Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002502.1 Hibiscus syriacus cultivar Beakdansim tig00005099_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: 67156
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:434 original size:55 final size:55
Alignment explanation
Indices: 350--458 Score: 191
Period size: 55 Copynumber: 2.0 Consensus size: 55
340 GCATCCATCG
* *
350 AACCTTCAACCCCGTTATGTGCAGGTGTGTAAACCTCGCAGACGGCACTATATCA
1 AACCTTCAACCCCATTATGTGCAGGTGTGTAAACCTCGCACACGGCACTATATCA
*
405 AACCTTCAGCCCCATTATGTGCAGGTGTGTAAACCTCGCACACGGCACTATATC
1 AACCTTCAACCCCATTATGTGCAGGTGTGTAAACCTCGCACACGGCACTATATC
459 GATCTCCCTT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (55 bp):
AACCTTCAACCCCATTATGTGCAGGTGTGTAAACCTCGCACACGGCACTATATCA
Found at i:11266 original size:18 final size:18
Alignment explanation
Indices: 11238--11272 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
11228 TATCCTTTAG
11238 GTAATTCTAAATATATTAT
1 GTAATTCTAAATA-ATTAT
11257 GTAA-TCTAAATAATTA
1 GTAATTCTAAATAATTA
11273 AATAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 8 0.50
19 4 0.25
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.43
Consensus pattern (18 bp):
GTAATTCTAAATAATTAT
Found at i:12258 original size:136 final size:136
Alignment explanation
Indices: 12014--12285 Score: 544
Period size: 136 Copynumber: 2.0 Consensus size: 136
12004 AAATTATTTA
12014 TAGGGTAAACTATACGGGAAACCATCAAACTATAGTCATTAATCAATCTTATCATCGAACTATTT
1 TAGGGTAAACTATACGGGAAACCATCAAACTATAGTCATTAATCAATCTTATCATCGAACTATTT
12079 TTTATCTCAATTCGATCATCAAACTTTTTAATTGATTCAATCAGACCACTCTCCGTTAAAAAAAT
66 TTTATCTCAATTCGATCATCAAACTTTTTAATTGATTCAATCAGACCACTCTCCGTTAAAAAAAT
12144 AACGGT
131 AACGGT
12150 TAGGGTAAACTATACGGGAAACCATCAAACTATAGTCATTAATCAATCTTATCATCGAACTATTT
1 TAGGGTAAACTATACGGGAAACCATCAAACTATAGTCATTAATCAATCTTATCATCGAACTATTT
12215 TTTATCTCAATTCGATCATCAAACTTTTTAATTGATTCAATCAGACCACTCTCCGTTAAAAAAAT
66 TTTATCTCAATTCGATCATCAAACTTTTTAATTGATTCAATCAGACCACTCTCCGTTAAAAAAAT
12280 AACGGT
131 AACGGT
12286 GCGTCCAACG
Statistics
Matches: 136, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
136 136 1.00
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (136 bp):
TAGGGTAAACTATACGGGAAACCATCAAACTATAGTCATTAATCAATCTTATCATCGAACTATTT
TTTATCTCAATTCGATCATCAAACTTTTTAATTGATTCAATCAGACCACTCTCCGTTAAAAAAAT
AACGGT
Found at i:16610 original size:130 final size:130
Alignment explanation
Indices: 16377--16636 Score: 520
Period size: 130 Copynumber: 2.0 Consensus size: 130
16367 CTGGTAACGC
16377 AATCAAAATTTTAATTAGTAAAATGGAAAAGACATTATTAACCTAATATGTTTTATGTATAAACT
1 AATCAAAATTTTAATTAGTAAAATGGAAAAGACATTATTAACCTAATATGTTTTATGTATAAACT
16442 CATTTTCTATACATTAATACACATGTTTCAATCTTTGCTTAGGTCAAGCTCCCTCTCTCCCACAT
66 CATTTTCTATACATTAATACACATGTTTCAATCTTTGCTTAGGTCAAGCTCCCTCTCTCCCACAT
16507 AATCAAAATTTTAATTAGTAAAATGGAAAAGACATTATTAACCTAATATGTTTTATGTATAAACT
1 AATCAAAATTTTAATTAGTAAAATGGAAAAGACATTATTAACCTAATATGTTTTATGTATAAACT
16572 CATTTTCTATACATTAATACACATGTTTCAATCTTTGCTTAGGTCAAGCTCCCTCTCTCCCACAT
66 CATTTTCTATACATTAATACACATGTTTCAATCTTTGCTTAGGTCAAGCTCCCTCTCTCCCACAT
16637 CATGCTTTGC
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
130 130 1.00
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.38
Consensus pattern (130 bp):
AATCAAAATTTTAATTAGTAAAATGGAAAAGACATTATTAACCTAATATGTTTTATGTATAAACT
CATTTTCTATACATTAATACACATGTTTCAATCTTTGCTTAGGTCAAGCTCCCTCTCTCCCACAT
Found at i:21895 original size:23 final size:22
Alignment explanation
Indices: 21835--21903 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 22
21825 AATTAGTAAA
* *
21835 ATATTTAAAAT-ATAT-TTATT
1 ATATTTATAATAATATAATATT
21855 AATATTTATAATAATATAATATT
1 -ATATTTATAATAATATAATATT
* * *
21878 ATATTTTTAATATCTATAATAAT
1 ATATTTATAATA-ATATAATATT
21901 ATA
1 ATA
21904 CTCAATTATA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
21 10 0.25
22 15 0.38
23 15 0.38
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (22 bp):
ATATTTATAATAATATAATATT
Found at i:21927 original size:31 final size:31
Alignment explanation
Indices: 21845--21962 Score: 91
Period size: 31 Copynumber: 3.7 Consensus size: 31
21835 ATATTTAAAA
*
21845 TATATTTATTAATATTTATAATAATATAATAT
1 TATATTTA-TAATATATATAATAATATAATAT
* * *
21877 TATATTTTTAATATCTATAATAATATACTCAAT
1 TATATTTATAATATATATAATAATATAAT--AT
* *
21910 TATA-TTATAATA-ATATAAGGTATTATACT-T
1 TATATTTATAATATATATAA--TAATATAATAT
*
21940 TTTATTT-TAATAATATATAATAA
1 TATATTTATAAT-ATATATAATAA
21963 ATTATCAATA
Statistics
Matches: 71, Mismatches: 8, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
30 10 0.14
31 27 0.38
32 20 0.28
33 14 0.20
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (31 bp):
TATATTTATAATATATATAATAATATAATAT
Found at i:51301 original size:2 final size:2
Alignment explanation
Indices: 51294--51319 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
51284 TTAAGCCGTT
51294 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
51320 AACAAACGAG
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:60422 original size:19 final size:19
Alignment explanation
Indices: 60395--60431 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
60385 TTAATAATAA
60395 TAATAATAATAATACATGG
1 TAATAATAATAATACATGG
*
60414 TAATTATAATAATACATG
1 TAATAATAATAATACATG
60432 ATATTTGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.35
Consensus pattern (19 bp):
TAATAATAATAATACATGG
Found at i:61804 original size:15 final size:17
Alignment explanation
Indices: 61784--61816 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
61774 CCATGTACAT
61784 TATTGAG-A-ATAGAGG
1 TATTGAGTACATAGAGG
61799 TATTGAGTACATAGAGG
1 TATTGAGTACATAGAGG
61816 T
1 T
61817 TGTGCACTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.36, C:0.03, G:0.30, T:0.30
Consensus pattern (17 bp):
TATTGAGTACATAGAGG
Found at i:63693 original size:40 final size:36
Alignment explanation
Indices: 63643--63725 Score: 94
Period size: 40 Copynumber: 2.2 Consensus size: 36
63633 TTAATCATTA
* * * *
63643 TTATTATATTTTTTAATCTAACGTTTTTATTATATTATTT
1 TTATTTTATTTTTT-ACCTAACATTTTT-GTATA-T-TTT
63683 TTATTTTATTTTTTACCTAACATTTTTGTATATTTT
1 TTATTTTATTTTTTACCTAACATTTTTGTATATTTT
63719 TTATTTT
1 TTATTTT
63726 TTATCATTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
36 10 0.26
37 1 0.03
38 4 0.10
39 11 0.28
40 13 0.33
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.67
Consensus pattern (36 bp):
TTATTTTATTTTTTACCTAACATTTTTGTATATTTT
Found at i:63803 original size:19 final size:18
Alignment explanation
Indices: 63779--63820 Score: 75
Period size: 19 Copynumber: 2.3 Consensus size: 18
63769 TTTTTTTAGT
63779 TTTTTTATTTCTATTTCTA
1 TTTTTTATTTCTATTT-TA
63798 TTTTTTATTTCTATTTTA
1 TTTTTTATTTCTATTTTA
63816 TTTTT
1 TTTTT
63821 ACTTATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTTATTTCTATTTTA
Found at i:63808 original size:13 final size:13
Alignment explanation
Indices: 63790--63814 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
63780 TTTTTATTTC
63790 TATTTCTATTTTT
1 TATTTCTATTTTT
63803 TATTTCTATTTT
1 TATTTCTATTTT
63815 ATTTTTACTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTTCTATTTTT
Done.