Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008112.1 Hibiscus syriacus cultivar Beakdansim tig00110650_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: 53998
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.34
Found at i:1594 original size:92 final size:92
Alignment explanation
Indices: 1427--1698 Score: 365
Period size: 92 Copynumber: 2.9 Consensus size: 92
1417 ATAAAGAATA
* *
1427 TGATAAGCAGAAAACGGCAGCA-TTACATAATGCAAGGAACTAAATCTTCA-TTTATACTTCAAA
1 TGATAAGCAGAAAAGGGCAGCACTT--A-AATGCAAGGAACTAAATCTTCATTTTATACTTCAAG
*
1490 CGACAAGCAGCAAGATTTAACAATATAGTC
63 CGACATGCAGCAAGATTTAACAATATAGTC
*
1520 TGATAAGCAGAAAAGGGCAGCACTTAAATGCAAGGAACTATATCTTCATTTTATACTTCAAGCGA
1 TGATAAGCAGAAAAGGGCAGCACTTAAATGCAAGGAACTAAATCTTCATTTTATACTTCAAGCGA
1585 CATGCAGCAAGATTTAACAATATAGTC
66 CATGCAGCAAGATTTAACAATATAGTC
* * *
1612 TGA-ATA--AGAAAGGGAAGCAGCACATAAATGTAAGGAACTAAATCTTCATTTTATACTTCAAG
1 TGATA-AGCAGAAAAGG--GCAGCACTTAAATGCAAGGAACTAAATCTTCATTTTATACTTCAAG
* * *
1674 CGACGTGCAGCGAGATTCAACAATA
63 CGACATGCAGCAAGATTTAACAATA
1699 AAACAACCAT
Statistics
Matches: 163, Mismatches: 11, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
90 7 0.04
91 22 0.13
92 111 0.68
93 21 0.13
94 2 0.01
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.24
Consensus pattern (92 bp):
TGATAAGCAGAAAAGGGCAGCACTTAAATGCAAGGAACTAAATCTTCATTTTATACTTCAAGCGA
CATGCAGCAAGATTTAACAATATAGTC
Found at i:8588 original size:31 final size:31
Alignment explanation
Indices: 8505--8597 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
8495 AAAGAAATTC
* * *
8505 TATAATAATTTGATAAATTTGATGATTA-TT
1 TATAATAATTTAATAAAATTAATGATTATTT
* ** * *
8535 TATATTGGTTTATTAAAGTTAATGATTATTT
1 TATAATAATTTAATAAAATTAATGATTATTT
*
8566 TATAATAATTTAATAAAATTAATAATTATTT
1 TATAATAATTTAATAAAATTAATGATTATTT
8597 T
1 T
8598 CAAAATTTTT
Statistics
Matches: 49, Mismatches: 13, Indels: 1
0.78 0.21 0.02
Matches are distributed among these distances:
30 21 0.43
31 28 0.57
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.52
Consensus pattern (31 bp):
TATAATAATTTAATAAAATTAATGATTATTT
Found at i:24512 original size:89 final size:89
Alignment explanation
Indices: 24361--24538 Score: 347
Period size: 89 Copynumber: 2.0 Consensus size: 89
24351 TACATCAAAT
*
24361 ATTGGTTTCCATGTTTAAGAAACAAATTCAGTTAGTTTCCTATTATATATGTTCTCTGAATCTGA
1 ATTGGTTTCCATGTTTAAGAAACAAATTCAGTTAGTTTCCAATTATATATGTTCTCTGAATCTGA
24426 TATAAGAAGTAATTACCAACCATG
66 TATAAGAAGTAATTACCAACCATG
24450 ATTGGTTTCCATGTTTAAGAAACAAATTCAGTTAGTTTCCAATTATATATGTTCTCTGAATCTGA
1 ATTGGTTTCCATGTTTAAGAAACAAATTCAGTTAGTTTCCAATTATATATGTTCTCTGAATCTGA
24515 TATAAGAAGTAATTACCAACCATG
66 TATAAGAAGTAATTACCAACCATG
24539 CTAAGGAGTG
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 88 1.00
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (89 bp):
ATTGGTTTCCATGTTTAAGAAACAAATTCAGTTAGTTTCCAATTATATATGTTCTCTGAATCTGA
TATAAGAAGTAATTACCAACCATG
Found at i:38530 original size:2 final size:2
Alignment explanation
Indices: 38523--38549 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38513 TTTGCAAGTA
38523 CT 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 CT C
38550 ACACACACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:47499 original size:35 final size:36
Alignment explanation
Indices: 47429--47499 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
47419 CATACCTCTG
*
47429 GTTTCTTATCACCTTAATTCTATATTGTACGTATAT
1 GTTTCTTATCACCTTAATTCTATATTGTACATATAT
*
47465 GTTTCTTATCACCTTAATTCTA-ATTGTATATATAT
1 GTTTCTTATCACCTTAATTCTATATTGTACATATAT
47500 ATTTATGGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
35 11 0.33
36 22 0.67
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.51
Consensus pattern (36 bp):
GTTTCTTATCACCTTAATTCTATATTGTACATATAT
Found at i:49293 original size:2 final size:2
Alignment explanation
Indices: 49288--49319 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
49278 ACACACACAC
49288 TA TA TA 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 TA TA TA
49320 CTTTTTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:51879 original size:14 final size:14
Alignment explanation
Indices: 51860--51887 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
51850 GAAAAGAAGC
51860 TATGTGATACGTGA
1 TATGTGATACGTGA
51874 TATGTGATACGTGA
1 TATGTGATACGTGA
51888 ATTACAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (14 bp):
TATGTGATACGTGA
Found at i:52291 original size:142 final size:148
Alignment explanation
Indices: 51986--52292 Score: 477
Period size: 149 Copynumber: 2.1 Consensus size: 148
51976 AAGTCGAGGG
* * *
51986 TCTACGC-GTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTATGTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
52050 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGAGGTCCTTATGGA-ATTATTA
52115 TATGGCACTACGATGCAAT
130 TATGGCACTACGATGCAAT
*
52134 TCTA-GCGGGTCCTTCGGGATATATATATATTATGTGGAACATGTGTGAAGTC-TGAAAGACACA
1 TCTACGC-GGTCCTTCGGGACATATATATATTATGTGGAACATGTGTGAAGTCTTGAAAGACACA
52197 TACTTGATCCCTAGTATA-GTATATGATTC-TAAGGAATAATAT-AGGTCCTTATGG-A-TATTA
65 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGAGGTCCTTATGGAATTATTA
*
52257 TATGGCACTACGGTGCAAT
130 TATGGCACTACGATGCAAT
*
52276 TCTACGCGGTACTTCGG
1 TCTACGCGGTCCTTCGG
52293 TGCAATTATA
Statistics
Matches: 149, Mismatches: 7, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
142 36 0.24
143 3 0.02
145 11 0.07
146 13 0.09
147 13 0.09
148 33 0.22
149 40 0.27
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (148 bp):
TCTACGCGGTCCTTCGGGACATATATATATTATGTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGAGGTCCTTATGGAATTATTAT
ATGGCACTACGATGCAAT
Found at i:52312 original size:142 final size:148
Alignment explanation
Indices: 52019--52292 Score: 436
Period size: 142 Copynumber: 1.9 Consensus size: 148
52009 GTATATTCTT
52019 TGGAACATGTGTGAAGTCTTGAAAGACACATACTTGATCCCTAGTATATGTATATGATTCTTAAG
1 TGGAACATGTGTGAAGTCTTGAAAGACACATACTTGATCCCTAGTATATGTATATGATTCTTAAG
* *
52084 GAATAATATGTGGTCCTTATGGACATTATTATATGGCACTACGATGCAATTCTAGCGGGTCCTTC
66 GAATAATATGAGGTCCTTATGGA-ATTATTATATGGCACTACGATGCAATTCTAGCGGGTACTTC
* *
52149 GGGATATATATATATTATG
130 GGGATATATATAGATGATG
52168 TGGAACATGTGTGAAGTC-TGAAAGACACATACTTGATCCCTAGTATA-GTATATGATTC-TAAG
1 TGGAACATGTGTGAAGTCTTGAAAGACACATACTTGATCCCTAGTATATGTATATGATTCTTAAG
*
52230 GAATAATAT-AGGTCCTTATGG-A-TATTATATGGCACTACGGTGCAATTCTA-CGCGGTACTTC
66 GAATAATATGAGGTCCTTATGGAATTATTATATGGCACTACGATGCAATTCTAGCG-GGTACTTC
52291 GG
130 GG
52293 TGCAATTATA
Statistics
Matches: 121, Mismatches: 3, Indels: 9
0.91 0.02 0.07
Matches are distributed among these distances:
141 2 0.02
142 36 0.30
143 1 0.01
145 11 0.09
146 13 0.11
147 11 0.09
148 29 0.24
149 18 0.15
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (148 bp):
TGGAACATGTGTGAAGTCTTGAAAGACACATACTTGATCCCTAGTATATGTATATGATTCTTAAG
GAATAATATGAGGTCCTTATGGAATTATTATATGGCACTACGATGCAATTCTAGCGGGTACTTCG
GGATATATATAGATGATG
Done.