Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001734.1 Hibiscus syriacus cultivar Beakdansim tig00003502_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: 40285
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3922 original size:23 final size:23
Alignment explanation
Indices: 3896--3941 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
3886 ATACTATCTA
3896 ATTTTTTTAAAGCATTTTGTTCT
1 ATTTTTTTAAAGCATTTTGTTCT
*
3919 ATTTTTTTAAAGTATTTTGTTCT
1 ATTTTTTTAAAGCATTTTGTTCT
3942 CCCAAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.07, G:0.09, T:0.63
Consensus pattern (23 bp):
ATTTTTTTAAAGCATTTTGTTCT
Found at i:10124 original size:21 final size:21
Alignment explanation
Indices: 10095--10138 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
10085 AATATGTAAA
10095 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
*
10116 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
10137 TC
1 TC
10139 ACAACGCGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.25, G:0.16, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:10147 original size:21 final size:21
Alignment explanation
Indices: 10102--10152 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
10092 AAATCGCATT
* ***
10102 GCGATTTTCCAAATTCGCGTT
1 GCGATTTTCCAAATTCACAAC
10123 GCGATTTTCCAAATTCACAAC
1 GCGATTTTCCAAATTCACAAC
10144 GCGAATTTT
1 GCG-ATTTT
10153 TAAATCGCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (21 bp):
GCGATTTTCCAAATTCACAAC
Found at i:10338 original size:22 final size:22
Alignment explanation
Indices: 10311--10355 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
10301 AACATCCGTC
*
10311 CCCCATCTCCGACGAAATTTGT
1 CCCCATCTCCGACGAAATCTGT
*
10333 CCCCATTTCCGACGAAATCTGT
1 CCCCATCTCCGACGAAATCTGT
10355 C
1 C
10356 TATCTCCATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.22, C:0.38, G:0.13, T:0.27
Consensus pattern (22 bp):
CCCCATCTCCGACGAAATCTGT
Found at i:11860 original size:20 final size:20
Alignment explanation
Indices: 11837--11898 Score: 106
Period size: 20 Copynumber: 3.1 Consensus size: 20
11827 AATAAGCGTT
11837 GCGATAGTCAAATTCGCAAC
1 GCGATAGTCAAATTCGCAAC
* *
11857 GCGAAAGTCAAATTCGCTAC
1 GCGATAGTCAAATTCGCAAC
11877 GCGATAGTCAAATTCGCAAC
1 GCGATAGTCAAATTCGCAAC
11897 GC
1 GC
11899 TTATTTCGTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.19
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCAAC
Found at i:12240 original size:18 final size:18
Alignment explanation
Indices: 12217--12252 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
12207 AAGCCGGTTG
*
12217 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
12235 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
12253 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:14544 original size:24 final size:24
Alignment explanation
Indices: 14510--14563 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
14500 CCATCACATC
14510 ATCAAAATCTGAATATTGACCAAG
1 ATCAAAATCTGAATATTGACCAAG
* * *
14534 ATCAAAGTCTGAGTATTGACCAAT
1 ATCAAAATCTGAATATTGACCAAG
14558 ATCAAA
1 ATCAAA
14564 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.26
Consensus pattern (24 bp):
ATCAAAATCTGAATATTGACCAAG
Found at i:15481 original size:19 final size:19
Alignment explanation
Indices: 15457--15523 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 19
15447 CTAAAACCTG
15457 TTGCGAAATTAAATTCGCA
1 TTGCGAAATTAAATTCGCA
*
15476 TTGCGAATTTAAAATT--CA
1 TTGCGAAATT-AAATTCGCA
* *
15494 GTTGCGAATTTAACTTTCGCA
1 -TTGCGAAATTAA-ATTCGCA
15515 TTGC-AAATT
1 TTGCGAAATT
15524 TGGAAAATAG
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
18 4 0.10
19 25 0.62
20 9 0.22
21 2 0.05
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (19 bp):
TTGCGAAATTAAATTCGCA
Found at i:15597 original size:20 final size:20
Alignment explanation
Indices: 15574--15647 Score: 112
Period size: 20 Copynumber: 3.7 Consensus size: 20
15564 TTACATATTC
15574 GAGTTGCGAAATTGGAAACT
1 GAGTTGCGAAATTGGAAACT
*
15594 GAGTTGTGAAATTGGAAACT
1 GAGTTGCGAAATTGGAAACT
**
15614 GAGTTGCGAAATTGGAATTT
1 GAGTTGCGAAATTGGAAACT
*
15634 GCGTTGCGAAATTG
1 GAGTTGCGAAATTG
15648 AGATCGTGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.30
Consensus pattern (20 bp):
GAGTTGCGAAATTGGAAACT
Found at i:15896 original size:21 final size:21
Alignment explanation
Indices: 15859--15898 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
15849 CTGCAAAGGA
*
15859 ATTTGGATATTGTGATTTATG
1 ATTTGGATATAGTGATTTATG
15880 ATTTGGATATAAG-GATTTA
1 ATTTGGATAT-AGTGATTTA
15899 AGGAATTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (21 bp):
ATTTGGATATAGTGATTTATG
Found at i:18608 original size:12 final size:12
Alignment explanation
Indices: 18587--18642 Score: 76
Period size: 12 Copynumber: 4.7 Consensus size: 12
18577 TGTTTCATCC
*
18587 GATTTATGTTCT
1 GATTTCTGTTCT
18599 GATTTCTGTTCT
1 GATTTCTGTTCT
*
18611 GAATTCTGTTCT
1 GATTTCTGTTCT
* *
18623 GAATTCTGTTAT
1 GATTTCTGTTCT
18635 GATTTCTG
1 GATTTCTG
18643 ATATCTCTGT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.16, C:0.12, G:0.18, T:0.54
Consensus pattern (12 bp):
GATTTCTGTTCT
Found at i:18821 original size:31 final size:32
Alignment explanation
Indices: 18786--18858 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
18776 TAAGATGACC
*
18786 CTTGGGTAGGCTCTACG-G-CCCTGAGATTTTT
1 CTTGGGTAGGC-CTACGTGACCCTGAGAATTTT
* *
18817 CTTGGGTAGGCCTCCGTGACCCTGATAATTTT
1 CTTGGGTAGGCCTACGTGACCCTGAGAATTTT
18849 CTTGGGTAGG
1 CTTGGGTAGG
18859 GTCGCAGGCC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.11
31 12 0.32
32 21 0.57
ACGTcount: A:0.14, C:0.22, G:0.30, T:0.34
Consensus pattern (32 bp):
CTTGGGTAGGCCTACGTGACCCTGAGAATTTT
Found at i:22844 original size:20 final size:18
Alignment explanation
Indices: 22807--22849 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
22797 ATTTAATTCT
22807 ATAAAATTTATTGTTTAAA
1 ATAAAATTTATTGTTT-AA
22826 ATAAATATTTATT-TATTAA
1 ATAAA-ATTTATTGT-TTAA
22845 ATAAA
1 ATAAA
22850 CTCGATTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
ATAAAATTTATTGTTTAA
Found at i:25456 original size:201 final size:197
Alignment explanation
Indices: 25073--25474 Score: 632
Period size: 201 Copynumber: 2.0 Consensus size: 197
25063 AAAAAATAAA
25073 TAATGTAAATAAATATAATAATAAAGAAGTAAAAAAATAGGGTAAAATACAAAATGTGTACATAT
1 TAATGTAAATAAATATAATAATAAAGAAGTAAAAAAATAGGGTAAAATACAAAATGTGTACA-AT
*
25138 ATACATATATATATATAATATAACACATAAATGAAATAATACTATACTAATAATAAATGTATACG
65 ATACATATATATATATAATATAACACATAAATGAAATAATACTATACTAATAATAAATATATACG
* * *
25203 AATGTATAAAAAACTAATAGTATAAAATATATAAATATTATAATGTAATATAAAAAGGTAATTAA
130 AATGTAAAAAAAACTAATAATATAAAATATATAAATATTATAATGTAATATAAAAAGATAATTAA
25268 AAC
195 AAC
*
25271 TAATGTAAATAAATATAATAATAAAGAAGTAAACAAATAGGGT-AAATACAAAATGTGTAC-ATA
1 TAATGTAAATAAATATAATAATAAAGAAGTAAAAAAATAGGGTAAAATACAAAATGTGTACAATA
* *
25334 TACATATATATATAT-ATATAACATATAAGTGAAATAATACTATACTAATAAT-AATATATACGA
66 TACATATATATATATAATATAACACATAAATGAAATAATACTATACTAATAATAAATATATACGA
25397 ATGTGTAAAAAAAAACTAATAATAATATAAAATATATATAAATATTATAATGTAATATAAAAAGA
131 A--TGT-AAAAAAAAC---TAATAATAT-AAA-ATATATAAATATTATAATGTAATATAAAAAGA
25462 TAATTAAAAC
188 TAATTAAAAC
25472 TAA
1 TAA
25475 AATCCCGAGA
Statistics
Matches: 189, Mismatches: 7, Indels: 13
0.90 0.03 0.06
Matches are distributed among these distances:
193 11 0.06
194 35 0.19
195 21 0.11
196 8 0.04
197 17 0.09
198 42 0.22
199 8 0.04
200 3 0.02
201 44 0.23
ACGTcount: A:0.57, C:0.05, G:0.08, T:0.30
Consensus pattern (197 bp):
TAATGTAAATAAATATAATAATAAAGAAGTAAAAAAATAGGGTAAAATACAAAATGTGTACAATA
TACATATATATATATAATATAACACATAAATGAAATAATACTATACTAATAATAAATATATACGA
ATGTAAAAAAAACTAATAATATAAAATATATAAATATTATAATGTAATATAAAAAGATAATTAAA
AC
Found at i:26924 original size:105 final size:105
Alignment explanation
Indices: 26742--27431 Score: 1344
Period size: 105 Copynumber: 6.6 Consensus size: 105
26732 CATGAGGTTG
*
26742 AGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT
1 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT
26807 GAGAAATGTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGA
66 GAGAAATGTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGA
26847 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT
1 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT
26912 GAGAAATGTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGA
66 GAGAAATGTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGA
*
26952 AGTTGAACTTGCGTTGTATGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT
1 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT
27017 GAGAAATGTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGA
66 GAGAAATGTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGA
27057 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT
1 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT
27122 GAGAAATGTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGA
66 GAGAAATGTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGA
27162 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT
1 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT
27227 GAGAAATGTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGA
66 GAGAAATGTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGA
27267 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT
1 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT
* *
27332 GGGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGA
66 GAGAAATGTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGA
27372 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
27432 GGTAAAACCT
Statistics
Matches: 580, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 580 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.34
Consensus pattern (105 bp):
AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT
GAGAAATGTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGA
Found at i:28228 original size:12 final size:12
Alignment explanation
Indices: 28211--28251 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
28201 ACCCTAAACG
28211 TTTTTCTCTTTT
1 TTTTTCTCTTTT
*
28223 TTTTTCTTTTTT
1 TTTTTCTCTTTT
28235 TTTTTCTCTTTT
1 TTTTTCTCTTTT
28247 TTTTT
1 TTTTT
28252 TCAACTTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (12 bp):
TTTTTCTCTTTT
Found at i:28238 original size:14 final size:14
Alignment explanation
Indices: 28219--28252 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
28209 CGTTTTTCTC
28219 TTTTTTTT-TCTTT
1 TTTTTTTTCTCTTT
28232 TTTTTTTTCTCTTT
1 TTTTTTTTCTCTTT
28246 TTTTTTT
1 TTTTTTT
28253 CAACTTAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (14 bp):
TTTTTTTTCTCTTT
Found at i:38833 original size:36 final size:37
Alignment explanation
Indices: 38793--38862 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 37
38783 ATGTACATGT
*
38793 AAAATA-ATAATAAAAAAATAAT-GAAAATAAAATAAG
1 AAAATATAT-ATAAAAAAATAATAGAAAAAAAAATAAG
* *
38829 AAAATATATATATAACAATAATAGAAAAAAAAAT
1 AAAATATATATAAAAAAATAATAGAAAAAAAAAT
38863 TGTAACATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 17 0.59
37 12 0.41
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.21
Consensus pattern (37 bp):
AAAATATATATAAAAAAATAATAGAAAAAAAAATAAG
Found at i:39207 original size:180 final size:186
Alignment explanation
Indices: 38984--39359 Score: 504
Period size: 185 Copynumber: 2.0 Consensus size: 186
38974 AAAAAATAAA
* *
38984 TAATGTAAAATATATAATAAAGAAGTAAAAAATAGGGTAAATACAAAATGTGTAC-ATAT-C-AT
1 TAATGTAAAAAATATAATAAAAAAGTAAAAAATAGGGTAAATACAAAATGTGTACAATATACAAT
*
39046 ATATATATAATA-ACACATAAA-TGAAATAATACTATACTAATAATAAATGTATACGAA-TGT-A
66 ATATATATAATATA-ACATAAAGTG-AATAATACTATACTAATAAT-AATATATACGAAGTGTAA
* * *
39107 TAAAAA-AATAATAGT-AATATATAATATTATAATGT-ATAT-AAAAGGTAATTAAAAC
128 AAAAAACAATAATAATAAATATATAATATTATAATGTAATATAAAAAGATAATTAAAAC
*
39162 TAATGTAAATAAATATAATAATAAAAGTAACAAATAGGGTAAATACAAAATGTGTACATATATAC
1 TAATGTAAA-AAATATAATAA-AAAAGTAAAAAATAGGGTAAATACAAAATGTGTACA-ATATAC
39227 ATATATATATATAATATAACATAAAGTGAATAATACTATACTAATAATAATATATACGAATGTGT
63 A-ATATATATATAATATAACATAAAGTGAATAATACTATACTAATAATAATATATACGAA-GTGT
39292 AAAAAAAAAACTAATAATAATAAAATATATAATATTATAATGTAATATAAAAAGATAATTAAAAC
126 --AAAAAAAAC-AATAATAAT-AAATATATAATATTATAATGTAATATAAAAAGATAATTAAAAC
39357 TAA
1 TAA
39360 AATCCCGAGA
Statistics
Matches: 171, Mismatches: 7, Indels: 23
0.85 0.03 0.11
Matches are distributed among these distances:
178 9 0.05
179 10 0.06
180 33 0.19
182 4 0.02
183 1 0.01
184 11 0.06
185 41 0.24
186 6 0.04
189 6 0.04
191 8 0.05
193 20 0.12
194 4 0.02
195 18 0.11
ACGTcount: A:0.57, C:0.05, G:0.08, T:0.30
Consensus pattern (186 bp):
TAATGTAAAAAATATAATAAAAAAGTAAAAAATAGGGTAAATACAAAATGTGTACAATATACAAT
ATATATATAATATAACATAAAGTGAATAATACTATACTAATAATAATATATACGAAGTGTAAAAA
AAACAATAATAATAAATATATAATATTATAATGTAATATAAAAAGATAATTAAAAC
Done.