Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002310.1 Kokia drynarioides strain JFW-HI SEQ_114351, 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: 30959
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:2548 original size:6 final size:6
Alignment explanation
Indices: 2531--2564 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
2521 AAAANNNAAA
*
2531 AAAAACT AAAAAT GAAAAT AAAAAT AAAAAT AAA
1 AAAAA-T AAAAAT AAAAAT AAAAAT AAAAAT AAA
2565 TGTACTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:4761 original size:9 final size:9
Alignment explanation
Indices: 4747--4775 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
4737 GAACAACATG
4747 ATCAATAAA
1 ATCAATAAA
4756 ATCAATAAA
1 ATCAATAAA
4765 ATCAATAAA
1 ATCAATAAA
4774 AT
1 AT
4776 AACATGAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.66, C:0.10, G:0.00, T:0.24
Consensus pattern (9 bp):
ATCAATAAA
Found at i:4785 original size:18 final size:18
Alignment explanation
Indices: 4741--4786 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
4731 AATTTTGAAC
4741 AACATG-ATCAATAAAAT
1 AACATGAATCAATAAAAT
* *
4758 CA-ATAAAATCAATAAAAT
1 AACAT-GAATCAATAAAAT
4776 AACATGAATCA
1 AACATGAATCA
4787 TCTTGCTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 5
0.71 0.13 0.16
Matches are distributed among these distances:
16 2 0.09
17 1 0.05
18 17 0.77
19 2 0.09
ACGTcount: A:0.61, C:0.13, G:0.04, T:0.22
Consensus pattern (18 bp):
AACATGAATCAATAAAAT
Found at i:8151 original size:25 final size:23
Alignment explanation
Indices: 8123--8168 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
8113 GTTGGATCCA
8123 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
8148 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
8169 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:10520 original size:94 final size:94
Alignment explanation
Indices: 10394--10565 Score: 256
Period size: 94 Copynumber: 1.8 Consensus size: 94
10384 GATAAAAAGG
* * *
10394 GGATTTGATATATTCTTTATCAAGTAAGGAAATAAAATTTAATTATTATTTAAAAGAGTTTTAGA
1 GGATTTGAGATATTCCTTATCAAGTAAGGAAATAAAATTTAATTATTATTTAAAAGAGGTTTAGA
*
10459 TAAATAATAATTAAAATTCAAAATCAAAT
66 TAAATAACAATTAAAATTCAAAATCAAAT
* * *
10488 GGATTTGAGATATTCCTTAT-GAGATAATGAAATAGAATTTAATTATTATTTAAAAGAGGTTTAG
1 GGATTTGAGATATTCCTTATCAAG-TAAGGAAATAAAATTTAATTATTATTTAAAAGAGGTTTAG
*
10552 ATAAGTAACAATTA
65 ATAAATAACAATTA
10566 TATTGTTATT
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
93 2 0.03
94 67 0.97
ACGTcount: A:0.45, C:0.04, G:0.13, T:0.38
Consensus pattern (94 bp):
GGATTTGAGATATTCCTTATCAAGTAAGGAAATAAAATTTAATTATTATTTAAAAGAGGTTTAGA
TAAATAACAATTAAAATTCAAAATCAAAT
Found at i:10615 original size:38 final size:38
Alignment explanation
Indices: 10535--10616 Score: 94
Period size: 38 Copynumber: 2.2 Consensus size: 38
10525 TTTAATTATT
* * * *
10535 ATTTAAAAGAGGTTTAGATAAGTAACAATTATATTGTT
1 ATTTAAAAGAGGTTTAGATAAATAACAATTAAATAGTA
* *
10573 ATTTAAAAGAGTTTTAGATAAATAATAATTAAAATAG-A
1 ATTTAAAAGAGGTTTAGATAAATAACAATT-AAATAGTA
10611 ATTTAA
1 ATTTAA
10617 TTATTATTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
38 33 0.89
39 4 0.11
ACGTcount: A:0.49, C:0.01, G:0.12, T:0.38
Consensus pattern (38 bp):
ATTTAAAAGAGGTTTAGATAAATAACAATTAAATAGTA
Found at i:10624 original size:49 final size:50
Alignment explanation
Indices: 10571--10684 Score: 126
Period size: 54 Copynumber: 2.2 Consensus size: 50
10561 AATTATATTG
*
10571 TTATTTAAAA-GAGTTTT-AGAT-AAATAATAATTAAAATAGAATTTAATTATTA
1 TTATTTAAAAGGAGTTTTGA-ATAAAAT-ATAATT-AAATAAAATTTAA--ATTA
*
10623 TTATTATTTAAAGGAGTTTTGAATAAAATATAATTAAATAAAATTTAAATTA
1 TTA-T-TTAAAAGGAGTTTTGAATAAAATATAATTAAATAAAATTTAAATTA
10675 TTATTTAAAA
1 TTATTTAAAA
10685 TAATTTTTTA
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
50 5 0.09
51 1 0.02
52 10 0.19
53 1 0.02
54 17 0.31
55 15 0.28
56 5 0.09
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (50 bp):
TTATTTAAAAGGAGTTTTGAATAAAATATAATTAAATAAAATTTAAATTA
Found at i:10668 original size:54 final size:56
Alignment explanation
Indices: 10561--10679 Score: 158
Period size: 55 Copynumber: 2.2 Consensus size: 56
10551 GATAAGTAAC
* *
10561 AATTA-TATTGTTATTTAAAAGAGTTTTAGATAAATAATAATTAAAATAGAATTT-
1 AATTATTATTATTATTTAAAAGAGTTTTAGATAAATAATAATTAAAATAAAATTTA
*
10615 AATTATTATTATTATTTAAAGGAGTTTT-GAATAAA-ATATAATT-AAATAAAATTTA
1 AATTATTATTATTATTTAAAAGAGTTTTAG-ATAAATA-ATAATTAAAATAAAATTTA
10670 AATTATTATT
1 AATTATTATT
10680 TAAAATAATT
Statistics
Matches: 58, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
54 17 0.29
55 41 0.71
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.45
Consensus pattern (56 bp):
AATTATTATTATTATTTAAAAGAGTTTTAGATAAATAATAATTAAAATAAAATTTA
Found at i:21809 original size:24 final size:24
Alignment explanation
Indices: 21775--21821 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
21765 TTTCATCTTT
*
21775 TATTAATTTGCTCTGAC-ATTTTA
1 TATTAATTTGCACTGACAATTTTA
21798 TATTATATTTGCACTGACAATTTT
1 TATTA-ATTTGCACTGACAATTTT
21822 TACCCTTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 11 0.52
25 5 0.24
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.51
Consensus pattern (24 bp):
TATTAATTTGCACTGACAATTTTA
Found at i:29583 original size:12 final size:12
Alignment explanation
Indices: 29581--29615 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
29571 AAGCAAGAGA
*
29581 AGAAGGAGAAAG
1 AGAAGAAGAAAG
29593 AGAAGAAGAAAG
1 AGAAGAAGAAAG
29605 AGAAGAAGAAA
1 AGAAGAAGAAA
29616 AATTTGCCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (12 bp):
AGAAGAAGAAAG
Found at i:29595 original size:15 final size:14
Alignment explanation
Indices: 29575--29613 Score: 55
Period size: 12 Copynumber: 2.9 Consensus size: 14
29565 ACAAAGAAGC
29575 AAGAGAAGAAGGAGA
1 AAGAGAAGAA-GAGA
29590 AAGAGAAG-A-AGA
1 AAGAGAAGAAGAGA
29602 AAGAGAAGAAGA
1 AAGAGAAGAAGA
29614 AAAATTTGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 11 0.50
13 1 0.05
14 2 0.09
15 8 0.36
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (14 bp):
AAGAGAAGAAGAGA
Found at i:29614 original size:15 final size:14
Alignment explanation
Indices: 29568--29614 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
29558 GAAGTCGACA
29568 AAGAAGCAAGAGAAG
1 AAGAAG-AAGAGAAG
*
29583 AAGGAGAA-AG-AG
1 AAGAAGAAGAGAAG
29595 AAGAAGAAAGAGAAG
1 AAGAAG-AAGAGAAG
29610 AAGAA
1 AAGAA
29615 AAATTTGCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
12 7 0.26
13 4 0.15
14 4 0.15
15 12 0.44
ACGTcount: A:0.64, C:0.02, G:0.34, T:0.00
Consensus pattern (14 bp):
AAGAAGAAGAGAAG
Found at i:30035 original size:17 final size:17
Alignment explanation
Indices: 30015--30051 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
30005 TTTTATTTAA
*
30015 ATTGTCATTGCATTTTT
1 ATTGTCACTGCATTTTT
*
30032 ATTGTCCCTGCATTTTT
1 ATTGTCACTGCATTTTT
30049 ATT
1 ATT
30052 TGTTTTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.16, C:0.16, G:0.11, T:0.57
Consensus pattern (17 bp):
ATTGTCACTGCATTTTT
Done.