Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011158.1 Kokia drynarioides strain JFW-HI SEQ_126132, 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: 302748
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 168 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:261243 original size:20 final size:21
Alignment explanation
Indices: 261220--261295 Score: 86
Period size: 20 Copynumber: 3.8 Consensus size: 21
261210 AAACAATAAG
*
261220 TATTGATACTT-TTAAAAATA
1 TATTGAGACTTATTAAAAATA
** *
261240 TATTGAGACTTATT-AAGTTT
1 TATTGAGACTTATTAAAAATA
*
261260 TATTGATACTT-TTAAAAATA
1 TATTGAGACTTATTAAAAATA
261280 TATTGAGACTTATTAA
1 TATTGAGACTTATTAA
261296 GTTTTATTGA
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
19 2 0.05
20 36 0.82
21 6 0.14
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.46
Consensus pattern (21 bp):
TATTGAGACTTATTAAAAATA
Found at i:261264 original size:40 final size:40
Alignment explanation
Indices: 261220--261308 Score: 178
Period size: 40 Copynumber: 2.2 Consensus size: 40
261210 AAACAATAAG
261220 TATTGATACTTTTAAAAATATATTGAGACTTATTAAGTTT
1 TATTGATACTTTTAAAAATATATTGAGACTTATTAAGTTT
261260 TATTGATACTTTTAAAAATATATTGAGACTTATTAAGTTT
1 TATTGATACTTTTAAAAATATATTGAGACTTATTAAGTTT
261300 TATTGATAC
1 TATTGATAC
261309 CATTTTTGCA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (40 bp):
TATTGATACTTTTAAAAATATATTGAGACTTATTAAGTTT
Found at i:261303 original size:20 final size:20
Alignment explanation
Indices: 261240--261305 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
261230 TTTAAAAATA
261240 TATTGAGACTTATTAAGTTT
1 TATTGAGACTTATTAAGTTT
* ** *
261260 TATTGATACTT-TTAAAAATA
1 TATTGAGACTTATT-AAGTTT
261280 TATTGAGACTTATTAAGTTT
1 TATTGAGACTTATTAAGTTT
261300 TATTGA
1 TATTGA
261306 TACCATTTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.06
20 32 0.89
21 2 0.06
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.48
Consensus pattern (20 bp):
TATTGAGACTTATTAAGTTT
Found at i:267781 original size:26 final size:27
Alignment explanation
Indices: 267733--267783 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
267723 CAATTTGAAG
**
267733 AAAAAAAATTATAAGTTCCAATTTTTT
1 AAAAAAAATTATAAGTAACAATTTTTT
*
267760 AAAAAAAATT-TAAGTAATAATTTT
1 AAAAAAAATTATAAGTAACAATTTT
267784 ATATTATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 11 0.52
27 10 0.48
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (27 bp):
AAAAAAAATTATAAGTAACAATTTTTT
Found at i:268214 original size:18 final size:18
Alignment explanation
Indices: 268178--268215 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
268168 AATTTAATTT
*
268178 AATTTTAATTAAATATAA
1 AATTTTAATTAAAAATAA
268196 AATTTT-ATTAAAAATTAA
1 AATTTTAATTAAAAA-TAA
268214 AA
1 AA
268216 ATCCAGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AATTTTAATTAAAAATAA
Found at i:274775 original size:22 final size:22
Alignment explanation
Indices: 274747--274788 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
274737 CAAATTTCAA
274747 TAATTATTTTTTAATCATTGAG
1 TAATTATTTTTTAATCATTGAG
274769 TAATTATTTTTTAATCATTG
1 TAATTATTTTTTAATCATTG
274789 TTATTAGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.57
Consensus pattern (22 bp):
TAATTATTTTTTAATCATTGAG
Found at i:280680 original size:149 final size:140
Alignment explanation
Indices: 280514--280791 Score: 362
Period size: 140 Copynumber: 1.9 Consensus size: 140
280504 AATATCTTTT
* * *
280514 TTTTTTATTTTTCTTTAAAATCTAAAACTAATGTTTCAAATTTATCATATTAAAATATTTTTTTA
1 TTTTTTATTTTTCTTTAAAATCTAAAACTAATGATTCAAATATATCATATT-AAATA----TATA
* *
280579 TTTTTCTTTTAAAAAAAGTTTTCAAATATATAT-AGTTTCAAATTTATTTGATCTAACATGAAAA
61 TATAT-TTTT---AAAAGTTTTCAAATATATATGA-TTTCAAATTTATTTGATCTAACATGAAAA
280643 TAATTATATGTTAAAATATC
121 TAATTATATGTTAAAATATC
* *
280663 TTTTTTATTTTGT-TTTAAAATCTAAAATTAATGATTCAAGTATATCATATTAAATATATATATA
1 TTTTTTATTTT-TCTTTAAAATCTAAAACTAATGATTCAAATATATCATATTAAATATATATATA
* *
280727 TTTTTAAAAGTTTTCAAATATTTATGATTTCAAATTTATTTGTTCTAACATGAAAATAATTATAT
65 TTTTTAAAAGTTTTCAAATATATATGATTTCAAATTTATTTGATCTAACATGAAAATAATTATAT
280792 TGTAATAAAA
Statistics
Matches: 118, Mismatches: 9, Indels: 13
0.84 0.06 0.09
Matches are distributed among these distances:
140 56 0.47
141 1 0.01
143 4 0.03
144 6 0.05
148 5 0.04
149 45 0.38
150 1 0.01
ACGTcount: A:0.39, C:0.06, G:0.05, T:0.50
Consensus pattern (140 bp):
TTTTTTATTTTTCTTTAAAATCTAAAACTAATGATTCAAATATATCATATTAAATATATATATAT
TTTTAAAAGTTTTCAAATATATATGATTTCAAATTTATTTGATCTAACATGAAAATAATTATATG
TTAAAATATC
Found at i:282303 original size:18 final size:17
Alignment explanation
Indices: 282280--282326 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
282270 TATTGTTTGT
282280 TTTTTATTATTTAATAAA
1 TTTTTATTATTTAA-AAA
* *
282298 TTTTTACT-TTTAAAAG
1 TTTTTATTATTTAAAAA
282314 TTTTTATCTATTT
1 TTTTTAT-TATTT
282327 TTGTAGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 8 0.33
17 6 0.25
18 10 0.42
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (17 bp):
TTTTTATTATTTAAAAA
Found at i:289715 original size:11 final size:11
Alignment explanation
Indices: 289701--289725 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
289691 TTAAAAAACT
289701 AAAAAAAATTA
1 AAAAAAAATTA
289712 AAAAAAAATTA
1 AAAAAAAATTA
289723 AAA
1 AAA
289726 TAATATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAAAAATTA
Found at i:292423 original size:20 final size:21
Alignment explanation
Indices: 292398--292437 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
292388 CACAACAGTT
292398 AAATAAAAATAATA-TAATAG
1 AAATAAAAATAATATTAATAG
**
292418 AAATAACGATAATATTAATA
1 AAATAAAAATAATATTAATA
292438 ATATTAATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (21 bp):
AAATAAAAATAATATTAATAG
Found at i:292520 original size:17 final size:15
Alignment explanation
Indices: 292490--292532 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 15
292480 GACATAGTTG
292490 AAAATAATAAATAAA
1 AAAATAATAAATAAA
*
292505 AAAATAATTAAAATAAG
1 AAAATAA-T-AAATAAA
292522 AAAATAA-AAAT
1 AAAATAATAAAT
292533 GATATAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 4 0.16
15 7 0.28
16 1 0.04
17 13 0.52
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (15 bp):
AAAATAATAAATAAA
Found at i:292769 original size:21 final size:22
Alignment explanation
Indices: 292734--292790 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 22
292724 ATTAAAATTG
*
292734 TAAACAAATTAAAGGCA-TAAAT
1 TAAACAAAATAAAGG-ATTAAAT
292756 TAAA-AAAATAAAGGATTAAAT
1 TAAACAAAATAAAGGATTAAAT
292777 TAAAACAAAATAAA
1 T-AAACAAAATAAA
292791 AATGCAGGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 1 0.03
21 15 0.48
22 7 0.23
23 8 0.26
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (22 bp):
TAAACAAAATAAAGGATTAAAT
Found at i:296907 original size:38 final size:38
Alignment explanation
Indices: 296865--296974 Score: 193
Period size: 38 Copynumber: 2.9 Consensus size: 38
296855 CCAAAGAAAT
296865 TTTGGACAGAATTTGTTCTGAAACTATTTAATTATTTC
1 TTTGGACAGAATTTGTTCTGAAACTATTTAATTATTTC
296903 TTTGGACAGAATTTGTTCTGAAACTATTTAATTATTTC
1 TTTGGACAGAATTTGTTCTGAAACTATTTAATTATTTC
* * *
296941 TTTGGACAGAATTCGTTCTGAAATTATATAATTA
1 TTTGGACAGAATTTGTTCTGAAACTATTTAATTA
296975 CATGAATGCT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 69 1.00
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45
Consensus pattern (38 bp):
TTTGGACAGAATTTGTTCTGAAACTATTTAATTATTTC
Done.