Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003750.1 Hibiscus syriacus cultivar Beakdansim tig00008028_pilon, 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: 35833
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Found at i:2804 original size:15 final size:16
Alignment explanation
Indices: 2770--2806 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2760 CAAAATCCTC
*
2770 TTTTCTTTCTCTCAAT
1 TTTTCTTTCTCTCAAA
2786 TTTTCTTTCTC-CAAA
1 TTTTCTTTCTCTCAAA
2801 TTTTCT
1 TTTTCT
2807 CATTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.14, C:0.24, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTCTTTCTCTCAAA
Found at i:7455 original size:145 final size:145
Alignment explanation
Indices: 7259--7551 Score: 577
Period size: 145 Copynumber: 2.0 Consensus size: 145
7249 ACTGTAGAGA
7259 ATTGGAAATGCTGAATAGAGGTTGGTTTCATGCTTGAATCAAATTGAAATCATGAAACCCCACCC
1 ATTGGAAATGCTGAATAGAGGTTGGTTTCATGCTTGAATCAAATTGAAATCATGAAACCCCACCC
7324 CTAAAATATTCGACCTAAGCTTTTGAAAGTGAGAAAAACTATGGAAAAATTATGTACGGGTTGGA
66 CTAAAATATTCGACCTAAGCTTTTGAAAGTGAGAAAAACTATGGAAAAATTATGTACGGGTTGGA
7389 AATTATGTAGAAATG
131 AATTATGTAGAAATG
7404 ATTGGAAATGCTGAATAGAGGTTGGTTTCATGCTTGAATCAAATTGAAATCATGAAACCCCACCC
1 ATTGGAAATGCTGAATAGAGGTTGGTTTCATGCTTGAATCAAATTGAAATCATGAAACCCCACCC
*
7469 CTAAAATATTCGACCTAAGCTTTTGAAAGTGAGAAAAACTATGGAAAAATTATTTACGGGTTGGA
66 CTAAAATATTCGACCTAAGCTTTTGAAAGTGAGAAAAACTATGGAAAAATTATGTACGGGTTGGA
7534 AATTATGTAGAAATG
131 AATTATGTAGAAATG
7549 ATT
1 ATT
7552 CTACAAGCCT
Statistics
Matches: 147, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
145 147 1.00
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (145 bp):
ATTGGAAATGCTGAATAGAGGTTGGTTTCATGCTTGAATCAAATTGAAATCATGAAACCCCACCC
CTAAAATATTCGACCTAAGCTTTTGAAAGTGAGAAAAACTATGGAAAAATTATGTACGGGTTGGA
AATTATGTAGAAATG
Found at i:7719 original size:19 final size:20
Alignment explanation
Indices: 7674--7721 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
7664 TGTACTATGC
* *
7674 TTGAAATTAATGTTAGAGTG
1 TTGAAATTGATGTTAGAATG
7694 TTGAAATTGATGTTAGAATG
1 TTGAAATTGATGTTAGAATG
7714 -TGAAATTG
1 TTGAAATTG
7722 GGTCACTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.35, C:0.00, G:0.25, T:0.40
Consensus pattern (20 bp):
TTGAAATTGATGTTAGAATG
Found at i:11182 original size:15 final size:16
Alignment explanation
Indices: 11148--11184 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
11138 CAAAATCCTC
*
11148 TTTTCTTTCTCTCAAT
1 TTTTCTTTCTCTCAAA
11164 TTTTCTTTCTC-CAAA
1 TTTTCTTTCTCTCAAA
11179 TTTTCT
1 TTTTCT
11185 CATTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.14, C:0.24, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTCTTTCTCTCAAA
Found at i:12795 original size:19 final size:20
Alignment explanation
Indices: 12750--12797 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
12740 TGTACTATGC
* *
12750 TTGAAATTAATGTTAGAGTG
1 TTGAAATTGATGTTAGAATG
12770 TTGAAATTGATGTTAGAATG
1 TTGAAATTGATGTTAGAATG
12790 -TGAAATTG
1 TTGAAATTG
12798 GGTCACTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.35, C:0.00, G:0.25, T:0.40
Consensus pattern (20 bp):
TTGAAATTGATGTTAGAATG
Found at i:14387 original size:17 final size:17
Alignment explanation
Indices: 14362--14397 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
14352 AATGCAATTT
14362 TAACATATGATTGAAGC
1 TAACATATGATTGAAGC
*
14379 TAACTTATGATTGAAGC
1 TAACATATGATTGAAGC
14396 TA
1 TA
14398 GCACATAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (17 bp):
TAACATATGATTGAAGC
Found at i:15640 original size:15 final size:16
Alignment explanation
Indices: 15606--15642 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
15596 CAAAATCCTC
*
15606 TTTTCTTTCTCTCAAT
1 TTTTCTTTCTCTCAAA
15622 TTTTCTTTCTC-CAAA
1 TTTTCTTTCTCTCAAA
15637 TTTTCT
1 TTTTCT
15643 CATTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.14, C:0.24, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTCTTTCTCTCAAA
Found at i:17250 original size:19 final size:20
Alignment explanation
Indices: 17205--17252 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
17195 TGTACTATGC
* *
17205 TTGAAATTAATGTTAGAGTG
1 TTGAAATTGATGTTAGAATG
17225 TTGAAATTGATGTTAGAATG
1 TTGAAATTGATGTTAGAATG
17245 -TGAAATTG
1 TTGAAATTG
17253 GGTCACTTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.35, C:0.00, G:0.25, T:0.40
Consensus pattern (20 bp):
TTGAAATTGATGTTAGAATG
Found at i:18208 original size:10 final size:10
Alignment explanation
Indices: 18195--18219 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
18185 AAATTATTAT
18195 TAATTAAAAA
1 TAATTAAAAA
18205 TAATTAAAAA
1 TAATTAAAAA
18215 TAATT
1 TAATT
18220 TTTATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
TAATTAAAAA
Found at i:20998 original size:15 final size:16
Alignment explanation
Indices: 20964--21000 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
20954 CAAAATCCTC
*
20964 TTTTCTTTCTCTCAAT
1 TTTTCTTTCTCTCAAA
20980 TTTTCTTTCTC-CAAA
1 TTTTCTTTCTCTCAAA
20995 TTTTCT
1 TTTTCT
21001 CATTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.14, C:0.24, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTCTTTCTCTCAAA
Found at i:22735 original size:15 final size:16
Alignment explanation
Indices: 22701--22738 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
22691 CAAACTCCTC
*
22701 TTTTCTTTCTCTCAAT
1 TTTTCTTTCTCTCAAA
22717 TTTTCTTTCTC-CAAA
1 TTTTCTTTCTCTCAAA
22732 TTTTCTT
1 TTTTCTT
22739 ATTGTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.13, C:0.24, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTTCTTTCTCTCAAA
Found at i:24332 original size:19 final size:20
Alignment explanation
Indices: 24289--24332 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
24279 TACTATATTG
*
24289 GAAATTAATGTTAGAGTGTT
1 GAAATTAATGTTAGAATGTT
*
24309 GAAATTGATGTTAGAATG-T
1 GAAATTAATGTTAGAATGTT
24328 GAAAT
1 GAAAT
24333 CGGGCCACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.39, C:0.00, G:0.25, T:0.36
Consensus pattern (20 bp):
GAAATTAATGTTAGAATGTT
Found at i:29879 original size:15 final size:16
Alignment explanation
Indices: 29845--29881 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
29835 CAAACTCCTC
*
29845 TTTTCTTTCTCTCAAT
1 TTTTCTTTCTCTCAAA
29861 TTTTCTTTCTC-CAAA
1 TTTTCTTTCTCTCAAA
29876 TTTTCT
1 TTTTCT
29882 CATTTTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.14, C:0.24, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTCTTTCTCTCAAA
Found at i:31341 original size:19 final size:19
Alignment explanation
Indices: 31317--31361 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
31307 TACTATGCTA
* *
31317 GAAATTGATATTAGAGTTT
1 GAAATTGATATTAGAATGT
*
31336 GAAATTGATGTTAGAATGT
1 GAAATTGATATTAGAATGT
31355 GAAATTG
1 GAAATTG
31362 GGTCACTTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.24, T:0.38
Consensus pattern (19 bp):
GAAATTGATATTAGAATGT
Found at i:33119 original size:19 final size:20
Alignment explanation
Indices: 33083--33121 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
33073 GGATAAGCTG
*
33083 AATCTGTTCTATTTTAACCA
1 AATCTGTTATATTTTAACCA
33103 AATCTGTTATA-TTTAACCA
1 AATCTGTTATATTTTAACCA
33122 TACACGCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.33, C:0.18, G:0.05, T:0.44
Consensus pattern (20 bp):
AATCTGTTATATTTTAACCA
Found at i:34250 original size:31 final size:30
Alignment explanation
Indices: 34193--34267 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
34183 AGGGCCACGG
34193 GGCCTACCCAAGAAAAATCCCAAGGTCGCAA
1 GGCCTACCCAAGAAAAATCCCAAGGTCG-AA
** * *
34224 GGCCTACCCAAGAATGATCTCGAGGTCGAA
1 GGCCTACCCAAGAAAAATCCCAAGGTCGAA
*
34254 GATCCTACCCAAGA
1 G-GCCTACCCAAGA
34268 GTCACAAGGT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
30 3 0.08
31 35 0.92
ACGTcount: A:0.35, C:0.31, G:0.21, T:0.13
Consensus pattern (30 bp):
GGCCTACCCAAGAAAAATCCCAAGGTCGAA
Done.