Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014123.1 Kokia drynarioides strain JFW-HI SEQ_129156, 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: 10136
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.34
Warning! 112 characters in sequence are not A, C, G, or T
Found at i:363 original size:29 final size:29
Alignment explanation
Indices: 245--684 Score: 350
Period size: 29 Copynumber: 14.9 Consensus size: 29
235 GGATTCTTGA
*
245 AGGGT-AAAATGGTAATTTTTGAAAGTTTCG
1 AGGGTAAAAATGG-AATTTTTGGAAG-TTCG
* *
275 -GTGTCAAAAATGGAAATTTTTAG-AGATTCG
1 AGGGT-AAAAATGG-AATTTTTGGAAG-TTCG
* * *
305 GGGGTAAAAATAGATTTTTTGGAAGTTTCG
1 AGGGTAAAAATGGAATTTTTGGAAG-TTCG
*
335 A-GATCAAAAATGGAATTTTTGGAAGTTCGGG
1 AGGGT-AAAAATGGAATTTTTGGAAGTTC--G
* * **
366 GGGGTAAAAATTGAATTTTT-GAAGTTTT
1 AGGGTAAAAATGGAATTTTTGGAAGTTCG
*
394 AGGGTTAAAAATGAAATTTTTGGAAGTTCG
1 AGGG-TAAAAATGGAATTTTTGGAAGTTCG
* **
424 ATGGT-AAAATGGAATTTTTGGAAGTTTT
1 AGGGTAAAAATGGAATTTTTGGAAGTTCG
* *
452 AGGGTCAAAAATGGGATTTTTGGAAATTCG
1 AGGGT-AAAAATGGAATTTTTGGAAGTTCG
**
482 AGGGTAAAAATGGAATTTTTGGAAGTTTT
1 AGGGTAAAAATGGAATTTTTGGAAGTTCG
*
511 AGGGTAAAAAT-GAGATTTTT-AAGAGTTCG
1 AGGGTAAAAATGGA-ATTTTTGGA-AGTTCG
540 AGGGTAAAAATGGAATTTTTGGAAGTTTC-
1 AGGGTAAAAATGGAATTTTTGGAAG-TTCG
* *
569 AGGGTAANAAATGGAATGTTTGGAAGTTTTG
1 AGGGTAA-AAATGGAATTTTTGGAAG-TTCG
* *
600 -GGGTTAAAAT-GAGATTTTTTGAAGTTTCG
1 AGGGTAAAAATGGA-ATTTTTGGAAG-TTCG
* *
629 A-GGTAAAAAATGGGA-TTTTAGAAGTTC-
1 AGGGT-AAAAATGGAATTTTTGGAAGTTCG
*
656 AGGGGTAAAAATGGAATTTTCGGACAGTT
1 A-GGGTAAAAATGGAATTTTTGGA-AGTT
685 TAGGGACCTC
Statistics
Matches: 330, Mismatches: 53, Indels: 54
0.76 0.12 0.12
Matches are distributed among these distances:
27 1 0.00
28 44 0.13
29 133 0.40
30 117 0.35
31 33 0.10
32 2 0.01
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (29 bp):
AGGGTAAAAATGGAATTTTTGGAAGTTCG
Found at i:462 original size:58 final size:59
Alignment explanation
Indices: 245--689 Score: 389
Period size: 58 Copynumber: 7.6 Consensus size: 59
235 GGATTCTTGA
* * *
245 AGGGT-AAAATGGTAATTTTTGAAAG-TTTCGGTGTCAAAAATGGAAATTTTTAG-AGATTCG
1 AGGGTAAAAATGG-AATTTTTGGAAGTTTTAGG-GTCAAAAAT-GAAATTTTTGGAAG-TTCG
* * * * * *
305 GGGGTAAAAATAGATTTTTTGGAAG-TTTCGAGATCAAAAATGGAATTTTTGGAAGTTCGGG
1 AGGGTAAAAATGGAATTTTTGGAAGTTTTAG-GGTCAAAAATGAAATTTTTGGAAGTTC--G
* * *
366 GGGGTAAAAATTGAATTTTT-GAAGTTTTAGGGTTAAAAATGAAATTTTTGGAAGTTCG
1 AGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGAAATTTTTGGAAGTTCG
* ** *
424 ATGGT-AAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGGGATTTTTGGAAATTCG
1 AGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGAAATTTTTGGAAGTTCG
* *
482 AGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGT-AAAAATGAGATTTTT-AAGAGTTCG
1 AGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGAAATTTTTGGA-AGTTCG
* * * *
540 AGGGTAAAAATGGAATTTTTGGAAGTTTCAGGGT-AANAAATGGAATGTTTGGAAGTTTTG
1 AGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTCAA-AAATGAAATTTTTGGAAG-TTCG
* * * * ** *
600 -GGGTTAAAAT-GAGATTTTTTGAAG-TTTCGAGGTAAAAAATGGGA-TTTTAGAAGTTC-
1 AGGGTAAAAATGGA-ATTTTTGGAAGTTTTAG-GGTCAAAAATGAAATTTTTGGAAGTTCG
*
656 AGGGGTAAAAATGGAATTTTCGGACAG-TTTAGGG
1 A-GGGTAAAAATGGAATTTTTGGA-AGTTTTAGGG
690 ACCTCTATGG
Statistics
Matches: 324, Mismatches: 42, Indels: 40
0.80 0.10 0.10
Matches are distributed among these distances:
57 16 0.05
58 126 0.39
59 89 0.27
60 63 0.19
61 30 0.09
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.34
Consensus pattern (59 bp):
AGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGAAATTTTTGGAAGTTCG
Found at i:2624 original size:6 final size:6
Alignment explanation
Indices: 2613--2721 Score: 61
Period size: 6 Copynumber: 19.0 Consensus size: 6
2603 AATGGGACTT
* * * ** *
2613 TTTAAA TTTAAA -ATAAT TTTAAT TTTAAA AGTAAA TTTAAA CTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
** * *
2659 TTTAAA TTTAAA TTTAAA -ACAAA CTTAAA TTTAAA -ATAAA -TTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
2704 TCTTATAA --TAAA TTTAAA
1 T-TTA-AA TTTAAA TTTAAA
2722 AAGGAATTTA
Statistics
Matches: 78, Mismatches: 17, Indels: 16
0.70 0.15 0.14
Matches are distributed among these distances:
4 2 0.03
5 20 0.26
6 51 0.65
7 3 0.04
8 2 0.03
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:2632 original size:17 final size:17
Alignment explanation
Indices: 2613--2721 Score: 121
Period size: 17 Copynumber: 6.4 Consensus size: 17
2603 AATGGGACTT
*
2613 TTTAAATTTAAAATAAT
1 TTTAAATTTAAAATAAA
*
2630 TTTAATTTTAAAAGTAAA
1 TTTAAATTTAAAA-TAAA
* **
2648 TTTAAACTTAATTTAAA
1 TTTAAATTTAAAATAAA
*
2665 TTTAAATTTAAAACAAA
1 TTTAAATTTAAAATAAA
*
2682 CTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
2699 -TTAAATCTTATAATAAA
1 TTTAAAT-TTAAAATAAA
2716 TTTAAA
1 TTTAAA
2722 AAGGAATTTA
Statistics
Matches: 76, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
16 6 0.08
17 53 0.70
18 17 0.22
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:2662 original size:11 final size:12
Alignment explanation
Indices: 2644--2676 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
2634 ATTTTAAAAG
2644 TAAATTTAAACT
1 TAAATTTAAACT
*
2656 T-AATTTAAATT
1 TAAATTTAAACT
2667 TAAATTTAAA
1 TAAATTTAAA
2677 ACAAACTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (12 bp):
TAAATTTAAACT
Found at i:2662 original size:23 final size:24
Alignment explanation
Indices: 2631--2676 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
2621 TAAAATAATT
2631 TTAATTTTAAAAGTAAATTTAAAC
1 TTAATTTTAAAAGTAAATTTAAAC
**
2655 TTAA-TTTAAATTTAAATTTAAA
1 TTAATTTTAAAAGTAAATTTAAA
2677 ACAAACTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (24 bp):
TTAATTTTAAAAGTAAATTTAAAC
Found at i:2662 original size:29 final size:29
Alignment explanation
Indices: 2615--2670 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
2605 TGGGACTTTT
*
2615 TAAATTTAAAATAATTTTAATTTTAAAAG
1 TAAATTTAAAATAATTTTAAATTTAAAAG
*
2644 TAAATTTAAACTTAA-TTTAAATTTAAA
1 TAAATTTAAA-ATAATTTTAAATTTAAA
2671 TTTAAAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.88
30 3 0.12
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (29 bp):
TAAATTTAAAATAATTTTAAATTTAAAAG
Found at i:2708 original size:23 final size:24
Alignment explanation
Indices: 2614--2708 Score: 65
Period size: 23 Copynumber: 4.1 Consensus size: 24
2604 ATGGGACTTT
* * *
2614 TTAAATTTAAA-ATAATTTTAATT
1 TTAAATTTAAATATAAATTAAATC
** *
2637 TTAAAAGTAAATTTAAACTT-AAT-
1 TTAAATTTAAATATAAA-TTAAATC
* **
2660 TTAAATTTAAATTTAAAACAAA-C
1 TTAAATTTAAATATAAATTAAATC
2683 TTAAATTTAAA-ATAAATTAAATC
1 TTAAATTTAAATATAAATTAAATC
2706 TTA
1 TTA
2709 TAATAAATTT
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
22 7 0.12
23 41 0.73
24 6 0.11
25 2 0.04
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (24 bp):
TTAAATTTAAATATAAATTAAATC
Found at i:3513 original size:200 final size:200
Alignment explanation
Indices: 3159--3560 Score: 583
Period size: 200 Copynumber: 2.0 Consensus size: 200
3149 TTTGCTAACA
* * *
3159 TCGAGAGTAGGTTTGATTTGGTCTTCTTTTTAGTATCTCATCTGGAAGATGACTACGTCGTTTGT
1 TCGAGAGTAGGTTTGATTTGGTCTTCTTCTCAGCATCTCATCTGGAAGATGACTACGTCGTTTGT
* * * * *
3224 TTCAATTCGCTTATCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTTATTATCTCATCAG
66 TTCAATTCGCTTATCTGTATCTCATCAAGAAGACGAATTTGGTTCACTCCTCAGTATCTCATCAA
* * * * *
3289 GAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAATGTCTCATCAGGAAGTTGGGGTTCGAAGA
131 GAAGCTAACCTCTTATTACTTCGACCTGCTTCTCAATATCTCATCAGGAAGCTGGAGTTCGAAGA
3354 CTTGC
196 CTTGC
* * *
3359 TCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGCATCTCAT-TAGGAAGATGAC-AGTGTCGTTT
1 TCGAGAGTAGGTTTGATTTGGTCTTCTTCTCAGCATCTCATCT-GGAAGATGACTA-CGTCGTTT
* *
3422 GTTTTAATTCGCTTATCTGTATCTCATCAAGAAGACGAATTTGGTTCACTCCTCCGTATCTCATC
64 GTTTCAATTCGCTTATCTGTATCTCATCAAGAAGACGAATTTGGTTCACTCCTCAGTATCTCATC
* *
3487 AAGAAGCTGACCTCTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGAGTTCGAA
129 AAGAAGCTAACCTCTTATTACTTCGACCTGCTTCTCAATATCTCATCAGGAAGCTGGAGTTCGAA
*
3552 GATTTGC
194 GACTTGC
3559 TC
1 TC
3561 ACTTTGAGCC
Statistics
Matches: 179, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
199 2 0.01
200 177 0.99
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (200 bp):
TCGAGAGTAGGTTTGATTTGGTCTTCTTCTCAGCATCTCATCTGGAAGATGACTACGTCGTTTGT
TTCAATTCGCTTATCTGTATCTCATCAAGAAGACGAATTTGGTTCACTCCTCAGTATCTCATCAA
GAAGCTAACCTCTTATTACTTCGACCTGCTTCTCAATATCTCATCAGGAAGCTGGAGTTCGAAGA
CTTGC
Done.