Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000680.1 Kokia drynarioides strain JFW-HI SEQ_111674, 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: 76402
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3618 original size:28 final size:28
Alignment explanation
Indices: 3558--3619 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 28
3548 TTTTCTCATC
*
3558 TTGATACTTAAAATTTTTTTTGTCACAAG
1 TTGATACCTAAAATTTTTTTTGT-ACAAG
3587 -TGATACCTAAATTATTTTTTTT-T-CAAG
1 TTGATACCTAAA--ATTTTTTTTGTACAAG
3614 TTGATA
1 TTGATA
3620 TCTCCGTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
27 4 0.14
28 15 0.52
29 1 0.03
30 9 0.31
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.50
Consensus pattern (28 bp):
TTGATACCTAAAATTTTTTTTGTACAAG
Found at i:9630 original size:29 final size:29
Alignment explanation
Indices: 9586--9673 Score: 149
Period size: 29 Copynumber: 3.0 Consensus size: 29
9576 TTCCAAATAT
*
9586 AAATATAATACGGATACAGTTACAGATGC
1 AAATATAATACAGATACAGTTACAGATGC
*
9615 AAATATAATACAGATACAGTTACAAATGC
1 AAATATAATACAGATACAGTTACAGATGC
*
9644 AAATATAATACAGATATAGTTACAGATGC
1 AAATATAATACAGATACAGTTACAGATGC
9673 A
1 A
9674 GATTCCTGCC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.25
Consensus pattern (29 bp):
AAATATAATACAGATACAGTTACAGATGC
Found at i:10452 original size:391 final size:389
Alignment explanation
Indices: 9716--10501 Score: 1482
Period size: 391 Copynumber: 2.0 Consensus size: 389
9706 TGTCTAACCC
9716 ATCACACCATATAGGTATATAATACCTATCCAGCCCTACACACCATATAATGTCGGTATGACGCG
1 ATCACACCATATAGGTATATAATACCTATCCAGCCCTACACACCATATAATGTCGGTATGACGCG
*
9781 TTGTAGTGTTTGCAGTCTCACTGTCAGTTCAAATATAATCAAGGGTGGTTTAACCACCGATTCAG
66 TTGTAGTGTTTGCAGTCTCACTGTCAATTCAAATATAATCAAGGGTGGTTTAACCACCGATTCAG
* *
9846 TACAGAACACTTCTTGCAATTCATATCTCCTGACCCATGCAGATGCAAAGAACAAATGACAGATA
131 TACAGAACACTTCTTGCAATTCATATCTCCCGACCCATGCAAATGCAAAGAACAAATGACAGATA
9911 TGTATAATTCACACACAGATGTGATCATACAATCCTAGTATAACAGTGTGCTGAGATTATTTGTA
196 TGTATAATTCACACACAGATGTGATCATACAATCCTAGTATAACAGTGTGCTGAGATTATTTGTA
9976 ACCATTTTGTACAATTATCTAGATATCACATATCCTTAATCAAAACAGTAACACAGAAGCGTACC
261 ACCATTTTGTACAATTATCTAGATATCACATATCCTTAATCAAAACAGTAACACAGAAGCGTACC
10041 TGTATGCTTAACAGAACACGAATCGTACCTGAATGGAATACACACTATAACACATCCAAACAAA
326 TGTATGCTTAACAGAACACGAATCGTACCTGAATGGAATACACACTATAACACATCCAAACAAA
*
10105 GTCACACCATATAGGTATATATAATACCTATCCAGCCCTACACACCATATAATGTCGGTATGACG
1 ATCACACCATATAGG--TATATAATACCTATCCAGCCCTACACACCATATAATGTCGGTATGACG
*
10170 CGTTGTAGTGTTTGCAGTCTCACTGTCAATTCAAATATAATCAAGGGTGGTTTAACCACCGATTT
64 CGTTGTAGTGTTTGCAGTCTCACTGTCAATTCAAATATAATCAAGGGTGGTTTAACCACCGATTC
*
10235 AGTACAGAACACTTCTTGCAATTCATATCTCCCGACCCATGCAAATGCAAAGAACAGATGACAGA
129 AGTACAGAACACTTCTTGCAATTCATATCTCCCGACCCATGCAAATGCAAAGAACAAATGACAGA
10300 TATGTATAATTCACACACAGATGTGATCATACAATCCTAGTATAACAGTGTGCTGAGATTATTTG
194 TATGTATAATTCACACACAGATGTGATCATACAATCCTAGTATAACAGTGTGCTGAGATTATTTG
*
10365 TAACCATTTTGTACAGTTATCTAGATATCACATATCCTTAATCAAAACAGTAACACAGAAGCGTA
259 TAACCATTTTGTACAATTATCTAGATATCACATATCCTTAATCAAAACAGTAACACAGAAGCGTA
*
10430 CTTGTATGCTTAACAGAACACGAATCGTACCTGAATGGAATACACACTATAACACATCCAAACAA
324 CCTGTATGCTTAACAGAACACGAATCGTACCTGAATGGAATACACACTATAACACATCCAAACAA
10495 A
389 A
10496 ATCACA
1 ATCACA
10502 TTACACATTA
Statistics
Matches: 386, Mismatches: 9, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
389 14 0.04
391 372 0.96
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (389 bp):
ATCACACCATATAGGTATATAATACCTATCCAGCCCTACACACCATATAATGTCGGTATGACGCG
TTGTAGTGTTTGCAGTCTCACTGTCAATTCAAATATAATCAAGGGTGGTTTAACCACCGATTCAG
TACAGAACACTTCTTGCAATTCATATCTCCCGACCCATGCAAATGCAAAGAACAAATGACAGATA
TGTATAATTCACACACAGATGTGATCATACAATCCTAGTATAACAGTGTGCTGAGATTATTTGTA
ACCATTTTGTACAATTATCTAGATATCACATATCCTTAATCAAAACAGTAACACAGAAGCGTACC
TGTATGCTTAACAGAACACGAATCGTACCTGAATGGAATACACACTATAACACATCCAAACAAA
Found at i:13182 original size:43 final size:42
Alignment explanation
Indices: 13095--13217 Score: 189
Period size: 43 Copynumber: 3.0 Consensus size: 42
13085 CTATTACACA
13095 TGTGCC-CCAAAACAGTATACAA-ACACCTTGACACACGCCCG
1 TGTGCCTCC-AAACAGTATACAACACACCTTGACACACGCCCG
* *
13136 TGTGCCTCCAAACAGTATACATACACACCCTGACACACGCCTG
1 TGTGCCTCCAAACAGTATACA-ACACACCTTGACACACGCCCG
13179 TGTGCCTCCAAACAGTATAC-ACACACCTTGACACACGCC
1 TGTGCCTCCAAACAGTATACAACACACCTTGACACACGCC
13218 ATTGTGCTAG
Statistics
Matches: 76, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
41 36 0.47
42 3 0.04
43 37 0.49
ACGTcount: A:0.32, C:0.37, G:0.14, T:0.17
Consensus pattern (42 bp):
TGTGCCTCCAAACAGTATACAACACACCTTGACACACGCCCG
Found at i:13224 original size:41 final size:40
Alignment explanation
Indices: 13095--13224 Score: 172
Period size: 41 Copynumber: 3.1 Consensus size: 40
13085 CTATTACACA
* *
13095 TGTGCC-CCAAAACAGTATACAAACACCTTGACACACGCCCG
1 TGTGCCTCC-AAACAGTATACACACACCTTGACACACG-CCT
*
13136 TGTGCCTCCAAACAGTATACATACACACCCTGACACACGCCT
1 TGTGCCTCCAAACAGTATAC--ACACACCTTGACACACGCCT
13178 GTGTGCCTCCAAACAGTATACACACACCTTGACACACGCCAT
1 -TGTGCCTCCAAACAGTATACACACACCTTGACACACGCC-T
13220 TGTGC
1 TGTGC
13225 TAGCCCGTGT
Statistics
Matches: 80, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
41 40 0.50
42 5 0.06
43 35 0.44
ACGTcount: A:0.31, C:0.36, G:0.15, T:0.18
Consensus pattern (40 bp):
TGTGCCTCCAAACAGTATACACACACCTTGACACACGCCT
Found at i:18187 original size:30 final size:29
Alignment explanation
Indices: 18153--18244 Score: 98
Period size: 30 Copynumber: 3.0 Consensus size: 29
18143 ACTGCTAAAG
18153 TTTAAGTTACACCCAAATAAGCCGTT-ACCA
1 TTTAA-TTACA-CCAAATAAGCCGTTAACCA
*
18183 TTTAATTGGCACCAAATAAAGCCGTTAACCA
1 TTTAATT-ACACCAAAT-AAGCCGTTAACCA
*
18214 -TTAATATACACCAAATTAAGCCATTAACCA
1 TTTAAT-TACACCAAA-TAAGCCGTTAACCA
18244 T
1 T
18245 AAATTTGTAC
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
29 8 0.15
30 39 0.74
31 6 0.11
ACGTcount: A:0.40, C:0.24, G:0.09, T:0.27
Consensus pattern (29 bp):
TTTAATTACACCAAATAAGCCGTTAACCA
Found at i:20698 original size:27 final size:27
Alignment explanation
Indices: 20668--20723 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
20658 ATAGTATTAC
20668 AATTTAAATAAAAAAAAACTTTCGAAT
1 AATTTAAATAAAAAAAAACTTTCGAAT
* * **
20695 AA-TTCAATGAATTAAAACTTTCGAAT
1 AATTTAAATAAAAAAAAACTTTCGAAT
20721 AAT
1 AAT
20724 ATGAACACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
26 22 0.92
27 2 0.08
ACGTcount: A:0.54, C:0.09, G:0.05, T:0.32
Consensus pattern (27 bp):
AATTTAAATAAAAAAAAACTTTCGAAT
Found at i:20800 original size:9 final size:9
Alignment explanation
Indices: 20758--20838 Score: 51
Period size: 9 Copynumber: 8.8 Consensus size: 9
20748 TATCTATACA
20758 ATTTTAAAT
1 ATTTTAAAT
* *
20767 GTTTTAAACA
1 ATTTTAAA-T
*
20777 ATATTTATAT
1 AT-TTTAAAT
20787 AATTTTAAAT
1 -ATTTTAAAT
*
20797 ATTTTACAGT
1 ATTTTA-AAT
20807 ATTATT-AAT
1 ATT-TTAAAT
*
20816 A-TTTACA-
1 ATTTTAAAT
20823 ATTTTAAAT
1 ATTTTAAAT
20832 ATTTTAA
1 ATTTTAA
20839 TATCGTATAA
Statistics
Matches: 54, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
7 3 0.06
8 7 0.13
9 23 0.43
10 12 0.22
11 9 0.17
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (9 bp):
ATTTTAAAT
Found at i:24911 original size:13 final size:13
Alignment explanation
Indices: 24895--24942 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
24885 TTTAATGTAA
24895 AATTTTATATATG
1 AATTTTATATATG
*
24908 AATTTTAATTTTATG
1 AATTTT-A-TATATG
24923 TAATTTTATATATG
1 -AATTTTATATATG
24937 AATTTT
1 AATTTT
24943 TTATTTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 12 0.40
14 6 0.20
15 6 0.20
16 6 0.20
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (13 bp):
AATTTTATATATG
Found at i:24943 original size:14 final size:14
Alignment explanation
Indices: 24897--24943 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
24887 TAATGTAAAA
24897 TTTTATATATGAAT
1 TTTTATATATGAAT
* *
24911 TTTAATTTTATGTAA-
1 TTTTA-TATATG-AAT
24926 TTTTATATATGAAT
1 TTTTATATATGAAT
24940 TTTT
1 TTTT
24944 TATTTAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
13 2 0.08
14 13 0.50
15 9 0.35
16 2 0.08
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (14 bp):
TTTTATATATGAAT
Found at i:24946 original size:25 final size:27
Alignment explanation
Indices: 24895--24953 Score: 77
Period size: 29 Copynumber: 2.2 Consensus size: 27
24885 TTTAATGTAA
24895 AATTTTATATATGAATTTTAATTTTATGT
1 AATTTTATATATGAA-TTT-ATTTTATGT
*
24924 AATTTTATATATGAA-TT-TTTTATTT
1 AATTTTATATATGAATTTATTTTATGT
24949 AATTT
1 AATTT
24954 AATTCTAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 12 0.41
27 2 0.07
29 15 0.52
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (27 bp):
AATTTTATATATGAATTTATTTTATGT
Found at i:26353 original size:42 final size:45
Alignment explanation
Indices: 26307--26409 Score: 131
Period size: 42 Copynumber: 2.4 Consensus size: 45
26297 CTCTATTAGG
*
26307 TGAAAGTATTTTCAACGGATTTATAAAAAAAAAA-A-ATTT-AAC
1 TGAAAGTATTTTCAACGGATTTACAAAAAAAAAACACATTTCAAC
* * *
26349 TGAAAGTGTTTTCAACGTATTTACAAAAAAAAAACACTTTTCAAC
1 TGAAAGTATTTTCAACGGATTTACAAAAAAAAAACACATTTCAAC
* *
26394 TAAAAGTTTTTTCAAC
1 TGAAAGTATTTTCAAC
26410 TGATATGACA
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
42 31 0.60
43 1 0.02
44 3 0.06
45 17 0.33
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.33
Consensus pattern (45 bp):
TGAAAGTATTTTCAACGGATTTACAAAAAAAAAACACATTTCAAC
Found at i:33707 original size:16 final size:16
Alignment explanation
Indices: 33686--33716 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33676 ATTCGACAAT
*
33686 AAATTTGAATCATTTC
1 AAATTTGAACCATTTC
33702 AAATTTGAACCATTT
1 AAATTTGAACCATTT
33717 TAATTTAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (16 bp):
AAATTTGAACCATTTC
Found at i:33828 original size:15 final size:14
Alignment explanation
Indices: 33808--33837 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
33798 ATTTTTTTAT
33808 AATCAAATTGAATTA
1 AATCAAATT-AATTA
33823 AATCAAATTAATTA
1 AATCAAATTAATTA
33837 A
1 A
33838 TAGAAAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (14 bp):
AATCAAATTAATTA
Found at i:37870 original size:21 final size:22
Alignment explanation
Indices: 37840--37884 Score: 83
Period size: 21 Copynumber: 2.1 Consensus size: 22
37830 GCCCAAAACA
37840 TTTGTTGCTAGGATCCTGAATT
1 TTTGTTGCTAGGATCCTGAATT
37862 TTTG-TGCTAGGATCCTGAATT
1 TTTGTTGCTAGGATCCTGAATT
37883 TT
1 TT
37885 CGTATCTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.18, C:0.13, G:0.22, T:0.47
Consensus pattern (22 bp):
TTTGTTGCTAGGATCCTGAATT
Found at i:41786 original size:22 final size:22
Alignment explanation
Indices: 41760--41811 Score: 95
Period size: 22 Copynumber: 2.3 Consensus size: 22
41750 TAAGTGATTA
41760 AATTGTACAGTGTACAAAAGTT
1 AATTGTACAGTGTACAAAAGTT
41782 AATTGTACAGTGTACAAAAGTT
1 AATTGTACAGTGTACAAAAGTT
41804 AATGTGTA
1 AAT-TGTA
41812 GAATATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 25 0.86
23 4 0.14
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (22 bp):
AATTGTACAGTGTACAAAAGTT
Found at i:46099 original size:2 final size:2
Alignment explanation
Indices: 46094--46128 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
46084 CCCTAGCTCT
*
46094 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46129 TTGTATGCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:53354 original size:3 final size:3
Alignment explanation
Indices: 53346--53390 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
53336 TATGCTGTAT
* * * *
53346 TCA TCA TCA TCG TCG TCA TCG TCA TCA TCA TCA TCA TCA TAA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
53391 CTCCTGATGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.29, C:0.31, G:0.07, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:55813 original size:30 final size:31
Alignment explanation
Indices: 55777--55915 Score: 99
Period size: 31 Copynumber: 4.5 Consensus size: 31
55767 ACGACCAATC
55777 AAAATTTTAAAAATTTTGAG-AGTTTTAATT
1 AAAATTTTAAAAATTTTGAGAAGTTTTAATT
* * * *
55807 AGAATTTTAAAAATTTTTG-GTAGATCTAATT
1 AAAATTTTAAAAA-TTTTGAGAAGTTTTAATT
* * *
55838 AAAACTTTAAAAATTTT-AGAAG-TTTGATA
1 AAAATTTTAAAAATTTTGAGAAGTTTTAATT
* * * *
55867 AAAATTTACAAAAGAATTTGAGAAG-TCTAACTG
1 AAAATTT-TAAAA-ATTTTGAGAAGTTTTAA-TT
*
55900 AAATTTTTAAAAATTT
1 AAAATTTTAAAAATTT
55916 CAAAGATTTA
Statistics
Matches: 84, Mismatches: 18, Indels: 13
0.73 0.16 0.11
Matches are distributed among these distances:
29 10 0.12
30 24 0.29
31 31 0.37
32 12 0.14
33 7 0.08
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.40
Consensus pattern (31 bp):
AAAATTTTAAAAATTTTGAGAAGTTTTAATT
Found at i:58647 original size:20 final size:19
Alignment explanation
Indices: 58604--58657 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 19
58594 CATACTATTT
58604 ATTTTTAAATTTTTATGAA
1 ATTTTTAAATTTTTATGAA
* * *
58623 CTTTTTAAAGTTTTTCTTAA
1 ATTTTTAAA-TTTTTATGAA
* *
58643 ATTTTGAAAATTTTA
1 ATTTTTAAATTTTTA
58658 AATAAATTAT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.57
Consensus pattern (19 bp):
ATTTTTAAATTTTTATGAA
Found at i:60992 original size:17 final size:18
Alignment explanation
Indices: 60970--61006 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
60960 ATAACTTTTA
*
60970 AAATTAAAA-CTAAAAAT
1 AAATTAAAATCAAAAAAT
60987 AAATTAAAATCAAAAAAT
1 AAATTAAAATCAAAAAAT
61005 AA
1 AA
61007 TATTTGATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (18 bp):
AAATTAAAATCAAAAAAT
Found at i:61642 original size:16 final size:18
Alignment explanation
Indices: 61603--61636 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
61593 GAAGATTATA
61603 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
61620 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
61637 AATTTAGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Done.