Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold316
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: 597962
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
File 4 of 5
Found at i:465970 original size:31 final size:30
Alignment explanation
Indices: 465919--466084 Score: 111
Period size: 31 Copynumber: 5.5 Consensus size: 30
465909 ATTCATATAT
*
465919 TTAT-ATTATATTTAAATATTTT-TATTTTA
1 TTATAATTTTATTTAAATATTTTATA-TTTA
465948 TTATAATTTTATTTAAAATATTTTATATTTA
1 TTATAATTTTATTT-AAATATTTTATATTTA
* *
465979 TT-TAAATTTTAATAGTTTAATAATTTATA-TTA
1 TTAT-AATTTT-AT--TTAAATATTTTATATTTA
*
466011 -TATAAATTTTA-ATAAATA-TTTATATTATA
1 TTAT-AATTTTATTTAAATATTTTATATT-TA
*
466040 TTATAATTATTTTATTAAA-A--TTATATTTA
1 TTATAATT-TTAT-TTAAATATTTTATATTTA
466069 -TATAAATTTTATTTAA
1 TTAT-AATTTTATTTAA
466085 TATGTGGCCC
Statistics
Matches: 114, Mismatches: 8, Indels: 32
0.74 0.05 0.21
Matches are distributed among these distances:
27 10 0.09
28 12 0.11
29 16 0.14
30 21 0.18
31 24 0.21
32 19 0.17
33 10 0.09
34 2 0.02
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (30 bp):
TTATAATTTTATTTAAATATTTTATATTTA
Found at i:465976 original size:16 final size:15
Alignment explanation
Indices: 465927--465978 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
465917 ATTTATATTA
465927 TATTT-AAATATTTT
1 TATTTAAAATATTTT
** *
465941 TATTTTATTATAATTT
1 TA-TTTAAAATATTTT
465957 TATTTAAAATATTTT
1 TATTTAAAATATTTT
465972 ATATTTA
1 -TATTTA
465979 TTTAAATTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
14 2 0.07
15 13 0.45
16 14 0.48
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TATTTAAAATATTTT
Found at i:466052 original size:32 final size:31
Alignment explanation
Indices: 465939--466071 Score: 89
Period size: 32 Copynumber: 4.2 Consensus size: 31
465929 TTTAAATATT
* *
465939 TTTATTTTAT-TATAATTTTATTTAAAA-TAT-
1 TTTATATTATATA-AATTTTA-ATAAAATTATA
* **
465969 TTTATATTTATTTAAATTTTAAT-AGTTTAATAA
1 TTTATA-TTATATAAATTTTAATAAAATT-AT-A
466002 TTTATATTATATAAATTTTAATAAATATT-TA
1 TTTATATTATATAAATTTTAATAAA-ATTATA
* *
466033 TATTATATTATA-ATTATTTTATTAAAATTATA
1 T-TTATATTATATA-AATTTTAATAAAATTATA
466065 TTTATAT
1 TTTATAT
466072 AAATTTTATT
Statistics
Matches: 83, Mismatches: 9, Indels: 21
0.73 0.08 0.19
Matches are distributed among these distances:
29 1 0.01
30 7 0.08
31 25 0.30
32 41 0.49
33 7 0.08
34 2 0.02
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.59
Consensus pattern (31 bp):
TTTATATTATATAAATTTTAATAAAATTATA
Found at i:466087 original size:16 final size:15
Alignment explanation
Indices: 465970--466083 Score: 53
Period size: 14 Copynumber: 7.6 Consensus size: 15
465960 TTAAAATATT
*
465970 TTATATTTATTTAAA
1 TTATATTTATATAAA
*
465985 TTTTAATAGTTTA-ATAAT
1 --TT-ATA-TTTATATAAA
466003 TTATA-TTATATAAA
1 TTATATTTATATAAA
* * * *
466017 TTTTA-ATAAAT-AT
1 TTATATTTATATAAA
466030 TTATA-TTATATTATAA
1 TTATATTTATA-TA-AA
466046 TTAT-TTTAT-TAAAA
1 TTATATTTATAT-AAA
466060 TTATATTTATATAAA
1 TTATATTTATATAAA
*
466075 TTTTATTTA
1 TTATATTTA
466084 ATATGTGGCC
Statistics
Matches: 75, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
13 11 0.15
14 20 0.27
15 20 0.27
16 12 0.16
17 2 0.03
18 6 0.08
19 4 0.05
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (15 bp):
TTATATTTATATAAA
Found at i:467396 original size:23 final size:23
Alignment explanation
Indices: 467354--467397 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
467344 TAAATTAATT
*
467354 AATAAAATTTATATAATATTTAA
1 AATAAAATTTATAAAATATTTAA
467377 AATAAAATTTA-AAAAGTATTT
1 AATAAAATTTATAAAA-TATTT
467398 TTAATACTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
AATAAAATTTATAAAATATTTAA
Found at i:467403 original size:23 final size:23
Alignment explanation
Indices: 467352--467403 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
467342 TTTAAATTAA
*
467352 TTAATAAAATTTATATAATATTT
1 TTAATAAAATTTATAAAATATTT
**
467375 AAAATAAAATTTA-AAAAGTATTT
1 TTAATAAAATTTATAAAA-TATTT
467398 TTAATA
1 TTAATA
467404 CTATTAATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TTAATAAAATTTATAAAATATTT
Found at i:467445 original size:21 final size:21
Alignment explanation
Indices: 467413--467475 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
467403 ACTATTAATT
467413 ATAA-TTAAATTAAAATTAAA
1 ATAATTTAAATTAAAATTAAA
**
467433 ATAATTTTTATTATAAA--AATA
1 ATAATTTAAATTA-AAATTAA-A
467454 ATAATTTAAATT-AAATTAAA
1 ATAATTTAAATTAAAATTAAA
467474 AT
1 AT
467476 TAAAATTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
19 3 0.09
20 9 0.26
21 19 0.56
22 3 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAATTTAAATTAAAATTAAA
Found at i:467746 original size:16 final size:16
Alignment explanation
Indices: 467725--467795 Score: 74
Period size: 16 Copynumber: 4.4 Consensus size: 16
467715 TTTAAATCCG
467725 AAATGATTCGAATAT-A
1 AAATGATTCGAAT-TCA
467741 AAATGATTCGAATTCA
1 AAATGATTCGAATTCA
**
467757 AAATGATTCGAACCCA
1 AAATGATTCGAATTCA
* *
467773 AAAT-AGTCTGAATTCG
1 AAATGATTC-GAATTCA
467789 AAATGAT
1 AAATGAT
467796 CCAAACCCGA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
15 4 0.09
16 40 0.89
17 1 0.02
ACGTcount: A:0.45, C:0.13, G:0.14, T:0.28
Consensus pattern (16 bp):
AAATGATTCGAATTCA
Found at i:467776 original size:32 final size:33
Alignment explanation
Indices: 467725--467810 Score: 86
Period size: 32 Copynumber: 2.7 Consensus size: 33
467715 TTTAAATCCG
*** *
467725 AAATGATTCGAATATAAAATGATTC-GAATTCA
1 AAATGATTCGAACCCAAAATGAGTCTGAATTCA
*
467757 AAATGATTCGAACCCAAAAT-AGTCTGAATTCG
1 AAATGATTCGAACCCAAAATGAGTCTGAATTCA
* * *
467789 AAATGATCCAAACCCGAAATGA
1 AAATGATTCGAACCCAAAATGA
467811 CCTGAATGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
31 3 0.07
32 40 0.91
33 1 0.02
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.24
Consensus pattern (33 bp):
AAATGATTCGAACCCAAAATGAGTCTGAATTCA
Found at i:468857 original size:53 final size:53
Alignment explanation
Indices: 468790--468895 Score: 124
Period size: 53 Copynumber: 2.0 Consensus size: 53
468780 TGAACTTAAT
** * * *
468790 TTAACCCGAATGTTAAACTTGATTAACCCGGATCC-AGAATGATCTGAACCCGA
1 TTAACCCGAATGTTAAACCCGATTAACCC-GAACCTAAAATGACCTGAACCCGA
* * *
468843 TTAACTCGAGTGTTAAACCCGATTGACCCGAACCTAAAATGACCTGAACCCGA
1 TTAACCCGAATGTTAAACCCGATTAACCCGAACCTAAAATGACCTGAACCCGA
468896 AACAACCCAA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
52 4 0.09
53 40 0.91
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (53 bp):
TTAACCCGAATGTTAAACCCGATTAACCCGAACCTAAAATGACCTGAACCCGA
Found at i:468939 original size:16 final size:16
Alignment explanation
Indices: 468909--468961 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
468899 AACCCAAACT
468909 CGAAATGA-TCCGAACC
1 CGAAATGACT-CGAACC
*
468925 CGAAATGACTTGAACC
1 CGAAATGACTCGAACC
* *
468941 CAAAATGACTCGAATC
1 CGAAATGACTCGAACC
468957 CGAAA
1 CGAAA
468962 ATTTTATAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 30 0.97
17 1 0.03
ACGTcount: A:0.42, C:0.26, G:0.17, T:0.15
Consensus pattern (16 bp):
CGAAATGACTCGAACC
Found at i:471140 original size:18 final size:19
Alignment explanation
Indices: 471080--471139 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
471070 TAAAGTGGAT
* *
471080 AAATCTAATTTATAATAAA
1 AAATCTTATTAATAATAAA
471099 AAATTACTTA-TAA-AATAAA
1 AAA-T-CTTATTAATAATAAA
471118 TAAATCTTATTAATAATAAA
1 -AAATCTTATTAATAATAAA
471138 AA
1 AA
471140 TTATTTACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
18 4 0.12
19 15 0.44
20 12 0.35
21 3 0.09
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
AAATCTTATTAATAATAAA
Found at i:471313 original size:16 final size:16
Alignment explanation
Indices: 471288--471318 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
471278 AAATTATTAT
471288 TTAATAATAAAAATAA
1 TTAATAATAAAAATAA
*
471304 TTAATTATAAAAATA
1 TTAATAATAAAAATA
471319 TATTTTTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TTAATAATAAAAATAA
Found at i:473183 original size:17 final size:17
Alignment explanation
Indices: 473161--473194 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
473151 CAAAAATTTT
* *
473161 GAAAAATCACTTTTCAA
1 GAAAAATAAATTTTCAA
473178 GAAAAATAAATTTTCAA
1 GAAAAATAAATTTTCAA
473195 AATCGGGTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.29
Consensus pattern (17 bp):
GAAAAATAAATTTTCAA
Found at i:473405 original size:24 final size:23
Alignment explanation
Indices: 473352--473408 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
473342 TTATAAAATT
473352 TGGAAAAATCATCTAATGGGTTA
1 TGGAAAAATCATCTAATGGGTTA
*
473375 TGGAAAAATCATCTAATGGGTTC
1 TGGAAAAATCATCTAATGGGTTA
473398 TGGAAAAATCA
1 TGGAAAAATCA
473409 AACTAGAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (23 bp):
TGGAAAAATCATCTAATGGGTTA
Found at i:478188 original size:20 final size:20
Alignment explanation
Indices: 478159--478202 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
478149 ACTTGGAGAC
478159 TTTTAAGTCATTTTA-TACAT
1 TTTTAAGTCATTTTAGT-CAT
*
478179 TTTTATGTCATTTTAGTCAT
1 TTTTAAGTCATTTTAGTCAT
478199 TTTT
1 TTTT
478203 CATTACTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.23, C:0.09, G:0.07, T:0.61
Consensus pattern (20 bp):
TTTTAAGTCATTTTAGTCAT
Found at i:480896 original size:2 final size:2
Alignment explanation
Indices: 480889--480928 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
480879 ATTGGCTTCC
480889 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
480929 GCTTTTATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:482831 original size:17 final size:19
Alignment explanation
Indices: 482808--482846 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
482798 TACTCGATGT
*
482808 TTTTTTAATT-TTTTATTA
1 TTTTTAAATTATTTTATTA
482826 TTTTTAAAATTATTTTATTA
1 TTTTT-AAATTATTTTATTA
482846 T
1 T
482847 AAAATTAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 4 0.22
20 9 0.50
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTTAAATTATTTTATTA
Found at i:483293 original size:22 final size:23
Alignment explanation
Indices: 483268--483311 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
483258 ATTAATTTCG
483268 AATTAATTAAA-TTT-AACATTTA
1 AATTAA-TAAAGTTTGAACATTTA
*
483290 AATTTATAAAGTTTGAACATTT
1 AATTAATAAAGTTTGAACATTT
483312 TGCATTTAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 8 0.42
23 7 0.37
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (23 bp):
AATTAATAAAGTTTGAACATTTA
Found at i:485142 original size:17 final size:15
Alignment explanation
Indices: 485121--485167 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 15
485111 TATATAACAT
485121 ATTTATATTTATATA
1 ATTTATATTTATATA
485136 ATTTTTATATATTA-ATA
1 A--TTTATAT-TTATATA
485153 ATTTATA-TTATATA
1 ATTTATATTTATATA
485167 A
1 A
485168 AGCTTGAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
13 3 0.11
14 4 0.14
15 7 0.25
17 11 0.39
18 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTATATTTATATA
Found at i:485157 original size:32 final size:31
Alignment explanation
Indices: 485108--485167 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
485098 CATATTATAA
485108 TTATATATAACATATTTATATTTATATAATTT
1 TTATATATAACATATTTATA-TTATATAATTT
*
485140 TTATATATTA-ATAATTTATATTATATAA
1 TTATATATAACAT-ATTTATATTATATAA
485168 AGCTTGAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 10 0.38
32 16 0.62
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (31 bp):
TTATATATAACATATTTATATTATATAATTT
Found at i:485311 original size:2 final size:2
Alignment explanation
Indices: 485306--485335 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
485296 GTGTGTGTGT
485306 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
485336 TGAAAGAGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:489274 original size:22 final size:21
Alignment explanation
Indices: 489241--489294 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 21
489231 TTTAGTGATC
489241 AATTAAATATAAAAT-ATTTTT
1 AATTAAA-ATAAAATAATTTTT
489262 AAATTAATAATAAAATAATTTTT
1 -AATTAA-AATAAAATAATTTTT
489285 AATTAAAATA
1 AATTAAAATA
489295 TATGTATACG
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.13
22 19 0.63
23 7 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AATTAAAATAAAATAATTTTT
Found at i:490206 original size:19 final size:17
Alignment explanation
Indices: 490163--490206 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
490153 TATATTATAT
490163 TTATATTTAAAATTTTA
1 TTATATTTAAAATTTTA
* *
490180 ATAAATTTAATAATTTTTA
1 TTATATTTAA-AA-TTTTA
490199 TTATATTT
1 TTATATTT
490207 TTATTTATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 8 0.38
18 2 0.10
19 11 0.52
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATATTTAAAATTTTA
Found at i:490223 original size:42 final size:41
Alignment explanation
Indices: 490129--490226 Score: 110
Period size: 42 Copynumber: 2.3 Consensus size: 41
490119 ATAATGTGAA
*
490129 ATATAATATAATATATTTAAAATATATATTATATTTATATTT
1 ATATAAT-TAATAAATTTAAAATATATATTATATTTATATTT
* * *
490171 A-A-AATTTTAATAAATTTAATAATTTTTATTATATTTTTATTT
1 ATATAA--TTAATAAATTTAA-AATATATATTATATTTATATTT
490213 ATATAATTAATAAA
1 ATATAATTAATAAA
490227 AAAATCAACA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
40 2 0.04
41 12 0.26
42 30 0.64
43 1 0.02
44 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (41 bp):
ATATAATTAATAAATTTAAAATATATATTATATTTATATTT
Found at i:491234 original size:2 final size:2
Alignment explanation
Indices: 491227--491306 Score: 85
Period size: 2 Copynumber: 41.5 Consensus size: 2
491217 TTTCAGATAG
*
491227 TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
491268 -A TC T- TT TT TG CA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
491307 TTACAAAGAG
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
1 3 0.04
2 65 0.96
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:491729 original size:24 final size:26
Alignment explanation
Indices: 491682--491729 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
491672 TTATACTATT
* *
491682 AAAATATTATTATTTTAATTTTTAAA
1 AAAATATTATTATTTAAATATTTAAA
491708 AAAAT-TTATTA-TTAAATATTTA
1 AAAATATTATTATTTAAATATTTA
491730 TAAAGCATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 9 0.45
25 6 0.30
26 5 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
AAAATATTATTATTTAAATATTTAAA
Found at i:495816 original size:16 final size:16
Alignment explanation
Indices: 495797--495827 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
495787 TTTTTAACGA
495797 AAGCTATTTTAAATAT
1 AAGCTATTTTAAATAT
*
495813 AAGCTATTTTGAATA
1 AAGCTATTTTAAATA
495828 ATAATTGTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (16 bp):
AAGCTATTTTAAATAT
Found at i:496979 original size:25 final size:25
Alignment explanation
Indices: 496948--497028 Score: 85
Period size: 25 Copynumber: 3.2 Consensus size: 25
496938 AGATATATAT
496948 AAATATAATATTAATAAAATAATTA
1 AAATATAATATTAATAAAATAATTA
*
496973 AAATATAATATAATATAAATATATATTA
1 AAATATAATATTA-ATAAA-ATA-ATTA
* *
497001 AAAT-TTATA-TAATATAAATTATTA
1 AAATATAATATTAATA-AAATAATTA
497025 AAAT
1 AAAT
497029 TTTAAAAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
24 8 0.17
25 17 0.35
26 8 0.17
27 7 0.15
28 8 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
AAATATAATATTAATAAAATAATTA
Found at i:496980 original size:16 final size:18
Alignment explanation
Indices: 496942--496997 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 18
496932 TAAATAAGAT
496942 ATATATAAATATAATAT--
1 ATATATAAA-ATAATATAA
496959 -TA-ATAAAATAAT-TAA
1 ATATATAAAATAATATAA
*
496974 A-ATATAATATAATATAA
1 ATATATAAAATAATATAA
496991 ATATATA
1 ATATATA
496998 TTAAAATTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
13 1 0.03
14 5 0.16
15 6 0.19
16 11 0.34
17 4 0.12
18 5 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATATATAAAATAATATAA
Found at i:497002 original size:11 final size:11
Alignment explanation
Indices: 496935--496995 Score: 58
Period size: 11 Copynumber: 5.8 Consensus size: 11
496925 CATATATTAA
496935 ATAAGATAT-AT
1 ATAA-ATATAAT
496946 ATAAATATAAT
1 ATAAATATAAT
*
496957 ATTAATA-AA-
1 ATAAATATAAT
* *
496966 ATAATTAAAAT
1 ATAAATATAAT
496977 AT-AATATAAT
1 ATAAATATAAT
496987 ATAAATATA
1 ATAAATATA
496996 TATTAAAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
9 5 0.12
10 16 0.39
11 20 0.49
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (11 bp):
ATAAATATAAT
Found at i:497016 original size:27 final size:26
Alignment explanation
Indices: 496950--497030 Score: 85
Period size: 24 Copynumber: 3.0 Consensus size: 26
496940 ATATATATAA
* *
496950 ATATAATATTAATAAAATAATTAAAATATA
1 ATATAATA-TAAT-ATAT-ATTAAAAT-TT
496980 ATATAATATAAATATATATTAAAATTT
1 ATATAATAT-AATATATATTAAAATTT
497007 ATATAATATAA-AT-TATTAAAATTT
1 ATATAATATAATATATATTAAAATTT
497031 TAAAAAATAT
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
24 11 0.23
25 2 0.04
26 2 0.04
27 10 0.21
28 8 0.17
29 4 0.08
30 11 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
ATATAATATAATATATATTAAAATTT
Found at i:497016 original size:32 final size:33
Alignment explanation
Indices: 496975--497098 Score: 91
Period size: 32 Copynumber: 3.7 Consensus size: 33
496965 AATAATTAAA
496975 ATATAATATAA-TATAAATATATATTAAAATTT
1 ATATAATATAATTATAAATATATATTAAAATTT
**
497007 ATATAATATAAATTATTAAA-AT-T-TTAAAAAAT
1 ATATAATAT-AATTA-TAAATATATATTAAAATTT
*
497039 ATATAATATTTTAATTATAATTATGATATAATAAAATATT
1 ATATAATA---TAATTATAA--AT-ATATATTAAAAT-TT
497079 -TA-AATATAA-TATAAATATAT
1 ATATAATATAATTATAAATATAT
497099 GAATTATTTT
Statistics
Matches: 74, Mismatches: 5, Indels: 27
0.70 0.05 0.25
Matches are distributed among these distances:
31 4 0.05
32 26 0.35
33 6 0.08
34 14 0.19
35 9 0.12
37 2 0.03
38 5 0.07
39 7 0.09
40 1 0.01
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.44
Consensus pattern (33 bp):
ATATAATATAATTATAAATATATATTAAAATTT
Found at i:497048 original size:25 final size:24
Alignment explanation
Indices: 496991--497048 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
496981 TATAATATAA
* *
496991 ATAT-ATATTAAAATTTATATAAT
1 ATATAATATTAAAATTTAAAAAAT
497014 ATA-AATTATTAAAATTTTAAAAAAT
1 ATATAA-TATTAAAA-TTTAAAAAAT
497039 ATATAATATT
1 ATATAATATT
497049 TTAATTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
23 4 0.14
24 8 0.28
25 15 0.52
26 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
ATATAATATTAAAATTTAAAAAAT
Found at i:497109 original size:29 final size:26
Alignment explanation
Indices: 497035--497109 Score: 69
Period size: 29 Copynumber: 2.7 Consensus size: 26
497025 AAATTTTAAA
*
497035 AAATATATAATATTTTAATTATAATT
1 AAATATATAATATTTTAAATATAATT
* *
497061 ATGATATAATAAAATATTTAAATATAATAT
1 A-AATAT-ATAATAT-TTTAAATATAAT-T
497091 AAATATATGAATTATTTTA
1 AAATATAT-AA-TATTTTA
497110 TTGCGATGGG
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
26 1 0.03
27 4 0.11
28 8 0.21
29 21 0.55
30 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (26 bp):
AAATATATAATATTTTAAATATAATT
Found at i:497852 original size:13 final size:13
Alignment explanation
Indices: 497836--497860 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
497826 TTCGAAACCA
497836 TTTCTCCATTTTT
1 TTTCTCCATTTTT
497849 TTTCTCCATTTT
1 TTTCTCCATTTT
497861 CCTTATTGGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTCTCCATTTTT
Found at i:498544 original size:14 final size:14
Alignment explanation
Indices: 498525--498566 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
498515 TAATTATTTA
498525 AAATATAATTAAAT
1 AAATATAATTAAAT
498539 AAATATATATT-AAT
1 AAATATA-ATTAAAT
*
498553 AATTATAATTAAAT
1 AAATATAATTAAAT
498567 TTAAATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 3 0.12
14 19 0.76
15 3 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AAATATAATTAAAT
Found at i:498636 original size:36 final size:36
Alignment explanation
Indices: 498565--498639 Score: 84
Period size: 36 Copynumber: 2.2 Consensus size: 36
498555 TTATAATTAA
** *
498565 ATTTAAATAAAAATAATTTTATTATATAAAATTATT
1 ATTTAAATAAAAATAATTTTAAAATAAAAAATTATT
* *
498601 ATTTAAATCAAATTAA-TTTAAAATAAAAAA-T-TT
1 ATTTAAATAAAAATAATTTTAAAATAAAAAATTATT
498634 ATTTAA
1 ATTTAA
498640 TTTCGGTCGA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
33 8 0.24
34 1 0.03
35 11 0.32
36 14 0.41
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (36 bp):
ATTTAAATAAAAATAATTTTAAAATAAAAAATTATT
Found at i:500760 original size:20 final size:20
Alignment explanation
Indices: 500737--500804 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
500727 AATAAATAAT
500737 AATTTAAATTTAATTAAATC
1 AATTTAAATTTAATTAAATC
* ** * **
500757 AATTCAAATAAAAATAAAAA
1 AATTTAAATTTAATTAAATC
*
500777 AATTTAAATTTAAATGAAATC
1 AATTTAAATTT-AATTAAATC
500798 AAATTTA
1 -AATTTA
500805 TAGGTGTAAA
Statistics
Matches: 33, Mismatches: 13, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
20 22 0.67
21 5 0.15
22 6 0.18
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.35
Consensus pattern (20 bp):
AATTTAAATTTAATTAAATC
Found at i:501912 original size:19 final size:19
Alignment explanation
Indices: 501888--501926 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
501878 TTATATACAT
501888 TCATAAATT-TAAATATTTA
1 TCAT-AATTATAAATATTTA
501907 TCATAATTAATAAATATTTA
1 TCATAATT-ATAAATATTTA
501927 ATTATTATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 4 0.22
20 10 0.56
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
TCATAATTATAAATATTTA
Found at i:503625 original size:11 final size:11
Alignment explanation
Indices: 503601--503630 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
503591 TTTTATATTA
503601 ATATTTAT-AT
1 ATATTTATAAT
503611 ATATTTATAAT
1 ATATTTATAAT
503622 ATATTTATA
1 ATATTTATA
503631 TAAAGATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.42
11 11 0.58
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
ATATTTATAAT
Found at i:503627 original size:21 final size:22
Alignment explanation
Indices: 503592--503632 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
503582 AATTTTTATT
*
503592 TTTATATTAATATTTATATATA
1 TTTATAATAATATTTATATATA
503614 TTTATAAT-ATATTTATATA
1 TTTATAATAATATTTATATA
503633 AAGATATTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTATAATAATATTTATATATA
Found at i:509667 original size:2 final size:2
Alignment explanation
Indices: 509660--509690 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
509650 AGAGATTCTT
509660 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
509691 TGGATGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:511501 original size:2 final size:2
Alignment explanation
Indices: 511460--511488 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
511450 AGATGAGAAA
511460 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
511489 CACATACTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:512981 original size:3 final size:3
Alignment explanation
Indices: 512969--513002 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
512959 CTGCTATTGC
* *
512969 TGG TGT TGG TGG TGG TGG TGG TGT TGG TGG TGG T
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG T
513003 AAGTTTTTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.59, T:0.41
Consensus pattern (3 bp):
TGG
Found at i:524464 original size:3 final size:3
Alignment explanation
Indices: 524456--524490 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
524446 TTGAGACTGT
524456 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
524491 TCGCCGATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.31, G:0.34, T:0.34
Consensus pattern (3 bp):
TGC
Found at i:530250 original size:21 final size:22
Alignment explanation
Indices: 530200--530272 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
530190 TATTTGAAAT
* *
530200 AATTTAGAATTAAATTTATTTTA
1 AATTTA-AATTAAATTGATTATA
* *
530223 TGA-TTAAATTATATTGATT-TA
1 -AATTTAAATTAAATTGATTATA
* *
530244 ATTTTAAATTAAATTTATTATA
1 AATTTAAATTAAATTGATTATA
530266 AATTTAA
1 AATTTAA
530273 TTGATTTATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
21 16 0.41
22 19 0.49
23 3 0.08
24 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (22 bp):
AATTTAAATTAAATTGATTATA
Found at i:530274 original size:21 final size:20
Alignment explanation
Indices: 530207--530288 Score: 67
Period size: 21 Copynumber: 4.0 Consensus size: 20
530197 AATAATTTAG
* *
530207 AATTAAATTTATTTTATGATTA
1 AATTAAATTTA-TTTA-AATTT
* * *
530229 AATTATATTGATTTAATTTT
1 AATTAAATTTATTTAAATTT
530249 AAATTAAATTTATTATAAATTT
1 -AATTAAATTTATT-TAAATTT
*
530271 AATT-GATTTATTTAAATT
1 AATTAAATTTATTTAAATT
530289 ATTATTTAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
19 6 0.12
20 9 0.18
21 19 0.39
22 15 0.31
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (20 bp):
AATTAAATTTATTTAAATTT
Found at i:530277 original size:37 final size:36
Alignment explanation
Indices: 530209--530289 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 36
530199 TAATTTAGAA
* *
530209 TTAAATTTATTTTATGATTAAATTATATTGATTTAATT
1 TTAAATTAAATTTATGATTAAATTATATTGATTT-A-T
*
530247 TTAAATTAAATTTATTA-TAAATT-TAATTGATTTAT
1 TTAAATTAAATTTATGATTAAATTAT-ATTGATTTAT
530282 TTAAATTA
1 TTAAATTA
530290 TTATTTAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
35 9 0.23
36 2 0.05
37 14 0.36
38 14 0.36
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.56
Consensus pattern (36 bp):
TTAAATTAAATTTATGATTAAATTATATTGATTTAT
Found at i:530304 original size:37 final size:37
Alignment explanation
Indices: 530209--530304 Score: 90
Period size: 37 Copynumber: 2.6 Consensus size: 37
530199 TAATTTAGAA
* * *
530209 TTAAATTTATTTTATGATTAAATTATATTGATTTAATT
1 TTAAATTAAATTTAT-AATAAATTATATTGATTTAATT
*
530247 TTAAATTAAATTTATTATAAATT-TAATTGATTT-A-T
1 TTAAATTAAATTTATAATAAATTAT-ATTGATTTAATT
*
530282 TTAAATTATTATTTAATAATAAA
1 TTAAATTA-AATTT-ATAATAAA
530305 AATAATATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
35 9 0.18
36 6 0.12
37 21 0.43
38 13 0.27
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (37 bp):
TTAAATTAAATTTATAATAAATTATATTGATTTAATT
Found at i:533395 original size:2 final size:2
Alignment explanation
Indices: 533388--533414 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
533378 TTATAAGTGT
533388 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
533415 GTGTGTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:536587 original size:2 final size:2
Alignment explanation
Indices: 536580--536614 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
536570 TCAAGTGTTG
536580 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
536615 ATCAATTTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:536892 original size:17 final size:17
Alignment explanation
Indices: 536851--536899 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
536841 TATTCTTCAC
*
536851 ATAATATAAATTATATA
1 ATAATATAAATTATAAA
536868 ATATATATAAA-TATAAA
1 ATA-ATATAAATTATAAA
*
536885 ATTAATATATATTAT
1 A-TAATATAAATTAT
536900 TATATAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAATATAAATTATAAA
Found at i:536892 original size:21 final size:21
Alignment explanation
Indices: 536866--536910 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
536856 ATAAATTATA
536866 TAATATATATAAATATAAAAT
1 TAATATATATAAATATAAAAT
* * *
536887 TAATATATATTATTATATAAT
1 TAATATATATAAATATAAAAT
536908 TAA
1 TAA
536911 AAAAATAGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAATATATATAAATATAAAAT
Found at i:539311 original size:22 final size:22
Alignment explanation
Indices: 539285--539328 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
539275 AAAGCTGCAT
539285 TGCTTTTATTAAAATGATATAA
1 TGCTTTTATTAAAATGATATAA
539307 TGCTTTTATTAAAATGATATAA
1 TGCTTTTATTAAAATGATATAA
539329 GCTAGTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (22 bp):
TGCTTTTATTAAAATGATATAA
Found at i:539339 original size:21 final size:22
Alignment explanation
Indices: 539291--539339 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
539281 GCATTGCTTT
**
539291 TATTAAAATGATATAATGCTTT
1 TATTAAAATGATATAATGCTAG
539313 TATTAAAATGATATAA-GCTAG
1 TATTAAAATGATATAATGCTAG
539334 TATTAA
1 TATTAA
539340 GTTTGATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (22 bp):
TATTAAAATGATATAATGCTAG
Found at i:539781 original size:20 final size:21
Alignment explanation
Indices: 539740--539783 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
539730 TTTCGGAGAG
*
539740 ATCAATCTCTTTTTACATATAA
1 ATCAATCTCTTTATACA-ATAA
539762 ATCAATCTCTTTATAC-ATAA
1 ATCAATCTCTTTATACAATAA
539782 AT
1 AT
539784 TTAGACGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.29
22 15 0.71
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.43
Consensus pattern (21 bp):
ATCAATCTCTTTATACAATAA
Found at i:540876 original size:2 final size:2
Alignment explanation
Indices: 540869--540900 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
540859 ATAAAAGCCA
540869 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
540901 GATTGAGTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:541411 original size:14 final size:14
Alignment explanation
Indices: 541383--541434 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
541373 AGGTCAAGTA
*
541383 ATACTATATACATAC
1 ATAC-ATATATATAC
541398 ATACATATATATAC
1 ATACATATATATAC
*
541412 ATATATATATATATC
1 ATACATATATATA-C
541427 ATA-ATATA
1 ATACATATA
541435 GAAGTTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
14 26 0.76
15 8 0.24
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (14 bp):
ATACATATATATAC
Found at i:546109 original size:31 final size:31
Alignment explanation
Indices: 546058--546136 Score: 142
Period size: 31 Copynumber: 2.5 Consensus size: 31
546048 AAATATATTT
546058 TTAAAATTTATATAATATTAATTATTATTATA
1 TTAAAATTTATA-AATATTAATTATTATTATA
546090 TTAAAATTTATAAATATTAATTATTATTATA
1 TTAAAATTTATAAATATTAATTATTATTATA
546121 TTAAAA-TTATAAATAT
1 TTAAAATTTATAAATAT
546137 AAATATATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
30 10 0.21
31 25 0.53
32 12 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
TTAAAATTTATAAATATTAATTATTATTATA
Found at i:546270 original size:25 final size:22
Alignment explanation
Indices: 546242--546298 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
546232 ATAAGTAATA
546242 ATAAATATAATTAGGTAAATATGAT
1 ATAAATATAATTA---AAATATGAT
* *
546267 ATAAAAATAATTAAAATATTAT
1 ATAAATATAATTAAAATATGAT
546289 ATAAATATAA
1 ATAAATATAA
546299 AAATATATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 17 0.59
25 12 0.41
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (22 bp):
ATAAATATAATTAAAATATGAT
Found at i:546297 original size:8 final size:8
Alignment explanation
Indices: 546286--546406 Score: 61
Period size: 8 Copynumber: 14.1 Consensus size: 8
546276 ATTAAAATAT
546286 TATATAAA
1 TATATAAA
*
546294 TATAAAAA
1 TATATAAA
546302 TATATAAA
1 TATATAAA
* *
546310 -ATTTTATA
1 TA-TATAAA
546318 TAATATAAA
1 T-ATATAAA
*
546327 T-TATTAAC
1 TATA-TAAA
546335 T-TATCAAAA
1 TATAT--AAA
546344 TTTATATAAA
1 -T-ATATAAA
546354 TATA-AAA
1 TATATAAA
*
546361 TATCTTAAA
1 TAT-ATAAA
546370 TATATTAAAA
1 TATA-T-AAA
546380 TATATAAAA
1 TATAT-AAA
546389 TAATATAAA
1 T-ATATAAA
546398 TATATAAA
1 TATATAAA
546406 T
1 T
546407 TATTTTATTT
Statistics
Matches: 89, Mismatches: 10, Indels: 28
0.70 0.08 0.22
Matches are distributed among these distances:
7 10 0.11
8 35 0.39
9 25 0.28
10 16 0.18
12 3 0.03
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (8 bp):
TATATAAA
Found at i:546297 original size:28 final size:29
Alignment explanation
Indices: 546265--546402 Score: 112
Period size: 28 Copynumber: 4.8 Consensus size: 29
546255 GGTAAATATG
546265 ATATAAAAATAAT-TAAAATATTATATAA
1 ATATAAAAATAATATAAAATATTATATAA
*
546293 ATATAAAAAT-ATATAAAATTTTATAT-A
1 ATATAAAAATAATATAAAATATTATATAA
*
546320 ATATAAATTATTAACTTATCAAAAT-TTATATAA
1 ATATAAA--AATAA--TAT-AAAATATTATATAA
* *
546353 ATAT-AAAAT-ATCTTAAATA-TAT-TAAA
1 ATATAAAAATAATATAAAATATTATAT-AA
546379 ATATATAAAATAATATAAATATAT
1 ATATA-AAAATAATATAAA-ATAT
546403 AAATTATTTT
Statistics
Matches: 88, Mismatches: 7, Indels: 27
0.72 0.06 0.22
Matches are distributed among these distances:
25 1 0.01
26 13 0.15
27 12 0.14
28 27 0.31
29 8 0.09
30 6 0.07
32 11 0.12
33 10 0.11
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (29 bp):
ATATAAAAATAATATAAAATATTATATAA
Found at i:546360 original size:17 final size:17
Alignment explanation
Indices: 546303--546361 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
546293 ATATAAAAAT
546303 ATATAAAATTT-TATATA
1 ATATAAAATTTATATA-A
546320 ATAT-AAA-TTAT-TAA
1 ATATAAAATTTATATAA
*
546334 CTTATCAAAATTTATATAA
1 -ATAT-AAAATTTATATAA
546353 ATATAAAAT
1 ATATAAAAT
546362 ATCTTAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
14 1 0.03
15 7 0.21
16 4 0.12
17 12 0.35
18 7 0.21
19 3 0.09
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATAAAATTTATATAA
Found at i:546363 original size:7 final size:8
Alignment explanation
Indices: 546346--546406 Score: 61
Period size: 9 Copynumber: 7.1 Consensus size: 8
546336 TATCAAAATT
546346 TATATAAA
1 TATATAAA
546354 TATA-AAA
1 TATATAAA
*
546361 TATCTTAAA
1 TAT-ATAAA
546370 TATATTAAAA
1 TATA-T-AAA
546380 TATATAAAA
1 TATAT-AAA
546389 TAATATAAA
1 T-ATATAAA
546398 TATATAAA
1 TATATAAA
546406 T
1 T
546407 TATTTTATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
7 6 0.13
8 12 0.26
9 17 0.37
10 11 0.24
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (8 bp):
TATATAAA
Found at i:546372 original size:9 final size:9
Alignment explanation
Indices: 546271--546410 Score: 52
Period size: 9 Copynumber: 16.0 Consensus size: 9
546261 TATGATATAA
546271 AAATA-ATT
1 AAATATATT
546279 AAAATATTATAT
1 -AAATA-TAT-T
*
546291 AAATATA-A
1 AAATATATT
546299 AAATATA-T
1 AAATATATT
*
546307 AAA-ATTTT
1 AAATATATT
*
546315 ATATA-ATAT
1 AAATATAT-T
546324 AAAT-TATT
1 AAATATATT
* *
546332 AACT-TATCA
1 AAATATAT-T
*
546341 AAATTTATAT
1 AAATATAT-T
546351 AAATATA--
1 AAATATATT
*
546358 AAATATCTT
1 AAATATATT
546367 AAATATATT
1 AAATATATT
*
546376 AAAATATATA
1 -AAATATATT
546386 AAATA-ATAT
1 AAATATAT-T
546395 AAATATA-T
1 AAATATATT
546403 AAAT-TATT
1 AAATATATT
546411 TTATTTATTA
Statistics
Matches: 100, Mismatches: 16, Indels: 31
0.68 0.11 0.21
Matches are distributed among these distances:
7 10 0.10
8 29 0.29
9 33 0.33
10 20 0.20
11 7 0.07
12 1 0.01
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (9 bp):
AAATATATT
Found at i:546532 original size:17 final size:17
Alignment explanation
Indices: 546505--546538 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
546495 AAAAATATAT
546505 AATTATAAAT-AATTAA
1 AATTATAAATAAATTAA
546521 AATTAGTAAATAAATTAA
1 AATTA-TAAATAAATTAA
546539 CATGTAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 5 0.31
18 6 0.38
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
AATTATAAATAAATTAA
Found at i:546582 original size:22 final size:24
Alignment explanation
Indices: 546557--546600 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
546547 GTTTATTCAA
546557 TATTTAAATTTTA-TA-AATTTAT
1 TATTTAAATTTTACTATAATTTAT
*
546579 TATTTTAATTTTACTATAATTT
1 TATTTAAATTTTACTATAATTT
546601 TTTTAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 2 0.11
24 5 0.26
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (24 bp):
TATTTAAATTTTACTATAATTTAT
Found at i:547321 original size:12 final size:11
Alignment explanation
Indices: 547297--547331 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
547287 AAATATCTGT
547297 ATATATTTTAA
1 ATATATTTTAA
547308 ATATATTATTAA
1 ATATATT-TTAA
547320 ATATATATTTAA
1 ATATAT-TTTAA
547332 TAAATTCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 7 0.32
12 14 0.64
13 1 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
ATATATTTTAA
Found at i:548268 original size:2 final size:2
Alignment explanation
Indices: 548261--548285 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
548251 ATTATTATTC
548261 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
548286 ACTCATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:548706 original size:20 final size:20
Alignment explanation
Indices: 548669--548767 Score: 81
Period size: 20 Copynumber: 5.2 Consensus size: 20
548659 AAAGTAGGTT
*
548669 TATAAATATATAATATATTTA
1 TATAAAT-TTTAATATATTTA
548690 TATAAAATTTT-ATATA-TTA
1 TAT-AAATTTTAATATATTTA
548709 -AT-AA--TT--TATA-TTA
1 TATAAATTTTAATATATTTA
548722 TATAAATTTTAATATATTTA
1 TATAAATTTTAATATATTTA
* *
548742 TATATATTTTAATTATTTTTA
1 TATAAATTTTAA-TATATTTA
548763 TATAA
1 TATAA
548768 TATAATCGTA
Statistics
Matches: 65, Mismatches: 4, Indels: 18
0.75 0.05 0.21
Matches are distributed among these distances:
13 7 0.11
14 4 0.06
15 2 0.03
16 2 0.03
17 2 0.03
18 2 0.03
19 7 0.11
20 19 0.29
21 16 0.25
22 4 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TATAAATTTTAATATATTTA
Found at i:548718 original size:15 final size:14
Alignment explanation
Indices: 548674--548747 Score: 54
Period size: 15 Copynumber: 5.5 Consensus size: 14
548664 AGGTTTATAA
548674 ATATATAATATATTT
1 ATATATAATA-ATTT
*
548689 ATATA-AA-ATTTT
1 ATATATAATAATTT
548701 ATATATTAATAATTT
1 ATATA-TAATAATTT
548716 ATAT-TATATAAATTT
1 ATATATA-AT-AATTT
548731 -TA-AT-AT-ATTT
1 ATATATAATAATTT
548741 ATATATA
1 ATATATA
548748 TTTTAATTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 20
0.69 0.03 0.29
Matches are distributed among these distances:
10 4 0.08
11 2 0.04
12 12 0.25
13 3 0.06
14 9 0.19
15 18 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATATATAATAATTT
Found at i:548737 original size:32 final size:31
Alignment explanation
Indices: 548678--548750 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
548668 TTATAAATAT
548678 ATAATATATTTATATAAAATTTTATATATTA
1 ATAATATATTTATATAAAATTTTATATATTA
* *
548709 ATAATTTATATTATAT-AAATTTTAATATATTT
1 ATAATATAT-TTATATAAAATTTT-ATATATTA
548741 AT-ATATATTT
1 ATAATATATTT
548751 TAATTATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
30 2 0.05
31 20 0.54
32 15 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (31 bp):
ATAATATATTTATATAAAATTTTATATATTA
Found at i:549309 original size:14 final size:15
Alignment explanation
Indices: 549290--549318 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
549280 TTAATTATTT
549290 TTAAA-TTAAAATTA
1 TTAAATTTAAAATTA
549304 TTAAATTTAAAATTA
1 TTAAATTTAAAATTA
549319 AACTAGATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAATTTAAAATTA
Found at i:550081 original size:23 final size:23
Alignment explanation
Indices: 550049--550093 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
550039 TAAACATATT
550049 ATAAAATAAGAAAATT-TTAAAG
1 ATAAAATAAGAAAATTATTAAAG
*
550071 ATAAAGATAAGAGAATTATTAAA
1 ATAAA-ATAAGAAAATTATTAAA
550094 ATACATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 10 0.50
24 5 0.25
ACGTcount: A:0.62, C:0.00, G:0.11, T:0.27
Consensus pattern (23 bp):
ATAAAATAAGAAAATTATTAAAG
Found at i:554590 original size:7 final size:6
Alignment explanation
Indices: 554578--554625 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
554568 TTCAATCTTT
* *
554578 TTTTTCC TTTTTC TTTTT- TTTTTC TTTTCTC TTCTTC TTTTTG TTTTT
1 TTTTT-C TTTTTC TTTTTC TTTTTC TTTT-TC TTTTTC TTTTTC TTTTT
554626 TCCCTCTTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
5 5 0.14
6 21 0.58
7 10 0.28
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:554596 original size:18 final size:18
Alignment explanation
Indices: 554575--554624 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
554565 TCTTTCAATC
*
554575 TTTTTTTTCCTTTT-TCT
1 TTTTTTTTTCTTTTCTCT
554592 TTTTTTTTTCTTTTCTCT
1 TTTTTTTTTCTTTTCTCT
* *
554610 TCTTCTTTTTGTTTT
1 T-TTTTTTTTCTTTT
554625 TTCCCTCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 13 0.46
18 4 0.14
19 11 0.39
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (18 bp):
TTTTTTTTTCTTTTCTCT
Found at i:554605 original size:24 final size:24
Alignment explanation
Indices: 554547--554625 Score: 81
Period size: 24 Copynumber: 3.2 Consensus size: 24
554537 AATTATTCTC
*
554547 TTTTTTCTTTTTCCTTCTTCTTTCA
1 TTTTTTCTTTTTCCTTCTTCTTT-T
* * *
554572 ATCTTT-TTTTTCCTTTTTCTTTT
1 TTTTTTCTTTTTCCTTCTTCTTTT
554595 TTTTTTC-TTTTCTCTTCTTCTTTT
1 TTTTTTCTTTTTC-CTTCTTCTTTT
554619 TGTTTTT
1 T-TTTTT
554626 TCCCTCTTTC
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
23 9 0.20
24 26 0.59
25 9 0.20
ACGTcount: A:0.03, C:0.19, G:0.01, T:0.77
Consensus pattern (24 bp):
TTTTTTCTTTTTCCTTCTTCTTTT
Found at i:554632 original size:23 final size:22
Alignment explanation
Indices: 554576--554634 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 22
554566 CTTTCAATCT
*
554576 TTTTTTTCCT-TTTTCTTTTTT
1 TTTTTTTCCTCTTTTCTTTTTG
*
554597 TTTTCTTTTCTCTTCTTCTTTTTG
1 TTTT-TTTCCTCTT-TTCTTTTTG
*
554621 TTTTTTCCCTCTTT
1 TTTTTTTCCTCTTT
554635 CATTAGAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
21 4 0.13
22 6 0.19
23 9 0.29
24 12 0.39
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (22 bp):
TTTTTTTCCTCTTTTCTTTTTG
Found at i:556203 original size:31 final size:31
Alignment explanation
Indices: 556154--556214 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
556144 ATAATGATGC
* * *
556154 CACATCATTTGTCAATGCCACGTGACATTAA
1 CACATCATTTGTAAATGCCACATGAAATTAA
556185 CACATCATTT-TAACATGCCACATGAAATTA
1 CACATCATTTGTAA-ATGCCACATGAAATTA
556215 TTAATTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.36, C:0.25, G:0.10, T:0.30
Consensus pattern (31 bp):
CACATCATTTGTAAATGCCACATGAAATTAA
Found at i:556305 original size:31 final size:29
Alignment explanation
Indices: 556269--556344 Score: 73
Period size: 31 Copynumber: 2.6 Consensus size: 29
556259 ATAAATTACA
**
556269 CTTTTGATCATTTAACTTTTCGATAATTTTT
1 CTTTTGATCATCCAACTTTT-GA-AATTTTT
* *
556300 CTTTTGGTCATCCAACTTTTGAAATTTCAT
1 CTTTTGATCATCCAACTTTTGAAATTT-TT
*
556330 ATTTTGATCA-CCAAC
1 CTTTTGATCATCCAAC
556345 GATTTATTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
29 10 0.26
30 11 0.29
31 17 0.45
ACGTcount: A:0.25, C:0.18, G:0.08, T:0.49
Consensus pattern (29 bp):
CTTTTGATCATCCAACTTTTGAAATTTTT
Found at i:557041 original size:231 final size:231
Alignment explanation
Indices: 556739--557205 Score: 934
Period size: 231 Copynumber: 2.0 Consensus size: 231
556729 TATAATCTTT
556739 ATTTCATAATTTTTTAAATCTTTTACATTTATATAAGTTTAGGTAATAAAAAATCTTAAGATTTT
1 ATTTCATAATTTTTTAAATCTTTTACATTTATATAAGTTTAGGTAATAAAAAATCTTAAGATTTT
556804 ATCTTTTTTTTGGTTAAATTCATATATTTATTACTAACAAATAAGCCTTTAATATTTAATTTATA
66 ATCTTTTTTTTGGTTAAATTCATATATTTATTACTAACAAATAAGCCTTTAATATTTAATTTATA
556869 AACAAATAAACATTTAATTTTAATCTTTGTCACAACATGCGCTCGACCCCGATGATAGGACAAAT
131 AACAAATAAACATTTAATTTTAATCTTTGTCACAACATGCGCTCGACCCCGATGATAGGACAAAT
556934 GAGGCGCGCCCGAATTAATATCCCTTGTGATTGGGG
196 GAGGCGCGCCCGAATTAATATCCCTTGTGATTGGGG
556970 ATTTCATAATTTTTTAAATCTTTTACATTTATATAAGTTTAGGTAATAAAAAATCTTAAGATTTT
1 ATTTCATAATTTTTTAAATCTTTTACATTTATATAAGTTTAGGTAATAAAAAATCTTAAGATTTT
557035 ATCTTTTTTTTGGTTAAATTCATATATTTATTACTAACAAATAAGCCTTTAATATTTAATTTATA
66 ATCTTTTTTTTGGTTAAATTCATATATTTATTACTAACAAATAAGCCTTTAATATTTAATTTATA
557100 AACAAATAAACATTTAATTTTAATCTTTGTCACAACATGCGCTCGACCCCGATGATAGGACAAAT
131 AACAAATAAACATTTAATTTTAATCTTTGTCACAACATGCGCTCGACCCCGATGATAGGACAAAT
557165 GAGGCGCGCCCGAATTAATATCCCTTGTGATTGGGG
196 GAGGCGCGCCCGAATTAATATCCCTTGTGATTGGGG
557201 ATTTC
1 ATTTC
557206 TATGGCATGG
Statistics
Matches: 236, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
231 236 1.00
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (231 bp):
ATTTCATAATTTTTTAAATCTTTTACATTTATATAAGTTTAGGTAATAAAAAATCTTAAGATTTT
ATCTTTTTTTTGGTTAAATTCATATATTTATTACTAACAAATAAGCCTTTAATATTTAATTTATA
AACAAATAAACATTTAATTTTAATCTTTGTCACAACATGCGCTCGACCCCGATGATAGGACAAAT
GAGGCGCGCCCGAATTAATATCCCTTGTGATTGGGG
Found at i:559317 original size:2 final size:2
Alignment explanation
Indices: 559310--559344 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
559300 GAGATTTTCA
*
559310 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
559345 AATAAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:559764 original size:20 final size:20
Alignment explanation
Indices: 559724--559773 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
559714 CATATGGTTT
* * *
559724 TTCCTTTTTTTTTCTTTTTC
1 TTCCTTTCTTTTTCATCTTC
559744 TTCCTTTCTTTTTCATCTTC
1 TTCCTTTCTTTTTCATCTTC
*
559764 TTTCTTTCTT
1 TTCCTTTCTT
559774 ACCTATAACC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (20 bp):
TTCCTTTCTTTTTCATCTTC
Found at i:559937 original size:21 final size:20
Alignment explanation
Indices: 559907--559955 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
559897 CGACCTCCTC
559907 TTTTTA-AATTCGGAGTTAGA
1 TTTTTATAATTC-GAGTTAGA
***
559927 TTTTTATAATTCTTTTTAGA
1 TTTTTATAATTCGAGTTAGA
559947 TTTTTATAA
1 TTTTTATAA
559956 ATCTACAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.29, C:0.04, G:0.10, T:0.57
Consensus pattern (20 bp):
TTTTTATAATTCGAGTTAGA
Found at i:564164 original size:8 final size:8
Alignment explanation
Indices: 564151--564222 Score: 51
Period size: 8 Copynumber: 8.8 Consensus size: 8
564141 TATCGACATG
564151 ATATAAAT
1 ATATAAAT
564159 ATATAAAT
1 ATATAAAT
*
564167 ATTTTAAA-
1 A-TATAAAT
564175 AT-TAATAT
1 ATATAA-AT
564183 AATATAAAT
1 -ATATAAAT
*
564192 -TATTAAT
1 ATATAAAT
*
564199 AAATAAATTT
1 ATATAAA--T
564209 ATATAAAT
1 ATATAAAT
564217 ATATAA
1 ATATAA
564223 TAAATTAAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
6 3 0.06
7 8 0.16
8 21 0.41
9 9 0.18
10 10 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
ATATAAAT
Found at i:564193 original size:15 final size:15
Alignment explanation
Indices: 564173--564219 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
564163 AAATATTTTA
564173 AAATTAATATAATAT
1 AAATTAATATAATAT
*
564188 AAATTATTAATAA-AT
1 AAATTAAT-ATAATAT
*
564203 AAATTTATATAAATAT
1 AAATTAATAT-AATAT
564219 A
1 A
564220 TAATAAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
14 2 0.08
15 17 0.65
16 7 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAATTAATATAATAT
Found at i:564210 original size:16 final size:18
Alignment explanation
Indices: 564175--564229 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
564165 ATATTTTAAA
564175 ATTAATATAATATAAATT
1 ATTAATATAATATAAATT
*
564193 ATTAATA-AATA-AATTT
1 ATTAATATAATATAAATT
564209 ATATAA-ATATATAATAAATT
1 AT-TAATATA-AT-ATAAATT
564229 A
1 A
564230 AATACGTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
16 7 0.23
17 8 0.27
18 9 0.30
19 1 0.03
20 5 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTAATATAATATAAATT
Found at i:564212 original size:25 final size:26
Alignment explanation
Indices: 564158--564232 Score: 77
Period size: 25 Copynumber: 3.0 Consensus size: 26
564148 ATGATATAAA
* *
564158 TATATAAATATTTTA-AAATT-AATAT
1 TATATAAATATATAATAAATTAAAT-T
*
564183 AATATAAAT-TATTAATAAA-TAAATT
1 TATATAAATATA-TAATAAATTAAATT
564208 TATATAAATATATAATAAATTAAAT
1 TATATAAATATATAATAAATTAAAT
564233 ACGTTTATGA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
24 1 0.02
25 27 0.66
26 13 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
TATATAAATATATAATAAATTAAATT
Found at i:564807 original size:20 final size:20
Alignment explanation
Indices: 564775--564816 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
564765 ATTACTTAAA
*
564775 ATTTAAAATATATAATTTAT
1 ATTTAAAATATATAATATAT
564795 ATTTATAAA-ATATAATATAT
1 ATTTA-AAATATATAATATAT
564815 AT
1 AT
564817 ACTAATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTTAAAATATATAATATAT
Found at i:567105 original size:18 final size:20
Alignment explanation
Indices: 567085--567121 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
567075 TCACCGTTTC
567085 TTTCCGTTTT-GTTCGTTCT
1 TTTCCGTTTTCGTTCGTTCT
*
567104 TTTCCTTTTTCGTTCGTT
1 TTTCCGTTTTCGTTCGTT
567122 GTTCTCCCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.00, C:0.22, G:0.14, T:0.65
Consensus pattern (20 bp):
TTTCCGTTTTCGTTCGTTCT
Found at i:568230 original size:2 final size:2
Alignment explanation
Indices: 568223--568269 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
568213 TTTTAGATGT
* *
568223 TA TA TA TA TA AA TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
568265 TA TA T
1 TA TA T
568270 TAGAATTTGG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:569401 original size:16 final size:16
Alignment explanation
Indices: 569376--569409 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
569366 TAATCATATT
* *
569376 AAATTTAATTATTTTA
1 AAATTAAATTAATTTA
569392 AAATTAAATTAATTTA
1 AAATTAAATTAATTTA
569408 AA
1 AA
569410 CTCAAATAAT
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATTAAATTAATTTA
Found at i:570332 original size:16 final size:17
Alignment explanation
Indices: 570296--570343 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
570286 TAATTTTATA
* *
570296 TTATTATTTATATATTT
1 TTATTAATTAAATATTT
570313 TT-TATAATTAAATATTT
1 TTAT-TAATTAAATATTT
570330 TTATTAATTAAATA
1 TTATTAATTAAATA
570344 ATTTAGGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 1 0.04
17 25 0.93
18 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTATTAATTAAATATTT
Found at i:570456 original size:29 final size:26
Alignment explanation
Indices: 570402--570457 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 26
570392 TTCCCTTGCT
* *
570402 TCAAAATAATTTCCAAGGAAATTTCC
1 TCAAAATAATTTCCAACGAAAATTCC
570428 TCAAAATATTATTTCCAAACGAAAATTCC
1 TCAAAATA--ATTTCC-AACGAAAATTCC
570457 T
1 T
570458 TGGAATGTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 8 0.32
28 6 0.24
29 11 0.44
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (26 bp):
TCAAAATAATTTCCAACGAAAATTCC
Found at i:570945 original size:19 final size:20
Alignment explanation
Indices: 570907--570945 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
570897 AAAATCAGAA
* *
570907 TATTTATAAATATTTTTATT
1 TATTTATAAAAATTTATATT
570927 TATTTA-AAAAATTTATATT
1 TATTTATAAAAATTTATATT
570946 AAATTAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TATTTATAAAAATTTATATT
Found at i:571095 original size:5 final size:5
Alignment explanation
Indices: 571076--571119 Score: 70
Period size: 5 Copynumber: 8.6 Consensus size: 5
571066 GAGGCAAGGG
*
571076 TTGGT TTGGGT TTGGA TTGGT TTGGT TTGGT TTGGT TTGGT TTG
1 TTGGT TT-GGT TTGGT TTGGT TTGGT TTGGT TTGGT TTGGT TTG
571120 TTGGTGGTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
5 31 0.86
6 5 0.14
ACGTcount: A:0.02, C:0.00, G:0.41, T:0.57
Consensus pattern (5 bp):
TTGGT
Found at i:571532 original size:19 final size:18
Alignment explanation
Indices: 571504--571543 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
571494 AAGTTTTTAT
*
571504 TATTTTAATAATTTATTAA
1 TATTTAAATAATTTA-TAA
*
571523 TATTTAAATATTTTATAA
1 TATTTAAATAATTTATAA
571541 TAT
1 TAT
571544 CATTACCGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTTAAATAATTTATAA
Found at i:571599 original size:15 final size:14
Alignment explanation
Indices: 571574--571613 Score: 62
Period size: 15 Copynumber: 2.8 Consensus size: 14
571564 TATTATAATT
571574 TTTAAAATATAAAA
1 TTTAAAATATAAAA
571588 TTTAATAATATAAAA
1 TTTAA-AATATAAAA
*
571603 ATTAAAATATA
1 TTTAAAATATA
571614 TTTTTACTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TTTAAAATATAAAA
Found at i:571807 original size:20 final size:20
Alignment explanation
Indices: 571750--571807 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 20
571740 TATTAAATAA
*
571750 AAATTATATAAT-TAATAATT
1 AAATTAAATAATATAAT-ATT
*
571770 -AA-TAAA-AATAT-TTATT
1 AAATTAAATAATATAATATT
571786 AAATTAAATAATATAATATT
1 AAATTAAATAATATAATATT
571806 AA
1 AA
571808 TAAAACTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
16 3 0.10
17 6 0.20
18 8 0.27
19 7 0.23
20 6 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATTAAATAATATAATATT
Found at i:573044 original size:27 final size:26
Alignment explanation
Indices: 573014--573064 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
573004 GTATTTTTAC
* *
573014 ATTTTAAAATATTATATATTTATATAA
1 ATTTTAAAATAATAT-TAATTATATAA
*
573041 ATTTTAATATAATATTAATTATAT
1 ATTTTAAAATAATATTAATTATAT
573065 TATATAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 8 0.38
27 13 0.62
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
ATTTTAAAATAATATTAATTATATAA
Found at i:573071 original size:31 final size:30
Alignment explanation
Indices: 573021--573082 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 30
573011 TACATTTTAA
573021 AATATTATATATTTATATAAATTTTAATAT
1 AATATTATATATTTATATAAATTTTAATAT
* *
573051 AATATTA-ATTATATTATATAATTTTTGATAT
1 AATATTATA-TAT-TTATATAAATTTTAATAT
573082 A
1 A
573083 TTCGTATCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 1 0.04
30 10 0.36
31 17 0.61
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (30 bp):
AATATTATATATTTATATAAATTTTAATAT
Found at i:573118 original size:22 final size:21
Alignment explanation
Indices: 573091--573149 Score: 84
Period size: 22 Copynumber: 2.8 Consensus size: 21
573081 TATTCGTATC
573091 TTTATATCATATTTATATTATT
1 TTTATATCATATTTA-ATTATT
*
573113 TTTATATAATAATTTAATTATT
1 TTTATATCAT-ATTTAATTATT
573135 TTT-TATCATATTTAA
1 TTTATATCATATTTAA
573150 CGTCGTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.18
21 5 0.15
22 18 0.53
23 5 0.15
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTATATCATATTTAATTATT
Found at i:573500 original size:30 final size:29
Alignment explanation
Indices: 573466--573533 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
573456 TGATGCGATT
573466 ATATAATATAAATATTAAAATATAAT-TAAA
1 ATATAATATAAA-A-TAAAATATAATATAAA
* **
573496 ATATAATTTAAAATATGATATAATATAAA
1 ATATAATATAAAATAAAATATAATATAAA
573525 ATAATAATA
1 AT-ATAATA
573534 CAAACACGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 9 0.28
29 7 0.22
30 16 0.50
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (29 bp):
ATATAATATAAAATAAAATATAATATAAA
Found at i:573508 original size:12 final size:12
Alignment explanation
Indices: 573470--573511 Score: 59
Period size: 11 Copynumber: 3.4 Consensus size: 12
573460 GCGATTATAT
573470 AATATAAATATTAA
1 AATAT-AAT-TTAA
573484 AATATAA-TTAA
1 AATATAATTTAA
573495 AATATAATTTAA
1 AATATAATTTAA
573507 AATAT
1 AATAT
573512 GATATAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 11 0.41
12 9 0.33
13 2 0.07
14 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AATATAATTTAA
Found at i:573937 original size:22 final size:22
Alignment explanation
Indices: 573912--573953 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
573902 TAAATTTTTT
573912 AAAT-TTAATTATAAAAATATGG
1 AAATATTAA-TATAAAAATATGG
573934 AAATATTAATATAAAAATAT
1 AAATATTAATATAAAAATAT
573954 TTTAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (22 bp):
AAATATTAATATAAAAATATGG
Found at i:573960 original size:22 final size:23
Alignment explanation
Indices: 573903--573961 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 23
573893 TTTAAAAAAT
*
573903 AAATTTTTTAA-ATTTAATTATAA
1 AAATATTTTAATA-TTAATTATAA
***
573926 AAATATGGAAATATTAA-TATAA
1 AAATATTTTAATATTAATTATAA
573948 AAATATTTTAATAT
1 AAATATTTTAATAT
573962 ATTTAAAATA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
22 16 0.57
23 11 0.39
24 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (23 bp):
AAATATTTTAATATTAATTATAA
Found at i:574646 original size:2 final size:2
Alignment explanation
Indices: 574634--574670 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
574624 GGAAGCTCCA
*
574634 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
574671 GAAATGTTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:575104 original size:2 final size:2
Alignment explanation
Indices: 575097--575136 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
575087 ATCAATATCA
*
575097 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT A- AT CT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
575137 TTTATCGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:575106 original size:12 final size:11
Alignment explanation
Indices: 575091--575136 Score: 53
Period size: 10 Copynumber: 4.4 Consensus size: 11
575081 ATCAATATCA
575091 ATATCAATATAT
1 ATAT-AATATAT
575103 ATAT-ATATAT
1 ATATAATATAT
575113 ATAT-ATATAT
1 ATATAATATAT
*
575123 A-ATAATCTAT
1 ATATAATATAT
575133 ATAT
1 ATAT
575137 TTTATCGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
9 2 0.06
10 23 0.74
11 2 0.06
12 4 0.13
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (11 bp):
ATATAATATAT
Found at i:575244 original size:16 final size:16
Alignment explanation
Indices: 575223--575259 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
575213 TTTTTAAATA
575223 TATATTTATATTATAT
1 TATATTTATATTATAT
* *
575239 TATATTTTTATTATTT
1 TATATTTATATTATAT
575255 TATAT
1 TATAT
575260 ATATCATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATATTTATATTATAT
Found at i:575248 original size:18 final size:20
Alignment explanation
Indices: 575220--575263 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
575210 AAATTTTTAA
575220 ATATATATTTA-TATTATAT
1 ATATATATTTATTATTATAT
* *
575239 -TATATTTTTATTATTTTAT
1 ATATATATTTATTATTATAT
575258 ATATAT
1 ATATAT
575264 CATATTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 9 0.43
19 7 0.33
20 5 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
ATATATATTTATTATTATAT
Found at i:575987 original size:26 final size:24
Alignment explanation
Indices: 575957--576013 Score: 78
Period size: 26 Copynumber: 2.3 Consensus size: 24
575947 TTGTCATCTG
* *
575957 TATATTTATATTATTTTATATTATA
1 TATATTTAAAATATTTTAT-TTATA
575982 TTATATTTAAAATATTTTATTTATA
1 -TATATTTAAAATATTTTATTTATA
576007 TATATTT
1 TATATTT
576014 TTTATATGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 7 0.24
25 5 0.17
26 17 0.59
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
TATATTTAAAATATTTTATTTATA
Found at i:576020 original size:24 final size:24
Alignment explanation
Indices: 575957--576053 Score: 79
Period size: 24 Copynumber: 3.9 Consensus size: 24
575947 TTGTCATCTG
575957 TATA-TTTATATTATTTTATATTATA
1 TATATTTTATA-TATTTTAT-TTATA
* *
575982 TTATATTTAAAATATTTTATTTATA
1 -TATATTTTATATATTTTATTTATA
* * * * *
576007 TATATTTTTTATATGTTAATAATT
1 TATATTTTATATATTTTATTTATA
576031 TATATTTTGATATATTTATATTT
1 TATATTTT-ATATATTT-TATTT
576054 TAAGTTCATA
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
24 25 0.45
25 11 0.20
26 15 0.27
27 4 0.07
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (24 bp):
TATATTTTATATATTTTATTTATA
Found at i:576032 original size:15 final size:16
Alignment explanation
Indices: 575957--576073 Score: 78
Period size: 16 Copynumber: 6.9 Consensus size: 16
575947 TTGTCATCTG
*
575957 TATATTTATATTATT-T
1 TATATTTATATT-TTAA
575973 TATATTATATTATATTTAA
1 TATATT-TA-TAT-TTTAA
*
575992 AATATTT-TATTTATATA
1 TATATTTATATTT-TA-A
* *
576009 TATTTTTTATATGTTAA
1 TA-TATTTATATTTTAA
*
576026 TA-ATTTATATTTTGA
1 TATATTTATATTTTAA
576041 TATATTTATATTTTAA
1 TATATTTATATTTTAA
576057 GTTCATATTTATATTTT
1 --T-ATATTTATATTTT
576074 TTTTATAATA
Statistics
Matches: 80, Mismatches: 9, Indels: 21
0.73 0.08 0.19
Matches are distributed among these distances:
15 14 0.17
16 23 0.29
17 7 0.09
18 13 0.16
19 23 0.29
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (16 bp):
TATATTTATATTTTAA
Found at i:576178 original size:28 final size:29
Alignment explanation
Indices: 576119--576180 Score: 76
Period size: 28 Copynumber: 2.1 Consensus size: 29
576109 ATTAAATTTT
576119 TAATTTTAATAATAACAAATTAAATATTGA
1 TAATTTTAATAATAACAAA-TAAATATTGA
576149 TAATTTTAAATATATAA-AAA-AAATA-TGA
1 TAATTTT-AATA-ATAACAAATAAATATTGA
576177 TAAT
1 TAAT
576181 GGTGTCGAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
28 7 0.23
29 5 0.17
30 7 0.23
31 7 0.23
32 4 0.13
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (29 bp):
TAATTTTAATAATAACAAATAAATATTGA
Found at i:576476 original size:3 final size:3
Alignment explanation
Indices: 576470--576501 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
576460 CATGGCAACT
576470 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
576502 TAATTTAGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:576761 original size:3 final size:3
Alignment explanation
Indices: 576753--576788 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
576743 TAAATCTTAA
576753 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
576789 GGTATTATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:576797 original size:3 final size:3
Alignment explanation
Indices: 576791--576824 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
576781 ATAATAATGG
576791 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
576825 GTTGTTGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:577352 original size:2 final size:2
Alignment explanation
Indices: 577347--577380 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
577337 TGCTTTTTTA
577347 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
577381 GTTAGGGCGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.