Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011739.1 Kokia drynarioides strain JFW-HI SEQ_126733, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 477670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 61 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:389196 original size:20 final size:20
Alignment explanation
Indices: 389160--389215 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
389150 TTTAATTTTT
389160 TTTATATT-TTATAATAA-TA
1 TTTATATTATT-TAATAAGTA
*
389179 TTTATATATATTTAATAAGTT
1 TTTATAT-TATTTAATAAGTA
*
389200 TTTATATTTTTTAATA
1 TTTATATTATTTAATA
389216 TTTTTTTCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 7 0.22
20 15 0.47
21 10 0.31
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
TTTATATTATTTAATAAGTA
Found at i:394968 original size:33 final size:33
Alignment explanation
Indices: 394926--394991 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
394916 AAGGAGTGAG
*
394926 ATCTCATTAATTTTAATTGCGTCGACAATTTAT
1 ATCTCATTAATTTTAATTACGTCGACAATTTAT
394959 ATCTCATTAATTTTAATTACGTCGACAATTTAT
1 ATCTCATTAATTTTAATTACGTCGACAATTTAT
394992 CAATCATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.32, C:0.15, G:0.08, T:0.45
Consensus pattern (33 bp):
ATCTCATTAATTTTAATTACGTCGACAATTTAT
Found at i:394999 original size:33 final size:33
Alignment explanation
Indices: 394929--394999 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
394919 GAGTGAGATC
* *
394929 TCATTAATTTTAATTGCGTCGACAATTTATATC
1 TCATTAATTTTAATTACGTCGACAATTTATATA
394962 TCATTAATTTTAATTACGTCGACAATTTATCA-A
1 TCATTAATTTTAATTACGTCGACAATTTAT-ATA
394995 TCATT
1 TCATT
395000 TTCCTTGTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 34 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.15, G:0.07, T:0.45
Consensus pattern (33 bp):
TCATTAATTTTAATTACGTCGACAATTTATATA
Found at i:399734 original size:33 final size:32
Alignment explanation
Indices: 399658--399735 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 32
399648 AAGCTTGTTC
*
399658 AAAA-TTGTTATTTTATTAATTTTGTTTTAAT
1 AAAATTTGTTATTTTATTAATTTTATTTTAAT
* * *
399689 TAAATTTGTTATTTTCTTAATTTTATTTTGACT
1 AAAATTTGTTATTTTATTAATTTTATTTT-AAT
399722 AAAATTAT-TTATTT
1 AAAATT-TGTTATTT
399736 AAGTAAATAG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
31 3 0.08
32 22 0.56
33 13 0.33
34 1 0.03
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (32 bp):
AAAATTTGTTATTTTATTAATTTTATTTTAAT
Found at i:400695 original size:16 final size:16
Alignment explanation
Indices: 400674--400705 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
400664 CTTCACCTTG
400674 TTTATTTCATTTTTAT
1 TTTATTTCATTTTTAT
*
400690 TTTATTTTATTTTTAT
1 TTTATTTCATTTTTAT
400706 CTCTAAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTATTTCATTTTTAT
Found at i:405407 original size:12 final size:12
Alignment explanation
Indices: 405390--405430 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
405380 GTTGCATGAA
405390 TTTCATTTAAAT
1 TTTCATTTAAAT
**
405402 TTTCA-TTGCA-
1 TTTCATTTAAAT
405412 TTTCATTTAAAT
1 TTTCATTTAAAT
405424 TTTCATT
1 TTTCATT
405431 GCATTTTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
10 5 0.22
11 6 0.26
12 12 0.52
ACGTcount: A:0.27, C:0.12, G:0.02, T:0.59
Consensus pattern (12 bp):
TTTCATTTAAAT
Found at i:405414 original size:22 final size:22
Alignment explanation
Indices: 405389--405436 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
405379 AGTTGCATGA
405389 ATTTCATTTAAATTTTCATTGC
1 ATTTCATTTAAATTTTCATTGC
405411 ATTTCATTTAAATTTTCATTGC
1 ATTTCATTTAAATTTTCATTGC
405433 ATTT
1 ATTT
405437 TTATTGTCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.27, C:0.12, G:0.04, T:0.56
Consensus pattern (22 bp):
ATTTCATTTAAATTTTCATTGC
Found at i:421054 original size:30 final size:30
Alignment explanation
Indices: 421017--421177 Score: 173
Period size: 30 Copynumber: 5.4 Consensus size: 30
421007 AAACCAGGTT
*
421017 AAATTTGACTTTTTGGAAAGTTTAGGGGTC
1 AAATTTGAATTTTTGGAAAGTTTAGGGGTC
* * *
421047 TAATTTGAATTTTTGGAAAGTTCAAGGGTC
1 AAATTTGAATTTTTGGAAAGTTTAGGGGTC
** *
421077 AAATTCAAATTTTTGGAAAGTTTAGAGGTC
1 AAATTTGAATTTTTGGAAAGTTTAGGGGTC
* * *
421107 AAATTTGAATTTTTGGAAAATTTGGGGGTA
1 AAATTTGAATTTTTGGAAAGTTTAGGGGTC
* * *
421137 AAACTT-AGATTTCTGGAAAG-TTCGAGGGTC
1 AAATTTGA-ATTTTTGGAAAGTTTAG-GGGTC
421167 AAATTTGAATT
1 AAATTTGAATT
421178 CTTAGATAGT
Statistics
Matches: 106, Mismatches: 22, Indels: 6
0.79 0.16 0.04
Matches are distributed among these distances:
29 4 0.04
30 101 0.95
31 1 0.01
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.38
Consensus pattern (30 bp):
AAATTTGAATTTTTGGAAAGTTTAGGGGTC
Found at i:421170 original size:90 final size:89
Alignment explanation
Indices: 421012--421198 Score: 223
Period size: 90 Copynumber: 2.1 Consensus size: 89
421002 CATTAAAACC
* * * ** * *
421012 AGGTTAAATTTGACTTTTTGGAAAGTTTAGGGGTCTAATTTGAATTTTTGGAAAGTTCAAGGGTC
1 AGGTCAAATTTGAATTTTTGGAAAATTTAGGGGTAAAATTAGAATTTCTGGAAAGTTCAAGGGTC
* *
421077 AAATTCAAATTTTTGGAAAGTTTAG
66 AAATTCAAATTCTTAGAAAG-TTAG
* *
421102 AGGTCAAATTTGAATTTTTGGAAAATTTGGGGGTAAAACTTAG-ATTTCTGGAAAGTTCGAGGGT
1 AGGTCAAATTTGAATTTTTGGAAAATTTAGGGGTAAAA-TTAGAATTTCTGGAAAGTTCAAGGGT
** *
421166 CAAATTTGAATTCTTAGATAGTTAG
65 CAAATTCAAATTCTTAGAAAGTTAG
421191 AGGTCAAA
1 AGGTCAAA
421199 ACACAATTTT
Statistics
Matches: 82, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
89 12 0.15
90 67 0.82
91 3 0.04
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.37
Consensus pattern (89 bp):
AGGTCAAATTTGAATTTTTGGAAAATTTAGGGGTAAAATTAGAATTTCTGGAAAGTTCAAGGGTC
AAATTCAAATTCTTAGAAAGTTAG
Found at i:424213 original size:36 final size:33
Alignment explanation
Indices: 424171--424262 Score: 113
Period size: 36 Copynumber: 2.8 Consensus size: 33
424161 TGGTAACAAG
424171 CATGACCTTTGGGTCAATAGGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAATAGGGAGTAAAA--AGC-T
*
424207 CATGACCTTTGGGTCAACAGGGAGT---AAGCT
1 CATGACCTTTGGGTCAATAGGGAGTAAAAAGCT
424237 --TGACCTTTGGGTCAATAGGGAGTAAA
1 CATGACCTTTGGGTCAATAGGGAGTAAA
424263 TCAGATATCT
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
28 22 0.43
30 1 0.02
31 3 0.06
33 1 0.02
36 24 0.47
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.25
Consensus pattern (33 bp):
CATGACCTTTGGGTCAATAGGGAGTAAAAAGCT
Found at i:430403 original size:63 final size:58
Alignment explanation
Indices: 430311--430477 Score: 198
Period size: 63 Copynumber: 2.8 Consensus size: 58
430301 TTATTATTTA
*
430311 TTTATTTATTTATCTATATTCATAAAATAATAAATAAATAACAAAACAAAATTAATATTAT
1 TTTATTTATTTATTTATATTCATAAAATAATAAATAAAT-A-AAAA-AAAATTAATATTAT
* * *
430372 TTTACATTTATTTATTTATATTCATACAATAATAAATAAAT--AAATAAGTTAATATTAT
1 TTT--ATTTATTTATTTATATTCATAAAATAATAAATAAATAAAAAAAAATTAATATTAT
*
430430 TTTA--TATTTATTTATATTCATATAATAAATAAATAAATAAAAATAAAA
1 TTTATTTATTTATTTATATTCATAAAAT-AATAAATAAATAAAAA-AAAA
430478 AAGATAAGAA
Statistics
Matches: 93, Mismatches: 7, Indels: 15
0.81 0.06 0.13
Matches are distributed among these distances:
54 21 0.23
55 11 0.12
56 1 0.01
57 3 0.03
58 17 0.18
59 3 0.03
61 3 0.03
63 34 0.37
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (58 bp):
TTTATTTATTTATTTATATTCATAAAATAATAAATAAATAAAAAAAAATTAATATTAT
Found at i:434715 original size:46 final size:47
Alignment explanation
Indices: 434664--434764 Score: 116
Period size: 46 Copynumber: 2.2 Consensus size: 47
434654 AGTTGGATCC
** * * *
434664 AAATTAAACTCTAAATTATA-AATTATAATCCTTAAAAGATAATTTA
1 AAATTAAACTCTAAACAATATAATAATAATCCTAAAAAGAGAATTTA
* *
434710 AAATTAAA-TCTAAACAATATCATAATAATCCTAAAAATAGAATTTA
1 AAATTAAACTCTAAACAATATAATAATAATCCTAAAAAGAGAATTTA
*
434756 AATTTAAAC
1 AAATTAAAC
434765 AAAGTTTTAT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
45 9 0.20
46 36 0.80
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (47 bp):
AAATTAAACTCTAAACAATATAATAATAATCCTAAAAAGAGAATTTA
Found at i:438141 original size:16 final size:16
Alignment explanation
Indices: 438109--438149 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
438099 TAAAAAAAGA
*
438109 AAATTAAAATTAAGTT
1 AAATTAAATTTAAGTT
* *
438125 AAGTTAAATTTACGTT
1 AAATTAAATTTAAGTT
438141 AAATTAAAT
1 AAATTAAAT
438150 AGTTGGTCAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.39
Consensus pattern (16 bp):
AAATTAAATTTAAGTT
Found at i:444733 original size:50 final size:50
Alignment explanation
Indices: 444670--444995 Score: 380
Period size: 50 Copynumber: 6.6 Consensus size: 50
444660 TATATAAATA
* * * * *
444670 CGTAAACGTATATATAAGTTGACGAGCGTAAACATGTGCAAGCTGGGGAG
1 CGTAAATGCATATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGGCGAG
* * *
444720 AGTAAATGCATATAT-AGTTGACAAGCGTAAACGTGTGCAAGCTGGCGAG
1 CGTAAATGCATATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGGCGAG
* * * *
444769 CGTAAACGCATATATAAGCTGGCGAGCGTAAACATGTGCAAGTTGGCGAG
1 CGTAAATGCATATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGGCGAG
444819 CGTAAA--C-TCATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGGCGAG
1 CGTAAATGCAT-ATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGGCGAG
* * * *
444867 CATAAATGCATATATAAGCTGACGAGAGTAAACGTGTGCAAGTTGGTGAG
1 CGTAAATGCATATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGGCGAG
* * * *
444917 CGTAAATGCATATAT-GGCTGACGAGTGTAAACGTTTGCAAGCTGACGAG
1 CGTAAATGCATATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGGCGAG
* *
444966 CGTAAA--CATATGA-AAGCTGGCGAGTGTAAA
1 CGTAAATGCATAT-ATAAGCTGACGAGCGTAAA
444996 ACATAATGAA
Statistics
Matches: 240, Mismatches: 29, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
47 6 0.03
48 57 0.24
49 78 0.32
50 98 0.41
51 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.22
Consensus pattern (50 bp):
CGTAAATGCATATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGGCGAG
Found at i:444771 original size:24 final size:24
Alignment explanation
Indices: 444743--444995 Score: 166
Period size: 24 Copynumber: 10.3 Consensus size: 24
444733 ATAGTTGACA
*
444743 AGCGTAAACGTGTGCAAGCTGGCG
1 AGCGTAAACGTATGCAAGCTGGCG
**
444767 AGCGTAAACGCATATATAAGCTGGCG
1 AGCGTAAACG--TATGCAAGCTGGCG
* * *
444793 AGCGTAAACATGTGCAAGTTGGCG
1 AGCGTAAACGTATGCAAGCTGGCG
** *
444817 AGCGTAAAC-TCATATAAGCTGACG
1 AGCGTAAACGT-ATGCAAGCTGGCG
*
444841 AGCGTAAACGTGTGCAAGCTGGCG
1 AGCGTAAACGTATGCAAGCTGGCG
* * ** *
444865 AGCATAAATGCATATATAAGCTGACG
1 AGCGTAAA--CGTATGCAAGCTGGCG
* * * *
444891 AGAGTAAACGTGTGCAAGTTGGTG
1 AGCGTAAACGTATGCAAGCTGGCG
* * ** * *
444915 AGCGTAAATGCATATATGGCTGACG
1 AGCGTAAACGTATGCA-AGCTGGCG
* * *
444940 AGTGTAAACGTTTGCAAGCTGACG
1 AGCGTAAACGTATGCAAGCTGGCG
* *
444964 AGCGTAAACATATGAAAGCTGGCG
1 AGCGTAAACGTATGCAAGCTGGCG
*
444988 AGTGTAAA
1 AGCGTAAA
444996 ACATAATGAA
Statistics
Matches: 167, Mismatches: 55, Indels: 14
0.71 0.23 0.06
Matches are distributed among these distances:
23 1 0.01
24 114 0.68
25 15 0.09
26 37 0.22
ACGTcount: A:0.33, C:0.17, G:0.30, T:0.21
Consensus pattern (24 bp):
AGCGTAAACGTATGCAAGCTGGCG
Found at i:444984 original size:147 final size:147
Alignment explanation
Indices: 444681--444972 Score: 408
Period size: 147 Copynumber: 2.0 Consensus size: 147
444671 GTAAACGTAT
* * * *
444681 ATATAAGTTGACGAGCGTAAACATGTGCAAGCTGGGGAGAGTAAATGCATATATAGTTGACAAGC
1 ATATAAGCTGACGAGCGTAAACATGTGCAAGCTGGCGAGAGTAAATGCATATATAGCTGACAAGA
*
444746 GTAAACGTGTGCAAGCTGGCGAGCGTAAACGCATATATAAGCTGGCGAGCGTAAACATGTGCAAG
66 GTAAACGTGTGCAAGCTGGCGAGCGTAAACGCATATATAAGCTGACGAGCGTAAACATGTGCAAG
* *
444811 TTGGCGAGCGTAAACTC
131 CTGACGAGCGTAAACTC
* *
444828 ATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGGCGAGCA-TAAATGCATATATAAGCTGACGA
1 ATATAAGCTGACGAGCGTAAACATGTGCAAGCTGGCGAG-AGTAAATGCATATAT-AGCTGACAA
* * * * * * *
444892 GAGTAAACGTGTGCAAGTTGGTGAGCGTAAATGCATATAT-GGCTGACGAGTGTAAACGTTTGCA
64 GAGTAAACGTGTGCAAGCTGGCGAGCGTAAACGCATATATAAGCTGACGAGCGTAAACATGTGCA
444956 AGCTGACGAGCGTAAAC
129 AGCTGACGAGCGTAAAC
444973 ATATGAAAGC
Statistics
Matches: 127, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
147 83 0.65
148 44 0.35
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (147 bp):
ATATAAGCTGACGAGCGTAAACATGTGCAAGCTGGCGAGAGTAAATGCATATATAGCTGACAAGA
GTAAACGTGTGCAAGCTGGCGAGCGTAAACGCATATATAAGCTGACGAGCGTAAACATGTGCAAG
CTGACGAGCGTAAACTC
Found at i:445666 original size:71 final size:71
Alignment explanation
Indices: 445575--445722 Score: 260
Period size: 71 Copynumber: 2.1 Consensus size: 71
445565 ACCTGTATCA
* *
445575 GTAGAAGTTGTAGGGAAAATCTACCTTGCTCTTTGGAACTTATTGTATCGGTAGCTGTATGGGTT
1 GTAGAAGTTATAGGGAAAATCTACCTTGCTCTTTGGAACTTATTGTATCGGTAGCTGTATGAGTT
445640 GTGTCG
66 GTGTCG
*
445646 GTAGAAGTTATAGGGCAAATCTACCTTGCTCTTTGGAACTTATTGTATCGGTAGCTGTATGAGTT
1 GTAGAAGTTATAGGGAAAATCTACCTTGCTCTTTGGAACTTATTGTATCGGTAGCTGTATGAGTT
445711 GTGTCG
66 GTGTCG
*
445717 ATAGAA
1 GTAGAA
445723 CCCATGCTTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 73 1.00
ACGTcount: A:0.24, C:0.13, G:0.28, T:0.36
Consensus pattern (71 bp):
GTAGAAGTTATAGGGAAAATCTACCTTGCTCTTTGGAACTTATTGTATCGGTAGCTGTATGAGTT
GTGTCG
Found at i:450123 original size:24 final size:24
Alignment explanation
Indices: 450069--450151 Score: 80
Period size: 24 Copynumber: 3.4 Consensus size: 24
450059 GCAAGTTGGC
450069 GAGCGTAAACGCATAT-ATAAGCTGACA
1 GAGCGTAAACG--TATGA-AAGCTGA-A
* *
450096 -AGCGTAAACGTGTGCAAGCTGAA
1 GAGCGTAAACGTATGAAAGCTGAA
**
450119 GAGCGTAAACGTATGAAAGCTGGC
1 GAGCGTAAACGTATGAAAGCTGAA
450143 GAGCGTAAA
1 GAGCGTAAA
450152 ATGCAATGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
23 1 0.02
24 37 0.77
26 10 0.21
ACGTcount: A:0.37, C:0.17, G:0.29, T:0.17
Consensus pattern (24 bp):
GAGCGTAAACGTATGAAAGCTGAA
Found at i:450124 original size:50 final size:50
Alignment explanation
Indices: 449982--450151 Score: 179
Period size: 49 Copynumber: 3.5 Consensus size: 50
449972 AAGAAAACAT
* *
449982 ATATATAAGCTGACGAGCGTAAACATGTACAAGCT-AGCGAGCATAAACGC
1 ATATATAAGCTGACGAGCGTAAACATGTGCAAGCTGA-CGAGCGTAAACGC
* * * * * *
450032 ATATAT-AGCTAATGAGCGGAAACTTGTGCAAGTTGGCGAGCGTAAACGC
1 ATATATAAGCTGACGAGCGTAAACATGTGCAAGCTGACGAGCGTAAACGC
* * *
450081 ATATATAAGCTGACAAGCGTAAACGTGTGCAAGCTGAAGAGCGTAAACG-
1 ATATATAAGCTGACGAGCGTAAACATGTGCAAGCTGACGAGCGTAAACGC
*
450130 -TATGA-AAGCTGGCGAGCGTAAA
1 ATAT-ATAAGCTGACGAGCGTAAA
450152 ATGCAATGAA
Statistics
Matches: 99, Mismatches: 18, Indels: 8
0.79 0.14 0.06
Matches are distributed among these distances:
48 18 0.18
49 41 0.41
50 40 0.40
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.19
Consensus pattern (50 bp):
ATATATAAGCTGACGAGCGTAAACATGTGCAAGCTGACGAGCGTAAACGC
Found at i:450802 original size:21 final size:21
Alignment explanation
Indices: 450786--450831 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
450776 GGTTGTTTCG
450786 GTAGAAC-CCATACTTGTATCA
1 GTAGAACACCA-ACTTGTATCA
* *
450807 GTAGAACACCAACTTCTACCA
1 GTAGAACACCAACTTGTATCA
450828 GTAG
1 GTAG
450832 GAAACTGCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (21 bp):
GTAGAACACCAACTTGTATCA
Found at i:455058 original size:23 final size:24
Alignment explanation
Indices: 455031--455094 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 24
455021 TTTAATGTTT
**
455031 ACGAACATGTTCATTTAAC-TTAA
1 ACGAACATGTTCATCGAACATTAA
* *
455054 TCGAACATGTTTA-CGAACATTAA
1 ACGAACATGTTCATCGAACATTAA
455077 ACGAACATGTTCAT-GAAC
1 ACGAACATGTTCATCGAAC
455095 GTATAATTGA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
22 3 0.09
23 30 0.91
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (24 bp):
ACGAACATGTTCATCGAACATTAA
Found at i:456040 original size:29 final size:29
Alignment explanation
Indices: 455960--456046 Score: 81
Period size: 29 Copynumber: 3.0 Consensus size: 29
455950 AAGATTTTCT
*
455960 AGAAAATATTATAAGAAAGTATTTCA-AAA
1 AGAAAATATTATAAGAAAATATTT-AGAAA
* ** **
455989 GGAAAA-A-TGCAATTAAATGATTTAGAAA
1 AGAAAATATTATAAGAAAAT-ATTTAGAAA
456017 AGAAAATATTATAAGAAAATATTTAGAAA
1 AGAAAATATTATAAGAAAATATTTAGAAA
456046 A
1 A
456047 CATATTGTCA
Statistics
Matches: 43, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
27 7 0.16
28 13 0.30
29 16 0.37
30 7 0.16
ACGTcount: A:0.59, C:0.02, G:0.13, T:0.26
Consensus pattern (29 bp):
AGAAAATATTATAAGAAAATATTTAGAAA
Found at i:456487 original size:2 final size:2
Alignment explanation
Indices: 456480--456506 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
456470 AAGAAAAATA
456480 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
456507 AAAATCTTAT
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:461142 original size:23 final size:23
Alignment explanation
Indices: 461054--461142 Score: 99
Period size: 23 Copynumber: 3.8 Consensus size: 23
461044 ACACTAGCGC
* * *
461054 GCCCTCTGTTTAGCACTGTGTGT
1 GCCCTCTGTTAAGCACTTTATGT
*
461077 GCCCTCTGTTAATAGCACTTCATGT
1 GCCCTCTGTT-A-AGCACTTTATGT
461102 GCCCTCTGATT-AGCACTTTATGT
1 GCCCTCTG-TTAAGCACTTTATGT
*
461125 GCCCTCTGTTAAGTACTT
1 GCCCTCTGTTAAGCACTT
461143 CGGTTTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
22 2 0.04
23 35 0.62
25 17 0.30
26 2 0.04
ACGTcount: A:0.16, C:0.27, G:0.19, T:0.38
Consensus pattern (23 bp):
GCCCTCTGTTAAGCACTTTATGT
Found at i:464970 original size:16 final size:17
Alignment explanation
Indices: 464949--464986 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
464939 ATTTGAAACG
*
464949 AAATAGCGAA-GAGAGA
1 AAATAGCAAATGAGAGA
*
464965 AAATAGTAAATGAGAGA
1 AAATAGCAAATGAGAGA
464982 AAATA
1 AAATA
464987 TGAGATTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.61, C:0.03, G:0.24, T:0.13
Consensus pattern (17 bp):
AAATAGCAAATGAGAGA
Found at i:477546 original size:20 final size:21
Alignment explanation
Indices: 477507--477551 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
477497 AAATTGAGTG
* *
477507 AAATAAAATTCGAGTTGAATC
1 AAATAAAATTCGAATCGAATC
*
477528 AAATAAAA-TCGAATCGAATG
1 AAATAAAATTCGAATCGAATC
477548 AAAT
1 AAAT
477552 TATTCAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.53, C:0.09, G:0.13, T:0.24
Consensus pattern (21 bp):
AAATAAAATTCGAATCGAATC
Done.