Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014270.1 Kokia drynarioides strain JFW-HI SEQ_129303, 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: 126680
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Warning! 42 characters in sequence are not A, C, G, or T
Found at i:1775 original size:30 final size:33
Alignment explanation
Indices: 1714--1775 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 33
1704 TTAAATCCGT
*
1714 ATTTAATCTTTTTTTCATCTAATTTGATACTTGA
1 ATTTAATCTTTTTTTCA-CTAATCTGATACTTGA
*
1748 ATTTAA-C-TTTTTTC-CTAATCTGGTACTT
1 ATTTAATCTTTTTTTCACTAATCTGATACTT
1776 AATCTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
30 12 0.46
32 7 0.27
33 1 0.04
34 6 0.23
ACGTcount: A:0.24, C:0.15, G:0.06, T:0.55
Consensus pattern (33 bp):
ATTTAATCTTTTTTTCACTAATCTGATACTTGA
Found at i:22064 original size:21 final size:21
Alignment explanation
Indices: 22021--22061 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
22011 TTTTTTCAAG
*
22021 TTTTTTATTTTTAATTAATAA
1 TTTTTTATTTTTAATAAATAA
22042 TTTTTTATTTTT-ATAAATAA
1 TTTTTTATTTTTAATAAATAA
22062 ATTAATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTTTATTTTTAATAAATAA
Found at i:22084 original size:28 final size:27
Alignment explanation
Indices: 22033--22089 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 27
22023 TTTTATTTTT
* * * *
22033 AATTAATAATTTTTTATTTTTATAAATA
1 AATTAATAATTATATAATTATAT-AATA
22061 AATTAATAATTATATAATTATATAATA
1 AATTAATAATTATATAATTATATAATA
22088 AA
1 AA
22090 AATATATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 6 0.24
28 19 0.76
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
AATTAATAATTATATAATTATATAATA
Found at i:22214 original size:18 final size:18
Alignment explanation
Indices: 22182--22216 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
22172 TATTTATGTC
22182 AAATATTATTATGATTTG
1 AAATATTATTATGATTTG
22200 AAATAATTATT-TGATTT
1 AAAT-ATTATTATGATTT
22217 TATTCCGGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (18 bp):
AAATATTATTATGATTTG
Found at i:23187 original size:39 final size:39
Alignment explanation
Indices: 23101--23192 Score: 91
Period size: 39 Copynumber: 2.3 Consensus size: 39
23091 ACCAATAAAA
* *
23101 TTAAAATATTTTAATTTAATAAAAATAATTTTTTTTACAAT
1 TTAAAATA-TTTAATTT-ATAAAAATAATTTTATATACAAT
*
23142 TT-AAATATTTAATTT-TAAAAATTATTTTGATATA-AATT
1 TTAAAATATTTAATTTATAAAAATAATTTT-ATATACAA-T
*
23180 TTAAAATAATTAA
1 TTAAAATATTTAA
23193 GTCCAAAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
37 14 0.32
38 6 0.14
39 17 0.39
40 5 0.11
41 2 0.05
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (39 bp):
TTAAAATATTTAATTTATAAAAATAATTTTATATACAAT
Found at i:28643 original size:40 final size:40
Alignment explanation
Indices: 28588--28674 Score: 165
Period size: 40 Copynumber: 2.2 Consensus size: 40
28578 TGAAATTATT
*
28588 GTTGTAATGTTTATTGCCATTTGTCACTTGCAGTGTGAGA
1 GTTGTAATGTTTATTGCCATTTGCCACTTGCAGTGTGAGA
28628 GTTGTAATGTTTATTGCCATTTGCCACTTGCAGTGTGAGA
1 GTTGTAATGTTTATTGCCATTTGCCACTTGCAGTGTGAGA
28668 GTTGTAA
1 GTTGTAA
28675 AAAGAAAACT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.21, C:0.13, G:0.25, T:0.41
Consensus pattern (40 bp):
GTTGTAATGTTTATTGCCATTTGCCACTTGCAGTGTGAGA
Found at i:29758 original size:20 final size:21
Alignment explanation
Indices: 29732--29779 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
29722 TTTGCCCTGA
* *
29732 TTAAAAATATTTATAAGTCA-T
1 TTAAAATTATTTAGAAG-CATT
29753 TTAAAATTATTTAGAAGCATT
1 TTAAAATTATTTAGAAGCATT
29774 TTAAAA
1 TTAAAA
29780 CGAGTTCTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (21 bp):
TTAAAATTATTTAGAAGCATT
Found at i:30967 original size:31 final size:31
Alignment explanation
Indices: 30910--30980 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
30900 TTGATGTAAG
* *
30910 TATACACGTGAAACTTTGATTATGATTCAAA
1 TATACACATGAAACTTTCATTATGATTCAAA
* * * *
30941 TATATACATGAAATTTTCATTTTGATTCAAT
1 TATACACATGAAACTTTCATTATGATTCAAA
30972 TATACACAT
1 TATACACAT
30981 TTAAAGAAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (31 bp):
TATACACATGAAACTTTCATTATGATTCAAA
Found at i:34351 original size:63 final size:63
Alignment explanation
Indices: 34283--34407 Score: 205
Period size: 63 Copynumber: 2.0 Consensus size: 63
34273 GAAACAATAG
* *
34283 GTGTGTGCTTCTCGTTGATCCGATCAACATGTTCCAAACGTCCAAAATCTACAGAGGAAGTAA
1 GTGTGTGCTTCTCGCTGATCCGATCAACATATTCCAAACGTCCAAAATCTACAGAGGAAGTAA
* * *
34346 GTGTGTGCTTCTCGCTGATCCGATCGACATATTCCAAATGTCTAAAATCTACAGAGGAAGTA
1 GTGTGTGCTTCTCGCTGATCCGATCAACATATTCCAAACGTCCAAAATCTACAGAGGAAGTA
34408 GTAACATGAG
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.28
Consensus pattern (63 bp):
GTGTGTGCTTCTCGCTGATCCGATCAACATATTCCAAACGTCCAAAATCTACAGAGGAAGTAA
Found at i:37161 original size:2 final size:2
Alignment explanation
Indices: 37154--37183 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
37144 AATCTTATTA
37154 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37184 TTTTTTTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38457 original size:23 final size:22
Alignment explanation
Indices: 38415--38462 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 22
38405 GACTGAATTT
38415 TTAAATTTCAATAAGTATAAATA
1 TTAAATTTCAATAAGTATAAA-A
38438 TTAAATTTGC-ATAA-TGATAAAA
1 TTAAATTT-CAATAAGT-ATAAAA
38460 TTA
1 TTA
38463 GTTCTTAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
22 5 0.22
23 17 0.74
24 1 0.04
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.40
Consensus pattern (22 bp):
TTAAATTTCAATAAGTATAAAA
Found at i:42655 original size:25 final size:25
Alignment explanation
Indices: 42627--42674 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
42617 ATCAATAATT
* *
42627 CAATATTTAGACATCATTAACAACG
1 CAATATTCAGACAACATTAACAACG
*
42652 CAATATTCGGACAACATTAACAA
1 CAATATTCAGACAACATTAACAA
42675 TGCATCACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.46, C:0.21, G:0.08, T:0.25
Consensus pattern (25 bp):
CAATATTCAGACAACATTAACAACG
Found at i:44528 original size:49 final size:49
Alignment explanation
Indices: 44467--44735 Score: 210
Period size: 49 Copynumber: 5.6 Consensus size: 49
44457 TAAGCCTTTC
* * *
44467 CATGCGTCTGGGAGCAGGATTATTATTCTACCTTCCATAAGTCTCCCCT
1 CATGCATCTGAGAGCAGGATTATTATTCTACCTTCCATAAGCCTCCCCT
* * * * *
44516 CATGCATATGGGAGCAAGATTGTTATTCTTCCTTCCATAAGCCTCCCC-
1 CATGCATCTGAGAGCAGGATTATTATTCTACCTTCCATAAGCCTCCCCT
* * * * * * **
44564 CATAG-GTATGAGAACAGGGTTATTATTTACTACCTTTCGTAAGCCTCCTAT
1 CAT-GCATCTGAGAGCAGGATTATTA-TT-CTACCTTCCATAAGCCTCCCCT
*** * *
44615 CATATGTCTGAGAACAAGG-TTATTATTCTACCTTCCGTAAGCCTCCCC-
1 CATGCATCTGAGAGC-AGGATTATTATTCTACCTTCCATAAGCCTCCCCT
* * *
44663 CATACATCTGAGAGCAAGATTATCATTCTACCTTCCATAAGCCT--CCT
1 CATGCATCTGAGAGCAGGATTATTATTCTACCTTCCATAAGCCTCCCCT
* * *
44710 -ATGCATCTGGGAGCAGGGTTGTTATT
1 CATGCATCTGAGAGCAGGATTATTATT
44736 TCAACAAAAG
Statistics
Matches: 178, Mismatches: 34, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
46 22 0.12
47 2 0.01
48 52 0.29
49 63 0.35
50 18 0.10
51 18 0.10
52 3 0.02
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (49 bp):
CATGCATCTGAGAGCAGGATTATTATTCTACCTTCCATAAGCCTCCCCT
Found at i:44691 original size:48 final size:48
Alignment explanation
Indices: 44473--44708 Score: 220
Period size: 48 Copynumber: 4.8 Consensus size: 48
44463 TTTCCATGCG
* * * *
44473 TCTGGGAGCAGGATTATTATTCTACCTTCCATAAGTCTCCCCTCATGCA
1 TCTGAGAGCAAGATTATTATTCTACCTTCCATAAGCCTCCCC-CATACA
* * * * **
44522 TATGGGAGCAAGATTGTTATTCTTCCTTCCATAAGCCTCCCCCATAGG
1 TCTGAGAGCAAGATTATTATTCTACCTTCCATAAGCCTCCCCCATACA
* * * * * * ** **
44570 TATGAGAACAGGGTTATTATTTACTACCTTTCGTAAGCCTCCTATCATATG
1 TCTGAGAGCAAGATTATTA-TT-CTACCTTCCATAAGCCTCC-CCCATACA
* * *
44621 TCTGAGAACAAGGTTATTATTCTACCTTCCGTAAGCCTCCCCCATACA
1 TCTGAGAGCAAGATTATTATTCTACCTTCCATAAGCCTCCCCCATACA
*
44669 TCTGAGAGCAAGATTATCATTCTACCTTCCATAAGCCTCC
1 TCTGAGAGCAAGATTATTATTCTACCTTCCATAAGCCTCC
44709 TATGCATCTG
Statistics
Matches: 154, Mismatches: 30, Indels: 7
0.81 0.16 0.04
Matches are distributed among these distances:
48 57 0.37
49 57 0.37
50 18 0.12
51 22 0.14
ACGTcount: A:0.25, C:0.27, G:0.15, T:0.32
Consensus pattern (48 bp):
TCTGAGAGCAAGATTATTATTCTACCTTCCATAAGCCTCCCCCATACA
Found at i:46316 original size:9 final size:9
Alignment explanation
Indices: 46302--46326 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
46292 TAATTTAAAT
46302 TTTTAAAAA
1 TTTTAAAAA
46311 TTTTAAAAA
1 TTTTAAAAA
46320 TTTTAAA
1 TTTTAAA
46327 TGGAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:46551 original size:21 final size:20
Alignment explanation
Indices: 46527--46566 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
46517 AAAATATTGT
46527 TTAT-AAATAAATTTATAATAA
1 TTATAAAAT-AATTT-TAATAA
46548 TTATAAAATAATTTTAATA
1 TTATAAAATAATTTTAATA
46567 TATTTTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTATAAAATAATTTTAATAA
Found at i:46917 original size:2 final size:2
Alignment explanation
Indices: 46910--46934 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
46900 AATTTTCATT
46910 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 T
46935 TTATTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:47025 original size:25 final size:26
Alignment explanation
Indices: 46970--47032 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 26
46960 TAATTTACAA
46970 TTTTTTTATTTTTTAAAAAAACTTTC
1 TTTTTTTATTTTTTAAAAAAACTTTC
* * * *
46996 ATTTTTTATTTTTTAAATAGA-TTTT
1 TTTTTTTATTTTTTAAAAAAACTTTC
47021 TTTTTTTATTTT
1 TTTTTTTATTTT
47033 CTTGGAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 14 0.44
26 18 0.56
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.70
Consensus pattern (26 bp):
TTTTTTTATTTTTTAAAAAAACTTTC
Found at i:52188 original size:30 final size:29
Alignment explanation
Indices: 52154--52214 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
52144 TGGTCACTCA
52154 TTTTAGCTTTTAAAAAGTAAGTTTATTTTT
1 TTTTA-CTTTTAAAAAGTAAGTTTATTTTT
* * * *
52184 TTTTATTTTTTAAAATTAATTTTATTTTT
1 TTTTACTTTTAAAAAGTAAGTTTATTTTT
52213 TT
1 TT
52215 CAAGTAAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.66
Consensus pattern (29 bp):
TTTTACTTTTAAAAAGTAAGTTTATTTTT
Found at i:52604 original size:12 final size:12
Alignment explanation
Indices: 52587--52618 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
52577 CTTTGAAAAA
52587 GATAAAATGAGT
1 GATAAAATGAGT
52599 GATAAAATGAGT
1 GATAAAATGAGT
52611 GACTAAAA
1 GA-TAAAA
52619 AGAAAACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.53, C:0.03, G:0.22, T:0.22
Consensus pattern (12 bp):
GATAAAATGAGT
Found at i:52744 original size:32 final size:32
Alignment explanation
Indices: 52708--52771 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
52698 TATTAAAGTT
*
52708 GGGTGACGAAAATCAAAATGGTTGCTAACGAC
1 GGGTGACGAAAATCAAAATGATTGCTAACGAC
*
52740 GGGTGACGAAAATGAAAATGATTGCTAACGAC
1 GGGTGACGAAAATCAAAATGATTGCTAACGAC
52772 AATGTTCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.39, C:0.14, G:0.28, T:0.19
Consensus pattern (32 bp):
GGGTGACGAAAATCAAAATGATTGCTAACGAC
Found at i:53094 original size:20 final size:20
Alignment explanation
Indices: 53071--53109 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
53061 TTCAGATATT
*
53071 TTTATTAATTTTTTTTGACA
1 TTTATTAATTTTTTATGACA
*
53091 TTTATTGATTTTTTATGAC
1 TTTATTAATTTTTTATGAC
53110 TTATACATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.05, G:0.08, T:0.64
Consensus pattern (20 bp):
TTTATTAATTTTTTATGACA
Found at i:58337 original size:21 final size:20
Alignment explanation
Indices: 58308--58353 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
58298 TAAAACAAGA
58308 TTTAAGATTT-ATAGTTTAGTG
1 TTTAAGATTTAAT-GTTTAG-G
*
58329 TTTAGGATTTAATGTTTAGG
1 TTTAAGATTTAATGTTTAGG
58349 TTTAA
1 TTTAA
58354 AAATTTGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 15 0.68
22 2 0.09
ACGTcount: A:0.28, C:0.00, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTAAGATTTAATGTTTAGG
Found at i:72831 original size:12 final size:12
Alignment explanation
Indices: 72814--72839 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
72804 AAGAATGAAT
72814 TCAACCAACAAA
1 TCAACCAACAAA
72826 TCAACCAACAAA
1 TCAACCAACAAA
72838 TC
1 TC
72840 CATGTTGGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.35, G:0.00, T:0.12
Consensus pattern (12 bp):
TCAACCAACAAA
Found at i:81643 original size:15 final size:16
Alignment explanation
Indices: 81623--81652 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
81613 AAGAATATAA
81623 AAATTAAAAT-TAATC
1 AAATTAAAATATAATC
81638 AAATTAAAATATAAT
1 AAATTAAAATATAAT
81653 TACTAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATTAAAATATAATC
Found at i:84848 original size:22 final size:22
Alignment explanation
Indices: 84816--84859 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
84806 AAATGATTTT
*
84816 TAATTTATTTTTAGTAATTTAA
1 TAATTTATTTTTAGTAAGTTAA
* *
84838 TAATTTCTTTTTATTAAGTTAA
1 TAATTTATTTTTAGTAAGTTAA
84860 GAAAGTATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (22 bp):
TAATTTATTTTTAGTAAGTTAA
Found at i:87056 original size:15 final size:14
Alignment explanation
Indices: 87038--87068 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
87028 TTATTCTCTC
87038 TTCTTTTTTTCTTTT
1 TTCTTTTTTT-TTTT
87053 TTCTTTTTTTTTTT
1 TTCTTTTTTTTTTT
87067 TT
1 TT
87069 AAATTTTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTCTTTTTTTTTTT
Found at i:96049 original size:12 final size:11
Alignment explanation
Indices: 96032--96058 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
96022 TTATCTTGAA
96032 TTTTTTTTTTC
1 TTTTTTTTTTC
96043 TTTTTTTTTTC
1 TTTTTTTTTTC
96054 TTTTT
1 TTTTT
96059 CATTAGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:106720 original size:6 final size:6
Alignment explanation
Indices: 106698--106795 Score: 69
Period size: 6 Copynumber: 16.5 Consensus size: 6
106688 GTTTAAGTTG
* * *
106698 ATTTAA ATTTAT TTTTAA ATTTAA ATTT-- ATCTTAA ATTTAA ATTTATCT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT-TTAA ATTTAA ATTTA--A
* * * **
106747 TTTTAA ATTTAA ATTT-G CTTTAA ATTTAA ATTT-A ATCAAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
106793 ATT
1 ATT
106796 GATATTAAAT
Statistics
Matches: 69, Mismatches: 16, Indels: 14
0.70 0.16 0.14
Matches are distributed among these distances:
4 2 0.03
5 8 0.12
6 53 0.77
7 2 0.03
8 4 0.06
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (6 bp):
ATTTAA
Found at i:106734 original size:17 final size:17
Alignment explanation
Indices: 106698--106806 Score: 105
Period size: 17 Copynumber: 6.2 Consensus size: 17
106688 GTTTAAGTTG
*
106698 ATTTAAATTTATTTTTAA
1 ATTTAAATTTA-TCTTAA
106716 ATTTAAATTTATCTTAA
1 ATTTAAATTTATCTTAA
106733 ATTTAAATTTATCTTTTTAA
1 ATTTAAATTTATC---TTAA
*
106753 ATTTAAATTT-GCTTTAA
1 ATTTAAATTTATC-TTAA
*
106770 ATTTAAATTTAATC-AAA
1 ATTTAAATTT-ATCTTAA
* *
106787 ATTTAAATTGATATTAA
1 ATTTAAATTTATCTTAA
106804 ATT
1 ATT
106807 AAAAACCCAA
Statistics
Matches: 78, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
16 2 0.03
17 49 0.63
18 11 0.14
19 2 0.03
20 14 0.18
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (17 bp):
ATTTAAATTTATCTTAA
Found at i:106757 original size:37 final size:35
Alignment explanation
Indices: 106698--106780 Score: 123
Period size: 37 Copynumber: 2.3 Consensus size: 35
106688 GTTTAAGTTG
*
106698 ATTTAAATTTATTTTTAAATTTAAATTT-ATCTTAA
1 ATTTAAATTTATTTTTAAATTTAAATTTGCT-TTAA
106733 ATTTAAATTTATCTTTTTAAATTTAAATTTGCTTTAA
1 ATTTAAATTTA--TTTTTAAATTTAAATTTGCTTTAA
106770 ATTTAAATTTA
1 ATTTAAATTTA
106781 ATCAAAATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
35 11 0.25
37 32 0.73
38 1 0.02
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.57
Consensus pattern (35 bp):
ATTTAAATTTATTTTTAAATTTAAATTTGCTTTAA
Found at i:106810 original size:23 final size:23
Alignment explanation
Indices: 106765--106810 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
106755 TTAAATTTGC
* *
106765 TTTAAATTTAAATTTAATCAAAA
1 TTTAAATTGAAATTAAATCAAAA
* *
106788 TTTAAATTGATATTAAATTAAAA
1 TTTAAATTGAAATTAAATCAAAA
106811 ACCCAAAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
TTTAAATTGAAATTAAATCAAAA
Found at i:107609 original size:34 final size:34
Alignment explanation
Indices: 107558--107622 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
107548 TAATAACTAT
*
107558 TTTATTAATAATAATAATAATAATAATAAATGGG
1 TTTAATAATAATAATAATAATAATAATAAATGGG
* *
107592 TTTAATAATAA-ATATAATATTTATAATAAAT
1 TTTAATAATAATA-ATAATAATAATAATAAAT
107623 AAATAAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 1 0.04
34 26 0.96
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.42
Consensus pattern (34 bp):
TTTAATAATAATAATAATAATAATAATAAATGGG
Found at i:108739 original size:25 final size:25
Alignment explanation
Indices: 108685--108740 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
108675 TTTCCAAAAT
* *
108685 TATATTTTGACCCCAAACTTATTCA
1 TATATTTTAACCCCAAACTTATCCA
*
108710 TATATTTTAACCCTCAAACTTCTCCA
1 TATATTTTAACCC-CAAACTTATCCA
108736 -ATATT
1 TATATT
108741 ATATTTTAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 17 0.63
26 10 0.37
ACGTcount: A:0.32, C:0.25, G:0.02, T:0.41
Consensus pattern (25 bp):
TATATTTTAACCCCAAACTTATCCA
Found at i:108744 original size:30 final size:29
Alignment explanation
Indices: 108670--108923 Score: 120
Period size: 30 Copynumber: 8.8 Consensus size: 29
108660 GGAGGTCCTT
*
108670 AAACTTTTCCAAAATTATATTTTGACCC-C
1 AAAC-TTTCCAAAATTATATTTTAACCCTC
*
108699 AAACTTATTC---A-TATATTTTAACCCTC
1 AAACTT-TCCAAAATTATATTTTAACCCTC
* *
108725 AAACTTCTCCAATATTATATTTTAACCCTT
1 AAACTT-TCCAAAATTATATTTTAACCCTC
* * * *
108755 AAACTTTCTAAAAATTAAATTTTTACCCCC
1 AAACTTTC-CAAAATTATATTTTAACCCTC
* *
108785 AAACTTTCCAAAATTCCAT-TTTTGACGCT-
1 AAACTTTCCAAAATT--ATATTTTAACCCTC
* *
108814 AAA-TTTCCAAAATTCCAT-TTTTGATCC-C
1 AAACTTTCCAAAATT--ATATTTTAACCCTC
* * * *
108842 AAACTTTTCAAAAATTACATTTTTACCCCC
1 AAAC-TTTCCAAAATTATATTTTAACCCTC
* * *
108872 GAAC-TTCCAAAAATTCCAT-TTTTGACCCTA
1 AAACTTTCC-AAAATT--ATATTTTAACCCTC
*
108902 AAAC-TTCTAAAAATTATATTTT
1 AAACTTTC-CAAAATTATATTTT
108924 TTACCCCTAA
Statistics
Matches: 176, Mismatches: 30, Indels: 38
0.72 0.12 0.16
Matches are distributed among these distances:
25 12 0.07
26 10 0.06
28 33 0.19
29 35 0.20
30 84 0.48
31 2 0.01
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.39
Consensus pattern (29 bp):
AAACTTTCCAAAATTATATTTTAACCCTC
Found at i:108914 original size:59 final size:59
Alignment explanation
Indices: 108818--109074 Score: 233
Period size: 59 Copynumber: 4.4 Consensus size: 59
108808 GACGCTAAAT
*
108818 TTCC-AAAATTCCATTTTTGATCCC--AAACTTTTCAAAAATTACATTTTTACCCCCGAA
1 TTCCAAAAATTCCATTTTTGA-CCCTAAAACTTCTCAAAAATTACATTTTTACCCCCGAA
* **
108875 CTTCCAAAAATTCCATTTTTGACCCTAAAACTTCT-AAAAATTATATTTTTTACCCCTAAA
1 -TTCCAAAAATTCCATTTTTGACCCTAAAACTTCTCAAAAATTACA-TTTTTACCCCCGAA
* * * * **
108935 CCTCCAAAAATTCTATTTTTGACCCCAAAACTT-TCAAAAATTACCA-TTTTACTCTTGAA
1 -TTCCAAAAATTCCATTTTTGACCCTAAAACTTCTCAAAAATTA-CATTTTTACCCCCGAA
* * ** * *
108994 TGTCCAAAAATTCCATTTTTGA-TCTCAATTTTC-CTAAAAATTACAATTTTACCCCCGGA
1 T-TCCAAAAATTCCATTTTTGACCCTAAAACTTCTC-AAAAATTACATTTTTACCCCCGAA
*
109053 TGTCCAAAAATTCCGTTTTTGA
1 T-TCCAAAAATTCCATTTTTGA
109075 TCTCGATTTT
Statistics
Matches: 166, Mismatches: 23, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
58 15 0.09
59 93 0.56
60 57 0.34
61 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (59 bp):
TTCCAAAAATTCCATTTTTGACCCTAAAACTTCTCAAAAATTACATTTTTACCCCCGAA
Found at i:108924 original size:30 final size:29
Alignment explanation
Indices: 108744--108984 Score: 145
Period size: 30 Copynumber: 8.1 Consensus size: 29
108734 CAATATTATA
* *
108744 TTTTAACCCTTAAACTTTCTAAAAATTAAAT
1 TTTTGACCC-TAAAC-TTCTAAAAATTACAT
* * *
108775 TTTT-ACCCCCAAACTT-TCCAAAATTCCAT
1 TTTTGA-CCCTAAACTTCT-AAAAATTACAT
* * * *
108804 TTTTGACGCTAAATTTC-CAAAATTCCAT
1 TTTTGACCCTAAACTTCTAAAAATTACAT
*
108832 TTTTGATCCC-AAACTTTTCAAAAATTACAT
1 TTTTGA-CCCTAAACTTCT-AAAAATTACAT
** * *
108862 TTTT-ACCCCCGAACTTCCAAAAATTCCAT
1 TTTTGA-CCCTAAACTTCTAAAAATTACAT
*
108891 TTTTGACCCTAAAACTTCTAAAAATTATAT
1 TTTTGACCCT-AAACTTCTAAAAATTACAT
* * *
108921 TTTTTACCCCTAAACCTCCAAAAATT-CTAT
1 TTTTGA-CCCTAAACTTCTAAAAATTAC-AT
*
108951 TTTTGACCCCAAAACTT-TCAAAAATTACCAT
1 TTTTGA-CCCTAAACTTCT-AAAAATTA-CAT
108982 TTT
1 TTT
108985 ACTCTTGAAT
Statistics
Matches: 165, Mismatches: 30, Indels: 30
0.73 0.13 0.13
Matches are distributed among these distances:
28 23 0.14
29 44 0.27
30 81 0.49
31 16 0.10
32 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.38
Consensus pattern (29 bp):
TTTTGACCCTAAACTTCTAAAAATTACAT
Found at i:109075 original size:59 final size:58
Alignment explanation
Indices: 108822--109130 Score: 230
Period size: 59 Copynumber: 5.2 Consensus size: 58
108812 CTAAATTTCC
* *
108822 AAAATTCCATTTTTGATCCCAAACTTTTC-AAAAATTACATTTTTACCCCCGAACT-TCCA
1 AAAATTCCATTTTTGATCTC-AA-TTTTCTAAAAATTACAATTTTACCCCCGAA-TGTCCA
* * ** * * ** **
108881 AAAATTCCATTTTTGACCCTAAAACTTCTAAAAATTATATTTTTTACCCCTAAACCTCCA
1 AAAATTCCATTTTTGA-TCTCAATTTTCTAAAAATTACA-ATTTTACCCCCGAATGTCCA
* * * * * * **
108941 AAAATTCTATTTTTGACCCCAAAACTTTC-AAAAATTACCATTTTACTCTTGAATGTCCA
1 AAAATTCCATTTTTGATCTC--AATTTTCTAAAAATTACAATTTTACCCCCGAATGTCCA
*
109000 AAAATTCCATTTTTGATCTCAATTTTCCTAAAAATTACAATTTTACCCCCGGATGTCCA
1 AAAATTCCATTTTTGATCTCAATTTT-CTAAAAATTACAATTTTACCCCCGAATGTCCA
* * * * ** * * *
109059 AAAATTCCGTTTTTGATCTCGATTTTTTTAAAAGTTACCGTTTTA-CCCCTAGGTGTCTA
1 AAAATTCCATTTTTGATCTC-AATTTTCTAAAAATTACAATTTTACCCCCGA-ATGTCCA
109118 AAAATTCCATTTT
1 AAAATTCCATTTT
109131 AACCTCGAAC
Statistics
Matches: 198, Mismatches: 42, Indels: 20
0.76 0.16 0.08
Matches are distributed among these distances:
57 5 0.03
58 8 0.04
59 135 0.68
60 45 0.23
61 5 0.03
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.39
Consensus pattern (58 bp):
AAAATTCCATTTTTGATCTCAATTTTCTAAAAATTACAATTTTACCCCCGAATGTCCA
Found at i:115101 original size:16 final size:17
Alignment explanation
Indices: 115070--115101 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
115060 ATTTAAATGC
115070 TTTAAATTATATAAAAT
1 TTTAAATTATATAAAAT
115087 TTTAAATTA-ATAAAA
1 TTTAAATTATATAAAA
115102 GTAAAATTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTAAATTATATAAAAT
Found at i:122331 original size:18 final size:19
Alignment explanation
Indices: 122310--122346 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
122300 TTTTTAAAAA
122310 TATAAAT-TTTAGAATTTT
1 TATAAATATTTAGAATTTT
*
122328 TATAAATATTTTGAATTTT
1 TATAAATATTTAGAATTTT
122347 AAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TATAAATATTTAGAATTTT
Found at i:123834 original size:2 final size:2
Alignment explanation
Indices: 123827--123854 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
123817 TCCTTAAAAC
123827 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
123855 GTTTTACTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:124137 original size:2 final size:2
Alignment explanation
Indices: 124130--124161 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
124120 CACTTCCTTA
124130 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
124162 TATTTTGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.