Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014009.1 Kokia drynarioides strain JFW-HI SEQ_129040, 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: 37061
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.33
Warning! 35 characters in sequence are not A, C, G, or T
Found at i:23401 original size:29 final size:28
Alignment explanation
Indices: 23369--23431 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
23359 CAAAAATAGG
23369 ATTTTTAACAGCTCGAGGG-TAAAATGGTA
1 ATTTTTAA-AGCTCG-GGGATAAAATGGTA
** *
23398 ATTTTGGAAGTTCGGGGATAAAATGGTA
1 ATTTTTAAAGCTCGGGGATAAAATGGTA
23426 ATTTTT
1 ATTTTT
23432 GGAAGGTTCG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 3 0.10
28 20 0.69
29 6 0.21
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.37
Consensus pattern (28 bp):
ATTTTTAAAGCTCGGGGATAAAATGGTA
Found at i:23479 original size:59 final size:59
Alignment explanation
Indices: 23389--23848 Score: 632
Period size: 59 Copynumber: 7.8 Consensus size: 59
23379 GCTCGAGGGT
* * * * * * *
23389 AAAATGGTAATTTTGGAAGTTCGGGGATAAAATGGTAATTTTTGGAAGGTTCGAGGTAA
1 AAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCA
* * *
23448 AAAATGGGGTTTTTGGAAGTTTAGGGGTAAAATGGTAACTTTTAGAAGGTTCGGGGTCA
1 AAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCA
* * *
23507 AAAATGAGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTTGGGGTCA
1 AAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCA
** * **
23566 AAAATGTTATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTCAAGGTCA
1 AAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCA
* * *
23625 AAAATGGGGTTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTGA
1 AAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCA
** * **
23684 AAAATGTTATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTAGAAGGTTCGACGTCA
1 AAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCA
* *
23743 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTTGGGGTCA
1 AAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCA
** * *
23802 AAAATGTTATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAA
1 AAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAA
23849 AGTTTAGGGT
Statistics
Matches: 354, Mismatches: 47, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 354 1.00
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (59 bp):
AAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCA
Found at i:23529 original size:118 final size:118
Alignment explanation
Indices: 23389--23848 Score: 697
Period size: 118 Copynumber: 3.9 Consensus size: 118
23379 GCTCGAGGGT
* * * * * *
23389 AAAATGGTAATTTTGGAAGTTCGGGGATAAAATGGTAATTTTTGGAAGGTTCGAGGTAAAAAATG
1 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATG
*** * *
23454 GGGTTTTTGGAAGTTT-AGGGGTAAAATGGTAACTTTTAGAAGGTTCGGGGTCA
66 TTATTTTTGGAAGTTTGA-GGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTCA
* *
23507 AAAATGAGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTTGGGGTCAAAAATG
1 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATG
* * *
23572 TTATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTCAAGGTCA
66 TTATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTCA
* ** *
23625 AAAATGGGGTTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTGAAAAATG
1 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATG
*
23690 TTATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTAGAAGGTTCGACGTCA
66 TTATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTCA
*
23743 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTTGGGGTCAAAAATG
1 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATG
*
23808 TTATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAA
66 TTATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTAGAA
23849 AGTTTAGGGT
Statistics
Matches: 309, Mismatches: 32, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
118 309 1.00
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (118 bp):
AAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATG
TTATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTCA
Found at i:23698 original size:177 final size:177
Alignment explanation
Indices: 23389--23848 Score: 706
Period size: 177 Copynumber: 2.6 Consensus size: 177
23379 GCTCGAGGGT
* * * *
23389 AAAATGGTAATTTTGGAAGTTCGGGGATAAAATGGTAATTTTTGGAAGGTTCGAGGTAAAAAATG
1 AAAATGGTATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTCAAAAATG
*
23454 GGGTTTTTGGAAGTTTAGGGGTAAAATGGTAACTTTTAGAAGGTTCGGGGTCAAAAATGAGATTT
66 GGGTTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGAGATTT
* * **
23519 TTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTTGGGGTCA
131 TTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTCGACGTCA
* *
23566 AAAATGTTATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTCAAGGTCAAAAATG
1 AAAATGGTATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTCAAAAATG
* **
23631 GGGTTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTGAAAAATGTTATTT
66 GGGTTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGAGATTT
*
23696 TTGGAAGTTTGAGGGTAAAATGGTAATTTTTAGAAGGTTCGACGTCA
131 TTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTCGACGTCA
* * *
23743 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTTGGGGTCAAAAATG
1 AAAATGGTATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTCAAAAATG
*** *
23808 TTATTTTTGGAAG-TTCGAGGGTAAAATGGTAATTTTTAGAA
66 GGGTTTTTGGAAGTTTAG-GGGTAAAATGGTAATTTTTAGAA
23849 AGTTTAGGGT
Statistics
Matches: 258, Mismatches: 24, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
176 3 0.01
177 255 0.99
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (177 bp):
AAAATGGTATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTCAAAAATG
GGGTTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGAGATTT
TTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTCGACGTCA
Found at i:25487 original size:15 final size:15
Alignment explanation
Indices: 25464--25570 Score: 110
Period size: 15 Copynumber: 7.3 Consensus size: 15
25454 CACTTTATAA
*
25464 TTGGACCATTTGTAT
1 TTGGGCCATTTGTAT
* *
25479 TTGGGCCATCTGTAA
1 TTGGGCCATTTGTAT
*
25494 CTGGGCCATTTGTAT
1 TTGGGCCATTTGTAT
* *
25509 TTGGGCCATCTGTAA
1 TTGGGCCATTTGTAT
*
25524 CTGGGCCATTTGT-T
1 TTGGGCCATTTGTAT
* *
25538 TTGGGCCATCTGTAA
1 TTGGGCCATTTGTAT
*
25553 CTGGGCCATTTGT-T
1 TTGGGCCATTTGTAT
25567 TTGG
1 TTGG
25571 ATTTTTTTTG
Statistics
Matches: 72, Mismatches: 19, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
14 14 0.19
15 58 0.81
ACGTcount: A:0.15, C:0.19, G:0.27, T:0.39
Consensus pattern (15 bp):
TTGGGCCATTTGTAT
Found at i:25550 original size:29 final size:30
Alignment explanation
Indices: 25469--25570 Score: 190
Period size: 30 Copynumber: 3.5 Consensus size: 30
25459 TATAATTGGA
25469 CCATTTGTATTTGGGCCATCTGTAACTGGG
1 CCATTTGTATTTGGGCCATCTGTAACTGGG
25499 CCATTTGTATTTGGGCCATCTGTAACTGGG
1 CCATTTGTATTTGGGCCATCTGTAACTGGG
25529 CCATTTGT-TTTGGGCCATCTGTAACTGGG
1 CCATTTGTATTTGGGCCATCTGTAACTGGG
25558 CCATTTGT-TTTGG
1 CCATTTGTATTTGG
25571 ATTTTTTTTG
Statistics
Matches: 72, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
29 34 0.47
30 38 0.53
ACGTcount: A:0.15, C:0.20, G:0.26, T:0.39
Consensus pattern (30 bp):
CCATTTGTATTTGGGCCATCTGTAACTGGG
Found at i:25617 original size:17 final size:18
Alignment explanation
Indices: 25595--25640 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
25585 CAGACTTTTC
*
25595 TAAA-TTAAATTTTATAA
1 TAAACTTAAATTTTAAAA
*
25612 TAAATTTAAA-TTTAAAA
1 TAAACTTAAATTTTAAAA
25629 TAAACTTAAATT
1 TAAACTTAAATT
25641 CAATTTCCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 19 0.76
18 6 0.24
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAACTTAAATTTTAAAA
Found at i:32574 original size:7 final size:7
Alignment explanation
Indices: 32562--32586 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
32552 ATTCGAAAAA
32562 AATTTCG
1 AATTTCG
32569 AATTTCG
1 AATTTCG
32576 AATTTCG
1 AATTTCG
32583 AATT
1 AATT
32587 ATTCGAATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (7 bp):
AATTTCG
Found at i:35226 original size:25 final size:25
Alignment explanation
Indices: 35189--35238 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
35179 TTCCTTGAGA
* *
35189 GTTGATATTTAGAAATTATAATAAT
1 GTTGACATCTAGAAATTATAATAAT
35214 GTTGACATCTAGAAATTATAATAAT
1 GTTGACATCTAGAAATTATAATAAT
35239 TAAAGTGAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.44, C:0.04, G:0.12, T:0.40
Consensus pattern (25 bp):
GTTGACATCTAGAAATTATAATAAT
Done.