Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009451.1 Kokia drynarioides strain JFW-HI SEQ_124158, 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: 47154
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:1910 original size:115 final size:113
Alignment explanation
Indices: 1737--1942 Score: 295
Period size: 115 Copynumber: 1.8 Consensus size: 113
1727 GGCTCAAAAC
* * * *
1737 GAGCATATTTCGAACCCCAGCTTCTTGATGAGATACTGAGAAGCAGGTCAAAGTAATAAAATGGT
1 GAGCAAATTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCAAAGCAATAAAA-GGT
*
1802 TAGCTTCCTGGTGAGACACAGAGAAGTATACCAACTCAGGGCTCGATGT
65 TAGCTTCCTGATGAGACACAGAGAAGTATACCAACTCAGGGCTCGATGT
* * *
1851 GAGCAAATCTTCGAATCTCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAGGT
1 GAGCAAAT-TTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCAAAGCAATAAAAGGT
* * *
1916 TAGCTTCTTGATGAGATACTGAGAAGT
65 TAGCTTCCTGATGAGACACAGAGAAGT
1943 GGACCGAATT
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
114 33 0.41
115 47 0.59
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (113 bp):
GAGCAAATTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCAAAGCAATAAAAGGTT
AGCTTCCTGATGAGACACAGAGAAGTATACCAACTCAGGGCTCGATGT
Found at i:2027 original size:49 final size:49
Alignment explanation
Indices: 1955--2075 Score: 226
Period size: 49 Copynumber: 2.5 Consensus size: 49
1945 ACCGAATTCG
1955 TCTTCCTGATGAGGTACAGAGAAGCGGATTGAAACAAGTAAGGCGGTCA
1 TCTTCCTGATGAGGTACAGAGAAGCGGATTGAAACAAGTAAGGCGGTCA
2004 TCTTCCTGATGAGGTACAGAGAAGCGGATTGAAACAAGTAAGGCGGTCA
1 TCTTCCTGATGAGGTACAGAGAAGCGGATTGAAACAAGTAAGGCGGTCA
2053 TCTTCCTGATG-GGATACAGAGAA
1 TCTTCCTGATGAGG-TACAGAGAA
2076 TAATACCAAC
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
48 2 0.03
49 69 0.97
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.21
Consensus pattern (49 bp):
TCTTCCTGATGAGGTACAGAGAAGCGGATTGAAACAAGTAAGGCGGTCA
Found at i:2674 original size:6 final size:6
Alignment explanation
Indices: 2665--2750 Score: 72
Period size: 6 Copynumber: 14.8 Consensus size: 6
2655 GATTTATTTA
* ** *
2665 TAAATT TAAATT T-ACTT TAAATT TAAATT TAAA-T GCATTT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
** *
2711 TAAATT T-GTTT TAAATT TAAATT T-AGTT TAAATT TGAAAT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT T-AAAT
2751 AATTTTAAAC
Statistics
Matches: 61, Mismatches: 14, Indels: 9
0.73 0.17 0.11
Matches are distributed among these distances:
5 13 0.21
6 44 0.72
7 4 0.07
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (6 bp):
TAAATT
Found at i:2685 original size:11 final size:11
Alignment explanation
Indices: 2667--2745 Score: 61
Period size: 11 Copynumber: 7.0 Consensus size: 11
2657 TTTATTTATA
2667 AATTTAAATTT
1 AATTTAAATTT
*
2678 ACTTTAAATTT
1 AATTTAAATTT
**
2689 AAATTTAAATGC
1 -AATTTAAATTT
*
2701 ATTTTAAATTT
1 AATTTAAATTT
**
2712 AAATTT-GTTTT
1 -AATTTAAATTT
2723 AAATTTAAATTT
1 -AATTTAAATTT
*
2735 AGTTTAAATTT
1 AATTTAAATTT
2746 GAAATAATTT
Statistics
Matches: 52, Mismatches: 13, Indels: 6
0.73 0.18 0.08
Matches are distributed among these distances:
11 37 0.71
12 15 0.29
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.53
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:2691 original size:23 final size:23
Alignment explanation
Indices: 2665--2717 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
2655 GATTTATTTA
**
2665 TAAATTTAAATTTACTTTAAATT
1 TAAATTTAAATGCACTTTAAATT
*
2688 TAAATTTAAATGCATTTTAAATT
1 TAAATTTAAATGCACTTTAAATT
2711 TAAATTT
1 TAAATTT
2718 GTTTTAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (23 bp):
TAAATTTAAATGCACTTTAAATT
Found at i:2757 original size:17 final size:17
Alignment explanation
Indices: 2651--2765 Score: 97
Period size: 17 Copynumber: 6.4 Consensus size: 17
2641 TAGATTAATT
*
2651 TTTAGATTTATTTATAAA
1 TTTAAATTTATTT-TAAA
*
2669 TTTAAATTTACTTTAAA
1 TTTAAATTTATTTTAAA
2686 TTTAAATTTAAATGCATTTTAAA
1 TTTAAA-TT---T--ATTTTAAA
*
2709 TTTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
*
2726 TTTAAATTTAGTTTAAA
1 TTTAAATTTATTTTAAA
*
2743 TTTGAAA-TAATTTTAAA
1 TTT-AAATTTATTTTAAA
*
2760 CTTAAA
1 TTTAAA
2766 ACTTTAAAAT
Statistics
Matches: 81, Mismatches: 9, Indels: 16
0.76 0.08 0.15
Matches are distributed among these distances:
16 3 0.04
17 45 0.56
18 16 0.20
19 1 0.01
21 1 0.01
22 2 0.02
23 13 0.16
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:3443 original size:3 final size:3
Alignment explanation
Indices: 3430--3539 Score: 69
Period size: 3 Copynumber: 34.7 Consensus size: 3
3420 TAAGTATCAT
* * *
3430 TAA TAA TTAA TAA TAA TAA TAA TAA TAA TAAA TAA CAA -AT TTA TAA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
* * * * * *
3476 TAA TGA TAT TAA TAA GTAT TAA TAA CAG TAA TTAA TAA TAA CTAT TAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA -TAA TAA TAA -TAA TAA
3524 TAA TTAA TAA TTAA TA
1 TAA -TAA TAA -TAA TA
3540 TTTAGTAATA
Statistics
Matches: 82, Mismatches: 17, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
2 1 0.01
3 62 0.76
4 19 0.23
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:3489 original size:33 final size:33
Alignment explanation
Indices: 3434--3533 Score: 96
Period size: 33 Copynumber: 2.9 Consensus size: 33
3424 TATCATTAAT
*
3434 AATTAATAATAATAATAATAATAATAAATAACA-
1 AATTAATAATAAT-ATATTAATAATAAATAACAG
*
3467 AATTTATAATAATGATATTAATAAGTATTAATAACAG
1 AATTAATAATAAT-ATATTAATAA-TA--AATAACAG
* *
3504 TAATTAATAATAA-CTATTAATAATTAATAA
1 -AATTAATAATAATATATTAATAATAAATAA
3534 TTAATATTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
33 26 0.46
34 2 0.04
35 1 0.02
36 16 0.29
38 11 0.20
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (33 bp):
AATTAATAATAATATATTAATAATAAATAACAG
Found at i:3489 original size:36 final size:37
Alignment explanation
Indices: 3434--3533 Score: 104
Period size: 36 Copynumber: 2.8 Consensus size: 37
3424 TATCATTAAT
3434 AATTAATAATAATA-A-TAATAA-TAATAAATAACA-
1 AATTAATAATAATATATTAATAAGTAATAAATAACAG
* *
3467 AATTTATAATAATGATATTAATAAGT-ATTAATAACAG
1 AATTAATAATAAT-ATATTAATAAGTAATAAATAACAG
* *
3504 TAATTAATAATAA-CTATTAATAATTAATAA
1 -AATTAATAATAATATATTAATAAGTAATAA
3534 TTAATATTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
33 12 0.22
34 1 0.02
35 1 0.02
36 25 0.46
37 4 0.07
38 11 0.20
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (37 bp):
AATTAATAATAATATATTAATAAGTAATAAATAACAG
Found at i:3548 original size:14 final size:14
Alignment explanation
Indices: 3415--3539 Score: 75
Period size: 13 Copynumber: 9.0 Consensus size: 14
3405 TTCAAAACGT
* *
3415 ATTAATAAGT-ATC
1 ATTAATAATTAATA
3428 ATTAATAATTAATA
1 ATTAATAATTAATA
3442 A-TAATAA-TAATA
1 ATTAATAATTAATA
* *
3454 A-TAATAAATAACAA
1 ATTAATAATTAA-TA
*
3468 ATTTATAA-TAATGA
1 ATTAATAATTAAT-A
* *
3482 TATTAATAAGTATTA
1 -ATTAATAATTAATA
*
3497 ATAACAGTAATTAATA
1 ATTA-A-TAATTAATA
3513 A-TAACT-ATTAATA
1 ATTAA-TAATTAATA
3526 ATTAATAATTAATA
1 ATTAATAATTAATA
3540 TTTAGTAATA
Statistics
Matches: 89, Mismatches: 12, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
12 12 0.13
13 27 0.30
14 24 0.27
15 15 0.17
16 11 0.12
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (14 bp):
ATTAATAATTAATA
Found at i:4702 original size:29 final size:28
Alignment explanation
Indices: 4635--4739 Score: 81
Period size: 29 Copynumber: 3.6 Consensus size: 28
4625 CCCTGGAGGT
4635 CCCT-AAACTGTCCAAAAATTATATTTTGA
1 CCCTGAAACT-TCC-AAAATTATATTTTGA
* *
4664 CCTTGAAACTTTCGAAAATTATATATTT-A
1 CCCTGAAAC-TTCCAAAATTATAT-TTTGA
*
4693 GCCCTG-AACTTCCAAAATTTCTATTTTTGA
1 -CCCTGAAACTTCCAAAA-TTATA-TTTTGA
**
4723 CCCCAAAACTTCCAAAA
1 CCCTGAAACTTCCAAAA
4740 AATACAATTT
Statistics
Matches: 61, Mismatches: 7, Indels: 15
0.73 0.08 0.18
Matches are distributed among these distances:
28 7 0.11
29 27 0.44
30 26 0.43
31 1 0.02
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.34
Consensus pattern (28 bp):
CCCTGAAACTTCCAAAATTATATTTTGA
Found at i:4774 original size:59 final size:59
Alignment explanation
Indices: 4645--4877 Score: 179
Period size: 59 Copynumber: 4.0 Consensus size: 59
4635 CCCTAAACTG
* *** * * * *
4645 TCCAAAAATTATA-TTTTGACCTTGAAACTTTCGAAAATTA-TATATTTAGCCCT-GAACT
1 TCCAAAAATTCTATTTTTGACCCCAAAACTTCCAAAAATTACCAT-TTTA-CCCTCGAACC
* * *
4703 TCCAAAATTTCTATTTTTGACCCCAAAACTTCCAAAAAATACAATTTTACCCTCGAACC
1 TCCAAAAATTCTATTTTTGACCCCAAAACTTCCAAAAATTACCATTTTACCCTCGAACC
* * * * * * * **
4762 TCTAAAAATTCTATTTTTGATCTCGAAACTTTCAAAATTTACCATTTTACCC-CAAGATG
1 TCCAAAAATTCTATTTTTGACCCCAAAACTTCCAAAAATTACCATTTTACCCTCGA-ACC
* * * *
4821 TCCAAAAACTCCATTTTTGACTCCAAGAC-TCTCAAAAATTACCATTTTACCCTCGAA
1 TCCAAAAATTCTATTTTTGACCCCAAAACTTC-CAAAAATTACCATTTTACCCTCGAA
4878 TGCCCAAAAT
Statistics
Matches: 136, Mismatches: 33, Indels: 11
0.76 0.18 0.06
Matches are distributed among these distances:
58 18 0.13
59 114 0.84
60 4 0.03
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (59 bp):
TCCAAAAATTCTATTTTTGACCCCAAAACTTCCAAAAATTACCATTTTACCCTCGAACC
Found at i:9512 original size:9 final size:9
Alignment explanation
Indices: 9473--9506 Score: 68
Period size: 9 Copynumber: 3.8 Consensus size: 9
9463 CATTTTTGTT
9473 TCACTTCCC
1 TCACTTCCC
9482 TCACTTCCC
1 TCACTTCCC
9491 TCACTTCCC
1 TCACTTCCC
9500 TCACTTC
1 TCACTTC
9507 ATTCACAGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.12, C:0.53, G:0.00, T:0.35
Consensus pattern (9 bp):
TCACTTCCC
Found at i:9512 original size:18 final size:18
Alignment explanation
Indices: 9472--9512 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
9462 CCATTTTTGT
*
9472 TTCACTTCCCTCACTTCC
1 TTCACTTCCCTCACTTCA
*
9490 CTCACTTCCCTCACTTCA
1 TTCACTTCCCTCACTTCA
9508 TTCAC
1 TTCAC
9513 AGTCTCTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.49, G:0.00, T:0.37
Consensus pattern (18 bp):
TTCACTTCCCTCACTTCA
Found at i:32105 original size:19 final size:19
Alignment explanation
Indices: 32077--32115 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
32067 TGCTAATATA
*
32077 TATAATTTTTTAAATAAAT
1 TATAACTTTTTAAATAAAT
32096 TATAACTTTTTAAATAAAT
1 TATAACTTTTTAAATAAAT
32115 T
1 T
32116 TTAAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (19 bp):
TATAACTTTTTAAATAAAT
Found at i:43882 original size:35 final size:37
Alignment explanation
Indices: 43836--43931 Score: 117
Period size: 35 Copynumber: 2.7 Consensus size: 37
43826 AACAGGCATG
43836 CCTTTGGGTCAATAGGGAGTAAAACGA-GCATCAT-A
1 CCTTTGGGTCAATAGGGAGTAAAACGATGCATCATAA
* * *
43871 CCTTTGGGTCAATATGGAGTAAGA-TATGCATCATAA
1 CCTTTGGGTCAATAGGGAGTAAAACGATGCATCATAA
* * *
43907 CCATTGGGTCAACAGAGAGTAAAAC
1 CCTTTGGGTCAATAGGGAGTAAAAC
43932 AAATAACGAT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
34 1 0.02
35 29 0.58
36 20 0.40
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (37 bp):
CCTTTGGGTCAATAGGGAGTAAAACGATGCATCATAA
Found at i:44705 original size:21 final size:21
Alignment explanation
Indices: 44679--44729 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
44669 ACTGTTTAAT
*
44679 GACTTGTATCAATAGAAGTGA
1 GACTTGTATCAATAGAACTGA
* *
44700 GACTTGTTTCGATAGAACTGA
1 GACTTGTATCAATAGAACTGA
*
44721 CACTTGTAT
1 GACTTGTAT
44730 TGGTAGAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (21 bp):
GACTTGTATCAATAGAACTGA
Done.