Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002554.1 Hibiscus syriacus cultivar Beakdansim tig00005184_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: 72856
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:2060 original size:21 final size:21
Alignment explanation
Indices: 2036--2110 Score: 114
Period size: 21 Copynumber: 3.6 Consensus size: 21
2026 CACCCCATTT
2036 GGTATCGATACTCCTTTTGTG
1 GGTATCGATACTCCTTTTGTG
2057 GGTATCGATACTCCTTTTGTG
1 GGTATCGATACTCCTTTTGTG
** *
2078 GGTATCGATACTCCCCTTATG
1 GGTATCGATACTCCTTTTGTG
*
2099 GGTATCAATACT
1 GGTATCGATACT
2111 GTAATGCCCC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (21 bp):
GGTATCGATACTCCTTTTGTG
Found at i:3017 original size:22 final size:22
Alignment explanation
Indices: 2989--3055 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 22
2979 CCGGTAGGGG
2989 GTATCGGTACCATAGTAGGGTA
1 GTATCGGTACCATAGTAGGGTA
3011 GTATCGGTACCATAGTAGGGTA
1 GTATCGGTACCATAGTAGGGTA
** *
3033 GTATCAATACCATGGTAAGGGTA
1 GTATCGGTACCATAGT-AGGGTA
3056 TCGATACTAG
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 35 0.85
23 6 0.15
ACGTcount: A:0.30, C:0.13, G:0.30, T:0.27
Consensus pattern (22 bp):
GTATCGGTACCATAGTAGGGTA
Found at i:3131 original size:117 final size:116
Alignment explanation
Indices: 2913--3139 Score: 276
Period size: 117 Copynumber: 1.9 Consensus size: 116
2903 ATACCGATGA
** * *
2913 GGTAGTATCGGTACCATGGAAAGGTATCGATACCAAGAAACATCGAATCTAATTTTGGTATCGAT
1 GGTAGTATCAATACCATGGAAAGGTATCGATACCAAGAAACATCGAACCTAATTTTGGTATCAAT
* * * * * *
2978 ACCGGTAGGGGGTATCGGTACCATAGTAGGGTAGTATCGGTACCATAGTAG
66 ACCGGAAGGGGGTATCAGTACCATAGAAGAGAAGTATCAGTACCATAGTAG
* * * * *
3029 GGTAGTATCAATACCATGGTAAGGGTATCGATACTAGGCAACATCGAACCTATTTTTGGTATCAA
1 GGTAGTATCAATACCATGG-AAAGGTATCGATACCAAGAAACATCGAACCTAATTTTGGTATCAA
* *
3094 TACTC-GAATGGGGTATCAGTACCATAGAATAGAAGTATCAGTACCA
65 TAC-CGGAAGGGGGTATCAGTACCATAGAAGAGAAGTATCAGTACCA
3140 GGGTAGTAGT
Statistics
Matches: 92, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
116 17 0.18
117 74 0.80
118 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.26
Consensus pattern (116 bp):
GGTAGTATCAATACCATGGAAAGGTATCGATACCAAGAAACATCGAACCTAATTTTGGTATCAAT
ACCGGAAGGGGGTATCAGTACCATAGAAGAGAAGTATCAGTACCATAGTAG
Found at i:3547 original size:54 final size:54
Alignment explanation
Indices: 3476--4069 Score: 768
Period size: 54 Copynumber: 11.3 Consensus size: 54
3466 TTACCAAATA
* * *
3476 GGCATTAAGTGTGCATTTCACGGAATTCATCTTATGTGGATGAATAACTGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* ** * *
3530 GGCACTAAGAGTGCATTTCAAAGAATTCAACCTACGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * *
3584 -G-AC--A-----CTTTTCACGGAATTCATCCTAAGTGGATGAATAATCGTTTT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* *
3629 GGCACTAAGAGTGCATTTCACGGAATTCATCATATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * * *
3683 GGCACTTAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAATCATTTT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
*
3737 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACAGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
3791 AGCACTAAGTGTGCATTTCACGG-A---ATCCTATGTGGATGAATTATCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
3841 GTCACTAAGTGTCCATTTCACGGAATTCATCCTATGTGGATTAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* *
3895 GACACTAAGTGTGCATTTCACGGAATTCATCATATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
3949 -GCACTAAATATGCATTTCACGGAATTCATCCTCTGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
4002 GGCACTAA-TGTGCATTTCATGGAATTCATCCTATGTGGATGAATAACCATTTT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
*
4055 GGCACTATGTGTGCA
1 GGCACTAAGTGTGCA
4070 AAGCACGAAA
Statistics
Matches: 467, Mismatches: 58, Indels: 30
0.84 0.10 0.05
Matches are distributed among these distances:
45 34 0.07
46 1 0.00
47 2 0.00
49 1 0.00
50 44 0.09
51 1 0.00
52 2 0.00
53 97 0.21
54 285 0.61
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
Found at i:3887 original size:158 final size:156
Alignment explanation
Indices: 3481--4069 Score: 694
Period size: 158 Copynumber: 3.7 Consensus size: 156
3471 AAATAGGCAT
* *
3481 TAAGTGTGCATTTCACGGAATTCATCTTATGTGGATGAATAACTGTTTCGGCACTAAGAGTGCAT
1 TAAGTGTGCATTTCACGGAA-TC--C-TATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCAT
** * * * * *
3546 TTCAAAGAATTCAACCTACGTGGATGAATAACC-GTTTCG-AC--A-----CTTTTCACGGAATT
62 TTCACGGAATTCATCCTATGTGGATGAATAACCATTTTGGCACTAAGTGTGCATTTCACGGAATT
* *
3602 CATCCTAAGTGGATGAATAATCGTTTTGGCAC
127 CATCCTATGTGGATGAATAA-CG-TTTCGCAC
* *
3634 TAAGAGTGCATTTCACGGAATTCATCATATGTGGATGAATAACCGTTTCGGCACTTAGTGTGCAT
1 TAAGTGTGCATTTCACGGAA-TC--C-TATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCAT
* *
3699 TTCACAGAATTCATCCTATGTGGATGAATAATCATTTTGGCACTAAGTGTGCATTTCACGGAATT
62 TTCACGGAATTCATCCTATGTGGATGAATAACCATTTTGGCACTAAGTGTGCATTTCACGGAATT
3764 CATCCTATGTGGATGAATAACAGTTTCAGCAC
127 CATCCTATGTGGATGAATAAC-GTTTC-GCAC
* * * *
3796 TAAGTGTGCATTTCACGGAATCCTATGTGGATGAATTATCGTTTCGTCACTAAGTGTCCATTTCA
1 TAAGTGTGCATTTCACGGAATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCA
* * * *
3861 CGGAATTCATCCTATGTGGATTAATAACCGTTTCGACACTAAGTGTGCATTTCACGGAATTCATC
66 CGGAATTCATCCTATGTGGATGAATAACCATTTTGGCACTAAGTGTGCATTTCACGGAATTCATC
*
3926 ATATGTGGATGAATAACCGTTTCGCAC
131 CTATGTGGATGAATAA-CGTTTCGCAC
* * *
3953 TAAATATGCATTTCACGGAATTCATCCTCTGTGGATGAATAACCGTTTCGGCACTAA-TGTGCAT
1 TAAGTGTGCATTTCACGG-A---ATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCAT
* *
4017 TTCATGGAATTCATCCTATGTGGATGAATAACCATTTTGGCACTATGTGTGCA
62 TTCACGGAATTCATCCTATGTGGATGAATAACCATTTTGGCACTAAGTGTGCA
4070 AAGCACGAAA
Statistics
Matches: 380, Mismatches: 40, Indels: 25
0.85 0.09 0.06
Matches are distributed among these distances:
153 89 0.23
154 4 0.01
155 2 0.01
157 21 0.06
158 117 0.31
159 2 0.01
160 53 0.14
161 36 0.09
162 56 0.15
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (156 bp):
TAAGTGTGCATTTCACGGAATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCA
CGGAATTCATCCTATGTGGATGAATAACCATTTTGGCACTAAGTGTGCATTTCACGGAATTCATC
CTATGTGGATGAATAACGTTTCGCAC
Found at i:7010 original size:26 final size:26
Alignment explanation
Indices: 6973--7026 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
6963 ACCAAAGTTC
* *
6973 TAATACATATAAGATTGTGCCCACCA
1 TAATACACATAAGATCGTGCCCACCA
*
6999 TAATACACATAAGGTCGTGCCCACCA
1 TAATACACATAAGATCGTGCCCACCA
7025 TA
1 TA
7027 TGCACTTAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.24
Consensus pattern (26 bp):
TAATACACATAAGATCGTGCCCACCA
Found at i:10861 original size:3 final size:3
Alignment explanation
Indices: 10848--10924 Score: 129
Period size: 3 Copynumber: 25.7 Consensus size: 3
10838 CAATATTAGC
*
10848 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
10895 TTA TTA TTA TATA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TT
10925 TAGACATCAT
Statistics
Matches: 70, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
2 2 0.03
3 65 0.93
4 3 0.04
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:11993 original size:26 final size:26
Alignment explanation
Indices: 11957--12006 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
11947 ACCAAAGGGT
*
11957 TAATACGCATAAGGTCGTGCCCACCA
1 TAATACACATAAGGTCGTGCCCACCA
*
11983 TAATACACATAAGGTTGTGCCCAC
1 TAATACACATAAGGTCGTGCCCAC
12007 TATATGCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (26 bp):
TAATACACATAAGGTCGTGCCCACCA
Found at i:15512 original size:20 final size:20
Alignment explanation
Indices: 15487--15526 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
15477 TTTGGGTTCG
*
15487 AGTATCGATACTAGATGAAT
1 AGTATCAATACTAGATGAAT
15507 AGTATCAATACTAGATGAAT
1 AGTATCAATACTAGATGAAT
15527 TAGGATGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.30
Consensus pattern (20 bp):
AGTATCAATACTAGATGAAT
Found at i:22946 original size:2 final size:2
Alignment explanation
Indices: 22939--22981 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
22929 TTCATGTGAT
*
22939 TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22981 T
1 T
22982 TATCATCAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:37371 original size:36 final size:37
Alignment explanation
Indices: 37297--37371 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 37
37287 TCAGTCAGAT
* * *
37297 GGCTCGATCGGCTCGGTTCCGTTCAGATGGCTCGGTC
1 GGCTCGATCGGCACGGCTCCGTTCAGATGGCTCAGTC
*
37334 GGCTCGATCGG-ACGGCTCGGTTCAGATGG-TCCAGTC
1 GGCTCGATCGGCACGGCTCCGTTCAGATGGCT-CAGTC
37370 GG
1 GG
37372 TTCAGACTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
35 1 0.03
36 21 0.64
37 11 0.33
ACGTcount: A:0.11, C:0.28, G:0.37, T:0.24
Consensus pattern (37 bp):
GGCTCGATCGGCACGGCTCCGTTCAGATGGCTCAGTC
Found at i:39370 original size:36 final size:36
Alignment explanation
Indices: 39330--39400 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
39320 TGGTCAACTC
* *
39330 GGCTCGGTCAGACGGCTTGGTCGGCTC-AGTTCAGAT
1 GGCTCAGTCAGACGGCTCGGTCGGCTCGA-TTCAGAT
39366 GGCTCAGTCAGACGGCTCGGTCGGCTCGATTCAGA
1 GGCTCAGTCAGACGGCTCGGTCGGCTCGATTCAGA
39401 CAGTCTAGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 31 0.97
37 1 0.03
ACGTcount: A:0.15, C:0.27, G:0.35, T:0.23
Consensus pattern (36 bp):
GGCTCAGTCAGACGGCTCGGTCGGCTCGATTCAGAT
Found at i:39382 original size:13 final size:14
Alignment explanation
Indices: 39351--39383 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
39341 ACGGCTTGGT
39351 CGGCTCAGTTCAGA
1 CGGCTCAGTTCAGA
*
39365 TGGCTCAG-TCAGA
1 CGGCTCAGTTCAGA
39378 CGGCTC
1 CGGCTC
39384 GGTCGGCTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.18, C:0.30, G:0.30, T:0.21
Consensus pattern (14 bp):
CGGCTCAGTTCAGA
Found at i:40905 original size:22 final size:22
Alignment explanation
Indices: 40855--40905 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
40845 ACTGTTCAAC
* *
40855 TCAGCTTGGTCAGATGGCTCAG
1 TCAGCTCGGTCAGACGGCTCAG
*
40877 TCGGCTCGGTCAGACGGCT-AGG
1 TCAGCTCGGTCAGACGGCTCA-G
40899 TCAGCTC
1 TCAGCTC
40906 AGTTTAGACG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.16, C:0.27, G:0.33, T:0.24
Consensus pattern (22 bp):
TCAGCTCGGTCAGACGGCTCAG
Found at i:42407 original size:20 final size:18
Alignment explanation
Indices: 42382--42430 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
42372 TAGTTCATTA
42382 TCTTAATTTTATCTTTATTT
1 TCTTAATTTTA-CTTT-TTT
*
42402 TCTTAATGTTACTTTTTT
1 TCTTAATTTTACTTTTTT
*
42420 TGTTCAATTTT
1 TCTT-AATTTT
42431 CTAGTAAACC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 6 0.24
19 9 0.36
20 10 0.40
ACGTcount: A:0.18, C:0.10, G:0.04, T:0.67
Consensus pattern (18 bp):
TCTTAATTTTACTTTTTT
Found at i:49051 original size:13 final size:13
Alignment explanation
Indices: 49033--49059 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
49023 CCATCAAAAT
49033 TTAAGCCTCCCTA
1 TTAAGCCTCCCTA
49046 TTAAGCCTCCCTA
1 TTAAGCCTCCCTA
49059 T
1 T
49060 GAAATAGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.37, G:0.07, T:0.33
Consensus pattern (13 bp):
TTAAGCCTCCCTA
Found at i:60189 original size:52 final size:52
Alignment explanation
Indices: 60111--60239 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
60101 AGAAAAAAGG
*
60111 CTATCTCTTGATGCTCTTACAGTGCCAAGACATATTTTACCAAAACCCAAGA
1 CTATCTCTCGATGCTCTTACAGTGCCAAGACATATTTTACCAAAACCCAAGA
* *
60163 CTATCTCTCGATGCTCTTACAGTGCCAAGACATGTTTTACCAAAACCCAAGG
1 CTATCTCTCGATGCTCTTACAGTGCCAAGACATATTTTACCAAAACCCAAGA
*
60215 CTATCTCTCGACGCTCTTACAGTGC
1 CTATCTCTCGATGCTCTTACAGTGC
60240 TAAGGTAAAA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (52 bp):
CTATCTCTCGATGCTCTTACAGTGCCAAGACATATTTTACCAAAACCCAAGA
Found at i:70467 original size:22 final size:24
Alignment explanation
Indices: 70439--70486 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
70429 GCCATCTCTC
*
70439 TTTCCTCA-TTT-TTTTATATCAT
1 TTTCCTCACTTTATATTATATCAT
70461 TTTCCTCACTTTACTATTATATCAT
1 TTTCCTCACTTTA-TATTATATCAT
70486 T
1 T
70487 CATTCTCAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 8 0.36
23 3 0.14
25 11 0.50
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTCCTCACTTTATATTATATCAT
Done.