Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007645.1 Kokia drynarioides strain JFW-HI SEQ_122276, 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: 25214
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:615 original size:7 final size:6
Alignment explanation
Indices: 594--632 Score: 51
Period size: 6 Copynumber: 6.0 Consensus size: 6
584 AATTATAAGT
594 ATAAAA ATAAAA ATAAATA ATAAAGA ATAAAAA ATAAAA
1 ATAAAA ATAAAA ATAAA-A ATAAA-A AT-AAAA ATAAAA
633 TTAATTGAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
6 15 0.50
7 12 0.40
8 3 0.10
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:1604 original size:29 final size:28
Alignment explanation
Indices: 1541--1597 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
1531 TTATTTTTGT
*
1541 ATTAATTTATATTTTTATAATTTTTAAAA
1 ATTAAATTA-ATTTTTATAATTTTTAAAA
*
1570 ATTTAAATTAATTTTTATTATTTTTAAA
1 A-TTAAATTAATTTTTATAATTTTTAAA
1598 GGATTAAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (28 bp):
ATTAAATTAATTTTTATAATTTTTAAAA
Found at i:2323 original size:59 final size:59
Alignment explanation
Indices: 2260--2403 Score: 186
Period size: 59 Copynumber: 2.4 Consensus size: 59
2250 TTATTGTTAA
2260 TAAATATAATTTAATAATAAATAATAAATAATTTAATAACATT-TTAACATAATTATTAT
1 TAAATATAATTTAATAA-AAATAATAAATAATTTAATAACATTCTTAACATAATTATTAT
* * * * *
2319 TAAATACAATTTAAT-AAAATAGTATATATTTTAATAACATTCTTAATATAATTATTAT
1 TAAATATAATTTAATAAAAATAATAAATAATTTAATAACATTCTTAACATAATTATTAT
*
2377 TAAAATATGAA-TTAATAAAAATCATAA
1 T-AAATAT-AATTTAATAAAAATAATAA
2404 TATATAATAT
Statistics
Matches: 72, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
57 22 0.31
58 17 0.24
59 24 0.33
60 9 0.12
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.41
Consensus pattern (59 bp):
TAAATATAATTTAATAAAAATAATAAATAATTTAATAACATTCTTAACATAATTATTAT
Found at i:2383 original size:29 final size:27
Alignment explanation
Indices: 2294--2380 Score: 86
Period size: 26 Copynumber: 3.1 Consensus size: 27
2284 TAAATAATTT
*
2294 AATAACATTTTAACATAATTATTATTA
1 AATAACATTTTAATATAATTATTATTA
* * *
2321 AAT-ACAATTTAATAAAATAGTATATATTTT
1 AATAACATTTTAATATAAT--TAT-TA-TTA
2351 AATAACATTCTTAATATAATTATTATTA
1 AATAACATT-TTAATATAATTATTATTA
2379 AA
1 AA
2381 ATATGAATTA
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
26 12 0.26
27 3 0.06
28 7 0.15
29 4 0.09
30 8 0.17
31 4 0.09
32 9 0.19
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44
Consensus pattern (27 bp):
AATAACATTTTAATATAATTATTATTA
Found at i:4916 original size:24 final size:24
Alignment explanation
Indices: 4882--4935 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
4872 GTGGATGTTC
* *
4882 AACCTTTCACCTTTGAT-CTCCCTT
1 AACCTTCCACCTTTCATCCT-CCTT
4906 AACCTTCCACCTTTCATCCTCCTT
1 AACCTTCCACCTTTCATCCTCCTT
4930 AACCTT
1 AACCTT
4936 TAACTTTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.19, C:0.41, G:0.02, T:0.39
Consensus pattern (24 bp):
AACCTTCCACCTTTCATCCTCCTT
Found at i:5732 original size:2 final size:2
Alignment explanation
Indices: 5725--5751 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5715 TAGAAGAGTT
5725 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 T
5752 GAATTTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13575 original size:37 final size:37
Alignment explanation
Indices: 13534--13605 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
13524 ATTCTTGCGA
* *
13534 CGATAGTTTTGGGTGCAATCTGGAAGTGCTCATGCAG
1 CGATAGTTTTGGGCGCAATCTAGAAGTGCTCATGCAG
13571 CGATAGTTTTGGGCGCAATCTAGAAGTGCTCATGC
1 CGATAGTTTTGGGCGCAATCTAGAAGTGCTCATGC
13606 TGCGGCATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (37 bp):
CGATAGTTTTGGGCGCAATCTAGAAGTGCTCATGCAG
Found at i:15653 original size:5 final size:5
Alignment explanation
Indices: 15645--15724 Score: 63
Period size: 5 Copynumber: 16.0 Consensus size: 5
15635 TTGACCCGAA
* * * ***
15645 ATGAT ATGAT ATGAT -TCAAT ATGGT ATGAT GTGAT ATGAT ATGAT CCAAT
1 ATGAT ATGAT ATGAT AT-GAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT
* * *
15695 ATGGT ATGAT GTGAT GTGAT ATGAT ATGAT
1 ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT
15725 CCAATATGGT
Statistics
Matches: 57, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
4 1 0.02
5 55 0.96
6 1 0.02
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.39
Consensus pattern (5 bp):
ATGAT
Found at i:15680 original size:30 final size:30
Alignment explanation
Indices: 15646--15751 Score: 142
Period size: 35 Copynumber: 3.4 Consensus size: 30
15636 TGACCCGAAA
*
15646 TGATATGATATGATTCAATATGGTATGATG
1 TGATATGATATGATCCAATATGGTATGATG
15676 TGATATGATATGATCCAATATGGTATGATGTGATG
1 TGATATGATATGATCCAATATGG--T-A--TGATG
15711 TGATATGATATGATCCAATATGGTATG-TG
1 TGATATGATATGATCCAATATGGTATGATG
*
15740 TGATATGTTATG
1 TGATATGATATG
15752 TTATGGTATG
Statistics
Matches: 69, Mismatches: 2, Indels: 11
0.84 0.02 0.13
Matches are distributed among these distances:
29 13 0.19
30 24 0.35
32 2 0.03
33 2 0.03
35 28 0.41
ACGTcount: A:0.31, C:0.05, G:0.25, T:0.40
Consensus pattern (30 bp):
TGATATGATATGATCCAATATGGTATGATG
Found at i:15684 original size:35 final size:35
Alignment explanation
Indices: 15645--15756 Score: 146
Period size: 30 Copynumber: 3.4 Consensus size: 35
15635 TTGACCCGAA
*
15645 ATGATATGATATGATTCAATATGGTATGA--TG--
1 ATGATATGATATGATCCAATATGGTATGATGTGAT
15676 -TGATATGATATGATCCAATATGGTATGATGTGAT
1 ATGATATGATATGATCCAATATGGTATGATGTGAT
*
15710 GTGATATGATATGATCCAATATGGTATG-TGTGAT
1 ATGATATGATATGATCCAATATGGTATGATGTGAT
* *
15744 ATGTTATGTTATG
1 ATGATATGATATG
15757 GTATGAAATA
Statistics
Matches: 72, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
30 27 0.38
32 2 0.03
34 16 0.22
35 27 0.38
ACGTcount: A:0.31, C:0.04, G:0.24, T:0.40
Consensus pattern (35 bp):
ATGATATGATATGATCCAATATGGTATGATGTGAT
Found at i:15717 original size:15 final size:15
Alignment explanation
Indices: 15646--15724 Score: 70
Period size: 15 Copynumber: 5.3 Consensus size: 15
15636 TGACCCGAAA
15646 TGATATGATATGAT-
1 TGATATGATATGATG
* *
15660 TCAATATGGTATGATG
1 T-GATATGATATGATG
*
15676 TGATATGATATGATC
1 TGATATGATATGATG
** *
15691 CAATATGGTATGATG
1 TGATATGATATGATG
* *
15706 TGATGTGATATGATA
1 TGATATGATATGATG
15721 TGAT
1 TGAT
15725 CCAATATGGT
Statistics
Matches: 49, Mismatches: 14, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
14 1 0.02
15 47 0.96
16 1 0.02
ACGTcount: A:0.33, C:0.04, G:0.24, T:0.39
Consensus pattern (15 bp):
TGATATGATATGATG
Found at i:16567 original size:20 final size:19
Alignment explanation
Indices: 16540--16577 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
16530 TATTATTGGT
16540 TATATTTAAATATTTAAAA
1 TATATTTAAATATTTAAAA
*
16559 TATAGTTTATATATTTAAA
1 TATA-TTTAAATATTTAAA
16578 TTAATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
TATATTTAAATATTTAAAA
Found at i:16589 original size:18 final size:20
Alignment explanation
Indices: 16543--16589 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
16533 TATTGGTTAT
*
16543 ATTTAAATATTTAAAATATA
1 ATTTATATATTTAAAATATA
*
16563 GTTTATATATTT-AAAT-TA
1 ATTTATATATTTAAAATATA
*
16581 ATTTTTATA
1 ATTTATATA
16590 AATGATTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 9 0.39
19 4 0.17
20 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
ATTTATATATTTAAAATATA
Found at i:17115 original size:17 final size:18
Alignment explanation
Indices: 17093--17129 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
17083 TTATTTTTTT
17093 AAAAATATTTTTGAA-AA
1 AAAAATATTTTTGAAGAA
17110 AAAAATATTTTTGAAGAA
1 AAAAATATTTTTGAAGAA
17128 AA
1 AA
17130 GTTAAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.32
Consensus pattern (18 bp):
AAAAATATTTTTGAAGAA
Found at i:22315 original size:13 final size:13
Alignment explanation
Indices: 22296--22334 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
22286 ATTGATAACT
22296 GTATTAATAATTA
1 GTATTAATAATTA
*
22309 TTATTAATAATTA
1 GTATTAATAATTA
*
22322 GTATTAATTATTA
1 GTATTAATAATTA
22335 AAAATAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (13 bp):
GTATTAATAATTA
Found at i:23363 original size:29 final size:28
Alignment explanation
Indices: 23323--23533 Score: 162
Period size: 30 Copynumber: 7.2 Consensus size: 28
23313 GAGGTCCCTA
*
23323 AACTATCCAAAAATTACCATTTTACCTTG
1 AACT-TCCAAAAATTACCATTTTACCTCG
*
23352 AACTTCCAAAAA-TCCCATTTTTAACCTCG
1 AACTTCCAAAAATTACCA-TTTT-ACCTCG
*
23381 AAACTTCCTAAAATTACCATTTTACCCTCG
1 -AACTTCCAAAAATTACCATTTTA-CCTCG
* *
23411 AACTTCCAAAAA-T-CTCATTTTTGACCCCA
1 AACTTCCAAAAATTAC-CA-TTTT-ACCTCG
23440 AACCTTCCAAAAATTACCATTTTACCCTCG
1 AA-CTTCCAAAAATTACCATTTTA-CCTCG
* * * * *
23470 AACTTTC-GAAAGTCCCATTTTTGACC-CATA
1 AACTTCCAAAAATTACCA-TTTT-ACCTC--G
23500 AACTTCCAAAAATTACCATTTTACCCTCG
1 AACTTCCAAAAATTACCATTTTA-CCTCG
23529 AACTT
1 AACTT
23534 TCTAAAATCC
Statistics
Matches: 144, Mismatches: 19, Indels: 38
0.72 0.09 0.19
Matches are distributed among these distances:
27 5 0.03
28 23 0.16
29 47 0.33
30 53 0.37
31 15 0.10
32 1 0.01
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.32
Consensus pattern (28 bp):
AACTTCCAAAAATTACCATTTTACCTCG
Found at i:23388 original size:30 final size:29
Alignment explanation
Indices: 23322--23564 Score: 144
Period size: 29 Copynumber: 8.2 Consensus size: 29
23312 GGAGGTCCCT
*
23322 AAACTATCCAAAAATTACCATTTT-ACCTTG
1 AAACT-TCCAAAAA-TACCATTTTAACCTCG
*
23352 -AACTTCCAAAAATCCCATTTTTAACCTCG
1 AAACTTCCAAAAATACCA-TTTTAACCTCG
* *
23381 AAACTTCCTAAAATTACCATTTTACCCTCG
1 AAACTTCC-AAAAATACCATTTTAACCTCG
* *
23411 -AACTTCCAAAAAT-CTCATTTTTGACC-CC
1 AAACTTCCAAAAATAC-CA-TTTTAACCTCG
*
23439 AAACCTTCCAAAAATTACCATTTTACCCTCG
1 AAA-CTTCCAAAAA-TACCATTTTAACCTCG
* * * * * *
23470 -AACTTTCGAAAGTCCCATTTTTGACC-CAT
1 AAACTTCCAAAAATACCA-TTTTAACCTC-G
*
23499 AAACTTCCAAAAATTACCATTTTACCCTCG
1 AAACTTCCAAAAA-TACCATTTTAACCTCG
* * * *
23529 -AACTTTCTAAAAT-CCAATTTTTGACCCCG
1 AAACTTCCAAAAATACC-A-TTTTAACCTCG
23558 AAACTTC
1 AAACTTC
23565 TTTAAATTAC
Statistics
Matches: 162, Mismatches: 32, Indels: 38
0.70 0.14 0.16
Matches are distributed among these distances:
27 7 0.04
28 27 0.17
29 55 0.34
30 55 0.34
31 17 0.10
32 1 0.01
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATACCATTTTAACCTCG
Found at i:23421 original size:59 final size:58
Alignment explanation
Indices: 23322--23582 Score: 335
Period size: 59 Copynumber: 4.4 Consensus size: 58
23312 GGAGGTCCCT
* *
23322 AAACTATCCAAAAATTACCATTTTA-CCTTGAACTTCCAAAAATCCCATTTTTAACCTCG
1 AAACT-TCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACC-CG
* * *
23381 AAACTTCCTAAAATTACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCCC
1 AAACTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCG
* * * *
23439 AAACCTTCCAAAAATTACCATTTTACCCTCGAACTTTCGAAAGTCCCATTTTTGACCCAT
1 AAA-CTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCC-G
* * *
23499 AAACTTCCAAAAATTACCATTTTACCCTCGAACTTTCTAAAATCCAATTTTTGACCCCG
1 AAACTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA-CCCG
***
23558 AAACTTCTTTAAATTACCATTTTAC
1 AAACTTCCAAAAATTACCATTTTAC
23583 TCCCGAATGT
Statistics
Matches: 180, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
58 22 0.12
59 152 0.84
60 6 0.03
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.33
Consensus pattern (58 bp):
AAACTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCG
Found at i:23588 original size:30 final size:28
Alignment explanation
Indices: 23333--23589 Score: 96
Period size: 30 Copynumber: 8.8 Consensus size: 28
23323 AACTATCCAA
** * *
23333 AAATTACCATTTTACCTTG-AACTTCCA
1 AAATTACCATTTTACCCCGAAACTTTCT
* * * *
23360 AAAATCCCATTTTTAACCTCGAAACTTCCT
1 AAATTACCA-TTTT-ACCCCGAAACTTTCT
* *
23390 AAAATTACCATTTTACCCTCG-AACTTCCA
1 -AAATTACCATTTTACCC-CGAAACTTTCT
* * *
23419 AAAAT-CTCATTTTTGACCCC-AAACCTTCCAA
1 AAATTAC-CA-TTTT-ACCCCGAAA-CTTTC-T
*
23450 AAATTACCATTTTACCCTCG-AACTTTCG
1 AAATTACCATTTTACCC-CGAAACTTTCT
* * ** * *
23478 AAAGTCCCATTTTTGACCCATAAACTTCCAA
1 AAATTACCA-TTTT-ACCCCGAAACTTTC-T
23509 AAATTACCATTTTACCCTCG-AACTTTCT
1 AAATTACCATTTTACCC-CGAAACTTTCT
* *
23537 AAAAT-CCAATTTTTGACCCCGAAACTTCTTT
1 AAATTACC-A-TTTT-ACCCCGAAACTT-TCT
23568 AAATTACCATTTTACTCCCGAA
1 AAATTACCATTTTAC-CCCGAA
23590 TGTCCGAAGA
Statistics
Matches: 177, Mismatches: 27, Indels: 49
0.70 0.11 0.19
Matches are distributed among these distances:
27 10 0.06
28 22 0.12
29 52 0.29
30 62 0.35
31 28 0.16
32 3 0.02
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (28 bp):
AAATTACCATTTTACCCCGAAACTTTCT
Done.