Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002839.1 Kokia drynarioides strain JFW-HI SEQ_115214, 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: 12749
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:612 original size:7 final size:8
Alignment explanation
Indices: 596--625 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
586 TTAATTAAAA
596 TTTTATTT
1 TTTTATTT
604 TTTTATTT
1 TTTTATTT
612 TTTTATTT
1 TTTTATTT
620 TTTTAT
1 TTTTAT
626 AAGTTACTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTATTT
Found at i:1189 original size:18 final size:18
Alignment explanation
Indices: 1157--1208 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
1147 ATGGGATGAG
1157 AATAAATTT--TTAATTA
1 AATAAATTTAATTAATTA
*
1173 AATAAATTTAATTAATTG
1 AATAAATTTAATTAATTA
*
1191 AA-AATTTTAAATTAATTA
1 AATAAATTT-AATTAATTA
1209 TAACTGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 9 0.30
17 5 0.17
18 16 0.53
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
AATAAATTTAATTAATTA
Found at i:4657 original size:66 final size:62
Alignment explanation
Indices: 4555--4719 Score: 237
Period size: 66 Copynumber: 2.6 Consensus size: 62
4545 GGTCTGTTAT
4555 TTATTTATTTATATTCAT-AA-AATAATAAATAAATAATAAAACAAAATTAATATTATTTTACA
1 TTATTTATTTATATTCATAAATAATAATAAATAAATAATAAAACAAAATTAATATTATTTT--A
*
4617 TTATTTATTTATATTCATACAATAATAAATAAATAAATAATAAAATAAAATTAATATTATTTTA
1 TTATTTATTTATATTCATA-AATAAT-AATAAATAAATAATAAAACAAAATTAATATTATTTTA
*
4681 -TATTTATTTATATTTATAAAAATAATAATAAATAAATAA
1 TTATTTATTTATATTCAT--AAATAATAATAAATAAATAA
4720 ATAATAATAA
Statistics
Matches: 95, Mismatches: 2, Indels: 11
0.88 0.02 0.10
Matches are distributed among these distances:
62 18 0.19
63 29 0.31
64 9 0.09
65 4 0.04
66 35 0.37
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (62 bp):
TTATTTATTTATATTCATAAATAATAATAAATAAATAATAAAACAAAATTAATATTATTTTA
Found at i:5363 original size:39 final size:39
Alignment explanation
Indices: 5257--5365 Score: 114
Period size: 40 Copynumber: 2.8 Consensus size: 39
5247 ATAGTTTTAG
** *
5257 GGGTAAAAGATTGGATTATTTCAATCTACTCCATGGTCA
1 GGGTAAAAGATTGGATTGCTTCAATCTGCTCCATGGTCA
* * * *
5296 GGGTAAGAGATCT-GATGGTCTTCAATCTGC-CCTCTGGTTA
1 GGGTAAAAGAT-TGGATTG-CTTCAATCTGCTCC-ATGGTCA
5336 GGGTAAAAGATTGGATTGCTTCAATCTGCT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCT
5366 GAATGGTCTT
Statistics
Matches: 56, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
39 27 0.48
40 29 0.52
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.33
Consensus pattern (39 bp):
GGGTAAAAGATTGGATTGCTTCAATCTGCTCCATGGTCA
Found at i:5400 original size:58 final size:58
Alignment explanation
Indices: 5310--5420 Score: 197
Period size: 58 Copynumber: 1.9 Consensus size: 58
5300 AAGAGATCTG
*
5310 ATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATTGCTTCAATCTGCTGA
1 ATGGTCTTCAATCTACCCTCTGGTTAGGGTAAAAGATTGGATTGCTTCAATCTGCTGA
5368 ATGGTCTTCAATCTACCCTCTGGTT-GAGGTAAAAGATTGGATTGCTTCAATCT
1 ATGGTCTTCAATCTACCCTCTGGTTAG-GGTAAAAGATTGGATTGCTTCAATCT
5421 ACCCCATAGT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
57 1 0.02
58 50 0.98
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (58 bp):
ATGGTCTTCAATCTACCCTCTGGTTAGGGTAAAAGATTGGATTGCTTCAATCTGCTGA
Found at i:5532 original size:80 final size:80
Alignment explanation
Indices: 5395--6486 Score: 1607
Period size: 80 Copynumber: 13.7 Consensus size: 80
5385 CTCTGGTTGA
* * * * * *
5395 GGTAAAAGATTGGATTG-CTTCAATC-TACCC-CATAGTTGGGGGAAAAGATTGGATTTCTTCAA
1 GGTAAAAGATCGGATGGTCTTCAATCTTGCCCTC-TGGTTAGGGTAAAAGATTGGATTTCTTCAA
5457 TCTGCCCCATGATCGG
65 TCTGCCCCATGATCGG
* * * *
5473 GGTGAAAGATTGGATGGTCTTCAATCTTGCCCTTTAGTTAGGGTAAAAGATTGGATTTCTTCAAT
1 GGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAAT
*
5538 CTGTCCCATGATCGG
66 CTGCCCCATGATCGG
*
5553 GGTAAAAGATCGGATGGTCTTCAATGTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAAT
1 GGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAAT
*
5618 CTGCCTCATGATCGG
66 CTGCCCCATGATCGG
* * * *
5633 GGTAAAAGATCGAATGGTGTTCAATCTTGCCCTCTAGTTAGGCTAAAAGATTGGATTTCTTCAAT
1 GGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAAT
* *
5698 TTGCCCCATGATTGG
66 CTGCCCCATGATCGG
** * * *
5713 GGTAAAAGATCAAATGATCTTCAATCTTGCCTTCTGGTTAGGCTAAAAGATTGGATTTCTTCAAT
1 GGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAAT
*
5778 CTGCCTCATGATCGG
66 CTGCCCCATGATCGG
* * * *
5793 GGTAAAAGATCGAATGGTCTTCAATCTTACCCTCTAGTTAGGTTAAAAGATTGGATTTCTTCAAT
1 GGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAAT
*
5858 CTACCCCAT-ATCGG
66 CTGCCCCATGATCGG
*
5872 GGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGAGTAAAAGATTGGATTTCTTCAAT
1 GGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAAT
*
5937 TTGCCCCATGATCGG
66 CTGCCCCATGATCGG
* *
5952 GGTAAAAGATCGGATGGTCTTCAATGTTGCCCTCTGGTTAGGGTAAAAGATTGAATTTCTTCAAT
1 GGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAAT
* * *
6017 CTGTCCAATGATCGT
66 CTGCCCCATGATCGG
* *
6032 GGTAAAAGATCGGATGGTCTTCAATGTTGCCCTCTGGTTAGGGTAAAAGATTGAATTTCTTCAAT
1 GGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAAT
*
6097 CTGCCCCATGATCGA
66 CTGCCCCATGATCGG
6112 GGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAAT
1 GGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAAT
* *
6177 CTGCCTCATGATCGA
66 CTGCCCCATGATCGG
* *
6192 GGTAAAAGATCGGATGATCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTTGATTTCTTCAAT
1 GGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAAT
* *
6257 CTTCCTCATGATCGG
66 CTGCCCCATGATCGG
* * * *
6272 GGTAAAAGATCGGATGGTCTTTAATCTTGCCCTCTGTTTAGGATAAAAGATTGGATTTCTTTAAT
1 GGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAAT
*
6337 CTGCCCTATGATCGG
66 CTGCCCCATGATCGG
* * * * * *
6352 GGTAAAAGATTGGATGATCTTCAATCTTACCCTCTAGTTAAGGTAAAAGATTAGATTTCTTCAAT
1 GGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAAT
* *
6417 CTGTCCCATGATTGG
66 CTGCCCCATGATCGG
*
6432 GGTAAAAGATCGGATGGTTTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGA
1 GGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGA
6487 GGTTGTAACT
Statistics
Matches: 919, Mismatches: 91, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
78 15 0.02
79 80 0.09
80 824 0.90
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (80 bp):
GGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAAT
CTGCCCCATGATCGG
Found at i:6604 original size:50 final size:50
Alignment explanation
Indices: 6540--6715 Score: 201
Period size: 50 Copynumber: 3.5 Consensus size: 50
6530 ATCCTTGTGA
* * * * *
6540 CTTCAATCTTCTCCTCTACAGCTTTAAGTGAATGAGATTTGCCATTACAG
1 CTTCAATCTGCACCTCTACAGCTTTAAGTGTATGAGATTTGTCATTGCAG
* * * **
6590 CTTCATTCTGCTCCTCTACAGCTTTAAGTGTATAAGATTTGTTGTTGCAG
1 CTTCAATCTGCACCTCTACAGCTTTAAGTGTATGAGATTTGTCATTGCAG
* * **
6640 TTTCAATCTGCACCTCCACAGCTTTTGGTGTATGAGATTTGTCATTGCAG
1 CTTCAATCTGCACCTCTACAGCTTTAAGTGTATGAGATTTGTCATTGCAG
*
6690 TTTCAATCTGCACCTAC-ACAGCTTTA
1 CTTCAATCTGCACCT-CTACAGCTTTA
6716 GGAGTAAAAG
Statistics
Matches: 107, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
50 106 0.99
51 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (50 bp):
CTTCAATCTGCACCTCTACAGCTTTAAGTGTATGAGATTTGTCATTGCAG
Found at i:6700 original size:100 final size:100
Alignment explanation
Indices: 6541--6735 Score: 248
Period size: 100 Copynumber: 1.9 Consensus size: 100
6531 TCCTTGTGAC
* * * * *
6541 TTCAATCTTCTCCTCTACAGCTTTAAGTGAATGAGATTTGCCATTACAGCTTCATTCTGCTCCT-
1 TTCAATCTGCACCTCCACAGCTTTAAGTGAATGAGATTTGCCATTACAGCTTCAATCTGCACCTA
* *
6605 CTACAGCTTTAAGTGTATAAGATTTGTTGTTGCAGT
66 C-ACAGCTTTAAGAGTAAAAGATTTGTTGTTGCAGT
** * * * *
6641 TTCAATCTGCACCTCCACAGCTTTTGGTGTATGAGATTTGTCATTGCAGTTTCAATCTGCACCTA
1 TTCAATCTGCACCTCCACAGCTTTAAGTGAATGAGATTTGCCATTACAGCTTCAATCTGCACCTA
*
6706 CACAGCTTTAGGAGTAAAAGATTTGTTGTT
66 CACAGCTTTAAGAGTAAAAGATTTGTTGTT
6736 CTATCACCAC
Statistics
Matches: 80, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
100 79 0.99
101 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (100 bp):
TTCAATCTGCACCTCCACAGCTTTAAGTGAATGAGATTTGCCATTACAGCTTCAATCTGCACCTA
CACAGCTTTAAGAGTAAAAGATTTGTTGTTGCAGT
Found at i:6798 original size:12 final size:12
Alignment explanation
Indices: 6781--6808 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
6771 TTGTTTTATG
6781 GGCCTCTATCTA
1 GGCCTCTATCTA
6793 GGCCTCTATCTA
1 GGCCTCTATCTA
6805 GGCC
1 GGCC
6809 ATGTAACTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.36, G:0.21, T:0.29
Consensus pattern (12 bp):
GGCCTCTATCTA
Found at i:7682 original size:21 final size:20
Alignment explanation
Indices: 7658--7721 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
7648 CCTTTTTTTA
7658 TTTTCTTATTTTTACTTGTCT
1 TTTTCTTATTTTT-CTTGTCT
*
7679 TTTTCTCT-TTTTTCCTT-TTT
1 TTTTCT-TATTTTT-CTTGTCT
* *
7699 TTTTTTTAATTTT-TTGTCT
1 TTTTCTTATTTTTCTTGTCT
7718 TTTT
1 TTTT
7722 TTTTTAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
18 2 0.06
19 7 0.20
20 11 0.31
21 14 0.40
22 1 0.03
ACGTcount: A:0.06, C:0.12, G:0.03, T:0.78
Consensus pattern (20 bp):
TTTTCTTATTTTTCTTGTCT
Done.