Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000555.1 Kokia drynarioides strain JFW-HI SEQ_111463, 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: 70585
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:6422 original size:29 final size:28
Alignment explanation
Indices: 6358--6528 Score: 101
Period size: 27 Copynumber: 6.1 Consensus size: 28
6348 AAGCCCATGC
* *
6358 TTTTATTAAAAATTATTAAAATT-TAAAA
1 TTTTAATAAAAACTA-TAAAATTATAAAA
*
6386 --TCAATAAAAACTATAAATATTATAAAA
1 TTTTAATAAAAACTATAAA-ATTATAAAA
*
6413 TTTTAATAAAAAAT-TCAAATATTA-AAAA
1 TTTTAATAAAAACTAT-AAA-ATTATAAAA
* * * *
6441 -TTTATTAAAAATTAGAAAAATATAAAAA
1 TTTTAATAAAAACTATAAAATTAT-AAAA
* *
6469 TTGTAA-AAAAA-TATAACAATTGTAAAA
1 TTTTAATAAAAACTATAA-AATTATAAAA
6496 TTTT-ATAAAAATCGTA-ATAAATTATAAAA
1 TTTTAATAAAAA-C-TATA-AAATTATAAAA
6525 TTTT
1 TTTT
6529 GTACAGTCGT
Statistics
Matches: 112, Mismatches: 16, Indels: 29
0.71 0.10 0.18
Matches are distributed among these distances:
25 4 0.04
26 17 0.15
27 35 0.31
28 18 0.16
29 35 0.31
30 3 0.03
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (28 bp):
TTTTAATAAAAACTATAAAATTATAAAA
Found at i:6478 original size:19 final size:19
Alignment explanation
Indices: 6456--6524 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
6446 TAAAAATTAG
6456 AAAAATATAAAAATTGTAA
1 AAAAATATAAAAATTGTAA
*
6475 AAAAATATAACAATTGTAA
1 AAAAATATAAAAATTGTAA
*** *
6494 AATTTTATAAAAATCGTAA
1 AAAAATATAAAAATTGTAA
* *
6513 TAAATTATAAAA
1 AAAAATATAAAA
6525 TTTTGTACAG
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.30
Consensus pattern (19 bp):
AAAAATATAAAAATTGTAA
Found at i:6796 original size:20 final size:21
Alignment explanation
Indices: 6759--6797 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
6749 TTAAAAAGAC
6759 TTTTTGATGCATTTTATAATG
1 TTTTTGATGCATTTTATAATG
6780 TTTTT-ATG-ATTTCTATAA
1 TTTTTGATGCATTT-TATAA
6798 AATTTTACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.24
20 8 0.47
21 5 0.29
ACGTcount: A:0.26, C:0.05, G:0.10, T:0.59
Consensus pattern (21 bp):
TTTTTGATGCATTTTATAATG
Found at i:15817 original size:18 final size:18
Alignment explanation
Indices: 15789--15824 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
15779 CATGCACAAG
15789 AAAGAAAGAAAA-AAAAA
1 AAAGAAAGAAAAGAAAAA
15806 AAAGAGAAGAAAAGAAAAA
1 AAAGA-AAGAAAAGAAAAA
15825 CATCCAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 7 0.41
19 5 0.29
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAGAAAGAAAAGAAAAA
Found at i:18623 original size:25 final size:26
Alignment explanation
Indices: 18576--18630 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
18566 TTCAAAAAAA
18576 TTAAAATATAAATATTATAGTTTTGAT
1 TTAAAATATAAATATTATAGTTTT-AT
18603 TTAAAA-ATAAA-ATTA-ATGTTTTAT
1 TTAAAATATAAATATTATA-GTTTTAT
18627 TTAA
1 TTAA
18631 TACGTTCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
24 7 0.26
25 9 0.33
26 5 0.19
27 6 0.22
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (26 bp):
TTAAAATATAAATATTATAGTTTTAT
Found at i:19255 original size:21 final size:21
Alignment explanation
Indices: 19231--19275 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
19221 GTATTGTTAG
*
19231 TATAGTT-CATTTTTATTATTT
1 TATAGTTACATTTTT-GTATTT
*
19252 TATATTTACATTTTTGTATTT
1 TATAGTTACATTTTTGTATTT
19273 TAT
1 TAT
19276 GTTTCTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (21 bp):
TATAGTTACATTTTTGTATTT
Found at i:20139 original size:24 final size:24
Alignment explanation
Indices: 20085--20150 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 24
20075 ACTCATAAAC
*
20085 ATTTTTAATTAATATAATAATATATT
1 ATTTTT-ATTAA-ATAATTATATATT
20111 A-TTTTATTAAATAATTATCAT-TT
1 ATTTTTATTAAATAATTAT-ATATT
*
20134 ATTTTTA-TGAATAATTA
1 ATTTTTATTAAATAATTA
20151 ATTTATACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
23 19 0.53
24 12 0.33
25 4 0.11
26 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
ATTTTTATTAAATAATTATATATT
Found at i:24891 original size:20 final size:20
Alignment explanation
Indices: 24866--24903 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
24856 TTAGAAGATG
24866 CTTTTATCTTTAC-TTATATT
1 CTTTTAT-TTTACATTATATT
24886 CTTTTATTTTACATTATA
1 CTTTTATTTTACATTATA
24904 CCATGTGGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.24, C:0.13, G:0.00, T:0.63
Consensus pattern (20 bp):
CTTTTATTTTACATTATATT
Found at i:38312 original size:3 final size:3
Alignment explanation
Indices: 38304--38328 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
38294 ACTATTAAGA
38304 GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT G
38329 CAAACAAATT
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:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:48078 original size:31 final size:30
Alignment explanation
Indices: 48022--48116 Score: 86
Period size: 31 Copynumber: 3.2 Consensus size: 30
48012 GCTAACCGTA
* *
48022 ATTAAA-AAAAAAATTT-AACAATTCAATG
1 ATTAAATAAAAACATTTAAATAATTCAATG
* * **
48050 AGTTAAATAAAAACTTTTAAATAGTTCAACA
1 A-TTAAATAAAAACATTTAAATAATTCAATG
* *
48081 ACTTAAATTAAAACATTTAAATAATTTAATG
1 A-TTAAATAAAAACATTTAAATAATTCAATG
48112 ATTAA
1 ATTAA
48117 TTTAATTTAT
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
28 1 0.02
29 5 0.10
30 12 0.24
31 33 0.65
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.34
Consensus pattern (30 bp):
ATTAAATAAAAACATTTAAATAATTCAATG
Found at i:48644 original size:25 final size:25
Alignment explanation
Indices: 48616--48663 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
48606 AGATATAGAC
48616 TATTAAAAATAAAAAAT-TAATTTTT
1 TATT-AAAATAAAAAATATAATTTTT
**
48641 TATTATCATAAAAAATATAATTT
1 TATTAAAATAAAAAATATAATTT
48664 AATTCCGTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (25 bp):
TATTAAAATAAAAAATATAATTTTT
Found at i:49045 original size:19 final size:18
Alignment explanation
Indices: 49018--49060 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
49008 AAATTAATTA
49018 AATTTATG-ATATTTAAAT
1 AATTTATGAAT-TTTAAAT
49036 AATTTAATGAATTTTAAAT
1 AATTT-ATGAATTTTAAAT
49055 ACATTT
1 A-ATTT
49061 TAAATAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.23
19 11 0.50
20 6 0.27
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (18 bp):
AATTTATGAATTTTAAAT
Found at i:50395 original size:23 final size:22
Alignment explanation
Indices: 50351--50399 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
50341 GAATTTTTGT
*
50351 TAAAATAAAATACAGTGATAAAA
1 TAAAATAAAATAAAGTGAT-AAA
*
50374 TAAAATAAAAGTAAAGT-TTAAA
1 TAAAATAAAA-TAAAGTGATAAA
50396 TAAA
1 TAAA
50400 CTAGACTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 7 0.30
23 11 0.48
24 5 0.22
ACGTcount: A:0.65, C:0.02, G:0.08, T:0.24
Consensus pattern (22 bp):
TAAAATAAAATAAAGTGATAAA
Found at i:53440 original size:17 final size:17
Alignment explanation
Indices: 53414--53448 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
53404 GGAGAACTTG
* *
53414 TTCGTTGAGAGTTCTTA
1 TTCGTAGAGAATTCTTA
53431 TTCGTAGAGAATTCTTA
1 TTCGTAGAGAATTCTTA
53448 T
1 T
53449 CAAGGTGGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.23, C:0.11, G:0.20, T:0.46
Consensus pattern (17 bp):
TTCGTAGAGAATTCTTA
Found at i:53536 original size:22 final size:22
Alignment explanation
Indices: 53491--53538 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
53481 AATTTTTGTA
*
53491 AAAATAAAATACAGTGGTAAAAT
1 AAAATAAAATAAAGT-GTAAAAT
53514 AAAATAAAAGTAAAGT-TAAAAT
1 AAAATAAAA-TAAAGTGTAAAAT
53536 AAA
1 AAA
53539 CTAGACTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 9 0.39
23 9 0.39
24 5 0.22
ACGTcount: A:0.67, C:0.02, G:0.10, T:0.21
Consensus pattern (22 bp):
AAAATAAAATAAAGTGTAAAAT
Found at i:56188 original size:17 final size:17
Alignment explanation
Indices: 56168--56205 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
56158 TAAATAAATT
* *
56168 ATTAAAAATTATAAAAA
1 ATTAAAAAATAGAAAAA
56185 ATTAAAAAATAGAAAAA
1 ATTAAAAAATAGAAAAA
56202 ATTA
1 ATTA
56206 GTTCAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
ATTAAAAAATAGAAAAA
Found at i:61633 original size:27 final size:27
Alignment explanation
Indices: 61595--61650 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
61585 TTAATATTAG
61595 ATCAATAATTTTATCCTGAATTTCAAA
1 ATCAATAATTTTATCCTGAATTTCAAA
*
61622 ATCAATAATTTTATCTTGAATTTCAAA
1 ATCAATAATTTTATCCTGAATTTCAAA
61649 AT
1 AT
61651 TTTTATTTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.41, C:0.12, G:0.04, T:0.43
Consensus pattern (27 bp):
ATCAATAATTTTATCCTGAATTTCAAA
Done.