Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012830.1 Kokia drynarioides strain JFW-HI SEQ_127843, 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: 40846
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3571 original size:2 final size:2
Alignment explanation
Indices: 3566--3592 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3556 AAGTAAAATA
3566 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3593 AAGAGAATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4290 original size:29 final size:30
Alignment explanation
Indices: 4234--4290 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
4224 ATTGATGATT
* *
4234 ATTTTTATTTTAGTCACTCAATTTTAATAA
1 ATTTTTATTTTAATCACTCAATGTTAATAA
*
4264 ATTTTTATTTTAATCAC-CACTGTTAAT
1 ATTTTTATTTTAATCACTCAATGTTAAT
4291 TCAATGTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.32, C:0.12, G:0.04, T:0.53
Consensus pattern (30 bp):
ATTTTTATTTTAATCACTCAATGTTAATAA
Found at i:6778 original size:2 final size:2
Alignment explanation
Indices: 6771--6798 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6761 ATTGTACCTA
6771 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
6799 TAATTCACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7610 original size:23 final size:23
Alignment explanation
Indices: 7580--7636 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
7570 ACTAAATTAG
7580 TTAATTTATTAATATTTTATAAA
1 TTAATTTATTAATATTTTATAAA
7603 TTAATTTATTAATATTTTATAAA
1 TTAATTTATTAATATTTTATAAA
7626 TTAATTTATTA
1 TTAATTTATTA
7637 TTAACCAGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TTAATTTATTAATATTTTATAAA
Found at i:14310 original size:12 final size:12
Alignment explanation
Indices: 14293--14320 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
14283 CACAACTATC
14293 TTCAAATAATGG
1 TTCAAATAATGG
14305 TTCAAATAATGG
1 TTCAAATAATGG
14317 TTCA
1 TTCA
14321 TGGTGAACTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (12 bp):
TTCAAATAATGG
Found at i:19948 original size:58 final size:59
Alignment explanation
Indices: 19841--19975 Score: 166
Period size: 58 Copynumber: 2.3 Consensus size: 59
19831 TTTACATTTT
* * * * * *
19841 GGTACCTGAACTTGGCTTAAGATTCAAATTGGTATCTAGGATTT-TTTTTGTCCAATTA
1 GGTACATGAACTTGGCTTAAGACTCAAATTAGTACCTACGATTTATTTTGGTCCAATTA
* * *
19899 GGTACTTGAACTTGGCTTAAGGCTCAATTTAGTACCTAACG-TTTATTTTGGTCCAATTA
1 GGTACATGAACTTGGCTTAAGACTCAAATTAGTACCT-ACGATTTATTTTGGTCCAATTA
19958 GGTACATGAACTTGGCTT
1 GGTACATGAACTTGGCTT
19976 CTTGGTTCAA
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
58 34 0.52
59 32 0.48
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (59 bp):
GGTACATGAACTTGGCTTAAGACTCAAATTAGTACCTACGATTTATTTTGGTCCAATTA
Found at i:20019 original size:31 final size:31
Alignment explanation
Indices: 19944--20019 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
19934 CTAACGTTTA
* *
19944 TTTTGGTCCAATTAGGTACATGAACTTGGCT
1 TTTTGGTCCAATTTGGTACATGAACTTGCCT
* * *
19975 TCTTGGTTCAATTTGGTACTTGAACTTGCCT
1 TTTTGGTCCAATTTGGTACATGAACTTGCCT
20006 TTTTGGTCCAATTT
1 TTTTGGTCCAATTT
20020 AATACCTAGC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.18, C:0.17, G:0.20, T:0.45
Consensus pattern (31 bp):
TTTTGGTCCAATTTGGTACATGAACTTGCCT
Found at i:21285 original size:31 final size:31
Alignment explanation
Indices: 21230--21305 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
21220 AAGTTATGTA
* *
21230 TTTAGTCCATATAC--TTTGATTTGATCAAT
1 TTTAGTCCTTATACTTTTTGAATTGATCAAT
21259 TTTAGTCCTTATACTTTTTGAATTGATCAAT
1 TTTAGTCCTTATACTTTTTGAATTGATCAAT
* *
21290 TTTAATCCTTGTACTT
1 TTTAGTCCTTATACTT
21306 CTTAATTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 13 0.32
31 28 0.68
ACGTcount: A:0.25, C:0.14, G:0.09, T:0.51
Consensus pattern (31 bp):
TTTAGTCCTTATACTTTTTGAATTGATCAAT
Found at i:30667 original size:15 final size:16
Alignment explanation
Indices: 30640--30669 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
30630 ATTTTATTTT
30640 AATAATCAATTTTAAC
1 AATAATCAATTTTAAC
30656 AATAAT-AATTTTAA
1 AATAATCAATTTTAA
30670 ATTTTACATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
AATAATCAATTTTAAC
Found at i:30723 original size:23 final size:22
Alignment explanation
Indices: 30697--30753 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 22
30687 TAACATATTA
* *
30697 TTAAAAATATTTATATTAACATT
1 TTAATAATATTTATATT-ACAAT
**
30720 TTAATAATAAATATATTACAAT
1 TTAATAATATTTATATTACAAT
30742 TT-ATAATATTTA
1 TTAATAATATTTA
30754 ATAATAAATG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
21 8 0.29
22 6 0.21
23 14 0.50
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (22 bp):
TTAATAATATTTATATTACAAT
Found at i:30747 original size:21 final size:23
Alignment explanation
Indices: 30708--30749 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
30698 TAAAAATATT
*
30708 TATATTAACATTTTAATAATAAA
1 TATATTAACAATTTAATAATAAA
30731 TATATT-ACAATTT-ATAATA
1 TATATTAACAATTTAATAATA
30750 TTTAATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 6 0.33
23 6 0.33
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (23 bp):
TATATTAACAATTTAATAATAAA
Found at i:32564 original size:16 final size:17
Alignment explanation
Indices: 32543--32577 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
32533 TTTTCATTTA
32543 TTTATTAAAATTT-ATT
1 TTTATTAAAATTTCATT
*
32559 TTTATTAAGATTTCATT
1 TTTATTAAAATTTCATT
32576 TT
1 TT
32578 AAATAGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (17 bp):
TTTATTAAAATTTCATT
Found at i:32777 original size:5 final size:6
Alignment explanation
Indices: 32751--32776 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
32741 AGTATTTTAA
32751 TTTATT TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TT
32777 AAATTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:33017 original size:5 final size:5
Alignment explanation
Indices: 33002--33040 Score: 62
Period size: 5 Copynumber: 7.8 Consensus size: 5
32992 ATTATCTCTA
33002 TTTACT TTTAT TTTAT TTTAT TTTAT TTTAT TTT-T TTTA
1 TTTA-T TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
33041 ATATTAACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 4 0.12
5 24 0.75
6 4 0.12
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:39407 original size:18 final size:18
Alignment explanation
Indices: 39386--39423 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
39376 ATAAATATAT
39386 AAATAAT-ATTAAGAATGA
1 AAATAATAATTAA-AATGA
39404 AAATAATGAATTAAAATGA
1 AAATAAT-AATTAAAATGA
39423 A
1 A
39424 GATTTCCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 6 0.33
20 5 0.28
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (18 bp):
AAATAATAATTAAAATGA
Found at i:39925 original size:17 final size:17
Alignment explanation
Indices: 39900--39947 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
39890 CTGGGTCCAA
*
39900 TAAACTTAAATTTATTT
1 TAAAATTAAATTTATTT
*
39917 TAAAATTAAGTTTATTT
1 TAAAATTAAATTTATTT
*
39934 TAAATTTAAATTTA
1 TAAAATTAAATTTA
39948 AAATTTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
TAAAATTAAATTTATTT
Done.