Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011580.1 Kokia drynarioides strain JFW-HI SEQ_126569, 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: 11844
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.33
Warning! 196 characters in sequence are not A, C, G, or T
Found at i:1653 original size:12 final size:12
Alignment explanation
Indices: 1636--1669 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1626 GAGCCTCAGG
1636 ACCAACCCGAGA
1 ACCAACCCGAGA
* *
1648 ACCAACCAGAGC
1 ACCAACCCGAGA
1660 ACCAACCCGA
1 ACCAACCCGA
1670 TCCCCAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.41, C:0.44, G:0.15, T:0.00
Consensus pattern (12 bp):
ACCAACCCGAGA
Found at i:2134 original size:30 final size:31
Alignment explanation
Indices: 2100--2171 Score: 105
Period size: 30 Copynumber: 2.4 Consensus size: 31
2090 ATTTTTTTTC
2100 CGTTTACT-TTTTAAATTTAATTTCTAATTT
1 CGTTTACTATTTTAAATTTAATTTCTAATTT
*
2130 CGTTT-TTATTTTAAATTTAATTTCTAATTT
1 CGTTTACTATTTTAAATTTAATTTCTAATTT
*
2160 CCTTTA-TATTTT
1 CGTTTACTATTTT
2172 TTTTCTAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 1 0.03
30 37 0.97
ACGTcount: A:0.25, C:0.10, G:0.03, T:0.62
Consensus pattern (31 bp):
CGTTTACTATTTTAAATTTAATTTCTAATTT
Found at i:2165 original size:23 final size:23
Alignment explanation
Indices: 2139--2199 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
2129 TCGTTTTTAT
*
2139 TTTAAATTTAATTTCTAATTTCC
1 TTTATATTTAATTTCTAATTTCC
**
2162 TTTATATTTTTTTTCTAATTTCC
1 TTTATATTTAATTTCTAATTTCC
*
2185 TGTATATTCTAATTT
1 TTTATATT-TAATTT
2200 TTTTTTAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
23 27 0.87
24 4 0.13
ACGTcount: A:0.25, C:0.11, G:0.02, T:0.62
Consensus pattern (23 bp):
TTTATATTTAATTTCTAATTTCC
Found at i:2183 original size:30 final size:30
Alignment explanation
Indices: 2108--2171 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
2098 TCCGTTTACT
* *
2108 TTTTAAATTTAATTTCTAATTTCGTTTTTA
1 TTTTAAATTTAATTTCTAATTTCCTTTATA
2138 TTTTAAATTTAATTTCTAATTTCCTTTATA
1 TTTTAAATTTAATTTCTAATTTCCTTTATA
2168 TTTT
1 TTTT
2172 TTTTCTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.64
Consensus pattern (30 bp):
TTTTAAATTTAATTTCTAATTTCCTTTATA
Found at i:2771 original size:62 final size:61
Alignment explanation
Indices: 2695--2874 Score: 242
Period size: 57 Copynumber: 3.0 Consensus size: 61
2685 TTACCAAATT
*
2695 AAAAGGGGGTGTCGATCATTTGATGGCCAACACCAAAAAAATTTGTAATTTTTTTATCCGAG
1 AAAAGGGGGTGTCGACCATTTGATGGCCAACACCAAAAAAATTTGTAATTTTTTT-TCCGAG
** * * *
2757 AAAAGGGGGTGTCGACCATTACATGACCAACA-CAAAAAAAATT-T-ATATTTTTT-CGAG
1 AAAAGGGGGTGTCGACCATTTGATGGCCAACACCAAAAAAATTTGTAATTTTTTTTCCGAG
* *
2814 AAAAGGGGGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGCAATTTTTTTCTCCGA
1 AAAAGGGGGTGTCGACCATTTGATGGCCAACACCAAAAAAATTTGTAATTTTTTT-TCCGA
2875 TGACACCCAA
Statistics
Matches: 100, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
57 32 0.32
58 11 0.11
59 7 0.07
60 8 0.08
61 11 0.11
62 31 0.31
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (61 bp):
AAAAGGGGGTGTCGACCATTTGATGGCCAACACCAAAAAAATTTGTAATTTTTTTTCCGAG
Found at i:2866 original size:57 final size:58
Alignment explanation
Indices: 2659--2866 Score: 222
Period size: 57 Copynumber: 3.5 Consensus size: 58
2649 CGTTGGAATA
* * * *
2659 GCCAACACCAAATAAAAATT-TAATTTTTACCAAATTAAAAGGGGGTGTCGATCATTTGATG
1 GCCAACACCAAA-AAAATTTGTAATTTTT-CC-GA-GAAAAGGGGGTGTCGACCATTTGATG
**
2720 GCCAACACCAAAAAAATTTGTAATTTTTTTATCCGAGAAAAGGGGGTGTCGACCATTACATG
1 GCCAACACCAAAAAAATTTGTAA---TTTT-TCCGAGAAAAGGGGGTGTCGACCATTTGATG
* * * * *
2782 ACCAACACAAAAAAAATTTAT-ATTTTTTCGAGAAAAGGGGGTGTCGGCCATTTGATG
1 GCCAACACCAAAAAAATTTGTAATTTTTCCGAGAAAAGGGGGTGTCGACCATTTGATG
*
2839 GCCAACACCAAAAAAATTTGCAATTTTT
1 GCCAACACCAAAAAAATTTGTAATTTTT
2867 TTCTCCGATG
Statistics
Matches: 124, Mismatches: 17, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
57 44 0.35
58 10 0.08
60 6 0.05
61 16 0.13
62 40 0.32
63 1 0.01
64 6 0.05
65 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.28
Consensus pattern (58 bp):
GCCAACACCAAAAAAATTTGTAATTTTTCCGAGAAAAGGGGGTGTCGACCATTTGATG
Found at i:2945 original size:58 final size:58
Alignment explanation
Indices: 2883--3287 Score: 297
Period size: 56 Copynumber: 7.0 Consensus size: 58
2873 GATGACACCC
* *
2883 AAAAATGTAAATTTTTTTTCGACAAAAGAGGGTGTCGGCCATTTGATGGCCAACACAA
1 AAAAATGTAAATTTTTTTTCGAGAAAAGAGGGTGTCGGCCATTTAATGGCCAACACAA
* * * * ** * **
2941 AAAAAAGTTGCAATTTTTTTATCCAAGAAAAGAGGGTGTCGACCATGCAATGGCTAACACCC
1 AAAAATG-T-AAATTTTTTT-T-CGAGAAAAGAGGGTGTCGGCCATTTAATGGCCAACACAA
* * * * * ** *
3003 AAAAATGCAATTTTTTTTTCAAGAAAAGGGGGTGTCGACCATGCAATGGCCAACACCCA
1 AAAAATGTAAATTTTTTTTCGAGAAAAGAGGGTGTCGGCCATTTAATGGCCAACA-CAA
* * * * *
3062 AAAAA-G-CAA-TTTTTTTCGAGAAAAGGGGGTATCGGCCATTTGATGGTCAACACCAA
1 AAAAATGTAAATTTTTTTTCGAGAAAAGAGGGTGTCGGCCATTTAATGGCCAACA-CAA
* * ** **
3118 AAAAATTTAAAATTTTTTTCTC-A-AAAAGAGGGTGTCGGCTATGCAATGGCCAACACTC
1 AAAAATGT-AAATTTTTTT-TCGAGAAAAGAGGGTGTCGGCCATTTAATGGCCAACACAA
* * *
3176 AAAAATGT-AA-TTTTTTTCGAGAAAAGGGGGTGTCAGCAATTTAATGGCCAACACAA
1 AAAAATGTAAATTTTTTTTCGAGAAAAGAGGGTGTCGGCCATTTAATGGCCAACACAA
* * * * * **
3232 AAAATTGT--ATTTTTTATCTGACAAAAAAGTGGTGTCGACCATTGCATGGCCAACAC
1 AAAAATGTAAATTTTTTTTC-GAGAAAAGAG-GGTGTCGGCCATTTAATGGCCAACAC
3288 TCCAAAATTT
Statistics
Matches: 275, Mismatches: 57, Indels: 30
0.76 0.16 0.08
Matches are distributed among these distances:
54 2 0.01
55 8 0.03
56 88 0.32
57 8 0.03
58 70 0.25
59 36 0.13
60 24 0.09
61 3 0.01
62 36 0.13
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (58 bp):
AAAAATGTAAATTTTTTTTCGAGAAAAGAGGGTGTCGGCCATTTAATGGCCAACACAA
Found at i:3151 original size:115 final size:112
Alignment explanation
Indices: 2989--3294 Score: 325
Period size: 115 Copynumber: 2.7 Consensus size: 112
2979 TCGACCATGC
* * * * *
2989 AATGGCTAACACCCAAAAA-TGCAATTTTTTTTTCAAGAAAAGGGGGTGTCGACCATGCAATGGC
1 AATGGCCAACA-CAAAAAATTGTAATTTTTTTCTC-A-AAAAGAGGGTGTCGACCATGCAATGGC
* *
3053 CAACACCCAAAAAAGCAATTTTTTTCGAGAAAAGGGGGTATCGGCCATTT
63 CAACACCCAAAAAAGCAATTTTTTTCGAGAAAAGGGGGTATCAGCAATTT
* * * *
3103 GATGGTCAACACCAAAAAAATT-TAAAATTTTTTTCTCAAAAAGAGGGTGTCGGCTATGCAATGG
1 AATGGCCAACA-C-AAAAAATTGT--AATTTTTTTCTCAAAAAGAGGGTGTCGACCATGCAATGG
* * * *
3167 CCAACACTCAAAAATGTAATTTTTTTCGAGAAAAGGGGGTGTCAGCAATTT
62 CCAACACCCAAAAAAGCAATTTTTTTCGAGAAAAGGGGGTATCAGCAATTT
3218 AATGGCCAACACAAAAAATTGT-ATTTTTTATCTGACAAAAA-AGTGGTGTCGACCATTGC-ATG
1 AATGGCCAACACAAAAAATTGTAATTTTTT-TCT--CAAAAAGAG-GGTGTCGACCA-TGCAATG
3280 GCCAACACTCCAAAA
61 GCCAACAC-CCAAAA
3295 TTTTTTTTTT
Statistics
Matches: 161, Mismatches: 20, Indels: 21
0.80 0.10 0.10
Matches are distributed among these distances:
111 7 0.04
112 3 0.02
113 10 0.06
114 38 0.24
115 90 0.56
116 2 0.01
117 11 0.07
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (112 bp):
AATGGCCAACACAAAAAATTGTAATTTTTTTCTCAAAAAGAGGGTGTCGACCATGCAATGGCCAA
CACCCAAAAAAGCAATTTTTTTCGAGAAAAGGGGGTATCAGCAATTT
Found at i:4162 original size:30 final size:33
Alignment explanation
Indices: 4119--4182 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 33
4109 TAATAATGGT
4119 AAAATTATAATTT-AT-TCTTAAAAATGATAAA
1 AAAATTATAATTTAATCTCTTAAAAATGATAAA
* *
4150 AAAATT-TAATTTAATCTTTTAAAAATTATAAA
1 AAAATTATAATTTAATCTCTTAAAAATGATAAA
4182 A
1 A
4183 TTATAACCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 6 0.21
31 8 0.28
32 15 0.52
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.41
Consensus pattern (33 bp):
AAAATTATAATTTAATCTCTTAAAAATGATAAA
Found at i:5600 original size:17 final size:17
Alignment explanation
Indices: 5569--5624 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 17
5559 TTTTTAATAA
*
5569 AAAAAATTTAGAATATAT
1 AAAAAA-TTAAAATATAT
5587 AAAAAATTAAAATAT-T
1 AAAAAATTAAAATATAT
*
5603 CTAAAAATTACAACATATAT
1 -AAAAAATTA-AA-ATATAT
5623 AA
1 AA
5625 TACGATCTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
16 1 0.03
17 16 0.52
18 8 0.26
19 5 0.16
20 1 0.03
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.30
Consensus pattern (17 bp):
AAAAAATTAAAATATAT
Found at i:6328 original size:18 final size:18
Alignment explanation
Indices: 6272--6330 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
6262 AACTTTTATA
*
6272 AGCTCGCTTCCTTGAGTG
1 AGCTCGCATCCTTGAGTG
* * * * *
6290 AACTTGAAACTTTGA-TG
1 AGCTCGCATCCTTGAGTG
6307 AGCTCGCATCCTTGAGTG
1 AGCTCGCATCCTTGAGTG
6325 AGCTCG
1 AGCTCG
6331 TAACTTTGAA
Statistics
Matches: 29, Mismatches: 11, Indels: 2
0.69 0.26 0.05
Matches are distributed among these distances:
17 12 0.41
18 17 0.59
ACGTcount: A:0.20, C:0.24, G:0.25, T:0.31
Consensus pattern (18 bp):
AGCTCGCATCCTTGAGTG
Found at i:6336 original size:35 final size:35
Alignment explanation
Indices: 6255--6350 Score: 111
Period size: 35 Copynumber: 2.7 Consensus size: 35
6245 TCACATGTAA
* * * *
6255 AGCTCGCAACTTTTATAAGCTCGCTTCCTTGAGTG
1 AGCTCGAAACTTTGATGAGCTCGCATCCTTGAGTG
* *
6290 AACTTGAAACTTTGATGAGCTCGCATCCTTGAGTG
1 AGCTCGAAACTTTGATGAGCTCGCATCCTTGAGTG
* *
6325 AGCTCGTAACTTTGAATGAGTTCGCA
1 AGCTCGAAACTTTG-ATGAGCTCGCA
6351 GATGTAGAGC
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
35 40 0.80
36 10 0.20
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (35 bp):
AGCTCGAAACTTTGATGAGCTCGCATCCTTGAGTG
Found at i:6339 original size:18 final size:18
Alignment explanation
Indices: 6283--6344 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 18
6273 GCTCGCTTCC
* *
6283 TTGAGTGAACTTGAAACT
1 TTGAGTGAGCTCGAAACT
* * *
6301 TTGA-TGAGCTCGCATCC
1 TTGAGTGAGCTCGAAACT
*
6318 TTGAGTGAGCTCGTAACT
1 TTGAGTGAGCTCGAAACT
*
6336 TTGAATGAG
1 TTGAGTGAG
6345 TTCGCAGATG
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
17 12 0.35
18 22 0.65
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (18 bp):
TTGAGTGAGCTCGAAACT
Done.