Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold365
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: 1826335
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 11 of 11
Found at i:1717596 original size:13 final size:13
Alignment explanation
Indices: 1717578--1717602 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1717568 CATAAAGTGT
1717578 TGTATCGATACAA
1 TGTATCGATACAA
1717591 TGTATCGATACA
1 TGTATCGATACA
1717603 TAAGTTTTGT
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:1717618 original size:32 final size:33
Alignment explanation
Indices: 1717558--1717623 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
1717548 TTCAACGATT
1717558 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*
1717591 TGTATCGATACAT-AAGTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1717623 T
1 T
1717624 TTAAGCTACT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 19 0.59
33 13 0.41
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:1717753 original size:52 final size:52
Alignment explanation
Indices: 1717697--1717821 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
1717687 CACTGATCTT
* *
1717697 TGTATCGATACATGTAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
1717749 TGTATCGATACATGCAGGAAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1717801 TGTATCGATACATGCAGGCAA
1 TGTATCGATACATGCAGGCAA
1717822 CTTTTCATAT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 68 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1730055 original size:61 final size:60
Alignment explanation
Indices: 1729958--1730085 Score: 159
Period size: 61 Copynumber: 2.1 Consensus size: 60
1729948 AAAGATGATG
* * * *
1729958 AAGATGAGAAGAGTCATAAAGATGCCGATATACTGATTCAAGGCTAGTGATATTGGGCATA
1 AAGATGAGAAGAGT-ATAAAGATGCCAATATACTGATGCAAGGCCAGCGATATTGGGCATA
* * *
1730019 AAGATGAGAAGGATGT-TAAAGGTGCCAATATGCTGATGCAAGGCCAGCGATATTGGGCTTA
1 AAGATGAGAA-GA-GTATAAAGATGCCAATATACTGATGCAAGGCCAGCGATATTGGGCATA
1730080 AAGATG
1 AAGATG
1730086 TGACAAATGT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
61 54 0.93
62 2 0.03
63 2 0.03
ACGTcount: A:0.36, C:0.12, G:0.29, T:0.23
Consensus pattern (60 bp):
AAGATGAGAAGAGTATAAAGATGCCAATATACTGATGCAAGGCCAGCGATATTGGGCATA
Found at i:1730116 original size:52 final size:51
Alignment explanation
Indices: 1730041--1730290 Score: 211
Period size: 52 Copynumber: 4.9 Consensus size: 51
1730031 ATGTTAAAGG
* * *
1730041 TGCCAATATGCTGATGCAAGGCCAGCGATATTGGGCTTAAAGATGTGACAAA
1 TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGTGA-AAA
* * * * * * **
1730093 TGTCAATGTGCTGATTCACGGCCAACGACATTAGACTTGAAGATAAGAAGAA
1 TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGTGAA-AA
* * * * * *
1730145 TGCCAATGTGTTGATTCAAGGCTAGTGACT-TTGGGCTT-AGGAATGTTAAAGA
1 TGCCAATGTGCTGATTCAAGGCCAGCGA-TATTGGACTTAAAG-ATGTGAAA-A
* * * * **
1730197 TGCCAATATACTGATTCAAGGCTAGCGATATCGGACTTAAAGA--TGAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGTGAAAA
*
1730246 TGTCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
1 TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
1730291 CTTATGTGCA
Statistics
Matches: 151, Mismatches: 39, Indels: 17
0.73 0.19 0.08
Matches are distributed among these distances:
49 38 0.25
50 3 0.02
51 5 0.03
52 103 0.68
53 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (51 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGTGAAAA
Found at i:1730312 original size:43 final size:46
Alignment explanation
Indices: 1730209--1730314 Score: 128
Period size: 49 Copynumber: 2.3 Consensus size: 46
1730199 CCAATATACT
* * *
1730209 GATTCAAGGCTAGCGATATCGGACTTAAAGATGAAGGTGTCAATGTGCT
1 GATTCAAGGCCAGCGATATCGGACTTAAAGAT--AGCTGT-AATGTGCA
*
1730258 GATTCAAGGCCAGCGATATTGGACTTAAAGAT-GCT-T-ATGTGCA
1 GATTCAAGGCCAGCGATATCGGACTTAAAGATAGCTGTAATGTGCA
1730301 GATTCAAGGCCAGC
1 GATTCAAGGCCAGC
1730315 AACATTAGGC
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
43 20 0.38
45 1 0.02
46 2 0.04
49 30 0.57
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.25
Consensus pattern (46 bp):
GATTCAAGGCCAGCGATATCGGACTTAAAGATAGCTGTAATGTGCA
Found at i:1730373 original size:32 final size:31
Alignment explanation
Indices: 1730337--1730517 Score: 202
Period size: 32 Copynumber: 5.7 Consensus size: 31
1730327 AGAAAGAGAA
1730337 GCCACCAACTTGTGTGGGCTTTTGAAAGGGTT
1 GCCACCAACTTGTGTGGGC-TTTGAAAGGGTT
* *
1730369 GCCACCGACTTGTGTGGGCTTTAAGAAGGGTT
1 GCCACCAACTTGTGTGGGCTTTGA-AAGGGTT
* * * * *
1730401 ACCACCAGCTTGTGTCGGCTTTGAAGGGGCT
1 GCCACCAACTTGTGTGGGCTTTGAAAGGGTT
** *
1730432 GCCACTGACTTGTGTGAGCTTTTG-AAGAGGTT
1 GCCACCAACTTGTGTGGGC-TTTGAAAG-GGTT
*
1730464 GCCACCAACTTGTGTGGGCTTTGAAGAAGGTT
1 GCCACCAACTTGTGTGGGCTTTGAA-AGGGTT
*
1730496 GCCACCAACTTGTGTAGGCTTT
1 GCCACCAACTTGTGTGGGCTTT
1730518 AGAGAAGGTT
Statistics
Matches: 122, Mismatches: 22, Indels: 10
0.79 0.14 0.06
Matches are distributed among these distances:
31 28 0.23
32 93 0.76
33 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.30
Consensus pattern (31 bp):
GCCACCAACTTGTGTGGGCTTTGAAAGGGTT
Found at i:1730442 original size:63 final size:63
Alignment explanation
Indices: 1730338--1730525 Score: 234
Period size: 63 Copynumber: 2.9 Consensus size: 63
1730328 GAAAGAGAAG
*
1730338 CCACCAACTTGTGTGGGCTTTTGAAAGGGTTGCCACCGACTTGTGTGGGCTTTAAGAAGGGTTA
1 CCACCAACTTGTGTGGGC-TTTGAAGGGGTTGCCACCGACTTGTGTGGGCTTTAAGAAGGGTTA
* * * * * * *
1730402 CCACCAGCTTGTGTCGGCTTTGAAGGGGCTGCCACTGACTTGTGTGAGCTTT-TGAAGAGGTTG
1 CCACCAACTTGTGTGGGCTTTGAAGGGGTTGCCACCGACTTGTGTGGGCTTTAAGAAG-GGTTA
* * *
1730465 CCACCAACTTGTGTGGGCTTTGAAGAAGGTTGCCACCAACTTGTGTAGGCTTTAGAGAAGG
1 CCACCAACTTGTGTGGGCTTTGAAG-GGGTTGCCACCGACTTGTGTGGGCTTTA-AGAAGG
1730526 TTTCTCCACT
Statistics
Matches: 103, Mismatches: 17, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
62 4 0.04
63 57 0.55
64 37 0.36
65 1 0.01
66 4 0.04
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (63 bp):
CCACCAACTTGTGTGGGCTTTGAAGGGGTTGCCACCGACTTGTGTGGGCTTTAAGAAGGGTTA
Found at i:1730475 original size:95 final size:95
Alignment explanation
Indices: 1730344--1730517 Score: 271
Period size: 95 Copynumber: 1.8 Consensus size: 95
1730334 GAAGCCACCA
* *
1730344 ACTTGTGTGGGCTTTTGAAAGGGTTGCCACCGACTTGTGTGGGCTTT-AAGAAGGGTTACCACCA
1 ACTTGTGTGAGCTTTTGAAAGGGTTGCCACCAACTTGTGTGGGCTTTGAAGAA-GGTTACCACCA
* *
1730408 GCTTGTGTCGGCTTTGAAGGGGCTGCCACTG
65 ACTTGTGTAGGCTTTGAAGGGGCTGCCACTG
*
1730439 ACTTGTGTGAGCTTTTG-AAGAGGTTGCCACCAACTTGTGTGGGCTTTGAAGAAGGTTGCCACCA
1 ACTTGTGTGAGCTTTTGAAAG-GGTTGCCACCAACTTGTGTGGGCTTTGAAGAAGGTTACCACCA
1730503 ACTTGTGTAGGCTTT
65 ACTTGTGTAGGCTTT
1730518 AGAGAAGGTT
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
94 3 0.04
95 64 0.89
96 5 0.07
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (95 bp):
ACTTGTGTGAGCTTTTGAAAGGGTTGCCACCAACTTGTGTGGGCTTTGAAGAAGGTTACCACCAA
CTTGTGTAGGCTTTGAAGGGGCTGCCACTG
Found at i:1730758 original size:28 final size:27
Alignment explanation
Indices: 1730699--1730759 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
1730689 TATACAGCAA
* *
1730699 GTGCCACTGATTGTGGACTTTGAAAAG
1 GTGCCACTAATTGTGGACTTCGAAAAG
* *
1730726 ATGCCACTAAGTTGTGGACTTCGAAGAG
1 GTGCCACTAA-TTGTGGACTTCGAAAAG
1730754 GTGCCA
1 GTGCCA
1730760 GTGACTAGTG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 8 0.29
28 20 0.71
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (27 bp):
GTGCCACTAATTGTGGACTTCGAAAAG
Found at i:1732090 original size:10 final size:10
Alignment explanation
Indices: 1732074--1732117 Score: 63
Period size: 10 Copynumber: 4.4 Consensus size: 10
1732064 TTTCTTCCCC
1732074 TTTTTGTTTG
1 TTTTTGTTTG
*
1732084 TTGTTGTTCT-
1 TTTTTGTT-TG
1732094 TTTTTGTTTG
1 TTTTTGTTTG
1732104 TTTTTGTTTG
1 TTTTTGTTTG
1732114 TTTT
1 TTTT
1732118 CTTTTTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 1 0.03
10 28 0.93
11 1 0.03
ACGTcount: A:0.00, C:0.02, G:0.18, T:0.80
Consensus pattern (10 bp):
TTTTTGTTTG
Found at i:1736913 original size:22 final size:19
Alignment explanation
Indices: 1736885--1736937 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 19
1736875 AATTCCCTTT
*
1736885 AAAAAAGAAATAGAAAAACATA
1 AAAAAAGAAA-AG-AAAA-AGA
1736907 AAAAAAGGAAAAGAAAAAGA
1 AAAAAA-GAAAAGAAAAAGA
1736927 AAAAAAGAAAA
1 AAAAAAGAAAA
1736938 AAAGCAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 5 0.17
20 8 0.28
21 4 0.14
22 8 0.28
23 4 0.14
ACGTcount: A:0.81, C:0.02, G:0.13, T:0.04
Consensus pattern (19 bp):
AAAAAAGAAAAGAAAAAGA
Found at i:1736918 original size:28 final size:28
Alignment explanation
Indices: 1736887--1736946 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
1736877 TTCCCTTTAA
* * * *
1736887 AAAAGAAATAGAAAAACATAAAAAAAGG
1 AAAAGAAAAAGAAAAAAAGAAAAAAAGC
1736915 AAAAGAAAAAGAAAAAAAGAAAAAAAGC
1 AAAAGAAAAAGAAAAAAAGAAAAAAAGC
1736943 AAAA
1 AAAA
1736947 AATGAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.80, C:0.03, G:0.13, T:0.03
Consensus pattern (28 bp):
AAAAGAAAAAGAAAAAAAGAAAAAAAGC
Found at i:1736940 original size:17 final size:17
Alignment explanation
Indices: 1736896--1736958 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
1736886 AAAAAGAAAT
* *
1736896 AGAAAAACATAAAAAAA
1 AGAAAAAAAGAAAAAAA
* *
1736913 GGAAAAGAAAAAGAAAAAA
1 AGAAAA-AAAGA-AAAAAA
*
1736932 AGAAAAAAAGCAAAAAA
1 AGAAAAAAAGAAAAAAA
*
1736949 TGAAAAAAAG
1 AGAAAAAAAG
1736959 TGCAGATAGT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
17 20 0.54
18 6 0.16
19 11 0.30
ACGTcount: A:0.79, C:0.03, G:0.14, T:0.03
Consensus pattern (17 bp):
AGAAAAAAAGAAAAAAA
Found at i:1737008 original size:18 final size:17
Alignment explanation
Indices: 1736920--1736996 Score: 54
Period size: 17 Copynumber: 4.4 Consensus size: 17
1736910 AAAGGAAAAG
1736920 AAAAAGA-AAAAAA-GA
1 AAAAAGAGAAAAAATGA
1736935 AAAAA-AGCAAAAAATGAA
1 AAAAAGAG-AAAAAATG-A
**
1736953 AAAAAGTGCAGATAGTAA-GA
1 AAAAA--G-AGA-AAAAATGA
1736973 AAAAAGAGAAAAAATGA
1 AAAAAGAGAAAAAATGA
1736990 AAAAAGA
1 AAAAAGA
1736997 AGAGGAAATG
Statistics
Matches: 48, Mismatches: 4, Indels: 18
0.69 0.06 0.26
Matches are distributed among these distances:
14 1 0.02
15 5 0.10
16 9 0.19
17 13 0.27
18 7 0.15
20 6 0.12
21 2 0.04
22 5 0.10
ACGTcount: A:0.74, C:0.03, G:0.17, T:0.06
Consensus pattern (17 bp):
AAAAAGAGAAAAAATGA
Found at i:1739440 original size:34 final size:34
Alignment explanation
Indices: 1739358--1739489 Score: 164
Period size: 31 Copynumber: 3.9 Consensus size: 34
1739348 GAAGTGATTG
*
1739358 AGAGGTTCTATCTTAGCCTTTAAGAAAGATA-GGA
1 AGAGGTTCTATCTTAGCCTTTGA-AAAGATAGGGA
* *
1739392 AGAAAGGTTCTATCTTAGCCTATGAGAAGATAGGGA
1 AG--AGGTTCTATCTTAGCCTTTGAAAAGATAGGGA
* *
1739428 AGAGGTTTTATCTTAGCCTGTGAAAAGAT-GGG-
1 AGAGGTTCTATCTTAGCCTTTGAAAAGATAGGGA
1739460 -GAGGTTCTATCTTAGCCTTTGAAAAGATAG
1 AGAGGTTCTATCTTAGCCTTTGAAAAGATAG
1739490 TGTTATAAGG
Statistics
Matches: 86, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
31 26 0.30
32 1 0.01
33 3 0.03
34 26 0.30
35 6 0.07
36 24 0.28
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.30
Consensus pattern (34 bp):
AGAGGTTCTATCTTAGCCTTTGAAAAGATAGGGA
Found at i:1740755 original size:164 final size:164
Alignment explanation
Indices: 1740421--1740768 Score: 406
Period size: 164 Copynumber: 2.1 Consensus size: 164
1740411 ATGGGAGTTT
* * *
1740421 AATAATATTATTAGATGAATTTTAAAAATTTTAAACCGAAGAAAATCCTCCCAAAAATATTTATA
1 AATAATAATATTTGATGAATTTTAAAAATTTTAAACCGAAGAAAATCCTCCCAAAAACATTTATA
* * ** *
1740486 GAATAGAAAACTAGATTTTTCAAAAATAGAGGAATTTTAGAGAAAATTTCGAAAATAATGAAAAT
66 GAATAGAAAACTAGATATTTCAAAAATAGAGAAATTCAAGAAAAAATTTC-AAAATAATGAAAAT
* *
1740551 GAATGAATTTTTTAAAACTGATTTAATGTGAATCA
130 GAATGAATTTTTCAAAACTGATTTAATGTCAATCA
*
1740586 AATAATAATATTTGATGAATTTTAAAAATTTTAAACC-AA-AAAATCC-CCTCGAAAACATTTAT
1 AATAATAATATTTGATGAATTTTAAAAATTTTAAACCGAAGAAAATCCTCC-CAAAAACATTTAT
* * *
1740648 GGAGTAGAAAATTCT-G-TATTTCAAAAATATGA-AAACTTCAAGGAAAAAATTT-AAAACTCAT
65 AGAATAGAAAA--CTAGATATTTCAAAAATA-GAGAAA-TTCAA-GAAAAAATTTCAAAA-TAAT
* * *
1740709 GAAAATGATTGAATTTTTCAAAACTGATTTACTAG-CAATTA
124 GAAAATGAATGAATTTTTCAAAACTGATTTAAT-GTCAATCA
1740750 AATAATAATATTTGATGAA
1 AATAATAATATTTGATGAA
1740769 AGTTAAAACT
Statistics
Matches: 158, Mismatches: 17, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
162 2 0.01
163 45 0.28
164 64 0.41
165 47 0.30
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.33
Consensus pattern (164 bp):
AATAATAATATTTGATGAATTTTAAAAATTTTAAACCGAAGAAAATCCTCCCAAAAACATTTATA
GAATAGAAAACTAGATATTTCAAAAATAGAGAAATTCAAGAAAAAATTTCAAAATAATGAAAATG
AATGAATTTTTCAAAACTGATTTAATGTCAATCA
Found at i:1741102 original size:164 final size:164
Alignment explanation
Indices: 1740824--1741322 Score: 484
Period size: 164 Copynumber: 3.0 Consensus size: 164
1740814 CAAAGTAGAA
* * * * * * *
1740824 AATTTTAAAAATTTTAAACCGAAGAAAATCCCCCCAAAAATATTTATGAAATAAAAAACTCGA-A
1 AATTTTAAAAATTTTAAACCGAA-AAAATCCCCTCGAAAACATTTATGGAATAGAAAATTCTATA
* * *
1740888 TTTTCGAAAACA-GAGGAATTTTAGAGAAAAATTCAAAACTCATGAAAATGAATGAATTTTTCAA
65 -TTTCGAAAATATGAGAAATTTAAGA-AAAAATTCAAAACTCATGAAAATGAATGAATTTTTCAA
* *
1740952 AATTGATTTAATGCGAATCAAATAATAATATTTAATG
128 AACTGATTTAATGCGAATCAAATAATAATATTTAAAG
*
1740989 AATTTTAAAAATTTTAAATC-AAAAAATCCCCTCGAAAACATTTATGGAATAGAAAATTCTATAT
1 AATTTTAAAAATTTTAAACCGAAAAAATCCCCTCGAAAACATTTATGGAATAGAAAATTCTATAT
*
1741053 TTCGAAAATATGA-AAATTTCAAGGAAAAAATTCAAAACTCATGAAAATGAATGAATTTTTCAGA
66 TTCGAAAATATGAGAAATTT-AA-GAAAAAATTCAAAACTCATGAAAATGAATGAATTTTTCAAA
* *
1741117 ACTGATTTAATAGC-AATGAAATAATAATATTTGACA-
129 ACTGATTTAAT-GCGAATCAAATAATAATATTT-AAAG
** * * * ** * *
1741153 AACGTTAAAAA-TTAAAAGCTAAAAAAT-CCCTCCGAAAACATTTACAGAGTAGAAAATT-TCGT
1 AATTTTAAAAATTTTAAACCGAAAAAATCCCCT-CGAAAACATTTATGGAATAGAAAATTCT-AT
* * * *
1741215 ATTTCAAAAATATGAGGAATTTTGAA-AAAAAA-TCAAAAACTCAT-AAAATAAAAGGAATTTTT
64 ATTTCGAAAATATGA-GAAATTT-AAGAAAAAATTC-AAAACTCATGAAAAT-GAATGAATTTTT
* * * *
1741277 CAAAACTGATTTAGTG-GAGATTAAATGATAATATTCAAAG
125 CAAAACTGATTTAATGCGA-ATCAAATAATAATATTTAAAG
1741317 AATTTT
1 AATTTT
1741323 GATGCTAGAA
Statistics
Matches: 281, Mismatches: 37, Indels: 33
0.80 0.11 0.09
Matches are distributed among these distances:
163 69 0.25
164 181 0.64
165 24 0.09
166 7 0.02
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.30
Consensus pattern (164 bp):
AATTTTAAAAATTTTAAACCGAAAAAATCCCCTCGAAAACATTTATGGAATAGAAAATTCTATAT
TTCGAAAATATGAGAAATTTAAGAAAAAATTCAAAACTCATGAAAATGAATGAATTTTTCAAAAC
TGATTTAATGCGAATCAAATAATAATATTTAAAG
Found at i:1741162 original size:386 final size:383
Alignment explanation
Indices: 1740438--1741211 Score: 1230
Period size: 386 Copynumber: 2.0 Consensus size: 383
1740428 TTATTAGATG
* * *
1740438 AATTTTAAAAATTTTAAACCGAAGAAAATCCTCCCAAAAATATTTATAGAATAGAAAACTAGATT
1 AATTTTAAAAATTTTAAACCGAAGAAAATCCCCCCAAAAATATTTATAGAATAAAAAACTAGAAT
* * *
1740503 TTTCAAAAATAGAGGAATTTTAGAGAAAATTTCGAAAATAATGAAAATGAATGAATTTTTTAAAA
66 TTTCAAAAACAGAGGAATTTTAGAGAAAAATTCGAAAATAATGAAAATGAATGAATTTTTCAAAA
* *
1740568 CTGATTTAATGTGAATCAAATAATAATATTTGATGAATTTTAAAAATTTTAAACCAAAAAATCCC
131 CTGATTTAATGCGAATCAAATAATAATATTTAATGAATTTTAAAAATTTTAAACCAAAAAATCCC
* *
1740633 CTCGAAAACATTTATGGAGTAGAAAATTCTGTATTTCAAAAATATGAAAACTTCAAGGAAAAAAT
196 CTCGAAAACATTTATGGAATAGAAAATTCTATATTTCAAAAATATGAAAACTTCAAGGAAAAAAT
* * * *
1740698 TTAAAACTCATGAAAATGATTGAATTTTTCAAAACTGATTTACTAGCAATTAAATAATAATATTT
261 TCAAAACTCATGAAAATGAATGAATTTTTCAAAACTGATTTAATAGCAATGAAATAATAATATTT
* * *
1740763 GATGAAAGTTAAAACTTAAAATCTAAAAAAAAATCCCTCCAAAAACATTTACAAAGTAGAA
326 GATCAAAGTTAAAAATTAAAAGCT---AAAAAATCCCTCCAAAAACATTTACAAAGTAGAA
*
1740824 AATTTTAAAAATTTTAAACCGAAGAAAATCCCCCCAAAAATATTTAT-GAAATAAAAAACTCGAA
1 AATTTTAAAAATTTTAAACCGAAGAAAATCCCCCCAAAAATATTTATAG-AATAAAAAACTAGAA
* *
1740888 TTTTCGAAAACAGAGGAATTTTAGAGAAAAATTC-AAAACTCATGAAAATGAATGAATTTTTCAA
65 TTTTCAAAAACAGAGGAATTTTAGAGAAAAATTCGAAAA-TAATGAAAATGAATGAATTTTTCAA
* *
1740952 AATTGATTTAATGCGAATCAAATAATAATATTTAATGAATTTTAAAAATTTTAAATCAAAAAATC
129 AACTGATTTAATGCGAATCAAATAATAATATTTAATGAATTTTAAAAATTTTAAACCAAAAAATC
* *
1741017 CCCTCGAAAACATTTATGGAATAGAAAATTCTATATTTCGAAAATATGAAAATTTCAAGGAAAAA
194 CCCTCGAAAACATTTATGGAATAGAAAATTCTATATTTCAAAAATATGAAAACTTCAAGGAAAAA
*
1741082 ATTCAAAACTCATGAAAATGAATGAATTTTTCAGAACTGATTTAATAGCAATGAAATAATAATAT
259 ATTCAAAACTCATGAAAATGAATGAATTTTTCAAAACTGATTTAATAGCAATGAAATAATAATAT
* *
1741147 TTGA-CAAACGTTAAAAATTAAAAGCTAAAAAATCCCTCCGAAAACATTTACAGAGTAGAA
324 TTGATCAAA-GTTAAAAATTAAAAGCTAAAAAATCCCTCCAAAAACATTTACAAAGTAGAA
1741207 AATTT
1 AATTT
1741212 CGTATTTCAA
Statistics
Matches: 358, Mismatches: 27, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
383 37 0.10
385 8 0.02
386 313 0.87
ACGTcount: A:0.49, C:0.11, G:0.10, T:0.30
Consensus pattern (383 bp):
AATTTTAAAAATTTTAAACCGAAGAAAATCCCCCCAAAAATATTTATAGAATAAAAAACTAGAAT
TTTCAAAAACAGAGGAATTTTAGAGAAAAATTCGAAAATAATGAAAATGAATGAATTTTTCAAAA
CTGATTTAATGCGAATCAAATAATAATATTTAATGAATTTTAAAAATTTTAAACCAAAAAATCCC
CTCGAAAACATTTATGGAATAGAAAATTCTATATTTCAAAAATATGAAAACTTCAAGGAAAAAAT
TCAAAACTCATGAAAATGAATGAATTTTTCAAAACTGATTTAATAGCAATGAAATAATAATATTT
GATCAAAGTTAAAAATTAAAAGCTAAAAAATCCCTCCAAAAACATTTACAAAGTAGAA
Found at i:1746268 original size:13 final size:13
Alignment explanation
Indices: 1746250--1746275 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1746240 CAATTTTTTG
1746250 TGTATCGATACAT
1 TGTATCGATACAT
1746263 TGTATCGATACAT
1 TGTATCGATACAT
1746276 ACTTGCTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1748842 original size:13 final size:13
Alignment explanation
Indices: 1748824--1748849 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1748814 ATAATCACCG
1748824 TGTATCGATACAA
1 TGTATCGATACAA
1748837 TGTATCGATACAA
1 TGTATCGATACAA
1748850 AGAAAAATGT
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):
TGTATCGATACAA
Found at i:1752783 original size:21 final size:21
Alignment explanation
Indices: 1752754--1752798 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1752744 AAGTTTTCAT
*
1752754 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1752774 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1752796 TTT
1 TTT
1752799 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1755035 original size:13 final size:13
Alignment explanation
Indices: 1755017--1755042 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1755007 CAATTTTTTA
1755017 TGTATCGATACAT
1 TGTATCGATACAT
1755030 TGTATCGATACAT
1 TGTATCGATACAT
1755043 ACTTGCTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1756435 original size:34 final size:34
Alignment explanation
Indices: 1756396--1756462 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
1756386 AGCCTGACTT
1756396 AAAATGGCCCTTAATTGTATGAATAATGAAGTAA
1 AAAATGGCCCTTAATTGTATGAATAATGAAGTAA
1756430 AAAATGGCCCTTAATTGTATGAATAATGAAGTA
1 AAAATGGCCCTTAATTGTATGAATAATGAAGTA
1756463 TTGTTATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.43, C:0.09, G:0.18, T:0.30
Consensus pattern (34 bp):
AAAATGGCCCTTAATTGTATGAATAATGAAGTAA
Found at i:1758641 original size:21 final size:21
Alignment explanation
Indices: 1758590--1758649 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
1758580 AGTCGTTGCG
1758590 TAAT-ATGTATCGATACAA-T
1 TAATCATGTATCGATACAATT
* * *
1758609 TCATCATATATCAATACAATT
1 TAATCATGTATCGATACAATT
1758630 TAATCATGTATCGATACAAT
1 TAATCATGTATCGATACAAT
1758650 GTATCGATAC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
19 3 0.09
20 12 0.36
21 18 0.55
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.37
Consensus pattern (21 bp):
TAATCATGTATCGATACAATT
Found at i:1758653 original size:13 final size:13
Alignment explanation
Indices: 1758635--1758660 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1758625 CAATTTAATC
1758635 ATGTATCGATACA
1 ATGTATCGATACA
1758648 ATGTATCGATACA
1 ATGTATCGATACA
1758661 GTCGAAGAGT
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:1759612 original size:11 final size:11
Alignment explanation
Indices: 1759596--1759675 Score: 87
Period size: 11 Copynumber: 7.5 Consensus size: 11
1759586 CAAATTTACT
1759596 TTTTTTCTCTC
1 TTTTTTCTCTC
1759607 TTTTTTCT-T-
1 TTTTTTCTCTC
*
1759616 TTTTTTCCTTTC
1 TTTTTT-CTCTC
1759628 TTTTTTCTCTC
1 TTTTTTCTCTC
*
1759639 TTTTTTCTC-A
1 TTTTTTCTCTC
*
1759649 TTTTTTCATTTC
1 TTTTTTC-TCTC
1759661 TTTTTTCTCT-
1 TTTTTTCTCTC
1759671 TTTTT
1 TTTTT
1759676 CTCATTTTTC
Statistics
Matches: 59, Mismatches: 5, Indels: 11
0.79 0.07 0.15
Matches are distributed among these distances:
9 6 0.10
10 15 0.25
11 25 0.42
12 13 0.22
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTTCTCTC
Found at i:1759632 original size:33 final size:32
Alignment explanation
Indices: 1759596--1759684 Score: 126
Period size: 32 Copynumber: 2.8 Consensus size: 32
1759586 CAAATTTACT
*
1759596 TTTTTTCTCTCTTTTTTCTTTTTTTTCCTTTC
1 TTTTTTCTCTCTTTTTTCTTTTTTTTCATTTC
*
1759628 TTTTTTCTCTCTTTTTTCTCATTTTTTCATTTC
1 TTTTTTCTCTCTTTTTTCT-TTTTTTTCATTTC
*
1759661 TTTTTTCTCT-TTTTTCTCATTTTT
1 TTTTTTCTCTCTTTTT-TCTTTTTT
1759685 CTCTCTCACT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
32 28 0.55
33 23 0.45
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.76
Consensus pattern (32 bp):
TTTTTTCTCTCTTTTTTCTTTTTTTTCATTTC
Found at i:1759678 original size:9 final size:9
Alignment explanation
Indices: 1759596--1759688 Score: 77
Period size: 9 Copynumber: 10.1 Consensus size: 9
1759586 CAAATTTACT
1759596 TTTTTTCTC
1 TTTTTTCTC
1759605 TCTTTTT-TC
1 T-TTTTTCTC
1759614 TTTTTT-T-
1 TTTTTTCTC
**
1759621 TCCTTTCT-
1 TTTTTTCTC
1759629 TTTTTCTCTC
1 TTTTT-TCTC
1759639 TTTTTTCTC
1 TTTTTTCTC
1759648 ATTTTTTCATTTC
1 -TTTTTTC---TC
1759661 TTTTTTCTC
1 TTTTTTCTC
1759670 TTTTTTCTC
1 TTTTTTCTC
*
1759679 ATTTTTCTC
1 TTTTTTCTC
1759688 T
1 T
1759689 CTCACTTTCC
Statistics
Matches: 70, Mismatches: 6, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
7 4 0.06
8 10 0.14
9 30 0.43
10 17 0.24
12 7 0.10
13 2 0.03
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTTTCTC
Found at i:1759684 original size:11 final size:10
Alignment explanation
Indices: 1759594--1759690 Score: 81
Period size: 11 Copynumber: 9.2 Consensus size: 10
1759584 AGCAAATTTA
1759594 CTTTTTTTCT
1 CTTTTTTTCT
1759604 CTCTTTTTTCT
1 CT-TTTTTTCT
1759615 -TTTTTTTCCT
1 CTTTTTTT-CT
*
1759625 TTCTTTTTTCT
1 CT-TTTTTTCT
1759636 CTCTTTTTTCT
1 CT-TTTTTTCT
*
1759647 CATTTTTTCAT
1 CTTTTTTTC-T
*
1759658 TTCTTTTTTCT
1 CT-TTTTTTCT
1759669 C-TTTTTTCT
1 CTTTTTTTCT
*
1759678 CATTTTTCTCT
1 C-TTTTTTTCT
1759689 CT
1 CT
1759691 CACTTTCCAA
Statistics
Matches: 73, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
9 15 0.21
10 13 0.18
11 32 0.44
12 13 0.18
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (10 bp):
CTTTTTTTCT
Found at i:1763334 original size:52 final size:52
Alignment explanation
Indices: 1763256--1763384 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
1763246 CAAAATATGA
* *
1763256 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
*
1763308 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
1763360 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1763385 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
Found at i:1763397 original size:52 final size:51
Alignment explanation
Indices: 1763256--1763404 Score: 219
Period size: 52 Copynumber: 2.9 Consensus size: 51
1763246 CAAAATATGA
*
1763256 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* *
1763308 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
1763360 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1763405 ATGTATTGAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 87 0.98
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:1767662 original size:20 final size:19
Alignment explanation
Indices: 1767637--1767713 Score: 91
Period size: 20 Copynumber: 3.9 Consensus size: 19
1767627 TTTTACTCAG
*
1767637 ATGTATTGATACATTCTTCA
1 ATGTATCGATACATT-TTCA
* *
1767657 ATGTATCGATACATGTATGA
1 ATGTATCGATACAT-TTTCA
*
1767677 ATATATCGATACATTTTTCA
1 ATGTATCGATACA-TTTTCA
1767697 ATGTATCGATACATTTT
1 ATGTATCGATACATTTT
1767714 GTCTTTTTAC
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
19 4 0.08
20 42 0.88
21 2 0.04
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (19 bp):
ATGTATCGATACATTTTCA
Found at i:1767757 original size:91 final size:90
Alignment explanation
Indices: 1767590--1767761 Score: 254
Period size: 91 Copynumber: 1.9 Consensus size: 90
1767580 TACCCAAATG
* * * *
1767590 TATCGATACATTTTTTAATGTATCAATACAATCTATCTTTTACTCAGATGTATTGATACATTCTT
1 TATCGATACATTTTTCAATGTATCAATACAATCTATCTTTTACCCAAATGTATCGATACATTCTT
1767655 CAATGTATCGATACATGTATGAATA
66 CAATGTATCGATACATGTATGAATA
* * * * *
1767680 TATCGATACATTTTTCAATGTATCGATACATTTTGTCTTTTTACCCAAATGTATCGATACATTTT
1 TATCGATACATTTTTCAATGTATCAATACAATCTATC-TTTTACCCAAATGTATCGATACATTCT
1767745 TCAATGTATCGATACAT
65 TCAATGTATCGATACAT
1767762 CTAGTTAAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 32 0.44
91 40 0.56
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.43
Consensus pattern (90 bp):
TATCGATACATTTTTCAATGTATCAATACAATCTATCTTTTACCCAAATGTATCGATACATTCTT
CAATGTATCGATACATGTATGAATA
Found at i:1774105 original size:11 final size:11
Alignment explanation
Indices: 1774089--1774123 Score: 56
Period size: 10 Copynumber: 3.4 Consensus size: 11
1774079 AACAACAAAA
1774089 AAAATAATAAT
1 AAAATAATAAT
1774100 AAAATAATAA-
1 AAAATAATAAT
1774110 AAAATAA-AAT
1 AAAATAATAAT
1774120 AAAA
1 AAAA
1774124 ATCGATTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 2 0.09
10 11 0.48
11 10 0.43
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:1774111 original size:23 final size:23
Alignment explanation
Indices: 1774062--1774121 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
1774052 TACTATGCGA
*
1774062 AAAAAAAATCAA-AATCAAACAAC
1 AAAAAAAAT-AATAATAAAACAAC
* *
1774085 AAAAAAAATAATAATAAAATAAT
1 AAAAAAAATAATAATAAAACAAC
1774108 AAAAAATAA-AATAA
1 AAAAAA-AATAATAA
1774122 AAATCGATTG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 2 0.06
23 28 0.88
24 2 0.06
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (23 bp):
AAAAAAAATAATAATAAAACAAC
Found at i:1774672 original size:17 final size:17
Alignment explanation
Indices: 1774650--1774690 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
1774640 AGTCTTAGGT
1774650 AGAATTCTGACAAGAAG
1 AGAATTCTGACAAGAAG
1774667 AGAATTCTGACAAGAAG
1 AGAATTCTGACAAGAAG
1774684 AGAATTC
1 AGAATTC
1774691 AACCTCTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.46, C:0.12, G:0.22, T:0.20
Consensus pattern (17 bp):
AGAATTCTGACAAGAAG
Found at i:1776082 original size:79 final size:79
Alignment explanation
Indices: 1775959--1776165 Score: 195
Period size: 79 Copynumber: 2.6 Consensus size: 79
1775949 TGCATTCCTC
* * * ** * *
1775959 GATGAAAAATTTAATATTTTGGAGATAAAGGCAGGGTTGAAGTATCCCCTCA-GAAATAACAAG-
1 GATGAAAAA-TCAATATTCTGGAAATAAAACCGGGGTTGGAGTATCCCCT-AGGAAATAA-AAGT
*
1776022 GTT-GAAGTATCCCTAAT
63 GTTAG-AGTATCCCCAAT
* * * * * *
1776039 GGTGAAAAATCGATGTTCTGGAAATAAAACCGGGGTTGGAGTATCCCATAGGGAATAATAGTGTT
1 GATGAAAAATCAATATTCTGGAAATAAAACCGGGGTTGGAGTATCCCCTAGGAAATAAAAGTGTT
*
1776104 AGAGTATCCCCGAT
66 AGAGTATCCCCAAT
* **
1776118 TATGAAAAATCAATATTCTGGAAATAAAATTGGGGTTGGAGTATCCCC
1 GATGAAAAATCAATATTCTGGAAATAAAACCGGGGTTGGAGTATCCCC
1776166 GATAGTGGAA
Statistics
Matches: 102, Mismatches: 22, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
78 3 0.03
79 90 0.88
80 9 0.09
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (79 bp):
GATGAAAAATCAATATTCTGGAAATAAAACCGGGGTTGGAGTATCCCCTAGGAAATAAAAGTGTT
AGAGTATCCCCAAT
Found at i:1776178 original size:51 final size:51
Alignment explanation
Indices: 1776105--1776216 Score: 127
Period size: 51 Copynumber: 2.2 Consensus size: 51
1776095 AATAGTGTTA
***
1776105 GAGTATCCCCGATTATGAAAAATCAATATTCTGGAAATAAAATTGGGGTTG
1 GAGTATCCCCGATTATGAAAAATCAATATTCTGGAAATAAAACCAGGGTTG
* *** * *
1776156 GAGTATCCCCGA-TAGTGGAAAATTGGTGTTTTGGAAATAAAACCAGGGTTG
1 GAGTATCCCCGATTA-TGAAAAATCAATATTCTGGAAATAAAACCAGGGTTG
1776207 GAGTATCCCC
1 GAGTATCCCC
1776217 TCGAAAATAA
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
50 2 0.04
51 49 0.96
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (51 bp):
GAGTATCCCCGATTATGAAAAATCAATATTCTGGAAATAAAACCAGGGTTG
Found at i:1776231 original size:79 final size:79
Alignment explanation
Indices: 1776150--1776591 Score: 457
Period size: 79 Copynumber: 5.6 Consensus size: 79
1776140 AATAAAATTG
* * * * *
1776150 GGGTTGGAGTATCCCCGATAGTGGAAAATTGGTGTTTTGGAAATAAAACCAGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCAATAGTGGAAAATCGATATTTTAGAAATAAAACCAGGGTTGGAGTATCC
*
1776215 CCTCGAAAATAATG
66 CCTCGAAAATAATA
* ** * ** *
1776229 GGGTTAGAGTATCCTTGATTA-TGGAAAATCGATATTTTAGAAATAAAACTGGGGTTAGTA-TAT
1 GGGTTGGAGTATCC-CCAATAGTGGAAAATCGATATTTTAGAAATAAAACCAGGGTT-GGAGTAT
*
1776292 CCCCTC-AGAAATAATG
64 CCCCTCGA-AAATAATA
* * *
1776308 GGGTTGGAGTATCCCCGATTGTGGAAAATCGATGTTTT-GAAAATAAAACCAGGGTTGGAGTATC
1 GGGTTGGAGTATCCCCAATAGTGGAAAATCGATATTTTAG-AAATAAAACCAGGGTTGGAGTATC
* * *
1776372 TCTTCGAAAATAACA
65 CCCTCGAAAATAATA
* * * *
1776387 GGGTTGGAGTATCCCCAATCGTGGAAAATTGGTATTTTGGAAATAAAA-CAGGAGTTGGAGTATC
1 GGGTTGGAGTATCCCCAATAGTGGAAAATCGATATTTTAGAAATAAAACCAGG-GTTGGAGTATC
1776451 CCCTCGAAAATAATA
65 CCCTCGAAAATAATA
* ** ** * * *
1776466 GGGTTGGAATATCCCCAACGGT-GAAAATTAATGTTTTAGAAATAAAGCCGGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCAATAGTGGAAAATCGATATTTTAGAAATAAAACCAGGGTTGGAGTATCC
*
1776530 CCTC-AGAAATAACA
66 CCTCGA-AAATAATA
* * *
1776544 GAGTTGGAGTATCCCCAATGGTGGAAAATCGGTATTTTAGAAATAAAA
1 GGGTTGGAGTATCCCCAATAGTGGAAAATCGATATTTTAGAAATAAAA
1776592 ACATGAATGA
Statistics
Matches: 299, Mismatches: 52, Indels: 24
0.80 0.14 0.06
Matches are distributed among these distances:
77 1 0.00
78 71 0.24
79 221 0.74
80 6 0.02
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (79 bp):
GGGTTGGAGTATCCCCAATAGTGGAAAATCGATATTTTAGAAATAAAACCAGGGTTGGAGTATCC
CCTCGAAAATAATA
Found at i:1776358 original size:158 final size:158
Alignment explanation
Indices: 1776148--1776591 Score: 547
Period size: 158 Copynumber: 2.8 Consensus size: 158
1776138 GAAATAAAAT
* *
1776148 TGGGGTTGGAGTATCCCCGATAGTGGAAAATTGGTGTTTTGGAAATAAAACCAGGGTTGGAGTAT
1 TGGGGTTGGAGTATCCCCGATAGTGGAAAATTGATGTTTTGAAAATAAAACCAGGGTTGGAGTAT
** * *** ** *
1776213 CCCCTCGAAAATAATGGGGTTAGAGTATCCTTGATTATGGAAAATCGATATTTTAGAAATAAAAC
66 CCCCTCGAAAATAACAGGGTTGGAGTATCCCCAATCGTGGAAAATCGGTATTTTAGAAATAAAAC
* * *
1776278 TGGGGTTAGTA-TATCCCCTC-AGAAATAA
131 AGGAGTT-GGAGTATCCCCTCGA-AAATAA
* *
1776306 TGGGGTTGGAGTATCCCCGATTGTGGAAAATCGATGTTTTGAAAATAAAACCAGGGTTGGAGTAT
1 TGGGGTTGGAGTATCCCCGATAGTGGAAAATTGATGTTTTGAAAATAAAACCAGGGTTGGAGTAT
* * * *
1776371 CTCTTCGAAAATAACAGGGTTGGAGTATCCCCAATCGTGGAAAATTGGTATTTTGGAAATAAAAC
66 CCCCTCGAAAATAACAGGGTTGGAGTATCCCCAATCGTGGAAAATCGGTATTTTAGAAATAAAAC
1776436 AGGAGTTGGAGTATCCCCTCGAAAATAA
131 AGGAGTTGGAGTATCCCCTCGAAAATAA
* * * ** * * *
1776464 TAGGGTTGGAATATCCCCAACGGT-GAAAATTAATGTTTT-AGAAATAAAGCCGGGGTTGGAGTA
1 TGGGGTTGGAGTATCCCCGATAGTGGAAAATTGATGTTTTGA-AAATAAAACCAGGGTTGGAGTA
* *
1776527 TCCCCTC-AGAAATAACAGAGTTGGAGTATCCCCAATGGTGGAAAATCGGTATTTTAGAAATAAA
65 TCCCCTCGA-AAATAACAGGGTTGGAGTATCCCCAATCGTGGAAAATCGGTATTTTAGAAATAAA
1776591 A
129 A
1776592 ACATGAATGA
Statistics
Matches: 247, Mismatches: 35, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
156 2 0.01
157 92 0.37
158 152 0.62
159 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (158 bp):
TGGGGTTGGAGTATCCCCGATAGTGGAAAATTGATGTTTTGAAAATAAAACCAGGGTTGGAGTAT
CCCCTCGAAAATAACAGGGTTGGAGTATCCCCAATCGTGGAAAATCGGTATTTTAGAAATAAAAC
AGGAGTTGGAGTATCCCCTCGAAAATAA
Found at i:1779524 original size:92 final size:92
Alignment explanation
Indices: 1779383--1779551 Score: 216
Period size: 92 Copynumber: 1.8 Consensus size: 92
1779373 TTTCCTCAAA
* * * *
1779383 CACTAGATGGTATTGATGCATCACAGAGCTTGATTTCCTTAAGATAAAGATAT-CCAGACCACAC
1 CACTAGATGGTATTGATGCATCACAAAGCCTGAATTCCTTAAGACAAAGATATCCCA-ACCACAC
1779447 ATTCCCAATCATATCCCTTTCATCCAAC
65 ATTCCCAATCATATCCCTTTCATCCAAC
** * * *
1779475 CACTAGATGGTATTGATGCATCACAAAGCCT-AATTCCTTGGGGGCAAAGATTTCCCAACCACTC
1 CACTAGATGGTATTGATGCATCACAAAGCCTGAATTCCTT-AAGACAAAGATATCCCAACCACAC
*
1779539 ATTCCTAATCATA
65 ATTCCCAATCATA
1779552 CCATTCTCTT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
91 7 0.11
92 55 0.85
93 3 0.05
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.28
Consensus pattern (92 bp):
CACTAGATGGTATTGATGCATCACAAAGCCTGAATTCCTTAAGACAAAGATATCCCAACCACACA
TTCCCAATCATATCCCTTTCATCCAAC
Found at i:1779762 original size:170 final size:170
Alignment explanation
Indices: 1779447--1779767 Score: 450
Period size: 170 Copynumber: 1.9 Consensus size: 170
1779437 CAGACCACAC
1779447 ATTCCCAATCATATCCCTTTCATCCAACCACTAGATGGTATTGATGCATCACAAAGCCTAATTCC
1 ATTCCCAATCATATCCCTTTCATCCAACCACTAGATGGTATTGATGCATCACAAAGCCTAATTCC
* * * ** *
1779512 TTGGGGGCAAAGATTTCCCAACCACTCATTCCTAATCATACCATTCTCTTTTAGTCACTAGATGA
66 TTGGGGGCAAAGATATCCCAACCACTCATTCCTAATCATACCATTCTCTCTCAACCACTAAATGA
* * *
1779577 TATTGGTGTATCACACGACCAGAAAAGGTGTAGCCCAAAT
131 TACTGATGCATCACACGACCAGAAAAGGTGTAGCCCAAAT
* ** *
1779617 ATTCCCAATCATATCGCC-TTCATTCATTCGCTAGATGGTATTGATGCATCACAAAGCCTAATTT
1 ATTCCCAATCATATC-CCTTTCATCCAACCACTAGATGGTATTGATGCATCACAAAGCCTAA-TT
* *
1779681 CCTT-GGGGCAAAGATATCTCAATCACTCATTCCTAATCATATCC-TTCTCTCTCAACCACTAAA
64 CCTTGGGGGCAAAGATATCCCAACCACTCATTCCTAATCATA-CCATTCTCTCTCAACCACTAAA
*
1779744 TGGTACTGATGCATCACACGACCA
128 TGATACTGATGCATCACACGACCA
1779768 TAAAGGGTAC
Statistics
Matches: 132, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
170 122 0.92
171 10 0.08
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (170 bp):
ATTCCCAATCATATCCCTTTCATCCAACCACTAGATGGTATTGATGCATCACAAAGCCTAATTCC
TTGGGGGCAAAGATATCCCAACCACTCATTCCTAATCATACCATTCTCTCTCAACCACTAAATGA
TACTGATGCATCACACGACCAGAAAAGGTGTAGCCCAAAT
Found at i:1780405 original size:70 final size:70
Alignment explanation
Indices: 1780284--1780667 Score: 323
Period size: 70 Copynumber: 5.5 Consensus size: 70
1780274 TCTTACCAAA
* ** * ** * *
1780284 CAAACTCTTTTTATCATTGTTTGGCTATATCTGGCCAAACA-CTTTTCATCATCGTTTGGCTGTA
1 CAAACTCTTTTCATCATCATTTGACTATATCTGGTTAAA-ATCTTTTTATCATCGTTTGACTGTA
*
1780348 TCTGGT
65 TCTAGT
* * * **
1780354 CAAA-TGCTTTTTATCATCATTTGACTATATTTGGTTAAAATCTTTTTATCATCATTCT-TTTGT
1 CAAACT-CTTTTCATCATCATTTGACTATATCTGGTTAAAATCTTTTTATCATCGTT-TGACTGT
*
1780417 ATCTGGT
64 ATCTAGT
* * * * *
1780424 CAAACTCTTTCCATCATCGTTTGATTATATCTAG-TCAAATC-TTTTATCATCGTTTGACTGTAT
1 CAAACTCTTTTCATCATCATTTGACTATATCTGGTTAAAATCTTTTTATCATCGTTTGACTGTAT
*
1780487 TTAGT
66 CTAGT
* * * * *
1780492 CAAACTCTTTTCATCATCATTTGACTATATTTGGTTGAACT-TTTTTCATCACCGTTTGTCTGTA
1 CAAACTCTTTTCATCATCATTTGACTATATCTGGTTAAAATCTTTTT-ATCATCGTTTGACTGTA
*
1780556 TCCAGT
65 TCTAGT
* * * * * * * *
1780562 CAAACTCATTTCATTATCATTTGACTATATCCGGTCAAACTCATTTCATCATCGTTTGACTTTAT
1 CAAACTCTTTTCATCATCATTTGACTATATCTGGTTAAAATCTTTTTATCATCGTTTGACTGTAT
1780627 CTAGT
66 CTAGT
* * * *
1780632 TAAACT-TATTTCATCCTCATTTGGCTGTATCTGGTT
1 CAAACTCT-TTTCATCATCATTTGACTATATCTGGTT
1780668 GTAGACACGT
Statistics
Matches: 251, Mismatches: 53, Indels: 20
0.77 0.16 0.06
Matches are distributed among these distances:
67 1 0.00
68 49 0.20
69 16 0.06
70 180 0.72
71 5 0.02
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.46
Consensus pattern (70 bp):
CAAACTCTTTTCATCATCATTTGACTATATCTGGTTAAAATCTTTTTATCATCGTTTGACTGTAT
CTAGT
Found at i:1780511 original size:103 final size:105
Alignment explanation
Indices: 1780311--1780512 Score: 273
Period size: 103 Copynumber: 1.9 Consensus size: 105
1780301 TGTTTGGCTA
* * * *
1780311 TATCTGGCCAAACACTTTTCATCATCGTTTGGCTGTATCTGGTCAAATGCTTTTTATCATCATTT
1 TATCTGGCCAAACACTTTCCATCATCGTTTGACTATATCTAGTCAAATGCTTTTTATCATCATTT
* * *
1780376 GACTATATTTGGTTAAAATCTTTTTATCATCATTCTTTTG
66 GACTATATTTAGTCAAAATCTTTTCATCATCATTCTTTTG
* * * *
1780416 TATCTGGTCAAACTCTTTCCATCATCGTTTGATTATATCTAGTCAAAT-C-TTTTATCATCGTTT
1 TATCTGGCCAAACACTTTCCATCATCGTTTGACTATATCTAGTCAAATGCTTTTTATCATCATTT
* *
1780479 GACTGTATTTAGTCAAACTCTTTTCATCATCATT
66 GACTATATTTAGTCAAAATCTTTTCATCATCATT
1780513 TGACTATATT
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
103 42 0.50
104 1 0.01
105 41 0.49
ACGTcount: A:0.24, C:0.19, G:0.11, T:0.46
Consensus pattern (105 bp):
TATCTGGCCAAACACTTTCCATCATCGTTTGACTATATCTAGTCAAATGCTTTTTATCATCATTT
GACTATATTTAGTCAAAATCTTTTCATCATCATTCTTTTG
Found at i:1780637 original size:35 final size:35
Alignment explanation
Indices: 1780284--1780646 Score: 232
Period size: 35 Copynumber: 10.4 Consensus size: 35
1780274 TCTTACCAAA
* * * * * *
1780284 CAAACTCTTTTTATCATTGTTTGGCTATATCTGGC
1 CAAACTCATTTCATCATCGTTTGACTATATCTAGT
* * * * *
1780319 CAAACACTTTTCATCATCGTTTGGCTGTATCTGGT
1 CAAACTCATTTCATCATCGTTTGACTATATCTAGT
* * * * *
1780354 CAAA-TGCTTTTTATCATCATTTGACTATATTTGGT
1 CAAACT-CATTTCATCATCGTTTGACTATATCTAGT
* * * * * ** * *
1780389 TAAAATCTTTTTATCATCATTCT-TTTGTATCTGGT
1 CAAACTCATTTCATCATCGTT-TGACTATATCTAGT
*
1780424 CAAACTC-TTTCCATCATCGTTTGATTATATCTAGT
1 CAAACTCATTT-CATCATCGTTTGACTATATCTAGT
* * *
1780459 CAAA-TC-TTTTATCATCGTTTGACTGTATTTAGT
1 CAAACTCATTTCATCATCGTTTGACTATATCTAGT
* * * *
1780492 CAAACTCTTTTCATCATCATTTGACTATATTTGGT
1 CAAACTCATTTCATCATCGTTTGACTATATCTAGT
** ** * * * *
1780527 TGAACTTTTTTCATCACCGTTTGTCTGTATCCAGT
1 CAAACTCATTTCATCATCGTTTGACTATATCTAGT
* * **
1780562 CAAACTCATTTCATTATCATTTGACTATATCCGGT
1 CAAACTCATTTCATCATCGTTTGACTATATCTAGT
*
1780597 CAAACTCATTTCATCATCGTTTGACTTTATCTAGT
1 CAAACTCATTTCATCATCGTTTGACTATATCTAGT
* *
1780632 TAAACTTATTTCATC
1 CAAACTCATTTCATC
1780647 CTCATTTGGC
Statistics
Matches: 263, Mismatches: 58, Indels: 14
0.79 0.17 0.04
Matches are distributed among these distances:
33 24 0.09
34 11 0.04
35 226 0.86
36 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.45
Consensus pattern (35 bp):
CAAACTCATTTCATCATCGTTTGACTATATCTAGT
Found at i:1783494 original size:20 final size:20
Alignment explanation
Indices: 1783454--1783494 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1783444 CTAAAATATC
* **
1783454 AATTTTTTACCATTGGGGAT
1 AATTTTCTACCATTGAAGAT
1783474 AATTTTCTACCATTGAAGAT
1 AATTTTCTACCATTGAAGAT
1783494 A
1 A
1783495 CTCCAACCCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (20 bp):
AATTTTCTACCATTGAAGAT
Found at i:1783609 original size:51 final size:51
Alignment explanation
Indices: 1783527--1783686 Score: 221
Period size: 51 Copynumber: 3.1 Consensus size: 51
1783517 GAGATATTCC
* *
1783527 AACCCCGGTTTTATTTCTAAAATATTGATTTTTTACCATCGGGGATACTCA
1 AACCCCGGTTTTATTTCTAAAATATTAATTTTTCACCATCGGGGATACTCA
** * *
1783578 AACCTTGGTTTTATTTCTAAAATATTAATTTTTCACTATCGGGGATACTCT
1 AACCCCGGTTTTATTTCTAAAATATTAATTTTTCACCATCGGGGATACTCA
* * * * *
1783629 AACCCCGGCTTTATTTCTAAAATATCAATTTTCCACCATCGAGGATACTCC
1 AACCCCGGTTTTATTTCTAAAATATTAATTTTTCACCATCGGGGATACTCA
1783680 AACCCCG
1 AACCCCG
1783687 TTATTTCTGA
Statistics
Matches: 95, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 95 1.00
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (51 bp):
AACCCCGGTTTTATTTCTAAAATATTAATTTTTCACCATCGGGGATACTCA
Found at i:1783752 original size:79 final size:80
Alignment explanation
Indices: 1783638--1783921 Score: 387
Period size: 79 Copynumber: 3.6 Consensus size: 80
1783628 TAACCCCGGC
*
1783638 TTTATTTCTAAAATATCAATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTCTG-AGGAGA
1 TTTATTTCTAAAATATCGATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTCTGAAGGAGA
* *
1783702 TACTCCGACCTTGAT
66 TACTCCAACCCTGAT
* *
1783717 TTTATTTTTAAAATATCGATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTTTGAAGG-GA
1 TTTATTTCTAAAATATCGATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTCTGAAGGAGA
1783781 TACTCCAACCCTGAT
66 TACTCCAACCCTGAT
* * *
1783796 TTTATTTCTAAAATATCGATTTTCCACCATTTGA-GATACTCCAACCGCATTATTTCTGAAGGA-
1 TTTATTTCTAAAATATCGATTTTCCACCA-TCGAGGATACTCCAACCCCGTTATTTCTGAAGGAG
* *
1783859 ATACTCTAACCCTGGT
65 ATACTCCAACCCTGAT
* * ** * *
1783875 TTTACTTCTAAAATATCGATTTTTCATTATCGGGGATTCTCCAACCC
1 TTTATTTCTAAAATATCGATTTTCCACCATCGAGGATACTCCAACCC
1783922 GGGTTTTATT
Statistics
Matches: 181, Mismatches: 20, Indels: 8
0.87 0.10 0.04
Matches are distributed among these distances:
78 2 0.01
79 173 0.96
80 6 0.03
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (80 bp):
TTTATTTCTAAAATATCGATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTCTGAAGGAGA
TACTCCAACCCTGAT
Found at i:1783908 original size:288 final size:288
Alignment explanation
Indices: 1783571--1784129 Score: 764
Period size: 288 Copynumber: 1.9 Consensus size: 288
1783561 ACCATCGGGG
* * * *
1783571 ATACTCAAACCTTGGTTTTATTTCTAAAATATTAATTTTTCACTATCGGGGATACTCTAACCCCG
1 ATACTCAAACCCTGGTTTTACTTCTAAAATATCAATTTTTCACTATCGGGGATACTCCAACCCCG
*
1783636 GCTTTATTTCTAAAATATCAATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTCTGAGGAG
66 GCTTTATTTCTAAAATATCAATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTCTAAGGAG
* *
1783701 ATACTCCGACCTTGATTTTATTTT-TAAAATATCGATTTTCCACCATCGAGGATACTCCAACCCC
131 ATACTCCAACCTTGATTTT-TTTTCTAAAATATCGATTTACCACCATCGAGGATACTCCAACCCC
* * * * **
1783765 GTTATTTTTGAA-GGGATACTCCAACC-CTGATTTTATTTCTAAAATATCGATTTTCCACCATTT
195 ATTA-TTTTCAAGGGGATACTCCAACCTC-GATTTGATTCCTAAAATATCGATTTTCCACCATCG
1783828 GAGATACTCCAACCGCATTATTTCTGAAGGA
258 GAGATACTCCAACCGCATTATTTCTGAAGGA
* * * * *
1783859 ATACTCTAACCCTGGTTTTACTTCTAAAATATCGATTTTTCATTATCGGGGATTCTCCAACCCGG
1 ATACTCAAACCCTGGTTTTACTTCTAAAATATCAATTTTTCACTATCGGGGATACTCCAACCCCG
* * * * * *
1783924 GTTTTATTTCTAAGATATCAATTTTCCACCATCGAGGATACTTCAACCTCGTTATTTTTAAGGGG
66 GCTTTATTTCTAAAATATCAATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTCTAAGGAG
* * * * * * *
1783989 ATACTCCAACCTTGATTTTTTTTCTAAAATATCGATTTACCGCTATTGGGGATGCTCTAACTCCA
131 ATACTCCAACCTTGATTTTTTTTCTAAAATATCGATTTACCACCATCGAGGATACTCCAACCCCA
* * *
1784054 TTATTTTCAAGGGGATACTCCAACCTCGGTTTGATTCCTAAAATATTGATTTTCCACCATCGGGG
196 TTATTTTCAAGGGGATACTCCAACCTCGATTTGATTCCTAAAATATCGATTTTCCACCATCGGAG
1784119 ATACTCCAACC
261 ATACTCCAACC
1784130 CTGTTATTTT
Statistics
Matches: 234, Mismatches: 34, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
287 10 0.04
288 223 0.95
289 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.36
Consensus pattern (288 bp):
ATACTCAAACCCTGGTTTTACTTCTAAAATATCAATTTTTCACTATCGGGGATACTCCAACCCCG
GCTTTATTTCTAAAATATCAATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTCTAAGGAG
ATACTCCAACCTTGATTTTTTTTCTAAAATATCGATTTACCACCATCGAGGATACTCCAACCCCA
TTATTTTCAAGGGGATACTCCAACCTCGATTTGATTCCTAAAATATCGATTTTCCACCATCGGAG
ATACTCCAACCGCATTATTTCTGAAGGA
Found at i:1783948 original size:130 final size:130
Alignment explanation
Indices: 1783777--1784026 Score: 324
Period size: 130 Copynumber: 1.9 Consensus size: 130
1783767 TATTTTTGAA
* * *
1783777 GGGATACTCCAACCCTGATTTTATTTCTAAAATATCGATTTTCCACCATTTGA-GATACTCCAAC
1 GGGATACTCCAACCCGGATTTTATTTCTAAAATATCAATTTTCCACCA-TCGAGGATACTCCAAC
* *
1783841 CGCATTATTTCTGAA-GGAATACTCTAACCCTGGTTTTACTTCTAAAATATCGATTTTTCATTAT
65 CGCATTATTT-TGAAGGGAATACTCCAACCCTGATTTTACTTCTAAAATATCGATTTTTCATTAT
1783905 CG
129 CG
* * * *
1783907 GGGATTCTCCAACCCGGGTTTTATTTCTAAGATATCAATTTTCCACCATCGAGGATACTTCAACC
1 GGGATACTCCAACCCGGATTTTATTTCTAAAATATCAATTTTCCACCATCGAGGATACTCCAACC
* * * * * **
1783972 TCGTTATTTTTAAGGGGATACTCCAACCTTGATTTTTTTTCTAAAATATCGATTT
66 GCATTATTTTGAAGGGAATACTCCAACCCTGATTTTACTTCTAAAATATCGATTT
1784027 ACCGCTATTG
Statistics
Matches: 102, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
129 6 0.06
130 96 0.94
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (130 bp):
GGGATACTCCAACCCGGATTTTATTTCTAAAATATCAATTTTCCACCATCGAGGATACTCCAACC
GCATTATTTTGAAGGGAATACTCCAACCCTGATTTTACTTCTAAAATATCGATTTTTCATTATCG
Found at i:1783955 original size:209 final size:209
Alignment explanation
Indices: 1783716--1784130 Score: 543
Period size: 209 Copynumber: 2.0 Consensus size: 209
1783706 CCGACCTTGA
* *
1783716 TTTTATTTTTAAAATATCGATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTTTGAA-GGG
1 TTTTATTTCTAAAATATCAATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTTT-AAGGGG
* *
1783780 ATACTCCAACCCTGATTTTATTTCTAAAATATCGATTTTCCACCATTTGAGATACTCCAAC-CGC
65 ATACTCCAACCCTGATTTTATTTCTAAAATATCGATTTACCACCATTGGAGATACTCCAACTC-C
* * * * **
1783844 ATTATTTCTGAA-GGAATACTCTAACC-CTGGTTTTACTT-CTAAAATATCGATTTTTCATTATC
129 ATTATTT-TCAAGGGAATACTCCAACCTC-GGTTTGA-TTCCTAAAATATCGATTTTCCACCATC
*
1783906 GGGGATTCTCCAACCCGGG
191 GGGGATACTCCAACCCGGG
* * *
1783925 TTTTATTTCTAAGATATCAATTTTCCACCATCGAGGATACTTCAACCTCGTTATTTTTAAGGGGA
1 TTTTATTTCTAAAATATCAATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTTTAAGGGGA
* * * * * * *
1783990 TACTCCAACCTTGATTTTTTTTCTAAAATATCGATTTACCGCTATTGGGGATGCTCTAACTCCAT
66 TACTCCAACCCTGATTTTATTTCTAAAATATCGATTTACCACCATTGGAGATACTCCAACTCCAT
* *
1784055 TATTTTCAAGGGGATACTCCAACCTCGGTTTGATTCCTAAAATATTGATTTTCCACCATCGGGGA
131 TATTTTCAAGGGAATACTCCAACCTCGGTTTGATTCCTAAAATATCGATTTTCCACCATCGGGGA
1784120 TACTCCAACCC
196 TACTCCAACCC
1784131 TGTTATTTTC
Statistics
Matches: 178, Mismatches: 23, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
208 7 0.04
209 169 0.95
210 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (209 bp):
TTTTATTTCTAAAATATCAATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTTTAAGGGGA
TACTCCAACCCTGATTTTATTTCTAAAATATCGATTTACCACCATTGGAGATACTCCAACTCCAT
TATTTTCAAGGGAATACTCCAACCTCGGTTTGATTCCTAAAATATCGATTTTCCACCATCGGGGA
TACTCCAACCCGGG
Found at i:1783971 original size:51 final size:51
Alignment explanation
Indices: 1783859--1783971 Score: 127
Period size: 51 Copynumber: 2.2 Consensus size: 51
1783849 TTCTGAAGGA
* * * * ** *
1783859 ATACTCTAACCCTGGTTTTACTTCTAAAATATCGATTTTTCATTATCGGGG
1 ATACTCCAACCCGGGTTTTACTTCTAAAATATCAATTTTCCACCATCGAGG
* * *
1783910 ATTCTCCAACCCGGGTTTTATTTCTAAGATATCAATTTTCCACCATCGAGG
1 ATACTCCAACCCGGGTTTTACTTCTAAAATATCAATTTTCCACCATCGAGG
*
1783961 ATACTTCAACC
1 ATACTCCAACC
1783972 TCGTTATTTT
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (51 bp):
ATACTCCAACCCGGGTTTTACTTCTAAAATATCAATTTTCCACCATCGAGG
Found at i:1783989 original size:79 final size:79
Alignment explanation
Indices: 1783906--1784206 Score: 306
Period size: 79 Copynumber: 3.8 Consensus size: 79
1783896 TTTCATTATC
* * * * *
1783906 GGGGATTCTCCAACC-CGGGTTTTATTTCTAAGATATCAATTTTCCACCATCGAGGATACTTCAA
1 GGGGATACTCCAACCTC-GATTTTATTTCTAAAATATCGATTTTCCACCATCGAGGATACTCCAA
*
1783970 CCTCGTTATTTTTAA
65 CCTCGTTATTTTCAA
* * * * * * * * *
1783985 GGGGATACTCCAACCTTGATTTTTTTTCTAAAATATCGATTTACCGCTATTGGGGATGCTCTAA-
1 GGGGATACTCCAACCTCGATTTTATTTCTAAAATATCGATTTTCCACCATCGAGGATACTCCAAC
*
1784049 CTCCATTATTTTCAA
66 CT-CGTTATTTTCAA
* * * * *
1784064 GGGGATACTCCAACCTCGGTTTGATTCCTAAAATATTGATTTTCCACCATCGGGGATACTCCAAC
1 GGGGATACTCCAACCTCGATTTTATTTCTAAAATATCGATTTTCCACCATCGAGGATACTCCAAC
*
1784129 C-CTGTTATTTTCGA
66 CTC-GTTATTTTCAA
* * * *
1784143 -GGGATACTCCAACCTCGATTTTATTTC-CAAATATCGATTTTTCACCATTGAAGATACTCCAAC
1 GGGGATACTCCAACCTCGATTTTATTTCTAAAATATCGATTTTCCACCATCGAGGATACTCCAAC
1784206 C
66 C
1784207 CCATTTTCAC
Statistics
Matches: 179, Mismatches: 39, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
77 31 0.17
78 27 0.15
79 120 0.67
80 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.36
Consensus pattern (79 bp):
GGGGATACTCCAACCTCGATTTTATTTCTAAAATATCGATTTTCCACCATCGAGGATACTCCAAC
CTCGTTATTTTCAA
Found at i:1784214 original size:29 final size:29
Alignment explanation
Indices: 1784181--1784237 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1784171 AAATATCGAT
*
1784181 TTTTCACCAT-TGAAGATACTCCAACCCCA
1 TTTTCACCATCGGAA-ATACTCCAACCCCA
*
1784210 TTTTCACCATCGGTAATACTCCAACCCC
1 TTTTCACCATCGGAAATACTCCAACCCC
1784238 GTTGTTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 23 0.92
30 2 0.08
ACGTcount: A:0.28, C:0.37, G:0.07, T:0.28
Consensus pattern (29 bp):
TTTTCACCATCGGAAATACTCCAACCCCA
Found at i:1785309 original size:46 final size:46
Alignment explanation
Indices: 1785259--1785364 Score: 140
Period size: 46 Copynumber: 2.3 Consensus size: 46
1785249 TTCCATCCTT
* *
1785259 ATTTGACTATATCAATTACCACCCTAGTCAAACACTTTTTGTTCTC
1 ATTTGACTATATCAATTACCACCCTAGTCAAACACTTTTCGTTCCC
* * * *
1785305 ATTTGATTGTATCAATTACCACTCTAGTCAAACCCTTTTCGTTCCC
1 ATTTGACTATATCAATTACCACCCTAGTCAAACACTTTTCGTTCCC
* *
1785351 AATTGACTTTATCA
1 ATTTGACTATATCA
1785365 GTTTTGCCTT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.27, C:0.25, G:0.08, T:0.40
Consensus pattern (46 bp):
ATTTGACTATATCAATTACCACCCTAGTCAAACACTTTTCGTTCCC
Found at i:1787078 original size:167 final size:163
Alignment explanation
Indices: 1786700--1787121 Score: 413
Period size: 167 Copynumber: 2.5 Consensus size: 163
1786690 TCTTGGTTTA
* * **
1786700 TAAATTTTAAAATTCATCAAATAGTATTATTTAACTCACAATT-AATTAGTTTCAAAACAATTCC
1 TAAATTTTAAAATTCATCAAATATTATCATTTAACTC-CAATTAAATTAGTTTTGAAA-AATT-C
* * ** * *
1786764 TTTTATTTCATTAATTTTTCATTTTTTCCTTAAAATTTCCTCGTTTTCAAAAACTGAGTTTTCTA
63 ATTTATTTCATGAATTTTTCATTTTTTCCTTAAAATCCCCTAGTTTTCAAAAACTGAATTTTCTA
* *** * *
1786829 TTCCATAAAGGTTTTTGTGGGGTTTTCTCTCGGTTC
128 TCCCATAAAGGTTTTCACGGGATTTTCTCTCAGTTC
* * * *
1786865 AAAAATTTTAAAATTCATCAAATATCATCATCTAA-TTCATATTAAATTAGTTTTGAAAAATTCA
1 -TAAATTTTAAAATTCATCAAATATTATCATTTAACTCCA-ATTAAATTAGTTTTGAAAAATTCA
* * * * *
1786929 TTTAATTTCATGAGTTTTTCATTTTTGTCCTTGAAATGCCCCTATTTTTGAATAACTGAATTTTC
64 TTT-ATTTCATGAATTTTTCATTTTT-TCCTTAAAAT-CCCCTAGTTTTCAAAAACTGAATTTTC
*
1786994 TATCCCATAAATGTTTTCACGAGGATTTTCT-TCAGTT-
126 TATCCCATAAAGGTTTTCACG-GGATTTTCTCTCAGTTC
* * * * *
1787031 TAAATTTTTCAAAATTCATCTAATATTGTCATTTAACTCCCATTAAATCAGTTTTGAAGAATTCA
1 TAAA-TTTT-AAAATTCATCAAATATTATCATTTAACTCCAATTAAATTAGTTTTGAAAAATTC-
*
1787096 ATTTATTTCATGAATTTTGC-TTTTTT
63 ATTTATTTCATGAATTTTTCATTTTTT
1787122 ATATATATTG
Statistics
Matches: 209, Mismatches: 37, Indels: 21
0.78 0.14 0.08
Matches are distributed among these distances:
164 6 0.03
165 32 0.15
166 59 0.28
167 98 0.47
168 14 0.07
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.46
Consensus pattern (163 bp):
TAAATTTTAAAATTCATCAAATATTATCATTTAACTCCAATTAAATTAGTTTTGAAAAATTCATT
TATTTCATGAATTTTTCATTTTTTCCTTAAAATCCCCTAGTTTTCAAAAACTGAATTTTCTATCC
CATAAAGGTTTTCACGGGATTTTCTCTCAGTTC
Found at i:1787618 original size:20 final size:21
Alignment explanation
Indices: 1787595--1787641 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
1787585 TTGGAAAGTG
*
1787595 AGAAAAAAAAAGGGA-AAAAA
1 AGAAAAAAAAAGAGAGAAAAA
*
1787615 AG-AAAAAGAAGAGAGAAAAA
1 AGAAAAAAAAAGAGAGAAAAA
1787635 AGAAAAA
1 AGAAAAA
1787642 TCAAGGTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 10 0.43
20 9 0.39
21 4 0.17
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (21 bp):
AGAAAAAAAAAGAGAGAAAAA
Found at i:1787621 original size:21 final size:20
Alignment explanation
Indices: 1787597--1787641 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1787587 GGAAAGTGAG
*
1787597 AAAAAAAAAGGGAAAAAAAGA
1 AAAAAAAAAGAG-AAAAAAGA
* *
1787618 AAAAGAAGAGAGAAAAAAGA
1 AAAAAAAAAGAGAAAAAAGA
1787638 AAAA
1 AAAA
1787642 TCAAGGTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGAGAAAAAAGA
Found at i:1788191 original size:23 final size:23
Alignment explanation
Indices: 1788157--1788200 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1788147 CCTCTCAATC
*
1788157 TCTTCAAGAATTATACCCCAAAT
1 TCTTCAAGAATTATAACCCAAAT
*
1788180 TCTT-AAGAAATTGTAACCCAA
1 TCTTCAAG-AATTATAACCCAA
1788201 TGTTGAATGC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.17
23 15 0.83
ACGTcount: A:0.41, C:0.23, G:0.07, T:0.30
Consensus pattern (23 bp):
TCTTCAAGAATTATAACCCAAAT
Found at i:1788623 original size:20 final size:20
Alignment explanation
Indices: 1788598--1788651 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
1788588 GTTGGGCATA
* * *
1788598 ATGTATCGATACATTTTACT
1 ATGTATCGATACAATGTACC
* *
1788618 ATGTATTGATACAATGTCCC
1 ATGTATCGATACAATGTACC
1788638 ATGTATCGATACAA
1 ATGTATCGATACAA
1788652 GTGGTAGGGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:1788703 original size:20 final size:20
Alignment explanation
Indices: 1788678--1788728 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1788668 TGCCAGTTTC
** *
1788678 ATGTATCGATACAACTCTAT
1 ATGTATCGATACAAAGCAAT
1788698 ATGTATCGATACAAAGCAAT
1 ATGTATCGATACAAAGCAAT
1788718 ATGTATCGATA
1 ATGTATCGATA
1788729 TTTCTAGGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAAAGCAAT
Found at i:1788742 original size:20 final size:21
Alignment explanation
Indices: 1788719--1788760 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1788709 CAAAGCAATA
1788719 TGTATCGATA-TTTCTAGGTT
1 TGTATCGATACTTTCTAGGTT
1788739 TGTATCGATACTTTCTAGGTT
1 TGTATCGATACTTTCTAGGTT
1788760 T
1 T
1788761 TGACCTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.50
Consensus pattern (21 bp):
TGTATCGATACTTTCTAGGTT
Found at i:1793278 original size:185 final size:185
Alignment explanation
Indices: 1792966--1793336 Score: 670
Period size: 185 Copynumber: 2.0 Consensus size: 185
1792956 ATGCAAAGGC
1792966 TAGCAATATTCTAATAGCTTATAACCTAGCTACAGGTGCATAGGTTACGTCATAGTCAATTCCTT
1 TAGCAATATTCTAATAGCTTATAACCTAGCTACAGGTGCATAGGTTACGTCATAGTCAATTCCTT
* *
1793031 CCTCTTGACTATAACCTTTTGCTGCTAGCCTAGCTTTATTTCTTGCTATGGTTCCATCTTCATCC
66 CCTCTTGACTATAACCTTTTACTACTAGCCTAGCTTTATTTCTTGCTATGGTTCCATCTTCATCC
1793096 AATTTATTTCTAAACACCCATTTAGTCCCTATAATTGAATGATCATTTGGTTTCT
131 AATTTATTTCTAAACACCCATTTAGTCCCTATAATTGAATGATCATTTGGTTTCT
* * *
1793151 TAGCAATATTCTAATAGCTTCTAACCTAGCTACGGGTGCATAGGTTTCGTCATAGTCAATTCCTT
1 TAGCAATATTCTAATAGCTTATAACCTAGCTACAGGTGCATAGGTTACGTCATAGTCAATTCCTT
* *
1793216 CCTCTTGACTATAATCTTTTACTACTAGCCTAGCTTTGTTTCTTGCTATGGTTCCATCTTCATCC
66 CCTCTTGACTATAACCTTTTACTACTAGCCTAGCTTTATTTCTTGCTATGGTTCCATCTTCATCC
*
1793281 AATTTATTTCTAAACACCCATTTAGTCCCTATAATTGGATGATCATTTGGTTTCT
131 AATTTATTTCTAAACACCCATTTAGTCCCTATAATTGAATGATCATTTGGTTTCT
1793336 T
1 T
1793337 GACTAAAGTC
Statistics
Matches: 178, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
185 178 1.00
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.41
Consensus pattern (185 bp):
TAGCAATATTCTAATAGCTTATAACCTAGCTACAGGTGCATAGGTTACGTCATAGTCAATTCCTT
CCTCTTGACTATAACCTTTTACTACTAGCCTAGCTTTATTTCTTGCTATGGTTCCATCTTCATCC
AATTTATTTCTAAACACCCATTTAGTCCCTATAATTGAATGATCATTTGGTTTCT
Found at i:1797663 original size:13 final size:13
Alignment explanation
Indices: 1797645--1797674 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1797635 ACATTTTACC
1797645 ATGTATCGATACA
1 ATGTATCGATACA
*
1797658 ATGTATCGATATA
1 ATGTATCGATACA
1797671 ATGT
1 ATGT
1797675 CCCATGTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1797664 original size:33 final size:33
Alignment explanation
Indices: 1797622--1797691 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1797612 GTCATTGGGC
* *
1797622 ACAATGTATCGATACATTTTACCATGTATCGAT
1 ACAATGTATCGATACAATGTACCATGTATCGAT
* *
1797655 ACAATGTATCGATATAATGTCCCATGTATCGAT
1 ACAATGTATCGATACAATGTACCATGTATCGAT
1797688 ACAA
1 ACAA
1797692 ACAGTGGTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.33
Consensus pattern (33 bp):
ACAATGTATCGATACAATGTACCATGTATCGAT
Found at i:1797744 original size:19 final size:20
Alignment explanation
Indices: 1797720--1797771 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
1797710 CTGCCAGTTT
*
1797720 CATGTATCGATACAATG-AA
1 CATGTATCGATACAAAGCAA
*
1797739 CATGTATCGATATAAAGCAA
1 CATGTATCGATACAAAGCAA
*
1797759 TATGTATCGATAC
1 CATGTATCGATAC
1797772 TTCTAGGCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.29
Consensus pattern (20 bp):
CATGTATCGATACAAAGCAA
Found at i:1797784 original size:20 final size:21
Alignment explanation
Indices: 1797761--1797799 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
1797751 TAAAGCAATA
1797761 TGTATCGATAC-TTCTAGGCT
1 TGTATCGATACTTTCTAGGCT
1797781 TGTATCGATACTTTCTAGG
1 TGTATCGATACTTTCTAGG
1797800 GTTTTGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (21 bp):
TGTATCGATACTTTCTAGGCT
Found at i:1799188 original size:17 final size:16
Alignment explanation
Indices: 1799166--1799197 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1799156 AGCAAGTGAG
1799166 AAGAAAAAGAGAAAAAA
1 AAGAAAAA-AGAAAAAA
1799183 AAGAAAAAAGAAAAA
1 AAGAAAAAAGAAAAA
1799198 TCAAGGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAGAAAAAA
Found at i:1800221 original size:21 final size:23
Alignment explanation
Indices: 1800186--1800227 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
1800176 GGGAATTTTG
1800186 AAAATAGAAAAAATAA-TAAAAT
1 AAAATAGAAAAAATAAGTAAAAT
*
1800208 AAAAT-GAAATAATAAGTAAA
1 AAAATAGAAAAAATAAGTAAA
1800228 TATTATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (23 bp):
AAAATAGAAAAAATAAGTAAAAT
Found at i:1806447 original size:48 final size:47
Alignment explanation
Indices: 1806382--1806529 Score: 147
Period size: 47 Copynumber: 3.1 Consensus size: 47
1806372 TTTTGAATCA
** *
1806382 ATACAATGAACGATGTATTGATATATCTGAGTTTTTCTAGAATGTATCG
1 ATACAATGAATAATGTATTGATACATCTG-G-TTTTCTAGAATGTATCG
* * *
1806431 ATACAA-GCAA-AATGTATCGATCCATCTGGATTTTCTAGAATGTATTG
1 ATACAATG-AATAATGTATTGATACATCTGG-TTTTCTAGAATGTATCG
* * * * *
1806478 ATATAATGAATAATGCATTGATACATCTGGGTTTCTAGATTGTGTCG
1 ATACAATGAATAATGTATTGATACATCTGGTTTTCTAGAATGTATCG
1806525 ATACA
1 ATACA
1806530 CTCACTAATG
Statistics
Matches: 81, Mismatches: 15, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
47 41 0.51
48 32 0.40
49 8 0.10
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (47 bp):
ATACAATGAATAATGTATTGATACATCTGGTTTTCTAGAATGTATCG
Found at i:1809873 original size:52 final size:51
Alignment explanation
Indices: 1809795--1809943 Score: 217
Period size: 52 Copynumber: 2.9 Consensus size: 51
1809785 CGAAATATGA
1809795 AAATTTACCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* * *
1809847 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
* **
1809899 AAATTTTCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTACCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
1809944 ATGTATCGAT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.95
53 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (51 bp):
AAATTTACCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:1809950 original size:13 final size:13
Alignment explanation
Indices: 1809932--1809956 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1809922 CAAAGATCAG
1809932 TGTATCGATACAA
1 TGTATCGATACAA
1809945 TGTATCGATACA
1 TGTATCGATACA
1809957 TTTAAGTGAT
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:1810034 original size:33 final size:33
Alignment explanation
Indices: 1809997--1810063 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1809987 AGTAGCTTAA
1809997 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1810030 ATTGTATCGATACAATACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1810063 A
1 A
1810064 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1810037 original size:13 final size:13
Alignment explanation
Indices: 1810019--1810043 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1810009 CAAAAAAATA
1810019 TGTATCGATACAT
1 TGTATCGATACAT
1810032 TGTATCGATACA
1 TGTATCGATACA
1810044 ATACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1811112 original size:91 final size:93
Alignment explanation
Indices: 1810940--1811119 Score: 285
Period size: 91 Copynumber: 1.9 Consensus size: 93
1810930 AAAAGGATGT
1810940 CAATGTGCTGATTCAAGGCGAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATT
1 CAATGTGCTGATTCAAGGCGAGCTACATTGAACTTAAAGATGG-AAAGGTGCCAATATGCTGATT
*
1811005 CAAGGCCAGCTATATTGGACTTAAGGTGC
65 CAAGGCCAGCGATATTGGACTTAAGGTGC
* *
1811034 CAATGTGCTGATTCAAGGTC-AGCTACATTGGACTTAAATAT-G-AAGGTGCCAATATGCTGATT
1 CAATGTGCTGATTCAAGG-CGAGCTACATTGAACTTAAAGATGGAAAGGTGCCAATATGCTGATT
*
1811096 TAAGGCCAGCGATATTGGACTTAA
65 CAAGGCCAGCGATATTGGACTTAA
1811120 AGGCAAGGTG
Statistics
Matches: 81, Mismatches: 4, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
91 42 0.52
93 1 0.01
94 37 0.46
95 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (93 bp):
CAATGTGCTGATTCAAGGCGAGCTACATTGAACTTAAAGATGGAAAGGTGCCAATATGCTGATTC
AAGGCCAGCGATATTGGACTTAAGGTGC
Found at i:1811113 original size:49 final size:49
Alignment explanation
Indices: 1811027--1811171 Score: 195
Period size: 49 Copynumber: 3.0 Consensus size: 49
1811017 TATTGGACTT
* * * *
1811027 AAGGTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAATATG-
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA-AGGC
* *
1811076 AAGGTGCCAATATGCTGATTTAAGGCCAGCGATATTGGACTT-AAAGGC
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAAGGC
* *
1811124 AAGGTGCCAATATGCTAATTCAAGGCCAGCTATATTGGGCTTAAAAGG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAAGG
1811172 AGACGCCACC
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
47 2 0.02
48 40 0.48
49 42 0.50
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.26
Consensus pattern (49 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAAGGC
Found at i:1811149 original size:48 final size:46
Alignment explanation
Indices: 1810940--1811168 Score: 232
Period size: 48 Copynumber: 4.8 Consensus size: 46
1810930 AAAAGGATGT
* * * *
1810940 CAATGTGCTGATTCAAGGCGAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A--G--AAGGTGC
1810992 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGGTGC
* * *
1811034 CAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAATATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-GAAGGTGC
* *
1811083 CAATATGCTGATTTAAGGCCAGCGATATTGGACTTAAAGGCAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA-G-AAGGTGC
* *
1811131 CAATATGCTAATTCAAGGCCAGCTATATTGGGCTTAAA
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
1811169 AGGAGACGCC
Statistics
Matches: 152, Mismatches: 17, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
42 39 0.26
47 2 0.01
48 43 0.28
49 37 0.24
52 31 0.20
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (46 bp):
CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGGTGC
Found at i:1811271 original size:30 final size:30
Alignment explanation
Indices: 1811212--1811316 Score: 178
Period size: 30 Copynumber: 3.6 Consensus size: 30
1811202 AGGTTTGCAT
* *
1811212 CACTGACTTGTGGGCTTTT--AAAGGTTGC
1 CACTAACTTGTGGGCTTTTGAAAAGGGTGC
1811240 CACTAACTTGTGGGCTTTTGAAAAGGGTGC
1 CACTAACTTGTGGGCTTTTGAAAAGGGTGC
1811270 CACTAACTTGTGGGCTTTTGAAAAGGGTGC
1 CACTAACTTGTGGGCTTTTGAAAAGGGTGC
1811300 CACTAACTTGTGGGCTT
1 CACTAACTTGTGGGCTT
1811317 AAAAAGAAAA
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
28 18 0.25
30 55 0.75
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (30 bp):
CACTAACTTGTGGGCTTTTGAAAAGGGTGC
Found at i:1811426 original size:27 final size:28
Alignment explanation
Indices: 1811388--1811449 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 28
1811378 TTCGAAAAAA
* *
1811388 AAGGGTGCCACTGATTTGTGGGC-TTTG
1 AAGGGTGCCACTGACTTGTGGACTTTTG
*
1811415 AAGGTTGCCACTGACTTGTGGACTTTTG
1 AAGGGTGCCACTGACTTGTGGACTTTTG
1811443 AAGGGTG
1 AAGGGTG
1811450 ATAAATGTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 20 0.67
28 10 0.33
ACGTcount: A:0.18, C:0.15, G:0.35, T:0.32
Consensus pattern (28 bp):
AAGGGTGCCACTGACTTGTGGACTTTTG
Found at i:1811432 original size:60 final size:62
Alignment explanation
Indices: 1811212--1811435 Score: 212
Period size: 60 Copynumber: 3.7 Consensus size: 62
1811202 AGGTTTGCAT
*
1811212 CACTGACTTGTGGGCTTTT-AAAGGTTGCCACTAACTTGTGGGCTTTTG----AAAAGGGTGC
1 CACTGACTTGTGGGCTTTTGAAAGGTTGCCACTAACTTGTGGGC-TTAGAAAAAAAAGGGTGC
* * * *
1811270 CACTAACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAAGAAAAAGAGTGC
1 CACTGACTTGTGGGCTTTTG-AAAGGTTGCCACTAACTTGTGGGCTTAGAAA-AAAAAGGGTGC
* * * * * * ** *
1811334 TA-TAGAGTTGTGAGCTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGAAAAAAAAGGGTGC
1 CACT-GACTTGTGGGCTTTTGAAAGGTTGCCACTAACTTGTGGGCTTAGAAAAAAAAGGGTGC
* *
1811396 CACTGATTTGTGGGC-TTTG-AAGGTTGCCACTGACTTGTGG
1 CACTGACTTGTGGGCTTTTGAAAGGTTGCCACTAACTTGTGG
1811436 ACTTTTGAAG
Statistics
Matches: 133, Mismatches: 24, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
58 18 0.14
59 2 0.02
60 41 0.31
61 3 0.02
62 20 0.15
63 27 0.20
64 22 0.17
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (62 bp):
CACTGACTTGTGGGCTTTTGAAAGGTTGCCACTAACTTGTGGGCTTAGAAAAAAAAGGGTGC
Found at i:1812886 original size:1 final size:1
Alignment explanation
Indices: 1812882--1813024 Score: 115
Period size: 1 Copynumber: 143.0 Consensus size: 1
1812872 CCGGACCCCC
* * * * * * * * *
1812882 TTTTTTTATTTTTGTTTGTTTTTTTATTGTTTTTGTTTTTTTTTTGTTTTTTTTTTGTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * ** * **
1812947 TTTTTGTTTTTTTTTTGTTTGTTTTTTTTTCATTTTTTTTTTGTTTTTTTTTCGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
1813012 TGTTTTATTTTTT
1 TTTTTTTTTTTTT
1813025 GGAGGACGCC
Statistics
Matches: 106, Mismatches: 36, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 106 1.00
ACGTcount: A:0.03, C:0.01, G:0.09, T:0.87
Consensus pattern (1 bp):
T
Found at i:1812943 original size:47 final size:43
Alignment explanation
Indices: 1812882--1813024 Score: 144
Period size: 47 Copynumber: 3.2 Consensus size: 43
1812872 CCGGACCCCC
*
1812882 TTTTTTTATTTTTGTTTGTTTTTTTATTGTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTGTTT-TTTTTTTATT-TTTTTGTTTTTTTTTT
*
1812927 GTTTTTTTTTTGTTTGTTTTTTTTTGTTTTTTTTTTGTTTGTTTTTTT
1 -TTTTTTTTTT-TTTG-TTTTTTTT-TTATTTTTTTGTTT-TTTTTTT
* ** *
1812975 TTCATTTTTTTTTTGTTTTTTTTTCGTTTTTTT-TTTTTGTTTT
1 TT-TTTTTTTTTTTGTTTTTTTTTTATTTTTTTGTTTTTTTTTT
*
1813018 ATTTTTT
1 TTTTTTT
1813025 GGAGGACGCC
Statistics
Matches: 84, Mismatches: 8, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
42 4 0.05
43 7 0.08
44 3 0.04
45 8 0.10
46 17 0.20
47 24 0.29
48 21 0.25
ACGTcount: A:0.03, C:0.01, G:0.09, T:0.87
Consensus pattern (43 bp):
TTTTTTTTTTTTTGTTTTTTTTTTATTTTTTTGTTTTTTTTTT
Found at i:1812946 original size:25 final size:24
Alignment explanation
Indices: 1812902--1813025 Score: 139
Period size: 25 Copynumber: 5.0 Consensus size: 24
1812892 TTTGTTTGTT
1812902 TTTTTATTGTTTTTGTTTTTTTTTTG
1 TTTTT-TT-TTTTTGTTTTTTTTTTG
1812928 TTTTTTTTTTGTT-TGTTTTTTTTTG
1 TTTTTTTTTT-TTGT-TTTTTTTTTG
1812953 --TTTTTTTTTTGTTTGTTTTTTT-
1 TTTTTTTTTTTTGTTT-TTTTTTTG
*
1812975 TTCATTTTTTTTTTGTTTTTTTTTCG
1 TT--TTTTTTTTTTGTTTTTTTTTTG
1813001 TTTTTTTTTTTTGTTTTATTTTTTG
1 TTTTTTTTTTTTGTTTT-TTTTTTG
1813026 GAGGACGCCG
Statistics
Matches: 86, Mismatches: 2, Indels: 21
0.79 0.02 0.19
Matches are distributed among these distances:
22 4 0.05
23 16 0.19
24 19 0.22
25 26 0.30
26 21 0.24
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.86
Consensus pattern (24 bp):
TTTTTTTTTTTTGTTTTTTTTTTG
Found at i:1812951 original size:36 final size:35
Alignment explanation
Indices: 1812882--1813025 Score: 159
Period size: 36 Copynumber: 3.9 Consensus size: 35
1812872 CCGGACCCCC
*
1812882 TTTTTTTATTTTTGTTTGTT-TTTTTATTGTTTTTGTTT
1 TTTTTTTGTTTTT-TTT-TTGTTTTT-TT-TTTTTGTTT
1812920 TTTTTTTGTTTTTTTTTTGTTTGTTTTTTTTTGTTT
1 TTTTTTTGTTTTTTTTTTGTTT-TTTTTTTTTGTTT
1812956 TTTTTTTGTTTGTTTTTTT-TTCATTTTTTTTTTGTTT
1 TTTTTTTGTTT-TTTTTTTGTT--TTTTTTTTTTGTTT
*
1812993 TTTTTTCGTTTTTTTTTT-TTGTTTTATTTTTTG
1 TTTTTTTGTTTTTTTTTTGTT-TTTT-TTTTTTG
1813026 GAGGACGCCG
Statistics
Matches: 97, Mismatches: 3, Indels: 14
0.85 0.03 0.12
Matches are distributed among these distances:
35 4 0.04
36 40 0.41
37 38 0.39
38 15 0.15
ACGTcount: A:0.03, C:0.01, G:0.10, T:0.86
Consensus pattern (35 bp):
TTTTTTTGTTTTTTTTTTGTTTTTTTTTTTTGTTT
Found at i:1813017 original size:11 final size:11
Alignment explanation
Indices: 1812884--1813025 Score: 133
Period size: 11 Copynumber: 12.0 Consensus size: 11
1812874 GGACCCCCTT
1812884 TTTTTATTTTTG
1 TTTTT-TTTTTG
*
1812896 TTTGTTTTTT-
1 TTTTTTTTTTG
* *
1812906 TATTGTTTTTG
1 TTTTTTTTTTG
1812917 TTTTTTTTTTG
1 TTTTTTTTTTG
1812928 TTTTTTTTTTG
1 TTTTTTTTTTG
1812939 TTTGTTTTTTTTTG
1 --T-TTTTTTTTTG
1812953 TTTTTTTTTTG
1 TTTTTTTTTTG
*
1812964 TTTGTTTTTTTTTCA
1 --T-TTTTTTTTT-G
1812979 TTTTTTTTTTG
1 TTTTTTTTTTG
*
1812990 TTTTTTTTTCGTT
1 TTTTTTTTT--TG
1813003 TTTTTTTTTTG
1 TTTTTTTTTTG
1813014 TTTTATTTTTTG
1 TTTT-TTTTTTG
1813026 GAGGACGCCG
Statistics
Matches: 109, Mismatches: 10, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
10 7 0.06
11 49 0.45
12 21 0.19
13 13 0.12
14 19 0.17
ACGTcount: A:0.03, C:0.01, G:0.10, T:0.86
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:1813040 original size:62 final size:62
Alignment explanation
Indices: 1812917--1813040 Score: 142
Period size: 62 Copynumber: 2.0 Consensus size: 62
1812907 ATTGTTTTTG
* *** ******
1812917 TTTTTTTTTTGTTTTTTTTTTGTTTGTTTTTTTTTGTTTTTTTTTTGTTTGTTTTTTTTTCA
1 TTTTTTTTTTGTTTTTTTTTCGTTTGTTTTTTTTTGTTTTTTTTTTGGAGGACGCCGTTTCA
1812979 TTTTTTTTTTGTTTTTTTTTCGTTT-TTTTTTTTTGTTTTATTTTTTGGAGGACGCCGTTTCA
1 TTTTTTTTTTGTTTTTTTTTCGTTTGTTTTTTTTTGTTTT-TTTTTTGGAGGACGCCGTTTCA
1813041 GGTTTTCGCC
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 14 0.27
62 37 0.73
ACGTcount: A:0.04, C:0.05, G:0.12, T:0.79
Consensus pattern (62 bp):
TTTTTTTTTTGTTTTTTTTTCGTTTGTTTTTTTTTGTTTTTTTTTTGGAGGACGCCGTTTCA
Found at i:1822730 original size:10 final size:10
Alignment explanation
Indices: 1822715--1822741 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1822705 ATGTATCAAG
1822715 CAAAAACAAA
1 CAAAAACAAA
1822725 CAAAAACAAA
1 CAAAAACAAA
1822735 CAAAAAC
1 CAAAAAC
1822742 TTAGTTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAACAAA
Done.