Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008425.1 Hibiscus syriacus cultivar Beakdansim tig00111208_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: 2340112
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 12
Found at i:2269201 original size:28 final size:28
Alignment explanation
Indices: 2269147--2269211 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
2269137 TTTTTTTTAT
* **
2269147 TTTTTAAACAAATCTTTGAGTCTGTTTC
1 TTTTGAAACAAATCTTTGAGTAGGTTTC
2269175 TTTTGAAACAAATCTTTGAGTAGGTTTC
1 TTTTGAAACAAATCTTTGAGTAGGTTTC
**
2269203 CCTTGAAAC
1 TTTTGAAAC
2269212 CATAATCACT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (28 bp):
TTTTGAAACAAATCTTTGAGTAGGTTTC
Found at i:2269418 original size:40 final size:39
Alignment explanation
Indices: 2269374--2269602 Score: 113
Period size: 40 Copynumber: 5.5 Consensus size: 39
2269364 CAAGAACTCT
*
2269374 TCATCACGTATAAGCCGTGTCATCCCCCGACCAAATTTCC
1 TCATCACGTATAA-CCGTGTCATCCCACGACCAAATTTCC
* * * ** *
2269414 TCATCACGTAGGAACCGTGTCA-CCCTTATATGGCCAAGAACTCT
1 TCATCACGTA-TAACCGTGTCATCCC----ACGACCAA-ATTTCC
** * *
2269458 TCATCACGTATGAGTCGTGTCATCCCCCGACCAGATTTCC
1 TCATCACGTAT-AACCGTGTCATCCCACGACCAAATTTCC
* * *
2269498 TCATCACGTAGGAACCGTGTCA-CCCTTAAACGACCAGAA-CTCT
1 TCATCACGTA-TAACCGTGTCATCCC----ACGACCA-AATTTCC
* ** * *
2269541 TCATCATGTATGATTCGTGTCATCCCTCGACCAGATTTCC
1 TCATCACGTAT-AACCGTGTCATCCCACGACCAAATTTCC
*
2269581 TCATCACGTAGGAACCGTGTCA
1 TCATCACGTA-TAACCGTGTCA
2269603 CTCTTAGACG
Statistics
Matches: 135, Mismatches: 36, Indels: 36
0.65 0.17 0.17
Matches are distributed among these distances:
39 7 0.05
40 64 0.47
41 6 0.04
43 30 0.22
44 25 0.19
45 3 0.02
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.26
Consensus pattern (39 bp):
TCATCACGTATAACCGTGTCATCCCACGACCAAATTTCC
Found at i:2269546 original size:43 final size:42
Alignment explanation
Indices: 2269414--2269645 Score: 170
Period size: 43 Copynumber: 5.5 Consensus size: 42
2269404 CCAAATTTCC
* *
2269414 TCATCACGTAGGAACCGTGTCACCCTTATATGGCCAAGAACTCT
1 TCATCACGTAGGAACCGTGTCACCCTTA-ACGACC-AGAACTCT
* ** * ** *
2269458 TCATCACGTATGAGTCGTGTCATCCC---CCGACCAGATTTCC
1 TCATCACGTAGGAACCGTGTCA-CCCTTAACGACCAGAACTCT
2269498 TCATCACGTAGGAACCGTGTCACCCTTAAACGACCAGAACTCT
1 TCATCACGTAGGAACCGTGTCACCCTT-AACGACCAGAACTCT
* * ** ** *
2269541 TCATCATGTATGATTCGTGTCATCCC-T--CGACCAGATTTCC
1 TCATCACGTAGGAACCGTGTCA-CCCTTAACGACCAGAACTCT
* * *
2269581 TCATCACGTAGGAACCGTGTCACTCTTAGACGACAAAAACTCT
1 TCATCACGTAGGAACCGTGTCACCCTTA-ACGACCAGAACTCT
* * *
2269624 TCATCGCGTATGAGCCGTGTCA
1 TCATCACGTAGGAACCGTGTCA
2269646 TCTCCACCAA
Statistics
Matches: 142, Mismatches: 36, Indels: 21
0.71 0.18 0.11
Matches are distributed among these distances:
39 5 0.04
40 53 0.37
41 3 0.02
43 56 0.39
44 22 0.15
45 3 0.02
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (42 bp):
TCATCACGTAGGAACCGTGTCACCCTTAACGACCAGAACTCT
Found at i:2269574 original size:83 final size:83
Alignment explanation
Indices: 2269366--2269647 Score: 420
Period size: 83 Copynumber: 3.4 Consensus size: 83
2269356 AAGATGGCCA
* *
2269366 AGAACTCTTCATCACGTATAAGCCGTGTCATCCCCCGACCAAATTTCCTCATCACGTAGGAACCG
1 AGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGATTTCCTCATCACGTAGGAACCG
* * *
2269431 TGTCACCCTTATATGGCC
66 TGTCACCCTTAAACGACC
*
2269449 AAGAACTCTTCATCACGTATGAGTCGTGTCATCCCCCGACCAGATTTCCTCATCACGTAGGAACC
1 -AGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGATTTCCTCATCACGTAGGAACC
2269514 GTGTCACCCTTAAACGACC
65 GTGTCACCCTTAAACGACC
* ** *
2269533 AGAACTCTTCATCATGTATGATTCGTGTCATCCCTCGACCAGATTTCCTCATCACGTAGGAACCG
1 AGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGATTTCCTCATCACGTAGGAACCG
* * *
2269598 TGTCACTCTTAGACGACA
66 TGTCACCCTTAAACGACC
* *
2269616 AAAACTCTTCATCGCGTATGAGCCGTGTCATC
1 AGAACTCTTCATCACGTATGAGCCGTGTCATC
2269648 TCCACCAACA
Statistics
Matches: 181, Mismatches: 17, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
83 104 0.57
84 77 0.43
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.26
Consensus pattern (83 bp):
AGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGATTTCCTCATCACGTAGGAACCG
TGTCACCCTTAAACGACC
Found at i:2270454 original size:14 final size:14
Alignment explanation
Indices: 2270435--2270467 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2270425 GAGAGGAACG
*
2270435 AAAAAAAAACCAGA
1 AAAAAAAAACAAGA
2270449 AAAAAAAAACAAGA
1 AAAAAAAAACAAGA
2270463 AAAAA
1 AAAAA
2270468 GAGAACTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.85, C:0.09, G:0.06, T:0.00
Consensus pattern (14 bp):
AAAAAAAAACAAGA
Found at i:2272900 original size:13 final size:13
Alignment explanation
Indices: 2272882--2272908 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2272872 GTTAATAAAA
2272882 AGCTTCTTCTGTC
1 AGCTTCTTCTGTC
2272895 AGCTTCTTCTGTC
1 AGCTTCTTCTGTC
2272908 A
1 A
2272909 TCTCTCCCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.11, C:0.30, G:0.15, T:0.44
Consensus pattern (13 bp):
AGCTTCTTCTGTC
Found at i:2281014 original size:13 final size:14
Alignment explanation
Indices: 2280991--2281044 Score: 67
Period size: 14 Copynumber: 3.9 Consensus size: 14
2280981 TAAATAATGA
2280991 AAACAATTAAATAC
1 AAACAATTAAATAC
2281005 AAAC-ATTAAATAC
1 AAACAATTAAATAC
* *
2281018 AAACGA-TACAATTC
1 AAACAATTA-AATAC
2281032 AAACAATTAAATA
1 AAACAATTAAATA
2281045 ATAAAAACTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 15 0.44
14 17 0.50
15 2 0.06
ACGTcount: A:0.61, C:0.15, G:0.02, T:0.22
Consensus pattern (14 bp):
AAACAATTAAATAC
Found at i:2282389 original size:22 final size:23
Alignment explanation
Indices: 2282358--2282400 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
2282348 TATTCAATGT
2282358 AAAAATAATTTCA-TTATATACTC
1 AAAAATAATTT-ATTTATATACTC
2282381 AAAAA-AATTTATTTATATAC
1 AAAAATAATTTATTTATATAC
2282401 GAACTCAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 1 0.05
22 13 0.68
23 5 0.26
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (23 bp):
AAAAATAATTTATTTATATACTC
Found at i:2283141 original size:22 final size:22
Alignment explanation
Indices: 2283116--2283163 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2283106 TGGATCTAAT
*
2283116 ATACGAATTAAAAAA-ATAATTA
1 ATACAAATTAAAAAATA-AATTA
*
2283138 ATACAAATTAAAATATAAATTA
1 ATACAAATTAAAAAATAAATTA
2283160 ATAC
1 ATAC
2283164 TAAAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.29
Consensus pattern (22 bp):
ATACAAATTAAAAAATAAATTA
Found at i:2290750 original size:19 final size:20
Alignment explanation
Indices: 2290711--2290751 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2290701 TGTCAAACTT
*
2290711 AATTAAAACTCGAAATCAAA
1 AATTAAAACTCGAAATAAAA
*
2290731 AATTGAAACTC-AAATAAAA
1 AATTAAAACTCGAAATAAAA
2290750 AA
1 AA
2290752 CTTGTAAGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.63, C:0.12, G:0.05, T:0.20
Consensus pattern (20 bp):
AATTAAAACTCGAAATAAAA
Found at i:2293741 original size:30 final size:30
Alignment explanation
Indices: 2293701--2293770 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
2293691 TAAAGTTTAG
* * *
2293701 TGAGCTAAATAGAAAATTTTGAAAGTACAA
1 TGAGCAAAATAGAAAAATTTAAAAGTACAA
* *
2293731 TGAGGAAAATAGAAAAATTTAAAAGTACAT
1 TGAGCAAAATAGAAAAATTTAAAAGTACAA
2293761 TGAGCAAAAT
1 TGAGCAAAAT
2293771 CAGAGAGAGT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.53, C:0.06, G:0.17, T:0.24
Consensus pattern (30 bp):
TGAGCAAAATAGAAAAATTTAAAAGTACAA
Found at i:2295538 original size:20 final size:20
Alignment explanation
Indices: 2295508--2295556 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2295498 AACTATTTTC
*
2295508 TTTTG-AAAACAAAAATG-GA
1 TTTTGAAAAAC-AAAATGAAA
2295527 TTTTGAAAAACAAAATGAAA
1 TTTTGAAAAACAAAATGAAA
2295547 TTTTGAAAAA
1 TTTTGAAAAA
2295557 ATGATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.55, C:0.04, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAAACAAAATGAAA
Found at i:2297069 original size:10 final size:10
Alignment explanation
Indices: 2297049--2297102 Score: 58
Period size: 10 Copynumber: 5.3 Consensus size: 10
2297039 TATTTTTTCC
2297049 AAAAAAA-AA
1 AAAAAAACAA
*
2297058 AACAAAACAA
1 AAAAAAACAA
2297068 AAAAAGGCAA-AA
1 AAAAA---AACAA
2297080 AAAAAAACAA
1 AAAAAAACAA
2297090 AAAAAAACAA
1 AAAAAAACAA
2297100 AAA
1 AAA
2297103 GCCAAAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
9 8 0.21
10 21 0.55
12 7 0.18
13 2 0.05
ACGTcount: A:0.87, C:0.09, G:0.04, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:2297085 original size:30 final size:30
Alignment explanation
Indices: 2297047--2297109 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 30
2297037 GCTATTTTTT
*
2297047 CCAAAAAAAAAAAC--AAAACAA-AAAAAG
1 CCAAAAAAAAAAACAAAAAAAAACAAAAAG
*
2297074 GCAAAAAAAAAAACAAAAAAAAACAAAAAG
1 CCAAAAAAAAAAACAAAAAAAAACAAAAAG
2297104 CCAAAA
1 CCAAAA
2297110 TTTCAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 13 0.43
29 6 0.20
30 11 0.37
ACGTcount: A:0.81, C:0.14, G:0.05, T:0.00
Consensus pattern (30 bp):
CCAAAAAAAAAAACAAAAAAAAACAAAAAG
Found at i:2297100 original size:22 final size:22
Alignment explanation
Indices: 2297049--2297102 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
2297039 TATTTTTTCC
*
2297049 AAAAA-AAAAAACAAAACAAAA
1 AAAAACAAAAAAAAAAACAAAA
**
2297070 AAAGGCAAAAAAAAAAACAAAA
1 AAAAACAAAAAAAAAAACAAAA
2297092 AAAAACAAAAA
1 AAAAACAAAAA
2297103 GCCAAAATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 3 0.11
22 24 0.89
ACGTcount: A:0.87, C:0.09, G:0.04, T:0.00
Consensus pattern (22 bp):
AAAAACAAAAAAAAAAACAAAA
Found at i:2305323 original size:17 final size:17
Alignment explanation
Indices: 2305301--2305334 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2305291 TGATGGATCT
2305301 GTGAGAATACCATATCC
1 GTGAGAATACCATATCC
2305318 GTGAGAATACCATATCC
1 GTGAGAATACCATATCC
2305335 TGATTGTCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.24
Consensus pattern (17 bp):
GTGAGAATACCATATCC
Found at i:2308591 original size:25 final size:25
Alignment explanation
Indices: 2308549--2308601 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
2308539 AGAAAATTTT
2308549 ATATAAAAGATTTAATTAGTATAAAA
1 ATATAAAAGATTTAATTAG-ATAAAA
* *
2308575 ATATAAAA-ATTTGATTAGATTAAA
1 ATATAAAAGATTTAATTAGATAAAA
2308599 ATA
1 ATA
2308602 ATCTAAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 8 0.32
25 9 0.36
26 8 0.32
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.36
Consensus pattern (25 bp):
ATATAAAAGATTTAATTAGATAAAA
Found at i:2325817 original size:24 final size:24
Alignment explanation
Indices: 2325785--2325839 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
2325775 AGTCAAGTGG
*
2325785 TGCGGCCCTAGAAGCATTATCACA
1 TGCGACCCTAGAAGCATTATCACA
*
2325809 TGCGACCCTAGAAGCATTATCACG
1 TGCGACCCTAGAAGCATTATCACA
2325833 TGCGACC
1 TGCGACC
2325840 ATCACTCCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.27, C:0.31, G:0.22, T:0.20
Consensus pattern (24 bp):
TGCGACCCTAGAAGCATTATCACA
Found at i:2326296 original size:12 final size:12
Alignment explanation
Indices: 2326279--2326303 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2326269 ACATTGGACC
2326279 CATGCGCATTAT
1 CATGCGCATTAT
2326291 CATGCGCATTAT
1 CATGCGCATTAT
2326303 C
1 C
2326304 TCGGTAGTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.32
Consensus pattern (12 bp):
CATGCGCATTAT
Found at i:2333999 original size:29 final size:30
Alignment explanation
Indices: 2333949--2334014 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
2333939 ACCAAAAGAA
2333949 TATTATTTTAACAAATAATATTATTTT-AG
1 TATTATTTTAACAAATAATATTATTTTGAG
* * * *
2333978 TGTTATTTTAATAGATATTATTATTTTGAG
1 TATTATTTTAACAAATAATATTATTTTGAG
2334008 TATTATT
1 TATTATT
2334015 CCCATAATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 23 0.74
30 8 0.26
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.56
Consensus pattern (30 bp):
TATTATTTTAACAAATAATATTATTTTGAG
Done.