Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014233.1 Kokia drynarioides strain JFW-HI SEQ_129266, 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: 58466
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Warning! 114 characters in sequence are not A, C, G, or T
Found at i:4398 original size:140 final size:140
Alignment explanation
Indices: 4146--4426 Score: 553
Period size: 140 Copynumber: 2.0 Consensus size: 140
4136 AAAGTAAGCC
4146 TTGTTTTATTTCTTTGCCTTGTGCTGAAACCTAAAGTAGCCTCATTCCATGATTAAATATATGCA
1 TTGTTTTATTTCTTTGCCTTGTGCTGAAACCTAAAGTAGCCTCATTCCATGATTAAATATATGCA
*
4211 TACCGCACTTCTATACATTTCAGTTTCTTCTCAAAGAGGCTTTGATTTTCTATTTTTGATGCTGA
66 TACCACACTTCTATACATTTCAGTTTCTTCTCAAAGAGGCTTTGATTTTCTATTTTTGATGCTGA
4276 CAACTGAAAT
131 CAACTGAAAT
4286 TTGTTTTATTTCTTTGCCTTGTGCTGAAACCTAAAGTAGCCTCATTCCATGATTAAATATATGCA
1 TTGTTTTATTTCTTTGCCTTGTGCTGAAACCTAAAGTAGCCTCATTCCATGATTAAATATATGCA
4351 TACCACACTTCTATACATTTCAGTTTCTTCTCAAAGAGGCTTTGATTTTCTATTTTTGATGCTGA
66 TACCACACTTCTATACATTTCAGTTTCTTCTCAAAGAGGCTTTGATTTTCTATTTTTGATGCTGA
4416 CAACTGAAAT
131 CAACTGAAAT
4426 T
1 T
4427 GCCTCTTATT
Statistics
Matches: 140, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 140 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (140 bp):
TTGTTTTATTTCTTTGCCTTGTGCTGAAACCTAAAGTAGCCTCATTCCATGATTAAATATATGCA
TACCACACTTCTATACATTTCAGTTTCTTCTCAAAGAGGCTTTGATTTTCTATTTTTGATGCTGA
CAACTGAAAT
Found at i:11471 original size:28 final size:29
Alignment explanation
Indices: 11416--11485 Score: 99
Period size: 28 Copynumber: 2.4 Consensus size: 29
11406 CAAATTATTT
*
11416 TAAAACTATTAAAATTATTTTTTAAAATA
1 TAAAATTATTAAAATTATTTTTTAAAATA
*
11445 TAAAAATT-TTAAAA-TATTTTTTTAAATA
1 T-AAAATTATTAAAATTATTTTTTAAAATA
11473 TAAAATTATTAAA
1 TAAAATTATTAAA
11486 TAATTTTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
27 6 0.16
28 19 0.51
29 7 0.19
30 5 0.14
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (29 bp):
TAAAATTATTAAAATTATTTTTTAAAATA
Found at i:11587 original size:34 final size:34
Alignment explanation
Indices: 11541--11615 Score: 111
Period size: 34 Copynumber: 2.3 Consensus size: 34
11531 CAATTTCATC
*
11541 TTCTT-TC-CCATTTTTCCATCTATCA-CATCTTT
1 TTCTTCTCACCATTTTTCCATCTAACACCA-CTTT
11573 TTCTTCTCACCATTTTTCCATCTAACACCACTTT
1 TTCTTCTCACCATTTTTCCATCTAACACCACTTT
11607 TTCTTCTCA
1 TTCTTCTCA
11616 TCATCCAAGC
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
32 5 0.13
33 2 0.05
34 30 0.77
35 2 0.05
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.49
Consensus pattern (34 bp):
TTCTTCTCACCATTTTTCCATCTAACACCACTTT
Found at i:11609 original size:19 final size:18
Alignment explanation
Indices: 11551--11609 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 18
11541 TTCTTTCCCA
11551 TTTTTCCATCTATCA-CATC
1 TTTTTCCATCTA-CACCA-C
*
11570 TTTTT-CTTCT-CACCA-
1 TTTTTCCATCTACACCAC
11585 TTTTTCCATCTAACACCAC
1 TTTTTCCATCT-ACACCAC
11604 TTTTTC
1 TTTTTC
11610 TTCTCATCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
15 5 0.15
16 6 0.18
17 2 0.06
18 9 0.27
19 11 0.33
ACGTcount: A:0.19, C:0.32, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTTTCCATCTACACCAC
Found at i:11943 original size:14 final size:15
Alignment explanation
Indices: 11903--11944 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
11893 ATTACACAGT
*
11903 GTTTAACCCATAAATC
1 GTTTATCCCA-AAATC
11919 GTTTATCCCAAAATC
1 GTTTATCCCAAAATC
*
11934 -TTTTTCCCAAA
1 GTTTATCCCAAA
11945 CCGTTTTGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 10 0.42
15 5 0.21
16 9 0.38
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.36
Consensus pattern (15 bp):
GTTTATCCCAAAATC
Found at i:12691 original size:30 final size:29
Alignment explanation
Indices: 12629--12694 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
12619 TTAGTAATAG
*
12629 TAAAAATTTACTTCAACTTTCAAAAATGA
1 TAAAAATTTAATTCAACTTTCAAAAATGA
* *
12658 TAAAAATTTAATTTAACCCTTT-AAAAATTA
1 TAAAAATTTAATTCAA--CTTTCAAAAATGA
12688 TAAAAAT
1 TAAAAAT
12695 ATAAACTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 14 0.44
30 14 0.44
31 4 0.12
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.36
Consensus pattern (29 bp):
TAAAAATTTAATTCAACTTTCAAAAATGA
Found at i:38243 original size:22 final size:21
Alignment explanation
Indices: 38218--38264 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
38208 AATAAGTTAG
*
38218 AATACAATTTTAAATTTAATTT
1 AATACAATTTGAAA-TTAATTT
**
38240 AATAGTATTTGAAATTAATTT
1 AATACAATTTGAAATTAATTT
38261 AATA
1 AATA
38265 TTATATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (21 bp):
AATACAATTTGAAATTAATTT
Found at i:38259 original size:21 final size:22
Alignment explanation
Indices: 38224--38264 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
38214 TTAGAATACA
*
38224 ATTTTAAATTTAATTTAATAGT
1 ATTTGAAATTTAATTTAATAGT
38246 ATTTGAAA-TTAATTTAATA
1 ATTTGAAATTTAATTTAATA
38265 TTATATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (22 bp):
ATTTGAAATTTAATTTAATAGT
Found at i:38289 original size:24 final size:24
Alignment explanation
Indices: 38253--38306 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
38243 AGTATTTGAA
* *
38253 ATTAATTTAATATTATATAAAAAT
1 ATTAAATTAATATAATATAAAAAT
* **
38277 ATTAAATTGATATAATATGTAAAT
1 ATTAAATTAATATAATATAAAAAT
38301 ATTAAA
1 ATTAAA
38307 AATTAAATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (24 bp):
ATTAAATTAATATAATATAAAAAT
Found at i:41563 original size:24 final size:25
Alignment explanation
Indices: 41522--41603 Score: 139
Period size: 25 Copynumber: 3.3 Consensus size: 25
41512 GAGGTACATA
*
41522 AGTGCTGGGGAAACAGAAGCACACAC
1 AGTGCT-GGGTAACAGAAGCACACAC
41548 A-TGCTGGGTAACAGAAGCACACAC
1 AGTGCTGGGTAACAGAAGCACACAC
41572 AGTGCTGGGTAACAGAAGCACACAC
1 AGTGCTGGGTAACAGAAGCACACAC
41597 AGTGCTG
1 AGTGCTG
41604 AACAGTAAAC
Statistics
Matches: 54, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
24 19 0.35
25 34 0.63
26 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.29, T:0.12
Consensus pattern (25 bp):
AGTGCTGGGTAACAGAAGCACACAC
Found at i:43530 original size:26 final size:26
Alignment explanation
Indices: 43445--43516 Score: 110
Period size: 26 Copynumber: 2.8 Consensus size: 26
43435 TAAGAATTTC
**
43445 TTTCT-TTCTTCTTCATTTTCATGCA
1 TTTCTCTTCTTCACCATTTTCATGCA
*
43470 TTTCTCTTATTCACCATTTTCATGCA
1 TTTCTCTTCTTCACCATTTTCATGCA
43496 TTTCTCTTCTTCACCATTTTC
1 TTTCTCTTCTTCACCATTTTC
43517 CTTCCTTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
25 5 0.12
26 37 0.88
ACGTcount: A:0.14, C:0.28, G:0.03, T:0.56
Consensus pattern (26 bp):
TTTCTCTTCTTCACCATTTTCATGCA
Found at i:43845 original size:27 final size:27
Alignment explanation
Indices: 43789--43856 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
43779 CTAAATAAAA
*
43789 AATAATAATAAATATTTAAGTAAAATATT
1 AATAA-AAT-AATATTTAACTAAAATATT
*
43818 AATAAAATAATATTTAACT-AATTAATT
1 AATAAAATAATATTTAACTAAAAT-ATT
43845 AATAAAA-AATAT
1 AATAAAATAATAT
43857 CTCCAAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
26 8 0.22
27 20 0.56
28 3 0.08
29 5 0.14
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (27 bp):
AATAAAATAATATTTAACTAAAATATT
Found at i:46586 original size:6 final size:6
Alignment explanation
Indices: 46575--46601 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
46565 ACAATTCATA
46575 TCACTT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCA
46602 ATTTTGATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.33, G:0.00, T:0.48
Consensus pattern (6 bp):
TCACTT
Found at i:51571 original size:6 final size:6
Alignment explanation
Indices: 51560--51585 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
51550 TGATGACCAC
51560 GATGAA GATGAA GATGAA GATGAA GA
1 GATGAA GATGAA GATGAA GATGAA GA
51586 CGAGGAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.35, T:0.15
Consensus pattern (6 bp):
GATGAA
Found at i:57027 original size:23 final size:23
Alignment explanation
Indices: 56992--57092 Score: 121
Period size: 23 Copynumber: 4.3 Consensus size: 23
56982 ACATCTCGTA
56992 CTCTCTGTTATTAGCACTGTGTGTG
1 CTCTCTG--ATTAGCACTGTGTGTG
* *
57017 CTCTCTGATTAGCACTTTGTATG
1 CTCTCTGATTAGCACTGTGTGTG
* * *
57040 CTCTCTGATTAGCATTTTGTGTA
1 CTCTCTGATTAGCACTGTGTGTG
* *
57063 CTCTCTGTTTAGCATTGTGTGTG
1 CTCTCTGATTAGCACTGTGTGTG
57086 CTCTCTG
1 CTCTCTG
57093 TTGCCCAGCA
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
23 61 0.90
25 7 0.10
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.46
Consensus pattern (23 bp):
CTCTCTGATTAGCACTGTGTGTG
Found at i:57133 original size:69 final size:70
Alignment explanation
Indices: 56989--57137 Score: 175
Period size: 69 Copynumber: 2.1 Consensus size: 70
56979 AGCACATCTC
56989 GTACTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTATGCTCTCTGATTAGCA
1 GTACTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTG-ATGCTCTCTGATTAGCA
*
57054 TTTTGT
65 CTTTGT
*
57060 GTACTCTCTG-T-TTAGCATTGTGTGTGCTCTCTG-TTGCCCAGCACTTATG-TGCTCTCT-ATT
1 GTACTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATT----AGCACTT-TGATGCTCTCTGATT
*
57120 AGTACTTTG-
61 AGCACTTTGT
57129 GTACTCTCT
1 GTACTCTCT
57138 ATTTGTTTCG
Statistics
Matches: 70, Mismatches: 3, Indels: 12
0.82 0.04 0.14
Matches are distributed among these distances:
68 2 0.03
69 30 0.43
70 11 0.16
71 18 0.26
72 7 0.10
73 2 0.03
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.44
Consensus pattern (70 bp):
GTACTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGATGCTCTCTGATTAGCAC
TTTGT
Done.