Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010738.1 Kokia drynarioides strain JFW-HI SEQ_125691, 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: 9282
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:530 original size:17 final size:18
Alignment explanation
Indices: 494--586 Score: 111
Period size: 17 Copynumber: 5.3 Consensus size: 18
484 TTATAGTAAT
*
494 TTTAAATTTGAAAATAAA
1 TTTAAATTTCAAAATAAA
* *
512 TTTAAACTT-AAATTAAA
1 TTTAAATTTCAAAATAAA
529 TTTAAA-TTCAAAATAAA
1 TTTAAATTTCAAAATAAA
546 TTTAAATTT-AAAATAAA
1 TTTAAATTTCAAAATAAA
** *
563 TTTAAATTTTTAAACAAA
1 TTTAAATTTCAAAATAAA
581 TTTAAA
1 TTTAAA
587 GGGAGTTTGG
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
16 2 0.03
17 43 0.64
18 22 0.33
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (18 bp):
TTTAAATTTCAAAATAAA
Found at i:559 original size:7 final size:6
Alignment explanation
Indices: 494--571 Score: 74
Period size: 6 Copynumber: 13.5 Consensus size: 6
484 TTATAGTAAT
* * *
494 TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA -TTAAA TTTAAA TTCAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
541 -ATAAA TTTAAA TTTAAA -ATAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
572 TTAAACAAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
5 15 0.26
6 40 0.69
7 3 0.05
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:569 original size:23 final size:23
Alignment explanation
Indices: 508--557 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
498 AATTTGAAAA
* *
508 TAAATTTAAACTTAAATTAAATT
1 TAAATTCAAACATAAATTAAATT
531 TAAATTCAAA-ATAAATTTAAATT
1 TAAATTCAAACATAAA-TTAAATT
554 TAAA
1 TAAA
558 ATAAATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (23 bp):
TAAATTCAAACATAAATTAAATT
Found at i:2595 original size:6 final size:6
Alignment explanation
Indices: 2584--2664 Score: 66
Period size: 6 Copynumber: 14.2 Consensus size: 6
2574 TGGACCCAAA
* * * *
2584 AAATTT AAATTT -ATTTT AAAGTT AAGTTT -ATTTT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
2630 --ATTT AAATTT --ATTAT AAATTT AAATTT AAAATTT A
1 AAATTT AAATTT AAATT-T AAATTT AAATTT -AAATTT A
2665 TTTAAATAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 16
0.72 0.08 0.19
Matches are distributed among these distances:
4 7 0.12
5 9 0.15
6 35 0.58
7 9 0.15
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:2635 original size:10 final size:10
Alignment explanation
Indices: 2620--2671 Score: 68
Period size: 10 Copynumber: 4.8 Consensus size: 10
2610 TTTATTTTAA
2620 ATTTAAATTT
1 ATTTAAATTT
2630 ATTTAAATTT
1 ATTTAAATTT
2640 ATTATAAATTT
1 ATT-TAAATTT
2651 AAATTTAAAATTT
1 --ATTT-AAATTT
2664 ATTTAAAT
1 ATTTAAAT
2672 AATATCCAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 17 0.45
11 11 0.29
12 1 0.03
13 9 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
ATTTAAATTT
Found at i:2635 original size:27 final size:27
Alignment explanation
Indices: 2605--2671 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
2595 TATTTTAAAG
* *
2605 TTAAGTTTATTTTAAATTTAAATTTAT
1 TTAAATTTATTATAAATTTAAATTTAT
2632 TTAAATTTATTATAAATTTAAATTTA-
1 TTAAATTTATTATAAATTTAAATTTAT
2658 --AAATTTATT-TAAAT
1 TTAAATTTATTATAAAT
2672 AATATCCAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
23 5 0.13
24 9 0.24
27 24 0.63
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (27 bp):
TTAAATTTATTATAAATTTAAATTTAT
Found at i:2650 original size:17 final size:16
Alignment explanation
Indices: 2584--2671 Score: 95
Period size: 17 Copynumber: 5.2 Consensus size: 16
2574 TGGACCCAAA
2584 AAATTTAAATTTATTTT
1 AAATTTAAATTTA-TTT
* *
2601 AAAGTTAAGTTTATTTT
1 AAATTTAAATTTA-TTT
2618 AAATTTAAATTTATTT
1 AAATTTAAATTTATTT
* **
2634 AAATTTATTATAAATTT
1 AAATTTA-AATTTATTT
2651 AAATTTAAAATTTATTT
1 AAATTT-AAATTTATTT
2668 AAAT
1 AAAT
2672 AATATCCAAG
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
16 10 0.17
17 48 0.81
18 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
AAATTTAAATTTATTT
Found at i:2668 original size:44 final size:43
Alignment explanation
Indices: 2586--2671 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 43
2576 GACCCAAAAA
* * *
2586 ATTTAAATTTATTTTAAAGTTAAGTTTATTTTAAATTTAAATTT
1 ATTTAAATTTATTATAAAGTTAAATTTAATTT-AATTTAAATTT
*
2630 ATTTAAATTTATTATAAATTTAAATTTAAAATTT-ATTTAAAT
1 ATTTAAATTTATTATAAAGTTAAATTT--AATTTAATTTAAAT
2672 AATATCCAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
44 32 0.89
46 4 0.11
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (43 bp):
ATTTAAATTTATTATAAAGTTAAATTTAATTTAATTTAAATTT
Found at i:3393 original size:3 final size:3
Alignment explanation
Indices: 3376--3451 Score: 73
Period size: 3 Copynumber: 25.0 Consensus size: 3
3366 TTCATAACAT
* * * * * *
3376 TAA TAA TAT TGA TAA TAA -ATA TAA TAT TAA TGA CAT TAA TTAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA -TAA TAA
3422 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3452 AGGAAAAGTG
Statistics
Matches: 58, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
2 1 0.02
3 53 0.91
4 4 0.07
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:4615 original size:30 final size:29
Alignment explanation
Indices: 4574--4898 Score: 316
Period size: 30 Copynumber: 11.0 Consensus size: 29
4564 TTCACCCTCG
*
4574 AACTTCCAAAAATCCCATTTTGACCCCGA
1 AACTTCCAAAAATCCCATTTTTACCCCGA
**
4603 AACTTCCAAAAAATTCCC-TTTTTACCCTTA
1 AACTTCC-AAAAA-TCCCATTTTTACCCCGA
* * *
4633 AACTCCCTAAAATCCCATTTTTACCCCCA
1 AACTTCCAAAAATCCCATTTTTACCCCGA
* * *
4662 AAGCTTCTAAAAATTCTATTTTTACCCC-A
1 AA-CTTCCAAAAATCCCATTTTTACCCCGA
* *
4691 AACTTTCAAAAATCCCATTTTTGACCTCGA
1 AACTTCCAAAAATCCCATTTTT-ACCCCGA
* **
4721 AACTTCCAAAAAATTCCATTTTTACCCTTA
1 AACTTCC-AAAAATCCCATTTTTACCCCGA
* * **
4751 AGCTTCCCAAAATCCCATTTTTAACCCTAA
1 AACTTCCAAAAATCCCATTTTT-ACCCCGA
* * *
4781 AACTTCTAAAAATTCTATTTTTACCCCG-
1 AACTTCCAAAAATCCCATTTTTACCCCGA
* * *
4809 AACTTCAAAAAATCTCATTTTTACCCTTG-
1 AACTTCCAAAAATCCCATTTTTACCC-CGA
*
4838 AACTTCCAAAAATCCGATTTTTTACCCCGA
1 AACTTCCAAAAATCCCA-TTTTTACCCCGA
4868 AACTTCCAAAAATCCCATTTTTACCCTCGA
1 AACTTCCAAAAATCCCATTTTTACCC-CGA
4898 A
1 A
4899 TGTGTAAAAA
Statistics
Matches: 241, Mismatches: 43, Indels: 23
0.79 0.14 0.07
Matches are distributed among these distances:
28 42 0.17
29 72 0.30
30 109 0.45
31 18 0.07
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33
Consensus pattern (29 bp):
AACTTCCAAAAATCCCATTTTTACCCCGA
Found at i:4787 original size:118 final size:118
Alignment explanation
Indices: 4574--4894 Score: 424
Period size: 118 Copynumber: 2.7 Consensus size: 118
4564 TTCACCCTCG
* * *
4574 AACTTCCAAAAATCCCA-TTTTGACCCCGAAACTTCCAAAAAATTCCCTTTTTACCCTTAAAC-T
1 AACTTTCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAAATTCCATTTTTACCCTTAAACTT
* * *
4637 CCCTAAAATCCCATTTTTACCCCCAAAGCTTCTAAAAATTCTATTTTTACCCCA
66 CCC-AAAATCCCATTTTTAACCCTAAAACTTCTAAAAATTCTATTTTTACCCCA
*
4691 AACTTTCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAAATTCCATTTTTACCCTTAAGCTT
1 AACTTTCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAAATTCCATTTTTACCCTTAAACTT
*
4756 CCCAAAATCCCATTTTTAACCCTAAAACTTCTAAAAATTCTATTTTTACCCCG
66 CCCAAAATCCCATTTTTAACCCTAAAACTTCTAAAAATTCTATTTTTACCCCA
* * **
4809 AAC-TTCAAAAAATCTCATTTTT-ACCCTTG-AACTTCC-AAAAA-TCCGATTTTTTACCCCGAA
1 AACTTTC-AAAAATCCCATTTTTGA-CCTCGAAACTTCCAAAAAATTCC-A-TTTTTACCCTTAA
*
4869 ACTTCCAAAAATCCCATTTTT-ACCCT
62 ACTTCCCAAAATCCCATTTTTAACCCT
4895 CGAATGTGTA
Statistics
Matches: 184, Mismatches: 14, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
115 3 0.02
116 11 0.06
117 57 0.31
118 109 0.59
119 4 0.02
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33
Consensus pattern (118 bp):
AACTTTCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAAATTCCATTTTTACCCTTAAACTT
CCCAAAATCCCATTTTTAACCCTAAAACTTCTAAAAATTCTATTTTTACCCCA
Found at i:4909 original size:59 final size:58
Alignment explanation
Indices: 4574--4898 Score: 302
Period size: 59 Copynumber: 5.5 Consensus size: 58
4564 TTCACCCTCG
* * * **
4574 AACTTCCAAAAATCCCATTTTGACCC-CGAAACTTCCAAAAAATTCC-CTTTTTACCCTTA
1 AACTTCCAAAAATCCCATTTTTACCCTCG-AACTT-CTAAAAA-TCCTATTTTTACCCCGA
* * * * *
4633 AACTCCCTAAAATCCCATTTTTACCCCCAAAGCTTCTAAAAATTCTATTTTTACCCC-A
1 AACTTCCAAAAATCCCATTTTTACCCTCGAA-CTTCTAAAAATCCTATTTTTACCCCGA
* * **
4691 AACTTTCAAAAATCCCATTTTTGA-CCTCGAAACTTCCAAAAAATTCC-ATTTTTACCCTTA
1 AACTTCCAAAAATCCCATTTTT-ACCCTCG-AACTT-CTAAAAA-TCCTATTTTTACCCCGA
* * ** *
4751 AGCTTCCCAAAATCCCATTTTTAACCCTAAAACTTCTAAAAATTCTATTTTTACCCCG-
1 AACTTCCAAAAATCCCATTTTT-ACCCTCGAACTTCTAAAAATCCTATTTTTACCCCGA
* * * * *
4809 AACTTCAAAAAATCTCATTTTTACCCTTGAACTTCCAAAAATCCGATTTTTTACCCCGA
1 AACTTCCAAAAATCCCATTTTTACCCTCGAACTTCTAAAAATCCTA-TTTTTACCCCGA
4868 AACTTCCAAAAATCCCATTTTTACCCTCGAA
1 AACTTCCAAAAATCCCATTTTTACCCTCGAA
4899 TGTGTAAAAA
Statistics
Matches: 216, Mismatches: 38, Indels: 24
0.78 0.14 0.09
Matches are distributed among these distances:
57 19 0.09
58 59 0.27
59 103 0.48
60 32 0.15
61 3 0.01
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33
Consensus pattern (58 bp):
AACTTCCAAAAATCCCATTTTTACCCTCGAACTTCTAAAAATCCTATTTTTACCCCGA
Found at i:4973 original size:28 final size:32
Alignment explanation
Indices: 4935--4997 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
4925 AATTTTCTCG
4935 AAATTACCA-TTT-CACCC-CCAAGAATCC-A
1 AAATTACCATTTTCCACCCTCCAAGAATCCGA
*
4963 AAATTACCATTTTCCCCCCTCCAAGAATCCGA
1 AAATTACCATTTTCCACCCTCCAAGAATCCGA
4995 AAA
1 AAA
4998 GTCTCATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 9 0.30
29 3 0.10
30 4 0.13
31 10 0.33
32 4 0.13
ACGTcount: A:0.38, C:0.35, G:0.05, T:0.22
Consensus pattern (32 bp):
AAATTACCATTTTCCACCCTCCAAGAATCCGA
Found at i:5333 original size:96 final size:96
Alignment explanation
Indices: 5215--5399 Score: 248
Period size: 96 Copynumber: 1.9 Consensus size: 96
5205 AAAACTTTAA
* *
5215 AATCGAGGCAATATTCTTTTATTTCGAATT-TCGAAAATTTGCGCCTTAACTTACTAGGTGCAAT
1 AATCGAGGCAATATTCTCTTATTTCGAATTCT-GAAAATTTGCGCCTTAACTTACTAGGTGCAAC
* *
5279 TTTTCTTCAAATCGAAATAATCGAATACCCTT
65 CTTTCCTCAAATCGAAATAATCGAATACCCTT
* *** * *
5311 AATCGAGGCAATGTT-TCCTTATTTTTTATTCTGAAAATTTGTGCCTTAACTTACTAGGTGTAAC
1 AATCGAGGCAATATTCT-CTTATTTCGAATTCTGAAAATTTGCGCCTTAACTTACTAGGTGCAAC
5375 CTTTCCTCAAATCGAAATAATCGAA
65 CTTTCCTCAAATCGAAATAATCGAA
5400 CATCCTTTTC
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
95 1 0.01
96 75 0.97
97 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (96 bp):
AATCGAGGCAATATTCTCTTATTTCGAATTCTGAAAATTTGCGCCTTAACTTACTAGGTGCAACC
TTTCCTCAAATCGAAATAATCGAATACCCTT
Done.