Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013453.1 Kokia drynarioides strain JFW-HI SEQ_128479, 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: 30517
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:482 original size:29 final size:30
Alignment explanation
Indices: 413--836 Score: 305
Period size: 30 Copynumber: 14.3 Consensus size: 30
403 GAACATTCGG
* *
413 GGGTAAAAATGGTAATTTTTGGAAGTTTTA
1 GGGTAAAAATGGGAATTTTTGGAAGTTTGA
*
443 GGGTCAAAAATGGGATTTTTTTGG-AGTTTGA
1 GGGT-AAAAATGGGA-ATTTTTGGAAGTTTGA
*
474 GGGT-AAAATGGTAA-TTTTGGAAGTTTCG-
1 GGGTAAAAATGGGAATTTTTGGAAGTTT-GA
*
502 GGGTTAAAAATGGG-ATTTTTTGAAGTTT-A
1 GGG-TAAAAATGGGAATTTTTGGAAGTTTGA
* *
531 GGGGT-AAAATGGTAATTTTTGGAAGTTTTA
1 -GGGTAAAAATGGGAATTTTTGGAAGTTTGA
* *
561 GGGTTAAAAATGAG-ATTTTTGGAAGTTCGA
1 GGG-TAAAAATGGGAATTTTTGGAAGTTTGA
* * * *
591 GGAT-AAAATGGTAATTTTTGAAATTTTCG-
1 GGGTAAAAATGGGAATTTTTGGAAGTTT-GA
* *
620 GAGTTAAAAATGGG-ATTTTTAGAAGTTT-A
1 G-GGTAAAAATGGGAATTTTTGGAAGTTTGA
*
649 GGGGT-AAAATGGTAATTTTTGGAAGTTTTGA
1 -GGGTAAAAATGGGAATTTTTGGAAG-TTTGA
* *
680 TGGTCAAAAATGAG-ATTTTTGGAAGTTTCGA
1 GGGT-AAAAATGGGAATTTTTGGAAGTTT-GA
* *
711 -GGTCAAAATGGG-ATTTTTGAAAGTTTTGA
1 GGGTAAAAATGGGAATTTTTGGAAG-TTTGA
* *
740 -GGTAAAAAATGTG-ATTTTTGGAAGTTTTGG
1 GGGT-AAAAATGGGAATTTTTGGAAG-TTTGA
* *
770 GGGT-AAAATGGTAATTTTTGAAAGTTTTG-
1 GGGTAAAAATGGGAATTTTTGGAAG-TTTGA
* *
799 GGGTCAAAAATGGG-ATTTTTAGAAGTTCGA
1 GGGT-AAAAATGGGAATTTTTGGAAGTTTGA
*
829 GGTTAAAA
1 GGGTAAAA
837 TGTTAATTTT
Statistics
Matches: 317, Mismatches: 45, Indels: 65
0.74 0.11 0.15
Matches are distributed among these distances:
27 6 0.02
28 28 0.09
29 92 0.29
30 122 0.38
31 56 0.18
32 13 0.04
ACGTcount: A:0.32, C:0.02, G:0.28, T:0.38
Consensus pattern (30 bp):
GGGTAAAAATGGGAATTTTTGGAAGTTTGA
Found at i:515 original size:59 final size:59
Alignment explanation
Indices: 413--846 Score: 445
Period size: 59 Copynumber: 7.3 Consensus size: 59
403 GAACATTCGG
*
413 GGGTAAAAATGGTAATTTTTGGAAGTTTTAGGGTCAAAAATGGGATTTTTTTGGAGTTTGA
1 GGGT-AAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGA-TTTTTTGGAGTTTGA
* * *
474 GGGTAAAATGGTAA-TTTTGGAAGTTTCGGGGTTAAAAATGGGATTTTTTGAAGTTT-A
1 GGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTTGGAGTTTGA
* * * *
531 GGGGTAAAATGGTAATTTTTGGAAGTTTTAGGGTTAAAAATGAGA-TTTTTGGAAGTTCGA
1 -GGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTTGG-AGTTTGA
* * * * * *
591 GGATAAAATGGTAATTTTT-GAAATTTTCGGAGTTAAAAATGGGATTTTTAGAAGTTT-A
1 GGGTAAAATGGTAATTTTTGGAAGTTTT-GGGGTCAAAAATGGGATTTTTTGGAGTTTGA
* *
649 GGGGTAAAATGGTAATTTTTGGAAGTTTTGATGGTCAAAAATGAGA-TTTTTGGAAGTTTCGA
1 -GGGTAAAATGGTAATTTTTGGAAGTTTTG-GGGTCAAAAATGGGATTTTTTGG-AGTTT-GA
* * * * * *
711 -GGTCAAAATGG-GATTTTTGAAAGTTTTGAGGTAAAAAATGTGA-TTTTTGGAAGTTTTGG
1 GGGT-AAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTTGG-AG-TTTGA
* * * *
770 GGGTAAAATGGTAATTTTTGAAAGTTTTGGGGTCAAAAATGGGATTTTTAGAAGTTCGA
1 GGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTTGGAGTTTGA
* *
829 GGTTAAAATGTTAATTTT
1 GGGTAAAATGGTAATTTT
847 CAGACAGTTT
Statistics
Matches: 315, Mismatches: 41, Indels: 36
0.80 0.10 0.09
Matches are distributed among these distances:
57 1 0.00
58 40 0.13
59 164 0.52
60 93 0.30
61 16 0.05
62 1 0.00
ACGTcount: A:0.32, C:0.02, G:0.28, T:0.38
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTTGGAGTTTGA
Found at i:578 original size:118 final size:117
Alignment explanation
Indices: 412--846 Score: 577
Period size: 118 Copynumber: 3.7 Consensus size: 117
402 CGAACATTCG
* *
412 GGGGTAAAAATGGTAATTTTTGGAAGTTTTAGGGTCAAAAATGGGATTTTTTTGG-AGTTTGAGG
1 GGGGT-AAAATGGTAATTTTTGGAAGTTTTAGGGTCAAAAATGAGA--TTTTTGGAAGTTCGAGG
* *
476 GTAAAATGGTAATTTTGGAAGTTTCGGGGTTAAAAATGGGATTTTTTGAAGTTTA
63 GTAAAATGGTAATTTTGAAAGTTTCGGGGTTAAAAATGGGATTTTTAGAAGTTTA
* *
531 GGGGTAAAATGGTAATTTTTGGAAGTTTTAGGGTTAAAAATGAGATTTTTGGAAGTTCGAGGATA
1 GGGGTAAAATGGTAATTTTTGGAAGTTTTAGGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGTA
* *
596 AAATGGTAATTTTTGAAATTTTCGGAGTTAAAAATGGGATTTTTAGAAGTTTA
66 AAATGGTAA-TTTTGAAAGTTTCGGGGTTAAAAATGGGATTTTTAGAAGTTTA
*
649 GGGGTAAAATGGTAATTTTTGGAAGTTTTGATGGTCAAAAATGAGATTTTTGGAAGTTTCGA-GG
1 GGGGTAAAATGGTAATTTTTGGAAGTTTT-AGGGTCAAAAATGAGATTTTTGGAAG-TTCGAGGG
* * * * * * * *
713 TCAAAATGGGATTTTTGAAAGTTTTGAGGTAAAAAATGTGATTTTTGGAAGTTTTG
64 T-AAAATGGTAATTTTGAAAGTTTCGGGGTTAAAAATGGGATTTTTAGAAG-TTTA
* * * * *
769 GGGGTAAAATGGTAATTTTTGAAAGTTTTGGGGTCAAAAATGGGATTTTTAGAAGTTCGAGGTTA
1 GGGGTAAAATGGTAATTTTTGGAAGTTTTAGGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGTA
*
834 AAATGTTAATTTT
66 AAATGGTAATTTT
847 CAGACAGTTT
Statistics
Matches: 279, Mismatches: 30, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
116 7 0.03
117 19 0.07
118 122 0.44
119 87 0.31
120 44 0.16
ACGTcount: A:0.31, C:0.02, G:0.28, T:0.38
Consensus pattern (117 bp):
GGGGTAAAATGGTAATTTTTGGAAGTTTTAGGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGTA
AAATGGTAATTTTGAAAGTTTCGGGGTTAAAAATGGGATTTTTAGAAGTTTA
Found at i:1152 original size:17 final size:17
Alignment explanation
Indices: 1107--1152 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
1097 TTAAAAATGA
1107 GTTTTAATAGCTATACC
1 GTTTTAATAGCTATACC
*
1124 -TTTCCCAA-AGCTATACC
1 GTTT--TAATAGCTATACC
1141 GTTTTAATAGCT
1 GTTTTAATAGCT
1153 TTTAAGAGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 8
0.70 0.06 0.24
Matches are distributed among these distances:
16 5 0.22
17 13 0.57
18 5 0.22
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (17 bp):
GTTTTAATAGCTATACC
Found at i:2558 original size:17 final size:16
Alignment explanation
Indices: 2536--2618 Score: 69
Period size: 17 Copynumber: 4.9 Consensus size: 16
2526 AAATAAATTT
2536 TAAATTTAGATTTATAA
1 TAAATTTA-ATTTATAA
**
2553 TAAATTTAAATTTCA-GC
1 TAAATTT-AATTT-ATAA
2570 TAAATTTAAGTTTATAA
1 TAAATTTAA-TTTATAA
* *
2587 TAAACTTAATTTTAAAA
1 TAAATTTAA-TTTATAA
2604 TAAATTTAAATTTAT
1 TAAATTT-AATTTAT
2619 TGGGCCCAGA
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
16 3 0.06
17 45 0.87
18 4 0.08
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (16 bp):
TAAATTTAATTTATAA
Found at i:2576 original size:34 final size:33
Alignment explanation
Indices: 2536--2618 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 33
2526 AAATAAATTT
* * **
2536 TAAATTTAGATTTATAATAAATTTAAATTTCAGC
1 TAAATTTA-ATTTATAATAAACTTAAATTTAAAA
*
2570 TAAATTTAAGTTTATAATAAACTTAATTTTAAAA
1 TAAATTTAA-TTTATAATAAACTTAAATTTAAAA
2604 TAAATTTAAATTTAT
1 TAAATTT-AATTTAT
2619 TGGGCCCAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
33 1 0.02
34 39 0.93
35 2 0.05
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (33 bp):
TAAATTTAATTTATAATAAACTTAAATTTAAAA
Found at i:7295 original size:25 final size:26
Alignment explanation
Indices: 7265--7313 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
7255 AATTAATAGT
*
7265 TTTAAAT-ACATTTTTATT-TTTTTAG
1 TTTAAATCA-ATTTTAATTATTTTTAG
7290 TTTAAATCAATTTTAATTATTTTT
1 TTTAAATCAATTTTAATTATTTTT
7314 TGATCATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTAAATCAATTTTAATTATTTTTAG
Found at i:12576 original size:15 final size:15
Alignment explanation
Indices: 12556--12586 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
12546 TTGTCATCCA
12556 TCGTAATCAAATTTG
1 TCGTAATCAAATTTG
12571 TCGTAATCAAATTTG
1 TCGTAATCAAATTTG
12586 T
1 T
12587 TATTAACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (15 bp):
TCGTAATCAAATTTG
Found at i:14974 original size:26 final size:26
Alignment explanation
Indices: 14938--14987 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
14928 CAAATCTTAA
*
14938 ACCAAATTTTTCAAAAGTACTTTTTT
1 ACCAAATTTTTCAAAAGCACTTTTTT
*
14964 ACCAAATTTTTTAAAAGCACTTTT
1 ACCAAATTTTTCAAAAGCACTTTT
14988 CAAAAGTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.36, C:0.16, G:0.04, T:0.44
Consensus pattern (26 bp):
ACCAAATTTTTCAAAAGCACTTTTTT
Found at i:16674 original size:30 final size:30
Alignment explanation
Indices: 16640--16706 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
16630 AGGTGGATGA
*
16640 AAAATGGCAGCTCCATTA-AGTTTGTAACGG
1 AAAATGGCAGCTCCATTACA-TCTGTAACGG
* **
16670 AAAATGGTAGCTCTGTTACATCTGTAACGG
1 AAAATGGCAGCTCCATTACATCTGTAACGG
16700 AAAATGG
1 AAAATGG
16707 TTAGTAGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 31 0.97
31 1 0.03
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (30 bp):
AAAATGGCAGCTCCATTACATCTGTAACGG
Found at i:16812 original size:18 final size:19
Alignment explanation
Indices: 16789--16827 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
16779 TTTACTTTTA
16789 TTATAAT-TTTTGATAA-TT
1 TTATAATATTTT-ATAACTT
16807 TTATAATATTTTATAACTT
1 TTATAATATTTTATAACTT
16826 TT
1 TT
16828 TAAATAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (19 bp):
TTATAATATTTTATAACTT
Found at i:17672 original size:14 final size:14
Alignment explanation
Indices: 17648--17689 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
17638 AGATTTTAAC
17648 AAATT-TTTTATTT
1 AAATTATTTTATTT
* *
17661 ACATTATTTTATTC
1 AAATTATTTTATTT
*
17675 AAATTATGTTATTT
1 AAATTATTTTATTT
17689 A
1 A
17690 TCTCTATACT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
13 4 0.17
14 19 0.83
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (14 bp):
AAATTATTTTATTT
Found at i:22985 original size:28 final size:28
Alignment explanation
Indices: 22945--23002 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
22935 ACCCCCAAAG
22945 AAAAACCCTTAACACCGACAGCTTAACC
1 AAAAACCCTTAACACCGACAGCTTAACC
22973 AAAAACCCTTAACACCGACAGCTTAACC
1 AAAAACCCTTAACACCGACAGCTTAACC
23001 AA
1 AA
23003 GATTATCTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.45, C:0.34, G:0.07, T:0.14
Consensus pattern (28 bp):
AAAAACCCTTAACACCGACAGCTTAACC
Found at i:29320 original size:31 final size:31
Alignment explanation
Indices: 29285--29350 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
29275 AAAAAATTAA
* * *
29285 ATGTATACAATTGAATTAAAATCGAAGTTTT
1 ATGTATACAATTAAATAAAAATCAAAGTTTT
*
29316 ATGTATACATTTAAATAAAAATCAAAGTTTT
1 ATGTATACAATTAAATAAAAATCAAAGTTTT
29347 ATGT
1 ATGT
29351 GCATAATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (31 bp):
ATGTATACAATTAAATAAAAATCAAAGTTTT
Found at i:29524 original size:17 final size:18
Alignment explanation
Indices: 29487--29525 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
29477 TATTGTTTAA
**
29487 AAAAACACTTTTAGATTG
1 AAAAACACTTTTAGAAAG
29505 AAAAACACTTTT-GAAAG
1 AAAAACACTTTTAGAAAG
29522 AAAA
1 AAAA
29526 GTTGTGCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.26
Consensus pattern (18 bp):
AAAAACACTTTTAGAAAG
Done.