Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005057.1 Kokia drynarioides strain JFW-HI SEQ_118850, 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: 3188
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Found at i:208 original size:29 final size:27
Alignment explanation
Indices: 160--259 Score: 74
Period size: 29 Copynumber: 3.4 Consensus size: 27
150 ATTTTCTAAA
* *
160 AAAATTACATTTCTACCCTCGAACTTCCC
1 AAAATT-CATTTTTAACCTCGAA-TTCCC
* * **
189 AAAATTCATTATTTGACCTCGTATGTCTA
1 AAAATTCATT-TTTAACCTCGAAT-TCCC
*
218 AAAATTTCATTTTTAACCTCGAATTTTCC
1 AAAA-TTCATTTTTAACCTCGAA-TTCCC
247 AAAATTACATTTT
1 AAAATT-CATTTT
260 ACCCGTAAAT
Statistics
Matches: 55, Mismatches: 11, Indels: 10
0.72 0.14 0.13
Matches are distributed among these distances:
28 7 0.13
29 41 0.75
30 7 0.13
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.40
Consensus pattern (27 bp):
AAAATTCATTTTTAACCTCGAATTCCC
Found at i:249 original size:58 final size:56
Alignment explanation
Indices: 98--491 Score: 244
Period size: 58 Copynumber: 6.8 Consensus size: 56
88 TGATGTCTTC
* * * * * *
98 AAAAATTACATTTTTACCCCCAAACTTTCCAAAATTCAAATTTTGACCTCGAATTTTCT
1 AAAAATTTCATTTTTAACCCCGAACCTTCCAAAATT-ACA-TTTGACCTCGAA-TGTCT
* * * *
157 AAAAAAATTACATTTCT-ACCCTCGAA-CTTCCCAAAATTCATTATTTGACCTCGTATGTCT
1 --AAAAATTTCATTTTTAACCC-CGAACCTT-CCAAAATT-A-CATTTGACCTCGAATGTCT
* ** * * *
217 AAAAATTTCATTTTTAACCTCGAATTTTCCAAAATTACATTTTACC-CGTAAATTTTT
1 AAAAATTTCATTTTTAACCCCGAACCTTCCAAAATTACATTTGACCTCG--AATGTCT
* * * *
274 GAAAA-TTCTATTTTTAACCCCGAACCTTCCAAAAATTACCATTTCACCTTGAATGTTT
1 AAAAATTTC-ATTTTTAACCCCGAACCTTCC-AAAATTA-CATTTGACCTCGAATGTCT
* * * * * *
332 AAAAATTCCA-TTTTGACCTCGAACCTTCAAAAAATTACCATTTTACTCCCGAATGTCT
1 AAAAATTTCATTTTTAACCCCGAACCTTC-CAAAATTA-CATTTGAC-CTCGAATGTCT
** *
390 AAAAATTT-AGTTTTTAACCCCGAATATTCCAAAAATTATCATTTTACCTCCGAATGT-T
1 AAAAATTTCA-TTTTTAACCCCGAACCTTCC-AAAATTA-CATTTGACCT-CGAATGTCT
* * *
448 AAAATTTTCATTTTTGACCACGAACCTTCCAAAAATTACCATTT
1 AAAAATTTCATTTTTAACCCCGAACCTTCC-AAAATTA-CATTT
492 TGCCCCCGAG
Statistics
Matches: 268, Mismatches: 46, Indels: 41
0.75 0.13 0.12
Matches are distributed among these distances:
55 2 0.01
56 10 0.04
57 59 0.22
58 96 0.36
59 52 0.19
60 10 0.04
61 38 0.14
62 1 0.00
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.37
Consensus pattern (56 bp):
AAAAATTTCATTTTTAACCCCGAACCTTCCAAAATTACATTTGACCTCGAATGTCT
Found at i:363 original size:28 final size:29
Alignment explanation
Indices: 285--376 Score: 89
Period size: 28 Copynumber: 3.2 Consensus size: 29
275 AAAATTCTAT
*
285 TTTTAACCCCGAACCTTCCAAAAATTACCA
1 TTTTAACCTCGAACCTT-CAAAAATTACCA
* * ** *
315 -TTTCACCTTGAATGTTTAAAAATT-CCA
1 TTTTAACCTCGAACCTTCAAAAATTACCA
*
342 TTTTGACCTCGAACCTTCAAAAAATTACCA
1 TTTTAACCTCGAACCTTC-AAAAATTACCA
372 TTTTA
1 TTTTA
377 CTCCCGAATG
Statistics
Matches: 47, Mismatches: 12, Indels: 6
0.72 0.18 0.09
Matches are distributed among these distances:
27 3 0.06
28 19 0.40
29 18 0.38
30 7 0.15
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (29 bp):
TTTTAACCTCGAACCTTCAAAAATTACCA
Found at i:393 original size:29 final size:28
Alignment explanation
Indices: 304--451 Score: 97
Period size: 29 Copynumber: 5.1 Consensus size: 28
294 CGAACCTTCC
* ** *
304 AAAAATTACCATTTCACCTTGAATGTTT
1 AAAAATTACCATTTTACCCCGAATGTCT
* *
332 AAAAATT-CCATTTTGACCTCGAACCT-TCA
1 AAAAATTACCATTTT-ACCCCGAA--TGTCT
361 AAAAATTACCATTTTACTCCCGAATGTCT
1 AAAAATTACCATTTTAC-CCCGAATGTCT
** * *
390 AAAAATTTA-GTTTTTAACCCCGAATATTCC
1 AAAAA-TTACCATTTT-ACCCCGAAT-GTCT
*
420 AAAAATTATCATTTTACCTCCGAATGT-T
1 AAAAATTACCATTTTACC-CCGAATGTCT
448 AAAA
1 AAAA
452 TTTTCATTTT
Statistics
Matches: 95, Mismatches: 14, Indels: 22
0.73 0.11 0.17
Matches are distributed among these distances:
27 6 0.06
28 19 0.20
29 35 0.37
30 35 0.37
ACGTcount: A:0.37, C:0.21, G:0.07, T:0.35
Consensus pattern (28 bp):
AAAAATTACCATTTTACCCCGAATGTCT
Found at i:407 original size:116 final size:117
Alignment explanation
Indices: 275--492 Score: 316
Period size: 116 Copynumber: 1.9 Consensus size: 117
265 TAAATTTTTG
* *
275 AAAATTCTATTTTTAACCCCGAACCTTCCAAAAATTACCATTTCACCT-TGAATGTTTAAAAATT
1 AAAATTCTATTTTTAACCCCGAACATTCCAAAAATTACCATTTCACCTCCGAATG-TTAAAAATT
*
339 CCA-TTTTGACCTCGAACCTTCAAAAAATTACCATTTTACTCCCGAATGTCTA
65 CCATTTTTGACCACGAACCTTCAAAAAATTACCATTTTACTCCCGAATGTCTA
* * * *
391 AAAATT-TAGTTTTTAACCCCGAATATTCCAAAAATTATCATTTTACCTCCGAATGTTAAAATTT
1 AAAATTCTA-TTTTTAACCCCGAACATTCCAAAAATTACCATTTCACCTCCGAATGTTAAAAATT
* *
455 TCATTTTTGACCACGAACCTTCCAAAAATTACCATTTT
65 CCATTTTTGACCACGAACCTTCAAAAAATTACCATTTT
493 GCCCCCGAGT
Statistics
Matches: 90, Mismatches: 9, Indels: 5
0.87 0.09 0.05
Matches are distributed among these distances:
115 2 0.02
116 51 0.57
117 37 0.41
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.36
Consensus pattern (117 bp):
AAAATTCTATTTTTAACCCCGAACATTCCAAAAATTACCATTTCACCTCCGAATGTTAAAAATTC
CATTTTTGACCACGAACCTTCAAAAAATTACCATTTTACTCCCGAATGTCTA
Found at i:492 original size:58 final size:57
Alignment explanation
Indices: 211--492 Score: 263
Period size: 58 Copynumber: 4.9 Consensus size: 57
201 TTGACCTCGT
* **
211 ATGTCTAAAAATTTCATTTTTAACCTCGAATTTTCC-AAAATTA-CATTTTAC-CCGTAA
1 ATGT-TAAAAATTTCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACTCCG--A
* * * *
268 ATTTTTGAAAA-TTCTATTTTTAACCCCGAACCTTCCAAAAATTACCATTTCAC-CTTGA
1 A-TGTTAAAAATTTC-ATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACTC-CGA
* * * *
326 ATGTTTAAAAATTCCA-TTTTGACCTCGAACCTTCAAAAAATTACCATTTTACTCCCGA
1 ATG-TTAAAAATTTCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACT-CCGA
** *
384 ATGTCTAAAAATTT-AGTTTTTAACCCCGAATATTCCAAAAATTATCATTTTACCTCCGA
1 ATGT-TAAAAATTTCA-TTTTTAACCCCGAACCTTCCAAAAATTACCATTTTA-CTCCGA
* * *
443 ATGTTAAAATTTTCATTTTTGACCACGAACCTTCCAAAAATTACCATTTT
1 ATGTTAAAAATTTCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTT
493 GCCCCCGAGT
Statistics
Matches: 183, Mismatches: 28, Indels: 27
0.77 0.12 0.11
Matches are distributed among these distances:
56 3 0.02
57 59 0.32
58 69 0.38
59 49 0.27
60 3 0.02
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.38
Consensus pattern (57 bp):
ATGTTAAAAATTTCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACTCCGA
Found at i:515 original size:28 final size:28
Alignment explanation
Indices: 479--538 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
469 GAACCTTCCA
* *
479 AAAATTACCATTTTGCCCCCGAGTATCC
1 AAAATTACCATTTTACCCCCGAGCATCC
* * *
507 AAAATTACCTTTTTACTCTCGAGCATCC
1 AAAATTACCATTTTACCCCCGAGCATCC
535 AAAA
1 AAAA
539 ATCACATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.33, C:0.28, G:0.08, T:0.30
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCCGAGCATCC
Found at i:520 original size:58 final size:59
Alignment explanation
Indices: 284--520 Score: 198
Period size: 58 Copynumber: 4.1 Consensus size: 59
274 GAAAATTCTA
* * * ** *
284 TTTTTAACCCCGAACCTTCCAAAAATTACCATTTCA-CCTTGAATGTTTAAAAA-TT-CC
1 TTTTTGACCACGAACCTTCCAAAAATTACCATTTTACCCCCGAATG-TCAAAAATTTACC
* * * * *
341 ATTTTGACCTCGAACCTTCAAAAAATTACCATTTTACTCCCGAATGTCTAAAAATTTA-G
1 TTTTTGACCACGAACCTTCCAAAAATTACCATTTTACCCCCGAATGTC-AAAAATTTACC
* * ** * * * * *
400 TTTTTAACCCCGAATATTCCAAAAATTATCATTTTACCTCCGAATGT-TAAAATTTTCA
1 TTTTTGACCACGAACCTTCCAAAAATTACCATTTTACCCCCGAATGTCAAAAATTTACC
* * * *
458 TTTTTGACCACGAACCTTCCAAAAATTACCATTTTGCCCCCGAGTATCCAAAA-TTACC
1 TTTTTGACCACGAACCTTCCAAAAATTACCATTTTACCCCCGAATGTCAAAAATTTACC
516 TTTTT
1 TTTTT
521 ACTCTCGAGC
Statistics
Matches: 140, Mismatches: 34, Indels: 11
0.76 0.18 0.06
Matches are distributed among these distances:
57 39 0.28
58 57 0.41
59 44 0.31
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.36
Consensus pattern (59 bp):
TTTTTGACCACGAACCTTCCAAAAATTACCATTTTACCCCCGAATGTCAAAAATTTACC
Found at i:2691 original size:15 final size:14
Alignment explanation
Indices: 2650--2700 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 14
2640 ATTTTGGTTA
2650 TTAAAATTAATTATTT
1 TTAAAATT--TTATTT
*
2666 TTAAGATTTTATTT
1 TTAAAATTTTATTT
2680 TATAAAATTTTATTT
1 T-TAAAATTTTATTT
2695 TTAAAA
1 TTAAAA
2701 AACTTTCACA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 12 0.38
15 13 0.41
16 7 0.22
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
TTAAAATTTTATTT
Done.