Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001375.1 Kokia drynarioides strain JFW-HI SEQ_112843, 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: 28238
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Found at i:1700 original size:17 final size:17
Alignment explanation
Indices: 1678--1712 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1668 CAGGAATGGA
1678 GTTTACACTTGAAAAAG
1 GTTTACACTTGAAAAAG
1695 GTTTACACTTGAAAAAG
1 GTTTACACTTGAAAAAG
1712 G
1 G
1713 ATCAAAGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (17 bp):
GTTTACACTTGAAAAAG
Found at i:4773 original size:19 final size:19
Alignment explanation
Indices: 4749--4794 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
4739 TGGTGGAAAT
* * *
4749 AATAAATTATGCATAATAA
1 AATAAAATATACAAAATAA
*
4768 AATAAAATATATAAAATAA
1 AATAAAATATACAAAATAA
4787 AATAAAAT
1 AATAAAAT
4795 GAAATTTTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (19 bp):
AATAAAATATACAAAATAA
Found at i:4781 original size:14 final size:14
Alignment explanation
Indices: 4764--4790 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4754 ATTATGCATA
4764 ATAAAATAAAATAT
1 ATAAAATAAAATAT
4778 ATAAAATAAAATA
1 ATAAAATAAAATA
4791 AAATGAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
ATAAAATAAAATAT
Found at i:7290 original size:18 final size:18
Alignment explanation
Indices: 7269--7303 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
7259 ATAGTTTATA
* *
7269 ATAATAAAATTAAAAAGT
1 ATAAAAAAATGAAAAAGT
7287 ATAAAAAAATGAAAAAG
1 ATAAAAAAATGAAAAAG
7304 GCAAAAAGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20
Consensus pattern (18 bp):
ATAAAAAAATGAAAAAGT
Found at i:7677 original size:5 final size:5
Alignment explanation
Indices: 7667--7691 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
7657 TATAAAGTGC
7667 ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT
7692 TACGAAGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:9466 original size:31 final size:30
Alignment explanation
Indices: 9393--9468 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 30
9383 TTTAATATCT
* * * * *
9393 TATATTTTTATTATTTTTAAATGATTAAAT
1 TATAATTTTATCATTTTTAAAGGATCAAAA
9423 TA-AATTTTTATCATTTTTAAAAGGATCAAAA
1 TATAA-TTTTATCATTTTT-AAAGGATCAAAA
9454 TATAATTTTATCATT
1 TATAATTTTATCATT
9469 ACCAATTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
29 1 0.03
30 14 0.37
31 21 0.55
32 2 0.05
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (30 bp):
TATAATTTTATCATTTTTAAAGGATCAAAA
Found at i:11883 original size:3 final size:3
Alignment explanation
Indices: 11875--11905 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
11865 TCACTTCTTG
*
11875 ATC ATC ATC ACC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
11906 CTTCTTTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.29
Consensus pattern (3 bp):
ATC
Found at i:16274 original size:22 final size:22
Alignment explanation
Indices: 16249--16295 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
16239 TTATTTGTTC
16249 AAATTTGA-ATATTATAAAGACT
1 AAATTTGACATATT-TAAAGACT
*
16271 AAA-TTGACCTATTTAAAGACT
1 AAATTTGACATATTTAAAGACT
16292 AAAT
1 AAAT
16296 ACTCTCCGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.34
Consensus pattern (22 bp):
AAATTTGACATATTTAAAGACT
Found at i:20195 original size:19 final size:19
Alignment explanation
Indices: 20164--20213 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 19
20154 TAATTAGTAT
20164 TTAAAAGATTATG-TTTTGAA
1 TTAAAA-ATTATGATTTT-AA
20184 TTAAAAATTATGATTTTAA
1 TTAAAAATTATGATTTTAA
20203 TTATAAAATTA
1 TTA-AAAATTA
20214 ATAAATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (19 bp):
TTAAAAATTATGATTTTAA
Found at i:20210 original size:21 final size:20
Alignment explanation
Indices: 20164--20205 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
20154 TAATTAGTAT
20164 TTAAAAGATTATGTTTTGAA
1 TTAAAAGATTATGTTTTGAA
20184 TTAAAA-ATTATGATTTT-AA
1 TTAAAAGATTATG-TTTTGAA
20203 TTA
1 TTA
20206 TAAAATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.48
Consensus pattern (20 bp):
TTAAAAGATTATGTTTTGAA
Found at i:20591 original size:55 final size:55
Alignment explanation
Indices: 20521--20663 Score: 169
Period size: 55 Copynumber: 2.6 Consensus size: 55
20511 TTTTTTTAAT
* * * *
20521 TGTTGGAATACTGCTTCTCTTGAATCAATTTTTTATATGTTTAAATTGATTGTCA
1 TGTTCGAATACTGCTTCTTTTGAATCAATTTTTTATACGTTTAAATCGATTGTCA
* * * * * *
20576 TGTTCGAATATTGCTTATTTTGAAGCTATTGTTTATACGTTTAAATCGATTGTTA
1 TGTTCGAATACTGCTTCTTTTGAATCAATTTTTTATACGTTTAAATCGATTGTCA
* * *
20631 TGTTCAAATACCGTTTCTTTTGAATCAATTTTT
1 TGTTCGAATACTGCTTCTTTTGAATCAATTTTT
20664 ACATAGCACA
Statistics
Matches: 70, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
55 70 1.00
ACGTcount: A:0.25, C:0.11, G:0.14, T:0.50
Consensus pattern (55 bp):
TGTTCGAATACTGCTTCTTTTGAATCAATTTTTTATACGTTTAAATCGATTGTCA
Found at i:22377 original size:43 final size:43
Alignment explanation
Indices: 22270--22479 Score: 169
Period size: 43 Copynumber: 4.7 Consensus size: 43
22260 ATAGAAACGT
*
22270 CGCTAAAGAACATGGTATTTAGC-A-GCGTTTCTACCACAAACAC
1 CGCTAAAGAACATGGTCTTTAGCGACG-GTTT-TACCACAAACAC
*
22313 CGCTAAA-AAGCGTGGTCTTTAGCGACGGTTTTACCACAAACAC
1 CGCTAAAGAA-CATGGTCTTTAGCGACGGTTTTACCACAAACAC
* * * * * * *
22356 CGTTAAAGAACATGATTTTTAGTGGCGCTTTTATCACAAACGCCGCTAGC
1 CGCTAAAGAACATGGTCTTTAGCGACGGTTTTACCACAAA-----C-A-C
* * *
22406 CGCTAAAGAACATGGTCTTTAGCGGCGCTTTT-CTCACAAACAT
1 CGCTAAAGAACATGGTCTTTAGCGACGGTTTTAC-CACAAACAC
*
22449 CGTTAAAGAACATGGTCTTTAGCGA-GGTTTT
1 CGCTAAAGAACATGGTCTTTAGCGACGGTTTT
22480 TCCTATAAAT
Statistics
Matches: 136, Mismatches: 19, Indels: 25
0.76 0.11 0.14
Matches are distributed among these distances:
42 7 0.05
43 82 0.60
44 8 0.06
45 2 0.01
48 1 0.01
49 1 0.01
50 35 0.26
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.28
Consensus pattern (43 bp):
CGCTAAAGAACATGGTCTTTAGCGACGGTTTTACCACAAACAC
Found at i:25274 original size:41 final size:41
Alignment explanation
Indices: 25190--25365 Score: 227
Period size: 41 Copynumber: 4.4 Consensus size: 41
25180 GCTGCTAGTA
*
25190 CTCTGACCTTTAGCGACACTTTCTCAT-AACGCCGCTAATG
1 CTCTGACCTTTAGCGACGCTTTCTCATAAACGCCGCTAATG
*
25230 CTCTGACCTTTAGC-AGCGCTTTTTCATAAACGCCGCTAATG
1 CTCTGACCTTTAGCGA-CGCTTTCTCATAAACGCCGCTAATG
* *
25271 CTCTGACCTTTAGCGACGCTTTCTCATAAATGACC-CTGATG
1 CTCTGACCTTTAGCGACGCTTTCTCATAAACG-CCGCTAATG
* * * *
25312 CTCTGACC--TAGCGACGCTTTCACATAAATGCTGTTAATG
1 CTCTGACCTTTAGCGACGCTTTCTCATAAACGCCGCTAATG
25351 CTCTGACCTTTAGCG
1 CTCTGACCTTTAGCG
25366 GCGTTTTTCC
Statistics
Matches: 120, Mismatches: 9, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
38 1 0.01
39 34 0.28
40 23 0.19
41 59 0.49
42 3 0.03
ACGTcount: A:0.22, C:0.30, G:0.17, T:0.31
Consensus pattern (41 bp):
CTCTGACCTTTAGCGACGCTTTCTCATAAACGCCGCTAATG
Found at i:25275 original size:81 final size:82
Alignment explanation
Indices: 25136--25365 Score: 251
Period size: 80 Copynumber: 2.9 Consensus size: 82
25126 GCTTATGGGA
* * * * *
25136 AAACGCCGCTATTGCT-TAACCTTTAGCAGCG--TTTACGAGAAAGCGCTGCTAGTACTCTGACC
1 AAACGCCGCTAATGCTCTGACCTTTAGCAGCGCTTTTAC-ATAAA-CGCTGCTAATGCTCTGACC
25198 TTTAGCGACACTTTCTCAT
64 TTTAGCGACACTTTCTCAT
* *
25217 -AACGCCGCTAATGCTCTGACCTTTAGCAGCGCTTTTTCATAAACGCCGCTAATGCTCTGACCTT
1 AAACGCCGCTAATGCTCTGACCTTTAGCAGCGCTTTTACATAAACGCTGCTAATGCTCTGACCTT
*
25281 TAGCGACGCTTTCTCAT
66 TAGCGACACTTTCTCAT
* * * * *
25298 AAATGACC-CTGATGCTCTGACC--TAGC-GACGCTTTCACATAAATGCTGTTAATGCTCTGACC
1 AAACG-CCGCTAATGCTCTGACCTTTAGCAG-CGCTTTTACATAAACGCTGCTAATGCTCTGACC
25359 TTTAGCG
64 TTTAGCG
25366 GCGTTTTTCC
Statistics
Matches: 128, Mismatches: 15, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
79 1 0.01
80 53 0.41
81 48 0.38
82 20 0.16
83 6 0.05
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.30
Consensus pattern (82 bp):
AAACGCCGCTAATGCTCTGACCTTTAGCAGCGCTTTTACATAAACGCTGCTAATGCTCTGACCTT
TAGCGACACTTTCTCAT
Found at i:25408 original size:121 final size:121
Alignment explanation
Indices: 25190--25409 Score: 284
Period size: 121 Copynumber: 1.8 Consensus size: 121
25180 GCTGCTAGTA
*
25190 CTCTGACCTTTAGCGACACTTTCTCATAACGCCGCTAATGCTCTGACCTTTAGCAGCGCTTTTTC
1 CTCTGACC-TTAGCGACACTTTCACATAACGCCGCTAATGCTCTGACCTTTAGCAGCGCTTTTTC
*
25255 ATAAACGCCGCTAATGCTCTGACCTTTAGCGACGCTTTCTCATAAATGACCCTGATG
65 ATAAACGCCGCTAATACTCTGACCTTTAGCGACGCTTTCTCATAAATGACCCTGATG
* * * * *
25312 CTCTGACC-TAGCGACGCTTTCACATAAATGCTGTTAATGCTCTGACCTTTAGCGGCG-TTTTTC
1 CTCTGACCTTAGCGACACTTTCACAT-AACGCCGCTAATGCTCTGACCTTTAGCAGCGCTTTTT-
* * * *
25375 CTATAAATGCCGCTATTACT-TTACCTTTTGCGACG
64 C-ATAAACGCCGCTAATACTCTGACCTTTAGCGACG
25410 TTTATGTCCA
Statistics
Matches: 84, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
120 20 0.24
121 41 0.49
122 23 0.27
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (121 bp):
CTCTGACCTTAGCGACACTTTCACATAACGCCGCTAATGCTCTGACCTTTAGCAGCGCTTTTTCA
TAAACGCCGCTAATACTCTGACCTTTAGCGACGCTTTCTCATAAATGACCCTGATG
Done.