Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013219.1 Kokia drynarioides strain JFW-HI SEQ_128238, 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: 24143
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.36
Warning! 23 characters in sequence are not A, C, G, or T
Found at i:2177 original size:19 final size:21
Alignment explanation
Indices: 2147--2198 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 21
2137 TATCTAATTG
2147 TTTATATTTATTTGCTT-TT-A
1 TTTAT-TTTATTTGCTTGTTCA
2167 TTTATTTTATTT-CTTGTTCA
1 TTTATTTTATTTGCTTGTTCA
2187 TTTA-TTTATTTG
1 TTTATTTTATTTG
2199 TTAATTATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 3 0.10
19 16 0.55
20 10 0.34
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71
Consensus pattern (21 bp):
TTTATTTTATTTGCTTGTTCA
Found at i:2445 original size:25 final size:25
Alignment explanation
Indices: 2408--2456 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
2398 TTATTTTAGA
2408 ATTTTTTCTCTATTGTAT-TTCCTAT
1 ATTTTTTCTCTATT-TATATTCCTAT
2433 ATTTATTTC-CTATTTATATTCCTA
1 ATTT-TTTCTCTATTTATATTCCTA
2457 ATTAATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 3 0.14
25 15 0.68
26 4 0.18
ACGTcount: A:0.20, C:0.16, G:0.02, T:0.61
Consensus pattern (25 bp):
ATTTTTTCTCTATTTATATTCCTAT
Found at i:3638 original size:18 final size:18
Alignment explanation
Indices: 3610--3645 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
3600 TACCTTAACC
3610 TTTATAATATTTTATTTAA
1 TTTATAATATTTT-TTTAA
3629 TTTA-AATATTTTTTTAA
1 TTTATAATATTTTTTTAA
3646 ATATATTGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 8 0.47
19 4 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTATAATATTTTTTTAA
Found at i:5425 original size:23 final size:21
Alignment explanation
Indices: 5399--5455 Score: 53
Period size: 23 Copynumber: 2.5 Consensus size: 21
5389 AAAAACTTTT
5399 AAATAGTTTAATAACTTAAATGA
1 AAATA-TTTAATAACTT-AATGA
5422 AAAT-TTTCAAATAACTTAATGA
1 AAATATTT--AATAACTTAATGA
*
5444 TAATAATTTAAT
1 AAAT-ATTTAAT
5456 GATAATAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
21 3 0.10
22 11 0.38
23 12 0.41
24 3 0.10
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (21 bp):
AAATATTTAATAACTTAATGA
Found at i:5441 original size:31 final size:31
Alignment explanation
Indices: 5379--5441 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
5369 AACAACCCAT
**
5379 TAACTTAAATAAAAACTTTTAAATAGTTTAA
1 TAACTTAAATAAAAACTTTTAAATAACTTAA
*
5410 TAACTTAAATGAAAA-TTTTCAAATAACTTAA
1 TAACTTAAATAAAAACTTTT-AAATAACTTAA
5441 T
1 T
5442 GATAATAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 4 0.14
31 24 0.86
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (31 bp):
TAACTTAAATAAAAACTTTTAAATAACTTAA
Found at i:5448 original size:14 final size:14
Alignment explanation
Indices: 5431--5473 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
5421 AAAATTTTCA
*
5431 AATAACTTAATGAT
1 AATAATTTAATGAT
5445 AATAATTTAATGAT
1 AATAATTTAATGAT
*
5459 AATAGTTTAATGAT
1 AATAATTTAATGAT
5473 A
1 A
5474 TGAAACGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (14 bp):
AATAATTTAATGAT
Found at i:6970 original size:15 final size:15
Alignment explanation
Indices: 6950--6980 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
6940 CCACTATAAC
6950 TAGCTTATTCAATCA
1 TAGCTTATTCAATCA
6965 TAGCTTATTCAATCA
1 TAGCTTATTCAATCA
6980 T
1 T
6981 GAGAAGAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.42
Consensus pattern (15 bp):
TAGCTTATTCAATCA
Found at i:10877 original size:158 final size:158
Alignment explanation
Indices: 10652--10954 Score: 435
Period size: 158 Copynumber: 1.9 Consensus size: 158
10642 TGTTACAGTT
* * ** * *
10652 ACAGCTTGTATGAACATTACATGTTATATGGGTTTTGGTCTTAAATGTCTTACCGATGGCTGGGG
1 ACAGCTCGTATGAACATTACAGGTTATATGGGTGCTGGTCCTAAATGTCTTACCGATGGCTGAGG
* * * *
10717 TCCTGCATTTGTTACGGATTCACCACAGCTCGTGTGAGCAGCATCGCGTAGCCTAACATCTCGAC
66 TCCGGCATTTATTACGAATTCACCACAGCTCGTGTGAGCAGCATCGCGTAGCCCAACATCTCGAC
*
10782 CCACAGCTTGTGTGAGCAGGCCCTTTTC
131 CCACAGCTCGTGTGAGCAGGCCCTTTTC
* * *
10810 ACAGCTCGTGTGAGCATTACAGGTTATATGGGTGCTGGTCCTAAATGTCTTACCGATGGTTGAGG
1 ACAGCTCGTATGAACATTACAGGTTATATGGGTGCTGGTCCTAAATGTCTTACCGATGGCTGAGG
* * * * *
10875 TCCGGCATTTATTTCGAATTCTCTACAGCTCGTGTGAGCAGCATCGTGTAGCCCCACATCTCGAC
66 TCCGGCATTTATTACGAATTCACCACAGCTCGTGTGAGCAGCATCGCGTAGCCCAACATCTCGAC
10940 CCACAGCTCGTGTGA
131 CCACAGCTCGTGTGA
10955 CCATATATGA
Statistics
Matches: 126, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
158 126 1.00
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.30
Consensus pattern (158 bp):
ACAGCTCGTATGAACATTACAGGTTATATGGGTGCTGGTCCTAAATGTCTTACCGATGGCTGAGG
TCCGGCATTTATTACGAATTCACCACAGCTCGTGTGAGCAGCATCGCGTAGCCCAACATCTCGAC
CCACAGCTCGTGTGAGCAGGCCCTTTTC
Found at i:13520 original size:24 final size:26
Alignment explanation
Indices: 13493--13540 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
13483 AGAGAAATGT
13493 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
13517 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
13541 CCCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:13639 original size:23 final size:22
Alignment explanation
Indices: 13601--13651 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 22
13591 GAACACTAGC
*
13601 GTGCTCTTGATTAGCACTGTGT
1 GTGCTCTTAATTAGCACTGTGT
*
13623 GTGCTCTCTAATTAGCACTTTGT
1 GTGCTCT-TAATTAGCACTGTGT
13646 GTGCTC
1 GTGCTC
13652 AGTATTTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.14, C:0.22, G:0.24, T:0.41
Consensus pattern (22 bp):
GTGCTCTTAATTAGCACTGTGT
Found at i:13691 original size:23 final size:24
Alignment explanation
Indices: 13657--13722 Score: 73
Period size: 23 Copynumber: 2.8 Consensus size: 24
13647 TGCTCAGTAT
*
13657 TTTGTGTACTCTCTGTT-TAGCAC
1 TTTGTGTGCTCTCTGTTCTAGCAC
*
13680 TTTGTGTGCTCTCTTTTGCCTAGCAC
1 TTTGTGTGCTCTCTGTT--CTAGCAC
*
13706 -TTATGTGCTCTCTGTTC
1 TTTGTGTGCTCTCTGTTC
13723 AGTACTTCGG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
23 16 0.44
25 14 0.39
26 6 0.17
ACGTcount: A:0.09, C:0.24, G:0.18, T:0.48
Consensus pattern (24 bp):
TTTGTGTGCTCTCTGTTCTAGCAC
Done.