Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004693.1 Kokia drynarioides strain JFW-HI SEQ_118251, 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: 56398
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:719 original size:23 final size:23
Alignment explanation
Indices: 669--723 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
659 TATGCGTGTT
* *
669 CATATTTGTTTAATTTGTATGAA
1 CATATTTATTTAATTTGAATGAA
*
692 TATATTTATTTAATTT-AATCGAA
1 CATATTTATTTAATTTGAAT-GAA
715 CATATTTAT
1 CATATTTAT
724 AAACTCAAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 2 0.07
23 25 0.93
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.53
Consensus pattern (23 bp):
CATATTTATTTAATTTGAATGAA
Found at i:912 original size:68 final size:69
Alignment explanation
Indices: 812--943 Score: 221
Period size: 68 Copynumber: 1.9 Consensus size: 69
802 GTGATGCTAC
*
812 GTGTGCTAAAGATTATAGATATTGGTAATTCTACGTTAACAGGGAAAAATAGAGTTTTGCATGTC
1 GTGTGCTAAAGATTATAGATATCGGTAATTCTACGTTAACAGGGAAAAATAGAGTTTTGCATGTC
877 TAAT
66 TAAT
* * *
881 GTGTGCT-AGGATTATATATATCGGTATTTCTACGTTAACAGGGAAAAATAGAGTTTTGCATGT
1 GTGTGCTAAAGATTATAGATATCGGTAATTCTACGTTAACAGGGAAAAATAGAGTTTTGCATGT
944 TCCTACTATT
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
68 52 0.88
69 7 0.12
ACGTcount: A:0.33, C:0.09, G:0.23, T:0.36
Consensus pattern (69 bp):
GTGTGCTAAAGATTATAGATATCGGTAATTCTACGTTAACAGGGAAAAATAGAGTTTTGCATGTC
TAAT
Found at i:3854 original size:45 final size:45
Alignment explanation
Indices: 3790--3881 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
3780 CTCTCAATTT
**
3790 TGTAAAAATAAATTGAGCCATGATGTGACCAAAATTTATGATAGC
1 TGTAAAAATAAATTGAGCCATGAACTGACCAAAATTTATGATAGC
* *
3835 TGTAAAAATAAATTGAGCCATGAACTGTCCAAATTTTATGATAGC
1 TGTAAAAATAAATTGAGCCATGAACTGACCAAAATTTATGATAGC
3880 TG
1 TG
3882 AAGAAAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.30
Consensus pattern (45 bp):
TGTAAAAATAAATTGAGCCATGAACTGACCAAAATTTATGATAGC
Found at i:3968 original size:50 final size:50
Alignment explanation
Indices: 3910--4011 Score: 177
Period size: 50 Copynumber: 2.0 Consensus size: 50
3900 TCAAGAGTCT
**
3910 TGGCAAGTATTATATCAATATAATAGAACCTAAATTTAAGTGTACTAAAA
1 TGGCAAGTATTATATCAATATAATAGAACCTAAATTTAAGTACACTAAAA
*
3960 TGGCAAGTATTATATCAATATAATAGAACGTAAATTTAAGTACACTAAAA
1 TGGCAAGTATTATATCAATATAATAGAACCTAAATTTAAGTACACTAAAA
4010 TG
1 TG
4012 TATAATAACA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31
Consensus pattern (50 bp):
TGGCAAGTATTATATCAATATAATAGAACCTAAATTTAAGTACACTAAAA
Found at i:5390 original size:66 final size:65
Alignment explanation
Indices: 5314--5543 Score: 176
Period size: 66 Copynumber: 3.5 Consensus size: 65
5304 AGCTGTCACG
* * * *
5314 TCCTTCGCTTCCTTCGCTTTTTCAGCTGCATAGTCTTTATACTCGGTCGCTTTTTCAACTGTGGT
1 TCCTTTGCTTCCTTAGCTTTTTCAGCTGCATAGTCTTTATACTCGGTCGCTTTTGC-ACTGTCGT
5379 A
65 A
* * * * * ** * *
5380 TCTTTTGCTTCCCTAGCTTTCTGC-GCTGCATAGTCTGTAAACTCGGAAGCCTTCTGCGCTGTCG
1 TCCTTTGCTTCCTTAGCTTT-TTCAGCTGCATAGTCTTTATACTCGGTCG-CTTTTGCACTGTCG
5444 TA
64 TA
* * * * * * * *
5446 TCCTTTGCTCCCTTGGCTTTCTCAGCTGCATAGTCCTTATATTCAGTCGCTTTTCCCATTG-CAG
1 TCCTTTGCTTCCTTAGCTTTTTCAGCTGCATAGTCTTTATACTCGGTCGCTTTT-GCACTGTC-G
*
5510 CA
64 TA
* **
5512 TCCTTTGCATCCTTAGCTTTTTGTGCTGCATA
1 TCCTTTGCTTCCTTAGCTTTTTCAGCTGCATA
5544 ATCTGTACAC
Statistics
Matches: 122, Mismatches: 37, Indels: 10
0.72 0.22 0.06
Matches are distributed among these distances:
65 6 0.05
66 109 0.89
67 7 0.06
ACGTcount: A:0.13, C:0.29, G:0.17, T:0.41
Consensus pattern (65 bp):
TCCTTTGCTTCCTTAGCTTTTTCAGCTGCATAGTCTTTATACTCGGTCGCTTTTGCACTGTCGTA
Found at i:5465 original size:132 final size:132
Alignment explanation
Indices: 5314--5731 Score: 437
Period size: 132 Copynumber: 3.2 Consensus size: 132
5304 AGCTGTCACG
* * * * * * * * * * * *
5314 TCCTTCGCTTCCTTCGCTTTTTCAGCTGCATAGTCTTTATACTCGGTCGCTTTTTCAACTGTGGT
1 TCCTTTGCTCCCTTGGCTTTCTCAGCTGCATAGTCATTATATTCAGTCGCTTTTCCCATTGTAGC
* * * * * *
5379 ATCTTTTGCTTCCCTAGCTTTCTGCGCTGCATAGTCTGTAAACTCGGAAGCCTTCTGCGCTGTCG
66 ATCCTTTGCATCCTTAGCTTTCTGTGCTGCATAGTCTGTAAACTCAGAAGCCTTTTGCGCTGTCG
5444 TA
131 TA
* *
5446 TCCTTTGCTCCCTTGGCTTTCTCAGCTGCATAGTCCTTATATTCAGTCGCTTTTCCCATTGCAGC
1 TCCTTTGCTCCCTTGGCTTTCTCAGCTGCATAGTCATTATATTCAGTCGCTTTTCCCATTGTAGC
* * * * *
5511 ATCCTTTGCATCCTTAGCTTTTTGTGCTGCATAATCTGTACACTCAGAAGCCTTTTGGGCTGTGG
66 ATCCTTTGCATCCTTAGCTTTCTGTGCTGCATAGTCTGTAAACTCAGAAGCCTTTTGCGCTGTCG
5576 TA
131 TA
** * * *
5578 T-CTCTTGC-CTCCTTGGCTTTCTGGGCTGTATAATCATTATATTCAGTCGCTTTCCCCATTGTA
1 TCCT-TTGCTC-CCTTGGCTTTCTCAGCTGCATAGTCATTATATTCAGTCGCTTTTCCCATTGTA
* * * * *
5641 GCATCCTTTGCATCCTTAGTTTTCTGTGCTGCATAGTCTGTATACTCTGATGCCTTTTGTGCTGT
64 GCATCCTTTGCATCCTTAGCTTTCTGTGCTGCATAGTCTGTAAACTCAGAAGCCTTTTGCGCTGT
* *
5706 GGTG
129 CGTA
* *
5710 TCTTTTGCGT-CCTTAGCTTTCT
1 TCCTTTGC-TCCCTTGGCTTTCT
5732 GGGCAGCATA
Statistics
Matches: 240, Mismatches: 41, Indels: 10
0.82 0.14 0.03
Matches are distributed among these distances:
131 3 0.01
132 236 0.98
133 1 0.00
ACGTcount: A:0.13, C:0.27, G:0.19, T:0.42
Consensus pattern (132 bp):
TCCTTTGCTCCCTTGGCTTTCTCAGCTGCATAGTCATTATATTCAGTCGCTTTTCCCATTGTAGC
ATCCTTTGCATCCTTAGCTTTCTGTGCTGCATAGTCTGTAAACTCAGAAGCCTTTTGCGCTGTCG
TA
Found at i:5732 original size:132 final size:131
Alignment explanation
Indices: 5383--5742 Score: 443
Period size: 132 Copynumber: 2.7 Consensus size: 131
5373 TGTGGTATCT
* * * * * * *
5383 TTTGCTTCCCTAGCTTTCTGCGCTGCATAGTCTGTAAACTCGGAAGCCTTCTGCGCTGTCGTATC
1 TTTGCATCCTTAGTTTTCTGTGCTGCATAGTCTGTAAACTCAGAAGCCTTTTGCGCTGTGGTATC
* ** * * *
5448 CTTTGCTCCCTTGGCTTTCTCAGCTGCATAGTCCTTATATTCAGTCGCTTTTCCCATTGCAGCAT
66 TTTTGCT-CCTTGGCTTTCTGGGCTGCATAATCATTATATTCAGTCGCTTTCCCCATTGCAGCAT
5513 CC
130 CC
* * *
5515 TTTGCATCCTTAGCTTTT-TGTGCTGCATAATCTGTACACTCAGAAGCCTTTTGGGCTGTGGTAT
1 TTTGCATCCTTAG-TTTTCTGTGCTGCATAGTCTGTAAACTCAGAAGCCTTTTGCGCTGTGGTAT
* * *
5579 CTCTTGCCTCCTTGGCTTTCTGGGCTGTATAATCATTATATTCAGTCGCTTTCCCCATTGTAGCA
65 CTTTTG-CTCCTTGGCTTTCTGGGCTGCATAATCATTATATTCAGTCGCTTTCCCCATTGCAGCA
5644 TCC
129 TCC
* * * * *
5647 TTTGCATCCTTAGTTTTCTGTGCTGCATAGTCTGTATACTCTGATGCCTTTTGTGCTGTGGTGTC
1 TTTGCATCCTTAGTTTTCTGTGCTGCATAGTCTGTAAACTCAGAAGCCTTTTGCGCTGTGGTATC
* *
5712 TTTTGCGTCCTTAGCTTTCTGGGCAGCATAA
66 TTTTGC-TCCTTGGCTTTCTGGGCTGCATAA
5743 CCGGTATACT
Statistics
Matches: 195, Mismatches: 29, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
131 5 0.03
132 185 0.95
133 5 0.03
ACGTcount: A:0.14, C:0.26, G:0.20, T:0.40
Consensus pattern (131 bp):
TTTGCATCCTTAGTTTTCTGTGCTGCATAGTCTGTAAACTCAGAAGCCTTTTGCGCTGTGGTATC
TTTTGCTCCTTGGCTTTCTGGGCTGCATAATCATTATATTCAGTCGCTTTCCCCATTGCAGCATC
C
Found at i:7602 original size:14 final size:13
Alignment explanation
Indices: 7582--7630 Score: 57
Period size: 14 Copynumber: 3.8 Consensus size: 13
7572 TCAACTTGAC
7582 TATTAAAAAATTA
1 TATTAAAAAATTA
7595 TAATTAAAAAA-TA
1 T-ATTAAAAAATTA
*
7608 T-TTAAAAAATAA
1 TATTAAAAAATTA
7620 TATTATAAAAA
1 TATTA-AAAAA
7631 CAAAACAACT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
11 8 0.26
12 2 0.06
13 7 0.23
14 14 0.45
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
TATTAAAAAATTA
Found at i:13112 original size:3 final size:3
Alignment explanation
Indices: 13104--13130 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
13094 TTCTTACCAT
13104 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
13131 ACAACTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:20947 original size:27 final size:26
Alignment explanation
Indices: 20902--20968 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
20892 CTAAAAATGT
*
20902 CTTTAAAAAGTTACTAAATATAATTTCA
1 CTTTAAAAA--TAATAAATATAATTTCA
* * *
20930 TTTTATAAAATAATAAATATTATTTTA
1 CTTTA-AAAATAATAAATATAATTTCA
20957 CTTTAAAAATAA
1 CTTTAAAAATAA
20969 ATTTATTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
26 7 0.21
27 18 0.55
28 4 0.12
29 4 0.12
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.43
Consensus pattern (26 bp):
CTTTAAAAATAATAAATATAATTTCA
Found at i:20973 original size:17 final size:17
Alignment explanation
Indices: 20953--20986 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
20943 TAAATATTAT
20953 TTTACTTTA-AAAATAAA
1 TTTA-TTTATAAAATAAA
20970 TTTATTTATAAAATAAA
1 TTTATTTATAAAATAAA
20987 AAATTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTATTTATAAAATAAA
Found at i:27184 original size:15 final size:16
Alignment explanation
Indices: 27150--27204 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
27140 CTTTTACTTT
27150 CTTTCTTTTCTTCTTC
1 CTTTCTTTTCTTCTTC
*
27166 CTTTCTTTT-TTCTTG
1 CTTTCTTTTCTTCTTC
*
27181 CTTTCTTTACTAT-TTC
1 CTTTCTTTTCT-TCTTC
27197 CTTTCTTT
1 CTTTCTTT
27205 AAAAAATGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
15 13 0.38
16 20 0.59
17 1 0.03
ACGTcount: A:0.04, C:0.25, G:0.02, T:0.69
Consensus pattern (16 bp):
CTTTCTTTTCTTCTTC
Found at i:27188 original size:31 final size:31
Alignment explanation
Indices: 27141--27204 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
27131 GCCACCAACC
* *
27141 TTTTACTTTCTTTCTTTTCT-TCTTCCTTTCT
1 TTTTACTTGCTTTCTTTACTAT-TTCCTTTCT
*
27172 TTTTTCTTGCTTTCTTTACTATTTCCTTTCT
1 TTTTACTTGCTTTCTTTACTATTTCCTTTCT
27203 TT
1 TT
27205 AAAAAATGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 28 0.97
32 1 0.03
ACGTcount: A:0.05, C:0.23, G:0.02, T:0.70
Consensus pattern (31 bp):
TTTTACTTGCTTTCTTTACTATTTCCTTTCT
Found at i:28367 original size:131 final size:133
Alignment explanation
Indices: 28145--28394 Score: 314
Period size: 132 Copynumber: 1.9 Consensus size: 133
28135 TATTTTTTAG
* *
28145 CCATTAGAATAAATAGGGTTATAAATGTCATTTTAATTTAATCTTATATTTTCATTTTTAATATT
1 CCATTAAAATAAATAGGGTTATAAATGTCATTTTAATTTAATCTTATATTTTCA-TTTTAAGATT
*
28210 TTTAAAGGAAGTAAATAGAGTTAGTTTAG-TCT-TTAAAATAGAGACAAAATATTAAATATAATA
65 TTTAAAGAAAGTAAATAGAGTTAGTTT-GTTCTCTTAAAATAGAGACAAAATATTAAATATAATA
28273 TAAAA
129 TAAAA
* * *
28278 CCATTAAAATAAATAGGG-TATAAATGTTATTTTAGTTTAATTTTATATTTATC-TTTTAAGATT
1 CCATTAAAATAAATAGGGTTATAAATGTCATTTTAATTTAATCTTATATTT-TCATTTTAAGATT
* * * * *
28341 TTTGAAGAAAGT--ATACGTGATTAGTTTGTTTTCTTAAAATATAGATAAAATATT
65 TTTAAAGAAAGTAAATA-GAG-TTAGTTTGTTCTCTTAAAATAGAGACAAAATATT
28395 TAAAACTTAA
Statistics
Matches: 101, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
129 3 0.03
130 3 0.03
131 28 0.28
132 48 0.48
133 19 0.19
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (133 bp):
CCATTAAAATAAATAGGGTTATAAATGTCATTTTAATTTAATCTTATATTTTCATTTTAAGATTT
TTAAAGAAAGTAAATAGAGTTAGTTTGTTCTCTTAAAATAGAGACAAAATATTAAATATAATATA
AAA
Found at i:28779 original size:25 final size:25
Alignment explanation
Indices: 28751--28800 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
28741 AAAACGAACA
*
28751 ATATTCTTAATTTAAATAA-AATATT
1 ATATT-TTAATTTAAACAACAATATT
28776 ATATTTTAATTTAAACAACAATATT
1 ATATTTTAATTTAAACAACAATATT
28801 CTATAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (25 bp):
ATATTTTAATTTAAACAACAATATT
Found at i:48604 original size:5 final size:5
Alignment explanation
Indices: 48590--48619 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
48580 TAATTATTAT
*
48590 TAAAA TAAAA AAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
48620 AGGTGTGTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
TAAAA
Found at i:51946 original size:3 final size:3
Alignment explanation
Indices: 51938--51973 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
51928 ATTCTATTTT
51938 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
51974 GTCAGCACCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:55501 original size:79 final size:78
Alignment explanation
Indices: 55372--55573 Score: 233
Period size: 80 Copynumber: 2.5 Consensus size: 78
55362 TGACTAGAGC
* * * * * *
55372 TGGGCTCACTTTCGTGGTTTATTCGCTAAGCACTGGGTGCTAGGATTTGATGGACTTTTGTTAGT
1 TGGGCTCACTTT-GCGGTTTATCCGCTAGGCACTGGGTGCCAAGAATTGATGGA-TTTTGTTAGT
*
55437 TCATCCAACTAGAAT
64 TAATCCAACTAGAAT
* * *
55452 TGGGCTTACTTTGCGGTTTATCCGCTAGGTACTGGGTGCCAAGAATTGATGGATTTTGTTGGTTA
1 TGGGCTCACTTTGCGGTTTATCCGCTAGGCACTGGGTGCCAAGAATTGATGGATTTTGTTAGTTA
*
55517 ATCCAACTAGAGT
66 ATCCAACTAGAAT
* * * *
55530 TGGGCTCACTTATTGCAGTTTATCCACTAGACACTGGGTACCAA
1 TGGGCTCAC-T-TTGCGGTTTATCCGCTAGGCACTGGGTGCCAA
55574 AATCGTCGGT
Statistics
Matches: 103, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
78 30 0.29
79 35 0.34
80 38 0.37
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.35
Consensus pattern (78 bp):
TGGGCTCACTTTGCGGTTTATCCGCTAGGCACTGGGTGCCAAGAATTGATGGATTTTGTTAGTTA
ATCCAACTAGAAT
Done.