Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000050.1 Hibiscus syriacus cultivar Beakdansim tig00000077_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: 80795
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:7429 original size:24 final size:24
Alignment explanation
Indices: 7402--7449 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
7392 TTCTTAACTA
*
7402 AAGGACTATATTAAACCATTAAAC
1 AAGGACTATATTAAACCACTAAAC
7426 AAGGACTATATTAAACCACTAAAC
1 AAGGACTATATTAAACCACTAAAC
7450 TGTTATTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (24 bp):
AAGGACTATATTAAACCACTAAAC
Found at i:7556 original size:4 final size:4
Alignment explanation
Indices: 7542--7571 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
7532 AAAATATATC
7542 ATAA TATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA -ATAA ATAA ATAA ATAA ATAA ATAA A
7572 ATTTTCATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:15694 original size:23 final size:23
Alignment explanation
Indices: 15644--15694 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
15634 TTAAATATAT
15644 TAATTATAAAACTAAACTATTTAA
1 TAATTATAAAACTAAAC-ATTTAA
*
15668 -AATTATTAAAATTAAA-ATTTAA
1 TAATTA-TAAAACTAAACATTTAA
15690 TAATT
1 TAATT
15695 TTGGAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
22 6 0.25
23 9 0.38
24 9 0.38
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (23 bp):
TAATTATAAAACTAAACATTTAA
Found at i:28538 original size:21 final size:22
Alignment explanation
Indices: 28506--28558 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
28496 AAATGTGTTA
*
28506 AAAAATATAAGAAAAACATCAT
1 AAAAATATAAGAAAAAAATCAT
*
28528 AAAAATA-AAGAAAAAAATTAT
1 AAAAATATAAGAAAAAAATCAT
*
28549 AAAGATATAA
1 AAAAATATAA
28559 TTATTAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.72, C:0.04, G:0.06, T:0.19
Consensus pattern (22 bp):
AAAAATATAAGAAAAAAATCAT
Found at i:28575 original size:33 final size:34
Alignment explanation
Indices: 28534--28613 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 34
28524 TCATAAAAAT
* *
28534 AAAGAAAAAAATTATAAAGATATAATTAT-TAAA
1 AAAGAAAAAAAATATAAAGATATAATAATATAAA
* * *
28567 AAATAAAAAAAATATTATGATATAATAATATAAA
1 AAAGAAAAAAAATATAAAGATATAATAATATAAA
28601 AAAGAAATAAAAA
1 AAAGAAA-AAAAA
28614 ATATCAACAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
33 24 0.62
34 10 0.26
35 5 0.13
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (34 bp):
AAAGAAAAAAAATATAAAGATATAATAATATAAA
Found at i:28578 original size:36 final size:34
Alignment explanation
Indices: 28528--28615 Score: 97
Period size: 34 Copynumber: 2.5 Consensus size: 34
28518 AAAACATCAT
*
28528 AAAAATAAAGAAAAAAATTATAAAGATATAATTAT-TA
1 AAAAATAAA-AAAAAAATTAT---GATATAATAATATA
*
28565 AAAAATAAAAAAAATATTATGATATAATAATATA
1 AAAAATAAAAAAAAAATTATGATATAATAATATA
* *
28599 AAAAAGAAATAAAAAAT
1 AAAAATAAAAAAAAAAT
28616 ATCAACAATA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
33 10 0.22
34 16 0.36
36 10 0.22
37 9 0.20
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (34 bp):
AAAAATAAAAAAAAAATTATGATATAATAATATA
Found at i:28616 original size:36 final size:33
Alignment explanation
Indices: 28527--28617 Score: 92
Period size: 36 Copynumber: 2.6 Consensus size: 33
28517 AAAAACATCA
* * *
28527 TAAAAATAAAGAAAAAAATTATAAAGATATAATTAT
1 TAAAAA-AAA-AAAAAAA-TATTATGATATAATAAT
*
28563 TAAAAAATAAAAAAAATATTATGATATAATAAT
1 TAAAAAAAAAAAAAAATATTATGATATAATAAT
28596 ATAAAAAAGAAATAAAAAATAT
1 -TAAAAAA-AAA-AAAAAATAT
28618 CAACAATAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
33 14 0.30
34 14 0.30
35 4 0.09
36 15 0.32
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.26
Consensus pattern (33 bp):
TAAAAAAAAAAAAAAATATTATGATATAATAAT
Found at i:29035 original size:18 final size:17
Alignment explanation
Indices: 28994--29043 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
28984 ATCAACTCTT
* *
28994 TTCTTCTT-TCTTCTTC
1 TTCTTCTTCTCCTCCTC
*
29010 TTCTTCTTCTCGTCCTC
1 TTCTTCTTCTCCTCCTC
29027 TTCCTTCTTCTCCTCCT
1 TT-CTTCTTCTCCTCCT
29044 TAAAACCCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 8 0.28
17 8 0.28
18 13 0.45
ACGTcount: A:0.00, C:0.40, G:0.02, T:0.58
Consensus pattern (17 bp):
TTCTTCTTCTCCTCCTC
Found at i:29165 original size:17 final size:16
Alignment explanation
Indices: 29096--29198 Score: 77
Period size: 17 Copynumber: 6.3 Consensus size: 16
29086 AACCCTATTG
*
29096 AAAATTATAACCTCCAC
1 AAAATCATAACC-CCAC
* *
29113 AAAATCAAAAACCCA-
1 AAAATCATAACCCCAC
*
29128 AAAATCATAA-CCCATTT
1 AAAATCATAACCCCA--C
29145 AAAATCATAACCTCCAC
1 AAAATCATAACC-CCAC
* *
29162 AAAATCAAAAAACCCA-
1 AAAATC-ATAACCCCAC
*
29178 AAAATCATAACCCTAC
1 AAAATCATAACCCCAC
29194 AAAAT
1 AAAAT
29199 ATGATAAGAT
Statistics
Matches: 69, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
14 4 0.06
15 15 0.22
16 14 0.20
17 28 0.41
18 5 0.07
19 3 0.04
ACGTcount: A:0.55, C:0.27, G:0.00, T:0.17
Consensus pattern (16 bp):
AAAATCATAACCCCAC
Found at i:29173 original size:50 final size:50
Alignment explanation
Indices: 29043--29192 Score: 212
Period size: 50 Copynumber: 3.0 Consensus size: 50
29033 CTTCTCCTCC
* * * * *
29043 TTAAAACCCTAACCTCCAAAAAATCAAAGACTCAAAAAATCATAACCCTAT
1 TTAAAATCATAACCTCCACAAAATCAAAAAC-CCAAAAATCATAACCCTAT
* *
29094 TGAAAATTATAACCTCCACAAAATCAAAAACCCAAAAATCATAACCC-AT
1 TTAAAATCATAACCTCCACAAAATCAAAAACCCAAAAATCATAACCCTAT
29143 TTAAAATCATAACCTCCACAAAATCAAAAAACCCAAAAATCATAACCCTA
1 TTAAAATCATAACCTCCACAAAATC-AAAAACCCAAAAATCATAACCCTA
29193 CAAAATATGA
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
49 25 0.28
50 37 0.42
51 26 0.30
ACGTcount: A:0.53, C:0.27, G:0.01, T:0.19
Consensus pattern (50 bp):
TTAAAATCATAACCTCCACAAAATCAAAAACCCAAAAATCATAACCCTAT
Found at i:29931 original size:32 final size:31
Alignment explanation
Indices: 29852--29936 Score: 100
Period size: 32 Copynumber: 2.7 Consensus size: 31
29842 TAGGATAATC
*
29852 ATTTTGTGG-GGTTATGATTTTTGGATTTTT
1 ATTTTGTGGAGGTTATGATTTTTGGATTTTG
* * *
29882 ATTTTTTTCGAGGTTATGATTTTTGGGTTTCTG
1 A-TTTTGTGGAGGTTATGATTTTTGGATTT-TG
*
29915 ATTTTGTGGAGCTTATGATTTT
1 ATTTTGTGGAGGTTATGATTTT
29937 CAATGGGGTT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
30 1 0.02
31 6 0.13
32 36 0.80
33 2 0.04
ACGTcount: A:0.14, C:0.04, G:0.25, T:0.58
Consensus pattern (31 bp):
ATTTTGTGGAGGTTATGATTTTTGGATTTTG
Found at i:29949 original size:50 final size:50
Alignment explanation
Indices: 29893--29989 Score: 133
Period size: 50 Copynumber: 1.9 Consensus size: 50
29883 TTTTTTTCGA
* *
29893 GGTTATGATTTTTGG-GTTTCTGATTTTGTGGAGCTTATGATTTTCAATGG
1 GGTTATGATTTTTGGAATTT-TGATTTTGTGGAGCTTAGGATTTTCAATGG
* * *
29943 GGTTATGATTTTTGGAATTTTGATTTTTTGGAGGTTAGGGTTTTCAA
1 GGTTATGATTTTTGGAATTTTGATTTTGTGGAGCTTAGGATTTTCAA
29990 ATAAGAAGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
50 38 0.93
51 3 0.07
ACGTcount: A:0.18, C:0.04, G:0.28, T:0.51
Consensus pattern (50 bp):
GGTTATGATTTTTGGAATTTTGATTTTGTGGAGCTTAGGATTTTCAATGG
Found at i:34022 original size:24 final size:23
Alignment explanation
Indices: 33989--34035 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 23
33979 AAACTCTTCC
33989 ATATAATTATGTTTACAGAATAT
1 ATATAATTATGTTTACAGAATAT
34012 ATATACATTATGTTTACAGAATAT
1 ATATA-ATTATGTTTACAGAATAT
34036 TTTTTAGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (23 bp):
ATATAATTATGTTTACAGAATAT
Found at i:44974 original size:2 final size:2
Alignment explanation
Indices: 44967--44994 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44957 CGTTCCTCTA
44967 AT 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 AT
44995 GTTAGCCGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51156 original size:4 final size:4
Alignment explanation
Indices: 51147--51171 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
51137 CTTGAATTTA
51147 ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
51172 GGTATATATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:51568 original size:27 final size:27
Alignment explanation
Indices: 51538--51590 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
51528 GAGCCGTAGA
51538 AGAAGAAAGAAGAGCCGAAGAAAGACG
1 AGAAGAAAGAAGAGCCGAAGAAAGACG
* **
51565 AGAAGAAGGCGGAGCCGAAGAAAGAC
1 AGAAGAAAGAAGAGCCGAAGAAAGAC
51591 CAGCCGAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.51, C:0.13, G:0.36, T:0.00
Consensus pattern (27 bp):
AGAAGAAAGAAGAGCCGAAGAAAGACG
Found at i:70095 original size:12 final size:12
Alignment explanation
Indices: 70080--70104 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
70070 TTATATTTTT
70080 TATAAAATATTA
1 TATAAAATATTA
70092 TATAAAATATTA
1 TATAAAATATTA
70104 T
1 T
70105 TTTTTTACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TATAAAATATTA
Found at i:70103 original size:42 final size:46
Alignment explanation
Indices: 70041--70154 Score: 120
Period size: 42 Copynumber: 2.6 Consensus size: 46
70031 TACGGTCAAA
** *
70041 AAAATATTATCGAAAGTATTAATATTTTTTTA-TA-TTTTT-TA-T
1 AAAATATTATATAAAATATTAATATTTTTTTACTAGTTTTTCTATT
70083 AAAATATTATATAAAATA-T--TATTTTTTTACTAGTTTTTCTATT
1 AAAATATTATATAAAATATTAATATTTTTTTACTAGTTTTTCTATT
70126 AAAA-ATTATATAGTAAA-ATTAATATTTTT
1 AAAATATTATATA--AAATATTAATATTTTT
70155 GATAGAACAA
Statistics
Matches: 60, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
39 10 0.17
40 2 0.03
41 6 0.10
42 25 0.42
43 6 0.10
44 4 0.07
46 7 0.12
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.53
Consensus pattern (46 bp):
AAAATATTATATAAAATATTAATATTTTTTTACTAGTTTTTCTATT
Found at i:77373 original size:18 final size:18
Alignment explanation
Indices: 77350--77385 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
77340 GTATGATGAA
77350 CGAATGTGACCTAAGGGC
1 CGAATGTGACCTAAGGGC
77368 CGAATGTGACCTAAGGGC
1 CGAATGTGACCTAAGGGC
77386 ATCCTTTGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.22, G:0.33, T:0.17
Consensus pattern (18 bp):
CGAATGTGACCTAAGGGC
Found at i:77448 original size:58 final size:58
Alignment explanation
Indices: 77358--77517 Score: 284
Period size: 58 Copynumber: 2.8 Consensus size: 58
77348 AACGAATGTG
*
77358 ACCTAAGGGCCGAATGTGACCTAAGGGCATCCTTTGCGATTCTTATCTTAGTAAAGTT
1 ACCTAATGGCCGAATGTGACCTAAGGGCATCCTTTGCGATTCTTATCTTAGTAAAGTT
*
77416 ACCTAATGGCCAAATGTGACCTAAGGGCATCCTTTGCGATTCTTATCTTAGTAAAGTT
1 ACCTAATGGCCGAATGTGACCTAAGGGCATCCTTTGCGATTCTTATCTTAGTAAAGTT
* *
77474 ACCTAATGGCTGAATGTGACCTAAGGGCATCCTTTGCGTTTCTT
1 ACCTAATGGCCGAATGTGACCTAAGGGCATCCTTTGCGATTCTT
77518 TGTGCAATAA
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 97 1.00
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (58 bp):
ACCTAATGGCCGAATGTGACCTAAGGGCATCCTTTGCGATTCTTATCTTAGTAAAGTT
Found at i:78613 original size:18 final size:18
Alignment explanation
Indices: 78587--78626 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
78577 GTCATTTTAG
*
78587 GGTTCGTCCTTTGTTCAT
1 GGTTAGTCCTTTGTTCAT
78605 GGTTAGTCCTTTGTTCAT
1 GGTTAGTCCTTTGTTCAT
78623 GGTT
1 GGTT
78627 GGTTTAGTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.07, C:0.17, G:0.25, T:0.50
Consensus pattern (18 bp):
GGTTAGTCCTTTGTTCAT
Done.