Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000337.1 Hibiscus syriacus cultivar Beakdansim tig00000627_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: 66925
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:7366 original size:185 final size:185
Alignment explanation
Indices: 7062--7427 Score: 662
Period size: 185 Copynumber: 2.0 Consensus size: 185
7052 AAATATTTTA
*
7062 TAATTAAAAAAATAGTTTATAATTAATTTAAATAATATATAATTATAAAATATAAATTTTATATA
1 TAATTAAAAAAATAGTTTACAATTAATTTAAATAATATATAATTATAAAATATAAATTTTATATA
* *
7127 AATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATATTAAATTATTAATTGGG
66 AATTTTTTAATTAATTAATATTAATTTAGGTTTAAAAATTATTGGATATTAAATTATTAATTGGG
7192 TTTTAAATGGTTTGGACTGAGCCCATATGTTATATATAATATATTTAAAAAATTT
131 TTTTAAATGGTTTGGACTGAGCCCATATGTTATATATAATATATTTAAAAAATTT
7247 TAATTCAAAAAAATAGTTTACAATTAATTTAAATAATATATAATTATAAAATATAAATTTTATAT
1 TAATT-AAAAAAATAGTTTACAATTAATTTAAATAATATATAATTATAAAATATAAATTTTATAT
* *
7312 AAA-TTTTTAATTAATTAATATTAATTTAGGTTTAAAAATTATTGGATCTTAAATTATTTATTGG
65 AAATTTTTTAATTAATTAATATTAATTTAGGTTTAAAAATTATTGGATATTAAATTATTAATTGG
*
7376 GTTTTAAATGGTTTGGACTGAGCTCATATGTTATATATAATATATTTAAAAA
130 GTTTTAAATGGTTTGGACTGAGCCCATATGTTATATATAATATATTTAAAAA
7428 TTAAAAATTT
Statistics
Matches: 174, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
185 113 0.65
186 61 0.35
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (185 bp):
TAATTAAAAAAATAGTTTACAATTAATTTAAATAATATATAATTATAAAATATAAATTTTATATA
AATTTTTTAATTAATTAATATTAATTTAGGTTTAAAAATTATTGGATATTAAATTATTAATTGGG
TTTTAAATGGTTTGGACTGAGCCCATATGTTATATATAATATATTTAAAAAATTT
Found at i:19667 original size:8 final size:7
Alignment explanation
Indices: 19646--19670 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
19636 AAAGAAGGTG
19646 AGTAAAA
1 AGTAAAA
19653 AGTAAAA
1 AGTAAAA
19660 AGTAAAA
1 AGTAAAA
19667 AGTA
1 AGTA
19671 GAGACTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (7 bp):
AGTAAAA
Found at i:25953 original size:28 final size:28
Alignment explanation
Indices: 25895--25958 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
25885 CCAAGGTTTG
*
25895 GGGGTATTTTAGGTTATTTCTCAATTCA
1 GGGGTATTTTAGGTCATTTCTCAATTCA
*
25923 GGGGTATTTT-GGTCATTT-TACAGTTCA
1 GGGGTATTTTAGGTCATTTCT-CAATTCA
*
25950 AGGGTATTT
1 GGGGTATTT
25959 CTGTCCTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 1 0.03
27 21 0.66
28 10 0.31
ACGTcount: A:0.20, C:0.09, G:0.25, T:0.45
Consensus pattern (28 bp):
GGGGTATTTTAGGTCATTTCTCAATTCA
Found at i:31577 original size:41 final size:41
Alignment explanation
Indices: 31531--31612 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
31521 AATTCCTCCA
31531 TAAACATTTTAGCGAACCAAAGGGTTTGGAGAACGAAAAGG
1 TAAACATTTTAGCGAACCAAAGGGTTTGGAGAACGAAAAGG
31572 TAAACATTTTAGCGAACCAAAGGGTTTGGAGAACGAAAAGG
1 TAAACATTTTAGCGAACCAAAGGGTTTGGAGAACGAAAAGG
31613 AGAGAGCGCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.41, C:0.12, G:0.27, T:0.20
Consensus pattern (41 bp):
TAAACATTTTAGCGAACCAAAGGGTTTGGAGAACGAAAAGG
Found at i:32082 original size:24 final size:23
Alignment explanation
Indices: 32020--32095 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 23
32010 AATAAACTCA
*
32020 TTTATTGCTTATTTATAAGT-TTG
1 TTTATTGCTTATTTATAA-TATCG
*
32043 TTTATCAT-CTTGTTTATAATATCG
1 TTTAT--TGCTTATTTATAATATCG
32067 TTTATTGGCTTATTTATAA-ACTCG
1 TTTATT-GCTTATTTATAATA-TCG
32091 TTTAT
1 TTTAT
32096 CGATTCTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
22 1 0.02
23 7 0.16
24 35 0.80
25 1 0.02
ACGTcount: A:0.24, C:0.09, G:0.11, T:0.57
Consensus pattern (23 bp):
TTTATTGCTTATTTATAATATCG
Found at i:32119 original size:48 final size:47
Alignment explanation
Indices: 32017--32120 Score: 113
Period size: 48 Copynumber: 2.2 Consensus size: 47
32007 ACGAATAAAC
** * *
32017 TCATTTATTGCTTATTTATAAGTTTGTTTATCATCTTGTTTATAATA
1 TCATTTATTGCTTATTTATAAACTCGTTTATCATCTTGTTTATAAGA
*
32064 TCGTTTATTGGCTTATTTATAAACTCGTTTATCGAT-TCT-TTTATAAGA
1 TCATTTATT-GCTTATTTATAAACTCGTTTATC-ATCT-TGTTTATAAGA
*
32112 TTATTTATT
1 TCATTTATT
32121 CGGTTCTCCT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
47 8 0.17
48 36 0.77
49 3 0.06
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.56
Consensus pattern (47 bp):
TCATTTATTGCTTATTTATAAACTCGTTTATCATCTTGTTTATAAGA
Found at i:32358 original size:23 final size:23
Alignment explanation
Indices: 32314--32370 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
32304 TTTACAGATG
*
32314 TTAAACGAACATGTTCACGAACA
1 TTAAACGAACATATTCACGAACA
* ** *
32337 TTAAACGAATATATTCGTGAACT
1 TTAAACGAACATATTCACGAACA
*
32360 TTAAATGAACA
1 TTAAACGAACA
32371 AATAAAAATA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (23 bp):
TTAAACGAACATATTCACGAACA
Found at i:35460 original size:12 final size:12
Alignment explanation
Indices: 35443--35468 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
35433 TTCATCTGCT
35443 AATGCTAGATGA
1 AATGCTAGATGA
35455 AATGCTAGATGA
1 AATGCTAGATGA
35467 AA
1 AA
35469 GTTTGTCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.08, G:0.23, T:0.23
Consensus pattern (12 bp):
AATGCTAGATGA
Found at i:47412 original size:21 final size:21
Alignment explanation
Indices: 47358--47412 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
47348 TTTGCACCCA
47358 ATGTGGCGATTCAAGGTGTTG
1 ATGTGGCGATTCAAGGTGTTG
* ** * *
47379 ACGTAACGCTTCAAGGTGTTT
1 ATGTGGCGATTCAAGGTGTTG
47400 ATGTGGCGATTCA
1 ATGTGGCGATTCA
47413 CAGTGGTGAT
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.22, C:0.15, G:0.31, T:0.33
Consensus pattern (21 bp):
ATGTGGCGATTCAAGGTGTTG
Found at i:47585 original size:21 final size:21
Alignment explanation
Indices: 47559--47605 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
47549 ACTATATAGA
*
47559 AAAAATAAATATAAAACTACT
1 AAAAATAAAAATAAAACTACT
* *
47580 AAAAATAAAAATTAAATTACT
1 AAAAATAAAAATAAAACTACT
47601 AAAAA
1 AAAAA
47606 AGTATATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAAATAAAAATAAAACTACT
Found at i:47908 original size:21 final size:21
Alignment explanation
Indices: 47857--47913 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 21
47847 TAAATATAAA
47857 TATATTTAAATTTTTAGTAATTT
1 TATATTT--ATTTTTAGTAATTT
* *
47880 GATTTTTATTTTTAGTAATTT
1 TATATTTATTTTTAGTAATTT
47901 TATATTTATTTTT
1 TATATTTATTTTT
47914 TCTATATTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 25 0.83
23 5 0.17
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (21 bp):
TATATTTATTTTTAGTAATTT
Found at i:47927 original size:23 final size:22
Alignment explanation
Indices: 47857--47932 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 22
47847 TAAATATAAA
*
47857 TATATTTAAATTTTTAGTAATTTG
1 TATATTT--ATTTTTACTAATTTG
* *
47881 -ATTTTTATTTTTAGTAATTT-
1 TATATTTATTTTTACTAATTTG
*
47901 TATATTTATTTTTTCTATATTTG
1 TATATTTATTTTTACTA-ATTTG
47924 TATAGTTTA
1 TATA-TTTA
47933 AATTTAAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
21 27 0.61
22 4 0.09
23 9 0.20
24 4 0.09
ACGTcount: A:0.28, C:0.01, G:0.07, T:0.64
Consensus pattern (22 bp):
TATATTTATTTTTACTAATTTG
Found at i:48864 original size:60 final size:60
Alignment explanation
Indices: 48811--48927 Score: 173
Period size: 60 Copynumber: 1.9 Consensus size: 60
48801 CAAATTATAT
* * * *
48811 CTTTTATTTTAAATTAGTCTTTAAACTTTTGAATATTTTAATCTCATCCTCAAACTACGA
1 CTTTCATTTTAAATTAGTCCTTAAACTTTTGAACATTCTAATCTCATCCTCAAACTACGA
*
48871 CTTTCATTTTAAATTAGTCCTTAAACTTTTGAACATTCTAATTTCATCC-CTAAACTA
1 CTTTCATTTTAAATTAGTCCTTAAACTTTTGAACATTCTAATCTCATCCTC-AAACTA
48928 TCCCCCTTTC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
59 1 0.02
60 50 0.98
ACGTcount: A:0.32, C:0.19, G:0.04, T:0.45
Consensus pattern (60 bp):
CTTTCATTTTAAATTAGTCCTTAAACTTTTGAACATTCTAATCTCATCCTCAAACTACGA
Found at i:59618 original size:21 final size:21
Alignment explanation
Indices: 59586--59641 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
59576 TGAGTTACCT
* *
59586 GCGACGGCCGCAATAGCGTCC
1 GCGACAGCCGCAATAGCGCCC
*
59607 GCGACAGTCGCAATAGCGCCC
1 GCGACAGCCGCAATAGCGCCC
*
59628 GCGACGGCCGCAAT
1 GCGACAGCCGCAAT
59642 CATGGTAGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.21, C:0.38, G:0.32, T:0.09
Consensus pattern (21 bp):
GCGACAGCCGCAATAGCGCCC
Found at i:64929 original size:32 final size:32
Alignment explanation
Indices: 64888--64976 Score: 108
Period size: 32 Copynumber: 2.8 Consensus size: 32
64878 AGTAGGCCCC
64888 TAATAATAAATATTAGAAAAAAATTGAACCCA
1 TAATAATAAATATTAGAAAAAAATTGAACCCA
** * * *
64920 TAATAATAAATATTAGAGGAAATTTGAACTCT
1 TAATAATAAATATTAGAAAAAAATTGAACCCA
* *
64952 TAATAATAATTATTA-AAAATAATTG
1 TAATAATAAATATTAGAAAAAAATTG
64977 GACCATATTA
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 6 0.13
32 41 0.87
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.33
Consensus pattern (32 bp):
TAATAATAAATATTAGAAAAAAATTGAACCCA
Done.