Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012365.1 Kokia drynarioides strain JFW-HI SEQ_127369, 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: 26733
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:712 original size:13 final size:13
Alignment explanation
Indices: 696--729 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
686 TAGCATCAAG
696 ATTTATTTCACTT
1 ATTTATTTCACTT
709 ATTTATTTCACTT
1 ATTTATTTCACTT
722 ATTTATTT
1 ATTTATTT
730 TATTTTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (13 bp):
ATTTATTTCACTT
Found at i:11383 original size:22 final size:22
Alignment explanation
Indices: 11357--11422 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
11347 TTGCAGTGTT
11357 TATAGTGTCACTGCCAGTTTAG
1 TATAGTGTCACTGCCAGTTTAG
* *
11379 TATA--G-CATTG-TAGTGTT--
1 TATAGTGTCACTGCCAGT-TTAG
*
11396 TACAGTGTCACTGCCAGTTTAG
1 TATAGTGTCACTGCCAGTTTAG
11418 TATAG
1 TATAG
11423 CATTGTAGCG
Statistics
Matches: 31, Mismatches: 6, Indels: 14
0.61 0.12 0.27
Matches are distributed among these distances:
17 3 0.10
18 3 0.10
19 7 0.23
20 7 0.23
21 3 0.10
22 8 0.26
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.38
Consensus pattern (22 bp):
TATAGTGTCACTGCCAGTTTAG
Found at i:11447 original size:39 final size:39
Alignment explanation
Indices: 11312--11492 Score: 227
Period size: 39 Copynumber: 4.6 Consensus size: 39
11302 ATAGTCTAAT
* * ** * * *
11312 AGTGTTTACAGTGTCACTACTACCTCAGTACAACATTGC
1 AGTGTTTACAGTGTCACTGCCAGTTTAGTATAGCATTGC
* *
11351 AGTGTTTATAGTGTCACTGCCAGTTTAGTATAGCATTGT
1 AGTGTTTACAGTGTCACTGCCAGTTTAGTATAGCATTGC
*
11390 AGTGTTTACAGTGTCACTGCCAGTTTAGTATAGCATTGT
1 AGTGTTTACAGTGTCACTGCCAGTTTAGTATAGCATTGC
* * * *
11429 AGCGTTTACAGTGTCACTGCCAATTTAGTATAGCGTTAC
1 AGTGTTTACAGTGTCACTGCCAGTTTAGTATAGCATTGC
*
11468 AGTGTTTATAGTGTCACTGCCAGTT
1 AGTGTTTACAGTGTCACTGCCAGTT
11493 CAGTCATTAT
Statistics
Matches: 124, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 124 1.00
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.36
Consensus pattern (39 bp):
AGTGTTTACAGTGTCACTGCCAGTTTAGTATAGCATTGC
Found at i:13350 original size:158 final size:158
Alignment explanation
Indices: 13053--13387 Score: 449
Period size: 158 Copynumber: 2.1 Consensus size: 158
13043 CACATACATG
* * *
13053 TAACC-ATATATGCTCACACGAGCTATGAAATGGGTCTGCTCACACGAGCTGTGGGTCGAGATGC
1 TAACCTATA-ATGCTCACACGAGCTATGAAATAGGCCTACTCACACGAGCTGTGGGTCGAGATGC
* * * *
13117 GGGGCTACACGATGTTGCTTACACGAGCTGTGAAGAATCCGCAATAAATGTCGGACCTCAACCAT
65 GAGGCTACACGATGCTGCTCACACGAGCTGTGAAGAATCCGCAACAAATGTCGGACCTCAACCAT
* * *
13182 CGGTAGGACATCTAAGACCAGCACCCATA
130 AGGTAAGACATCCAAGACCAGCACCCATA
* **
13211 TAACCTATAATGCTCACACGAGCTATGAAATAGGCCTACTCACACGAGCTGTGGGTTGAGATGTT
1 TAACCTATAATGCTCACACGAGCTATGAAATAGGCCTACTCACACGAGCTGTGGGTCGAGATGCG
** * * * * *
13276 AGGCTATGCGATGCTGCTCACACGAGTTGTGGAGAATTCGCAACCAATG-CAGGACCTCAGCCAT
66 AGGCTACACGATGCTGCTCACACGAGCTGTGAAGAATCCGCAACAAATGTC-GGACCTCAACCAT
13340 AGGTAAGACATCCAAGACCAGCACCCATA
130 AGGTAAGACATCCAAGACCAGCACCCATA
*
13369 TAACCTGTAATGCTCACAC
1 TAACCTATAATGCTCACAC
13388 AAGCAGTAAC
Statistics
Matches: 154, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
157 1 0.01
158 150 0.97
159 3 0.02
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (158 bp):
TAACCTATAATGCTCACACGAGCTATGAAATAGGCCTACTCACACGAGCTGTGGGTCGAGATGCG
AGGCTACACGATGCTGCTCACACGAGCTGTGAAGAATCCGCAACAAATGTCGGACCTCAACCATA
GGTAAGACATCCAAGACCAGCACCCATA
Found at i:14444 original size:18 final size:18
Alignment explanation
Indices: 14418--14456 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
14408 TTGATCTAAA
* *
14418 TAATAATTCCCATCAATT
1 TAATAATTCCAATAAATT
*
14436 TAATCATTCCAATAAATT
1 TAATAATTCCAATAAATT
14454 TAA
1 TAA
14457 ATATTTAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (18 bp):
TAATAATTCCAATAAATT
Found at i:14763 original size:23 final size:22
Alignment explanation
Indices: 14737--14779 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
14727 TAAAAACTCA
14737 AAAACTCT-TCAAAATCATTAATG
1 AAAACTCTCT-AAAATC-TTAATG
*
14760 AAAATTCTCTAAAATCTTAA
1 AAAACTCTCTAAAATCTTAA
14780 CAGTTTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 13 0.72
24 1 0.06
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAACTCTCTAAAATCTTAATG
Found at i:17564 original size:36 final size:36
Alignment explanation
Indices: 17515--17587 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
17505 AAAATCGATG
*
17515 TCGCCTGACAGTTTGATAGCACCCTTAAATATATAT
1 TCGCCGGACAGTTTGATAGCACCCTTAAATATATAT
*
17551 TCGCCGGATAGTTTGATAGCACCCTTAAATATATAT
1 TCGCCGGACAGTTTGATAGCACCCTTAAATATATAT
17587 T
1 T
17588 TTTTGTCTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (36 bp):
TCGCCGGACAGTTTGATAGCACCCTTAAATATATAT
Found at i:19767 original size:21 final size:21
Alignment explanation
Indices: 19733--19789 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
19723 CTTGTTGCCT
* * *
19733 CTGCTTCCTTCGCTTCTCTCG
1 CTGCTGCCTCCGCTTCCCTCG
19754 CTGCTGCCTCCGCTTCCCTCG
1 CTGCTGCCTCCGCTTCCCTCG
* *
19775 CTACTGCCTCGGCTT
1 CTGCTGCCTCCGCTT
19790 TAAGTTGTAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.02, C:0.46, G:0.18, T:0.35
Consensus pattern (21 bp):
CTGCTGCCTCCGCTTCCCTCG
Found at i:26243 original size:21 final size:21
Alignment explanation
Indices: 26217--26267 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
26207 AAGATAAGAT
26217 TGAAGAAGAGAAGGGCGTGCG
1 TGAAGAAGAGAAGGGCGTGCG
*
26238 TGAAGAAGGGAAGGGCGTGCG
1 TGAAGAAGAGAAGGGCGTGCG
26259 TGAAGAAGA
1 TGAAGAAGA
26268 AGGTAATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.35, C:0.08, G:0.47, T:0.10
Consensus pattern (21 bp):
TGAAGAAGAGAAGGGCGTGCG
Found at i:26644 original size:10 final size:11
Alignment explanation
Indices: 26617--26657 Score: 52
Period size: 10 Copynumber: 4.0 Consensus size: 11
26607 AAATTAAAAG
*
26617 TTATTATCAA-
1 TTATTATTAAT
26627 TTATTATTAAT
1 TTATTATTAAT
26638 TTA-TATT-AT
1 TTATTATTAAT
26647 TTATTATTAAT
1 TTATTATTAAT
26658 ATTAAGTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
9 5 0.19
10 17 0.63
11 5 0.19
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (11 bp):
TTATTATTAAT
Found at i:26684 original size:23 final size:23
Alignment explanation
Indices: 26651--26729 Score: 115
Period size: 23 Copynumber: 3.4 Consensus size: 23
26641 TATTATTTAT
*
26651 TATTAATATTAAGTAATTAATAA
1 TATTTATATTAAGTAATTAATAA
*
26674 TCTTTATATTAAGTAATTAATAA
1 TATTTATATTAAGTAATTAATAA
26697 TATTTATATTAA-TAATTAATATA
1 TATTTATATTAAGTAATTAATA-A
*
26720 TTTTTATATT
1 TATTTATATT
26730 TATA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
22 9 0.18
23 42 0.82
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (23 bp):
TATTTATATTAAGTAATTAATAA
Done.