Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007156.1 Hibiscus syriacus cultivar Beakdansim tig00018739_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: 59444
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:554 original size:30 final size:33
Alignment explanation
Indices: 494--556 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 33
484 ATTATTTAAT
*
494 AATAATAATATAATATAATAAATATTAAAAAAA
1 AATAATAATATAATATAATAAATATGAAAAAAA
527 AATAATAATA-AATA-AA-ACAA-ATGAAAAAAA
1 AATAATAATATAATATAATA-AATATGAAAAAAA
557 TAGTGTCTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
30 10 0.36
31 4 0.14
32 4 0.14
33 10 0.36
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (33 bp):
AATAATAATATAATATAATAAATATGAAAAAAA
Found at i:1037 original size:112 final size:111
Alignment explanation
Indices: 796--1421 Score: 827
Period size: 109 Copynumber: 5.7 Consensus size: 111
786 AGTTCTCTCA
* * * *
796 TATGAACTTCCTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAAAC--T-TCTGGCAATGCTG
1 TATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG-AACTTTCTCTGGAAAAGCTG
* * *
858 AT-CATCAAATGATGAA-TCAAAG-AAAAGGTTGAACAAATTCTTCTTAT
65 ATCCATCAAGTGATGAATTC-AAGCAAAAGGTTGAAC-AACTCTT-TCAT
* *
905 TATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTTGAAATGCTGA
1 TATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGA
* ** *
970 TCCATCAAGTGATGGATTTGAGTAAAAGGTTGAACAACTCTTCTCAT
66 TCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAACTCTT-TCAT
1017 TATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGA
1 TATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGA
* *
1082 TCCATCGAA-TGATGAATTCAAACAAAAGGTTGAACAAATTCTTTCAT
66 TCCATC-AAGTGATGAATTCAAGCAAAAGGTTGAAC-AACTCTTTCAT
* *
1129 TATGAA---CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGTAAAAGTTGA
1 TATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGA
* **
1191 TCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTC-TTCAT
66 TCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAA-CTCTTTCAT
*
1237 TATGAACTTCTTCTTCCTTCTTCAGATGAG-T-TT-TCATTATGAAC-TTCTCTGGAAAGGCTGA
1 TATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGA
* *
1298 TCCATCGAA-TGATGAATTCAAACAAAAGGTTGAACAAAT-TTTCAT
66 TCCATC-AAGTGATGAATTCAAGCAAAAGGTTGAACAACTCTTTCAT
*
1343 TATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGA
1 TATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGA
*
1408 TCCATCGAGTGATG
66 TCCATCAAGTGATG
1422 GATTGAATCT
Statistics
Matches: 461, Mismatches: 36, Indels: 39
0.86 0.07 0.07
Matches are distributed among these distances:
106 35 0.08
107 45 0.10
108 33 0.07
109 140 0.30
110 29 0.06
111 34 0.07
112 124 0.27
113 21 0.05
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (111 bp):
TATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGA
TCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAACTCTTTCAT
Found at i:1053 original size:221 final size:222
Alignment explanation
Indices: 789--1425 Score: 982
Period size: 221 Copynumber: 2.9 Consensus size: 222
779 TCAGATGAGT
* * *
789 TCTCTCA-TATGAACTTCCTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAAAC-T-TCTGGC
1 TCTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG-AACTTCTCTGGA
* * *
851 AATGCTGAT-CATCAAATGATGAA-TCAAAGAAAAGGTTGAACAAATTCTTCTTATTATGAACTT
65 AAAGCTGATCCATCGAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTC-TATTATGAA-TT
*
914 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTTGAAATGCTGATCCATCAAG
128 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTTGAAAAGCTGATCCATCAAG
*
979 TGATGGATTTGAGTAAAAGGTTGAACAA-C
193 TGATGGATTTGAGCAAAAGGTTGAACAAGC
1008 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
1 TC-TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTGG
1073 AAAAGCTGATCCATCGAATGATGAATTCAAACAAAAGGTTGAACAAATTCTT-TCATTATGAA--
64 AAAAGCTGATCCATCGAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCT-ATTATGAATT
*
1135 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC-TGTAAAAGTTGATCCATCAA
128 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTTG-AAAAGCTGATCCATCAA
1199 GTGATGGATTTGAGCAAAAGGTTGAACAAGC
192 GTGATGGATTTGAGCAAAAGGTTGAACAAGC
1230 TCT-TCATTATGAACTTCTTCTTCCTTCTTCAGATGAG-T-TT-TCATTATGAACTTCTCTGGAA
1 TCTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAA
*
1291 AGGCTGATCCATCGAATGATGAATTCAAACAAAAGGTTGAACAAATT-TTC-ATTATGAATTTCT
66 AAGCTGATCCATCGAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTATTATGAA-TTCT
* *
1354 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTG
130 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTTGAAAAGCTGATCCATCAAGTG
1419 ATGGATT
195 ATGGATT
1426 GAATCTTTGC
Statistics
Matches: 390, Mismatches: 13, Indels: 32
0.90 0.03 0.07
Matches are distributed among these distances:
214 8 0.02
215 2 0.01
216 56 0.14
217 80 0.21
218 3 0.01
219 3 0.01
220 44 0.11
221 130 0.33
222 4 0.01
223 14 0.04
224 21 0.05
225 25 0.06
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (222 bp):
TCTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAA
AAGCTGATCCATCGAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTATTATGAATTCTT
CTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTTGAAAAGCTGATCCATCAAGTGA
TGGATTTGAGCAAAAGGTTGAACAAGC
Found at i:10206 original size:15 final size:15
Alignment explanation
Indices: 10183--10214 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
10173 TGCAATGAAT
10183 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
10198 AATGCATGTATGCAA
1 AATGAATGTATGCAA
10213 AA
1 AA
10215 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:13564 original size:28 final size:27
Alignment explanation
Indices: 13513--13566 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
13503 ATATTAATAA
* *
13513 AATAATATATATAAATACTATGAAAAT
1 AATAATATATATAAAAAATATGAAAAT
*
13540 AATAAGTATATATAAAAAATTTGAAAA
1 AATAA-TATATATAAAAAATATGAAAA
13567 GAAAGAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (27 bp):
AATAATATATATAAAAAATATGAAAAT
Found at i:14317 original size:18 final size:18
Alignment explanation
Indices: 14294--14331 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
14284 GCCCTTTCTT
14294 AATATTGAAAA-ATAAATA
1 AATATT-AAAACATAAATA
*
14312 AATATTAAAACATAATTA
1 AATATTAAAACATAAATA
14330 AA
1 AA
14332 ATAAGTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (18 bp):
AATATTAAAACATAAATA
Found at i:15795 original size:3 final size:3
Alignment explanation
Indices: 15789--15841 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
15779 ATTATTTCTT
* *
15789 TAA TAA TAA TAA T-A TAG T-A TAA TAA TAA TAT TAA -AA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
15833 TAA TAA TAA
1 TAA TAA TAA
15842 ATAAAACAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
2 7 0.17
3 35 0.83
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:15811 original size:19 final size:19
Alignment explanation
Indices: 15789--15842 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
15779 ATTATTTCTT
* *
15789 TAATAATAATAATATAGTA
1 TAATAATAATAATAAAATA
*
15808 TAATAATAATATTAAAATA
1 TAATAATAATAATAAAATA
*
15827 AAATAATAATAATAAA
1 TAATAATAATAATAAA
15843 TAAAACAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
TAATAATAATAATAAAATA
Found at i:15852 original size:22 final size:22
Alignment explanation
Indices: 15789--15847 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
15779 ATTATTTCTT
* **
15789 TAATAATAATAATATAGTATAA
1 TAATAATAATAAAATAAAATAA
*
15811 TAATAATATTAAAATAAAATAA
1 TAATAATAATAAAATAAAATAA
15833 TAATAATAAATAAAA
1 TAATAAT-AATAAAA
15848 CAAATGAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
22 25 0.81
23 6 0.19
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (22 bp):
TAATAATAATAAAATAAAATAA
Found at i:20481 original size:23 final size:23
Alignment explanation
Indices: 20410--20492 Score: 89
Period size: 23 Copynumber: 3.7 Consensus size: 23
20400 GCACTTAACA
* *
20410 GTGCATCGATGTACCCCTTTGAAT
1 GTGCATCGATGCACACC-TTGAAT
* *
20434 GTGCATCGAT--ACACCATGAAG
1 GTGCATCGATGCACACCTTGAAT
* *
20455 GTGCACCGATGCACTCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
20478 GTGCATCGATGCACA
1 GTGCATCGATGCACA
20493 GGGCCATGCA
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
21 13 0.27
22 4 0.08
23 21 0.44
24 10 0.21
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (23 bp):
GTGCATCGATGCACACCTTGAAT
Found at i:20590 original size:2 final size:2
Alignment explanation
Indices: 20583--20607 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20573 TCTTTGCCGC
20583 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
20608 AATTCTCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:22839 original size:12 final size:13
Alignment explanation
Indices: 22806--22838 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
22796 GTGAGTAATT
*
22806 TTTTCAAAATTGA
1 TTTTCAAAATTAA
22819 -TTTCAAAATTAA
1 TTTTCAAAATTAA
22831 TTTTCAAA
1 TTTTCAAA
22839 TCTTAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.45
Consensus pattern (13 bp):
TTTTCAAAATTAA
Found at i:23162 original size:20 final size:20
Alignment explanation
Indices: 23133--23170 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
23123 TTTCAAAGGA
23133 ATGCAACGATGCACCAATCC
1 ATGCAACGATGCACCAATCC
*
23153 ATGCATCGATGCACCAAT
1 ATGCAACGATGCACCAAT
23171 GAATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCAACGATGCACCAATCC
Found at i:23311 original size:65 final size:63
Alignment explanation
Indices: 23181--23333 Score: 186
Period size: 65 Copynumber: 2.4 Consensus size: 63
23171 GAATAAATTG
*
23181 AACATCGAATGCATTGTATGCATCGATGCACATACCATGCATCGATGCACTCAGGTTTCTATGAA
1 AACATCGAATGCATTG-ATGCATCGATGCACATAACATGCATCGATGCACTCAGGTTTCTATG-A
*
23246 AACATCGAATGCATTTGATGCATTGATGCACA-AGACATGCATCGATGCACTCAGGCTATT-T-T
1 AACATCGAATGCA-TTGATGCATCGATGCACATA-ACATGCATCGATGCACTCAGG-T-TTCTAT
23308 GA
62 GA
* *
23310 AACATTGAATGCACTTCATGCATC
1 AACATCGAATGCA-TTGATGCATC
23334 AAAGCACTCT
Statistics
Matches: 78, Mismatches: 6, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
64 22 0.28
65 49 0.63
66 5 0.06
67 2 0.03
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTGATGCATCGATGCACATAACATGCATCGATGCACTCAGGTTTCTATGA
Found at i:26111 original size:30 final size:30
Alignment explanation
Indices: 26052--26112 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
26042 TCTTAAAATA
*
26052 TATTCTTCTCTTCTTCGTCTCTCTCTCTTC
1 TATTCTTCTCTTCTTCGTCTATCTCTCTTC
* *
26082 TATTCTTCTCTTCTTCGTCTATTTTTCTTC
1 TATTCTTCTCTTCTTCGTCTATCTCTCTTC
26112 T
1 T
26113 CTAATCGCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.05, C:0.31, G:0.03, T:0.61
Consensus pattern (30 bp):
TATTCTTCTCTTCTTCGTCTATCTCTCTTC
Found at i:26605 original size:103 final size:103
Alignment explanation
Indices: 26426--26617 Score: 280
Period size: 103 Copynumber: 1.9 Consensus size: 103
26416 AATAAAACCC
* * *
26426 TTTTTAAATATCACCGATATAGAAGTTTTGGTTTCTAATCCCTTTTAATTCAAGTTCGAGGAAGA
1 TTTTTAAATATCACCGATATAGAAGTTGTGGTTTCTAATCCCGTATAATTCAAGTTCGAGGAAGA
26491 TAGGGAACTTTTGTGAATGTGGTTAGTTTCTAATCTCT
66 TAGGGAACTTTTGTGAATGTGGTTAGTTTCTAATCTCT
* * * *
26529 TTTTTAAGTATCACCTATATATGAA-TTGTGGTTTCTAATCCCGTATAATTTGAA-TTTGAGGAA
1 TTTTTAAATATCACCGATATA-GAAGTTGTGGTTTCTAATCCCGTATAA-TTCAAGTTCGAGGAA
*
26592 GATAGGGAACTTTTGTTAATGTGGTT
64 GATAGGGAACTTTTGTGAATGTGGTT
26618 GGACTCTTGC
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
103 72 0.91
104 7 0.09
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (103 bp):
TTTTTAAATATCACCGATATAGAAGTTGTGGTTTCTAATCCCGTATAATTCAAGTTCGAGGAAGA
TAGGGAACTTTTGTGAATGTGGTTAGTTTCTAATCTCT
Found at i:30737 original size:24 final size:23
Alignment explanation
Indices: 30697--30743 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
30687 GGGGTTTTAT
**
30697 TTTTTTATTTTTTAAAAAATAAA
1 TTTTTTATTTTAAAAAAAATAAA
*
30720 TTTTTTATTATTAAAAAAATTAAA
1 TTTTTTATT-TTAAAAAAAATAAA
30744 AATATAATGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTTTTATTTTAAAAAAAATAAA
Found at i:43016 original size:21 final size:22
Alignment explanation
Indices: 42976--43016 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
42966 TATTAAGAAA
*
42976 AGTATCGATACCTCAGACTAGG
1 AGTATCGATACCTCAAACTAGG
*
42998 AGTATCTATA-CTCAAACTA
1 AGTATCGATACCTCAAACTA
43017 TAATATTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.27
Consensus pattern (22 bp):
AGTATCGATACCTCAAACTAGG
Found at i:43100 original size:20 final size:20
Alignment explanation
Indices: 43061--43100 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
43051 AGTAAGTCAG
* *
43061 TAGTATTGATACCGAGAGGT
1 TAGTATCGATACCCAGAGGT
*
43081 TAGTATCGATACCCATAGGT
1 TAGTATCGATACCCAGAGGT
43101 CATTCCATGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (20 bp):
TAGTATCGATACCCAGAGGT
Done.