Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 212 of 221
Found at i:61904714 original size:6 final size:6
Alignment explanation
Indices: 61904698--61904738 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
61904688 CTGTGAGTTA
* *
61904698 CTGTT- CTGTTG CTGTTG CTGTTG CAGTTG CTGCTG CTGTTG
1 CTGTTG CTGTTG CTGTTG CTGTTG CTGTTG CTGTTG CTGTTG
61904739 ATGCAACTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.02, C:0.20, G:0.32, T:0.46
Consensus pattern (6 bp):
CTGTTG
Found at i:61905382 original size:30 final size:30
Alignment explanation
Indices: 61905346--61905403 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
61905336 ATCACATTAT
* *
61905346 TTAGATTCCAAATATACAAGTAATATGAAC
1 TTAGATTCCAAATAAACAAGTAAAATGAAC
*
61905376 TTAGATTCCAAATAAATAAGTAAAATGA
1 TTAGATTCCAAATAAACAAGTAAAATGA
61905404 CCCGAGTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.29
Consensus pattern (30 bp):
TTAGATTCCAAATAAACAAGTAAAATGAAC
Found at i:61906586 original size:6 final size:6
Alignment explanation
Indices: 61906420--61906583 Score: 178
Period size: 6 Copynumber: 28.3 Consensus size: 6
61906410 CTGTGGTGGC
* * *
61906420 TGCTGC TGCTGT TGCTG- T--TGT TGCTGC TGTTGT TGCTGT TGCTGT
1 TGCTGT TGCTGT TGCTGT TGCTGT TGCTGT TGCTGT TGCTGT TGCTGT
* *
61906465 TGTTGT TGTTGT TGCTGT TGCTGT TGCTGT TGCTGT TGCTGT TGC---
1 TGCTGT TGCTGT TGCTGT TGCTGT TGCTGT TGCTGT TGCTGT TGCTGT
* * * *
61906510 TGCTGT TGCTGT TGCTGT TGCTGC TGCTGT TGCTGC TGCTGT TGTTGC
1 TGCTGT TGCTGT TGCTGT TGCTGT TGCTGT TGCTGT TGCTGT TGCTGT
* * *
61906558 TGCTGT TGTTGC TGCTGT TGTTGT TG
1 TGCTGT TGCTGT TGCTGT TGCTGT TG
61906584 TTGGGCATGC
Statistics
Matches: 132, Mismatches: 20, Indels: 12
0.80 0.12 0.07
Matches are distributed among these distances:
3 5 0.04
4 1 0.01
5 1 0.01
6 125 0.95
ACGTcount: A:0.00, C:0.16, G:0.34, T:0.50
Consensus pattern (6 bp):
TGCTGT
Found at i:61906686 original size:12 final size:12
Alignment explanation
Indices: 61906624--61906687 Score: 56
Period size: 12 Copynumber: 5.1 Consensus size: 12
61906614 CATCTGCAGT
61906624 TGTTGCTGCTGC
1 TGTTGCTGCTGC
* *
61906636 TGTTGCTGTTGA
1 TGTTGCTGCTGC
* *
61906648 TGTTGAGGCTGTTGA
1 TGTT---GCTGCTGC
*
61906663 GGTTGCTGCTGC
1 TGTTGCTGCTGC
61906675 TGTTGCTGCTGC
1 TGTTGCTGCTGC
61906687 T
1 T
61906688 CCCGTGCTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
12 32 0.74
15 11 0.26
ACGTcount: A:0.05, C:0.17, G:0.36, T:0.42
Consensus pattern (12 bp):
TGTTGCTGCTGC
Found at i:61908651 original size:10 final size:10
Alignment explanation
Indices: 61908639--61908673 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
61908629 TTTTGAGAGC
61908639 TTTTTT-TTT
1 TTTTTTCTTT
*
61908648 CTTTTTCTTT
1 TTTTTTCTTT
61908658 TTTTTTCTTT
1 TTTTTTCTTT
61908668 TTTTTT
1 TTTTTT
61908674 TTGGTGTATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 5 0.22
10 18 0.78
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:61908657 original size:16 final size:16
Alignment explanation
Indices: 61908638--61908675 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
61908628 TTTTTGAGAG
61908638 CTTTTTTTTTCTTTTT
1 CTTTTTTTTTCTTTTT
61908654 CTTTTTTTTTCTTTTT
1 CTTTTTTTTTCTTTTT
61908670 -TTTTTT
1 CTTTTTT
61908676 GGTGTATGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (16 bp):
CTTTTTTTTTCTTTTT
Found at i:61912392 original size:31 final size:31
Alignment explanation
Indices: 61912352--61912474 Score: 101
Period size: 31 Copynumber: 4.0 Consensus size: 31
61912342 TTAAAATGAG
*
61912352 TATAATTGAATCAAC-ATTAAAGTTTCATGTA
1 TATAATTGAA-CAACAATCAAAGTTTCATGTA
* * *
61912383 TATATTTGAACCACAATCAAAGTTTCATGTG
1 TATAATTGAACAACAATCAAAGTTTCATGTA
* * * *
61912414 CACAATTGCACCA-AATCAAAG-TTCATGTA
1 TATAATTGAACAACAATCAAAGTTTCATGTA
* * *
61912443 TCTAATTGCACATTCAATCAAAG-TTCATGTA
1 TATAATTGAACA-ACAATCAAAGTTTCATGTA
61912474 T
1 T
61912475 CATTTTGAGA
Statistics
Matches: 75, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
29 15 0.20
30 11 0.15
31 49 0.65
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (31 bp):
TATAATTGAACAACAATCAAAGTTTCATGTA
Found at i:61921498 original size:249 final size:240
Alignment explanation
Indices: 61920719--61921501 Score: 568
Period size: 242 Copynumber: 3.2 Consensus size: 240
61920709 CCATATCTAA
* * * *
61920719 CATATCCCTAAGCTACACCTATTTATTGTTTAGGCACTTAATTCAACAATTAAAAAGTGCCACTT
1 CATATCCCTAAACCACACCTATTTCTTGTTTAGGCACTTAATTCAACAACTAAAAAGTGCCACTT
* * * * * ** *
61920784 AACAGTCGGGTGACCAAAAAGAACAATTTCGAAAAGTTTAGTGACCAATTTGTAA-TTTTTTTAG
66 AACAGTCGAGTGA-CAAAAA-AACAATTTCAAAAAGTTCAATGACCAAATTACAACATTTTTTAG
* * * * *
61920848 TTAA-TGGGCCAAAATAAAAACTTAGCCATAGTTTAGTGA-CTAATGACATATTTATTCCTTTTT
129 TTAAGT-GACCAAAACAAAAACTTACCCATAATTTAGT-ATCTAATGACATATTTA-TCCTTCTT
* * * * * ** ** ** ** *
61920911 AATACAACATTGAGGGTGAGAGACGGGAGTCACATGGT-TTGAACCCGTATCAAAT
191 AATACAATATTAAAGAT--GCGACTTGA---AC-CCGTATCAAACGAGTATCATAT
** * * * * *
61920966 GGGTAT-CGT--ATCATATCC--CTTCTTGTTTAGGCACTTAATTCAACAATTAAAAAGTGCCAC
1 -CATATCCCTAAACCACA-CCTATTTCTTGTTTAGGCACTTAATTCAACAACTAAAAAGTGCCAC
* * * * * * *
61921026 TTAATAGTCGGGTGACAAAAAAATAATTTCAAAAAGTTTAGTGACCAAATTGCAACATTTTTTGG
64 TTAACAGTCGAGTGACAAAAAAACAATTTCAAAAAGTTCAATGACCAAATTACAACATTTTTTAG
* ** * * *
61921091 TTAAGTGACCGAAATGAAAACTTACCCATAATTTAGTGTCTAATGGCGTATTTATCCTTCTTAAT
129 TTAAGTGACCAAAACAAAAACTTACCCATAATTTAGTATCTAATGACATATTTATCCTTCTTAAT
* * * * * *
61921156 ACAATGTTGAAGGTGTGACTTGAACTCGTGTCAAACGAGTATCATAT
194 ACAATATTAAAGATGCGACTTGAACCCGTATCAAACGAGTATCATAT
* * * * *
61921203 CATATCCCTAAGCCACGCCTATTTCTTGTTTAGGCACTAAATTCAACAACTAAAAAGTGTCATTT
1 CATATCCCTAAACCACACCTATTTCTTGTTTAGGCACTTAATTCAACAACTAAAAAGTGCCACTT
* *
61921268 AACAGTCGAGTGACCAAAAAAACAATTTCAAAAAAGTTCAATGACTAAATTATAAC-TTTTTTAG
66 AACAGTCGAGTGA-CAAAAAAACAATTTC-AAAAAGTTCAATGACCAAATTACAACATTTTTTAG
* * * *
61921332 TTAAGTG-CCTAAAACAAAAACTCT-TCCATAATTTAGTCAT-TAATGATATAATTTGCTCTTTT
129 TTAAGTGACC-AAAACAAAAACT-TACCCATAATTTAGT-ATCTAATGACAT-ATTT-ATC-CTT
* * * *
61921394 TTTAATACAATATTAAAGATGAACGACTGAATTAACCCGTATCAAATGAGTGTCATAT
188 CTTAATACAATATTAAAGATG--CGACT---TGAACCCGTATCAAACGAGTATCATAT
*
61921452 CATA-CTCTTAAACCACACCTATTTCTTGTTTAGGCACTTAATTCAACAAC
1 CATATC-CCTAAACCACACCTATTTCTTGTTTAGGCACTTAATTCAACAAC
61921502 GCGGGTTCAA
Statistics
Matches: 429, Mismatches: 82, Indels: 47
0.77 0.15 0.08
Matches are distributed among these distances:
236 6 0.01
237 16 0.04
238 2 0.00
239 2 0.00
240 58 0.14
241 55 0.13
242 78 0.18
243 58 0.14
244 74 0.17
245 2 0.00
246 6 0.01
247 2 0.00
248 4 0.01
249 66 0.15
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (240 bp):
CATATCCCTAAACCACACCTATTTCTTGTTTAGGCACTTAATTCAACAACTAAAAAGTGCCACTT
AACAGTCGAGTGACAAAAAAACAATTTCAAAAAGTTCAATGACCAAATTACAACATTTTTTAGTT
AAGTGACCAAAACAAAAACTTACCCATAATTTAGTATCTAATGACATATTTATCCTTCTTAATAC
AATATTAAAGATGCGACTTGAACCCGTATCAAACGAGTATCATAT
Found at i:61942061 original size:235 final size:231
Alignment explanation
Indices: 61941645--61942095 Score: 642
Period size: 235 Copynumber: 1.9 Consensus size: 231
61941635 TAATGCCTCG
*
61941645 GAATTTATGGAGTAAGTTAGAAGAAACTCCCTATCTAATTTTCACAAATTCCAAATTTAATTATT
1 GAATTTATGGAGTAAGTTAGAACAAACTCCCTATCTAATTTTCACAAATTCCAAATTTAATTATT
*
61941710 TTAATTTTAAAATTTTAAAATGTAAGTACAATTATTAATATTGTTAACATTTTTTTATTAAATTT
66 TTAATTTTAAAATTTTAAAATGTAAGTACAATTATTAAGATTGTTAACA-TTTTTTATTAAATTT
* * * *
61941775 ATCAAATGATATTTTGAAATAAAAATTACTAATTTGATAGTCATGTAATTAAAAAATTTTGATAT
130 ATCAAATGACATTTTGAAATAAAAAATACTAATTTGATACTCATGTAATTAAAAAA--ATGATAT
*
61941840 TTTAATTAATTTAAATTTAACAATATTAACCATTGAACCT
193 TTTAA-TAACTTAAATTTAACAATATTAACCATTGAACCT
* *
61941880 GAATTTATGGAGTAAGTTAGAACAAACTCCCTAT-TAATTTTCATAAATTCCAAATTTAGTTATT
1 GAATTTATGGAGTAAGTTAGAACAAACTCCCTATCTAATTTTCACAAATTCCAAATTTAATTATT
* *
61941944 TTAATTTTTAAAA-TTTAAAATTTAAGTCCAATTATTAACGA-TGTTAACA-TTTTTATTAAATT
66 TTAA-TTTTAAAATTTTAAAATGTAAGTACAATTATTAA-GATTGTTAACATTTTTTATTAAATT
* **
61942006 TATTAGCTTGACATTTTGAAATAAAAAAAATACTAATTTGATAACT-ATGTAATTAAAAAAATGA
129 TATCA-AATGACATTTTGAAAT--AAAAAATACTAATTTGAT-ACTCATGTAATTAAAAAAATGA
*
61942070 TGTTTTAATAACTTAAATTTAACAAT
190 TATTTTAATAACTTAAATTTAACAAT
61942096 GTTAGTTCGA
Statistics
Matches: 195, Mismatches: 15, Indels: 15
0.87 0.07 0.07
Matches are distributed among these distances:
232 34 0.17
233 23 0.12
234 63 0.32
235 73 0.37
236 2 0.01
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (231 bp):
GAATTTATGGAGTAAGTTAGAACAAACTCCCTATCTAATTTTCACAAATTCCAAATTTAATTATT
TTAATTTTAAAATTTTAAAATGTAAGTACAATTATTAAGATTGTTAACATTTTTTATTAAATTTA
TCAAATGACATTTTGAAATAAAAAATACTAATTTGATACTCATGTAATTAAAAAAATGATATTTT
AATAACTTAAATTTAACAATATTAACCATTGAACCT
Found at i:61952079 original size:19 final size:19
Alignment explanation
Indices: 61952042--61952079 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
61952032 TACGGTAAAA
*
61952042 TTAGGTTTTTCTTTGATAT
1 TTAGGTTTTTCTTTCATAT
61952061 TTAGG-TTTTCTTATCATAT
1 TTAGGTTTTTCTT-TCATAT
61952080 ATGTATTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.18, C:0.08, G:0.13, T:0.61
Consensus pattern (19 bp):
TTAGGTTTTTCTTTCATAT
Found at i:61962596 original size:25 final size:25
Alignment explanation
Indices: 61962550--61962597 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
61962540 AAAGAATAAA
* *
61962550 ATATATAATAAAAATTAGAAATTGT
1 ATATATAATAAAAAGTAAAAATTGT
* *
61962575 ATATATAATATATAGTAAAAATT
1 ATATATAATAAAAAGTAAAAATT
61962598 AAAAAAACTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (25 bp):
ATATATAATAAAAAGTAAAAATTGT
Found at i:61964874 original size:22 final size:21
Alignment explanation
Indices: 61964833--61964875 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
61964823 AGATTAAAGG
61964833 GAGAGAAAAAAATTAAAAAAAA
1 GAGAGAAAAAAA-TAAAAAAAA
*
61964855 GAGAGGAAAAAAA-AACAAAAA
1 GAGA-GAAAAAAATAAAAAAAA
61964876 TCACAGTGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 7 0.37
22 4 0.21
23 8 0.42
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.05
Consensus pattern (21 bp):
GAGAGAAAAAAATAAAAAAAA
Found at i:61971556 original size:28 final size:28
Alignment explanation
Indices: 61971525--61971581 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
61971515 AGTACACATG
61971525 TAGGATACATATTTGACAAGTATATGGT
1 TAGGATACATATTTGACAAGTATATGGT
61971553 TAGGATACATATTTGACAAGTATATGGT
1 TAGGATACATATTTGACAAGTATATGGT
61971581 T
1 T
61971582 TACTATCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.07, G:0.21, T:0.37
Consensus pattern (28 bp):
TAGGATACATATTTGACAAGTATATGGT
Found at i:61971674 original size:9 final size:9
Alignment explanation
Indices: 61971660--61971684 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
61971650 TAGCCAAAGC
61971660 CAAACAATG
1 CAAACAATG
61971669 CAAACAATG
1 CAAACAATG
61971678 CAAACAA
1 CAAACAA
61971685 AATCCAAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.24, G:0.08, T:0.08
Consensus pattern (9 bp):
CAAACAATG
Found at i:61973054 original size:29 final size:29
Alignment explanation
Indices: 61972992--61973047 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
61972982 TTCTTTTTTG
*
61972992 GTCACCGAACTATGAAAAGTTACAAAACA
1 GTCACCCAACTATGAAAAGTTACAAAACA
* *
61973021 GTCACCCAATTATGAAAATTTACAAAA
1 GTCACCCAACTATGAAAAGTTACAAAA
61973048 TGATCACTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.48, C:0.20, G:0.11, T:0.21
Consensus pattern (29 bp):
GTCACCCAACTATGAAAAGTTACAAAACA
Found at i:61973198 original size:18 final size:18
Alignment explanation
Indices: 61973175--61973221 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 18
61973165 GATGATCTGC
61973175 AACTTTTCATAGTTGGGT
1 AACTTTTCATAGTTGGGT
61973193 AACTTTTAGTTCATAGTTGGGT
1 AAC--TT--TTCATAGTTGGGT
61973215 AACTTTT
1 AACTTTT
61973222 ACTGTGTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
18 5 0.20
20 4 0.16
22 16 0.64
ACGTcount: A:0.23, C:0.11, G:0.19, T:0.47
Consensus pattern (18 bp):
AACTTTTCATAGTTGGGT
Found at i:61973208 original size:22 final size:22
Alignment explanation
Indices: 61973180--61973222 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
61973170 TCTGCAACTT
61973180 TTCATAGTTGGGTAACTTTTAG
1 TTCATAGTTGGGTAACTTTTAG
61973202 TTCATAGTTGGGTAACTTTTA
1 TTCATAGTTGGGTAACTTTTA
61973223 CTGTGTTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.09, G:0.21, T:0.47
Consensus pattern (22 bp):
TTCATAGTTGGGTAACTTTTAG
Found at i:61974685 original size:3 final size:3
Alignment explanation
Indices: 61974666--61974701 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
61974656 GGCATATCAG
* *
61974666 GCA GAA GCA GAA GCA GCA GCA GCA GCA GCA GCA GCA
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA
61974702 ACAACAACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.39, C:0.28, G:0.33, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:61974841 original size:6 final size:6
Alignment explanation
Indices: 61974818--61974852 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
61974808 GGTAGGAGTG
* *
61974818 GAGGTA GAGGAA GAGGTA GGGGTA GAGGTA GAGGT
1 GAGGTA GAGGTA GAGGTA GAGGTA GAGGTA GAGGT
61974853 GCGCAAATGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.31, C:0.00, G:0.54, T:0.14
Consensus pattern (6 bp):
GAGGTA
Found at i:61979170 original size:18 final size:18
Alignment explanation
Indices: 61979144--61979181 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
61979134 GGTACTAAAC
*
61979144 TATATAGTAAAATAGACA
1 TATAGAGTAAAATAGACA
61979162 TATAGAGTAAAATAGACA
1 TATAGAGTAAAATAGACA
61979180 TA
1 TA
61979182 GAATACAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.55, C:0.05, G:0.13, T:0.26
Consensus pattern (18 bp):
TATAGAGTAAAATAGACA
Found at i:61985905 original size:11 final size:11
Alignment explanation
Indices: 61985885--61985950 Score: 63
Period size: 11 Copynumber: 6.4 Consensus size: 11
61985875 ATAAATATCA
61985885 AAAAATTATTTT
1 AAAAA-TATTTT
61985897 AAAAATATTTT
1 AAAAATATTTT
61985908 --AAA-A--TT
1 AAAAATATTTT
*
61985914 AAAAA-AATTT
1 AAAAATATTTT
61985924 AAAAAGTATTTT
1 AAAAA-TATTTT
61985936 AAAAATATTTT
1 AAAAATATTTT
61985947 AAAA
1 AAAA
61985951 TTAAAAATAA
Statistics
Matches: 47, Mismatches: 1, Indels: 13
0.77 0.02 0.21
Matches are distributed among these distances:
6 2 0.04
8 5 0.11
9 3 0.06
10 7 0.15
11 16 0.34
12 14 0.30
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:61985934 original size:39 final size:39
Alignment explanation
Indices: 61985885--61986008 Score: 180
Period size: 39 Copynumber: 3.1 Consensus size: 39
61985875 ATAAATATCA
*
61985885 AAAAATTATTTTAAAAATATTTTAAAATTAAAAAAATTT
1 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTT
*
61985924 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAATAA-TG
1 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAA-AATTT
61985963 AAAAAGGTATTTT-AAAATATTTTAAAATTAAAAAAAAATTT
1 AAAAA-GTATTTTAAAAATATTTTAAAATT--AAAAAAATTT
61986004 AAAAA
1 AAAAA
61986009 TAAATATATT
Statistics
Matches: 77, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
39 55 0.71
40 11 0.14
41 11 0.14
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (39 bp):
AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTT
Found at i:61995110 original size:20 final size:20
Alignment explanation
Indices: 61995092--61995127 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 20
61995082 ATGTGTGAAT
61995092 AAATATA-GA-TATGTATGA
1 AAATATACGAGTATGTATGA
61995110 AAATATACGAGTATGTAT
1 AAATATACGAGTATGTAT
61995128 ATAAATGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.44
19 2 0.12
20 7 0.44
ACGTcount: A:0.47, C:0.03, G:0.17, T:0.33
Consensus pattern (20 bp):
AAATATACGAGTATGTATGA
Found at i:61995133 original size:20 final size:19
Alignment explanation
Indices: 61995090--61995133 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
61995080 AAATGTGTGA
61995090 ATAAATATAGATATGTATG
1 ATAAATATAGATATGTATG
61995109 A-AAATATACGAGTATGTAT-
1 ATAAATATA-GA-TATGTATG
61995128 ATAAAT
1 ATAAAT
61995134 GTATTTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 7 0.32
19 4 0.18
20 11 0.50
ACGTcount: A:0.50, C:0.02, G:0.14, T:0.34
Consensus pattern (19 bp):
ATAAATATAGATATGTATG
Found at i:61995506 original size:18 final size:19
Alignment explanation
Indices: 61995474--61995511 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
61995464 TAGTAAAAAT
*
61995474 ACATAAATAACAGTATTAA
1 ACATAAATAACAGTAGTAA
*
61995493 ACAT-AATAATAGTAGTAA
1 ACATAAATAACAGTAGTAA
61995511 A
1 A
61995512 AATACTGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.26
Consensus pattern (19 bp):
ACATAAATAACAGTAGTAA
Found at i:61997105 original size:88 final size:88
Alignment explanation
Indices: 61996987--61997430 Score: 470
Period size: 88 Copynumber: 5.1 Consensus size: 88
61996977 AGATCTGGTT
* * * ** * * *
61996987 TCTTCGATCTGCTTCACCGTCAGTACAGGAAGGCAAGATCCACTATCTTCAACTAACTCCACTAC
1 TCTTCGATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTGCTGTCTTCAACCAGCTCCACTAC
61997052 AACCGAGAGAGGCAAGGTTTGTG
66 AACCGAGAGAGGCAAGGTTTGTG
* * *
61997075 TCTTCGACCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACCAC
1 TCTTCGATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTGCTGTCTTCAACCAGCTCCACTAC
61997140 AACCGAGAGAGGCAAGGTTTGTG
66 AACCGAGAGAGGCAAGGTTTGTG
* * * * **
61997163 TCTTCGATCTGCTTCGTTGTTAATGCAGGAAGGCAAGATCTGCTGTTTTCAACCAGCTCTGCTAC
1 TCTTCGATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTGCTGTCTTCAACCAGCTCCACTAC
*
61997228 ACCCGAGAGAGGCAAGGTTTGTG
66 AACCGAGAGAGGCAAGGTTTGTG
* ** * * * * * * *
61997251 TCTTCGATCTGCTTCGCTGTTAATGTAGGAATGCAGGATCTGCTATCTTTAAACAGCTCCATTGC
1 TCTTCGATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTGCTGTCTTCAACCAGCTCCACTAC
* *
61997316 AACCAATG-GAGGCAAGGTTT-TA
66 AACCGA-GAGAGGCAAGGTTTGTG
* * * * * *
61997338 T-TCTCGATCTGCTTCGCTATTAATGCAGGAGGGCAAGATCTGCT-TCTTTAACCAGCTCCACTG
1 TCT-TCGATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTGCTGTCTTCAACCAGCTCCACTA
* *
61997401 CAACCAATGA-AGGCAAGGCTTGT-
65 CAACCGA-GAGAGGCAAGGTTTGTG
61997424 T-TTCGAT
1 TCTTCGAT
61997431 GTTCACTGAT
Statistics
Matches: 308, Mismatches: 44, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
85 5 0.02
86 39 0.13
87 39 0.13
88 224 0.73
89 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (88 bp):
TCTTCGATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTGCTGTCTTCAACCAGCTCCACTAC
AACCGAGAGAGGCAAGGTTTGTG
Found at i:61997109 original size:44 final size:44
Alignment explanation
Indices: 61997061--61997199 Score: 115
Period size: 44 Copynumber: 3.2 Consensus size: 44
61997051 CAACCGAGAG
61997061 AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGGA
1 AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGGA
* * * * ** *
61997105 AGGCAAGATCTGTTGTCTTCAACCAGC-TC-C-ACCACA-ACCGAGA
1 AGGCAAGGTTTG-TGTCTTCGACCTGCTTCGCTGTCA-ATACAG-GA
* * * *
61997148 GAGGCAAGGTTTGTGTCTTCGATCTGCTTCGTTGTTAATGCAGGA
1 -AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGGA
61997193 AGGCAAG
1 AGGCAAG
61997200 ATCTGCTGTT
Statistics
Matches: 69, Mismatches: 18, Indels: 16
0.67 0.17 0.16
Matches are distributed among these distances:
42 5 0.07
43 15 0.22
44 31 0.45
45 15 0.22
46 3 0.04
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.27
Consensus pattern (44 bp):
AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGGA
Found at i:61997167 original size:43 final size:43
Alignment explanation
Indices: 61997032--61997167 Score: 116
Period size: 44 Copynumber: 3.1 Consensus size: 43
61997022 AGATCCACTA
* * *
61997032 TCTTCAACTAACTCCACTACAACCGAGAGAGGCAAGGTTTGTG
1 TCTTCAACCAGCTCCACCACAACCGAGAGAGGCAAGGTTTGTG
* * ** * * *
61997075 TCTTCGACCTGCTTCGCTGTCA-ATACAG-GA-AGGCAAGATCTGTTG
1 TCTTCAACCAGC-TC-C-ACCACA-ACCGAGAGAGGCAAGGTTTG-TG
61997120 TCTTCAACCAGCTCCACCACAACCGAGAGAGGCAAGGTTTGTG
1 TCTTCAACCAGCTCCACCACAACCGAGAGAGGCAAGGTTTGTG
61997163 TCTTC
1 TCTTC
61997168 GATCTGCTTC
Statistics
Matches: 68, Mismatches: 17, Indels: 16
0.67 0.17 0.16
Matches are distributed among these distances:
42 5 0.07
43 19 0.28
44 24 0.35
45 16 0.24
46 4 0.06
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (43 bp):
TCTTCAACCAGCTCCACCACAACCGAGAGAGGCAAGGTTTGTG
Found at i:61999148 original size:13 final size:12
Alignment explanation
Indices: 61999114--61999161 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
61999104 TCTTTTTCTT
*
61999114 TTTTATTTTTTA
1 TTTTGTTTTTTA
* *
61999126 TTTTGATTTTGA
1 TTTTGTTTTTTA
*
61999138 TTTTGTTTTTTT
1 TTTTGTTTTTTA
61999150 TTCTTGTTTTTT
1 TT-TTGTTTTTT
61999162 GAATCGGATC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
12 20 0.69
13 9 0.31
ACGTcount: A:0.08, C:0.02, G:0.08, T:0.81
Consensus pattern (12 bp):
TTTTGTTTTTTA
Found at i:62004110 original size:20 final size:20
Alignment explanation
Indices: 62004092--62004127 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 20
62004082 ATGTGTGAAT
62004092 AAATATA-GA-TATGTATGA
1 AAATATACGAGTATGTATGA
62004110 AAATATACGAGTATGTAT
1 AAATATACGAGTATGTAT
62004128 ATAAATGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.44
19 2 0.12
20 7 0.44
ACGTcount: A:0.47, C:0.03, G:0.17, T:0.33
Consensus pattern (20 bp):
AAATATACGAGTATGTATGA
Found at i:62004133 original size:20 final size:19
Alignment explanation
Indices: 62004090--62004133 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
62004080 AAATGTGTGA
62004090 ATAAATATAGATATGTATG
1 ATAAATATAGATATGTATG
62004109 A-AAATATACGAGTATGTAT-
1 ATAAATATA-GA-TATGTATG
62004128 ATAAAT
1 ATAAAT
62004134 GTATTTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 7 0.32
19 4 0.18
20 11 0.50
ACGTcount: A:0.50, C:0.02, G:0.14, T:0.34
Consensus pattern (19 bp):
ATAAATATAGATATGTATG
Found at i:62004507 original size:18 final size:19
Alignment explanation
Indices: 62004475--62004512 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
62004465 TAGTAAAAAT
*
62004475 ACATAAATAACAGTATTAA
1 ACATAAATAACAGTAGTAA
*
62004494 ACAT-AATAATAGTAGTAA
1 ACATAAATAACAGTAGTAA
62004512 A
1 A
62004513 AATACTGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.26
Consensus pattern (19 bp):
ACATAAATAACAGTAGTAA
Found at i:62011964 original size:29 final size:29
Alignment explanation
Indices: 62011930--62011985 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
62011920 ATAAGGATTA
*
62011930 GATCAAATTAGTCACTT-TATTATTAAATG
1 GATCAAATTAGTC-CTTATACTATTAAATG
*
62011959 GATCAATTTAGTCCTTATACTATTAAA
1 GATCAAATTAGTCCTTATACTATTAAA
62011986 AAGAATCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (29 bp):
GATCAAATTAGTCCTTATACTATTAAATG
Found at i:62030016 original size:30 final size:30
Alignment explanation
Indices: 62029970--62030093 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
62029960 TTTTATTATG
*
62029970 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
62030001 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
62030031 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
62030061 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
62030091 CCA
1 CCA
62030094 TAAATATGGA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 81 0.92
31 7 0.08
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:62030025 original size:15 final size:15
Alignment explanation
Indices: 62029980--62030087 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
62029970 CCAATATCTC
62029980 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
62029995 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
62030010 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
62030025 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
62030040 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
62030055 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
62030070 GATACCCATATCTTT
1 GATACCCATATCTTT
62030085 GAT
1 GAT
62030088 TTTCCATAAA
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.26, C:0.22, G:0.07, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:62034711 original size:30 final size:30
Alignment explanation
Indices: 62034661--62034784 Score: 185
Period size: 30 Copynumber: 4.1 Consensus size: 30
62034651 TTTTATTATG
* *
62034661 CCAATATCTCGATACTCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
62034692 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
62034722 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * * *
62034752 CTATTATTTGATACCTATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
62034782 CCA
1 CCA
62034785 TAAATATGGA
Statistics
Matches: 86, Mismatches: 7, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
30 79 0.92
31 7 0.08
ACGTcount: A:0.26, C:0.23, G:0.06, T:0.45
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:62034716 original size:15 final size:15
Alignment explanation
Indices: 62034671--62034778 Score: 60
Period size: 15 Copynumber: 7.2 Consensus size: 15
62034661 CCAATATCTC
*
62034671 GATACTCATATCTTT
1 GATACCCATATCTTT
** *
62034686 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
62034701 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
62034716 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
62034731 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
62034746 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
*
62034761 GATACCTATATCTTT
1 GATACCCATATCTTT
62034776 GAT
1 GAT
62034779 TTTCCATAAA
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 13 0.19
15 43 0.64
16 11 0.16
ACGTcount: A:0.26, C:0.20, G:0.07, T:0.46
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:62039620 original size:21 final size:20
Alignment explanation
Indices: 62039565--62039610 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
62039555 AAGAAAAAAA
* *
62039565 AGAAAGAAAAAAAG-GAA-G
1 AGAAAGAACAAAGGAGAAGG
62039583 AGAAAGAACAAAGGAGAAGG
1 AGAAAGAACAAAGGAGAAGG
62039603 AGAAAGAA
1 AGAAAGAA
62039611 AAGTAGGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 12 0.50
19 3 0.12
20 9 0.38
ACGTcount: A:0.67, C:0.02, G:0.30, T:0.00
Consensus pattern (20 bp):
AGAAAGAACAAAGGAGAAGG
Found at i:62049643 original size:15 final size:15
Alignment explanation
Indices: 62049623--62049653 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
62049613 GAAACTTGTC
62049623 ATTATTGATTTCTTG
1 ATTATTGATTTCTTG
62049638 ATTATTGATTTCTTG
1 ATTATTGATTTCTTG
62049653 A
1 A
62049654 AGAGATTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.06, G:0.13, T:0.58
Consensus pattern (15 bp):
ATTATTGATTTCTTG
Found at i:62051591 original size:3 final size:3
Alignment explanation
Indices: 62051583--62051611 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
62051573 TACTAAACTA
62051583 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
62051612 CTTTTACTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:62051870 original size:21 final size:21
Alignment explanation
Indices: 62051844--62051894 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
62051834 GTACATACAT
62051844 ATATATTATT-TATATTTTAAA
1 ATATATT-TTATATATTTTAAA
62051865 ATATATTTTATATATTTT---
1 ATATATTTTATATATTTTAAA
62051883 ATATATTTTATA
1 ATATATTTTATA
62051895 ATTCACATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 12 0.41
20 2 0.07
21 15 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATATTTTATATATTTTAAA
Found at i:62051877 original size:9 final size:9
Alignment explanation
Indices: 62051843--62051894 Score: 61
Period size: 9 Copynumber: 5.4 Consensus size: 9
62051833 TGTACATACA
62051843 TATATATTAT
1 TATATATT-T
62051853 T-TATATTT
1 TATATATTT
62051861 TAAAATATATTT
1 T---ATATATTT
62051873 TATATATTT
1 TATATATTT
62051882 TATATATTT
1 TATATATTT
62051891 TATA
1 TATA
62051895 ATTCACATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
8 2 0.05
9 27 0.71
10 1 0.03
12 8 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TATATATTT
Found at i:62060683 original size:13 final size:14
Alignment explanation
Indices: 62060658--62060686 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
62060648 AAAGGGGAAT
62060658 GAAGAACAAAATGG
1 GAAGAACAAAATGG
62060672 GAAGAA-AAAATGG
1 GAAGAACAAAATGG
62060685 GA
1 GA
62060687 GTGAAGGGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.59, C:0.03, G:0.31, T:0.07
Consensus pattern (14 bp):
GAAGAACAAAATGG
Found at i:62070138 original size:35 final size:35
Alignment explanation
Indices: 62070099--62070195 Score: 95
Period size: 27 Copynumber: 3.0 Consensus size: 35
62070089 ACTTCACTTC
62070099 TAGCTTTACTTCTAGCTTCTTAACATTTGATTTTT
1 TAGCTTTACTTCTAGCTTCTTAACATTTGATTTTT
* * *
62070134 TAGCTTTACTTC--G-TGGC-T---A--TGGTTCTT
1 TAGCTTTACTTCTAGCT-TCTTAACATTTGATTTTT
62070161 TAGCTTTACTTCTAGCTTCTTAACATTTGATTTTT
1 TAGCTTTACTTCTAGCTTCTTAACATTTGATTTTT
62070196 CAAAGATTGC
Statistics
Matches: 46, Mismatches: 6, Indels: 20
0.64 0.08 0.28
Matches are distributed among these distances:
27 18 0.39
29 3 0.07
30 2 0.04
32 2 0.04
33 3 0.07
35 18 0.39
ACGTcount: A:0.18, C:0.18, G:0.12, T:0.53
Consensus pattern (35 bp):
TAGCTTTACTTCTAGCTTCTTAACATTTGATTTTT
Found at i:62070757 original size:52 final size:52
Alignment explanation
Indices: 62070684--62070788 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 52
62070674 ACTTAAGTTA
*
62070684 AATTACAAAAATGCTATACTTAGGCAATTAAAGAGGCAAACTCTTAGAAATT
1 AATTACAAAAACGCTATACTTAGGCAATTAAAGAGGCAAACTCTTAGAAATT
* **
62070736 AATTACAGAAACGCTATACTTAGGCAATTAAAGAGGTGAACTCTTAGAAATT
1 AATTACAAAAACGCTATACTTAGGCAATTAAAGAGGCAAACTCTTAGAAATT
62070788 A
1 A
62070789 GTGACTTTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (52 bp):
AATTACAAAAACGCTATACTTAGGCAATTAAAGAGGCAAACTCTTAGAAATT
Found at i:62078196 original size:5 final size:5
Alignment explanation
Indices: 62078182--62078215 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
62078172 ATTATTAGTA
*
62078182 AAAAT TAAAT AAAAT AAAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAA
62078216 TTTTATTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:62078201 original size:16 final size:16
Alignment explanation
Indices: 62078180--62078215 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
62078170 GCATTATTAG
*
62078180 TAAAAATTAAATAAAA
1 TAAAAATAAAATAAAA
62078196 TAAAAATAAAATAAAA
1 TAAAAATAAAATAAAA
62078212 TAAA
1 TAAA
62078216 TTTTATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
TAAAAATAAAATAAAA
Found at i:62104151 original size:36 final size:36
Alignment explanation
Indices: 62104111--62104187 Score: 86
Period size: 36 Copynumber: 2.1 Consensus size: 36
62104101 ATGCATATAA
* *
62104111 ATATACATACT-TATAAAAATAAAAAT-ATGTATATGT
1 ATATACATA-TATATAAAAAGAAAAATGA-GTATACGT
* *
62104147 ATATAGATATATATAAAAAGAAATATGAGTATACGT
1 ATATACATATATATAAAAAGAAAAATGAGTATACGT
62104183 ATATA
1 ATATA
62104188 TATTAAACAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
35 1 0.03
36 33 0.94
37 1 0.03
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.34
Consensus pattern (36 bp):
ATATACATATATATAAAAAGAAAAATGAGTATACGT
Found at i:62104332 original size:3 final size:3
Alignment explanation
Indices: 62104321--62104373 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
62104311 CAATAATACC
* * *
62104321 AAT ACT AAT AAT AAT AA- AGAT GAT AAT AAT GAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
62104366 AAT AAT AA
1 AAT AAT AA
62104374 AGTTAACAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
2 1 0.02
3 41 0.98
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:62109255 original size:2 final size:2
Alignment explanation
Indices: 62109248--62109277 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
62109238 AATATGAATG
62109248 AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
62109278 GTAAGTAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62111284 original size:14 final size:14
Alignment explanation
Indices: 62111265--62111295 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
62111255 TTTTCAAATT
62111265 TTGGAATTTTAATA
1 TTGGAATTTTAATA
62111279 TTGGAATTTTAATA
1 TTGGAATTTTAATA
62111293 TTG
1 TTG
62111296 ACCCGAACTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (14 bp):
TTGGAATTTTAATA
Found at i:62112603 original size:246 final size:245
Alignment explanation
Indices: 62112157--62112728 Score: 932
Period size: 246 Copynumber: 2.3 Consensus size: 245
62112147 AATTTTAGTG
62112157 ATTAATTAATATGAGAATAGAGTGGGGGAGTGAAGGAGTAAGCATAGAGACCCCACCCCACTATT
1 ATTAATTAATATGAGAATAGAGT-GGGGAGTGAAGGAGTAAGCATAGAGACCCCACCCCACTATT
* * *
62112222 GTCGTGATTATTGA--TTTTTTTTAACAATATTATTATAGGTTAAGATCATATTTGTTATTTTTA
65 GTCGTGATTATTGACTTTTTTTTTAACAATATCATTATAAGTTAAGATCATATTTGTTAGTTTTA
* *
62112285 ACATAATACTTAGAATTATTCATAGTTCTTCCCTAACTCATAAATAAAAAGATAATGCATTTCAG
130 ACATAATACTTAGAATTATTCATAGTTCTTCACTAACTCATAAATAAAAAGATAATACATTTCAG
62112350 CACACTCAAACTTACGTATCGTGTATTGACAATAATATTCATACTAATCAA
195 CACACTCAAACTTACGTATCGTGTATTGACAATAATATTCATACTAATCAA
*
62112401 ATTAATTAATATGAGAATAGAGTGGGGAGTGAAGGAGTAAGCATAGAGACCCCACCCTACTATTG
1 ATTAATTAATATGAGAATAGAGTGGGGAGTGAAGGAGTAAGCATAGAGACCCCACCCCACTATTG
*
62112466 TCGTGATTATTGACTTTTTTTTTAACAATATCATTATAAGTTAAAGATCATATTTGTTCGTTTTA
66 TCGTGATTATTGACTTTTTTTTTAACAATATCATTATAAGTT-AAGATCATATTTGTTAGTTTTA
* * * *
62112531 ACATAATACTTAGAATTATTCGTAGTTTTTTACTAACTCATAAATAAAAAGATAATACATTTTAG
130 ACATAATACTTAGAATTATTCATAGTTCTTCACTAACTCATAAATAAAAAGATAATACATTTCAG
* * * * *
62112596 TACACTCAAATTTACGTATCGTGTATTGATAATACTATTTATACTAATCAA
195 CACACTCAAACTTACGTATCGTGTATTGACAATAATATTCATACTAATCAA
* * *
62112647 ATTAATTAAGATGAGAATAGAGTGAGGAGTGAAGGAGTAAGCATGGAGACCCCACCCCACTATTG
1 ATTAATTAATATGAGAATAGAGTGGGGAGTGAAGGAGTAAGCATAGAGACCCCACCCCACTATTG
*
62112712 TCGTAATTATTGACTTT
66 TCGTGATTATTGACTTT
62112729 GCAATTTGCA
Statistics
Matches: 304, Mismatches: 21, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
243 54 0.18
244 23 0.08
245 25 0.08
246 202 0.66
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.35
Consensus pattern (245 bp):
ATTAATTAATATGAGAATAGAGTGGGGAGTGAAGGAGTAAGCATAGAGACCCCACCCCACTATTG
TCGTGATTATTGACTTTTTTTTTAACAATATCATTATAAGTTAAGATCATATTTGTTAGTTTTAA
CATAATACTTAGAATTATTCATAGTTCTTCACTAACTCATAAATAAAAAGATAATACATTTCAGC
ACACTCAAACTTACGTATCGTGTATTGACAATAATATTCATACTAATCAA
Found at i:62117351 original size:30 final size:30
Alignment explanation
Indices: 62117273--62117351 Score: 72
Period size: 28 Copynumber: 2.7 Consensus size: 30
62117263 TAAATTTTTG
* * **
62117273 GGGGTCTAATTAAAATTTTTAAAAAATCTA
1 GGGGTCTAATGAAAATTTTAAAAAAAAATA
* * * *
62117303 GGAGTTTAATG-AGA-TTTAAAAAAAAATT
1 GGGGTCTAATGAAAATTTTAAAAAAAAATA
62117331 GGGGTCTAATGAAAATTTTAA
1 GGGGTCTAATGAAAATTTTAA
62117352 TTTTTTGTGA
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
28 19 0.53
29 4 0.11
30 13 0.36
ACGTcount: A:0.44, C:0.04, G:0.18, T:0.34
Consensus pattern (30 bp):
GGGGTCTAATGAAAATTTTAAAAAAAAATA
Found at i:62117624 original size:28 final size:28
Alignment explanation
Indices: 62117588--62117648 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
62117578 AATTACTAGT
*
62117588 GTCTCGATCCCAATTTTCTACTGAAACG
1 GTCTTGATCCCAATTTTCTACTGAAACG
* *
62117616 GTCTTGATCTCAATTTTCTATTGAAACG
1 GTCTTGATCCCAATTTTCTACTGAAACG
*
62117644 ATCTT
1 GTCTT
62117649 AAAAGTGTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.39
Consensus pattern (28 bp):
GTCTTGATCCCAATTTTCTACTGAAACG
Found at i:62120602 original size:8 final size:8
Alignment explanation
Indices: 62120589--62120615 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
62120579 TATTAAATCT
62120589 AAATTTTA
1 AAATTTTA
62120597 AAATTTTA
1 AAATTTTA
62120605 AAATTTTA
1 AAATTTTA
62120613 AAA
1 AAA
62120616 ATAGAAAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
AAATTTTA
Found at i:62120629 original size:31 final size:31
Alignment explanation
Indices: 62120597--62120654 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
62120587 CTAAATTTTA
*
62120597 AAATTTTAAAATTTT-AAAAATAGAAAGATT
1 AAATTTTAAAATTTTGAAAAATACAAAGATT
* *
62120627 AAATTTTTAATTTTTGAAAAATACAAAG
1 AAATTTTAAAATTTTGAAAAATACAAAG
62120655 GCTATACGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 13 0.54
31 11 0.46
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (31 bp):
AAATTTTAAAATTTTGAAAAATACAAAGATT
Found at i:62120758 original size:18 final size:18
Alignment explanation
Indices: 62120735--62120784 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
62120725 AAATCGAAAA
62120735 AATTCGGTTAACCGACTG
1 AATTCGGTTAACCGACTG
62120753 AATTCGGTTAACCGACTG
1 AATTCGGTTAACCGACTG
62120771 AATTCGGTTAACCG
1 AATTCGGTTAACCG
62120785 GTCGGTTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (18 bp):
AATTCGGTTAACCGACTG
Found at i:62121127 original size:9 final size:9
Alignment explanation
Indices: 62121108--62121180 Score: 94
Period size: 9 Copynumber: 8.2 Consensus size: 9
62121098 TCGGGTATTT
62121108 TTCGG-TAA
1 TTCGGTTAA
62121116 TTCGGTTAA
1 TTCGGTTAA
62121125 TTCGGTTAA
1 TTCGGTTAA
*
62121134 TTCAGTTAA
1 TTCGGTTAA
*
62121143 TTCGGATAA
1 TTCGGTTAA
*
62121152 TTCGGATAA
1 TTCGGTTAA
*
62121161 TTCGGGTAA
1 TTCGGTTAA
*
62121170 TTCGGGTAA
1 TTCGGTTAA
62121179 TT
1 TT
62121181 TTTAACCAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
8 5 0.08
9 55 0.92
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (9 bp):
TTCGGTTAA
Found at i:62121358 original size:12 final size:12
Alignment explanation
Indices: 62121341--62121365 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
62121331 AGTAATTTCG
62121341 GGTCGGTTAACC
1 GGTCGGTTAACC
62121353 GGTCGGTTAACC
1 GGTCGGTTAACC
62121365 G
1 G
62121366 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:62126024 original size:16 final size:16
Alignment explanation
Indices: 62126005--62126042 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
62125995 ATATATAATA
62126005 TATATAATATATTTTT
1 TATATAATATATTTTT
*
62126021 TATATAATGTATTTTT
1 TATATAATATATTTTT
62126037 TATATA
1 TATATA
62126043 TGTTTTATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
TATATAATATATTTTT
Found at i:62126884 original size:15 final size:15
Alignment explanation
Indices: 62126851--62126899 Score: 71
Period size: 15 Copynumber: 3.2 Consensus size: 15
62126841 ACTGAATTAA
*
62126851 ATAATATATATTATAT
1 ATAATATAT-TTTTAT
62126867 ATAATATATTTTTAT
1 ATAATATATTTTTAT
*
62126882 ATAATGTATTTTTAT
1 ATAATATATTTTTAT
62126897 ATA
1 ATA
62126900 TGTTTTATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
15 22 0.71
16 9 0.29
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (15 bp):
ATAATATATTTTTAT
Found at i:62127194 original size:859 final size:859
Alignment explanation
Indices: 62125499--62128072 Score: 4240
Period size: 859 Copynumber: 3.0 Consensus size: 859
62125489 CGACCTTGTA
* *
62125499 GTGCCCTAAACCGGCAGCGCGTGTGGAATGAACTGAAAATTGCGGCAAGACTCGTACAAGCACAT
1 GTGCCCTAAACCGGCAGCGTGTGTGGACTGAACTGAAAATTGCGGCAAGACTCGTACAAGCACAT
*
62125564 GACTTGGGCAACATATTTCCTTACATGCGACTTATTTCAATCACTAGGACCCTACTCTGATGCCC
66 GACTTGGGCAACATATTTCCTTACATGCGACTTATTTCAATCACTAGGACCCTACTATGATGCCC
*
62125629 ACTGCAGAGCCACCCTAATGGCACAGGTCAAAATAAGATTCAAATTTTAAACCCAAAATTAGCAT
131 ACTGCAGAGCCACCCTAATGGCACAGGTCAAAATAAGATTGAAATTTTAAACCCAAAATTAGCAT
** * *
62125694 GAAAAACTTAGACTCGTTTGAGATTATATTTTAGTACAATGAGATATCGTGTAATCTTTTCTAAA
196 GAAAATTTTAGACACGTTTAAGA-TATATTTTAGTACAATGAGATATCGTGTAATCTTTTCTAAA
* * * * *
62125759 TTAATGATTGTGGTTAAAATATAAAATCGAGGAAGCTGTAACCATTTGATCAAATTACAACAGAA
260 TTAATGATTGTGGTTAAAAAATAAAATCGAGGAGGTTGTAACCGTTTGATCAAATCACAACAGAA
* *
62125824 ATTAGAGGTGCTCATAGTTCGGTTAAAGTCGAATTAACTGACCAAACCGATCTAATTCAGTTAAT
325 ATTAGAGGTGTTCATAGTTCGGTTAAAATCGAATTAACTGACCAAACCGATCTAATTCAGTTAAT
*
62125889 CGATCAATGCTCGAATTTAGTTCGGTCTGATGTGGATTAATGATTTTTTGAAATTTTAATTATCA
390 CGATCAATGCTCGAATTTAGTTCGGTCTGATGTCGATTAATGATTTTTTGAAATTTTAATTATCA
* ** *
62125954 GTTAATTCAGTTCGAAATTAAGTAATTAACTGAATTAAATAATATATAATATATATAATATATTT
455 GTTAATTCGGTTCGAAATCGAGTAATTAACTGAATTAAATAATATATATTATATATAATATATTT
*
62126019 TTTATATAATGTATTTTTTATATATGTTTTATACTTATTTTAACCAAAAGACAAAAACATACAAA
520 TTTATATAATGTATTTTTTATATATGTTTTATACTTATTTTAACCAAAAGACAAAAACATATAAA
62126084 TTTTAGTTAATTCAGTTAAGTTATTGGGTTGCTAAGTTTTCTTTTTAAATCCAGCTAGTGAGCTC
585 TTTTAGTTAATTCAGTTAAGTTATTGGGTTGCTAAGTTTTC-TTTTAAATCCAGCTAGTGAGCTC
*
62126149 CAAGTATCGATTCGACAAACGGTGCGATGGATCAGTATCTATCGACGAGTAGAATAACATATCTT
649 CAAGTGTCGATTCGACAAACGGTGCGATGGATCAGTATCTATCGACGAGTAGAATAACATATCTT
* * * *
62126214 ACATCCAAATCGATTTGATGGTCAGTGTTAGAGATTGGAGAATAAAACTATTTAAA-TTTAATTT
714 AAATCCAAGTCGATTTGATGGTCAGTGTTAGAGATTGAAGAATAAAACTATTTAAATTTTGATTT
* *
62126278 ATAGATTTGTAAATTTTAAAGTTGTTTAATGAAAAAA-AAACTAAACTATAGAAGAGAAGATGAA
779 ATAGATTCGTGAATTTTAAAGTTGTTTAATGAAAAAATAAACTAAACTATAGAAGAGAAGATGAA
*
62126342 TGAAAGCTTTCGATTG
844 TGAAAGCTTTCGACTG
* *
62126358 GTGCCCTAAACCGGCAGTGTGTGTGGACTGAACTGAAAATTGCGGCAAGACTCGTACAAGTACAT
1 GTGCCCTAAACCGGCAGCGTGTGTGGACTGAACTGAAAATTGCGGCAAGACTCGTACAAGCACAT
62126423 GAACTTGGGCAACATATTTCCTTACATGCGACTTATTTCAATCACTAGGACCCTACTATGATGCC
66 G-ACTTGGGCAACATATTTCCTTACATGCGACTTATTTCAATCACTAGGACCCTACTATGATGCC
*
62126488 CACTGCAGAGCCACCCTAATGGCACACGTCAAAATAAGATTGAAATTTTAAACCCAAAATTAGCA
130 CACTGCAGAGCCACCCTAATGGCACAGGTCAAAATAAGATTGAAATTTTAAACCCAAAATTAGCA
*
62126553 TGAAAATTTTAGACACGTTTAAGATATATTTTAGTACAATGAGATATCGTCTAATCTTTTCTAAA
195 TGAAAATTTTAGACACGTTTAAGATATATTTTAGTACAATGAGATATCGTGTAATCTTTTCTAAA
62126618 TTAATGATTGTGGTTAAAAAATAAAATCGAGGAGGTTGTAACCGTTTGATCAAATCACAACAGAA
260 TTAATGATTGTGGTTAAAAAATAAAATCGAGGAGGTTGTAACCGTTTGATCAAATCACAACAGAA
* * *
62126683 ATTAAAGGTGTTCATAGTTCGGTTAAAATCGAATTAACAGACCGAACCGATCTAATTCAGTTAAT
325 ATTAGAGGTGTTCATAGTTCGGTTAAAATCGAATTAACTGACCAAACCGATCTAATTCAGTTAAT
*
62126748 CGATCAATGCTCGAATTTAGTTTGGTCTGATGTCGATTAATGATTTTTTGAAATTTTAATTATCA
390 CGATCAATGCTCGAATTTAGTTCGGTCTGATGTCGATTAATGATTTTTTGAAATTTTAATTATCA
*
62126813 GTTAATTCGGTTCAAAATCGAGTAATTAACTGAATTAAATAATATATATTATATATAATATA-TT
455 GTTAATTCGGTTCGAAATCGAGTAATTAACTGAATTAAATAATATATATTATATATAATATATTT
* *
62126877 TTTATATAATGTA-TTTTTATATATGTTTTATGCTTATTTTAACCAAAAGACAAAAATATATAAA
520 TTTATATAATGTATTTTTTATATATGTTTTATACTTATTTTAACCAAAAGACAAAAACATATAAA
* *
62126941 TTTTAGTTAATTCAGTTAAGTTATTGGGTTGCTAAATTTTCTTTATAAATCTAGCTAGTGAGCTC
585 TTTTAGTTAATTCAGTTAAGTTATTGGGTTGCTAAGTTTTCTTT-TAAATCCAGCTAGTGAGCTC
* * * *
62127006 CAAATGTCGATTCGACAAACGGTGCGGTGGATCAGTACCTATCGACGAATAGAATAACATATCTT
649 CAAGTGTCGATTCGACAAACGGTGCGATGGATCAGTATCTATCGACGAGTAGAATAACATATCTT
* * ** *
62127071 AGATTCAAGTCGATTTGATGACCAGTGTTAGAGATTGAAGGATAAAACTATTTAAATTTTGATTT
714 AAATCCAAGTCGATTTGATGGTCAGTGTTAGAGATTGAAGAATAAAACTATTTAAATTTTGATTT
* * * * * *
62127136 ATAGATTCGCGAATTTTAAAATTGTTGAATGAAAAAATTAAACTATA-TATAAAAGAGAAAATGA
779 ATAGATTCGTGAATTTTAAAGTTGTTTAATGAAAAAA-TAAACTAAACTATAGAAGAGAAGATGA
*
62127200 ATGAAAGTTTTCGACTG
843 ATGAAAGCTTTCGACTG
*
62127217 GTG-------CCGGCAGCGTGTGTGGACTGAACTGAAAATTGCGGCAAGACTCGTACAAGCATAT
1 GTGCCCTAAACCGGCAGCGTGTGTGGACTGAACTGAAAATTGCGGCAAGACTCGTACAAGCACAT
62127275 GACTTGGGCAACATATTTCCTTACATGCGACTTATTTCAATCACTAGGACCCTACTATGATGCCC
66 GACTTGGGCAACATATTTCCTTACATGCGACTTATTTCAATCACTAGGACCCTACTATGATGCCC
62127340 ACTGCAGAGCCACCCTAATGGCACAGGTCAAAATAAGATTGAAATTTTAAACCCAAAATTAGCAT
131 ACTGCAGAGCCACCCTAATGGCACAGGTCAAAATAAGATTGAAATTTTAAACCCAAAATTAGCAT
62127405 GAAAATTTTAGACACGTTTAAGATGATATTTTAGTACAATGAGATATCGTGTAATCTTTTCTAAA
196 GAAAATTTTAGACACGTTTAAGAT-ATATTTTAGTACAATGAGATATCGTGTAATCTTTTCTAAA
* * **
62127470 TTAATGATTGTGGTTAAAAAATAAAATTGAAGAGGTTGTAATAGTTTGATCAAATCACAACAGAA
260 TTAATGATTGTGGTTAAAAAATAAAATCGAGGAGGTTGTAACCGTTTGATCAAATCACAACAGAA
* * *
62127535 ATTAGAGATGTTCATAGTTCGGTTAAAATCGAATTAACTGACCAAACCTATCTAATTCAGTTTAT
325 ATTAGAGGTGTTCATAGTTCGGTTAAAATCGAATTAACTGACCAAACCGATCTAATTCAGTTAAT
* ** * *
62127600 CAATCAATGCTTTAATTTAGTTCGGTCTGATGTCGATTAATGATTTTTTAAAATTTCAATTATCA
390 CGATCAATGCTCGAATTTAGTTCGGTCTGATGTCGATTAATGATTTTTTGAAATTTTAATTATCA
* *
62127665 ATTAATTCGGTTCGAAATCGAGTAATTAACTGAATTAAATAATATATATTATATTTAATATATTT
455 GTTAATTCGGTTCGAAATCGAGTAATTAACTGAATTAAATAATATATATTATATATAATATATTT
*
62127730 TTTATATAATTTATTTTTTATATATGTTTTATACTTATTTTAACCAAAAGACAAAAACATATAAA
520 TTTATATAATGTATTTTTTATATATGTTTTATACTTATTTTAACCAAAAGACAAAAACATATAAA
*
62127795 TTTTAGTTAATTCAGTTAAGTTATTGGGTTGCTAAGTTTTCTTTTCAAATCCAACTAGTGAGCTC
585 TTTTAGTTAATTCAGTTAAGTTATTGGGTTGCTAAGTTTTCTTTT-AAATCCAGCTAGTGAGCTC
* * *
62127860 CAAGTGTCGATTCAACGAACGGTGCGATGGATCAGTATCTATCGACGAGTAGAATAACATATATT
649 CAAGTGTCGATTCGACAAACGGTGCGATGGATCAGTATCTATCGACGAGTAGAATAACATATCTT
**
62127925 AAATCCAAGTCGATTTGATGGTCAGTGTTAGAGATTGAAGAATAAAACTATTTGGATTTTGATTT
714 AAATCCAAGTCGATTTGATGGTCAGTGTTAGAGATTGAAGAATAAAACTATTTAAATTTTGATTT
* * *
62127990 ATAGATTCGTGAATTTCAAAGTTGTTTAATG-AAATA-AAACTAAACTATAGAAGATAAGATGAA
779 ATAGATTCGTGAATTTTAAAGTTGTTTAATGAAAAAATAAACTAAACTATAGAAGAGAAGATGAA
62128053 TGAAAGCTTTCGACTG
844 TGAAAGCTTTCGACTG
62128069 GTGC
1 GTGC
62128073 AAATGACGCA
Statistics
Matches: 1593, Mismatches: 111, Indels: 28
0.92 0.06 0.02
Matches are distributed among these distances:
851 159 0.10
852 363 0.23
853 19 0.01
854 252 0.16
856 3 0.00
857 216 0.14
858 54 0.03
859 375 0.24
860 152 0.10
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (859 bp):
GTGCCCTAAACCGGCAGCGTGTGTGGACTGAACTGAAAATTGCGGCAAGACTCGTACAAGCACAT
GACTTGGGCAACATATTTCCTTACATGCGACTTATTTCAATCACTAGGACCCTACTATGATGCCC
ACTGCAGAGCCACCCTAATGGCACAGGTCAAAATAAGATTGAAATTTTAAACCCAAAATTAGCAT
GAAAATTTTAGACACGTTTAAGATATATTTTAGTACAATGAGATATCGTGTAATCTTTTCTAAAT
TAATGATTGTGGTTAAAAAATAAAATCGAGGAGGTTGTAACCGTTTGATCAAATCACAACAGAAA
TTAGAGGTGTTCATAGTTCGGTTAAAATCGAATTAACTGACCAAACCGATCTAATTCAGTTAATC
GATCAATGCTCGAATTTAGTTCGGTCTGATGTCGATTAATGATTTTTTGAAATTTTAATTATCAG
TTAATTCGGTTCGAAATCGAGTAATTAACTGAATTAAATAATATATATTATATATAATATATTTT
TTATATAATGTATTTTTTATATATGTTTTATACTTATTTTAACCAAAAGACAAAAACATATAAAT
TTTAGTTAATTCAGTTAAGTTATTGGGTTGCTAAGTTTTCTTTTAAATCCAGCTAGTGAGCTCCA
AGTGTCGATTCGACAAACGGTGCGATGGATCAGTATCTATCGACGAGTAGAATAACATATCTTAA
ATCCAAGTCGATTTGATGGTCAGTGTTAGAGATTGAAGAATAAAACTATTTAAATTTTGATTTAT
AGATTCGTGAATTTTAAAGTTGTTTAATGAAAAAATAAACTAAACTATAGAAGAGAAGATGAATG
AAAGCTTTCGACTG
Found at i:62127596 original size:852 final size:852
Alignment explanation
Indices: 62125509--62128072 Score: 4199
Period size: 852 Copynumber: 3.0 Consensus size: 852
62125499 GTGCCCTAAA
* *
62125509 CCGGCAGCGCGTGTGGAATGAACTGAAAATTGCGGCAAGACTCGTACAAGCACATGACTTGGGCA
1 CCGGCAGCGTGTGTGGACTGAACTGAAAATTGCGGCAAGACTCGTACAAGCACATGACTTGGGCA
*
62125574 ACATATTTCCTTACATGCGACTTATTTCAATCACTAGGACCCTACTCTGATGCCCACTGCAGAGC
66 ACATATTTCCTTACATGCGACTTATTTCAATCACTAGGACCCTACTATGATGCCCACTGCAGAGC
* **
62125639 CACCCTAATGGCACAGGTCAAAATAAGATTCAAATTTTAAACCCAAAATTAGCATGAAAAACTTA
131 CACCCTAATGGCACAGGTCAAAATAAGATTGAAATTTTAAACCCAAAATTAGCATGAAAATTTTA
* *
62125704 GACTCGTTTGAGATTATATTTTAGTACAATGAGATATCGTGTAATCTTTTCTAAATTAATGATTG
196 GACACGTTTAAGA-TATATTTTAGTACAATGAGATATCGTGTAATCTTTTCTAAATTAATGATTG
* * * *
62125769 TGGTTAAAATATAAAATCGAGGAAGCTGTAACCA-TTTGATCAAATTACAACAGAAATTAGAGGT
260 TGGTTAAAAAATAAAATCGAGGAGGTTGTAA-CAGTTTGATCAAATCACAACAGAAATTAGAGGT
* *
62125833 GCTCATAGTTCGGTTAAAGTCGAATTAACTGACCAAACCGATCTAATTCAGTTAATCGATCAATG
324 GTTCATAGTTCGGTTAAAATCGAATTAACTGACCAAACCGATCTAATTCAGTTAATCGATCAATG
* *
62125898 CTCGAATTTAGTTCGGTCTGATGTGGATTAATGATTTTTTGAAATTTTAATTATCAGTTAATTCA
389 CTCGAATTTAGTTCGGTCTGATGTCGATTAATGATTTTTTGAAATTTTAATTATCAGTTAATTCG
** *
62125963 GTTCGAAATTAAGTAATTAACTGAATTAAATAATATATAATATATATAATATATTTTTTATATAA
454 GTTCGAAATCGAGTAATTAACTGAATTAAATAATATATATTATATATAATATATTTTTTATATAA
*
62126028 TGTATTTTTTATATATGTTTTATACTTATTTTAACCAAAAGACAAAAACATACAAATTTTAGTTA
519 TGTATTTTTTATATATGTTTTATACTTATTTTAACCAAAAGACAAAAACATATAAATTTTAGTTA
*
62126093 ATTCAGTTAAGTTATTGGGTTGCTAAGTTTTCTTTTTAAATCCAGCTAGTGAGCTCCAAGTATCG
584 ATTCAGTTAAGTTATTGGGTTGCTAAGTTTTC-TTTTAAATCCAGCTAGTGAGCTCCAAGTGTCG
* *
62126158 ATTCGACAAACGGTGCGATGGATCAGTATCTATCGACGAGTAGAATAACATATCTTACATCCAAA
648 ATTCGACAAACGGTGCGATGGATCAGTATCTATCGACGAGTAGAATAACATATCTTAAATCCAAG
* * *
62126223 TCGATTTGATGGTCAGTGTTAGAGATTGGAGAATAAAACTATTTAAA-TTTAATTTATAGATTTG
713 TCGATTTGATGGTCAGTGTTAGAGATTGAAGAATAAAACTATTTAAATTTTGATTTATAGATTCG
*
62126287 TAAATTTTAAAGTTGTTTAATGAAAAAA-AAACTAAACTATAGAAGAGAAGATGAATGAAAGCTT
778 TGAATTTTAAAGTTGTTTAATGAAAAAATAAACTAAACTATAGAAGAGAAGATGAATGAAAGCTT
*
62126351 TCGATTGGTG
843 TCGACTGGTG
* *
62126361 CCCTAAACCGGCAGTGTGTGTGGACTGAACTGAAAATTGCGGCAAGACTCGTACAAGTACATGAA
1 -------CCGGCAGCGTGTGTGGACTGAACTGAAAATTGCGGCAAGACTCGTACAAGCACATG-A
62126426 CTTGGGCAACATATTTCCTTACATGCGACTTATTTCAATCACTAGGACCCTACTATGATGCCCAC
58 CTTGGGCAACATATTTCCTTACATGCGACTTATTTCAATCACTAGGACCCTACTATGATGCCCAC
*
62126491 TGCAGAGCCACCCTAATGGCACACGTCAAAATAAGATTGAAATTTTAAACCCAAAATTAGCATGA
123 TGCAGAGCCACCCTAATGGCACAGGTCAAAATAAGATTGAAATTTTAAACCCAAAATTAGCATGA
*
62126556 AAATTTTAGACACGTTTAAGATATATTTTAGTACAATGAGATATCGTCTAATCTTTTCTAAATTA
188 AAATTTTAGACACGTTTAAGATATATTTTAGTACAATGAGATATCGTGTAATCTTTTCTAAATTA
*
62126621 ATGATTGTGGTTAAAAAATAAAATCGAGGAGGTTGTAACCGTTTGATCAAATCACAACAGAAATT
253 ATGATTGTGGTTAAAAAATAAAATCGAGGAGGTTGTAACAGTTTGATCAAATCACAACAGAAATT
* * *
62126686 AAAGGTGTTCATAGTTCGGTTAAAATCGAATTAACAGACCGAACCGATCTAATTCAGTTAATCGA
318 AGAGGTGTTCATAGTTCGGTTAAAATCGAATTAACTGACCAAACCGATCTAATTCAGTTAATCGA
*
62126751 TCAATGCTCGAATTTAGTTTGGTCTGATGTCGATTAATGATTTTTTGAAATTTTAATTATCAGTT
383 TCAATGCTCGAATTTAGTTCGGTCTGATGTCGATTAATGATTTTTTGAAATTTTAATTATCAGTT
*
62126816 AATTCGGTTCAAAATCGAGTAATTAACTGAATTAAATAATATATATTATATATAATATA-TTTTT
448 AATTCGGTTCGAAATCGAGTAATTAACTGAATTAAATAATATATATTATATATAATATATTTTTT
* *
62126880 ATATAATGTA-TTTTTATATATGTTTTATGCTTATTTTAACCAAAAGACAAAAATATATAAATTT
513 ATATAATGTATTTTTTATATATGTTTTATACTTATTTTAACCAAAAGACAAAAACATATAAATTT
* *
62126944 TAGTTAATTCAGTTAAGTTATTGGGTTGCTAAATTTTCTTTATAAATCTAGCTAGTGAGCTCCAA
578 TAGTTAATTCAGTTAAGTTATTGGGTTGCTAAGTTTTCTTT-TAAATCCAGCTAGTGAGCTCCAA
* * * * *
62127009 ATGTCGATTCGACAAACGGTGCGGTGGATCAGTACCTATCGACGAATAGAATAACATATCTTAGA
642 GTGTCGATTCGACAAACGGTGCGATGGATCAGTATCTATCGACGAGTAGAATAACATATCTTAAA
* ** *
62127074 TTCAAGTCGATTTGATGACCAGTGTTAGAGATTGAAGGATAAAACTATTTAAATTTTGATTTATA
707 TCCAAGTCGATTTGATGGTCAGTGTTAGAGATTGAAGAATAAAACTATTTAAATTTTGATTTATA
* * * * * *
62127139 GATTCGCGAATTTTAAAATTGTTGAATGAAAAAATTAAACTATA-TATAAAAGAGAAAATGAATG
772 GATTCGTGAATTTTAAAGTTGTTTAATGAAAAAA-TAAACTAAACTATAGAAGAGAAGATGAATG
*
62127203 AAAGTTTTCGACTGGTG
836 AAAGCTTTCGACTGGTG
*
62127220 CCGGCAGCGTGTGTGGACTGAACTGAAAATTGCGGCAAGACTCGTACAAGCATATGACTTGGGCA
1 CCGGCAGCGTGTGTGGACTGAACTGAAAATTGCGGCAAGACTCGTACAAGCACATGACTTGGGCA
62127285 ACATATTTCCTTACATGCGACTTATTTCAATCACTAGGACCCTACTATGATGCCCACTGCAGAGC
66 ACATATTTCCTTACATGCGACTTATTTCAATCACTAGGACCCTACTATGATGCCCACTGCAGAGC
62127350 CACCCTAATGGCACAGGTCAAAATAAGATTGAAATTTTAAACCCAAAATTAGCATGAAAATTTTA
131 CACCCTAATGGCACAGGTCAAAATAAGATTGAAATTTTAAACCCAAAATTAGCATGAAAATTTTA
62127415 GACACGTTTAAGATGATATTTTAGTACAATGAGATATCGTGTAATCTTTTCTAAATTAATGATTG
196 GACACGTTTAAGAT-ATATTTTAGTACAATGAGATATCGTGTAATCTTTTCTAAATTAATGATTG
* * * *
62127480 TGGTTAAAAAATAAAATTGAAGAGGTTGTAATAGTTTGATCAAATCACAACAGAAATTAGAGATG
260 TGGTTAAAAAATAAAATCGAGGAGGTTGTAACAGTTTGATCAAATCACAACAGAAATTAGAGGTG
* * *
62127545 TTCATAGTTCGGTTAAAATCGAATTAACTGACCAAACCTATCTAATTCAGTTTATCAATCAATGC
325 TTCATAGTTCGGTTAAAATCGAATTAACTGACCAAACCGATCTAATTCAGTTAATCGATCAATGC
** * * *
62127610 TTTAATTTAGTTCGGTCTGATGTCGATTAATGATTTTTTAAAATTTCAATTATCAATTAATTCGG
390 TCGAATTTAGTTCGGTCTGATGTCGATTAATGATTTTTTGAAATTTTAATTATCAGTTAATTCGG
*
62127675 TTCGAAATCGAGTAATTAACTGAATTAAATAATATATATTATATTTAATATATTTTTTATATAAT
455 TTCGAAATCGAGTAATTAACTGAATTAAATAATATATATTATATATAATATATTTTTTATATAAT
*
62127740 TTATTTTTTATATATGTTTTATACTTATTTTAACCAAAAGACAAAAACATATAAATTTTAGTTAA
520 GTATTTTTTATATATGTTTTATACTTATTTTAACCAAAAGACAAAAACATATAAATTTTAGTTAA
*
62127805 TTCAGTTAAGTTATTGGGTTGCTAAGTTTTCTTTTCAAATCCAACTAGTGAGCTCCAAGTGTCGA
585 TTCAGTTAAGTTATTGGGTTGCTAAGTTTTCTTTT-AAATCCAGCTAGTGAGCTCCAAGTGTCGA
* * *
62127870 TTCAACGAACGGTGCGATGGATCAGTATCTATCGACGAGTAGAATAACATATATTAAATCCAAGT
649 TTCGACAAACGGTGCGATGGATCAGTATCTATCGACGAGTAGAATAACATATCTTAAATCCAAGT
**
62127935 CGATTTGATGGTCAGTGTTAGAGATTGAAGAATAAAACTATTTGGATTTTGATTTATAGATTCGT
714 CGATTTGATGGTCAGTGTTAGAGATTGAAGAATAAAACTATTTAAATTTTGATTTATAGATTCGT
* * *
62128000 GAATTTCAAAGTTGTTTAATG-AAATA-AAACTAAACTATAGAAGATAAGATGAATGAAAGCTTT
779 GAATTTTAAAGTTGTTTAATGAAAAAATAAACTAAACTATAGAAGAGAAGATGAATGAAAGCTTT
62128063 CGACTGGTG
844 CGACTGGTG
62128072 C
1 C
62128073 AAATGACGCA
Statistics
Matches: 1583, Mismatches: 111, Indels: 29
0.92 0.06 0.02
Matches are distributed among these distances:
851 159 0.10
852 364 0.23
853 19 0.01
854 252 0.16
856 3 0.00
857 216 0.14
858 55 0.03
859 363 0.23
860 152 0.10
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (852 bp):
CCGGCAGCGTGTGTGGACTGAACTGAAAATTGCGGCAAGACTCGTACAAGCACATGACTTGGGCA
ACATATTTCCTTACATGCGACTTATTTCAATCACTAGGACCCTACTATGATGCCCACTGCAGAGC
CACCCTAATGGCACAGGTCAAAATAAGATTGAAATTTTAAACCCAAAATTAGCATGAAAATTTTA
GACACGTTTAAGATATATTTTAGTACAATGAGATATCGTGTAATCTTTTCTAAATTAATGATTGT
GGTTAAAAAATAAAATCGAGGAGGTTGTAACAGTTTGATCAAATCACAACAGAAATTAGAGGTGT
TCATAGTTCGGTTAAAATCGAATTAACTGACCAAACCGATCTAATTCAGTTAATCGATCAATGCT
CGAATTTAGTTCGGTCTGATGTCGATTAATGATTTTTTGAAATTTTAATTATCAGTTAATTCGGT
TCGAAATCGAGTAATTAACTGAATTAAATAATATATATTATATATAATATATTTTTTATATAATG
TATTTTTTATATATGTTTTATACTTATTTTAACCAAAAGACAAAAACATATAAATTTTAGTTAAT
TCAGTTAAGTTATTGGGTTGCTAAGTTTTCTTTTAAATCCAGCTAGTGAGCTCCAAGTGTCGATT
CGACAAACGGTGCGATGGATCAGTATCTATCGACGAGTAGAATAACATATCTTAAATCCAAGTCG
ATTTGATGGTCAGTGTTAGAGATTGAAGAATAAAACTATTTAAATTTTGATTTATAGATTCGTGA
ATTTTAAAGTTGTTTAATGAAAAAATAAACTAAACTATAGAAGAGAAGATGAATGAAAGCTTTCG
ACTGGTG
Found at i:62127739 original size:16 final size:16
Alignment explanation
Indices: 62127703--62127753 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
62127693 ACTGAATTAA
* *
62127703 ATAATATATATTATAT
1 ATAATATATTTTTTAT
*
62127719 TTAATATATTTTTTAT
1 ATAATATATTTTTTAT
*
62127735 ATAATTTATTTTTTAT
1 ATAATATATTTTTTAT
62127751 ATA
1 ATA
62127754 TGTTTTATAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATAATATATTTTTTAT
Found at i:62131231 original size:26 final size:26
Alignment explanation
Indices: 62131195--62131314 Score: 117
Period size: 26 Copynumber: 4.8 Consensus size: 26
62131185 CGCAGCTTTT
*
62131195 ATGAGCGTCCCGATATATGGCTCTTC
1 ATGAGCTTCCCGATATATGGCTCTTC
*
62131221 ATGAGCTTCCCGATAAATGGCTCTT-
1 ATGAGCTTCCCGATATATGGCTCTTC
*
62131246 ATGAGCTTCCCGTTA-ATGGCTCTTC
1 ATGAGCTTCCCGATATATGGCTCTTC
* * * *
62131271 -GGAACTTTCC-A-ATATGGCTC-GC
1 ATGAGCTTCCCGATATATGGCTCTTC
* *
62131293 TTGAACTTCCCGATATATGGCT
1 ATGAGCTTCCCGATATATGGCT
62131315 ACCCGGAGCT
Statistics
Matches: 79, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
22 2 0.03
23 15 0.19
24 17 0.22
25 22 0.28
26 23 0.29
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.33
Consensus pattern (26 bp):
ATGAGCTTCCCGATATATGGCTCTTC
Found at i:62135019 original size:17 final size:16
Alignment explanation
Indices: 62134995--62135033 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
62134985 CTTTTCATTA
62134995 TGTTTTCCTTTCTTTT-
1 TGTTTTCCTTT-TTTTC
62135011 TGTTGTTCCTTTTTTTC
1 TGTT-TTCCTTTTTTTC
62135028 TGTTTT
1 TGTTTT
62135034 GTGCATGCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.00, C:0.15, G:0.10, T:0.74
Consensus pattern (16 bp):
TGTTTTCCTTTTTTTC
Found at i:62139037 original size:29 final size:29
Alignment explanation
Indices: 62138995--62139052 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
62138985 AATATTACTT
62138995 AGAGAGTTTAAGTTAGAATTTTTTTAGTA
1 AGAGAGTTTAAGTTAGAATTTTTTTAGTA
62139024 AGAGAGTTTAAGTTAGAATTTTTTTAGTA
1 AGAGAGTTTAAGTTAGAATTTTTTTAGTA
62139053 CAAGATTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (29 bp):
AGAGAGTTTAAGTTAGAATTTTTTTAGTA
Found at i:62139164 original size:37 final size:35
Alignment explanation
Indices: 62139088--62139166 Score: 88
Period size: 34 Copynumber: 2.2 Consensus size: 35
62139078 AGAGTTCTAA
* * *
62139088 AATATTAAATAATAAAATATTTTTTTAAATCAAAT
1 AATAATAAATAATAAAATATTGTTTGAAATCAAAT
* *
62139123 -ATAATAAATAATAAAATGTATTGTTTGAAATTAATT
1 AATAATAAATAATAAAA--TATTGTTTGAAATCAAAT
62139159 AATAATAA
1 AATAATAA
62139167 CACTTGAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
34 15 0.42
36 14 0.39
37 7 0.19
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (35 bp):
AATAATAAATAATAAAATATTGTTTGAAATCAAAT
Found at i:62141274 original size:14 final size:15
Alignment explanation
Indices: 62141246--62141274 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
62141236 AATCCTATTT
62141246 AATATTTTAATATAA
1 AATATTTTAATATAA
62141261 AATATTTT-ATATAA
1 AATATTTTAATATAA
62141275 TACATCTGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AATATTTTAATATAA
Found at i:62143028 original size:36 final size:35
Alignment explanation
Indices: 62142979--62143058 Score: 126
Period size: 36 Copynumber: 2.3 Consensus size: 35
62142969 TAAACTTAAA
62142979 ATTAAAAA-ATAAAACTTTAATAAATTCTTCAATC
1 ATTAAAAACATAAAACTTTAATAAATTCTTCAATC
* *
62143013 ATTAAAAACAGTAAAACTTTAATAAATTCTTTAATT
1 ATTAAAAACA-TAAAACTTTAATAAATTCTTCAATC
62143049 ATTAAAAACA
1 ATTAAAAACA
62143059 AATAATGTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
34 8 0.19
35 1 0.02
36 33 0.79
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.35
Consensus pattern (35 bp):
ATTAAAAACATAAAACTTTAATAAATTCTTCAATC
Found at i:62147541 original size:18 final size:18
Alignment explanation
Indices: 62147518--62147583 Score: 51
Period size: 18 Copynumber: 3.3 Consensus size: 18
62147508 TGTAATTAAT
62147518 TTCACTGTATATTACTAA
1 TTCACTGTATATTACTAA
* * *
62147536 TTCACTTTACCATAAATTATTCAT
1 TTCACTGT---AT--ATTACT-AA
62147560 TTCACTGTATATTACTAA
1 TTCACTGTATATTACTAA
62147578 TTCACT
1 TTCACT
62147584 TTATTATCTC
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
18 14 0.39
19 5 0.14
21 4 0.11
23 5 0.14
24 8 0.22
ACGTcount: A:0.32, C:0.20, G:0.03, T:0.45
Consensus pattern (18 bp):
TTCACTGTATATTACTAA
Found at i:62148854 original size:3 final size:3
Alignment explanation
Indices: 62148846--62148877 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
62148836 GCTTAGTTGC
*
62148846 AAG AAG AAG AAG AAG AAG AAG ATG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
62148878 TAGTTTGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:62152653 original size:16 final size:18
Alignment explanation
Indices: 62152627--62152659 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
62152617 TTGAATTATC
62152627 TAAATTAA-TTTCTCAAT
1 TAAATTAATTTTCTCAAT
62152644 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
62152660 CTCAATTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:62154667 original size:22 final size:21
Alignment explanation
Indices: 62154635--62154680 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
62154625 TATATCCAAT
* *
62154635 ACCCAAGACCATAAACTCTTAA
1 ACCCAAAACCATAAA-TCCTAA
62154657 ACCCAAAACCATAAATCCTAA
1 ACCCAAAACCATAAATCCTAA
62154678 ACC
1 ACC
62154681 ATAGATCCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.48, C:0.35, G:0.02, T:0.15
Consensus pattern (21 bp):
ACCCAAAACCATAAATCCTAA
Found at i:62162394 original size:2 final size:2
Alignment explanation
Indices: 62162387--62162422 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
62162377 TGTGCGTGCA
*
62162387 TG TG TG TG TG TG TA TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
62162423 AGAGAGAGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (2 bp):
TG
Found at i:62171039 original size:31 final size:30
Alignment explanation
Indices: 62170966--62171044 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
62170956 ATGCAATTTG
* *
62170966 ATACATGAAA-TTTGATTTGGTACAATTAT
1 ATACATGAAACTTTGATTTAGTACAAATAT
* * * *
62170995 ACACATAAAACTTTGATTGTAGTTCAAATGT
1 ATACATGAAACTTTGATT-TAGTACAAATAT
62171026 ATACATGAAACTTTGATTT
1 ATACATGAAACTTTGATTT
62171045 TGATTCGATC
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
29 8 0.20
30 8 0.20
31 24 0.60
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (30 bp):
ATACATGAAACTTTGATTTAGTACAAATAT
Found at i:62172396 original size:40 final size:40
Alignment explanation
Indices: 62172341--62172421 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
62172331 CCAGCAACAC
62172341 ATACCATACCAAACAGCATATTGTGTTTCCATGGTAGTCT
1 ATACCATACCAAACAGCATATTGTGTTTCCATGGTAGTCT
62172381 ATACCATACCAAACAGCATATTGTGTTTCCATGGTAGTCT
1 ATACCATACCAAACAGCATATTGTGTTTCCATGGTAGTCT
62172421 A
1 A
62172422 ATAATAGTCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (40 bp):
ATACCATACCAAACAGCATATTGTGTTTCCATGGTAGTCT
Found at i:62175702 original size:38 final size:38
Alignment explanation
Indices: 62175660--62175740 Score: 153
Period size: 38 Copynumber: 2.1 Consensus size: 38
62175650 GTAGCCTTTC
62175660 ACTTATAAAAACAAACAAAAAGATACCTTTATTTTCTT
1 ACTTATAAAAACAAACAAAAAGATACCTTTATTTTCTT
*
62175698 ACTTATAAAAACAAACAAAAAGATATCTTTATTTTCTT
1 ACTTATAAAAACAAACAAAAAGATACCTTTATTTTCTT
62175736 ACTTA
1 ACTTA
62175741 ATGCTGCAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.47, C:0.15, G:0.02, T:0.36
Consensus pattern (38 bp):
ACTTATAAAAACAAACAAAAAGATACCTTTATTTTCTT
Found at i:62176490 original size:35 final size:35
Alignment explanation
Indices: 62176451--62176522 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
62176441 AGTAATAGAG
62176451 AATGGCAATTGAGAACAGTATAACACCATTTTAAT
1 AATGGCAATTGAGAACAGTATAACACCATTTTAAT
62176486 AATGGCAATTGAGAACAGTATAACACCATTTTAAT
1 AATGGCAATTGAGAACAGTATAACACCATTTTAAT
62176521 AA
1 AA
62176523 ACCCGAGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (35 bp):
AATGGCAATTGAGAACAGTATAACACCATTTTAAT
Found at i:62183955 original size:19 final size:20
Alignment explanation
Indices: 62183928--62183980 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
62183918 AGATGGATTA
62183928 TTATATATTTTTAAAT-TTT
1 TTATATATTTTTAAATATTT
* *
62183947 TTATGTATTTTTATATATTT
1 TTATATATTTTTAAATATTT
*
62183967 TTA-AAATTTTTAAA
1 TTATATATTTTTAAA
62183981 ATTAAGATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 22 0.79
20 6 0.21
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
TTATATATTTTTAAATATTT
Found at i:62183957 original size:10 final size:10
Alignment explanation
Indices: 62183928--62183978 Score: 61
Period size: 10 Copynumber: 5.3 Consensus size: 10
62183918 AGATGGATTA
62183928 TTATATATTT
1 TTATATATTT
*
62183938 TTAAAT-TTT
1 TTATATATTT
*
62183947 TTATGTATTT
1 TTATATATTT
62183957 TTATATATTT
1 TTATATATTT
*
62183967 TTA-AAATTT
1 TTATATATTT
62183976 TTA
1 TTA
62183979 AAATTAAGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 15 0.43
10 20 0.57
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (10 bp):
TTATATATTT
Found at i:62183976 original size:29 final size:29
Alignment explanation
Indices: 62183910--62183978 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 29
62183900 GATATTAATA
**
62183910 TAAAATTTAGATGGATTATTATATATTTT
1 TAAAATTTTTATGGATTATTATATATTTT
* * *
62183939 TAAATTTTTTATGTATTTTTATATATTTT
1 TAAAATTTTTATGGATTATTATATATTTT
62183968 TAAAATTTTTA
1 TAAAATTTTTA
62183979 AAATTAAGAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (29 bp):
TAAAATTTTTATGGATTATTATATATTTT
Found at i:62185995 original size:32 final size:32
Alignment explanation
Indices: 62185954--62186014 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
62185944 CAAATTTAGC
62185954 TATACATTCAATTTCTAGGAAGAGAACTTGTA
1 TATACATTCAATTTCTAGGAAGAGAACTTGTA
*
62185986 TATACATTCAATTTCTAGGAAGAGGACTT
1 TATACATTCAATTTCTAGGAAGAGAACTT
62186015 TACTTATACC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.34
Consensus pattern (32 bp):
TATACATTCAATTTCTAGGAAGAGAACTTGTA
Found at i:62187709 original size:98 final size:98
Alignment explanation
Indices: 62187592--62187787 Score: 392
Period size: 98 Copynumber: 2.0 Consensus size: 98
62187582 ATTGTGTCGA
62187592 TTGTTTGGTTGTTTTTTCTTGGATAATTTCTTATTGATTGTTTTGTTTTAAAAATTGCTAAGAGT
1 TTGTTTGGTTGTTTTTTCTTGGATAATTTCTTATTGATTGTTTTGTTTTAAAAATTGCTAAGAGT
62187657 CACAAGTATTTGAACTTCTCTTTCTACTGGCAT
66 CACAAGTATTTGAACTTCTCTTTCTACTGGCAT
62187690 TTGTTTGGTTGTTTTTTCTTGGATAATTTCTTATTGATTGTTTTGTTTTAAAAATTGCTAAGAGT
1 TTGTTTGGTTGTTTTTTCTTGGATAATTTCTTATTGATTGTTTTGTTTTAAAAATTGCTAAGAGT
62187755 CACAAGTATTTGAACTTCTCTTTCTACTGGCAT
66 CACAAGTATTTGAACTTCTCTTTCTACTGGCAT
62187788 ATACTTAAAT
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 98 1.00
ACGTcount: A:0.21, C:0.11, G:0.16, T:0.51
Consensus pattern (98 bp):
TTGTTTGGTTGTTTTTTCTTGGATAATTTCTTATTGATTGTTTTGTTTTAAAAATTGCTAAGAGT
CACAAGTATTTGAACTTCTCTTTCTACTGGCAT
Found at i:62194799 original size:20 final size:19
Alignment explanation
Indices: 62194756--62194802 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
62194746 CACTTTATTT
62194756 TATTT-TATTTAATAATAG
1 TATTTATATTTAATAATAG
62194774 TAATTTATATTTAATTAATTA-
1 T-ATTTATATTTAA-TAA-TAG
62194795 TATTTATA
1 TATTTATA
62194803 ACACTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 1 0.04
19 4 0.16
20 14 0.56
21 4 0.16
22 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
TATTTATATTTAATAATAG
Found at i:62201708 original size:24 final size:26
Alignment explanation
Indices: 62201658--62201711 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
62201648 TTTTAACTTC
**
62201658 ATAATTTTTTTCCACATTATCTCTTTT
1 ATAATTTTTTTCCACATTA-CGATTTT
62201685 ATAATTTTTTTCCACA-TA-GATTTT
1 ATAATTTTTTTCCACATTACGATTTT
62201709 ATA
1 ATA
62201712 GAACTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.28
26 2 0.08
27 16 0.64
ACGTcount: A:0.28, C:0.15, G:0.02, T:0.56
Consensus pattern (26 bp):
ATAATTTTTTTCCACATTACGATTTT
Found at i:62213967 original size:3 final size:3
Alignment explanation
Indices: 62213961--62214009 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
62213951 ATACTTGACC
62213961 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
62214008 AT
1 AT
62214010 AATTTTAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:62216374 original size:16 final size:16
Alignment explanation
Indices: 62216355--62216385 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
62216345 TTGAAAGAGT
62216355 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
62216371 TTTCAAATTTATATG
1 TTTCAAATATATATG
62216386 CTCTAACATG
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:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:62217130 original size:24 final size:24
Alignment explanation
Indices: 62217076--62217131 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
62217066 ATTCTATATT
**
62217076 TTATTTAATATATAATTAATTTTA
1 TTATTTAATATATAAAAAATTTTA
* *
62217100 TTTTTTATTATATAAAAATATTTTA
1 TTATTTAATATATAAAAA-ATTTTA
62217125 -TATTTAA
1 TTATTTAA
62217132 AATAATGAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TTATTTAATATATAAAAAATTTTA
Found at i:62218391 original size:19 final size:20
Alignment explanation
Indices: 62218338--62218392 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
62218328 ATTTTTTAAA
62218338 ATTAAAAAATATAAATATTCT
1 ATTAAAAAATATAAA-ATTCT
* *
62218359 TTTTAAAAAT-TAAAATTC-
1 ATTAAAAAATATAAAATTCT
62218377 ATTAAAAAATATAAAA
1 ATTAAAAAATATAAAA
62218393 GATATTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 8 0.28
19 9 0.31
20 4 0.14
21 8 0.28
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (20 bp):
ATTAAAAAATATAAAATTCT
Found at i:62218631 original size:28 final size:29
Alignment explanation
Indices: 62218587--62218642 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
62218577 TTAACTAACT
62218587 TTTTTAAAAATTAAAAAATTA-TAAAAATC
1 TTTTTAAAAATT-AAAAATTATTAAAAATC
62218616 TTTTTAAAAATT-AAAATTATTAAAAAT
1 TTTTTAAAAATTAAAAATTATTAAAAAT
62218643 ATAAAAACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 7 0.27
28 7 0.27
29 12 0.46
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (29 bp):
TTTTTAAAAATTAAAAATTATTAAAAATC
Found at i:62218675 original size:37 final size:38
Alignment explanation
Indices: 62218592--62218675 Score: 102
Period size: 37 Copynumber: 2.2 Consensus size: 38
62218582 TAACTTTTTT
62218592 AAAAATTAAAAAATTATAAAAATCTTTTTAAAAATTAA
1 AAAAATTAAAAAATTATAAAAATCTTTTTAAAAATTAA
** *
62218630 AATTATT-AAAAA-TATAAAAA-CATTTTTTAAAATTTAA
1 AAAAATTAAAAAATTATAAAAATC--TTTTTAAAAATTAA
62218667 AAAAATTAA
1 AAAAATTAA
62218676 TTAAATGATG
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
35 1 0.03
36 8 0.21
37 23 0.61
38 6 0.16
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (38 bp):
AAAAATTAAAAAATTATAAAAATCTTTTTAAAAATTAA
Found at i:62218679 original size:20 final size:19
Alignment explanation
Indices: 62218628--62218680 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
62218618 TTTAAAAATT
62218628 AAAATTATTAAAAATATAAA
1 AAAATTATT-AAAATATAAA
* * *
62218648 AACATTTTTTAAAATTTAAA
1 AA-AATTATTAAAATATAAA
62218668 AAAATTAATTAAA
1 AAAATT-ATTAAA
62218681 TGATGACATG
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 3 0.12
20 18 0.69
21 5 0.19
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAATTATTAAAATATAAA
Found at i:62219061 original size:16 final size:16
Alignment explanation
Indices: 62219040--62219070 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
62219030 TTTGCAACTC
62219040 GATTTAAATTTAGACG
1 GATTTAAATTTAGACG
62219056 GATTTAAATTTAGAC
1 GATTTAAATTTAGAC
62219071 AAATTTAAGC
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:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (16 bp):
GATTTAAATTTAGACG
Found at i:62219076 original size:16 final size:16
Alignment explanation
Indices: 62219041--62219078 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
62219031 TTGCAACTCG
**
62219041 ATTTAAATTTAGACGG
1 ATTTAAATTTAGACAA
62219057 ATTTAAATTTAGACAA
1 ATTTAAATTTAGACAA
62219073 ATTTAA
1 ATTTAA
62219079 GCATAATTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (16 bp):
ATTTAAATTTAGACAA
Found at i:62219828 original size:33 final size:31
Alignment explanation
Indices: 62219770--62219832 Score: 74
Period size: 33 Copynumber: 2.0 Consensus size: 31
62219760 AACTTTGGTT
*
62219770 TTCTGAATTTTTTGAATTAATTATTTTATTTA
1 TTCTGAATTTTTTGAACTAATTA-TTTATTTA
*
62219802 TTCTCGAATTTTTTTATACTAA-TATTTATTT
1 TTCT-GAATTTTTTGA-ACTAATTATTTATTT
62219833 TTCGTTGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 11 0.41
33 12 0.44
34 4 0.15
ACGTcount: A:0.27, C:0.06, G:0.05, T:0.62
Consensus pattern (31 bp):
TTCTGAATTTTTTGAACTAATTATTTATTTA
Found at i:62219850 original size:37 final size:37
Alignment explanation
Indices: 62219809--62219906 Score: 105
Period size: 37 Copynumber: 2.7 Consensus size: 37
62219799 TTATTCTCGA
62219809 ATTTT-TTTATACT-AATATTTATTTTTCGTTGGA-AAAT
1 ATTTTATTTA-ACTCAATATTT-TTTTTCGTT-GACAAAT
*
62219846 ATTTTATTTAACTCAATCTTTTTTTTCGTTGACAAAT
1 ATTTTATTTAACTCAATATTTTTTTTCGTTGACAAAT
** *
62219883 ATTTGGTTTAAC-CAAAATTTTTTT
1 ATTTTATTTAACTCAATATTTTTTT
62219907 GTGTAGTCTT
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
36 12 0.23
37 31 0.58
38 10 0.19
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.55
Consensus pattern (37 bp):
ATTTTATTTAACTCAATATTTTTTTTCGTTGACAAAT
Found at i:62221667 original size:43 final size:43
Alignment explanation
Indices: 62221619--62221721 Score: 179
Period size: 43 Copynumber: 2.4 Consensus size: 43
62221609 TAACCGAAAT
*
62221619 GATACACATTCTTTAACAGGTAACTACAAACAAAGATACTCAA
1 GATACACATTCTTTAACAGCTAACTACAAACAAAGATACTCAA
*
62221662 GATACACATTCTTTAACAGCTACCTACAAACAAAGATACTCAA
1 GATACACATTCTTTAACAGCTAACTACAAACAAAGATACTCAA
*
62221705 GATATACATTCTTTAAC
1 GATACACATTCTTTAAC
62221722 CGAAATGATA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (43 bp):
GATACACATTCTTTAACAGCTAACTACAAACAAAGATACTCAA
Found at i:62227479 original size:36 final size:36
Alignment explanation
Indices: 62227432--62227534 Score: 206
Period size: 36 Copynumber: 2.9 Consensus size: 36
62227422 TTTAATGTAA
62227432 ATTTCTGTAACCAAGACTTACCATTACAAGATGGAC
1 ATTTCTGTAACCAAGACTTACCATTACAAGATGGAC
62227468 ATTTCTGTAACCAAGACTTACCATTACAAGATGGAC
1 ATTTCTGTAACCAAGACTTACCATTACAAGATGGAC
62227504 ATTTCTGTAACCAAGACTTACCATTACAAGA
1 ATTTCTGTAACCAAGACTTACCATTACAAGA
62227535 GAAAAGAACA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 67 1.00
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (36 bp):
ATTTCTGTAACCAAGACTTACCATTACAAGATGGAC
Found at i:62228228 original size:20 final size:20
Alignment explanation
Indices: 62228181--62228229 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
62228171 AATTTAGTAC
* * *
62228181 TTTAATAAATAATAATTATA
1 TTTATTAAAAAATAAATATA
62228201 -TTATTTAAAAAATAAATATA
1 TTTA-TTAAAAAATAAATATA
62228221 TTTATTAAA
1 TTTATTAAA
62228230 GAAACTATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 3 0.12
20 18 0.75
21 3 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTATTAAAAAATAAATATA
Found at i:62229705 original size:11 final size:11
Alignment explanation
Indices: 62229691--62229718 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
62229681 AAAAATAAAA
62229691 AAAAATATTTT
1 AAAAATATTTT
62229702 AAAAATATTTT
1 AAAAATATTTT
62229713 AAAAAT
1 AAAAAT
62229719 TAAAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:62230073 original size:10 final size:10
Alignment explanation
Indices: 62230058--62230082 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
62230048 AAAAAGAAAA
62230058 GATATGATTT
1 GATATGATTT
62230068 GATATGATTT
1 GATATGATTT
62230078 GATAT
1 GATAT
62230083 TTTCTAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (10 bp):
GATATGATTT
Found at i:62231677 original size:30 final size:30
Alignment explanation
Indices: 62231643--62231700 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
62231633 TATTATCATG
62231643 GGAATTCCTTGATGCTGGACCAACCTTTAA
1 GGAATTCCTTGATGCTGGACCAACCTTTAA
*
62231673 GGAATTCCTTGATGTTGGACCAACCTTT
1 GGAATTCCTTGATGCTGGACCAACCTTT
62231701 CAGAAATTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (30 bp):
GGAATTCCTTGATGCTGGACCAACCTTTAA
Found at i:62235451 original size:21 final size:21
Alignment explanation
Indices: 62235410--62235451 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
62235400 TTTTCTTCAA
* *
62235410 TCGAGTCGAATGAGATGGAAT
1 TCGAATCGAATGAGATCGAAT
62235431 TCGAATCGAATCGA-ATCGAAT
1 TCGAATCGAAT-GAGATCGAAT
62235452 ATATTTGTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (21 bp):
TCGAATCGAATGAGATCGAAT
Found at i:62236132 original size:29 final size:31
Alignment explanation
Indices: 62236094--62236152 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
62236084 GGAGGTGGGA
*
62236094 TGGGAAGGGAATAAAAGTTTT-GGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTGGGGGAAAAG
*
62236124 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTGGGGGAAAA
62236153 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.39, C:0.00, G:0.41, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTGGGGGAAAAG
Found at i:62236298 original size:30 final size:31
Alignment explanation
Indices: 62236257--62236317 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
62236247 GGGTTGGGAG
**
62236257 GGGAGAGGAGTAAAAGTTTTGGGGGAAAAGT
1 GGGAGAGGAGTAAAAGTTTTAAGGGAAAAGT
62236288 GGGA-AGGAGTAAAAGTTTTAAGGGAAAAGT
1 GGGAGAGGAGTAAAAGTTTTAAGGGAAAAGT
62236318 AAAAAAGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.41, T:0.20
Consensus pattern (31 bp):
GGGAGAGGAGTAAAAGTTTTAAGGGAAAAGT
Found at i:62236380 original size:9 final size:9
Alignment explanation
Indices: 62236366--62236402 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
62236356 TATAGTTTGA
62236366 TATTCGAAT
1 TATTCGAAT
62236375 TATTCGAAT
1 TATTCGAAT
*
62236384 TATTCGAGT
1 TATTCGAAT
62236393 TATTCGAAT
1 TATTCGAAT
62236402 T
1 T
62236403 CGAAAATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:62237108 original size:44 final size:44
Alignment explanation
Indices: 62237044--62237130 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
62237034 GCTAAGTCTT
* **
62237044 ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACAAATCTC
1 ATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCGACAAATCTC
* *
62237088 ATCTCCTTGAAGTTATAGTGGAGCAGATTGAAGCGACAAATCT
1 ATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCGACAAATCT
62237131 TGTACCTCTA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (44 bp):
ATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCGACAAATCTC
Found at i:62238530 original size:16 final size:17
Alignment explanation
Indices: 62238509--62238541 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
62238499 ATGTCTAGGT
62238509 AAATT-ATTAATTGAGA
1 AAATTAATTAATTGAGA
62238525 AAATTAGATTAATTGAG
1 AAATTA-ATTAATTGAG
62238542 GAGTTAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
18 10 0.67
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
AAATTAATTAATTGAGA
Found at i:62241369 original size:41 final size:41
Alignment explanation
Indices: 62241203--62241358 Score: 285
Period size: 41 Copynumber: 3.8 Consensus size: 41
62241193 TTTATCGTTA
* *
62241203 GTGACATAATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
62241244 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
62241285 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
62241326 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
62241359 AAGAGCCGGT
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 112 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.27
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:62241627 original size:33 final size:32
Alignment explanation
Indices: 62241572--62241634 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
62241562 GATAGATATG
62241572 TATATATATATGTTGCATTCGGCATAGGTGGA
1 TATATATATATGTTGCATTCGGCATAGGTGGA
* *
62241604 TATATTTATGTGTATGCATTCGGCATAGGTG
1 TATATATATATGT-TGCATTCGGCATAGGTG
62241635 AAAATAAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (32 bp):
TATATATATATGTTGCATTCGGCATAGGTGGA
Found at i:62241651 original size:33 final size:33
Alignment explanation
Indices: 62241578--62241651 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
62241568 TATGTATATA
* * **
62241578 TATATGT-TGCATTCGGCATAGGTGGATATATT
1 TATATGTATGCATTCGGCATAGGTGAAAATAAG
*
62241610 TATGTGTATGCATTCGGCATAGGTGAAAATAAG
1 TATATGTATGCATTCGGCATAGGTGAAAATAAG
*
62241643 TGTATGTAT
1 TATATGTAT
62241652 CTATGCATTC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
32 6 0.18
33 28 0.82
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (33 bp):
TATATGTATGCATTCGGCATAGGTGAAAATAAG
Found at i:62242901 original size:46 final size:46
Alignment explanation
Indices: 62242834--62243064 Score: 372
Period size: 46 Copynumber: 5.0 Consensus size: 46
62242824 CATGGCAAAG
* * *
62242834 TGTGAAACGTAGGTATGGTATTTCAGTGAAGAAAACTATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTGAAGAAAACCATACTGAGT
* *
62242880 TGTGAAAAGTAGGTATGGTATTCCGGTAAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTGAAGAAAACCATACTGAGT
* *
62242926 TGTGAAAAGTATGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTGAAGAAAACCATACTGAGT
* *
62242972 TGTGAAAAGTAGGTATGGTGTTTTGGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTGAAGAAAACCATACTGAGT
*
62243018 TGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTGAAGAAAACCATACTGAGT
62243064 T
1 T
62243065 ATAGCAATGT
Statistics
Matches: 171, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 171 1.00
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.29
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCGGTGAAGAAAACCATACTGAGT
Found at i:62243718 original size:11 final size:11
Alignment explanation
Indices: 62243702--62243726 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
62243692 GTATTAGAAA
62243702 TTTCTTTTATT
1 TTTCTTTTATT
62243713 TTTCTTTTATT
1 TTTCTTTTATT
62243724 TTT
1 TTT
62243727 AAACTATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTCTTTTATT
Found at i:62244349 original size:3 final size:3
Alignment explanation
Indices: 62244332--62244429 Score: 74
Period size: 3 Copynumber: 33.0 Consensus size: 3
62244322 CGTTATTTTC
* * * *
62244332 ATT ATT AGT AGT ATT ATT ATT -TAT ATT ATT ATT AAT AAT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT
* * * * * * *
62244377 ATT AAT GTC ATC ATT ACT A-T AGT ATT ATT ACT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
62244424 ATT ATT
1 ATT ATT
62244430 CACTTATTTA
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
2 3 0.04
3 74 0.95
4 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:62244559 original size:2 final size:2
Alignment explanation
Indices: 62244552--62244639 Score: 54
Period size: 2 Copynumber: 44.5 Consensus size: 2
62244542 ACTTTTGTAA
* * * * *
62244552 AT AT AT AT AC AC AT AT TT AT AT AT AT AT AT AT AT AT AT TT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
62244594 AT TT TT AT -T TT CAT A- AT TT TT AT AT AT AT TT AT AT AT AT AT
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
62244635 AT AT A
1 AT AT A
62244640 CATACGTGCG
Statistics
Matches: 70, Mismatches: 13, Indels: 6
0.79 0.15 0.07
Matches are distributed among these distances:
1 2 0.03
2 67 0.96
3 1 0.01
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (2 bp):
AT
Found at i:62259354 original size:21 final size:21
Alignment explanation
Indices: 62259328--62259368 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
62259318 AGACGAGCAA
* *
62259328 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
62259349 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
62259369 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:62263057 original size:20 final size:20
Alignment explanation
Indices: 62263021--62263059 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
62263011 TTAGATTACG
62263021 ATAAAATAATTATTTAAAAA
1 ATAAAATAATTATTTAAAAA
*
62263041 ATAAATATATTTA-TTAAAA
1 ATAAA-ATAATTATTTAAAA
62263060 GATTATGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATAAAATAATTATTTAAAAA
Found at i:62266250 original size:21 final size:22
Alignment explanation
Indices: 62266224--62266264 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
62266214 AAATATTTTG
62266224 AATTTTAAAAATTA-TTTTTCA
1 AATTTTAAAAATTACTTTTTCA
62266245 AATTTTAAAAATTACTTTTT
1 AATTTTAAAAATTACTTTTT
62266265 TTTTTGTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (22 bp):
AATTTTAAAAATTACTTTTTCA
Found at i:62270423 original size:25 final size:25
Alignment explanation
Indices: 62270394--62270443 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
62270384 AACAACTTCA
62270394 TTTCATTTCTAAGGGCGAACAATGT
1 TTTCATTTCTAAGGGCGAACAATGT
62270419 TTTCATTTCTAAGGGCGAACAATGT
1 TTTCATTTCTAAGGGCGAACAATGT
62270444 AGATCTTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (25 bp):
TTTCATTTCTAAGGGCGAACAATGT
Done.