Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003800.1 Kokia drynarioides strain JFW-HI SEQ_116786, 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: 34473
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:462 original size:20 final size:20
Alignment explanation
Indices: 437--679 Score: 202
Period size: 20 Copynumber: 12.2 Consensus size: 20
427 ATATATATAT
437 TCAGGCTTTGTGCCGGTGTA
1 TCAGGCTTTGTGCCGGTGTA
* * *
457 TCAGGCTTTATGTCGGTGAA
1 TCAGGCTTTGTGCCGGTGTA
* * **
477 TCAAGCTTCGTGCTAGTGTA
1 TCAGGCTTTGTGCCGGTGTA
** * *
497 TCAGGCTTCATACCGATGTA
1 TCAGGCTTTGTGCCGGTGTA
*
517 TCAGGCTTGGTGCCGGTGTA
1 TCAGGCTTTGTGCCGGTGTA
* * *
537 TTAGGCTTTGTGCCAGTGAA
1 TCAGGCTTTGTGCCGGTGTA
* * *
557 TCAGGCTTCGTGTCGATGTA
1 TCAGGCTTTGTGCCGGTGTA
* * * *
577 GCAGGCTTTGTACCGATGCAA
1 TCAGGCTTTGTGCCGGTG-TA
*
598 T-AGGCTTTGTGCCGTTGTA
1 TCAGGCTTTGTGCCGGTGTA
* *
617 GCAAGCTTTGTGCCGGTGTA
1 TCAGGCTTTGTGCCGGTGTA
* *
637 TCAAG-TCTTGTGCCAGTGTA
1 TCAGGCT-TTGTGCCGGTGTA
*
657 TCAGGCTTTGTGCCAGTGTA
1 TCAGGCTTTGTGCCGGTGTA
677 TCA
1 TCA
680 AAGAACAAGT
Statistics
Matches: 174, Mismatches: 45, Indels: 8
0.77 0.20 0.04
Matches are distributed among these distances:
19 2 0.01
20 170 0.98
21 2 0.01
ACGTcount: A:0.17, C:0.20, G:0.30, T:0.33
Consensus pattern (20 bp):
TCAGGCTTTGTGCCGGTGTA
Found at i:662 original size:80 final size:80
Alignment explanation
Indices: 437--667 Score: 270
Period size: 80 Copynumber: 2.9 Consensus size: 80
427 ATATATATAT
* * *
437 TCAGGCTTTGTGCCGGTGTATCAGGCTTTATGTCGGTGAATCAAGCTTCGTGCTAGTGTATCAGG
1 TCAGGCTTTGTGCCGGTGTATCAGGCTTTGTGCCGGTGAATCAAGCTTCGTGCCAGTGTATCAGG
** *
502 CTTCATACCGATGTA
66 CTTTGTACCGATGAA
* * * * * *
517 TCAGGCTTGGTGCCGGTGTATTAGGCTTTGTGCCAGTGAATCAGGCTTCGTGTC-GATGTAGCAG
1 TCAGGCTTTGTGCCGGTGTATCAGGCTTTGTGCCGGTGAATCAAGCTTCGTGCCAG-TGTATCAG
581 GCTTTGTACCGATGCAA
65 GCTTTGTACCGATG-AA
* * * *
598 T-AGGCTTTGTGCCGTTGTAGCAAGCTTTGTGCCGGTGTATCAAGTCTT-GTGCCAGTGTATCAG
1 TCAGGCTTTGTGCCGGTGTATCAGGCTTTGTGCCGGTGAATCAAG-CTTCGTGCCAGTGTATCAG
661 GCTTTGT
65 GCTTTGT
668 GCCAGTGTAT
Statistics
Matches: 125, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
79 1 0.01
80 118 0.94
81 6 0.05
ACGTcount: A:0.17, C:0.19, G:0.30, T:0.34
Consensus pattern (80 bp):
TCAGGCTTTGTGCCGGTGTATCAGGCTTTGTGCCGGTGAATCAAGCTTCGTGCCAGTGTATCAGG
CTTTGTACCGATGAA
Found at i:6798 original size:20 final size:20
Alignment explanation
Indices: 6773--7135 Score: 334
Period size: 20 Copynumber: 18.1 Consensus size: 20
6763 CTATATATAT
*
6773 TCAGGCTTTGTGCCGTTGTA
1 TCAGGCTTTGTGCCGGTGTA
* *
6793 TCAGGCTTTGTGCAGGTGAA
1 TCAGGCTTTGTGCCGGTGTA
* *
6813 TCAGGCTTCGTGTCGGTGTA
1 TCAGGCTTTGTGCCGGTGTA
*
6833 TCAGGCTTCGTGCCGGTGTA
1 TCAGGCTTTGTGCCGGTGTA
* * * *
6853 TCCGACTTTGTGCCAGTGAA
1 TCAGGCTTTGTGCCGGTGTA
*
6873 TCAGGCTTCT-TGCTGGTGTA
1 TCAGGCTT-TGTGCCGGTGTA
* *
6893 ACAGGCTTTGTGCCAGTGTA
1 TCAGGCTTTGTGCCGGTGTA
**
6913 TCAGGCTTCATGCCGGTGTA
1 TCAGGCTTTGTGCCGGTGTA
* * *
6933 TCAAGCTTTGTACTGGTGTA
1 TCAGGCTTTGTGCCGGTGTA
* * *
6953 TCCA-GCTTTGTACTGGTGAA
1 T-CAGGCTTTGTGCCGGTGTA
* *
6973 TCAGGCTTCGTGCTGGTGTA
1 TCAGGCTTTGTGCCGGTGTA
* *
6993 TCAGGCTTTATACCGGTGTA
1 TCAGGCTTTGTGCCGGTGTA
* *
7013 TCAGGCTTTGTGCTGGTGAA
1 TCAGGCTTTGTGCCGGTGTA
* **
7033 TTAGGCTTCATGCCGGTGTA
1 TCAGGCTTTGTGCCGGTGTA
*
7053 TCAGGCTTTGTGACGGTGTA
1 TCAGGCTTTGTGCCGGTGTA
* **
7073 TCAGGTTTTGTAACGGTGTA
1 TCAGGCTTTGTGCCGGTGTA
* * *
7093 TCAAGCTTGGTGCCGATGTA
1 TCAGGCTTTGTGCCGGTGTA
* **
7113 TCAAGCTTTGTGCTAGTGTA
1 TCAGGCTTTGTGCCGGTGTA
7133 TCA
1 TCA
7136 CAGAACAAGT
Statistics
Matches: 276, Mismatches: 63, Indels: 8
0.80 0.18 0.02
Matches are distributed among these distances:
19 3 0.01
20 270 0.98
21 3 0.01
ACGTcount: A:0.16, C:0.19, G:0.30, T:0.35
Consensus pattern (20 bp):
TCAGGCTTTGTGCCGGTGTA
Found at i:8414 original size:16 final size:16
Alignment explanation
Indices: 8393--8424 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
8383 AGGAAAGATG
8393 AAGAATAAAAATAAAA
1 AAGAATAAAAATAAAA
*
8409 AAGAATAATAATAAAA
1 AAGAATAAAAATAAAA
8425 TCGTATCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (16 bp):
AAGAATAAAAATAAAA
Found at i:13682 original size:26 final size:27
Alignment explanation
Indices: 13631--13694 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 27
13621 CAATTCAAGC
*
13631 TCATTTTTTTTTTCATTTTCAATTTTT
1 TCATTTTTTTATTCATTTTCAATTTTT
*
13658 TCATTTTTTTATT-ATTATT-ATTTTTT
1 TCATTTTTTTATTCATT-TTCAATTTTT
*
13684 TCATGTTTTTA
1 TCATTTTTTTA
13695 GAACAAAGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 19 0.58
27 14 0.42
ACGTcount: A:0.17, C:0.08, G:0.02, T:0.73
Consensus pattern (27 bp):
TCATTTTTTTATTCATTTTCAATTTTT
Found at i:14640 original size:12 final size:11
Alignment explanation
Indices: 14625--14777 Score: 82
Period size: 12 Copynumber: 13.2 Consensus size: 11
14615 CCGATAAAAC
14625 AATAAAAGTAAA
1 AATAAAA-TAAA
14637 AATAAAATAAA
1 AATAAAATAAA
*
14648 ACATATAAGTCTAAA
1 A-ATA-AA--ATAAA
*
14663 ATACAAAATAAA
1 A-ATAAAATAAA
*
14675 AA-CAAATAACAA
1 AATAAAAT-A-AA
14687 AATTAAAATAAA
1 AA-TAAAATAAA
*
14699 AATAGAAATAGA
1 AATA-AAATAAA
14711 AATAAAAATAAA
1 AAT-AAAATAAA
14723 AAT-AAATAAA
1 AATAAAATAAA
14733 ACATAAAACT--A
1 A-ATAAAA-TAAA
*
14744 AATAAAATATA
1 AATAAAATAAA
* *
14755 AAT-AATTCAA
1 AATAAAATAAA
*
14765 AAGAAAATAAA
1 AATAAAATAAA
14776 AA
1 AA
14778 ATCTAATAAT
Statistics
Matches: 111, Mismatches: 14, Indels: 33
0.70 0.09 0.21
Matches are distributed among these distances:
9 1 0.01
10 24 0.22
11 24 0.22
12 44 0.40
13 5 0.05
14 6 0.05
15 7 0.06
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.19
Consensus pattern (11 bp):
AATAAAATAAA
Found at i:14642 original size:6 final size:6
Alignment explanation
Indices: 14625--14745 Score: 79
Period size: 6 Copynumber: 20.0 Consensus size: 6
14615 CCGATAAAAC
* * * *
14625 AATAAA AGTAAA AAT-AA AATAAA ACATATA AGTCTAA AATACAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA A-ATAAA AAT-AAA AATA-AA AATAAA
* * * * *
14675 AACAAA TAA-CAA AATTAA AATAAA AATAGA AATAGA AATAAA AATAAA
1 AATAAA -AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
*
14723 AAT--A AATAAA ACATAAA ACTAAA
1 AATAAA AATAAA A-ATAAA AATAAA
14746 TAAAATATAA
Statistics
Matches: 91, Mismatches: 15, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
4 4 0.04
5 7 0.08
6 58 0.64
7 22 0.24
ACGTcount: A:0.73, C:0.06, G:0.03, T:0.18
Consensus pattern (6 bp):
AATAAA
Found at i:14647 original size:17 final size:17
Alignment explanation
Indices: 14625--14756 Score: 87
Period size: 17 Copynumber: 7.7 Consensus size: 17
14615 CCGATAAAAC
*
14625 AATAAAAGTAAAAATAA
1 AATAAAAATAAAAATAA
**
14642 AATAAAACATATAAGTCTAA
1 AATAAAA-ATA-AA-AATAA
*
14662 AATACAAAATAAAAA-CA
1 AATA-AAAATAAAAATAA
* *
14679 AAT---AACAAAATTAA
1 AATAAAAATAAAAATAA
*
14693 AATAAAAATAGAAATAGA
1 AATAAAAATAAAAATA-A
14711 AATAAAAATAAAAAT-A
1 AATAAAAATAAAAATAA
*
14727 AATAAAACATAAAACT-A
1 AATAAAA-ATAAAAATAA
14744 AATAAAATATAAA
1 AATAAAA-ATAAA
14757 TAATTCAAAA
Statistics
Matches: 90, Mismatches: 15, Indels: 20
0.72 0.12 0.16
Matches are distributed among these distances:
13 6 0.07
14 4 0.04
16 8 0.09
17 38 0.42
18 17 0.19
19 4 0.04
20 10 0.11
21 3 0.03
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.19
Consensus pattern (17 bp):
AATAAAAATAAAAATAA
Found at i:14663 original size:25 final size:24
Alignment explanation
Indices: 14618--14699 Score: 69
Period size: 25 Copynumber: 3.2 Consensus size: 24
14608 AAAACAACCG
* *
14618 ATAAAACAATAAAAGTAAAAATAAA
1 ATAAAAC-ATATAAGTCAAAATAAA
14643 ATAAAACATATAAGTCTAAAATACAAA
1 ATAAAACATATAAGTC-AAAAT--AAA
*
14670 ATAAAAACAAATAA--CAAAATTAAA
1 AT-AAAACATATAAGTCAAAA-TAAA
14694 ATAAAA
1 ATAAAA
14700 ATAGAAATAG
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
23 4 0.08
24 12 0.24
25 16 0.33
26 2 0.04
27 5 0.10
28 10 0.20
ACGTcount: A:0.72, C:0.07, G:0.02, T:0.18
Consensus pattern (24 bp):
ATAAAACATATAAGTCAAAATAAA
Found at i:22285 original size:24 final size:24
Alignment explanation
Indices: 22225--22295 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 24
22215 CAAGATGCGT
* *
22225 CGTTGTGGTCAAACCACTAAATAG
1 CGTTGTGGTCAAGCCACTAAATAA
* * * * *
22249 TGTTATGGGCAAGTCACTCAATAA
1 CGTTGTGGTCAAGCCACTAAATAA
22273 CGTTGTGGTCAAGCCACTAAATA
1 CGTTGTGGTCAAGCCACTAAATA
22296 TTGCAGTAAA
Statistics
Matches: 35, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (24 bp):
CGTTGTGGTCAAGCCACTAAATAA
Found at i:22430 original size:42 final size:42
Alignment explanation
Indices: 22383--22485 Score: 134
Period size: 42 Copynumber: 2.5 Consensus size: 42
22373 TTCAGTGGAC
**
22383 ATGCTTAACATGTGAATCAAATTTATAATCAACATAGTCGGG
1 ATGCTTAACATGTGAATCAAATTTATAATCAACATAGTCGAA
* ** *
22425 ATGCTTAAGATGTGAATCGGATTTATAATCAACATAGTTGAA
1 ATGCTTAACATGTGAATCAAATTTATAATCAACATAGTCGAA
* *
22467 ATGCTAAACATGCGAATCA
1 ATGCTTAACATGTGAATCA
22486 TATCTCAATT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (42 bp):
ATGCTTAACATGTGAATCAAATTTATAATCAACATAGTCGAA
Found at i:23357 original size:16 final size:16
Alignment explanation
Indices: 23336--23368 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
23326 ATGTTTTTTC
*
23336 TTTTTATTTAGTTACA
1 TTTTTATTTAATTACA
23352 TTTTTATTTAATTACA
1 TTTTTATTTAATTACA
23368 T
1 T
23369 GTTGATTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.64
Consensus pattern (16 bp):
TTTTTATTTAATTACA
Found at i:29085 original size:19 final size:20
Alignment explanation
Indices: 29054--29092 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
29044 AAATCTAATT
29054 CCAATATCAAAAA-AAGAAA
1 CCAATATCAAAAATAAGAAA
29073 CCAA-ATCAGAAAATAAGAAA
1 CCAATATCA-AAAATAAGAAA
29093 ATATCTAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 8 0.44
20 6 0.33
ACGTcount: A:0.67, C:0.15, G:0.08, T:0.10
Consensus pattern (20 bp):
CCAATATCAAAAATAAGAAA
Done.