Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015245.1 Kokia drynarioides strain JFW-HI SEQ_130290, 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: 767229
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 115 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:695214 original size:103 final size:103
Alignment explanation
Indices: 695027--695261 Score: 319
Period size: 103 Copynumber: 2.3 Consensus size: 103
695017 TGTTTAAAAG
* * * *
695027 GGTCTGATGACTATGTGTCATCGTGAGTATATGAATCATTTACGGATTATGAGGTATAATGACTA
1 GGTCCGATGACTATGTGTCATCATGAGTATATGAATCA-TTACGAATTATAAGGTATAATGACTA
* * ***
695092 TGTTTCATTGTGAGTATATGAATTCTTTACGGGTTATGA
65 TGTATCATTGTGAGTATATGAATCCTTTACAAATTATGA
* * *
695131 GGTCCGTTGACTATGTGTCATCATGAGTATATGAATTC-TTACGAATTATAAGGTCTGATGACTA
1 GGTCCGATGACTATGTGTCATCATGAGTATATGAA-TCATTACGAATTATAAGGTATAATGACTA
695195 TGTATCATTGTGAGTATATGAATCCTTTACAAATTATGA
65 TGTATCATTGTGAGTATATGAATCCTTTACAAATTATGA
**
695234 GGTTTGATGACTATGTGTCATCATGAGT
1 GGTCCGATGACTATGTGTCATCATGAGT
695262 GTTAAATGAA
Statistics
Matches: 115, Mismatches: 15, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
103 81 0.70
104 32 0.28
105 2 0.02
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.39
Consensus pattern (103 bp):
GGTCCGATGACTATGTGTCATCATGAGTATATGAATCATTACGAATTATAAGGTATAATGACTAT
GTATCATTGTGAGTATATGAATCCTTTACAAATTATGA
Found at i:696030 original size:21 final size:21
Alignment explanation
Indices: 695997--696049 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
695987 GAGTTTTCAG
* *
695997 TATCGGTACAAGCATTACTTA
1 TATCGGTAGAAGCATGACTTA
* *
696018 TATCAGTAGAAGCATGACTTG
1 TATCGGTAGAAGCATGACTTA
696039 TATCGGTAGAA
1 TATCGGTAGAA
696050 CTTACTCAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (21 bp):
TATCGGTAGAAGCATGACTTA
Found at i:698970 original size:2 final size:2
Alignment explanation
Indices: 698950--698986 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
698940 CAACATTTAT
*
698950 TA TA TA -A TA -A TA TA CA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
698987 TTCTTTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:699581 original size:3 final size:3
Alignment explanation
Indices: 699573--699614 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
699563 GTCGGGACAA
*
699573 CTT CTT CTT CTT CTT CTT CTT CTT CTT TTT CCTT C-T CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT -CTT CTT CTT CTT
699615 TTCCTTTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.89
4 2 0.06
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:699615 original size:15 final size:14
Alignment explanation
Indices: 699573--699648 Score: 66
Period size: 15 Copynumber: 5.3 Consensus size: 14
699563 GTCGGGACAA
*
699573 CTTCTTCTTCTTCTT
1 CTTC-TCTTCTTTTT
699588 CTTCTTCTTCTTTTT
1 CTTC-TCTTCTTTTT
*
699603 CCTTCTCTTCTTTTC
1 -CTTCTCTTCTTTTT
699618 CTT-T-TTCTTTTAT
1 CTTCTCTTCTTTT-T
* *
699631 GTTCTCTTCTTTTG
1 CTTCTCTTCTTTTT
699645 CTTC
1 CTTC
699649 AATACCCTCA
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
12 7 0.14
13 3 0.06
14 7 0.14
15 30 0.59
16 4 0.08
ACGTcount: A:0.01, C:0.29, G:0.03, T:0.67
Consensus pattern (14 bp):
CTTCTCTTCTTTTT
Found at i:699625 original size:27 final size:26
Alignment explanation
Indices: 699575--699648 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 26
699565 CGGGACAACT
699575 TCTTCTTCTTCTTCTTCTTCTTCTTTT-
1 TCTTC-TCTTCTT-TTCTTCTTCTTTTA
*
699602 TCCTTCTCTTCTTTTCCTTTTTCTTTTA
1 T-CTTCTCTTCTTTT-CTTCTTCTTTTA
*
699630 TGTTCTCTTCTTTTGCTTC
1 TCTTCTCTTCTTTT-CTTC
699649 AATACCCTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
26 2 0.05
27 33 0.82
28 5 0.12
ACGTcount: A:0.01, C:0.28, G:0.03, T:0.68
Consensus pattern (26 bp):
TCTTCTCTTCTTTTCTTCTTCTTTTA
Found at i:701333 original size:27 final size:27
Alignment explanation
Indices: 701303--701356 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
701293 AATCAACCGG
*
701303 CGTGATTCTTTCCTGAAATGCTTCACT
1 CGTGATTCTTTCCCGAAATGCTTCACT
701330 CGTGATTCTTTCCCGAAATGCTTCACT
1 CGTGATTCTTTCCCGAAATGCTTCACT
701357 GAGTCATCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.19, C:0.28, G:0.15, T:0.39
Consensus pattern (27 bp):
CGTGATTCTTTCCCGAAATGCTTCACT
Found at i:701454 original size:13 final size:12
Alignment explanation
Indices: 701430--701476 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
701420 TTATTCCTAC
*
701430 AAAAACTAAAGA
1 AAAAATTAAAGA
701442 AACAAATTAAAG-
1 AA-AAATTAAAGA
*
701454 AAAAATAAAAGA
1 AAAAATTAAAGA
701466 CAAAAATTAAA
1 -AAAAATTAAA
701477 AAATTTTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 8 0.28
12 4 0.14
13 17 0.59
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.13
Consensus pattern (12 bp):
AAAAATTAAAGA
Found at i:716581 original size:245 final size:245
Alignment explanation
Indices: 716151--716641 Score: 946
Period size: 245 Copynumber: 2.0 Consensus size: 245
716141 CGCAACGTCG
*
716151 TGTAAAAGTATAACTTTCTTGTTACCAATAGCACTCAAGGGTAGCTTCCCACACACAAGATAGTT
1 TGTAAAAATATAACTTTCTTGTTACCAATAGCACTCAAGGGTAGCTTCCCACACACAAGATAGTT
716216 GACAACATCAGCATACCAGGGCGATGCATCGACAAAGAGCAACTGCTCATCTGGAAATGCATCAA
66 GACAACATCAGCATACCAGGGCGATGCATCGACAAAGAGCAACTGCTCATCTGGAAATGCATCAA
716281 CAATTTGGACTTTATTCTCATCTTCACTTCCAACTTCTAATCAAGACAAGTGGTCAGCTACTTGA
131 CAATTTGGACTTTATTCTCATCTTCACTTCCAACTTCTAATCAAGACAAGTGGTCAGCTACTTGA
716346 TTTTCATATCCCTTTCTATCCTTGATTTCAACATCAAACTCTTGTAGCAA
196 TTTTCATATCCCTTTCTATCCTTGATTTCAACATCAAACTCTTGTAGCAA
716396 TGTAAAAATATAACTTTCTTGTTACCAATAGCACTCAAGGGTAGCTTCCCACACACAAGATAGTT
1 TGTAAAAATATAACTTTCTTGTTACCAATAGCACTCAAGGGTAGCTTCCCACACACAAGATAGTT
* *
716461 GACAACATCAGCATACCAGGGTGATGCATCGACAAAGAGTAACTGCTCATCTGGAAATGCATCAA
66 GACAACATCAGCATACCAGGGCGATGCATCGACAAAGAGCAACTGCTCATCTGGAAATGCATCAA
716526 CAATTTGGACTTTATTCTCATCTTCACTTCCAACTTCTAATCAAGACAAGTGGTCAGCTACTTGA
131 CAATTTGGACTTTATTCTCATCTTCACTTCCAACTTCTAATCAAGACAAGTGGTCAGCTACTTGA
*
716591 TTTTCATATCCCTTTCTATCCTTGATTTCAACATCAAATTCTTGTAGCAA
196 TTTTCATATCCCTTTCTATCCTTGATTTCAACATCAAACTCTTGTAGCAA
716641 T
1 T
716642 AGGATCCATC
Statistics
Matches: 242, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
245 242 1.00
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.31
Consensus pattern (245 bp):
TGTAAAAATATAACTTTCTTGTTACCAATAGCACTCAAGGGTAGCTTCCCACACACAAGATAGTT
GACAACATCAGCATACCAGGGCGATGCATCGACAAAGAGCAACTGCTCATCTGGAAATGCATCAA
CAATTTGGACTTTATTCTCATCTTCACTTCCAACTTCTAATCAAGACAAGTGGTCAGCTACTTGA
TTTTCATATCCCTTTCTATCCTTGATTTCAACATCAAACTCTTGTAGCAA
Found at i:731605 original size:54 final size:54
Alignment explanation
Indices: 731541--731648 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
731531 TGGTAGAAAA
731541 GAATTAACTTGTTGAGCCTACTGATTGTGTTGTAAGGTCACAAATCCTTTAGGT
1 GAATTAACTTGTTGAGCCTACTGATTGTGTTGTAAGGTCACAAATCCTTTAGGT
731595 GAATTAACTTGTTGAGCCTACTGATTGTGTTGTAAGGTCACAAATCCTTTAGGT
1 GAATTAACTTGTTGAGCCTACTGATTGTGTTGTAAGGTCACAAATCCTTTAGGT
731649 CATAGTGTTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (54 bp):
GAATTAACTTGTTGAGCCTACTGATTGTGTTGTAAGGTCACAAATCCTTTAGGT
Found at i:735926 original size:37 final size:37
Alignment explanation
Indices: 735601--735924 Score: 346
Period size: 37 Copynumber: 8.8 Consensus size: 37
735591 ATTTAAGTAA
* *
735601 TCAGCCTATGTGCCTAGTAGGCTTCGTGCCGGTGTAT
1 TCAGGCTATGTGCCTAGCAGGCTTCGTGCCGGTGTAT
* * * *
735638 TCAAGCTATTTGCCTAGTAGGCTTCAT-CCAGGTGTAT
1 TCAGGCTATGTGCCTAGCAGGCTTCGTGCC-GGTGTAT
** *
735675 TCAGGCTATGTGCCTAGCAGGCTTTATGCCGGTGAAT
1 TCAGGCTATGTGCCTAGCAGGCTTCGTGCCGGTGTAT
* *
735712 TCAGGCTATGTGCCTAGTAGGCTTCGTGCCAGTGTAT
1 TCAGGCTATGTGCCTAGCAGGCTTCGTGCCGGTGTAT
* * * *
735749 TCAGGCTATGTGCCTAGCGGGTTTTGTGCCGGTGAAT
1 TCAGGCTATGTGCCTAGCAGGCTTCGTGCCGGTGTAT
* *
735786 TTAGGCTATGTGCCTAGCAGGCTTCGTGCCAGTGTAT
1 TCAGGCTATGTGCCTAGCAGGCTTCGTGCCGGTGTAT
* * ** **
735823 TCAGGCTATATGCCTAGCAAGCTTTATGCCAATGTAT
1 TCAGGCTATGTGCCTAGCAGGCTTCGTGCCGGTGTAT
* * * * *
735860 TTAGGCTATGTGCCTAACAGGCTTTGTGTCGGTGTAC
1 TCAGGCTATGTGCCTAGCAGGCTTCGTGCCGGTGTAT
* *
735897 T-AGGGATATGTGCCTAGTAGGCTTCGTG
1 TCA-GGCTATGTGCCTAGCAGGCTTCGTG
735925 TCAGTGTTCA
Statistics
Matches: 239, Mismatches: 45, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
36 3 0.01
37 234 0.98
38 2 0.01
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.33
Consensus pattern (37 bp):
TCAGGCTATGTGCCTAGCAGGCTTCGTGCCGGTGTAT
Found at i:741918 original size:30 final size:30
Alignment explanation
Indices: 741884--741940 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
741874 AGAGAAAGTC
741884 ATGAGTAAGAAATCATGATAGAAGGGACAA
1 ATGAGTAAGAAATCATGATAGAAGGGACAA
741914 ATGAGTAAGAAATCATGATAGAAGGGA
1 ATGAGTAAGAAATCATGATAGAAGGGA
741941 TAAAGTCACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.49, C:0.05, G:0.28, T:0.18
Consensus pattern (30 bp):
ATGAGTAAGAAATCATGATAGAAGGGACAA
Found at i:756306 original size:15 final size:15
Alignment explanation
Indices: 756278--756322 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
756268 GAGGAGATGT
756278 AGAAGAGAAAGAAGA
1 AGAAGAGAAAGAAGA
756293 AGAA-AGAAAG--GA
1 AGAAGAGAAAGAAGA
* *
756305 AGACGAGAAAGAGGA
1 AGAAGAGAAAGAAGA
756320 AGA
1 AGA
756323 CGTTGTCGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 5 0.19
13 6 0.23
14 6 0.23
15 9 0.35
ACGTcount: A:0.62, C:0.02, G:0.36, T:0.00
Consensus pattern (15 bp):
AGAAGAGAAAGAAGA
Done.