Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010670.1 Kokia drynarioides strain JFW-HI SEQ_125616, 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: 3056
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Found at i:1186 original size:201 final size:206
Alignment explanation
Indices: 837--1773 Score: 1234
Period size: 218 Copynumber: 4.5 Consensus size: 206
827 AAAGACGCGG
* * **
837 TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTTGGCATGAGCAAATCT
1 TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAACCAAACCCACGCTCGATATGAGCAAATCT
* *
902 TTGAACCACAGCTTCCTAATGAGATACTGAGAAG-A-C-G--GTTAGCTTCCTGACCATCTTCCT
66 TCGAACCACAGCTTCCTGATGAGATACTGAGAAGAAGCAGAAGTTAGCTTCCTGACCATCTTCCT
* *
962 GATGAGGTATGGAGAAATGGACCAAATTCATCTTCGTGATGAGATACAGAGAAGCGAATTGAAAC
131 GATGAGGTATGGAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAGAGAAGCGAATTGAAAC
1027 AGACGACGTGA
196 AGACGACGTGA
* *
1038 TCATCTTCCTGATGAGATACTGAGAAGAAGCCCAAACCAAACCCACGCTCGATGTGAGCAAATCT
1 TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAACCAAACCCACGCTCGATATGAGCAAATCT
* *
1103 TCGAACCACAGCTTCCTGATGAGAGACTGAGAAG-A-C-G-A-TTAGCTTTCTGACCATCTTCCT
66 TCGAACCACAGCTTCCTGATGAGATACTGAGAAGAAGCAGAAGTTAGCTTCCTGACCATCTTCCT
*
1163 GATGAGGTATGGAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAAAGAAGCGAATTGAAAC
131 GATGAGGTATGGAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAGAGAAGCGAATTGAAAC
*
1228 AGACGACGTGG
196 AGACGACGTGA
* *
1239 TCATCTTCCTGATGAGATACTGAGAATAAGACCAAACCAAACCCACGCTCGGTATGAGCAAATCT
1 TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAACCAAACCCACGCTCGATATGAGCAAATCT
1304 TCGAACCACAGCTTCCTGATGAGATACTGAGAAGCAAGTCAAAGTAATAAAACGGTTAGCTTCCT
66 TCGAACCACAGCTTCCTGATGAGATACTGAGAAG-AAG-C--AG------AA--GTTAGCTTCCT
*
1369 GACCATCTTCCTGATGAGGTATGGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAA
119 GACCATCTTCCTGATGAGGTATGGAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAGAGAA
* *
1434 GCGAATTAAAACAGACGACGTGG
184 GCGAATTGAAACAGACGACGTGA
* *
1457 TCATCTTCCTGATGAGATATTGAGAAGAAGACCAAACCAAACCCACGCTCGATATGAGAAAATCT
1 TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAACCAAACCCACGCTCGATATGAGCAAATCT
*
1522 TCGAACCACAACTTCCTGATGAGATACTGAGAAGCAAGTCAAAGTAATAAAACGGTTAGCTTCCT
66 TCGAACCACAGCTTCCTGATGAGATACTGAGAAG-AAG-C--AG------AA--GTTAGCTTCCT
*
1587 GACCATCTTCCTGATGAGGTACGGAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAGAGAA
119 GACCATCTTCCTGATGAGGTATGGAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAGAGAA
* *
1652 GCGAATTGAAACAGATGACG-CA
184 GCGAATTGAAACAGACGACGTGA
* * * * * *
1674 GTCATCTT-CTCGATGAGATACCGAGAAAAAGACCAAATCAAACTCACG-TCCGATGTGAGAAAA
1 -TCATCTTCCT-GATGAGATACTGAGAAGAAGACCAAACCAAACCCACGCT-CGATATGAGCAAA
* * *
1737 TATTCGAACCCCAGCTTCCTGATGAGACACTGAGAAG
63 TCTTCGAACCACAGCTTCCTGATGAGATACTGAGAAG
1774 TAGGTCGAAG
Statistics
Matches: 671, Mismatches: 44, Indels: 25
0.91 0.06 0.03
Matches are distributed among these distances:
201 280 0.42
203 1 0.00
205 1 0.00
208 1 0.00
215 1 0.00
217 3 0.00
218 384 0.57
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (206 bp):
TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAACCAAACCCACGCTCGATATGAGCAAATCT
TCGAACCACAGCTTCCTGATGAGATACTGAGAAGAAGCAGAAGTTAGCTTCCTGACCATCTTCCT
GATGAGGTATGGAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAGAGAAGCGAATTGAAAC
AGACGACGTGA
Found at i:2252 original size:17 final size:18
Alignment explanation
Indices: 2229--2327 Score: 103
Period size: 18 Copynumber: 5.6 Consensus size: 18
2219 CCATACTCCC
2229 TTTAAATTTATTTTAAAA
1 TTTAAATTTATTTTAAAA
* *
2247 -TTAAATTTGTTTAAAAA
1 TTTAAATTTATTTTAAAA
*
2264 TTTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAAAA
* * *
2282 TTTAAATTTAATTT-GAG
1 TTTAAATTTATTTTAAAA
* *
2299 TTTAAAATTATTTTCAAA
1 TTTAAATTTATTTTAAAA
2317 TTTAAAGTTTA
1 TTTAAA-TTTA
2328 AAATAAATAA
Statistics
Matches: 66, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
17 28 0.42
18 35 0.53
19 3 0.05
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (18 bp):
TTTAAATTTATTTTAAAA
Found at i:2288 original size:24 final size:24
Alignment explanation
Indices: 2261--2307 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2251 ATTTGTTTAA
*
2261 AAATTTAAATTTG-TTTTAAAATTT
1 AAATTT-AATTTGAGTTTAAAATTT
2285 AAATTTAATTTGAGTTTAAAATT
1 AAATTTAATTTGAGTTTAAAATT
2308 ATTTTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (24 bp):
AAATTTAATTTGAGTTTAAAATTT
Found at i:2303 original size:35 final size:36
Alignment explanation
Indices: 2229--2327 Score: 76
Period size: 35 Copynumber: 2.8 Consensus size: 36
2219 CCATACTCCC
* * *
2229 TTTAAATTTATTTTAAAA-TTAAATTTGTTTAAAAA
1 TTTAAATTTAATTTAAAATTTAAATTTATTTTAAAA
** * * *
2264 TTTAAATTTGTTTTAAAATTTAAATTTAATTT-GAG
1 TTTAAATTTAATTTAAAATTTAAATTTATTTTAAAA
* * *
2299 TTTAAAATTATTTTCAAATTTAAAGTTTA
1 TTTAAATTTAATTTAAAATTTAAA-TTTA
2328 AAATAAATAA
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
35 39 0.74
36 14 0.26
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (36 bp):
TTTAAATTTAATTTAAAATTTAAATTTATTTTAAAA
Done.