Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008885.1 Hibiscus syriacus cultivar Beakdansim tig00112131_pilon, 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: 671647
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:512329 original size:24 final size:26
Alignment explanation
Indices: 512293--512348 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
512283 AAAAAATAAA
512293 TTTTATATATTTA-T-ATATT-TACTT
1 TTTTATATATTTATTGATATTATA-TT
*
512317 TTTTATATTTTTATTGATATTATATT
1 TTTTATATATTTATTGATATTATATT
512343 TTTTAT
1 TTTTAT
512349 CTTAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 12 0.43
25 1 0.04
26 13 0.46
27 2 0.07
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (26 bp):
TTTTATATATTTATTGATATTATATT
Found at i:516614 original size:26 final size:26
Alignment explanation
Indices: 516585--516637 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
516575 TTATAATCAA
516585 TATCATGGTTCAATGAT-TTGTTTTGG
1 TATCATGGTT-AATGATCTTGTTTTGG
* *
516611 TATCATGGTTTATGTTCTTGTTTTGG
1 TATCATGGTTAATGATCTTGTTTTGG
516637 T
1 T
516638 GTTTTTGATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.15, C:0.08, G:0.23, T:0.55
Consensus pattern (26 bp):
TATCATGGTTAATGATCTTGTTTTGG
Found at i:530547 original size:30 final size:29
Alignment explanation
Indices: 530513--530581 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
530503 GTCATTTTCG
* *
530513 ATAATCATGACTGTTTATTTAATATTTTTA
1 ATAATTATGACTATTTA-TTAATATTTTTA
* *
530543 ATAATTGTGAGTATTTATTAATATTTTTA
1 ATAATTATGACTATTTATTAATATTTTTA
530572 ATAATTATGA
1 ATAATTATGA
530582 GTAGATAAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 21 0.62
30 13 0.38
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.52
Consensus pattern (29 bp):
ATAATTATGACTATTTATTAATATTTTTA
Found at i:530570 original size:29 final size:30
Alignment explanation
Indices: 530526--530584 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
530516 ATCATGACTG
*
530526 TTTATTTAATATTTTTAATAATTGTGAGTA
1 TTTATTTAATATTTTTAATAATTATGAGTA
530556 TTTA-TTAATATTTTTAATAATTATGAGTA
1 TTTATTTAATATTTTTAATAATTATGAGTA
530585 GATAAAGAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (30 bp):
TTTATTTAATATTTTTAATAATTATGAGTA
Found at i:531037 original size:13 final size:13
Alignment explanation
Indices: 531019--531045 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
531009 GTTTAGGGGT
531019 CGGAAAGTTTGGG
1 CGGAAAGTTTGGG
531032 CGGAAAGTTTGGG
1 CGGAAAGTTTGGG
531045 C
1 C
531046 TTCATCAGTC
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:0.22, C:0.11, G:0.44, T:0.22
Consensus pattern (13 bp):
CGGAAAGTTTGGG
Found at i:540679 original size:23 final size:23
Alignment explanation
Indices: 540652--540703 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
540642 CTGAGTGGCA
* *
540652 TATGAAATTTGTCCC-TATGGACC
1 TATGAAATATGTCCCGAAT-GACC
540675 TATG-AATATGTCCCGAATGACC
1 TATGAAATATGTCCCGAATGACC
540697 TATGAAA
1 TATGAAA
540704 CCCTCGAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (23 bp):
TATGAAATATGTCCCGAATGACC
Found at i:552133 original size:15 final size:15
Alignment explanation
Indices: 552092--552134 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
552082 TGGCACCCAA
552092 AGCTGAGAAGAAGCC
1 AGCTGAGAAGAAGCC
* *
552107 AGCGGATAAGAAGCC
1 AGCTGAGAAGAAGCC
*
552122 AGCTGAGGAGAAG
1 AGCTGAGAAGAAG
552135 AAAACAGTCG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.40, C:0.16, G:0.37, T:0.07
Consensus pattern (15 bp):
AGCTGAGAAGAAGCC
Found at i:555141 original size:61 final size:61
Alignment explanation
Indices: 555069--555271 Score: 361
Period size: 61 Copynumber: 3.3 Consensus size: 61
555059 ATGATTTGTT
* *
555069 CTGATACTGAATGATTTATTTTTATGTCATAATTCTATCTTTATGTGTATCGCAGTTCATC
1 CTGATACTGAATGATTTATTTGTATGTCATAATTCTATCTTTATGTGTATCGCAGTTTATC
*
555130 CTGATACTGAATGATTTATTTGTATGTCATAATTCTATCTTTATGTGTATTGCAGTTTATC
1 CTGATACTGAATGATTTATTTGTATGTCATAATTCTATCTTTATGTGTATCGCAGTTTATC
*
555191 CTGATACTGAATGATTTATTTGTATGTCATAATTCTATCTTTATGTGTATCACAGTTTATC
1 CTGATACTGAATGATTTATTTGTATGTCATAATTCTATCTTTATGTGTATCGCAGTTTATC
*
555252 CTGATAATGAATGATTTATT
1 CTGATACTGAATGATTTATT
555272 CTTACTAGAA
Statistics
Matches: 136, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 136 1.00
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (61 bp):
CTGATACTGAATGATTTATTTGTATGTCATAATTCTATCTTTATGTGTATCGCAGTTTATC
Found at i:561637 original size:23 final size:23
Alignment explanation
Indices: 561611--561658 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
561601 ATAAAGTACA
*
561611 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
561634 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
561657 AT
1 AT
561659 TTACATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:562100 original size:21 final size:22
Alignment explanation
Indices: 562075--562126 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
562065 ATACTTTACA
*
562075 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
562098 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
562121 ATATAA
1 ATATAA
562127 GCGCTATCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:562111 original size:23 final size:23
Alignment explanation
Indices: 562085--562147 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
562075 ATATAACCAC
562085 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
562108 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
* *
562131 TATCTATTACATCATAT
1 TACCTATTACATTATAT
562148 TTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:562531 original size:21 final size:22
Alignment explanation
Indices: 562506--562557 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
562496 ATACTTTACA
*
562506 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
562529 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
562552 ATATAA
1 ATATAA
562558 GCGCTATCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:562534 original size:431 final size:430
Alignment explanation
Indices: 561732--562784 Score: 1982
Period size: 431 Copynumber: 2.4 Consensus size: 430
561722 TTATAATATG
*
561732 TTGAAAGTGCCCATACTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
*
561797 TCAATTTTTTTTAATATTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
*
561862 CAAAAAATTATTTAATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATAA
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATAA
561927 TATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAAC
196 TATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAAC
*
561992 TCACTCAAAAGATAATCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAA
261 TCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAA
562057 AAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTA
326 AAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTA
562122 TATAAGCGCTATCTATTACATCATATTTTTACCTATTATA
391 TATAAGCGCTATCTATTACATCATATTTTTACCTATTATA
* *
562162 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
562227 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
562292 CAAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATA
131 C-AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATA
562357 ATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAA
195 ATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAA
562422 CTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAA
260 CTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAA
562487 AAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATT
325 AAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATT
562552 ATATAAGCGCTATCTATTACATCATATTTTTACCTATTATA
390 ATATAAGCGCTATCTATTACATCATATTTTTACCTATTATA
*
562593 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATACTTTTTATAAAAAAGATCGATACTTTTTTT-AAAGTTATGTAATTTATGT
* *
562658 TTCAA-TTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTAC
65 TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
* *
562722 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAAAATTTAAATTTAACAA
130 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAA
562785 CATTAACCAA
Statistics
Matches: 609, Mismatches: 12, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
430 186 0.31
431 399 0.66
432 24 0.04
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.41
Consensus pattern (430 bp):
TTGAAAGTGTCCATACTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATAA
TATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAAC
TCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAA
AAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTA
TATAAGCGCTATCTATTACATCATATTTTTACCTATTATA
Found at i:562542 original size:23 final size:23
Alignment explanation
Indices: 562516--562578 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
562506 ATATAACCAC
562516 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
562539 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
* *
562562 TATCTATTACATCATAT
1 TACCTATTACATTATAT
562579 TTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:562948 original size:25 final size:25
Alignment explanation
Indices: 562920--562984 Score: 103
Period size: 25 Copynumber: 2.6 Consensus size: 25
562910 ACTCAAAAGA
* *
562920 TGTATATACCTAAATATGTAGTTAT
1 TGTACATACCTAAATATATAGTTAT
*
562945 TGTACATATCTAAATATATAGTTAT
1 TGTACATACCTAAATATATAGTTAT
562970 TGTACATACCTAAAT
1 TGTACATACCTAAAT
562985 TTAATGATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (25 bp):
TGTACATACCTAAATATATAGTTAT
Found at i:564167 original size:183 final size:183
Alignment explanation
Indices: 563642--564134 Score: 925
Period size: 183 Copynumber: 2.7 Consensus size: 183
563632 TTAAAATTAC
563642 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
563707 ATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
* *
563772 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
563825 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
563890 ATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
563955 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
*
564008 CGACACTTTTTGACAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
1 CGACACTTTTTTA-AATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
* *
564072 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCG
65 TATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCG
564135 ATAGCATTGC
Statistics
Matches: 304, Mismatches: 5, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
183 301 0.99
184 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (183 bp):
CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
ATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
Found at i:564552 original size:23 final size:23
Alignment explanation
Indices: 564526--564576 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
564516 AACCACTACA
564526 TATTACATTATATAA-ACGATACC
1 TATTACATTATATAAGA-GATACC
*
564549 TATTACATTATATAAGAGCTACC
1 TATTACATTATATAAGAGATACC
564572 TATTA
1 TATTA
564577 TATCATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 25 0.96
24 1 0.04
ACGTcount: A:0.41, C:0.16, G:0.06, T:0.37
Consensus pattern (23 bp):
TATTACATTATATAAGAGATACC
Found at i:566182 original size:3 final size:3
Alignment explanation
Indices: 566174--566218 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
566164 ACTTGTTTGG
* * *
566174 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
566219 GTCAGCTTCA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.27, C:0.33, G:0.02, T:0.38
Consensus pattern (3 bp):
ATC
Found at i:566197 original size:18 final size:18
Alignment explanation
Indices: 566174--566247 Score: 67
Period size: 18 Copynumber: 4.1 Consensus size: 18
566164 ACTTGTTTGG
566174 ATCATCATCTTCATCATC
1 ATCATCATCTTCATCATC
* *
566192 ATCATCATCATCGTCATC
1 ATCATCATCTTCATCATC
* * * *
566210 ATCTTCATCGTCAGCTTC
1 ATCATCATCTTCATCATC
* * *
566228 ATCGTCAGCTTCATCTTC
1 ATCATCATCTTCATCATC
566246 AT
1 AT
566248 TGACTGCTTG
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.23, C:0.32, G:0.07, T:0.38
Consensus pattern (18 bp):
ATCATCATCTTCATCATC
Found at i:566247 original size:6 final size:6
Alignment explanation
Indices: 566178--566247 Score: 59
Period size: 6 Copynumber: 11.7 Consensus size: 6
566168 GTTTGGATCA
* * * * * * *
566178 TCATCT TCATCA TCATCA TCATCA TCGTCA TCATCT TCATCG TCAGCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* *
566226 TCATCG TCAGCT TCATCT TCAT
1 TCATCT TCATCT TCATCT TCAT
566248 TGACTGCTTG
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.21, C:0.33, G:0.07, T:0.39
Consensus pattern (6 bp):
TCATCT
Found at i:568329 original size:199 final size:199
Alignment explanation
Indices: 567711--568684 Score: 1770
Period size: 200 Copynumber: 4.9 Consensus size: 199
567701 TTTAAATTAG
*
567711 TATCGACACAAACT-AAAAAGTATCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
567775 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCAATATTTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
* *
567840 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTTATTCTGGACCA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
567905 AAAA
196 AAAA
*
567909 TATTGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
567974 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGTTTTTGGGA
568039 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAAC
130 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAAC
568104 AAAAA
195 AAAAA
*
568109 TATCGACACAAACTAAAAAAGTGTCGACATATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
568174 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
*
568239 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCTTGTTTTCCATTCATTCTGGAACA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
568304 AAAA
196 AAAA
*
568308 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATG
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
568373 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGTTTTTGGGA
* *
568438 TCTACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
130 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAAC
568503 AAAAA
195 AAAAA
*
568508 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACTGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
568573 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGG-TTCGATGTTTTTGGGA
* *
568638 TCGACACTTTTTATATATGGTTCGACACTTTATGGTTGCACCTTGTT
130 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
568685 GGCCATATTG
Statistics
Matches: 749, Mismatches: 23, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
198 13 0.02
199 291 0.39
200 445 0.59
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (199 bp):
TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
AAAA
Found at i:568463 original size:399 final size:399
Alignment explanation
Indices: 567711--568684 Score: 1815
Period size: 399 Copynumber: 2.4 Consensus size: 399
567701 TTTAAATTAG
*
567711 TATCGACACAAACT-AAAAAGTATCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
567775 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCAATATTTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
* * *
567840 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTTATTCTGGACCA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCTTGTTTTCCATTCATTCTGGAACA
*
567905 AAAATATTGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
196 AAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
567970 TATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTT
261 TATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTT
568035 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTG
326 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTG
568100 GAACAAAAA
391 GAACAAAAA
*
568109 TATCGACACAAACTAAAAAAGTGTCGACATATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
568174 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
568239 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCTTGTTTTCCATTCATTCTGGAACA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCTTGTTTTCCATTCATTCTGGAACA
568304 AAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
196 AAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
*
568369 TATGCTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTT
261 TATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTT
*
568434 GGGATCTACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTG
326 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTG
*
568499 GACCAAAAA
391 GAACAAAAA
*
568508 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACTGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
568573 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGG-TTCGATGTTTTTGGGA
*
568638 TCGACACTTTTTATATATGGTTCGACACTTTATGGTTGCACCTTGTT
130 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCTTGTT
568685 GGCCATATTG
Statistics
Matches: 560, Mismatches: 14, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
398 14 0.03
399 484 0.86
400 62 0.11
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (399 bp):
TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCTTGTTTTCCATTCATTCTGGAACA
AAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
TATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTT
GGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTG
GAACAAAAA
Found at i:568849 original size:19 final size:19
Alignment explanation
Indices: 568803--568851 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
568793 TTATATTCAC
*
568803 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
568822 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
568841 ATACAAAATTA
1 ATACAAAATTA
568852 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:570675 original size:33 final size:33
Alignment explanation
Indices: 570638--570703 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
570628 CATCTTAATA
*
570638 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
570671 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
570704 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:570762 original size:21 final size:21
Alignment explanation
Indices: 570737--570780 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
570727 CCCCTTATGC
570737 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
570758 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
570779 CT
1 CT
570781 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:572834 original size:24 final size:24
Alignment explanation
Indices: 572797--572849 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
572787 CCGTTCTATC
572797 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
572821 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
572845 TATTT
1 TATTT
572850 AACCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:573040 original size:20 final size:19
Alignment explanation
Indices: 572994--573040 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
572984 TCCGGTATCA
572994 TTTTACCGATTTTATCATT
1 TTTTACCGATTTTATCATT
* *
573013 TTGATACCGGTTTTATCATAT
1 TT-TTACCGATTTTATCAT-T
573034 TTTTACC
1 TTTTACC
573041 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.53
Consensus pattern (19 bp):
TTTTACCGATTTTATCATT
Found at i:573265 original size:181 final size:181
Alignment explanation
Indices: 572961--573429 Score: 687
Period size: 181 Copynumber: 2.6 Consensus size: 181
572951 CGTACTTACG
* * * *
572961 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGATTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTA-CCTTTTACCGGTTTTATCATTTTGATACCGATTT
* *
573026 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
65 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTTAAAGTATCGACACATTAT
* *
573091 AGGCGCTAAAACTGTTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
130 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* *
573142 AAAGTATCGACACTTTTAATATATCCGGTAACCTTTTACCGGTTTTATCGTTTTGATACCGATTT
1 AAAGTATCGACACTTTAAATATATCCGGT-ACCTTTTACCGGTTTTATCATTTTGATACCGATTT
* * *
573207 TATCATATTTTTACATGGTATATCGTTTTGGATCGATACATTTTTTTAAAGTATCGACACTTTAT
65 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTTAAAGTATCGACACATTAT
**
573272 AGGATTTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
130 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* *
573324 AAAGTACCGACACTTTAAATGTATCCGGT--C-TTTACCGGTTTTATCATTTCT-ATACCGATTT
1 AAAGTATCGACACTTTAAATATATCCGGTACCTTTTACCGGTTTTATCATTT-TGATACCGATTT
* * * *
573385 TGTCATAGTTTTACCTGTTATATCATTTTGGATCGACACATTTTT
65 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
573430 AATTTGGATC
Statistics
Matches: 261, Mismatches: 24, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
178 67 0.26
179 2 0.01
181 164 0.63
182 28 0.11
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (181 bp):
AAAGTATCGACACTTTAAATATATCCGGTACCTTTTACCGGTTTTATCATTTTGATACCGATTTT
ATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTTAAAGTATCGACACATTATA
GGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:574444 original size:22 final size:23
Alignment explanation
Indices: 574400--574445 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
574390 GTCAATATTA
* * *
574400 TTTAAGAATATATTAATTTTAAT
1 TTTAAGAATATAGTAAATATAAT
574423 TTTAA-AATATAGTAAATATAAT
1 TTTAAGAATATAGTAAATATAAT
574445 T
1 T
574446 GATTTCAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (23 bp):
TTTAAGAATATAGTAAATATAAT
Found at i:576332 original size:2 final size:2
Alignment explanation
Indices: 576325--576361 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
576315 CTCAATTAAA
576325 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
576362 AGGTATAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:576817 original size:24 final size:24
Alignment explanation
Indices: 576790--576864 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 24
576780 TCAATAATTA
576790 TATTTAATTATATAAATAAAAATG
1 TATTTAATTATATAAATAAAAATG
* **
576814 TA-TTAA--AT-TCAATAATTATG
1 TATTTAATTATATAAATAAAAATG
*
576834 --TTTAATTATATAAATAAAAATT
1 TATTTAATTATATAAATAAAAATG
*
576856 TATTAAATT
1 TATTTAATT
576865 CAATTTAAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 12
0.65 0.14 0.21
Matches are distributed among these distances:
19 4 0.11
20 9 0.24
21 4 0.11
22 8 0.22
23 4 0.11
24 8 0.22
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (24 bp):
TATTTAATTATATAAATAAAAATG
Found at i:576828 original size:42 final size:42
Alignment explanation
Indices: 576777--576868 Score: 166
Period size: 42 Copynumber: 2.2 Consensus size: 42
576767 TTGAAATTTT
576777 AATTCAATAATTATATTTAATTATATAAATAAAAATGTATTA
1 AATTCAATAATTATATTTAATTATATAAATAAAAATGTATTA
* *
576819 AATTCAATAATTATGTTTAATTATATAAATAAAAATTTATTA
1 AATTCAATAATTATATTTAATTATATAAATAAAAATGTATTA
576861 AATTCAAT
1 AATTCAAT
576869 TTAAAAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.43
Consensus pattern (42 bp):
AATTCAATAATTATATTTAATTATATAAATAAAAATGTATTA
Found at i:576956 original size:7 final size:8
Alignment explanation
Indices: 576912--576961 Score: 50
Period size: 9 Copynumber: 6.1 Consensus size: 8
576902 CTAAATATTT
576912 TTTTTATA
1 TTTTTATA
*
576920 TTTGATATA
1 TTT-TTATA
576929 TATTTTATTA
1 T-TTTTA-TA
576939 TTTTTATA
1 TTTTTATA
576947 TTTTTA-A
1 TTTTTATA
576954 -TTTTATA
1 TTTTTATA
576961 T
1 T
576962 CAACTATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
6 5 0.14
7 2 0.06
8 11 0.31
9 12 0.34
10 5 0.14
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (8 bp):
TTTTTATA
Found at i:590648 original size:19 final size:19
Alignment explanation
Indices: 590624--590672 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
590614 AACCACAGTA
590624 AACTCATTAAATTATCAAC
1 AACTCATTAAATTATCAAC
590643 AACTCATTAAATTATCAAC
1 AACTCATTAAATTATCAAC
*
590662 AACTAATTAAA
1 AACTCATTAAA
590673 ATTTTAACCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (19 bp):
AACTCATTAAATTATCAAC
Found at i:592931 original size:26 final size:26
Alignment explanation
Indices: 592895--592957 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
592885 ATGGTTTTGG
*
592895 AGGTTAAGCTTAGCAATCTTGATAGT
1 AGGTTTAGCTTAGCAATCTTGATAGT
592921 AGGTTTAGCTTAGCAATCTTGATAGT
1 AGGTTTAGCTTAGCAATCTTGATAGT
592947 AGGTTTAGCTT
1 AGGTTTAGCTT
592958 TTGGACTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.38
Consensus pattern (26 bp):
AGGTTTAGCTTAGCAATCTTGATAGT
Found at i:593457 original size:19 final size:19
Alignment explanation
Indices: 593430--593466 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
593420 TCATCCTTAT
*
593430 ATTATTAAATTTACTTTAA
1 ATTAATAAATTTACTTTAA
593449 ATTAATAAATTTACTTTA
1 ATTAATAAATTTACTTTA
593467 TATATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTAATAAATTTACTTTAA
Found at i:594296 original size:57 final size:56
Alignment explanation
Indices: 594218--594326 Score: 164
Period size: 57 Copynumber: 1.9 Consensus size: 56
594208 TCATTTATAC
* * *
594218 GCTTGCTGAAATTTATAAAAATTAATCAAAAAGCAGTAAATGTAAAAGCAATAACAT
1 GCTTGCTAAAATTCATAAAAATTAATCAAAAA-CAGTAAATGTAAAAACAATAACAT
* *
594275 GCTTGCTAAAATTCATGAAAATTAATGAAAAACAGTAAATGTAAAAACAATA
1 GCTTGCTAAAATTCATAAAAATTAATCAAAAACAGTAAATGTAAAAACAATA
594327 GCACCCTACA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
56 19 0.40
57 28 0.60
ACGTcount: A:0.52, C:0.10, G:0.12, T:0.26
Consensus pattern (56 bp):
GCTTGCTAAAATTCATAAAAATTAATCAAAAACAGTAAATGTAAAAACAATAACAT
Found at i:599076 original size:18 final size:16
Alignment explanation
Indices: 599050--599172 Score: 91
Period size: 16 Copynumber: 7.8 Consensus size: 16
599040 CATAAACCGG
*
599050 AAAATAAATAAATAACA
1 AAAACAAATAAATAA-A
599067 GAAAACAAATAAA-AAA
1 -AAAACAAATAAATAAA
599083 ATAAACTAAAT-AAT-AA
1 A-AAAC-AAATAAATAAA
* *
599099 AAAATAAATAAA-ATAG
1 AAAACAAATAAATA-AA
599115 AAAACAAA-AAATAAA
1 AAAACAAATAAATAAA
599130 AATAA-AAATAAA-AATA
1 AA-AACAAATAAATAA-A
*
599146 AAAATAAA-AAATAAA
1 AAAACAAATAAATAAA
599161 AAAACAAATAAA
1 AAAACAAATAAA
599173 AAACATAAAA
Statistics
Matches: 86, Mismatches: 6, Indels: 28
0.72 0.05 0.23
Matches are distributed among these distances:
14 4 0.05
15 30 0.35
16 35 0.41
17 6 0.07
18 11 0.13
ACGTcount: A:0.80, C:0.04, G:0.02, T:0.15
Consensus pattern (16 bp):
AAAACAAATAAATAAA
Found at i:599102 original size:19 final size:17
Alignment explanation
Indices: 599073--599175 Score: 98
Period size: 18 Copynumber: 5.6 Consensus size: 17
599063 AACAGAAAAC
599073 AAATAAAAAAATAAACTAA
1 AAAT-AAAAAATAAA-TAA
599092 ATAATAAAAAATAAATAA
1 A-AATAAAAAATAAATAA
* *
599110 AATAGAAAACAAAAAATAA
1 AA-ATAAAA-AATAAATAA
*
599129 AAATAAAAATAAAAATAA
1 AAATAAAAA-ATAAATAA
*
599147 AAATAAAAAATAAAAAAA
1 AAATAAAAAAT-AAATAA
599165 CAAATAAAAAA
1 -AAATAAAAAA
599176 CATAAAACAA
Statistics
Matches: 73, Mismatches: 5, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
17 3 0.04
18 36 0.49
19 31 0.42
20 3 0.04
ACGTcount: A:0.82, C:0.03, G:0.01, T:0.15
Consensus pattern (17 bp):
AAATAAAAAATAAATAA
Found at i:599108 original size:31 final size:31
Alignment explanation
Indices: 599050--599181 Score: 121
Period size: 31 Copynumber: 4.3 Consensus size: 31
599040 CATAAACCGG
* * *
599050 AAAATAAA-TAAATAACAGAAAACAAATAAA
1 AAAATAAACTAAAAAATAAAAAACAAATAAA
* *
599080 AAAATAAACTAAATAATAAAAAATAAATAAA
1 AAAATAAACTAAAAAATAAAAAACAAATAAA
* *
599111 ATAGA-AAAC-AAAAAATAAAAATAAAAATAAA
1 A-AAATAAACTAAAAAATAAAAA-ACAAATAAA
599142 AATAA-AAA-TAAAAAATAAAAAAACAAATAAA
1 AA-AATAAACTAAAAAAT-AAAAAACAAATAAA
599173 AAACATAAA
1 AAA-ATAAA
599182 ACAATATAAG
Statistics
Matches: 86, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
30 21 0.24
31 55 0.64
32 10 0.12
ACGTcount: A:0.80, C:0.05, G:0.02, T:0.14
Consensus pattern (31 bp):
AAAATAAACTAAAAAATAAAAAACAAATAAA
Found at i:599123 original size:23 final size:23
Alignment explanation
Indices: 599050--599129 Score: 81
Period size: 23 Copynumber: 3.3 Consensus size: 23
599040 CATAAACCGG
*
599050 AAAATAAATAAATAACAGAAAACAA
1 AAAATAAAT-AA-AATAGAAAACAA
* * *
599075 ATAAAAAAATAAACTA-AATAATAA
1 A-AAATAAATAAAATAGAA-AACAA
599099 AAAATAAATAAAATAGAAAACAA
1 AAAATAAATAAAATAGAAAACAA
599122 AAAATAAA
1 AAAATAAA
599130 AATAAAAATA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
23 26 0.58
24 9 0.20
25 3 0.07
26 7 0.16
ACGTcount: A:0.78, C:0.05, G:0.03, T:0.15
Consensus pattern (23 bp):
AAAATAAATAAAATAGAAAACAA
Found at i:599130 original size:12 final size:11
Alignment explanation
Indices: 599077--599175 Score: 83
Period size: 12 Copynumber: 8.3 Consensus size: 11
599067 GAAAACAAAT
599077 AAAAAAATAAA
1 AAAAAAATAAA
* *
599088 CTAAATAATAAA
1 -AAAAAAATAAA
*
599100 AAATAAATAAA
1 AAAAAAATAAA
599111 ATAGAAAACA-AAA
1 A-A-AAAA-ATAAA
599124 AATAAAAATAAA
1 AA-AAAAATAAA
599136 AATAAAAATAAAA
1 AA-AAAAAT-AAA
599149 ATAAAAAATAAA
1 A-AAAAAATAAA
599161 AAAACAAATAAA
1 AAAA-AAATAAA
599173 AAA
1 AAA
599176 CATAAAACAA
Statistics
Matches: 73, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
11 13 0.18
12 41 0.56
13 17 0.23
14 2 0.03
ACGTcount: A:0.82, C:0.03, G:0.01, T:0.14
Consensus pattern (11 bp):
AAAAAAATAAA
Found at i:599182 original size:18 final size:18
Alignment explanation
Indices: 599050--599190 Score: 83
Period size: 19 Copynumber: 7.6 Consensus size: 18
599040 CATAAACCGG
* * *
599050 AAAATAAATAAATAACAG
1 AAAACAAATAAAAAACAA
599068 AAAACAAAT-AAAAA-AA
1 AAAACAAATAAAAAACAA
*
599084 TAAACTAAATAATAAAA-AA
1 AAAAC-AAATAA-AAAACAA
*
599103 TAAATA-AAATAGAAAACAA
1 -AAA-ACAAATAAAAAACAA
* * *
599122 AAAATAAAAATAAAAATAA
1 AAAACAAATA-AAAAACAA
* *
599141 AAATAAAAATAAAAAATAAA
1 AAA-ACAAATAAAAAA-CAA
*
599161 AAAACAAATAAAAAACAT
1 AAAACAAATAAAAAACAA
599179 AAAACAATATAA
1 AAAACAA-ATAA
599191 GAATCAACTA
Statistics
Matches: 97, Mismatches: 15, Indels: 21
0.73 0.11 0.16
Matches are distributed among these distances:
16 5 0.05
17 9 0.09
18 28 0.29
19 42 0.43
20 12 0.12
21 1 0.01
ACGTcount: A:0.79, C:0.05, G:0.01, T:0.15
Consensus pattern (18 bp):
AAAACAAATAAAAAACAA
Found at i:599182 original size:19 final size:19
Alignment explanation
Indices: 599050--599182 Score: 75
Period size: 18 Copynumber: 7.2 Consensus size: 19
599040 CATAAACCGG
* * *
599050 AAAATAAATAAATAACA-G
1 AAAACAAATAAAAAACATA
599068 AAAACAAATAAAAAA-AT-
1 AAAACAAATAAAAAACATA
*
599085 -AAACTAAATAATAAAAAATA
1 AAAAC-AAATAA-AAAACATA
* *
599105 AATA-AAATAGAAAACA-A
1 AAAACAAATAAAAAACATA
*
599122 AAAATAAA-AATAAAA-ATAA
1 AAAACAAATAA-AAAACAT-A
* * *
599141 AAATAAAAATAAAAAATAAA
1 AAA-ACAAATAAAAAACATA
599161 AAAACAAATAAAAAACATA
1 AAAACAAATAAAAAACATA
599180 AAA
1 AAA
599183 CAATATAAGA
Statistics
Matches: 90, Mismatches: 12, Indels: 25
0.71 0.09 0.20
Matches are distributed among these distances:
16 4 0.04
17 13 0.14
18 29 0.32
19 27 0.30
20 12 0.13
21 5 0.06
ACGTcount: A:0.80, C:0.05, G:0.02, T:0.14
Consensus pattern (19 bp):
AAAACAAATAAAAAACATA
Found at i:599190 original size:10 final size:9
Alignment explanation
Indices: 599068--599190 Score: 53
Period size: 9 Copynumber: 13.2 Consensus size: 9
599058 TAAATAACAG
599068 AAAACAAAT
1 AAAACAAAT
599077 AAAA-AAAT
1 AAAACAAAT
599085 -AAACTAAAT
1 AAAAC-AAAT
*
599094 AATAAAAAAT
1 AA-AACAAAT
599104 AAATA-AAAT
1 AAA-ACAAAT
599113 AGAAAACAAA-
1 --AAAACAAAT
*
599123 AAATAAAAAT
1 AAA-ACAAAT
599133 AAAA-ATAA-
1 AAAACA-AAT
*
599141 AAATAAAAAT
1 AAA-ACAAAT
* *
599151 AAAAAATAAA
1 AAAACA-AAT
599161 AAAACAAAT
1 AAAACAAAT
599170 AAAA-AACAT
1 AAAACAA-AT
599179 AAAACAATAT
1 AAAACAA-AT
599189 AA
1 AA
599191 GAATCAACTA
Statistics
Matches: 91, Mismatches: 6, Indels: 33
0.70 0.05 0.25
Matches are distributed among these distances:
7 3 0.03
8 13 0.14
9 38 0.42
10 29 0.32
11 8 0.09
ACGTcount: A:0.80, C:0.05, G:0.01, T:0.15
Consensus pattern (9 bp):
AAAACAAAT
Found at i:599211 original size:21 final size:21
Alignment explanation
Indices: 599187--599247 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
599177 ATAAAACAAT
599187 ATAAGAATCAACTAATTCATA
1 ATAAGAATCAACTAATTCATA
*
599208 AT-A-ATTC-AC--ATT-A-A
1 ATAAGAATCAACTAATTCATA
599222 CATAAGAATCAACTAATTCATA
1 -ATAAGAATCAACTAATTCATA
599244 ATAA
1 ATAA
599248 TTCACATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 16
0.62 0.04 0.33
Matches are distributed among these distances:
14 1 0.03
15 3 0.10
16 4 0.13
17 3 0.10
18 4 0.13
19 3 0.10
20 4 0.13
21 7 0.23
22 1 0.03
ACGTcount: A:0.52, C:0.15, G:0.03, T:0.30
Consensus pattern (21 bp):
ATAAGAATCAACTAATTCATA
Found at i:599225 original size:18 final size:18
Alignment explanation
Indices: 599204--599262 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
599194 TCAACTAATT
599204 CATAATAATTCACATTAA
1 CATAATAATTCACATTAA
* *
599222 CATAAGAA-TCA-ACTAA
1 CATAATAATTCACATTAA
599238 TTCATAATAATTCACATTAA
1 --CATAATAATTCACATTAA
599258 CATAA
1 CATAA
599263 GAATCAACTA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
16 4 0.12
17 3 0.09
18 19 0.58
19 3 0.09
20 4 0.12
ACGTcount: A:0.51, C:0.17, G:0.02, T:0.31
Consensus pattern (18 bp):
CATAATAATTCACATTAA
Found at i:599227 original size:36 final size:36
Alignment explanation
Indices: 599187--599306 Score: 178
Period size: 36 Copynumber: 3.4 Consensus size: 36
599177 ATAAAACAAT
599187 ATAAGAATCAACTAATTCATAATAATTCACATTAAC
1 ATAAGAATCAACTAATTCATAATAATTCACATTAAC
599223 ATAAGAATCAACTAATTCATAATAATTCACATTAAC
1 ATAAGAATCAACTAATTCATAATAATTCACATTAAC
**
599259 ATAAGAATCAACT-A---AT-ATCCTTCACATTAAC
1 ATAAGAATCAACTAATTCATAATAATTCACATTAAC
599290 ATTAAGAATCAACTAAT
1 A-TAAGAATCAACTAAT
599307 ACCCTTCAAA
Statistics
Matches: 79, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
31 14 0.18
32 14 0.18
33 1 0.01
35 1 0.01
36 49 0.62
ACGTcount: A:0.49, C:0.17, G:0.03, T:0.30
Consensus pattern (36 bp):
ATAAGAATCAACTAATTCATAATAATTCACATTAAC
Found at i:599301 original size:32 final size:31
Alignment explanation
Indices: 599212--599322 Score: 132
Period size: 32 Copynumber: 3.4 Consensus size: 31
599202 TTCATAATAA
**
599212 TTCACATTAACATAAGAATCAACTAATTCATAATAA
1 TTCACATTAACATAAGAATCAACT-A---AT-ATCC
599248 TTCACATTAACATAAGAATCAACTAATATCC
1 TTCACATTAACATAAGAATCAACTAATATCC
*
599279 TTCACATTAACATTAAGAATCAACTAATACCC
1 TTCACATTAACA-TAAGAATCAACTAATATCC
*
599311 TTCAAATTAACA
1 TTCACATTAACA
599323 AATAAAAACA
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
31 14 0.20
32 31 0.44
35 1 0.01
36 24 0.34
ACGTcount: A:0.47, C:0.21, G:0.03, T:0.30
Consensus pattern (31 bp):
TTCACATTAACATAAGAATCAACTAATATCC
Found at i:599380 original size:31 final size:31
Alignment explanation
Indices: 599342--599404 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 31
599332 ATAAAACAAT
*
599342 ATAAGAAT-AAGCTAATATCCTTCACATTAAC
1 ATAAGAATCAA-CTAATATCCTTCACATCAAC
599373 ATAAGAATCAACTAATATCCTTCACATCAAC
1 ATAAGAATCAACTAATATCCTTCACATCAAC
599404 A
1 A
599405 AATAAAAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.46, C:0.22, G:0.05, T:0.27
Consensus pattern (31 bp):
ATAAGAATCAACTAATATCCTTCACATCAAC
Found at i:599408 original size:82 final size:82
Alignment explanation
Indices: 599259--599470 Score: 291
Period size: 82 Copynumber: 2.5 Consensus size: 82
599249 TCACATTAAC
*
599259 ATAAGAATCAA-CTAATATCCTTCACATTAACATTAAGAATCAACTAATACCCTTCAAATTAACA
1 ATAAGAAT-AAGCTAATATCCTTCACATTAACA-TAAGAATCAACTAATACCCTTCAAATCAACA
*
599323 AATAAAAACATAAAACAAT
64 AATAAAAACAGAAAACAAT
* *
599342 ATAAGAATAAGCTAATATCCTTCACATTAACATAAGAATCAACTAATATCCTTCACATCAACAAA
1 ATAAGAATAAGCTAATATCCTTCACATTAACATAAGAATCAACTAATACCCTTCAAATCAACAAA
*
599407 TAAAAACAGAAAATAAT
66 TAAAAACAGAAAACAAT
* *
599424 ATAAAAATCAGCTAATTCAAAGTCCTTCACATTAACATAAGAATCAA
1 ATAAGAATAAGCTAA-T---A-TCCTTCACATTAACATAAGAATCAA
599471 AAAACAAAAA
Statistics
Matches: 116, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
82 60 0.52
83 30 0.26
86 1 0.01
87 25 0.22
ACGTcount: A:0.52, C:0.19, G:0.04, T:0.25
Consensus pattern (82 bp):
ATAAGAATAAGCTAATATCCTTCACATTAACATAAGAATCAACTAATACCCTTCAAATCAACAAA
TAAAAACAGAAAACAAT
Found at i:599546 original size:7 final size:7
Alignment explanation
Indices: 599534--599586 Score: 63
Period size: 7 Copynumber: 7.4 Consensus size: 7
599524 TGAACTTATG
599534 AAAAACA
1 AAAAACA
599541 AAAAACA
1 AAAAACA
599548 AATAAA-A
1 AA-AAACA
*
599555 AATAAATA
1 AA-AAACA
*
599563 GAAAACA
1 AAAAACA
599570 AAAAACA
1 AAAAACA
599577 AAAAACA
1 AAAAACA
599584 AAA
1 AAA
599587 GCATATAATG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
7 36 0.88
8 5 0.12
ACGTcount: A:0.83, C:0.09, G:0.02, T:0.06
Consensus pattern (7 bp):
AAAAACA
Found at i:599623 original size:18 final size:18
Alignment explanation
Indices: 599600--599655 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
599590 TATAATGTAT
599600 ACATAAAACAAATAA-AAA
1 ACATAAAACAAA-AAGAAA
*
599618 ACATAAAAGAAAAAGAAA
1 ACATAAAACAAAAAGAAA
*
599636 ACATAAAACATAAAATAAA
1 ACATAAAACA-AAAAGAAA
599655 A
1 A
599656 AAAACATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
17 2 0.06
18 23 0.70
19 8 0.24
ACGTcount: A:0.77, C:0.09, G:0.04, T:0.11
Consensus pattern (18 bp):
ACATAAAACAAAAAGAAA
Found at i:599645 original size:25 final size:23
Alignment explanation
Indices: 599615--599689 Score: 71
Period size: 25 Copynumber: 3.0 Consensus size: 23
599605 AAACAAATAA
599615 AAAACATAAAAGAAAAAGAAAACAT
1 AAAACATAAAA-AAAAA-AAAACAT
*
599640 AAAACATAAAATAAAAAAAACAT
1 AAAACATAAAAAAAAAAAAACAT
*
599663 ATAAA-ATTTAAAAAAAATAAAAGCAT
1 A-AAACA--TAAAAAAAA-AAAAACAT
599689 A
1 A
599690 TAAAAAAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
23 9 0.21
24 7 0.16
25 19 0.44
26 8 0.19
ACGTcount: A:0.75, C:0.07, G:0.04, T:0.15
Consensus pattern (23 bp):
AAAACATAAAAAAAAAAAAACAT
Found at i:600532 original size:31 final size:30
Alignment explanation
Indices: 600482--600541 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
600472 GAAAAGAAAT
600482 AAAAAAAAACAAATAATAAAAAACAAAAAC
1 AAAAAAAAACAAATAATAAAAAACAAAAAC
*
600512 AAAAACAAAACAGAAT-ATAAAAAAGAAAAA
1 AAAAA-AAAACA-AATAATAAAAAACAAAAA
600542 AAATTAACAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 5 0.19
31 19 0.70
32 3 0.11
ACGTcount: A:0.82, C:0.08, G:0.03, T:0.07
Consensus pattern (30 bp):
AAAAAAAAACAAATAATAAAAAACAAAAAC
Found at i:600541 original size:26 final size:26
Alignment explanation
Indices: 600482--600585 Score: 70
Period size: 27 Copynumber: 3.8 Consensus size: 26
600472 GAAAAGAAAT
*
600482 AAAAAAA-AACAAATAATAAAAAACAAAA
1 AAAAAAATAACAAAT-AT-AAAAAC-AGA
*
600510 ACAAAAACAAAACAGAATATAAAAA-AGA
1 A-AAAAA-ATAACA-AATATAAAAACAGA
*
600538 AAAAAAATTAACACATATAAAAACAGA
1 AAAAAAA-TAACAAATATAAAAACAGA
* * *
600565 AAACAAA-ACCAAATAAAAAAA
1 AAAAAAATAACAAATATAAAAA
600586 TAAACATTGT
Statistics
Matches: 63, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
25 11 0.17
26 10 0.16
27 18 0.29
28 4 0.06
29 5 0.08
30 6 0.10
31 6 0.10
32 3 0.05
ACGTcount: A:0.78, C:0.11, G:0.03, T:0.09
Consensus pattern (26 bp):
AAAAAAATAACAAATATAAAAACAGA
Found at i:600550 original size:27 final size:28
Alignment explanation
Indices: 600520--600572 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
600510 ACAAAAACAA
600520 AACAGAATATAAAAA-AGAAAA-AAAATT
1 AACA-AATATAAAAACAGAAAACAAAATT
*
600547 AACACATATAAAAACAGAAAACAAAA
1 AACAAATATAAAAACAGAAAACAAAA
600573 CCAAATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 9 0.39
27 10 0.43
28 4 0.17
ACGTcount: A:0.74, C:0.09, G:0.06, T:0.11
Consensus pattern (28 bp):
AACAAATATAAAAACAGAAAACAAAATT
Found at i:600568 original size:51 final size:49
Alignment explanation
Indices: 600459--600591 Score: 136
Period size: 50 Copynumber: 2.7 Consensus size: 49
600449 CATACTATTA
*
600459 AAAAACAGAAAACGAAA-AGAA-ATAAAAAAAAACAAATAATAAAAAAC
1 AAAAACAGAAAACAAAACAGAATATAAAAAAAAACAAATAATAAAAAAC
* *
600506 AAAAACA-AAAACAAAACAGAATATAAAAAAGAAA-AAA-AATTAACACATAT
1 AAAAACAGAAAACAAAACAGAATATAAAAAA-AAACAAATAA-TAA-A-AAAC
600556 AAAAACAGAAAACAAAACCA-AATA-AAAAAATAAACA
1 AAAAACAGAAAACAAAA-CAGAATATAAAAAA-AAACA
600592 TTGTGGTTTT
Statistics
Matches: 73, Mismatches: 4, Indels: 14
0.80 0.04 0.15
Matches are distributed among these distances:
46 8 0.11
47 13 0.18
48 14 0.19
49 4 0.05
50 18 0.25
51 14 0.19
52 2 0.03
ACGTcount: A:0.77, C:0.11, G:0.05, T:0.08
Consensus pattern (49 bp):
AAAAACAGAAAACAAAACAGAATATAAAAAAAAACAAATAATAAAAAAC
Found at i:600589 original size:57 final size:59
Alignment explanation
Indices: 600473--600589 Score: 134
Period size: 57 Copynumber: 2.0 Consensus size: 59
600463 ACAGAAAACG
* *
600473 AAAAGAAATAAAAAAAAACAAATAATAAAAAACAAAAACAAAAACAAAACAGAATATAA
1 AAAAGAAATAAAAAAAAACAAATAATAAAAAACAAAAACAAAAACAAAACAAAAAATAA
** * *
600532 AAAAGAAA-AAAAATTAACACAT-AT-AAAAACAGAAAACAAAACCAAATA-AAAAAATAA
1 AAAAGAAATAAAAAAAAACAAATAATAAAAAACA-AAAACAAAAACAAA-ACAAAAAATAA
600589 A
1 A
600590 CATTGTGGTT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
56 7 0.14
57 23 0.46
58 12 0.24
59 8 0.16
ACGTcount: A:0.78, C:0.09, G:0.03, T:0.09
Consensus pattern (59 bp):
AAAAGAAATAAAAAAAAACAAATAATAAAAAACAAAAACAAAAACAAAACAAAAAATAA
Found at i:600814 original size:16 final size:16
Alignment explanation
Indices: 600793--600823 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
600783 AGTCAAGAAT
600793 AGAAGATGAGGAGTCG
1 AGAAGATGAGGAGTCG
*
600809 AGAAGATGAGTAGTC
1 AGAAGATGAGGAGTC
600824 ACGAATAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.06, G:0.39, T:0.16
Consensus pattern (16 bp):
AGAAGATGAGGAGTCG
Found at i:600928 original size:16 final size:16
Alignment explanation
Indices: 600904--600940 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
600894 ATAGAACTAT
*
600904 AGAAAATGAGGAGTCA
1 AGAAGATGAGGAGTCA
*
600920 AGAAGATGAGGAGTTA
1 AGAAGATGAGGAGTCA
600936 AGAAG
1 AGAAG
600941 GTGGAGGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.49, C:0.03, G:0.35, T:0.14
Consensus pattern (16 bp):
AGAAGATGAGGAGTCA
Found at i:601500 original size:2 final size:2
Alignment explanation
Indices: 601493--602198 Score: 145
Period size: 2 Copynumber: 353.0 Consensus size: 2
601483 AACTTAAACT
*
601493 TA TA TA TA TA TA TA TA TA TA TA TA TA CTA -A TA T- TA TA CTT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA
* * * * * *
601535 -A TA CTT TA AA TA TA TA TA CT- TA TT TA -A TT TA GTCC TA TG TA
1 TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -T-A TA TA TA
*
601576 TA TA TA TA TA TT TA TA T- TA TA -A TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
601615 TA TA TA CTA TG TGG TT TA TA TA TA GTT TA TA T- TA -A TA AA CTA
1 TA TA TA -TA TA T-A TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA
* * * *
601657 TA TA -A TT TA TA -A T- TA TA TA GTA TA TA AA TA TA AA CTA TA CA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA
* * * * *
601698 -A TT TA TA TA TA TA GTT TA TT TA CTA T- TA TG TA TA AA CTA TA
1 TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA -TA TA
* * * **
601739 TA GTT TA TA TA TA AA CTA TA TA TA -A T- TA TA TA AA T- TA -A CCC
1 TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * * *
601780 TA AA CCA TA TA TA T- TA TA TA TA TA AA CTA TA TA GTT TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA
* * *
601822 TA TA GTA TA CA TA GTT TA TA TT TA TA T- TA T- TA TA T- TA TA TA
1 TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
601863 TA TA TA AA TCA TA TA GTT TA TA TT TA TA TA TA TA TA TA TA CTA
1 TA TA TA TA T-A TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * *
601906 TG TA TA -A T- TA TA AA T- TA TA TA TA -A TA TA TA AA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
601943 TA GTT TA TA CT- TA TA TA T- TA CTA TG TA TA AA CTA TA TA TA T-
1 TA -TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA
* * * * *
601984 TA TG TA TA AA T- TA TA TA GTT TA TA TA TA AA CTC TA TA TGA -A
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA T-A TA
* *
602025 CTA TG TA TA GT- TCA TA TA TA GTA TA TA -A GTA TA AA CTA TA TA
1 -TA TA TA TA -TA T-A TA TA TA -TA TA TA TA -TA TA TA -TA TA TA
* * *
602067 -A TT TA TA TA TA AA CTC TA TA TGA -A CTA TA TA TA GT- TCA TA TA
1 TA TA TA TA TA TA TA -TA TA TA T-A TA -TA TA TA TA -TA T-A TA TA
* * * * *
602109 TA -A TT TA TA TA TA GTA TA TA AA TA TA AA T- TA TA T- TG TT TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
602149 TA TA T- TA TA T- TA T- TA TA TA GTT TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
602189 -A TA TA T- TA TA
1 TA TA TA TA TA TA
602199 ATTTTTTTCA
Statistics
Matches: 502, Mismatches: 110, Indels: 184
0.63 0.14 0.23
Matches are distributed among these distances:
1 46 0.09
2 402 0.80
3 54 0.11
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:601607 original size:11 final size:11
Alignment explanation
Indices: 601574--602200 Score: 80
Period size: 11 Copynumber: 57.1 Consensus size: 11
601564 TAGTCCTATG
601574 TATATATATATA
1 TATATATATA-A
*
601586 TTTATATTATAA
1 TATATA-TATAA
601598 TATATATAT-A
1 TATATATATAA
601608 TATATAT-T-A
1 TATATATATAA
* **
601617 TATACTATGTGG
1 TATA-TATATAA
* *
601629 TTTATATATAG
1 TATATATATAA
*
601640 TTTATAT-TAA
1 TATATATATAA
*
601650 TAAACTATATAA
1 TATA-TATATAA
* *
601662 TTTATA-ATTA
1 TATATATATAA
601672 TATAGTATATAAA
1 TATA-TATAT-AA
*
601685 TATAAACTATACA
1 TATATA-TATA-A
*
601698 -ATTTATATATA
1 TATATATATA-A
* * *
601709 TAGTTTATTTAC
1 TA-TATATATAA
*
601721 TATTATGTATAA
1 TA-TATATATAA
* *
601733 -A-CTATATAG
1 TATATATATAA
*
601742 TTTATATATAA
1 TATATATATAA
601753 -ACTATATATAA
1 TA-TATATATAA
601764 T-TATATA-AA
1 TATATATATAA
**
601773 T-TA-ACCCTAA
1 TATATA-TATAA
* *
601783 -ACCATATATAT
1 TA-TATATATAA
601794 TATATATATAA
1 TATATATATAA
*
601805 -ACTATATAGT-T
1 TA-TATATA-TAA
*
601816 TATATATATAG
1 TATATATATAA
* *
601827 TATACATAGT-T
1 TATATATA-TAA
* *
601838 TATATTTATAT
1 TATATATATAA
*
601849 TAT-TATATTA
1 TATATATATAA
601859 TATATATATAA
1 TATATATATAA
*
601870 -ATCATATAGT-T
1 TAT-ATATA-TAA
*
601881 TATATTTAT-A
1 TATATATATAA
601891 TATATATAT-A
1 TATATATATAA
*
601901 TACTATGTAT-A
1 TA-TATATATAA
601912 -AT-TATA-AA
1 TATATATATAA
601920 T-TATATATAA
1 TATATATATAA
* *
601930 TATATAAATTA
1 TATATATATAA
* *
601941 TATAGTTTATAC
1 TATA-TATATAA
601953 T-TATATAT--
1 TATATATATAA
*
601961 TACTATGTATAA
1 TA-TATATATAA
601973 -ACTATATAT-A
1 TA-TATATATAA
*
601983 T-TATGTATAA
1 TATATATATAA
*
601993 -AT-TATATAG
1 TATATATATAA
*
602002 TTTATATATAA
1 TATATATATAA
*
602013 -ACTCTATATGAA
1 TA-TATATAT-AA
*
602025 CTATGTATAGTTCATA
1 -TATATATA--T-A-A
602041 TATAGTATATAA
1 TATA-TATATAA
602053 GTATAAACTATATAA
1 -TAT--A-TATATAA
*
602068 TTTATATATAA
1 TATATATATAA
*
602079 -ACTCTATATGAA
1 TA-TATATAT-AA
* *
602091 -CTATATATAG
1 TATATATATAA
602101 T-TCATATATAA
1 TAT-ATATATAA
*
602112 TTTATATATAGTA
1 TATATATATA--A
*
602125 TATAAATATAA
1 TATATATATAA
**
602136 -AT-TATATTG
1 TATATATATAA
* *
602145 TTTATATATTA
1 TATATATATAA
*
602156 TATTATTATATAG
1 TA-TA-TATATAA
*
602169 TTTATATAT-A
1 TATATATATAA
602179 TATATATATAA
1 TATATATATAA
602190 TATAT-TATAA
1 TATATATATAA
602200 T
1 T
602201 TTTTTTCATT
Statistics
Matches: 447, Mismatches: 96, Indels: 146
0.65 0.14 0.21
Matches are distributed among these distances:
8 7 0.02
9 36 0.08
10 90 0.20
11 191 0.43
12 57 0.13
13 44 0.10
14 4 0.01
15 13 0.03
16 5 0.01
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (11 bp):
TATATATATAA
Found at i:601800 original size:9 final size:9
Alignment explanation
Indices: 601786--602198 Score: 107
Period size: 9 Copynumber: 45.3 Consensus size: 9
601776 ACCCTAAACC
601786 ATATATATT
1 ATATATATT
*
601795 ATATATATAA
1 ATATATAT-T
601805 ACTATATAGTTT
1 A-TATATA--TT
601817 ATATATATAGT
1 ATATATAT--T
*
601828 ATACATAGTT
1 ATATATA-TT
601838 -TATAT-TT
1 ATATATATT
601845 ATAT-TATT
1 ATATATATT
601853 ATAT-TA-T
1 ATATATATT
*
601860 ATATATATAA
1 ATATATAT-T
601870 ATCATATAGTT
1 AT-ATATA-TT
601881 -TATAT-TT
1 ATATATATT
601888 ATATATA-T
1 ATATATATT
*
601896 ATATATACT
1 ATATATATT
*
601905 ATGTATAATT
1 ATATAT-ATT
601915 ATA-A-ATT
1 ATATATATT
*
601922 ATATATAAT
1 ATATATATT
*
601931 ATATAAATT
1 ATATATATT
601940 ATATAGT-TT
1 ATATA-TATT
601949 ATACT-TA-T
1 ATA-TATATT
601957 ATATTACTATGT
1 ATA-TA-TAT-T
*
601969 ATA-A-ACT
1 ATATATATT
601976 ATATATATT
1 ATATATATT
*
601985 ATGTATAAATT
1 A--TATATATT
601996 ATATAGT-TT
1 ATATA-TATT
602005 ATATATAAACTCT
1 ATATAT--A-T-T
*
602018 ATATGA-ACT
1 ATAT-ATATT
*
602027 ATGTATAGTT
1 ATATATA-TT
*
602037 CATATATAGT
1 -ATATATATT
*
602047 ATATA-AGT
1 ATATATATT
*
602055 ATA-A-ACT
1 ATATATATT
602062 ATATA-ATTT
1 ATATATA-TT
602071 ATATATAAACTCT
1 ATATAT--A-T-T
*
602084 ATATGA-ACT
1 ATAT-ATATT
602093 ATATATAGTT
1 ATATATA-TT
602103 CATATATAATT
1 -ATATAT-ATT
602114 -TATATA-T
1 ATATATATT
*
602121 AGTATATA-A
1 A-TATATATT
*
602130 ATATAAATT
1 ATATATATT
*
602139 ATAT-TGTT
1 ATATATATT
602147 -TATATATT
1 ATATATATT
602155 ATAT-TATT
1 ATATATATT
602163 ATATAGT-TT
1 ATATA-TATT
602172 ATATATA-T
1 ATATATATT
602180 ATATATA-T
1 ATATATATT
602188 A-ATATATT
1 ATATATATT
602196 ATA
1 ATA
602199 ATTTTTTTCA
Statistics
Matches: 308, Mismatches: 34, Indels: 124
0.66 0.07 0.27
Matches are distributed among these distances:
7 35 0.11
8 78 0.25
9 106 0.34
10 17 0.06
11 48 0.16
12 11 0.04
13 11 0.04
14 2 0.01
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.48
Consensus pattern (9 bp):
ATATATATT
Found at i:601946 original size:67 final size:73
Alignment explanation
Indices: 601816--601960 Score: 203
Period size: 67 Copynumber: 2.1 Consensus size: 73
601806 CTATATAGTT
* * *
601816 TATATATATAGTATACATAGTTTATATTTATATTATTATATTATATATATATAAATCATATAGTT
1 TATATATATAGTATACATAGTGTATAATTATATAATTATATTATATATATATAAATCATATAGTT
*
601881 TATATTTA
66 TATACTTA
*
601889 TATATATATA-TATAC-TA-TGTATAATTATA-AATTATA-TATA-ATATATAAATTATATAGTT
1 TATATATATAGTATACATAGTGTATAATTATATAATTATATTATATATATATAAATCATATAGTT
601948 TATACTTA
66 TATACTTA
601956 TATAT
1 TATAT
601961 TACTATGTAT
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
67 30 0.45
68 4 0.06
69 6 0.09
70 10 0.15
71 2 0.03
72 5 0.07
73 10 0.15
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (73 bp):
TATATATATAGTATACATAGTGTATAATTATATAATTATATTATATATATATAAATCATATAGTT
TATACTTA
Found at i:602010 original size:67 final size:60
Alignment explanation
Indices: 601787--602201 Score: 204
Period size: 59 Copynumber: 7.0 Consensus size: 60
601777 CCCTAAACCA
* * * *
601787 TATATATTATATATATAAACTATATAGTTTATATATATAGTATACATAGTTTA-TATTTATATTA
1 TATATA-T-TATATATAAATTATATAGTTTATATATATA-TATATATA-TATACTATGTATA--A
601851 T
60 T
* *
601852 TATATTATATATATATAAATCATATAGTTTATATTTATATATATATATATACTATGTATAAT
1 TATA-TAT-TATATATAAATTATATAGTTTATATATATATATATATATATACTATGTATAAT
* ** *
601914 TATAAATTATATAT-AA-TATATAAATTATATAGTTTATACT-TATATATTACTATGTATAAACT
1 TATATATTATATATAAATTATATAGTTTATATA-TATATA-TATATATA-TACTATGTAT-AA-T
* * *
601976 ATATATATTATGTATAAATTATATAGTTTATATATA-A-ACTCTATATGA-ACTATGTATAGT
1 -TATATATTATATATAAATTATATAGTTTATATATATATA-TATATAT-ATACTATGTATAAT
* * * * * * * *
602036 TCATATA-TAGTATAT-AAGTATAAACTATATA-ATTTATATATAAACTCTA-TATG-A-ACT
1 T-ATATATTA-TATATAAATTATATAGTTTATATATATATATATATA-TATACTATGTATAAT
* * *
602093 ATATATAGTTCATATAT-AATT-TATA---TATAGTATATAAATATAAAT-TA-TAT-TGT--T
1 -TATATA-TT-ATATATAAATTATATAGTTTATA-TATATATATATATATATACTATGTATAAT
602147 TATATATTATAT-T--ATTATATAGTTTATATATATATATATATA-ATA-TAT-TATAAT
1 TATATATTATATATAAATTATATAGTTTATATATATATATATATATATACTATGTATAAT
602201 T
1 T
602202 TTTTTCATTT
Statistics
Matches: 281, Mismatches: 36, Indels: 77
0.71 0.09 0.20
Matches are distributed among these distances:
49 3 0.01
50 5 0.02
51 4 0.01
52 21 0.07
53 10 0.04
54 3 0.01
55 9 0.03
56 1 0.00
57 18 0.06
58 18 0.06
59 46 0.16
60 32 0.11
61 5 0.02
62 19 0.07
63 21 0.07
64 18 0.06
65 46 0.16
66 2 0.01
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.48
Consensus pattern (60 bp):
TATATATTATATATAAATTATATAGTTTATATATATATATATATATATACTATGTATAAT
Found at i:602072 original size:66 final size:64
Alignment explanation
Indices: 601975--602110 Score: 218
Period size: 66 Copynumber: 2.1 Consensus size: 64
601965 ATGTATAAAC
* * * *
601975 TATATATATTATGTATAAATTATATAGTTTATATATAAACTCTATATGAACTATGTATAGTTCA
1 TATATATATTAAGTATAAACTATATAATTTATATATAAACTCTATATGAACTATATATAGTTCA
602039 TATATAGTATATAAGTATAAACTATATAATTTATATATAAACTCTATATGAACTATATATAGTTC
1 TATATA-TAT-TAAGTATAAACTATATAATTTATATATAAACTCTATATGAACTATATATAGTTC
602104 A
64 A
602105 TATATA
1 TATATA
602111 ATTTATATAT
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
64 6 0.09
65 3 0.05
66 57 0.86
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (64 bp):
TATATATATTAAGTATAAACTATATAATTTATATATAAACTCTATATGAACTATATATAGTTCA
Found at i:605366 original size:2 final size:2
Alignment explanation
Indices: 605359--605413 Score: 96
Period size: 2 Copynumber: 28.5 Consensus size: 2
605349 AATAGAAGTG
605359 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
605401 AT AT -T AT A- AT AT A
1 AT AT AT AT AT AT AT A
605414 GGTTATGTAA
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 49 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:610355 original size:2 final size:2
Alignment explanation
Indices: 610348--610384 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
610338 AATAGAAGTG
610348 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
610385 GGTTATGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:610571 original size:20 final size:20
Alignment explanation
Indices: 610544--610740 Score: 80
Period size: 20 Copynumber: 9.7 Consensus size: 20
610534 ACGCGAAATA
610544 AAAATCGCAACGCGATTCCC
1 AAAATCGCAACGCGATTCCC
* ** *
610564 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGA-TTCCC
**
610584 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATTC-CC
* *
610605 AAAATCGCAATGCGATAGT-AC
1 AAAATCGCAACGCGAT--TCCC
* ** *
610626 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGA-TTCCC
* ***
610647 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTCCC
* *
610667 AAAATCGCAACGCGA-ACAC
1 AAAATCGCAACGCGATTCCC
*
610686 ATAAATCGCAACGCG-TATCCG
1 A-AAATCGCAACGCGAT-TCCC
* * *
610707 TAAATCGCAACGTG-TATCCG
1 AAAATCGCAACGCGAT-TCCC
*
610727 TAAATCGCAACGCG
1 AAAATCGCAACGCG
610741 TATGGGTAAA
Statistics
Matches: 134, Mismatches: 33, Indels: 20
0.72 0.18 0.11
Matches are distributed among these distances:
19 2 0.01
20 87 0.65
21 43 0.32
22 1 0.01
23 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCCC
Found at i:610610 original size:21 final size:20
Alignment explanation
Indices: 610524--610681 Score: 95
Period size: 21 Copynumber: 7.8 Consensus size: 20
610514 AAATGACCAA
**
610524 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* **
610543 AAAAATCGCAACGCGATTCC
1 CAAAATCGCAACGCGATTTT
* ** *
610563 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
610583 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
610604 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
610625 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
610645 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
610666 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
610682 ACACATAAAT
Statistics
Matches: 105, Mismatches: 28, Indels: 11
0.73 0.19 0.08
Matches are distributed among these distances:
19 16 0.15
20 42 0.40
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:610697 original size:40 final size:40
Alignment explanation
Indices: 610648--610821 Score: 172
Period size: 40 Copynumber: 4.3 Consensus size: 40
610638 CGATTTTCCA
* ** *
610648 AAATCGCAACGCGAATATGAAAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTAAC-CAT
* * *
610688 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTAACCAT
** * * *
610728 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTAACCAT
* * *
610768 ATATCGCAACGCGTATCCGTAAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTAA-CCAT
610808 AAAATCGCAACGCG
1 -AAATCGCAACGCG
610822 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 20, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
39 2 0.02
40 95 0.86
41 14 0.13
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGTAACCAT
Found at i:610732 original size:60 final size:60
Alignment explanation
Indices: 610648--610821 Score: 213
Period size: 60 Copynumber: 2.9 Consensus size: 60
610638 CGATTTTCCA
* ** * *
610648 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
610708 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
610768 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCG
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCG
610822 ATATTTAAAG
Statistics
Matches: 93, Mismatches: 20, Indels: 1
0.82 0.18 0.01
Matches are distributed among these distances:
60 81 0.87
61 12 0.13
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:610743 original size:20 final size:20
Alignment explanation
Indices: 610648--610798 Score: 187
Period size: 20 Copynumber: 7.5 Consensus size: 20
610638 CGATTTTCCA
* ** *
610648 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
610668 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
610688 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
610708 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
610728 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
610748 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
610768 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
610788 AAATCGCAACG
1 AAATCGCAACG
610799 ATAATACATA
Statistics
Matches: 112, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
19 1 0.01
20 109 0.97
21 2 0.02
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:611243 original size:33 final size:33
Alignment explanation
Indices: 611204--611274 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
611194 TTCACTTAGA
* *
611204 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGAGAT
* * *
611237 TTTCATTTCGCGTTGCTATTCTCTCGTTGATAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGAGAT
611270 TTTCA
1 TTTCA
611275 AGTTAGTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.13, C:0.21, G:0.17, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGAGAT
Found at i:611427 original size:21 final size:21
Alignment explanation
Indices: 611357--611429 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
611347 AGAAGAGTCA
*
611357 CAACGAGATAAATGAAAATCG
1 CAACGAGAGAAATGAAAATCG
***
611378 CAACGAGAG-AATGACTGTCG
1 CAACGAGAGAAATGAAAATCG
611398 CAACGAGAGAAATGAAAATCG
1 CAACGAGAGAAATGAAAATCG
611419 CAACGAGAGAA
1 CAACGAGAGAA
611430 TCGCAACGCG
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 17 0.39
21 27 0.61
ACGTcount: A:0.48, C:0.16, G:0.25, T:0.11
Consensus pattern (21 bp):
CAACGAGAGAAATGAAAATCG
Found at i:611433 original size:14 final size:14
Alignment explanation
Indices: 611414--611469 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
611404 GAGAAATGAA
611414 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
611428 AATCGCAACGCGAAATG
1 AATCGCAA--CGAGA-G
611445 AAATCGCAACGAGAG
1 -AATCGCAACGAGAG
611460 AATCGCAACG
1 AATCGCAACG
611470 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 18 0.50
15 1 0.03
16 8 0.22
17 1 0.03
18 8 0.22
ACGTcount: A:0.43, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:611453 original size:32 final size:33
Alignment explanation
Indices: 611406--611485 Score: 135
Period size: 32 Copynumber: 2.5 Consensus size: 33
611396 CGCAACGAGA
611406 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
611439 GAAATG-AAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
611471 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
611486 TTGCGATTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
32 30 0.68
33 14 0.32
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:611503 original size:19 final size:19
Alignment explanation
Indices: 611481--611608 Score: 87
Period size: 19 Copynumber: 7.1 Consensus size: 19
611471 GAAACCAAAA
*
611481 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
611500 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
611514 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
611533 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
611547 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
611567 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
611587 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
611607 TC
1 TC
611609 AACCAAAAGA
Statistics
Matches: 87, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
14 20 0.23
16 6 0.07
17 6 0.07
19 22 0.25
20 19 0.22
21 14 0.16
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:611522 original size:14 final size:14
Alignment explanation
Indices: 611503--611559 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
611493 TTTCATTTCG
611503 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
611517 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
611536 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
611550 CGTTGCGATT
1 CGTTGCGATT
611560 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:611528 original size:33 final size:33
Alignment explanation
Indices: 611486--611608 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
611476 CAAAATCGCA
611486 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
611519 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
611552 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
611593 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
611609 AACCAAAAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 45 0.56
34 2 0.02
35 6 0.07
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.02
41 21 0.26
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:611570 original size:21 final size:21
Alignment explanation
Indices: 611544--611608 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
611534 CGCGTTGCGA
611544 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
611565 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
611585 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
611606 TTC
1 TTC
611609 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:613798 original size:93 final size:93
Alignment explanation
Indices: 613307--613775 Score: 922
Period size: 93 Copynumber: 5.1 Consensus size: 93
613297 TAGATTGCTT
*
613307 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
613372 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
613400 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
613465 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
613493 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
613558 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
613586 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
613651 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
613679 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
613744 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
613771 AGTAA
1 AGTAA
613776 TGTAATCCAT
Statistics
Matches: 375, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
92 6 0.02
93 369 0.98
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:613943 original size:19 final size:19
Alignment explanation
Indices: 613823--613937 Score: 159
Period size: 19 Copynumber: 6.3 Consensus size: 19
613813 TAGTTTACTT
* *
613823 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
613843 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
613862 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
613881 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
613900 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
613914 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
613933 TCGCA
1 TCGCA
613938 TTGCGATTTT
Statistics
Matches: 86, Mismatches: 4, Indels: 11
0.85 0.04 0.11
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 57 0.66
20 13 0.15
ACGTcount: A:0.46, C:0.30, G:0.16, T:0.08
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:613955 original size:19 final size:19
Alignment explanation
Indices: 613933--614086 Score: 148
Period size: 19 Copynumber: 8.6 Consensus size: 19
613923 GAAACCAAAA
*
613933 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
613952 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
613968 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
613985 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
614001 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
614018 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
614037 TCTCGTTGCGATTATCATT
1 TCGCGTTGCGATTTTCATT
*
614056 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
614076 TCGTGTTGCGA
1 TCGCGTTGCGA
614087 AAGTAAACTA
Statistics
Matches: 109, Mismatches: 15, Indels: 21
0.75 0.10 0.14
Matches are distributed among these distances:
14 15 0.14
16 11 0.10
17 11 0.10
19 60 0.55
20 12 0.11
ACGTcount: A:0.12, C:0.19, G:0.23, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:613974 original size:14 final size:14
Alignment explanation
Indices: 613955--614011 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
613945 TTTCATTTCG
613955 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
613969 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
613986 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
614002 CGTTGCGATT
1 CGTTGCGATT
614012 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:613980 original size:33 final size:33
Alignment explanation
Indices: 613938--614068 Score: 181
Period size: 33 Copynumber: 3.8 Consensus size: 33
613928 CAAAATCGCA
613938 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
* *
613971 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
*
614004 TTGCGATTTTCATTTCGCGTTGCGATTTTGGTTTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGA--TT--CTT-TCG
*
614042 TTGCGATTATCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
614069 TTAAGTTTCG
Statistics
Matches: 87, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
33 55 0.63
35 2 0.02
36 2 0.02
37 1 0.01
38 27 0.31
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
Found at i:616030 original size:14 final size:14
Alignment explanation
Indices: 616011--616046 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
616001 ATTGTTTAAT
616011 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
616025 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
616039 TGATTTGT
1 TGATTTGT
616047 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:616169 original size:19 final size:19
Alignment explanation
Indices: 616153--616250 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
616143 AAAAATGACT
616153 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
616172 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
616191 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
616205 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
616224 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
616244 ATCGCAA
1 ATCGCAA
616251 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:616282 original size:53 final size:53
Alignment explanation
Indices: 616153--616269 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
616143 AAAAATGACT
616153 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
616205 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
616258 ATCGCAATGCGA
1 ATCGCAATGCGA
616270 TTTTAATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:616287 original size:19 final size:19
Alignment explanation
Indices: 616259--616461 Score: 203
Period size: 19 Copynumber: 11.7 Consensus size: 19
616249 AACGAGAGAA
* *
616259 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
616278 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
616294 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
616311 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
616330 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
616346 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
616363 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
616382 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
616398 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
616415 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
616433 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
616449 TCGCATTGCGATT
1 TCGCATTGCGATT
616462 CTCTCGTTGC
Statistics
Matches: 153, Mismatches: 10, Indels: 42
0.75 0.05 0.20
Matches are distributed among these distances:
14 29 0.19
16 23 0.15
17 19 0.12
18 3 0.02
19 67 0.44
20 12 0.08
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:616322 original size:52 final size:52
Alignment explanation
Indices: 616259--616433 Score: 323
Period size: 52 Copynumber: 3.3 Consensus size: 52
616249 AACGAGAGAA
* *
616259 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
616311 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
616363 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
616415 TCCGCATTGCGATTTTCAT
1 T-CGCATTGCGATTTTCAT
616434 GTTGGGATTT
Statistics
Matches: 120, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
52 103 0.86
53 17 0.14
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:616483 original size:33 final size:33
Alignment explanation
Indices: 616265--616475 Score: 223
Period size: 33 Copynumber: 6.2 Consensus size: 33
616255 AGAATCGCAA
*
616265 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
616298 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * * *
616336 TGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGT
616369 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
616402 TGCGATTTTCATTTCCGCATTGCGATTTTCAT-GT
1 TGCGATTTTCATTT-CGCATTGCGATTCTC-TCGT
*
616436 TGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
616469 TGCGATT
1 TGCGATT
616476 GTAATTTCCG
Statistics
Matches: 147, Mismatches: 17, Indels: 28
0.77 0.09 0.15
Matches are distributed among these distances:
31 9 0.06
32 6 0.04
33 71 0.48
34 29 0.20
35 6 0.04
36 4 0.03
37 2 0.01
38 8 0.05
39 3 0.02
40 9 0.06
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:618775 original size:12 final size:12
Alignment explanation
Indices: 618758--618782 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
618748 TCTTCGGGGA
618758 CTTTTTCTTCTT
1 CTTTTTCTTCTT
618770 CTTTTTCTTCTT
1 CTTTTTCTTCTT
618782 C
1 C
618783 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:618991 original size:24 final size:24
Alignment explanation
Indices: 618957--619003 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
618947 CTGAAACATC
618957 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
618981 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
619004 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:619714 original size:20 final size:20
Alignment explanation
Indices: 619686--619915 Score: 212
Period size: 20 Copynumber: 11.5 Consensus size: 20
619676 AAATTTTAGT
* * *
619686 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
619706 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
619726 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
***
619746 GTTGCGATTTACGGATTATT
1 GTTGCGATTTACGGATTCGC
*
619766 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
619786 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
619806 ATTG-GAATTTACCCATACGC
1 GTTGCG-ATTTACGGATTCGC
* *
619826 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
619846 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
619866 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
619886 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
619906 GTTGCGATTT
1 GTTGCGATTT
619916 TGGAAAATCG
Statistics
Matches: 178, Mismatches: 28, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
19 1 0.01
20 175 0.98
21 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:619932 original size:21 final size:21
Alignment explanation
Indices: 619902--619984 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
619892 ATTTTCATAT
*
619902 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
619923 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
619944 TCGCATTGCGATTTT-TAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
619965 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
619985 CTGATTTGCG
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
20 2 0.04
21 44 0.92
22 2 0.04
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:619975 original size:42 final size:43
Alignment explanation
Indices: 619882--619980 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
619872 ATTTATGTGT
*
619882 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGGAAAA
** *
619923 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-TAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGGAA-AA
*
619965 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
619981 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.38
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGGAAAA
Found at i:634563 original size:170 final size:170
Alignment explanation
Indices: 634336--634677 Score: 684
Period size: 170 Copynumber: 2.0 Consensus size: 170
634326 GTATATTTTT
634336 TATATTATTCATTATTAAAAGAATAAATTAACTTGACTTGAACTTGAAACTTTTAATTGAAAATT
1 TATATTATTCATTATTAAAAGAATAAATTAACTTGACTTGAACTTGAAACTTTTAATTGAAAATT
634401 CACTCCGCACCTCATTCACCCTTGATTTTCAAATCTGTCAAAGAATAATTGAAAAATATTGATGT
66 CACTCCGCACCTCATTCACCCTTGATTTTCAAATCTGTCAAAGAATAATTGAAAAATATTGATGT
634466 AAAAAACTTTAGTTCTTTATTTGCGCATATTCAAAAATGG
131 AAAAAACTTTAGTTCTTTATTTGCGCATATTCAAAAATGG
634506 TATATTATTCATTATTAAAAGAATAAATTAACTTGACTTGAACTTGAAACTTTTAATTGAAAATT
1 TATATTATTCATTATTAAAAGAATAAATTAACTTGACTTGAACTTGAAACTTTTAATTGAAAATT
634571 CACTCCGCACCTCATTCACCCTTGATTTTCAAATCTGTCAAAGAATAATTGAAAAATATTGATGT
66 CACTCCGCACCTCATTCACCCTTGATTTTCAAATCTGTCAAAGAATAATTGAAAAATATTGATGT
634636 AAAAAACTTTAGTTCTTTATTTGCGCATATTCAAAAATGG
131 AAAAAACTTTAGTTCTTTATTTGCGCATATTCAAAAATGG
634676 TA
1 TA
634678 GGCTCTTATT
Statistics
Matches: 172, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
170 172 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (170 bp):
TATATTATTCATTATTAAAAGAATAAATTAACTTGACTTGAACTTGAAACTTTTAATTGAAAATT
CACTCCGCACCTCATTCACCCTTGATTTTCAAATCTGTCAAAGAATAATTGAAAAATATTGATGT
AAAAAACTTTAGTTCTTTATTTGCGCATATTCAAAAATGG
Found at i:636074 original size:24 final size:24
Alignment explanation
Indices: 636042--636090 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
636032 AAGTAAGTAT
636042 TAAAAGTTAAAATTCATAATTTTA
1 TAAAAGTTAAAATTCATAATTTTA
636066 TAAAAGTTAAAATTCATAATTTTA
1 TAAAAGTTAAAATTCATAATTTTA
636090 T
1 T
636091 CATTTTGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (24 bp):
TAAAAGTTAAAATTCATAATTTTA
Found at i:646020 original size:11 final size:11
Alignment explanation
Indices: 646006--646031 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
645996 TATATAAATT
646006 AATTATAGTAG
1 AATTATAGTAG
646017 AATTATAGTAG
1 AATTATAGTAG
646028 AATT
1 AATT
646032 CAACTTGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (11 bp):
AATTATAGTAG
Found at i:646196 original size:16 final size:16
Alignment explanation
Indices: 646175--646225 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
646165 TAATGTGTTA
*
646175 GGTAATGTTACATTCC
1 GGTAATCTTACATTCC
**
646191 GGTAATCTTATTTTCGCC
1 GGTAATCTTACATT--CC
646209 GGTAATCTTACATTCC
1 GGTAATCTTACATTCC
646225 G
1 G
646226 TGAACCAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
16 14 0.50
18 14 0.50
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.39
Consensus pattern (16 bp):
GGTAATCTTACATTCC
Found at i:654359 original size:20 final size:20
Alignment explanation
Indices: 654315--654359 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
654305 ATATTATGAT
654315 ATTTATGTAATATCTTAAAA
1 ATTTATGTAATATCTTAAAA
* *
654335 TTTTAT-TAATTTCTTAATAA
1 ATTTATGTAATATCTTAA-AA
654355 ATTTA
1 ATTTA
654360 AAATTTTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (20 bp):
ATTTATGTAATATCTTAAAA
Found at i:655503 original size:23 final size:23
Alignment explanation
Indices: 655436--655511 Score: 57
Period size: 23 Copynumber: 3.3 Consensus size: 23
655426 TCGATAACGC
* * *
655436 TAAACAAAATGTTTGCGAATATA
1 TAAACAACATGTTAGCGAACATA
* *
655459 TAAACGAACATGTTAACAAACAT-
1 TAAAC-AACATGTTAGCGAACATA
* *
655482 TAAACTAACATGTTCGCGAACACA
1 TAAAC-AACATGTTAGCGAACATA
655506 -AAACAA
1 TAAACAA
655512 ACGAACACAA
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
22 2 0.05
23 27 0.66
24 12 0.29
ACGTcount: A:0.50, C:0.17, G:0.11, T:0.22
Consensus pattern (23 bp):
TAAACAACATGTTAGCGAACATA
Found at i:655510 original size:69 final size:68
Alignment explanation
Indices: 655376--655512 Score: 157
Period size: 69 Copynumber: 2.0 Consensus size: 68
655366 ACAAATGAAC
* * * * * * *
655376 ATGTTTGTGAATATATAATCGAATACTAAACAAATATTAAACGAACATATTCGATAACGCTAAAC
1 ATGTTTGCGAATATATAAACGAACACTAAACAAACATTAAACGAACATATTCGAGAACACAAAAC
655441 AAA
66 AAA
* * * * *
655444 ATGTTTGCGAATATATAAACGAACATGTTAACAAACATTAAACTAACATGTTCGCGAACACAAAA
1 ATGTTTGCGAATATATAAACGAACA-CTAAACAAACATTAAACGAACATATTCGAGAACACAAAA
655509 CAAA
65 CAAA
655513 CGAACACAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
68 22 0.39
69 34 0.61
ACGTcount: A:0.48, C:0.15, G:0.11, T:0.26
Consensus pattern (68 bp):
ATGTTTGCGAATATATAAACGAACACTAAACAAACATTAAACGAACATATTCGAGAACACAAAAC
AAA
Found at i:665825 original size:20 final size:20
Alignment explanation
Indices: 665800--665892 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
665790 TTTTCCCAAT
665800 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
665820 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
665840 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
665861 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
665882 TCGCAATGCGA
1 TCGCAATGCGA
665893 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:665842 original size:41 final size:41
Alignment explanation
Indices: 665797--665892 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
665787 CGATTTTCCC
665797 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
665838 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
665879 AAATCGCAATGCGA
1 AATTCGCAATGCGA
665893 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:665846 original size:21 final size:20
Alignment explanation
Indices: 665800--665892 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
665790 TTTTCCCAAT
*
665800 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
665820 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
665840 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
665861 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
665882 TCGCAATGCGA
1 TCGCAATGCGA
665893 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:665905 original size:41 final size:41
Alignment explanation
Indices: 665819--665953 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
665809 GAATAAGTAA
* * *
665819 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
665860 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
665901 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
665942 TTCGCAACGCGA
1 ATCGCAACGCGA
665954 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:665906 original size:20 final size:20
Alignment explanation
Indices: 665881--665974 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
665871 AATTGGGAAA
*
665881 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
665901 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
665922 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
665942 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
665962 TTCGCAACGCGAT
1 ATCGCAACGCGAT
665975 TTACTTAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:666520 original size:20 final size:19
Alignment explanation
Indices: 666495--666546 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
666485 CGAGAATGAA
666495 ATCGCAAAGCGGAAATAACT
1 ATCGCAAAGC-GAAATAACT
* *
666515 ATCGCAACGCGAAATAA-A
1 ATCGCAAAGCGAAATAACT
*
666533 ATCGCAACGCGAAA
1 ATCGCAAAGCGAAA
666547 CCAAAATCGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 14 0.47
19 7 0.23
20 9 0.30
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (19 bp):
ATCGCAAAGCGAAATAACT
Found at i:666538 original size:18 final size:18
Alignment explanation
Indices: 666493--666557 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 18
666483 TTCGAGAATG
*
666493 AAATCGCAAAGCGGAAATA
1 AAATCGCAACGC-GAAATA
*
666512 ACTATCGCAACGCGAAATA
1 A-AATCGCAACGCGAAATA
*
666531 AAATCGCAACGCGAAACCA
1 AAATCGCAACGCGAAA-TA
666550 AAATCGCA
1 AAATCGCA
666558 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
18 14 0.35
19 17 0.43
20 9 0.22
ACGTcount: A:0.48, C:0.25, G:0.17, T:0.11
Consensus pattern (18 bp):
AAATCGCAACGCGAAATA
Found at i:666554 original size:19 final size:18
Alignment explanation
Indices: 666515--666557 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
666505 GGAAATAACT
*
666515 ATCGCAACGCGAAATAAA
1 ATCGCAACGCGAAACAAA
666533 ATCGCAACGCGAAACCAAA
1 ATCGCAACGCGAAA-CAAA
666552 ATCGCA
1 ATCGCA
666558 TTGCGATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.47, C:0.28, G:0.16, T:0.09
Consensus pattern (18 bp):
ATCGCAACGCGAAACAAA
Found at i:666633 original size:19 final size:19
Alignment explanation
Indices: 666553--666622 Score: 131
Period size: 19 Copynumber: 3.7 Consensus size: 19
666543 GAAACCAAAA
*
666553 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
666572 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
666591 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
666610 TCGCGTTGCGATT
1 TCGCGTTGCGATT
666623 CTCTCGTCGC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:666633 original size:38 final size:38
Alignment explanation
Indices: 666553--666633 Score: 119
Period size: 38 Copynumber: 2.1 Consensus size: 38
666543 GAAACCAAAA
* * *
666553 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATG
666591 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTC-TCG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCAT-G
666629 TCGCG
1 TCGCG
666634 ATAGTCATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
37 1 0.03
38 38 0.97
ACGTcount: A:0.10, C:0.25, G:0.22, T:0.43
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATG
Found at i:666642 original size:33 final size:33
Alignment explanation
Indices: 666605--666692 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
666595 GTTGCGATTT
*
666605 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
* *
666638 TCATTTCGCGTTGTGATTCTCTCATTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
*
666671 TCATTTCCGCGTTGCAATTCTC
1 TCATTT-CGCGTTGCGATTCTC
666693 ATTATCTCGT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 36 0.73
34 13 0.27
ACGTcount: A:0.14, C:0.26, G:0.20, T:0.40
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
Found at i:668762 original size:42 final size:42
Alignment explanation
Indices: 668702--668824 Score: 115
Period size: 42 Copynumber: 2.9 Consensus size: 42
668692 GCCCGACTCG
* * *
668702 CCTATCATCCATCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCATCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* *
668744 CCTATCATTCC-TCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCA-TCCATCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
668786 ACTGTCATCGTTGAAGATGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCATCAAGA-GTCCACTCCCACCGTTCAAGAG
668825 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 2 0.03
42 58 0.87
43 7 0.10
ACGTcount: A:0.24, C:0.36, G:0.17, T:0.24
Consensus pattern (42 bp):
CCTATCATCCATCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:668782 original size:21 final size:21
Alignment explanation
Indices: 668758--668824 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
668748 TCATTCCTCG
668758 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
668779 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
668800 AGATGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
668821 AGAG
1 AGAG
668825 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.19, T:0.21
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:670184 original size:14 final size:14
Alignment explanation
Indices: 670165--670200 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
670155 ATTGTTTAAT
670165 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
670179 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
670193 TGATTTGT
1 TGATTTGT
670201 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:670428 original size:20 final size:19
Alignment explanation
Indices: 670378--670429 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
670368 CGAAATTAAA
** *
670378 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATAGTAAT
*
670397 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATAGTAAT
670416 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
670430 GGACATTAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.15, C:0.21, G:0.23, T:0.40
Consensus pattern (19 bp):
TTCGCGTTGCGATAGTAAT
Done.