Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006995.1 Hibiscus syriacus cultivar Beakdansim tig00018039_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: 83566
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1705 original size:13 final size:11
Alignment explanation
Indices: 1667--1747 Score: 60
Period size: 13 Copynumber: 6.9 Consensus size: 11
1657 AGATAGAGTC
1667 CATCACCAT-T
1 CATCACCATAT
1677 -ATCAGCCTATAT
1 CATCA-CC-ATAT
1689 CATCACCATAGT
1 CATCACCATA-T
1701 CCATCACCATTAT
1 -CATCACCA-TAT
*
1714 CATGC-CTATAT
1 CAT-CACCATAT
1725 CATCACCATATT
1 CATCACCATA-T
1737 CCATCACCATA
1 -CATCACCATA
1748 CCACGCCTAT
Statistics
Matches: 58, Mismatches: 2, Indels: 19
0.73 0.03 0.24
Matches are distributed among these distances:
9 4 0.07
10 3 0.05
11 15 0.26
12 10 0.17
13 24 0.41
14 2 0.03
ACGTcount: A:0.32, C:0.35, G:0.04, T:0.30
Consensus pattern (11 bp):
CATCACCATAT
Found at i:1709 original size:35 final size:36
Alignment explanation
Indices: 1663--1767 Score: 160
Period size: 35 Copynumber: 3.0 Consensus size: 36
1653 TATAAGATAG
1663 AGTCCATCACCATTATCA-GCCTATATCATCACCAT
1 AGTCCATCACCATTATCACGCCTATATCATCACCAT
*
1698 AGTCCATCACCATTATCATGCCTATATCATCACCAT
1 AGTCCATCACCATTATCACGCCTATATCATCACCAT
* * *
1734 ATTCCATCACCA-TACCACGCCTATATTATCACCA
1 AGTCCATCACCATTATCACGCCTATATCATCACCA
1768 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
35 37 0.57
36 28 0.43
ACGTcount: A:0.31, C:0.35, G:0.05, T:0.29
Consensus pattern (36 bp):
AGTCCATCACCATTATCACGCCTATATCATCACCAT
Found at i:4141 original size:2 final size:2
Alignment explanation
Indices: 4134--4160 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4124 CAAACACATC
4134 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 A
4161 CATGTTCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7231 original size:14 final size:15
Alignment explanation
Indices: 7197--7243 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
7187 AATTTGGAGT
7197 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
7212 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
7226 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
7243 G
1 G
7244 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:37397 original size:38 final size:38
Alignment explanation
Indices: 37346--37431 Score: 172
Period size: 38 Copynumber: 2.3 Consensus size: 38
37336 CCTTCATCCT
37346 TTCCATTATCCATCTTCTTCACTCCTAAACCATCACCA
1 TTCCATTATCCATCTTCTTCACTCCTAAACCATCACCA
37384 TTCCATTATCCATCTTCTTCACTCCTAAACCATCACCA
1 TTCCATTATCCATCTTCTTCACTCCTAAACCATCACCA
37422 TTCCATTATC
1 TTCCATTATC
37432 ATTTTATCAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.26, C:0.38, G:0.00, T:0.36
Consensus pattern (38 bp):
TTCCATTATCCATCTTCTTCACTCCTAAACCATCACCA
Found at i:42820 original size:33 final size:33
Alignment explanation
Indices: 42759--42826 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
42749 GTTGATGAAT
*
42759 GAAGGATGATTTAATGGTGATGAAATGGTAATG
1 GAAGGATGATTTAATGGCGATGAAATGGTAATG
* * *
42792 GAAGGATGATGTTATTGGCG-TGATATGGTGATG
1 GAAGGATGAT-TTAATGGCGATGAAATGGTAATG
42825 GA
1 GA
42827 CAGATTGTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 23 0.77
34 7 0.23
ACGTcount: A:0.31, C:0.01, G:0.37, T:0.31
Consensus pattern (33 bp):
GAAGGATGATTTAATGGCGATGAAATGGTAATG
Found at i:47265 original size:33 final size:33
Alignment explanation
Indices: 47204--47271 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
47194 GTTGATGAAT
*
47204 GAAGGATGATTTAATGGTGATGAAATGGTAATG
1 GAAGGATGATTTAATGGCGATGAAATGGTAATG
* * *
47237 GAAGGATGATGTTATTGGCG-TGATATGGTGATG
1 GAAGGATGAT-TTAATGGCGATGAAATGGTAATG
47270 GA
1 GA
47272 CAGATTGTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 23 0.77
34 7 0.23
ACGTcount: A:0.31, C:0.01, G:0.37, T:0.31
Consensus pattern (33 bp):
GAAGGATGATTTAATGGCGATGAAATGGTAATG
Found at i:51711 original size:33 final size:33
Alignment explanation
Indices: 51650--51717 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
51640 GTTGATGAAT
*
51650 GAAGGATGATTTAATGGTGATGAAATGGTAATG
1 GAAGGATGATTTAATGGCGATGAAATGGTAATG
* * *
51683 GAAGGATGATGTTATTGGCG-TGATATGGTGATG
1 GAAGGATGAT-TTAATGGCGATGAAATGGTAATG
51716 GA
1 GA
51718 CAGATTGTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 23 0.77
34 7 0.23
ACGTcount: A:0.31, C:0.01, G:0.37, T:0.31
Consensus pattern (33 bp):
GAAGGATGATTTAATGGCGATGAAATGGTAATG
Found at i:63425 original size:19 final size:20
Alignment explanation
Indices: 63382--63427 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
63372 GACTATGCTG
*
63382 GAAATTAATGTTAAAGTGTT
1 GAAATTGATGTTAAAGTGTT
63402 GAAATTGATGTTAGAA-TG-T
1 GAAATTGATGTTA-AAGTGTT
63421 GAAATTG
1 GAAATTG
63428 GTCTATTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 8 0.33
20 14 0.58
21 2 0.08
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (20 bp):
GAAATTGATGTTAAAGTGTT
Found at i:67761 original size:42 final size:42
Alignment explanation
Indices: 67669--67763 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 42
67659 AAATATTGCA
** * *
67669 GTGTTTTTCTTACAAACGCTGCAAAAGGTCAAGCTCTATAGTG
1 GTGTTTTTC-TACAAACGCAACAAAAGGTCAAGATCTATAGCG
** * *
67712 GCATTTTTCTACAAATGCAACAAAATGTCAAGATCTATAGCG
1 GTGTTTTTCTACAAACGCAACAAAAGGTCAAGATCTATAGCG
67754 GTGTTTTTCT
1 GTGTTTTTCT
67764 TATAAACACC
Statistics
Matches: 42, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
42 35 0.83
43 7 0.17
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (42 bp):
GTGTTTTTCTACAAACGCAACAAAAGGTCAAGATCTATAGCG
Found at i:67866 original size:43 final size:43
Alignment explanation
Indices: 67818--67899 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
67808 TCAAATGCCA
*
67818 CAAATCTTTAT-GCCAATGGTGGCATTTCCATCACAAAACGCCG
1 CAAATCTTTATAG-CAATAGTGGCATTTCCATCACAAAACGCCG
* * *
67861 CAAATCTTTATAGCATTAGTGTCGTTTCCATCACAAAAC
1 CAAATCTTTATAGCAATAGTGGCATTTCCATCACAAAAC
67900 ACAACTAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 33 0.97
44 1 0.03
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (43 bp):
CAAATCTTTATAGCAATAGTGGCATTTCCATCACAAAACGCCG
Found at i:71069 original size:141 final size:139
Alignment explanation
Indices: 70914--71211 Score: 359
Period size: 141 Copynumber: 2.1 Consensus size: 139
70904 GCGTTTATTT
* * *
70914 TAAAAAATGCCACTAAAGGTTCT-GGATGATAAAATACTCAAAAATTGCGACATTTGTAATTAAT
1 TAAAAAATGCCACTAAAGGTCCTGGGATGATAAAAGACTCAAAAATTGCGACATTTATAATTAA-
* * * * *
70978 AACGCCACTAAGGTATTGAA-AACTTGTGGCATTTAATAAAAAAGCCACTATATATGATATA-TA
65 AACGCCACTAAAGTACT-AACAAATTGTGGCATTTAATAAAAAA-CAAATATATATGATA-ACTA
* *
71041 TTGTGGCATTTGA
127 TTGCGGCACTTGA
* ***
71054 CTAAAAAATGCCACTAAAGGTCCTGGGATGATAAAAGACTCAGAAATTGCGGTGTTTATAATTAA
1 -TAAAAAATGCCACTAAAGGTCCTGGGATGATAAAAGACTCAAAAATTGCGACATTTATAATTAA
* * * *
71119 AATGCCATTAAAGTACTAACAAATTGTGGCGTTTAATAAAAAATAAATATATATGATAACTATTG
65 AACGCCACTAAAGTACTAACAAATTGTGGCATTTAATAAAAAACAAATATATATGATAACTATTG
71184 CGGCACTTGA
130 CGGCACTTGA
*
71194 TTAAAAATGCCACTAAAG
1 TAAAAAATGCCACTAAAG
71212 TACGAGTCTT
Statistics
Matches: 135, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
139 18 0.13
140 27 0.20
141 56 0.41
142 34 0.25
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (139 bp):
TAAAAAATGCCACTAAAGGTCCTGGGATGATAAAAGACTCAAAAATTGCGACATTTATAATTAAA
ACGCCACTAAAGTACTAACAAATTGTGGCATTTAATAAAAAACAAATATATATGATAACTATTGC
GGCACTTGA
Found at i:73275 original size:53 final size:53
Alignment explanation
Indices: 73210--73323 Score: 192
Period size: 53 Copynumber: 2.2 Consensus size: 53
73200 CAACATCATT
*
73210 TAGCAAAATTTAAAAGAAAAACTAATAATTATTTTGTAAAAAACAGCAGCGTA
1 TAGCAAAATTTAAAAGAAAAACTAACAATTATTTTGTAAAAAACAGCAGCGTA
* * *
73263 TAGCAAATTTTAAAAGAAAAACTAACAATTATTTTGTAAAAAGCAGCAGCGTT
1 TAGCAAAATTTAAAAGAAAAACTAACAATTATTTTGTAAAAAACAGCAGCGTA
73316 TAGCAAAA
1 TAGCAAAA
73324 AATCAGAAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.51, C:0.11, G:0.12, T:0.26
Consensus pattern (53 bp):
TAGCAAAATTTAAAAGAAAAACTAACAATTATTTTGTAAAAAACAGCAGCGTA
Found at i:73828 original size:20 final size:20
Alignment explanation
Indices: 73803--73840 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
73793 AAATATAGAA
*
73803 AATTTAGATAAATTAAAAAT
1 AATTTAAATAAATTAAAAAT
*
73823 AATTTAAATAATTTAAAA
1 AATTTAAATAAATTAAAA
73841 TAGTAAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (20 bp):
AATTTAAATAAATTAAAAAT
Found at i:78134 original size:22 final size:23
Alignment explanation
Indices: 78104--78150 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
78094 AAAATATATT
78104 TATTAATA-TTTCTAATAATATAA
1 TATTAATATTTTC-AATAATATAA
*
78127 TATT-ATATTTTCAATATTATAA
1 TATTAATATTTTCAATAATATAA
78149 TA
1 TA
78151 AAATAATCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTAATATTTTCAATAATATAA
Found at i:78189 original size:23 final size:23
Alignment explanation
Indices: 78140--78193 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
78130 TATATTTTCA
**
78140 ATATTATAATAAAATAATCAATT
1 ATATTATAATAAAATAATCAAAG
*
78163 ATATTATAATAATATAAT-ATAAG
1 ATATTATAATAAAATAATCA-AAG
78186 ATATTATA
1 ATATTATA
78194 TTTTTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
ATATTATAATAAAATAATCAAAG
Found at i:78494 original size:25 final size:25
Alignment explanation
Indices: 78454--78507 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
78444 ATCCAATATT
*
78454 AATATTTTTATTAATAAAATTATAAA
1 AATATTATTATTAAT-AAATTATAAA
* *
78480 AATATTATT-TTAATATATTTTAAA
1 AATATTATTATTAATAAATTATAAA
78504 AATA
1 AATA
78508 ATAATATGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 12 0.48
25 5 0.20
26 8 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
AATATTATTATTAATAAATTATAAA
Found at i:78650 original size:14 final size:14
Alignment explanation
Indices: 78628--78662 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
78618 CAAACATCGT
*
78628 AAAACGTTTTCTAG
1 AAAATGTTTTCTAG
*
78642 AAAATGTTTTTTAG
1 AAAATGTTTTCTAG
78656 AAAATGT
1 AAAATGT
78663 AATTCATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.40, C:0.06, G:0.14, T:0.40
Consensus pattern (14 bp):
AAAATGTTTTCTAG
Done.