Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005660.1 Kokia drynarioides strain JFW-HI SEQ_119831, 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: 50289
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Warning! 32 characters in sequence are not A, C, G, or T
Found at i:9692 original size:3 final size:3
Alignment explanation
Indices: 9684--9708 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
9674 ATCATATTCA
9684 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
9709 TATGTCGGGG
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:17316 original size:17 final size:17
Alignment explanation
Indices: 17294--17354 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 17
17284 CTAAATTTTT
17294 TTAAATTTATTTTAAGA
1 TTAAATTTATTTTAAGA
*
17311 TTAAATTTGTTTTAA-A
1 TTAAATTTATTTTAAGA
** *
17327 TTTAAATTTAGCTTAAGT
1 -TTAAATTTATTTTAAGA
17345 TTAAATTTAT
1 TTAAATTTAT
17355 CTTTGAATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
16 1 0.03
17 35 0.97
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.54
Consensus pattern (17 bp):
TTAAATTTATTTTAAGA
Found at i:19074 original size:29 final size:29
Alignment explanation
Indices: 19018--19370 Score: 181
Period size: 29 Copynumber: 12.1 Consensus size: 29
19008 CCTTGAAGGT
*
19018 CCCTAAACTAT-CCAAAAATCTCATTTTTAC
1 CCCTAAACT-TCCCAAAATTC-CATTTTTAC
19048 CCCTAAACTTCCCAAAATTCCATTTTTA-
1 CCCTAAACTTCCCAAAATTCCATTTTTAC
* * * *
19076 ACCTCAAATTTTCCAAAAATTACATTTTTAC
1 CCCT-AAA-CTTCCCAAAATTCCATTTTTAC
*
19107 CCC-AAACATT-CCAAAATTCCAATTTTA-
1 CCCTAAAC-TTCCCAAAATTCCATTTTTAC
* * ** *
19134 ACCTCAAATTTTCTAAAAATTACATTTTTAC
1 CCCT-AAA-CTTCCCAAAATTCCATTTTTAC
* **
19165 CCCCAAACTTTTCAAAATTCCATTTTTGAC
1 CCCTAAACTTCCCAAAATTCCATTTTT-AC
* * ** * *
19195 CTC-GATTTTCCAAAAATTACATTTTTAC
1 CCCTAAACTTCCCAAAATTCCATTTTTAC
* *
19223 CCTTAAACTT-CCAAAATTTCATTTTTGA-
1 CCCTAAACTTCCCAAAATTCCATTTTT-AC
* * * *
19251 CCCTAAATTTTCCAAATATTACAATTTTA-
1 CCCTAAACTTCCCAAA-ATTCCATTTTTAC
* *
19280 CCCTCAAACTTTCCAAGAA-TCCATTTTTAT
1 CCCT-AAACTTCCCAA-AATTCCATTTTTAC
* ** * *
19310 CCC-AAATTTTCTAAAAATTACTTTTTTAC
1 CCCTAAA-CTTCCCAAAATTCCATTTTTAC
* *
19339 ACCTAAACTTTCCAAAATTACCA-TTTTAC
1 CCCTAAACTTCCCAAAATT-CCATTTTTAC
19368 CCC
1 CCC
19371 CGAATGTCTA
Statistics
Matches: 242, Mismatches: 59, Indels: 45
0.70 0.17 0.13
Matches are distributed among these distances:
27 2 0.01
28 47 0.19
29 106 0.44
30 82 0.34
31 5 0.02
ACGTcount: A:0.35, C:0.26, G:0.01, T:0.38
Consensus pattern (29 bp):
CCCTAAACTTCCCAAAATTCCATTTTTAC
Found at i:19143 original size:58 final size:58
Alignment explanation
Indices: 19028--19365 Score: 409
Period size: 58 Copynumber: 5.8 Consensus size: 58
19018 CCCTAAACTA
*
19028 TCCAAAAATCT-CATTTTTACCCCTAAACTTCCCAAAATTCCATTTTTAACCTCAAATTT
1 TCCAAAAAT-TACATTTTTACCCC-AAACTTTCCAAAATTCCATTTTTAACCTCAAATTT
* *
19087 TCCAAAAATTACATTTTTACCCCAAACATTCCAAAATTCCAATTTTAACCTCAAATTT
1 TCCAAAAATTACATTTTTACCCCAAACTTTCCAAAATTCCATTTTTAACCTCAAATTT
* * * *
19145 TCTAAAAATTACATTTTTACCCCCAAACTTTTCAAAATTCCATTTTTGACCTC-GATTT
1 TCCAAAAATTACATTTTTA-CCCCAAACTTTCCAAAATTCCATTTTTAACCTCAAATTT
* * *
19203 TCCAAAAATTACATTTTTACCCTTAAAC-TTCCAAAATTTCATTTTTGACC-CTAAATTT
1 TCCAAAAATTACATTTTTACCC-CAAACTTTCCAAAATTCCATTTTTAACCTC-AAATTT
* * *
19261 TCCAAATATTACAATTTTACCCTCAAACTTTCCAAGAA-TCCATTTTTATCC-CAAATTT
1 TCCAAAAATTACATTTTTACCC-CAAACTTTCCAA-AATTCCATTTTTAACCTCAAATTT
* * *
19319 TCTAAAAATTACTTTTTTACACCTAAACTTTCCAAAATTACCATTTT
1 TCCAAAAATTACATTTTTAC-CCCAAACTTTCCAAAATT-CCATTTT
19366 ACCCCCGAAT
Statistics
Matches: 244, Mismatches: 25, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
56 1 0.00
57 25 0.10
58 140 0.57
59 76 0.31
60 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.01, T:0.39
Consensus pattern (58 bp):
TCCAAAAATTACATTTTTACCCCAAACTTTCCAAAATTCCATTTTTAACCTCAAATTT
Found at i:22470 original size:22 final size:22
Alignment explanation
Indices: 22442--22488 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
22432 GACTCATGAC
**
22442 AATTTTTTAAAGTTGCCTGTGA
1 AATTTTTTAAAACTGCCTGTGA
*
22464 AATTTTTTAAAACTGTCTGTGA
1 AATTTTTTAAAACTGCCTGTGA
22486 AAT
1 AAT
22489 AAAAAAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.45
Consensus pattern (22 bp):
AATTTTTTAAAACTGCCTGTGA
Found at i:24026 original size:22 final size:20
Alignment explanation
Indices: 23986--24026 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
23976 TGATGGTGGC
*
23986 TTTTATTTGGTAATTGTGTA
1 TTTTATTTGGTAATGGTGTA
24006 TTTTATTTGTGATAATGGTGT
1 TTTTATTTG-G-TAATGGTGT
24027 TTAAGGTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 1 0.06
22 8 0.44
ACGTcount: A:0.20, C:0.00, G:0.22, T:0.59
Consensus pattern (20 bp):
TTTTATTTGGTAATGGTGTA
Found at i:27723 original size:29 final size:29
Alignment explanation
Indices: 27690--27764 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 29
27680 AAAATTTTTT
*
27690 TTTTTTAAGGAGTAGAAATTAAA-TTAT-A
1 TTTTTTAAGGAGTA-AAAATAAATTTATAA
* *
27718 TATTTTTACGAGAGTAAAAATATATTTATAA
1 T-TTTTTAAG-GAGTAAAAATAAATTTATAA
*
27749 TTTTTTAAGGATTAAA
1 TTTTTTAAGGAGTAAA
27765 TCAAAATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
28 1 0.03
29 19 0.50
30 16 0.42
31 2 0.05
ACGTcount: A:0.43, C:0.01, G:0.12, T:0.44
Consensus pattern (29 bp):
TTTTTTAAGGAGTAAAAATAAATTTATAA
Found at i:28869 original size:2 final size:2
Alignment explanation
Indices: 28862--28896 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
28852 TAGTCCCTGC
28862 TA TA 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 TA TA T
28897 GGGATTTGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:36541 original size:29 final size:29
Alignment explanation
Indices: 36499--36576 Score: 70
Period size: 31 Copynumber: 2.6 Consensus size: 29
36489 GTGTAAATTG
*
36499 ATACAT-AAATTTTTATTTGACGT-AATTAT
1 ATACATGAAA-TTTTATTTGA-GTCAAATAT
* * *
36528 ATATATGATATTTTGATTGTGATTCAAATAT
1 ATACATGAAATTTT-ATT-TGAGTCAAATAT
36559 ATACATGAAATTTTATTT
1 ATACATGAAATTTTATTT
36577 TTAATTCAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
29 10 0.26
30 9 0.23
31 20 0.51
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (29 bp):
ATACATGAAATTTTATTTGAGTCAAATAT
Found at i:39401 original size:362 final size:362
Alignment explanation
Indices: 38736--39461 Score: 1443
Period size: 362 Copynumber: 2.0 Consensus size: 362
38726 TCGAGGGAGT
38736 TTAGTGTTTTAGTGAGGGTGTTTTTTGTGATTAGTAAGCAGGATTGTATGCTTGCGGGTTAAGAG
1 TTAGTGTTTTAGTGAGGGTGTTTTTTGTGATTAGTAAGCAGGATTGTATGCTTGCGGGTTAAGAG
*
38801 ATGCTGTTGTGTCTGGTTTTTGGCTCTGCTACTAGTTGTAGCAGTGTTCTGTTTCCGTACTGGCA
66 ACGCTGTTGTGTCTGGTTTTTGGCTCTGCTACTAGTTGTAGCAGTGTTCTGTTTCCGTACTGGCA
38866 TGGTCTTTCCACTGCCTTAGACTTTGTCTTAATTTGAATGAGCTAAAAAAAAAGAGCTTTGTTTT
131 TGGTCTTTCCACTGCCTTAGACTTTGTCTTAATTTGAATGAGCTAAAAAAAAAGAGCTTTGTTTT
38931 TGTGGTTTAAGGTTTGTTTGTTTTTCATACTATTTTCATCTTGTACTCATTCATATATTATTTGT
196 TGTGGTTTAAGGTTTGTTTGTTTTTCATACTATTTTCATCTTGTACTCATTCATATATTATTTGT
38996 CATTTTAGTAAAATTTTATTCGCCAGTGAATTTTTATTCTCTACAAAAGAATTTTTTACGTAAAA
261 CATTTTAGTAAAATTTTATTCGCCAGTGAATTTTTATTCTCTACAAAAGAATTTTTTACGTAAAA
39061 CATTTGTGTTTAATTTTCTATACATTTTTCTATTTTG
326 CATTTGTGTTTAATTTTCTATACATTTTTCTATTTTG
39098 TTAGTGTTTTAGTGAGGGTGTTTTTTGTGATTAGTAAGCAGGATTGTATGCTTGCGGGTTAAGAG
1 TTAGTGTTTTAGTGAGGGTGTTTTTTGTGATTAGTAAGCAGGATTGTATGCTTGCGGGTTAAGAG
39163 ACGCTGTTGTGTCTGGTTTTTGGCTCTGCTACTAGTTGTAGCAGTGTTCTGTTTCCGTACTGGCA
66 ACGCTGTTGTGTCTGGTTTTTGGCTCTGCTACTAGTTGTAGCAGTGTTCTGTTTCCGTACTGGCA
39228 TGGTCTTTCCACTGCCTTAGACTTTGTCTTAATTTGAATGAGCTAAAAAAAAAGAGCTTTGTTTT
131 TGGTCTTTCCACTGCCTTAGACTTTGTCTTAATTTGAATGAGCTAAAAAAAAAGAGCTTTGTTTT
39293 TGTGGTTTAAGGTTTGTTTGTTTTTCATACTATTTTCATCTTGTACTCATTCATATATTATTTGT
196 TGTGGTTTAAGGTTTGTTTGTTTTTCATACTATTTTCATCTTGTACTCATTCATATATTATTTGT
39358 CATTTTAGTAAAATTTTATTCGCCAGTGAATTTTTATTCTCTACAAAAGAATTTTTTACGTAAAA
261 CATTTTAGTAAAATTTTATTCGCCAGTGAATTTTTATTCTCTACAAAAGAATTTTTTACGTAAAA
39423 CATTTGTGTTTAATTTTCTATACATTTTTCTATTTTG
326 CATTTGTGTTTAATTTTCTATACATTTTTCTATTTTG
39460 TT
1 TT
39462 GTTTATACGA
Statistics
Matches: 363, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
362 363 1.00
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (362 bp):
TTAGTGTTTTAGTGAGGGTGTTTTTTGTGATTAGTAAGCAGGATTGTATGCTTGCGGGTTAAGAG
ACGCTGTTGTGTCTGGTTTTTGGCTCTGCTACTAGTTGTAGCAGTGTTCTGTTTCCGTACTGGCA
TGGTCTTTCCACTGCCTTAGACTTTGTCTTAATTTGAATGAGCTAAAAAAAAAGAGCTTTGTTTT
TGTGGTTTAAGGTTTGTTTGTTTTTCATACTATTTTCATCTTGTACTCATTCATATATTATTTGT
CATTTTAGTAAAATTTTATTCGCCAGTGAATTTTTATTCTCTACAAAAGAATTTTTTACGTAAAA
CATTTGTGTTTAATTTTCTATACATTTTTCTATTTTG
Found at i:40531 original size:10 final size:10
Alignment explanation
Indices: 40518--40606 Score: 53
Period size: 10 Copynumber: 9.0 Consensus size: 10
40508 AGTTTAAAAT
40518 TTAAAAATTA
1 TTAAAAATTA
*
40528 TTAAAAGA-TC
1 TTAAAA-ATTA
* *
40538 GTAAAAACTA
1 TTAAAAATTA
*
40548 TAAACAAAATTTA
1 TTAA--AAA-TTA
*
40561 TAAAAAATTA
1 TTAAAAATTA
40571 -TAAAAA--A
1 TTAAAAATTA
40578 TT-AAAATTA
1 TTAAAAATTA
*
40587 TAAAAAATTA
1 TTAAAAATTA
40597 TTAAAAATTA
1 TTAAAAATTA
40607 ACAATATTGA
Statistics
Matches: 61, Mismatches: 9, Indels: 18
0.69 0.10 0.20
Matches are distributed among these distances:
7 5 0.08
8 1 0.02
9 8 0.13
10 34 0.56
11 4 0.07
12 3 0.05
13 6 0.10
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.31
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:40585 original size:16 final size:16
Alignment explanation
Indices: 40564--40596 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
40554 AAATTTATAA
40564 AAAATTATAAAAAATT
1 AAAATTATAAAAAATT
40580 AAAATTATAAAAAATT
1 AAAATTATAAAAAATT
40596 A
1 A
40597 TTAAAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATTATAAAAAATT
Found at i:40590 original size:26 final size:27
Alignment explanation
Indices: 40553--40607 Score: 94
Period size: 26 Copynumber: 2.1 Consensus size: 27
40543 AACTATAAAC
40553 AAAATTTATAAAAAATTATAAAAAATT
1 AAAATTTATAAAAAATTATAAAAAATT
*
40580 AAAA-TTATAAAAAATTATTAAAAATT
1 AAAATTTATAAAAAATTATAAAAAATT
40606 AA
1 AA
40608 CAATATTGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 23 0.85
27 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (27 bp):
AAAATTTATAAAAAATTATAAAAAATT
Found at i:40603 original size:11 final size:10
Alignment explanation
Indices: 40553--40606 Score: 62
Period size: 10 Copynumber: 5.8 Consensus size: 10
40543 AACTATAAAC
*
40553 AAAATTTATA
1 AAAAATTATA
40563 AAAAATTATA
1 AAAAATTATA
40573 AAAAA-T-T-
1 AAAAATTATA
40580 -AAAATTATA
1 AAAAATTATA
*
40589 AAAAATTATT
1 AAAAATTATA
40599 AAAAATTA
1 AAAAATTA
40607 ACAATATTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
6 4 0.11
7 1 0.03
8 2 0.05
9 1 0.03
10 30 0.79
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAAATTATA
Found at i:47756 original size:14 final size:14
Alignment explanation
Indices: 47737--47764 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
47727 GTAACAAGAG
47737 ATTGTTTTATCACC
1 ATTGTTTTATCACC
47751 ATTGTTTTATCACC
1 ATTGTTTTATCACC
47765 TACGAGTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.50
Consensus pattern (14 bp):
ATTGTTTTATCACC
Done.