Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004607.1 Kokia drynarioides strain JFW-HI SEQ_118110, 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: 2557
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.38
Found at i:1134 original size:29 final size:29
Alignment explanation
Indices: 1026--1255 Score: 98
Period size: 29 Copynumber: 7.9 Consensus size: 29
1016 TTTAACCTCG
* **
1026 AAACTTCTAAAAATTCCATTTTTTACCCCG
1 AAACTTCTAAAAATTACA-TTTTTACCCTA
** **
1056 AAAC-TCTTTAAATTACCATTTTTACCCCC
1 AAACTTCTAAAAATTA-CATTTTTACCCTA
* * **
1085 AAACTTCCAAAAA-AATTTTTTTACCCTA
1 AAACTTCTAAAAATTACATTTTTACCCTA
1113 AAACTTCTAAAAATTACA-TTTTACCTCT-
1 AAACTTCTAAAAATTACATTTTTACC-CTA
* * * ** *
1141 GAACCTCTAAAAATTCAAATTTGAACCC-G
1 AAACTTCTAAAAATT-ACATTTTTACCCTA
* * *
1170 AAACTT-TCAAAAATTACAATTTTGCCCTC
1 AAACTTCT-AAAAATTACATTTTTACCCTA
* * * *
1199 AAA-TGTCCAAAAAATCCATTTTTGACCCAA
1 AAACT-TCTAAAAATTACATTTTT-ACCCTA
* *
1229 AAAC-TCTTAAAATTACCGTTTTTACCC
1 AAACTTCTAAAAATTA-CATTTTTACCC
1256 CCGAATGTCC
Statistics
Matches: 145, Mismatches: 41, Indels: 29
0.67 0.19 0.13
Matches are distributed among these distances:
28 50 0.34
29 67 0.46
30 28 0.19
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.34
Consensus pattern (29 bp):
AAACTTCTAAAAATTACATTTTTACCCTA
Found at i:1343 original size:58 final size:60
Alignment explanation
Indices: 1237--1352 Score: 139
Period size: 58 Copynumber: 2.0 Consensus size: 60
1227 AAAAACTCTT
* * *
1237 AAAATTACCGTTTTTACCCCCGAATGTCCAAAAATTCTATTTTTATCCC-GATTTTTCTA
1 AAAATTACCGTTTTTACCCCCGAATGTCCAAAAATTCCATTTTAATCCCTAATTTTTCTA
** * *
1296 AAAATTACCG-TTTTACCTTCGGATGT-CTAAAATTCCATTTTAAATCCCTAATTTTTC
1 AAAATTACCGTTTTTACCCCCGAATGTCCAAAAATTCCATTTT-AATCCCTAATTTTTC
1353 CAAAGTTACC
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
57 13 0.27
58 18 0.38
59 17 0.35
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.41
Consensus pattern (60 bp):
AAAATTACCGTTTTTACCCCCGAATGTCCAAAAATTCCATTTTAATCCCTAATTTTTCTA
Found at i:2257 original size:20 final size:20
Alignment explanation
Indices: 2232--2319 Score: 79
Period size: 20 Copynumber: 4.3 Consensus size: 20
2222 CTATATTATC
2232 GTTTTGGTG-TTTTCTTTACT
1 GTTTTGGTGCTTTT-TTTACT
* * *
2252 GTTTTGCTTGCTCTTTTTTGCA
1 GTTTTG-GTGCT-TTTTTTACT
* **
2274 GTTTTTGTATTTTTTTTACT
1 GTTTTGGTGCTTTTTTTACT
*
2294 GTTTTGGTGCTTTTTTTATT
1 GTTTTGGTGCTTTTTTTACT
2314 GTTTTG
1 GTTTTG
2320 TTTGTTATTT
Statistics
Matches: 52, Mismatches: 13, Indels: 6
0.73 0.18 0.08
Matches are distributed among these distances:
20 35 0.67
21 4 0.08
22 10 0.19
23 3 0.06
ACGTcount: A:0.06, C:0.09, G:0.18, T:0.67
Consensus pattern (20 bp):
GTTTTGGTGCTTTTTTTACT
Found at i:2330 original size:23 final size:23
Alignment explanation
Indices: 2304--2356 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
2294 GTTTTGGTGC
* *
2304 TTTTTTTATTG-TTTTGTTTGTTA
1 TTTTTGTATTGTTTTTG-CTGTTA
*
2327 TTTTCGTATTGTTTTTGCTGTTA
1 TTTTTGTATTGTTTTTGCTGTTA
2350 TTTTTGT
1 TTTTTGT
2357 TGCTATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.08, C:0.04, G:0.15, T:0.74
Consensus pattern (23 bp):
TTTTTGTATTGTTTTTGCTGTTA
Found at i:2353 original size:12 final size:12
Alignment explanation
Indices: 2315--2372 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
2305 TTTTTTATTG
2315 TTTTGTTTGTTAT
1 TTTTG-TTGTTAT
* * *
2328 TTTCG-TATTGT
1 TTTTGTTGTTAT
*
2339 TTTTGCTGTTAT
1 TTTTGTTGTTAT
*
2351 TTTTGTTGCTAT
1 TTTTGTTGTTAT
2363 TTTTGTTGTT
1 TTTTGTTGTT
2373 TTTAATGTTG
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
11 8 0.23
12 23 0.66
13 4 0.11
ACGTcount: A:0.07, C:0.05, G:0.17, T:0.71
Consensus pattern (12 bp):
TTTTGTTGTTAT
Found at i:2428 original size:44 final size:43
Alignment explanation
Indices: 2313--2430 Score: 103
Period size: 44 Copynumber: 2.6 Consensus size: 43
2303 CTTTTTTTAT
* * * *
2313 TGTTTTGTTTGTTATTTTCGTATTGTTTTTGCTGTTATTTTTGTTGC
1 TGTTTTGGTTGTTATTTT--T-TT-TGTTTGCTATTATTTTTGCTGC
* * * *
2360 TATTTTTGTTGTT-TTTAATGTTGTTTGCTATTAATTTTTGCTGC
1 TGTTTTGGTTGTTATTT-TTTTTGTTTGCTATT-ATTTTTGCTGC
2404 TGTTTTGGTTGTTATTTTTTTTGTTTG
1 TGTTTTGGTTGTTATTTTTTTTGTTTG
2431 GATGTTACTT
Statistics
Matches: 56, Mismatches: 12, Indels: 9
0.73 0.16 0.12
Matches are distributed among these distances:
43 9 0.16
44 30 0.54
45 4 0.07
46 3 0.05
47 10 0.18
ACGTcount: A:0.08, C:0.05, G:0.19, T:0.68
Consensus pattern (43 bp):
TGTTTTGGTTGTTATTTTTTTTGTTTGCTATTATTTTTGCTGC
Done.