Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005040.1 Hibiscus syriacus cultivar Beakdansim tig00011313_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: 42929
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:46 original size:25 final size:26
Alignment explanation
Indices: 5--56 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
1 TAAA
* *
5 ATTTTAAAGGCTTATT-ATAATATTT
1 ATTTTAAAGGCTAATTAAAAATATTT
30 ATTTTAAA-GCTAAATTAAAAATATTT
1 ATTTTAAAGGCT-AATTAAAAATATTT
56 A
1 A
57 ATAATGTGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 3 0.13
25 11 0.48
26 9 0.39
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (26 bp):
ATTTTAAAGGCTAATTAAAAATATTT
Found at i:1107 original size:29 final size:28
Alignment explanation
Indices: 1009--1152 Score: 76
Period size: 29 Copynumber: 4.9 Consensus size: 28
999 ACTTAGGGAT
* * *
1009 TAAATAG-AAAAATAAAAATTAAAGTAC
1 TAAATAGTAAAAACAATAATTAAAGAAC
* * * * *
1036 AAAATA-TCACAAACAAAAACTTAATGTAC
1 TAAATAGT-AAAAACAATAA-TTAAAGAAC
*
1065 TAAAATAATAAAAACATATAATTAAAGAAC
1 T-AAATAGTAAAAACA-ATAATTAAAGAAC
* * *
1095 TAAATAGTAAAAATAGAAAATTAAGGAAC
1 TAAATAGTAAAAACA-ATAATTAAAGAAC
*
1124 TAGAATAAGAAAAAAGCAATAATTCAAAG
1 TA-AAT-AGTAAAAA-CAATAATT-AAAG
1153 GAAAATAATT
Statistics
Matches: 89, Mismatches: 18, Indels: 15
0.73 0.15 0.12
Matches are distributed among these distances:
27 5 0.06
28 9 0.10
29 33 0.37
30 22 0.25
31 16 0.18
32 4 0.04
ACGTcount: A:0.63, C:0.08, G:0.08, T:0.21
Consensus pattern (28 bp):
TAAATAGTAAAAACAATAATTAAAGAAC
Found at i:3065 original size:128 final size:128
Alignment explanation
Indices: 2911--3768 Score: 872
Period size: 128 Copynumber: 6.7 Consensus size: 128
2901 TTTAGGAAAT
* * * * *
2911 GTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCTAGGTTGACATAGTTCCTACATAT
1 GTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACAGCTCCTACATAA
* * ** * * * * *
2976 TGAGGAAGTCTAATCGGGTGATGACACGACTCATACGTGATGAAGATTTCTGGCCATCTAAGG
66 TGAGGAAATTTGGTCGGGTGATGACACGATTCATACGCGATGAGGATGTCAGGCCATCTAAGG
** * * *
3039 GTGATAACACGGTTCCTACGTGATGAGGATTGATGGTTATCTGGGTTGACACAACTCTTACATAA
1 GTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACAGCTCCTACATAA
* * * * * **
3104 TGAAGAGATTTGGTCGGGTGATGACACGGTTCCTACGTGATGAGGATGGAAGGCCATCTAAGG
66 TGAGGAAATTTGGTCGGGTGATGACACGATTCATACGCGATGAGGATGTCAGGCCATCTAAGG
* * * * *
3167 GTGATAACACGCTTCCTACGTGATGCGGACGGCTGGTTATCTGGGTTCACACAACTCCTAGATAA
1 GTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACAGCTCCTACATAA
* * * * * * *
3232 TGAGGAAATCTGGTCGGATGATGAAACGGTTTC-TACGCGAAGAGGACGAT-AGGCCATCCAAGG
66 TGAGGAAATTTGGTCGGGTGATGACAC-GATTCATACGCGATGAGGATG-TCAGGCCATCTAAGG
* * * *
3295 GTGATAACATGGTTCTTACGTGATGAGGACGGCTGGTTATTTGGGTTGACACAGCTTCTACATAA
1 GTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACAGCTCCTACATAA
* * * * *
3360 TGAGGATATATGGTCGGGTGATGACACGGTTCCTACGCGATGAGGATGAT-ATGCCATCTAAGG
66 TGAGGAAATTTGGTCGGGTGATGACACGATTCATACGCGATGAGGATG-TCAGGCCATCTAAGG
* * * * *
3423 GTAATAACACGATTCCTACGAGATGAGGATGGTTGGTTATCTGGGTTGACACAGCTCCTACATAA
1 GTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACAGCTCCTACATAA
* * * * *
3488 TGAGGAAATTTGGTCGGGTGATGACAC-AGTTCATAAGCGATGAGGACGGCAAGTCATCTAAGG
66 TGAGGAAATTTGGTCGGGTGATGACACGA-TTCATACGCGATGAGGATGTCAGGCCATCTAAGG
* * * *
3551 GTGATAACACGGTTCCTATGTGATGAGTACGGCTGCTTATCTGAGTT-AGCACAGCTCCTACATA
1 GTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGA-CACAGCTCCTACATA
* * * * * *
3615 ATGAGGAAATTTGGTCAGGTGATGACACTG-CTCAT---CTATTCATGA-GTCTTGGCCATCTAA
65 ATGAGGAAATTTGGTCGGGTGATGACAC-GATTCATACGCGA-TGAGGATGTC-AGGCCATCTAA
*
3675 AG
127 GG
* * * * * * *
3677 GTGAGAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCTGAGTTCAGACATCTCCCACATAA
1 GTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACAGCTCCTACATAA
* * *
3742 TGAGGAGATCTGGTCAGGTGATGACAC
66 TGAGGAAATTTGGTCGGGTGATGACAC
3769 TACTCAAATG
Statistics
Matches: 611, Mismatches: 108, Indels: 24
0.82 0.15 0.03
Matches are distributed among these distances:
125 4 0.01
126 93 0.15
127 6 0.01
128 504 0.82
129 4 0.01
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (128 bp):
GTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACAGCTCCTACATAA
TGAGGAAATTTGGTCGGGTGATGACACGATTCATACGCGATGAGGATGTCAGGCCATCTAAGG
Found at i:3620 original size:384 final size:381
Alignment explanation
Indices: 2911--3774 Score: 1033
Period size: 384 Copynumber: 2.3 Consensus size: 381
2901 TTTAGGAAAT
* *
2911 GTGATAAC-TCGGTTCCTACGTGATGAGGACGGCTGGTTATCTAGGTTGACATAG-TTCCTACAT
1 GTGATAACAT-GGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACAGCTT-CTACAT
* ** * * *
2974 ATTGAGGAAGTCTAATCGGGTGATGACACGACTCATACGTGATGAAGATTTCTGGCCATCTAAGG
64 AATGAGGAA-TCTGGTCGGGTGATGACACGACTCATACGCGATGAAGATATATGGCCATCTAAGG
* * * * *
3039 GTGATAACACGGTTCCTACGTGATGAGGATTGATGGTTATCTGGGTTGACACAACTCTTACATAA
128 GTAATAACACGATTCCTACGAGATGAGGATGGATGGTTATCTGGGTTGACACAACTCCTACATAA
* * * * * *
3104 TGAAGAGATTTGGTCGGGTGATGACACGGTTCCTACGTGATGAGGATGGAAGGCCATCTAAGGGT
193 TGAAGAAATTTGGTCGGGTGATGACACAGTTCATAAGCGATGAGGACGGAAGGCCATCTAAGGGT
* * * *
3169 GATAACACGCTTCCTACGTGATGCGGACGGCTGGTTATCTGGGTTCACACAACTCCTAGATAATG
258 GATAACACGCTTCCTACGTGATGAGGACGGCTGCTTATCTGAGTTCACACAACTCCTACATAATG
* * *
3234 AGGAAATCTGGTC-GGATGATGAAAC-GGT-TTCTACGCGAAGAGGACGATAGGCCATCCAAGG
323 AGGAAATCTGGTCAGG-TGATGAAACTGCTCATCTACGC-AAGA-GAC--TAGGCCATCCAAAG
* *
3295 GTGATAACATGGTTCTTACGTGATGAGGACGGCTGGTTATTTGGGTTGACACAGCTTCTACATAA
1 GTGATAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACAGCTTCTACATAA
* ** * *
3360 TGAGGATATATGGTCGGGTGATGACACGGTTCCTACGCGATGAGGATGATAT-GCCATCTAAGGG
66 TGAGGA-ATCTGGTCGGGTGATGACACGACTCATACGCGATGAAGAT-ATATGGCCATCTAAGGG
* *
3424 TAATAACACGATTCCTACGAGATGAGGATGGTTGGTTATCTGGGTTGACACAGCTCCTACATAAT
129 TAATAACACGATTCCTACGAGATGAGGATGGATGGTTATCTGGGTTGACACAACTCCTACATAAT
* *
3489 GAGGAAATTTGGTCGGGTGATGACACAGTTCATAAGCGATGAGGACGGCAA-GTCATCTAAGGGT
194 GAAGAAATTTGGTCGGGTGATGACACAGTTCATAAGCGATGAGGACGG-AAGGCCATCTAAGGGT
* * * *
3553 GATAACACGGTTCCTATGTGATGAGTACGGCTGCTTATCTGAGTT-AGCACAGCTCCTACATAAT
258 GATAACACGCTTCCTACGTGATGAGGACGGCTGCTTATCTGAGTTCA-CACAACTCCTACATAAT
* * ** * * * *
3617 GAGGAAATTTGGTCAGGTGATGACACTGCTCATCTATTCATGAGTCTTGGCCATCTAAAG
322 GAGGAAATCTGGTCAGGTGATGAAACTGCTCATCTACGCAAGAGACTAGGCCATCCAAAG
* * * * * * *
3677 GTGAGAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCTGAGTTCAGACATCTCCCACATAA
1 GTGATAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACAGCTTCTACATAA
* *
3742 TGAGGAGATCTGGTCAGGTGATGACACTACTCA
66 TGAGGA-ATCTGGTCGGGTGATGACACGACTCA
3775 AATGTTCATG
Statistics
Matches: 406, Mismatches: 65, Indels: 20
0.83 0.13 0.04
Matches are distributed among these distances:
382 93 0.23
383 1 0.00
384 292 0.72
385 15 0.04
386 5 0.01
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (381 bp):
GTGATAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACAGCTTCTACATAA
TGAGGAATCTGGTCGGGTGATGACACGACTCATACGCGATGAAGATATATGGCCATCTAAGGGTA
ATAACACGATTCCTACGAGATGAGGATGGATGGTTATCTGGGTTGACACAACTCCTACATAATGA
AGAAATTTGGTCGGGTGATGACACAGTTCATAAGCGATGAGGACGGAAGGCCATCTAAGGGTGAT
AACACGCTTCCTACGTGATGAGGACGGCTGCTTATCTGAGTTCACACAACTCCTACATAATGAGG
AAATCTGGTCAGGTGATGAAACTGCTCATCTACGCAAGAGACTAGGCCATCCAAAG
Found at i:4095 original size:32 final size:32
Alignment explanation
Indices: 4047--4136 Score: 99
Period size: 32 Copynumber: 2.8 Consensus size: 32
4037 TTCGTATCAG
* * *
4047 GATGTTAAATCCCCAAAGATTCCCCAACATTT
1 GATGTTGAATCTCCAAAGATGCCCCAACATTT
* * ** *
4079 GATTTTGAATCTCCAAAGGTGCCTTAACGTTT
1 GATGTTGAATCTCCAAAGATGCCCCAACATTT
*
4111 GATGTTGAATCTTCAAAGATGCCCCA
1 GATGTTGAATCTCCAAAGATGCCCCA
4137 TCGTTCCTCA
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (32 bp):
GATGTTGAATCTCCAAAGATGCCCCAACATTT
Found at i:5345 original size:2 final size:2
Alignment explanation
Indices: 5338--5367 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5328 ACAACAAGGG
*
5338 AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5368 GGATAAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:8591 original size:30 final size:29
Alignment explanation
Indices: 8550--8663 Score: 88
Period size: 30 Copynumber: 3.7 Consensus size: 29
8540 CAAAAAAAAC
*
8550 TTAAGGTACTAAAATAATAAAAACATATAA
1 TTAAGGAACTAAAATAATAAAAACA-ATAA
* *
8580 TTAAGGAACTAAAATAGTAAACATAGAA-AA
1 TTAAGGAACTAAAATAATAAA-A-ACAATAA
* * *
8610 ATAAGGAACTAGAATAGCAAAAAAATCAATAA
1 TTAAGGAACTAAAATA--ATAAAAA-CAATAA
8642 TTCAAAGG-ACTAAAATAATAAA
1 TT--AAGGAACTAAAATAATAAA
8664 CGTAAGAACT
Statistics
Matches: 65, Mismatches: 11, Indels: 15
0.71 0.12 0.16
Matches are distributed among these distances:
30 36 0.55
31 9 0.14
32 8 0.12
33 8 0.12
34 4 0.06
ACGTcount: A:0.61, C:0.08, G:0.11, T:0.21
Consensus pattern (29 bp):
TTAAGGAACTAAAATAATAAAAACAATAA
Found at i:21051 original size:26 final size:27
Alignment explanation
Indices: 21022--21073 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
21012 GTCAAAACAT
* *
21022 CTAAA-TTTTGGAAATTTCACTTTTGC
1 CTAAACTTTTGAAAATTACACTTTTGC
*
21048 CTAAACTTTTGAAAATTACCCTTTTG
1 CTAAACTTTTGAAAATTACACTTTTG
21074 GTCATTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.44
Consensus pattern (27 bp):
CTAAACTTTTGAAAATTACACTTTTGC
Found at i:26682 original size:22 final size:20
Alignment explanation
Indices: 26657--26699 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
26647 AAAATATTGG
*
26657 TTTGAAATGGAATTGATTGAAA
1 TTTGAAATGCAA-TGATT-AAA
*
26679 TTTGATATGCAATGATTAAA
1 TTTGAAATGCAATGATTAAA
26699 T
1 T
26700 GGATGGTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 5 0.26
22 10 0.53
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.40
Consensus pattern (20 bp):
TTTGAAATGCAATGATTAAA
Found at i:27528 original size:2 final size:2
Alignment explanation
Indices: 27521--27546 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
27511 TTAGTACTAA
27521 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
27547 GTGTGTGTGT
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
Found at i:33781 original size:14 final size:14
Alignment explanation
Indices: 33762--33789 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
33752 AAGTTTAAAA
33762 ATTTATTAATAAGT
1 ATTTATTAATAAGT
33776 ATTTATTAATAAGT
1 ATTTATTAATAAGT
33790 TACTCCCACT
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:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATTTATTAATAAGT
Found at i:40762 original size:49 final size:48
Alignment explanation
Indices: 40642--40763 Score: 154
Period size: 49 Copynumber: 2.5 Consensus size: 48
40632 CGATGAGTAA
*
40642 CACCTTTTATGCCAAAAATAAACCGTTATGCATTTAACTTTCATTAGTGG
1 CACCTTTTATGCC--AAATACACCGTTATGCATTTAACTTTCATTAGTGG
** * *
40692 CACCTTTTATGTTGAAATACACCGTTATGCATTTAACTTTCGTTTGTGG
1 CACCTTTTATG-CCAAATACACCGTTATGCATTTAACTTTCATTAGTGG
*
40741 TACCTTTTATGCCAAAGTACACC
1 CACCTTTTATGCCAAA-TACACC
40764 TCTTACTCTT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
48 3 0.05
49 48 0.77
50 11 0.18
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (48 bp):
CACCTTTTATGCCAAATACACCGTTATGCATTTAACTTTCATTAGTGG
Done.