Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005092.1 Kokia drynarioides strain JFW-HI SEQ_118910, whole genome shotgun sequence
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: 85203
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 18 characters in sequence are not A, C, G, or T
Found at i:557 original size:30 final size:30
Alignment explanation
Indices: 501--557 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
491 CCTTAAAGGT
*
501 CCCTAAACTATTTAAAAATTATATTTTGAC
1 CCCTAAACTATTTAAAAATTACATTTTGAC
* *
531 CCCTAAACT-TCTTTAAAATTCCATTTT
1 CCCTAAACTAT-TTAAAAATTACATTTT
558 TAACCTCGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 1 0.04
30 22 0.96
ACGTcount: A:0.35, C:0.21, G:0.02, T:0.42
Consensus pattern (30 bp):
CCCTAAACTATTTAAAAATTACATTTTGAC
Found at i:579 original size:30 final size:29
Alignment explanation
Indices: 545--705 Score: 105
Period size: 30 Copynumber: 5.5 Consensus size: 29
535 AAACTTCTTT
* **
545 AAAATTCCATTTTTAACCTCGATTTTTTCA
1 AAAATTACATTTTTAACCTCGA-AATTTCA
* * *
575 AAAATTAC-TATTTTACCCTC-AAACTTCC
1 AAAATTACAT-TTTTAACCTCGAAATTTCA
* * **
603 AAAATTCCATTTTTGACCTAAAAACTTTCA
1 AAAATTACATTTTTAACCTCGAAA-TTTCA
* * *
633 AAAATTACATTTTTACCCTCG-AACTTCC
1 AAAATTACATTTTTAACCTCGAAATTTCA
**
661 AAAATT-CTATTTTTAACCTCGATCTTTTCA
1 AAAATTAC-ATTTTTAACCTCGA-AATTTCA
*
691 TAAATTACATTTTTA
1 AAAATTACATTTTTA
706 CCCTTTGAAC
Statistics
Matches: 98, Mismatches: 25, Indels: 16
0.71 0.18 0.12
Matches are distributed among these distances:
27 1 0.01
28 38 0.39
29 8 0.08
30 50 0.51
31 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.02, T:0.42
Consensus pattern (29 bp):
AAAATTACATTTTTAACCTCGAAATTTCA
Found at i:627 original size:29 final size:27
Alignment explanation
Indices: 585--675 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 27
575 AAAATTACTA
*
585 TTTTACCCTCAAACTTCCAAAATTCCAT
1 TTTTA-CCTAAAACTTCCAAAATTCCAT
* *
613 TTTTGACCTAAAAACTTTCAAAAATTACAT
1 TTTT-ACCT-AAAAC-TTCCAAAATTCCAT
** *
643 TTTTACCCTCGAACTTCCAAAATTCTAT
1 TTTTA-CCTAAAACTTCCAAAATTCCAT
671 TTTTA
1 TTTTA
676 ACCTCGATCT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
28 23 0.45
29 9 0.18
30 19 0.37
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.40
Consensus pattern (27 bp):
TTTTACCTAAAACTTCCAAAATTCCAT
Found at i:784 original size:29 final size:30
Alignment explanation
Indices: 545--903 Score: 173
Period size: 29 Copynumber: 12.2 Consensus size: 30
535 AAACTTCTTT
* ** *
545 AAAATT-CCATTTTTAACCTCGATTTTTTCA
1 AAAATTACCATTTTTACCCTCGA-ACTTCCA
* *
575 AAAATTACTA-TTTTACCCTCAAACTTCC-
1 AAAATTACCATTTTTACCCTCGAACTTCCA
** *
603 AAAATT-CCATTTTTGA-CCTAAAAACTTTCA
1 AAAATTACCATTTTT-ACCCT-CGAACTTCCA
633 AAAATTA-CATTTTTACCCTCGAACTTCC-
1 AAAATTACCATTTTTACCCTCGAACTTCCA
* * * *
661 AAAATT-CTATTTTTAACCTCGATCTTTTCA
1 AAAATTACCATTTTTACCCTCGAAC-TTCCA
* * *
691 TAAATTA-CATTTTTACCCTTTGAACTTCAAA
1 AAAATTACCATTTTTACCC-TCGAACTTC-CA
* * *
722 AAAATCT-CTATTTTGACCC-CGAAACTTCTA
1 AAAAT-TACCATTTTTACCCTCG-AACTTCCA
*
752 AAAATTACCA-TTTTACCCTCGAACCTCCA
1 AAAATTACCATTTTTACCCTCGAACTTCCA
*
781 AAAATT-CCATTTTTGACCC-CGAAAC-TCTTA
1 AAAATTACCATTTTT-ACCCTCG-AACTTC-CA
* * * *
811 AAAATTACTA-TTTTACCCCCAAACTT-CT
1 AAAATTACCATTTTTACCCTCGAACTTCCA
* *** *
839 GAAATT-CCATTTTTTACCCAAAAACTTTCA
1 AAAATTACCA-TTTTTACCCTCGAACTTCCA
* *
869 AAAATTACC-CTTTTACCCTCGGA-TGTCCA
1 AAAATTACCATTTTTACCCTCGAACT-TCCA
898 AAAATT
1 AAAATT
904 TCGTTTTTGA
Statistics
Matches: 250, Mismatches: 49, Indels: 61
0.69 0.14 0.17
Matches are distributed among these distances:
27 4 0.02
28 42 0.17
29 88 0.35
30 85 0.34
31 21 0.08
32 10 0.04
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (30 bp):
AAAATTACCATTTTTACCCTCGAACTTCCA
Found at i:806 original size:59 final size:60
Alignment explanation
Indices: 545--948 Score: 305
Period size: 58 Copynumber: 6.9 Consensus size: 60
535 AAACTTCTTT
* * ** * * *
545 AAAATTCCATTTTTAACCTCG-ATTTTTTCAAAAATTACTATTTTACCCTCAAACTTCC-
1 AAAATTCCATTTTTGACCCCGAAACTTCTCAAAAATTACCATTTTACCCTCGAACTTCCA
***
603 AAAATTCCATTTTTGACCTAAAAACTT-TCAAAAATTA-CATTTTTACCCTCGAACTTCC-
1 AAAATTCCATTTTTGACCCCGAAACTTCTCAAAAATTACCA-TTTTACCCTCGAACTTCCA
* * * * * * * *
661 AAAATTCTATTTTTAACCTCG-ATCTTTTCATAAATTA-CATTTTTACCCTTTGAACTTCAA
1 AAAATTCCATTTTTGACCCCGAAACTTCTCAAAAATTACCA-TTTTACCC-TCGAACTTCCA
* *
721 AAAAATCTC-TATTTTGACCCCGAAACTTCT-AAAAATTACCATTTTACCCTCGAACCTCCA
1 AAAATTC-CAT-TTTTGACCCCGAAACTTCTCAAAAATTACCATTTTACCCTCGAACTTCCA
* * * * *
781 AAAATTCCATTTTTGACCCCGAAAC-TCTTAAAAATTACTATTTTACCCCCAAACTT-CT
1 AAAATTCCATTTTTGACCCCGAAACTTCTCAAAAATTACCATTTTACCCTCGAACTTCCA
* * ** * *
839 GAAATTCCATTTTTTACCCAAAAACTT-TCAAAAATTACCCTTTTACCCTCGGA-TGTCCA
1 AAAATTCCATTTTTGACCCCGAAACTTCTCAAAAATTACCATTTTACCCTCGAACT-TCCA
* * * ** * * *
898 AAAATTTCGTTTTTGATCCCG-ATTTTTTCTAAAATTACCGTTTTACCCTCG
1 AAAATTCCATTTTTGACCCCGAAACTTCTCAAAAATTACCATTTTACCCTCG
949 GGTGTCTAAA
Statistics
Matches: 278, Mismatches: 53, Indels: 29
0.77 0.15 0.08
Matches are distributed among these distances:
57 6 0.02
58 131 0.47
59 88 0.32
60 22 0.08
61 24 0.09
62 7 0.03
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (60 bp):
AAAATTCCATTTTTGACCCCGAAACTTCTCAAAAATTACCATTTTACCCTCGAACTTCCA
Found at i:1043 original size:28 final size:28
Alignment explanation
Indices: 987--1046 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
977 AAACTTTCCT
* * *
987 AAAATTCCCATTTTGCCCCTATTAGTCC
1 AAAATTACCATTTTGCCCCGAGTAGTCC
1015 AAAATTACCATTTTGCCCCCGAGTA-TCC
1 AAAATTACCATTTTG-CCCCGAGTAGTCC
1043 AAAA
1 AAAA
1047 AGTCTCATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 21 0.75
29 7 0.25
ACGTcount: A:0.32, C:0.30, G:0.08, T:0.30
Consensus pattern (28 bp):
AAAATTACCATTTTGCCCCGAGTAGTCC
Found at i:6559 original size:18 final size:16
Alignment explanation
Indices: 6538--6606 Score: 52
Period size: 17 Copynumber: 4.1 Consensus size: 16
6528 AAAAAATAAG
6538 GAAAAAAGATGAAGAAAA
1 GAAAAAA-A-GAAGAAAA
*
6556 GAAAGAAA-AAGAAAA
1 GAAAAAAAGAAGAAAA
6571 GCAAAAACAAGAAGAAAA
1 G-AAAAA-AAGAAGAAAA
*
6589 -ACAAAAATAGAAAAAAA
1 GA-AAAAA-AGAAGAAAA
6606 G
1 G
6607 GGAAAGGTCG
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
15 8 0.19
16 6 0.14
17 15 0.36
18 13 0.31
ACGTcount: A:0.75, C:0.04, G:0.17, T:0.03
Consensus pattern (16 bp):
GAAAAAAAGAAGAAAA
Found at i:7884 original size:50 final size:49
Alignment explanation
Indices: 7812--8101 Score: 191
Period size: 50 Copynumber: 5.8 Consensus size: 49
7802 TGAAGACGTG
* *
7812 AAGGGAAAGATCTAAGACCGCAACGGCAGATCTAGTACCACAAAGATACAA
1 AAGGGAAAGATCTAAG-CCGCAACGGCGGATCCAGTACCACAAAGA-ACAA
* * * *
7863 AAGGGAAAGGTTTAAGTCGCAACGGCGGA-CCGTGTACCTTA-AAAG-ACAA
1 AAGGGAAAGATCTAAGCCGCAACGGCGGATCC-AGTACC--ACAAAGAACAA
* * * * ** *
7912 GAAGGGAAAGATTTAAGCCACAACGACGAATCCAGTACCATGAAG-ACATG
1 -AAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACAAAGAACA-A
7962 AAGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACAAAGACACAA
1 AAGGGAAAGATCTAAG-CCGCAACGGCGGATCCAGTACCACAAAGA-ACAA
* * * * *
8013 AA-GGAAAAAGTCTAAGTCGCAACAGTGGA-CCGTGTACCTTA-AAAG-ACAA
1 AAGGGAAAGA-TCTAAGCCGCAACGGCGGATCC-AGTACC--ACAAAGAACAA
* * * * *
8062 GAAGGGAAAGATTTAAGTCGTAACGACGAATCCAGTACCA
1 -AAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCA
8102 TGAAGACATC
Statistics
Matches: 188, Mismatches: 34, Indels: 37
0.73 0.13 0.14
Matches are distributed among these distances:
48 2 0.01
49 32 0.17
50 109 0.58
51 40 0.21
52 5 0.03
ACGTcount: A:0.42, C:0.20, G:0.24, T:0.14
Consensus pattern (49 bp):
AAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACAAAGAACAA
Found at i:8065 original size:150 final size:150
Alignment explanation
Indices: 7794--8110 Score: 526
Period size: 150 Copynumber: 2.1 Consensus size: 150
7784 CTACAGGTCT
* * *
7794 CAGTACCATGAAGACGTGAAGGGAAAGATCTAAGACCGCAACGGCAGATCTAGTACCACAAAGAT
1 CAGTACCATGAAGACATGAAGGGAAAGATCTAAGACCGCAACGGCAGATCCAGTACCACAAAGAC
* * * *
7859 ACAAAAGGGAAAGGTTTAAGTCGCAACGGCGGACCGTGTACCTTAAAAGACAAGAAGGGAAAGAT
66 ACAAAAGGAAAAAGTCTAAGTCGCAACAGCGGACCGTGTACCTTAAAAGACAAGAAGGGAAAGAT
7924 TTAAGCCACAACGACGAATC
131 TTAAGCCACAACGACGAATC
*
7944 CAGTACCATGAAGACATGAAGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACAAAGAC
1 CAGTACCATGAAGACATGAAGGGAAAGATCTAAGACCGCAACGGCAGATCCAGTACCACAAAGAC
*
8009 ACAAAAGGAAAAAGTCTAAGTCGCAACAGTGGACCGTGTACCTTAAAAGACAAGAAGGGAAAGAT
66 ACAAAAGGAAAAAGTCTAAGTCGCAACAGCGGACCGTGTACCTTAAAAGACAAGAAGGGAAAGAT
* **
8074 TTAAGTCGTAACGACGAATC
131 TTAAGCCACAACGACGAATC
8094 CAGTACCATGAAGACAT
1 CAGTACCATGAAGACAT
8111 CTAAGACCGC
Statistics
Matches: 155, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
150 155 1.00
ACGTcount: A:0.41, C:0.20, G:0.24, T:0.14
Consensus pattern (150 bp):
CAGTACCATGAAGACATGAAGGGAAAGATCTAAGACCGCAACGGCAGATCCAGTACCACAAAGAC
ACAAAAGGAAAAAGTCTAAGTCGCAACAGCGGACCGTGTACCTTAAAAGACAAGAAGGGAAAGAT
TTAAGCCACAACGACGAATC
Found at i:8144 original size:138 final size:138
Alignment explanation
Indices: 7821--8390 Score: 647
Period size: 138 Copynumber: 4.0 Consensus size: 138
7811 GAAGGGAAAG
* * *
7821 ATCTAAGACCGCAACGGCAGATCTAGTACCACAAAGATACAAAAGGGAAAGGTTTAAGTCGCAAC
1 ATCTAAGACCGCAACGGCAGATCTAGTACCACAAAGATACAAAAGGAAAAAGTCTAAGTCGCAAC
7886 GGCGGACCGTGTACCTTAAAAGACAAGAAGGGAAAGATTTAAGCCACAACGACGAATCCAGTACC
66 GGCGGACCGTGTACCTTAAAAGACAAGAAGGGAAAGATTTAAGCCACAACGACGAATCCAGTACC
7951 ATGAAGAC
131 ATGAAGAC
* * *
7959 ATGAAGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACAAAGACACAAAAGGAAAAAGT
1 ------------ATCTAAGACCGCAACGGCAGATCTAGTACCACAAAGATACAAAAGGAAAAAGT
* * * **
8024 CTAAGTCGCAACAGTGGACCGTGTACCTTAAAAGACAAGAAGGGAAAGATTTAAGTCGTAACGAC
54 CTAAGTCGCAACGGCGGACCGTGTACCTTAAAAGACAAGAAGGGAAAGATTTAAGCCACAACGAC
8089 GAATCCAGTACCATGAAGAC
119 GAATCCAGTACCATGAAGAC
* ** *
8109 ATCTAAGACCGCAATGGTGGATCTAGTACCACAAAGATACAAAAGGGAAAAGTCTAAGTCGCAAC
1 ATCTAAGACCGCAACGGCAGATCTAGTACCACAAAGATACAAAAGGAAAAAGTCTAAGTCGCAAC
* * * * *
8174 GGTGGACCGTGTACCTTAGAAGACAAGAAGGGAAAGATTTAAACCACAACGACGAATCTAATACC
66 GGCGGACCGTGTACCTTAAAAGACAAGAAGGGAAAGATTTAAGCCACAACGACGAATCCAGTACC
8239 ATGAAGAC
131 ATGAAGAC
* * * *
8247 ATGAACGATCCAAGATCGCAATGGCAGATCTAGTACCACAAAGATACAAAA-GAGAAAGGTTTAA
1 AT---C--T--AAGACCGCAACGGCAGATCTAGTACCACAAAGATACAAAAGGA-AAAAGTCTAA
* * ** * * * * *
8311 GTTGTAACGGCGGACCACGTACCTCAGAAGACAAGAAGGGAAAGATTTAAGCCGCAATGGCGAAT
58 GTCGCAACGGCGGACCGTGTACCTTAAAAGACAAGAAGGGAAAGATTTAAGCCACAACGACGAAT
*
8376 CCAGTACCACGAAGA
123 CCAGTACCATGAAGA
8391 TTTGAAGAGG
Statistics
Matches: 369, Mismatches: 43, Indels: 21
0.85 0.10 0.05
Matches are distributed among these distances:
138 127 0.34
141 1 0.00
143 1 0.00
144 1 0.00
145 112 0.30
150 127 0.34
ACGTcount: A:0.41, C:0.20, G:0.24, T:0.15
Consensus pattern (138 bp):
ATCTAAGACCGCAACGGCAGATCTAGTACCACAAAGATACAAAAGGAAAAAGTCTAAGTCGCAAC
GGCGGACCGTGTACCTTAAAAGACAAGAAGGGAAAGATTTAAGCCACAACGACGAATCCAGTACC
ATGAAGAC
Found at i:8693 original size:101 final size:101
Alignment explanation
Indices: 8515--8713 Score: 292
Period size: 101 Copynumber: 2.0 Consensus size: 101
8505 CAAAACTACT
* * *
8515 ATAGCAAGTCTTTAACTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTTAACGTCAATTCCTA
1 ATAGCAAGTCTTTAACTCTCTGAAGTTGCAGTAAAAGCAAGATGAAGCTTTAACATCAAATCCTA
* * *
8580 TCCTCTTGAAGTTGCAGTAAAGTTGGATTAAAAACA
66 TCCTCTTAAAGTTGCAGCAAAGTTGGAATAAAAACA
* *
8616 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAAAGCAAGATGAAG-TTTCAACATCAAATCCT
1 ATAGCAAGTCTTTAACTCTCTGAAGTTGCAGTAAAAGCAAGATGAAGCTTT-AACATCAAATCCT
* *
8680 ATCTTCTTAAAGTTGCAGCGAAGTTGGAATAAAA
65 ATCCTCTTAAAGTTGCAGCAAAGTTGGAATAAAA
8714 CTACAGCAGC
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
100 3 0.03
101 84 0.97
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (101 bp):
ATAGCAAGTCTTTAACTCTCTGAAGTTGCAGTAAAAGCAAGATGAAGCTTTAACATCAAATCCTA
TCCTCTTAAAGTTGCAGCAAAGTTGGAATAAAAACA
Found at i:8834 original size:39 final size:39
Alignment explanation
Indices: 8775--9064 Score: 189
Period size: 39 Copynumber: 7.4 Consensus size: 39
8765 TTACATCGTT
8775 AACCAATCTCTTACCCCGAGCCTGGGGCAGATCATCATC
1 AACCAATCTCTTACCCCGAGCCTGGGGCAGATCATCATC
* ** *
8814 AACCAATCTCTTACCTCGAGCCTGAAGCAGAT--TGAAGTC
1 AACCAATCTCTTACCCCGAGCCTGGGGCAGATCAT-CA-TC
**** * * *
8853 ATTTGATCTTTTACCCCGAGCTTAGGGCAGATCATCATC
1 AACCAATCTCTTACCCCGAGCCTGGGGCAGATCATCATC
* * *
8892 AACCAATATCTTACCCCGAGCTTGGGGCAGAT--TGA--
1 AACCAATCTCTTACCCCGAGCCTGGGGCAGATCATCATC
* * * *
8927 AGCCATTTGATTTTTTACCCCGAGCCTGGGGCAAATCATCATC
1 AACCA----ATCTCTTACCCCGAGCCTGGGGCAGATCATCATC
* * * * *
8970 AACCAATCTCTTACCCCGAGCCAGAGGCAGATTA-GAGCC
1 AACCAATCTCTTACCCCGAGCCTGGGGCAGATCATCA-TC
** * * **
9009 ATTCGATCTCTTACCCCGAGCTTGGGGCAGATCATTGTC
1 AACCAATCTCTTACCCCGAGCCTGGGGCAGATCATCATC
* *
9048 AACCAAACTCCTACCCC
1 AACCAATCTCTTACCCC
9065 AATCACGGGG
Statistics
Matches: 184, Mismatches: 53, Indels: 28
0.69 0.20 0.11
Matches are distributed among these distances:
35 4 0.02
37 3 0.02
38 2 0.01
39 167 0.91
40 1 0.01
41 3 0.02
43 4 0.02
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (39 bp):
AACCAATCTCTTACCCCGAGCCTGGGGCAGATCATCATC
Found at i:8922 original size:78 final size:78
Alignment explanation
Indices: 8780--9064 Score: 383
Period size: 78 Copynumber: 3.7 Consensus size: 78
8770 TCGTTAACCA
* *
8780 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAACCAATCTCTTACCTCGAGCCTGAAGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAACCAATCTCTTACCCCGAGCCTGAGGCAGA
*
8845 TTGAAGTCATTTG
66 TTGAAGCCATTTG
* * * * * *
8858 ATCTTTTACCCCGAGCTTAGGGCAGATCATCATCAACCAATATCTTACCCCGAGCTTGGGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAACCAATCTCTTACCCCGAGCCTGAGGCAGA
8923 TTGAAGCCATTTG
66 TTGAAGCCATTTG
* * * *
8936 ATTTTTTACCCCGAGCCTGGGGCAAATCATCATCAACCAATCTCTTACCCCGAGCCAGAGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAACCAATCTCTTACCCCGAGCCTGAGGCAGA
*
9001 TT-AGAGCCATTCG
66 TTGA-AGCCATTTG
* ** * *
9014 ATCTCTTACCCCGAGCTTGGGGCAGATCATTGTCAACCAAACTCCTACCCC
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAACCAATCTCTTACCCC
9065 AATCACGGGG
Statistics
Matches: 180, Mismatches: 26, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
77 1 0.01
78 179 0.99
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.25
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAACCAATCTCTTACCCCGAGCCTGAGGCAGA
TTGAAGCCATTTG
Found at i:9075 original size:156 final size:156
Alignment explanation
Indices: 8785--9080 Score: 425
Period size: 156 Copynumber: 1.9 Consensus size: 156
8775 AACCAATCTC
* * *
8785 TTACCCCGAGCCTGGGGCAGATCATCATCAACCAATCTCTTACCTCGAGCCTGAAGCAGATTGAA
1 TTACCCCGAGCCTGGGGCAAATCATCATCAACCAATCTCTTACCCCGAGCCAGAAGCAGATTGAA
* * * * * **
8850 GTCATTTGATCTTTTACCCCGAGCTTAGGGCAGATCATCATCAACCAATATCTTACCCCGAGCTT
66 GCCATTCGATCTCTTACCCCGAGCTTAGGGCAGATCATCATCAACCAATATCCTACCCCAAGCAC
8915 GGGGCAGATTGAAGCCATTTGATTTT
131 GGGGCAGATTGAAGCCATTTGATTTT
*
8941 TTACCCCGAGCCTGGGGCAAATCATCATCAACCAATCTCTTACCCCGAGCCAGAGGCAGATT-AG
1 TTACCCCGAGCCTGGGGCAAATCATCATCAACCAATCTCTTACCCCGAGCCAGAAGCAGATTGA-
* ** *
9005 AGCCATTCGATCTCTTACCCCGAGCTTGGGGCAGATCATTGTCAACCAA-ACTCCTACCCCAATC
65 AGCCATTCGATCTCTTACCCCGAGCTTAGGGCAGATCATCATCAACCAATA-TCCTACCCCAAGC
9069 ACGGGGCAGATT
129 ACGGGGCAGATT
9081 ACGATTATCC
Statistics
Matches: 123, Mismatches: 15, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
155 2 0.02
156 121 0.98
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (156 bp):
TTACCCCGAGCCTGGGGCAAATCATCATCAACCAATCTCTTACCCCGAGCCAGAAGCAGATTGAA
GCCATTCGATCTCTTACCCCGAGCTTAGGGCAGATCATCATCAACCAATATCCTACCCCAAGCAC
GGGGCAGATTGAAGCCATTTGATTTT
Found at i:9839 original size:206 final size:206
Alignment explanation
Indices: 9370--9846 Score: 661
Period size: 206 Copynumber: 2.3 Consensus size: 206
9360 CGAATCCCAA
* * * *
9370 CTTCATGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCAGAT
1 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCATGATGAGATATAGAGAAGCGGAT
* * ** **
9435 TGAAACAAACGACATGATTATCTTCCTGATGAGATGCTGAGAAGAAGACCAAATCAAACCCACGC
66 TGAAACAAACGACACGATCATCTTCCTGATGAGACACAAAGAAGAAGACCAAATCAAACCCACGC
* * *
9500 TTGAGGTGAGCAAATCTTCGAATCCCAGCATCCTGATGAGATACTGAGAAGCGGGTCGAAGCAAT
131 TCGAGGTGAACAAATCTTCGAATCCCAGCATCCTGATGAGATACTGAGAAGCAGGTCGAAGCAAT
9565 AAAATGGTTAG
196 AAAATGGTTAG
* *
9576 TTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCATGATGAGATATAGAGAAGCGGAT
1 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCATGATGAGATATAGAGAAGCGGAT
* *
9641 TGTAACAAACGACACGGTCATCTTCCTGATGAGACACAAAGAAGAAGACCAAATCAAACCCACGC
66 TGAAACAAACGACACGATCATCTTCCTGATGAGACACAAAGAAGAAGACCAAATCAAACCCACGC
* * *
9706 TCGATGTGAACAAATCTTCGAA-CCCTAGCTTCCTGATGAGATACTGATAAGCAGGTCGAAGCAA
131 TCGAGGTGAACAAATCTTCGAATCCC-AGCATCCTGATGAGATACTGAGAAGCAGGTCGAAGCAA
* *
9770 TAAAGTGGTTGG
195 TAAAATGGTTAG
* * * * * * *
9782 CTTCCTGATGAGATAC-GAAGAAGTGAATCTAATCCGTCTTCCTGATGAAACATAGAGAAGTGGA
1 CTTCCTGATGAGATACTG-AGAAGTGAACCAAATTCGTCTTCATGATGAGATATAGAGAAGCGGA
9846 T
65 T
9847 CAAAACAAGT
Statistics
Matches: 238, Mismatches: 31, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
205 4 0.02
206 234 0.98
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (206 bp):
CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCATGATGAGATATAGAGAAGCGGAT
TGAAACAAACGACACGATCATCTTCCTGATGAGACACAAAGAAGAAGACCAAATCAAACCCACGC
TCGAGGTGAACAAATCTTCGAATCCCAGCATCCTGATGAGATACTGAGAAGCAGGTCGAAGCAAT
AAAATGGTTAG
Found at i:9892 original size:206 final size:206
Alignment explanation
Indices: 9370--9903 Score: 640
Period size: 206 Copynumber: 2.6 Consensus size: 206
9360 CGAATCCCAA
* * * * * * *
9370 CTTCATGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCAGAT
1 CTTCCTGATGAGATACTGAGAAGTGAACCAAATCCGTCTTCATGATGAAACATAGAGAAGCGGAT
** * * * *
9435 TGAAACAAACGACATGATTATCTTCCTGATGAGATGCTGAGAAGAAGACCAAATCAAACCCACGC
66 CAAAACAAACGACACGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
* * *
9500 TTGAGGTGAGCAAATCTTCGAATCCCAGCATCCTGATGAGATACTGAGAAGCGGGTCGAAGCAAT
131 TCGAGGTGAACAAATCTTCGAATCCCAGCATCCTGATGAGATACTGAGAAGCAGGTCGAAGCAAT
9565 AAAATGGTTAG
196 AAAATGGTTAG
* * * * *
9576 TTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCATGATGAGATATAGAGAAGCGGAT
1 CTTCCTGATGAGATACTGAGAAGTGAACCAAATCCGTCTTCATGATGAAACATAGAGAAGCGGAT
*** * **
9641 TGTAACAAACGACACGGTCATCTTCCTGATGAGACACAAAGAAGAAGACCAAATCAAACCCACGC
66 CAAAACAAACGACACGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
* * *
9706 TCGATGTGAACAAATCTTCGAA-CCCTAGCTTCCTGATGAGATACTGATAAGCAGGTCGAAGCAA
131 TCGAGGTGAACAAATCTTCGAATCCC-AGCATCCTGATGAGATACTGAGAAGCAGGTCGAAGCAA
* *
9770 TAAAGTGGTTGG
195 TAAAATGGTTAG
* * * *
9782 CTTCCTGATGAGATAC-GAAGAAGTGAATCTAATCCGTCTTCCTGATGAAACATAGAGAAGTGGA
1 CTTCCTGATGAGATACTG-AGAAGTGAACCAAATCCGTCTTCATGATGAAACATAGAGAAGCGGA
** ** * * * *
9846 TCAAAACAAGTGATGCGGTCATCTTCCCGATAAGATACTGAGAAGAAGGCCAAGTCAA
65 TCAAAACAAACGACACGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAA
9904 TGAAACCAGA
Statistics
Matches: 281, Mismatches: 45, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
205 4 0.01
206 277 0.99
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (206 bp):
CTTCCTGATGAGATACTGAGAAGTGAACCAAATCCGTCTTCATGATGAAACATAGAGAAGCGGAT
CAAAACAAACGACACGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
TCGAGGTGAACAAATCTTCGAATCCCAGCATCCTGATGAGATACTGAGAAGCAGGTCGAAGCAAT
AAAATGGTTAG
Found at i:10313 original size:16 final size:16
Alignment explanation
Indices: 10235--10329 Score: 66
Period size: 16 Copynumber: 5.7 Consensus size: 16
10225 GAGTCTAATT
*
10235 TTTAATTTTAATTTAC
1 TTTAATTTAAATTTAC
* *
10251 TTTAAGTTTGAATTT-G
1 TTTAA-TTTAAATTTAC
* *
10267 TTCTAAATTTAAATTCATT
1 TT-T-AATTTAAATTTA-C
*
10286 TTTGAGTTTAAATTTAC
1 TTT-AATTTAAATTTAC
10303 TTTAATTTAAATTTAC
1 TTTAATTTAAATTTAC
* *
10319 TGTAAATTAAA
1 TTTAATTTAAA
10330 ATTAATTAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
16 28 0.45
17 19 0.31
18 13 0.21
19 2 0.03
ACGTcount: A:0.35, C:0.05, G:0.06, T:0.54
Consensus pattern (16 bp):
TTTAATTTAAATTTAC
Found at i:10405 original size:26 final size:25
Alignment explanation
Indices: 10376--10465 Score: 135
Period size: 26 Copynumber: 3.5 Consensus size: 25
10366 CTTACAAAGA
10376 CCAAATTGGGTCCGATCCTAACAAAC
1 CCAAATTGGG-CCGATCCTAACAAAC
*
10402 CCAAATTAGGCCCGATCCTAACAAAC
1 CCAAATT-GGGCCGATCCTAACAAAC
*
10428 CCAAATTGGGCTCAATCCTAACAAAC
1 CCAAATTGGGC-CGATCCTAACAAAC
10454 CCAAATTGGGCC
1 CCAAATTGGGCC
10466 TAAATTTCAA
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
25 4 0.07
26 53 0.90
27 2 0.03
ACGTcount: A:0.36, C:0.32, G:0.14, T:0.18
Consensus pattern (25 bp):
CCAAATTGGGCCGATCCTAACAAAC
Found at i:11146 original size:21 final size:21
Alignment explanation
Indices: 11122--11162 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
11112 AATATATTAA
11122 TAATAATAATAAATATTTTTT
1 TAATAATAATAAATATTTTTT
11143 TAATAATAATAAATATTTTT
1 TAATAATAATAAATATTTTT
11163 GGTAATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TAATAATAATAAATATTTTTT
Found at i:12520 original size:29 final size:29
Alignment explanation
Indices: 12328--12579 Score: 117
Period size: 29 Copynumber: 8.6 Consensus size: 29
12318 CCGATTTTTT
* * *
12328 CAAAAATTACTATTTTAACCC-CAAACTTC
1 CAAAAATT-CCATTTTTACCCTCGAACTTC
* *
12357 CAAAAA-TACATTTTTACCCTTGAACTTTC
1 CAAAAATTCCATTTTTACCCTCGAAC-TTC
* * *
12386 C-AAAATTCCATTTTTAACCT-TAATCTTTT
1 CAAAAATTCCATTTTTACCCTCGAA-C-TTC
* * * *
12415 CATAGATTACATTTTTACCCCCCGAACTTC
1 CAAAAATTCCATTTTTA-CCCTCGAACTTC
* * *
12445 CAAAAAATCTC-TATTTTAACCTCGAAACTTT
1 CAAAAATTC-CAT-TTTTACCCTCG-AACTTC
* *
12476 TAAAAATTGCCA-TTTTACCCTCGAACCTC
1 CAAAAATT-CCATTTTTACCCTCGAACTTC
*** *
12505 CAAAAATTCCATTTTTGACCCAAAAACTTT
1 CAAAAATTCCATTTTT-ACCCTCGAACTTC
*
12535 CAAAAATTAC-TCTTTTACCCTC-ATA-TGTC
1 CAAAAATTCCAT-TTTTACCCTCGA-ACT-TC
*
12564 CAAAAATTCCTTTTTT
1 CAAAAATTCCATTTTT
12580 TATCTTGATT
Statistics
Matches: 166, Mismatches: 39, Indels: 36
0.69 0.16 0.15
Matches are distributed among these distances:
27 9 0.05
28 15 0.09
29 62 0.37
30 56 0.34
31 21 0.13
32 3 0.02
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (29 bp):
CAAAAATTCCATTTTTACCCTCGAACTTC
Found at i:13469 original size:2 final size:2
Alignment explanation
Indices: 13462--13489 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13452 TGGTTTCGAC
13462 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
13490 TTCTATCCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14712 original size:43 final size:40
Alignment explanation
Indices: 14632--14711 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
14622 TTCAAAAAAA
*
14632 AAAAATCCTAAATTAAGCTTCCAAATTCATTTTTCTTCTTT
1 AAAAATCCTAAATTAACCTTCC-AATTCATTTTTCTTCTTT
*
14673 AAAAATCCCTAAATTAAACCTTCC-ATTC-TTCTTCTTCTT
1 AAAAAT-CCTAAATT-AACCTTCCAATTCATTTTTCTTCTT
14712 CATTAGTTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
40 10 0.29
41 10 0.29
42 8 0.23
43 7 0.20
ACGTcount: A:0.33, C:0.24, G:0.01, T:0.42
Consensus pattern (40 bp):
AAAAATCCTAAATTAACCTTCCAATTCATTTTTCTTCTTT
Found at i:15822 original size:28 final size:29
Alignment explanation
Indices: 15761--15822 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
15751 ATGTAACAAT
*
15761 ATTTTATTTTTTTTAAATGTCATTTTTATC
1 ATTTTATTTATTTTAAATGT-ATTTTTATC
*
15791 -TTTTATTTATTTT-AATG-ATTTTTTTTC
1 ATTTTATTTATTTTAAATGTA-TTTTTATC
15818 ATTTT
1 ATTTT
15823 TCTCCTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
26 1 0.04
27 7 0.25
28 8 0.29
29 12 0.43
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (29 bp):
ATTTTATTTATTTTAAATGTATTTTTATC
Found at i:16750 original size:2 final size:2
Alignment explanation
Indices: 16737--16790 Score: 99
Period size: 2 Copynumber: 26.5 Consensus size: 2
16727 TGAAGCACAT
16737 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16780 TA TA TA TA TA T
1 TA TA TA TA TA T
16791 TAATTTTTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 49 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21196 original size:51 final size:51
Alignment explanation
Indices: 21136--21234 Score: 180
Period size: 51 Copynumber: 1.9 Consensus size: 51
21126 ACTCATAACT
*
21136 TTCAAAAGAATGGTGATATAAATGCTTAGCAGATATATTCAAATAGTCTCA
1 TTCAAAAGAATGGTGATATAAATGCTTAGCAGATACATTCAAATAGTCTCA
*
21187 TTCAAAAGAATGGTGATATAAATGCTTGGCAGATACATTCAAATAGTC
1 TTCAAAAGAATGGTGATATAAATGCTTAGCAGATACATTCAAATAGTC
21235 AATTGAAAGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.30
Consensus pattern (51 bp):
TTCAAAAGAATGGTGATATAAATGCTTAGCAGATACATTCAAATAGTCTCA
Found at i:24334 original size:17 final size:17
Alignment explanation
Indices: 24291--24334 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
24281 ACTTTTCGTA
*
24291 TTTTATTACTTTTATTAT
1 TTTTATTA-TTTTAATAT
*
24309 TTTTCTTATTTTAATAT
1 TTTTATTATTTTAATAT
24326 TTTTATTAT
1 TTTTATTAT
24335 CTTATAAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATTATTTTAATAT
Found at i:25062 original size:48 final size:48
Alignment explanation
Indices: 24952--25114 Score: 202
Period size: 48 Copynumber: 3.4 Consensus size: 48
24942 AAAGCTACTT
* * * * *
24952 AATACGTTATGGATGAACCACTAGTCGAGTAGAT-GACTGCCAACTAA
1 AATACGTTGTGGATAAACCACTAGTCGAGTAGATAAACTACCGACTAA
* * * *
24999 AATACGTTGTGGATAAACCACTAGTCGAGTAGGTAAACTATCGAGTTA
1 AATACGTTGTGGATAAACCACTAGTCGAGTAGATAAACTACCGACTAA
* * *
25047 AATACGTTGTGGATAAACCACTAGTTGAGCAAATAAACTACCGACTAA
1 AATACGTTGTGGATAAACCACTAGTCGAGTAGATAAACTACCGACTAA
*
25095 AATACATTGTGGATAAACCA
1 AATACGTTGTGGATAAACCA
25115 TTGGTTAATC
Statistics
Matches: 98, Mismatches: 17, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
47 31 0.32
48 67 0.68
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.25
Consensus pattern (48 bp):
AATACGTTGTGGATAAACCACTAGTCGAGTAGATAAACTACCGACTAA
Found at i:25140 original size:48 final size:48
Alignment explanation
Indices: 24994--25141 Score: 163
Period size: 48 Copynumber: 3.1 Consensus size: 48
24984 ATGACTGCCA
* * *
24994 ACTAAAATACGTTGTGGATAAACCACTAGTCGAGT-AGGTAAACTATCG
1 ACTAAAATACGTTGTGGATAAACCACTAGT-TAATCAGATAAACTATCG
* * * * * *
25042 AGTTAAATACGTTGTGGATAAACCACTAGTTGAGCAAATAAACTACCG
1 ACTAAAATACGTTGTGGATAAACCACTAGTTAATCAGATAAACTATCG
* * * *
25090 ACTAAAATACATTGTGGATAAACCATTGGTTAATCAGATAAACTGTCG
1 ACTAAAATACGTTGTGGATAAACCACTAGTTAATCAGATAAACTATCG
25138 ACTA
1 ACTA
25142 CTTCCTCCGT
Statistics
Matches: 80, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
48 80 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.26
Consensus pattern (48 bp):
ACTAAAATACGTTGTGGATAAACCACTAGTTAATCAGATAAACTATCG
Found at i:30740 original size:9 final size:9
Alignment explanation
Indices: 30726--30755 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
30716 TTATATTTTC
30726 TTTTTGAAT
1 TTTTTGAAT
30735 TTTTTG-AT
1 TTTTTGAAT
30743 TTTTTGAAT
1 TTTTTGAAT
30752 TTTT
1 TTTT
30756 AAATATCGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.73
Consensus pattern (9 bp):
TTTTTGAAT
Found at i:31471 original size:8 final size:8
Alignment explanation
Indices: 31460--31484 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
31450 TACATTTATA
31460 AAAATATT
1 AAAATATT
31468 AAAATATT
1 AAAATATT
31476 AAAATATT
1 AAAATATT
31484 A
1 A
31485 TTTTACACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
AAAATATT
Found at i:31744 original size:29 final size:31
Alignment explanation
Indices: 31690--31747 Score: 93
Period size: 29 Copynumber: 1.9 Consensus size: 31
31680 TATATTTTAT
31690 ATATTTGGATAAATATATTTTATAAAATTTG
1 ATATTTGGATAAATATATTTTATAAAATTTG
*
31721 ATATTT-GATATATAT-TTTTATAAAATT
1 ATATTTGGATAAATATATTTTATAAAATT
31748 GGATGTGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 12 0.46
30 8 0.31
31 6 0.23
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (31 bp):
ATATTTGGATAAATATATTTTATAAAATTTG
Found at i:31763 original size:28 final size:31
Alignment explanation
Indices: 31701--31766 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 31
31691 TATTTGGATA
* * *
31701 AATATATTTTATAAAATTTGATATTTGATAT
1 AATATATTTTATAAAATTTGAGATGTGAAAT
31732 -ATAT-TTTTATAAAA-TTG-GATGTGAAAT
1 AATATATTTTATAAAATTTGAGATGTGAAAT
31759 AATATATT
1 AATATATT
31767 AATAATATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 7 0.23
28 7 0.23
29 12 0.40
30 4 0.13
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.48
Consensus pattern (31 bp):
AATATATTTTATAAAATTTGAGATGTGAAAT
Found at i:41246 original size:67 final size:67
Alignment explanation
Indices: 41138--41271 Score: 268
Period size: 67 Copynumber: 2.0 Consensus size: 67
41128 CCATTTATGC
41138 TAATGGCATATGAAACAGTCGAAACACATTGCATAATCTTCTCTACCCATTCAGGCGCAAAGCCT
1 TAATGGCATATGAAACAGTCGAAACACATTGCATAATCTTCTCTACCCATTCAGGCGCAAAGCCT
41203 AT
66 AT
41205 TAATGGCATATGAAACAGTCGAAACACATTGCATAATCTTCTCTACCCATTCAGGCGCAAAGCCT
1 TAATGGCATATGAAACAGTCGAAACACATTGCATAATCTTCTCTACCCATTCAGGCGCAAAGCCT
41270 AT
66 AT
41272 AGCCCCCATC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.25
Consensus pattern (67 bp):
TAATGGCATATGAAACAGTCGAAACACATTGCATAATCTTCTCTACCCATTCAGGCGCAAAGCCT
AT
Found at i:44657 original size:21 final size:22
Alignment explanation
Indices: 44618--44658 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
44608 AATATATTGT
*
44618 TTTTAAAATATATTTAATAATA
1 TTTTAAAATATATTAAATAATA
*
44640 TTTTAGAAT-TATTAAATAA
1 TTTTAAAATATATTAAATAA
44659 AGAAATTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TTTTAAAATATATTAAATAATA
Found at i:46539 original size:29 final size:30
Alignment explanation
Indices: 46302--46576 Score: 238
Period size: 30 Copynumber: 9.3 Consensus size: 30
46292 AAAAATTATG
* * ****
46302 TTTTAACCCCTAAGCTTTTCCAAAATTGTG
1 TTTTAACCCCTAAACTTTCCCAAAATCACA
* * **
46332 TTTTAACCCTTAAA-TTTCTCAAAATTTGCA
1 TTTTAACCCCTAAACTTTCCCAAAA-TCACA
* * * * *
46362 TTTTGATCCTTAAAC-TTCTCAAAAATTACA
1 TTTTAACCCCTAAACTTTC-CCAAAATCACA
* * *
46392 TTTTAACACTTAAACTTTTCCAAAATCACA
1 TTTTAACCCCTAAACTTTCCCAAAATCACA
**
46422 TTTTAACCCCTAAACTTTTTCAAAATCACA
1 TTTTAACCCCTAAACTTTCCCAAAATCACA
*
46452 TTTTAACCCCCAAACTTTCCCAAAATCACA
1 TTTTAACCCCTAAACTTTCCCAAAATCACA
*
46482 TTTTAA-CCC-AAACTTTCCTAAAA-CTACA
1 TTTTAACCCCTAAACTTTCCCAAAATC-ACA
*
46510 TTTTAACTCCTAAAC-TTCCCAAAATCACA
1 TTTTAACCCCTAAACTTTCCCAAAATCACA
* * * *
46539 TTTTTACCCCTAAACTTTCCCAAATTTATA
1 TTTTAACCCCTAAACTTTCCCAAAATCACA
46569 TTTTAACC
1 TTTTAACC
46577 TTAATTTCTC
Statistics
Matches: 204, Mismatches: 32, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
27 1 0.00
28 22 0.11
29 37 0.18
30 138 0.68
31 6 0.03
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.37
Consensus pattern (30 bp):
TTTTAACCCCTAAACTTTCCCAAAATCACA
Found at i:46556 original size:87 final size:89
Alignment explanation
Indices: 46383--46577 Score: 254
Period size: 87 Copynumber: 2.2 Consensus size: 89
46373 AAACTTCTCA
* **
46383 AAAATTACATTTTAACACTTAAACTTTTCCAAAATCACATTTTAACCCCTAAACTTTTTCAAAAT
1 AAAATTACATTTTAAC-CTCAAACTTTTCCAAAATCACATTTTAACCCCTAAACTTTCCCAAAAT
46448 CACATTTTAACCCCCAAACTTTCCC
65 CACATTTTAACCCCCAAACTTTCCC
* *
46473 AAAATCACATTTTAACC-CAAAC-TTTCCTAAAA-CTACATTTTAACTCCTAAAC-TTCCCAAAA
1 AAAATTACATTTTAACCTCAAACTTTTCC-AAAATC-ACATTTTAACCCCTAAACTTTCCCAAAA
* *
46534 TCACATTTTTACCCCTAAACTTTCCC
64 TCACATTTTAACCCCCAAACTTTCCC
* *
46560 AAATTTATATTTTAACCT
1 AAAATTACATTTTAACCT
46578 TAATTTCTCC
Statistics
Matches: 92, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
87 51 0.55
88 25 0.27
89 1 0.01
90 15 0.16
ACGTcount: A:0.37, C:0.28, G:0.00, T:0.35
Consensus pattern (89 bp):
AAAATTACATTTTAACCTCAAACTTTTCCAAAATCACATTTTAACCCCTAAACTTTCCCAAAATC
ACATTTTAACCCCCAAACTTTCCC
Found at i:63457 original size:17 final size:17
Alignment explanation
Indices: 63435--63483 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
63425 ATAATTTTAT
63435 AAAATTTAAAAATATAA
1 AAAATTTAAAAATATAA
**
63452 AAAA-TTAAAAATACTTT
1 AAAATTTAAAAATA-TAA
*
63469 AAAATTCAAAAATAT
1 AAAATTTAAAAATAT
63484 TTTTTTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 9 0.33
17 10 0.37
18 8 0.30
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAATTTAAAAATATAA
Found at i:66815 original size:30 final size:30
Alignment explanation
Indices: 66710--66964 Score: 290
Period size: 30 Copynumber: 8.6 Consensus size: 30
66700 TTTGGGCGTT
*
66710 AAAATGTGA-TTTTGAAAAGTTTACGGGTA
1 AAAATGTGATTTTTGAAAAGTTTAAGGGTA
* *
66739 AAAATGT-AATTTTAAAAAGTTT-AGGGTAA
1 AAAATGTGATTTTTGAAAAGTTTAAGGGT-A
* * *
66768 AAAATGTTA-TTTAGAAAAGTTTGA-GGTAA
1 AAAATGTGATTTTTGAAAAGTTTAAGGGT-A
* *
66797 AAAATATGATTTTTGAAAAGTTTAAGGGTT
1 AAAATGTGATTTTTGAAAAGTTTAAGGGTA
*
66827 AAAATG-GAATTTTTGAAAAGTTTAAGGGTT
1 AAAATGTG-ATTTTTGAAAAGTTTAAGGGTA
* *
66857 AAAATGTGATTTTTGAAAAGTTTAGGGGTC
1 AAAATGTGATTTTTGAAAAGTTTAAGGGTA
*
66887 AAAATGTGATTTTTGAAAAGTTTAA-TGTCAA
1 AAAATGTGATTTTTGAAAAGTTTAAGGGT--A
*
66918 AAAATGTGATTTTTGAAAAGTTTAAGGGTT
1 AAAATGTGATTTTTGAAAAGTTTAAGGGTA
*
66948 AAAATGTAATTTTTGAA
1 AAAATGTGATTTTTGAA
66965 TAAAATAGGG
Statistics
Matches: 197, Mismatches: 18, Indels: 21
0.83 0.08 0.09
Matches are distributed among these distances:
28 5 0.03
29 53 0.27
30 108 0.55
31 29 0.15
32 2 0.01
ACGTcount: A:0.41, C:0.01, G:0.21, T:0.37
Consensus pattern (30 bp):
AAAATGTGATTTTTGAAAAGTTTAAGGGTA
Found at i:69117 original size:208 final size:208
Alignment explanation
Indices: 68600--69567 Score: 1221
Period size: 208 Copynumber: 4.7 Consensus size: 208
68590 GTTGCATCTC
* * * * *
68600 TTGGTTTACTTCTCTACATCTCAT-AAGGAAGATGACCGCTTCATTGTTTTAATCCACTTCTCTG
1 TTGGTCTACTTCTCTATATCTCATCAA-GAAGATGATCGCCTCATTGTTTCAATCCACTTCTCTG
* * *
68664 TATCTCATTAGGAAGACGGATTTGGTTCACTCCTCTGCATCTCGTCAA-GAAAATGAACACTTTA
65 TATCTCATTAGGAAGACGGATTTGGTTCACTTCTCTGCATCTCGT-AAGGAAGATGACCACTTTA
* * * * *
68728 TTGCTTCAACTCACTCCTCTATATCTCATCAAGAAGATGGGGTTTGGAAGTTTCACTCATATTAA
129 TTGCTTCGACCCACTTCTCTATATCTCATCAGGAAGATGGGGTTT-GAAGTCTCACTCATATTAA
*
68793 GCTTCACTTCATTGAA-
193 GCTTCGCTTCATT-AAT
* * * * * *
68809 TTGGTCTTCTTCTCTATATCTCATC-AGAAAGATGATCGCTTCATTATTTTAATACACTTCTTTG
1 TTGGTCTACTTCTCTATATCTCATCAAG-AAGATGATCGCCTCATTGTTTCAATCCACTTCTCTG
* * * ** *
68873 TATCTCATTAGGAAGATGGATTTAGTTCATTTCTCTGCATCTCGTAAAAAAGATGAACACTTTAT
65 TATCTCATTAGGAAGACGGATTTGGTTCACTTCTCTGCATCTCGTAAGGAAGATGACCACTTTAT
* * * *
68938 TGCTTCGACCCACTTTTCTATATCTCATCAGGAAGATGGGGTTTGAAGTGTCATTCATATTGAGC
130 TGCTTCGACCCACTTCTCTATATCTCATCAGGAAGATGGGGTTTGAAGTCTCACTCATATTAAGC
69003 TTCGCTTCATTAAT
195 TTCGCTTCATTAAT
* * * *
69017 TTGGTCTACTTATCTGTATCTCATCAAGAAGATGACCGCCTCATTGTTTCAATCCACTTCTTTGT
1 TTGGTCTACTTCTCTATATCTCATCAAGAAGATGATCGCCTCATTGTTTCAATCCACTTCTCTGT
* * *
69082 ATCTCATCAGGAAGACGGATTTGGTTCACTTCTCTGCATCTCATTAGGAAGATGACCA-TTTATT
66 ATCTCATTAGGAAGACGGATTTGGTTCACTTCTCTGCATCTCGTAAGGAAGATGACCACTTTATT
* * * * *
69146 AG-TTCGACCCACTTCTATGTATCTCATCAGAAAGATGGGGTTTGAAGTCTCATTCATATTGAGC
131 -GCTTCGACCCACTTCTCTATATCTCATCAGGAAGATGGGGTTTGAAGTCTCACTCATATTAAGC
*
69210 TTCGCTTCATTTAT
195 TTCGCTTCATTAAT
69224 TTGGTCTACTTCTCTATATCTCATCAAGAAGATGATCGCCTCATTGTTTCAATCCACTTCTCTGT
1 TTGGTCTACTTCTCTATATCTCATCAAGAAGATGATCGCCTCATTGTTTCAATCCACTTCTCTGT
* * * * * * * *
69289 ATCTCATCAGGAAGACAGATTTGATCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATT
66 ATCTCATTAGGAAGACGGATTTGGTTCACTTCTCTGCATCTCGTAAGGAAGATGACCACTTTATT
* * *
69354 GCTTTGACCCACTTCTCTATATCTCATCAGGAAGATGGGGTTTGAAGTCTCACCCGTATTAAGCT
131 GCTTCGACCCACTTCTCTATATCTCATCAGGAAGATGGGGTTTGAAGTCTCACTCATATTAAGCT
* *
69419 TCGCTTCAATGAT
196 TCGCTTCATTAAT
* * * * ** *
69432 TTGGTCTACTTTTCTATATCTTATTAGGAAGATGATTACCTTATTGATTT-AATCCACTTCTCTG
1 TTGGTCTACTTCTCTATATCTCATCAAGAAGATGATCGCCTCATTG-TTTCAATCCACTTCTCTG
** * *
69496 TATCTCATTAAAAAGACGGAATTGGTTCACTTCTCTGCATCTCGTTAGGAAGATGACCACTTTAT
65 TATCTCATTAGGAAGACGGATTTGGTTCACTTCTCTGCATCTCGTAAGGAAGATGACCACTTTAT
69561 TGCTTCG
130 TGCTTCG
69568 GATGACTTCA
Statistics
Matches: 666, Mismatches: 84, Indels: 19
0.87 0.11 0.02
Matches are distributed among these distances:
207 192 0.29
208 320 0.48
209 154 0.23
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (208 bp):
TTGGTCTACTTCTCTATATCTCATCAAGAAGATGATCGCCTCATTGTTTCAATCCACTTCTCTGT
ATCTCATTAGGAAGACGGATTTGGTTCACTTCTCTGCATCTCGTAAGGAAGATGACCACTTTATT
GCTTCGACCCACTTCTCTATATCTCATCAGGAAGATGGGGTTTGAAGTCTCACTCATATTAAGCT
TCGCTTCATTAAT
Found at i:69366 original size:85 final size:85
Alignment explanation
Indices: 69222--69388 Score: 228
Period size: 85 Copynumber: 2.0 Consensus size: 85
69212 CGCTTCATTT
* * * *
69222 ATTTGGTCTACTTCTCTATATCTCATCAAGAAGATGATCGCCTCATTGTTTCAATCCACTTCTCT
1 ATTTGATCCACTTCTCTATATCTCATCAAGAAGATGACCGCCTCATTGTTTCAACCCACTTCTCT
*
69287 GTATCTCATCAGGAAGACAG
66 ATATCTCATCAGGAAGACAG
* * * * *
69307 ATTTGATCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTT-GACCCACTTCTC
1 ATTTGATCCACTTCTCTATATCTCATCAAGAAGATGACCGCCTCATTG-TTTCAACCCACTTCTC
69371 TATATCTCATCAGGAAGA
65 TATATCTCATCAGGAAGA
69389 TGGGGTTTGA
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
85 68 0.96
86 3 0.04
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.35
Consensus pattern (85 bp):
ATTTGATCCACTTCTCTATATCTCATCAAGAAGATGACCGCCTCATTGTTTCAACCCACTTCTCT
ATATCTCATCAGGAAGACAG
Found at i:69389 original size:415 final size:415
Alignment explanation
Indices: 68600--69566 Score: 1253
Period size: 415 Copynumber: 2.3 Consensus size: 415
68590 GTTGCATCTC
* * * *
68600 TTGGTTTACTTCTCTACATCTCATAAGGAAGATGACCGCTTCATTGTTTTAATCCACTTCTCTGT
1 TTGGTCTACTTATCTATATCTCATAA-GAAGATGACCGCCTCATTG-TTTAATCCACTTCTCTGT
* * * * *
68665 ATCTCATTAGGAAGACGGATTTGGTTCACTCCTCTGCATCTCGTCAAGAAAATGAACACTTTATT
64 ATCTCATTAGGAAGACGGATTTGGTTCACTTCTCTGCATCTCGTTAGGAAGATGACCACTTTATT
* * *
68730 GCTTCAACTCACTCCTCTATATCTCATCAAGAAGATGGGGTTTGGAAGTTTCACTCATATTAAGC
129 GCTTCAACCCACTCCTATATATCTCATCAAGAAGATGGGGTTTGGAAGTCTCACTCATATTAAGC
* * *
68795 TTCACTTCATTGAATTGGTCTTCTTCTCTATATCTCATCAGAAAGATGATCGCTTCATTATTTTA
194 TTCACTTCATTGAATTGGTCTACTTCTCTATATCTCATCAGAAAGATGATCGCCTCATTATTTCA
* * ** * * *
68860 ATACACTTCTTTGTATCTCATTAGGAAGATGGATTTAGTTCATTTCTCTGCATCTCGTAAAAAAG
259 ATACACTTCTCTGTATCTCATCAGGAAGACAGATTTAGTCCACTTCTCTGCATCTCATAAAAAAG
* *
68925 ATGAACACTTTATTGCTTCGACCCACTTTTCTATATCTCATCAGGAAGATGGGGTTTGAAGTGTC
324 ATGAACACTTTATTGCTTCGACCCACTTCTCTATATCTCATCAGGAAGATGGGGTTTGAAGTCTC
** * *
68990 ATTCATATTGAGCTTCGCTTCATTAAT
389 ACCCATATTAAGCTTCGCTTCAATAAT
* *
69017 TTGGTCTACTTATCTGTATCTCATCAAGAAGATGACCGCCTCATTGTTTCAATCCACTTCTTTGT
1 TTGGTCTACTTATCTATATCTCAT-AAGAAGATGACCGCCTCATTGTTT-AATCCACTTCTCTGT
* *
69082 ATCTCATCAGGAAGACGGATTTGGTTCACTTCTCTGCATCTCATTAGGAAGATGACCA-TTTATT
64 ATCTCATTAGGAAGACGGATTTGGTTCACTTCTCTGCATCTCGTTAGGAAGATGACCACTTTATT
* * * * *
69146 AG-TTCGACCCACTTCTATGTATCTCATC-AGAAAGATGGGGTTT-GAAGTCTCATTCATATTGA
129 -GCTTCAACCCACTCCTATATATCTCATCAAG-AAGATGGGGTTTGGAAGTCTCACTCATATTAA
* * * *
69208 GCTTCGCTTCATTTATTTGGTCTACTTCTCTATATCTCATCA-AGAAGATGATCGCCTCATTGTT
192 GCTTCACTTCATTGAATTGGTCTACTTCTCTATATCTCATCAGA-AAGATGATCGCCTCATTATT
* * * *
69272 TCAATCCACTTCTCTGTATCTCATCAGGAAGACAGATTT-GATCCACTTCTCTGTATCTCATCAG
256 TCAATACACTTCTCTGTATCTCATCAGGAAGACAGATTTAG-TCCACTTCTCTGCATCTCATAAA
* * * *
69336 GAAGATGACCGCTTTATTGCTTTGACCCACTTCTCTATATCTCATCAGGAAGATGGGGTTTGAAG
320 AAAGATGAACACTTTATTGCTTCGACCCACTTCTCTATATCTCATCAGGAAGATGGGGTTTGAAG
* *
69401 TCTCACCCGTATTAAGCTTCGCTTCAATGAT
385 TCTCACCCATATTAAGCTTCGCTTCAATAAT
* * * *** *
69432 TTGGTCTACTTTTCTATATCTTATTAGGAAGATGATTACCTTATTGATTTAATCCACTTCTCTGT
1 TTGGTCTACTTATCTATATCTCA-TAAGAAGATGACCGCCTCATTG-TTTAATCCACTTCTCTGT
** *
69497 ATCTCATTAAAAAGACGGAATTGGTTCACTTCTCTGCATCTCGTTAGGAAGATGACCACTTTATT
64 ATCTCATTAGGAAGACGGATTTGGTTCACTTCTCTGCATCTCGTTAGGAAGATGACCACTTTATT
69562 GCTTC
129 GCTTC
69567 GGATGACTTC
Statistics
Matches: 475, Mismatches: 65, Indels: 21
0.85 0.12 0.04
Matches are distributed among these distances:
414 2 0.00
415 312 0.66
416 55 0.12
417 104 0.22
418 2 0.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.38
Consensus pattern (415 bp):
TTGGTCTACTTATCTATATCTCATAAGAAGATGACCGCCTCATTGTTTAATCCACTTCTCTGTAT
CTCATTAGGAAGACGGATTTGGTTCACTTCTCTGCATCTCGTTAGGAAGATGACCACTTTATTGC
TTCAACCCACTCCTATATATCTCATCAAGAAGATGGGGTTTGGAAGTCTCACTCATATTAAGCTT
CACTTCATTGAATTGGTCTACTTCTCTATATCTCATCAGAAAGATGATCGCCTCATTATTTCAAT
ACACTTCTCTGTATCTCATCAGGAAGACAGATTTAGTCCACTTCTCTGCATCTCATAAAAAAGAT
GAACACTTTATTGCTTCGACCCACTTCTCTATATCTCATCAGGAAGATGGGGTTTGAAGTCTCAC
CCATATTAAGCTTCGCTTCAATAAT
Found at i:69665 original size:41 final size:40
Alignment explanation
Indices: 69620--70014 Score: 405
Period size: 41 Copynumber: 9.7 Consensus size: 40
69610 AGCTACAAAT
* *
69620 TGCCCCTCTTGATTAGGGGTAAAAGATCGAAATCTCCAATC
1 TGCCCCTCTTGATTAAGGGTAAAAGA-CGAAATCTTCAATC
* * *
69661 TGCCCTTCTTGATTAAGGATAAAAGACTAGAATCTTCAA-C
1 TGCCCCTCTTGATTAAGGGTAAAAGACGA-AATCTTCAATC
* * * * *
69701 TTGCCCCTTTTGATTAGGGGTAAAAGATTGGAATCTTCAATG
1 -TGCCCCTCTTGATTAAGGGTAAAAGA-CGAAATCTTCAATC
*
69743 TGTCCCTCTTGATTAAGGGTAAAAGACTGAAATCTTCAATC
1 TGCCCCTCTTGATTAAGGGTAAAAGAC-GAAATCTTCAATC
** * * * *
69784 TGCCTTTTTTTATTAAGGGTAAAAGACTGGAATCTTTAATC
1 TGCCCCTCTTGATTAAGGGTAAAAGAC-GAAATCTTCAATC
* *
69825 AGCCTCTCTTGATTAAGGGTAAAAGACTGAAATCTTCAATC
1 TGCCCCTCTTGATTAAGGGTAAAAGAC-GAAATCTTCAATC
* * *
69866 TGCCCTTCTTGATTAAGTGTAAAAGATTGAAATCTTCAATC
1 TGCCCCTCTTGATTAAGGGTAAAAGA-CGAAATCTTCAATC
* * ** *
69907 AGTCATTCTTGATTAAGGGTAAAAGACCAAATCTTCAATC
1 TGCCCCTCTTGATTAAGGGTAAAAGACGAAATCTTCAATC
* * *
69947 TACCCTTCTTGATTAAGGGTAAAAGACTGGAATCTTCAATC
1 TGCCCCTCTTGATTAAGGGTAAAAGAC-GAAATCTTCAATC
**
69988 TGCCCCTCTTGACTTTGGGGTAAAAGA
1 TGCCCCTCTTGA-TTAAGGGTAAAAGA
70015 TTGGAATGAT
Statistics
Matches: 293, Mismatches: 53, Indels: 15
0.81 0.15 0.04
Matches are distributed among these distances:
40 38 0.13
41 243 0.83
42 12 0.04
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (40 bp):
TGCCCCTCTTGATTAAGGGTAAAAGACGAAATCTTCAATC
Found at i:69807 original size:123 final size:121
Alignment explanation
Indices: 69623--70015 Score: 477
Period size: 123 Copynumber: 3.2 Consensus size: 121
69613 TACAAATTGC
* * * *
69623 CCCTCTTGATTAGGGGTAAAAGATCGAAATCTCCAATCTGCCCTTCTTGATTAAGGATAAAAGAC
1 CCCTCTTGATTAAGGGTAAAAGAT-GAAATCTTCAATCTGCCATTCTTGATTAAGGGTAAAAGAC
* * *
69688 TAGAATCTTCAA-CTTGCCCCTTTTGATTAGGGGTAAAAGATTGGAATCTTCAATGTG
65 TAGAATCTTCAATC-TGCCCCTTTTGATTAAGGGTAAAAGACTGGAATCTTCAATCTG
* * *
69745 TCCCTCTTGATTAAGGGTAAAAGACTGAAATCTTCAATCTGCCTTTTTTTATTAAGGGTAAAAGA
1 -CCCTCTTGATTAAGGGTAAAAGA-TGAAATCTTCAATCTGCCATTCTTGATTAAGGGTAAAAGA
* * * * * *
69810 CTGGAATCTTTAATCAGCCTCTCTTGATTAAGGGTAAAAGACTGAAATCTTCAATCTG
64 CTAGAATCTTCAATCTGCCCCTTTTGATTAAGGGTAAAAGACTGGAATCTTCAATCTG
* * *
69868 CCCTTCTTGATTAAGTGTAAAAGATTGAAATCTTCAATCAGTCATTCTTGATTAAGGGTAAAAGA
1 CCC-TCTTGATTAAGGGTAAAAGA-TGAAATCTTCAATCTGCCATTCTTGATTAAGGGTAAAAGA
* *
69933 CCA-AATCTTCAATCT-ACCCTTCTTGATTAAGGGTAAAAGACTGGAATCTTCAATCTG
64 CTAGAATCTTCAATCTGCCCCTT-TTGATTAAGGGTAAAAGACTGGAATCTTCAATCTG
**
69990 CCCCTCTTGACTTTGGGGTAAAAGAT
1 -CCCTCTTGA-TTAAGGGTAAAAGAT
70016 TGGAATGATA
Statistics
Matches: 231, Mismatches: 33, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
121 3 0.01
122 54 0.23
123 172 0.74
124 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (121 bp):
CCCTCTTGATTAAGGGTAAAAGATGAAATCTTCAATCTGCCATTCTTGATTAAGGGTAAAAGACT
AGAATCTTCAATCTGCCCCTTTTGATTAAGGGTAAAAGACTGGAATCTTCAATCTG
Found at i:70484 original size:50 final size:50
Alignment explanation
Indices: 70272--70598 Score: 233
Period size: 50 Copynumber: 6.6 Consensus size: 50
70262 AGGTTCATAT
* * * * **
70272 TTGCGACCTCAACCTTTTCCTTCA-ACTCTTC-ATGGTACCGGGCTCGCTG
1 TTGCGGCCTCAACCTTTCCCTTCACA-TCTTCTAAGGTACCGGGTTCGCCA
* * * * * **
70321 TTGCAGCCTCAACATTTCCCATCACAT-TTCATCAA---ACCAGATTTACCA
1 TTGCGGCCTCAACCTTTCCCTTCACATCTTC-T-AAGGTACCGGGTTCGCCA
* * * *
70369 TTGCGGCCTCAATCC-TCCCCATCACATCTTCTAAGGTACCGGATTCGTCA
1 TTGCGGCCTCAA-CCTTTCCCTTCACATCTTCTAAGGTACCGGGTTCGCCA
* * * * *
70419 TTACGACCTCGACCTTTCCCTTCACATTTTCTAAGGTACCGGGTTCACCA
1 TTGCGGCCTCAACCTTTCCCTTCACATCTTCTAAGGTACCGGGTTCGCCA
70469 TTGCGGCCTCAACCTTT-CCTATCACATCTTCTAAGGTACCGGGTTCGCCA
1 TTGCGGCCTCAACCTTTCCCT-TCACATCTTCTAAGGTACCGGGTTCGCCA
* * ** * * * ***
70519 TTGTGACCTCAAATTTTCCCTCCAAATC-T-TAATGGTACTGGGTTCGTTG
1 TTGCGGCCTCAACCTTTCCCTTCACATCTTCTAA-GGTACCGGGTTCGCCA
*
70568 TTGCGGCCTCAACCTTTCCCTTCAAATCTTC
1 TTGCGGCCTCAACCTTTCCCTTCACATCTTC
70599 ATGGTACTGC
Statistics
Matches: 214, Mismatches: 49, Indels: 28
0.74 0.17 0.10
Matches are distributed among these distances:
47 2 0.01
48 35 0.16
49 65 0.30
50 108 0.50
51 4 0.02
ACGTcount: A:0.20, C:0.33, G:0.15, T:0.32
Consensus pattern (50 bp):
TTGCGGCCTCAACCTTTCCCTTCACATCTTCTAAGGTACCGGGTTCGCCA
Found at i:71412 original size:7 final size:6
Alignment explanation
Indices: 71385--71466 Score: 57
Period size: 7 Copynumber: 13.5 Consensus size: 6
71375 GACCTCTCTC
*
71385 TTTCTT TTTC-T TGT-TT TTTCTAT TTTCTT TTTCCTT TTTCTT TTT-TT
1 TTTCTT TTTCTT TTTCTT TTTCT-T TTTCTT TTT-CTT TTTCTT TTTCTT
*
71432 CTT-TT TTTCATT TTTCCTT TCTT-TT CTTTCTT TTT
1 TTTCTT TTTC-TT TTT-CTT T-TTCTT -TTTCTT TTT
71467 TATTTAATTT
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
5 14 0.23
6 22 0.35
7 23 0.37
8 3 0.05
ACGTcount: A:0.02, C:0.17, G:0.01, T:0.79
Consensus pattern (6 bp):
TTTCTT
Found at i:71424 original size:30 final size:30
Alignment explanation
Indices: 71388--71471 Score: 90
Period size: 29 Copynumber: 2.9 Consensus size: 30
71378 CTCTCTCTTT
71388 CTTTTTCTTGTTTTT-TCTATTTTC-TTTTTC
1 CTTTTTCTT-TTTTTCT-TATTTTCATTTTTC
*
71418 CTTTTTCTTTTTTTCTTTTTTTCATTTTTC
1 CTTTTTCTTTTTTTCTTATTTTCATTTTTC
71448 C--TTTCTTTTCTTTCTT-TTTT-ATTT
1 CTTTTTCTTTT-TTTCTTATTTTCATTT
71472 AATTTTCTTC
Statistics
Matches: 50, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
27 4 0.08
28 12 0.24
29 17 0.34
30 17 0.34
ACGTcount: A:0.04, C:0.17, G:0.01, T:0.79
Consensus pattern (30 bp):
CTTTTTCTTTTTTTCTTATTTTCATTTTTC
Found at i:71430 original size:29 final size:30
Alignment explanation
Indices: 71388--71471 Score: 97
Period size: 28 Copynumber: 2.9 Consensus size: 30
71378 CTCTCTCTTT
*
71388 CTTTTTCTTGTTTTTTCTATTTTC-TTTTTC
1 CTTTTTCTT-TTTTTTCTTTTTTCATTTTTC
71418 CTTTTTC-TTTTTTTCTTTTTTTCATTTTTC
1 CTTTTTCTTTTTTTTC-TTTTTTCATTTTTC
*
71448 C--TTTCTTTTCTTTCTTTTTT-ATTT
1 CTTTTTCTTTTTTTTCTTTTTTCATTT
71472 AATTTTCTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
27 4 0.08
28 17 0.35
29 14 0.29
30 14 0.29
ACGTcount: A:0.04, C:0.17, G:0.01, T:0.79
Consensus pattern (30 bp):
CTTTTTCTTTTTTTTCTTTTTTCATTTTTC
Found at i:71452 original size:20 final size:20
Alignment explanation
Indices: 71429--71466 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
71419 TTTTTCTTTT
71429 TTTCTTTT-TTTCATTTTTCC
1 TTTCTTTTCTTTC-TTTTTCC
71449 TTTCTTTTCTTTCTTTTT
1 TTTCTTTTCTTTCTTTTT
71467 TATTTAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTCTTTTCTTTCTTTTTCC
Found at i:72115 original size:20 final size:21
Alignment explanation
Indices: 72090--72130 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
72080 TTTCATCTTG
72090 ACTTTTCTTT-CTTTT-TTTTT
1 ACTTTT-TTTGCTTTTCTTTTT
72110 ACTTTTTTTGCTTTTCTTTTT
1 ACTTTTTTTGCTTTTCTTTTT
72131 TATAACACGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.16
20 11 0.58
21 5 0.26
ACGTcount: A:0.05, C:0.15, G:0.02, T:0.78
Consensus pattern (21 bp):
ACTTTTTTTGCTTTTCTTTTT
Found at i:76666 original size:30 final size:30
Alignment explanation
Indices: 76604--76783 Score: 160
Period size: 30 Copynumber: 6.2 Consensus size: 30
76594 TTGAAATGTG
* * * *
76604 ATTTTGGGAAACTTTAGGGGT--TAATATG
1 ATTTTGGAAAAGTTTAGGGGTAAAAATATA
76632 ATTTTGGAAAAGTTTAGGGGTAAAAATATA
1 ATTTTGGAAAAGTTTAGGGGTAAAAATATA
* *
76662 ATTTT-GAAAAGTTT-GAGGGTGAAAAATGTT
1 ATTTTGGAAAAGTTTAG-GGGT-AAAAATATA
* *
76692 ATTTTGGAAAA-TTT-TGGGTAAAAATGTA
1 ATTTTGGAAAAGTTTAGGGGTAAAAATATA
* * * *
76720 ATTTTTGAAAAGTTTAAGGGTCAAAATGTA
1 ATTTTGGAAAAGTTTAGGGGTAAAAATATA
*
76750 GATTTT-GAAAAGTTTA-GGGTTAAAATATA
1 -ATTTTGGAAAAGTTTAGGGGTAAAAATATA
76779 ATTTT
1 ATTTT
76784 TTAATAAAAT
Statistics
Matches: 131, Mismatches: 13, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
28 43 0.33
29 31 0.24
30 47 0.36
31 10 0.08
ACGTcount: A:0.38, C:0.01, G:0.23, T:0.38
Consensus pattern (30 bp):
ATTTTGGAAAAGTTTAGGGGTAAAAATATA
Found at i:76681 original size:29 final size:28
Alignment explanation
Indices: 76626--76783 Score: 165
Period size: 30 Copynumber: 5.4 Consensus size: 28
76616 TTTAGGGGTT
*
76626 AATATGATTTTGGAAAAGTTTAGGGGTAAA
1 AATATAATTTT-GAAAAGTTTA-GGGTAAA
76656 AATATAATTTTGAAAAGTTTGAGGGTGAAA
1 AATATAATTTTGAAAAGTTT-AGGGT-AAA
* * *
76686 AATGTTATTTTGGAAAA-TTTTGGGTAAA
1 AATATAATTTT-GAAAAGTTTAGGGTAAA
* *
76714 AATGTAATTTTTGAAAAGTTTAAGGGTCAA
1 AATATAA-TTTTGAAAAGTTT-AGGGTAAA
* *
76744 AATGTAGATTTTGAAAAGTTTAGGGTTAA
1 AATATA-ATTTTGAAAAGTTTAGGGTAAA
76773 AATATAATTTT
1 AATATAATTTT
76784 TTAATAAAAT
Statistics
Matches: 112, Mismatches: 9, Indels: 16
0.82 0.07 0.12
Matches are distributed among these distances:
28 19 0.17
29 36 0.32
30 51 0.46
31 6 0.05
ACGTcount: A:0.40, C:0.01, G:0.22, T:0.38
Consensus pattern (28 bp):
AATATAATTTTGAAAAGTTTAGGGTAAA
Found at i:76740 original size:59 final size:60
Alignment explanation
Indices: 76631--76784 Score: 208
Period size: 59 Copynumber: 2.6 Consensus size: 60
76621 GGGTTAATAT
*
76631 GATTTTGGAAAAGTTTAGGGGTAAAAATATAA-TTTTGAAAAGTTTGAGGGTGAAAAATGT-
1 GATTTTGGAAAAGTTTA-GGGTAAAAATATAATTTTTGAAAAGTTTAAGGGT-AAAAATGTA
* * * *
76691 TATTTTGGAAAA-TTTTGGGTAAAAATGTAATTTTTGAAAAGTTTAAGGGTCAAAATGTA
1 GATTTTGGAAAAGTTTAGGGTAAAAATATAATTTTTGAAAAGTTTAAGGGTAAAAATGTA
*
76750 GATTTT-GAAAAGTTTAGGGTTAAAATATAATTTTT
1 GATTTTGGAAAAGTTTAGGGTAAAAATATAATTTTT
76785 TAATAAAATA
Statistics
Matches: 82, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
58 25 0.30
59 46 0.56
60 11 0.13
ACGTcount: A:0.39, C:0.01, G:0.22, T:0.38
Consensus pattern (60 bp):
GATTTTGGAAAAGTTTAGGGTAAAAATATAATTTTTGAAAAGTTTAAGGGTAAAAATGTA
Found at i:77617 original size:16 final size:17
Alignment explanation
Indices: 77592--77624 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
77582 TTCTTTGAAT
*
77592 CTATT-TTTTTTTTTTG
1 CTATTCTTTTTATTTTG
77608 CTATTCTTTTTATTTTG
1 CTATTCTTTTTATTTTG
77625 ATTTTTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.76
Consensus pattern (17 bp):
CTATTCTTTTTATTTTG
Found at i:84001 original size:16 final size:15
Alignment explanation
Indices: 83980--84013 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
83970 TTCTATTAAA
83980 TAATTTATTTTAATTT
1 TAATTTATTTT-ATTT
83996 TAATTTATTTTATTT
1 TAATTTATTTTATTT
84011 TAA
1 TAA
84014 AATAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TAATTTATTTTATTT
Found at i:84413 original size:2 final size:2
Alignment explanation
Indices: 84406--84438 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
84396 TCACAAGTAT
*
84406 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
84439 GCATTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Done.