Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002262.1 Hibiscus syriacus cultivar Beakdansim tig00004602_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: 46317
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Found at i:769 original size:26 final size:26
Alignment explanation
Indices: 740--817 Score: 72
Period size: 26 Copynumber: 3.1 Consensus size: 26
730 TTATGCACTA
740 TTAAATTCTAATGTTTTTATACACAT
1 TTAAATTCTAATGTTTTTATACACAT
* * * *
766 TTAAATTCGACTATATTTATACAC-T
1 TTAAATTCTAATGTTTTTATACACAT
* *
791 ATTAAA-CCTATTGTTTTT-TACACAT
1 -TTAAATTCTAATGTTTTTATACACAT
816 TT
1 TT
818 TAAACATGTT
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
24 7 0.17
25 9 0.22
26 25 0.61
ACGTcount: A:0.33, C:0.14, G:0.04, T:0.49
Consensus pattern (26 bp):
TTAAATTCTAATGTTTTTATACACAT
Found at i:836 original size:24 final size:24
Alignment explanation
Indices: 781--836 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
771 TTCGACTATA
*
781 TTTATACACTATTAAACCTATTGT
1 TTTATACACTATTAAACATATTGT
* * *
805 TTTTTACACATTTTAAACATGTTG-
1 TTTATACAC-TATTAAACATATTGT
829 TTTATACA
1 TTTATACA
837 ATATAAAGCC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 15 0.58
25 11 0.42
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.48
Consensus pattern (24 bp):
TTTATACACTATTAAACATATTGT
Found at i:3506 original size:25 final size:25
Alignment explanation
Indices: 3478--3530 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
3468 AGATTGGGAT
*
3478 TGGTCAATGCTCACCTTTGCTAGGA
1 TGGTCAATGCTCACCTTTGCCAGGA
*
3503 TGGTTAATGCTCACCTTTGCCAGGA
1 TGGTCAATGCTCACCTTTGCCAGGA
3528 TGG
1 TGG
3531 ACCATTCATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (25 bp):
TGGTCAATGCTCACCTTTGCCAGGA
Found at i:3823 original size:13 final size:13
Alignment explanation
Indices: 3805--3830 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3795 TGATTCTCTT
3805 TTATTTTATTTTA
1 TTATTTTATTTTA
3818 TTATTTTATTTTA
1 TTATTTTATTTTA
3831 AATATTGATG
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTATTTTATTTTA
Found at i:34052 original size:14 final size:14
Alignment explanation
Indices: 34035--34093 Score: 82
Period size: 14 Copynumber: 4.2 Consensus size: 14
34025 TGGAAAATAG
*
34035 ATTTCGAAAAATGC
1 ATTTCGAAAAATGA
*
34049 ATTTCGAAAAATAA
1 ATTTCGAAAAATGA
*
34063 ATTTCGTAAAATGA
1 ATTTCGAAAAATGA
*
34077 ATTTCGTAAAATGA
1 ATTTCGAAAAATGA
34091 ATT
1 ATT
34094 ACATTTTCTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 41 1.00
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.34
Consensus pattern (14 bp):
ATTTCGAAAAATGA
Found at i:34066 original size:28 final size:28
Alignment explanation
Indices: 34028--34093 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
34018 TGTTTCATGG
* *
34028 AAAATAGATTTCGAAAAATGCATTTCGA
1 AAAATAAATTTCGAAAAATGAATTTCGA
* *
34056 AAAATAAATTTCGTAAAATGAATTTCGT
1 AAAATAAATTTCGAAAAATGAATTTCGA
*
34084 AAAATGAATT
1 AAAATAAATT
34094 ACATTTTCTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (28 bp):
AAAATAAATTTCGAAAAATGAATTTCGA
Found at i:34351 original size:22 final size:20
Alignment explanation
Indices: 34314--34382 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 20
34304 ATTAAAATAA
34314 AATTATTAGTATAAATTATATT
1 AATTATTA-T-TAAATTATATT
* *
34336 AATTATCTATTAAAATAATAAT
1 AATTAT-TATT-AAATTATATT
*
34358 AATATATTATT-ATTTATATT
1 AAT-TATTATTAAATTATATT
34378 AATTA
1 AATTA
34383 AATTTGAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
19 2 0.05
20 9 0.23
21 1 0.03
22 22 0.56
23 5 0.13
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (20 bp):
AATTATTATTAAATTATATT
Found at i:34365 original size:78 final size:75
Alignment explanation
Indices: 34278--34439 Score: 163
Period size: 75 Copynumber: 2.1 Consensus size: 75
34268 CTATAATTTT
* * * *
34278 ATAAAATATTAATAATATTATATTTTATTAAA-ATAAAATTATTAGTATAAAT-TATATTAATTA
1 ATAATATATTAATAAT-TTATA-TTAATTAAATATAAAA-TATTATTA-AAATAT-TATAAATTA
*
34341 T-CTATTAAAATAATA
61 TAATATTAAAATAA-A
* * *
34356 ATAATATATT-ATTATTTATATTAATTAAATTTGAAATATTATTAAAATATTATAAATTATAATA
1 ATAATATATTAATAATTTATATTAATTAAATATAAAATATTATTAAAATATTATAAATTATAATA
34420 TTAAAATAAA
66 TTAAAATAAA
34430 AT-ATATATTA
1 ATAATATATTA
34440 CTTTAAAGAG
Statistics
Matches: 72, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
73 7 0.10
74 16 0.22
75 27 0.38
76 9 0.12
77 4 0.06
78 9 0.12
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (75 bp):
ATAATATATTAATAATTTATATTAATTAAATATAAAATATTATTAAAATATTATAAATTATAATA
TTAAAATAAA
Found at i:34416 original size:41 final size:42
Alignment explanation
Indices: 34323--34432 Score: 111
Period size: 41 Copynumber: 2.7 Consensus size: 42
34313 AAATTATTAG
** *
34323 TATAAATTATATTAATTATCTATTAAAATAATAATAATATAT
1 TATAAATTATATTAATTAAATATTAAAATAATAATAAAATAT
* * * * *
34365 TATTATTTATATTAATTAAAT-TTGAAATATTATTAAAATAT
1 TATAAATTATATTAATTAAATATTAAAATAATAATAAAATAT
*
34406 TATAAATTATAAT-ATTAAA-A-TAAAATA
1 TATAAATTATATTAATTAAATATTAAAATA
34433 TATATTACTT
Statistics
Matches: 55, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
39 6 0.11
40 6 0.11
41 26 0.47
42 17 0.31
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (42 bp):
TATAAATTATATTAATTAAATATTAAAATAATAATAAAATAT
Found at i:34419 original size:15 final size:14
Alignment explanation
Indices: 34396--34433 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
34386 TTGAAATATT
34396 ATTAAAATATTATAA
1 ATTAAAATATTA-AA
*
34411 ATTATAATATTAAA
1 ATTAAAATATTAAA
34425 A-TAAAATAT
1 ATTAAAATAT
34434 ATATTACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 7 0.33
14 3 0.14
15 11 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATTAAAATATTAAA
Found at i:34537 original size:21 final size:21
Alignment explanation
Indices: 34504--34592 Score: 53
Period size: 21 Copynumber: 4.4 Consensus size: 21
34494 TTAATAAATA
* *
34504 ATATTTTTTAATATTTATTAT
1 ATATTATTAAATATTTATTAT
**
34525 ATATTATTAAATAAATATTAT
1 ATATTATTAAATATTTATTAT
* *
34546 AT-GTATT-AATA-TAATTAT
1 ATATTATTAAATATTTATTAT
** *
34564 A-ACAATAAAATATTATATTAT
1 ATATTATTAAATATT-TATTAT
34585 ATA-TATTA
1 ATATTATTA
34593 TAAAATTATT
Statistics
Matches: 50, Mismatches: 13, Indels: 10
0.68 0.18 0.14
Matches are distributed among these distances:
18 8 0.16
19 8 0.16
20 5 0.10
21 28 0.56
22 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (21 bp):
ATATTATTAAATATTTATTAT
Found at i:34628 original size:23 final size:23
Alignment explanation
Indices: 34568--34628 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
34558 AATTATAACA
* *
34568 ATAAAATATTATATTATATATATT
1 ATAAAAT-TAATATTAAATATATT
*
34592 ATAAAATTATTATTAAATATAATT
1 ATAAAATTAATATTAAATAT-ATT
*
34616 -TATAATTAATATT
1 ATAAAATTAATATT
34629 TTATTAAATG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 21 0.68
24 10 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATAAAATTAATATTAAATATATT
Found at i:35414 original size:14 final size:14
Alignment explanation
Indices: 35395--35422 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
35385 TTACGTTATC
35395 ATCGTAAGTTAATA
1 ATCGTAAGTTAATA
35409 ATCGTAAGTTAATA
1 ATCGTAAGTTAATA
35423 CTATAGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (14 bp):
ATCGTAAGTTAATA
Found at i:40575 original size:50 final size:52
Alignment explanation
Indices: 40493--40591 Score: 148
Period size: 50 Copynumber: 1.9 Consensus size: 52
40483 TTCATTAATT
*
40493 CATTAATATATATATATATATATCGATCAATAATAATTACTCAACAATTTAC
1 CATTAATACATATATATATATATCGATCAATAATAATTACTCAACAATTTAC
* * *
40545 CATTAATACATATATGT-T-TATCTATCAATAATAATTACTCGACAATT
1 CATTAATACATATATATATATATCGATCAATAATAATTACTCAACAATT
40592 CGACTCTATC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
50 27 0.63
51 1 0.02
52 15 0.35
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.39
Consensus pattern (52 bp):
CATTAATACATATATATATATATCGATCAATAATAATTACTCAACAATTTAC
Found at i:45374 original size:152 final size:154
Alignment explanation
Indices: 45022--45381 Score: 485
Period size: 154 Copynumber: 2.4 Consensus size: 154
45012 CTCCTTCATT
* * *
45022 TTAAGTCATTTTTACCAAATTTGACCCACATGCTCCTAAACCATAGTAGAATACATCTGTACTTT
1 TTAAGTCCTTTTTACCAAATTTGAACCACATGCTCCTAAACCATAATAGAATACATCTGTACTTT
* * *
45087 CAATTACTCTTTTTGATAACAATTTTTTATTTTTCAATTTAGTCATTCAATTTTTTATAATCTCC
66 CAATTACTCTTTTTGATAACAATTTTTTATTTTTCAATTTAATCACTCAATTTTTCATAATCTCC
* * *
45152 TTATTTCTTCATTCGTCATTTATT
131 TTATTCCTTAATTCGTCATTTATG
* * *
45176 TTAAGTCCATTTTACCAAATTTGAGCCACATGCTCCTAAACCATAATAGAATACATTTGTACTTT
1 TTAAGTCCTTTTTACCAAATTTGAACCACATGCTCCTAAACCATAATAGAATACATCTGTACTTT
*
45241 CAATTCCTCTTTTTGATAAC-A-TTTTTATTTTTCAATTTAATC-CTCAATTTTTCATAATCTCC
66 CAATTACTCTTTTTGATAACAATTTTTTATTTTTCAATTTAATCACTCAATTTTTCATAATCTCC
* *
45303 TTATTCCTTTAATTTGTGATTTA-G
131 TTATTCC-TTAATTCGTCATTTATG
* ** * * *
45327 TTAATTATTTTTTTACCAAATTTGAACCACATGCTCATATACCATAATAAAATAC
1 TTAAGT-CCTTTTTACCAAATTTGAACCACATGCTCCTAAACCATAATAGAATAC
45382 CTATGTAACT
Statistics
Matches: 182, Mismatches: 22, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
151 29 0.16
152 73 0.40
153 1 0.01
154 79 0.43
ACGTcount: A:0.30, C:0.19, G:0.06, T:0.45
Consensus pattern (154 bp):
TTAAGTCCTTTTTACCAAATTTGAACCACATGCTCCTAAACCATAATAGAATACATCTGTACTTT
CAATTACTCTTTTTGATAACAATTTTTTATTTTTCAATTTAATCACTCAATTTTTCATAATCTCC
TTATTCCTTAATTCGTCATTTATG
Found at i:45395 original size:152 final size:154
Alignment explanation
Indices: 45022--45406 Score: 483
Period size: 152 Copynumber: 2.5 Consensus size: 154
45012 CTCCTTCATT
* * * *
45022 TTAAGTCATTTTTACCAAATTTGACCCACATGCTCCTAAACCATAGTAGAATACATCTGTACTTT
1 TTAAGTCCTTTTTACCAAATTTGAACCACATGCTCCTAAACCATAATAGAATACATATGTACTTT
* * *
45087 CAATTACTCTTTTTGATAACAATTTTTTATTTTTCAATTTAGTCATTCAATTTTTTATAATCTCC
66 CAATTACTCTTTTTGATAACAATTTTTTATTTTTCAATTTAATCACTCAATTTTTCATAATCTCC
* * *
45152 TTATTTCTTCATTCGTCATTTATT
131 TTATTCCTTAATTCGTCATTTATG
* * *
45176 TTAAGTCCATTTTACCAAATTTGAGCCACATGCTCCTAAACCATAATAGAATACATTTGTACTTT
1 TTAAGTCCTTTTTACCAAATTTGAACCACATGCTCCTAAACCATAATAGAATACATATGTACTTT
*
45241 CAATTCCTCTTTTTGATAAC-A-TTTTTATTTTTCAATTTAATC-CTCAATTTTTCATAATCTCC
66 CAATTACTCTTTTTGATAACAATTTTTTATTTTTCAATTTAATCACTCAATTTTTCATAATCTCC
* *
45303 TTATTCCTTTAATTTGTGATTTA-G
131 TTATTCC-TTAATTCGTCATTTATG
* ** * * * *
45327 TTAATTATTTTTTTACCAAATTTGAACCACATGCTCATATACCATAATAAAATACCTATGTAAC-
1 TTAAGT-CCTTTTTACCAAATTTGAACCACATGCTCCTAAACCATAATAGAATACATATGT-ACT
* *
45391 TTCAATTGCTATTTTT
64 TTCAATTACTCTTTTT
45407 TCACTAAAGA
Statistics
Matches: 202, Mismatches: 26, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
151 29 0.14
152 91 0.45
153 3 0.01
154 79 0.39
ACGTcount: A:0.30, C:0.19, G:0.06, T:0.46
Consensus pattern (154 bp):
TTAAGTCCTTTTTACCAAATTTGAACCACATGCTCCTAAACCATAATAGAATACATATGTACTTT
CAATTACTCTTTTTGATAACAATTTTTTATTTTTCAATTTAATCACTCAATTTTTCATAATCTCC
TTATTCCTTAATTCGTCATTTATG
Found at i:45758 original size:14 final size:14
Alignment explanation
Indices: 45738--45770 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
45728 TTAGTACAGA
45738 AACTCGAATAACTC
1 AACTCGAATAACTC
*
45752 GACTCGAATAACTC
1 AACTCGAATAACTC
45766 AACTC
1 AACTC
45771 AAATTTCCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.39, C:0.30, G:0.09, T:0.21
Consensus pattern (14 bp):
AACTCGAATAACTC
Found at i:45922 original size:85 final size:85
Alignment explanation
Indices: 45766--45966 Score: 350
Period size: 85 Copynumber: 2.4 Consensus size: 85
45756 CGAATAACTC
* *
45766 AACTCAAATTTCCTAAACTCGACTTGATTCG-AAAAAAAATTCAAGTTAAGTTCGAGTTGTAAAA
1 AACTCAAATTTCTTAAACTCGACTTGACTCGAAAAAAAAATTCAAGTTAAGTTCGAGTTGTAAAA
45830 TACGACTCGTCAACTCAAAT
66 TACGACTCGTCAACTCAAAT
45850 AACTCAAATTTCTTAAACTCGACTTGACTCGAAAAAAAAATTCAAGTTAAGTTCGAGTTGTAAAA
1 AACTCAAATTTCTTAAACTCGACTTGACTCGAAAAAAAAATTCAAGTTAAGTTCGAGTTGTAAAA
*
45915 TATGACTCGTCAACTCAAAT
66 TACGACTCGTCAACTCAAAT
* *
45935 AACTCAAATTTTTTAAACTCGACTCGACTCGA
1 AACTCAAATTTCTTAAACTCGACTTGACTCGA
45967 TCAAATGCTC
Statistics
Matches: 111, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
84 29 0.26
85 82 0.74
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.29
Consensus pattern (85 bp):
AACTCAAATTTCTTAAACTCGACTTGACTCGAAAAAAAAATTCAAGTTAAGTTCGAGTTGTAAAA
TACGACTCGTCAACTCAAAT
Done.