Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014545.1 Kokia drynarioides strain JFW-HI SEQ_129584, 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: 38043
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:2154 original size:39 final size:39
Alignment explanation
Indices: 2091--2173 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 39
2081 TGTTAATATC
*
2091 TAATATACTACTGAATTGGAAGTGACACTGTAAACACTG
1 TAATATACTACTGAACTGGAAGTGACACTGTAAACACTG
* * * *
2130 TAATGTACTATTGAACTGGTAGTGACACTTTAAACACTG
1 TAATATACTACTGAACTGGAAGTGACACTGTAAACACTG
*
2169 CAATA
1 TAATA
2174 CTACAATTGG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (39 bp):
TAATATACTACTGAACTGGAAGTGACACTGTAAACACTG
Found at i:11396 original size:86 final size:86
Alignment explanation
Indices: 11250--11424 Score: 325
Period size: 86 Copynumber: 2.0 Consensus size: 86
11240 ATGAACTGCC
11250 TGAAAGCAAGCAATGGCCTTGGTTGTAAATGCTGAAGGGACGTCCTCTTGTAGCAGTGCCTTAGA
1 TGAAAGCAAGCAATGGCCTTGGTTGTAAATGCTGAAGGGACGTCCTCTTGTAGCAGTGCCTTAGA
11315 TACT-AAAACTCTGCCATTTT
66 TACTAAAAACTCTGCCATTTT
11335 TNGAAAGCAAGCAATGGCCTTGGTTGTAAATGCTGAAGGGACGTCCTCTTGTAGCAGTGCCTTAG
1 T-GAAAGCAAGCAATGGCCTTGGTTGTAAATGCTGAAGGGACGTCCTCTTGTAGCAGTGCCTTAG
11400 ATACTAAAAAACTCTGCCATTTT
65 ATACT-AAAAACTCTGCCATTTT
11423 TG
1 TG
11425 TCACGAGCTA
Statistics
Matches: 87, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
85 1 0.01
86 68 0.78
87 1 0.01
88 17 0.20
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.29
Consensus pattern (86 bp):
TGAAAGCAAGCAATGGCCTTGGTTGTAAATGCTGAAGGGACGTCCTCTTGTAGCAGTGCCTTAGA
TACTAAAAACTCTGCCATTTT
Found at i:16886 original size:29 final size:29
Alignment explanation
Indices: 16842--16919 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
16832 TATAATAATG
*
16842 TAAAAAAAGAAAGAAAATG-ATGAAAGAAT
1 TAAAAAAAGAAAGAAAA-GAATAAAAGAAT
* *
16871 TATAAAAAGAAAGAAAAGAATAAAATAAT
1 TAAAAAAAGAAAGAAAAGAATAAAAGAAT
16900 TAAAAAAAGAAAG-AAAGAAT
1 TAAAAAAAGAAAGAAAAGAAT
16920 TCGAAATGAG
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 8 0.18
29 36 0.82
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (29 bp):
TAAAAAAAGAAAGAAAAGAATAAAAGAAT
Found at i:21466 original size:13 final size:13
Alignment explanation
Indices: 21438--21473 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
21428 CAAAAATAGA
*
21438 TATATGAAATGGT
1 TATATGAAGTGGT
*
21451 TATATGAAGTGTT
1 TATATGAAGTGGT
21464 TATATGAAGT
1 TATATGAAGT
21474 ATTAGTAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.22, T:0.42
Consensus pattern (13 bp):
TATATGAAGTGGT
Found at i:22314 original size:33 final size:33
Alignment explanation
Indices: 22277--22354 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
22267 TGATGTAAAG
* * * *
22277 AAAAAGAGAGAAAATGATGAAATAATTAAAAAA
1 AAAAAGAAAGAAAATAATAAAAGAATTAAAAAA
22310 AAAAAGAAAGAAAATAATAAAAGAATTAAAAAA
1 AAAAAGAAAGAAAATAATAAAAGAATTAAAAAA
*
22343 AGAAAGAAAGAA
1 AAAAAGAAAGAA
22355 TTAGAAATGA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (33 bp):
AAAAAGAAAGAAAATAATAAAAGAATTAAAAAA
Found at i:22340 original size:17 final size:16
Alignment explanation
Indices: 22300--22350 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
22290 ATGATGAAAT
22300 AATTAAAAAAAAAAAG
1 AATTAAAAAAAAAAAG
** *
22316 AAAGAAAATAATAAAAG
1 AATTAAAA-AAAAAAAG
*
22333 AATTAAAAAAAGAAAG
1 AATTAAAAAAAAAAAG
22349 AA
1 AA
22351 AGAATTAGAA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
16 14 0.52
17 13 0.48
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (16 bp):
AATTAAAAAAAAAAAG
Found at i:24602 original size:42 final size:42
Alignment explanation
Indices: 24538--24678 Score: 228
Period size: 42 Copynumber: 3.3 Consensus size: 42
24528 TCTTGATGCA
*
24538 TAAATGGAAGACTCATGTCTCGGGATGAGAATGAGATTATATT
1 TAAA-GGAAGACTCATGTCTCGGGATGAGAATGAGATTATGTT
24581 TAAAGGAAGACTCATGTCTCGGGATGAGAATGAGATTATGTT
1 TAAAGGAAGACTCATGTCTCGGGATGAGAATGAGATTATGTT
* *
24623 TAAAGGAAGACTCATGTCTCGGAATGAGCATGAGATTATGTT
1 TAAAGGAAGACTCATGTCTCGGGATGAGAATGAGATTATGTT
24665 TGAAAAGGAAGACT
1 T--AAAGGAAGACT
24679 TATACCTGGG
Statistics
Matches: 93, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
42 78 0.84
43 4 0.04
44 11 0.12
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.28
Consensus pattern (42 bp):
TAAAGGAAGACTCATGTCTCGGGATGAGAATGAGATTATGTT
Found at i:26134 original size:158 final size:158
Alignment explanation
Indices: 25846--26143 Score: 427
Period size: 158 Copynumber: 1.9 Consensus size: 158
25836 GTTATAGCTA
* * *
25846 TGTGAGCATTACATGTTATATGGGTGCTGGTCTTAGATGTCCTATCGATGGCTGATGTCCGACAT
1 TGTGAGCATTACAGGTTATATGGGTGCTGGTCTTAGATGTCCTACCGATGGCTGAGGTCCGACAT
* * * *
25911 TTATTACGGATTCTTCACAACTCTTGTGAGCAACATCATGTAGCCTAACATCTCAATACATAGCT
66 TTATTACGGATTCTTCACAACTCGTGTAAGCAACATCATGTAGCCTAACATCTCAACACACAGCT
25976 CGTGTGAGCAAGCCCATTTCATATCTCG
131 CGTGTGAGCAAGCCCATTTCATATCTCG
26004 TGTGAGCATTACAGGTTATATGGGTGCTGGTCTTAGATGTCCTACCGATGGCTGAGGTCCGACAT
1 TGTGAGCATTACAGGTTATATGGGTGCTGGTCTTAGATGTCCTACCGATGGCTGAGGTCCGACAT
** *** * * * * *
26069 TTATTGTGGATTCTTCAGTGCTCGTGTAAGCAGCATCGTGTAGTCC-CACATCTCGACCCACAGC
66 TTATTACGGATTCTTCACAACTCGTGTAAGCAACATCATGTAG-CCTAACATCTCAACACACAGC
26133 TCGTGTGAGCA
130 TCGTGTGAGCA
26144 TATATGGTTA
Statistics
Matches: 122, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
158 120 0.98
159 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.32
Consensus pattern (158 bp):
TGTGAGCATTACAGGTTATATGGGTGCTGGTCTTAGATGTCCTACCGATGGCTGAGGTCCGACAT
TTATTACGGATTCTTCACAACTCGTGTAAGCAACATCATGTAGCCTAACATCTCAACACACAGCT
CGTGTGAGCAAGCCCATTTCATATCTCG
Found at i:32131 original size:18 final size:18
Alignment explanation
Indices: 32108--32190 Score: 71
Period size: 18 Copynumber: 4.6 Consensus size: 18
32098 GTTCAATGTG
32108 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
*
32126 TAATTAATTTATTTAATTTT
1 TAATTAATTTA--AAATTTT
* * * * * *
32146 T-TTTCAGTT-CAATGTG
1 TAATTAATTTAAAATTTT
32162 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
32180 TAATTAATTTA
1 TAATTAATTTA
32191 TTTATTCAAT
Statistics
Matches: 48, Mismatches: 13, Indels: 8
0.70 0.19 0.12
Matches are distributed among these distances:
16 5 0.10
17 5 0.10
18 26 0.54
19 5 0.10
20 7 0.15
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:32153 original size:54 final size:54
Alignment explanation
Indices: 32088--32194 Score: 214
Period size: 54 Copynumber: 2.0 Consensus size: 54
32078 GACGAGCGGG
32088 TTTTTTTTCAGTTCAATGTGTAATTAATTTAAAATTTTTAATTAATTTATTTAA
1 TTTTTTTTCAGTTCAATGTGTAATTAATTTAAAATTTTTAATTAATTTATTTAA
32142 TTTTTTTTCAGTTCAATGTGTAATTAATTTAAAATTTTTAATTAATTTATTTA
1 TTTTTTTTCAGTTCAATGTGTAATTAATTTAAAATTTTTAATTAATTTATTTA
32195 TTCAATTAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.58
Consensus pattern (54 bp):
TTTTTTTTCAGTTCAATGTGTAATTAATTTAAAATTTTTAATTAATTTATTTAA
Found at i:33578 original size:125 final size:125
Alignment explanation
Indices: 33355--33585 Score: 356
Period size: 125 Copynumber: 1.8 Consensus size: 125
33345 TTTTTCATGC
* * *
33355 AATTTTTTTTCTTGTATGCTTGTTTTGTTTGCATTGTGGAATTAGTGTTCTTAGATTATCACAGA
1 AATTTATTTTCTTGTATGCTTGTTTTGTTTACATTGTGGAATTAGTGTTCTTAGATGATCACAGA
* * * * *
33420 TGTGGCCGAAAGCTAAACCGGTGTGGCAGCTTTTAGATAATGGTTTCTCTATAGATTTTG
66 CGCGGCCGAAAGCTAAACCAGTGAGGCACCTTTTAGATAATGGTTTCTCTATAGATTTTG
*
33480 AATTTATTTTCTTGTATGCTTGTTTTGTTTACATTGTGGAATTAGTGTTCTTAGATGGTCACA-A
1 AATTTATTTTCTTGTATGCTTGTTTTGTTTACATTGTGGAATTAGTGTTCTTAGATGATCACAGA
*
33544 GCGCGGCCGAAAGCTAAACCAGTGAGGCTCCTTTTAGATAAT
66 -CGCGGCCGAAAGCTAAACCAGTGAGGCACCTTTTAGATAAT
33586 AGATTTTGAA
Statistics
Matches: 95, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
124 1 0.01
125 94 0.99
ACGTcount: A:0.23, C:0.13, G:0.22, T:0.42
Consensus pattern (125 bp):
AATTTATTTTCTTGTATGCTTGTTTTGTTTACATTGTGGAATTAGTGTTCTTAGATGATCACAGA
CGCGGCCGAAAGCTAAACCAGTGAGGCACCTTTTAGATAATGGTTTCTCTATAGATTTTG
Found at i:35553 original size:19 final size:19
Alignment explanation
Indices: 35529--35566 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
35519 AGTATACAAC
35529 ATATATCAGATGAAGCAAG
1 ATATATCAGATGAAGCAAG
35548 ATATATCAGATGAAGCAAG
1 ATATATCAGATGAAGCAAG
35567 TTTTCCATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.11, G:0.21, T:0.21
Consensus pattern (19 bp):
ATATATCAGATGAAGCAAG
Done.