Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000599.1 Kokia drynarioides strain JFW-HI SEQ_111537, 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: 50464
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Warning! 43 characters in sequence are not A, C, G, or T
Found at i:624 original size:29 final size:29
Alignment explanation
Indices: 583--873 Score: 285
Period size: 29 Copynumber: 9.8 Consensus size: 29
573 GAAAGACCCT
**
583 AAACTATCCAAAAATTTCATTTTTACCCCC
1 AAACT-TCCAAAAATCCCATTTTTACCCCC
* * *
613 AAACTTCTAAAAATCACATTTTTTACCCCG
1 AAACTTCCAAAAATCCCA-TTTTTACCCCC
*
643 AAACTATCCAAAAATTCCATTTTTTACCCCC
1 AAACT-TCCAAAAATCCCA-TTTTTACCCCC
* * *
674 GAACTTCCAAAAATCCCATTTTTAACCTCG
1 AAACTTCCAAAAATCCCATTTTT-ACCCCC
** *
704 AAACTTCCAAAAATTTCATTTTTACCCTC
1 AAACTTCCAAAAATCCCATTTTTACCCCC
* * * * *
733 GAACTTCCAAAAATCACATTTTTGATCTCG
1 AAACTTCCAAAAATCCCATTTTT-ACCCCC
*
763 AAACTTCCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATCCCATTTTTACCCCC
* * ***
792 GAACTTCCAAAAATCCCATTTTGACCTTA
1 AAACTTCCAAAAATCCCATTTTTACCCCC
**
821 AAACTTCCAAAAATTTCATTTTTACCCCC
1 AAACTTCCAAAAATCCCATTTTTACCCCC
* *
850 GAACTTCAAAAAATCCCATTTTTA
1 AAACTTCCAAAAATCCCATTTTTA
874 ACTCCGAATT
Statistics
Matches: 209, Mismatches: 48, Indels: 9
0.79 0.18 0.03
Matches are distributed among these distances:
29 106 0.51
30 78 0.37
31 25 0.12
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATCCCATTTTTACCCCC
Found at i:745 original size:59 final size:59
Alignment explanation
Indices: 583--875 Score: 417
Period size: 59 Copynumber: 4.9 Consensus size: 59
573 GAAAGACCCT
* * * * *
583 AAACTATCCAAAAATTTCATTTTTACCCCCAAACTTCTAAAAATCACATTTTTTACCCCG
1 AAACT-TCCAAAAATTTCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCG
*
643 AAACTATCCAAAAATTCCATTTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCG
1 AAACT-TCCAAAAATTTCA-TTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCG
* * * *
704 AAACTTCCAAAAATTTCATTTTTACCCTCGAACTTCCAAAAATCACATTTTTGATCTCG
1 AAACTTCCAAAAATTTCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCG
* * **
763 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCA-TTTTGACCTTA
1 AAACTTCCAAAAATTTCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCG
*
821 AAACTTCCAAAAATTTCATTTTTACCCCCGAACTTCAAAAAATCCCATTTTTAAC
1 AAACTTCCAAAAATTTCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAAC
876 TCCGAATTTT
Statistics
Matches: 211, Mismatches: 20, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
58 53 0.25
59 87 0.41
60 30 0.14
61 41 0.19
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (59 bp):
AAACTTCCAAAAATTTCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCG
Found at i:2549 original size:31 final size:31
Alignment explanation
Indices: 2512--2576 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
2502 AACAACCAAG
* *
2512 TGACTTAAATAAAAACTTTT-GAATAGTTTAA
1 TGACTTAAATAAAAA-TTTTAAAATAATTTAA
*
2543 TGACTTATATAAAAATTTTAAAATAATTTAA
1 TGACTTAAATAAAAATTTTAAAATAATTTAA
2574 TGA
1 TGA
2577 TTATTTTGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.48, C:0.05, G:0.08, T:0.40
Consensus pattern (31 bp):
TGACTTAAATAAAAATTTTAAAATAATTTAA
Found at i:6589 original size:3 final size:3
Alignment explanation
Indices: 6581--6612 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
6571 TCATAATCAT
6581 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
6613 TTGTTTGGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:9281 original size:25 final size:25
Alignment explanation
Indices: 9253--9301 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
9243 TATAAATCAA
*
9253 ATTTA-TTATTTATTTCATAAATTTT
1 ATTTATTTATATATTTCA-AAATTTT
*
9278 ATTTATTTATATATTTTAAAATTT
1 ATTTATTTATATATTTCAAAATTT
9302 ATTAATGGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (25 bp):
ATTTATTTATATATTTCAAAATTTT
Found at i:9295 original size:17 final size:18
Alignment explanation
Indices: 9258--9295 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
9248 ATCAAATTTA
9258 TTATTTATTTCATAAATT
1 TTATTTATTTCATAAATT
*
9276 TTATTTATTT-ATATATT
1 TTATTTATTTCATAAATT
9293 TTA
1 TTA
9296 AAATTTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (18 bp):
TTATTTATTTCATAAATT
Found at i:19689 original size:177 final size:176
Alignment explanation
Indices: 19392--19730 Score: 493
Period size: 177 Copynumber: 1.9 Consensus size: 176
19382 GGGAAGTGAT
*
19392 GCTTATTATTGAAGAAAAGTTAACAAAATAAAAACAAAAAAAAATCATTATTTGTATATGTTTGT
1 GCTTATTATTAAAGAAAAGTTAACAAAATAAAAAC--AAAAAAATCATTATTTGTATATGTTTGT
* *
19457 ATTTAGGATGTGTTGCATTTGATTCTAATAGGTCTCATGATTTGATCACTTTGAAGTGGTTAATT
64 ATTAAAGATGTGTTGCATTTGATTCTAATAGGTCTCATGATTTGATCACTTTGAAGTGGTTAATT
*
19522 CCCTATGATTAGATCAGCTCTGAGAGTGTGTTCTCAAACTTTTATAAA
129 CCCTATGATTAGATCACCTCTGAGAGTGTGTTCTCAAACTTTTATAAA
* ** * * *
19570 GCTTATTATTAAAGCAAAGTTGGCAAAATGAAAAC-AAAAAGTCCTTATTTGTATAGATGTTTGT
1 GCTTATTATTAAAGAAAAGTTAACAAAATAAAAACAAAAAAATCATTATTTGTAT--ATGTTTGT
* * *
19634 ATTAAAGATG-GATTGCATTTGATTCTAATAGGTCTCATGGTTTTATCACTTTGAAGTGGTTCAT
64 ATTAAAGATGTG-TTGCATTTGATTCTAATAGGTCTCATGATTTGATCACTTTGAAGTGGTTAAT
*
19698 TCCCTATGATTGGATCACCTCTGAGAGTGTGTT
128 TCCCTATGATTAGATCACCTCTGAGAGTGTGTT
19731 TCTTAGACTT
Statistics
Matches: 144, Mismatches: 14, Indels: 7
0.87 0.08 0.04
Matches are distributed among these distances:
175 17 0.12
176 1 0.01
177 96 0.67
178 30 0.21
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (176 bp):
GCTTATTATTAAAGAAAAGTTAACAAAATAAAAACAAAAAAATCATTATTTGTATATGTTTGTAT
TAAAGATGTGTTGCATTTGATTCTAATAGGTCTCATGATTTGATCACTTTGAAGTGGTTAATTCC
CTATGATTAGATCACCTCTGAGAGTGTGTTCTCAAACTTTTATAAA
Found at i:28040 original size:13 final size:13
Alignment explanation
Indices: 28014--28043 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
28004 AAAGTATAAT
28014 AAAATATTTAAAA
1 AAAATATTTAAAA
28027 AAAATCATTTAAAA
1 AAAAT-ATTTAAAA
28041 AAA
1 AAA
28044 GAGATGTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (13 bp):
AAAATATTTAAAA
Found at i:28424 original size:18 final size:18
Alignment explanation
Indices: 28403--28437 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28393 AATTAATTAA
* *
28403 AATAATAATAATAATATC
1 AATAAGAATAAAAATATC
28421 AATAAGAATAAAAATAT
1 AATAAGAATAAAAATAT
28438 TTATCAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (18 bp):
AATAAGAATAAAAATATC
Found at i:37818 original size:18 final size:20
Alignment explanation
Indices: 37785--37825 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
37775 TCATTTATGG
*
37785 TTTTTATTAATTAAAATA-C
1 TTTTTATTAATAAAAATATC
37804 TTTTTATTAA-AAAAATATC
1 TTTTTATTAATAAAAATATC
37823 TTT
1 TTT
37826 GCCATATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTTATTAATAAAAATATC
Found at i:37980 original size:15 final size:16
Alignment explanation
Indices: 37950--37989 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
37940 ATAAAAATAT
37950 ATAATTTCATTATTTTG
1 ATAATTT-ATTATTTTG
*
37967 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTG
37982 ATAATTTA
1 ATAATTTA
37990 AAAAATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.64
16 1 0.05
17 7 0.32
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (16 bp):
ATAATTTATTATTTTG
Found at i:38021 original size:27 final size:27
Alignment explanation
Indices: 37967--38047 Score: 74
Period size: 27 Copynumber: 3.0 Consensus size: 27
37957 CATTATTTTG
* * * **
37967 ATAATTTATATTTTTATAATTTAAAAA
1 ATAAATTAAATTTTTATTATTTTTAAA
37994 ATAAATTAAATTTTTATTATTTTTAAA
1 ATAAATTAAATTTTTATTATTTTTAAA
* *
38021 ATTAAAATATAA-TTTTATTATTATTAA
1 A-TAAATTA-AATTTTTATTATTTTTAA
38048 TTTAAAATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
27 23 0.51
28 20 0.44
29 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
ATAAATTAAATTTTTATTATTTTTAAA
Found at i:38021 original size:28 final size:28
Alignment explanation
Indices: 37967--38047 Score: 76
Period size: 28 Copynumber: 2.9 Consensus size: 28
37957 CATTATTTTG
* * * *
37967 ATAATTTATATTTTTA-TAATTTAAAAA
1 ATAAATTAAATTTTTATTATTTTTAAAA
37994 ATAAATTAAATTTTTATTATTTTTAAAA
1 ATAAATTAAATTTTTATTATTTTTAAAA
* * *
38022 TTAAAATATAA-TTTTATTATTATTAA
1 ATAAATTA-AATTTTTATTATTTTTAA
38048 TTTAAAATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
27 14 0.31
28 29 0.64
29 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
ATAAATTAAATTTTTATTATTTTTAAAA
Found at i:43880 original size:37 final size:39
Alignment explanation
Indices: 43825--43897 Score: 116
Period size: 37 Copynumber: 1.9 Consensus size: 39
43815 ATCGAGACAC
43825 CTTTTTATATATTATTAAGCATTGTT-AAGTTGAGTCAA
1 CTTTTTATATATTATTAAGCATTGTTAAAGTTGAGTCAA
43863 CTTTTT-TATATCT-TTAAGCATTGTTAAAGTTGAGT
1 CTTTTTATATAT-TATTAAGCATTGTTAAAGTTGAGT
43898 AAAAATGACA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
37 17 0.52
38 16 0.48
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.49
Consensus pattern (39 bp):
CTTTTTATATATTATTAAGCATTGTTAAAGTTGAGTCAA
Found at i:45814 original size:50 final size:49
Alignment explanation
Indices: 45739--45835 Score: 142
Period size: 50 Copynumber: 1.9 Consensus size: 49
45729 GTCAGACAGA
*
45739 CGTGTGTCCAGGCTGTGTAACTCACTGTTTCTG-TATTAAGGCCACANGGG
1 CGTGTGTCCAAGCTGTGTAACTCACTGTTT-TGATATTAAGGCCACA-GGG
*
45789 CGTGTGTTCAAGCTGTGTAACTCACTGTTTTGAATATTAAGGCCACA
1 CGTGTGTCCAAGCTGTGTAACTCACTGTTTTG-ATATTAAGGCCACA
45836 CGGTTGACAC
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
49 2 0.05
50 28 0.65
51 13 0.30
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (49 bp):
CGTGTGTCCAAGCTGTGTAACTCACTGTTTTGATATTAAGGCCACAGGG
Found at i:47152 original size:7 final size:7
Alignment explanation
Indices: 47153--47189 Score: 58
Period size: 7 Copynumber: 5.3 Consensus size: 7
47143 CTTACCCCTT
47153 CCCTTTC
1 CCCTTTC
47160 TCCC-TTC
1 -CCCTTTC
47167 CCCTTTC
1 CCCTTTC
47174 CCCTTTC
1 CCCTTTC
47181 CCCTTTC
1 CCCTTTC
47188 CC
1 CC
47190 TTCTATTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 3 0.11
7 22 0.79
8 3 0.11
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (7 bp):
CCCTTTC
Found at i:47172 original size:14 final size:13
Alignment explanation
Indices: 47142--47189 Score: 62
Period size: 14 Copynumber: 3.6 Consensus size: 13
47132 TTTTTTGTTA
*
47142 CCTTACCCCTT-C
1 CCTTTCCCCTTCC
47154 CCTTTCTCCCTTCC
1 CCTTTC-CCCTTCC
47168 CCTTTCCCCTTTCC
1 CCTTTCCCC-TTCC
47182 CCTTTCCC
1 CCTTTCCC
47190 TTCTATTTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 5 0.16
13 8 0.25
14 19 0.59
ACGTcount: A:0.02, C:0.58, G:0.00, T:0.40
Consensus pattern (13 bp):
CCTTTCCCCTTCC
Found at i:49323 original size:22 final size:23
Alignment explanation
Indices: 49275--49332 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 23
49265 TTTCTCACCT
*
49275 TGTGTGCCTACTGATTTGCGCTA
1 TGTGTGCCTACTGATTTGCACTA
* * *
49298 TGTGCGCCTACTGA-TTGCATTG
1 TGTGTGCCTACTGATTTGCACTA
*
49320 TGTGTGCTTACTG
1 TGTGTGCCTACTG
49333 TTTCCCCAGC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
22 16 0.55
23 13 0.45
ACGTcount: A:0.12, C:0.21, G:0.28, T:0.40
Consensus pattern (23 bp):
TGTGTGCCTACTGATTTGCACTA
Found at i:50398 original size:33 final size:33
Alignment explanation
Indices: 50361--50427 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
50351 AAAGTGACAA
50361 AACCACCAAATGTTAGGGACTAATTTTGAACTT
1 AACCACCAAATGTTAGGGACTAATTTTGAACTT
50394 AACCACCAAATGTTAGGGACTAATTTTGAACTT
1 AACCACCAAATGTTAGGGACTAATTTTGAACTT
50427 A
1 A
50428 TGCCATTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (33 bp):
AACCACCAAATGTTAGGGACTAATTTTGAACTT
Done.