Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013280.1 Kokia drynarioides strain JFW-HI SEQ_128301, 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: 13538
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Found at i:653 original size:17 final size:16
Alignment explanation
Indices: 634--690 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
624 TTAATTAAGT
*
634 TTTAAATCCATTTAAA
1 TTTAAATCAATTTAAA
* *
650 TTTTAATTAAATTTAAA
1 -TTTAAATCAATTTAAA
*
667 TTTAAAGCAAATTTAAA
1 TTTAAATC-AATTTAAA
684 TTTAAAT
1 TTTAAAT
691 TTAAAATAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
16 5 0.16
17 27 0.84
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (16 bp):
TTTAAATCAATTTAAA
Found at i:657 original size:6 final size:6
Alignment explanation
Indices: 643--734 Score: 77
Period size: 6 Copynumber: 16.2 Consensus size: 6
633 TTTTAAATCC
* **
643 ATTTAA ATTTTA A-TTAA ATTTAA ATTTAA A-GCAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * ** *
689 ATTTAA A-ATAA TTTTAA ATTTAA AAATAA ATTTGA A--TAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
734 A
1 A
735 CCCAATAAAA
Statistics
Matches: 65, Mismatches: 16, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
4 3 0.05
5 10 0.15
6 52 0.80
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.43
Consensus pattern (6 bp):
ATTTAA
Found at i:661 original size:11 final size:11
Alignment explanation
Indices: 643--708 Score: 53
Period size: 11 Copynumber: 5.8 Consensus size: 11
633 TTTTAAATCC
*
643 ATTTAAATTTTA
1 ATTTAAA-TTAA
655 A-TTAAATTTAA
1 ATTTAAA-TTAA
**
666 ATTTAAAGCAA
1 ATTTAAATTAA
677 ATTTAAATTTAA
1 ATTTAAA-TTAA
*
689 ATTTAAAATAA
1 ATTTAAATTAA
*
700 TTTTAAATT
1 ATTTAAATT
709 TAAAAATAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
11 29 0.66
12 15 0.34
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (11 bp):
ATTTAAATTAA
Found at i:671 original size:23 final size:23
Alignment explanation
Indices: 643--734 Score: 75
Period size: 23 Copynumber: 4.0 Consensus size: 23
633 TTTTAAATCC
643 ATTTAAATTTTAA-TTAAATTTAA
1 ATTTAAA-TTTAATTTAAATTTAA
***
666 ATTTAAAGCAAATTTAAATTTAA
1 ATTTAAATTTAATTTAAATTTAA
*
689 ATTTAAA-ATAATTTTAAATTTAA
1 ATTTAAATTTAA-TTTAAATTTAA
**
712 AAATAAATTTGAA--TAAATTTAA
1 ATTTAAATTT-AATTTAAATTTAA
734 A
1 A
735 CCCAATAAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
22 14 0.25
23 40 0.70
24 1 0.02
25 2 0.04
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.43
Consensus pattern (23 bp):
ATTTAAATTTAATTTAAATTTAA
Found at i:707 original size:29 final size:28
Alignment explanation
Indices: 675--734 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
665 AATTTAAAGC
** *
675 AAATTTAAATTTAAATTTAAAATAATTTT
1 AAATTTAAAAATAAATTT-AAATAAATTT
*
704 AAATTTAAAAATAAATTTGAATAAATTT
1 AAATTTAAAAATAAATTTAAATAAATTT
732 AAA
1 AAA
735 CCCAATAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 11 0.41
29 16 0.59
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (28 bp):
AAATTTAAAAATAAATTTAAATAAATTT
Found at i:1425 original size:206 final size:205
Alignment explanation
Indices: 1061--1721 Score: 1099
Period size: 206 Copynumber: 3.2 Consensus size: 205
1051 TCTGATTTCA
* * * * ** *
1061 TTGACTTGGCCTTCTTCTCAGTATCTCATCCGGAAGAAGACCATATCACTTGTTTCAATCCACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTT
*
1126 CTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACTGT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCGT
* *
1191 TTATTGCTTCGACCTGCTTCTCGGTGTCTCATCAGGAAGCTGGGGTTCGAAGATCTTGCTCACTT
131 TTATTGCTTCGACCTGCTTCTCGGTGTCTCATCAGGAAGCTGGGGTTCG-AGATTTTGCTCGCTT
1256 TGAGCGTGGGT
195 TGAGCGTGGGT
*
1267 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTT
* * *
1332 CTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTTATCAAGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCGT
1397 TTATTGCTTCGACCTGCTTCTCGGTGTCTCATCAGGAAGCTGGGGTTC-AGATTTTTTGCTCGCT
131 TTATTGCTTCGACCTGCTTCTCGGTGTCTCATCAGGAAGCTGGGGTTCGAGA--TTTTGCTCGCT
1461 TTGAGCGTGGGT
194 TTGAGCGTGGGT
* *
1473 TTGATTTGGTCTTCTTCTCAGTATCTCATTAGGAAGATGACCGCATCATTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTT
*
1538 CTCTGTATCTCATCAAGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCGT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCGT
*
1603 TTATTGCTTCGACCTGCTTCTCGATGTCTCATCAGGAAGCTGGGGTTCGGAGATTTTGCTCGCTT
131 TTATTGCTTCGACCTGCTTCTCGGTGTCTCATCAGGAAGCTGGGGTTC-GAGATTTTGCTCGCTT
*
1668 TGAGCATGGGT
195 TGAGCGTGGGT
*
1679 TTGATTTGGTCTTCTTCTCAGTATCTCATTAGGAAGATGACCG
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCG
1722 TGTCGTTTAT
Statistics
Matches: 428, Mismatches: 23, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
204 3 0.01
206 422 0.99
208 3 0.01
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (205 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTT
CTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCGT
TTATTGCTTCGACCTGCTTCTCGGTGTCTCATCAGGAAGCTGGGGTTCGAGATTTTGCTCGCTTT
GAGCGTGGGT
Found at i:2268 original size:27 final size:29
Alignment explanation
Indices: 2218--2278 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
2208 TCAAGAATTC
* *
2218 TATT-AAAAAGAGGATCGAATG-AAACAA
1 TATTAAAAAACAGGATCGAAAGAAAACAA
2245 TATTAAAAAACAGGATC-AAAGAAAACAA
1 TATTAAAAAACAGGATCGAAAGAAAACAA
2273 TCATTA
1 T-ATTA
2279 GTTGAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 7 0.24
28 18 0.62
29 4 0.14
ACGTcount: A:0.57, C:0.10, G:0.13, T:0.20
Consensus pattern (29 bp):
TATTAAAAAACAGGATCGAAAGAAAACAA
Found at i:9617 original size:37 final size:37
Alignment explanation
Indices: 9567--9640 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
9557 GCAGAGCTTT
9567 TTCCTTTATCAGCCATGCTTTGTTTAACTTGCGCTAA
1 TTCCTTTATCAGCCATGCTTTGTTTAACTTGCGCTAA
*
9604 TTCCTTTATCAGCCATGCTTTGTTTTACTTGCGCTAA
1 TTCCTTTATCAGCCATGCTTTGTTTAACTTGCGCTAA
9641 GTTCTCTGCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.18, C:0.24, G:0.14, T:0.45
Consensus pattern (37 bp):
TTCCTTTATCAGCCATGCTTTGTTTAACTTGCGCTAA
Found at i:9659 original size:37 final size:37
Alignment explanation
Indices: 9574--9650 Score: 109
Period size: 37 Copynumber: 2.0 Consensus size: 37
9564 TTTTTCCTTT
**
9574 ATCAGCCATGCTTTGTTTAACTTGCGCTAATTCCTTT
1 ATCAGCCATGCTTTGTTTAACTTGCGCTAATTCCTGC
*
9611 ATCAGCCATGCTTTGTTTTACTTGCGCTAAGTTCTCTGC
1 ATCAGCCATGCTTTGTTTAACTTGCGCTAA-TTC-CTGC
9650 A
1 A
9651 CATCATGCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
37 29 0.83
38 3 0.09
39 3 0.09
ACGTcount: A:0.18, C:0.25, G:0.16, T:0.42
Consensus pattern (37 bp):
ATCAGCCATGCTTTGTTTAACTTGCGCTAATTCCTGC
Found at i:13040 original size:30 final size:29
Alignment explanation
Indices: 13001--13326 Score: 298
Period size: 29 Copynumber: 11.0 Consensus size: 29
12991 CGGACATCCG
13001 GGGGT-AAAATGGTAATTTTTGGAAGTTTC
1 GGGGTAAAAATGG-AATTTTTGGAAGTTTC
* * *
13030 GGGGTCAAAATGGGATTTTTAGAAGTTTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTC
* * *
13059 GGAGTAAAAATGAAATTTTTGGAAGTTTT
1 GGGGTAAAAATGGAATTTTTGGAAGTTTC
* * * * *
13088 GAGGTCAAAATTGGGATTTTGGGAAGTTTG
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTC
*
13118 GGGGTAAAAATAGAATTTTTGGAAGTTTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTC
*
13147 GAGGTTAAAAATTGG-ATTTTTGGAAGTTT-
1 G-GGGTAAAAA-TGGAATTTTTGGAAGTTTC
* *
13176 GGAGGTAAAAATAGAATTTTGGGAAGTTTC
1 GG-GGTAAAAATGGAATTTTTGGAAGTTTC
* * * *
13206 GGGATCAAAAATGGGATTTTTTGAAGTTTGA
1 GGGGT-AAAAATGGAATTTTTGGAAGTTT-C
* *
13237 GGGGTAAAAAAGGAATTTTTTGGAAGTTTT
1 GGGGTAAAAATGGAA-TTTTTGGAAGTTTC
* *
13267 GGGGTTAAAAAATGGGATTTTTGGAAGTTTT
1 GGGG-T-AAAAATGGAATTTTTGGAAGTTTC
* * *
13298 GGAGTAAAAACGAAATTTTTGGATAGTTT
1 GGGGTAAAAATGGAATTTTTGGA-AGTTT
13327 AGGGACCTTC
Statistics
Matches: 241, Mismatches: 43, Indels: 25
0.78 0.14 0.08
Matches are distributed among these distances:
28 3 0.01
29 103 0.43
30 91 0.38
31 36 0.15
32 8 0.03
ACGTcount: A:0.32, C:0.02, G:0.29, T:0.36
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTC
Found at i:13114 original size:59 final size:59
Alignment explanation
Indices: 13014--13326 Score: 334
Period size: 59 Copynumber: 5.3 Consensus size: 59
13004 GTAAAATGGT
* *
13014 AATTTTTGGAAGTTTCG-GGGTC-AAAATGGGATTTTTAGAAGTTTCGGAGTAAAAATGA
1 AATTTTTGGAAGTTTCGAGGTTCAAAAATGGGATTTTTGGAAGTTT-GGAGTAAAAATGA
* * * *
13072 AATTTTTGGAAGTTTTGAGG-TCAAAATTGGGATTTTGGGAAGTTTGGGGGTAAAAAT-A
1 AATTTTTGGAAGTTTCGAGGTTCAAAAATGGGATTTTTGGAAGTTT-GGAGTAAAAATGA
*
13130 GAATTTTTGGAAGTTTCGAGGTT-AAAAATTGGATTTTTGGAAGTTTGGAGGTAAAAAT-A
1 -AATTTTTGGAAGTTTCGAGGTTCAAAAATGGGATTTTTGGAAGTTTGGA-GTAAAAATGA
* * * * *
13189 GAATTTTGGGAAGTTTCG-GGATCAAAAATGGGATTTTTTGAAGTTTGAGGGGTAAAAAAGGA
1 -AATTTTTGGAAGTTTCGAGGTTCAAAAATGGGATTTTTGGAAGTTT--GGAGT-AAAAATGA
* * * * *
13251 ATTTTTTGGAAGTTTTGGGGTTAAAAAATGGGATTTTTGGAAGTTTTGGAGTAAAAACGA
1 AATTTTTGGAAGTTTCGAGGTTCAAAAATGGGATTTTTGGAAG-TTTGGAGTAAAAATGA
13311 AATTTTTGGATAGTTT
1 AATTTTTGGA-AGTTT
13327 AGGGACCTTC
Statistics
Matches: 216, Mismatches: 26, Indels: 23
0.82 0.10 0.09
Matches are distributed among these distances:
58 24 0.11
59 117 0.54
60 19 0.09
61 30 0.14
62 23 0.11
63 3 0.01
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.36
Consensus pattern (59 bp):
AATTTTTGGAAGTTTCGAGGTTCAAAAATGGGATTTTTGGAAGTTTGGAGTAAAAATGA
Done.