Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004578.1 Kokia drynarioides strain JFW-HI SEQ_118066, 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: 112507
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 48 characters in sequence are not A, C, G, or T
Found at i:67 original size:18 final size:19
Alignment explanation
Indices: 41--84 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
31 TTTTTTTTCC
*
41 TCTCCTTCTTCC-CCTTCT
1 TCTCTTTCTTCCTCCTTCT
*
59 TCTCTTTCTTCCTTCTTCT
1 TCTCTTTCTTCCTCCTTCT
78 T-TCTTTC
1 TCTCTTTC
85 CTTCTTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (19 bp):
TCTCTTTCTTCCTCCTTCT
Found at i:74 original size:16 final size:15
Alignment explanation
Indices: 53--111 Score: 70
Period size: 16 Copynumber: 4.0 Consensus size: 15
43 TCCTTCTTCC
53 CCTTCTTCTCTTTCTT
1 CCTTCTT-TCTTTCTT
69 CCTTC-TTCTTTCTTT
1 CCTTCTTTCTTTC-TT
84 CCTTCTTTCTTTC-T
1 CCTTCTTTCTTTCTT
*
98 -CTTTTTTCTTTCTT
1 CCTTCTTTCTTTCTT
112 TTTTCCTTCA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
13 11 0.28
14 8 0.21
15 8 0.21
16 12 0.31
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (15 bp):
CCTTCTTTCTTTCTT
Found at i:93 original size:4 final size:4
Alignment explanation
Indices: 55--116 Score: 58
Period size: 4 Copynumber: 15.8 Consensus size: 4
45 CTTCTTCCCC
* * *
55 TTCT TCTCT TTC- TTCC TTC- TTCT TTCT TTCC TTCT TTCT TTCT CTTTT
1 TTCT T-TCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT -TTCT
103 TTCT TTCT TT-T TTC
1 TTCT TTCT TTCT TTC
117 CTTCATTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
3 9 0.18
4 33 0.67
5 7 0.14
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (4 bp):
TTCT
Found at i:113 original size:11 final size:11
Alignment explanation
Indices: 55--127 Score: 56
Period size: 11 Copynumber: 6.3 Consensus size: 11
45 CTTCTTCCCC
*
55 TTCTTCTCTTTC
1 TTCTT-TCTTTT
* *
67 TTCCTTCTTCT
1 TTCTTTCTTTT
*
78 TTCTTTCCTTCT
1 TTCTTT-CTTTT
90 TTCTTTCTCTTTT
1 TTC-TT-TCTTTT
103 TTCTTTCTTTT
1 TTCTTTCTTTT
* *
114 TTCCTTCATTT
1 TTCTTTCTTTT
125 TTC
1 TTC
128 GTTGCCCCCC
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
11 27 0.53
12 14 0.27
13 9 0.18
14 1 0.02
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (11 bp):
TTCTTTCTTTT
Found at i:125 original size:12 final size:11
Alignment explanation
Indices: 73--127 Score: 60
Period size: 11 Copynumber: 5.0 Consensus size: 11
63 TTTCTTCCTT
73 CTTCTTTCTTTC
1 CTTCTTT-TTTC
85 CTTCTTTCTTT-
1 CTTCTTT-TTTC
96 C-TCTTTTTTC
1 CTTCTTTTTTC
*
106 TTTCTTTTTTC
1 CTTCTTTTTTC
*
117 CTTCATTTTTC
1 CTTCTTTTTTC
128 GTTGCCCCCC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
9 3 0.08
10 5 0.13
11 19 0.50
12 11 0.29
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (11 bp):
CTTCTTTTTTC
Found at i:4611 original size:20 final size:19
Alignment explanation
Indices: 4588--4630 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
4578 TTTAAAAATA
4588 TTTTTT-ATAATTTATATT
1 TTTTTTAATAATTTATATT
* *
4606 CTTTTTTAATAGTTTTTATT
1 -TTTTTTAATAATTTATATT
4626 TTTTT
1 TTTTT
4631 GAACTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTTTTAATAATTTATATT
Found at i:6766 original size:14 final size:14
Alignment explanation
Indices: 6741--6778 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
6731 AATTAAATTT
6741 AAATATAT-TTTTA
1 AAATATATGTTTTA
6754 CAAATA-ATGTTTTA
1 -AAATATATGTTTTA
6768 AAATATATGTT
1 AAATATATGTT
6779 ACTTTGCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (14 bp):
AAATATATGTTTTA
Found at i:12117 original size:31 final size:31
Alignment explanation
Indices: 12079--12148 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 31
12069 TTTATTATTC
*
12079 AGTCACTCCCGTTAGATAAGTTGTTAATTTT
1 AGTCACTCCCGTTAGATAAGTTGTCAATTTT
*
12110 AGTCACTCTCGTTAGATAAGTTGTCAATTTT
1 AGTCACTCCCGTTAGATAAGTTGTCAATTTT
*
12141 AATCACTC
1 AGTCACTC
12149 TATCGTTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (31 bp):
AGTCACTCCCGTTAGATAAGTTGTCAATTTT
Found at i:12733 original size:33 final size:35
Alignment explanation
Indices: 12668--12733 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
12658 GTTAAGAATT
* * * *
12668 ATATATATTTTTATGTCTTTTTATATTAATAAATA
1 ATATATATTTTCAAGTCTTTTAAAATTAATAAATA
12703 ATATATATTTTCAAGT-TTTTAAAATT-ATAAA
1 ATATATATTTTCAAGTCTTTTAAAATTAATAAA
12734 ATTTTAGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 5 0.19
34 8 0.30
35 14 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (35 bp):
ATATATATTTTCAAGTCTTTTAAAATTAATAAATA
Found at i:15671 original size:2 final size:2
Alignment explanation
Indices: 15664--15688 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15654 GCTTACTTAT
15664 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
15689 ACTTGTCCAT
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16783 original size:3 final size:3
Alignment explanation
Indices: 16775--16801 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
16765 ATCTGGTTGA
16775 GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
16802 ATAAGTGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:18154 original size:2 final size:2
Alignment explanation
Indices: 18149--18174 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18139 AACCCCCCCC
18149 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
18175 TTCTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:19804 original size:3 final size:3
Alignment explanation
Indices: 19796--19820 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
19786 TTTCCTCCCG
19796 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
19821 TAACGCAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:21933 original size:2 final size:2
Alignment explanation
Indices: 21926--21950 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21916 ATGAAATGAA
21926 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
21951 TATATATTTG
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:28974 original size:4 final size:4
Alignment explanation
Indices: 28967--28996 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
28957 ATATGCATGC
28967 ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
28997 AGACACAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:34424 original size:18 final size:16
Alignment explanation
Indices: 34398--34463 Score: 55
Period size: 17 Copynumber: 4.1 Consensus size: 16
34388 AAGCCCTTTT
*
34398 AAAATTTATAAATTATTA
1 AAAAATTAT-AATTA-TA
34416 AAAAATTATAATTATA
1 AAAAATTATAATTATA
*
34432 AAAAA-TA-AGTTATA
1 AAAAATTATAATTATA
* *
34446 AAAATTTTAAAATTATA
1 AAAA-ATTATAATTATA
34463 A
1 A
34464 TTTTTTTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
14 10 0.24
15 2 0.05
16 9 0.22
17 12 0.29
18 8 0.20
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
AAAAATTATAATTATA
Found at i:34428 original size:17 final size:17
Alignment explanation
Indices: 34398--34437 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
34388 AAGCCCTTTT
*
34398 AAAATTTATAAATTATTA
1 AAAAATTATAAATTA-TA
34416 AAAAATTAT-AATTATA
1 AAAAATTATAAATTATA
34432 AAAAAT
1 AAAAAT
34438 AAGTTATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 5 0.24
18 8 0.38
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAAATTATAAATTATA
Found at i:38223 original size:29 final size:30
Alignment explanation
Indices: 38190--38248 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
38180 TCATATATCA
*
38190 AATTGCACA-AAATCACAGTTCATGTATAC
1 AATTGCACATAAATCACAATTCATGTATAC
*
38219 AATTGCACATTAAATCATAATTCATGTATA
1 AATTGCACA-TAAATCACAATTCATGTATA
38249 ATTTTGAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 9 0.35
31 17 0.65
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.32
Consensus pattern (30 bp):
AATTGCACATAAATCACAATTCATGTATAC
Found at i:38251 original size:29 final size:28
Alignment explanation
Indices: 38170--38249 Score: 79
Period size: 31 Copynumber: 2.7 Consensus size: 28
38160 AATTGAATCG
* *
38170 AATCAAAATGTCATATATCAAATTGCACAA
1 AATCACAAT-TCATGTAT-AAATTGCACAA
*
38200 AATCACAGTTCATGTATACAATTGCACATTA
1 AATCACAATTCATGTATA-AATTGCACA--A
*
38231 AATCATAATTCATGTATAA
1 AATCACAATTCATGTATAA
38250 TTTTGAGATT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
28 1 0.02
29 16 0.38
30 8 0.19
31 17 0.40
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.31
Consensus pattern (28 bp):
AATCACAATTCATGTATAAATTGCACAA
Found at i:39837 original size:3 final size:3
Alignment explanation
Indices: 39829--39871 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
39819 ATAATATTCT
39829 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
39872 CTACAAACTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:41039 original size:25 final size:25
Alignment explanation
Indices: 41011--41062 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
41001 ATAACTTTAT
41011 TTTACATT-AATAAAATTAGCATAAC
1 TTTACATTAAATAAAATTAGCA-AAC
**
41036 TTTATTTTAAAATAAAATTAGCAAAC
1 TTTACATT-AAATAAAATTAGCAAAC
41062 T
1 T
41063 CTTTTTAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 6 0.26
26 4 0.17
27 13 0.57
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.38
Consensus pattern (25 bp):
TTTACATTAAATAAAATTAGCAAAC
Found at i:41057 original size:27 final size:29
Alignment explanation
Indices: 41001--41062 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 29
40991 TGTTTAAGTA
41001 ATAACTTTATTTTACATTAATAAAATTAGC
1 ATAACTTTATTTTACA-TAATAAAATTAGC
41031 ATAACTTTATTTTA-A-AATAAAATTAGC
1 ATAACTTTATTTTACATAATAAAATTAGC
41058 A-AACT
1 ATAACT
41063 CTTTTTAGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
26 4 0.12
27 13 0.41
29 1 0.03
30 14 0.44
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (29 bp):
ATAACTTTATTTTACATAATAAAATTAGC
Found at i:41217 original size:36 final size:37
Alignment explanation
Indices: 41155--41233 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 37
41145 TAAATTTCTA
* ** *
41155 TTTAAA-TAATAATTCTATTTTAAAATTAGCATAATT
1 TTTAAATTAATAATTATAAATTAAAATTAGAATAATT
* *
41191 TTTAAATTAATAATTATAAATT-AAATTATAATTATT
1 TTTAAATTAATAATTATAAATTAAAATTAGAATAATT
41227 TTTAAAT
1 TTTAAAT
41234 GTTTAATTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
36 24 0.67
37 12 0.33
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (37 bp):
TTTAAATTAATAATTATAAATTAAAATTAGAATAATT
Found at i:41298 original size:44 final size:44
Alignment explanation
Indices: 41210--41299 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 44
41200 ATAATTATAA
* * ** *
41210 ATTAAATTATAATTATTTTTAAATGTTTAATTATTGTAATTTCT
1 ATTAAATTATAATGATTTTTAAATGTGTAATTATCATAACTTCT
*
41254 ATTAAATTATAATGATTTTTAAATGTGTAGTTATCATAACTTCT
1 ATTAAATTATAATGATTTTTAAATGTGTAATTATCATAACTTCT
41298 AT
1 AT
41300 GTTAGCTTAG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (44 bp):
ATTAAATTATAATGATTTTTAAATGTGTAATTATCATAACTTCT
Found at i:43255 original size:12 final size:12
Alignment explanation
Indices: 43237--43266 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
43227 CAAGCATTCA
43237 AGAGAGGGAGAG
1 AGAGAGGGAGAG
*
43249 GGAGAGGGAGAG
1 AGAGAGGGAGAG
43261 AGAGAG
1 AGAGAG
43267 AGACATGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (12 bp):
AGAGAGGGAGAG
Found at i:43771 original size:6 final size:6
Alignment explanation
Indices: 43760--43787 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
43750 TAATATAATG
43760 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
43788 TTGAATAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:53479 original size:28 final size:27
Alignment explanation
Indices: 53423--53480 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
53413 GAAAATTATT
*
53423 TTTAAAAATTAAAAATCATTAACATTA
1 TTTAAAAATTAAAAATCATTAACAATA
53450 TTTAAAAAGTATAAAAAT-A-TAACAAATA
1 TTTAAAAA-T-TAAAAATCATTAAC-AATA
53478 TTT
1 TTT
53481 TTGAATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 12 0.44
28 8 0.30
29 7 0.26
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (27 bp):
TTTAAAAATTAAAAATCATTAACAATA
Found at i:53769 original size:25 final size:23
Alignment explanation
Indices: 53714--53761 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
53704 CCTAGTAACC
* *
53714 ATAAACCTAAATTTAACAATATA
1 ATAAACTTAAATTTAACAAAATA
53737 ATAAACTTAAATTTAACAAAATA
1 ATAAACTTAAATTTAACAAAATA
53760 AT
1 AT
53762 TTAAACTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.31
Consensus pattern (23 bp):
ATAAACTTAAATTTAACAAAATA
Found at i:64975 original size:13 final size:13
Alignment explanation
Indices: 64957--64989 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
64947 TTGACTAATC
64957 GGAGGGAAACTTG
1 GGAGGGAAACTTG
64970 GGAGGGAAACTTG
1 GGAGGGAAACTTG
64983 GGAGGGA
1 GGAGGGA
64990 TTTGGAGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.30, C:0.06, G:0.52, T:0.12
Consensus pattern (13 bp):
GGAGGGAAACTTG
Found at i:65163 original size:17 final size:17
Alignment explanation
Indices: 65141--65182 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
65131 GCTGATTTTT
65141 TTTATATTTGTATTATA
1 TTTATATTTGTATTATA
** *
65158 TTTATAAATGTATTGTA
1 TTTATATTTGTATTATA
65175 TTTATATT
1 TTTATATT
65183 AACCACTTAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (17 bp):
TTTATATTTGTATTATA
Found at i:66537 original size:17 final size:16
Alignment explanation
Indices: 66502--66544 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
66492 ACTAATCAAT
66502 AATATTACAAATATATA
1 AATATTA-AAATATATA
*
66519 AATATTAAATTATATTA
1 AATATTAAAATATA-TA
*
66536 AAAATTAAA
1 AATATTAAA
66545 GTAAGATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 6 0.26
17 17 0.74
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
AATATTAAAATATATA
Found at i:68862 original size:28 final size:27
Alignment explanation
Indices: 68831--68886 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
68821 ACAAATAATA
*
68831 TTAAATAATAATATTTTACTTAAAAAAT
1 TTAAATAAT-ATATTTTAATTAAAAAAT
* * *
68859 TTAATTGATATGTTTTAATTAAAAAAT
1 TTAAATAATATATTTTAATTAAAAAAT
68886 T
1 T
68887 ATTGTTATAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 17 0.71
28 7 0.29
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (27 bp):
TTAAATAATATATTTTAATTAAAAAAT
Found at i:69626 original size:17 final size:16
Alignment explanation
Indices: 69604--69695 Score: 58
Period size: 17 Copynumber: 5.3 Consensus size: 16
69594 CATGATTGCT
69604 TTTATTTTATTTATTTA
1 TTTATTTT-TTTATTTA
*
69621 TTTATTATTTTTATGTTG
1 TTTATT-TTTTTAT-TTA
* * *
69639 TTTGTATTTTTACCTTCA
1 TTTATTTTTTTA--TTTA
*
69657 TTTAGTTTTATTTATTCA
1 TTTA-TTTT-TTTATTTA
* *
69675 TTGATATTTTTATTTA
1 TTTATTTTTTTATTTA
69691 TTTAT
1 TTTAT
69696 ATGCCATATT
Statistics
Matches: 58, Mismatches: 11, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
16 11 0.19
17 20 0.34
18 19 0.33
19 4 0.07
20 4 0.07
ACGTcount: A:0.21, C:0.04, G:0.05, T:0.70
Consensus pattern (16 bp):
TTTATTTTTTTATTTA
Found at i:70830 original size:14 final size:13
Alignment explanation
Indices: 70808--70837 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
70798 CAAAATTTTA
70808 TTTTTTATATAAT
1 TTTTTTATATAAT
70821 TTTTTATATATAAT
1 TTTTT-TATATAAT
70835 TTT
1 TTT
70838 AAATAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTTATATAAT
Found at i:71755 original size:14 final size:15
Alignment explanation
Indices: 71736--71768 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
71726 ATTAAAAGGA
*
71736 ATTTTAGACA-AATT
1 ATTTTAAACATAATT
71750 ATTTTAAACATAATT
1 ATTTTAAACATAATT
71765 ATTT
1 ATTT
71769 GATATTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (15 bp):
ATTTTAAACATAATT
Found at i:87152 original size:25 final size:24
Alignment explanation
Indices: 87107--87153 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
87097 TAAAAATGAA
*
87107 ATTATTAATTAAATGTGAAAAACC
1 ATTATTAATTAAATGTAAAAAACC
87131 ATTATTAAATTAAAAT-TAAAAAA
1 ATTATT-AATT-AAATGTAAAAAA
87154 TAATGAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 6 0.30
25 10 0.50
26 4 0.20
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.34
Consensus pattern (24 bp):
ATTATTAATTAAATGTAAAAAACC
Found at i:98398 original size:21 final size:21
Alignment explanation
Indices: 98373--98412 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
98363 TACTTACTAC
98373 TACTAACAAAATAAAATTACT
1 TACTAACAAAATAAAATTACT
* *
98394 TACTAACGAAATTAAATTA
1 TACTAACAAAATAAAATTA
98413 AGTTAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.12, G:0.03, T:0.30
Consensus pattern (21 bp):
TACTAACAAAATAAAATTACT
Found at i:98523 original size:30 final size:32
Alignment explanation
Indices: 98471--98552 Score: 84
Period size: 30 Copynumber: 2.7 Consensus size: 32
98461 TTACCCAACT
* *
98471 AAATAA-AAATATTAA-ATAACAAATCAA-TTA
1 AAATAATAAATATAAACAAAACAAAT-AACTTA
*
98501 AAA-ATTAAAT-TAAACAAAACAAATAACTTA
1 AAATAATAAATATAAACAAAACAAATAACTTA
98531 AAATAATAAATACTAAACAAAA
1 AAATAATAAATA-TAAACAAAA
98553 TATATAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
29 6 0.14
30 21 0.50
31 6 0.14
33 9 0.21
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.23
Consensus pattern (32 bp):
AAATAATAAATATAAACAAAACAAATAACTTA
Found at i:100520 original size:35 final size:37
Alignment explanation
Indices: 100453--100529 Score: 95
Period size: 35 Copynumber: 2.1 Consensus size: 37
100443 CTCCCATATT
* * * **
100453 TTTTTAATATTTTTTTAAAATATTTTATTTATTTTAA
1 TTTTTAATAATTTTATAAAATATTTTAATTATTGAAA
100490 TTTTTAATAATTTTAT-AAATA-TTTAATTATTGAAA
1 TTTTTAATAATTTTATAAAATATTTTAATTATTGAAA
100525 TTTTT
1 TTTTT
100530 TATACAGTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
35 16 0.46
36 5 0.14
37 14 0.40
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (37 bp):
TTTTTAATAATTTTATAAAATATTTTAATTATTGAAA
Found at i:100530 original size:36 final size:38
Alignment explanation
Indices: 100452--100531 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 38
100442 CCTCCCATAT
* * * **
100452 TTTTTTAATATTTTTTTAAAATATTTTATTTATTTTAA
1 TTTTTTAATAATTTTATAAAATATTTTAATTATTGAAA
100490 -TTTTTAATAATTTTAT-AAATA-TTTAATTATTGAAA
1 TTTTTTAATAATTTTATAAAATATTTTAATTATTGAAA
100525 TTTTTTA
1 TTTTTTA
100532 TACAGTCATT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
35 11 0.31
36 11 0.31
37 14 0.39
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (38 bp):
TTTTTTAATAATTTTATAAAATATTTTAATTATTGAAA
Found at i:107815 original size:180 final size:179
Alignment explanation
Indices: 107481--107831 Score: 616
Period size: 180 Copynumber: 2.0 Consensus size: 179
107471 AGGGTGTGCC
107481 TATATGTATTTTTTTGTTTTTGGATGGAACTGTTATTGAAACTCAGCTGACAGTATACTTATAGT
1 TATATGTATTTTTTTGTTTTTGGATGGAACTGTTATTGAAACTCAGCTGACAGTATACTTATAGT
*
107546 CATCTTCTCAAGAACCTAGAAAGAGTCTTTCTATTTTAAGAGTTTTTTCTCCTCCACCATTCTCT
66 CATCTTCTCAAGAACCTAGAAAGAGTCTTGCTATTTTAAGAGTTTTTTCTCCTCCACCATTCTCT
107611 CTTTCTTCCTTTTCTTTTGAAGGGATTGGGGATTAAGGATGACAATAAG
131 CTTTCTTCCTTTTCTTTTGAAGGGATTGGGGATTAAGGATGACAATAAG
*
107660 TATATGTATTATTTTTGTTTTTGGATGGAACTGTTATTGAAACTCAGCTGA-TGATATACTTATA
1 TATATGTATT-TTTTTGTTTTTGGATGGAACTGTTATTGAAACTCAGCTGACAG-TATACTTATA
107724 GTCATCTTCTCAAGAACCTAGAAAGAGTCTTGCTATTTTAAGAGTTTTTTCTCCT-CACCATTCT
64 GTCATCTTCTCAAGAACCTAGAAAGAGTCTTGCTATTTTAAGAGTTTTTTCTCCTCCACCATTCT
* * *
107788 CTCTTTCTTCTTTTTCTTTTGGAAGGGATTGGGGGTTCAGGATG
129 CTCTTTCTTCCTTTTCTTTT-GAAGGGATTGGGGATTAAGGATG
107832 GGTGTAGAAT
Statistics
Matches: 164, Mismatches: 5, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
179 39 0.24
180 125 0.76
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.43
Consensus pattern (179 bp):
TATATGTATTTTTTTGTTTTTGGATGGAACTGTTATTGAAACTCAGCTGACAGTATACTTATAGT
CATCTTCTCAAGAACCTAGAAAGAGTCTTGCTATTTTAAGAGTTTTTTCTCCTCCACCATTCTCT
CTTTCTTCCTTTTCTTTTGAAGGGATTGGGGATTAAGGATGACAATAAG
Found at i:108518 original size:18 final size:17
Alignment explanation
Indices: 108487--108520 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
108477 CCCAGTATTT
108487 TTATTTGAAATTTGTTA
1 TTATTTGAAATTTGTTA
*
108504 TTATTATGAATTTTGTT
1 TTATT-TGAAATTTGTT
108521 CAGTTGAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.26, C:0.00, G:0.12, T:0.62
Consensus pattern (17 bp):
TTATTTGAAATTTGTTA
Done.