Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015077.1 Kokia drynarioides strain JFW-HI SEQ_130121, 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: 92567
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Warning! 46 characters in sequence are not A, C, G, or T
Found at i:3547 original size:20 final size:20
Alignment explanation
Indices: 3522--3569 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
3512 GCTTGTGCGG
3522 GTTTGCAC-TTTGGTGCCTCT
1 GTTTGCACATTT-GTGCCTCT
*
3542 GTTTGCACATTTGTGTCTCT
1 GTTTGCACATTTGTGCCTCT
*
3562 GTCTGCAC
1 GTTTGCAC
3570 CTCGGTGACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 22 0.88
21 3 0.12
ACGTcount: A:0.08, C:0.25, G:0.23, T:0.44
Consensus pattern (20 bp):
GTTTGCACATTTGTGCCTCT
Found at i:6711 original size:29 final size:29
Alignment explanation
Indices: 6652--6720 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
6642 AGTATATTTT
* * * *
6652 TTTATAATTTTTAAAAGATTAAATTAAAA
1 TTTATTATTTTTAAAAAAATAAATAAAAA
6681 TTTATTATTTTTAAAAAAATAAA-AAATAA
1 TTTATTATTTTTAAAAAAATAAATAAA-AA
6710 -TT-TTATTTTTA
1 TTTATTATTTTTA
6721 CTAATTTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
27 9 0.26
28 4 0.11
29 22 0.63
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (29 bp):
TTTATTATTTTTAAAAAAATAAATAAAAA
Found at i:7863 original size:21 final size:20
Alignment explanation
Indices: 7837--7877 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
7827 TTAAAAACTG
*
7837 AAAAAAATAATTGAACCCCTT
1 AAAAAAA-AAATGAACCCCTT
*
7858 AAAAAAAAAATGAATCCCTT
1 AAAAAAAAAATGAACCCCTT
7878 TTAACTTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.56, C:0.17, G:0.05, T:0.22
Consensus pattern (20 bp):
AAAAAAAAAATGAACCCCTT
Found at i:9998 original size:24 final size:24
Alignment explanation
Indices: 9969--10024 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
9959 TGTGTCATCT
9969 TATTATTAATGGATGGTACATAAAA
1 TATTATTAAT-GATGGTACATAAAA
* * *
9994 T-TTATGTACTGATGGTTCATTAAA
1 TATTAT-TAATGATGGTACATAAAA
10018 TATTATT
1 TATTATT
10025 TATCCTTTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
24 18 0.69
25 8 0.31
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (24 bp):
TATTATTAATGATGGTACATAAAA
Found at i:13231 original size:20 final size:21
Alignment explanation
Indices: 13208--13250 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
13198 TTTGAAATAA
13208 TTTTTAT-AA-TTTTATAATTT
1 TTTTTATGAATTTTTA-AATTT
13228 TTTTTATGAATTTTTAAATTT
1 TTTTTATGAATTTTTAAATTT
13249 TT
1 TT
13251 AAAAAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.33
21 9 0.43
22 5 0.24
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (21 bp):
TTTTTATGAATTTTTAAATTT
Found at i:13239 original size:21 final size:19
Alignment explanation
Indices: 13208--13250 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
13198 TTTGAAATAA
*
13208 TTTTTATAATTTTATAATTT
1 TTTTTATAATTTT-TAAATT
13228 TTTTTATGAATTTTTAAATT
1 TTTTTAT-AATTTTTAAATT
13248 TTT
1 TTT
13251 AAAAAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTTTATAATTTTTAAATT
Found at i:37627 original size:23 final size:24
Alignment explanation
Indices: 37559--37635 Score: 106
Period size: 23 Copynumber: 3.3 Consensus size: 24
37549 ATACTAGCGC
37559 GCTTACT--ATTCAGCACTGTGTGT
1 GCTTACTAGATTC-GCACTGTGTGT
*
37582 GCTTACTTGATTCGCACTGTGTGT
1 GCTTACTAGATTCGCACTGTGTGT
*
37606 GCTTACTAGATT-GTACTGTGTGT
1 GCTTACTAGATTCGCACTGTGTGT
37629 GCTTACT
1 GCTTACT
37636 GTTGCCCAGC
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
23 24 0.48
24 22 0.44
25 4 0.08
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (24 bp):
GCTTACTAGATTCGCACTGTGTGT
Found at i:37870 original size:78 final size:78
Alignment explanation
Indices: 37777--37931 Score: 276
Period size: 78 Copynumber: 2.0 Consensus size: 78
37767 AACTATGATG
* *
37777 GCTAAATTGTAAAAGATAAAAGAATGTGTAAATTGTGATATTGAGGTAAGT-ATAAAGATGAACA
1 GCTAAATTGTAAAAGATAAAAGAATGTGCAAATTGTGATATTGAAGTAAGTGA-AAAGATGAACA
37841 TATGAAAGATAAGA
65 TATGAAAGATAAGA
37855 GCTAAATTGTAAAAGATAAAAGAATGTGCAAATTGTGATATTGAAGTAAGTGAAAAGATGAACAT
1 GCTAAATTGTAAAAGATAAAAGAATGTGCAAATTGTGATATTGAAGTAAGTGAAAAGATGAACAT
37920 ATGAAAGATAAG
66 ATGAAAGATAAG
37932 TATTATTTGT
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
78 73 0.99
79 1 0.01
ACGTcount: A:0.49, C:0.03, G:0.22, T:0.26
Consensus pattern (78 bp):
GCTAAATTGTAAAAGATAAAAGAATGTGCAAATTGTGATATTGAAGTAAGTGAAAAGATGAACAT
ATGAAAGATAAGA
Found at i:41266 original size:27 final size:28
Alignment explanation
Indices: 41234--41306 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 28
41224 AGAAACTAAC
*
41234 TTAAAACAATAACTTAAATTTAAA-CTT
1 TTAAAACAATAATTTAAATTTAAATCTT
*
41261 TTAAAA-ACAT--TTTAAGTTTAAATCTT
1 TTAAAACA-ATAATTTAAATTTAAATCTT
41287 TT-AAACAATAATTTAAATTT
1 TTAAAACAATAATTTAAATTT
41307 TTTATTGAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
25 15 0.39
26 7 0.18
27 16 0.42
ACGTcount: A:0.48, C:0.08, G:0.01, T:0.42
Consensus pattern (28 bp):
TTAAAACAATAATTTAAATTTAAATCTT
Found at i:41275 original size:25 final size:27
Alignment explanation
Indices: 41237--41306 Score: 81
Period size: 25 Copynumber: 2.7 Consensus size: 27
41227 AACTAACTTA
* *
41237 AAACAATAACTTAAATTTAAA-CTTTT
1 AAACAACAATTTAAATTTAAATCTTTT
* *
41263 AAA-AACATTTTAAGTTTAAATCTTTT
1 AAACAACAATTTAAATTTAAATCTTTT
*
41289 AAACAATAATTTAAATTT
1 AAACAACAATTTAAATTT
41307 TTTATTGAGT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
25 13 0.37
26 11 0.31
27 11 0.31
ACGTcount: A:0.49, C:0.09, G:0.01, T:0.41
Consensus pattern (27 bp):
AAACAACAATTTAAATTTAAATCTTTT
Found at i:65583 original size:56 final size:56
Alignment explanation
Indices: 65497--65607 Score: 222
Period size: 56 Copynumber: 2.0 Consensus size: 56
65487 TTTTGAGTGA
65497 CAAGAGAAGTATCAGATTCAAAGGATTAAAGAACTGAAAGGTGTAAATCATTGATG
1 CAAGAGAAGTATCAGATTCAAAGGATTAAAGAACTGAAAGGTGTAAATCATTGATG
65553 CAAGAGAAGTATCAGATTCAAAGGATTAAAGAACTGAAAGGTGTAAATCATTGAT
1 CAAGAGAAGTATCAGATTCAAAGGATTAAAGAACTGAAAGGTGTAAATCATTGAT
65608 CCTTTTAATT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
CAAGAGAAGTATCAGATTCAAAGGATTAAAGAACTGAAAGGTGTAAATCATTGATG
Found at i:67273 original size:2 final size:2
Alignment explanation
Indices: 67261--67290 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
67251 AAAATAATAG
*
67261 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
67291 ATTGATGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:69286 original size:58 final size:59
Alignment explanation
Indices: 69221--69452 Score: 207
Period size: 59 Copynumber: 4.0 Consensus size: 59
69211 TAGACACTCA
69221 AGGGTAAAATGGTAA-TTTTGGAAAAATTAGGGTCAAAAATGGAATTTTAAGAAGTTCG
1 AGGGTAAAATGGTAATTTTTGGAAAAATTAGGGTCAAAAATGGAATTTTAAGAAGTTCG
** * * *
69279 -GGAGTAAAATGGTAATTTTTGGTGAATTTGGGGTTAAAAATGGAATTTTGGAA-AA-TTCG
1 AGG-GTAAAATGGTAATTTTTGGAAAAATTAGGGTCAAAAATGGAATTTT--AAGAAGTTCG
* * ** *
69338 AGGGTAAAAAT-GTTATTTTTGAAAAAATCGGGGT-AAAAATGGAATTTT-GGAAAGTTCG
1 AGGGT-AAAATGGTAATTTTTGGAAAAATTAGGGTCAAAAATGGAATTTTAAG-AAGTTCG
*
69396 AGGGTAAAAT-GTAATTTTTGG-AAAGTTCAAGGGTCAAAATAT--AATTTTAGAGAAGTT
1 AGGGTAAAATGGTAATTTTTGGAAAAATT--AGGGTCAAAA-ATGGAATTTTA-AGAAGTT
69453 TAGAGGTTAA
Statistics
Matches: 141, Mismatches: 18, Indels: 29
0.75 0.10 0.15
Matches are distributed among these distances:
56 4 0.03
57 18 0.13
58 45 0.32
59 60 0.43
60 12 0.09
61 2 0.01
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.32
Consensus pattern (59 bp):
AGGGTAAAATGGTAATTTTTGGAAAAATTAGGGTCAAAAATGGAATTTTAAGAAGTTCG
Found at i:69323 original size:59 final size:58
Alignment explanation
Indices: 69221--69419 Score: 212
Period size: 59 Copynumber: 3.4 Consensus size: 58
69211 TAGACACTCA
* *
69221 AGGGTAAAATGGTAA-TTTTGGAAAAATTAGGGTCAAAAATGGAATTTTAAGAAGTTCG
1 AGGGTAAAAT-GTAATTTTTGGAAAAATTGGGGTTAAAAATGGAATTTTAAGAAGTTCG
** *
69279 -GGAGTAAAATGGTAATTTTTGGTGAATTTGGGGTTAAAAATGGAATTTTGGAA-AA-TTCG
1 AGG-GTAAAAT-GTAATTTTTGGAAAAATTGGGGTTAAAAATGGAATTTT--AAGAAGTTCG
* * * *
69338 AGGGTAAAAATGTTATTTTTGAAAAAATCGGGG-TAAAAATGGAATTTT-GGAAAGTTCG
1 AGGGT-AAAATGTAATTTTTGGAAAAATTGGGGTTAAAAATGGAATTTTAAG-AAGTTCG
69396 AGGGTAAAATGTAATTTTTGGAAA
1 AGGGTAAAATGTAATTTTTGGAAA
69420 GTTCAAGGGT
Statistics
Matches: 118, Mismatches: 14, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
57 21 0.18
58 36 0.31
59 50 0.42
60 9 0.08
61 2 0.02
ACGTcount: A:0.39, C:0.03, G:0.27, T:0.32
Consensus pattern (58 bp):
AGGGTAAAATGTAATTTTTGGAAAAATTGGGGTTAAAAATGGAATTTTAAGAAGTTCG
Found at i:69400 original size:29 final size:29
Alignment explanation
Indices: 69221--69435 Score: 153
Period size: 29 Copynumber: 7.4 Consensus size: 29
69211 TAGACACTCA
69221 AGGGT-AAAATGGTAATTTTGGAAAAATT--
1 AGGGTAAAAATGG-AATTTTGG-AAAATTCG
69249 AGGGTCAAAAATGGAATTTT--AAGAAGTTCG
1 AGGGT-AAAAATGGAATTTTGGAA-AA-TTCG
** *
69279 -GGAGT-AAAATGGTAATTTTTGGTGAATTTG
1 AGG-GTAAAAATGG-AA-TTTTGGAAAATTCG
69309 -GGGTTAAAAATGGAATTTTGGAAAATTCG
1 AGGG-TAAAAATGGAATTTTGGAAAATTCG
* * * *
69338 AGGGTAAAAATGTTATTTTTGAAAAAATCG
1 AGGGTAAAAATG-GAATTTTGGAAAATTCG
*
69368 -GGGTAAAAATGGAATTTTGGAAAGTTCG
1 AGGGTAAAAATGGAATTTTGGAAAATTCG
* * *
69396 AGGGT-AAAATGTAATTTTTGGAAAGTTCA
1 AGGGTAAAAATGGAA-TTTTGGAAAATTCG
*
69425 AGGGTCAAAAT
1 AGGGTAAAAAT
69436 ATAATTTTAG
Statistics
Matches: 152, Mismatches: 17, Indels: 34
0.75 0.08 0.17
Matches are distributed among these distances:
26 2 0.01
27 2 0.01
28 34 0.22
29 63 0.41
30 42 0.28
31 9 0.06
ACGTcount: A:0.39, C:0.03, G:0.27, T:0.32
Consensus pattern (29 bp):
AGGGTAAAAATGGAATTTTGGAAAATTCG
Found at i:69441 original size:30 final size:29
Alignment explanation
Indices: 69382--69481 Score: 105
Period size: 29 Copynumber: 3.4 Consensus size: 29
69372 AAAAATGGAA
* *
69382 TTTTGGAAAGTTCGAGGGTAAAATGTAAT
1 TTTTGGAAAGTTCAAGGGTAAAATATAAT
69411 TTTTGGAAAGTTCAAGGGTCAAAATATAA-
1 TTTTGGAAAGTTCAAGGGT-AAAATATAAT
* * *
69440 TTTTAGAGAAGTT-TAGAGGTTAAATATAAT
1 TTTTGGA-AAGTTCAAG-GGTAAAATATAAT
*
69470 TTTTGGACAGTT
1 TTTTGGAAAGTT
69482 TAGGGACCTT
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
29 38 0.63
30 22 0.37
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.37
Consensus pattern (29 bp):
TTTTGGAAAGTTCAAGGGTAAAATATAAT
Found at i:76339 original size:58 final size:55
Alignment explanation
Indices: 76272--76486 Score: 259
Period size: 58 Copynumber: 3.7 Consensus size: 55
76262 ATCGAGGTAA
** *
76272 AAAATGGAATTTTAGGAAGATAGAGGGTAAAATGGTAATTTTTGGTGAAATCGGAATC
1 AAAATGGAATTTT-GGAAGATAG-GGGTAAAAT-GTAATTTTTGGTGAAATCGGGGTT
* *
76330 AAAATGGAATTTTGGAAAGTTCGGGGCTAAAATGGTAATTTTTGGTGAAATCGGGGTT
1 AAAATGGAATTTTGG-AAGATAGGGG-TAAAAT-GTAATTTTTGGTGAAATCGGGGTT
* * * *
76388 AAAATGGAATTTTGAAAAGTTCGAGGTAAAATGTAATTTTTGGTGAAATCGGGGTT
1 AAAATGGAATTTTG-GAAGATAGGGGTAAAATGTAATTTTTGGTGAAATCGGGGTT
*
76444 AAAATGGAATTTTGGAAAATTTAGGGGTAAAATGTAATTTTTG
1 AAAATGGAATTTTGGAAGA--TAGGGGTAAAATGTAATTTTTG
76487 AAAAGTTTAA
Statistics
Matches: 140, Mismatches: 12, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
55 2 0.01
56 38 0.27
57 31 0.22
58 69 0.49
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.33
Consensus pattern (55 bp):
AAAATGGAATTTTGGAAGATAGGGGTAAAATGTAATTTTTGGTGAAATCGGGGTT
Found at i:76361 original size:28 final size:26
Alignment explanation
Indices: 76272--76489 Score: 129
Period size: 28 Copynumber: 7.7 Consensus size: 26
76262 ATCGAGGTAA
*
76272 AAAATGGAATTTTAGGAAGA-TAGAGGGT
1 AAAATGGAATTTT-GGAA-ATTCG-GGGT
**
76300 AAAATGGTAATTTTTGGTGAAA-TCGGAAT
1 AAAATGG-AA-TTTT-G-GAAATTCGGGGT
76329 CAAAATGGAATTTTGGAAAGTTCGGGGCT
1 -AAAATGGAATTTTGGAAA-TTCGGGG-T
76358 AAAATGGTAATTTTTGGTGAAA-TCGGGGTT
1 AAAATGG-AA-TTTT-G-GAAATTCGGGG-T
* *
76388 AAAATGGAATTTTGAAAAGTTCGAGGT
1 AAAATGGAATTTTGGAAA-TTCGGGGT
*
76415 AAAATGTAATTTTTGGTGAAA-TCGGGGTT
1 AAAATGGAA-TTTT-G-GAAATTCGGGG-T
*
76444 AAAATGGAATTTTGGAAAATTTAGGGGT
1 AAAATGGAATTTTGG-AAA-TTCGGGGT
* *
76472 AAAATGTAATTTTTGAAA
1 AAAATGGAATTTTGGAAA
76490 AGTTTAAGGG
Statistics
Matches: 154, Mismatches: 16, Indels: 41
0.73 0.08 0.19
Matches are distributed among these distances:
26 8 0.05
27 18 0.12
28 58 0.38
29 26 0.17
30 36 0.23
31 4 0.03
32 4 0.03
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.33
Consensus pattern (26 bp):
AAAATGGAATTTTGGAAATTCGGGGT
Found at i:76441 original size:56 final size:57
Alignment explanation
Indices: 76296--76486 Score: 287
Period size: 58 Copynumber: 3.4 Consensus size: 57
76286 GGAAGATAGA
** * *
76296 GGGTAAAATGGTAATTTTTGGTGAAATCGGAATCAAAATGGAATTTTGGAAAGTTCG
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGAATTTTGAAAAGTTCG
76353 GGGCTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGAATTTTGAAAAGTTCG
1 GGG-TAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGAATTTTGAAAAGTTCG
* * *
76411 AGGTAAAAT-GTAATTTTTGGTGAAATCGGGGTTAAAATGGAATTTTGGAAAATTTAG
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGAATTTT-GAAAAGTTCG
76468 GGGTAAAAT-GTAATTTTTG
1 GGGTAAAATGGTAATTTTTG
76487 AAAAGTTTAA
Statistics
Matches: 124, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
56 37 0.30
57 35 0.28
58 52 0.42
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.34
Consensus pattern (57 bp):
GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGAATTTTGAAAAGTTCG
Found at i:76470 original size:29 final size:29
Alignment explanation
Indices: 76330--76536 Score: 133
Period size: 30 Copynumber: 7.2 Consensus size: 29
76320 AATCGGAATC
* *
76330 AAAATGGAATTTTGG-AAAGTTCGGGGCT
1 AAAATGGAATTTTGGAAAATTTCGGGGTT
*
76358 AAAATGGTAATTTTTGGTGAAA--TCGGGGTT
1 AAAATGG-AA-TTTTGG-AAAATTTCGGGGTT
* *
76388 AAAATGGAATTTT-GAAAAGTTCGAGG-T
1 AAAATGGAATTTTGGAAAATTTCGGGGTT
* *
76415 AAAATGTAATTTTTGGTGAAA--TCGGGGTT
1 AAAATGGAA-TTTTGG-AAAATTTCGGGGTT
*
76444 AAAATGGAATTTTGGAAAATTTAGGGG-T
1 AAAATGGAATTTTGGAAAATTTCGGGGTT
* * ** *
76472 AAAATGTAATTTTTGAAAAGTTTAAGGGTC
1 AAAATGGAATTTTGGAAAA-TTTCGGGGTT
** * * *
76502 AAAATATAATTTTAGAGAAGTTTAGGGGTT
1 AAAATGGAATTTTGGA-AAATTTCGGGGTT
76532 AAAAT
1 AAAAT
76537 ATAATTTTTG
Statistics
Matches: 146, Mismatches: 18, Indels: 28
0.76 0.09 0.15
Matches are distributed among these distances:
26 3 0.02
27 13 0.09
28 49 0.34
29 26 0.18
30 50 0.34
31 2 0.01
32 3 0.02
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (29 bp):
AAAATGGAATTTTGGAAAATTTCGGGGTT
Found at i:76506 original size:114 final size:116
Alignment explanation
Indices: 76292--76547 Score: 272
Period size: 114 Copynumber: 2.2 Consensus size: 116
76282 TTTAGGAAGA
*
76292 TAGAGGGTAAAATGGTAATTTTTGGTGAAATCGGAATCAAAATGGAATTTTGGAAAGTTCGGGGC
1 TAGA-GGTAAAAT-GTAATTTTTGGTGAAATCGGAATCAAAATGGAATTTTGGAAAGTTAGGGGC
* ** * *
76357 TAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGAATTTT-GAAAAG-T
64 TAAAATGGTAATTTTTGGTAAAATAAGGGTCAAAATAGAATTTTAGAAAAGTT
* ** * *
76408 TCGAGGTAAAATGTAATTTTTGGTGAAATCGGGGTTAAAATGGAATTTTGGAAAATTTAGGGG-T
1 TAGAGGTAAAATGTAATTTTTGGTGAAATCGGAATCAAAATGGAATTTTGG-AAAGTTAGGGGCT
* *
76472 AAAAT-GTAATTTTT-G-AAAAGTTTAAGGGTCAAAATATAATTTTAGAGAAGTT
65 AAAATGGTAATTTTTGGTAAAA---TAAGGGTCAAAATAGAATTTTAGAAAAGTT
* *
76524 TAGGGGTTAAAATATAATTTTTGG
1 TAGAGG-TAAAATGTAATTTTTGG
76548 ATAGTTTATG
Statistics
Matches: 117, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
111 3 0.03
112 1 0.01
113 9 0.08
114 58 0.50
115 22 0.19
116 8 0.07
117 16 0.14
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.34
Consensus pattern (116 bp):
TAGAGGTAAAATGTAATTTTTGGTGAAATCGGAATCAAAATGGAATTTTGGAAAGTTAGGGGCTA
AAATGGTAATTTTTGGTAAAATAAGGGTCAAAATAGAATTTTAGAAAAGTT
Found at i:76512 original size:30 final size:29
Alignment explanation
Indices: 76451--76555 Score: 122
Period size: 30 Copynumber: 3.6 Consensus size: 29
76441 GTTAAAATGG
* *
76451 AATTTTGGAAAA-TTTAGGGGTAAAATGT
1 AATTTTTGAAAAGTTTAGGGGTAAAATAT
*
76479 AATTTTTGAAAAGTTTAAGGGTCAAAATAT
1 AATTTTTGAAAAGTTTAGGGGT-AAAATAT
* *
76509 AATTTTAGAGAAGTTTAGGGGTTAAAATAT
1 AATTTTTGAAAAGTTTAGGGG-TAAAATAT
* *
76539 AATTTTTGGATAGTTTA
1 AATTTTTGAAAAGTTTA
76556 TGGACCTTTA
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 11 0.17
29 8 0.12
30 44 0.69
31 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.21, T:0.39
Consensus pattern (29 bp):
AATTTTTGAAAAGTTTAGGGGTAAAATAT
Found at i:77683 original size:21 final size:21
Alignment explanation
Indices: 77628--77684 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
77618 CTTCCTTTTT
* *
77628 TTATTAATTAT-TTATTATTA
1 TTATTAATAATATTATTACTA
* *
77648 TTATTAA-ATTCATTATTACTG
1 TTATTAATAAT-ATTATTACTA
77669 TTATTAATAATATTAT
1 TTATTAATAATATTAT
77685 CATTAATAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
19 1 0.03
20 7 0.24
21 19 0.66
22 2 0.07
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (21 bp):
TTATTAATAATATTATTACTA
Found at i:77684 original size:36 final size:34
Alignment explanation
Indices: 77643--77719 Score: 86
Period size: 36 Copynumber: 2.2 Consensus size: 34
77633 AATTATTTAT
* *
77643 TATTATTATTAA-ATTCATTATTACTGTTATTAATAA
1 TATTATTATTAATAAT-ATTATTA-AGTTATTAA-AA
*
77679 TATTATCATTAATAATATTATTAAGTTATTAAAA
1 TATTATTATTAATAATATTATTAAGTTATTAAAA
77713 TA-TATTA
1 TATTATTA
77720 ATTACTAGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
33 4 0.11
34 4 0.11
35 8 0.22
36 18 0.50
37 2 0.06
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.51
Consensus pattern (34 bp):
TATTATTATTAATAATATTATTAAGTTATTAAAA
Found at i:77691 original size:15 final size:15
Alignment explanation
Indices: 77671--77699 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
77661 TATTACTGTT
77671 ATTAATAATATTATC
1 ATTAATAATATTATC
77686 ATTAATAATATTAT
1 ATTAATAATATTAT
77700 TAAGTTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTAATAATATTATC
Found at i:78463 original size:6 final size:6
Alignment explanation
Indices: 78452--78508 Score: 73
Period size: 6 Copynumber: 9.8 Consensus size: 6
78442 GAAAATATAA
* *
78452 TTAAAT TTAAAT TT-ACT TTAAAT TTAAAT TTAAAT TTAAA- ATAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
78498 CTAAAT TTAAA
1 TTAAAT TTAAA
78509 ACAAATTTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
5 8 0.18
6 36 0.82
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (6 bp):
TTAAAT
Found at i:78471 original size:11 final size:11
Alignment explanation
Indices: 78450--78490 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
78440 TTGAAAATAT
*
78450 AATTAAATTTA
1 AATTTAATTTA
*
78461 AATTTACTTTA
1 AATTTAATTTA
78472 AATTTAAATTTA
1 AATTT-AATTTA
78484 AATTTAA
1 AATTTAA
78491 AATAAATCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 16 0.62
12 10 0.38
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (11 bp):
AATTTAATTTA
Found at i:78482 original size:23 final size:23
Alignment explanation
Indices: 78433--78508 Score: 91
Period size: 23 Copynumber: 3.3 Consensus size: 23
78423 GGGACATAAT
78433 TTTAAATTTGAAAATATAA-TTAAA
1 TTTAAATTT-AAAATA-AATTTAAA
***
78457 TTTAAATTTACTTTAAATTTAAA
1 TTTAAATTTAAAATAAATTTAAA
*
78480 TTTAAATTTAAAATAAATCTAAA
1 TTTAAATTTAAAATAAATTTAAA
78503 TTTAAA
1 TTTAAA
78509 ACAAATTTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
22 2 0.05
23 33 0.75
24 9 0.20
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (23 bp):
TTTAAATTTAAAATAAATTTAAA
Found at i:78496 original size:11 final size:12
Alignment explanation
Indices: 78453--78524 Score: 53
Period size: 11 Copynumber: 6.3 Consensus size: 12
78443 AAAATATAAT
78453 TAAATTTAAAT-
1 TAAATTTAAATA
* * *
78464 TTACTTTAAATT
1 TAAATTTAAATA
*
78476 TAAATTTAAATT
1 TAAATTTAAATA
* *
78488 TAAA-ATAAATC
1 TAAATTTAAATA
78499 TAAATTTAAA-A
1 TAAATTTAAATA
*
78510 CAAATTTAAA-A
1 TAAATTTAAATA
78521 TAAA
1 TAAA
78525 CTTAGAAGGG
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
11 31 0.63
12 18 0.37
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (12 bp):
TAAATTTAAATA
Found at i:78496 original size:17 final size:17
Alignment explanation
Indices: 78476--78519 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
78466 ACTTTAAATT
78476 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
78493 TAAATCTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
78510 CAAATTTAAA
1 TAAATTTAAA
78520 ATAAACTTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:81234 original size:23 final size:20
Alignment explanation
Indices: 81134--81268 Score: 64
Period size: 21 Copynumber: 6.7 Consensus size: 20
81124 AATAACATCC
*
81134 AAACAACAAAAATAACAATCAA
1 AAACAACAAAAA-AAC-AGCAA
* * * **
81156 ACAGCAGCAAAACAACATAAA
1 A-AACAACAAAAAAACAGCAA
*
81177 AAAAAACAAAAATAACAGCAA
1 AAACAACAAAAA-AACAGCAA
**
81198 AAACAACACGAAAACAGCAACCA
1 AAACAACAAAAAAACAGC-A--A
81221 AAACAACAAAAAAAC--C-A
1 AAACAACAAAAAAACAGCAA
**
81238 AAACAGTAAAAAAACA-CAA
1 AAACAACAAAAAAACAGCAA
*
81257 AAAGAA-AAAAAA
1 AAACAACAAAAAA
81269 TAGCAACCAA
Statistics
Matches: 87, Mismatches: 19, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
17 14 0.16
18 7 0.08
19 5 0.06
20 13 0.15
21 22 0.25
22 4 0.05
23 22 0.25
ACGTcount: A:0.72, C:0.19, G:0.05, T:0.04
Consensus pattern (20 bp):
AAACAACAAAAAAACAGCAA
Found at i:81252 original size:40 final size:42
Alignment explanation
Indices: 81208--81307 Score: 117
Period size: 40 Copynumber: 2.5 Consensus size: 42
81198 AAACAACACG
81208 AAAACAGCAACCAAAACAACAAAA-A-AACCAAAACAGTAAA
1 AAAACAGCAACCAAAACAACAAAATACAACCAAAACAGTAAA
*
81248 AAAACA-CAA--AAAGA-AAAAAAATAGCAACCAAAACAGTAAA
1 AAAACAGCAACCAAA-ACAACAAAATA-CAACCAAAACAGTAAA
81288 AAAA-AGC-ACCAAAACAACAA
1 AAAACAGCAACCAAAACAACAA
81308 TATAATTTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
37 9 0.18
38 2 0.04
39 5 0.10
40 27 0.54
41 7 0.14
ACGTcount: A:0.71, C:0.20, G:0.06, T:0.03
Consensus pattern (42 bp):
AAAACAGCAACCAAAACAACAAAATACAACCAAAACAGTAAA
Found at i:81265 original size:17 final size:17
Alignment explanation
Indices: 81216--81268 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
81206 CGAAAACAGC
81216 AACCAAAACA-ACAAAAA
1 AACCAAAACAGA-AAAAA
*
81233 AACCAAAACAGTAAAAA
1 AACCAAAACAGAAAAAA
81250 AACACAAAA-AGAAAAAA
1 AAC-CAAAACAGAAAAAA
81267 AA
1 AA
81269 TAGCAACCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 27 0.84
18 5 0.16
ACGTcount: A:0.77, C:0.17, G:0.04, T:0.02
Consensus pattern (17 bp):
AACCAAAACAGAAAAAA
Found at i:81984 original size:16 final size:16
Alignment explanation
Indices: 81963--81996 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
81953 TTTTCCCCTA
*
81963 TTAATTATAAACTCAT
1 TTAATTACAAACTCAT
*
81979 TTAATTACAAAGTCAT
1 TTAATTACAAACTCAT
81995 TT
1 TT
81997 CACTATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.12, G:0.03, T:0.44
Consensus pattern (16 bp):
TTAATTACAAACTCAT
Found at i:88399 original size:70 final size:71
Alignment explanation
Indices: 88271--88412 Score: 196
Period size: 70 Copynumber: 2.0 Consensus size: 71
88261 AAAACATCTG
* ** * **
88271 ATACCATAGAATGAACAGGAGAAGCAAGATTTCAACTAGGAAAAGTAAACACTTCTTAGGAAAGA
1 ATACCATAGAATAAACAGGAGAAGCAAGAAGTCAACCAGGAAAAAAAAACACTTCTTAGGAAAGA
88336 ACCAAA
66 ACCAAA
* * *
88342 ATACCATGGAATAAACATGAGAAGCAAGAAGTCGACCA-GAAAAAAAAACACTTCTTAGGAAAGA
1 ATACCATAGAATAAACAGGAGAAGCAAGAAGTCAACCAGGAAAAAAAAACACTTCTTAGGAAAGA
88406 ACCAAA
66 ACCAAA
88412 A
1 A
88413 ACATTTGATA
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
70 31 0.50
71 31 0.50
ACGTcount: A:0.51, C:0.16, G:0.18, T:0.15
Consensus pattern (71 bp):
ATACCATAGAATAAACAGGAGAAGCAAGAAGTCAACCAGGAAAAAAAAACACTTCTTAGGAAAGA
ACCAAA
Found at i:89311 original size:106 final size:106
Alignment explanation
Indices: 89126--89337 Score: 424
Period size: 106 Copynumber: 2.0 Consensus size: 106
89116 TCAAAGTTTG
89126 TCTTCGAGAGTTCTTTGGTGAGTACATCAGCAATATGTTGTTTTTTAGGAGCAAATGGCTTGCAC
1 TCTTCGAGAGTTCTTTGGTGAGTACATCAGCAATATGTTGTTTTTTAGGAGCAAATGGCTTGCAC
89191 ACTTGGCCTTCTTCAATCTTCTCCTTGATGAAGTGTCTATC
66 ACTTGGCCTTCTTCAATCTTCTCCTTGATGAAGTGTCTATC
89232 TCTTCGAGAGTTCTTTGGTGAGTACATCAGCAATATGTTGTTTTTTAGGAGCAAATGGCTTGCAC
1 TCTTCGAGAGTTCTTTGGTGAGTACATCAGCAATATGTTGTTTTTTAGGAGCAAATGGCTTGCAC
89297 ACTTGGCCTTCTTCAATCTTCTCCTTGATGAAGTGTCTATC
66 ACTTGGCCTTCTTCAATCTTCTCCTTGATGAAGTGTCTATC
89338 AATCTAAACA
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 106 1.00
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.39
Consensus pattern (106 bp):
TCTTCGAGAGTTCTTTGGTGAGTACATCAGCAATATGTTGTTTTTTAGGAGCAAATGGCTTGCAC
ACTTGGCCTTCTTCAATCTTCTCCTTGATGAAGTGTCTATC
Done.