Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015136.1 Kokia drynarioides strain JFW-HI SEQ_130180, 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: 601175
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Warning! 598 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:543904 original size:21 final size:20
Alignment explanation
Indices: 543880--543925 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
543870 TTGAAAATAA
*
543880 TTTTT-GAAAAATTATTTATT
1 TTTTTAGAAAAATTA-ATATT
*
543900 TTTTTAGAAATATTAATATT
1 TTTTTAGAAAAATTAATATT
543920 TTTTTA
1 TTTTTA
543926 TGTTCAGATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (20 bp):
TTTTTAGAAAAATTAATATT
Found at i:549461 original size:25 final size:23
Alignment explanation
Indices: 549426--549472 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
549416 GAAATTGTTA
549426 TTTTTTTTAATTTAATATTTAAT
1 TTTTTTTTAATTTAATATTTAAT
**
549449 TTTTTTATCTAATTTGGTATTTAA
1 TTTTTT-T-TAATTTAATATTTAA
549473 ATTTGACATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 1 0.05
25 13 0.65
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (23 bp):
TTTTTTTTAATTTAATATTTAAT
Found at i:549493 original size:31 final size:31
Alignment explanation
Indices: 549435--549530 Score: 106
Period size: 32 Copynumber: 3.0 Consensus size: 31
549425 ATTTTTTTTA
549435 ATTTAATATTT-A-ATTTTTTTATCTAATTTGGT
1 ATTTAA-ATTTGACATTTTTTT-T-TAATTTGGT
*
549467 ATTTAAATTTGACATTTTTTTTTAATTTAGT
1 ATTTAAATTTGACATTTTTTTTTAATTTGGT
* * *
549498 ATTTAAACTTGACCTTTTTTTTTTAAATTGGT
1 ATTTAAATTTGA-CATTTTTTTTTAATTTGGT
549530 A
1 A
549531 CGTAATTTCT
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
31 23 0.41
32 25 0.45
33 8 0.14
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.59
Consensus pattern (31 bp):
ATTTAAATTTGACATTTTTTTTTAATTTGGT
Found at i:549517 original size:32 final size:31
Alignment explanation
Indices: 549448--549523 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
549438 TAATATTTAA
* * *
549448 TTTTTTTATCTAATTTGGTATTTAAATTTGAC
1 TTTTTTT-TTTAATTTAGTATTTAAACTTGAC
*
549480 ATTTTTTTTTAATTTAGTATTTAAACTTGACC
1 TTTTTTTTTTAATTTAGTATTTAAACTTGA-C
549512 TTTTTTTTTTAA
1 TTTTTTTTTTAA
549524 ATTGGTACGT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
31 20 0.53
32 18 0.47
ACGTcount: A:0.25, C:0.07, G:0.07, T:0.62
Consensus pattern (31 bp):
TTTTTTTTTTAATTTAGTATTTAAACTTGAC
Found at i:551769 original size:23 final size:24
Alignment explanation
Indices: 551725--551769 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
551715 TCATTTTAAA
*
551725 TTATAGAAAACTTAATAAATATGT
1 TTATACAAAACTTAATAAATATGT
*
551749 TTATACAAAA-TTAATATATAT
1 TTATACAAAACTTAATAAATAT
551770 AACAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (24 bp):
TTATACAAAACTTAATAAATATGT
Found at i:564623 original size:12 final size:13
Alignment explanation
Indices: 564606--564638 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
564596 AAGTTGTTTG
564606 TTTATTTTC-TTA
1 TTTATTTTCATTA
564618 TTTATTTTCATTA
1 TTTATTTTCATTA
564631 TTTATTTT
1 TTTATTTT
564639 TATTTCACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTTCATTA
Found at i:564642 original size:19 final size:19
Alignment explanation
Indices: 564618--564657 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
564608 TATTTTCTTA
*
564618 TTTATTTTCA-TTATTTATT
1 TTTA-TTTCACTTATCTATT
564637 TTTATTTCACTTATCTATT
1 TTTATTTCACTTATCTATT
564656 TT
1 TT
564658 ATGGTTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTATTTCACTTATCTATT
Found at i:569558 original size:21 final size:21
Alignment explanation
Indices: 569534--569592 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
569524 TAGAAATAAG
569534 ACTTGTTTCGGTAGAAGAGAC
1 ACTTGTTTCGGTAGAAGAGAC
* ** *
569555 ACTTGTATCGGTAGAATTGTC
1 ACTTGTTTCGGTAGAAGAGAC
569576 ACTTGTATT-GGTAGAAG
1 ACTTGT-TTCGGTAGAAG
569593 CCTGTACTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34
Consensus pattern (21 bp):
ACTTGTTTCGGTAGAAGAGAC
Found at i:573913 original size:25 final size:25
Alignment explanation
Indices: 573885--573934 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
573875 TGTTTATCAT
573885 CCACAGACTGATGGTCAATCAGAGC
1 CCACAGACTGATGGTCAATCAGAGC
573910 CCACAGACTGATGGTCAATCAGAGC
1 CCACAGACTGATGGTCAATCAGAGC
573935 GGGTGATACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.28, G:0.24, T:0.16
Consensus pattern (25 bp):
CCACAGACTGATGGTCAATCAGAGC
Found at i:577397 original size:15 final size:15
Alignment explanation
Indices: 577379--577414 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
577369 TCTTCTTTCT
*
577379 CTTCTTCTCGTGCTC
1 CTTCATCTCGTGCTC
*
577394 CTTCATCTCGTGCTT
1 CTTCATCTCGTGCTC
577409 CTTCAT
1 CTTCAT
577415 TGGCTCCCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.06, C:0.36, G:0.11, T:0.47
Consensus pattern (15 bp):
CTTCATCTCGTGCTC
Found at i:580860 original size:138 final size:138
Alignment explanation
Indices: 580627--580904 Score: 529
Period size: 138 Copynumber: 2.0 Consensus size: 138
580617 GATAAGTGGT
* *
580627 CTGCTACTTGGTTTTCTGATCCTTTCCTGTCCTTGATCTCAACGTCAAATTCTTGCAGGAAAAGG
1 CTGCTACTTGGGTTTCTGATCCTTTCCTGTCCTTGATCTCAACGTCAAATTCTTGCAGCAAAAGG
580692 ATCCATCTGATCAACTTGGGCTTGGCATCTTTCTTAGAAAAAAAGTATCTTAAAGCAGAATGATC
66 ATCCATCTGATCAACTTGGGCTTGGCATCTTTCTTAGAAAAAAAGTATCTTAAAGCAGAATGATC
580757 AGTGTATA
131 AGTGTATA
580765 CTGCTACTTGGGTTTCTGATCCTTTCCTGTCCTTGATCTCAACGTCAAATTCTTGCAGCAAAAGG
1 CTGCTACTTGGGTTTCTGATCCTTTCCTGTCCTTGATCTCAACGTCAAATTCTTGCAGCAAAAGG
*
580830 ATCCATCTGATCAACTTGGGCTTGGCATCTTTCTTAGAAAAAATGTATCTTAAAGCAGAATGATC
66 ATCCATCTGATCAACTTGGGCTTGGCATCTTTCTTAGAAAAAAAGTATCTTAAAGCAGAATGATC
580895 AGTGTATA
131 AGTGTATA
580903 CT
1 CT
580905 ATAACTTTTG
Statistics
Matches: 137, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
138 137 1.00
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (138 bp):
CTGCTACTTGGGTTTCTGATCCTTTCCTGTCCTTGATCTCAACGTCAAATTCTTGCAGCAAAAGG
ATCCATCTGATCAACTTGGGCTTGGCATCTTTCTTAGAAAAAAAGTATCTTAAAGCAGAATGATC
AGTGTATA
Found at i:584682 original size:21 final size:21
Alignment explanation
Indices: 584656--584697 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
584646 TCTAGATCTT
584656 TCTCTCTTCTCAGATCTAACA
1 TCTCTCTTCTCAGATCTAACA
584677 TCTCTCTTCTCAGATCTAACA
1 TCTCTCTTCTCAGATCTAACA
584698 CCTTTTTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.33, G:0.05, T:0.38
Consensus pattern (21 bp):
TCTCTCTTCTCAGATCTAACA
Found at i:586662 original size:21 final size:22
Alignment explanation
Indices: 586633--586706 Score: 75
Period size: 21 Copynumber: 3.5 Consensus size: 22
586623 GGAGTTTTTA
*
586633 GTATCGGTAGAACTA-AGACTT
1 GTATCGGTAGAACTAGACACTT
* *
586654 GTTTCGGTAGAA-GAGACACTT
1 GTATCGGTAGAACTAGACACTT
*
586675 GTATCGGTAGAACT-G-TACTT
1 GTATCGGTAGAACTAGACACTT
*
586695 GTATCGTTAGAA
1 GTATCGGTAGAA
586707 TTCTGCACTA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
20 16 0.36
21 28 0.64
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.31
Consensus pattern (22 bp):
GTATCGGTAGAACTAGACACTT
Found at i:589610 original size:18 final size:19
Alignment explanation
Indices: 589578--589614 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
589568 CCTAAAAAAT
*
589578 TAAAAATTAATTAAACAAA
1 TAAAAATTAAATAAACAAA
589597 TAAAAA-TAAATAAACAAA
1 TAAAAATTAAATAAACAAA
589615 ATTAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (19 bp):
TAAAAATTAAATAAACAAA
Found at i:591146 original size:50 final size:50
Alignment explanation
Indices: 591040--591134 Score: 172
Period size: 50 Copynumber: 1.9 Consensus size: 50
591030 TGCTTCTATT
*
591040 GATACTAAAAACTCTAAAGAGCTAAGACATTTAATCCTGTAACTTCTACC
1 GATACTAAAAACTCCAAAGAGCTAAGACATTTAATCCTGTAACTTCTACC
*
591090 GATACTAAAAACTCCAAAGAGCTAAGACATTTTATCCTGTAACTT
1 GATACTAAAAACTCCAAAGAGCTAAGACATTTAATCCTGTAACTT
591135 TTGTCGATAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (50 bp):
GATACTAAAAACTCCAAAGAGCTAAGACATTTAATCCTGTAACTTCTACC
Found at i:600373 original size:16 final size:16
Alignment explanation
Indices: 600352--600382 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
600342 TTCAAAACTT
600352 ATAAAAATAATATAAA
1 ATAAAAATAATATAAA
*
600368 ATAAAATTAATATAA
1 ATAAAAATAATATAA
600383 TTAATCATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
ATAAAAATAATATAAA
Done.