Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011426.1 Kokia drynarioides strain JFW-HI SEQ_126410, 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: 550552
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Warning! 325 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:380089 original size:21 final size:22
Alignment explanation
Indices: 380064--380104 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
380054 ATCATAATTA
380064 AAAAATATATTTAAA-ATCAAT
1 AAAAATATATTTAAATATCAAT
*
380085 AAAAATATTTTTAAATATCA
1 AAAAATATATTTAAATATCA
380105 TAATTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAAATATATTTAAATATCAAT
Found at i:381532 original size:11 final size:11
Alignment explanation
Indices: 381508--381594 Score: 63
Period size: 11 Copynumber: 7.9 Consensus size: 11
381498 AAGCCCAATC
*
381508 TTTAA-TTAAA
1 TTTAATTTAAT
*
381518 TTTATTTTAAT
1 TTTAATTTAAT
381529 TTTAATTT-AT
1 TTTAATTTAAT
*
381539 TTTAAGTTTAAA
1 TTTAA-TTTAAT
*
381551 TTTAATTTAAAC
1 TTTAATTT-AAT
**
381563 TAAAATTT-AT
1 TTTAATTTAAT
381573 TTTAAATTTAAT
1 TTT-AATTTAAT
*
381585 TTTAAATTAA
1 TTTAATTTAA
381595 GTTCAAAGTC
Statistics
Matches: 60, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
10 13 0.22
11 28 0.47
12 19 0.32
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (11 bp):
TTTAATTTAAT
Found at i:381552 original size:17 final size:17
Alignment explanation
Indices: 381513--381588 Score: 91
Period size: 17 Copynumber: 4.5 Consensus size: 17
381503 CAATCTTTAA
381513 TTAAATTTATTTT-AAT
1 TTAAATTTATTTTAAAT
* *
381529 TTTAATTTATTTTAAGT
1 TTAAATTTATTTTAAAT
* *
381546 TTAAATTTAATTTAAAC
1 TTAAATTTATTTTAAAT
*
381563 TAAAATTTATTTTAAAT
1 TTAAATTTATTTTAAAT
*
381580 TTAATTTTA
1 TTAAATTTA
381589 AATTAAGTTC
Statistics
Matches: 48, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
16 12 0.25
17 36 0.75
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (17 bp):
TTAAATTTATTTTAAAT
Found at i:381557 original size:5 final size:5
Alignment explanation
Indices: 381508--381560 Score: 52
Period size: 5 Copynumber: 10.0 Consensus size: 5
381498 AAGCCCAATC
* * *
381508 TTTAA TTAAA TTTAT TTTAA TTTTAA TTTAT TTTAA GTTTAAA TTTAA
1 TTTAA TTTAA TTTAA TTTAA -TTTAA TTTAA TTTAA -TTT-AA TTTAA
381556 TTTAA
1 TTTAA
381561 ACTAAAATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
5 26 0.67
6 11 0.28
7 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (5 bp):
TTTAA
Found at i:381591 original size:12 final size:12
Alignment explanation
Indices: 381523--381592 Score: 67
Period size: 11 Copynumber: 6.2 Consensus size: 12
381513 TTAAATTTAT
381523 TTTAATTTT-AA
1 TTTAATTTTAAA
*
381534 TTT-ATTTTAAG
1 TTTAATTTTAAA
*
381545 TTTAAATTT-AA
1 TTTAATTTTAAA
** *
381556 TTTAAACTAAAA
1 TTTAATTTTAAA
381568 TTT-ATTTTAAA
1 TTTAATTTTAAA
381579 TTTAATTTTAAA
1 TTTAATTTTAAA
381591 TT
1 TT
381593 AAGTTCAAAG
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
10 5 0.11
11 23 0.49
12 19 0.40
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (12 bp):
TTTAATTTTAAA
Found at i:381640 original size:16 final size:17
Alignment explanation
Indices: 381604--381641 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
381594 AGTTCAAAGT
381604 CCAATTACAAATTAGGAC
1 CCAATTACAAATTA-GAC
*
381622 CCAATTTCAAATT-GAC
1 CCAATTACAAATTAGAC
381638 CCAA
1 CCAA
381642 ACAAGCCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
18 12 0.63
ACGTcount: A:0.42, C:0.26, G:0.08, T:0.24
Consensus pattern (17 bp):
CCAATTACAAATTAGAC
Found at i:383403 original size:30 final size:29
Alignment explanation
Indices: 383363--383724 Score: 196
Period size: 30 Copynumber: 12.4 Consensus size: 29
383353 CCCCTAAGCT
*
383363 TTTCCAAAATTCCATTTTTTACATCGAAC
1 TTTCCAAAATTCCATTTTTTACCTCGAAC
*
383392 TTTCCATAAATT--ATATTTTACCCTCGAAC
1 TTTCCA-AAATTCCATTTTTTA-CCTCGAAC
* * * *
383421 TTTCCAAAATTCCATTTTTGACCCCAAAT
1 TTTCCAAAATTCCATTTTTTACCTCGAAC
* * * *
383450 TTTCCAAAAATTACATTTTTTACCCCTAAAT
1 TTTCC-AAAATTCCATTTTTTACCTC-GAAC
*
383481 TTTCCAAAATTCCATTTTTGACCTCGAAC
1 TTTCCAAAATTCCATTTTTTACCTCGAAC
**
383510 TTTCCAAAATT--ATCATTTACCCTCGAAC
1 TTTCCAAAATTCCATTTTTTA-CCTCGAAC
* *
383538 -TTCCAAAAATTTCA-TTTTGACCTCGAAC
1 TTTCC-AAAATTCCATTTTTTACCTCGAAC
*
383566 -TTCCTGAAAATTACCA--TTTTACCTTGAAC
1 TTTCC--AAAATT-CCATTTTTTACCTCGAAC
* * * *
383595 -TTCCAAAAATTCTATTTTTGACCCCAAAC
1 TTTCC-AAAATTCCATTTTTTACCTCGAAC
* *
383624 TTCTCAAAAATTACCA--TTTTACCCCCGAAC
1 TT-TCCAAAATT-CCATTTTTTA-CCTCGAAC
* * * *
383654 TTCTCAAAAATTACC--GTTTTACCCCCAAAC
1 TT-TCCAAAATT-CCATTTTTTA-CCTCGAAC
* *
383684 -TTCCAAAGATTCCATTTTTAACCTCAAAC
1 TTTCCAAA-ATTCCATTTTTTACCTCGAAC
*
383713 CTTCCGAAAATT
1 TTTCC-AAAATT
383725 ATCATTTTGT
Statistics
Matches: 270, Mismatches: 39, Indels: 47
0.76 0.11 0.13
Matches are distributed among these distances:
27 11 0.04
28 51 0.19
29 90 0.33
30 102 0.38
31 16 0.06
ACGTcount: A:0.32, C:0.27, G:0.04, T:0.36
Consensus pattern (29 bp):
TTTCCAAAATTCCATTTTTTACCTCGAAC
Found at i:383576 original size:57 final size:58
Alignment explanation
Indices: 383364--383665 Score: 241
Period size: 58 Copynumber: 5.2 Consensus size: 58
383354 CCCTAAGCTT
* * * *
383364 TTCC-AAAATTCCATTTTTTACATCGAACTTTCC-ATAAATTA-TATTTTACCCTCGAAC
1 TTCCAAAAATTTCATTTTTGACCTCGAAC-TTCCTA-AAATTACCATTTTACCCTCGAAC
* * * * * * *
383421 TTTCC-AAAATTCCATTTTTGACCCCAAATTTTCCAAAAATTA-CATTTTTTACCC-CTAAATT
1 -TTCCAAAAATTTCATTTTTGACCTCGAA-CTTCCTAAAATTACCA--TTTTACCCTC-GAA-C
* *
383482 TTCC-AAAATTCCATTTTTGACCTCGAACTTTCC-AAAATTATCA-TTTACCCTCGAAC
1 TTCCAAAAATTTCATTTTTGACCTCGAAC-TTCCTAAAATTACCATTTTACCCTCGAAC
*
383538 TTCCAAAAATTTCA-TTTTGACCTCGAACTTCCTGAAAATTACCATTTTA-CCTTGAAC
1 TTCCAAAAATTTCATTTTTGACCTCGAACTTCCT-AAAATTACCATTTTACCCTCGAAC
* * * *
383595 TTCCAAAAA-TTCTATTTTTGACCCCAAACTTCTCAAAAATTACCATTTTACCCCCGAAC
1 TTCCAAAAATTTC-ATTTTTGACCTCGAACTTC-CTAAAATTACCATTTTACCCTCGAAC
383654 TTCTCAAAAATT
1 TTC-CAAAAATT
383666 ACCGTTTTAC
Statistics
Matches: 204, Mismatches: 21, Indels: 35
0.78 0.08 0.13
Matches are distributed among these distances:
55 4 0.02
56 21 0.10
57 43 0.21
58 69 0.34
59 19 0.09
60 47 0.23
61 1 0.00
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.37
Consensus pattern (58 bp):
TTCCAAAAATTTCATTTTTGACCTCGAACTTCCTAAAATTACCATTTTACCCTCGAAC
Found at i:393026 original size:3 final size:3
Alignment explanation
Indices: 393018--393051 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
393008 CTTTTAATTA
393018 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
393052 TGAATGTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:393845 original size:16 final size:16
Alignment explanation
Indices: 393822--393858 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
393812 TAAGTTGTTC
393822 AAAAAATG-AAAACAT
1 AAAAAATGAAAAACAT
393837 AAAAGAATGAAAAACAT
1 AAAA-AATGAAAAACAT
393854 AAAAA
1 AAAAA
393859 GAACTATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.20
16 5 0.25
17 11 0.55
ACGTcount: A:0.76, C:0.05, G:0.08, T:0.11
Consensus pattern (16 bp):
AAAAAATGAAAAACAT
Found at i:395653 original size:17 final size:18
Alignment explanation
Indices: 395625--395663 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
395615 TTTTTTTTAA
395625 ATAATAAATATTATTATT
1 ATAATAAATATTATTATT
* *
395643 ATAAT-AATATTTTTTTT
1 ATAATAAATATTATTATT
395660 ATAA
1 ATAA
395664 AATTTATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATAATAAATATTATTATT
Found at i:413882 original size:111 final size:109
Alignment explanation
Indices: 413743--414086 Score: 321
Period size: 123 Copynumber: 3.0 Consensus size: 109
413733 AGTGGTGGCT
* *
413743 GCGGTGGTTGTGGTGCTGGATGTGGAAACATGGTGAAGAGTGGTGGTTGTGGTGGTGGTTGCGGC
1 GCGGTGGTTGTGGTGCTGGATGTGGAAACATGGTGAAGAGTGGTGG-TGTGGTGGTGGCTGTGG-
*
413808 AGTGGGTGTGGGGGTGGGTGTGGAAGCATAGTGAATAGCGGCGGCC
64 AGTGGGTGTGGGGGTGGTTGTGGAAGCATAGTGAATAGCGGCGGCC
* ***** *
413854 GCGGCGGTTGTGGTGCTGGATGTGGAAACATGGNNNNNNNNNNATGTGGAAACATGGTGAAGAGT
1 GCGGTGGTTGTGGTGCTGGATGTGGAAACATGG-----TGAAGA-GTGG-----TGGTG-TG-GT
* * * *
413919 GGTGGCTGTGGTGGTGGGTGCGGGGGTGGTTGTGGAAGCATAGTGAATAGCGGCAGCT
53 GGTGGCTGTGG-AGTGGGTGTGGGGGTGGTTGTGGAAGCATAGTGAATAGCGGCGGCC
* *
413977 GCGGTGGTTGTGGTGCTGGATGTGGAAACTTGGTGAAGAGTGGTGGCTGTGGCT-CTGGCTGTGG
1 GCGGTGGTTGTGGTGCTGGATGTGGAAACATGGTGAAGAGTGGTGG-TGTGG-TGGTGGCTGTGG
* * * * *
414041 TGCTGGCTGTGGGGGTGGTTGCGGAAGCGTAGTGAATAGCAGCGGC
64 AG-TGGGTGTGGGGGTGGTTGTGGAAGCATAGTGAATAGCGGCGGC
414087 TGTGGCTCTG
Statistics
Matches: 186, Mismatches: 31, Indels: 32
0.75 0.12 0.13
Matches are distributed among these distances:
110 1 0.01
111 79 0.42
112 5 0.03
113 2 0.01
116 1 0.01
117 8 0.04
118 1 0.01
121 2 0.01
122 4 0.02
123 83 0.45
ACGTcount: A:0.15, C:0.10, G:0.48, T:0.24
Consensus pattern (109 bp):
GCGGTGGTTGTGGTGCTGGATGTGGAAACATGGTGAAGAGTGGTGGTGTGGTGGTGGCTGTGGAG
TGGGTGTGGGGGTGGTTGTGGAAGCATAGTGAATAGCGGCGGCC
Found at i:413953 original size:51 final size:48
Alignment explanation
Indices: 413897--414028 Score: 129
Period size: 48 Copynumber: 2.7 Consensus size: 48
413887 NNNNNNNNNN
*
413897 ATGTGGAAACATGGTGAAGAGTGGTGGCTGTGGTGGTGGGTGCGGGGGTGG
1 ATGTGGAAACATGGTGAAGAGTGGTGGCTGTGGTGGT---TGCGGGGCTGG
* * * * * ** * * *
413948 TTGTGGAAGCATAGTGAATAGCGGCAGCTGCGGTGGTTGTGGTGCTGG
1 ATGTGGAAACATGGTGAAGAGTGGTGGCTGTGGTGGTTGCGGGGCTGG
*
413996 ATGTGGAAACTTGGTGAAGAGTGGTGGCTGTGG
1 ATGTGGAAACATGGTGAAGAGTGGTGGCTGTGG
414029 CTCTGGCTGT
Statistics
Matches: 61, Mismatches: 20, Indels: 3
0.73 0.24 0.04
Matches are distributed among these distances:
48 32 0.52
51 29 0.48
ACGTcount: A:0.17, C:0.08, G:0.48, T:0.26
Consensus pattern (48 bp):
ATGTGGAAACATGGTGAAGAGTGGTGGCTGTGGTGGTTGCGGGGCTGG
Found at i:414037 original size:12 final size:12
Alignment explanation
Indices: 414020--414052 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
414010 TGAAGAGTGG
414020 TGGCTGTGGCT-C
1 TGGCTGTGG-TGC
414032 TGGCTGTGGTGC
1 TGGCTGTGGTGC
414044 TGGCTGTGG
1 TGGCTGTGG
414053 GGGTGGTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 1 0.05
12 19 0.95
ACGTcount: A:0.00, C:0.18, G:0.48, T:0.33
Consensus pattern (12 bp):
TGGCTGTGGTGC
Found at i:414142 original size:60 final size:61
Alignment explanation
Indices: 414021--414163 Score: 177
Period size: 60 Copynumber: 2.4 Consensus size: 61
414011 GAAGAGTGGT
* * *
414021 GGCTGTGGCTCTGGCTGTGGTGCTGGCTGTGGGGGTGGTTGCGGAAGCGTAGTGAATAGCAGC
1 GGCTGTGGCTCTGGCTGTGGTG--GGCTGCGGGGGAGGTTGCGGAAGCATAGTGAATAGCAGC
* * * *
414084 GGCTGTGGCTCTGGCTGTGGTGGG-TGCGGTGGAGGTTGTGGAAGCATGGTGAATAGCAGT
1 GGCTGTGGCTCTGGCTGTGGTGGGCTGCGGGGGAGGTTGCGGAAGCATAGTGAATAGCAGC
414144 GGCTGTGG---TGGCTGTGGTGG
1 GGCTGTGGCTCTGGCTGTGGTGG
414164 TGGGTGCGGT
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
57 12 0.16
60 37 0.51
61 2 0.03
63 22 0.30
ACGTcount: A:0.10, C:0.13, G:0.50, T:0.27
Consensus pattern (61 bp):
GGCTGTGGCTCTGGCTGTGGTGGGCTGCGGGGGAGGTTGCGGAAGCATAGTGAATAGCAGC
Found at i:415305 original size:16 final size:16
Alignment explanation
Indices: 415255--415297 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
415245 TTTAAACTTG
**
415255 AATTTAAATGTTTA-A
1 AATTTAAATCATTACA
415270 AA-TTAAATCATTACA
1 AATTTAAATCATTACA
415285 AATTTAAATCATT
1 AATTTAAATCATT
415298 TCTAATTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 9 0.38
15 5 0.21
16 10 0.42
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (16 bp):
AATTTAAATCATTACA
Found at i:425224 original size:62 final size:62
Alignment explanation
Indices: 425142--425263 Score: 199
Period size: 62 Copynumber: 2.0 Consensus size: 62
425132 CCACTACATG
* * * *
425142 ATTACACCGATCGAGGTGAATTCGTTTTTATGATTTCATAAGTTATCAACAAGAGCAAATGA
1 ATTACACCGATCAAGATGAATTCGTTTTTATGATTCCATAAATTATCAACAAGAGCAAATGA
*
425204 ATTACACCGATCAAGATGAATTCGTTTTTATGATTCCATAAATTCTCAACAAGAGCAAAT
1 ATTACACCGATCAAGATGAATTCGTTTTTATGATTCCATAAATTATCAACAAGAGCAAAT
425264 AGTACTATCA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (62 bp):
ATTACACCGATCAAGATGAATTCGTTTTTATGATTCCATAAATTATCAACAAGAGCAAATGA
Found at i:426269 original size:25 final size:27
Alignment explanation
Indices: 426227--426277 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
426217 AGTTATTCTA
* *
426227 TTTTTGTTTTCAAGAATTTAGTTTTAT
1 TTTTTATTTTCAAGAATTTAGGTTTAT
426254 TTTTTATTTT-AA-AATTTAGGTTTA
1 TTTTTATTTTCAAGAATTTAGGTTTA
426278 ATTATGCTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 11 0.50
26 2 0.09
27 9 0.41
ACGTcount: A:0.25, C:0.02, G:0.10, T:0.63
Consensus pattern (27 bp):
TTTTTATTTTCAAGAATTTAGGTTTAT
Found at i:432803 original size:6 final size:6
Alignment explanation
Indices: 432792--432823 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
432782 TACACATATC
432792 TCATCT TCATCT TCATCT TCATCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TC
432824 TTCCCTTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.34, G:0.00, T:0.50
Consensus pattern (6 bp):
TCATCT
Found at i:434504 original size:14 final size:13
Alignment explanation
Indices: 434474--434511 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
434464 AAATAAGTTG
*
434474 AATTTTTATTTTA
1 AATTTTAATTTTA
434487 AATTTTAATTTATA
1 AATTTTAATTT-TA
434501 AATTTTAATTT
1 AATTTTAATTT
434512 GGTATAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
AATTTTAATTTTA
Found at i:435169 original size:15 final size:15
Alignment explanation
Indices: 435150--435206 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 15
435140 CATTTGATAA
435150 ATTGAAAAATTAAGG
1 ATTGAAAAATTAAGG
* * *
435165 GTTG-AAAAGTAAGT
1 ATTGAAAAATTAAGG
*
435179 ATTGAAAAATTAAGT
1 ATTGAAAAATTAAGG
* *
435194 AATGAAAATTTAA
1 ATTGAAAAATTAA
435207 ATAGTATTGA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
14 11 0.32
15 23 0.68
ACGTcount: A:0.53, C:0.00, G:0.18, T:0.30
Consensus pattern (15 bp):
ATTGAAAAATTAAGG
Found at i:440814 original size:2 final size:2
Alignment explanation
Indices: 440807--440831 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
440797 AAGTTAGTTG
440807 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 A
440832 GTTGAGATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:447197 original size:13 final size:13
Alignment explanation
Indices: 447179--447203 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
447169 AGTACCTTCC
447179 GTTTTTTTTTTTT
1 GTTTTTTTTTTTT
447192 GTTTTTTTTTTT
1 GTTTTTTTTTTT
447204 NNNNNNNNNN
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (13 bp):
GTTTTTTTTTTTT
Found at i:447317 original size:44 final size:44
Alignment explanation
Indices: 447254--447337 Score: 168
Period size: 44 Copynumber: 1.9 Consensus size: 44
447244 NNNNNNNNNN
447254 AGGATTTTAATGCATAGAACAGTAAGGCTTCAGTGAACTTAAAA
1 AGGATTTTAATGCATAGAACAGTAAGGCTTCAGTGAACTTAAAA
447298 AGGATTTTAATGCATAGAACAGTAAGGCTTCAGTGAACTT
1 AGGATTTTAATGCATAGAACAGTAAGGCTTCAGTGAACTT
447338 TATTTTCCCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (44 bp):
AGGATTTTAATGCATAGAACAGTAAGGCTTCAGTGAACTTAAAA
Found at i:454317 original size:28 final size:28
Alignment explanation
Indices: 454273--454341 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 28
454263 GTATTCATAT
*
454273 TATATTATTTTAATATTTAATAATTTTA
1 TATATTATTTTAATATTGAATAATTTTA
* **
454301 TATATT-TTTTATTTATTGAATTTTTTTA
1 TATATTATTTTA-ATATTGAATAATTTTA
*
454329 TATAGTAATTTTA
1 TATA-TTATTTTA
454342 GCATTATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
27 5 0.15
28 22 0.67
29 1 0.03
30 5 0.15
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (28 bp):
TATATTATTTTAATATTGAATAATTTTA
Found at i:461000 original size:18 final size:17
Alignment explanation
Indices: 460977--461020 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
460967 TTTATATGTT
* *
460977 TAAAAATATTAATTATTA
1 TAAAAATATT-AGTATAA
460995 TAAAAATTATTAGTATAA
1 TAAAAA-TATTAGTATAA
461013 TAAAAATA
1 TAAAAATA
461021 ATTTTTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 17 0.74
19 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
TAAAAATATTAGTATAA
Found at i:461706 original size:16 final size:18
Alignment explanation
Indices: 461679--461711 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
461669 ATTAAGTAAA
461679 AAAATAATATAA-ATTTT
1 AAAATAATATAATATTTT
461696 AAAAT-ATATAATATTT
1 AAAATAATATAATATTT
461712 ATTAAAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAATAATATAATATTTT
Found at i:462293 original size:19 final size:20
Alignment explanation
Indices: 462266--462304 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
462256 TCCAGTTGTT
*
462266 CTAAATTTAGTGG-TACCCA
1 CTAAATTTAATGGTTACCCA
*
462285 CTAATTTTAATGGTTACCCA
1 CTAAATTTAATGGTTACCCA
462305 AACATTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.36
Consensus pattern (20 bp):
CTAAATTTAATGGTTACCCA
Found at i:463439 original size:22 final size:24
Alignment explanation
Indices: 463387--463440 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
463377 ACAGTTTTTT
*
463387 AAATTAAATATATTTTATTTATTT
1 AAATTAAATATATTTTATTTATTA
*
463411 AATTTAAAT-T-TTTTA-TTATGTA
1 AAATTAAATATATTTTATTTAT-TA
463433 AAATTAAA
1 AAATTAAA
463441 AAGTAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 4 0.15
22 13 0.50
23 1 0.04
24 8 0.31
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
AAATTAAATATATTTTATTTATTA
Found at i:464079 original size:14 final size:14
Alignment explanation
Indices: 464048--464123 Score: 57
Period size: 14 Copynumber: 5.4 Consensus size: 14
464038 TGTAAGGTTC
*
464048 AAAAATCATAAAACA
1 AAAAATC-TAAAAAA
* *
464063 AAATATTTAAAAAA
1 AAAAATCTAAAAAA
464077 AAAAATCTAAAAACA
1 AAAAATCTAAAAA-A
* *
464092 TAAAATC-AAAAAGT
1 AAAAATCTAAAAA-A
*
464106 GAAAAT-TAAAAAA
1 AAAAATCTAAAAAA
464119 AAAAA
1 AAAAA
464124 AAATCGAAAA
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
13 4 0.08
14 32 0.67
15 12 0.25
ACGTcount: A:0.74, C:0.07, G:0.03, T:0.17
Consensus pattern (14 bp):
AAAAATCTAAAAAA
Found at i:465909 original size:27 final size:28
Alignment explanation
Indices: 465852--465910 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
465842 TTATCTACTC
* *
465852 CTCCTTCCCCTAAATCCCCTTCTAGTTT
1 CTCCTTCCCCTAAATCCACTTCTAGTGT
*
465880 CTCCTT-CCTTAAATCCACTCTCT-GTGT
1 CTCCTTCCCCTAAATCCACT-TCTAGTGT
465907 CTCC
1 CTCC
465911 AAAGTAAGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 18 0.67
28 9 0.33
ACGTcount: A:0.14, C:0.42, G:0.05, T:0.39
Consensus pattern (28 bp):
CTCCTTCCCCTAAATCCACTTCTAGTGT
Found at i:479837 original size:99 final size:100
Alignment explanation
Indices: 479682--479883 Score: 298
Period size: 99 Copynumber: 2.0 Consensus size: 100
479672 AAATTTTCAC
** * *
479682 CTCATATTAAATTTTGAGGTTTTTTTTTCAATTCATCATAAGTTAAGAAGGAATTTAGGGATTAG
1 CTCATATTAAATTTTGAGGCCTTTTTTTCAATTCATCATAAGTGAAGAAGGAATTTAGGGATTAA
479747 GGTATTTTCTCGATTTTTTTTCTTTTCTTCTCCAT
66 GGTATTTTCTCGATTTTTTTTCTTTTCTTCTCCAT
* ** * * *
479782 CTCATATTTAATTTTGA-GCCTTTTTTTCAATTCATCATGTGTGAGGATGGGATTTAGGGATTAA
1 CTCATATTAAATTTTGAGGCCTTTTTTTCAATTCATCATAAGTGAAGAAGGAATTTAGGGATTAA
*
479846 GGTATTTTCTTGATTTTTTTTCTTTTCTTCTCCAT
66 GGTATTTTCTCGATTTTTTTTCTTTTCTTCTCCAT
479881 CTC
1 CTC
479884 TATACTGTTA
Statistics
Matches: 91, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
99 75 0.82
100 16 0.18
ACGTcount: A:0.21, C:0.13, G:0.15, T:0.50
Consensus pattern (100 bp):
CTCATATTAAATTTTGAGGCCTTTTTTTCAATTCATCATAAGTGAAGAAGGAATTTAGGGATTAA
GGTATTTTCTCGATTTTTTTTCTTTTCTTCTCCAT
Found at i:487043 original size:59 final size:57
Alignment explanation
Indices: 486980--487090 Score: 143
Period size: 58 Copynumber: 1.9 Consensus size: 57
486970 AATTGAATCC
* *
486980 AAAAAAGTTCAGAA-ACCAAATTAGAAAAAAAATATCAAGCTCGAGTACCAAATAGATCA
1 AAAAAAGTT--GAAGACCAAATTA-AAAAAAAATATCAAGCTCAAATACCAAATAGATCA
* *
487039 AAAAAAGTTGAAGTACCAAATTAAAAAAAAGTATCAAGTTCAAATACCAAAT
1 AAAAAAGTTGAAG-ACCAAATTAAAAAAAAATATCAAGCTCAAATACCAAAT
487091 GTTATATCGG
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
57 3 0.07
58 25 0.54
59 18 0.39
ACGTcount: A:0.57, C:0.14, G:0.11, T:0.19
Consensus pattern (57 bp):
AAAAAAGTTGAAGACCAAATTAAAAAAAAATATCAAGCTCAAATACCAAATAGATCA
Found at i:492822 original size:30 final size:30
Alignment explanation
Indices: 492757--492830 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 30
492747 AAACTTTAAA
492757 TTAAAAATAATAAAATTACAATTTAACCCT
1 TTAAAAATAATAAAATTACAATTTAACCCT
* * * **
492787 CTAAAAATAGTAAAAATT-TAATTTAACTTT
1 TTAAAAATAAT-AAAATTACAATTTAACCCT
*
492817 TTAAAAATTATAAA
1 TTAAAAATAATAAA
492831 TATATAAGCT
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
29 3 0.09
30 26 0.74
31 6 0.17
ACGTcount: A:0.54, C:0.08, G:0.01, T:0.36
Consensus pattern (30 bp):
TTAAAAATAATAAAATTACAATTTAACCCT
Found at i:493898 original size:23 final size:22
Alignment explanation
Indices: 493868--493911 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
493858 TATTTATGTT
*
493868 AACATTGTTTGAACTGTAATATC
1 AACATTGTTTGAAAT-TAATATC
493891 AACATTGTTTGAAATTAATAT
1 AACATTGTTTGAAATTAATAT
493912 TTAATCCGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (22 bp):
AACATTGTTTGAAATTAATATC
Found at i:496433 original size:36 final size:36
Alignment explanation
Indices: 496392--496503 Score: 206
Period size: 36 Copynumber: 3.1 Consensus size: 36
496382 AAAGTCAAAG
496392 TAAACAATTAAATTGCCAGTAAAAGAAAAGAATAAA
1 TAAACAATTAAATTGCCAGTAAAAGAAAAGAATAAA
496428 TAAACAATTAAATTGCCAGTAAAAGAAAAGAATAAA
1 TAAACAATTAAATTGCCAGTAAAAGAAAAGAATAAA
* *
496464 TAAACAATTAAATTGCCAGCAGAAGAAAAGAATAAA
1 TAAACAATTAAATTGCCAGTAAAAGAAAAGAATAAA
496500 TAAA
1 TAAA
496504 AGAAACAGAC
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 74 1.00
ACGTcount: A:0.61, C:0.09, G:0.12, T:0.19
Consensus pattern (36 bp):
TAAACAATTAAATTGCCAGTAAAAGAAAAGAATAAA
Found at i:497262 original size:29 final size:29
Alignment explanation
Indices: 497229--497286 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
497219 ATTTGTAATT
497229 TAAAAATTATAAAATA-AAATAAAATAAAA
1 TAAAAA-TATAAAATAGAAATAAAATAAAA
* * *
497258 TAAAAATATATATTAGTAATAAAATAAAA
1 TAAAAATATAAAATAGAAATAAAATAAAA
497287 AATTGGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.28
Consensus pattern (29 bp):
TAAAAATATAAAATAGAAATAAAATAAAA
Found at i:497285 original size:5 final size:5
Alignment explanation
Indices: 497237--497262 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
497227 TTTAAAAATT
497237 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
497263 ATATATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:497442 original size:37 final size:39
Alignment explanation
Indices: 497380--497452 Score: 114
Period size: 37 Copynumber: 1.9 Consensus size: 39
497370 TGGCCATGCA
*
497380 ATGGTCGACATCCCCTTTTTAATCTGATAAAAAAATTGC
1 ATGGTCGACATCCCCTATTTAATCTGATAAAAAAATTGC
*
497419 ATGGTTGACA-CCCCTATTT-ATCTGATAAAAAAAT
1 ATGGTCGACATCCCCTATTTAATCTGATAAAAAAAT
497453 CAAATTTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
37 15 0.47
38 8 0.25
39 9 0.28
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (39 bp):
ATGGTCGACATCCCCTATTTAATCTGATAAAAAAATTGC
Found at i:497631 original size:61 final size:59
Alignment explanation
Indices: 497418--497800 Score: 258
Period size: 61 Copynumber: 6.4 Consensus size: 59
497408 AAAAAAATTG
* * * * * *
497418 CATGGTTGACA-CCCCTATTTATCTGATAAAAAAATCAAATTTTTGGGTGTTGACCATGC
1 CATGGTCGACACCCCCT-TTTTTCAGATAAAAAATTCAAATTTTTTGGTGTTGGCCATGC
* * ** * *
497477 AATAGTCGACA-ATCCTTTTTTCAAATAAAAAATTTTCAAAATTTTTTGGTGTTGGTCATGC
1 CATGGTCGACACCCCCTTTTTTCAGATAAAAAA--TTC-AAATTTTTTGGTGTTGGCCATGC
* *
497538 AATAG-CGGACACCCCC-TTTTTCAGATAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGC
1 CATGGTC-GACACCCCCTTTTTTCAGAT-AAAAAA-TTC-AAATTTTTTGGTGTTGGCCATGC
* ** * * *
497599 CATGGTCGACACCCCCTTTTTGTCAGATAAAAAGTTTGATTTTTTTTGTGTTGGCCATCC
1 CATGGTCGACACCCCCTTTTT-TCAGATAAAAAATTCAAATTTTTTGGTGTTGGCCATGC
* * * * * **
497659 CATGGCCGACACTCCCTTTTTT-ATTTGGTAAAAAAATCAAATTTTTTTGTGTTGATCATGC
1 CATGGTCGACACCCCCTTTTTTCA---GATAAAAAATTCAAATTTTTTGGTGTTGGCCATGC
* ** * **
497720 AATGACCGACACCCCCTTTTTGT--GATAAAAAATTCAAAATTTTTTTAGTGTTGTTCATGC
1 CATGGTCGACACCCCCTTTTT-TCAGATAAAAAATTC-AAA-TTTTTTGGTGTTGGCCATGC
* * *
497780 CATAGACGATACCCCCTTTTT
1 CATGGTCGACACCCCCTTTTT
497801 ATTTGGTAAA
Statistics
Matches: 262, Mismatches: 47, Indels: 29
0.78 0.14 0.09
Matches are distributed among these distances:
58 24 0.09
59 15 0.06
60 75 0.29
61 123 0.47
62 19 0.07
63 6 0.02
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (59 bp):
CATGGTCGACACCCCCTTTTTTCAGATAAAAAATTCAAATTTTTTGGTGTTGGCCATGC
Found at i:497730 original size:121 final size:119
Alignment explanation
Indices: 497425--497813 Score: 308
Period size: 121 Copynumber: 3.2 Consensus size: 119
497415 TTGCATGGTT
* * * * *
497425 GACA-CCCCTATTTATCTGATAAAAAAATCAAATTTTTGGGTGTTGACCATGCAAT-AGTCGACA
1 GACACCCCCTTTTTATTTGGTAAAAAAATCAAATTTTTTGGTGTTGACCATGCAATGA-CCGACA
** * *** * * * *
497488 ATCCTTTTTTCAAATAAAAAATTTTCAAAA-TTTTTTGGTGTTGGTCATGCAATAG-C
65 CCCCCTTTTTGTGATAAAAAA--TT-AAAATTTTTTTAGTGTTGGCCATCCCATAGAC
* * * **
497544 GGACACCCCCTTTTTCA---GATAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGCCATGGTC
1 -GACACCCCCTTTTT-ATTTGGTAAAAAAA--TC-AAATTTTTTGGTGTTGACCATGCAATGACC
* ** * * *
497606 GACACCCCCTTTTTGTCAGATAAAAAGTT-TGATTTTTTTTGTGTTGGCCATCCCATGGCC
61 GACACCCCCTTTTTGT--GATAAAAAATTAAAATTTTTTTAGTGTTGGCCATCCCATAGAC
* * *
497666 GACACTCCCTTTTTTATTTGGTAAAAAAATCAAATTTTTTTGTGTTGATCATGCAATGACCGACA
1 GACAC-CCCCTTTTTATTTGGTAAAAAAATCAAATTTTTTGGTGTTGACCATGCAATGACCGACA
** *
497731 CCCCCTTTTTGTGATAAAAAATTCAAAATTTTTTTAGTGTTGTTCATGCCATAGAC
65 CCCCCTTTTTGTGATAAAAAATT-AAAATTTTTTTAGTGTTGGCCATCCCATAGAC
*
497787 GATACCCCCTTTTTATTTGGTAAAAAA
1 GACACCCCCTTTTTATTTGGTAAAAAA
497814 TTAAAAAAAA
Statistics
Matches: 215, Mismatches: 38, Indels: 32
0.75 0.13 0.11
Matches are distributed among these distances:
119 20 0.09
120 26 0.12
121 103 0.48
122 50 0.23
124 16 0.07
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (119 bp):
GACACCCCCTTTTTATTTGGTAAAAAAATCAAATTTTTTGGTGTTGACCATGCAATGACCGACAC
CCCCTTTTTGTGATAAAAAATTAAAATTTTTTTAGTGTTGGCCATCCCATAGAC
Found at i:498641 original size:17 final size:16
Alignment explanation
Indices: 498621--498675 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 16
498611 AAAAAATAAT
498621 AATTAGAATATACAGGA
1 AATTAGAATATACA-GA
*
498638 AATTAGAA-AT-TA-A
1 AATTAGAATATACAGA
*
498651 AATTAAAATATACAGAA
1 AATTAGAATATACAG-A
498668 AATTAGAA
1 AATTAGAA
498676 ATTAAATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
13 8 0.27
14 2 0.07
15 2 0.07
16 2 0.07
17 16 0.53
ACGTcount: A:0.60, C:0.04, G:0.11, T:0.25
Consensus pattern (16 bp):
AATTAGAATATACAGA
Found at i:498655 original size:30 final size:30
Alignment explanation
Indices: 498621--498711 Score: 119
Period size: 30 Copynumber: 3.0 Consensus size: 30
498611 AAAAAATAAT
*
498621 AATTAGAATATACAGGAAATTAGAAATTAA
1 AATTAAAATATACAGGAAATTAGAAATTAA
*
498651 AATTAAAATATACAGAAAATTAGAAATTAA
1 AATTAAAATATACAGGAAATTAGAAATTAA
* * * * *
498681 ATTTAAAATAAAAACGAAATTACAAATTAA
1 AATTAAAATATACAGGAAATTAGAAATTAA
498711 A
1 A
498712 TTTTAAAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.62, C:0.04, G:0.08, T:0.26
Consensus pattern (30 bp):
AATTAAAATATACAGGAAATTAGAAATTAA
Found at i:498712 original size:30 final size:30
Alignment explanation
Indices: 498636--498730 Score: 113
Period size: 30 Copynumber: 3.1 Consensus size: 30
498626 GAATATACAG
* * *
498636 GAAATTAGAAATTAAAATTAAAATATACA-
1 GAAATTAGAAATTAAATTTAAAATAAAAAC
498665 GAAAATTAGAAATTAAATTTAAAATAAAAAC
1 G-AAATTAGAAATTAAATTTAAAATAAAAAC
*
498696 GAAATTACAAATTAAATTTTAAAA-AATAAAC
1 GAAATTAGAAATTAAA-TTTAAAATAA-AAAC
498727 GAAA
1 GAAA
498731 AAAAAAATCA
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
29 1 0.02
30 41 0.71
31 16 0.28
ACGTcount: A:0.63, C:0.04, G:0.06, T:0.26
Consensus pattern (30 bp):
GAAATTAGAAATTAAATTTAAAATAAAAAC
Found at i:499812 original size:22 final size:22
Alignment explanation
Indices: 499787--499839 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
499777 TAAGATTTTT
499787 TGTAAAAAAAATATTTCGAAAA
1 TGTAAAAAAAATATTTCGAAAA
******
499809 TGTATTTTTTATATTTCGAAAA
1 TGTAAAAAAAATATTTCGAAAA
499831 TGTAAAAAA
1 TGTAAAAAA
499840 TATCATATAT
Statistics
Matches: 20, Mismatches: 11, Indels: 0
0.65 0.35 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (22 bp):
TGTAAAAAAAATATTTCGAAAA
Found at i:499912 original size:21 final size:20
Alignment explanation
Indices: 499867--499914 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
499857 TTAAAAATTC
*
499867 AAAAATATAAAAAACATTTA
1 AAAAATAGAAAAAACATTTA
* *
499887 GAAAATAGAAAAAAATATTATA
1 AAAAATAG-AAAAAACATT-TA
499909 AAAAAT
1 AAAAAT
499915 TCAAAAATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 6 0.27
21 9 0.41
22 7 0.32
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (20 bp):
AAAAATAGAAAAAACATTTA
Found at i:499922 original size:30 final size:30
Alignment explanation
Indices: 499867--499923 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
499857 TTAAAAATTC
*
499867 AAAAATATAAAAAACATTTAGAAAATAGAA
1 AAAAATATAAAAAACATTCAGAAAATAGAA
499897 AAAAATATTATAAAAA-ATTCA-AAAATA
1 AAAAATA-TA-AAAAACATTCAGAAAATA
499924 TATTTTACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 13 0.54
31 6 0.25
32 5 0.21
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.23
Consensus pattern (30 bp):
AAAAATATAAAAAACATTCAGAAAATAGAA
Found at i:501184 original size:84 final size:84
Alignment explanation
Indices: 501091--501634 Score: 717
Period size: 83 Copynumber: 6.5 Consensus size: 84
501081 ATTTAAAAAC
* *
501091 TGATAAAAATTGTAATATTATAACAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGTATT
1 TGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGTATT
*
501156 GTCAAATCAATACATTATT
66 GTCAAATCAACACATTATT
* * *
501175 TGATAAAAATTATAATATAATAATAA-TATTTATTTAAATATTTAAAATTAGTAAATAATATATT
1 TGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGTATT
501239 GTCAAATCAACACATTATT
66 GTCAAATCAACACATTATT
501258 TGATAAAAATTGTAATATAATAATAA-TTTTTATTTAAATATTTAAAATTAGTAAATAATGTATT
1 TGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGTATT
*
501322 GTCAAATCAACATATTATAT
66 GTCAAATCAACACATTAT-T
* *
501342 T-ATAAAAAGTGTAATATAATAAT-ATTTTTTATTTAAATA-TGAAAATTTTA-TAAATAATGTA
1 TGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAA--TTAGTAAATAATGTA
*
501403 TTGTCAAATCAACATATTATT
64 TTGTCAAATCAACACATTATT
* * * * *
501424 TGATAAAAATTGTAATATAATAATAATAATTTT-TTTAAATATTTAAATTTAATAAATAATATGT
1 TGATAAAAATTGTAATATAATAATAAT-TTTTTATTTAAATATTTAAAATTAGTAAATAATGTAT
*
501488 TGTCAAATCAACACATAATT
65 TGTCAAATCAACACATTATT
* * * * *
501508 TGATAAAAATTGTAACATAATAATAATTTATAATTTAAATA-TGAAAATTTGATAAATAATGTAT
1 TGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAG-TAAATAATGTAT
* * * * *
501572 TGTTAACTGAAGACAATATT
65 TGTCAAATCAACACATTATT
* *
501592 TGATATAAATTGAAATATAATAATAATCTTTTTTATTTAAATA
1 TGATAAAAATTGTAATATAATAATAA--TTTTTTATTTAAATA
501635 ATGTTAAATT
Statistics
Matches: 406, Mismatches: 41, Indels: 24
0.86 0.09 0.05
Matches are distributed among these distances:
82 8 0.02
83 230 0.57
84 147 0.36
85 8 0.02
86 13 0.03
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (84 bp):
TGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGTATT
GTCAAATCAACACATTATT
Found at i:501278 original size:45 final size:43
Alignment explanation
Indices: 501218--501445 Score: 108
Period size: 45 Copynumber: 5.4 Consensus size: 43
501208 TTAAATATTT
501218 AAAATTAGTAAATAATATATTGTCAAATCAACACATTATTTGATA
1 AAAATT-GTAAATAATATATTGTCAAATCAACA-ATTATTTGATA
** **
501263 AAAATTGTAATATAATAATAATT-T-TTATTTA-AA-TA-TT--T-
1 AAAATTGTAA-ATAAT-AT-ATTGTCAAATCAACAATTATTTGATA
*
501301 AAAATTAGTAAATAATGTATTGTCAAATCAACATATTATATT-ATA
1 AAAATT-GTAAATAATATATTGTCAAATCAACA-ATTAT-TTGATA
* *** **
501346 AAAAGTGTAATATAATAATATT-TTTTATTTA-AA-TA--TGA-A
1 AAAATTGTAA-ATAAT-ATATTGTCAAATCAACAATTATTTGATA
** * *
501385 AATTTTATAAATAATGTATTGTCAAATCAACATATTATTTGATA
1 AAAATTGTAAATAATATATTGTCAAATCAACA-ATTATTTGATA
501429 AAAATTGTAATATAATA
1 AAAATTGTAA-ATAATA
501446 ATAATAATTT
Statistics
Matches: 129, Mismatches: 30, Indels: 48
0.62 0.14 0.23
Matches are distributed among these distances:
36 3 0.02
37 6 0.05
38 23 0.18
39 15 0.12
40 3 0.02
41 6 0.05
42 4 0.03
43 7 0.05
44 19 0.15
45 33 0.26
46 7 0.05
47 3 0.02
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.41
Consensus pattern (43 bp):
AAAATTGTAAATAATATATTGTCAAATCAACAATTATTTGATA
Found at i:501337 original size:38 final size:38
Alignment explanation
Indices: 501129--501337 Score: 104
Period size: 38 Copynumber: 5.1 Consensus size: 38
501119 TTTTATTTAA
*
501129 ATATTTAAAATTAGTAAATAATGTATTGTCAAATCAATAC
1 ATATTTAAAATTAGTAAATAATATATTGTCAAATC-A-AC
* * ** * *
501169 ATTATTTGATAAAAATTA-TAATATAATAATAATATTTATTTAA-
1 A-TA-TT--T-AAAATTAGTAA-ATAAT-ATATTGTCAAATCAAC
501212 ATATTTAAAATTAGTAAATAATATATTGTCAAATCAACAC
1 ATATTTAAAATTAGTAAATAATATATTGTCAAATC-A-AC
** * *
501252 ATTATTTGATAAAAATT-GTAATATAATAATAATT-TTTATTTAA-
1 A-TA-TT--T-AAAATTAGTAA-ATAAT-AT-ATTGTCAAATCAAC
*
501295 ATATTTAAAATTAGTAAATAATGTATTGTCAAATCAAC
1 ATATTTAAAATTAGTAAATAATATATTGTCAAATCAAC
501333 ATATT
1 ATATT
501338 ATATTATAAA
Statistics
Matches: 125, Mismatches: 22, Indels: 46
0.65 0.11 0.24
Matches are distributed among these distances:
36 3 0.02
37 13 0.10
38 29 0.23
39 10 0.08
40 2 0.02
41 8 0.06
42 8 0.06
43 2 0.02
44 11 0.09
45 25 0.20
46 11 0.09
47 3 0.02
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (38 bp):
ATATTTAAAATTAGTAAATAATATATTGTCAAATCAAC
Found at i:504691 original size:60 final size:59
Alignment explanation
Indices: 504612--505087 Score: 299
Period size: 61 Copynumber: 7.9 Consensus size: 59
504602 AGGGGAAGTT
* **
504612 GGTGTCGACCATTAAATGACCAACACCAAAAAAAATT-AATTTTTTACTAAATAAAAAGG
1 GGTGTCGGCCATTGCATGACCAACACCAAAAAAAATTAAATTTTTTACTAAA-AAAAAGG
* * * ** *
504671 AAGTGTCGGCTATGGCATGACCAACATAAAAAAAAATTAAATTTTTTATTACACAAAAAAGG
1 -GGTGTCGGCCATTGCATGACCAACACCAAAAAAAATTAAATTTTTTACTA-A-AAAAAAGG
* * * * * *
504733 GGTGCCGGCCATTGCATAACCAACA-CAGAAAAAATTGATTTTTTTACCATATAAAAAAGG
1 GGTGTCGGCCATTGCATGACCAACACCAAAAAAAATTAAATTTTTTA-C-TAAAAAAAAGG
* * * * * * * * *
504793 TGGTGTCGACCATGGCATGGCTAAC-GCAAAAAAAAATAAATTTTTTATTTGACAAAAAGG
1 -GGTGTCGGCCATTGCATGACCAACACCAAAAAAAATTAAATTTTTTA-CTAAAAAAAAGG
* * * * ** *
504853 GGTGTCGGTCATGGCATGACTAACATCAAAAAATTTTAAATTTTTTTTATCTGAAAAAAA-G
1 GGTGTCGGCCATTGCATGACCAACACCAAAAAAAATTAAA--TTTTTTA-CTAAAAAAAAGG
* * * * *
504914 GGTGTCAGTCATTGAATGACCAACACTAAAAAAATTTAAATTTTTTTTATCT-AAAAAAAGG
1 GGTGTCGGCCATTGCATGACCAACACCAAAAAAAATTAAA--TTTTTTA-CTAAAAAAAAGG
** * ** * *
504975 GAGTGTCGGCCATTGCATG-GTAACACC--CAAAAATTTGATTTTTTA-TCAGATAAATAGG
1 G-GTGTCGGCCATTGCATGACCAACACCAAAAAAAATTAAATTTTTTACT-A-AAAAAAAGG
* * *
505033 GGTGTCGACCATTGCATGACCAACACC--AAAAAATTGAATTTTTTATCTGAAAAAA
1 GGTGTCGGCCATTGCATGACCAACACCAAAAAAAATTAAATTTTTTA-CTAAAAAAA
505088 GGTCAACACC
Statistics
Matches: 326, Mismatches: 72, Indels: 38
0.75 0.17 0.09
Matches are distributed among these distances:
55 1 0.00
57 23 0.07
58 33 0.10
59 28 0.09
60 81 0.25
61 119 0.37
62 40 0.12
63 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (59 bp):
GGTGTCGGCCATTGCATGACCAACACCAAAAAAAATTAAATTTTTTACTAAAAAAAAGG
Found at i:504971 original size:181 final size:181
Alignment explanation
Indices: 504639--504998 Score: 392
Period size: 181 Copynumber: 2.0 Consensus size: 181
504629 GACCAACACC
* *
504639 AAAAAAAATTAATTTTTTACTAAATAAAAAGGAAGTGTCGGCTATGGCATGACCAACATAAAAAA
1 AAAAAAAATAAATTTTTTACTAAACAAAAAGGAAGTGTCGGCTATGGCATGACCAACATAAAAAA
* * *
504704 AAATTAAATTTTTTATTACACAAAAAAGGGGTGCCGGCCATTGCATAACCAACACAGAAAAAATT
66 AAATTAAATTTTTTATTACACAAAAAAAGGGTGCCAGCCATTGAATAACCAACACAGAAAAAATT
*
504769 GATTTTTTTACCATAT-AAAAAAGGTG-GTGTCGACCATGGCATGGCTAACGCA
131 AATTTTTTTA-CATATAAAAAAAGG-GAGTGTCGACCATGGCATGG-TAACGCA
* ** * * *
504821 AAAAAAAATAAATTTTTTATTTGACAAAAAGG-GGTGTCGG-TCATGGCATGACTAACATCAAAA
1 AAAAAAAATAAATTTTTTACTAAACAAAAAGGAAGTGTCGGCT-ATGGCATGACCAACATAAAAA
** ** * * *
504884 AATTTTAAATTTTTT-TTATCTGAAAAAAAGGGTGTCAGTCATTGAATGACCAACACTA-AAAAA
65 AAAATTAAATTTTTTATTA-CACAAAAAAAGGGTGCCAGCCATTGAATAACCAACAC-AGAAAAA
* * * *
504947 ATTTAAATTTTTTT-TATCTAAAAAAAGGGAGTGTCGGCCATTGCATGGTAAC
128 A-TT-AATTTTTTTACATATAAAAAAAGGGAGTGTCGACCATGGCATGGTAAC
504999 ACCCAAAAAT
Statistics
Matches: 148, Mismatches: 23, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
180 4 0.03
181 82 0.55
182 54 0.36
183 8 0.05
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (181 bp):
AAAAAAAATAAATTTTTTACTAAACAAAAAGGAAGTGTCGGCTATGGCATGACCAACATAAAAAA
AAATTAAATTTTTTATTACACAAAAAAAGGGTGCCAGCCATTGAATAACCAACACAGAAAAAATT
AATTTTTTTACATATAAAAAAAGGGAGTGTCGACCATGGCATGGTAACGCA
Found at i:507416 original size:21 final size:22
Alignment explanation
Indices: 507374--507416 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
507364 TTGGACTCTT
*
507374 CCCTCCTCCATTTTCTCATCAA
1 CCCTCCTCCATTTTCACATCAA
* *
507396 CCCTTCTCC-TTTTCACTTCAA
1 CCCTCCTCCATTTTCACATCAA
507417 TAGCGTCTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.16, C:0.44, G:0.00, T:0.40
Consensus pattern (22 bp):
CCCTCCTCCATTTTCACATCAA
Found at i:508178 original size:83 final size:83
Alignment explanation
Indices: 508039--508205 Score: 334
Period size: 83 Copynumber: 2.0 Consensus size: 83
508029 TTTAAAAATA
508039 AAAAACAAAATTCCTATGAAGTGGACCTATTCCGGAATATGATCAGACGGTGGAAGATTGAAAAT
1 AAAAACAAAATTCCTATGAAGTGGACCTATTCCGGAATATGATCAGACGGTGGAAGATTGAAAAT
508104 CAATGAACATGATGGATG
66 CAATGAACATGATGGATG
508122 AAAAACAAAATTCCTATGAAGTGGACCTATTCCGGAATATGATCAGACGGTGGAAGATTGAAAAT
1 AAAAACAAAATTCCTATGAAGTGGACCTATTCCGGAATATGATCAGACGGTGGAAGATTGAAAAT
508187 CAATGAACATGATGGATG
66 CAATGAACATGATGGATG
508205 A
1 A
508206 TTCGGGTTGA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 84 1.00
ACGTcount: A:0.41, C:0.13, G:0.23, T:0.23
Consensus pattern (83 bp):
AAAAACAAAATTCCTATGAAGTGGACCTATTCCGGAATATGATCAGACGGTGGAAGATTGAAAAT
CAATGAACATGATGGATG
Found at i:518085 original size:36 final size:36
Alignment explanation
Indices: 518041--518218 Score: 218
Period size: 36 Copynumber: 4.9 Consensus size: 36
518031 GAAAACAGCA
518041 TGGTGTTAGCAATGGTATGGGGCCAGGCCGGCCTGG
1 TGGTGTTAGCAATGGTATGGGGCCAGGCCGGCCTGG
*
518077 TGGTGTTAGCAATGGTATGGGGCCTGGCCGGCCTGG
1 TGGTGTTAGCAATGGTATGGGGCCAGGCCGGCCTGG
* * * *
518113 TGGTGCTAGCAATGGTATGGGGCCCGGTCGGCCTGC
1 TGGTGTTAGCAATGGTATGGGGCCAGGCCGGCCTGG
* *
518149 TGGTGCTAGCAATGGTACT-GGGCCTA-GCCGACCTGG
1 TGGTGTTAGCAATGGTA-TGGGGCC-AGGCCGGCCTGG
* * *
518185 TGGTGTAAACAATGGTACT-GGGCCAGGTCGGCCT
1 TGGTGTTAGCAATGGTA-TGGGGCCAGGCCGGCCT
518219 AACAGTGGGT
Statistics
Matches: 125, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
35 1 0.01
36 123 0.98
37 1 0.01
ACGTcount: A:0.15, C:0.22, G:0.40, T:0.23
Consensus pattern (36 bp):
TGGTGTTAGCAATGGTATGGGGCCAGGCCGGCCTGG
Found at i:524467 original size:24 final size:24
Alignment explanation
Indices: 524435--524482 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
524425 TTTTATCAAA
524435 CTATGAATGTAAAAAAAGTATGTG
1 CTATGAATGTAAAAAAAGTATGTG
524459 CTATGAATGTAAAAAAAGTATGTG
1 CTATGAATGTAAAAAAAGTATGTG
524483 TTGCACAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.21, T:0.29
Consensus pattern (24 bp):
CTATGAATGTAAAAAAAGTATGTG
Found at i:526856 original size:39 final size:39
Alignment explanation
Indices: 526801--526884 Score: 141
Period size: 39 Copynumber: 2.2 Consensus size: 39
526791 TGGAGGAGGA
*
526801 GTAAGTCATTATTTATATAACTTCAAGAAGCATCATGGG
1 GTAAGTCATTAATTATATAACTTCAAGAAGCATCATGGG
* *
526840 GTAAGTCGTTAATTATATAACTTCAAGAAGTATCATGGG
1 GTAAGTCATTAATTATATAACTTCAAGAAGCATCATGGG
526879 GTAAGT
1 GTAAGT
526885 TTAGTGGTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (39 bp):
GTAAGTCATTAATTATATAACTTCAAGAAGCATCATGGG
Found at i:526919 original size:51 final size:51
Alignment explanation
Indices: 526839--526938 Score: 191
Period size: 51 Copynumber: 2.0 Consensus size: 51
526829 AGCATCATGG
526839 GGTAAGTCGTTAATTATATAACTTCAAGAAGTATCATGGGGTAAGTTTAGT
1 GGTAAGTCGTTAATTATATAACTTCAAGAAGTATCATGGGGTAAGTTTAGT
*
526890 GGTAAGTCGTTAATTATATAACTTTAAGAAGTATCATGGGGTAAGTTTA
1 GGTAAGTCGTTAATTATATAACTTCAAGAAGTATCATGGGGTAAGTTTA
526939 AGTGTTCAGG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36
Consensus pattern (51 bp):
GGTAAGTCGTTAATTATATAACTTCAAGAAGTATCATGGGGTAAGTTTAGT
Found at i:527849 original size:97 final size:97
Alignment explanation
Indices: 527683--527878 Score: 383
Period size: 97 Copynumber: 2.0 Consensus size: 97
527673 ATTCATGGTT
527683 TTTGTTTTAAAAAGTCTTGTTACCTGATGTTTTATAGGGTTCTTTCTGGGTAAGTTAACAAATTT
1 TTTGTTTTAAAAAGTCTTGTTACCTGATGTTTTATAGGGTTCTTTCTGGGTAAGTTAACAAATTT
527748 CTTTTAATGAATTAACCATAGTATTTGCATCC
66 CTTTTAATGAATTAACCATAGTATTTGCATCC
527780 TTTGTTTTAAAAAGTCTTGTTACCTGATGTTTTATAGGGTTCTTTCTGGGTAAGTTAACAAATTT
1 TTTGTTTTAAAAAGTCTTGTTACCTGATGTTTTATAGGGTTCTTTCTGGGTAAGTTAACAAATTT
*
527845 CTTTTGATGAATTAACCATAGTATTTGCATCC
66 CTTTTAATGAATTAACCATAGTATTTGCATCC
527877 TT
1 TT
527879 CATTCTTTTT
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 98 1.00
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (97 bp):
TTTGTTTTAAAAAGTCTTGTTACCTGATGTTTTATAGGGTTCTTTCTGGGTAAGTTAACAAATTT
CTTTTAATGAATTAACCATAGTATTTGCATCC
Found at i:539434 original size:46 final size:46
Alignment explanation
Indices: 539336--539434 Score: 135
Period size: 46 Copynumber: 2.2 Consensus size: 46
539326 TGTTTGAATC
* * *
539336 GCATCGAATTCCTTACCATTCAATTCAATAAACTGTTAGTAGAATA
1 GCATCGAATTCCTTACCATTCAATTCAACAAACTGTTAGTAAAACA
** * *
539382 ATATCGAATTCCTTACCATTCAATTCCACGAACTGTTAGTAAAACA
1 GCATCGAATTCCTTACCATTCAATTCAACAAACTGTTAGTAAAACA
539428 GCATCGA
1 GCATCGA
539435 GTTCTGTACT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.30
Consensus pattern (46 bp):
GCATCGAATTCCTTACCATTCAATTCAACAAACTGTTAGTAAAACA
Found at i:548475 original size:17 final size:17
Alignment explanation
Indices: 548454--548507 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
548444 TAAGCCATTT
548454 TAAAATTA-AAAACTATTA
1 TAAAATTATAAAA--ATTA
548472 -AAAATTATAAAAATTA
1 TAAAATTATAAAAATTA
* *
548488 TAAAATTATTATAATTA
1 TAAAATTATAAAAATTA
548505 TAA
1 TAA
548508 TTTTTTCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 4 0.12
17 24 0.75
18 4 0.12
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (17 bp):
TAAAATTATAAAAATTA
Found at i:548484 original size:26 final size:26
Alignment explanation
Indices: 548455--548507 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
548445 AAGCCATTTT
548455 AAAATTA-AAAACTATTAAAAATTATA
1 AAAATTATAAAACTATT-AAAATTATA
* *
548481 AAAATTATAAAATTATTATAATTATA
1 AAAATTATAAAACTATTAAAATTATA
548507 A
1 A
548508 TTTTTTCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (26 bp):
AAAATTATAAAACTATTAAAATTATA
Found at i:548500 original size:11 final size:9
Alignment explanation
Indices: 548460--548507 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
548450 ATTTTAAAAT
*
548460 TAAAAACTA
1 TAAAAATTA
548469 TTAAAAATTA
1 -TAAAAATTA
548479 TAAAAATTA
1 TAAAAATTA
548488 T-AAAATTA
1 TAAAAATTA
* *
548496 TTATAATTA
1 TAAAAATTA
548505 TAA
1 TAA
548508 TTTTTTCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
8 8 0.24
9 18 0.53
10 8 0.24
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (9 bp):
TAAAAATTA
Done.