Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008602.1 Kokia drynarioides strain JFW-HI SEQ_123280, 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: 7291
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Found at i:4306 original size:172 final size:172
Alignment explanation
Indices: 4020--4386 Score: 563
Period size: 172 Copynumber: 2.1 Consensus size: 172
4010 ATTCGTCTTT
* * * * *
4020 CTGATGAGATACAGAGAAGAGGATTAAAATAATGAAGCGGTCATTTTCCTGATGAGATACTGAGA
1 CTGATGAGATACAGAGAAGTGAATTAAAATAATGAAGCGATCATCTTCCTAATGAGATACTGAGA
* * * *
4085 AGTAGACCAATTCAATGAAGCGAAGCTCAATGTGAGTGAAATTTCAAACCCCCATCTTCCTGATG
66 AGTAGACCAAATCAATAAAGCAAAGCTCAATGTGAGTGAAACTTCAAACCCCCATCTTCCTGATG
4150 AGATACAAAGAAGTGGGTAAAAGCAATAAAGCGGTTACCTTC
131 AGATACAAAGAAGTGGGTAAAAGCAATAAAGCGGTTACCTTC
* * *
4192 CTGATGAGATACAGAGAGGTGAATTAAAATAATGAGGCGATCATCTTCCTAATGAGATATTGAGA
1 CTGATGAGATACAGAGAAGTGAATTAAAATAATGAAGCGATCATCTTCCTAATGAGATACTGAGA
* * *
4257 AGTAGACCAAATCAATAAAGCAAAGCTCAATTTGAGTGAAACTTCAAACCCTCATCTTCTTGATG
66 AGTAGACCAAATCAATAAAGCAAAGCTCAATGTGAGTGAAACTTCAAACCCCCATCTTCCTGATG
* * *
4322 AGATACAGAGAAGTGGGTCAAAGCAATAAAGTGGTTACCTTC
131 AGATACAAAGAAGTGGGTAAAAGCAATAAAGCGGTTACCTTC
*
4364 CTAATGAGATACAGAGAAGTGAA
1 CTGATGAGATACAGAGAAGTGAA
4387 CCAAATCCGT
Statistics
Matches: 175, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
172 175 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.24
Consensus pattern (172 bp):
CTGATGAGATACAGAGAAGTGAATTAAAATAATGAAGCGATCATCTTCCTAATGAGATACTGAGA
AGTAGACCAAATCAATAAAGCAAAGCTCAATGTGAGTGAAACTTCAAACCCCCATCTTCCTGATG
AGATACAAAGAAGTGGGTAAAAGCAATAAAGCGGTTACCTTC
Found at i:4475 original size:85 final size:85
Alignment explanation
Indices: 4311--4468 Score: 217
Period size: 85 Copynumber: 1.9 Consensus size: 85
4301 CAAACCCTCA
* * * * *
4311 TCTTCTTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGTGGTTACCTTCCTAATGAGATAC
1 TCTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATAAAGCGGTCACCTTCCTAATGAGATAC
4376 AGAGAAGTGAACCAAATCCG
66 AGAGAAGTGAACCAAATCCG
* * * * *
4396 TCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAATGAGGCGGTCATCTTCCTGATGAGATAC
1 TCTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATAAAGCGGTCACCTTCCTAATGAGATAC
*
4461 TGAGAAGT
66 AGAGAAGT
4469 AGACCAATTC
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
85 62 1.00
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.25
Consensus pattern (85 bp):
TCTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATAAAGCGGTCACCTTCCTAATGAGATAC
AGAGAAGTGAACCAAATCCG
Found at i:4549 original size:161 final size:161
Alignment explanation
Indices: 4367--4660 Score: 480
Period size: 161 Copynumber: 1.8 Consensus size: 161
4357 TACCTTCCTA
* * *
4367 ATGAGATACAGAGAAGTGAACCAAATCCGTCTTCCTGATGAGATACAGAGAAGTGGATTAAAACA
1 ATGAGATACAGAGAAGTGAACCAAATACGTCTTCATGATGAGATACAAAGAAGTGGATTAAAACA
* * *
4432 ATGAGGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAATTCAATGAAGCGAAGCTCAAT
66 ATGAGGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAGCAAAGCCCAAT
4497 GTGAGTGAAATTTCAAATCCTCATCTTCTTG
131 GTGAGTGAAATTTCAAATCCTCATCTTCTTG
* * *
4528 ATGAGCTACAGAGAAGTGAACCAAATATGTCTTTATGATGAGATACAAAGAAGTGGATTAAAACA
1 ATGAGATACAGAGAAGTGAACCAAATACGTCTTCATGATGAGATACAAAGAAGTGGATTAAAACA
* * *
4593 ATGAGGTGGTCATCTTCTTGATGAGATACTGAGAAGTAGACCAAATCAATGAAGTAAAGCCCAAT
66 ATGAGGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAGCAAAGCCCAAT
4658 GTG
131 GTG
4661 TGAGCGAAAC
Statistics
Matches: 121, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
161 121 1.00
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.24
Consensus pattern (161 bp):
ATGAGATACAGAGAAGTGAACCAAATACGTCTTCATGATGAGATACAAAGAAGTGGATTAAAACA
ATGAGGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAGCAAAGCCCAAT
GTGAGTGAAATTTCAAATCCTCATCTTCTTG
Found at i:4617 original size:209 final size:212
Alignment explanation
Indices: 4140--4629 Score: 522
Period size: 209 Copynumber: 2.3 Consensus size: 212
4130 AAACCCCCAT
* * * *
4140 CTTCCTGATGAGATACAAAGAAGTGGGTAAAAGCAATAAAGCGGTTACCTTCCTGATGAGATACA
1 CTTCATGATGAGATACAAAGAAGT-GGTAAAA-CAAT--AGTGGTCATCTTCCTGATGAGATACA
* * *
4205 GAGAGGTGAATTAAAATAATGAGGCGATCATCTTCCTAATGAGATATTGAGAAGTAGACCAAATC
62 GAGAAGTGAATTAAAACAATGAGGCGATCATCTTCCTAATGAGATACTGAGAAGTAGACCAAATC
*
4270 AATAAAGCAAAGCTCAATTTGAGTGAAACTTCAAACCCTCATCTTCTTGATGAGATACAGAGAAG
127 AATAAAGCAAAGCTCAATGTGAGTGAAACTTCAAACCCTCATCTTCTTGATGAGATACAGAGAAG
*
4335 TGGGTCAAAGCAATAAAGTGGTTA
192 T-GG--AAACCAATAAAGTGGTTA
* * * * * *
4359 CCTTCCTAATGAGATACAGAGAAGT-G--AACCAA-A-T--CCGTCTTCCTGATGAGATACAGAG
1 -CTTCATGATGAGATACAAAGAAGTGGTAAAACAATAGTGGTCATCTTCCTGATGAGATACAGAG
* * * *
4417 AAGTGGATTAAAACAATGAGGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAATTCAAT
65 AAGTGAATTAAAACAATGAGGCGATCATCTTCCTAATGAGATACTGAGAAGTAGACCAAATCAAT
* * * * *
4482 GAAGCGAAGCTCAATGTGAGTGAAATTTCAAATCCTCATCTTCTTGATGAGCTACAGAGAAGT-G
130 AAAGCAAAGCTCAATGTGAGTGAAACTTCAAACCCTCATCTTCTTGATGAGATACAGAGAAGTGG
*
4546 -AACCAA-ATA-T-G-T-
195 AAACCAATAAAGTGGTTA
* * *
4558 CTTTATGATGAGATACAAAGAAGTGGATTAAAACAATGAGGTGGTCATCTTCTTGATGAGATACT
1 CTTCATGATGAGATACAAAGAAGTGG--TAAAACAAT-A-GTGGTCATCTTCCTGATGAGATACA
4623 GAGAAGT
62 GAGAAGT
4630 AGACCAAATC
Statistics
Matches: 227, Mismatches: 32, Indels: 33
0.78 0.11 0.11
Matches are distributed among these distances:
198 20 0.09
199 1 0.00
200 1 0.00
201 1 0.00
202 1 0.00
203 7 0.03
204 5 0.02
205 1 0.00
207 2 0.01
209 159 0.70
212 1 0.00
215 3 0.01
216 2 0.01
218 1 0.00
220 22 0.10
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (212 bp):
CTTCATGATGAGATACAAAGAAGTGGTAAAACAATAGTGGTCATCTTCCTGATGAGATACAGAGA
AGTGAATTAAAACAATGAGGCGATCATCTTCCTAATGAGATACTGAGAAGTAGACCAAATCAATA
AAGCAAAGCTCAATGTGAGTGAAACTTCAAACCCTCATCTTCTTGATGAGATACAGAGAAGTGGA
AACCAATAAAGTGGTTA
Found at i:5675 original size:24 final size:24
Alignment explanation
Indices: 5648--5695 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
5638 AAAAAAAAGG
*
5648 GGGTTTATAGAAGACAGATTTTTA
1 GGGTTCATAGAAGACAGATTTTTA
5672 GGGTTCATAGAAGACAGATTTTTA
1 GGGTTCATAGAAGACAGATTTTTA
5696 AAAAAATAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.35
Consensus pattern (24 bp):
GGGTTCATAGAAGACAGATTTTTA
Done.