Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012408.1 Kokia drynarioides strain JFW-HI SEQ_127412, 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: 24106
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:2870 original size:29 final size:28
Alignment explanation
Indices: 2817--2871 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
2807 GGGAGGGGAA
* **
2817 TAAAAGTTTTGGGGAAAGTGGAAATGAG
1 TAAAAGTTTTGGGGAAAATAAAAATGAG
2845 TAAAAGTTTTGGGGGAAAATAAAAATG
1 TAAAAGTTTT-GGGGAAAATAAAAATG
2872 TTTGGGGTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 10 0.43
29 13 0.57
ACGTcount: A:0.44, C:0.00, G:0.31, T:0.25
Consensus pattern (28 bp):
TAAAAGTTTTGGGGAAAATAAAAATGAG
Found at i:2884 original size:21 final size:21
Alignment explanation
Indices: 2852--2892 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2842 GAGTAAAAGT
*
2852 TTTGGGGGAAAATA-AAAATG
1 TTTGGGGAAAAATATAAAATG
2872 TTTGGGGTAAAAATATAAAAT
1 TTTGGGG-AAAAATATAAAAT
2893 ATTATAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 6 0.33
22 5 0.28
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (21 bp):
TTTGGGGAAAAATATAAAATG
Found at i:3615 original size:35 final size:35
Alignment explanation
Indices: 3531--3626 Score: 99
Period size: 33 Copynumber: 2.8 Consensus size: 35
3521 TAATGATATT
* *
3531 TTGCACCCAGCGCTAGTCAGAT-AACCGGCAAAAG
1 TTGCGCCCAGCGCTAGTCAGATAAACCGACAAAAG
* * * *
3565 -TGTGCCCAGCACTAGTCAGATAAACTGACAAAGG
1 TTGCGCCCAGCGCTAGTCAGATAAACCGACAAAAG
* *
3599 TTGCGCCCAACGCTAGTCGGAT-AACCGA
1 TTGCGCCCAGCGCTAGTCAGATAAACCGA
3627 TGAATTTAAT
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
33 18 0.37
34 14 0.29
35 17 0.35
ACGTcount: A:0.31, C:0.28, G:0.24, T:0.17
Consensus pattern (35 bp):
TTGCGCCCAGCGCTAGTCAGATAAACCGACAAAAG
Found at i:7620 original size:46 final size:50
Alignment explanation
Indices: 7544--7653 Score: 122
Period size: 50 Copynumber: 2.3 Consensus size: 50
7534 TAATTATATA
* *
7544 GTGTAATACTAATTATGCACTTTAACAATA-T-T-T-TAGTTATAATGTT
1 GTGTACTACTAATTATGCACTTTAACAATATTATCTATAGTTATAATGTG
* * *
7590 GTGTACTACTAATTATGTAC-TTAGATAATATTATCTATAGTTATTATGTG
1 GTGTACTACTAATTATGCACTTTA-ACAATATTATCTATAGTTATAATGTG
*
7640 GTGTACTATTAATT
1 GTGTACTACTAATT
7654 TATAATATTA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
45 3 0.06
46 23 0.43
47 1 0.02
48 1 0.02
49 1 0.02
50 24 0.45
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (50 bp):
GTGTACTACTAATTATGCACTTTAACAATATTATCTATAGTTATAATGTG
Found at i:8391 original size:16 final size:18
Alignment explanation
Indices: 8370--8403 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
8360 AATAAACTTA
8370 AAATAAA-TTT-AATTTT
1 AAATAAACTTTAAATTTT
8386 AAATAAACTTTAAATTTT
1 AAATAAACTTTAAATTTT
8404 TAATTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 3 0.19
18 6 0.38
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATAAACTTTAAATTTT
Found at i:8411 original size:25 final size:26
Alignment explanation
Indices: 8353--8424 Score: 101
Period size: 25 Copynumber: 2.8 Consensus size: 26
8343 ATCATTAAAA
8353 AATTTTAAATAAACTTAAAATAAATTT
1 AATTTTAAATAAACTTAAAAT-AATTT
* *
8380 AATTTTAAATAAACTTTAAAT-TTTT
1 AATTTTAAATAAACTTAAAATAATTT
*
8405 AATTTTAAATAGACTTAAAA
1 AATTTTAAATAAACTTAAAA
8425 CCTCCCAACT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 21 0.51
27 20 0.49
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (26 bp):
AATTTTAAATAAACTTAAAATAATTT
Found at i:10489 original size:22 final size:21
Alignment explanation
Indices: 10445--10489 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
10435 TTAATTTTAA
* *
10445 ATTAATTTGGATTAGATTAAT
1 ATTAATTTGGATTAAAATAAT
*
10466 ATTAATTTAGGATTAAAATCAT
1 ATTAATTT-GGATTAAAATAAT
10488 AT
1 AT
10490 GTATTTTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.44
Consensus pattern (21 bp):
ATTAATTTGGATTAAAATAAT
Found at i:10535 original size:20 final size:20
Alignment explanation
Indices: 10510--10547 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
10500 ACAGTTGGAA
*
10510 TTAATAACTTGAATTTAATT
1 TTAATAAATTGAATTTAATT
*
10530 TTAATAAATTTAATTTAA
1 TTAATAAATTGAATTTAA
10548 GTTGCTCATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (20 bp):
TTAATAAATTGAATTTAATT
Found at i:14557 original size:2 final size:2
Alignment explanation
Indices: 14550--14583 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
14540 CAAATTGCAT
14550 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14584 AACACACATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16442 original size:2 final size:2
Alignment explanation
Indices: 16437--16466 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16427 AATTATATCA
16437 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16467 CAAACAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16443 original size:20 final size:20
Alignment explanation
Indices: 16398--16465 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 20
16388 AGTATGTAAT
16398 TATATAATAAAAATATATAA
1 TATATAATAAAAATATATAA
* *
16418 TCTATAA-AAAATTATATCAA
1 TATATAATAAAAATATAT-AA
* *
16438 TATATATATATATATATATATA
1 TATATA-ATAAAAATATATA-A
16460 TATATA
1 TATATA
16466 TCAAACAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 9 0.24
20 13 0.34
21 2 0.05
22 14 0.37
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
TATATAATAAAAATATATAA
Found at i:16599 original size:108 final size:102
Alignment explanation
Indices: 16448--16703 Score: 245
Period size: 103 Copynumber: 2.5 Consensus size: 102
16438 TATATATATA
* * * * * *
16448 TATATATATATATATATATCAAACAAATTTGTTAAAAATAAAATACATTTAACAA-AATTATAAA
1 TATATATATATATATATAT-AAA-AGAGTTATT-AATA-AAAATAAATTTAA-AATAATGAT--A
16512 TATAAAAAATATATATAATTTCATTATACAATTACATATTTAGTAATT
59 TATAAAAAATATAT-T--TTTCATTATACAATTACATATTTA-TAATT
** *
16560 TATATATATATATATATATAAAAGAGTTATTAATAAAAATATTTTTAAAATAATGATATATATAA
1 TATATATATATATATATATAAAAGAGTTATTAATAAAAATAAATTTAAAATAATGATATATAAAA
* * *
16625 AATATATTTTTTATTATATAATTACATATTTATTATT
66 AATATATTTTTCATTATACAATTACATATTTATAATT
*
16662 T-TAT-T-TATATA-A-ATAACAGAGTTATTAATTAAAAATAAATTT
1 TATATATATATATATATATAAAAGAGTTATTAA-TAAAAATAAATTT
16704 GAAAGTTTGA
Statistics
Matches: 128, Mismatches: 14, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
97 15 0.12
98 12 0.09
99 6 0.05
100 1 0.01
101 3 0.02
102 5 0.04
103 22 0.17
105 1 0.01
106 14 0.11
107 2 0.02
108 16 0.12
109 3 0.02
110 6 0.05
111 3 0.02
112 19 0.15
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (102 bp):
TATATATATATATATATATAAAAGAGTTATTAATAAAAATAAATTTAAAATAATGATATATAAAA
AATATATTTTTCATTATACAATTACATATTTATAATT
Found at i:16686 original size:29 final size:27
Alignment explanation
Indices: 16629--16688 Score: 68
Period size: 29 Copynumber: 2.2 Consensus size: 27
16619 ATATAAAATA
* * *
16629 TATT-TTTTATTATATAATTACATATT
1 TATTATTTTATTATATAATAACAGAGT
16655 TATTATTTTATTTATATAAATAACAGAGT
1 TATTATTTTA-TTATAT-AATAACAGAGT
16684 TATTA
1 TATTA
16689 ATTAAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 4 0.14
27 5 0.18
28 6 0.21
29 13 0.46
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.55
Consensus pattern (27 bp):
TATTATTTTATTATATAATAACAGAGT
Found at i:21375 original size:16 final size:17
Alignment explanation
Indices: 21354--21388 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
21344 AATGGTATTA
*
21354 ATATAAAT-TTTTTTAT
1 ATATAAATATTGTTTAT
21370 ATATAAATATTGTTTAT
1 ATATAAATATTGTTTAT
21387 AT
1 AT
21389 TAATATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
ATATAAATATTGTTTAT
Done.