Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014990.1 Kokia drynarioides strain JFW-HI SEQ_130034, 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: 743029
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 631 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:690736 original size:23 final size:23
Alignment explanation
Indices: 690710--690755 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
690700 AATTTGCCAC
*
690710 TTGTCATCACCCTTTTGTGCAGT
1 TTGTCATCACCCCTTTGTGCAGT
690733 TTGTCATCACCCCTTTGTGCAGT
1 TTGTCATCACCCCTTTGTGCAGT
690756 GTAAGTGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.13, C:0.28, G:0.17, T:0.41
Consensus pattern (23 bp):
TTGTCATCACCCCTTTGTGCAGT
Found at i:690972 original size:12 final size:12
Alignment explanation
Indices: 690955--690979 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
690945 AATGTAGTGT
690955 ATTTATTTTTAA
1 ATTTATTTTTAA
690967 ATTTATTTTTAA
1 ATTTATTTTTAA
690979 A
1 A
690980 GTTTTTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTTATTTTTAA
Found at i:693039 original size:43 final size:42
Alignment explanation
Indices: 692957--693049 Score: 107
Period size: 43 Copynumber: 2.2 Consensus size: 42
692947 ATTAACATGT
* * *
692957 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTA
1 TAAATTATATTACTTGACTCGTATCAATATGCTTGCATGTTA
* *
692999 CTAAATTATATTACTTTACTCTTATCAATA-GCTTGACATGTTA
1 -TAAATTATATTACTTGACTCGTATCAATATGCTTG-CATGTTA
*
693042 TTAATTAT
1 TAAATTAT
693050 GCAGTTCATC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
42 11 0.26
43 32 0.74
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.46
Consensus pattern (42 bp):
TAAATTATATTACTTGACTCGTATCAATATGCTTGCATGTTA
Found at i:693909 original size:21 final size:21
Alignment explanation
Indices: 693863--693910 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
693853 TTTTATATTT
*
693863 ATAAACCCTAAATCCTAAACC
1 ATAAACCCTAAATCCTAAACA
* *
693884 TTAAACCCTAAAT-TTAAAACA
1 ATAAACCCTAAATCCT-AAACA
693905 ATAAAC
1 ATAAAC
693911 TTTAAATTCG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.52, C:0.25, G:0.00, T:0.23
Consensus pattern (21 bp):
ATAAACCCTAAATCCTAAACA
Found at i:696479 original size:24 final size:24
Alignment explanation
Indices: 696452--696498 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
696442 TACCATATAC
*
696452 GGAGTTGGATCTTCATTTTCTACT
1 GGAGTTAGATCTTCATTTTCTACT
696476 GGAGTTAGATCTTCATTTTCTAC
1 GGAGTTAGATCTTCATTTTCTAC
696499 AAGTTCCACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.45
Consensus pattern (24 bp):
GGAGTTAGATCTTCATTTTCTACT
Found at i:696965 original size:4 final size:4
Alignment explanation
Indices: 696956--697001 Score: 83
Period size: 4 Copynumber: 11.2 Consensus size: 4
696946 TTTCTCATTC
696956 TTCT TTCT TTCAT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT T
1 TTCT TTCT TTC-T TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT T
697002 CTGTCCGTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 37 0.90
5 4 0.10
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (4 bp):
TTCT
Found at i:706919 original size:28 final size:28
Alignment explanation
Indices: 706875--706936 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
706865 ATTTGGTACG
*
706875 TAAAC-TTTTTTGACCCAACTTGATACC
1 TAAACTTTTTTTAACCCAACTTGATACC
* *
706902 TAAACTTTTTTTAACCCAATTTGGTACC
1 TAAACTTTTTTTAACCCAACTTGATACC
706930 TAAACTT
1 TAAACTT
706937 GACAATTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
27 5 0.16
28 26 0.84
ACGTcount: A:0.31, C:0.23, G:0.06, T:0.40
Consensus pattern (28 bp):
TAAACTTTTTTTAACCCAACTTGATACC
Found at i:707027 original size:58 final size:58
Alignment explanation
Indices: 706898--707028 Score: 183
Period size: 58 Copynumber: 2.3 Consensus size: 58
706888 CCCAACTTGA
706898 TACCTAAACTTTTTTTAACCCAATTTGGTACCTAAACTTGACAATTTTTCCTAATTTG
1 TACCTAAACTTTTTTTAACCCAATTTGGTACCTAAACTTGACAATTTTTCCTAATTTG
* ** * * *
706956 TATCTAAACTTTTTTGGACCCAATTTGGTACCTGAATTTGACATTTTTTCCTAATTT-
1 TACCTAAACTTTTTTTAACCCAATTTGGTACCTAAACTTGACAATTTTTCCTAATTTG
* *
707013 TACCTGAGCTTTTTTT
1 TACCTAAACTTTTTTT
707029 TAGATTCAAG
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
57 12 0.19
58 51 0.81
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (58 bp):
TACCTAAACTTTTTTTAACCCAATTTGGTACCTAAACTTGACAATTTTTCCTAATTTG
Found at i:709170 original size:19 final size:20
Alignment explanation
Indices: 709148--709200 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
709138 TAAATTATTT
709148 AAAAAATCATAAAAT-TAAA
1 AAAAAATCATAAAATATAAA
* *
709167 AAAAAA-CTAAAAAATATTAA
1 AAAAAATC-ATAAAATATAAA
709187 AAAAAAT-ATAAAAT
1 AAAAAATCATAAAAT
709201 CCAATTCAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 1 0.04
19 18 0.64
20 9 0.32
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAAAATCATAAAATATAAA
Found at i:726529 original size:6 final size:6
Alignment explanation
Indices: 726520--726598 Score: 86
Period size: 6 Copynumber: 13.2 Consensus size: 6
726510 AGATGAAGGA
* * * **
726520 GATGAT GATGGT GATGGT GATGAT GATGGT GATCGT GACCGT GATGGT
1 GATGGT GATGGT GATGGT GATGGT GATGGT GATGGT GATGGT GATGGT
* * *
726568 GATCGT GATCGC GATGGT GATGGT GATGGT G
1 GATGGT GATGGT GATGGT GATGGT GATGGT G
726599 CACTAGTTAC
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.19, C:0.08, G:0.43, T:0.30
Consensus pattern (6 bp):
GATGGT
Found at i:728942 original size:19 final size:19
Alignment explanation
Indices: 728920--728956 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
728910 AAAAAAGAAG
728920 TTAAATGTAAAAAATTACA
1 TTAAATGTAAAAAATTACA
728939 TTAAATGTAAAAAATTAC
1 TTAAATGTAAAAAATTAC
728957 TGCTTTTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.32
Consensus pattern (19 bp):
TTAAATGTAAAAAATTACA
Found at i:733551 original size:6 final size:6
Alignment explanation
Indices: 733540--733583 Score: 79
Period size: 6 Copynumber: 7.3 Consensus size: 6
733530 CCACAGATGA
*
733540 TTGCTT TTGCTT TTACTT TTGCTT TTGCTT TTGCTT TTGCTT TT
1 TTGCTT TTGCTT TTGCTT TTGCTT TTGCTT TTGCTT TTGCTT TT
733584 AGTTTTTGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.02, C:0.16, G:0.14, T:0.68
Consensus pattern (6 bp):
TTGCTT
Found at i:734496 original size:20 final size:19
Alignment explanation
Indices: 734471--734519 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
734461 CTCCTCCTCT
734471 TTTTTCTTCTCTTCATCTTC
1 TTTTTCTTCTCTTC-TCTTC
* * *
734491 TTTTTCTTCTTTTCTTTTT
1 TTTTTCTTCTCTTCTCTTC
734510 TTTTTCTTCT
1 TTTTTCTTCT
734520 TAAACCCTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTTCTTCTCTTCTCTTC
Found at i:736601 original size:20 final size:20
Alignment explanation
Indices: 736576--736643 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
736566 TCTCTTCTTC
736576 TCTTCCCAACTTCTTCATCT
1 TCTTCCCAACTTCTTCATCT
*
736596 TCTTCCCCAC-TC--CATCT
1 TCTTCCCAACTTCTTCATCT
** *
736613 TCTTATCAACTCCTTCATCTT
1 TCTTCCCAACTTCTTCATC-T
736634 TCTTCCCAAC
1 TCTTCCCAAC
736644 ACAATCAACC
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
17 12 0.32
18 1 0.03
19 2 0.05
20 13 0.35
21 9 0.24
ACGTcount: A:0.16, C:0.43, G:0.00, T:0.41
Consensus pattern (20 bp):
TCTTCCCAACTTCTTCATCT
Found at i:737153 original size:16 final size:15
Alignment explanation
Indices: 737115--737162 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
737105 TAAAAGATAA
737115 TTTAATTAAAGTAAA-
1 TTTAATTAAAG-AAAT
*
737130 TGTAATTAAACGAAAT
1 TTTAATTAAA-GAAAT
737146 TTTAATTAAAGGAAAT
1 TTTAATTAAA-GAAAT
737162 T
1 T
737163 ATAAATATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (15 bp):
TTTAATTAAAGAAAT
Found at i:739641 original size:12 final size:12
Alignment explanation
Indices: 739626--739650 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
739616 TTTTAATAGT
739626 TTTAATAATTTA
1 TTTAATAATTTA
739638 TTTAATAATTTA
1 TTTAATAATTTA
739650 T
1 T
739651 ATATTTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTAATAATTTA
Found at i:739684 original size:39 final size:39
Alignment explanation
Indices: 739600--739686 Score: 95
Period size: 39 Copynumber: 2.2 Consensus size: 39
739590 AATCACTCTC
* * * *
739600 AAAATATTTTATATATTTTTAATAGTTTTAATAATTTAT
1 AAAATAATTTATATATTTTTAAAAGTTTTAATAATTAAA
** *
739639 TTAATAATTTATATATTTTTAAAATTTTTAA-ATATTAAA
1 AAAATAATTTATATATTTTTAAAAGTTTTAATA-ATTAAA
739678 AAAATAATT
1 AAAATAATT
739687 AATTGTTAAT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
38 1 0.03
39 37 0.97
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (39 bp):
AAAATAATTTATATATTTTTAAAAGTTTTAATAATTAAA
Done.