Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1808
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: 79399
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1559 original size:41 final size:41
Alignment explanation
Indices: 1496--1579 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 41
1486 ACTTTGTATC
*
1496 AACACTTATGTATCGATGCATTTACTATTTGTATCGATACA
1 AACACTTATGTATCGATACATTTACTATTTGTATCGATACA
* * *
1537 AACACTTATGTATTGATACATTTATTGTTTGTATCGATACA
1 AACACTTATGTATCGATACATTTACTATTTGTATCGATACA
1578 AA
1 AA
1580 TTATGAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.40
Consensus pattern (41 bp):
AACACTTATGTATCGATACATTTACTATTTGTATCGATACA
Found at i:1575 original size:21 final size:20
Alignment explanation
Indices: 1499--1577 Score: 68
Period size: 21 Copynumber: 3.9 Consensus size: 20
1489 TTGTATCAAC
* *
1499 ACTTATGTATCGATGCATTT
1 ACTTTTGTATCGATACATTT
***
1519 ACTATTTGTATCGATACAAAC
1 ACT-TTTGTATCGATACATTT
* *
1540 ACTTATGTATTGATACATTT
1 ACTTTTGTATCGATACATTT
*
1560 ATTGTTTGTATCGATACA
1 ACT-TTTGTATCGATACA
1578 AATTATGAAA
Statistics
Matches: 44, Mismatches: 13, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
20 17 0.39
21 27 0.61
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (20 bp):
ACTTTTGTATCGATACATTT
Found at i:2501 original size:12 final size:12
Alignment explanation
Indices: 2471--2505 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
2461 AATATACACA
*
2471 TATTTTAAATAT
1 TATTTAAAATAT
2483 T-TTTAAAATAT
1 TATTTAAAATAT
2494 TATTTAAAATAT
1 TATTTAAAATAT
2506 AAAACTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TATTTAAAATAT
Found at i:2606 original size:84 final size:85
Alignment explanation
Indices: 2447--2617 Score: 274
Period size: 84 Copynumber: 2.0 Consensus size: 85
2437 AAATATGAAA
*
2447 AATATGTGTATATTAATATACACATATTTTAAATATTTTTAAAATATTATTTAAAATATAAAACT
1 AATATGTGTATATTAATATACACATATTTTAAATATTTTTAAAATATTATTTAAAATATAAAAAT
*
2512 AATTGCATATTAATAATTTT
66 AATTGAATATTAATAATTTT
* * *
2532 AATATGTGTATA-TATTATTACACATATTTTTAATA-TTTTAAAATATTATTTAAAGTATAAAAA
1 AATATGTGTATATTAATA-TACACATATTTTAAATATTTTTAAAATATTATTTAAAATATAAAAA
2595 TAATTGAATATTAATAATTTT
65 TAATTGAATATTAATAATTTT
2616 AA
1 AA
2618 ACTTTTTGAA
Statistics
Matches: 80, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
84 52 0.65
85 28 0.35
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (85 bp):
AATATGTGTATATTAATATACACATATTTTAAATATTTTTAAAATATTATTTAAAATATAAAAAT
AATTGAATATTAATAATTTT
Found at i:5501 original size:27 final size:26
Alignment explanation
Indices: 5457--5540 Score: 98
Period size: 26 Copynumber: 3.2 Consensus size: 26
5447 TTGAATTTTG
* *
5457 AAATTTGGATAAAAATTTTAAAATTC
1 AAATTTGAATAATAATTTTAAAATTC
* *
5483 AAATTTTAGATAATGATTTT-AAATTC
1 AAATTTGA-ATAATAATTTTAAAATTC
*
5509 AAGATTTGAATAGTAATTTTAAAATTC
1 AA-ATTTGAATAATAATTTTAAAATTC
5536 AAATT
1 AAATT
5541 GTTCAAGTAG
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
26 26 0.54
27 22 0.46
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (26 bp):
AAATTTGAATAATAATTTTAAAATTC
Found at i:5549 original size:26 final size:24
Alignment explanation
Indices: 5470--5549 Score: 63
Period size: 26 Copynumber: 3.0 Consensus size: 24
5460 TTTGGATAAA
5470 AATTTTAAAATTCAAATTTT-AGAT
1 AATTTTAAAATTCAAATTTTAAG-T
* *
5494 AATGATTTTAAATTCAAGATTTGAATAGT
1 AAT--TTTAAAATTCAA-ATTT-TA-AGT
5523 AATTTTAAAATTCAAATTGTTCAAGT
1 AATTTTAAAATTCAAATT-TT-AAGT
5549 A
1 A
5550 GGATATTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
24 3 0.07
26 18 0.41
27 17 0.39
29 4 0.09
30 2 0.05
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (24 bp):
AATTTTAAAATTCAAATTTTAAGT
Found at i:7082 original size:20 final size:20
Alignment explanation
Indices: 7059--7133 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 20
7049 AAGTACCCAG
7059 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
7079 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
7099 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
*
7119 ATGTATCAATACATT
1 ATGTATCGATACATT
7134 CTGTCTTTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:21075 original size:20 final size:20
Alignment explanation
Indices: 21050--21126 Score: 72
Period size: 19 Copynumber: 3.9 Consensus size: 20
21040 CTTCATACCC
21050 AAAAAACAAACAAAAAATAG
1 AAAAAACAAACAAAAAATAG
*
21070 AAAAAAACCAAAAAAAAAATA-
1 -AAAAAA-CAAACAAAAAATAG
*
21091 AAAAAACAAA-AAAACCA-AG
1 AAAAAACAAACAAAA-AATAG
21110 AAAAAA-ATAACAAAAAA
1 AAAAAACA-AACAAAAAA
21127 AACAAAAAGG
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
18 6 0.12
19 14 0.29
20 10 0.21
21 6 0.12
22 12 0.25
ACGTcount: A:0.83, C:0.10, G:0.03, T:0.04
Consensus pattern (20 bp):
AAAAAACAAACAAAAAATAG
Found at i:21081 original size:22 final size:20
Alignment explanation
Indices: 21050--21128 Score: 81
Period size: 22 Copynumber: 3.8 Consensus size: 20
21040 CTTCATACCC
*
21050 AAAAAACAAACAAAAAATAGA
1 AAAAAACAAAAAAAAAATA-A
21071 AAAAAACCAAAAAAAAAAT-A
1 AAAAAA-CAAAAAAAAAATAA
21091 AAAAAACAAAAAAACCAAGA-AA
1 AAAAAACAAAAAAA--AA-ATAA
21113 AAAATAACAAAAAAAA
1 AAAA-AACAAAAAAAA
21129 CAAAAAGGGG
Statistics
Matches: 51, Mismatches: 1, Indels: 12
0.80 0.02 0.19
Matches are distributed among these distances:
19 8 0.16
20 7 0.14
21 9 0.18
22 17 0.33
23 10 0.20
ACGTcount: A:0.84, C:0.10, G:0.03, T:0.04
Consensus pattern (20 bp):
AAAAAACAAAAAAAAAATAA
Found at i:21082 original size:9 final size:9
Alignment explanation
Indices: 21051--21134 Score: 60
Period size: 9 Copynumber: 8.6 Consensus size: 9
21041 TTCATACCCA
21051 AAAAACAAAC
1 AAAAA-AAAC
* *
21061 AAAAAATAG
1 AAAAAAAAC
*
21070 AAAAAAACC
1 AAAAAAAAC
*
21079 AAAAAAAAA
1 AAAAAAAAC
21088 ATAAAAAAAC
1 A-AAAAAAAC
*
21098 AAAAAAACCAAGA
1 -AAAAAA--AA-C
21111 AAAAAATAAC
1 AAAAAA-AAC
21121 AAAAAAAAC
1 AAAAAAAAC
21130 AAAAA
1 AAAAA
21135 GGGGTCCAGA
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
9 24 0.41
10 23 0.40
11 3 0.05
12 8 0.14
ACGTcount: A:0.83, C:0.11, G:0.02, T:0.04
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:21093 original size:28 final size:28
Alignment explanation
Indices: 21048--21134 Score: 102
Period size: 29 Copynumber: 3.0 Consensus size: 28
21038 TTCTTCATAC
* * *
21048 CCAAAAAACAAACAAAAAATAGAAAAAAA
1 CCAAAAAAAAAATAAAAAA-ACAAAAAAA
21077 CCAAAAAAAAAATAAAAAAACAAAAAAA
1 CCAAAAAAAAAATAAAAAAACAAAAAAA
* *
21105 CCAAGAAAAAAATAACAAAAAAAACAAAAA
1 CCAAAAAAAAAATAA-AAAAACAA-AAAAA
21135 GGGGTCCAGA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
28 22 0.43
29 24 0.47
30 5 0.10
ACGTcount: A:0.82, C:0.13, G:0.02, T:0.03
Consensus pattern (28 bp):
CCAAAAAAAAAATAAAAAAACAAAAAAA
Found at i:21112 original size:40 final size:41
Alignment explanation
Indices: 21050--21134 Score: 104
Period size: 40 Copynumber: 2.1 Consensus size: 41
21040 CTTCATACCC
*
21050 AAAAAACAAACAAAAAATAGAAAAAAACCAA-AAAAAAAATA
1 AAAAAACAAACAAAAAATAGAAAAAAA-CAACAAAAAAAACA
* *
21091 AAAAAACAAA-AAAACCA-AGAAAAAAATAACAAAAAAAACA
1 AAAAAACAAACAAAA-AATAGAAAAAAACAACAAAAAAAACA
21131 AAAA
1 AAAA
21135 GGGGTCCAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
39 2 0.05
40 26 0.67
41 11 0.28
ACGTcount: A:0.84, C:0.11, G:0.02, T:0.04
Consensus pattern (41 bp):
AAAAAACAAACAAAAAATAGAAAAAAACAACAAAAAAAACA
Found at i:21133 original size:20 final size:19
Alignment explanation
Indices: 21050--21134 Score: 80
Period size: 20 Copynumber: 4.2 Consensus size: 19
21040 CTTCATACCC
*
21050 AAAAAACAAACAAAAAATAGA
1 AAAAAACAAA-AAAAAA-ACA
*
21071 AAAAAACCAAAAAAAAAATA
1 AAAAAA-CAAAAAAAAAACA
* *
21091 AAAAAACAAAAAAACCAAGA
1 AAAAAACAAAAAAA-AAACA
*
21111 AAAAAATAACAAAAAAAACA
1 AAAAAACAA-AAAAAAAACA
21131 AAAA
1 AAAA
21135 GGGGTCCAGA
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
19 8 0.15
20 26 0.47
21 17 0.31
22 4 0.07
ACGTcount: A:0.84, C:0.11, G:0.02, T:0.04
Consensus pattern (19 bp):
AAAAAACAAAAAAAAAACA
Found at i:22389 original size:28 final size:28
Alignment explanation
Indices: 22349--22768 Score: 615
Period size: 28 Copynumber: 14.9 Consensus size: 28
22339 TGTTCATCTC
22349 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
22377 TTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* *
22406 TTTAAAGCCCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
22434 TTCAAAGCCCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
22462 TTCAAAGCCCACAAGTTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* *
22491 TTCAAAACCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
22519 TTCAAAGACCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
22547 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
22575 TTCAAAGCTCACAAGTTAGTGGCACTTCT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
*
22604 TTCAAAGCCCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
22632 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * **
22660 TTCAAAACCCACAAGTCAATGGCATTCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
22688 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
22716 TTCAAAGCCCACAAGTCAGTGGCACCAT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
22744 TTCAAAGCCCACAAGTTAGTGGCAC
1 TTCAAAGCCCACAAGTCAGTGGCAC
22769 TTTTTTCAAG
Statistics
Matches: 357, Mismatches: 32, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
28 282 0.79
29 75 0.21
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.22
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:22492 original size:85 final size:85
Alignment explanation
Indices: 22349--22768 Score: 639
Period size: 85 Copynumber: 5.0 Consensus size: 85
22339 TGTTCATCTC
* * *
22349 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTTAAAGC
1 TTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
22414 CCACAAGTTAGTGGCACCCT
66 CCACAAGTTAGTGGCACCCT
* * *
22434 TTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAAC
1 TTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
* *
22499 CCACAAGTCAGTGGCATCCT
66 CCACAAGTTAGTGGCACCCT
*
22519 TTCAAAGACCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGC
1 TTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
* *
22583 TCACAAGTTAGTGGCACTTCT
66 CCACAAGTTAGTGGCAC-CCT
*
22604 TTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAAC
1 TTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
* * **
22668 CCACAAGTCAATGGCATTCT
66 CCACAAGTTAGTGGCACCCT
* * *
22688 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCAC-CATTTCAAAGC
1 TTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
22752 CCACAAGTTAGTGGCAC
66 CCACAAGTTAGTGGCAC
22769 TTTTTTCAAG
Statistics
Matches: 305, Mismatches: 27, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
84 99 0.32
85 206 0.68
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.22
Consensus pattern (85 bp):
TTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
CCACAAGTTAGTGGCACCCT
Found at i:22547 original size:113 final size:113
Alignment explanation
Indices: 22349--22768 Score: 639
Period size: 113 Copynumber: 3.7 Consensus size: 113
22339 TGTTCATCTC
* *
22349 TTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTTAAAG
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAG
*
22413 CCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACCCT
65 CCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCT
* * * *
22462 TTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAACCCACAAGTCAGTGGCATCCTTTCAAAGA
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
22527 CCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCT
66 CCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCT
* * * * *
22575 TTCAAAGCTCACAAGTTAGTGGCACTTCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
* * * * **
22640 CCACAAGTCAGTGGCATCCTTTCAAAACCCACAAGTCAATGGCATTCT
66 CCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCT
22688 TTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCA-CCATTTCAAAG
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAG
22751 CCCACAAGTTAGTGGCAC
65 CCCACAAGTTAGTGGCAC
22769 TTTTTTCAAG
Statistics
Matches: 279, Mismatches: 26, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
111 2 0.01
112 50 0.18
113 202 0.72
114 25 0.09
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.22
Consensus pattern (113 bp):
TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
CCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:22868 original size:32 final size:30
Alignment explanation
Indices: 22349--22867 Score: 268
Period size: 28 Copynumber: 18.1 Consensus size: 30
22339 TGTTCATCTC
* **
22349 TTCAAAGCCCAC-AAGTCAGTGGCAC-CCT
1 TTCAAAGCCCACAAAGTCAGTGGTACTTTT
*
22377 TTCAAAGCCCAC-AAGTCAGTGGCACTCTTT
1 TTCAAAGCCCACAAAGTCAGTGGTACT-TTT
* * **
22407 TT-AAAGCCCAC-AAGTTAGTGGCAC-CCT
1 TTCAAAGCCCACAAAGTCAGTGGTACTTTT
* * **
22434 TTCAAAGCCCAC-AAGTTAGTGGCAC-CCT
1 TTCAAAGCCCACAAAGTCAGTGGTACTTTT
* * *
22462 TTCAAAGCCCAC-AAGTTAGTGGCACTCTT
1 TTCAAAGCCCACAAAGTCAGTGGTACTTTT
* * **
22491 TTCAAAACCCAC-AAGTCAGTGGCA-TCCT
1 TTCAAAGCCCACAAAGTCAGTGGTACTTTT
* * * **
22519 TTCAAAGACCAC-AAGTTAGTGGCAC-CCT
1 TTCAAAGCCCACAAAGTCAGTGGTACTTTT
* **
22547 TTCAAAGCCCAC-AAGTCAGTGGCAC-CCT
1 TTCAAAGCCCACAAAGTCAGTGGTACTTTT
* * * *
22575 TTCAAAGCTCAC-AAGTTAGTGGCACTTCT
1 TTCAAAGCCCACAAAGTCAGTGGTACTTTT
* * **
22604 TTCAAAGCCCAC-AAGTTAGTGGCAC-CCT
1 TTCAAAGCCCACAAAGTCAGTGGTACTTTT
* **
22632 TTCAAAGCCCAC-AAGTCAGTGGCA-TCCT
1 TTCAAAGCCCACAAAGTCAGTGGTACTTTT
* * * *
22660 TTCAAAACCCAC-AAGTCAATGGCA-TTCT
1 TTCAAAGCCCACAAAGTCAGTGGTACTTTT
* **
22688 TTCAAAGCCCAC-AAGTCAGTGGCA-TCCT
1 TTCAAAGCCCACAAAGTCAGTGGTACTTTT
* **
22716 TTCAAAGCCCAC-AAGTCAGTGGCAC-CAT
1 TTCAAAGCCCACAAAGTCAGTGGTACTTTT
* *
22744 TTCAAAGCCCAC-AAGTTAGTGGCACTTTT
1 TTCAAAGCCCACAAAGTCAGTGGTACTTTT
* *
22773 TTC-AAGACCCACAAA-CCAGTAGTAACTTTT
1 TTCAAAG-CCCACAAAGTCAGTGGT-ACTTTT
* * * *
22803 TTCAAAGCCTACACGAGTCGGTGGCAACTTTT
1 TTCAAAGCCCACA-AAGTCAGTGG-TACTTTT
*
22835 TTCAAAGCCCACATAAGTTAGTGGTACTTTT
1 TTCAAAGCCCACA-AAGTCAGTGGTACTTTT
22866 TT
1 TT
22868 TAAAAAAAAA
Statistics
Matches: 429, Mismatches: 46, Indels: 29
0.85 0.09 0.06
Matches are distributed among these distances:
27 3 0.01
28 282 0.66
29 84 0.20
30 19 0.04
31 12 0.03
32 29 0.07
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (30 bp):
TTCAAAGCCCACAAAGTCAGTGGTACTTTT
Found at i:23705 original size:20 final size:20
Alignment explanation
Indices: 23677--23751 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
23667 AAGGACCTAG
23677 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * * *
23697 ATATATCGATATATGTATGA
1 ATGTATCGATACATTTTTCA
*
23717 ATGTATGGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
23737 ATGTATCGATACATT
1 ATGTATCGATACATT
23752 CTGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:27131 original size:79 final size:80
Alignment explanation
Indices: 27007--27487 Score: 449
Period size: 79 Copynumber: 6.2 Consensus size: 80
26997 AAATCGGAGG
* * ** *
27007 TGGAGTATCCCCTC-GAAAATAATGGGGTCGGAGTATCCATGATTGTGGAAAATTAG-TATTTT-
1 TGGAGTATCCCCTCAG-AAATAACGGGGTTGGAGTATCCCCGATTGTGGAAAATTCGATATTTTA
27069 GAAAGTAAAACTGGGGT
65 GAAA-TAAAACTGGGGT
** * * *
27086 TAAAGTATCCCCTCAGAAGTAACGGGGTTGGAGTATCCCCAATTGTGAAAAATT-GATATTTTAG
1 TGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGGAAAATTCGATATTTTAG
27150 AAATAAAA-TCGGGGT
66 AAATAAAACT-GGGGT
* *
27165 TGGAGTATCCCCTCAGAAATAACAGGGTTGGAGTATCCCCGATTGTGGAAAA-TCGATGTTTT--
1 TGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGGAAAATTCGATATTTTAG
*
27227 -AA-AAATC-GGGGT
66 AAATAAAACTGGGGT
** * * * *
27239 TGGAGTAT-CCCTTTGAAAATAACAGGGTTTGAGTATCCTCGATTATGGAAAA-TCGATATTTTA
1 TGGAGTATCCCCTCAG-AAATAACGGGGTTGGAGTATCCCCGATTGTGGAAAATTCGATATTTTA
*
27302 GAAATAAAATTGGGGT
65 GAAATAAAACTGGGGT
* * * * * *
27318 TGGAGTATCTCCTGAGAAATAACGGGGTTGAAGTATCCCCAATTATGGAAAA-TCGATGTTTTAG
1 TGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGGAAAATTCGATATTTTAG
* *
27382 AAATAAAACCGAGGT
66 AAATAAAACTGGGGT
** ** * * * *
27397 TGGAGTATCCTTTC-GAAAATAACAAGGTTGGAGTATCCCCAATTAT-GAAAAATCGATGTTTT-
1 TGGAGTATCCCCTCAG-AAATAACGGGGTTGGAGTATCCCCGATTGTGGAAAATTCGATATTTTA
27459 GAAAATAAAA-TCGGGGT
65 G-AAATAAAACT-GGGGT
27476 TGGAGTATCCCC
1 TGGAGTATCCCC
27488 GATTGTAAAA
Statistics
Matches: 337, Mismatches: 48, Indels: 34
0.80 0.11 0.08
Matches are distributed among these distances:
73 5 0.01
74 55 0.16
75 3 0.01
76 2 0.01
77 2 0.01
78 13 0.04
79 248 0.74
80 9 0.03
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (80 bp):
TGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGGAAAATTCGATATTTTAG
AAATAAAACTGGGGT
Found at i:27317 original size:153 final size:155
Alignment explanation
Indices: 27105--27487 Score: 531
Period size: 153 Copynumber: 2.5 Consensus size: 155
27095 CCCTCAGAAG
* * *
27105 TAACGGGGTTGGAGTATCCCCAATTGTGAAAAATTGATATTTTAGAAATAAAATCGGGGTTGGAG
1 TAACAGGGTTGGAGTATCCCCAATTATGAAAAATCGATATTTTAGAAATAAAATCGGGGTTGGAG
* * * *
27170 TATCCCCTCAGAAATAACAGGGTTGGAGTATCCCCGATTGTGGAAAATCGATGTTTT-A-AAAAT
66 TATCCCCTCAGAAATAACAGGGTTGAAGTATCCCCAATTATGGAAAATCGATGTTTTAATAAAAC
*
27233 CGGGGTTGGAGTATCCCTTT-GAAAA
131 CGAGGTTGGAGTAT-CCTTTCGAAAA
* * * * *
27258 TAACAGGGTTTGAGTATCCTCGATTATGGAAAATCGATATTTTAGAAATAAAATTGGGGTTGGAG
1 TAACAGGGTTGGAGTATCCCCAATTATGAAAAATCGATATTTTAGAAATAAAATCGGGGTTGGAG
* * *
27323 TATCTCCTGAGAAATAACGGGGTTGAAGTATCCCCAATTATGGAAAATCGATGTTTTAGAAATAA
66 TATCCCCTCAGAAATAACAGGGTTGAAGTATCCCCAATTATGGAAAATCGATGTTTT---AATAA
27388 AACCGAGGTTGGAGTATCCTTTCGAAAA
128 AACCGAGGTTGGAGTATCCTTTCGAAAA
* *
27416 TAACAAGGTTGGAGTATCCCCAATTATGAAAAATCGATGTTTT-GAAAATAAAATCGGGGTTGGA
1 TAACAGGGTTGGAGTATCCCCAATTATGAAAAATCGATATTTTAG-AAATAAAATCGGGGTTGGA
27480 GTATCCCC
65 GTATCCCC
27488 GATTGTAAAA
Statistics
Matches: 199, Mismatches: 24, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
153 108 0.54
157 7 0.04
158 84 0.42
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (155 bp):
TAACAGGGTTGGAGTATCCCCAATTATGAAAAATCGATATTTTAGAAATAAAATCGGGGTTGGAG
TATCCCCTCAGAAATAACAGGGTTGAAGTATCCCCAATTATGGAAAATCGATGTTTTAATAAAAC
CGAGGTTGGAGTATCCTTTCGAAAA
Found at i:27402 original size:232 final size:234
Alignment explanation
Indices: 26994--27487 Score: 624
Period size: 232 Copynumber: 2.1 Consensus size: 234
26984 GCGATAGAAG
** *
26994 ATAAAATCGGAGG-TGGAGTATCCCCTCGAAAATAATGGGGTCGGAGTATCCATGATTGTGGAAA
1 ATAAAATCGG-GGTTGGAGTATCCCCTCGAAAATAACAGGGTCGGAGTATCCATGATTATGGAAA
* * *
27058 ATTAGTATTTTGAAAGTAAAACTGGGGTTAAAGTATCCCCTCAGAAGTAACGGGGTTGGAGTATC
65 ATGAGTATTTTGAAAGTAAAACTGGGGTTAAAGTATCCCCTCAGAAATAACGGGGTTGAAGTATC
* * * *
27123 CCCAATTGTGAAAAATTGATATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTC-AGAAATAA
130 CCCAATTATGAAAAATCGATATTTTAGAAATAAAACCGAGGTTGGAGTATCCCCTCGA-AAATAA
* * * *
27187 CAGGGTTGGAGTATCCCCGATTGTGGAAAATCGATGTTTT-
194 CAAGGTTGGAGTATCCCCAATTATGAAAAATCGATGTTTTA
* * **
27227 A-AAAATCGGGGTTGGAGTATCCCTTTGAAAATAACAGGGTTTGAGTATCC-TCGATTATGGAAA
1 ATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTCGGAGTATCCAT-GATTATGGAAA
* ** * *
27290 ATCGA-TATTTTAGAAA-TAAAATTGGGGTTGGAGTATCTCCTGAGAAATAACGGGGTTGAAGTA
65 AT-GAGTATTTT-GAAAGTAAAACTGGGGTTAAAGTATCCCCTCAGAAATAACGGGGTTGAAGTA
* * **
27353 TCCCCAATTATGGAAAATCGATGTTTTAGAAATAAAACCGAGGTTGGAGTATCCTTTCGAAAATA
128 TCCCCAATTATGAAAAATCGATATTTTAGAAATAAAACCGAGGTTGGAGTATCCCCTCGAAAATA
27418 ACAAGGTTGGAGTATCCCCAATTATGAAAAATCGATGTTTTGAAA
193 ACAAGGTTGGAGTATCCCCAATTATGAAAAATCGATGTTTT---A
27463 ATAAAATCGGGGTTGGAGTATCCCC
1 ATAAAATCGGGGTTGGAGTATCCCC
27488 GATTGTAAAA
Statistics
Matches: 223, Mismatches: 28, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
231 3 0.01
232 190 0.85
233 7 0.03
236 1 0.00
237 22 0.10
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.28
Consensus pattern (234 bp):
ATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTCGGAGTATCCATGATTATGGAAAA
TGAGTATTTTGAAAGTAAAACTGGGGTTAAAGTATCCCCTCAGAAATAACGGGGTTGAAGTATCC
CCAATTATGAAAAATCGATATTTTAGAAATAAAACCGAGGTTGGAGTATCCCCTCGAAAATAACA
AGGTTGGAGTATCCCCAATTATGAAAAATCGATGTTTTA
Found at i:27484 original size:51 final size:51
Alignment explanation
Indices: 27422--27538 Score: 162
Period size: 51 Copynumber: 2.3 Consensus size: 51
27412 AAAATAACAA
* * * *
27422 GGTTGGAGTATCCCCAATTATGAAAAATCGATGTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCAATTATAAAAAATCGATATTTTAAAAATAAAATCAG
* * *
27473 GGTTGGAGTATCCCCGATTGTAAAAAATTGATATTTTAAAAATAAAATCAG
1 GGTTGGAGTATCCCCAATTATAAAAAATCGATATTTTAAAAATAAAATCAG
*
27524 GTTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
27539 TCAGAAATAA
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.31
Consensus pattern (51 bp):
GGTTGGAGTATCCCCAATTATAAAAAATCGATATTTTAAAAATAAAATCAG
Found at i:27587 original size:130 final size:130
Alignment explanation
Indices: 27340--27598 Score: 301
Period size: 130 Copynumber: 2.0 Consensus size: 130
27330 TGAGAAATAA
** * *
27340 CGGGGTTGAAGTATCCCCAATTATGGAAAATCGATGTTTTAGAAATAAAACCGAGGTTGGAGTAT
1 CGGGGTTGAAGTATCCCCAATTATAAAAAATCGATATTTTAAAAATAAAACCGAGGTTGGAGTAT
** *
27405 CCTTTCGAAAATAACAAGGTTGGAGTATCCCCAATTATGAAAAATCGATGTTTT-GAAAATAAAA
66 CCCCTCGAAAATAACAAGGTTGGAGTATCCCCAATTATGAAAAATAGATGTTTTAG-AAATAAAA
27469 T
130 T
* * * * *
27470 CGGGGTTGGAGTATCCCCGATTGTAAAAAATTGATATTTTAAAAATAAAATC-AGGTTTGGAGTA
1 CGGGGTTGAAGTATCCCCAATTATAAAAAATCGATATTTTAAAAATAAAACCGAGG-TTGGAGTA
** * * *
27534 TCCCCTC-AGAAATAACGGGGTTGGAGTATCCCCGATTGTAGAAAATTAG-TGTTTTAGAAATAA
65 TCCCCTCGA-AAATAACAAGGTTGGAGTATCCCCAATTAT-GAAAAATAGATGTTTTAGAAATAA
27597 AA
128 AA
27599 ACATGAATGA
Statistics
Matches: 108, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
129 4 0.04
130 96 0.89
131 8 0.07
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.29
Consensus pattern (130 bp):
CGGGGTTGAAGTATCCCCAATTATAAAAAATCGATATTTTAAAAATAAAACCGAGGTTGGAGTAT
CCCCTCGAAAATAACAAGGTTGGAGTATCCCCAATTATGAAAAATAGATGTTTTAGAAATAAAAT
Found at i:33909 original size:52 final size:51
Alignment explanation
Indices: 33831--33979 Score: 235
Period size: 52 Copynumber: 2.9 Consensus size: 51
33821 CGAAATATGA
33831 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
33883 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
* *
33935 AAATTTTCCTGCATGTATCGATACAATGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
33980 ATGTATCGAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 3 0.03
52 84 0.94
53 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:33986 original size:13 final size:13
Alignment explanation
Indices: 33968--33992 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33958 CAATGATCAG
33968 TGTATCGATACAA
1 TGTATCGATACAA
33981 TGTATCGATACA
1 TGTATCGATACA
33993 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:34060 original size:20 final size:20
Alignment explanation
Indices: 34031--34088 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
34021 GCAGTAGCTT
34031 AAAT-TGTATCGATACAAAA
1 AAATATGTATCGATACAAAA
*
34050 AAATATGTATCGATACAACA
1 AAATATGTATCGATACAAAA
***
34070 CTTTATGTATCGATACAAA
1 AAATATGTATCGATACAAA
34089 TCGTTGAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (20 bp):
AAATATGTATCGATACAAAA
Found at i:34481 original size:45 final size:44
Alignment explanation
Indices: 34394--34628 Score: 215
Period size: 45 Copynumber: 5.3 Consensus size: 44
34384 ACACTACTGC
* * * * *
34394 TTGAGGAC-AAAGGAAAAAAAGGAAAAAAAAGTGCGTTCTGCTCT
1 TTGAGGACAAAAAGAAAAAAAAG-AAATAAAGTGTGTCCTGCTCT
* *
34438 TTGAGGACAAAAAAGAAAAAAAAGAAATAAAGTATGTCATGCTCT
1 TTGAGGAC-AAAAAGAAAAAAAAGAAATAAAGTGTGTCCTGCTCT
** * * * *
34483 TTGAGGACAAAGGGAAAATAAGGAAATAAGGTGTGCCCTGCTCT
1 TTGAGGACAAAAAGAAAAAAAAGAAATAAAGTGTGTCCTGCTCT
* * *
34527 TTGAGGAC-AAAGGAAAAAAGAA-AAAAAAAGTGTGTCCTACTCT
1 TTGAGGACAAAAAGAAAAAA-AAGAAATAAAGTGTGTCCTGCTCT
* * * * *
34570 TTGAGGATAAAAGAGAAAATAAGGAAATGAAGTGTGTCCTACTCT
1 TTGAGGACAAAA-AGAAAAAAAAGAAATAAAGTGTGTCCTGCTCT
*
34615 TTGAGGACTAAAAG
1 TTGAGGACAAAAAG
34629 GTGACACCAA
Statistics
Matches: 155, Mismatches: 30, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
43 33 0.21
44 51 0.33
45 59 0.38
46 12 0.08
ACGTcount: A:0.45, C:0.11, G:0.24, T:0.20
Consensus pattern (44 bp):
TTGAGGACAAAAAGAAAAAAAAGAAATAAAGTGTGTCCTGCTCT
Found at i:34824 original size:63 final size:62
Alignment explanation
Indices: 34605--35444 Score: 887
Period size: 63 Copynumber: 13.9 Consensus size: 62
34595 AATGAAGTGT
* * *
34605 GTCCTACTCTTTGAGGACTAAAAGGTGACACCAACTTGTGTGGGCTTT-AAAAGAGGAAAAGAAA
1 GTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGA--AAAAG---
*
34669 GT
61 GC
* * * *
34671 GTCCTGCTCCTTGAGGACTAAAGAGTGCCACCAACTCGTGTGGGTTTTGAAAAGAAAAAGGC
1 GTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGC
* *
34733 G-----CTCTTTAAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGGC
1 GTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGC
*
34790 GTCCTACTCTTTGAGGACTAAAAGGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAAAGGC
1 GTCCTACTCTTTGAGGACT-AAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAA-GAAAAAGGC
* *
34854 ATCCTACTCTTTAAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAAAGGC
1 GTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAA-GAAAAAGGC
* * * * * *
34917 ATCTTGCTCTTTGAGTACTAGAGGGTGCCACCAACTCGTGTGAGC-TT-----G--AAAGGC
1 GTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGC
* * * *
34971 GTCCTGCTCTTTAAGGACTAAAGGGTGCCACCAGCTCGTGTGGGCTTTGAAAAGAAAAAGAC
1 GTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGC
* * *
35033 GTCCTACTTTTTGAGGGCTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAGAGAAAAA---
1 GTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGC
** * * * ** *
35092 -----AAACTTTGAAGACTAAAGTGTGCCACCAACTCATGTAAGCTTTGAAAAGAAAAAAGC
1 GTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGC
* * * * *
35149 GTCCTCCTCTTTAAAGACTAAAGGGTGCCACCCACTCGTGTGGGCTTTGAAAAAGAAAAAGGT
1 GTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTG-AAAAGAAAAAGGC
* * * **
35212 ATTCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGGAAAAAAAC
1 GTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAA-GAAAAAGGC
* *
35275 GTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTAAAAAGGAAAAAGGC
1 GTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAA-GAAAAAGGC
* * **
35338 ATCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGC-TT-----G--AAAGTT
1 GTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGC
* *
35392 GTCC-AGCTTTTTGAGGACTAAAGGGTGCCACCAACTCGTGTAGGCTTTGAAAA
1 GTCCTA-CTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAA
35445 AAGGATGTCA
Statistics
Matches: 657, Mismatches: 84, Indels: 72
0.81 0.10 0.09
Matches are distributed among these distances:
54 132 0.20
55 4 0.01
56 2 0.00
57 52 0.08
60 1 0.00
62 115 0.18
63 273 0.42
64 26 0.04
65 5 0.01
66 41 0.06
67 6 0.01
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.24
Consensus pattern (62 bp):
GTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGC
Found at i:35083 original size:117 final size:117
Alignment explanation
Indices: 34848--35443 Score: 561
Period size: 116 Copynumber: 5.0 Consensus size: 117
34838 TGAAAAGGAA
34848 AAAGGCATCCTACTCTTTAAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAA
1 AAAGGCATCCTACTCTTTAAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAA-GAAAA
* * * * * * *
34913 AGGCATCTTGCTCTTTGAGTACTAGAGGGTGCCACCAACTCGTGTGAGC-TTG
65 AGACGTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTG
* * *
34965 AAAGGCGTCCTGCTCTTTAAGGACTAAAGGGTGCCACCAGCTCGTGTGGGCTTTGAAAAGAAAAA
1 AAAGGCATCCTACTCTTTAAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAA
* *
35030 GACGTCCTACTTTTTGAGGGCTAAAGGGTGCCACCAACTCGTGTGGGCTTTG
66 GACGTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTG
** **** * * * **
35082 AAGAGAAAAAAAACT-TTGAA-GACTAAAGTGTGCCACCAACTCATGTAAGCTTTGAAAAGAAAA
1 AA-AGGCATCCTACTCTTTAAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAA
* * * *
35145 A-AGCGTCCTCCTCTTTAAAGACTAAAGGGTGCCACCCACTCGTGTGGGCTTTGAAAAAG
65 AGA-CGTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT------G
* * * *
35204 AAAAAGGTATTCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGGAA
1 --AAAGGCATCCTACTCTTTAAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAA-GAA
* *
35269 AAAAACGTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTAAAAAGG
63 AAAGACGTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT------G
* *
35330 AAAAAGGCATCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGC-TT-----G--A
1 --AAAGGCATCCTACTCTTTAAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAA
** * *
35387 AAGTTGTCC-AGCTTTTTGAGGACTAAAGGGTGCCACCAACTCGTGTAGGCTTTG
64 AAGACGTCCTA-CTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTG
35441 AAA
1 AAA
35444 AAAGGATGTC
Statistics
Matches: 403, Mismatches: 60, Indels: 40
0.80 0.12 0.08
Matches are distributed among these distances:
109 3 0.01
111 1 0.00
115 1 0.00
116 128 0.32
117 111 0.28
118 4 0.01
119 1 0.00
122 1 0.00
123 6 0.01
124 5 0.01
125 37 0.09
126 104 0.26
127 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.24
Consensus pattern (117 bp):
AAAGGCATCCTACTCTTTAAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAA
GACGTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTG
Found at i:36719 original size:31 final size:32
Alignment explanation
Indices: 36666--36745 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 32
36656 GTCGTTCCCA
* *
36666 TTTTATTCATTCTTTTT-GTTTT-TTTCTCTTG
1 TTTTTTTCATT-TTTTTATTTTTGTTTCTCTTG
36697 TTTTTTTCATTTTTTTCATTTTTGTTTCTCTTG
1 TTTTTTTCATTTTTTT-ATTTTTGTTTCTCTTG
* *
36730 TGTTTCTCATTTTTTT
1 TTTTTTTCATTTTTTT
36746 GCTTTTACCC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
30 5 0.12
31 10 0.24
32 4 0.10
33 23 0.55
ACGTcount: A:0.06, C:0.12, G:0.06, T:0.75
Consensus pattern (32 bp):
TTTTTTTCATTTTTTTATTTTTGTTTCTCTTG
Found at i:36730 original size:33 final size:32
Alignment explanation
Indices: 36684--36745 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 32
36674 ATTCTTTTTG
* *
36684 TTTTTTTCTCTTGTTTTTTTCATTTTTTTCAT
1 TTTTTTTCTCTTGTGTTTCTCATTTTTTTCAT
36716 TTTTGTTTCTCTTGTGTTTCTCATTTTTTT
1 TTTT-TTTCTCTTGTGTTTCTCATTTTTTT
36746 GCTTTTACCC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 4 0.15
33 23 0.85
ACGTcount: A:0.05, C:0.13, G:0.06, T:0.76
Consensus pattern (32 bp):
TTTTTTTCTCTTGTGTTTCTCATTTTTTTCAT
Found at i:43502 original size:133 final size:131
Alignment explanation
Indices: 43181--43542 Score: 471
Period size: 133 Copynumber: 2.7 Consensus size: 131
43171 ATTATTTTTT
* *
43181 AATAAAAAATAATATTTAATTAAATTTAAAAAAATACATTAACAAATTAAAATATTAA-TATTAT
1 AATAAAAAATAATATTTAATTAAGTTTAAAAATATACATTAACAAATTAAAATATTAATTATTAT
* **** * * **
43245 ATTTTTTATAAAAAATAAAAAATTTTAAA-T-AAGAAATAAAAAAGGTTTTTTTATTATTTTTTA
66 -GTTTTTAT-AAAAATAAAAAATTTTAAATTAAAGAAATAAAAAAAAAATTATTATTAATTCCTA
43308 ATA
129 ATA
* *
43311 AATAAAAACTAATATTTAATTAAGTTTTAGAAAATCTACATTAACAAATTAAAATATTAATTATT
1 AATAAAAAATAATATTTAATTAAG-TTTA-AAAATATACATTAACAAATTAAAATATTAATTATT
43376 ATGTTTTTATAAAAATAAAAAATTTTAAATTAAAGAAATAAAAAAAAAAATTATTA-TAATTCCT
64 ATGTTTTTATAAAAATAAAAAATTTTAAATTAAAGAAAT-AAAAAAAAAATTATTATTAATTCCT
43440 AATAA
128 AAT-A
* * *
43445 AATAAAAAATAATATTTAATTAAGTTTAAAAATTTTTCATTAACAAATTAAAATATTAATTGTTA
1 AATAAAAAATAATATTTAATTAAGTTTAAAAA-TATACATTAACAAATTAAAATATTAATTATTA
* *
43510 TGTTTTTTTTAAAATAAAAAATTTTAAATTAAA
65 TGTTTTTATAAAAATAAAAAATTTTAAATTAAA
43543 AAAACTTAAT
Statistics
Matches: 205, Mismatches: 19, Indels: 13
0.86 0.08 0.05
Matches are distributed among these distances:
130 22 0.11
131 23 0.11
132 40 0.20
133 85 0.41
134 35 0.17
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (131 bp):
AATAAAAAATAATATTTAATTAAGTTTAAAAATATACATTAACAAATTAAAATATTAATTATTAT
GTTTTTATAAAAATAAAAAATTTTAAATTAAAGAAATAAAAAAAAAATTATTATTAATTCCTAAT
A
Found at i:43543 original size:14 final size:15
Alignment explanation
Indices: 43516--43545 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
43506 GTTATGTTTT
43516 TTTTAAAATAAAAAA
1 TTTTAAAATAAAAAA
*
43531 TTTTAAATTAAAAAA
1 TTTTAAAATAAAAAA
43546 ACTTAATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TTTTAAAATAAAAAA
Found at i:43642 original size:16 final size:15
Alignment explanation
Indices: 43621--43663 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
43611 TTAATTCCTT
43621 AAATATGTTTTTAAGA
1 AAATATGTTTTTAA-A
*
43637 AAATAT-TTTTCAAA
1 AAATATGTTTTTAAA
43651 AAATATGTTTTTA
1 AAATATGTTTTTA
43664 TTAATATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 7 0.29
15 11 0.46
16 6 0.25
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (15 bp):
AAATATGTTTTTAAA
Found at i:47060 original size:51 final size:51
Alignment explanation
Indices: 47001--47146 Score: 249
Period size: 50 Copynumber: 2.9 Consensus size: 51
46991 TTTTAACTAG
*
47001 ATGTATTGATACATTAAAAAATGTATCGATACATCTAGGTAAAAAGACAGA
1 ATGTATTGATACATTGAAAAATGTATCGATACATCTAGGTAAAAAGACAGA
*
47052 ATGTATTGATACATTGAAAAATGTATCGATACATCTGGGT-AAAAGACAGA
1 ATGTATTGATACATTGAAAAATGTATCGATACATCTAGGTAAAAAGACAGA
* *
47102 ATGTATCGATACATTGAAAAATGTATCAATACATCTAGGTAAAAA
1 ATGTATTGATACATTGAAAAATGTATCGATACATCTAGGTAAAAA
47147 TGTGACTTTT
Statistics
Matches: 89, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
50 47 0.53
51 42 0.47
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.28
Consensus pattern (51 bp):
ATGTATTGATACATTGAAAAATGTATCGATACATCTAGGTAAAAAGACAGA
Found at i:49842 original size:20 final size:20
Alignment explanation
Indices: 49817--49918 Score: 78
Period size: 20 Copynumber: 4.5 Consensus size: 20
49807 TTTTAACTAG
49817 ATGTATCGATACATTAAAAA
1 ATGTATCGATACATTAAAAA
49837 ATGTATCGATACATCTAGTTAAAAAGACAAA
1 ATGTATCGAT--A-C-A-TT---AA-A-A-A
* * *
49868 ATGTATCGATACATTCATAC
1 ATGTATCGATACATTAAAAA
49888 ATGTATCGATACATTAAAAA
1 ATGTATCGATACATTAAAAA
49908 ATGTATCGATA
1 ATGTATCGATA
49919 AATCCGTGTA
Statistics
Matches: 65, Mismatches: 6, Indels: 22
0.70 0.06 0.24
Matches are distributed among these distances:
20 38 0.58
21 1 0.02
22 1 0.02
23 2 0.03
24 1 0.02
25 2 0.03
26 2 0.03
27 1 0.02
28 3 0.05
29 2 0.03
30 1 0.02
31 11 0.17
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACATTAAAAA
Found at i:49950 original size:70 final size:71
Alignment explanation
Indices: 49817--49971 Score: 206
Period size: 70 Copynumber: 2.2 Consensus size: 71
49807 TTTTAACTAG
*
49817 ATGTATCGATACATTAAAAAATGTATCGATACATCTAGTTAAAAAGACAAAATGTATCGATACAT
1 ATGTATCGATACATTAAAAAATGTATCGATAAATCTAGTTAAAAAGACAAAATGTATCGATACAT
* *
49882 TCATAC
66 TCAAAA
* * **
49888 ATGTATCGATACATTAAAAAATGTATCGATAAATC-CGTGT-AAAAGATAGGATGTATCGATACA
1 ATGTATCGATACATTAAAAAATGTATCGATAAATCTAGT-TAAAAAGACAAAATGTATCGATACA
*
49951 TTGAAAA
65 TTCAAAA
*
49958 ATGTATCAATACAT
1 ATGTATCGATACAT
49972 CTGGTAAAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
70 39 0.53
71 35 0.47
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.30
Consensus pattern (71 bp):
ATGTATCGATACATTAAAAAATGTATCGATAAATCTAGTTAAAAAGACAAAATGTATCGATACAT
TCAAAA
Found at i:51585 original size:33 final size:31
Alignment explanation
Indices: 51544--51655 Score: 127
Period size: 32 Copynumber: 3.5 Consensus size: 31
51534 CGACATTAGG
*
51544 TTTAGAAGGGTTGCCACCAATTTGTGTGGAC
1 TTTAGAAGGGTTGCCACCAACTTGTGTGGAC
* * *
51575 TTTAGAGAAGGCTGCCACCAACTTGTGTGGGC
1 TTTAGA-AGGGTTGCCACCAACTTGTGTGGAC
** *
51607 TTTAGAAGGGTTGCCACTGACTTATGT-GAGC
1 TTTAGAAGGGTTGCCACCAACTTGTGTGGA-C
51638 TTTAGAAGAGGTTGCCAC
1 TTTAGAAG-GGTTGCCAC
51656 TGACTTGTAG
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
30 1 0.01
31 31 0.46
32 36 0.53
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.29
Consensus pattern (31 bp):
TTTAGAAGGGTTGCCACCAACTTGTGTGGAC
Found at i:51682 original size:28 final size:28
Alignment explanation
Indices: 51600--52390 Score: 787
Period size: 28 Copynumber: 27.7 Consensus size: 28
51590 CACCAACTTG
*
51600 TGTGGGCTTT-AGAAGGGTTGCCACTGACTT
1 TGTGGGCTTTGA-AAAGG-TGCCACTGAC-T
* *
51630 ATGTGAGCTTTAGAAGAGGTTGCCACTGACT
1 -TGTGGGCTTT-GAAAAGG-TGCCACTGACT
*
51661 TGTAGGCTTTGAAAAGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
* *
51689 TGTGAGTTTTGAAAAGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
*
51717 TATGGGCTTTG-AAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAAGG-TGCCACTGACT
*
51745 TGTGGGCTTTG-AAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAAGG-TGCCACTGACT
* * *
51773 TATGGGCTTTGAAAAAGGTGCCACTAATT
1 TGTGGGCTTTG-AAAAGGTGCCACTGACT
** * *
51802 TGCAGGCTTTGAAAAGATGCTACTGACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
* *
51830 TGTGGGCTTTGAAAAGATGCCACTTACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
*
51858 TGTGGGCTTTG-AAAGGATGCCATTGACT
1 TGTGGGCTTTGAAAAGG-TGCCACTGACT
** *
51886 TGCAGGCTTTGAAAAAGATGCCACTGACT
1 TGTGGGCTTTG-AAAAGGTGCCACTGACT
* * *
51915 TGCGGGCTTTGAAAAGATGCCATTGACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
* *
51943 TATGGGCTTTG-AAAGGATGCCATTGACT
1 TGTGGGCTTTGAAAAGG-TGCCACTGACT
* * *
51971 TATGGGCTTTGAAAAGGGATGTCGCTGACT
1 TGTGGGCTTTGAAAA-GG-TGCCACTGACT
* *
52001 CGTGGGCTTTGAAAAGGGATGCCGCTGACT
1 TGTGGGCTTTGAAAA-GG-TGCCACTGACT
52031 TGTGGGCTTTGAAAAGGGATGCCACTGACT
1 TGTGGGCTTTGAAAA-GG-TGCCACTGACT
*
52061 CGTGGGCTTTG-AAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAAGG-TGCCACTGACT
* *
52089 TGCGGGCTTTGAAAAGGTGCCACTAACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
*
52117 TGTGGGCTTT-AAAAGGTGCCACTGGCT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
* *
52144 TGTGGGCTTTAAAAAGGGTTGCCACTAACT
1 TGTGGGCTTTGAAAA-GG-TGCCACTGACT
*
52174 TGTGAG-TTCTG-AAAGGATGCCACTGACT
1 TGTGGGCTT-TGAAAAGG-TGCCACTGACT
52202 TGTGGGCTTTG-AAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAAGG-TGCCACTGACT
* *
52230 TGTGGGCTCT-AAAATGATGCCACTGACT
1 TGTGGGCTTTGAAAA-GGTGCCACTGACT
52258 TGTGGGCTTT-AAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAA-GGTGCCACTGACT
*** * *
52286 TGCAAGCTTTGAAAATGTGCTACTGACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
* * *
52314 TGTAGGCTTTGAAAAGGTGCCATTAACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
**
52342 TGTGAACTTTGAAAAAGGATGCCACTGACT
1 TGTGGGCTTTG-AAAAGG-TGCCACTGACT
*
52372 CGTGGGCTTTGAAAAGGTG
1 TGTGGGCTTTGAAAAGGTG
52391 TCGTATTGAC
Statistics
Matches: 653, Mismatches: 85, Indels: 47
0.83 0.11 0.06
Matches are distributed among these distances:
27 38 0.06
28 384 0.59
29 81 0.12
30 125 0.19
31 10 0.02
32 14 0.02
33 1 0.00
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTGAAAAGGTGCCACTGACT
Found at i:51797 original size:113 final size:113
Alignment explanation
Indices: 51600--52390 Score: 871
Period size: 113 Copynumber: 6.9 Consensus size: 113
51590 CACCAACTTG
* * * * *
51600 TGTGGGCTTTAGAAGGGTTGCCACTGACTTATGTGAGCTTTAGAAGAGGTTGCCACTGACTTGTA
1 TGTGGGCTTT-GAAAGGATGCCACTGAC-T-TGTGGGCTTT-GAA-AGGATGCCACTGACTTGTG
* *
51665 GGCTTTG-AAAAGGTGCCACTGACTTGTGAGTTTTGAAAAGGTGCCACTGACT
61 GGCTTTGAAAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACT
* * *
51717 TATGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTTATGGGCTT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTT
* * ** * *
51782 TGAAAAAGGTGCCACTAATTTGCAGGCTTTGAAAAGATGCTACTGACT
66 TGAAAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACT
* * * **
51830 TGTGGGCTTTGAAAAGATGCCACTTACTTGTGGGCTTTGAAAGGATGCCATTGACTTGCAGGCTT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTT
* * * *
51895 TGAAAAAGATGCCACTGACTTGCGGGCTTTGAAAAGATGCCATTGACT
66 TGAAAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACT
* * * * * *
51943 TATGGGCTTTGAAAGGATGCCATTGACTTATGGGCTTTGAAAAGGGATGTCGCTGACTCGTGGGC
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG-AAA-GGATGCCACTGACTTGTGGGC
* *
52008 TTTGAAAAGGGATGCCGCTGACTTGTGGGCTTTGAAAAGGGATGCCACTGACT
64 TTTGAAAAAGG-TGCCACTGACTTGTGGGCTTTGAAAA-GG-TGCCACTGACT
* * *
52061 CGTGGGCTTTGAAAGGATGCCACTGACTTGCGGGCTTTGAAAAGG-TGCCACTAACTTGTGGGCT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG-AAAGGATGCCACTGACTTGTGGGCT
* * *
52125 TT--AAAAGGTGCCACTGGCTTGTGGGCTTTAAAAAGGGTTGCCACTAACT
65 TTGAAAAAGGTGCCACTGACTTGTGGGCTTTGAAAA-GG-TGCCACTGACT
*
52174 TGTGAG-TTCTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCT
1 TGTGGGCTT-TGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCT
* * *
52238 CT-AAAATGATGCCACTGACTTGTGGGCTTT-AAAAGGGTGCCACTGACT
65 TTGAAAAAGGTGCCACTGACTTGTGGGCTTTGAAAA-GGTGCCACTGACT
*** * * * * * **
52286 TGCAAGCTTTGAAAATG-TGCTACTGACTTGTAGGCTTTGAAAAGG-TGCCATTAACTTGTGAAC
1 TGTGGGCTTTG-AAAGGATGCCACTGACTTGTGGGCTTTG-AAAGGATGCCACTGACTTGTGGGC
*
52349 TTTGAAAAAGGATGCCACTGACTCGTGGGCTTTGAAAAGGTG
64 TTTGAAAAAGG-TGCCACTGACTTGTGGGCTTTGAAAAGGTG
52391 TCGTATTGAC
Statistics
Matches: 575, Mismatches: 84, Indels: 33
0.83 0.12 0.05
Matches are distributed among these distances:
112 81 0.14
113 284 0.49
114 65 0.11
115 29 0.05
116 56 0.10
117 12 0.02
118 48 0.08
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (113 bp):
TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTT
TGAAAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACT
Found at i:64202 original size:11 final size:11
Alignment explanation
Indices: 64176--64207 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
64166 TGATTATGAC
64176 ATAATA-AAAT
1 ATAATATAAAT
64186 AT-ATATAAAT
1 ATAATATAAAT
64196 ATAATATAAAT
1 ATAATATAAAT
64207 A
1 A
64208 CGATAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 3 0.15
10 8 0.40
11 9 0.45
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:69187 original size:20 final size:20
Alignment explanation
Indices: 69162--69316 Score: 76
Period size: 20 Copynumber: 6.7 Consensus size: 20
69152 TTTTAACTAC
69162 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
69182 ATGTATCGATACATCTAGGTAAAAAGACAGA
1 ATGTATCGATACAT-T--G-----A-A-A-A
* * *
69213 ATGTATCGATACATTCATAC
1 ATGTATCGATACATTGAAAA
*
69233 ATGTATTGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
69253 ATGTATCGATACATCTAGGTAAAAGATAGA
1 ATGTATCGATACAT-T--G----A-A-A-A
*
69283 ATGTATCGATAAATTGAAAA
1 ATGTATCGATACATTGAAAA
69303 ATGTATCGATACAT
1 ATGTATCGATACAT
69317 CTAGGTAAAA
Statistics
Matches: 104, Mismatches: 10, Indels: 42
0.67 0.06 0.27
Matches are distributed among these distances:
20 57 0.55
21 4 0.04
22 1 0.01
23 4 0.04
27 2 0.02
28 2 0.02
29 3 0.03
30 16 0.15
31 15 0.14
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:69275 original size:71 final size:70
Alignment explanation
Indices: 69159--69316 Score: 253
Period size: 71 Copynumber: 2.2 Consensus size: 70
69149 TAATTTTAAC
69159 TACATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAAGACAGAATGTATCGATA
1 TACATGTATCGATACATTGAAAAATGTATCGATACATCTAGGT-AAAAGACAGAATGTATCGATA
*
69224 CATTCA
65 AATTCA
* *
69230 TACATGTATTGATACATTGAAAAATGTATCGATACATCTAGGTAAAAGATAGAATGTATCGATAA
1 TACATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAGACAGAATGTATCGATAA
*
69295 ATTGA
66 ATTCA
* *
69300 AAAATGTATCGATACAT
1 TACATGTATCGATACAT
69317 CTAGGTAAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
70 38 0.47
71 42 0.52
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (70 bp):
TACATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAGACAGAATGTATCGATAA
ATTCA
Found at i:69326 original size:24 final size:24
Alignment explanation
Indices: 69249--69330 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 24
69239 TGATACATTG
69249 AAAAATGTATCGATACATCTAGGT
1 AAAAATGTATCGATACATCTAGGT
*
69273 AAAAGATAGAATGTATCGATAAAT-T--G-
1 ---A-A-A-AATGTATCGATACATCTAGGT
69299 AAAAATGTATCGATACATCTAGGT
1 AAAAATGTATCGATACATCTAGGT
69323 AAAAATGT
1 AAAAATGT
69331 GACTTTTCCA
Statistics
Matches: 46, Mismatches: 2, Indels: 17
0.71 0.03 0.26
Matches are distributed among these distances:
20 14 0.30
21 2 0.04
22 1 0.02
23 2 0.04
24 8 0.17
27 2 0.04
28 1 0.02
29 2 0.04
30 14 0.30
ACGTcount: A:0.46, C:0.09, G:0.17, T:0.28
Consensus pattern (24 bp):
AAAAATGTATCGATACATCTAGGT
Found at i:70890 original size:95 final size:94
Alignment explanation
Indices: 70645--71072 Score: 560
Period size: 94 Copynumber: 4.6 Consensus size: 94
70635 CCTTATAGTC
* * * * *
70645 TTTTTTCTATAAAAAAGAATC-GATTTTAAGATATAATTCATACATTAGTCTAATCCTTACAATC
1 TTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTGCAGTC
70709 TGACATTTACAATCAATCAACTTTTCTTT
66 TGACATTTACAATCAATCAACTTTTCTTT
* ** * * *
70738 TTTTTTCTATAAAAAAAAATCCAATTCTCAGATATAATTAATGCATTAGTCTAATCCTTGTAGTT
1 TTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTGCAGTC
**
70803 TGACATTTACACCCAATCAACTTTTCTTT
66 TGACATTTACAATCAATCAACTTTTCTTT
* * * *
70832 ATTTTTTCTATAAAAAAGAATTTAATTTTCAGATATAATTTATGCATTAGTCTAATCCTTGCAGT
1 -TTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTGCAGT
* * * *
70897 TTAATATTTACACTCAATCAACTTTTCTTT
65 CTGACATTTACAATCAATCAACTTTTCTTT
* * * *
70927 TTTTTT-TATAAAAAAAGAATCTGATTCTCATATATAATTTATACATTAGTCTAATCCTTTCAGT
1 TTTTTTCTAT-AAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTGCAGT
*
70991 CTGATATTTACAATCAATCAACTTTTC--T
65 CTGACATTTACAATCAATCAACTTTTCTTT
*
71019 TTTTTTCTATAAAAAA-AATCTGATTCTCAAATATAATTCATGCATTAGTCTAAT
1 TTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAAT
71073 ATATATAAAG
Statistics
Matches: 298, Mismatches: 33, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
91 35 0.12
92 13 0.04
93 26 0.09
94 139 0.47
95 85 0.29
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.43
Consensus pattern (94 bp):
TTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTGCAGTC
TGACATTTACAATCAATCAACTTTTCTTT
Found at i:70964 original size:189 final size:186
Alignment explanation
Indices: 70645--71072 Score: 576
Period size: 189 Copynumber: 2.3 Consensus size: 186
70635 CCTTATAGTC
* * *
70645 TTTTTTCTATAAAAAAGAA-TCGATTTTAAGATATAATTCATACATTAGTCTAATCCTTACAATC
1 TTTTTTCTATAAAAAAGAATTTGATTTTCAGATATAATTCATGCATTAGTCTAATCCTTACAATC
*
70709 TGACATTTACAATCAATCAACTTTTCTTTTTTTTTCTATAAAAAAAAATCCAATTCTCAGATATA
66 TAACATTTACAATCAATCAACTTTTCTTTTTTTTTCTATAAAAAAAAATCCAATTCTCAGATATA
* * *
70774 ATTAATGCATTAGTCTAATCCTTGT-AGTTTGACATTTACACCCAATCAACTTTTCTTT
131 ATTAATACATTAGTCTAATCCTT-TCAGTCTGACATTTACAACCAATCAACTTTTC--T
* * * *
70832 ATTTTTTCTATAAAAAAGAATTTAATTTTCAGATATAATTTATGCATTAGTCTAATCCTTGCAGT
1 -TTTTTTCTATAAAAAAGAATTTGATTTTCAGATATAATTCATGCATTAGTCTAATCCTTACAAT
* * * ** *
70897 TTAATATTTACACTCAATCAACTTTTCTTTTTTTTT-TATAAAAAAAGAATCTGATTCTCATATA
65 CTAACATTTACAATCAATCAACTTTTCTTTTTTTTTCTATAAAAAAA-AATCCAATTCTCAGATA
* * *
70961 TAATTTATACATTAGTCTAATCCTTTCAGTCTGATATTTACAATCAATCAACTTTTCT
129 TAATTAATACATTAGTCTAATCCTTTCAGTCTGACATTTACAACCAATCAACTTTTCT
* * *
71019 TTTTTTCTATAAAAAA-AATCTGATTCTCAAATATAATTCATGCATTAGTCTAAT
1 TTTTTTCTATAAAAAAGAATTTGATTTTCAGATATAATTCATGCATTAGTCTAAT
71073 ATATATAAAG
Statistics
Matches: 212, Mismatches: 25, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
185 33 0.16
186 16 0.08
187 1 0.00
188 30 0.14
189 132 0.62
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.43
Consensus pattern (186 bp):
TTTTTTCTATAAAAAAGAATTTGATTTTCAGATATAATTCATGCATTAGTCTAATCCTTACAATC
TAACATTTACAATCAATCAACTTTTCTTTTTTTTTCTATAAAAAAAAATCCAATTCTCAGATATA
ATTAATACATTAGTCTAATCCTTTCAGTCTGACATTTACAACCAATCAACTTTTCT
Found at i:71868 original size:15 final size:15
Alignment explanation
Indices: 71848--71878 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
71838 AACTCTTTTT
71848 ATTTTTTAATTTAAA
1 ATTTTTTAATTTAAA
*
71863 ATTTTTTATTTTAAA
1 ATTTTTTAATTTAAA
71878 A
1 A
71879 AATATAATAA
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTTTTTAATTTAAA
Found at i:71968 original size:133 final size:128
Alignment explanation
Indices: 71704--72457 Score: 954
Period size: 126 Copynumber: 5.9 Consensus size: 128
71694 AATTATTATT
*
71704 ATAATAAAAAGCCTTTTTATTTTTTAATTTAAAATTTTTTATTTTTAAAAAA-AATAATTAATAT
1 ATAATAAAAAACCTTTTTATTTTTTAATTTAAAATTTTTTATTTTTAAAAAATAATAATTAATAT
* * *
71768 TTTAATTTGTTAATGTAATTTTTTTAAACTCAATT-AA-A-TATTTTTTATTTTATTAAAAATT
66 TTTAATTTATTAATGTAA-TTTTTTAAACTTAATTAAATATTATTTTTTATTTTATTAAAAATA
*
71829 ATAATAAAAAACTCTTTTTATTTTTTAATTTAAAATTTTTTATTTTAAAAAATATAATAATTAAT
1 ATAATAAAAAAC-CTTTTTATTTTTTAATTTAAAATTTTTTATTTTTAAAAA-ATAATAATTAAT
* * *
71894 ATTTTAATATGTTAATGTCAAGTTTTTTTAAACTTAATCAAATATTATTTTTTATTTTATTAAAA
64 ATTTTAATTTATTAATGT-AA--TTTTTTAAACTTAATTAAATATTATTTTTTATTTTATTAAAA
71959 ATA
126 ATA
* * * *
71962 ATAATAACAAATCCTTTCTATTTTTTTAATTT-AATTTTTTTATTTTTTAAAATATAATAATTAA
1 ATAATAA-AAAACCTTTTTA-TTTTTTAATTTAAAATTTTTTA-TTTTTAAAAAATAATAATTAA
* * *
72026 TATTTTAATTTATTAAGGTAAAGTTTTTAAACTTAATTAAATATTATTTTTTATTTTATCAAAAA
63 TATTTTAATTTATTAATGT-AATTTTTTAAACTTAATTAAATATTATTTTTTATTTTAT--TAAA
72091 AATA
125 AATA
72095 ATAATAAAAAACC----T-TTTTTTAA-TTAAAATTTTTTATTTTTAAAAAGATAATAATTAAAT
1 ATAATAAAAAACCTTTTTATTTTTTAATTTAAAATTTTTTATTTTTAAAAA-ATAATAATT-AAT
* *
72154 ATTTTAATTTATT-ATGTAAAGTTTTTAAAACGT-ATTAAATATTATTTTTTA-TTTATT-AAAA
64 ATTTTAATTTATTAATGT-AA-TTTTTTAAACTTAATTAAATATTATTTTTTATTTTATTAAAAA
72215 -A
127 TA
* **
72216 ATAATAAAAAACCTTTTTATTTTTTTATTTAAAA-TTTTTATTTAAAAAAAAATAATAATTAATA
1 ATAATAAAAAACCTTTTTATTTTTTAATTTAAAATTTTTTATTT-TTAAAAAATAATAATTAATA
* *
72280 GTTTAATTTGTTAATGTAAATTTTTTAAACTTAATTAAATATTATTTTTTATTTTATTAAAAATA
65 TTTTAATTTATTAATGT-AATTTTTTAAACTTAATTAAATATTATTTTTTATTTTATTAAAAATA
* *
72345 ATAATAAAAAGCCTTTTTATTTTTT-ATTT-AAATTTTTAATTTTTTTAAAAAATAATAATTAAT
1 ATAATAAAAAACCTTTTTATTTTTTAATTTAAAATTTTT--TATTTTTAAAAAATAATAATTAAT
*
72408 ATTTTAATTTATTAATGTAAATTTTTT-AATTTAATTAAATATTATTTTTT
64 ATTTTAATTTATTAATGT-AATTTTTTAAACTTAATTAAATATTATTTTTT
72458 TAAAAAATAA
Statistics
Matches: 557, Mismatches: 40, Indels: 61
0.85 0.06 0.09
Matches are distributed among these distances:
121 14 0.03
122 4 0.01
125 52 0.09
126 138 0.25
127 46 0.08
128 62 0.11
129 69 0.12
130 19 0.03
131 37 0.07
132 6 0.01
133 87 0.16
134 23 0.04
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (128 bp):
ATAATAAAAAACCTTTTTATTTTTTAATTTAAAATTTTTTATTTTTAAAAAATAATAATTAATAT
TTTAATTTATTAATGTAATTTTTTAAACTTAATTAAATATTATTTTTTATTTTATTAAAAATA
Found at i:72263 original size:14 final size:13
Alignment explanation
Indices: 72237--72262 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
72227 CCTTTTTATT
72237 TTTTTATTTAAAA
1 TTTTTATTTAAAA
72250 TTTTTATTTAAAA
1 TTTTTATTTAAAA
72263 AAAAATAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTTATTTAAAA
Found at i:72406 original size:23 final size:23
Alignment explanation
Indices: 72380--72475 Score: 58
Period size: 22 Copynumber: 4.2 Consensus size: 23
72370 ATTTAAATTT
72380 TTAATTTTTTTAAAAAATAATAA
1 TTAATTTTTTTAAAAAATAATAA
* ** *
72403 TTAA-TATTTT--AATTTATTAA
1 TTAATTTTTTTAAAAAATAATAA
* * *
72423 TGTAAATTTTTTAATTTAATTAA-ATA
1 T-TAATTTTTTTAA--AAAATAATA-A
72449 TT-ATTTTTTTAAAAAATAATAA
1 TTAATTTTTTTAAAAAATAATAA
72471 TTAAT
1 TTAAT
72476 ATATTAATAA
Statistics
Matches: 53, Mismatches: 11, Indels: 18
0.65 0.13 0.22
Matches are distributed among these distances:
20 8 0.15
21 3 0.06
22 18 0.34
23 7 0.13
24 9 0.17
25 2 0.04
26 6 0.11
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (23 bp):
TTAATTTTTTTAAAAAATAATAA
Found at i:72466 original size:68 final size:69
Alignment explanation
Indices: 72383--72513 Score: 203
Period size: 68 Copynumber: 1.9 Consensus size: 69
72373 TAAATTTTTA
* * *
72383 ATTTTTTTAAAAAATAATAATTAATATTTTAAT-TTATTAATGT-AAATTTTTTAATTTAATTAA
1 ATTTTTTTAAAAAATAATAATTAATATATTAATAATATTAAT-TAAAATTTTTAAATTTAATTAA
72446 ATATT
65 ATATT
*
72451 ATTTTTTTAAAAAATAATAATTAATATATTAATAATATTTATTAAAATTTTTAAATTTAATTA
1 ATTTTTTTAAAAAATAATAATTAATATATTAATAATATTAATTAAAATTTTTAAATTTAATTA
72514 TTTTATATGA
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
68 33 0.58
69 24 0.42
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.53
Consensus pattern (69 bp):
ATTTTTTTAAAAAATAATAATTAATATATTAATAATATTAATTAAAATTTTTAAATTTAATTAAA
TATT
Found at i:76531 original size:99 final size:98
Alignment explanation
Indices: 76422--76603 Score: 242
Period size: 99 Copynumber: 1.8 Consensus size: 98
76412 GAGTATCTTA
*
76422 TTAGAGGAATGAGTTTGGAGTGTCCCCGATGATAAACAATTTAAGCAAAAAATAAGA-TTTAAAT
1 TTAGAGGAATGAGGTTGGAGTGTCCCCGATGAT-AACAATTTAAG-AAAAAATAA-ATTTTAAAT
* *
76486 -CTTGACGAGTTTAAAAATGACGTTAGAGTTTTCAT
63 GCTTAACAAGTTTAAAAATGACGTTAGAGTTTTCAT
* ** * * *
76521 TTAGAGGAATGGGGTTGGAGTGTCCTTGATGATAACAATTTATGTAGAAATAAATTTTAAATGCT
1 TTAGAGGAATGAGGTTGGAGTGTCCCCGATGATAACAATTTAAGAAAAAATAAATTTTAAATGCT
76586 TAACAAGTTTAAAAATGA
66 TAACAAGTTTAAAAATGA
76604 GGTTGAAGTA
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
96 1 0.01
97 14 0.19
98 28 0.39
99 29 0.40
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.32
Consensus pattern (98 bp):
TTAGAGGAATGAGGTTGGAGTGTCCCCGATGATAACAATTTAAGAAAAAATAAATTTTAAATGCT
TAACAAGTTTAAAAATGACGTTAGAGTTTTCAT
Found at i:76629 original size:98 final size:94
Alignment explanation
Indices: 76424--76683 Score: 247
Period size: 98 Copynumber: 2.6 Consensus size: 94
76414 GTATCTTATT
* * * *
76424 AGAGGAATGAGTTTGGAGTGTCCCCGATGATAAACAATTTAAGCAAAAAATAAGATTTAAATCTT
1 AGAGGAATGGGGTTGGAGTGT-CCCGATGAT-AACAATTTAAG-TAGAAATAA-ATTTAAATCTT
* * *
76489 GACGAGTTTAAAAATGACGTTAGAGTTTTCATTT
62 AACAAGTTTAAAAATGACGTTAGAGTTTTCA-TC
* *
76523 AGAGGAATGGGGTTGGAGTGTCCTTGATGATAACAATTTATGTAGAAATAAATTTTAAATGCTTA
1 AGAGGAATGGGGTTGGAGTGTCC-CGATGATAACAATTTAAGTAGAAATAAA-TTTAAAT-CTTA
*
76588 ACAAGTTTAAAAATGAGGTT-GAAGTATTTTC-TC
63 ACAAGTTTAAAAATGACGTTAG-AG--TTTTCATC
* * * *
76621 GGAGGAATGGGGTTGGAATGTTCCCGATGATGAC-ATTTCAAGTGGAAATAAAATTTAAATCTT
1 AGAGGAATGGGGTTGGAGTG-TCCCGATGATAACAATTT-AAGTAGAAAT-AAATTTAAATCTT
76684 GGAAATGTTC
Statistics
Matches: 136, Mismatches: 16, Indels: 20
0.79 0.09 0.12
Matches are distributed among these distances:
96 1 0.01
97 22 0.16
98 77 0.57
99 31 0.23
100 5 0.04
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.32
Consensus pattern (94 bp):
AGAGGAATGGGGTTGGAGTGTCCCGATGATAACAATTTAAGTAGAAATAAATTTAAATCTTAACA
AGTTTAAAAATGACGTTAGAGTTTTCATC
Found at i:78996 original size:20 final size:21
Alignment explanation
Indices: 78971--79021 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
78961 CAATGCTAAC
78971 ATGTATCGATACATTCACTT-
1 ATGTATCGATACATTCACTTG
* *
78991 ATGTATTGATACATTGACTTG
1 ATGTATCGATACATTCACTTG
*
79012 TTGTATCGAT
1 ATGTATCGAT
79022 GCAAATCGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (21 bp):
ATGTATCGATACATTCACTTG
Done.