Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005010.1 Kokia drynarioides strain JFW-HI SEQ_118769, 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: 44854
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:5908 original size:15 final size:15
Alignment explanation
Indices: 5888--5919 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
5878 ATTGAAGGAC
5888 TAAGCATAATTTAAG
1 TAAGCATAATTTAAG
5903 TAAGCATAATTTAAG
1 TAAGCATAATTTAAG
5918 TA
1 TA
5920 CGGACTGGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.34
Consensus pattern (15 bp):
TAAGCATAATTTAAG
Found at i:15742 original size:15 final size:15
Alignment explanation
Indices: 15704--15740 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
15694 TGCAACAAGA
15704 TTTATTTTACTTTAT
1 TTTATTTTACTTTAT
*
15719 TTTATTTTA-TTTGT
1 TTTATTTTACTTTAT
15733 TTTATTTT
1 TTTATTTT
15741 TAGTTTAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.78
Consensus pattern (15 bp):
TTTATTTTACTTTAT
Found at i:22648 original size:14 final size:14
Alignment explanation
Indices: 22629--22656 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
22619 AATTCTCAAA
22629 ACTTCAACAACAAT
1 ACTTCAACAACAAT
22643 ACTTCAACAACAAT
1 ACTTCAACAACAAT
22657 TTGATTTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (14 bp):
ACTTCAACAACAAT
Found at i:36540 original size:37 final size:38
Alignment explanation
Indices: 36489--36573 Score: 109
Period size: 38 Copynumber: 2.3 Consensus size: 38
36479 AATAAACTTT
* *
36489 TAATCCTAGCCCTAGATATAAA-CCTAAAGATATCTTA
1 TAATCCTAGCCCTAGATATAAATCCTAAAGATAACTAA
* * * *
36526 TAATCCTTGTCCTAGATTTAAATCCTAAAGGTAACTAA
1 TAATCCTAGCCCTAGATATAAATCCTAAAGATAACTAA
36564 TAATCCTAGC
1 TAATCCTAGC
36574 TATCTATCTA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
37 19 0.49
38 20 0.51
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (38 bp):
TAATCCTAGCCCTAGATATAAATCCTAAAGATAACTAA
Found at i:36626 original size:16 final size:15
Alignment explanation
Indices: 36592--36630 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
36582 TATATGTCTA
*
36592 ATAAT-AAATAAGAC
1 ATAATAAAATAACAC
36606 ATAATAAAATAACATC
1 ATAATAAAATAACA-C
36622 ATAATAAAA
1 ATAATAAAA
36631 AAGCTTACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.23
15 7 0.32
16 10 0.45
ACGTcount: A:0.67, C:0.08, G:0.03, T:0.23
Consensus pattern (15 bp):
ATAATAAAATAACAC
Found at i:40111 original size:32 final size:32
Alignment explanation
Indices: 40075--40136 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
40065 ATTGAAAAAG
*
40075 AGTTTAGGTATCAAATTGAAAAAAAAAAAATC
1 AGTTTAGATATCAAATTGAAAAAAAAAAAATC
* * *
40107 AGTTTAGATATTAAATTGGAATAAAAAAAA
1 AGTTTAGATATCAAATTGAAAAAAAAAAAA
40137 CTTAATTACT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.56, C:0.03, G:0.13, T:0.27
Consensus pattern (32 bp):
AGTTTAGATATCAAATTGAAAAAAAAAAAATC
Found at i:40868 original size:19 final size:20
Alignment explanation
Indices: 40837--40885 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
40827 TTAAATATAA
*
40837 ATTTTGAAATTTTTATAAA-T
1 ATTTTG-AATTTTTAAAAATT
40857 ATTTTGAA-TTTTAAAAATT
1 ATTTTGAATTTTTAAAAATT
40876 ATTTTGAATT
1 ATTTTGAATT
40886 ACTTTGTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 8 0.31
19 11 0.42
20 7 0.27
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (20 bp):
ATTTTGAATTTTTAAAAATT
Found at i:44388 original size:15 final size:16
Alignment explanation
Indices: 44368--44397 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
44358 AAGGAAACAA
44368 AGAAAA-GAAAAAGAG
1 AGAAAATGAAAAAGAG
44383 AGAAAATGAAAAAGA
1 AGAAAATGAAAAAGA
44398 AAATAAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.03
Consensus pattern (16 bp):
AGAAAATGAAAAAGAG
Found at i:44400 original size:12 final size:11
Alignment explanation
Indices: 44370--44411 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
44360 GGAAACAAAG
44370 AAAAGAAAA-A
1 AAAAGAAAATA
* *
44380 GAGAGAAAATGA
1 AAAAGAAAAT-A
44392 AAAAGAAAATA
1 AAAAGAAAATA
44403 AAAAGAAAA
1 AAAAGAAAA
44412 AAGAGGTACA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 7 0.27
11 10 0.38
12 9 0.35
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.05
Consensus pattern (11 bp):
AAAAGAAAATA
Done.