Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014494.1 Kokia drynarioides strain JFW-HI SEQ_129533, 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: 13424
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:587 original size:29 final size:29
Alignment explanation
Indices: 567--738 Score: 204
Period size: 29 Copynumber: 5.9 Consensus size: 29
557 GTAAAAGGGT
*
567 AATTTTTGAAAGTTTTTGGGTTAAAAATGG
1 AATTTTTGAAAG-TTTTGGGGTAAAAATGG
*
597 AATTTTTGAAAGTTTAGGGGTAAAAATGG
1 AATTTTTGAAAGTTTTGGGGTAAAAATGG
* * * *
626 AAATTTTGGAAG-TTTAGGGTAAAAATGT
1 AATTTTTGAAAGTTTTGGGGTAAAAATGG
* *
654 AATTTTTGGAAGTTTTGGGGTCAAAATGG
1 AATTTTTGAAAGTTTTGGGGTAAAAATGG
* *
683 AATTTTTGGAAA-TTTTGAGGTCAAAATGG
1 AATTTTT-GAAAGTTTTGGGGTAAAAATGG
*
712 AATTTTTAGAAAGTTTGGGGGTAAAAA
1 AATTTTT-GAAAGTTTTGGGGTAAAAA
739 CAAAATTTCT
Statistics
Matches: 122, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
28 24 0.20
29 72 0.59
30 26 0.21
ACGTcount: A:0.35, C:0.01, G:0.26, T:0.37
Consensus pattern (29 bp):
AATTTTTGAAAGTTTTGGGGTAAAAATGG
Found at i:656 original size:87 final size:88
Alignment explanation
Indices: 553--738 Score: 234
Period size: 86 Copynumber: 2.1 Consensus size: 88
543 TTAGACATCA
* * *
553 GAGGGTAAAAGGGTAATTTTTGAAAGTTTTTGGGTTAAAAATGGAATTTTT-GAAAGTTTAGGGG
1 GAGGGTAAAAAGGTAATTTTTGAAAG-TTTTGGGGTAAAAATGGAATTTTTGGAAA-TTTAGAGG
*
617 TAAAAATGGAAATTTT-GGAAGTTT
64 TAAAAATGGAAATTTTAGAAAGTTT
* * * * *
641 -AGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTCAAAATGGAATTTTTGGAAATTTTGAGGTC
1 GAGGGTAAAAAGGTAATTTTTGAAAGTTTTGGGGTAAAAATGGAATTTTTGGAAATTTAGAGGTA
*
705 AAAATGGAATTTTTAGAAAGTTT
66 AAAATGGAAATTTTAGAAAGTTT
*
728 GGGGGTAAAAA
1 GAGGGTAAAAA
739 CAAAATTTCT
Statistics
Matches: 84, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
86 42 0.50
87 33 0.39
88 9 0.11
ACGTcount: A:0.35, C:0.01, G:0.28, T:0.35
Consensus pattern (88 bp):
GAGGGTAAAAAGGTAATTTTTGAAAGTTTTGGGGTAAAAATGGAATTTTTGGAAATTTAGAGGTA
AAAATGGAAATTTTAGAAAGTTT
Found at i:667 original size:57 final size:57
Alignment explanation
Indices: 570--738 Score: 212
Period size: 57 Copynumber: 2.9 Consensus size: 57
560 AAAGGGTAAT
*
570 TTTTGAAAGTTTTTGGGTTAAAAATGGAATTTTTGAAAGTTTAGGGGTAAAAATGGAAA
1 TTTTGGAAG-TTTTGGG-TAAAAATGGAATTTTTGAAAGTTTAGGGGTAAAAATGGAAA
* * * * * *
629 TTTTGGAAGTTTAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTCAAAATGGAAT
1 TTTTGGAAGTTTTGGGTAAAAATGGAATTTTTGAAAGTTTAGGGGTAAAAATGGAAA
* * *
686 TTTTGGAAATTTTGAGGTCAAAATGGAATTTTTAGAAAGTTTGGGGGTAAAAA
1 TTTTGGAAGTTTTG-GGTAAAAATGGAATTTTT-GAAAGTTTAGGGGTAAAAA
739 CAAAATTTCT
Statistics
Matches: 94, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
57 48 0.51
58 22 0.23
59 24 0.26
ACGTcount: A:0.35, C:0.01, G:0.27, T:0.37
Consensus pattern (57 bp):
TTTTGGAAGTTTTGGGTAAAAATGGAATTTTTGAAAGTTTAGGGGTAAAAATGGAAA
Found at i:768 original size:30 final size:29
Alignment explanation
Indices: 597--785 Score: 73
Period size: 29 Copynumber: 6.4 Consensus size: 29
587 TTAAAAATGG
* * **
597 AATTTTTGAAAGTTTAGGGGTAAAAATGGA
1 AATTTTGGAAAGTTTGGGGGTAAAAA-CAA
* **
627 AATTTTGG-AAGTTT-AGGGTAAAAATGTA
1 AATTTTGGAAAGTTTGGGGGTAAAAA-CAA
* * ***
655 ATTTTTGG-AAGTTTTGGGGTCAAAATGGA
1 AATTTTGGAAAGTTTGGGGGT-AAAAACAA
* * * ***
684 ATTTTTGGAAA-TTTTGAGGTCAAAATGGA
1 AATTTTGGAAAGTTTGGGGGT-AAAAACAA
* *
713 ATTTTTAGAAAGTTTGGGGGTAAAAACAA
1 AATTTTGGAAAGTTTGGGGGTAAAAACAA
* * *
742 AATTTCTGGAAAGTTT-GGTGTCAAAAATAT
1 AATTT-TGGAAAGTTTGGGGGT-AAAAACAA
772 AATTTTGGAGAAGT
1 AATTTTGGA-AAGT
786 CGAGGGTCAA
Statistics
Matches: 133, Mismatches: 19, Indels: 14
0.80 0.11 0.08
Matches are distributed among these distances:
28 25 0.19
29 64 0.48
30 44 0.33
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (29 bp):
AATTTTGGAAAGTTTGGGGGTAAAAACAA
Found at i:1924 original size:22 final size:22
Alignment explanation
Indices: 1896--1941 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
1886 TTTCGATTTT
* *
1896 TTTAATACTATTATTATTATTA
1 TTTAATAATATTATTATTAATA
1918 TTTAATAATATTATTATTAATA
1 TTTAATAATATTATTATTAATA
1940 TT
1 TT
1942 CATTCAATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTAATAATATTATTATTAATA
Found at i:1931 original size:16 final size:15
Alignment explanation
Indices: 1910--1939 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1900 ATACTATTAT
1910 TATTATTATTTAATAA
1 TATTATTA-TTAATAA
1926 TATTATTATTAATA
1 TATTATTATTAATA
1940 TTCATTCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTATTATTAATAA
Found at i:2704 original size:6 final size:6
Alignment explanation
Indices: 2659--2725 Score: 61
Period size: 6 Copynumber: 11.5 Consensus size: 6
2649 CTTTATTTAT
* * *
2659 TTTAAA TTTATAA --TAAT TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
2706 -TTAAA TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTT
2726 TAAAACAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
4 1 0.02
5 10 0.20
6 34 0.68
7 5 0.10
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:2721 original size:41 final size:41
Alignment explanation
Indices: 2676--2757 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
2666 TTATAATAAT
* *
2676 TTTAAATTTGAAAATAAATTTAAACTTAAATTAAATTTAAA
1 TTTAAATTTGAAAACAAATTTAAACTTAAAATAAATTTAAA
* *
2717 TTTAAATTTTAAAACAAATTTAATCTTAAAATAAATTTAAA
1 TTTAAATTTGAAAACAAATTTAAACTTAAAATAAATTTAAA
2758 ATGAGTTTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (41 bp):
TTTAAATTTGAAAACAAATTTAAACTTAAAATAAATTTAAA
Found at i:2724 original size:17 final size:17
Alignment explanation
Indices: 2659--2724 Score: 80
Period size: 17 Copynumber: 3.8 Consensus size: 17
2649 CTTTATTTAT
*
2659 TTTAAATTTATAA-TAAT
1 TTTAAATTTA-AATTAAA
*
2676 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAATTAAA
*
2694 TTTAAACTTAAATTAAA
1 TTTAAATTTAAATTAAA
2711 TTTAAATTTAAATT
1 TTTAAATTTAAATT
2725 TTAAAACAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
17 31 0.72
18 12 0.28
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (17 bp):
TTTAAATTTAAATTAAA
Found at i:2737 original size:18 final size:18
Alignment explanation
Indices: 2714--2757 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
2704 AATTAAATTT
*
2714 AAATTTAAATTTTAAAAC
1 AAATTTAAATCTTAAAAC
*
2732 AAATTT-AATCTTAAAAT
1 AAATTTAAATCTTAAAAC
2749 AAATTTAAA
1 AAATTTAAA
2758 ATGAGTTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATTTAAATCTTAAAAC
Found at i:7301 original size:31 final size:30
Alignment explanation
Indices: 7266--7325 Score: 102
Period size: 31 Copynumber: 2.0 Consensus size: 30
7256 ATCAATCAAA
*
7266 ATTTACATGCTTGAAAGATACCAATACATAT
1 ATTTACATGCTTGAAAGATACAAAT-CATAT
7297 ATTTACATGCTTGAAAGATACAAATCATA
1 ATTTACATGCTTGAAAGATACAAATCATA
7326 AGAATGTTCG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 4 0.14
31 24 0.86
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.32
Consensus pattern (30 bp):
ATTTACATGCTTGAAAGATACAAATCATAT
Found at i:11681 original size:13 final size:14
Alignment explanation
Indices: 11649--11682 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
11639 TTATCACAAG
*
11649 ATATAAATAAACAT
1 ATATTAATAAACAT
11663 ATATTAATAAACA-
1 ATATTAATAAACAT
11676 ATATTAA
1 ATATTAA
11683 AATATTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (14 bp):
ATATTAATAAACAT
Done.