Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold41
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2798036
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 10448 characters in sequence are not A, C, G, or T
File 16 of 21
Found at i:1879477 original size:13 final size:13
Alignment explanation
Indices: 1879459--1879484 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1879449 ACAAAGATCG
1879459 ATGTATTGATACA
1 ATGTATTGATACA
1879472 ATGTATTGATACA
1 ATGTATTGATACA
1879485 TTTCCTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
ATGTATTGATACA
Found at i:1879497 original size:21 final size:21
Alignment explanation
Indices: 1879471--1879512 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1879461 GTATTGATAC
*
1879471 AATGTATTGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
1879492 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
1879513 GGTAGTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.45
Consensus pattern (21 bp):
AATGTATCGATACATTTCCTT
Found at i:1879547 original size:13 final size:13
Alignment explanation
Indices: 1879529--1879580 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
1879519 AGCTTCGTAG
1879529 CGATACATTGTAT
1 CGATACATTGTAT
1879542 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
1879561 CGATACATTGTAT
1 CGATACATTGTAT
1879574 CGATACA
1 CGATACA
1879581 ACACTTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:1879570 original size:32 final size:32
Alignment explanation
Indices: 1879529--1879601 Score: 119
Period size: 32 Copynumber: 2.3 Consensus size: 32
1879519 AGCTTCGTAG
1879529 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
* *
1879561 CGATACATTGTATCGATACAACACTTATTTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
1879593 CGATGCATT
1 CGATACATT
1879602 TTCTGTTTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:1880229 original size:51 final size:52
Alignment explanation
Indices: 1880113--1880251 Score: 192
Period size: 51 Copynumber: 2.7 Consensus size: 52
1880103 AATAGCCTGC
* *
1880113 ATGTATCGATACATTGAAGAATGTATCAATACATTTGGGTCAAAAACCCAAG
1 ATGTATCGATACAATGAAAAATGTATCAATACATTTGGGTCAAAAACCCAAG
* *
1880165 ATGTATCGATACAATGAAAAATGTATTAATACATTTGGGT-TAAAACCC-AG
1 ATGTATCGATACAATGAAAAATGTATCAATACATTTGGGTCAAAAACCCAAG
* * *
1880215 AATGTATTGATACAATGAAAAATATATCGATACATTT
1 -ATGTATCGATACAATGAAAAATGTATCAATACATTT
1880252 TTTTTCTAGA
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
50 2 0.03
51 39 0.50
52 37 0.47
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (52 bp):
ATGTATCGATACAATGAAAAATGTATCAATACATTTGGGTCAAAAACCCAAG
Found at i:1880940 original size:63 final size:62
Alignment explanation
Indices: 1880728--1881172 Score: 313
Period size: 63 Copynumber: 7.0 Consensus size: 62
1880718 AGTAGATAGA
* * * * *
1880728 TGCCACCAACTTAG-GTGGGCTTTGAGAAAGAAAAAGAGC--CTTGCTCTTTGTGGACTAAAAAA
1 TGCCACCAGCTT-GTGTGGGCTTT-AAAAAGAAAAAG-GCGTCCTACTCTTTGAGGACT--AAAA
1880790 GAG
61 G-G
* * * ** * * * *
1880793 TGCTACCAACTTATGTGGGCTTTAAAAAGAAAAAAAAGATGTCCTGCTCTTTGATGACAAAAATG
1 TGCCACCAGCTTGTGTGGGCTTTAAAAAG---AAAAAGGCGTCCTACTCTTTGAGGACTAAAAGG
* * *
1880858 TGCCACCAGCTTGTATGGGCTTTTAAAAAGAAAAAGGCGTTCTACTTTTTGAGGACTAAAAGG
1 TGCCACCAGCTTGTGTGGGC-TTTAAAAAGAAAAAGGCGTCCTACTCTTTGAGGACTAAAAGG
* ** * ** * *
1880921 TGCTACCAATTTGTGTGGGCTTTTAAAAAGGAAAATACGTCCTACTTTTTGAGGATTAAAAGG
1 TGCCACCAGCTTGTGTGGGC-TTTAAAAAGAAAAAGGCGTCCTACTCTTTGAGGACTAAAAGG
* * * * * * *
1880984 TGCCACCAGCTTGTATGGGCTTTAAAAGAAAAAAAAAGTGTCTTGCTCTATGAGGACTAAAAGG
1 TGCCACCAGCTTGTGTGGGCTTT-AAA-AAGAAAAAGGCGTCCTACTCTTTGAGGACTAAAAGG
* * * * * * * * *
1881048 TGCCACCAGTTTGTGTGGGCTTT-AAGAGGACAAGGCATCTTGCTCTTTAAGGATTAAAAGG
1 TGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAAGGCGTCCTACTCTTTGAGGACTAAAAGG
* * * * *
1881109 TGCCACCAGCTTGTGTGGGCTTTAAAAGGAAAAAAAGCAGTCCTATTTTTTGAAGACTAAAAGG
1 TGCCACCAGCTTGTGTGGGCTTTAAAAAG-AAAAAGGC-GTCCTACTCTTTGAGGACTAAAAGG
1881173 ATAAAATGTT
Statistics
Matches: 297, Mismatches: 71, Indels: 25
0.76 0.18 0.06
Matches are distributed among these distances:
61 48 0.16
62 8 0.03
63 103 0.35
64 69 0.23
65 37 0.12
66 13 0.04
67 6 0.02
68 13 0.04
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.28
Consensus pattern (62 bp):
TGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAAGGCGTCCTACTCTTTGAGGACTAAAAGG
Found at i:1881123 original size:61 final size:61
Alignment explanation
Indices: 1880972--1881142 Score: 207
Period size: 61 Copynumber: 2.8 Consensus size: 61
1880962 CTACTTTTTG
* ** ** *
1880972 AGGATTAAAAGGTGCCACCAGCTTGTATGGGCTTTAAAAGAAAAAAAAAGTGTCTTGCTCTATG
1 AGGATTAAAAGGTGCCACCAGCTTGTGTGGGCTTT--AAG-AGGAAAAAGCATCTTGCTCTATA
* * * * *
1881036 AGGACTAAAAGGTGCCACCAGTTTGTGTGGGCTTTAAGAGGACAAGGCATCTTGCTCTTTA
1 AGGATTAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAGAGGAAAAAGCATCTTGCTCTATA
*
1881097 AGGATTAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGGAAAAA
1 AGGATTAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAGAGGAAAAA
1881143 AAGCAGTCCT
Statistics
Matches: 91, Mismatches: 16, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
61 56 0.62
62 3 0.03
64 32 0.35
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (61 bp):
AGGATTAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAGAGGAAAAAGCATCTTGCTCTATA
Found at i:1881167 original size:125 final size:126
Alignment explanation
Indices: 1880852--1881172 Score: 378
Period size: 125 Copynumber: 2.5 Consensus size: 126
1880842 TTTGATGACA
* * * *
1880852 AAAATGTGCCACCAGCTTGTATGGGCTTTTAAAAAG-AAAAAGGCGTTCTACTTTTTGAGGACTA
1 AAAAGGTGCCACCAGCTTGTATGGGC-TTTAAAAGGAAAAAAAGCGTCCTACTTTTTGAGGACTA
* * * * *
1880916 AAAGGTGCTACCAATTTGTGTGGGCTTTTAAAAAGGAAAATACGTCCTACTTTTTGAGGATT
65 AAAGGTGCCACCAATTTGTGTGGGCTTTTAAAAAGGAAAAGACATCCTACTCTTTAAGGATT
* * * * * *
1880978 AAAAGGTGCCACCAGCTTGTATGGGCTTTAAAAGAAAAAAAAAGTGTCTTGCTCTATGAGGACTA
1 AAAAGGTGCCACCAGCTTGTATGGGCTTTAAAAG-GAAAAAAAGCGTCCTACTTTTTGAGGACTA
* * * * * *
1881043 AAAGGTGCCACCAGTTTGTGTGGGC-TTT-AAGAGGACAAGGCATCTTGCTCTTTAAGGATT
65 AAAGGTGCCACCAATTTGTGTGGGCTTTTAAAAAGGAAAAGACATCCTACTCTTTAAGGATT
* * *
1881103 AAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGGAAAAAAAGCAGTCCTATTTTTTGAAGACTA
1 AAAAGGTGCCACCAGCTTGTATGGGCTTTAAAAGGAAAAAAAGC-GTCCTACTTTTTGAGGACTA
1881168 AAAGG
65 AAAGG
1881173 ATAAAATGTT
Statistics
Matches: 162, Mismatches: 30, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
124 8 0.05
125 82 0.51
126 28 0.17
127 44 0.27
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (126 bp):
AAAAGGTGCCACCAGCTTGTATGGGCTTTAAAAGGAAAAAAAGCGTCCTACTTTTTGAGGACTAA
AAGGTGCCACCAATTTGTGTGGGCTTTTAAAAAGGAAAAGACATCCTACTCTTTAAGGATT
Found at i:1882184 original size:22 final size:21
Alignment explanation
Indices: 1882159--1882199 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1882149 TGTTCTTTCG
*
1882159 TGTTTTTGTTTTTACTTTTTTA
1 TGTTTTT-TTTTTAATTTTTTA
1882181 TGTTTTTTTTTTAATTTTT
1 TGTTTTTTTTTTAATTTTT
1882200 GTGATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.10, C:0.02, G:0.07, T:0.80
Consensus pattern (21 bp):
TGTTTTTTTTTTAATTTTTTA
Found at i:1890465 original size:20 final size:20
Alignment explanation
Indices: 1890440--1890509 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
1890430 ATATATTTTC
1890440 AATGTATCGATACATGTATG
1 AATGTATCGATACATGTATG
* *
1890460 AATGTATTGATATAT-T-T-
1 AATGTATCGATACATGTATG
* *
1890477 --TGTATCAATACATGCATG
1 AATGTATCGATACATGTATG
1890495 AATGTATCGATACAT
1 AATGTATCGATACAT
1890510 TATATTTTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
15 10 0.26
17 1 0.03
18 1 0.03
19 1 0.03
20 25 0.66
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATGTATG
Found at i:1890488 original size:35 final size:37
Alignment explanation
Indices: 1890421--1890506 Score: 113
Period size: 35 Copynumber: 2.3 Consensus size: 37
1890411 TTTTTACCCA
* *
1890421 AATGTATTGATATATTTTCAATGTATCGATACATGTATG
1 AATGTATTGATATATTTT--ATGTATCAATACATGCATG
1890460 AATGTATTGATATA-TTT-TGTATCAATACATGCATG
1 AATGTATTGATATATTTTATGTATCAATACATGCATG
*
1890495 AATGTATCGATA
1 AATGTATTGATA
1890507 CATTATATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
35 27 0.61
38 3 0.07
39 14 0.32
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (37 bp):
AATGTATTGATATATTTTATGTATCAATACATGCATG
Found at i:1895565 original size:63 final size:63
Alignment explanation
Indices: 1895492--1895618 Score: 236
Period size: 63 Copynumber: 2.0 Consensus size: 63
1895482 AAAGTTAGGT
*
1895492 AAGAAATTATATGCTATCTTACTTTTTTCTAGACAAAAGTGACTAACAAGCTAAATGTGAAGG
1 AAGAAATTATATGCTATCTTACTTTCTTCTAGACAAAAGTGACTAACAAGCTAAATGTGAAGG
*
1895555 AAGAAATTATATGCTATCTTACTTTCTTCTAGACAAAAGTGACTAACGAGCTAAATGTGAAGG
1 AAGAAATTATATGCTATCTTACTTTCTTCTAGACAAAAGTGACTAACAAGCTAAATGTGAAGG
1895618 A
1 A
1895619 GTGGTACATA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (63 bp):
AAGAAATTATATGCTATCTTACTTTCTTCTAGACAAAAGTGACTAACAAGCTAAATGTGAAGG
Found at i:1900120 original size:101 final size:101
Alignment explanation
Indices: 1899945--1900150 Score: 376
Period size: 101 Copynumber: 2.0 Consensus size: 101
1899935 TTCACCAAAG
1899945 GTAACTTTTCCAACATTCTTGTGCATTCATTATGGGTCATATGATTTGGAGCACTTACTGTCAAG
1 GTAACTTTTCCAACATTCTTGTGCATTCATTATGGGTCATATGATTTGGAGCACTTACTGTCAAG
* *
1900010 GTTCCAATTGATCTTCATTGCTGTAGTTGCCTTGTA
66 GTTCCAATTGATCCTCATTGCTGTAATTGCCTTGTA
1900046 GTAACTTTTCCAACATTCTTGTGCATTCATTATGGGTCATATGATTTGGAGCACTTACTGTCAAG
1 GTAACTTTTCCAACATTCTTGTGCATTCATTATGGGTCATATGATTTGGAGCACTTACTGTCAAG
**
1900111 GTTCCAATTGATCCTCATTTTTGTAATTGCCTTGTA
66 GTTCCAATTGATCCTCATTGCTGTAATTGCCTTGTA
1900147 GTAA
1 GTAA
1900151 TGCTCTTTTT
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
101 101 1.00
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (101 bp):
GTAACTTTTCCAACATTCTTGTGCATTCATTATGGGTCATATGATTTGGAGCACTTACTGTCAAG
GTTCCAATTGATCCTCATTGCTGTAATTGCCTTGTA
Found at i:1900638 original size:21 final size:21
Alignment explanation
Indices: 1900606--1900659 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1900596 CACTTGCAAC
1900606 TCATTT-TTTTCTCCTCTAAT
1 TCATTTATTTTCTCCTCTAAT
**
1900626 TCATTTATTTTCTTTTCTAAT
1 TCATTTATTTTCTCCTCTAAT
* *
1900647 TCACTTAATTTCT
1 TCATTTATTTTCT
1900660 TTTCAAGAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 6 0.21
21 23 0.79
ACGTcount: A:0.19, C:0.20, G:0.00, T:0.61
Consensus pattern (21 bp):
TCATTTATTTTCTCCTCTAAT
Found at i:1900660 original size:21 final size:21
Alignment explanation
Indices: 1900620--1900663 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1900610 TTTTTTCTCC
* *
1900620 TCTAATTCATTTATTTTCTTT
1 TCTAATTCACTTAATTTCTTT
1900641 TCTAATTCACTTAATTTCTTT
1 TCTAATTCACTTAATTTCTTT
1900662 TC
1 TC
1900664 AAGAATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.18, G:0.00, T:0.61
Consensus pattern (21 bp):
TCTAATTCACTTAATTTCTTT
Found at i:1901043 original size:14 final size:14
Alignment explanation
Indices: 1901010--1901036 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1901000 TTTCAACATT
1901010 TCTCTTCTAGGATG
1 TCTCTTCTAGGATG
1901024 TCTCTTCTAGGAT
1 TCTCTTCTAGGAT
1901037 AGGTCTTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (14 bp):
TCTCTTCTAGGATG
Found at i:1902462 original size:20 final size:20
Alignment explanation
Indices: 1902437--1902554 Score: 78
Period size: 20 Copynumber: 5.7 Consensus size: 20
1902427 CCATTGAACT
1902437 CAATGTATCGATACTATTCA
1 CAATGTATCGATACTATTCA
**
1902457 CAATGTATCGATAC-ATGAA
1 CAATGTATCGATACTATTCA
** *
1902476 CAGTGATGTATTAATATTATTCA
1 CA---ATGTATCGATACTATTCA
**
1902499 CAATGTATCGATAC-ATGAA
1 CAATGTATCGATACTATTCA
** *
1902518 CAGTGATGTATTAATATTATTCA
1 CA---ATGTATCGATACTATTCA
1902541 CAATGTATCGATAC
1 CAATGTATCGATAC
1902555 ATGAACAGTG
Statistics
Matches: 70, Mismatches: 20, Indels: 16
0.66 0.19 0.15
Matches are distributed among these distances:
19 10 0.14
20 32 0.46
22 18 0.26
23 10 0.14
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (20 bp):
CAATGTATCGATACTATTCA
Found at i:1902497 original size:42 final size:42
Alignment explanation
Indices: 1902451--1902567 Score: 234
Period size: 42 Copynumber: 2.8 Consensus size: 42
1902441 GTATCGATAC
1902451 TATTCACAATGTATCGATACATGAACAGTGATGTATTAATAT
1 TATTCACAATGTATCGATACATGAACAGTGATGTATTAATAT
1902493 TATTCACAATGTATCGATACATGAACAGTGATGTATTAATAT
1 TATTCACAATGTATCGATACATGAACAGTGATGTATTAATAT
1902535 TATTCACAATGTATCGATACATGAACAGTGATG
1 TATTCACAATGTATCGATACATGAACAGTGATG
1902568 AGCAGTGATG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (42 bp):
TATTCACAATGTATCGATACATGAACAGTGATGTATTAATAT
Found at i:1902573 original size:10 final size:10
Alignment explanation
Indices: 1902555--1902585 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1902545 GTATCGATAC
1902555 ATGAACAGTG
1 ATGAACAGTG
*
1902565 ATGAGCAGTG
1 ATGAACAGTG
1902575 ATGAACAGTG
1 ATGAACAGTG
1902585 A
1 A
1902586 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.39, C:0.10, G:0.32, T:0.19
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:1905220 original size:79 final size:78
Alignment explanation
Indices: 1905128--1905312 Score: 196
Period size: 78 Copynumber: 2.3 Consensus size: 78
1905118 CTAAGATGAA
* * * * * *
1905128 AAAAATTTAATATTTT-AAAAGTGAAAATGGGGTTGGAGTATCCCCTC-AGAAGTGATGGGGTTG
1 AAAAA-TTGATATTTTGAAAA-TAAAAATAGGGTTAGAGTATCCCCTCGA-AAATAAT-GGGTTG
1905191 GAGTATC-CTCGATGGTG
62 GAGTATCTC-CGATGGTG
*
1905208 AAAAATTGATATTTTGTAAATAAAAATAGGGTTAGAGTATCCCCTCGAAAATAATGGGTTGGAGT
1 AAAAATTGATATTTTGAAAATAAAAATAGGGTTAGAGTATCCCCTCGAAAATAATGGGTTGGAGT
1905273 ATCTCCGATGGTG
66 ATCTCCGATGGTG
* * * * *
1905286 CAAAATCGATTTTTTGGAGATAAAAAT
1 AAAAATTGATATTTTGAAAATAAAAAT
1905313 CTCACTACTG
Statistics
Matches: 90, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
78 43 0.48
79 38 0.42
80 9 0.10
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (78 bp):
AAAAATTGATATTTTGAAAATAAAAATAGGGTTAGAGTATCCCCTCGAAAATAATGGGTTGGAGT
ATCTCCGATGGTG
Found at i:1905301 original size:78 final size:79
Alignment explanation
Indices: 1905151--1905312 Score: 204
Period size: 78 Copynumber: 2.1 Consensus size: 79
1905141 TTTAAAAGTG
* * * * *
1905151 AAAATGGGGTTGGAGTATCCCCTCAGAAGTGATGGGGTTGGAGTATCCTCGATGGTGAAAAATTG
1 AAAATAGGGTTAGAGTATCCCCTCAGAAATAATGGGGTTGGAGTATCCTCGATGGTGAAAAATCG
*
1905216 ATATTTTGTAAATA
66 ATATTTTGGAAATA
*
1905230 AAAATAGGGTTAGAGTATCCCCTC-GAAAATAAT-GGGTTGGAGTAT-CTCCGATGGTGCAAAAT
1 AAAATAGGGTTAGAGTATCCCCTCAG-AAATAATGGGGTTGGAGTATCCT-CGATGGTGAAAAAT
* *
1905292 CGATTTTTTGGAGATA
64 CGATATTTTGGAAATA
1905308 AAAAT
1 AAAAT
1905313 CTCACTACTG
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
77 2 0.03
78 43 0.60
79 27 0.38
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.30
Consensus pattern (79 bp):
AAAATAGGGTTAGAGTATCCCCTCAGAAATAATGGGGTTGGAGTATCCTCGATGGTGAAAAATCG
ATATTTTGGAAATA
Found at i:1906953 original size:20 final size:20
Alignment explanation
Indices: 1906915--1906954 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1906905 TTGATACAAC
* **
1906915 AAGTTAATGTATCGGTACAT
1 AAGTGAATGTATCAATACAT
1906935 AAGTGAATGTATCAATACAT
1 AAGTGAATGTATCAATACAT
1906955 GCTTGCACTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (20 bp):
AAGTGAATGTATCAATACAT
Found at i:1908529 original size:48 final size:46
Alignment explanation
Indices: 1908472--1908980 Score: 300
Period size: 49 Copynumber: 11.0 Consensus size: 46
1908462 AGACACCTCA
* * * *
1908472 TAAGCCCAATATCGCTGGCCTTGAATTAGCATATTAGCACCTTGTATT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT-T-TT
* *
1908520 TAAGACCAATGTCGCTAGCCTTGAATCAGCACATTGGCACC---TT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTTT
* *
1908563 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CTTCATCTT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT--T-TT
* *
1908611 TAAGACCAATGTTGCTGGCCTTGAATCAGCACATTGGCA-C-----
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTTT
* * *
1908651 -AAGCCCAATATCGCTGGCCATGAATCAGCATATTGGCACCATTATCTT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACC-TT-T-TT
* * *
1908699 TAAGACCAATGTCGCTAGCCCTGAATCAGCACATTGGCA-------
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTTT
* * * *
1908738 -AGAGCCCAATATTGCTGGCCTTGAATCAACATATTGGCACCTTCATCTT
1 TA-AGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT--T-TT
* ** * * *
1908787 TAAAACTGATGTCGTTGGCCTTGAATCAGCACATTAGCACCTTAACCATCTT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT-----T-TT
* * * * *
1908839 TAAGTCCAATGTCGCTGGCTTTGAATCAGCACATTGGTACGTTCATCTT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT--T-TT
** * * *
1908888 TAAGTTCGATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT--T-TT
* * * * *
1908937 TAAGTCCGATATCGTTGGCCTTGAATCAGCATATTGGCATCTTT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTT
1908981 AACATTCCTA
Statistics
Matches: 370, Mismatches: 60, Indels: 63
0.75 0.12 0.13
Matches are distributed among these distances:
38 1 0.00
39 63 0.17
40 1 0.00
42 1 0.00
43 37 0.10
47 1 0.00
48 73 0.20
49 152 0.41
50 1 0.00
52 40 0.11
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.30
Consensus pattern (46 bp):
TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTTT
Found at i:1908632 original size:91 final size:92
Alignment explanation
Indices: 1908472--1909430 Score: 535
Period size: 101 Copynumber: 10.0 Consensus size: 92
1908462 AGACACCTCA
* * * *
1908472 TAAGCCCAATATCGCTGGCCTTGAATTAGCATATTAGCACCTT-GTATTTAAGACCAATGTCGCT
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCGCT
*
1908536 AGCCTTGAATCAGCACATTGGCACCTT
66 GGCCTTGAATCAGCACATTGGCACCTT
* *
1908563 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CTTCATCTTTAAGACCAATGTTGCT
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCGCT
1908627 GGCCTTGAATCAGCACATTGGCA-C--
66 GGCCTTGAATCAGCACATTGGCACCTT
*
1908651 -AAGCCCAATATCGCTGGCCATGAATCAGCATATTGGCACCATT-ATCTTTAAGACCAATGTCGC
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTCATCTTTAAGACCAATGTCGC
* *
1908714 TAGCCCTGAATCAGCACATTGGCA----
65 TGGCCTTGAATCAGCACATTGGCACCTT
* * * ** *
1908738 -AGAGCCCAATATTGCTGGCCTTGAATCAACATATTGGCACCTTCATCTTTAAAACTGATGTCGT
1 TA-AGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCGC
*
1908802 TGGCCTTGAATCAGCACATTAGCACCTTAACCATCTT
65 TGGCCTTGAATCAGCACATT-G--GC---A-C--CTT
* * * * * * ** *
1908839 TAAGTCCAATGTCGCTGGCTTTGAATCAGCACATTGGTACGTTCATCTTTAAGTTCGATGTCGCT
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCGCT
1908904 GGCCTTGAATCAGCACATTGGCATCTTCATCTT
66 GGCCTTGAATCAGCACATTGGCA----C--CTT
* * * * * * *
1908937 TAAGTCCGATATCGTTGGCCTTGAATCAGCATATTGGCATCTTTAACATTCCTAAGCCCAATGTC
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC-TT--TAAGACCAATGTC
* * ** * * *
1909002 ACTAGCCTTGTCTTAACACATTGGCATTTTTCTT
63 GCTGGCCTTGAATCAGCACATTGGCA----CCTT
* * * * ** * * * * ** * *
1909036 CAAGTCTAATGTCGCTGGCCAAGAATCAGCACAATGTCATTCTTCGCATCTTCGAGCCCAATATC
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CCTT--CATCTTTAAGACCAATGTC
* * * ** *
1909101 GCTAG-C-TGCATATTAGCTCCTTTATCCTTTTTCTCATCTT
63 GCTGGCCTTG-A-ATCAG---C---A--C--ATTGGCACCTT
* * * * * *
1909141 TAAGCCCAATATCGTTGGCCTTGAATTAGCATATTGGCACTTTCATTTTTAAGACCGATGTCGTT
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCGCT
1909206 GGCCTTGAATCAGCACATTGGCACCTTAACCATCTT
66 GGCCTTGAATCAGCACATTGG---C---A-C--CTT
* * * * * * *
1909242 TAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCACGTTCATCTTTAA-ATTCGATGTCGC
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGA-CCAATGTCGC
1909306 TGGCCTTGAATCAGCACATTGGCATCTTCATCTT
65 TGGCCTTGAATCAGCACATTGGCA----C--CTT
* * * * * * * *
1909340 TAAGTCCGATATCGTTGGCCTTGAATCAGCATATTAGCATCTTGAACGTTTTTAAGCCCAATGTC
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT---CATCTTTAAGACCAATGTC
* **
1909405 GCTAGCCTTGTCTCAGCACATTGGCA
63 GCTGGCCTTGAATCAGCACATTGGCA
1909431 TTCTTCTTCA
Statistics
Matches: 676, Mismatches: 133, Indels: 108
0.74 0.15 0.12
Matches are distributed among these distances:
87 39 0.06
88 112 0.17
89 3 0.00
90 4 0.01
91 77 0.11
92 2 0.00
94 2 0.00
95 3 0.00
96 1 0.00
97 2 0.00
98 88 0.13
99 52 0.08
100 6 0.01
101 217 0.32
102 24 0.04
103 2 0.00
104 4 0.01
105 33 0.05
107 1 0.00
109 4 0.01
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (92 bp):
TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCGCT
GGCCTTGAATCAGCACATTGGCACCTT
Found at i:1908727 original size:49 final size:49
Alignment explanation
Indices: 1908655--1909474 Score: 481
Period size: 49 Copynumber: 16.6 Consensus size: 49
1908645 TGGCACAAGC
* * * *
1908655 CCAATATCGCTGGCCATGAATCAGCATATTGGCACCATT-ATCTTTAAGA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-TTCATCTTTAAGT
* * * *
1908704 CCAATGTCGCTAGCCCTGAATCAGCACATTGGCA-----A-----GAGC
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * * * **
1908743 CCAATATTGCTGGCCTTGAATCAACATATTGGCACCTTCATCTTTAAAA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
** * *
1908792 CTGATGTCGTTGGCCTTGAATCAGCACATTAGCACCTTAACCATCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT---CATCTTTAAGT
* * *
1908844 CCAATGTCGCTGGCTTTGAATCAGCACATTGGTACGTTCATCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * *
1908893 TCGATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * * * * * * *
1908942 CCGATATCGTTGGCCTTGAATCAGCATATTGGCATCTTTAACATTCCTAAGC
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC-TT--TAAGT
* * ** * * ** *
1908994 CCAATGTCACTAGCCTTGTCTTAACACATTGGCA--TTTTTCTTCAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* ** * * * ** *
1909041 CTAATGTCGCTGGCCAAGAATCAGCACAATGTCATTCTTCGCATCTTCGAGC
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CCTT--CATCTTTAAGT
* * * * * * *
1909093 CCAATATCGCTAG-C-TGCATATTAGCTCCTT--TATCCTTTTTCTCATCTTTAAGC
1 CCAATGTCGCTGGCCTTG-A-ATCAGCACATTGGCA-CC----T-TCATCTTTAAGT
* * * * * * *
1909146 CCAATATCGTTGGCCTTGAATTAGCATATTGGCACTTTCATTTTTAAGA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* *
1909195 CCGATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTAACCATCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT---CATCTTTAAGT
* * *
1909247 CCAATGTCGCTAGCCTTGAATCAGCACATTGGCACGTTCATCTTTAAAT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * *
1909296 TCGATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * * * * * * * *
1909345 CCGATATCGTTGGCCTTGAATCAGCATATTAGCATCTTGAACGTTTTTAAGC
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT---CATCTTTAAGT
* ** * *
1909397 CCAATGTCGCTAGCCTTGTCTCAGCACATTGGCA--TTCTTCTTCAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* ** *
1909444 CTAATGTCGGGGGCCATGAATCAGCACATTG
1 CCAATGTCGCTGGCCTTGAATCAGCACATTG
1909475 TCATTCTTTG
Statistics
Matches: 593, Mismatches: 140, Indels: 78
0.73 0.17 0.10
Matches are distributed among these distances:
39 30 0.05
44 2 0.00
47 57 0.10
49 282 0.48
50 15 0.03
51 2 0.00
52 169 0.28
53 28 0.05
54 4 0.01
55 4 0.01
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.33
Consensus pattern (49 bp):
CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
Found at i:1908736 original size:88 final size:88
Alignment explanation
Indices: 1908473--1908826 Score: 473
Period size: 88 Copynumber: 4.0 Consensus size: 88
1908463 GACACCTCAT
* * * *
1908473 AAGCCCAATATCGCTGGCCTTGAATTAGCATATTAGCACCTT-GTATTTAAGACCAATGTCGCTA
1 AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCGCTA
1908537 GCCTTGAATCAGCACATTGGCACC
66 GCCTTGAATCAGCACATTGGCA-C
* *
1908561 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CTTCATCTTTAAGACCAATGTTG
1 ---AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCG
*
1908625 CTGGCCTTGAATCAGCACATTGGCAC
63 CTAGCCTTGAATCAGCACATTGGCAC
*
1908651 AAGCCCAATATCGCTGGCCATGAATCAGCATATTGGCACCATT-ATCTTTAAGACCAATGTCGCT
1 AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTCATCTTTAAGACCAATGTCGCT
*
1908715 AGCCCTGAATCAGCACATTGGCA-
65 AGCCTTGAATCAGCACATTGGCAC
* * * ** *
1908738 AGAGCCCAATATTGCTGGCCTTGAATCAACATATTGGCACCTTCATCTTTAAAACTGATGTCGTT
1 A-AGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCGCT
* *
1908803 GGCCTTGAATCAGCACATTAGCAC
65 AGCCTTGAATCAGCACATTGGCAC
1908827 CTTAACCATC
Statistics
Matches: 235, Mismatches: 22, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
87 39 0.17
88 115 0.49
89 2 0.01
90 4 0.02
91 75 0.32
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (88 bp):
AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCGCTA
GCCTTGAATCAGCACATTGGCAC
Found at i:1909022 original size:150 final size:150
Alignment explanation
Indices: 1908751--1909025 Score: 347
Period size: 150 Copynumber: 1.8 Consensus size: 150
1908741 GCCCAATATT
* * *
1908751 GCTGGCCTTGAATCAACATATTGGCACCTTCATCTTTAAAACTGATGTCGTTGGCCTTGAATCAG
1 GCTGGCCTTGAATCAACACATTGGCACCTTCATCTTTAAAACCGATATCGTTGGCCTTGAATCAG
* * * * * *
1908816 CACATTAGCACCTTAACCATCTTTAAGTCCAATGTCGCTGGCTTTGAATCAGCACATTGGTACGT
66 CACATTAGCACCTTAACCATCTCTAAGCCCAATGTCACTAGCCTTGAATCAACACATTGGTACGT
1908881 TCATCTTTAAGTTCGATGTC
131 TCATCTTTAAGTTCGATGTC
* * **
1908901 GCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCGATATCGTTGGCCTTGAATCAG
1 GCTGGCCTTGAATCAACACATTGGCACCTTCATCTTTAAAACCGATATCGTTGGCCTTGAATCAG
* * * ** *
1908966 CATATTGGCATCTTTAA-CAT-TCCTAAGCCCAATGTCACTAGCCTTGTCTTAACACATTGG
66 CACATTAGCA-CCTTAACCATCT-CTAAGCCCAATGTCACTAGCCTTGAATCAACACATTGG
1909026 CATTTTTCTT
Statistics
Matches: 104, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
149 1 0.01
150 98 0.94
151 5 0.05
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (150 bp):
GCTGGCCTTGAATCAACACATTGGCACCTTCATCTTTAAAACCGATATCGTTGGCCTTGAATCAG
CACATTAGCACCTTAACCATCTCTAAGCCCAATGTCACTAGCCTTGAATCAACACATTGGTACGT
TCATCTTTAAGTTCGATGTC
Found at i:1909349 original size:150 final size:150
Alignment explanation
Indices: 1909156--1909430 Score: 401
Period size: 150 Copynumber: 1.8 Consensus size: 150
1909146 CCAATATCGT
* * * *
1909156 TGGCCTTGAATTAGCATATTGGCACTTTCATTTTTAAGACCGATGTCGTTGGCCTTGAATCAGCA
1 TGGCCTTGAATCAGCACATTGGCACTTTCATCTTTAAGACCGATATCGTTGGCCTTGAATCAGCA
* *
1909221 CATTGGCACCTT-AACCATCTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCACGTT
66 CATTAGCACCTTGAA-CATCTTTAAGCCCAATGTCGCTAGCCTTGAATCAGCACATTGGCACGTT
1909285 CATCTTTAAATTCGATGTCGC
130 CATCTTTAAATTCGATGTCGC
*
1909306 TGGCCTTGAATCAGCACATTGGCA-TCTTCATCTTTAAGTCCGATATCGTTGGCCTTGAATCAGC
1 TGGCCTTGAATCAGCACATTGGCACT-TTCATCTTTAAGACCGATATCGTTGGCCTTGAATCAGC
* * * * **
1909370 ATATTAGCATCTTGAACGTTTTTAAGCCCAATGTCGCTAGCCTTGTCTCAGCACATTGGCA
65 ACATTAGCACCTTGAACATCTTTAAGCCCAATGTCGCTAGCCTTGAATCAGCACATTGGCA
1909431 TTCTTCTTCA
Statistics
Matches: 110, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
149 1 0.01
150 107 0.97
151 2 0.02
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (150 bp):
TGGCCTTGAATCAGCACATTGGCACTTTCATCTTTAAGACCGATATCGTTGGCCTTGAATCAGCA
CATTAGCACCTTGAACATCTTTAAGCCCAATGTCGCTAGCCTTGAATCAGCACATTGGCACGTTC
ATCTTTAAATTCGATGTCGC
Found at i:1909490 original size:403 final size:403
Alignment explanation
Indices: 1908740--1909571 Score: 1376
Period size: 403 Copynumber: 2.1 Consensus size: 403
1908730 CATTGGCAAG
* * *
1908740 AGCCCAATATTGCTGGCCTTGAATCAACATATTGGCACCTTCATCTTTAAAACTGATGTCGTTGG
1 AGCCCAATATCGTTGGCCTTGAATCAACATATTGGCACCTTCATCTTTAAAACCGATGTCGTTGG
* *
1908805 CCTTGAATCAGCACATTAGCACCTTAACCATCTTTAAGTCCAATGTCGCTGGCTTTGAATCAGCA
66 CCTTGAATCAGCACATTAGCACCTTAACCATCTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCA
* *
1908870 CATTGGTACGTTCATCTTTAAGTTCGATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
131 CATTGGCACGTTCATCTTTAAATTCGATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
* *
1908935 TTTAAGTCCGATATCGTTGGCCTTGAATCAGCATATTGGCATCTTTAACATTCCTAAGCCCAATG
196 TTTAAGTCCGATATCGTTGGCCTTGAATCAGCATATTAGCATCTTGAACATTCCTAAGCCCAATG
* * *
1909000 TCACTAGCCTTGTCTTAACACATTGGCATTTTTCTTCAAGTCTAATGTCGCTGGCCAAGAATCAG
261 TCACTAGCCTTGTCTCAACACATTGGCATTCTTCTTCAAGTCTAATGTCGCGGGCCAAGAATCAG
* *
1909065 CACAATGTCATTCTTCGCATCTTCGAGCCCAATATCGCTAGCTGCATATTAGCTCCTTTATCCTT
326 CACAATGTCATTCTTCGCATCTTCGAGCCCAATATCGCTAGCAGCACATTAGCTCCTTTATCCTT
*
1909130 TTTCTCATCTTTA
391 TTTCTCATCTTCA
* * * * *
1909143 AGCCCAATATCGTTGGCCTTGAATTAGCATATTGGCACTTTCATTTTTAAGACCGATGTCGTTGG
1 AGCCCAATATCGTTGGCCTTGAATCAACATATTGGCACCTTCATCTTTAAAACCGATGTCGTTGG
*
1909208 CCTTGAATCAGCACATTGGCACCTTAACCATCTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCA
66 CCTTGAATCAGCACATTAGCACCTTAACCATCTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCA
1909273 CATTGGCACGTTCATCTTTAAATTCGATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
131 CATTGGCACGTTCATCTTTAAATTCGATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
* **
1909338 TTTAAGTCCGATATCGTTGGCCTTGAATCAGCATATTAGCATCTTGAACGTTTTTAAGCCCAATG
196 TTTAAGTCCGATATCGTTGGCCTTGAATCAGCATATTAGCATCTTGAACATTCCTAAGCCCAATG
* * * *
1909403 TCGCTAGCCTTGTCTCAGCACATTGGCATTCTTCTTCAAGTCTAATGTCGGGGGCCATGAATCAG
261 TCACTAGCCTTGTCTCAACACATTGGCATTCTTCTTCAAGTCTAATGTCGCGGGCCAAGAATCAG
* *
1909468 CACATTGTCATTCTTTGCATCTTCGAGCCCAATATCGCTAGCAGCACATTAGCTCCTTTATCCTT
326 CACAATGTCATTCTTCGCATCTTCGAGCCCAATATCGCTAGCAGCACATTAGCTCCTTTATCCTT
1909533 TTTCTCATCTTCA
391 TTTCTCATCTTCA
* *
1909546 AGCTCAATATCGTTGGCCGTGAATCA
1 AGCCCAATATCGTTGGCCTTGAATCA
1909572 GCGTATGGTC
Statistics
Matches: 396, Mismatches: 33, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
403 396 1.00
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (403 bp):
AGCCCAATATCGTTGGCCTTGAATCAACATATTGGCACCTTCATCTTTAAAACCGATGTCGTTGG
CCTTGAATCAGCACATTAGCACCTTAACCATCTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCA
CATTGGCACGTTCATCTTTAAATTCGATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
TTTAAGTCCGATATCGTTGGCCTTGAATCAGCATATTAGCATCTTGAACATTCCTAAGCCCAATG
TCACTAGCCTTGTCTCAACACATTGGCATTCTTCTTCAAGTCTAATGTCGCGGGCCAAGAATCAG
CACAATGTCATTCTTCGCATCTTCGAGCCCAATATCGCTAGCAGCACATTAGCTCCTTTATCCTT
TTTCTCATCTTCA
Found at i:1914497 original size:14 final size:14
Alignment explanation
Indices: 1914478--1914505 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1914468 TGTCCCTAGG
1914478 CATCATAATGCCTA
1 CATCATAATGCCTA
1914492 CATCATAATGCCTA
1 CATCATAATGCCTA
1914506 ATGTTGGGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (14 bp):
CATCATAATGCCTA
Found at i:1915628 original size:101 final size:98
Alignment explanation
Indices: 1915452--1915685 Score: 265
Period size: 101 Copynumber: 2.4 Consensus size: 98
1915442 ATCCTTTTTC
* * * *
1915452 TCATCTTTAAGCCCAATATCGTTGGCCTTGAATCAGCATATTGGCAGCTTCATCTTTAAGACCGA
1 TCATCTTTAAGTCCAATATCGTTGGCCTTGAATCAACACATTCGCAGCTTCATCTTTAAGACCGA
* *
1915517 TGTTGTTGGCCTTGAATAAACACATTAGCACCT
66 TGTCGCTGGCCTTGAATAAACACATTAGCACCT
* *
1915550 TAACCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAACACATTCGCATG-TTCATCTTTAA-A
1 T---CATCTTTAAGTCCAATATCGTTGGCCTTGAATCAACACATTCGCA-GCTTCATCTTTAAGA
* * * * *
1915613 TTCGATGTCGCTGGCCTTGAATCAGCACATTGGCATCT
62 -CCGATGTCGCTGGCCTTGAATAAACACATTAGCACCT
* * *
1915651 TTATCTTTAAGTCCGATATCATTGGCCTTGAATCA
1 TCATCTTTAAGTCCAATATCGTTGGCCTTGAATCA
1915686 GCATATTGGC
Statistics
Matches: 113, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
98 30 0.27
100 1 0.01
101 81 0.72
102 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.34
Consensus pattern (98 bp):
TCATCTTTAAGTCCAATATCGTTGGCCTTGAATCAACACATTCGCAGCTTCATCTTTAAGACCGA
TGTCGCTGGCCTTGAATAAACACATTAGCACCT
Found at i:1915702 original size:49 final size:49
Alignment explanation
Indices: 1915452--1915700 Score: 264
Period size: 49 Copynumber: 5.0 Consensus size: 49
1915442 ATCCTTTTTC
* * * * *
1915452 TCATCTTTAAGCCCAATATCGTTGGCCTTGAATCAGCATATTGGCAGCT
1 TCATCTTTAAGTCCGATGTCGTTGGCCTTGAATCAGCACATTGGCATCT
* * * * * *
1915501 TCATCTTTAAGACCGATGTTGTTGGCCTTGAATAAACACATTAGCACCT
1 TCATCTTTAAGTCCGATGTCGTTGGCCTTGAATCAGCACATTGGCATCT
* * * * *
1915550 TAACCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAACACATTCGCATGT
1 T---CATCTTTAAGTCCGATGTCGTTGGCCTTGAATCAGCACATTGGCATCT
* * *
1915602 TCATCTTTAAATTCGATGTCGCTGGCCTTGAATCAGCACATTGGCATCT
1 TCATCTTTAAGTCCGATGTCGTTGGCCTTGAATCAGCACATTGGCATCT
* * * *
1915651 TTATCTTTAAGTCCGATATCATTGGCCTTGAATCAGCATATTGGCATCT
1 TCATCTTTAAGTCCGATGTCGTTGGCCTTGAATCAGCACATTGGCATCT
1915700 T
1 T
1915701 TAACGTTTCT
Statistics
Matches: 167, Mismatches: 30, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
49 126 0.75
52 41 0.25
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (49 bp):
TCATCTTTAAGTCCGATGTCGTTGGCCTTGAATCAGCACATTGGCATCT
Found at i:1915725 original size:150 final size:148
Alignment explanation
Indices: 1915474--1915792 Score: 338
Period size: 150 Copynumber: 2.1 Consensus size: 148
1915464 CCAATATCGT
* * **
1915474 TGGCCTTGAATCAGCATATTGGCAGCTTCATCTTTAAGACCGATGTTGTTGGCCTTGAATAAACA
1 TGGCCTTGAATCAGCACATTGGCAGCTTCATCTTTAAGACCGATATCATTGGCCTTGAATAAACA
* * *
1915539 CATTAGCACCTTAACCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAACACATTCGCATGTTC
66 CATTAGCACCTTAACCATCTTTAAGCCCAATATCGCTAGCCTTGAATCAACACATTCGCA--TTC
*
1915604 ATCTTTAAATTC-GATGTCGC
129 ATC-TTAAATTCTAATGTCGC
* * * * *
1915624 TGGCCTTGAATCAGCACATTGGCATCTTTATCTTTAAGTCCGATATCATTGGCCTTGAATCAGCA
1 TGGCCTTGAATCAGCACATTGGCAGCTTCATCTTTAAGACCGATATCATTGGCCTTGAATAAACA
* * * * ** * *
1915689 TATTGGCATCTTTAA-CGT-TTCTAAGCCCAATATCGCTAGCCTTGTCTCAGCACATTGGCATTC
66 CATTAGCA-CCTTAACCATCTT-TAAGCCCAATATCGCTAGCCTTGAATCAACACATTCGCATTC
* *
1915752 TTCTTCAATTCTAATGTCGC
129 ATCTTAAATTCTAATGTCGC
* * *
1915772 TGGTCATGAATCAGTACATTG
1 TGGCCTTGAATCAGCACATTG
1915793 TCATTCTTCG
Statistics
Matches: 140, Mismatches: 26, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
147 7 0.05
148 30 0.21
149 2 0.01
150 96 0.69
151 5 0.04
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (148 bp):
TGGCCTTGAATCAGCACATTGGCAGCTTCATCTTTAAGACCGATATCATTGGCCTTGAATAAACA
CATTAGCACCTTAACCATCTTTAAGCCCAATATCGCTAGCCTTGAATCAACACATTCGCATTCAT
CTTAAATTCTAATGTCGC
Found at i:1916640 original size:13 final size:13
Alignment explanation
Indices: 1916622--1916649 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1916612 ATACAAAGAT
1916622 CAATGTATCGATA
1 CAATGTATCGATA
1916635 CAATGTATCGATA
1 CAATGTATCGATA
1916648 CA
1 CA
1916650 TTGAATAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1916642 original size:33 final size:33
Alignment explanation
Indices: 1916603--1916669 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
1916593 CTGCCAAGGA
1916603 AATGTATCGATACAAAG-ATCAATGTATCGATAC
1 AATGTATCGATACAAAGAAT-AATGTATCGATAC
**
1916636 AATGTATCGATACATTGAATAATGTATCGATAC
1 AATGTATCGATACAAAGAATAATGTATCGATAC
1916669 A
1 A
1916670 TCTGGGAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 29 0.94
34 2 0.06
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (33 bp):
AATGTATCGATACAAAGAATAATGTATCGATAC
Found at i:1922331 original size:43 final size:43
Alignment explanation
Indices: 1922270--1922442 Score: 265
Period size: 43 Copynumber: 4.0 Consensus size: 43
1922260 ATTTATTTTC
* *
1922270 TTTCACTTTCTTAAAGGAGAAAAGCTTGGAAAAGGTATAATGT
1 TTTCACTTTCTTAGAGGAGAAAAGCTTGGAAAAGGTATAATAT
* *
1922313 TTTCACTTTCTTAGAGGAGAAAAGCTTGGAAAAAGTATAATTT
1 TTTCACTTTCTTAGAGGAGAAAAGCTTGGAAAAGGTATAATAT
*
1922356 TGTTCGCTTTCTTAGAGGAGAAAAGCTTGGAAAAGGTATAATTTAT
1 T-TTCACTTTCTTAGAGGAGAAAAGCTTGGAAAAGGTATAA--TAT
*
1922402 TTTCACTTTCTTAGAGGAGAAAAGCTTGGAAAAGCTATAAT
1 TTTCACTTTCTTAGAGGAGAAAAGCTTGGAAAAGGTATAAT
1922443 TTCTTTCGTA
Statistics
Matches: 119, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
43 42 0.35
44 37 0.31
45 37 0.31
46 3 0.03
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.34
Consensus pattern (43 bp):
TTTCACTTTCTTAGAGGAGAAAAGCTTGGAAAAGGTATAATAT
Found at i:1922426 original size:45 final size:44
Alignment explanation
Indices: 1922264--1922449 Score: 284
Period size: 44 Copynumber: 4.2 Consensus size: 44
1922254 TAAACTATTT
*
1922264 ATTTTCTTTCACTTTCTTAAAGGAGAAAAGCTTGGAAAAGGTATA
1 ATTTT-TTTCACTTTCTTAGAGGAGAAAAGCTTGGAAAAGGTATA
* *
1922309 A-TGTTTTCACTTTCTTAGAGGAGAAAAGCTTGGAAAAAGTATA
1 ATTTTTTTCACTTTCTTAGAGGAGAAAAGCTTGGAAAAGGTATA
* *
1922352 ATTTTGTTCGCTTTCTTAGAGGAGAAAAGCTTGGAAAAGGTATA
1 ATTTTTTTCACTTTCTTAGAGGAGAAAAGCTTGGAAAAGGTATA
*
1922396 ATTTATTTTCACTTTCTTAGAGGAGAAAAGCTTGGAAAAGCTATA
1 ATTT-TTTTCACTTTCTTAGAGGAGAAAAGCTTGGAAAAGGTATA
*
1922441 ATTTCTTTC
1 ATTTTTTTC
1922450 GTATCTTTTA
Statistics
Matches: 128, Mismatches: 11, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
43 38 0.30
44 48 0.38
45 42 0.33
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (44 bp):
ATTTTTTTCACTTTCTTAGAGGAGAAAAGCTTGGAAAAGGTATA
Found at i:1922441 original size:89 final size:87
Alignment explanation
Indices: 1922275--1922444 Score: 288
Period size: 89 Copynumber: 1.9 Consensus size: 87
1922265 TTTTCTTTCA
*
1922275 CTTTCTTAAAGGAGAAAAGCTTGGAAAAGGTATAATGTTTTCACTTTCTTAGAGGAGAAAAGCTT
1 CTTTCTTAAAGGAGAAAAGCTTGGAAAAGGTATAATATTTTCACTTTCTTAGAGGAGAAAAGCTT
1922340 GGAAAAAGTATAATTTTGTTCG
66 GGAAAAAGTATAATTTTGTTCG
*
1922362 CTTTCTTAGAGGAGAAAAGCTTGGAAAAGGTATAATTTATTTTCACTTTCTTAGAGGAGAAAAGC
1 CTTTCTTAAAGGAGAAAAGCTTGGAAAAGGTATAA--TATTTTCACTTTCTTAGAGGAGAAAAGC
1922427 TTGG-AAAAGCTATAATTT
64 TTGGAAAAAG-TATAATTT
1922445 CTTTCGTATC
Statistics
Matches: 78, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
87 34 0.44
88 5 0.06
89 39 0.50
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.34
Consensus pattern (87 bp):
CTTTCTTAAAGGAGAAAAGCTTGGAAAAGGTATAATATTTTCACTTTCTTAGAGGAGAAAAGCTT
GGAAAAAGTATAATTTTGTTCG
Found at i:1923961 original size:30 final size:30
Alignment explanation
Indices: 1923925--1923985 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
1923915 GAAAACTAGA
1923925 GACAAAGAAGAATAGAGAGGAATGCTACTT
1 GACAAAGAAGAATAGAGAGGAATGCTACTT
1923955 GACAAAGAAGAATAGAGAGGAATGCTACTT
1 GACAAAGAAGAATAGAGAGGAATGCTACTT
1923985 G
1 G
1923986 TATTTCTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.46, C:0.10, G:0.28, T:0.16
Consensus pattern (30 bp):
GACAAAGAAGAATAGAGAGGAATGCTACTT
Found at i:1925374 original size:165 final size:164
Alignment explanation
Indices: 1924993--1925374 Score: 375
Period size: 165 Copynumber: 2.3 Consensus size: 164
1924983 AGGGTTTTTT
* ** * * * * *
1924993 TTTTCTTCTTCATAAATTTTTTAGAAGGATTTTCATAGGTTTAAAATTTTGATAATTCATCAAAT
1 TTTTCTAC-TCATAAATTTTTTAGGGGGATTTTCTTTGGTTTAAAATTTTTAAAACTCATCAAAT
* * * *
1925058 ATATTTATTTAATTCATATTAAATTAGCTTTCTAAAAATTCATTTATTTTCATAAATTTTCATTT
65 ATATTCATTTAATTCATACTAAATTAGCTTTCTAAAAATTCATTCATTTTCATAAATTTTCAGTT
* *
1925123 TTTCCTTAAAATTCTCCTATTTCTAAAATACAGAG
130 TTTCCTTAAAATTCTCATATTTCTAAAAAACAGAG
* * * * ***
1925158 TTTTCTAATCGTAAATCTTTTCAAGGGGATTTT-TCTTGGTTTTTGATTTTTAAAACTCATCAAA
1 TTTTCTACTCATAAAT-TTTTTAGGGGGATTTTCT-TTGGTTTAAAATTTTTAAAACTCATCAAA
* * *
1925222 TAT-TGTCATTTGATTCATACTAAATTAG-TTT-TAAAACATTCATTCATTTTCATAAGTTTTGG
64 TATAT-TCATTTAATTCATACTAAATTAGCTTTCTAAAA-ATTCATTCATTTTCATAAATTTT-C
* *
1925284 AGTTTTT-CTTGGAAA-TGTCAT-TTTCTCAAAAAACTA-AG
126 AGTTTTTCCTT-AAAATTCTCATATTTCT-AAAAAAC-AGAG
1925322 TTTTCTACTCCATAAATATTTTTAGGGGGATTTTCTTTGGTTTAAAATTTTTA
1 TTTTCTACT-CATAAAT-TTTTTAGGGGGATTTTCTTTGGTTTAAAATTTTTA
1925375 GAAGTTATCT
Statistics
Matches: 173, Mismatches: 34, Indels: 20
0.76 0.15 0.09
Matches are distributed among these distances:
163 10 0.06
164 55 0.32
165 107 0.62
166 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.48
Consensus pattern (164 bp):
TTTTCTACTCATAAATTTTTTAGGGGGATTTTCTTTGGTTTAAAATTTTTAAAACTCATCAAATA
TATTCATTTAATTCATACTAAATTAGCTTTCTAAAAATTCATTCATTTTCATAAATTTTCAGTTT
TTCCTTAAAATTCTCATATTTCTAAAAAACAGAG
Found at i:1925968 original size:11 final size:12
Alignment explanation
Indices: 1925935--1925966 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
1925925 TAGGTTAGCT
1925935 GAAAAAAAGAGA
1 GAAAAAAAGAGA
1925947 GAAAGAAAAGAGA
1 GAAA-AAAAGAGA
1925960 GAAAAAA
1 GAAAAAA
1925967 GAAAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (12 bp):
GAAAAAAAGAGA
Found at i:1927732 original size:156 final size:155
Alignment explanation
Indices: 1927448--1927992 Score: 564
Period size: 156 Copynumber: 3.5 Consensus size: 155
1927438 TCCTTCACGC
* * * * * ** **
1927448 TTTTAAGTCTTTTAGGGTTAAC-AAAGTACTTTTATGTCGAAGGTATACCTATA-CAGTTTTTTC
1 TTTTAAGTCCTTTAGGGTTATCGAGA-TACTTTCATGTCGAAGGTATACCCATAGGGGCATTTTC
* * * * * * * * * *
1927511 ATAATTTCTAAGAATCGAGTCCTAGGTTGTCACCGGGTCCT-TTTTTATGCTGAAGGTAGATATT
65 GTAATTTTTTAGAACCTAGTCTTAGGTTGTCACCGGGT-CTGCTTTTATGCCGAAGGTGGGTATT
1927575 TAGGATAGGTTCATCCCTTTTAAAATCTT
129 TAGGATAGGTTCATCCCTTTT-AAATC-T
* * *
1927604 TTTTAA-ACTCTGTAGGGTTATCGGGATACTTTCATGTCGAAGGTATACCCATA-GGGCATTTTC
1 TTTTAAGTC-CTTTAGGGTTATCGAGATACTTTCATGTCGAAGGTATACCCATAGGGGCATTTTC
* * *
1927667 GCAATTTTTTAGAACTTAGTCTTAGGTTGTCACCGGGTCTGCTTTTATGCCGAAGGTGGGCATTT
65 GTAATTTTTTAGAACCTAGTCTTAGGTTGTCACCGGGTCTGCTTTTATGCCGAAGGTGGGTATTT
* *
1927732 AGGATAGGTTCATCTCGTCTCT-AATCT
130 AGGATAGGTTCATC-CCT-TTTAAATCT
* * * *
1927759 TTTTAAGTCCTTTAGGGTTACCGAAAAACTTTCATGTCGAAGGTATACCTATAGGGGCATTTTCG
1 TTTTAAGTCCTTTAGGGTTATCGAGATACTTTCATGTCGAAGGTATACCCATAGGGGCATTTTCG
* * *** *
1927824 TAGTTTTTTAAAACCTAGT-TCTAGGTTGTCACCACATCCGCTTTTATGCCGAAGGTGGGTATTT
66 TAATTTTTTAGAACCTAGTCT-TAGGTTGTCACCGGGTCTGCTTTTATGCCGAAGGTGGGTATTT
* *
1927888 AGGATAGGTTCATCCCATCTTGAATCT
130 AGGATAGGTTCATCCC-TTTTAAATCT
* * * *
1927915 TTTTAGGTCCTTTAGGGTTATCGAGATACTTTCATGTTGAAAGTATACCCATAGGGGCATTTTCA
1 TTTTAAGTCCTTTAGGGTTATCGAGATACTTTCATGTCGAAGGTATACCCATAGGGGCATTTTCG
*
1927980 TAATTCTTTAGAA
66 TAATTTTTTAGAA
1927993 TCGAGTCCTG
Statistics
Matches: 322, Mismatches: 57, Indels: 20
0.81 0.14 0.05
Matches are distributed among these distances:
155 51 0.16
156 266 0.83
157 3 0.01
158 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (155 bp):
TTTTAAGTCCTTTAGGGTTATCGAGATACTTTCATGTCGAAGGTATACCCATAGGGGCATTTTCG
TAATTTTTTAGAACCTAGTCTTAGGTTGTCACCGGGTCTGCTTTTATGCCGAAGGTGGGTATTTA
GGATAGGTTCATCCCTTTTAAATCT
Found at i:1935392 original size:2 final size:2
Alignment explanation
Indices: 1935385--1935410 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1935375 TGATTGTGTA
1935385 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1935411 CTTCAATGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1944195 original size:19 final size:18
Alignment explanation
Indices: 1944171--1944222 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
1944161 GATACACTGC
**
1944171 ATCGATACATGATTTTGGT
1 ATCGATACATGAACTT-GT
1944190 ATCGATACATAGTAACTTGT
1 ATCGATACAT-G-AACTTGT
1944210 ATCGATACATGAA
1 ATCGATACATGAA
1944223 ACTGGCAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 2 0.07
19 11 0.38
20 13 0.45
21 3 0.10
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (18 bp):
ATCGATACATGAACTTGT
Found at i:1944274 original size:20 final size:20
Alignment explanation
Indices: 1944249--1944302 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
1944239 CTACCACTGT
*
1944249 TTGTATCGATACATGGTACA
1 TTGTATCGATACATGGTAAA
*
1944269 TTGTATCGATATATGGTAAA
1 TTGTATCGATACATGGTAAA
**
1944289 AAGTATCGATACAT
1 TTGTATCGATACAT
1944303 TGTGCCTAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (20 bp):
TTGTATCGATACATGGTAAA
Found at i:1950228 original size:16 final size:17
Alignment explanation
Indices: 1950209--1950242 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1950199 TTTAGTGTTT
1950209 TTGTGATT-ATTGTTGA
1 TTGTGATTAATTGTTGA
*
1950225 TTGTGTTTAATTGTTGA
1 TTGTGATTAATTGTTGA
1950242 T
1 T
1950243 AAATTTGGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.18, C:0.00, G:0.24, T:0.59
Consensus pattern (17 bp):
TTGTGATTAATTGTTGA
Found at i:1952263 original size:20 final size:21
Alignment explanation
Indices: 1952209--1952264 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
1952199 TTTAGAAACA
*
1952209 AAAAGAGGGAGAGATGTTTTTG
1 AAAAG-GGGAGAAATGTTTTTG
*
1952231 AAAACGGGAAGAAAT-TTTATT-
1 AAAA-GGGGAGAAATGTTT-TTG
1952252 AAAAGGGGAGAAA
1 AAAAGGGGAGAAA
1952265 AATTTTTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 8 0.28
21 7 0.24
22 13 0.45
23 1 0.03
ACGTcount: A:0.46, C:0.02, G:0.30, T:0.21
Consensus pattern (21 bp):
AAAAGGGGAGAAATGTTTTTG
Found at i:1955180 original size:22 final size:23
Alignment explanation
Indices: 1955149--1955200 Score: 88
Period size: 22 Copynumber: 2.3 Consensus size: 23
1955139 CATGTTAAAG
*
1955149 ATGCACGAAACATAAT-AAAAAA
1 ATGCATGAAACATAATAAAAAAA
1955171 ATGCATGAAACATAATAAAAAAA
1 ATGCATGAAACATAATAAAAAAA
1955194 ATGCATG
1 ATGCATG
1955201 GTCAAAGGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 15 0.54
23 13 0.46
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.17
Consensus pattern (23 bp):
ATGCATGAAACATAATAAAAAAA
Found at i:1956157 original size:20 final size:20
Alignment explanation
Indices: 1956134--1956184 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1956124 CTGTAGAATA
* *
1956134 TATCGATACATTCATACATG
1 TATCGATACATTCAAAAATG
* *
1956154 TATCGATATATTGAAAAATG
1 TATCGATACATTCAAAAATG
1956174 TATCGATACAT
1 TATCGATACAT
1956185 CAGGGTATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (20 bp):
TATCGATACATTCAAAAATG
Found at i:1956901 original size:28 final size:28
Alignment explanation
Indices: 1956792--1961063 Score: 4142
Period size: 28 Copynumber: 148.8 Consensus size: 28
1956782 CACTGACACA
* **
1956792 TGTGGGCTTTGAAAAGAGTGTTACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
*
1956821 TGCGTGGGCTTTAAAAGGGTGCCACTGACT
1 T--GTGGGCTTTGAAAGGGTGCCACTGACT
* *
1956851 TGCGTGGGCTTTGGAAGGATGCCACTGACT
1 T--GTGGGCTTTGAAAGGGTGCCACTGACT
* *
1956881 CGTGGGCTTTGAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
1956909 TGTGGGCTTTGAAA-GGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1956936 CGTGGGCTTTGAAAAGGTACCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1956964 CGTGGGC-TTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1956991 TATGGGCTTTGAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1957019 CGTGGGCTTTGAAAAGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
1957047 TGCGTGGGCTTTGAAAGGAGTGCCACTGACTT
1 T--GTGGGCTTTGAAAGG-GTGCCACTGAC-T
1957079 GTGTGGGCTTTGAAAGGAGTGCCACTGACTT
1 -TGTGGGCTTTGAAAGG-GTGCCACTGAC-T
* *
1957110 GTGTGGGCTTTGAAAGGGTGCCATTAACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1957139 TGTAGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1957167 TGTGGGCTTTGAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
1957195 CGTGGGCTTTGAAAAGGTACTACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1957223 TGCGTGAGCTTTAAAAGGAGTGCCACTGACT
1 T--GTGGGCTTTGAAAGG-GTGCCACTGACT
1957254 TGCGTGGGCTTTGAAAAGGGTGCCACTGACT
1 T--GTGGGCTTTG-AAAGGGTGCCACTGACT
1957285 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1957313 TGTGGGCTTTGAAAAGAGTGCCAATAACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
1957342 TGTGGGCTTTCAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
1957370 TACGTGGGCTTTGAAAGGGGTGCCACTGACT
1 T--GTGGGCTTTGAAA-GGGTGCCACTGACT
*
1957401 TGTGGGCTTTGAAAGGGTGCCACCGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1957429 TGTGTAGGCTTTGAAAGGATGCCACTAACT
1 TGTG--GGCTTTGAAAGGGTGCCACTGACT
*
1957459 TGTGGGCTTTGAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1957487 CGTGGGCTTTGAAAAGGTACCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1957515 TGCGTGAGCTTTAAAAGGAGTGCCACTGACAT
1 T--GTGGGCTTTGAAAGG-GTGCCACTGAC-T
* *
1957547 GTGTAGGCTTTAAAAGGGTGCCACTGACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1957576 TGTGGGCTTTGAAAGAGTGCCACTAAAT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
1957604 TGTGGGCTTCGCAATGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1957632 TGTGGGCTTCGAAAGGGTGCCACTTACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
1957660 TGCGTGGGCTTTGAAAAGGGTGCCACTGACT
1 T--GTGGGCTTTG-AAAGGGTGCCACTGACT
*
1957691 TGCGTGGGCTTTGAAAAGTGTGCCACTGACT
1 T--GTGGGCTTTG-AAAGGGTGCCACTGACT
*
1957722 TGTGGGCTTTGAAAGGGTGCCATTGAC-
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
1957749 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
** * *
1957777 TGTGGGCTTTGAAAAAAGTGCCAATAACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
1957806 TGTGGGCTTTAAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1957834 TGCGTGGGCTTTGAAAGGGGTGCCACTAACT
1 T--GTGGGCTTTGAAA-GGGTGCCACTGACT
*
1957865 TGTGGGCTTTGAAAGGGTGCCACCGACTT
1 TGTGGGCTTTGAAAGGGTGCCACTGAC-T
* *
1957894 GTGTGGGCTTTGAAAGGATGCCACAGACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1957923 TGTGGACTTTAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
** * * *
1957951 CATGGGTTTTGAAAAGGTACCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1957979 TGCGTGAGCTTTAAAAGAAGTGCCACTGACTT
1 T--GTGGGCTTTGAAAG-GGTGCCACTGAC-T
*
1958011 GTGTGGGCTTTAAAAGGGTGCCACTGACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1958040 TGTGGGCTTTGAAAGAGTGCCACTGAAT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1958068 TGTGGGCTTCGCAAA-GGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
*
1958096 TGTGGGCTTCGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
1958124 TGCGTGGGCTTTGAAAAGGGTGCCACTGACT
1 T--GTGGGCTTTG-AAAGGGTGCCACTGACT
* *
1958155 TGTGGACTTTGAAAAGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1958183 TGTGGGCTTTGAAAAGAGTGCCAATAACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
1958212 TGTGGGCTTTAAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
1958240 TGCGTGGGCTTTGAAAGGGGTGCCACTGACT
1 T--GTGGGCTTTGAAA-GGGTGCCACTGACT
*
1958271 TGTGGGCTTTGAAAGGGTGCCACCGACTT
1 TGTGGGCTTTGAAAGGGTGCCACTGAC-T
*
1958300 GTGTGGGCTTTGAAAGGATGCCACTGACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1958329 TGTGGGCTTTGGAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1958357 CGTGGGCTTTGAAAAGGTACCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
1958385 TGCGTGAGCTTTAAAAAGAGTGCCACTAACTT
1 T--GTGGGCTTT-GAAAGGGTGCCACTGAC-T
* *
1958417 GTGTGGGCTTTAAAAGGGTGCCACTAACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1958446 TGTGGGCTTTGAAAGAGTGCCACTGAAT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1958474 TGTGGGCTTCGCAATGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1958502 TGTGGGCTTCGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1958530 TGCGTGGGCTTTAAAAAGGGTGCCACTGACT
1 T--GTGGGCTTT-GAAAGGGTGCCACTGACT
1958561 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
** * *
1958589 TGTGGGCTTTGAAAAGAATGCCAATAACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* * *
1958618 TGTTGGCTTTAAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1958646 TGCGTGGGCTTTGAAAAGGGTGCCACTAACT
1 T--GTGGGCTTTG-AAAGGGTGCCACTGACT
*
1958677 TGTGGGCTTTGAAAGGGTGCCACCGACTT
1 TGTGGGCTTTGAAAGGGTGCCACTGAC-T
*
1958706 GTGTGGGCTTTGAAAGGATGCCACTGACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1958735 TGTGGGCTTTGAAAGAGTGGCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1958763 CGTGGGCTTTGAAAAGGTACCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1958791 TGCGTGAGCTTTAAAAGGTGTGCCACTGACTT
1 T--GTGGGCTTTGAAAGG-GTGCCACTGAC-T
*
1958823 GTGTGGGCTTTAAAAGGGTGCCACTGACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1958852 TGTGGGCTTTGAAAGAGTGCCACTAAAT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
1958880 TGTGGGCTTCGCAATGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1958908 TGTGGGCTTCGAAAGGGTGCCCCTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
1958936 TGCATGGGCTTTGAAAAGGGTGCCACTGACT
1 TG--TGGGCTTTG-AAAGGGTGCCACTGACT
* *
1958967 TGTAGGCTTTGAAAGGGTGGCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1958995 TGTGGGCTTTGAAAAGGGTGCCAATAACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* * *
1959024 TGTGGGCTTTAAAAGGGTGCCCCTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
1959052 TGCGTGGGCTTTGAAAGGGGTGCCACTGACT
1 T--GTGGGCTTTGAAA-GGGTGCCACTGACT
*
1959083 TGTGGGCTTTGAAAGGGTGCCACCGACTT
1 TGTGGGCTTTGAAAGGGTGCCACTGAC-T
*
1959112 GTGTGGGCTTTGAAAGGATGCCACTGACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1959141 TGTGGACTTTGAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1959169 CGTGGGCTTTGAAAAGGTACCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1959197 TGCGTGAGCTTTGAAAGGAGTGCCACTGACTT
1 T--GTGGGCTTTGAAAGG-GTGCCACTGAC-T
*
1959229 GTGTGGGCTTTAAAAGGGTGCCACTGACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1959258 TGTGGGCTTTGAAAGAGTGCCACTGAAT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1959286 TGTGGGCTTCGCAATGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1959314 TGTGGGCTTCGAAAGGGTACCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1959342 TGCGTGGGCTTTAAAAAGGGTGCCACTGACT
1 T--GTGGGCTTT-GAAAGGGTGCCACTGACT
1959373 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1959401 TGTGGGCTTTGAAAAGAGTGCCAATAACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
1959430 TGTGGGCTTTAAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
1959458 TGCGTGGGCTTTGAAAGGGGTGCCACTGACT
1 T--GTGGGCTTTGAAA-GGGTGCCACTGACT
*
1959489 TGTGGGCTTTGAAAGGGTGCCACCGACTT
1 TGTGGGCTTTGAAAGGGTGCCACTGAC-T
*
1959518 GTGTGGGCTTTGAAAGGATGCCACTGACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1959547 TGTGGGCTTTGAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1959575 CGTGGGCTTTGAAAAGGTACCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1959603 TGCGTGAGCTTTAAAAGGAGTGCCACTGACTT
1 T--GTGGGCTTTGAAAGG-GTGCCACTGAC-T
*
1959635 GTGTGGGCTTTAAAAGGGTGCCACTGACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1959664 TGTGGGCTTTGAAAGAGG-GCCACTGAAT
1 TGTGGGCTTTGAAAG-GGTGCCACTGACT
* *
1959692 TGTGGGCTTTGCAATGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1959720 TGTGGGCTTCGAAAGGGTGCCAATGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1959748 TGTGGGCTCTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
1959776 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1959804 TGTGGGCTTTGAAAAGAGTGCCACTGATT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
1959833 TGTGGGCTTTGAAAAGAGGT-CCACTGACT
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACT
*
1959862 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
*
1959891 TGTGGGCTTTGAAAGGAGTGCCACTGATTT
1 TGTGGGCTTTGAAAGG-GTGCCACTGA-CT
*
1959921 GTGTGGGCTTTAAAAGGGTGCCACTGACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1959950 TGTGGGCTTTGAAAGAGTGCCACTGAAT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1959978 TGTGGGCTTCG-TAGTGGTGCCACTGACT
1 TGTGGGCTTTGAAAG-GGTGCCACTGACT
*
1960006 TGTGGGCTTCGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
1960034 TGCGTGGGCTTTGAAAAGGGTGCCACTGACT
1 T--GTGGGCTTTG-AAAGGGTGCCACTGACT
1960065 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1960093 TGTGGGCTTTGAAAAGAGTGCCACTAACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
1960122 TGTGGGCTTTAAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
1960150 TGCGTGGGCTTTGAAAGGGGTGCCACTGACT
1 T--GTGGGCTTTGAAA-GGGTGCCACTGACT
*
1960181 TGTGGGCTTTGAAAGGGTGCCACCGACTT
1 TGTGGGCTTTGAAAGGGTGCCACTGAC-T
* *
1960210 GTGTGGGCTTTGAAATGGGTTCCCACCGACTT
1 -TGTGGGCTTTGAAA-GGG-TGCCACTGAC-T
1960242 GTGTGGGCTTTGAAATGGGTTGCCACTGACTT
1 -TGTGGGCTTTGAAA-GGG-TGCCACTGAC-T
* * *
1960274 GTGTGGGCTTTGAAATAGGTGCCACAGAGT
1 -TGTGGGCTTTGAAA-GGGTGCCACTGACT
** * * * *
1960304 TGTGGATTTTAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
** * * *
1960332 TGTGGATTTTAAAAGGGTGCCACAGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* ** * * *
1960360 TGTGGAC-TCAAAAGAGATGCCACGGAGT
1 TGTGGGCTTTGAAAG-GGTGCCACTGACT
* * * * *
1960388 TATGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * * *
1960415 TATGGTC-TTAAAAGGATGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * **
1960442 TGTGGAC-TTAAAAGGGTGCCACGGTGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
1960469 TGTGGAC-TTAAAAGGGTGCCACAGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
1960496 TGTGGAC-TTAAAAGGGTGCCACAGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
1960523 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* ** * **
1960550 TGTGGAC-TAAAAAGGGTGCCACGGTGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
1960577 TGTGGACTTTAAAAGGGTGCCACAGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
1960605 TGTGGAC-TTAAAAGAGATGCCACGGAGT
1 TGTGGGCTTTGAAAG-GGTGCCACTGACT
* * * * *
1960633 TATGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
1960660 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
1960687 TGTGGTC-TTAAAAGGGATGCCACGGAGT
1 TGTGGGCTTTGAAAGGG-TGCCACTGACT
* * * *
1960715 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1960742 TGTGGAC-TTAAAAGGGTGCCA-TGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACT-GACT
* * ** * *
1960769 TGTGGAC-TTAAAAGAATGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
1960796 TGTGGACTTTAAAAGGATGCCAC-GAAGT
1 TGTGGGCTTTGAAAGGGTGCCACTG-ACT
* * * *
1960824 TGTGGAC-TTAAAAGGGATGCCACGGAGT
1 TGTGGGCTTTGAAAGGG-TGCCACTGACT
* * * *
1960852 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
1960879 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
1960906 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
1960933 TGTTGACTTTAAAAGGGTGCCACAGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
1960961 TGTGGAC-TTAAAAGAGATGCCACGGAGT
1 TGTGGGCTTTGAAAG-GGTGCCACTGACT
* * * * *
1960989 TATGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
1961016 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1961043 TGTGGACTTTAAAAGGGTGCC
1 TGTGGGCTTTGAAAGGGTGCC
1961064 GCAGAGTTGT
Statistics
Matches: 3721, Mismatches: 391, Indels: 263
0.85 0.09 0.06
Matches are distributed among these distances:
27 515 0.14
28 1663 0.45
29 442 0.12
30 522 0.14
31 501 0.13
32 71 0.02
33 7 0.00
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.27
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:1957935 original size:406 final size:401
Alignment explanation
Indices: 1956824--1960298 Score: 2610
Period size: 406 Copynumber: 8.6 Consensus size: 401
1956814 ACTGACTTGC
* * * *
1956824 GTGGGCTTTAAAAGGGTGCCACTGACTTGCGTGGGCTTTGGAAGGATGCCACTGACTCGTGGGCT
1 GTGGGCTTTGAAAGGGTGCCACTGACTT--GTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
* * * *
1956889 TTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAA-GGTGCCACTGAC-T-CGTGGGCTTTGAAA
64 TTGAAAAGAGTGCCAATAACTTGTGGGCTTTAAAAGGGTGCCACTAACTTGCGTGGGCTTTGAAA
* * * * *
1956950 -AGGTACCACTGACTCGTGGGC-TTGAAAGGGTGCCACTGAC-T-TATGGGCTTTGAAA-GAGTG
129 GGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACCGACTTGTGTGGGCTTTGAAAGGA-TG
* * *
1957010 CCACTGACTCGTGGGCTTTGAAA-AGGTGCCACTGACTTGCGTGGGCTTTGAAAGGAGTGCCACT
193 CCACTGACTTGTGGGCTTTGAAAGA-GTGCCACTGAC-T-CGTGGGCTTTGAAAAG-GTACCACT
* * * * * * *
1957074 GACTTGTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCATTAACT
254 GACTT-CGTGAGCTTT-AAAAGAGTGCCACTGAATTGTGTGGGCTTTAAAAGGGTGCCACTGACT
* * * * *
1957139 TGTAGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTT
317 TGTGGGCTTTGAAAGGGTGCCACTGAATTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTT
* * * *
1957204 TGAAAAGGTACTACTGACTT
382 CGAAAGGGTGCCACTGACTT
* *
1957224 GCGTGAGCTTTAAAAGGAGTGCCACTGACTTGCGTGGGCTTTGAAAAGGGTGCCACTGACTTGTG
1 --GTGGGCTTTGAAAGG-GTGCCACTGACTT--GTGGGCTTTG-AAAGGGTGCCACTGACTTGTG
* * * * *
1957289 GGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCAATAACTT--GTGGGCTT
60 GGCTTTGAAAAGAGTGCCAATAACTTGTGGGCTTT-AAAAGGGTGCCACTAACTTGCGTGGGCTT
* * *
1957351 TCAAA-GGGTGCCACTAACTTACGTGGGCTTTGAAAGGGGTGCCACTGAC-T-TGTGGGCTTTGA
124 TGAAAGGGGTGCCACTGACTT--GTGGGCTTTGAAA-GGGTGCCACCGACTTGTGTGGGCTTTGA
* * * *
1957413 AAGGGTGCCACCGACTTGTGTAGGCTTTGAAAG-GATGCCACTAACTTGTGGGCTTTG-AAAGAG
186 AAGGATGCCACTGACTTGTG--GGCTTTGAAAGAG-TGCCACTGACTCGTGGGCTTTGAAAAG-G
* * * * * *
1957476 TGCCACTGAC-TCGTGGGCTTTGAAAAG-GTACCACTGACTTGCGTGAGCTTTAAAAGGAGTGCC
247 TACCACTGACTTCGTGAGCTTT-AAAAGAGTGCCACTGAATTGTGTGGGCTTTAAAAGG-GTGCC
* * * * * *
1957539 ACTGACATGTGTAGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTAAAT
310 ACTGAC-T-TGTGGGCTTTGAAAGGGTGCCACTGAATTGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1957604 TGTGGGCTTCGCAATGGTGCCACTAACTT
373 TGTGGGCTTCGAAAGGGTGCCACTGACTT
* *
1957633 GTGGGCTTCGAAAGGGTGCCACTTACTTGCGTGGGCTTTGAAAAGGGTGCCACTGACTTGCGTGG
1 GTGGGCTTTGAAAGGGTGCCACTGACTT--GTGGGCTTTG-AAAGGGTGCCACTGACTT--GTGG
* * * * * *
1957698 GCTTTGAAAAGTGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCATTGAC-T--GTGGGCTTTG
61 GCTTTGAAAAGAGTGCCAATAACTTGTGGGCTTTAAAAGGGTGCCACTAACTTGCGTGGGCTTTG
** *** *
1957760 AAA-GGGTGCCACTGACTTGTGGGCTTTGAAAAAAGTGCCAATAAC-T-TGTGGGCTTTAAAAGG
126 AAAGGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACCGACTTGTGTGGGCTTTGAAAGG
* * * * * * *
1957822 GTGCCACTAACTTGCGTGGGCTTTGAAAGGGGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCA
190 ATGCCACTGACTT--GTGGGCTTTGAAA-GAGTGCCACTGACTCGTGGGCTTTGAAAAGGTACCA
* * * * * * * *
1957887 CCGACTTGTGTGGGCTTTGAAAG-GATGCCACAG-ACT-TGTGGACTTTAAAAGAGTGCCACTGA
252 CTGACTT-CGTGAGCTTTAAAAGAG-TGCCACTGAATTGTGTGGGCTTTAAAAGGGTGCCACTGA
** * * * * * * *
1957949 CTCATGGGTTTTGAAAAGGTACCACTGACTTGCGTGAGCTTTAAAAGAAGTGCCACTGACTTGTG
315 CTTGTGGGCTTTGAAAGGGTGCCACTGAATT--GTGGGCTTTGAAAG-GGTGCCACTGAC-T-TG
**
1958014 TGGGCTTTAAAAGGGTGCCACTGACTT
375 TGGGCTTCGAAAGGGTGCCACTGACTT
* * *
1958041 GTGGGCTTTGAAAGAGTGCCACTGAATTGTGGGCTTCGCAAA-GGTGCCACTGACTTGTGGGCTT
1 GTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTT
* * * * * *
1958105 CG-AAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAAGGGTGCCACTGACTT--GTGGACTTTGA
65 TGAAAAGAGTGCCAATAACTT--GTGGGCTTT-AAAAGGGTGCCACTAACTTGCGTGGGCTTTGA
* * *** * *
1958167 AA-AGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCAATAAC-T-TGTGGGCTTTAAAAGGG
127 AAGGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACCGACTTGTGTGGGCTTTGAAAGGA
* * * * *
1958229 TGCCACTAACTTGCGTGGGCTTTGAAAGGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCAC
191 TGCCACTGACTT--GTGGGCTTTGAAA-GAGTGCCACTGACTCGTGGGCTTTGAAAAGGTACCAC
* * * * * ** *
1958294 CGACTTGTGTGGGCTTTGAAAG-GATGCCACTG-ACT-TGTGGGCTTTGGAAGAGTGCCACTGAC
253 TGACTT-CGTGAGCTTTAAAAGAG-TGCCACTGAATTGTGTGGGCTTTAAAAGGGTGCCACTGAC
* * * * * * * *
1958356 TCGTGGGCTTTGAAAAGGTACCACTGACTTGCGTGAGCTTTAAAAAGAGTGCCACTAACTTGTGT
316 TTGTGGGCTTTGAAAGGGTGCCACTGAATT--GTGGGCTTT-GAAAGGGTGCCACTGAC-T-TGT
** *
1958421 GGGCTTTAAAAGGGTGCCACTAACTT
376 GGGCTTCGAAAGGGTGCCACTGACTT
* * * * * *
1958447 GTGGGCTTTGAAAGAGTGCCACTGAATTGTGGGCTTCGCAATGGTGCCACTGACTTGTGGGCTTC
1 GTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTT
* * * *
1958512 G-AAAGGGTGCCACTGACTTGCGTGGGCTTTAAAAAGGGTGCCACTGACTT--GTGGGCTTTGAA
66 GAAAAGAGTGCCAATAACTT--GTGGGCTTT-AAAAGGGTGCCACTAACTTGCGTGGGCTTTGAA
** *** * *
1958574 A-GGGTGCCACTGACTTGTGGGCTTTGAAAAGAATGCCAATAACTTGT-T-GGCTTTAAAAGGGT
128 AGGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACCGACTTGTGTGGGCTTTGAAAGGAT
* * * * * * *
1958636 GCCACTAACTTGCGTGGGCTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACC
192 GCCACTGACTT--GTGGGCTTTG-AAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTACCACT
* * * * * * *
1958701 GACTTGTGTGGGCTTTGAAAG-GATGCCACTG-ACT-TGTGGGCTTTGAAAGAGTGGCACTGACT
254 GACTT-CGTGAGCTTTAAAAGAG-TGCCACTGAATTGTGTGGGCTTTAAAAGGGTGCCACTGACT
* * * * * *
1958763 CGTGGGCTTTGAAAAGGTACCACTGACTTGCGTGAGCTTTAAAAGGTGTGCCACTGACTTGTGTG
317 TGTGGGCTTTGAAAGGGTGCCACTGAATT--GTGGGCTTTGAAAGG-GTGCCACTGAC-T-TGTG
**
1958828 GGCTTTAAAAGGGTGCCACTGACTT
377 GGCTTCGAAAGGGTGCCACTGACTT
* * * * * * * *
1958853 GTGGGCTTTGAAAGAGTGCCACTAAATTGTGGGCTTCGCAATGGTGCCACTAACTTGTGGGCTTC
1 GTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTT
* ** * * *
1958918 G-AAAGGGTGCCCCTGACTTGCATGGGCTTTGAAAAGGGTGCCACTGACTT--GTAGGCTTTGAA
66 GAAAAGAGTGCCAATAACTTG--TGGGCTTT-AAAAGGGTGCCACTAACTTGCGTGGGCTTTGAA
* *** * *
1958980 A-GGGTGGCACTGACTTGTGGGCTTTGAAAAGGGTGCCAATAAC-T-TGTGGGCTTTAAAAGGGT
128 AGGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACCGACTTGTGTGGGCTTTGAAAGGAT
* * * * * * *
1959042 GCCCCTAACTTGCGTGGGCTTTGAAAGGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACC
192 GCCACTGACTT--GTGGGCTTTGAAA-GAGTGCCACTGACTCGTGGGCTTTGAAAAGGTACCACT
* * * * * * *
1959107 GACTTGTGTGGGCTTTGAAAG-GATGCCACTG-ACT-TGTGGACTTTGAAAGAGTGCCACTGACT
254 GACTT-CGTGAGCTTTAAAAGAG-TGCCACTGAATTGTGTGGGCTTTAAAAGGGTGCCACTGACT
* * * * *
1959169 CGTGGGCTTTGAAAAGGTACCACTGACTTGCGTGAGCTTTGAAAGGAGTGCCACTGACTTGTGTG
317 TGTGGGCTTTGAAAGGGTGCCACTGAATT--GTGGGCTTTGAAAGG-GTGCCACTGAC-T-TGTG
**
1959234 GGCTTTAAAAGGGTGCCACTGACTT
377 GGCTTCGAAAGGGTGCCACTGACTT
* * * * * *
1959259 GTGGGCTTTGAAAGAGTGCCACTGAATTGTGGGCTTCGCAATGGTGCCACTGACTTGTGGGCTTC
1 GTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTT
* * * * *
1959324 G-AAAGGGTACCACTGACTTGCGTGGGCTTTAAAAAGGGTGCCACTGACTT--GTGGGCTTTGAA
66 GAAAAGAGTGCCAATAACTT--GTGGGCTTT-AAAAGGGTGCCACTAACTTGCGTGGGCTTTGAA
* *** * *
1959386 A-GGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCAATAAC-T-TGTGGGCTTTAAAAGGGT
128 AGGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACCGACTTGTGTGGGCTTTGAAAGGAT
* * * * * *
1959448 GCCACTAACTTGCGTGGGCTTTGAAAGGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACC
192 GCCACTGACTT--GTGGGCTTTGAAA-GAGTGCCACTGACTCGTGGGCTTTGAAAAGGTACCACT
* * * * * *
1959513 GACTTGTGTGGGCTTTGAAAG-GATGCCACTG-ACT-TGTGGGCTTTGAAAGAGTGCCACTGACT
254 GACTT-CGTGAGCTTTAAAAGAG-TGCCACTGAATTGTGTGGGCTTTAAAAGGGTGCCACTGACT
* * * * * *
1959575 CGTGGGCTTTGAAAAGGTACCACTGACTTGCGTGAGCTTTAAAAGGAGTGCCACTGACTTGTGTG
317 TGTGGGCTTTGAAAGGGTGCCACTGAATT--GTGGGCTTTGAAAGG-GTGCCACTGAC-T-TGTG
**
1959640 GGCTTTAAAAGGGTGCCACTGACTT
377 GGCTTCGAAAGGGTGCCACTGACTT
* * *
1959665 GTGGGCTTTGAAAGAGG-GCCACTGAATTGTGGGCTTTGCAATGGTGCCACTGACTTGTGGGCTT
1 GTGGGCTTTGAAAG-GGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTT
* * * * * *
1959729 CG-AAAGGGTGCCAATGAGTTGTGGGCTCTGAAAGGGTGCCACTAACTT--GTGGGCTTTGAAA-
65 TGAAAAGAGTGCCAATAACTTGTGGGCTTTAAAAGGGTGCCACTAACTTGCGTGGGCTTTGAAAG
* * * *
1959790 GGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGA-TT-TGTGGGCTTTGAAAAGAGGT
130 GGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACCGACTTGTGTGGGCTTTGAAAGGATG-
* * *
1959853 CCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGA
193 CCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTCGTGGGCTTTGAAAAG-GTACCACTGA
* * * * * * * *
1959918 TTTGTGTGGGCTTTAAAAGGGTGCCACTG-ACT-TGTGGGCTTTGAAAGAGTGCCACTGAATTGT
256 CTT-CGTGAGCTTTAAAAGAGTGCCACTGAATTGTGTGGGCTTTAAAAGGGTGCCACTGACTTGT
* * * *
1959981 GGGCTTCG-TAGTGGTGCCACTGACTTGTGGGCTTCGAAAGGGTGCCACTGACTTGCGTGGGCTT
320 GGGCTTTGAAAG-GGTGCCACTGAATTGTGGGCTTTGAAAGGGTGCCACTGACTT--GTGGGCTT
*
1960045 TGAAAAGGGTGCCACTGACTT
382 CG-AAAGGGTGCCACTGACTT
* *
1960066 GTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTT
1 GTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTT
* * * *
1960131 T-AAAAGGGTGCCACTAACTTGCGTGGGCTTTGAAAGGGGTGCCACTGACTT--GTGGGCTTTGA
65 TGAAAAGAGTGCCAATAACTT--GTGGGCTTT-AAAAGGGTGCCACTAACTTGCGTGGGCTTTGA
* *
1960193 AA-GGGTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTCCCACCGACTTGTGTGGGCTTTGAAA
127 AAGGGGTGCCACTGAC-T-TGTGGGCTTTGAAA-GGG-TGCCACCGACTTGTGTGGGCTTTGAAA
* *
1960257 TGGGTTGCCACTGACTTGTGTGGGCTTTGAAATAGGTGCCAC
188 --GGATGCCACTGAC-T-TGTGGGCTTTGAAAGA-GTGCCAC
1960299 AGAGTTGTGG
Statistics
Matches: 2801, Mismatches: 194, Indels: 145
0.89 0.06 0.05
Matches are distributed among these distances:
398 1 0.00
399 1 0.00
400 22 0.01
401 64 0.02
402 108 0.04
403 230 0.08
404 89 0.03
405 164 0.06
406 1675 0.60
407 102 0.04
408 103 0.04
409 123 0.04
410 64 0.02
411 11 0.00
412 26 0.01
413 18 0.01
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.28
Consensus pattern (401 bp):
GTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTT
GAAAAGAGTGCCAATAACTTGTGGGCTTTAAAAGGGTGCCACTAACTTGCGTGGGCTTTGAAAGG
GGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACCGACTTGTGTGGGCTTTGAAAGGATGCCA
CTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTACCACTGACTTCG
TGAGCTTTAAAAGAGTGCCACTGAATTGTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTT
TGAAAGGGTGCCACTGAATTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTCGAAAGGGT
GCCACTGACTT
Found at i:1960443 original size:82 final size:81
Alignment explanation
Indices: 1959644--1961112 Score: 1234
Period size: 82 Copynumber: 17.4 Consensus size: 81
1959634 TGTGTGGGCT
* * * * * * * ** *
1959644 TTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGG-GCCACTGAATTGTGGGCTTTGCAATG
1 TTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAG-GGTGCCACGGAGTTGTGGAC-TTAAAAGG
* * *
1959708 GTGCCACTGACTTGTGGGC
63 GTGCCACGGAGTTGTGGAC
* ** * * ** * * *
1959727 TTCGAAAGGGTGCCAATGAGTTGTGGGCTCTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGG
1 TT-AAAAGGGTGCCACGGAGTTGTGGACT-TAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGG
* * *
1959792 GTGCCACTGACTTGTGGGC
63 GTGCCACGGAGTTGTGGAC
* * * * * * *
1959811 TTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGAGGT-CCACTGACTTGTGGGCTTTGAA
1 -TT-AAAAGGGTGCCACGGAGTTGTGGAC-TT-AAAAG-GGTGCCACGGAGTTGTGGAC-TT-AA
* * * *
1959875 AAGAGTGCCACTGACTTGTGGGC
59 AAGGGTGCCACGGAGTTGTGGAC
* * * * * * * *
1959898 TTTGAAAGGAGTGCCACTGATTTGTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAA
1 -TTAAAAGG-GTGCCACGGA-GT-TGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAA
* * * *
1959963 AGAGTGCCACTGAATTGTGGGC
60 AGGGTGCCACGGAGTTGTGGAC
*** * * * * * * *
1959985 TTCGTAGTGGTGCCACTGACTTGTGGGCTTCGAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAA
1 TTAAAAG-GGTGCCACGGAGTTGTGGACTT-AAAAGGGTGCCACGGAGTT--GTGGAC-TT-AAA
* * *
1960050 AGGGTGCCACTGACTTGTGGGC
60 AGGGTGCCACGGAGTTGTGGAC
* * * * * ** * *
1960072 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTAAAAG
1 -TTAAAAGGGTGCCACGGAGTTGTGGAC-TT-AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAG
** * *
1960137 GGTGCCACTAACTTGCGTGGGC
62 GGTGCCACGGAGTT--GTGGAC
* * * * * * * *
1960159 TTTGAAAGGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACCGACTTGTGTGGGCTTTGAA
1 -TT-AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGA-GT-TGTGGAC-TT-AA
* * * * *
1960224 ATGGGTTCCCACCGACTTGTGTGGGC
59 AAGGG-TGCCACGGA-GT-TGTGGAC
* * * * * *
1960250 TTTGAAATGGGTTGCCACTGACTTGTGTGGGCTTTGAAATA-GGTGCCACAGAGTTGTGGATTTT
1 -TT-AAAAGGG-TGCCACGGA-GT-TGTGGAC-TT-AAA-AGGGTGCCACGGAGTTGTGGA-CTT
* *
1960314 AAAAGAGTGCCACGGAGTTGTGGATT
57 AAAAGGGTGCCACGGAGTTGTGGA-C
* * * *
1960340 TTAAAAGGGTGCCACAGAGTTGTGGACTCAAAAGAGATGCCACGGAGTTATGGACTTAAAAGGGT
1 TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG-GGTGCCACGGAGTTGTGGACTTAAAAGGGT
* *
1960405 GCCACGGAGTTATGGTC
65 GCCACGGAGTTGTGGAC
* *
1960422 TTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGTGTTGTGGACTTAAAAGGGTG
1 TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTG
*
1960487 CCACAGAGTTGTGGAC
66 CCACGGAGTTGTGGAC
* *
1960503 TTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTAAAAAGGGTG
1 TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTG
*
1960568 CCACGGTGTTGTGGAC
66 CCACGGAGTTGTGGAC
* * *
1960584 TTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGATGCCACGGAGTTATGGACTTAAAAGGG
1 -TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG-GGTGCCACGGAGTTGTGGACTTAAAAGGG
1960649 TGCCACGGAGTTGTGGAC
64 TGCCACGGAGTTGTGGAC
*
1960667 TTAAAAGGGTGCCACGGAGTTGTGGTCTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGT
1 TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGT
1960732 GCCACGGAGTTGTGGAC
65 GCCACGGAGTTGTGGAC
* ** *
1960749 TTAAAAGGGTGCCATGGAGTTGTGGACTTAAAAGAATGCCACGGAGTTGTGGACTTTAAAAGGAT
1 TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGT
*
1960814 GCCACGAAGTTGTGGAC
65 GCCACGGAGTTGTGGAC
1960831 TTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGT
1 TTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGT
1960896 GCCACGGAGTTGTGGAC
65 GCCACGGAGTTGTGGAC
* * *
1960913 TTAAAAGGGTGCCACGGAGTTGTTGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGA
1 TTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG-GG
*
1960978 TGCCACGGAGTTATGGAC
64 TGCCACGGAGTTGTGGAC
1960996 TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGT
1 TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGT
* *
1961061 GCCGCAGAGTTGTGGAC
65 GCCACGGAGTTGTGGAC
* * *
1961078 TTAAAAAGATGCCACAGAGTTGTGGACTTTAAAAG
1 TTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAG
1961113 AAAATGCCAC
Statistics
Matches: 1218, Mismatches: 122, Indels: 92
0.85 0.09 0.06
Matches are distributed among these distances:
81 152 0.12
82 341 0.28
83 176 0.14
84 111 0.09
85 49 0.04
86 60 0.05
87 137 0.11
88 81 0.07
89 27 0.02
90 7 0.01
91 29 0.02
92 15 0.01
93 9 0.01
94 11 0.01
95 12 0.01
96 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.34, T:0.26
Consensus pattern (81 bp):
TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTG
CCACGGAGTTGTGGAC
Found at i:1960675 original size:137 final size:135
Alignment explanation
Indices: 1959644--1961112 Score: 1234
Period size: 137 Copynumber: 10.5 Consensus size: 135
1959634 TGTGTGGGCT
* * * * * * * ** *
1959644 TTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGG-GCCACTGAATTGTGGGCTTTGCAATG
1 TTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAG-GGTGCCACGGAGTTGTGGAC-TTAAAAGG
* * * * ** * * **
1959708 GTGCCACTGACTTGTGGGCTTCGAAAGGGTGCCAATGAGTTGTGGGCTCTGAAAGGGTGCCACTA
63 GTGCCACGGAGTTGTGGACTT-AAAAGGGTGCCACGGAGTTGTGGACT-TAAAAGGGTGCCACGG
* *
1959773 ACTTGTGGGC
126 AGTTGTGGAC
* * * * * * * *
1959783 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAA
1 -TTAAAAGGGTGCCACGGAGTTGTGGAC-TT-AAAAGGGTGCCACGGAGTTGTGGAC-TT-AAAA
* * * * * * * *
1959848 GAGGT-CCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGC
61 G-GGTGCCACGGAGTTGTGGAC-TT-AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGG-GTGC
* * *
1959912 CACTGATTTGTGTGGGC
121 CACGGA-GT-TGTGGAC
* * * * * * * * ***
1959929 TTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGAATTGTGGGCTTCGTAGTG
1 -TTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG-G
* * * * * * *
1959994 GTGCCACTGACTTGTGGGCTTCGAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAAGGGTGCCA
63 GTGCCACGGAGTTGTGGACTT-AAAAGGGTGCCACGGAGTT--GTGGAC-TT-AAAAGGGTGCCA
* * *
1960059 CTGACTTGTGGGC
123 CGGAGTTGTGGAC
* * * * * ** * *
1960072 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTAAAAG
1 -TTAAAAGGGTGCCACGGAGTTGTGGAC-TT-AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAG
** * * * * * * *
1960137 GGTGCCACTAACTTGCGTGGGCTTTGAAAGGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCC
62 GGTGCCACGGAGTT--GTGGAC-TT-AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCC
* * *
1960202 ACCGACTTGTGTGGGC
122 ACGGA-GT-TGTGGAC
* * * * * * * * *
1960218 TTTGAAATGGGTTCCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACTGACTTGTGTGGGCT
1 -TT-AAAAGGG-TGCCACGGA-GT-TGTGGAC-TT-AAAAGGG-TGCCACGGA-GT-TGTGGAC-
* * * *
1960283 TTGAAATA-GGTGCCACAGAGTTGTGGATTTTAAAAGAGTGCCACGGAGTTGTGGATTTTAAAAG
55 TT-AAA-AGGGTGCCACGGAGTTGTGGA-CTTAAAAGGGTGCCACGGAGTTGTGGA-CTTAAAAG
*
1960347 GGTGCCACAGAGTTGTGGAC
116 GGTGCCACGGAGTTGTGGAC
* * * * * *
1960367 TCAAAAGAGATGCCACGGAGTTATGGACTTAAAAGGGTGCCACGGAGTTATGGTCTTAAAAGGAT
1 TTAAAAG-GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGT
* *
1960432 GCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGTGTTGTGGACTTAAAAGGGTGCCACAGAGTT
65 GCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTT
1960497 GTGGAC
130 GTGGAC
* *
1960503 TTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTAAAAAGGGTG
1 TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTG
* * *
1960568 CCACGGTGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGATGCCACGGAGT
66 CCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG-GGTGCCACGGAGT
*
1960633 TATGGAC
129 TGTGGAC
*
1960640 TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGTCTTAAAAGGGAT
1 TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG-T
*
1960705 GCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCATGGAGTT
65 GCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTT
1960770 GTGGAC
130 GTGGAC
** * *
1960776 TTAAAAGAATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGAAGTTGTGGACTTAAAAGGGA
1 TTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG-
1960841 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
64 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
1960906 TGTGGAC
129 TGTGGAC
* * *
1960913 TTAAAAGGGTGCCACGGAGTTGTTGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGA
1 TTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG-GG
*
1960978 TGCCACGGAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
64 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
1961043 TGTGGAC
129 TGTGGAC
* * * * *
1961050 TTTAAAAGGGTGCCGCAGAGTTGTGGACTTAAAAAGATGCCACAGAGTTGTGGACTTTAAAAG
1 -TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAG
1961113 AAAATGCCAC
Statistics
Matches: 1165, Mismatches: 124, Indels: 82
0.85 0.09 0.06
Matches are distributed among these distances:
135 66 0.06
136 107 0.09
137 392 0.34
138 69 0.06
139 2 0.00
140 35 0.03
141 24 0.02
142 26 0.02
143 100 0.09
144 80 0.07
145 62 0.05
146 59 0.05
147 35 0.03
148 9 0.01
149 7 0.01
150 17 0.01
151 43 0.04
152 7 0.01
153 10 0.01
154 14 0.01
155 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.34, T:0.26
Consensus pattern (135 bp):
TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTG
CCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTG
TGGAC
Found at i:1962497 original size:23 final size:23
Alignment explanation
Indices: 1962472--1962514 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1962462 TTTTGCCCTT
*
1962472 TTTTTCTTTTCA-TTTTTTGTGC
1 TTTTGCTTTTCACTTTTTTGTGC
*
1962494 TTTTGCTTTTGACTTTTTTGT
1 TTTTGCTTTTCACTTTTTTGT
1962515 CATTTTGAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.05, C:0.12, G:0.12, T:0.72
Consensus pattern (23 bp):
TTTTGCTTTTCACTTTTTTGTGC
Found at i:1968669 original size:22 final size:23
Alignment explanation
Indices: 1968638--1968689 Score: 88
Period size: 22 Copynumber: 2.3 Consensus size: 23
1968628 CATGTTAAAG
*
1968638 ATGCACGAAACATAAT-AAAAAA
1 ATGCATGAAACATAATAAAAAAA
1968660 ATGCATGAAACATAATAAAAAAA
1 ATGCATGAAACATAATAAAAAAA
1968683 ATGCATG
1 ATGCATG
1968690 GTCAAAGGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 15 0.54
23 13 0.46
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.17
Consensus pattern (23 bp):
ATGCATGAAACATAATAAAAAAA
Found at i:1969646 original size:20 final size:20
Alignment explanation
Indices: 1969623--1969673 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1969613 CTGTAGAATA
* *
1969623 TATCGATACATTCATACATG
1 TATCGATACATTCAAAAATG
* *
1969643 TATCGATATATTGAAAAATG
1 TATCGATACATTCAAAAATG
1969663 TATCGATACAT
1 TATCGATACAT
1969674 CAGGGTATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (20 bp):
TATCGATACATTCAAAAATG
Found at i:1969921 original size:20 final size:22
Alignment explanation
Indices: 1969886--1969926 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
1969876 ACAAAGGTCA
*
1969886 AAACCTTAGAAAGTATTGATAC
1 AAACCTTAGAAAGTATCGATAC
1969908 AAACC-TAG-AAGTATCGATA
1 AAACCTTAGAAAGTATCGATA
1969927 TATATTGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 3 0.17
22 5 0.28
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (22 bp):
AAACCTTAGAAAGTATCGATAC
Found at i:1969995 original size:20 final size:19
Alignment explanation
Indices: 1969949--1970007 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
1969939 TATCGGTACA
*
1969949 TTGTATCGATACAT-GATC
1 TTGTATCGATACATAGAAC
1969967 TTGGTATCGATACATAGTAAC
1 TT-GTATCGATACATAG-AAC
* *
1969988 TTGTATCGATGCATAAAAC
1 TTGTATCGATACATAGAAC
1970007 T
1 T
1970008 GGCTGTAGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 2 0.06
19 16 0.46
20 13 0.37
21 4 0.11
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATAGAAC
Found at i:1972195 original size:20 final size:20
Alignment explanation
Indices: 1972170--1972211 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1972160 AAGCTGCTAG
1972170 ACCAGATCATTAGGCATATA
1 ACCAGATCATTAGGCATATA
1972190 ACCAGATCATTAGGCATATA
1 ACCAGATCATTAGGCATATA
1972210 AC
1 AC
1972212 TTATACTCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.24
Consensus pattern (20 bp):
ACCAGATCATTAGGCATATA
Found at i:1979481 original size:36 final size:36
Alignment explanation
Indices: 1979441--1979519 Score: 149
Period size: 36 Copynumber: 2.2 Consensus size: 36
1979431 TGAAAAACAA
*
1979441 GAAAAGTTAAAATGGTGGTGAAAACCATAAAACCAT
1 GAAAAATTAAAATGGTGGTGAAAACCATAAAACCAT
1979477 GAAAAATTAAAATGGTGGTGAAAACCATAAAACCAT
1 GAAAAATTAAAATGGTGGTGAAAACCATAAAACCAT
1979513 GAAAAAT
1 GAAAAAT
1979520 GATGAAGTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.53, C:0.10, G:0.18, T:0.19
Consensus pattern (36 bp):
GAAAAATTAAAATGGTGGTGAAAACCATAAAACCAT
Found at i:1980289 original size:34 final size:34
Alignment explanation
Indices: 1980253--1980517 Score: 194
Period size: 34 Copynumber: 8.0 Consensus size: 34
1980243 TAAGCATTTT
* * *
1980253 TTAAGGATGTTTTAAGAGATTTCACAAGCCCCTT
1 TTAAGGATGTTTTAAAAGATTTCACAAGCCTCTC
*
1980287 TTAAAGATGTTTTAAAAGATCTT-ACAAGCCTCTC
1 TTAAGGATGTTTTAAAAGAT-TTCACAAGCCTCTC
* * *
1980321 TT---GA---TTCAGAA-ATTTCACAAGCCTCTG
1 TTAAGGATGTTTTAAAAGATTTCACAAGCCTCTC
* * *
1980348 TTGAGGATATTTTAAAAGAATTTCA-AGAGTCTCTC
1 TTAAGGATGTTTTAAAAG-ATTTCACA-AGCCTCTC
* ** * *
1980383 TTAAGGATGTTTTAAAAAAAATCA-AGGGCTTCTC
1 TTAAGGATGTTTTAAAAGATTTCACA-AGCCTCTC
* *
1980417 TTGAGGATGTTTTAAAAGATTTCACAATCCAT-TC
1 TTAAGGATGTTTTAAAAGATTTCACAAGCC-TCTC
* *
1980451 TTGAGGATGTTTTCAAAA-ATTTCACAAGCCTCCC
1 TTAAGGATGTTTT-AAAAGATTTCACAAGCCTCTC
* * *
1980485 TTAAGAATGTTTTAAGAGATTTCAAAAGCCTCT
1 TTAAGGATGTTTTAAAAGATTTCACAAGCCTCT
1980518 TTTGAGGGCA
Statistics
Matches: 182, Mismatches: 33, Indels: 32
0.74 0.13 0.13
Matches are distributed among these distances:
26 2 0.01
27 14 0.08
28 5 0.03
30 2 0.01
31 2 0.01
33 9 0.05
34 113 0.62
35 35 0.19
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Consensus pattern (34 bp):
TTAAGGATGTTTTAAAAGATTTCACAAGCCTCTC
Found at i:1985109 original size:43 final size:41
Alignment explanation
Indices: 1985039--1985123 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 41
1985029 TGCTCTTGCG
1985039 ATGCATCAGGTGTGTATATATATATATATATCCAAATCTTA
1 ATGCATCAGGTGTGTATATATATATATATATCCAAATCTTA
1985080 ATGCATCATGTGTGTGTATATATATATATATATCCAAATCTTA
1 ATGCATCA-G-GTGTGTATATATATATATATATCCAAATCTTA
1985123 A
1 A
1985124 GTAGTCATCT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
41 8 0.19
42 1 0.02
43 33 0.79
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (41 bp):
ATGCATCAGGTGTGTATATATATATATATATCCAAATCTTA
Found at i:1987549 original size:13 final size:13
Alignment explanation
Indices: 1987531--1987557 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1987521 ACATGCTGCT
1987531 TTGTATCGATACA
1 TTGTATCGATACA
1987544 TTGTATCGATACA
1 TTGTATCGATACA
1987557 T
1 T
1987558 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1987566 original size:19 final size:19
Alignment explanation
Indices: 1987542--1987598 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
1987532 TGTATCGATA
**
1987542 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGGC
*
1987561 CATTGTATCGATGCATGGC
1 CATTGTATCGATACATGGC
1987580 CAAATTGTATCGATACATG
1 C--ATTGTATCGATACATG
1987599 AAACTGGCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 17 0.53
21 15 0.47
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (19 bp):
CATTGTATCGATACATGGC
Found at i:1995626 original size:36 final size:36
Alignment explanation
Indices: 1995581--1995655 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
1995571 AAGGGGGAGA
* * *
1995581 AGATAATCGTTTAAGGGGGAGAATTTTTTTTAGAGG
1 AGATAATCGTTTAAAGGGGAGAATATTTTTAAGAGG
* *
1995617 AGATAATCGTTTAAAGGGGCGAATATTTTTAAGGGG
1 AGATAATCGTTTAAAGGGGAGAATATTTTTAAGAGG
1995653 AGA
1 AGA
1995656 AAAACGATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.32
Consensus pattern (36 bp):
AGATAATCGTTTAAAGGGGAGAATATTTTTAAGAGG
Found at i:1996659 original size:27 final size:27
Alignment explanation
Indices: 1996621--1996691 Score: 124
Period size: 27 Copynumber: 2.6 Consensus size: 27
1996611 GGTTGAAAAT
*
1996621 GGGGTTGAAGTATCCCCTCGGAAGAAC
1 GGGGTTGGAGTATCCCCTCGGAAGAAC
*
1996648 GGGGTTGGAGTATCCCCTCGGAAGAAT
1 GGGGTTGGAGTATCCCCTCGGAAGAAC
1996675 GGGGTTGGAGTATCCCC
1 GGGGTTGGAGTATCCCC
1996692 GATGAATAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.21, C:0.21, G:0.37, T:0.21
Consensus pattern (27 bp):
GGGGTTGGAGTATCCCCTCGGAAGAAC
Found at i:1998894 original size:52 final size:52
Alignment explanation
Indices: 1998816--1998944 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
1998806 CAAAATATGA
*
1998816 AAATTTGCCTGCATGTATCAATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
1998868 AAATTTGCCTGTATGTATCGATACATTTCTTAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
1998920 AAATTTGCCTGCATGTATTGATACA
1 AAATTTGCCTGCATGTATCGATACA
1998945 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:1998955 original size:52 final size:51
Alignment explanation
Indices: 1998816--1998964 Score: 208
Period size: 52 Copynumber: 2.9 Consensus size: 51
1998806 CAAAATATGA
*
1998816 AAATTTGCCTGCATGTATCAATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTCATAGTGTATCGATACATCTGGGC
* *
1998868 AAATTTGCCTGTATGTATCGATACATTTCTTAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTCATAGTGTATCGATACATCTGGGC
* ***
1998920 AAATTTGCCTGCATGTATTGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTCAT-AGTGTATCGATACA
1998965 ATGTATCGAT
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
51 1 0.01
52 86 0.99
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTCATAGTGTATCGATACATCTGGGC
Found at i:1998971 original size:13 final size:13
Alignment explanation
Indices: 1998953--1998977 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1998943 CAAAGATCAG
1998953 TGTATCGATACAA
1 TGTATCGATACAA
1998966 TGTATCGATACA
1 TGTATCGATACA
1998978 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1999040 original size:13 final size:13
Alignment explanation
Indices: 1999022--1999105 Score: 60
Period size: 13 Copynumber: 5.5 Consensus size: 13
1999012 AGCTTCGTAG
1999022 CGATACATTGTAT
1 CGATACATTGTAT
1999035 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
1999054 CGATACATTGTAT
1 CGATACATTGTAT
1999067 CGATACAACACTTATGTAT
1 CGAT---ACA--T-TGTAT
1999086 CGATACATTGTAT
1 CGATACATTGTAT
1999099 CGATACA
1 CGATACA
1999106 ACACTTATCG
Statistics
Matches: 59, Mismatches: 0, Indels: 24
0.71 0.00 0.29
Matches are distributed among these distances:
13 26 0.44
14 1 0.02
15 2 0.03
16 8 0.14
17 2 0.03
18 1 0.02
19 19 0.32
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:1999054 original size:19 final size:18
Alignment explanation
Indices: 1999030--1999092 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
1999020 AGCGATACAT
1999030 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
1999049 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1999062 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1999081 TGTATCGATACA
1 TGTATCGATACA
1999093 TTGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:1999063 original size:32 final size:32
Alignment explanation
Indices: 1999022--1999113 Score: 175
Period size: 32 Copynumber: 2.9 Consensus size: 32
1999012 AGCTTCGTAG
*
1999022 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
1999054 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
1999086 CGATACATTGTATCGATACAACACTTAT
1 CGATACATTGTATCGATACAACACTTAT
1999114 CGATATGTAT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 59 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:2000061 original size:52 final size:51
Alignment explanation
Indices: 1999783--2000426 Score: 676
Period size: 49 Copynumber: 12.8 Consensus size: 51
1999773 GATAAAAGGA
* * * * **
1999783 CCAATATGTTGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAAAAGGATG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAG---AAGG-TG
* * * * * * * *
1999838 TCAATGTGCTGATTCACGGTCAGCGACATTTAGACCTGAAGATGAGAAGAATG
1 CCAATATGCTGATTCAAGGCCAGCGACA-TTGGACTTAAAGATGAGAAG-GTG
* * * * * **
1999891 CCAATGTGTTGTTTCAAGGCTAACGACATTGGGTTTTAAAGATGACGAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATT-GGACTTAAAGATGA-GAAGGTG
*
1999944 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--GAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGTG
* *
1999993 CCAATGTGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATGATGAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA-GAAGGTG
*
2000045 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA-GAAGGTG
* * *
2000097 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGCG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA-GAAGGTG
* * * *
2000149 CCAATATGCTGATTCAAGGCCAGTGATATTGGACTAAAAAAT--GAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGTG
*
2000198 CCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT-A-AAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGTG
* * *
2000247 CCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGA-CA-AAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGTG
*
2000296 CCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T-A-AAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGTG
* * *
2000339 CCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGA-CA-AAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGTG
* * *
2000388 CCAATATGTTGATTCAAGGCCAGCGATATTGGGCTTAAA
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAA
2000427 AGTGCCAATG
Statistics
Matches: 508, Mismatches: 64, Indels: 40
0.83 0.10 0.07
Matches are distributed among these distances:
43 38 0.07
44 1 0.00
48 1 0.00
49 213 0.42
52 156 0.31
53 61 0.12
54 4 0.01
55 22 0.04
56 12 0.02
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (51 bp):
CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGTG
Found at i:2000350 original size:43 final size:43
Alignment explanation
Indices: 2000142--2000460 Score: 296
Period size: 49 Copynumber: 6.9 Consensus size: 43
2000132 TAAAGATGAC
* * *
2000142 AAAGGCGCCAATATGCTGATTCAAGGCCAGTGATATTGGACTAAAAAAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACT------T
* *
2000191 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGAC-T-----T
* *
2000240 AAAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTT
*
2000283 AAAGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 ------AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTT
* *
2000332 AAAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTT
* * *
2000375 AAAGACAAAGGTGCCAATATGTTGATTCAAGGCCAGCGATATTGGGCTT
1 ------AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTT
*
2000424 AAAAGTGCCAATGTGCTGATTCAAGGCCAGCGATATT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATT
2000461 AGGCTTAGAA
Statistics
Matches: 235, Mismatches: 22, Indels: 32
0.81 0.08 0.11
Matches are distributed among these distances:
43 75 0.32
48 1 0.00
49 158 0.67
50 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.23
Consensus pattern (43 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTT
Found at i:2000379 original size:92 final size:92
Alignment explanation
Indices: 2000142--2000452 Score: 442
Period size: 92 Copynumber: 3.3 Consensus size: 92
2000132 TAAAGATGAC
* * ** * * * ** *
2000142 AAAGGCGCCAATATGCTGATTCAAGGCCAGTGATATTGGACTAAAAAATGAAGGTGCCAATGTGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGACAAAGGTGCCAATATGC
*
2000207 TGATTCAAGGCCAGCGACATTGGACTTAAAGAT
66 TGATTCAAGGCCAGCGATATTGGAC-T-----T
2000240 AAAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGACAAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGACAAAGGTGCCAATATGC
2000305 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
*
2000332 AAAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGACAAAGGTGCCAATATGT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGACAAAGGTGCCAATATGC
*
2000397 TGATTCAAGGCCAGCGATATTGGGCTT
66 TGATTCAAGGCCAGCGATATTGGACTT
*
2000424 AAAAGTGCCAATGTGCTGATTCAAGGCCA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCA
2000453 GCGATATTAG
Statistics
Matches: 199, Mismatches: 14, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
92 119 0.60
97 1 0.01
98 79 0.40
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGACAAAGGTGCCAATATGC
TGATTCAAGGCCAGCGATATTGGACTT
Found at i:2000509 original size:33 final size:33
Alignment explanation
Indices: 2000467--2000563 Score: 169
Period size: 33 Copynumber: 3.0 Consensus size: 33
2000457 TATTAGGCTT
*
2000467 AGAAGGGTTGCCACCAACTTGTGTGGGCTTTAG
1 AGAATGGTTGCCACCAACTTGTGTGGGCTTTAG
2000500 AGAATGGTTGCCACCAACTTGTGTGGGCTTTAG
1 AGAATGGTTGCCACCAACTTGTGTGGGCTTTAG
*
2000533 AGAATGGTTGCCACCGACTTGTGTGGG-TTTA
1 AGAATGGTTGCCACCAACTTGTGTGGGCTTTA
2000564 AAAGGAAAAG
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 4 0.06
33 58 0.94
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.30
Consensus pattern (33 bp):
AGAATGGTTGCCACCAACTTGTGTGGGCTTTAG
Found at i:2000614 original size:34 final size:34
Alignment explanation
Indices: 2000563--2000861 Score: 257
Period size: 34 Copynumber: 9.0 Consensus size: 34
2000553 GTGTGGGTTT
* *
2000563 AAAAGGAAAAGGATGCCACAGAGTTGTGGACTTTG
1 AAAAGAAAAAGG-TGCCACGGAGTTGTGGACTTTG
* *
2000598 AAAAGAAAAAGGTGCCATGGAGTTGTGGACTTAG
1 AAAAGAAAAAGGTGCCACGGAGTTGTGGACTTTG
* * * *
2000632 -AAGGAAAAAGAGTGCCATGGAGTTGTGGGCTTTA
1 AAAAGAAAAAG-GTGCCACGGAGTTGTGGACTTTG
* *
2000666 AAAAGAAAAAGGTGCCACAGAGTTGTGGACTTAG
1 AAAAGAAAAAGGTGCCACGGAGTTGTGGACTTTG
* * * *
2000700 -AAGGAAAAAGAGTGCCACAGAGTTATGGGC-TT-
1 AAAAGAAAAAG-GTGCCACGGAGTTGTGGACTTTG
* *
2000732 AAATGAAAAAGGTGCCACGGAGTTGTGGACTTAG
1 AAAAGAAAAAGGTGCCACGGAGTTGTGGACTTTG
*
2000766 -AAGGAAAAAGAGTGCCACGGAGTTGTAGG-CTTT-
1 AAAAGAAAAAG-GTGCCACGGAGTTGT-GGACTTTG
*
2000799 AAAAG-----GGTGCCACAGAGTTGTGGAC-TT-
1 AAAAGAAAAAGGTGCCACGGAGTTGTGGACTTTG
* *
2000826 AAAAGGAAAAAGAGTGCCACGGAGTTATGGGCTTTG
1 AAAA-GAAAAAG-GTGCCACGGAGTTGTGGACTTTG
2000862 CAGAAAAGGA
Statistics
Matches: 215, Mismatches: 30, Indels: 37
0.76 0.11 0.13
Matches are distributed among these distances:
27 8 0.04
28 16 0.07
29 1 0.00
32 16 0.07
33 39 0.18
34 111 0.52
35 24 0.11
ACGTcount: A:0.36, C:0.11, G:0.32, T:0.20
Consensus pattern (34 bp):
AAAAGAAAAAGGTGCCACGGAGTTGTGGACTTTG
Found at i:2000641 original size:68 final size:67
Alignment explanation
Indices: 2000565--2000860 Score: 408
Period size: 68 Copynumber: 4.5 Consensus size: 67
2000555 GTGGGTTTAA
* * * **
2000565 AAGGAAAAGGA-TGCCACAGAGTTGTGGACTTTGAAAAGAAAAAGGTGCCATGGAGTTGTGGACT
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAGAAAAAGGTGCCACAGAGTTGTGGACT
2000629 TAG
65 TAG
*
2000632 AAGGAAAAAGAGTGCCATGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACAGAGTTGTGGACT
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAGAAAAAGGTGCCACAGAGTTGTGGACT
2000697 TAG
65 TAG
* * * *
2000700 AAGGAAAAAGAGTGCCACAGAGTTATGGGC-TTAAATGAAAAAGGTGCCACGGAGTTGTGGACTT
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACAGAGTTGTGGACTT
2000764 AG
66 AG
*
2000766 AAGGAAAAAGAGTGCCACGGAGTTGTAGGCTTTAAAAG-----GGTGCCACAGAGTTGTGGACTT
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACAGAGTTGTGGACTT
*
2000826 AA
66 AG
*
2000828 AAGGAAAAAGAGTGCCACGGAGTTATGGGCTTT
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
2000861 GCAGAAAAGG
Statistics
Matches: 207, Mismatches: 20, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
62 53 0.26
66 59 0.29
67 18 0.09
68 77 0.37
ACGTcount: A:0.35, C:0.11, G:0.32, T:0.21
Consensus pattern (67 bp):
AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACAGAGTTGTGGACTT
AG
Found at i:2000754 original size:134 final size:129
Alignment explanation
Indices: 2000561--2000859 Score: 440
Period size: 134 Copynumber: 2.3 Consensus size: 129
2000551 TTGTGTGGGT
* * * *
2000561 TTAAAAGGAAAAGGA-TGCCACAGAGTTGTGGACTTTGAAAAGAAAAAGGTGCCATGGAGTTGTG
1 TTAAAAGGAAAAAGAGTGCCACAGAGTTATGGGC-TTGAAAAGAAAAAGGTGCCACGGAGTTGTG
* *
2000625 GACTTAGAAGGAAAAAGAGTGCCATGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACAGAGTT
65 GACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTAGGCTTT-AAAAG-----GGTGCCACAGAGTT
2000690 GTGGAC
124 GTGGAC
* *
2000696 TTAGAAGGAAAAAGAGTGCCACAGAGTTATGGGCTT-AAATGAAAAAGGTGCCACGGAGTTGTGG
1 TTAAAAGGAAAAAGAGTGCCACAGAGTTATGGGCTTGAAAAGAAAAAGGTGCCACGGAGTTGTGG
2000760 ACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTAGGCTTTAAAAGGGTGCCACAGAGTTGTGGAC
66 ACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTAGGCTTTAAAAGGGTGCCACAGAGTTGTGGAC
*
2000824 TTAAAAGGAAAAAGAGTGCCACGGAGTTATGGGCTT
1 TTAAAAGGAAAAAGAGTGCCACAGAGTTATGGGCTT
2000860 TGCAGAAAAG
Statistics
Matches: 153, Mismatches: 10, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
128 54 0.35
133 5 0.03
134 63 0.41
135 15 0.10
136 16 0.10
ACGTcount: A:0.36, C:0.11, G:0.32, T:0.21
Consensus pattern (129 bp):
TTAAAAGGAAAAAGAGTGCCACAGAGTTATGGGCTTGAAAAGAAAAAGGTGCCACGGAGTTGTGG
ACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTAGGCTTTAAAAGGGTGCCACAGAGTTGTGGAC
Found at i:2000811 original size:28 final size:27
Alignment explanation
Indices: 2000771--2000831 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 27
2000761 CTTAGAAGGA
* *
2000771 AAAAGAGTGCCACGGAGTTGTAGG-CTTT
1 AAAAGGGTGCCACAGAGTTGT-GGAC-TT
2000799 AAAAGGGTGCCACAGAGTTGTGGACTT
1 AAAAGGGTGCCACAGAGTTGTGGACTT
2000826 AAAAGG
1 AAAAGG
2000832 AAAAAGAGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 10 0.33
28 20 0.67
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.21
Consensus pattern (27 bp):
AAAAGGGTGCCACAGAGTTGTGGACTT
Found at i:2000889 original size:128 final size:128
Alignment explanation
Indices: 2000561--2000908 Score: 377
Period size: 128 Copynumber: 2.7 Consensus size: 128
2000551 TTGTGTGGGT
* * * * * * **
2000561 TTAAAAGGAAAAGGA-TGCCACAGAGTTGTGGACTTTGAAAAGAAAAAGGTGCCATGGAGTTGTG
1 TTAAAAGGAAAAAGAGTGCCACAGAGTTATGGGC-TT---ATGAAAAAGGTGCCACGAAGTCATG
* *
2000625 GACTTAGAAGGAAAAAGAGTGCCATGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACAGAGTT
62 GACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTAGGCTTTAAAAAG----AGGTGCCACAGAGTT
2000690 GTGGAC
123 GTGGAC
* * **
2000696 TTAGAAGGAAAAAGAGTGCCACAGAGTTATGGGCTTAAATGAAAAAGGTGCCACGGAGTTGTGGA
1 TTAAAAGGAAAAAGAGTGCCACAGAGTTATGGGCTT--ATGAAAAAGGTGCCACGAAGTCATGGA
2000761 CTTAGAAGGAAAAAGAGTGCCACGGAGTTGTAGGCTTT-AAAAG-GGTGCCACAGAGTTGTGGAC
64 CTTAGAAGGAAAAAGAGTGCCACGGAGTTGTAGGCTTTAAAAAGAGGTGCCACAGAGTTGTGGAC
* *
2000824 TTAAAAGGAAAAAGAGTGCCACGGAGTTATGGGCTT-TGCAGAAAAGGATGCCACTAAGTCATGG
1 TTAAAAGGAAAAAGAGTGCCACAGAGTTATGGGCTTATG-A-AAAAGG-TGCCACGAAGTCATGG
*
2000888 ACTTTGAA-G-AAAAGA-TGCCAC
63 ACTTAGAAGGAAAAAGAGTGCCAC
2000909 TAAATCGTGG
Statistics
Matches: 194, Mismatches: 15, Indels: 18
0.85 0.07 0.08
Matches are distributed among these distances:
125 8 0.04
126 7 0.04
127 7 0.04
128 73 0.38
133 5 0.03
134 63 0.32
135 15 0.08
136 16 0.08
ACGTcount: A:0.36, C:0.12, G:0.31, T:0.20
Consensus pattern (128 bp):
TTAAAAGGAAAAAGAGTGCCACAGAGTTATGGGCTTATGAAAAAGGTGCCACGAAGTCATGGACT
TAGAAGGAAAAAGAGTGCCACGGAGTTGTAGGCTTTAAAAAGAGGTGCCACAGAGTTGTGGAC
Found at i:2000908 original size:31 final size:31
Alignment explanation
Indices: 2000833--2000928 Score: 104
Period size: 32 Copynumber: 3.1 Consensus size: 31
2000823 CTTAAAAGGA
** * * *
2000833 AAAAGAGTGCCACGGAGTTATGGGCTTTGCAG
1 AAAAGA-TGCCACTAAGTCATGGACTTTGAAG
2000865 AAAAGGATGCCACTAAGTCATGGACTTTGAAG
1 AAAA-GATGCCACTAAGTCATGGACTTTGAAG
* *
2000897 AAAAGATGCCACTAAATCGTGGACTTT-AAG
1 AAAAGATGCCACTAAGTCATGGACTTTGAAG
2000927 AA
1 AA
2000929 GGTATTTGAA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
30 5 0.09
31 21 0.38
32 28 0.50
33 2 0.04
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.22
Consensus pattern (31 bp):
AAAAGATGCCACTAAGTCATGGACTTTGAAG
Found at i:2002185 original size:19 final size:21
Alignment explanation
Indices: 2002146--2002192 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
2002136 TTTACATTGT
*
2002146 TTTTTGTGTGTTTTCCTTTTG-
1 TTTTT-TGTGTTTTACTTTTGA
2002167 TTTTTTGTG-TTTACTTTTGA
1 TTTTTTGTGTTTTACTTTTGA
2002187 TTTTTT
1 TTTTTT
2002193 ATCATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 9 0.38
20 10 0.42
21 5 0.21
ACGTcount: A:0.04, C:0.06, G:0.15, T:0.74
Consensus pattern (21 bp):
TTTTTTGTGTTTTACTTTTGA
Found at i:2004236 original size:13 final size:13
Alignment explanation
Indices: 2004218--2004244 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2004208 ACATGCTGCT
2004218 TTGTATCGATACA
1 TTGTATCGATACA
2004231 TTGTATCGATACA
1 TTGTATCGATACA
2004244 T
1 T
2004245 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2004239 original size:33 final size:32
Alignment explanation
Indices: 2004197--2004263 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
2004187 TACATAGCTA
*
2004197 ATTGTATCGATACATGCTGCTTTGTATCGATAC
1 ATTGTATCGATACATG-TGCATTGTATCGATAC
*
2004230 ATTGTATCGATACATGTTCATTGTATCGATAC
1 ATTGTATCGATACATGTGCATTGTATCGATAC
2004262 AT
1 AT
2004264 GGCCAAATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 16 0.50
33 16 0.50
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.40
Consensus pattern (32 bp):
ATTGTATCGATACATGTGCATTGTATCGATAC
Found at i:2004253 original size:19 final size:19
Alignment explanation
Indices: 2004180--2004264 Score: 74
Period size: 20 Copynumber: 4.7 Consensus size: 19
2004170 CATACTCAAA
* *
2004180 GTATCGATACATAGCTAATT
1 GTATCGATACAT-GTTCATT
* *
2004200 GTATCGATACATGCTGCTTT
1 GTATCGATACATG-TTCATT
2004220 GTATCGAT--A----CATT
1 GTATCGATACATGTTCATT
2004233 GTATCGATACATGTTCATT
1 GTATCGATACATGTTCATT
2004252 GTATCGATACATG
1 GTATCGATACATG
2004265 GCCAAATTGT
Statistics
Matches: 53, Mismatches: 5, Indels: 15
0.73 0.07 0.21
Matches are distributed among these distances:
13 11 0.21
15 1 0.02
18 1 0.02
19 18 0.34
20 22 0.42
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (19 bp):
GTATCGATACATGTTCATT
Found at i:2004280 original size:52 final size:53
Alignment explanation
Indices: 2004180--2004283 Score: 131
Period size: 52 Copynumber: 2.0 Consensus size: 53
2004170 CATACTCAAA
****
2004180 GTATCGATACATAGCTAATTGTATCGATACATGCTGCTTTGTATCGATACATT
1 GTATCGATACATAGCTAATTGTATCGATACATGCCAAATTGTATCGATACATT
* *
2004233 GTATCGATACAT-GTTCATTGTATCGATACATGGCCAAATTGTA-CGATACAT
1 GTATCGATACATAGCTAATTGTATCGATACAT-GCCAAATTGTATCGATACAT
2004284 GAAACTGGCA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
52 25 0.57
53 19 0.43
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (53 bp):
GTATCGATACATAGCTAATTGTATCGATACATGCCAAATTGTATCGATACATT
Found at i:2010237 original size:3 final size:3
Alignment explanation
Indices: 2010229--2010319 Score: 123
Period size: 3 Copynumber: 30.0 Consensus size: 3
2010219 TGAAAAACAA
2010229 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
* *
2010275 AAAT AAT AAAT AAT AAT -AT TAT AAT AAT AAT AAT -AT AGT AAT AAT
1 -AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2010320 TAATTAATTA
Statistics
Matches: 81, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
2 4 0.05
3 67 0.83
4 10 0.12
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:2010689 original size:13 final size:15
Alignment explanation
Indices: 2010650--2010690 Score: 61
Period size: 13 Copynumber: 2.9 Consensus size: 15
2010640 GCAAAAATAG
2010650 TGCATTGCATTTCAT
1 TGCATTGCATTTCAT
2010665 TGCATTGC-TTTCA-
1 TGCATTGCATTTCAT
2010678 TGCA-TGCATTTCA
1 TGCATTGCATTTCA
2010691 CACATGAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.12
13 9 0.36
14 5 0.20
15 8 0.32
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.44
Consensus pattern (15 bp):
TGCATTGCATTTCAT
Found at i:2011028 original size:23 final size:22
Alignment explanation
Indices: 2010994--2011040 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
2010984 CAAAGAATAT
2010994 AAAAGAGAATGGACAGCAGCTC
1 AAAAGAGAATGGACAGCAGCTC
* *
2011016 AAAATGAGGATGGACAGCAGTTC
1 AAAA-GAGAATGGACAGCAGCTC
2011039 AA
1 AA
2011041 GAGATCATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.45, C:0.15, G:0.28, T:0.13
Consensus pattern (22 bp):
AAAAGAGAATGGACAGCAGCTC
Found at i:2011101 original size:19 final size:19
Alignment explanation
Indices: 2011077--2011113 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2011067 AAAAAAAAAA
*
2011077 TAGAATAGAAACAGCAAAC
1 TAGAATAGAAACACCAAAC
*
2011096 TAGAATCGAAACACCAAA
1 TAGAATAGAAACACCAAA
2011114 ACAAAAGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.19, G:0.14, T:0.11
Consensus pattern (19 bp):
TAGAATAGAAACACCAAAC
Found at i:2017783 original size:13 final size:13
Alignment explanation
Indices: 2017765--2017790 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2017755 TACACAAAGT
2017765 ATGTATCGATACA
1 ATGTATCGATACA
2017778 ATGTATCGATACA
1 ATGTATCGATACA
2017791 TAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2017788 original size:32 final size:33
Alignment explanation
Indices: 2017747--2017810 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
2017737 TAGCCAAACT
**
2017747 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
*
2017779 TGTATCGATACATAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
2017811 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:2018918 original size:21 final size:20
Alignment explanation
Indices: 2018888--2018961 Score: 85
Period size: 21 Copynumber: 3.6 Consensus size: 20
2018878 TTCTACAATT
2018888 TGTATCGATACAATAAGTGAA
1 TGTATCGATAC-ATAAGTGAA
*
2018909 TGTATTGATACATAAGTGAA
1 TGTATCGATACATAAGTGAA
* ***
2018929 TGTATCGATATATGCTTGAAA
1 TGTATCGATACATAAGTG-AA
2018950 TGTATCGATACA
1 TGTATCGATACA
2018962 AGACCATGTA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 22 0.49
21 23 0.51
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (20 bp):
TGTATCGATACATAAGTGAA
Found at i:2018925 original size:20 final size:21
Alignment explanation
Indices: 2018888--2018938 Score: 86
Period size: 20 Copynumber: 2.5 Consensus size: 21
2018878 TTCTACAATT
2018888 TGTATCGATACAATAAGTGAA
1 TGTATCGATACAATAAGTGAA
*
2018909 TGTATTGATAC-ATAAGTGAA
1 TGTATCGATACAATAAGTGAA
2018929 TGTATCGATA
1 TGTATCGATA
2018939 TATGCTTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 18 0.64
21 10 0.36
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (21 bp):
TGTATCGATACAATAAGTGAA
Found at i:2021546 original size:101 final size:101
Alignment explanation
Indices: 2021395--2021597 Score: 288
Period size: 101 Copynumber: 2.0 Consensus size: 101
2021385 TCCAACCCCG
* * *
2021395 TTTTTAAACTTGTCAAGATTTAAATCTTATTTTTGTCTAAATTATCATCATC-GGAGACGCACCA
1 TTTTTAAACTTGTCAAGATTTAAATCTTATTTTTGGCAAAATTATCATCATCAGG-GACACACCA
2021459 ACCCCATTCTTAC-AAGGGGATACTCCAACC-CTATTTT
65 ACCCCATTCTT-CTAAGGGGATACTCCAACCTC-ATTTT
* * *
2021496 TTTTTAAACTTGTCAAGATTTAAATCTTA-TTTTGGCAAAGATTGTTATCATCAGGGACACTCCA
1 TTTTTAAACTTGTCAAGATTTAAATCTTATTTTTGGCAAA-ATTATCATCATCAGGGACACACCA
2021560 ACCCCATTCTTCTAAGGGGATACTCCAACCTCATTTT
65 ACCCCATTCTTCTAAGGGGATACTCCAACCTCATTTT
2021597 T
1 T
2021598 CAACTAAAAT
Statistics
Matches: 92, Mismatches: 6, Indels: 8
0.87 0.06 0.08
Matches are distributed among these distances:
100 9 0.10
101 80 0.87
102 3 0.03
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (101 bp):
TTTTTAAACTTGTCAAGATTTAAATCTTATTTTTGGCAAAATTATCATCATCAGGGACACACCAA
CCCCATTCTTCTAAGGGGATACTCCAACCTCATTTT
Found at i:2024389 original size:137 final size:137
Alignment explanation
Indices: 2024137--2024394 Score: 367
Period size: 137 Copynumber: 1.9 Consensus size: 137
2024127 TTTCGGCATG
* *
2024137 AAAGCATTCCGGTGACAACCTAAGACTCGGTTTTAATAAAATTATAAAAATGCCCTTATAGGTAT
1 AAAGCATTCCGGTGACAACCTAAGACTCGGTTCTAAAAAAATTATAAAAATGCCCTTATAGGTAT
* * *
2024202 ACTTTCAACATGAAAGTATCCCGGTAACTCTAAAGGACTCAAAAAGGATCATAAATATCTACCTT
66 ACTTTCAACATGAAAGTATCCCGATAACCCTAAAAGACTCAAAAAGGATCATAAATATCTACCTT
2024267 TGACATA
131 TGACATA
* *
2024274 AAAGCA-TCTCGGTGACAACCTAAGAGTCGGTTCTAAAAAAATTATAAAAATGCCCTTATGGGTA
1 AAAGCATTC-CGGTGACAACCTAAGACTCGGTTCTAAAAAAATTATAAAAATGCCCTTATAGGTA
** *** *
2024338 TACTTTTGACATGAAAGTATTTTGATAACCCTAAAAGACTTAGAAAA-GATCATAAAT
65 TACTTTCAACATGAAAGTATCCCGATAACCCTAAAAGACTCA-AAAAGGATCATAAAT
2024395 GGGAGGAACC
Statistics
Matches: 106, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
136 2 0.02
137 100 0.94
138 4 0.04
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (137 bp):
AAAGCATTCCGGTGACAACCTAAGACTCGGTTCTAAAAAAATTATAAAAATGCCCTTATAGGTAT
ACTTTCAACATGAAAGTATCCCGATAACCCTAAAAGACTCAAAAAGGATCATAAATATCTACCTT
TGACATA
Found at i:2025552 original size:16 final size:17
Alignment explanation
Indices: 2025531--2025564 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2025521 AAAACCAATA
2025531 CAAATACAACAA-AAAT
1 CAAATACAACAACAAAT
*
2025547 CAAATACATCAACAAAT
1 CAAATACAACAACAAAT
2025564 C
1 C
2025565 CATAAACTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.62, C:0.24, G:0.00, T:0.15
Consensus pattern (17 bp):
CAAATACAACAACAAAT
Found at i:2027681 original size:19 final size:19
Alignment explanation
Indices: 2027638--2027693 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
2027628 CTGCTAGTTT
2027638 CATGTATCGATACAATTGAG
1 CATGTATCGATACAA-TGAG
*
2027658 TATGTATCGATACAATGAG
1 CATGTATCGATACAATGAG
* *
2027677 CATGTGTCGATATAATG
1 CATGTATCGATACAATG
2027694 TATTGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAG
Found at i:2030178 original size:21 final size:21
Alignment explanation
Indices: 2030129--2030180 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
2030119 TGTTTTTATT
2030129 GATG-ATTTTGATGAAAAATA
1 GATGAATTTTGATGAAAAATA
* *
2030149 GAT-AGTTTTGATGTGAAAA-A
1 GATGAATTTTGATG-AAAAATA
2030169 GATGAATTTTGA
1 GATGAATTTTGA
2030181 AAAGGATTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.37
Consensus pattern (21 bp):
GATGAATTTTGATGAAAAATA
Found at i:2030308 original size:13 final size:13
Alignment explanation
Indices: 2030290--2030326 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
2030280 ATAGTAATCT
*
2030290 TGTATCAATACAA
1 TGTATCGATACAA
*
2030303 TGTATCGATATAA
1 TGTATCGATACAA
2030316 TGTATCGATAC
1 TGTATCGATAC
2030327 TTAGAACATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2033508 original size:307 final size:307
Alignment explanation
Indices: 2032933--2033538 Score: 1106
Period size: 307 Copynumber: 2.0 Consensus size: 307
2032923 TGTTAAGGAG
*
2032933 TTCTAGGAGCTAAGAAATTATGGCTAATACCGTTTTCATTACAAAAGTTATTAAAACCAAGATTC
1 TTCTAAGAGCTAAGAAATTATGGCTAATACCGTTTTCATTACAAAAGTTATTAAAACCAAGATTC
*
2032998 TCAAATTCTCTACCATGGTCACTTCTTATGCTAGATAAGGTGTAACCTTTTTTGTTTTGAACAAT
66 TCAAATTCTCTACCATGGTCACTTCTTATGCTAGATAAGGTGTAACCTTTTTCGTTTTGAACAAT
*
2033063 TTTACAAAAAGTGATGAATTTTTATAAAGCTTCATCTTTAGTGCTTAAGAATAAAACCCAAGTAT
131 TTTACAAAAAGTGATAAATTTTTATAAAGCTTCATCTTTAGTGCTTAAGAATAAAACCCAAGTAT
* * **
2033128 ATTTAGAATAATCATCCACAATAACAAATCCATATCTTTTACCACTTAGACTTGACATTCTAGTT
196 ATCTAGAATAATCATCCACAATAACAAATCAATATCTTTTACCACTTAGACTTGACATTAGAGTT
*
2033193 AGACCAAATAAATCGATGTGAACTAGTTACAAAACTCTAGATGAATT
261 AAACCAAATAAATCGATGTGAACTAGTTACAAAACTCTAGATGAATT
2033240 TTCTAAGAGCTAAGAAATTATGGCTAATACCGTTTTCATTACAAAAGTTATTAAAACCAAGATTC
1 TTCTAAGAGCTAAGAAATTATGGCTAATACCGTTTTCATTACAAAAGTTATTAAAACCAAGATTC
2033305 TCAAATTCTCTACCATGGTCACTTCTTATGCTAGATAAGGTGTAACCTTTTTCGTTTTGAACAAT
66 TCAAATTCTCTACCATGGTCACTTCTTATGCTAGATAAGGTGTAACCTTTTTCGTTTTGAACAAT
*
2033370 TTTACAAAAAGTGATAAATTTTTCTAAAGCTTCATCTTTAGTGCTTAAGAATAAAACCCAAGTAT
131 TTTACAAAAAGTGATAAATTTTTATAAAGCTTCATCTTTAGTGCTTAAGAATAAAACCCAAGTAT
2033435 ATCTAGAATAATCATCCACAATAACAAATCAATATCTTTTACCACTTAGACTTTG-CATTAGAGT
196 ATCTAGAATAATCATCCACAATAACAAATCAATATCTTTTACCACTTAGAC-TTGACATTAGAGT
*
2033499 TAAACCAAATAAGTCGATGTGAACTAGTTACAAAACTCTA
260 TAAACCAAATAAATCGATGTGAACTAGTTACAAAACTCTA
2033539 AATGTCGTGA
Statistics
Matches: 288, Mismatches: 10, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
307 285 0.99
308 3 0.01
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (307 bp):
TTCTAAGAGCTAAGAAATTATGGCTAATACCGTTTTCATTACAAAAGTTATTAAAACCAAGATTC
TCAAATTCTCTACCATGGTCACTTCTTATGCTAGATAAGGTGTAACCTTTTTCGTTTTGAACAAT
TTTACAAAAAGTGATAAATTTTTATAAAGCTTCATCTTTAGTGCTTAAGAATAAAACCCAAGTAT
ATCTAGAATAATCATCCACAATAACAAATCAATATCTTTTACCACTTAGACTTGACATTAGAGTT
AAACCAAATAAATCGATGTGAACTAGTTACAAAACTCTAGATGAATT
Found at i:2036862 original size:33 final size:33
Alignment explanation
Indices: 2036796--2036862 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
2036786 CGTTGGGCAT
* *
2036796 AATGTATCGATACAATTCTTCATGTATCGATAC
1 AATGTATCGATACAATTCTCCATGTATCAATAC
* *
2036829 AATGTATCGATATAATATC-CCATGTATTAATAC
1 AATGTATCGATACAAT-TCTCCATGTATCAATAC
2036862 A
1 A
2036863 TTTCACTTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 27 0.93
34 2 0.07
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.36
Consensus pattern (33 bp):
AATGTATCGATACAATTCTCCATGTATCAATAC
Found at i:2036916 original size:19 final size:19
Alignment explanation
Indices: 2036891--2036945 Score: 92
Period size: 19 Copynumber: 2.9 Consensus size: 19
2036881 CTGCCAGTTT
2036891 CATGTATCGATACAATGAG
1 CATGTATCGATACAATGAG
* *
2036910 TATGTATCGATACAATAAG
1 CATGTATCGATACAATGAG
2036929 CATGTATCGATACAATG
1 CATGTATCGATACAATG
2036946 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAG
Found at i:2036948 original size:13 final size:13
Alignment explanation
Indices: 2036930--2036957 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2036920 TACAATAAGC
2036930 ATGTATCGATACA
1 ATGTATCGATACA
2036943 ATGTATCGATACA
1 ATGTATCGATACA
2036956 AT
1 AT
2036958 TAGATGTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2036952 original size:32 final size:32
Alignment explanation
Indices: 2036911--2036974 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
2036901 TACAATGAGT
2036911 ATGTATCGATACAATAAGCA-TGTATCGATACA
1 ATGTATCGATACAATAAG-AGTGTATCGATACA
*
2036943 ATGTATCGATACAATTAGATGTGTATCGATAC
1 ATGTATCGATACAATAAGA-GTGTATCGATAC
2036975 TTTCAGGGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 1 0.03
32 17 0.59
33 11 0.38
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (32 bp):
ATGTATCGATACAATAAGAGTGTATCGATACA
Found at i:2038235 original size:50 final size:50
Alignment explanation
Indices: 2038165--2038372 Score: 258
Period size: 50 Copynumber: 4.2 Consensus size: 50
2038155 GCTTAGAGTT
* * * * *
2038165 AACAATTACAGCCACATCTCTCTATTGTTAAAGGTTGGTGAAGAATCGTC
1 AACAATTACGGCTACATCTCTCGATTGTCAAAGGTTGGTGAAGAATAGTC
* *
2038215 AACAATTACGGCTACCTCTCTCGATTGTCAAAGGTTGTTGAAGAATAGTC
1 AACAATTACGGCTACATCTCTCGATTGTCAAAGGTTGGTGAAGAATAGTC
* * * * *
2038265 AATAATTACGGCCT-CCTCTCTCAATTGTCCAAGGTTGGTGAAGAATCGTC
1 AACAATTACGG-CTACATCTCTCGATTGTCAAAGGTTGGTGAAGAATAGTC
* *
2038315 AACAATTACGG-TCACATCTCTCGATTGTGAAAGGTTGGTAAAGAATAGTC
1 AACAATTACGGCT-ACATCTCTCGATTGTCAAAGGTTGGTGAAGAATAGTC
2038365 AACAATTA
1 AACAATTA
2038373 GTTTTGGTGG
Statistics
Matches: 136, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
48 1 0.01
50 133 0.98
51 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (50 bp):
AACAATTACGGCTACATCTCTCGATTGTCAAAGGTTGGTGAAGAATAGTC
Found at i:2038341 original size:100 final size:100
Alignment explanation
Indices: 2038165--2038372 Score: 301
Period size: 100 Copynumber: 2.1 Consensus size: 100
2038155 GCTTAGAGTT
* * * * *
2038165 AACAATTACAGCCACATCTCTCTATTGTTAAAGGTTGGTGAAGAATCGTCAACAATTACGGCTAC
1 AACAATTACGGCCTCCTCTCTCAATTGTCAAAGGTTGGTGAAGAATCGTCAACAATTACGGCTAC
* * *
2038230 CTCTCTCGATTGTCAAAGGTTGTTGAAGAATAGTC
66 ATCTCTCGATTGTCAAAGGTTGGTAAAGAATAGTC
* *
2038265 AATAATTACGGCCTCCTCTCTCAATTGTCCAAGGTTGGTGAAGAATCGTCAACAATTACGG-TCA
1 AACAATTACGGCCTCCTCTCTCAATTGTCAAAGGTTGGTGAAGAATCGTCAACAATTACGGCT-A
*
2038329 CATCTCTCGATTGTGAAAGGTTGGTAAAGAATAGTC
65 CATCTCTCGATTGTCAAAGGTTGGTAAAGAATAGTC
2038365 AACAATTA
1 AACAATTA
2038373 GTTTTGGTGG
Statistics
Matches: 95, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
99 1 0.01
100 94 0.99
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (100 bp):
AACAATTACGGCCTCCTCTCTCAATTGTCAAAGGTTGGTGAAGAATCGTCAACAATTACGGCTAC
ATCTCTCGATTGTCAAAGGTTGGTAAAGAATAGTC
Found at i:2042318 original size:34 final size:35
Alignment explanation
Indices: 2042280--2042346 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
2042270 CCTTACAACA
2042280 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
2042314 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
2042347 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:2042843 original size:13 final size:13
Alignment explanation
Indices: 2042825--2042850 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2042815 CTATTTATGA
2042825 TGTATCGATACAC
1 TGTATCGATACAC
2042838 TGTATCGATACAC
1 TGTATCGATACAC
2042851 ACAAATATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:2042971 original size:21 final size:22
Alignment explanation
Indices: 2042940--2042995 Score: 96
Period size: 21 Copynumber: 2.6 Consensus size: 22
2042930 ACAGTGACCT
*
2042940 ATGAATAGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
2042962 ATGAA-AGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
2042983 ATGAACAGTGATG
1 ATGAACAGTGATG
2042996 AATAGTGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.38, C:0.09, G:0.25, T:0.29
Consensus pattern (22 bp):
ATGAACAGTGATGTATCGATAC
Found at i:2043101 original size:53 final size:53
Alignment explanation
Indices: 2043037--2043173 Score: 238
Period size: 53 Copynumber: 2.6 Consensus size: 53
2043027 CTACTTCCAA
2043037 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* * *
2043090 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGTCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
2043143 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
2043174 TATGCAATTT
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 66 0.84
54 13 0.16
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:2043186 original size:20 final size:21
Alignment explanation
Indices: 2043161--2043214 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
2043151 TACATATTTG
2043161 TGTGTATCGATACTATGC-AA
1 TGTGTATCGATACTATGCAAA
* *
2043181 TTTGTATCGATAC-ATTCAAA
1 TGTGTATCGATACTATGCAAA
2043201 TGTGTATCGATACT
1 TGTGTATCGATACT
2043215 TTTCAGGGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 3 0.10
20 26 0.90
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.39
Consensus pattern (21 bp):
TGTGTATCGATACTATGCAAA
Found at i:2043279 original size:21 final size:21
Alignment explanation
Indices: 2043253--2043293 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2043243 GTCAACCTTG
2043253 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
2043274 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
2043294 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:2044381 original size:50 final size:49
Alignment explanation
Indices: 2044291--2044481 Score: 238
Period size: 50 Copynumber: 3.8 Consensus size: 49
2044281 TATGGCTATT
* *
2044291 TCTCTCTATTGTCAAAGTTGGTGAAGAATCGTCAACAATTACGATCACC
1 TCTCTCGATTGTCAAAGTTGGTGAAGAATAGTCAACAATTACGATCACC
*
2044340 TCTCTCGATTGTCAAAGGTTGGTGAAGAATAGTCAATAATTACGATCACC
1 TCTCTCGATTGTCAAA-GTTGGTGAAGAATAGTCAACAATTACGATCACC
* * * * *
2044390 TTTCTCGATTGTCCAAAGTTAGTGAAGAATCGTCAACAATTACGACCACA
1 TCTCTCGATTGT-CAAAGTTGGTGAAGAATAGTCAACAATTACGATCACC
* * * * *
2044440 TTTTTCGATTGTCAAAGATTGATGAAGAGTAGTCAATAATTA
1 TCTCTCGATTGTCAAAG-TTGGTGAAGAATAGTCAACAATTA
2044482 ATTTTGATGA
Statistics
Matches: 124, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
49 20 0.16
50 100 0.81
51 4 0.03
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (49 bp):
TCTCTCGATTGTCAAAGTTGGTGAAGAATAGTCAACAATTACGATCACC
Found at i:2044448 original size:100 final size:99
Alignment explanation
Indices: 2044293--2044481 Score: 288
Period size: 100 Copynumber: 1.9 Consensus size: 99
2044283 TGGCTATTTC
* * * * *
2044293 TCTCTATTGTCAAAGTTGGTGAAGAATCGTCAACAATTACGATCACCTCTCTCGATTGTCAAAGG
1 TCTCGATTGTCAAAGTTAGTGAAGAATCGTCAACAATTACGACCACATCTCTCGATTGTCAAAGA
*
2044358 TTGGTGAAGAATAGTCAATAATTACGATCACCTT
66 TTGATGAAGAATAGTCAATAATTACGATCACCTT
* *
2044392 TCTCGATTGTCCAAAGTTAGTGAAGAATCGTCAACAATTACGACCACATTTTTCGATTGTCAAAG
1 TCTCGATTGT-CAAAGTTAGTGAAGAATCGTCAACAATTACGACCACATCTCTCGATTGTCAAAG
*
2044457 ATTGATGAAGAGTAGTCAATAATTA
65 ATTGATGAAGAATAGTCAATAATTA
2044482 ATTTTGATGA
Statistics
Matches: 80, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
99 9 0.11
100 71 0.89
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Consensus pattern (99 bp):
TCTCGATTGTCAAAGTTAGTGAAGAATCGTCAACAATTACGACCACATCTCTCGATTGTCAAAGA
TTGATGAAGAATAGTCAATAATTACGATCACCTT
Found at i:2046587 original size:28 final size:28
Alignment explanation
Indices: 2046551--2046605 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
2046541 TAATAAAATA
2046551 AATATAATATAA-CACCTTTAAATTAATT
1 AATATAATATAATCA-CTTTAAATTAATT
*
2046579 AATATAATATAATTACTTTAAATTAAT
1 AATATAATATAATCACTTTAAATTAAT
2046606 ATAAGTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (28 bp):
AATATAATATAATCACTTTAAATTAATT
Found at i:2048877 original size:6 final size:6
Alignment explanation
Indices: 2048866--2048896 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
2048856 TTTTCTAATT
*
2048866 TTTTTG TTTTTG CTTTTG TTTTTG TTTTTG T
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG T
2048897 GTGTGTTGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.03, G:0.16, T:0.81
Consensus pattern (6 bp):
TTTTTG
Found at i:2050444 original size:12 final size:12
Alignment explanation
Indices: 2050411--2050445 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2050401 AATGCTTGTG
2050411 CAACAGCAGCAA
1 CAACAGCAGCAA
*
2050423 CAACAACAGCAA
1 CAACAGCAGCAA
*
2050435 CAGCAGCAGCA
1 CAACAGCAGCA
2050446 GTTCCTCCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.49, C:0.34, G:0.17, T:0.00
Consensus pattern (12 bp):
CAACAGCAGCAA
Found at i:2059937 original size:16 final size:18
Alignment explanation
Indices: 2059901--2059938 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
2059891 GTCTAACAAT
*
2059901 AAATCAATTTGAAATTTA
1 AAATCAATTTGAAACTTA
2059919 AAAT-AATTTG-AACTTA
1 AAATCAATTTGAAACTTA
2059935 AAAT
1 AAAT
2059939 GATCCGAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 6 0.32
18 4 0.21
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (18 bp):
AAATCAATTTGAAACTTA
Done.