Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold14
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: 2879421
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 64274 characters in sequence are not A, C, G, or T
File 11 of 17
Found at i:1726041 original size:20 final size:20
Alignment explanation
Indices: 1726016--1726068 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
1726006 ACATCTTTTT
1726016 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
1726036 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
1726056 CATGTATCGATAC
1 CATGTATCGATAC
1726069 TTTGAATTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:1728532 original size:13 final size:13
Alignment explanation
Indices: 1728514--1728551 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1728504 ATAATCCCCC
1728514 TGTATCGATACAG
1 TGTATCGATACAG
*
1728527 TGTATCGATACAT
1 TGTATCGATACAG
1728540 TGTATCGATACA
1 TGTATCGATACA
1728552 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1730429 original size:15 final size:15
Alignment explanation
Indices: 1730409--1730439 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1730399 ATTTCGTTTG
*
1730409 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1730424 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1730439 G
1 G
1730440 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1734527 original size:13 final size:13
Alignment explanation
Indices: 1734509--1734534 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1734499 ATATTTTTTA
1734509 TGTATCGATACAT
1 TGTATCGATACAT
1734522 TGTATCGATACAT
1 TGTATCGATACAT
1734535 ATTTTGTGTA
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:1734550 original size:32 final size:33
Alignment explanation
Indices: 1734488--1734552 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
1734478 TACAAGCCAA
1734488 TGTATCGATACATATTTTTTATGTATCGATACAT
1 TGTATCGATACATA-TTTTTATGTATCGATACAT
*
1734522 TGTATCGATACATA-TTTTGTGTATCGATACA
1 TGTATCGATACATATTTTTATGTATCGATACA
1734553 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 16 0.53
34 14 0.47
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATATTTTTATGTATCGATACAT
Found at i:1747648 original size:92 final size:92
Alignment explanation
Indices: 1747524--1747822 Score: 377
Period size: 92 Copynumber: 3.2 Consensus size: 92
1747514 TCCTCAACCG
1747524 CTAGATGGTATTGATGCATCACAAAGCCTGATCTCTTTGGGGCAAAGATATCTAGACCACACATT
1 CTAGATGGTATTGATGCATCACAAAGCCTGATCTCTTTGGGGCAAAGATATCTAGACCACACATT
*
1747589 CCTATTCGTATCCCTTTCATCCAATCA
66 CCTAATCGTATCCCTTTCATCCAATCA
* * * * *
1747616 CTAGATGGTATTGATGCATCATAAAGCTTGATCTCCTTGGGGCAAGGATATCCAGACCACACATT
1 CTAGATGGTATTGATGCATCACAAAGCCTGATCTCTTTGGGGCAAAGATATCTAGACCACACATT
* * *
1747681 CATAAACGTATCCCCTTCATCCAATCA
66 CCTAATCGTATCCCTTTCATCCAATCA
* * * * *
1747708 CTAAATGGTATTGATGCATCACAAAACCTGAT-TCTTTTTGGGCAAAGATATCTCGACCACTCAT
1 CTAGATGGTATTGATGCATCACAAAGCCTGATCTC-TTTGGGGCAAAGATATCTAGACCACACAT
* * * * *
1747772 TCCTAATCATA-CCATTCTCTTTCGATCA
65 TCCTAATCGTATCCCTT-TCATCCAATCA
* *
1747800 CTAGATGATATTGGTGCATCACA
1 CTAGATGGTATTGATGCATCACA
1747823 TGATCACAAA
Statistics
Matches: 175, Mismatches: 30, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
91 5 0.03
92 170 0.97
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.30
Consensus pattern (92 bp):
CTAGATGGTATTGATGCATCACAAAGCCTGATCTCTTTGGGGCAAAGATATCTAGACCACACATT
CCTAATCGTATCCCTTTCATCCAATCA
Found at i:1748568 original size:45 final size:45
Alignment explanation
Indices: 1748419--1748585 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 45
1748409 TTACTAAACA
* * ** * *
1748419 AAACCTTTTTCATCCTCATTTGACTCTATCGGTTATCACCCTGATC
1 AAACCCTTTTCATTCTTGTTTGACTGTATCGGTTA-CACCCTGGTC
* *
1748465 AAACCTTTTTCATTCTTGTTTGACTGTATCGGTTACTATCCTGGTC
1 AAACCCTTTTCATTCTTGTTTGACTGTATCGGTTAC-ACCCTGGTC
* *
1748511 AAACCCTTTTCA-TCTATGTTTGACTGTATTGATTACACCCTGGTC
1 AAACCCTTTTCATTCT-TGTTTGACTGTATCGGTTACACCCTGGTC
1748556 AAACCCTTTTCATTCTTGTTTGACTGTATC
1 AAACCCTTTTCATTCTTGTTTGACTGTATC
1748586 AGCTACCACA
Statistics
Matches: 107, Mismatches: 11, Indels: 7
0.86 0.09 0.06
Matches are distributed among these distances:
45 37 0.35
46 70 0.65
ACGTcount: A:0.20, C:0.25, G:0.12, T:0.43
Consensus pattern (45 bp):
AAACCCTTTTCATTCTTGTTTGACTGTATCGGTTACACCCTGGTC
Found at i:1748786 original size:40 final size:40
Alignment explanation
Indices: 1748664--1748788 Score: 126
Period size: 40 Copynumber: 3.1 Consensus size: 40
1748654 TACTCTGTTC
* * * **
1748664 GCTTTATCAATTTCGCCCTAGCCAACCTTCCAATTGGTTG
1 GCTTTATCGATTTCACCCTAGCCAACTTTTTAATTGGTTG
* * * * *
1748704 ACTTTATCGGTTTTACCCTAGTCAACCTTTTTAATCT-ATTG
1 GCTTTATCGATTTCACCCTAGCCAA-CTTTTTAAT-TGGTTG
*
1748745 GCTTTATCGATTTCATCCTAGCCAACTTTTTAATTGGTTG
1 GCTTTATCGATTTCACCCTAGCCAACTTTTTAATTGGTTG
1748785 GCTT
1 GCTT
1748789 GTCGGTTTAA
Statistics
Matches: 66, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
39 1 0.02
40 35 0.53
41 29 0.44
42 1 0.02
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.42
Consensus pattern (40 bp):
GCTTTATCGATTTCACCCTAGCCAACTTTTTAATTGGTTG
Found at i:1748816 original size:81 final size:81
Alignment explanation
Indices: 1748664--1748820 Score: 183
Period size: 81 Copynumber: 2.0 Consensus size: 81
1748654 TACTCTGTTC
* *
1748664 GCTTTATCAATTTCGCCCTAGCCAACCTTCCAATTGGTTGACTTTATCGGTTTTACCCTAGTCAA
1 GCTTTATCAATTTCACCCTAGCCAACCTTCCAATTGGTTGACTTTATCGGTTTAACCCTAGTCAA
1748729 CCTTTTTAATCTATTG
66 CCTTTTTAATCTATTG
* * * ** * * *
1748745 GCTTTATCGATTTCATCCTAGCCAACTTTTTAATTGGTTGGC-TTGTCGGTTTAATCCC-GGTCA
1 GCTTTATCAATTTCACCCTAGCCAACCTTCCAATTGGTTGACTTTATCGGTTTAA-CCCTAGTCA
* *
1748808 ACATTTTTTATCT
65 ACCTTTTTAATCT
1748821 TTTTTTAACC
Statistics
Matches: 63, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
80 25 0.40
81 38 0.60
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.43
Consensus pattern (81 bp):
GCTTTATCAATTTCACCCTAGCCAACCTTCCAATTGGTTGACTTTATCGGTTTAACCCTAGTCAA
CCTTTTTAATCTATTG
Found at i:1748954 original size:44 final size:43
Alignment explanation
Indices: 1748896--1749039 Score: 125
Period size: 41 Copynumber: 3.3 Consensus size: 43
1748886 CCCGATCAAT
* *
1748896 CTTTTGTAACCTTTGTCTACCTATCAGCTCAGTCCCTGGTAAATC
1 CTTTT-TATCCTTTGTCTACCTGTCAGCTCAGT-CCTGGTAAATC
* * * *
1748941 CTTTTTATCCTTTGT-TAACTTGTCAGTTCA-TCTTGGTCAA-C
1 CTTTTTATCCTTTGTCT-ACCTGTCAGCTCAGTCCTGGTAAATC
* * *
1748982 TTTTTTATCCTTTGTCTACCTGTCAACTTAGTCCTGGGTAAAT-
1 CTTTTTATCCTTTGTCTACCTGTCAGCTCAGTCCT-GGTAAATC
* *
1749025 CTTTTTGTCATTTGT
1 CTTTTTATCCTTTGT
1749040 TGGCTTGTTA
Statistics
Matches: 78, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
41 24 0.31
42 11 0.14
43 19 0.24
44 19 0.24
45 5 0.06
ACGTcount: A:0.17, C:0.23, G:0.13, T:0.47
Consensus pattern (43 bp):
CTTTTTATCCTTTGTCTACCTGTCAGCTCAGTCCTGGTAAATC
Found at i:1748996 original size:85 final size:87
Alignment explanation
Indices: 1748840--1749040 Score: 214
Period size: 85 Copynumber: 2.4 Consensus size: 87
1748830 CTGTTGGCTT
* * * *
1748840 AGTCTTGGGCAAATCC-TTTAATCCTTTGTTGACTTATCAATTCAATCCCGATCAATCTTTTGTA
1 AGTCCTGGGTAAATCCTTTTTATCCTTTGTTAACTTATCAATTCAATCCCGATCAATCTTTTGTA
*
1748904 ACCTTTGTCTACCTATCAGCTC
66 ACCTTTGTCTACCTATCAACTC
* * ** * *
1748926 AGTCCCT-GGTAAATCCTTTTTATCCTTTGTTAACTTGTCAGTTC-ATCTTGGTCAA-CTTTTTT
1 AGT-CCTGGGTAAATCCTTTTTATCCTTTGTTAACTTATCAATTCAATCCCGATCAATCTTTTGT
* * *
1748988 ATCCTTTGTCTACCTGTCAACTT
65 AACCTTTGTCTACCTATCAACTC
* *
1749011 AGTCCTGGGTAAAT-CTTTTTGTCATTTGTT
1 AGTCCTGGGTAAATCCTTTTTATCCTTTGTT
1749041 GGCTTGTTAG
Statistics
Matches: 96, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
84 17 0.18
85 35 0.36
86 19 0.20
87 25 0.26
ACGTcount: A:0.20, C:0.23, G:0.13, T:0.44
Consensus pattern (87 bp):
AGTCCTGGGTAAATCCTTTTTATCCTTTGTTAACTTATCAATTCAATCCCGATCAATCTTTTGTA
ACCTTTGTCTACCTATCAACTC
Found at i:1749006 original size:41 final size:44
Alignment explanation
Indices: 1748891--1749030 Score: 128
Period size: 44 Copynumber: 3.2 Consensus size: 44
1748881 TCAATCCCGA
* * *
1748891 TCAATCTTTTGTAACCTTTGTCTACCTATCAGCTCAGTCCCTGG
1 TCAATCTTTTTTATCCTTTGTCTACCTGTCAGCTCAGTCCCTGG
* * * * *
1748935 TAAATCCTTTTTATCCTTTGT-TAACTTGTCAGTTCA-T-CTTGG
1 TCAATCTTTTTTATCCTTTGTCT-ACCTGTCAGCTCAGTCCCTGG
* *
1748977 TCAA-CTTTTTTATCCTTTGTCTACCTGTCAACTTAGT-CCTGGG
1 TCAATCTTTTTTATCCTTTGTCTACCTGTCAGCTCAGTCCCT-GG
*
1749020 TAAATCTTTTT
1 TCAATCTTTTT
1749031 GTCATTTGTT
Statistics
Matches: 75, Mismatches: 16, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
41 24 0.32
42 11 0.15
43 7 0.09
44 33 0.44
ACGTcount: A:0.19, C:0.24, G:0.12, T:0.46
Consensus pattern (44 bp):
TCAATCTTTTTTATCCTTTGTCTACCTGTCAGCTCAGTCCCTGG
Found at i:1749065 original size:85 final size:86
Alignment explanation
Indices: 1748891--1749087 Score: 188
Period size: 85 Copynumber: 2.3 Consensus size: 86
1748881 TCAATCCCGA
* * * * *
1748891 TCAATCTTTTGTAACCTTTGTCTACCTATCAGCTCAGTCCCTGGTAAATCCTTTTTATCCTTTGT
1 TCAACCTTTTTTATCCTTTGTCTACCTATCAACTCAGTCCCTGGTAAATCCTTTTTATCATTTGT
* * * *
1748956 TAACTTGTCAGTTCATCTTGG
66 TAACTTGTCAGTTAACCGTAG
* * *
1748977 TCAA-CTTTTTTATCCTTTGTCTACCTGTCAACTTAGT-CCTGGGTAAAT-CTTTTTGTCATTTG
1 TCAACCTTTTTTATCCTTTGTCTACCTATCAACTCAGTCCCT-GGTAAATCCTTTTTATCATTTG
** *
1749039 TTGGCTTGTTAGTTTAACCGTAG
65 TTAACTTGTCAG-TTAACCGTAG
*
1749062 TCAACCTTTGTTT-T-CTTTATCTACCT
1 TCAACCTTT-TTTATCCTTTGTCTACCT
1749088 TTTGGTTTAA
Statistics
Matches: 92, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
84 24 0.26
85 56 0.61
86 9 0.10
87 3 0.03
ACGTcount: A:0.18, C:0.22, G:0.13, T:0.47
Consensus pattern (86 bp):
TCAACCTTTTTTATCCTTTGTCTACCTATCAACTCAGTCCCTGGTAAATCCTTTTTATCATTTGT
TAACTTGTCAGTTAACCGTAG
Found at i:1750639 original size:14 final size:15
Alignment explanation
Indices: 1750620--1750649 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1750610 TAAGAGTTAA
1750620 TTTTAATTTT-AATT
1 TTTTAATTTTCAATT
1750634 TTTTAATTTTCAATT
1 TTTTAATTTTCAATT
1750649 T
1 T
1750650 ATTTTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTAATTTTCAATT
Found at i:1750650 original size:20 final size:19
Alignment explanation
Indices: 1750616--1750655 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
1750606 TTGCTAAGAG
1750616 TTAATTTTAATTTTAATTTT
1 TTAATTTTAATTTT-ATTTT
1750636 TTAATTTTCAA-TTTATTTT
1 TTAATTTT-AATTTTATTTT
1750655 T
1 T
1750656 ATTTACTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.32
20 11 0.58
21 2 0.11
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (19 bp):
TTAATTTTAATTTTATTTT
Found at i:1750995 original size:12 final size:12
Alignment explanation
Indices: 1750971--1751013 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
1750961 AACTTTGGGC
*
1750971 AAAG-GAGAAAA
1 AAAGAGAGAGAA
1750982 AAAGAGAGAGAA
1 AAAGAGAGAGAA
*
1750994 AAAGAAAGAGATA
1 AAAGAGAGAGA-A
1751007 AAAGAGA
1 AAAGAGA
1751014 AAATAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 4 0.15
12 16 0.59
13 7 0.26
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (12 bp):
AAAGAGAGAGAA
Found at i:1751032 original size:23 final size:24
Alignment explanation
Indices: 1750980--1751032 Score: 56
Period size: 23 Copynumber: 2.2 Consensus size: 24
1750970 CAAAGGAGAA
*
1750980 AAAAAGAGAGAGAAAAAGAAAGAG
1 AAAAAGAGAGAGAAAAAGAAACAG
*
1751004 ATAAAAGAGA-A-AATAAGAAAACAG
1 A-AAAAGAGAGAGAAAAAG-AAACAG
1751028 AAAAA
1 AAAAA
1751033 AAATAGTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 9 0.36
24 8 0.32
25 8 0.32
ACGTcount: A:0.74, C:0.02, G:0.21, T:0.04
Consensus pattern (24 bp):
AAAAAGAGAGAGAAAAAGAAACAG
Found at i:1751408 original size:14 final size:14
Alignment explanation
Indices: 1751385--1751416 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1751375 GACCAAGTTG
1751385 TAAA-AAAATAAAA
1 TAAATAAAATAAAA
1751398 TAAATAAAATAAAA
1 TAAATAAAATAAAA
1751412 TAAAT
1 TAAAT
1751417 TGTTATATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAATAAAATAAAA
Found at i:1751834 original size:16 final size:16
Alignment explanation
Indices: 1751813--1751844 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1751803 TTTTAATATT
*
1751813 CCTACTGGTATCCGTA
1 CCTACTAGTATCCGTA
1751829 CCTACTAGTATCCGTA
1 CCTACTAGTATCCGTA
1751845 GGGGTATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.31, G:0.16, T:0.31
Consensus pattern (16 bp):
CCTACTAGTATCCGTA
Found at i:1758223 original size:33 final size:33
Alignment explanation
Indices: 1758186--1758252 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1758176 TTCAACGATT
1758186 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1758219 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1758252 T
1 T
1758253 TTAAGCTACT
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:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1758224 original size:13 final size:13
Alignment explanation
Indices: 1758206--1758230 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1758196 CATAAAATGT
1758206 TGTATCGATACAA
1 TGTATCGATACAA
1758219 TGTATCGATACA
1 TGTATCGATACA
1758231 TATTTTTTTG
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:1758311 original size:13 final size:13
Alignment explanation
Indices: 1758293--1758317 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1758283 ATTACTCAAA
1758293 TGTATCGATACAT
1 TGTATCGATACAT
1758306 TGTATCGATACA
1 TGTATCGATACA
1758318 CTGATCTTTG
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:1758419 original size:52 final size:52
Alignment explanation
Indices: 1758326--1758453 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
1758316 CACTGATCTT
*
1758326 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
1758377 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1758429 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1758454 TCATATTTCG
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 19 0.26
52 52 0.70
53 3 0.04
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:1765347 original size:18 final size:17
Alignment explanation
Indices: 1765326--1765361 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1765316 CGGAACAGTC
*
1765326 AAAAGAAAACACAAAAAA
1 AAAACAAAACA-AAAAAA
1765344 AAAACAAAACAAAAAAA
1 AAAACAAAACAAAAAAA
1765361 A
1 A
1765362 GTGCAAAGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.86, C:0.11, G:0.03, T:0.00
Consensus pattern (17 bp):
AAAACAAAACAAAAAAA
Found at i:1765632 original size:16 final size:16
Alignment explanation
Indices: 1765602--1765632 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1765592 TCTTTTCCAA
*
1765602 AAAAAAGAAACAAAAC
1 AAAAAAGAAAAAAAAC
1765618 AAAAAAGAAAAAAAA
1 AAAAAAGAAAAAAAA
1765633 GAGGAAAAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.87, C:0.06, G:0.06, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAAAAAAC
Found at i:1766629 original size:31 final size:31
Alignment explanation
Indices: 1766591--1766735 Score: 199
Period size: 31 Copynumber: 4.7 Consensus size: 31
1766581 AAAAAAAAAA
1766591 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
*
1766622 AAAGTCCACGACTCAGTGGCAATCTCTGCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
*
1766653 AAAGTCCACGACGCAGTGGC-ATC-CTTCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
*
1766682 TTTAAAGTCCACGACTCAGTGGC-AT-TTTGTCTC
1 ---AAAGTCCACGACTCAGTGGCAATCTCT-TCTC
1766715 AAAGTCCACGACTCAGTGGCA
1 AAAGTCCACGACTCAGTGGCA
1766736 TTTTTTCTTT
Statistics
Matches: 103, Mismatches: 5, Indels: 12
0.86 0.04 0.10
Matches are distributed among these distances:
29 5 0.05
30 23 0.22
31 49 0.48
32 22 0.21
33 4 0.04
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (31 bp):
AAAGTCCACGACTCAGTGGCAATCTCTTCTC
Found at i:1766736 original size:62 final size:62
Alignment explanation
Indices: 1766591--1766766 Score: 218
Period size: 62 Copynumber: 2.9 Consensus size: 62
1766581 AAAAAAAAAA
1766591 AAAGTCCACGACTCAGTGGCAATCTCTTCTC---AAAGTCCACGACTCAGTGGCAATCTCTGCTC
1 AAAGTCCACGACTCAGTGGC-ATC-CTTCTCTTTAAAGTCCACGACTCAGTGGC-ATCTCTGCTC
* *
1766653 AAAGTCCACGACGCAGTGGCATCCTTCTCTTTAAAGTCCACGACTCAGTGGCAT-TTTGTCTC
1 AAAGTCCACGACTCAGTGGCATCCTTCTCTTTAAAGTCCACGACTCAGTGGCATCTCTG-CTC
* * * * *
1766715 AAAGTCCACGACTCAGTGGCAT-TTTTTCTTTAAAGCCCACAACTCCGTGGCA
1 AAAGTCCACGACTCAGTGGCATCCTTCTCTTTAAAGTCCACGACTCAGTGGCA
1766767 CCTTGTTCCT
Statistics
Matches: 102, Mismatches: 8, Indels: 9
0.86 0.07 0.08
Matches are distributed among these distances:
60 6 0.06
61 31 0.30
62 45 0.44
63 20 0.20
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (62 bp):
AAAGTCCACGACTCAGTGGCATCCTTCTCTTTAAAGTCCACGACTCAGTGGCATCTCTGCTC
Found at i:1766857 original size:34 final size:33
Alignment explanation
Indices: 1766720--1767278 Score: 418
Period size: 34 Copynumber: 17.6 Consensus size: 33
1766710 GTCTCAAAGT
* * *
1766720 CCACGACTCAGTGGCA-TTTTTTC-TTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCATTTTAAGC
* * * *
1766751 CCACAACTCCGTGGCACCTTGTTCCTTTTAAGT
1 CCACAACTCCGTGGCACTTTTTTCATTTTAAGC
**
1766784 CCACAACTCCGTGGCACCCTTTT-A----AAGC
1 CCACAACTCCGTGGCACTTTTTTCATTTTAAGC
* * *
1766812 CCATAATTCCGTGGCACTTTTTTCATCTTTAAGT
1 CCACAACTCCGTGGCACTTTTTTCAT-TTTAAGC
**
1766846 CCACAACTCCGTGGCACCCTTTT-A----AAGC
1 CCACAACTCCGTGGCACTTTTTTCATTTTAAGC
* *
1766874 CCACAATTCCGTGGCACTTTTTTTCATCTTTAAGT
1 CCACAACTCCGTGGCAC-TTTTTTCAT-TTTAAGC
**
1766909 CCACAACTCCGTGGCACCCTTTT-A----AAGC
1 CCACAACTCCGTGGCACTTTTTTCATTTTAAGC
* *
1766937 CCACAATTCCGTGGCACTTTTTTCATCTTTAAGT
1 CCACAACTCCGTGGCACTTTTTTCAT-TTTAAGC
* *
1766971 CCACAACTCCGTGGCACCTTCTTC-TTTTCAAAGC
1 CCACAACTCCGTGGCACTTTTTTCATTTT--AAGC
* *
1767005 CCACAACTCTGTGGCACCTTTTTC-TTTTCAATGC
1 CCACAACTCCGTGGCACTTTTTTCATTTT-AA-GC
*
1767039 CCACGACTCCGTGGCACTCTTTTT-A----AAGC
1 CCACAACTCCGTGGCACT-TTTTTCATTTTAAGC
*
1767068 CCACGACTCCGTGGCACTCTTTTT-A----AAGC
1 CCACAACTCCGTGGCACT-TTTTTCATTTTAAGC
* *
1767097 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
1 CCACAACTCCGTGGCACT-TTTTTCATTTTAAGC
*
1767131 CCACAACTCCGTGGCAC------CCTTTTAAGC
1 CCACAACTCCGTGGCACTTTTTTCATTTTAAGC
*
1767158 CCACAACTCCGTGGCACTTTTTTCATCTTTAAGT
1 CCACAACTCCGTGGCACTTTTTTCAT-TTTAAGC
* *
1767192 CCACAACTCCGTGGCACCTTTTT--TTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCATTTTAAGC
* *
1767223 CCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGT
1 CCACAACTCCGTGGCACT-TTTTT-CATTTTAAGC
1767258 CCACAACTCCGTGGCATCTTT
1 CCACAACTCCGTGGCA-CTTT
1767279 CTCTCTTCCT
Statistics
Matches: 432, Mismatches: 53, Indels: 82
0.76 0.09 0.14
Matches are distributed among these distances:
27 26 0.06
28 64 0.15
29 60 0.14
30 3 0.01
31 36 0.08
32 14 0.03
33 34 0.08
34 145 0.34
35 48 0.11
36 2 0.00
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (33 bp):
CCACAACTCCGTGGCACTTTTTTCATTTTAAGC
Found at i:1766859 original size:62 final size:62
Alignment explanation
Indices: 1766743--1767091 Score: 461
Period size: 62 Copynumber: 5.5 Consensus size: 62
1766733 GCATTTTTTC
* * *
1766743 TTTAAAGCCCACAACTCCGTGGCACCTTGTTCCT-TTTAAGTCCACAACTCCGTGGCACCCT
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCCT
* *
1766804 TTTAAAGCCCATAATTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCCT
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCCT
*
1766866 TTTAAAGCCCACAATTCCGTGGCACTTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCCT
1 TTTAAAGCCCACAACTCCGTGGCAC-TTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCCT
*
1766929 TTTAAAGCCCACAATTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTCTT
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCA-C--C--
1766994 CT
61 CT
* * * * *
1766996 TTTCAAAGCCCACAACTCTGTGGCACCTTTTTC-T-TTTCAATGCCCACGACTCCGTGGCACTCT
1 TTT-AAAGCCCACAACTCCGTGGCACTTTTTTCATCTTT-AA-GTCCACAACTCCGTGGCAC-CC
1767059 T
62 T
*
1767060 TTTAAAGCCCACGACTCCGTGGCACTCTTTTT
1 TTTAAAGCCCACAACTCCGTGGCACT-TTTTT
1767092 AAAGCCCACA
Statistics
Matches: 262, Mismatches: 15, Indels: 19
0.89 0.05 0.06
Matches are distributed among these distances:
61 29 0.11
62 84 0.32
63 83 0.32
64 9 0.03
65 1 0.00
66 5 0.02
67 9 0.03
68 42 0.16
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (62 bp):
TTTAAAGCCCACAACTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCCT
Found at i:1766925 original size:125 final size:125
Alignment explanation
Indices: 1766743--1767174 Score: 498
Period size: 125 Copynumber: 3.5 Consensus size: 125
1766733 GCATTTTTTC
*
1766743 TTTAAAGCCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTA
1 TTTAAAGCCCACAACTCCGTGGCACCTT-TTTCTTTTAAGTCCACAACTCCGTGGCACCCTTTTA
*
1766808 AAGCCCATAATTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCA-C-C-CT
65 AAGCCCACAATTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTCTCT
* *
1766866 TTTAAAGCCCACAATTCCGTGGCACTTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCCTTT
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTTC-T-TTTAAGTCCACAACTCCGTGGCACCCTTT
1766931 TAAAGCCCACAATTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTCTTCT
63 TAAAGCCCACAATTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACC-TC-TCT
* * * *
1766996 TTTCAAAGCCCACAACTCTGTGGCACCTTTTTCTTTTCAATGCCCACGACTCCGTGGCACTCTTT
1 TTT-AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT-AA-GTCCACAACTCCGTGGCAC-CCTT
* * * *
1767061 TTAAAGCCCACGACTCCGTGGCACTCTTTTT-A-----AAGCCCACAACTCCGTGGCA-CTCTTT
62 TTAAAGCCCACAATTCCGTGGCACT-TTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTC-TC
1767119 T
125 T
* *
1767120 TCCTTCTAAGCCCACAACTCCGTGGCACC-----CTTTTAAGCCCACAACTCCGTGGCAC
1 T--TT-AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAGTCCACAACTCCGTGGCAC
1767175 TTTTTTCATC
Statistics
Matches: 277, Mismatches: 17, Indels: 34
0.84 0.05 0.10
Matches are distributed among these distances:
119 18 0.06
120 2 0.01
121 5 0.02
123 27 0.10
124 9 0.03
125 85 0.31
126 44 0.16
128 4 0.01
129 3 0.01
130 28 0.10
131 47 0.17
132 5 0.02
ACGTcount: A:0.21, C:0.34, G:0.14, T:0.31
Consensus pattern (125 bp):
TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAA
AGCCCACAATTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTCTCT
Found at i:1767151 original size:27 final size:27
Alignment explanation
Indices: 1767121--1767174 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
1767111 CACTCTTTTT
1767121 CCTTCTAAGCCCACAACTCCGTGGCAC
1 CCTTCTAAGCCCACAACTCCGTGGCAC
*
1767148 CCTTTTAAGCCCACAACTCCGTGGCAC
1 CCTTCTAAGCCCACAACTCCGTGGCAC
1767175 TTTTTTCATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.22, C:0.43, G:0.15, T:0.20
Consensus pattern (27 bp):
CCTTCTAAGCCCACAACTCCGTGGCAC
Found at i:1767217 original size:126 final size:124
Alignment explanation
Indices: 1766715--1767273 Score: 422
Period size: 126 Copynumber: 4.4 Consensus size: 124
1766705 ATTTTGTCTC
* * *
1766715 AAAGTCCACGACTCAGTGGCA-T-TTTTT-CTT-TAAAGCCCACAACTCCGTGGCACCTTGTTCC
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT-AAGCCCACAACTCCGTGGCACC----T-C
* * * * *
1766776 TTTT-AA-GTCCACAACTCCGTGGCAC-CCTTTTAAAGCCCATAATTCCGTGGCACTTTTTTCAT
60 TTTTCAATGCCCACAACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTT--T
1766838 CTT
123 -TT
* * * * * * *
1766841 TAAGTCCACAACTCCGTGGCAC-C--CTT--TT-AAAGCCCACAATTCCGTGGCACTTTTTTTCA
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACCTCTTTTCA
* * * * *
1766900 TCTTTAAGTCCACAACTCCGTGGCAC-CCTTTTAAAGCCCACAATTCCGTGGCACTTTTTTCATC
66 -----ATGCCCACAACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTT--T-
1766964 TT
123 TT
* * * * * *
1766966 TAAGTCCACAACTCCGTGGCAC-CTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTTTTCT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTC-CTTCTAAGCCCACAACTCCGTGGCACC----TCT
* * *
1767030 TTTCAATGCCCACGACTCCGTGGCACTCTTTTTAAAGCCCACGACTCCGTGGCA-C-TCTTTTT
61 TTTCAATGCCCACAACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTTTT
1767092 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACC-CTTTT-A
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACCTCTTTTCA
*
1767155 A-GCCCACAACTCCGTGGCACT-TTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTTTTTT
66 ATGCCCACAACTCCGTGGCACTCTTTTT-A-----AAGCCCACAACTCCGTGGCACCTTTTTTTT
* *
1767218 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGTCCACAACTCCGTGGCA
1 AAAGCCCACAACTCCGTGGCACTCTTTTT-CCTTCTAAGCCCACAACTCCGTGGCA
1767274 TCTTTCTCTC
Statistics
Matches: 370, Mismatches: 33, Indels: 59
0.80 0.07 0.13
Matches are distributed among these distances:
118 9 0.02
119 22 0.06
120 2 0.01
121 5 0.01
123 20 0.05
124 21 0.06
125 84 0.23
126 99 0.27
127 34 0.09
129 3 0.01
130 20 0.05
131 44 0.12
135 7 0.02
ACGTcount: A:0.21, C:0.33, G:0.14, T:0.32
Consensus pattern (124 bp):
AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACCTCTTTTCA
ATGCCCACAACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTTTT
Found at i:1767319 original size:32 final size:32
Alignment explanation
Indices: 1767283--1767391 Score: 168
Period size: 32 Copynumber: 3.4 Consensus size: 32
1767273 ATCTTTCTCT
1767283 CTTCCTAAAGCCCACACAAGTCGGTGGCAACC
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACC
* *
1767315 CTTCCCAAAGCCCACACAAGTTGGTGGCAACC
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACC
*
1767347 ATTCTCTAAAGCCCACACAAGTCGGTGGCAACC
1 CTTC-CTAAAGCCCACACAAGTCGGTGGCAACC
1767380 CTT-CT-AAGCCCA
1 CTTCCTAAAGCCCA
1767392 ATATAGCTGG
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
30 7 0.10
31 2 0.03
32 33 0.47
33 28 0.40
ACGTcount: A:0.28, C:0.37, G:0.17, T:0.17
Consensus pattern (32 bp):
CTTCCTAAAGCCCACACAAGTCGGTGGCAACC
Found at i:1767448 original size:49 final size:49
Alignment explanation
Indices: 1767384--1767672 Score: 383
Period size: 49 Copynumber: 6.0 Consensus size: 49
1767374 GCAACCCTTC
* * * *
1767384 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
1767433 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
1767482 TAAGACCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
1767531 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
1767574 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
* *
1767626 TAAATCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATC
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
1767673 ATCTCTAAAA
Statistics
Matches: 211, Mismatches: 20, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
43 40 0.19
49 128 0.61
50 3 0.01
52 40 0.19
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.30
Consensus pattern (49 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
Found at i:1767589 original size:43 final size:43
Alignment explanation
Indices: 1767528--1767617 Score: 162
Period size: 43 Copynumber: 2.1 Consensus size: 43
1767518 GCACCTTTAT
*
1767528 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
*
1767571 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
1767614 CTTT
1 CTTT
1767618 TCCATCTTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:1767676 original size:52 final size:52
Alignment explanation
Indices: 1767571--1767681 Score: 152
Period size: 52 Copynumber: 2.1 Consensus size: 52
1767561 ACATTGGCAC
* * *
1767571 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCAT
1 CTTTAAATCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTATCCAT
* *
1767623 CTTTAAATCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT-CAT
1 CTTTAAATCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT-ATCCAT
*
1767675 CTCTAAA
1 CTTTAAA
1767682 AACCCAATGA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
52 51 0.98
53 1 0.02
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.32
Consensus pattern (52 bp):
CTTTAAATCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTATCCAT
Found at i:1767709 original size:54 final size:52
Alignment explanation
Indices: 1767579--1767715 Score: 143
Period size: 52 Copynumber: 2.6 Consensus size: 52
1767569 ACCTTTAAGT
* * * * * *
1767579 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAAT
1 CCAATGTAGCTGGCCATGAATCAGCACATTGGCACCTTATCCATCTTAAAAC
* *
1767631 CCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT-CATCTCTAAAAAC
1 CCAATGTAGCTGGCCATGAATCAGCACATTGGCACCTT-ATCCATCT-T-AAAAC
*
1767685 CCAATG-ACGCTGGTCATGAATCAGCACATTG
1 CCAATGTA-GCTGGCCATGAATCAGCACATTG
1767716 TCATTTTTCG
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
52 40 0.56
53 3 0.04
54 29 0.40
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (52 bp):
CCAATGTAGCTGGCCATGAATCAGCACATTGGCACCTTATCCATCTTAAAAC
Found at i:1771711 original size:33 final size:33
Alignment explanation
Indices: 1771674--1771740 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1771664 TTCAACGATT
1771674 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1771707 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1771740 T
1 T
1771741 TTAAGCTACT
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:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1771712 original size:13 final size:13
Alignment explanation
Indices: 1771694--1771718 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1771684 CATAAAATGT
1771694 TGTATCGATACAA
1 TGTATCGATACAA
1771707 TGTATCGATACA
1 TGTATCGATACA
1771719 TATTTTTTTG
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:1771799 original size:13 final size:13
Alignment explanation
Indices: 1771781--1771805 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1771771 ATTACTCAAA
1771781 TGTATCGATACAT
1 TGTATCGATACAT
1771794 TGTATCGATACA
1 TGTATCGATACA
1771806 CTGATCTTTG
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:1771907 original size:52 final size:52
Alignment explanation
Indices: 1771814--1771941 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
1771804 CACTGATCTT
*
1771814 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
1771865 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1771917 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1771942 TCATATTTCG
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 19 0.26
52 52 0.70
53 3 0.04
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:1778850 original size:32 final size:32
Alignment explanation
Indices: 1778814--1779033 Score: 241
Period size: 32 Copynumber: 6.9 Consensus size: 32
1778804 ATCTCTCTTC
*
1778814 TCAAAGTCCATGACTTAGTGGCATCTTTTTCT
1 TCAAAGTCCATGACTCAGTGGCATCTTTTTCT
* *
1778846 TCAAAGTCCATAACTCAGTGGCATCTCTTTC-
1 TCAAAGTCCATGACTCAGTGGCATCTTTTTCT
* * *
1778877 CCAAAGTCCACGACTCAGTAGCATCCTTTTT-T
1 TCAAAGTCCATGACTCAGTGGCAT-CTTTTTCT
* *
1778909 TCAAAGTCCACGACTCAGTGGCATCTTTTGCT
1 TCAAAGTCCATGACTCAGTGGCATCTTTTTCT
** * *
1778941 TCAAAGTCCACAACTCAGTGGCATCTCTTTCC
1 TCAAAGTCCATGACTCAGTGGCATCTTTTTCT
*
1778973 T-AAAGTCCATGACTTAGTGGCATCTTTTTTCT
1 TCAAAGTCCATGACTCAGTGGCATC-TTTTTCT
* * *
1779005 TTAATA-TCCATGACTCAATAGCATCTTTT
1 TCAA-AGTCCATGACTCAGTGGCATCTTTT
1779034 CCAAAAGTCT
Statistics
Matches: 159, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
31 45 0.28
32 95 0.60
33 18 0.11
34 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.14, T:0.35
Consensus pattern (32 bp):
TCAAAGTCCATGACTCAGTGGCATCTTTTTCT
Found at i:1778912 original size:63 final size:62
Alignment explanation
Indices: 1778804--1778997 Score: 230
Period size: 63 Copynumber: 3.1 Consensus size: 62
1778794 AATTCTTTAA
* * *
1778804 ATCTCTCTTCTCAAAGTCCATGACTTAGTGGCATCTTTTTCTTCAAAGTCCATAACTCAGTGGC
1 ATCTCT-TTCTCAAAGTCCACGACTCAGTGGCATCTTTTT-TTCAAAGTCCATGACTCAGTGGC
* * *
1778868 ATCTCTTTCCCAAAGTCCACGACTCAGTAGCATCCTTTTTTTCAAAGTCCACGACTCAGTGGC
1 ATCTCTTTCTCAAAGTCCACGACTCAGTGGCAT-CTTTTTTTCAAAGTCCATGACTCAGTGGC
* * * *
1778931 ATCT-TTTGCTTCAAAGTCCACAACTCAGTGGCATC-TCTTTCCTAAAGTCCATGACTTAGTGGC
1 ATCTCTTT-C-TCAAAGTCCACGACTCAGTGGCATCTTTTTTTC-AAAGTCCATGACTCAGTGGC
1778994 ATCT
1 ATCT
1778998 TTTTTCTTTA
Statistics
Matches: 113, Mismatches: 13, Indels: 9
0.84 0.10 0.07
Matches are distributed among these distances:
62 8 0.07
63 72 0.64
64 33 0.29
ACGTcount: A:0.24, C:0.28, G:0.14, T:0.34
Consensus pattern (62 bp):
ATCTCTTTCTCAAAGTCCACGACTCAGTGGCATCTTTTTTTCAAAGTCCATGACTCAGTGGC
Found at i:1778978 original size:95 final size:94
Alignment explanation
Indices: 1778814--1779002 Score: 297
Period size: 95 Copynumber: 2.0 Consensus size: 94
1778804 ATCTCTCTTC
* * * *
1778814 TCAAAGTCCATGACTTAGTGGCATCTTTTTCTTCAAAGTCCATAACTCAGTGGCATCTCTTTCCC
1 TCAAAGTCCACGACTCAGTGGCATCTTTTGCTTCAAAGTCCACAACTCAGTGGCATCTCTTTCCC
1778879 AAAGTCCACGACTCAGTAGCATCCTTTTTT
66 AAAGTCCACGACTCAGTAGCAT-CTTTTTT
*
1778909 TCAAAGTCCACGACTCAGTGGCATCTTTTGCTTCAAAGTCCACAACTCAGTGGCATCTCTTTCCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTGCTTCAAAGTCCACAACTCAGTGGCATCTCTTTCCC
* * *
1778974 AAAGTCCATGACTTAGTGGCATCTTTTTT
66 AAAGTCCACGACTCAGTAGCATCTTTTTT
1779003 CTTTAATATC
Statistics
Matches: 86, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
94 7 0.08
95 79 0.92
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.34
Consensus pattern (94 bp):
TCAAAGTCCACGACTCAGTGGCATCTTTTGCTTCAAAGTCCACAACTCAGTGGCATCTCTTTCCC
AAAGTCCACGACTCAGTAGCATCTTTTTT
Found at i:1779035 original size:63 final size:62
Alignment explanation
Indices: 1778814--1779042 Score: 203
Period size: 63 Copynumber: 3.6 Consensus size: 62
1778804 ATCTCTCTTC
* * * * **
1778814 TCAAAGTCCATGACTTAGTGGCATCTTTTTCTTCAAAGTCCATAACTCAGTGGCATCTCTTT-C-
1 TCAAAGTCCACGACTCAGTAGCATC-TTTTCCT-AAAGTCCACGACTCAGTGGCATCT-TTTGCT
* **
1778877 CCAAAGTCCACGACTCAGTAGCATCCTTTTTTTCAAAGTCCACGACTCAGTGGCATCTTTTGCT
1 TCAAAGTCCACGACTCAGTAGCAT-CTTTTCCT-AAAGTCCACGACTCAGTGGCATCTTTTGCT
* * * * *
1778941 TCAAAGTCCACAACTCAGTGGCATCTCTTTCCTAAAGTCCATGACTTAGTGGCATCTTTTTTCT
1 TCAAAGTCCACGACTCAGTAGCATCT-TTTCCTAAAGTCCACGACTCAGTGGCATC-TTTTGCT
* * * *
1779005 TTAATA-TCCATGACTCAATAGCATCTTTTCCAAAAGTC
1 TCAA-AGTCCACGACTCAGTAGCATCTTTTCCTAAAGTC
1779043 TGTGACTCCG
Statistics
Matches: 139, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
62 3 0.02
63 84 0.60
64 51 0.37
65 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.34
Consensus pattern (62 bp):
TCAAAGTCCACGACTCAGTAGCATCTTTTCCTAAAGTCCACGACTCAGTGGCATCTTTTGCT
Found at i:1779145 original size:34 final size:32
Alignment explanation
Indices: 1779061--1779617 Score: 389
Period size: 27 Copynumber: 18.0 Consensus size: 32
1779051 CGTGGCACCT
1779061 TTTTAAGTCCACAACTCTGTGGCACC-----C
1 TTTTAAGTCCACAACTCTGTGGCACCTTTTTC
*
1779088 TATTAAGTCCACAACT-TCGTGGCACCTTTTTC
1 TTTTAAGTCCACAACTCT-GTGGCACCTTTTTC
* *
1779120 TTTTTAAAGCCCACAACTCTATGGCACTCTTTTTCC
1 -TTTT-AAGTCCACAACTCTGTGGCAC-CTTTTT-C
*
1779156 TTTTAAGTCCACAACTCCGTGGCACC-----C
1 TTTTAAGTCCACAACTCTGTGGCACCTTTTTC
* *
1779183 TTTTAAGTCCACAACACCGTGGCACCTTTTTCC
1 TTTTAAGTCCACAACTCTGTGGCACCTTTTT-C
1779216 TTTTAAGTCCACAACT-TCGTGGCACC-----C
1 TTTTAAGTCCACAACTCT-GTGGCACCTTTTTC
* *
1779243 TTTTAAGCCCACAACTCCGTGGCACCTTTTTC
1 TTTTAAGTCCACAACTCTGTGGCACCTTTTTC
*
1779275 TTTTTAAGTCCACAACTCCGTGGCACC-----C
1 -TTTTAAGTCCACAACTCTGTGGCACCTTTTTC
*
1779303 TTTTAAGTCCACAACTCTGTGGAACCTTTTTCC
1 TTTTAAGTCCACAACTCTGTGGCACCTTTTT-C
* * *
1779336 TTTTAAAGCCCACAACTCTGTTGCACTATTTTTC
1 TTTT-AAGTCCACAACTCTGTGGCAC-CTTTTTC
*
1779370 TTTTTAAGTCCACGACTCTGTGGCACC-----C
1 -TTTTAAGTCCACAACTCTGTGGCACCTTTTTC
*
1779398 TTTTAAGCTCC-CAACTCTGTTGCACTCTTTTTC
1 TTTTAAG-TCCACAACTCTGTGGCAC-CTTTTTC
*
1779431 TTTTTAAGTCCACGACTCTGTGGCACC-----C
1 -TTTTAAGTCCACAACTCTGTGGCACCTTTTTC
* * *
1779459 TTTTAAGCCCACAACTCCGTGGCATTCTTTTTCC
1 TTTTAAGTCCACAACTCTGTGGCA-CCTTTTT-C
* *
1779493 TTTTAAGTCAACAACTCCGTGGCACC-----C
1 TTTTAAGTCCACAACTCTGTGGCACCTTTTTC
* * *
1779520 TTTTAAGTCCACAACTCTGTAGCGCCTTGTTCC
1 TTTTAAGTCCACAACTCTGTGGCACCTT-TTTC
* * * *
1779553 TTTTAAGTCCATAACTCCGTGGCATCTTTCTCC
1 TTTTAAGTCCACAACTCTGTGGCACCTTT-TTC
* * * *
1779586 TTTTAAGCCCACAAGTCAGTGGCACCCTTTTC
1 TTTTAAGTCCACAACTCTGTGGCACCTTTTTC
1779618 AAAAGCCCAC
Statistics
Matches: 423, Mismatches: 50, Indels: 109
0.73 0.09 0.19
Matches are distributed among these distances:
26 1 0.00
27 160 0.38
28 8 0.02
32 5 0.01
33 114 0.27
34 114 0.27
35 20 0.05
36 1 0.00
ACGTcount: A:0.20, C:0.32, G:0.13, T:0.35
Consensus pattern (32 bp):
TTTTAAGTCCACAACTCTGTGGCACCTTTTTC
Found at i:1779167 original size:95 final size:94
Alignment explanation
Indices: 1779061--1779523 Score: 295
Period size: 95 Copynumber: 5.0 Consensus size: 94
1779051 CGTGGCACCT
* ** *
1779061 TTTTAAGTCCACAACTCTGTGGCACCCTATTAAGTCCACAACTTCGTGGCACCTTTTTCTTTTTA
1 TTTTAAGTCCACAACTCCGTGGCACCCTATTAAGTCCACAACACCGTGGCACCTTTTTCCTTTT-
1779126 AAGCCCACAACTCTATGGCACTCTTTTTCC
65 AAGCCCACAACTCTATGGCACTCTTTTTCC
*
1779156 TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACACCGTGGCACCTTTTTCCTTTTA
1 TTTTAAGTCCACAACTCCGTGGCACCCTATTAAGTCCACAACACCGTGGCACCTTTTTCCTTTTA
* *
1779221 AGTCCACAACT-TCGTGGCA--C-----CC
66 AGCCCACAACTCT-ATGGCACTCTTTTTCC
* * *
1779243 TTTTAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAGTCCACAACTCCGTGGCA-C-----C
1 TTTTAAGTCCACAACTCCGTGGCACC-----C-TATTAAGTCCACAACACCGTGGCACCTTTTTC
* * *
1779302 CTTTTAAGTCCACAACTCTGTGGAAC-CTTTTTCC
60 CTTTTAAGCCCACAACTCTATGGCACTCTTTTTCC
* * * * * * * *
1779336 TTTTAAAGCCCACAACTCTGTTGCACTATTTTTCTTTTTAAGTCCACGACTCTGTGGCA-C----
1 TTTT-AAGTCCACAACTCCGTGGCAC-------CCTATTAAGTCCACAACACCGTGGCACCTTTT
* * *
1779396 -CCTTTTAAGCTCC-CAACTCTGTTGCACTCTTTTTCT
58 TCCTTTTAAGC-CCACAACTCTATGGCACTCTTTTTCC
* * * * * *
1779432 TTTTAAGTCCACGACTCTGTGGCACCCTTTTAAGCCCACAACTCCGTGGCATTCTTTTTCCTTTT
1 TTTTAAGTCCACAACTCCGTGGCACCCTATTAAGTCCACAACACCGTGGCA-CCTTTTTCCTTTT
* * ** *
1779497 AAGTCAACAACTCCGTGGCACCCTTTT
65 AAGCCCACAACTCTATGGCACTCTTTT
1779524 AAGTCCACAA
Statistics
Matches: 305, Mismatches: 31, Indels: 64
0.76 0.08 0.16
Matches are distributed among these distances:
87 50 0.16
88 24 0.08
90 1 0.00
92 3 0.01
93 30 0.10
94 36 0.12
95 147 0.48
96 13 0.04
101 1 0.00
ACGTcount: A:0.21, C:0.32, G:0.13, T:0.35
Consensus pattern (94 bp):
TTTTAAGTCCACAACTCCGTGGCACCCTATTAAGTCCACAACACCGTGGCACCTTTTTCCTTTTA
AGCCCACAACTCTATGGCACTCTTTTTCC
Found at i:1779220 original size:60 final size:60
Alignment explanation
Indices: 1779047--1779353 Score: 374
Period size: 60 Copynumber: 5.1 Consensus size: 60
1779037 AAAGTCTGTG
* *
1779047 ACTCCGTGGCACCTTTTTAAGTCCACAACTCTGTGGCA-C-----CCTATTAAGTCCACA
1 ACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCCTTTTAAGTCCACA
* * *
1779101 ACTTCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCTATGGCACTCTTTTTCCTTTTAAGTCC
1 ACTCCGTGGCACC-----C-TTTT-AAGTCCACAACTCTGTGGCAC-CTTTTTCCTTTTAAGTCC
1779166 ACA
58 ACA
* *
1779169 ACTCCGTGGCACCCTTTTAAGTCCACAACACCGTGGCACCTTTTTCCTTTTAAGTCCACA
1 ACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCCTTTTAAGTCCACA
* * * *
1779229 ACTTCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAGTCCACA
1 ACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCCTTTTAAGTCCACA
* *
1779289 ACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGAACCTTTTTCCTTTTAAAGCCCACA
1 ACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCCTTTT-AAGTCCACA
1779350 ACTC
1 ACTC
1779354 TGTTGCACTA
Statistics
Matches: 218, Mismatches: 20, Indels: 23
0.84 0.08 0.09
Matches are distributed among these distances:
54 12 0.06
60 127 0.58
61 47 0.22
62 4 0.02
63 2 0.01
68 26 0.12
ACGTcount: A:0.22, C:0.33, G:0.13, T:0.33
Consensus pattern (60 bp):
ACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCCTTTTAAGTCCACA
Found at i:1779291 original size:215 final size:217
Alignment explanation
Indices: 1779059--1779616 Score: 788
Period size: 215 Copynumber: 2.6 Consensus size: 217
1779049 TCCGTGGCAC
* * *
1779059 CTTTTTAAGTCCACAACTCTGTGGCACCCTATTAAGTCCACAACT-TCGTGGCACCTTTTTCTTT
1 CTTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCT-GTGGCACCTTTTTCCTT
* *
1779123 TTAAAGCCCACAACTCTATGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTA
65 TTAAAGCCCACAACTCTGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCAGTGGCACCCTTTTA
1779188 AG-TCCACAACACCGTGGCAC-CTTTTTCCTTTTAAGTCCACAACT-TCGTGGCACCCTTTTAAG
130 AGCTCC-CAACACCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCT-GTGGCACCCTTTTAAG
1779250 CCCACAACTCCGTGGCA-CCTTTTT
193 CCCACAACTCCGTGGCATCCTTTTT
*
1779274 CTTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGAACCTTTTTCCTTT
1 CTTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCCTTT
* * * * *
1779339 TAAAGCCCACAACTCTGTTGCACTATTTTTCTTTTTAAGTCCACGACTCTGTGGCACCCTTTTAA
66 TAAAGCCCACAACTCTGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCAGTGGCACCCTTTTAA
* * * * *
1779404 GCTCCCAACTCTGTTGCACTCTTTTTCTTTTTAAGTCCACGACTCTGTGGCACCCTTTTAAGCCC
131 GCTCCCAACACCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGCCC
*
1779469 ACAACTCCGTGGCATTCTTTTT
196 ACAACTCCGTGGCATCCTTTTT
* * * * *
1779491 CCTTTTAAGTCAACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTAGCGCCTTGTTCCTTT
1 CTTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCCTTT
* * * * * *
1779556 T-AAGTCCATAACTCCGTGGCA-TCTTTCTCCTTTTAAGCCCACAAGTCAGTGGCACCCTTTT
66 TAAAGCCCACAACTCTGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCAGTGGCACCCTTTT
1779617 CAAAAGCCCA
Statistics
Matches: 305, Mismatches: 33, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
215 163 0.53
216 75 0.25
217 67 0.22
ACGTcount: A:0.20, C:0.32, G:0.13, T:0.35
Consensus pattern (217 bp):
CTTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCCTTT
TAAAGCCCACAACTCTGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCAGTGGCACCCTTTTAA
GCTCCCAACACCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGCCC
ACAACTCCGTGGCATCCTTTTT
Found at i:1779413 original size:61 final size:61
Alignment explanation
Indices: 1779334--1779563 Score: 311
Period size: 61 Copynumber: 3.8 Consensus size: 61
1779324 GAACCTTTTT
*
1779334 CCTTTTAAAGCCCACAACTCTGTTGCACTATTTTTCTTTTTAAGTCCACGACTCTGTGGCAC
1 CCTTTT-AAGCCCACAACTCTGTTGCACTCTTTTTCTTTTTAAGTCCACGACTCTGTGGCAC
1779396 CCTTTTAAGCTCC-CAACTCTGTTGCACTCTTTTTCTTTTTAAGTCCACGACTCTGTGGCAC
1 CCTTTTAAGC-CCACAACTCTGTTGCACTCTTTTTCTTTTTAAGTCCACGACTCTGTGGCAC
* * * * * * *
1779457 CCTTTTAAGCCCACAACTCCGTGGCATTCTTTTTCCTTTTAAGTCAACAACTCCGTGGCAC
1 CCTTTTAAGCCCACAACTCTGTTGCACTCTTTTTCTTTTTAAGTCCACGACTCTGTGGCAC
* * * * *
1779518 CCTTTTAAGTCCACAACTCTGTAGCGC-CTTGTTCCTTTTAAGTCCA
1 CCTTTTAAGCCCACAACTCTGTTGCACTCTTTTTCTTTTTAAGTCCA
1779564 TAACTCCGTG
Statistics
Matches: 151, Mismatches: 15, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
60 19 0.13
61 124 0.82
62 8 0.05
ACGTcount: A:0.20, C:0.31, G:0.13, T:0.37
Consensus pattern (61 bp):
CCTTTTAAGCCCACAACTCTGTTGCACTCTTTTTCTTTTTAAGTCCACGACTCTGTGGCAC
Found at i:1779661 original size:29 final size:30
Alignment explanation
Indices: 1779590--1779714 Score: 141
Period size: 29 Copynumber: 4.3 Consensus size: 30
1779580 TTCTCCTTTT
*
1779590 AAGCCCACAAGTCAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCACCCCTTTCAA
1779620 AAGCCCACAAGTCAGTGGCACCCCTTTC-A
1 AAGCCCACAAGTCAGTGGCACCCCTTTCAA
* * *
1779649 AAGCCCACAAGTCAATAGCA-ACC-TTCAA
1 AAGCCCACAAGTCAGTGGCACCCCTTTCAA
* * ** *
1779677 AGGCACACAAGTTGGT-GCAACCCTTTCAA
1 AAGCCCACAAGTCAGTGGCACCCCTTTCAA
1779706 AAGCCCACA
1 AAGCCCACA
1779715 CAAGTTGGTG
Statistics
Matches: 80, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
27 6 0.08
28 16 0.20
29 31 0.39
30 27 0.34
ACGTcount: A:0.34, C:0.34, G:0.16, T:0.17
Consensus pattern (30 bp):
AAGCCCACAAGTCAGTGGCACCCCTTTCAA
Found at i:1779709 original size:57 final size:58
Alignment explanation
Indices: 1779590--1779714 Score: 146
Period size: 57 Copynumber: 2.2 Consensus size: 58
1779580 TTCTCCTTTT
* * * * *
1779590 AAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCACCCCTTTCA
1 AAGCCCACAAGTCAATAGCAACC-TTTCAAAAGCACACAAGTCAGTGGCAACCCTTTCA
* **
1779649 AAGCCCACAAGTCAATAGCAACC-TTCAAAGGCACACAAGTTGGT-GCAACCCTTTCAA
1 AAGCCCACAAGTCAATAGCAACCTTTCAAAAGCACACAAGTCAGTGGCAACCCTTTC-A
1779706 AAGCCCACA
1 AAGCCCACA
1779715 CAAGTTGGTG
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
56 10 0.18
57 27 0.47
59 20 0.35
ACGTcount: A:0.34, C:0.34, G:0.16, T:0.17
Consensus pattern (58 bp):
AAGCCCACAAGTCAATAGCAACCTTTCAAAAGCACACAAGTCAGTGGCAACCCTTTCA
Found at i:1779856 original size:52 final size:49
Alignment explanation
Indices: 1779734--1780693 Score: 532
Period size: 49 Copynumber: 20.8 Consensus size: 49
1779724 GACATCTTCT
* *
1779734 TCTAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTCATC
1 TCTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * *
1779783 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATC
1 TCTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCATC
* * *
1779835 TCTAAGACCAATGTTGCTGGCCTTGAATCAACATATTGG------CA--
1 TCTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * * *
1779876 --TAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCA-CTTTATC
1 TCTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * * * *
1779922 TTTAAGACCAATGTCGCTGGCCTTGAATCAACACATTGGCATCTTCATC
1 TCTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * * *
1779971 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
1 TCTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * * * * *
1780020 TTTAAGACCAATATTGCCGGCCTTGAATCAGTATATTGGCACCTT-ATC
1 TCTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * *
1780068 TCTCAGACCAATGTCGTTGGCCTTGAATCAGCACT-TTGG------CA--
1 TCTAAGTCCAATGTCGCTGGCCTTGAATCAGCA-TATTGGCACCTTCATC
* * * *
1780109 --TAAGCCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTT-GTC
1 TCTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * *
1780155 TCTAAGACCAATGTCGCTGGCCTTGAATCGGCACATTGG------CA--
1 TCTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * * *
1780196 --TAAGCCCAATATCGCTGGTCTTGAATCAGCATATTGGCACCTTTATC
1 TCTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * *
1780243 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGG------CA--
1 TCTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * *
1780284 --TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-GTC
1 TCTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * * *
1780330 TCTAAGACCAATGTTGCTGGTCTTGAATCAGCACATTGG------CA--
1 TCTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * * * * *
1780371 --TAAGCCCAATATCGCTAGCCTTGAATCAACATATTGGCACCTT-GTT
1 TCTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * * *
1780417 TTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGG------CA--
1 TCTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * * * *
1780458 -C-AAGCCCAATATCACTAGCCTTGAATCAGCATATTGGTACCTTTGTCATC
1 TCTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCATC
* ** * *
1780508 TTTAAAACCATTGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
1 TCTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * * *
1780557 -CTTAAGTCCAATATCGTTGGCCTTGAATCAGCGTATTGGCATCTTTAACAT-
1 TC-TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA-CCTT--CATC
* * ** * *
1780608 TCCTAAGCCCAATGTCGTTGGCCTTGTCTCAGCACATTGGCA--TTCTTC
1 T-CTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * * * *
1780656 T-TCAAGTCTAATGTTGCTAGCCATGAATCAGCACATTG
1 TCT-AAGTCCAATGTCGCTGGCCTTGAATCAGCATATTG
1780694 TCATTCTTCG
Statistics
Matches: 711, Mismatches: 120, Indels: 162
0.72 0.12 0.16
Matches are distributed among these distances:
38 1 0.00
39 192 0.27
43 4 0.01
44 1 0.00
45 1 0.00
46 1 0.00
47 29 0.04
48 165 0.23
49 204 0.29
50 4 0.01
51 1 0.00
52 107 0.15
53 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (49 bp):
TCTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
Found at i:1780129 original size:39 final size:39
Alignment explanation
Indices: 1780075--1780494 Score: 266
Period size: 39 Copynumber: 9.8 Consensus size: 39
1780065 ATCTCTCAGA
* *
1780075 CCAATGTCGTTGGCCTTGAATCAGCACT-TTGGCATAAGC
1 CCAATATCGCTGGCCTTGAATCAGCA-TATTGGCATAAGC
* *
1780114 CCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCA---------TAAGC
* * *
1780162 CCAATGTCGCTGGCCTTGAATCGGCACATTGGCATAAGC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCATAAGC
* *
1780201 CCAATATCGCTGGTCTTGAATCAGCATATTGGCACCTTTATCTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCATATTGG---C---A----TAAGC
* *
1780250 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATAAGC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCATAAGC
*
1780289 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCA---------TAAGC
* * * *
1780337 CCAATGTTGCTGGTCTTGAATCAGCACATTGGCATAAGC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCATAAGC
* * *
1780376 CCAATATCGCTAGCCTTGAATCAACATATTGGCACCTTGTTTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCA---------TAAGC
* * * *
1780424 CCAATGTCACTGGCCTTGAATCAGCACATTGGCACAAGC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCATAAGC
* *
1780463 CCAATATCACTAGCCTTGAATCAGCATATTGG
1 CCAATATCGCTGGCCTTGAATCAGCATATTGG
1780495 TACCTTTGTC
Statistics
Matches: 302, Mismatches: 41, Indels: 76
0.72 0.10 0.18
Matches are distributed among these distances:
38 1 0.00
39 163 0.54
42 1 0.00
43 1 0.00
45 1 0.00
46 1 0.00
48 101 0.33
49 33 0.11
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (39 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCATAAGC
Found at i:1780176 original size:87 final size:87
Alignment explanation
Indices: 1780022--1780548 Score: 775
Period size: 87 Copynumber: 6.0 Consensus size: 87
1780012 TCTTCATCTT
* * * * * * *
1780022 TAAGACCAATATTGCCGGCCTTGAATCAGTATATTGGCACCTTATCTCTCAGACCAATGTCGTTG
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTG
*
1780087 GCCTTGAATCAGCACTTTGGCA
66 GCCTTGAATCAGCACATTGGCA
*
1780109 TAAGCCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTG
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTG
*
1780174 GCCTTGAATCGGCACATTGGCA
66 GCCTTGAATCAGCACATTGGCA
* * *
1780196 TAAGCCCAATATCGCTGGTCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCGCT
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTGTCTCTAAGACCAATGTCGCT
1780261 GGCCTTGAATCAGCACATTGGCA
65 GGCCTTGAATCAGCACATTGGCA
*
1780284 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTTGCTG
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTG
*
1780349 GTCTTGAATCAGCACATTGGCA
66 GCCTTGAATCAGCACATTGGCA
* * * * *
1780371 TAAGCCCAATATCGCTAGCCTTGAATCAACATATTGGCACCTTGTTTTTAAGACCAATGTCACTG
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTG
1780436 GCCTTGAATCAGCACATTGGCA
66 GCCTTGAATCAGCACATTGGCA
* * * * * *
1780458 CAAGCCCAATATCACTAGCCTTGAATCAGCATATTGGTACCTTTGTCATCTTTAAAACCATTGTC
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTGTC-TC--TAAGACCAATGTC
1780523 GCTGGCCTTGAATCAGCACATTGGCA
62 GCTGGCCTTGAATCAGCACATTGGCA
1780549 CCTTCATCCT
Statistics
Matches: 399, Mismatches: 36, Indels: 6
0.90 0.08 0.01
Matches are distributed among these distances:
87 275 0.69
88 87 0.22
89 1 0.00
91 36 0.09
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (87 bp):
TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTG
GCCTTGAATCAGCACATTGGCA
Found at i:1780287 original size:175 final size:175
Alignment explanation
Indices: 1780022--1780650 Score: 796
Period size: 175 Copynumber: 3.5 Consensus size: 175
1780012 TCTTCATCTT
* * * * * * *
1780022 TAAGACCAATATTGCCGGCCTTGAATCAGTATATTGGCACC-TTATCTCTCAGACCAATGTCGTT
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCGCT
* *
1780086 GGCCTTGAATCAGCACTTTGGCATAAGCCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCT
66 GGCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCT
*
1780151 TGTCTCTAAGACCAATGTCGCTGGCCTTGAATCGGCACATTGGCA
131 TGTCTCTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
*
1780196 TAAGCCCAATATCGCTGGTCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCGCT
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCGCT
1780261 GGCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCT
66 GGCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCT
* *
1780326 TGTCTCTAAGACCAATGTTGCTGGTCTTGAATCAGCACATTGGCA
131 TGTCTCTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
* * *
1780371 TAAGCCCAATATCGCTAGCCTTGAATCAACATATTGGCACCTTGT-T-TTTAAGACCAATGTCAC
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-TATCTTTAAGACCAATGTCGC
* * * *
1780434 TGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCACTAGCCTTGAATCAGCATATTGGTACC
65 TGGCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC
* *
1780499 TTTGTCATCTTTAAAACCATTGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
130 -TTGTC-TC--TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGG------CA
* * * * * *
1780555 TCCTTAAGTCCAATATCGTTGGCCTTGAATCAGCGTATTGGCATCTTTAACATTCCTAAGCCCAA
1 ----TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC-TT--TAAGACCAA
* **
1780620 TGTCGTTGGCCTTGTCTCAGCACATTGGCAT
59 TGTCGCTGGCCTTGAATCAGCACATTGGCAT
1780651 TCTTCTTCAA
Statistics
Matches: 396, Mismatches: 38, Indels: 24
0.86 0.08 0.05
Matches are distributed among these distances:
174 113 0.29
175 171 0.43
176 3 0.01
178 33 0.08
184 2 0.01
187 1 0.00
188 37 0.09
190 2 0.01
192 34 0.09
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (175 bp):
TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCGCT
GGCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCT
TGTCTCTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
Found at i:1780406 original size:262 final size:263
Alignment explanation
Indices: 1779924--1780548 Score: 865
Period size: 262 Copynumber: 2.3 Consensus size: 263
1779914 ACTTTATCTT
* * * * * *
1779924 TAAGACCAATGTCGCTGGCCTTGAATCAACACATTGGCATCTTCATCTTTAAGACCAATGTCGCT
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCGCT
* *
1779989 GGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGACCAATATTGCCGGCCTTGAATCAGTAT
66 GGCCTTGAATCAGCACATTGG------CA---TTAAGACCAATATCGCCGGCCTTGAATCAGCAT
* * *
1780054 ATTGGCACCTTATCTCTCAGACCAATGTCGTTGGCCTTGAATCAGCACTTTGGCATAAGCCCAAT
122 ATTGGCACCTTATCTCTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATAAGCCCAAT
* * * *
1780119 ATCGTTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTGGCCTTGAATC
187 ATCGCTAGCCTTGAATCAACATATTGGCACCTTGTCTCTAAGACCAATGTCACTGGCCTTGAATC
*
1780184 GGCACATTGGCA
252 AGCACATTGGCA
*
1780196 TAAGCCCAATATCGCTGGTCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCGCT
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCGCT
* *
1780261 GGCCTTGAATCAGCACATTGGCA-TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC
66 GGCCTTGAATCAGCACATTGGCATTAAGACCAATATCGCCGGCCTTGAATCAGCATATTGGCACC
* * *
1780325 TTGTCTCTAAGACCAATGTTGCTGGTCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTAGC
131 TTATCTCTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTAGC
* *
1780390 CTTGAATCAACATATTGGCACCTTGTTTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTG
196 CTTGAATCAACATATTGGCACCTTGTCTCTAAGACCAATGTCACTGGCCTTGAATCAGCACATTG
1780455 GCA
261 GCA
* * * * * *
1780458 CAAGCCCAATATCACTAGCCTTGAATCAGCATATTGGTACCTTTGTCATCTTTAAAACCATTGTC
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TT-T-ATCTTTAAGACCAATGTC
1780523 GCTGGCCTTGAATCAGCACATTGGCA
63 GCTGGCCTTGAATCAGCACATTGGCA
1780549 CCTTCATCCT
Statistics
Matches: 319, Mismatches: 31, Indels: 13
0.88 0.09 0.04
Matches are distributed among these distances:
262 193 0.61
263 2 0.01
264 1 0.00
265 42 0.13
266 2 0.01
272 79 0.25
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (263 bp):
TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCGCT
GGCCTTGAATCAGCACATTGGCATTAAGACCAATATCGCCGGCCTTGAATCAGCATATTGGCACC
TTATCTCTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTAGC
CTTGAATCAACATATTGGCACCTTGTCTCTAAGACCAATGTCACTGGCCTTGAATCAGCACATTG
GCA
Found at i:1784569 original size:18 final size:18
Alignment explanation
Indices: 1784546--1784583 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1784536 GCCCGAAATG
1784546 ATCGGTGGTGACTCCAAA
1 ATCGGTGGTGACTCCAAA
1784564 ATCGGTGGTGACTCCAAA
1 ATCGGTGGTGACTCCAAA
1784582 AT
1 AT
1784584 TTCGGTCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (18 bp):
ATCGGTGGTGACTCCAAA
Found at i:1787541 original size:13 final size:13
Alignment explanation
Indices: 1787523--1787562 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1787513 ACAATGTTCT
1787523 TTGTATCGATACA
1 TTGTATCGATACA
* *
1787536 TTGTATCAATATA
1 TTGTATCGATACA
*
1787549 ATGTATCGATACA
1 TTGTATCGATACA
1787562 T
1 T
1787563 AGGTTACTAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1790085 original size:20 final size:20
Alignment explanation
Indices: 1790062--1790123 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
1790052 TGCTTTGTAT
*
1790062 TGATACATTGTATCAATACA
1 TGATACATTGTATCGATACA
*
1790082 TGAT-CATTGCATCGATACA
1 TGATACATTGTATCGATACA
*
1790101 TG-CACAATTGTATCGATACA
1 TGATAC-ATTGTATCGATACA
1790121 TGA
1 TGA
1790124 AACTGGCAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 16 0.46
20 19 0.54
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (20 bp):
TGATACATTGTATCGATACA
Found at i:1796486 original size:20 final size:21
Alignment explanation
Indices: 1796450--1796489 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1796440 TCTATAATTT
*
1796450 GTATTGATACAATAAGTGAAC
1 GTATCGATACAATAAGTGAAC
1796471 GTATCGATAC-ATAAGTGAA
1 GTATCGATACAATAAGTGAA
1796490 TGTTTTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.28
Consensus pattern (21 bp):
GTATCGATACAATAAGTGAAC
Found at i:1796500 original size:21 final size:20
Alignment explanation
Indices: 1796450--1796504 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
1796440 TCTATAATTT
1796450 GTATTGATACAATAAGTGAAC
1 GTATTGATAC-ATAAGTGAAC
* *
1796471 GTATCGATACATAAGTGAAT
1 GTATTGATACATAAGTGAAC
*
1796491 GTTTTTGATACATA
1 G-TATTGATACATA
1796505 TCTGAAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 10 0.34
21 19 0.66
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (20 bp):
GTATTGATACATAAGTGAAC
Found at i:1799310 original size:79 final size:79
Alignment explanation
Indices: 1799036--1799397 Score: 325
Period size: 79 Copynumber: 4.5 Consensus size: 79
1799026 AATCTCAGGA
* * * * ** * *
1799036 ATACTCTAACCCTATCATTTCCAAAGGGATACTCCAACCCTATTTTTACTTCCATAATGTTGAAT
1 ATACTCCAACCCCATCATTTTCGAAGGGATACTCCAACCCCGTTTTTACTTCCAAAATATTG-A-
* *
1799101 TTTTTTCACCATCGGGG
64 TTTTTT-ACCATCAGAG
* * * * *
1799118 ATACTCCAACCCGATCATTTTTG-AGAGGATACTCCAACCCCGTTTCTCCTTCCAAAAGCATTGA
1 ATACTCCAACCCCATCATTTTCGAAG-GGATACTCCAACCCCGTTTTTACTTCCAAAA-TATTG-
* *
1799182 ATTTTTCACCATCAGGG
63 ATTTTTTACCATCAGAG
* * * * * * *
1799199 ATACTCAAATCCCATCATTTTCGATGGAATACTCCAACCCCGTTTTTATTTTCAAAATATCGATT
1 ATACTCCAACCCCATCATTTTCGAAGGGATACTCCAACCCCGTTTTTACTTCCAAAATATTGATT
* *
1799264 TTTTAGCATTAGAG
66 TTTTACCATCAGAG
* *
1799278 ATATTCCAACCCCATCATTTTCGAAGGGATACTCCAACCCCGTTTTTACTTCCAAAATATTAATT
1 ATACTCCAACCCCATCATTTTCGAAGGGATACTCCAACCCCGTTTTTACTTCCAAAATATTGATT
*
1799343 TTTT-CCATCTTAGGG
66 TTTTACCATC--AGAG
* * * *
1799358 ATACTCTAACCCCACCATCTCCG-AGGAGATACTCCAACCC
1 ATACTCCAACCCCATCATTTTCGAAGG-GATACTCCAACCC
1799398 TGATTTTCAC
Statistics
Matches: 227, Mismatches: 47, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
78 3 0.01
79 76 0.33
80 37 0.16
81 56 0.25
82 50 0.22
83 5 0.02
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.33
Consensus pattern (79 bp):
ATACTCCAACCCCATCATTTTCGAAGGGATACTCCAACCCCGTTTTTACTTCCAAAATATTGATT
TTTTACCATCAGAG
Found at i:1805075 original size:18 final size:18
Alignment explanation
Indices: 1805052--1805095 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1805042 TAGAGGAAAG
1805052 AGAGAATAGA-AGAAAAAA
1 AGAGAA-AGAGAGAAAAAA
*
1805070 AGAGAAAGAGAGAACAAA
1 AGAGAAAGAGAGAAAAAA
1805088 AGAAGAAA
1 AG-AGAAA
1805096 AGAAAAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 3 0.13
18 15 0.65
19 5 0.22
ACGTcount: A:0.70, C:0.02, G:0.25, T:0.02
Consensus pattern (18 bp):
AGAGAAAGAGAGAAAAAA
Found at i:1805080 original size:26 final size:26
Alignment explanation
Indices: 1805047--1805104 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
1805037 CTATTTAGAG
* *
1805047 GAAAGAGAGAATAGAAGAAAAAAAGA
1 GAAAGAGAGAACAAAAGAAAAAAAGA
*
1805073 GAAAGAGAGAACAAAAGAAGAAAAGA
1 GAAAGAGAGAACAAAAGAAAAAAAGA
*
1805099 AAAAGA
1 GAAAGA
1805105 AGTCTAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.71, C:0.02, G:0.26, T:0.02
Consensus pattern (26 bp):
GAAAGAGAGAACAAAAGAAAAAAAGA
Found at i:1807475 original size:72 final size:72
Alignment explanation
Indices: 1807351--1807748 Score: 679
Period size: 72 Copynumber: 5.5 Consensus size: 72
1807341 GATGAAACGA
* * * *
1807351 TAATTCGAGATAATCTGCACGATAAATACAATCAACAACTATTTTTGCATATTTAAAACTACTAT
1 TAATCCGAGATAATCTGCACGATAACTACAATCAACAAATATTTCTGCATATTTAAAACTACTAT
1807416 CAACAAC
66 CAACAAC
* * *
1807423 TAATCCAAGATAATATGCACGATAACTACAATTAACAAATATTTCTGCATATTTAAAACTACTAT
1 TAATCCGAGATAATCTGCACGATAACTACAATCAACAAATATTTCTGCATATTTAAAACTACTAT
1807488 CAACAAC
66 CAACAAC
* *
1807495 TAATCCGAGATAATCTGCACGATAACTACAATCAACAAATATTTCTACATATTTAAAACTGCTAT
1 TAATCCGAGATAATCTGCACGATAACTACAATCAACAAATATTTCTGCATATTTAAAACTACTAT
1807560 CAACAAC
66 CAACAAC
1807567 TAATCCGAGATAATCTGCACGATAACTACAATCAACAAATATTTCTGCATATTTAAAACTACTAT
1 TAATCCGAGATAATCTGCACGATAACTACAATCAACAAATATTTCTGCATATTTAAAACTACTAT
*
1807632 CAATAAC
66 CAACAAC
*
1807639 TAACCCGAGATAATCTGCACGATAACTACAATCAACAAATATTTCTGCATATTTAAAACTACTAT
1 TAATCCGAGATAATCTGCACGATAACTACAATCAACAAATATTTCTGCATATTTAAAACTACTAT
1807704 CAACAAC
66 CAACAAC
* *
1807711 TAATCCGAGATAATTTGCACGATAACTACAAGCAACAA
1 TAATCCGAGATAATCTGCACGATAACTACAATCAACAA
1807749 CTTTGTATGC
Statistics
Matches: 306, Mismatches: 20, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 306 1.00
ACGTcount: A:0.44, C:0.21, G:0.07, T:0.28
Consensus pattern (72 bp):
TAATCCGAGATAATCTGCACGATAACTACAATCAACAAATATTTCTGCATATTTAAAACTACTAT
CAACAAC
Found at i:1808183 original size:15 final size:15
Alignment explanation
Indices: 1808160--1808201 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
1808150 CTGGGTAAAT
1808160 AGGTGGTGGATGCAC
1 AGGTGGTGGATGCAC
*
1808175 AGGTTGTGGATGCAC
1 AGGTGGTGGATGCAC
* *
1808190 GGGTGGTAGATG
1 AGGTGGTGGATG
1808202 GACAAGATCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.19, C:0.10, G:0.48, T:0.24
Consensus pattern (15 bp):
AGGTGGTGGATGCAC
Found at i:1808687 original size:7 final size:7
Alignment explanation
Indices: 1808616--1808684 Score: 120
Period size: 7 Copynumber: 9.9 Consensus size: 7
1808606 TTATATTATA
1808616 TGGCACT
1 TGGCACT
1808623 TGGCACT
1 TGGCACT
1808630 TGGCACT
1 TGGCACT
1808637 TGGCACT
1 TGGCACT
1808644 TGGCACT
1 TGGCACT
1808651 TGGCACT
1 TGGCACT
1808658 TGGCACT
1 TGGCACT
*
1808665 TGGCACG
1 TGGCACT
*
1808672 TGGCACG
1 TGGCACT
1808679 TGGCAC
1 TGGCAC
1808685 GTGCAGGTGC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 61 1.00
ACGTcount: A:0.14, C:0.29, G:0.32, T:0.25
Consensus pattern (7 bp):
TGGCACT
Found at i:1810848 original size:13 final size:13
Alignment explanation
Indices: 1810830--1810854 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1810820 ACACACTTTG
1810830 TGTATCGATACAA
1 TGTATCGATACAA
1810843 TGTATCGATACA
1 TGTATCGATACA
1810855 CAAAAAGTTG
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:1812802 original size:33 final size:34
Alignment explanation
Indices: 1812743--1812807 Score: 98
Period size: 33 Copynumber: 1.9 Consensus size: 34
1812733 CTACTTATGC
1812743 ATTAATATAATTAATAATATTATATTAATTTTTTA
1 ATTAATATAATTAATAATATTATATT-ATTTTTTA
*
1812778 ATTAAT-TAATT-ATATTATTATATTATTTTT
1 ATTAATATAATTAATAATATTATATTATTTTT
1812808 ATTTGTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 6 0.21
33 12 0.41
34 5 0.17
35 6 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (34 bp):
ATTAATATAATTAATAATATTATATTATTTTTTA
Found at i:1812804 original size:8 final size:9
Alignment explanation
Indices: 1812761--1812802 Score: 54
Period size: 8 Copynumber: 5.0 Consensus size: 9
1812751 AATTAATAAT
1812761 ATTATATTA
1 ATTATATTA
*
1812770 ATT-TTTTA
1 ATTATATTA
1812778 ATTA-ATTA
1 ATTATATTA
1812786 ATTATATT-
1 ATTATATTA
1812794 ATTATATTA
1 ATTATATTA
1812803 TTTTTATTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
8 22 0.79
9 6 0.21
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
ATTATATTA
Found at i:1823022 original size:12 final size:11
Alignment explanation
Indices: 1823005--1823031 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1822995 GATTAATAGA
1823005 TTTTTTTTTTC
1 TTTTTTTTTTC
1823016 TTTTTTTTTTC
1 TTTTTTTTTTC
1823027 TTTTT
1 TTTTT
1823032 GTTCATCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:1824608 original size:20 final size:23
Alignment explanation
Indices: 1824569--1824610 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 23
1824559 TAAATTTATC
1824569 TAATTATATGTTGATTTGATTTT
1 TAATTATATGTTGATTTGATTTT
1824592 TAATT-TAT-TTG-TTTGATTT
1 TAATTATATGTTGATTTGATTT
1824611 AATCTATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
21 3 0.16
22 3 0.16
23 5 0.26
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (23 bp):
TAATTATATGTTGATTTGATTTT
Found at i:1836241 original size:32 final size:32
Alignment explanation
Indices: 1836200--1836261 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
1836190 ATTAATAGGT
*
1836200 CATCAAGTTTCAACGTATTTAAGTTCAACGAA
1 CATCAAGTTTCAACCTATTTAAGTTCAACGAA
* *
1836232 CATCAAGTTTTAACCTCTTTAAGTTCAACG
1 CATCAAGTTTCAACCTATTTAAGTTCAACG
1836262 GAGTACTACA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (32 bp):
CATCAAGTTTCAACCTATTTAAGTTCAACGAA
Found at i:1840194 original size:16 final size:15
Alignment explanation
Indices: 1840115--1840212 Score: 82
Period size: 16 Copynumber: 6.7 Consensus size: 15
1840105 TTTTAATATC
*
1840115 AAATTTAAATTATTT
1 AAATTTAAATAATTT
* *
1840130 ACATCTTAAATTATCTT
1 AAAT-TTAAATAAT-TT
* *
1840147 AAATTCAAATAATCT
1 AAATTTAAATAATTT
1840162 AAATTTAAAT--TTT
1 AAATTTAAATAATTT
1840175 -AATTTAAAATAATTT
1 AAATTT-AAATAATTT
1840190 AAATTTAAA-AA-TT
1 AAATTTAAATAATTT
1840203 -AATTTAAATA
1 AAATTTAAATA
1840213 TTTTTAATTG
Statistics
Matches: 69, Mismatches: 7, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
12 13 0.19
13 9 0.13
14 2 0.03
15 19 0.28
16 21 0.30
17 5 0.07
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (15 bp):
AAATTTAAATAATTT
Found at i:1840219 original size:28 final size:28
Alignment explanation
Indices: 1840153--1840210 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
1840143 TCTTAAATTC
* **
1840153 AAATAATCTAAATTTAAATTTTAATTTA
1 AAATAATTTAAATTTAAAAATTAATTTA
1840181 AAATAATTTAAATTTAAAAATTAATTTA
1 AAATAATTTAAATTTAAAAATTAATTTA
1840209 AA
1 AA
1840211 TATTTTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (28 bp):
AAATAATTTAAATTTAAAAATTAATTTA
Found at i:1840662 original size:30 final size:30
Alignment explanation
Indices: 1840624--1840695 Score: 96
Period size: 28 Copynumber: 2.5 Consensus size: 30
1840614 CATCTCATTC
*
1840624 AAAAATATATATATATATAGTAA-AA-AAT
1 AAAAATATATATATATATATTAATAATAAT
*
1840652 AAAAATATATACATATATATTAATAATAAT
1 AAAAATATATATATATATATTAATAATAAT
*
1840682 ATAAATATAT-TATA
1 AAAAATATATATATA
1840696 AATACATGCA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 21 0.55
29 5 0.13
30 12 0.32
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (30 bp):
AAAAATATATATATATATATTAATAATAAT
Found at i:1841282 original size:25 final size:26
Alignment explanation
Indices: 1841226--1841296 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 26
1841216 TATTTTATTT
*
1841226 ATAAATATAATAAATATT-ATTATAA
1 ATAATTATAATAAATATTAATTATAA
*
1841251 TTAATTATAATAAATATTAACTT-TAA
1 ATAATTATAATAAATATTAA-TTATAA
*
1841277 AT-ATTAATAATAAAAATTAA
1 ATAATT-ATAATAAATATTAA
1841297 AATTATTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
25 19 0.49
26 18 0.46
27 2 0.05
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (26 bp):
ATAATTATAATAAATATTAATTATAA
Found at i:1841290 original size:13 final size:13
Alignment explanation
Indices: 1841232--1841296 Score: 55
Period size: 13 Copynumber: 5.1 Consensus size: 13
1841222 ATTTATAAAT
1841232 ATAATAAATATT-
1 ATAATAAATATTA
* *
1841244 ATTATAATTAATT-
1 ATAATAAAT-ATTA
1841257 ATAATAAATATTA
1 ATAATAAATATTA
*
1841270 ACT-TTAAATATTA
1 A-TAATAAATATTA
*
1841283 ATAATAAAAATTA
1 ATAATAAATATTA
1841296 A
1 A
1841297 AATTATTAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
12 11 0.26
13 30 0.71
14 1 0.02
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (13 bp):
ATAATAAATATTA
Found at i:1843609 original size:18 final size:17
Alignment explanation
Indices: 1843566--1843613 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
1843556 AATTTATATA
* *
1843566 AAAATATTTTTTATT-C
1 AAAATATTTTTAATTAT
1843582 AAAATATTTTTAATTAT
1 AAAATATTTTTAATTAT
1843599 AAAATTATTTTTAAT
1 AAAA-TATTTTTAAT
1843614 CACTATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 14 0.50
17 4 0.14
18 10 0.36
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
AAAATATTTTTAATTAT
Found at i:1844024 original size:10 final size:10
Alignment explanation
Indices: 1844009--1844037 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
1843999 AGAGATAAAA
1844009 TATATTTTTT
1 TATATTTTTT
1844019 TATATTTTTT
1 TATATTTTTT
1844029 TATATTTTT
1 TATATTTTT
1844038 ATTTTTTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
TATATTTTTT
Found at i:1844107 original size:28 final size:28
Alignment explanation
Indices: 1844069--1844130 Score: 70
Period size: 31 Copynumber: 2.1 Consensus size: 28
1844059 CCACTAAATT
* *
1844069 TTTAAATAATAATAATTAATTAATTAATTAA
1 TTTAAATAAAAATAA-T--TTAATAAATTAA
*
1844100 TTTAAATAAAAATAATTTAATAAATTTA
1 TTTAAATAAAAATAATTTAATAAATTAA
1844128 TTT
1 TTT
1844131 TAAAGTTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 13 0.46
30 1 0.04
31 14 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
TTTAAATAAAAATAATTTAATAAATTAA
Found at i:1844222 original size:16 final size:16
Alignment explanation
Indices: 1844201--1844231 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1844191 AAAATATAAC
1844201 TTAATAATAATTAAAT
1 TTAATAATAATTAAAT
1844217 TTAATAATAATTAAA
1 TTAATAATAATTAAA
1844232 AATAATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTAATAATAATTAAAT
Found at i:1844237 original size:16 final size:16
Alignment explanation
Indices: 1844202--1844237 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1844192 AAATATAACT
**
1844202 TAATAATAATTAAATT
1 TAATAATAATTAAAAA
1844218 TAATAATAATTAAAAA
1 TAATAATAATTAAAAA
1844234 TAAT
1 TAAT
1844238 TTTAAGATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATAATAATTAAAAA
Found at i:1844410 original size:29 final size:29
Alignment explanation
Indices: 1844351--1844461 Score: 111
Period size: 30 Copynumber: 3.7 Consensus size: 29
1844341 AAAATAATAA
* *
1844351 ATTAAGAAGATAATTATATTTTTTATCAAAT
1 ATTAA-AAAATAAATATATTTTTTAT-AAAT
1844382 -TTGAAAAAATAAATATATATTTTT-TAAAT
1 ATT-AAAAAATAAATATAT-TTTTTATAAAT
1844411 ATT-AAAAATAAATATATTTTTTTATAAAT
1 ATTAAAAAATAAATATA-TTTTTTATAAAT
* *
1844440 ATTTAAAAGATAAATATCTTTT
1 A-TTAAAAAATAAATATATTTT
1844462 ACTCCTTATA
Statistics
Matches: 69, Mismatches: 4, Indels: 15
0.78 0.05 0.17
Matches are distributed among these distances:
28 18 0.26
29 11 0.16
30 22 0.32
31 18 0.26
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.46
Consensus pattern (29 bp):
ATTAAAAAATAAATATATTTTTTATAAAT
Found at i:1844417 original size:28 final size:30
Alignment explanation
Indices: 1844360--1844456 Score: 112
Period size: 28 Copynumber: 3.3 Consensus size: 30
1844350 AATTAAGAAG
* *
1844360 ATAATTATAT-TTTTTATCAAAT-TTGAAAAA
1 ATAAATATATATTTTTAT-AAATATT-TAAAA
1844390 ATAAATATATATTTTT-TAAATA-TTAAAA
1 ATAAATATATATTTTTATAAATATTTAAAA
*
1844418 ATAAATATATTTTTTTATAAATATTTAAAA
1 ATAAATATATATTTTTATAAATATTTAAAA
1844448 GATAAATAT
1 -ATAAATAT
1844457 CTTTTACTCC
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
28 19 0.32
29 11 0.19
30 16 0.27
31 13 0.22
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (30 bp):
ATAAATATATATTTTTATAAATATTTAAAA
Found at i:1845753 original size:13 final size:13
Alignment explanation
Indices: 1845735--1845760 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1845725 CAATTATATT
1845735 TTTGAGTTTTAAA
1 TTTGAGTTTTAAA
1845748 TTTGAGTTTTAAA
1 TTTGAGTTTTAAA
1845761 CTCGAAAACA
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:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
TTTGAGTTTTAAA
Found at i:1845831 original size:19 final size:19
Alignment explanation
Indices: 1845809--1845869 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
1845799 GCTTTTCTTG
1845809 TTTTTTTAATTTTTATTTA
1 TTTTTTTAATTTTTATTTA
1845828 TTTTTTTAATTTTTATTT-
1 TTTTTTTAATTTTTATTTA
1845846 TATTTTTT-ATTATTT-TTTA
1 T-TTTTTTAATT-TTTATTTA
1845865 TTTTT
1 TTTTT
1845870 AAAAAATACA
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
18 11 0.28
19 28 0.72
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTTTAATTTTTATTTA
Found at i:1845835 original size:41 final size:41
Alignment explanation
Indices: 1845790--1845867 Score: 95
Period size: 41 Copynumber: 1.9 Consensus size: 41
1845780 TTAGTTTTTA
* * *
1845790 TTTT-ATTTTGCTTTTCTTGTTTTTTTAATTTTTATTTATTT
1 TTTTAATTTTGATTTTATT-TTTTATTAATTTTTATTTATTT
* *
1845831 TTTTAATTTTTATTTTATTTTTTATTATTTTTTATTT
1 TTTTAATTTTGATTTTATTTTTTATTAATTTTTATTT
1845868 TTAAAAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 20 0.65
42 11 0.35
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (41 bp):
TTTTAATTTTGATTTTATTTTTTATTAATTTTTATTTATTT
Found at i:1845844 original size:15 final size:13
Alignment explanation
Indices: 1845818--1845870 Score: 52
Period size: 15 Copynumber: 3.8 Consensus size: 13
1845808 GTTTTTTTAA
*
1845818 TTTTTATTTATTT
1 TTTTTTTTTATTT
1845831 TTTTAATTTTTATTT
1 TTTT--TTTTTATTT
1845846 TATTTTTTATTATTT
1 T-TTTTTT-TTATTT
*
1845861 TTTATTTTTA
1 TTTTTTTTTA
1845871 AAAAATACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
13 7 0.21
14 8 0.24
15 16 0.47
16 3 0.09
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTTTTTATTT
Found at i:1845864 original size:10 final size:10
Alignment explanation
Indices: 1845809--1845866 Score: 57
Period size: 11 Copynumber: 5.8 Consensus size: 10
1845799 GCTTTTCTTG
*
1845809 TTTTT-TTAA
1 TTTTTATTAT
1845818 TTTTTATTTAT
1 TTTTTA-TTAT
*
1845829 TTTTT-TAAT
1 TTTTTATTAT
*
1845838 TTTTATTTTAT
1 TTTT-TATTAT
1845849 TTTTTATTAT
1 TTTTTATTAT
1845859 TTTTTATT
1 TTTTTATT
1845867 TTTAAAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
9 12 0.29
10 14 0.34
11 15 0.37
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTATTAT
Found at i:1846628 original size:16 final size:16
Alignment explanation
Indices: 1846550--1846672 Score: 61
Period size: 16 Copynumber: 7.7 Consensus size: 16
1846540 TTATACTTAA
* *
1846550 TTTAAATTCAAGTTAT
1 TTTAAATTTAAATTAT
** *
1846566 TTTTTATTTAAATAAT
1 TTTAAATTTAAATTAT
* * *
1846582 TTTGAAA-TCAAATCAA
1 TTT-AAATTTAAATTAT
* * *
1846598 TTTATATATATATTAT
1 TTTAAATTTAAATTAT
*
1846614 TTTAAATTTAGATTAT
1 TTTAAATTTAAATTAT
* * **
1846630 TTTGAGTTTATTTTAT
1 TTTAAATTTAAATTAT
*
1846646 TTTATAA-TTAAATTAA
1 TTTA-AATTTAAATTAT
1846662 TTTAAATTTAA
1 TTTAAATTTAA
1846673 TTTAAATTTA
Statistics
Matches: 75, Mismatches: 28, Indels: 8
0.68 0.25 0.07
Matches are distributed among these distances:
15 4 0.05
16 69 0.92
17 2 0.03
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.54
Consensus pattern (16 bp):
TTTAAATTTAAATTAT
Found at i:1846674 original size:11 final size:11
Alignment explanation
Indices: 1846653--1846683 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1846643 TATTTTATAA
1846653 TTAAA-TTAAT
1 TTAAATTTAAT
1846663 TTAAATTTAAT
1 TTAAATTTAAT
1846674 TTAAATTTAA
1 TTAAATTTAA
1846684 ATCAATTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.25
11 15 0.75
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:1853163 original size:16 final size:16
Alignment explanation
Indices: 1853142--1853172 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1853132 TAGCCATTAC
*
1853142 TTTAACTAAGCACTAT
1 TTTAACTAACCACTAT
1853158 TTTAACTAACCACTA
1 TTTAACTAACCACTA
1853173 CACATGCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.35
Consensus pattern (16 bp):
TTTAACTAACCACTAT
Found at i:1856609 original size:50 final size:50
Alignment explanation
Indices: 1856534--1856792 Score: 407
Period size: 50 Copynumber: 5.2 Consensus size: 50
1856524 AGTTATTGTC
*
1856534 ATTGTTGACTA-TCATTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1 ATTGTTGACAATTC-TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
1856584 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGA-AGGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATA
* *
1856634 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTAGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* *
1856684 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGA-AGGAGGTGGTCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATA
*
1856734 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1856784 ATTGTTGAC
1 ATTGTTGAC
1856793 TCTAAGTATA
Statistics
Matches: 193, Mismatches: 11, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
49 1 0.01
50 190 0.98
51 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (50 bp):
ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Found at i:1856658 original size:100 final size:100
Alignment explanation
Indices: 1856534--1856792 Score: 466
Period size: 100 Copynumber: 2.6 Consensus size: 100
1856524 AGTTATTGTC
* *
1856534 ATTGTTGACTA-TCATTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTC
1 ATTGTTGACAATTC-TTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACGATTC
1856598 TTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
65 TTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
*
1856634 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTAGCCATAATTGTTGACGATTCT
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACGATTCT
*
1856699 TCACCAACCTTTGACAATAGAAGGAGGTGGTCATA
66 TCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
1856734 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGAC
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGAC
1856793 TCTAAGTATA
Statistics
Matches: 153, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
100 151 0.99
101 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (100 bp):
ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACGATTCT
TCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
Found at i:1861266 original size:50 final size:50
Alignment explanation
Indices: 1861191--1861449 Score: 416
Period size: 50 Copynumber: 5.2 Consensus size: 50
1861181 AGTTATTGTC
*
1861191 ATTGTTGACTA-TCATTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1 ATTGTTGACAATTC-TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* *
1861241 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGA-AGGAAGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATA
*
1861291 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
1861341 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGA-AGGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATA
*
1861391 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1861441 ATTGTTGAC
1 ATTGTTGAC
1861450 TCTAAGTATA
Statistics
Matches: 195, Mismatches: 9, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
49 1 0.01
50 192 0.98
51 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.29
Consensus pattern (50 bp):
ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Found at i:1861364 original size:100 final size:100
Alignment explanation
Indices: 1861191--1861449 Score: 475
Period size: 100 Copynumber: 2.6 Consensus size: 100
1861181 AGTTATTGTC
* *
1861191 ATTGTTGACTA-TCATTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTC
1 ATTGTTGACAATTC-TTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACGATTC
1861255 TTCACCAACCTTTGACAATAGAAGGAAGTGGCCATA
65 TTCACCAACCTTTGACAATAGAAGGAAGTGGCCATA
1861291 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACGATTCT
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACGATTCT
*
1861356 TCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
66 TCACCAACCTTTGACAATAGAAGGAAGTGGCCATA
1861391 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGAC
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGAC
1861450 TCTAAGTATA
Statistics
Matches: 155, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
100 153 0.99
101 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.29
Consensus pattern (100 bp):
ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACGATTCT
TCACCAACCTTTGACAATAGAAGGAAGTGGCCATA
Found at i:1868755 original size:2 final size:2
Alignment explanation
Indices: 1868748--1868781 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1868738 CAAGATAAGT
1868748 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1868782 CACACACTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1869934 original size:23 final size:24
Alignment explanation
Indices: 1869908--1869955 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
1869898 AATTTAGTAG
1869908 TATGGTCAC-AAACTTTATACTAT
1 TATGGTCACAAAACTTTATACTAT
*
1869931 TATGGTCACAAAACTTTATATTAT
1 TATGGTCACAAAACTTTATACTAT
1869955 T
1 T
1869956 GTCTTCATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (24 bp):
TATGGTCACAAAACTTTATACTAT
Found at i:1871252 original size:20 final size:20
Alignment explanation
Indices: 1871227--1871266 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1871217 TGGAAGCCTA
1871227 GTAAACTTCTTAGGTGCTCG
1 GTAAACTTCTTAGGTGCTCG
* *
1871247 GTAAACTTTTTGGGTGCTCG
1 GTAAACTTCTTAGGTGCTCG
1871267 ACAGATCATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.38
Consensus pattern (20 bp):
GTAAACTTCTTAGGTGCTCG
Found at i:1874203 original size:15 final size:16
Alignment explanation
Indices: 1874167--1874210 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
1874157 TTTTCAATCG
1874167 CAAAAAA-ATTTTGGT
1 CAAAAAATATTTTGGT
*
1874182 GACAAAAATATTTT-GT
1 CA-AAAAATATTTTGGT
1874198 CAAAAAATATTTT
1 CAAAAAATATTTT
1874211 TTTTAAAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 12 0.48
16 8 0.32
17 5 0.20
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.36
Consensus pattern (16 bp):
CAAAAAATATTTTGGT
Found at i:1875921 original size:14 final size:14
Alignment explanation
Indices: 1875902--1875930 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1875892 CAATCTATAT
1875902 ATAGAAATAAAAAA
1 ATAGAAATAAAAAA
1875916 ATAGAAATAAAAAA
1 ATAGAAATAAAAAA
1875930 A
1 A
1875931 CAAGTAATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (14 bp):
ATAGAAATAAAAAA
Found at i:1881710 original size:14 final size:16
Alignment explanation
Indices: 1881691--1881728 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1881681 ATATTTTGAC
1881691 TTTTA-AAAAAG-TCA
1 TTTTATAAAAAGATCA
1881705 TTTTAATAAAAAGATCA
1 TTTT-ATAAAAAGATCA
1881722 TTTTATA
1 TTTTATA
1881729 TTTCTTGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 4 0.19
15 1 0.05
16 9 0.43
17 7 0.33
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (16 bp):
TTTTATAAAAAGATCA
Found at i:1891808 original size:2 final size:2
Alignment explanation
Indices: 1891789--1891825 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1891779 TGTATTTTTA
* *
1891789 TG TG TT TG TG TT TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1891826 AATAACTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.43, T:0.57
Consensus pattern (2 bp):
TG
Found at i:1892503 original size:17 final size:16
Alignment explanation
Indices: 1892460--1892503 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
1892450 CCTGTGTGTT
*
1892460 AGAACAGAAAACAGTTA
1 AGAA-AGAAAACAGCTA
*
1892477 AGAGAGAAAACAGCTA
1 AGAAAGAAAACAGCTA
1892493 AGGAAAGAAAA
1 A-GAAAGAAAA
1892504 AGAACAGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.61, C:0.09, G:0.23, T:0.07
Consensus pattern (16 bp):
AGAAAGAAAACAGCTA
Found at i:1893120 original size:24 final size:25
Alignment explanation
Indices: 1893088--1893135 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
1893078 CTTAGCAGTT
1893088 TCACGG-TTTCATTTCAGT-TCCTTC
1 TCACGGTTTTCA-TTCAGTATCCTTC
*
1893112 TCACTGTTTTCATTCAGTATCCTT
1 TCACGGTTTTCATTCAGTATCCTT
1893136 ATATACAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.15, C:0.27, G:0.10, T:0.48
Consensus pattern (25 bp):
TCACGGTTTTCATTCAGTATCCTTC
Found at i:1896513 original size:18 final size:19
Alignment explanation
Indices: 1896492--1896529 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1896482 TTTTAAAATA
*
1896492 ATATTTTAT-ATTAATTTT
1 ATATTTTATAATTAAATTT
1896510 ATATTTTATAATTAAATTT
1 ATATTTTATAATTAAATTT
1896529 A
1 A
1896530 AATAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATATTTTATAATTAAATTT
Found at i:1896607 original size:16 final size:15
Alignment explanation
Indices: 1896586--1896615 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1896576 AATTTTATAC
1896586 ATAAATTTAACTTAAT
1 ATAAATTTAA-TTAAT
1896602 ATAAATTTAATTAA
1 ATAAATTTAATTAA
1896616 AAATATTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
ATAAATTTAATTAAT
Found at i:1897708 original size:17 final size:15
Alignment explanation
Indices: 1897653--1897741 Score: 63
Period size: 12 Copynumber: 6.3 Consensus size: 15
1897643 AATATAGTAT
1897653 TATATAAAA-ATT-A
1 TATATAAAATATTAA
1897666 -ATATAAAATA--AA
1 TATATAAAATATTAA
*
1897678 TATATCATAA-ATTACA
1 TATAT-AAAATATTA-A
1897694 TAATATAAAATATTAA
1 T-ATATAAAATATTAA
1897710 TATATAAAA-ATT--
1 TATATAAAATATTAA
1897722 TATATAAACAT-TTAA
1 TATATAAA-ATATTAA
1897737 TATAT
1 TATAT
1897742 TATATATAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 24
0.70 0.02 0.28
Matches are distributed among these distances:
12 17 0.28
13 9 0.15
14 6 0.10
15 14 0.23
16 7 0.11
17 8 0.13
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
TATATAAAATATTAA
Found at i:1897736 original size:27 final size:26
Alignment explanation
Indices: 1897653--1897741 Score: 81
Period size: 27 Copynumber: 3.2 Consensus size: 26
1897643 AATATAGTAT
* *
1897653 TATATAAAAATTAATATAAAA-TAAA
1 TATATAAAAATTTATATAAAATTTAA
*
1897678 TATATCATAAATTACATAATATAAAATATTAA
1 TATAT-AAAAATT---T-ATATAAAAT-TTAA
1897710 TATATAAAAATTTATATAAACATTTAA
1 TATATAAAAATTTATATAAA-ATTTAA
1897737 TATAT
1 TATAT
1897742 TATATATAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
25 5 0.10
26 6 0.12
27 16 0.31
28 3 0.06
30 8 0.15
31 6 0.12
32 8 0.15
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (26 bp):
TATATAAAAATTTATATAAAATTTAA
Found at i:1897762 original size:57 final size:56
Alignment explanation
Indices: 1897629--1897762 Score: 130
Period size: 57 Copynumber: 2.3 Consensus size: 56
1897619 CACAACGTTA
*
1897629 ATATAATATAAAA-AAATATAGTATTATATAAAAATTAATATAAAATAAATATATCAT
1 ATATAAT-TAAAATAAATATA-TAATATATAAAAATTAATATAAAATAAATATATCAT
* * * * *
1897686 AAATTACA-TAATATAAA-ATATTAATATATAAAAATTTATATAAACATTTAATATATTAT
1 ATA-TA-ATTAAAATAAATATA-TAATATATAAAAATTAATATAAA-A-TAAATATATCAT
1897745 ATATAATTAAAATAAATA
1 ATATAATTAAAATAAATA
1897763 AAAACATATT
Statistics
Matches: 61, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
57 31 0.51
58 16 0.26
59 14 0.23
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (56 bp):
ATATAATTAAAATAAATATATAATATATAAAAATTAATATAAAATAAATATATCAT
Found at i:1898199 original size:6 final size:6
Alignment explanation
Indices: 1898183--1898231 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
1898173 ACAACTTTTA
* *
1898183 AAATA- AAATAT AAATAT AAA-AT -AATAT TAATAT TAATAT -AATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
1898227 AAATA
1 AAATA
1898232 AAACATATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
4 2 0.05
5 14 0.35
6 24 0.60
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
AAATAT
Found at i:1900613 original size:21 final size:21
Alignment explanation
Indices: 1900587--1900637 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
1900577 AGGGAGTTAA
1900587 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGCAACTTGGAC
*
1900608 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGCAACTTGGAC
1900629 AAAAA-AGAA
1 AAAAAGAGAA
1900638 ACAGCATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.59, C:0.10, G:0.22, T:0.10
Consensus pattern (21 bp):
AAAAAGAGAAGCAACTTGGAC
Found at i:1900672 original size:16 final size:16
Alignment explanation
Indices: 1900643--1900685 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
1900633 AAGAAACAGC
** *
1900643 ATATATATTTATATTT
1 ATATATATACATATAT
*
1900659 ATTTATATACATATAT
1 ATATATATACATATAT
1900675 ATATATATACA
1 ATATATATACA
1900686 CGAACATAGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATATATACATATAT
Found at i:1902304 original size:22 final size:22
Alignment explanation
Indices: 1902276--1902317 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1902266 GTTCAAACTC
1902276 TGTTCTATTACTTGAGTATCAA
1 TGTTCTATTACTTGAGTATCAA
1902298 TGTTCTATTACTTGAGTATC
1 TGTTCTATTACTTGAGTATC
1902318 GACGTCCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.48
Consensus pattern (22 bp):
TGTTCTATTACTTGAGTATCAA
Found at i:1903675 original size:20 final size:20
Alignment explanation
Indices: 1903652--1903785 Score: 69
Period size: 20 Copynumber: 6.6 Consensus size: 20
1903642 CATTATGCTT
1903652 TGTATCGATACAATGTGTCA
1 TGTATCGATACAATGTGTCA
* *
1903672 TGTATCGATACAAACAGTGACA
1 TGTATCGATAC-AA-TGTGTCA
* * * *
1903694 GGGTAGCTACTGCCAAT-T-TCA
1 -TGTATCGA-T-ACAATGTGTCA
*
1903715 TGTATCGATACAAT-TGTATA
1 TGTATCGATACAATGTGT-CA
**
1903735 TGTATCGATACAATG-AACA
1 TGTATCGATACAATGTGTCA
* ** *
1903754 TGTATCGATACAAAGCATAA
1 TGTATCGATACAATGTGTCA
1903774 TGTATCGATACA
1 TGTATCGATACA
1903786 TCTAGATGTG
Statistics
Matches: 86, Mismatches: 19, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
18 5 0.06
19 17 0.20
20 45 0.52
21 4 0.05
22 6 0.07
23 5 0.06
24 3 0.03
25 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (20 bp):
TGTATCGATACAATGTGTCA
Found at i:1908958 original size:71 final size:72
Alignment explanation
Indices: 1908865--1909008 Score: 236
Period size: 73 Copynumber: 2.0 Consensus size: 72
1908855 GGTACATAAC
*
1908865 GAATACGACTGCTCTTTAGCCTTTTAT-AAAGGATGAATTCTTTAACCTTCAAAACTTAAAATAG
1 GAATACCACTGCTCTTTAGCCTTTTATAAAAGGATGAATTCTTTAACCTTCAAAACTTAAAATAG
1908929 ATGACAA
66 ATGACAA
* * *
1908936 GAATACCACTGTTCTTTAGCCTTTTATAAAAAGGATGAATTCTTTAGCCTTCAATACTTAAAATA
1 GAATACCACTGCTCTTTAGCCTTTTAT-AAAAGGATGAATTCTTTAACCTTCAAAACTTAAAATA
1909001 GATGACAA
65 GATGACAA
1909009 TAATGGGAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
71 25 0.37
73 42 0.63
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (72 bp):
GAATACCACTGCTCTTTAGCCTTTTATAAAAGGATGAATTCTTTAACCTTCAAAACTTAAAATAG
ATGACAA
Found at i:1910621 original size:333 final size:332
Alignment explanation
Indices: 1909998--1910644 Score: 1231
Period size: 333 Copynumber: 1.9 Consensus size: 332
1909988 AAAGAGGAAA
*
1909998 TGCAATCATTTTGGTATGAATGCTATGCAAACAAATTAAACAGCAATCAACACCATAAATGAATA
1 TGCAATCATTTTGGTATGAATGCTATGCAAACAAATTAAACAGCAAGCAACACCATAAATGAATA
* *
1910063 AATAATTTCAAATATCCAAAAACTTCTACAATCAATTAGACTTTCATGTTGGCCAAAGTTCAAAA
66 AATAATTTCAAATATCCAAAAACCTCTACAATCAATTAGACTTTCATGTTGGCCAAACTTCAAAA
1910128 AGCTTGAAACTTTGAAACTTGCAAAAAGCTAACTTCCTTAAAAGTGAAATAGATCTTAAAGTTGC
131 AGCTTGAAACTTTGAAACTTGCAAAAAGCTAACTTCCTTAAAAGTGAAATAGATCTTAAAGTTGC
*
1910193 AATTATTGTCTCTTGTTCACTTGAAGAATATGATGTATTTTTATATATAGCATCATTATTGAGTG
196 AATTATTGTCTCCTGTTCACTTGAAGAATATGATGTATTTTTATATATAGCATCATTATTGAGTG
1910258 CGACATCAACAGCTATGACCTGAAGTACATCTTCGAGCTCATATTGCCGAGTTTCATTTTTGAAA
261 CGACATCAACAGCTATGACCTGAAGTACATCTTCGAGCTCATATTGCCGAGTTTCATTTTTGAAA
1910323 CTTTGAG
326 CTTTGAG
1910330 TGCAATCATTTTGGTATGAATGCTATGCAAACAAATTAAACAGCAAGCAACACCATAAATGAATA
1 TGCAATCATTTTGGTATGAATGCTATGCAAACAAATTAAACAGCAAGCAACACCATAAATGAATA
1910395 AATAATTTCAAATATCCAAAAACCTCTACAATCAATTAGACTTTCATGTTGGCCAAACTTCAAAA
66 AATAATTTCAAATATCCAAAAACCTCTACAATCAATTAGACTTTCATGTTGGCCAAACTTCAAAA
*
1910460 AGCTTGAAACTTTGAAAACTTGCAAAAAGCTAACTTCCTTAAAAGTGAAATGGATCTTAAAGTTG
131 AGCTTGAAACTTTG-AAACTTGCAAAAAGCTAACTTCCTTAAAAGTGAAATAGATCTTAAAGTTG
*
1910525 CAATTATTGTCTCCTGTTCACTTGAAGAATATGATGTATTTTTTTATATAGCATCATTATTGAGT
195 CAATTATTGTCTCCTGTTCACTTGAAGAATATGATGTATTTTTATATATAGCATCATTATTGAGT
1910590 GCGACATCAACAGCTATGACCTGAAGTACATCTTCGAGCTCATATTGCCGAGTTT
260 GCGACATCAACAGCTATGACCTGAAGTACATCTTCGAGCTCATATTGCCGAGTTT
1910645 TAGGAGAAGT
Statistics
Matches: 308, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
332 141 0.46
333 167 0.54
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (332 bp):
TGCAATCATTTTGGTATGAATGCTATGCAAACAAATTAAACAGCAAGCAACACCATAAATGAATA
AATAATTTCAAATATCCAAAAACCTCTACAATCAATTAGACTTTCATGTTGGCCAAACTTCAAAA
AGCTTGAAACTTTGAAACTTGCAAAAAGCTAACTTCCTTAAAAGTGAAATAGATCTTAAAGTTGC
AATTATTGTCTCCTGTTCACTTGAAGAATATGATGTATTTTTATATATAGCATCATTATTGAGTG
CGACATCAACAGCTATGACCTGAAGTACATCTTCGAGCTCATATTGCCGAGTTTCATTTTTGAAA
CTTTGAG
Found at i:1914596 original size:29 final size:31
Alignment explanation
Indices: 1914553--1914610 Score: 75
Period size: 29 Copynumber: 1.9 Consensus size: 31
1914543 TAAAATTTAA
* *
1914553 AAAGATTATTCTTTTTAGATAAAAAAATGAG
1 AAAGATTATTCTTTTCAAATAAAAAAATGAG
*
1914584 AAAG-TTATT-TTTTCAAATAACAAAATG
1 AAAGATTATTCTTTTCAAATAAAAAAATG
1914611 GGTCATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 15 0.62
30 5 0.21
31 4 0.17
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.36
Consensus pattern (31 bp):
AAAGATTATTCTTTTCAAATAAAAAAATGAG
Done.