Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006875.1 Hibiscus syriacus cultivar Beakdansim tig00017512_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: 67661
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.31
Found at i:845 original size:31 final size:31
Alignment explanation
Indices: 810--877 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
800 GGGTGACCAC
*
810 ATCTTAACTAAATAAAAACGAAAGTGATCA-T
1 ATCTTAACTAAATAAAAACGAAAGAGAT-ATT
*
841 ATCTTAATTAAATAAAAACGAAAGAGATATT
1 ATCTTAACTAAATAAAAACGAAAGAGATATT
872 ATCTTA
1 ATCTTA
878 TGTTCTTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 1 0.03
31 33 0.97
ACGTcount: A:0.51, C:0.10, G:0.09, T:0.29
Consensus pattern (31 bp):
ATCTTAACTAAATAAAAACGAAAGAGATATT
Found at i:12277 original size:15 final size:15
Alignment explanation
Indices: 12257--12286 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12247 TGAAAATACA
*
12257 AAAATTTAAATAAAT
1 AAAATTAAAATAAAT
12272 AAAATTAAAATAAAT
1 AAAATTAAAATAAAT
12287 TAATTTGTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAATTAAAATAAAT
Found at i:12826 original size:19 final size:19
Alignment explanation
Indices: 12800--12843 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
12790 TATATTTTTT
*
12800 AAATTTTTTAAAAATAAAA
1 AAATTTTTTAAAAAGAAAA
* *
12819 ATATTTTTTTAAAAGAAAA
1 AAATTTTTTAAAAAGAAAA
12838 AAATTT
1 AAATTT
12844 AAAAAACTCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
AAATTTTTTAAAAAGAAAA
Found at i:12838 original size:20 final size:19
Alignment explanation
Indices: 12803--12843 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
12793 ATTTTTTAAA
12803 TTTTTTAAAAATAAAAATAT
1 TTTTTTAAAAATAAAAA-AT
12823 TTTTTTAAAAGA-AAAAAAT
1 TTTTTTAAAA-ATAAAAAAT
12842 TT
1 TT
12844 AAAAAACTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.20
20 15 0.75
21 1 0.05
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
TTTTTTAAAAATAAAAAAT
Found at i:13764 original size:31 final size:31
Alignment explanation
Indices: 13729--13840 Score: 197
Period size: 31 Copynumber: 3.6 Consensus size: 31
13719 TCCATAGATT
*
13729 CCGAAGAACCTAGGTAAACAATCCATATGTC
1 CCGAAGAACATAGGTAAACAATCCATATGTC
13760 CCGAAGAACATAGGTAAACAATCCATATGTC
1 CCGAAGAACATAGGTAAACAATCCATATGTC
* *
13791 CCGAAGAACATAGGTAAACATTCCATATGCC
1 CCGAAGAACATAGGTAAACAATCCATATGTC
13822 CCGAAGAACATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
13841 CTTCAACCCT
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 78 1.00
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.18
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAATCCATATGTC
Found at i:14156 original size:34 final size:32
Alignment explanation
Indices: 14103--14172 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
14093 CTTACAAAAC
*
14103 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
14135 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
14169 TCCC
1 TCCC
14173 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:14598 original size:30 final size:31
Alignment explanation
Indices: 14547--14637 Score: 150
Period size: 31 Copynumber: 3.0 Consensus size: 31
14537 AAATTTTGAA
* *
14547 TAAACTCAATT-AAGTCTAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
14576 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
14607 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
14638 CCTTAAATTG
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
29 10 0.17
30 10 0.17
31 38 0.66
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:16606 original size:98 final size:98
Alignment explanation
Indices: 16437--16616 Score: 333
Period size: 98 Copynumber: 1.8 Consensus size: 98
16427 CTGCACCTAT
* *
16437 TGTTAGCAAAAACTTCTTTAGGATCTAGATTGTATTTTGAGAAGTAGTTTAGGTACTAAAAAGTG
1 TGTTAGCAAAAACTTCTTTAGGATCTAGATTGTATTTTGAGAAGTAATTTAGGCACTAAAAAGTG
16502 TATTAAGCCTTTATTTTGAGATCTAGATTATAG
66 TATTAAGCCTTTATTTTGAGATCTAGATTATAG
*
16535 TGTTAGCAAAAACTTCTTTAGGATCTAGATTGTATTTTGAGATGTAATTTAGGCACTAAAAAGTG
1 TGTTAGCAAAAACTTCTTTAGGATCTAGATTGTATTTTGAGAAGTAATTTAGGCACTAAAAAGTG
16600 TATTAAGCCTTTATTTT
66 TATTAAGCCTTTATTTT
16617 AATATTTATG
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 79 1.00
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (98 bp):
TGTTAGCAAAAACTTCTTTAGGATCTAGATTGTATTTTGAGAAGTAATTTAGGCACTAAAAAGTG
TATTAAGCCTTTATTTTGAGATCTAGATTATAG
Found at i:23648 original size:21 final size:21
Alignment explanation
Indices: 23624--23666 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
23614 TGATATGAAT
*
23624 TGTAACGAACATGAATGGTAA
1 TGTAACGAACATGAATGATAA
* *
23645 TGTAATGAAGATGAATGATAA
1 TGTAACGAACATGAATGATAA
23666 T
1 T
23667 ACAGCGTGGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.05, G:0.23, T:0.28
Consensus pattern (21 bp):
TGTAACGAACATGAATGATAA
Found at i:24045 original size:21 final size:21
Alignment explanation
Indices: 24019--24059 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
24009 AAATTAAAAC
*
24019 AAATATAAATAACAATACAAT
1 AAATATAAATAACAAAACAAT
* *
24040 AAATATTAATGACAAAACAA
1 AAATATAAATAACAAAACAA
24060 CAAAATCAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.66, C:0.10, G:0.02, T:0.22
Consensus pattern (21 bp):
AAATATAAATAACAAAACAAT
Found at i:25715 original size:31 final size:31
Alignment explanation
Indices: 25690--25894 Score: 356
Period size: 31 Copynumber: 6.6 Consensus size: 31
25680 TCCATAAATT
* *
25690 CCGAAGAACCTAGGTAATCAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
*
25721 CCGAAGAACATAGGTAAACAATCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
*
25752 CCAAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
*
25783 CCGAAGGACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
*
25814 TCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
25845 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
25876 CCGAAGAACATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
25895 CCTCGACCCT
Statistics
Matches: 164, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 164 1.00
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGTCCATATGTC
Found at i:33705 original size:21 final size:21
Alignment explanation
Indices: 33681--33741 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
33671 AACTTTGAAA
33681 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
33702 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
33716 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
33737 AAATG
1 AAATG
33742 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:33719 original size:35 final size:35
Alignment explanation
Indices: 33680--33789 Score: 168
Period size: 35 Copynumber: 3.1 Consensus size: 35
33670 CAACTTTGAA
33680 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
33715 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
* * *
33750 AAAAATAGTTTCTCAAAGTTTGGTAGATATTT-TTTG
1 -AAAATGGTTT-TCAAAGTTTGGTAAATGTTTCTTTG
33786 AAAA
1 AAAA
33790 ATGATAATGG
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
35 39 0.56
36 13 0.19
37 18 0.26
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (35 bp):
AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
Found at i:38437 original size:23 final size:23
Alignment explanation
Indices: 38370--38456 Score: 88
Period size: 23 Copynumber: 3.7 Consensus size: 23
38360 TCGTATAAAT
*
38370 TTGCACCGTAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
38393 TTTTGTC-CCGAAG-GACCGCGTAGAA
1 --TTG-CACCGAAGTG-CCACGTAGAA
*
38418 ATGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
38441 TTGCACCGTAGTGCCA
1 TTGCACCGAAGTGCCA
38457 TATAATATGT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
22 1 0.02
23 31 0.60
24 2 0.04
25 17 0.33
26 1 0.02
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:44908 original size:2 final size:2
Alignment explanation
Indices: 44901--44926 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
44891 TTACCCATCT
44901 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
44927 CAATTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55248 original size:20 final size:20
Alignment explanation
Indices: 55223--55263 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
55213 TGGAGGAGCT
55223 CCCAACACTAACCAAATCCA
1 CCCAACACTAACCAAATCCA
55243 CCCAACACTAACCAAATCCA
1 CCCAACACTAACCAAATCCA
55263 C
1 C
55264 ATGAGTGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.46, G:0.00, T:0.10
Consensus pattern (20 bp):
CCCAACACTAACCAAATCCA
Found at i:55707 original size:23 final size:23
Alignment explanation
Indices: 55679--55724 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
55669 ATCTTTGATG
55679 TAACATGGAAGGTGGTAACAAAA
1 TAACATGGAAGGTGGTAACAAAA
55702 TAACATGGAAGGTGGTAACAAAA
1 TAACATGGAAGGTGGTAACAAAA
55725 ATATTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.09, G:0.26, T:0.17
Consensus pattern (23 bp):
TAACATGGAAGGTGGTAACAAAA
Found at i:56820 original size:20 final size:20
Alignment explanation
Indices: 56782--56832 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
56772 TCATATTAAT
* **
56782 ATATAATATAATAAATAAATG
1 ATATCATAT-ATAAATAAAAA
*
56803 ATATCATATATAACTAAAAA
1 ATATCATATATAAATAAAAA
56823 ATATCATATA
1 ATATCATATA
56833 AATGTATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (20 bp):
ATATCATATATAAATAAAAA
Done.