Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005295.1 Kokia drynarioides strain JFW-HI SEQ_119221, 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: 15538
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:1011 original size:16 final size:17
Alignment explanation
Indices: 981--1014 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
971 AAAAAAATCA
*
981 ATTTTTTAATTAAAATT
1 ATTTTTTAATAAAAATT
998 ATTTTTT-ATAAAAATT
1 ATTTTTTAATAAAAATT
1014 A
1 A
1015 AAAAATGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTTTAATAAAAATT
Found at i:1129 original size:22 final size:22
Alignment explanation
Indices: 1104--1154 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
1094 CTCAATGATA
* *
1104 AAATATTATAACGCGATAATTT
1 AAATATTAAAACGCAATAATTT
* *
1126 AAATGATTAAAACGTAATATTTT
1 AAAT-ATTAAAACGCAATAATTT
1149 AAATAT
1 AAATAT
1155 AGATAACTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (22 bp):
AAATATTAAAACGCAATAATTT
Found at i:6318 original size:21 final size:21
Alignment explanation
Indices: 6292--6331 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
6282 TTCCAGATCC
6292 TATGTCCTCCCCTGAAAATTT
1 TATGTCCTCCCCTGAAAATTT
*
6313 TATGTCCTTCCCTGAAAAT
1 TATGTCCTCCCCTGAAAAT
6332 CTATAAACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.28, G:0.10, T:0.38
Consensus pattern (21 bp):
TATGTCCTCCCCTGAAAATTT
Found at i:9570 original size:4 final size:4
Alignment explanation
Indices: 9563--9627 Score: 60
Period size: 4 Copynumber: 16.0 Consensus size: 4
9553 AAACAAACGG
* * * *
9563 GAAA GAAA AAAA GAAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
*
9613 -AAA GAAG GAAA GAAA
1 GAAA GAAA GAAA GAAA
9628 AATAATGTGT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
3 3 0.06
4 39 0.78
5 8 0.16
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:13007 original size:21 final size:20
Alignment explanation
Indices: 12970--13036 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
12960 GGTTTAGAGT
* *
12970 TTTAAGTCT-AGTATTTACGG
1 TTTAAGTTTAAGT-TTTAGGG
12990 TTTAAGGTTTTAAG-TTTAGGG
1 TTTAA-G-TTTAAGTTTTAGGG
13011 TTTCAAGTTTAAGTTTTAGGG
1 TTT-AAGTTTAAGTTTTAGGG
13032 TTTAA
1 TTTAA
13037 TGTTATGAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
20 13 0.32
21 21 0.52
22 4 0.10
23 2 0.05
ACGTcount: A:0.25, C:0.04, G:0.22, T:0.48
Consensus pattern (20 bp):
TTTAAGTTTAAGTTTTAGGG
Found at i:13012 original size:14 final size:14
Alignment explanation
Indices: 12989--13023 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
12979 AGTATTTACG
*
12989 GTTTAAGGTTTTAA
1 GTTTAAGGTTTCAA
*
13003 GTTTAGGGTTTCAA
1 GTTTAAGGTTTCAA
13017 GTTTAAG
1 GTTTAAG
13024 TTTTAGGGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.26, C:0.03, G:0.26, T:0.46
Consensus pattern (14 bp):
GTTTAAGGTTTCAA
Found at i:13272 original size:21 final size:21
Alignment explanation
Indices: 13246--13290 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
13236 TAGGGTCCAT
*
13246 TTGCCCTGA-AGGAGTAAAGTA
1 TTGCCC-GAGAGGAATAAAGTA
*
13267 TTGCCCGAGAGGAATAGAGTA
1 TTGCCCGAGAGGAATAAAGTA
13288 TTG
1 TTG
13291 TGGTGGCTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.24
Consensus pattern (21 bp):
TTGCCCGAGAGGAATAAAGTA
Found at i:13414 original size:45 final size:45
Alignment explanation
Indices: 13283--13419 Score: 202
Period size: 45 Copynumber: 3.0 Consensus size: 45
13273 GAGAGGAATA
* ** **
13283 GAGTATTGTGGTGGCTCGTCAAACTCAACCTGATATCCTTCCCTT
1 GAGTATTGTGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
* * *
13328 GAGTATTGCGGTGGCTCGTCAAATTGAGGCTGATATTCTTGGCTT
1 GAGTATTGTGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
13373 GAGTATTGTGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
1 GAGTATTGTGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
13418 GA
1 GA
13420 TGAACTATGC
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 81 1.00
ACGTcount: A:0.19, C:0.20, G:0.28, T:0.34
Consensus pattern (45 bp):
GAGTATTGTGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
Found at i:15240 original size:29 final size:28
Alignment explanation
Indices: 15208--15301 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 28
15198 CCAAAATGTG
15208 TTATTTACTAAAATGGTACAAATATATAT
1 TTATTTACTAAAATGGTACAAATA-ATAT
* * * * * **
15237 TTATATACCAAAATAGTATCCACACACCA-
1 TTATTTACTAAAATGGTA--CAAATAATAT
15266 TTATTTACTAAAATGGTACAAAATAAATAT
1 TTATTTACTAAAATGGTAC-AAAT-AATAT
15296 TTATTT
1 TTATTT
15302 TGTACCATTT
Statistics
Matches: 46, Mismatches: 14, Indels: 9
0.67 0.20 0.13
Matches are distributed among these distances:
27 1 0.02
28 2 0.04
29 32 0.70
30 7 0.15
31 4 0.09
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.37
Consensus pattern (28 bp):
TTATTTACTAAAATGGTACAAATAATAT
Found at i:15355 original size:16 final size:16
Alignment explanation
Indices: 15334--15382 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
15324 TGATGGATAT
15334 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
15350 ATTATTTTTAT-ATT-
1 ATTATTTTGATAATTA
*
15364 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
15379 ATTA
1 ATTA
15383 GCTAGGTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
13 7 0.26
14 4 0.15
15 4 0.15
16 12 0.44
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Done.