Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003422.1 Kokia drynarioides strain JFW-HI SEQ_116190, 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: 51868
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:8347 original size:52 final size:52
Alignment explanation
Indices: 8202--8438 Score: 336
Period size: 52 Copynumber: 4.6 Consensus size: 52
8192 AAATCCAAAA
8202 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * *
8254 AGGTCCGAGGAC--TGTGTCATCGTAAGCATATGAATCATTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
8304 AGGTCCGATGACTACGTGTCATCGTGAGTATGTGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * *
8356 AGCTCCGATGACTATGTGTCATCGTGAGCATATGAATCCTTTTATGGATT-TA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCC-TTTACGGATTATG
* *
8408 AGGTCCGATGACTTTGTGTCATTGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
8439 TAAATGGGAA
Statistics
Matches: 162, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
50 46 0.28
52 107 0.66
53 9 0.06
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.34
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:13028 original size:344 final size:344
Alignment explanation
Indices: 12397--13086 Score: 1326
Period size: 344 Copynumber: 2.0 Consensus size: 344
12387 GCTTGTGTTG
12397 GTCAGCCATTGATATCCCTAAGACATATTAAACATGCTTGTTAGGACATATTAAATGGGCAACAA
1 GTCAGCCATTGATATCCCTAAGACATATTAAACATGCTTGTTAGGACATATTAAATGGGCAACAA
* *
12462 TATTTGACTAAAACTAACAACTAACTTAGGACATATTTAAAGACTTAACAAAATAATACAAAACA
66 TATTTGACTAAAACTAACAACTAACTTAGGAAATATTTAAAGACTTAACAAAATAATACAAAAAA
12527 TAATTAAAACTTAAACTAAGATAACTAAATTTTTTAAAATCCATTTCCAGCAATTAAATTGACTA
131 TAATTAAAACTTAAACTAAGATAACTAAATTTTTTAAAATCCATTTCCAGCAATTAAATTGACTA
12592 AGTAAATTAAGGTTTTATGTGCAGCACATTGCATGGTATACATGTGTTGCAAGAAGTGCACGAGT
196 AGTAAATTAAGGTTTTATGTGCAGCACATTGCATGGTATACATGTGTTGCAAGAAGTGCACGAGT
12657 TATATGAAATGCATGGAATGCATGATGTGTTTTCCCAAACTCGTTTAATTAAACCCGTGACAGCT
261 TATATGAAATGCATGGAATGCATGATGTGTTTTCCCAAACTCGTTTAATTAAACCCGTGACAGCT
*
12722 TCTTTGAACTTCTTGGCTT
326 TCTTTGAACTTATTGGCTT
12741 GTCAGCCATTGATATCCCTAAGACATATTAAACATGCTTGTTAGGACATATTAAATGGGCAACAA
1 GTCAGCCATTGATATCCCTAAGACATATTAAACATGCTTGTTAGGACATATTAAATGGGCAACAA
12806 TATTTGACTAAAACTAACAACTAACTTAGGAAATATTTAAAGACTTAACAAAATAATACAAAAAA
66 TATTTGACTAAAACTAACAACTAACTTAGGAAATATTTAAAGACTTAACAAAATAATACAAAAAA
*
12871 TAATTAAAACTTAAACTAAGATAACTAAATTTTTTAAAATCCATTTCTAGCAATTAAATTGACTA
131 TAATTAAAACTTAAACTAAGATAACTAAATTTTTTAAAATCCATTTCCAGCAATTAAATTGACTA
*
12936 AGTAAATTAAGGTTTTATGTGCAGCACATTGCATGGTATATATGTGTTGCAAGAAGTGCACGAGT
196 AGTAAATTAAGGTTTTATGTGCAGCACATTGCATGGTATACATGTGTTGCAAGAAGTGCACGAGT
*
13001 TATATGAAATGCATGGAATGTATGATGTGTTTTCCCAAACTCGTTTAATTAAACCCGTGACAGCT
261 TATATGAAATGCATGGAATGCATGATGTGTTTTCCCAAACTCGTTTAATTAAACCCGTGACAGCT
13066 TCTTTGAACTTATTGGCTT
326 TCTTTGAACTTATTGGCTT
13085 GT
1 GT
13087 GCTCGCGTGA
Statistics
Matches: 340, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
344 340 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (344 bp):
GTCAGCCATTGATATCCCTAAGACATATTAAACATGCTTGTTAGGACATATTAAATGGGCAACAA
TATTTGACTAAAACTAACAACTAACTTAGGAAATATTTAAAGACTTAACAAAATAATACAAAAAA
TAATTAAAACTTAAACTAAGATAACTAAATTTTTTAAAATCCATTTCCAGCAATTAAATTGACTA
AGTAAATTAAGGTTTTATGTGCAGCACATTGCATGGTATACATGTGTTGCAAGAAGTGCACGAGT
TATATGAAATGCATGGAATGCATGATGTGTTTTCCCAAACTCGTTTAATTAAACCCGTGACAGCT
TCTTTGAACTTATTGGCTT
Found at i:16155 original size:18 final size:18
Alignment explanation
Indices: 16115--16149 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
16105 TAAATAATAA
*
16115 AATATTATTATTTATTAT
1 AATATTATTATTAATTAT
16133 AATATTATTATTAATTA
1 AATATTATTATTAATTA
16150 ATATATCAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AATATTATTATTAATTAT
Found at i:17229 original size:21 final size:21
Alignment explanation
Indices: 17203--17243 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
17193 CACAAGGATG
17203 ACTGTCTTCTATCCATTAATA
1 ACTGTCTTCTATCCATTAATA
* *
17224 ACTGTCTTCTGTCTATTAAT
1 ACTGTCTTCTATCCATTAAT
17244 GTCAGTGCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.22, G:0.07, T:0.46
Consensus pattern (21 bp):
ACTGTCTTCTATCCATTAATA
Found at i:25522 original size:21 final size:21
Alignment explanation
Indices: 25498--25537 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
25488 GTACACGATT
**
25498 TTGATGTGGCTGCATCTGATC
1 TTGATGTGAATGCATCTGATC
25519 TTGATGTGAATGCATCTGA
1 TTGATGTGAATGCATCTGA
25538 GTATTATGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.15, G:0.28, T:0.38
Consensus pattern (21 bp):
TTGATGTGAATGCATCTGATC
Found at i:28580 original size:18 final size:18
Alignment explanation
Indices: 28539--28612 Score: 62
Period size: 16 Copynumber: 3.9 Consensus size: 18
28529 CAATTCTTCT
28539 CTTTTTTTTCTCTCA--A
1 CTTTTTTTTCTCTCATTA
* *
28555 GTTCTTTTTCTCTCATTA
1 CTTTTTTTTCTCTCATTA
28573 CTTTTTTTCTTCTCTCTATTTA
1 C-TTTTTT-TTCTCTC-A-TTA
*
28595 TTTTATTTTTCTCTCATT
1 CTTT-TTTTTCTCTCATT
28613 TTCTCTCATT
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
16 13 0.28
18 1 0.02
19 7 0.15
20 8 0.17
21 11 0.24
22 6 0.13
ACGTcount: A:0.11, C:0.22, G:0.01, T:0.66
Consensus pattern (18 bp):
CTTTTTTTTCTCTCATTA
Found at i:28606 original size:21 final size:20
Alignment explanation
Indices: 28559--28613 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 20
28549 TCTCAAGTTC
28559 TTTTTCTCTCA-TTACTTTT
1 TTTTTCTCTCATTTACTTTT
28578 TTTCTTCTCTCTATTTA-TTTT
1 TTT-TTCTCTC-ATTTACTTTT
28599 ATTTTTCTCTCATTT
1 -TTTTTCTCTCATTT
28614 TCTCTCATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
19 3 0.09
20 11 0.34
21 12 0.38
22 6 0.19
ACGTcount: A:0.11, C:0.20, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTTCTCTCATTTACTTTT
Found at i:34471 original size:22 final size:23
Alignment explanation
Indices: 34446--34497 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
34436 CTTCTAACTA
34446 CTAAATAATATTTTAAAC-TT-CT
1 CTAAATAATA-TTTAAACATTACT
*
34468 CTAAATCA-ATTTAAACATTACT
1 CTAAATAATATTTAAACATTACT
34490 CT-AATAAT
1 CTAAATAAT
34498 TTAGAGAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 7 0.28
21 7 0.28
22 11 0.44
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.40
Consensus pattern (23 bp):
CTAAATAATATTTAAACATTACT
Found at i:34498 original size:20 final size:18
Alignment explanation
Indices: 34451--34500 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 18
34441 AACTACTAAA
*
34451 TAATATTTTAAACTTCTC
1 TAATAATTTAAACTTCTC
34469 TAAATCAATTTAAACATTACTC
1 T-AAT-AATTTAAAC-TT-CTC
34491 TAATAATTTA
1 TAATAATTTA
34501 GAGAGATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 1 0.04
19 3 0.11
20 14 0.52
21 5 0.19
22 4 0.15
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (18 bp):
TAATAATTTAAACTTCTC
Found at i:37676 original size:7 final size:7
Alignment explanation
Indices: 37653--37773 Score: 138
Period size: 7 Copynumber: 17.3 Consensus size: 7
37643 AGTACATTTA
37653 TTTTCA-
1 TTTTCAT
37659 TTTTCATT
1 TTTTCA-T
37667 TTTTCATT
1 TTTTCA-T
37675 TTTTCAT
1 TTTTCAT
37682 TTTTCAT
1 TTTTCAT
37689 TTTTCAT
1 TTTTCAT
37696 TTTTCAT
1 TTTTCAT
37703 TTTTCAT
1 TTTTCAT
37710 TTTTCAT
1 TTTTCAT
*
37717 CTTTCAT
1 TTTTCAT
* *
37724 CTTTAAT
1 TTTTCAT
*
37731 CTTTCAT
1 TTTTCAT
*
37738 CTTTCAT
1 TTTTCAT
*
37745 CTTTCAT
1 TTTTCAT
37752 TTTTCAT
1 TTTTCAT
*
37759 CTTT-AT
1 TTTTCAT
*
37765 TTTTAAT
1 TTTTCAT
37772 TT
1 TT
37774 AATTTAATTT
Statistics
Matches: 106, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
6 11 0.10
7 81 0.76
8 14 0.13
ACGTcount: A:0.16, C:0.17, G:0.00, T:0.68
Consensus pattern (7 bp):
TTTTCAT
Found at i:38745 original size:20 final size:19
Alignment explanation
Indices: 38719--38759 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
38709 GAAAAAATCG
38719 AAAAGA-AAAATTGAA-AAA
1 AAAAGAGAAAATT-AAGAAA
38737 AAAAGAGAAAATTAAGAAA
1 AAAAGAGAAAATTAAGAAA
38756 AAAA
1 AAAA
38760 CCGACAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (19 bp):
AAAAGAGAAAATTAAGAAA
Found at i:39868 original size:23 final size:25
Alignment explanation
Indices: 39841--39886 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
39831 CCATTTAGGA
39841 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
39864 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
39887 TGTATCAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:46405 original size:20 final size:21
Alignment explanation
Indices: 46363--46405 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
46353 TTCGTTCCAT
* * *
46363 TTTAAGATTTAATCTATACAC
1 TTTAAGATTTAATATAAAAAC
46384 TTTAA-ATTTAATATAAAAAC
1 TTTAAGATTTAATATAAAAAC
46404 TT
1 TT
46406 CAGGATGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (21 bp):
TTTAAGATTTAATATAAAAAC
Found at i:48571 original size:36 final size:36
Alignment explanation
Indices: 48312--48561 Score: 288
Period size: 36 Copynumber: 7.0 Consensus size: 36
48302 TTGTTGCGAA
* * *
48312 AGTAAATATGTTACTATGTTATTCATGTC-TGTGAT
1 AGTAAATATGTGAGTATGTTATTCATGCCATGTGAT
* * *
48347 AGTAAATATGTGAGTATGTTATCCATTCCATGAGAT
1 AGTAAATATGTGAGTATGTTATTCATGCCATGTGAT
* * *
48383 AGTAAACATGTGTGTATGTTATTCACGCCATGTGAT
1 AGTAAATATGTGAGTATGTTATTCATGCCATGTGAT
* * * **
48419 AGTAAAAATAT-AGGTATGTTATTTATGCCATGAAAT
1 AGTAAATATGTGA-GTATGTTATTCATGCCATGTGAT
* * **
48455 AGTAAATATGTGGGTTTGTTATTCATGGAATGTGAT
1 AGTAAATATGTGAGTATGTTATTCATGCCATGTGAT
* *
48491 AGTAAATATGTGAGTATGTTATTCATGCCATGAGAC
1 AGTAAATATGTGAGTATGTTATTCATGCCATGTGAT
*
48527 AGTAAATATGTGAGTATGTTATTCATACCATGTGA
1 AGTAAATATGTGAGTATGTTATTCATGCCATGTGA
48562 CAGAGAATAT
Statistics
Matches: 176, Mismatches: 36, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
35 24 0.14
36 152 0.86
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (36 bp):
AGTAAATATGTGAGTATGTTATTCATGCCATGTGAT
Found at i:48995 original size:23 final size:23
Alignment explanation
Indices: 48969--49175 Score: 306
Period size: 23 Copynumber: 9.0 Consensus size: 23
48959 TAGATGTGCA
*
48969 TTAAATATTAATATGATTTATGC
1 TTAAATATTAATGTGATTTATGC
* *
48992 TTAAATATTAATATGATTTGTGC
1 TTAAATATTAATGTGATTTATGC
* *
49015 TTAAATATTAATTTGATTTGTGC
1 TTAAATATTAATGTGATTTATGC
* *
49038 TTAAATATTAATGTGATTTGTGT
1 TTAAATATTAATGTGATTTATGC
*
49061 TTAAATATTAATGTGATTTGTGC
1 TTAAATATTAATGTGATTTATGC
*
49084 TTAAATATTAATGTGATTTATTC
1 TTAAATATTAATGTGATTTATGC
* *
49107 TTAAATGTTAATATGATTTATGC
1 TTAAATATTAATGTGATTTATGC
49130 TTAAATATTAATGTGATTTATGC
1 TTAAATATTAATGTGATTTATGC
49153 TTAAAATATTAATGTGATTTATG
1 TT-AAATATTAATGTGATTTATG
49176 TGTAAATGGA
Statistics
Matches: 171, Mismatches: 12, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
23 151 0.88
24 20 0.12
ACGTcount: A:0.34, C:0.03, G:0.13, T:0.49
Consensus pattern (23 bp):
TTAAATATTAATGTGATTTATGC
Found at i:49203 original size:69 final size:69
Alignment explanation
Indices: 48988--49203 Score: 206
Period size: 69 Copynumber: 3.1 Consensus size: 69
48978 AATATGATTT
* * * * * * * * **
48988 ATGCTTAAATATTAATATGATTTGTGCTTAAATATTAATTTGATTTGTGCTTAAATATTAATGTG
1 ATGCTTAAATATTAATGTGATTTATGCTTAAATATTAATGTGATTTATTCGTAAATGTGAACATG
*
49053 ATTTG
66 A-ATG
* * * * *
49058 -TGTTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGATTTATTCTTAAATGTTAATATG
1 ATGCTTAAATATTAATGTGATTTATGCTTAAATATTAATGTGATTTATTCGTAAATGTGAACATG
* *
49122 ATTT
66 AATG
49126 ATGCTTAAATATTAATGTGATTTATGCTTAAAATATTAATGTGATTTATGT-GTAAATG-GAACC
1 ATGCTTAAATATTAATGTGATTTATGCTT-AAATATTAATGTGATTTAT-TCGTAAATGTGAA-C
49189 ATGAATG
63 ATGAATG
49196 ATG-TTAAA
1 ATGCTTAAA
49204 ATGTATGTAA
Statistics
Matches: 127, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
68 2 0.02
69 91 0.72
70 33 0.26
71 1 0.01
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.46
Consensus pattern (69 bp):
ATGCTTAAATATTAATGTGATTTATGCTTAAATATTAATGTGATTTATTCGTAAATGTGAACATG
AATG
Done.