Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007801.1 Kokia drynarioides strain JFW-HI SEQ_122436, 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: 28565
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Warning! 88 characters in sequence are not A, C, G, or T
Found at i:10139 original size:17 final size:17
Alignment explanation
Indices: 10119--10188 Score: 70
Period size: 17 Copynumber: 4.1 Consensus size: 17
10109 ATTCATTTTG
**
10119 AGTTTAAATTTAGTTTA
1 AGTTTAAATTTAAATTA
*
10136 AGTTAAAATTTAAATTA
1 AGTTTAAATTTAAATTA
* *
10153 AGTTTAAATCTAATTTGA
1 AGTTTAAATTTAAATT-A
10171 A-TTTAAAATTTAAATTA
1 AGTTT-AAATTTAAATTA
10188 A
1 A
10189 TTAAAAGTTC
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
17 32 0.74
18 11 0.26
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.46
Consensus pattern (17 bp):
AGTTTAAATTTAAATTA
Found at i:12011 original size:29 final size:28
Alignment explanation
Indices: 11967--12223 Score: 187
Period size: 29 Copynumber: 8.8 Consensus size: 28
11957 CCTAAATTGT
*
11967 CAAAAAATTACATTTTGACCCTC-AACTTC
1 CAAAAAA-TACATTTTTACCC-CAAACTTC
* *
11996 CAAAAAATATATTTTTAACCCCGAAACCTC
1 CAAAAAATACATTTTT-ACCCC-AAACTTC
* **
12026 CAAAAATTACATTTTTACCCTTGAACTTC
1 CAAAAAATACATTTTTACCC-CAAACTTC
*
12055 CAAAAAATCCATTTTTTACCCCAAAACTTC
1 CAAAAAATACA-TTTTTACCCC-AAACTTC
* * *
12085 CAAAAATTACATTTTAACCCCTATACTTC
1 CAAAAAATACATTTTTACCCC-AAACTTC
* * *
12114 TAAAAAATCCATTTTTGACCCTAAAACTTC
1 CAAAAAATACATTTTT-ACCC-CAAACTTC
* *
12144 CAAAAATTACATTTTTACCCCTAGA-TGTC
1 CAAAAAATACATTTTTACCCC-AAACT-TC
* * *
12173 CAAAAACTTCATTTTTGACCCCAATACTTT
1 CAAAAAATACATTTTT-ACCCCAA-ACTTC
*
12203 CAAAAATTACCA-TTTTACCCC
1 CAAAAAATA-CATTTTTACCCC
12224 CCTAATGTCT
Statistics
Matches: 180, Mismatches: 34, Indels: 28
0.74 0.14 0.12
Matches are distributed among these distances:
28 9 0.05
29 84 0.47
30 84 0.47
31 3 0.02
ACGTcount: A:0.38, C:0.27, G:0.03, T:0.33
Consensus pattern (28 bp):
CAAAAAATACATTTTTACCCCAAACTTC
Found at i:12061 original size:59 final size:57
Alignment explanation
Indices: 11969--12277 Score: 284
Period size: 59 Copynumber: 5.2 Consensus size: 57
11959 TAAATTGTCA
* ** * *
11969 AAAAATTACATTTTGACCCTCAACTTCCAAAAAATATATTTTTAACCCCGAAACCTCC
1 AAAAATTACATTTTTACCCT-AACTTCCAAAAAATCCATTTTTAACCCCAAAACTTCC
*
12027 AAAAATTACATTTTTACCCTTGAACTTCCAAAAAATCCATTTTTTACCCCAAAACTTCC
1 AAAAATTACATTTTTACCC-T-AACTTCCAAAAAATCCATTTTTAACCCCAAAACTTCC
* * * *
12086 AAAAATTACATTTTAACCCCTATACTTCTAAAAAATCCATTTTTGACCCTAAAACTTCC
1 AAAAATTACATTTTTA-CCCTA-ACTTCCAAAAAATCCATTTTTAACCCCAAAACTTCC
* * * * *
12145 AAAAATTACATTTTTACCCCTAGA-TGTCCAAAAACTTCATTTTTGACCCCAATACTTTC
1 AAAAATTACATTTTTA-CCCTA-ACT-TCCAAAAAATCCATTTTTAACCCCAAAACTTCC
* * * *
12204 AAAAATTACCA-TTTTACCCCCCTAA-TGT-CTAAAATTTCATTTTTAACCCCAAAATTTCC
1 AAAAATTA-CATTTTTA---CCCTAACT-TCCAAAAAATCCATTTTTAACCCCAAAACTTCC
*
12263 CAAAATTACCATTTT
1 AAAAATTA-CATTTT
12278 GCCCCCCTAA
Statistics
Matches: 217, Mismatches: 26, Indels: 14
0.84 0.10 0.05
Matches are distributed among these distances:
58 20 0.09
59 179 0.82
60 12 0.06
61 6 0.03
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (57 bp):
AAAAATTACATTTTTACCCTAACTTCCAAAAAATCCATTTTTAACCCCAAAACTTCC
Found at i:12268 original size:30 final size:30
Alignment explanation
Indices: 11969--12277 Score: 217
Period size: 30 Copynumber: 10.5 Consensus size: 30
11959 TAAATTGTCA
*
11969 AAAAATTACA-TTTTGACCCTC--AACTTCC
1 AAAAATTACATTTTTAACCC-CAAAACTTCC
* * * *
11997 AAAAAATATATTTTTAACCCCGAAACCTCC
1 AAAAATTACATTTTTAACCCCAAAACTTCC
***
12027 AAAAATTACATTTTT-ACCCTTGAACTTCC
1 AAAAATTACATTTTTAACCCCAAAACTTCC
* * *
12056 AAAAAATCCATTTTTTACCCCAAAACTTCC
1 AAAAATTACATTTTTAACCCCAAAACTTCC
* * *
12086 AAAAATTACA-TTTTAACCCCTATACTTCT
1 AAAAATTACATTTTTAACCCCAAAACTTCC
* * * *
12115 AAAAAATCCATTTTTGACCCTAAAACTTCC
1 AAAAATTACATTTTTAACCCCAAAACTTCC
* *
12145 AAAAATTACATTTTT-ACCCCTAGA-TGTCC
1 AAAAATTACATTTTTAACCCCAAAACT-TCC
* * *
12174 AAAAACTT-CATTTTTGACCCCAATACTTTC
1 AAAAA-TTACATTTTTAACCCCAAAACTTCC
* **
12204 AAAAATTACCA-TTTTACCCCCCTAA-TGT-C
1 AAAAATTA-CATTTTTAACCCCAAAACT-TCC
* * *
12233 TAAAATTTCATTTTTAACCCCAAAATTTCC
1 AAAAATTACATTTTTAACCCCAAAACTTCC
*
12263 CAAAATTACCATTTT
1 AAAAATTA-CATTTT
12278 GCCCCCCTAA
Statistics
Matches: 217, Mismatches: 48, Indels: 29
0.74 0.16 0.10
Matches are distributed among these distances:
28 12 0.06
29 97 0.45
30 99 0.46
31 9 0.04
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (30 bp):
AAAAATTACATTTTTAACCCCAAAACTTCC
Found at i:12323 original size:29 final size:30
Alignment explanation
Indices: 12262--12326 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
12252 CCAAAATTTC
* *
12262 CCAAAATTACCATTTTGCCCCCCTAAGAGT
1 CCAAAATTACCATTTTGCCCCCCGAACAGT
*
12292 CCAAAATTACCATTTTGCCCCCCGGACA-T
1 CCAAAATTACCATTTTGCCCCCCGAACAGT
12321 CCAAAA
1 CCAAAA
12327 AATCTCATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 7 0.22
30 25 0.78
ACGTcount: A:0.32, C:0.35, G:0.09, T:0.23
Consensus pattern (30 bp):
CCAAAATTACCATTTTGCCCCCCGAACAGT
Found at i:14359 original size:2 final size:2
Alignment explanation
Indices: 14352--14392 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
14342 GTTGTTATTT
14352 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14393 TTTAATAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18722 original size:21 final size:21
Alignment explanation
Indices: 18683--18723 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
18673 TTTTTTTAAT
18683 TTTAAATTTCTTTATATATTC
1 TTTAAATTTCTTTATATATTC
*
18704 TTTAGAATTTTTTTA-ATATT
1 TTTA-AATTTCTTTATATATT
18724 TATAACTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTAAATTTCTTTATATATTC
Found at i:23947 original size:22 final size:22
Alignment explanation
Indices: 23922--23974 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
23912 TATAATAACC
**
23922 AAATAATAACAAAATGATAGCA
1 AAATAATAACAAAACAATAGCA
* * * *
23944 AAATGACATCAAAACAATAGTA
1 AAATAATAACAAAACAATAGCA
23966 AAATAATAA
1 AAATAATAA
23975 TAATAAAAAT
Statistics
Matches: 22, Mismatches: 9, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.64, C:0.09, G:0.08, T:0.19
Consensus pattern (22 bp):
AAATAATAACAAAACAATAGCA
Found at i:24395 original size:18 final size:18
Alignment explanation
Indices: 24361--24409 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
24351 TAATTTTAGG
* *
24361 TTATTTAATTAAATAAATT
1 TTATTTTATT-AATAAATA
24380 TTATTTTATTAATAAATA
1 TTATTTTATTAATAAATA
*
24398 TAATTTTATTAA
1 TTATTTTATTAA
24410 AGATTTCATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 18 0.67
19 9 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTATTTTATTAATAAATA
Found at i:24406 original size:23 final size:25
Alignment explanation
Indices: 24348--24407 Score: 81
Period size: 23 Copynumber: 2.5 Consensus size: 25
24338 GATTATAAAT
**
24348 ATATAATTTTAGGTTATTTAATTAA
1 ATATAATTTTATTTTATTTAATTAA
24373 ATA-AATTTTATTTTA-TTAA-TAA
1 ATATAATTTTATTTTATTTAATTAA
24395 ATATAATTTTATT
1 ATATAATTTTATT
24408 AAAGATTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 6 0.19
23 13 0.41
24 10 0.31
25 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (25 bp):
ATATAATTTTATTTTATTTAATTAA
Done.