Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009010.1 Kokia drynarioides strain JFW-HI SEQ_123708, 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: 35957
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:1583 original size:5 final size:6
Alignment explanation
Indices: 1553--1586 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
1543 TTTAAAAATC
*
1553 ATAAAA ATTATAA ATAAAA ATAAAA ATAAAA ATA
1 ATAAAA A-TAAAA ATAAAA ATAAAA ATAAAA ATA
1587 TATTAAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (6 bp):
ATAAAA
Found at i:2113 original size:2 final size:2
Alignment explanation
Indices: 2106--2136 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2096 AATTTAACCG
2106 TA TA TA 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 TA TA TA T
2137 TATTTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3535 original size:10 final size:11
Alignment explanation
Indices: 3504--3548 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 11
3494 TCTTCAATTT
3504 ATATATTAT-A
1 ATATATTATAA
* *
3514 ATAAAATATAA
1 ATATATTATAA
3525 ATATATT-TAA
1 ATATATTATAA
3535 ATA-ATTATAA
1 ATATATTATAA
3545 ATAT
1 ATAT
3549 TAAATATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
9 3 0.11
10 19 0.68
11 6 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
ATATATTATAA
Found at i:6240 original size:19 final size:19
Alignment explanation
Indices: 6216--6259 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
6206 AACGATCAAA
* *
6216 GTCAATGGGTTTGGGTCGG
1 GTCAATGAGTTCGGGTCGG
6235 GTCAATGAGTTCGGGTCGG
1 GTCAATGAGTTCGGGTCGG
*
6254 GCCAAT
1 GTCAAT
6260 CGGGCTTGGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.16, C:0.16, G:0.41, T:0.27
Consensus pattern (19 bp):
GTCAATGAGTTCGGGTCGG
Found at i:7444 original size:24 final size:25
Alignment explanation
Indices: 7406--7456 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
7396 AACGGTCAAC
*
7406 GGTTTGGGTTCGGGTTC-GATCAATG
1 GGTTCGGGTTCGGGTTCAG-TCAATG
7431 GGTTCGGGTT-GGGTTCAGTCAATG
1 GGTTCGGGTTCGGGTTCAGTCAATG
7455 GG
1 GG
7457 AGAGTCAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.12, C:0.12, G:0.43, T:0.33
Consensus pattern (25 bp):
GGTTCGGGTTCGGGTTCAGTCAATG
Found at i:7519 original size:21 final size:22
Alignment explanation
Indices: 7470--7534 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
7460 GTCAAATCGA
* *
7470 ATTGGG-TTTAAGGTTTAGGTG
1 ATTGGGTTTTATGGTTTGGGTG
*
7491 ATTTGGTTTTATGGTTTGGGT-
1 ATTGGGTTTTATGGTTTGGGTG
7512 ATTGGGTTTTTATGGTTTTGGGT
1 ATTGGG-TTTTATGG-TTTGGGT
7535 TTTGCACACA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 10 0.27
22 20 0.54
23 7 0.19
ACGTcount: A:0.12, C:0.00, G:0.35, T:0.52
Consensus pattern (22 bp):
ATTGGGTTTTATGGTTTGGGTG
Found at i:11159 original size:2 final size:2
Alignment explanation
Indices: 11152--11176 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11142 ATATACATTC
11152 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
11177 CAGTCTATAA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17580 original size:57 final size:57
Alignment explanation
Indices: 17492--17605 Score: 210
Period size: 57 Copynumber: 2.0 Consensus size: 57
17482 CCAGCAAGAG
*
17492 TAGACTCTTCCACAATATCCCACCAATTTTAGGCCTCACCCCTTTGTAAAGAAACAT
1 TAGACTCTTCCACAATATCCCACCAATTTTAGGCCTCACCCATTTGTAAAGAAACAT
*
17549 TAGACTCTTTCACAATATCCCACCAATTTTAGGCCTCACCCATTTGTAAAGAAACAT
1 TAGACTCTTCCACAATATCCCACCAATTTTAGGCCTCACCCATTTGTAAAGAAACAT
17606 CAGCCCTAAC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.32, C:0.30, G:0.09, T:0.29
Consensus pattern (57 bp):
TAGACTCTTCCACAATATCCCACCAATTTTAGGCCTCACCCATTTGTAAAGAAACAT
Found at i:18588 original size:13 final size:13
Alignment explanation
Indices: 18555--18581 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
18545 ATGAAATCCC
18555 AATATAAAATAAT
1 AATATAAAATAAT
18568 AATATAAAATAAT
1 AATATAAAATAAT
18581 A
1 A
18582 TAATAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AATATAAAATAAT
Found at i:19618 original size:14 final size:13
Alignment explanation
Indices: 19599--19640 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 13
19589 AACCCAAAAA
*
19599 GTCAACGGTTAACT
1 GTCAACGGTCAA-T
19613 GTCAACGGTCAAT
1 GTCAACGGTCAAT
19626 GATCAACGGTCAAT
1 G-TCAACGGTCAAT
19640 G
1 G
19641 GTCTGCGTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 2 0.08
14 24 0.92
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (13 bp):
GTCAACGGTCAAT
Found at i:19756 original size:22 final size:22
Alignment explanation
Indices: 19709--19762 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
19699 TTAAATTGGG
*
19709 TTTAGGGTTTGGGTGATTTAGT
1 TTTAGGGTTTGGGTGATTCAGT
*
19731 TTTAGGGTTTGGGT-ATTCGGT
1 TTTAGGGTTTGGGTGATTCAGT
*
19752 CTTTATGGTTT
1 -TTTAGGGTTT
19763 TAGGTTTGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 5 0.18
22 23 0.82
ACGTcount: A:0.11, C:0.04, G:0.33, T:0.52
Consensus pattern (22 bp):
TTTAGGGTTTGGGTGATTCAGT
Found at i:25136 original size:28 final size:28
Alignment explanation
Indices: 25096--25163 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
25086 AATCCTAACC
25096 TACAACTTGTGTGAGCAGACCCGTATTA
1 TACAACTTGTGTGAGCAGACCCGTATTA
* * *
25124 TACAACTTGTGTGAGTAGACCTGTTTTA
1 TACAACTTGTGTGAGCAGACCCGTATTA
*
25152 TACAGCTTGTGT
1 TACAACTTGTGT
25164 AAACAAATCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (28 bp):
TACAACTTGTGTGAGCAGACCCGTATTA
Found at i:32121 original size:16 final size:14
Alignment explanation
Indices: 32097--32137 Score: 64
Period size: 16 Copynumber: 2.8 Consensus size: 14
32087 GTTGTAATGT
32097 AATTTAAATTTTAA
1 AATTTAAATTTTAA
32111 AATACTTAAATTTTAA
1 AAT--TTAAATTTTAA
32127 AATTTAAATTT
1 AATTTAAATTT
32138 GAAAGCTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 11 0.44
16 14 0.56
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (14 bp):
AATTTAAATTTTAA
Found at i:32432 original size:44 final size:47
Alignment explanation
Indices: 32382--32469 Score: 146
Period size: 44 Copynumber: 1.9 Consensus size: 47
32372 TGTTCACGTT
32382 AGAGAATCTCACTGTTCA-TTT-TTTTTT-TTGCAAAGAATATTGTC
1 AGAGAATCTCACTGTTCACTTTATTTTTTCTTGCAAAGAATATTGTC
*
32426 AGAGAATCTCACTGTTCACTTTATTTTTTCTTGCAGAGAATATT
1 AGAGAATCTCACTGTTCACTTTATTTTTTCTTGCAAAGAATATT
32470 TCCAGTTCAT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
44 18 0.45
45 3 0.08
46 6 0.15
47 13 0.32
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (47 bp):
AGAGAATCTCACTGTTCACTTTATTTTTTCTTGCAAAGAATATTGTC
Found at i:35296 original size:13 final size:13
Alignment explanation
Indices: 35278--35317 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
35268 AATTAATTAT
35278 TTTTTAAAAATAA
1 TTTTTAAAAATAA
35291 TTTTTAAAAAT-A
1 TTTTTAAAAATAA
*
35303 -TTTTAAAATTAA
1 TTTTTAAAAATAA
35315 TTT
1 TTT
35318 AAAATTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 9 0.38
12 2 0.08
13 13 0.54
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTTTTAAAAATAA
Found at i:35297 original size:24 final size:24
Alignment explanation
Indices: 35270--35329 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
35260 TTAGCAAAAA
35270 TTAATTATTTTTTAAAAATAATTT
1 TTAATTATTTTTTAAAAATAATTT
** * *
35294 TTAAAAATATTTTAAAATTAATTT
1 TTAATTATTTTTTAAAAATAATTT
**
35318 AAAATTATTTTT
1 TTAATTATTTTT
35330 ATATATAAAA
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TTAATTATTTTTTAAAAATAATTT
Found at i:35308 original size:11 final size:11
Alignment explanation
Indices: 35279--35328 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
35269 ATTAATTATT
35279 TTTTAAAAATAA
1 TTTTAAAAAT-A
35291 TTTTTAAAAATA
1 -TTTTAAAAATA
*
35303 TTTTAAAATTA
1 TTTTAAAAATA
* *
35314 ATTTAAAATTA
1 TTTTAAAAATA
35325 TTTT
1 TTTT
35329 TATATATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
11 23 0.68
12 1 0.03
13 10 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTTAAAAATA
Done.