Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015332.1 Kokia drynarioides strain JFW-HI SEQ_130379, 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: 389104
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 724 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:366661 original size:24 final size:25
Alignment explanation
Indices: 366634--366690 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
366624 AAAAAACAGA
* *
366634 TATAAATAAAATC-TATAATAAAAT
1 TATAAATAAAAACTTAAAATAAAAT
* *
366658 TATAAAAAAAAACTTAAAATAAATT
1 TATAAATAAAAACTTAAAATAAAAT
366683 TATAAATA
1 TATAAATA
366691 CATATAAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 11 0.41
25 16 0.59
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.32
Consensus pattern (25 bp):
TATAAATAAAAACTTAAAATAAAAT
Found at i:366668 original size:12 final size:13
Alignment explanation
Indices: 366634--366690 Score: 50
Period size: 12 Copynumber: 4.6 Consensus size: 13
366624 AAAAAACAGA
366634 TATAAATAAAATC
1 TATAAATAAAATC
366647 TAT-AATAAAAT-
1 TATAAATAAAATC
* *
366658 TATAAAAAAAAAC
1 TATAAATAAAATC
*
366671 T-TAAA-ATAAATT
1 TATAAATA-AAATC
366683 TATAAATA
1 TATAAATA
366691 CATATAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
11 4 0.11
12 22 0.63
13 8 0.23
14 1 0.03
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
TATAAATAAAATC
Found at i:367658 original size:15 final size:14
Alignment explanation
Indices: 367638--367677 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 14
367628 TGAAATGATA
367638 AAATTAAATGATTTT
1 AAATTAAAT-ATTTT
367653 AAATTATAATATTTT
1 AAATTA-AATATTTT
367668 AAATTTAAAT
1 AAA-TTAAAT
367678 CTCACAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 17 0.74
16 6 0.26
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
AAATTAAATATTTT
Found at i:368225 original size:13 final size:13
Alignment explanation
Indices: 368181--368227 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
368171 CTAGATTTTT
368181 TATTTT-TTTAAA
1 TATTTTATTTAAA
* *
368193 TATTTATTTTTAAT
1 TATTT-TATTTAAA
*
368207 TGTTTTATTTAAA
1 TATTTTATTTAAA
368220 TATTTTAT
1 TATTTTAT
368228 AATAATAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
12 5 0.18
13 14 0.50
14 9 0.32
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (13 bp):
TATTTTATTTAAA
Found at i:368234 original size:3 final size:3
Alignment explanation
Indices: 368226--368251 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
368216 TAAATATTTT
368226 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
368252 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:369207 original size:17 final size:17
Alignment explanation
Indices: 369173--369227 Score: 83
Period size: 17 Copynumber: 3.2 Consensus size: 17
369163 GTTTAAGTTG
369173 ATTTAAATTTATTCTTAA
1 ATTTAAATTTA-TCTTAA
369191 ATTTAAATTTATCTTAA
1 ATTTAAATTTATCTTAA
* *
369208 ATTTAAATTGATATTAA
1 ATTTAAATTTATCTTAA
369225 ATT
1 ATT
369228 AAAAACCCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
17 24 0.69
18 11 0.31
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (17 bp):
ATTTAAATTTATCTTAA
Found at i:369946 original size:22 final size:21
Alignment explanation
Indices: 369920--369973 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
369910 TCTGTGGTAT
* *
369920 TTAATAAATAAGCAATAAATA
1 TTAATAAATAAGAAAAAAATA
**
369941 TATAATAAATATTAAAAAAATA
1 T-TAATAAATAAGAAAAAAATA
369963 TTAATAAATAA
1 TTAATAAATAA
369974 TATTAATAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (21 bp):
TTAATAAATAAGAAAAAAATA
Found at i:369947 original size:11 final size:11
Alignment explanation
Indices: 369933--369996 Score: 57
Period size: 11 Copynumber: 6.2 Consensus size: 11
369923 ATAAATAAGC
369933 AATAAATATAT
1 AATAAATATAT
369944 AATAAATAT-T
1 AATAAATATAT
*
369954 AA-AAAAATATT
1 AATAAATATA-T
369965 AATAAATA-AT
1 AATAAATATAT
*
369975 -ATTAATA-AT
1 AATAAATATAT
*
369984 AATAAATAAAT
1 AATAAATATAT
369995 AA
1 AA
369997 AGGGAGTCAA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
9 13 0.30
10 10 0.23
11 17 0.39
12 4 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AATAAATATAT
Found at i:369977 original size:13 final size:13
Alignment explanation
Indices: 369948--369996 Score: 63
Period size: 11 Copynumber: 4.2 Consensus size: 13
369938 ATATATAATA
369948 AATATTAA-AAA-
1 AATATTAATAAAT
369959 AATATTAATAAAT
1 AATATTAATAAAT
369972 AATATTAAT-AAT
1 AATATTAATAAAT
369984 AATA--AATAAAT
1 AATATTAATAAAT
369995 AA
1 AA
369997 AGGGAGTCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
10 3 0.09
11 13 0.37
12 10 0.29
13 9 0.26
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AATATTAATAAAT
Found at i:371109 original size:29 final size:29
Alignment explanation
Indices: 371027--371167 Score: 176
Period size: 29 Copynumber: 4.8 Consensus size: 29
371017 TCCCTAAAAT
* **
371027 TTCCAAAAATTCCATTTTTGATCTGGAAAC
1 TTCCAAAAATTCCATTTTT-ACCCCGAAAC
*
371057 TCCCAAAAATTCCATTTTTAACCCCGAAAC
1 TTCCAAAAATTCCATTTTT-ACCCCGAAAC
* *
371087 TTCCAAAAATTACATTTTTACCCCCAAAC
1 TTCCAAAAATTCCATTTTTACCCCGAAAC
*
371116 TTCCAAAAATTCCATTTTAACCCCGAAAC
1 TTCCAAAAATTCCATTTTTACCCCGAAAC
*
371145 TTTCAAAAATTACCA-TTTTACCC
1 TTCCAAAAATT-CCATTTTTACCC
371168 TCAAATGTCC
Statistics
Matches: 97, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
29 52 0.54
30 45 0.46
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.32
Consensus pattern (29 bp):
TTCCAAAAATTCCATTTTTACCCCGAAAC
Found at i:371152 original size:58 final size:59
Alignment explanation
Indices: 371053--371199 Score: 194
Period size: 58 Copynumber: 2.5 Consensus size: 59
371043 TTTGATCTGG
*
371053 AAACTCCCAAAAATTCCATTTTTAACCCCGAAACTTCCAAAAATTA-CATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTAACCCCGAAACTTCCAAAAATTACCA-TTTTACCCCC
* *
371112 AAACTTCCAAAAATTCCA-TTTTAACCCCGAAACTTTCAAAAATTACCATTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTAACCCCGAAACTTCCAAAAATTACCATTTTACCCCC
* * *
371170 AAA-TGTCC-AAATTTCTATTTTTAATCCCGA
1 AAACT-TCCAAAAATTCCATTTTTAACCCCGA
371200 TTTTTTAAAA
Statistics
Matches: 79, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
57 8 0.10
58 52 0.66
59 19 0.24
ACGTcount: A:0.37, C:0.29, G:0.03, T:0.32
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTAACCCCGAAACTTCCAAAAATTACCATTTTACCCCC
Found at i:371180 original size:29 final size:30
Alignment explanation
Indices: 371027--371163 Score: 179
Period size: 30 Copynumber: 4.6 Consensus size: 30
371017 TCCCTAAAAT
* * **
371027 TTCCAAAAATTCCATTTTTGATCTGGAAAC
1 TTCCAAAAATTCCATTTTTAACCCCGAAAC
*
371057 TCCCAAAAATTCCATTTTTAACCCCGAAAC
1 TTCCAAAAATTCCATTTTTAACCCCGAAAC
* *
371087 TTCCAAAAATTACATTTTT-ACCCCCAAAC
1 TTCCAAAAATTCCATTTTTAACCCCGAAAC
371116 TTCCAAAAATTCCA-TTTTAACCCCGAAAC
1 TTCCAAAAATTCCATTTTTAACCCCGAAAC
*
371145 TTTCAAAAATTACCATTTT
1 TTCCAAAAATT-CCATTTT
371164 ACCCTCAAAT
Statistics
Matches: 93, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
28 4 0.04
29 41 0.44
30 45 0.48
31 3 0.03
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (30 bp):
TTCCAAAAATTCCATTTTTAACCCCGAAAC
Found at i:371286 original size:59 final size:57
Alignment explanation
Indices: 371060--371288 Score: 173
Period size: 58 Copynumber: 3.9 Consensus size: 57
371050 TGGAAACTCC
* * *
371060 CAAAAATTCCATTTTTAACCCCGAAAC-TTCCAAAAATTA-CATTTTTACCCCCAAACT-T
1 CAAAAATTCCATTTTTAA-CCCG-AACTTTTCAAAAATTACCA-TTTTACCCTCGAA-TGT
*
371118 CCAAAAATTCCA-TTTTAACCCCGAAAC-TTTCAAAAATTACCATTTTACCCTCAAATGT
1 -CAAAAATTCCATTTTTAA-CCCG-AACTTTTCAAAAATTACCATTTTACCCTCGAATGT
* * * * * * * **
371176 CCAAATTTCTATTTTTAATCCCG-ATTTTTTAAAAAGTTACCGTTTCACCCTCGGGTAGT
1 CAAAAATTCCATTTTTAA-CCCGAACTTTTCAAAAA-TTACCATTTTACCCTCGAAT-GT
* * *
371235 TAAAAATTCCATTTTTAACCTCGAACTTTTCCAAAATTACCATTTTGCCCTCGA
1 CAAAAATTCCATTTTTAACC-CGAACTTTTCAAAAATTACCATTTTACCCTCGA
371289 GAATCCAAAA
Statistics
Matches: 138, Mismatches: 24, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
56 1 0.01
57 17 0.12
58 66 0.48
59 45 0.33
60 9 0.07
ACGTcount: A:0.33, C:0.26, G:0.06, T:0.35
Consensus pattern (57 bp):
CAAAAATTCCATTTTTAACCCGAACTTTTCAAAAATTACCATTTTACCCTCGAATGT
Found at i:380277 original size:33 final size:31
Alignment explanation
Indices: 380237--380319 Score: 93
Period size: 32 Copynumber: 2.7 Consensus size: 31
380227 AATCCTTTAT
*
380237 TTTTTAAATTTTAAATTTAATTATTA-ATATTA
1 TTTTTAAA-TTCAAATTT-ATTATTATATATTA
*
380269 TTTATTAAATTCAAATTTATTATTATATATTC
1 TTT-TTAAATTCAAATTTATTATTATATATTA
380301 TTTTT-AATT-AAA-TTATTAT
1 TTTTTAAATTCAAATTTATTAT
380320 CAAATAACTA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
28 7 0.15
29 3 0.06
30 4 0.09
31 9 0.19
32 19 0.40
33 5 0.11
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (31 bp):
TTTTTAAATTCAAATTTATTATTATATATTA
Found at i:381634 original size:15 final size:15
Alignment explanation
Indices: 381614--381651 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
381604 AAATTTATTT
381614 TAAATTTAAATTTAA
1 TAAATTTAAATTTAA
*
381629 TAAATTT-AATTTCA
1 TAAATTTAAATTTAA
381643 -AAATTTAAA
1 TAAATTTAAA
381652 AAGTCCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 6 0.29
14 8 0.38
15 7 0.33
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
TAAATTTAAATTTAA
Found at i:382393 original size:13 final size:13
Alignment explanation
Indices: 382375--382399 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
382365 TTGATAACTG
382375 TATTAATAATTAT
1 TATTAATAATTAT
382388 TATTAATAATTA
1 TATTAATAATTA
382400 GAATTAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TATTAATAATTAT
Found at i:385655 original size:163 final size:158
Alignment explanation
Indices: 385415--385742 Score: 586
Period size: 163 Copynumber: 2.1 Consensus size: 158
385405 CGTTTACGCT
*
385415 TGAA-GTTTCGATTCTTGAGGAGCCTGCTCAGCTAAATGTCAATACTCATCATATGGTAACATAG
1 TGAAGGTTTCGATTCTTGAGGAGCCTACTCAGCTAAATGTCAATACTCATCATATGGTAACATAG
*
385479 TCTAAAGCTGGTATTTTCAAACCAAAAGTATTGGCTATTGAAGTTGCTGAGAAAGAGCCACGTAC
66 TCTAAAGCTGGTATTTTCAAACCAAAAGTACTGGCTATTGAAGTTGCTGAGAAAGAGCCACGTAC
385544 AATTGAAGAAGCGTTTGCTCATAAGGAA
131 AATTGAAGAAGCGTTTGCTCATAAGGAA
385572 TGAAGGTTNTCGATTCTTGAGGAGCCTACTCAGCTAAATAAATGTCAATACTCATCATATGGTAA
1 TGAAGGTT-TCGATTCTTGAGGAGCCTACTCAGC----TAAATGTCAATACTCATCATATGGTAA
385637 CATAGTCTAAAGCTGGTATTTTCAAACCAAAAGTACTGGCTATTGAAGTTGCTGAGAAAGAGCCA
61 CATAGTCTAAAGCTGGTATTTTCAAACCAAAAGTACTGGCTATTGAAGTTGCTGAGAAAGAGCCA
385702 CGTACAATTGAAGAAGCGTTTGCTCATAAGGAA
126 CGTACAATTGAAGAAGCGTTTGCTCATAAGGAA
385735 TGAAGGTT
1 TGAAGGTT
385743 AGCAGCTCAA
Statistics
Matches: 163, Mismatches: 2, Indels: 6
0.95 0.01 0.04
Matches are distributed among these distances:
157 4 0.02
158 3 0.02
159 24 0.15
163 132 0.81
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (158 bp):
TGAAGGTTTCGATTCTTGAGGAGCCTACTCAGCTAAATGTCAATACTCATCATATGGTAACATAG
TCTAAAGCTGGTATTTTCAAACCAAAAGTACTGGCTATTGAAGTTGCTGAGAAAGAGCCACGTAC
AATTGAAGAAGCGTTTGCTCATAAGGAA
Done.