Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002892.1 Kokia drynarioides strain JFW-HI SEQ_115306, 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: 50995
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:2092 original size:6 final size:6
Alignment explanation
Indices: 2077--2111 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
2067 TTCAGCCACT
*
2077 TGAGCC TGAGCT TGAGCC TGAGCC TGAGCC TGAGC
1 TGAGCC TGAGCC TGAGCC TGAGCC TGAGCC TGAGC
2112 ACTATTCGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.17, C:0.29, G:0.34, T:0.20
Consensus pattern (6 bp):
TGAGCC
Found at i:2695 original size:26 final size:26
Alignment explanation
Indices: 2640--2715 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
2630 GCTAAACCTC
**
2640 ATTAAATAAATTCAAACATAAAAATT
1 ATTAAATAAATTCAAACATAAAAAGA
** *
2666 ATTAAATAAATTCAAATTTAAACAGA
1 ATTAAATAAATTCAAACATAAAAAGA
* *
2692 ATTAATTCCAAATTCAATCATAAA
1 ATTAAAT--AAATTCAAACATAAA
2716 CTTAATTAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
26 27 0.69
28 12 0.31
ACGTcount: A:0.57, C:0.11, G:0.01, T:0.32
Consensus pattern (26 bp):
ATTAAATAAATTCAAACATAAAAAGA
Found at i:6033 original size:16 final size:16
Alignment explanation
Indices: 5979--6033 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
5969 TTATTTAAGT
*
5979 TATTAATTTTTTTTTG
1 TATTATTTTTTTTTTG
* **
5995 TATTA-TATTTTGGTG
1 TATTATTTTTTTTTTG
*
6010 TATAATTTTTTTTTTG
1 TATTATTTTTTTTTTG
6026 TATTATTT
1 TATTATTT
6034 ATGTCAAAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
15 11 0.37
16 19 0.63
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.71
Consensus pattern (16 bp):
TATTATTTTTTTTTTG
Found at i:7766 original size:21 final size:22
Alignment explanation
Indices: 7742--7793 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
7732 TGTCAAAAAA
**
7742 TTATACTTTTTAAAAA-TTAAT
1 TTATACTTTAAAAAAATTTAAT
7763 TTATA-TTTAAAAAAATTTAAT
1 TTATACTTTAAAAAAATTTAAT
7784 TTATATCTTT
1 TTATA-CTTT
7794 CATGTACCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 8 0.31
21 15 0.58
23 3 0.12
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (22 bp):
TTATACTTTAAAAAAATTTAAT
Found at i:7779 original size:16 final size:16
Alignment explanation
Indices: 7736--7786 Score: 50
Period size: 18 Copynumber: 3.0 Consensus size: 16
7726 TAAATTTGTC
*
7736 AAAAAATTATACTTTTTA
1 AAAAAATT-TA-TATTTA
7754 AAAATTAATTTATATTTA
1 AAAA--AATTTATATTTA
7772 AAAAAATTTA-ATTTA
1 AAAAAATTTATATTTA
7787 TATCTTTCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 5 0.17
16 6 0.20
18 13 0.43
19 2 0.07
20 4 0.13
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
AAAAAATTTATATTTA
Found at i:9987 original size:23 final size:21
Alignment explanation
Indices: 9963--10059 Score: 72
Period size: 23 Copynumber: 4.2 Consensus size: 21
9953 CTAGCGTGCT
9963 CTCTGATTAGCACTGTATGCC
1 CTCTGATTAGCACTGTATGCC
*
9984 CTCTG-TTCAGCACTGTGTGTGCC
1 CTCTGATT-AGCAC--TGTATGCC
10007 CTCTGTTATTAGCACT-TCATGTACC
1 CTCTG--ATTAGCACTGT-ATG--CC
*
10032 CTCTGATTAGCACTTTGTGTGCC
1 CTCTGATTAGCAC--TGTATGCC
10055 CTCTG
1 CTCTG
10060 TTACCCAGCA
Statistics
Matches: 61, Mismatches: 3, Indels: 22
0.71 0.03 0.26
Matches are distributed among these distances:
20 2 0.03
21 10 0.16
22 1 0.02
23 30 0.49
25 15 0.25
26 3 0.05
ACGTcount: A:0.14, C:0.29, G:0.20, T:0.37
Consensus pattern (21 bp):
CTCTGATTAGCACTGTATGCC
Found at i:10033 original size:25 final size:24
Alignment explanation
Indices: 9968--10087 Score: 99
Period size: 25 Copynumber: 5.0 Consensus size: 24
9958 GTGCTCTCTG
9968 ATTAGCACTGTA--TGCCCTCTG-T
1 ATTAGCACT-TATGTGCCCTCTGTT
* *
9990 -TCAGCACTGTGTGTGCCCTCTGTT
1 ATTAGCACT-TATGTGCCCTCTGTT
*
10014 ATTAGCACTTCATGTACCCTCTG--
1 ATTAGCACTT-ATGTGCCCTCTGTT
*
10037 ATTAGCACTTTGTGTGCCCTCTGTT
1 ATTAGCAC-TTATGTGCCCTCTGTT
**
10062 ACCCAGCACTTATGTGCCCTCTGTT
1 A-TTAGCACTTATGTGCCCTCTGTT
10087 A
1 A
10088 AGTACTTCGG
Statistics
Matches: 79, Mismatches: 10, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
21 9 0.11
23 27 0.34
24 4 0.05
25 34 0.43
26 5 0.06
ACGTcount: A:0.16, C:0.29, G:0.18, T:0.37
Consensus pattern (24 bp):
ATTAGCACTTATGTGCCCTCTGTT
Found at i:10044 original size:48 final size:48
Alignment explanation
Indices: 9982--10086 Score: 142
Period size: 48 Copynumber: 2.2 Consensus size: 48
9972 GCACTGTATG
**
9982 CCCTCTGTTCAGCACTGTGTGTGCCCTCTGTTA-TTAGCACTTCATGTA
1 CCCTCTGTTCAGCACTGTGTGTGCCCTCTGTTACCCAGCACTT-ATGTA
* *
10030 CCCTCTGATT-AGCACTTTGTGTGCCCTCTGTTACCCAGCACTTATGTG
1 CCCTCTG-TTCAGCACTGTGTGTGCCCTCTGTTACCCAGCACTTATGTA
10078 CCCTCTGTT
1 CCCTCTGTT
10087 AAGTACTTCG
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
47 2 0.04
48 40 0.78
49 9 0.18
ACGTcount: A:0.13, C:0.31, G:0.18, T:0.37
Consensus pattern (48 bp):
CCCTCTGTTCAGCACTGTGTGTGCCCTCTGTTACCCAGCACTTATGTA
Found at i:11458 original size:32 final size:30
Alignment explanation
Indices: 11384--11458 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 30
11374 AAGCGCACTC
*
11384 ATATTTATT-TTTAAATTTTTAAAAAATATAT
1 ATATTT-TTATTT-AATGTTTAAAAAATATAT
*
11415 -TATTTTAATTTAATGTTTAATAATAATATAT
1 ATATTTTTATTTAATGTTTAA-AA-AATATAT
11446 ATATTTTTATTTA
1 ATATTTTTATTTA
11459 TTAAAATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
29 9 0.24
30 10 0.27
31 7 0.19
32 11 0.30
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (30 bp):
ATATTTTTATTTAATGTTTAAAAAATATAT
Found at i:16171 original size:9 final size:9
Alignment explanation
Indices: 16147--16194 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
16137 AATGAAAGAA
*
16147 AAAGACAAG
1 AAAGAAAAG
16156 AAAAGAAAAG
1 -AAAGAAAAG
*
16166 AAAGAACAG
1 AAAGAAAAG
16175 AAAG-AAAG
1 AAAGAAAAG
*
16183 AGAGAAAAG
1 AAAGAAAAG
16192 AAA
1 AAA
16195 CGTTCATAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
8 6 0.19
9 18 0.56
10 8 0.25
ACGTcount: A:0.73, C:0.04, G:0.23, T:0.00
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:16191 original size:13 final size:12
Alignment explanation
Indices: 16141--16194 Score: 51
Period size: 13 Copynumber: 4.6 Consensus size: 12
16131 TTTAAGAATG
16141 AAAGAAA-AAGA
1 AAAGAAAGAAGA
*
16152 CAAG-AA-AAGA
1 AAAGAAAGAAGA
*
16162 AAAGAAAGAACA
1 AAAGAAAGAAGA
16174 GAAAGAAAGAGAGA
1 -AAAGAAAGA-AGA
16188 AAAGAAA
1 AAAGAAA
16195 CGTTCATAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 9 0.26
11 5 0.14
12 3 0.09
13 16 0.46
14 2 0.06
ACGTcount: A:0.74, C:0.04, G:0.22, T:0.00
Consensus pattern (12 bp):
AAAGAAAGAAGA
Found at i:25445 original size:29 final size:30
Alignment explanation
Indices: 25412--25475 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
25402 CAATTCAAGT
* *
25412 TTCATATATATAATT-ACATCAAATTAAAA
1 TTCATATATAAAATTAACATCAAAATAAAA
*
25441 TTCATGTATAAAATTACACATCAAAATAAAA
1 TTCATATATAAAATTA-ACATCAAAATAAAA
25472 TTCA
1 TTCA
25476 CGCATTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 13 0.43
31 17 0.57
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.34
Consensus pattern (30 bp):
TTCATATATAAAATTAACATCAAAATAAAA
Found at i:26365 original size:26 final size:25
Alignment explanation
Indices: 26336--26409 Score: 94
Period size: 26 Copynumber: 2.9 Consensus size: 25
26326 TTAAAAGTAA
*
26336 TTTTCAAAATCACTTTTTCAAAACAC
1 TTTTTAAAATCA-TTTTTCAAAACAC
* *
26362 TTTTTAAAGTCATTTTTTCAAAACAT
1 TTTTTAAAATCA-TTTTTCAAAACAC
*
26388 TTTTTAAAAGCATTTTTCAAAA
1 TTTTTAAAATCATTTTTCAAAA
26410 GCAATGCTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
25 10 0.24
26 32 0.76
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.45
Consensus pattern (25 bp):
TTTTTAAAATCATTTTTCAAAACAC
Found at i:26410 original size:13 final size:14
Alignment explanation
Indices: 26336--26412 Score: 76
Period size: 13 Copynumber: 5.9 Consensus size: 14
26326 TTAAAAGTAA
*
26336 TTTTCAAAATCACT
1 TTTTCAAAAGCACT
26350 TTTTCAAAA-CACT
1 TTTTCAAAAGCACT
*
26363 TTTT--AAAGTCATT
1 TTTTCAAAAG-CACT
26376 TTTTCAAAA-CA-T
1 TTTTCAAAAGCACT
*
26388 TTTTTAAAAGCA-T
1 TTTTCAAAAGCACT
26401 TTTTCAAAAGCA
1 TTTTCAAAAGCA
26413 ATGCTAAACT
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
11 3 0.05
12 9 0.16
13 31 0.56
14 9 0.16
15 3 0.05
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.43
Consensus pattern (14 bp):
TTTTCAAAAGCACT
Found at i:32046 original size:22 final size:22
Alignment explanation
Indices: 32016--32089 Score: 85
Period size: 22 Copynumber: 3.2 Consensus size: 22
32006 CTGCTGGGGA
*
32016 AACAAAAGCACACACAATGCTG
1 AACAGAAGCACACACAATGCTG
* *
32038 AACAGAAGCACACATAGTGCTGGGG
1 AACAGAAGCACACACAATGCT---G
32063 AAACAGAAGCACACACAATGCTG
1 -AACAGAAGCACACACAATGCTG
32086 AACA
1 AACA
32090 AAAGTGCGCT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
22 22 0.51
23 1 0.02
25 1 0.02
26 19 0.44
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.09
Consensus pattern (22 bp):
AACAGAAGCACACACAATGCTG
Found at i:32067 original size:26 final size:26
Alignment explanation
Indices: 32007--32085 Score: 103
Period size: 26 Copynumber: 3.2 Consensus size: 26
31997 AGTACATAAC
*
32007 TGCTGGGGAAACAAAAGCACACACAA
1 TGCTGGGGAAACAGAAGCACACACAA
* *
32033 TGCT---G-AACAGAAGCACACATAG
1 TGCTGGGGAAACAGAAGCACACACAA
32055 TGCTGGGGAAACAGAAGCACACACAA
1 TGCTGGGGAAACAGAAGCACACACAA
32081 TGCTG
1 TGCTG
32086 AACAAAAGTG
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
22 18 0.41
23 1 0.02
25 1 0.02
26 24 0.55
ACGTcount: A:0.41, C:0.23, G:0.25, T:0.11
Consensus pattern (26 bp):
TGCTGGGGAAACAGAAGCACACACAA
Found at i:35133 original size:18 final size:20
Alignment explanation
Indices: 35102--35140 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
35092 AATAAAACAT
*
35102 ATTTTATGATAATT-TTAAA
1 ATTTAATGATAATTATTAAA
35121 ATTTAATGA-AATTATTAAA
1 ATTTAATGATAATTATTAAA
35140 A
1 A
35141 AATTAATTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (20 bp):
ATTTAATGATAATTATTAAA
Found at i:35193 original size:21 final size:21
Alignment explanation
Indices: 35169--35231 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
35159 TAAAATTTAA
35169 TTATAATGATAATTTTTATAT
1 TTATAATGATAATTTTTATAT
* *
35190 TTATAATAAT-ATTATT-TAT
1 TTATAATGATAATTTTTATAT
* *
35209 CTCT-ATGATAATTTTATATAT
1 TTATAATGATAATTTT-TATAT
35230 TT
1 TT
35232 GCATTTTTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
18 4 0.12
19 9 0.28
20 6 0.19
21 13 0.41
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (21 bp):
TTATAATGATAATTTTTATAT
Found at i:37773 original size:43 final size:43
Alignment explanation
Indices: 37690--37794 Score: 113
Period size: 43 Copynumber: 2.4 Consensus size: 43
37680 TACATATCTG
** * * * *
37690 AACTTAAACTAAAATAAATTTGGACAGAGTCTACACATGGTTA
1 AACTTAAACTAAAATAAATTTAAACAAACTCTACAAATGGTGA
*
37733 AACTTAAACTAGAATAAATTTAAACAAAACTC-ACAAATGGTGA
1 AACTTAAACTAAAATAAATTTAAAC-AAACTCTACAAATGGTGA
* *
37776 AACTTGAACCAAAATAAAT
1 AACTTAAACTAAAATAAAT
37795 ATGGAGATAA
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
43 47 0.92
44 4 0.08
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.25
Consensus pattern (43 bp):
AACTTAAACTAAAATAAATTTAAACAAACTCTACAAATGGTGA
Found at i:47058 original size:12 final size:12
Alignment explanation
Indices: 47041--47070 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
47031 TTTCATATGG
47041 AAGAAACAGTGA
1 AAGAAACAGTGA
47053 AAGAAACAGTGA
1 AAGAAACAGTGA
47065 AAGAAA
1 AAGAAA
47071 AGGAATTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.63, C:0.07, G:0.23, T:0.07
Consensus pattern (12 bp):
AAGAAACAGTGA
Found at i:47518 original size:22 final size:22
Alignment explanation
Indices: 47490--47577 Score: 113
Period size: 22 Copynumber: 3.8 Consensus size: 22
47480 TTTCGTGCCC
47490 TCTGTTCAGCACTATGTGTGCT
1 TCTGTTCAGCACTATGTGTGCT
*
47512 TCTGTTCAGCACTGTGTGTGCT
1 TCTGTTCAGCACTATGTGTGCT
* *
47534 TCTGTTTAGCACTTTGTGTGCT
1 TCTGTTCAGCACTATGTGTGCT
47556 TACTGTTTCCAGCACTTATGTG
1 T-CTG-TT-CAGCAC-TATGTG
47578 CCCTCTGATA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
22 42 0.74
23 3 0.05
24 2 0.04
25 5 0.09
26 5 0.09
ACGTcount: A:0.12, C:0.22, G:0.23, T:0.43
Consensus pattern (22 bp):
TCTGTTCAGCACTATGTGTGCT
Found at i:48815 original size:107 final size:107
Alignment explanation
Indices: 48629--48911 Score: 406
Period size: 107 Copynumber: 2.7 Consensus size: 107
48619 ACAAATAGAA
* * * ** *
48629 TTTGCGCCCAGCACTAGTCGGATAAACCGACGAATGTGTGCGTAGCATTAGTTAATTAAACTGAC
1 TTTGCGCCCAACGCTAGTCGGATAAATCGACGAATGTGTGCACAGCAATAGTTAATTAAACTGAC
* *
48694 AAACAATAAGTAAGCTCAACTCTAGTTAGATTAACCAACGGT
66 AAACAATAAGTAAGCCCAACTCTAGTTAGATTAACCAACGAT
* *
48736 TTTGCGTCCAACGCTAGTCGGATAAATCGACGAATGTGTGCACAGCACTAGTTAATTAAACTGAC
1 TTTGCGCCCAACGCTAGTCGGATAAATCGACGAATGTGTGCACAGCAATAGTTAATTAAACTGAC
* *
48801 AAACAATAAGTAAGCCCAACTCTAGTTGGATTAACTAACGAT
66 AAACAATAAGTAAGCCCAACTCTAGTTAGATTAACCAACGAT
** * * *
48843 TTTGCGCCCAACGCTAGTCAAATAAATCGACG-ATATGTGCCCAGCAATAGTCAATTAAACTGAC
1 TTTGCGCCCAACGCTAGTCGGATAAATCGACGAATGTGTGCACAGCAATAGTTAATTAAACTGAC
48907 AAACA
66 AAACA
48912 TTTAGTAAAT
Statistics
Matches: 158, Mismatches: 18, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
106 33 0.21
107 125 0.79
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (107 bp):
TTTGCGCCCAACGCTAGTCGGATAAATCGACGAATGTGTGCACAGCAATAGTTAATTAAACTGAC
AAACAATAAGTAAGCCCAACTCTAGTTAGATTAACCAACGAT
Done.