Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000251.1 Hibiscus syriacus cultivar Beakdansim tig00000453_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: 648719
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:351736 original size:16 final size:16
Alignment explanation
Indices: 351682--351761 Score: 54
Period size: 16 Copynumber: 4.9 Consensus size: 16
351672 TTATTATATT
*
351682 AATAATAATAATAATA
1 AATAATATTAATAATA
* * *
351698 AATAAAATAAAATATTTA
1 AATAATAT-TAATA-ATA
*
351716 TAATAATATTTATAATA
1 -AATAATATTAATAATA
* *
351733 AATAAAACTAATAATA
1 AATAATATTAATAATA
*
351749 AA-AATATAAATAA
1 AATAATATTAATAA
351762 AAACAAATGG
Statistics
Matches: 47, Mismatches: 14, Indels: 7
0.69 0.21 0.10
Matches are distributed among these distances:
15 8 0.17
16 21 0.45
17 6 0.13
18 5 0.11
19 7 0.15
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAATATTAATAATA
Found at i:352159 original size:17 final size:17
Alignment explanation
Indices: 352137--352186 Score: 59
Period size: 16 Copynumber: 3.0 Consensus size: 17
352127 GTTGAACAAG
352137 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
* *
352154 TTCTTCTTCA-AATG-AG
1 TTCTTC-TCATTATGAAC
352170 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
352187 ACTTCTGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
15 3 0.12
16 10 0.38
17 10 0.38
18 3 0.12
ACGTcount: A:0.24, C:0.22, G:0.08, T:0.46
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:352557 original size:110 final size:113
Alignment explanation
Indices: 352230--352677 Score: 613
Period size: 113 Copynumber: 4.0 Consensus size: 113
352220 ATAGAGTCAT
* *
352230 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTATTCTTCTTCAGATAAGTTCTTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC-T-TCCTTCTTCAGATAAGTTCTTC
** * * * * * *
352295 TCATTATGAACTCTTTCTGGAAAAGTTGATCCGTCGAGTGATGAATTCAA
64 TCATTATGAACTCTACCTGGCAATGCTGATCCATCAAGTGATGAATTCGA
* *
352345 ACAAAAGGTTTGAACAAATTCTTCTCATTATGAA-TTTTTCTTCCTTCTTCAGATAAGTTCTTCT
1 GCAAAAGG-TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCT
352409 CATTATGAACTCTACCTGGCAATGCTGATCCATCAAGTGATGAATTCGA
65 CATTATGAACTCTACCTGGCAATGCTGATCCATCAAGTGATGAATTCGA
* * *
352458 GCAAAAGGTTGAACAAATTCTTCTCATTATTAATTTCTTCTTCCTTCTTCAGATGAGTTC-T-T-
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
352520 ATTATGAACTCTACCTGGCAATGCTGATCCATCAAGTGATGAATT-GA
66 ATTATGAACTCTACCTGGCAATGCTGATCCATCAAGTGATGAATTCGA
* * *
352567 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTT-AGATGAGTTATTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
* * * **
352631 ATTATGAACACTACCTTGC-ATGTTGATCCATTGAGTGATGAATTCGA
66 ATTATGAACTCTACCTGGCAATGCTGATCCATCAAGTGATGAATTCGA
352678 ATCTTTACTA
Statistics
Matches: 302, Mismatches: 25, Indels: 16
0.88 0.07 0.05
Matches are distributed among these distances:
108 9 0.03
109 49 0.16
110 68 0.23
111 20 0.07
112 25 0.08
113 94 0.31
114 1 0.00
115 12 0.04
116 24 0.08
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
ATTATGAACTCTACCTGGCAATGCTGATCCATCAAGTGATGAATTCGA
Found at i:355523 original size:14 final size:14
Alignment explanation
Indices: 355504--355530 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
355494 TTTTTCATCA
355504 TTTTTCATTTTTTC
1 TTTTTCATTTTTTC
355518 TTTTTCATTTTTT
1 TTTTTCATTTTTT
355531 TTCTTCAAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTCATTTTTTC
Found at i:366132 original size:22 final size:21
Alignment explanation
Indices: 366090--366140 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 21
366080 TTAATAAAAA
366090 ATAATAATATATATATATATAT
1 ATAA-AATATATATATATATAT
366112 ATAAAATATATA-ATAAGTATAT
1 ATAAAATATATATAT-A-TATAT
366134 ATAAAAT
1 ATAAAAT
366141 TTTGAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 2 0.07
21 9 0.33
22 16 0.59
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
ATAAAATATATATATATATAT
Found at i:366137 original size:13 final size:12
Alignment explanation
Indices: 366090--366137 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 12
366080 TTAATAAAAA
366090 ATAATAATATAT
1 ATAATAATATAT
366102 AT-AT-ATATAT
1 ATAATAATATAT
366112 AT-A-AA-ATAT
1 ATAATAATATAT
366121 ATAATAAGTATAT
1 ATAATAA-TATAT
366134 ATAA
1 ATAA
366138 AATTTTGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
9 6 0.19
10 11 0.35
11 4 0.13
12 2 0.06
13 8 0.26
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (12 bp):
ATAATAATATAT
Found at i:366642 original size:2 final size:2
Alignment explanation
Indices: 366635--366668 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
366625 TTTTAAGAAA
366635 AT AT AT AT AT AT -T A- 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
366669 TTATTTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:367395 original size:21 final size:21
Alignment explanation
Indices: 367371--367413 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
367361 AGAGGACCAA
367371 ATCTATTATTTTACCTAAAAT
1 ATCTATTATTTTACCTAAAAT
**
367392 ATCTATTATTTTATGTAAAAT
1 ATCTATTATTTTACCTAAAAT
367413 A
1 A
367414 AAATAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (21 bp):
ATCTATTATTTTACCTAAAAT
Found at i:368495 original size:30 final size:30
Alignment explanation
Indices: 368456--368525 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 30
368446 TTTATTATAT
368456 TATTAATAATAATAATAAAA-TAA-AATAAAA
1 TATTAATAAT-A-AATAAAACTAATAATAAAA
*
368486 TATTTATAATAAATAAAACTAATAATAAAAA
1 TATTAATAATAAATAAAACTAATAAT-AAAA
*
368517 TATAAATAA
1 TATTAATAA
368526 AAACAAATGG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 7 0.21
29 4 0.12
30 12 0.35
31 11 0.32
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.31
Consensus pattern (30 bp):
TATTAATAATAAATAAAACTAATAATAAAA
Found at i:368513 original size:19 final size:18
Alignment explanation
Indices: 368460--368525 Score: 64
Period size: 18 Copynumber: 3.6 Consensus size: 18
368450 TTATATTATT
368460 AATAATAATAATAA-AATAA
1 AATAA-AATAATAATAAT-A
* *
368479 AATAAAATATTTATAATA
1 AATAAAATAATAATAATA
368497 AATAAAACTAATAATAA-A
1 AATAAAA-TAATAATAATA
368515 AATATAAATAA
1 AATA-AAATAA
368526 AAACAAATGG
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
18 22 0.55
19 18 0.45
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.29
Consensus pattern (18 bp):
AATAAAATAATAATAATA
Found at i:368521 original size:24 final size:23
Alignment explanation
Indices: 368459--368527 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 23
368449 ATTATATTAT
368459 TAATAATAATAATA-AAATAAAA
1 TAATAATAATAATATAAATAAAA
* *
368481 TAA-AATATTTATAATAAATAAAA
1 TAATAATAATAAT-ATAAATAAAA
*
368504 CTAATAATAAAAATATAAATAAAA
1 -TAATAATAATAATATAAATAAAA
368528 ACAAATGGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 7 0.18
22 4 0.11
23 8 0.21
24 13 0.34
25 6 0.16
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.29
Consensus pattern (23 bp):
TAATAATAATAATATAAATAAAA
Found at i:370955 original size:40 final size:40
Alignment explanation
Indices: 370911--371030 Score: 222
Period size: 40 Copynumber: 3.0 Consensus size: 40
370901 CGTAGTGCTG
*
370911 CACATAAGGTCGTACCCACCATATACACCGAAGTGTATTA
1 CACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTA
*
370951 CACATAAGGTCGTGCCCACCATATAAACCGAAGTGTATTA
1 CACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTA
370991 CACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTA
1 CACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTA
371031 TAAACCTGCA
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 77 1.00
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
CACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTA
Found at i:378383 original size:40 final size:40
Alignment explanation
Indices: 378339--378420 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
378329 ACCGTAGTGC
* *
378339 TACACATAAGGTTGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
378379 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
378419 TA
1 TA
378421 TAAACCTGCA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
Found at i:379432 original size:30 final size:29
Alignment explanation
Indices: 379367--379433 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
379357 CATTCCTAAC
*
379367 TTTTTCTAAAATTACAAATTGGTCCCCCAA
1 TTTTT-TAAAATTACAAATTGGTCCCCAAA
* *
379397 CTTTTTAAAAGTTACAAAATT-GTGCCCAAA
1 TTTTTTAAAA-TTAC-AAATTGGTCCCCAAA
379427 TTTTTTA
1 TTTTTTA
379434 TAAGGCATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
29 5 0.16
30 21 0.68
31 5 0.16
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.40
Consensus pattern (29 bp):
TTTTTTAAAATTACAAATTGGTCCCCAAA
Found at i:381748 original size:18 final size:18
Alignment explanation
Indices: 381727--381763 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
381717 CAATTGAAGG
381727 AAAAAGGTCAATCAAAGA
1 AAAAAGGTCAATCAAAGA
381745 AAAAAGGTCAATCAAAGA
1 AAAAAGGTCAATCAAAGA
381763 A
1 A
381764 TAAACACAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.62, C:0.11, G:0.16, T:0.11
Consensus pattern (18 bp):
AAAAAGGTCAATCAAAGA
Found at i:385820 original size:21 final size:23
Alignment explanation
Indices: 385790--385839 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
385780 GGGAATCGAC
385790 CCCCCCTTG-A-GGGAACCGATT
1 CCCCCCTTGAAGGGGAACCGATT
*
385811 CCCCCTTTGAAGGGGAACCGATT
1 CCCCCCTTGAAGGGGAACCGATT
385834 CCCCCC
1 CCCCCC
385840 ACAGGGGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 8 0.32
22 1 0.04
23 16 0.64
ACGTcount: A:0.18, C:0.42, G:0.22, T:0.18
Consensus pattern (23 bp):
CCCCCCTTGAAGGGGAACCGATT
Found at i:385865 original size:20 final size:21
Alignment explanation
Indices: 385821--385860 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
385811 CCCCCTTTGA
*
385821 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
385842 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
385861 TAGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:389977 original size:30 final size:30
Alignment explanation
Indices: 389941--390013 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 30
389931 AAAATTACAT
* *
389941 TTTGGTCACTAAACTTT-TCAAAGTTTATAC
1 TTTGGTCACTAAACTTTACCAAA-TTTATAA
*
389971 TTTGGTCACCAAACTTTACCAAATTTATAA
1 TTTGGTCACTAAACTTTACCAAATTTATAA
390001 TTTGGTCACTAAA
1 TTTGGTCACTAAA
390014 TAAATCCATT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 34 0.89
31 4 0.11
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.40
Consensus pattern (30 bp):
TTTGGTCACTAAACTTTACCAAATTTATAA
Found at i:395080 original size:35 final size:35
Alignment explanation
Indices: 395032--395098 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
395022 ATATTAAAGT
* *
395032 AAATACTTCAATTATATTTTAAACCCCAAATTCTA
1 AAATACTTCAATTACATTATAAACCCCAAATTCTA
* *
395067 AAATACTTTAATTACATTATAAACCCTAAATT
1 AAATACTTCAATTACATTATAAACCCCAAATT
395099 AAAGTATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.37
Consensus pattern (35 bp):
AAATACTTCAATTACATTATAAACCCCAAATTCTA
Found at i:395445 original size:7 final size:7
Alignment explanation
Indices: 395433--395466 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
395423 TTGTTTTAGT
395433 GGTTAAA
1 GGTTAAA
395440 GGTTAAA
1 GGTTAAA
*
395447 AGTTAAA
1 GGTTAAA
*
395454 GATTAAA
1 GGTTAAA
395461 GGTTAA
1 GGTTAA
395467 TAGTCAATAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.24, T:0.29
Consensus pattern (7 bp):
GGTTAAA
Found at i:395544 original size:13 final size:13
Alignment explanation
Indices: 395526--395555 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
395516 TATAATCACC
395526 ATAAATTATTAAA
1 ATAAATTATTAAA
395539 ATAAATTATTAAA
1 ATAAATTATTAAA
395552 ATAA
1 ATAA
395556 TAATAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATAAATTATTAAA
Found at i:395557 original size:3 final size:3
Alignment explanation
Indices: 395551--395586 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
395541 AAATTATTAA
*
395551 AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
395587 CCCTTATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:397509 original size:21 final size:20
Alignment explanation
Indices: 397423--397579 Score: 93
Period size: 20 Copynumber: 7.8 Consensus size: 20
397413 AAATGACCAA
**
397423 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
397442 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
397462 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
397482 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
397503 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
397523 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
397543 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
397564 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
397580 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 9
0.73 0.20 0.06
Matches are distributed among these distances:
19 16 0.15
20 56 0.54
21 32 0.31
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:397532 original size:41 final size:41
Alignment explanation
Indices: 397423--397579 Score: 126
Period size: 41 Copynumber: 3.9 Consensus size: 41
397413 AAATGACCAA
* **
397423 CAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGA-TCCC
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
* ** * *
397462 CAGAATCGCAAATC-AGTTTCCAAAATCGCAACGCGATTCTT-
1 CAAAATCGCAACGCGAATAT-CAAAATCGCAACGCGATT-TTC
* * * **
397503 GAAAATCGCAATGCG-ATAGTCAAATTCGCATTGCGATTTTC
1 CAAAATCGCAACGCGAATA-TCAAAATCGCAACGCGATTTTC
*
397544 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGA
397580 ACACATAAAT
Statistics
Matches: 87, Mismatches: 23, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
38 1 0.01
39 12 0.14
40 17 0.20
41 53 0.61
42 4 0.05
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (41 bp):
CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
Found at i:397589 original size:20 final size:20
Alignment explanation
Indices: 397566--397739 Score: 109
Period size: 20 Copynumber: 8.7 Consensus size: 20
397556 GCGAATATGA
397566 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTAAC-CAT
* * *
397586 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
397606 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTAACCAT
****
397626 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTAACCAT
* * *
397646 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * **
397666 ATATCGCAACGCGTATCGGT
1 AAATCGCAACGCGTAACCAT
* *
397686 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGTAA-CCAT
* * *
397706 AAAATCGCAACTCGTATCCGT
1 -AAATCGCAACGCGTAACCAT
397727 AAATCGCAACGCG
1 AAATCGCAACGCG
397740 ATATTTAAAG
Statistics
Matches: 124, Mismatches: 26, Indels: 8
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.02
20 106 0.85
21 14 0.11
22 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (20 bp):
AAATCGCAACGCGTAACCAT
Found at i:397610 original size:40 final size:39
Alignment explanation
Indices: 397546--397740 Score: 174
Period size: 40 Copynumber: 4.9 Consensus size: 39
397536 CGATTTTCCA
* ** *
397546 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CAT
* * * *
397586 AAATCGCAATGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCAT
** * * *
397626 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCAT
* * ** *
397666 ATATCGCAACGCGTATCGGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT
*
397706 AAAATCGCAACTCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
397741 TATTTAAAGC
Statistics
Matches: 126, Mismatches: 26, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
39 1 0.01
40 94 0.75
41 31 0.25
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (39 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACCAT
Found at i:397631 original size:60 final size:60
Alignment explanation
Indices: 397546--397739 Score: 237
Period size: 60 Copynumber: 3.2 Consensus size: 60
397536 CGATTTTCCA
* ** * *
397546 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
* * ***
397606 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
* * **
397666 ATATCGCAACGCGTATCGGTAAATCGCAACGATAATACATAAAATCGCAACT-CGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAA-TGCGTATCCGT
397727 AAATCGCAACGCG
1 AAATCGCAACGCG
397740 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
60 81 0.72
61 30 0.27
62 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
Found at i:398159 original size:33 final size:33
Alignment explanation
Indices: 398120--398190 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
398110 TTCACTTAGA
398120 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
398153 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
398186 TTTCA
1 TTTCA
398191 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:398294 original size:20 final size:20
Alignment explanation
Indices: 398269--398338 Score: 81
Period size: 19 Copynumber: 3.5 Consensus size: 20
398259 TGCAGAAGAG
398269 TCGCAACGAGATAAATGA-AA
1 TCGCAACGAGA-AAATGACAA
* **
398289 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGACAA
*
398309 TCGCAACGCG-AAATGACAA
1 TCGCAACGAGAAAATGACAA
398328 TCGCAACGAGA
1 TCGCAACGAGA
398339 GAATCGCAAC
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 20 0.50
20 20 0.50
ACGTcount: A:0.41, C:0.21, G:0.24, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAAAATGACAA
Found at i:398323 original size:19 final size:20
Alignment explanation
Indices: 398269--398342 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
398259 TGCAGAAGAG
*
398269 TCGCAACGAGATAAATGA-AA
1 TCGCAACGAGA-GAATGACAA
**
398289 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGACAA
*
398309 TCGCAACGCGA-AATGACAA
1 TCGCAACGAGAGAATGACAA
398328 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
398343 CGCAACGCGA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
19 21 0.47
20 24 0.53
ACGTcount: A:0.42, C:0.20, G:0.24, T:0.14
Consensus pattern (20 bp):
TCGCAACGAGAGAATGACAA
Found at i:398345 original size:14 final size:14
Alignment explanation
Indices: 398326--398381 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
398316 GCGAAATGAC
398326 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
398340 AATCGCAACGCGAAATG
1 AATCGCAA--CGAGA-G
398357 AAATCGCAACGAGAG
1 -AATCGCAACGAGAG
398372 AATCGCAACG
1 AATCGCAACG
398382 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:398367 original size:32 final size:32
Alignment explanation
Indices: 398281--398396 Score: 151
Period size: 32 Copynumber: 3.4 Consensus size: 32
398271 GCAACGAGAT
398281 AAATGAAATCGCAACGAGAGAATGACTGTCGCAACGCG
1 AAATGAAATCGCAACGAGAG-A--A---TCGCAACGCG
398319 AAATGACAATCGCAACGAGAGAATCGCAACGCG
1 AAATGA-AATCGCAACGAGAGAATCGCAACGCG
398352 AAATGAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAATCGCAACGAGAGAATCGCAACGCG
**
398384 AAACCAAATCGCA
1 AAATGAAATCGCA
398397 TTGCGATTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 8
0.88 0.02 0.09
Matches are distributed among these distances:
32 37 0.49
33 16 0.21
36 1 0.01
38 7 0.09
39 14 0.19
ACGTcount: A:0.43, C:0.23, G:0.23, T:0.10
Consensus pattern (32 bp):
AAATGAAATCGCAACGAGAGAATCGCAACGCG
Found at i:398433 original size:14 final size:14
Alignment explanation
Indices: 398414--398503 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
398404 TTTTATTTCG
398414 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
398428 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
398447 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
398461 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
398480 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
398494 CGTTGCGATT
1 CGTTGCGATT
398504 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:398439 original size:33 final size:33
Alignment explanation
Indices: 398397--398511 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
398387 CCAAATCGCA
*
398397 TTGCGATTTTTATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
398430 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
398463 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
398496 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
398512 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:398485 original size:19 final size:18
Alignment explanation
Indices: 398392--398489 Score: 77
Period size: 19 Copynumber: 5.7 Consensus size: 18
398382 CGAAACCAAA
* *
398392 TCGCATTGCGATTTTTATT
1 TCGCGTTGCGA-TTTCATT
398411 TCGCGTTGCGA-TTC---
1 TCGCGTTGCGATTTCATT
*
398425 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
398444 TCGCGTTGCGA-TTC---
1 TCGCGTTGCGATTTCATT
*
398458 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATT-TCATT
398477 TCGCGTTGCGATT
1 TCGCGTTGCGATT
398490 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
15 1 0.02
16 5 0.08
17 5 0.08
19 32 0.51
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.45
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:400363 original size:93 final size:93
Alignment explanation
Indices: 400204--400486 Score: 541
Period size: 93 Copynumber: 3.1 Consensus size: 93
400194 TAGATTGCTT
*
400204 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
400269 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
400297 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
400362 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
400390 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTTTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
400455 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
400482 AGTAA
1 AGTAA
400487 TGCAATCCAT
Statistics
Matches: 188, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
92 6 0.03
93 182 0.97
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:400559 original size:20 final size:19
Alignment explanation
Indices: 400534--400747 Score: 162
Period size: 19 Copynumber: 12.3 Consensus size: 19
400524 TAGTTTACTT
* *
400534 TCGCAACACGAAAGTTAAAA
1 TCGCAACGCGAAA-TCAAAA
*
400554 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATCAAAA
*
400573 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATCAAAA
*
400592 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAATCAAAA
*
400606 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATCAAAA
*
400625 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAATCAAAA
*
400639 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATCAAAA
*
400658 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATCAAAA
*
400677 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAATCAAAA
*
400691 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATCAAAA
*
400710 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAATCAAAA
*
400724 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATCAAAA
400743 TCGCA
1 TCGCA
400748 TTGCGATTTT
Statistics
Matches: 157, Mismatches: 17, Indels: 41
0.73 0.08 0.19
Matches are distributed among these distances:
14 38 0.24
15 4 0.03
16 8 0.05
17 8 0.05
18 4 0.03
19 83 0.53
20 12 0.08
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (19 bp):
TCGCAACGCGAAATCAAAA
Found at i:400613 original size:33 final size:32
Alignment explanation
Indices: 400570--400665 Score: 156
Period size: 33 Copynumber: 2.9 Consensus size: 32
400560 CGCGAAACCA
**
400570 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
400602 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
400635 AAGATCGCAACGCGAAACCAAAATCGCAACG
1 AA-ATCGCAACGCGAAACCAAAATCGCAACG
400666 CGAAATGAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.03
33 58 0.97
ACGTcount: A:0.46, C:0.28, G:0.19, T:0.07
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:400660 original size:52 final size:52
Alignment explanation
Indices: 400550--400717 Score: 209
Period size: 52 Copynumber: 3.2 Consensus size: 52
400540 CACGAAAGTT
* ** *
400550 AAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-AT-GAAAATCGCAACGAC
1 AAAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGATCGCAACGCGAAAC--C
*
400602 AGAATCGCAACGCGAAACCAAAATCGCAACGACAAGATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACCAAAATCGCAACGACAAGATCGCAACGCGAAACC
**
400654 AAAATCGCAACGCGAAATGAAAATCGCAACGAC-AGAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACCAAAATCGCAACGACAAG-ATCGCAACGCGAAACC
400706 AAAATCGCAACG
1 AAAATCGCAACG
400718 ACAAGATCGC
Statistics
Matches: 104, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
51 2 0.02
52 91 0.88
53 3 0.03
54 8 0.08
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.07
Consensus pattern (52 bp):
AAAATCGCAACGCGAAACCAAAATCGCAACGACAAGATCGCAACGCGAAACC
Found at i:400693 original size:33 final size:32
Alignment explanation
Indices: 400655--400747 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
400645 CGCGAAACCA
**
400655 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
400687 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
400720 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
400748 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:400696 original size:85 final size:85
Alignment explanation
Indices: 400553--400747 Score: 390
Period size: 85 Copynumber: 2.3 Consensus size: 85
400543 GAAAGTTAAA
400553 ATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACGACAGAATCGCAACGCGAA
1 ATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACGACAGAATCGCAACGCGAA
400618 ACCAAAATCGCAACGACAAG
66 ACCAAAATCGCAACGACAAG
400638 ATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACGACAGAATCGCAACGCGAA
1 ATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACGACAGAATCGCAACGCGAA
400703 ACCAAAATCGCAACGACAAG
66 ACCAAAATCGCAACGACAAG
400723 ATCGCAACGCGAAACCAAAATCGCA
1 ATCGCAACGCGAAACCAAAATCGCA
400748 TTGCGATTTT
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 110 1.00
ACGTcount: A:0.46, C:0.29, G:0.18, T:0.07
Consensus pattern (85 bp):
ATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACGACAGAATCGCAACGCGAA
ACCAAAATCGCAACGACAAG
Found at i:400745 original size:52 final size:51
Alignment explanation
Indices: 400604--400747 Score: 139
Period size: 52 Copynumber: 2.8 Consensus size: 51
400594 GCAACGACAG
** * * *
400604 AATCGCAACGCGAAACCAAAATCGCAACGACAAGATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAATGAAAAGCGAAAC-ACAAAATCGCAACGCGAAACCAA
* * *
400656 AATCGCAACGCGAAATGAAAATCGCAACGACAGAATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAATGAAAAGCGAAAC-ACAAAATCGCAACGCGAAACCAA
* *
400708 AATCGCAACGAC-AAGATCGCAACGCGAAAC-CAAAATCGCA
1 AATCGCAACG-CGAA-AT-GAAAAGCGAAACACAAAATCGCA
400748 TTGCGATTTT
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
52 69 0.86
53 3 0.04
54 8 0.10
ACGTcount: A:0.46, C:0.29, G:0.18, T:0.07
Consensus pattern (51 bp):
AATCGCAACGCGAAATGAAAAGCGAAACACAAAATCGCAACGCGAAACCAA
Found at i:400765 original size:19 final size:19
Alignment explanation
Indices: 400743--400861 Score: 123
Period size: 19 Copynumber: 6.8 Consensus size: 19
400733 GAAACCAAAA
*
400743 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
400762 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
400778 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
400795 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
400811 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
400828 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
400847 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
400862 AAGTTTTGTG
Statistics
Matches: 83, Mismatches: 7, Indels: 20
0.75 0.06 0.18
Matches are distributed among these distances:
14 15 0.18
16 11 0.13
17 11 0.13
19 46 0.55
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:400784 original size:14 final size:14
Alignment explanation
Indices: 400765--400821 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
400755 TTTCATTTCG
400765 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
400779 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
400796 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
400812 CGTTGCGATT
1 CGTTGCGATT
400822 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:400790 original size:33 final size:33
Alignment explanation
Indices: 400748--400840 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
400738 CAAAATCGCA
*
400748 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
400781 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
400814 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
400841 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:400874 original size:20 final size:19
Alignment explanation
Indices: 400812--400877 Score: 80
Period size: 19 Copynumber: 3.4 Consensus size: 19
400802 GCGATTCTGT
400812 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTT-AGTTTCG
*
400831 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTAGTTTCG
*
400850 CGTTGCGATTTTAAGTTTTG
1 CGTTGCGATTTT-AGTTTCG
*
400870 TGTTGCGA
1 CGTTGCGA
400878 AAGTAAACTA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.11, C:0.15, G:0.27, T:0.47
Consensus pattern (19 bp):
CGTTGCGATTTTAGTTTCG
Found at i:402810 original size:14 final size:14
Alignment explanation
Indices: 402791--402826 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
402781 CTTATTTAAT
402791 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
402805 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
402819 TGATTTGT
1 TGATTTGT
402827 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:402949 original size:19 final size:19
Alignment explanation
Indices: 402933--403034 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
402923 AAAAATGACT
402933 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
402952 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
402971 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
402985 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
403004 ATCGCAATGCGGAATGAAA
1 ATCGCAATGCGAAATGAAA
403023 ATCGCAATGCGA
1 ATCGCAATGCGA
403035 TTTTCATTTC
Statistics
Matches: 74, Mismatches: 4, Indels: 10
0.84 0.05 0.11
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 58 0.78
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:403046 original size:19 final size:19
Alignment explanation
Indices: 403024--403316 Score: 348
Period size: 19 Copynumber: 16.7 Consensus size: 19
403014 GGAATGAAAA
*
403024 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
403043 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
403059 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
403076 TCGCATTGCGA--TTC-TT
1 TCGCATTGCGATTTTCATT
403092 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
403109 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
403128 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
403147 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
403166 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
403185 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
403201 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
403218 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
403237 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
403253 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
403270 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
403288 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
403304 TCGCGTTGCGATT
1 TCGCATTGCGATT
403317 GTAATTTCCG
Statistics
Matches: 239, Mismatches: 9, Indels: 52
0.80 0.03 0.17
Matches are distributed among these distances:
14 35 0.15
16 31 0.13
17 28 0.12
18 3 0.01
19 130 0.54
20 12 0.05
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:403067 original size:14 final size:14
Alignment explanation
Indices: 403048--403102 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
403038 TCATTTCGCA
*
403048 TTGCGATTCTCTCG
1 TTGCGATTCTTTCG
403062 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TTTCG
403079 CATTGCGATTCTTTCG
1 --TTGCGATTCTTTCG
403095 TTGCGATT
1 TTGCGATT
403103 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 14 0.40
16 8 0.23
17 7 0.20
19 6 0.17
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.47
Consensus pattern (14 bp):
TTGCGATTCTTTCG
Found at i:403072 original size:33 final size:33
Alignment explanation
Indices: 403030--403230 Score: 294
Period size: 33 Copynumber: 5.8 Consensus size: 33
403020 AAAATCGCAA
*
403030 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTTTCGT
403063 TGCGATTTTCATTTCGCATTGCGATTCTTTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTTTCGT
403096 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--T
403134 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--T
*
403172 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTTTCGT
403205 TGCGATTTTCATTTCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATT
403231 TTCATTTCGC
Statistics
Matches: 161, Mismatches: 2, Indels: 10
0.93 0.01 0.06
Matches are distributed among these distances:
33 83 0.52
35 7 0.04
36 8 0.05
38 63 0.39
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTTTCGT
Found at i:403080 original size:52 final size:54
Alignment explanation
Indices: 403024--403288 Score: 263
Period size: 52 Copynumber: 5.0 Consensus size: 54
403014 GGAATGAAAA
*
403024 TCGCAATGCGATTTTCATTTCGCATTGCGA-TTC-TCTCG-TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCG-ATTGCGATTTCATCTCGATTGCGATTTTCATT
*
403076 TCGCATTGCGA--TTC-TTTCG-TTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGATTGCGA-TTTCATCTCG-ATTGCGATTTTCATT
*
403128 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCG-ATTGCGA-TTTCATCTCG-ATTGCGATTTTCATT
* *
403185 TCGCATTGCGA--TTC-TCTCG-TTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGATTGCGA-TTTCATCTCG-ATTGCGATTTTCATT
* *
403237 TCGCATTGCGA--TTC-TCTCG-TTGCGATTTTCATTTCCGCATTGCGATTTTCAT
1 TCGCATTGCGATTTTCATTTCGATTGCGA-TTTCATCT-CG-ATTGCGATTTTCAT
403289 GTTGGGATTT
Statistics
Matches: 199, Mismatches: 3, Indels: 21
0.89 0.01 0.09
Matches are distributed among these distances:
47 6 0.03
49 8 0.04
50 7 0.04
52 102 0.51
53 17 0.09
54 7 0.04
55 8 0.04
57 44 0.22
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (54 bp):
TCGCATTGCGATTTTCATTTCGATTGCGATTTCATCTCGATTGCGATTTTCATT
Found at i:405607 original size:12 final size:12
Alignment explanation
Indices: 405590--405614 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
405580 TCTTCGGAGA
405590 CTTTTTCTTCTT
1 CTTTTTCTTCTT
405602 CTTTTTCTTCTT
1 CTTTTTCTTCTT
405614 C
1 C
405615 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:405828 original size:24 final size:23
Alignment explanation
Indices: 405789--405834 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
405779 CTGAAACATC
405789 ATCAAATCCGTGTATTGACCAAT
1 ATCAAATCCGTGTATTGACCAAT
405812 ATCAAAGTCCG-GATATTGACCAA
1 ATCAAA-TCCGTG-TATTGACCAA
405835 GACCAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (23 bp):
ATCAAATCCGTGTATTGACCAAT
Found at i:406538 original size:20 final size:20
Alignment explanation
Indices: 406510--406719 Score: 206
Period size: 20 Copynumber: 10.5 Consensus size: 20
406500 AAATTTCAGT
* * *
406510 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
406530 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
406550 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
406570 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
406590 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
406610 GTTGCGATATACGGAAACGC
1 GTTGCGATTTACGGATTCGC
* *
406630 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
406650 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
406670 ATTGCGATTTATTTG-TTCGC
1 GTTGCGATTTA-CGGATTCGC
* **
406690 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
406710 GTTGCGATTT
1 GTTGCGATTT
406720 TGGAAAATCG
Statistics
Matches: 163, Mismatches: 25, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 162 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:406736 original size:21 final size:20
Alignment explanation
Indices: 406686--406783 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
406676 ATTTATTTGT
* * * *
406686 TCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTGAAAA
*
406706 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTT-GAAAA
* * **
406727 TCGCAATGCGAATTTGACTA
1 TCGCATTGCGATTTTGAAAA
*
406747 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAA-AA
*
406768 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
406784 GACACTGATT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 32 0.52
21 29 0.48
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTTGAAAA
Found at i:406778 original size:41 final size:41
Alignment explanation
Indices: 406686--406842 Score: 110
Period size: 41 Copynumber: 3.9 Consensus size: 41
406676 ATTTATTTGT
* * *
406686 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
** *
406727 TCGCAATGCGAATTTGACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGA-TATTCGCATTGCGATTTTGCAA-AA
* * * ***
406768 TCGCGTTGCGATTTTGGACACT-G-ATTTGCGATTCTG-GGGA
1 TCGCGTTGCGATTTT-GATATTCGCA-TTGCGATTTTGCAAAA
* *
406808 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTG
406843 TTGGTCATTT
Statistics
Matches: 89, Mismatches: 19, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
38 1 0.01
39 12 0.13
40 19 0.21
41 52 0.58
42 5 0.06
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
Found at i:409128 original size:41 final size:42
Alignment explanation
Indices: 409055--409134 Score: 99
Period size: 41 Copynumber: 1.9 Consensus size: 42
409045 GCCATCAGCA
* * * *
409055 AGTCTTTCAAGCATGATGATTAAATCTTTCGGGTCATCTGTT
1 AGTCGTTCAAGCAAGATGATTAAATCCTTCGGGCCATCTGTT
* *
409097 AGTCGTTCGAGCAAGATGA-TAAGTCCTTCGGGCCATCT
1 AGTCGTTCAAGCAAGATGATTAAATCCTTCGGGCCATCT
409135 ATAAGACCTA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
41 16 0.50
42 16 0.50
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.34
Consensus pattern (42 bp):
AGTCGTTCAAGCAAGATGATTAAATCCTTCGGGCCATCTGTT
Found at i:409318 original size:20 final size:20
Alignment explanation
Indices: 409293--409343 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
409283 CAAAAATGAG
409293 TAAGTCCTTCGGGCCTTCAA
1 TAAGTCCTTCGGGCCTTCAA
409313 TAAGTCCTTCGGGCCTTCAA
1 TAAGTCCTTCGGGCCTTCAA
*
409333 TAAGTCTTTCG
1 TAAGTCCTTCG
409344 AGCGAGATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (20 bp):
TAAGTCCTTCGGGCCTTCAA
Found at i:409618 original size:21 final size:21
Alignment explanation
Indices: 409594--409667 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
409584 TAGGTCATCT
409594 ATAAGCCTTTTAAGCAATATG
1 ATAAGCCTTTTAAGCAATATG
* *
409615 ATAAGTCC-TTTAGGTC-ATGT-
1 ATAAG-CCTTTTAAG-CAATATG
* *
409635 ATAAGTCTTTCAAGCAATATG
1 ATAAGCCTTTTAAGCAATATG
*
409656 ATAAGTCTTTTA
1 ATAAGCCTTTTA
409668 GGCCATCTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
19 2 0.05
20 12 0.29
21 24 0.59
22 3 0.07
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.38
Consensus pattern (21 bp):
ATAAGCCTTTTAAGCAATATG
Found at i:409632 original size:41 final size:41
Alignment explanation
Indices: 409528--409680 Score: 157
Period size: 41 Copynumber: 3.7 Consensus size: 41
409518 ATTTCCAAAA
* * * *
409528 ATGAGTAAGTCCTTCAGGTCA-CCAGTAAGTCTTTCGAGC-AT
1 ATGA-TAAGTCCTTTAGGTCATCTA-TAAGCCTTTCAAGCAAT
* * *
409569 GATGATTAAATCATTTAGGTCATCTATAAGCCTTTTAAGCAAT
1 -ATGA-TAAGTCCTTTAGGTCATCTATAAGCCTTTCAAGCAAT
* *
409612 ATGATAAGTCCTTTAGGTCATGTATAAGTCTTTCAAGCAAT
1 ATGATAAGTCCTTTAGGTCATCTATAAGCCTTTCAAGCAAT
* *
409653 ATGATAAGTCTTTTAGGCCATCTATAAG
1 ATGATAAGTCCTTTAGGTCATCTATAAG
409681 ATATTCGGGC
Statistics
Matches: 93, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
41 57 0.61
42 32 0.34
43 4 0.04
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (41 bp):
ATGATAAGTCCTTTAGGTCATCTATAAGCCTTTCAAGCAAT
Found at i:410045 original size:12 final size:12
Alignment explanation
Indices: 410030--410091 Score: 65
Period size: 12 Copynumber: 5.2 Consensus size: 12
410020 AAAACAACAA
410030 AAAGGAAAAAGG
1 AAAGGAAAAAGG
410042 AAAGG-AAAAGG
1 AAAGGAAAAAGG
*
410053 AAAAGGAAAAATG
1 -AAAGGAAAAAGG
*
410066 AAAAGAAAAAGG
1 AAAGGAAAAAGG
* *
410078 AGA-TAAAAAGG
1 AAAGGAAAAAGG
410089 AAA
1 AAA
410092 AAGAATATTA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
11 15 0.36
12 22 0.52
13 5 0.12
ACGTcount: A:0.69, C:0.00, G:0.27, T:0.03
Consensus pattern (12 bp):
AAAGGAAAAAGG
Found at i:410056 original size:24 final size:24
Alignment explanation
Indices: 410029--410074 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
410019 AAAAACAACA
*
410029 AAAAGGAAAAAGGAAAGGAAAAGG
1 AAAAGGAAAAAGGAAAAGAAAAGG
*
410053 AAAAGGAAAAATGAAAAGAAAA
1 AAAAGGAAAAAGGAAAAGAAAA
410075 AGGAGATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (24 bp):
AAAAGGAAAAAGGAAAAGAAAAGG
Found at i:410092 original size:6 final size:6
Alignment explanation
Indices: 410029--410078 Score: 57
Period size: 6 Copynumber: 8.2 Consensus size: 6
410019 AAAAACAACA
* *
410029 AAAAGG AAAAAGG -AAAGG AAAAGG AAAAGG AAAAATG AAAAGA AAAAGG
1 AAAAGG -AAAAGG AAAAGG AAAAGG AAAAGG -AAAAGG AAAAGG AAAAGG
410078 A
1 A
410079 GATAAAAAGG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
5 5 0.14
6 21 0.57
7 11 0.30
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (6 bp):
AAAAGG
Found at i:410104 original size:18 final size:17
Alignment explanation
Indices: 410029--410096 Score: 57
Period size: 18 Copynumber: 3.8 Consensus size: 17
410019 AAAAACAACA
*
410029 AAAAGGAAAAAGGAAAGG
1 AAAAGGAAAAA-GAAATG
*
410047 AAAAGGAAAAGGAAAAATG
1 AAAAGGAAAA--AGAAATG
* *
410066 AAAA-GAAAAAGGAGATA
1 AAAAGGAAAAA-GAAATG
410083 AAAAGGAAAAAGAA
1 AAAAGGAAAAAGAA
410097 TATTAAAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
16 1 0.03
17 9 0.22
18 21 0.52
19 8 0.20
20 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.03
Consensus pattern (17 bp):
AAAAGGAAAAAGAAATG
Found at i:428565 original size:10 final size:10
Alignment explanation
Indices: 428536--429280 Score: 321
Period size: 10 Copynumber: 75.0 Consensus size: 10
428526 TTTTTATACA
*
428536 ATATAGTATT
1 ATATATTATT
428546 ATA-ATATATT
1 ATATAT-TATT
428556 ATATATTATT
1 ATATATTATT
*
428566 -TCATA-TAGT
1 AT-ATATTATT
*
428575 ATATGTTA-T
1 ATATATTATT
*
428584 ATAGTATGGTACT
1 ATA-TAT--TATT
**
428597 ATATAGCA-T
1 ATATATTATT
* *
428606 ATATAATATA
1 ATATATTATT
428616 ATAT-TTATAT
1 ATATATTAT-T
428626 AGTATATTATT
1 A-TATATTATT
428637 ATATAGTATATT
1 ATATA-T-TATT
428649 ATTATATATATT
1 A-TATAT-TATT
428661 ATAGTATTA-T
1 ATA-TATTATT
428671 AT-TA-TATT
1 ATATATTATT
428679 ATAT-TATATT
1 ATATAT-TATT
428689 ATATATTA-T
1 ATATATTATT
428698 ATTATATTATATT
1 A-TATA-T-TATT
428711 ATATATTA-T
1 ATATATTATT
428720 ATTATATATATT
1 A-TATAT-TATT
428732 ATATA-TA-T
1 ATATATTATT
428740 ATTATATTATT
1 A-TATATTATT
428751 ATATTATATATAT
1 ATA-TAT-TAT-T
428764 ATATATTA-T
1 ATATATTATT
428773 ATTATATTA-T
1 A-TATATTATT
428783 ATTATATTA-T
1 A-TATATTATT
428793 ATTATATTA-T
1 A-TATATTATT
428803 ATTATATTA-T
1 A-TATATTATT
428813 ATTATATTA-T
1 A-TATATTATT
428823 ATTATATTA-T
1 A-TATATTATT
428833 ATTATATTA-T
1 A-TATATTATT
428843 ATTATATTA-T
1 A-TATATTATT
428853 ATTATATTA-T
1 A-TATATTATT
428863 ATTATATTA-T
1 A-TATATTATT
428873 ATTATATTA-T
1 A-TATATTATT
428883 ATTATATTA-T
1 A-TATATTATT
428893 ATTATATTA-T
1 A-TATATTATT
428903 ATTATATTA-T
1 A-TATATTATT
428913 ATTATATATATT
1 A-TATAT-TATT
428925 ATATATTA-T
1 ATATATTATT
428934 ATATATTA-T
1 ATATATTATT
428943 ATTATATTA-T
1 A-TATATTATT
428953 ATTATATTA-T
1 A-TATATTATT
428963 ATTATATTA-T
1 A-TATATTATT
428973 ATATATATATT
1 ATATAT-TATT
428984 ATTATATTTATT
1 A-TATA-TTATT
428996 ATAT-TATATT
1 ATATAT-TATT
429006 ATAT-TATATT
1 ATATAT-TATT
429016 ATAT-TATATT
1 ATATAT-TATT
429026 ATAT-TATATT
1 ATATAT-TATT
429036 ATAT-TATATT
1 ATATAT-TATT
429046 ATAT-TATATT
1 ATATAT-TATT
429056 ATAT-TATATT
1 ATATAT-TATT
429066 AT-TA-TATT
1 ATATATTATT
429074 ATAT-TATATT
1 ATATAT-TATT
429084 ATAT-TATATT
1 ATATAT-TATT
429094 ATATATTA-T
1 ATATATTATT
429103 AT-TA-TATT
1 ATATATTATT
429111 ATATA-TA-T
1 ATATATTATT
429119 -TATATTA-T
1 ATATATTATT
429127 ATATATTATT
1 ATATATTATT
429137 ATATTATTA-T
1 ATA-TATTATT
429147 ATTATATATATT
1 A-TATAT-TATT
429159 ATAT-TATATT
1 ATATAT-TATT
429169 ATAT-TATATT
1 ATATAT-TATT
* *
429179 ATATGTTCTCGT
1 ATATATTAT--T
429191 -TAT-TTATT
1 ATATATTATT
429199 ATAGTA-TA-T
1 ATA-TATTATT
*
429208 ATAT-TTAAT
1 ATATATTATT
429217 ATATATTA-T
1 ATATATTATT
*
429226 ATTATATTATA
1 A-TATATTATT
*
429237 ACATA-T-TT
1 ATATATTATT
*
429245 AAAT-TATATT
1 ATATAT-TATT
429255 ATATATTATT
1 ATATATTATT
429265 -TAT-TTATT
1 ATATATTATT
429273 -TAT-TTATT
1 ATATATTATT
429281 TAATAATTTC
Statistics
Matches: 644, Mismatches: 18, Indels: 148
0.80 0.02 0.18
Matches are distributed among these distances:
7 8 0.01
8 43 0.07
9 85 0.13
10 383 0.59
11 59 0.09
12 51 0.08
13 15 0.02
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (10 bp):
ATATATTATT
Found at i:428673 original size:5 final size:5
Alignment explanation
Indices: 428605--429258 Score: 843
Period size: 5 Copynumber: 131.0 Consensus size: 5
428595 CTATATAGCA
* * * *
428605 TATAT AATAT AATAT T-TA- TATAG TATAT TAT-T ATATAG TATAT TATTAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT -TATAT TATAT TA-TAT
*
428654 ATATAT TATA- -GTAT TATAT TATAT TATAT TATATT ATATAT TATAT
1 -TATAT TATAT TATAT TATAT TATAT TATAT TATA-T -TATAT TATAT
428700 TATAT TATATT ATATAT TATAT TATA- TATAT TATAT ATATAT TATA-
1 TATAT TATA-T -TATAT TATAT TATAT TATAT TATAT -TATAT TATAT
428746 T-TAT TATAT TATA- TATAT ATATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT -TATAT TATAT TATAT TATAT TATAT TATAT
428795 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
428845 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
428895 TATAT TATAT TATAT TATAT TATA- TATAT TATA- TATTAT ATATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TA-TAT -TATAT TATAT
428945 TATAT TATAT TATAT TATAT TATAT TATA- TATAT ATATTAT TATAT T-TAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT -TA-TAT TATAT TATAT
428995 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
429045 TATAT TATAT TATAT TATA- T-TAT TATAT TATAT TATAT TATAT TATATT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA-T
429094 ATATAT TATAT TATAT TATA- TATAT TATAT TATA- TATAT TAT-T ATATTAT
1 -TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT -TA-TAT
*
429144 TATAT TATA- TATAT TATAT TATAT TATAT TATAT TATAT GT-TCT CGT-TAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT -TATAT --TATAT
* * *
429194 T-TAT TATAG TATA- TATAT T-TAAT ATATAT TATAT TATAT TATAA CATATT
1 TATAT TATAT TATAT TATAT TAT-AT -TATAT TATAT TATAT TATAT TATA-T
*
429244 TAAAT TATAT TATAT
1 TATAT TATAT TATAT
429259 ATTATTTATT
Statistics
Matches: 589, Mismatches: 16, Indels: 88
0.85 0.02 0.13
Matches are distributed among these distances:
3 7 0.01
4 54 0.09
5 465 0.79
6 42 0.07
7 21 0.04
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:431463 original size:16 final size:16
Alignment explanation
Indices: 431442--431475 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
431432 CGGGTAGTAA
431442 TAAAAAACATGTGAGG
1 TAAAAAACATGTGAGG
* *
431458 TAAAAATCATGTGGGG
1 TAAAAAACATGTGAGG
431474 TA
1 TA
431476 GGAATTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.26, T:0.24
Consensus pattern (16 bp):
TAAAAAACATGTGAGG
Found at i:432405 original size:21 final size:21
Alignment explanation
Indices: 432379--432425 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
432369 CGAAGACCAG
*
432379 CCACCCGCCAGTGTCAAACCT
1 CCACCCGCCAGTGCCAAACCT
432400 CCACCCGCCAGTGCCAAACCT
1 CCACCCGCCAGTGCCAAACCT
432421 CCACC
1 CCACC
432426 TAGACCGCCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.23, C:0.53, G:0.13, T:0.11
Consensus pattern (21 bp):
CCACCCGCCAGTGCCAAACCT
Found at i:433116 original size:4 final size:4
Alignment explanation
Indices: 433103--433136 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
433093 TTTTTGGACC
*
433103 TAAA -AAA TAAA TAAA CAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
433137 GTATATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (4 bp):
TAAA
Found at i:433269 original size:37 final size:36
Alignment explanation
Indices: 433231--433383 Score: 204
Period size: 37 Copynumber: 4.2 Consensus size: 36
433221 TTTCAAAATG
* *
433231 TTTTCAAAAA-TATTTTCTAAACTATATATTATATATG
1 TTTTCAAAAATTATTTTCAAAACTATATA--ATATATA
*
433268 TTTTCAAAAATTGTTTTCAAAACTATAT-A-ATATA
1 TTTTCAAAAATTATTTTCAAAACTATATAATATATA
* *
433302 TTTTCAAAAAATATTTTCAAATCTATATAATATATA
1 TTTTCAAAAATTATTTTCAAAACTATATAATATATA
*
433338 TTTTCAAAAAATTCTTTTCAAAACTATATAATATATA
1 TTTTC-AAAAATTATTTTCAAAACTATATAATATATA
433375 TTTTCAAAA
1 TTTTCAAAA
433384 CTATATAATA
Statistics
Matches: 103, Mismatches: 9, Indels: 9
0.85 0.07 0.07
Matches are distributed among these distances:
34 29 0.28
35 2 0.02
36 14 0.14
37 43 0.42
38 15 0.15
ACGTcount: A:0.44, C:0.09, G:0.01, T:0.45
Consensus pattern (36 bp):
TTTTCAAAAATTATTTTCAAAACTATATAATATATA
Found at i:433308 original size:71 final size:72
Alignment explanation
Indices: 433231--433383 Score: 224
Period size: 71 Copynumber: 2.1 Consensus size: 72
433221 TTTCAAAATG
* *
433231 TTTTCAAAAATATTTTCTAAA-CTATATATTATATATGTTTTC-AAAAATTGTTTTCAAAACTAT
1 TTTTCAAAAATATTTTC-AAATCTATATA--ATATATATTTTCAAAAAATTCTTTTCAAAACTAT
433294 AT-A-ATATA
63 ATAATATATA
433302 TTTTCAAAAAATATTTTCAAATCTATATAATATATATTTTCAAAAAATTCTTTTCAAAACTATAT
1 TTTTC-AAAAATATTTTCAAATCTATATAATATATATTTTCAAAAAATTCTTTTCAAAACTATAT
433367 AATATATA
65 AATATATA
433375 TTTTCAAAA
1 TTTTCAAAA
433384 CTATATAATA
Statistics
Matches: 75, Mismatches: 2, Indels: 9
0.87 0.02 0.10
Matches are distributed among these distances:
70 11 0.15
71 30 0.40
72 24 0.32
73 10 0.13
ACGTcount: A:0.44, C:0.09, G:0.01, T:0.45
Consensus pattern (72 bp):
TTTTCAAAAATATTTTCAAATCTATATAATATATATTTTCAAAAAATTCTTTTCAAAACTATATA
ATATATA
Found at i:433380 original size:60 final size:59
Alignment explanation
Indices: 433312--433498 Score: 222
Period size: 60 Copynumber: 3.2 Consensus size: 59
433302 TTTTCAAAAA
*
433312 ATATTTTCAAATCTATATAATATATATTTTCAAAAAATTCTTTTCAAAACTATATAATAT
1 ATATTTTCAAATCTATATAATATATATTTTCAAAAAATTATTTTCAAAACTATAT-ATAT
* *
433372 ATATTTTCAAAACTATATAATATATATTTTCAAAAAATTATTTTC-AAATTATATA-AT
1 ATATTTTCAAATCTATATAATATATATTTTCAAAAAATTATTTTCAAAACTATATATAT
* * *** *
433429 ATGTTTTCAAAAT-TATATAATATATGTGTTT--AAATCGTATTTTCAAAACCATATTATAT
1 ATATTTTC-AAATCTATATAATATATAT-TTTCAAAAAATTATTTTCAAAACTATA-TATAT
433488 ATATTTTCAAA
1 ATATTTTCAAA
433499 AATCAATTTT
Statistics
Matches: 110, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
56 10 0.09
57 28 0.25
58 12 0.11
59 17 0.15
60 43 0.39
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.45
Consensus pattern (59 bp):
ATATTTTCAAATCTATATAATATATATTTTCAAAAAATTATTTTCAAAACTATATATAT
Found at i:433408 original size:25 final size:23
Alignment explanation
Indices: 433352--433406 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
433342 CAAAAAATTC
433352 TTTTCAAAACTATATAATATATA
1 TTTTCAAAACTATATAATATATA
433375 TTTTCAAAACTATATAATATATA
1 TTTTCAAAACTATATAATATATA
433398 TTTTCAAAA
1 TTTTCAAAA
433407 AATTATTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (23 bp):
TTTTCAAAACTATATAATATATA
Found at i:433437 original size:20 final size:21
Alignment explanation
Indices: 433412--433451 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
433402 CAAAAAATTA
433412 TTTTC-AAATTATATAATATG
1 TTTTCAAAATTATATAATATG
433432 TTTTCAAAATTATATAATAT
1 TTTTCAAAATTATATAATAT
433452 ATGTGTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (21 bp):
TTTTCAAAATTATATAATATG
Found at i:433502 original size:38 final size:37
Alignment explanation
Indices: 433460--433603 Score: 111
Period size: 38 Copynumber: 3.9 Consensus size: 37
433450 ATATGTGTTT
*
433460 AAATCGTATTTTCAAAACCATATTATATATATTTTCAA
1 AAATC-TATTTTCAAAACTATATTATATATATTTTCAA
* * *
433498 AAATCAATTTTTTAAAACTATA-TATTATATGTTTTCAA
1 AAATCTA-TTTTCAAAACTATATTA-TATATATTTTCAA
* * * *
433536 TAACCGT-TTTCTAAAAACTATATGT-TATACATTTTCAA
1 AAATC-TATTT-TCAAAACTATAT-TATATATATTTTCAA
433574 AAA--TATTTTCAAAAACTATATTATAT-TATT
1 AAATCTATTTTC-AAAACTATATTATATATATT
433604 ATATATTGAA
Statistics
Matches: 84, Mismatches: 13, Indels: 21
0.71 0.11 0.18
Matches are distributed among these distances:
35 6 0.07
36 16 0.19
37 6 0.07
38 55 0.65
40 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.44
Consensus pattern (37 bp):
AAATCTATTTTCAAAACTATATTATATATATTTTCAA
Found at i:434266 original size:201 final size:201
Alignment explanation
Indices: 433914--434279 Score: 561
Period size: 201 Copynumber: 1.8 Consensus size: 201
433904 TCTTGTTTCC
* **
433914 AAATCGTAGTCAACCTTGGTCTTCTTCTCGGTTTAAAGACCTCAATTTAAGCTTCAACCAGAAAC
1 AAATCGCAGTCAACCCAGGTCTTCTTCTCGGTTTAAAGACCTCAATTTAAGCTTCAACCAGAAAC
* * * * * *
433979 TAGTTCCTCGCTACTACCATGCGGTTGATATGTCATTGAGCTTAATGGAATCAAACTCGAAAGTT
66 TAGTTCATCGCTACTACCATGCAGTTAATATGCCATCGAGCTGAATGGAATCAAACTCGAAAGTT
* * * *
434044 TTTGTTAACAGATAGCCCTTCTCGCCTTGAGCTATGTTGTGAATTTGACTGGGATATAGTTCCTT
131 TTTATCAACAGATAGCCCTTCTCGCATTGAACTATGTTGTGAATTTGACTGGGATATAGTTCCTT
434109 ATTGCT
196 ATTGCT
* * * * *
434115 AAATCGCAGTCAACCCAGGTCTTCTTCTTGGTTTAAAGACCTCAGTTTAAGCTTCAATCGGAAAG
1 AAATCGCAGTCAACCCAGGTCTTCTTCTCGGTTTAAAGACCTCAATTTAAGCTTCAACCAGAAAC
434180 TAGTTCATCGCTACTACCATGCAGTTAATATGCCATCGAGCTGAATGGAATCAAACTCGAAAGTT
66 TAGTTCATCGCTACTACCATGCAGTTAATATGCCATCGAGCTGAATGGAATCAAACTCGAAAGTT
*
434245 TTTATCGACAGATAGCCCTTCTCGCATTGAACTAT
131 TTTATCAACAGATAGCCCTTCTCGCATTGAACTAT
434280 ACTATAATAG
Statistics
Matches: 146, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
201 146 1.00
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.33
Consensus pattern (201 bp):
AAATCGCAGTCAACCCAGGTCTTCTTCTCGGTTTAAAGACCTCAATTTAAGCTTCAACCAGAAAC
TAGTTCATCGCTACTACCATGCAGTTAATATGCCATCGAGCTGAATGGAATCAAACTCGAAAGTT
TTTATCAACAGATAGCCCTTCTCGCATTGAACTATGTTGTGAATTTGACTGGGATATAGTTCCTT
ATTGCT
Found at i:434679 original size:186 final size:184
Alignment explanation
Indices: 434342--434890 Score: 736
Period size: 186 Copynumber: 3.0 Consensus size: 184
434332 ATGAAACTTA
* * * *
434342 AGTCAATTCATTTGGGCATGATATCCTTATTCGTGAATTTGAAATCGCGGATGGCTCCTTCATTT
1 AGTCAATTCATTTGGGCATGATAT-CTTCTTCGTGAAATTGAAATCGTGGATGGCTCCTTCATTG
* * * *
434407 TGAAGTTGAGCTTTGAATTGGATGTCCTTCGTTGTGAAGTTGAAATCCAATCTCGAGCTATAATG
65 TGAAGTTGAGCTTTGAATTGGATGTTCTTCGTTGTGAAGTTGAAATCCAAT-TCGAGTTGTAGTG
* *
434472 CTTCGCCAAATTGTCTTTGGGTTTGATATCCTTCATTGTGAAGTTTAAATCCAATC
129 CTTCGCCAAATTGGCTTTGGGTTTGATATCCTTCATTGTGAAGTTAAAATCCAATC
* * ** * **
434528 AGTCAATCCATTTGGGCACGATATCATTCTTTATGAAATTGAAATCGTGTATGGCTCCTTCGCTG
1 AGTCAATTCATTTGGGCATGATATC-TTCTTCGTGAAATTGAAATCGTGGATGGCTCCTTCATTG
* *
434593 TGAAGTTGAGCTTTGAATTGGATGTTCTTCGTTGTGAAGTTGAAATCCAATATCGAATTGTAGTA
65 TGAAGTTGAGCTTTGAATTGGATGTTCTTCGTTGTGAAGTTGAAATCCAAT-TCGAGTTGTAGTG
* * *
434658 CTTCGCAAAATTGGATTTGGG-TTG-GA----T-ATTGTGAAGTTAAAATCCAATC
129 CTTCGCCAAATTGGCTTTGGGTTTGATATCCTTCATTGTGAAGTTAAAATCCAATC
* *
434707 AGTCAATTCATTTGGGCATGATATCTTCTTCGTGAAGTTGAAATCGTGGATGGCTTCTTCATTGT
1 AGTCAATTCATTTGGGCATGATATCTTCTTCGTGAAATTGAAATCGTGGATGGCTCCTTCATTGT
* * *
434772 GTAGTTCAACTTTGAATTGGATG-TCATTCGTTGTGAAGTTGAAATCCAATTCGAGTTGTAGTGC
66 GAAGTTGAGCTTTGAATTGGATGTTC-TTCGTTGTGAAGTTGAAATCCAATTCGAGTTGTAGTGC
* *
434836 TTCGCCAAATTGGCTTTGGGTTAGATATCCTTCATTGTGAAGTTGAAATCCAATC
130 TTCGCCAAATTGGCTTTGGGTTTGATATCCTTCATTGTGAAGTTAAAATCCAATC
434891 TTGTATAAGT
Statistics
Matches: 312, Mismatches: 42, Indels: 20
0.83 0.11 0.05
Matches are distributed among these distances:
177 32 0.10
178 79 0.25
179 45 0.14
180 1 0.00
183 1 0.00
184 22 0.07
185 4 0.01
186 128 0.41
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (184 bp):
AGTCAATTCATTTGGGCATGATATCTTCTTCGTGAAATTGAAATCGTGGATGGCTCCTTCATTGT
GAAGTTGAGCTTTGAATTGGATGTTCTTCGTTGTGAAGTTGAAATCCAATTCGAGTTGTAGTGCT
TCGCCAAATTGGCTTTGGGTTTGATATCCTTCATTGTGAAGTTAAAATCCAATC
Found at i:439782 original size:22 final size:22
Alignment explanation
Indices: 439757--439800 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
439747 AGGCTCCCTA
**
439757 TTGGGGCCGTTTTCGATTATTT
1 TTGGGGCCGTTCCCGATTATTT
*
439779 TTGGGGTCGTTCCCGATTATTT
1 TTGGGGCCGTTCCCGATTATTT
439801 CGGGGTCATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.48
Consensus pattern (22 bp):
TTGGGGCCGTTCCCGATTATTT
Found at i:439807 original size:21 final size:22
Alignment explanation
Indices: 439770--439812 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
439760 GGGCCGTTTT
* *
439770 CGATTATTTTTGGGGTCGTTCC
1 CGATTATTTTCGGGGTCATTCC
439792 CGATTA-TTTCGGGGTCATTCC
1 CGATTATTTTCGGGGTCATTCC
439813 TGATCATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.12, C:0.21, G:0.26, T:0.42
Consensus pattern (22 bp):
CGATTATTTTCGGGGTCATTCC
Found at i:440120 original size:12 final size:11
Alignment explanation
Indices: 440070--440111 Score: 66
Period size: 12 Copynumber: 3.6 Consensus size: 11
440060 TTTTTGGACC
440070 TAAAAAATAAA
1 TAAAAAATAAA
440081 TAAACAAATAAA
1 TAAA-AAATAAA
440093 TAAAAAATAAAA
1 TAAAAAAT-AAA
440105 TAAAAAA
1 TAAAAAA
440112 GTATATAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 8 0.28
12 21 0.72
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (11 bp):
TAAAAAATAAA
Found at i:440277 original size:36 final size:36
Alignment explanation
Indices: 440205--440418 Score: 333
Period size: 36 Copynumber: 5.9 Consensus size: 36
440195 TTTCAAAATG
* *
440205 TTTTCAAAAA-TGTTTTTCTAAACTATATATTATATATG
1 TTTTCAAAAATTG-TTTTCAAAACTATATA--ATATATA
440243 TTTTCAAAAATTGTTTTCAAAACTATATAATATATA
1 TTTTCAAAAATTGTTTTCAAAACTATATAATATATA
* * *
440279 TTTTCAAAAATTATTTTCAAAACAATATATTATATA
1 TTTTCAAAAATTGTTTTCAAAACTATATAATATATA
440315 TTTTCAAAAATTGTTTTCAAAACTATATAATATATA
1 TTTTCAAAAATTGTTTTCAAAACTATATAATATATA
*
440351 TTTTCAAAAATTATTTTCAAAACTATAT-ATATATA
1 TTTTCAAAAATTGTTTTCAAAACTATATAATATATA
440386 TTTTCAAAAATTGTTTTCAAAACTATATAATAT
1 TTTTCAAAAATTGTTTTCAAAACTATATAATAT
440419 GTTTTCAAAA
Statistics
Matches: 164, Mismatches: 10, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
35 34 0.21
36 103 0.63
38 25 0.15
39 2 0.01
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.46
Consensus pattern (36 bp):
TTTTCAAAAATTGTTTTCAAAACTATATAATATATA
Found at i:440295 original size:13 final size:13
Alignment explanation
Indices: 440277--440372 Score: 55
Period size: 13 Copynumber: 7.8 Consensus size: 13
440267 ATATAATATA
440277 TATTTTCAAAAAT
1 TATTTTCAAAAAT
*
440290 TATTTTCAAAACAA
1 TATTTTCAAAA-AT
* *
440304 TATATT---ATA-
1 TATTTTCAAAAAT
440313 TATTTTCAAAAAT
1 TATTTTCAAAAAT
* *
440326 TGTTTTC-AAAAC
1 TATTTTCAAAAAT
* *
440338 TA-TAT--AATAT
1 TATTTTCAAAAAT
440348 ATATTTTCAAAAAT
1 -TATTTTCAAAAAT
440362 TATTTTCAAAA
1 TATTTTCAAAA
440373 CTATATATAT
Statistics
Matches: 61, Mismatches: 13, Indels: 18
0.66 0.14 0.20
Matches are distributed among these distances:
9 5 0.08
10 4 0.07
11 5 0.08
12 9 0.15
13 28 0.46
14 10 0.16
ACGTcount: A:0.46, C:0.08, G:0.01, T:0.45
Consensus pattern (13 bp):
TATTTTCAAAAAT
Found at i:440338 original size:72 final size:72
Alignment explanation
Indices: 440205--440418 Score: 369
Period size: 72 Copynumber: 3.0 Consensus size: 72
440195 TTTCAAAATG
*
440205 TTTTCAAAAATGT-TTTTCTAAACTATATATTATATATGTTTTCAAAAATTGTTTTCAAAACTAT
1 TTTTCAAAAAT-TATTTTCAAAACTATATATTATATA--TTTTCAAAAATTGTTTTCAAAACTAT
440269 ATAATATATA
63 ATAATATATA
*
440279 TTTTCAAAAATTATTTTCAAAACAATATATTATATATTTTCAAAAATTGTTTTCAAAACTATATA
1 TTTTCAAAAATTATTTTCAAAACTATATATTATATATTTTCAAAAATTGTTTTCAAAACTATATA
440344 ATATATA
66 ATATATA
440351 TTTTCAAAAATTATTTTCAAAACTATATA-TATATATTTTCAAAAATTGTTTTCAAAACTATATA
1 TTTTCAAAAATTATTTTCAAAACTATATATTATATATTTTCAAAAATTGTTTTCAAAACTATATA
440415 ATAT
66 ATAT
440419 GTTTTCAAAA
Statistics
Matches: 136, Mismatches: 3, Indels: 5
0.94 0.02 0.03
Matches are distributed among these distances:
71 39 0.29
72 64 0.47
73 1 0.01
74 32 0.24
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.46
Consensus pattern (72 bp):
TTTTCAAAAATTATTTTCAAAACTATATATTATATATTTTCAAAAATTGTTTTCAAAACTATATA
ATATATA
Found at i:440423 original size:21 final size:22
Alignment explanation
Indices: 440397--440446 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
440387 TTTCAAAAAT
440397 TGTTTTCAAAACTATATA-ATA
1 TGTTTTCAAAACTATATAGATA
*
440418 TGTTTTCAAAATTATATAGTATA
1 TGTTTTCAAAACTATATAG-ATA
440441 TGTTTT
1 TGTTTT
440447 ATATCGTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 17 0.65
23 9 0.35
ACGTcount: A:0.36, C:0.06, G:0.08, T:0.50
Consensus pattern (22 bp):
TGTTTTCAAAACTATATAGATA
Found at i:440428 original size:92 final size:95
Alignment explanation
Indices: 440326--440524 Score: 244
Period size: 92 Copynumber: 2.1 Consensus size: 95
440316 TTTCAAAAAT
* *
440326 TGTTTTCAAAACTATATAATATATATTTTCAAAAATTATTTTCAAAACTATA-TATATATATTTT
1 TGTTTTCAAAACTATATAATATATATTTT-AAAAAGTATTTTCAAAACCATATTATATATATTTT
440390 C-AAA-AATTGTTTTCAAAACTATATA-ATA
65 CAAAATAATTGTTTTCAAAACTATATATATA
* * * * **
440418 TGTTTTCAAAATTATATAGTATATGTTTTATATCGTATTTTCAAAACCATATTATATATATTTTC
1 TGTTTTCAAAACTATATAATATATATTTTAAAAAGTATTTTCAAAACCATATTATATATATTTTC
* *
440483 AAAATCTAATTTTTTTTAAAACTATATATTATA
66 AAAA--TAATTGTTTTCAAAACTATATA-TATA
440516 TGTTTTCAA
1 TGTTTTCAA
440525 TAATCGTTTT
Statistics
Matches: 90, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
91 17 0.19
92 39 0.43
93 3 0.03
96 19 0.21
98 12 0.13
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.48
Consensus pattern (95 bp):
TGTTTTCAAAACTATATAATATATATTTTAAAAAGTATTTTCAAAACCATATTATATATATTTTC
AAAATAATTGTTTTCAAAACTATATATATA
Found at i:446117 original size:13 final size:13
Alignment explanation
Indices: 446101--446167 Score: 102
Period size: 13 Copynumber: 5.3 Consensus size: 13
446091 TTCTGGAAAA
*
446101 CATTTCTTCCTTT
1 CATTTCTTCATTT
446114 CATTTCTTCATTT
1 CATTTCTTCATTT
446127 CATTTCTT--TTT
1 CATTTCTTCATTT
*
446138 CATTTCTTCCTTT
1 CATTTCTTCATTT
446151 CATTTCTTCATTT
1 CATTTCTTCATTT
446164 CATT
1 CATT
446168 ATTATATCAT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
11 11 0.22
13 39 0.78
ACGTcount: A:0.12, C:0.25, G:0.00, T:0.63
Consensus pattern (13 bp):
CATTTCTTCATTT
Found at i:451008 original size:15 final size:15
Alignment explanation
Indices: 450988--451043 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
450978 ATATAACATA
450988 TATTATATAGTATGG
1 TATTATATAGTATGG
*
451003 TATTATATAGCATAT-A
1 TATTATATAG--TATGG
*
451019 TAGTATATAGTATGG
1 TATTATATAGTATGG
451034 TATTATATAG
1 TATTATATAG
451044 CATATATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 3 0.09
15 19 0.56
16 9 0.26
17 3 0.09
ACGTcount: A:0.38, C:0.02, G:0.16, T:0.45
Consensus pattern (15 bp):
TATTATATAGTATGG
Found at i:451020 original size:31 final size:31
Alignment explanation
Indices: 450985--451113 Score: 148
Period size: 31 Copynumber: 4.4 Consensus size: 31
450975 TTCATATAAC
450985 ATATATTATATAGTATGGTATTATATAGCAT
1 ATATATTATATAGTATGGTATTATATAGCAT
*
451016 ATATAGTATATAGTATGGTATTATATAGCAT
1 ATATATTATATAGTATGGTATTATATAGCAT
*
451047 ATATATTATA-A-TA---T-TTATATAGTAT
1 ATATATTATATAGTATGGTATTATATAGCAT
**
451072 ATA-ATTATATAGTATAATATTATATA-CATT
1 ATATATTATATAGTATGGTATTATATAGCA-T
451102 ATAGTATTATAT
1 ATA-TATTATAT
451114 TAATATTATA
Statistics
Matches: 85, Mismatches: 4, Indels: 17
0.80 0.04 0.16
Matches are distributed among these distances:
24 6 0.07
25 14 0.16
26 3 0.04
29 4 0.05
30 12 0.14
31 39 0.46
32 7 0.08
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (31 bp):
ATATATTATATAGTATGGTATTATATAGCAT
Found at i:451050 original size:55 final size:54
Alignment explanation
Indices: 450991--451119 Score: 145
Period size: 55 Copynumber: 2.4 Consensus size: 54
450981 TAACATATAT
** **
450991 TATATAGTATGGTA-TTATATAGCATATATAGTATATAGTATGGTATTATATAGCA
1 TATATAGTATAATATTTATATAGCATATA-AGTATATAGTATAATATTATATA-CA
* * *
451046 TATATATTATAATATTTATATAGTATATAATTATATAGTATAATATTATATACA
1 TATATAGTATAATATTTATATAGCATATAAGTATATAGTATAATATTATATACA
* *
451100 T-TATAGTATTATATTAATAT
1 TATATAGTATAATATTTATAT
451120 TATATTATAT
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
53 16 0.25
54 3 0.05
55 31 0.49
56 13 0.21
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (54 bp):
TATATAGTATAATATTTATATAGCATATAAGTATATAGTATAATATTATATACA
Found at i:451096 original size:5 final size:5
Alignment explanation
Indices: 451048--451273 Score: 110
Period size: 5 Copynumber: 46.6 Consensus size: 5
451038 ATATAGCATA
* *
451048 TATAT TATAA TAT-T TATA- TAGTA- TATAAT TATA- TAGTAT AATAT
1 TATAT TATAT TATAT TATAT TA-TAT TAT-AT TATAT TA-TAT TATAT
* *
451092 TATA- TACAT TATA- -GTAT TATAT TAATAT TATATT ATATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT T-ATAT TATA-T -TATAT TATAT
* *
451137 GT-TA- TATAT TATAG TATA- TATAT T-TAT TATAG TATATT TATAT TATA-
1 -TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA-T TATAT TATAT
* * * *
451184 TGTAT TATAC TATA- TATAT TATAG TATA- TATAT T-TAT TATGTAT TGTAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TA--TAT TATAT
* * *
451233 TGTAG TATATT TAAAT TATAT TATA- TATA- TATAT TAT-T TAT
1 TATAT TATA-T TATAT TATAT TATAT TATAT TATAT TATAT TAT
451274 TTAATCATTT
Statistics
Matches: 174, Mismatches: 21, Indels: 53
0.70 0.08 0.21
Matches are distributed among these distances:
3 3 0.02
4 48 0.28
5 96 0.55
6 19 0.11
7 8 0.05
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (5 bp):
TATAT
Found at i:451145 original size:14 final size:13
Alignment explanation
Indices: 451057--451269 Score: 106
Period size: 14 Copynumber: 16.2 Consensus size: 13
451047 ATATATTATA
451057 ATATTTATATAGTAT
1 ATATTTATATA-T-T
* *
451072 ATAATTATATAGT
1 ATATTTATATATT
*
451085 ATA-ATAT-TA-T
1 ATATTTATATATT
*
451095 ATACATTATAGTATT
1 ATA-TTTATA-TATT
451110 ATA-TTA-ATATT
1 ATATTTATATATT
451121 ATA-TTATATATT
1 ATATTTATATATT
451133 ATATGTTATATATT
1 ATAT-TTATATATT
*
451147 ATAGTATATATATT
1 ATA-TTTATATATT
451161 -TATTATAGTATATTT
1 ATATT-TA-TATA-TT
*
451176 ATATTATATGTATT
1 ATATT-TATATATT
*
451190 ATACTATATATATT
1 ATA-TTTATATATT
*
451204 ATAGTATATATATT
1 ATA-TTTATATATT
*
451218 -TA-TTATGTATT
1 ATATTTATATATT
*
451229 GTATTGTAGTATATT
1 ATATT-TA-TATATT
**
451244 -TAAAT-TATATT
1 ATATTTATATATT
*
451255 ATATATATATATT
1 ATATTTATATATT
451268 AT
1 AT
451270 TTATTTAATC
Statistics
Matches: 162, Mismatches: 16, Indels: 42
0.74 0.07 0.19
Matches are distributed among these distances:
10 4 0.02
11 25 0.15
12 22 0.14
13 23 0.14
14 55 0.34
15 26 0.16
16 7 0.04
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.54
Consensus pattern (13 bp):
ATATTTATATATT
Found at i:451200 original size:69 final size:67
Alignment explanation
Indices: 451045--451269 Score: 184
Period size: 69 Copynumber: 3.3 Consensus size: 67
451035 ATTATATAGC
** *
451045 ATATATATTATA-ATAT-TTATATAGTATATA-A-TTA-TATAGTATAATATTATA-TACATTAT
1 ATAT-TATTATATATATATTATATAGTATATATATTTATTATA-TATTGTATTATAGTATATT-T
*
451104 AGTATT
63 A-AATT
451110 ATATTAATATTATATTATATATTATAT-GT-TATATATTATAGTATATATATT-TATTATAGTAT
1 ATA-T--TATTATA-TATATATTATATAGTATATATATT-TA-T-TATATATTGTATTATAGTAT
*
451172 ATTTATATT
59 ATTTAAATT
* *
451181 ATATGTATTATACTATATA-TATTATAGTATATATATTTATTATGTATTGTATTGTAGTATATTT
1 ATAT-TATTATA-TATATATTA-TATAGTATATATATTTATTATATATTGTATTATAGTATATTT
451245 AAATT
63 AAATT
451250 ATATTA-TATATATATATTAT
1 ATATTATTATATATATATTAT
451270 TTATTTAATC
Statistics
Matches: 136, Mismatches: 7, Indels: 33
0.77 0.04 0.19
Matches are distributed among these distances:
65 3 0.02
66 8 0.06
67 14 0.10
68 15 0.11
69 46 0.34
70 12 0.09
71 17 0.12
72 9 0.07
73 8 0.06
74 4 0.03
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.53
Consensus pattern (67 bp):
ATATTATTATATATATATTATATAGTATATATATTTATTATATATTGTATTATAGTATATTTAAA
TT
Found at i:451217 original size:57 final size:56
Alignment explanation
Indices: 451057--451269 Score: 118
Period size: 57 Copynumber: 3.9 Consensus size: 56
451047 ATATATTATA
* *
451057 ATATTTA-TATAGTATATAATTATA-TAGTATA--ATATTATATACATTATAGTAT-T
1 ATATTTATTATAGTATAT-ATTATATTA-TATATTATATGATATATATTATAGTATAT
* *
451110 ATATTAATATTATATTATATATTATATGTTATATATTATA-GTATATATATT-TATTATAGT
1 ATATT--TATTATAGTATATATTATA--TTATATATTATATG-ATATATATTATAGTATA-T
*
451170 ATATTTA-TATTA-TATGTATTATACTATATATATTATA-GTATATATATT-TA-T-TAT
1 ATATTTATTA-TAGTATATATTATA-T-TATATATTATATG-ATATATATTATAGTATAT
* * *
451224 GTATTGTATTGTAGTATAT-TTA-AAT-TATATTATAT-ATATATATTAT
1 ATATT-TATTATAGTATATATTATATTATATATTATATGATATATATTAT
451270 TTATTTAATC
Statistics
Matches: 132, Mismatches: 10, Indels: 38
0.73 0.06 0.21
Matches are distributed among these distances:
50 9 0.07
51 10 0.08
52 1 0.01
53 5 0.04
54 6 0.05
55 17 0.13
56 16 0.12
57 40 0.30
58 11 0.08
59 11 0.08
60 6 0.05
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.54
Consensus pattern (56 bp):
ATATTTATTATAGTATATATTATATTATATATTATATGATATATATTATAGTATAT
Found at i:452477 original size:4 final size:5
Alignment explanation
Indices: 452438--452487 Score: 52
Period size: 5 Copynumber: 10.4 Consensus size: 5
452428 CTGCAATATC
* *
452438 TTTT- TTTTA TTTTA GTATT- TTTAA TTTTA TTTTA -TTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
452486 TT
1 TT
452488 GTTTAACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
4 10 0.26
5 25 0.66
6 3 0.08
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:452479 original size:20 final size:19
Alignment explanation
Indices: 452438--452487 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
452428 CTGCAATATC
452438 TTTT-TTTTATTTTAGTAT
1 TTTTATTTTATTTTAGTAT
*
452456 TTTTAATTTTATTTTA-TTT
1 TTTT-ATTTTATTTTAGTAT
452475 ATTTTATTTTATT
1 -TTTTATTTTATT
452488 GTTTAACATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 4 0.14
19 10 0.36
20 14 0.50
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (19 bp):
TTTTATTTTATTTTAGTAT
Found at i:452482 original size:14 final size:14
Alignment explanation
Indices: 452438--452487 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
452428 CTGCAATATC
*
452438 TTTTTTTTATTTTA
1 TTTTATTTATTTTA
*
452452 GTATTT-TTAATTTTA
1 -T-TTTATTTATTTTA
452467 TTTTATTTATTTTA
1 TTTTATTTATTTTA
452481 TTTTATT
1 TTTTATT
452488 GTTTAACATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 3 0.10
14 16 0.52
15 9 0.29
16 3 0.10
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (14 bp):
TTTTATTTATTTTA
Found at i:452958 original size:16 final size:16
Alignment explanation
Indices: 452937--452995 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 16
452927 ATTTAACAAG
452937 AATGGTATATTATTCA
1 AATGGTATATTATTCA
* *
452953 AATGGTCACATAGTTTTTGAA
1 AATGGT---ATA-TTATT-CA
452974 AATGGTATATTATTCA
1 AATGGTATATTATTCA
452990 AATGGT
1 AATGGT
452996 CACATAGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
16 13 0.38
17 4 0.12
18 3 0.09
19 3 0.09
20 4 0.12
21 7 0.21
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.41
Consensus pattern (16 bp):
AATGGTATATTATTCA
Found at i:452978 original size:21 final size:21
Alignment explanation
Indices: 452952--453010 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
452942 TATATTATTC
452952 AAATGGTCACATAGTTTTTGA
1 AAATGGTCACATAGTTTTTGA
* *
452973 AAATGGT---ATA-TTATT-C
1 AAATGGTCACATAGTTTTTGA
452989 AAATGGTCACATAGTTTTTGA
1 AAATGGTCACATAGTTTTTGA
453010 A
1 A
453011 GTGTTATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 10
0.67 0.09 0.23
Matches are distributed among these distances:
16 7 0.24
17 4 0.14
18 3 0.10
19 3 0.10
20 4 0.14
21 8 0.28
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (21 bp):
AAATGGTCACATAGTTTTTGA
Found at i:452987 original size:37 final size:37
Alignment explanation
Indices: 452937--453010 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
452927 ATTTAACAAG
452937 AATGGTATATTATTCAAATGGTCACATAGTTTTTGAA
1 AATGGTATATTATTCAAATGGTCACATAGTTTTTGAA
452974 AATGGTATATTATTCAAATGGTCACATAGTTTTTGAA
1 AATGGTATATTATTCAAATGGTCACATAGTTTTTGAA
453011 GTGTTATTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.41
Consensus pattern (37 bp):
AATGGTATATTATTCAAATGGTCACATAGTTTTTGAA
Found at i:453564 original size:5 final size:5
Alignment explanation
Indices: 453554--453617 Score: 50
Period size: 5 Copynumber: 13.6 Consensus size: 5
453544 TCAAGGGACA
*
453554 ATAAT ATAAT ATAAT -TAAT ATAA- ATAACT -T-AT ATAAT ATATT A-AATT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAA-T ATAAT ATAAT ATAAT ATAA-T
*
453601 ATTAT ATAAT AT-AT ATA
1 ATAAT ATAAT ATAAT ATA
453618 CACACTATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
3 1 0.02
4 15 0.32
5 30 0.64
6 1 0.02
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (5 bp):
ATAAT
Found at i:453574 original size:9 final size:10
Alignment explanation
Indices: 453554--453617 Score: 50
Period size: 9 Copynumber: 6.8 Consensus size: 10
453544 TCAAGGGACA
453554 ATAATATAAT
1 ATAATATAAT
453564 ATAAT-TAAT
1 ATAATATAAT
453573 ATAA-ATAACT
1 ATAATATAA-T
453583 -T-ATATAAT
1 ATAATATAAT
*
453591 ATATTA-AATT
1 ATAATATAA-T
*
453601 ATTATATAAT
1 ATAATATAAT
453611 AT-ATATA
1 ATAATATA
453618 CACACTATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 15
0.71 0.05 0.24
Matches are distributed among these distances:
8 2 0.05
9 24 0.55
10 16 0.36
11 2 0.05
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (10 bp):
ATAATATAAT
Found at i:453587 original size:13 final size:14
Alignment explanation
Indices: 453555--453597 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 14
453545 CAAGGGACAA
453555 TAATATAATATAAT
1 TAATATAATATAAT
453569 TAATATAA-ATAACT
1 TAATATAATATAA-T
453583 T-ATATAATAT-AT
1 TAATATAATATAAT
453595 TAA
1 TAA
453598 ATTATTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
12 2 0.08
13 12 0.46
14 12 0.46
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (14 bp):
TAATATAATATAAT
Found at i:453590 original size:22 final size:21
Alignment explanation
Indices: 453553--453616 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 21
453543 GTCAAGGGAC
453553 AATAATATAATATAATTA-ATATA
1 AATAAT-T-ATATAATTATAT-TA
453576 AATAACTTATATAA-TATATTA
1 AATAA-TTATATAATTATATTA
*
453597 AATTATTATATAATATATAT
1 AATAATTATATAAT-TATAT
453617 ACACACTATA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
20 8 0.22
21 8 0.22
22 13 0.36
23 6 0.17
24 1 0.03
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
AATAATTATATAATTATATTA
Found at i:453594 original size:20 final size:19
Alignment explanation
Indices: 453571--453615 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
453561 AATATAATTA
453571 ATATAAATAACTTATATAAT
1 ATATAAATAA-TTATATAAT
*
453591 ATATTAAATTATTATATAAT
1 ATA-TAAATAATTATATAAT
453611 ATATA
1 ATATA
453616 TACACACTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 2 0.09
20 15 0.65
21 6 0.26
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATAAATAATTATATAAT
Found at i:453721 original size:20 final size:20
Alignment explanation
Indices: 453676--453723 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
453666 TAATATATAT
*
453676 ATATATATATATCTTCTAAA
1 ATATTTATATATCTTCTAAA
* *
453696 AAATTTATATAT-TTTTAAA
1 ATATTTATATATCTTCTAAA
453715 CATATTTAT
1 -ATATTTAT
453724 TATAATATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTTATATATCTTCTAAA
Found at i:454453 original size:225 final size:223
Alignment explanation
Indices: 454043--454636 Score: 596
Period size: 225 Copynumber: 2.7 Consensus size: 223
454033 AATCTAGCTC
* * * *
454043 AAAGTTGTA-TTCGAAAAGATTAGACTGGAAGATGGCGT-CTCGCCATTGAGTTAAGCCAAATTG
1 AAAGTTG-ACTTCAAAAAGATTTGACCGGAAGATGGC-TCCTCGCCGTTGAGTTAAGCCAAATTG
* * * * *
454106 CAATAGCTCTGAATGCGCTT-TCGAGTCAAGTATCAATTACCGT-GAAGTTGAAACTTGGCCTGA
64 CAATAGTTCTGAATGTGCTTCTAGA-TCAAGTATC-ATTTCC-TAAAAGTTGAAACTTGGCCTGA
* * * * * ** * * * * *
454169 ATACTTCAACTGATAACTAGCTCCTCGTTGCTGAGTTAAGCTATATTGTAGTTGATTCTGAATTG
126 AAACTTCAACAGAGAACTAGCCCCCCGCCGCTGAGTTAAGCCAAACTGCAGTCGATTCTGAATTG
454234 GCTTTCGAACCCAATATCCTCCCTCGTGGAGTT
191 GCTTTCGAACCCAATATCCTCCCTCGTGGAGTT
* * * * *
454267 GAAGTTGGCTTTAAAAAGATTTGCCCGGAAGATGGCTCCTCACCGTTGAGTTAAGCCAAATTGCA
1 AAAGTTGACTTCAAAAAGATTTGACCGGAAGATGGCTCCTCGCCGTTGAGTTAAGCCAAATTGCA
* * *
454332 GTCAGTTATGAATGTGCTTCTAGATCAAGTATCATTTCCTACAAAGTTGAAATTTGGCCTGAAAA
66 AT-AGTTCTGAATGTGCTTCTAGATCAAGTATCATTTCCTA-AAAGTTGAAACTTGGCCTGAAAA
* *
454397 CTTCAACAGGGAACTA-CCCCCCAGCCGTTGAGTTAAGCCAAACTGCAGTCGATTCTGAATTGGC
129 CTTCAACAGAGAACTAGCCCCCC-GCCGCTGAGTTAAGCCAAACTGCAGTCGATTCTGAATTGGC
* ** *
454461 TTTCGAATCCAATATCCTCTGTCGTGGTGTT
193 TTTCGAACCCAATATCCTCCCTCGTGGAGTT
* * * * * *
454492 AAAGTTGACTTCAAAAATATTTGACTGTAAGATGTCTCCTCGCAG-TGAGTTAAGAC-AATTGCA
1 AAAGTTGACTTCAAAAAGATTTGACCGGAAGATGGCTCCTCGCCGTTGAGTTAAGCCAAATTGCA
* * * *
454555 ATTAGTTCTTAATGTGCTTCTGGGTCAAGTATCATTCTCCATGAAA-TT-AATACTTGGCCTGAA
66 A-TAGTTCTGAATGTGCTTCTAGATCAAGTATCATT-TCC-TAAAAGTTGAA-ACTTGGCCTGAA
*
454618 AACTTCAACTGA-AACTAGC
127 AACTTCAACAGAGAACTAGC
454637 TCCTATGCTA
Statistics
Matches: 303, Mismatches: 55, Indels: 25
0.79 0.14 0.07
Matches are distributed among these distances:
222 7 0.02
223 62 0.20
224 80 0.26
225 151 0.50
226 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (223 bp):
AAAGTTGACTTCAAAAAGATTTGACCGGAAGATGGCTCCTCGCCGTTGAGTTAAGCCAAATTGCA
ATAGTTCTGAATGTGCTTCTAGATCAAGTATCATTTCCTAAAAGTTGAAACTTGGCCTGAAAACT
TCAACAGAGAACTAGCCCCCCGCCGCTGAGTTAAGCCAAACTGCAGTCGATTCTGAATTGGCTTT
CGAACCCAATATCCTCCCTCGTGGAGTT
Found at i:460844 original size:24 final size:24
Alignment explanation
Indices: 460801--460853 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 24
460791 ATAAAGTTAT
*
460801 TTTTTCTTTTCTTTTCAAGTTTTCA
1 TTTTTCTTTTATTTTCAAGTTTT-A
460826 TTTTTCTTTTATTTT-AAGTTTTA
1 TTTTTCTTTTATTTTCAAGTTTTA
460849 TTTTT
1 TTTTT
460854 AAACATGCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 6 0.22
24 7 0.26
25 14 0.52
ACGTcount: A:0.13, C:0.09, G:0.04, T:0.74
Consensus pattern (24 bp):
TTTTTCTTTTATTTTCAAGTTTTA
Found at i:466850 original size:45 final size:45
Alignment explanation
Indices: 466750--466994 Score: 406
Period size: 44 Copynumber: 5.5 Consensus size: 45
466740 CAATTTAATC
* *
466750 CCATAAGCTTGTAAGCTTATTTTACCAACAT-CATACCATTTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
* *
466794 TCATAAGCTCGTAAGCTTATTTTACCAACATACTTATCATTTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
466839 CCATAAGCTCGTAAGCTTATTTTACCAACAT-CTTACCATTTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
466883 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
* * *
466928 TCATAAGCTCGTAAGTTTATTTTACCAACATACTTGCCA-TTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
466972 CCATAAGCTCGTAAGCTTATTTT
1 CCATAAGCTCGTAAGCTTATTTT
466995 CATACTTACC
Statistics
Matches: 188, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
44 98 0.52
45 90 0.48
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (45 bp):
CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
Found at i:466856 original size:89 final size:89
Alignment explanation
Indices: 466750--466994 Score: 411
Period size: 89 Copynumber: 2.8 Consensus size: 89
466740 CAATTTAATC
* * *
466750 CCATAAGCTTGTAAGCTTATTTTACCAACATCATACCATTTATTTCATAAGCTCGTAAGCTTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATCTTACCATTTATTCCATAAGCTCGTAAGCTTATT
*
466815 TTACCAACATACTTATCATTTATT
66 TTACCAACATACTTACCATTTATT
466839 CCATAAGCTCGTAAGCTTATTTTACCAACATCTTACCATTTATTCCATAAGCTCGTAAGCTTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATCTTACCATTTATTCCATAAGCTCGTAAGCTTATT
466904 TTACCAACATACTTACCATTTATT
66 TTACCAACATACTTACCATTTATT
* * *
466928 TCATAAGCTCGTAAGTTTATTTTACCAACATACTTGCCA-TTATTCCATAAGCTCGTAAGCTTAT
1 CCATAAGCTCGTAAGCTTATTTTACCAACAT-CTTACCATTTATTCCATAAGCTCGTAAGCTTAT
466992 TTT
65 TTT
466995 CATACTTACC
Statistics
Matches: 148, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
89 142 0.96
90 6 0.04
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (89 bp):
CCATAAGCTCGTAAGCTTATTTTACCAACATCTTACCATTTATTCCATAAGCTCGTAAGCTTATT
TTACCAACATACTTACCATTTATT
Found at i:473725 original size:45 final size:45
Alignment explanation
Indices: 473627--473871 Score: 388
Period size: 44 Copynumber: 5.5 Consensus size: 45
473617 CAATTTAATC
* * * *
473627 CCATAAGCTTGTAAGCTTATTTAACCAATAT-CTTATCATTTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
*
473671 TCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
* *
473716 CCATAAGCTCGTAAACTTATTTTACCTACAT-CTTACCATTTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
*
473760 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTATCATTTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
*
473805 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTGCCA-TTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
473849 CCATAAGCTCGTAAGCTTATTTT
1 CCATAAGCTCGTAAGCTTATTTT
473872 CATACTTACC
Statistics
Matches: 186, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
44 97 0.52
45 89 0.48
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.40
Consensus pattern (45 bp):
CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
Found at i:473778 original size:89 final size:89
Alignment explanation
Indices: 473627--473871 Score: 393
Period size: 89 Copynumber: 2.8 Consensus size: 89
473617 CAATTTAATC
* * * * *
473627 CCATAAGCTTGTAAGCTTATTTAACCAATATCTTATCATTTATTTCATAAGCTCGTAAGCTTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATCTTACCATTTATTCCATAAGCTCGTAAGCTTATT
473692 TTACCAACATACTTACCATTTATT
66 TTACCAACATACTTACCATTTATT
* *
473716 CCATAAGCTCGTAAACTTATTTTACCTACATCTTACCATTTATTCCATAAGCTCGTAAGCTTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATCTTACCATTTATTCCATAAGCTCGTAAGCTTATT
*
473781 TTACCAACATACTTATCATTTATT
66 TTACCAACATACTTACCATTTATT
*
473805 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTGCCA-TTATTCCATAAGCTCGTAAGCTTAT
1 CCATAAGCTCGTAAGCTTATTTTACCAACAT-CTTACCATTTATTCCATAAGCTCGTAAGCTTAT
473869 TTT
65 TTT
473872 CATACTTACC
Statistics
Matches: 144, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
89 138 0.96
90 6 0.04
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.40
Consensus pattern (89 bp):
CCATAAGCTCGTAAGCTTATTTTACCAACATCTTACCATTTATTCCATAAGCTCGTAAGCTTATT
TTACCAACATACTTACCATTTATT
Found at i:475053 original size:14 final size:14
Alignment explanation
Indices: 475034--475062 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
475024 AACATAATTT
475034 TTTGCAGAATCTGC
1 TTTGCAGAATCTGC
475048 TTTGCAGAATCTGC
1 TTTGCAGAATCTGC
475062 T
1 T
475063 GTCTGATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (14 bp):
TTTGCAGAATCTGC
Found at i:476972 original size:24 final size:24
Alignment explanation
Indices: 476929--476981 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 24
476919 ATAAAGTTAT
*
476929 TTTTTCTTTTCTTTTCAAGTTTTCA
1 TTTTTCTTTTATTTTCAAGTTTT-A
476954 TTTTTCTTTTATTTT-AAGTTTTA
1 TTTTTCTTTTATTTTCAAGTTTTA
476977 TTTTT
1 TTTTT
476982 AAACATGCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 6 0.22
24 7 0.26
25 14 0.52
ACGTcount: A:0.13, C:0.09, G:0.04, T:0.74
Consensus pattern (24 bp):
TTTTTCTTTTATTTTCAAGTTTTA
Found at i:478860 original size:18 final size:18
Alignment explanation
Indices: 478837--478872 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
478827 TAACCGAAAC
478837 CGTTTAACATTAATAGTT
1 CGTTTAACATTAATAGTT
478855 CGTTTAACATTAATAGTT
1 CGTTTAACATTAATAGTT
478873 ATCGATTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (18 bp):
CGTTTAACATTAATAGTT
Found at i:481233 original size:21 final size:21
Alignment explanation
Indices: 481204--481279 Score: 125
Period size: 21 Copynumber: 3.6 Consensus size: 21
481194 AAACTAATAC
481204 CAGTATCGATACCACCCTTTG
1 CAGTATCGATACCACCCTTTG
* *
481225 TAATATCGATACCACCCTTTG
1 CAGTATCGATACCACCCTTTG
*
481246 CAGTATCGATACCACCATTTG
1 CAGTATCGATACCACCCTTTG
481267 CAGTATCGATACC
1 CAGTATCGATACC
481280 CCTACCTTGA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.28, C:0.30, G:0.13, T:0.29
Consensus pattern (21 bp):
CAGTATCGATACCACCCTTTG
Found at i:484573 original size:13 final size:14
Alignment explanation
Indices: 484550--484586 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
484540 ATTAATAATA
484550 ATATAATATAAATT
1 ATATAATATAAATT
*
484564 ATATAA-ATAACTT
1 ATATAATATAAATT
484577 ATATAATATA
1 ATATAATATA
484587 TTAAATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATAATATAAATT
Found at i:484695 original size:22 final size:20
Alignment explanation
Indices: 484671--484723 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
484661 TAATGTGTGT
*
484671 ATATATATATATTGT-AAAA
1 ATATATATATATTTTCAAAA
*
484690 ATTATATATATATTTTCAAAC
1 A-TATATATATATTTTCAAAA
484711 ATATATATATATT
1 ATATATATATATT
484724 ATACATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 1 0.03
20 25 0.83
21 4 0.13
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (20 bp):
ATATATATATATTTTCAAAA
Found at i:484740 original size:35 final size:34
Alignment explanation
Indices: 484693--484768 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 34
484683 TGTAAAAATT
* *
484693 ATATATATATTTTCAAACATA-TATATATATTATAC
1 ATATATACATTTTCAAA-AGACTATATATA-TATAC
* *
484728 ATATATACATTTTTAAAAGACTATATATATATAT
1 ATATATACATTTTCAAAAGACTATATATATATAC
484762 ATATATA
1 ATATATA
484769 AACAATATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 13 0.36
35 23 0.64
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.45
Consensus pattern (34 bp):
ATATATACATTTTCAAAAGACTATATATATATAC
Found at i:485442 original size:5 final size:5
Alignment explanation
Indices: 485432--485487 Score: 64
Period size: 5 Copynumber: 11.6 Consensus size: 5
485422 TTGAACCTGA
* *
485432 ATAAT ATAAT ATAA- GTAAT ATAAAT ATAAT ATAAT ATATT A-AAT -TAAT
1 ATAAT ATAAT ATAAT ATAAT AT-AAT ATAAT ATAAT ATAAT ATAAT ATAAT
485480 ATAAT ATA
1 ATAAT ATA
485488 TACGATATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
4 8 0.19
5 30 0.70
6 5 0.12
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (5 bp):
ATAAT
Done.