Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013000.1 Kokia drynarioides strain JFW-HI SEQ_128018, 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: 58134
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:5250 original size:20 final size:21
Alignment explanation
Indices: 5215--5260 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
5205 CATTAACAGG
5215 TCGTTAACCGTTGATCGTTGA
1 TCGTTAACCGTTGATCGTTGA
5236 TCGTTAACC-TTGATCGTTGA
1 TCGTTAACCGTTGATCGTTGA
*
5256 CCGTT
1 TCGTT
5261 GACTTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (21 bp):
TCGTTAACCGTTGATCGTTGA
Found at i:6163 original size:16 final size:16
Alignment explanation
Indices: 6121--6154 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
6111 TGTTGATTTA
6121 TAAATACTTTAGGTTG
1 TAAATACTTTAGGTTG
6137 TAAATACTTTAGGTTG
1 TAAATACTTTAGGTTG
6153 TA
1 TA
6155 TGTACTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (16 bp):
TAAATACTTTAGGTTG
Found at i:6276 original size:3 final size:3
Alignment explanation
Indices: 6268--6308 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
6258 TTGCATCATT
6268 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
6309 TTGGTTTTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:22450 original size:16 final size:16
Alignment explanation
Indices: 22425--22458 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
22415 TCAATTAAGA
* *
22425 AAAAGGGGTAAATATT
1 AAAAGAGGTAAAAATT
22441 AAAAGAGGTAAAAATT
1 AAAAGAGGTAAAAATT
22457 AA
1 AA
22459 TTGCTATTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.21, T:0.21
Consensus pattern (16 bp):
AAAAGAGGTAAAAATT
Found at i:24411 original size:43 final size:43
Alignment explanation
Indices: 24350--24663 Score: 201
Period size: 42 Copynumber: 7.4 Consensus size: 43
24340 AAATCAATTG
* *
24350 ATGTATAAATAGAAGACTCATGTCTCTGAATGAGCGTGAGATT
1 ATGTATAAATGGAAGACTCATGTCTCTGAATGAGCATGAGATT
* * *
24393 ATGTATAAATGGAAGACTCGTGACT-TGGGATGAGCATGAGATT
1 ATGTATAAATGGAAGACTCATGTCTCT-GAATGAGCATGAGATT
* *
24436 ATGTATAAATGGAGGACTCATGTCTC-GAGATGAGCTTGAGATT
1 ATGTATAAATGGAAGACTCATGTCTCTGA-ATGAGCATGAGATT
* * * *
24479 ATGTTTAAA-GGAAGACTTATGTCTCAG-ATAGAGCATAAGA-T
1 ATGTATAAATGGAAGACTCATGTCTCTGAAT-GAGCATGAGATT
* * * *
24520 -TGTATTAAAAGGAAGACTTATGTCTC-GGATAGAGCATAAGA-T
1 ATGTA-TAAATGGAAGACTCATGTCTCTGAAT-GAGCATGAGATT
* * * *
24562 -TGTATTAAAAGGAAGATTTATGTCT-TGGATAGAGCAT-A-A-T
1 ATGTA-TAAATGGAAGACTCATGTCTCTGAAT-GAGCATGAGATT
* * * *
24602 ATTGTATTAAAAGGAAGACTTATGTCTCAG-ATAGAGCATAAGA-T
1 A-TGTA-TAAATGGAAGACTCATGTCTCTGAAT-GAGCATGAGATT
*
24646 -TGTATTAAAAGGAAGACT
1 ATGTA-TAAATGGAAGACT
24664 TATGACTCGG
Statistics
Matches: 238, Mismatches: 19, Indels: 29
0.83 0.07 0.10
Matches are distributed among these distances:
40 5 0.02
41 9 0.04
42 140 0.59
43 82 0.34
44 2 0.01
ACGTcount: A:0.37, C:0.09, G:0.24, T:0.30
Consensus pattern (43 bp):
ATGTATAAATGGAAGACTCATGTCTCTGAATGAGCATGAGATT
Found at i:24520 original size:42 final size:42
Alignment explanation
Indices: 24437--24685 Score: 322
Period size: 42 Copynumber: 6.0 Consensus size: 42
24427 CATGAGATTA
* * * * *
24437 TGTA-TAAATGGAGGACTCATGTCTCGAGAT-GAGCTTGAGAT
1 TGTATTAAAAGGAAGACTTATGTCTC-AGATAGAGCATAAGAT
* * *
24478 TATGTTTAAAGGAAGACTTATGTCTCAGATAGAGCATAAGAT
1 TGTATTAAAAGGAAGACTTATGTCTCAGATAGAGCATAAGAT
*
24520 TGTATTAAAAGGAAGACTTATGTCTCGGATAGAGCATAAGAT
1 TGTATTAAAAGGAAGACTTATGTCTCAGATAGAGCATAAGAT
* ** *
24562 TGTATTAAAAGGAAGATTTATGTCTTGGATAGAGCATAATAT
1 TGTATTAAAAGGAAGACTTATGTCTCAGATAGAGCATAAGAT
24604 TGTATTAAAAGGAAGACTTATGTCTCAGATAGAGCATAAGAT
1 TGTATTAAAAGGAAGACTTATGTCTCAGATAGAGCATAAGAT
* * * *
24646 TGTATTAAAAGGAAGACTTATGACTCGGTTTGAGCATAAG
1 TGTATTAAAAGGAAGACTTATGTCTCAGATAGAGCATAAG
24686 GTTAATTCAG
Statistics
Matches: 183, Mismatches: 23, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
41 6 0.03
42 177 0.97
ACGTcount: A:0.37, C:0.09, G:0.24, T:0.31
Consensus pattern (42 bp):
TGTATTAAAAGGAAGACTTATGTCTCAGATAGAGCATAAGAT
Found at i:36009 original size:17 final size:17
Alignment explanation
Indices: 35989--36043 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
35979 ATTGTGATCA
35989 CATTCTCATTGTCATTG
1 CATTCTCATTGTCATTG
* * *
36006 CATTTTAATTGTCACTG
1 CATTCTCATTGTCATTG
* *
36023 CATTCGCATTGTTATTG
1 CATTCTCATTGTCATTG
36040 CATT
1 CATT
36044 TCCATTTGTC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.47
Consensus pattern (17 bp):
CATTCTCATTGTCATTG
Found at i:36049 original size:17 final size:17
Alignment explanation
Indices: 35995--36049 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
35985 ATCACATTCT
*
35995 CATTGTCATTGCATTTT
1 CATTGTCATTGCATTTC
* *
36012 AATTGTCACTGCA-TTC
1 CATTGTCATTGCATTTC
*
36028 GCATTGTTATTGCATTTC
1 -CATTGTCATTGCATTTC
36046 CATT
1 CATT
36050 TGTCTTTGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
16 2 0.07
17 25 0.83
18 3 0.10
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.47
Consensus pattern (17 bp):
CATTGTCATTGCATTTC
Found at i:36631 original size:30 final size:30
Alignment explanation
Indices: 36596--36654 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
36586 CAATGACATC
*
36596 TCTCAGTCACATAATCTATATATATATATA
1 TCTCAGTCACATAAACTATATATATATATA
*
36626 TCTCAGTCACATAAAGTATATATATATAT
1 TCTCAGTCACATAAACTATATATATATAT
36655 GCATATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.39
Consensus pattern (30 bp):
TCTCAGTCACATAAACTATATATATATATA
Found at i:39195 original size:14 final size:14
Alignment explanation
Indices: 39178--39218 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 14
39168 TTTAAACTCT
39178 AAAAGATAAATACA
1 AAAAGATAAATACA
39192 AAAAGAT-AA-ACA
1 AAAAGATAAATACA
*
39204 TAAAG-TAAATACA
1 AAAAGATAAATACA
39217 AA
1 AA
39219 TTTAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
11 1 0.04
12 9 0.39
13 6 0.26
14 7 0.30
ACGTcount: A:0.71, C:0.07, G:0.07, T:0.15
Consensus pattern (14 bp):
AAAAGATAAATACA
Found at i:39233 original size:19 final size:19
Alignment explanation
Indices: 39209--39251 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
39199 AAACATAAAG
39209 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
39228 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
39247 TAAAT
1 TAAAT
39252 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:40627 original size:28 final size:28
Alignment explanation
Indices: 40588--40642 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
40578 TTTAGATAAT
40588 TATGTTTATTTATTTTT-TAATTTTTTG
1 TATGTTTATTTATTTTTATAATTTTTTG
*
40615 TATGATTTATTTATTTTTATTATTTTTT
1 TATG-TTTATTTATTTTTATAATTTTTT
40643 ACATATAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 4 0.16
28 13 0.52
29 8 0.32
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (28 bp):
TATGTTTATTTATTTTTATAATTTTTTG
Found at i:43471 original size:69 final size:72
Alignment explanation
Indices: 43379--43523 Score: 183
Period size: 72 Copynumber: 2.1 Consensus size: 72
43369 GTGAGTGATA
* *
43379 ATTTATTCACTATTTTAATT-AAAAAGTT-GA-TTTTAGTCCC-TCATTGATTAGAGAATA-TCA
1 ATTTATTCACTATTTTAATTAAAAAAGTTAAATTTTTAATCCCAT-ATTGATTAGAGAATATTC-
*
43439 TCATAACTC
64 CCATAACTC
* * *
43448 ATTTCTTCACTATTTTCATTAAAAAAGTTAAATTTTTAATCCCATATTTATTAGAGAATATTCCC
1 ATTTATTCACTATTTTAATTAAAAAAGTTAAATTTTTAATCCCATATTGATTAGAGAATATTCCC
43513 ATAACTC
66 ATAACTC
43520 ATTT
1 ATTT
43524 TTCTTTATTC
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
69 18 0.28
70 8 0.12
71 1 0.02
72 35 0.54
73 3 0.05
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.43
Consensus pattern (72 bp):
ATTTATTCACTATTTTAATTAAAAAAGTTAAATTTTTAATCCCATATTGATTAGAGAATATTCCC
ATAACTC
Found at i:43653 original size:35 final size:35
Alignment explanation
Indices: 43607--43679 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
43597 CATGCTCACA
* ** *
43607 TTTACCTTATAAATAAGTGTTAAGTTTTTTACTAT
1 TTTACCTTATAAATAAGTGTCAAACTTTTCACTAT
*
43642 TTTACTTTATAAATAAGTGTCAAACTTTTCACTAT
1 TTTACCTTATAAATAAGTGTCAAACTTTTCACTAT
43677 TTT
1 TTT
43680 TATTAAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.32, C:0.11, G:0.07, T:0.51
Consensus pattern (35 bp):
TTTACCTTATAAATAAGTGTCAAACTTTTCACTAT
Found at i:45803 original size:53 final size:53
Alignment explanation
Indices: 45740--45846 Score: 123
Period size: 53 Copynumber: 2.0 Consensus size: 53
45730 AAAATAGAAC
45740 AAGTACTGAAAATAAA-AAAT-ACTGAAAAGTAAATGAT-AAAATAAAGGGTAAACT
1 AAGTACTGAAAA-AAATAAATGA-T-AAAA-TAAATGATAAAAATAAAGGGTAAACT
* *
45794 AAGTA-TGAAAAAAATAAATGATAAAATAAATGCTGAAAAATAAATGGTAAACT
1 AAGTACTGAAAAAAATAAATGATAAAATAAATGAT-AAAAATAAAGGGTAAACT
45847 GTAAATGGAG
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
51 7 0.15
52 7 0.15
53 27 0.57
54 6 0.13
ACGTcount: A:0.60, C:0.05, G:0.14, T:0.21
Consensus pattern (53 bp):
AAGTACTGAAAAAAATAAATGATAAAATAAATGATAAAAATAAAGGGTAAACT
Found at i:45806 original size:26 final size:27
Alignment explanation
Indices: 45772--45846 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 27
45762 TGAAAAGTAA
* * *
45772 ATGATAAAATAAAGGGTAAACTAAGT-
1 ATGAAAAAATAAATGGTAAACTAAATG
* *
45798 ATGAAAAAAATAAATGATAAAATAAATG
1 ATG-AAAAAATAAATGGTAAACTAAATG
*
45826 CTG-AAAAATAAATGGTAAACT
1 ATGAAAAAATAAATGGTAAACT
45847 GTAAATGGAG
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
26 19 0.49
27 18 0.46
28 2 0.05
ACGTcount: A:0.59, C:0.04, G:0.15, T:0.23
Consensus pattern (27 bp):
ATGAAAAAATAAATGGTAAACTAAATG
Found at i:45821 original size:12 final size:12
Alignment explanation
Indices: 45764--45844 Score: 54
Period size: 12 Copynumber: 6.2 Consensus size: 12
45754 AAAAATACTG
45764 AAAAGTAAATGAT
1 AAAA-TAAATGAT
* *
45777 AAAATAAAGGGT
1 AAAATAAATGAT
* *
45789 AAACTAAGTATGAAA
1 AAAATAA--ATG-AT
45804 AAAATAAATGAT
1 AAAATAAATGAT
*
45816 AAAATAAATGCT
1 AAAATAAATGAT
*
45828 GAAAAATAAATGGT
1 --AAAATAAATGAT
45842 AAA
1 AAA
45845 CTGTAAATGG
Statistics
Matches: 53, Mismatches: 10, Indels: 11
0.72 0.14 0.15
Matches are distributed among these distances:
12 27 0.51
13 7 0.13
14 13 0.25
15 6 0.11
ACGTcount: A:0.62, C:0.02, G:0.15, T:0.21
Consensus pattern (12 bp):
AAAATAAATGAT
Found at i:45996 original size:17 final size:19
Alignment explanation
Indices: 45976--46014 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
45966 GTTTATCTAC
45976 AAGATAA-A-TTTAATATT
1 AAGATAACACTTTAATATT
45993 AAGATAATCACTTTAATATT
1 AAGATAA-CACTTTAATATT
46013 AA
1 AA
46015 ATTAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
19 1 0.05
20 11 0.58
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (19 bp):
AAGATAACACTTTAATATT
Done.