Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011612.1 Kokia drynarioides strain JFW-HI SEQ_126602, 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: 42342
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Found at i:378 original size:17 final size:16
Alignment explanation
Indices: 358--423 Score: 60
Period size: 17 Copynumber: 3.9 Consensus size: 16
348 AAATAAACTT
358 TAAATTTAAATTTATAA
1 TAAATTTAAATTTA-AA
* *
375 TAAACTTAAATTTCAAC
1 TAAATTTAAATTT-AAA
*
392 CAAATTTAAATTTAAAA
1 TAAATTTAAATTT-AAA
**
409 TAAAAATAAATTTAA
1 TAAATTTAAATTTAA
424 GTTTACTGGG
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
16 2 0.05
17 36 0.92
18 1 0.03
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:1494 original size:27 final size:28
Alignment explanation
Indices: 1464--1524 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
1454 CCAAGAATTC
*
1464 TATTAAAAG-AGGATCGAAGGAAACAAT
1 TATTAAAAGCAGGATCAAAGGAAACAAT
*
1491 TATTAAAAGCAGGATTAAAGGAAACAAT
1 TATTAAAAGCAGGATCAAAGGAAACAAT
*
1519 CATTAA
1 TATTAA
1525 TGTCAAGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 9 0.30
28 21 0.70
ACGTcount: A:0.52, C:0.08, G:0.18, T:0.21
Consensus pattern (28 bp):
TATTAAAAGCAGGATCAAAGGAAACAAT
Found at i:12554 original size:6 final size:6
Alignment explanation
Indices: 12545--12620 Score: 66
Period size: 6 Copynumber: 12.2 Consensus size: 6
12535 AATATCCATG
* * *
12545 AAATAA AAATAA AAATAA AAA-AT AAA-AA AAATGAAA AAATGA AAATGA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAAT--AA AAATAA AAATAA
12593 AAATGAA AATATAA AAATATA AAATAA A
1 AAAT-AA AA-ATAA AAATA-A AAATAA A
12621 CGTACTAATT
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
5 8 0.13
6 31 0.52
7 13 0.22
8 8 0.13
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:12595 original size:24 final size:23
Alignment explanation
Indices: 12545--12610 Score: 55
Period size: 26 Copynumber: 2.7 Consensus size: 23
12535 AATATCCATG
*
12545 AAATAAAAAT-AAAAATAAAAAA
1 AAATAAAAATAAAAAATGAAAAA
12567 TAAA-AAAAATGAAAAAATGAAAATGA
1 -AAATAAAAAT-AAAAAATGAAAA--A
*
12593 AAATGAAAATATAAAAAT
1 AAATAAAAATA-AAAAAT
12611 ATAAAATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
22 6 0.17
23 3 0.09
24 10 0.29
25 4 0.11
26 12 0.34
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (23 bp):
AAATAAAAATAAAAAATGAAAAA
Found at i:13885 original size:87 final size:87
Alignment explanation
Indices: 13775--13943 Score: 266
Period size: 87 Copynumber: 1.9 Consensus size: 87
13765 TTGTTTTGAA
* * *
13775 ATCTAGTTTCAGAAACTAAAATAAATTTAGAAAGCATCTCTTCAAGGTTTGATTTTTGCTCTTGC
1 ATCTAGTTTCAGAAACCAAAATAAATTTAGAAAGCATCTCTTCAAGGTTTAATTTTTGCTCTTAC
13840 TCATAAGGTTGCTGAAATGTCG
66 TCATAAGGTTGCTGAAATGTCG
* *
13862 ATCTAGTTTCAGAAACCGAAATAAATTTAGCAAGCATCTCTTCAAGGTTTAATTTTTGCTCTTAC
1 ATCTAGTTTCAGAAACCAAAATAAATTTAGAAAGCATCTCTTCAAGGTTTAATTTTTGCTCTTAC
* * *
13927 TGATCAGGTTGTTGAAA
66 TCATAAGGTTGCTGAAA
13944 AGTCAGAGCG
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 74 1.00
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (87 bp):
ATCTAGTTTCAGAAACCAAAATAAATTTAGAAAGCATCTCTTCAAGGTTTAATTTTTGCTCTTAC
TCATAAGGTTGCTGAAATGTCG
Found at i:23451 original size:21 final size:22
Alignment explanation
Indices: 23401--23453 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
23391 GATAGTGCAG
* *
23401 ACTTCTACCGATACAAGTGACT
1 ACTTCTACCGAAACAAATGACT
* *
23423 -CTTTTACCGAAACAAAT-ATT
1 ACTTCTACCGAAACAAATGACT
23443 ACTTCTACCGA
1 ACTTCTACCGA
23454 TACTAAAAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.30
Consensus pattern (22 bp):
ACTTCTACCGAAACAAATGACT
Found at i:23570 original size:21 final size:24
Alignment explanation
Indices: 23518--23572 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
23508 AGAACATAAT
23518 CTACCGATACTTCTAATTATAGAA
1 CTACCGATACTTCTAATTATAGAA
*
23542 CTATCGATACTTACT-A-T-TA-AA
1 CTACCGATACTT-CTAATTATAGAA
23563 CTACCGATAC
1 CTACCGATAC
23573 AACTCAAGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 11 0.39
22 2 0.07
23 1 0.04
24 12 0.43
25 2 0.07
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.33
Consensus pattern (24 bp):
CTACCGATACTTCTAATTATAGAA
Found at i:24248 original size:26 final size:26
Alignment explanation
Indices: 24219--24300 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 26
24209 GTCATCAGAC
*
24219 CTCATAATCCGTAAAGGATTCATATA
1 CTCATAATCCATAAAGGATTCATATA
* * * * * *
24245 CTCACAATGACACATAGTCA-TCAGA-A
1 CTCATAAT-CCATAAAG-GATTCATATA
24271 CTCATAATCCATAAAGGATTCATATA
1 CTCATAATCCATAAAGGATTCATATA
24297 CTCA
1 CTCA
24301 CAATGACACA
Statistics
Matches: 39, Mismatches: 13, Indels: 8
0.65 0.22 0.13
Matches are distributed among these distances:
24 1 0.03
25 9 0.23
26 20 0.51
27 8 0.21
28 1 0.03
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (26 bp):
CTCATAATCCATAAAGGATTCATATA
Found at i:24262 original size:52 final size:52
Alignment explanation
Indices: 24190--24322 Score: 216
Period size: 52 Copynumber: 2.6 Consensus size: 52
24180 ATTTCGTTTA
* * *
24190 ATACTCACGAA-GACAGATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCAC-AATGACACATAGTCATCAGAACTCATAATCCATAAAGGATTCAT
24242 ATACTCACAATGACACATAGTCATCAGAACTCATAATCCATAAAGGATTCAT
1 ATACTCACAATGACACATAGTCATCAGAACTCATAATCCATAAAGGATTCAT
24294 ATACTCACAATGACACATAGTCATC-GAAC
1 ATACTCACAATGACACATAGTCATCAGAAC
24323 CCTTTTTAAT
Statistics
Matches: 77, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
51 6 0.08
52 71 0.92
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.23
Consensus pattern (52 bp):
ATACTCACAATGACACATAGTCATCAGAACTCATAATCCATAAAGGATTCAT
Found at i:36460 original size:13 final size:13
Alignment explanation
Indices: 36442--36473 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
36432 CTTAAACCAA
36442 ACTTTTCAAAAAT
1 ACTTTTCAAAAAT
*
36455 ACTTTTCAAAATT
1 ACTTTTCAAAAAT
36468 ACTTTT
1 ACTTTT
36474 TTAAAGCACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.47
Consensus pattern (13 bp):
ACTTTTCAAAAAT
Found at i:36484 original size:13 final size:13
Alignment explanation
Indices: 36468--36504 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
36458 TTTCAAAATT
*
36468 ACTTTTTTAAAGC
1 ACTTTTTAAAAGC
36481 ACTTTTTAAAAGC
1 ACTTTTTAAAAGC
*
36494 ACTTCTTAAAA
1 ACTTTTTAAAA
36505 ATAATGCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.41
Consensus pattern (13 bp):
ACTTTTTAAAAGC
Found at i:38897 original size:18 final size:20
Alignment explanation
Indices: 38869--38910 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
38859 AATTTGATTT
38869 TTTTAATAAATAATTTT-AA
1 TTTTAATAAATAATTTTGAA
*
38888 TTTTAA-AAATTATTTTGAA
1 TTTTAATAAATAATTTTGAA
38907 TTTT
1 TTTT
38911 TTTTAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
TTTTAATAAATAATTTTGAA
Found at i:39352 original size:19 final size:20
Alignment explanation
Indices: 39316--39355 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
39306 ATAAAGTCCA
* *
39316 TTTTCTTAAAACAGAAATTT
1 TTTTATTAAAACACAAATTT
39336 TTTTATTAAAA-ACAAATTT
1 TTTTATTAAAACACAAATTT
39355 T
1 T
39356 AAAACTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.47
Consensus pattern (20 bp):
TTTTATTAAAACACAAATTT
Found at i:41340 original size:17 final size:17
Alignment explanation
Indices: 41320--41388 Score: 68
Period size: 17 Copynumber: 4.1 Consensus size: 17
41310 TAATTTTAAA
*
41320 TAAGTTTGAATTTATTT
1 TAAGTTTAAATTTATTT
* *
41337 TAAGTTAAAATTCATTT
1 TAAGTTTAAATTTATTT
* *
41354 TGAA-TTTGAATTTAATT
1 T-AAGTTTAAATTTATTT
*
41371 TAAATTTAAATTTATTT
1 TAAGTTTAAATTTATTT
41388 T
1 T
41389 CAATTAAAAT
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
16 2 0.05
17 37 0.90
18 2 0.05
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.55
Consensus pattern (17 bp):
TAAGTTTAAATTTATTT
Found at i:41362 original size:34 final size:34
Alignment explanation
Indices: 41324--41393 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 34
41314 TTTAAATAAG
* * *
41324 TTTGAATTTATTTTAAGTTAAAATTCATTTTGAA
1 TTTGAATTTAATTTAAATTAAAATTCATTTTCAA
* *
41358 TTTGAATTTAATTTAAATTTAAATTTATTTTCAA
1 TTTGAATTTAATTTAAATTAAAATTCATTTTCAA
41392 TT
1 TT
41394 AAAATTAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.56
Consensus pattern (34 bp):
TTTGAATTTAATTTAAATTAAAATTCATTTTCAA
Found at i:41393 original size:17 final size:16
Alignment explanation
Indices: 41328--41399 Score: 63
Period size: 17 Copynumber: 4.2 Consensus size: 16
41318 AATAAGTTTG
41328 AATTTATTTTAAGTTAA
1 AATTTATTTTAA-TTAA
* **
41345 AATTCATTTTGAATTTG
1 AATTTATTTT-AATTAA
* *
41362 AATTTAATTTAAATTTA
1 AATTT-ATTTTAATTAA
41379 AATTTATTTTCAATTAA
1 AATTTATTTT-AATTAA
41396 AATT
1 AATT
41400 AATTAAAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
16 4 0.09
17 34 0.77
18 6 0.14
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (16 bp):
AATTTATTTTAATTAA
Found at i:42117 original size:3 final size:3
Alignment explanation
Indices: 42109--42152 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
42099 ATAAATTCAT
* *
42109 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAT TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
42153 TTAAATAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Done.