Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004427.1 Kokia drynarioides strain JFW-HI SEQ_117815, 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: 48227
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Warning! 24 characters in sequence are not A, C, G, or T
Found at i:3685 original size:21 final size:20
Alignment explanation
Indices: 3636--3687 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
3626 AATACTTTCT
*
3636 TCTTCTTCCTTCTCCTCTTCC
1 TCTTCTTCTTTCTCCTCTT-C
* *
3657 TTTTCTTCTTTCTCTTCTTC
1 TCTTCTTCTTTCTCCTCTTC
3677 TCTTGCTTCTT
1 TCTT-CTTCTT
3688 CATCTCGTGC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.00, C:0.37, G:0.02, T:0.62
Consensus pattern (20 bp):
TCTTCTTCTTTCTCCTCTTC
Found at i:3687 original size:15 final size:15
Alignment explanation
Indices: 3644--3703 Score: 56
Period size: 15 Copynumber: 4.3 Consensus size: 15
3634 CTTCTTCTTC
* *
3644 CTTCTCCTCTTCCTT
1 CTTCTTCTCTTGCTT
3659 -TTCTTCT-TT-C-T
1 CTTCTTCTCTTGCTT
3670 CTTCTTCTCTTGCTT
1 CTTCTTCTCTTGCTT
* *
3685 CTTCATCTCGTGCTT
1 CTTCTTCTCTTGCTT
3700 CTTC
1 CTTC
3704 ATTGGCTCCA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
11 1 0.03
12 8 0.21
13 4 0.11
14 7 0.18
15 18 0.47
ACGTcount: A:0.02, C:0.37, G:0.05, T:0.57
Consensus pattern (15 bp):
CTTCTTCTCTTGCTT
Found at i:14263 original size:16 final size:16
Alignment explanation
Indices: 14242--14274 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
14232 GAATAAAGTG
*
14242 TTTTTGAGACTTTTAA
1 TTTTTGAGACTTGTAA
14258 TTTTTGAGACTTGTAA
1 TTTTTGAGACTTGTAA
14274 T
1 T
14275 GTTAGGATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.06, G:0.15, T:0.55
Consensus pattern (16 bp):
TTTTTGAGACTTGTAA
Found at i:20305 original size:35 final size:31
Alignment explanation
Indices: 20266--20330 Score: 85
Period size: 35 Copynumber: 2.0 Consensus size: 31
20256 ACTTTAAATA
20266 ATAAATTTGTATAAAATTCTAAAATACATATATAC
1 ATAAATTT-TA-AAAATTC-AAAATA-ATATATAC
*
20301 ATAAATTTTAAATATTCAAAATAATATATA
1 ATAAATTTTAAAAATTCAAAATAATATATA
20331 AAAATTGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 7 0.24
32 6 0.21
33 6 0.21
34 2 0.07
35 8 0.28
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (31 bp):
ATAAATTTTAAAAATTCAAAATAATATATAC
Found at i:20332 original size:20 final size:18
Alignment explanation
Indices: 20304--20362 Score: 55
Period size: 20 Copynumber: 3.1 Consensus size: 18
20294 TATATACATA
* *
20304 AATTTTAAATATTCAAAAT
1 AATTATAAAAATT-AAAAT
*
20323 AATATATAAAAATTGAAAAAC
1 AAT-TATAAAAATT--AAAAT
20344 AATTATAAAAATTAAAAT
1 AATTATAAAAATTAAAAT
20362 A
1 A
20363 GGTATCTAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
18 5 0.15
19 3 0.09
20 18 0.55
21 7 0.21
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (18 bp):
AATTATAAAAATTAAAAT
Found at i:22340 original size:23 final size:23
Alignment explanation
Indices: 22310--22353 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
22300 CTTCCACCTG
22310 AAGTTAG-AGAGGCTCAAGAAAAT
1 AAGTTAGAAG-GGCTCAAGAAAAT
*
22333 AAGTTAGAAGGGCTTAAGAAA
1 AAGTTAGAAGGGCTCAAGAAA
22354 CAACAGGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.48, C:0.07, G:0.27, T:0.18
Consensus pattern (23 bp):
AAGTTAGAAGGGCTCAAGAAAAT
Found at i:33364 original size:21 final size:21
Alignment explanation
Indices: 33302--33357 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
33292 GTGGCTATCT
* *
33302 CACATGCCCGTGTGACTACCC
1 CACACGCCCATGTGACTACCC
33323 CACACGCCCATGTGACTACCC
1 CACACGCCCATGTGACTACCC
33344 CACACGCCCATGTG
1 CACACGCCCATGTG
33358 CTTACCCATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.21, C:0.45, G:0.18, T:0.16
Consensus pattern (21 bp):
CACACGCCCATGTGACTACCC
Found at i:33742 original size:21 final size:21
Alignment explanation
Indices: 33705--33771 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
33695 ACTTTTACTG
*
33705 ATACAAGTGATAGTTCTACCA
1 ATACAAGTGATACTTCTACCA
33726 ATACAAGTGACT-CTTCTACCGA
1 ATACAAGTGA-TACTTCTACC-A
* ** *
33748 A-ACAACTCTTACTTCTATCA
1 ATACAAGTGATACTTCTACCA
33768 ATAC
1 ATAC
33772 TAAAAACTCT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
20 3 0.08
21 31 0.84
22 3 0.08
ACGTcount: A:0.36, C:0.25, G:0.09, T:0.30
Consensus pattern (21 bp):
ATACAAGTGATACTTCTACCA
Found at i:33989 original size:50 final size:50
Alignment explanation
Indices: 33879--33993 Score: 155
Period size: 50 Copynumber: 2.3 Consensus size: 50
33869 TCTAGTAGTA
* *
33879 CTATCGATACAATGCAAGTCAGAATATAACCTTTCTCCTACCCAGTACTT
1 CTATCAATACAATGCAAGTCAGAATATAACCTCTCTCCTACCCAGTACTT
*
33929 CTAT-AGATACAATGCAAGTCAGAATATAATCTCTCTCCTACCCTA-TACTT
1 CTATCA-ATACAATGCAAGTCAGAATATAACCTCTCTCCTACCC-AGTACTT
*
33979 TTATCAATAC-ATGCA
1 CTATCAATACAATGCA
33994 TTAGATCTAC
Statistics
Matches: 58, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
49 5 0.09
50 51 0.88
51 2 0.03
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (50 bp):
CTATCAATACAATGCAAGTCAGAATATAACCTCTCTCCTACCCAGTACTT
Found at i:37182 original size:10 final size:10
Alignment explanation
Indices: 37169--37207 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
37159 TCTTTTCTCT
*
37169 TTTCTTCTTA
1 TTTCTTTTTA
*
37179 TTTCTTTTTC
1 TTTCTTTTTA
37189 TTTCTTTTTA
1 TTTCTTTTTA
37199 TTTCTTTTT
1 TTTCTTTTT
37208 GTGAATGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTCTTTTTA
Found at i:37194 original size:20 final size:21
Alignment explanation
Indices: 37157--37207 Score: 77
Period size: 20 Copynumber: 2.4 Consensus size: 21
37147 ATATATTTAT
37157 TTTCTTTTCTCTTTTCTTCTTA
1 TTTCTTTT-TCTTTTCTTCTTA
*
37179 TTTCTTTTTC-TTTCTTTTTA
1 TTTCTTTTTCTTTTCTTCTTA
37199 TTTCTTTTT
1 TTTCTTTTT
37208 GTGAATGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 18 0.64
21 2 0.07
22 8 0.29
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTCTTTTTCTTTTCTTCTTA
Found at i:37699 original size:17 final size:18
Alignment explanation
Indices: 37678--37719 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
37668 TATAAGAATG
37678 GAAATGCAACT-AC-AAT
1 GAAATGCAACTAACAAAT
37694 GCAAATGC-ACTAACAAAT
1 G-AAATGCAACTAACAAAT
37712 GAAATGCA
1 GAAATGCA
37720 TTGACAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 4 0.18
17 14 0.64
18 4 0.18
ACGTcount: A:0.50, C:0.19, G:0.14, T:0.17
Consensus pattern (18 bp):
GAAATGCAACTAACAAAT
Found at i:37890 original size:21 final size:21
Alignment explanation
Indices: 37865--37908 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
37855 GCCATCCTCT
*
37865 TTGTGCTTTTTCTTCTTATCC
1 TTGTGCTTTCTCTTCTTATCC
*
37886 TTGTGCTTTCTCTTCTTGTCC
1 TTGTGCTTTCTCTTCTTATCC
37907 TT
1 TT
37909 TGAATCAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.02, C:0.25, G:0.11, T:0.61
Consensus pattern (21 bp):
TTGTGCTTTCTCTTCTTATCC
Done.