Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 122 of 186
Found at i:40434549 original size:34 final size:34
Alignment explanation
Indices: 40434506--40434581 Score: 100
Period size: 34 Copynumber: 2.2 Consensus size: 34
40434496 TTACATACTG
40434506 TACTGAAATGGGCT-AAGGCCCAAACTGTCACTAA
1 TACTGAAATGGGCTCAA-GCCCAAACTGTCACTAA
* * **
40434540 TACTGAAATGGGCTCAAGCCCAGACTGTTACTGC
1 TACTGAAATGGGCTCAAGCCCAAACTGTCACTAA
40434574 TACTGAAA
1 TACTGAAA
40434582 GAGGGGCTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
34 35 0.95
35 2 0.05
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (34 bp):
TACTGAAATGGGCTCAAGCCCAAACTGTCACTAA
Found at i:40439843 original size:38 final size:38
Alignment explanation
Indices: 40439792--40439868 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
40439782 AGCTAGCCCA
40439792 AGTACTAATTCATAATACTGTCAAATTTTTGAAAATTT
1 AGTACTAATTCATAATACTGTCAAATTTTTGAAAATTT
40439830 AGTACTAATTCATAATACTGTCAAATTTTTGAAAATTT
1 AGTACTAATTCATAATACTGTCAAATTTTTGAAAATTT
40439868 A
1 A
40439869 CCATTTTTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (38 bp):
AGTACTAATTCATAATACTGTCAAATTTTTGAAAATTT
Found at i:40441210 original size:28 final size:28
Alignment explanation
Indices: 40441170--40441268 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
40441160 GTGTTTCTTG
40441170 TTTTTTAGATTTTATAATTTTGCCCCTA
1 TTTTTTAGATTTTATAATTTTGCCCCTA
* **
40441198 TTTTTTGGATTTTATAATTTTGCCTATA
1 TTTTTTAGATTTTATAATTTTGCCCCTA
* **
40441226 TTTTTTTAGATTTTATAGTTTTTTCCCTA
1 -TTTTTTAGATTTTATAATTTTGCCCCTA
40441255 TTTTTTAGATTTTA
1 TTTTTTAGATTTTA
40441269 CAAAATTTCC
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
28 39 0.64
29 22 0.36
ACGTcount: A:0.20, C:0.09, G:0.08, T:0.63
Consensus pattern (28 bp):
TTTTTTAGATTTTATAATTTTGCCCCTA
Found at i:40441284 original size:28 final size:27
Alignment explanation
Indices: 40441170--40441286 Score: 101
Period size: 28 Copynumber: 4.1 Consensus size: 27
40441160 GTGTTTCTTG
* *
40441170 TTTTTTAGATTTTATAATTTTGCCCCTA
1 TTTTTTAGATTTTAAAATTTT-CCCTTA
* * *
40441198 TTTTTTGGATTTTATAATTTTGCCTATA
1 TTTTTTAGATTTTAAAATTTTCCCT-TA
**
40441226 TTTTTTTAGATTTTATAGTTTTTTCCC-TA
1 -TTTTTTAGATTTTA-A-AATTTTCCCTTA
*
40441255 TTTTTTAGATTTTACAAAATTTCCCTTA
1 TTTTTTAGATTTTA-AAATTTTCCCTTA
40441283 TTTT
1 TTTT
40441287 CCAAATTTTA
Statistics
Matches: 72, Mismatches: 12, Indels: 10
0.77 0.13 0.11
Matches are distributed among these distances:
27 8 0.11
28 43 0.60
29 15 0.21
31 6 0.08
ACGTcount: A:0.21, C:0.11, G:0.07, T:0.61
Consensus pattern (27 bp):
TTTTTTAGATTTTAAAATTTTCCCTTA
Found at i:40441285 original size:57 final size:57
Alignment explanation
Indices: 40441170--40441286 Score: 155
Period size: 57 Copynumber: 2.1 Consensus size: 57
40441160 GTGTTTCTTG
* * * *
40441170 TTTTTTAGATTTTATAATTTTGCCCCTATTTTTTGGATTTTATAATTTTGCCTATAT
1 TTTTTTAGATTTTATAATTTTGCCCCTATTTTTTAGATTTTAAAAATTTCCCTATAT
* **
40441227 TTTTTTAGATTTTATAGTTTTTTCCCTATTTTTTAGATTTTACAAAATTTCCCT-TAT
1 TTTTTTAGATTTTATAATTTTGCCCCTATTTTTTAGATTTTA-AAAATTTCCCTATAT
40441284 TTT
1 TTT
40441287 CCAAATTTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
57 44 0.85
58 8 0.15
ACGTcount: A:0.21, C:0.11, G:0.07, T:0.61
Consensus pattern (57 bp):
TTTTTTAGATTTTATAATTTTGCCCCTATTTTTTAGATTTTAAAAATTTCCCTATAT
Found at i:40441929 original size:89 final size:90
Alignment explanation
Indices: 40441817--40442031 Score: 335
Period size: 90 Copynumber: 2.4 Consensus size: 90
40441807 CCTGCAAATA
* *** *
40441817 TGTTGTGCATCTACAATGTAGTGGCAGATTTTATCTGTGATATTTTGCTGTGTACCCACAGCC-A
1 TGTTGTGCATCCACAGCCTAGTGGCAGATTTTATCTGCGATATTTTGCTGTGTACCCACAGCCTA
40441881 GTGACAGGTTTCATCTGC-GAATTTT
66 GTGACAGGTTTCATCT-CTGAATTTT
* * *
40441906 TGTTGTGTATTCACAGCCTAGTGGCAAATTTTATCTGCGATATTTTGCTGTGTACCCACAGCCTA
1 TGTTGTGCATCCACAGCCTAGTGGCAGATTTTATCTGCGATATTTTGCTGTGTACCCACAGCCTA
40441971 GTGACAGGTTTCATCTCTGAATTTT
66 GTGACAGGTTTCATCTCTGAATTTT
40441996 TGTTGTGCATCCACAGCCTAGTGGCAGATTTTATCT
1 TGTTGTGCATCCACAGCCTAGTGGCAGATTTTATCT
40442032 ATGAAACCAG
Statistics
Matches: 113, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
89 56 0.50
90 57 0.50
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (90 bp):
TGTTGTGCATCCACAGCCTAGTGGCAGATTTTATCTGCGATATTTTGCTGTGTACCCACAGCCTA
GTGACAGGTTTCATCTCTGAATTTT
Found at i:40441952 original size:45 final size:45
Alignment explanation
Indices: 40441835--40442031 Score: 213
Period size: 45 Copynumber: 4.4 Consensus size: 45
40441825 ATCTACAATG
*
40441835 TAGTGGCAGATTTTATCTGTG-ATATTTTGCTGTGTACCCACAGCC
1 TAGTGGCAGATTTTATCTGCGAAT-TTTTGCTGTGTACCCACAGCC
* * * * **
40441880 -AGTGACAGGTTTCATCTGCGAATTTTTGTTGTGTATTCACAGCC
1 TAGTGGCAGATTTTATCTGCGAATTTTTGCTGTGTACCCACAGCC
*
40441924 TAGTGGCAAATTTTATCTGCG-ATATTTTGCTGTGTACCCACAGCC
1 TAGTGGCAGATTTTATCTGCGAAT-TTTTGCTGTGTACCCACAGCC
* * * * * *
40441969 TAGTGACAGGTTTCATCT-CTGAATTTTTGTTGTGCATCCACAGCC
1 TAGTGGCAGATTTTATCTGC-GAATTTTTGCTGTGTACCCACAGCC
40442014 TAGTGGCAGATTTTATCT
1 TAGTGGCAGATTTTATCT
40442032 ATGAAACCAG
Statistics
Matches: 123, Mismatches: 24, Indels: 10
0.78 0.15 0.06
Matches are distributed among these distances:
44 37 0.30
45 84 0.68
46 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (45 bp):
TAGTGGCAGATTTTATCTGCGAATTTTTGCTGTGTACCCACAGCC
Found at i:40442641 original size:20 final size:20
Alignment explanation
Indices: 40442616--40442656 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
40442606 AACAAAGTAA
40442616 AAAAAAATCACTTTTCCGCT
1 AAAAAAATCACTTTTCCGCT
40442636 AAAAAAATCACTTTTCCGCT
1 AAAAAAATCACTTTTCCGCT
40442656 A
1 A
40442657 CTAGATTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.24, G:0.05, T:0.29
Consensus pattern (20 bp):
AAAAAAATCACTTTTCCGCT
Found at i:40445509 original size:48 final size:46
Alignment explanation
Indices: 40445302--40445509 Score: 163
Period size: 46 Copynumber: 4.4 Consensus size: 46
40445292 TGTCATATCT
* * ** * *
40445302 CAGACACGATCTTACACTAGCTTATATCTC-AAGTCGAAGCCATGTCC
1 CAGACATG-TCTTACACTAGCCTACGTCTCGAAGCCGATG-CATGTCC
* * * * * *
40445349 CAGACATGGTCTTACACT-GACTACCATCTTGTAGTCGACGCATGTCC
1 CAGACAT-GTCTTACACTAGCCTA-CGTCTCGAAGCCGATGCATGTCC
* * *
40445396 CAGACATGTCTTACACTGGCTTACGTCTCGAAGCCGATGTATGTCC
1 CAGACATGTCTTACACTAGCCTACGTCTCGAAGCCGATGCATGTCC
* *
40445442 CAGACATGTCTTACACTAGCACT-CGTCTC-AATTCCGATGCCATGTCG
1 CAGACATGTCTTACACTAGC-CTACGTCTCGAA-GCCGATG-CATGTCC
40445489 CAGACATGGTCTTACACTAGC
1 CAGACAT-GTCTTACACTAGC
40445510 TCTCACAAAT
Statistics
Matches: 133, Mismatches: 20, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
45 2 0.02
46 61 0.46
47 49 0.37
48 21 0.16
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (46 bp):
CAGACATGTCTTACACTAGCCTACGTCTCGAAGCCGATGCATGTCC
Found at i:40449139 original size:29 final size:29
Alignment explanation
Indices: 40449078--40449193 Score: 144
Period size: 29 Copynumber: 4.0 Consensus size: 29
40449068 TACCTGTATC
* *
40449078 TGGCCCACCAGGCCC-AATCACATTTGTA
1 TGGCCCATCAGGCCCAAATCACATTTATA
* * * **
40449106 TGGCCCATTAGGCCTAATTTGCATTTATA
1 TGGCCCATCAGGCCCAAATCACATTTATA
*
40449135 TGGCCCATCAGACCCAAATCACATTTATA
1 TGGCCCATCAGGCCCAAATCACATTTATA
*
40449164 TGGCCCATCAGGCCCAAATCACATTCATA
1 TGGCCCATCAGGCCCAAATCACATTTATA
40449193 T
1 T
40449194 TCATGCTCGC
Statistics
Matches: 72, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
28 12 0.17
29 60 0.83
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.27
Consensus pattern (29 bp):
TGGCCCATCAGGCCCAAATCACATTTATA
Found at i:40449432 original size:24 final size:24
Alignment explanation
Indices: 40449405--40449455 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
40449395 GTAGCCAAAC
*
40449405 TTTCGACTTTTCGGCATTTCAGCT
1 TTTCGACTTTTCAGCATTTCAGCT
40449429 TTTCGACTTTTCAGCATTTCAGCT
1 TTTCGACTTTTCAGCATTTCAGCT
40449453 TTT
1 TTT
40449456 GCCGATCTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.14, C:0.24, G:0.14, T:0.49
Consensus pattern (24 bp):
TTTCGACTTTTCAGCATTTCAGCT
Found at i:40450134 original size:4 final size:4
Alignment explanation
Indices: 40450125--40450149 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
40450115 ATATTTATAC
40450125 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
40450150 CACCTACACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:40462419 original size:28 final size:28
Alignment explanation
Indices: 40462364--40462421 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
40462354 TACAGGGGTT
*
40462364 TTCACACGGCCTGTCACACGCCCGTGTCC
1 TTCACACGGCCTG-CACACACCCGTGTCC
*
40462393 TTCACACGGCCATG-ACACACTCGTGTCC
1 TTCACACGGCC-TGCACACACCCGTGTCC
40462421 T
1 T
40462422 AGCCCCTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 13 0.50
29 11 0.42
30 2 0.08
ACGTcount: A:0.17, C:0.41, G:0.19, T:0.22
Consensus pattern (28 bp):
TTCACACGGCCTGCACACACCCGTGTCC
Found at i:40463509 original size:46 final size:46
Alignment explanation
Indices: 40463426--40463542 Score: 139
Period size: 46 Copynumber: 2.5 Consensus size: 46
40463416 AAGTTGAAGC
* *
40463426 CATGTCACAGACATGGTCTTACACTGACTATCATCTTGTA-GCCGACG
1 CATGTCCCAGACAT-GTCTTACACTGACTATCATCTTG-AGGCCGACA
* * *
40463473 CATGTCCCAGACATGTCTTACACTGGCT-TACGTCTTGAGGCCGATA
1 CATGTCCCAGACATGTCTTACACTGACTAT-CATCTTGAGGCCGACA
*
40463519 CATGTCCCAAACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
40463543 AGCACTCGTC
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
45 2 0.03
46 47 0.76
47 13 0.21
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTGACTATCATCTTGAGGCCGACA
Found at i:40465935 original size:46 final size:47
Alignment explanation
Indices: 40465877--40466008 Score: 164
Period size: 46 Copynumber: 2.8 Consensus size: 47
40465867 ATCTCGTAGT
* * *
40465877 CGATGCATGTCCCAAACATGTCTTATACTAGCTTA-T-GTCTTAAGGC
1 CGATGCATGTCCCAAACATGTCTTACACTAGC-TACTCATCTCAAGGC
* *
40465923 CGATGCATGTCCCAGACATGTCTTACACTAGC-ACTCATCTCAATGC
1 CGATGCATGTCCCAAACATGTCTTACACTAGCTACTCATCTCAAGGC
40465969 CGATGCCATGTCCCAAACATGGTCTTACACTAGCT-CTCAT
1 CGATG-CATGTCCCAAACAT-GTCTTACACTAGCTACTCAT
40466009 AATGTATCCA
Statistics
Matches: 75, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
44 1 0.01
45 1 0.01
46 42 0.56
47 13 0.17
48 18 0.24
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.29
Consensus pattern (47 bp):
CGATGCATGTCCCAAACATGTCTTACACTAGCTACTCATCTCAAGGC
Found at i:40465973 original size:92 final size:94
Alignment explanation
Indices: 40465829--40466003 Score: 245
Period size: 92 Copynumber: 1.9 Consensus size: 94
40465819 GTATATCTGT
* *
40465829 GCCGATGCCATGTCCCAGACATGGTCTTACACTGACATATCTCGTAGTCGATG-CATGTCCCAAA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGACATATCTCATAGCCGATGCCATGTCCCAAA
*
40465893 CAT-GTCTTATACTAGCTTATGTCTTAAG
66 CATGGTCTTACACTAGCTTATGTCTTAAG
40465921 GCCGATG-CATGTCCCAGACAT-GTCTTACACT-AGCACTCATCTCA-ATGCCGATGCCATGTCC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGA-CA-T-ATCTCATA-GCCGATGCCATGTCC
40465982 CAAACATGGTCTTACACTAGCT
62 CAAACATGGTCTTACACTAGCT
40466004 CTCATAATGT
Statistics
Matches: 74, Mismatches: 3, Indels: 10
0.85 0.03 0.11
Matches are distributed among these distances:
89 1 0.01
90 12 0.16
91 16 0.22
92 18 0.24
93 14 0.19
94 13 0.18
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (94 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGACATATCTCATAGCCGATGCCATGTCCCAAA
CATGGTCTTACACTAGCTTATGTCTTAAG
Found at i:40466026 original size:47 final size:47
Alignment explanation
Indices: 40465879--40466050 Score: 158
Period size: 46 Copynumber: 3.7 Consensus size: 47
40465869 CTCGTAGTCG
* * * * *
40465879 ATGCATGTCCCAAACAT-GTCTTATACTAGCT-T-ATGTCTTAAGGCCG
1 ATGCATGTCCCAGACATGGTCTTACACTAGCTCTCATATC--AATGCCA
* * *
40465925 ATGCATGTCCCAGACAT-GTCTTACACTAGCACTCATCTCAATGCCG
1 ATGCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGCCA
* **
40465971 ATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATAATGTAT-CCA
1 ATG-CATGTCCCAGACATGGTCTTACACTAGCTCTCAT-ATCAATGCCA
*
40466019 ATGCATGTCCCAGACATGG-CTTACTCTAGCTC
1 ATGCATGTCCCAGACATGGTCTTACACTAGCTC
40466051 ACACAAGTGA
Statistics
Matches: 108, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
46 49 0.45
47 29 0.27
48 27 0.25
49 3 0.03
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (47 bp):
ATGCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGCCA
Found at i:40473047 original size:28 final size:28
Alignment explanation
Indices: 40473006--40473085 Score: 108
Period size: 29 Copynumber: 2.8 Consensus size: 28
40472996 CATACATGCT
* *
40473006 TATGGTCCACTAGGCCCAATCTCAT-TCA
1 TATGGCCCACTAGGCCCAATCACATCT-A
*
40473034 TATGGCCCATTAGGCCCAAATCACATCTA
1 TATGGCCCACTAGGCCC-AATCACATCTA
40473063 TATGGCCCACTAGGCCCAATCAC
1 TATGGCCCACTAGGCCCAATCAC
40473086 TTTTACAGTC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
28 21 0.46
29 24 0.52
30 1 0.02
ACGTcount: A:0.28, C:0.34, G:0.15, T:0.24
Consensus pattern (28 bp):
TATGGCCCACTAGGCCCAATCACATCTA
Found at i:40473066 original size:29 final size:28
Alignment explanation
Indices: 40473006--40473085 Score: 108
Period size: 28 Copynumber: 2.8 Consensus size: 28
40472996 CATACATGCT
* *
40473006 TATGGTCCACTAGGCCCAATCTCATTCA
1 TATGGCCCACTAGGCCCAATCACATTCA
*
40473034 TATGGCCCATTAGGCCCAAATCACA-TCTA
1 TATGGCCCACTAGGCCC-AATCACATTC-A
40473063 TATGGCCCACTAGGCCCAATCAC
1 TATGGCCCACTAGGCCCAATCAC
40473086 TTTTACAGTC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
28 23 0.50
29 23 0.50
ACGTcount: A:0.28, C:0.34, G:0.15, T:0.24
Consensus pattern (28 bp):
TATGGCCCACTAGGCCCAATCACATTCA
Found at i:40476038 original size:21 final size:21
Alignment explanation
Indices: 40476008--40476054 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
40475998 ACACCAACTA
40476008 AATTAAAAGAACTTAAAAT-AC
1 AATTAAAAGAAC-TAAAATCAC
* *
40476029 AATTATAAGAACTCAAATCAC
1 AATTAAAAGAACTAAAATCAC
40476050 AATTA
1 AATTA
40476055 CAATAATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.57, C:0.13, G:0.04, T:0.26
Consensus pattern (21 bp):
AATTAAAAGAACTAAAATCAC
Found at i:40478628 original size:40 final size:41
Alignment explanation
Indices: 40478549--40478633 Score: 120
Period size: 40 Copynumber: 2.1 Consensus size: 41
40478539 TGAATCCATG
40478549 AAAAGGTTGAAAAGGAAGTTATCTGAAAAGGATAGCAAATA
1 AAAAGGTTGAAAAGGAAGTTATCTGAAAAGGATAGCAAATA
* * *
40478590 AAAAGGTTGAAAAGGATG-TAT-TCGAAAAGGATATCAAATG
1 AAAAGGTTGAAAAGGAAGTTATCT-GAAAAGGATAGCAAATA
40478630 AAAA
1 AAAA
40478634 TGCTGTAAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
39 1 0.03
40 22 0.55
41 17 0.43
ACGTcount: A:0.52, C:0.05, G:0.24, T:0.20
Consensus pattern (41 bp):
AAAAGGTTGAAAAGGAAGTTATCTGAAAAGGATAGCAAATA
Found at i:40478644 original size:40 final size:41
Alignment explanation
Indices: 40478546--40478676 Score: 131
Period size: 41 Copynumber: 3.2 Consensus size: 41
40478536 TTTTGAATCC
* * *
40478546 ATGAAAAGGTTGAAAAGGA-AGTTATCTGAAAAGGATAGCAA
1 ATGAAAAGGCTGAAAAGGATAG-TATCCGAAAAGGATAACAA
* * * *
40478587 ATAAAAAGGTTGAAAAGGAT-GTATTCGAAAAGGATATCAA
1 ATGAAAAGGCTGAAAAGGATAGTATCCGAAAAGGATAACAA
* * * * *
40478627 ATGAAAATGCTGTAAAGGATATTATCCAAAAAGGGTAACAA
1 ATGAAAAGGCTGAAAAGGATAGTATCCGAAAAGGATAACAA
40478668 ATGAAAAGG
1 ATGAAAAGG
40478677 GTGTGTTTGA
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
40 32 0.43
41 42 0.57
ACGTcount: A:0.50, C:0.06, G:0.24, T:0.21
Consensus pattern (41 bp):
ATGAAAAGGCTGAAAAGGATAGTATCCGAAAAGGATAACAA
Found at i:40486403 original size:15 final size:15
Alignment explanation
Indices: 40486355--40486404 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
40486345 TTTATCAAAT
40486355 TTATATTGATTGAAA
1 TTATATTGATTGAAA
* * *
40486370 TCATTTTGATTGAAT
1 TTATATTGATTGAAA
40486385 TTATATTGATTGAAA
1 TTATATTGATTGAAA
40486400 TTATA
1 TTATA
40486405 ATATATATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (15 bp):
TTATATTGATTGAAA
Found at i:40491732 original size:55 final size:56
Alignment explanation
Indices: 40491658--40491780 Score: 142
Period size: 55 Copynumber: 2.2 Consensus size: 56
40491648 GTTAATTTAA
* * *
40491658 CAGGTTCGACCA-TGATTCTTCCACATGGGCGTGTCGAACGCCCATGCAGTTTTGG
1 CAGGCTCGACCACTGATTCTTCCACACGGGCATGTCGAACGCCCATGCAGTTTTGG
* * ** **
40491713 CAGGCTCGACCACTG-TTCTTCCACACGGGCATGTCGCATGCCTGTGTTGTTTTGG
1 CAGGCTCGACCACTGATTCTTCCACACGGGCATGTCGAACGCCCATGCAGTTTTGG
*
40491768 CAGGCTCAACCAC
1 CAGGCTCGACCAC
40491781 GGCCATATCG
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
55 55 0.96
56 2 0.04
ACGTcount: A:0.17, C:0.30, G:0.26, T:0.27
Consensus pattern (56 bp):
CAGGCTCGACCACTGATTCTTCCACACGGGCATGTCGAACGCCCATGCAGTTTTGG
Found at i:40502050 original size:16 final size:16
Alignment explanation
Indices: 40502022--40502060 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
40502012 GTTGGGAAGC
*
40502022 ATGTTATTGAATGCTTA
1 ATGTTAATGAATG-TTA
40502039 AT-TTAATGAATGTTA
1 ATGTTAATGAATGTTA
40502054 ATGTTAA
1 ATGTTAA
40502061 GTTTAATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 5 0.25
16 13 0.65
17 2 0.10
ACGTcount: A:0.36, C:0.03, G:0.15, T:0.46
Consensus pattern (16 bp):
ATGTTAATGAATGTTA
Found at i:40503479 original size:25 final size:25
Alignment explanation
Indices: 40503451--40503532 Score: 130
Period size: 25 Copynumber: 3.3 Consensus size: 25
40503441 GAAGTTATCC
40503451 AAAAAGGATAA-AAATGAAAAGGTT
1 AAAAAGGATAACAAATGAAAAGGTT
*
40503475 AAAAAGGATAACAAATGAAAGGGTT
1 AAAAAGGATAACAAATGAAAAGGTT
*
40503500 AAAAAGGATAACAAATTAAAAGGTT
1 AAAAAGGATAACAAATGAAAAGGTT
*
40503525 GAAAAGGA
1 AAAAAGGA
40503533 AGTATCTGAA
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
24 11 0.21
25 42 0.79
ACGTcount: A:0.60, C:0.02, G:0.22, T:0.16
Consensus pattern (25 bp):
AAAAAGGATAACAAATGAAAAGGTT
Found at i:40503546 original size:40 final size:40
Alignment explanation
Indices: 40503501--40503641 Score: 183
Period size: 40 Copynumber: 3.5 Consensus size: 40
40503491 GAAAGGGTTA
* *
40503501 AAAAGGATAACAAATTAAAAGGTTGAAAAGGAAGTATCTG
1 AAAAGGATAACAAATGAAAAGGTTGAAAAGGAAGTAACTG
* * * *
40503541 AAAAGGATAACAGATGAAAAGGTTGAAAAGGATGTACCCG
1 AAAAGGATAACAAATGAAAAGGTTGAAAAGGAAGTAACTG
* * *
40503581 AAAAGGATATCAAATGAAAATGTTGAAAAGGATATTAACTG
1 AAAAGGATAACAAATGAAAAGGTTGAAAAGGA-AGTAACTG
*
40503622 AAAAGGGTAACAAATGAAAA
1 AAAAGGATAACAAATGAAAA
40503642 TGATGTGTTT
Statistics
Matches: 86, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
40 64 0.74
41 22 0.26
ACGTcount: A:0.52, C:0.06, G:0.23, T:0.18
Consensus pattern (40 bp):
AAAAGGATAACAAATGAAAAGGTTGAAAAGGAAGTAACTG
Found at i:40503795 original size:21 final size:21
Alignment explanation
Indices: 40503771--40503810 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
40503761 ATATATTGAG
* *
40503771 ATATTATGCATGATATGTTAC
1 ATATTATGAATAATATGTTAC
40503792 ATATTATGAATAATATGTT
1 ATATTATGAATAATATGTT
40503811 CTTATATTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (21 bp):
ATATTATGAATAATATGTTAC
Found at i:40505798 original size:49 final size:48
Alignment explanation
Indices: 40505696--40505898 Score: 180
Period size: 49 Copynumber: 4.2 Consensus size: 48
40505686 TGGGAGCCTG
* * * * * *
40505696 TGTAAGACTTGTCTGGGACATGGCATCGGCCTA-AAGATACGGAAGCTAA
1 TGTAAGACCTGTCTGGGACATGGCATCGACCTAGATG-TA-GAAAGCCAC
*
40505745 TGTAAGACCTGTCTGGGACATGCCATCGACAC-AGATAAGTA-AAAGCCAC
1 TGTAAGACCTGTCTGGGACATGGCATCGAC-CTAGAT--GTAGAAAGCCAC
* * * * *
40505794 TGTAAGACCTGTTTGGGAAATGGCATCGACCTCGATGTATGAAAGTCAT
1 TGTAAGACCTGTCTGGGACATGGCATCGACCTAGATGTA-GAAAGCCAC
* * * *
40505843 TGTAAGACCTGTCTGGGACATGGCATCGACTTAGATGT-GAGAGTCAA
1 TGTAAGACCTGTCTGGGACATGGCATCGACCTAGATGTAGAAAGCCAC
40505890 TGTAAGACC
1 TGTAAGACC
40505899 ATGTTTGGAA
Statistics
Matches: 128, Mismatches: 19, Indels: 16
0.79 0.12 0.10
Matches are distributed among these distances:
47 19 0.15
48 1 0.01
49 103 0.80
50 2 0.02
51 2 0.02
52 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (48 bp):
TGTAAGACCTGTCTGGGACATGGCATCGACCTAGATGTAGAAAGCCAC
Found at i:40505817 original size:98 final size:98
Alignment explanation
Indices: 40505696--40505872 Score: 232
Period size: 98 Copynumber: 1.8 Consensus size: 98
40505686 TGGGAGCCTG
* * * *
40505696 TGTAAGACTTGTCTGGGACATGGCATCGGCCT-AAAGATACGGAAG-CTAATGTAAGACCTGTCT
1 TGTAAGACCTGTCTGGGAAATGGCATCGACCTCAAAG-TACGAAAGTC-AATGTAAGACCTGTCT
40505759 GGGACATGCCATCGACACAGATAAGTAAAAGCCAC
64 GGGACATGCCATCGACACAGATAAGTAAAAGCCAC
* * * * *
40505794 TGTAAGACCTGTTTGGGAAATGGCATCGACCTCGATGTATGAAAGTCATTGTAAGACCTGTCTGG
1 TGTAAGACCTGTCTGGGAAATGGCATCGACCTCAAAGTACGAAAGTCAATGTAAGACCTGTCTGG
*
40505859 GACATGGCATCGAC
66 GACATGCCATCGAC
40505873 TTAGATGTGA
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
98 64 0.96
99 3 0.04
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (98 bp):
TGTAAGACCTGTCTGGGAAATGGCATCGACCTCAAAGTACGAAAGTCAATGTAAGACCTGTCTGG
GACATGCCATCGACACAGATAAGTAAAAGCCAC
Found at i:40507146 original size:21 final size:20
Alignment explanation
Indices: 40507113--40507151 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
40507103 GTCAAGAATG
40507113 CCACACGGACGTGTAGCCCTT
1 CCACACGGACGTGT-GCCCTT
40507134 CCACAC-GAGCGTGTGCCC
1 CCACACGGA-CGTGTGCCC
40507152 CTATTTCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.18, C:0.41, G:0.26, T:0.15
Consensus pattern (20 bp):
CCACACGGACGTGTGCCCTT
Found at i:40508750 original size:7 final size:7
Alignment explanation
Indices: 40508738--40508771 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
40508728 TTCTTCGTCA
40508738 TCACATC
1 TCACATC
40508745 TCACATC
1 TCACATC
40508752 TCACATC
1 TCACATC
* *
40508759 TTACATA
1 TCACATC
40508766 TCACAT
1 TCACAT
40508772 ATTCGTGGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.32, C:0.35, G:0.00, T:0.32
Consensus pattern (7 bp):
TCACATC
Found at i:40509292 original size:89 final size:89
Alignment explanation
Indices: 40509137--40509498 Score: 708
Period size: 89 Copynumber: 4.1 Consensus size: 89
40509127 AAGTGTCCAT
40509137 AATC-ACTATAATTCAAACACACTTGGTATTACAATTCATTTGACACTCCAAAGTACATACCACA
1 AATCTACTATAATTCAAACACACTTGGTATTACAATTCATTTGACACTCCAAAGTACATACCACA
40509201 TATAACCAAGTTAAAATGATTAAA
66 TATAACCAAGTTAAAATGATTAAA
40509225 AATCTACTATAATTCAAACACACTTGGTATTACAATTCATTTGACACTCCAAAGTACATACCACA
1 AATCTACTATAATTCAAACACACTTGGTATTACAATTCATTTGACACTCCAAAGTACATACCACA
40509290 TATAACCAAGTTAAAATGATTAAA
66 TATAACCAAGTTAAAATGATTAAA
40509314 AATCTACTATAATTCAAACACACTTGGTATTACAATTCATTTGACACTCCAAAGTACATACCACA
1 AATCTACTATAATTCAAACACACTTGGTATTACAATTCATTTGACACTCCAAAGTACATACCACA
40509379 TATAACCAAGTTAAAATGATTAAA
66 TATAACCAAGTTAAAATGATTAAA
40509403 AATCTACTATAATTCAAACACACTTGGTATTACAATTCATTTGACACTCCAAAGTACATACCACA
1 AATCTACTATAATTCAAACACACTTGGTATTACAATTCATTTGACACTCCAAAGTACATACCACA
*
40509468 TATAACCAAGTTAAAATTATTAAA
66 TATAACCAAGTTAAAATGATTAAA
40509492 AATCTAC
1 AATCTAC
40509499 CTAATCAAGA
Statistics
Matches: 272, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
88 4 0.01
89 268 0.99
ACGTcount: A:0.44, C:0.20, G:0.06, T:0.29
Consensus pattern (89 bp):
AATCTACTATAATTCAAACACACTTGGTATTACAATTCATTTGACACTCCAAAGTACATACCACA
TATAACCAAGTTAAAATGATTAAA
Found at i:40518043 original size:26 final size:27
Alignment explanation
Indices: 40518014--40518066 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
40518004 TATGTGAGCA
* *
40518014 TGGCTGTA-AATGTTATTTGGGCCTAG
1 TGGCCGTAGAATGTGATTTGGGCCTAG
40518040 TGGCCGTATGAATGTGATTTGGGCCTA
1 TGGCCGTA-GAATGTGATTTGGGCCTA
40518067 ATGGGCCACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 7 0.30
28 16 0.70
ACGTcount: A:0.19, C:0.13, G:0.32, T:0.36
Consensus pattern (27 bp):
TGGCCGTAGAATGTGATTTGGGCCTAG
Found at i:40518118 original size:28 final size:28
Alignment explanation
Indices: 40518030--40518133 Score: 104
Period size: 28 Copynumber: 3.7 Consensus size: 28
40518020 TAAATGTTAT
* * *
40518030 TTGGGCCTAGT-GGCCGTATGAATGTGA
1 TTGGGCCTAATGGGCCATATGAAAGTGA
*
40518057 TTTGGGCCTAATGGGCCACAT-AAATGTGA
1 -TTGGGCCTAATGGGCCATATGAAA-GTGA
* *
40518086 ATGGGCCTAATGGGCCATATGAAAGAGA
1 TTGGGCCTAATGGGCCATATGAAAGTGA
* *
40518114 TTGGGCCTAGTGGGTCATAT
1 TTGGGCCTAATGGGCCATAT
40518134 ATATATAGGT
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
28 50 0.79
29 13 0.21
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.27
Consensus pattern (28 bp):
TTGGGCCTAATGGGCCATATGAAAGTGA
Found at i:40520395 original size:27 final size:27
Alignment explanation
Indices: 40520343--40520403 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
40520333 TATTATAAAA
*
40520343 TTAATTAAAATTCAATATGTTAATAAT
1 TTAATTAAAATTCAATATCTTAATAAT
* *
40520370 TTAATTATAATTTAATCATCTT-ATAA-
1 TTAATTAAAATTCAAT-ATCTTAATAAT
40520396 -TAATTAAA
1 TTAATTAAA
40520404 TATTTTTCGA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
25 7 0.24
27 18 0.62
28 4 0.14
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.46
Consensus pattern (27 bp):
TTAATTAAAATTCAATATCTTAATAAT
Found at i:40523271 original size:24 final size:25
Alignment explanation
Indices: 40523229--40523276 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
40523219 TTAATTAGTA
*
40523229 TGAAATATTAATAATTC-AATAAAT
1 TGAAAAATTAATAATTCAAATAAAT
40523253 TGAAAAATTAATTAA-TCAAATAAA
1 TGAAAAATTAA-TAATTCAAATAAA
40523277 ATTAAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.33
Consensus pattern (25 bp):
TGAAAAATTAATAATTCAAATAAAT
Found at i:40524818 original size:301 final size:301
Alignment explanation
Indices: 40524276--40524832 Score: 1001
Period size: 301 Copynumber: 1.9 Consensus size: 301
40524266 CTCTTAGACA
*
40524276 GAATTTATTAAAACATACTAATCCCAAAAAATATACCCTAAATAATTTATTTAAAAAGGAAAATA
1 GAATTTATTAAAACATACTAATCCCAAAAAATATACCCTAAATAATTTATTTAAAAAGGAAAACA
40524341 AGAAAAATTAATCATCTGATAAATGAACGAGATATGATCCTGTTCAATTTTATCTCCCCAGTATT
66 AGAAAAATTAATCATCTGATAAATGAACGAGATATGATCCTGTTCAATTTTATCTCCCCAGTATT
*
40524406 GTTTTGAGCGTTGAGCATTAACTCAAAAAAATTACCTCTCTTACTTTGAAGTTCGACAACTCCGT
131 GTTTTGAGCGATGAGCATTAACTCAAAAAAATTACCTCTCTTACTTTGAAGTTCGACAACTCCGT
40524471 ATGGATAAAATCGGTGAATCACAAATGGACCGAACCAATGTGATTTTAACTTACCTGGAAAAAAC
196 ATGGATAAAATCGGTGAATCACAAATGGACCGAACCAATGTGATTTTAACTTACCTGGAAAAAAC
40524536 CTTAATTTGGAATTCAATAACAAGACTTGCTGACCTGCTTC
261 CTTAATTTGGAATTCAATAACAAGACTTGCTGACCTGCTTC
*
40524577 GAATTTATTAAAACATACTAATCCC-AAAAATATACCCTAAATGATTTATTTAAAAAGGAAAACA
1 GAATTTATTAAAACATACTAATCCCAAAAAATATACCCTAAATAATTTATTTAAAAAGGAAAACA
* *
40524641 AGAAAAATTAATCATCTGATAAAATGAATGAGATTTGATCCCT-TTCAATTTTATCTCCCCAGTA
66 AGAAAAATTAATCATCTGAT-AAATGAACGAGATATGAT-CCTGTTCAATTTTATCTCCCCAGTA
* * *
40524705 TTGTTTTGAGCGATGAGCATTAACTTAAAAAAATTGCCTCTCTTACTTTGAAGTTTGACAACTCC
129 TTGTTTTGAGCGATGAGCATTAACTCAAAAAAATTACCTCTCTTACTTTGAAGTTCGACAACTCC
*
40524770 GTATGGATAAAATCGGTGAATCACAAATGGACCGGACCAATGTGATTTTAACTTACCTGGAAA
194 GTATGGATAAAATCGGTGAATCACAAATGGACCGAACCAATGTGATTTTAACTTACCTGGAAA
40524833 GAACTCAAAT
Statistics
Matches: 245, Mismatches: 9, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
300 57 0.23
301 185 0.76
302 3 0.01
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (301 bp):
GAATTTATTAAAACATACTAATCCCAAAAAATATACCCTAAATAATTTATTTAAAAAGGAAAACA
AGAAAAATTAATCATCTGATAAATGAACGAGATATGATCCTGTTCAATTTTATCTCCCCAGTATT
GTTTTGAGCGATGAGCATTAACTCAAAAAAATTACCTCTCTTACTTTGAAGTTCGACAACTCCGT
ATGGATAAAATCGGTGAATCACAAATGGACCGAACCAATGTGATTTTAACTTACCTGGAAAAAAC
CTTAATTTGGAATTCAATAACAAGACTTGCTGACCTGCTTC
Found at i:40524957 original size:12 final size:12
Alignment explanation
Indices: 40524940--40524965 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40524930 AAAACAGGGC
40524940 TTTAGCGGCGTT
1 TTTAGCGGCGTT
40524952 TTTAGCGGCGTT
1 TTTAGCGGCGTT
40524964 TT
1 TT
40524966 ACCAAAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTAGCGGCGTT
Found at i:40525056 original size:41 final size:41
Alignment explanation
Indices: 40524996--40525277 Score: 286
Period size: 41 Copynumber: 6.9 Consensus size: 41
40524986 TGTAAAACAT
* *
40524996 AGAGCAATAGCGGCGTTTTTGGTAAAACGCCGCTAAAAA-C
1 AGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACC
* ** * * *
40525036 AGAGCAATAGCGGCATTTTTTGTTAAAATGCTGCTAAAAA-C
1 AGAGCATTAGCGGC-GCTTTTGGTAAAACGCCGCTAAAAACC
* *** **
40525077 AGAGCAATAGCGGCG-TTTTACCAAAAACGCCGCTAAAAATG
1 AGAGCATTAGCGGCGCTTTT-GGTAAAACGCCGCTAAAAACC
*
40525118 AGAGCATTAGCGGCGCTTTTGGTAAAACGCCACTAAAAACC
1 AGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACC
* *
40525159 -GAAGCATTAACGGCGCTTTTGGTAAAATGCCGCTAAAAACC
1 AG-AGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACC
* * *
40525200 GGAGTATTAGCGGCGCTTTTGGTAAAACGTCGCTAAAAACC
1 AGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACC
* * * *
40525241 GGAGCATTAGCGGGGCTTTCGGGAAAACGCCG-TAAAA
1 AGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAA
40525278 GTCATATAAC
Statistics
Matches: 206, Mismatches: 30, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
39 4 0.02
40 34 0.17
41 163 0.79
42 5 0.02
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.21
Consensus pattern (41 bp):
AGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACC
Found at i:40525321 original size:19 final size:18
Alignment explanation
Indices: 40525273--40525322 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
40525263 GAAAACGCCG
*
40525273 TAAAAGTCATATAA-CCCC
1 TAAAAATCATA-AACCCCC
*
40525291 TAAAAA-CCTAAACCCCC
1 TAAAAATCATAAACCCCC
40525308 TAAAAAATCATAAAC
1 T-AAAAATCATAAAC
40525323 ACTAATCTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 2 0.08
17 8 0.31
18 10 0.38
19 6 0.23
ACGTcount: A:0.52, C:0.28, G:0.02, T:0.18
Consensus pattern (18 bp):
TAAAAATCATAAACCCCC
Found at i:40525607 original size:22 final size:21
Alignment explanation
Indices: 40525582--40525623 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
40525572 ATTTTAAGTT
*
40525582 TTATGGATTATGGGTTTAGGGA
1 TTATGGATTAAGGG-TTAGGGA
*
40525604 TTATGGTTTAAGGGTTAGGG
1 TTATGGATTAAGGGTTAGGG
40525624 GTCTAAGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.40
Consensus pattern (21 bp):
TTATGGATTAAGGGTTAGGGA
Found at i:40525617 original size:15 final size:15
Alignment explanation
Indices: 40525581--40525613 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
40525571 TATTTTAAGT
*
40525581 TTTATGGATTATGGG
1 TTTAGGGATTATGGG
40525596 TTTAGGGATTAT-GG
1 TTTAGGGATTATGGG
40525610 TTTA
1 TTTA
40525614 AGGGTTAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.48
Consensus pattern (15 bp):
TTTAGGGATTATGGG
Found at i:40525663 original size:14 final size:15
Alignment explanation
Indices: 40525646--40525683 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
40525636 GAGTTTATAT
40525646 TTTAGGATTT-AGGA
1 TTTAGGATTTAAGGA
*
40525660 TTTAGGGTTTAAGGA
1 TTTAGGATTTAAGGA
*
40525675 TTAAGGATT
1 TTTAGGATT
40525684 AAGAGTTTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (15 bp):
TTTAGGATTTAAGGA
Found at i:40525681 original size:22 final size:22
Alignment explanation
Indices: 40525649--40525692 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
40525639 TTTATATTTT
* * *
40525649 AGGATTTAGGATTTAGGGTTTA
1 AGGATTAAGGATTAAGAGTTTA
40525671 AGGATTAAGGATTAAGAGTTTA
1 AGGATTAAGGATTAAGAGTTTA
40525693 GGGTTTAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.30, T:0.36
Consensus pattern (22 bp):
AGGATTAAGGATTAAGAGTTTA
Found at i:40525958 original size:22 final size:22
Alignment explanation
Indices: 40525920--40525985 Score: 57
Period size: 22 Copynumber: 3.0 Consensus size: 22
40525910 GGGTTATGGG
40525920 TTTAGGG-TTAATG-GTTTATAT
1 TTTAGGGATTAA-GAGTTTATAT
* * *
40525941 TTTA-GGACTTTAGAGTTTAGAG
1 TTTAGGGA-TTAAGAGTTTATAT
*
40525963 TTTAGGGATTAAGGGTTTATAT
1 TTTAGGGATTAAGAGTTTATAT
40525985 T
1 T
40525986 AATTAGTGTT
Statistics
Matches: 34, Mismatches: 7, Indels: 7
0.71 0.15 0.15
Matches are distributed among these distances:
20 2 0.06
21 5 0.15
22 24 0.71
23 3 0.09
ACGTcount: A:0.26, C:0.02, G:0.26, T:0.47
Consensus pattern (22 bp):
TTTAGGGATTAAGAGTTTATAT
Found at i:40528879 original size:7 final size:7
Alignment explanation
Indices: 40528867--40528899 Score: 52
Period size: 6 Copynumber: 5.0 Consensus size: 7
40528857 ACATAATATT
40528867 TAAATTC
1 TAAATTC
40528874 TAAATT-
1 TAAATTC
40528880 TAAATTC
1 TAAATTC
40528887 TAAATT-
1 TAAATTC
40528893 TAAATTC
1 TAAATTC
40528900 ATCAATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 12 0.50
7 12 0.50
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (7 bp):
TAAATTC
Found at i:40528880 original size:13 final size:13
Alignment explanation
Indices: 40528864--40528899 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
40528854 TAAACATAAT
40528864 ATTTAAATTCTAA
1 ATTTAAATTCTAA
40528877 ATTTAAATTCTAA
1 ATTTAAATTCTAA
40528890 ATTTAAATTC
1 ATTTAAATTC
40528900 ATCAATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTTAAATTCTAA
Found at i:40530609 original size:43 final size:43
Alignment explanation
Indices: 40530458--40530607 Score: 162
Period size: 43 Copynumber: 3.5 Consensus size: 43
40530448 GAAAAGCGCC
* * *
40530458 GCTAAAGGTCGTGATCTTTAGCAGCATTTGT-AAAAAAGAGTC
1 GCTAAAGGTCGTGATCTTTAGCAGCGTTTGTGGAAAAAGAGTT
* *
40530500 GCTAAAGGTCGTGATCTTTAGTAGCGTTTGTAGG-AAAAGCGTT
1 GCTAAAGGTCGTGATCTTTAGCAGCGTTTGT-GGAAAAAGAGTT
* * * *
40530543 G-TCATAGGTCTTGATCTTTAGCGGCGTTTGTGGAAAAAGTGTT
1 GCT-AAAGGTCGTGATCTTTAGCAGCGTTTGTGGAAAAAGAGTT
* *
40530586 GCTATAGGTCTTGATCTTTAGC
1 GCTAAAGGTCGTGATCTTTAGC
40530608 GGTGTTTTTT
Statistics
Matches: 93, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
42 32 0.34
43 60 0.65
44 1 0.01
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.34
Consensus pattern (43 bp):
GCTAAAGGTCGTGATCTTTAGCAGCGTTTGTGGAAAAAGAGTT
Found at i:40530729 original size:22 final size:22
Alignment explanation
Indices: 40530698--40530756 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
40530688 AGCGGCGCTT
*
40530698 AAAAGCGTCGCTAAAGACCTTA
1 AAAAACGTCGCTAAAGACCTTA
*
40530720 AAAAATGTCGCTAAAGACCTTA
1 AAAAACGTCGCTAAAGACCTTA
40530742 AAAAACGTCGCTAAA
1 AAAAACGTCGCTAAA
40530757 AGTCAATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.46, C:0.20, G:0.15, T:0.19
Consensus pattern (22 bp):
AAAAACGTCGCTAAAGACCTTA
Found at i:40531008 original size:49 final size:49
Alignment explanation
Indices: 40530948--40531044 Score: 167
Period size: 49 Copynumber: 2.0 Consensus size: 49
40530938 TGTCTTGTAT
*
40530948 GTTGTCCTGTAGGCCCATAAAGCATCATCCAATCTTTTGGACCAATCTC
1 GTTGTCCTGTAGGCCCATAAAGCATCATACAATCTTTTGGACCAATCTC
* *
40530997 GTTGTCTTGTAGGCCCATAAAGCATCATACAGTCTTTTGGACCAATCT
1 GTTGTCCTGTAGGCCCATAAAGCATCATACAATCTTTTGGACCAATCT
40531045 TTTCGGTTCA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (49 bp):
GTTGTCCTGTAGGCCCATAAAGCATCATACAATCTTTTGGACCAATCTC
Found at i:40537006 original size:21 final size:20
Alignment explanation
Indices: 40536977--40537018 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
40536967 CGAAATGCAA
*
40536977 TCAACCTATTATGAATTAAAT
1 TCAACCTA-TATCAATTAAAT
*
40536998 TCAAGCTATATCAATTAAAT
1 TCAACCTATATCAATTAAAT
40537018 T
1 T
40537019 AAACAATTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.38
Consensus pattern (20 bp):
TCAACCTATATCAATTAAAT
Found at i:40537558 original size:11 final size:11
Alignment explanation
Indices: 40537542--40537575 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
40537532 CGCATCCAGT
40537542 TTTGTTCTTGA
1 TTTGTTCTTGA
*
40537553 TTTGTTCTTAA
1 TTTGTTCTTGA
*
40537564 TTTATTCTTGA
1 TTTGTTCTTGA
40537575 T
1 T
40537576 GATTTGACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.15, C:0.09, G:0.12, T:0.65
Consensus pattern (11 bp):
TTTGTTCTTGA
Found at i:40537694 original size:22 final size:22
Alignment explanation
Indices: 40537666--40537708 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
40537656 TCATGTTAAA
40537666 TTATTGAGAATGAATTGATTCT
1 TTATTGAGAATGAATTGATTCT
** *
40537688 TTATTGATTATGGATTGATTC
1 TTATTGAGAATGAATTGATTC
40537709 GTTTTTCTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.28, C:0.05, G:0.19, T:0.49
Consensus pattern (22 bp):
TTATTGAGAATGAATTGATTCT
Found at i:40537822 original size:20 final size:20
Alignment explanation
Indices: 40537799--40537843 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
40537789 GTTTTGATTC
*
40537799 TTTAAATAAAATTTTAAGGT
1 TTTAAATAAAATTTTAAAGT
*
40537819 TTTAAATAAAGTTTTAAAGT
1 TTTAAATAAAATTTTAAAGT
40537839 TTTAA
1 TTTAA
40537844 TTTTCGTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (20 bp):
TTTAAATAAAATTTTAAAGT
Found at i:40540361 original size:29 final size:28
Alignment explanation
Indices: 40540296--40540400 Score: 133
Period size: 28 Copynumber: 3.7 Consensus size: 28
40540286 ACATACATGC
* *
40540296 ATATGGCCCA-CTATGCCCAATCCCATTT
1 ATATGGCCCATC-AGGCCCAATCTCATTT
*
40540324 ATATGGCCCATCCGGCCCAAT-TCATGTT
1 ATATGGCCCATCAGGCCCAATCTCAT-TT
40540352 CATATGGCCCATCAGGCCCAATCTCATTT
1 -ATATGGCCCATCAGGCCCAATCTCATTT
*
40540381 ATATGGCCCATCTGGCCCAA
1 ATATGGCCCATCAGGCCCAA
40540401 ATCACATTAT
Statistics
Matches: 68, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
27 3 0.04
28 38 0.56
29 23 0.34
30 4 0.06
ACGTcount: A:0.24, C:0.34, G:0.15, T:0.27
Consensus pattern (28 bp):
ATATGGCCCATCAGGCCCAATCTCATTT
Found at i:40540410 original size:28 final size:28
Alignment explanation
Indices: 40540296--40540412 Score: 123
Period size: 28 Copynumber: 4.1 Consensus size: 28
40540286 ACATACATGC
* *
40540296 ATATGGCCCA-CTATGCCCAATCCCATTT
1 ATATGGCCCATCT-GGCCCAATCACATTT
* *
40540324 ATATGGCCCATCCGGCCCAAT-TCATGTT
1 ATATGGCCCATCTGGCCCAATCACAT-TT
* *
40540352 CATATGGCCCATCAGGCCCAATCTCATTT
1 -ATATGGCCCATCTGGCCCAATCACATTT
40540381 ATATGGCCCATCTGGCCCAAATCACA-TT
1 ATATGGCCCATCTGGCCC-AATCACATTT
40540409 ATAT
1 ATAT
40540413 TCATGCTCAC
Statistics
Matches: 78, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
27 3 0.04
28 42 0.54
29 29 0.37
30 4 0.05
ACGTcount: A:0.26, C:0.32, G:0.14, T:0.28
Consensus pattern (28 bp):
ATATGGCCCATCTGGCCCAATCACATTT
Found at i:40540503 original size:9 final size:9
Alignment explanation
Indices: 40540490--40540540 Score: 66
Period size: 9 Copynumber: 5.4 Consensus size: 9
40540480 CAGCCCATCG
40540490 GGCCCATTT
1 GGCCCATTT
* *
40540499 AGCCCATTCC
1 GGCCCATT-T
40540509 GGCCCATTT
1 GGCCCATTT
40540518 GGCCCATTT
1 GGCCCATTT
40540527 CGGCCCATTT
1 -GGCCCATTT
40540537 GGCC
1 GGCC
40540541 TATTCACAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
9 20 0.56
10 16 0.44
ACGTcount: A:0.12, C:0.39, G:0.22, T:0.27
Consensus pattern (9 bp):
GGCCCATTT
Found at i:40540514 original size:19 final size:19
Alignment explanation
Indices: 40540481--40540536 Score: 78
Period size: 19 Copynumber: 3.0 Consensus size: 19
40540471 TGGGCCCAAC
*
40540481 AGCCCA-TCGGGCCCATTT
1 AGCCCATTCCGGCCCATTT
40540499 AGCCCATTCCGGCCCATTT
1 AGCCCATTCCGGCCCATTT
* *
40540518 GGCCCATTTCGGCCCATTT
1 AGCCCATTCCGGCCCATTT
40540537 GGCCTATTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
18 6 0.18
19 28 0.82
ACGTcount: A:0.14, C:0.39, G:0.20, T:0.27
Consensus pattern (19 bp):
AGCCCATTCCGGCCCATTT
Found at i:40540537 original size:19 final size:19
Alignment explanation
Indices: 40540490--40540545 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
40540480 CAGCCCATCG
*
40540490 GGCCCATTTAGCCCATTCC
1 GGCCCATTTGGCCCATTCC
*
40540509 GGCCCATTTGGCCCATTTC
1 GGCCCATTTGGCCCATTCC
*
40540528 GGCCCATTTGGCCTATTC
1 GGCCCATTTGGCCCATTC
40540546 ACAACCAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.12, C:0.38, G:0.20, T:0.30
Consensus pattern (19 bp):
GGCCCATTTGGCCCATTCC
Found at i:40545491 original size:11 final size:11
Alignment explanation
Indices: 40545475--40545508 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
40545465 CGCATCTATT
40545475 TTTGTTCTTGA
1 TTTGTTCTTGA
*
40545486 TTTGTTCTTAA
1 TTTGTTCTTGA
*
40545497 TTTATTCTTGA
1 TTTGTTCTTGA
40545508 T
1 T
40545509 GATTTGACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.15, C:0.09, G:0.12, T:0.65
Consensus pattern (11 bp):
TTTGTTCTTGA
Found at i:40545746 original size:24 final size:25
Alignment explanation
Indices: 40545715--40545763 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
40545705 AGGAAACAAT
*
40545715 GAAAAATG-GAAGGGAA-TGAAGAGA
1 GAAAAATGAGAA-AGAAGTGAAGAGA
40545739 GAAAAATGAGAAAGAAGTGAAGAGA
1 GAAAAATGAGAAAGAAGTGAAGAGA
40545764 TGAGAAGGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.57, C:0.00, G:0.35, T:0.08
Consensus pattern (25 bp):
GAAAAATGAGAAAGAAGTGAAGAGA
Found at i:40554881 original size:40 final size:40
Alignment explanation
Indices: 40554819--40554895 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
40554809 ACGGTACCAT
* **
40554819 TTGGTGTGTAGGGTTGGATGGGTTGATTTTATCCCCATAC
1 TTGGTGTGTAGGGATGGATGGGTCAATTTTATCCCCATAC
*
40554859 TTGGTGTGTAGGGATGGGTGGGTCAATTTTATCCCCA
1 TTGGTGTGTAGGGATGGATGGGTCAATTTTATCCCCA
40554896 CATGGTGTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.16, C:0.13, G:0.34, T:0.38
Consensus pattern (40 bp):
TTGGTGTGTAGGGATGGATGGGTCAATTTTATCCCCATAC
Found at i:40561724 original size:42 final size:42
Alignment explanation
Indices: 40561677--40561762 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
40561667 GAAATAAGAA
40561677 AATGTCGATTATAATTCAAACAAACTCATAATGCTTTCATCT
1 AATGTCGATTATAATTCAAACAAACTCATAATGCTTTCATCT
40561719 AATGTCGATTATAATTCAAACAAACTCATAATGCTTTCATCT
1 AATGTCGATTATAATTCAAACAAACTCATAATGCTTTCATCT
40561761 AA
1 AA
40561763 CATACAAATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.35
Consensus pattern (42 bp):
AATGTCGATTATAATTCAAACAAACTCATAATGCTTTCATCT
Found at i:40562338 original size:26 final size:26
Alignment explanation
Indices: 40562309--40562364 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
40562299 TGATAAAAAT
40562309 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
40562335 TGATAATGGGTTATGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
40562361 TGAT
1 TGAT
40562365 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:0.30, C:0.07, G:0.25, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:40563904 original size:26 final size:26
Alignment explanation
Indices: 40563852--40563904 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
40563842 TTTACAATTT
*
40563852 TACCCCTAGGAGATAAATTATCGAAA
1 TACCCCTAGGAGATAAATTACCGAAA
* *
40563878 TACCCCTAGG-GTTAAATTGACCTAAA
1 TACCCCTAGGAGATAAATT-ACCGAAA
40563904 T
1 T
40563905 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (26 bp):
TACCCCTAGGAGATAAATTACCGAAA
Found at i:40565525 original size:12 final size:12
Alignment explanation
Indices: 40565504--40565534 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
40565494 ACTCGGGGAA
*
40565504 GAGGCTGTGGTC
1 GAGGCCGTGGTC
40565516 GAGGCCGTGGTC
1 GAGGCCGTGGTC
40565528 GAGGCCG
1 GAGGCCG
40565535 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:0.10, C:0.23, G:0.52, T:0.16
Consensus pattern (12 bp):
GAGGCCGTGGTC
Found at i:40569469 original size:26 final size:26
Alignment explanation
Indices: 40569440--40569495 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
40569430 TGATAAAAAT
*
40569440 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAACGGGTTAGGTAAATGTTCCA
*
40569466 TGATAACGGGTTAGGTAAATGTTCTA
1 TGATAACGGGTTAGGTAAATGTTCCA
40569492 TGAT
1 TGAT
40569496 GGGCATTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.36
Consensus pattern (26 bp):
TGATAACGGGTTAGGTAAATGTTCCA
Found at i:40572892 original size:48 final size:48
Alignment explanation
Indices: 40572820--40572943 Score: 160
Period size: 48 Copynumber: 2.6 Consensus size: 48
40572810 GTCTCATAAT
*
40572820 AATGCCATGTCCCAGACATGGTCTTACACTAGCA-CACATATCAACGCC
1 AATGCCATGTCCCAGACATGGTCTTACACGAG-ATCACATATCAACGCC
* * * * * *
40572868 GATGCCATGTCCCAGACATGGTCTTATACGAGATCTCATCTCGATGCC
1 AATGCCATGTCCCAGACATGGTCTTACACGAGATCACATATCAACGCC
*
40572916 AATGCCATGCCCCAGACATGGTCTTACA
1 AATGCCATGTCCCAGACATGGTCTTACA
40572944 TGGGATCTCA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
47 1 0.02
48 64 0.98
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.23
Consensus pattern (48 bp):
AATGCCATGTCCCAGACATGGTCTTACACGAGATCACATATCAACGCC
Found at i:40579728 original size:26 final size:26
Alignment explanation
Indices: 40579698--40579807 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
40579688 TGATACAAAT
40579698 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
40579724 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
40579750 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
40579776 TGGTAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
40579802 TGATAA
1 TGATAA
40579808 GAATTTCATG
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 79 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:40581468 original size:27 final size:27
Alignment explanation
Indices: 40581427--40581539 Score: 111
Period size: 27 Copynumber: 4.2 Consensus size: 27
40581417 GAGGAAGCGT
*
40581427 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
40581454 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * * *
40581481 TCTAGTGGCTCTACCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
40581509 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
40581535 TCTGG
1 TCTGG
40581540 CAGCCATGCT
Statistics
Matches: 71, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
26 5 0.07
27 53 0.75
28 13 0.18
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:40582717 original size:49 final size:49
Alignment explanation
Indices: 40582658--40582763 Score: 160
Period size: 49 Copynumber: 2.2 Consensus size: 49
40582648 GATATAGGTC
* * *
40582658 TCGCGTCATTGAACATCAAATGGGATTTCTGA-TAGCTCAAAGTTGGGTG
1 TCGCGACATTGAACATCAAATGGAACTTCTGACT-GCTCAAAGTTGGGTG
*
40582707 TCGCGACATTGAACATCAAATGGAACTTCTGACTGCTCGAAGTTGGGTG
1 TCGCGACATTGAACATCAAATGGAACTTCTGACTGCTCAAAGTTGGGTG
40582756 TCGCGACA
1 TCGCGACA
40582764 CTTGTCTTCC
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
49 51 0.98
50 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.27
Consensus pattern (49 bp):
TCGCGACATTGAACATCAAATGGAACTTCTGACTGCTCAAAGTTGGGTG
Found at i:40583861 original size:170 final size:170
Alignment explanation
Indices: 40583554--40583875 Score: 452
Period size: 170 Copynumber: 1.9 Consensus size: 170
40583544 GTGGCACTAG
* * * * *
40583554 AAATGATGGTTCCAGAACTCCGTATACAGATCATTGATTCCGTAAATATTAATTATTAATATTTA
1 AAATGATGGTTCCAGAACACCGTATACAGATAATCGATTCAGTAAATATTAATTACTAATATTTA
* * * *
40583619 TGAGTTAACTTTAGATTTATATTGAGTTTTGGTCTAGTAATTTTAGTAGACAACTAGTACTTAAA
66 TGAGTTAACTTGAGATTTATATCGAGATTTGGTCTAGTAATTTTAGTAGACAACTAGTAATTAAA
*
40583684 GTACAAGGACTAAATCATAAAATTTGTAAAAGTGTACCAA
131 ATACAAGGACTAAATCATAAAATTTGTAAAAGTGTACCAA
* *
40583724 AAATGATTGTTTCAGAACACCGTATACCA-ATAATCGATTCAGTAAATATTAATTACTAATATTT
1 AAATGATGGTTCCAGAACACCGTATA-CAGATAATCGATTCAGTAAATATTAATTACTAATATTT
* * *
40583788 ATGAGCTT-ACTTGAGATTTATATCGAGATTTGGT-TAGGTAATTTTATTAGACGATTAGTAATT
65 ATGAG-TTAACTTGAGATTTATATCGAGATTTGGTCTA-GTAATTTTAGTAGACAACTAGTAATT
*
40583851 AAAATACAAGGACTAAATCGTAAAA
128 AAAATACAAGGACTAAATCATAAAA
40583876 ACTATAAAAG
Statistics
Matches: 133, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
169 2 0.02
170 127 0.95
171 4 0.03
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.36
Consensus pattern (170 bp):
AAATGATGGTTCCAGAACACCGTATACAGATAATCGATTCAGTAAATATTAATTACTAATATTTA
TGAGTTAACTTGAGATTTATATCGAGATTTGGTCTAGTAATTTTAGTAGACAACTAGTAATTAAA
ATACAAGGACTAAATCATAAAATTTGTAAAAGTGTACCAA
Found at i:40585517 original size:27 final size:27
Alignment explanation
Indices: 40585485--40585539 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
40585475 ATGTAGGCTT
40585485 ATCATTAAATTCTTAAAGTACTTACTA
1 ATCATTAAATTCTTAAAGTACTTACTA
*
40585512 ATCATTAAATTCTTGAAGTACTTACTA
1 ATCATTAAATTCTTAAAGTACTTACTA
40585539 A
1 A
40585540 GTTGTTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.40
Consensus pattern (27 bp):
ATCATTAAATTCTTAAAGTACTTACTA
Found at i:40585746 original size:12 final size:12
Alignment explanation
Indices: 40585729--40585754 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40585719 ATGAAAACTT
40585729 TACTTATTTTGG
1 TACTTATTTTGG
40585741 TACTTATTTTGG
1 TACTTATTTTGG
40585753 TA
1 TA
40585755 TCATATGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.08, G:0.15, T:0.58
Consensus pattern (12 bp):
TACTTATTTTGG
Found at i:40586029 original size:18 final size:18
Alignment explanation
Indices: 40586006--40586040 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40585996 AAACAGAATG
40586006 CATTTTTGGTATCGATAA
1 CATTTTTGGTATCGATAA
* *
40586024 CATTTTTTGTATTGATA
1 CATTTTTGGTATCGATA
40586041 TTGGGGACAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.09, G:0.14, T:0.51
Consensus pattern (18 bp):
CATTTTTGGTATCGATAA
Found at i:40587284 original size:12 final size:12
Alignment explanation
Indices: 40587267--40587292 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40587257 AAAATAGGGC
40587267 TTTAGCGGCGTT
1 TTTAGCGGCGTT
40587279 TTTAGCGGCGTT
1 TTTAGCGGCGTT
40587291 TT
1 TT
40587293 GACAAAAACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTAGCGGCGTT
Found at i:40587399 original size:41 final size:41
Alignment explanation
Indices: 40587339--40587475 Score: 231
Period size: 41 Copynumber: 3.4 Consensus size: 41
40587329 TTTTTTGTTA
* * *
40587339 AAACGGCGCTAAA-AACAGAGCATTAGCGGTGCTTTTGGTG
1 AAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGGTG
*
40587379 AAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGGTA
1 AAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGGTG
40587420 AAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGGTG
1 AAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGGTG
40587461 AAACGCCGCTAAAGA
1 AAACGCCGCTAAAGA
40587476 TACCAACTAG
Statistics
Matches: 91, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
40 12 0.13
41 79 0.87
ACGTcount: A:0.31, C:0.23, G:0.28, T:0.19
Consensus pattern (41 bp):
AAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGGTG
Found at i:40587636 original size:7 final size:7
Alignment explanation
Indices: 40587566--40587666 Score: 60
Period size: 7 Copynumber: 14.1 Consensus size: 7
40587556 TTAAGGGTTG
40587566 GGGTTTA
1 GGGTTTA
*
40587573 AGGTTTA
1 GGGTTTA
40587580 -GGTGTTA
1 GGGT-TTA
*
40587587 GGGGTTA
1 GGGTTTA
*
40587594 GGGGTTCA
1 -GGGTTTA
* *
40587602 TGGTTCA
1 GGGTTTA
* *
40587609 TGGTTCA
1 GGGTTTA
40587616 GGGTTTA
1 GGGTTTA
* *
40587623 TGTTTTA
1 GGGTTTA
40587630 GGGTTTA
1 GGGTTTA
**
40587637 ATGTTTA
1 GGGTTTA
*
40587644 GGGATTA
1 GGGTTTA
40587651 GGAGTTTA
1 GG-GTTTA
40587659 GGGTTTA
1 GGGTTTA
40587666 G
1 G
40587667 ATTAGTTAGT
Statistics
Matches: 73, Mismatches: 17, Indels: 8
0.74 0.17 0.08
Matches are distributed among these distances:
6 3 0.04
7 57 0.78
8 13 0.18
ACGTcount: A:0.18, C:0.03, G:0.38, T:0.42
Consensus pattern (7 bp):
GGGTTTA
Found at i:40588302 original size:16 final size:16
Alignment explanation
Indices: 40588281--40588312 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40588271 AAAAATCTTC
*
40588281 ATAAAAAATTTAAAAA
1 ATAAAAAACTTAAAAA
40588297 ATAAAAAACTTAAAAA
1 ATAAAAAACTTAAAAA
40588313 TTTAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (16 bp):
ATAAAAAACTTAAAAA
Found at i:40590274 original size:22 final size:22
Alignment explanation
Indices: 40590249--40590293 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
40590239 TTTAATAAAG
40590249 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
*
40590271 AAAATATTTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
40590293 A
1 A
40590294 CACTCCCCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:40594050 original size:22 final size:22
Alignment explanation
Indices: 40594025--40594069 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
40594015 TTTAATAAAG
40594025 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* * *
40594047 AAAATATTTATAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
40594069 A
1 A
40594070 CATATATTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:40596065 original size:27 final size:27
Alignment explanation
Indices: 40596030--40596082 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
40596020 TATTTTGATA
40596030 ATGAATTTTA-AACT-TTTTATATTTTTC
1 ATGAATTTTATAA-TATTTTAT-TTTTTC
*
40596057 ATGACTTTTATAATATTTTATTTTTT
1 ATGAATTTTATAATATTTTATTTTTT
40596083 AAAATTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (27 bp):
ATGAATTTTATAATATTTTATTTTTTC
Found at i:40596157 original size:43 final size:43
Alignment explanation
Indices: 40596096--40596234 Score: 215
Period size: 43 Copynumber: 3.2 Consensus size: 43
40596086 ATTTTATGAC
* *
40596096 CTTTAGCGGCGTTTGCGGGAAAAGCGCCGCGAAAAGTCCTAGA
1 CTTTAGCGGCGTTTGCGGGAAAAGCGCCGCGAAAAGTCCTGGT
40596139 CTTTAGCGGCGTTTGCGGGAAAAGCGCCGCGAAAAGTCCTGGT
1 CTTTAGCGGCGTTTGCGGGAAAAGCGCCGCGAAAAGTCCTGGT
**** *
40596182 CTTTAGCGGCGTTTTTTAGAAAAGCGCCGCTAAAAGTCCTGGT
1 CTTTAGCGGCGTTTGCGGGAAAAGCGCCGCGAAAAGTCCTGGT
40596225 CTTTAGCGGC
1 CTTTAGCGGC
40596235 CTTTTTTCGA
Statistics
Matches: 89, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 89 1.00
ACGTcount: A:0.22, C:0.23, G:0.31, T:0.24
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGCGGGAAAAGCGCCGCGAAAAGTCCTGGT
Found at i:40598447 original size:39 final size:39
Alignment explanation
Indices: 40598404--40598544 Score: 219
Period size: 39 Copynumber: 3.6 Consensus size: 39
40598394 CATATTCACT
* * *
40598404 TTTAAGCATGTATCACATTACACATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* *
40598443 TTTAAGCATATATCATAATACTTATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
*
40598482 TTTAAGCAAATATCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
*
40598521 TTCAAGCATATATCACAATACTCA
1 TTTAAGCATATATCACAATACTCA
40598545 AAAACATGTT
Statistics
Matches: 92, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 92 1.00
ACGTcount: A:0.45, C:0.20, G:0.04, T:0.31
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACTCATATAATCACATAACA
Found at i:40600356 original size:46 final size:46
Alignment explanation
Indices: 40600306--40600664 Score: 396
Period size: 46 Copynumber: 7.7 Consensus size: 46
40600296 TGGTTGAGCA
*
40600306 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAGG
* * *
40600352 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--AGG
*
40600397 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAGG
* * *
40600445 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--AGG
*
40600490 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAGG
* * *
40600538 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--AGG
* *
40600583 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAGG
*
40600631 -CTCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TC-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
40600665 GGGGCAGGTT
Statistics
Matches: 265, Mismatches: 26, Indels: 44
0.79 0.08 0.13
Matches are distributed among these distances:
43 18 0.07
45 13 0.05
46 118 0.45
47 87 0.33
48 12 0.05
50 17 0.06
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAGG
Found at i:40600462 original size:93 final size:93
Alignment explanation
Indices: 40600303--40600659 Score: 671
Period size: 93 Copynumber: 3.8 Consensus size: 93
40600293 GGATGGTTGA
40600303 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
40600368 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
40600396 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
40600461 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
40600489 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
40600554 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
40600582 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CTCGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTC-CGAACTCGTTGAG
40600646 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
40600660 ACTTAGGGGC
Statistics
Matches: 260, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
92 1 0.00
93 259 1.00
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:40600925 original size:19 final size:20
Alignment explanation
Indices: 40600888--40600925 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
40600878 ATAAGGTGGT
40600888 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
40600908 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
40600926 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:40601654 original size:296 final size:296
Alignment explanation
Indices: 40601120--40601713 Score: 1170
Period size: 296 Copynumber: 2.0 Consensus size: 296
40601110 GGTAAATGGT
40601120 TTGTACAACTACTTAAGTATGGCATGTATAGCAATATACCTATTTTGTGTAAATAATTTTATGAT
1 TTGTACAACTACTTAAGTATGGCATGTATAGCAATATACCTATTTTGTGTAAATAATTTTATGAT
40601185 ATGGCCATGTTTGGTTGAGAAAATGTTTGATATTGATAAGTCATGGTGATGGCTAATTTAGATCA
66 ATGGCCATGTTTGGTTGAGAAAATGTTTGATATTGATAAGTCATGGTGATGGCTAATTTAGATCA
40601250 TGTTTGATATCATGGAAGTTTAACAGGTTATCTAGTTCATAAAAATTCATGGAAAGATGAAACTT
131 TGTTTGATATCATGGAAGTTTAACAGGTTATCTAGTTCATAAAAATTCATGGAAAGATGAAACTT
40601315 GCCTTAAAACAGAATATTGCTGCAGCAATGACATGAATTTGAAAAATCACTAAAAATAGTATAAA
196 GCCTTAAAACAGAATATTGCTGCAGCAATGACATGAATTTGAAAAATCACTAAAAATAGTATAAA
40601380 TGGAACTAAATAATGAGTAAGTTACGAAATTGAAGC
261 TGGAACTAAATAATGAGTAAGTTACGAAATTGAAGC
40601416 TTGTACAACTACTTAAGTATGGCATGTATAGCAATATACCTATTTTGTGTAAATAATTTTATGAT
1 TTGTACAACTACTTAAGTATGGCATGTATAGCAATATACCTATTTTGTGTAAATAATTTTATGAT
40601481 ATGGCCATGTTTGGTTGAGAAAATGTTTGATATTGATAAGTCATGGTGATGGCTAATTTAGATCA
66 ATGGCCATGTTTGGTTGAGAAAATGTTTGATATTGATAAGTCATGGTGATGGCTAATTTAGATCA
40601546 TGTTTGATATCATGGAAGTTTAACAGGTTATCTAGTTCATAAAAATTCATGGAAAGATGAAACTT
131 TGTTTGATATCATGGAAGTTTAACAGGTTATCTAGTTCATAAAAATTCATGGAAAGATGAAACTT
*
40601611 GCCTTAAAACAGAATATTGTTGCAGCAATGACATGAATTTGAAAAATCACTAAAAATAGTATAAA
196 GCCTTAAAACAGAATATTGCTGCAGCAATGACATGAATTTGAAAAATCACTAAAAATAGTATAAA
*
40601676 TGGAACTAAATAATGAGTAAGTTATGAAATTGAAGC
261 TGGAACTAAATAATGAGTAAGTTACGAAATTGAAGC
40601712 TT
1 TT
40601714 AATGAGTCTA
Statistics
Matches: 296, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
296 296 1.00
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.34
Consensus pattern (296 bp):
TTGTACAACTACTTAAGTATGGCATGTATAGCAATATACCTATTTTGTGTAAATAATTTTATGAT
ATGGCCATGTTTGGTTGAGAAAATGTTTGATATTGATAAGTCATGGTGATGGCTAATTTAGATCA
TGTTTGATATCATGGAAGTTTAACAGGTTATCTAGTTCATAAAAATTCATGGAAAGATGAAACTT
GCCTTAAAACAGAATATTGCTGCAGCAATGACATGAATTTGAAAAATCACTAAAAATAGTATAAA
TGGAACTAAATAATGAGTAAGTTACGAAATTGAAGC
Found at i:40607302 original size:23 final size:23
Alignment explanation
Indices: 40607276--40607324 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
40607266 AGTTTTAAAA
40607276 ACTCTGCAACTACCTCACTTTTC
1 ACTCTGCAACTACCTCACTTTTC
40607299 ACTCTGCAACTACCTCACTTTTC
1 ACTCTGCAACTACCTCACTTTTC
40607322 ACT
1 ACT
40607325 TATTTTTCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.22, C:0.39, G:0.04, T:0.35
Consensus pattern (23 bp):
ACTCTGCAACTACCTCACTTTTC
Found at i:40608773 original size:22 final size:21
Alignment explanation
Indices: 40608748--40608805 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 21
40608738 ACTTATTTCT
40608748 ATTGATGTATTATGCCAATATA
1 ATTGATGT-TTATGCCAATATA
* *
40608770 ATTGATTGGTTGTGCCAATATA
1 ATTGA-TGTTTATGCCAATATA
40608792 ATTGAATGTTTATG
1 ATTG-ATGTTTATG
40608806 TGTTAAAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 27 0.90
23 3 0.10
ACGTcount: A:0.31, C:0.07, G:0.19, T:0.43
Consensus pattern (21 bp):
ATTGATGTTTATGCCAATATA
Found at i:40611206 original size:21 final size:21
Alignment explanation
Indices: 40611180--40611221 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
40611170 GGAGATTAAG
40611180 TATACCTCAAGTTGCAACCAT
1 TATACCTCAAGTTGCAACCAT
40611201 TATACCTCAAGTTGCAACCAT
1 TATACCTCAAGTTGCAACCAT
40611222 ATAGGTAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.29, G:0.10, T:0.29
Consensus pattern (21 bp):
TATACCTCAAGTTGCAACCAT
Found at i:40622103 original size:44 final size:44
Alignment explanation
Indices: 40622040--40622127 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
40622030 CGCTGCAGCC
*
40622040 TAGGATTATACCTTTACGAGGGGAACAGCAAATGAAGCAGGAAT
1 TAGGATTATACCTTTACGAGGGGAACAGCAAATGAAGAAGGAAT
40622084 TAGGATTATACCTTTACGAGGGGAACAGCAAATGAAGAAGGAAT
1 TAGGATTATACCTTTACGAGGGGAACAGCAAATGAAGAAGGAAT
40622128 GAATGAGAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.40, C:0.12, G:0.27, T:0.20
Consensus pattern (44 bp):
TAGGATTATACCTTTACGAGGGGAACAGCAAATGAAGAAGGAAT
Found at i:40625892 original size:6 final size:6
Alignment explanation
Indices: 40625881--40625924 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
40625871 AAACAGAGGC
40625881 CATTTT CATTTT CATTTT CATTTT CATTTT CATTTT CATTTT CA
1 CATTTT CATTTT CATTTT CATTTT CATTTT CATTTT CATTTT CA
40625925 AAAAGGAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (6 bp):
CATTTT
Found at i:40648383 original size:24 final size:24
Alignment explanation
Indices: 40648356--40648427 Score: 144
Period size: 24 Copynumber: 3.0 Consensus size: 24
40648346 CAGTTAAACC
40648356 ATTTTAATTTTCTATAATTATATT
1 ATTTTAATTTTCTATAATTATATT
40648380 ATTTTAATTTTCTATAATTATATT
1 ATTTTAATTTTCTATAATTATATT
40648404 ATTTTAATTTTCTATAATTATATT
1 ATTTTAATTTTCTATAATTATATT
40648428 TGAAATTAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTTTAATTTTCTATAATTATATT
Found at i:40648793 original size:13 final size:13
Alignment explanation
Indices: 40648775--40648806 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
40648765 AATGTTGTGG
40648775 AAAAGTGCTTTTA
1 AAAAGTGCTTTTA
*
40648788 AGAAGTGCTTTTA
1 AAAAGTGCTTTTA
40648801 AAAAGT
1 AAAAGT
40648807 TTGTTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.34
Consensus pattern (13 bp):
AAAAGTGCTTTTA
Found at i:40649870 original size:17 final size:17
Alignment explanation
Indices: 40649854--40649892 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
40649844 ATATAATAAT
40649854 TAAA-ATTATTTTTTAA
1 TAAAGATTATTTTTTAA
40649870 TAAAGATTATTTTTTAA
1 TAAAGATTATTTTTTAA
*
40649887 CAAAGA
1 TAAAGA
40649893 ATTGATGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (17 bp):
TAAAGATTATTTTTTAA
Found at i:40650797 original size:55 final size:55
Alignment explanation
Indices: 40650737--40650847 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
40650727 GAAAGACAAC
40650737 GTACTTCAATAGATAATTTAAACGACTTCGTAATCTCATAAAAAAATCAAAATGA
1 GTACTTCAATAGATAATTTAAACGACTTCGTAATCTCATAAAAAAATCAAAATGA
*
40650792 GTACTTCAATAGATAATTTAAACGAGTTCGTAATCTCATAAAAAAATCAAAATGA
1 GTACTTCAATAGATAATTTAAACGACTTCGTAATCTCATAAAAAAATCAAAATGA
40650847 G
1 G
40650848 CATTTGATTC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.29
Consensus pattern (55 bp):
GTACTTCAATAGATAATTTAAACGACTTCGTAATCTCATAAAAAAATCAAAATGA
Found at i:40652357 original size:68 final size:69
Alignment explanation
Indices: 40652278--40652412 Score: 195
Period size: 68 Copynumber: 2.0 Consensus size: 69
40652268 TTTAATATAT
* * * *
40652278 TTAATATTAAATTTAATTTAATACTT-A-CCTTGATAA-TATTTTATTAATTTAATGTTAAAGTT
1 TTAATATTAAATTTAATCTAATA-TTCATCC-TGATAAGTATTATATTAATTTAATATTAAAGTG
40652340 ATTATC
64 ATTATC
40652346 TTAATATTAAATTTAATCTAATATTCATCCTGATAAGTATTATATTAATTTAATATTAAAGTGAT
1 TTAATATTAAATTTAATCTAATATTCATCCTGATAAGTATTATATTAATTTAATATTAAAGTGAT
40652411 TA
66 TA
40652413 AGTTTAATCA
Statistics
Matches: 60, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
67 2 0.03
68 29 0.48
69 29 0.48
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.49
Consensus pattern (69 bp):
TTAATATTAAATTTAATCTAATATTCATCCTGATAAGTATTATATTAATTTAATATTAAAGTGAT
TATC
Found at i:40668150 original size:14 final size:15
Alignment explanation
Indices: 40668119--40668151 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
40668109 GCTTTTAGAG
40668119 TTTATTAATTAGGGT
1 TTTATTAATTAGGGT
40668134 TTTATT-ATTAGGGT
1 TTTATTAATTAGGGT
40668148 TTTA
1 TTTA
40668152 GGTTTTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (15 bp):
TTTATTAATTAGGGT
Found at i:40668167 original size:23 final size:23
Alignment explanation
Indices: 40668141--40668204 Score: 110
Period size: 23 Copynumber: 2.7 Consensus size: 23
40668131 GGTTTTATTA
40668141 TTAGGGTTTTAGGTTTTTTAGGG
1 TTAGGGTTTTAGGTTTTTTAGGG
40668164 TTAGGGTTTTAGGTTTTTTAGGG
1 TTAGGGTTTTAGGTTTTTTAGGG
*
40668187 TTAGTGTTTTATGGTTTT
1 TTAGGGTTTTA-GGTTTT
40668205 AATTGATTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
23 33 0.85
24 6 0.15
ACGTcount: A:0.12, C:0.00, G:0.31, T:0.56
Consensus pattern (23 bp):
TTAGGGTTTTAGGTTTTTTAGGG
Found at i:40668355 original size:29 final size:29
Alignment explanation
Indices: 40668306--40668438 Score: 178
Period size: 29 Copynumber: 4.6 Consensus size: 29
40668296 AAAAATTGAA
* *
40668306 ATGGGTTCTG-AAAAATTATTTTGATGAG
1 ATGGGTTCTGAAAAAATAATTTTGACGAG
* * *
40668334 ATAGGTTCTGGAAACATAATTTTGACGAG
1 ATGGGTTCTGAAAAAATAATTTTGACGAG
*
40668363 ATGAGTTCTGAAAAAATAATTTTGACGAG
1 ATGGGTTCTGAAAAAATAATTTTGACGAG
* *
40668392 ATGGGTTCTAAAAAAATAATTTTGACTAG
1 ATGGGTTCTGAAAAAATAATTTTGACGAG
*
40668421 ATGGGTTCTAAAAAAATA
1 ATGGGTTCTGAAAAAATA
40668439 TCCTGGGATT
Statistics
Matches: 93, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
28 9 0.10
29 84 0.90
ACGTcount: A:0.39, C:0.07, G:0.21, T:0.33
Consensus pattern (29 bp):
ATGGGTTCTGAAAAAATAATTTTGACGAG
Found at i:40668666 original size:19 final size:19
Alignment explanation
Indices: 40668619--40668716 Score: 164
Period size: 19 Copynumber: 5.2 Consensus size: 19
40668609 AATCTTTAAG
40668619 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40668638 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40668655 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40668674 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40668693 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
40668714 GAT
1 GAT
40668717 CTTGTAATTT
Statistics
Matches: 75, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.23
19 49 0.65
21 9 0.12
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:40673893 original size:75 final size:75
Alignment explanation
Indices: 40673765--40674065 Score: 593
Period size: 75 Copynumber: 4.0 Consensus size: 75
40673755 TTATTTCACC
*
40673765 TACAATTTTCGAGTATTGATACCTAATAAAAGGGTATTGATATTTTTTTGTAATAAATTCTAATT
1 TACAGTTTTCGAGTATTGATACCTAATAAAAGGGTATTGATATTTTTTTGTAATAAATTCTAATT
40673830 CAGTGACCGT
66 CAGTGACCGT
40673840 TACAGTTTTCGAGTATTGATACCTAATAAAAGGGTATTGATATTTTTTTGTAATAAATTCTAATT
1 TACAGTTTTCGAGTATTGATACCTAATAAAAGGGTATTGATATTTTTTTGTAATAAATTCTAATT
40673905 CAGTGACCGT
66 CAGTGACCGT
40673915 TACAGTTTTCGAGTATTGATACCTAATAAAAGGGTATTGATATTTTTTTGTAATAAATTCTAATT
1 TACAGTTTTCGAGTATTGATACCTAATAAAAGGGTATTGATATTTTTTTGTAATAAATTCTAATT
40673980 CAGTGACCGT
66 CAGTGACCGT
40673990 TACAGTTTTCGAGTATTGATACCTAATAAAAGGGTATTGATATTTTTTTGTAATAAATTCTAATT
1 TACAGTTTTCGAGTATTGATACCTAATAAAAGGGTATTGATATTTTTTTGTAATAAATTCTAATT
40674055 CAGTGACCGT
66 CAGTGACCGT
40674065 T
1 T
40674066 GGGATTTATT
Statistics
Matches: 225, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 225 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (75 bp):
TACAGTTTTCGAGTATTGATACCTAATAAAAGGGTATTGATATTTTTTTGTAATAAATTCTAATT
CAGTGACCGT
Found at i:40678762 original size:46 final size:46
Alignment explanation
Indices: 40678686--40678915 Score: 291
Period size: 46 Copynumber: 5.0 Consensus size: 46
40678676 TGATGTCATA
* * * *
40678686 GTATCTTTAAACTATGGTTTTACTCGTTTTC-TGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTC-ATTTCATGTCATGTTGCCATG
* **
40678732 GTATCTTTCAACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCA-TTTCATGTCATGTTGCCATG
*
40678779 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGCCATG
* * * *
40678825 GTATCTTTCAAACATGGTCTTATTCATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGCCATG
* * * *
40678871 GTATCTTTCAACCATGGTCTTACCCATTTAATATCAGGTTGCCAT
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGCCAT
40678916 AGGCCTGTAT
Statistics
Matches: 163, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
46 124 0.76
47 39 0.24
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.42
Consensus pattern (46 bp):
GTATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGCCATG
Found at i:40691727 original size:8 final size:8
Alignment explanation
Indices: 40691714--40691744 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
40691704 GCACCCGGAT
40691714 TCACATAG
1 TCACATAG
40691722 TCACATAG
1 TCACATAG
40691730 TCACATAG
1 TCACATAG
*
40691738 ACACATA
1 TCACATA
40691745 ATCTCATGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.23
Consensus pattern (8 bp):
TCACATAG
Found at i:40692982 original size:38 final size:38
Alignment explanation
Indices: 40692931--40693005 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
40692921 ATCATAGATC
* * *
40692931 TCATAATAATCATAAAATATTTTTTTCTACTTTGGATA
1 TCATAATAATCATAAAATAATTATTGCTACTTTGGATA
40692969 TCATAATAATCATAAAATAATTATTGCTACTTTGGAT
1 TCATAATAATCATAAAATAATTATTGCTACTTTGGAT
40693006 TTGTAGTCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.44
Consensus pattern (38 bp):
TCATAATAATCATAAAATAATTATTGCTACTTTGGATA
Found at i:40693344 original size:33 final size:33
Alignment explanation
Indices: 40693302--40693368 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
40693292 TAGAACTATT
*
40693302 TTACCTTTTTGGACATGATCTCTAATGAAATGA
1 TTACCTTTTTGGACATGACCTCTAATGAAATGA
40693335 TTACCTTTTTGGACATGACCTCTAATGAAATGA
1 TTACCTTTTTGGACATGACCTCTAATGAAATGA
40693368 T
1 T
40693369 GTCTAATTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (33 bp):
TTACCTTTTTGGACATGACCTCTAATGAAATGA
Found at i:40696524 original size:31 final size:31
Alignment explanation
Indices: 40696486--40696547 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
40696476 ACAAAAGAGA
40696486 ATGTGCATAGCCTTGGCGTTGAGTTGCATGC
1 ATGTGCATAGCCTTGGCGTTGAGTTGCATGC
* *
40696517 ATGTGCATGGCCTTGGCGTTGAGTTTCATGC
1 ATGTGCATAGCCTTGGCGTTGAGTTGCATGC
40696548 TCTTCTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.15, C:0.19, G:0.32, T:0.34
Consensus pattern (31 bp):
ATGTGCATAGCCTTGGCGTTGAGTTGCATGC
Found at i:40698456 original size:12 final size:12
Alignment explanation
Indices: 40698423--40698456 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
40698413 GACACACGCT
*
40698423 CGTGTGGCTGGC
1 CGTGTGGCTTGC
40698435 CGTGTGGCTTGC
1 CGTGTGGCTTGC
40698447 CGTGTGGCTT
1 CGTGTGGCTT
40698457 ACACGACCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.44, T:0.32
Consensus pattern (12 bp):
CGTGTGGCTTGC
Found at i:40699022 original size:24 final size:26
Alignment explanation
Indices: 40698991--40699043 Score: 74
Period size: 24 Copynumber: 2.1 Consensus size: 26
40698981 TTTCTTTTTT
40698991 TAATAAATAAAAAAC-TTT-AAAATA
1 TAATAAATAAAAAACATTTAAAAATA
* *
40699015 TAATAAATCAAATACATTTAAAAATA
1 TAATAAATAAAAAACATTTAAAAATA
40699041 TAA
1 TAA
40699044 AAACAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 13 0.52
25 3 0.12
26 9 0.36
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (26 bp):
TAATAAATAAAAAACATTTAAAAATA
Found at i:40700208 original size:90 final size:90
Alignment explanation
Indices: 40700055--40700911 Score: 1696
Period size: 90 Copynumber: 9.5 Consensus size: 90
40700045 CTATGACCTA
* *
40700055 GCCATGGTCTTACATTCGTAGTGCCATAACCCAGTTATGGTCTTATCATCAGAGTGCCATAGCCC
1 GCCATGGTCTTATATTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAGTGCCATAGCCC
40700120 AGCTATGATCTTACATATAAACACT
66 AGCTATGATCTTACATATAAACACT
40700145 GCCATGGTCTTATATTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAGTGCCATAGCCC
1 GCCATGGTCTTATATTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAGTGCCATAGCCC
40700210 AGCTATGATCTTACATATAAACACT
66 AGCTATGATCTTACATATAAACACT
40700235 GCCATGGTCTTATATTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAGTGCCATAGCCC
1 GCCATGGTCTTATATTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAGTGCCATAGCCC
40700300 AGCTATGATCTTACATATAAACACT
66 AGCTATGATCTTACATATAAACACT
40700325 GCCATGGTCTTATATTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAGTGCCATAGCCC
1 GCCATGGTCTTATATTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAGTGCCATAGCCC
40700390 AGCTATGATCTTACATATAAACACT
66 AGCTATGATCTTACATATAAACACT
40700415 GCCATGGTCTTATATTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAGTGCCATAGCCC
1 GCCATGGTCTTATATTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAGTGCCATAGCCC
40700480 AGCTATGATCTTACATATAAACACT
66 AGCTATGATCTTACATATAAACACT
40700505 GCCATGGTCTTATATTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAGTGCCATAGCCC
1 GCCATGGTCTTATATTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAGTGCCATAGCCC
40700570 AGCTATGATCTTACATATAAACACT
66 AGCTATGATCTTACATATAAACACT
40700595 GCCATGGTCTTATATTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAGTGCCATAGCCC
1 GCCATGGTCTTATATTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAGTGCCATAGCCC
40700660 AGCTATGATCTTACATATAAACACT
66 AGCTATGATCTTACATATAAACACT
40700685 GCCATGGTCTTATATTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAGTGCCATAGCCC
1 GCCATGGTCTTATATTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAGTGCCATAGCCC
40700750 AGCTATGATCTTACATATAAACACT
66 AGCTATGATCTTACATATAAACACT
40700775 GCCATGGTCTTATATTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAGTGCCATAGCCC
1 GCCATGGTCTTATATTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAGTGCCATAGCCC
40700840 AGCTATGATCTTACATATAAACACT
66 AGCTATGATCTTACATATAAACACT
40700865 GCCATGGTCTTATATTCATAGTGCCATAACCCAGTTATGGTCTTATC
1 GCCATGGTCTTATATTCATAGTGCCATAACCCAGTTATGGTCTTATC
40700912 CGTTAATTCA
Statistics
Matches: 765, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 765 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (90 bp):
GCCATGGTCTTATATTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAGTGCCATAGCCC
AGCTATGATCTTACATATAAACACT
Found at i:40703000 original size:17 final size:19
Alignment explanation
Indices: 40702959--40703003 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
40702949 ATCTAATCTG
*
40702959 AAAAAATCATTTAAAAAGT
1 AAAAAATTATTTAAAAAGT
*
40702978 ATAAAATTA-TTAAAAA-T
1 AAAAAATTATTTAAAAAGT
40702995 AAAAAATTA
1 AAAAAATTA
40703004 AAAATAAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 9 0.39
18 7 0.30
19 7 0.30
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAAAATTATTTAAAAAGT
Found at i:40703005 original size:14 final size:14
Alignment explanation
Indices: 40702986--40703012 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40702976 GTATAAAATT
40702986 ATTAAAAATAAAAA
1 ATTAAAAATAAAAA
40703000 ATTAAAAATAAAA
1 ATTAAAAATAAAA
40703013 CAAATTCTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
ATTAAAAATAAAAA
Found at i:40703121 original size:17 final size:16
Alignment explanation
Indices: 40703064--40703122 Score: 55
Period size: 16 Copynumber: 3.5 Consensus size: 16
40703054 AATAAATCTC
* *
40703064 TAAAAAATTTAAATCA
1 TAAAAAATATAAATTA
*
40703080 TAAAATAATAGAAAACTTA
1 TAAAA-AATA-TAAA-TTA
40703099 TAAAAAATATAAATTA
1 TAAAAAATATAAATTA
*
40703115 TTAAAAAT
1 TAAAAAAT
40703123 TTGTTTCACG
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
16 15 0.43
17 6 0.17
18 7 0.20
19 7 0.20
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (16 bp):
TAAAAAATATAAATTA
Found at i:40705078 original size:27 final size:27
Alignment explanation
Indices: 40705031--40705082 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
40705021 TTGGTGCTAG
* *
40705031 GGTTAATTCTAAATGGGTTTTGGGTGA
1 GGTTAATACTAAATGGATTTTGGGTGA
40705058 GGTTAATACTAAA-GCGATTTTGGGT
1 GGTTAATACTAAATG-GATTTTGGGT
40705083 CAAGTTGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 1 0.05
27 21 0.95
ACGTcount: A:0.25, C:0.06, G:0.31, T:0.38
Consensus pattern (27 bp):
GGTTAATACTAAATGGATTTTGGGTGA
Found at i:40711986 original size:16 final size:17
Alignment explanation
Indices: 40711965--40712001 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
40711955 TTCAATAAGA
40711965 TTTAAAA-ATAATTTTT
1 TTTAAAATATAATTTTT
40711981 TTTAAAATTATAATTTTT
1 TTTAAAA-TATAATTTTT
40711999 TTT
1 TTT
40712002 TGTAAAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.37
18 12 0.63
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTAAAATATAATTTTT
Found at i:40712002 original size:21 final size:21
Alignment explanation
Indices: 40711976--40712017 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
40711966 TTAAAAATAA
40711976 TTTTTTT-TAAAA-TTATAATT
1 TTTTTTTGTAAAACTTA-AATT
40711996 TTTTTTTGTAAAACTTAAATT
1 TTTTTTTGTAAAACTTAAATT
40712017 T
1 T
40712018 GGTATTACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.35
21 10 0.50
22 3 0.15
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (21 bp):
TTTTTTTGTAAAACTTAAATT
Found at i:40720769 original size:3 final size:3
Alignment explanation
Indices: 40720763--40720789 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
40720753 AAAAAAAAAA
40720763 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
40720790 CAATTCATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:40723104 original size:30 final size:29
Alignment explanation
Indices: 40723065--40723126 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
40723055 TTTTATAAAT
* *
40723065 AATTAATATTT-ATTTCTTAAAATTATTTAA
1 AATTAATATTTCATATATTAAAA-TA-TTAA
*
40723095 AATTTATATTTCATATATTAAAATATTAA
1 AATTAATATTTCATATATTAAAATATTAA
40723124 AAT
1 AAT
40723127 AAAGTTATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 7 0.25
30 12 0.43
31 9 0.32
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (29 bp):
AATTAATATTTCATATATTAAAATATTAA
Done.