Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006707.1 Hibiscus syriacus cultivar Beakdansim tig00016715_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: 101821
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:10532 original size:61 final size:61
Alignment explanation
Indices: 10437--10560 Score: 221
Period size: 61 Copynumber: 2.0 Consensus size: 61
10427 CATCTGATCG
10437 AGCGTCAAAGTAACAACCATCAAAAACGTATTCTCAATTAAAATAAACTGATCTTAATGTT
1 AGCGTCAAAGTAACAACCATCAAAAACGTATTCTCAATTAAAATAAACTGATCTTAATGTT
* * *
10498 AGCGTCATAGTAGCAACCATCAAAAAGGTATTCTCAATTAAAATAAACTGATCTTAATGTT
1 AGCGTCAAAGTAACAACCATCAAAAACGTATTCTCAATTAAAATAAACTGATCTTAATGTT
10559 AG
1 AG
10561 GATTGATAAC
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.28
Consensus pattern (61 bp):
AGCGTCAAAGTAACAACCATCAAAAACGTATTCTCAATTAAAATAAACTGATCTTAATGTT
Found at i:19958 original size:19 final size:19
Alignment explanation
Indices: 19936--19972 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
19926 TAAAAAAATA
19936 AAAAATT-CCATAAAATCTC
1 AAAAATTCCCA-AAAATCTC
19955 AAAAATTCCCAAAAATCT
1 AAAAATTCCCAAAAATCT
19973 TAATCTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.54, C:0.22, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAAATTCCCAAAAATCTC
Found at i:20190 original size:17 final size:17
Alignment explanation
Indices: 20168--20202 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
20158 ATTGAGGTTA
20168 TGATAGTCCAATGAGGG
1 TGATAGTCCAATGAGGG
20185 TGATAGTCCAATGAGGG
1 TGATAGTCCAATGAGGG
20202 T
1 T
20203 AGTTTTATGA
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:0.29, C:0.11, G:0.34, T:0.26
Consensus pattern (17 bp):
TGATAGTCCAATGAGGG
Found at i:28534 original size:123 final size:123
Alignment explanation
Indices: 28315--28683 Score: 738
Period size: 123 Copynumber: 3.0 Consensus size: 123
28305 ATTAGTTGTT
28315 GTTGAACTTCTTCCTTGAACCTCTTCATTTTCTCACCAAACAATCATTGTTTGGGAAGGAAAAAG
1 GTTGAACTTCTTCCTTGAACCTCTTCATTTTCTCACCAAACAATCATTGTTTGGGAAGGAAAAAG
28380 AAAATGGTGAAAATATAAAATTTTTGTGAAGAAAATAAAAACTTACTCAATAATCAAA
66 AAAATGGTGAAAATATAAAATTTTTGTGAAGAAAATAAAAACTTACTCAATAATCAAA
28438 GTTGAACTTCTTCCTTGAACCTCTTCATTTTCTCACCAAACAATCATTGTTTGGGAAGGAAAAAG
1 GTTGAACTTCTTCCTTGAACCTCTTCATTTTCTCACCAAACAATCATTGTTTGGGAAGGAAAAAG
28503 AAAATGGTGAAAATATAAAATTTTTGTGAAGAAAATAAAAACTTACTCAATAATCAAA
66 AAAATGGTGAAAATATAAAATTTTTGTGAAGAAAATAAAAACTTACTCAATAATCAAA
28561 GTTGAACTTCTTCCTTGAACCTCTTCATTTTCTCACCAAACAATCATTGTTTGGGAAGGAAAAAG
1 GTTGAACTTCTTCCTTGAACCTCTTCATTTTCTCACCAAACAATCATTGTTTGGGAAGGAAAAAG
28626 AAAATGGTGAAAATATAAAATTTTTGTGAAGAAAATAAAAACTTACTCAATAATCAAA
66 AAAATGGTGAAAATATAAAATTTTTGTGAAGAAAATAAAAACTTACTCAATAATCAAA
28684 TGACAGTGTA
Statistics
Matches: 246, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
123 246 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (123 bp):
GTTGAACTTCTTCCTTGAACCTCTTCATTTTCTCACCAAACAATCATTGTTTGGGAAGGAAAAAG
AAAATGGTGAAAATATAAAATTTTTGTGAAGAAAATAAAAACTTACTCAATAATCAAA
Found at i:42445 original size:15 final size:16
Alignment explanation
Indices: 42425--42455 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
42415 TGTATGGGTG
42425 GTGAAAGAGT-ATGGA
1 GTGAAAGAGTCATGGA
42440 GTGAAAGAGTCATGGA
1 GTGAAAGAGTCATGGA
42456 CCGAACTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.39, T:0.19
Consensus pattern (16 bp):
GTGAAAGAGTCATGGA
Found at i:45367 original size:18 final size:18
Alignment explanation
Indices: 45344--45382 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
45334 TCTTGAGAAT
*
45344 TTATTTAT-ATATTTAACA
1 TTATTTATGAT-TTTAAAA
45362 TTATTTATGATTTTAAAA
1 TTATTTATGATTTTAAAA
45380 TTA
1 TTA
45383 CTTGTGGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (18 bp):
TTATTTATGATTTTAAAA
Found at i:47268 original size:27 final size:27
Alignment explanation
Indices: 47208--47262 Score: 78
Period size: 25 Copynumber: 2.1 Consensus size: 27
47198 TTTAAGTTTT
47208 TTCTATTAGAAAAAAGTTTCTAAAAAG
1 TTCTATTAGAAAAAAGTTTCTAAAAAG
* *
47235 TTCTATTA-AAAAAGGTTT-TTAAAAG
1 TTCTATTAGAAAAAAGTTTCTAAAAAG
47260 TTC
1 TTC
47263 ACTATTGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 9 0.35
26 9 0.35
27 8 0.31
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (27 bp):
TTCTATTAGAAAAAAGTTTCTAAAAAG
Found at i:48055 original size:35 final size:35
Alignment explanation
Indices: 48008--48121 Score: 165
Period size: 35 Copynumber: 3.3 Consensus size: 35
47998 AAAACAATCC
* *
48008 TCAATTTCATTCTAAACCCCAAATTCTAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCTAAAATAAT
* * *
48043 TCAATTTTATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTAATTCTAAACCCCAAATTCTAAAATAAT
* *
48078 TCAATTAAATTCTAAACCCCAAATTCTAAAATATT
1 TCAATTTAATTCTAAACCCCAAATTCTAAAATAAT
48113 TCAATTTAA
1 TCAATTTAA
48122 GGTTTAGAAT
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 69 1.00
ACGTcount: A:0.43, C:0.20, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCTAAAATAAT
Found at i:48154 original size:35 final size:35
Alignment explanation
Indices: 48115--48189 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
48105 AAAATATTTC
* * *
48115 AATTTAAGGTTTAGAATGTAATTGAATTATTTTGG
1 AATTTAAGGTTTAAAATGAAATTGAATTACTTTGG
*
48150 AATTTAGGGTTTAAAATGAAATTGAATTACTTTGG
1 AATTTAAGGTTTAAAATGAAATTGAATTACTTTGG
48185 AATTT
1 AATTT
48190 TGAACATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.36, C:0.01, G:0.19, T:0.44
Consensus pattern (35 bp):
AATTTAAGGTTTAAAATGAAATTGAATTACTTTGG
Found at i:48193 original size:24 final size:24
Alignment explanation
Indices: 48166--48237 Score: 62
Period size: 24 Copynumber: 3.0 Consensus size: 24
48156 GGGTTTAAAA
48166 TGAAATTGAATTACTTTGGAATTT
1 TGAAATTGAATTACTTTGGAATTT
*
48190 TGAACA-TGAATTTACTATTTAGAA---
1 TGAA-ATTGAA-TTAC--TTTGGAATTT
*
48214 TAAAATTGAATTACTTTGGAATTT
1 TGAAATTGAATTACTTTGGAATTT
48238 GGGGTTTAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 16
0.66 0.05 0.29
Matches are distributed among these distances:
21 6 0.16
23 5 0.14
24 15 0.41
25 5 0.14
27 6 0.16
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.43
Consensus pattern (24 bp):
TGAAATTGAATTACTTTGGAATTT
Found at i:49660 original size:30 final size:30
Alignment explanation
Indices: 49602--49660 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
49592 ATTTTTTAAT
* *
49602 TAAATATTTAAAGTATTTTTTCAGTCAAAA
1 TAAATATTTAAAGTATTATTTCACTCAAAA
*
49632 TAAATATTTAAACTTATTATTT-ACTCAAA
1 TAAATATTTAAA-GTATTATTTCACTCAAA
49661 TCAGGTACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (30 bp):
TAAATATTTAAAGTATTATTTCACTCAAAA
Found at i:51962 original size:15 final size:16
Alignment explanation
Indices: 51936--51965 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
51926 AGTAGTTCGG
51936 TCCATGACTCTTTCAC
1 TCCATGACTCTTTCAC
51952 TCCAT-ACTCTTTCA
1 TCCATGACTCTTTCA
51966 TCACCCATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.20, C:0.37, G:0.03, T:0.40
Consensus pattern (16 bp):
TCCATGACTCTTTCAC
Found at i:53460 original size:22 final size:22
Alignment explanation
Indices: 53428--53471 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
53418 ATCTTGTCTT
*
53428 CTTCATTGTGTTAATTAGTGTG
1 CTTCATAGTGTTAATTAGTGTG
53450 CTTCATAGTGTTAATTAGTGTG
1 CTTCATAGTGTTAATTAGTGTG
53472 ATGTTGTGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.09, G:0.23, T:0.48
Consensus pattern (22 bp):
CTTCATAGTGTTAATTAGTGTG
Found at i:65016 original size:30 final size:30
Alignment explanation
Indices: 64980--65036 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
64970 AGGGAAACCT
* *
64980 CCAAACCCACCGCCTGCACCAGCTCCACCG
1 CCAAACCCACCACCTGCACCACCTCCACCG
*
65010 CCAAACCCACCACCTGCGCCACCTCCA
1 CCAAACCCACCACCTGCACCACCTCCA
65037 GCTCCGCCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.25, C:0.58, G:0.11, T:0.07
Consensus pattern (30 bp):
CCAAACCCACCACCTGCACCACCTCCACCG
Found at i:65055 original size:24 final size:24
Alignment explanation
Indices: 65028--65089 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
65018 ACCACCTGCG
* *
65028 CCACCTCCAGCTCCGCCTCCAAAT
1 CCACCTCCACCTCCGCCACCAAAT
* *
65052 CCACCTCCACCACCTCCACCAAAT
1 CCACCTCCACCTCCGCCACCAAAT
*
65076 CCACCACCACCTCC
1 CCACCTCCACCTCC
65090 AGCTCCCGCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.24, C:0.60, G:0.03, T:0.13
Consensus pattern (24 bp):
CCACCTCCACCTCCGCCACCAAAT
Found at i:65310 original size:24 final size:24
Alignment explanation
Indices: 65283--65338 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
65273 ACCTAACCCT
65283 CCTCCACCTCCACCACCACCAAAA
1 CCTCCACCTCCACCACCACCAAAA
* * * *
65307 CCTCCGCCTCCACCTCCTCCTAAA
1 CCTCCACCTCCACCACCACCAAAA
*
65331 CCACCACC
1 CCTCCACC
65339 AATTCCCGGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.25, C:0.61, G:0.02, T:0.12
Consensus pattern (24 bp):
CCTCCACCTCCACCACCACCAAAA
Found at i:77098 original size:23 final size:20
Alignment explanation
Indices: 77068--77111 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 20
77058 CGTTCGACGT
77068 TTACATAACAATAATATGATAAA
1 TTACATAA-AATAA-AT-ATAAA
77091 TTACATAAAATAAATATAAA
1 TTACATAAAATAAATATAAA
77111 T
1 T
77112 ATAATATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.29
21 2 0.10
22 5 0.24
23 8 0.38
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.32
Consensus pattern (20 bp):
TTACATAAAATAAATATAAA
Found at i:79527 original size:22 final size:21
Alignment explanation
Indices: 79502--79542 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
79492 TACATTTAAA
79502 ATTTTAACTAATTTATAATTCT
1 ATTTT-ACTAATTTATAATTCT
* *
79524 ATTTTAGTACTTTATAATT
1 ATTTTACTAATTTATAATT
79543 TAAAATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTTTACTAATTTATAATTCT
Found at i:79552 original size:15 final size:15
Alignment explanation
Indices: 79495--79583 Score: 78
Period size: 15 Copynumber: 6.1 Consensus size: 15
79485 CATTAATTAC
79495 ATTTAAAATTTTAACTA
1 ATTTAAAATTTT-A-TA
* *
79512 ATTTATAATTCTAT-
1 ATTTAAAATTTTATA
** *
79526 -TTTAGTACTTTATA
1 ATTTAAAATTTTATA
79540 ATTTAAAATTTTATA
1 ATTTAAAATTTTATA
*
79555 AATT--AATTTTATA
1 ATTTAAAATTTTATA
79568 ATTTAAAATTTTATA
1 ATTTAAAATTTTATA
79583 A
1 A
79584 ATTACTTAGT
Statistics
Matches: 57, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
13 21 0.37
15 25 0.44
16 1 0.02
17 10 0.18
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (15 bp):
ATTTAAAATTTTATA
Found at i:79564 original size:13 final size:13
Alignment explanation
Indices: 79546--79587 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
79536 TATAATTTAA
79546 AATTTTATAAATT
1 AATTTTATAAATT
*
79559 AATTTTATAATTT
1 AATTTTATAAATT
79572 AAAATTTTATAAATT
1 --AATTTTATAAATT
79587 A
1 A
79588 CTTAGTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 13 0.52
15 12 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATTTTATAAATT
Found at i:79565 original size:28 final size:28
Alignment explanation
Indices: 79534--79587 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
79524 ATTTTAGTAC
79534 TTTATAATTTAAAATTTTATAAATTAAT
1 TTTATAATTTAAAATTTTATAAATTAAT
79562 TTTATAATTTAAAATTTTATAAATTA
1 TTTATAATTTAAAATTTTATAAATTA
79588 CTTAGTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
TTTATAATTTAAAATTTTATAAATTAAT
Found at i:81204 original size:17 final size:14
Alignment explanation
Indices: 81167--81218 Score: 68
Period size: 14 Copynumber: 3.5 Consensus size: 14
81157 AAAAACCGAT
81167 AAACCGAACCGAAA
1 AAACCGAACCGAAA
*
81181 AACCCGAACCGTTAAAA
1 AAACCGAACCG---AAA
81198 AAACCGAACCGAAA
1 AAACCGAACCGAAA
81212 AAACCGA
1 AAACCGA
81219 TTTCGATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 20 0.61
17 13 0.39
ACGTcount: A:0.54, C:0.29, G:0.13, T:0.04
Consensus pattern (14 bp):
AAACCGAACCGAAA
Found at i:85856 original size:13 final size:13
Alignment explanation
Indices: 85838--85863 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
85828 ATAACAATGG
85838 CGAAAAGTGATTT
1 CGAAAAGTGATTT
85851 CGAAAAGTGATTT
1 CGAAAAGTGATTT
85864 TCTGCTGCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (13 bp):
CGAAAAGTGATTT
Done.