Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008339.1 Hibiscus syriacus cultivar Beakdansim tig00111061_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: 1048908
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1028742 original size:4 final size:4
Alignment explanation
Indices: 1028718--1028774 Score: 71
Period size: 4 Copynumber: 14.0 Consensus size: 4
1028708 TTTTTAATTA
* *
1028718 ATTT ATTA ATTT ATCT ATTT ATTT ATTT ATTT ATTTT CATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT A-TTT -ATTT ATTT ATTT
1028768 A-TT ATTT
1 ATTT ATTT
1028775 GTTTCAGGTC
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
3 3 0.07
4 36 0.78
5 6 0.13
6 1 0.02
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (4 bp):
ATTT
Found at i:1030207 original size:22 final size:22
Alignment explanation
Indices: 1030161--1030211 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
1030151 TTCTTGCAAC
*
1030161 TTTTATTTTTATTTTTCATTTT
1 TTTTATTTTTATTTTTCATTCT
1030183 TTTTAATTTGTTA-TTTT-ATTC-
1 TTTT-ATTT-TTATTTTTCATTCT
1030204 TTTTATTT
1 TTTTATTT
1030212 ACTCTTGATC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 4 0.15
21 4 0.15
22 7 0.27
23 8 0.31
24 3 0.12
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (22 bp):
TTTTATTTTTATTTTTCATTCT
Found at i:1035367 original size:18 final size:20
Alignment explanation
Indices: 1035346--1035383 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1035336 AATATTAAAA
1035346 ATTATA-AAT-TAATTTTTT
1 ATTATATAATATAATTTTTT
*
1035364 ATTATATAATATTATTTTTT
1 ATTATATAATATAATTTTTT
1035384 TGAGTTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 3 0.18
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTATATAATATAATTTTTT
Found at i:1037037 original size:19 final size:18
Alignment explanation
Indices: 1036995--1037045 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
1036985 ACAATATATT
1036995 TAAAAACAATAAAATAAA
1 TAAAAACAATAAAATAAA
* *
1037013 TGAAAACATATAAAATAAC
1 TAAAAACA-ATAAAATAAA
1037032 TAAAAA-AATAAAAT
1 TAAAAACAATAAAAT
1037046 TAAAAATCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 7 0.24
18 8 0.28
19 14 0.48
ACGTcount: A:0.73, C:0.06, G:0.02, T:0.20
Consensus pattern (18 bp):
TAAAAACAATAAAATAAA
Found at i:1037874 original size:28 final size:28
Alignment explanation
Indices: 1037820--1037882 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
1037810 TAGTTTGGAT
*
1037820 TTTCTC-TGTTTTTTTTTTCTATATCTC
1 TTTCTCGTCTTTTTTTTTTCTATATCTC
* *
1037847 TTTCTCGTCTTTTTTTTTTCTGTCTCTC
1 TTTCTCGTCTTTTTTTTTTCTATATCTC
*
1037875 TGTCTCGT
1 TTTCTCGT
1037883 TGTATATCTC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 6 0.19
28 25 0.81
ACGTcount: A:0.03, C:0.22, G:0.08, T:0.67
Consensus pattern (28 bp):
TTTCTCGTCTTTTTTTTTTCTATATCTC
Found at i:1038356 original size:3 final size:3
Alignment explanation
Indices: 1038348--1038457 Score: 136
Period size: 3 Copynumber: 37.7 Consensus size: 3
1038338 TTAATATATT
* *
1038348 TAA TAA TAA TAG TAA AAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
1038395 AAA TAA T-A TAA T-A TAT TAA TAA TGA TAA TAA TAT TAG TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1038441 TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
1038458 GGATAAAAAT
Statistics
Matches: 91, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
2 6 0.07
3 85 0.93
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1039067 original size:221 final size:224
Alignment explanation
Indices: 1038740--1039481 Score: 1092
Period size: 221 Copynumber: 3.3 Consensus size: 224
1038730 AGATAATATC
* * *
1038740 AAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTT
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
*
1038804 TCATTCATGAACTTTCTCTGGCAATGTTGATCCATC-AATGATGAATTTAAACAAAAAGTTGAAC
66 TCATT-ATGAACTTTCTCTGGAAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAAC
1038868 AAGTTTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
130 AAGTTTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
1038933 TGGTAATGTTGATCCATCAAATGATGAATT
195 TGGTAATGTTGATCCATCAAATGATGAATT
*
1038963 AAACAAAAAGTTGAACAAGTTC-T-TCATTATG-ACCTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* *
1039025 TCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAAC-AAAAGTTG-ACA
66 TCATTATGAACTTTCTCTGGAAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACA
*
1039088 AGTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCT
131 AGTTTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCT
1039153 GGTAATGTTGATCCATCAAATGATGAATTT
196 GGTAATGTTGATCCATCAAATGATGAA-TT
*
1039183 AAACAAAAAGTTGAACAAG-TCTTCTCATT-TGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * * * * *** *
1039246 TCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACA
66 TCATTATGAACTTTCTCTGGAAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACA
* * *
1039311 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG-ACTTTCTC
131 AGTT-TTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
* * * * *
1039375 TGGGAAAGATGATCCACCAAATGATGGATT
195 TGGTAATGTTGATCCATCAAATGATGAATT
*** * *
1039405 CAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATGAGTTCTT
1 -AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTT
1039469 CTCATTATGAACT
65 CTCATTATGAACT
1039482 CTACCTTGCA
Statistics
Matches: 472, Mismatches: 35, Indels: 23
0.89 0.07 0.04
Matches are distributed among these distances:
219 96 0.20
220 60 0.13
221 126 0.27
222 17 0.04
223 54 0.11
224 108 0.23
225 11 0.02
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (224 bp):
AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
TCATTATGAACTTTCTCTGGAAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACA
AGTTTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCT
GGTAATGTTGATCCATCAAATGATGAATT
Found at i:1039276 original size:111 final size:112
Alignment explanation
Indices: 1038740--1039481 Score: 1065
Period size: 111 Copynumber: 6.7 Consensus size: 112
1038730 AGATAATATC
* *
1038740 AAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTT
1 AAACAAAAAGTTGAACAAG-TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
*
1038804 TCATTCATGAACTTTCTCTGGCAATGTTGATCCATC-AATGATGAATTT
65 TCATT-ATGAACTTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
* *
1038852 AAACAAAAAGTTGAACAAGTTTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AAACAAAAAGTTGAACAAGTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
*
1038917 CATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAA-TT
66 CATTATGAACTTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
*
1038963 AAACAAAAAGTTGAACAAG--TTCTTCATTATG-ACCTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTCTTC-TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
*
1039025 TCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
65 TCATTATGAACTTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
*
1039073 AAAC-AAAAGTTG-ACAAGTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AAACAAAAAGTTGAACAAGTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
*
1039136 CATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
66 CATTATGAACTTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
*
1039183 AAACAAAAAGTTGAACAAGTCTTCTCATT-TGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCT
1 AAACAAAAAGTTGAACAAGTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * * * *
1039247 CATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTC
66 CATTATGAACTTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
*** * *
1039294 AGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAAC-AAGTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * * * * *
1039359 TCATTATG-ACTTTCTCTGGGAAAGATGATCCACCAAATGATGGATTC
65 TCATTATGAACTTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
*** * *
1039406 AGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAAC-AAGTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1039470 TCATTATGAACT
65 TCATTATGAACT
1039482 CTACCTTGCA
Statistics
Matches: 596, Mismatches: 22, Indels: 24
0.93 0.03 0.04
Matches are distributed among these distances:
108 5 0.01
109 95 0.16
110 100 0.17
111 172 0.29
112 170 0.29
113 54 0.09
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (112 bp):
AAACAAAAAGTTGAACAAGTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
CATTATGAACTTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
Found at i:1040496 original size:82 final size:81
Alignment explanation
Indices: 1040230--1040705 Score: 661
Period size: 82 Copynumber: 5.8 Consensus size: 81
1040220 GTTCTGTAAT
* * *
1040230 TTCTACCAAACCAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATATTCATTT
1 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG-ACACATTCA-TT
*
1040295 TCCCACTTCAATGATTGA
64 TCCCACTTCAATGATTGG
* * *
1040313 TTATGTCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATC
1 TTCTG-CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGACACATTCAT-
* *
1040377 TTCCAAATTCAATGATTGG
63 TTCCCACTTCAATGATTGG
* *
1040396 TTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGACACATTCTTCTT
1 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGACACATTCAT-TT
* *
1040461 CCAAATTCAATGATTGG
65 CCCACTTCAATGATTGG
*
1040478 TTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA-ACTATTCATTT
1 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGACAC-ATTCATTT
1040542 CCCACTTCAATGATTGG
65 CCCACTTCAATGATTGG
* *
1040559 TTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATATTCATTT
1 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG-ACACATTCATTT
*
1040624 CCCACTTCAATGATTGA
65 CCCACTTCAATGATTGG
* * *
1040641 TTATGTCC-AACCAGATCAGATAACTCAAATAACACTTCCAGAAGATGCTATGAACATATTCATT
1 TTCTG-CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG-ACACATTCATT
1040705 T
64 T
1040706 GTTCTATTTA
Statistics
Matches: 364, Mismatches: 21, Indels: 17
0.91 0.05 0.04
Matches are distributed among these distances:
81 71 0.20
82 174 0.48
83 115 0.32
84 4 0.01
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (81 bp):
TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGACACATTCATTTC
CCACTTCAATGATTGG
Found at i:1040597 original size:163 final size:163
Alignment explanation
Indices: 1040230--1040705 Score: 735
Period size: 163 Copynumber: 2.9 Consensus size: 163
1040220 GTTCTGTAAT
* * *
1040230 TTCTACCAAACCAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATATTCATTT
1 TTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATATTC-TTT
1040295 TCCCACTTCAATGATTGATTATGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
65 TCCCACTTCAATGATTGATTATGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
1040360 CTATTGGCAA--ATTCATCTTCCAAATTCAATGATTGG
130 CTA-T-G-AACTATTCAT-TTCCAAATTCAATGATTGG
*
1040396 TTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG-ACACATTCTTCT
1 TTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATATTCTT-T
* * * * *
1040460 TCCAAATTCAATGATTGGTTCTG-CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
65 TCCCACTTCAATGATTGATTATGTCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
* *
1040524 GCTATGAACTATTCATTTCCCACTTCAATGATTGG
129 GCTATGAACTATTCATTTCCAAATTCAATGATTGG
*
1040559 TTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATATTCATTT
1 TTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATATTCTTTT
*
1040624 CCCACTTCAATGATTGATTATGTCCAACCAGATCAGATAACTCAAATAACACTTCCAGAAGATGC
66 CCCACTTCAATGATTGATTATGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC
1040689 TATGAACATATTCATTT
131 TATGAAC-TATTCATTT
1040706 GTTCTATTTA
Statistics
Matches: 284, Mismatches: 19, Indels: 16
0.89 0.06 0.05
Matches are distributed among these distances:
162 2 0.01
163 135 0.48
164 30 0.11
165 68 0.24
166 49 0.17
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (163 bp):
TTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATATTCTTTT
CCCACTTCAATGATTGATTATGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC
TATGAACTATTCATTTCCAAATTCAATGATTGG
Found at i:1041850 original size:26 final size:26
Alignment explanation
Indices: 1041820--1041888 Score: 68
Period size: 27 Copynumber: 2.6 Consensus size: 26
1041810 ACCCCCTTTC
1041820 TTTTTCTTCTCTTTTTTTCATTTCTA
1 TTTTTCTTCTCTTTTTTTCATTTCTA
* * *
1041846 TTTTT-TTCTTTTCTTTTTTCTTTTCTT
1 TTTTTCTTC-TCT-TTTTTTCATTTCTA
*
1041873 TTCTTTCTTTTCTTTT
1 TT-TTTCTTCTCTTTT
1041889 CTTTTTCCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
25 3 0.09
26 7 0.21
27 17 0.50
28 5 0.15
29 2 0.06
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (26 bp):
TTTTTCTTCTCTTTTTTTCATTTCTA
Found at i:1041865 original size:22 final size:21
Alignment explanation
Indices: 1041815--1041893 Score: 73
Period size: 19 Copynumber: 4.0 Consensus size: 21
1041805 CCTTGACCCC
*
1041815 CTTTC-TTTTTCTTCTCTTTT
1 CTTTCTTTTTTCTTTTCTTTT
*
1041835 -TTTC--ATTTCTATTT-TTTT
1 CTTTCTTTTTTCT-TTTCTTTT
1041853 CTTTTCTTTTTTCTTTTCTTTT
1 C-TTTCTTTTTTCTTTTCTTTT
1041875 CTTTC--TTTTCTTTTCTTTT
1 CTTTCTTTTTTCTTTTCTTTT
1041894 TCCTTCAAGC
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
18 9 0.18
19 20 0.40
20 4 0.08
21 7 0.14
22 10 0.20
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (21 bp):
CTTTCTTTTTTCTTTTCTTTT
Found at i:1041892 original size:14 final size:13
Alignment explanation
Indices: 1041820--1041888 Score: 86
Period size: 14 Copynumber: 5.2 Consensus size: 13
1041810 ACCCCCTTTC
*
1041820 TTTTTCTTCTCTT
1 TTTTTCTTTTCTT
*
1041833 TTTTTCATTTCTATT
1 TTTTTC-TTT-TCTT
1041848 TTTTTCTTTTC-T
1 TTTTTCTTTTCTT
1041860 TTTTTCTTTTCTT
1 TTTTTCTTTTCTT
1041873 TTCTTTCTTTTCTT
1 TT-TTTCTTTTCTT
1041887 TT
1 TT
1041889 CTTTTTCCTT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
12 12 0.24
13 10 0.20
14 18 0.37
15 9 0.18
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTCTTTTCTT
Done.