Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 137 of 187
Found at i:41088039 original size:64 final size:64
Alignment explanation
Indices: 41087938--41088063 Score: 225
Period size: 64 Copynumber: 2.0 Consensus size: 64
41087928 AGGAAAGACC
* * *
41087938 ATTTTCTTTTGCCGTTCATCGATCAAATGATAGATAGATTAGTGAGAAAAGTCTTTTATTGCTA
1 ATTTTCTTTTGCCATTCATCGATCAAATGATAGATAGATTAGCGAGAAAAGCCTTTTATTGCTA
41088002 ATTTTCTTTTGCCATTCATCGATCAAATGATAGATAGATTAGCGAGAAAAGCCTTTTATTGC
1 ATTTTCTTTTGCCATTCATCGATCAAATGATAGATAGATTAGCGAGAAAAGCCTTTTATTGC
41088064 ATTTTAGATG
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (64 bp):
ATTTTCTTTTGCCATTCATCGATCAAATGATAGATAGATTAGCGAGAAAAGCCTTTTATTGCTA
Found at i:41096061 original size:483 final size:483
Alignment explanation
Indices: 41095155--41096124 Score: 1769
Period size: 483 Copynumber: 2.0 Consensus size: 483
41095145 AATAGGCGTT
*
41095155 ATTTCGAAGAATGCAAATTGAGATATGGATCGTGCTTTAAATGTGGTTCTTATGACCATTTTCTT
1 ATTTCGAAGAATGCAAATTGAGAGATGGATCGTGCTTTAAATGTGGTTCTTATGACCATTTTCTT
* *
41095220 CGAGACTGCCTTGAAAGATCTGATAGGGAGAAAGCTCAGAACAGTCGTTCGAGTAACACGACTGC
66 CGAGACTACCTTGAAAGATCTGATAGGGAGAAAGCTCAGAACACTCGTTCGAGTAACACGACTGC
*
41095285 GAGAGGGAGACCATCCAGAAATAGTGGAAATACGGGTAATAGTCGATGTGGAATGAAATATTCTA
131 GAGAGGGAGACCATCCAGAAATAGTGGAAATACAGGTAATAGTCGATGTGGAATGAAATATTCTA
41095350 CGGTTAGATCTGAGGCTCGGGCATATGCAATTCGAGCTCGTGAGAAAGCTTCAGCACCTGATGTG
196 CGGTTAGATCTGAGGCTCGGGCATATGCAATTCGAGCTCGTGAGAAAGCTTCAGCACCTGATGTG
* * * *
41095415 ATTATTGGTACATTTTCTATCTTTGATACTAATGTTAATGCTTTGATTGACTCGAGGTCAACACC
261 ATTACTGGTACATTTTCTATCTTTGATACTAATGTTAATGATCTGATTGACCCGAGGTCAACACC
41095480 CTCATATATATGCACAACCTTAGTGTCAGATAAGAAAATACCTTATGAGCCAACTGAATTTGTGA
326 CTCATATATATGCACAACCTTAGTGTCAGATAAGAAAATACCTTATGAGCCAACTGAATTTGTGA
* *
41095545 TTAAAGTAACGAATCCTTTAGACCAGTATGTGTTAGTTGATAAAGTTTGTAGAAACTGTCTTTTG
391 TTAAAGTAACGAATCATTTAGACCAGTATGTGTTAGTTGATAAAGTTTGTAGAAACTATCTTTTG
41095610 ATGATTCAGGATTGCAACTTTCTTGCTG
456 ATGATTCAGGATTGCAACTTTCTTGCTG
41095638 ATTTCGAAGAATGCAAATTGAGAGATGGATCGTGCTTTAAATGTGGTTCTTATGACCATTTTCTT
1 ATTTCGAAGAATGCAAATTGAGAGATGGATCGTGCTTTAAATGTGGTTCTTATGACCATTTTCTT
* *
41095703 CGAGACTACCTTGAAAGATCTGATAGGGAGAAAGCTCAGAACACTCGTTCGAGTAACACGGCTGG
66 CGAGACTACCTTGAAAGATCTGATAGGGAGAAAGCTCAGAACACTCGTTCGAGTAACACGACTGC
*
41095768 GAGAGGGAGACCATCTAGAAATAGTGGAAATACAGGTAATAGTCGATGTGGAATGAAATATTCTA
131 GAGAGGGAGACCATCCAGAAATAGTGGAAATACAGGTAATAGTCGATGTGGAATGAAATATTCTA
*
41095833 CGGTTAGATCTGAGGCTCGGGCATATGCAATTCGAGCTCGTGAGGAAGCTTCAGCACCTGATGTG
196 CGGTTAGATCTGAGGCTCGGGCATATGCAATTCGAGCTCGTGAGAAAGCTTCAGCACCTGATGTG
41095898 ATTACTGGTACATTTTCTATCTTTGATACTAATGTTAATGATCTGATTGACCCGAGGTCAACACC
261 ATTACTGGTACATTTTCTATCTTTGATACTAATGTTAATGATCTGATTGACCCGAGGTCAACACC
* * *
41095963 GTCATATATATGCACGACCTTAGTGTCAGATAAGAAAATACCTTATGAGTCAACTGAATTTGTGA
326 CTCATATATATGCACAACCTTAGTGTCAGATAAGAAAATACCTTATGAGCCAACTGAATTTGTGA
* *
41096028 TTAAAGTAACGAATCATTTAGGCCAGTATGTGTTAGTTGGTAAAGTTTGTAGAAACTATCTTTTG
391 TTAAAGTAACGAATCATTTAGACCAGTATGTGTTAGTTGATAAAGTTTGTAGAAACTATCTTTTG
41096093 ATGATTCAGGATTGCAACTTTCTTGCTG
456 ATGATTCAGGATTGCAACTTTCTTGCTG
41096121 ATTT
1 ATTT
41096125 GATGCTATTA
Statistics
Matches: 468, Mismatches: 19, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
483 468 1.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (483 bp):
ATTTCGAAGAATGCAAATTGAGAGATGGATCGTGCTTTAAATGTGGTTCTTATGACCATTTTCTT
CGAGACTACCTTGAAAGATCTGATAGGGAGAAAGCTCAGAACACTCGTTCGAGTAACACGACTGC
GAGAGGGAGACCATCCAGAAATAGTGGAAATACAGGTAATAGTCGATGTGGAATGAAATATTCTA
CGGTTAGATCTGAGGCTCGGGCATATGCAATTCGAGCTCGTGAGAAAGCTTCAGCACCTGATGTG
ATTACTGGTACATTTTCTATCTTTGATACTAATGTTAATGATCTGATTGACCCGAGGTCAACACC
CTCATATATATGCACAACCTTAGTGTCAGATAAGAAAATACCTTATGAGCCAACTGAATTTGTGA
TTAAAGTAACGAATCATTTAGACCAGTATGTGTTAGTTGATAAAGTTTGTAGAAACTATCTTTTG
ATGATTCAGGATTGCAACTTTCTTGCTG
Found at i:41104348 original size:14 final size:14
Alignment explanation
Indices: 41104331--41104363 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
41104321 TAAATATTGC
*
41104331 CCATTAAAAATCAT
1 CCATGAAAAATCAT
41104345 CCATGAAAAATCAT
1 CCATGAAAAATCAT
41104359 CCATG
1 CCATG
41104364 CACCGTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.45, C:0.24, G:0.06, T:0.24
Consensus pattern (14 bp):
CCATGAAAAATCAT
Found at i:41129690 original size:21 final size:19
Alignment explanation
Indices: 41129625--41129718 Score: 152
Period size: 19 Copynumber: 4.8 Consensus size: 19
41129615 AATTTTTGAG
41129625 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
41129644 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
41129663 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
41129682 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
41129703 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
41129719 AGATATGATT
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
19 51 0.73
21 19 0.27
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:41129700 original size:40 final size:38
Alignment explanation
Indices: 41129625--41129725 Score: 152
Period size: 40 Copynumber: 2.7 Consensus size: 38
41129615 AATTTTTGAG
41129625 GATATGCAATCTTAGATATGATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATATGATATGCAATCCTAGATAT
*
41129663 GATATGCAATCTTAGATATGATATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATATG--ATATGCAATCCTAGATAT
*
41129703 GATATGTAATCTTAGA-A-GATATG
1 GATATGCAATCTTAGATATGATATG
41129726 ATTTTGTAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
36 5 0.08
38 21 0.36
39 1 0.02
40 32 0.54
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (38 bp):
GATATGCAATCTTAGATATGATATGCAATCCTAGATAT
Found at i:41129737 original size:23 final size:22
Alignment explanation
Indices: 41129657--41129741 Score: 81
Period size: 21 Copynumber: 4.0 Consensus size: 22
41129647 ATGCAATCCT
*
41129657 AGATATGATATGCAATCTTAG-
1 AGATATGATATGTAATCTTAGA
* *
41129678 ATATGAT-ATATGCAATCTT---
1 AGAT-ATGATATGTAATCTTAGA
41129697 AGATATGATATGTAATCTTAGA
1 AGATATGATATGTAATCTTAGA
*
41129719 AGATATGATTTTGTAATCTTAGA
1 AGATATGA-TATGTAATCTTAGA
41129742 GATTTAATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
18 2 0.04
19 14 0.26
21 15 0.28
22 10 0.19
23 13 0.24
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.39
Consensus pattern (22 bp):
AGATATGATATGTAATCTTAGA
Found at i:41129751 original size:22 final size:23
Alignment explanation
Indices: 41129707--41129751 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
41129697 AGATATGATA
*
41129707 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
41129730 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
41129752 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:41130401 original size:25 final size:26
Alignment explanation
Indices: 41130358--41130407 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
41130348 CATATATATA
41130358 TATATTTTTTTAAACGAATATTTTCC
1 TATATTTTTTTAAACGAATATTTTCC
*
41130384 TATATTTTTTT-AATGAATATTTTC
1 TATATTTTTTTAAACGAATATTTTC
41130408 ATATTTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.30, C:0.08, G:0.04, T:0.58
Consensus pattern (26 bp):
TATATTTTTTTAAACGAATATTTTCC
Found at i:41130522 original size:30 final size:29
Alignment explanation
Indices: 41130431--41130526 Score: 83
Period size: 30 Copynumber: 3.3 Consensus size: 29
41130421 TATATTTACA
41130431 TTTTTTTAAGTGATTAAATACTCACCCTTTTT
1 TTTTTTTAA-TGATTAAATACTCA--CTTTTT
* * ** *
41130463 TTTCTTT-CTTTTTAAATA-T-AC-TTAT
1 TTTTTTTAATGATTAAATACTCACTTTTT
41130488 TTTTTTTAATGATTAAATACTCACTTTTT
1 TTTTTTTAATGATTAAATACTCACTTTTT
41130517 CTTTTTTTAA
1 -TTTTTTTAA
41130527 ATATACCTAT
Statistics
Matches: 49, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
25 9 0.18
26 9 0.18
27 1 0.02
28 3 0.06
29 4 0.08
30 17 0.35
32 6 0.12
ACGTcount: A:0.25, C:0.12, G:0.03, T:0.59
Consensus pattern (29 bp):
TTTTTTTAATGATTAAATACTCACTTTTT
Found at i:41130530 original size:49 final size:54
Alignment explanation
Indices: 41130431--41130540 Score: 149
Period size: 49 Copynumber: 2.1 Consensus size: 54
41130421 TATATTTACA
*
41130431 TTTTTTTAAGTGATTAAATACTCACCCTTTTTTTTCTTTCTTTTTAAATATACTTAT
1 TTTTTTTAAGTGATTAAATACTCA-CC--TTTTTTCTTTCTTTTTAAATATACCTAT
41130488 TTTTTTTAA-TGATTAAATACTCA-C-TTTTTC-TT-TTTTTAAATATACCTAT
1 TTTTTTTAAGTGATTAAATACTCACCTTTTTTCTTTCTTTTTAAATATACCTAT
41130537 TTTT
1 TTTT
41130541 ATTATTTTAT
Statistics
Matches: 52, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
49 20 0.38
50 2 0.04
51 6 0.12
54 1 0.02
56 14 0.27
57 9 0.17
ACGTcount: A:0.25, C:0.13, G:0.03, T:0.59
Consensus pattern (54 bp):
TTTTTTTAAGTGATTAAATACTCACCTTTTTTCTTTCTTTTTAAATATACCTAT
Found at i:41131239 original size:98 final size:98
Alignment explanation
Indices: 41131122--41131514 Score: 723
Period size: 98 Copynumber: 4.0 Consensus size: 98
41131112 TTAAAAATCA
** * * *
41131122 TAAAGGAAATATTTTGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
41131187 TTAAATCTTGGATTAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATTAGTGGATGTTCTTTTAAAG
41131220 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
41131285 TTAAATCTTGGATTAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATTAGTGGATGTTCTTTTAAAG
41131318 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
41131383 TTAAATCTTGGATTAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATTAGTGGATGTTCTTTTAAAG
41131416 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
* *
41131481 TTAAATCTTGGATAAGTGGATATTCTTTTAAAG
66 TTAAATCTTGGATTAGTGGATGTTCTTTTAAAG
41131514 T
1 T
41131515 TTTATTGTAC
Statistics
Matches: 288, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 288 1.00
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.38
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATTAGTGGATGTTCTTTTAAAG
Found at i:41132196 original size:17 final size:17
Alignment explanation
Indices: 41132174--41132206 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41132164 ATGAATGAAA
41132174 AAATGCTAGGGAAATTG
1 AAATGCTAGGGAAATTG
*
41132191 AAATGCTATGGAAATT
1 AAATGCTAGGGAAATT
41132207 CTCAAAGAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.24, T:0.27
Consensus pattern (17 bp):
AAATGCTAGGGAAATTG
Found at i:41134682 original size:17 final size:19
Alignment explanation
Indices: 41134651--41134693 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
41134641 TTGTTTTTAC
41134651 TTTTCATTTGCATAT-T-T
1 TTTTCATTTGCATATGTGT
**
41134668 TTTTCATTTTTATATGTGT
1 TTTTCATTTGCATATGTGT
41134687 TTTTCAT
1 TTTTCAT
41134694 GCATTTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 13 0.59
18 1 0.05
19 8 0.36
ACGTcount: A:0.16, C:0.09, G:0.07, T:0.67
Consensus pattern (19 bp):
TTTTCATTTGCATATGTGT
Found at i:41134698 original size:23 final size:21
Alignment explanation
Indices: 41134672--41134721 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
41134662 ATATTTTTTT
41134672 CATTTTTATATGTGTTTTTCA-TG
1 CATTTTTA-AT-TG-TTTTCATTG
*
41134695 CATTTATAATTGTTTTCATTG
1 CATTTTTAATTGTTTTCATTG
41134716 CATTTT
1 CATTTT
41134722 CTACATATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 6 0.25
21 9 0.38
22 2 0.08
23 7 0.29
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.60
Consensus pattern (21 bp):
CATTTTTAATTGTTTTCATTG
Found at i:41137730 original size:76 final size:76
Alignment explanation
Indices: 41137604--41137755 Score: 259
Period size: 76 Copynumber: 2.0 Consensus size: 76
41137594 CTTGAATCTT
* * *
41137604 CTTTTTAGCATTTTTGAGTGAGTACATATGTGCATTGGTTGCTAGATGGAGAAGAATCGGCTAGG
1 CTTTTTAGCATTTTTGAGTGAGCACATATGTGCATTGGTTGCTAAATGGAGAAGAATCGGCTAGC
*
41137669 AAGTTGTGTGC
66 AAGATGTGTGC
*
41137680 CTTTTTAGCATTTTTGTGTGAGCACATATGTGCATTGGTTGCTAAATGGAGAAGAATCGGCTAGC
1 CTTTTTAGCATTTTTGAGTGAGCACATATGTGCATTGGTTGCTAAATGGAGAAGAATCGGCTAGC
41137745 AAGATGTGTGC
66 AAGATGTGTGC
41137756 TAAGGCCGAA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
76 71 1.00
ACGTcount: A:0.24, C:0.12, G:0.29, T:0.35
Consensus pattern (76 bp):
CTTTTTAGCATTTTTGAGTGAGCACATATGTGCATTGGTTGCTAAATGGAGAAGAATCGGCTAGC
AAGATGTGTGC
Found at i:41138512 original size:39 final size:40
Alignment explanation
Indices: 41138308--41138530 Score: 227
Period size: 40 Copynumber: 5.6 Consensus size: 40
41138298 TTGAATGCTG
* * * * * *
41138308 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
** * * *
41138348 TCCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
41138388 TCCGGGTTAAGTCCCGAAGACATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
**
41138428 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
41138468 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
41138507 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
41138531 TGAACGAGGA
Statistics
Matches: 159, Mismatches: 21, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
39 35 0.22
40 116 0.73
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:41138550 original size:79 final size:80
Alignment explanation
Indices: 41138383--41138565 Score: 217
Period size: 79 Copynumber: 2.3 Consensus size: 80
41138373 GTGCGAGATA
* * * *
41138383 CTAAATCCGGGTTAAGTCCCGAAGACATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
41138448 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * *
41138463 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
41138527 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
41138542 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
41138566 TACGTGATTT
Statistics
Matches: 86, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
78 14 0.16
79 46 0.53
80 26 0.30
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:41151754 original size:28 final size:28
Alignment explanation
Indices: 41151686--41151867 Score: 276
Period size: 28 Copynumber: 6.5 Consensus size: 28
41151676 CATGAGATTG
* * * *
41151686 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
*
41151715 GCACTAAGTGTGCGAGTTAGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
41151743 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
* *
41151771 GCACTAAGTGTGCAAGTTTGATTATGTA
1 GCACTAAGTGTGCGAGTTTGATTATATA
41151799 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
41151827 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
41151854 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
41151868 GACTTAATAT
Statistics
Matches: 142, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
27 24 0.17
28 101 0.71
29 17 0.12
ACGTcount: A:0.28, C:0.12, G:0.27, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:41153868 original size:13 final size:13
Alignment explanation
Indices: 41153850--41153874 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41153840 CATTTTTATT
41153850 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
41153863 TTTTTTCTTTTT
1 TTTTTTCTTTTT
41153875 TAGAAGTCTC
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:41163224 original size:7 final size:7
Alignment explanation
Indices: 41163212--41163261 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
41163202 ACTATATATT
41163212 AATAATA
1 AATAATA
41163219 AATAATAA
1 AATAAT-A
41163227 AATAATA
1 AATAATA
*
41163234 TATAAT-
1 AATAATA
41163240 AA-AATA
1 AATAATA
*
41163246 TATAATA
1 AATAATA
*
41163253 TATAATA
1 AATAATA
41163260 AA
1 AA
41163262 AGCTATAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
5 3 0.08
6 2 0.06
7 24 0.67
8 7 0.19
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AATAATA
Found at i:41163232 original size:15 final size:15
Alignment explanation
Indices: 41163212--41163250 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
41163202 ACTATATATT
41163212 AATAATAAATAATAA
1 AATAATAAATAATAA
*
41163227 AATAATATATAATAA
1 AATAATAAATAATAA
41163242 AATATATAA
1 AATA-ATAA
41163251 TATATAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 18 0.86
16 3 0.14
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AATAATAAATAATAA
Found at i:41163250 original size:19 final size:19
Alignment explanation
Indices: 41163228--41163334 Score: 75
Period size: 19 Copynumber: 5.7 Consensus size: 19
41163218 AAATAATAAA
41163228 ATAATATATAATAAAATAT
1 ATAATATATAATAAAATAT
41163247 ATAATATATAATAAAAGCTAT
1 ATAATATATAATAAAA--TAT
*
41163268 A-AATAAAATATATAAAATAT
1 ATAAT-ATATA-ATAAAATAT
* *
41163288 A-AATAACATGAT-AAATA-
1 ATAAT-ATATAATAAAATAT
*
41163305 AT-ACATA-AATAAAA-AT
1 ATAATATATAATAAAATAT
*
41163321 ATTATATATAATAA
1 ATAATATATAATAA
41163335 TTTTACATGT
Statistics
Matches: 72, Mismatches: 7, Indels: 19
0.73 0.07 0.19
Matches are distributed among these distances:
15 3 0.04
16 7 0.10
17 6 0.08
18 10 0.14
19 18 0.25
20 14 0.19
21 8 0.11
22 6 0.08
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.32
Consensus pattern (19 bp):
ATAATATATAATAAAATAT
Found at i:41163317 original size:47 final size:50
Alignment explanation
Indices: 41163266--41163385 Score: 115
Period size: 47 Copynumber: 2.4 Consensus size: 50
41163256 AATAAAAGCT
41163266 ATAAATAAAATATATAAAATATAAATAACATG-ATAAATAATA-CAT-AA
1 ATAAATAAAATATATAAAATATAAATAACATGTATAAATAATATCATAAA
* * ** * *
41163313 ATAAA-AATATTATATATAATA-ATTTTACATGTATAAATAATATTTATAAAA
1 ATAAATAA-AATATATAAAATATAAATAACATGTATAAATAATA-TCAT-AAA
*
41163364 ATAAATAATATATATAAAATAT
1 ATAAATAAAATATATAAAATAT
41163386 TTAAAATAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
46 9 0.16
47 26 0.46
49 2 0.04
51 17 0.30
52 2 0.04
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.35
Consensus pattern (50 bp):
ATAAATAAAATATATAAAATATAAATAACATGTATAAATAATATCATAAA
Found at i:41163331 original size:15 final size:15
Alignment explanation
Indices: 41163313--41163426 Score: 63
Period size: 15 Copynumber: 7.4 Consensus size: 15
41163303 TAATACATAA
41163313 ATAAAAATATTATAT
1 ATAAAAATATTATAT
* * *
41163328 ATAATAATTTTACAT
1 ATAAAAATATTATAT
* * * *
41163343 GTATAAATAATATTT
1 ATAAAAATATTATAT
*
41163358 ATAAAAATAAATAATAT
1 ATAAAAAT--ATTATAT
*
41163375 ATATAAAATATT-TAAA
1 ATA-AAAATATTAT-AT
41163391 ATAAACAA-ATTATAT
1 ATAAA-AATATTATAT
*
41163406 AT-AAAATGTATATAT
1 ATAAAAATAT-TATAT
41163421 ATAAAA
1 ATAAAA
41163427 GGATTAAAAT
Statistics
Matches: 71, Mismatches: 19, Indels: 17
0.66 0.18 0.16
Matches are distributed among these distances:
13 2 0.03
14 3 0.04
15 42 0.59
16 12 0.17
17 7 0.10
18 5 0.07
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (15 bp):
ATAAAAATATTATAT
Found at i:41163367 original size:19 final size:19
Alignment explanation
Indices: 41163345--41163382 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
41163335 TTTTACATGT
*
41163345 ATAAATAATATTTATAAAA
1 ATAAATAATATATATAAAA
41163364 ATAAATAATATATATAAAA
1 ATAAATAATATATATAAAA
41163383 TATTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
ATAAATAATATATATAAAA
Found at i:41163407 original size:78 final size:79
Alignment explanation
Indices: 41163265--41163409 Score: 190
Period size: 78 Copynumber: 1.8 Consensus size: 79
41163255 TAATAAAAGC
41163265 TATAAATAAAATATATAAAATATAAATAACATGATAAATAATACATAAATAAAAATATTATATAT
1 TATAAATAAAATATATAAAATATAAATAACATGATAAATAATACATAAATAAAAATATTATATAT
41163330 AATAATTTTACATG
66 AATAATTTTACATG
* * * **
41163344 TATAAATAATATTTATAAAA-ATAAATAATAT-ATATAA-AATATTTAAAATAAACAA-ATTATA
1 TATAAATAAAATATATAAAATATAAATAACATGATA-AATAATACAT-AAATAAA-AATATTATA
41163405 TATAA
63 TATAA
41163410 AATGTATATA
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
77 8 0.14
78 30 0.52
79 20 0.34
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (79 bp):
TATAAATAAAATATATAAAATATAAATAACATGATAAATAATACATAAATAAAAATATTATATAT
AATAATTTTACATG
Found at i:41168137 original size:26 final size:26
Alignment explanation
Indices: 41168108--41168157 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
41168098 AATAAAAGAA
41168108 AACATTCAATATTTCAATTTAATTCT
1 AACATTCAATATTTCAATTTAATTCT
*
41168134 AACATTCAATATTTCAGTTTAATT
1 AACATTCAATATTTCAATTTAATT
41168158 AGCATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.46
Consensus pattern (26 bp):
AACATTCAATATTTCAATTTAATTCT
Found at i:41172363 original size:25 final size:25
Alignment explanation
Indices: 41172335--41172388 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
41172325 GAATACGTTA
41172335 CAATAAAAGAAAACATTCAATATTT
1 CAATAAAAGAAAACATTCAATATTT
**
41172360 CAATTTAAGAAAACATTCAATATTT
1 CAATAAAAGAAAACATTCAATATTT
41172385 CAAT
1 CAAT
41172389 TTAATTCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.52, C:0.13, G:0.04, T:0.31
Consensus pattern (25 bp):
CAATAAAAGAAAACATTCAATATTT
Found at i:41172407 original size:26 final size:26
Alignment explanation
Indices: 41172344--41172421 Score: 113
Period size: 25 Copynumber: 3.0 Consensus size: 26
41172334 ACAATAAAAG
*
41172344 AAAACATTCAATATTTCAATTTAA-G
1 AAAACATTCAATATTTCAATTTAATT
41172369 AAAACATTCAATATTTCAATTTAATT
1 AAAACATTCAATATTTCAATTTAATT
** *
41172395 CTAACATTCAATATTTCAGTTTAATT
1 AAAACATTCAATATTTCAATTTAATT
41172421 A
1 A
41172422 GCATTAATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
25 24 0.51
26 23 0.49
ACGTcount: A:0.44, C:0.13, G:0.03, T:0.41
Consensus pattern (26 bp):
AAAACATTCAATATTTCAATTTAATT
Found at i:41173165 original size:255 final size:255
Alignment explanation
Indices: 41172714--41173221 Score: 1007
Period size: 255 Copynumber: 2.0 Consensus size: 255
41172704 CTATTTTTCT
41172714 AATTTTGTGTAGTTGTGTATGTACATGTTATGTTGATGGTTAAAAATTCACGTGCATCTCAAAAT
1 AATTTTGTGTAGTTGTGTATGTACATGTTATGTTGATGGTTAAAAATTCACGTGCATCTCAAAAT
41172779 TGAATGAGCTATACTAGATTCCCCTAACAGTGATATGAATGTGCCACAATGTAGAAATAATTATG
66 TGAATGAGCTATACTAGATTCCCCTAACAGTGATATGAATGTGCCACAATGTAGAAATAATTATG
41172844 CAAACATAAAATCTTATACCCTTGTTGTTGTTAAAAAGTTTTTATCAGACATACCGTATTTGTAA
131 CAAACATAAAATCTTATACCCTTGTTGTTGTTAAAAAGTTTTTATCAGACATACCGTATTTGTAA
*
41172909 AATGTAAAATGGCAACTAAATGATTGACATTCAAAATTAATTCATTAACAATATTTCATG
196 AATGTAAAATGGCAACTAAATGATTGACATTCAAAATTAATTCATCAACAATATTTCATG
41172969 AATTTTGTGTAGTTGTGTATGTACATGTTATGTTGATGGTTAAAAATTCACGTGCATCTCAAAAT
1 AATTTTGTGTAGTTGTGTATGTACATGTTATGTTGATGGTTAAAAATTCACGTGCATCTCAAAAT
41173034 TGAATGAGCTATACTAGATTCCCCTAACAGTGATATGAATGTGCCACAATGTAGAAATAATTATG
66 TGAATGAGCTATACTAGATTCCCCTAACAGTGATATGAATGTGCCACAATGTAGAAATAATTATG
41173099 CAAACATAAAATCTTATACCCTTGTTGTTGTTAAAAAGTTTTTATCAGACATACCGTATTTGTAA
131 CAAACATAAAATCTTATACCCTTGTTGTTGTTAAAAAGTTTTTATCAGACATACCGTATTTGTAA
41173164 AATGTAAAATGGCAACTAAATGATTGACATTCAAAATTAATTCATCAACAATATTTCA
196 AATGTAAAATGGCAACTAAATGATTGACATTCAAAATTAATTCATCAACAATATTTCA
41173222 CCTTCTGATA
Statistics
Matches: 252, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
255 252 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (255 bp):
AATTTTGTGTAGTTGTGTATGTACATGTTATGTTGATGGTTAAAAATTCACGTGCATCTCAAAAT
TGAATGAGCTATACTAGATTCCCCTAACAGTGATATGAATGTGCCACAATGTAGAAATAATTATG
CAAACATAAAATCTTATACCCTTGTTGTTGTTAAAAAGTTTTTATCAGACATACCGTATTTGTAA
AATGTAAAATGGCAACTAAATGATTGACATTCAAAATTAATTCATCAACAATATTTCATG
Found at i:41174475 original size:81 final size:81
Alignment explanation
Indices: 41174340--41174502 Score: 281
Period size: 81 Copynumber: 2.0 Consensus size: 81
41174330 AGGATTTTCA
* *
41174340 AGAGTCCTCTTTACTAATGTTGAGTGGCAAAATTTTCCCAACACAACAAGTTCGCCGCAACACTT
1 AGAGTCCTCTTTACTAATGCTGAGTGGCAAAATTTTCCCAACACAACAAGTTCGCCACAACACTT
41174405 GTTAGAAATAATCCCT
66 GTTAGAAATAATCCCT
* *
41174421 AGAGTCCTCTTTACTAATGCTGAGTGGCAAACTTTTCCCAACACAACAAGTTCGCCACAGCACTT
1 AGAGTCCTCTTTACTAATGCTGAGTGGCAAAATTTTCCCAACACAACAAGTTCGCCACAACACTT
*
41174486 GTTAGAAATACTCCCT
66 GTTAGAAATAATCCCT
41174502 A
1 A
41174503 TATTGAAAAT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 77 1.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (81 bp):
AGAGTCCTCTTTACTAATGCTGAGTGGCAAAATTTTCCCAACACAACAAGTTCGCCACAACACTT
GTTAGAAATAATCCCT
Found at i:41174828 original size:26 final size:26
Alignment explanation
Indices: 41174796--41174845 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
41174786 AATAAAAGAA
41174796 AACATTCAAT-TTTACAATTTAATTCT
1 AACATTCAATATTT-CAATTTAATTCT
*
41174822 AACATTCAATATTTCAGTTTAATT
1 AACATTCAATATTTCAATTTAATT
41174846 AGCATTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 19 0.86
27 3 0.14
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.46
Consensus pattern (26 bp):
AACATTCAATATTTCAATTTAATTCT
Found at i:41178960 original size:12 final size:12
Alignment explanation
Indices: 41178930--41178960 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
41178920 ACTCGGGGAA
*
41178930 GAGGCCATGGTC
1 GAGGCCGTGGTC
41178942 GAGGCCGTGGTC
1 GAGGCCGTGGTC
41178954 GAGGCCG
1 GAGGCCG
41178961 AGGTAGTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.13, C:0.26, G:0.48, T:0.13
Consensus pattern (12 bp):
GAGGCCGTGGTC
Found at i:41183781 original size:26 final size:26
Alignment explanation
Indices: 41183752--41183807 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
41183742 TGATAAAAAT
*
41183752 TGATAATGGGTTAGGTCAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
41183778 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
41183804 TGAT
1 TGAT
41183808 GGGCATTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.29, C:0.09, G:0.27, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:41186285 original size:66 final size:66
Alignment explanation
Indices: 41186166--41186295 Score: 165
Period size: 66 Copynumber: 2.0 Consensus size: 66
41186156 ATACTGCCCA
*
41186166 TATGATCTTTTCGTTACTTCCTCATGAAAACAGACTCATCGAGCTTCGATTACATAATTTATTCC
1 TATGATCTTTTCGTTACTTCCTCATGAAAACAGACTCATCAAGCTTCGATTACATAATTTATTCC
41186231 G
66 G
** * * * *
41186232 TATGAT-TGTTTCGTTACTTTCCT-ATGAAAGTAGATTCATCAAGGTTTGTTTACATAATTTATT
1 TATGATCT-TTTCGTTAC-TTCCTCATGAAAACAGACTCATCAAGCTTCGATTACATAATTTATT
41186295 C
64 C
41186296 ACTATTTAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
65 1 0.02
66 49 0.89
67 5 0.09
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (66 bp):
TATGATCTTTTCGTTACTTCCTCATGAAAACAGACTCATCAAGCTTCGATTACATAATTTATTCC
G
Found at i:41187206 original size:39 final size:39
Alignment explanation
Indices: 41187084--41187354 Score: 438
Period size: 39 Copynumber: 6.9 Consensus size: 39
41187074 GCTCCTCGTT
* *
41187084 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
41187124 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
*
41187164 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGTA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
41187203 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
41187242 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
41187281 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
41187320 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCT
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCT
41187355 TTAGTAACTC
Statistics
Matches: 221, Mismatches: 8, Indels: 5
0.94 0.03 0.02
Matches are distributed among these distances:
39 173 0.78
40 46 0.21
41 2 0.01
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
Found at i:41187713 original size:74 final size:74
Alignment explanation
Indices: 41187588--41187737 Score: 273
Period size: 74 Copynumber: 2.0 Consensus size: 74
41187578 TTAAAACATG
* *
41187588 ATCTAATCACATCATAATTTAAGCTCTCTTACTCAAGAACTTACCTTGGGTGTTGTTGAACGATT
1 ATCTAATCACATCATAATTTAAGCTCTCTTACTCAAGAACTTACCTCGGGTGTTGTCGAACGATT
41187653 CCGATAGCT
66 CCGATAGCT
*
41187662 ATCTAATCACATCATAATTTAAGCTCTTTTACTCAAGAACTTACCTCGGGTGTTGTCGAACGATT
1 ATCTAATCACATCATAATTTAAGCTCTCTTACTCAAGAACTTACCTCGGGTGTTGTCGAACGATT
41187727 CCGATAGCT
66 CCGATAGCT
41187736 AT
1 AT
41187738 TCGACCACTT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.35
Consensus pattern (74 bp):
ATCTAATCACATCATAATTTAAGCTCTCTTACTCAAGAACTTACCTCGGGTGTTGTCGAACGATT
CCGATAGCT
Found at i:41195408 original size:16 final size:17
Alignment explanation
Indices: 41195384--41195416 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
41195374 AAAGCAAACT
*
41195384 TACACATAGTTTCAATG
1 TACACATAGTTACAATG
41195401 TACA-ATAGTTACAATG
1 TACACATAGTTACAATG
41195417 GCGTTTTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (17 bp):
TACACATAGTTACAATG
Found at i:41198025 original size:30 final size:30
Alignment explanation
Indices: 41197989--41198046 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
41197979 CGTGTTGGCA
* *
41197989 GTTATCTACTGGCCCTTCGGGGTGACACTG
1 GTTATCTACTAGCCCTTCGGGGTAACACTG
* *
41198019 GTTATCTACTAGTCCTTTGGGGTAACAC
1 GTTATCTACTAGCCCTTCGGGGTAACAC
41198047 CATGTTGATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.17, C:0.24, G:0.26, T:0.33
Consensus pattern (30 bp):
GTTATCTACTAGCCCTTCGGGGTAACACTG
Found at i:41198157 original size:35 final size:36
Alignment explanation
Indices: 41198074--41198157 Score: 89
Period size: 35 Copynumber: 2.3 Consensus size: 36
41198064 ACTAGTCTTT
* * *
41198074 CGGGGTGACACTGTGTAAATGGTATATAAAGGTCTTT
1 CGGGGTGACACCGTGTAAATGG-ATATAAAGGTCCTA
* ** *
41198111 TGGGGCAACACCGTGTAAATGG-TATACAGGTCCTA
1 CGGGGTGACACCGTGTAAATGGATATAAAGGTCCTA
41198146 CGGGGTGACACC
1 CGGGGTGACACC
41198158 TCGAAAAGGG
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
35 19 0.51
37 18 0.49
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (36 bp):
CGGGGTGACACCGTGTAAATGGATATAAAGGTCCTA
Found at i:41204735 original size:16 final size:16
Alignment explanation
Indices: 41204714--41204746 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
41204704 TTGAGTTGAG
41204714 AAAATT-ATTGAATTAA
1 AAAATTAATT-AATTAA
41204730 AAAATTAATTAATTAA
1 AAAATTAATTAATTAA
41204746 A
1 A
41204747 TAATATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
AAAATTAATTAATTAA
Found at i:41210965 original size:17 final size:18
Alignment explanation
Indices: 41210934--41210969 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
41210924 GATATTCCCC
41210934 TTTCCCTTTCCAATCCCTA
1 TTTCCCTTT-CAATCCCTA
41210953 TTTCCCTTT-AATCCCTA
1 TTTCCCTTTCAATCCCTA
41210970 ATCCCTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
19 9 0.53
ACGTcount: A:0.17, C:0.39, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTCCCTTTCAATCCCTA
Found at i:41221130 original size:20 final size:20
Alignment explanation
Indices: 41221065--41221130 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
41221055 AGAATAAATC
41221065 ATTTTATCTTTTAGTAGTTT
1 ATTTTATCTTTTAGTAGTTT
** * * *
41221085 ATTAGATATTCTAGGAATATTTT
1 ATTTTATCTTTTA-G--TAGTTT
41221108 ATTTTATCTTTTAGTAGTTT
1 ATTTTATCTTTTAGTAGTTT
41221128 ATT
1 ATT
41221131 AGAATAAGGG
Statistics
Matches: 33, Mismatches: 10, Indels: 6
0.67 0.20 0.12
Matches are distributed among these distances:
20 17 0.52
21 1 0.03
22 1 0.03
23 14 0.42
ACGTcount: A:0.26, C:0.05, G:0.11, T:0.59
Consensus pattern (20 bp):
ATTTTATCTTTTAGTAGTTT
Found at i:41221195 original size:16 final size:16
Alignment explanation
Indices: 41221174--41221208 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
41221164 GACTATTTTC
41221174 TCTATTTAAATTCAGT
1 TCTATTTAAATTCAGT
41221190 TCTATTTAAATTCAGT
1 TCTATTTAAATTCAGT
41221206 TCT
1 TCT
41221209 TTAATTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.14, G:0.06, T:0.51
Consensus pattern (16 bp):
TCTATTTAAATTCAGT
Found at i:41229350 original size:22 final size:22
Alignment explanation
Indices: 41229325--41229367 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
41229315 TTACACAATT
41229325 TAAAAAA-TTAAATTCTTAAAAA
1 TAAAAAATTTAAATT-TTAAAAA
41229347 TAAAAAATTTAAATTTTAAAA
1 TAAAAAATTTAAATTTTAAAA
41229368 TTTTAAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAAAAATTTAAATTTTAAAAA
Found at i:41229830 original size:16 final size:16
Alignment explanation
Indices: 41229809--41229839 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41229799 TTTTGTATTA
*
41229809 TTTTAATATTAAATAT
1 TTTTAAAATTAAATAT
41229825 TTTTAAAATTAAATA
1 TTTTAAAATTAAATA
41229840 ATATTAATAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTTAAAATTAAATAT
Found at i:41230177 original size:3 final size:3
Alignment explanation
Indices: 41230171--41230208 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
41230161 AAGTGATGAT
41230171 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
41230209 ATTAAATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:41236216 original size:24 final size:24
Alignment explanation
Indices: 41236189--41236242 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
41236179 AAAAGCCTAC
41236189 AACGGGTAGCTCCAAAGAGCACTT
1 AACGGGTAGCTCCAAAGAGCACTT
***
41236213 AACGGGTAGCTTTGAAGAGCACTT
1 AACGGGTAGCTCCAAAGAGCACTT
41236237 AACGGG
1 AACGGG
41236243 AAGCACTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.31, C:0.20, G:0.30, T:0.19
Consensus pattern (24 bp):
AACGGGTAGCTCCAAAGAGCACTT
Found at i:41252630 original size:50 final size:50
Alignment explanation
Indices: 41252505--41252801 Score: 292
Period size: 50 Copynumber: 5.8 Consensus size: 50
41252495 ATTTGGGTAA
* *
41252505 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATG
* * *
41252561 AGAGGTTCGATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
41252611 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * *
41252661 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGAACCTATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * * *
41252711 AGAACTCTCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACAAG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** * * *
41252760 AAACATCCCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
41252802 TGTTATATTC
Statistics
Matches: 204, Mismatches: 36, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
49 36 0.18
50 126 0.62
53 3 0.01
55 1 0.00
56 38 0.19
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:41266190 original size:13 final size:12
Alignment explanation
Indices: 41266172--41266239 Score: 56
Period size: 13 Copynumber: 5.8 Consensus size: 12
41266162 ATTTTCTTGT
41266172 TTTTCTTTTCAC
1 TTTTCTTTTCAC
41266184 ATTTTCTTTTCAC
1 -TTTTCTTTTCAC
41266197 -TTTCTTTTTCTAC
1 TTTTC-TTTTC-AC
*
41266210 TTTTGTTTT--C
1 TTTTCTTTTCAC
*
41266220 -TTT-TTTTCAT
1 TTTTCTTTTCAC
41266230 TTTTCTTTTC
1 TTTTCTTTTC
41266240 TTTTTCACTT
Statistics
Matches: 46, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
8 4 0.09
9 3 0.07
10 1 0.02
11 7 0.15
12 10 0.22
13 18 0.39
14 3 0.07
ACGTcount: A:0.07, C:0.19, G:0.01, T:0.72
Consensus pattern (12 bp):
TTTTCTTTTCAC
Found at i:41266219 original size:19 final size:19
Alignment explanation
Indices: 41266197--41266262 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 19
41266187 TTCTTTTCAC
*
41266197 TTTCTTTTTCTACTTTTGT
1 TTTCTTTTTCTACTTTTCT
* *
41266216 TTTCTTTTTTTCATTTTTCT
1 TTTCTTTTTCT-ACTTTTCT
41266236 TTTCTTTTTC-ACTTCCTTCT
1 TTTCTTTTTCTACTT--TTCT
41266256 TTT-TTTT
1 TTTCTTTT
41266263 CCTTTTTCAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 3 0.08
19 14 0.36
20 22 0.56
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTCTTTTTCTACTTTTCT
Found at i:41266224 original size:20 final size:20
Alignment explanation
Indices: 41266153--41266244 Score: 78
Period size: 22 Copynumber: 4.2 Consensus size: 20
41266143 CAATCAGGCC
41266153 TTTTTTCACATTTTCTTGTT-T
1 TTTTTTCAC-TTTTCTT-TTCT
41266174 TTCTTTTCACATTTTCTTTTCACTT
1 TT-TTTTCAC-TTTTCTTTT--C-T
*
41266199 TCTTTTTCTACTTTTGTTTTCT
1 T-TTTTTC-ACTTTTCTTTTCT
*
41266221 TTTTTTCATTTTTCTTTTCT
1 TTTTTTCACTTTTCTTTTCT
41266241 TTTT
1 TTTT
41266245 CACTTCCTTC
Statistics
Matches: 61, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
20 15 0.25
21 10 0.16
22 17 0.28
23 1 0.02
25 15 0.25
26 3 0.05
ACGTcount: A:0.08, C:0.17, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTTTTCACTTTTCTTTTCT
Found at i:41270532 original size:29 final size:30
Alignment explanation
Indices: 41270481--41270541 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 30
41270471 TGAATTGTTT
*
41270481 TTAAAAATTTGGTTGCTCTTTTTGTAAATA
1 TTAAAAATTAGGTTGCTCTTTTTGTAAATA
*
41270511 TTAAAAATTAGGTT-CTTTTTTTGTAAATA
1 TTAAAAATTAGGTTGCTCTTTTTGTAAATA
41270540 TT
1 TT
41270542 TTCAAAAAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 16 0.55
30 13 0.45
ACGTcount: A:0.31, C:0.05, G:0.11, T:0.52
Consensus pattern (30 bp):
TTAAAAATTAGGTTGCTCTTTTTGTAAATA
Found at i:41270645 original size:16 final size:15
Alignment explanation
Indices: 41270605--41270651 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
41270595 AGATGATAAT
41270605 TATTAATATATAATTA
1 TATTAAT-TATAATTA
41270621 TATCT-ATTATAATATA
1 TAT-TAATTATAAT-TA
*
41270637 TATTAATTATTATTA
1 TATTAATTATAATTA
41270652 GCTTTATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
15 9 0.33
16 17 0.63
17 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTAATTATAATTA
Found at i:41270650 original size:10 final size:11
Alignment explanation
Indices: 41270603--41270651 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 11
41270593 AAAGATGATA
41270603 ATTATTAATAT
1 ATTATTAATAT
* *
41270614 ATAATTATATCT
1 ATTATTA-ATAT
41270626 ATTA-TAATAT
1 ATTATTAATAT
41270636 A-TATTAAT-T
1 ATTATTAATAT
41270645 ATTATTA
1 ATTATTA
41270652 GCTTTATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
9 4 0.13
10 13 0.42
11 8 0.26
12 6 0.19
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (11 bp):
ATTATTAATAT
Found at i:41270650 original size:22 final size:23
Alignment explanation
Indices: 41270603--41270651 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
41270593 AAAGATGATA
41270603 ATTATTAATATATAATTATATCT
1 ATTATTAATATATAATTATATCT
41270626 ATTA-TAATATAT-ATTA-AT-T
1 ATTATTAATATATAATTATATCT
41270645 ATTATTA
1 ATTATTA
41270652 GCTTTATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 5 0.20
20 4 0.16
21 4 0.16
22 8 0.32
23 4 0.16
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
ATTATTAATATATAATTATATCT
Found at i:41270819 original size:12 final size:12
Alignment explanation
Indices: 41270802--41270831 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
41270792 TTTAAGAACT
*
41270802 CTACTCTAGCTC
1 CTACTCTAGCGC
41270814 CTACTCTAGCGC
1 CTACTCTAGCGC
41270826 CTACTC
1 CTACTC
41270832 CTTTCACTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.43, G:0.10, T:0.30
Consensus pattern (12 bp):
CTACTCTAGCGC
Found at i:41278148 original size:16 final size:16
Alignment explanation
Indices: 41278127--41278159 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
41278117 AAGTTAGGTT
41278127 ATAACTCGATATCATC
1 ATAACTCGATATCATC
41278143 ATAACTCGATATCATC
1 ATAACTCGATATCATC
41278159 A
1 A
41278160 GGAGTGAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.30
Consensus pattern (16 bp):
ATAACTCGATATCATC
Found at i:41288461 original size:7 final size:7
Alignment explanation
Indices: 41288445--41288480 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
41288435 TTTAAATTTC
41288445 TTTT-AA
1 TTTTAAA
41288451 TTTTAAA
1 TTTTAAA
41288458 TTTTAAA
1 TTTTAAA
41288465 TTTTAAA
1 TTTTAAA
41288472 TTTTAAA
1 TTTTAAA
41288479 TT
1 TT
41288481 AAGTATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 4 0.14
7 25 0.86
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
TTTTAAA
Found at i:41294231 original size:18 final size:19
Alignment explanation
Indices: 41294200--41294236 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
41294190 TTCCATTAGG
41294200 TTAATTTAGGTTAATTAAT
1 TTAATTTAGGTTAATTAAT
*
41294219 TTAA-TTAGTTTAATTAAT
1 TTAATTTAGGTTAATTAAT
41294237 CCATTGGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (19 bp):
TTAATTTAGGTTAATTAAT
Found at i:41306135 original size:20 final size:21
Alignment explanation
Indices: 41306115--41306192 Score: 77
Period size: 21 Copynumber: 3.7 Consensus size: 21
41306105 ATACCAATAT
41306115 AAAAATATCGATACTTTTATA
1 AAAAATATCGATACTTTTATA
* **
41306136 AAAAAAATTAATACTTTTATTAA
1 AAAAATATCGATACTTTTA-T-A
* **
41306159 AAAAATATCGATACTCTT-GG
1 AAAAATATCGATACTTTTATA
41306179 AAAAATATCGATAC
1 AAAAATATCGATAC
41306193 CACTGGGGTT
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
20 14 0.30
21 16 0.35
22 1 0.02
23 15 0.33
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.33
Consensus pattern (21 bp):
AAAAATATCGATACTTTTATA
Found at i:41306172 original size:23 final size:22
Alignment explanation
Indices: 41306115--41306173 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
41306105 ATACCAATAT
41306115 AAAAATATCGATACTTTTATAA
1 AAAAATATCGATACTTTTATAA
**
41306137 AAAAA-ATTAATACTTTTATTAA
1 AAAAATATCGATACTTTTA-TAA
41306159 AAAAATATCGATACT
1 AAAAATATCGATACT
41306174 CTTGGAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 11 0.35
22 13 0.42
23 7 0.23
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.36
Consensus pattern (22 bp):
AAAAATATCGATACTTTTATAA
Found at i:41308378 original size:20 final size:20
Alignment explanation
Indices: 41308341--41308379 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41308331 AAATCAATTT
*
41308341 AAAATGATTTTAACCAAGTC
1 AAAATGATTTCAACCAAGTC
* *
41308361 AAAATTATTTCAATCAAGT
1 AAAATGATTTCAACCAAGT
41308380 TGAAGTCATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.33
Consensus pattern (20 bp):
AAAATGATTTCAACCAAGTC
Found at i:41308856 original size:27 final size:27
Alignment explanation
Indices: 41308825--41308879 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
41308815 CCAACGACTC
41308825 TATTCATGACACCAGCAACCTCAACGG
1 TATTCATGACACCAGCAACCTCAACGG
41308852 TATTCATGACACCAGCAACCTCAACGG
1 TATTCATGACACCAGCAACCTCAACGG
41308879 T
1 T
41308880 TGGAAATCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.33, G:0.15, T:0.20
Consensus pattern (27 bp):
TATTCATGACACCAGCAACCTCAACGG
Found at i:41309774 original size:64 final size:64
Alignment explanation
Indices: 41309699--41309834 Score: 245
Period size: 64 Copynumber: 2.1 Consensus size: 64
41309689 GTAATGGTAT
*
41309699 ATAATAAGGGAGTGTTAAGTCATTGTAATATATTAGAATGACTCTATGATTAAATAAATTATAA
1 ATAATAAGGGAGAGTTAAGTCATTGTAATATATTAGAATGACTCTATGATTAAATAAATTATAA
* *
41309763 ATAATAAGGGAGAGTTATGTCATTGTACTATATTAGAATGACTCTATGATTAAATAAATTATAA
1 ATAATAAGGGAGAGTTAAGTCATTGTAATATATTAGAATGACTCTATGATTAAATAAATTATAA
41309827 ATAATAAG
1 ATAATAAG
41309835 TGAAGAGCCA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 69 1.00
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.35
Consensus pattern (64 bp):
ATAATAAGGGAGAGTTAAGTCATTGTAATATATTAGAATGACTCTATGATTAAATAAATTATAA
Found at i:41314327 original size:283 final size:283
Alignment explanation
Indices: 41313820--41314366 Score: 1094
Period size: 283 Copynumber: 1.9 Consensus size: 283
41313810 TCTTTCCTTC
41313820 TAAATTTATCAATAATCTTTTAGTTGCTGACATTTTTTAATAAGGTTAAAATAGTAGTCTATTAC
1 TAAATTTATCAATAATCTTTTAGTTGCTGACATTTTTTAATAAGGTTAAAATAGTAGTCTATTAC
41313885 AAAGGAGTGAATTGTATTTTTAAAAGTAGCCTAATCACTTATTTCCCCATCCAATTTTATAAAAA
66 AAAGGAGTGAATTGTATTTTTAAAAGTAGCCTAATCACTTATTTCCCCATCCAATTTTATAAAAA
41313950 AAAAAACTCATTTTTAACCCCCATTTTAATTTCTTTTCTTTCTTTAGCTTTTGAACATGCATTAT
131 AAAAAACTCATTTTTAACCCCCATTTTAATTTCTTTTCTTTCTTTAGCTTTTGAACATGCATTAT
41314015 TCGTTAAATCACCTTAAAATGGATGAAAAAGTTAATGTTTGTTAACTTTGTTGATGTGGCAGTCC
196 TCGTTAAATCACCTTAAAATGGATGAAAAAGTTAATGTTTGTTAACTTTGTTGATGTGGCAGTCC
41314080 ACATTCCGATCTATGTGGTGCCT
261 ACATTCCGATCTATGTGGTGCCT
41314103 TAAATTTATCAATAATCTTTTAGTTGCTGACATTTTTTAATAAGGTTAAAATAGTAGTCTATTAC
1 TAAATTTATCAATAATCTTTTAGTTGCTGACATTTTTTAATAAGGTTAAAATAGTAGTCTATTAC
41314168 AAAGGAGTGAATTGTATTTTTAAAAGTAGCCTAATCACTTATTTCCCCATCCAATTTTATAAAAA
66 AAAGGAGTGAATTGTATTTTTAAAAGTAGCCTAATCACTTATTTCCCCATCCAATTTTATAAAAA
41314233 AAAAAACTCATTTTTAACCCCCATTTTAATTTCTTTTCTTTCTTTAGCTTTTGAACATGCATTAT
131 AAAAAACTCATTTTTAACCCCCATTTTAATTTCTTTTCTTTCTTTAGCTTTTGAACATGCATTAT
41314298 TCGTTAAATCACCTTAAAATGGATGAAAAAGTTAATGTTTGTTAACTTTGTTGATGTGGCAGTCC
196 TCGTTAAATCACCTTAAAATGGATGAAAAAGTTAATGTTTGTTAACTTTGTTGATGTGGCAGTCC
41314363 ACAT
261 ACAT
41314367 GTATGTCACA
Statistics
Matches: 264, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
283 264 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.41
Consensus pattern (283 bp):
TAAATTTATCAATAATCTTTTAGTTGCTGACATTTTTTAATAAGGTTAAAATAGTAGTCTATTAC
AAAGGAGTGAATTGTATTTTTAAAAGTAGCCTAATCACTTATTTCCCCATCCAATTTTATAAAAA
AAAAAACTCATTTTTAACCCCCATTTTAATTTCTTTTCTTTCTTTAGCTTTTGAACATGCATTAT
TCGTTAAATCACCTTAAAATGGATGAAAAAGTTAATGTTTGTTAACTTTGTTGATGTGGCAGTCC
ACATTCCGATCTATGTGGTGCCT
Found at i:41314419 original size:13 final size:13
Alignment explanation
Indices: 41314403--41314444 Score: 52
Period size: 11 Copynumber: 3.3 Consensus size: 13
41314393 TTTTTTAAAA
41314403 ATTTTAAAATAAT
1 ATTTTAAAATAAT
*
41314416 ATTTTTTAAA-AAT
1 A-TTTTAAAATAAT
41314429 -TTTTAAAATAAT
1 ATTTTAAAATAAT
41314441 ATTT
1 ATTT
41314445 ATAAGTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
11 7 0.29
12 3 0.12
13 7 0.29
14 7 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTAAAATAAT
Found at i:41314425 original size:24 final size:25
Alignment explanation
Indices: 41314389--41314444 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
41314379 AGCAATTAAT
41314389 TAAT-TTTTTTAAAAA-TTTTAAAA
1 TAATATTTTTTAAAAATTTTTAAAA
41314412 TAATATTTTTTAAAAATTTTTAAAA
1 TAATATTTTTTAAAAATTTTTAAAA
41314437 TAATATTT
1 TAATATTT
41314445 ATAAGTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 4 0.13
24 11 0.35
25 16 0.52
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TAATATTTTTTAAAAATTTTTAAAA
Found at i:41319801 original size:28 final size:28
Alignment explanation
Indices: 41319748--41319805 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
41319738 CAAACAAAGG
*
41319748 CATGAATTTAATATGTAATATACTAAGA
1 CATGAATTTAATATGTAACATACTAAGA
* *
41319776 CATG-ATTTAAATATGTAGCATGCTAAGA
1 CATGAATTT-AATATGTAACATACTAAGA
41319804 CA
1 CA
41319806 AAATAATGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 4 0.15
28 22 0.85
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (28 bp):
CATGAATTTAATATGTAACATACTAAGA
Found at i:41324347 original size:141 final size:141
Alignment explanation
Indices: 41324092--41324375 Score: 523
Period size: 141 Copynumber: 2.0 Consensus size: 141
41324082 TCCAGCAACC
41324092 TGTTAAGACAAATTTTAAACACACGATTAAAGCTTCAATAAGACAATATTGAACACAATTAAATA
1 TGTTAAGACAAATTTTAAACACACGATTAAAGCTTCAATAAGACAATATTGAACACAATTAAATA
*
41324157 TGTAATAAGCTAAGACACATTAAGAAAACTAATTTGCTAATATGTAATAAATCTGTCTGAAATTG
66 TGTAATAAGCTAAGACACATTAAGAAAACTAATTTGCTAATATGCAATAAATCTGTCTGAAATTG
41324222 GACATGCTTAA
131 GACATGCTTAA
* * *
41324233 TGTTAAGACACATTTTAAACACACGATTAAAGCTTCAATAGGGCAATATTGAACACAATTAAATA
1 TGTTAAGACAAATTTTAAACACACGATTAAAGCTTCAATAAGACAATATTGAACACAATTAAATA
41324298 TGTAATAAGCTAAGACACATTAAGAAAACTAATTTGCTAATATGCAATAAATCTGTCTGAAATTG
66 TGTAATAAGCTAAGACACATTAAGAAAACTAATTTGCTAATATGCAATAAATCTGTCTGAAATTG
*
41324363 GACTTGCTTAA
131 GACATGCTTAA
41324374 TG
1 TG
41324376 GACAAACAAA
Statistics
Matches: 138, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
141 138 1.00
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (141 bp):
TGTTAAGACAAATTTTAAACACACGATTAAAGCTTCAATAAGACAATATTGAACACAATTAAATA
TGTAATAAGCTAAGACACATTAAGAAAACTAATTTGCTAATATGCAATAAATCTGTCTGAAATTG
GACATGCTTAA
Found at i:41324441 original size:28 final size:28
Alignment explanation
Indices: 41324384--41324443 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
41324374 TGGACAAACA
*
41324384 AAGACATTAATTTAATATGTAATATACT
1 AAGACATTAATTTAATATGTAACATACT
* * *
41324412 AAGACA-TGATTTAAATATGTAGCATGCT
1 AAGACATTAATTT-AATATGTAACATACT
41324440 AAGA
1 AAGA
41324444 AAAAATAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.33
Consensus pattern (28 bp):
AAGACATTAATTTAATATGTAACATACT
Found at i:41331223 original size:25 final size:25
Alignment explanation
Indices: 41331189--41331241 Score: 90
Period size: 25 Copynumber: 2.1 Consensus size: 25
41331179 ATTTTACCTG
41331189 AATCTTATTCGAGAACT-TCGTTATC
1 AATCTTATTCGAGAACTCT-GTTATC
41331214 AATCTTATTCGAGAACTCTGTTATC
1 AATCTTATTCGAGAACTCTGTTATC
41331239 AAT
1 AAT
41331242 ATTCTTTGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 26 0.96
26 1 0.04
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (25 bp):
AATCTTATTCGAGAACTCTGTTATC
Found at i:41332199 original size:20 final size:20
Alignment explanation
Indices: 41332157--41332199 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
41332147 GAATGTTAAA
*
41332157 TTAGTATGTTTTGACATGTT
1 TTAGTATGTTTTGACATGGT
*
41332177 TTAGTGTGTTTTGA-ATAGGT
1 TTAGTATGTTTTGACAT-GGT
41332197 TTA
1 TTA
41332200 AAATGTTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.21, C:0.02, G:0.23, T:0.53
Consensus pattern (20 bp):
TTAGTATGTTTTGACATGGT
Found at i:41346673 original size:38 final size:40
Alignment explanation
Indices: 41346588--41346685 Score: 130
Period size: 38 Copynumber: 2.5 Consensus size: 40
41346578 ATATTATAAG
* *
41346588 TATAATTACCATAATTATAATAATGTTTGACCCAAAAAAT
1 TATAATTACAATAATTATAATAATATTTGACCCAAAAAAT
* *
41346628 TACAATTACAATAATTATAATAATATTCT-A-TC-AAAAAT
1 TATAATTACAATAATTATAATAATATT-TGACCCAAAAAAT
41346666 TATAATTACAATAATTATAA
1 TATAATTACAATAATTATAA
41346686 CAAGGATTTC
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
38 25 0.48
39 1 0.02
40 25 0.48
41 1 0.02
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (40 bp):
TATAATTACAATAATTATAATAATATTTGACCCAAAAAAT
Found at i:41364500 original size:23 final size:24
Alignment explanation
Indices: 41364464--41364511 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
41364454 TTCATCAAAT
41364464 GTTTCTCATCAAGTTTTTAAGCAA
1 GTTTCTCATCAAGTTTTTAAGCAA
*
41364488 GTTTC-CATCAAGTTTTTAATCAA
1 GTTTCTCATCAAGTTTTTAAGCAA
41364511 G
1 G
41364512 CTTTTATCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (24 bp):
GTTTCTCATCAAGTTTTTAAGCAA
Found at i:41364509 original size:12 final size:12
Alignment explanation
Indices: 41364471--41364517 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
41364461 AATGTTTCTC
41364471 ATCAAGTTTTTA
1 ATCAAGTTTTTA
* **
41364483 AGCAAG-TTTCC
1 ATCAAGTTTTTA
41364494 ATCAAGTTTTTA
1 ATCAAGTTTTTA
*
41364506 ATCAAGCTTTTA
1 ATCAAGTTTTTA
41364518 TCTTTTGAGT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
11 8 0.30
12 19 0.70
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.43
Consensus pattern (12 bp):
ATCAAGTTTTTA
Found at i:41372032 original size:27 final size:27
Alignment explanation
Indices: 41372002--41372056 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
41371992 CAAACAATTG
* *
41372002 ATTACAACTTTATTCCATTGCATCTCT
1 ATTACAACTCTATTCCATTACATCTCT
* *
41372029 ATTATAGCTCTATTCCATTACATCTCT
1 ATTACAACTCTATTCCATTACATCTCT
41372056 A
1 A
41372057 GTATAGCTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.27, C:0.25, G:0.04, T:0.44
Consensus pattern (27 bp):
ATTACAACTCTATTCCATTACATCTCT
Found at i:41372061 original size:27 final size:27
Alignment explanation
Indices: 41372012--41372069 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
41372002 ATTACAACTT
* *
41372012 TATTCCATTGCATCTCTATTATAGCTC
1 TATTCCATTACATCTCTAGTATAGCTC
41372039 TATTCCATTACATCTCTAGTATAGCTC
1 TATTCCATTACATCTCTAGTATAGCTC
41372066 TATT
1 TATT
41372070 TCAATGAACC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.24, C:0.24, G:0.07, T:0.45
Consensus pattern (27 bp):
TATTCCATTACATCTCTAGTATAGCTC
Found at i:41377671 original size:7 final size:7
Alignment explanation
Indices: 41377656--41377716 Score: 77
Period size: 7 Copynumber: 8.6 Consensus size: 7
41377646 GTTTTGAGGT
41377656 TTTAGGG
1 TTTAGGG
*
41377663 TTTATGG
1 TTTAGGG
*
41377670 TTTAGTGT
1 TTTAG-GG
*
41377678 TTTAAGG
1 TTTAGGG
41377685 TTTAGGG
1 TTTAGGG
41377692 TTTAGGG
1 TTTAGGG
41377699 TTTAGGG
1 TTTAGGG
*
41377706 TTTGGGG
1 TTTAGGG
41377713 TTTA
1 TTTA
41377717 ATGTTAAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
7 40 0.89
8 5 0.11
ACGTcount: A:0.15, C:0.00, G:0.36, T:0.49
Consensus pattern (7 bp):
TTTAGGG
Found at i:41377681 original size:15 final size:14
Alignment explanation
Indices: 41377646--41377704 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
41377636 CGTTTTGCCT
*
41377646 GTTTTGAGGTTTTAG
1 GTTTTAAGG-TTTAG
* *
41377661 GGTTTATGGTTTAG
1 GTTTTAAGGTTTAG
41377675 TGTTTTAAGGTTTAG
1 -GTTTTAAGGTTTAG
* *
41377690 GGTTTAGGGTTTAG
1 GTTTTAAGGTTTAG
41377704 G
1 G
41377705 GTTTGGGGTT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
14 18 0.50
15 18 0.50
ACGTcount: A:0.15, C:0.00, G:0.36, T:0.49
Consensus pattern (14 bp):
GTTTTAAGGTTTAG
Found at i:41377700 original size:29 final size:30
Alignment explanation
Indices: 41377645--41377708 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 30
41377635 GCGTTTTGCC
* *
41377645 TGTTTTGAGGTTTTAGGGTTTATGGTTTAG
1 TGTTTTAAGGTTTTAGGGTTTAGGGTTTAG
41377675 TGTTTTAAGG-TTTAGGGTTTAGGGTTTAG
1 TGTTTTAAGGTTTTAGGGTTTAGGGTTTAG
*
41377704 GGTTT
1 TGTTT
41377709 GGGGTTTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 22 0.71
30 9 0.29
ACGTcount: A:0.14, C:0.00, G:0.34, T:0.52
Consensus pattern (30 bp):
TGTTTTAAGGTTTTAGGGTTTAGGGTTTAG
Found at i:41378344 original size:6 final size:6
Alignment explanation
Indices: 41378330--41378373 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
41378320 AAAAATCAGA
* *
41378330 TTAGGG TTAGTG TTAAGG TTAGGG TTAGGG TTAGGG TTAGGG TT
1 TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TT
41378374 TTTGTTAGGG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.18, C:0.00, G:0.43, T:0.39
Consensus pattern (6 bp):
TTAGGG
Found at i:41378380 original size:18 final size:18
Alignment explanation
Indices: 41378330--41378385 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
41378320 AAAAATCAGA
*
41378330 TTAGGGTTAGTGTTAAGG
1 TTAGGGTTAGTGTTAGGG
*
41378348 TTAGGGTTAGGGTTAGGG
1 TTAGGGTTAGTGTTAGGG
**
41378366 TTAGGGTTTTTGTTAGGG
1 TTAGGGTTAGTGTTAGGG
41378384 TT
1 TT
41378386 TTGGTGTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.16, C:0.00, G:0.41, T:0.43
Consensus pattern (18 bp):
TTAGGGTTAGTGTTAGGG
Found at i:41378635 original size:249 final size:229
Alignment explanation
Indices: 41378187--41378765 Score: 730
Period size: 230 Copynumber: 2.4 Consensus size: 229
41378177 GAACACCTCT
* * * *
41378187 AGTTTAGGGTTTGTCAATTAAATCATTTAAAAAATTTTAAAAATTGGATTTGTTTTCGTGTTTAT
1 AGTTTAGGGTTTGTCAATTAAATTATTTATAAAATTTTCAAAATTGGATTAGTTTTCGTGTTTAT
*
41378252 TATTTTTAAGAAAAAATCAATTAAATTAGGGTTTAGGATTACTTGAGTAATTTAATTAAAAAAAT
66 TATTTTT---AAAAAATCAATTAAATTAGGGTTTAGGATTACTTGAGTAATTTAATTAAAAAAAA
* *
41378317 TTTAAAAATCAGATTAGGGTTAGTGTTAAGGTTAGGGTTAGGGTTAGGGTTAGGGTTTTTGTTAG
128 TTTAAAAATCAGATTAGGGTTAGGGTTAAGGTTAGGATTAGGGTTAGGGTTAGGG--TTT-TTA-
41378382 GGTTTTGGTGTTTTTAAGGGTTTTTAAGAAAAAATCAAATAAGTTAGGGTTTAG
189 ---------G---TTAAGGG-TTTTAAGAAAAAATCAAATAAGTTAGGGTTTAG
* *
41378436 AGTTTAGGGTTTATCAATTAAATTATTTATAAATTTTTCAAAATTGGATTAGTTTTCGTGTTTAT
1 AGTTTAGGGTTTGTCAATTAAATTATTTATAAAATTTTCAAAATTGGATTAGTTTTCGTGTTTAT
*
41378501 TA-TTTTAAAAAATCAATTAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAAAATTT
66 TATTTTTAAAAAATCAATTAAATTAGGGTTTAGGATTACTTGAGTAATTTAATTAAAAAAAATTT
* * *** *
41378565 -AAAATTAGATTAGGGTTAGGGTTAGGGTTAGGATTTTTGTTAGGGTTTTGGTGTTTTTAAGTTA
131 AAAAATCAGATTAGGGTTAGGGTTAAGGTTAGGATTAGGGTTAGGG-TTAGG-GTTTTT-AGTTA
41378629 AGGGTTTTAAGAAAAAATCAAATAAGTTAGGGTTTAG
193 AGGGTTTTAAGAAAAAATCAAATAAGTTAGGGTTTAG
* *
41378666 AGTTTAGGGTTTGTCAATTAAATTATTTATAAAGTTTTCAAAATTAGATTAGTTTTCGTGTTTAT
1 AGTTTAGGGTTTGTCAATTAAATTATTTATAAAATTTTCAAAATTGGATTAGTTTTCGTGTTTAT
*
41378731 TATTTTTTAGGAAAATATGAATTAAATTAGGGTTT
66 TA-TTTTTA--AAAA-ATCAATTAAATTAGGGTTT
41378766 TGGTGTTTTT
Statistics
Matches: 302, Mismatches: 20, Indels: 30
0.86 0.06 0.09
Matches are distributed among these distances:
230 97 0.32
231 7 0.02
232 5 0.02
234 5 0.02
235 18 0.06
243 2 0.01
244 42 0.14
245 60 0.20
246 1 0.00
248 4 0.01
249 61 0.20
ACGTcount: A:0.34, C:0.03, G:0.20, T:0.43
Consensus pattern (229 bp):
AGTTTAGGGTTTGTCAATTAAATTATTTATAAAATTTTCAAAATTGGATTAGTTTTCGTGTTTAT
TATTTTTAAAAAATCAATTAAATTAGGGTTTAGGATTACTTGAGTAATTTAATTAAAAAAAATTT
AAAAATCAGATTAGGGTTAGGGTTAAGGTTAGGATTAGGGTTAGGGTTAGGGTTTTTAGTTAAGG
GTTTTAAGAAAAAATCAAATAAGTTAGGGTTTAG
Found at i:41380625 original size:18 final size:18
Alignment explanation
Indices: 41380599--41380641 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
41380589 GACTCAAAAA
* * *
41380599 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
41380617 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
41380635 AGGATAC
1 AGGATAC
41380642 GCACCTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:41382505 original size:11 final size:11
Alignment explanation
Indices: 41382472--41382499 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
41382462 TAAGAGAAAT
41382472 TTGAGAGCAAA
1 TTGAGAGCAAA
41382483 TTGAGAGCAAA
1 TTGAGAGCAAA
41382494 TTGAGA
1 TTGAGA
41382500 TTAAATAGGG
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:0.43, C:0.07, G:0.29, T:0.21
Consensus pattern (11 bp):
TTGAGAGCAAA
Found at i:41382513 original size:51 final size:51
Alignment explanation
Indices: 41382451--41382550 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
41382441 AATAATTAAA
*
41382451 AAATAGGGATTTAAGAGAAATTT-GAGAGCAAATTGAGAGCAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTTGGAAAG-AAATTGAGAGCAAATTGAGATT
* *
41382502 AAATAGGGATTTGAGAGAAATTTGGAAAGAAATTGAGAGGAAATTGAGA
1 AAATAGGGATTTAAGAGAAATTTGGAAAGAAATTGAGAGCAAATTGAGA
41382551 GAATAATAGA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 41 0.91
52 4 0.09
ACGTcount: A:0.46, C:0.02, G:0.28, T:0.24
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTGGAAAGAAATTGAGAGCAAATTGAGATT
Found at i:41388058 original size:31 final size:32
Alignment explanation
Indices: 41387999--41388063 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
41387989 AGCAAATTAC
41387999 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
41388031 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
41388062 AA
1 AA
41388064 ATTATCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:41388556 original size:41 final size:41
Alignment explanation
Indices: 41388497--41388578 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
41388487 ACACTATACT
41388497 CAGCAGGAAGATCAATGCGATAAGCATTGTCATTTATTTTC
1 CAGCAGGAAGATCAATGCGATAAGCATTGTCATTTATTTTC
*
41388538 CAGCAGGAAGATCGATGCGATAAGCATTGTCATTTATTTTC
1 CAGCAGGAAGATCAATGCGATAAGCATTGTCATTTATTTTC
41388579 TCGAGTACTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (41 bp):
CAGCAGGAAGATCAATGCGATAAGCATTGTCATTTATTTTC
Found at i:41389111 original size:13 final size:13
Alignment explanation
Indices: 41389093--41389121 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
41389083 AACACCTTCC
41389093 AAAAGTGACTAAG
1 AAAAGTGACTAAG
41389106 AAAAGTGACTAAG
1 AAAAGTGACTAAG
41389119 AAA
1 AAA
41389122 TTTTGCATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.59, C:0.07, G:0.21, T:0.14
Consensus pattern (13 bp):
AAAAGTGACTAAG
Found at i:41391618 original size:106 final size:106
Alignment explanation
Indices: 41391214--41391632 Score: 551
Period size: 107 Copynumber: 4.0 Consensus size: 106
41391204 AGGAATGTTT
* *
41391214 TTCT-AAATAAGGCAATATTTCGCATTTGGAAAATCGAGGAAACGTACCCTAACGTGTTGGGTTT
1 TTCTCAAATAAGGCAATATTTCGCATTTGGAAAATTGAGGAAACGTGCCCTAACGTGTTGGGTTT
41391278 CGACTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAA
66 CGACTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAA
** * * * *
41391319 TT-TCAAAGCGAGGCAATATTT-GCGTTTGGAAAATTGAGAAAACATGCCCTAACGTGTTAGGTT
1 TTCTCAAA-TAAGGCAATATTTCGCATTTGGAAAATTGAGGAAACGTGCCCTAACGTGTTGGGTT
* *
41391382 TCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAAC
65 TCGACTTCTCGTTCGACCAAATAGCCAAATATCC-TTTTAAAA
* * *
41391425 TTTTAAAATAAGGCAATATTTCGCATTTGGAAAATTGAGGAAATGTGCCCTAACGTGTTGGGTTT
1 TTCTCAAATAAGGCAATATTTCGCATTTGGAAAATTGAGGAAACGTGCCCTAACGTGTTGGGTTT
*
41391490 CGACTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAA
66 CGACTTCTCGTTCGACCAAATAGCCAAATATCCTTTT-AAAA
* * * * *
41391532 TTCTCAAATAAGGCAATGTTTTGCGTTTGG-AAATTCGAGG-AACGTGCCCTAATGTGCTGGGTT
1 TTCTCAAATAAGGCAATATTTCGCATTTGGAAAATT-GAGGAAACGTGCCCTAACGTGTTGGGTT
* * ** *
41391595 TTGATTTCTCGTTTAACTAAATAGCCAAATATCCTTTT
65 TCGACTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
41391633 GAATTTCAAT
Statistics
Matches: 272, Mismatches: 35, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
104 1 0.00
105 74 0.27
106 92 0.34
107 105 0.39
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (106 bp):
TTCTCAAATAAGGCAATATTTCGCATTTGGAAAATTGAGGAAACGTGCCCTAACGTGTTGGGTTT
CGACTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAA
Found at i:41392565 original size:16 final size:16
Alignment explanation
Indices: 41392544--41392578 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
41392534 ACTTATTTTG
* *
41392544 TTTTGATTGCATGGCA
1 TTTTGACTGCATGGAA
41392560 TTTTGACTGCATGGAA
1 TTTTGACTGCATGGAA
41392576 TTT
1 TTT
41392579 CATTATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.20, C:0.11, G:0.23, T:0.46
Consensus pattern (16 bp):
TTTTGACTGCATGGAA
Found at i:41402762 original size:107 final size:107
Alignment explanation
Indices: 41402540--41402904 Score: 502
Period size: 107 Copynumber: 3.4 Consensus size: 107
41402530 TCTTATCCAT
* ***
41402540 TGTTGGGTTTCGACTTCTCGTTCGACCAAATAGCCAAATATCC-TTTTAAAATTTCAAAGCGAGG
1 TGTTGGGTTTCGACTTCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAAATTTTAAAATAAGG
* *
41402604 CAATA-TTTGCGTTTGGAAAATTGAGAAAACGTGCCCTAACG
66 CAATATTTTGCGTTTGGAAAATCGAGGAAACGTGCCCTAACG
* *
41402645 TGTTGGGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAACTTTTAAAATAAGG
1 TGTTGGGTTTCGACTTCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAAATTTTAAAATAAGG
*
41402710 CAATATTTTGCATTTGGAAAATCGAGGAAACGTGCCCTAACG
66 CAATATTTTGCGTTTGGAAAATCGAGGAAACGTGCCCTAACG
* * * *
41402752 TGTTGGGTTTCGACTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAATTCTCAAATAAGG
1 TGTTGGGTTTCGACTTCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAAATTTTAAAATAAGG
* * * *
41402817 CAATGTTTCGCGTTTGGAAATTCGAGG-AACGTGCCCTAATG
66 CAATATTTTGCGTTTGGAAAATCGAGGAAACGTGCCCTAACG
* * * ** *
41402858 TGCTGGGTTTTGATTTCTCGTTTAACTAAATAGCCAAATATCCTTTT
1 TGTTGGGTTTCGACTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
41402905 GAATTTCAAT
Statistics
Matches: 231, Mismatches: 27, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
105 42 0.18
106 74 0.32
107 115 0.50
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (107 bp):
TGTTGGGTTTCGACTTCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAAATTTTAAAATAAGG
CAATATTTTGCGTTTGGAAAATCGAGGAAACGTGCCCTAACG
Found at i:41413711 original size:8 final size:8
Alignment explanation
Indices: 41413698--41413769 Score: 62
Period size: 8 Copynumber: 9.1 Consensus size: 8
41413688 ATGTTATATA
41413698 ACATTAAT
1 ACATTAAT
41413706 ACATTAAT
1 ACATTAAT
41413714 ACATTAATAT
1 ACATT-A-AT
41413724 AACATTAAT
1 -ACATTAAT
*
41413733 --ATAAAT
1 ACATTAAT
**
41413739 -TTTTAAT
1 ACATTAAT
41413746 A-ATTAAT
1 ACATTAAT
41413753 ACATTAAT
1 ACATTAAT
41413761 ACATTAAT
1 ACATTAAT
41413769 A
1 A
41413770 TAACATTAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
6 5 0.09
7 10 0.19
8 28 0.52
9 3 0.06
10 3 0.06
11 5 0.09
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.40
Consensus pattern (8 bp):
ACATTAAT
Found at i:41413716 original size:39 final size:37
Alignment explanation
Indices: 41413662--41413780 Score: 131
Period size: 39 Copynumber: 3.2 Consensus size: 37
41413652 TAAAAGAATT
* *
41413662 TTTAATAATTAATACATTAATATAAGATGTTATATAACA
1 TTTAATAATTAATACATTAATATAACAT-TAATATAA-A
41413701 -TTAATACATTAATACATTAATATAACATTAATATAAA
1 TTTAATA-ATTAATACATTAATATAACATTAATATAAA
41413738 TTTTTAATAATTAATACATT-A-AT-ACATTAATATAACA
1 --TTTAATAATTAATACATTAATATAACATTAATATAA-A
41413775 -TTAATA
1 TTTAATA
41413781 CAAGCTTACA
Statistics
Matches: 73, Mismatches: 2, Indels: 15
0.81 0.02 0.17
Matches are distributed among these distances:
34 6 0.08
36 12 0.16
37 4 0.05
38 14 0.19
39 31 0.42
40 6 0.08
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (37 bp):
TTTAATAATTAATACATTAATATAACATTAATATAAA
Found at i:41413722 original size:47 final size:44
Alignment explanation
Indices: 41413663--41413769 Score: 128
Period size: 47 Copynumber: 2.3 Consensus size: 44
41413653 AAAAGAATTT
*
41413663 TTAATA-ATTAATACATTAATATAAGATGTTATATAA-CATTAATACA
1 TTAATACATTAATACATTAATATAA-AT-TT-T-TAATAATTAATACA
41413709 TTAATACATTAATATAACATTAATATAAATTTTTAATAATTAATACA
1 TTAATACATT-A-AT-ACATTAATATAAATTTTTAATAATTAATACA
41413756 TTAATACATTAATA
1 TTAATACATTAATA
41413770 TAACATTAAT
Statistics
Matches: 55, Mismatches: 1, Indels: 12
0.81 0.01 0.18
Matches are distributed among these distances:
44 1 0.02
45 2 0.04
46 10 0.18
47 23 0.42
48 3 0.05
49 4 0.07
50 12 0.22
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (44 bp):
TTAATACATTAATACATTAATATAAATTTTTAATAATTAATACA
Found at i:41418117 original size:57 final size:58
Alignment explanation
Indices: 41418056--41418212 Score: 205
Period size: 57 Copynumber: 2.8 Consensus size: 58
41418046 ACATTAACCC
* * * **
41418056 ATAAGATTATACCAATTACA-ATTAAATCATTTCAATGACATATCCCA-TTATCAATTT
1 ATAAGGTTATACCAATTACACA-TAATTCATTTCAATGACATATCCAAGTTATCAATCG
* * *
41418113 ATAAGGTTATACTATTTACACATAATTCATTTCAATTACATAT-CAAGTTATCAATCG
1 ATAAGGTTATACCAATTACACATAATTCATTTCAATGACATATCCAAGTTATCAATCG
41418170 ATAAGGTTATACCAATTACACATAATTCATTTCAATG-CATATC
1 ATAAGGTTATACCAATTACACATAATTCATTTCAATGACATATC
41418213 AAATTATTTT
Statistics
Matches: 86, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
56 7 0.08
57 78 0.91
58 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.37
Consensus pattern (58 bp):
ATAAGGTTATACCAATTACACATAATTCATTTCAATGACATATCCAAGTTATCAATCG
Found at i:41419725 original size:17 final size:19
Alignment explanation
Indices: 41419682--41419726 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
41419672 AAACTACCTC
41419682 AAACT-AATATAGACAAAA
1 AAACTAAATATAGACAAAA
*
41419700 AAATTTAAATATA-A-AAAA
1 AAA-CTAAATATAGACAAAA
41419718 AAACTAAAT
1 AAACTAAAT
41419727 TTACGGATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 5 0.22
18 10 0.43
19 2 0.09
20 6 0.26
ACGTcount: A:0.69, C:0.07, G:0.02, T:0.22
Consensus pattern (19 bp):
AAACTAAATATAGACAAAA
Found at i:41420033 original size:14 final size:15
Alignment explanation
Indices: 41420009--41420037 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
41419999 TTCGATTTCA
41420009 AAAATAAATTTAAAT
1 AAAATAAATTTAAAT
41420024 AAAA-AAATTTAAAT
1 AAAATAAATTTAAAT
41420038 CCATTTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAAATAAATTTAAAT
Found at i:41431007 original size:45 final size:45
Alignment explanation
Indices: 41430943--41431029 Score: 156
Period size: 45 Copynumber: 1.9 Consensus size: 45
41430933 AACAGATACT
* *
41430943 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
41430988 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGAT
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGAT
41431030 ATTCGGTTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.24
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:41431100 original size:51 final size:51
Alignment explanation
Indices: 41431033--41431228 Score: 218
Period size: 51 Copynumber: 3.9 Consensus size: 51
41431023 CAATGATATT
* * * *
41431033 CGGTTCACATAGTAGCCTGCACATAGTACTACGCATGTGACCATTACCATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTACCATC
** * * *
41431084 CAATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGA-AACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATTACCATC
** * * * *
41431135 CGGTATGCATAGTAGCCTGCACATAGTACTACACATGCGACC-TT-TCATTC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTACCA-TC
41431185 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
41431229 CACTTTCACT
Statistics
Matches: 116, Mismatches: 25, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
49 1 0.01
50 40 0.34
51 73 0.63
52 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.24
Consensus pattern (51 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTACCATC
Found at i:41431216 original size:101 final size:102
Alignment explanation
Indices: 41431040--41431224 Score: 302
Period size: 101 Copynumber: 1.8 Consensus size: 102
41431030 ATTCGGTTCA
* *
41431040 CATAGTAGCCTGCACATAGTACTACGCATGTGACCATTACCATCCAATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATTACCATCCAATACACGTAGTAGCCTGCA
41431105 CATAGTACTACACACGTGATCGAAACTATCCGGTATG
66 CATAGTACTACACACGTGATCGAAACTATCCGGTATG
* **
41431142 CATAGTAGCCTGCACATAGTACTACACATGCGACC-TT-TCATTCCGGTACACGTAGTAGCCTGC
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATTACCA-TCCAATACACGTAGTAGCCTGC
41431205 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
41431225 CCATCACTTT
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
100 2 0.03
101 42 0.55
102 33 0.43
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (102 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATTACCATCCAATACACGTAGTAGCCTGCA
CATAGTACTACACACGTGATCGAAACTATCCGGTATG
Found at i:41436834 original size:16 final size:15
Alignment explanation
Indices: 41436807--41436836 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
41436797 AAATTCACAT
41436807 TTATACTATATATAA
1 TTATACTATATATAA
41436822 TTATACATATATATA
1 TTATAC-TATATATA
41436837 TTTCCAACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (15 bp):
TTATACTATATATAA
Found at i:41441910 original size:27 final size:26
Alignment explanation
Indices: 41441863--41441917 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
41441853 TAGGTTAATT
* *
41441863 TTAAAATAAATAATATGTAAAATAAC
1 TTAAAATAAATAACATATAAAATAAC
*
41441889 TTAAAATAAAATGACATATAAAATAAC
1 TTAAAAT-AAATAACATATAAAATAAC
41441916 TT
1 TT
41441918 GAAACAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.31
Consensus pattern (26 bp):
TTAAAATAAATAACATATAAAATAAC
Found at i:41452247 original size:40 final size:40
Alignment explanation
Indices: 41452164--41452426 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
41452154 TTGAATGCTG
* * * * * *
41452164 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
41452204 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
41452244 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
41452284 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
41452324 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
41452364 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
41452403 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
41452427 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:41452446 original size:79 final size:80
Alignment explanation
Indices: 41452203--41452461 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
41452193 AAGTGAATAT
* * * * * *
41452203 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
41452267 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
41452283 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
41452348 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
41452363 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
41452427 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
41452442 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
41452462 TACGTGATTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:41460198 original size:40 final size:40
Alignment explanation
Indices: 41460115--41460377 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
41460105 TTGAATGCTG
* * * * * *
41460115 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
41460155 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
41460195 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
41460235 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
41460275 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
41460315 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
41460354 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
41460378 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:41460397 original size:79 final size:80
Alignment explanation
Indices: 41460154--41460412 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
41460144 AAGTGAATAT
* * * * * *
41460154 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
41460218 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
41460234 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
41460299 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
41460314 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
41460378 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
41460393 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
41460413 TACGTGATTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:41465705 original size:16 final size:17
Alignment explanation
Indices: 41465678--41465726 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
41465668 GTCTAAAATT
*
41465678 ATATGTATTAATTTATA
1 ATATATATTAATTTATA
41465695 ATATA-ATTAATTT-TA
1 ATATATATTAATTTATA
*
41465710 ATTTATATTCAATTTAT
1 ATATATATT-AATTTAT
41465727 TTTGGGTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 6 0.22
16 11 0.41
17 9 0.33
18 1 0.04
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
ATATATATTAATTTATA
Found at i:41469779 original size:10 final size:10
Alignment explanation
Indices: 41469764--41469814 Score: 54
Period size: 9 Copynumber: 5.4 Consensus size: 10
41469754 TTAATAAATG
41469764 TTTTATATAT
1 TTTTATATAT
41469774 TTTTATAT-T
1 TTTTATATAT
*
41469783 TTTTGTA-AT
1 TTTTATATAT
* *
41469792 TTTTTTATAA
1 TTTTATATAT
41469802 TTTTATA-AT
1 TTTTATATAT
41469811 TTTT
1 TTTT
41469815 GCAAGTATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
9 19 0.56
10 15 0.44
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (10 bp):
TTTTATATAT
Found at i:41469795 original size:19 final size:19
Alignment explanation
Indices: 41469764--41469814 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
41469754 TTAATAAATG
* *
41469764 TTTTAT-ATATTTTTATATT
1 TTTTATAATTTTTTTATA-A
*
41469783 TTTTGTAATTTTTTTATAA
1 TTTTATAATTTTTTTATAA
41469802 TTTTATAATTTTT
1 TTTTATAATTTTT
41469815 GCAAGTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTTATAATTTTTTTATAA
Found at i:41469797 original size:11 final size:11
Alignment explanation
Indices: 41469748--41469805 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
41469738 AAAATTTCCA
*
41469748 AATTTTTTAAT
1 AATTTTTTTAT
* *
41469759 AAATGTTTTAT
1 AATTTTTTTAT
*
41469770 -ATATTTTTAT
1 AATTTTTTTAT
*
41469780 -A-TTTTTTGT
1 AATTTTTTTAT
41469789 AATTTTTTTAT
1 AATTTTTTTAT
41469800 AATTTT
1 AATTTT
41469806 ATAATTTTTG
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
9 6 0.17
10 9 0.25
11 21 0.58
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.67
Consensus pattern (11 bp):
AATTTTTTTAT
Found at i:41469805 original size:28 final size:27
Alignment explanation
Indices: 41469764--41469842 Score: 77
Period size: 28 Copynumber: 2.9 Consensus size: 27
41469754 TTAATAAATG
* * * *
41469764 TTTTATATATTTTTATATTTTTTGTAA
1 TTTTTTATAATTTTATAATTTTTGCAA
41469791 TTTTTTTATAATTTTATAATTTTTGCAA
1 -TTTTTTATAATTTTATAATTTTTGCAA
* * *
41469819 GTATTTATAATTTTAATACTTTTT
1 TTTTTTATAATTTT-ATAATTTTT
41469843 AAATAAATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 12 0.28
28 31 0.72
ACGTcount: A:0.28, C:0.03, G:0.04, T:0.66
Consensus pattern (27 bp):
TTTTTTATAATTTTATAATTTTTGCAA
Found at i:41477895 original size:17 final size:18
Alignment explanation
Indices: 41477849--41477896 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
41477839 AATTACAAAC
41477849 AAATAGAGAAAAATCATAA
1 AAATAG-GAAAAATCATAA
* * *
41477868 ATATA-AAAAAAACATAA
1 AAATAGGAAAAATCATAA
41477885 AAATAGGAAAAA
1 AAATAGGAAAAA
41477897 AGAACCACTC
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
17 14 0.61
18 5 0.22
19 4 0.17
ACGTcount: A:0.73, C:0.04, G:0.08, T:0.15
Consensus pattern (18 bp):
AAATAGGAAAAATCATAA
Found at i:41479699 original size:31 final size:31
Alignment explanation
Indices: 41479657--41479721 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
41479647 CTTAAATATA
* *
41479657 ATAAATTATATTTATATAATTTAATATAATG
1 ATAAATGATATTTAAATAATTTAATATAATG
*
41479688 ATAAATGATATTTAAATAATTTGATATAATG
1 ATAAATGATATTTAAATAATTTAATATAATG
41479719 ATA
1 ATA
41479722 CATAAATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (31 bp):
ATAAATGATATTTAAATAATTTAATATAATG
Found at i:41479735 original size:31 final size:31
Alignment explanation
Indices: 41479657--41479746 Score: 92
Period size: 31 Copynumber: 2.9 Consensus size: 31
41479647 CTTAAATATA
* * *
41479657 ATAAATTATATTTATATAATTTAATATAATG
1 ATAAATGAAATTTAAATAATTTAATATAATG
* *
41479688 ATAAATGATATTTAAATAATTTGATATAATG
1 ATAAATGAAATTTAAATAATTTAATATAATG
* *
41479719 ATACAT-AAATTATAAATTAATCTAATAT
1 ATAAATGAAATT-TAAA-TAATTTAATAT
41479747 TTTTTTAGAT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
30 4 0.08
31 37 0.74
32 9 0.18
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.43
Consensus pattern (31 bp):
ATAAATGAAATTTAAATAATTTAATATAATG
Found at i:41480378 original size:39 final size:39
Alignment explanation
Indices: 41480335--41480412 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
41480325 TAGTTATAAT
41480335 CACGATATGAGTGGTTTCATATAAAATCAATATCTAAAC
1 CACGATATGAGTGGTTTCATATAAAATCAATATCTAAAC
*
41480374 CACGATATGAGTGGTTTCATATAAAATTAATATCTAAAC
1 CACGATATGAGTGGTTTCATATAAAATCAATATCTAAAC
41480413 ATCATTAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (39 bp):
CACGATATGAGTGGTTTCATATAAAATCAATATCTAAAC
Found at i:41480784 original size:17 final size:17
Alignment explanation
Indices: 41480762--41480794 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41480752 ATAATTTATT
*
41480762 TTTCTTTTTATAAAATA
1 TTTCTTTTTAAAAAATA
41480779 TTTCTTTTTAAAAAAT
1 TTTCTTTTTAAAAAAT
41480795 CGTGGCTCCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTCTTTTTAAAAAATA
Found at i:41485164 original size:40 final size:41
Alignment explanation
Indices: 41485088--41485166 Score: 106
Period size: 40 Copynumber: 1.9 Consensus size: 41
41485078 AAGTACTTTG
***
41485088 TCCACGTGGACAGAAAACGCTTCCTTGAGGGCGCGCTTTGTA
1 TCCACGTGGACA-AAAACGCTTCCTTGAGAAAGCGCTTTGTA
*
41485130 TCCACGTGGAC-AAAGCGCTTCCTTGAGAAAGCGCTTT
1 TCCACGTGGACAAAAACGCTTCCTTGAGAAAGCGCTTT
41485167 TCCGGTCTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 22 0.67
42 11 0.33
ACGTcount: A:0.23, C:0.27, G:0.27, T:0.24
Consensus pattern (41 bp):
TCCACGTGGACAAAAACGCTTCCTTGAGAAAGCGCTTTGTA
Found at i:41485227 original size:15 final size:15
Alignment explanation
Indices: 41485195--41485237 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
41485185 GCAATCAAGG
*
41485195 TTAGGGTTTGAGATTT
1 TTAGGGTTTTA-ATTT
41485211 TT-GGGATTTTAATTT
1 TTAGGG-TTTTAATTT
41485226 TTAGGGTTTTAA
1 TTAGGGTTTTAA
41485238 GAAAAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.53
Consensus pattern (15 bp):
TTAGGGTTTTAATTT
Done.