Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012324.1 Kokia drynarioides strain JFW-HI SEQ_127326, 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: 26059
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Found at i:9592 original size:30 final size:30
Alignment explanation
Indices: 9556--9652 Score: 146
Period size: 30 Copynumber: 3.3 Consensus size: 30
9546 ACTTTGCATC
*
9556 TGGAAGTTTTGGGGTCAAAAATAGGATTTT
1 TGGAAGTTTCGGGGTCAAAAATAGGATTTT
9586 TGGAAG-TTCGGGCGT-AAAAAT-GGAATTTT
1 TGGAAGTTTCGGG-GTCAAAAATAGG-ATTTT
9615 TGGAAGTTTCGGGGTCAAAAATAGGATTTT
1 TGGAAGTTTCGGGGTCAAAAATAGGATTTT
9645 TGGAAGTT
1 TGGAAGTT
9653 CGACAGTAAA
Statistics
Matches: 61, Mismatches: 1, Indels: 10
0.85 0.01 0.14
Matches are distributed among these distances:
28 2 0.03
29 24 0.39
30 33 0.54
31 2 0.03
ACGTcount: A:0.30, C:0.05, G:0.31, T:0.34
Consensus pattern (30 bp):
TGGAAGTTTCGGGGTCAAAAATAGGATTTT
Found at i:9613 original size:29 final size:29
Alignment explanation
Indices: 9572--9654 Score: 125
Period size: 29 Copynumber: 2.8 Consensus size: 29
9562 TTTTGGGGTC
9572 AAAAATAGGATTTTTGGAAGTTCGGGCGT
1 AAAAATAGGATTTTTGGAAGTTCGGGCGT
9601 AAAAAT-GGAATTTTTGGAAGTTTCGGG-GT
1 AAAAATAGG-ATTTTTGGAAG-TTCGGGCGT
9630 CAAAAATAGGATTTTTGGAAGTTCG
1 -AAAAATAGGATTTTTGGAAGTTCG
9655 ACAGTAAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
28 2 0.04
29 23 0.46
30 23 0.46
31 2 0.04
ACGTcount: A:0.33, C:0.06, G:0.29, T:0.33
Consensus pattern (29 bp):
AAAAATAGGATTTTTGGAAGTTCGGGCGT
Found at i:9648 original size:59 final size:59
Alignment explanation
Indices: 9556--9688 Score: 205
Period size: 59 Copynumber: 2.2 Consensus size: 59
9546 ACTTTGCATC
* * *
9556 TGGAAGTTTTGGGGTCAAAAATAGGATTTTTGGAAGTTCGGGC-GTAAAAATGGAATTTT
1 TGGAAGTTTAGGGGTCAAAAATAGGATTTTTGGAAGTTC-GACAGTAAAAACGGAATTTT
*
9615 TGGAAGTTTCGGGGTCAAAAATAGGATTTTTGGAAGTTCGACAGTAAAAACGGAATTTT
1 TGGAAGTTTAGGGGTCAAAAATAGGATTTTTGGAAGTTCGACAGTAAAAACGGAATTTT
9674 TGGACAGTTTAGGGG
1 TGGA-AGTTTAGGGG
9689 ACCACAAGGG
Statistics
Matches: 68, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
58 2 0.03
59 57 0.84
60 9 0.13
ACGTcount: A:0.31, C:0.07, G:0.31, T:0.32
Consensus pattern (59 bp):
TGGAAGTTTAGGGGTCAAAAATAGGATTTTTGGAAGTTCGACAGTAAAAACGGAATTTT
Found at i:9663 original size:29 final size:28
Alignment explanation
Indices: 9572--9682 Score: 104
Period size: 29 Copynumber: 3.8 Consensus size: 28
9562 TTTTGGGGTC
9572 AAAAATAGG-ATTTTTGGAAGTTCGGGCGT
1 AAAAATAGGAATTTTTGGAAGTTC--GCGT
*
9601 AAAAAT-GGAATTTTTGGAAGTTTCGGGGT
1 AAAAATAGGAATTTTTGGAAG-TTC-GCGT
9630 CAAAAATAGG-ATTTTTGGAAGTTCGACAGT
1 -AAAAATAGGAATTTTTGGAAGTTCG-C-GT
*
9660 AAAAA-CGGAATTTTTGGACAGTT
1 AAAAATAGGAATTTTTGGA-AGTT
9683 TAGGGGACCA
Statistics
Matches: 71, Mismatches: 3, Indels: 15
0.80 0.03 0.17
Matches are distributed among these distances:
28 5 0.07
29 38 0.54
30 26 0.37
31 2 0.03
ACGTcount: A:0.34, C:0.07, G:0.27, T:0.32
Consensus pattern (28 bp):
AAAAATAGGAATTTTTGGAAGTTCGCGT
Found at i:10693 original size:12 final size:12
Alignment explanation
Indices: 10676--10718 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
10666 CCTTTTTTTA
10676 TTATTAATATTT
1 TTATTAATATTT
10688 TTATTAATA---
1 TTATTAATATTT
*
10697 TTATTAATAATT
1 TTATTAATATTT
10709 TTATTAATAT
1 TTATTAATAT
10719 CTATTAATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
9 9 0.33
12 18 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTATTAATATTT
Found at i:10700 original size:21 final size:21
Alignment explanation
Indices: 10674--10726 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
10664 TCCCTTTTTT
*
10674 TATTATTAATATTTTTATTAA
1 TATTATTAATAATTTTATTAA
10695 TATTATTAATAATTTTATTAA
1 TATTATTAATAATTTTATTAA
10716 TATCTATTAAT
1 TAT-TATTAAT
10727 GTCATTATTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 23 0.77
22 7 0.23
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TATTATTAATAATTTTATTAA
Found at i:11357 original size:6 final size:6
Alignment explanation
Indices: 11348--11425 Score: 67
Period size: 6 Copynumber: 13.5 Consensus size: 6
11338 CTTTTTTTAT
* * *
11348 TTTAAA TTTATAA --TAAT TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
*
11395 -TTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
11426 TTAAACAAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
4 1 0.02
5 14 0.24
6 38 0.66
7 5 0.09
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:11368 original size:17 final size:17
Alignment explanation
Indices: 11348--11457 Score: 89
Period size: 17 Copynumber: 6.4 Consensus size: 17
11338 CTTTTTTTAT
*
11348 TTTAAATTTATAATAAT
1 TTTAAATTTATAATAAA
*
11365 TTTAAATTTGAAAATAAA
1 TTTAAATTT-ATAATAAA
*
11383 TTTAAACTTA-AATTAAA
1 TTTAAATTTATAA-TAAA
**
11400 TTTAAATTTATTTTAAA
1 TTTAAATTTATAATAAA
* *
11417 TTTAAATTTTTAAACAAA
1 TTTAAATTTAT-AATAAA
* *
11435 TTT-AATCCTAAAATAAA
1 TTTAAAT-TTATAATAAA
11452 TTTAAA
1 TTTAAA
11458 ATGAGTTTGG
Statistics
Matches: 73, Mismatches: 14, Indels: 11
0.74 0.14 0.11
Matches are distributed among these distances:
16 2 0.03
17 48 0.66
18 23 0.32
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (17 bp):
TTTAAATTTATAATAAA
Found at i:11404 original size:11 final size:11
Alignment explanation
Indices: 11366--11424 Score: 57
Period size: 11 Copynumber: 5.2 Consensus size: 11
11356 TATAATAATT
11366 TTAAATTTGAAA
1 TTAAATTT-AAA
*
11378 ATAAATTTAAA
1 TTAAATTTAAA
11389 CTTAAA-TTAAA
1 -TTAAATTTAAA
**
11400 TTTAAATTTATT
1 -TTAAATTTAAA
11412 TTAAATTTAAA
1 TTAAATTTAAA
11423 TT
1 TT
11425 TTTAAACAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
11 24 0.63
12 14 0.37
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:11405 original size:52 final size:52
Alignment explanation
Indices: 11348--11457 Score: 139
Period size: 52 Copynumber: 2.1 Consensus size: 52
11338 CTTTTTTTAT
* * * *
11348 TTTAAATTTATAATAATTTTAAATTTGAAAATAAATTTAAACTTAAATTAAA
1 TTTAAATTTATAATAAATTTAAATTTGAAAACAAATTTAAACCTAAAATAAA
** ** *
11400 TTTAAATTTATTTTAAATTTAAATTTTTAAACAAATTTAATCCTAAAATAAA
1 TTTAAATTTATAATAAATTTAAATTTGAAAACAAATTTAAACCTAAAATAAA
11452 TTTAAA
1 TTTAAA
11458 ATGAGTTTGG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (52 bp):
TTTAAATTTATAATAAATTTAAATTTGAAAACAAATTTAAACCTAAAATAAA
Found at i:20778 original size:45 final size:45
Alignment explanation
Indices: 20697--20787 Score: 112
Period size: 45 Copynumber: 2.0 Consensus size: 45
20687 ATAGAAATAA
* * *
20697 AGAAATGGAAAACATTCGGAAATGATTATGGTTTTCTTCGAAATGG
1 AGAAATGGAAAACATTCGGAAATGAATATGATTTTC-TCAAAATGG
* * *
20743 AGAAATGG-AATCATTTGGAAATGAATGTGATTTTCTCAAAATGG
1 AGAAATGGAAAACATTCGGAAATGAATATGATTTTCTCAAAATGG
20787 A
1 A
20788 AATGAAAATC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 9 0.23
45 22 0.56
46 8 0.21
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (45 bp):
AGAAATGGAAAACATTCGGAAATGAATATGATTTTCTCAAAATGG
Found at i:23689 original size:11 final size:12
Alignment explanation
Indices: 23666--23694 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
23656 ATTCACTAAA
23666 AAATAATTATCT
1 AAATAATTATCT
23678 AAATAA-TATCT
1 AAATAATTATCT
23689 AAATAA
1 AAATAA
23695 AATTATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (12 bp):
AAATAATTATCT
Done.