Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004944.1 Kokia drynarioides strain JFW-HI SEQ_118655, 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: 62882
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Found at i:511 original size:29 final size:30
Alignment explanation
Indices: 479--787 Score: 309
Period size: 29 Copynumber: 10.5 Consensus size: 30
469 CTAAACTATT
*
479 CAAAAATTACATTTTT-ACCCTCAAACTTC
1 CAAAAATTCCATTTTTGACCCTCAAACTTC
*
508 C-AAAATTCCATTTTTTACCC-CAAAACTTC
1 CAAAAATTCCATTTTTGACCCTC-AAACTTC
* *
537 CAAAAAATCCATTTTT-ACCCCCAAACTTC
1 CAAAAATTCCATTTTTGACCCTCAAACTTC
** *
566 CAAAAATTATATTTTTGACCC-AAAACTTC
1 CAAAAATTCCATTTTTGACCCTCAAACTTC
*
595 CAAAAATTCCATTTTT-ACCCTCAAACTTT
1 CAAAAATTCCATTTTTGACCCTCAAACTTC
624 CAAAAATTCCATTTTTGACCC-CAAAACTTC
1 CAAAAATTCCATTTTTGACCCTC-AAACTTC
* *
654 CAAAAATT-CATTTTTCACCCTCGAACTTC
1 CAAAAATTCCATTTTTGACCCTCAAACTTC
* * *
683 CAAAAATTCCATTTTTGACCAC-GAAAATTT
1 CAAAAATTCCATTTTTGACC-CTCAAACTTC
** *
713 CAAAAATAACATTTTT-ACCCTCGAACCTT-
1 CAAAAATTCCATTTTTGACCCTC-AAACTTC
* * *
742 CAAAATTTCCATTTTTGA-CCTCGAATCTTT
1 CAAAAATTCCATTTTTGACCCTC-AAACTTC
772 CAAAAATTACCATTTT
1 CAAAAATT-CCATTTT
788 CTCCCGGATG
Statistics
Matches: 236, Mismatches: 28, Indels: 30
0.80 0.10 0.10
Matches are distributed among these distances:
28 19 0.08
29 132 0.56
30 77 0.33
31 8 0.03
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (30 bp):
CAAAAATTCCATTTTTGACCCTCAAACTTC
Found at i:580 original size:59 final size:59
Alignment explanation
Indices: 479--761 Score: 353
Period size: 58 Copynumber: 4.8 Consensus size: 59
469 CTAAACTATT
* * *
479 CAAAAATTACATTTTTACCCTCAAACTTCC-AAAATTCCATTTTTTACCCCAAAACTTC
1 CAAAAAATCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTC
* **
537 CAAAAAATCCATTTTTACCCCCAAACTTCCAAAAATTATATTTTTGA-CCCAAAACTTC
1 CAAAAAATCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTC
* *
595 CAAAAATTCCATTTTTACCCTCAAACTTTCAAAAATTCCATTTTTGACCCCAAAACTTC
1 CAAAAAATCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTC
* * * *
654 C-AAAAATTCATTTTTCACCCTCGAACTTCCAAAAATTCCATTTTTGACCACGAAAA-TTT
1 CAAAAAATCCATTTTT-ACCCTCAAACTTCCAAAAATTCCATTTTTGACC-CCAAAACTTC
* * *
713 C-AAAAATAACATTTTTACCCTCGAACCTT-CAAAATTTCCATTTTTGACC
1 CAAAAAAT-CCATTTTTACCCTC-AAACTTCCAAAAATTCCATTTTTGACC
762 TCGAATCTTT
Statistics
Matches: 198, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
58 92 0.46
59 90 0.45
60 16 0.08
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.34
Consensus pattern (59 bp):
CAAAAAATCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTC
Found at i:773 original size:59 final size:60
Alignment explanation
Indices: 479--787 Score: 352
Period size: 59 Copynumber: 5.2 Consensus size: 60
469 CTAAACTATT
*
479 CAAAAATTA-CATTTTTACCCTC-AAACTTCC-AAAATTCCATTTTTTACCCCAAAACTTC
1 CAAAAA-TACCATTTTTACCCTCGAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTC
* **
537 CAAAAA-ATCCATTTTTACCC-CCAAACTTCCAAAAATTATATTTTTGA-CCCAAAACTTC
1 CAAAAATA-CCATTTTTACCCTCGAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTC
* *
595 CAAAAATTCCATTTTTACCCTC-AAACTTTCAAAAATTCCATTTTTGACCCCAAAACTTC
1 CAAAAATACCATTTTTACCCTCGAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTC
* * *
654 CAAAAAT-TCATTTTTCACCCTCG-AACTTCCAAAAATTCCATTTTTGACCACGAAAA-TTT
1 CAAAAATACCATTTTT-ACCCTCGAAACTTCCAAAAATTCCATTTTTGACC-CCAAAACTTC
* * * * * * *
713 CAAAAATAACATTTTTACCCTCGAACCTT-CAAAATTTCCATTTTTGACCTCGAATCTTT
1 CAAAAATACCATTTTTACCCTCGAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTC
772 CAAAAATTACCATTTT
1 CAAAAA-TACCATTTT
788 CTCCCGGATG
Statistics
Matches: 218, Mismatches: 19, Indels: 26
0.83 0.07 0.10
Matches are distributed among these distances:
56 1 0.00
57 1 0.00
58 85 0.39
59 107 0.49
60 24 0.11
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (60 bp):
CAAAAATACCATTTTTACCCTCGAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTC
Found at i:902 original size:58 final size:59
Alignment explanation
Indices: 479--902 Score: 315
Period size: 58 Copynumber: 7.3 Consensus size: 59
469 CTAAACTATT
* * * * *
479 CAAAAATTACATTTTTACCCTCAAACTTCC-AAAATTCCATTTTTTACC-CCAAAACTTC
1 CAAAAATTACATTTTTACCCCCGAACTTCCAAAAATTTCATTTTTGACCTCGAAAAC-TC
* * *
537 CAAAAAATCCATTTTTACCCCCAAACTTCCAAAAATTAT-ATTTTTGACC-C-AAAACTTC
1 CAAAAATTACATTTTTACCCCCGAACTTCCAAAAATT-TCATTTTTGACCTCGAAAAC-TC
* * * * * *
595 CAAAAATTCCATTTTTACCCTCAAACTTTCAAAAATTCCATTTTTGACC-CCAAAACTTC
1 CAAAAATTACATTTTTACCCCCGAACTTCCAAAAATTTCATTTTTGACCTCGAAAAC-TC
* * * * *
654 CAAAAATT-CATTTTTCACCCTCGAACTTCCAAAAATTCCATTTTTGACCACGAAAATTT
1 CAAAAATTACATTTTT-ACCCCCGAACTTCCAAAAATTTCATTTTTGACCTCGAAAACTC
* * * *
713 CAAAAATAACATTTTTACCCTCGAACCTT-C-AAAATTTCCATTTTTGACCTCG-AATCTTT
1 CAAAAATTACATTTTTACCCCCGAA-CTTCCAAAAATTT-CATTTTTGACCTCGAAAAC-TC
* * * * ** *
772 CAAAAATTACCA-TTTT-CTCCCGGA-TGTCCAAAAACTTCATTTTCGATATTG-AAACTC
1 CAAAAATTA-CATTTTTACCCCCGAACT-TCCAAAAATTTCATTTTTGACCTCGAAAACTC
** * *
829 TTAAAATTACCTTTTTACCCCCGAA-TGTCCAAAAATTTCATTTTTGACCTCGAGAA-TC
1 CAAAAATTACATTTTTACCCCCGAACT-TCCAAAAATTTCATTTTTGACCTCGAAAACTC
887 C-AAAATTAACATTTTT
1 CAAAAATT-ACATTTTT
903 GGTATCCAAA
Statistics
Matches: 305, Mismatches: 43, Indels: 36
0.79 0.11 0.09
Matches are distributed among these distances:
56 2 0.01
57 19 0.06
58 151 0.50
59 116 0.38
60 17 0.06
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (59 bp):
CAAAAATTACATTTTTACCCCCGAACTTCCAAAAATTTCATTTTTGACCTCGAAAACTC
Found at i:2403 original size:103 final size:103
Alignment explanation
Indices: 2224--2430 Score: 387
Period size: 103 Copynumber: 2.0 Consensus size: 103
2214 CTTATTTGCA
*
2224 TTGCATCTTCATATTAGGAAAGGTATTGATTTAAGATCAATTACTAATAGATAATTGCTCATGTA
1 TTGCATCTTCATATTAGGAAAGGTATTGATTTAAGATCAATTACTAATAGATAATTGCTCATGGA
2289 AAAGGGATATCTTGATAAGGTGGAGGATAATGTGACCG
66 AAAGGGATATCTTGATAAGGTGGAGGATAATGTGACCG
* *
2327 TTGCATCTTCATATTAGGAAAGGTATTGATTTAAGATCAATTACTAGTAGATAATTGGTCATGGA
1 TTGCATCTTCATATTAGGAAAGGTATTGATTTAAGATCAATTACTAATAGATAATTGCTCATGGA
2392 AAAGGGATATCTTGATAAGGTGGAGGATAATGTGACCG
66 AAAGGGATATCTTGATAAGGTGGAGGATAATGTGACCG
2430 T
1 T
2431 GCGCATGTGG
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 101 1.00
ACGTcount: A:0.34, C:0.09, G:0.24, T:0.33
Consensus pattern (103 bp):
TTGCATCTTCATATTAGGAAAGGTATTGATTTAAGATCAATTACTAATAGATAATTGCTCATGGA
AAAGGGATATCTTGATAAGGTGGAGGATAATGTGACCG
Found at i:4619 original size:3 final size:3
Alignment explanation
Indices: 4611--4647 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
4601 AAAAAATCAT
4611 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
4648 AGATCCTCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:9184 original size:14 final size:13
Alignment explanation
Indices: 9156--9219 Score: 56
Period size: 13 Copynumber: 4.6 Consensus size: 13
9146 TCAAACTAGC
*
9156 AAAAAAAAAAAAG
1 AAAAAAAAAAGAG
*
9169 AAACAGAAAAAGAG
1 AAA-AAAAAAAGAG
*
9183 AAAAAAAAAAGAA
1 AAAAAAAAAAGAG
*
9196 AAAAGAGGAAAAAAAG
1 AAAA-A--AAAAAGAG
9212 AAAAAAAA
1 AAAAAAAA
9220 GAAAAAGAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
13 18 0.44
14 12 0.29
15 1 0.02
16 10 0.24
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGAG
Found at i:9186 original size:19 final size:17
Alignment explanation
Indices: 9160--9227 Score: 59
Period size: 18 Copynumber: 3.9 Consensus size: 17
9150 ACTAGCAAAA
*
9160 AAAAAAAAGAAACAGA-
1 AAAAAAAAGAAAAAGAG
*
9176 AAAAGAGAAA-AAAAAAAG
1 AAAA-A-AAAGAAAAAGAG
* *
9194 AAAAAAGAGGAAAAAAAG
1 AAAAAA-AAGAAAAAGAG
9212 AAAAAAAAGAAAAAGA
1 AAAAAAAAGAAAAAGA
9228 AGGTCCGAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
16 5 0.12
17 16 0.38
18 21 0.50
ACGTcount: A:0.82, C:0.01, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAAAAAGAAAAAGAG
Found at i:9186 original size:20 final size:19
Alignment explanation
Indices: 9162--9225 Score: 69
Period size: 21 Copynumber: 3.3 Consensus size: 19
9152 TAGCAAAAAA
9162 AAAAAAGAAACAGAAAAAGAG
1 AAAAAA-AAA-AGAAAAAGAG
9183 AAAAAAAAAAGAAAAAAGAGG
1 AAAAAAAAAAG-AAAAAGA-G
*
9204 AAAAAAAGAA-AAAAA-AG
1 AAAAAAAAAAGAAAAAGAG
9221 AAAAA
1 AAAAA
9226 GAAGGTCCGA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
17 6 0.15
18 1 0.03
19 7 0.17
20 10 0.25
21 16 0.40
ACGTcount: A:0.83, C:0.02, G:0.16, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAGAAAAAGAG
Found at i:9186 original size:21 final size:23
Alignment explanation
Indices: 9161--9219 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 23
9151 CTAGCAAAAA
9161 AAAAAAAGAAACAG-AAAAAGA-G
1 AAAAAAAGAAA-AGAAAAAAGAGG
9183 -AAAAAA-AAAAGAAAAAAGAGG
1 AAAAAAAGAAAAGAAAAAAGAGG
9204 AAAAAAAGAAAA-AAAA
1 AAAAAAAGAAAAGAAAA
9220 GAAAAAGAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
19 2 0.06
20 10 0.30
21 7 0.21
22 10 0.30
23 4 0.12
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (23 bp):
AAAAAAAGAAAAGAAAAAAGAGG
Found at i:9188 original size:29 final size:30
Alignment explanation
Indices: 9156--9228 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
9146 TCAAACTAGC
*
9156 AAAAAAAAAAAAGAAACA-GAAAAAGAGAA
1 AAAAAAAAAAAAGAAACAGGAAAAAAAGAA
* *
9185 AAAAAAAAGAAA-AAAGAGGAAAAAAAGAA
1 AAAAAAAAAAAAGAAACAGGAAAAAAAGAA
*
9214 AAAAAAGAAAAAGAA
1 AAAAAAAAAAAAGAA
9229 GGTCCGAGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 4 0.11
29 31 0.84
30 2 0.05
ACGTcount: A:0.84, C:0.01, G:0.15, T:0.00
Consensus pattern (30 bp):
AAAAAAAAAAAAGAAACAGGAAAAAAAGAA
Found at i:9197 original size:18 final size:18
Alignment explanation
Indices: 9156--9217 Score: 72
Period size: 18 Copynumber: 3.3 Consensus size: 18
9146 TCAAACTAGC
9156 AAAAAA-AAAAAAGAAACAG
1 AAAAAAGAAAAAA-AAA-AG
9175 AAAAAGAGAAAAAAAAAAG
1 AAAAA-AGAAAAAAAAAAG
**
9194 AAAAAAGAGGAAAAAAAG
1 AAAAAAGAAAAAAAAAAG
9212 AAAAAA
1 AAAAAA
9218 AAGAAAAAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
18 17 0.44
19 12 0.31
20 4 0.10
21 6 0.15
ACGTcount: A:0.84, C:0.02, G:0.15, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAAAAAAAAAG
Found at i:10399 original size:49 final size:48
Alignment explanation
Indices: 10340--10478 Score: 134
Period size: 49 Copynumber: 2.8 Consensus size: 48
10330 AATCGAAGGG
* * *
10340 GGAAATATTGAAGCCACAACGGCGGATCTTACACCTTAAAATTGAAAAA
1 GGAAAGATTGAA-CCGCAACGACGGATCTTACACCTTAAAATTGAAAAA
* * * * * * *
10389 GGATAGATTGAACTCGTAATGACGGATCTAACACCCTAAAATTGAAGAG
1 GGAAAGATTGAAC-CGCAACGACGGATCTTACACCTTAAAATTGAAAAA
* * *
10438 GGAAAGATTGAATCCGCAACGATGAATCTTACACTTTAAAA
1 GGAAAGATTGAA-CCGCAACGACGGATCTTACACCTTAAAA
10479 AAACTAAACA
Statistics
Matches: 70, Mismatches: 18, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
48 1 0.01
49 68 0.97
50 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.22
Consensus pattern (48 bp):
GGAAAGATTGAACCGCAACGACGGATCTTACACCTTAAAATTGAAAAA
Found at i:10553 original size:45 final size:44
Alignment explanation
Indices: 10503--10833 Score: 367
Period size: 45 Copynumber: 7.3 Consensus size: 44
10493 AAAGTCACCA
* * * *
10503 CATCCAGTCTTTTA-CCCTAAATCTAAAGGGGCAAATTGAAGCTAA
1 CATCCAGTCTTTTACCCCT-AATCCAGAGGGGCAGATTGAAGC-AC
* * * *
10548 CATCCAGTCTTTTACCCCTAATCCAAAGAGGTAGATTGAAGCAAT
1 CATCCAGTCTTTTACCCCTAATCCAGAGGGGCAGATTGAAGC-AC
* * * * *
10593 CATCCAATCTTTCACCCTTAATCCAGAGGGACAGAATGAAGACAC
1 CATCCAGTCTTTTACCCCTAATCCAGAGGGGCAGATTGAAG-CAC
* * * *
10638 CATCTAATCATTTACTCCTAATCCAGAGGGGCAGATTGAAGCCAC
1 CATCCAGTCTTTTACCCCTAATCCAGAGGGGCAGATTGAAG-CAC
* *
10683 CATCCAGTCTTTTACCCCTAATCCAGAGGGACAAATTGAAGCCAC
1 CATCCAGTCTTTTACCCCTAATCCAGAGGGGCAGATTGAAG-CAC
10728 CATCCAGTCTTTTACCCCTAATCCAGAGGGGCAGATTGAAGTCAC
1 CATCCAGTCTTTTACCCCTAATCCAGAGGGGCAGATTGAAG-CAC
* *
10773 CATCCAATCATTTACCCCTAATCCAGAGGGGCAGATTGAAGTCAC
1 CATCCAGTCTTTTACCCCTAATCCAGAGGGGCAGATTGAAG-CAC
*
10818 CAAATCCAATCTTTTA
1 C--ATCCAGTCTTTTA
10834 TCTTTAAATC
Statistics
Matches: 247, Mismatches: 35, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
45 230 0.93
46 5 0.02
47 12 0.05
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (44 bp):
CATCCAGTCTTTTACCCCTAATCCAGAGGGGCAGATTGAAGCAC
Found at i:10819 original size:135 final size:134
Alignment explanation
Indices: 10486--10833 Score: 412
Period size: 135 Copynumber: 2.5 Consensus size: 134
10476 AAAAAACTAA
* * * * * * *
10486 ACAGATTAAAGTCACCACATCCAGTCTTTTA-CCCTAAATCTAAAGGGGCAAATTGAAGCTAACA
1 ACAGATTGAAGTCA-C-CATCCAATCATTTACCCCT-AATCCAGAGGGGCAGATTGAAGC-ACCA
* * * *
10550 TCCAGTCTTTTACCCCTAATCCAAAGAGGTAGATTGAAGCAATCATCCAATCTTTCACCCTTAAT
62 TCCAGTCTTTTACCCCTAATCCAAAGAGGCAAATTGAAGCAACCATCCAATCTTTCACCCCTAAT
10615 CCAGAGGG
127 CCAGAGGG
* * * *
10623 ACAGAATGAAGACACCATCTAATCATTTACTCCTAATCCAGAGGGGCAGATTGAAGCCACCATCC
1 ACAGATTGAAGTCACCATCCAATCATTTACCCCTAATCCAGAGGGGCAGATTGAAG-CACCATCC
* * * *
10688 AGTCTTTTACCCCTAATCCAGAG-GGACAAATTGAAGCCACCATCCAGTCTTTTACCCCTAATCC
65 AGTCTTTTACCCCTAATCCAAAGAGG-CAAATTGAAGCAACCATCCAATCTTTCACCCCTAATCC
10752 AGAGGG
129 AGAGGG
*
10758 GCAGATTGAAGTCACCATCCAATCATTTACCCCTAATCCAGAGGGGCAGATTGAAGTCACCAAAT
1 ACAGATTGAAGTCACCATCCAATCATTTACCCCTAATCCAGAGGGGCAGATTGAAG-CACC--AT
*
10823 CCAATCTTTTA
63 CCAGTCTTTTA
10834 TCTTTAAATC
Statistics
Matches: 180, Mismatches: 26, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
134 2 0.01
135 150 0.83
136 5 0.03
137 23 0.13
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (134 bp):
ACAGATTGAAGTCACCATCCAATCATTTACCCCTAATCCAGAGGGGCAGATTGAAGCACCATCCA
GTCTTTTACCCCTAATCCAAAGAGGCAAATTGAAGCAACCATCCAATCTTTCACCCCTAATCCAG
AGGG
Found at i:11309 original size:22 final size:23
Alignment explanation
Indices: 11267--11318 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
11257 GAGAGGAATT
* *
11267 TTTTTTTAATAAGATTCAGAG-A
1 TTTTTTTAACAACATTCAGAGAA
11289 TTTTTTTAACAACACTT-AGAGAA
1 TTTTTTTAACAACA-TTCAGAGAA
11312 TTTTTTT
1 TTTTTTT
11319 GAGACTTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 16 0.62
23 10 0.38
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.50
Consensus pattern (23 bp):
TTTTTTTAACAACATTCAGAGAA
Found at i:11540 original size:3 final size:3
Alignment explanation
Indices: 11532--11575 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
11522 GAGTTTGTCT
11532 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
11576 TAGTTGTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:11607 original size:4 final size:4
Alignment explanation
Indices: 11598--11639 Score: 52
Period size: 4 Copynumber: 11.0 Consensus size: 4
11588 TTGACATTCA
* *
11598 ATTT ATTT ATTT -TTT GTTT ATTT ATTT ATTT -GTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
11640 TCATGCTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
3 5 0.15
4 28 0.85
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.76
Consensus pattern (4 bp):
ATTT
Found at i:11701 original size:6 final size:6
Alignment explanation
Indices: 11657--11732 Score: 61
Period size: 6 Copynumber: 12.5 Consensus size: 6
11647 TAATCTAAAT
* *
11657 TTTTTA TTGTTTA -TATT- TTTTTA -TTTTA GTATTTAA TTTTTA TTTTTA
1 TTTTTA TT-TTTA TTTTTA TTTTTA TTTTTA -T-TTTTA TTTTTA TTTTTA
11705 TTTTTA TTTTTA TTTATT- TTATTTA TTT
1 TTTTTA TTTTTA TTT-TTA TT-TTTA TTT
11733 ATCTTGTTGT
Statistics
Matches: 57, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
5 10 0.18
6 33 0.58
7 10 0.18
8 4 0.07
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:11729 original size:19 final size:19
Alignment explanation
Indices: 11599--11766 Score: 78
Period size: 19 Copynumber: 8.3 Consensus size: 19
11589 TGACATTCAA
*
11599 TTTATTTATTTTTTGTTTA-
1 TTTATTTA-TTTTTATTTAT
11618 TTTATTTATTTGTTATTTAT
1 TTTATTTATTT-TTATTTAT
* ** *
11638 TTTCATGCTTAATCTAAATTTTT
1 TTT-AT--TT-ATTTTTATTTAT
*
11661 TATTGTTTATATTTT-TTTATT
1 T-TTATTTAT-TTTTATTTA-T
11682 TTAGTATTTAATTTTTATTT-T
1 TT--TATTT-ATTTTTATTTAT
11703 TATT-TTTATTTTTATTTAT
1 T-TTATTTATTTTTATTTAT
*
11722 TTTATTTA--TTTATCTTGT
1 TTTATTTATTTTTAT-TTAT
*
11740 TGTTATTTATTTTCATGTTAT
1 T-TTATTTATTTTTAT-TTAT
11761 TTTATT
1 TTTATT
11767 GTTATCTCTT
Statistics
Matches: 114, Mismatches: 15, Indels: 39
0.68 0.09 0.23
Matches are distributed among these distances:
17 5 0.04
18 19 0.17
19 30 0.26
20 15 0.13
21 17 0.15
22 9 0.08
23 14 0.12
24 5 0.04
ACGTcount: A:0.20, C:0.03, G:0.05, T:0.72
Consensus pattern (19 bp):
TTTATTTATTTTTATTTAT
Found at i:11733 original size:29 final size:29
Alignment explanation
Indices: 11666--11830 Score: 88
Period size: 28 Copynumber: 5.4 Consensus size: 29
11656 TTTTTTATTG
11666 TTTATATT-TTTTTATTTTAGTATTTAATTTT-
1 TTTAT-TTATTTTTATTTT--TATTT-ATTTTA
11697 TATT-TTTATTTTTATTTTTATTTATTTTA
1 T-TTATTTATTTTTATTTTTATTTATTTTA
* * *
11726 TTTATTTA-TCTTGTTGTTATTTATTTTCA
1 TTTATTTATTTTTATTTTTATTTATTTT-A
*
11755 TGTTATTTTATTGTTATCTCTTTTATTATTATTTTA
1 T-TTA-TTTATT-TT-TAT-TTTTA-T-TTATTTTA
** * * *
11791 TTTAATTTACATTAATTTTTA-TTATCTTG
1 TTT-ATTTATTTTTATTTTTATTTATTTTA
11820 TTTATTTATTT
1 TTTATTTATTT
11831 ATCATTAAAT
Statistics
Matches: 106, Mismatches: 14, Indels: 31
0.70 0.09 0.21
Matches are distributed among these distances:
28 29 0.27
29 21 0.20
30 5 0.05
31 16 0.15
32 8 0.08
33 2 0.02
34 4 0.04
35 10 0.09
36 4 0.04
37 7 0.07
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.72
Consensus pattern (29 bp):
TTTATTTATTTTTATTTTTATTTATTTTA
Found at i:11758 original size:15 final size:14
Alignment explanation
Indices: 11600--11799 Score: 71
Period size: 15 Copynumber: 13.9 Consensus size: 14
11590 GACATTCAAT
*
11600 TTATTTATTTTTTG
1 TTATTTATTTTATG
*
11614 TTTATTTATTTATTTG
1 -TTATTTATTT-TATG
11630 TTATTTATTTTCATG
1 TTATTTATTTT-ATG
* *
11645 CTTAATCTAAATTT-T-
1 -TT-AT-TTATTTTATG
*
11660 TTATTGT-TTATAT-
1 TTATT-TATTTTATG
*
11673 TTTTTTATTTTA-G
1 TTATTTATTTTATG
*
11686 -TATTTAATTTT-TA
1 TTATTT-ATTTTATG
*
11699 TT-TTTATTTTTATTT
1 TTATTTA-TTTTA-TG
11714 TTATTTATTTTAT-
1 TTATTTATTTTATG
11727 TTATTTATCTTGT-TG
1 TTATTTAT-TT-TATG
11742 TTATTTATTTTCATG
1 TTATTTATTTT-ATG
*
11757 TTATTTTATTGTTATC
1 TTA-TTTATT-TTATG
*
11773 TCT-TTTATTATTATT
1 T-TATTTATT-TTATG
*
11788 TTATTTAATTTA
1 TTATTTATTTTA
11800 CATTAATTTT
Statistics
Matches: 145, Mismatches: 15, Indels: 51
0.69 0.07 0.24
Matches are distributed among these distances:
12 9 0.06
13 32 0.22
14 14 0.10
15 60 0.41
16 20 0.14
17 5 0.03
18 5 0.03
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (14 bp):
TTATTTATTTTATG
Found at i:11778 original size:26 final size:26
Alignment explanation
Indices: 11694--11792 Score: 83
Period size: 26 Copynumber: 3.7 Consensus size: 26
11684 AGTATTTAAT
* * *
11694 TTTTATTTTTATTTTTATTTTTATTTA
1 TTTTATTATTA-TTTTATTGTTATCTA
* * *
11721 TTTTATTTATTTATCTTGTTGTTATTTA
1 TTTTA-TTA-TTATTTTATTGTTATCTA
* *
11749 TTTTCA-TGTTATTTTATTGTTATCTC
1 TTTT-ATTATTATTTTATTGTTATCTA
11775 TTTTATTATTATTTTATT
1 TTTTATTATTATTTTATT
11793 TAATTTACAT
Statistics
Matches: 58, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
25 1 0.02
26 29 0.50
27 6 0.10
28 18 0.31
29 4 0.07
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.74
Consensus pattern (26 bp):
TTTTATTATTATTTTATTGTTATCTA
Found at i:11812 original size:32 final size:31
Alignment explanation
Indices: 11775--11866 Score: 107
Period size: 33 Copynumber: 2.9 Consensus size: 31
11765 TTGTTATCTC
*
11775 TTTTATTATTATTTTATTTAATTTACATTAAT
1 TTTTATTATT-TTTTATTTAATTTACATTAAA
11807 TTTTATTATCTTGTTTATTT-ATTTATCATTAAA
1 TTTTATTAT-TT-TTTATTTAATTTA-CATTAAA
*
11840 TTTTATTTTCTTTTTATTTAA-TTACAT
1 TTTTATTAT-TTTTTATTTAATTTACAT
11867 GTTAATTAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
31 3 0.06
32 25 0.46
33 26 0.48
ACGTcount: A:0.27, C:0.05, G:0.01, T:0.66
Consensus pattern (31 bp):
TTTTATTATTTTTTATTTAATTTACATTAAA
Found at i:11837 original size:33 final size:31
Alignment explanation
Indices: 11775--11866 Score: 114
Period size: 32 Copynumber: 2.9 Consensus size: 31
11765 TTGTTATCTC
*
11775 TTTTATTAT-TATTTTATTTAATTTACATTAAT
1 TTTTATTATCT-TTTTATTT-ATTTACATTAAA
11807 TTTTATTATCTTGTTTATTTATTTATCATTAAA
1 TTTTATTATCTT-TTTATTTATTTA-CATTAAA
* *
11840 TTTTATTTTCTTTTTATTTAATTACAT
1 TTTTATTATCTTTTTATTTATTTACAT
11867 GTTAATTAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
31 3 0.06
32 26 0.48
33 25 0.46
ACGTcount: A:0.27, C:0.05, G:0.01, T:0.66
Consensus pattern (31 bp):
TTTTATTATCTTTTTATTTATTTACATTAAA
Found at i:11953 original size:16 final size:17
Alignment explanation
Indices: 11913--11953 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
11903 TTATGGTTGC
11913 ATTTCATATATTTATTT
1 ATTTCATATATTTATTT
*
11930 -TTTGATATATTTATTT
1 ATTTCATATATTTATTT
11946 ATTT-ATAT
1 ATTTCATAT
11954 GCCATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (17 bp):
ATTTCATATATTTATTT
Found at i:14071 original size:21 final size:21
Alignment explanation
Indices: 14047--14092 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
14037 GCCCAGACCG
14047 CGTGTGGCTA-TCCCACACGCT
1 CGTGTGGCTACT-CCACACGCT
*
14068 CGTGTGGCTACTCCACATGCT
1 CGTGTGGCTACTCCACACGCT
14089 CGTG
1 CGTG
14093 AGCTCACCCG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.13, C:0.35, G:0.26, T:0.26
Consensus pattern (21 bp):
CGTGTGGCTACTCCACACGCT
Found at i:18345 original size:31 final size:31
Alignment explanation
Indices: 18310--18372 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
18300 ACCTTTTAGG
18310 TGTTTGGACTTCTTGTCTAAGATACATTTCA
1 TGTTTGGACTTCTTGTCTAAGATACATTTCA
* *
18341 TGTTTGGACTTTTTGTCTGAGATACATTTCA
1 TGTTTGGACTTCTTGTCTAAGATACATTTCA
18372 T
1 T
18373 AAGTTATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.48
Consensus pattern (31 bp):
TGTTTGGACTTCTTGTCTAAGATACATTTCA
Found at i:21752 original size:13 final size:13
Alignment explanation
Indices: 21734--21758 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21724 GTCACCAAAT
21734 AAAATAATTTAAA
1 AAAATAATTTAAA
21747 AAAATAATTTAA
1 AAAATAATTTAA
21759 TCATGTCAAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAATAATTTAAA
Found at i:23108 original size:18 final size:17
Alignment explanation
Indices: 23078--23111 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
23068 ATAATTGTAA
23078 TTTAAATTATAATTATT
1 TTTAAATTATAATTATT
*
23095 TTTAAATGTGTAATTAT
1 TTTAAAT-TATAATTAT
23112 CACAACTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (17 bp):
TTTAAATTATAATTATT
Found at i:23706 original size:21 final size:21
Alignment explanation
Indices: 23682--23723 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
23672 TGATTGTTAC
*
23682 AGTACTAATATAATCGTTAAT
1 AGTACTAATATAACCGTTAAT
* *
23703 AGTAGTAATATGACCGTTAAT
1 AGTACTAATATAACCGTTAAT
23724 GATACTGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (21 bp):
AGTACTAATATAACCGTTAAT
Found at i:24710 original size:6 final size:6
Alignment explanation
Indices: 24699--24742 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
24689 AAAGTATACA
24699 TTGTGG TTGTGG TTGTGG TTGTGG TTGTGG TTGTGG TTGTGG TT
1 TTGTGG TTGTGG TTGTGG TTGTGG TTGTGG TTGTGG TTGTGG TT
24743 TAAACTAATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (6 bp):
TTGTGG
Found at i:29581 original size:61 final size:61
Alignment explanation
Indices: 29486--29608 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
29476 TTATATGTTG
29486 AATAAACTAAAAATGAAATTATTGAAGGGATTGGATATATGAATAGAAAGGAAATTACTAC
1 AATAAACTAAAAATGAAATTATTGAAGGGATTGGATATATGAATAGAAAGGAAATTACTAC
29547 AATAAACTAAAAATGAAATTATTGAAGGGATTGGATATATGAATAGAAAGGAAATTACTAC
1 AATAAACTAAAAATGAAATTATTGAAGGGATTGGATATATGAATAGAAAGGAAATTACTAC
29608 A
1 A
29609 CATGATTGAG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.51, C:0.05, G:0.18, T:0.26
Consensus pattern (61 bp):
AATAAACTAAAAATGAAATTATTGAAGGGATTGGATATATGAATAGAAAGGAAATTACTAC
Found at i:35938 original size:25 final size:25
Alignment explanation
Indices: 35887--35959 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 25
35877 TTTTCAAAAA
* *
35887 ATATATAATAATAAATTTAAAT-TTT
1 ATAT-TAATAATAAATTAAAATAATT
*
35912 ATATTAATATTAAATTAAAATAATT
1 ATATTAATAATAAATTAAAATAATT
* ** *
35937 ATGTTAATGCTAAATAAAAATAA
1 ATATTAATAATAAATTAAAATAA
35960 AAAGACCCTC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
24 15 0.38
25 25 0.62
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (25 bp):
ATATTAATAATAAATTAAAATAATT
Found at i:38849 original size:178 final size:177
Alignment explanation
Indices: 38551--38897 Score: 493
Period size: 178 Copynumber: 2.0 Consensus size: 177
38541 TGTTATCTAA
*
38551 TTTGGGAGTTAATCATTAGACTTATTATTTTGTTGTGTGCCTTAGAACAAATCCATTGCATATTC
1 TTTGGGAATTAATCATTAGACTTATTATTTTGTTGTGTGCCTTAGAACAAATCCATTGCATATTC
* * * *
38616 TGTGGCTCCGATAAAATGTTTTGTTTGCTTTTGTGTCGCTACGAGGTGTTCAGAGAACTAGAAAT
66 TGTGACTCCGATAAAATGTTTTGTTTGCTTTTGTGGCGCTACAAGGTGTTCAGAGAACCAGAAAT
* * * *
38681 TTTAAGCTTGATCTTCAGTTTAGTTTA-TTATATTTAGCTTTATCTGT
131 GTAAAGCTTAATCTTCAGTTTACTTTAGTT-TATTTAGCTTTATCTGT
* * *
38728 TTTGGGAATTAATC-TTGCGACTTATTTTTTTGTTGTGTGCTTTAGAAACAAATCCATTGCATAT
1 TTTGGGAATTAATCATT-AGACTTATTATTTTGTTGTGTGCCTTAG-AACAAATCCATTGCATAT
** * *
38792 TCTGTGACTGTGATCAAATGTTTTGTTTGCTTTTGTGGCGGTTA-AAGGTGTTCAGAGAACCAGA
64 TCTGTGACTCCGATAAAATGTTTTGTTTGCTTTTGTGGC-GCTACAAGGTGTTCAGAGAACCAGA
38856 AATGTAAAGCTTAATCTTCAGTTTACTTTAGTTTATTTAGCT
128 AATGTAAAGCTTAATCTTCAGTTTACTTTAGTTTATTTAGCT
38898 CTATATATTA
Statistics
Matches: 150, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
176 2 0.01
177 38 0.25
178 105 0.70
179 5 0.03
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.44
Consensus pattern (177 bp):
TTTGGGAATTAATCATTAGACTTATTATTTTGTTGTGTGCCTTAGAACAAATCCATTGCATATTC
TGTGACTCCGATAAAATGTTTTGTTTGCTTTTGTGGCGCTACAAGGTGTTCAGAGAACCAGAAAT
GTAAAGCTTAATCTTCAGTTTACTTTAGTTTATTTAGCTTTATCTGT
Found at i:39935 original size:31 final size:31
Alignment explanation
Indices: 39844--39942 Score: 87
Period size: 31 Copynumber: 3.2 Consensus size: 31
39834 ATTTGGTATT
*
39844 TGAACTTGACACTTTTTCCTAATTTTGTACC
1 TGAACTTGACACTTTTTCCTAATTTAGTACC
* ** * *
39875 TTAACTT---TTTTTTTGACCCAATTTGGTACC
1 TGAACTTGACACTTTTT--CCTAATTTAGTACC
*
39905 TGAACTTGACCCTTTTTCCTAATTTAGTACC
1 TGAACTTGACACTTTTTCCTAATTTAGTACC
*
39936 TAAACTT
1 TGAACTT
39943 TTTTTGGACC
Statistics
Matches: 52, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
28 5 0.10
30 18 0.35
31 24 0.46
33 5 0.10
ACGTcount: A:0.23, C:0.22, G:0.09, T:0.45
Consensus pattern (31 bp):
TGAACTTGACACTTTTTCCTAATTTAGTACC
Found at i:39974 original size:60 final size:61
Alignment explanation
Indices: 39834--39999 Score: 226
Period size: 60 Copynumber: 2.7 Consensus size: 61
39824 TTAATATAAC
* * * *
39834 ATTTGGTATTTGAACTTGACACTTTTTCCTAATTTTGTACCTTAACTTTTTTTTTGACCCA
1 ATTTGGTACTTGAACTTGACACTTTTTCCTAATTTAGTACCTAAACTTTTTTTTGGACCCA
* * *
39895 ATTTGGTACCTGAACTTGACCCTTTTTCCTAATTTAGTACCTAAAC-TTTTTTTGGACCTA
1 ATTTGGTACTTGAACTTGACACTTTTTCCTAATTTAGTACCTAAACTTTTTTTTGGACCCA
* * * *
39955 ATTTGGTACTTGAACTTGACATTTTTTCTTAATTTGGTATCTAAA
1 ATTTGGTACTTGAACTTGACACTTTTTCCTAATTTAGTACCTAAA
40000 TTTATTAAAT
Statistics
Matches: 92, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
60 51 0.55
61 41 0.45
ACGTcount: A:0.23, C:0.17, G:0.11, T:0.48
Consensus pattern (61 bp):
ATTTGGTACTTGAACTTGACACTTTTTCCTAATTTAGTACCTAAACTTTTTTTTGGACCCA
Found at i:42870 original size:43 final size:43
Alignment explanation
Indices: 42790--42886 Score: 133
Period size: 43 Copynumber: 2.3 Consensus size: 43
42780 TAAATGATGT
* * **
42790 ATATGAAAAAGATTGATGCTTTTGTGTAATAGCTAGGCAGGAA
1 ATATGAAAAAGATTGATGCGTCTGTGTAATAAATAGGCAGGAA
*
42833 ATATGAAAAAGATTGATG-GTCTGTTTAGATAAATAGGCAGGAA
1 ATATGAAAAAGATTGATGCGTCTGTGTA-ATAAATAGGCAGGAA
42876 ATATGAAAAAG
1 ATATGAAAAAG
42887 GTGTGTCTGA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 6 0.12
43 42 0.88
ACGTcount: A:0.42, C:0.05, G:0.25, T:0.28
Consensus pattern (43 bp):
ATATGAAAAAGATTGATGCGTCTGTGTAATAAATAGGCAGGAA
Found at i:46052 original size:11 final size:11
Alignment explanation
Indices: 46036--46070 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
46026 TACTTTGAAA
*
46036 TTTTTATACTT
1 TTTTTATAATT
46047 TTTTTATAATT
1 TTTTTATAATT
*
46058 TTTTTTTAATT
1 TTTTTATAATT
46069 TT
1 TT
46071 GAATTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTATAATT
Found at i:46077 original size:18 final size:18
Alignment explanation
Indices: 46048--46098 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
46038 TTTATACTTT
* *
46048 TTTTATAATTTTTTTTTAA
1 TTTTA-AATTTTTTATAAA
*
46067 TTTTGAATTTTTTATAAA
1 TTTTAAATTTTTTATAAA
*
46085 TTTTAAATTATTTA
1 TTTTAAATTTTTTA
46099 CTTGACATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 23 0.85
19 4 0.15
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTTAAATTTTTTATAAA
Found at i:46840 original size:2 final size:2
Alignment explanation
Indices: 46794--46822 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
46784 CTTTAGCTTG
46794 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
46823 GAATTAGACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:50340 original size:22 final size:20
Alignment explanation
Indices: 50315--50355 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
50305 GTCAAACAAA
50315 TAATAAAAACATCAAAAAAATT
1 TAAT-AAAACA-CAAAAAAATT
*
50337 TAATAAATCACAAAAAAAT
1 TAATAAAACACAAAAAAAT
50356 ACGAAAAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 5 0.28
22 4 0.22
ACGTcount: A:0.68, C:0.10, G:0.00, T:0.22
Consensus pattern (20 bp):
TAATAAAACACAAAAAAATT
Found at i:51581 original size:9 final size:9
Alignment explanation
Indices: 51567--51613 Score: 62
Period size: 9 Copynumber: 5.3 Consensus size: 9
51557 AAAAAAATAT
51567 TTTTTATTA
1 TTTTTATTA
51576 TTTTTATTA
1 TTTTTATTA
51585 TTTTTA-TA
1 TTTTTATTA
51593 TTTTT-TTA
1 TTTTTATTA
*
51601 ATTTTATATA
1 TTTTTAT-TA
51611 TTT
1 TTT
51614 CAAAAAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
8 13 0.39
9 16 0.48
10 4 0.12
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTTATTA
Found at i:51588 original size:19 final size:19
Alignment explanation
Indices: 51564--51613 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
51554 ATTAAAAAAA
51564 TATTTTT-TATTATTTTTAT
1 TATTTTTATATT-TTTTTAT
51583 TATTTTTATATTTTTTTA-
1 TATTTTTATATTTTTTTAT
51601 -ATTTTATATATTT
1 TATTTT-TATATTT
51614 CAAAAAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.17
18 7 0.24
19 13 0.45
20 4 0.14
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (19 bp):
TATTTTTATATTTTTTTAT
Found at i:56291 original size:15 final size:15
Alignment explanation
Indices: 56262--56299 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
56252 TATTTGTTAT
56262 ATTAA-TTTAAATTA
1 ATTAATTTTAAATTA
*
56276 ATTAATTTTTAATTA
1 ATTAATTTTAAATTA
*
56291 AATAATTTT
1 ATTAATTTT
56300 CTCAATCCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTAATTTTAAATTA
Done.