Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012644.1 Kokia drynarioides strain JFW-HI SEQ_127654, 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: 4582
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.33
Warning! 88 characters in sequence are not A, C, G, or T
Found at i:414 original size:29 final size:30
Alignment explanation
Indices: 382--771 Score: 347
Period size: 29 Copynumber: 13.3 Consensus size: 30
372 AACATTCGGT
*
382 GGGT-AAAATGGTAATTTTTGGAAGGTTCA
1 GGGTCAAAATGGTAATTTTTGGAAGGTTCG
*
411 GGGTCAAAAATGG-GATTTTTGGAA-GTTCG
1 GGGTC-AAAATGGTAATTTTTGGAAGGTTCG
440 AGGGT-AAAATGGTAA-TTTTGGAAGGTTCG
1 -GGGTCAAAATGGTAATTTTTGGAAGGTTCG
* *
469 AGGTCAAAAATGG-GATTTTTGGAA-GTTCG
1 GGGTC-AAAATGGTAATTTTTGGAAGGTTCG
*
498 AGGGT-GAAATGGTAATTTTTGGAAGGTTC-
1 -GGGTCAAAATGGTAATTTTTGGAAGGTTCG
* *
527 GGGTCAAAAATGG-GATTTTTGGAA-TTTCGG
1 GGGTC-AAAATGGTAATTTTTGGAAGGTTC-G
* * *
557 GGGT-GAAATAGTAATTTTTTGAAGGTTCG
1 GGGTCAAAATGGTAATTTTTGGAAGGTTCG
*
586 GGGTCAAAAATAGG--ATTTTTGGAA-GTACG
1 GGGTC-AAAAT-GGTAATTTTTGGAAGGTTCG
* * *
615 GTGGT-GAAATGGTAATTTTTGAAAGGTTTG
1 G-GGTCAAAATGGTAATTTTTGGAAGGTTCG
* *
645 GGGTCAAAAAT-G-AGATTTTTGGAAGTTTGG
1 GGGTC-AAAATGGTA-ATTTTTGGAAGGTTCG
675 GGGT-AAAATGGTAATTTTTGGAAGGTTCG
1 GGGTCAAAATGGTAATTTTTGGAAGGTTCG
*
704 GGGTCAAAAAT-GAAATTTTTGGAA-GTTCAG
1 GGGTC-AAAATGGTAATTTTTGGAAGGTTC-G
*
734 AGGT-AAAATGGTAATTTTTGGAAGGTTCG
1 GGGTCAAAATGGTAATTTTTGGAAGGTTCG
763 GGGTCAAAA
1 GGGTCAAAA
772 ATGAGATTTC
Statistics
Matches: 292, Mismatches: 34, Indels: 69
0.74 0.09 0.17
Matches are distributed among these distances:
27 2 0.01
28 50 0.17
29 111 0.38
30 108 0.37
31 20 0.07
32 1 0.00
ACGTcount: A:0.30, C:0.05, G:0.32, T:0.33
Consensus pattern (30 bp):
GGGTCAAAATGGTAATTTTTGGAAGGTTCG
Found at i:423 original size:59 final size:59
Alignment explanation
Indices: 376--780 Score: 589
Period size: 59 Copynumber: 6.9 Consensus size: 59
366 ATTTCAAACA
*
376 TTCGGTGGGTAAAATGGTAATTTTTGGAAGGTTCAGGGTCAAAAATGGGATTTTTGGAAG
1 TTCGG-GGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAG
* *
436 TTCGAGGGTAAAATGGTAA-TTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAG
* * *
494 TTCGAGGGTGAAATGGTAATTTTTGGAAGGTTC-GGGTCAAAAATGGGATTTTTGGAAT
1 TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAG
* * * *
552 TTCGGGGGTGAAATAGTAATTTTTTGAAGGTTCGGGGTCAAAAATAGGATTTTTGGAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAG
* * * * * *
611 TACGGTGGTGAAATGGTAATTTTTGAAAGGTTTGGGGTCAAAAATGAGATTTTTGGAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAG
* **
670 TTTGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGAAATTTTTGGAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAG
* * *
729 TTCAGAGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGAGATTT
1 TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTT
781 CTTGACAATT
Statistics
Matches: 313, Mismatches: 30, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
58 108 0.35
59 201 0.64
60 4 0.01
ACGTcount: A:0.30, C:0.05, G:0.32, T:0.33
Consensus pattern (59 bp):
TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAG
Found at i:2591 original size:6 final size:6
Alignment explanation
Indices: 2577--2623 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
2567 AATTCGAAAA
* *
2577 TAAATT TAAAAT TAAATT TAAA-A TAAATT TAAATT T-AATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
2623 T
1 T
2624 TTAACAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
5 9 0.26
6 26 0.74
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
TAAATT
Found at i:2603 original size:11 final size:11
Alignment explanation
Indices: 2573--2620 Score: 69
Period size: 11 Copynumber: 4.3 Consensus size: 11
2563 TTTAAATTCG
2573 AAAATAAATTT
1 AAAATAAATTT
2584 AAAATTAAATTT
1 AAAA-TAAATTT
2596 AAAATAAATTT
1 AAAATAAATTT
* *
2607 AAATTTAATTT
1 AAAATAAATTT
2618 AAA
1 AAA
2621 TTTTTAACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
11 23 0.68
12 11 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AAAATAAATTT
Found at i:2608 original size:17 final size:17
Alignment explanation
Indices: 2546--2654 Score: 78
Period size: 17 Copynumber: 6.4 Consensus size: 17
2536 TGGACCTTAT
* *
2546 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
*
2563 TTTAAATTCGAAAATAAA
1 TTTAAATT-TAAAATAAA
* *
2581 TTTAAAATTAAATTTAAA
1 TTTAAATTTAAA-ATAAA
* * *
2599 -ATAAATTTAAATTTAA
1 TTTAAATTTAAAATAAA
** *
2615 TTTAAATTTTTAACAAA
1 TTTAAATTTAAAATAAA
2632 TTT-AATCTTAAAATAAA
1 TTTAAAT-TTAAAATAAA
2649 TTTAAA
1 TTTAAA
2655 GGGGAGTTTT
Statistics
Matches: 69, Mismatches: 18, Indels: 9
0.72 0.19 0.09
Matches are distributed among these distances:
16 7 0.10
17 43 0.62
18 19 0.28
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:3355 original size:152 final size:152
Alignment explanation
Indices: 3084--3363 Score: 440
Period size: 152 Copynumber: 1.8 Consensus size: 152
3074 CTTCTCTGTA
3084 TCTCATCAGGAAGACGAATTTGGTTCACTTTCCAGTATCTCATCAGGAAGCTAACCATTTATTGC
1 TCTCATCAGGAAGACGAATTTGGTTCACTTTCCAGTATCTCATCAGGAAGCTAACCATTTATTGC
* * * * *
3149 TTTCACCTGCTTCTCAGTGTCTCATTAGGAAGCTGAGTTTTGAAGGTTTCGCTCG-TTTCGAGCC
66 TTTCACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTCGCTCGCTTT-GAGCC
3213 TCGTTTGGGTCTTCTTCTCAATG
130 TCGTTTGGGTCTTCTTCTCAATG
3236 TCTCATCAGGAAGACGAATTTGGTTCACTTCTCC-GTATCTCATCAGGAAGCTAACCATTTATTG
1 TCTCATCAGGAAGACGAATTTGGTTCACTT-TCCAGTATCTCATCAGGAAGCTAACCATTTATTG
* * *
3300 C-TTCGACCTGCTTCTCGGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCGCTTTGAGC
65 CTTTC-ACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTCGCTCGCTTTGAGC
3364 GTAGGCCTGA
Statistics
Matches: 117, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
151 3 0.03
152 108 0.92
153 6 0.05
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (152 bp):
TCTCATCAGGAAGACGAATTTGGTTCACTTTCCAGTATCTCATCAGGAAGCTAACCATTTATTGC
TTTCACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTCGCTCGCTTTGAGCCT
CGTTTGGGTCTTCTTCTCAATG
Done.