Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014277.1 Kokia drynarioides strain JFW-HI SEQ_129310, 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: 41053
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Warning! 39 characters in sequence are not A, C, G, or T
Found at i:8732 original size:29 final size:29
Alignment explanation
Indices: 8681--8752 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 29
8671 AGAAGGGTAG
8681 AGTGAG-AAAAAAAACAATCGACAAATAC
1 AGTGAGAAAAAAAAACAATCGACAAATAC
* *
8709 AGTGAGAAAAAAAAACAAAT-GACAGATAT
1 AGTGAGAAAAAAAAAC-AATCGACAAATAC
8738 AGTGAGAAAAAAAAA
1 AGTGAGAAAAAAAAA
8753 ATATAGGGAG
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
28 6 0.15
29 31 0.77
30 3 0.08
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11
Consensus pattern (29 bp):
AGTGAGAAAAAAAAACAATCGACAAATAC
Found at i:17781 original size:12 final size:12
Alignment explanation
Indices: 17764--17789 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
17754 AGGCCAAAAC
17764 ACGTGACCTACA
1 ACGTGACCTACA
17776 ACGTGACCTACA
1 ACGTGACCTACA
17788 AC
1 AC
17790 TTTAGAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.35, G:0.15, T:0.15
Consensus pattern (12 bp):
ACGTGACCTACA
Found at i:22255 original size:30 final size:31
Alignment explanation
Indices: 22220--22287 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 31
22210 CATACATTTT
*
22220 AAATTTAATTTCA-ATACTTTTTTAT-TTTAG
1 AAATTTAA-TTCATATACTTTTTTATATTTAA
* *
22250 AAATTTAATTCATTTACTTTTTTTTATTTAA
1 AAATTTAATTCATATACTTTTTTATATTTAA
22281 AAATTTA
1 AAATTTA
22288 GGTTCAATTG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 4 0.12
30 18 0.55
31 11 0.33
ACGTcount: A:0.35, C:0.06, G:0.01, T:0.57
Consensus pattern (31 bp):
AAATTTAATTCATATACTTTTTTATATTTAA
Found at i:24033 original size:11 final size:11
Alignment explanation
Indices: 24002--24037 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
23992 TAGACCATGC
24002 TTAACCTTTAA
1 TTAACCTTTAA
*
24013 TTAATC-TTAA
1 TTAACCTTTAA
24023 TTAACCTTTAA
1 TTAACCTTTAA
24034 TTAA
1 TTAA
24038 ACATGTTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (11 bp):
TTAACCTTTAA
Found at i:31238 original size:57 final size:57
Alignment explanation
Indices: 31166--31428 Score: 393
Period size: 57 Copynumber: 4.6 Consensus size: 57
31156 TAACCAATTT
* * * * *
31166 ATACCATTTTCACAT-ATCTCATCTCAATGTCATATTCTATCATTAATCCATAAGATC
1 ATACCAATTTCACATAAT-TCATTTCAATGTCATATTCCATTATCAATCCATAAGATC
* * *
31223 ATACCAATTTTACATAATTCATTTCAACGTCCTATTCCATTATCAATCCATAAGATC
1 ATACCAATTTCACATAATTCATTTCAATGTCATATTCCATTATCAATCCATAAGATC
* * *
31280 ATACCAAATTCACATAATTCATTTCAATGTCATATTCCATTGTCAATCTATAAGATC
1 ATACCAATTTCACATAATTCATTTCAATGTCATATTCCATTATCAATCCATAAGATC
* *
31337 ATACCAATTTCACATAATTCATTTCAATGTCATATTCCATTGTCAATCTATAAGATC
1 ATACCAATTTCACATAATTCATTTCAATGTCATATTCCATTATCAATCCATAAGATC
31394 ATACCAATTTCACATAATTCATTTCAATGTCATAT
1 ATACCAATTTCACATAATTCATTTCAATGTCATAT
31429 CAAATTGGTT
Statistics
Matches: 190, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
57 188 0.99
58 2 0.01
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.38
Consensus pattern (57 bp):
ATACCAATTTCACATAATTCATTTCAATGTCATATTCCATTATCAATCCATAAGATC
Found at i:34428 original size:12 final size:12
Alignment explanation
Indices: 34395--34455 Score: 56
Period size: 12 Copynumber: 5.1 Consensus size: 12
34385 TTAAATTTTA
34395 ATAATTTAATA-
1 ATAATTTAATAT
*
34406 ATAATAATAATAT
1 ATAAT-TTAATAT
34419 ATAATTTAATA-
1 ATAATTTAATAT
34430 A-AATTCTTAATAT
1 ATAA-T-TTAATAT
*
34443 ATATTTTAATAT
1 ATAATTTAATAT
34455 A
1 A
34456 ATTTAAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
10 2 0.05
11 7 0.17
12 24 0.59
13 7 0.17
14 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (12 bp):
ATAATTTAATAT
Found at i:34458 original size:24 final size:24
Alignment explanation
Indices: 34395--34458 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
34385 TTAAATTTTA
**
34395 ATAATTTAATAATAA-TAATAATAT
1 ATAATTTAATAA-AATTCTTAATAT
34419 ATAATTTAATAAAATTCTTAATAT
1 ATAATTTAATAAAATTCTTAATAT
* *
34443 ATATTTTAATATAATT
1 ATAATTTAATAAAATT
34459 TAAAATAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 2 0.06
24 33 0.94
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
ATAATTTAATAAAATTCTTAATAT
Found at i:37253 original size:61 final size:61
Alignment explanation
Indices: 37179--37294 Score: 232
Period size: 61 Copynumber: 1.9 Consensus size: 61
37169 GGGATATAGG
37179 CCAATTCCTTTGTGAGTCCGTTGGGAAGCCGGTCAAACCCCCAACAATTGTAAGGGAGAAA
1 CCAATTCCTTTGTGAGTCCGTTGGGAAGCCGGTCAAACCCCCAACAATTGTAAGGGAGAAA
37240 CCAATTCCTTTGTGAGTCCGTTGGGAAGCCGGTCAAACCCCCAACAATTGTAAGG
1 CCAATTCCTTTGTGAGTCCGTTGGGAAGCCGGTCAAACCCCCAACAATTGTAAGG
37295 TGTTTTCTCC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (61 bp):
CCAATTCCTTTGTGAGTCCGTTGGGAAGCCGGTCAAACCCCCAACAATTGTAAGGGAGAAA
Done.