Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012598.1 Kokia drynarioides strain JFW-HI SEQ_127607, 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: 29725
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:649 original size:18 final size:18
Alignment explanation
Indices: 626--660 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
616 CATCTAATAC
*
626 TGTTCCTTGTAATTATTT
1 TGTTCCTTGTAAATATTT
644 TGTTCCTTGTAAATATT
1 TGTTCCTTGTAAATATT
661 CGGCAATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.11, G:0.11, T:0.57
Consensus pattern (18 bp):
TGTTCCTTGTAAATATTT
Found at i:1227 original size:49 final size:50
Alignment explanation
Indices: 1087--1554 Score: 293
Period size: 49 Copynumber: 9.5 Consensus size: 50
1077 GTACCACGAA
* * * *
1087 ACATGAAGGGAAAGATTTAAGCCGCAATGACGAATCCAATACC-AAGAAG
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCTCAGAAG
* * ** * * *
1136 ATATAAAGGGAAATG-TTTAAATCGCAGCGGC-AAACCGTGTACCTCAGAAG
1 ACATGAAGGGAAA-GATTTAAGCCGCAACGGCGAATCC-AGTACCTCAGAAG
*
1186 -CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACA-AAG
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCTCAGAAG
** * * * * ** *
1234 ACACAAAGGGAAGGGTTTAAGTCACAACGGCGAACTTTA-TACCTGAG-AG
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAA-TCCAGTACCTCAGAAG
* * * *
1283 ACATGAAGGGAAATATTTAAGCTGAAACGGCGAATCCAGTACCAC-GAAG
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCTCAGAAG
* * * * * * *
1332 ACA-CAAGGGAAAGGTCTAAGTCACAATGACGAA-CCTAGTACCTCAG-AG
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCTCAGAAG
* * * *
1380 ACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCTAGTACCGCA-AAG
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCTCAGAAG
* ** * * ** *
1429 ATACA-AAAGGGAAAGGCTTAAGTCGCAATGATGAA-CCTAGCACCTCA-AAG
1 --ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCTCAGAAG
** *
1479 ACATGAAGGGAAAGATTTAAGCCGCAACGGTAAATCCAGTACCAC-GAAG
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCTCAGAAG
* ** * *
1528 GCACAAAGGGAAAGGTTTAAGTCGCAA
1 ACATGAAGGGAAAGATTTAAGCCGCAA
1555 TGGTAACCTT
Statistics
Matches: 310, Mismatches: 88, Indels: 42
0.70 0.20 0.10
Matches are distributed among these distances:
47 2 0.01
48 46 0.15
49 213 0.69
50 46 0.15
51 3 0.01
ACGTcount: A:0.40, C:0.20, G:0.25, T:0.15
Consensus pattern (50 bp):
ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCTCAGAAG
Found at i:1474 original size:99 final size:98
Alignment explanation
Indices: 1087--1556 Score: 527
Period size: 98 Copynumber: 4.8 Consensus size: 98
1077 GTACCACGAA
* * * * * *
1087 ACATGAAGGGAAAGATTTAAGCCGCAATGACGAATCCAATACCA-AGAAGATATAAAGGGAAATG
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACA-AAGACACAAAGGGAAAGG
* * ** * *
1151 TTTAAATCGCAGCGGCAAACCGT-GTACCTCAGA-
65 TTTAAGTCACAATGACGAACC-TAGTACCTCAGAG
*
1184 AGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAAAGACACAAAGGGAAGGG
1 A-CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAAAGACACAAAGGGAAAGG
* * * *
1249 TTTAAGTCACAACGGCGAACTTTA-TACCTGAGAG
65 TTTAAGTCACAATGACGAAC-CTAGTACCTCAGAG
* * * *
1283 ACATGAAGGGAAATATTTAAGCTGAAACGGCGAATCCAGTACCACGAAGACAC-AAGGGAAAGGT
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAAAGACACAAAGGGAAAGGT
*
1347 CTAAGTCACAATGACGAACCTAGTACCTCAGAG
66 TTAAGTCACAATGACGAACCTAGTACCTCAGAG
* * * * *
1380 ACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCTAGTACCGCAAAGATACAAAAGGGAAAGG
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAAAGACAC-AAAGGGAAAGG
* * * * *
1445 CTTAAGTCGCAATGATGAACCTAGCACCTCAAAG
65 TTTAAGTCACAATGACGAACCTAGTACCTCAGAG
** * *
1479 ACATGAAGGGAAAGATTTAAGCCGCAACGGTAAATCCAGTACCACGAAGGCACAAAGGGAAAGGT
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAAAGACACAAAGGGAAAGGT
*
1544 TTAAGTCGCAATG
66 TTAAGTCACAATG
1557 GTAACCTTGT
Statistics
Matches: 317, Mismatches: 48, Indels: 15
0.83 0.13 0.04
Matches are distributed among these distances:
96 2 0.01
97 80 0.25
98 151 0.48
99 84 0.26
ACGTcount: A:0.40, C:0.20, G:0.25, T:0.16
Consensus pattern (98 bp):
ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAAAGACACAAAGGGAAAGGT
TTAAGTCACAATGACGAACCTAGTACCTCAGAG
Found at i:2282 original size:17 final size:17
Alignment explanation
Indices: 2260--2341 Score: 74
Period size: 17 Copynumber: 4.8 Consensus size: 17
2250 TGTGGATTGT
*
2260 TTTTAAATTTTAAGTTA
1 TTTTAAATTTAAAGTTA
* *
2277 TTTTAAGTTTAAATTTA
1 TTTTAAATTTAAAGTTA
*
2294 TTTTAAATTTAAACTTA
1 TTTTAAATTTAAAGTTA
* *** *
2311 CTTTGGGTTTAAATTTA
1 TTTTAAATTTAAAGTTA
2328 TTTTAAAATTTAAA
1 TTTT-AAATTTAAA
2342 TTTAAAAGTC
Statistics
Matches: 50, Mismatches: 14, Indels: 1
0.77 0.22 0.02
Matches are distributed among these distances:
17 44 0.88
18 6 0.12
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (17 bp):
TTTTAAATTTAAAGTTA
Found at i:2303 original size:34 final size:34
Alignment explanation
Indices: 2260--2340 Score: 108
Period size: 34 Copynumber: 2.4 Consensus size: 34
2250 TGTGGATTGT
* *
2260 TTTTAAATTTTAAGTTATTTTAAGTTTAAATTTA
1 TTTTAAATTTTAACTTACTTTAAGTTTAAATTTA
* **
2294 TTTTAAATTTAAACTTACTTTGGGTTTAAATTTA
1 TTTTAAATTTTAACTTACTTTAAGTTTAAATTTA
*
2328 TTTTAAAATTTAA
1 TTTTAAATTTTAA
2341 ATTTAAAAGT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.56
Consensus pattern (34 bp):
TTTTAAATTTTAACTTACTTTAAGTTTAAATTTA
Found at i:3155 original size:20 final size:20
Alignment explanation
Indices: 3060--3168 Score: 68
Period size: 18 Copynumber: 5.5 Consensus size: 20
3050 ACATTAATAA
*
3060 TAATAAT-AATAATAA-TAA
1 TAATAATAAATAATAATTAT
*
3078 TAATAATAAA-AATAA-TAC
1 TAATAATAAATAATAATTAT
* * *
3096 TAATAAT-ATTGATAA-CAT
1 TAATAATAAATAATAATTAT
3114 TAATAACTGTAATAATAATAATTAT
1 TAATAA---T-A-AATAATAATTAT
* *
3139 TAATAATAAATATTAATTTT
1 TAATAATAAATAATAATTAT
3159 TAATAATAAA
1 TAATAATAAA
3169 AAAGAAAAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 16
0.73 0.10 0.16
Matches are distributed among these distances:
17 1 0.01
18 32 0.44
19 2 0.03
20 20 0.28
21 2 0.03
22 1 0.01
24 6 0.08
25 8 0.11
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.38
Consensus pattern (20 bp):
TAATAATAAATAATAATTAT
Found at i:3167 original size:3 final size:3
Alignment explanation
Indices: 3054--3147 Score: 91
Period size: 3 Copynumber: 31.0 Consensus size: 3
3044 TTGATAACAT
* *
3054 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA AAA TAA TAC TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
3102 TAT TGA TAA CAT TAA TAA CT-G TAA TAA TAA TAA TTAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA -TAA TAA TAA TAA
3148 ATATTAATTT
Statistics
Matches: 72, Mismatches: 16, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
2 1 0.01
3 68 0.94
4 3 0.04
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:4383 original size:58 final size:58
Alignment explanation
Indices: 4288--4496 Score: 187
Period size: 57 Copynumber: 3.6 Consensus size: 58
4278 CCTTAAAGGT
* * * ** ***
4288 CCCTAAATTGTCCATAAATTACATTTTTATTCCGAACTTTCCAAAATTTTATTTTTGA
1 CCCTGAATTTTCCAAAAATTACATTTTTACCCCGAACTTTCCAAAATACAATTTTTGA
*
4346 CCCT-AATTTTCCAAAAATTACTTTTTTAGCCCCGAACTTTCCAAAATACAATTTTTGA
1 CCCTGAATTTTCCAAAAATTACATTTTTA-CCCCGAACTTTCCAAAATACAATTTTTGA
* * * *
4404 -CCTGGATTTTTCTAAAAATTACATTTTTACCCTCGAAC-TTCTAAAATACCA-TTTTGA
1 CCCT-GAATTTTCCAAAAATTACATTTTTACCC-CGAACTTTCCAAAATACAATTTTTGA
* * *
4461 CCCAG-ATTCTTTCAAAAATTACCA-TTTTCCCCCGAA
1 CCCTGAATT-TTCCAAAAATTA-CATTTTTACCCCGAA
4497 TGTCTAAAAA
Statistics
Matches: 126, Mismatches: 18, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
56 6 0.05
57 48 0.38
58 46 0.37
59 26 0.21
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.39
Consensus pattern (58 bp):
CCCTGAATTTTCCAAAAATTACATTTTTACCCCGAACTTTCCAAAATACAATTTTTGA
Found at i:4507 original size:57 final size:57
Alignment explanation
Indices: 4340--4505 Score: 164
Period size: 59 Copynumber: 2.9 Consensus size: 57
4330 AAAATTTTAT
* * * * *
4340 TTTTGACCCTA-A-TTTTCCAAAAATTACTTTTTTAGCCCCGAACTTTCCAAAATACAA
1 TTTTGACCC-AGATTTTTCTAAAAATTACATTTTTACCCCCGAAC-TTCTAAAATACCA
** *
4397 TTTTTGACCTGGATTTTTCTAAAAATTACATTTTTACCCTCGAACTTCTAAAATACCA
1 -TTTTGACCCAGATTTTTCTAAAAATTACATTTTTACCCCCGAACTTCTAAAATACCA
4455 TTTTGACCCAGATTCTTTC-AAAAATTACCA-TTTT-CCCCCGAA-TGTCTAAAA
1 TTTTGACCCAGATT-TTTCTAAAAATTA-CATTTTTACCCCCGAACT-TCTAAAA
4506 ATCCCGTTTT
Statistics
Matches: 92, Mismatches: 11, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
55 1 0.01
56 14 0.15
57 24 0.26
58 26 0.28
59 27 0.29
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.38
Consensus pattern (57 bp):
TTTTGACCCAGATTTTTCTAAAAATTACATTTTTACCCCCGAACTTCTAAAATACCA
Found at i:4594 original size:29 final size:29
Alignment explanation
Indices: 4533--4592 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
4523 GAATTTGCCC
**
4533 AAATTACTATTTTGCCCCTCAAGTGTCCA
1 AAATTACTATTTTGCCCCTCAAGCATCCA
*
4562 AAATTACTATTTTG-CCCTCGAGCATCCA
1 AAATTACTATTTTGCCCCTCAAGCATCCA
4590 AAA
1 AAA
4593 ATCTCGTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.32, C:0.27, G:0.10, T:0.32
Consensus pattern (29 bp):
AAATTACTATTTTGCCCCTCAAGCATCCA
Found at i:18956 original size:19 final size:19
Alignment explanation
Indices: 18934--18978 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
18924 TTGTGTTACA
*
18934 AGTAATTAGGGAAGTTAGG
1 AGTAATTAGAGAAGTTAGG
18953 AGTAATTAGAGAAGTTAGG
1 AGTAATTAGAGAAGTTAGG
18972 AGTAATT
1 AGTAATT
18979 TATGGGATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.31, T:0.29
Consensus pattern (19 bp):
AGTAATTAGAGAAGTTAGG
Done.