Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001416.1 Kokia drynarioides strain JFW-HI SEQ_112912, 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: 47168
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Warning! 108 characters in sequence are not A, C, G, or T
Found at i:7171 original size:30 final size:30
Alignment explanation
Indices: 7135--7199 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
7125 CAACTTAACA
*
7135 AACAAATGTCTCTAAAATAATAATAAAATT
1 AACAAATGTCTCTAAAATAATAACAAAATT
7165 AACAAATGTCTCTAAAATAATAACAAAATT
1 AACAAATGTCTCTAAAATAATAACAAAATT
7195 AACAA
1 AACAA
7200 TAAAATAAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.58, C:0.12, G:0.03, T:0.26
Consensus pattern (30 bp):
AACAAATGTCTCTAAAATAATAACAAAATT
Found at i:13739 original size:16 final size:16
Alignment explanation
Indices: 13715--13750 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
13705 AGAATAAGTA
* *
13715 AATATTTAATATAAAT
1 AATACTTAAAATAAAT
13731 AATACTTAAAATAAAT
1 AATACTTAAAATAAAT
13747 AATA
1 AATA
13751 TTTTGTAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (16 bp):
AATACTTAAAATAAAT
Found at i:13925 original size:16 final size:16
Alignment explanation
Indices: 13904--13938 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
13894 ATGCAGATAG
13904 TAATTTTTTTTAGTTA
1 TAATTTTTTTTAGTTA
13920 TAATTTTTTTTAGTTA
1 TAATTTTTTTTAGTTA
13936 TAA
1 TAA
13939 AATAATTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.66
Consensus pattern (16 bp):
TAATTTTTTTTAGTTA
Found at i:16633 original size:24 final size:24
Alignment explanation
Indices: 16572--16645 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
16562 AGAAATAATC
* *
16572 TTTCAGTTAAACTCTGTTTGTTT-
1 TTTCAATTAAACTCTGTTTATTTG
* *
16595 TTTTAATTAAGCTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
*
16619 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
16643 TTT
1 TTT
16646 GTATCAAACT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 19 0.44
24 24 0.56
ACGTcount: A:0.22, C:0.11, G:0.09, T:0.58
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:16654 original size:24 final size:24
Alignment explanation
Indices: 16580--16657 Score: 68
Period size: 24 Copynumber: 3.3 Consensus size: 24
16570 TCTTTCAGTT
* * * *
16580 AAACTCTGTTTGTTT-TTTTAATT
1 AAACTCTATTTATTTGTTTCAATC
* * *
16603 AAGCTCTGTTTATTTGTTTCAATT
1 AAACTCTATTTATTTGTTTCAATC
**
16627 AAACTCTATTTATTTGTTTGTATC
1 AAACTCTATTTATTTGTTTCAATC
16651 AAACTCT
1 AAACTCT
16658 TATTAGTCTA
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
23 13 0.28
24 33 0.72
ACGTcount: A:0.24, C:0.13, G:0.09, T:0.54
Consensus pattern (24 bp):
AAACTCTATTTATTTGTTTCAATC
Found at i:19520 original size:42 final size:42
Alignment explanation
Indices: 19379--19501 Score: 201
Period size: 42 Copynumber: 2.9 Consensus size: 42
19369 ATATCAGTTA
* *
19379 AGATTTGATTTGCACGTTAAGCATGACGACTATGTTGATATG
1 AGATTTGGTTTGCATGTTAAGCATGACGACTATGTTGATATG
*
19421 AGATTTGGTTTACATGTTAAGCATGACGACTATGTTGATATG
1 AGATTTGGTTTGCATGTTAAGCATGACGACTATGTTGATATG
* *
19463 AGATTTGGTTTGCATGTTAAGCATGCCAACTATGTTGAT
1 AGATTTGGTTTGCATGTTAAGCATGACGACTATGTTGAT
19502 CATAAATTTG
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (42 bp):
AGATTTGGTTTGCATGTTAAGCATGACGACTATGTTGATATG
Found at i:19644 original size:24 final size:24
Alignment explanation
Indices: 19611--19671 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
19601 TTACTATAAA
19611 ATTGAGTGGCTTGACCACAATGCT
1 ATTGAGTGGCTTGACCACAATGCT
* *
19635 ATTGAATGGCTTGACCATAATGCT
1 ATTGAGTGGCTTGACCACAATGCT
*
19659 ATCGAGTGGCTTG
1 ATTGAGTGGCTTG
19672 GCCATACGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (24 bp):
ATTGAGTGGCTTGACCACAATGCT
Found at i:22317 original size:18 final size:16
Alignment explanation
Indices: 22296--22352 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 16
22286 AAATAAAAAT
22296 TAAATTTAATGAATGAAA
1 TAAA-TTAATGAAT-AAA
*
22314 TAAAATTAATAAATAAA
1 T-AAATTAATGAATAAA
*
22331 TATAAATAATGAATAAAA
1 TA-AATTAATGAAT-AAA
22349 TAAA
1 TAAA
22353 ATGGACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
16 1 0.03
17 15 0.45
18 14 0.42
19 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (16 bp):
TAAATTAATGAATAAA
Found at i:22350 original size:35 final size:37
Alignment explanation
Indices: 22283--22371 Score: 103
Period size: 35 Copynumber: 2.5 Consensus size: 37
22273 TTTCATAAAA
*
22283 AATAAATAAAAATTAAATTTAATGAATGAAATAAAATT
1 AATAAATAAAAATTAAA-TTAATGAATAAAATAAAATT
* *
22321 AATAAATAAATA-TAAA-TAATGAATAAAATAAAATG
1 AATAAATAAAAATTAAATTAATGAATAAAATAAAATT
* *
22356 GACAAA-AAAAATTAAA
1 AATAAATAAAAATTAAA
22372 AAAATTGGGG
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
34 4 0.09
35 25 0.57
37 4 0.09
38 11 0.25
ACGTcount: A:0.67, C:0.01, G:0.06, T:0.26
Consensus pattern (37 bp):
AATAAATAAAAATTAAATTAATGAATAAAATAAAATT
Found at i:22354 original size:17 final size:16
Alignment explanation
Indices: 22302--22354 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 16
22292 AAATTAAATT
22302 TAATGAATGAAATAAAA
1 TAATGAAT-AAATAAAA
*
22319 TTAATAAATAAATATAAA
1 -TAATGAATAAATA-AAA
22337 TAATGAATAAAATAAAA
1 TAATGAAT-AAATAAAA
22354 T
1 T
22355 GGACAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 16 0.52
18 15 0.48
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (16 bp):
TAATGAATAAATAAAA
Found at i:23961 original size:50 final size:49
Alignment explanation
Indices: 23869--24023 Score: 131
Period size: 50 Copynumber: 3.1 Consensus size: 49
23859 GCAAATTTAG
* * * *
23869 GGGTATAAGATTTGGTTTTGT-GACTTTAATCTGA-CCTACTATAACTTCAA
1 GGGTATAGGATTTGGTTTCGTAG-CTTTAATC-CACCCT-CTATAGCTTCAA
*
23919 GGGTATAGGATTTGGTTTCGTAGCTTTAATCCACTCCTCTATAGCTT-TA
1 GGGTATAGGATTTGGTTTCGTAGCTTTAATCCAC-CCTCTATAGCTTCAA
* * *
23968 GGAGTATAGGATTT-ATTTCTTTAGCTTTAATCCGCCCCTCT-TCAGCTTCAA
1 GG-GTATAGGATTTGGTTTC-GTAGCTTTAATCC-ACCCTCTAT-AGCTTCAA
24019 GGGTA
1 GGGTA
24024 AAAGATTCAC
Statistics
Matches: 88, Mismatches: 9, Indels: 16
0.78 0.08 0.14
Matches are distributed among these distances:
49 9 0.10
50 71 0.81
51 8 0.09
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.39
Consensus pattern (49 bp):
GGGTATAGGATTTGGTTTCGTAGCTTTAATCCACCCTCTATAGCTTCAA
Found at i:24056 original size:50 final size:51
Alignment explanation
Indices: 24002--24119 Score: 127
Period size: 50 Copynumber: 2.4 Consensus size: 51
23992 CTTTAATCCG
* * *
24002 CCCCTCTTCAGCTTCA-AGG-GTAAAAGATTCACTCTTTCGACTTCAATCTA
1 CCCCTCTACAGCTT-ATAGGTGTAAAAGATTCACCCTTGCGACTTCAATCTA
* ** *
24052 CCCCTCTACAAC-TATAGGTGTATGAGATTCACCCTTGCGACTTCAATCTG
1 CCCCTCTACAGCTTATAGGTGTAAAAGATTCACCCTTGCGACTTCAATCTA
*
24102 CTCCTCTACAGCTT-TAGG
1 CCCCTCTACAGCTTATAGG
24120 GGTATAGGAT
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
48 1 0.02
49 4 0.07
50 50 0.89
51 1 0.02
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.31
Consensus pattern (51 bp):
CCCCTCTACAGCTTATAGGTGTAAAAGATTCACCCTTGCGACTTCAATCTA
Found at i:35474 original size:21 final size:21
Alignment explanation
Indices: 35436--35475 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
35426 AAATAAAAGT
* *
35436 AATAAATTAAATTAAATAATG
1 AATAAAATAAAATAAATAATG
*
35457 AATAAAATAAAATGAATAA
1 AATAAAATAAAATAAATAA
35476 AAAAATTAGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (21 bp):
AATAAAATAAAATAAATAATG
Done.