Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 101 of 132
Found at i:30905304 original size:17 final size:17
Alignment explanation
Indices: 30905263--30905306 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
30905253 TTTATATTTT
30905263 TTTATAATTTCAAAAATAA
1 TTTA-AATTT-AAAAATAA
30905282 --TAAATTTAAAAATAA
1 TTTAAATTTAAAAATAA
30905297 TTTAAATTTA
1 TTTAAATTTA
30905307 CATGTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 8 0.35
16 5 0.22
17 10 0.43
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAAAATAA
Found at i:30906592 original size:48 final size:48
Alignment explanation
Indices: 30906530--30906633 Score: 163
Period size: 48 Copynumber: 2.2 Consensus size: 48
30906520 CCAGACTAAC
* * *
30906530 CAATGCCACCGCCAAACCGGAACCCATCACACCCATGGGCAGACTGCT
1 CAATGCCACAGCCAAACCGGAACCCACCACACCCATGGACAGACTGCT
* *
30906578 CAATGCCATAGCCAAACTGGAACCCACCACACCCATGGACAGACTGCT
1 CAATGCCACAGCCAAACCGGAACCCACCACACCCATGGACAGACTGCT
30906626 CAATGCCA
1 CAATGCCA
30906634 GGGTAAGCAC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.32, C:0.39, G:0.17, T:0.12
Consensus pattern (48 bp):
CAATGCCACAGCCAAACCGGAACCCACCACACCCATGGACAGACTGCT
Found at i:30909892 original size:48 final size:48
Alignment explanation
Indices: 30909823--30909937 Score: 167
Period size: 48 Copynumber: 2.4 Consensus size: 48
30909813 GGTCATGGCC
* * * * *
30909823 AGACTACCCAATGCCACAGCCAAACTGGAAGCCATCACACCCATGGGC
1 AGACTGCCCAATGCCATAGCCAAACTGGAACCCACCACACCCATGGGA
**
30909871 AGACTGTTCAATGCCATAGCCAAACTGGAACCCACCACACCCATGGGA
1 AGACTGCCCAATGCCATAGCCAAACTGGAACCCACCACACCCATGGGA
30909919 AGACTGCCCAATGCCATAG
1 AGACTGCCCAATGCCATAG
30909938 TCAATCCCTT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 58 1.00
ACGTcount: A:0.33, C:0.35, G:0.19, T:0.13
Consensus pattern (48 bp):
AGACTGCCCAATGCCATAGCCAAACTGGAACCCACCACACCCATGGGA
Found at i:30910576 original size:42 final size:42
Alignment explanation
Indices: 30910517--30910651 Score: 162
Period size: 42 Copynumber: 3.2 Consensus size: 42
30910507 CGAAAAAACG
* *
30910517 CCGCTAAAGATCATGTTCTTTAGCGGCGTTTTTTCCACAAGCA
1 CCGCTAAA-ACCATGTTCTTTAGCGGCGTTTTTCCCACAAGCA
* ** * *
30910560 CCGTTAAAACCATGTTCTTTAGTAGCGTTTTTCCCTCAAGCG
1 CCGCTAAAACCATGTTCTTTAGCGGCGTTTTTCCCACAAGCA
* * * *
30910602 CCGCTAAAACCATGTTCTTTAGCGGCGCTTTTCCCTCATGCG
1 CCGCTAAAACCATGTTCTTTAGCGGCGTTTTTCCCACAAGCA
30910644 CCGCTAAA
1 CCGCTAAA
30910652 TTAACAGATT
Statistics
Matches: 80, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
42 73 0.91
43 7 0.09
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.32
Consensus pattern (42 bp):
CCGCTAAAACCATGTTCTTTAGCGGCGTTTTTCCCACAAGCA
Found at i:30910735 original size:15 final size:15
Alignment explanation
Indices: 30910715--30910747 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
30910705 TTTTTCTGTA
*
30910715 AATTCAAATCCAACC
1 AATTCAAATCCAAAC
30910730 AATTCAAATCCAAAC
1 AATTCAAATCCAAAC
30910745 AAT
1 AAT
30910748 AACTTCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.27, G:0.00, T:0.21
Consensus pattern (15 bp):
AATTCAAATCCAAAC
Found at i:30910942 original size:21 final size:21
Alignment explanation
Indices: 30910917--30910959 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
30910907 CTGTTTCCTT
*
30910917 CGCTTGCCTCGCTGCTGCCTC
1 CGCTTGCCTCGCTACTGCCTC
30910938 CGCTTGCCTCGCTACTGCCTC
1 CGCTTGCCTCGCTACTGCCTC
30910959 C
1 C
30910960 ACTTTAAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.02, C:0.49, G:0.21, T:0.28
Consensus pattern (21 bp):
CGCTTGCCTCGCTACTGCCTC
Found at i:30911031 original size:66 final size:66
Alignment explanation
Indices: 30910955--30911102 Score: 269
Period size: 66 Copynumber: 2.2 Consensus size: 66
30910945 CTCGCTACTG
* *
30910955 CCTCCACTTTAAGTTGTAGGTGGAGTTCATCATATTTTTTTTGAGCCTTTGCTTCTCTCGCTGCA
1 CCTCCTCTTTAAGTTGTAGGTGGAGTTCATCATATTTTTTTTGAGCCTCTGCTTCTCTCGCTGCA
30911020 A
66 A
30911021 CCTCCTCTTTAAGTTGTAGGTGGAGTTCATCATATTTTTTTTGAGCCTCTGCTTCTCTCGCTGCA
1 CCTCCTCTTTAAGTTGTAGGTGGAGTTCATCATATTTTTTTTGAGCCTCTGCTTCTCTCGCTGCA
*
30911086 G
66 A
30911087 CCTCCTCTTTAAGTTG
1 CCTCCTCTTTAAGTTG
30911103 AGCAATTTGC
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 79 1.00
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.43
Consensus pattern (66 bp):
CCTCCTCTTTAAGTTGTAGGTGGAGTTCATCATATTTTTTTTGAGCCTCTGCTTCTCTCGCTGCA
A
Found at i:30911897 original size:15 final size:14
Alignment explanation
Indices: 30911876--30911914 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
30911866 TAAATCTCTA
30911876 AAAATTATAAAAAT
1 AAAATTATAAAAAT
*
30911890 ATAAATTATTAAAGAT
1 A-AAATTA-TAAAAAT
30911906 AAAATTATA
1 AAAATTATA
30911915 TTTTTACAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 3 0.14
15 12 0.55
16 7 0.32
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (14 bp):
AAAATTATAAAAAT
Found at i:30912883 original size:7 final size:7
Alignment explanation
Indices: 30912871--30912913 Score: 59
Period size: 7 Copynumber: 5.9 Consensus size: 7
30912861 GGGATCATGG
30912871 TAAATTT
1 TAAATTT
30912878 TAAATTT
1 TAAATTT
*
30912885 TAACCTTT
1 TAA-ATTT
30912893 TATAATTT
1 TA-AATTT
30912901 TAAATTT
1 TAAATTT
30912908 TAAATT
1 TAAATT
30912914 AATAATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 21 0.66
8 10 0.31
9 1 0.03
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (7 bp):
TAAATTT
Found at i:30915330 original size:69 final size:69
Alignment explanation
Indices: 30915046--30915323 Score: 299
Period size: 69 Copynumber: 4.0 Consensus size: 69
30915036 ATGAACAACG
* * * *
30915046 AGGTGATATTGAGCACAAGGGTCAGGAAGAATCACA-TGTTGAAGCCGGAGGAAAGACCGATGGT
1 AGGTGATAATGAGCAAAAGGGTAAGGAAGAATCACAGT-TTGAAGCCGGAGGAAAGACGGATGGT
*
30915110 GGAGA
65 GGAAA
* * * * *
30915115 AGGTGATAATGTGCAAAAGGCTAAGCAAGAATCACATTTTGATGCCGGAGGAAAGACGGATGGTG
1 AGGTGATAATGAGCAAAAGGGTAAGGAAGAATCACAGTTTGAAGCCGGAGGAAAGACGGATGGTG
30915180 GAAA
66 GAAA
* * * * * * *
30915184 AGGTGATAATGAGCACAAGGGTAAGGACGAATCACAGTTTAAAGCTGTAGGAAA-AGTGGACGGT
1 AGGTGATAATGAGCAAAAGGGTAAGGAAGAATCACAGTTTGAAGCCGGAGGAAAGA-CGGATGGT
**
30915248 ACAAA
65 GGAAA
* * * * * *
30915253 AGGTGATAACGAGCAAAAGGGTAAGGAAGAATCGCGGTTTGAAGCCGGGGGAAAGGCAGATGGTG
1 AGGTGATAATGAGCAAAAGGGTAAGGAAGAATCACAGTTTGAAGCCGGAGGAAAGACGGATGGTG
30915318 GAAA
66 GAAA
30915322 AG
1 AG
30915324 ACGATAAGGA
Statistics
Matches: 168, Mismatches: 38, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
68 1 0.01
69 166 0.99
70 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.35, T:0.16
Consensus pattern (69 bp):
AGGTGATAATGAGCAAAAGGGTAAGGAAGAATCACAGTTTGAAGCCGGAGGAAAGACGGATGGTG
GAAA
Found at i:30918250 original size:30 final size:30
Alignment explanation
Indices: 30918186--30918250 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
30918176 AAATTGAGAT
* *
30918186 TAAAAAAATATTAAAACAAGTAAACTTATT
1 TAAAAAAAAATTAAAACAAGTAAACTTATG
*
30918216 TAAAAAAAAATTATAACAA-TAACAACTTA-G
1 TAAAAAAAAATTAAAACAAGT-A-AACTTATG
30918246 TAAAA
1 TAAAA
30918251 TGTGCTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 1 0.03
30 23 0.77
31 6 0.20
ACGTcount: A:0.63, C:0.08, G:0.03, T:0.26
Consensus pattern (30 bp):
TAAAAAAAAATTAAAACAAGTAAACTTATG
Found at i:30918701 original size:22 final size:22
Alignment explanation
Indices: 30918682--30918736 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
30918672 TAGAAAAATG
30918682 ACAGCAAAACAGTGAGAAAACA
1 ACAGCAAAACAGTGAGAAAACA
* * *
30918704 ATAGCAAAATAGTGAGAAACCA
1 ACAGCAAAACAGTGAGAAAACA
*
30918726 ACAGTAAAACA
1 ACAGCAAAACA
30918737 ACATTTTTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.58, C:0.16, G:0.16, T:0.09
Consensus pattern (22 bp):
ACAGCAAAACAGTGAGAAAACA
Found at i:30924536 original size:17 final size:18
Alignment explanation
Indices: 30924503--30924536 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
30924493 AATTTAATTT
30924503 TAATTAGATTATTTAAAA
1 TAATTAGATTATTTAAAA
*
30924521 TAATTA-ATTTTTTAAA
1 TAATTAGATTATTTAAA
30924537 TTATAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TAATTAGATTATTTAAAA
Found at i:30924593 original size:20 final size:20
Alignment explanation
Indices: 30924570--30924608 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
30924560 CTAAAAACCA
30924570 GAACCCCAAACTTTAAACTC
1 GAACCCCAAACTTTAAACTC
*
30924590 GAACCCTAAACTTTAAACT
1 GAACCCCAAACTTTAAACT
30924609 TCAAGATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.31, G:0.05, T:0.23
Consensus pattern (20 bp):
GAACCCCAAACTTTAAACTC
Found at i:30930396 original size:53 final size:51
Alignment explanation
Indices: 30930322--30930509 Score: 231
Period size: 53 Copynumber: 3.7 Consensus size: 51
30930312 TTCACATTTG
30930322 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATTCGTAATAGGATTCAT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATTCGT--TAGGATTCAT
** * *
30930375 ATAACTCACGATGACGTAGAGTCATGGGACCTTTAATCCGTGTTAGGATTCAT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATTC--GTTAGGATTCAT
* * *
30930428 ATAACTCACGGTGACACAGAGTCATTGGACC-TT--GT-GTTAGGATTCAT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATTCGTTAGGATTCAT
* *
30930475 ATAACTCACGATGACATAGAGTCATCGAACCTTTA
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTA
30930510 TGCTTTTATG
Statistics
Matches: 117, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
47 39 0.33
48 2 0.02
52 2 0.02
53 72 0.62
55 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (51 bp):
ATAACTCACGATGACACAGAGTCATCGGACCTTTAATTCGTTAGGATTCAT
Found at i:30930507 original size:100 final size:104
Alignment explanation
Indices: 30930322--30930509 Score: 276
Period size: 100 Copynumber: 1.8 Consensus size: 104
30930312 TTCACATTTG
*
30930322 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATTCGTAATAGGATTCATATAACTCACGAT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTT-AGTCGT-ATAGGATTCATATAACTCACGAT
* * *
30930387 GACGTAGAGTCATGGGACCTTTAATCCGTGTTAGGATTCAT
64 GACATAGAGTCATCGAACCTTTAATCCGTGTTAGGATTCAT
* *
30930428 ATAACTCACGGTGACACAGAGTCATTGGACC-TT-GT-GT-TAGGATTCATATAACTCACGATGA
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAGTCGTATAGGATTCATATAACTCACGATGA
30930489 CATAGAGTCATCGAACCTTTA
66 CATAGAGTCATCGAACCTTTA
30930510 TGCTTTTATG
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
100 42 0.55
102 2 0.03
103 1 0.01
105 2 0.03
106 29 0.38
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (104 bp):
ATAACTCACGATGACACAGAGTCATCGGACCTTTAGTCGTATAGGATTCATATAACTCACGATGA
CATAGAGTCATCGAACCTTTAATCCGTGTTAGGATTCAT
Found at i:30939623 original size:29 final size:30
Alignment explanation
Indices: 30939569--30939648 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
30939559 ATCTCAAAAT
*
30939569 TATACATGAACTATGATTTAATGTGCAATTG
1 TATACATGAACTTTGATTT-ATGTGCAATTG
* *
30939600 TATACATGAACTTTGATTT-TGTGCTATTT
1 TATACATGAACTTTGATTTATGTGCAATTG
* *
30939629 TATATATGAAATTTTGATTT
1 TATACATG-AACTTTGATTT
30939649 GATCCAAACT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 15 0.35
30 10 0.23
31 18 0.42
ACGTcount: A:0.31, C:0.07, G:0.14, T:0.47
Consensus pattern (30 bp):
TATACATGAACTTTGATTTATGTGCAATTG
Found at i:30939875 original size:29 final size:30
Alignment explanation
Indices: 30939792--30939878 Score: 104
Period size: 31 Copynumber: 2.9 Consensus size: 30
30939782 ATTCAATCAA
* * *
30939792 AATTAAAATTTTAAGTATATATTTGAACCAC
1 AATTAAAA-TTTATGTATATAATTGTACCAC
* *
30939823 AATTAAAATTTCATGTGTATAATTGTACC-T
1 AATTAAAATTT-ATGTATATAATTGTACCAC
30939853 AATTAAAATTTATGTATATAATTGTA
1 AATTAAAATTTATGTATATAATTGTA
30939879 TATTAAATCA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
29 14 0.29
30 14 0.29
31 21 0.43
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.43
Consensus pattern (30 bp):
AATTAAAATTTATGTATATAATTGTACCAC
Found at i:30943200 original size:29 final size:29
Alignment explanation
Indices: 30943142--30943216 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 29
30943132 TAAAATCGAT
* *
30943142 CTTTTGGAAAATTTGAGGTCGAAAATGTGA
1 CTTTTGG-AAATTTGGGGGCGAAAATGTGA
*
30943172 CTTTTGGAAATTTGGGGGC-AAATTGGTGA
1 CTTTTGGAAATTTGGGGGCGAAAAT-GTGA
*
30943201 -TTTTCGGATATTTGGG
1 CTTTT-GGAAATTTGGG
30943217 ATAAAATGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
28 8 0.21
29 24 0.62
30 7 0.18
ACGTcount: A:0.25, C:0.07, G:0.31, T:0.37
Consensus pattern (29 bp):
CTTTTGGAAATTTGGGGGCGAAAATGTGA
Found at i:30943283 original size:28 final size:30
Alignment explanation
Indices: 30943243--30943319 Score: 104
Period size: 28 Copynumber: 2.6 Consensus size: 30
30943233 GGAAAAGTTC
* *
30943243 AGGGTTAAAATGTAATTTTGA-GATATTCG
1 AGGGTCAAAATGTAATTTTGATGAAATTCG
*
30943272 A-GGTCAAAATGTAATTTTGATGAAATTTG
1 AGGGTCAAAATGTAATTTTGATGAAATTCG
*
30943301 AGGGTCAAAATATAATTTT
1 AGGGTCAAAATGTAATTTT
30943320 CAAAGAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 18 0.43
29 8 0.19
30 16 0.38
ACGTcount: A:0.38, C:0.04, G:0.21, T:0.38
Consensus pattern (30 bp):
AGGGTCAAAATGTAATTTTGATGAAATTCG
Found at i:30945446 original size:39 final size:39
Alignment explanation
Indices: 30945397--30945932 Score: 301
Period size: 39 Copynumber: 13.7 Consensus size: 39
30945387 GGATGGTTAC
*
30945397 AATCTGCCCCAGGCTCGAGGTAAAAGATTGGCTGATGGT
1 AATCTGCCCCAGGCTCGAGGTAAAAGATTGGATGATGGT
* * * * *
30945436 AATTTACCCCAGGCTCGAGATAAAAGATCGGATGACT-GC
1 AATCTGCCCCAGGCTCGAGGTAAAAGATTGGATGA-TGGT
* * *
30945475 AATCTGCCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGT
1 AATCTG-CCCCAGGCTCGAGGTAAAAGATTGGATGATGGT
* * * * * * * * *
30945515 GATCTGCCTCAAGCTCGGGGCAAGAGATCGGATGGCT-GC
1 AATCTGCCCCAGGCTCGAGGTAAAAGATTGGAT-GATGGT
* * * ** *
30945554 AATTTGCCCCAAGCTCGGGGTATGAGATTGGTTGATGGT
1 AATCTGCCCCAGGCTCGAGGTAAAAGATTGGATGATGGT
* * * * *
30945593 GATCTGCCCCTA-GCTCGGGGTAAAAGATCGGATGGCT-GC
1 AATCTGCCCC-AGGCTCGAGGTAAAAGATTGGAT-GATGGT
* * * *
30945632 ACTCTGCCCTAGGCTCGAGGTAAGAGATTGGCTGATGGT
1 AATCTGCCCCAGGCTCGAGGTAAAAGATTGGATGATGGT
* * * * * **
30945671 GATCTGTCCCAAGCTCGAGGTAAAAGATCGGATGGTTAT
1 AATCTGCCCCAGGCTCGAGGTAAAAGATTGGATGATGGT
* * * * *
30945710 AATCTGCCCTAAGCTCGGGGTAAGAGATTGGTTGATGGT
1 AATCTGCCCCAGGCTCGAGGTAAAAGATTGGATGATGGT
* ** * * * * *
30945749 GATCCACCCCAAGCTCGAGGTAAAAAATCGGATGGCT-GC
1 AATCTGCCCCAGGCTCGAGGTAAAAGATTGGAT-GATGGT
* * * * *
30945788 AATCTGCCCGAGGCTTGGGGTAAGAGATTGGCTGATGGT
1 AATCTGCCCCAGGCTCGAGGTAAAAGATTGGATGATGGT
* * * *** * * *
30945827 GATCTACCCCAAGCTC-AGGATAAAAGATCAAATGGTTGC
1 AATCTGCCCCAGGCTCGAGG-TAAAAGATTGGATGATGGT
* * * * *
30945866 AATTTACCTCAGGCTCGAGGTAAGAGATTGGCTGATGGT
1 AATCTGCCCCAGGCTCGAGGTAAAAGATTGGATGATGGT
* *
30945905 AATTTGCCCCAGGCTCGGGGTAAAAGAT
1 AATCTGCCCCAGGCTCGAGGTAAAAGAT
30945933 CAGATCTTCA
Statistics
Matches: 361, Mismatches: 123, Indels: 26
0.71 0.24 0.05
Matches are distributed among these distances:
38 9 0.02
39 311 0.86
40 41 0.11
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (39 bp):
AATCTGCCCCAGGCTCGAGGTAAAAGATTGGATGATGGT
Found at i:30945593 original size:78 final size:78
Alignment explanation
Indices: 30945387--30945933 Score: 644
Period size: 78 Copynumber: 7.0 Consensus size: 78
30945377 CTAATATATT
* * * * * * * *
30945387 GGATGGTTACAATCTGCCCCAGGCTCGAGGTAAAAGATTGGCTGATGGTAATTTACCCCAGGCTC
1 GGATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTC
* *
30945452 GAGATAAAAGATC
66 GGGGTAAAAGATC
* *
30945465 GGATGACTGCAATCTGCCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCTCAAGCT
1 GGATGGCTGCAATCTG-CCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCT
* *
30945530 CGGGGCAAGAGATC
65 CGGGGTAAAAGATC
* * * * *
30945544 GGATGGCTGCAATTTGCCCCAAGCTCGGGGTATGAGATTGGTTGATGGTGATCTGCCCCTAGCTC
1 GGATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTC
30945609 GGGGTAAAAGATC
66 GGGGTAAAAGATC
* * * *
30945622 GGATGGCTGCACTCTGCCCTAGGCTCGAGGTAAGAGATTGGCTGATGGTGATCTGTCCCAAGCTC
1 GGATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTC
*
30945687 GAGGTAAAAGATC
66 GGGGTAAAAGATC
* ** * * * **
30945700 GGATGGTTATAATCTGCCCTAAGCTCGGGGTAAGAGATTGGTTGATGGTGATCCACCCCAAGCTC
1 GGATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTC
* *
30945765 GAGGTAAAAAATC
66 GGGGTAAAAGATC
* * *
30945778 GGATGGCTGCAATCTGCCCGAGGCTTGGGGTAAGAGATTGGCTGATGGTGATCTACCCCAAGCTC
1 GGATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTC
* *
30945843 AGGATAAAAGATC
66 GGGGTAAAAGATC
** * * * * * * * *
30945856 AAATGGTTGCAATTTACCTCAGGCTCGAGGTAAGAGATTGGCTGATGGTAATTTGCCCCAGGCTC
1 GGATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTC
30945921 GGGGTAAAAGATC
66 GGGGTAAAAGATC
30945934 AGATCTTCAA
Statistics
Matches: 397, Mismatches: 71, Indels: 2
0.84 0.15 0.00
Matches are distributed among these distances:
78 332 0.84
79 65 0.16
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (78 bp):
GGATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTC
GGGGTAAAAGATC
Found at i:30955947 original size:29 final size:28
Alignment explanation
Indices: 30955888--30955947 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
30955878 TTTGAGGTCG
* *
30955888 AAAATGTGACTTTTGGAAATTTGGGGGA
1 AAAATGTGACTTTTGGAAATTCGAGGGA
* * *
30955916 AAAATGGTGATTTTTGGATATTCGAGGTA
1 AAAAT-GTGACTTTTGGAAATTCGAGGGA
30955945 AAA
1 AAA
30955948 TGATAATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.33
Consensus pattern (28 bp):
AAAATGTGACTTTTGGAAATTCGAGGGA
Found at i:30956008 original size:30 final size:30
Alignment explanation
Indices: 30955944--30956016 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 30
30955934 TATTCGAGGT
* * *
30955944 AAAATGATAATTTTGGAAAAGTTTAGGTTT
1 AAAATGATAATTTTGGAAAAATTTAGGGTC
*
30955974 AAAATG-TAATTTTGGGAAAAATTTGGGGTC
1 AAAATGATAATTTT-GGAAAAATTTAGGGTC
*
30956004 AAAAT-ATATTTTT
1 AAAATGATAATTTT
30956017 AAGGAATTCG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 7 0.19
30 29 0.81
ACGTcount: A:0.40, C:0.01, G:0.19, T:0.40
Consensus pattern (30 bp):
AAAATGATAATTTTGGAAAAATTTAGGGTC
Found at i:30957058 original size:4 final size:4
Alignment explanation
Indices: 30957049--30957074 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
30957039 TTCTACTCAT
30957049 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
30957075 ATTATTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:30979311 original size:21 final size:23
Alignment explanation
Indices: 30979281--30979326 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
30979271 AAAATTCAAA
30979281 AAATAATTCAA-GT-TTTGAATT
1 AAATAATTCAATGTATTTGAATT
* *
30979302 AAATAGTTCAATTTATTTGAATT
1 AAATAATTCAATGTATTTGAATT
30979325 AA
1 AA
30979327 TCATGTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
22 1 0.05
23 10 0.48
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.43
Consensus pattern (23 bp):
AAATAATTCAATGTATTTGAATT
Found at i:30980009 original size:15 final size:17
Alignment explanation
Indices: 30979983--30980015 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
30979973 ATTTTATATG
30979983 TTAAATTATTATG-AAT
1 TTAAATTATTATGTAAT
30979999 TTAAATT-TTATGTAAT
1 TTAAATTATTATGTAAT
30980015 T
1 T
30980016 AACAAAGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (17 bp):
TTAAATTATTATGTAAT
Found at i:30983383 original size:28 final size:27
Alignment explanation
Indices: 30983352--30983434 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
30983342 AGTGAAATTT
30983352 TATAAAAATCGTAAAAAATTATAAAATA
1 TATAAAAATCGTAAAAAATTATAAAA-A
* * *
30983380 TATAGAAAT-ATAAAAAAATATAAAAA
1 TATAAAAATCGTAAAAAATTATAAAAA
* * *
30983406 TTTATTAAGTCGTAATAAAATTATAAAAA
1 TATA-AAAATCGTAA-AAAATTATAAAAA
30983435 ATGTTTTATA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
26 4 0.09
27 17 0.39
28 11 0.25
29 12 0.27
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (27 bp):
TATAAAAATCGTAAAAAATTATAAAAA
Found at i:30983397 original size:56 final size:55
Alignment explanation
Indices: 30983328--30983433 Score: 126
Period size: 56 Copynumber: 1.9 Consensus size: 55
30983318 AAAAAGCATA
* * *
30983328 AGAAAATAGAAAAAA-GTGAAATTTTATAAAAATCGTAA-AAAATTATAAAATATAT
1 AGAAAATA-AAAAAATATAAAAATTTAT-AAAATCGTAATAAAATTATAAAATATAT
* *
30983383 AGAAATATAAAAAAATATAAAAATTTATTAAGTCGTAATAAAATTATAAAA
1 AGAAA-ATAAAAAAATATAAAAATTTATAAAATCGTAATAAAATTATAAAA
30983434 AATGTTTTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
55 19 0.44
56 24 0.56
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.28
Consensus pattern (55 bp):
AGAAAATAAAAAAATATAAAAATTTATAAAATCGTAATAAAATTATAAAATATAT
Found at i:30983547 original size:9 final size:9
Alignment explanation
Indices: 30983507--30983547 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
30983497 TTTATAATTT
30983507 TTTTTA-TA
1 TTTTTATTA
30983515 TATTTTATATA
1 T-TTTTAT-TA
30983526 TTTTTATT-
1 TTTTTATTA
30983534 TTTTTATTA
1 TTTTTATTA
30983543 TTTTT
1 TTTTT
30983548 CGTCCATGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 9 0.31
9 11 0.38
10 6 0.21
11 3 0.10
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTTATTA
Found at i:30983676 original size:10 final size:9
Alignment explanation
Indices: 30983663--30983798 Score: 87
Period size: 9 Copynumber: 14.4 Consensus size: 9
30983653 TTTTTATGCA
30983663 TTTTATAAT
1 TTTTATAAT
30983672 CTTTTATAAT
1 -TTTTATAAT
*
30983682 TTTTATAAAA
1 TTTTAT-AAT
*
30983692 TTTTACAAT
1 TTTTATAAT
*
30983701 TTTATATAAA
1 TTT-TATAAT
*
30983711 TTTTCTAAT
1 TTTTATAAT
* *
30983720 TTTTAAAAA
1 TTTTATAAT
* *
30983729 ATTTAAATAT
1 TTTTATA-AT
30983739 TCTTTAT-AT
1 T-TTTATAAT
*
30983748 TTTTATTAAAA
1 TTTTA-T-AAT
*
30983759 TTTAATAAT
1 TTTTATAAT
30983768 TTTTATAACT
1 TTTTATAA-T
*
30983778 TTTT-TTAT
1 TTTTATAAT
30983786 TTTTATAAT
1 TTTTATAAT
30983795 TTTT
1 TTTT
30983799 TGCTGCATGT
Statistics
Matches: 97, Mismatches: 20, Indels: 19
0.71 0.15 0.14
Matches are distributed among these distances:
8 9 0.09
9 49 0.51
10 30 0.31
11 9 0.09
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (9 bp):
TTTTATAAT
Found at i:30983685 original size:19 final size:18
Alignment explanation
Indices: 30983663--30983798 Score: 78
Period size: 19 Copynumber: 7.2 Consensus size: 18
30983653 TTTTTATGCA
*
30983663 TTTTATAATCTTTTATAAT
1 TTTTATAA-ATTTTATAAT
*
30983682 TTTTATAAAATTTTACAAT
1 TTTTAT-AAATTTTATAAT
*
30983701 TTTATATAAATTTTCTAAT
1 TTT-TATAAATTTTATAAT
* * *
30983720 TTTTAAAAAATTTAAATAT
1 TTTTATAAATTTTATA-AT
* *
30983739 TCTTTAT-ATTTTTATTAAAA
1 T-TTTATAAATTTTA-T-AAT
* *
30983759 TTTAATAATTTTTATAACT
1 TTTTATAAATTTTATAA-T
* *
30983778 TTTT-TTATTTTTATAAT
1 TTTTATAAATTTTATAAT
30983795 TTTT
1 TTTT
30983799 TGCTGCATGT
Statistics
Matches: 92, Mismatches: 17, Indels: 18
0.72 0.13 0.14
Matches are distributed among these distances:
17 5 0.05
18 22 0.24
19 46 0.50
20 18 0.20
21 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTATAAATTTTATAAT
Found at i:30983765 original size:28 final size:28
Alignment explanation
Indices: 30983709--30983774 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
30983699 ATTTTATATA
30983709 AATTTTCTA-ATTTTTAAAAAATTTAAAT
1 AATTTT-TATATTTTTAAAAAATTTAAAT
*
30983737 -ATTCTTTATATTTTTATTAAAATTT-AAT
1 AATT-TTTATATTTTTA-AAAAATTTAAAT
30983765 AATTTTTATA
1 AATTTTTATA
30983775 ACTTTTTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
27 5 0.15
28 18 0.55
29 10 0.30
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (28 bp):
AATTTTTATATTTTTAAAAAATTTAAAT
Found at i:30985621 original size:16 final size:17
Alignment explanation
Indices: 30985600--30985639 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
30985590 AAATTTTTTA
30985600 GCTTTTT-CTCAAAAGT
1 GCTTTTTGCTCAAAAGT
30985616 GCTTTTTGGCTCAAAAGT
1 GCTTTTT-GCTCAAAAGT
*
30985634 ACTTTT
1 GCTTTT
30985640 AAAAAGCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.33
18 14 0.67
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.45
Consensus pattern (17 bp):
GCTTTTTGCTCAAAAGT
Found at i:30997247 original size:15 final size:15
Alignment explanation
Indices: 30997229--30997279 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
30997219 ACTGTGTGGG
*
30997229 GATTGACTTGAAGAT
1 GATTGACTTGGAGAT
*
30997244 GATTGAATATGGAG-T
1 GATTGACT-TGGAGAT
30997259 GACTT-ACTTGGAGAT
1 GA-TTGACTTGGAGAT
30997274 GATTGA
1 GATTGA
30997280 GTTTGGGGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
14 7 0.24
15 16 0.55
16 6 0.21
ACGTcount: A:0.31, C:0.06, G:0.29, T:0.33
Consensus pattern (15 bp):
GATTGACTTGGAGAT
Found at i:31002554 original size:29 final size:29
Alignment explanation
Indices: 31002499--31002814 Score: 222
Period size: 29 Copynumber: 10.9 Consensus size: 29
31002489 TTCAACAATC
* **
31002499 ACATTTTGA-CCTCATACTTCTTAAAAATT
1 ACATTTTGACCCTCAAACTT-TCCAAAATT
* * *
31002528 ACATTTTTACCCTCAAACTTTTCAAAAAAT
1 ACATTTTGACCCTCAAAC-TTTCCAAAATT
* *
31002558 ACATTTTGACCCTCGAACTTTCCAAAAATC
1 ACATTTTGACCCTCAAACTTTCC-AAAATT
* **
31002588 ACATATTGA-CCTTGAACTTTCCAAAATT
1 ACATTTTGACCCTCAAACTTTCCAAAATT
* * *
31002616 ATATTTTTACCC-CTAAAC-TTCCAAAAATC
1 ACATTTTGACCCTC-AAACTTTCC-AAAATT
*
31002645 ACATTTTGACCC-CAAACTTTCTAAAATT
1 ACATTTTGACCCTCAAACTTTCCAAAATT
* * *
31002673 ACATTTTTACCCTCGAAC-TTCCAACAATC
1 ACATTTTGACCCTCAAACTTTCCAA-AATT
* *
31002702 ACGTTTTGACCCTCGAACTTTCCAAAATT
1 ACATTTTGACCCTCAAACTTTCCAAAATT
* * * *
31002731 ATATTTTAGCCCCTCGAAC-ATCCAAAATTT
1 ACATTTT-GACCCTCAAACTTTCCAAAA-TT
* *
31002761 ACCATTTTGACCC-CGAAC-ATCCAAAATT
1 A-CATTTTGACCCTCAAACTTTCCAAAATT
*
31002789 ACCATTTT-ACCCTTAAA-TTTCCAAAA
1 A-CATTTTGACCCTCAAACTTTCCAAAA
31002815 ATCATATTTT
Statistics
Matches: 234, Mismatches: 38, Indels: 31
0.77 0.13 0.10
Matches are distributed among these distances:
27 4 0.02
28 59 0.25
29 99 0.42
30 65 0.28
31 7 0.03
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (29 bp):
ACATTTTGACCCTCAAACTTTCCAAAATT
Found at i:31002555 original size:30 final size:29
Alignment explanation
Indices: 31002488--31002844 Score: 219
Period size: 29 Copynumber: 12.3 Consensus size: 29
31002478 GTCCTTGATT
* * *
31002488 TTTCAACAATCACATTTTGA-CCTCATAC
1 TTTCAAAAATTACATTTTGACCCTCAAAC
* *
31002516 TTCTTAAAAATTACATTTTTACCCTCAAAC
1 TT-TCAAAAATTACATTTTGACCCTCAAAC
* *
31002546 TTTTCAAAAAATACATTTTGACCCTCGAAC
1 -TTTCAAAAATTACATTTTGACCCTCAAAC
* * **
31002576 TTTCCAAAAATCACATATTGA-CCTTGAAC
1 TTT-CAAAAATTACATTTTGACCCTCAAAC
* * *
31002605 TTTCCAAAATTATATTTTTACCC-CTAAAC
1 TTTCAAAAATTACATTTTGACCCTC-AAAC
* *
31002634 TTCCAAAAATCACATTTTGACCC-CAAAC
1 TTTCAAAAATTACATTTTGACCCTCAAAC
* * *
31002662 TTTCTAAAATTACATTTTTACCCTCGAAC
1 TTTCAAAAATTACATTTTGACCCTCAAAC
* * * * *
31002691 TTCCAACAATCACGTTTTGACCCTCGAAC
1 TTTCAAAAATTACATTTTGACCCTCAAAC
* * * *
31002720 TTTCCAAAATTATATTTTAGCCCCTCGAAC
1 TTTCAAAAATTACATTTT-GACCCTCAAAC
* * * *
31002750 ATCCAAAATTTACCATTTTGACCC-CGAAC
1 TTTCAAAAATTA-CATTTTGACCCTCAAAC
* * *
31002779 -ATCCAAAATTACCATTTT-ACCCTTAAA-
1 TTTCAAAAATTA-CATTTTGACCCTCAAAC
* * *
31002806 TTTCCAAAAATCATATTTTTGA-CCTCAAAT
1 TTT-CAAAAATTACA-TTTTGACCCTCAAAC
*
31002836 TTTCTAAAA
1 TTTCAAAAA
31002845 GTTCGATGTT
Statistics
Matches: 253, Mismatches: 61, Indels: 29
0.74 0.18 0.08
Matches are distributed among these distances:
27 4 0.02
28 55 0.22
29 117 0.46
30 70 0.28
31 7 0.03
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (29 bp):
TTTCAAAAATTACATTTTGACCCTCAAAC
Found at i:31002639 original size:57 final size:57
Alignment explanation
Indices: 31002521--31002829 Score: 268
Period size: 57 Copynumber: 5.3 Consensus size: 57
31002511 CATACTTCTT
* * * * * *
31002521 AAAAATTACATTTTTACCCTCAAACTTTTCAAAAAATACATTTTGA-CCCTCGAACTTTCC
1 AAAAATCACATTTTGACCC-CGAAC-TTTCCAAAATTACATTTT-ACCCCTCAAAC-TTCC
* ** *
31002581 AAAAATCACATATTGACCTTGAACTTTCCAAAATTATATTTTTACCCCT-AAACTTCC
1 AAAAATCACATTTTGACCCCGAACTTTCCAAAATTACA-TTTTACCCCTCAAACTTCC
* * *
31002638 AAAAATCACATTTTGACCCCAAACTTTCTAAAATTACATTTTTA-CCCTCGAACTTCC
1 AAAAATCACATTTTGACCCCGAACTTTCCAAAATTACA-TTTTACCCCTCAAACTTCC
* * * * *
31002695 AACAATCACGTTTTGACCCTCGAACTTTCCAAAATTATATTTTAGCCCCTCGAACATCC
1 AAAAATCACATTTTGACCC-CGAACTTTCCAAAATTACATTTTA-CCCCTCAAACTTCC
* * * * *
31002754 AAAATTTACCATTTTGACCCCGAAC-ATCCAAAATTACCATTTTA-CCCTTAAATTTCC
1 AAAAATCA-CATTTTGACCCCGAACTTTCCAAAATTA-CATTTTACCCCTCAAACTTCC
*
31002811 AAAAATCATATTTTTGACC
1 AAAAATCACA-TTTTGACC
31002830 TCAAATTTTC
Statistics
Matches: 204, Mismatches: 36, Indels: 21
0.78 0.14 0.08
Matches are distributed among these distances:
56 5 0.02
57 94 0.46
58 41 0.20
59 39 0.19
60 25 0.12
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.34
Consensus pattern (57 bp):
AAAAATCACATTTTGACCCCGAACTTTCCAAAATTACATTTTACCCCTCAAACTTCC
Found at i:31003820 original size:150 final size:151
Alignment explanation
Indices: 31003518--31003823 Score: 569
Period size: 150 Copynumber: 2.0 Consensus size: 151
31003508 TCCTTTCGTT
31003518 TTCAAAATTATTTTATAAATAAACCTTTAAACCCGAGGCAATGTCCTTTTCATGTGGAAATCTCG
1 TTCAAAATTATTTTATAAATAAACCTTTAAACCCGAGGCAATGTCCTTTTCATGTGGAAATCTCG
* *
31003583 AAAACCCATGCCCTAACGTGCTGGGTGTGATTTTCGTATAATTCACACGGTCGAATATCCTCTTT
66 AAAAACCATGCCCTAACGTGCTCGGTGTGATTTTCGTATAATTCACACGGTCGAATATCCTCTTT
31003648 TAAAATCCTTTCAAAATGTTC
131 TAAAATCCTTTCAAAATGTTC
*
31003669 TTCAAAATTATTTTATAAATAAACCTTTAAACCCGGGGCAATGTCCTTTTCATGTGGAAATCTCG
1 TTCAAAATTATTTTATAAATAAACCTTTAAACCCGAGGCAATGTCCTTTTCATGTGGAAATCTCG
*
31003734 AAAAACCATG-CCTAACGTGCTCGGTGTGATTTTCGTATAATTCACGCGGTCGAATATCCTCTTT
66 AAAAACCATGCCCTAACGTGCTCGGTGTGATTTTCGTATAATTCACACGGTCGAATATCCTCTTT
31003798 TAAAATCCTTTCAAAATGTTC
131 TAAAATCCTTTCAAAATGTTC
31003819 TTCAA
1 TTCAA
31003824 TTTCGAAATT
Statistics
Matches: 151, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
150 78 0.52
151 73 0.48
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (151 bp):
TTCAAAATTATTTTATAAATAAACCTTTAAACCCGAGGCAATGTCCTTTTCATGTGGAAATCTCG
AAAAACCATGCCCTAACGTGCTCGGTGTGATTTTCGTATAATTCACACGGTCGAATATCCTCTTT
TAAAATCCTTTCAAAATGTTC
Found at i:31010259 original size:50 final size:50
Alignment explanation
Indices: 31010176--31010679 Score: 472
Period size: 50 Copynumber: 10.2 Consensus size: 50
31010166 AGGATCGCGA
* * * * * *
31010176 CCGCGACGACGAATCCGGCACCTTAGAAGATGTGATGGGAAAGGTTAAGG
1 CCGCAACGGCGAACCCGGTACCTAAGAAGATGTGATGGGAAAGGTTGAGG
*
31010226 CCGCAACGGCGAACCCGATACCTAAGAAGATGTGATGGGAAAGGTTGAGG
1 CCGCAACGGCGAACCCGGTACCTAAGAAGATGTGATGGGAAAGGTTGAGG
* * * *
31010276 CCACAACGGCGAACCCGGTACC-ATGAAGA-GATGAAGGG-AAGCATTGAGG
1 CCGCAACGGCGAACCCGGTACCTAAGAAGATG-TGATGGGAAAG-GTTGAGG
* * ** *
31010325 CCGCAACGGCGAATCCGATACCT--GAAGATACGAAGGGAAAGGTTGAGG
1 CCGCAACGGCGAACCCGGTACCTAAGAAGATGTGATGGGAAAGGTTGAGG
** * * *
31010373 CCGCAATAGCGAACCCGGTACCTGAGAAGACGTGATGGGAAAGGTTGAAG
1 CCGCAACGGCGAACCCGGTACCTAAGAAGATGTGATGGGAAAGGTTGAGG
* * * * * *
31010423 TCGCAACGACGAACCCGGTACC-AAGAGGA-GATGA-AGGAAATGATTGAAG
1 CCGCAACGGCGAACCCGGTACCTAAGAAGATG-TGATGGGAAA-GGTTGAGG
* * * * *
31010472 CCACGATGGCGAATCCGGTACCTTAGAAGATGTGATGGGAAAGGTTGAGG
1 CCGCAACGGCGAACCCGGTACCTAAGAAGATGTGATGGGAAAGGTTGAGG
* * ** *
31010522 CTGCAACGACGAACCCGGTACC-ACA-AAGA-GACAAAGGGAAAGGTTGAGG
1 CCGCAACGGCGAACCCGGTACCTA-AGAAGATG-TGATGGGAAAGGTTGAGG
* *
31010571 CCGCAATGGCGAACTCGGTACCTAAGAAGATGTGATGGGAAAGGTTGAGG
1 CCGCAACGGCGAACCCGGTACCTAAGAAGATGTGATGGGAAAGGTTGAGG
* * * * **
31010621 CTGCAACGGCGAACCCGGTACCTTAGAAGATATAAAAGGAAAGGTTGAGG
1 CCGCAACGGCGAACCCGGTACCTAAGAAGATGTGATGGGAAAGGTTGAGG
31010671 CCGCAACGG
1 CCGCAACGG
31010680 TAAACCTAGC
Statistics
Matches: 365, Mismatches: 72, Indels: 34
0.77 0.15 0.07
Matches are distributed among these distances:
48 47 0.13
49 109 0.30
50 202 0.55
51 7 0.02
ACGTcount: A:0.33, C:0.20, G:0.33, T:0.14
Consensus pattern (50 bp):
CCGCAACGGCGAACCCGGTACCTAAGAAGATGTGATGGGAAAGGTTGAGG
Found at i:31010395 original size:147 final size:146
Alignment explanation
Indices: 31010176--31010676 Score: 526
Period size: 147 Copynumber: 3.4 Consensus size: 146
31010166 AGGATCGCGA
* * * * * * *
31010176 CCGCGACGACGAATCCGGCACCTTAGAAGATGTGATGGGAAAGGTTAAGGCCGCAACGGCGAACC
1 CCGCAACGGCGAATCCGGTACCTTAGAAGATATGAAGGGAAAGGTTGAGGCCGCAA-AGCGAACC
* * *
31010241 CGATACCTAAGAAGATGTGATGGGAAAGGTTGAGGCCACAACGGCGAACCCGGTACCATGAAGAG
65 CGGTACCTAAGAAGA-GTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCAAGAAGAG
31010306 ATGAAGGGAAGCATTGAGG
129 ATGAAGGGAAG-ATTGAGG
* *
31010325 CCGCAACGGCGAATCCGATACC-T-GAAGATACGAAGGGAAAGGTTGAGGCCGCAATAGCGAACC
1 CCGCAACGGCGAATCCGGTACCTTAGAAGATATGAAGGGAAAGGTTGAGGCCGCAA-AGCGAACC
* * * * *
31010388 CGGTACCTGAGAAGACGTGATGGGAAAGGTTGAAGTCGCAACGACGAACCCGGTACCAAGAGGAG
65 CGGTACCTAAGAAGA-GTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCAAGAAGAG
* *
31010453 ATGAAGGAAATGATTGAAG
129 ATGAAGGGAA-GATTGAGG
* * * * * * *
31010472 CCACGATGGCGAATCCGGTACCTTAGAAGATGTGATGGGAAAGGTTGAGGCTGCAACGACGAACC
1 CCGCAACGGCGAATCCGGTACCTTAGAAGATATGAAGGGAAAGGTTGAGGCCGCAAAG-CGAACC
** * * *
31010537 CGGTACC-ACA-AAGAGACAAAGGGAAAGGTTGAGGCCGCAATGGCGAACTCGGTACCTAAGAAG
65 CGGTACCTA-AGAAGAG-TGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACC-AAGAAG
* *
31010600 ATG-TGATGGGAAAGGTTGAGG
127 A-GATGAAGGG-AAGATTGAGG
* * * *
31010621 CTGCAACGGCGAACCCGGTACCTTAGAAGATATAAAAGGAAAGGTTGAGGCCGCAA
1 CCGCAACGGCGAATCCGGTACCTTAGAAGATATGAAGGGAAAGGTTGAGGCCGCAA
31010677 CGGTAAACCT
Statistics
Matches: 289, Mismatches: 54, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
147 124 0.43
148 40 0.14
149 122 0.42
150 3 0.01
ACGTcount: A:0.33, C:0.20, G:0.33, T:0.14
Consensus pattern (146 bp):
CCGCAACGGCGAATCCGGTACCTTAGAAGATATGAAGGGAAAGGTTGAGGCCGCAAAGCGAACCC
GGTACCTAAGAAGAGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCAAGAAGAGAT
GAAGGGAAGATTGAGG
Found at i:31010704 original size:99 final size:99
Alignment explanation
Indices: 31010185--31010676 Score: 521
Period size: 99 Copynumber: 5.0 Consensus size: 99
31010175 ACCGCGACGA
* * * * *
31010185 CGAATCCGGCACCTTAGAAGATGTGATGGGAAAGGTTAAGGCCGCAACGGCGAACCCGATACCTA
1 CGAACCCGGTACCTTAGAAGATGTGATGGGAAAGGTTGAGGCTGCAACGGCGAACCCGGTACC-A
* * * * *
31010250 AGAAGATGTGATGGGAAAGGTTGAGGCCACAACGG
65 AGAAGATATAAAGGGAAAGGTTGAGGCCGCAATGG
* * * * * *
31010285 CGAACCCGGTACCAT-GAAGA-GATGAAGGG-AAGCATTGAGGCCGCAACGGCGAATCCGATACC
1 CGAACCCGGTACCTTAGAAGATG-TGATGGGAAAG-GTTGAGGCTGCAACGGCGAACCCGGTACC
* ** *
31010347 -TGAAGATACGAAGGGAAAGGTTGAGGCCGCAATAG
64 AAGAAGATATAAAGGGAAAGGTTGAGGCCGCAATGG
* * * *
31010382 CGAACCCGGTACCTGAGAAGACGTGATGGGAAAGGTTGAAG-TCGCAACGACGAACCCGGTACCA
1 CGAACCCGGTACCTTAGAAGATGTGATGGGAAAGGTTGAGGCT-GCAACGGCGAACCCGGTACCA
* * * * * * *
31010446 AGAGGAGATGAA-GGAAATGATTGAAGCCACGATGG
65 AGAAGATATAAAGGGAAA-GGTTGAGGCCGCAATGG
* *
31010481 CGAATCCGGTACCTTAGAAGATGTGATGGGAAAGGTTGAGGCTGCAACGACGAACCCGGTACCAC
1 CGAACCCGGTACCTTAGAAGATGTGATGGGAAAGGTTGAGGCTGCAACGGCGAACCCGGTACCA-
* *
31010546 A-AAGAGACAAAGGGAAAGGTTGAGGCCGCAATGG
65 AGAAGATATAAAGGGAAAGGTTGAGGCCGCAATGG
* * *
31010580 CGAACTCGGTACCTAAGAAGATGTGATGGGAAAGGTTGAGGCTGCAACGGCGAACCCGGTACCTT
1 CGAACCCGGTACCTTAGAAGATGTGATGGGAAAGGTTGAGGCTGCAACGGCGAACCCGGTACC-A
*
31010645 AGAAGATATAAAAGGAAAGGTTGAGGCCGCAA
65 AGAAGATATAAAGGGAAAGGTTGAGGCCGCAA
31010677 CGGTAAACCT
Statistics
Matches: 328, Mismatches: 51, Indels: 26
0.81 0.13 0.06
Matches are distributed among these distances:
97 41 0.12
98 42 0.13
99 199 0.61
100 46 0.14
ACGTcount: A:0.34, C:0.19, G:0.33, T:0.14
Consensus pattern (99 bp):
CGAACCCGGTACCTTAGAAGATGTGATGGGAAAGGTTGAGGCTGCAACGGCGAACCCGGTACCAA
GAAGATATAAAGGGAAAGGTTGAGGCCGCAATGG
Found at i:31011105 original size:7 final size:7
Alignment explanation
Indices: 31011093--31011124 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
31011083 AATTGAACCC
31011093 AATTTTA
1 AATTTTA
31011100 AATTTTA
1 AATTTTA
31011107 AATTTTA
1 AATTTTA
31011114 AATTTTA
1 AATTTTA
31011121 AATT
1 AATT
31011125 ATTTTAAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AATTTTA
Found at i:31011179 original size:17 final size:17
Alignment explanation
Indices: 31011137--31011182 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
31011127 TTTAAGTTTA
*
31011137 AATTTAAACTTATTTTG
1 AATTTAAATTTATTTTG
*
31011154 AGTTTAAATTTATTTTG
1 AATTTAAATTTATTTTG
31011171 AATTTAAATTTA
1 AATTTAAATTTA
31011183 AAATAAAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (17 bp):
AATTTAAATTTATTTTG
Found at i:31011184 original size:23 final size:22
Alignment explanation
Indices: 31011101--31011165 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 22
31011091 CCAATTTTAA
*
31011101 ATTTTAAATTTTAAATTTTAAATT
1 ATTTT-AAGTTTAAA-TTTAAATT
31011125 ATTTTAAGTTTAAATTTAAACTT
1 ATTTTAAGTTTAAATTTAAA-TT
*
31011148 ATTTTGAGTTTAAATTTA
1 ATTTTAAGTTTAAATTTA
31011166 TTTTGAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
22 6 0.16
23 27 0.71
24 5 0.13
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (22 bp):
ATTTTAAGTTTAAATTTAAATT
Found at i:31011186 original size:7 final size:6
Alignment explanation
Indices: 31011096--31011184 Score: 51
Period size: 6 Copynumber: 15.0 Consensus size: 6
31011086 TGAACCCAAT
* *
31011096 TTTAAA TTTTAAA TTTTAAA TTTTAAA -TT-AT TTTAAG TTTAAA TTTAAA
1 TTTAAA -TTTAAA -TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * * *
31011145 CTT-AT TTTGAG TTTAAA TTT-AT TTTGAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
31011185 ATAAAAGTTC
Statistics
Matches: 66, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
4 1 0.02
5 11 0.17
6 34 0.52
7 20 0.30
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:31011816 original size:9 final size:9
Alignment explanation
Indices: 31011802--31011853 Score: 59
Period size: 9 Copynumber: 5.4 Consensus size: 9
31011792 TTCAAAACAT
31011802 AATATATTA
1 AATATATTA
31011811 AATATATTA
1 AATATATTA
*
31011820 AATGTATAATA
1 AA--TATATTA
31011831 AATGATATTA
1 AAT-ATATTA
*
31011841 AAAATATTA
1 AATATATTA
31011850 AATA
1 AATA
31011854 AAAAATAAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
9 21 0.58
10 7 0.19
11 8 0.22
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (9 bp):
AATATATTA
Found at i:31011840 original size:21 final size:20
Alignment explanation
Indices: 31011804--31011842 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31011794 CAAAACATAA
*
31011804 TATATTAAATATATTAAATG
1 TATAATAAATATATTAAATG
31011824 TATAATAAATGATATTAAA
1 TATAATAAAT-ATATTAAA
31011843 AATATTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (20 bp):
TATAATAAATATATTAAATG
Found at i:31011861 original size:30 final size:30
Alignment explanation
Indices: 31011805--31011862 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
31011795 AAAACATAAT
* ** *
31011805 ATATTAAATATATTAAATGTATAATAAATG
1 ATATTAAAAATATTAAATAAAAAATAAATG
31011835 ATATTAAAAATATTAAATAAAAAATAAA
1 ATATTAAAAATATTAAATAAAAAATAAA
31011863 GAAAAATTCG
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:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (30 bp):
ATATTAAAAATATTAAATAAAAAATAAATG
Found at i:31013023 original size:60 final size:58
Alignment explanation
Indices: 31012957--31013206 Score: 274
Period size: 60 Copynumber: 4.2 Consensus size: 58
31012947 GTACTTCTTA
* * *
31012957 AAAATTACA-TTTTTACCACTAAACTTTTTAAAAATTACATTTTGACCCCCAAATTTTCC
1 AAAATTACATTTTTTACC-CTAAAC-TTCTAAAAATCACATTTTGACCCCCAAACTTTCC
31013016 TAAAATTACATTTTTTACCCTTAAACTTCTAAAAATCACATTTTGACCCCTCAAACTTTCC
1 -AAAATTACATTTTTTACCC-TAAACTTCTAAAAATCACATTTTGACCCC-CAAACTTTCC
* *
31013077 AAAATTACATTTTTTACCCCTAAACTTCCAAAAATCACATTTTGACCCTCAAACTTTCC
1 AAAATTACATTTTTTA-CCCTAAACTTCTAAAAATCACATTTTGACCCCCAAACTTTCC
* * * * * * *
31013136 AAAACTATA-TTTTTACCCCAGAACATCCAAAAATTACCATTTT-ACCCTCAAA-TTTCC
1 AAAATTACATTTTTTACCCTA-AACTTCTAAAAATCA-CATTTTGACCCCCAAACTTTCC
*
31013193 AAAAATCACATTTT
1 -AAAATTACATTTT
31013207 CGACCTCAAA
Statistics
Matches: 169, Mismatches: 13, Indels: 17
0.85 0.07 0.09
Matches are distributed among these distances:
57 9 0.05
58 34 0.20
59 26 0.15
60 75 0.44
61 25 0.15
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.36
Consensus pattern (58 bp):
AAAATTACATTTTTTACCCTAAACTTCTAAAAATCACATTTTGACCCCCAAACTTTCC
Found at i:31013136 original size:30 final size:30
Alignment explanation
Indices: 31012956--31013296 Score: 235
Period size: 30 Copynumber: 11.5 Consensus size: 30
31012946 CGTACTTCTT
* **
31012956 AAAAATTACATTTTTACCACT-AAACTTTTT
1 AAAAATTACATTTTGACC-CTCAAACTTTCC
* *
31012986 AAAAATTACATTTTGACCCCCAAATTTTCC
1 AAAAATTACATTTTGACCCTCAAACTTTCC
* * * *
31013016 TAAAATTACATTTTTTACCCTTAAAC-TTCT
1 AAAAATTACA-TTTTGACCCTCAAACTTTCC
*
31013046 AAAAATCACATTTTGACCCCTCAAACTTTCC
1 AAAAATTACATTTTGA-CCCTCAAACTTTCC
*
31013077 -AAAATTACATTTTTTACCC-CTAAAC-TTCC
1 AAAAATTACA-TTTTGACCCTC-AAACTTTCC
*
31013106 AAAAATCACATTTTGACCCTCAAACTTTCC
1 AAAAATTACATTTTGACCCTCAAACTTTCC
* * * *
31013136 -AAAACTATATTTTTACCC-CAGAAC-ATCC
1 AAAAATTACATTTTGACCCTCA-AACTTTCC
31013164 AAAAATTACCATTTT-ACCCTCAAA-TTTCC
1 AAAAATTA-CATTTTGACCCTCAAACTTTCC
* *
31013193 AAAAATCACATTTTCGA-CCTCAAATTTTCC
1 AAAAATTACATTTT-GACCCTCAAACTTTCC
* * * * *
31013223 AAAAGTT-CGATGTTAATCCT-AAATTTTCC
1 AAAAATTAC-ATTTTGACCCTCAAACTTTCC
* *
31013252 AAAAATTTCAATTTTGATCCCT-AAA-TTCCTC
1 AAAAATTAC-ATTTTGA-CCCTCAAACTTTC-C
*
31013283 GAAAATTACATTTT
1 AAAAATTACATTTT
31013297 TATCCCGAAT
Statistics
Matches: 248, Mismatches: 41, Indels: 44
0.74 0.12 0.13
Matches are distributed among these distances:
28 11 0.04
29 86 0.35
30 118 0.48
31 33 0.13
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (30 bp):
AAAAATTACATTTTGACCCTCAAACTTTCC
Found at i:31013153 original size:29 final size:29
Alignment explanation
Indices: 31012956--31013226 Score: 200
Period size: 29 Copynumber: 9.1 Consensus size: 29
31012946 CGTACTTCTT
**
31012956 AAAAATTACATTTTTACCACT-AAACTTTTT
1 AAAAA-TACATTTTTACC-CTCAAACTTTCC
* * *
31012986 AAAAATTACATTTTGACCCCCAAATTTTCC
1 AAAAA-TACATTTTTACCCTCAAACTTTCC
* * *
31013016 TAAAATTACATTTTTTACCCTTAAAC-TTCT
1 -AAAAATACA-TTTTTACCCTCAAACTTTCC
*
31013046 AAAAATCACATTTTGACCCCTCAAACTTTCC
1 AAAAAT-ACATTTTTA-CCCTCAAACTTTCC
*
31013077 AAAATTACATTTTTTACCC-CTAAAC-TTCC
1 AAAAATACA-TTTTTACCCTC-AAACTTTCC
*
31013106 AAAAATCACATTTTGACCCTCAAACTTTCC
1 AAAAAT-ACATTTTTACCCTCAAACTTTCC
* * *
31013136 AAAACTATATTTTTACCC-CAGAAC-ATCC
1 AAAAATACATTTTTACCCTCA-AACTTTCC
31013164 AAAAATTACCA-TTTTACCCTCAAA-TTTCC
1 AAAAA-TA-CATTTTTACCCTCAAACTTTCC
* *
31013193 AAAAATCACATTTTCGA-CCTCAAATTTTCC
1 AAAAAT-ACATTTT-TACCCTCAAACTTTCC
31013223 AAAA
1 AAAA
31013227 GTTCGATGTT
Statistics
Matches: 194, Mismatches: 27, Indels: 40
0.74 0.10 0.15
Matches are distributed among these distances:
28 12 0.06
29 77 0.40
30 77 0.40
31 28 0.14
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.35
Consensus pattern (29 bp):
AAAAATACATTTTTACCCTCAAACTTTCC
Found at i:31014674 original size:19 final size:20
Alignment explanation
Indices: 31014645--31014695 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
31014635 AAATATAATT
*
31014645 TTTGAAATTTTT-ATAAATAC
1 TTTG-AATTTTTGACAAATAC
* *
31014665 TTTGAATTTTTGACAATTAT
1 TTTGAATTTTTGACAAATAC
31014685 TTTGAATTTTT
1 TTTGAATTTTT
31014696 TTGCAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 7 0.26
20 20 0.74
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.57
Consensus pattern (20 bp):
TTTGAATTTTTGACAAATAC
Found at i:31022095 original size:24 final size:22
Alignment explanation
Indices: 31022040--31022104 Score: 62
Period size: 24 Copynumber: 2.9 Consensus size: 22
31022030 TTGAATATAG
*
31022040 TTTT-TTAT-TTAAATTAATTT
1 TTTTATTATATTAATTTAATTT
*
31022060 TTTTATCCATATTAATTTAATTT
1 TTTTAT-TATATTAATTTAATTT
*
31022083 TGTTATATTATATTTATTTAAT
1 T-TT-TATTATATTAATTTAAT
31022105 AAATAAATAG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 4 0.11
21 1 0.03
22 2 0.06
23 12 0.33
24 14 0.39
25 3 0.08
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTTATTATATTAATTTAATTT
Found at i:31022427 original size:22 final size:23
Alignment explanation
Indices: 31022396--31022464 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 23
31022386 TTTAAACATT
*
31022396 AATATGTTTTAAAATTTTAAA-A
1 AATATTTTTTAAAATTTTAAATA
**
31022418 AATATTTTTTAGTATTTTAAATA
1 AATATTTTTTAAAATTTTAAATA
*
31022441 ATTTATTTTTTAAAATATTTAAAT
1 A-ATATTTTTTAAAAT-TTTAAAT
31022465 TTATTTAATG
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
22 18 0.47
23 2 0.05
24 11 0.29
25 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (23 bp):
AATATTTTTTAAAATTTTAAATA
Found at i:31022459 original size:26 final size:28
Alignment explanation
Indices: 31022428--31022487 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 28
31022418 AATATTTTTT
* *
31022428 AGTATTTTAAA-TAATTTATTTTTTAAA
1 AGTATTTTAAATTAATTTAATGTTTAAA
*
31022455 A-TA-TTTAAATTTATTTAATGTTTAAA
1 AGTATTTTAAATTAATTTAATGTTTAAA
31022481 AGTATTT
1 AGTATTT
31022488 ATTACATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
25 6 0.22
26 16 0.59
27 3 0.11
28 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (28 bp):
AGTATTTTAAATTAATTTAATGTTTAAA
Found at i:31022525 original size:21 final size:20
Alignment explanation
Indices: 31022497--31022536 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
31022487 TATTACATTT
31022497 TTATAATTAAAAAATATATA
1 TTATAATTAAAAAATATATA
**
31022517 TTATCAATTTCAAAATATAT
1 TTAT-AATTAAAAAATATAT
31022537 GTTACTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (20 bp):
TTATAATTAAAAAATATATA
Found at i:31025702 original size:23 final size:23
Alignment explanation
Indices: 31025667--31025826 Score: 230
Period size: 23 Copynumber: 7.0 Consensus size: 23
31025657 ATCTTAATTC
31025667 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * * *
31025690 TTTAATCATAAATGATATTAATA
1 TTTAAGCACAAATCACATTAATA
31025713 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
31025736 TTTAAACGCAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
31025759 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
31025782 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
31025805 TTTAAGTATAAATCACATTAAT
1 TTTAAGCACAAATCACATTAAT
31025827 TGTAACAATC
Statistics
Matches: 119, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 119 1.00
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.34
Consensus pattern (23 bp):
TTTAAGCACAAATCACATTAATA
Found at i:31027972 original size:21 final size:21
Alignment explanation
Indices: 31027946--31027999 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
31027936 AGAGTTTTTA
*
31027946 GTATCGGTAGTAG-TATGACTT
1 GTATCGGTAGAAGTTAT-ACTT
31027967 GTATCGGTAGAAGTTATACTT
1 GTATCGGTAGAAGTTATACTT
31027988 GTATCGGTAGAA
1 GTATCGGTAGAA
31028000 CTAGTACAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 28 0.90
22 3 0.10
ACGTcount: A:0.28, C:0.09, G:0.28, T:0.35
Consensus pattern (21 bp):
GTATCGGTAGAAGTTATACTT
Found at i:31031331 original size:23 final size:23
Alignment explanation
Indices: 31031292--31031676 Score: 536
Period size: 23 Copynumber: 16.7 Consensus size: 23
31031282 TTTGGGTGTT
* *
31031292 ACATTAATACTTGAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
*
31031315 ATATTAATATTTAAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
*
31031338 ACATTAACATTTAAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
31031361 ACATTAATATTTAAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
* *
31031384 ACATTAATATTTAATCATAAATC
1 ACATTAATATTTAAGCACAAATC
*
31031407 ACATTAATATTTGAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
* *
31031430 ATATTAATATTTAAGAACAAATC
1 ACATTAATATTTAAGCACAAATC
* * *
31031453 ACATTGATATTTGAGCATAAATC
1 ACATTAATATTTAAGCACAAATC
* *
31031476 ATATTAATATTTAAGCATAAATC
1 ACATTAATATTTAAGCACAAATC
*
31031499 ACATTAATACTTAAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
*
31031522 ACATTAATATTTAAGCATAAATC
1 ACATTAATATTTAAGCACAAATC
*
31031545 ACATTAATATTTGAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
*
31031568 ATATTAATATTTAAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
* * *
31031591 TCATTAATATTTGAGCACAAACC
1 ACATTAATATTTAAGCACAAATC
* *
31031614 AAATTAATATTTAAGCATAAATC
1 ACATTAATATTTAAGCACAAATC
* * *
31031637 GCATAAATACTTAAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
31031660 ACATTAATATTTAAGCA
1 ACATTAATATTTAAGCA
31031677 TAGATATAAG
Statistics
Matches: 314, Mismatches: 48, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 314 1.00
ACGTcount: A:0.46, C:0.16, G:0.06, T:0.32
Consensus pattern (23 bp):
ACATTAATATTTAAGCACAAATC
Found at i:31035501 original size:46 final size:46
Alignment explanation
Indices: 31035434--31035525 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
31035424 GTTTGTTTGG
*
31035434 ATGGTTCTTCTTCCTTCAATATTATTCCCTAGTTCTCTTTCTTAAA
1 ATGGTTCTTCTTCCTTCAATATTATTCCCTAATTCTCTTTCTTAAA
*
31035480 ATGGTTCTTCTTCCTTCAATATTATTCTCTAATTCTCTTTCTTAAA
1 ATGGTTCTTCTTCCTTCAATATTATTCCCTAATTCTCTTTCTTAAA
31035526 CTTAAATGTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (46 bp):
ATGGTTCTTCTTCCTTCAATATTATTCCCTAATTCTCTTTCTTAAA
Found at i:31045243 original size:23 final size:23
Alignment explanation
Indices: 31045217--31045260 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
31045207 TATTTTGGAC
31045217 AATAAAAAATAAATATTGAATTG
1 AATAAAAAATAAATATTGAATTG
** *
31045240 AATAAATTATAAGTATTGAAT
1 AATAAAAAATAAATATTGAAT
31045261 AAAAATTCAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (23 bp):
AATAAAAAATAAATATTGAATTG
Found at i:31046094 original size:13 final size:13
Alignment explanation
Indices: 31046076--31046100 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31046066 GTTACAAAAT
31046076 AAAAATTAAAGCA
1 AAAAATTAAAGCA
31046089 AAAAATTAAAGC
1 AAAAATTAAAGC
31046101 TATAGGTAAC
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:0.68, C:0.08, G:0.08, T:0.16
Consensus pattern (13 bp):
AAAAATTAAAGCA
Found at i:31049550 original size:31 final size:30
Alignment explanation
Indices: 31049499--31049556 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
31049489 ATTTCTACCC
*
31049499 ATAACCTTCAATTCTCAAATTATAAAATCA
1 ATAACCTTCAATTCTCAAATTAAAAAATCA
*
31049529 ATAACCTCTCAA-TCTTTAAATTAAAAAA
1 ATAACCT-TCAATTC-TCAAATTAAAAAA
31049557 AAACACATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 9 0.38
31 15 0.62
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.33
Consensus pattern (30 bp):
ATAACCTTCAATTCTCAAATTAAAAAATCA
Found at i:31050460 original size:18 final size:18
Alignment explanation
Indices: 31050437--31050479 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
31050427 ATTCAAAGTG
31050437 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
31050455 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
31050473 TAATTAA
1 TAATTAA
31050480 AAAAATATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:31057898 original size:37 final size:37
Alignment explanation
Indices: 31057856--31057932 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
31057846 CATAGAATAA
31057856 TAACCCCAACTTAAATTTGTCTATTGCTATATAATCT
1 TAACCCCAACTTAAATTTGTCTATTGCTATATAATCT
31057893 TAACCCCAACTTAAATTTGTCTATTGCTATATAATCT
1 TAACCCCAACTTAAATTTGTCTATTGCTATATAATCT
31057930 TAA
1 TAA
31057933 AAAAAATTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.40
Consensus pattern (37 bp):
TAACCCCAACTTAAATTTGTCTATTGCTATATAATCT
Found at i:31061150 original size:22 final size:23
Alignment explanation
Indices: 31061112--31061179 Score: 79
Period size: 22 Copynumber: 3.1 Consensus size: 23
31061102 TCTCCGTTAT
*
31061112 TTTA-CACGTATAGTGCTCTCCG
1 TTTAGCACGTATAGTGCTCTCCA
*
31061134 TTTAGCACGTTTA-TGCTCTCCA
1 TTTAGCACGTATAGTGCTCTCCA
* *
31061156 TTTAGCACCT-TGGTGCTCTCCA
1 TTTAGCACGTATAGTGCTCTCCA
31061178 TT
1 TT
31061180 CTTTAGTGCA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.03
22 32 0.80
23 7 0.17
ACGTcount: A:0.16, C:0.28, G:0.16, T:0.40
Consensus pattern (23 bp):
TTTAGCACGTATAGTGCTCTCCA
Found at i:31061691 original size:15 final size:15
Alignment explanation
Indices: 31061673--31061703 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
31061663 TTGTAATGGA
31061673 ACATTTTGGTCTCAT
1 ACATTTTGGTCTCAT
31061688 ACATTTTGGTCTCAT
1 ACATTTTGGTCTCAT
31061703 A
1 A
31061704 AGTTACCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (15 bp):
ACATTTTGGTCTCAT
Found at i:31067926 original size:48 final size:48
Alignment explanation
Indices: 31067874--31067973 Score: 200
Period size: 48 Copynumber: 2.1 Consensus size: 48
31067864 TAGAAGTATT
31067874 TTGAATTGAGTCATCTCTAATCTTTGCATATTTCCAGTAAGTTTGTTA
1 TTGAATTGAGTCATCTCTAATCTTTGCATATTTCCAGTAAGTTTGTTA
31067922 TTGAATTGAGTCATCTCTAATCTTTGCATATTTCCAGTAAGTTTGTTA
1 TTGAATTGAGTCATCTCTAATCTTTGCATATTTCCAGTAAGTTTGTTA
31067970 TTGA
1 TTGA
31067974 TTGTACATGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.25, C:0.14, G:0.15, T:0.46
Consensus pattern (48 bp):
TTGAATTGAGTCATCTCTAATCTTTGCATATTTCCAGTAAGTTTGTTA
Found at i:31070703 original size:15 final size:15
Alignment explanation
Indices: 31070683--31070711 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
31070673 AGGGCATCTC
31070683 ATTTCTGCTTGATAT
1 ATTTCTGCTTGATAT
31070698 ATTTCTGCTTGATA
1 ATTTCTGCTTGATA
31070712 AGCATAAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.52
Consensus pattern (15 bp):
ATTTCTGCTTGATAT
Found at i:31076418 original size:7 final size:7
Alignment explanation
Indices: 31076406--31076431 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
31076396 AGAGAAGAAA
31076406 GATGAGG
1 GATGAGG
31076413 GATGAGG
1 GATGAGG
31076420 GATGAGG
1 GATGAGG
31076427 GATGA
1 GATGA
31076432 TTAGAAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.54, T:0.15
Consensus pattern (7 bp):
GATGAGG
Found at i:31077735 original size:25 final size:25
Alignment explanation
Indices: 31077696--31077808 Score: 145
Period size: 25 Copynumber: 4.5 Consensus size: 25
31077686 TAGATTAACA
* *
31077696 CTCTTACAAGTCAGATAGAATATCG
1 CTCTTACAAGCCAGACAGAATATCG
* *
31077721 CTCTTACAATCCAGACAGAGTATCG
1 CTCTTACAAGCCAGACAGAATATCG
*
31077746 CTCTTACGAGCCAGACAGAATATCG
1 CTCTTACAAGCCAGACAGAATATCG
* * *
31077771 CTCTTACGAGCCAAACAGATTATCG
1 CTCTTACAAGCCAGACAGAATATCG
*
31077796 CTCTTATAAGCCA
1 CTCTTACAAGCCA
31077809 AACTTCAGAG
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 77 1.00
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.25
Consensus pattern (25 bp):
CTCTTACAAGCCAGACAGAATATCG
Found at i:31079176 original size:3 final size:3
Alignment explanation
Indices: 31079170--31079230 Score: 77
Period size: 3 Copynumber: 20.0 Consensus size: 3
31079160 TTTTTTTCAC
* * *
31079170 ATT ATT ATT ATT ATT ACT ACT ATT ATT ATT ATT ATT ATT ATC ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
31079218 ATA ATTT ATT ATT
1 ATT A-TT ATT ATT
31079231 TAAAACATCA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
3 49 0.96
4 2 0.04
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:31095272 original size:18 final size:16
Alignment explanation
Indices: 31095246--31095293 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
31095236 TTTTAGCTTT
*
31095246 TTTTATTCTCCATTCTC
1 TTTTCTTCTCC-TTCTC
*
31095263 TTTTGCTTCTCCTTCTG
1 TTTT-CTTCTCCTTCTC
31095280 TTTTCTTC-CCTTCT
1 TTTTCTTCTCCTTCT
31095294 TCATTTCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 6 0.21
16 4 0.14
17 12 0.43
18 6 0.21
ACGTcount: A:0.04, C:0.31, G:0.04, T:0.60
Consensus pattern (16 bp):
TTTTCTTCTCCTTCTC
Found at i:31095293 original size:15 final size:17
Alignment explanation
Indices: 31095251--31095293 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
31095241 GCTTTTTTTA
31095251 TTCTCCATTCTCTTTTGC
1 TTCTCC-TTCTCTTTTGC
*
31095269 TTCTCCTTCTGTTTT-C
1 TTCTCCTTCTCTTTTGC
31095285 TTC-CCTTCT
1 TTCTCCTTCT
31095294 TCATTTCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 6 0.25
16 4 0.17
17 8 0.33
18 6 0.25
ACGTcount: A:0.02, C:0.35, G:0.05, T:0.58
Consensus pattern (17 bp):
TTCTCCTTCTCTTTTGC
Found at i:31095505 original size:19 final size:19
Alignment explanation
Indices: 31095483--31095520 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
31095473 AAGCAAAAGT
31095483 GAATGAAAATTAAAAAAAA
1 GAATGAAAATTAAAAAAAA
*
31095502 GAATGGAAATTAAAAAAAA
1 GAATGAAAATTAAAAAAAA
31095521 CATAAAAGAA
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:0.71, C:0.00, G:0.13, T:0.16
Consensus pattern (19 bp):
GAATGAAAATTAAAAAAAA
Found at i:31096689 original size:39 final size:40
Alignment explanation
Indices: 31096628--31096705 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 40
31096618 ATTTAAGTAA
* **
31096628 TTATCTATTTACACGGATCGAAGCTGAGATAGAAAACTAG
1 TTATCTATTTACACGGAACGAAGAAGAGATAGAAAACTAG
31096668 TTAT-TATTTACACGGAACGAAGAAGAGATAGAAAACTA
1 TTATCTATTTACACGGAACGAAGAAGAGATAGAAAACTA
31096706 ATTTATACAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 31 0.89
40 4 0.11
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (40 bp):
TTATCTATTTACACGGAACGAAGAAGAGATAGAAAACTAG
Found at i:31123616 original size:19 final size:19
Alignment explanation
Indices: 31123570--31123635 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 19
31123560 TATAAAATAA
*
31123570 TCAAAATAATTTTCAAAATT
1 TCAAAATAATTTT-AAAAAT
* *
31123590 TGAAAATAATTTTTAAAAT
1 TCAAAATAATTTTAAAAAT
31123609 TCAAAAT-ATTTTAAAAAAT
1 TCAAAATAATTTT-AAAAAT
31123628 TCTAAAAT
1 TC-AAAAT
31123636 TTTTATTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
18 5 0.13
19 17 0.44
20 17 0.44
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (19 bp):
TCAAAATAATTTTAAAAAT
Found at i:31123639 original size:19 final size:19
Alignment explanation
Indices: 31123553--31123640 Score: 67
Period size: 20 Copynumber: 4.6 Consensus size: 19
31123543 TCTCTCTTAA
*
31123553 CAAAA-ATTATAAAATAA-T
1 CAAAATATTTTAAAA-AATT
* *
31123571 CAAAATAATTTTCAAAATTT
1 CAAAAT-ATTTTAAAAAATT
* *
31123591 GAAAATAATTTT-TAAAATT
1 CAAAAT-ATTTTAAAAAATT
31123610 CAAAATATTTTAAAAAATT
1 CAAAATATTTTAAAAAATT
31123629 CTAAAAT-TTTTA
1 C-AAAATATTTTA
31123641 TTTTTTTAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
18 10 0.18
19 23 0.40
20 24 0.42
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.39
Consensus pattern (19 bp):
CAAAATATTTTAAAAAATT
Found at i:31127754 original size:14 final size:14
Alignment explanation
Indices: 31127731--31127762 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
31127721 TATATCTATT
*
31127731 AATAACATTATCAA
1 AATAAAATTATCAA
31127745 AATAAAATTATCAA
1 AATAAAATTATCAA
31127759 AATA
1 AATA
31127763 TATTAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.28
Consensus pattern (14 bp):
AATAAAATTATCAA
Found at i:31131079 original size:24 final size:24
Alignment explanation
Indices: 31131037--31131120 Score: 134
Period size: 24 Copynumber: 3.5 Consensus size: 24
31131027 ATTTAGCCCA
31131037 TACGAGCCCA-AATGGTTAGCTCT
1 TACGAGCCCAGAATGGTTAGCTCT
*
31131060 TACGAGCCCAGAATGGTTAGATCT
1 TACGAGCCCAGAATGGTTAGCTCT
* *
31131084 TACGAGTCCAGAATGATTAGCTCT
1 TACGAGCCCAGAATGGTTAGCTCT
31131108 TACGAGCCCAGAA
1 TACGAGCCCAGAA
31131121 CCAGAATAAC
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
23 10 0.18
24 45 0.82
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.24
Consensus pattern (24 bp):
TACGAGCCCAGAATGGTTAGCTCT
Found at i:31131879 original size:3 final size:3
Alignment explanation
Indices: 31131871--31131912 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
31131861 TATTAGCCGT
31131871 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
31131913 ATTAGAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:31138565 original size:16 final size:15
Alignment explanation
Indices: 31138524--31138590 Score: 61
Period size: 16 Copynumber: 4.5 Consensus size: 15
31138514 ATATACTTTG
*
31138524 AAATTAAATTTATTT
1 AAATTTAATTTATTT
31138539 AAATTT-A---ATTT
1 AAATTTAATTTATTT
*
31138550 AAGTTTGAATTTATTT
1 AAATTT-AATTTATTT
31138566 AAATTTAATATTATTGT
1 AAATTTAAT-TTATT-T
31138583 AAATTTAA
1 AAATTTAA
31138591 ATGTTCATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
11 9 0.21
13 1 0.02
14 1 0.02
15 8 0.19
16 14 0.33
17 9 0.21
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (15 bp):
AAATTTAATTTATTT
Found at i:31141654 original size:30 final size:29
Alignment explanation
Indices: 31141593--31141749 Score: 138
Period size: 30 Copynumber: 5.4 Consensus size: 29
31141583 AACTATCGAG
* * * *
31141593 AAATTATA-TTTTAACCCCGAAACATCTAA
1 AAATTACATTTTTACCCCCG-AACTTCCAA
*
31141622 AAATTACATTTTTACCCCTCGAACTTTCAA
1 AAATTACATTTTTACCCC-CGAACTTCCAA
* * ** *
31141652 AAATTATATTTTTTACCTCAAAACTTCTAA
1 AAATTACA-TTTTTACCCCCGAACTTCCAA
* *
31141682 ATATTACATTTTTGCCCCCGAACTTCCAA
1 AAATTACATTTTTACCCCCGAACTTCCAA
* *
31141711 AAATTCCA-TTTTAACCCCGAACTTCCAA
1 AAATTACATTTTTACCCCCGAACTTCCAA
*
31141739 AAATTTCATTT
1 AAATTACATTT
31141750 ATGATCCCGA
Statistics
Matches: 101, Mismatches: 23, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
28 25 0.25
29 31 0.31
30 34 0.34
31 11 0.11
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.36
Consensus pattern (29 bp):
AAATTACATTTTTACCCCCGAACTTCCAA
Found at i:31141704 original size:59 final size:59
Alignment explanation
Indices: 31141593--31141728 Score: 175
Period size: 60 Copynumber: 2.3 Consensus size: 59
31141583 AACTATCGAG
* *
31141593 AAATTATATTTTAACCCCGAAACATCTAAAAATTACATTTTTACCCCTCGAACTTTCAA
1 AAATTATATTTTAACCCCAAAACATCTAAAAATTACATTTTTACCCCTCGAACTTCCAA
* * * * *
31141652 AAATTATATTTTTTACCTCAAAACTTCTAAATATTACATTTTTGCCCC-CGAACTTCCAA
1 AAATTATA-TTTTAACCCCAAAACATCTAAAAATTACATTTTTACCCCTCGAACTTCCAA
**
31141711 AAATTCCATTTTAACCCC
1 AAATTATATTTTAACCCC
31141729 GAACTTCCAA
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
58 8 0.12
59 24 0.37
60 33 0.51
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (59 bp):
AAATTATATTTTAACCCCAAAACATCTAAAAATTACATTTTTACCCCTCGAACTTCCAA
Found at i:31141731 original size:28 final size:28
Alignment explanation
Indices: 31141593--31141808 Score: 137
Period size: 29 Copynumber: 7.4 Consensus size: 28
31141583 AACTATCGAG
* * *
31141593 AAATTATATTTTAACCCCGAAACATCTAA
1 AAATTACATTTTAACCCCG-AACTTCCAA
* *
31141622 AAATTACATTTTTACCCCTCGAACTTTCAA
1 AAATTACA-TTTTAACCC-CGAACTTCCAA
* * ** *
31141652 AAATTATATTTTTTACCTCAAAACTTCTAA
1 AAATTACA-TTTTAACC-CCGAACTTCCAA
* **
31141682 ATATTACATTTTTGCCCCCGAACTTCCAA
1 AAATTACA-TTTTAACCCCGAACTTCCAA
*
31141711 AAATTCCATTTTAACCCCGAACTTCCAA
1 AAATTACATTTTAACCCCGAACTTCCAA
* * * * *
31141739 AAATTTCATTTATGATCCCGATTCTT-CTA
1 AAATTACATTT-TAACCCCGA-ACTTCCAA
* * *
31141768 AAATTACAATTTAACCCCTAAATATCCAA
1 AAATTACATTTTAACCCCGAACT-TCCAA
*
31141797 AAATTCCATTTT
1 AAATTACATTTT
31141809 TGATTCTGAT
Statistics
Matches: 142, Mismatches: 38, Indels: 14
0.73 0.20 0.07
Matches are distributed among these distances:
27 1 0.01
28 35 0.25
29 52 0.37
30 51 0.36
31 3 0.02
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (28 bp):
AAATTACATTTTAACCCCGAACTTCCAA
Found at i:31141759 original size:57 final size:58
Alignment explanation
Indices: 31141698--31141844 Score: 136
Period size: 58 Copynumber: 2.5 Consensus size: 58
31141688 CATTTTTGCC
* * * *
31141698 CCCGA-ACTTCCAAAAATTCCATTTTAACCCCGAACT-TCCAAAAATTTCATTTATGAT
1 CCCGATACTT-CAAAAATTACAATTTAACCCCGAAATATCCAAAAATTCCATTTATGAT
* * * *
31141755 CCCGATTCTTCTAAAATTACAATTTAACCCCTAAATATCCAAAAATTCCATTTTTGAT
1 CCCGATACTTCAAAAATTACAATTTAACCCCGAAATATCCAAAAATTCCATTTATGAT
* * * * * *
31141813 TCTGATTCTTCTAAAATTTACCATTTTACCCC
1 CCCGATACTTC-AAAAATTACAATTTAACCCC
31141845 CATATGTCCG
Statistics
Matches: 73, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
57 26 0.36
58 31 0.42
59 16 0.22
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (58 bp):
CCCGATACTTCAAAAATTACAATTTAACCCCGAAATATCCAAAAATTCCATTTATGAT
Found at i:31141866 original size:59 final size:59
Alignment explanation
Indices: 31141716--31141948 Score: 220
Period size: 59 Copynumber: 4.0 Consensus size: 59
31141706 TCCAAAAATT
* * * * *
31141716 CCATTTTAACCCCGAACT-TCCAAAAATTTCATTTATGATCCCGATTCTTCTAAAA-TTA
1 CCATTTT-ACCCCCAAATGTCCAAAAATTCCATTTTTGATCCTGATTCTTCTAAAATTTA
* * * * *
31141774 CAATTTAACCCCTAAATATCCAAAAATTCCATTTTTGATTCTGATTCTTCTAAAATTTA
1 CCATTTTACCCCCAAATGTCCAAAAATTCCATTTTTGATCCTGATTCTTCTAAAATTTA
* * * * * *
31141833 CCATTTTACCCCCATATGTCCGAAAATTTCATTTTTAATCCTGATTTTTCTAAAAATTA
1 CCATTTTACCCCCAAATGTCCAAAAATTCCATTTTTGATCCTGATTCTTCTAAAATTTA
* * *** * *
31141892 TCGTTTTACCCCCGGGTGTCCAAAAATTCCATTTTTTAT-CTCGATTTTTCTAAAATT
1 CCATTTTACCCCCAAATGTCCAAAAATTCCATTTTTGATCCT-GATTCTTCTAAAATT
31141949 ATCGTTTTAC
Statistics
Matches: 144, Mismatches: 28, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
57 8 0.06
58 40 0.28
59 96 0.67
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.41
Consensus pattern (59 bp):
CCATTTTACCCCCAAATGTCCAAAAATTCCATTTTTGATCCTGATTCTTCTAAAATTTA
Found at i:31141997 original size:58 final size:57
Alignment explanation
Indices: 31141734--31141989 Score: 174
Period size: 59 Copynumber: 4.4 Consensus size: 57
31141724 ACCCCGAACT
* * * * * *** *
31141734 TCCAAAAATTTCATTTATGATCCCGATTCTTCTAAAATTA-CAATTTAACCCCTAAATA
1 TCCAAAAATTTCATTT-TTAACCCGATTTTTCTAAAATTATC-GTTTTACCCCCGGATG
* ** * * * * **
31141792 TCCAAAAATTCCATTTTTGATTCTGATTCTTCTAAAATTTACCATTTTACCCCCATATG
1 TCCAAAAATTTCATTTTT-AACCCGATTTTTCTAAAA-TTATCGTTTTACCCCCGGATG
* * *
31141851 TCCGAAAATTTCATTTTTAATCCTGATTTTTCTAAAAATTATCGTTTTACCCCCGGGTG
1 TCCAAAAATTTCATTTTTAA-CCCGATTTTTCT-AAAATTATCGTTTTACCCCCGGATG
* * * **
31141910 TCCAAAAATTCCATTTTTTATCTCGATTTTTCTAAAATTATCGTTTTACCCTTGGAT-
1 TCCAAAAATTTCA-TTTTTAACCCGATTTTTCTAAAATTATCGTTTTACCCCCGGATG
***
31141967 TTTTAAAATTTCATTTTTAACCC
1 TCCAAAAATTTCATTTTTAACCC
31141990 CAAATTTTCC
Statistics
Matches: 160, Mismatches: 32, Indels: 14
0.78 0.16 0.07
Matches are distributed among these distances:
56 8 0.05
57 10 0.06
58 53 0.33
59 78 0.49
60 11 0.07
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.43
Consensus pattern (57 bp):
TCCAAAAATTTCATTTTTAACCCGATTTTTCTAAAATTATCGTTTTACCCCCGGATG
Found at i:31142061 original size:28 final size:29
Alignment explanation
Indices: 31141999--31142061 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
31141989 CCAAATTTTC
* *
31141999 CCAAAATTACCATTTTGCTTCTCGGGAGT
1 CCAAAATTACCATTTTACTCCTCGGGAGT
* *
31142028 CTAAAATTACTATTTTAC-CCTCGGGTA-T
1 CCAAAATTACCATTTTACTCCTCGGG-AGT
31142056 CCAAAA
1 CCAAAA
31142062 AGTCTCGTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
28 12 0.43
29 16 0.57
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (29 bp):
CCAAAATTACCATTTTACTCCTCGGGAGT
Found at i:31147572 original size:14 final size:14
Alignment explanation
Indices: 31147545--31147584 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
31147535 CAATGAATAA
31147545 AAGAAAAGAAAAAAG
1 AAGAAAA-AAAAAAG
31147560 AAGAAAAAAAAAAG
1 AAGAAAAAAAAAAG
*
31147574 ATGAAAAAAAA
1 AAGAAAAAAAA
31147585 TAAAAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 17 0.71
15 7 0.29
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (14 bp):
AAGAAAAAAAAAAG
Found at i:31147595 original size:15 final size:15
Alignment explanation
Indices: 31147540--31147597 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 15
31147530 GGATTCAATG
31147540 AATAAAAGAAAAGAAAA
1 AATAAAA-AAAA-AAAA
*
31147557 AAGAAGAAAAAAAAAA
1 AATAA-AAAAAAAAAA
* *
31147573 GATGAAAAAAAATAAA
1 AAT-AAAAAAAAAAAA
31147589 AATAAAAAA
1 AATAAAAAA
31147598 GGGAAAGGTC
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
15 6 0.18
16 16 0.47
17 10 0.29
18 2 0.06
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (15 bp):
AATAAAAAAAAAAAA
Found at i:31147603 original size:24 final size:26
Alignment explanation
Indices: 31147553--31147603 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
31147543 AAAAGAAAAG
*
31147553 AAAAAAGAAGAAAAAAAAAAGATGAA
1 AAAAAAGAAGAAAAAAAAAAGAGGAA
* *
31147579 AAAAAATAA-AAATAAAAAAG-GGAA
1 AAAAAAGAAGAAAAAAAAAAGAGGAA
31147603 A
1 A
31147604 GGTCGAGGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 4 0.18
25 10 0.45
26 8 0.36
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (26 bp):
AAAAAAGAAGAAAAAAAAAAGAGGAA
Found at i:31149202 original size:92 final size:92
Alignment explanation
Indices: 31149045--31149570 Score: 759
Period size: 92 Copynumber: 5.5 Consensus size: 92
31149035 TCAGATCAAA
* *
31149045 ATAGCAAGTCTTTATCTCTCTAAAGTTGTAGTAAGAGCAAGATGAAACTTCAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
31149110 ATCCTCTTGAAGTTGCAGTAAAGTTGG
66 ATCCTCTTGAAGTTGCAGTAAAGTTGG
*
31149137 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGGAAGATGAAGCTTCAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
31149202 ATCCTCTTGAAGTTGCAGTAAAGTTGG
66 ATCCTCTTGAAGTTGCAGTAAAGTTGG
31149229 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
31149294 ATCCTCTTGAAGTTGCAGTAAAGTTGG
66 ATCCTCTTGAAGTTGCAGTAAAGTTGG
*
31149321 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTTAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
31149386 ATCCTCTTGAAGTTGCAGTAAAGTTGG
66 ATCCTCTTGAAGTTGCAGTAAAGTTGG
* ** * * *
31149413 ATAGCAAGTCTATTGGATAGCAAGTCT-TTATCTCTCTGAAGT-TGTAGTAAGAGGAAGATGAAG
1 ATAGCAAGTCT-TT--AT--C---TCTCTGA--AGT-TGTAGTAAG-AG-CA-A----GATGAAG
31149476 CTTCAAACATCAATTCCTATCCTCTTGAAGTTGCAGTAAAGTTGG
48 CTTCAAACATCAATTCCTATCCTCTTGAAGTTGCAGTAAAGTTGG
* * *
31149521 ATAGCAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAACAAGATAAAGCTT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTT
31149571 TGGCACCAAA
Statistics
Matches: 394, Mismatches: 20, Indels: 40
0.87 0.04 0.09
Matches are distributed among these distances:
92 291 0.74
93 2 0.01
95 2 0.01
96 1 0.00
97 2 0.01
98 6 0.02
99 4 0.01
100 6 0.02
101 4 0.01
102 7 0.02
103 2 0.01
104 1 0.00
105 2 0.01
107 2 0.01
108 62 0.16
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (92 bp):
ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
ATCCTCTTGAAGTTGCAGTAAAGTTGG
Found at i:31149354 original size:184 final size:189
Alignment explanation
Indices: 31149045--31149570 Score: 846
Period size: 184 Copynumber: 2.8 Consensus size: 189
31149035 TCAGATCAAA
* *
31149045 ATAGCAAGTCTTTATCTCTCTAAAGTTGTAGTAAGAGCAAGATGAAACTTCAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
*
31149110 ATCCTCTTGAAGTTGCAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGG
66 ATCCTCTTGAAGTTGCAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGC
31149175 AAGATGAAGCTTCAAACATCAATTCCTATCCTCTTGAAGTTGC-A-G-TA-AAG-TTGG
131 AAGATGAAGCTTCAAACATCAATTCCTATCCTCTTGAAGTTGCAAGGATACAAGTTTGG
31149229 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
31149294 ATCCTCTTGAAGTTGCAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGC
66 ATCCTCTTGAAGTTGCAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGC
*
31149359 AAGATGAAGCTTTAAACATCAATTCCTATCCTCTTGAAGTTGCAGTAAAGTTGGATAGCAAGTCT
131 AAGATGAAGCTTCAAACATCAATTCCTATCCTCTTGAAGTTGC----AA---GGATA-CAAG--T
31149424 ATTGG
186 -TTGG
*
31149429 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGGAAGATGAAGCTTCAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
* *
31149494 ATCCTCTTGAAGTTGCAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAAC
66 ATCCTCTTGAAGTTGCAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGC
*
31149559 AAGATAAAGCTT
131 AAGATGAAGCTT
31149571 TGGCACCAAA
Statistics
Matches: 318, Mismatches: 8, Indels: 16
0.93 0.02 0.05
Matches are distributed among these distances:
184 169 0.53
189 1 0.00
193 1 0.00
194 2 0.01
196 3 0.01
200 142 0.45
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (189 bp):
ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
ATCCTCTTGAAGTTGCAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGC
AAGATGAAGCTTCAAACATCAATTCCTATCCTCTTGAAGTTGCAAGGATACAAGTTTGG
Found at i:31149430 original size:16 final size:16
Alignment explanation
Indices: 31149409--31149439 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
31149399 TGCAGTAAAG
31149409 TTGGATAGCAAGTCTA
1 TTGGATAGCAAGTCTA
31149425 TTGGATAGCAAGTCT
1 TTGGATAGCAAGTCT
31149440 TTATCTCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (16 bp):
TTGGATAGCAAGTCTA
Found at i:31149506 original size:108 final size:108
Alignment explanation
Indices: 31149317--31149531 Score: 412
Period size: 108 Copynumber: 2.0 Consensus size: 108
31149307 TGCAGTAAAG
*
31149317 TTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTTAAACATCAAT
1 TTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAAT
31149382 TCCTATCCTCTTGAAGTTGCAGTAAAGTTGGATAGCAAGTCTA
66 TCCTATCCTCTTGAAGTTGCAGTAAAGTTGGATAGCAAGTCTA
*
31149425 TTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGGAAGATGAAGCTTCAAACATCAAT
1 TTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAAT
31149490 TCCTATCCTCTTGAAGTTGCAGTAAAGTTGGATAGCAAGTCT
66 TCCTATCCTCTTGAAGTTGCAGTAAAGTTGGATAGCAAGTCT
31149532 TTATCTCTCT
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
108 105 1.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (108 bp):
TTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAAT
TCCTATCCTCTTGAAGTTGCAGTAAAGTTGGATAGCAAGTCTA
Found at i:31149571 original size:200 final size:199
Alignment explanation
Indices: 31149225--31149603 Score: 659
Period size: 200 Copynumber: 1.9 Consensus size: 199
31149215 TGCAGTAAAG
31149225 TTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAAT
1 TTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAAT
*
31149290 TCCTATCCTCTTGAAGTTGCAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAA
66 TCCTATCCTCTTGAAGTTGCAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGCAGTAA
* * * * *
31149355 GAGCAAGATGAAGCTTTAAACATCAATTCCTATCCTCTTGAAGTTGCAGTAAAGTTGGATAGCAA
131 GAACAAGATAAAGCTTT-AACACCAAATCCTATCCTCATGAAGTTGCAGTAAAGTTGGATAGCAA
31149420 GTCTA
195 GTCTA
*
31149425 TTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGGAAGATGAAGCTTCAAACATCAAT
1 TTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAAT
31149490 TCCTATCCTCTTGAAGTTGCAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGCAGTAA
66 TCCTATCCTCTTGAAGTTGCAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGCAGTAA
** *
31149555 GAACAAGATAAAGCTTTGGCACCAAATCCTATCTTCATGAAGTTGCAGT
131 GAACAAGATAAAGCTTTAACACCAAATCCTATCCTCATGAAGTTGCAGT
31149604 GGAGTTTGGA
Statistics
Matches: 169, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
199 26 0.15
200 143 0.85
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (199 bp):
TTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAAT
TCCTATCCTCTTGAAGTTGCAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGCAGTAA
GAACAAGATAAAGCTTTAACACCAAATCCTATCCTCATGAAGTTGCAGTAAAGTTGGATAGCAAG
TCTA
Found at i:31149784 original size:38 final size:40
Alignment explanation
Indices: 31149712--31149815 Score: 133
Period size: 38 Copynumber: 2.7 Consensus size: 40
31149702 CTGTTAGTCA
*
31149712 ATCTCTTACCCCGAGTCTAAGGCAGA-TAACAGCCATTCG
1 ATCTCTTACCCCGAGCCTAAGGCAGATTAACAGCCATTCG
* *
31149751 ATCTCTTACCCCGAGCCT-AGGCAGATTGA-AGCCATTTG
1 ATCTCTTACCCCGAGCCTAAGGCAGATTAACAGCCATTCG
* **
31149789 ATCTCTTCCCCCGAGCCTGGGGCAGAT
1 ATCTCTTACCCCGAGCCTAAGGCAGAT
31149816 CACCATCAAC
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
38 32 0.55
39 26 0.45
ACGTcount: A:0.23, C:0.32, G:0.21, T:0.24
Consensus pattern (40 bp):
ATCTCTTACCCCGAGCCTAAGGCAGATTAACAGCCATTCG
Found at i:31150235 original size:11 final size:11
Alignment explanation
Indices: 31150219--31150302 Score: 84
Period size: 11 Copynumber: 7.5 Consensus size: 11
31150209 TACTTTGAAA
*
31150219 TTAAATTTATT
1 TTAAATTTAAT
31150230 TTAAATTTTAAT
1 TTAAA-TTTAAT
31150242 TT-AATTTATAT
1 TTAAATTTA-AT
*
31150253 TTATATTT-AT
1 TTAAATTTAAT
31150263 TTAAATTTAAT
1 TTAAATTTAAT
*
31150274 TTAAGTTTAAAT
1 TTAAATTT-AAT
31150286 TT-AATTTAAAT
1 TTAAATTT-AAT
31150297 TTAAAT
1 TTAAAT
31150303 ATCTATTAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
10 13 0.21
11 30 0.48
12 19 0.31
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:31150284 original size:17 final size:16
Alignment explanation
Indices: 31150205--31150302 Score: 108
Period size: 17 Copynumber: 5.9 Consensus size: 16
31150195 ACCATTTAAA
* *
31150205 AATTTACTTTGAAATTA
1 AATTTAATTT-AAATTT
*
31150222 AATTTATTTTAAATTTT
1 AATTTAATTTAAA-TTT
*
31150239 AATTTAATTTATATTT
1 AATTTAATTTAAATTT
31150255 ATATTT-ATTTAAATTT
1 A-ATTTAATTTAAATTT
31150271 AATTTAAGTTTAAATTT
1 AATTTAA-TTTAAATTT
31150288 AATTTAAATTTAAAT
1 AATTT-AATTTAAAT
31150303 ATCTATTAAT
Statistics
Matches: 71, Mismatches: 5, Indels: 10
0.83 0.06 0.12
Matches are distributed among these distances:
15 4 0.06
16 18 0.25
17 47 0.66
18 2 0.03
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (16 bp):
AATTTAATTTAAATTT
Found at i:31150300 original size:6 final size:6
Alignment explanation
Indices: 31150219--31150302 Score: 81
Period size: 6 Copynumber: 15.0 Consensus size: 6
31150209 TACTTTGAAA
* * * *
31150219 TTAAAT TT-ATT TTAAAT TTTAAT TT-AAT TTATAT TTATAT TT--AT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
31150263 TTAAAT TT-AAT TTAAGT TTAAAT TT-AAT TTAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
31150303 ATCTATTAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
4 4 0.06
5 19 0.29
6 43 0.65
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (6 bp):
TTAAAT
Found at i:31153305 original size:29 final size:29
Alignment explanation
Indices: 31153262--31153478 Score: 214
Period size: 29 Copynumber: 7.5 Consensus size: 29
31153252 GGAGGTCCCT
* * *
31153262 AAACTATCCAAAAATTATATTTTAACCTCG
1 AAACT-TCTAAAAATTACATTTTAACCCCG
*
31153292 AAACTTCTAAAAATTACATTTT-TCCCC-
1 AAACTTCTAAAAATTACATTTTAACCCCG
* *
31153319 AAACTT-TCAAAAATTATATTTTTGACCCCG
1 AAACTTCT-AAAAATTACA-TTTTAACCCCG
* * *
31153349 AAACTT-TGGAAAATTACATTTTTACCCCT
1 AAACTTCT-AAAAATTACATTTTAACCCCG
*
31153378 AAACTTTCT-AAAATTACATTTTAACCCCA
1 AAAC-TTCTAAAAATTACATTTTAACCCCG
*
31153407 AAACTTCTAAAAATTACATTTTTACCCCG
1 AAACTTCTAAAAATTACATTTTAACCCCG
*
31153436 -AACTTCTAAAAATTCCATTTTTAACCCCG
1 AAACTTCTAAAAATTACA-TTTTAACCCCG
*
31153465 -AACTTCAAAAAATT
1 AAACTTCTAAAAATT
31153479 TTATTTTTGC
Statistics
Matches: 161, Mismatches: 18, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
26 1 0.01
27 15 0.09
28 27 0.17
29 95 0.59
30 22 0.14
31 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.35
Consensus pattern (29 bp):
AAACTTCTAAAAATTACATTTTAACCCCG
Found at i:31153486 original size:57 final size:58
Alignment explanation
Indices: 31153262--31153478 Score: 250
Period size: 57 Copynumber: 3.8 Consensus size: 58
31153252 GGAGGTCCCT
* * *
31153262 AAACTATCCAAAAATTATA-TTTTAACCTCGAAACTTCTAAAAATTACATTTTT-CCCC
1 AAACT-TCTAAAAATTACATTTTTAACCCCGAAACTTCTAAAAATTACATTTTTACCCC
* * *
31153319 AAACTT-TCAAAAATTATATTTTTGACCCCGAAACTT-TGGAAAATTACATTTTTACCCC
1 AAACTTCT-AAAAATTACATTTTTAACCCCGAAACTTCT-AAAAATTACATTTTTACCCC
*
31153377 TAAACTTTCT-AAAATTACA-TTTTAACCCCAAAACTTCTAAAAATTACATTTTTACCCC
1 -AAAC-TTCTAAAAATTACATTTTTAACCCCGAAACTTCTAAAAATTACATTTTTACCCC
* * *
31153435 GAACTTCTAAAAATTCCATTTTTAACCCCG-AACTTCAAAAAATT
1 AAACTTCTAAAAATTACATTTTTAACCCCGAAACTTCTAAAAATT
31153479 TTATTTTTGC
Statistics
Matches: 138, Mismatches: 12, Indels: 20
0.81 0.07 0.12
Matches are distributed among these distances:
56 16 0.12
57 58 0.42
58 48 0.35
59 13 0.09
60 2 0.01
61 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.35
Consensus pattern (58 bp):
AAACTTCTAAAAATTACATTTTTAACCCCGAAACTTCTAAAAATTACATTTTTACCCC
Found at i:31155164 original size:24 final size:24
Alignment explanation
Indices: 31155127--31155173 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
31155117 AGTTGGATCC
*
31155127 AAATTCAATTCTAAAAAAATAATTA
1 AAATTCAAATCT-AAAAAATAATTA
*
31155152 AAATT-AAATCTAAACAATAATT
1 AAATTCAAATCTAAAAAATAATT
31155174 TCCTAATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 5 0.25
25 5 0.25
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.32
Consensus pattern (24 bp):
AAATTCAAATCTAAAAAATAATTA
Found at i:31163070 original size:2 final size:2
Alignment explanation
Indices: 31163063--31163110 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
31163053 AACTAGACAA
31163063 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31163105 AT AT AT
1 AT AT AT
31163111 TGAAAATAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31165502 original size:16 final size:16
Alignment explanation
Indices: 31165482--31165520 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
31165472 TAAAATAAAT
31165482 TATTATAATTACGTTAA
1 TATTATAATTA-GTTAA
*
31165499 -ATTATATTTAGTTAA
1 TATTATAATTAGTTAA
31165514 TATTATA
1 TATTATA
31165521 CTTTTATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (16 bp):
TATTATAATTAGTTAA
Found at i:31189293 original size:42 final size:42
Alignment explanation
Indices: 31189246--31189479 Score: 260
Period size: 42 Copynumber: 5.5 Consensus size: 42
31189236 TCTTATGCTC
* *
31189246 TATCGAGTCATAAGTCTTCCTTTAATCATATTCTCATTCTCA
1 TATCGAGACATGAGTCTTCCTTTAATCATATTCTCATTCTCA
31189288 TATCGAGACATGAGTCTTCCTTTAATCATAATT-TCATTCTCA
1 TATCGAGACATGAGTCTTCCTTTAATCAT-ATTCTCATTCTCA
* * * *
31189330 TCTCGAGACATGAGTTTTCCTTTAATCATAATCTCATTCTTA
1 TATCGAGACATGAGTCTTCCTTTAATCATATTCTCATTCTCA
* * *
31189372 TCTCGAGACATGAGTCTTCCTTTAATCATATTTTCATGT-ACA
1 TATCGAGACATGAGTCTTCCTTTAATCATATTCTCAT-TCTCA
* * * * *
31189414 TTTCGAGTCACGAGTCTTCCATTTATAT-AAATTCTCATGCTCA
1 TATCGAGACATGAGTCTTCC-TTTA-ATCATATTCTCATTCTCA
*
31189457 -ACCCGAGACATGAGTCTTCCTTT
1 TA-TCGAGACATGAGTCTTCCTTT
31189480 TTATACATCA
Statistics
Matches: 163, Mismatches: 22, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
41 2 0.01
42 126 0.77
43 33 0.20
44 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.11, T:0.40
Consensus pattern (42 bp):
TATCGAGACATGAGTCTTCCTTTAATCATATTCTCATTCTCA
Found at i:31189389 original size:84 final size:84
Alignment explanation
Indices: 31189248--31189479 Score: 290
Period size: 84 Copynumber: 2.8 Consensus size: 84
31189238 TTATGCTCTA
* * *
31189248 TCGAGTCATAAGTCTTCCTTTAATCATATTCTCATTCTCATATCGAGACATGAGTCTTCCTTTAA
1 TCGAGTCATGAGTCTTCCTTTAATCATAATCTCATTCTCATCTCGAGACATGAGTCTTCCTTTAA
*
31189313 TCATAATTTCAT-TCTCATC
66 TCATAATTTCATGT-ACATC
* * *
31189332 TCGAGACATGAGTTTTCCTTTAATCATAATCTCATTCTTATCTCGAGACATGAGTCTTCCTTTAA
1 TCGAGTCATGAGTCTTCCTTTAATCATAATCTCATTCTCATCTCGAGACATGAGTCTTCCTTTAA
* *
31189397 TCATATTTTCATGTACATT
66 TCATAATTTCATGTACATC
* * * *
31189416 TCGAGTCACGAGTCTTCCATTT-AT-ATAAATTCTCATGCTCAACCCGAGACATGAGTCTTCCTT
1 TCGAGTCATGAGTCTTCC-TTTAATCAT-AA-TCTCATTCTCATCTCGAGACATGAGTCTTCCTT
31189479 T
63 T
31189480 TTATACATCA
Statistics
Matches: 128, Mismatches: 16, Indels: 7
0.85 0.11 0.05
Matches are distributed among these distances:
83 2 0.02
84 92 0.72
85 34 0.27
ACGTcount: A:0.26, C:0.23, G:0.11, T:0.40
Consensus pattern (84 bp):
TCGAGTCATGAGTCTTCCTTTAATCATAATCTCATTCTCATCTCGAGACATGAGTCTTCCTTTAA
TCATAATTTCATGTACATC
Found at i:31190305 original size:21 final size:20
Alignment explanation
Indices: 31190281--31190324 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
31190271 ACTTTCATCA
* *
31190281 TTAAGCTTTAATTAACCCTTT
1 TTAAGC-TTAATTAAACCTAT
*
31190302 TTAATCTTAATTAAACCTAT
1 TTAAGCTTAATTAAACCTAT
31190322 TTA
1 TTA
31190325 TACTTAGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.34, C:0.16, G:0.02, T:0.48
Consensus pattern (20 bp):
TTAAGCTTAATTAAACCTAT
Found at i:31208406 original size:42 final size:42
Alignment explanation
Indices: 31208357--31208521 Score: 224
Period size: 42 Copynumber: 3.9 Consensus size: 42
31208347 TATCGAGCCC
* *
31208357 TAAGTCTTTCTTTAATCATATTCTCATTCTCATAC-CGAGACA
1 TAAGTCTTCCTTTAATCATAATCTCATTCTCAT-CTCGAGACA
31208399 TAAGTCTTCCTTTAATCATAATCTCATTCTCATCTCGAGACA
1 TAAGTCTTCCTTTAATCATAATCTCATTCTCATCTCGAGACA
* *
31208441 TGAGTCTTCCTTTAATCATAATCTCATTCTCATCTCGAGATA
1 TAAGTCTTCCTTTAATCATAATCTCATTCTCATCTCGAGACA
* * * * * *
31208483 TGAGTGTTCCTTTAATCATATTTTCATGCTCATTTCGAG
1 TAAGTCTTCCTTTAATCATAATCTCATTCTCATCTCGAG
31208522 TCACGAGTAT
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
41 1 0.01
42 112 0.99
ACGTcount: A:0.26, C:0.23, G:0.10, T:0.41
Consensus pattern (42 bp):
TAAGTCTTCCTTTAATCATAATCTCATTCTCATCTCGAGACA
Found at i:31209406 original size:21 final size:20
Alignment explanation
Indices: 31209382--31209425 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
31209372 ACTTTCATCA
* *
31209382 TTAAGCTTTAATTAACCCTTT
1 TTAAGC-TTAATTAAACCTAT
*
31209403 TTAATCTTAATTAAACCTAT
1 TTAAGCTTAATTAAACCTAT
31209423 TTA
1 TTA
31209426 TACTTAGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.34, C:0.16, G:0.02, T:0.48
Consensus pattern (20 bp):
TTAAGCTTAATTAAACCTAT
Found at i:31217354 original size:41 final size:41
Alignment explanation
Indices: 31217297--31217378 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
31217287 AAGTCAAAAT
*
31217297 TATATAGGCTTATTTAGCACATTTTTACTTAGAGTTTGTGC
1 TATATAGGCTTATTTAGCACATTTTTACTTAGAATTTGTGC
*
31217338 TATATAGGTTTATTTAGCACATTTTTACTTAGAATTTGTGC
1 TATATAGGCTTATTTAGCACATTTTTACTTAGAATTTGTGC
31217379 AAATTCCGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.48
Consensus pattern (41 bp):
TATATAGGCTTATTTAGCACATTTTTACTTAGAATTTGTGC
Found at i:31217785 original size:208 final size:208
Alignment explanation
Indices: 31217427--31217842 Score: 796
Period size: 208 Copynumber: 2.0 Consensus size: 208
31217417 TTCAAATTGA
31217427 GACATTGGGCATAATTTAAGTAAAGTTTGTAATTTTACATTTTTACATAATTTTGGAAAATTATG
1 GACATTGGGCATAATTTAAGTAAAGTTTGTAATTTTACATTTTTACATAATTTTGGAAAATTATG
*
31217492 CTACATTATAATTTCTTTCTTAAAATGCACCAGTATCAACCATTAAATTATACAATGATAGGAGA
66 CTACATTATAATTTCTTTCTTAAAATGCAACAGTATCAACCATTAAATTATACAATGATAGGAGA
* *
31217557 AAATAAGGGAACACATGCAAGTGACCTAATTATCCAATAAATTGGACGAAAAATTTGATGAATTG
131 AAATAAGGGAACACATGCAAGTGACCTAATTATCCAATAAATTGGACGAAAAAGTTGATGAATTA
31217622 GGCTCATAAAAAT
196 GGCTCATAAAAAT
31217635 GACATTGGGCATAATTTAAGTAAAGTTTGTAATTTTACATTTTTACATAATTTTGGAAAATTATG
1 GACATTGGGCATAATTTAAGTAAAGTTTGTAATTTTACATTTTTACATAATTTTGGAAAATTATG
*
31217700 CTACATTATAATTTCTTTCTTAAAATGCAACAGTATCAACCATTAAATTATACAATGATAGGAGC
66 CTACATTATAATTTCTTTCTTAAAATGCAACAGTATCAACCATTAAATTATACAATGATAGGAGA
31217765 AAATAAGGGAACACATGCAAGTGACCTAATTATCCAATAAATTGGACGAAAAAGTTGATGAATTA
131 AAATAAGGGAACACATGCAAGTGACCTAATTATCCAATAAATTGGACGAAAAAGTTGATGAATTA
31217830 GGCTCATAAAAAT
196 GGCTCATAAAAAT
31217843 TTTCTTGACC
Statistics
Matches: 204, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
208 204 1.00
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (208 bp):
GACATTGGGCATAATTTAAGTAAAGTTTGTAATTTTACATTTTTACATAATTTTGGAAAATTATG
CTACATTATAATTTCTTTCTTAAAATGCAACAGTATCAACCATTAAATTATACAATGATAGGAGA
AAATAAGGGAACACATGCAAGTGACCTAATTATCCAATAAATTGGACGAAAAAGTTGATGAATTA
GGCTCATAAAAAT
Found at i:31224554 original size:16 final size:16
Alignment explanation
Indices: 31224533--31224570 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
31224523 TAGAATGGAA
31224533 AGAAAATTAG-AAAGAT
1 AGAAAATT-GTAAAGAT
*
31224549 AGAAAATTGTAAGGAT
1 AGAAAATTGTAAAGAT
31224565 AGAAAA
1 AGAAAA
31224571 AGAGAAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 1 0.05
16 19 0.95
ACGTcount: A:0.61, C:0.00, G:0.21, T:0.18
Consensus pattern (16 bp):
AGAAAATTGTAAAGAT
Found at i:31233678 original size:117 final size:117
Alignment explanation
Indices: 31233541--31233806 Score: 417
Period size: 117 Copynumber: 2.3 Consensus size: 117
31233531 AGAAGTAAAA
*
31233541 ACAAGACCCCGGTCGCCACACACAGGCGTGTTAATGACCGTGTGTCTACTGGAGCATA-ATTTCA
1 ACAAGACCACGGTCGCCACACACAGGCGTGTTAATGACCGTGTGTCTACTGGAGC-TAGATTTCA
** *
31233605 CAAAATTTCGAAATGACACATGGCTTATAGACACGGGCGTGGGAAAAGCGAAG
65 CAAAATTTCGAAACAACACATGACTTATAGACACGGGCGTGGGAAAAGCGAAG
* **
31233658 ACAAGACCACGGTCGCCACACACGGGCGTGTTAATGACCGTGTGTCTACTGGAGCTAGATTTTGC
1 ACAAGACCACGGTCGCCACACACAGGCGTGTTAATGACCGTGTGTCTACTGGAGCTAGATTTCAC
* * *
31233723 AAAATTTTGAAACAACACATGACTTATGGACACGGGCGTGGGAGAAGCGAAG
66 AAAATTTCGAAACAACACATGACTTATAGACACGGGCGTGGGAAAAGCGAAG
*
31233775 ACAAGTCCACGGTCGCCACACACAGGCGTGTT
1 ACAAGACCACGGTCGCCACACACAGGCGTGTT
31233807 CCGAGACCGT
Statistics
Matches: 136, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
116 2 0.01
117 134 0.99
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.20
Consensus pattern (117 bp):
ACAAGACCACGGTCGCCACACACAGGCGTGTTAATGACCGTGTGTCTACTGGAGCTAGATTTCAC
AAAATTTCGAAACAACACATGACTTATAGACACGGGCGTGGGAAAAGCGAAG
Found at i:31234101 original size:22 final size:22
Alignment explanation
Indices: 31234059--31234101 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
31234049 TTCACCACCG
* *
31234059 CCCTCCCTCAACAAACCACCCA
1 CCCTCCATCAACAAACAACCCA
31234081 CCCTCCATCAACCAAA-AACCC
1 CCCTCCATCAA-CAAACAACCC
31234102 GTCCTACCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.35, C:0.56, G:0.00, T:0.09
Consensus pattern (22 bp):
CCCTCCATCAACAAACAACCCA
Found at i:31234509 original size:3 final size:3
Alignment explanation
Indices: 31234416--31234489 Score: 62
Period size: 3 Copynumber: 24.7 Consensus size: 3
31234406 TTATTTAGCT
* * * *
31234416 TTA TTA TTA TTA TTG TTA TTG TTG TTA TTG TTA TTA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
31234463 TTTA TTTA TTA TT- TTT TTA TTA CTA TT
1 -TTA -TTA TTA TTA TTA TTA TTA TTA TT
31234490 TCTACTACTG
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
2 4 0.07
3 48 0.81
4 7 0.12
ACGTcount: A:0.23, C:0.01, G:0.05, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:31237001 original size:12 final size:11
Alignment explanation
Indices: 31236978--31237067 Score: 74
Period size: 11 Copynumber: 7.6 Consensus size: 11
31236968 TATTATTTAG
31236978 AAAAAGAAAAA
1 AAAAAGAAAAA
**
31236989 AAATTGAAAAA
1 AAAAAGAAAAA
31237000 AAAAAGAAAAA
1 AAAAAGAAAAA
31237011 AAAAAGAAAATTGA
1 AAAAAGAAAA---A
31237025 AAAAA-AAAAGA
1 AAAAAGAAAA-A
31237036 AAAAATTGAGAAAA
1 AAAAA--GA-AAAA
* *
31237050 AAAAAGAGAAG
1 AAAAAGAAAAA
31237061 AAAAAGA
1 AAAAAGA
31237068 CAAAGATATG
Statistics
Matches: 66, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
11 44 0.67
12 2 0.03
13 4 0.06
14 13 0.20
15 3 0.05
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:31237009 original size:20 final size:19
Alignment explanation
Indices: 31237005--31237056 Score: 79
Period size: 18 Copynumber: 2.7 Consensus size: 19
31236995 AAAAAAAAAA
31237005 GAAAAAAAAAAG-AAAATT
1 GAAAAAAAAAAGAAAAATT
31237023 GAAAAAAAAAAGAAAAAATT
1 GAAAAAAAAAAG-AAAAATT
31237043 GAGAAAAAAAAAGA
1 GA-AAAAAAAAAGA
31237057 GAAGAAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.39
20 9 0.29
21 10 0.32
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (19 bp):
GAAAAAAAAAAGAAAAATT
Done.