Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold507
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: 914714
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
File 4 of 8
Found at i:402356 original size:22 final size:23
Alignment explanation
Indices: 402290--402369 Score: 80
Period size: 22 Copynumber: 3.6 Consensus size: 23
402280 TAAAATTATT
*
402290 TATATTAAT-TTAAT-TATAAAAA
1 TATA-TAATATTAATATTTAAAAA
402312 TATATAATATTAATATTTAAAAA
1 TATATAATATTAATATTTAAAAA
*
402335 -ATATAAT-TTAATATTTTTAAAA
1 TATATAATATTAATA-TTTAAAAA
*
402357 TA-ATAAAATTAAT
1 TATATAATATTAAT
402370 TTATAAATAA
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
21 10 0.20
22 27 0.54
23 13 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATATAATATTAATATTTAAAAA
Found at i:402371 original size:21 final size:21
Alignment explanation
Indices: 402299--402386 Score: 63
Period size: 20 Copynumber: 4.1 Consensus size: 21
402289 TTATATTAAT
* * *
402299 TTAATTATAAAAATATATAATA
1 TTAATTTTTAAAATA-ATAAAA
* *
402321 TTAATATTTAAAA-AATATAAT
1 TTAATTTTTAAAATAATA-AAA
402342 TTAATATTTTTAAAATAATAAAA
1 TT-A-ATTTTTAAAATAATAAAA
* *
402365 TTAATTTAT-AAATAAAAAAA
1 TTAATTTTTAAAATAATAAAA
402385 TT
1 TT
402387 TTAAATGTCG
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
20 15 0.28
21 9 0.17
22 12 0.23
23 13 0.25
24 4 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAATTTTTAAAATAATAAAA
Found at i:404467 original size:18 final size:18
Alignment explanation
Indices: 404446--404501 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
404436 CCATTCCTAT
404446 ATTCATCCCCATGCCAGG
1 ATTCATCCCCATGCCAGG
**
404464 ATTCA-CGCCCATG---TT
1 ATTCATC-CCCATGCCAGG
404479 ATTCATCCCCATGCCAGG
1 ATTCATCCCCATGCCAGG
404497 ATTCA
1 ATTCA
404502 CGCCCATGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 10
0.67 0.09 0.23
Matches are distributed among these distances:
15 11 0.38
16 1 0.03
17 1 0.03
18 16 0.55
ACGTcount: A:0.23, C:0.36, G:0.14, T:0.27
Consensus pattern (18 bp):
ATTCATCCCCATGCCAGG
Found at i:404482 original size:33 final size:33
Alignment explanation
Indices: 404445--404553 Score: 154
Period size: 33 Copynumber: 3.4 Consensus size: 33
404435 CCCATTCCTA
404445 TATTCATCCCCATGCCAGGATTCACGCCCATGT
1 TATTCATCCCCATGCCAGGATTCACGCCCATGT
404478 TATTCATCCCCATGCCAGGATTCACGCCCATG-
1 TATTCATCCCCATGCCAGGATTCACGCCCATGT
* *
404510 --TTCATCCCCATGCCCAGG-TTCATGCCCGTGT
1 TATTCATCCCCATG-CCAGGATTCACGCCCATGT
*
404541 TGTTCATCCCCAT
1 TATTCATCCCCAT
404554 TCCCATGCCC
Statistics
Matches: 70, Mismatches: 2, Indels: 8
0.88 0.03 0.10
Matches are distributed among these distances:
30 22 0.31
31 5 0.07
33 43 0.61
ACGTcount: A:0.18, C:0.38, G:0.16, T:0.28
Consensus pattern (33 bp):
TATTCATCCCCATGCCAGGATTCACGCCCATGT
Found at i:404507 original size:18 final size:18
Alignment explanation
Indices: 404453--404509 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
404443 TATATTCATC
404453 CCCATGCCAGGATTCACG
1 CCCATGCCAGGATTCACG
**
404471 CCCATG---TTATTCATC-
1 CCCATGCCAGGATTCA-CG
404486 CCCATGCCAGGATTCACG
1 CCCATGCCAGGATTCACG
404504 CCCATG
1 CCCATG
404510 TTCATCCCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
15 11 0.37
16 1 0.03
17 1 0.03
18 17 0.57
ACGTcount: A:0.21, C:0.39, G:0.18, T:0.23
Consensus pattern (18 bp):
CCCATGCCAGGATTCACG
Found at i:405474 original size:33 final size:33
Alignment explanation
Indices: 405423--405649 Score: 177
Period size: 33 Copynumber: 6.9 Consensus size: 33
405413 ATTAGCACTT
* * *
405423 GGCTGGCTGTATGGGTTAGCATTCGGCTGTGCA
1 GGCTGGCCGTATGGATTAGCATTTGGCTGTGCA
* * * * *
405456 GGTTGGCCATATGGGTTAGCGTTTGGTTGTGCA
1 GGCTGGCCGTATGGATTAGCATTTGGCTGTGCA
* * * **
405489 AGTTGGCCGTATGGATTAGCATTAGGCTGTGTG
1 GGCTGGCCGTATGGATTAGCATTTGGCTGTGCA
* *
405522 GGCTGGCTGTATGGATTAGCATTTGGTTGTGCA
1 GGCTGGCCGTATGGATTAGCATTTGGCTGTGCA
* * *
405555 GGCTGGCCGTAGGGATCAGCATTTGGTTGTGC-
1 GGCTGGCCGTATGGATTAGCATTTGGCTGTGCA
* * * * ** **
405587 GAACTGGCTGTAGGGATTAGAAGCTGGCTGCCCA
1 G-GCTGGCCGTATGGATTAGCATTTGGCTGTGCA
* * *
405621 GGTTGGCCGTAGGGATTAGCACTTGGCTG
1 GGCTGGCCGTATGGATTAGCATTTGGCTG
405650 CCCGTTGTGG
Statistics
Matches: 153, Mismatches: 39, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
32 1 0.01
33 151 0.99
34 1 0.01
ACGTcount: A:0.15, C:0.16, G:0.38, T:0.30
Consensus pattern (33 bp):
GGCTGGCCGTATGGATTAGCATTTGGCTGTGCA
Found at i:405604 original size:99 final size:99
Alignment explanation
Indices: 405423--405606 Score: 246
Period size: 99 Copynumber: 1.9 Consensus size: 99
405413 ATTAGCACTT
* * * *
405423 GGCTGGCTGTATGGGTTAGCATTCGGCTGTGCAGGTTGGCCATATGGGTTAGCGTTTGGTTGTGC
1 GGCTGGCTGTATGGATTAGCATTCGGCTGTGCAGGCTGGCCATATGGGTCAGCATTTGGTTGTGC
* *
405488 AAGTTGGCCGTATGGATTAGCATTAGGCTGTGTG
66 AAGCTGGCCGTAGGGATTAGCATTAGGCTGTGTG
* * *
405522 GGCTGGCTGTATGGATTAGCATTTGGTTGTGCAGGCTGGCCGTA-GGGATCAGCATTTGGTTGTG
1 GGCTGGCTGTATGGATTAGCATTCGGCTGTGCAGGCTGGCCATATGGG-TCAGCATTTGGTTGTG
*
405586 CGAA-CTGGCTGTAGGGATTAG
65 C-AAGCTGGCCGTAGGGATTAG
405607 AAGCTGGCTG
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
98 3 0.04
99 68 0.93
100 2 0.03
ACGTcount: A:0.15, C:0.14, G:0.39, T:0.32
Consensus pattern (99 bp):
GGCTGGCTGTATGGATTAGCATTCGGCTGTGCAGGCTGGCCATATGGGTCAGCATTTGGTTGTGC
AAGCTGGCCGTAGGGATTAGCATTAGGCTGTGTG
Found at i:405650 original size:33 final size:34
Alignment explanation
Indices: 405597--405715 Score: 113
Period size: 33 Copynumber: 3.6 Consensus size: 34
405587 GAACTGGCTG
* *
405597 TAGGGATTAGAAGC-TGGCTGCCCAGGTTGGCCG
1 TAGGGATTAGCAGCTTGGCTGCCCAGGTTGGCCA
*
405630 TAGGGATTAGCA-CTTGGCTGCCC-GTTGTGGCCA
1 TAGGGATTAGCAGCTTGGCTGCCCAGGT-TGGCCA
* * * * *
405663 TATGAATTAG-AGCTAGGCTGCACAGGCTGGCCA
1 TAGGGATTAGCAGCTTGGCTGCCCAGGTTGGCCA
*
405696 TATGGATTAGCA-CTTGGCTG
1 TAGGGATTAGCAGCTTGGCTG
405716 TGTGGGTTGG
Statistics
Matches: 70, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
32 4 0.06
33 64 0.91
34 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.34, T:0.25
Consensus pattern (34 bp):
TAGGGATTAGCAGCTTGGCTGCCCAGGTTGGCCA
Found at i:406548 original size:172 final size:171
Alignment explanation
Indices: 406259--406604 Score: 665
Period size: 172 Copynumber: 2.0 Consensus size: 171
406249 AAAAAAAAAA
406259 TCAACAACAATGTCCACTTGAAATAAAGAACAAAGACAAAGTTAAGAGGCATAATTAGGGGAAAG
1 TCAACAACAATGTCCACTTGAAATAAAGAACAAAGACAAAGTTAAGAGGCATAATTAGGGGAAAG
406324 AAAGCAAAGAGGAAGGAAATAAAGCAAAATGTAGCAATGCGTTATATTCATAATCAGTTAAGTGA
66 AAAGCAAAGAGGAAGGAAATAAAGCAAAATGTAGCAATGCGTTATATTCATAATCAGTTAAGTGA
406389 TATAATTCTAAACAAAATTTCACCTTTATATTTTTTGAAAT
131 TATAATTCTAAACAAAATTTCACCTTTATATTTTTTGAAAT
406430 TCAACAACAATGTCCACTTGAAATAAAGAACAAAGACAAAGTTAAGAGGCATAATTACGGGGAAA
1 TCAACAACAATGTCCACTTGAAATAAAGAACAAAGACAAAGTTAAGAGGCATAATTA-GGGGAAA
* *
406495 GAAAGCAAAGAGGAAGGAAATAAAGCAAAATGTAGCACTGGGTTATATTCATAATCAGTTAAGTG
65 GAAAGCAAAGAGGAAGGAAATAAAGCAAAATGTAGCAATGCGTTATATTCATAATCAGTTAAGTG
406560 ATATAATTCTAAACAAAATTTCACCTTTATATTTTTTGAAAT
130 ATATAATTCTAAACAAAATTTCACCTTTATATTTTTTGAAAT
406602 TCA
1 TCA
406605 CCCTAAAACC
Statistics
Matches: 172, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
171 57 0.33
172 115 0.67
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.26
Consensus pattern (171 bp):
TCAACAACAATGTCCACTTGAAATAAAGAACAAAGACAAAGTTAAGAGGCATAATTAGGGGAAAG
AAAGCAAAGAGGAAGGAAATAAAGCAAAATGTAGCAATGCGTTATATTCATAATCAGTTAAGTGA
TATAATTCTAAACAAAATTTCACCTTTATATTTTTTGAAAT
Found at i:410109 original size:13 final size:13
Alignment explanation
Indices: 410091--410143 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
410081 GAGGAAAAGT
410091 AAAATATGTACAG
1 AAAATATGTACAG
* *
410104 AAAATATGGAAAG
1 AAAATATGTACAG
*
410117 TAAAATATAGTACAC
1 -AAAATAT-GTACAG
*
410132 AAAAAATGTACA
1 AAAATATGTACA
410144 TCATAACACA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
13 16 0.50
14 13 0.41
15 3 0.09
ACGTcount: A:0.58, C:0.08, G:0.13, T:0.21
Consensus pattern (13 bp):
AAAATATGTACAG
Found at i:410123 original size:14 final size:14
Alignment explanation
Indices: 410086--410124 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
410076 AAACGGAGGA
*
410086 AAAGTAAAATATGT
1 AAAGTAAAATATGG
*
410100 ACAG-AAAATATGG
1 AAAGTAAAATATGG
410113 AAAGTAAAATAT
1 AAAGTAAAATAT
410125 AGTACACAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.59, C:0.03, G:0.15, T:0.23
Consensus pattern (14 bp):
AAAGTAAAATATGG
Found at i:413059 original size:46 final size:48
Alignment explanation
Indices: 412995--413095 Score: 120
Period size: 46 Copynumber: 2.1 Consensus size: 48
412985 ATTGTAATAT
* * *
412995 TTATTTGACTTAATTATTT-TTATTATTTTTTATTTTACTTAATTATTTA
1 TTATTT-ACTTAATTATTTATTA-TAATATTTATTTTACTTAATAATTTA
*
413044 TTATTTA-TTAA-TATTTATTATAATATTTATTTTATTTAATAATTTA
1 TTATTTACTTAATTATTTATTATAATATTTATTTTACTTAATAATTTA
413090 -TATTTA
1 TTATTTA
413096 AAAATAATTC
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
45 6 0.13
46 27 0.57
47 7 0.15
48 1 0.02
49 6 0.13
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (48 bp):
TTATTTACTTAATTATTTATTATAATATTTATTTTACTTAATAATTTA
Found at i:413060 original size:29 final size:28
Alignment explanation
Indices: 412996--413089 Score: 86
Period size: 29 Copynumber: 3.2 Consensus size: 28
412986 TTGTAATATT
*
412996 TATTTGACTTAATTATTTTTATTATTTTTTA
1 TATTT-ACTTAATTA--TTTATTATTTTTAA
413027 T-TTTACTTAATTATTTATTATTTATTAA
1 TATTTACTTAATTATTTATTATTT-TTAA
*
413055 TATTTA-TTATAATATTTATT-TTATTTAA
1 TATTTACTTA-ATTATTTATTATT-TTTAA
413083 TAATTTA
1 T-ATTTA
413090 TATTTAAAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
27 10 0.18
28 14 0.25
29 28 0.50
30 3 0.05
31 1 0.02
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (28 bp):
TATTTACTTAATTATTTATTATTTTTAA
Found at i:413159 original size:7 final size:7
Alignment explanation
Indices: 413147--413227 Score: 56
Period size: 7 Copynumber: 10.6 Consensus size: 7
413137 AATTTAAAAG
413147 AATTAAA
1 AATTAAA
413154 AATTAAAA
1 AATT-AAA
*
413162 TAATTTAA
1 -AATTAAA
413170 AATTAAA
1 AATTAAA
413177 TTAA-TAAA
1 --AATTAAA
413185 AATTAAAA
1 AATT-AAA
413193 TAATTTAAA
1 -AA-TTAAA
**
413202 TTTTAAA
1 AATTAAA
413209 TAATTAAA
1 -AATTAAA
413217 AATTAAA
1 AATTAAA
413224 AATT
1 AATT
413228 TATTTAATTT
Statistics
Matches: 59, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
6 2 0.03
7 27 0.46
8 17 0.29
9 11 0.19
10 2 0.03
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (7 bp):
AATTAAA
Found at i:413169 original size:10 final size:10
Alignment explanation
Indices: 413137--413201 Score: 50
Period size: 10 Copynumber: 6.8 Consensus size: 10
413127 ATTTAACTTA
*
413137 AATTTAAAAG
1 AATTTAAAAT
413147 AA-TT-AAA-
1 AATTTAAAAT
413154 AA-TTAAAAT
1 AATTTAAAAT
413163 AATTTAAAATT
1 AATTTAAAA-T
*
413174 AAATTAATAA-
1 AATTTAA-AAT
*
413184 AAATTAAAAT
1 AATTTAAAAT
413194 AATTTAAA
1 AATTTAAA
413202 TTTTAAATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
7 4 0.09
8 6 0.13
9 6 0.13
10 22 0.47
11 7 0.15
12 2 0.04
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (10 bp):
AATTTAAAAT
Found at i:413176 original size:32 final size:32
Alignment explanation
Indices: 413134--413224 Score: 139
Period size: 31 Copynumber: 2.9 Consensus size: 32
413124 ACTATTTAAC
*
413134 TTAAATTTAAAAGAATTAAAAATTAAAATAAT
1 TTAAATTTAAAATAATTAAAAATTAAAATAAT
* *
413166 TTAAAATTAAATTAA-TAAAAATTAAAATAAT
1 TTAAATTTAAAATAATTAAAAATTAAAATAAT
*
413197 TTAAATTTTAAATAATTAAAAATTAAAA
1 TTAAATTTAAAATAATTAAAAATTAAAA
413225 ATTTATTTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
31 28 0.54
32 24 0.46
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (32 bp):
TTAAATTTAAAATAATTAAAAATTAAAATAAT
Found at i:413186 original size:15 final size:16
Alignment explanation
Indices: 413140--413224 Score: 109
Period size: 16 Copynumber: 5.4 Consensus size: 16
413130 TAACTTAAAT
*
413140 TTAAAAGAATTAAAAA
1 TTAAAATAATTAAAAA
*
413156 TTAAAATAATTTAAAA
1 TTAAAATAATTAAAAA
*
413172 TTAAATTAA-TAAAAA
1 TTAAAATAATTAAAAA
* *
413187 TTAAAATAATTTAAAT
1 TTAAAATAATTAAAAA
*
413203 TTTAAATAATTAAAAA
1 TTAAAATAATTAAAAA
413219 TTAAAA
1 TTAAAA
413225 ATTTATTTAA
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
15 13 0.23
16 44 0.77
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (16 bp):
TTAAAATAATTAAAAA
Found at i:414684 original size:14 final size:15
Alignment explanation
Indices: 414645--414685 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
414635 GCAAGTTAAG
*
414645 TATAAATA-AAAAAT
1 TATAAATATTAAAAT
414659 TATAAATATTAAAAT
1 TATAAATATTAAAAT
*
414674 T-TAAATTTTAAA
1 TATAAATATTAAA
414686 TATATCAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 18 0.75
15 6 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TATAAATATTAAAAT
Found at i:414704 original size:22 final size:21
Alignment explanation
Indices: 414655--414704 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
414645 TATAAATAAA
* *
414655 AAATTATAAATATTAAAATTT
1 AAATTTTAAATATTAAAATAT
*
414676 AAATTTTAAATATATCAAATAT
1 AAATTTTAAATAT-TAAAATAT
*
414698 AATTTTT
1 AAATTTT
414705 TAAAAATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
AAATTTTAAATATTAAAATAT
Found at i:414846 original size:2 final size:2
Alignment explanation
Indices: 414839--414885 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
414829 TTAAGATAGA
414839 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
414881 AT AT A
1 AT AT A
414886 ACCTTTTCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:415741 original size:21 final size:22
Alignment explanation
Indices: 415702--415743 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
415692 TATTCATTGA
415702 TATATTTAGTTATTGTTTAAATT
1 TATATTTA-TTATTGTTTAAATT
*
415725 TATATTT-TTATTTTTTAAA
1 TATATTTATTATTGTTTAAA
415744 AAATAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
23 7 0.39
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (22 bp):
TATATTTATTATTGTTTAAATT
Found at i:416218 original size:13 final size:13
Alignment explanation
Indices: 416192--416246 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
416182 TTTTTAAATA
416192 AATTTTATTTTTTT
1 AATTTTA-TTTTTT
416206 AATTTTATTTTTT
1 AATTTTATTTTTT
*
416219 AAATTTATTATTTAT
1 AATTTTATT-TTT-T
416234 AA--TTATTTTTT
1 AATTTTATTTTTT
416245 AA
1 AA
416247 ATTATCGAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
11 3 0.08
12 3 0.08
13 19 0.50
14 10 0.26
15 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
AATTTTATTTTTT
Found at i:418095 original size:20 final size:23
Alignment explanation
Indices: 418070--418119 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 23
418060 TTTGTGTTAT
418070 TTAAATATTA-ATTCAAAT-T-A
1 TTAAATATTATATTCAAATCTAA
*
418090 TTAAATATTATATTTAAATCTAA
1 TTAAATATTATATTCAAATCTAA
418113 TTAAATA
1 TTAAATA
418120 CAGATAAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.38
21 7 0.27
22 1 0.04
23 8 0.31
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (23 bp):
TTAAATATTATATTCAAATCTAA
Found at i:418346 original size:22 final size:21
Alignment explanation
Indices: 418309--418349 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
418299 TATTTTTATT
418309 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
418330 TAAATATTAA-TATTAAAATA
1 TAAAT-TTAATTA-TAAAATA
418350 ACTTTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:418592 original size:22 final size:21
Alignment explanation
Indices: 418567--418610 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
418557 AAATAATTAA
*
418567 TTTAATTTAAATAGTTAAAAAT
1 TTTAACTTAAATA-TTAAAAAT
**
418589 TTTAACTTATTTATTAAAAAT
1 TTTAACTTAAATATTAAAAAT
418610 T
1 T
418611 AAATTAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (21 bp):
TTTAACTTAAATATTAAAAAT
Found at i:419916 original size:105 final size:105
Alignment explanation
Indices: 419729--419919 Score: 296
Period size: 105 Copynumber: 1.8 Consensus size: 105
419719 ATATTGCACT
*
419729 TAATATTTTCACGTATAGTATATTGATCGATGCGCATTGCAAGGATGGGATGATTTCGGAAGCTG
1 TAATATTTTCACGTATAGTATATTGATCGATGCACATTGCAAGGATGGGATGATTTCGGAAGCTG
*
419794 TAGATATCGTTGACACAATGAGAAAGCAAGGCATTGAGCC
66 AAGATATCGTTGACACAATGAGAAAGCAAGGCATTGAGCC
* * *
419834 TAATGTTTTCACGTATAGTATATT-AGTTGATGCACATTGCAAGGA-GGGTATGGTTTCGGAAGC
1 TAATATTTTCACGTATAGTATATTGA-TCGATGCACATTGCAAGGATGGG-ATGATTTCGGAAGC
*
419897 TGAAGATATTGTTGACACAATGA
64 TGAAGATATCGTTGACACAATGA
419920 TAGAGAAATG
Statistics
Matches: 78, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
104 4 0.05
105 74 0.95
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.31
Consensus pattern (105 bp):
TAATATTTTCACGTATAGTATATTGATCGATGCACATTGCAAGGATGGGATGATTTCGGAAGCTG
AAGATATCGTTGACACAATGAGAAAGCAAGGCATTGAGCC
Found at i:419933 original size:105 final size:105
Alignment explanation
Indices: 419729--419945 Score: 294
Period size: 105 Copynumber: 2.1 Consensus size: 105
419719 ATATTGCACT
* *
419729 TAATATTTTCACGTATAGTATATTGATCGATGCGCATTGCAAGGATGGGATGATTTCGGAAGCTG
1 TAATGTTTTCACGTATAGTATATTGATCGATGCACATTGCAAGGATGGGATGATTTCGGAAGCTG
* * *
419794 TAGATATCGTTGACACAATGAGAAAGCAAGGCATTGAGCC
66 AAGATATCGTTGACACAATGAGAAAGAAAGGCATTGAACC
* *
419834 TAATGTTTTCACGTATAGTATATT-AGTTGATGCACATTGCAAGGA-GGGTATGGTTTCGGAAGC
1 TAATGTTTTCACGTATAGTATATTGA-TCGATGCACATTGCAAGGATGGG-ATGATTTCGGAAGC
* * * *
419897 TGAAGATATTGTTGACACAATGATAGAGAAATGCATTGAACC
64 TGAAGATATCGTTGACACAATGAGAAAGAAAGGCATTGAACC
*
419939 TGATGTT
1 TAATGTT
419946 GCTACCTATA
Statistics
Matches: 98, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
104 4 0.04
105 94 0.96
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.31
Consensus pattern (105 bp):
TAATGTTTTCACGTATAGTATATTGATCGATGCACATTGCAAGGATGGGATGATTTCGGAAGCTG
AAGATATCGTTGACACAATGAGAAAGAAAGGCATTGAACC
Found at i:419977 original size:105 final size:105
Alignment explanation
Indices: 419758--419978 Score: 241
Period size: 105 Copynumber: 2.1 Consensus size: 105
419748 ATATTGATCG
* * *
419758 ATGCGCATTGCAAGGATGGGATGATTTCGGAAGCTGTAGATATCGTTGACACAATGAGAAAGCAA
1 ATGCACATTGCAAGGATGGGATGATTTCGGAAGCTGAAGATATCGTTGACACAATGAGAAAGAAA
* * * * * **
419823 GGCATTGAGCCTAATGTTTTCACGTATAGTATATTAGTTG
66 GGCATTGAACCTAATGTTCTCACCTATAGTACATTAATAA
* * * *
419863 ATGCACATTGCAAGGA-GGGTATGGTTTCGGAAGCTGAAGATATTGTTGACACAATGATAGAGAA
1 ATGCACATTGCAAGGATGGG-ATGATTTCGGAAGCTGAAGATATCGTTGACACAATGAGAAAGAA
* * *
419927 ATGCATTGAACCTGATGTTGCT-ACCTATAGTGCATTAATAA
65 AGGCATTGAACCTAATGTT-CTCACCTATAGTACATTAATAA
419968 ATGGC-CATTGC
1 AT-GCACATTGC
419979 TTGCAAAACA
Statistics
Matches: 96, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
104 3 0.03
105 90 0.94
106 3 0.03
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (105 bp):
ATGCACATTGCAAGGATGGGATGATTTCGGAAGCTGAAGATATCGTTGACACAATGAGAAAGAAA
GGCATTGAACCTAATGTTCTCACCTATAGTACATTAATAA
Found at i:422974 original size:21 final size:19
Alignment explanation
Indices: 422945--422985 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 19
422935 TATTTTTATT
422945 TAAATTTAATATAAAATATA
1 TAAATTTAATATAAAA-ATA
422965 TAAATATTAATATAAAAATA
1 TAAAT-TTAATATAAAAATA
422985 T
1 T
422986 TTTTTTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TAAATTTAATATAAAAATA
Found at i:424913 original size:31 final size:31
Alignment explanation
Indices: 424875--424935 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
424865 TTTATTTAAA
424875 TTTAATTTTAAAATATATAAAT-ATAAATATT
1 TTTAATTTTAAAAT-TATAAATAATAAATATT
**
424906 TTTAATTTTTTAATTATAAATAATAAATAT
1 TTTAATTTTAAAATTATAAATAATAAATAT
424936 AAAAATTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 7 0.26
31 20 0.74
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
TTTAATTTTAAAATTATAAATAATAAATATT
Found at i:426499 original size:105 final size:105
Alignment explanation
Indices: 426333--426523 Score: 283
Period size: 105 Copynumber: 1.8 Consensus size: 105
426323 ATATTGCACT
* *
426333 TAATATTTTCACGTATAATATATTGATCGATGCACATTGCAAGGATGGGATGATTTTGGAAGCTC
1 TAATATTTTCACGTATAATATATTGATCGATGCACATTGCAAGGAGGGGATGATTTCGGAAGCTC
*
426398 TAGATATCGTTGACACAATGAGAAAGCAAGGCATTGAGCC
66 AAGATATCGTTGACACAATGAGAAAGCAAGGCATTGAGCC
* * * * * *
426438 TAATGTTTTCATGTATAGTATATTGGTCGATGCACATTGCAAGGAGGGGATGGTTTCGGAAGCTG
1 TAATATTTTCACGTATAATATATTGATCGATGCACATTGCAAGGAGGGGATGATTTCGGAAGCTC
* *
426503 AATATATTGTTGACACAATGA
66 AAGATATCGTTGACACAATGA
426524 TAGAGAAATG
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
105 75 1.00
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (105 bp):
TAATATTTTCACGTATAATATATTGATCGATGCACATTGCAAGGAGGGGATGATTTCGGAAGCTC
AAGATATCGTTGACACAATGAGAAAGCAAGGCATTGAGCC
Found at i:426537 original size:105 final size:105
Alignment explanation
Indices: 426333--426549 Score: 281
Period size: 105 Copynumber: 2.1 Consensus size: 105
426323 ATATTGCACT
* * *
426333 TAATATTTTCACGTATAATATATTGATCGATGCACATTGCAAGGATGGGATGATTTTGGAAGCTC
1 TAATGTTTTCACGTATAATATATTGATCGATGCACATTGCAAGGAGGGGATGATTTCGGAAGCTC
* * *
426398 TAGATATCGTTGACACAATGAGAAAGCAAGGCATTGAGCC
66 AAGATATCGTTGACACAATGAGAAAGAAAGGCATTGAACC
* * * * *
426438 TAATGTTTTCATGTATAGTATATTGGTCGATGCACATTGCAAGGAGGGGATGGTTTCGGAAGCTG
1 TAATGTTTTCACGTATAATATATTGATCGATGCACATTGCAAGGAGGGGATGATTTCGGAAGCTC
* * * * * *
426503 AATATATTGTTGACACAATGATAGAGAAATGCATTGAACT
66 AAGATATCGTTGACACAATGAGAAAGAAAGGCATTGAACC
426543 TAATGTT
1 TAATGTT
426550 GTTACCTATA
Statistics
Matches: 95, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
105 95 1.00
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (105 bp):
TAATGTTTTCACGTATAATATATTGATCGATGCACATTGCAAGGAGGGGATGATTTCGGAAGCTC
AAGATATCGTTGACACAATGAGAAAGAAAGGCATTGAACC
Found at i:428709 original size:19 final size:20
Alignment explanation
Indices: 428673--428714 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
428663 TTTTATATCA
* *
428673 ATATGGATCAGTAAAAATTG
1 ATATGGATCAATAAAAATCG
*
428693 ATAT-GATCAATATAAATCG
1 ATATGGATCAATAAAAATCG
428712 ATA
1 ATA
428715 CAAAAATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (20 bp):
ATATGGATCAATAAAAATCG
Found at i:432874 original size:105 final size:105
Alignment explanation
Indices: 432691--432901 Score: 269
Period size: 105 Copynumber: 2.0 Consensus size: 105
432681 ATATTGCACT
* * * *
432691 TAATATTTTCACGTATAATATATTGATCAATGCACGTTGCAAGGATGGGATGCTTTCGGAAGCTT
1 TAATATTTTCACATATAATATATTGATCAATGCACATTGCAAGGAGGGGATGCTTTCGGAAGCTG
* * *
432756 TAGATATCATTGACACAATGAGAAAGCAAGGCATTGAGCC
66 AAGATATCATTGACACAATGAGAAAGAAACGCATTGAGCC
* ** * *
432796 TAATATTTTCACATATAATATATTGGTTGATGCGCATTGCAAGGAGGGGATGGTTTCGGAAGCTG
1 TAATATTTTCACATATAATATATTGATCAATGCACATTGCAAGGAGGGGATGCTTTCGGAAGCTG
* ** * *
432861 AATATATTGTTGACACAATGATAGAGAAACGCATTGAGCC
66 AAGATATCATTGACACAATGAGAAAGAAACGCATTGAGCC
432901 T
1 T
432902 GATGTTGCTA
Statistics
Matches: 89, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
105 89 1.00
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (105 bp):
TAATATTTTCACATATAATATATTGATCAATGCACATTGCAAGGAGGGGATGCTTTCGGAAGCTG
AAGATATCATTGACACAATGAGAAAGAAACGCATTGAGCC
Found at i:437331 original size:17 final size:17
Alignment explanation
Indices: 437309--437359 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
437299 TTTAAAAATT
437309 TATTTAATAAAATTAAA
1 TATTTAATAAAATTAAA
*
437326 TATTTAA-AGAATTTAAA
1 TATTTAATA-AAATTAAA
*
437343 TATCTAATAAATATTAA
1 TATTTAATAAA-ATTAA
437360 CTGAATCTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 1 0.04
17 22 0.79
18 5 0.18
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (17 bp):
TATTTAATAAAATTAAA
Found at i:439060 original size:17 final size:18
Alignment explanation
Indices: 439047--439095 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
439037 ATTTAAAATT
439047 TTTTATTTTTTAAATAAA
1 TTTTATTTTTTAAATAAA
**
439065 TTTTA-TTTTTATTTAAA
1 TTTTATTTTTTAAATAAA
*
439082 -TTTATTTTTAAAAT
1 TTTTATTTTTTAAAT
439096 TTATTATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 4 0.16
17 16 0.64
18 5 0.20
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTATTTTTTAAATAAA
Found at i:439079 original size:21 final size:20
Alignment explanation
Indices: 439042--439082 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
439032 TTTGAATTTA
439042 AAATTTTTTATTTTTTAAAT
1 AAATTTTTTATTTTTTAAAT
439062 AAATTTTATT-TTTATTTAAAT
1 AAATTTT-TTATTT-TTTAAAT
439083 TTATTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
AAATTTTTTATTTTTTAAAT
Found at i:439085 original size:16 final size:17
Alignment explanation
Indices: 439047--439117 Score: 69
Period size: 16 Copynumber: 4.2 Consensus size: 17
439037 ATTTAAAATT
**
439047 TTTTATTTTTTAAATAAA
1 TTTTA-TTTTTATTTAAA
439065 TTTTATTTTTATTTAAA
1 TTTTATTTTTATTTAAA
439082 -TTTATTTTTA---AAA
1 TTTTATTTTTATTTAAA
439095 TTTATTATTTTTATTTAAA
1 -TT-TTATTTTTATTTAAA
439114 TTTT
1 TTTT
439118 TTTAAATATC
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
13 3 0.07
15 1 0.02
16 19 0.42
17 12 0.27
18 7 0.16
19 3 0.07
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTATTTTTATTTAAA
Found at i:442217 original size:105 final size:105
Alignment explanation
Indices: 442003--442218 Score: 229
Period size: 105 Copynumber: 2.1 Consensus size: 105
441993 GATCGACACA
* * * * *
442003 CATTGCAAGGATGGGATGATTTCGGAAGCTGTAGATATCGTTGACACTATGAGAAAGCAAGGCAT
1 CATTGCAAGGAGGGGATGATTTCGGAAGCTGAAGATATCGATGACACAATGAGAAAGAAAGGCAT
* * * ** **
442068 TGAGCCTAATGTTTTCACCTATAGTATATTGGTCGATGCG
66 TGAACCTAATGTTTTCACCTATAATACATTAATAAATGCG
* * * * *
442108 CATTGCAAGGAGGGGATGGTTTCGGAAGCTGAAGATATTGATGACACAATGATAGAGAAATGCAT
1 CATTGCAAGGAGGGGATGATTTCGGAAGCTGAAGATATCGATGACACAATGAGAAAGAAAGGCAT
* *
442173 TGAACCTAATGTTGTT-TCCTATAATGCATTAATAAATG-G
66 TGAACCTAATGTT-TTCACCTATAATACATTAATAAATGCG
442212 CCATTGC
1 -CATTGC
442219 TTGCAAAACA
Statistics
Matches: 90, Mismatches: 19, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
104 1 0.01
105 87 0.97
106 2 0.02
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.29
Consensus pattern (105 bp):
CATTGCAAGGAGGGGATGATTTCGGAAGCTGAAGATATCGATGACACAATGAGAAAGAAAGGCAT
TGAACCTAATGTTTTCACCTATAATACATTAATAAATGCG
Found at i:445176 original size:18 final size:19
Alignment explanation
Indices: 445149--445185 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
445139 AATTTGAAAG
445149 AATAT-TTTTTATTAAAAT
1 AATATATTTTTATTAAAAT
445167 AATATATTTTTATTAAAAT
1 AATATATTTTTATTAAAAT
445186 TTAATTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AATATATTTTTATTAAAAT
Found at i:447228 original size:17 final size:18
Alignment explanation
Indices: 447181--447233 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 18
447171 CAAAATTTTT
447181 TATTTAAATTTAATTATAAAA
1 TATTTAAATTT--TT-TAAAA
*
447202 TATATAAATTTTTTAAAA
1 TATTTAAATTTTTTAAAA
*
447220 T-TTTAAATTATTTA
1 TATTTAAATTTTTTA
447234 TTAATAATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 11 0.38
18 6 0.21
19 2 0.07
21 10 0.34
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATTTAAATTTTTTAAAA
Found at i:447386 original size:14 final size:13
Alignment explanation
Indices: 447357--447383 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
447347 TTTTATATTA
447357 TAAAAAATAAAAT
1 TAAAAAATAAAAT
447370 TAAAAAATAAAAT
1 TAAAAAATAAAAT
447383 T
1 T
447384 TAATTTGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
TAAAAAATAAAAT
Found at i:448802 original size:105 final size:105
Alignment explanation
Indices: 448627--448829 Score: 264
Period size: 105 Copynumber: 1.9 Consensus size: 105
448617 CTTAATATTT
* *
448627 TCACGTATAATATATTGGTCGATGCACATTGCAAGGATGGGATGATTTCAGAAGCTGCAGATATC
1 TCACGTATAATATATTGGTCGATGCACATTGCAAGGAGGGGATGATTTCAGAAGCTGAAGATATC
** *
448692 ATTGACTTAATGAGAAAGCAAGGCATTGAGCCTAACGTTG
66 ATTGACAAAATGAGAAAGAAAGGCATTGAGCCTAACGTTG
** * * *
448732 TCACGTATGGTATATTGGTCGATGCGCATTGCAAGGAGGGGATGGTTTCGGAAGCTGAAGATAAT
1 TCACGTATAATATATTGGTCGATGCACATTGCAAGGAGGGGATGATTTCAGAAGCTGAAGAT-AT
* * * *
448797 -GTTGACAAAATGATAGAGAAATGCATTGAGCCT
65 CATTGACAAAATGAGAAAGAAAGGCATTGAGCCT
448830 GATGTCGTTA
Statistics
Matches: 83, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
105 81 0.98
106 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.28, T:0.27
Consensus pattern (105 bp):
TCACGTATAATATATTGGTCGATGCACATTGCAAGGAGGGGATGATTTCAGAAGCTGAAGATATC
ATTGACAAAATGAGAAAGAAAGGCATTGAGCCTAACGTTG
Found at i:458622 original size:39 final size:41
Alignment explanation
Indices: 458548--458664 Score: 113
Period size: 38 Copynumber: 3.0 Consensus size: 41
458538 ATTATATAAA
* * *
458548 AATTAATTAAAATATGAATGATATAAAAA-TAATATAAATAC-
1 AATT-ATTAATATATAAAT-ATATAAAAATTTATATAAATACG
458589 AA-TATTAATATATAAATATATAAAAATTTATAT-AATACG
1 AATTATTAATATATAAATATATAAAAATTTATATAAATACG
* *
458628 AATTATTAATATTTTAAATAT-T--ATATTTATATAAATA
1 AATTATTAATA-TATAAATATATAAAAATTTATATAAATA
458665 ACACATGATT
Statistics
Matches: 66, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
38 23 0.35
39 23 0.35
40 10 0.15
41 10 0.15
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.40
Consensus pattern (41 bp):
AATTATTAATATATAAATATATAAAAATTTATATAAATACG
Found at i:459236 original size:3 final size:3
Alignment explanation
Indices: 459230--459275 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
459220 ATAATAATAA
459230 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
459276 GGCCATAGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:460189 original size:24 final size:25
Alignment explanation
Indices: 460162--460211 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
460152 AAATATAATA
*
460162 TAATATTTAAATTTTAT-TTTAAAT
1 TAATATTTAAATTTTATAATTAAAT
*
460186 TAATATTTATATTTTATAATTAAAT
1 TAATATTTAAATTTTATAATTAAAT
460211 T
1 T
460212 TAAATAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TAATATTTAAATTTTATAATTAAAT
Found at i:460212 original size:13 final size:13
Alignment explanation
Indices: 460164--460212 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
460154 ATATAATATA
460164 ATATTTAAATTTT
1 ATATTTAAATTTT
*
460177 AT-TTTAAA-TTA
1 ATATTTAAATTTT
*
460188 ATATTTATATTTT
1 ATATTTAAATTTT
*
460201 ATAATTAAATTT
1 ATATTTAAATTT
460213 AAATAATAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
11 4 0.14
12 11 0.38
13 14 0.48
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATATTTAAATTTT
Found at i:461564 original size:10 final size:10
Alignment explanation
Indices: 461544--461577 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
461534 ATTAAGTTAA
461544 AATTATTTTAT
1 AATT-TTTTAT
461555 AATTTTTTAT
1 AATTTTTTAT
461565 AATTTGTTTAT
1 AATTT-TTTAT
461576 AA
1 AA
461578 ATATTATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 11 0.50
11 11 0.50
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (10 bp):
AATTTTTTAT
Found at i:462618 original size:20 final size:22
Alignment explanation
Indices: 462583--462638 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
462573 ATATGATATG
* *
462583 ATTATACTTA-ATTTTT-TAAA
1 ATTATATTTATATTTTTAAAAA
462603 ATT-TATTTATATTTTTAAAAA
1 ATTATATTTATATTTTTAAAAA
462624 ATTATATTTATATTT
1 ATTATATTTATATTT
462639 AAATATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.16
20 9 0.29
21 6 0.19
22 11 0.35
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTATATTTATATTTTTAAAAA
Found at i:462670 original size:11 final size:12
Alignment explanation
Indices: 462633--462681 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 12
462623 AATTATATTT
*
462633 ATATTTAAATAT
1 ATATTTAAATAA
*
462645 ATATTAAATATAA
1 ATATTTAA-ATAA
462658 ATATTTAAA-AA
1 ATATTTAAATAA
462669 AT-TTTAAA-AA
1 ATATTTAAATAA
462679 ATA
1 ATA
462682 AAATAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
10 10 0.31
11 4 0.12
12 8 0.25
13 10 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATTTAAATAA
Found at i:462894 original size:12 final size:12
Alignment explanation
Indices: 462865--462897 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
462855 CAATATTTAA
*
462865 AAATTTATATTT
1 AAATATATATTT
462877 -AATATATATTT
1 AAATATATATTT
462888 AAATATATAT
1 AAATATATAT
462898 CAAGTATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
AAATATATATTT
Found at i:463272 original size:8 final size:8
Alignment explanation
Indices: 463259--463300 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
463249 TTGGATATTG
463259 AATATAAA
1 AATATAAA
*
463267 AATATAAT
1 AATATAAA
*
463275 TATATAAA
1 AATATAAA
*
463283 TATATAAA
1 AATATAAA
463291 AAT-TAAA
1 AATATAAA
463298 AAT
1 AAT
463301 GAAATATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
7 7 0.23
8 23 0.77
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AATATAAA
Found at i:463513 original size:19 final size:19
Alignment explanation
Indices: 463489--463527 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
463479 AAATTTGATA
* *
463489 ATTTATGTATTTGTATTAT
1 ATTTATATATATGTATTAT
*
463508 ATTTATATATATGTGTTAT
1 ATTTATATATATGTATTAT
463527 A
1 A
463528 ATTTCATTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (19 bp):
ATTTATATATATGTATTAT
Found at i:463989 original size:9 final size:8
Alignment explanation
Indices: 463961--463986 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
463951 ACTATTTAAA
463961 TTAATTTT
1 TTAATTTT
463969 TTAATTTT
1 TTAATTTT
463977 TTAATTTT
1 TTAATTTT
463985 TT
1 TT
463987 TAACTGTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
TTAATTTT
Found at i:464061 original size:5 final size:5
Alignment explanation
Indices: 464015--464102 Score: 60
Period size: 5 Copynumber: 18.0 Consensus size: 5
464005 TTAATAAATA
* * *
464015 ATATT ATA-T ATATT ATGA-T ATATT -TAAT ATCTT CAAATT ATATT ATATT
1 ATATT ATATT ATATT AT-ATT ATATT ATATT ATATT -ATATT ATATT ATATT
* * *
464064 ATATT TTAATT ATTTT ATATT ATA-T A-ATT ATATA ATATT
1 ATATT AT-ATT ATATT ATATT ATATT ATATT ATATT ATATT
464103 CATAGTTATC
Statistics
Matches: 63, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
3 1 0.02
4 12 0.19
5 42 0.67
6 8 0.13
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (5 bp):
ATATT
Found at i:464081 original size:16 final size:18
Alignment explanation
Indices: 464056--464102 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
464046 TTCAAATTAT
464056 ATTATATTATATT-T-TA
1 ATTATATTATATTATATA
*
464072 ATTATTTTATATTATATA
1 ATTATATTATATTATATA
*
464090 ATTATATAATATT
1 ATTATATTATATT
464103 CATAGTTATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
18 13 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTATATTATATTATATA
Found at i:469655 original size:2 final size:2
Alignment explanation
Indices: 469650--469684 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
469640 TAAAAAAGGG
469650 TA TA 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 TA TA T
469685 CAAAGAATTC
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:469982 original size:14 final size:14
Alignment explanation
Indices: 469959--469993 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
469949 ATGAAGTCTC
*
469959 TAATTAAATTAGTA
1 TAATTGAATTAGTA
469973 TAATTGAATTAGTA
1 TAATTGAATTAGTA
*
469987 TCATTGA
1 TAATTGA
469994 TACGAGGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (14 bp):
TAATTGAATTAGTA
Found at i:470048 original size:11 final size:11
Alignment explanation
Indices: 470024--470064 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
470014 TTTAATTTAA
* *
470024 AAAATTATATT
1 AAAATTAAAAT
470035 AAAATTAAAAT
1 AAAATTAAAAT
470046 -AAA-TAAAAT
1 AAAATTAAAAT
470055 AAAATTAAAA
1 AAAATTAAAA
470065 GTATTTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 6 0.23
10 6 0.23
11 14 0.54
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AAAATTAAAAT
Found at i:470326 original size:2 final size:2
Alignment explanation
Indices: 470319--470351 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
470309 TTTGTGTAAG
*
470319 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
470352 AAACATTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:470932 original size:2 final size:2
Alignment explanation
Indices: 470925--470962 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
470915 ATTTGATTTG
*
470925 AT AT AT AT CT A- AT AT CAT 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
470963 GTTTACTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.91
3 2 0.06
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:473282 original size:19 final size:21
Alignment explanation
Indices: 473254--473298 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
473244 TTTAGTTAAT
473254 TTTTTAATTTT-CTCAAGTTA
1 TTTTTAATTTTACTCAAGTTA
* *
473274 TTTTT-ATTTTATTCAATTTA
1 TTTTTAATTTTACTCAAGTTA
473294 TTTTT
1 TTTTT
473299 TTATTTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTTTAATTTTACTCAAGTTA
Found at i:473305 original size:27 final size:27
Alignment explanation
Indices: 473285--473341 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
473275 TTTTATTTTA
473285 TTCAATTTATTTTTTTATTTTAATTAAG
1 TTCAA-TTATTTTTTTATTTTAATTAAG
** *
473313 TTTTATTATTTTTTTATTTTAATTGAG
1 TTCAATTATTTTTTTATTTTAATTAAG
473340 TT
1 TT
473342 TTTAATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 23 0.88
28 3 0.12
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (27 bp):
TTCAATTATTTTTTTATTTTAATTAAG
Found at i:473345 original size:28 final size:27
Alignment explanation
Indices: 473291--473343 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
473281 TTTATTCAAT
473291 TTATTTTTTTATTTTAATTAAGTTTTA
1 TTATTTTTTTATTTTAATTAAGTTTTA
*
473318 TTATTTTTTTATTTTAATTGAGTTTT
1 TTATTTTTTTATTTTAATTAAGTTTT
473344 TAATTTTAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.72
Consensus pattern (27 bp):
TTATTTTTTTATTTTAATTAAGTTTTA
Found at i:474615 original size:16 final size:15
Alignment explanation
Indices: 474586--474632 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
474576 AAATTTAATG
* *
474586 ATTATTTTATTAAAAT
1 ATTATTATA-TAAAAA
474602 ATTAATTATATAAAAA
1 ATT-ATTATATAAAAA
474618 ATTA-TATATAAAAA
1 ATTATTATATAAAAA
474632 A
1 A
474633 CTCGCTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 11 0.39
15 1 0.04
16 11 0.39
17 5 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATTATTATATAAAAA
Found at i:475758 original size:138 final size:135
Alignment explanation
Indices: 475578--475961 Score: 417
Period size: 138 Copynumber: 2.9 Consensus size: 135
475568 CATGACTAGG
***
475578 GACATTTGCTTAATAGACAACCTAAGTGTGAAATCTCAATAGAAACCCAATTATGCATCATTAAT
1 GACATTTGCTTAATAGA-AACCTAAACATGAAATCTCAATAGAAACCCAATTATGCATCATTAAT
* * **
475643 CCATAATAATCCCAACATGTCTCTCAAATTATACATCAAATACCCAATTAATCCCCCTT-TAACA
65 CCAAAATTATCCCAACATGTCTCTCAAACCATACATCAAATACCCAATTAAT--CCCTTATAACA
*
475707 CCACCGAT
128 CCACCAAT
*
475715 GACATTTGCTTAAATAGATAACCTAAACATGAAATCTCGATAG-AACCCAATTATGCATCATTAA
1 GACATTTGCTT-AATAGA-AACCTAAACATGAAATCTCAATAGAAACCCAATTATGCATCATTAA
** * * **
475779 TCCAAAATTATCCCTAACACATCTCTAAAACCATACATCAAATACCTAATTAATCTTTTCATAAC
64 TCCAAAATTATCCC-AACATGTCTCTCAAACCATACATCAAATACCCAATTAATCCCTT-ATAAC
* *
475844 ACGACTAAT
127 ACCACCAAT
* *
475853 GACATTTGCTTAAT--AAA-C--AACATGAAATCTCAATA-AAACTCAATTATACATCATTAATC
1 GACATTTGCTTAATAGAAACCTAAACATGAAATCTCAATAGAAACCCAATTATGCATCATTAATC
* * * * *
475912 CAAAATTATCCTAACATGTGTCTCTAACCCTACA-CCAATGACCCAATTAA
66 CAAAATTATCCCAACATGTCTCTCAAACCATACATCAAAT-ACCCAATTAA
475962 CTAAAAAAAG
Statistics
Matches: 211, Mismatches: 30, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
129 4 0.02
130 25 0.12
131 48 0.23
133 1 0.00
134 2 0.01
135 1 0.00
136 3 0.01
137 47 0.22
138 80 0.38
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.28
Consensus pattern (135 bp):
GACATTTGCTTAATAGAAACCTAAACATGAAATCTCAATAGAAACCCAATTATGCATCATTAATC
CAAAATTATCCCAACATGTCTCTCAAACCATACATCAAATACCCAATTAATCCCTTATAACACCA
CCAAT
Found at i:476105 original size:15 final size:15
Alignment explanation
Indices: 476085--476134 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
476075 AACTATTATT
*
476085 TTTTTATTTATAAAA
1 TTTTTATTAATAAAA
476100 TTTTTAATTAAATAAAA
1 TTTTT-ATT-AATAAAA
* *
476117 TTATAATTAATAAAA
1 TTTTTATTAATAAAA
476132 TTT
1 TTT
476135 ATTTAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 14 0.48
16 6 0.21
17 9 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTTTATTAATAAAA
Found at i:476136 original size:16 final size:17
Alignment explanation
Indices: 476094--476136 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
476084 TTTTTTATTT
*
476094 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATTAA
476111 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
476126 ATAAAATTTAT
1 ATAAAATTTAT
476137 TTAAAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 11 0.46
17 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:476832 original size:17 final size:18
Alignment explanation
Indices: 476806--476840 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
476796 AATTAATAAC
*
476806 ATTTTTAATT-TTTTTAA
1 ATTTTAAATTATTTTTAA
476823 ATTTTAAATTATTTTTAA
1 ATTTTAAATTATTTTTAA
476841 TAAAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTTTAAATTATTTTTAA
Found at i:477075 original size:24 final size:23
Alignment explanation
Indices: 477048--477093 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
477038 ATATGAAAAA
*
477048 TAAAACTATGACATAAAAAATAAT
1 TAAAAC-ATAACATAAAAAATAAT
*
477072 TAAAACATAATATAAAAAATAA
1 TAAAACATAACATAAAAAATAA
477094 ATATGACACG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.24
Consensus pattern (23 bp):
TAAAACATAACATAAAAAATAAT
Found at i:477093 original size:12 final size:12
Alignment explanation
Indices: 477060--477093 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
477050 AAACTATGAC
477060 ATAAAAAATAAT
1 ATAAAAAATAAT
*
477072 -TAAAACATAAT
1 ATAAAAAATAAT
477083 ATAAAAAATAA
1 ATAAAAAATAA
477094 ATATGACACG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAAAAAATAAT
Found at i:478038 original size:33 final size:34
Alignment explanation
Indices: 477983--478048 Score: 80
Period size: 33 Copynumber: 1.9 Consensus size: 34
477973 AATTATTAGT
*
477983 ATATAAAAAATATACAAAAATAT-AATATTTTAA
1 ATATAAAAAATAAACAAAAATATAAATATTTTAA
* **
478016 ATATAAAAAATAAATACCAATATACAATATTTT
1 ATATAAAAAATAAACAAAAATATA-AATATTTT
478049 TCTTTTTCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 19 0.70
35 8 0.30
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (34 bp):
ATATAAAAAATAAACAAAAATATAAATATTTTAA
Found at i:478091 original size:25 final size:25
Alignment explanation
Indices: 478044--478092 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
478034 AATATACAAT
* *
478044 ATTTTTCTTTTTCTTTTTTTTTCTC
1 ATTTTTCTTTTTCTCTTTCTTTCTC
* *
478069 ATTTTTTTTTTTTTCTTTCTTTCT
1 ATTTTTCTTTTTCTCTTTCTTTCT
478093 TTCCTTCCTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (25 bp):
ATTTTTCTTTTTCTCTTTCTTTCTC
Found at i:478211 original size:2 final size:2
Alignment explanation
Indices: 478166--478193 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
478156 ATAGTTAAAT
478166 TA TA TA TA 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
478194 AATAGATAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:478304 original size:22 final size:22
Alignment explanation
Indices: 478278--478347 Score: 58
Period size: 18 Copynumber: 3.3 Consensus size: 22
478268 AGGAACCAAC
478278 CTAAAAATTGAAAATTATTGAA
1 CTAAAAATTGAAAATTATTGAA
** ***
478300 CT-AAAA---AAAAGGAACCAA
1 CTAAAAATTGAAAATTATTGAA
478318 CCTAAAAATTGAAAATTATTGAA
1 C-TAAAAATTGAAAATTATTGAA
478341 CTAAAAA
1 CTAAAAA
478348 AAGGAACCAA
Statistics
Matches: 33, Mismatches: 10, Indels: 10
0.62 0.19 0.19
Matches are distributed among these distances:
18 8 0.24
19 1 0.03
20 4 0.12
21 4 0.12
22 8 0.24
23 8 0.24
ACGTcount: A:0.59, C:0.10, G:0.09, T:0.23
Consensus pattern (22 bp):
CTAAAAATTGAAAATTATTGAA
Found at i:478319 original size:41 final size:41
Alignment explanation
Indices: 478263--478383 Score: 226
Period size: 40 Copynumber: 3.0 Consensus size: 41
478253 TTGAGCACCG
478263 AAAAAAGGAACCAACCTAAAAATTGAAAATTATTGAACTAA
1 AAAAAAGGAACCAACCTAAAAATTGAAAATTATTGAACTAA
478304 AAAAAAGGAACCAACCTAAAAATTGAAAATTATTGAACT-A
1 AAAAAAGGAACCAACCTAAAAATTGAAAATTATTGAACTAA
*
478344 AAAAAAGGAACCAACCTAAAAATTGAAAATTATTGCACTA
1 AAAAAAGGAACCAACCTAAAAATTGAAAATTATTGAACTA
478384 GAAGTTGAAA
Statistics
Matches: 78, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
40 39 0.50
41 39 0.50
ACGTcount: A:0.57, C:0.13, G:0.10, T:0.20
Consensus pattern (41 bp):
AAAAAAGGAACCAACCTAAAAATTGAAAATTATTGAACTAA
Found at i:478675 original size:21 final size:21
Alignment explanation
Indices: 478649--478690 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
478639 AAAATATTAT
478649 TTTTATAA-TAATATTTAAATA
1 TTTTATAATTAA-ATTTAAATA
478670 TTTTATAATTAAATTTAAATA
1 TTTTATAATTAAATTTAAATA
478691 AAATTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTTATAATTAAATTTAAATA
Found at i:478731 original size:29 final size:29
Alignment explanation
Indices: 478640--478734 Score: 72
Period size: 29 Copynumber: 3.3 Consensus size: 29
478630 AAAAATAACA
*
478640 AAATATTATTTTTATAATAAT-ATTTAAA-T
1 AAAT-TTATTATTA-AATAATAATTTAAATT
* * * * *
478669 -ATTTTATAATTAAAT-TTAAATAAAATT
1 AAATTTATTATTAAATAATAATTTAAATT
**
478696 ATTTTTATTATTAAATAATAATTTAAATT
1 AAATTTATTATTAAATAATAATTTAAATT
478725 AAATTTATTA
1 AAATTTATTA
478735 ATTTTAAAAA
Statistics
Matches: 49, Mismatches: 13, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
25 1 0.02
26 8 0.16
27 8 0.16
28 15 0.31
29 17 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
AAATTTATTATTAAATAATAATTTAAATT
Found at i:478751 original size:19 final size:19
Alignment explanation
Indices: 478725--478772 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
478715 AATTTAAATT
**
478725 AAATTTA-TTAATTTTAAA
1 AAATTTATTTAAAATTAAA
478743 AAATATTATTTAAAATTAAA
1 AAAT-TTATTTAAAATTAAA
478763 AAA-TTATTTA
1 AAATTTATTTA
478773 TAACATGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 11 0.42
19 3 0.12
20 12 0.46
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AAATTTATTTAAAATTAAA
Found at i:478754 original size:34 final size:34
Alignment explanation
Indices: 478681--478762 Score: 87
Period size: 34 Copynumber: 2.4 Consensus size: 34
478671 TTTATAATTA
* * * *
478681 AATTTAAATAAAATTATTTTTATTATTAAATAAT
1 AATTTAAATTAAATTATATTAATTATTAAAAAAT
478715 AATTTAAATTAAATT-TATTAATT-TTAAAAAAT
1 AATTTAAATTAAATTATATTAATTATTAAAAAAT
478747 ATTATTTAAAATTAAA
1 A--ATTT-AAATTAAA
478763 AAATTATTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
32 9 0.22
33 6 0.15
34 18 0.44
35 8 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (34 bp):
AATTTAAATTAAATTATATTAATTATTAAAAAAT
Found at i:481714 original size:60 final size:60
Alignment explanation
Indices: 481621--481735 Score: 176
Period size: 60 Copynumber: 1.9 Consensus size: 60
481611 TATTTGGTTT
* * *
481621 GTGAAACAATGATGACAATAGGAAGTATTACATAGGCCTTTTCTTCCATAATTCACGATA
1 GTGAAACAATGATGACAATAGAAAGCATTACATAGGCCTTTTCTACCATAATTCACGATA
** *
481681 GTGAAACAATGATGATGATAGAAAGCATTACATAGGTCTTTTCTACCATAATTCA
1 GTGAAACAATGATGACAATAGAAAGCATTACATAGGCCTTTTCTACCATAATTCA
481736 GGATGCAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (60 bp):
GTGAAACAATGATGACAATAGAAAGCATTACATAGGCCTTTTCTACCATAATTCACGATA
Found at i:487700 original size:16 final size:17
Alignment explanation
Indices: 487676--487708 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
487666 GAGACAATGC
487676 TTTTGTTTTGTTTTTGT
1 TTTTGTTTTGTTTTTGT
*
487693 TTTT-TTTTTTTTTTGT
1 TTTTGTTTTGTTTTTGT
487709 ATACAAAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (17 bp):
TTTTGTTTTGTTTTTGT
Found at i:488079 original size:22 final size:22
Alignment explanation
Indices: 488053--488105 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
488043 TATTAAAAAT
*
488053 AATTTAAATAATTTTGT-ATTA
1 AATTTAAATAATTTTATAATTA
* *
488074 ATATTTATATATTTTTATAATTA
1 A-ATTTAAATAATTTTATAATTA
488097 AATTTAAAT
1 AATTTAAAT
488106 TAAAAATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 1 0.04
22 20 0.77
23 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
AATTTAAATAATTTTATAATTA
Found at i:488451 original size:28 final size:28
Alignment explanation
Indices: 488419--488475 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
488409 AAAAAATAAT
488419 AAAATT-ATTAAAAATAAATTTTATATTA
1 AAAATTAATTAAAAATAAATTTT-TATTA
** *
488447 AAAATTAATTAATTATATATTTTTATTA
1 AAAATTAATTAAAAATAAATTTTTATTA
488475 A
1 A
488476 TTATTTATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 12 0.48
29 13 0.52
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
AAAATTAATTAAAAATAAATTTTTATTA
Found at i:488476 original size:21 final size:19
Alignment explanation
Indices: 488450--488493 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 19
488440 TATATTAAAA
488450 ATTAATTAATTATATATTTTT
1 ATTAATTAATTAT-TA-TTTT
*
488471 ATTAATTATTTATTATTTT
1 ATTAATTAATTATTATTTT
488490 ATTA
1 ATTA
488494 CACCAAGTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.36
20 2 0.09
21 12 0.55
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTAATTAATTATTATTTT
Found at i:488853 original size:2 final size:2
Alignment explanation
Indices: 488846--488882 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
488836 AAAATAAACA
488846 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
488883 AAGAAAGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:489037 original size:29 final size:29
Alignment explanation
Indices: 489003--489060 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
488993 TTAAAAATGA
* *
489003 ATTTATTTTGCTAAACA-AAAAATGAATTT
1 ATTTATTTTGATAAA-ATAAAAATAAATTT
489032 ATTTATTTTGATAAAATAAAAATAAATTT
1 ATTTATTTTGATAAAATAAAAATAAATTT
489061 CAAAATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 25 0.96
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.43
Consensus pattern (29 bp):
ATTTATTTTGATAAAATAAAAATAAATTT
Found at i:489060 original size:25 final size:26
Alignment explanation
Indices: 488994--489060 Score: 66
Period size: 29 Copynumber: 2.5 Consensus size: 26
488984 TTACAAAGTT
* *
488994 TAAAAATGAATTTATTTTGCTAAACA
1 TAAAAATAAATTTATTTTGATAAACA
489020 -AAAAATGAATTTATTTATTTTGATAAA-A
1 TAAAAAT-AA---ATTTATTTTGATAAACA
489048 TAAAAATAAATTT
1 TAAAAATAAATTT
489061 CAAAATTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
25 10 0.29
26 1 0.03
28 3 0.09
29 20 0.59
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.40
Consensus pattern (26 bp):
TAAAAATAAATTTATTTTGATAAACA
Found at i:489776 original size:4 final size:5
Alignment explanation
Indices: 489756--489793 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
489746 CTTTCCATTC
489756 AAAAT AAAAT AAAAT -AAAT AAAAT AATAAT AATAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT AA-AAT AA
489794 TAAAGCCTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 4 0.13
5 16 0.52
6 11 0.35
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (5 bp):
AAAAT
Found at i:489839 original size:12 final size:12
Alignment explanation
Indices: 489822--489855 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
489812 AAACCTTCCA
489822 TTTTCTCTCTGT
1 TTTTCTCTCTGT
*
489834 TTTTCTCTCAGT
1 TTTTCTCTCTGT
*
489846 TTCTCTCTCT
1 TTTTCTCTCT
489856 TTCTCTCCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.03, C:0.29, G:0.06, T:0.62
Consensus pattern (12 bp):
TTTTCTCTCTGT
Found at i:496136 original size:2 final size:2
Alignment explanation
Indices: 496129--496154 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
496119 ACACCAAAGC
496129 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
496155 GTCAACATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:496629 original size:15 final size:15
Alignment explanation
Indices: 496601--496638 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
496591 AATTATATAG
496601 TATATATTATATTTA
1 TATATATTATATTTA
496616 TATATGATTA-ATTTA
1 TATAT-ATTATATTTA
496631 TATCATAT
1 TAT-ATAT
496639 AAAAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (15 bp):
TATATATTATATTTA
Found at i:498845 original size:14 final size:13
Alignment explanation
Indices: 498810--498850 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
498800 ATTTATATTT
*
498810 TATAAAGATTAAA
1 TATAAATATTAAA
498823 TATATAATATTATAA
1 TATA-AATATTA-AA
498838 TATAAATATTAAA
1 TATAAATATTAAA
498851 AAATATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 6 0.24
14 13 0.52
15 6 0.24
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (13 bp):
TATAAATATTAAA
Found at i:499703 original size:2 final size:2
Alignment explanation
Indices: 499696--499720 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
499686 ATGGAAACAT
499696 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 T
499721 TAATCAAAGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:501290 original size:113 final size:113
Alignment explanation
Indices: 501096--501384 Score: 465
Period size: 113 Copynumber: 2.6 Consensus size: 113
501086 AAAACTTAAG
* * * * * *
501096 TTTCGTGCAGCCCCACCTGTGTA-AGTAACAGCAAGCAAAGCGA-CAAGCTTATTTAAACAACAC
1 TTTCGAGCAGCCCCACCGGCGTACCGCAACAGCAAGCAAAGTGATC-AGCTTATTTAAACAACAC
* *
501159 AGCCGGTTACCACTCGTTTCTGTCCTGTGACTATAACTTAATACCTAAA
65 AGCCGGTTACCACACGTTTATGTCCTGTGACTATAACTTAATACCTAAA
501208 TTTCGAGCAGCCCCACCGGCGTACCGCAACAGCAAGCAAAGTGATCAGCTTATTTAAACAACACA
1 TTTCGAGCAGCCCCACCGGCGTACCGCAACAGCAAGCAAAGTGATCAGCTTATTTAAACAACACA
* *
501273 GCCGGTTTCCACACGTTTATGTCCTGTGACTATAGCTTAATACCTAAA
66 GCCGGTTACCACACGTTTATGTCCTGTGACTATAACTTAATACCTAAA
501321 TTTCGAGCAGCCCCACCGGCGTACCGCAACAGCAAGCAAAGTGATCAGCTTATTTAAACAACAC
1 TTTCGAGCAGCCCCACCGGCGTACCGCAACAGCAAGCAAAGTGATCAGCTTATTTAAACAACAC
501385 TGTGACCCGT
Statistics
Matches: 165, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
112 20 0.12
113 144 0.87
114 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.23
Consensus pattern (113 bp):
TTTCGAGCAGCCCCACCGGCGTACCGCAACAGCAAGCAAAGTGATCAGCTTATTTAAACAACACA
GCCGGTTACCACACGTTTATGTCCTGTGACTATAACTTAATACCTAAA
Found at i:502010 original size:10 final size:10
Alignment explanation
Indices: 501987--502020 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
501977 ACTATTAATT
501987 TTAATTTAAAC
1 TTAATTT-AAC
501998 TTAATTTAAC
1 TTAATTTAAC
502008 TTAATTTAA-
1 TTAATTTAAC
502017 TTAA
1 TTAA
502021 AAAAATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 4 0.17
10 12 0.52
11 7 0.30
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (10 bp):
TTAATTTAAC
Found at i:502151 original size:15 final size:16
Alignment explanation
Indices: 502093--502192 Score: 98
Period size: 16 Copynumber: 6.2 Consensus size: 16
502083 ACTCGAGTTA
* *
502093 TAAATTTAAAATAATA
1 TAAACTTAAAATAATT
*
502109 TAAACTCAAAATAATT
1 TAAACTTAAAATAATT
* *
502125 TAAACATAAAATAACT
1 TAAACTTAAAATAATT
502141 TAAA-TTAAAATAATT
1 TAAACTTAAAATAATT
502156 TAAA-TTAAAAAATAATT
1 TAAACTT--AAAATAATT
*
502173 TAAAAATTAAAA-AATT
1 T-AAACTTAAAATAATT
502189 TAAA
1 TAAA
502193 ATAATTTAAT
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
15 18 0.25
16 35 0.49
17 14 0.19
18 3 0.04
19 2 0.03
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAACTTAAAATAATT
Found at i:502168 original size:48 final size:48
Alignment explanation
Indices: 502093--502211 Score: 125
Period size: 48 Copynumber: 2.5 Consensus size: 48
502083 ACTCGAGTTA
* * * *
502093 TAAATTTAAAATAATATAAACT-CAAAATAATTTAAACA-TAAAATAACT
1 TAAA-TTAAAATAATTTAAATTAAAAAATAATTTAAAAATTAAAA-AACT
*
502141 TAAATTAAAATAATTTAAATTAAAAAATAATTTAAAAATTAAAAAATT
1 TAAATTAAAATAATTTAAATTAAAAAATAATTTAAAAATTAAAAAACT
* ** *
502189 TAAAATAATTTAATTCAAATTAA
1 TAAATTAAAATAATTTAAATTAA
502212 TTTAGTCAGG
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
47 15 0.25
48 40 0.67
49 5 0.08
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.34
Consensus pattern (48 bp):
TAAATTAAAATAATTTAAATTAAAAAATAATTTAAAAATTAAAAAACT
Found at i:502181 original size:19 final size:17
Alignment explanation
Indices: 502116--502187 Score: 78
Period size: 15 Copynumber: 4.3 Consensus size: 17
502106 ATATAAACTC
* *
502116 AAAATAATTTAAA-CAT
1 AAAATAATTTAAATTAA
*
502132 AAAATAACTTAAATT--
1 AAAATAATTTAAATTAA
502147 AAAATAATTTAAATTAA
1 AAAATAATTTAAATTAA
502164 AAAATAATTTAAAAATTAA
1 AAAATAATTT--AAATTAA
502183 AAAAT
1 AAAAT
502188 TTAAAATAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
15 14 0.29
16 12 0.25
17 10 0.21
19 12 0.25
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATAATTTAAATTAA
Found at i:502203 original size:15 final size:15
Alignment explanation
Indices: 502095--502215 Score: 70
Period size: 15 Copynumber: 8.1 Consensus size: 15
502085 TCGAGTTATA
*
502095 AATTTAAAATAATATA
1 AATTTAAAATAAT-TT
* *
502111 AACTCAAAATAATTT
1 AATTTAAAATAATTT
** *
502126 AAACATAAAATAACTT
1 -AATTTAAAATAATTT
*
502142 AAATTAAAATAATTT
1 AATTTAAAATAATTT
*
502157 AAATTAAAA-AA--T
1 AATTTAAAATAATTT
**
502169 AATTTAAAAATTAA-AA
1 AATTT-AAAA-TAATTT
502185 AATTTAAAATAATTT
1 AATTTAAAATAATTT
* *
502200 AATTCAAATTAATTT
1 AATTTAAAATAATTT
502215 A
1 A
502216 GTCAGGAATC
Statistics
Matches: 84, Mismatches: 15, Indels: 13
0.75 0.13 0.12
Matches are distributed among these distances:
12 5 0.06
13 4 0.05
14 5 0.06
15 42 0.50
16 28 0.33
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (15 bp):
AATTTAAAATAATTT
Found at i:502572 original size:23 final size:22
Alignment explanation
Indices: 502524--502566 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
502514 TTTTTAAAAG
* *
502524 TAAAAAATATTTTATAAATATA
1 TAAAAAAAAATTTATAAATATA
502546 TAAAAAAAAATTTA-AAATATA
1 TAAAAAAAAATTTATAAATATA
502567 AATAAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAAAAAAAATTTATAAATATA
Found at i:505855 original size:26 final size:26
Alignment explanation
Indices: 505825--505891 Score: 116
Period size: 26 Copynumber: 2.6 Consensus size: 26
505815 ATATTGAAAT
*
505825 AATATCGAGTCAAAACCAATGAAACC
1 AATATCAAGTCAAAACCAATGAAACC
*
505851 AATATCAAGTCAAAACCAATGAAACT
1 AATATCAAGTCAAAACCAATGAAACC
505877 AATATCAAGTCAAAA
1 AATATCAAGTCAAAA
505892 TGTAGCTAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.54, C:0.19, G:0.09, T:0.18
Consensus pattern (26 bp):
AATATCAAGTCAAAACCAATGAAACC
Found at i:506425 original size:16 final size:16
Alignment explanation
Indices: 506406--506444 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
506396 TATTATGTTA
506406 TATTTTTTATTTAAAG
1 TATTTTTTATTTAAAG
* * *
506422 TATTTTATATTTATAT
1 TATTTTTTATTTAAAG
506438 TATTTTT
1 TATTTTT
506445 GATATATTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (16 bp):
TATTTTTTATTTAAAG
Found at i:506468 original size:32 final size:29
Alignment explanation
Indices: 506425--506506 Score: 83
Period size: 32 Copynumber: 2.7 Consensus size: 29
506415 TTTAAAGTAT
*
506425 TTTATATTTATATTATTTTTGATATATTAATAA
1 TTTATA-TTATATTATTTTTGAGATA--AAT-A
* *
506458 TTTATATTATATAAATTTTGAGATAAATA
1 TTTATATTATATTATTTTTGAGATAAATA
*
506487 TTTTTATTATATTATATTTT
1 TTTATATTATATTAT-TTTT
506507 AATTACTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
29 13 0.31
30 7 0.17
32 16 0.38
33 6 0.14
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (29 bp):
TTTATATTATATTATTTTTGAGATAAATA
Found at i:506505 original size:16 final size:16
Alignment explanation
Indices: 506388--506511 Score: 55
Period size: 17 Copynumber: 7.8 Consensus size: 16
506378 CAAATAATTC
*
506388 ATATATTTTATTATGTT
1 ATAT-TTTTATTATATT
*
506405 ATATTTTTTATT-TA-A
1 ATA-TTTTTATTATATT
506420 AGTATTTTATATTTATATT
1 A-TATTTT-TA-TTATATT
*
506439 AT-TTTTGA-TATATT
1 ATATTTTTATTATATT
*
506453 AATAATTTATATTATA-T
1 -AT-ATTTTTATTATATT
* * * *
506470 AAATTTTGA-GATA-A
1 ATATTTTTATTATATT
506484 ATATTTTTATTATATT
1 ATATTTTTATTATATT
*
506500 ATATTTTAATTA
1 ATATTTTTATTA
506512 CTTTATATGT
Statistics
Matches: 79, Mismatches: 16, Indels: 25
0.66 0.13 0.21
Matches are distributed among these distances:
14 16 0.20
15 15 0.19
16 18 0.23
17 21 0.27
18 8 0.10
19 1 0.01
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (16 bp):
ATATTTTTATTATATT
Found at i:507599 original size:12 final size:13
Alignment explanation
Indices: 507567--507622 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
507557 CTTTTAATAA
507567 AATATTTAAAATTT
1 AATATTT-AAATTT
507581 AAT-TTTAAA-TT
1 AATATTTAAATTT
507592 AATATTTATATATTT
1 AATATTTA-A-ATTT
* *
507607 TATAATTAAATTT
1 AATATTTAAATTT
507620 AAT
1 AAT
507623 TAAAAATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
11 5 0.14
12 7 0.20
13 10 0.29
14 5 0.14
15 8 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATATTTAAATTT
Found at i:511120 original size:35 final size:35
Alignment explanation
Indices: 511074--511141 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
511064 ATTGGCCGAT
*
511074 GTTTGGTGTTACTTGCATATTTGTAATGTTTTGCC
1 GTTTGCTGTTACTTGCATATTTGTAATGTTTTGCC
511109 GTTTGCTGTTACTTGCATATTTGTAATGTTTTG
1 GTTTGCTGTTACTTGCATATTTGTAATGTTTTG
511142 ACTTTTGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.15, C:0.10, G:0.22, T:0.53
Consensus pattern (35 bp):
GTTTGCTGTTACTTGCATATTTGTAATGTTTTGCC
Found at i:514896 original size:20 final size:18
Alignment explanation
Indices: 514835--514905 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 18
514825 ACTATTGAAA
*
514835 TAAAAAAAT-ATAAATAT
1 TAAATAAATAATAAATAT
* *
514852 TAAATAAATGATCTAATAT
1 TAAATAAATAAT-AAATAT
514871 TAAATAAATAATAAATAT
1 TAAATAAATAATAAATAT
*
514889 AGTAAATAATTAATAAA
1 --TAAATAAATAATAAA
514906 AATATATATT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
17 8 0.18
18 7 0.16
19 16 0.36
20 14 0.31
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.32
Consensus pattern (18 bp):
TAAATAAATAATAAATAT
Found at i:515516 original size:19 final size:19
Alignment explanation
Indices: 515481--515520 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
515471 TTAAAAAATT
515481 ATTTTTAATTAATATTTAA
1 ATTTTTAATTAATATTTAA
515500 ATTTTATAATTAA-ATTTAA
1 ATTTT-TAATTAATATTTAA
515519 AT
1 AT
515521 AAAAATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTTTAATTAATATTTAA
Found at i:515559 original size:48 final size:48
Alignment explanation
Indices: 515472--515591 Score: 118
Period size: 48 Copynumber: 2.4 Consensus size: 48
515462 ATTAAAATAT
**
515472 TAAAAAATTATTTTTAATTAATATTTAAATTTTATAATTAAATTTAAA
1 TAAAAAATTATTTTTAATTAATAAATAAATTTTATAATTAAATTTAAA
*
515520 TAAAAATATTA-TTTTAATTAATAAATAGTAATTTAAATTAAATT-AATTTAAA
1 TAAAAA-ATTATTTTTAATTAATAAATA--AATTT-TA-T-AATTAAATTTAAA
* *
515572 TTAAAAAATAATTTTAAATT
1 -TAAAAAATTATTTTTAATT
515592 TAAATCAAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 11
0.79 0.07 0.15
Matches are distributed among these distances:
48 20 0.34
49 4 0.07
50 5 0.08
51 1 0.02
52 12 0.20
53 17 0.29
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.47
Consensus pattern (48 bp):
TAAAAAATTATTTTTAATTAATAAATAAATTTTATAATTAAATTTAAA
Found at i:515562 original size:5 final size:5
Alignment explanation
Indices: 515552--515610 Score: 52
Period size: 5 Copynumber: 12.0 Consensus size: 5
515542 AAATAGTAAT
* * *
515552 TTAAA TTAAA TTAAT TTAAA TTAAA --AAA -TAATT TTAAA TTTAAA TCAAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAA-A TTAAA -TTAAA TTAAA
515601 TTAAA TTAAA
1 TTAAA TTAAA
515611 AAAAATTATT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
3 3 0.07
4 2 0.05
5 31 0.70
6 8 0.18
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (5 bp):
TTAAA
Found at i:515587 original size:18 final size:18
Alignment explanation
Indices: 515512--515612 Score: 83
Period size: 17 Copynumber: 5.8 Consensus size: 18
515502 TTTATAATTA
515512 AATTTAAA-TAAAAATAT
1 AATTTAAATTAAAAATAT
* *
515529 TATTTTAATTAATAAATAGT
1 AATTTAAATTAA-AAATA-T
515549 AATTTAAATT--AAAT-T
1 AATTTAAATTAAAAATAT
515564 AATTTAAATTAAAAA-AT
1 AATTTAAATTAAAAATAT
*
515581 AATTTTAAATT-TAAATCA-
1 AA-TTTAAATTAAAAAT-AT
515599 AA-TTAAATTAAAAA
1 AATTTAAATTAAAAA
515613 AAATTATTGA
Statistics
Matches: 68, Mismatches: 6, Indels: 20
0.72 0.06 0.21
Matches are distributed among these distances:
15 11 0.16
16 7 0.10
17 22 0.32
18 13 0.19
19 6 0.09
20 9 0.13
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (18 bp):
AATTTAAATTAAAAATAT
Found at i:515595 original size:34 final size:32
Alignment explanation
Indices: 515551--515617 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 32
515541 TAAATAGTAA
* *
515551 TTTAAATTAAATTAATTTAAATTAAAAAATAAT
1 TTTAAATTAAATCAAATTAAATTAAAAAA-AAT
515584 TTTAAATTTAAATCAAATTAAATTAAAAAAAAT
1 TTTAAA-TTAAATCAAATTAAATTAAAAAAAAT
515617 T
1 T
515618 ATTGACTCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 10 0.32
34 21 0.68
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (32 bp):
TTTAAATTAAATCAAATTAAATTAAAAAAAAT
Found at i:515946 original size:29 final size:27
Alignment explanation
Indices: 515909--515998 Score: 82
Period size: 28 Copynumber: 3.4 Consensus size: 27
515899 ATATGTACTA
*
515909 ATTTTTTTTAATTTAATTATGTATATTAT
1 ATTTATTTT-ATTTAATTAT-TATATTAT
*
515938 ATTTATTTTATTTTATT-TTAT-TT-T
1 ATTTATTTTATTTAATTATTATATTAT
515962 A-TTATTTT-TTTAATTATTTATATTAT
1 ATTTATTTTATTTAATTA-TTATATTAT
*
515988 AATTATATTTA
1 ATTTAT-TTTA
515999 AAATAAATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
22 6 0.12
23 7 0.14
24 6 0.12
25 4 0.08
26 5 0.10
27 5 0.10
28 10 0.20
29 8 0.16
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (27 bp):
ATTTATTTTATTTAATTATTATATTAT
Found at i:515971 original size:10 final size:10
Alignment explanation
Indices: 515934--515964 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
515924 ATTATGTATA
515934 TTATATTTATT
1 TTAT-TTTATT
515945 TTATTTTATT
1 TTATTTTATT
515955 TTATTTTATT
1 TTATTTTATT
515965 ATTTTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 16 0.80
11 4 0.20
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (10 bp):
TTATTTTATT
Found at i:515990 original size:15 final size:13
Alignment explanation
Indices: 515914--515998 Score: 61
Period size: 15 Copynumber: 6.4 Consensus size: 13
515904 TACTAATTTT
515914 TTTTAATTTAATTA
1 TTTT-ATTTAATTA
* *
515928 TGTATATTATATTTA
1 T-TTTATT-TAATTA
515943 TTTTA-TT--TTA
1 TTTTATTTAATTA
*
515953 TTTTATTTTATTA
1 TTTTATTTAATTA
515966 TTTT-TTTAATTA
1 TTTTATTTAATTA
515978 TTTATATTATAATTA
1 TTT-TATT-TAATTA
515993 TATTTA
1 T-TTTA
515999 AAATAAATTT
Statistics
Matches: 58, Mismatches: 4, Indels: 17
0.73 0.05 0.22
Matches are distributed among these distances:
10 8 0.14
11 2 0.03
12 11 0.19
13 9 0.16
14 9 0.16
15 17 0.29
16 2 0.03
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (13 bp):
TTTTATTTAATTA
Found at i:516154 original size:18 final size:18
Alignment explanation
Indices: 516128--516182 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
516118 TTTTCATATA
*
516128 TATTATTATATTATTTTTT
1 TATT-TTATATTATATTTT
516147 TATTTTATATTATA-TTT
1 TATTTTATATTATATTTT
*
516164 TAATTTATTATATATATTT
1 TATTTTA-TAT-TATATTT
516183 ATAATAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 9 0.29
18 12 0.39
19 8 0.26
20 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TATTTTATATTATATTTT
Found at i:516187 original size:20 final size:19
Alignment explanation
Indices: 516130--516187 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 19
516120 TTCATATATA
516130 TTATTATAT-TATTTT--T
1 TTATTATATATATTTTAAT
516146 TTATTTTATATTATATTTTAAT
1 TTA--TTATA-TATATTTTAAT
516168 TTATTATATATATTTATAAT
1 TTATTATATATATTT-TAAT
516188 AATATAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
16 3 0.09
18 5 0.14
19 8 0.23
20 15 0.43
22 4 0.11
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATTATATATATTTTAAT
Found at i:516717 original size:19 final size:18
Alignment explanation
Indices: 516683--516732 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
516673 TTGTTTATAT
516683 TATATTTTTTATTTTTAA
1 TATATTTTTTATTTTTAA
*
516701 TTTATTTTTTATCTTTTAA
1 TATATTTTTTAT-TTTTAA
*
516720 TAAATTTTTTATT
1 TATATTTTTTATT
516733 AATATTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 12 0.43
19 16 0.57
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (18 bp):
TATATTTTTTATTTTTAA
Found at i:516900 original size:20 final size:20
Alignment explanation
Indices: 516877--516937 Score: 50
Period size: 22 Copynumber: 3.0 Consensus size: 20
516867 ACATTTTTAA
*
516877 TTAAAAATCTTTATTCAAGT
1 TTAAAAATCTTTATTCAAGC
* * **
516897 TTAACTAAAGCTATATTCGTGC
1 TTAA--AAATCTTTATTCAAGC
*
516919 TTAAAATTCTTTATTCAAG
1 TTAAAAATCTTTATTCAAG
516938 GTCTATTTTT
Statistics
Matches: 29, Mismatches: 10, Indels: 4
0.67 0.23 0.09
Matches are distributed among these distances:
20 14 0.48
22 15 0.52
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.43
Consensus pattern (20 bp):
TTAAAAATCTTTATTCAAGC
Done.