Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002806.1 Kokia drynarioides strain JFW-HI SEQ_115155, 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: 6862
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Warning! 22 characters in sequence are not A, C, G, or T
Found at i:3382 original size:29 final size:28
Alignment explanation
Indices: 3303--3645 Score: 249
Period size: 29 Copynumber: 12.0 Consensus size: 28
3293 CGGACACCCG
*
3303 GGGGT-AAAATGGTAATTTTTGGGAAAATTC
1 GGGGTAAAAATGG-AATTTTT-GG-AAGTTC
*
3333 GGGGTTAAAAATGGGAA-TTTTGGAAGTGC
1 GGGG-TAAAAAT-GGAATTTTTGGAAGTTC
*
3362 AGGGGTAAAAATGGAATTTTTGAAAGTTTC
1 -GGGGTAAAAATGGAATTTTTGGAAG-TTC
* * *
3392 GAGGTCAAAAATGGGATTTTTAGAAGTTC
1 GGGGT-AAAAATGGAATTTTTGGAAGTTC
*
3421 GAGGGTAAAAATGGAATTTTTGAAAGTTTC
1 G-GGGTAAAAATGGAATTTTTGGAAG-TTC
* * * *
3451 AGCGTTAAAAATAGG-GTTTTTGAAAGTTC
1 -GGGGTAAAAAT-GGAATTTTTGGAAGTTC
* *
3480 GAGGGT-GAAATGGAATTTTTGG--GGTC
1 G-GGGTAAAAATGGAATTTTTGGAAGTTC
*
3506 -----AAAAATGGGATTTTTGGAAGTTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTC
* *
3529 GAGGGTAAAAATGGAATTTTTTGAAGTTTT
1 G-GGGTAAAAATGGAATTTTTGGAAG-TTC
*
3559 GGGGTCAAAAATGGGATTTTTGGAAGTTC
1 GGGGT-AAAAATGGAATTTTTGGAAGTTC
* *
3588 GGGGGTAAAAATGGATTTTTTGGAAGTTTT
1 -GGGGTAAAAATGGAATTTTTGGAAG-TTC
* *
3618 GGGGTCAAAATAGAATTTTTGGACAGTT
1 GGGGTAAAAATGGAATTTTTGGA-AGTT
3646 TAGGGACCTT
Statistics
Matches: 250, Mismatches: 36, Indels: 55
0.73 0.11 0.16
Matches are distributed among these distances:
21 14 0.06
23 3 0.01
26 3 0.01
27 2 0.01
28 15 0.06
29 113 0.45
30 83 0.33
31 8 0.03
32 7 0.03
33 2 0.01
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (28 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTC
Found at i:3427 original size:59 final size:59
Alignment explanation
Indices: 3304--3645 Score: 347
Period size: 59 Copynumber: 5.9 Consensus size: 59
3294 GGACACCCGG
* * * *
3304 GGGT-AAAATGGTAATTTTTGGGAAA-ATTCGGGGTTAAAAATGGGAATTTTGGAAGTGC-A
1 GGGTAAAAATGG-AATTTTT--GAAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGA
* *
3363 GGGGTAAAAATGGAATTTTTGAAAGTTTCGAGGTCAAAAATGGGATTTTTAGAAGTTCGA
1 -GGGTAAAAATGGAATTTTTGAAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGA
* * * *
3423 GGGTAAAAATGGAATTTTTGAAAGTTTCAGCGTTAAAAATAGGG-TTTTTGAAAGTTCGA
1 GGGTAAAAATGGAATTTTTGAAAGTTTCGGGGTCAAAAAT-GGGATTTTTGGAAGTTCGA
*
3482 GGGT-GAAATGGAA---TT-----TTT-GGGGTCAAAAATGGGATTTTTGGAAGTTCGA
1 GGGTAAAAATGGAATTTTTGAAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGA
* *
3531 GGGTAAAAATGGAATTTTTTG-AAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGG
1 GGGTAAAAATGGAA-TTTTTGAAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGA
* * * * *
3590 GGGTAAAAATGGATTTTTTGGAAGTTTTGGGGTC-AAAATAGAATTTTTGGACAGTT
1 GGGTAAAAATGGAATTTTTGAAAGTTTCGGGGTCAAAAATGGGATTTTTGGA-AGTT
3646 TAGGGACCTT
Statistics
Matches: 243, Mismatches: 22, Indels: 35
0.81 0.07 0.12
Matches are distributed among these distances:
48 3 0.01
49 27 0.11
50 11 0.05
54 2 0.01
55 2 0.01
58 36 0.15
59 140 0.58
60 15 0.06
61 7 0.03
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (59 bp):
GGGTAAAAATGGAATTTTTGAAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGA
Found at i:3586 original size:108 final size:109
Alignment explanation
Indices: 3394--3610 Score: 314
Period size: 108 Copynumber: 2.0 Consensus size: 109
3384 AAAGTTTCGA
*
3394 GGTCAAAAATGGGATTTTTAGAAGTTCGAGGGTAAAAATGGAATTTTTGAAAGTTTCAGCGTTAA
1 GGTCAAAAATGGGATTTTTAGAAGTTCGAGGGTAAAAATGGAATTTTTGAAAGTTTCAGCGTCAA
*
3459 AAATAGGGTTTTTGAAAGTTCGAGGGT-GAAATGGAATTTTTGG
66 AAATAGGGTTTTTGAAAGTTCGAGGGTAAAAATGGAATTTTTGG
* ** *
3502 GGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTTG-AAGTTTTGGGGTCA
1 GGTCAAAAATGGGATTTTTAGAAGTTCGAGGGTAAAAATGGAA-TTTTTGAAAGTTTCAGCGTCA
* * *
3566 AAAAT-GGGATTTTTGGAAGTTCGGGGGTAAAAATGGATTTTTTGG
65 AAAATAGGG-TTTTTGAAAGTTCGAGGGTAAAAATGGAATTTTTGG
3611 AAGTTTTGGG
Statistics
Matches: 97, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
107 3 0.03
108 74 0.76
109 20 0.21
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.34
Consensus pattern (109 bp):
GGTCAAAAATGGGATTTTTAGAAGTTCGAGGGTAAAAATGGAATTTTTGAAAGTTTCAGCGTCAA
AAATAGGGTTTTTGAAAGTTCGAGGGTAAAAATGGAATTTTTGG
Found at i:4685 original size:3 final size:3
Alignment explanation
Indices: 4677--4749 Score: 76
Period size: 3 Copynumber: 24.0 Consensus size: 3
4667 ATTTCGACTT
* * *
4677 TTA TTA TTA TTA TTA TTA TTA TTAA TTA ATA TTA TCA TTA TTA -CA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA
* *
4722 ATA TTTA TTA TTA TTA ATA TTA TTA TTA
1 TTA -TTA TTA TTA TTA TTA TTA TTA TTA
4750 ATAACCATTT
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
2 1 0.02
3 52 0.90
4 5 0.09
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:5491 original size:11 final size:11
Alignment explanation
Indices: 5475--5522 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 11
5465 TAAATATATT
5475 TAAATTTAAAA
1 TAAATTTAAAA
5486 TAAATTTAAATATA
1 TAAATTT-AA-A-A
5500 TTTAAATTTAAAA
1 --TAAATTTAAAA
5513 TAAATTTAAA
1 TAAATTTAAA
5523 TTCTAAAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
11 17 0.53
12 2 0.06
13 2 0.06
14 2 0.06
15 2 0.06
16 7 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:5492 original size:17 final size:17
Alignment explanation
Indices: 5421--5557 Score: 112
Period size: 17 Copynumber: 8.4 Consensus size: 17
5411 AATTTTATTT
* *
5421 ATTTTAATTTATAATAA
1 ATTTAAATTTAAAATAA
* *
5438 TTTTAAATTTGAAAATGA
1 ATTTAAATTT-AAAATAA
* *
5456 ATTTAAACTT-AAATAT
1 ATTTAAATTTAAAATAA
5472 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
5489 ATTTAAA--T---AT--
1 ATTTAAATTTAAAATAA
5499 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
*
5516 ATTTAAATTCTAAAACAA
1 ATTTAAATT-TAAAATAA
*
5534 ATTT-AGTCTTAAAATAA
1 ATTTAAAT-TTAAAATAA
5551 ATTTAAA
1 ATTTAAA
5558 ATGAGTTTGA
Statistics
Matches: 94, Mismatches: 14, Indels: 23
0.72 0.11 0.18
Matches are distributed among these distances:
10 7 0.07
12 3 0.03
15 3 0.03
16 13 0.14
17 42 0.45
18 26 0.28
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:5494 original size:27 final size:27
Alignment explanation
Indices: 5459--5523 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
5449 AAAATGAATT
*
5459 TAAACTTAAATATATTTAAATTTAAAA
1 TAAATTTAAATATATTTAAATTTAAAA
5486 TAAATTTAAATATATTTAAATTTAAAA
1 TAAATTTAAATATATTTAAATTTAAAA
5513 TAAATTTAAAT
1 TAAATTTAAAT
5524 TCTAAAACAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (27 bp):
TAAATTTAAATATATTTAAATTTAAAA
Found at i:5529 original size:7 final size:6
Alignment explanation
Indices: 5455--5529 Score: 54
Period size: 6 Copynumber: 13.3 Consensus size: 6
5445 TTTGAAAATG
* * *
5455 AATTTA AACTTA AA--TA TATTTA AATTTA AA-ATA AATTTA AA--TA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* *
5498 TATTTA AATTTA AA-ATA AATTTA AATTCTA AA
1 AATTTA AATTTA AATTTA AATTTA AATT-TA AA
5530 ACAAATTTAG
Statistics
Matches: 53, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
4 6 0.11
5 8 0.15
6 35 0.66
7 4 0.08
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.43
Consensus pattern (6 bp):
AATTTA
Done.