Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002717.1 Kokia drynarioides strain JFW-HI SEQ_115012, 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: 36969
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:300 original size:55 final size:55
Alignment explanation
Indices: 230--338 Score: 191
Period size: 55 Copynumber: 2.0 Consensus size: 55
220 GTGTATGTTG
*
230 ATGATTTAAATATCATTAAGACTCCTGAAGAAAATTTAGTGATAATGGAGTGCTA
1 ATGATTTAAATATCATTAAGACTCCTAAAGAAAATTTAGTGATAATGGAGTGCTA
* *
285 ATGATTTAAATATCATTAAGACTGCTAAAGAGAATTTAGTGATAATGGAGTGCT
1 ATGATTTAAATATCATTAAGACTCCTAAAGAAAATTTAGTGATAATGGAGTGCT
339 TAAAGAAAGA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.33
Consensus pattern (55 bp):
ATGATTTAAATATCATTAAGACTCCTAAAGAAAATTTAGTGATAATGGAGTGCTA
Found at i:1216 original size:17 final size:17
Alignment explanation
Indices: 1196--1236 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
1186 TCCTTTGACG
1196 TTTAACCTTCCATATTC
1 TTTAACCTTCCATATTC
*
1213 TTTAACCTTTCATATTC
1 TTTAACCTTCCATATTC
1230 TTGTAAC
1 TT-TAAC
1237 TACTTTGTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.24, C:0.24, G:0.02, T:0.49
Consensus pattern (17 bp):
TTTAACCTTCCATATTC
Found at i:12185 original size:27 final size:27
Alignment explanation
Indices: 12140--12192 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
12130 ATTGTCAGTT
* * * *
12140 GTGTTCGCTAGTGTGTTTGGCGAGCTG
1 GTGTTCGCCAATGTATTTGGAGAGCTG
12167 GTGTTCGCCAATGTATTTGGAGAGCT
1 GTGTTCGCCAATGTATTTGGAGAGCT
12193 AGGATTCACT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.13, C:0.15, G:0.36, T:0.36
Consensus pattern (27 bp):
GTGTTCGCCAATGTATTTGGAGAGCTG
Found at i:19283 original size:25 final size:25
Alignment explanation
Indices: 19247--19297 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
19237 TGTAATTCAA
19247 AGAACAAGAATAAAGTGAAAGAATG
1 AGAACAAGAATAAAGTGAAAGAATG
* *
19272 AGAACAATAATAAATTGAAAGAATG
1 AGAACAAGAATAAAGTGAAAGAATG
19297 A
1 A
19298 AAAATGATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.61, C:0.04, G:0.20, T:0.16
Consensus pattern (25 bp):
AGAACAAGAATAAAGTGAAAGAATG
Found at i:22314 original size:21 final size:21
Alignment explanation
Indices: 22288--22341 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
22278 GAGTCACAGA
* *
22288 ATTCCACACCTGAATCGCCGG
1 ATTCCACACCCGAATCACCGG
*
22309 ATTCCACACCCGAATCACCTG
1 ATTCCACACCCGAATCACCGG
*
22330 ATTCCATACCCG
1 ATTCCACACCCG
22342 CGGCACCTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.26, C:0.41, G:0.13, T:0.20
Consensus pattern (21 bp):
ATTCCACACCCGAATCACCGG
Found at i:23794 original size:13 final size:13
Alignment explanation
Indices: 23755--23796 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
23745 ACACATTTAC
*
23755 AATTTGATAGAATA
1 AATTTGATATAA-A
23769 AATTT-AT-TAAA
1 AATTTGATATAAA
23780 AATTTGATATAAA
1 AATTTGATATAAA
23793 AATT
1 AATT
23797 AAATATGACT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 6 0.24
12 4 0.16
13 10 0.40
14 5 0.20
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.40
Consensus pattern (13 bp):
AATTTGATATAAA
Found at i:24567 original size:3 final size:3
Alignment explanation
Indices: 24559--24583 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
24549 AACTCGTTCA
24559 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
24584 TAATATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:28734 original size:21 final size:21
Alignment explanation
Indices: 28701--28752 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
28691 GGAGTTTTTA
*
28701 GTATCGGTAGAAG-CATGACAT
1 GTATCGATAGAAGTCAT-ACAT
* *
28722 GTTTCGATAGAAGTCATACTT
1 GTATCGATAGAAGTCATACAT
28743 GTATCGATAG
1 GTATCGATAG
28753 TATTGTCTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (21 bp):
GTATCGATAGAAGTCATACAT
Found at i:29605 original size:42 final size:42
Alignment explanation
Indices: 29557--29654 Score: 137
Period size: 42 Copynumber: 2.3 Consensus size: 42
29547 CCGAGTAATA
*
29557 AGTCTTCCTTTAATCATATTGTCATTCTCATCCCT-AGACAT-
1 AGTCTTCCTTTAATCATATTCTCATTCTCAT-CCTGAGACATG
* *
29598 AGGTCTTCCTTTGATCATATTCTCATTCTCATCTTGAGACATG
1 A-GTCTTCCTTTAATCATATTCTCATTCTCATCCTGAGACATG
29641 AGTCTTCCTTTAAT
1 AGTCTTCCTTTAAT
29655 AAATCATCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
41 3 0.06
42 46 0.92
43 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.10, T:0.43
Consensus pattern (42 bp):
AGTCTTCCTTTAATCATATTCTCATTCTCATCCTGAGACATG
Found at i:30257 original size:23 final size:23
Alignment explanation
Indices: 30214--30260 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
30204 AAATTTATCT
* *
30214 TTTAAATTTAAATTTGCTTTAAA
1 TTTAAATTTAAATTGGATTTAAA
30237 TTTAAATTTAAA-TGGAATTTAAA
1 TTTAAATTTAAATTGG-ATTTAAA
30260 T
1 T
30261 GGATTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 19 0.90
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (23 bp):
TTTAAATTTAAATTGGATTTAAA
Found at i:30268 original size:10 final size:11
Alignment explanation
Indices: 30241--30269 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
30231 TTTAAATTTA
30241 AATTTAAATGG
1 AATTTAAATGG
30252 AATTTAAATGG
1 AATTTAAATGG
30263 -ATTTAAA
1 AATTTAAA
30270 ACTTTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (11 bp):
AATTTAAATGG
Found at i:30303 original size:47 final size:46
Alignment explanation
Indices: 30252--30340 Score: 169
Period size: 47 Copynumber: 1.9 Consensus size: 46
30242 ATTTAAATGG
30252 AATTTAAATGGATTTAAAACTTTTAAAAGTCCAATGTCGCAAATTTA
1 AATTTAAATGGATTTAAAACTTTTAAAAGTCCAATGTC-CAAATTTA
30299 AATTTAAATGGATTTAAAACTTTTAAAAGTCCAATGTCCAAA
1 AATTTAAATGGATTTAAAACTTTTAAAAGTCCAATGTCCAAA
30341 GTCCATTTAC
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 4 0.10
47 38 0.90
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.35
Consensus pattern (46 bp):
AATTTAAATGGATTTAAAACTTTTAAAAGTCCAATGTCCAAATTTA
Found at i:31028 original size:13 final size:13
Alignment explanation
Indices: 30995--31033 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
30985 GTTGATAACT
*
30995 GTATTAAAAATTA
1 GTATTAATAATTA
*
31008 TTATTAATAATTA
1 GTATTAATAATTA
*
31021 GTATTAATTATTA
1 GTATTAATAATTA
31034 ATAAAAAGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (13 bp):
GTATTAATAATTA
Found at i:32316 original size:30 final size:28
Alignment explanation
Indices: 32251--32611 Score: 292
Period size: 30 Copynumber: 12.5 Consensus size: 28
32241 GGAGGTGCCT
*
32251 AAACTATCCAAAAATTCCATTTTTACCCCT
1 AAACT-TCCAAAAA-TCCATTTTTACCCCA
* *
32281 GAACTTCTAAAAATCCTATTTTTGACCCCA
1 AAACTTCCAAAAATCC-ATTTTT-ACCCCA
*
32311 AAAC-T-------TCCATTTTTACCCCT
1 AAACTTCCAAAAATCCATTTTTACCCCA
32331 AAACTTCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAAT-CCATTTTT-ACCCCA
32361 AAACTTCCAAAAATTCCATTTTTACCCTC-
1 AAACTTCCAAAAA-TCCATTTTTACCC-CA
* * *
32390 GAACTTCCAAAAATCCCATTTTTGACCTCG
1 AAACTTCCAAAAAT-CCATTTTT-ACCCCA
*
32420 AAACTTCCAAAAATTCCATTTTTATCCTC-
1 AAACTTCCAAAAA-TCCATTTTTA-CCCCA
* ** *
32449 GAACTTCCAAAAATCCCATTTTTAACATCG
1 AAACTTCCAAAAAT-CCATTTTT-ACCCCA
* *
32479 AAACTTCTAAAAATTCCATTTTTACCCCCC
1 AAACTTCCAAAAA-TCCATTTTTA-CCCCA
* *
32509 GAACTTCCAAAAATCCCATTTTTGACCCTA
1 AAACTTCCAAAAAT-CCATTTTT-ACCCCA
*
32539 AAACTTCCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAA-TCCATTTTTACCCCA
* *
32568 GAGCTTCCAAAAATCCCATTTTTAACCCCA
1 AAACTTCCAAAAAT-CCATTTTT-ACCCCA
32598 AAACTTCCAAAAAT
1 AAACTTCCAAAAAT
32612 TATCATTTTA
Statistics
Matches: 274, Mismatches: 28, Indels: 58
0.76 0.08 0.16
Matches are distributed among these distances:
20 9 0.03
21 7 0.03
22 3 0.01
28 7 0.03
29 96 0.35
30 147 0.54
31 5 0.02
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (28 bp):
AAACTTCCAAAAATCCATTTTTACCCCA
Found at i:32319 original size:50 final size:50
Alignment explanation
Indices: 32258--32369 Score: 188
Period size: 50 Copynumber: 2.2 Consensus size: 50
32248 CCTAAACTAT
* * * *
32258 CCAAAAATTCCATTTTTACCCCTGAACTTCTAAAAATCCTATTTTTGACC
1 CCAAAACTTCCATTTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACC
32308 CCAAAACTTCCATTTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACC
1 CCAAAACTTCCATTTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACC
32358 CCAAAACTTCCA
1 CCAAAACTTCCA
32370 AAAATTCCAT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 58 1.00
ACGTcount: A:0.33, C:0.32, G:0.03, T:0.32
Consensus pattern (50 bp):
CCAAAACTTCCATTTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACC
Found at i:32322 original size:21 final size:20
Alignment explanation
Indices: 32298--32339 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
32288 TAAAAATCCT
32298 ATTTTTGACCCCAAAACTTCC
1 ATTTTT-ACCCCAAAACTTCC
*
32319 ATTTTTACCCCTAAACTTCC
1 ATTTTTACCCCAAAACTTCC
32339 A
1 A
32340 AAAATCCCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.29, C:0.33, G:0.02, T:0.36
Consensus pattern (20 bp):
ATTTTTACCCCAAAACTTCC
Found at i:32400 original size:59 final size:59
Alignment explanation
Indices: 32308--32627 Score: 462
Period size: 59 Copynumber: 5.4 Consensus size: 59
32298 ATTTTTGACC
* **
32308 CCAAAACTTCCATTTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTT
1 CCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTT
* * *
32367 CCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCGAAACTT
1 CCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTT
* * * ** *
32426 CCAAAAATTCCATTTTTATCCTCGAACTTCCAAAAATCCCATTTTTAACATCGAAACTT
1 CCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTT
* *
32485 CTAAAAATTCCATTTTTACCCCCCGAACTTCCAAAAATCCCATTTTTGACCCTAAAACTT
1 CCAAAAATTCCATTTTTA-CCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTT
* *
32545 CCAAAAATTCCATTTTTACCCCCGAGCTTCCAAAAATCCCATTTTTAACCCCAAAACTT
1 CCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTT
*
32604 CCAAAAATTATCA-TTTTACCCCCG
1 CCAAAAATT-CCATTTTTACCCCCG
32628 GATGTCCGAA
Statistics
Matches: 237, Mismatches: 22, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
59 184 0.78
60 53 0.22
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (59 bp):
CCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTT
Found at i:32625 original size:29 final size:29
Alignment explanation
Indices: 32308--32611 Score: 324
Period size: 30 Copynumber: 10.3 Consensus size: 29
32298 ATTTTTGACC
* * *
32308 CCAAAACTTCCATTTTTACCCCTAAACTT
1 CCAAAAATCCCATTTTTACCCCAAAACTT
32337 CCAAAAATCCCATTTTTGACCCCAAAACTT
1 CCAAAAATCCCATTTTT-ACCCCAAAACTT
* *
32367 CCAAAAATTCCATTTTTACCCTC-GAACTT
1 CCAAAAATCCCATTTTTACCC-CAAAACTT
* *
32396 CCAAAAATCCCATTTTTGACCTCGAAACTT
1 CCAAAAATCCCATTTTT-ACCCCAAAACTT
* * *
32426 CCAAAAATTCCATTTTTATCCTC-GAACTT
1 CCAAAAATCCCATTTTTA-CCCCAAAACTT
** *
32455 CCAAAAATCCCATTTTTAACATCGAAACTT
1 CCAAAAATCCCATTTTT-ACCCCAAAACTT
* * **
32485 CTAAAAATTCCATTTTTACCCCCCGAACTT
1 CCAAAAATCCCATTTTTA-CCCCAAAACTT
*
32515 CCAAAAATCCCATTTTTGACCCTAAAACTT
1 CCAAAAATCCCATTTTT-ACCCCAAAACTT
* ** *
32545 CCAAAAATTCCATTTTTACCCCCGAGCTT
1 CCAAAAATCCCATTTTTACCCCAAAACTT
32574 CCAAAAATCCCATTTTTAACCCCAAAACTT
1 CCAAAAATCCCATTTTT-ACCCCAAAACTT
32604 CCAAAAAT
1 CCAAAAAT
32612 TATCATTTTA
Statistics
Matches: 232, Mismatches: 33, Indels: 19
0.82 0.12 0.07
Matches are distributed among these distances:
29 91 0.39
30 140 0.60
31 1 0.00
ACGTcount: A:0.35, C:0.31, G:0.03, T:0.31
Consensus pattern (29 bp):
CCAAAAATCCCATTTTTACCCCAAAACTT
Done.