Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009817.1 Kokia drynarioides strain JFW-HI SEQ_124538, 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: 9481
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.33
Found at i:1128 original size:23 final size:22
Alignment explanation
Indices: 1098--1293 Score: 148
Period size: 23 Copynumber: 8.5 Consensus size: 22
1088 ACGCTAGCGC
1098 GCTTACTG-TTCAGCACTGTGTGT
1 GCTTACTGTTTC-GCACT-TGTGT
1121 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTT-GTGT
*
1144 GCTTACAGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTT-GTGT
1167 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTT-GTGT
* * * *
1190 GCCTACT-TATTTGCGCTATGTGC
1 GCTTACTGT-TTCGCACT-TGTGT
* **
1213 GCCTACTAATT-GCACTGTGTGT
1 GCTTACTGTTTCGCACT-TGTGT
*
1235 GCTTACTGGATT-GCACTGTGTGT
1 GCTTACT-GTTTCGCACT-TGTGT
1258 GCTTACTGTTTCCCTAGCACTTGTGT
1 GCTTACTGTTT--C--GCACTTGTGT
*
1284 ACTTACTGTT
1 GCTTACTGTT
1294 AAGTACTTCG
Statistics
Matches: 148, Mismatches: 14, Indels: 19
0.82 0.08 0.10
Matches are distributed among these distances:
22 19 0.13
23 106 0.72
24 4 0.03
26 14 0.09
27 5 0.03
ACGTcount: A:0.13, C:0.24, G:0.22, T:0.41
Consensus pattern (22 bp):
GCTTACTGTTTCGCACTTGTGT
Found at i:2311 original size:20 final size:20
Alignment explanation
Indices: 2288--2363 Score: 54
Period size: 20 Copynumber: 3.8 Consensus size: 20
2278 ATTTTAAAAT
2288 TTTTATATTTTAAAAATTAA
1 TTTTATATTTTAAAAATTAA
2308 TTTTA-A----AAAAATGTAATAA
1 TTTTATATTTTAAAAA--T--TAA
*
2327 TTTTATATTTTAAAAAATAA
1 TTTTATATTTTAAAAATTAA
2347 TTTTAATAATTTTAAAA
1 TTTT-AT-ATTTTAAAA
2364 TCATTTGTTG
Statistics
Matches: 44, Mismatches: 1, Indels: 20
0.68 0.02 0.31
Matches are distributed among these distances:
15 5 0.11
17 1 0.02
19 9 0.20
20 13 0.30
21 2 0.05
22 9 0.20
24 5 0.11
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (20 bp):
TTTTATATTTTAAAAATTAA
Found at i:2329 original size:40 final size:39
Alignment explanation
Indices: 2268--2352 Score: 118
Period size: 39 Copynumber: 2.2 Consensus size: 39
2258 ATTATTATAT
* * *
2268 TTTTAAAATAATTTTAAAATTTTTATATTTTAAAAATTAA
1 TTTTAAAATAAATGTAAAA-TTTTATATTTTAAAAAATAA
2308 TTTTAAAA-AAATGTAATAATTTTATATTTTAAAAAATAA
1 TTTTAAAATAAATGTAA-AATTTTATATTTTAAAAAATAA
2347 TTTTAA
1 TTTTAA
2353 TAATTTTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
39 31 0.76
40 10 0.24
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (39 bp):
TTTTAAAATAAATGTAAAATTTTATATTTTAAAAAATAA
Found at i:2364 original size:20 final size:19
Alignment explanation
Indices: 2322--2363 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
2312 AAAAAAATGT
2322 AATAATTTTATATTTTAAAA
1 AATAATTTTATATTTT-AAA
2342 AATAATTTTAATAATTTTAAA
1 AATAATTTT-AT-ATTTTAAA
2363 A
1 A
2364 TCATTTGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 9 0.45
21 6 0.30
22 5 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AATAATTTTATATTTTAAA
Found at i:2511 original size:29 final size:29
Alignment explanation
Indices: 2448--2517 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
2438 AAAAAAATTT
* * *
2448 GTCATGTCAACACGGTTAGTCAACTAATG
1 GTCACGTCAACACCGTTAGTCAACTAACG
* *
2477 GCCACGTCAGCACCGTTAGTCAACTAACG
1 GTCACGTCAACACCGTTAGTCAACTAACG
*
2506 GTCACGCCAACA
1 GTCACGTCAACA
2518 AGACCGTTAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (29 bp):
GTCACGTCAACACCGTTAGTCAACTAACG
Found at i:9355 original size:12 final size:12
Alignment explanation
Indices: 9340--9378 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
9330 AAATTGAAGG
*
9340 AAAAAAGAATGA
1 AAAAAAGAAAGA
9352 AAAAAGAGAAAGA
1 AAAAA-AGAAAGA
9365 AAAAAAGAAAGA
1 AAAAAAGAAAGA
9377 AA
1 AA
9379 GAAGAAGGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 14 0.56
13 11 0.44
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (12 bp):
AAAAAAGAAAGA
Done.