Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004773.1 Hibiscus syriacus cultivar Beakdansim tig00010766_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: 68706
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:7793 original size:2 final size:2
Alignment explanation
Indices: 7788--7824 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
7778 TTTTTTAATA
7788 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7825 ATCAATTAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20684 original size:21 final size:21
Alignment explanation
Indices: 20658--20702 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
20648 GATTTCTGGG
* *
20658 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
20679 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
20700 CAA
1 CAA
20703 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:22427 original size:23 final size:22
Alignment explanation
Indices: 22368--22434 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
22358 TATGGACATC
*
22368 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
22390 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
22412 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
22435 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:26530 original size:15 final size:15
Alignment explanation
Indices: 26505--26539 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
26495 ACATCATTCA
*
26505 ATTAATTTATAAAAT
1 ATTAATCTATAAAAT
*
26520 GTTAATCTATAAAAT
1 ATTAATCTATAAAAT
26535 ATTAA
1 ATTAA
26540 ATGTATGATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (15 bp):
ATTAATCTATAAAAT
Found at i:30050 original size:45 final size:45
Alignment explanation
Indices: 29999--30133 Score: 216
Period size: 45 Copynumber: 3.0 Consensus size: 45
29989 CGTTAGTGAT
* * * *
29999 TTGCTGCTAAGCATAGCTACTGAAACATCATTCTAAAATGGGATA
1 TTGCTGCTGATCATGGCTACTCAAACATCATTCTAAAATGGGATA
*
30044 TTGCTGCTGATCATGGCTACTCAGACATCATTCTAAAATGGGATA
1 TTGCTGCTGATCATGGCTACTCAAACATCATTCTAAAATGGGATA
*
30089 TTGCTGCTGATCATGGCTACTCAAACATCATTCTCAAATGGGATA
1 TTGCTGCTGATCATGGCTACTCAAACATCATTCTAAAATGGGATA
30134 ATATGCTAGT
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 83 1.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (45 bp):
TTGCTGCTGATCATGGCTACTCAAACATCATTCTAAAATGGGATA
Found at i:34817 original size:48 final size:48
Alignment explanation
Indices: 34679--34824 Score: 184
Period size: 48 Copynumber: 3.0 Consensus size: 48
34669 GGGTTGTTCT
* * *
34679 TCTTCGGCTACTAGGGGATCCTGAATATGTTGGTTGAGCTGCTCCTCT
1 TCTTCGGCTACTAGGGGCTCCTGAATATGTTGGTTGAGCTGTTCCTCA
* ** *
34727 TCTTCGGCTACTAGGGGCTCCTGAATATGTAGGTTGAGCTGTTTGTGA
1 TCTTCGGCTACTAGGGGCTCCTGAATATGTTGGTTGAGCTGTTCCTCA
** * * *
34775 TCTTTTGCTTCTAGGGGCTCCTGAATATGTTGGTTGATCTGTTCCCCA
1 TCTTCGGCTACTAGGGGCTCCTGAATATGTTGGTTGAGCTGTTCCTCA
34823 TC
1 TC
34825 GTCCTCGATT
Statistics
Matches: 82, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 82 1.00
ACGTcount: A:0.14, C:0.21, G:0.27, T:0.38
Consensus pattern (48 bp):
TCTTCGGCTACTAGGGGCTCCTGAATATGTTGGTTGAGCTGTTCCTCA
Found at i:46442 original size:18 final size:19
Alignment explanation
Indices: 46395--46442 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
46385 GTTCAATTGA
* *
46395 GTTGTTCTTGATTTAGGGAT
1 GTTGTT-TTGAGTTAGAGAT
46415 GTTGGTTTTGAGTTAGAGAT
1 GTT-GTTTTGAGTTAGAGAT
46435 -TTGTTTTG
1 GTTGTTTTG
46443 GTGTTATTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 6 0.24
19 2 0.08
20 14 0.56
21 3 0.12
ACGTcount: A:0.15, C:0.02, G:0.31, T:0.52
Consensus pattern (19 bp):
GTTGTTTTGAGTTAGAGAT
Found at i:52040 original size:13 final size:13
Alignment explanation
Indices: 52022--52046 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52012 AATAAAAAAA
52022 AATCAAGTTTTTG
1 AATCAAGTTTTTG
52035 AATCAAGTTTTT
1 AATCAAGTTTTT
52047 CTTACCCCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.48
Consensus pattern (13 bp):
AATCAAGTTTTTG
Found at i:52516 original size:19 final size:19
Alignment explanation
Indices: 52492--52529 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
52482 AAAAGTAATT
* *
52492 TATTTTTTATAAATCATAA
1 TATTTTTTAAAAAACATAA
52511 TATTTTTTAAAAAACATAA
1 TATTTTTTAAAAAACATAA
52530 GATAATTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
TATTTTTTAAAAAACATAA
Found at i:59266 original size:23 final size:26
Alignment explanation
Indices: 59211--59269 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 26
59201 TTTAAGTATA
59211 ATAATAAAATTTCTGACTAAAAATTAT
1 ATAATAAAATTTCTGACTAAAAA-TAT
*
59238 ATAATAAAA-TTCT-ATTAAAAA-AT
1 ATAATAAAATTTCTGACTAAAAATAT
59261 ATAATAAAA
1 ATAATAAAA
59270 GTTTTGAGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 11 0.35
25 7 0.23
26 4 0.13
27 9 0.29
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (26 bp):
ATAATAAAATTTCTGACTAAAAATAT
Found at i:59267 original size:26 final size:28
Alignment explanation
Indices: 59207--59267 Score: 83
Period size: 25 Copynumber: 2.3 Consensus size: 28
59197 ATTATTTAAG
*
59207 TATAATAATAAAATTTCTGACTAAAAAT
1 TATAATAATAAAATTTCTGACTAAAAAA
*
59235 TAT-ATAATAAAA-TTCT-ATTAAAAAA
1 TATAATAATAAAATTTCTGACTAAAAAA
59260 TATAATAA
1 TATAATAA
59268 AAGTTTTGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 10 0.33
26 8 0.27
27 9 0.30
28 3 0.10
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (28 bp):
TATAATAATAAAATTTCTGACTAAAAAA
Found at i:60990 original size:22 final size:22
Alignment explanation
Indices: 60965--61008 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
60955 CACCACAGCT
*
60965 CGTATAAATGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
* *
60987 CGTAGAATTGCACCGCAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
61009 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.27, C:0.30, G:0.25, T:0.18
Consensus pattern (22 bp):
CGTAGAAATGCACCGAAGTGCC
Found at i:61259 original size:144 final size:144
Alignment explanation
Indices: 60987--61285 Score: 492
Period size: 144 Copynumber: 2.0 Consensus size: 144
60977 CCGAAGTGCC
* *
60987 CGTAGAATTGCACCGCAGTGCCATATAATGATGTCCATAAGGACCACGTAGAATTCTTAAGAATC
1 CGTAGAATTGCACCGCAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTAAGAATC
61052 ATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACATGTTCCAAAGAATATATAT
66 ATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACATGTTCCAAAGAATATATAT
61117 GTCCCGAAGAACCG
131 GTCCCGAAGAACCG
*
61131 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGCAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTC-TTAAGAAT
*
61196 CATATACATATGCTAGGGATCAAGTATGTGTC-TTCTAGACTTCACACATGTTCCAAAGAATATA
65 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTT--CACATGTTCCAAAGAATAT-
*
61260 CATATGTCTCGAAGAAACCG
127 -ATATGTCCCGAAG-AACCG
61280 CGTAGA
1 CGTAGA
61286 CCCTCGACTC
Statistics
Matches: 144, Mismatches: 5, Indels: 7
0.92 0.03 0.04
Matches are distributed among these distances:
144 62 0.43
145 40 0.28
146 19 0.13
148 12 0.08
149 11 0.08
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (144 bp):
CGTAGAATTGCACCGCAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTAAGAATC
ATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACATGTTCCAAAGAATATATAT
GTCCCGAAGAACCG
Found at i:63775 original size:16 final size:17
Alignment explanation
Indices: 63736--63778 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
63726 ATAGCATCAG
*
63736 TTTATCACTCAAAATCC
1 TTTATCAATCAAAATCC
* *
63753 TTAATCAATC-AAATTC
1 TTTATCAATCAAAATCC
63769 TTTATCAATC
1 TTTATCAATC
63779 TTTAATTACC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40
Consensus pattern (17 bp):
TTTATCAATCAAAATCC
Found at i:65945 original size:23 final size:23
Alignment explanation
Indices: 65919--65963 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
65909 CACCACAGCT
* *
65919 CGTATAAATGCACTGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
65942 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
65964 ATATAATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:66205 original size:144 final size:145
Alignment explanation
Indices: 65943--66229 Score: 483
Period size: 144 Copynumber: 2.0 Consensus size: 145
65933 GAAGTGCCCC
* *
65943 GTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACGTAGAATTCTTTAAGAATC
1 GTAGAATTGCACCGTAGTGCCATATAATGATATCCATAAGGACCACATAGAATTCTTTAAGAATC
66008 ATATACATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACAT
66 ATATACATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACAT
66073 ATGTCCCGAAGAACCG
131 ATGTCCCG-AGAACCG
66089 GTAGAATTGCACCGTAGTGCCATATAAT-A-ATCCATAAGGACCACATAGAATTCTTTAAGAATC
1 GTAGAATTGCACCGTAGTGCCATATAATGATATCCATAAGGACCACATAGAATTCTTTAAGAATC
*
66152 ATATACATATGCTAGGGATCAAGTATGTGT-TTT-TAGACTTCACACATGTTCCAAAGAATATAC
66 ATATAC--ATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATAC
*
66215 ATATGTCTCGAGAAC
129 ATATGTCCCGAGAAC
66230 GCGTAGACCC
Statistics
Matches: 135, Mismatches: 4, Indels: 7
0.92 0.03 0.05
Matches are distributed among these distances:
143 5 0.04
144 76 0.56
145 4 0.03
146 50 0.37
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (145 bp):
GTAGAATTGCACCGTAGTGCCATATAATGATATCCATAAGGACCACATAGAATTCTTTAAGAATC
ATATACATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACAT
ATGTCCCGAGAACCG
Found at i:66968 original size:21 final size:22
Alignment explanation
Indices: 66927--66983 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 22
66917 CATTTCATTC
*
66927 ATATATAATTATAT-ATATATAT
1 ATATATCA-TATATCATATATAT
* *
66949 TTCTATCATATATCAT-TATAT
1 ATATATCATATATCATATATAT
*
66970 ATATATTATATATC
1 ATATATCATATATC
66984 CTCAAGATTA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 21 0.75
22 7 0.25
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (22 bp):
ATATATCATATATCATATATAT
Found at i:67828 original size:20 final size:20
Alignment explanation
Indices: 67800--67840 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
67790 ATTTGTCGTT
* *
67800 TGAAGGGGTATCGGTTCCCC
1 TGAAGGGGTACCGATTCCCC
*
67820 TGAATGGGTACCGATTCCCC
1 TGAAGGGGTACCGATTCCCC
67840 T
1 T
67841 TGCCCAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (20 bp):
TGAAGGGGTACCGATTCCCC
Done.