Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 80 of 135
Found at i:31369654 original size:21 final size:21
Alignment explanation
Indices: 31369614--31369662 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
31369604 ATAAATAAAA
*
31369614 TCATTCA-TGTCAATTCCCTG
1 TCATTCATTGACAATTCCCTG
*
31369634 TCATTCATTGACAATTTCCTG
1 TCATTCATTGACAATTCCCTG
31369655 TCATTCAT
1 TCATTCAT
31369663 AACTTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.22, C:0.27, G:0.08, T:0.43
Consensus pattern (21 bp):
TCATTCATTGACAATTCCCTG
Found at i:31369939 original size:21 final size:21
Alignment explanation
Indices: 31369835--31369933 Score: 105
Period size: 21 Copynumber: 4.8 Consensus size: 21
31369825 TGAATACACC
31369835 AACAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCGTAAGAGCTG
* *
31369856 AACAGAAGCTTG-AA-AGCTA
1 AACAGAAGCTCGTAAGAGCTG
* *
31369875 AATAGAAGCTCGTAAGAGCTA
1 AACAGAAGCTCGTAAGAGCTG
* * *
31369896 AACAAAAACTCAG-AAGAGTTG
1 AACAGAAGCTC-GTAAGAGCTG
31369917 AACAGAAGCTCGTAAGA
1 AACAGAAGCTCGTAAGA
31369934 ATTGAATATA
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
19 14 0.22
20 5 0.08
21 43 0.68
22 1 0.02
ACGTcount: A:0.45, C:0.16, G:0.23, T:0.15
Consensus pattern (21 bp):
AACAGAAGCTCGTAAGAGCTG
Found at i:31370103 original size:17 final size:17
Alignment explanation
Indices: 31370083--31370121 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
31370073 AAATCCAATT
31370083 CAATAATAT-AATTCCAA
1 CAATAAT-TCAATTCCAA
31370100 CAATAATTCAATTCCAA
1 CAATAATTCAATTCCAA
31370117 CAATA
1 CAATA
31370122 GAATAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 1 0.05
17 20 0.95
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (17 bp):
CAATAATTCAATTCCAA
Found at i:31377386 original size:31 final size:31
Alignment explanation
Indices: 31377343--31377420 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
31377333 CCTTTTTCTT
31377343 TTTTAGATTTTATAAGAATTATCTAATTTCAA
1 TTTT-GATTTTATAAGAATTATCTAATTTCAA
31377375 TTTTGATTTTATAAGAATTATCTAATTTCAA
1 TTTTGATTTTATAAGAATTATCTAATTTCAA
31377406 TTTTGATCTTTATAA
1 TTTTGAT-TTTATAA
31377421 TATATTTAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
31 34 0.76
32 11 0.24
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (31 bp):
TTTTGATTTTATAAGAATTATCTAATTTCAA
Found at i:31388941 original size:89 final size:89
Alignment explanation
Indices: 31388790--31389017 Score: 393
Period size: 89 Copynumber: 2.6 Consensus size: 89
31388780 AAAAAAGCTA
* * *
31388790 AAAATTAGGAAGAAAAATCTGATTTGTCATTCTCCTATTAGAAAGGGATATGGATGACGTGGAAT
1 AAAATTAGGAAGAAAAATCTGATTTATCTTTCTCCTATTGGAAAGGGATATGGATGACGTGGAAT
31388855 CACAATTTAGTACAATCTCTCCTC
66 CACAATTTAGTACAATCTCTCCTC
31388879 AAAATTAGGAAGAAAAATCTGATTTATCTTTCTCCTATTGGAAAGGGATATGGATGACGTGGAAT
1 AAAATTAGGAAGAAAAATCTGATTTATCTTTCTCCTATTGGAAAGGGATATGGATGACGTGGAAT
*
31388944 CACAATTTCGTACAATCTCTCCTC
66 CACAATTTAGTACAATCTCTCCTC
* * *
31388968 AAAATCAGGAAGAAAAATCTGATTTATCTTTCTCCTATTGAAAAGAGATA
1 AAAATTAGGAAGAAAAATCTGATTTATCTTTCTCCTATTGGAAAGGGATA
31389018 GGGGTGAACT
Statistics
Matches: 132, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
89 132 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (89 bp):
AAAATTAGGAAGAAAAATCTGATTTATCTTTCTCCTATTGGAAAGGGATATGGATGACGTGGAAT
CACAATTTAGTACAATCTCTCCTC
Found at i:31391469 original size:21 final size:22
Alignment explanation
Indices: 31391430--31391478 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
31391420 TCCTATTTAG
* *
31391430 TATATTTTAAATTCTAATATAA-
1 TATATTTAAAATTCAAATA-AAT
31391452 TATATTTAAAATT-AAATAAAT
1 TATATTTAAAATTCAAATAAAT
31391473 TATATT
1 TATATT
31391479 AGTATCATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 10 0.42
22 12 0.50
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
TATATTTAAAATTCAAATAAAT
Found at i:31392464 original size:13 final size:15
Alignment explanation
Indices: 31392438--31392472 Score: 56
Period size: 13 Copynumber: 2.5 Consensus size: 15
31392428 ATGGAGGCAA
31392438 AAAAAAAGCAAAAAC
1 AAAAAAAGCAAAAAC
31392453 AAAAAAA-C-AAAAC
1 AAAAAAAGCAAAAAC
31392466 AAAAAAA
1 AAAAAAA
31392473 AACCTCTACC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 12 0.60
14 1 0.05
15 7 0.35
ACGTcount: A:0.86, C:0.11, G:0.03, T:0.00
Consensus pattern (15 bp):
AAAAAAAGCAAAAAC
Found at i:31392473 original size:14 final size:14
Alignment explanation
Indices: 31392436--31392473 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
31392426 CAATGGAGGC
31392436 AAAAAAAAAGCAAA
1 AAAAAAAAAGCAAA
31392450 AACAAAAAAA-CAAA
1 AA-AAAAAAAGCAAA
31392464 ACAAAAAAAA
1 A-AAAAAAAA
31392474 ACCTCTACCG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.87, C:0.11, G:0.03, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAGCAAA
Found at i:31393974 original size:44 final size:45
Alignment explanation
Indices: 31393852--31394039 Score: 213
Period size: 43 Copynumber: 4.3 Consensus size: 45
31393842 TGAAGTCATT
** * *
31393852 AAAGCAGATCTTGTCTTCATGTATTGGTAG-GAAGTGGATCGAAG
1 AAAGCAGATCTTGTCTTCACATACTGGTAGCGAAGTAGATCGAAG
* * *
31393896 -ATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAG
1 AAAGCAGATCTTGTCTTCACATACTGGTAGCGAAGTAGATCGAAG
** * *
31393940 AAAGCAGATCTTGTCTTCATGTATTGGTAG-GAAGTGGATCGAAG
1 AAAGCAGATCTTGTCTTCACATACTGGTAGCGAAGTAGATCGAAG
* * *
31393984 -ATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAG
1 AAAGCAGATCTTGTCTTCACATACTGGTAGCGAAGTAGATCGAAG
*
31394028 AAAACAGATCTT
1 AAAGCAGATCTT
31394040 ATCTCTCTAA
Statistics
Matches: 117, Mismatches: 23, Indels: 7
0.80 0.16 0.05
Matches are distributed among these distances:
43 46 0.39
44 39 0.33
45 32 0.27
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (45 bp):
AAAGCAGATCTTGTCTTCACATACTGGTAGCGAAGTAGATCGAAG
Found at i:31394001 original size:88 final size:88
Alignment explanation
Indices: 31393852--31394039 Score: 367
Period size: 88 Copynumber: 2.1 Consensus size: 88
31393842 TGAAGTCATT
31393852 AAAGCAGATCTTGTCTTCATGTATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCAT
1 AAAGCAGATCTTGTCTTCATGTATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCAT
31393917 ACTGGTGGCGAAGTAGATCGAAG
66 ACTGGTGGCGAAGTAGATCGAAG
31393940 AAAGCAGATCTTGTCTTCATGTATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCAT
1 AAAGCAGATCTTGTCTTCATGTATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCAT
31394005 ACTGGTGGCGAAGTAGATCGAAG
66 ACTGGTGGCGAAGTAGATCGAAG
*
31394028 AAAACAGATCTT
1 AAAGCAGATCTT
31394040 ATCTCTCTAA
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 99 1.00
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (88 bp):
AAAGCAGATCTTGTCTTCATGTATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCAT
ACTGGTGGCGAAGTAGATCGAAG
Found at i:31394186 original size:50 final size:50
Alignment explanation
Indices: 31394105--31394586 Score: 268
Period size: 50 Copynumber: 9.6 Consensus size: 50
31394095 ACAGTAGAGC
* * * * * * *
31394105 AGATTAAAGCTACGACGGTGAATCTTGCTTCCCTGATATTGCAATTTAAA
1 AGATTGAAGCTGCAACGGCGAATCTTACTTCCCTGACATTGCAATTGAAA
* * * * * * *
31394155 AGATTGAAGCCGCAACGGCGAATCTTACTTCCCTGGCAGTACAGTGGAAC
1 AGATTGAAGCTGCAACGGCGAATCTTACTTCCCTGACATTGCAATTGAAA
* * * * * ** * *
31394205 TGATTAAAGCTACAACGACGAATCTTGCTTCCCCAACATTGTAATTTAAA
1 AGATTGAAGCTGCAACGGCGAATCTTACTTCCCTGACATTGCAATTGAAA
* * ** * **** *** * *
31394255 AGATTGAAGCCGCAGCAACGAATCTTACTTCCTTGGTGGTGCAGCGGGAC
1 AGATTGAAGCTGCAACGGCGAATCTTACTTCCCTGACATTGCAATTGAAA
* * * * * *
31394305 TGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTTAAA
1 AGATTGAAGCTGCAACGGCGAATCTTACTTCCCTGACATTGCAATTGAAA
* * * * * * * **
31394355 AGATTGAATAC-GCAATGGCGAATCTTACTTCCATGGCAATGCAGTGGAGT
1 AGATTGAA-GCTGCAACGGCGAATCTTACTTCCCTGACATTGCAATTGAAA
* * * * *
31394405 AGATTAAAGCTACAACGGTGAATCTTGCTTCCCTGACATTGCAATTAAAA
1 AGATTGAAGCTGCAACGGCGAATCTTACTTCCCTGACATTGCAATTGAAA
* * * * * * * **
31394455 AGATTGAAGCCGCAATGGCGAATCTTACTTCCTTGGCGA-TACAGTGGAGC
1 AGATTGAAGCTGCAACGGCGAATCTTACTTCCCTGAC-ATTGCAATTGAAA
* * * * * *
31394505 AGATTAAAGCTACGACGGTGAATCTTACTTCCCCGACATTGCAATTTAAA
1 AGATTGAAGCTGCAACGGCGAATCTTACTTCCCTGACATTGCAATTGAAA
31394555 AGATTGAAGCTGCAACAGG-GAATCTTACTTCC
1 AGATTGAAGCTGCAAC-GGCGAATCTTACTTCC
31394587 TTAGTGGTGC
Statistics
Matches: 295, Mismatches: 132, Indels: 10
0.68 0.30 0.02
Matches are distributed among these distances:
49 2 0.01
50 289 0.98
51 4 0.01
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (50 bp):
AGATTGAAGCTGCAACGGCGAATCTTACTTCCCTGACATTGCAATTGAAA
Found at i:31394260 original size:100 final size:100
Alignment explanation
Indices: 31394088--31394647 Score: 683
Period size: 100 Copynumber: 5.6 Consensus size: 100
31394078 CTTATCTCTC
* * * * * * *
31394088 TGGCGGTACAGTAGAGCAGATTAAAGCTACGACGGTGAATCTTGCTTCCCTGATATTGCAATTTA
1 TGGCGGTACAGTGGAACTGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTTA
*
31394153 AAAGATTGAAGCCGCAACGGCGAATCTTACTTCCC
66 AAAGATTGAAGCCGCAACGGCGAATCTTACTTCCT
* * * *
31394188 TGGCAGTACAGTGGAACTGATTAAAGCTACAACGACGAATCTTGCTTCCCCAACATTGTAATTTA
1 TGGCGGTACAGTGGAACTGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTTA
* **
31394253 AAAGATTGAAGCCGCAGCAACGAATCTTACTTCCT
66 AAAGATTGAAGCCGCAACGGCGAATCTTACTTCCT
* * * *
31394288 TGGTGGTGCAGCGGGACTGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTTA
1 TGGCGGTACAGTGGAACTGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTTA
** * *
31394353 AAAGATTGAATACGCAATGGCGAATCTTACTTCCA
66 AAAGATTGAAGCCGCAACGGCGAATCTTACTTCCT
** * * * * *
31394388 TGGCAATGCAGTGG-AGTAGATTAAAGCTACAACGGTGAATCTTGCTTCCCTGACATTGCAATTA
1 TGGCGGTACAGTGGAACT-GATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTT
*
31394452 AAAAGATTGAAGCCGCAATGGCGAATCTTACTTCCT
65 AAAAGATTGAAGCCGCAACGGCGAATCTTACTTCCT
* * * * * *
31394488 TGGCGATACAGTGGAGCAGATTAAAGCTACGACGGTGAATCTTACTTCCCCGACATTGCAATTTA
1 TGGCGGTACAGTGGAACTGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTTA
*
31394553 AAAGATTGAAGCTGCAACAGG-GAATCTTACTTCCT
66 AAAGATTGAAGCCGCAAC-GGCGAATCTTACTTCCT
* * * ** * *
31394588 TAGTGGTGCAGCAGAACTGATTAAAGCTAGAACAGCGAATCTTGCTTCCCCGACATTGCA
1 TGGCGGTACAGTGGAACTGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCA
31394648 GTTAATCGGA
Statistics
Matches: 392, Mismatches: 65, Indels: 6
0.85 0.14 0.01
Matches are distributed among these distances:
99 2 0.01
100 388 0.99
101 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (100 bp):
TGGCGGTACAGTGGAACTGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTTA
AAAGATTGAAGCCGCAACGGCGAATCTTACTTCCT
Found at i:31394767 original size:43 final size:43
Alignment explanation
Indices: 31394711--31394954 Score: 177
Period size: 44 Copynumber: 5.7 Consensus size: 43
31394701 TTGCATCAAG
31394711 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAATAAACCAA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAATAAACCAA
* * ** * *
31394754 TCCTATCTCCCTAA--AGTTACAATGGAGCAGATTAAA-ACCACAAA
1 TCTTATCTCCCTAAGCAG-T--AGTGGAGCAGACGAAATA-AACCAA
* *
31394798 ACTTATCTCCCTAAGCAGTAGTGGAGCAGATCG-CAT----CAGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAATAAACCA-A
*
31394838 TATTATCTCCCTAAGCAGTAGTGGAGCAGACGAAATAAACCAA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAATAAACCAA
* * * * ** *
31394881 TCCTATCTCCCTGAAGTTA-CAGTGGAGCGGA-TTAA-AACCACAGA
1 TCTTATCTCCCT-AAG-CAGTAGTGGAGCAGACGAAATAAAC-CA-A
31394925 TCTTATCTCCCTAAGCAGTAGTGGAGCAGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGA
31394955 NNNNNNNCTC
Statistics
Matches: 154, Mismatches: 28, Indels: 38
0.70 0.13 0.17
Matches are distributed among these distances:
39 3 0.02
40 31 0.20
41 2 0.01
42 5 0.03
43 53 0.34
44 56 0.36
45 2 0.01
46 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.23
Consensus pattern (43 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAATAAACCAA
Found at i:31394816 original size:127 final size:127
Alignment explanation
Indices: 31394656--31394954 Score: 492
Period size: 127 Copynumber: 2.4 Consensus size: 127
31394646 CAGTTAATCG
* * * * *
31394656 GATTAAAACTACAAATCTTATCTCCCTATGCAGTAGTGGAACAGATTGCATCA-AGTCTTATCTC
1 GATTAAAACCACAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAGA-TATTATCTC
31394720 CCTAAGCAGTAGTGGAGCAGACGAAATAAACCAATCCTATCTCCCTAAAGTTACAATGGAGCA
65 CCTAAGCAGTAGTGGAGCAGACGAAATAAACCAATCCTATCTCCCTAAAGTTACAATGGAGCA
*
31394783 GATTAAAACCACAAAACTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAGATATTATCTCC
1 GATTAAAACCACAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAGATATTATCTCC
* * *
31394848 CTAAGCAGTAGTGGAGCAGACGAAATAAACCAATCCTATCTCCCTGAAGTTACAGTGGAGCG
66 CTAAGCAGTAGTGGAGCAGACGAAATAAACCAATCCTATCTCCCTAAAGTTACAATGGAGCA
*
31394910 GATTAAAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
1 GATTAAAACCACAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
31394955 NNNNNNNCTC
Statistics
Matches: 160, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
127 159 0.99
128 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.23
Consensus pattern (127 bp):
GATTAAAACCACAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAGATATTATCTCC
CTAAGCAGTAGTGGAGCAGACGAAATAAACCAATCCTATCTCCCTAAAGTTACAATGGAGCA
Found at i:31395043 original size:40 final size:40
Alignment explanation
Indices: 31394975--31395197 Score: 196
Period size: 40 Copynumber: 5.3 Consensus size: 40
31394965 CCTGAAGTGC
*
31394975 AGTGGAGCAGATTAAAACCACAGATCTTATCTCCCTAAGCAGT
1 AGTGGAGCAGA-TCAAACCA-AG-TCTTATCTCCCTAAGCAGT
** *
31395018 AGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGT
1 AGTGGAGCAGATCAAACCAAGTCTTATCTCCCTAAGCAGT
* * ** *
31395058 AGTGGAGCAGACCGAAAAAAACCAA-TCCTATCTCCCTAAAGTTGC
1 AGTGGAGCAGATC-----AAACCAAGTCTTATCTCCCT-AAGCAGT
* * *
31395103 AGTGGAGCGGATTAAAACCACAGATCTTACCTCCCTAAGCAGT
1 AGTGGAGCAGA-TCAAACCA-AG-TCTTATCTCCCTAAGCAGT
* * *
31395146 AGTGGAGCAGATCACATCAAGTTTTATCTCCCTAAGCAGT
1 AGTGGAGCAGATCAAACCAAGTCTTATCTCCCTAAGCAGT
31395186 AGTGGAGCAGAT
1 AGTGGAGCAGAT
31395198 AAAAGAAACC
Statistics
Matches: 144, Mismatches: 26, Indels: 23
0.75 0.13 0.12
Matches are distributed among these distances:
40 60 0.42
41 10 0.07
42 10 0.07
43 25 0.17
44 21 0.15
45 18 0.12
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (40 bp):
AGTGGAGCAGATCAAACCAAGTCTTATCTCCCTAAGCAGT
Found at i:31396845 original size:18 final size:20
Alignment explanation
Indices: 31396822--31396864 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
31396812 CATATACATG
31396822 CATACATTTT-A-TAATACA
1 CATACATTTTAATTAATACA
31396840 CATACATTTTAATTAATACA
1 CATACATTTTAATTAATACA
31396860 CATAC
1 CATAC
31396865 TTATACATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 10 0.43
19 1 0.04
20 12 0.52
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.37
Consensus pattern (20 bp):
CATACATTTTAATTAATACA
Found at i:31405025 original size:15 final size:16
Alignment explanation
Indices: 31404979--31405031 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
31404969 GAGATATTAA
31404979 ATCTAATTTAATATTT
1 ATCTAATTTAATATTT
31404995 ATCTAGA--TAATA-TT
1 ATCTA-ATTTAATATTT
31405009 AT-TAATTTAATATTT
1 ATCTAATTTAATATTT
*
31405024 ATGTAATT
1 ATCTAATT
31405032 AATTCTAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
12 1 0.03
13 2 0.06
14 9 0.28
15 9 0.28
16 10 0.31
17 1 0.03
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (16 bp):
ATCTAATTTAATATTT
Found at i:31406685 original size:23 final size:23
Alignment explanation
Indices: 31406659--31406709 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
31406649 TCCTTCCGCT
* *
31406659 TGTAATATCTCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
31406682 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
31406705 AGTAA
1 TGTAA
31406710 GAAAGTAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:31429017 original size:167 final size:171
Alignment explanation
Indices: 31428710--31429019 Score: 430
Period size: 167 Copynumber: 1.8 Consensus size: 171
31428700 ATAGATAATC
* * * *
31428710 AAGAAAAGTTGTTCAGTATTCATCACTGTTTCATTTCAGCTATCTAATGAAGTTCCAGTTCCAAC
1 AAGAAAAGCTGTTCAATATTCATCAATGTTTCATTTCAGCAATCTAATGAA----CAGTTCCAAC
* * * *
31428775 TTCCAACACAGATGAATTAATGATTGTCTAATTAACAGGTGCTAGTTCAAGAACAATGACTTCCA
62 TTCCAACACAGATCAATGAATGATTGTCTAATTAACAGCTGCTAGTTCAAGAACAATAACTTCCA
31428840 ATTATTACCCAATATTTAACGTTTCATTTCAGCAATTTGTAAATA
127 ATTATTACCCAATATTTAACGTTTCATTTCAGCAATTTGTAAATA
*
31428885 AAGAAAA-CTGTTCAATATTCATCAATGTTTCATTTCAGCAATTTAATG-A-AGTTCCAA-TTCC
1 AAGAAAAGCTGTTCAATATTCATCAATGTTTCATTTCAGCAATCTAATGAACAGTTCCAACTTCC
* * * * *
31428946 AATACAGATCAATGAATGATTGTGTAATTAACAGCTGCTAGTTCAAGAACAATAACTTTCATTTT
66 AACACAGATCAATGAATGATTGTCTAATTAACAGCTGCTAGTTCAAGAACAATAACTTCCAATTA
31429011 TTACCCAAT
131 TTACCCAAT
31429020 CTTTCAAGCA
Statistics
Matches: 121, Mismatches: 14, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
167 69 0.57
168 8 0.07
173 1 0.01
174 36 0.30
175 7 0.06
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (171 bp):
AAGAAAAGCTGTTCAATATTCATCAATGTTTCATTTCAGCAATCTAATGAACAGTTCCAACTTCC
AACACAGATCAATGAATGATTGTCTAATTAACAGCTGCTAGTTCAAGAACAATAACTTCCAATTA
TTACCCAATATTTAACGTTTCATTTCAGCAATTTGTAAATA
Found at i:31431634 original size:25 final size:26
Alignment explanation
Indices: 31431598--31431722 Score: 92
Period size: 25 Copynumber: 4.5 Consensus size: 26
31431588 ATGGTGGAGA
*
31431598 AGAGGAACAAAGAACCGGCACAGGGC
1 AGAGGAACAAAGAACCAGCACAGGGC
*
31431624 AGAGG-ACAAAGAACCAGCAGAGGGC
1 AGAGGAACAAAGAACCAGCACAGGGC
*
31431649 AGAGATGAGGGCAAAGAACCAGCGTAGCAGAGGGC
1 AGAG--GA--ACAAAGAACCAGC--A-C--AGGGC
* * *
31431684 AGAGAAACAAAGAACCAGCAGAGAGC
1 AGAGGAACAAAGAACCAGCACAGGGC
*
31431710 AGA-GAGCAAAGAA
1 AGAGGAACAAAGAA
31431723 GAGTACTGGG
Statistics
Matches: 79, Mismatches: 10, Indels: 21
0.72 0.09 0.19
Matches are distributed among these distances:
25 30 0.38
26 12 0.15
27 1 0.01
29 1 0.01
30 12 0.15
31 12 0.15
32 1 0.01
33 1 0.01
35 9 0.11
ACGTcount: A:0.46, C:0.18, G:0.34, T:0.02
Consensus pattern (26 bp):
AGAGGAACAAAGAACCAGCACAGGGC
Found at i:31433720 original size:21 final size:21
Alignment explanation
Indices: 31433696--31433742 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
31433686 GTGATTGTCT
31433696 AGATTGACAATACATCA-AACA
1 AGATTGACAATACAT-ATAACA
* *
31433717 AGATCGACAATGCATATAACA
1 AGATTGACAATACATATAACA
31433738 AGATT
1 AGATT
31433743 CGAGTTGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.49, C:0.17, G:0.13, T:0.21
Consensus pattern (21 bp):
AGATTGACAATACATATAACA
Found at i:31434983 original size:21 final size:20
Alignment explanation
Indices: 31434959--31434997 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
31434949 GACTAAACCG
31434959 AAAACTCAAAGAATTTTTCAC
1 AAAACTCAAA-AATTTTTCAC
* *
31434980 AAAATTCCAAAATTTTTC
1 AAAACTCAAAAATTTTTC
31434998 CTATATGCAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.46, C:0.18, G:0.03, T:0.33
Consensus pattern (20 bp):
AAAACTCAAAAATTTTTCAC
Found at i:31435816 original size:42 final size:42
Alignment explanation
Indices: 31435756--31435892 Score: 150
Period size: 42 Copynumber: 3.3 Consensus size: 42
31435746 CCAAAGGCTG
* * * * * *
31435756 AACAAAAGCTCATGAGAGCTAAAAAGAAACCCATAAGGGTTG
1 AACAGAAGCTCATAAGAGCTGAACAGAAACCCATAAAGGTTA
* *
31435798 AACGGAAGCTCGTAAGAGCTGAACAGAAACCCATAAAGGTTA
1 AACAGAAGCTCATAAGAGCTGAACAGAAACCCATAAAGGTTA
* * *
31435840 AACAGAAGCTCAAAAGAGCTGAACAGAAACTCAT-ATGAGTTA
1 AACAGAAGCTCATAAGAGCTGAACAGAAACCCATAAAG-GTTA
*
31435882 AATAGAAGCTC
1 AACAGAAGCTC
31435893 GTGAAAGCTA
Statistics
Matches: 80, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
41 2 0.03
42 78 0.98
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTGAACAGAAACCCATAAAGGTTA
Found at i:31435864 original size:21 final size:21
Alignment explanation
Indices: 31435811--31435872 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
31435801 GGAAGCTCGT
*
31435811 AAGAGCTGAACAGAAACCCATA
1 AAGAGCTGAACAGAAACTCA-A
* * *
31435833 AAG-GTTAAACAGAAGCTCAA
1 AAGAGCTGAACAGAAACTCAA
31435853 AAGAGCTGAACAGAAACTCA
1 AAGAGCTGAACAGAAACTCA
31435873 TATGAGTTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 4 0.12
21 25 0.78
22 3 0.09
ACGTcount: A:0.50, C:0.19, G:0.19, T:0.11
Consensus pattern (21 bp):
AAGAGCTGAACAGAAACTCAA
Found at i:31442053 original size:21 final size:21
Alignment explanation
Indices: 31441994--31442153 Score: 74
Period size: 21 Copynumber: 7.6 Consensus size: 21
31441984 AAGCCCGAAG
* *
31441994 GCTGAACAAAAGCTCATGAGA
1 GCTGAACGAAAGCTCATAAGA
* * *
31442015 GCTAAACAGAAA-CCCATAAGG
1 GCTGAAC-GAAAGCTCATAAGA
*
31442036 GTTGAACGAAAGCTCATAAGA
1 GCTGAACGAAAGCTCATAAGA
* * *
31442057 GCTGAATAGAAA-CCCATAAGG
1 GCTGAA-CGAAAGCTCATAAGA
* * *
31442078 GTTAAAC-ATAAGCTCAAAAGA
1 GCTGAACGA-AAGCTCATAAGA
* * *
31442099 GCTCAACGAAAGCTTATATGA
1 GCTGAACGAAAGCTCATAAGA
* * * * *
31442120 GTTAAACAAAAGCTCGTGAGA
1 GCTGAACGAAAGCTCATAAGA
*
31442141 GCTAAACGGAAAG
1 GCTGAAC-GAAAG
31442154 TAAACATGAA
Statistics
Matches: 99, Mismatches: 33, Indels: 13
0.68 0.23 0.09
Matches are distributed among these distances:
19 1 0.01
20 6 0.06
21 80 0.81
22 12 0.12
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.16
Consensus pattern (21 bp):
GCTGAACGAAAGCTCATAAGA
Found at i:31442058 original size:42 final size:41
Alignment explanation
Indices: 31441996--31442109 Score: 140
Period size: 42 Copynumber: 2.7 Consensus size: 41
31441986 GCCCGAAGGC
*
31441996 TGAACAAAAGCTCATGAGAGCTAAACAGAAACCCATAAGGGT
1 TGAAC-AAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
* *
31442038 TGAACGAAAGCTCATAAGAGCTGAATAGAAACCCATAAGGGT
1 TGAAC-AAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
* * *
31442080 TAAACATAAGCTCAAAAGAGCTCAAC-GAAA
1 TGAACA-AAGCTCATAAGAGCTAAACAGAAA
31442110 GCTTATATGA
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
41 5 0.08
42 58 0.92
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.15
Consensus pattern (41 bp):
TGAACAAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
Found at i:31444734 original size:13 final size:13
Alignment explanation
Indices: 31444716--31444764 Score: 62
Period size: 13 Copynumber: 3.6 Consensus size: 13
31444706 TAAAAATAAT
31444716 TTAATTAAGAGAA
1 TTAATTAAGAGAA
* *
31444729 TTAATTAAAAATAA
1 TTAATT-AAGAGAA
31444743 TTTAATTAAGAGAA
1 -TTAATTAAGAGAA
31444757 TTAATTAA
1 TTAATTAA
31444765 ATTTATTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
13 14 0.47
14 10 0.33
15 6 0.20
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (13 bp):
TTAATTAAGAGAA
Found at i:31444744 original size:28 final size:28
Alignment explanation
Indices: 31444696--31444779 Score: 132
Period size: 28 Copynumber: 3.0 Consensus size: 28
31444686 TAATAAAATT
31444696 AGAATTAAGTTAAAAATAATTTAATTAAG
1 AGAATTAA-TTAAAAATAATTTAATTAAG
31444725 AGAATTAATTAAAAATAATTTAATTAAG
1 AGAATTAATTAAAAATAATTTAATTAAG
** *
31444753 AGAATTAATTAAATTTATTTTAATTAA
1 AGAATTAATTAAAAATAATTTAATTAA
31444780 TTAAAAATAA
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 44 0.85
29 8 0.15
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (28 bp):
AGAATTAATTAAAAATAATTTAATTAAG
Found at i:31444749 original size:15 final size:15
Alignment explanation
Indices: 31444700--31444751 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 15
31444690 AAAATTAGAA
31444700 TTAAGTTAAAAATAAT
1 TTAA-TTAAAAATAAT
* *
31444716 TTAATT-AAGAGAA-
1 TTAATTAAAAATAAT
31444729 TTAATTAAAAATAAT
1 TTAATTAAAAATAAT
31444744 TTAATTAA
1 TTAATTAA
31444752 GAGAATTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
13 6 0.20
14 10 0.33
15 10 0.33
16 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (15 bp):
TTAATTAAAAATAAT
Found at i:31448410 original size:11 final size:11
Alignment explanation
Indices: 31448394--31448418 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31448384 AGTTTCACCG
31448394 TTGATAATTTT
1 TTGATAATTTT
31448405 TTGATAATTTT
1 TTGATAATTTT
31448416 TTG
1 TTG
31448419 TGTTTGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (11 bp):
TTGATAATTTT
Found at i:31448748 original size:21 final size:21
Alignment explanation
Indices: 31448707--31448749 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
31448697 AATAAAGTAG
*
31448707 ATTATATATTATTTTTATAGT
1 ATTATATATTATATTTATAGT
31448728 ATTATATATTATGATTT-TAGT
1 ATTATATATTAT-ATTTATAGT
31448749 A
1 A
31448750 AATTCATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (21 bp):
ATTATATATTATATTTATAGT
Found at i:31448791 original size:17 final size:18
Alignment explanation
Indices: 31448766--31448810 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
31448756 TATAAGAATA
*
31448766 ATTATATTA-AGAATTTT
1 ATTAAATTATAGAATTTT
* *
31448783 ATTAAATTATATATTTTT
1 ATTAAATTATAGAATTTT
31448801 ATTAAATTAT
1 ATTAAATTAT
31448811 GTTTAATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
ATTAAATTATAGAATTTT
Found at i:31448912 original size:59 final size:59
Alignment explanation
Indices: 31448732--31448913 Score: 139
Period size: 59 Copynumber: 3.1 Consensus size: 59
31448722 TATAGTATTA
*
31448732 TATATTATGA--TT-TTAGTAAATTCATATAAGAATAATTATATTAAGAATTTTATTAAAT
1 TATATTATGATTTTATTAGTAAATTCATATAAGAAT-ATT-TATTAACAATTTTATTAAAT
* ** * * * * * *
31448790 TATA-TAT--TTTTATTAAATTATGTTTA-ATAATAATTATTT-TAAATTATATTTTAGT-ATT
1 TATATTATGATTTTATT--AGTAAATTCATATAAGAA-TATTTATTAA-CA-ATTTTATTAAAT
31448848 ATATATTATGATTTTATTAGTAAATTCATATAAGAATATTTATTAACAATTTTATTAAAT
1 -TATATTATGATTTTATTAGTAAATTCATATAAGAATATTTATTAACAATTTTATTAAAT
31448908 TATATT
1 TATATT
31448914 TTATAACAGT
Statistics
Matches: 91, Mismatches: 18, Indels: 29
0.66 0.13 0.21
Matches are distributed among these distances:
57 8 0.09
58 10 0.11
59 33 0.36
60 24 0.26
61 9 0.10
62 7 0.08
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (59 bp):
TATATTATGATTTTATTAGTAAATTCATATAAGAATATTTATTAACAATTTTATTAAAT
Found at i:31449198 original size:16 final size:16
Alignment explanation
Indices: 31449145--31449198 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
31449135 TTAAATTACT
*
31449145 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
* *
31449161 ATTACAGCTCTATTCT
1 ATTACACCTCTATTCC
31449177 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
31449193 ATTACA
1 ATTACA
31449199 GCGAAACAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.26, C:0.31, G:0.04, T:0.39
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:31449511 original size:21 final size:20
Alignment explanation
Indices: 31449483--31449521 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
31449473 GATCTAATTT
31449483 TTTATTTAATAATAAAAACA
1 TTTATTTAATAATAAAAACA
* *
31449503 TTTAGTTTAGTTATAAAAA
1 TTTA-TTTAATAATAAAAA
31449522 TATAAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.44
Consensus pattern (20 bp):
TTTATTTAATAATAAAAACA
Found at i:31450366 original size:11 final size:11
Alignment explanation
Indices: 31450352--31450396 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
31450342 ATTTTTTTAA
31450352 TTTTAAAATAC
1 TTTTAAAATAC
*
31450363 TTTTAAAAT-T
1 TTTTAAAATAC
31450373 TTTTAAAA-A-
1 TTTTAAAATAC
31450382 TTTTAAAATAC
1 TTTTAAAATAC
31450393 TTTT
1 TTTT
31450397 TTTAATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
9 8 0.27
10 9 0.30
11 13 0.43
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:31451174 original size:20 final size:20
Alignment explanation
Indices: 31451151--31451191 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
31451141 TAAATTTTTA
31451151 TAAAAAC-ATATAAAAATTAT
1 TAAAAACTA-ATAAAAATTAT
*
31451171 TAAAAACTAATAAATATTAT
1 TAAAAACTAATAAAAATTAT
31451191 T
1 T
31451192 CAATTTTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAAAACTAATAAAAATTAT
Found at i:31451701 original size:18 final size:17
Alignment explanation
Indices: 31451671--31451704 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
31451661 TACCTAATAA
*
31451671 TTATAGTATATTCGAAT
1 TTATAGTAAATTCGAAT
31451688 TTATGAGTAAATTCGAA
1 TTAT-AGTAAATTCGAA
31451705 GAATTTATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.41
Consensus pattern (17 bp):
TTATAGTAAATTCGAAT
Found at i:31456298 original size:2 final size:2
Alignment explanation
Indices: 31456291--31456317 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31456281 CTGTTAGGTC
31456291 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
31456318 CATATCTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:31469659 original size:17 final size:19
Alignment explanation
Indices: 31469639--31469675 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
31469629 TTATAATAAA
31469639 TTATAAAA-T-ATATTTTT
1 TTATAAAATTAATATTTTT
31469656 TTATAAAATTAATATTTTT
1 TTATAAAATTAATATTTTT
31469675 T
1 T
31469676 AAAAAAACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 1 0.06
19 9 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTATAAAATTAATATTTTT
Found at i:31470684 original size:4 final size:4
Alignment explanation
Indices: 31470675--31470716 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
31470665 AGCCCAAAGT
31470675 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CA
31470717 AAAGAGGTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:31472793 original size:31 final size:30
Alignment explanation
Indices: 31472758--31472824 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 30
31472748 TTTTTCTTAT
31472758 TTTTATAGA-AATTT-AATATGTTGTTATAAAA
1 TTTTATA-ATAATTTAAATATGTT-TTAT-AAA
*
31472789 TTTTA-AATAATTTAAATATGTTTTATTAA
1 TTTTATAATAATTTAAATATGTTTTATAAA
31472818 TTTTATA
1 TTTTATA
31472825 NNNNNNNNNN
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
29 8 0.25
30 11 0.34
31 13 0.41
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (30 bp):
TTTTATAATAATTTAAATATGTTTTATAAA
Found at i:31472896 original size:10 final size:9
Alignment explanation
Indices: 31472847--31472917 Score: 58
Period size: 9 Copynumber: 7.7 Consensus size: 9
31472837 NNNNNNNNNN
31472847 TTTTTATATA
1 TTTTTA-ATA
31472857 TTTTTTAA-A
1 -TTTTTAATA
*
31472866 TATTTAATAA
1 TTTTTAAT-A
*
31472876 TTTGT-ATA
1 TTTTTAATA
31472884 TTTTTAAATA
1 TTTTT-AATA
31472894 TTTTT-ATGA
1 TTTTTAAT-A
31472903 TTTTTAATA
1 TTTTTAATA
31472912 TTTTTA
1 TTTTTA
31472918 TAGGAAAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
8 13 0.26
9 16 0.32
10 15 0.30
11 6 0.12
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (9 bp):
TTTTTAATA
Found at i:31472896 original size:18 final size:17
Alignment explanation
Indices: 31472847--31472919 Score: 74
Period size: 18 Copynumber: 4.0 Consensus size: 17
31472837 NNNNNNNNNN
*
31472847 TTTTTATATATTTTTTAAA
1 TTTTTA-ATA-TTTTTATA
* *
31472866 TATTTAATAATTTGTATA
1 TTTTTAAT-ATTTTTATA
31472884 TTTTTAAATATTTTTATGA
1 TTTTT-AATATTTTTAT-A
31472903 TTTTTAATATTTTTATA
1 TTTTTAATATTTTTATA
31472920 GGAAAAATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
17 1 0.02
18 30 0.65
19 15 0.33
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
TTTTTAATATTTTTATA
Found at i:31475031 original size:115 final size:114
Alignment explanation
Indices: 31474893--31475287 Score: 602
Period size: 115 Copynumber: 3.6 Consensus size: 114
31474883 CAAAGAATTA
* **
31474893 TTTTTCTTTGTACTGTGTACTGGGTGTCGGCCATTGACAGGCCAGCACCCCAATTTTTTTTTTAA
1 TTTTTCTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCCAAAATTTTTTTTAA
31474958 -TTTTTTCGTATTTTTTATCTGATTCTGACACGAAAAAAAAGATAAATTTT
66 TTTTTTTCGTATTTTTTATCTGATTCTGACACG-AAAAAAA-ATAAATTTT
*
31475008 TTTTTCTTTGTACTGCGTACTGGGTGCCGGCCATTGACAGGCCAGCA-CCCAAAATTTTTTTTAA
1 TTTTTCTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCCAAAATTTTTTTTAA
31475072 TTTTTTTCGTATTTTTTTATCTGATTCTGACACGAAAAAAAATAAATTTT
66 TTTTTTTCGTA-TTTTTTATCTGATTCTGACACGAAAAAAAATAAATTTT
31475122 TTTTTCTTTGTACTGTGTA-----TGCCGGCCATTGACAGGCCAGCACCCCAAAAATTTTTTTTA
1 TTTTTCTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCC-AAAATTTTTTTTA
31475182 ATTTTTTTCGTATTTTTTATCTGATTCTGACACG-AAAAAAATAAA----
65 ATTTTTTTCGTATTTTTTATCTGATTCTGACACGAAAAAAAATAAATTTT
* *
31475227 ATTTT-TTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCA-CCCAAATTTTTTTTT
1 TTTTTCTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCCAAAATTTTTTTT
31475288 TTGTTTTTTT
Statistics
Matches: 264, Mismatches: 7, Indels: 26
0.89 0.02 0.09
Matches are distributed among these distances:
104 13 0.05
105 4 0.02
107 11 0.04
108 3 0.01
109 57 0.22
110 25 0.09
111 25 0.09
114 42 0.16
115 62 0.23
116 22 0.08
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.42
Consensus pattern (114 bp):
TTTTTCTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCCAAAATTTTTTTTAA
TTTTTTTCGTATTTTTTATCTGATTCTGACACGAAAAAAAATAAATTTT
Found at i:31484021 original size:37 final size:39
Alignment explanation
Indices: 31483948--31484023 Score: 95
Period size: 37 Copynumber: 2.0 Consensus size: 39
31483938 TAGTCCCATT
* *
31483948 TTAAAAACAAATTAATATTTATATATTAAATCAATTAAA
1 TTAAAAACAAATTAATATTTATATACTAAAGCAATTAAA
*
31483987 TTAAAAA-AAATTAAT-TTTAT-TACTAACGCTAATTAAA
1 TTAAAAACAAATTAATATTTATATACTAAAGC-AATTAAA
31484024 ATATTGAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 6 0.18
37 12 0.36
38 8 0.24
39 7 0.21
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.38
Consensus pattern (39 bp):
TTAAAAACAAATTAATATTTATATACTAAAGCAATTAAA
Found at i:31500748 original size:35 final size:35
Alignment explanation
Indices: 31500702--31500772 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
31500692 TTAGTGCAAG
31500702 ATATGGGTATATATGCCTGACATGAGAATGCTCAA
1 ATATGGGTATATATGCCTGACATGAGAATGCTCAA
31500737 ATATGGGTATATATGCCTGACATGAGAATGCTCAA
1 ATATGGGTATATATGCCTGACATGAGAATGCTCAA
31500772 A
1 A
31500773 ATTTTCAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (35 bp):
ATATGGGTATATATGCCTGACATGAGAATGCTCAA
Found at i:31503690 original size:21 final size:21
Alignment explanation
Indices: 31503649--31503691 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
31503639 ACCCCAAACT
* *
31503649 CTCAAATCTTTTTACTTTTCC
1 CTCAAAACTTTTTACTCTTCC
31503670 CTCAAAAC-TTTTACTCCTTCC
1 CTCAAAACTTTTTACT-CTTCC
31503691 C
1 C
31503692 ACTTTCCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.21, C:0.35, G:0.00, T:0.44
Consensus pattern (21 bp):
CTCAAAACTTTTTACTCTTCC
Found at i:31504015 original size:20 final size:20
Alignment explanation
Indices: 31503987--31504024 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
31503977 CCTCAAACTT
*
31503987 TTATTCCCCAAAACTTTTTA
1 TTATCCCCCAAAACTTTTTA
*
31504007 TTATCCCCCTAAACTTTT
1 TTATCCCCCAAAACTTTT
31504025 ACTTCTCACC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.29, G:0.00, T:0.45
Consensus pattern (20 bp):
TTATCCCCCAAAACTTTTTA
Found at i:31507776 original size:16 final size:16
Alignment explanation
Indices: 31507755--31507788 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
31507745 TTCATTCTTG
31507755 ATATTTATTAATTTAT
1 ATATTTATTAATTTAT
*
31507771 ATATTTTTTAATTTAT
1 ATATTTATTAATTTAT
31507787 AT
1 AT
31507789 CTATCATGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATATTTATTAATTTAT
Found at i:31511611 original size:23 final size:24
Alignment explanation
Indices: 31511580--31511625 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
31511570 AAAATACTAT
*
31511580 AAAATTTTTTTATTTATCAAAAAA
1 AAAATTTTTTTATTTACCAAAAAA
31511604 AAAATTTTTTTATTTACCAAAA
1 AAAATTTTTTTATTTACCAAAA
31511626 TATATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (24 bp):
AAAATTTTTTTATTTACCAAAAAA
Found at i:31511732 original size:27 final size:27
Alignment explanation
Indices: 31511702--31511768 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
31511692 CGCCAATGGG
*
31511702 ATTGGCGGCACCAAAGGTGCCAAAACC
1 ATTGGCGGCACCAAAGGTGCCAAAACA
* *
31511729 ATTGGCGGCACCAATGGTGCCAATACA
1 ATTGGCGGCACCAAAGGTGCCAAAACA
*
31511756 ATTGGTGGCACCA
1 ATTGGCGGCACCA
31511769 GTGTATATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAAAACA
Found at i:31511823 original size:4 final size:4
Alignment explanation
Indices: 31511814--31511938 Score: 109
Period size: 4 Copynumber: 31.0 Consensus size: 4
31511804 GAAGGAGAGG
*
31511814 GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AA -AAA GAAG GAAA GAAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA
* *
31511861 GGAAA G-GA GAAGA GAAA AAAA GAAA GAAA G-AA G-AA GAAAA GGAAA
1 -GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAAA G-AAA -GAAA
*
31511906 GGAGAA G-AA GAAA GAAA GAAA GAAG GAAA GAAA
1 -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
31511939 AGGAAAGGAA
Statistics
Matches: 102, Mismatches: 8, Indels: 22
0.77 0.06 0.17
Matches are distributed among these distances:
3 15 0.15
4 64 0.63
5 19 0.19
6 4 0.04
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:31511941 original size:34 final size:31
Alignment explanation
Indices: 31511815--31511944 Score: 122
Period size: 34 Copynumber: 4.0 Consensus size: 31
31511805 AAGGAGAGGG
*
31511815 AAAGAAAGAAAGAAAGAAAGAAAG-AAA-GAA
1 AAAGAAAGAAAG-AAGAAGGAAAGAAAAGGAA
* *
31511845 AAAGAAGGAAAGAA-AAGGAAAGGAGAAGAGAAAA
1 AAAGAAAGAAAGAAGAAGGAAA-GA-AA-AG-GAA
* *
31511879 AAAGAAAGAAAGAAGAAGAAAAGGAAAGGAGA
1 AAAGAAAGAAAGAAGAAGGAAAGAAAAGGA-A
31511911 AGAAGAAAGAAAGAAAGAAGGAAAGAAAAGGAA
1 A-AAGAAAGAAAG-AAGAAGGAAAGAAAAGGAA
31511944 A
1 A
31511945 GGAAAGGAGA
Statistics
Matches: 81, Mismatches: 9, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
28 6 0.07
29 3 0.04
30 11 0.14
31 3 0.04
32 5 0.06
33 15 0.19
34 32 0.40
35 6 0.07
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (31 bp):
AAAGAAAGAAAGAAGAAGGAAAGAAAAGGAA
Found at i:31512003 original size:89 final size:89
Alignment explanation
Indices: 31511819--31511979 Score: 219
Period size: 84 Copynumber: 1.9 Consensus size: 89
31511809 AGAGGGAAAG
31511819 AAAGAAAGAAAGAAAGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGA
1 AAAG-AAGAAAGAAAGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGA
**
31511884 AAGAAAGAAGAAGAAAAGGAAAGGA
65 AAGAAAGAAGAAGAAAAGGAAAAAA
* * *
31511909 GAAGAAGAAAGAAAGAAAG-AAG-GAAAG-A--AAAGGAAAGGAAAGGAGAAGAGAAAAAAA-AA
1 AAAGAAGAAAGAAAGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAA
31511968 AG-AAGAAGAAGA
66 AGAAAGAAGAAGA
31511980 GGGAAGGAAG
Statistics
Matches: 68, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
82 10 0.15
83 4 0.06
84 28 0.41
86 1 0.01
87 4 0.06
88 3 0.04
89 15 0.22
90 3 0.04
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (89 bp):
AAAGAAGAAAGAAAGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAA
AGAAAGAAGAAGAAAAGGAAAAAA
Found at i:31512008 original size:79 final size:82
Alignment explanation
Indices: 31511824--31512004 Score: 217
Period size: 84 Copynumber: 2.2 Consensus size: 82
31511814 GAAAGAAAGA
* ** *
31511824 AAGAAAGAAAGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAAAGAA
1 AAGAAA-AAAAAAAGAAAGAAGGA-AAGAAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAAAGAA
31511889 AGAAGAAGAAAAGGAAAGGAG
64 AGAAGAAG--AAGGAAAGGAG
* * *
31511910 AAGAAGAAAGAAAGAAAGAAGGAAAGAAAAGGAAAGGAAAGGAGAAGAGAAAAAAA-AAAG-AAG
1 AAGAAAAAAAAAAGAAAGAAGGAAAGAAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAAAGAAAG
*
31511973 AAGAAG-AGGGAAGGA-
66 AAGAAGAAGGAAAGGAG
*
31511988 AGGAAAAAAAAAAGAAA
1 AAGAAAAAAAAAAGAAA
31512005 AGAAAAGGTA
Statistics
Matches: 86, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
78 14 0.16
79 8 0.09
82 9 0.10
83 4 0.05
84 31 0.36
85 15 0.17
86 5 0.06
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (82 bp):
AAGAAAAAAAAAAGAAAGAAGGAAAGAAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAAAGAAAG
AAGAAGAAGGAAAGGAG
Found at i:31513163 original size:23 final size:25
Alignment explanation
Indices: 31513137--31513202 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 25
31513127 GTTTTTTTTG
31513137 ATATATTTTGGTAAAT-AAAAAA-T
1 ATATATTTTGGTAAATAAAAAAATT
*
31513160 ATATATTTTGATAAATAAAAAAATTT
1 ATATATTTTGGTAAATAAAAAAA-TT
31513186 ATAGTATTTTGGTAAAT
1 ATA-TATTTTGGTAAAT
31513203 TTTATTTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.41
24 6 0.16
26 4 0.11
27 12 0.32
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (25 bp):
ATATATTTTGGTAAATAAAAAAATT
Found at i:31517020 original size:29 final size:29
Alignment explanation
Indices: 31516988--31517082 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 29
31516978 TTGGTCATAT
31516988 AACTATGAAAAGTTACAAAATGGTCACTC
1 AACTATGAAAAGTTACAAAATGGTCACTC
* * * * **** *
31517017 AACTATTAGTAATTTTCTTTTTTGGTCA-TAT
1 AACTATGA-AAAGTTAC-AAAATGGTCACT-C
31517048 AACTATGAAAAGTTACAAAATGGTCACTC
1 AACTATGAAAAGTTACAAAATGGTCACTC
31517077 AACTAT
1 AACTAT
31517083 TAGTAAATTT
Statistics
Matches: 44, Mismatches: 18, Indels: 8
0.63 0.26 0.11
Matches are distributed among these distances:
29 19 0.43
30 12 0.27
31 13 0.30
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.35
Consensus pattern (29 bp):
AACTATGAAAAGTTACAAAATGGTCACTC
Found at i:31517044 original size:31 final size:31
Alignment explanation
Indices: 31517008--31517122 Score: 96
Period size: 31 Copynumber: 3.8 Consensus size: 31
31516998 AGTTACAAAA
*
31517008 TGGTCACTCAACTATTAGTAATTTTCTTTTT
1 TGGTCACTCAACTATTAGTAAATTTCTTTTT
* * * ****
31517039 TGGTCA-TATAACTA-T-GAAAAGTTAC-AAAA
1 TGGTCACT-CAACTATTAGTAAA-TTTCTTTTT
31517068 TGGTCACTCAACTATTAGTAAATTTCTTTTT
1 TGGTCACTCAACTATTAGTAAATTTCTTTTT
*
31517099 TGGTCACTCAACTA-TATTAAATTT
1 TGGTCACTCAACTATTAGTAAATTT
31517123 TTGAATGTTT
Statistics
Matches: 62, Mismatches: 16, Indels: 13
0.68 0.18 0.14
Matches are distributed among these distances:
29 14 0.23
30 19 0.31
31 29 0.47
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (31 bp):
TGGTCACTCAACTATTAGTAAATTTCTTTTT
Found at i:31517050 original size:60 final size:60
Alignment explanation
Indices: 31516969--31517104 Score: 256
Period size: 60 Copynumber: 2.3 Consensus size: 60
31516959 TCTAACTATG
31516969 ATTTT-TTTTTTGGTCATATAACTATGAAAAGTTACAAAATGGTCACTCAACTATTAGTA
1 ATTTTCTTTTTTGGTCATATAACTATGAAAAGTTACAAAATGGTCACTCAACTATTAGTA
31517028 ATTTTCTTTTTTGGTCATATAACTATGAAAAGTTACAAAATGGTCACTCAACTATTAGTA
1 ATTTTCTTTTTTGGTCATATAACTATGAAAAGTTACAAAATGGTCACTCAACTATTAGTA
*
31517088 AATTTCTTTTTTGGTCA
1 ATTTTCTTTTTTGGTCA
31517105 CTCAACTATA
Statistics
Matches: 75, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
59 5 0.07
60 70 0.93
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (60 bp):
ATTTTCTTTTTTGGTCATATAACTATGAAAAGTTACAAAATGGTCACTCAACTATTAGTA
Found at i:31526762 original size:23 final size:24
Alignment explanation
Indices: 31526726--31526776 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
31526716 AAATTATTTC
*
31526726 TATTTTTCATGTTATTATTATAAT
1 TATTTTTCATGTTACTATTATAAT
* *
31526750 TATTTTTTA-GTTACTATTATTAT
1 TATTTTTCATGTTACTATTATAAT
31526773 TATT
1 TATT
31526777 CCTATTGCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (24 bp):
TATTTTTCATGTTACTATTATAAT
Found at i:31527356 original size:20 final size:20
Alignment explanation
Indices: 31527318--31527363 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
31527308 TTAACCATAC
31527318 ATCAAA-GTTATTTTCTTGA
1 ATCAAAGGTTATTTTCTTGA
* *
31527337 ATCAAAGGTTTTTTTTTTGA
1 ATCAAAGGTTATTTTCTTGA
*
31527357 ATAAAAG
1 ATCAAAG
31527364 CAATATTCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.46
Consensus pattern (20 bp):
ATCAAAGGTTATTTTCTTGA
Found at i:31528251 original size:21 final size:21
Alignment explanation
Indices: 31528226--31528278 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
31528216 CATTGTTTCA
* *
31528226 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAATAACC
*
31528247 AATCTCACCGCTACAATAACT
1 AATCTCACCGCTACAATAACC
31528268 AATCTCACCGC
1 AATCTCACCGC
31528279 CACCACTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.38, G:0.08, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAATAACC
Found at i:31537714 original size:3 final size:3
Alignment explanation
Indices: 31537706--31537732 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
31537696 TTTGATGTGA
31537706 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
31537733 TTCTAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:31537784 original size:42 final size:43
Alignment explanation
Indices: 31537723--31537809 Score: 167
Period size: 42 Copynumber: 2.0 Consensus size: 43
31537713 TTATTATTAT
31537723 TATTATTATTTTCTAAATTTTAATTCGATTTTTATTATGCGTA
1 TATTATTATTTTCTAAATTTTAATTCGATTTTTATTATGCGTA
31537766 TATTATTA-TTTCTAAATTTTAATTCGATTTTTATTATGCGTA
1 TATTATTATTTTCTAAATTTTAATTCGATTTTTATTATGCGTA
31537808 TA
1 TA
31537810 AATTAAACTA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 36 0.82
43 8 0.18
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (43 bp):
TATTATTATTTTCTAAATTTTAATTCGATTTTTATTATGCGTA
Found at i:31541087 original size:46 final size:46
Alignment explanation
Indices: 31541024--31541125 Score: 186
Period size: 46 Copynumber: 2.2 Consensus size: 46
31541014 GAAAATGCAG
31541024 TTTTCTTAATCTTAAAGTCCAGTGTAGTTTAGCATCCCTACCCAGT
1 TTTTCTTAATCTTAAAGTCCAGTGTAGTTTAGCATCCCTACCCAGT
*
31541070 TTTTCTTAATCTTAAAGTCCAGTGTAGTTTAGCATCCTTACCCAGT
1 TTTTCTTAATCTTAAAGTCCAGTGTAGTTTAGCATCCCTACCCAGT
*
31541116 TGTTCTTAAT
1 TTTTCTTAAT
31541126 GTTACCCAAG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 54 1.00
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.42
Consensus pattern (46 bp):
TTTTCTTAATCTTAAAGTCCAGTGTAGTTTAGCATCCCTACCCAGT
Found at i:31548918 original size:23 final size:23
Alignment explanation
Indices: 31548860--31548918 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
31548850 ATGATTTTTA
31548860 ATTAAATAAAATATTTAAAATTAAG
1 ATTAAA-AAAA-ATTTAAAATTAAG
* * *
31548885 ATTCAATAAAATTTAAATTTAA-
1 ATTAAAAAAAATTTAAAATTAAG
31548907 ATTTAAAAAAAA
1 A-TTAAAAAAAA
31548919 AATCGTCTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
22 1 0.04
23 19 0.68
24 3 0.11
25 5 0.18
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (23 bp):
ATTAAAAAAAATTTAAAATTAAG
Found at i:31554967 original size:6 final size:6
Alignment explanation
Indices: 31554956--31554981 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
31554946 ACTTCACCAT
31554956 CCCCAG CCCCAG CCCCAG CCCCAG CC
1 CCCCAG CCCCAG CCCCAG CCCCAG CC
31554982 TCTGCACACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.69, G:0.15, T:0.00
Consensus pattern (6 bp):
CCCCAG
Found at i:31561785 original size:15 final size:16
Alignment explanation
Indices: 31561762--31561841 Score: 78
Period size: 15 Copynumber: 5.2 Consensus size: 16
31561752 TCTCGATACT
31561762 CATATATTTGACTTTC
1 CATATATTTGACTTTC
**
31561778 CA-ATATTTGA-TACC
1 CATATATTTGACTTTC
31561792 CATATATTTGACTTTC
1 CATATATTTGACTTTC
* **
31561808 TAT-TATTTGA-TACC
1 CATATATTTGACTTTC
*
31561822 CATATCTTTGACTTTC
1 CATATATTTGACTTTC
31561838 CATA
1 CATA
31561842 AATATGGATG
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
14 8 0.16
15 29 0.59
16 12 0.24
ACGTcount: A:0.28, C:0.20, G:0.06, T:0.46
Consensus pattern (16 bp):
CATATATTTGACTTTC
Found at i:31561796 original size:30 final size:30
Alignment explanation
Indices: 31561746--31561839 Score: 134
Period size: 30 Copynumber: 3.1 Consensus size: 30
31561736 ATTTCTTATG
* *
31561746 CCAATATCTCGATACTCATATATTTGACTTT
1 CCAATAT-TTGATACCCATATATTTGACTTT
31561777 CCAATATTTGATACCCATATATTTGACTTT
1 CCAATATTTGATACCCATATATTTGACTTT
* * *
31561807 CTATTATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATATTTGACTTT
31561837 CCA
1 CCA
31561840 TAAATATGGA
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 50 0.88
31 7 0.12
ACGTcount: A:0.28, C:0.22, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATATTTGACTTT
Found at i:31567393 original size:7 final size:8
Alignment explanation
Indices: 31567371--31567396 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
31567361 ATAAATTTAA
31567371 ATATTTTT
1 ATATTTTT
31567379 ATATTTTT
1 ATATTTTT
31567387 ATATTTTT
1 ATATTTTT
31567395 AT
1 AT
31567397 CCTTTTAAGA
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:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
ATATTTTT
Found at i:31570915 original size:16 final size:15
Alignment explanation
Indices: 31570885--31570920 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
31570875 GAGGAAGAAA
*
31570885 AAAGGAAAAAGATAT
1 AAAGTAAAAAGATAT
31570900 AAAGTAAAAAGAATAT
1 AAAGTAAAAAG-ATAT
31570916 AAAGT
1 AAAGT
31570921 TTTAAAGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
AAAGTAAAAAGATAT
Found at i:31577146 original size:13 final size:13
Alignment explanation
Indices: 31577128--31577158 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
31577118 TTCCAGCAAC
31577128 TATGAATTTATTT
1 TATGAATTTATTT
31577141 TATGAATTTATTT
1 TATGAATTTATTT
*
31577154 GATGA
1 TATGA
31577159 TGATCCAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:31581112 original size:58 final size:59
Alignment explanation
Indices: 31581020--31581180 Score: 193
Period size: 58 Copynumber: 2.7 Consensus size: 59
31581010 TTGCATTTTG
* * *
31581020 ACCCCT-AAACTTCTCTAAAATTTCATTTTGACCCCTAAACTTTCTCAAAATTACAGTTAA
1 ACCCCTAAAATTTCT-TAAAATTACATTTTGACCCCTAAACTTT-TAAAAATTACAGTTAA
* *
31581080 ACCCCTAAAATTT-TT-AAATTACATTTTGACCCCTAAACTTTTAAAAATTACATTTTA
1 ACCCCTAAAATTTCTTAAAATTACATTTTGACCCCTAAACTTTTAAAAATTACAGTTAA
* * * * *
31581137 ACTCCTAAACTTTCTTAAAATTACGTTTTGACCCCAAAAGTTTT
1 ACCCCTAAAATTTCTTAAAATTACATTTTGACCCCTAAACTTTT
31581181 GCTGCCATTA
Statistics
Matches: 88, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
57 24 0.27
58 27 0.31
59 25 0.28
60 7 0.08
61 5 0.06
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.38
Consensus pattern (59 bp):
ACCCCTAAAATTTCTTAAAATTACATTTTGACCCCTAAACTTTTAAAAATTACAGTTAA
Found at i:31581143 original size:29 final size:29
Alignment explanation
Indices: 31581013--31581171 Score: 187
Period size: 30 Copynumber: 5.4 Consensus size: 29
31581003 TAATTTTTTG
*
31581013 CATTTTGACCCCTAAACTTCTCTAAAATTT
1 CATTTTGACCCCTAAACTT-TCTAAAATTA
31581043 CATTTTGACCCCTAAACTTTCTCAAAATTA
1 CATTTTGACCCCTAAACTTTCT-AAAATTA
* ** * *
31581073 CAGTTAAACCCCTAAAATTT-TTAAATTA
1 CATTTTGACCCCTAAACTTTCTAAAATTA
31581101 CATTTTGACCCCTAAACTTT-TAAAAATTA
1 CATTTTGACCCCTAAACTTTCT-AAAATTA
* *
31581130 CATTTTAACTCCTAAACTTTCTTAAAATTA
1 CATTTTGACCCCTAAACTTTC-TAAAATTA
*
31581160 CGTTTTGACCCC
1 CATTTTGACCCC
31581172 AAAAGTTTTG
Statistics
Matches: 109, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
28 23 0.21
29 28 0.26
30 57 0.52
31 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (29 bp):
CATTTTGACCCCTAAACTTTCTAAAATTA
Found at i:31581171 original size:87 final size:87
Alignment explanation
Indices: 31581013--31581180 Score: 225
Period size: 87 Copynumber: 1.9 Consensus size: 87
31581003 TAATTTTTTG
* *
31581013 CATTTTGACCCCTAAACTTCTCTAAAATTTCATTTTGACCCCTAAACTTTCTCAAAATTACAGTT
1 CATTTTGACCCCTAAACTTCTCTAAAATTACATTTTAACCCCTAAACTTTCTCAAAATTACAGTT
*
31581078 AAACCCCTAAAATTTTTAAATTA
66 AAACCCC-AAAAGTTTTAAATTA
* *
31581101 CATTTTGACCCCTAAACTT-T-TAAAAATTACATTTTAACTCCTAAACTTTCTTAAAATTAC-GT
1 CATTTTGACCCCTAAACTTCTCT-AAAATTACATTTTAACCCCTAAACTTTCTCAAAATTACAG-
**
31581163 TTTGACCCCAAAAGTTTT
64 TTAAACCCCAAAAGTTTT
31581181 GCTGCCATTA
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
86 10 0.14
87 42 0.59
88 19 0.27
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.39
Consensus pattern (87 bp):
CATTTTGACCCCTAAACTTCTCTAAAATTACATTTTAACCCCTAAACTTTCTCAAAATTACAGTT
AAACCCCAAAAGTTTTAAATTA
Found at i:31581646 original size:4 final size:4
Alignment explanation
Indices: 31581637--31581691 Score: 73
Period size: 4 Copynumber: 14.5 Consensus size: 4
31581627 GCTGATCGGA
31581637 AAAG AAAG AAAG AAAG -AA- AAAG AGAAG AAAG AAAG AAAG -AAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG A-AAG AAAG AAAG AAAG AAAG AAAG
31581683 -AAG AAAG AA
1 AAAG AAAG AA
31581692 GAGAGAAGAG
Statistics
Matches: 46, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
3 10 0.22
4 32 0.70
5 4 0.09
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:31581666 original size:15 final size:15
Alignment explanation
Indices: 31581641--31581690 Score: 68
Period size: 15 Copynumber: 3.3 Consensus size: 15
31581631 ATCGGAAAAG
31581641 AAAGA-AAGAAAGAA
1 AAAGAGAAGAAAGAA
31581655 AAAGAGAAGAAAGAA
1 AAAGAGAAGAAAGAA
31581670 AGAA-AGAAGAAAGAA
1 A-AAGAGAAGAAAGAA
31581685 GAAAGA
1 -AAAGA
31581691 AGAGAGAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.16
15 23 0.72
16 4 0.12
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (15 bp):
AAAGAGAAGAAAGAA
Found at i:31581701 original size:7 final size:7
Alignment explanation
Indices: 31581638--31581700 Score: 81
Period size: 7 Copynumber: 8.6 Consensus size: 7
31581628 CTGATCGGAA
31581638 AAGAAAG
1 AAGAAAG
31581645 AAAGAAAG
1 -AAGAAAG
*
31581653 AAAAAGAG
1 AAGAA-AG
31581661 AAGAAAG
1 AAGAAAG
31581668 AAAGAAAG
1 -AAGAAAG
31581676 AAGAAAG
1 AAGAAAG
31581683 AAGAAAG
1 AAGAAAG
*
31581690 AAGAGAG
1 AAGAAAG
31581697 AAGA
1 AAGA
31581701 GGGGAAAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
7 30 0.60
8 20 0.40
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (7 bp):
AAGAAAG
Found at i:31581841 original size:23 final size:20
Alignment explanation
Indices: 31581812--31581861 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
31581802 AAGCAGCGAA
31581812 AAAAAAACAAAAAACAAAGCAG
1 AAAAAAA-AAAAAA-AAAGCAG
*
31581834 AAAAAAAAAAGAAAAAGCAG
1 AAAAAAAAAAAAAAAAGCAG
*
31581854 CAAAAAAA
1 AAAAAAAA
31581862 TAGCAGGCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 14 0.54
21 5 0.19
22 7 0.27
ACGTcount: A:0.80, C:0.10, G:0.10, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAAAAAAAAGCAG
Found at i:31581843 original size:20 final size:21
Alignment explanation
Indices: 31581812--31581861 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
31581802 AAGCAGCGAA
*
31581812 AAAAAAACAAAAAACAAAGCAG-
1 AAAAAAA-AAAGAA-AAAGCAGC
31581834 AAAAAAAAAAGAAAAAGCAGC
1 AAAAAAAAAAGAAAAAGCAGC
31581855 AAAAAAA
1 AAAAAAA
31581862 TAGCAGGCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 7 0.27
21 12 0.46
22 7 0.27
ACGTcount: A:0.80, C:0.10, G:0.10, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAAGAAAAAGCAGC
Found at i:31581848 original size:25 final size:26
Alignment explanation
Indices: 31581800--31581849 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
31581790 TAGTCAAGCC
*
31581800 CAAAGCAGCGAAAAAAAAACAAAAAA
1 CAAAGCAGCAAAAAAAAAACAAAAAA
*
31581826 CAAAGCAG-AAAAAAAAAAGAAAAA
1 CAAAGCAGCAAAAAAAAAACAAAAA
31581850 GCAGCAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.76, C:0.12, G:0.12, T:0.00
Consensus pattern (26 bp):
CAAAGCAGCAAAAAAAAAACAAAAAA
Found at i:31582475 original size:18 final size:18
Alignment explanation
Indices: 31582452--31582757 Score: 144
Period size: 18 Copynumber: 16.4 Consensus size: 18
31582442 CAATTTTAAA
31582452 AAAAATTTGTCGTG-TTTC
1 AAAAATTT-TCGTGTTTTC
*
31582470 AAAAA-TTTCGAGTTTTC
1 AAAAATTTTCGTGTTTTC
* *
31582487 AAAAAAATTTCTCAT-ATTTC
1 --AAAAATTT-TCGTGTTTTC
31582507 AAAAATTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
**
31582525 AAAAAATTCCCGTGTTTTC
1 -AAAAATTTTCGTGTTTTC
31582544 AAAATTTTCATGTTTTCGTGTTTTC
1 AAAA-----A--TTTTCGTGTTTTC
* *
31582569 AAAAAATTCTCGTGTTTTTTTAA
1 -AAAAATTTTCGTG---TTTT-C
** * *
31582592 AAAAAAATTCATGTTTTA
1 AAAAATTTTCGTGTTTTC
** *
31582610 AAAAAAATTCATGTTTTC
1 AAAAATTTTCGTGTTTTC
*
31582628 -GAAATTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
*
31582645 AAAATTTTTCGTG---TC
1 AAAAATTTTCGTGTTTTC
* * *
31582660 AAAAAATTCTCATG-TATC
1 -AAAAATTTTCGTGTTTTC
* * *
31582678 GAAAATTTCCTTGTTTTC
1 AAAAATTTTCGTGTTTTC
* *
31582696 AAAAAAATTCCGTGTTTTC
1 -AAAAATTTTCGTGTTTTC
31582715 AAAAAATTTTCGTG-TTTC
1 -AAAAATTTTCGTGTTTTC
*
31582733 AAAAATCTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
31582751 AAAAATT
1 AAAAATT
31582758 ATTATTGTGT
Statistics
Matches: 224, Mismatches: 38, Indels: 52
0.71 0.12 0.17
Matches are distributed among these distances:
15 2 0.01
16 14 0.06
17 43 0.19
18 68 0.30
19 59 0.26
20 6 0.03
21 3 0.01
22 13 0.06
23 1 0.00
25 11 0.05
26 4 0.02
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.44
Consensus pattern (18 bp):
AAAAATTTTCGTGTTTTC
Found at i:31582507 original size:37 final size:38
Alignment explanation
Indices: 31582445--31582530 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 38
31582435 TATGGCACAA
* * * *
31582445 TTTTAAAAAAAATTTGTCGTGTTTCAAAAA-TTTCGAG
1 TTTTCAAAAAAATTTCTCATATTTCAAAAATTTTCGAG
*
31582482 TTTTCAAAAAAATTTCTCATATTTCAAAAATTTTCGTG
1 TTTTCAAAAAAATTTCTCATATTTCAAAAATTTTCGAG
31582520 TTTTCAAAAAA
1 TTTTCAAAAAA
31582531 TTCCCGTGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
37 26 0.60
38 17 0.40
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (38 bp):
TTTTCAAAAAAATTTCTCATATTTCAAAAATTTTCGAG
Found at i:31582531 original size:19 final size:19
Alignment explanation
Indices: 31582451--31582755 Score: 165
Period size: 19 Copynumber: 16.3 Consensus size: 19
31582441 ACAATTTTAA
31582451 AAAAAATTTGTCGTG-TTTC
1 AAAAAATTT-TCGTGTTTTC
*
31582470 -AAAAA-TTTCGAGTTTTC
1 AAAAAATTTTCGTGTTTTC
* *
31582487 AAAAAAATTTCTCAT-ATTTC
1 -AAAAAATTT-TCGTGTTTTC
31582507 -AAAAATTTTCGTGTTTTC
1 AAAAAATTTTCGTGTTTTC
**
31582525 AAAAAATTCCCGTGTTTTC
1 AAAAAATTTTCGTGTTTTC
*
31582544 AAAATTTTCATGTTTTCGTGTTTTC
1 AAAA-----A-ATTTTCGTGTTTTC
* *
31582569 AAAAAATTCTCGTGTTTTTTTA
1 AAAAAATTTTCGTG---TTTTC
** *
31582591 AAAAAAAATTCATGTTTT-
1 AAAAAATTTTCGTGTTTTC
** *
31582609 AAAAAAAATTCATGTTTTC
1 AAAAAATTTTCGTGTTTTC
*
31582628 --GAAATTTTCGTGTTTTC
1 AAAAAATTTTCGTGTTTTC
*
31582645 -AAAATTTTTCGTG---TC
1 AAAAAATTTTCGTGTTTTC
* * *
31582660 AAAAAATTCTCATG-TATC
1 AAAAAATTTTCGTGTTTTC
* * *
31582678 -GAAAATTTCCTTGTTTTC
1 AAAAAATTTTCGTGTTTTC
* *
31582696 AAAAAAATTCCGTGTTTTC
1 AAAAAATTTTCGTGTTTTC
31582715 AAAAAATTTTCGTG-TTTC
1 AAAAAATTTTCGTGTTTTC
*
31582733 -AAAAATCTTCGTGTTTTC
1 AAAAAATTTTCGTGTTTTC
31582751 AAAAA
1 AAAAA
31582756 TTATTATTGT
Statistics
Matches: 223, Mismatches: 38, Indels: 50
0.72 0.12 0.16
Matches are distributed among these distances:
15 2 0.01
16 14 0.06
17 43 0.19
18 58 0.26
19 67 0.30
20 7 0.03
21 2 0.01
22 14 0.06
24 1 0.00
25 15 0.07
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (19 bp):
AAAAAATTTTCGTGTTTTC
Found at i:31582557 original size:17 final size:18
Alignment explanation
Indices: 31582452--31582560 Score: 75
Period size: 17 Copynumber: 6.0 Consensus size: 18
31582442 CAATTTTAAA
*
31582452 AAAAATTTGTCGTG-TTTC
1 AAAAATTT-TCATGTTTTC
31582470 AAAAA-TTTCGA-GTTTTC
1 AAAAATTTTC-ATGTTTTC
*
31582487 AAAAAAATTTCTCAT-ATTTC
1 --AAAAATTT-TCATGTTTTC
*
31582507 AAAAATTTTCGTGTTTTC
1 AAAAATTTTCATGTTTTC
** *
31582525 AAAAAATTCCCGTGTTTTC
1 -AAAAATTTTCATGTTTTC
31582544 -AAAATTTTCATGTTTTC
1 AAAAATTTTCATGTTTTC
31582561 GTGTTTTCAA
Statistics
Matches: 73, Mismatches: 9, Indels: 19
0.72 0.09 0.19
Matches are distributed among these distances:
16 3 0.04
17 23 0.32
18 17 0.23
19 21 0.29
20 7 0.10
21 2 0.03
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (18 bp):
AAAAATTTTCATGTTTTC
Found at i:31582584 original size:27 final size:25
Alignment explanation
Indices: 31582535--31582586 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
31582525 AAAAAATTCC
*
31582535 CGTGTTTTCAAAATTTTCATGTTTT
1 CGTGTTTTCAAAATTCTCATGTTTT
*
31582560 CGTGTTTTCAAAAAATTCTCGTGTTTT
1 CGTGTTTTC--AAAATTCTCATGTTTT
31582587 TTTAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 9 0.39
27 14 0.61
ACGTcount: A:0.21, C:0.13, G:0.13, T:0.52
Consensus pattern (25 bp):
CGTGTTTTCAAAATTCTCATGTTTT
Found at i:31582746 original size:36 final size:38
Alignment explanation
Indices: 31582688--31582773 Score: 108
Period size: 36 Copynumber: 2.3 Consensus size: 38
31582678 GAAAATTTCC
31582688 TTGT-TTTCAAAAAAATTCCGTGTTTTCAAAAA-ATT-
1 TTGTGTTTCAAAAAAATTCCGTGTTTTCAAAAATATTA
**
31582723 TTCGTGTTTCAAAAATCTT-CGTGTTTTCAAAAATTATTA
1 TT-GTGTTTCAAAAAAATTCCGTGTTTTCAAAAA-TATTA
31582762 TTGTGTTTCAAA
1 TTGTGTTTCAAA
31582774 GTTCTCGTGT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
35 2 0.05
36 16 0.36
37 11 0.25
38 13 0.30
39 2 0.05
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (38 bp):
TTGTGTTTCAAAAAAATTCCGTGTTTTCAAAAATATTA
Found at i:31585454 original size:29 final size:29
Alignment explanation
Indices: 31585387--31585481 Score: 111
Period size: 30 Copynumber: 3.2 Consensus size: 29
31585377 ACAAAAAATA
**
31585387 TAAATTACATTTTGGCCCCTAAACTTTT-
1 TAAATTACATTTTAACCCCTAAACTTTTC
*
31585415 TAAAAATTACATTTTAACCTCTAAACTTTTC
1 T--AAATTACATTTTAACCCCTAAACTTTTC
*
31585446 TAAATTACATTTCAACCCCTAAACTTTCTC
1 TAAATTACATTTTAACCCCTAAACTTT-TC
*
31585476 AAAATT
1 TAAATT
31585482 GTGTGTGTGC
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
28 1 0.02
29 24 0.42
30 31 0.54
31 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.02, T:0.40
Consensus pattern (29 bp):
TAAATTACATTTTAACCCCTAAACTTTTC
Found at i:31587806 original size:87 final size:86
Alignment explanation
Indices: 31587660--31587829 Score: 304
Period size: 87 Copynumber: 2.0 Consensus size: 86
31587650 TAGAAACAGA
31587660 GAGTTCTGTATTCTGAATACTGAAGCTTGAAAATCTTTTTTACACCATGTTTATGTATTTATAGT
1 GAGTTCTGTATTCTGAATACTGAAGCTTGAAAATCTTTTTTACACCATGTTTATGTATTTATAGT
*
31587725 TTAGGCCCTTAATCATTTCAGG
66 TTA-ACCCTTAATCATTTCAGG
*
31587747 GAGTTCTGTATTCTGAATATTGAAGCTTGAAAATCTTTTTTACACCATGTTTATGTATTTATAGT
1 GAGTTCTGTATTCTGAATACTGAAGCTTGAAAATCTTTTTTACACCATGTTTATGTATTTATAGT
*
31587812 TTAATCCTTAATCATTTC
66 TTAACCCTTAATCATTTC
31587830 TTAACTACTT
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
86 13 0.16
87 67 0.84
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (86 bp):
GAGTTCTGTATTCTGAATACTGAAGCTTGAAAATCTTTTTTACACCATGTTTATGTATTTATAGT
TTAACCCTTAATCATTTCAGG
Found at i:31587872 original size:43 final size:43
Alignment explanation
Indices: 31587824--31587910 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
31587814 AATCCTTAAT
31587824 CATTTCTTAA-CTACTTAACTATTATAACTAACAACCCAATAAC
1 CATTTCTTAATC-ACTTAACTATTATAACTAACAACCCAATAAC
* * * * *
31587867 CATTTCTTAATCATTTGATTATTATAATTAACAACTCAATAAC
1 CATTTCTTAATCACTTAACTATTATAACTAACAACCCAATAAC
31587910 C
1 C
31587911 CACTATTAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
43 37 0.97
44 1 0.03
ACGTcount: A:0.40, C:0.22, G:0.01, T:0.37
Consensus pattern (43 bp):
CATTTCTTAATCACTTAACTATTATAACTAACAACCCAATAAC
Found at i:31590970 original size:25 final size:25
Alignment explanation
Indices: 31590936--31590989 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
31590926 CTTAACTAAC
*
31590936 TAAAACAGTCATGTCCATATATAAT
1 TAAAACAGTCATGACCATATATAAT
31590961 TAAAACAGTCATGACCATATATAAT
1 TAAAACAGTCATGACCATATATAAT
31590986 TAAA
1 TAAA
31590990 TTTTCACACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (25 bp):
TAAAACAGTCATGACCATATATAAT
Found at i:31591103 original size:112 final size:113
Alignment explanation
Indices: 31590984--31591194 Score: 318
Period size: 113 Copynumber: 1.9 Consensus size: 113
31590974 ACCATATATA
31590984 ATTAAATTT-TCACACAATTTTAAAAAATTAAAATATAAAATTACCACCATACTA-TTAACAACA
1 ATTAAATTTGTCACACAATTTTAAAAAA-TAAAATATAAAATTACCACCATACTATTTAACAACA
* * * *
31591047 TTAAAAATCGTAATTATATTTTATTTTGATTAATATTTATCTTTATAGG
65 TTAAAAATCGCAACTAAATTTTATTTCGATTAATATTTATCTTTATAGG
* * *
31591096 ATTAAATTTGTCACACAATTTTAAAAAATAAAATGTAAAATTACCACCATACTATTTAATAATAT
1 ATTAAATTTGTCACACAATTTTAAAAAATAAAATATAAAATTACCACCATACTATTTAACAACAT
* *
31591161 TAAAAATTGCCACTAAATTTTATTTCGATTAATA
66 TAAAAATCGCAACTAAATTTTATTTCGATTAATA
31591195 ATTGTCACTA
Statistics
Matches: 88, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
112 34 0.39
113 54 0.61
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.39
Consensus pattern (113 bp):
ATTAAATTTGTCACACAATTTTAAAAAATAAAATATAAAATTACCACCATACTATTTAACAACAT
TAAAAATCGCAACTAAATTTTATTTCGATTAATATTTATCTTTATAGG
Found at i:31599695 original size:2 final size:2
Alignment explanation
Indices: 31599679--31599716 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
31599669 CTATCCATAG
*
31599679 TA TA -A TA TT TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31599717 AAGTAAGGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:31601309 original size:5 final size:5
Alignment explanation
Indices: 31601299--31601369 Score: 135
Period size: 5 Copynumber: 14.4 Consensus size: 5
31601289 TTTAAAATAC
31601299 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
31601349 TATAT TATAT TATAT TA-AT TA
1 TATAT TATAT TATAT TATAT TA
31601370 AAAAAATATT
Statistics
Matches: 66, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
4 4 0.06
5 62 0.94
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:31603172 original size:19 final size:19
Alignment explanation
Indices: 31603148--31603185 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
31603138 AAATACAAAA
*
31603148 TTTTTATATG-AAATATTAT
1 TTTTTAAATGTAAAT-TTAT
31603167 TTTTTAAATGTAAATTTAT
1 TTTTTAAATGTAAATTTAT
31603186 ATATAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (19 bp):
TTTTTAAATGTAAATTTAT
Found at i:31603453 original size:18 final size:20
Alignment explanation
Indices: 31603410--31603447 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
31603400 AGACTTTTAG
* *
31603410 GTTTCTTTATAAATTTTCTA
1 GTTTTTTTAAAAATTTTCTA
31603430 GTTTTTTTAAAAATTTTC
1 GTTTTTTTAAAAATTTTC
31603448 ATTTTTCATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.61
Consensus pattern (20 bp):
GTTTTTTTAAAAATTTTCTA
Found at i:31624489 original size:29 final size:30
Alignment explanation
Indices: 31624423--31624491 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 30
31624413 AAATATCGAT
* *
31624423 TTTATACATTAACTTTGTTTTCATGTGTAA
1 TTTATACATGAACTTTGATTTCATGTGTAA
31624453 TTTGATACATGAACTTTGATTT-A-GTGTAA
1 TTT-ATACATGAACTTTGATTTCATGTGTAA
31624482 TTATATACAT
1 TT-TATACAT
31624492 AAAACTTGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 14 0.40
30 5 0.14
31 16 0.46
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.49
Consensus pattern (30 bp):
TTTATACATGAACTTTGATTTCATGTGTAA
Found at i:31625538 original size:29 final size:30
Alignment explanation
Indices: 31625492--31625571 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 30
31625482 AAATTTAATC
*
31625492 AAATCAAAATTTAATATATAAAATCGCACA-
1 AAATCAAAA-TTCATATATAAAATCGCACAT
* *
31625522 AAATCAAAATTCATATATAACATTGCACATT
1 AAATCAAAATTCATATATAAAATCGCACA-T
* *
31625553 AAATTAAAATTCATGTATA
1 AAATCAAAATTCATATATA
31625572 GTTTAATATT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 17 0.40
30 9 0.21
31 17 0.40
ACGTcount: A:0.53, C:0.12, G:0.04, T:0.31
Consensus pattern (30 bp):
AAATCAAAATTCATATATAAAATCGCACAT
Found at i:31631464 original size:14 final size:14
Alignment explanation
Indices: 31631447--31631491 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
31631437 ATTTAATTAT
31631447 TTTAATCTTTGTAC
1 TTTAATCTTTGTAC
31631461 TTTAAT-TTAAT-TA-
1 TTTAATCTT--TGTAC
31631474 TTTAATCTTTGTAC
1 TTTAATCTTTGTAC
31631488 TTTA
1 TTTA
31631492 CTATTTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
12 1 0.04
13 10 0.38
14 14 0.54
15 1 0.04
ACGTcount: A:0.27, C:0.09, G:0.04, T:0.60
Consensus pattern (14 bp):
TTTAATCTTTGTAC
Found at i:31631485 original size:27 final size:28
Alignment explanation
Indices: 31631437--31631491 Score: 103
Period size: 27 Copynumber: 2.0 Consensus size: 28
31631427 ATTTATTCTT
31631437 ATTTAATTATTTTAATCTTTGTACTTTA
1 ATTTAATTATTTTAATCTTTGTACTTTA
31631465 ATTTAATTA-TTTAATCTTTGTACTTTA
1 ATTTAATTATTTTAATCTTTGTACTTTA
31631492 CTATTTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 18 0.67
28 9 0.33
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.60
Consensus pattern (28 bp):
ATTTAATTATTTTAATCTTTGTACTTTA
Found at i:31631502 original size:27 final size:25
Alignment explanation
Indices: 31631438--31631506 Score: 88
Period size: 27 Copynumber: 2.7 Consensus size: 25
31631428 TTTATTCTTA
31631438 TTTAA-TTAT-TTTAATCTTTGTAC
1 TTTAATTTATATTTAATCTTTGTAC
31631461 TTTAATTTAATTATTTAATCTTTGTAC
1 TTTAATTT-A-TATTTAATCTTTGTAC
31631488 TTTACTATTTATATTTAAT
1 TTTA--ATTTATATTTAAT
31631507 TTATACTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
23 5 0.12
24 2 0.05
25 1 0.03
26 1 0.03
27 26 0.65
28 1 0.03
29 4 0.10
ACGTcount: A:0.29, C:0.07, G:0.03, T:0.61
Consensus pattern (25 bp):
TTTAATTTATATTTAATCTTTGTAC
Found at i:31634020 original size:6 final size:6
Alignment explanation
Indices: 31634009--31634033 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
31633999 TACTTTACAA
31634009 CGATGG CGATGG CGATGG CGATGG C
1 CGATGG CGATGG CGATGG CGATGG C
31634034 CAGCAAGCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.20, G:0.48, T:0.16
Consensus pattern (6 bp):
CGATGG
Found at i:31637984 original size:20 final size:20
Alignment explanation
Indices: 31637961--31637998 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
31637951 GCTTATTGTT
*
31637961 AATTAAGTAAAGGTTAATTA
1 AATTAAGTAAAGATTAATTA
*
31637981 AATTAATTAAAGATTAAT
1 AATTAAGTAAAGATTAAT
31637999 CTAAGTATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.37
Consensus pattern (20 bp):
AATTAAGTAAAGATTAATTA
Found at i:31640488 original size:13 final size:13
Alignment explanation
Indices: 31640470--31640499 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
31640460 AGCCCAAACT
31640470 CAATTACCCAACC
1 CAATTACCCAACC
31640483 CAATTACCCAACC
1 CAATTACCCAACC
31640496 CAAT
1 CAAT
31640500 AAAATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:31660080 original size:16 final size:16
Alignment explanation
Indices: 31660059--31660091 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
31660049 TAAATATATA
31660059 TTAAGTTTTTTATGTT
1 TTAAGTTTTTTATGTT
31660075 TTAAGTTTTTTATGTT
1 TTAAGTTTTTTATGTT
31660091 T
1 T
31660092 AAAAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.70
Consensus pattern (16 bp):
TTAAGTTTTTTATGTT
Found at i:31660183 original size:20 final size:20
Alignment explanation
Indices: 31660160--31660219 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
31660150 CCCCTGACAG
31660160 TTTAAGTTTTCAATTTTATT
1 TTTAAGTTTTCAATTTTATT
*
31660180 TTTATGTTTTCAATTTTATT
1 TTTAAGTTTTCAATTTTATT
*
31660200 TTT-AGTTTTCAATTTCATT
1 TTTAAGTTTTCAATTTTATT
31660219 T
1 T
31660220 CCCCGACAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
19 15 0.41
20 22 0.59
ACGTcount: A:0.22, C:0.07, G:0.05, T:0.67
Consensus pattern (20 bp):
TTTAAGTTTTCAATTTTATT
Found at i:31660477 original size:16 final size:16
Alignment explanation
Indices: 31660456--31660498 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
31660446 ATTTTGTTAC
* *
31660456 AACAATTAATATACTT
1 AACAATTAATACAATT
31660472 AACAATTAATACAATT
1 AACAATTAATACAATT
31660488 AACAATTAATA
1 AACAATTAATA
31660499 AGTTGATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.33
Consensus pattern (16 bp):
AACAATTAATACAATT
Found at i:31660526 original size:16 final size:16
Alignment explanation
Indices: 31660505--31660546 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
31660495 AATAAGTTGA
*
31660505 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
31660521 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
31660537 TAATTTTAAT
1 TAATTTTAAT
31660547 TTTATCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:31669598 original size:47 final size:45
Alignment explanation
Indices: 31669547--31669714 Score: 141
Period size: 47 Copynumber: 3.6 Consensus size: 45
31669537 TATTTAATAT
*
31669547 TAATTATTTTAAATTGTATAAATTCATATAAGAAAAATTATTATCAA
1 TAATTATTTTAAATT-TATAAATTCATATAAGAAAATTTATTAT-AA
* * **
31669594 TAATT-TTATGAAA-TTATATATT-AT-T-ATTAAATTATATGTAATAA
1 TAATTATT-TTAAATTTATAAATTCATATAAGAAAATT-TAT-T-ATAA
* *
31669638 TAATTATTTTAAATTATACAAATTCATATAAGAAAATTTATTAGTTA
1 TAATTATTTTAAATT-TATAAATTCATATAAGAAAATTTATTA-TAA
31669685 TAATTATTTTAAATTTTATTAAA-TCATATA
1 TAATTATTTTAAA-TTTA-TAAATTCATATA
31669715 TTTTAATTAA
Statistics
Matches: 96, Mismatches: 12, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
42 5 0.05
43 4 0.04
44 14 0.15
45 12 0.12
46 10 0.10
47 36 0.38
48 9 0.09
49 6 0.06
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (45 bp):
TAATTATTTTAAATTTATAAATTCATATAAGAAAATTTATTATAA
Found at i:31669641 original size:44 final size:43
Alignment explanation
Indices: 31669511--31669655 Score: 116
Period size: 44 Copynumber: 3.2 Consensus size: 43
31669501 AAGAATTTTA
* *
31669511 TGAAATTATATATCATTATTAAATTATATTTAATATTAATTATT
1 TGAAATTATATATAATTATTAAATTATA-TTAATAATAATTATT
* * * *
31669555 TTAAATTGTATA-AATTCATATAAGA-AAAATTATTATCAATAATT-TT
1 TGAAATTATATATAATT-AT-TAA-ATTATATTA--AT-AATAATTATT
*
31669601 ATGAAATTATATATTATTATTAAATTATATGTAATAATAATTATT
1 -TGAAATTATATATAATTATTAAATTATAT-TAATAATAATTATT
*
31669646 TTAAATTATA
1 TGAAATTATA
31669656 CAAATTCATA
Statistics
Matches: 78, Mismatches: 12, Indels: 22
0.70 0.11 0.20
Matches are distributed among these distances:
43 3 0.04
44 31 0.40
45 10 0.13
46 11 0.14
47 20 0.26
48 3 0.04
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.48
Consensus pattern (43 bp):
TGAAATTATATATAATTATTAAATTATATTAATAATAATTATT
Found at i:31669649 original size:26 final size:28
Alignment explanation
Indices: 31669595--31669655 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
31669585 TATTATCAAT
* *
31669595 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
31669623 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
31669649 AATTATA
1 AATTATA
31669656 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:31669699 original size:91 final size:91
Alignment explanation
Indices: 31669495--31669680 Score: 300
Period size: 91 Copynumber: 2.0 Consensus size: 91
31669485 NNNNNNNNNN
* * * *
31669495 ATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAA
1 ATTATCAATAATTTTATGAAATTATATATCATTATTAAATTATATGTAATAATAATTATTTTAAA
* *
31669560 TTGTATAAATTCATATAAGAAAAATT
66 TTATACAAATTCATATAAGAAAAATT
*
31669586 ATTATCAATAATTTTATGAAATTATATATTATTATTAAATTATATGTAATAATAATTATTTTAAA
1 ATTATCAATAATTTTATGAAATTATATATCATTATTAAATTATATGTAATAATAATTATTTTAAA
*
31669651 TTATACAAATTCATATAAGAAAATTT
66 TTATACAAATTCATATAAGAAAAATT
31669677 ATTA
1 ATTA
31669681 GTTATAATTA
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 87 1.00
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
ATTATCAATAATTTTATGAAATTATATATCATTATTAAATTATATGTAATAATAATTATTTTAAA
TTATACAAATTCATATAAGAAAAATT
Found at i:31669817 original size:16 final size:15
Alignment explanation
Indices: 31669796--31669825 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
31669786 TAAATTCATA
31669796 TAAGAATTTTGATTAT
1 TAAGAATTTT-ATTAT
31669812 TAAGAATTTTATTA
1 TAAGAATTTTATTA
31669826 AATTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (15 bp):
TAAGAATTTTATTAT
Found at i:31669845 original size:18 final size:17
Alignment explanation
Indices: 31669817--31669851 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
31669807 ATTATTAAGA
*
31669817 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
31669834 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
31669852 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:31669964 original size:18 final size:17
Alignment explanation
Indices: 31669936--31669970 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
31669926 ATTATTAAGA
*
31669936 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
31669953 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
31669971 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:31669979 original size:119 final size:119
Alignment explanation
Indices: 31669696--31670111 Score: 726
Period size: 119 Copynumber: 3.5 Consensus size: 119
31669686 AATTATTTTA
* * * *
31669696 AATTTTATTAAATCATATATTTTAATTAAAATATTTTTAATATTAATTACT-TCAAATTATATTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTA-TGTTAAATTATATTT
* *
31669760 TATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATTTTGATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAG-ATATTGATTATTAAG
31669816 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
31669881 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGATATTGATTATTAAG
31669935 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
31670000 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGATATTGATTATTAAG
* *
31670054 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATTATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
31670112 ATAATTAAAT
Statistics
Matches: 286, Mismatches: 8, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
119 183 0.64
120 103 0.36
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (119 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGATATTGATTATTAAG
Found at i:31670333 original size:45 final size:44
Alignment explanation
Indices: 31670235--31670345 Score: 133
Period size: 45 Copynumber: 2.6 Consensus size: 44
31670225 TTTTCCATTA
31670235 TGCTATTACACCTCTATTCCA-T----TCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACACTCAACCAAACACAAGAT
* * ***
31670274 TACTATTACGCCTCTATTCCATTACACTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACACTCAACCAAACACAAGA-T
31670319 TGCTATTACACCTCTATTCCATTACAC
1 TGCTATTACACCTCTATTCCATTACAC
31670346 CTCTATTCCA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 19 0.32
40 1 0.02
44 13 0.22
45 26 0.44
ACGTcount: A:0.32, C:0.31, G:0.05, T:0.32
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACACTCAACCAAACACAAGAT
Found at i:31670344 original size:16 final size:16
Alignment explanation
Indices: 31670323--31670392 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
31670313 TTGATTTGCT
*
31670323 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
*
31670339 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
31670355 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
31670371 AATACACCTCTAATCC
1 ATTACACCTCTAATCC
*
31670387 AATACA
1 ATTACA
31670393 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.31
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:31671747 original size:23 final size:23
Alignment explanation
Indices: 31671721--31671772 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
31671711 TAATTTTTTA
*
31671721 ATTTTGAATTATTTAGTGATAAT
1 ATTTAGAATTATTTAGTGATAAT
31671744 ATTTAGAATTATTTAGTGATAAT
1 ATTTAGAATTATTTAGTGATAAT
*
31671767 GTTTAG
1 ATTTAG
31671773 GAAAAATCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (23 bp):
ATTTAGAATTATTTAGTGATAAT
Done.