Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008692.1 Kokia drynarioides strain JFW-HI SEQ_123374, 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: 76308
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 30 characters in sequence are not A, C, G, or T
Found at i:2049 original size:3 final size:3
Alignment explanation
Indices: 2041--2081 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2031 ATTGAACCAA
2041 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
2082 TATTATTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:2086 original size:3 final size:3
Alignment explanation
Indices: 2080--2106 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2070 CATCATCATC
2080 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
2107 TAAGTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2756 original size:18 final size:18
Alignment explanation
Indices: 2716--2758 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2706 TTTTCAATTG
2716 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
2734 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
2752 TAATTAA
1 TAATTAA
2759 AAAATTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:3065 original size:18 final size:18
Alignment explanation
Indices: 3042--3078 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3032 CTAAACTATT
3042 ATTTTAATATTT-TTATAC
1 ATTTTAAT-TTTATTATAC
3060 ATTTTAATTTTATTATAC
1 ATTTTAATTTTATTATAC
3078 A
1 A
3079 CACTTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTTAATTTTATTATAC
Found at i:7151 original size:24 final size:25
Alignment explanation
Indices: 7114--7160 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
7104 TGATCAGATT
* *
7114 TTTTATTATAAATATATTAAAATCA
1 TTTTATTATAAATAAAATAAAATCA
7139 TTTT-TTATAAATAAAATAAAAT
1 TTTTATTATAAATAAAATAAAAT
7161 ATTATTTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
TTTTATTATAAATAAAATAAAATCA
Found at i:8576 original size:23 final size:23
Alignment explanation
Indices: 8549--8601 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
8539 AGATTTATTT
*
8549 TTATTTAATTT-TTTTTTTAAAAA
1 TTATTTAATTTACTTTTTT-AAAA
* *
8572 TTATTAAATTTACTTTTTTAATA
1 TTATTTAATTTACTTTTTTAAAA
8595 TTATTTA
1 TTATTTA
8602 CCCTAAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (23 bp):
TTATTTAATTTACTTTTTTAAAA
Found at i:16677 original size:7 final size:7
Alignment explanation
Indices: 16665--16690 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
16655 AAGGTAATGA
16665 GAAGATT
1 GAAGATT
16672 GAAGATT
1 GAAGATT
16679 GAAGATT
1 GAAGATT
16686 GAAGA
1 GAAGA
16691 AAGACAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (7 bp):
GAAGATT
Found at i:16717 original size:5 final size:5
Alignment explanation
Indices: 16699--16734 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
16689 GAAAGACAAA
16699 TGAA- TGAA- TGAAG TGAAG TGAAG TGAAG TGAAG TGA
1 TGAAG TGAAG TGAAG TGAAG TGAAG TGAAG TGAAG TGA
16735 TGGAGGTCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 8 0.26
5 23 0.74
ACGTcount: A:0.42, C:0.00, G:0.36, T:0.22
Consensus pattern (5 bp):
TGAAG
Found at i:20505 original size:16 final size:16
Alignment explanation
Indices: 20484--20514 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
20474 TCAACTGATA
20484 TTCTTTTTTTTTTTTT
1 TTCTTTTTTTTTTTTT
20500 TTCTTTTTTTTTTTT
1 TTCTTTTTTTTTTTT
20515 GATTTGTCGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (16 bp):
TTCTTTTTTTTTTTTT
Found at i:20508 original size:13 final size:13
Alignment explanation
Indices: 20490--20514 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20480 GATATTCTTT
20490 TTTTTTTTTTTTC
1 TTTTTTTTTTTTC
20503 TTTTTTTTTTTT
1 TTTTTTTTTTTT
20515 GATTTGTCGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.04, G:0.00, T:0.96
Consensus pattern (13 bp):
TTTTTTTTTTTTC
Found at i:22338 original size:19 final size:19
Alignment explanation
Indices: 22301--22344 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
22291 AAACACAGGT
*
22301 GCTTAATTTTATTATTTTA
1 GCTTAATTTTATAATTTTA
22320 GCTT-ATTTTATAATATTTA
1 GCTTAATTTTATAAT-TTTA
*
22339 GGTTAA
1 GCTTAA
22345 GTATTAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 9 0.43
19 11 0.52
20 1 0.05
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.57
Consensus pattern (19 bp):
GCTTAATTTTATAATTTTA
Found at i:34594 original size:11 final size:11
Alignment explanation
Indices: 34578--34628 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
34568 TTTTTAAAAA
34578 TTCTTTTATTT
1 TTCTTTTATTT
34589 TTCTTTTTATTT
1 TTC-TTTTATTT
34601 TT-TTTCTATTT
1 TTCTTT-TATTT
* *
34612 TTTTTTTCTTT
1 TTCTTTTATTT
34623 CTTCTT
1 -TTCTT
34629 CTTTTATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
10 3 0.09
11 14 0.41
12 17 0.50
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (11 bp):
TTCTTTTATTT
Found at i:34596 original size:12 final size:11
Alignment explanation
Indices: 34581--34618 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
34571 TTAAAAATTC
34581 TTTTATTTTTCT
1 TTTTATTTTT-T
34593 TTTTATTTTTT
1 TTTTATTTTTT
*
34604 TTCTATTTTTT
1 TTTTATTTTTT
34615 TTTT
1 TTTT
34619 CTTTCTTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.08, C:0.05, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTATTTTTT
Found at i:34601 original size:17 final size:15
Alignment explanation
Indices: 34581--34625 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
34571 TTAAAAATTC
*
34581 TTTTATTTTTCTTTT
1 TTTTTTTTTTCTTTT
*
34596 TATTTTTTTTCTATTT
1 TTTTTTTTTTCT-TTT
34612 TTTTTTTCTTTCTT
1 TTTTTTT-TTTCTT
34626 CTTCTTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 10 0.40
16 10 0.40
17 5 0.20
ACGTcount: A:0.07, C:0.09, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTTTTTTCTTTT
Found at i:34630 original size:23 final size:23
Alignment explanation
Indices: 34578--34630 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
34568 TTTTTAAAAA
*
34578 TTCTTTTATTTTTCTTTTTATTT
1 TTCTTCTATTTTTCTTTTTATTT
* *
34601 TTTTTCTATTTTT-TTTTTCTTT
1 TTCTTCTATTTTTCTTTTTATTT
34623 CTTCTTCT
1 -TTCTTCT
34631 TTTATAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (23 bp):
TTCTTCTATTTTTCTTTTTATTT
Found at i:46680 original size:19 final size:19
Alignment explanation
Indices: 46656--46736 Score: 69
Period size: 20 Copynumber: 4.4 Consensus size: 19
46646 TTGAAATTTT
46656 TTTTTATATATTTTTATAA
1 TTTTTATATATTTTTATAA
* * *
46675 TTTTTAAATTATTTTCATTA
1 TTTTTATA-TATTTTTATAA
*
46695 TTTTTAT-T-TTTTAATAA
1 TTTTTATATATTTTTATAA
** *
46712 AATTTATATA-TTTTATTA
1 TTTTTATATATTTTTATAA
46730 TTTTTAT
1 TTTTTAT
46737 TTAAAATACT
Statistics
Matches: 47, Mismatches: 12, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
17 12 0.26
18 13 0.28
19 7 0.15
20 15 0.32
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTTATATATTTTTATAA
Found at i:46705 original size:35 final size:34
Alignment explanation
Indices: 46664--46738 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 34
46654 TTTTTTTATA
**
46664 TATTTTT-ATAATTTTTAAATTATTTTCATTATTTT
1 TATTTTTAATAAAATTTAAA-TATTTT-ATTATTTT
*
46699 TATTTTTTAATAAAATTTATATATTTTATTATTTT
1 TA-TTTTTAATAAAATTTAAATATTTTATTATTTT
46734 TATTT
1 TATTT
46739 AAAATACTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
34 3 0.09
35 12 0.34
36 11 0.31
37 9 0.26
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (34 bp):
TATTTTTAATAAAATTTAAATATTTTATTATTTT
Found at i:46737 original size:9 final size:9
Alignment explanation
Indices: 46656--46737 Score: 60
Period size: 9 Copynumber: 8.9 Consensus size: 9
46646 TTGAAATTTT
46656 TTTTTATATA
1 TTTTTAT-TA
*
46666 TTTTTATAA
1 TTTTTATTA
46675 TTTTTAAATTA
1 TTTTT--ATTA
*
46686 TTTTCATTA
1 TTTTTATTA
46695 TTTTTATT-
1 TTTTTATTA
* *
46703 TTTTAATAA
1 TTTTTATTA
**
46712 AATTTA-TA
1 TTTTTATTA
46720 TATTTTATTA
1 T-TTTTATTA
46730 TTTTTATT
1 TTTTTATT
46738 TAAAATACTG
Statistics
Matches: 55, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
8 7 0.13
9 31 0.56
10 10 0.18
11 7 0.13
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTTATTA
Found at i:52312 original size:8 final size:8
Alignment explanation
Indices: 52299--52327 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
52289 AAATAATAAT
52299 TTTTTTAA
1 TTTTTTAA
52307 TTTTTTAA
1 TTTTTTAA
52315 TTTTTTAA
1 TTTTTTAA
52323 TTTTT
1 TTTTT
52328 CTCTTTCCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTAA
Found at i:52342 original size:12 final size:12
Alignment explanation
Indices: 52325--52351 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
52315 TTTTTTAATT
52325 TTTCTCTTTCCC
1 TTTCTCTTTCCC
52337 TTTCTCTTTCCC
1 TTTCTCTTTCCC
52349 TTT
1 TTT
52352 TTTTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTCTCTTTCCC
Found at i:55560 original size:68 final size:68
Alignment explanation
Indices: 55485--55626 Score: 266
Period size: 68 Copynumber: 2.1 Consensus size: 68
55475 ACAAATATAA
55485 AACTAATACAACACAAATGAACCCCCCAAGTAATCACAAAGTATAGTCAAACTACTAAAACACAA
1 AACTAATACAACACAAATGAACCCCCCAAGTAATCACAAAGTATAGTCAAACTACTAAAACACAA
55550 ATG
66 ATG
* *
55553 GACTAATACAACACAAATGAACCGCCCAAGTAATCACAAAGTATAGTCAAACTACTAAAACACAA
1 AACTAATACAACACAAATGAACCCCCCAAGTAATCACAAAGTATAGTCAAACTACTAAAACACAA
55618 ATG
66 ATG
55621 AACTAA
1 AACTAA
55627 GAACTAGTAC
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 71 1.00
ACGTcount: A:0.51, C:0.24, G:0.08, T:0.16
Consensus pattern (68 bp):
AACTAATACAACACAAATGAACCCCCCAAGTAATCACAAAGTATAGTCAAACTACTAAAACACAA
ATG
Found at i:58281 original size:17 final size:15
Alignment explanation
Indices: 58259--58292 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 15
58249 AATTTTTATT
58259 AATAAAATTTATAAAAA
1 AATAAAA-TTA-AAAAA
58276 AATAAAATTAAAAAA
1 AATAAAATTAAAAAA
58291 AA
1 AA
58293 CTAGTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 3 0.18
17 7 0.41
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAAAATTAAAAAA
Found at i:58292 original size:16 final size:17
Alignment explanation
Indices: 58259--58292 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
58249 AATTTTTATT
*
58259 AATAAAATTTATAAAAA
1 AATAAAATTTAAAAAAA
58276 AATAAAA-TTAAAAAAA
1 AATAAAATTTAAAAAAA
58292 A
1 A
58293 CTAGTAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AATAAAATTTAAAAAAA
Found at i:69887 original size:21 final size:21
Alignment explanation
Indices: 69861--69932 Score: 108
Period size: 21 Copynumber: 3.4 Consensus size: 21
69851 ACAAAAAATT
*
69861 ATGTTTGTAACTTTCCTCATA
1 ATGTTTGTAACTCTCCTCATA
*
69882 ATGTTTGTAACTCTCCTTATA
1 ATGTTTGTAACTCTCCTCATA
*
69903 ATGTTTTGTAACTCTCCTCATT
1 ATG-TTTGTAACTCTCCTCATA
69925 ATGTTTGT
1 ATGTTTGT
69933 TTTAAATTTC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
21 27 0.59
22 19 0.41
ACGTcount: A:0.21, C:0.18, G:0.11, T:0.50
Consensus pattern (21 bp):
ATGTTTGTAACTCTCCTCATA
Found at i:69913 original size:22 final size:22
Alignment explanation
Indices: 69864--69930 Score: 100
Period size: 22 Copynumber: 3.1 Consensus size: 22
69854 AAAAATTATG
*
69864 TTTGTAACTTTCCTCATAATG-
1 TTTGTAACTCTCCTCATAATGT
*
69885 TTTGTAACTCTCCTTATAATGT
1 TTTGTAACTCTCCTCATAATGT
*
69907 TTTGTAACTCTCCTCATTATGT
1 TTTGTAACTCTCCTCATAATGT
69929 TT
1 TT
69931 GTTTTAAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
21 19 0.46
22 22 0.54
ACGTcount: A:0.21, C:0.19, G:0.09, T:0.51
Consensus pattern (22 bp):
TTTGTAACTCTCCTCATAATGT
Found at i:73936 original size:20 final size:20
Alignment explanation
Indices: 73900--73944 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
73890 ATCCAAATAT
*
73900 AAAAAATATTAACTTTTTCA
1 AAAAAATATTAACTTTTCCA
*
73920 AAAAAATAATTCA-TTTTCCA
1 AAAAAAT-ATTAACTTTTCCA
73940 AAAAA
1 AAAAA
73945 CATTTCCCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAAATATTAACTTTTCCA
Found at i:74804 original size:20 final size:20
Alignment explanation
Indices: 74779--74846 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
74769 ATAATAAAAA
74779 TTATATATATTTTCAATAAT
1 TTATATATATTTTCAATAAT
**
74799 TTATATCAATATGAATCAATAA-
1 TTATAT--ATAT-TTTCAATAAT
* *
74821 TTATATTTTTTTTCAATAAT
1 TTATATATATTTTCAATAAT
74841 TTATAT
1 TTATAT
74847 CAATACGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
19 7 0.18
20 14 0.37
22 10 0.26
23 7 0.18
ACGTcount: A:0.40, C:0.06, G:0.01, T:0.53
Consensus pattern (20 bp):
TTATATATATTTTCAATAAT
Done.