Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005200.1 Hibiscus syriacus cultivar Beakdansim tig00011748_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: 68461
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:13106 original size:18 final size:18
Alignment explanation
Indices: 13079--13123 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
13069 GGAAATATTC
*
13079 TTTTACTTTATTCCTTTA
1 TTTTACTTTATTCCATTA
* *
13097 TTTTATTTTATTTCATTA
1 TTTTACTTTATTCCATTA
13115 TTTTTACTT
1 -TTTTACTT
13124 GTCTCTCCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTACTTTATTCCATTA
Found at i:14364 original size:13 final size:13
Alignment explanation
Indices: 14328--14380 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
14318 ACCCGTGAAT
*
14328 AGTGAACAATAAC
1 AGTGAACAGTAAC
* * *
14341 AATGTATAGTAAC
1 AGTGAACAGTAAC
*
14354 AGTGAACAGTACC
1 AGTGAACAGTAAC
*
14367 TGTGAACAGTAAC
1 AGTGAACAGTAAC
14380 A
1 A
14381 TGCCACTAAT
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.45, C:0.15, G:0.19, T:0.21
Consensus pattern (13 bp):
AGTGAACAGTAAC
Found at i:14730 original size:47 final size:45
Alignment explanation
Indices: 14660--14785 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
14650 TATAAAATCT
*
14660 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
14705 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * * *
14752 CTTGCCA-TTATTTCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
14786 GCATGGTTAC
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
44 22 0.31
45 10 0.14
46 2 0.03
47 38 0.53
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:14950 original size:40 final size:40
Alignment explanation
Indices: 14889--15010 Score: 201
Period size: 40 Copynumber: 3.0 Consensus size: 40
14879 ACCGTAGTGC
* *
14889 TACACATAAGGTCGTGT-CCACCATATACATCGAATTGTAT
1 TACACATAAGGTCGT-TCCCACCATATACACCGAAGTGTAT
14929 TACACATAAGGTCGTTCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTTCCCACCATATACACCGAAGTGTAT
*
14969 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTTCCCACCATATACACCGAAGTGTAT
15009 TA
1 TA
15011 TAAACCTGCA
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
39 1 0.01
40 77 0.99
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (40 bp):
TACACATAAGGTCGTTCCCACCATATACACCGAAGTGTAT
Found at i:21317 original size:26 final size:26
Alignment explanation
Indices: 21250--21326 Score: 93
Period size: 26 Copynumber: 3.0 Consensus size: 26
21240 TTAATTGAAC
* * *
21250 TAAAAGAGCTAATAAATCTATTATAA
1 TAAAAGAGCAAATAAATCTCTTTTAA
*
21276 TAAAATAGCAAATAAATCTCTTTTAA
1 TAAAAGAGCAAATAAATCTCTTTTAA
*
21302 TAAAAGATG-AATTAAATCTCTTTTA
1 TAAAAGA-GCAAATAAATCTCTTTTA
21327 TATTTATCTT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
26 43 0.98
27 1 0.02
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.35
Consensus pattern (26 bp):
TAAAAGAGCAAATAAATCTCTTTTAA
Found at i:26574 original size:26 final size:26
Alignment explanation
Indices: 26510--26576 Score: 107
Period size: 26 Copynumber: 2.6 Consensus size: 26
26500 TAAAATATCT
* **
26510 AATAAATCTCTTCTAATAAAAGAGGA
1 AATAAATCTCTTTTAATAAAAGAAAA
26536 AATAAATCTCTTTTAATAAAAGAAAA
1 AATAAATCTCTTTTAATAAAAGAAAA
26562 AATAAATCTCTTTTA
1 AATAAATCTCTTTTA
26577 TATTTATCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.51, C:0.10, G:0.06, T:0.33
Consensus pattern (26 bp):
AATAAATCTCTTTTAATAAAAGAAAA
Found at i:28804 original size:19 final size:19
Alignment explanation
Indices: 28780--28845 Score: 78
Period size: 19 Copynumber: 3.5 Consensus size: 19
28770 GCCTCGGGGG
*
28780 TACTGTTCAAACAGTGATT
1 TACTGTTCAAACAGTAATT
*
28799 TACTGTTCAAATAGTAATT
1 TACTGTTCAAACAGTAATT
* * *
28818 TAATGTTCAAATAGTAAAT
1 TACTGTTCAAACAGTAATT
*
28837 TACTATTCA
1 TACTGTTCA
28846 TAAAAACATT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (19 bp):
TACTGTTCAAACAGTAATT
Found at i:28961 original size:30 final size:30
Alignment explanation
Indices: 28910--28989 Score: 128
Period size: 30 Copynumber: 2.7 Consensus size: 30
28900 AAACTTTGAA
*
28910 TAAATTCAATT-AAGTCAAAATA-GATTTTG
1 TAAATTCAATTCAAGTCCAAATACG-TTTTG
28939 TAAATTCAATTCAAGTCCAAATACGTTTTG
1 TAAATTCAATTCAAGTCCAAATACGTTTTG
28969 TAAATTCAATTCAAGTCCAAA
1 TAAATTCAATTCAAGTCCAAA
28990 AACCATTTTG
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
29 11 0.23
30 36 0.75
31 1 0.02
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (30 bp):
TAAATTCAATTCAAGTCCAAATACGTTTTG
Found at i:29711 original size:12 final size:12
Alignment explanation
Indices: 29694--29723 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
29684 CATTAAAACC
29694 AATTTTGACCAA
1 AATTTTGACCAA
29706 AATTTTGACCAA
1 AATTTTGACCAA
29718 AATTTT
1 AATTTT
29724 ATTATGATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (12 bp):
AATTTTGACCAA
Found at i:30322 original size:20 final size:20
Alignment explanation
Indices: 30285--30332 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
30275 CTAAATCCTT
*
30285 TTTCAAAATTTCATTTTTGGC
1 TTTCAAAATCTCATTTTT-GC
*
30306 TTTCAAAATCT-ATTTTTGT
1 TTTCAAAATCTCATTTTTGC
30325 TTTCAAAA
1 TTTCAAAA
30333 GAAGATCGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 9 0.36
20 6 0.24
21 10 0.40
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTCAAAATCTCATTTTTGC
Found at i:34410 original size:21 final size:21
Alignment explanation
Indices: 34384--34423 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
34374 AGAACCCCAG
*
34384 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
34405 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
34424 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:34453 original size:21 final size:23
Alignment explanation
Indices: 34405--34464 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
34395 ATTCCCCTGT
34405 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTTCCCCTTCAA
* *
34428 AGGGGGAATCGGTT-TCC-TCAA
1 GGGGGGAATCGGTTCCCCTTCAA
*
34449 GGGGGG-ATCGATTCCC
1 GGGGGGAATCGGTTCCC
34465 TCTATACCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
20 6 0.19
21 10 0.32
22 2 0.06
23 13 0.42
ACGTcount: A:0.18, C:0.23, G:0.37, T:0.22
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCTTCAA
Found at i:34466 original size:20 final size:20
Alignment explanation
Indices: 34406--34466 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
34396 TTCCCCTGTG
*
34406 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATT-CCC-TC-AA
* *
34429 GGGGGAATCGGTTTCCTCAA
1 GGGGGAATCGATTCCCTCAA
*
34449 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
34467 TATACCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 2 0.06
23 13 0.38
ACGTcount: A:0.18, C:0.25, G:0.34, T:0.23
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAA
Found at i:39599 original size:19 final size:20
Alignment explanation
Indices: 39567--39604 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
39557 GTGTTGCGGC
*
39567 ACACAAATCTATGCAAGTAT
1 ACACAAATCGATGCAAGTAT
*
39587 ACAC-AATCGATGCGAGTA
1 ACACAAATCGATGCAAGTA
39605 ATATAGTAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.42, C:0.21, G:0.16, T:0.21
Consensus pattern (20 bp):
ACACAAATCGATGCAAGTAT
Found at i:57030 original size:20 final size:20
Alignment explanation
Indices: 56991--57036 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
56981 TTTGTGGGTA
*
56991 CGATACTAACCCTTCAGTAT
1 CGATACTAAACCTTCAGTAT
* **
57011 TGATACTAAACCTTTGGTAT
1 CGATACTAAACCTTCAGTAT
57031 CGATAC
1 CGATAC
57037 CTACCTGTTG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (20 bp):
CGATACTAAACCTTCAGTAT
Found at i:57047 original size:20 final size:19
Alignment explanation
Indices: 57020--57057 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
57010 TTGATACTAA
57020 ACCTTTGGTATCGATACCT
1 ACCTTTGGTATCGATACCT
57039 ACCTGTTGGTATCGATACC
1 ACCT-TTGGTATCGATACC
57058 CCCTGACTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (19 bp):
ACCTTTGGTATCGATACCT
Found at i:57138 original size:22 final size:22
Alignment explanation
Indices: 57110--57165 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
57100 CCTATTATGA
57110 GTATCGATACTTTGGTATTGGG
1 GTATCGATACTTTGGTATTGGG
57132 GTATCGATACTTTGGTATTGGG
1 GTATCGATACTTTGGTATTGGG
57154 GTATCGATACTT
1 GTATCGATACTT
57166 GACTGAGTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.20, C:0.11, G:0.29, T:0.41
Consensus pattern (22 bp):
GTATCGATACTTTGGTATTGGG
Found at i:60370 original size:28 final size:27
Alignment explanation
Indices: 60343--60419 Score: 70
Period size: 28 Copynumber: 2.9 Consensus size: 27
60333 ATCTTCATAT
60343 TATTTAAACAATATAATATTATTAATA
1 TATTTAAACAATATAATATTATTAATA
** * * *
60370 TATCAAATACAATCTAAAATTATAAATA
1 TATTTAA-ACAATATAATATTATTAATA
*
60398 TATTT--ACAATATTATATT-TTAA
1 TATTTAAACAATATAATATTATTAA
60420 AGAAGATATT
Statistics
Matches: 38, Mismatches: 11, Indels: 5
0.70 0.20 0.09
Matches are distributed among these distances:
24 3 0.08
25 10 0.26
27 5 0.13
28 20 0.53
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (27 bp):
TATTTAAACAATATAATATTATTAATA
Found at i:65689 original size:2 final size:2
Alignment explanation
Indices: 65682--65707 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
65672 TCTTTAAAAC
65682 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
65708 CATTTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.