Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010655.1 Kokia drynarioides strain JFW-HI SEQ_125598, 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: 28351
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Warning! 93 characters in sequence are not A, C, G, or T
Found at i:4723 original size:38 final size:37
Alignment explanation
Indices: 4662--4748 Score: 99
Period size: 39 Copynumber: 2.4 Consensus size: 37
4652 GGATATTATG
4662 AAAAAATT--AAAAACTCTTTAAATTTTA-AAAAATA
1 AAAAAATTAAAAAAACTCTTTAAATTTTATAAAAATA
*
4696 AAAAAATTAAAAAAATTCATTTAAAATTTTATAAAAATA
1 AAAAAATTAAAAAAACTC-TTT-AAATTTTATAAAAATA
* *
4735 TAAAAGTATAAAAA
1 AAAAAAT-TAAAAA
4749 GTTTCAAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
34 8 0.18
36 7 0.16
37 3 0.07
38 8 0.18
39 12 0.27
40 6 0.14
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.31
Consensus pattern (37 bp):
AAAAAATTAAAAAAACTCTTTAAATTTTATAAAAATA
Found at i:9087 original size:217 final size:214
Alignment explanation
Indices: 8712--9141 Score: 779
Period size: 217 Copynumber: 2.0 Consensus size: 214
8702 CTTCATACTT
* *
8712 CTAATTTATCATCATAAGAGTGCAATATGTTGTTTCTCAGACTTGAAAATGCTTTGGAAGCAACA
1 CTAATTTATCATCATAAGAGTGCAACATGTTGTTTCTCAGACTTGAAAATGCTTTGGAAGCAAAA
*
8777 ATTTTACCCCTAGGAGATACAGCATTTGATCATATGTTAGAAAATGTCCGTTGGTGATAGGATTT
66 ATTTTACCCCTAGGAGATACAGCATTTGATCATATGTTAGAAAATGTCCGATGGTGATAGGATTT
*
8842 CCGATACTGTTATAAGAGATATTTGAATGCTAGGTTTATATATATGCTCAACTTCTTGTTTGGAG
131 CCGATACTGTTATAAGAGATATTTGAATGCTAGATTTATATATATGCTCAA---CTTGTTTGGAG
8907 TTAACTGTGATTTCCTGTACAG
193 TTAACTGTGATTTCCTGTACAG
8929 CTAATTTATCATCATAAGAGTGCAACATGTTGTTTCTCAGACTTGAAAATGCTTTGGAAGCAAAA
1 CTAATTTATCATCATAAGAGTGCAACATGTTGTTTCTCAGACTTGAAAATGCTTTGGAAGCAAAA
8994 ATTTTACCCCTAGGAGATACAGCATTTGATCATATGTTAGAAAATGTCCGATGGTGATAGGATTT
66 ATTTTACCCCTAGGAGATACAGCATTTGATCATATGTTAGAAAATGTCCGATGGTGATAGGATTT
* *
9059 CCGATGCTGTTATAAGAGATATTTGAATGCTAGATTTATATATATGCTTAACTTGTTTGGAGTTA
131 CCGATACTGTTATAAGAGATATTTGAATGCTAGATTTATATATATGCTCAACTTGTTTGGAGTTA
9124 ACTGTGATTTCCTGTACA
196 ACTGTGATTTCCTGTACA
9142 ACAAAGAGTT
Statistics
Matches: 207, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
214 32 0.15
217 175 0.85
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (214 bp):
CTAATTTATCATCATAAGAGTGCAACATGTTGTTTCTCAGACTTGAAAATGCTTTGGAAGCAAAA
ATTTTACCCCTAGGAGATACAGCATTTGATCATATGTTAGAAAATGTCCGATGGTGATAGGATTT
CCGATACTGTTATAAGAGATATTTGAATGCTAGATTTATATATATGCTCAACTTGTTTGGAGTTA
ACTGTGATTTCCTGTACAG
Found at i:17414 original size:14 final size:14
Alignment explanation
Indices: 17397--17511 Score: 68
Period size: 14 Copynumber: 8.1 Consensus size: 14
17387 GCCCCTGCAT
* *
17397 GCGAATCCCTTTAG
1 GCGAACCCCTATAG
17411 GCGAACCCCATATAG
1 GCGAACCCC-TATAG
* * * *
17426 GCTAGCCCCTGTAA
1 GCGAACCCCTATAG
17440 GCGAACCCCTTATAG
1 GCGAACCCC-TATAG
** * *
17455 GCGAGTCCCTGTAT
1 GCGAACCCCTATAG
17469 GCGAACCCCTATAG
1 GCGAACCCCTATAG
* ** * *
17483 GTGAGGCCCTGTAT
1 GCGAACCCCTATAG
*
17497 GCAAACCCCTATAG
1 GCGAACCCCTATAG
17511 G
1 G
17512 TGAGCCTTTA
Statistics
Matches: 70, Mismatches: 29, Indels: 4
0.68 0.28 0.04
Matches are distributed among these distances:
14 49 0.70
15 21 0.30
ACGTcount: A:0.24, C:0.31, G:0.23, T:0.21
Consensus pattern (14 bp):
GCGAACCCCTATAG
Found at i:17443 original size:29 final size:28
Alignment explanation
Indices: 17411--17511 Score: 123
Period size: 29 Copynumber: 3.5 Consensus size: 28
17401 ATCCCTTTAG
*
17411 GCGAACCCCATATAGGCTAGCCCCTGTAA
1 GCGAACCCC-TATAGGCTAGCCCCTGTAT
* *
17440 GCGAACCCCTTATAGGCGAGTCCCTGTAT
1 GCGAACCCC-TATAGGCTAGCCCCTGTAT
*
17469 GCGAACCCCTATAGG-TGAGGCCCTGTAT
1 GCGAACCCCTATAGGCT-AGCCCCTGTAT
*
17497 GCAAACCCCTATAGG
1 GCGAACCCCTATAGG
17512 TGAGCCTTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
28 30 0.47
29 34 0.53
ACGTcount: A:0.25, C:0.32, G:0.24, T:0.20
Consensus pattern (28 bp):
GCGAACCCCTATAGGCTAGCCCCTGTAT
Found at i:17492 original size:28 final size:29
Alignment explanation
Indices: 17411--17517 Score: 130
Period size: 28 Copynumber: 3.8 Consensus size: 29
17401 ATCCCTTTAG
*
17411 GCGAACCCCATATAGGCT-AGCCCCTGTAA
1 GCGAACCCCATATAGG-TGAGCCCCTGTAT
* * *
17440 GCGAACCCCTTATAGGCGAGTCCCTGTAT
1 GCGAACCCCATATAGGTGAGCCCCTGTAT
*
17469 GCGAACCCC-TATAGGTGAGGCCCTGTAT
1 GCGAACCCCATATAGGTGAGCCCCTGTAT
*
17497 GCAAACCCC-TATAGGTGAGCC
1 GCGAACCCCATATAGGTGAGCC
17518 TTTATATGTG
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
28 36 0.52
29 33 0.48
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.20
Consensus pattern (29 bp):
GCGAACCCCATATAGGTGAGCCCCTGTAT
Found at i:17564 original size:17 final size:17
Alignment explanation
Indices: 17542--17580 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
17532 CCTGTAGGCC
* *
17542 AACCCCTTGTATATGTG
1 AACCCCCTGTATATGCG
*
17559 AACCCCCTGTATGTGCG
1 AACCCCCTGTATATGCG
17576 AACCC
1 AACCC
17581 ATATGCTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.23, C:0.33, G:0.18, T:0.26
Consensus pattern (17 bp):
AACCCCCTGTATATGCG
Found at i:27015 original size:18 final size:18
Alignment explanation
Indices: 26992--27029 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
26982 NNTTGCTTTT
26992 TCAGCTACT-TTTTTCTCA
1 TCAGCTACTCTTTTT-TCA
*
27010 TCAGCTTCTCTTTTTTCA
1 TCAGCTACTCTTTTTTCA
27028 TC
1 TC
27030 TTCTTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.13, C:0.29, G:0.05, T:0.53
Consensus pattern (18 bp):
TCAGCTACTCTTTTTTCA
Done.