Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009705.1 Kokia drynarioides strain JFW-HI SEQ_124424, 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: 6667
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Found at i:1546 original size:23 final size:23
Alignment explanation
Indices: 1518--1571 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
1508 GTTTCTGGTA
* *
1518 TTGTTTTTGGCGTTATTTCATTG
1 TTGTTTTTGGCGCTATTTCACTG
* *
1541 TTGTTTTTTGTGCTATTTCACTG
1 TTGTTTTTGGCGCTATTTCACTG
1564 TTGTTTTT
1 TTGTTTTT
1572 AATGTTGTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.07, C:0.09, G:0.19, T:0.65
Consensus pattern (23 bp):
TTGTTTTTGGCGCTATTTCACTG
Found at i:2321 original size:17 final size:17
Alignment explanation
Indices: 2299--2386 Score: 88
Period size: 17 Copynumber: 5.1 Consensus size: 17
2289 CAAACTCTCT
2299 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
*
2316 TTAAATTT-GTTTAAAA
1 TTAAATTTATTTTAAAA
*
2332 TTTTAAATTTATTTTAAAT
1 --TTAAATTTATTTTAAAA
* **
2351 TTAAATTTAATTTAAGT
1 TTAAATTTATTTTAAAA
* *
2368 TTAAAATTATTTTCAAA
1 TTAAATTTATTTTAAAA
2385 TT
1 TT
2387 TAAAATTATC
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
16 7 0.12
17 37 0.64
18 8 0.14
19 6 0.10
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:2345 original size:11 final size:11
Alignment explanation
Indices: 2331--2388 Score: 55
Period size: 11 Copynumber: 5.1 Consensus size: 11
2321 TTTGTTTAAA
2331 ATTTTAAATTT
1 ATTTTAAATTT
2342 ATTTTAAATTT
1 ATTTTAAATTT
*
2353 AAATTT-AATTT
1 -ATTTTAAATTT
* *
2364 AAGTTTAAAATT
1 -ATTTTAAATTT
2376 ATTTTCAAATTT
1 ATTTT-AAATTT
2388 A
1 A
2389 AAATTATCAT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
11 25 0.64
12 14 0.36
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (11 bp):
ATTTTAAATTT
Found at i:2372 original size:52 final size:52
Alignment explanation
Indices: 2298--2407 Score: 125
Period size: 52 Copynumber: 2.1 Consensus size: 52
2288 CCAAACTCTC
* * **
2298 TTTAAATTTATTTTAAAATT-AAATT-TGTTTAAAATTTTAAATTTATTTTAAA
1 TTTAAATTTAATTTAAAATTAAAATTAT-TTTAAAA-TTTAAAATTATCATAAA
** *
2350 TTTAAATTTAATTTAAGTTTAAAATTATTTTCAAATTTAAAATTATCATAAA
1 TTTAAATTTAATTTAAAATTAAAATTATTTTAAAATTTAAAATTATCATAAA
2402 TTTAAA
1 TTTAAA
2408 ATAAATAAAG
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
52 37 0.76
53 11 0.22
54 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (52 bp):
TTTAAATTTAATTTAAAATTAAAATTATTTTAAAATTTAAAATTATCATAAA
Found at i:2375 original size:35 final size:35
Alignment explanation
Indices: 2301--2409 Score: 116
Period size: 35 Copynumber: 3.1 Consensus size: 35
2291 AACTCTCTTT
* * *
2301 AAATTTATTTTAAAATTAAATTTGTTTAAAATTTT
1 AAATTTATTTTAAATTTAAATTTATTTAAAATTTA
*
2336 AAATTTATTTTAAATTTAAATTTAATTT-AAGTTTA
1 AAATTTATTTTAAATTTAAATTT-ATTTAAAATTTA
* *
2371 AAA-TTATTTTCAAATTTAAAATTA-TCATAAATTTA
1 AAATTTATTTT-AAATTTAAATTTATTTA-AAATTTA
2406 AAAT
1 AAAT
2410 AAATAAAGCC
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
33 1 0.02
34 8 0.13
35 50 0.81
36 3 0.05
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (35 bp):
AAATTTATTTTAAATTTAAATTTATTTAAAATTTA
Found at i:2404 original size:17 final size:18
Alignment explanation
Indices: 2367--2409 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2357 TTAATTTAAG
**
2367 TTTAAAATTATTTTCAAA
1 TTTAAAATTATCATCAAA
2385 TTTAAAATTATCAT-AAA
1 TTTAAAATTATCATCAAA
2402 TTTAAAAT
1 TTTAAAAT
2410 AAATAAAGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTAAAATTATCATCAAA
Found at i:4279 original size:30 final size:30
Alignment explanation
Indices: 4239--4565 Score: 308
Period size: 30 Copynumber: 11.0 Consensus size: 30
4229 TTTACCCCTG
* *
4239 AACTTTCAAAAATCCCAATTTTAACATCGA
1 AACTTTCAAAAATCCCATTTTTAACCTCGA
* * * *
4269 AACTTCCAAAAAATTCCATTTTT-ACCCCTA
1 AACTTTC-AAAAATCCCATTTTTAACCTCGA
* * *
4299 AATTTTCAAAAATCCCATTTTTAACCCCAA
1 AACTTTCAAAAATCCCATTTTTAACCTCGA
* * *
4329 AACTTCCAAAAATTCCATTTTTACCCTC-A
1 AACTTTCAAAAATCCCATTTTTAACCTCGA
*
4358 AACTTTCAAAAATCCCATTTTTGACCTCGA
1 AACTTTCAAAAATCCCATTTTTAACCTCGA
* * *
4388 AACTTCCAAAAATTCCATTTTTACCCTC-A
1 AACTTTCAAAAATCCCATTTTTAACCTCGA
* * *
4417 AACTTTCGAAAATCCCATTTTTGACCCCGA
1 AACTTTCAAAAATCCCATTTTTAACCTCGA
* * *
4447 AACTTTAAAAAATTCCATTTTTTACCCTCG-
1 AACTTTCAAAAATCCCA-TTTTTAACCTCGA
*
4477 AACTTTCAAAAATCCCATTTTTGACCTCGA
1 AACTTTCAAAAATCCCATTTTTAACCTCGA
** * * *
4507 AA-TTTCAAAAAATTACGTTTTTACCCCCG-
1 AACTTTC-AAAAATCCCATTTTTAACCTCGA
* *
4536 AACTTCCAAAAATCCCA-TTTTAACCCCGA
1 AACTTTCAAAAATCCCATTTTTAACCTCGA
4565 A
1 A
4566 TTTTCCCAAA
Statistics
Matches: 238, Mismatches: 50, Indels: 19
0.78 0.16 0.06
Matches are distributed among these distances:
28 10 0.04
29 86 0.36
30 120 0.50
31 22 0.09
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.33
Consensus pattern (30 bp):
AACTTTCAAAAATCCCATTTTTAACCTCGA
Found at i:4349 original size:59 final size:60
Alignment explanation
Indices: 4208--4592 Score: 453
Period size: 59 Copynumber: 6.5 Consensus size: 60
4198 AAAGGTCCCT
* * * **
4208 AAACTATCCAAAAATTCCGTTTTTACCCCT-GAACTTTCAAAAATCCCAATTTTAACATCG
1 AAACT-TCCAAAAATTCCATTTTTACCCCTCAAACTTTCAAAAATCCCATTTTTAACCCCG
* *
4268 AAACTTCCAAAAAATTCCATTTTTACCCCT-AAATTTTCAAAAATCCCATTTTTAACCCCA
1 AAACTTCC-AAAAATTCCATTTTTACCCCTCAAACTTTCAAAAATCCCATTTTTAACCCCG
* *
4328 AAACTTCCAAAAATTCCATTTTTA-CCCTCAAACTTTCAAAAATCCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTTACCCCTCAAACTTTCAAAAATCCCATTTTTAACCCCG
* *
4387 AAACTTCCAAAAATTCCATTTTTA-CCCTCAAACTTTCGAAAATCCCATTTTTGACCCCG
1 AAACTTCCAAAAATTCCATTTTTACCCCTCAAACTTTCAAAAATCCCATTTTTAACCCCG
** * * *
4446 AAACTTTAAAAAATTCCATTTTTTA-CCCTCGAACTTTCAAAAATCCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCA-TTTTTACCCCTCAAACTTTCAAAAATCCCATTTTTAACCCCG
* * * * * *
4506 AAATTTCAAAAAATTACGTTTTTACCCC-CGAACTTCCAAAAATCCCA-TTTTAACCCCG
1 AAACTTCCAAAAATTCCATTTTTACCCCTCAAACTTTCAAAAATCCCATTTTTAACCCCG
** *
4564 AATTTTCCCAAAATTACCA-TTTTACCCCT
1 AAACTTCCAAAAATT-CCATTTTTACCCCT
4593 GGTATCCTAA
Statistics
Matches: 289, Mismatches: 30, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
58 34 0.12
59 143 0.49
60 112 0.39
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (60 bp):
AAACTTCCAAAAATTCCATTTTTACCCCTCAAACTTTCAAAAATCCCATTTTTAACCCCG
Found at i:4366 original size:119 final size:119
Alignment explanation
Indices: 4208--4590 Score: 499
Period size: 119 Copynumber: 3.2 Consensus size: 119
4198 AAAGGTCCCT
* * * *
4208 AAACTATCCAAAAATTCCGTTTTTACCC-CTGAACTTTCAAAAATCCCAATTTTAACATCGAAAC
1 AAACT-TCCAAAAATTCCATTTTTACCCTC-GAACTTTCAAAAATCCCATTTTTGACCTCGAAAC
* *
4272 TTCCAAAAAATTCCATTTTTACCCCTAAATTTTCAAAAATCCCATTTTTAACCCCA
64 TTCCAAAAAATTCCATTTTTACCCCTAAACTTTCAAAAATCCCATTTTTAACCCCG
*
4328 AAACTTCCAAAAATTCCATTTTTACCCTCAAACTTTCAAAAATCCCATTTTTGACCTCGAAACTT
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTTCAAAAATCCCATTTTTGACCTCGAAACTT
* *
4393 CC-AAAAATTCCATTTTTA-CCCTCAAACTTTCGAAAATCCCATTTTTGACCCCG
66 CCAAAAAATTCCATTTTTACCCCT-AAACTTTCAAAAATCCCATTTTTAACCCCG
**
4446 AAACTTTAAAAAATTCCATTTTTTACCCTCGAACTTTCAAAAATCCCATTTTTGACCTCGAAA-T
1 AAACTTCCAAAAATTCCA-TTTTTACCCTCGAACTTTCAAAAATCCCATTTTTGACCTCGAAACT
* * * ** *
4510 TTCAAAAAATTACGTTTTTACCCCCGAACTTCCAAAAATCCCA-TTTTAACCCCG
65 TCCAAAAAATTCCATTTTTACCCCTAAACTTTCAAAAATCCCATTTTTAACCCCG
** *
4564 AATTTTCCCAAAATTACCA-TTTTACCC
1 AAACTTCCAAAAATT-CCATTTTTACCC
4591 CTGGTATCCT
Statistics
Matches: 232, Mismatches: 25, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
117 12 0.05
118 81 0.35
119 130 0.56
120 9 0.04
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (119 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTTCAAAAATCCCATTTTTGACCTCGAAACTT
CCAAAAAATTCCATTTTTACCCCTAAACTTTCAAAAATCCCATTTTTAACCCCG
Found at i:4575 original size:30 final size:29
Alignment explanation
Indices: 4209--4591 Score: 282
Period size: 30 Copynumber: 13.0 Consensus size: 29
4199 AAGGTCCCTA
* * *
4209 AACTATCCAAAAATTCCGTTTTTACCCCTG
1 AACTTTCCAAAAATCCCATTTTTACCCC-G
* **
4239 AACTTT-CAAAAATCCCAATTTTAACATCG
1 AACTTTCCAAAAATCCC-ATTTTTACCCCG
* *
4268 AAAC-TTCCAAAAAATTCCATTTTTACCCCT
1 -AACTTTCC-AAAAATCCCATTTTTACCCCG
* * *
4298 AAATTTTCAAAAATCCCATTTTTAACCCCAA
1 AACTTTCCAAAAATCCCATTTTT-ACCCC-G
* *
4329 AAC-TTCCAAAAATTCCATTTTTACCCTCA
1 AACTTTCCAAAAATCCCATTTTTACCC-CG
*
4358 AACTTT-CAAAAATCCCATTTTTGACCTCG
1 AACTTTCCAAAAATCCCATTTTT-ACCCCG
* *
4387 AAAC-TTCCAAAAATTCCATTTTTACCCTCA
1 -AACTTTCCAAAAATCCCATTTTTACCC-CG
*
4417 AACTTT-CGAAAATCCCATTTTTGACCCCG
1 AACTTTCCAAAAATCCCATTTTT-ACCCCG
* *
4446 AAACTTT-AAAAAATTCCATTTTTTACCCTCG
1 -AACTTTCCAAAAATCCCA-TTTTTACCC-CG
*
4477 AACTTT-CAAAAATCCCATTTTTGACCTCG
1 AACTTTCCAAAAATCCCATTTTT-ACCCCG
* * ** *
4506 AAATTTCAAAAAATTACGTTTTTACCCCCG
1 AACTTTCCAAAAATCCCATTTTTA-CCCCG
*
4536 AAC-TTCCAAAAATCCCATTTTAACCCCG
1 AACTTTCCAAAAATCCCATTTTTACCCCG
* * *
4564 AATTTTCCCAAAATTACCA-TTTTACCCC
1 AACTTT-CCAAAAATCCCATTTTTACCCC
4592 TGGTATCCTA
Statistics
Matches: 281, Mismatches: 49, Indels: 47
0.75 0.13 0.12
Matches are distributed among these distances:
28 7 0.02
29 113 0.40
30 144 0.51
31 17 0.06
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (29 bp):
AACTTTCCAAAAATCCCATTTTTACCCCG
Done.