Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014425.1 Kokia drynarioides strain JFW-HI SEQ_129463, 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: 16717
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:662 original size:15 final size:16
Alignment explanation
Indices: 625--662 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
615 TTTAAATTAA
*
625 TTAATTTTATTTTATT
1 TTAATTTTATTTCATT
641 TTAATTTT-TTTCATT
1 TTAATTTTATTTCATT
*
656 TTCATTT
1 TTAATTT
663 GCTTCTAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (16 bp):
TTAATTTTATTTCATT
Found at i:3501 original size:10 final size:10
Alignment explanation
Indices: 3453--3491 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
3443 CATGTTTTTA
3453 AAAAAAATTG
1 AAAAAAATTG
*
3463 AAAAAAATTT
1 AAAAAAATTG
3473 AAAAAAATTTTG
1 AAAAAAA--TTG
3485 AAAAAAA
1 AAAAAAA
3492 AAATTGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 16 0.64
12 9 0.36
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (10 bp):
AAAAAAATTG
Found at i:3537 original size:13 final size:13
Alignment explanation
Indices: 3519--3543 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3509 AAAAAATAGT
3519 ATATTTATTTTTC
1 ATATTTATTTTTC
3532 ATATTTATTTTT
1 ATATTTATTTTT
3544 AGTTTTATTT
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:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (13 bp):
ATATTTATTTTTC
Found at i:3550 original size:12 final size:11
Alignment explanation
Indices: 3522--3576 Score: 58
Period size: 12 Copynumber: 4.7 Consensus size: 11
3512 AAATAGTATA
3522 TTTATTTTTCAT
1 TTTATTTTT-AT
3534 ATTTATTTTTAGT
1 -TTTATTTTTA-T
3547 TTTA-TTTTAT
1 TTTATTTTTAT
3557 TTTATTTTTAAT
1 TTTATTTTT-AT
*
3569 TATATTTT
1 TTTATTTT
3577 AATTATGCAC
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
10 5 0.13
11 9 0.24
12 14 0.37
13 10 0.26
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:3563 original size:22 final size:22
Alignment explanation
Indices: 3535--3577 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3525 ATTTTTCATA
* *
3535 TTTATTTTTAGTTTTATTTTAT
1 TTTATTTTTAATTATATTTTAT
3557 TTTATTTTTAATTATATTTTA
1 TTTATTTTTAATTATATTTTA
3578 ATTATGCACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTATTTTTAATTATATTTTAT
Found at i:3574 original size:17 final size:17
Alignment explanation
Indices: 3518--3577 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
3508 AAAAAAATAG
3518 TATA-TTTATTTTTCATAT
1 TATATTTTATTTTT-A-AT
*
3536 T-TATTTTTAGTTTT-AT
1 TATA-TTTTATTTTTAAT
*
3552 TTTATTTTATTTTTAAT
1 TATATTTTATTTTTAAT
3569 TATATTTTA
1 TATATTTTA
3578 ATTATGCACT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
16 12 0.34
17 14 0.40
18 1 0.03
19 8 0.23
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (17 bp):
TATATTTTATTTTTAAT
Found at i:3871 original size:23 final size:23
Alignment explanation
Indices: 3836--3890 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
3826 CGTGGCGTCC
*
3836 AGTCAGCAGCTTCTAAAAGGTCT
1 AGTCAGCAACTTCTAAAAGGTCT
* *
3859 AGTTAGCAACTTCTAGAAGGTCT
1 AGTCAGCAACTTCTAAAAGGTCT
3882 AGTCAGCAA
1 AGTCAGCAA
3891 GGATGGACGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (23 bp):
AGTCAGCAACTTCTAAAAGGTCT
Found at i:4528 original size:41 final size:41
Alignment explanation
Indices: 4452--4742 Score: 372
Period size: 41 Copynumber: 7.2 Consensus size: 41
4442 TATATAAACA
* *
4452 CCGCAAAAGGT-AGAGCAATAGC-G-GCTTAAGGGAAAGCG
1 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCG
*
4490 CCGCTAAAGGTCAAAGCAATAGCGGCGCTTATGGGAAAGCG
1 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCG
* * *
4531 CCGCTAAAAGTCAGAGCAATAGCGGTGCTTATGGGAAAGCA
1 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCG
* * *
4572 CCGCTAAAGGTCAGAACAATAGCGGCGCTTATGGGCAAGAG
1 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCG
* * * * *
4613 TCGTTAAAAGTCAGAGCAATAGCGGCGCTTATGGGCAAGTG
1 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCG
* * * * *
4654 CTGCTAAAAGTTAGAGCAATAGTGACGCTTATGGGAAAGCG
1 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCG
*
4695 CCGCTAAAGGTCAAAGCAATAGCGGCGCTTATGGGAAAGCG
1 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCG
*
4736 CTGCTAA
1 CCGCTAA
4743 TTTATTTAAA
Statistics
Matches: 217, Mismatches: 33, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
38 10 0.05
39 10 0.05
40 1 0.00
41 196 0.90
ACGTcount: A:0.33, C:0.20, G:0.31, T:0.17
Consensus pattern (41 bp):
CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCG
Found at i:7928 original size:17 final size:16
Alignment explanation
Indices: 7906--7970 Score: 58
Period size: 17 Copynumber: 3.8 Consensus size: 16
7896 CGACCCTAAC
7906 AAATTTAAATTTATATT
1 AAATTTAAATTTAT-TT
**
7923 AAATTTAAATCCATTT
1 AAATTTAAATTTATTT
*
7939 GGAATTTAAATTTATTAT
1 -AAATTTAAATTTATT-T
*
7957 AAATATTAAGTTTA
1 AAAT-TTAAATTTA
7971 AATTTATTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
16 2 0.05
17 27 0.71
18 9 0.24
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.48
Consensus pattern (16 bp):
AAATTTAAATTTATTT
Found at i:9766 original size:58 final size:57
Alignment explanation
Indices: 9633--9886 Score: 257
Period size: 58 Copynumber: 4.4 Consensus size: 57
9623 CGGAGGTCCT
* * *
9633 CAAA-TTTCCAAAATTCCA-TTTTAAACCTGAACTTTTCATAAA-TTACATTTTA-CCT
1 CAAACTTTCCAAAATTCCATTTTTAACCCT-AAATTTTCA-AAATTTACATTTTACCCC
*
9688 CAAACTTTCCAAAATTCCATTTTTGACCCTAAATTTTCTAAAATTTACATTTTACCCC
1 CAAACTTTCCAAAATTCCATTTTTAACCCTAAATTTTC-AAAATTTACATTTTACCCC
* * *
9746 CAAACTTTCCAAAATTCCATTTTTTA-CCTCAATTTTCCAAATATTACATTTTTACCCC
1 CAAACTTTCCAAAATTCCATTTTTAACCCTAAATTTTCAAAAT-TTACA-TTTTACCCC
** * * * * * **
9804 TGAACATTCCAAAATTCCATTTTTAACCTTGATTTTTCCAAAAATTACCATTTTACCTT
1 CAAACTTTCCAAAATTCCATTTTTAACCCTAAATTTT-CAAAATTTA-CATTTTACCCC
*
9863 CGAACTTTCCAAAATTCCATTTTT
1 CAAACTTTCCAAAATTCCATTTTT
9887 TACCTCAATT
Statistics
Matches: 169, Mismatches: 20, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
55 4 0.02
56 28 0.17
57 34 0.20
58 58 0.34
59 39 0.23
60 6 0.04
ACGTcount: A:0.33, C:0.24, G:0.02, T:0.41
Consensus pattern (57 bp):
CAAACTTTCCAAAATTCCATTTTTAACCCTAAATTTTCAAAATTTACATTTTACCCC
Found at i:9773 original size:30 final size:29
Alignment explanation
Indices: 9630--9910 Score: 197
Period size: 29 Copynumber: 9.7 Consensus size: 29
9620 CCTCGGAGGT
* *
9630 CCTCAAA-TTTCCAAAATTCCATTTTAAA
1 CCTCAAACTTTCCAAAATTCCATTTTTAC
* * *
9658 CCT-GAACTTTTCATAAATTACA-TTTTA-
1 CCTCAAACTTTCCA-AAATTCCATTTTTAC
9685 CCTCAAACTTTCCAAAATTCCATTTTTGAC
1 CCTCAAACTTTCCAAAATTCCATTTTT-AC
* * *
9715 CCT-AAATTTTCTAAAATTTACA-TTTTAC
1 CCTCAAACTTTCCAAAA-TTCCATTTTTAC
*
9743 CCCCAAACTTTCCAAAATTCCATTTTTTA-
1 CCTCAAACTTTCCAAAATTCCA-TTTTTAC
* *
9772 CCTC-AATTTTCCAAATATTACATTTTTAC
1 CCTCAAACTTTCCAAA-ATTCCATTTTTAC
* * *
9801 CC-CTGAACATTCCAAAATTCCATTTTTAA
1 CCTC-AAACTTTCCAAAATTCCATTTTTAC
** **
9830 CCTTGATTTTTCCAAAAATTACCA-TTTTAC
1 CCTCAAACTTTCC-AAAATT-CCATTTTTAC
* *
9860 CTTCGAACTTTCCAAAATTCCATTTTTTA-
1 CCTCAAACTTTCCAAAATTCCA-TTTTTAC
**
9889 CCTCAATTTTTCCAAAAGTTCC
1 CCTCAAACTTTCCAAAA-TTCC
9911 TAAAATTCCA
Statistics
Matches: 199, Mismatches: 34, Indels: 38
0.73 0.13 0.14
Matches are distributed among these distances:
27 12 0.06
28 52 0.26
29 82 0.41
30 50 0.25
31 3 0.02
ACGTcount: A:0.32, C:0.25, G:0.02, T:0.41
Consensus pattern (29 bp):
CCTCAAACTTTCCAAAATTCCATTTTTAC
Found at i:9873 original size:59 final size:56
Alignment explanation
Indices: 9633--9905 Score: 289
Period size: 59 Copynumber: 4.8 Consensus size: 56
9623 CGGAGGTCCT
* * * *
9633 CAAA-TTTCCAAAATTCCATTTTAAACCTGAACTTTT-CATAAATTACATTTTACCT
1 CAAACTTTCCAAAATTCCATTTTTAACCT-AAATTTTCCAAAAATTACATTTTACCC
* * *
9688 CAAACTTTCCAAAATTCCATTTTTGACCCTAAATTTTCTAAAATTTACATTTTACCCC
1 CAAACTTTCCAAAATTCCATTTTT-AACCTAAATTTTCCAAAAATTACATTTTA-CCC
* * *
9746 CAAACTTTCCAAAATTCCATTTTTTACCTCAATTTTCCAAATATTACATTTTTACCC
1 CAAACTTTCCAAAATTCCATTTTTAACCTAAATTTTCCAAAAATTACA-TTTTACCC
* * * * *
9803 CTGAACATTCCAAAATTCCATTTTTAACCTTGATTTTTCCAAAAATTACCATTTTACCTT
1 C-AAACTTTCCAAAATTCCATTTTTAACC-TAAATTTTCCAAAAATTA-CATTTTACC-C
* * *
9863 CGAACTTTCCAAAATTCCATTTTTTACCTCAATTTTTCCAAAA
1 CAAACTTTCCAAAATTCCATTTTTAACCT-AAATTTTCCAAAA
9906 GTTCCTAAAA
Statistics
Matches: 185, Mismatches: 23, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
55 4 0.02
56 24 0.13
57 39 0.21
58 56 0.30
59 59 0.32
60 3 0.02
ACGTcount: A:0.33, C:0.25, G:0.02, T:0.41
Consensus pattern (56 bp):
CAAACTTTCCAAAATTCCATTTTTAACCTAAATTTTCCAAAAATTACATTTTACCC
Found at i:9936 original size:39 final size:38
Alignment explanation
Indices: 9869--9944 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 38
9859 CCTTCGAACT
*
9869 TTCCAAAATTCCATTTTTTACCTCAATTTTTCCAAAAG
1 TTCCAAAATTCCATTTTTTACCTCAATTTTTCAAAAAG
*
9907 TTCCTAAAATTCCATTTTTTA-CTGTAATTTTTCAAAAA
1 TTCC-AAAATTCCATTTTTTACCT-CAATTTTTCAAAAA
9945 TTACCATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 6 0.18
39 28 0.82
ACGTcount: A:0.33, C:0.20, G:0.03, T:0.45
Consensus pattern (38 bp):
TTCCAAAATTCCATTTTTTACCTCAATTTTTCAAAAAG
Found at i:9998 original size:97 final size:97
Alignment explanation
Indices: 9810--10002 Score: 216
Period size: 97 Copynumber: 2.0 Consensus size: 97
9800 CCCCTGAACA
* * *
9810 TTCCAAAATTCCATTTTTAACCTTGATTTTTCCAAAAATTACCATTTTACCTTCGAACTTTCCAA
1 TTCCAAAATTCCATTTTTAACCTTAATTTTTCCAAAAATTACCATTTTACCTTCGAACTGTCAAA
** * **
9875 AATTCCATTTTTTACCTCAATTTTTCCAAAAG
66 AATTCCATTTTAAACCCCAAACTTTCCAAAAG
* *
9907 TTCCTAAAATTCCATTTTTTA-CTGTAATTTTT-CAAAAATTACCATTTTA-CTAGT-GGA-TGT
1 TTCC-AAAATTCCATTTTTAACCT-TAATTTTTCCAAAAATTACCATTTTACCT--TCGAACTGT
9967 CTAAAAATTCCATTTTAAACCCCAAACTTTCCAAAA
62 C-AAAAATTCCATTTTAAACCCCAAACTTTCCAAAA
10003 AATACCATTT
Statistics
Matches: 81, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
96 5 0.06
97 53 0.65
98 23 0.28
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.41
Consensus pattern (97 bp):
TTCCAAAATTCCATTTTTAACCTTAATTTTTCCAAAAATTACCATTTTACCTTCGAACTGTCAAA
AATTCCATTTTAAACCCCAAACTTTCCAAAAG
Found at i:10055 original size:27 final size:28
Alignment explanation
Indices: 10000--10068 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
9990 AAACTTTCCA
* * *
10000 AAAAATACCATTTTGCCCTCGAGTGTCC
1 AAAAATACCATTTTGCCCCCCAGTATCC
*
10028 AAAATTACCATTTTGCCCCCCA-TATCC
1 AAAAATACCATTTTGCCCCCCAGTATCC
10055 AAAAAT-CTCATTTT
1 AAAAATAC-CATTTT
10069 CGACTCTGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 1 0.03
27 15 0.43
28 19 0.54
ACGTcount: A:0.32, C:0.29, G:0.07, T:0.32
Consensus pattern (28 bp):
AAAAATACCATTTTGCCCCCCAGTATCC
Found at i:10059 original size:28 final size:29
Alignment explanation
Indices: 9996--10060 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 29
9986 CCCCAAACTT
* * * *
9996 TCCAAAAAATACCATTTTGCCCTCGAGTG
1 TCCAAAAATTACCATTTTGCCCCCCAGTA
10025 TCC-AAAATTACCATTTTGCCCCCCA-TA
1 TCCAAAAATTACCATTTTGCCCCCCAGTA
10052 TCCAAAAAT
1 TCCAAAAAT
10061 CTCATTTTCG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 4 0.13
28 24 0.77
29 3 0.10
ACGTcount: A:0.34, C:0.31, G:0.08, T:0.28
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTGCCCCCCAGTA
Done.