Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012533.1 Kokia drynarioides strain JFW-HI SEQ_127541, 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: 30116
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:24122 original size:29 final size:29
Alignment explanation
Indices: 24090--24169 Score: 74
Period size: 28 Copynumber: 2.8 Consensus size: 29
24080 TTTTAGCAAA
*
24090 TTTTTTATATTTTTATATTGTTTTTTTTT
1 TTTTTTATATTTTTATATTGTTTTTATTT
* * * * *
24119 TTTTTTGTAATTTTATAAT-CTTATATTT
1 TTTTTTATATTTTTATATTGTTTTTATTT
* *
24147 TTTTTTCTATTTTTA-ATAGTTTT
1 TTTTTTATATTTTTATATTGTTTT
24170 AACCATTTTT
Statistics
Matches: 38, Mismatches: 12, Indels: 3
0.72 0.23 0.06
Matches are distributed among these distances:
27 1 0.03
28 21 0.55
29 16 0.42
ACGTcount: A:0.19, C:0.03, G:0.04, T:0.75
Consensus pattern (29 bp):
TTTTTTATATTTTTATATTGTTTTTATTT
Found at i:24170 original size:37 final size:37
Alignment explanation
Indices: 24092--24170 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 37
24082 TTAGCAAATT
* * * **
24092 TTTTATATTTTTATATTGTTTTTTTTTTTTTTTGTAA
1 TTTTATAATCTTATATTGTTTTTTTTATTTTTAATAA
*
24129 TTTTATAATCTTATATT-TTTTTTTCTATTTTTAATAG
1 TTTTATAATCTTATATTGTTTTTTT-TATTTTTAATAA
24166 TTTTA
1 TTTTA
24171 ACCATTTTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
36 7 0.20
37 28 0.80
ACGTcount: A:0.20, C:0.03, G:0.04, T:0.73
Consensus pattern (37 bp):
TTTTATAATCTTATATTGTTTTTTTTATTTTTAATAA
Found at i:27334 original size:11 final size:11
Alignment explanation
Indices: 27318--27366 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
27308 ATCGGGCCCT
27318 TTTTAAATTTA
1 TTTTAAATTTA
27329 TTTTAAATTTGA
1 TTTTAAATTT-A
* * *
27341 ATTTGAATTAA
1 TTTTAAATTTA
*
27352 ATTTAAATTTA
1 TTTTAAATTTA
27363 TTTT
1 TTTT
27367 CAAAATTTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
11 23 0.74
12 8 0.26
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (11 bp):
TTTTAAATTTA
Found at i:29341 original size:30 final size:30
Alignment explanation
Indices: 29250--29438 Score: 169
Period size: 29 Copynumber: 6.5 Consensus size: 30
29240 AAACTATTTG
* *
29250 AAAATTACATTTTTACCC-CTAAACTTCCA
1 AAAATTCCATTTTTACCCTCGAAACTTCCA
*
29279 AAAATTCCATTCTTACCCTCG-AACTTCCA
1 AAAATTCCATTTTTACCCTCGAAACTTCCA
* *
29308 AAAATTCTATTTTTGA-CCTCGAAACTTCTA
1 AAAATTCCATTTTT-ACCCTCGAAACTTCCA
** * *
29338 AAAATTATATTTTTACCCCCG-AACTTTCA
1 AAAATTCCATTTTTACCCTCGAAACTTCCA
**
29367 AAAATTCCATTTTTAATC-CGAAACTTCCA
1 AAAATTCCATTTTTACCCTCGAAACTTCCA
* *
29396 AAAATTACC-CTTTTACCCCCG-AA-TGTCCA
1 AAAATT-CCATTTTTACCCTCGAAACT-TCCA
*
29425 AAAATTCTATTTTT
1 AAAATTCCATTTTT
29439 GATCCCGATT
Statistics
Matches: 131, Mismatches: 20, Indels: 18
0.78 0.12 0.11
Matches are distributed among these distances:
28 4 0.03
29 97 0.74
30 30 0.23
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (30 bp):
AAAATTCCATTTTTACCCTCGAAACTTCCA
Found at i:29500 original size:59 final size:59
Alignment explanation
Indices: 29250--29502 Score: 243
Period size: 59 Copynumber: 4.3 Consensus size: 59
29240 AAACTATTTG
* * * *
29250 AAAATTACATTTTT-ACCCCTAAACTTCCAAAAATT-CCATTCTTACCCTCGAACT-TCCA
1 AAAATTCCATTTTTGATCCCGAAACTTCCAAAAATTACCATT-TTACCCCCGAA-TGTCCA
* * * *
29308 AAAATTCTATTTTTGA-CCTCGAAACTTCTAAAAATTA-TATTTTTACCCCCGAACT-TTCA
1 AAAATTCCATTTTTGATCC-CGAAACTTCCAAAAATTACCA-TTTTACCCCCGAA-TGTCCA
* *
29367 AAAATTCCATTTTTAAT-CCGAAACTTCCAAAAATTACCCTTTTACCCCCGAATGTCCA
1 AAAATTCCATTTTTGATCCCGAAACTTCCAAAAATTACCATTTTACCCCCGAATGTCCA
* ** * * *
29425 AAAATTCTATTTTTGATCCCG-ATTTTCCTAAATATTACCATTTTACCCTCGGATGTCCA
1 AAAATTCCATTTTTGATCCCGAAACTTCC-AAAAATTACCATTTTACCCCCGAATGTCCA
*
29484 AAAATTCCGTTTTTGATCC
1 AAAATTCCATTTTTGATCC
29503 TAATTTTTTT
Statistics
Matches: 163, Mismatches: 23, Indels: 17
0.80 0.11 0.08
Matches are distributed among these distances:
57 1 0.01
58 67 0.41
59 93 0.57
60 2 0.01
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (59 bp):
AAAATTCCATTTTTGATCCCGAAACTTCCAAAAATTACCATTTTACCCCCGAATGTCCA
Found at i:29606 original size:28 final size:28
Alignment explanation
Indices: 29573--29632 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
29563 AAACTTTCCT
*
29573 AAAATTATCATTTTGCCCCCGAGAATCC
1 AAAATTACCATTTTGCCCCCGAGAATCC
* * *
29601 AAAATTACCATTTTGCCCTCGGGTATCC
1 AAAATTACCATTTTGCCCCCGAGAATCC
29629 AAAA
1 AAAA
29633 AGTCTCATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.28
Consensus pattern (28 bp):
AAAATTACCATTTTGCCCCCGAGAATCC
Done.