Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003009.1 Kokia drynarioides strain JFW-HI SEQ_115515, 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: 48321
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 132 characters in sequence are not A, C, G, or T
Found at i:14768 original size:28 final size:28
Alignment explanation
Indices: 14728--14784 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
14718 CTTATGTTTC
14728 CTTTGTTTCTTTTTTCTTTTTCTTCAAA
1 CTTTGTTTCTTTTTTCTTTTTCTTCAAA
14756 CTTTGTTTCTTTTTTCTTTTTCTTCAAA
1 CTTTGTTTCTTTTTTCTTTTTCTTCAAA
14784 C
1 C
14785 CAACCACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.11, C:0.19, G:0.04, T:0.67
Consensus pattern (28 bp):
CTTTGTTTCTTTTTTCTTTTTCTTCAAA
Found at i:17392 original size:13 final size:14
Alignment explanation
Indices: 17350--17383 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
17340 TAAAAGAAGC
*
17350 AATTAAAATA-AAT
1 AATTAAAATAGAAA
17363 AATTAAAATAGAAA
1 AATTAAAATAGAAA
17377 AATTAAA
1 AATTAAA
17384 TAATTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (14 bp):
AATTAAAATAGAAA
Found at i:21858 original size:2 final size:2
Alignment explanation
Indices: 21851--21880 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
21841 TTATTTCAAT
21851 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21881 AAAAAAATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22979 original size:39 final size:39
Alignment explanation
Indices: 22906--22996 Score: 105
Period size: 39 Copynumber: 2.3 Consensus size: 39
22896 TTTAGATCGA
* *
22906 AAACGTCACAAAAGGTAAAGCAATAGCTACGTTTT-TCAT
1 AAACGCCACAAAAGGTAAAGCAATAGCTA-GTTTTCCCAT
* *
22945 AAACGCCGCAAAAGGTAAAGCAATAATGGT-GTTTTCCCAT
1 AAACGCCACAAAAGGTAAAGCAAT-A-GCTAGTTTTCCCAT
22985 AAACGCCACAAA
1 AAACGCCACAAA
22997 GATAAAGTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
39 27 0.61
40 15 0.34
41 2 0.05
ACGTcount: A:0.42, C:0.21, G:0.16, T:0.21
Consensus pattern (39 bp):
AAACGCCACAAAAGGTAAAGCAATAGCTAGTTTTCCCAT
Found at i:26287 original size:21 final size:21
Alignment explanation
Indices: 26263--26314 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
26253 TACAACTTAA
* *
26263 AGCAGAGGCAGCAACGAGGGT
1 AGCAGAGGCAGCAACAAGGGC
*
26284 AGCAGAGGCAGCAGCAAGGGC
1 AGCAGAGGCAGCAACAAGGGC
26305 AGCAGAGGCA
1 AGCAGAGGCA
26315 ACAAGAAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.35, C:0.21, G:0.42, T:0.02
Consensus pattern (21 bp):
AGCAGAGGCAGCAACAAGGGC
Found at i:26681 original size:43 final size:43
Alignment explanation
Indices: 26623--26793 Score: 184
Period size: 43 Copynumber: 4.0 Consensus size: 43
26613 TAATGTTAGT
* * *
26623 GGCGTTTGT-AGGAAAAGCGCCGCTAAAGATCATGTTCTATAAC
1 GGCGTTTGTGA-GAAAAACGCCGCTAAAGACCATGTTCTATAGC
* *
26666 GGCATTTGTGAGAAAAACGCCGCTAAGGACCATGTTCTATAGC
1 GGCGTTTGTGAGAAAAACGCCGCTAAAGACCATGTTCTATAGC
* * **
26709 GGCGTTTATGGGAAAAACATCGCTAAAGACCATGTTCTATAGC
1 GGCGTTTGTGAGAAAAACGCCGCTAAAGACCATGTTCTATAGC
* * * * *
26752 GACGTTTGT-AGGAGAAGCGCCGCTAAAAATCATGTTCTATAG
1 GGCGTTTGTGA-GAAAAACGCCGCTAAAGACCATGTTCTATAG
26794 ACATTTTCCC
Statistics
Matches: 106, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
43 105 0.99
44 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (43 bp):
GGCGTTTGTGAGAAAAACGCCGCTAAAGACCATGTTCTATAGC
Found at i:32095 original size:11 final size:10
Alignment explanation
Indices: 32062--32189 Score: 51
Period size: 11 Copynumber: 11.5 Consensus size: 10
32052 AAAACTAGAT
*
32062 AATAACAATA
1 AATAAAAATA
32072 AATAAAAATTA
1 AATAAAAA-TA
32083 AATAGAAAATAAA
1 AATA-AAAAT--A
*
32096 AATATCAAATA
1 AATA-AAAATA
32107 AATAAAACACATA
1 AAT-AAA-A-ATA
*
32120 AA-AATAATAA
1 AATAAAAAT-A
*
32130 AGATAAAATTA
1 A-ATAAAAATA
*
32141 AATAAAAGTGGA
1 AATAAAAAT--A
*
32153 AATATAAATA
1 AATAAAAATA
* *
32163 ACATAAAATTG
1 A-ATAAAAATA
32174 AATAACAAATA
1 AATAA-AAATA
32185 AATAA
1 AATAA
32190 GTGAAAGAAC
Statistics
Matches: 89, Mismatches: 15, Indels: 27
0.68 0.11 0.21
Matches are distributed among these distances:
9 2 0.02
10 23 0.26
11 32 0.36
12 18 0.20
13 14 0.16
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.22
Consensus pattern (10 bp):
AATAAAAATA
Found at i:32098 original size:24 final size:25
Alignment explanation
Indices: 32071--32126 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 25
32061 TAATAACAAT
*
32071 AAATAAAAATTAAATAGAA-A-ATAA
1 AAATAAAAA-TAAATAAAACACATAA
*
32095 AAATATCAAATAAATAAAACACATAA
1 AAATA-AAAATAAATAAAACACATAA
32121 AAATAA
1 AAATAA
32127 TAAAGATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
24 13 0.50
25 4 0.15
26 9 0.35
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (25 bp):
AAATAAAAATAAATAAAACACATAA
Found at i:32170 original size:57 final size:57
Alignment explanation
Indices: 32042--32170 Score: 154
Period size: 57 Copynumber: 2.2 Consensus size: 57
32032 AATTTTAGTG
* * *
32042 ATAAATAAATAAAACTAGATAATAACAATAAATAAAAATTAAATAGAAAATAAAAAT
1 ATAAATAAATAAAACTACATAAAAACAATAAAGAAAAATTAAATAGAAAATAAAAAT
* * **
32099 ATCAAATAAATAAAAC-ACATAAAAATAATAAAGATAAAATTAAATA-AAAGTGGAAAT
1 AT-AAATAAATAAAACTACATAAAAACAATAAAGA-AAAATTAAATAGAAAATAAAAAT
32156 ATAAATAACATAAAA
1 ATAAATAA-ATAAAA
32171 TTGAATAACA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
56 6 0.10
57 32 0.52
58 24 0.39
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.22
Consensus pattern (57 bp):
ATAAATAAATAAAACTACATAAAAACAATAAAGAAAAATTAAATAGAAAATAAAAAT
Found at i:36035 original size:17 final size:17
Alignment explanation
Indices: 36010--36052 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
36000 CAGAGCTTGC
*
36010 TAAAAAGGGTAAACTTA
1 TAAAGAGGGTAAACTTA
*
36027 TAAAGAGGGTAAATTTA
1 TAAAGAGGGTAAACTTA
36044 TAAAGAGGG
1 TAAAGAGGG
36053 ATTTACTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.49, C:0.02, G:0.26, T:0.23
Consensus pattern (17 bp):
TAAAGAGGGTAAACTTA
Found at i:38072 original size:19 final size:18
Alignment explanation
Indices: 38048--38132 Score: 66
Period size: 19 Copynumber: 4.4 Consensus size: 18
38038 TAAGATAACT
38048 ATATAAAATTTTTTAAAAA
1 ATATAAAA-TTTTTAAAAA
38067 ATATAAAATTTTT-AAAA
1 ATATAAAATTTTTAAAAA
* **
38084 TTATTAAATATTAAAATAAAACA
1 ATA-TAAA-ATT--TTTAAAA-A
38107 ATATAAATATTTTTAAAAA
1 ATATAAA-ATTTTTAAAAA
38126 AT-TAAAA
1 ATATAAAA
38133 AAATAATATG
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
17 7 0.13
18 13 0.24
19 14 0.26
20 5 0.09
21 1 0.02
22 11 0.20
23 3 0.06
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATAAAATTTTTAAAAA
Found at i:38459 original size:36 final size:36
Alignment explanation
Indices: 38412--38485 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
38402 TTATTCACTA
38412 TAACTTCACCTTAACATCACTTTGTAATTAATTCAC
1 TAACTTCACCTTAACATCACTTTGTAATTAATTCAC
38448 TAACTTCACCTTAACATCACTTTGTAATTAATTCAC
1 TAACTTCACCTTAACATCACTTTGTAATTAATTCAC
38484 TA
1 TA
38486 CTTAATTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39
Consensus pattern (36 bp):
TAACTTCACCTTAACATCACTTTGTAATTAATTCAC
Found at i:42392 original size:19 final size:19
Alignment explanation
Indices: 42368--42407 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
42358 TGGTCAAGAA
42368 AAAGTCAACAATCAAAGTC
1 AAAGTCAACAATCAAAGTC
*
42387 AAAGTCAACGATCAAAGTC
1 AAAGTCAACAATCAAAGTC
42406 AA
1 AA
42408 CGAGTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.53, C:0.20, G:0.12, T:0.15
Consensus pattern (19 bp):
AAAGTCAACAATCAAAGTC
Found at i:42401 original size:13 final size:13
Alignment explanation
Indices: 42385--42410 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42375 ACAATCAAAG
42385 TCAAAGTCAACGA
1 TCAAAGTCAACGA
42398 TCAAAGTCAACGA
1 TCAAAGTCAACGA
42411 GTTAAAAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.15, T:0.15
Consensus pattern (13 bp):
TCAAAGTCAACGA
Done.