Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014703.1 Kokia drynarioides strain JFW-HI SEQ_129742, 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: 42861
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:567 original size:29 final size:29
Alignment explanation
Indices: 525--795 Score: 136
Period size: 29 Copynumber: 9.5 Consensus size: 29
515 CTAAACTATT
*
525 CAAAAATTACATTTTTACCCCCGAACTTC
1 CAAAAATTCCATTTTTACCCCCGAACTTC
554 CAAAAATTCCATTTTT------G-AC-TC
1 CAAAAATTCCATTTTTACCCCCGAACTTC
* ** *
575 CAAAAATTCCATTTTGACCCCAAAATTTC
1 CAAAAATTCCATTTTTACCCCCGAACTTC
*
604 CAAAAATTCCA-TTTTACCCTCGAACTTC
1 CAAAAATTCCATTTTTACCCCCGAACTTC
** *** *
632 CAAATTTTCCATTTTTGACCCTAAAACTTT
1 CAAAAATTCCATTTTT-ACCCCCGAACTTC
* * *
662 CAAAAATTACAATTTTGCCCCCGAA-TGTC
1 CAAAAATTCCATTTTTACCCCCGAACT-TC
* * * *
691 CAAAAACTCCATTTTCAACCTCGAAAC-TC
1 CAAAAATTCCATTTTTACCCCCG-AACTTC
* * * *
720 TAAAAAATTACACTTTTACCCCC-AAATATC
1 -CAAAAATTCCATTTTTACCCCCGAACT-TC
* * *
750 TAAAAAATTCCA-TTTTAACCCCAAACTTTC
1 -CAAAAATTCCATTTTTACCCCCGAAC-TTC
*
780 CCAAAATTACCATTTT
1 CAAAAATT-CCATTTT
796 GCCCTCAAGA
Statistics
Matches: 179, Mismatches: 43, Indels: 38
0.69 0.17 0.15
Matches are distributed among these distances:
21 17 0.09
22 2 0.01
23 1 0.01
28 25 0.14
29 71 0.40
30 59 0.33
31 4 0.02
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.32
Consensus pattern (29 bp):
CAAAAATTCCATTTTTACCCCCGAACTTC
Found at i:589 original size:20 final size:21
Alignment explanation
Indices: 552--605 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 21
542 CCCCCGAACT
552 TCCAAAAATTCCATTTTTGAC
1 TCCAAAAATTCCATTTTTGAC
573 TCCAAAAATTCCA-TTTTGAC
1 TCCAAAAATTCCATTTTTGAC
* *
593 CCCAAAATTTCCA
1 TCCAAAAATTCCA
606 AAAATTCCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 18 0.58
21 13 0.42
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (21 bp):
TCCAAAAATTCCATTTTTGAC
Found at i:703 original size:59 final size:58
Alignment explanation
Indices: 573--795 Score: 186
Period size: 59 Copynumber: 3.8 Consensus size: 58
563 CATTTTTGAC
* * *
573 TCCAAAAATTCCATTTTGACCCCAAAA-TTTCCAAAAATT-CCATTTTACCCTCGAACT
1 TCCAAAAATTCCATTTTGACCCTAAAACTTTCCAAAAATTACAATTTTACCCCCGAA-T
** *
630 TCCAAATTTTCCATTTTTGACCCTAAAACTTT-CAAAAATTACAATTTTGCCCCCGAAT
1 TCCAAAAATTCCA-TTTTGACCCTAAAACTTTCCAAAAATTACAATTTTACCCCCGAAT
* * * * * * * *
688 GTCCAAAAACTCCATTTTCAACCTCGAAACTCT-AAAAAATTACACTTTTACCCCCAAAT
1 -TCCAAAAATTCCATTTTGACCCT-AAAACTTTCCAAAAATTACAATTTTACCCCCGAAT
* * * * *
747 ATCTAAAAAATTCCATTTTAACCC-CAAACTTTCCCAAAATTACCATTTT
1 -TC-CAAAAATTCCATTTTGACCCTAAAACTTTCCAAAAATTACAATTTT
796 GCCCTCAAGA
Statistics
Matches: 131, Mismatches: 28, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
57 11 0.08
58 36 0.27
59 68 0.52
60 16 0.12
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.32
Consensus pattern (58 bp):
TCCAAAAATTCCATTTTGACCCTAAAACTTTCCAAAAATTACAATTTTACCCCCGAAT
Found at i:752 original size:30 final size:29
Alignment explanation
Indices: 718--774 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
708 ACCTCGAAAC
*
718 TCTAAAAAATTACACTTTTACCCCCAAATA
1 TCTAAAAAATTACA-TTTTAACCCCAAATA
*
748 TCTAAAAAATTCCATTTTAACCCCAAA
1 TCTAAAAAATTACATTTTAACCCCAAA
775 CTTTCCCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.30
Consensus pattern (29 bp):
TCTAAAAAATTACATTTTAACCCCAAATA
Found at i:1368 original size:111 final size:112
Alignment explanation
Indices: 1174--1398 Score: 443
Period size: 111 Copynumber: 2.0 Consensus size: 112
1164 GCAATGTTTC
1174 CTTATCTTCGATTCTAATATTTGCGCCTTAACTTACTAGGTGCAACCTTTCTTCAAATCGAGATA
1 CTTATCTTCGATTCTAATATTTGCGCCTTAACTTACTAGGTGCAACCTTTCTTCAAATCGAGATA
1239 ATCGAATATCCTTTTCCCAAAAATTTAAAAAG-TTTACAAAGGAAAG
66 ATCGAATATCCTTTTCCCAAAAATTTAAAAAGTTTTACAAAGGAAAG
1285 CTTATCTTCGATTCTAATATTTGCGCCTTAACTTACTAGGTGCAACCTTTCTTCAAATCGAGATA
1 CTTATCTTCGATTCTAATATTTGCGCCTTAACTTACTAGGTGCAACCTTTCTTCAAATCGAGATA
1350 ATCGAATATCCTTTTCCCAAAAATTTAAAAAGTTTTACAAAGGAAAG
66 ATCGAATATCCTTTTCCCAAAAATTTAAAAAGTTTTACAAAGGAAAG
1397 CT
1 CT
1399 CGTTATTTCT
Statistics
Matches: 113, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
111 97 0.86
112 16 0.14
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.35
Consensus pattern (112 bp):
CTTATCTTCGATTCTAATATTTGCGCCTTAACTTACTAGGTGCAACCTTTCTTCAAATCGAGATA
ATCGAATATCCTTTTCCCAAAAATTTAAAAAGTTTTACAAAGGAAAG
Found at i:1904 original size:19 final size:20
Alignment explanation
Indices: 1880--1921 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1870 TAAGTTATAG
**
1880 AAATTAGATGGAT-ATTTAA
1 AAATTAGATAAATCATTTAA
1899 AAATTAGATAAATCATTTAA
1 AAATTAGATAAATCATTTAA
1919 AAA
1 AAA
1922 ATTATAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.55, C:0.02, G:0.10, T:0.33
Consensus pattern (20 bp):
AAATTAGATAAATCATTTAA
Found at i:5140 original size:19 final size:19
Alignment explanation
Indices: 5113--5162 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
5103 AAATAAATAA
* * *
5113 AATTGTAAACATCATAGAC
1 AATTTTAAAAATCATAAAC
*
5132 AATTTTAAAAATTATAAAC
1 AATTTTAAAAATCATAAAC
*
5151 AATATTAAAAAT
1 AATTTTAAAAAT
5163 ACACAAAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.32
Consensus pattern (19 bp):
AATTTTAAAAATCATAAAC
Found at i:15528 original size:3 final size:3
Alignment explanation
Indices: 15520--15554 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
15510 AACCTCTGCT
15520 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
15555 ATTTTCCAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.66, T:0.34
Consensus pattern (3 bp):
TGG
Found at i:16834 original size:30 final size:30
Alignment explanation
Indices: 16794--16855 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
16784 CTTAACAAAT
*
16794 AAATGCCTCTAAAATAGTAACAAAATTAAC
1 AAATGCCTCTAAAATAATAACAAAATTAAC
* *
16824 AAATGTCTCTAAAATAATAATAAAATTAAC
1 AAATGCCTCTAAAATAATAACAAAATTAAC
16854 AA
1 AA
16856 TAAAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.56, C:0.13, G:0.05, T:0.26
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAACAAAATTAAC
Found at i:16932 original size:22 final size:22
Alignment explanation
Indices: 16884--16932 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
16874 ATATACAAAT
*
16884 AATAACAATAAAATAGTAGTAA
1 AATAACAATAAAATAGTAGCAA
* * * *
16906 CATAATAATGAAATTGTAGCAA
1 AATAACAATAAAATAGTAGCAA
16928 AATAA
1 AATAA
16933 AGAGGAAATA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.59, C:0.06, G:0.10, T:0.24
Consensus pattern (22 bp):
AATAACAATAAAATAGTAGCAA
Found at i:30012 original size:27 final size:27
Alignment explanation
Indices: 29982--30036 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
29972 ACATCCCTTA
29982 GTGCCGCCACTT-GATATTCCTCCATTG
1 GTGCCGCCACTTCG-TATTCCTCCATTG
*
30009 GTGCCGCCACTTCGTGTTCCTCCATTG
1 GTGCCGCCACTTCGTATTCCTCCATTG
30036 G
1 G
30037 GTGTCAGGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 25 0.96
28 1 0.04
ACGTcount: A:0.11, C:0.35, G:0.22, T:0.33
Consensus pattern (27 bp):
GTGCCGCCACTTCGTATTCCTCCATTG
Found at i:34109 original size:3 final size:3
Alignment explanation
Indices: 34092--34144 Score: 92
Period size: 3 Copynumber: 18.3 Consensus size: 3
34082 ACAAATTTAC
34092 ATT ATT -TT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
34138 ATT ATT A
1 ATT ATT A
34145 ATATACTTTG
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.08
3 44 0.92
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:36361 original size:31 final size:29
Alignment explanation
Indices: 36325--36387 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 29
36315 ATCGAAGTTC
*
36325 AAAATGAGACTTTTCGGATTCTCGGGGGGCA
1 AAAATGAGAATTTT-GGATTCTC-GGGGGCA
*
36356 AAAATGATAATTTTGGATTCTCGGGGGCA
1 AAAATGAGAATTTTGGATTCTCGGGGGCA
36385 AAA
1 AAA
36388 CGATAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 10 0.33
30 8 0.27
31 12 0.40
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.27
Consensus pattern (29 bp):
AAAATGAGAATTTTGGATTCTCGGGGGCA
Found at i:36374 original size:30 final size:28
Alignment explanation
Indices: 36324--36399 Score: 98
Period size: 28 Copynumber: 2.6 Consensus size: 28
36314 AATCGAAGTT
* *
36324 CAAAATGAGACTTTTCGGATTCTCGGGGGG
1 CAAAATGATAATTTT-GGATTCTC-GGGGG
36354 CAAAAATGATAATTTTGGATTCTCGGGGG
1 C-AAAATGATAATTTTGGATTCTCGGGGG
*
36383 CAAAACGATAATTTTGG
1 CAAAATGATAATTTTGG
36400 GAAAATTCGG
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 15 0.36
29 6 0.14
30 9 0.21
31 12 0.29
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.29
Consensus pattern (28 bp):
CAAAATGATAATTTTGGATTCTCGGGGG
Found at i:36504 original size:29 final size:29
Alignment explanation
Indices: 36442--36846 Score: 158
Period size: 29 Copynumber: 13.8 Consensus size: 29
36432 ATCCGGGGGT
36442 AAAATGGTAATTTTAGGAAGTTTCGGAGTCA
1 AAAATGG-AATTTTAGGAAGTTTCGGAGT-A
* *
36473 AAAATGGAATTTTAGGGAG-TTCGGGGCTA
1 AAAATGGAATTTTAGGAAGTTTCGGAG-TA
* *
36502 AAAATGGAATTTTA-GAAGTTTCAGTGTTA
1 AAAATGGAATTTTAGGAAGTTTCGGAG-TA
* *
36531 AAAATGGAATTTT-GGAAGTTTTAGG-GTTT
1 AAAATGGAATTTTAGGAAG-TTTCGGAG-TA
* ** *
36560 AAAATGAGATTTTTA-GAAGTTAAGGGGTA
1 AAAATG-GAATTTTAGGAAGTTTCGGAGTA
** * * *
36589 AAAAAAGATTTTTTGGAAGTTTC-AAGATAA
1 AAAATGGAATTTTAGGAAGTTTCGGAG-T-A
* *
36619 AAAATGGGATTTTTA-GAAG-TTCGAGGGT-
1 AAAAT-GGAATTTTAGGAAGTTTCG-GAGTA
* * *
36647 AAAATGGTACTTTTTGGAAGTTTCGGGGTTA
1 AAAATGG-AATTTTAGGAAGTTTCGGAG-TA
* ** * *
36678 AAAATGGGATTTTTTGAAGTTTAGGGGT-
1 AAAATGGAATTTTAGGAAGTTTCGGAGTA
* * *
36706 AAAATGGTAATTTTA-AAAGTTTTATGG-TTA
1 AAAATGG-AATTTTAGGAAG-TTT-CGGAGTA
* * *
36736 AAAATGGGACTTTT-GGAAGTTTGGGGGT-
1 AAAAT-GGAATTTTAGGAAGTTTCGGAGTA
* * *
36764 AAAATGGTAATTTTTGGAAGTTTTGGGGTAA
1 AAAATGG-AATTTTAGGAAGTTTCGGAGT-A
* * *
36795 AAAATGGGACTTTT-GGAAGTTTGGGGGT-
1 AAAAT-GGAATTTTAGGAAGTTTCGGAGTA
*
36823 AAAATGGTAATTTTCGGATAGTTT
1 AAAATGG-AATTTTAGGA-AGTTT
36847 AGGGACCATT
Statistics
Matches: 297, Mismatches: 44, Indels: 67
0.73 0.11 0.16
Matches are distributed among these distances:
27 6 0.02
28 53 0.18
29 111 0.37
30 91 0.31
31 34 0.11
32 2 0.01
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.36
Consensus pattern (29 bp):
AAAATGGAATTTTAGGAAGTTTCGGAGTA
Found at i:36593 original size:59 final size:58
Alignment explanation
Indices: 36500--36850 Score: 325
Period size: 59 Copynumber: 6.0 Consensus size: 58
36490 AGTTCGGGGC
* * *
36500 TAAAAAT-GGAATTTTAGAAGTTTCAGTGTTAAAAATGG-AATTTTGGAAGTTTTAGGGT
1 TAAAAATGGGATTTTTAGAAGTTT-AGGGGT-AAAATGGTAATTTTGGAAGTTTTAGGGT
* * * ** * * * *
36558 TTAAAATGAGATTTTTAGAAGTTAAGGGGTAAAAAAAG-ATTTTTTGGAAGTTTCAAGAT
1 TAAAAATGGGATTTTTAGAAGTTTAGGGGT-AAAATGGTA-ATTTTGGAAGTTTTAGGGT
* * * **
36617 AAAAAATGGGATTTTTAGAAG-TTCGAGGGTAAAATGGTACTTTTTGGAAGTTTCGGGGT
1 TAAAAATGGGATTTTTAGAAGTTTAG-GGGTAAAATGGTA-ATTTTGGAAGTTTTAGGGT
* ** *
36676 TAAAAATGGGATTTTTTGAAGTTTAGGGGTAAAATGGTAATTTTAAAAGTTTTATGGT
1 TAAAAATGGGATTTTTAGAAGTTTAGGGGTAAAATGGTAATTTTGGAAGTTTTAGGGT
* * * *
36734 TAAAAATGGGACTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGT
1 TAAAAATGGGATTTTTAGAAGTTTAGGGGTAAAATGGTAA-TTTTGGAAGTTTTAGGGT
* * * *
36793 AAAAAATGGGACTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTCGGATAG-TTTAGGG
1 TAAAAATGGGATTTTTAGAAGTTTAGGGGTAAAATGGTAATTTT-GGA-AGTTTTAGGG
36851 ACCATTGGGG
Statistics
Matches: 244, Mismatches: 41, Indels: 15
0.81 0.14 0.05
Matches are distributed among these distances:
58 78 0.32
59 161 0.66
60 5 0.02
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.36
Consensus pattern (58 bp):
TAAAAATGGGATTTTTAGAAGTTTAGGGGTAAAATGGTAATTTTGGAAGTTTTAGGGT
Found at i:36779 original size:117 final size:117
Alignment explanation
Indices: 36501--36836 Score: 358
Period size: 117 Copynumber: 2.9 Consensus size: 117
36491 GTTCGGGGCT
* * * *
36501 AAAAAT-GGAATTTTAGAAGTTTC-AGTGTTAAAAATGG-AA-TTTTGGAAGTTTTAGGGTTTAA
1 AAAAATGGGACTTTTAGAAG-TTCGAG-GGT-AAAATGGTAATTTTTGGAAGTTTTGGGGTTAAA
* * ** * **
36562 AATGAGATTTTTAGAAGTTAAGGGGTAAAAAAAG-ATTTTTTGGAAGTTTCAAGATA
63 AATGGGATTTTTAGAAGTTTAGGGGT-AAAATGGTA-ATTTTAAAAGTTTCAAGATA
* * *
36618 AAAAATGGGATTTTTAGAAGTTCGAGGGTAAAATGGTACTTTTTGGAAGTTTCGGGGTTAAAAAT
1 AAAAATGGGACTTTTAGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTTAAAAAT
* * * * *
36683 GGGATTTTTTGAAGTTTAGGGGTAAAATGGTAATTTTAAAAGTTTTATGGTT
66 GGGATTTTTAGAAGTTTAGGGGTAAAATGGTAATTTTAAAAGTTTCAAGATA
* * * *
36735 AAAAATGGGACTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTAAAAAAT
1 AAAAATGGGACTTTTAGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTTAAAAAT
* * *
36800 GGGACTTTTGGAAGTTTGGGGGTAAAATGGTAATTTT
66 GGGATTTTTAGAAGTTTAGGGGTAAAATGGTAATTTT
36837 CGGATAGTTT
Statistics
Matches: 186, Mismatches: 28, Indels: 10
0.83 0.12 0.04
Matches are distributed among these distances:
116 7 0.04
117 122 0.66
118 57 0.31
ACGTcount: A:0.34, C:0.02, G:0.27, T:0.37
Consensus pattern (117 bp):
AAAAATGGGACTTTTAGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTTAAAAAT
GGGATTTTTAGAAGTTTAGGGGTAAAATGGTAATTTTAAAAGTTTCAAGATA
Found at i:37641 original size:34 final size:36
Alignment explanation
Indices: 37597--37670 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 36
37587 AAAAAAAAAC
*
37597 TTTCCCTTTTC-CCTTTTATTTTT-AGAACTCCTCT
1 TTTCCCTTTTCGCCTTTTATTTTTAAAAACTCCTCT
* ** *
37631 TTTCCTTTTTCGTTTTTTTTTTTTAAAAACTCCTCT
1 TTTCCCTTTTCGCCTTTTATTTTTAAAAACTCCTCT
37667 TTTC
1 TTTC
37671 TCTCTTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
34 10 0.30
35 9 0.27
36 14 0.42
ACGTcount: A:0.12, C:0.24, G:0.03, T:0.61
Consensus pattern (36 bp):
TTTCCCTTTTCGCCTTTTATTTTTAAAAACTCCTCT
Found at i:38454 original size:30 final size:29
Alignment explanation
Indices: 38418--38478 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
38408 TTTAAATTTT
38418 AAATAATTAA-ATTAT-ATTTTAATTCTTTAA
1 AAATAA-TAATATTATGA-TTTAATT-TTTAA
*
38448 AAATAATAATATTTTGATTTAATTTTTAA
1 AAATAATAATATTATGATTTAATTTTTAA
38477 AA
1 AA
38479 TTTATAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.36
30 17 0.61
31 1 0.04
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (29 bp):
AAATAATAATATTATGATTTAATTTTTAA
Found at i:38496 original size:17 final size:17
Alignment explanation
Indices: 38474--38514 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
38464 ATTTAATTTT
38474 TAAAATTTATAAAAAT-A
1 TAAAATTT-TAAAAATAA
*
38491 TAAAATATTAAAAATAA
1 TAAAATTTTAAAAATAA
38508 TAAAATT
1 TAAAATT
38515 ATATTTTTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAAATTTTAAAAATAA
Found at i:38698 original size:32 final size:32
Alignment explanation
Indices: 38658--38719 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
38648 TAAAAATATA
* * *
38658 TTTTTTAAAATATTAAATTAAAATTTTATTAT
1 TTTTTTAAAAAATAAAAATAAAATTTTATTAT
*
38690 TTTTTTAAAAAATAAAAATATAATTTTATT
1 TTTTTTAAAAAATAAAAATAAAATTTTATT
38720 TTTATTAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (32 bp):
TTTTTTAAAAAATAAAAATAAAATTTTATTAT
Found at i:38702 original size:27 final size:27
Alignment explanation
Indices: 38672--38739 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 27
38662 TTAAAATATT
38672 AAATTAAAATTTTATTATT-TTTTTAAA
1 AAATTAAAATTTTATT-TTATTTTTAAA
* * * **
38699 AAATAAAAATATAATTTTATTTTTATT
1 AAATTAAAATTTTATTTTATTTTTAAA
*
38726 AATTTAAAATTTTA
1 AAATTAAAATTTTA
38740 AAAAATTTTA
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
26 2 0.06
27 29 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
AAATTAAAATTTTATTTTATTTTTAAA
Found at i:39690 original size:18 final size:18
Alignment explanation
Indices: 39650--39700 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 18
39640 TTTTCGATTG
39650 TAATTAATTTAAAATTT-TC
1 TAATTAA-TT-AAATTTATC
39669 -AATTAATTAAATTTATC
1 TAATTAATTAAATTTATC
39686 TAATTAA--AAATTTAT
1 TAATTAATTAAATTTAT
39701 TCTCATTCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 14 0.47
17 4 0.13
18 12 0.40
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATTAATTAAATTTATC
Found at i:41517 original size:15 final size:16
Alignment explanation
Indices: 41497--41537 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
41487 TGAATTTTTA
*
41497 TTTAAAAATA-AATTT
1 TTTAAAAATATAATAT
41512 TTTAAAAATATAATAT
1 TTTAAAAATATAATAT
*
41528 ATTAAAAATA
1 TTTAAAAATA
41538 CTCATAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TTTAAAAATATAATAT
Found at i:41585 original size:39 final size:38
Alignment explanation
Indices: 41525--41610 Score: 111
Period size: 39 Copynumber: 2.2 Consensus size: 38
41515 AAAAATATAA
* * *
41525 TATATTAAAAATACTCATAAATATAATAAATGTTTTAT
1 TATATTAAAAATACACATAAATACAATAAATATTTTAT
41563 TATATTAAAAA-ACACAAATAAATACAATAAATATTTTAT
1 TATATTAAAAATACAC--ATAAATACAATAAATATTTTAT
*
41602 TGTATTAAA
1 TATATTAAA
41611 TACAATTTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
37 3 0.07
38 11 0.26
39 28 0.67
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.38
Consensus pattern (38 bp):
TATATTAAAAATACACATAAATACAATAAATATTTTAT
Found at i:41767 original size:20 final size:20
Alignment explanation
Indices: 41699--41767 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
41689 ATTACTATTG
*
41699 AATTAATAATTTAATATAAAT
1 AATTAAT-ATTTAATATATAT
* * *
41720 -ATAAATA-TAAACATATAT
1 AATTAATATTTAATATATAT
41738 AA-TAATTATTTAATATATAT
1 AATTAA-TATTTAATATATAT
41758 AATTAATATT
1 AATTAATATT
41768 ATTTTTTAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
18 10 0.27
19 4 0.11
20 20 0.54
21 3 0.08
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (20 bp):
AATTAATATTTAATATATAT
Done.