Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007709.1 Kokia drynarioides strain JFW-HI SEQ_122340, 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: 2743
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Found at i:644 original size:7 final size:7
Alignment explanation
Indices: 632--676 Score: 56
Period size: 7 Copynumber: 6.4 Consensus size: 7
622 AATGGAATCC
632 AATTTTA
1 AATTTTA
639 AATTTTA
1 AATTTTA
646 AATTTTA
1 AATTTTA
*
653 AATTATTT
1 AATT-TTA
*
661 AAGTTTA
1 AATTTTA
668 AA-TTTA
1 AATTTTA
674 AAT
1 AAT
677 AAATTTAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
6 6 0.18
7 22 0.67
8 5 0.15
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (7 bp):
AATTTTA
Found at i:673 original size:6 final size:6
Alignment explanation
Indices: 635--744 Score: 67
Period size: 6 Copynumber: 19.5 Consensus size: 6
625 GGAATCCAAT
*
635 TTTAAA TTTTAAA TTTTAAA -TT--A TTTAAG TTTAAA TTTAAA --TAAA
1 TTTAAA -TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * * * *
680 TTTAAA CTT-AT TTTGAG TTTGAA TTT-AT TTTAAA TTTAAA TTT-AT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
725 TTTAAA -TTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTT
745 TAAAAGTCCA
Statistics
Matches: 83, Mismatches: 11, Indels: 19
0.73 0.10 0.17
Matches are distributed among these distances:
3 1 0.01
4 6 0.07
5 18 0.22
6 45 0.54
7 13 0.16
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:682 original size:22 final size:22
Alignment explanation
Indices: 642--684 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
632 AATTTTAAAT
*
642 TTTAAATTTTAAATTATTTAAG
1 TTTAAATTTTAAATAATTTAAG
664 TTTAAA-TTTAAATAAATTTAA
1 TTTAAATTTTAAAT-AATTTAA
685 ACTTATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TTTAAATTTTAAATAATTTAAG
Found at i:736 original size:16 final size:17
Alignment explanation
Indices: 640--739 Score: 100
Period size: 17 Copynumber: 6.1 Consensus size: 17
630 CCAATTTTAA
640 ATTTTAAATTTTAAA-TT
1 ATTTTAAA-TTTAAATTT
*
657 A-TTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
** *
673 A-AATAAATTTAAACTT
1 ATTTTAAATTTAAATTT
* * *
689 ATTTTGAGTTTGAATTT
1 ATTTTAAATTTAAATTT
706 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
723 ATTTTAAA-TTAAATTT
1 ATTTTAAATTTAAATTT
739 A
1 A
740 AATTTTAAAA
Statistics
Matches: 67, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
15 6 0.09
16 29 0.43
17 32 0.48
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:765 original size:23 final size:23
Alignment explanation
Indices: 739--786 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
729 AATTAAATTT
*
739 AAATTTTAAAAGTCCAAATACAA
1 AAATTCTAAAAGTCCAAATACAA
*
762 AAATTCTAAAAGTCCAAATCCAA
1 AAATTCTAAAAGTCCAAATACAA
785 AA
1 AA
787 TCCAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.56, C:0.17, G:0.04, T:0.23
Consensus pattern (23 bp):
AAATTCTAAAAGTCCAAATACAA
Found at i:1341 original size:15 final size:13
Alignment explanation
Indices: 1309--1373 Score: 60
Period size: 13 Copynumber: 4.8 Consensus size: 13
1299 CTAAACGTTT
1309 TAATAAATAAATA
1 TAATAAATAAATA
*
1322 TAATAAATATACTAA
1 TAATAAATA-AAT-A
*
1337 TAATAAATAAGTA
1 TAATAAATAAATA
*
1350 TAAT-ATTAAATAGA
1 TAATAAATAAAT--A
1364 TAATAAATAA
1 TAATAAATAA
1374 TAATAAAAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
12 5 0.12
13 14 0.33
14 9 0.21
15 14 0.33
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (13 bp):
TAATAAATAAATA
Found at i:2498 original size:30 final size:29
Alignment explanation
Indices: 2458--2564 Score: 108
Period size: 30 Copynumber: 3.6 Consensus size: 29
2448 TAACTTTTCT
2458 AAAATCACATTTTGACCCCCGAACTTCTTA
1 AAAAT-ACATTTTGACCCCCGAACTTCTTA
* *
2488 AAAAGTACATTTTTACTCCCGAACTTCTTA
1 AAAA-TACATTTTGACCCCCGAACTTCTTA
* * ** *
2518 AAAATTACTTTTTTACCCTTGAACTTCCT-
1 AAAA-TACATTTTGACCCCCGAACTTCTTA
2547 AAAATCACATTTTGACCC
1 AAAAT-ACATTTTGACCC
2565 TTAAACTTCT
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
28 1 0.02
29 14 0.22
30 49 0.75
31 1 0.02
ACGTcount: A:0.33, C:0.26, G:0.06, T:0.36
Consensus pattern (29 bp):
AAAATACATTTTGACCCCCGAACTTCTTA
Found at i:2614 original size:25 final size:26
Alignment explanation
Indices: 2573--2654 Score: 78
Period size: 26 Copynumber: 3.1 Consensus size: 26
2563 CCTTAAACTT
2573 CTAAAAATTAGATTTTTGCCCCCAAA
1 CTAAAAATTAGATTTTTGCCCCCAAA
*
2599 CTAAAAATT-GCATTTTT-CTCCCAAA
1 CTAAAAATTAG-ATTTTTGCCCCCAAA
* * *
2624 CTTCTAAAAATTACATTTTTACCCTCAAA
1 ---CTAAAAATTAGATTTTTGCCCCCAAA
2653 CT
1 CT
2655 TCCAAAGATC
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
25 8 0.17
26 17 0.37
28 15 0.33
29 6 0.13
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (26 bp):
CTAAAAATTAGATTTTTGCCCCCAAA
Found at i:2668 original size:29 final size:28
Alignment explanation
Indices: 2415--2739 Score: 148
Period size: 29 Copynumber: 11.4 Consensus size: 28
2405 CATATCTTGA
*
2415 ACCC-CAAACTTTCCAAAATTACATTTTA
1 ACCCTCAAAC-TTCCAAAATTACATTTTT
* * * *
2443 ACCCT-TAACTTTTCTAAAATCACATTTTG
1 ACCCTCAAAC--TTCCAAAATTACATTTTT
* * * *
2472 ACCCCCGAACTTCTTAAAAAGTACATTTTT
1 ACCCTCAAACTTC--CAAAATTACATTTTT
* * *
2502 ACTCC-CGAACTTCTTAAAAATTACTTTTTT
1 AC-CCTCAAACTTC--CAAAATTACATTTTT
** * *
2532 ACCCTTGAACTTCCTAAAATCACATTTTG
1 ACCCTCAAACTTCC-AAAATTACATTTTT
* * *
2561 ACCCTTAAACTTCTAAAAATTAGATTTTT
1 ACCCTCAAACTTC-CAAAATTACATTTTT
* * * *
2590 GCCCCCAAAC-T-AAAAATTGCATTTTT
1 ACCCTCAAACTTCCAAAATTACATTTTT
*
2616 -CTCC-CAAACTTCTAAAAATTACATTTTT
1 AC-CCTCAAACTTC-CAAAATTACATTTTT
* * *
2644 ACCCTCAAACTTCCAAAGATCACATGTCT
1 ACCCTCAAACTTCCAAA-ATTACATTTTT
* *
2673 A-CCTCGAACTTCCCCAAAATGACA-TTTT
1 ACCCTCAAACTT--CCAAAATTACATTTTT
* * *
2701 CCCCTAAAACTTTCCAAAATTACATTTTA
1 ACCCTCAAAC-TTCCAAAATTACATTTTT
2730 ACCC-CAAACT
1 ACCCTCAAACT
2740 CTTC
Statistics
Matches: 233, Mismatches: 43, Indels: 43
0.73 0.13 0.13
Matches are distributed among these distances:
25 6 0.03
26 16 0.07
27 1 0.00
28 55 0.24
29 98 0.42
30 55 0.24
31 2 0.01
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.34
Consensus pattern (28 bp):
ACCCTCAAACTTCCAAAATTACATTTTT
Done.