Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006110.1 Hibiscus syriacus cultivar Beakdansim tig00014483_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: 52737
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:833 original size:16 final size:16
Alignment explanation
Indices: 796--837 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
786 CAGATCAAGA
* *
796 AAACATACATCAATAT
1 AAACATACATCAACAC
812 AAACATACATCAACAC
1 AAACATACATCAACAC
*
828 ATACATACAT
1 AAACATACAT
838 AATACATGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.21
Consensus pattern (16 bp):
AAACATACATCAACAC
Found at i:2079 original size:196 final size:192
Alignment explanation
Indices: 1814--2309 Score: 610
Period size: 191 Copynumber: 2.6 Consensus size: 192
1804 CATCGCGTAT
* *
1814 GAGCAGTGTCATCTTCAGATAATCAGACTTTCTCATCACAAAGGAACTGTATTGTCCTCAAATTA
1 GAGCAGTGTCATCTTCAGAAAATCAGAC-TTCTCATCACAAAGGAACCGTATTGTCCTCAAATTA
* *
1879 TCTCCTGATTGACCCGATTTCCTCAACGCGCGAATGAACAACTTCATTTACCCAAAAACGACCAG
65 TCTCCTGATTGACCCGATTTCCTCAAC-CGCGAAGGAACAACGTCATTTACCC--AAACGACCAG
* *
1944 ATCTCTTCAACACGGATCAACAGTGTCGTCTTCATA-ATCAAATTGACCTAATCTCCTCACCACG
127 ATCTCTTCAACACGGATCAACAGTGTCATCTTCA-ACATCAAATTGACC-AATCTCCTCAACACG
2008 AAG
190 AAG
* *
2011 GAGCAGTGTCATTTTCAGAAAATCAGAC-TCATCATCACGAAA-GAACCGTATTATCCTCAAATT
1 GAGCAGTGTCATCTTCAGAAAATCAGACTTC-TCATCAC-AAAGGAACCGTATTGTCCTCAAATT
* * * * * *
2074 ATCTCCTGATTAACCCGATTTCCTCAA-TGCGAAGGAACAACGTCATTTACTCAAATGACTATAT
64 ATCTCCTGATTGACCCGATTTCCTCAACCGCGAAGGAACAACGTCATTTACCCAAACGACCAGAT
* ** * *
2138 CTCTTCAACACGGATGAGTAGTGTCATCTTCAACATCAAATTGACCGATCTCCTCAACATGAAG
129 CTCTTCAACACGGATCAACAGTGTCATCTTCAACATCAAATTGACCAATCTCCTCAACACGAAG
* * * * *
2202 GATCAATGTCATCTTCAGACAATC-GACTTCCTCATCACAAAGGGACCGTATTGT-CTCCAATTA
1 GAGCAGTGTCATCTTCAGAAAATCAGACTT-CTCATCACAAAGGAACCGTATTGTCCTCAAATTA
* * * *
2265 TCTCTTGATTGACCCGATTTCCTCAA-CTCAAAGGAACAACATCAT
65 TCTCCTGATTGACCCGATTTCCTCAACCGCGAAGGAACAACGTCAT
2310 CTTCAACAAA
Statistics
Matches: 261, Mismatches: 32, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
190 53 0.20
191 54 0.21
192 50 0.19
194 21 0.08
195 2 0.01
196 52 0.20
197 29 0.11
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.28
Consensus pattern (192 bp):
GAGCAGTGTCATCTTCAGAAAATCAGACTTCTCATCACAAAGGAACCGTATTGTCCTCAAATTAT
CTCCTGATTGACCCGATTTCCTCAACCGCGAAGGAACAACGTCATTTACCCAAACGACCAGATCT
CTTCAACACGGATCAACAGTGTCATCTTCAACATCAAATTGACCAATCTCCTCAACACGAAG
Found at i:2594 original size:20 final size:20
Alignment explanation
Indices: 2569--2611 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2559 ACACCAATTC
2569 CACCAACTCCACTAATGTCG
1 CACCAACTCCACTAATGTCG
* *
2589 CACCAACTCCATTAATGTTG
1 CACCAACTCCACTAATGTCG
2609 CAC
1 CAC
2612 ACCACCCATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.37, G:0.09, T:0.23
Consensus pattern (20 bp):
CACCAACTCCACTAATGTCG
Found at i:19580 original size:65 final size:66
Alignment explanation
Indices: 19458--19584 Score: 177
Period size: 65 Copynumber: 1.9 Consensus size: 66
19448 CATTAAAAAG
** * *
19458 CAATTAAGGGTTGAAATACTCAGGCCAATGTAAAACTTTGACCTTACTTCGTTTATATATATTAA
1 CAATTAAGGGTTGAAATACTCAGGAAAATGTAAAACTTTGACCTTACTTCATATATATATATTAA
19523 A
66 A
* *
19524 CAATTAAGGG-TGAAATATTCAGGGAAAATGTAAAAC-TTGACCTTACTTTATATATATATAT
1 CAATTAAGGGTTGAAATACTCA-GGAAAATGTAAAACTTTGACCTTACTTCATATATATATAT
19585 GTGTGTGTGT
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
65 32 0.59
66 22 0.41
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.35
Consensus pattern (66 bp):
CAATTAAGGGTTGAAATACTCAGGAAAATGTAAAACTTTGACCTTACTTCATATATATATATTAA
A
Found at i:24754 original size:31 final size:31
Alignment explanation
Indices: 24718--24780 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
24708 GACCATTATT
* *
24718 TAAATTCA-AATATTTAATTCAAT-TATACTCA
1 TAAATT-ATAATAATTAATTAAATATATA-TCA
24749 TAAATTATAATAATTAATTAAATATATATCA
1 TAAATTATAATAATTAATTAAATATATATCA
24780 T
1 T
24781 CCATTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 1 0.04
31 23 0.82
32 4 0.14
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (31 bp):
TAAATTATAATAATTAATTAAATATATATCA
Found at i:35017 original size:174 final size:174
Alignment explanation
Indices: 34719--35076 Score: 565
Period size: 174 Copynumber: 2.1 Consensus size: 174
34709 CCCATCAGCC
*
34719 CCAGAATAAGAACTTGCTGGGATGACACCGATATCGCTGCTTTCAACACCAGTGGTTCCTTCCAT
1 CCAGAAT-AGAACTTGCTGGGATGACACCGATATCGCTGCTTTCAACACCAGTGGTTCCTCCCAT
* * * * *
34784 CTGGCCCGTCTCATTTCCTCGAAGAGAACAAGTTGATCCATGTGGAGTAGAAGAGGCAAC-GAGA
65 CTGGACCGTCTCATTTCCACGAAAAGAACAAGTTGATCCATGTAGAGCAGAAGAGGCAACAG-GA
*
34848 TCATTGTTGGCATTACAAGAATTAGGGACCAAATCATCACCTTCGG
129 TCATTGTTGGCATTACAAGAATTAGGGACCAAACCATCACCTTCGG
*
34894 TCAGAATAGAACTTGCTGGGATGACACCGATATCGCTGCTTTCAACACCAGTGGTTCCTCCCATC
1 CCAGAATAGAACTTGCTGGGATGACACCGATATCGCTGCTTTCAACACCAGTGGTTCCTCCCATC
* * * *
34959 TGGACTGTCTCATTTCCAGGAAAAGAACATGTTGATCCATGTAGTGCAGAAGAGGCAACAGGATC
66 TGGACCGTCTCATTTCCACGAAAAGAACAAGTTGATCCATGTAGAGCAGAAGAGGCAACAGGATC
**
35024 ATTGTTGGCATTACAAGAATTAGGGACCAAACCATTGCCTTCGG
131 ATTGTTGGCATTACAAGAATTAGGGACCAAACCATCACCTTCGG
35068 CCAGAATAG
1 CCAGAATAG
35077 CAGTCGGTTG
Statistics
Matches: 167, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
174 160 0.96
175 7 0.04
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (174 bp):
CCAGAATAGAACTTGCTGGGATGACACCGATATCGCTGCTTTCAACACCAGTGGTTCCTCCCATC
TGGACCGTCTCATTTCCACGAAAAGAACAAGTTGATCCATGTAGAGCAGAAGAGGCAACAGGATC
ATTGTTGGCATTACAAGAATTAGGGACCAAACCATCACCTTCGG
Found at i:42603 original size:21 final size:21
Alignment explanation
Indices: 42577--42616 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
42567 AAACCATTCA
42577 GGGGGAATCGGTACCCTCTTG
1 GGGGGAATCGGTACCCTCTTG
*
42598 GGGGGAATCGGTTCCCTCT
1 GGGGGAATCGGTACCCTCT
42617 GAGCAATCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.25, G:0.38, T:0.25
Consensus pattern (21 bp):
GGGGGAATCGGTACCCTCTTG
Found at i:45337 original size:22 final size:22
Alignment explanation
Indices: 45258--45338 Score: 87
Period size: 23 Copynumber: 3.7 Consensus size: 22
45248 AGAACCCCAG
45258 GGGGGTATCGATTCCCC-T--A
1 GGGGGTATCGATTCCCCTTCAA
*
45277 GTGGGGAATCGATTCCCCTTCAA
1 G-GGGGTATCGATTCCCCTTCAA
** *
45300 AAGGGTAATCGGTTCCCCTTCAA
1 GGGGGT-ATCGATTCCCCTTCAA
45323 GGGGGTATCGATTCCC
1 GGGGGTATCGATTCCC
45339 TCTGCCCTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
19 1 0.02
20 15 0.31
21 1 0.02
22 12 0.24
23 20 0.41
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.26
Consensus pattern (22 bp):
GGGGGTATCGATTCCCCTTCAA
Done.