Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002973.1 Kokia drynarioides strain JFW-HI SEQ_115452, 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: 3968
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.35
Found at i:1240 original size:6 final size:6
Alignment explanation
Indices: 1231--1299 Score: 88
Period size: 6 Copynumber: 11.7 Consensus size: 6
1221 TTAATTTTAT
* * *
1231 TTTAAA TTTAGA TTT-AT TTTAAA TTTGAA TTTAAA TCTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
1279 -TTAAA TTTAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTA
1300 TTTTCAAAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
5 8 0.15
6 40 0.74
7 6 0.11
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:1246 original size:17 final size:17
Alignment explanation
Indices: 1220--1313 Score: 98
Period size: 17 Copynumber: 5.4 Consensus size: 17
1210 CAGGCCCATT
*
1220 TTTAATTTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
1237 TTTAGATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
1254 TTTGAATTTAAATCTTAAA
1 TTTAAATTT--ATTTTAAA
* *
1273 TTTAAATTAAATTTAAA
1 TTTAAATTTATTTTAAA
1290 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
*
1308 ATTAAA
1 TTTAAA
1314 ATCCACAAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
17 40 0.65
18 8 0.13
19 14 0.23
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:2097 original size:24 final size:24
Alignment explanation
Indices: 2068--2113 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2058 TTATATATTA
*
2068 AATAATTTCATTAATGATAATAAT
1 AATAATTTCATTAAAGATAATAAT
*
2092 AATAATTTTATTAAAGATAATA
1 AATAATTTCATTAAAGATAATA
2114 TTTATTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.41
Consensus pattern (24 bp):
AATAATTTCATTAAAGATAATAAT
Found at i:2130 original size:18 final size:17
Alignment explanation
Indices: 2089--2131 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
2079 TAATGATAAT
2089 AATAATAAT-TTTATTA
1 AATAATAATATTTATTA
*
2105 AA-GATAATATTTATTA
1 AATAATAATATTTATTA
2121 AATAATTAATA
1 AATAA-TAATA
2132 ATAAAAAGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 5 0.23
16 11 0.50
17 1 0.05
18 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
AATAATAATATTTATTA
Found at i:3196 original size:29 final size:29
Alignment explanation
Indices: 3155--3339 Score: 171
Period size: 29 Copynumber: 6.3 Consensus size: 29
3145 AAACTATTCG
*
3155 AAAATTCCATTTTTACCCCCGAACTTCCA
1 AAAATTCCATTTTTACCCCCAAACTTCCA
***
3184 AAAATTCCATTTTTGACCTTAAAACTTCCA
1 AAAATTCCATTTTT-ACCCCCAAACTTCCA
* **
3214 AAAATTCCA-TTTTACCCCTAAACTTAAA
1 AAAATTCCATTTTTACCCCCAAACTTCCA
* **
3242 AAAATTCCATTTTGACCCTAAAACTTCC-
1 AAAATTCCATTTTTACCCCCAAACTTCCA
*
3270 AAAATTCCATTTTTGA-CCCCAAA-TGTCTA
1 AAAATTCCATTTTT-ACCCCCAAACT-TCCA
* * *
3299 AAAATTCCATTTTTAACCCCAAATTTTCCC
1 AAAATTCCATTTTTACCCCCAAA-CTTCCA
3329 AAAATTACCAT
1 AAAATT-CCAT
3340 GTCACCCCGA
Statistics
Matches: 127, Mismatches: 20, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
27 1 0.01
28 40 0.31
29 53 0.42
30 28 0.22
31 5 0.04
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAATTCCATTTTTACCCCCAAACTTCCA
Found at i:3245 original size:28 final size:29
Alignment explanation
Indices: 3155--3311 Score: 162
Period size: 28 Copynumber: 5.4 Consensus size: 29
3145 AAACTATTCG
* ***
3155 AAAATTCCATTTTTACCCCCGAACTTCCA
1 AAAATTCCATTTTGACCCTAAAACTTCCA
*
3184 AAAATTCCATTTTTGACCTTAAAACTTCCA
1 AAAATTCCA-TTTTGACCCTAAAACTTCCA
**
3214 AAAATTCCATTTT-ACCCCT-AAACTTAAA
1 AAAATTCCATTTTGA-CCCTAAAACTTCCA
3242 AAAATTCCATTTTGACCCTAAAACTTCC-
1 AAAATTCCATTTTGACCCTAAAACTTCCA
* *
3270 AAAATTCCATTTTTGACCC-CAAA-TGTCTA
1 AAAATTCCA-TTTTGACCCTAAAACT-TCCA
3299 AAAATTCCATTTT
1 AAAATTCCATTTT
3312 TAACCCCAAA
Statistics
Matches: 109, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
27 1 0.01
28 43 0.39
29 41 0.38
30 24 0.22
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAATTCCATTTTGACCCTAAAACTTCCA
Found at i:3302 original size:57 final size:57
Alignment explanation
Indices: 3155--3311 Score: 194
Period size: 57 Copynumber: 2.7 Consensus size: 57
3145 AAACTATTCG
* * *
3155 AAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCTTAAAACTTCCA
1 AAAATTCCATTTTTA-CCCCGAAATTCAAAAAATTCCA-TTTTGACCCTAAAACTTCCA
* *
3214 AAAATTCCA-TTTTACCCCTAAACTTAAAAAAATTCCATTTTGACCCTAAAACTTCC-
1 AAAATTCCATTTTTACCCCGAAA-TTCAAAAAATTCCATTTTGACCCTAAAACTTCCA
*
3270 AAAATTCCATTTTTGACCCC-AAATGTCTAAAAATTCCATTTT
1 AAAATTCCATTTTT-ACCCCGAAAT-TCAAAAAATTCCATTTT
3312 TAACCCCAAA
Statistics
Matches: 87, Mismatches: 7, Indels: 10
0.84 0.07 0.10
Matches are distributed among these distances:
56 10 0.11
57 46 0.53
58 22 0.25
59 9 0.10
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.34
Consensus pattern (57 bp):
AAAATTCCATTTTTACCCCGAAATTCAAAAAATTCCATTTTGACCCTAAAACTTCCA
Done.