Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001827.1 Kokia drynarioides strain JFW-HI SEQ_113571, 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: 41954
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Warning! 21 characters in sequence are not A, C, G, or T
Found at i:775 original size:21 final size:22
Alignment explanation
Indices: 741--783 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
731 TATTTCTTTC
741 AATTCTGTTTTCTTTTATTTTT
1 AATTCTGTTTTCTTTTATTTTT
763 AATTCTG-TTTCTTTTATTTTT
1 AATTCTGTTTTCTTTTATTTTT
784 CCTCAGATCG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.14, C:0.09, G:0.05, T:0.72
Consensus pattern (22 bp):
AATTCTGTTTTCTTTTATTTTT
Found at i:6889 original size:30 final size:30
Alignment explanation
Indices: 6853--6909 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
6843 AACAGAAGGG
6853 TAATTTAGAACGACGAGACGACGAATTGGA
1 TAATTTAGAACGACGAGACGACGAATTGGA
6883 TAATTTAGAACGACGAGACGACGAATT
1 TAATTTAGAACGACGAGACGACGAATT
6910 AAATCAGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.21
Consensus pattern (30 bp):
TAATTTAGAACGACGAGACGACGAATTGGA
Found at i:7033 original size:22 final size:22
Alignment explanation
Indices: 6991--7042 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
6981 CTCAAAGGAA
6991 GGAAGAGAGACGTTTCAAAAAG
1 GGAAGAGAGACGTTTCAAAAAG
* *
7013 GGAACGAGAGGCGTTTGAAAAGAG
1 GGAA-GAGAGACGTTTCAAAA-AG
*
7037 AGAAGA
1 GGAAGA
7043 AACGGAGGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 4 0.16
23 16 0.64
24 5 0.20
ACGTcount: A:0.44, C:0.08, G:0.37, T:0.12
Consensus pattern (22 bp):
GGAAGAGAGACGTTTCAAAAAG
Found at i:8515 original size:30 final size:31
Alignment explanation
Indices: 8449--8533 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 31
8439 TTTTGGATCT
* *
8449 CTTAAAAGTTGGAAAAAAAAATTTTAAACCT
1 CTTAAAAGTTAGAAAAAAAAATTTTAAACCC
* * *
8480 ATTAAAAGTTAG-TAAAAAAATTTTGAACCC
1 CTTAAAAGTTAGAAAAAAAAATTTTAAACCC
* * *
8510 CTTAAAA-ATCGAAAAAATAATTTT
1 CTTAAAAGTTAGAAAAAAAAATTTT
8534 TTTGAACCTC
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
29 2 0.05
30 31 0.72
31 10 0.23
ACGTcount: A:0.52, C:0.09, G:0.08, T:0.31
Consensus pattern (31 bp):
CTTAAAAGTTAGAAAAAAAAATTTTAAACCC
Found at i:8547 original size:33 final size:34
Alignment explanation
Indices: 8500--8565 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 34
8490 AGTAAAAAAA
*
8500 TTTTGAACCCCTTAAAAATCGAAA-AAATAATTT
1 TTTTGAACCCCTTAAAAATCGAAACAAAAAATTT
* *
8533 TTTTGAACCTCTTAAAAATTGAAACAAAAAATT
1 TTTTGAACCCCTTAAAAATCGAAACAAAAAATT
8566 GAACCCTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 22 0.76
34 7 0.24
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.33
Consensus pattern (34 bp):
TTTTGAACCCCTTAAAAATCGAAACAAAAAATTT
Found at i:8908 original size:24 final size:24
Alignment explanation
Indices: 8859--8908 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
8849 ATGAATGTCA
* * *
8859 AATATTATAATTTTTAATATTTTT
1 AATATTATAATTTTCAACATTATT
8883 AATATTATAATTTTCAACATTATT
1 AATATTATAATTTTCAACATTATT
8907 AA
1 AA
8909 ACAAATATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (24 bp):
AATATTATAATTTTCAACATTATT
Found at i:11623 original size:14 final size:15
Alignment explanation
Indices: 11591--11623 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
11581 AGAGTTATGG
11591 AATGGATTTACAAAAC
1 AATGGATTTAC-AAAC
11607 AATGGATTTAC-AAC
1 AATGGATTTACAAAC
11621 AAT
1 AAT
11624 TAAAACATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
16 11 0.65
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.27
Consensus pattern (15 bp):
AATGGATTTACAAAC
Found at i:12223 original size:42 final size:42
Alignment explanation
Indices: 12131--12210 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
12121 AATGTAAGAA
* * *
12131 CAAGATCAAGACCTAACTTGAAAAAAAAAACAATTACCAAGT
1 CAAGTTCAAGACCTAACTTGAAAAAAAAAACAATAAACAAGT
*
12173 CAAGTTCAAGATCTAACTTGAAAAAAAAAA-AA-AAACAA
1 CAAGTTCAAGACCTAACTTGAAAAAAAAAACAATAAACAA
12211 TTACCAAGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 4 0.12
41 2 0.06
42 28 0.82
ACGTcount: A:0.59, C:0.16, G:0.09, T:0.16
Consensus pattern (42 bp):
CAAGTTCAAGACCTAACTTGAAAAAAAAAACAATAAACAAGT
Found at i:12242 original size:48 final size:47
Alignment explanation
Indices: 12151--12242 Score: 114
Period size: 47 Copynumber: 1.9 Consensus size: 47
12141 ACCTAACTTG
* ***
12151 AAAAAAAAAACAATTACCAAGTCAAGTTCAAGATCTAACTTGAAAAA
1 AAAAAAAAAACAATTACCAAGTCAAGTACAAGAAAAAACTTGAAAAA
*
12198 AAAAAAAAAACAATTACCAAGTTCAA-TACACAGAAAAAAGTTGAA
1 AAAAAAAAAACAATTACCAAG-TCAAGTACA-AGAAAAAACTTGAA
12243 CCTTTAAAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
47 24 0.63
48 14 0.37
ACGTcount: A:0.60, C:0.14, G:0.09, T:0.17
Consensus pattern (47 bp):
AAAAAAAAAACAATTACCAAGTCAAGTACAAGAAAAAACTTGAAAAA
Found at i:18803 original size:16 final size:16
Alignment explanation
Indices: 18773--18828 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
18763 AAACTTTTTT
* *
18773 CCCAAATTCTAAAATC
1 CCCAAATTGTGAAATC
* *
18789 CCCAACTTGTTAAATTC
1 CCCAAATTGTGAAA-TC
*
18806 CCCAAATTGTGAAACC
1 CCCAAATTGTGAAATC
18822 CCCAAAT
1 CCCAAAT
18829 CCATAACATT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
16 19 0.58
17 14 0.42
ACGTcount: A:0.38, C:0.32, G:0.05, T:0.25
Consensus pattern (16 bp):
CCCAAATTGTGAAATC
Found at i:19474 original size:13 final size:13
Alignment explanation
Indices: 19446--19481 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
19436 TGGAAATAGA
*
19446 TATATGAAATGAT
1 TATATGAAGTGAT
*
19459 TATATGAAGTGTT
1 TATATGAAGTGAT
19472 TATATGAAGT
1 TATATGAAGT
19482 ATTTGTAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.19, T:0.42
Consensus pattern (13 bp):
TATATGAAGTGAT
Found at i:21117 original size:7 final size:7
Alignment explanation
Indices: 21101--21144 Score: 70
Period size: 7 Copynumber: 6.3 Consensus size: 7
21091 GGAGATTTTG
*
21101 AAAATAA
1 AAAATTA
21108 AAAATTA
1 AAAATTA
*
21115 AAAATAA
1 AAAATTA
21122 AAAATTA
1 AAAATTA
21129 AAAATTA
1 AAAATTA
21136 AAAATTA
1 AAAATTA
21143 AA
1 AA
21145 GAATGTGTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (7 bp):
AAAATTA
Found at i:21120 original size:14 final size:14
Alignment explanation
Indices: 21101--21144 Score: 79
Period size: 14 Copynumber: 3.1 Consensus size: 14
21091 GGAGATTTTG
21101 AAAATAAAAAATTA
1 AAAATAAAAAATTA
21115 AAAATAAAAAATTA
1 AAAATAAAAAATTA
*
21129 AAAATTAAAAATTA
1 AAAATAAAAAATTA
21143 AA
1 AA
21145 GAATGTGTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAATAAAAAATTA
Found at i:24258 original size:24 final size:25
Alignment explanation
Indices: 24217--24265 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
24207 AATAAATATT
24217 TTTTTCTTCTTTTCTTTTCTCTTTC
1 TTTTTCTTCTTTTCTTTTCTCTTTC
*
24242 TTTTTC-TCATTTT-TTTTCTTTTTC
1 TTTTTCTTC-TTTTCTTTTCTCTTTC
24266 AAGTAACTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (25 bp):
TTTTTCTTCTTTTCTTTTCTCTTTC
Found at i:24264 original size:10 final size:11
Alignment explanation
Indices: 24215--24264 Score: 57
Period size: 12 Copynumber: 4.3 Consensus size: 11
24205 GCAATAAATA
24215 TTTTTTTCTTCT
1 TTTTTTTC-TCT
24227 TTTCTTTTCTCT
1 TTT-TTTTCTCT
24239 TTCTTTTTCTCAT
1 TT-TTTTTCTC-T
24252 TTTTTTTCT-T
1 TTTTTTTCTCT
24262 TTT
1 TTT
24265 CAAGTAACTG
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 4 0.11
12 22 0.63
13 9 0.26
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTTTCTCT
Found at i:26748 original size:41 final size:41
Alignment explanation
Indices: 26700--26829 Score: 163
Period size: 41 Copynumber: 3.2 Consensus size: 41
26690 AAGACTCATT
* * *
26700 AATGAGATTTTTATTAAAGAAGACTCATGTCTTGAAATGAG
1 AATGAGATTTTCATTAAGGAAGACTCATGTCTCGAAATGAG
* *
26741 AATGAGATTATGCA-TAAGGAAGACTCATGTCTCAAAATGAG
1 AATGAGATT-TTCATTAAGGAAGACTCATGTCTCGAAATGAG
* * **
26782 AATGATATTTTGATTAAGGAAGACTCATGTCTCGAGTTGAG
1 AATGAGATTTTCATTAAGGAAGACTCATGTCTCGAAATGAG
26823 AATGAGA
1 AATGAGA
26830 ATATGGTTAA
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
40 2 0.03
41 71 0.95
42 2 0.03
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.30
Consensus pattern (41 bp):
AATGAGATTTTCATTAAGGAAGACTCATGTCTCGAAATGAG
Found at i:27553 original size:20 final size:21
Alignment explanation
Indices: 27513--27557 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
27503 TTAGAGTTTT
27513 TAGTATCAGTAGAAATACAAC
1 TAGTATCAGTAGAAATACAAC
* *
27534 TAGTATCGGTA-AAGTACAAC
1 TAGTATCAGTAGAAATACAAC
27554 TAGT
1 TAGT
27558 TTCGCTAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (21 bp):
TAGTATCAGTAGAAATACAAC
Found at i:41763 original size:24 final size:24
Alignment explanation
Indices: 41730--41853 Score: 142
Period size: 24 Copynumber: 5.2 Consensus size: 24
41720 TAGTGAGTGG
* * *
41730 AAACGCAAAGTGGTTGACGAGCAA
1 AAACGTAAAGTGGCTGACGAGCAT
*
41754 AAACGTAAAGTGGCCGACGAGCAT
1 AAACGTAAAGTGGCTGACGAGCAT
*
41778 AAACGTAAAGTGGCTGAAGAGCAT
1 AAACGTAAAGTGGCTGACGAGCAT
* * *
41802 AGACGTAGAGTGGTTGACGAGCAT
1 AAACGTAAAGTGGCTGACGAGCAT
* *
41826 AAACGTATAGT-GCATGATGAGCAT
1 AAACGTAAAGTGGC-TGACGAGCAT
41850 AAAC
1 AAAC
41854 ATAATTGAAA
Statistics
Matches: 85, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
23 1 0.01
24 84 0.99
ACGTcount: A:0.39, C:0.15, G:0.29, T:0.17
Consensus pattern (24 bp):
AAACGTAAAGTGGCTGACGAGCAT
Done.