Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003320.1 Kokia drynarioides strain JFW-HI SEQ_116013, 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: 8633
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:1423 original size:33 final size:32
Alignment explanation
Indices: 1376--1450 Score: 82
Period size: 34 Copynumber: 2.3 Consensus size: 32
1366 ACTTAATGTA
* * *
1376 TTTATATAAA-ATTTAT-CAAAATTATTAAAT
1 TTTATAAAAATATTTATAAAAAATTATAAAAT
*
1406 TTTAATGAAAAATATTTATAAAAAATTGTAAAAT
1 TTT-AT-AAAAATATTTATAAAAAATTATAAAAT
1440 TTTATAAAAAT
1 TTTATAAAAAT
1451 CATAAAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
30 3 0.08
31 2 0.05
32 10 0.27
33 8 0.22
34 14 0.38
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (32 bp):
TTTATAAAAATATTTATAAAAAATTATAAAAT
Found at i:1458 original size:20 final size:21
Alignment explanation
Indices: 1413--1463 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
1403 AATTTTAATG
**
1413 AAAAATATTTATAAAAAATTGT
1 AAAAAT-TTTATAAAAAATCAT
1435 -AAAATTTTAT-AAAAATCAT
1 AAAAATTTTATAAAAAATCAT
1454 AAAAATTTTA
1 AAAAATTTTA
1464 GCAATTGATC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 7 0.27
20 14 0.54
21 5 0.19
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
AAAAATTTTATAAAAAATCAT
Found at i:2346 original size:21 final size:20
Alignment explanation
Indices: 2320--2375 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 20
2310 CAATACTCAT
* *
2320 TAATAATAATAAATGTTTTGA
1 TAATAATAATAAAT-TATTAA
2341 TAATAATAATAATATTATTAA
1 TAATAATAATAA-ATTATTAA
2362 TAATAATTAATAAA
1 TAATAA-TAATAAA
2376 AAAAAGGGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 23 0.74
22 8 0.26
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (20 bp):
TAATAATAATAAATTATTAA
Found at i:3429 original size:29 final size:29
Alignment explanation
Indices: 3379--3686 Score: 335
Period size: 29 Copynumber: 10.7 Consensus size: 29
3369 GAGGTCCCTG
*
3379 AACTGTCCAAAAATCCCA-TTTTACCCCCG
1 AACT-TCCAAAAATCCCATTTTTACCCCCA
* *
3408 AACTTCCAAAAATCCCATTTTTAACCACAA
1 AACTTCCAAAAATCCCATTTTT-ACCCCCA
* *
3438 AACTTCTAAAAATCCCA-TTTTATCCCCA
1 AACTTCCAAAAATCCCATTTTTACCCCCA
* *
3466 AACTTCTAAAAATCCCATTTTTAACCCCAA
1 AACTTCCAAAAATCCCATTTTT-ACCCCCA
*
3496 AACTTCCAAAAATTCCATTTTTACCCCCA
1 AACTTCCAAAAATCCCATTTTTACCCCCA
* *
3525 AACTTCAAAAAATCCCA--TTT----CAA
1 AACTTCCAAAAATCCCATTTTTACCCCCA
* *
3548 AACTTCCAAAAATCACATTTTTACCCCTA
1 AACTTCCAAAAATCCCATTTTTACCCCCA
*
3577 AACTTCCAAAAATCCCATTTTTGACCCCAA
1 AACTTCCAAAAATCCCATTTTT-ACCCCCA
* * * *
3607 AATTTCTAAAAATCTCATTTTTACCCTCA
1 AACTTCCAAAAATCCCATTTTTACCCCCA
*
3636 AACTTCCAAAAATCCCATTTTTACCCCGA
1 AACTTCCAAAAATCCCATTTTTACCCCCA
* *
3665 AACTTTCAAAAATTACCATTTT
1 AACTTCCAAAAA-TCCCATTTT
3687 GCCCCTCGGG
Statistics
Matches: 235, Mismatches: 32, Indels: 23
0.81 0.11 0.08
Matches are distributed among these distances:
23 17 0.07
25 3 0.01
27 3 0.01
28 34 0.14
29 100 0.43
30 78 0.33
ACGTcount: A:0.38, C:0.31, G:0.01, T:0.31
Consensus pattern (29 bp):
AACTTCCAAAAATCCCATTTTTACCCCCA
Found at i:3552 original size:23 final size:23
Alignment explanation
Indices: 3524--3567 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
3514 TTTTACCCCC
*
3524 AAACTTCAAAAAATCCCATTTCA
1 AAACTTCAAAAAATCACATTTCA
*
3547 AAACTTCCAAAAATCACATTT
1 AAACTTCAAAAAATCACATTT
3568 TTACCCCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (23 bp):
AAACTTCAAAAAATCACATTTCA
Found at i:3618 original size:59 final size:58
Alignment explanation
Indices: 3379--3686 Score: 355
Period size: 59 Copynumber: 5.4 Consensus size: 58
3369 GAGGTCCCTG
* * *
3379 AACTGTCCAAAAATCCCA-TTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCACAA
1 AACT-TCCAAAAATCACATTTTTACCCCCAAACTTCCAAAAATCCCATTTTT-ACCCCAA
* * * *
3438 AACTTCTAAAAATCCCA-TTTTATCCCCAAACTTCTAAAAATCCCATTTTTAACCCCAA
1 AACTTCCAAAAATCACATTTTTACCCCCAAACTTCCAAAAATCCCATTTTT-ACCCCAA
*
3496 AACTTCCAAAAATTC-CATTTTTACCCCCAAACTTCAAAAAATCCCA--TTT----CAA
1 AACTTCCAAAAA-TCACATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTACCCCAA
*
3548 AACTTCCAAAAATCACATTTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCAA
1 AACTTCCAAAAATCACATTTTTACCCCCAAACTTCCAAAAATCCCATTTTT-ACCCCAA
* * * * *
3607 AATTTCTAAAAATCTCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTACCCCGA
1 AACTTCCAAAAATCACATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTACCCCAA
* *
3665 AACTTTCAAAAATTACCATTTT
1 AACTTCCAAAAATCA-CATTTT
3687 GCCCCTCGGG
Statistics
Matches: 217, Mismatches: 21, Indels: 22
0.83 0.08 0.08
Matches are distributed among these distances:
51 2 0.01
52 44 0.20
54 3 0.01
57 3 0.01
58 78 0.36
59 87 0.40
ACGTcount: A:0.38, C:0.31, G:0.01, T:0.31
Consensus pattern (58 bp):
AACTTCCAAAAATCACATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTACCCCAA
Found at i:6192 original size:21 final size:21
Alignment explanation
Indices: 6168--6218 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
6158 ATAATAGCAT
6168 AATCCAAATATAAAATTTAGA
1 AATCCAAATATAAAATTTAGA
* * *
6189 AATCCAAACATAAAGTTTATA
1 AATCCAAATATAAAATTTAGA
6210 AATCCAAAT
1 AATCCAAAT
6219 TACATAATTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.55, C:0.14, G:0.04, T:0.27
Consensus pattern (21 bp):
AATCCAAATATAAAATTTAGA
Done.