Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004691.1 Kokia drynarioides strain JFW-HI SEQ_118249, 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: 35950
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 47 characters in sequence are not A, C, G, or T
Found at i:12217 original size:11 final size:11
Alignment explanation
Indices: 12153--12217 Score: 53
Period size: 11 Copynumber: 5.9 Consensus size: 11
12143 ATATTGTTAT
12153 TTTTG-TGCTG
1 TTTTGTTGCTG
* *
12163 TTTTTTTACTG
1 TTTTGTTGCTG
*
12174 TTTTAG-TGTTG
1 TTTT-GTTGCTG
12185 TTTTGGTTGCTG
1 TTTT-GTTGCTG
*
12197 TTTGGTTGCTG
1 TTTTGTTGCTG
*
12208 TTTTGATGCT
1 TTTTGTTGCT
12218 ATTATTTTTG
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
10 4 0.10
11 31 0.74
12 7 0.17
ACGTcount: A:0.05, C:0.08, G:0.26, T:0.62
Consensus pattern (11 bp):
TTTTGTTGCTG
Found at i:12252 original size:24 final size:24
Alignment explanation
Indices: 12145--12278 Score: 89
Period size: 24 Copynumber: 5.7 Consensus size: 24
12135 AAAAATATAT
*
12145 ATTGTTATTTTTG-TGCTGTTTT-
1 ATTGCTATTTTTGTTGCTGTTTTG
* * * * *
12167 TTTACTGTTTTAG-TGTTGTTTTG
1 ATTGCTATTTTTGTTGCTGTTTTG
* * *
12190 GTTGCT-GTTTGGTTGCTGTTTTG
1 ATTGCTATTTTTGTTGCTGTTTTG
*
12213 A-TGCTATTATTTTTGTTGCTGTTTTT
1 ATTGC---TATTTTTGTTGCTGTTTTG
*
12239 ATTGCTATTTTTGTTGTTGTTTTG
1 ATTGCTATTTTTGTTGCTGTTTTG
* *
12263 ATTGTTATTTTGGTTG
1 ATTGCTATTTTTGTTG
12279 TTTGGATGTT
Statistics
Matches: 86, Mismatches: 19, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
22 23 0.27
23 13 0.15
24 31 0.36
25 1 0.01
26 15 0.17
27 3 0.03
ACGTcount: A:0.08, C:0.05, G:0.22, T:0.64
Consensus pattern (24 bp):
ATTGCTATTTTTGTTGCTGTTTTG
Found at i:12288 original size:20 final size:21
Alignment explanation
Indices: 12254--12293 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
12244 TATTTTTGTT
*
12254 GTTGTTTTGATTGTTATTTTG
1 GTTGTTTGGATTGTTATTTTG
12275 GTTGTTTGGA-TGTTATTTT
1 GTTGTTTGGATTGTTATTTT
12294 TATGCATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.10, C:0.00, G:0.25, T:0.65
Consensus pattern (21 bp):
GTTGTTTGGATTGTTATTTTG
Found at i:12294 original size:21 final size:23
Alignment explanation
Indices: 12219--12294 Score: 68
Period size: 24 Copynumber: 3.3 Consensus size: 23
12209 TTTGATGCTA
* **
12219 TTATTTTTGTTGCTGTTTTTATTG
1 TTATTTTTG-TGTTGTTTGGATTG
* *
12243 CTATTTTTGTTGTTGTTTTGATTG
1 TTATTTTTG-TGTTGTTTGGATTG
12267 TTA-TTTTG-GTTGTTTGGA-TG
1 TTATTTTTGTGTTGTTTGGATTG
12287 TTATTTTT
1 TTATTTTT
12295 ATGCATTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.11
21 13 0.28
23 5 0.11
24 23 0.50
ACGTcount: A:0.09, C:0.03, G:0.20, T:0.68
Consensus pattern (23 bp):
TTATTTTTGTGTTGTTTGGATTG
Found at i:12491 original size:38 final size:38
Alignment explanation
Indices: 12409--12493 Score: 93
Period size: 38 Copynumber: 2.2 Consensus size: 38
12399 ATATAAAGAA
* * * *
12409 TTTTTAATGTATTTTAAATTTGTTTATTTTTTAATGTT
1 TTTTTAATGTATTTTAAATTTATTTATATATTAATGAT
12447 TATTTTAATGT-TTTTAAATTTATTTGATATATTATAT-AT
1 T-TTTTAATGTATTTTAAATTTATTT-ATATATTA-ATGAT
12486 TTTTTAAT
1 TTTTTAAT
12494 TTGTTGTATA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
38 21 0.52
39 17 0.43
40 2 0.05
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (38 bp):
TTTTTAATGTATTTTAAATTTATTTATATATTAATGAT
Found at i:15372 original size:21 final size:21
Alignment explanation
Indices: 15328--15372 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
15318 AATGATATTT
* ** *
15328 TTTAAATTTTATTTTTTATTA
1 TTTAAATTTTATTATAGATAA
15349 TTTAAATTTTATTATAGATAA
1 TTTAAATTTTATTATAGATAA
15370 TTT
1 TTT
15373 TTGAAAATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTAAATTTTATTATAGATAA
Found at i:16025 original size:31 final size:31
Alignment explanation
Indices: 15981--16043 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
15971 TCCTTAAATC
* *
15981 TCTTTATGCAACAAATTGCTCTTTCAACTAT
1 TCTTTATACAACAAATTACTCTTTCAACTAT
* * *
16012 TCTTTATATAACAATTTACTGTTTCAACTAT
1 TCTTTATACAACAAATTACTCTTTCAACTAT
16043 T
1 T
16044 GCATAAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.46
Consensus pattern (31 bp):
TCTTTATACAACAAATTACTCTTTCAACTAT
Found at i:16617 original size:26 final size:26
Alignment explanation
Indices: 16588--16644 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
16578 TTTTTTTATA
*
16588 ATTTAATGAAATTTT-CATATTTTTCT
1 ATTTAATG-AATTTTAAATATTTTTCT
* *
16614 ATTTTATGAATTTTAAATATTTTTTT
1 ATTTAATGAATTTTAAATATTTTTCT
16640 ATTTA
1 ATTTA
16645 TAATGTATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 6 0.23
26 20 0.77
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.61
Consensus pattern (26 bp):
ATTTAATGAATTTTAAATATTTTTCT
Found at i:16727 original size:17 final size:17
Alignment explanation
Indices: 16700--16733 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
16690 TTTTTTTCCA
16700 ATAAATTTTAAT-CTTT
1 ATAAATTTTAATACTTT
16716 ATAAATTTTTAATACTTT
1 ATAAA-TTTTAATACTTT
16734 TCGGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 7 0.44
18 4 0.25
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
ATAAATTTTAATACTTT
Found at i:28831 original size:3 final size:3
Alignment explanation
Indices: 28823--28898 Score: 152
Period size: 3 Copynumber: 25.3 Consensus size: 3
28813 AGTTTTTAGG
28823 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28871 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
28899 ATAAAGCTTG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:30287 original size:20 final size:20
Alignment explanation
Indices: 30262--30316 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
30252 ACGTGGCACT
30262 ATTATTTTAAAATTATTAAA
1 ATTATTTTAAAATTATTAAA
30282 ATTATTTTTTAAAA-TA-TAAA
1 ATTA--TTTTAAAATTATTAAA
30302 ATTA--TTAAAATTATT
1 ATTATTTTAAAATTATT
30317 TTTTTGAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
16 6 0.19
17 2 0.06
18 1 0.03
20 12 0.39
21 2 0.06
22 8 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTATTTTAAAATTATTAAA
Found at i:30302 original size:29 final size:31
Alignment explanation
Indices: 30269--30341 Score: 123
Period size: 29 Copynumber: 2.4 Consensus size: 31
30259 ACTATTATTT
30269 TAAAATTATTAAAATTA-TTTTTTAAAAT-A
1 TAAAATTATTAAAATTATTTTTTTAAAATAA
*
30298 TAAAATTATTAAAATTATTTTTTTGAAATAA
1 TAAAATTATTAAAATTATTTTTTTAAAATAA
30329 TAAAATTATTAAA
1 TAAAATTATTAAA
30342 TAATTTTAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 17 0.41
30 10 0.24
31 14 0.34
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (31 bp):
TAAAATTATTAAAATTATTTTTTTAAAATAA
Found at i:30308 original size:23 final size:23
Alignment explanation
Indices: 30261--30308 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 23
30251 GACGTGGCAC
*
30261 TATTATTTTAAAATTATTAAAAT
1 TATTATTTTAAAATTATAAAAAT
30284 TATT-TTTTAAAA-TAT-AAAAT
1 TATTATTTTAAAATTATAAAAAT
30304 TATTA
1 TATTA
30309 AAATTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 8 0.33
23 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TATTATTTTAAAATTATAAAAAT
Found at i:30348 original size:30 final size:29
Alignment explanation
Indices: 30269--30348 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 29
30259 ACTATTATTT
*
30269 TAAAATTATTAAA-ATTATTTTTTAAAATA
1 TAAAATTATTAAATAAT-TTTTTTAAAATA
* *
30298 TAAAATTATTAAAATTATTTTTTTGAAATAA
1 TAAAATTATT-AAATAATTTTTTTAAAAT-A
30329 TAAAATTATTAAATAATTTT
1 TAAAATTATTAAATAATTTT
30349 AATTTTCAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
29 10 0.23
30 22 0.50
31 12 0.27
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (29 bp):
TAAAATTATTAAATAATTTTTTTAAAATA
Found at i:31574 original size:29 final size:30
Alignment explanation
Indices: 31517--31592 Score: 111
Period size: 29 Copynumber: 2.5 Consensus size: 30
31507 ATTGAAAATT
*
31517 AAAATTATTTAATAATTTTATTATTTTTAA
1 AAAATAATTTAATAATTTTATTATTTTTAA
31547 AAAATAATGTTAATAATTTTA-TA-TTTTAA
1 AAAATAAT-TTAATAATTTTATTATTTTTAA
31576 AAAATAATTTTAATAAT
1 AAAATAA-TTTAATAAT
31593 ATTAAAATCA
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
29 21 0.49
30 10 0.23
31 12 0.28
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (30 bp):
AAAATAATTTAATAATTTTATTATTTTTAA
Found at i:33248 original size:23 final size:22
Alignment explanation
Indices: 33212--33266 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
33202 ATAAAAGAAG
* *
33212 TTTAGTTTTATTTA-GACTTTACT
1 TTTA-TTTTATTTACCACTGTA-T
33235 TTTATTTTATTTTACCACTGTAT
1 TTTATTTTA-TTTACCACTGTAT
33258 TTTATTTTA
1 TTTATTTTA
33267 ACAAGAATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 5 0.18
23 18 0.64
24 5 0.18
ACGTcount: A:0.22, C:0.09, G:0.05, T:0.64
Consensus pattern (22 bp):
TTTATTTTATTTACCACTGTAT
Done.