Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000827.1 Kokia drynarioides strain JFW-HI SEQ_111921, 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: 174284
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 42 characters in sequence are not A, C, G, or T
Found at i:2920 original size:5 final size:5
Alignment explanation
Indices: 2910--2937 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2900 ATTCCTGTTA
2910 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
2938 GACTACACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:3040 original size:49 final size:48
Alignment explanation
Indices: 2964--3056 Score: 141
Period size: 49 Copynumber: 1.9 Consensus size: 48
2954 TCCGTATAAA
* *
2964 AGTACATTCTTCTATTTGATATTGATTAGAATAAGGTGTTTCAATATT
1 AGTACATTCTTCTATTAGAGATTGATTAGAATAAGGTGTTTCAATATT
* *
3012 AGTACATTACTTTTATTAGAGATTGATTAGAATAAGGTTTTTCAA
1 AGTACATT-CTTCTATTAGAGATTGATTAGAATAAGGTGTTTCAA
3057 CCTATCAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
48 8 0.20
49 32 0.80
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (48 bp):
AGTACATTCTTCTATTAGAGATTGATTAGAATAAGGTGTTTCAATATT
Found at i:3508 original size:2 final size:2
Alignment explanation
Indices: 3501--3539 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3491 ATTTTGGTGT
3501 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3540 GCATGGTTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4676 original size:12 final size:11
Alignment explanation
Indices: 4655--4684 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
4645 AGGACGATGG
4655 TCGACGACAGA
1 TCGACGACAGA
4666 TCGAGCGACAGA
1 TCGA-CGACAGA
4678 TCGACGA
1 TCGACGA
4685 TTGAGGAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.33, C:0.27, G:0.30, T:0.10
Consensus pattern (11 bp):
TCGACGACAGA
Found at i:5146 original size:30 final size:30
Alignment explanation
Indices: 5112--5369 Score: 131
Period size: 30 Copynumber: 8.7 Consensus size: 30
5102 TATTTTAGCT
5112 AAAAATTACATTTTAACCCCTAAACTTTCC
1 AAAAATTACATTTTAACCCCTAAACTTTCC
* * * *
5142 AAAAACTATATTTTGATCCCTAAACTTTCC
1 AAAAATTACATTTTAACCCCTAAACTTTCC
* ** *
5172 ATAAATTTGATTTTGAA-CCCTCAAAC-TTCT
1 AAAAATTACATTTT-AACCCCT-AAACTTTCC
**
5202 AAAAATTTGATTTTAACCCCTAAACTTTCC
1 AAAAATTACATTTTAACCCCTAAACTTTCC
* ** ** * **
5232 ATAAATTTGATTTTGGCACCTAAACTTTTT
1 AAAAATTACATTTTAACCCCTAAACTTTCC
* *
5262 TAAAATTA-ATTTTTTGACCCC-AAACTTTTCC
1 AAAAATTACA--TTTTAACCCCTAAAC-TTTCC
* **
5293 -AAAATTACATTTTGA-CTATAAAAC-TTCC
1 AAAAATTACATTTTAACCCCT-AAACTTTCC
* * *
5321 TAAAATCACATTTTAACCCC-AAA-TTCTTC
1 AAAAATTACATTTTAACCCCTAAACTT-TCC
*
5350 AAAACTT-CATTTTTAACCCC
1 AAAAATTACA-TTTTAACCCC
5370 GTTTCTTTCT
Statistics
Matches: 178, Mismatches: 35, Indels: 31
0.73 0.14 0.13
Matches are distributed among these distances:
28 11 0.06
29 42 0.24
30 108 0.61
31 17 0.10
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.38
Consensus pattern (30 bp):
AAAAATTACATTTTAACCCCTAAACTTTCC
Found at i:5206 original size:60 final size:61
Alignment explanation
Indices: 5121--5259 Score: 171
Period size: 60 Copynumber: 2.3 Consensus size: 61
5111 TAAAAATTAC
* *
5121 ATTTT-AACCCCTAAACTTTCCAAAAACTAT-ATTTTGATCCCTAAACTTTCCATAAATTTG
1 ATTTTGAACCCCTAAACTTTCCAAAAA-TATGATTTTAACCCCTAAACTTTCCATAAATTTG
* *
5181 ATTTTGAA-CCCTCAAAC-TTCTAAAAATTTGATTTTAACCCCTAAACTTTCCATAAATTTG
1 ATTTTGAACCCCT-AAACTTTCCAAAAATATGATTTTAACCCCTAAACTTTCCATAAATTTG
* *
5241 ATTTTG-GCACCTAAACTTT
1 ATTTTGAACCCCTAAACTTT
5260 TTTAAAATTA
Statistics
Matches: 68, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
59 6 0.09
60 56 0.82
61 6 0.09
ACGTcount: A:0.34, C:0.22, G:0.05, T:0.39
Consensus pattern (61 bp):
ATTTTGAACCCCTAAACTTTCCAAAAATATGATTTTAACCCCTAAACTTTCCATAAATTTG
Found at i:5305 original size:90 final size:90
Alignment explanation
Indices: 5110--5305 Score: 213
Period size: 90 Copynumber: 2.2 Consensus size: 90
5100 CCTATTTTAG
*
5110 CTAAAAATTACATTTTAACCCCTAAACTTTCCAAAAACTATATTTTGATCCCTAAACTTTCCATA
1 CTAAAAATTACATTTTAACCCCTAAACTTTCCAAAAACTATATTTTGAGCCCTAAACTTTCCATA
* *
5175 AATTTGATTTTGAACCCTCAAACTT
66 AAATTAATTTTGAACCCTCAAACTT
** * * **
5200 CTAAAAATTTGATTTTAACCCCTAAACTTTCCATAAA-TTTGATTTTG-GCACCTAAACTTT-TT
1 CTAAAAATTACATTTTAACCCCTAAACTTTCCAAAAACTAT-ATTTTGAGC-CCTAAACTTTCCA
5262 TAAAATTAATTTTTTG-ACCC-CAAACTT
64 TAAAATTAA--TTTTGAACCCTCAAACTT
* *
5289 TTCCAAAATTACATTTT
1 CT-AAAAATTACATTTT
5306 GACTATAAAA
Statistics
Matches: 88, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
89 18 0.20
90 65 0.74
91 5 0.06
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.40
Consensus pattern (90 bp):
CTAAAAATTACATTTTAACCCCTAAACTTTCCAAAAACTATATTTTGAGCCCTAAACTTTCCATA
AAATTAATTTTGAACCCTCAAACTT
Found at i:13757 original size:93 final size:93
Alignment explanation
Indices: 13590--13759 Score: 322
Period size: 93 Copynumber: 1.8 Consensus size: 93
13580 AGATAATGGG
*
13590 TAATGGGCTAATATCACAAGGAATACAAGGATCTACGTGTATTATTCTAGAAATTTTCTAAATGA
1 TAATAGGCTAATATCACAAGGAATACAAGGATCTACGTGTATTATTCTAGAAATTTTCTAAATGA
*
13655 TACAGGGACCTAAAAAAGGACTACCAGT
66 TACAAGGACCTAAAAAAGGACTACCAGT
13683 TAATAGGCTAATATCACAAGGAATACAAGGATCTACGTGTATTATTCTAGAAATTTTCTAAATGA
1 TAATAGGCTAATATCACAAGGAATACAAGGATCTACGTGTATTATTCTAGAAATTTTCTAAATGA
13748 TACAAGGACCTA
66 TACAAGGACCTA
13760 TTACCAAATA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (93 bp):
TAATAGGCTAATATCACAAGGAATACAAGGATCTACGTGTATTATTCTAGAAATTTTCTAAATGA
TACAAGGACCTAAAAAAGGACTACCAGT
Found at i:14155 original size:49 final size:49
Alignment explanation
Indices: 14088--14862 Score: 562
Period size: 49 Copynumber: 15.7 Consensus size: 49
14078 CAGTATCTTA
* * * *
14088 GAAGATGTGATGGGAAAGGTTAAGGCCGTAACGGTGAACCCAGTACCAT
1 GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCAGTACCAT
* * * * * *
14137 GAATATATGAAGGGAAAGGTTGAGGTCACAACGGCGAACTC-GATACCTT
1 GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCAG-TACCAT
* * * * *** *
14186 AGAAGATGTG-ATGGAAAGGTTAAAGCCGCAATATTGAACCCGGTACCAT
1 -GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCAGTACCAT
* *
14235 GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTT
1 GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCAGTACCAT
* * * ***
14284 AGAAGATGTGATGGGAAAGGTTAAGGTTACAACGGTGAACCC-GATACCAT
1 -GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCAG-TACCAT
* * * * * *
14334 GAAGATTTGAAGGG-AAGGATTGAGGCCGTAATGGTGAATCCAATACCTT
1 GAAGATATGAAGGGAAAGG-TTGAGGCCGCAACGGTGAACCCAGTACCAT
* * * * * * *
14383 AGAAGATGT-AATAGGAAAGGTTAAGGCCGCAATGATGAACCC-GATTCTAT
1 -GAAGATATGAA-GGGAAAGGTTGAGGCCGCAACGGTGAACCCAG-TACCAT
* * * * ** *
14433 GAAGAGATTAAGGAAAAGGTTGAGGCTGCAACGGCAAACCC-GATACCTT
1 GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCAG-TACCAT
* * *
14482 AGAAGATGTGATA-GGAAAGGTTAAGGCCGCAAAGGTGAACCCAGTACCAT
1 -GAAGATATGA-AGGGAAAGGTTGAGGCCGCAACGGTGAACCCAGTACCAT
* * * *
14532 GAAGATATGAAGGGAAAGGTTGAGGCCACAACGGTGAACTCGGTACCTT
1 GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCAGTACCAT
* * *
14581 AGAAGATATGATGGGAAAGGTTGAGGTCGCAACGGTGAACCCAATACCAT
1 -GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCAGTACCAT
* * * * * **** *
14631 GAAGATTTGAAGGG-AAGGACTGAGGTCGCGACGATGAATTTGGTACCTT
1 GAAGATATGAAGGGAAAGG-TTGAGGCCGCAACGGTGAACCCAGTACCAT
* * *** *
14680 AGAAGATGTGATGGGAAAGGTTGAGGCCGCAACAACGAACCCGGTACCAT
1 -GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCAGTACCAT
* * * **
14730 GAAGATATGAAGGGAAAGGTTGAGGCTGCAACGATGAACCGAACACCAT
1 GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCAGTACCAT
* * * * *
14779 GAAGATATGAAGGGAAAGGTTGAGGCTGTAACGGCGAACCTAGTACCTT
1 GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCAGTACCAT
* * * * *
14828 AGAA-ACATGACGGGAAAGATTGAAGCCACAACGGT
1 -GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGT
14863 AAATCTTATA
Statistics
Matches: 562, Mismatches: 142, Indels: 44
0.75 0.19 0.06
Matches are distributed among these distances:
48 18 0.03
49 341 0.61
50 193 0.34
51 10 0.02
ACGTcount: A:0.35, C:0.16, G:0.31, T:0.19
Consensus pattern (49 bp):
GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCAGTACCAT
Found at i:14357 original size:99 final size:99
Alignment explanation
Indices: 14084--14769 Score: 788
Period size: 99 Copynumber: 6.9 Consensus size: 99
14074 AATCCAGTAT
* *
14084 CTTAGAAGATGTGATGGGAAAGGTTAAGGCCGTAACGGTGAACCC-AGTACCATGAATATATGAA
1 CTTAGAAGATGTGATGGGAAAGGTTAAGGCCGCAACGGTGAACCCGA-TACCATGAAGATATGAA
* * * * *
14148 GGGAAAGGTTGAGGTCACAACGGCGAACTCGATAC
65 GGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTAC
* *** *
14183 CTTAGAAGATGTGAT-GGAAAGGTTAAAGCCGCAATATTGAACCCGGTACCATGAAGATATGAAG
1 CTTAGAAGATGTGATGGGAAAGGTTAAGGCCGCAACGGTGAACCCGATACCATGAAGATATGAAG
14247 GGAAAGGTTGAGGCCGCAACGGTGAACCCGGTAC
66 GGAAAGGTTGAGGCCGCAACGGTGAACCCGGTAC
*** *
14281 CTTAGAAGATGTGATGGGAAAGGTTAAGGTTACAACGGTGAACCCGATACCATGAAGATTTGAAG
1 CTTAGAAGATGTGATGGGAAAGGTTAAGGCCGCAACGGTGAACCCGATACCATGAAGATATGAAG
* * * **
14346 GG-AAGGATTGAGGCCGTAATGGTGAATCCAATAC
66 GGAAAGG-TTGAGGCCGCAACGGTGAACCCGGTAC
* * * * * * * *
14380 CTTAGAAGATGTAATAGGAAAGGTTAAGGCCGCAATGATGAACCCGATTCTATGAAGAGATTAAG
1 CTTAGAAGATGTGATGGGAAAGGTTAAGGCCGCAACGGTGAACCCGATACCATGAAGATATGAAG
* * ** *
14445 GAAAAGGTTGAGGCTGCAACGGCAAACCCGATAC
66 GGAAAGGTTGAGGCCGCAACGGTGAACCCGGTAC
* *
14479 CTTAGAAGATGTGATAGGAAAGGTTAAGGCCGCAAAGGTGAACCC-AGTACCATGAAGATATGAA
1 CTTAGAAGATGTGATGGGAAAGGTTAAGGCCGCAACGGTGAACCCGA-TACCATGAAGATATGAA
* *
14543 GGGAAAGGTTGAGGCCACAACGGTGAACTCGGTAC
65 GGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTAC
* * * * *
14578 CTTAGAAGATATGATGGGAAAGGTTGAGGTCGCAACGGTGAACCCAATACCATGAAGATTTGAAG
1 CTTAGAAGATGTGATGGGAAAGGTTAAGGCCGCAACGGTGAACCCGATACCATGAAGATATGAAG
* * * * ***
14643 GG-AAGGACTGAGGTCGCGACGATGAATTTGGTAC
66 GGAAAGG-TTGAGGCCGCAACGGTGAACCCGGTAC
* *** *
14677 CTTAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACAACGAACCCGGTACCATGAAGATATGAAG
1 CTTAGAAGATGTGATGGGAAAGGTTAAGGCCGCAACGGTGAACCCGATACCATGAAGATATGAAG
* *
14742 GGAAAGGTTGAGGCTGCAACGATGAACC
66 GGAAAGGTTGAGGCCGCAACGGTGAACC
14770 GAACACCATG
Statistics
Matches: 492, Mismatches: 87, Indels: 16
0.83 0.15 0.03
Matches are distributed among these distances:
98 94 0.19
99 389 0.79
100 9 0.02
ACGTcount: A:0.35, C:0.16, G:0.31, T:0.19
Consensus pattern (99 bp):
CTTAGAAGATGTGATGGGAAAGGTTAAGGCCGCAACGGTGAACCCGATACCATGAAGATATGAAG
GGAAAGGTTGAGGCCGCAACGGTGAACCCGGTAC
Found at i:14596 original size:297 final size:296
Alignment explanation
Indices: 14073--14762 Score: 972
Period size: 297 Copynumber: 2.3 Consensus size: 296
14063 TTGCAACAGC
* * *
14073 GAATCCAGTATCTTAGAAGATGTGATGGGAAAGGTTAAGGCCGTAACGGTGAACCC-AGTACCAT
1 GAATCCAGTACCTTAGAAGATGTGATGGGAAAGGTTAAGGCCGCAACGATGAACCCGA-TACCAT
* * * *
14137 GAATATATGAAGGGAAAGGTTGAGG-TCACAACGGCGAACTCGATACCTTAGAAGATGTGATGGA
65 GAAGATATGAAGGGAAAGGTTGAGGCT-GCAACGGCAAACCCGATACCTTAGAAGATGTGATGGA
* * *
14201 AAGGTTAAAGCCGCAATATTGAACCCGGTACCATGAAGATATGAAGGGAAAGGTTGAGGCCGCAA
129 AAGGTTAAAGCCGCAATAGTGAACCCAGTACCATGAAGATATGAAGGGAAAGGTTGAGGCCACAA
* * *
14266 CGGTGAACCCGGTACCTTAGAAGATGTGATGGGAAAGGTTAAGGTTACAACGGTGAACCCGATAC
194 CGGTGAACCCGGTACCTTAGAAGATATGATGGGAAAGGTTAAGGTCACAACGGTGAACCCAATAC
* * * *
14331 CATGAAGATTTGAAGGGAAGGATTGAGGCCGTAATGGT
259 CATGAAGATTTGAAGGGAAGGACTGAGGCCGCAACGAT
* * * * * *
14369 GAATCCAATACCTTAGAAGATGTAATAGGAAAGGTTAAGGCCGCAATGATGAACCCGATTCTATG
1 GAATCCAGTACCTTAGAAGATGTGATGGGAAAGGTTAAGGCCGCAACGATGAACCCGATACCATG
* * *
14434 AAGAGATTAAGGAAAAGGTTGAGGCTGCAACGGCAAACCCGATACCTTAGAAGATGTGATAGGAA
66 AAGATATGAAGGGAAAGGTTGAGGCTGCAACGGCAAACCCGATACCTTAGAAGATGTGAT-GGAA
*
14499 AGGTTAAGGCCGCAA-AGGTGAACCCAGTACCATGAAGATATGAAGGGAAAGGTTGAGGCCACAA
130 AGGTTAAAGCCGCAATA-GTGAACCCAGTACCATGAAGATATGAAGGGAAAGGTTGAGGCCACAA
* * *
14563 CGGTGAACTCGGTACCTTAGAAGATATGATGGGAAAGGTTGAGGTCGCAACGGTGAACCCAATAC
194 CGGTGAACCCGGTACCTTAGAAGATATGATGGGAAAGGTTAAGGTCACAACGGTGAACCCAATAC
* *
14628 CATGAAGATTTGAAGGGAAGGACTGAGGTCGCGACGAT
259 CATGAAGATTTGAAGGGAAGGACTGAGGCCGCAACGAT
*** * * * *
14666 GAATTTGGTACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACAACGAACCCGGTACCATG
1 GAATCCAGTACCTTAGAAGATGTGATGGGAAAGGTTAAGGCCGCAACGATGAACCCGATACCATG
14731 AAGATATGAAGGGAAAGGTTGAGGCTGCAACG
66 AAGATATGAAGGGAAAGGTTGAGGCTGCAACG
14763 ATGAACCGAA
Statistics
Matches: 342, Mismatches: 48, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
296 106 0.31
297 236 0.69
ACGTcount: A:0.34, C:0.16, G:0.31, T:0.19
Consensus pattern (296 bp):
GAATCCAGTACCTTAGAAGATGTGATGGGAAAGGTTAAGGCCGCAACGATGAACCCGATACCATG
AAGATATGAAGGGAAAGGTTGAGGCTGCAACGGCAAACCCGATACCTTAGAAGATGTGATGGAAA
GGTTAAAGCCGCAATAGTGAACCCAGTACCATGAAGATATGAAGGGAAAGGTTGAGGCCACAACG
GTGAACCCGGTACCTTAGAAGATATGATGGGAAAGGTTAAGGTCACAACGGTGAACCCAATACCA
TGAAGATTTGAAGGGAAGGACTGAGGCCGCAACGAT
Found at i:14860 original size:98 final size:98
Alignment explanation
Indices: 14495--14860 Score: 254
Period size: 99 Copynumber: 3.7 Consensus size: 98
14485 AGATGTGATA
* ** * * *
14495 GGAAAGGTTAAGGCCGCAA-AGGTGAACCCAGTACCATGAAGATATGAAGGGAAAGGTTGAGGCC
1 GGAAAGGTTGAGGCCGCAACA-ACGAACCCAGTACCATGAAGACATGAAGGGAAAGATTGAAGCC
* ** * *
14559 ACAACGGTGAACTCG-GTACCTTAGAAGATATGATG
65 ACAACGATGAAC-CGAACACCAT-GAAGATATGAAG
* *** * ** * * * * *
14594 GGAAAGGTTGAGGTCGCAACGGTGAACCCAATACCATGAAGATTTGAAGGGAAGGACTGAGGTCG
1 GGAAAGGTTGAGGCCGCAACAACGAACCCAGTACCATGAAGACATGAAGGGAAAGATTGAAGCCA
* ** ** * * *
14659 CGACGATGAATTTG-GTACCTTAGAAGATGTGATG
66 CAACGATGAA-CCGAACACCAT-GAAGATATGAAG
* * * * **
14693 GGAAAGGTTGAGGCCGCAACAACGAACCCGGTACCATGAAGATATGAAGGGAAAGGTTGAGGCTG
1 GGAAAGGTTGAGGCCGCAACAACGAACCCAGTACCATGAAGACATGAAGGGAAAGATTGAAGCCA
14758 CAACGATGAACCGAACACCATGAAGATATGAAG
66 CAACGATGAACCGAACACCATGAAGATATGAAG
* * ** * * *
14791 GGAAAGGTTGAGGCTGTAACGGCGAACCTAGTACCTTAGAA-ACATGACGGGAAAGATTGAAGCC
1 GGAAAGGTTGAGGCCGCAACAACGAACCCAGTACCAT-GAAGACATGAAGGGAAAGATTGAAGCC
14855 ACAACG
65 ACAACG
14861 GTAAATCTTA
Statistics
Matches: 215, Mismatches: 48, Indels: 9
0.79 0.18 0.03
Matches are distributed among these distances:
98 64 0.30
99 151 0.70
ACGTcount: A:0.35, C:0.17, G:0.31, T:0.17
Consensus pattern (98 bp):
GGAAAGGTTGAGGCCGCAACAACGAACCCAGTACCATGAAGACATGAAGGGAAAGATTGAAGCCA
CAACGATGAACCGAACACCATGAAGATATGAAG
Found at i:15295 original size:209 final size:209
Alignment explanation
Indices: 14934--15317 Score: 588
Period size: 209 Copynumber: 1.8 Consensus size: 209
14924 TTGAAGTTAC
* * *
14934 AGTGGATTAAAATAATGAAGCAGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAATTCAATG
1 AGTGGATTAAAACAATGAACCAGTCATCTTCCTGATGAGATACAGAGAAGAAGACCAATTCAATG
* * *
14999 AAGCGAAGCTCAATATGAGTGAAACTTCCAAACCCCATATTCTTGATGAGATACAGAGAAGAGAG
66 AAGCGAAGCTCAATATGAGTGAAACTTCCAAACACCATATTCCTGATGAGATACAAAGAAGAGAG
*** *
15064 TCAAAGCAATAAAGTGATCATCTTCCTAATGAGATGCAGAGAAGTGAACCAAATCCGTCTTCTTG
131 TCAAAGCAATAAAACAATCATCTTCCTAATGAGATACAGAGAAGTGAACCAAATCCGTCTTCTTG
15129 ATGAGATATAAAGA
196 ATGAGATATAAAGA
15143 AGTGGATTAAAACAATGAACCAGTCATCTTCCTGATGAGATACAGAGAAGAAGACCAATTCAATG
1 AGTGGATTAAAACAATGAACCAGTCATCTTCCTGATGAGATACAGAGAAGAAGACCAATTCAATG
* * * * * *
15208 AAGTGAAGCTCAATGTGAGTGAAACTTCCAAACACCATGTTCCTGATGAGATACAAAGAGGTGGG
66 AAGCGAAGCTCAATATGAGTGAAACTTCCAAACACCATATTCCTGATGAGATACAAAGAAGAGAG
** * *
15273 TTGAAGTAATAAAACAATCATCTTCCTGATGAGATACAGAGAAGT
131 TCAAAGCAATAAAACAATCATCTTCCTAATGAGATACAGAGAAGT
15318 AGACCAAGAG
Statistics
Matches: 155, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
209 155 1.00
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (209 bp):
AGTGGATTAAAACAATGAACCAGTCATCTTCCTGATGAGATACAGAGAAGAAGACCAATTCAATG
AAGCGAAGCTCAATATGAGTGAAACTTCCAAACACCATATTCCTGATGAGATACAAAGAAGAGAG
TCAAAGCAATAAAACAATCATCTTCCTAATGAGATACAGAGAAGTGAACCAAATCCGTCTTCTTG
ATGAGATATAAAGA
Found at i:17357 original size:57 final size:59
Alignment explanation
Indices: 17174--17454 Score: 245
Period size: 57 Copynumber: 4.8 Consensus size: 59
17164 TTATTTTATC
* * *
17174 TAAAATTTACATTTTAACCCTTAAACTTTCAAAAAATTACATTTTAACCCTTAAACTTTC
1 TAAAAATTACATTTTAACCCTTAAACTTTC-AAAAATTACATTTTAACCCCTAAACTTTT
** * * * *
17234 TAAAAATTTGATTTTGACCCTTAAACTTTCCAAAAATT-CAATTTTGA-TCCTAAACTTTCA
1 TAAAAATTACATTTTAACCCTTAAACTTT-CAAAAATTAC-ATTTTAACCCCTAAACTTT-T
* * *
17294 AAAAAATTA-ATTTTAACCC-CAAACTTTCAAAAATT-CAATTTTGACCCCTAAACTTTT
1 TAAAAATTACATTTTAACCCTTAAACTTTCAAAAATTAC-ATTTTAACCCCTAAACTTTT
* * ** *
17351 TCAAAATTACA-TTT-ACCCTTAAAATTTTTAAAATTACATTTTAACTCCTAAACTTTT
1 TAAAAATTACATTTTAACCCTTAAACTTTCAAAAATTACATTTTAACCCCTAAACTTTT
** * * * *
17408 CCAAAATAATATTTTAACCC-CAAACTTTTCTAAAATTACATTTTAAC
1 TAAAAATTACATTTTAACCCTTAAAC-TTTCAAAAATTACATTTTAAC
17455 TCTAAAACCT
Statistics
Matches: 183, Mismatches: 28, Indels: 21
0.79 0.12 0.09
Matches are distributed among these distances:
56 4 0.02
57 65 0.36
58 25 0.14
59 43 0.23
60 45 0.25
61 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.01, T:0.39
Consensus pattern (59 bp):
TAAAAATTACATTTTAACCCTTAAACTTTCAAAAATTACATTTTAACCCCTAAACTTTT
Found at i:17407 original size:29 final size:28
Alignment explanation
Indices: 17174--17486 Score: 206
Period size: 30 Copynumber: 10.7 Consensus size: 28
17164 TTATTTTATC
*
17174 TAAAATTTACATTTTAACCCTTAAACTTT
1 TAAAAATTACATTTTAACCC-TAAACTTT
*
17203 CAAAAAATTACATTTTAACCCTTAAACTTT
1 -TAAAAATTACATTTTAACCC-TAAACTTT
** *
17233 CTAAAAATTTGATTTTGACCCTTAAACTTT
1 -TAAAAATTACATTTTAACCC-TAAACTTT
* * *
17263 CCAAAAATT-CAATTTTGATCCTAAACTTT
1 -TAAAAATTAC-ATTTTAACCCTAAACTTT
* *
17292 CAAAAAAATTA-ATTTTAACCCCAAACTTT
1 --TAAAAATTACATTTTAACCCTAAACTTT
* *
17321 CAAAAATT-CAATTTTGACCCCTAAACTTTT
1 TAAAAATTAC-ATTTT-AACCCTAAAC-TTT
* *
17351 TCAAAATTACA-TTT-ACCCTTAAAATTT
1 TAAAAATTACATTTTAACCC-TAAACTTT
*
17378 TTAAAATTACATTTTAACTCCTAAACTTT
1 TAAAAATTACATTTTAAC-CCTAAACTTT
* * * *
17407 TCCAAAATAATATTTTAACCCCAAACTTT
1 T-AAAAATTACATTTTAACCCTAAACTTT
* * *
17436 TCTAAAATTACATTTTAACTCTAAAACCTTCC
1 T-AAAAATTACATTTTAACCCT-AAA-CTT-T
*
17468 T-AAAATAACATTTTAACCC
1 TAAAAATTACATTTTAACCC
17487 CAAATTCTTC
Statistics
Matches: 232, Mismatches: 35, Indels: 32
0.78 0.12 0.11
Matches are distributed among these distances:
27 23 0.10
28 12 0.05
29 70 0.30
30 122 0.53
31 4 0.02
32 1 0.00
ACGTcount: A:0.40, C:0.20, G:0.01, T:0.38
Consensus pattern (28 bp):
TAAAAATTACATTTTAACCCTAAACTTT
Found at i:17454 original size:59 final size:59
Alignment explanation
Indices: 17184--17509 Score: 236
Period size: 59 Copynumber: 5.6 Consensus size: 59
17174 TAAAATTTAC
* * *
17184 ATTTTAACCCTTAAAC-TTTCAAAAAATTACATTTTAAC-CCTTAAACTTTCTAAAA-ATTT
1 ATTTTAACCCTCAAACTTTTC-AAAAATTACATTTTAACTCC-TAAACTTTCCAAAATA-AT
* * * * *
17243 GATTTTGACCCTTAAACTTTCCAAAAATT-CAATTTTGA-TCCTAAACTTT-CAAAAAAATT
1 -ATTTTAACCCTCAAACTTTTCAAAAATTAC-ATTTTAACTCCTAAACTTTCCAAAATAA-T
* * * * *
17302 AATTTTAACCC-CAAAC-TTTCAAAAATT-CAATTTTGACCCCTAAACTTTTTCAAAATTAC
1 -ATTTTAACCCTCAAACTTTTCAAAAATTAC-ATTTTAACTCCTAAAC-TTTCCAAAATAAT
* * *
17361 A-TTT-ACCCTTAAAATTTT-TAAAATTACATTTTAACTCCTAAACTTTTCCAAAATAAT
1 ATTTTAACCCTCAAACTTTTCAAAAATTACATTTTAACTCCTAAAC-TTTCCAAAATAAT
* * *
17418 ATTTTAACCC-CAAACTTTTCTAAAATTACATTTTAACT-CTAAAACCTTCCTAAAATAAC
1 ATTTTAACCCTCAAACTTTTCAAAAATTACATTTTAACTCCT-AAACTTTCC-AAAATAAT
*
17477 ATTTTAACCC-CAAA-TTCTTCAAAACTT-CATTTT
1 ATTTTAACCCTCAAACTT-TTCAAAAATTACATTTT
17510 GGACCCAGTT
Statistics
Matches: 222, Mismatches: 27, Indels: 36
0.78 0.09 0.13
Matches are distributed among these distances:
56 4 0.02
57 57 0.26
58 44 0.20
59 78 0.35
60 36 0.16
61 3 0.01
ACGTcount: A:0.39, C:0.21, G:0.01, T:0.39
Consensus pattern (59 bp):
ATTTTAACCCTCAAACTTTTCAAAAATTACATTTTAACTCCTAAACTTTCCAAAATAAT
Found at i:20638 original size:17 final size:17
Alignment explanation
Indices: 20607--20640 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20597 CCGTAATACT
**
20607 AAAATGCAATGACAATG
1 AAAATGCAACAACAATG
20624 AAAATGCAACAACAATG
1 AAAATGCAACAACAATG
20641 CTTACTAACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (17 bp):
AAAATGCAACAACAATG
Found at i:24683 original size:56 final size:56
Alignment explanation
Indices: 24597--24706 Score: 211
Period size: 56 Copynumber: 2.0 Consensus size: 56
24587 GGGTTTGAGG
24597 TGTCACATTAAAACAAAAGAGCCTTCCAGTATAATCAACTTAATCGTTTTCTCCAT
1 TGTCACATTAAAACAAAAGAGCCTTCCAGTATAATCAACTTAATCGTTTTCTCCAT
*
24653 TGTCACATTAAAACAAAAGAGCCTTCCAGTATAATCAACTTAATTGTTTTCTCC
1 TGTCACATTAAAACAAAAGAGCCTTCCAGTATAATCAACTTAATCGTTTTCTCC
24707 GCCAAAGGCG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.33
Consensus pattern (56 bp):
TGTCACATTAAAACAAAAGAGCCTTCCAGTATAATCAACTTAATCGTTTTCTCCAT
Found at i:31424 original size:23 final size:23
Alignment explanation
Indices: 31397--31906 Score: 662
Period size: 23 Copynumber: 22.2 Consensus size: 23
31387 ATCTTAATTC
*
31397 TTTAAGCACAAATCAGATTAATA
1 TTTAAGCACAAATCACATTAATA
*
31420 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
31443 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
31466 TTTAAGTATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
31489 TTTGAGCAGAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
31512 TTTAAGCACAAAACACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
31535 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
31558 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
31581 CTTAAACACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
** * *
31604 TTTAAATATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
31627 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
31650 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
31673 TTTAATCATAAATCATATT-ATA
1 TTTAAGCACAAATCACATTAATA
*
31695 TTTAAACACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
31718 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
31741 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
31764 TTTAAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* * * *
31787 TTTGAGAACAAATCATATTAGTA
1 TTTAAGCACAAATCACATTAATA
*
31810 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
31833 CTTAAGTACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
31856 TTTAATCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
31879 TTTAATCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
31902 TTTAA
1 TTTAA
31907 ACATAGATAT
Statistics
Matches: 426, Mismatches: 60, Indels: 2
0.87 0.12 0.00
Matches are distributed among these distances:
22 19 0.04
23 407 0.96
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.35
Consensus pattern (23 bp):
TTTAAGCACAAATCACATTAATA
Found at i:39769 original size:16 final size:16
Alignment explanation
Indices: 39748--39778 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39738 ATAATGTGAA
39748 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
39764 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
39779 GGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:40657 original size:38 final size:38
Alignment explanation
Indices: 40606--40706 Score: 100
Period size: 38 Copynumber: 2.7 Consensus size: 38
40596 GGATGCAATT
* * *
40606 GAATACTTATGCAGTGACA-TTTCTGGGTGCAATTT-GAA
1 GAATATTTATGCAGCGACAGTCT-TGGGTGC-ATTTCGAA
40644 GAATATTTATGCAGCGACAGTCTTGGGTGCATTTCGAA
1 GAATATTTATGCAGCGACAGTCTTGGGTGCATTTCGAA
** * *
40682 -AATATTCCTGCGGCGACAGTTTTGG
1 GAATATTTATGCAGCGACAGTCTTGG
40707 TGAAATCTGG
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
37 25 0.46
38 27 0.50
39 2 0.04
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.33
Consensus pattern (38 bp):
GAATATTTATGCAGCGACAGTCTTGGGTGCATTTCGAA
Found at i:40698 original size:37 final size:38
Alignment explanation
Indices: 40577--40706 Score: 105
Period size: 37 Copynumber: 3.6 Consensus size: 38
40567 TCTGTACATG
* *
40577 TTCATGCAGCGACATTCTTGGATGCAA-TT---GAATA
1 TTCATGCAGCGACAGTCTTGGGTGCAATTTGAAGAATA
* *
40611 CTT-ATGCAGTGACA-TTTCTGGGTGCAATTTGAAGAATA
1 -TTCATGCAGCGACAGTCT-TGGGTGCAATTTGAAGAATA
*
40649 TTTATGCAGCGACAGTCTTGGGTGC-ATTTCGAA-AATA
1 TTCATGCAGCGACAGTCTTGGGTGCAATTT-GAAGAATA
* * *
40686 TTCCTGCGGCGACAGTTTTGG
1 TTCATGCAGCGACAGTCTTGG
40707 TGAAATCTGG
Statistics
Matches: 78, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
33 2 0.03
34 18 0.23
35 4 0.05
37 27 0.35
38 25 0.32
39 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (38 bp):
TTCATGCAGCGACAGTCTTGGGTGCAATTTGAAGAATA
Found at i:40767 original size:38 final size:38
Alignment explanation
Indices: 40690--40793 Score: 133
Period size: 38 Copynumber: 2.8 Consensus size: 38
40680 AAAATATTCC
*
40690 TGCGGCGACAGTTTTGGTG---AAATCTGGAAGTGCTCA
1 TGCGGCGACAGTTTTGG-GCACAAATTTGGAAGTGCTCA
* *
40726 TGCGGTGACAGTTTTGGGCACAAATTTGGAAGTGCTTA
1 TGCGGCGACAGTTTTGGGCACAAATTTGGAAGTGCTCA
* *
40764 TGCGGCGATAGTTTTGGGCGCAAATTTGGA
1 TGCGGCGACAGTTTTGGGCACAAATTTGGA
40794 TGTTATTTTG
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
35 1 0.02
36 16 0.27
38 42 0.71
ACGTcount: A:0.22, C:0.14, G:0.34, T:0.30
Consensus pattern (38 bp):
TGCGGCGACAGTTTTGGGCACAAATTTGGAAGTGCTCA
Found at i:41449 original size:15 final size:18
Alignment explanation
Indices: 41415--41452 Score: 55
Period size: 15 Copynumber: 2.3 Consensus size: 18
41405 GGAAAGAGCC
41415 TGTGAACTGAGATAGAAT
1 TGTGAACTGAGATAGAAT
41433 TGTGAACT-AG-T-GAAT
1 TGTGAACTGAGATAGAAT
41448 TGTGA
1 TGTGA
41453 GCTACCTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 9 0.45
16 1 0.05
17 2 0.10
18 8 0.40
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (18 bp):
TGTGAACTGAGATAGAAT
Found at i:48944 original size:16 final size:16
Alignment explanation
Indices: 48923--48954 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
48913 TAGAAATTTT
*
48923 ATGTTAAAGGACTAAA
1 ATGTTAAAGGAATAAA
48939 ATGTTAAAGGAATAAA
1 ATGTTAAAGGAATAAA
48955 TTTGTAAGGA
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:0.53, C:0.03, G:0.19, T:0.25
Consensus pattern (16 bp):
ATGTTAAAGGAATAAA
Found at i:49718 original size:93 final size:93
Alignment explanation
Indices: 49580--49856 Score: 360
Period size: 93 Copynumber: 3.0 Consensus size: 93
49570 ATTGTTAGGG
* * *
49580 AACAATTATATGTATAGATACCATATCGATGACTGAGGTACCGCATATGTTACGAGTCCTCGTCA
1 AACAATTATATGTA-CGATATCATATCGATGGCTGAGGTACCGCATATGTTACGAGTCCTCGTCA
49645 GCTTAGTGTGAGCAGCATCGTATACTAGT
65 GCTTAGTGTGAGCAGCATCGTATACTAGT
* * ** *
49674 AACAATTATATGTACGATATCGTATCAATGGCTGAGGTACCGCATATGTTTTGAGTCATCGTCAG
1 AACAATTATATGTACGATATCATATCGATGGCTGAGGTACCGCATATGTTACGAGTCCTCGTCAG
*
49739 CTTAGTGTGA-CTAGCATCGTATACTGGT
66 CTTAGTGTGAGC-AGCATCGTATACTAGT
* * * * *
49767 AACAGTTATATGAAC-ATATACCATATTGATGGCTGAGGTACCGCATATGTTGCGAGTCCTTGTC
1 AACAATTATATGTACGATAT--CATATCGATGGCTGAGGTACCGCATATGTTACGAGTCCTCGTC
* *
49831 AGCTTAGTGTGAGCAGTATCATATAC
64 AGCTTAGTGTGAGCAGCATCGTATAC
49857 CGATAACAAA
Statistics
Matches: 159, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
92 5 0.03
93 81 0.51
94 72 0.45
95 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (93 bp):
AACAATTATATGTACGATATCATATCGATGGCTGAGGTACCGCATATGTTACGAGTCCTCGTCAG
CTTAGTGTGAGCAGCATCGTATACTAGT
Found at i:49864 original size:94 final size:95
Alignment explanation
Indices: 49580--49865 Score: 341
Period size: 94 Copynumber: 3.1 Consensus size: 95
49570 ATTGTTAGGG
* * * *
49580 AACAATTATATGTA-TAGATACCATATCGATGACTGAGGTACCGCATATGTTACGAGTCCTCGTC
1 AACAATTATATGAACGATATACCATATCGATGGCTGAGGTACCGCATATGTTACGAGTCCTCGTC
*
49644 AGCTTAGTGTGAGCAGCATCGTATA-CTAGT
66 AGCTTAGTGTGAGCAGCATCGTATACCGA-T
* * * ** *
49674 AACAATTATATGTACGATAT--CGTATCAATGGCTGAGGTACCGCATATGTTTTGAGTCATCGTC
1 AACAATTATATGAACGATATACCATATCGATGGCTGAGGTACCGCATATGTTACGAGTCCTCGTC
* *
49737 AGCTTAGTGTGA-CTAGCATCGTATACTGGT
66 AGCTTAGTGTGAGC-AGCATCGTATACCGAT
* * * *
49767 AACAGTTATATGAAC-ATATACCATATTGATGGCTGAGGTACCGCATATGTTGCGAGTCCTTGTC
1 AACAATTATATGAACGATATACCATATCGATGGCTGAGGTACCGCATATGTTACGAGTCCTCGTC
* *
49831 AGCTTAGTGTGAGCAGTATCATATACCGAT
66 AGCTTAGTGTGAGCAGCATCGTATACCGAT
49861 AACAA
1 AACAA
49866 AAATGACATT
Statistics
Matches: 161, Mismatches: 25, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
92 5 0.03
93 74 0.46
94 78 0.48
95 4 0.02
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (95 bp):
AACAATTATATGAACGATATACCATATCGATGGCTGAGGTACCGCATATGTTACGAGTCCTCGTC
AGCTTAGTGTGAGCAGCATCGTATACCGAT
Found at i:55278 original size:94 final size:94
Alignment explanation
Indices: 55003--55293 Score: 306
Period size: 94 Copynumber: 3.1 Consensus size: 94
54993 GCATATTCTC
* * * * * *
55003 GTCAGCTTAGTGTTAGCACCATCGT-TA--GGGAACAGTTATATGTACACATATTGTATCGATGG
1 GTCAGCTTAGTGTAAGCAACATCGTATACTGGTAACAGTTATATGAACAAATATCGTATCGATGG
* *
55065 CTGAGGTACCGCATATGTTGC-ATGTACTC
66 CTGAGGTACCGCATATGTTGCGA-GTCCTT
* * * * * * *
55094 GTCAGCTTAATGTGAGCAACATCATATACTAGTAAAAATTATATGTATC-AATA-CTGTATCGAT
1 GTCAGCTTAGTGTAAGCAACATCGTATACTGGTAACAGTTATATG-AACAAATATC-GTATCGAT
55157 GGCTGAGGTACCGCATATGTTGCGAGTCCTT
64 GGCTGAGGTACCGCATATGTTGCGAGTCCTT
* *
55188 GTCAGCTTAGTGTAAGCAGCATCGTATACTGGTAACAGTTATATGAACAAATATCATATCGATGG
1 GTCAGCTTAGTGTAAGCAACATCGTATACTGGTAACAGTTATATGAACAAATATCGTATCGATGG
* * * *
55253 TTGAGGTAACGTATACGTTGCGAGTCCTT
66 CTGAGGTACCGCATATGTTGCGAGTCCTT
* *
55282 ATCAACTTAGTG
1 GTCAGCTTAGTG
55294 ATAGCATTAG
Statistics
Matches: 163, Mismatches: 29, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
91 21 0.13
92 2 0.01
93 2 0.01
94 135 0.83
95 3 0.02
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (94 bp):
GTCAGCTTAGTGTAAGCAACATCGTATACTGGTAACAGTTATATGAACAAATATCGTATCGATGG
CTGAGGTACCGCATATGTTGCGAGTCCTT
Found at i:59879 original size:108 final size:108
Alignment explanation
Indices: 59690--59909 Score: 440
Period size: 108 Copynumber: 2.0 Consensus size: 108
59680 CATGTTGAGA
59690 TTTCCTATGTGGAGAAATATGGAAGGTGAAAGAAGGAGAGATAAAACGGTGAGTGGGAAAGGGTT
1 TTTCCTATGTGGAGAAATATGGAAGGTGAAAGAAGGAGAGATAAAACGGTGAGTGGGAAAGGGTT
59755 ACTATAGGGGAAAAATAGGGATTAGTACAATGTGCCAAACTAT
66 ACTATAGGGGAAAAATAGGGATTAGTACAATGTGCCAAACTAT
59798 TTTCCTATGTGGAGAAATATGGAAGGTGAAAGAAGGAGAGATAAAACGGTGAGTGGGAAAGGGTT
1 TTTCCTATGTGGAGAAATATGGAAGGTGAAAGAAGGAGAGATAAAACGGTGAGTGGGAAAGGGTT
59863 ACTATAGGGGAAAAATAGGGATTAGTACAATGTGCCAAACTAT
66 ACTATAGGGGAAAAATAGGGATTAGTACAATGTGCCAAACTAT
59906 TTTC
1 TTTC
59910 GTGTTTGTAA
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 112 1.00
ACGTcount: A:0.38, C:0.08, G:0.31, T:0.23
Consensus pattern (108 bp):
TTTCCTATGTGGAGAAATATGGAAGGTGAAAGAAGGAGAGATAAAACGGTGAGTGGGAAAGGGTT
ACTATAGGGGAAAAATAGGGATTAGTACAATGTGCCAAACTAT
Found at i:63675 original size:16 final size:19
Alignment explanation
Indices: 63654--63696 Score: 65
Period size: 16 Copynumber: 2.4 Consensus size: 19
63644 ATCGTAAATT
63654 TTTTTCTT-CTTTTT-TC-
1 TTTTTCTTCCTTTTTCTCA
63670 TTTTTCTTCCTTTTTCTCA
1 TTTTTCTTCCTTTTTCTCA
63689 TTTTTCTT
1 TTTTTCTT
63697 TTTCAAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.33
17 6 0.25
18 2 0.08
19 8 0.33
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTTCTTCCTTTTTCTCA
Found at i:64365 original size:31 final size:31
Alignment explanation
Indices: 64330--64391 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
64320 TATTATAGCT
64330 ACATGATATGCATGAAAACTAAACTAAGTGC
1 ACATGATATGCATGAAAACTAAACTAAGTGC
64361 ACATGATATGCATGAAAACTAAACTAAGTGC
1 ACATGATATGCATGAAAACTAAACTAAGTGC
64392 TAAAAAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (31 bp):
ACATGATATGCATGAAAACTAAACTAAGTGC
Found at i:71769 original size:19 final size:19
Alignment explanation
Indices: 71735--71884 Score: 153
Period size: 19 Copynumber: 8.1 Consensus size: 19
71725 GAAATAATTC
* *
71735 CTTACGATCCAATATTGCT
1 CTTACGAGCCAGTATTGCT
* *
71754 CTTACAAGCTAGTATTGCT
1 CTTACGAGCCAGTATTGCT
* * *
71773 C-AACAAGCCAGTATTACT
1 CTTACGAGCCAGTATTGCT
*
71791 CTTACGAGCCAATATTGCT
1 CTTACGAGCCAGTATTGCT
* *
71810 C-AACGAGCCAGTATTACT
1 CTTACGAGCCAGTATTGCT
*
71828 CTTACGAGCCAATATTGCT
1 CTTACGAGCCAGTATTGCT
* *
71847 C-AACGAGCCAGTATTGAT
1 CTTACGAGCCAGTATTGCT
*
71865 CTTACGAGCCAATATTGCT
1 CTTACGAGCCAGTATTGCT
71884 C
1 C
71885 AATGAGCTAG
Statistics
Matches: 105, Mismatches: 23, Indels: 6
0.78 0.17 0.04
Matches are distributed among these distances:
18 45 0.43
19 60 0.57
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.29
Consensus pattern (19 bp):
CTTACGAGCCAGTATTGCT
Found at i:71780 original size:18 final size:19
Alignment explanation
Indices: 71747--71901 Score: 147
Period size: 18 Copynumber: 8.4 Consensus size: 19
71737 TACGATCCAA
* * *
71747 TATTGCTCTTACAAGCTAG
1 TATTGCTCTAACGAGCCAG
*
71766 TATTGCTC-AACAAGCCAG
1 TATTGCTCTAACGAGCCAG
* * *
71784 TATTACTCTTACGAGCCAA
1 TATTGCTCTAACGAGCCAG
71803 TATTGCTC-AACGAGCCAG
1 TATTGCTCTAACGAGCCAG
* * *
71821 TATTACTCTTACGAGCCAA
1 TATTGCTCTAACGAGCCAG
71840 TATTGCTC-AACGAGCCAG
1 TATTGCTCTAACGAGCCAG
* * *
71858 TATTGATCTTACGAGCCAA
1 TATTGCTCTAACGAGCCAG
* *
71877 TATTGCTC-AATGAGCTAG
1 TATTGCTCTAACGAGCCAG
71895 TATTGCT
1 TATTGCT
71902 ATTCTCTCTA
Statistics
Matches: 110, Mismatches: 23, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
18 58 0.53
19 52 0.47
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (19 bp):
TATTGCTCTAACGAGCCAG
Found at i:71807 original size:37 final size:37
Alignment explanation
Indices: 71738--71898 Score: 225
Period size: 37 Copynumber: 4.4 Consensus size: 37
71728 ATAATTCCTT
* * * * * *
71738 ACGATCCAATATTGCTCTTACAAGCTAGTATTGCTCA
1 ACGAGCCAGTATTACTCTTACGAGCCAATATTGCTCA
*
71775 ACAAGCCAGTATTACTCTTACGAGCCAATATTGCTCA
1 ACGAGCCAGTATTACTCTTACGAGCCAATATTGCTCA
71812 ACGAGCCAGTATTACTCTTACGAGCCAATATTGCTCA
1 ACGAGCCAGTATTACTCTTACGAGCCAATATTGCTCA
71849 ACGAGCCAGTATTGA-TCTTACGAGCCAATATTGCTCA
1 ACGAGCCAGTATT-ACTCTTACGAGCCAATATTGCTCA
* *
71886 ATGAGCTAGTATT
1 ACGAGCCAGTATT
71899 GCTATTCTCT
Statistics
Matches: 113, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
37 112 0.99
38 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.29
Consensus pattern (37 bp):
ACGAGCCAGTATTACTCTTACGAGCCAATATTGCTCA
Found at i:77626 original size:46 final size:46
Alignment explanation
Indices: 77576--77701 Score: 209
Period size: 46 Copynumber: 2.7 Consensus size: 46
77566 TACTAAACTT
*
77576 TACCATGACATTATTTCTTTGTCATGACATTAACATACATTGACTA
1 TACCATGACATTATTTCTTTGTCATGACATTAACATACAGTGACTA
77622 TACCATGACATTATTTCTTTGTCATGACATTAACATACAGTGACTA
1 TACCATGACATTATTTCTTTGTCATGACATTAACATACAGTGACTA
* *
77668 TACCAGGACATTA-TTCTTTTGTCATGACAATAAC
1 TACCATGACATTATTTC-TTTGTCATGACATTAAC
77702 TTAATCAGAT
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
45 3 0.04
46 73 0.96
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (46 bp):
TACCATGACATTATTTCTTTGTCATGACATTAACATACAGTGACTA
Found at i:81596 original size:44 final size:41
Alignment explanation
Indices: 81484--81629 Score: 134
Period size: 42 Copynumber: 3.4 Consensus size: 41
81474 GAGCATTAGA
* * **
81484 TTATGTTTAAAAGGAAGACTCGTGACTCAGGAAGAGCCTGAGG
1 TTATGTTT-AAAGGAAGACTAGTGACTC-GAAAGAGTATGAGG
81527 TTATGATTT-AAGGAAGACTCA-TGACTCGAAAGGAGTATGAGG
1 TTATG-TTTAAAGGAAGACT-AGTGACTCGAAA-GAGTATGAGG
* * *
81569 TTATGTTTTAAAAGGAAGACTAGTGACTTGAGATGAGTATGAGA
1 TTATG-TTT-AAAGGAAGACTAGTGACTCGA-AAGAGTATGAGG
*
81613 TTTTGTTTAAAGGAAGA
1 TTATGTTTAAAGGAAGA
81630 TTTACGACTC
Statistics
Matches: 87, Mismatches: 9, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
41 3 0.03
42 41 0.47
43 9 0.10
44 33 0.38
45 1 0.01
ACGTcount: A:0.35, C:0.08, G:0.28, T:0.29
Consensus pattern (41 bp):
TTATGTTTAAAGGAAGACTAGTGACTCGAAAGAGTATGAGG
Found at i:81639 original size:86 final size:85
Alignment explanation
Indices: 81484--81641 Score: 185
Period size: 86 Copynumber: 1.8 Consensus size: 85
81474 GAGCATTAGA
* * * *
81484 TTATGTTTAAAAGGAAGACTCGTGACTCAGGAAGAGCCTGAGGTTATGATTTAAGGAAGACTCAT
1 TTATGTTTAAAAGGAAGACTAGTGACTCAGGAAGAGCATGAGATTATGATTTAAGGAAGACTCAC
81549 GACTCGAAAGGAGTATGAGG
66 GACTCGAAAGGAGTATGAGG
* * * * *
81569 TTATGTTTTAAAAGGAAGACTAGTGACT-TGAGATGAGTATGAGATTTTG-TTTAAAGGAAGATT
1 TTATG-TTTAAAAGGAAGACTAGTGACTCAG-GAAGAGCATGAGATTATGATTT-AAGGAAGACT
*
81632 TACGACTCGA
63 CACGACTCGA
81642 TTGATTATGT
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
85 9 0.15
86 51 0.85
ACGTcount: A:0.34, C:0.09, G:0.27, T:0.29
Consensus pattern (85 bp):
TTATGTTTAAAAGGAAGACTAGTGACTCAGGAAGAGCATGAGATTATGATTTAAGGAAGACTCAC
GACTCGAAAGGAGTATGAGG
Found at i:84134 original size:19 final size:19
Alignment explanation
Indices: 84112--84156 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
84102 TTTTATTAGG
84112 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
84131 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
84150 ATTTAAT
1 ATTTAAT
84157 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:86553 original size:21 final size:21
Alignment explanation
Indices: 86538--86577 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
86528 TAGCAATCTA
86538 TAGATTTTCAAAAGCAAACAG
1 TAGATTTTCAAAAGCAAACAG
*
86559 TAGATTTTCAAAAGAAAAC
1 TAGATTTTCAAAAGCAAAC
86578 TGAGGCATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.25
Consensus pattern (21 bp):
TAGATTTTCAAAAGCAAACAG
Found at i:90556 original size:13 final size:13
Alignment explanation
Indices: 90538--90570 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
90528 ACCTAATTAT
90538 TTTTATTTTTCTA
1 TTTTATTTTTCTA
*
90551 TTTTATTTTTTTA
1 TTTTATTTTTCTA
90564 TTTTATT
1 TTTTATT
90571 ATATGTCTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTATTTTTCTA
Found at i:91533 original size:103 final size:101
Alignment explanation
Indices: 91343--91541 Score: 215
Period size: 103 Copynumber: 2.0 Consensus size: 101
91333 ATTTGGAGTG
* * *
91343 TGTTAGGCTGAGTAATCGGAGTGGAGTGCTTGGCTGTCATTTCACTTTGCGTCAAAAGGGCTAAC
1 TGTTAGGCTGAGTAACCGGAGTGGAGTGCTTGGCTGTCATTTCACTTTGCATCAAAAGGGCCAAC
*
91408 ACATTCTACAAAAAGAAGAAGAAACAAAATTGAGAGCA
66 ACATTCTACAAAAAGAAAAAG-AA-AAAATTGAGAGCA
* * * * * *
91446 TGTTGGGCTGAGTAACCGG-GATGGAGTGCTTGGGTGTTATTTTATTTTGCATCAAAAGGTCCAA
1 TGTTAGGCTGAGTAACCGGAG-TGGAGTGCTTGGCTGTCATTTCACTTTGCATCAAAAGGGCCAA
***
91510 TGTATTCTTA-AAGAAA-AAAAAGAAAAAATTGA
65 CACATTC-TACAA-AAAGAAAAAGAAAAAATTGA
91542 CAAAATAAAT
Statistics
Matches: 80, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
101 8 0.10
102 3 0.04
103 64 0.80
104 5 0.06
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.28
Consensus pattern (101 bp):
TGTTAGGCTGAGTAACCGGAGTGGAGTGCTTGGCTGTCATTTCACTTTGCATCAAAAGGGCCAAC
ACATTCTACAAAAAGAAAAAGAAAAAATTGAGAGCA
Found at i:92118 original size:19 final size:19
Alignment explanation
Indices: 92096--92140 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
92086 TTTTATTAGG
92096 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
92115 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
92134 ATTTAAT
1 ATTTAAT
92141 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:99467 original size:44 final size:41
Alignment explanation
Indices: 99344--99501 Score: 165
Period size: 42 Copynumber: 3.7 Consensus size: 41
99334 GTCTTGGGAT
* * *
99344 GAGCATGAGATTAAGTTAAAAAGGAAGACTCGTGACTCGAGAA
1 GAGCATGAGGTTATGTT-TAAAGGAAGACTCGTGACTCGA-AA
* *
99387 GAGCATGATGTTATGATTT-AAGGAAGACTCATGACTCGAAA
1 GAGCATGAGGTTATG-TTTAAAGGAAGACTCGTGACTCGAAA
* *
99428 GGAGTATGAGGTTATGTTTTAAAAGGAAGACTCGTGACTCGATAT
1 -GAGCATGAGGTTATG-TTT-AAAGGAAGACTCGTGACTCGA-AA
* *
99473 GAGCATGAGATTTTGTTTAAAGGAAGACT
1 GAGCATGAGGTTATGTTTAAAGGAAGACT
99502 TACAACTCGG
Statistics
Matches: 97, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
41 2 0.02
42 46 0.47
43 15 0.15
44 33 0.34
45 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.27, T:0.27
Consensus pattern (41 bp):
GAGCATGAGGTTATGTTTAAAGGAAGACTCGTGACTCGAAA
Found at i:99735 original size:13 final size:13
Alignment explanation
Indices: 99717--99741 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
99707 ATCTAGTACT
99717 AAAATGTAATGCC
1 AAAATGTAATGCC
99730 AAAATGTAATGC
1 AAAATGTAATGC
99742 TAAGTGTTGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (13 bp):
AAAATGTAATGCC
Found at i:102973 original size:29 final size:26
Alignment explanation
Indices: 102937--103039 Score: 84
Period size: 29 Copynumber: 3.7 Consensus size: 26
102927 TTGAACTTAA
*
102937 TTTAAAAAAATAAAAATACATAAATAT
1 TTTATAAAAATAAAAATA-ATAAATAT
102964 TTTCATAAAAATATAAAATAAATTAAATA-
1 TTT-ATAAAAATA-AAAAT-AA-TAAATAT
* *
102993 TATATAAAAATAAAAA-AATTAATATT
1 TTTATAAAAATAAAAATAATAAATA-T
103019 TTTACTGTAAAAATAAAAATA
1 TTTA---TAAAAATAAAAATA
103040 TATACTATAA
Statistics
Matches: 62, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
24 5 0.08
25 2 0.03
26 3 0.05
27 7 0.11
28 17 0.27
29 20 0.32
30 8 0.13
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (26 bp):
TTTATAAAAATAAAAATAATAAATAT
Found at i:102999 original size:28 final size:28
Alignment explanation
Indices: 102942--103008 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
102932 CTTAATTTAA
* *
102942 AAAAATAAAAATACATAAATATTTTCAT
1 AAAAATAAAAATAAATAAATATTATCAT
102970 AAAAATATAAAATAAATTAAATA-TAT-AT
1 AAAAATA-AAAATAAA-TAAATATTATCAT
102998 AAAAATAAAAA
1 AAAAATAAAAA
103009 AATTAATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
27 4 0.11
28 16 0.46
29 9 0.26
30 6 0.17
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (28 bp):
AAAAATAAAAATAAATAAATATTATCAT
Found at i:103011 original size:20 final size:20
Alignment explanation
Indices: 102974--103011 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
102964 TTTCATAAAA
*
102974 ATATAAAATAAATTAAATAT
1 ATATAAAATAAATAAAATAT
102994 ATATAAAAATAAA-AAAAT
1 ATAT-AAAATAAATAAAAT
103012 TAATATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
ATATAAAATAAATAAAATAT
Found at i:104380 original size:8 final size:8
Alignment explanation
Indices: 104369--104399 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
104359 ATTTTACTAA
104369 TTTAAAAT
1 TTTAAAAT
104377 TTTAAAAT
1 TTTAAAAT
104385 TTTAAAAT
1 TTTAAAAT
104393 TTTAAAA
1 TTTAAAA
104400 AATCTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
TTTAAAAT
Found at i:106163 original size:21 final size:21
Alignment explanation
Indices: 106134--106177 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
106124 AGGCCAATTC
*
106134 AAGACAAGGTG-ACTCTTCAA
1 AAGACAAGGGGAACTCTTCAA
106154 AAGATCAAGGGGAAACTCTTCAA
1 AAGA-CAAGGGG-AACTCTTCAA
106177 A
1 A
106178 TGTTGATCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 6 0.30
23 10 0.50
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.18
Consensus pattern (21 bp):
AAGACAAGGGGAACTCTTCAA
Found at i:108340 original size:77 final size:77
Alignment explanation
Indices: 108213--108365 Score: 306
Period size: 77 Copynumber: 2.0 Consensus size: 77
108203 GTTAAGTCGA
108213 GCTTGACATCAGAAAACATACACACAAAAGAAACAATGTGTTAAGTATAAGGCTTAGTAAGATAA
1 GCTTGACATCAGAAAACATACACACAAAAGAAACAATGTGTTAAGTATAAGGCTTAGTAAGATAA
108278 TATGGAAATTAG
66 TATGGAAATTAG
108290 GCTTGACATCAGAAAACATACACACAAAAGAAACAATGTGTTAAGTATAAGGCTTAGTAAGATAA
1 GCTTGACATCAGAAAACATACACACAAAAGAAACAATGTGTTAAGTATAAGGCTTAGTAAGATAA
108355 TATGGAAATTA
66 TATGGAAATTA
108366 CTCATTATAC
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.24
Consensus pattern (77 bp):
GCTTGACATCAGAAAACATACACACAAAAGAAACAATGTGTTAAGTATAAGGCTTAGTAAGATAA
TATGGAAATTAG
Found at i:112500 original size:14 final size:15
Alignment explanation
Indices: 112481--112511 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
112471 CTTTACTTTA
112481 TTTTATTTTTAT-CT
1 TTTTATTTTTATGCT
112495 TTTTATTTTTATGCT
1 TTTTATTTTTATGCT
112510 TT
1 TT
112512 CAAACAACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.13, C:0.06, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTTATTTTTATGCT
Found at i:121602 original size:16 final size:16
Alignment explanation
Indices: 121581--121612 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
121571 GGCTAAGAAT
121581 GGTCTCCCAAGGATGA
1 GGTCTCCCAAGGATGA
121597 GGTCTCCCAAGGATGA
1 GGTCTCCCAAGGATGA
121613 TCGACACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.25, G:0.31, T:0.19
Consensus pattern (16 bp):
GGTCTCCCAAGGATGA
Found at i:125090 original size:14 final size:15
Alignment explanation
Indices: 125066--125096 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
125056 GAGTTGTTTT
125066 AAAGCATAAAAATAA
1 AAAGCATAAAAATAA
125081 AAAG-ATAAAAATAA
1 AAAGCATAAAAATAA
125095 AA
1 AA
125097 TAAAGTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.13
Consensus pattern (15 bp):
AAAGCATAAAAATAA
Found at i:132510 original size:25 final size:25
Alignment explanation
Indices: 132473--132531 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
132463 TAGAAATTAA
* *
132473 AATTTCTCATGTCGAAATTCTATTG
1 AATTCCTCGTGTCGAAATTCTATTG
132498 AATTCCTCGTGTCGAAATTCTATTG
1 AATTCCTCGTGTCGAAATTCTATTG
132523 AATTCCTCG
1 AATTCCTCG
132532 ATATATTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (25 bp):
AATTCCTCGTGTCGAAATTCTATTG
Found at i:133514 original size:19 final size:19
Alignment explanation
Indices: 133490--133528 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
133480 CCAAAGTTAG
133490 TTGTTAGTTTTTAATCAAA
1 TTGTTAGTTTTTAATCAAA
*
133509 TTGTTAGTTTTTAGTCAAA
1 TTGTTAGTTTTTAATCAAA
133528 T
1 T
133529 ATTGCTGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.05, G:0.13, T:0.54
Consensus pattern (19 bp):
TTGTTAGTTTTTAATCAAA
Found at i:163572 original size:16 final size:17
Alignment explanation
Indices: 163549--163591 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
163539 CTTAGAACAA
163549 TCTCAAGCTCGAAT-TAT
1 TCTCAAGCTCGAATCT-T
163566 T-TCAAGCTC-AATCTT
1 TCTCAAGCTCGAATCTT
163581 TCTCAAGCTCG
1 TCTCAAGCTCG
163592 GATCAGCTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 5 0.22
16 17 0.74
17 1 0.04
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.35
Consensus pattern (17 bp):
TCTCAAGCTCGAATCTT
Found at i:164231 original size:18 final size:18
Alignment explanation
Indices: 164208--164247 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
164198 GAATGAATTT
164208 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
164226 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
164244 TTAA
1 TTAA
164248 GTACACCTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:164900 original size:18 final size:19
Alignment explanation
Indices: 164866--164917 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
164856 TCAAAATTTT
*
164866 ATTTTAATATTT-TTATAC-
1 ATTTTAAT-TTTAATATACA
164884 ATTTTAATTTTAATATACA
1 ATTTTAATTTTAATATACA
*
164903 ATTTTTTATTTTAAT
1 A-TTTTAATTTTAAT
164918 TACGTAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 3 0.10
18 13 0.45
19 1 0.03
20 12 0.41
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTTAATTTTAATATACA
Found at i:166810 original size:25 final size:26
Alignment explanation
Indices: 166764--166814 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
166754 AATTATACTT
* *
166764 TTTTTTAATATAAGTTGTTACTTAAA
1 TTTTTTAATAGAAGTTGATACTTAAA
*
166790 TTTTTTATTAGAAG-TGATACTTAAA
1 TTTTTTAATAGAAGTTGATACTTAAA
166815 CTATACTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.35, C:0.04, G:0.10, T:0.51
Consensus pattern (26 bp):
TTTTTTAATAGAAGTTGATACTTAAA
Found at i:169161 original size:19 final size:19
Alignment explanation
Indices: 169133--169170 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
169123 ATTCAACCCG
169133 TTGACAGTTGATCATTGAC
1 TTGACAGTTGATCATTGAC
* *
169152 TTGACCGTTGATCGTTGAC
1 TTGACAGTTGATCATTGAC
169171 CGTTGATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (19 bp):
TTGACAGTTGATCATTGAC
Found at i:170545 original size:12 final size:12
Alignment explanation
Indices: 170525--170556 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
170515 CATCTTTATT
170525 AAACCCAATTAC
1 AAACCCAATTAC
*
170537 AAGCCCAATTAC
1 AAACCCAATTAC
170549 AAACCCAA
1 AAACCCAA
170557 ACCTAAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.50, C:0.34, G:0.03, T:0.12
Consensus pattern (12 bp):
AAACCCAATTAC
Found at i:173244 original size:32 final size:32
Alignment explanation
Indices: 173207--173272 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 32
173197 TATATATATG
* **
173207 ATCCTTTGCATTTTCTATTAAATATTATGATA
1 ATCCTTTGCATTTTCTATGAAATACCATGATA
* *
173239 ATCCTTTTCATTTTCTGTGAAATACCATGATA
1 ATCCTTTGCATTTTCTATGAAATACCATGATA
173271 AT
1 AT
173273 ATTATTGCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.30, C:0.15, G:0.08, T:0.47
Consensus pattern (32 bp):
ATCCTTTGCATTTTCTATGAAATACCATGATA
Done.