Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014852.1 Kokia drynarioides strain JFW-HI SEQ_129895, 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: 730378
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 125 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:441139 original size:22 final size:22
Alignment explanation
Indices: 441107--441148 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
441097 TACTCTCTCA
*
441107 TTTTGTGTTTTTACTCATTTTCT
1 TTTTGTGTTTTCACT-ATTTTCT
441130 TTTTGT-TTTTCACTATTTT
1 TTTTGTGTTTTCACTATTTT
441149 TCTCTTCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 7 0.39
23 6 0.33
ACGTcount: A:0.10, C:0.12, G:0.07, T:0.71
Consensus pattern (22 bp):
TTTTGTGTTTTCACTATTTTCT
Found at i:441151 original size:22 final size:22
Alignment explanation
Indices: 441107--441148 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
441097 TACTCTCTCA
441107 TTTTGTGTTTTTACTCATTTTC
1 TTTTGTGTTTTTACTCATTTTC
441129 TTTT-TGTTTTTCACT-ATTTT
1 TTTTGTGTTTTT-ACTCATTTT
441149 TCTCTTCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.10, C:0.12, G:0.07, T:0.71
Consensus pattern (22 bp):
TTTTGTGTTTTTACTCATTTTC
Found at i:443647 original size:41 final size:39
Alignment explanation
Indices: 443597--443680 Score: 141
Period size: 41 Copynumber: 2.1 Consensus size: 39
443587 GGTGTGGGTA
*
443597 TTTTTAGGGTTTTAGGTGTTAAAAATTGGATAAATGTTGGG
1 TTTTTAGGGTTTTAGGTGTTAAAAA-TCGA-AAATGTTGGG
443638 TTTTTAGGGTTTTAGGTGTTAAAAATCGAAAATGTTGGG
1 TTTTTAGGGTTTTAGGTGTTAAAAATCGAAAATGTTGGG
443677 TTTT
1 TTTT
443681 GCCACCAAGT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
39 14 0.33
40 3 0.07
41 25 0.60
ACGTcount: A:0.26, C:0.01, G:0.27, T:0.45
Consensus pattern (39 bp):
TTTTTAGGGTTTTAGGTGTTAAAAATCGAAAATGTTGGG
Found at i:453607 original size:8 final size:8
Alignment explanation
Indices: 453594--453619 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
453584 AGGAAGTAAA
453594 AAAGGAAG
1 AAAGGAAG
453602 AAAGGAAG
1 AAAGGAAG
453610 AAAGGAAG
1 AAAGGAAG
453618 AA
1 AA
453620 CCTACTGTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (8 bp):
AAAGGAAG
Found at i:455064 original size:21 final size:21
Alignment explanation
Indices: 455026--455065 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
455016 TTATTTTTTA
* **
455026 GCATTTTTTAACTTAGTGACT
1 GCATTTTCTAACCCAGTGACT
455047 GCATTTTCTAACCCAGTGA
1 GCATTTTCTAACCCAGTGA
455066 TGCTCGGTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (21 bp):
GCATTTTCTAACCCAGTGACT
Found at i:456584 original size:30 final size:30
Alignment explanation
Indices: 456521--456601 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
456511 CTAAACTTCC
* * *
456521 CTAAAAATTCAAATTTAACCCCTGAGCTTT
1 CTAAAAATTCAATTTTAACCCCTGAACTAT
*
456551 CTAAAAATTCAATTTTGACACCC-GAACTAT
1 CTAAAAATTCAATTTTAAC-CCCTGAACTAT
* *
456581 CTAAAATTTCATTTTTAACCC
1 CTAAAAATTCAATTTTAACCC
456602 TCAATCTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 2 0.05
30 38 0.88
31 3 0.07
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.35
Consensus pattern (30 bp):
CTAAAAATTCAATTTTAACCCCTGAACTAT
Found at i:456594 original size:29 final size:28
Alignment explanation
Indices: 456538--456764 Score: 163
Period size: 30 Copynumber: 7.6 Consensus size: 28
456528 TTCAAATTTA
* *
456538 ACCCCTGAGCTTTCTAAAAATTCAATTTTG
1 ACCCC-GAACTTTCTAAAATTTC-ATTTTG
* *
456568 ACACCCGAACTATCTAAAATTTCATTTTTA
1 AC-CCCGAACTTTCTAAAATTTCA-TTTTG
* *
456598 ACCCTC-AATCTTTTTGGAAATTTCATTTTG
1 ACCC-CGAA-CTTTCT-AAAATTTCATTTTG
* *
456628 ACCCC-AAGCTTTCTAAAATTTTATTTTTT
1 ACCCCGAA-CTTTCTAAAATTTCA-TTTTG
* *
456657 ACCCCTAAACTTACTAAAATTTCATTTTTG
1 ACCCC-GAACTTTCTAAAATTTCA-TTTTG
*
456687 ACCCTCGATA-TTTCTAAAAATTTCATTTTA
1 ACCC-CGA-ACTTTCT-AAAATTTCATTTTG
*
456717 ACCTCGAACTTTCTAAAAATTTCATTTTG
1 ACCCCGAACTTTCT-AAAATTTCATTTTG
* *
456746 ACCCTTGAACTTTCCAAAA
1 ACCC-CGAACTTTCTAAAA
456765 AATTACATTC
Statistics
Matches: 160, Mismatches: 24, Indels: 27
0.76 0.11 0.13
Matches are distributed among these distances:
28 8 0.05
29 51 0.32
30 77 0.48
31 24 0.15
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.41
Consensus pattern (28 bp):
ACCCCGAACTTTCTAAAATTTCATTTTG
Found at i:456645 original size:89 final size:90
Alignment explanation
Indices: 456545--456749 Score: 231
Period size: 89 Copynumber: 2.3 Consensus size: 90
456535 TTAACCCCTG
* *
456545 AGCTTTCTAAAAATTCAATTTTGACACCC-GAAC-TATCTAAAATTTCATTTTTAACCCTCAATC
1 AGCTTTCTAAAAATTCAATTTTGAC-CCCTAAACTTA-CTAAAATTTCATTTTTAACCCTCAATA
* ** *
456608 TTTTTGGAAATTTCATTTTGACC-CCA
64 TTTCTAAAAATTTCATTTTAACCTCCA
* * * * * *
456634 AGCTTTCTAAAATTTTATTTTTTACCCCTAAACTTACTAAAATTTCATTTTTGACCCTCGATATT
1 AGCTTTCTAAAAATTCAATTTTGACCCCTAAACTTACTAAAATTTCATTTTTAACCCTCAATATT
*
456699 TCTAAAAATTTCATTTTAACCTCGA
66 TCTAAAAATTTCATTTTAACCTCCA
456724 A-CTTTCTAAAAATTTC-ATTTTGACCC
1 AGCTTTCTAAAAA-TTCAATTTTGACCC
456750 TTGAACTTTC
Statistics
Matches: 95, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
88 3 0.03
89 85 0.89
90 7 0.07
ACGTcount: A:0.31, C:0.21, G:0.05, T:0.42
Consensus pattern (90 bp):
AGCTTTCTAAAAATTCAATTTTGACCCCTAAACTTACTAAAATTTCATTTTTAACCCTCAATATT
TCTAAAAATTTCATTTTAACCTCCA
Found at i:456757 original size:89 final size:88
Alignment explanation
Indices: 456521--456757 Score: 223
Period size: 89 Copynumber: 2.6 Consensus size: 88
456511 CTAAACTTCC
* * *
456521 CTAAAAA-TTCAAATTTAACCCCTGAGCTTTCTAAAAA-TTCAATTTTGACACCCGAAC-TATCT
1 CTAAAAATTTC-ATTTTAA-CCC-GAACTTTCTAAAAATTTC-ATTTTGAC-CCTGAACTTATCT
*
456583 AAAATTTCATTTTTAACCCTCAATCTTT
61 AAAATTTCATTTTTAACCCTCAATATTT
* ** * * * * *
456611 TTGGAAATTTCATTTTGACCCCAAGCTTTCT-AAAATTTTATTTTTTACCCCTAAACTTA-CTAA
1 CTAAAAATTTCATTTTAACCCGAA-CTTTCTAAAAATTTCA-TTTTGA-CCCTGAACTTATCTAA
* *
456674 AATTTCATTTTTGACCCTCGATATTT
63 AATTTCATTTTTAACCCTCAATATTT
456700 CTAAAAATTTCATTTTAACCTCGAACTTTCTAAAAATTTCATTTTGACCCTTGAACTT
1 CTAAAAATTTCATTTTAACC-CGAACTTTCTAAAAATTTCATTTTGACCC-TGAACTT
456758 TCCAAAAAAT
Statistics
Matches: 116, Mismatches: 22, Indels: 19
0.74 0.14 0.12
Matches are distributed among these distances:
88 9 0.08
89 81 0.70
90 23 0.20
91 3 0.03
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (88 bp):
CTAAAAATTTCATTTTAACCCGAACTTTCTAAAAATTTCATTTTGACCCTGAACTTATCTAAAAT
TTCATTTTTAACCCTCAATATTT
Found at i:456765 original size:59 final size:57
Alignment explanation
Indices: 456547--456765 Score: 178
Period size: 59 Copynumber: 3.7 Consensus size: 57
456537 AACCCCTGAG
* *
456547 CTTTCTAAAAA-TTCAATTTTGACACCCGAACTATCTAAAATTTCATTTTTAACCCTCAA
1 CTTTCTAAAAATTTC-ATTTTGAC-CCCGAACTTTCAAAAATTTCATTTTTAA-CCTCAA
* ** * * * *
456606 TCTTTTTGGAAATTTCATTTTGACCCC-AAGCTTTCTAAAATTTTATTTTTTACCCCTAAA
1 -CTTTCTAAAAATTTCATTTTGACCCCGAA-CTTTCAAAAATTTCA-TTTTTA-ACCTCAA
*
456666 CTTACT-AAAATTTCATTTTTGACCCTCGATA-TTTCTAAAAATTTCA-TTTTAACCTCGAA
1 CTTTCTAAAAATTTCA-TTTTGACCC-CGA-ACTTTC-AAAAATTTCATTTTTAACCTC-AA
*
456725 CTTTCTAAAAATTTCATTTTGACCCTTGAACTTTCCAAAAA
1 CTTTCTAAAAATTTCATTTTGACCC-CGAACTTT-CAAAAA
456766 ATTACATTCT
Statistics
Matches: 130, Mismatches: 16, Indels: 27
0.75 0.09 0.16
Matches are distributed among these distances:
58 14 0.11
59 61 0.47
60 42 0.32
61 12 0.09
62 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.05, T:0.42
Consensus pattern (57 bp):
CTTTCTAAAAATTTCATTTTGACCCCGAACTTTCAAAAATTTCATTTTTAACCTCAA
Found at i:463042 original size:49 final size:49
Alignment explanation
Indices: 462986--463272 Score: 193
Period size: 49 Copynumber: 5.8 Consensus size: 49
462976 CAAGAAGATT
*
462986 TGAAGGGAAAGGTTGAGGCCGCAACAGTGAACCTGGTACCATGAAAATA
1 TGAAGGGAAAGGTTGAGGCCGCAACAGCGAACCTGGTACCATGAAAATA
** * * ** * * * * *
463035 TGAAGGGAAAGGTTGAGGTTGTAACCGTAAAACTGGCACCTTAAAAGATG
1 TGAAGGGAAAGGTTGAGGCCGCAACAGCGAACCTGGTACCATGAAA-ATA
* * * * *
463085 TGATGGGAAAGGTTGAGGCCACAACAGCAAACCTGGTACCATGAAGATT
1 TGAAGGGAAAGGTTGAGGCCGCAACAGCGAACCTGGTACCATGAAAATA
* * * * * *
463134 TGAAGGGATAGGTTGAGGACGCAACAGCGAACTTAGTACCTTAGAAGATA
1 TGAAGGGAAAGGTTGAGGCCGCAACAGCGAACCTGGTACCAT-GAAAATA
* * * * * * *
463184 TGATGGG-AAGGATTTAGGCCGTAACGGCGAACCTAGTACCCT-AAAGATT
1 TGAAGGGAAAGG-TTGAGGCCGCAACAGCGAACCTGGTACCATGAAA-ATA
* * * * *
463233 TGAAGGAAAAGGTT-AGGGTCGTAACAGCAAACCCGGTACC
1 TGAAGGGAAAGGTTGA-GGCCGCAACAGCGAACCTGGTACC
463273 TTAGAAGATG
Statistics
Matches: 183, Mismatches: 49, Indels: 12
0.75 0.20 0.05
Matches are distributed among these distances:
48 3 0.02
49 104 0.57
50 76 0.42
ACGTcount: A:0.35, C:0.16, G:0.30, T:0.19
Consensus pattern (49 bp):
TGAAGGGAAAGGTTGAGGCCGCAACAGCGAACCTGGTACCATGAAAATA
Found at i:463175 original size:99 final size:99
Alignment explanation
Indices: 462980--463246 Score: 277
Period size: 99 Copynumber: 2.7 Consensus size: 99
462970 AGGAAACAAG
* * * * *
462980 AAGATTTGAAGGGAAAGGTTGAGGCCGCAACAGTGAACCTGGTACCATGAAAATATGAAGGGAAA
1 AAGATATGATGGGAAAGGTTGAGGCCGCAACAGCGAACCTGGTACCATGAAGATTTGAAGGGAAA
** * * *
463045 GGTTGAGGTTGTAACCGTAAAACTGGCACCTTAA
66 GGTTGAGGACGCAACAGTAAAACTAGCACCTTAA
* * * *
463079 AAGATGTGATGGGAAAGGTTGAGGCCACAACAGCAAACCTGGTACCATGAAGATTTGAAGGGATA
1 AAGATATGATGGGAAAGGTTGAGGCCGCAACAGCGAACCTGGTACCATGAAGATTTGAAGGGAAA
** * *
463144 GGTTGAGGACGCAACAG-CGAACTTAGTACCTTAG
66 GGTTGAGGACGCAACAGTAAAAC-TAGCACCTTAA
* * * * * * *
463178 AAGATATGATGGG-AAGGATTTAGGCCGTAACGGCGAACCTAGTACCCTAAAGATTTGAAGGAAA
1 AAGATATGATGGGAAAGG-TTGAGGCCGCAACAGCGAACCTGGTACCATGAAGATTTGAAGGGAA
463242 AGGTT
65 AGGTT
463247 AGGGTCGTAA
Statistics
Matches: 138, Mismatches: 28, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
98 7 0.05
99 131 0.95
ACGTcount: A:0.36, C:0.15, G:0.30, T:0.20
Consensus pattern (99 bp):
AAGATATGATGGGAAAGGTTGAGGCCGCAACAGCGAACCTGGTACCATGAAGATTTGAAGGGAAA
GGTTGAGGACGCAACAGTAAAACTAGCACCTTAA
Found at i:463259 original size:99 final size:99
Alignment explanation
Indices: 462978--463286 Score: 255
Period size: 99 Copynumber: 3.1 Consensus size: 99
462968 CAAGGAAACA
* * * ** * * *
462978 AGAAGATTTGAAGGGAAAGGTTGAGGCCGCAACAGTGAACCTGGTACCATGAAA-ATATGAAGGG
1 AGAAGATGTGATGGGAAAGGTTGAGGCCACAACAGCAAACCTAGTACCAT-AAAGATTTGAAGGA
** * * * * ** *
463042 AAAGGTTGAGGTTGTAACCGTAAAACTGGCACCTT
65 AAAGGTTGAGGACGCAACAGCAAACCCAGTACCTT
* * * *
463077 AAAAGATGTGATGGGAAAGGTTGAGGCCACAACAGCAAACCTGGTACCATGAAGATTTGAAGGGA
1 AGAAGATGTGATGGGAAAGGTTGAGGCCACAACAGCAAACCTAGTACCATAAAGATTTGAAGGAA
* * **
463142 TAGGTTGAGGACGCAACAGCGAACTTAGTACCTT
66 AAGGTTGAGGACGCAACAGCAAACCCAGTACCTT
* * ** * * *
463176 AGAAGATATGATGGG-AAGGATTTAGGCCGTAACGGCGAACCTAGTACCCTAAAGATTTGAAGGA
1 AGAAGATGTGATGGGAAAGG-TTGAGGCCACAACAGCAAACCTAGTACCATAAAGATTTGAAGGA
* * *
463240 AAAGGTT-AGGGTCGTAACAGCAAACCCGGTACCTT
65 AAAGGTTGA-GGACGCAACAGCAAACCCAGTACCTT
463275 AGAAGATGTGAT
1 AGAAGATGTGAT
463287 TAAGGCCACA
Statistics
Matches: 169, Mismatches: 38, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
98 7 0.04
99 162 0.96
ACGTcount: A:0.35, C:0.15, G:0.29, T:0.20
Consensus pattern (99 bp):
AGAAGATGTGATGGGAAAGGTTGAGGCCACAACAGCAAACCTAGTACCATAAAGATTTGAAGGAA
AAGGTTGAGGACGCAACAGCAAACCCAGTACCTT
Found at i:463581 original size:38 final size:38
Alignment explanation
Indices: 463530--463759 Score: 255
Period size: 38 Copynumber: 6.0 Consensus size: 38
463520 GCGAAGACAT
* *
463530 CATCCAATCTCTTACCCCAATCATGTGGCAGATTGAAG
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAG
***
463568 CATCCAATCTCTTATATCGATCATGGGGCAGATTGAAG
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAG
* * *
463606 CATCCAATCTCTTACCCTGATCATGGGGTAGATTTAAG
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAG
* * *
463644 CATCCAATCTCTTATCCTGATCATAGGGCAGATTGAAG
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAG
** * *
463682 CATCCAATCTCTTACCCTAATCA-GAGGGTATATTGAAG
1 CATCCAATCTCTTACCCCGATCATG-GGGCAGATTGAAG
* * * *
463720 ACACACCAATCTCTTACCCCGTTCGTGGGGCAGGTTGAAG
1 -CA-TCCAATCTCTTACCCCGATCATGGGGCAGATTGAAG
463760 TAATCAGAAG
Statistics
Matches: 160, Mismatches: 28, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
38 131 0.82
39 2 0.01
40 26 0.16
41 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (38 bp):
CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAG
Found at i:463656 original size:76 final size:76
Alignment explanation
Indices: 463530--463735 Score: 281
Period size: 76 Copynumber: 2.7 Consensus size: 76
463520 GCGAAGACAT
* * * * *
463530 CATCCAATCTCTTACCCCAATCATGTGGCAGATTGAAGCATCCAATCTCTTAT-ATCGATCATGG
1 CATCCAATCTCTTACCCTAATCATGGGGTAGATTGAAGCATCCAATCTCTTATCCT-GATCATAG
463594 GGCAGATTGAAG
65 GGCAGATTGAAG
* *
463606 CATCCAATCTCTTACCCTGATCATGGGGTAGATTTAAGCATCCAATCTCTTATCCTGATCATAGG
1 CATCCAATCTCTTACCCTAATCATGGGGTAGATTGAAGCATCCAATCTCTTATCCTGATCATAGG
463671 GCAGATTGAAG
66 GCAGATTGAAG
* *
463682 CATCCAATCTCTTACCCTAATCA-GAGGGTATATTGAAGACACACCAATCTCTTA
1 CATCCAATCTCTTACCCTAATCATG-GGGTAGATTGAAG-CA-TCCAATCTCTTA
463736 CCCCGTTCGT
Statistics
Matches: 115, Mismatches: 11, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
75 1 0.01
76 100 0.87
77 3 0.03
78 11 0.10
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.29
Consensus pattern (76 bp):
CATCCAATCTCTTACCCTAATCATGGGGTAGATTGAAGCATCCAATCTCTTATCCTGATCATAGG
GCAGATTGAAG
Found at i:463840 original size:42 final size:43
Alignment explanation
Indices: 463783--464130 Score: 348
Period size: 42 Copynumber: 8.4 Consensus size: 43
463773 AATTAAAGAC
* * * *
463783 CATCCAATCTTTTACCCTAATTA-GAGGGCAAATTGAAGACAT
1 CATCCAATCTCTTACCCTGATCATGAGGGCAGATTGAAGACAT
* * * *
463825 CATCCAATCTCTTACCCCGATCAT-AGGGCAGATTAAAAAAAT
1 CATCCAATCTCTTACCCTGATCATGAGGGCAGATTGAAGACAT
* * * *
463867 CATCCAATCTCTTACCCCGATCATG-GGGTAAATTAAAGACAT
1 CATCCAATCTCTTACCCTGATCATGAGGGCAGATTGAAGACAT
*
463909 CATCTAATCTCTTATCCC-GATCATG-GGGCAGATTGAAGACAT
1 CATCCAATCTCTTA-CCCTGATCATGAGGGCAGATTGAAGACAT
* * * * * *
463951 CATCCAATTTCTTACCCTTATCATG-GAGCAGATTGAATATAC
1 CATCCAATCTCTTACCCTGATCATGAGGGCAGATTGAAGACAT
* *
463993 CATCCAATCTCTTACCCTGATCATGA-GGCAAATTGGAG-C-T
1 CATCCAATCTCTTACCCTGATCATGAGGGCAGATTGAAGACAT
* * *
464033 -ATCCAATCTCTTACCCCGATCAT-AGGGTAGATTGAAGATAT
1 CATCCAATCTCTTACCCTGATCATGAGGGCAGATTGAAGACAT
*
464074 CATCCAATCTCTTACCCTAATCATGA-GGCAGATTGAAG---T
1 CATCCAATCTCTTACCCTGATCATGAGGGCAGATTGAAGACAT
*
464113 CATCCAATCTTTTACCCT
1 CATCCAATCTCTTACCCT
464131 TAAGTCAAGA
Statistics
Matches: 256, Mismatches: 40, Indels: 23
0.80 0.13 0.07
Matches are distributed among these distances:
38 1 0.00
39 49 0.19
41 4 0.02
42 198 0.77
43 4 0.02
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (43 bp):
CATCCAATCTCTTACCCTGATCATGAGGGCAGATTGAAGACAT
Found at i:464015 original size:126 final size:121
Alignment explanation
Indices: 463768--464130 Score: 390
Period size: 126 Copynumber: 2.9 Consensus size: 121
463758 AGTAATCAGA
* * ** * * *
463768 AGGCAAATTAAAGACCATCCAATCTTTTACCCTAATTAGAGGGCAAATTGAAGACATCATCCAAT
1 AGGCAAATTAAAG-CTATCCAATCTCTTACCCCGATCATAGGGCAGATTGAAGACATCATCCAAT
** * * *
463833 CTCTTACCCCGATCATAGG-GCAGATTAAAAAAATCATCCAATCTCTTACCCCGATCATG
65 CTCTTACCCTAATCAT-GGAGCAGATT-GAAATA-CATCCAATCTCTTACCCTGATCATG
* * * * *
463892 GGGTAAATTAAAGACATCATCTAATCTCTTATCCCGATCATGGGGCAGATTGAAGACATCATCCA
1 AGGCAAATTAAAG-C-T-ATCCAATCTCTTACCCCGATCATAGGGCAGATTGAAGACATCATCCA
* *
463957 ATTTCTTACCCTTATCATGGAGCAGATTGAATATACCATCCAATCTCTTACCCTGATCATG
63 ATCTCTTACCCTAATCATGGAGCAGATTGAA-ATA-CATCCAATCTCTTACCCTGATCATG
** * *
464018 AGGCAAATTGGAGCTATCCAATCTCTTACCCCGATCATAGGGTAGATTGAAGATATCATCCAATC
1 AGGCAAATTAAAGCTATCCAATCTCTTACCCCGATCATAGGGCAGATTGAAGACATCATCCAATC
* *
464083 TCTTACCCTAATCAT-GAGGCAGATTGAAGT-CATCCAATCTTTTACCCT
66 TCTTACCCTAATCATGGA-GCAGATTGAAATACATCCAATCTCTTACCCT
464131 TAAGTCAAGA
Statistics
Matches: 202, Mismatches: 32, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
120 17 0.08
122 3 0.01
123 68 0.34
124 14 0.07
125 5 0.02
126 95 0.47
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.28
Consensus pattern (121 bp):
AGGCAAATTAAAGCTATCCAATCTCTTACCCCGATCATAGGGCAGATTGAAGACATCATCCAATC
TCTTACCCTAATCATGGAGCAGATTGAAATACATCCAATCTCTTACCCTGATCATG
Found at i:464201 original size:47 final size:46
Alignment explanation
Indices: 464114--464202 Score: 115
Period size: 47 Copynumber: 1.9 Consensus size: 46
464104 GATTGAAGTC
* * **
464114 ATCCAATCTTTTACCCTTAAGTCAAGAAAGGCAGTTTGAAGCCACT
1 ATCCAATCTTTTACCCTAAAATCAAGAAAGGCAGACTGAAGCCACT
**
464160 ATCCAATCTTTTACCCCTAAAATCAAGAGGGGCAGACTGAAGC
1 ATCCAATCTTTTA-CCCTAAAATCAAGAAAGGCAGACTGAAGC
464203 TACCATCTCA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
46 13 0.36
47 23 0.64
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (46 bp):
ATCCAATCTTTTACCCTAAAATCAAGAAAGGCAGACTGAAGCCACT
Found at i:466020 original size:30 final size:30
Alignment explanation
Indices: 465983--466202 Score: 195
Period size: 30 Copynumber: 7.4 Consensus size: 30
465973 AACCCCTGAG
465983 CTTTCTAAAAATTCATTTTTGACCCTCAAA
1 CTTTCTAAAAATTCATTTTTGACCCTCAAA
* * * * *
466013 CTCTCTAAAATTTAATTTTTAACCCTCAAT
1 CTTTCTAAAAATTCATTTTTGACCCTCAAA
*
466043 CTTTCTAAAAATTTCA-TTTTAACCC-CTAAA
1 CTTTCTAAAAA-TTCATTTTTGACCCTC-AAA
* * * *
466073 CTTT-TGAAAATTGTATTTTTAACCCTTAAA
1 CTTTCTAAAAATT-CATTTTTGACCCTCAAA
*
466103 CTTTCT-AAAATGTCATTTTTGACCC-CTAAC
1 CTTTCTAAAAAT-TCATTTTTGACCCTC-AAA
* *
466133 CTTTTTAAAAATTTCA-TTTTGA-CCTCGAA
1 CTTTCTAAAAA-TTCATTTTTGACCCTCAAA
466162 CTTTCTAAAAATTTCA-TTTTGACCCTCAAA
1 CTTTCTAAAAA-TTCATTTTTGACCCTCAAA
*
466192 GTTTCTAAAAA
1 CTTTCTAAAAA
466203 ATTGCATTCT
Statistics
Matches: 156, Mismatches: 22, Indels: 24
0.77 0.11 0.12
Matches are distributed among these distances:
28 2 0.01
29 31 0.20
30 110 0.71
31 12 0.08
32 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.04, T:0.42
Consensus pattern (30 bp):
CTTTCTAAAAATTCATTTTTGACCCTCAAA
Found at i:466047 original size:60 final size:59
Alignment explanation
Indices: 465944--466202 Score: 221
Period size: 60 Copynumber: 4.3 Consensus size: 59
465934 ATATATTTCA
* ** * *
465944 ACCCC-AAACTTCCCTAAAAATTTACATTTAACCCCTGAGCTTTCTAAAAA-TTCATTTTTG
1 ACCCCTAAACTT-TCTAAAAATTTATTTTTAA-CCCTCAACTTTCTAAAAATTTCA-TTTTG
* *
466004 A-CCCTCAAACTCTCT-AAAATTTAATTTTTAACCCTCAATCTTTCTAAAAATTTCATTTTA
1 ACCCCT-AAACTTTCTAAAAATTT-ATTTTTAACCCTCAA-CTTTCTAAAAATTTCATTTTG
* * *
466064 ACCCCTAAACTTT-TGAAAATTGTATTTTTAACCCTTAAACTTTCT-AAAATGTCATTTTTG
1 ACCCCTAAACTTTCTAAAAATT-TATTTTTAACCC-TCAACTTTCTAAAAATTTCA-TTTTG
* * *
466124 ACCCCTAACCTTTTTAAAAATTTCA-TTTTGA-CCTCGAACTTTCTAAAAATTTCATTTTG
1 ACCCCTAAACTTTCTAAAAATTT-ATTTTTAACCCTC-AACTTTCTAAAAATTTCATTTTG
*
466183 A-CCCTCAAAGTTTCTAAAAA
1 ACCCCT-AAACTTTCTAAAAA
466203 ATTGCATTCT
Statistics
Matches: 165, Mismatches: 19, Indels: 31
0.77 0.09 0.14
Matches are distributed among these distances:
58 5 0.03
59 51 0.31
60 84 0.51
61 25 0.15
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.39
Consensus pattern (59 bp):
ACCCCTAAACTTTCTAAAAATTTATTTTTAACCCTCAACTTTCTAAAAATTTCATTTTG
Found at i:466098 original size:90 final size:90
Alignment explanation
Indices: 465957--466201 Score: 257
Period size: 90 Copynumber: 2.7 Consensus size: 90
465947 CCAAACTTCC
* * *
465957 CTAAAAATTTACA-TTTAACCCCTGAGCTTTCTAAAAATTCATTTTTGACCCTCAAACTCTCTAA
1 CTAAAAATTT-CATTTTAACCCCTAAACTTTCTAAAAATTCATTTTTAACCCTCAAACTCTCTAA
* *
466021 AATTTAATTTTTAA-CCCTCAATCTTT
65 AATGTAATTTTTAACCCCT-AACCTTT
* * * *
466047 CTAAAAATTTCATTTTAACCCCTAAACTTT-TGAAAATTGTATTTTTAACCCTTAAACTTTCTAA
1 CTAAAAATTTCATTTTAACCCCTAAACTTTCTAAAAATT-CATTTTTAACCCTCAAACTCTCTAA
* *
466111 AATGTCATTTTTGACCCCTAACCTTT
65 AATGTAATTTTTAACCCCTAACCTTT
* * * * * * *
466137 TTAAAAATTTCATTTTGACCTC-GAACTTTCTAAAAATTTCA-TTTTGACCCTCAAAGTTTCTAA
1 CTAAAAATTTCATTTTAACCCCTAAACTTTCTAAAAA-TTCATTTTTAACCCTCAAACTCTCTAA
466200 AA
65 AA
466202 AATTGCATTC
Statistics
Matches: 130, Mismatches: 20, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
89 36 0.28
90 88 0.68
91 6 0.05
ACGTcount: A:0.33, C:0.21, G:0.04, T:0.41
Consensus pattern (90 bp):
CTAAAAATTTCATTTTAACCCCTAAACTTTCTAAAAATTCATTTTTAACCCTCAAACTCTCTAAA
ATGTAATTTTTAACCCCTAACCTTT
Found at i:471456 original size:10 final size:10
Alignment explanation
Indices: 471441--471481 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
471431 AATTTTAAAT
471441 AAATAAATAA
1 AAATAAATAA
*
471451 AAAT-AAGAA
1 AAATAAATAA
471460 AAATAAA-ATA
1 AAATAAATA-A
471470 AAATAAATAA
1 AAATAAATAA
471480 AA
1 AA
471482 TCATATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
9 9 0.33
10 17 0.63
11 1 0.04
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (10 bp):
AAATAAATAA
Found at i:471493 original size:14 final size:14
Alignment explanation
Indices: 471437--471482 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
471427 AAACAATTTT
471437 AAAT-AAATAAATAA
1 AAATAAAATAAAT-A
471451 AAATAAGAA-AAATA
1 AAATAA-AATAAATA
471465 AAATAAAATAAATA
1 AAATAAAATAAATA
471479 AAAT
1 AAAT
471483 CATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
13 2 0.07
14 20 0.69
15 5 0.17
16 2 0.07
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (14 bp):
AAATAAAATAAATA
Found at i:484690 original size:33 final size:33
Alignment explanation
Indices: 484650--484718 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
484640 AAATTAAAAA
*
484650 TAACCAAATCAAATATTAGCTCAACAAAATAAC
1 TAACCAAATAAAATATTAGCTCAACAAAATAAC
* *
484683 TAACCAAATAAAATGTTAGCTCAACAATATAAC
1 TAACCAAATAAAATATTAGCTCAACAAAATAAC
484716 TAA
1 TAA
484719 AATCTTACTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.54, C:0.19, G:0.04, T:0.23
Consensus pattern (33 bp):
TAACCAAATAAAATATTAGCTCAACAAAATAAC
Found at i:489778 original size:41 final size:40
Alignment explanation
Indices: 489720--489832 Score: 118
Period size: 41 Copynumber: 2.8 Consensus size: 40
489710 AGGCGTCTTC
* * *
489720 AGGGGTTTGTCGCGACATAAACATGCTTTGTTGTGACATA
1 AGGGGTTTCTCGCGACATAAACATGCTATGTTGCGACATA
* * *
489760 GAGGGGTTTCTCGTGACATAGACATTCTATGTTGCGACATA
1 -AGGGGTTTCTCGCGACATAAACATGCTATGTTGCGACATA
* * * *
489801 AGGGGGTTTGTTGCAACATAGACATGCTATGT
1 A-GGGGTTTCTCGCGACATAAACATGCTATGT
489833 CGTGAAGAAG
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
40 1 0.02
41 59 0.98
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (40 bp):
AGGGGTTTCTCGCGACATAAACATGCTATGTTGCGACATA
Found at i:490442 original size:5 final size:5
Alignment explanation
Indices: 490432--490456 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
490422 CTTTGTTCAT
490432 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
490457 GCATGTTGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:502355 original size:15 final size:15
Alignment explanation
Indices: 502335--502364 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
502325 CCATCTCCTC
502335 AAACCATCTACAGAT
1 AAACCATCTACAGAT
502350 AAACCATCTACAGAT
1 AAACCATCTACAGAT
502365 TCTTTCTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.27, G:0.07, T:0.20
Consensus pattern (15 bp):
AAACCATCTACAGAT
Found at i:505001 original size:18 final size:21
Alignment explanation
Indices: 504958--505005 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
504948 AATCACTTGA
*
504958 AAGAAAAAAAATGAGAAAAAG
1 AAGAAATAAAATGAGAAAAAG
504979 AAGAAATAAAA-GA-AAAAAG
1 AAGAAATAAAATGAGAAAAAG
504998 -AG-AATAAA
1 AAGAAATAAA
505006 TTGCAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 6 0.23
18 2 0.08
19 6 0.23
20 2 0.08
21 10 0.38
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (21 bp):
AAGAAATAAAATGAGAAAAAG
Found at i:523056 original size:9 final size:9
Alignment explanation
Indices: 523042--523092 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
523032 AATCACGTAT
523042 AAAAAAAGA
1 AAAAAAAGA
*
523051 AAAAAAGGA
1 AAAAAAAGA
523060 AAAAAGAAGA
1 AAAAA-AAGA
*
523070 AGAAAAAGA
1 AAAAAAAGA
**
523079 AAGCAAAGA
1 AAAAAAAGA
523088 AAAAA
1 AAAAA
523093 GGAAAAGCAG
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
9 26 0.79
10 7 0.21
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:523064 original size:16 final size:16
Alignment explanation
Indices: 523043--523109 Score: 55
Period size: 17 Copynumber: 3.9 Consensus size: 16
523033 ATCACGTATA
523043 AAAAAAGAAAAAAAGG
1 AAAAAAGAAAAAAAGG
*
523059 AAAAAAGAAGAAGAAAAAG
1 AAAAAAG-A-AA-AAAAGG
523078 AAAGCAAAG-AAAAAAGG
1 AAA--AAAGAAAAAAAGG
*
523095 AAAAGCAGAAAAAAA
1 AAAA-AAGAAAAAAA
523110 ATATATTGCT
Statistics
Matches: 41, Mismatches: 3, Indels: 13
0.72 0.05 0.23
Matches are distributed among these distances:
15 1 0.02
16 9 0.22
17 15 0.37
18 4 0.10
19 8 0.20
21 4 0.10
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAAAAAGG
Found at i:537590 original size:14 final size:15
Alignment explanation
Indices: 537571--537605 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
537561 TAGCAAACAT
*
537571 TTTTTCTTCTTTT-C
1 TTTTTCTTATTTTCC
537585 TTTTTCTTATTTTCC
1 TTTTTCTTATTTTCC
537600 TTTTTC
1 TTTTTC
537606 AAGTAACTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTCTTATTTTCC
Found at i:553694 original size:34 final size:34
Alignment explanation
Indices: 553646--553711 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
553636 GTTAGTATGT
*
553646 ATTGTCATCACATTCACATTGTCATTACATTTTA
1 ATTGTCATCACATTCACATTATCATTACATTTTA
** * *
553680 ATTGTCATTGCATTCGCATTATCATTGCATTT
1 ATTGTCATCACATTCACATTATCATTACATTT
553712 CCATTTGTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.26, C:0.20, G:0.09, T:0.45
Consensus pattern (34 bp):
ATTGTCATCACATTCACATTATCATTACATTTTA
Found at i:554256 original size:14 final size:15
Alignment explanation
Indices: 554221--554256 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
554211 ATATATATAT
554221 AAAAAAAGAGAAAAG
1 AAAAAAAGAGAAAAG
*
554236 AGAAAAAG-GAAAAG
1 AAAAAAAGAGAAAAG
554250 AAAAAAA
1 AAAAAAA
554257 TATATGTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAGAAAAG
Found at i:555520 original size:16 final size:16
Alignment explanation
Indices: 555495--555567 Score: 92
Period size: 16 Copynumber: 4.5 Consensus size: 16
555485 CGTTTGGTTC
555495 GCTGTAATGGAATAAA
1 GCTGTAATGGAATAAA
* *
555511 GCTATAATGGAATACA
1 GCTGTAATGGAATAAA
* *
555527 GCTGTAATGTAATATA
1 GCTGTAATGGAATAAA
*
555543 GCTTGTAATGGAATAAG
1 GC-TGTAATGGAATAAA
555560 GCTGTAAT
1 GCTGTAAT
555568 TAGTAGTTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
16 35 0.73
17 13 0.27
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.30
Consensus pattern (16 bp):
GCTGTAATGGAATAAA
Found at i:555556 original size:33 final size:32
Alignment explanation
Indices: 555495--555567 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 32
555485 CGTTTGGTTC
555495 GCTGTAATGGAATAAAGCTATAATGGAATACA-
1 GCTGTAATGGAATAAAGCTATAATGGAATA-AG
* * *
555527 GCTGTAATGTAATATAGCTTGTAATGGAATAAG
1 GCTGTAATGGAATAAAGC-TATAATGGAATAAG
555560 GCTGTAAT
1 GCTGTAAT
555568 TAGTAGTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 17 0.47
33 19 0.53
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.30
Consensus pattern (32 bp):
GCTGTAATGGAATAAAGCTATAATGGAATAAG
Found at i:555822 original size:60 final size:61
Alignment explanation
Indices: 555742--555904 Score: 185
Period size: 56 Copynumber: 2.7 Consensus size: 61
555732 TTAATAAGAT
* * *
555742 TATTATTAAATATAATTTAATAAAAAAATAATAAATAATTTAATTATA-TTTTAACATAAC
1 TATTATTAAATACAATTTAATAAAAAAATAATATATAATTTAATAATATTTTTAACATAAC
* *
555802 TATTATTAAATACAATTTAAT----AAATAATATATAATTTAATAATATTTTTAATATAAT
1 TATTATTAAATACAATTTAATAAAAAAATAATATATAATTTAATAATATTTTTAACATAAC
* *
555859 TATTATTAAAATATGAA-TTAATAAAAATCATAATATATAATATTAA
1 TATTATT-AAATA-CAATTTAATAAAAA-AATAATATATAAT-TTAA
555905 AAAAATAATA
Statistics
Matches: 87, Mismatches: 7, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
56 21 0.24
57 17 0.20
58 10 0.11
59 2 0.02
60 20 0.23
62 1 0.01
63 12 0.14
64 4 0.05
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (61 bp):
TATTATTAAATACAATTTAATAAAAAAATAATATATAATTTAATAATATTTTTAACATAAC
Found at i:557663 original size:19 final size:18
Alignment explanation
Indices: 557637--557672 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
557627 GTTTTTCCTT
557637 CATCATAAAATATTGATA
1 CATCATAAAATATTGATA
*
557655 CATCAATAAACTATTGAT
1 CATC-ATAAAATATTGAT
557673 TGCATGCTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.33
Consensus pattern (18 bp):
CATCATAAAATATTGATA
Found at i:562429 original size:3 final size:3
Alignment explanation
Indices: 562423--562451 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
562413 TGAAGATCGG
562423 ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
562452 TATCCTAGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:569025 original size:21 final size:21
Alignment explanation
Indices: 569001--569040 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
568991 TGGTAGAGGA
*
569001 GTCAATTGTATTAGTAGAACT
1 GTCAATTGTATCAGTAGAACT
*
569022 GTCACTTGTATCAGTAGAA
1 GTCAATTGTATCAGTAGAA
569041 ATCTGCACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (21 bp):
GTCAATTGTATCAGTAGAACT
Found at i:572468 original size:14 final size:15
Alignment explanation
Indices: 572451--572489 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
572441 TACTGTTTAT
572451 CATTTATTTTTCT-A-
1 CATTTATTTTT-TAAG
572465 CATTTATTTTTTAAG
1 CATTTATTTTTTAAG
572480 CATTTATTTT
1 CATTTATTTT
572490 CCCATACCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.04
14 12 0.52
15 10 0.43
ACGTcount: A:0.23, C:0.10, G:0.03, T:0.64
Consensus pattern (15 bp):
CATTTATTTTTTAAG
Found at i:579953 original size:17 final size:17
Alignment explanation
Indices: 579933--579966 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
579923 GAATAGGTAG
579933 CTCAAAGCAATAGTTGT
1 CTCAAAGCAATAGTTGT
579950 CTCAAAGCAATAGTTGT
1 CTCAAAGCAATAGTTGT
579967 TCATGACTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (17 bp):
CTCAAAGCAATAGTTGT
Found at i:581896 original size:57 final size:57
Alignment explanation
Indices: 581798--581915 Score: 159
Period size: 57 Copynumber: 2.1 Consensus size: 57
581788 ATATAAATGG
*
581798 TGAAATGGAGAAATAAGAAACATTTAGGAAATGATTATGGTTTTCTCCAAAATGAAAA
1 TGAAATGGAGAAATAAGAAACATTTAGGAAATGAATATGGTTTTCT-CAAAATGAAAA
* * * *
581856 TGAAATTGGAGAAAT-GGAATCATTT-GGAAATGAATGTGGTTTTCTCAAAATGGAAA
1 TGAAA-TGGAGAAATAAGAAACATTTAGGAAATGAATATGGTTTTCTCAAAATGAAAA
581912 TGAA
1 TGAA
581916 TTCATTTACA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
56 14 0.26
57 18 0.33
58 13 0.24
59 9 0.17
ACGTcount: A:0.43, C:0.06, G:0.22, T:0.29
Consensus pattern (57 bp):
TGAAATGGAGAAATAAGAAACATTTAGGAAATGAATATGGTTTTCTCAAAATGAAAA
Found at i:586461 original size:6 final size:6
Alignment explanation
Indices: 586450--586476 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
586440 TAGTATTCAT
586450 AATCTC AATCTC AATCTC AATCTC AAT
1 AATCTC AATCTC AATCTC AATCTC AAT
586477 TAAAGTAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.30, G:0.00, T:0.33
Consensus pattern (6 bp):
AATCTC
Found at i:589458 original size:42 final size:42
Alignment explanation
Indices: 589411--589494 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
589401 AAAATATCAT
*
589411 TTAGTCTAGAAATCAAGTGTACTTCCATATAAACATGAAATA
1 TTAGTCTAGAAATCAAGTGTACTTCCATACAAACATGAAATA
589453 TTAGTCTAGAAATCAAGTGTACTTCCATACAAACATGAAATA
1 TTAGTCTAGAAATCAAGTGTACTTCCATACAAACATGAAATA
589495 AACATTAATC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.30
Consensus pattern (42 bp):
TTAGTCTAGAAATCAAGTGTACTTCCATACAAACATGAAATA
Found at i:591005 original size:17 final size:17
Alignment explanation
Indices: 590983--591015 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
590973 AATAACATTT
590983 AAATGCAATGACAATGA
1 AAATGCAATGACAATGA
591000 AAATGCAATGACAATG
1 AAATGCAATGACAATG
591016 CTTAATAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.12, G:0.18, T:0.18
Consensus pattern (17 bp):
AAATGCAATGACAATGA
Found at i:592958 original size:39 final size:39
Alignment explanation
Indices: 592915--592993 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
592905 TACTAAGTGT
592915 CGCTCACAAGGTATGAAAGGATAGGTGATTGTCGCTACA
1 CGCTCACAAGGTATGAAAGGATAGGTGATTGTCGCTACA
*
592954 CGCTCACAAGGTATGAAAGGATAGGTGGTTGTCGCTACA
1 CGCTCACAAGGTATGAAAGGATAGGTGATTGTCGCTACA
592993 C
1 C
592994 TAGAGTGAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (39 bp):
CGCTCACAAGGTATGAAAGGATAGGTGATTGTCGCTACA
Found at i:593757 original size:55 final size:55
Alignment explanation
Indices: 593662--593768 Score: 160
Period size: 55 Copynumber: 1.9 Consensus size: 55
593652 TTATCCGGAC
* *
593662 AGCTATCAGATGCAACGACAATTTTGAGCGTAATTCTGGATATGCTAATGCAACG
1 AGCTATCAGATGCAACGACAATTCTGAGCGCAATTCTGGATATGCTAATGCAACG
* * * *
593717 AGCTGTCAGATGCAACGACAATTCTGGGCGCAATTTTGGATATGCTCATGCA
1 AGCTATCAGATGCAACGACAATTCTGAGCGCAATTCTGGATATGCTAATGCA
593769 GTGACATTAG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 46 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (55 bp):
AGCTATCAGATGCAACGACAATTCTGAGCGCAATTCTGGATATGCTAATGCAACG
Found at i:609111 original size:23 final size:23
Alignment explanation
Indices: 609085--609157 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
609075 ATTTATCCAA
609085 ACAAATCCTTGAAATTGTGGAAG
1 ACAAATCCTTGAAATTGTGGAAG
** ** *
609108 ACAAATGCCTACACTTTAGT-CAA-
1 ACAAAT-CCTTGAAATT-GTGGAAG
*
609131 ACAAATCTTTGAAATTGTGGAAG
1 ACAAATCCTTGAAATTGTGGAAG
609154 ACAA
1 ACAA
609158 CTTGACTTGA
Statistics
Matches: 35, Mismatches: 11, Indels: 8
0.65 0.20 0.15
Matches are distributed among these distances:
21 2 0.06
22 7 0.20
23 16 0.46
24 8 0.23
25 2 0.06
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.26
Consensus pattern (23 bp):
ACAAATCCTTGAAATTGTGGAAG
Found at i:609132 original size:46 final size:46
Alignment explanation
Indices: 609038--609157 Score: 172
Period size: 46 Copynumber: 2.6 Consensus size: 46
609028 GATAAAAGAG
* * *
609038 AAACAAATCCCTGAAATTGTGGAATAC-AATGCCTATAATTTATCC
1 AAACAAATCCTTGAAATTGTGGAAGACAAATGCCTACAATTTATCC
*
609083 AAACAAATCCTTGAAATTGTGGAAGACAAATGCCTACACTTTAGT-C
1 AAACAAATCCTTGAAATTGTGGAAGACAAATGCCTACAATTTA-TCC
*
609129 AAACAAATCTTTGAAATTGTGGAAGACAA
1 AAACAAATCCTTGAAATTGTGGAAGACAA
609158 CTTGACTTGA
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
45 25 0.37
46 42 0.62
47 1 0.01
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (46 bp):
AAACAAATCCTTGAAATTGTGGAAGACAAATGCCTACAATTTATCC
Found at i:609757 original size:17 final size:18
Alignment explanation
Indices: 609725--609758 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
609715 CCTTTGTTTT
*
609725 CTTTTGCTCTTCCAATTA
1 CTTTTGATCTTCCAATTA
609743 CTTTTGATC-TCCAATT
1 CTTTTGATCTTCCAATT
609759 CCTAATTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.18, C:0.26, G:0.06, T:0.50
Consensus pattern (18 bp):
CTTTTGATCTTCCAATTA
Found at i:610761 original size:36 final size:36
Alignment explanation
Indices: 610721--610939 Score: 279
Period size: 36 Copynumber: 6.2 Consensus size: 36
610711 CTGTTGTGAA
*
610721 AGTAAATATGTGGGTATGTTATTCATGTCATGAGAC
1 AGTAAATATGTGGGTATGTTATTCATGCCATGAGAC
*
610757 AGTAAATATGTGGGTATGTTATTCATGCCATGTG--
1 AGTAAATATGTGGGTATGTTATTCATGCCATGAGAC
* * *
610791 -GT-AGT-TGTGGATATGTTATTCTTGCCATGAGAC
1 AGTAAATATGTGGGTATGTTATTCATGCCATGAGAC
* *
610824 AGTAAATATGTGGGTATG-TATTAATGCCATGTGAC
1 AGTAAATATGTGGGTATGTTATTCATGCCATGAGAC
* * *
610859 AGTAAATATGTGAGTATGCTATTTATGCCATGAGAC
1 AGTAAATATGTGGGTATGTTATTCATGCCATGAGAC
* *
610895 AGTAAATATGTGGGTGTGTTATTCATGCCATGTGAC
1 AGTAAATATGTGGGTATGTTATTCATGCCATGAGAC
*
610931 AGTGAATAT
1 AGTAAATAT
610940 AATGTGCTAA
Statistics
Matches: 157, Mismatches: 20, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
31 23 0.15
32 2 0.01
33 2 0.01
34 2 0.01
35 33 0.21
36 95 0.61
ACGTcount: A:0.29, C:0.10, G:0.26, T:0.36
Consensus pattern (36 bp):
AGTAAATATGTGGGTATGTTATTCATGCCATGAGAC
Found at i:610837 original size:67 final size:70
Alignment explanation
Indices: 610721--610929 Score: 277
Period size: 67 Copynumber: 3.0 Consensus size: 70
610711 CTGTTGTGAA
* * *
610721 AGTAAATATGTGGGTATGTTATTCATGTCATGAGACAGTAAATATGTGGGTATGTTATTCATGCC
1 AGTAAATATGTGGATATGTTATTCTTGCCATGAGACAGTAAATATGTGGGTATGTTATTCATGCC
610786 ATGTG
66 ATGTG
* *
610791 -GT-AGT-TGTGGATATGTTATTCTTGCCATGAGACAGTAAATATGTGGGTATG-TATTAATGCC
1 AGTAAATATGTGGATATGTTATTCTTGCCATGAGACAGTAAATATGTGGGTATGTTATTCATGCC
610852 ATGTG
66 ATGTG
* *
610857 ACAGTAAATATGT-GAGTATGCTATT-TATGCCATGAGACAGTAAATATGTGGGTGTGTTATTCA
1 --AGTAAATATGTGGA-TATGTTATTCT-TGCCATGAGACAGTAAATATGTGGGTATGTTATTCA
610920 TGCCATGTG
62 TGCCATGTG
610929 A
1 A
610930 CAGTGAATAT
Statistics
Matches: 122, Mismatches: 9, Indels: 16
0.83 0.06 0.11
Matches are distributed among these distances:
66 14 0.11
67 43 0.35
68 2 0.02
69 4 0.03
70 6 0.05
71 39 0.32
72 14 0.11
ACGTcount: A:0.28, C:0.10, G:0.26, T:0.36
Consensus pattern (70 bp):
AGTAAATATGTGGATATGTTATTCTTGCCATGAGACAGTAAATATGTGGGTATGTTATTCATGCC
ATGTG
Found at i:611753 original size:23 final size:23
Alignment explanation
Indices: 611330--611746 Score: 636
Period size: 23 Copynumber: 18.1 Consensus size: 23
611320 ATTAAATGTG
* *
611330 TTAAATATTAATGTGATTTAAGC
1 TTAAATGTTAATGTGATTTATGC
** *
611353 TTAAATGTTAATACGATTTATAC
1 TTAAATGTTAATGTGATTTATGC
* *
611376 TTAAAAGTTAATGTGATTTATAC
1 TTAAATGTTAATGTGATTTATGC
* *
611399 TTAAATGATAATATGATTTATGC
1 TTAAATGTTAATGTGATTTATGC
*
611422 TTAAAAGTTAATGTGATTTATGC
1 TTAAATGTTAATGTGATTTATGC
*
611445 TTAAATGTTAATATGATTTATGC
1 TTAAATGTTAATGTGATTTATGC
*
611468 TTAAAAGTTAATGTGATTTATGC
1 TTAAATGTTAATGTGATTTATGC
611491 TTAAATGTTAATGTGATTTATGC
1 TTAAATGTTAATGTGATTTATGC
* *
611514 TTAAAAGTTAATGTGATTTACGC
1 TTAAATGTTAATGTGATTTATGC
611537 TTAAATGTTAATGTGATTTATGC
1 TTAAATGTTAATGTGATTTATGC
*
611560 TTAAAAGTTAATGTGATTTATGC
1 TTAAATGTTAATGTGATTTATGC
*
611583 TTAAATGTTAAAGTGATTTATGC
1 TTAAATGTTAATGTGATTTATGC
*
611606 TTAAATGTTAATATGATTTATGC
1 TTAAATGTTAATGTGATTTATGC
*
611629 TTAAAAGTTAATGTGATTTATGC
1 TTAAATGTTAATGTGATTTATGC
*
611652 TTAAATGTTAATATGATTTATGC
1 TTAAATGTTAATGTGATTTATGC
*
611675 TTAAAAGTTAATGTGATTTATGC
1 TTAAATGTTAATGTGATTTATGC
*
611698 TTAAATGTTAATGTAATTTATGC
1 TTAAATGTTAATGTGATTTATGC
*
611721 TTAAAAGTTAATGTGATTTATGC
1 TTAAATGTTAATGTGATTTATGC
611744 TTA
1 TTA
611747 GTAGTTAGTA
Statistics
Matches: 355, Mismatches: 39, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 355 1.00
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (23 bp):
TTAAATGTTAATGTGATTTATGC
Found at i:615270 original size:18 final size:18
Alignment explanation
Indices: 615225--615272 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
615215 AGGAGGAAGA
*
615225 TGAAGAGGAAGAAGAAAG
1 TGAAGAGGAGGAAGAAAG
*
615243 TGAATAGGAGGAAGAAAG
1 TGAAGAGGAGGAAGAAAG
615261 TGAAGAGGAGGA
1 TGAAGAGGAGGA
615273 GGATGAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.50, C:0.00, G:0.42, T:0.08
Consensus pattern (18 bp):
TGAAGAGGAGGAAGAAAG
Found at i:650718 original size:69 final size:69
Alignment explanation
Indices: 650607--650744 Score: 267
Period size: 69 Copynumber: 2.0 Consensus size: 69
650597 AATAAAATGA
*
650607 AGGATCCCCCCATTTTCTCTTGCTCATGGTCAACCACTCTTTATGGAGTTGGTGCTTGGTTGTTT
1 AGGATCCCCCCATTTTCTCTTGCGCATGGTCAACCACTCTTTATGGAGTTGGTGCTTGGTTGTTT
650672 ACTT
66 ACTT
650676 AGGATCCCCCCATTTTCTCTTGCGCATGGTCAACCACTCTTTATGGAGTTGGTGCTTGGTTGTTT
1 AGGATCCCCCCATTTTCTCTTGCGCATGGTCAACCACTCTTTATGGAGTTGGTGCTTGGTTGTTT
650741 ACTT
66 ACTT
650745 GATTTAAGCA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.14, C:0.25, G:0.21, T:0.40
Consensus pattern (69 bp):
AGGATCCCCCCATTTTCTCTTGCGCATGGTCAACCACTCTTTATGGAGTTGGTGCTTGGTTGTTT
ACTT
Found at i:656177 original size:22 final size:24
Alignment explanation
Indices: 656128--656184 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
656118 AGGTCAAAGT
* *
656128 AATTAAATTAACCCAATTATTTAAC
1 AATTAAATAAACCCAATTATGT-AC
656153 AATTAAATAAACCCAATT-TGT-C
1 AATTAAATAAACCCAATTATGTAC
*
656175 AATGAAATAA
1 AATTAAATAA
656185 TGTATATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 10 0.34
24 2 0.07
25 17 0.59
ACGTcount: A:0.51, C:0.14, G:0.04, T:0.32
Consensus pattern (24 bp):
AATTAAATAAACCCAATTATGTAC
Found at i:662236 original size:413 final size:399
Alignment explanation
Indices: 661476--662288 Score: 1313
Period size: 413 Copynumber: 2.0 Consensus size: 399
661466 TCACCAAAAG
* * *
661476 TACTCCGACAAAGGCAAAGCTCCCATGGAACCTTAATCTGACTTGAAGGATGGTTGAAGTGTTTT
1 TACTCCAACAAAGGCAAAGCTCCCATGGAACCTTAATCCGACTTGAAGGATGATTGAAGTGTTTT
*
661541 GGATTTATTTACTTTAAAGACTTGTAATAATTAGATGATTTTTGGGTTTTGTTAAGACTTATATA
66 GGATTTATTTACTTTAAAGACTTGTAATAATTAGATGATTTTTGAGTTTTGTTAAGACTTATATA
*
661606 ATTTTTAGGAGTAGGATTAGGATTAGGATTTACTTTTGCACATATATGCATTAACCCCACAATAT
131 ATTTTTAGGAGTAGGAGTAGGATTAGGATTTACTTTTGCACATATATGCATTAACCCCACAATAT
*
661671 GAAGACACAAAAATTTTGAGCATTATGCCAAGAGGGAGAAGGATAACAACCACAAGAAGAAAAGG
196 GAAGACACAAAAATTTCGAGCATTATGCCAAGAGGGAGAAGGATAACAACCACAAGAAGAAAAGG
661736 ACTTTCACGAGAAATCAGGTAACTTCTTTCCTTATTATTTATGAGGCTACATATTGAGGACAATA
261 ACTTTCACGAGAAATCAGGTAACTTCTTTCCTTATTATTTATGAGGCTACATATTGAGGACAATA
* * * *
661801 TATTTTCTGAAGTGTGGAGGTTAACATAGGATTTTTGCCTATAGTTTTAATTTCTAGTTTTTATG
326 TATTTTCTAAAGAGTGGAGGTTAACAAAGGATATTTGCCTATAGTTTTAATTTCTAGTTTTTATG
661866 TTTTTTTTT
391 TTTTTTTTT
661875 TACTCCAACAAAGGCAAAGCTCCCATGGAACCTTAATCCGACTTGAAGGATGATTGAAGTGTTTT
1 TACTCCAACAAAGGCAAAGCTCCCATGGAACCTTAATCCGACTTGAAGGATGATTGAAGTGTTTT
*
661940 GGATTTATTTACTTTAAAGACTTGTAATAGTTAGATGA-TTTTGAGTTTTGTTAAGACTTATATA
66 GGATTTATTTACTTTAAAGACTTGTAATAATTAGATGATTTTTGAGTTTTGTTAAGACTTATATA
*
662004 ATTTTTAGGAGTAGTAGTAGGATTAGGATTTACTTTTGCACATATATGCATTAATTCTTTTTGTA
131 ATTTTTAGGAGTAGGAGTAGGATTAGGATTTACTTTTGCACATATATGC----A-------T-T-
* *
662069 GGAACCCCACAATATGAAGACACAAAAATTTCGAGCATTATGCCAAGGGGGAGAAGGATAACAGC
183 --AACCCCACAATATGAAGACACAAAAATTTCGAGCATTATGCCAAGAGGGAGAAGGATAACAAC
* *
662134 CACAGGAAGAAAAGGACTTTCACGAGAAATCAGGTAACTTCTTTCCTTATTATTTATGGGGCTAC
246 CACAAGAAGAAAAGGACTTTCACGAGAAATCAGGTAACTTCTTTCCTTATTATTTATGAGGCTAC
* *
662199 ATATTGAGGACAATATGTTTTCTAAAGAGTGGAGGTTAACAAAGGATATTTGTCTATAGTTTTAA
311 ATATTGAGGACAATATATTTTCTAAAGAGTGGAGGTTAACAAAGGATATTTGCCTATAGTTTTAA
*
662264 TTTTTAGTTTTTATGTTTTTTTTT
376 TTTCTAGTTTTTATGTTTTTTTTT
662288 T
1 T
662289 GCTTGAGCTT
Statistics
Matches: 380, Mismatches: 19, Indels: 16
0.92 0.05 0.04
Matches are distributed among these distances:
398 72 0.19
399 99 0.26
402 1 0.00
409 1 0.00
410 1 0.00
413 206 0.54
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.36
Consensus pattern (399 bp):
TACTCCAACAAAGGCAAAGCTCCCATGGAACCTTAATCCGACTTGAAGGATGATTGAAGTGTTTT
GGATTTATTTACTTTAAAGACTTGTAATAATTAGATGATTTTTGAGTTTTGTTAAGACTTATATA
ATTTTTAGGAGTAGGAGTAGGATTAGGATTTACTTTTGCACATATATGCATTAACCCCACAATAT
GAAGACACAAAAATTTCGAGCATTATGCCAAGAGGGAGAAGGATAACAACCACAAGAAGAAAAGG
ACTTTCACGAGAAATCAGGTAACTTCTTTCCTTATTATTTATGAGGCTACATATTGAGGACAATA
TATTTTCTAAAGAGTGGAGGTTAACAAAGGATATTTGCCTATAGTTTTAATTTCTAGTTTTTATG
TTTTTTTTT
Found at i:665994 original size:70 final size:70
Alignment explanation
Indices: 665917--666057 Score: 282
Period size: 70 Copynumber: 2.0 Consensus size: 70
665907 AATAAATTCT
665917 AATCCTACTCCTATGAATTATATAAGTCTGAAAATAAAAACCAAAAATTATCCAAAATTTACAAA
1 AATCCTACTCCTATGAATTATATAAGTCTGAAAATAAAAACCAAAAATTATCCAAAATTTACAAA
665982 ATTAA
66 ATTAA
665987 AATCCTACTCCTATGAATTATATAAGTCTGAAAATAAAAACCAAAAATTATCCAAAATTTACAAA
1 AATCCTACTCCTATGAATTATATAAGTCTGAAAATAAAAACCAAAAATTATCCAAAATTTACAAA
666052 ATTAA
66 ATTAA
666057 A
1 A
666058 TTATTTCAGA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.52, C:0.16, G:0.04, T:0.28
Consensus pattern (70 bp):
AATCCTACTCCTATGAATTATATAAGTCTGAAAATAAAAACCAAAAATTATCCAAAATTTACAAA
ATTAA
Found at i:670917 original size:53 final size:53
Alignment explanation
Indices: 670752--670980 Score: 302
Period size: 53 Copynumber: 4.3 Consensus size: 53
670742 TACACATGTG
* * * * * * * *
670752 ATAACTCACAATGACATAGAGCCATTGGACCATTAATCCGTAATAGGATTCAT
1 ATAACTCACGATGACACAAAGTCATCGAACCTTTAATCCGTGATAGGATTCAT
*
670805 ATAACTCACGATGACACAGAGTCATC-AGACCTTT-ATCCGTGATAGGATTCAT
1 ATAACTCACGATGACACAAAGTCATCGA-ACCTTTAATCCGTGATAGGATTCAT
* *
670857 ATAACTCACTATAACACAAAGTCATCGAACCTTTAATCCGTGATAGGATTCAT
1 ATAACTCACGATGACACAAAGTCATCGAACCTTTAATCCGTGATAGGATTCAT
* *
670910 ATAACTCA-TAGTGACACAAAGTCATCGGACCTTTAATCCGTGATAGGATTCAT
1 ATAACTCACGA-TGACACAAAGTCATCGAACCTTTAATCCGTGATAGGATTCAT
670963 ATAACTCACGATGACACA
1 ATAACTCACGATGACACA
670981 GAGTTACTGA
Statistics
Matches: 158, Mismatches: 13, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
52 48 0.30
53 109 0.69
54 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (53 bp):
ATAACTCACGATGACACAAAGTCATCGAACCTTTAATCCGTGATAGGATTCAT
Found at i:670934 original size:105 final size:106
Alignment explanation
Indices: 670784--670980 Score: 317
Period size: 105 Copynumber: 1.9 Consensus size: 106
670774 CATTGGACCA
* *
670784 TTAATCCGTAATAGGATTCATATAACTCACGATGACACAGAGTCATCAGACCTTT-ATCCGTGAT
1 TTAATCCGTAATAGGATTCATATAACTCAAGATGACACAAAGTCATCAGACCTTTAATCCGTGAT
*
670848 AGGATTCATATAACTCACTATAACACAAAGTCATCGAACCT
66 AGGATTCATATAACTCACGATAACACAAAGTCATCGAACCT
* *
670889 TTAATCCGTGATAGGATTCATATAACTCATAG-TGACACAAAGTCATCGGACCTTTAATCCGTGA
1 TTAATCCGTAATAGGATTCATATAACTCA-AGATGACACAAAGTCATCAGACCTTTAATCCGTGA
*
670953 TAGGATTCATATAACTCACGATGACACA
65 TAGGATTCATATAACTCACGATAACACA
670981 GAGTTACTGA
Statistics
Matches: 84, Mismatches: 6, Indels: 3
0.90 0.06 0.03
Matches are distributed among these distances:
105 49 0.58
106 35 0.42
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.28
Consensus pattern (106 bp):
TTAATCCGTAATAGGATTCATATAACTCAAGATGACACAAAGTCATCAGACCTTTAATCCGTGAT
AGGATTCATATAACTCACGATAACACAAAGTCATCGAACCT
Found at i:677002 original size:16 final size:17
Alignment explanation
Indices: 676967--677004 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
676957 ACATAGCCAG
676967 ATGCAACCACAAGCTAGA
1 ATGCAACCACAA-CTAGA
*
676985 ATGCAGCCACAA-TAGA
1 ATGCAACCACAACTAGA
677001 ATGC
1 ATGC
677005 GCTTCCACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
18 11 0.58
ACGTcount: A:0.42, C:0.26, G:0.18, T:0.13
Consensus pattern (17 bp):
ATGCAACCACAACTAGA
Found at i:682112 original size:32 final size:32
Alignment explanation
Indices: 682071--682133 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
682061 GCCATCCATA
* *
682071 CATGTACCTGAAATATATTAATCAGCTAATTG
1 CATGTACCTGAAACATATTAATCAACTAATTG
682103 CATGTACCTGAAACATATTAATCAACTAATT
1 CATGTACCTGAAACATATTAATCAACTAATT
682134 AATTTCAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (32 bp):
CATGTACCTGAAACATATTAATCAACTAATTG
Found at i:682229 original size:38 final size:39
Alignment explanation
Indices: 682181--682276 Score: 142
Period size: 39 Copynumber: 2.5 Consensus size: 39
682171 AATTTGTCTT
* *
682181 AAACTTAGACACCTTAAAAA-AACTATTAAATATGTATCA
1 AAACTAAGACACATTAAAAACAACTATTAAATATGTAT-A
*
682220 AAA-TAAGACACATTAAAAACAACTATTCAATATGTATA
1 AAACTAAGACACATTAAAAACAACTATTAAATATGTATA
682258 AAACTAAGACACATTAAAA
1 AAACTAAGACACATTAAAA
682277 CCCTATTTAA
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
38 18 0.35
39 34 0.65
ACGTcount: A:0.55, C:0.15, G:0.05, T:0.25
Consensus pattern (39 bp):
AAACTAAGACACATTAAAAACAACTATTAAATATGTATA
Found at i:695886 original size:13 final size:13
Alignment explanation
Indices: 695868--695894 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
695858 TCTTGCGTCG
695868 ATAATTTAGCCCT
1 ATAATTTAGCCCT
695881 ATAATTTAGCCCT
1 ATAATTTAGCCCT
695894 A
1 A
695895 GTCAGTTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.37
Consensus pattern (13 bp):
ATAATTTAGCCCT
Found at i:698294 original size:17 final size:17
Alignment explanation
Indices: 698271--698318 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
698261 TAGATTGCAT
698271 ACATTTTTATTGTCATC
1 ACATTTTTATTGTCATC
* * *
698288 GCATTTTATTTTGTCATT
1 ACATTTT-TATTGTCATC
*
698306 ACATTTCTATTGT
1 ACATTTTTATTGT
698319 TAATTTAGTT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.21, C:0.15, G:0.08, T:0.56
Consensus pattern (17 bp):
ACATTTTTATTGTCATC
Found at i:700790 original size:53 final size:53
Alignment explanation
Indices: 700701--701045 Score: 310
Period size: 53 Copynumber: 6.6 Consensus size: 53
700691 TTCACATGTG
* * *
700701 ATAACTCACGATGACATAGAGTCATCGGACCTTTAATCC-AAGATCGGATT-AGT
1 ATAACTCATGATGACACAGAGTCATCGGACCTTTAATCCGAA-ATAGGATTCA-T
* * *
700754 GTAACTCATGATGACACAGAGTCATTC-GACCCTTAATCCGTAATAGGATTCAT
1 ATAACTCATGATGACACAGAGTCA-TCGGACCTTTAATCCGAAATAGGATTCAT
* * ** **
700807 ATAATTAATGATGACACAGAGTCATCGGACCTTTAATCCGTGATTTGATTCAT
1 ATAACTCATGATGACACAGAGTCATCGGACCTTTAATCCGAAATAGGATTCAT
* * * **
700860 ATAACTCACGATGACA-A-AGTCATCAGACCTTTAATTCGTGATAGGATTCAT
1 ATAACTCATGATGACACAGAGTCATCGGACCTTTAATCCGAAATAGGATTCAT
* * * *
700911 ATAACTCATAATGACACAAAGTCATCGGACCTTTAATCCGTGACT-GGATTCAT
1 ATAACTCATGATGACACAGAGTCATCGGACCTTTAATCCG-AAATAGGATTCAT
* * * * ** **
700964 ATAACTCACGATGATACAAAGTCATCAGACCTTTAATTTGTGATAGGATTCAT
1 ATAACTCATGATGACACAGAGTCATCGGACCTTTAATCCGAAATAGGATTCAT
** *
701017 ATAACTCACAATG--ACATAGTCATCGGACC
1 ATAACTCATGATGACACAGAGTCATCGGACC
701046 ATTTTGCTTT
Statistics
Matches: 245, Mismatches: 39, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
51 58 0.24
52 5 0.02
53 177 0.72
54 5 0.02
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (53 bp):
ATAACTCATGATGACACAGAGTCATCGGACCTTTAATCCGAAATAGGATTCAT
Found at i:701007 original size:157 final size:157
Alignment explanation
Indices: 700701--701045 Score: 426
Period size: 157 Copynumber: 2.2 Consensus size: 157
700691 TTCACATGTG
* * *
700701 ATAACTCACGATGACATAGAGTCATCGGACCTTTAATCCAAGATCGGATTAGTGTAACTCATGAT
1 ATAACTCACGATGACA-A-AGTCATCGGACCTTTAATCCAAGATAGGATTAGTATAACTCATAAT
* * * *
700766 GACACAGAGTCATTCGACCCTTAATCCGTAATAGGATTCATATAATTAATGATGACACAGAGTCA
64 GACACAAAGTCATTCGACCCTTAATCCGTAATAGGATTCATATAACTAACGATGACACAAAGTCA
* **
700831 TCGGACCTTTAATCCGTGATTTGATTCAT
129 TCAGACCTTTAATCCGTGATAGGATTCAT
* * **
700860 ATAACTCACGATGACAAAGTCATCAGACCTTTAATTCGTGATAGGATTCA-TATAACTCATAATG
1 ATAACTCACGATGACAAAGTCATCGGACCTTTAATCCAAGATAGGATT-AGTATAACTCATAATG
* * * *
700924 ACACAAAGTCA-TCGGACCTTTAATCCGTGACT-GGATTCATATAACTCACGATGATACAAAGTC
65 ACACAAAGTCATTC-GACCCTTAATCCGT-AATAGGATTCATATAACTAACGATGACACAAAGTC
**
700987 ATCAGACCTTTAATTTGTGATAGGATTCAT
128 ATCAGACCTTTAATCCGTGATAGGATTCAT
* *
701017 ATAACTCACAATGACATAGTCATCGGACC
1 ATAACTCACGATGACAAAGTCATCGGACC
701046 ATTTTGCTTT
Statistics
Matches: 160, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
156 2 0.01
157 138 0.86
158 4 0.03
159 16 0.10
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (157 bp):
ATAACTCACGATGACAAAGTCATCGGACCTTTAATCCAAGATAGGATTAGTATAACTCATAATGA
CACAAAGTCATTCGACCCTTAATCCGTAATAGGATTCATATAACTAACGATGACACAAAGTCATC
AGACCTTTAATCCGTGATAGGATTCAT
Found at i:701032 original size:106 final size:104
Alignment explanation
Indices: 700701--701045 Score: 421
Period size: 104 Copynumber: 3.3 Consensus size: 104
700691 TTCACATGTG
* * ** * *
700701 ATAACTCACGATGACATAGAGTCATCGGACCTTTAATCCAAGATCGGATT-AGTGTAACTCATGA
1 ATAACTCACAATGACACAGAGTCATCGGACCTTTAATCCGTGAT-GGATTCA-TATAACTCACGA
* * * *
700765 TGACACAGAGTCATTC-GACCCTTAATCCGTAATAGGATTCAT
64 TGA-ACAAAGTCA-TCAGACCTTTAATTCGTGATAGGATTCAT
* * ** *
700807 ATAATTAATGATGACACAGAGTCATCGGACCTTTAATCCGTGATTTGATTCATATAACTCACGAT
1 ATAACTCACAATGACACAGAGTCATCGGACCTTTAATCCGTGA-TGGATTCATATAACTCACGAT
700872 G-ACAAAGTCATCAGACCTTTAATTCGTGATAGGATTCAT
65 GAACAAAGTCATCAGACCTTTAATTCGTGATAGGATTCAT
* *
700911 ATAACTCATAATGACACAAAGTCATCGGACCTTTAATCCGTGACTGGATTCATATAACTCACGAT
1 ATAACTCACAATGACACAGAGTCATCGGACCTTTAATCCGTGA-TGGATTCATATAACTCACGAT
*
700976 GATACAAAGTCATCAGACCTTTAATTTGTGATAGGATTCAT
65 GA-ACAAAGTCATCAGACCTTTAATTCGTGATAGGATTCAT
*
701017 ATAACTCACAATG--ACATAGTCATCGGACC
1 ATAACTCACAATGACACAGAGTCATCGGACC
701046 ATTTTGCTTT
Statistics
Matches: 212, Mismatches: 22, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
103 2 0.01
104 106 0.50
106 102 0.48
107 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (104 bp):
ATAACTCACAATGACACAGAGTCATCGGACCTTTAATCCGTGATGGATTCATATAACTCACGATG
AACAAAGTCATCAGACCTTTAATTCGTGATAGGATTCAT
Found at i:703353 original size:45 final size:45
Alignment explanation
Indices: 703302--703392 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
703292 AATATGTAGG
703302 TTTACATCATGAAGATGCTAGAGAGCATCTCAAACCGTTTTCTAT
1 TTTACATCATGAAGATGCTAGAGAGCATCTCAAACCGTTTTCTAT
703347 TTTACATCATGAAGATGCTAGAGAGCATCTCAAACCGTTTTCTAT
1 TTTACATCATGAAGATGCTAGAGAGCATCTCAAACCGTTTTCTAT
703392 T
1 T
703393 CATATGCGCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (45 bp):
TTTACATCATGAAGATGCTAGAGAGCATCTCAAACCGTTTTCTAT
Found at i:708487 original size:15 final size:15
Alignment explanation
Indices: 708467--708514 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
708457 ATGTCAAGAA
708467 GAAGAGAAGGATAAT
1 GAAGAGAAGGATAAT
708482 GAAGAGGAA--A-AA-
1 GAAGA-GAAGGATAAT
708494 GAAGAGAAGGATAAT
1 GAAGAGAAGGATAAT
708509 GAAGAG
1 GAAGAG
708515 GAAGAAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
11 3 0.11
12 5 0.18
13 3 0.11
14 3 0.11
15 11 0.39
16 3 0.11
ACGTcount: A:0.56, C:0.00, G:0.35, T:0.08
Consensus pattern (15 bp):
GAAGAGAAGGATAAT
Found at i:708503 original size:27 final size:27
Alignment explanation
Indices: 708465--708517 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
708455 TTATGTCAAG
708465 AAGAAGAGAAGGATAATGAAGAGGAAA
1 AAGAAGAGAAGGATAATGAAGAGGAAA
708492 AAGAAGAGAAGGATAATGAAGAGGAA
1 AAGAAGAGAAGGATAATGAAGAGGAA
708518 GAAAAACCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.58, C:0.00, G:0.34, T:0.08
Consensus pattern (27 bp):
AAGAAGAGAAGGATAATGAAGAGGAAA
Found at i:713368 original size:35 final size:35
Alignment explanation
Indices: 713321--713406 Score: 156
Period size: 35 Copynumber: 2.5 Consensus size: 35
713311 TAATTCCTTT
*
713321 AGATCAAT-CAGTGCCATTCTGTATGGAGGAATCG
1 AGATCGATGCAGTGCCATTCTGTATGGAGGAATCG
713355 AGATCGATGCAGTGCCATTCTGTATGGAGGAATCG
1 AGATCGATGCAGTGCCATTCTGTATGGAGGAATCG
713390 AGATCGATGCAGTGCCA
1 AGATCGATGCAGTGCCA
713407 GGTACTAAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
34 7 0.14
35 43 0.86
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (35 bp):
AGATCGATGCAGTGCCATTCTGTATGGAGGAATCG
Found at i:724579 original size:18 final size:17
Alignment explanation
Indices: 724548--724581 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
724538 TAGTTTTTGC
724548 ATTTTTATTGTCACTGG
1 ATTTTTATTGTCACTGG
*
724565 ATTTTATATTTTCACTG
1 ATTTT-TATTGTCACTG
724582 CACTCATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.21, C:0.12, G:0.12, T:0.56
Consensus pattern (17 bp):
ATTTTTATTGTCACTGG
Found at i:726594 original size:24 final size:25
Alignment explanation
Indices: 726547--726594 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
726537 TCTACCGATA
*
726547 CAAGTACAAAATCTATCGATACTTT
1 CAAGTACAAAATCTACCGATACTTT
*
726572 CAAGTACAGAA-CTACCGATACTT
1 CAAGTACAAAATCTACCGATACTT
726595 ACTAATCAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (25 bp):
CAAGTACAAAATCTACCGATACTTT
Found at i:727197 original size:53 final size:53
Alignment explanation
Indices: 727128--727420 Score: 324
Period size: 53 Copynumber: 5.6 Consensus size: 53
727118 TTCACATGTG
* * * * *
727128 ATAACTCATGACGACACAAAGTCATCGGAGCTTTAATCCATGATAAGATTTC-T
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCATGATAGGA-TTCAT
* * * * * *
727181 GTAACTCATGAGGACAC--AGTCATCGGACCCTTAATTTC-TAATAGGATTCAT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAA-TCCATGATAGGATTCAT
* * *
727232 ATAACTCACGATGACACTGAGTCATCAGACCTTTAATCTATGATAGGATTCAT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCATGATAGGATTCAT
* ** * *
727285 ATAACTCACGATGACACTGAGTCATCTAACCTTTAATCCGTGATAAGATTCAT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCATGATAGGATTCAT
* * * *
727338 ATAACTCATGATGACACAGAGTCATCAGACCTTTAATTCGTGATAGGATTCAT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCATGATAGGATTCAT
*
727391 ATAACTCACGATGACACAAAGTCATCGGAC
1 ATAACTCACGATGACACAGAGTCATCGGAC
727421 ATTTTCACAT
Statistics
Matches: 206, Mismatches: 29, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
50 3 0.01
51 36 0.17
52 3 0.01
53 164 0.80
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (53 bp):
ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCATGATAGGATTCAT
Done.