Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001130.1 Kokia drynarioides strain JFW-HI SEQ_112419, 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: 13232
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
Found at i:8479 original size:18 final size:18
Alignment explanation
Indices: 8446--8481 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
8436 TCACGAACTC
*
8446 TAAACATAAATCATAAAA
1 TAAACATAAAACATAAAA
*
8464 TAAACATAAAAGATAAAA
1 TAAACATAAAACATAAAA
8482 AAAAAATCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.69, C:0.08, G:0.03, T:0.19
Consensus pattern (18 bp):
TAAACATAAAACATAAAA
Found at i:8854 original size:17 final size:19
Alignment explanation
Indices: 8819--8855 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
8809 ATCCTTGTCA
8819 TCTCTGCTTCTTCACTTTC
1 TCTCTGCTTCTTCACTTTC
*
8838 TCTCT-CTTTTTCA-TTTC
1 TCTCTGCTTCTTCACTTTC
8855 T
1 T
8856 GTTGATACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 5 0.29
18 7 0.41
19 5 0.29
ACGTcount: A:0.05, C:0.32, G:0.03, T:0.59
Consensus pattern (19 bp):
TCTCTGCTTCTTCACTTTC
Found at i:11559 original size:96 final size:96
Alignment explanation
Indices: 11382--11566 Score: 259
Period size: 96 Copynumber: 1.9 Consensus size: 96
11372 GAAAAGGATG
* ** *
11382 TTCGATTATCTCGATTTGATGAAAGGTTGCACCTAGTAAGTTAAGGCGCAAATTTTTAGAATCGA
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTGAGAATCGA
*
11447 AGATAAGGAAACATTGCCTCGATTCAGGGTA
66 AGATAAAGAAACATTGCCTCGATTCAGGGTA
*
11478 TTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCGA-AACTC
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTT-GAGAA-TC
*
11542 GAA-ATAAA-AGAATATTGCCTCGATT
64 GAAGATAAAGA-AACATTGCCTCGATT
11567 TTAAAGTTTT
Statistics
Matches: 79, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
95 1 0.01
96 72 0.91
97 6 0.08
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.31
Consensus pattern (96 bp):
TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTGAGAATCGA
AGATAAAGAAACATTGCCTCGATTCAGGGTA
Found at i:11977 original size:59 final size:59
Alignment explanation
Indices: 11852--12047 Score: 175
Period size: 59 Copynumber: 3.4 Consensus size: 59
11842 GGAAAATTTA
* * * ** * * *
11852 GGGTTAAAAA-GGAGATTTTAAACATTCG-GGGGTAAAGGGTAA-TTTCGAGAGTTTCG
1 GGGTCAAAAATGGAAATTTTGAACATTCGAGGGAAAAATGGTAATTTTTGAAAGTTTCG
* * **
11908 AGGTCGAAAATGGAGTTTTTGAACATTCGAGGGAAAAATGGTAATTTTTGAAAGTTTCG
1 GGGTCAAAAATGGAAATTTTGAACATTCGAGGGAAAAATGGTAATTTTTGAAAGTTTCG
* ** ** *
11967 GGGTCAAAAATGGAAATTTTGGAGGTTTAAGGGTAAAAATGG-AATTTTTTAGAAGTTTCG
1 GGGTCAAAAATGGAAATTTTGAACATTCGAGGG-AAAAATGGTAATTTTTGA-AAGTTTCG
*
12027 GGGTCAAAAATGGAATTTTTG
1 GGGTCAAAAATGGAAATTTTG
12048 GGAGTTCGAG
Statistics
Matches: 114, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
56 7 0.06
57 16 0.14
58 11 0.10
59 44 0.39
60 36 0.32
ACGTcount: A:0.34, C:0.06, G:0.29, T:0.32
Consensus pattern (59 bp):
GGGTCAAAAATGGAAATTTTGAACATTCGAGGGAAAAATGGTAATTTTTGAAAGTTTCG
Found at i:12010 original size:29 final size:29
Alignment explanation
Indices: 11937--12235 Score: 271
Period size: 30 Copynumber: 10.1 Consensus size: 29
11927 TGAACATTCG
* *
11937 AGGG-AAAAATGGTAATTTTTGAAAGTTTC
1 AGGGTAAAAATGG-AATTTTTGGAAGTTTA
* * *
11966 GGGGTCAAAAATGGAAATTTTGGAGGTTTA
1 AGGGT-AAAAATGGAATTTTTGGAAGTTTA
* *
11996 AGGGTAAAAATGGAATTTTTTAGAAGTTTC
1 AGGGTAAAAATGGAA-TTTTTGGAAGTTTA
* * **
12026 GGGGTCAAAAATGGAATTTTTGGGAGTTCG
1 AGGGT-AAAAATGGAATTTTTGGAAGTTTA
* * * *
12056 AGGGTTAAAATGAAAATTTTGGAAG-TTC
1 AGGGTAAAAATGGAATTTTTGGAAGTTTA
12084 AGAGGTAAAAATGGAATTTTTGGAAGTTT-
1 AG-GGTAAAAATGGAATTTTTGGAAGTTTA
* *
12113 TGAGGTAAAAAATGGAATTTTTGGAAGTTCA
1 AG-GGT-AAAAATGGAATTTTTGGAAGTTTA
* * *
12144 GGGGTGAAAATGGAATTTTTGGAAGTTTC
1 AGGGTAAAAATGGAATTTTTGGAAGTTTA
* * **
12173 GGGGTCGAAAATGGAATTTTTGGAAGTTCG
1 AGGGT-AAAAATGGAATTTTTGGAAGTTTA
*
12203 ATGGTAAAAATGGAATTTTTGGACAGTTTA
1 AGGGTAAAAATGGAATTTTTGGA-AGTTTA
12233 AGG
1 AGG
12236 ACCTTTAGGG
Statistics
Matches: 221, Mismatches: 39, Indels: 19
0.79 0.14 0.07
Matches are distributed among these distances:
28 3 0.01
29 97 0.44
30 102 0.46
31 19 0.09
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (29 bp):
AGGGTAAAAATGGAATTTTTGGAAGTTTA
Found at i:12074 original size:30 final size:29
Alignment explanation
Indices: 11914--12230 Score: 308
Period size: 29 Copynumber: 10.7 Consensus size: 29
11904 TTCGAGGTCG
* *
11914 AAAATGGAGTTTTT-GAACATTCGAGGG-A
1 AAAATGGAATTTTTGGAA-GTTCGAGGGTA
*
11942 AAAATGGTAATTTTTGAAAGTTTCG-GGGTCA
1 AAAATGG-AATTTTTGGAAG-TTCGAGGGT-A
* * **
11973 AAAATGGAAATTTTGGAGGTTTAAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
*
12002 AAAATGGAATTTTTTAGAAGTTTCG-GGGTCA
1 AAAATGGAA-TTTTTGGAAG-TTCGAGGGT-A
* *
12033 AAAATGGAATTTTTGGGAGTTCGAGGGTT
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
* *
12062 AAAATGAAAATTTTGGAAGTTC-AGAGGTA
1 AAAATGGAATTTTTGGAAGTTCGAG-GGTA
*
12091 AAAATGGAATTTTTGGAAGTTTTGA-GGTAA
1 AAAATGGAATTTTTGGAAG-TTCGAGGGT-A
*
12121 AAAATGGAATTTTTGGAAGTTC-AGGGGTG
1 AAAATGGAATTTTTGGAAGTTCGA-GGGTA
*
12150 AAAATGGAATTTTTGGAAGTTTCG-GGGTCG
1 AAAATGGAATTTTTGGAAG-TTCGAGGGT-A
*
12180 AAAATGGAATTTTTGGAAGTTCGATGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
12209 AAAATGGAATTTTTGGACAGTT
1 AAAATGGAATTTTTGGA-AGTT
12231 TAAGGACCTT
Statistics
Matches: 241, Mismatches: 27, Indels: 40
0.78 0.09 0.13
Matches are distributed among these distances:
28 10 0.04
29 113 0.47
30 97 0.40
31 21 0.09
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTA
Found at i:12137 original size:59 final size:58
Alignment explanation
Indices: 11914--12231 Score: 333
Period size: 59 Copynumber: 5.4 Consensus size: 58
11904 TTCGAGGTCG
* ** *
11914 AAAATGGAGTTTTT-GAACATTCGAGGG-AAAAATGGTAATTTTTGAAAGTTTCGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGAGGGTAAAAATGG-AATTTTTGGAAG-TTCGGGGT-A
* * * *
11973 AAAATGGAAATTTTGGAGGTTT-AAGGGTAAAAATGGAATTTTTTAGAAGTTTCGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGAGGGTAAAAATGGAA-TTTTTGGAAG-TTCGGGGT-A
* * * * *
12033 AAAATGGAATTTTTGGGAG-TTCGAGGGTTAAAATGAAAATTTTGGAAGTTCAGAGGTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGGTAAAAATGGAATTTTTGGAAGTTC-GGGGTA
* *
12091 AAAATGGAATTTTTGGAAGTTTTGA-GGTAAAAAATGGAATTTTTGGAAGTTCAGGGGTG
1 AAAATGGAATTTTTGGAAGTTTCGAGGGT-AAAAATGGAATTTTTGGAAGTTC-GGGGTA
* *
12150 AAAATGGAATTTTTGGAAGTTTCG-GGGTCGAAAATGGAATTTTTGGAAGTTCGATGGTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGGT-AAAAATGGAATTTTTGGAAGTTCG-GGGTA
12209 AAAATGGAATTTTTGGACAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
12232 AAGGACCTTT
Statistics
Matches: 220, Mismatches: 29, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
58 26 0.12
59 129 0.59
60 65 0.30
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (58 bp):
AAAATGGAATTTTTGGAAGTTTCGAGGGTAAAAATGGAATTTTTGGAAGTTCGGGGTA
Done.