Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 162 of 190
Found at i:47268593 original size:25 final size:26
Alignment explanation
Indices: 47268560--47268608 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
47268550 AAAAAGTTTT
47268560 GGGAATAAAAGGTT-GAGGGAAAAGG
1 GGGAATAAAAGGTTGGAGGGAAAAGG
* **
47268585 GGGAGTAAAATTTTGGAGGGAAAA
1 GGGAATAAAAGGTTGGAGGGAAAA
47268609 TATTAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 11 0.55
26 9 0.45
ACGTcount: A:0.43, C:0.00, G:0.41, T:0.16
Consensus pattern (26 bp):
GGGAATAAAAGGTTGGAGGGAAAAGG
Found at i:47268694 original size:31 final size:30
Alignment explanation
Indices: 47268659--47268718 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
47268649 GGAGGTGGGA
*
47268659 TGGGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AGAGAATAAAAATTTTAGGGGAAAAG
* * *
47268690 TGGGAGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAGAGAATAAAAATTTTAGGGGAAAA
47268719 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (30 bp):
TGGGAGAGAATAAAAATTTTAGGGGAAAAG
Found at i:47269715 original size:25 final size:26
Alignment explanation
Indices: 47269699--47269789 Score: 77
Period size: 25 Copynumber: 3.7 Consensus size: 26
47269689 TTTCTGTTAT
47269699 TTGGCTCTCACGAGC-TTCTTGATAA
1 TTGGCTCTCACGAGCTTTCTTGATAA
* *
47269724 TTGGCTCTCATGAGC-TTCTCGATTAA
1 TTGGCTCTCACGAGCTTTCTTGA-TAA
*
47269750 -TGGCTCTCTA-GAGC-TTCCTGAT-A
1 TTGGCTCTC-ACGAGCTTTCTTGATAA
* *
47269773 TTGGCTCGCATGAGCTT
1 TTGGCTCTCACGAGCTT
47269790 CCCGTTACAT
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
23 2 0.04
24 12 0.21
25 38 0.68
26 4 0.07
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (26 bp):
TTGGCTCTCACGAGCTTTCTTGATAA
Found at i:47269802 original size:49 final size:50
Alignment explanation
Indices: 47269700--47269804 Score: 144
Period size: 49 Copynumber: 2.1 Consensus size: 50
47269690 TTCTGTTATT
* * *
47269700 TGGCTCTCACGAGCTTCTTGATAATTGGCTCTCATGAGCTTCTCGATTAA
1 TGGCTCTCACGAGCTTCCTGATAATTGGCTCGCATGAGCTTCCCGATTAA
47269750 TGGCTCTCTA-GAGCTTCCTGAT-ATTGGCTCGCATGAGCTTCCCG-TTACA
1 TGGCTCTC-ACGAGCTTCCTGATAATTGGCTCGCATGAGCTTCCCGATTA-A
47269799 TGGCTC
1 TGGCTC
47269805 GGAATAGCTT
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
48 3 0.06
49 27 0.54
50 19 0.38
51 1 0.02
ACGTcount: A:0.17, C:0.27, G:0.22, T:0.34
Consensus pattern (50 bp):
TGGCTCTCACGAGCTTCCTGATAATTGGCTCGCATGAGCTTCCCGATTAA
Found at i:47270340 original size:2 final size:2
Alignment explanation
Indices: 47270333--47270361 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
47270323 GCCCATTTCG
47270333 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
47270362 GTAAATCAAT
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:47271429 original size:17 final size:17
Alignment explanation
Indices: 47271407--47271441 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
47271397 AGTAAGATTC
*
47271407 AGACTGTGACAAGCACA
1 AGACTGTCACAAGCACA
*
47271424 AGACTGTCACTAGCACA
1 AGACTGTCACAAGCACA
47271441 A
1 A
47271442 TGCATATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.26, G:0.20, T:0.14
Consensus pattern (17 bp):
AGACTGTCACAAGCACA
Found at i:47274534 original size:125 final size:125
Alignment explanation
Indices: 47274308--47274727 Score: 583
Period size: 125 Copynumber: 3.4 Consensus size: 125
47274298 GGACGTCAAT
* * * * *
47274308 AATTTGTGAAATCGCGCCCCCCTGGATGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTT
1 AATTTGTGAAATCACGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTT
*
47274373 GAGTTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGAGAAG
66 GAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGAGAAG
* * * *
47274433 AATTTGTTAAATCACGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCT-GAAAAAATTATTTC
1 AATTTGTGAAATCACGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTT
* * * * * *
47274497 GAGTTGACGTTTCTGAGCAAATAGTACAAAAAACGCTTCAAGCAGGCTACTATT-TGAGAAG
66 GAGTTGACGTTTCTGAGCAAATAGTA-TAAAATCGCTTCTACCAGGATGCT-TTATGAGAAG
* * * *
47274558 AATTTCTGAAATCACGCCCTCGTGGACGCGCTTTTGCTATAGTTGGTCCTGGAAGAAATAATTTT
1 AATTTGTGAAATCACGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTT
47274623 GAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGAGAAG
66 GAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGAGAAG
* * * * *
47274683 AATTTGTGAAATCGCGTCCACATGGACGCGCTTTTACCACAGTAG
1 AATTTGTGAAATCACGCCCACGTGGACGCGCTTTTGCTACAGTAG
47274728 CATGTTTGGG
Statistics
Matches: 252, Mismatches: 39, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
124 38 0.15
125 175 0.69
126 39 0.15
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (125 bp):
AATTTGTGAAATCACGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTT
GAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGAGAAG
Found at i:47277871 original size:25 final size:25
Alignment explanation
Indices: 47277837--47277884 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
47277827 TCGAAAAAAT
47277837 TTCTATTTTATTACATCAAATAAAC
1 TTCTATTTTATTACATCAAATAAAC
47277862 TTCTATTTTATTACATCAAATAA
1 TTCTATTTTATTACATCAAATAA
47277885 TATCAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.46
Consensus pattern (25 bp):
TTCTATTTTATTACATCAAATAAAC
Found at i:47277879 original size:70 final size:70
Alignment explanation
Indices: 47277799--47277929 Score: 237
Period size: 70 Copynumber: 1.9 Consensus size: 70
47277789 TAAGCTCATG
*
47277799 TTATTACATCAAATAATATCAAAATAACTCG-AAAAAATTTCTATTTTATTACATCAAATAAACT
1 TTATTACATCAAATAATATCAAAATAACT-GAAAAAAATTTCTATTTTATTACATAAAATAAACT
47277863 TCTATT
65 TCTATT
47277869 TTATTACATCAAATAATATCAAAATAACTGAAAAAAATTTCTATTTTATTACATAAAATAA
1 TTATTACATCAAATAATATCAAAATAACTGAAAAAAATTTCTATTTTATTACATAAAATAA
47277930 TATCAAAATA
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
69 1 0.02
70 58 0.98
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (70 bp):
TTATTACATCAAATAATATCAAAATAACTGAAAAAAATTTCTATTTTATTACATAAAATAAACTT
CTATT
Found at i:47278381 original size:18 final size:18
Alignment explanation
Indices: 47278358--47278397 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
47278348 GACTCGAAAA
*
47278358 AGGATACATATAAGGGTT
1 AGGATACATATAAGGGCT
47278376 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
47278394 AGGA
1 AGGA
47278398 AACGCACCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.07, G:0.30, T:0.23
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:47280271 original size:51 final size:51
Alignment explanation
Indices: 47280200--47280297 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
47280190 AATTATTTAA
* *
47280200 AAATAGGGATTTAAGCGAAA-TTTAAGAAGAACTTGAGAGCAAATTGAAATT
1 AAATACGGATTTAAGAGAAATTTTAA-AAGAACTTGAGAGCAAATTGAAATT
* * *
47280251 AAATACGGATTTGAGAGAAATTTTAAAGGAATTTGAGAGCAAATTGA
1 AAATACGGATTTAAGAGAAATTTTAAAAGAACTTGAGAGCAAATTGA
47280298 GAGGAAATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
51 36 0.88
52 5 0.12
ACGTcount: A:0.46, C:0.05, G:0.22, T:0.27
Consensus pattern (51 bp):
AAATACGGATTTAAGAGAAATTTTAAAAGAACTTGAGAGCAAATTGAAATT
Found at i:47280302 original size:22 final size:23
Alignment explanation
Indices: 47280259--47280313 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
47280249 TTAAATACGG
*
47280259 ATTTGAGAGAAATTTTAAAGG-A
1 ATTTGAGAGAAATTTGAAAGGAA
*
47280281 ATTTGAGAGCAAA-TTGAGAGGAA
1 ATTTGAGAG-AAATTTGAAAGGAA
*
47280304 ATTTAAGAGA
1 ATTTGAGAGA
47280314 GGATTAGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 16 0.57
23 12 0.43
ACGTcount: A:0.45, C:0.02, G:0.25, T:0.27
Consensus pattern (23 bp):
ATTTGAGAGAAATTTGAAAGGAA
Found at i:47283713 original size:13 final size:13
Alignment explanation
Indices: 47283695--47283719 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47283685 AACGAATATC
47283695 AAATAAAATAAAT
1 AAATAAAATAAAT
47283708 AAATAAAATAAA
1 AAATAAAATAAA
47283720 ATTAGTAACC
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATAAAATAAAT
Found at i:47287762 original size:3 final size:3
Alignment explanation
Indices: 47287754--47287779 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
47287744 AATATTTTAA
47287754 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
47287780 CAAAAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:47304351 original size:2 final size:2
Alignment explanation
Indices: 47304344--47304383 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
47304334 NNNNNNNNNN
47304344 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
47304384 CTCAAATGCA
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:47304780 original size:41 final size:41
Alignment explanation
Indices: 47304720--47304834 Score: 131
Period size: 41 Copynumber: 2.8 Consensus size: 41
47304710 TGATTCGGTA
* * * * * *
47304720 CACCGGCCTTTAGCTTGCTAGACCTATAGTCTGAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAATATAT
* * *
47304761 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGTATTATTT
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAATATAT
* *
47304802 CACCGGTATCAAGCCTGCTAGACGTAAAGTCTG
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTG
47304835 TATTACATTC
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAATATAT
Found at i:47304835 original size:41 final size:41
Alignment explanation
Indices: 47304760--47304839 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
47304750 CTGAAATGTA
*
47304760 TCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGTATTATT
1 TCACCGGCATCAAGCCTGCTAGACGTAAAGTCTGTATTATT
*
47304801 TCACCGGTATCAAGCCTGCTAGACGTAAAGTCTGTATTA
1 TCACCGGCATCAAGCCTGCTAGACGTAAAGTCTGTATTA
47304840 CATTCGATCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (41 bp):
TCACCGGCATCAAGCCTGCTAGACGTAAAGTCTGTATTATT
Found at i:47305101 original size:2 final size:2
Alignment explanation
Indices: 47305094--47305126 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
47305084 CTCAAAAACT
*
47305094 TA TA TA TA TA TA TA CA 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 T
47305127 TCGAGTATCA
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:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:47307009 original size:16 final size:17
Alignment explanation
Indices: 47306986--47307024 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
47306976 TTTTTATAGA
*
47306986 ATTTTTTTATA-AATTT
1 ATTTTTTTACATAATTT
47307002 ATTTTTTTACATAATTT
1 ATTTTTTTACATAATTT
47307019 -TTTTTT
1 ATTTTTT
47307025 CACTCAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTTTTACATAATTT
Found at i:47314140 original size:53 final size:51
Alignment explanation
Indices: 47314060--47314161 Score: 177
Period size: 53 Copynumber: 2.0 Consensus size: 51
47314050 AAACTGATGC
*
47314060 AATTTATATTATCTTTTTTCATGACAGTCGAAGGGCCCATCACAACCTAACTT
1 AATTTATATTATCTTTTTTCATGACAGT-GAAGAGCCC-TCACAACCTAACTT
47314113 AATTTATATTATCTTTTTTCATGACAGTGAAGAGCCCTCACAACCTAAC
1 AATTTATATTATCTTTTTTCATGACAGTGAAGAGCCCTCACAACCTAAC
47314162 ATCAATTTGA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
51 12 0.25
52 8 0.17
53 28 0.58
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (51 bp):
AATTTATATTATCTTTTTTCATGACAGTGAAGAGCCCTCACAACCTAACTT
Found at i:47315993 original size:25 final size:25
Alignment explanation
Indices: 47315965--47316067 Score: 93
Period size: 25 Copynumber: 4.1 Consensus size: 25
47315955 ATGTAAACCA
* *
47315965 GAAGCTCTTCCGAGCCATATAACGG
1 GAAGCTCTTACGAGCCATATATCGG
* ** *
47315990 GAAGCTCATACGAGCTGTATATTGG
1 GAAGCTCTTACGAGCCATATATCGG
* * *
47316015 GAAGCTCTTGCGAGCCAAATATCGA
1 GAAGCTCTTACGAGCCATATATCGG
47316040 GAAGCTCATTA-GAGCCA-AGTATCGG
1 GAAGCTC-TTACGAGCCATA-TATCGG
47316065 GAA
1 GAA
47316068 ACTCAAGAGA
Statistics
Matches: 61, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
24 1 0.02
25 58 0.95
26 2 0.03
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.21
Consensus pattern (25 bp):
GAAGCTCTTACGAGCCATATATCGG
Found at i:47316067 original size:50 final size:50
Alignment explanation
Indices: 47315965--47316067 Score: 111
Period size: 50 Copynumber: 2.1 Consensus size: 50
47315955 ATGTAAACCA
* * ** *
47315965 GAAGCTCTTCCGAGCCATATAACGGGAAGCTCATACGAGCTGTATATTGG
1 GAAGCTCTTCCGAGCCAAATAACGAGAAGCTCATACGAGCTCAATATCGG
* *
47316015 GAAGCTCTTGCGAGCCAAATATCGAGAAGCTCATTA-GAGC-CAAGTATCGG
1 GAAGCTCTTCCGAGCCAAATAACGAGAAGCTCA-TACGAGCTCAA-TATCGG
47316065 GAA
1 GAA
47316068 ACTCAAGAGA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
49 1 0.02
50 41 0.93
51 2 0.05
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.21
Consensus pattern (50 bp):
GAAGCTCTTCCGAGCCAAATAACGAGAAGCTCATACGAGCTCAATATCGG
Found at i:47316078 original size:25 final size:25
Alignment explanation
Indices: 47316026--47316079 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
47316016 AAGCTCTTGC
* **
47316026 GAGCCAAATATCGAGAAGCTCATTA
1 GAGCCAAATATCGAGAAACTCAAGA
* *
47316051 GAGCCAAGTATCGGGAAACTCAAGA
1 GAGCCAAATATCGAGAAACTCAAGA
47316076 GAGC
1 GAGC
47316080 TGTGGTGTGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.26, T:0.15
Consensus pattern (25 bp):
GAGCCAAATATCGAGAAACTCAAGA
Found at i:47316427 original size:16 final size:15
Alignment explanation
Indices: 47316387--47316429 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
47316377 TATACGAATG
* *
47316387 AATTTAACTCAATTT
1 AATTTAATTCAATTC
*
47316402 AATATAATTCATATTC
1 AATTTAATTCA-ATTC
47316418 AATTTAATTCAA
1 AATTTAATTCAA
47316430 CACACATCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTTAATTCAATTC
Found at i:47320420 original size:2 final size:2
Alignment explanation
Indices: 47320413--47320442 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
47320403 CAAACAAATG
47320413 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
47320443 ATCCGTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47326332 original size:19 final size:21
Alignment explanation
Indices: 47326292--47326330 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
47326282 AAAATATGAG
*
47326292 AAAAGATATTTTAAATTAAAT
1 AAAAGATATTTAAAATTAAAT
47326313 AAAA-ATATTTAAAATTAA
1 AAAAGATATTTAAAATTAA
47326331 TATTGTTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (21 bp):
AAAAGATATTTAAAATTAAAT
Found at i:47328640 original size:40 final size:40
Alignment explanation
Indices: 47328532--47328706 Score: 197
Period size: 40 Copynumber: 4.3 Consensus size: 40
47328522 ACCTAAGCCC
* * *
47328532 AAAGCGCCGCTAATGCTCGGGGATTTTGCGGTATTTTTGAA
1 AAAGCGCCGCTAATGCTCGGGGATTTAGCAGCATTTTTG-A
* * * * * *
47328573 AAAGTGCCTCTAATACTTGGGGCTTTAGCAGCGTTTTTGA
1 AAAGCGCCGCTAATGCTCGGGGATTTAGCAGCATTTTTGA
*
47328613 AAAGCGCCGCTAATGCTCGGGGATTTAGCGGCATTTTTGA
1 AAAGCGCCGCTAATGCTCGGGGATTTAGCAGCATTTTTGA
* * * * *
47328653 ACAGCGCCGCTAATGTTCGGGGCTTTAGCAGCGTTTTTAAA
1 AAAGCGCCGCTAATGCTCGGGGATTTAGCAGCATTTTT-GA
47328694 AAAGCGCCGCTAA
1 AAAGCGCCGCTAA
47328707 AAACATTTTA
Statistics
Matches: 110, Mismatches: 23, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
40 67 0.61
41 43 0.39
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.29
Consensus pattern (40 bp):
AAAGCGCCGCTAATGCTCGGGGATTTAGCAGCATTTTTGA
Found at i:47328697 original size:81 final size:81
Alignment explanation
Indices: 47328532--47328706 Score: 255
Period size: 81 Copynumber: 2.2 Consensus size: 81
47328522 ACCTAAGCCC
* * * *
47328532 AAAGCGCCGCTAATGCTCGGGGATTTTGCGGTATTTTTGAAAAAGTGCCTCTAATACTTGGGGCT
1 AAAGCGCCGCTAATGCTCGGGGATTTAGCGGCATTTTTGAAAAAGCGCCGCTAATACTTGGGGCT
*
47328597 TTAGCAGCGTTTTTGA
66 TTAGCAGCGTTTTTAA
* *
47328613 AAAGCGCCGCTAATGCTCGGGGATTTAGCGGCATTTTTG-AACAGCGCCGCTAAT-GTTCGGGGC
1 AAAGCGCCGCTAATGCTCGGGGATTTAGCGGCATTTTTGAAAAAGCGCCGCTAATACTT-GGGGC
47328676 TTTAGCAGCGTTTTTAAA
65 TTTAGCAGCGTTTTT-AA
47328694 AAAGCGCCGCTAA
1 AAAGCGCCGCTAA
47328707 AAACATTTTA
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
79 2 0.02
80 32 0.38
81 51 0.60
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.29
Consensus pattern (81 bp):
AAAGCGCCGCTAATGCTCGGGGATTTAGCGGCATTTTTGAAAAAGCGCCGCTAATACTTGGGGCT
TTAGCAGCGTTTTTAA
Found at i:47329095 original size:14 final size:15
Alignment explanation
Indices: 47329066--47329099 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
47329056 GTTTAAGGAG
47329066 TATGGATTTAGAGAT
1 TATGGATTTAGAGAT
*
47329081 TATGGA-TTAGGGAT
1 TATGGATTTAGAGAT
47329095 TATGG
1 TATGG
47329100 TTCAAAGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.38
Consensus pattern (15 bp):
TATGGATTTAGAGAT
Found at i:47329319 original size:7 final size:7
Alignment explanation
Indices: 47329307--47329355 Score: 53
Period size: 7 Copynumber: 7.0 Consensus size: 7
47329297 TATAATTATA
47329307 GTTTAAG
1 GTTTAAG
47329314 GTTTAAG
1 GTTTAAG
*
47329321 GTTTAGG
1 GTTTAAG
* *
47329328 GTATATG
1 GTTTAAG
* *
47329335 GTGTAGG
1 GTTTAAG
47329342 GTTTAAG
1 GTTTAAG
47329349 GTTTAAG
1 GTTTAAG
47329356 AGTTACTATT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.41
Consensus pattern (7 bp):
GTTTAAG
Found at i:47329437 original size:15 final size:15
Alignment explanation
Indices: 47329415--47329490 Score: 61
Period size: 14 Copynumber: 5.3 Consensus size: 15
47329405 GGGTTAGGAT
47329415 TTTA-GGTTTAGGGG
1 TTTAGGGTTTAGGGG
47329429 TTTAGGGTTTAGGGG
1 TTTAGGGTTTAGGGG
* * * *
47329444 -CTATGTTTTA-TGG
1 TTTAGGGTTTAGGGG
*
47329457 TTTATGGTTTAGGGG
1 TTTAGGGTTTAGGGG
* *
47329472 ATAAGGGTTTA-GGG
1 TTTAGGGTTTAGGGG
47329486 TTTAG
1 TTTAG
47329491 ATTAATTAGT
Statistics
Matches: 47, Mismatches: 12, Indels: 6
0.72 0.18 0.09
Matches are distributed among these distances:
13 2 0.04
14 25 0.53
15 20 0.43
ACGTcount: A:0.17, C:0.01, G:0.38, T:0.43
Consensus pattern (15 bp):
TTTAGGGTTTAGGGG
Found at i:47329438 original size:7 final size:7
Alignment explanation
Indices: 47329415--47329490 Score: 55
Period size: 7 Copynumber: 10.7 Consensus size: 7
47329405 GGGTTAGGAT
47329415 TTTA-GG
1 TTTAGGG
47329421 TTTAGGGG
1 TTTA-GGG
47329429 TTTAGGG
1 TTTAGGG
47329436 TTTAGGG
1 TTTAGGG
** * *
47329443 GCTATGT
1 TTTAGGG
*
47329450 TTTATGG
1 TTTAGGG
*
47329457 TTTATGG
1 TTTAGGG
47329464 TTTAGGGG
1 TTTA-GGG
* *
47329472 ATAAGGG
1 TTTAGGG
47329479 TTTAGGG
1 TTTAGGG
47329486 TTTAG
1 TTTAG
47329491 ATTAATTAGT
Statistics
Matches: 55, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
6 4 0.07
7 41 0.75
8 10 0.18
ACGTcount: A:0.17, C:0.01, G:0.38, T:0.43
Consensus pattern (7 bp):
TTTAGGG
Found at i:47329865 original size:19 final size:19
Alignment explanation
Indices: 47329841--47329889 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
47329831 AAATTATAAC
*
47329841 AAATAAAAATAAAATACAA
1 AAATAAAAATAAAACACAA
*
47329860 AAATAAAAATGAAACACAA
1 AAATAAAAATAAAACACAA
47329879 AAACTAAAAAT
1 AAA-TAAAAAT
47329890 TATAATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.76, C:0.08, G:0.02, T:0.14
Consensus pattern (19 bp):
AAATAAAAATAAAACACAA
Found at i:47336696 original size:16 final size:17
Alignment explanation
Indices: 47336677--47336713 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
47336667 ATATGAAGAA
47336677 TATTATTTAAAA-TTAT
1 TATTATTTAAAATTTAT
47336693 TATT-TTTAAAATTTAT
1 TATTATTTAAAATTTAT
47336709 TATTA
1 TATTA
47336714 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTATTTAAAATTTAT
Found at i:47355481 original size:51 final size:51
Alignment explanation
Indices: 47355417--47355555 Score: 158
Period size: 51 Copynumber: 2.7 Consensus size: 51
47355407 TGTTCGGTTT
* * * *
47355417 ACATACTAGCCTGCACATAGTATTACACATGTGACCATTACCATCC-GATAC
1 ACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACCATCCAG-TAC
* * * *
47355468 ACGTAGTAGCCTGCACATAGTACTATACACGTGATCGA-AACTATCCAGTAC
1 ACATAGTAGCCTGCACATAGTACTACACACGTGA-CCATAACCATCCAGTAC
*
47355519 GCATAGTAG-CTGCACATAGTACTACACACGTGACCAT
1 ACATAGTAGCCTGCACATAGTACTACACACGTGACCAT
47355556 CACTTTCACT
Statistics
Matches: 73, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
49 2 0.03
50 23 0.32
51 45 0.62
52 3 0.04
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (51 bp):
ACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACCATCCAGTAC
Found at i:47357254 original size:2 final size:2
Alignment explanation
Indices: 47357214--47357245 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
47357204 TAAAATTTGG
*
47357214 AT AT AT AT TT 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
47357246 GCGTATATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:47360360 original size:3 final size:3
Alignment explanation
Indices: 47360352--47360377 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
47360342 CTTTTTGTTT
47360352 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
47360378 GTAAACTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:47362959 original size:22 final size:23
Alignment explanation
Indices: 47362934--47362977 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
47362924 GTTTTTATTT
47362934 TAATAATAAATTTTAAA-AATAA
1 TAATAATAAATTTTAAATAATAA
**
47362956 TAATTTTAAATTTTAAATAATA
1 TAATAATAAATTTTAAATAATA
47362978 TTCTCCATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TAATAATAAATTTTAAATAATAA
Found at i:47362962 original size:15 final size:16
Alignment explanation
Indices: 47362935--47362965 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
47362925 TTTTTATTTT
47362935 AATAATAAATTTTAAA
1 AATAATAAATTTTAAA
47362951 AATAAT-AATTTTAAA
1 AATAATAAATTTTAAA
47362966 TTTTAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAATAAATTTTAAA
Found at i:47363422 original size:18 final size:17
Alignment explanation
Indices: 47363381--47363435 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 17
47363371 GACTAAATCA
* *
47363381 TTATTAGAAAATAATATC
1 TTATTATAAAATAA-ATT
47363399 TTATTATAAAATAAATT
1 TTATTATAAAATAAATT
47363416 TTGATTATCAAAATGAAATT
1 TT-ATTAT-AAAAT-AAATT
47363436 GTACTATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 4 0.12
18 18 0.56
19 5 0.16
20 5 0.16
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (17 bp):
TTATTATAAAATAAATT
Found at i:47368557 original size:12 final size:11
Alignment explanation
Indices: 47368522--47368548 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
47368512 AACAGAAGGG
47368522 GAAAAAGGAAA
1 GAAAAAGGAAA
47368533 GAAAAAGGAAA
1 GAAAAAGGAAA
47368544 GAAAA
1 GAAAA
47368549 GGAGAAAGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (11 bp):
GAAAAAGGAAA
Found at i:47369244 original size:24 final size:24
Alignment explanation
Indices: 47369217--47369263 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
47369207 ATTGAAATGG
47369217 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
47369241 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
47369264 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:47380267 original size:15 final size:15
Alignment explanation
Indices: 47380247--47380275 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
47380237 AGATGAATTA
47380247 AAAATAATATATTTG
1 AAAATAATATATTTG
47380262 AAAATAATATATTT
1 AAAATAATATATTT
47380276 ATTAATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
AAAATAATATATTTG
Found at i:47384833 original size:3 final size:3
Alignment explanation
Indices: 47384825--47384872 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
47384815 AATAAGGAGA
47384825 AAT AAT AAT AAT 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 AAT AAT AAT AAT
47384873 TAAATTTTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:47385705 original size:5 final size:5
Alignment explanation
Indices: 47385697--47385746 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
47385687 TATTTAATTT
* *
47385697 ATATA ATATA ATACA ATATA ATATA TTATATT ATATA ATA-A A-ATA ATATA
1 ATATA ATATA ATATA ATATA ATATA --ATATA ATATA ATATA ATATA ATATA
47385747 TAAAAAACAT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
3 1 0.03
4 4 0.11
5 28 0.76
7 4 0.11
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:47385726 original size:27 final size:25
Alignment explanation
Indices: 47385695--47385747 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 25
47385685 TCTATTTAAT
47385695 TTATATAATATAATACAATATAATATA
1 TTATATAATATAATA-AA-ATAATATA
*
47385722 TTATATTATATAATAAAATAATATA
1 TTATATAATATAATAAAATAATATA
47385747 T
1 T
47385748 AAAAAACATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 9 0.36
26 2 0.08
27 14 0.56
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
TTATATAATATAATAAAATAATATA
Found at i:47386407 original size:9 final size:9
Alignment explanation
Indices: 47386393--47386423 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
47386383 TTTGGTTAAA
47386393 AATTAACCG
1 AATTAACCG
47386402 AATTAACCG
1 AATTAACCG
*
47386411 AATTAACCA
1 AATTAACCG
47386420 AATT
1 AATT
47386424 GAATCACTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.48, C:0.19, G:0.06, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:47392878 original size:15 final size:15
Alignment explanation
Indices: 47392826--47392879 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
47392816 GAAAATTTAT
47392826 GTTTTCCATCCTTCTA
1 GTTTT-CATCCTTCTA
*
47392842 GTTTTCTACGCCTTCTA
1 GTTTTC-A-TCCTTCTA
* *
47392859 TTTTTCATCCTTCTG
1 GTTTTCATCCTTCTA
47392874 GTTTTC
1 GTTTTC
47392880 TTTCCACTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
15 12 0.39
16 7 0.23
17 12 0.39
ACGTcount: A:0.09, C:0.28, G:0.09, T:0.54
Consensus pattern (15 bp):
GTTTTCATCCTTCTA
Found at i:47404014 original size:31 final size:31
Alignment explanation
Indices: 47403926--47404015 Score: 153
Period size: 31 Copynumber: 2.9 Consensus size: 31
47403916 ATTAAGAACA
* *
47403926 AAATCTTTTCAAAAGTGCTCAAATAAGGACT
1 AAATCTTTTTAAAAGTGCTCAAATAATGACT
*
47403957 AAATTTTTTTAAAAGTGCTCAAATAATGACT
1 AAATCTTTTTAAAAGTGCTCAAATAATGACT
47403988 AAATCTTTTTAAAAGTGCTCAAATAATG
1 AAATCTTTTTAAAAGTGCTCAAATAATG
47404016 GCTTCTAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.34
Consensus pattern (31 bp):
AAATCTTTTTAAAAGTGCTCAAATAATGACT
Found at i:47407410 original size:22 final size:22
Alignment explanation
Indices: 47407385--47407431 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
47407375 TTAAAATAAT
* *
47407385 TAATATATAAAATAACTTAAAA
1 TAATATACAAAACAACTTAAAA
* *
47407407 TAATATACAAAGCAACTTAACA
1 TAATATACAAAACAACTTAAAA
47407429 TAA
1 TAA
47407432 ATAATTTACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.60, C:0.11, G:0.02, T:0.28
Consensus pattern (22 bp):
TAATATACAAAACAACTTAAAA
Found at i:47428297 original size:18 final size:17
Alignment explanation
Indices: 47428260--47428311 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
47428250 CTAAATGACG
* *
47428260 ACAAATAATCGATAAAT
1 ACAAATAAGCAATAAAT
47428277 ACAAATAAGCAATACAAT
1 ACAAATAAGCAATA-AAT
*
47428295 ACACATGAGAGCAATAA
1 ACAAAT-A-AGCAATAA
47428312 TCTTACATCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 12 0.41
18 8 0.28
19 2 0.07
20 7 0.24
ACGTcount: A:0.58, C:0.15, G:0.10, T:0.17
Consensus pattern (17 bp):
ACAAATAAGCAATAAAT
Found at i:47431299 original size:46 final size:46
Alignment explanation
Indices: 47431233--47431531 Score: 480
Period size: 46 Copynumber: 6.6 Consensus size: 46
47431223 TTTGAGTACT
47431233 TCTGATC-AGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
47431278 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGTTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
** *
47431324 TCTGATCAAAAGACAAAGTGATAAGTGGTAGCTTTATCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
47431370 TCTGATCCAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
47431416 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
47431462 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CTCGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
47431507 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
47431532 ATCATACGTA
Statistics
Matches: 238, Mismatches: 15, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
43 12 0.05
44 5 0.02
45 25 0.11
46 196 0.82
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:47439007 original size:27 final size:28
Alignment explanation
Indices: 47438953--47439025 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 28
47438943 ATAACTATTA
* * *
47438953 AATT-TATATATGAATTTTTATTTAGTG
1 AATTATATATATGAAATTTGAATTAGTG
47438980 AATTATATATATGAAATTTGAATT-GTG
1 AATTATATATATGAAATTTGAATTAGTG
* * * *
47439007 ATTTACATACATAAAATTT
1 AATTATATATATGAAATTT
47439026 TGATTTTAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
27 22 0.58
28 16 0.42
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.48
Consensus pattern (28 bp):
AATTATATATATGAAATTTGAATTAGTG
Found at i:47447607 original size:2 final size:2
Alignment explanation
Indices: 47447600--47447645 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
47447590 TTCAAAAAGA
47447600 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
47447642 AT AT
1 AT AT
47447646 CAATGGTGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47449429 original size:19 final size:20
Alignment explanation
Indices: 47449405--47449448 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
47449395 AATATATTAA
*
47449405 TATTAATA-TTAAATTTTTT
1 TATTAATAGCTAAATTTTTT
47449424 TATTAA-AGCTAAATTTTTT
1 TATTAATAGCTAAATTTTTT
47449443 T-TTAAT
1 TATTAAT
47449449 TTTTTCTGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (20 bp):
TATTAATAGCTAAATTTTTT
Found at i:47454076 original size:20 final size:21
Alignment explanation
Indices: 47454053--47454102 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
47454043 AATAAATACC
47454053 AAAAATTTATTTTAAAAATTA
1 AAAAATTTATTTTAAAAATTA
* *
47454074 AAAAA-GTATTTTAAAATTTA
1 AAAAATTTATTTTAAAAATTA
47454094 AAAAATTTA
1 AAAAATTTA
47454103 AAAAGTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
AAAAATTTATTTTAAAAATTA
Found at i:47454092 original size:28 final size:28
Alignment explanation
Indices: 47454061--47454125 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
47454051 CCAAAAATTT
47454061 ATTTTAAAAATTAAAAAAGTATTTTAAA
1 ATTTTAAAAATTAAAAAAGTATTTTAAA
* *
47454089 ATTTAAAAAATTTAAAAAGTATTTTAAA
1 ATTTTAAAAATTAAAAAAGTATTTTAAA
47454117 ATATTTAAA
1 AT-TTTAAA
47454126 TTAAAATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 28 0.85
29 5 0.15
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (28 bp):
ATTTTAAAAATTAAAAAAGTATTTTAAA
Found at i:47454173 original size:34 final size:33
Alignment explanation
Indices: 47454069--47454174 Score: 100
Period size: 34 Copynumber: 3.3 Consensus size: 33
47454059 TTATTTTAAA
47454069 AATTAAAAAAGTATTTTAAAAT--TTA--AAAA-
1 AATT-AAAAAGTATTTTAAAATAATTATTAAAAT
* *
47454098 ATTTAAAAAGTATTTTAAAATATTTAAATTAAAAT
1 AATTAAAAAGTATTTTAAAATAATT--ATTAAAAT
47454133 AA-TAAAAAGTATTTTTAAAATAATT-TTAAAATT
1 AATTAAAAAGTA-TTTTAAAATAATTATTAAAA-T
47454166 AATTAAAAA
1 AATTAAAAA
47454175 ATAAATATAT
Statistics
Matches: 64, Mismatches: 3, Indels: 15
0.78 0.04 0.18
Matches are distributed among these distances:
28 17 0.27
29 3 0.05
30 2 0.03
32 7 0.11
33 3 0.05
34 19 0.30
35 13 0.20
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (33 bp):
AATTAAAAAGTATTTTAAAATAATTATTAAAAT
Found at i:47457585 original size:36 final size:37
Alignment explanation
Indices: 47457540--47457615 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 37
47457530 TTCCCTTTTC
* * *
47457540 TTTTCTAAATTCAAATTAAAAATTTATTAATATC-AT
1 TTTTATAAATTCAAATTAAAAACTTACTAATATCTAT
** *
47457576 TTTTATAAATTTTAATTAAAAACTTACTAATTTCTAT
1 TTTTATAAATTCAAATTAAAAACTTACTAATATCTAT
47457613 TTT
1 TTT
47457616 ATTTCCTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
36 28 0.85
37 5 0.15
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (37 bp):
TTTTATAAATTCAAATTAAAAACTTACTAATATCTAT
Found at i:47465805 original size:38 final size:38
Alignment explanation
Indices: 47465754--47465830 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
47465744 CTGGAAGTAT
47465754 ATTCTTTCAATCTCTAAAGATTCATTATTATTCATTTA
1 ATTCTTTCAATCTCTAAAGATTCATTATTATTCATTTA
47465792 ATTCTTTCAATCTCTAAAGATTCATTATTATTCATTTA
1 ATTCTTTCAATCTCTAAAGATTCATTATTATTCATTTA
47465830 A
1 A
47465831 ACTGACCATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.32, C:0.16, G:0.03, T:0.49
Consensus pattern (38 bp):
ATTCTTTCAATCTCTAAAGATTCATTATTATTCATTTA
Found at i:47475651 original size:16 final size:16
Alignment explanation
Indices: 47475630--47475669 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
47475620 CTCAACACCA
47475630 TACCTATCAATATTTC
1 TACCTATCAATATTTC
*
47475646 TACCTATCGATATTTC
1 TACCTATCAATATTTC
47475662 TACCTATC
1 TACCTATC
47475670 CCACACACCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.28, C:0.28, G:0.03, T:0.42
Consensus pattern (16 bp):
TACCTATCAATATTTC
Found at i:47475842 original size:2 final size:2
Alignment explanation
Indices: 47475835--47475877 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
47475825 GTGCTTAAAG
47475835 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
47475877 T
1 T
47475878 GCAACTCTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:47476023 original size:21 final size:21
Alignment explanation
Indices: 47475999--47476039 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
47475989 GATAATTTTA
*
47475999 AATACAATATAATTA-AAAAAC
1 AATACAA-AAAATTATAAAAAC
47476020 AATACAAAAAATTATAAAAA
1 AATACAAAAAATTATAAAAA
47476040 TATAAATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.22
Consensus pattern (21 bp):
AATACAAAAAATTATAAAAAC
Found at i:47476061 original size:26 final size:24
Alignment explanation
Indices: 47476020--47476067 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
47476010 ATTAAAAAAC
*
47476020 AATACAAAAAATTATAAAAATATA
1 AATACAAAAAAATATAAAAATATA
*
47476044 AATACAGAACAAAATATACAAATA
1 AATACA-AA-AAAATATAAAAATA
47476068 ATTATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 2 0.10
26 12 0.60
ACGTcount: A:0.69, C:0.08, G:0.02, T:0.21
Consensus pattern (24 bp):
AATACAAAAAAATATAAAAATATA
Found at i:47481776 original size:2 final size:2
Alignment explanation
Indices: 47481769--47481797 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
47481759 TTTTAAGTTT
47481769 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 T
47481798 TATTTGCTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:47482233 original size:13 final size:13
Alignment explanation
Indices: 47482196--47482227 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
47482186 TCTTTTTACA
47482196 TTTTTAT-AATTT
1 TTTTTATAAATTT
47482208 TTTTTATAAATTT
1 TTTTTATAAATTT
47482221 TTTTTAT
1 TTTTTAT
47482228 TTATTTACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTTTATAAATTT
Found at i:47483832 original size:21 final size:20
Alignment explanation
Indices: 47483806--47483843 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
47483796 AAATAGAAGT
47483806 ATTTCTCTTGTATTTTTTTAG
1 ATTTCTCTT-TATTTTTTTAG
47483827 ATTTCTCTTT-TTTTTTT
1 ATTTCTCTTTATTTTTTT
47483844 TGCATGCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 1 0.06
21 9 0.53
ACGTcount: A:0.11, C:0.11, G:0.05, T:0.74
Consensus pattern (20 bp):
ATTTCTCTTTATTTTTTTAG
Found at i:47486571 original size:31 final size:29
Alignment explanation
Indices: 47486533--47486610 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
47486523 CTAACGGCTC
* *
47486533 AGTGACTAAAATGTTACAACGTGATAACATA
1 AGTGACTAAAATGTAAC-ACGTCA-AACATA
* **
47486564 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACACGTCAAACATA
47486593 AGTGACTAAAATGTAACA
1 AGTGACTAAAATGTAACA
47486611 TGAGCCAAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 23 0.56
30 3 0.07
31 15 0.37
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AGTGACTAAAATGTAACACGTCAAACATA
Found at i:47491423 original size:16 final size:17
Alignment explanation
Indices: 47491390--47491424 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
47491380 AACAATTCTA
*
47491390 ATAATTTTAAATACAAT
1 ATAATTATAAATACAAT
47491407 ATAATTATAAA-ACAAT
1 ATAATTATAAATACAAT
47491423 AT
1 AT
47491425 GAAAATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (17 bp):
ATAATTATAAATACAAT
Found at i:47494457 original size:16 final size:16
Alignment explanation
Indices: 47494438--47494468 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
47494428 TAATTTAATT
47494438 AATTTAAAATTTTTTA
1 AATTTAAAATTTTTTA
*
47494454 AATTTTAAATTTTTT
1 AATTTAAAATTTTTT
47494469 TAAAACTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
AATTTAAAATTTTTTA
Found at i:47494462 original size:17 final size:17
Alignment explanation
Indices: 47494440--47494472 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
47494430 ATTTAATTAA
47494440 TTTAAAATTTTTTAAAT
1 TTTAAAATTTTTTAAAT
*
47494457 TTTAAATTTTTTTAAA
1 TTTAAAATTTTTTAAA
47494473 ACTTTTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTAAAATTTTTTAAAT
Found at i:47496370 original size:32 final size:31
Alignment explanation
Indices: 47496331--47496423 Score: 159
Period size: 32 Copynumber: 2.9 Consensus size: 31
47496321 ATAGATATTG
47496331 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
1 ATTATGTTTTAAGCTTGTT-GATATTGAATTT
47496363 ATTATGTTTTAAGCTTGTTGAATATTGAATTT
1 ATTATGTTTTAAGCTTGTTG-ATATTGAATTT
47496395 ATTATGTTTTAAGCTTGTTGGATATTGAA
1 ATTATGTTTTAAGCTTGTT-GATATTGAA
47496424 ATAATTGACA
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
31 1 0.02
32 57 0.97
33 1 0.02
ACGTcount: A:0.28, C:0.03, G:0.17, T:0.52
Consensus pattern (31 bp):
ATTATGTTTTAAGCTTGTTGATATTGAATTT
Found at i:47497825 original size:14 final size:14
Alignment explanation
Indices: 47497801--47497838 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
47497791 CCAGAAAAGT
47497801 AAAATATTTTCCA-
1 AAAATATTTTCCAG
47497814 AAAATCATTTTCCAG
1 AAAAT-ATTTTCCAG
47497829 AAAATATTTT
1 AAAATATTTT
47497839 ACTGGAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.22
14 13 0.57
15 5 0.22
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (14 bp):
AAAATATTTTCCAG
Found at i:47505004 original size:40 final size:40
Alignment explanation
Indices: 47504952--47505035 Score: 159
Period size: 40 Copynumber: 2.1 Consensus size: 40
47504942 GTCTCAGAGA
47504952 ACATGCACAATGTCCTTAGTATCATGACCACATAATGAGC
1 ACATGCACAATGTCCTTAGTATCATGACCACATAATGAGC
*
47504992 ACATGCATAATGTCCTTAGTATCATGACCACATAATGAGC
1 ACATGCACAATGTCCTTAGTATCATGACCACATAATGAGC
47505032 ACAT
1 ACAT
47505036 ATTGTTTTGC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (40 bp):
ACATGCACAATGTCCTTAGTATCATGACCACATAATGAGC
Found at i:47509772 original size:14 final size:14
Alignment explanation
Indices: 47509753--47509783 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
47509743 AAGCTTATGG
47509753 TTTCTTTTTCTTTT
1 TTTCTTTTTCTTTT
*
47509767 TTTCTTTTTGTTTT
1 TTTCTTTTTCTTTT
47509781 TTT
1 TTT
47509784 ATTGAATTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.87
Consensus pattern (14 bp):
TTTCTTTTTCTTTT
Found at i:47510440 original size:25 final size:25
Alignment explanation
Indices: 47510412--47510461 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
47510402 TATGTGAATT
47510412 GATGCATTTCCTATAAAAATTATTC
1 GATGCATTTCCTATAAAAATTATTC
47510437 GATGCATTTCCTATAAAAATTATTC
1 GATGCATTTCCTATAAAAATTATTC
47510462 TCTCTCTCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (25 bp):
GATGCATTTCCTATAAAAATTATTC
Found at i:47512499 original size:14 final size:14
Alignment explanation
Indices: 47512480--47512510 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
47512470 TAAATGATTT
47512480 TTTAATTAATTAAA
1 TTTAATTAATTAAA
47512494 TTTAATTAATTAAA
1 TTTAATTAATTAAA
47512508 TTT
1 TTT
47512511 TCTAAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTAATTAATTAAA
Found at i:47514370 original size:41 final size:40
Alignment explanation
Indices: 47514298--47514376 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 40
47514288 AAGTCAACGC
**
47514298 TTTTTTTTATTTTATTTTAAAAATATATTATTTTAGTTGT
1 TTTTTTTTATTTTAAATTAAAAATATATTATTTTAGTTGT
*
47514338 TTTTTTTTACTTTTTAAATTAAAAA-ATGTTATTTTAGTT
1 TTTTTTTTA--TTTTAAATTAAAAATATATTATTTTAGTT
47514377 TAAGAATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 9 0.26
41 13 0.38
42 12 0.35
ACGTcount: A:0.29, C:0.01, G:0.05, T:0.65
Consensus pattern (40 bp):
TTTTTTTTATTTTAAATTAAAAATATATTATTTTAGTTGT
Found at i:47516497 original size:3 final size:3
Alignment explanation
Indices: 47516489--47516513 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
47516479 ATTGATTTTC
47516489 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
47516514 TTGTTTTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:47521508 original size:21 final size:20
Alignment explanation
Indices: 47521467--47521524 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 20
47521457 AATTATTTAT
* *
47521467 TAAATATATATTTTATTTTAA
1 TAAATATATTTTTTA-TTAAA
47521488 TCAAATATACTTTTTTATTAAA
1 T-AAATATA-TTTTTTATTAAA
*
47521510 TATATATATTTTTTA
1 TAAATATATTTTTTA
47521525 GATTTTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
20 7 0.22
21 7 0.22
22 12 0.38
23 6 0.19
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (20 bp):
TAAATATATTTTTTATTAAA
Found at i:47523542 original size:21 final size:21
Alignment explanation
Indices: 47523516--47523566 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
47523506 TTTCCCTAAG
* *
47523516 ATGTAACTTGGATTGAATTGA
1 ATGTAAATTGGATTAAATTGA
*
47523537 ATGTAAATTGTATTAAATTG-
1 ATGTAAATTGGATTAAATTGA
47523557 ATGTTAAATT
1 ATG-TAAATT
47523567 TACTCGTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.37, C:0.02, G:0.18, T:0.43
Consensus pattern (21 bp):
ATGTAAATTGGATTAAATTGA
Found at i:47524058 original size:24 final size:24
Alignment explanation
Indices: 47524021--47524080 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
47524011 TATATGGCTA
* *
47524021 TTCGGTGCTTCCCGTTAAGTGCTC
1 TTCGGAGCTACCCGTTAAGTGCTC
*
47524045 TTCGGAGCTACCCGTTAATTGCTC
1 TTCGGAGCTACCCGTTAAGTGCTC
*
47524069 TTCGGAGATACC
1 TTCGGAGCTACC
47524081 AATTATAGGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.15, C:0.28, G:0.23, T:0.33
Consensus pattern (24 bp):
TTCGGAGCTACCCGTTAAGTGCTC
Found at i:47525380 original size:17 final size:17
Alignment explanation
Indices: 47525339--47525386 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
47525329 GAATTTAGAA
*
47525339 GAATTTT-TGAATTAGT
1 GAATTTTGTGATTTAGT
* *
47525355 GACTTTTGTGATTTATT
1 GAATTTTGTGATTTAGT
47525372 GAATTTTGTGATTTA
1 GAATTTTGTGATTTA
47525387 AAAAGAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 6 0.22
17 21 0.78
ACGTcount: A:0.25, C:0.02, G:0.19, T:0.54
Consensus pattern (17 bp):
GAATTTTGTGATTTAGT
Found at i:47526739 original size:46 final size:46
Alignment explanation
Indices: 47526602--47526740 Score: 224
Period size: 46 Copynumber: 3.0 Consensus size: 46
47526592 TGGCAAAGTG
* * *
47526602 TGAAACGTAGGTATCGTATTTCAGTGAAGAAAACCATACTGAGTTG
1 TGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTA
*
47526648 TGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTA
1 TGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTA
* *
47526694 TGCAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGTTA
1 TGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTA
47526740 T
1 T
47526741 AGCAGTGTGA
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 86 1.00
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (46 bp):
TGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTA
Found at i:47527384 original size:5 final size:5
Alignment explanation
Indices: 47527374--47527398 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
47527364 ATTTTTTTTA
47527374 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
47527399 TGCAATGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:47534780 original size:24 final size:24
Alignment explanation
Indices: 47534747--47534807 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
47534737 GGTGCTTCCT
47534747 GTTAAGTGCTCTTCAGAGCTACCC
1 GTTAAGTGCTCTTCAGAGCTACCC
* * *
47534771 GTTAATTGCTCTTCGGAGCTACTC
1 GTTAAGTGCTCTTCAGAGCTACCC
* *
47534795 GTTATGGGCTCTT
1 GTTAAGTGCTCTT
47534808 TGTGAACTTC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (24 bp):
GTTAAGTGCTCTTCAGAGCTACCC
Found at i:47535975 original size:49 final size:48
Alignment explanation
Indices: 47535885--47535981 Score: 140
Period size: 49 Copynumber: 2.0 Consensus size: 48
47535875 TTTCTTTGCT
* *
47535885 TAAAAACGCCTAAGTCAGCCTAACTCACAATGATAACGGATTCAACAG
1 TAAAAACACCTAAGTCAGCCTAACTCACAATGATAAAGGATTCAACAG
* * *
47535933 TAAAAACACCTAAGTTAGCTTAATCTCGCAATGATAAAGGATTCAACAG
1 TAAAAACACCTAAGTCAGCCTAA-CTCACAATGATAAAGGATTCAACAG
47535982 AATCCCCTCA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
48 20 0.47
49 23 0.53
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.22
Consensus pattern (48 bp):
TAAAAACACCTAAGTCAGCCTAACTCACAATGATAAAGGATTCAACAG
Found at i:47539843 original size:23 final size:24
Alignment explanation
Indices: 47539802--47539847 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
47539792 AAATTGAAAG
*
47539802 TTAAATACCAAAATGATAAAAAAA
1 TTAAATACCAAAATAATAAAAAAA
*
47539826 TTAAAT-CTAAAATAATAAAAAA
1 TTAAATACCAAAATAATAAAAAA
47539848 TAAATATTTA
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 (24 bp):
TTAAATACCAAAATAATAAAAAAA
Found at i:47540217 original size:32 final size:29
Alignment explanation
Indices: 47540181--47540248 Score: 57
Period size: 32 Copynumber: 2.2 Consensus size: 29
47540171 AATTAGTAAA
* *
47540181 GATAAAATTAT-ACTTTAATTCACTTTAAAAAT
1 GATAAAATT-TGA-TTTAATTC-TTTAAAAA-T
47540213 GATAAAAATTTGATTTAATTCTTTAAAAAT
1 GATA-AAATTTGATTTAATTCTTTAAAAAT
*
47540243 TATAAA
1 GATAAA
47540249 GATAGATGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
29 2 0.06
30 4 0.13
31 6 0.19
32 13 0.42
33 6 0.19
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (29 bp):
GATAAAATTTGATTTAATTCTTTAAAAAT
Found at i:47552004 original size:2 final size:2
Alignment explanation
Indices: 47551997--47552021 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
47551987 AAAACAAACA
47551997 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
47552022 AAACTTAAGA
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:47560712 original size:30 final size:30
Alignment explanation
Indices: 47560676--47560785 Score: 202
Period size: 30 Copynumber: 3.7 Consensus size: 30
47560666 NATTGTATTT
*
47560676 TGTATTTTAAAAATAAAAAAATATATGTAA
1 TGTATTTTAAAAATAAAAAAATATATGTAG
*
47560706 TGTATTTTAAAAATAAAGAAATATATGTAG
1 TGTATTTTAAAAATAAAAAAATATATGTAG
47560736 TGTATTTTAAAAATAAAAAAATATATGTAG
1 TGTATTTTAAAAATAAAAAAATATATGTAG
47560766 TGTATTTTAAAAATAAAAAA
1 TGTATTTTAAAAATAAAAAA
47560786 TATTTATCAT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 77 1.00
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (30 bp):
TGTATTTTAAAAATAAAAAAATATATGTAG
Found at i:47560808 original size:60 final size:60
Alignment explanation
Indices: 47560684--47560810 Score: 168
Period size: 60 Copynumber: 2.1 Consensus size: 60
47560674 TTTGTATTTT
* **
47560684 AAAAATAAAAAAATATATGTAATGTATTTTAAAAATAAAGAAATATATGTAGTGTATTTT
1 AAAAATAAAAAAATATATGTAATGTATTTTAAAAATAAAGAAATATATATAGTGTATTAA
* * *
47560744 AAAAATAAAAAAATATATGTAGTGTATTTTAAAAATAAA-AAATATTTATCATTGT-TATAA
1 AAAAATAAAAAAATATATGTAATGTATTTTAAAAATAAAGAAATATATAT-AGTGTAT-TAA
47560804 AAAAATA
1 AAAAATA
47560811 TTTAATTATA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
59 9 0.15
60 50 0.85
ACGTcount: A:0.56, C:0.01, G:0.08, T:0.35
Consensus pattern (60 bp):
AAAAATAAAAAAATATATGTAATGTATTTTAAAAATAAAGAAATATATATAGTGTATTAA
Found at i:47560829 original size:23 final size:23
Alignment explanation
Indices: 47560778--47560831 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
47560768 TATTTTAAAA
* *
47560778 ATAAAAAATATTTATCATTGTTAT
1 ATAAAAAATATTTA-CATTATAAT
47560802 A-AAAAAATATTTA-ATTATAACT
1 ATAAAAAATATTTACATTATAA-T
47560824 ATAAAAAA
1 ATAAAAAA
47560832 GTTAAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 5 0.19
22 2 0.08
23 18 0.69
24 1 0.04
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (23 bp):
ATAAAAAATATTTACATTATAAT
Found at i:47561110 original size:21 final size:21
Alignment explanation
Indices: 47561084--47561136 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
47561074 CATTGTTTCT
*
47561084 AATCTCACCGCTACAGTACCC
1 AATCTCACCGCTACAGTAACC
* *
47561105 AATCTCACTGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
47561126 AATCTCACCGC
1 AATCTCACCGC
47561137 CACCGCTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.30, C:0.38, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:47561461 original size:37 final size:39
Alignment explanation
Indices: 47561397--47561477 Score: 112
Period size: 37 Copynumber: 2.1 Consensus size: 39
47561387 TTGCAGAAAG
47561397 AAAACTAAACTAGAGAAGAAGGAACTAAAACCAGAATACA
1 AAAACTAAACTA-AGAAGAAGGAACTAAAACCAGAATACA
* * *
47561437 AAAACTAAACT-A-AAGAATGAACTAAAATCAGAATGCA
1 AAAACTAAACTAAGAAGAAGGAACTAAAACCAGAATACA
47561474 AAAA
1 AAAA
47561478 GTAGTCTGCT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
37 26 0.68
38 1 0.03
40 11 0.29
ACGTcount: A:0.62, C:0.14, G:0.12, T:0.12
Consensus pattern (39 bp):
AAAACTAAACTAAGAAGAAGGAACTAAAACCAGAATACA
Found at i:47564032 original size:11 final size:11
Alignment explanation
Indices: 47564016--47564042 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
47564006 TAGGCAACTT
47564016 TTTTTTTGCGG
1 TTTTTTTGCGG
47564027 TTTTTTTGCGG
1 TTTTTTTGCGG
47564038 TTTTT
1 TTTTT
47564043 GCTTCTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.22, T:0.70
Consensus pattern (11 bp):
TTTTTTTGCGG
Found at i:47564086 original size:19 final size:19
Alignment explanation
Indices: 47564029--47564086 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
47564019 TTTTGCGGTT
*
47564029 TTTTTGCGGTTTTTGCTTCTTC
1 TTTTTGCTGTTTTT--TT-TTC
*
47564051 TTTTTTCT-TTTTCTTTTTC
1 TTTTTGCTGTTTT-TTTTTC
47564070 TTTTTGCTGTTTTTTTT
1 TTTTTGCTGTTTTTTTT
47564087 AAAGAACAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 14 0.45
20 6 0.19
21 4 0.13
22 7 0.23
ACGTcount: A:0.00, C:0.14, G:0.10, T:0.76
Consensus pattern (19 bp):
TTTTTGCTGTTTTTTTTTC
Found at i:47564686 original size:31 final size:32
Alignment explanation
Indices: 47564627--47564691 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
47564617 GGCAAATTAC
47564627 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
47564659 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
47564690 AA
1 AA
47564692 ATTATCTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:47564788 original size:3 final size:3
Alignment explanation
Indices: 47564780--47564804 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
47564770 GAATTAAGTA
47564780 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
47564805 TACATAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:47569652 original size:196 final size:196
Alignment explanation
Indices: 47569276--47569672 Score: 460
Period size: 196 Copynumber: 2.0 Consensus size: 196
47569266 TCATTTTAAC
* * * *
47569276 AAACGCCGCAAAAGATCAAGCATTAGGGGCGCTTATAGAAAAACGCCGCAAAAAAGTTGGGCAAA
1 AAACGCCGCAAAAGATCAAACATTAGCGGCGCTTACAGAAAAACGCCGCAAAAAAGTTGAGCAAA
* * * * *
47569341 ACGACGCCATTTTCTTTTTTGAGCTTTGGTGCCATTAGCGGCACTTTTTAACAAACGCCACAAAA
66 ACGACACCACTCTCTATTTTGAGCTTTAGTGCCATTAGCGGCACTTTTTAACAAACGCCACAAAA
* ** ** * * * *
47569406 AAATTAGAATTAGCGGTGCTTTTTTAAAATGCCGCTAAAGATCGAGCATTAGCGGCGCCTCTTGT
131 AAATGAGAATTAGCGACGCTTTTAAAAAACGCAGCTAAAGATCAAGCATTAGCGGCGCCTCTTGG
47569471 A
196 A
* *
47569472 AAACGCCGCTAAAGGTCAAACATTAGCGGCGCATTACAG-AAAACGCCGCAAAAAAGTTGAG-AA
1 AAACGCCGCAAAAGATCAAACATTAGCGGCGC-TTACAGAAAAACGCCGCAAAAAAGTTGAGCAA
* * * * * *
47569535 AATGACATCGCTCTCTATTTTGAGCTTTAGTAG-TATTAGCGGCGCTTTTTAACAAACGCCGC-A
65 AACGACACCACTCTCTATTTTGAGCTTTAGT-GCCATTAGCGGCACTTTTTAACAAACGCCACAA
* * * *
47569598 ATAGATCGAGAATTAGCGACGCTTTCTAAAAAACGCAGCTATAGATCAAGCATTAGCGGCGCCTT
129 AAAAAT-GAGAATTAGCGACGCTTT-TAAAAAACGCAGCTAAAGATCAAGCATTAGCGGCGCCTC
47569663 TTGGA
192 TTGGA
47569668 AAACG
1 AAACG
47569673 TCACAAAAAA
Statistics
Matches: 167, Mismatches: 30, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
194 5 0.03
195 66 0.40
196 91 0.54
197 5 0.03
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (196 bp):
AAACGCCGCAAAAGATCAAACATTAGCGGCGCTTACAGAAAAACGCCGCAAAAAAGTTGAGCAAA
ACGACACCACTCTCTATTTTGAGCTTTAGTGCCATTAGCGGCACTTTTTAACAAACGCCACAAAA
AAATGAGAATTAGCGACGCTTTTAAAAAACGCAGCTAAAGATCAAGCATTAGCGGCGCCTCTTGG
A
Found at i:47569672 original size:40 final size:39
Alignment explanation
Indices: 47569569--47569664 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 39
47569559 CTTTAGTAGT
* * *
47569569 ATTAGCGGCGCTTTTTAACAAACGCCGCAATAGATCGAGA
1 ATTAGCGGCGC-TTTTAAAAAACGCAGCAATAGATCAAGA
* * *
47569609 ATTAGCGACGCTTTCTAAAAAACGCAGCTATAGATCAAGC
1 ATTAGCGGCGCTTT-TAAAAAACGCAGCAATAGATCAAGA
47569649 ATTAGCGGCGCCTTTT
1 ATTAGCGGCG-CTTTT
47569665 GGAAAACGTC
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
39 3 0.06
40 40 0.85
41 4 0.09
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (39 bp):
ATTAGCGGCGCTTTTAAAAAACGCAGCAATAGATCAAGA
Found at i:47570511 original size:9 final size:9
Alignment explanation
Indices: 47570494--47570844 Score: 201
Period size: 9 Copynumber: 39.7 Consensus size: 9
47570484 TTACATTTCA
47570494 AACTTACAT
1 AACTTACAT
*
47570503 AATTTACAT
1 AACTTACAT
* *
47570512 AA-ATATAT
1 AACTTACAT
* * *
47570520 ATCATATCAA
1 AACTTA-CAT
47570530 AACTTACAT
1 AACTTACAT
47570539 AACTTACAT
1 AACTTACAT
*
47570548 AATTTACAT
1 AACTTACAT
* *
47570557 AACTTTAAAG
1 AAC-TTACAT
* * * *
47570567 AAATAAAAAA
1 AACT-TACAT
47570577 AACTTACAT
1 AACTTACAT
47570586 AACTTACAT
1 AACTTACAT
*
47570595 AATTTACAT
1 AACTTACAT
47570604 AACTTACAT
1 AACTTACAT
47570613 AA--TACAT
1 AACTTACAT
* *
47570620 AAATATATAT
1 AACT-TACAT
* *
47570630 ATCATATCAT
1 AACTTA-CAT
47570640 AACTTACAT
1 AACTTACAT
**
47570649 AACTTATTT
1 AACTTACAT
47570658 ATACTTACAT
1 A-ACTTACAT
*
47570668 AA--TACGT
1 AACTTACAT
47570675 AACTTACAT
1 AACTTACAT
47570684 AA-TCTACAT
1 AACT-TACAT
47570693 AACTTACAT
1 AACTTACAT
*
47570702 AACTTATAT
1 AACTTACAT
47570711 AA--TACAT
1 AACTTACAT
*
47570718 AA---ATAT
1 AACTTACAT
47570724 AACTTACAT
1 AACTTACAT
*
47570733 AAGTTACAT
1 AACTTACAT
* *
47570742 AA-ATATAT
1 AACTTACAT
* * *
47570750 ATCATATCAA
1 AACTTA-CAT
47570760 AACTTACAT
1 AACTTACAT
*
47570769 AATTTACAT
1 AACTTACAT
*
47570778 AACTCACAT
1 AACTTACAT
47570787 AACTTACAT
1 AACTTACAT
47570796 AACTTACAT
1 AACTTACAT
47570805 AA--TACAT
1 AACTTACAT
* *
47570812 AA-ATATAT
1 AACTTACAT
* *
47570820 ATCATATCAT
1 AACTTA-CAT
47570830 AACTTACAT
1 AACTTACAT
47570839 AACTTA
1 AACTTA
47570845 TTTATACTTA
Statistics
Matches: 264, Mismatches: 57, Indels: 42
0.73 0.16 0.12
Matches are distributed among these distances:
6 5 0.02
7 26 0.10
8 16 0.06
9 170 0.64
10 47 0.18
ACGTcount: A:0.48, C:0.16, G:0.01, T:0.35
Consensus pattern (9 bp):
AACTTACAT
Found at i:47570670 original size:120 final size:118
Alignment explanation
Indices: 47570530--47570800 Score: 291
Period size: 120 Copynumber: 2.3 Consensus size: 118
47570520 ATCATATCAA
47570530 AACTTACATAACTTACATAATTTACATAACTTTAAAGAAATAAAAAAAACTTACATAACTTACAT
1 AACTTACATAACTTACATAA-TTACATAACTTTAAA-AAATAAAAAAAACTTACATAACTTACAT
* *
47570595 AAT-T-TACATAACTTACATAA-TACATAAATATATATATCATATCATAACTTACAT
64 AATATAAACATAACTTACATAAGTACAT-AA-ATATATATCATATCAAAACTTACAT
** * * * ** * * *
47570649 AACTTATTTATACTTACATAA-TACGTAAC-TTACATAATCTACATAACTTACATAACTTATATA
1 AACTTACATA-ACTTACATAATTACATAACTTTAAAAAATAAAAAAAACTTACATAACTTACATA
*
47570712 ATACATAAATATAACTTACATAAGTTACATAAATATATATCATATCAAAACTTACAT
65 AT--ATAAACATAACTTACATAAG-TACATAAATATATATCATATCAAAACTTACAT
* *
47570769 AATTTACATAACTCACATAACTTACATAACTT
1 AACTTACATAACTTACATAA-TTACATAACTT
47570801 ACATAATACA
Statistics
Matches: 124, Mismatches: 18, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
116 25 0.20
117 4 0.03
118 7 0.06
119 18 0.15
120 55 0.44
121 9 0.07
122 6 0.05
ACGTcount: A:0.48, C:0.16, G:0.01, T:0.35
Consensus pattern (118 bp):
AACTTACATAACTTACATAATTACATAACTTTAAAAAATAAAAAAAACTTACATAACTTACATAA
TATAAACATAACTTACATAAGTACATAAATATATATCATATCAAAACTTACAT
Found at i:47570706 original size:98 final size:97
Alignment explanation
Indices: 47570577--47570855 Score: 365
Period size: 94 Copynumber: 2.9 Consensus size: 97
47570567 AAATAAAAAA
*
47570577 AACTTACATAACTTACATAATTTACATAACTTACATAATACATAAATATATATATCATATCATAA
1 AACTTACATAAC-TACATAACTTACATAACTTACATAATACAT-AA-ATATATATCATATCATAA
* *
47570642 CTTACATAACTTATTTATACTTA-CATAA-TACGT
63 CTTACATAACTTATTTATACTTATCAAAACTACAT
* * *
47570675 AACTTACATAATCTACATAACTTACATAACTTATATAATACATAAATATA-A-CTTA-CATAAGT
1 AACTTACATAA-CTACATAACTTACATAACTTACATAATACATAAATATATATCATATCATAACT
* * *
47570737 TACATAA-ATATATAT-CATATCAAAACTTACAT
65 TACATAACTTATTTATACTTATCAAAAC-TACAT
*
47570769 AATTTACATAACTCACATAACTTACATAACTTACATAATACATAAATATATATCATATCATAACT
1 AACTTACATAACT-ACATAACTTACATAACTTACATAATACATAAATATATATCATATCATAACT
47570834 TACATAACTTATTTATACTTAT
65 TACATAACTTATTTATACTTAT
47570856 AAATAAACAA
Statistics
Matches: 155, Mismatches: 16, Indels: 19
0.82 0.08 0.10
Matches are distributed among these distances:
91 3 0.02
92 10 0.06
93 15 0.10
94 52 0.34
95 2 0.01
96 8 0.05
97 15 0.10
98 45 0.29
99 5 0.03
ACGTcount: A:0.46, C:0.16, G:0.01, T:0.37
Consensus pattern (97 bp):
AACTTACATAACTACATAACTTACATAACTTACATAATACATAAATATATATCATATCATAACTT
ACATAACTTATTTATACTTATCAAAACTACAT
Found at i:47570728 original size:22 final size:23
Alignment explanation
Indices: 47570700--47570748 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
47570690 CATAACTTAC
*
47570700 ATAACTTATATAA-TACATAAAT
1 ATAACTTACATAAGTACATAAAT
47570722 ATAACTTACATAAGTTACATAAAT
1 ATAACTTACATAAG-TACATAAAT
47570746 ATA
1 ATA
47570749 TATCATATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 12 0.50
24 12 0.50
ACGTcount: A:0.53, C:0.10, G:0.02, T:0.35
Consensus pattern (23 bp):
ATAACTTACATAAGTACATAAAT
Found at i:47572167 original size:43 final size:43
Alignment explanation
Indices: 47572114--47572285 Score: 184
Period size: 43 Copynumber: 4.0 Consensus size: 43
47572104 GGAGAGAAAC
* *
47572114 GTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGTTAAAG
1 GTCATCTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGATAAAG
*** * * * * *
47572157 GTCATCTTCTTTAATAGTGATTGTGATAGAAGCGCTGCTAAAG
1 GTCATCTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGATAAAG
* * * *
47572200 GTCATGTTCTTTAGCGGCGTTTGTGGTAAAAGCGTCGATAAAA
1 GTCATCTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGATAAAG
* *
47572243 GTCATGCTT-TTTAGCGGCATTTGTGATAAAAGCGCCGGTAAAG
1 GTCAT-CTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGATAAAG
47572286 AACATGGCCT
Statistics
Matches: 101, Mismatches: 27, Indels: 2
0.78 0.21 0.02
Matches are distributed among these distances:
43 99 0.98
44 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.33
Consensus pattern (43 bp):
GTCATCTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGATAAAG
Found at i:47572267 original size:86 final size:86
Alignment explanation
Indices: 47572114--47572277 Score: 217
Period size: 86 Copynumber: 1.9 Consensus size: 86
47572104 GGAGAGAAAC
* * *
47572114 GTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGTTAAAGGTCATCTTCTTTAATAGTGATT
1 GTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGATAAAAGTCATCTTCTTTAAGAGTGATT
*
47572179 GTGATAGAAGCGCTGCTAAAG
66 GTGATAAAAGCGCTGCTAAAG
* * *
47572200 GTCATGTTCTTTAGCGGCGTTTGTGGTAAAAGCGTCGATAAAAGTCATGCTT-TTT-AGCG-GCA
1 GTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGATAAAAGTCAT-CTTCTTTAAGAGTG-A
47572262 TTTGTGATAAAAGCGC
64 -TTGTGATAAAAGCGC
47572278 CGGTAAAGAA
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
84 1 0.01
85 3 0.04
86 61 0.90
87 3 0.04
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (86 bp):
GTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGATAAAAGTCATCTTCTTTAAGAGTGATT
GTGATAAAAGCGCTGCTAAAG
Found at i:47579576 original size:2 final size:2
Alignment explanation
Indices: 47579569--47579602 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
47579559 CTCTTATCAA
47579569 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
47579603 TTAAAAAAAA
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
Found at i:47579699 original size:15 final size:16
Alignment explanation
Indices: 47579679--47579733 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
47579669 TTTTTATTTA
47579679 AATTTA-AATTTATAT
1 AATTTAGAATTTATAT
47579694 AATTTAGGAATTTATAT
1 AATTTA-GAATTTATAT
* *
47579711 ATTTTATGGATTTATAT
1 AATTTA-GAATTTATAT
47579728 ACATTT
1 A-ATTT
47579734 TTTAAAGATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 6 0.18
17 24 0.73
18 3 0.09
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (16 bp):
AATTTAGAATTTATAT
Found at i:47579707 original size:17 final size:18
Alignment explanation
Indices: 47579685--47579733 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
47579675 TTTAAATTTA
47579685 AATTTATATAATTTA-GG
1 AATTTATATAATTTATGG
*
47579702 AATTTATATATTTTATGG
1 AATTTATATAATTTATGG
47579720 -ATTTATATACATTT
1 AATTTATATA-ATTT
47579734 TTTAAAGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 23 0.82
18 5 0.18
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.53
Consensus pattern (18 bp):
AATTTATATAATTTATGG
Found at i:47581594 original size:294 final size:288
Alignment explanation
Indices: 47581071--47581608 Score: 801
Period size: 294 Copynumber: 1.8 Consensus size: 288
47581061 AATCTAGTAT
* * * *
47581071 ATTGATAATATTGTTGGTTGAGTTGGTGTCATAAGCTAACTCAACAGTAACTCAAGATTCATGAT
1 ATTGATAATATGGTTGATTGAGTTGGTGTCACAAACTAACTCAACAGTAACTCAAGATTCATGAT
* * *
47581136 AAACAATTTTTGTTCATTTAATATTCTTAATTTGATGTATTTAAATTTTATTTTGCTCACAATTT
66 AAACAATTTTTGTACATTCAATATTCTTAATTTGATGTATTTAAATTTTATTTTACTCACAATTT
* * *
47581201 AATCTACTTTTTCATTTTAATATCATATATATTTAATGTGTTATTATTAATCAATTTCAAACCAT
131 AATCTACTTTTTCATTTTAATATCATACATACTTAATATGTTATTATTAATCAATTTCAAACCAT
47581266 AAGTTTCATTATATCATATGTTATTTTTAAATACCCCTATGTGTTCTAAATACGTAGTTTCCACG
196 AAGTTTCATTATATCATATGTTATTTTTAAATACCCCTATGTGTTCTAAATACGTAGTTTCCACG
47581331 TGCATACACGAATGATAGAATTTTTAGC
261 TGCATACACGAATGATAGAATTTTTAGC
* * * *
47581359 ATTGATAATGTGGTTGATTGAGTTGGTGTCACAAACTAAGTCAATATTAACTCAAGATTCATGAT
1 ATTGATAATATGGTTGATTGAGTTGGTGTCACAAACTAACTCAACAGTAACTCAAGATTCATGAT
* *
47581424 AAACAATTTTTGTACATTCAGTATTCTTAATTTGAAGTATTTACGTATTTAAATTTTGTTTTACT
66 AAACAATTTTTGTACATTCAATATTCTTAATTT---G-A--T--GTATTTAAATTTTATTTTACT
* * *
47581489 CACAATTT-ATTTA-TTTTTCATTTTAATATCATACATACTTCATATGTTATTATTAATTAATTT
123 CACAATTTAATCTACTTTTTCATTTTAATATCATACATACTTAATATGTTATTATTAATCAATTT
* *
47581552 CAAACCATACGTTTTATTATATCATATGTTATTTTTAAATACCCCTATGTGTTCTAA
188 CAAACCATAAGTTTCATTATATCATATGTTATTTTTAAATACCCCTATGTGTTCTAA
47581609 GTACATAAAG
Statistics
Matches: 221, Mismatches: 21, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
288 87 0.39
291 1 0.00
292 1 0.00
294 101 0.46
295 4 0.02
296 27 0.12
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.45
Consensus pattern (288 bp):
ATTGATAATATGGTTGATTGAGTTGGTGTCACAAACTAACTCAACAGTAACTCAAGATTCATGAT
AAACAATTTTTGTACATTCAATATTCTTAATTTGATGTATTTAAATTTTATTTTACTCACAATTT
AATCTACTTTTTCATTTTAATATCATACATACTTAATATGTTATTATTAATCAATTTCAAACCAT
AAGTTTCATTATATCATATGTTATTTTTAAATACCCCTATGTGTTCTAAATACGTAGTTTCCACG
TGCATACACGAATGATAGAATTTTTAGC
Found at i:47582526 original size:11 final size:11
Alignment explanation
Indices: 47582512--47582549 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
47582502 CAATATCCTT
47582512 TCAAATTTCTC
1 TCAAATTTCTC
47582523 TCAAATTTCTC
1 TCAAATTTCTC
* *
47582534 TTAAATTCCTC
1 TCAAATTTCTC
47582545 TCAAA
1 TCAAA
47582550 GCTCTCTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.42
Consensus pattern (11 bp):
TCAAATTTCTC
Found at i:47582539 original size:22 final size:22
Alignment explanation
Indices: 47582514--47582563 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
47582504 ATATCCTTTC
**
47582514 AAATTTCTCTCAAATTTCTCTT
1 AAATTTCTCTCAAAGCTCTCTT
*
47582536 AAATTCCTCTCAAAGCTCTCTT
1 AAATTTCTCTCAAAGCTCTCTT
*
47582558 TAATTT
1 AAATTT
47582564 TTTTTCGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.28, C:0.24, G:0.02, T:0.46
Consensus pattern (22 bp):
AAATTTCTCTCAAAGCTCTCTT
Found at i:47583644 original size:11 final size:11
Alignment explanation
Indices: 47583630--47583657 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
47583620 AAGAGAGCTC
47583630 TGAGAGAAATT
1 TGAGAGAAATT
47583641 TGAGAGAAATT
1 TGAGAGAAATT
47583652 TGAGAG
1 TGAGAG
47583658 GATATTGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.32, T:0.25
Consensus pattern (11 bp):
TGAGAGAAATT
Found at i:47586903 original size:11 final size:11
Alignment explanation
Indices: 47586887--47586913 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
47586877 CCCATTTTTC
47586887 TATTTTTAACT
1 TATTTTTAACT
47586898 TATTTTTAACT
1 TATTTTTAACT
47586909 TATTT
1 TATTT
47586914 GATCCCATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (11 bp):
TATTTTTAACT
Found at i:47589432 original size:17 final size:17
Alignment explanation
Indices: 47589395--47589442 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
47589385 GAATTTAGAA
*
47589395 GAATTTT-TGAATTAGT
1 GAATTTTGTGATTTAGT
*
47589411 GAATTTTGTGATTTATT
1 GAATTTTGTGATTTAGT
47589428 GAATTTTGTGATTTA
1 GAATTTTGTGATTTA
47589443 AAAAGAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (17 bp):
GAATTTTGTGATTTAGT
Found at i:47591472 original size:24 final size:24
Alignment explanation
Indices: 47591440--47591489 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
47591430 TTCATATGGC
47591440 TGAACTTTTATGATTAATTGTTAA
1 TGAACTTTTATGATTAATTGTTAA
47591464 TGAACTTTTATGATTAATTGTTAA
1 TGAACTTTTATGATTAATTGTTAA
47591488 TG
1 TG
47591490 TGGGAATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.32, C:0.04, G:0.14, T:0.50
Consensus pattern (24 bp):
TGAACTTTTATGATTAATTGTTAA
Found at i:47591731 original size:46 final size:45
Alignment explanation
Indices: 47591660--47591846 Score: 259
Period size: 46 Copynumber: 4.1 Consensus size: 45
47591650 TCCATGGAAA
* *
47591660 AGTT-TGAAACGTAGGTATGGTATTTCAGTGAATAAAACCATACTG
1 AGTTGTGAAAAGTAGGTATGGTATTTC-GTGAAGAAAACCATACTG
* *
47591705 AGTTGTGAAAAGTAGGTATGGTATTTCGATAAAGAAAACCATATTG
1 AGTTGTGAAAAGTAGGTATGGTATTTCG-TGAAGAAAACCATACTG
* *
47591751 AGTTGTGAAAAGTAGGTATGATGTTTCAGTGAAGAAAACCATACTG
1 AGTTGTGAAAAGTAGGTATGGTATTTC-GTGAAGAAAACCATACTG
**
47591797 AGTTACGAAAAGTAGGTATGGTATTTTCGTGAAGAAAACCATACTG
1 AGTTGTGAAAAGTAGGTATGGTA-TTTCGTGAAGAAAACCATACTG
47591843 AGTT
1 AGTT
47591847 ATAGCAATGT
Statistics
Matches: 126, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
45 5 0.04
46 116 0.92
47 5 0.04
ACGTcount: A:0.37, C:0.09, G:0.24, T:0.30
Consensus pattern (45 bp):
AGTTGTGAAAAGTAGGTATGGTATTTCGTGAAGAAAACCATACTG
Found at i:47600409 original size:23 final size:23
Alignment explanation
Indices: 47600367--47600410 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
47600357 CTTTCTTACT
* *
47600367 GTAGTAATTTTCGGGGTATTATA
1 GTAGTAATTTTCAGGATATTATA
*
47600390 GTAGTAATTTTTAGGATATTA
1 GTAGTAATTTTCAGGATATTA
47600411 AATTAGTCGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.02, G:0.23, T:0.45
Consensus pattern (23 bp):
GTAGTAATTTTCAGGATATTATA
Found at i:47600417 original size:23 final size:23
Alignment explanation
Indices: 47600367--47600417 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
47600357 CTTTCTTACT
* * *
47600367 GTAGTAATTTTCGGGGTATTATA
1 GTAGTAATTTTCAGGATATTAAA
*
47600390 GTAGTAATTTTTAGGATATTAAA
1 GTAGTAATTTTCAGGATATTAAA
*
47600413 TTAGT
1 GTAGT
47600418 CGTCGAGACA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.31, C:0.02, G:0.22, T:0.45
Consensus pattern (23 bp):
GTAGTAATTTTCAGGATATTAAA
Done.