Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007876.1 Kokia drynarioides strain JFW-HI SEQ_122517, 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: 9304
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:8 original size:3 final size:3
Alignment explanation
Indices: 1--132 Score: 63
Period size: 3 Copynumber: 42.7 Consensus size: 3
** * * *
1 TAA TAA TAA TTT TAA TAA TAA CAA TAA TAG TAA TAA TAA TAAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
* * * ** **
47 TTA TAA -AA T-C TAA TAAA TAC TTT TGC TAA TAA TAAA TAGA TTAA TTAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA T-AA TA-A -TAA -TAA
*
95 TAA TAA TAA TAA TAA TAA TAA TAA -ATA TAA TAT TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA
133 CAAAAAAAGA
Statistics
Matches: 97, Mismatches: 23, Indels: 18
0.70 0.17 0.13
Matches are distributed among these distances:
2 4 0.04
3 75 0.77
4 16 0.16
5 2 0.02
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1218 original size:30 final size:32
Alignment explanation
Indices: 1182--1264 Score: 102
Period size: 30 Copynumber: 2.7 Consensus size: 32
1172 CTCTAAGCTG
1182 TCCAAAAATTACATTTTTACCCT-TAAA-CTT
1 TCCAAAAATTACATTTTTACCCTCTAAATCTT
* * *
1212 TCCAAAAA-TCCATTTTTTA-TCTCTAAATTTT
1 TCCAAAAATTACA-TTTTTACCCTCTAAATCTT
1243 TCCAAAAATTACATTTTTACCC
1 TCCAAAAATTACATTTTTACCC
1265 CCGAACTTCT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
29 5 0.12
30 18 0.42
31 16 0.37
32 4 0.09
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (32 bp):
TCCAAAAATTACATTTTTACCCTCTAAATCTT
Found at i:1286 original size:29 final size:29
Alignment explanation
Indices: 1246--1426 Score: 104
Period size: 29 Copynumber: 6.2 Consensus size: 29
1236 AAATTTTTCC
*
1246 AAAAATTACATTTTTACCCCCGAACTTCT
1 AAAAATTCCATTTTTACCCCCGAACTTCT
* *
1275 AAAAATTCCATTTTTGA-TCCCG-ATTTCTT
1 AAAAATTCCATTTTT-ACCCCCGAACTTC-T
* * * * *
1304 CGAAAATTACCA-TTTTACCCCTGTATTTCC
1 -AAAAATT-CCATTTTTACCCCCGAACTTCT
* * * *
1334 AACAATTCCATTTTTTA-TCCCGATCTTTCC
1 AAAAATTCCA-TTTTTACCCCCGAAC-TTCT
*
1364 AAAAATTACCA-TTTTACCCCCGGA-TGTCT
1 AAAAATT-CCATTTTTACCCCCGAACT-TCT
* * *
1393 AAAAATTCCGTTTTAAACCCCGAACTTCT
1 AAAAATTCCATTTTTACCCCCGAACTTCT
1422 AAAAA
1 AAAAA
1427 ATCACCATTT
Statistics
Matches: 115, Mismatches: 23, Indels: 28
0.69 0.14 0.17
Matches are distributed among these distances:
28 10 0.09
29 60 0.52
30 34 0.30
31 11 0.10
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.36
Consensus pattern (29 bp):
AAAAATTCCATTTTTACCCCCGAACTTCT
Found at i:1341 original size:59 final size:59
Alignment explanation
Indices: 1182--1385 Score: 191
Period size: 59 Copynumber: 3.4 Consensus size: 59
1172 CTCTAAGCTG
*** * ** *
1182 TCCAAAAATTA-CATTTTTACCCTTAAACTTTCCAAAAA-TCCATTTTTTATCTCTAAATTTT
1 TCCAAAAATTACCA-TTTTACCCCCGAAC-TTCCAAAAATTCCATTTTTGATC-C-CGATCTT
*
1243 TCCAAAAATTA-CATTTTTACCCCCGAACTTCTAAAAATTCCATTTTTGATCCCGAT-TT
1 TCCAAAAATTACCA-TTTTACCCCCGAACTTCCAAAAATTCCATTTTTGATCCCGATCTT
* * * * * * *
1301 CTTCGAAAATTACCATTTTACCCCTGTATTTCCAACAATTCCATTTTTTATCCCGATCTT
1 -TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGATCCCGATCTT
1361 TCCAAAAATTACCATTTTACCCCCG
1 TCCAAAAATTACCATTTTACCCCCG
1386 GATGTCTAAA
Statistics
Matches: 121, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
58 2 0.02
59 69 0.57
60 13 0.11
61 37 0.31
ACGTcount: A:0.30, C:0.26, G:0.03, T:0.40
Consensus pattern (59 bp):
TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGATCCCGATCTT
Found at i:1363 original size:30 final size:30
Alignment explanation
Indices: 1209--1378 Score: 111
Period size: 30 Copynumber: 5.7 Consensus size: 30
1199 TACCCTTAAA
**
1209 CTTTCCAAAAA-TCCATTTTTTATCTCTAAAT
1 CTTTCCAAAAATTCCATTTTTTATC-C-CGAT
* * * *
1240 TTTTCCAAAAATTACA-TTTTTACCCCCGAA
1 CTTTCCAAAAATTCCATTTTTTA-TCCCGAT
* *
1270 C-TTCTAAAAATTCCATTTTTGATCCCGAT
1 CTTTCCAAAAATTCCATTTTTTATCCCGAT
* * *
1299 -TTCTTCGAAAATTACCA--TTTTACCCCTG-T
1 CTT-TCCAAAAATT-CCATTTTTTATCCC-GAT
* *
1328 ATTTCCAACAATTCCATTTTTTATCCCGAT
1 CTTTCCAAAAATTCCATTTTTTATCCCGAT
1358 CTTTCCAAAAATTACCATTTT
1 CTTTCCAAAAATT-CCATTTT
1379 ACCCCCGGAT
Statistics
Matches: 104, Mismatches: 23, Indels: 24
0.69 0.15 0.16
Matches are distributed among these distances:
28 3 0.03
29 34 0.33
30 36 0.35
31 27 0.26
32 4 0.04
ACGTcount: A:0.29, C:0.25, G:0.04, T:0.42
Consensus pattern (30 bp):
CTTTCCAAAAATTCCATTTTTTATCCCGAT
Found at i:1400 original size:59 final size:59
Alignment explanation
Indices: 1241--1503 Score: 218
Period size: 59 Copynumber: 4.5 Consensus size: 59
1231 TCTCTAAATT
*
1241 TTTCCAAAAATTA-CATTTTTACCCCCGAACT-TCTAAAAATTCCATTTTTGATCCCGAT-
1 TTTCCAAAAATTACCA-TTTTACCCCCGGA-TGTCTAAAAATTCCATTTTTGATCCCGATC
* * * * * * * *
1299 TTCTTCGAAAATTACCATTTTACCCCTGTATTTCCAACAATTCCATTTTTTATCCCGATC
1 TT-TCCAAAAATTACCATTTTACCCCCGGATGTCTAAAAATTCCATTTTTGATCCCGATC
* ** * *
1359 TTTCCAAAAATTACCATTTTACCCCCGGATGTCTAAAAATTCCGTTTTAAACCCCGAAC
1 TTTCCAAAAATTACCATTTTACCCCCGGATGTCTAAAAATTCCATTTTTGATCCCGATC
* * * * *
1418 -TTCTAAAAAATCACCATTTTACTCCCGGGTGTCT-AAAATTCTATTTTTGA-CCC-ATAAC
1 TTTC-CAAAAATTACCATTTTACCCCCGGATGTCTAAAAATTCCATTTTTGATCCCGAT--C
* *
1476 TTTTTC-AAAATTACCATTTCACCCCCGG
1 -TTTCCAAAAATTACCATTTTACCCCCGG
1504 GTATCCAAAA
Statistics
Matches: 163, Mismatches: 33, Indels: 18
0.76 0.15 0.08
Matches are distributed among these distances:
56 1 0.01
57 3 0.02
58 38 0.23
59 115 0.71
60 6 0.04
ACGTcount: A:0.29, C:0.27, G:0.07, T:0.37
Consensus pattern (59 bp):
TTTCCAAAAATTACCATTTTACCCCCGGATGTCTAAAAATTCCATTTTTGATCCCGATC
Found at i:1428 original size:118 final size:119
Alignment explanation
Indices: 1210--1439 Score: 272
Period size: 118 Copynumber: 1.9 Consensus size: 119
1200 ACCCTTAAAC
*
1210 TTTCCAAAAATCCATTTTTTATCTCTAAATTTTTCCAAAAATTACATTTTTACCCCCGAACTTCT
1 TTTCCAAAAATCCATTTTTTATCTCTAAATCTTTCCAAAAATTACATTTTTACCCCCGAACTTCT
** * * ** *
1275 AAAAATTCCATTTTTGATCCCGATTTCTTCGAAAATTACCATTTTACCCCTGTA
66 AAAAATTCCATTTTAAACCCCGACTTCTTAAAAAATCACCATTTTACCCCTGTA
* ** *
1329 TTTCCAACAATTCCATTTTTTATC-C-CGATCTTTCCAAAAATTACCA-TTTTACCCCCGGA-TG
1 TTTCCAA-AAATCCATTTTTTATCTCTAAATCTTTCCAAAAATTA-CATTTTTACCCCCGAACT-
*
1390 TCTAAAAATTCCGTTTTAAACCCCGAACTTC-TAAAAAATCACCATTTTAC
63 TCTAAAAATTCCATTTTAAACCCCG-ACTTCTTAAAAAATCACCATTTTAC
1440 TCCCGGGTGT
Statistics
Matches: 94, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
117 1 0.01
118 64 0.68
119 14 0.15
120 15 0.16
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.38
Consensus pattern (119 bp):
TTTCCAAAAATCCATTTTTTATCTCTAAATCTTTCCAAAAATTACATTTTTACCCCCGAACTTCT
AAAAATTCCATTTTAAACCCCGACTTCTTAAAAAATCACCATTTTACCCCTGTA
Found at i:1492 original size:58 final size:59
Alignment explanation
Indices: 1364--1523 Score: 162
Period size: 58 Copynumber: 2.7 Consensus size: 59
1354 CGATCTTTCC
* * *
1364 AAAAATTACCATTTTACCCCCGGATGTCTAAAAATTCCGTTTTAAACCCCGAACTTCTA
1 AAAAATTACCATTTTACCCCCGGGTGTCTAAAAATTCCATTTTAAACCCAGAACTTCTA
* * * ** * * *
1423 AAAAATCACCATTTTACTCCCGGGTGTCT-AAAATTCTATTTTTGACCCATAACTTTTT
1 AAAAATTACCATTTTACCCCCGGGTGTCTAAAAATTCCATTTTAAACCCAGAACTTCTA
* * * *
1481 CAAAATTACCATTTCACCCCCGGGTATCCAAAAA-TCACATTTT
1 AAAAATTACCATTTTACCCCCGGGTGTCTAAAAATTC-CATTTT
1524 CATCTCCGAT
Statistics
Matches: 81, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
58 46 0.57
59 35 0.43
ACGTcount: A:0.33, C:0.26, G:0.08, T:0.33
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCCCGGGTGTCTAAAAATTCCATTTTAAACCCAGAACTTCTA
Found at i:2969 original size:17 final size:18
Alignment explanation
Indices: 2949--2991 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
2939 TTCGAAATCG
* *
2949 AATTTAATTCTAT-TTTT
1 AATTTAATTATATAATTT
2966 AATTTAA-TATATAATTT
1 AATTTAATTATATAATTT
2983 AATTTAATT
1 AATTTAATT
2992 TTTATTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 4 0.18
17 17 0.77
18 1 0.05
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
AATTTAATTATATAATTT
Found at i:3580 original size:10 final size:10
Alignment explanation
Indices: 3565--3598 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
3555 ACACGTGTTT
3565 TTTATTATTA
1 TTTATTATTA
3575 TTTATTATTA
1 TTTATTATTA
3585 TTT-TTATATA
1 TTTATTAT-TA
3595 TTTA
1 TTTA
3599 AAAATAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTATTATTA
Found at i:3927 original size:4 final size:4
Alignment explanation
Indices: 3918--3983 Score: 71
Period size: 4 Copynumber: 16.2 Consensus size: 4
3908 AAATAAACGG
* * *
3918 GAAA GAAA GAAA GAAAA GAAA GAAA GAAA GGAA GAAG GAGA GAAAA GAAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA GAAA
*
3968 G-AA GAAG GAAA GAAA G
1 GAAA GAAA GAAA GAAA G
3984 GTAATGTGTT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
3 3 0.06
4 41 0.80
5 7 0.14
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:3940 original size:17 final size:19
Alignment explanation
Indices: 3917--3983 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 19
3907 CAAATAAACG
3917 GGAAAGAAAGAAAGAA-AA
1 GGAAAGAAAGAAAGAAGAA
3935 -GAAAGAAAGAAAGGAAGAA
1 GGAAAGAAAGAAA-GAAGAA
*
3954 GGAGAGAAAAGAAAGAAGAA
1 GGAAAG-AAAGAAAGAAGAA
3974 GGAAAGAAAG
1 GGAAAGAAAG
3984 GTAATGTGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
17 12 0.28
18 3 0.07
19 6 0.14
20 15 0.35
21 7 0.16
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (19 bp):
GGAAAGAAAGAAAGAAGAA
Found at i:3984 original size:29 final size:31
Alignment explanation
Indices: 3917--3984 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 31
3907 CAAATAAACG
3917 GGAAAGAAA-GAAAGAAAAGAAAGAAAGAAA
1 GGAAAGAAAGGAAAGAAAAGAAAGAAAGAAA
*
3947 GG-AAG-AAGGAGAGAAAAGAAAG-AAG-AA
1 GGAAAGAAAGGAAAGAAAAGAAAGAAAGAAA
3974 GGAAAGAAAGG
1 GGAAAGAAAGG
3985 TAATGTGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
27 4 0.12
28 8 0.24
29 20 0.59
30 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (31 bp):
GGAAAGAAAGGAAAGAAAAGAAAGAAAGAAA
Found at i:7096 original size:28 final size:28
Alignment explanation
Indices: 7064--7123 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
7054 CAATTTAGCA
*
7064 TTTACGGTTTA-GAGTTTCAAGTCTAGTG
1 TTTACGGTTTATG-GTTTCAAGTCTAGGG
*
7092 TTTACGGTTTATGGTTTCAAGTGTAGGG
1 TTTACGGTTTATGGTTTCAAGTCTAGGG
7120 TTTA
1 TTTA
7124 TAATTTAGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.20, C:0.08, G:0.27, T:0.45
Consensus pattern (28 bp):
TTTACGGTTTATGGTTTCAAGTCTAGGG
Found at i:7391 original size:21 final size:21
Alignment explanation
Indices: 7365--7407 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
7355 TAGGGTCCAT
*
7365 TTGCCCCGGAGGAGTAGAGTA
1 TTGCCCCGGAGGAATAGAGTA
*
7386 TTGCCCGGGAGGAATAGAGTA
1 TTGCCCCGGAGGAATAGAGTA
7407 T
1 T
7408 CACGGTGGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.16, G:0.37, T:0.21
Consensus pattern (21 bp):
TTGCCCCGGAGGAATAGAGTA
Found at i:7468 original size:45 final size:45
Alignment explanation
Indices: 7412--7538 Score: 141
Period size: 45 Copynumber: 2.8 Consensus size: 45
7402 GAGTATCACG
* *
7412 GTGGCTTGTCAAACTCAGCCTGATATCCTT-CCTTTGAGTATTGCA
1 GTGGCTCGTCAAACTGAGCCTGATATCCTTGCC-TTGAGTATTGCA
* * *
7457 GTGGCTCGTCAAATTGAGGCC-GATATCCTTGGCTTGAGTATTGCG
1 GTGGCTCGTCAAACTGA-GCCTGATATCCTTGCCTTGAGTATTGCA
* ** *
7502 GTGGCTCGTAAAACTGAGGTTGATATCCTTGGCTTGA
1 GTGGCTCGTCAAACTGAGCCTGATATCCTTGCCTTGA
7539 TGAGCTATGC
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
44 1 0.01
45 65 0.93
46 4 0.06
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (45 bp):
GTGGCTCGTCAAACTGAGCCTGATATCCTTGCCTTGAGTATTGCA
Done.