Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013327.1 Kokia drynarioides strain JFW-HI SEQ_128349, 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: 18760
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:439 original size:29 final size:29
Alignment explanation
Indices: 372--839 Score: 495
Period size: 29 Copynumber: 15.9 Consensus size: 29
362 CTCGAGGGTT
* ** *
372 AAATGGTAATTTTGGGAAAATTCAGGGTTAA
1 AAATGG-AATTTTTGGAAGTTTGAGGG-TAA
* *
403 AAATGGAATTTTTGGAAGTTCGAGGCTAA
1 AAATGGAATTTTTGGAAGTTTGAGGGTAA
*
432 AAATGGAATTTTTGGAAGTTTTAGGGTAA
1 AAATGGAATTTTTGGAAGTTTGAGGGTAA
* * *
461 AAATGGGATTTTTTGAAGTTTGGGGGTAA
1 AAATGGAATTTTTGGAAGTTTGAGGGTAA
*
490 AAATGGAATTTTTGGAAGTTTGGGGGTAA
1 AAATGGAATTTTTGGAAGTTTGAGGGTAA
* *
519 AAATAGAATTTTTGGAACTTTTG-GGGTCAA
1 AAATGGAATTTTTGGAA-GTTTGAGGGT-AA
*
549 AAATGGGATTTTTGGAAGTTTG-GGGATAA
1 AAATGGAATTTTTGGAAGTTTGAGGG-TAA
*
578 AAATGGAATTTTTGGAACTTTTG-GGGTAAA
1 AAATGGAATTTTTGGAA-GTTTGAGGGT-AA
* *
608 AAATGGGATTTTAGGAAGTTT-AGGGGTAA
1 AAATGGAATTTTTGGAAGTTTGA-GGGTAA
*
637 AAATGGAATTTTTTGAAGTTTTG-GGGTCAA
1 AAATGGAATTTTTGGAAG-TTTGAGGGT-AA
*
667 AAATGGGATTTTTGGAAGTTT-AGGAGTAA
1 AAATGGAATTTTTGGAAGTTTGAGG-GTAA
696 AAATGGAATTTTTGGAAGTTTTG-GGGTTAA
1 AAATGGAATTTTTGGAAG-TTTGAGGG-TAA
* *
726 AAATGGGATTTTTGGAAGTTCG-GGGTTAA
1 AAATGGAATTTTTGGAAGTTTGAGGG-TAA
* * *
755 AAATGGAATTTTTAGAAGTTTTAAGGTCAA
1 AAATGGAATTTTTGGAAGTTTGAGGGT-AA
* *
785 AAATGGGATTTTTGGAAGTTCGAGGGTAA
1 AAATGGAATTTTTGGAAGTTTGAGGGTAA
814 AAATGGAATTTTTGGACAGTTT-AGGG
1 AAATGGAATTTTTGGA-AGTTTGAGGG
840 ACCTTCAGGG
Statistics
Matches: 374, Mismatches: 45, Indels: 38
0.82 0.10 0.08
Matches are distributed among these distances:
29 226 0.60
30 142 0.38
31 6 0.02
ACGTcount: A:0.33, C:0.02, G:0.30, T:0.35
Consensus pattern (29 bp):
AAATGGAATTTTTGGAAGTTTGAGGGTAA
Found at i:442 original size:59 final size:57
Alignment explanation
Indices: 395--835 Score: 535
Period size: 59 Copynumber: 7.5 Consensus size: 57
385 GGGAAAATTC
* * *
395 AGGGTTAAAAATGGAATTTTTGGAAGTTCGAGG-CTAAAAATGGAATTTTTGGAAGTTTT
1 AGGG-TAAAAATGGAATTTTTGGAAGTTTGGGGTC-AAAAATGGGATTTTTGGAAG-TTT
* * *
454 AGGGTAAAAATGGGATTTTTTGAAGTTTGGGGGT-AAAAATGGAATTTTTGGAAGTTT
1 AGGGTAAAAATGGAATTTTTGGAAGTTT-GGGGTCAAAAATGGGATTTTTGGAAGTTT
* * *
511 GGGGGTAAAAATAGAATTTTTGGAACTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTT
1 -AGGGTAAAAATGGAATTTTTGGAA-GTTTGGGGTCAAAAATGGGATTTTTGGAAGTTT
* * * *
570 GGGGATAAAAATGGAATTTTTGGAACTTTTGGGGTAAAAAATGGGATTTTAGGAAGTTT
1 AGGG-TAAAAATGGAATTTTTGGAA-GTTTGGGGTCAAAAATGGGATTTTTGGAAGTTT
*
629 AGGGGTAAAAATGGAATTTTTTGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTT
1 A-GGGTAAAAATGGAATTTTTGGAAG-TTTGGGGTCAAAAATGGGATTTTTGGAAGTTT
* *
688 AGGAGTAAAAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTC
1 AGG-GTAAAAATGGAATTTTTGGAAG-TTTGGGGTCAAAAATGGGATTTTTGGAAGTTT
* * ** *
747 GGGGTTAAAAATGGAATTTTTAGAAGTTTTAAGGTCAAAAATGGGATTTTTGGAAGTTCG
1 AGGG-TAAAAATGGAATTTTTGGAAG-TTTGGGGTCAAAAATGGGATTTTTGGAAGTT-T
807 AGGGTAAAAATGGAATTTTTGGACAGTTT
1 AGGGTAAAAATGGAATTTTTGGA-AGTTT
836 AGGGACCTTC
Statistics
Matches: 341, Mismatches: 29, Indels: 24
0.87 0.07 0.06
Matches are distributed among these distances:
57 3 0.01
58 73 0.21
59 257 0.75
60 8 0.02
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (57 bp):
AGGGTAAAAATGGAATTTTTGGAAGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTT
Found at i:649 original size:118 final size:116
Alignment explanation
Indices: 395--835 Score: 591
Period size: 118 Copynumber: 3.8 Consensus size: 116
385 GGGAAAATTC
* * * *
395 AGGGTTAAAAATGGAATTTTTGGAAG-TTCGAGG-CTAAAAATGGAATTTTTGGAAGTTTTAGGG
1 AGGGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTC-AAAAATGGGATTTTTGGAAG-TTTGGGG
* * * *
458 TAAAAATGGGATTTTTTGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTT
64 TAAAAATGGAATTTTTGGAAGTTTTGGGGTAAAAATGGGATTTTTGGAAGTTT
* * * *
511 GGGGGTAAAAATAGAATTTTTGGAACTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGAT
1 AGGGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGG-T
* *
576 AAAAATGGAATTTTTGGAACTTTTGGGGTAAAAAATGGGATTTTAGGAAGTTT
65 AAAAATGGAATTTTTGGAAGTTTTGGGGT-AAAAATGGGATTTTTGGAAGTTT
* * *
629 AGGGGTAAAAATGGAATTTTTTGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTAGGAGT
1 AGGGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTGGAAGTTT-GGGGT
694 AAAAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAG-TT
65 AAAAATGGAATTTTTGGAAGTTTTGGGG-TAAAAATGGGATTTTTGGAAGTTT
* * * *
746 CGGGGTTAAAAATGGAATTTTTAGAAGTTTTAAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGG
1 AGGGG-TAAAAATGGAATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTGGAAGTTTG-GGG
811 TAAAAATGGAATTTTTGGACAGTTT
64 TAAAAATGGAATTTTTGGA-AGTTT
836 AGGGACCTTC
Statistics
Matches: 289, Mismatches: 27, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
116 28 0.10
117 57 0.20
118 195 0.67
119 9 0.03
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (116 bp):
AGGGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGTA
AAAATGGAATTTTTGGAAGTTTTGGGGTAAAAATGGGATTTTTGGAAGTTT
Found at i:1865 original size:11 final size:11
Alignment explanation
Indices: 1851--1875 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1841 TTCTTTTTAT
1851 TTATTAATTAA
1 TTATTAATTAA
1862 TTATTAATTAA
1 TTATTAATTAA
1873 TTA
1 TTA
1876 ATAAATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TTATTAATTAA
Found at i:1871 original size:15 final size:15
Alignment explanation
Indices: 1847--1877 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1837 CGTTTTCTTT
*
1847 TTATTTATTAATTAA
1 TTATTAATTAATTAA
1862 TTATTAATTAATTAA
1 TTATTAATTAATTAA
1877 T
1 T
1878 AAATATTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATTAATTAATTAA
Found at i:2514 original size:30 final size:30
Alignment explanation
Indices: 2480--2572 Score: 143
Period size: 30 Copynumber: 3.1 Consensus size: 30
2470 TAGGCTTAGG
* *
2480 GTATTTGGGCTGACTTGGGCCATTT-AGTAT
1 GTATTTGGGCCGATTTGGGCCATTTGA-TAT
2510 GTATTTGGGCCGATTTGGGCCATTTGATAT
1 GTATTTGGGCCGATTTGGGCCATTTGATAT
*
2540 GTATTTGGGCCGATTTGGGCCATTTGATTT
1 GTATTTGGGCCGATTTGGGCCATTTGATAT
2570 GTA
1 GTA
2573 AATGGACTTT
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
30 58 0.98
31 1 0.02
ACGTcount: A:0.16, C:0.13, G:0.30, T:0.41
Consensus pattern (30 bp):
GTATTTGGGCCGATTTGGGCCATTTGATAT
Found at i:2636 original size:17 final size:16
Alignment explanation
Indices: 2596--2640 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
2586 CAAAAAAAAA
*
2596 ATTTAAAGTTAAATTT
1 ATTTAAATTTAAATTT
*
2612 ATGATAAATTTAAATTT
1 AT-TTAAATTTAAATTT
2629 CATTTAAATTTA
1 -ATTTAAATTTA
2641 TAATAAATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 2 0.08
17 20 0.83
18 2 0.08
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (16 bp):
ATTTAAATTTAAATTT
Found at i:2657 original size:17 final size:18
Alignment explanation
Indices: 2637--2676 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
2627 TTCATTTAAA
2637 TTTATAATAAA-TTCAAT
1 TTTATAATAAATTTCAAT
* *
2654 TTTAAAATAAATTTTAAT
1 TTTATAATAAATTTCAAT
2672 TTTAT
1 TTTAT
2677 TGGGCCCAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTATAATAAATTTCAAT
Found at i:2664 original size:28 final size:28
Alignment explanation
Indices: 2594--2671 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 28
2584 GACAAAAAAA
* * *
2594 AAATTTAAAGTTAAATTTATGATAAATTT
1 AAATTTAAA-ATAAATTTATAATAAATTC
* **
2623 AAATTTCATTTAAATTTATAATAAATTC
1 AAATTTAAAATAAATTTATAATAAATTC
*
2651 AATTTTAAAATAAATTT-TAAT
1 AAATTTAAAATAAATTTATAAT
2672 TTTATTGGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 4 0.10
28 30 0.73
29 7 0.17
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (28 bp):
AAATTTAAAATAAATTTATAATAAATTC
Found at i:10586 original size:63 final size:62
Alignment explanation
Indices: 10510--10707 Score: 227
Period size: 63 Copynumber: 3.1 Consensus size: 62
10500 GGGCAGTGGT
* * * * *
10510 CACAAGAGCAAGCCATACTA-GTGTGTGCTAGACCATGTGTGGCTACTGTTTTCTGATTGGAGG
1 CACACGAGCAAGCCATAC-AGGCGTGTGCTAGATCGTGTGTGACTACTGTTTTCTGATT-GAGG
* * * *
10573 CACACGAGTAAGCCATAAAGGCGTGTGCTAGATCGTGTGTTACTATTGTTTTCTGATTTGAGG
1 CACACGAGCAAGCCATACAGGCGTGTGCTAGATCGTGTGTGACTACTGTTTTCTGA-TTGAGG
* * * * *
10636 CACACGGGCAAACCACACAGGCGTGTGCTAGATCGTGTGTGCCTACTATTTTCTGAGTTGAGG
1 CACACGAGCAAGCCATACAGGCGTGTGCTAGATCGTGTGTGACTACTGTTTTCTGA-TTGAGG
10699 CACACGAGC
1 CACACGAGC
10708 GTGTGCAAGA
Statistics
Matches: 113, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
62 1 0.01
63 110 0.97
64 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (62 bp):
CACACGAGCAAGCCATACAGGCGTGTGCTAGATCGTGTGTGACTACTGTTTTCTGATTGAGG
Found at i:18524 original size:23 final size:24
Alignment explanation
Indices: 18494--18663 Score: 114
Period size: 23 Copynumber: 7.3 Consensus size: 24
18484 ATGCTAGCGC
18494 GCTTACTG-TTCAGCACTGTGTGT
1 GCTTACTGATTCAGCACTGTGTGT
*
18517 GCTTACTGTTTC-GCACT-TCGTGT
1 GCTTACTGATTCAGCACTGT-GTGT
*
18540 GCTTACT-ATTTCA-CACCT-CGTGT
1 GCTTACTGA-TTCAGCA-CTGTGTGT
*
18563 GCCTACTGATT--GCACTGTGTGT
1 GCTTACTGATTCAGCACTGTGTGT
*
18585 GCCTACTGATT-A-CACTGTGTGT
1 GCTTACTGATTCAGCACTGTGTGT
* *
18607 GCCTACTGGATT--GCATTGTGTGT
1 GCTTACT-GATTCAGCACTGTGTGT
* *
18630 GGTTACTGTTTCCCTAGCACT-TGTGT
1 GCTTACTGATT--C-AGCACTGTGTGT
18656 GCTTACTG
1 GCTTACTG
18664 TTAAGTACTT
Statistics
Matches: 121, Mismatches: 10, Indels: 29
0.76 0.06 0.18
Matches are distributed among these distances:
21 2 0.02
22 38 0.31
23 59 0.49
24 6 0.05
26 12 0.10
27 4 0.03
ACGTcount: A:0.14, C:0.24, G:0.24, T:0.39
Consensus pattern (24 bp):
GCTTACTGATTCAGCACTGTGTGT
Found at i:18587 original size:22 final size:22
Alignment explanation
Indices: 18506--18630 Score: 119
Period size: 23 Copynumber: 5.5 Consensus size: 22
18496 TTACTGTTCA
* *
18506 GCACTGTGTGTGCTTACTGTTT
1 GCACTGTGTGTGCCTACTGATT
*
18528 CGCACT-TCGTGTGCTTACT-ATT
1 -GCACTGT-GTGTGCCTACTGATT
* **
18550 TCACACCTCGTGTGCCTACTGATT
1 GCAC-TGT-GTGTGCCTACTGATT
18574 GCACTGTGTGTGCCTACTGATT
1 GCACTGTGTGTGCCTACTGATT
*
18596 ACACTGTGTGTGCCTACTGGATT
1 GCACTGTGTGTGCCTACT-GATT
*
18619 GCATTGTGTGTG
1 GCACTGTGTGTG
18631 GTTACTGTTT
Statistics
Matches: 87, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
21 3 0.03
22 35 0.40
23 43 0.49
24 6 0.07
ACGTcount: A:0.14, C:0.23, G:0.25, T:0.38
Consensus pattern (22 bp):
GCACTGTGTGTGCCTACTGATT
Done.