Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004442.1 Hibiscus syriacus cultivar Beakdansim tig00009742_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: 74356
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:3468 original size:33 final size:31
Alignment explanation
Indices: 3407--3468 Score: 79
Period size: 33 Copynumber: 1.9 Consensus size: 31
3397 TATTATTACT
* *
3407 TTTATTTATAAAAATAATCAACATTAAATAA
1 TTTAATTATAAAAATAATCAACAATAAATAA
*
3438 TTTAATTATCAAATAATATTCAACAATAAAT
1 TTTAATTAT-AAA-AATAATCAACAATAAAT
3469 TTGTTTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 8 0.31
32 3 0.12
33 15 0.58
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (31 bp):
TTTAATTATAAAAATAATCAACAATAAATAA
Found at i:3840 original size:17 final size:17
Alignment explanation
Indices: 3818--3883 Score: 132
Period size: 17 Copynumber: 3.9 Consensus size: 17
3808 CTCTAATGAT
3818 TTAGTTCTAATGATTCA
1 TTAGTTCTAATGATTCA
3835 TTAGTTCTAATGATTCA
1 TTAGTTCTAATGATTCA
3852 TTAGTTCTAATGATTCA
1 TTAGTTCTAATGATTCA
3869 TTAGTTCTAATGATT
1 TTAGTTCTAATGATT
3884 TGTCTCTTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 49 1.00
ACGTcount: A:0.29, C:0.11, G:0.12, T:0.48
Consensus pattern (17 bp):
TTAGTTCTAATGATTCA
Found at i:6474 original size:70 final size:67
Alignment explanation
Indices: 6379--6573 Score: 181
Period size: 63 Copynumber: 2.9 Consensus size: 67
6369 ACTAGATATC
* *
6379 TTTTAATATTCAAATTTAAACAGATATAATAATATCTTTTAATTTGAAATATTCAAAAGATAAAG
1 TTTTAATATTCAAACTTAAATAGATATAATAATA-CTTTTAATTTGAAATATTCAAAAGATAAA-
6444 TCACA
64 TCA-A
* *
6449 TTTTACTATTCAAACTTAAATAG--AT-AT--TA-TTTTAATTTGAAATATTTAAAATGATATAA
1 TTTTAATATTCAAACTTAAATAGATATAATAATACTTTTAATTTGAAATATTCAAAA-GATA-AA
* *
6508 TTAT
64 TCAA
* * * *
6512 TTTTAATATTCAAAGTTAACTAGATA-ACA-AATACCTTTTAATTTGACATATTCAAATGATAA
1 TTTTAATATTCAAACTTAAATAGATATA-ATAATA-CTTTTAATTTGAAATATTCAAAAGATAA
6574 TTATCCTACT
Statistics
Matches: 103, Mismatches: 12, Indels: 23
0.75 0.09 0.17
Matches are distributed among these distances:
63 41 0.40
64 6 0.06
65 5 0.05
66 1 0.01
67 5 0.05
68 6 0.06
69 19 0.18
70 20 0.19
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.42
Consensus pattern (67 bp):
TTTTAATATTCAAACTTAAATAGATATAATAATACTTTTAATTTGAAATATTCAAAAGATAAATC
AA
Found at i:10746 original size:5 final size:5
Alignment explanation
Indices: 10736--10769 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
10726 ACTTCTTAAG
10736 AAAAT AAAAT AAAAT AAAAT -AAAT AGAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT AAAA
10770 ATACTCTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 18 0.67
6 5 0.19
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:11228 original size:21 final size:20
Alignment explanation
Indices: 11204--11242 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
11194 CACTTTTTAC
11204 TATTTAAACTTAAATATATAT
1 TATTTAAACTTAAA-ATATAT
* *
11225 TATTTTAATTTAAAATAT
1 TATTTAAACTTAAAATAT
11243 TTAAAATGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTTAAACTTAAAATATAT
Found at i:22873 original size:25 final size:25
Alignment explanation
Indices: 22845--22904 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
22835 ATATTTTAAT
*
22845 CTATTATATTTAGAGAAACATCTAC
1 CTATGATATTTAGAGAAACATCTAC
* * *
22870 CTATGGTATTTAGAGAAATATCTGC
1 CTATGATATTTAGAGAAACATCTAC
*
22895 CTATGGTATT
1 CTATGATATT
22905 ATATATATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (25 bp):
CTATGATATTTAGAGAAACATCTAC
Found at i:23347 original size:6 final size:6
Alignment explanation
Indices: 23326--23392 Score: 102
Period size: 6 Copynumber: 11.5 Consensus size: 6
23316 GACACGTATT
**
23326 ACCACG ACCATT ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
23374 ACCACG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACC
23393 CGAGACGAGA
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
5 10 0.18
6 47 0.82
ACGTcount: A:0.31, C:0.51, G:0.15, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:33468 original size:29 final size:29
Alignment explanation
Indices: 33426--33484 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
33416 ATTTTCACCT
33426 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
33455 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
33484 A
1 A
33485 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:38138 original size:29 final size:29
Alignment explanation
Indices: 38096--38154 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
38086 ATTTTCACCT
38096 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
38125 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
38154 A
1 A
38155 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:40151 original size:33 final size:33
Alignment explanation
Indices: 40107--40171 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
40097 CCTGGATTGT
*
40107 TTAGGTAGAAACTCTCTTGTAGTAATGAGGAAC
1 TTAGGTAGAAACTCACTTGTAGTAATGAGGAAC
* * * *
40140 TTAGGTGGAAACTGAGTTGTAGTCATGAGGAA
1 TTAGGTAGAAACTCACTTGTAGTAATGAGGAA
40172 ATTTCGGTAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.29
Consensus pattern (33 bp):
TTAGGTAGAAACTCACTTGTAGTAATGAGGAAC
Found at i:43351 original size:31 final size:31
Alignment explanation
Indices: 43300--43433 Score: 189
Period size: 31 Copynumber: 4.3 Consensus size: 31
43290 GTTCATTTTT
* * *
43300 AATTTGACTCTTAAATTTTAGATAAAATATC
1 AATTTGACCCATAAACTTTAGATAAAATATC
*
43331 AATTTGATTCC-TAAACTTTAGATAAAATATC
1 AATTTGA-CCCATAAACTTTAGATAAAATATC
*
43362 AATTTGACCCATAAACTTTAGTTAAAATATC
1 AATTTGACCCATAAACTTTAGATAAAATATC
*
43393 AATTTGACCCATAAACTTTAGTTAAAATATC
1 AATTTGACCCATAAACTTTAGATAAAATATC
*
43424 AATTTAACCC
1 AATTTGACCC
43434 TTAATTCTAA
Statistics
Matches: 95, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
30 2 0.02
31 92 0.97
32 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.37
Consensus pattern (31 bp):
AATTTGACCCATAAACTTTAGATAAAATATC
Found at i:48154 original size:37 final size:37
Alignment explanation
Indices: 48113--48184 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
48103 ATGACCTATG
*
48113 TAACTGTCCATATGTTCCGAAAAACATAGGTAAACTA
1 TAACTGTCCATATGTCCCGAAAAACATAGGTAAACTA
*
48150 TAACTGTCCATATGTCCCGAAAGACATAGGTAAAC
1 TAACTGTCCATATGTCCCGAAAAACATAGGTAAAC
48185 CCTCGACTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.25
Consensus pattern (37 bp):
TAACTGTCCATATGTCCCGAAAAACATAGGTAAACTA
Found at i:57209 original size:27 final size:26
Alignment explanation
Indices: 57152--57210 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
57142 AAAAATCAAG
57152 GAAAAATAAAATAAAATAAAAAGAAC
1 GAAAAATAAAATAAAATAAAAAGAAC
57178 G-AAAATAGAAATTAAAATAGAAAA-AA-
1 GAAAAATA-AAA-TAAAATA-AAAAGAAC
57204 GAAAAAT
1 GAAAAAT
57211 TGGGTTGCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
25 6 0.21
26 5 0.17
27 14 0.48
28 4 0.14
ACGTcount: A:0.75, C:0.02, G:0.10, T:0.14
Consensus pattern (26 bp):
GAAAAATAAAATAAAATAAAAAGAAC
Found at i:63252 original size:27 final size:26
Alignment explanation
Indices: 63195--63253 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
63185 AAAAATCAAG
63195 GAAAAATAAAATAAAATAAAAAGAAC
1 GAAAAATAAAATAAAATAAAAAGAAC
63221 G-AAAATAGAAATTAAAATAGAAAA-AA-
1 GAAAAATA-AAA-TAAAATA-AAAAGAAC
63247 GAAAAAT
1 GAAAAAT
63254 TGGGTTGCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
25 6 0.21
26 5 0.17
27 14 0.48
28 4 0.14
ACGTcount: A:0.75, C:0.02, G:0.10, T:0.14
Consensus pattern (26 bp):
GAAAAATAAAATAAAATAAAAAGAAC
Found at i:70003 original size:18 final size:21
Alignment explanation
Indices: 69958--70013 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
69948 AGTTGCATTC
*
69958 TATATAATTTGAATTTATTTA
1 TATAAAATTTGAATTTATTTA
69979 TATAAAATTT-AATTT-TTTA
1 TATAAAATTTGAATTTATTTA
69998 -ATAAAATATTAGAATT
1 TATAAAAT-TT-GAATT
70014 ATTAAAGAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
18 7 0.23
19 6 0.19
20 5 0.16
21 13 0.42
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (21 bp):
TATAAAATTTGAATTTATTTA
Done.