Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005129.1 Kokia drynarioides strain JFW-HI SEQ_118964, 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: 41924
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 79 characters in sequence are not A, C, G, or T
Found at i:764 original size:25 final size:25
Alignment explanation
Indices: 670--779 Score: 75
Period size: 25 Copynumber: 4.3 Consensus size: 25
660 TGTTAATAAT
* *
670 TTAAATTAAATAAT-TTTTTATCTA
1 TTAAATTAAATACTATTTTTATTTA
* * *
694 TTAAATTTTATTACCTATTTTCTGTTTAA
1 TTAAA-TTAAATA-CTATTTT-TATTT-A
723 TTTAAATTAAATA--ATTTTTATTTA
1 -TTAAATTAAATACTATTTTTATTTA
* *
747 TTAAATTATATACTATTTATA-TTA
1 TTAAATTAAATACTATTTTTATTTA
771 TATAAATTA
1 T-TAAATTA
780 GTATTTATTT
Statistics
Matches: 67, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
23 11 0.16
24 10 0.15
25 22 0.33
26 6 0.09
27 4 0.06
28 3 0.04
29 6 0.09
30 5 0.07
ACGTcount: A:0.39, C:0.05, G:0.01, T:0.55
Consensus pattern (25 bp):
TTAAATTAAATACTATTTTTATTTA
Found at i:789 original size:25 final size:23
Alignment explanation
Indices: 724--779 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
714 TCTGTTTAAT
* * *
724 TTAAATTAAATAATTTTTATTTA
1 TTAAATTATATACTATTTATTTA
747 TTAAATTATATACTATTTATATTA
1 TTAAATTATATACTATTTAT-TTA
771 TATAAATTA
1 T-TAAATTA
780 GTATTTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 17 0.61
24 4 0.14
25 7 0.25
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
TTAAATTATATACTATTTATTTA
Found at i:795 original size:25 final size:24
Alignment explanation
Indices: 724--798 Score: 66
Period size: 23 Copynumber: 3.1 Consensus size: 24
714 TCTGTTTAAT
* * *
724 TTAAATTAAATAAT-TTTTATTTA
1 TTAAATTATATACTATTTTAATTA
747 TTAAATTATATACTA-TTTATATTA
1 TTAAATTATATACTATTTTA-ATTA
*
771 TATAAATTAGTAT-TTATTTTAATTA
1 T-TAAATTA-TATACTATTTTAATTA
796 TTA
1 TTA
799 GCATATACTA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
23 16 0.37
24 6 0.14
25 14 0.33
26 7 0.16
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (24 bp):
TTAAATTATATACTATTTTAATTA
Found at i:1035 original size:21 final size:21
Alignment explanation
Indices: 1011--1052 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1001 ACCTCAAACT
*
1011 TTAAATCCTGAATCCCAAATC
1 TTAAATACTGAATCCCAAATC
* *
1032 TTAAATATTGAATCCCGAATC
1 TTAAATACTGAATCCCAAATC
1053 CCAAATTTCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.24, G:0.07, T:0.31
Consensus pattern (21 bp):
TTAAATACTGAATCCCAAATC
Found at i:1058 original size:21 final size:21
Alignment explanation
Indices: 1019--1058 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1009 CTTTAAATCC
**
1019 TGAATCCCAAATCTTAAATAT
1 TGAATCCCAAATCCCAAATAT
*
1040 TGAATCCCGAATCCCAAAT
1 TGAATCCCAAATCCCAAAT
1059 TTCGAACACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.25, G:0.07, T:0.28
Consensus pattern (21 bp):
TGAATCCCAAATCCCAAATAT
Found at i:1092 original size:7 final size:7
Alignment explanation
Indices: 1080--1111 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
1070 AATTCGGATC
1080 TCGAGTT
1 TCGAGTT
1087 TCGAGTT
1 TCGAGTT
1094 TCGAGTT
1 TCGAGTT
1101 TCGAG-T
1 TCGAGTT
1107 TCGAG
1 TCGAG
1112 ATTCAAGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.16, C:0.16, G:0.31, T:0.38
Consensus pattern (7 bp):
TCGAGTT
Found at i:4284 original size:27 final size:27
Alignment explanation
Indices: 4252--4310 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
4242 GAAATGAGAC
4252 TTTGGA-TACCCGGAGCAAAATGATAAT
1 TTTGGACT-CCCGGAGCAAAATGATAAT
** * *
4279 TTTGGACTTTCGGGGCAAGATGATAAT
1 TTTGGACTCCCGGAGCAAAATGATAAT
4306 TTTGG
1 TTTGG
4311 GGAAGTTCGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 26 0.96
28 1 0.04
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32
Consensus pattern (27 bp):
TTTGGACTCCCGGAGCAAAATGATAAT
Found at i:4457 original size:30 final size:31
Alignment explanation
Indices: 4321--4464 Score: 110
Period size: 29 Copynumber: 4.9 Consensus size: 31
4311 GGAAGTTCGA
* * *
4321 GGTTAAAAGATGGAATTTTTAGACA-TTTAGG
1 GGTTAAAAAATGGAATTTTTGGA-AGTTTTGG
* *
4352 TG-T-AAAAATGGAATTTTTGAAAGTTTTGG
1 GGTTAAAAAATGGAATTTTTGGAAGTTTTGG
* *
4381 GGTT--AAAATAGAATTTTTGGACA--TTCGG
1 GGTTAAAAAATGGAATTTTTGGA-AGTTTTGG
**
4409 GG--GCAAAATGGTAATTTTTGGAAGTTTTGG
1 GGTTAAAAAATGG-AATTTTTGGAAGTTTTGG
4439 GGTTAAAAAAT-GAATTTTTGGAAGTT
1 GGTTAAAAAATGGAATTTTTGGAAGTT
4465 CGGGTGCAAA
Statistics
Matches: 90, Mismatches: 13, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
28 14 0.16
29 46 0.51
30 23 0.26
31 2 0.02
32 5 0.06
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.38
Consensus pattern (31 bp):
GGTTAAAAAATGGAATTTTTGGAAGTTTTGG
Found at i:4484 original size:29 final size:29
Alignment explanation
Indices: 4392--4486 Score: 88
Period size: 29 Copynumber: 3.2 Consensus size: 29
4382 GTTAAAATAG
*
4392 AATTTTTGGACA-TTCGGGGGC-AAAATGGT
1 AATTTTTGGA-AGTTCGGGTGCAAAAAT-GT
* **
4421 AATTTTTGGAAGTTTTGGGGTTAAAAAATG-
1 AATTTTTGGAAG--TTCGGGTGCAAAAATGT
4451 AATTTTTGGAAGTTCGGGTGCAAAAATGT
1 AATTTTTGGAAGTTCGGGTGCAAAAATGT
*
4480 GATTTTT
1 AATTTTT
4487 AGATAGTTTA
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
28 14 0.26
29 16 0.30
30 12 0.23
31 6 0.11
32 5 0.09
ACGTcount: A:0.29, C:0.05, G:0.27, T:0.38
Consensus pattern (29 bp):
AATTTTTGGAAGTTCGGGTGCAAAAATGT
Found at i:4485 original size:59 final size:58
Alignment explanation
Indices: 4333--4495 Score: 179
Period size: 58 Copynumber: 2.8 Consensus size: 58
4323 TTAAAAGATG
* ** * * *
4333 GAATTTTTAGACATTTAGGTGTAAAAATG-GAATTTTTGAAAGTTTTGGGGTTAAAATA
1 GAATTTTTGGACATTCGGGTGCAAAAATGTG-ATTTTTGGAAGTTTTGGGGTTAAAAAA
* *
4391 GAATTTTTGGACATTCGGGGGC-AAAATGGTAATTTTTGGAAGTTTTGGGGTTAAAAAA
1 GAATTTTTGGACATTCGGGTGCAAAAAT-GTGATTTTTGGAAGTTTTGGGGTTAAAAAA
*
4449 TGAATTTTTGGA-AGTTCGGGTGCAAAAATGTGATTTTTAGATAGTTT
1 -GAATTTTTGGACA-TTCGGGTGCAAAAATGTGATTTTTGGA-AGTTT
4496 AGGGACCTCC
Statistics
Matches: 88, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
57 5 0.06
58 44 0.50
59 29 0.33
60 10 0.11
ACGTcount: A:0.32, C:0.04, G:0.26, T:0.39
Consensus pattern (58 bp):
GAATTTTTGGACATTCGGGTGCAAAAATGTGATTTTTGGAAGTTTTGGGGTTAAAAAA
Found at i:6214 original size:16 final size:19
Alignment explanation
Indices: 6169--6208 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
6159 TTGACTTGTG
*
6169 AATTTGGG-CTAGAGATGT
1 AATTTGGGTTTAGAGATGT
6187 AATTTGGGTTTAGAG-TGT
1 AATTTGGGTTTAGAGATGT
6205 AATT
1 AATT
6209 GGTTTATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.28, C:0.03, G:0.30, T:0.40
Consensus pattern (19 bp):
AATTTGGGTTTAGAGATGT
Found at i:6325 original size:17 final size:17
Alignment explanation
Indices: 6300--6389 Score: 74
Period size: 17 Copynumber: 5.1 Consensus size: 17
6290 GGACTTTTAA
* **
6300 TTAAGTTTTAAATCCAT
1 TTAAATTTTAAATAAAT
*
6317 TTAAATTTTAATTAAAT
1 TTAAATTTTAAATAAAT
*
6334 TTAAA-TTTAAAGCAAAT
1 TTAAATTTTAAA-TAAAT
*
6351 TTAAATTTAGAACATAAAT
1 TTAAATTT-TAA-ATAAAT
*
6370 TTAAATTTAAAAATAAAT
1 TTAAATTT-TAAATAAAT
6388 TT
1 TT
6390 GAATAAATTT
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
16 5 0.08
17 27 0.45
18 10 0.17
19 17 0.28
20 1 0.02
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.43
Consensus pattern (17 bp):
TTAAATTTTAAATAAAT
Found at i:6329 original size:6 final size:6
Alignment explanation
Indices: 6315--6403 Score: 69
Period size: 6 Copynumber: 15.3 Consensus size: 6
6305 TTTTAAATCC
* **
6315 ATTTAA ATTTTA A-TTAA ATTTAA ATTTAA A-GCAA ATTTAA ATTTAGA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTA-A
** ** *
6362 ACATAA ATTTAA ATTTAA AAATAA ATTTGA A--TAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT
6404 CCAATAAAAA
Statistics
Matches: 62, Mismatches: 16, Indels: 10
0.70 0.18 0.11
Matches are distributed among these distances:
4 3 0.05
5 7 0.11
6 48 0.77
7 4 0.06
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (6 bp):
ATTTAA
Found at i:12539 original size:5 final size:5
Alignment explanation
Indices: 12529--12573 Score: 81
Period size: 5 Copynumber: 9.0 Consensus size: 5
12519 CCATAAGAAT
*
12529 GTTGG GTTGG GTTGG GTTGG GTTGG GTTGG GTTGG GTTAG GTTGG
1 GTTGG GTTGG GTTGG GTTGG GTTGG GTTGG GTTGG GTTGG GTTGG
12574 ATCGGGTCGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.02, C:0.00, G:0.58, T:0.40
Consensus pattern (5 bp):
GTTGG
Found at i:12787 original size:27 final size:23
Alignment explanation
Indices: 12743--12790 Score: 60
Period size: 27 Copynumber: 1.9 Consensus size: 23
12733 ATTTTAAATG
12743 TATTTATTTTATTTTAAATTAAA
1 TATTTATTTTATTTTAAATTAAA
12766 TATTTAATTGTTATCTTATAAATTA
1 TATTT-ATT-TTAT-TT-TAAATTA
12791 CCTAATGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 4 0.19
26 2 0.10
27 7 0.33
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (23 bp):
TATTTATTTTATTTTAAATTAAA
Found at i:12838 original size:28 final size:27
Alignment explanation
Indices: 12807--12859 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
12797 GTATACAAAT
12807 AAAATAA-CATTACATATTATAAACTTAA
1 AAAATAATCATTA-ATATT-TAAACTTAA
*
12835 AAAATAATCATTAATGTTTAAACTT
1 AAAATAATCATTAATATTTAAACTT
12860 GAGTTCAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 7 0.30
28 11 0.48
29 5 0.22
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.36
Consensus pattern (27 bp):
AAAATAATCATTAATATTTAAACTTAA
Found at i:23556 original size:14 final size:13
Alignment explanation
Indices: 23549--23574 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23539 TTTTTCGATA
23549 AAAATTTTTATAT
1 AAAATTTTTATAT
23562 AAAATTTTTATAT
1 AAAATTTTTATAT
23575 TTTTATTATT
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:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AAAATTTTTATAT
Found at i:24944 original size:21 final size:21
Alignment explanation
Indices: 24920--24960 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
24910 TTTTCTTATC
24920 TTTTCACAAAA-TGATTTTTTT
1 TTTTCA-AAAATTGATTTTTTT
*
24941 TTTTCAAAAATTTATTTTTT
1 TTTTCAAAAATTGATTTTTT
24961 GTTTCATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (21 bp):
TTTTCAAAAATTGATTTTTTT
Found at i:27127 original size:20 final size:20
Alignment explanation
Indices: 27105--27141 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
27095 ATATTGGATT
27105 TTTTATA-TTATTATTCTTC
1 TTTTATAGTTATTATTCTTC
*
27124 TTTTATAGTTATTTTTCT
1 TTTTATAGTTATTATTCT
27142 AATTTGTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.19, C:0.08, G:0.03, T:0.70
Consensus pattern (20 bp):
TTTTATAGTTATTATTCTTC
Found at i:34618 original size:5 final size:5
Alignment explanation
Indices: 34608--34637 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
34598 GTGCCCGCTT
34608 CATCC CATCC CATCC CATCC CATCC CATCC
1 CATCC CATCC CATCC CATCC CATCC CATCC
34638 GTTTCTGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.60, G:0.00, T:0.20
Consensus pattern (5 bp):
CATCC
Done.