Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008380.1 Hibiscus syriacus cultivar Beakdansim tig00111140_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: 24607
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Found at i:2798 original size:29 final size:28
Alignment explanation
Indices: 2714--2801 Score: 86
Period size: 31 Copynumber: 2.9 Consensus size: 28
2704 TGATCCAATC
* *
2714 AAGAAAAAAAAGAAAAGAAGCAAAAAAAAA
1 AAGAAAAAAAA-ACAAGAA-CAAAGAAAAA
* *
2744 AAGAAAAAGAGAAACACGAACAAAAGGAAAA
1 AAGAAAAA-A-AAACAAGAAC-AAAGAAAAA
2775 AAGAAAAAAAAACAAGAATCAAAGAAA
1 AAGAAAAAAAAACAAGAA-CAAAGAAA
2802 GAGGAACAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
29 14 0.29
30 11 0.23
31 21 0.44
32 2 0.04
ACGTcount: A:0.77, C:0.07, G:0.15, T:0.01
Consensus pattern (28 bp):
AAGAAAAAAAAACAAGAACAAAGAAAAA
Found at i:2801 original size:44 final size:45
Alignment explanation
Indices: 2720--2814 Score: 115
Period size: 44 Copynumber: 2.1 Consensus size: 45
2710 AATCAAGAAA
2720 AAAAAGAAAAGAAGCAAAAAAAAAAAGAAAAAGAGAAACACGAAC
1 AAAAAGAAAAGAAGCAAAAAAAAAAAGAAAAAGAGAAACACGAAC
* * * *
2765 AAAAGGAAAA-AAG-AAAAAAAAACAAGAATCAA-AGAAAGAGGAAC
1 AAAAAGAAAAGAAGCAAAAAAAAA-AAGAA-AAAGAGAAACACGAAC
2809 AAAAAG
1 AAAAAG
2815 CACATGCAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
43 9 0.21
44 23 0.53
45 11 0.26
ACGTcount: A:0.75, C:0.07, G:0.17, T:0.01
Consensus pattern (45 bp):
AAAAAGAAAAGAAGCAAAAAAAAAAAGAAAAAGAGAAACACGAAC
Found at i:5629 original size:105 final size:105
Alignment explanation
Indices: 5049--6039 Score: 1296
Period size: 105 Copynumber: 9.5 Consensus size: 105
5039 GACGAAGGGG
** * * * *
5049 CTTCCCAATTTCAGAGTAAATTTCAACTTCACAGCGAATGATATTGGACTCAAGACAACACAAGT
1 CTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGT
* *
5114 TCAACTTCACAATGAAGGGA-CGACTGGTTGTCAACAAACAA
66 TCAACTTCACGACGAAGGGACCG-CTGGTTGTCAAC-AACAA
* * * * *
5155 TTTCCCAGTTTCAGAGCCAATTTCAACTTTACAGCAAAGGATATTGGACTCCAGACAACGCAAGT
1 CTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGT
5220 TCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAA
66 TCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-AACAA
* * * *
5261 CTTCTCAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCAAGACAACACAAGT
1 CTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGT
* * * *
5326 TCAACTTCACAACGAAGGGACGGCTAGTTGTCAACAATAA
66 TCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAA
* * * * * * *
5366 TTTCCTAATTTCAGAGCCAGTTTCAACTTCCCAGCAAAGGATATTTGACTCCAGAC-ACGCAAGT
1 CTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGT
* * *
5430 TCAACTTCACAACGAAGGGACCGTTGGTTGTCAATAACAA
66 TCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAA
*
5470 CTTCCC-ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGT
1 CTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGT
*
5534 TCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAA
66 TCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAA
* *
5574 CTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGT
1 CTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGT
*
5639 TCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAA
66 TCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAA
* * * * *
5679 CTTCCCAATATCAAAGTCAATTTCAACTTCACAACGAAGGATATTGGAATCCAGACAATGCAAGT
1 CTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGT
*
5744 TCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAA
66 TCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAA
* * *
5784 CTTCCCAATCTCAGAGCCAATTTTAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGT
1 CTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGT
* * * * *
5849 TTAACTTCAGGACGAAGGGACCGTTGTTTGTCAATAA-AA
66 TCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAA
* ** * * *
5888 -TT-TC-A-TTCAGATTCAATTTCAACTTCACAATGAAGGATATTGGACTCGAGACAACACAAGT
1 CTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGT
* * *
5949 TCAACTTCACAACGAAGAGACGGCTGGTTGTCAACAAACAA
66 TCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-AACAA
* * ** * * *
5990 TTTTCCGGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGGACT
1 CTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
6040 TGGAACAATG
Statistics
Matches: 783, Mismatches: 93, Indels: 18
0.88 0.10 0.02
Matches are distributed among these distances:
100 77 0.10
101 3 0.00
102 3 0.00
103 49 0.06
104 98 0.13
105 335 0.43
106 216 0.28
107 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (105 bp):
CTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGT
TCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAA
Found at i:6631 original size:34 final size:34
Alignment explanation
Indices: 6588--6712 Score: 120
Period size: 34 Copynumber: 3.8 Consensus size: 34
6578 TCCGTCCTAC
*
6588 TAGGATTCAAACTCCTAAAAATAGGATATAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
6622 TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
6657 GCTAGGATTC--A-----AAAAATAGGATAGAATTT
1 --TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * *
6686 TATGATTTAAACTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
6713 CCACAAGCAC
Statistics
Matches: 73, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
27 6 0.08
29 4 0.05
30 13 0.18
34 38 0.52
35 4 0.05
37 8 0.11
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.32
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:7107 original size:18 final size:17
Alignment explanation
Indices: 7068--7110 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
7058 ATTATATGGA
7068 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
7084 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
7102 TATTATTAT
1 TATTATTAT
7111 GTATATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:7161 original size:10 final size:10
Alignment explanation
Indices: 7146--7199 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 10
7136 CATTTGATTT
7146 TTTTATTATA
1 TTTTATTATA
7156 TTTTATTATA
1 TTTTATTATA
7166 TTATTATATATA
1 TT-TTAT-TATA
7178 TTTCT-TTAATA
1 TTT-TATT-ATA
7189 TTTTACTTATA
1 TTTTA-TTATA
7200 AATCTAATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
10 14 0.37
11 15 0.39
12 9 0.24
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTATTATA
Found at i:7373 original size:15 final size:17
Alignment explanation
Indices: 7343--7374 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
7333 TGTTTATGTA
7343 ATATATCTTATAATTTT
1 ATATATCTTATAATTTT
7360 ATATAT-TTAT-ATTTT
1 ATATATCTTATAATTTT
7375 TTTATTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 4 0.27
17 6 0.40
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
ATATATCTTATAATTTT
Found at i:8287 original size:3 final size:3
Alignment explanation
Indices: 8279--8308 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
8269 ATATTAATTT
8279 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
8309 TATTCTTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:8598 original size:12 final size:12
Alignment explanation
Indices: 8581--8613 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
8571 TATAATTTAA
*
8581 TAATTAAAATTT
1 TAATTAAAATGT
8593 TAATTAAAATGT
1 TAATTAAAATGT
8605 TAA-TAAAAT
1 TAATTAAAAT
8614 AGTATAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (12 bp):
TAATTAAAATGT
Found at i:10308 original size:2 final size:2
Alignment explanation
Indices: 10303--10342 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
10293 ATTATAAAAA
10303 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10343 CCAAGAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11449 original size:3 final size:3
Alignment explanation
Indices: 11441--11476 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
11431 GTATGAATTT
11441 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
11477 TATTCTTGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:11770 original size:12 final size:12
Alignment explanation
Indices: 11753--11785 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
11743 TATAATTTAA
*
11753 TAATTAAAATTT
1 TAATTAAAATGT
11765 TAATTAAAATGT
1 TAATTAAAATGT
11777 TAA-TAAAAT
1 TAATTAAAAT
11786 AGTATAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (12 bp):
TAATTAAAATGT
Found at i:14840 original size:12 final size:12
Alignment explanation
Indices: 14823--14855 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
14813 TATAATTTAA
*
14823 TAATTAAAATTT
1 TAATTAAAATGT
14835 TAATTAAAATGT
1 TAATTAAAATGT
14847 TAA-TAAAAT
1 TAATTAAAAT
14856 AGTATAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (12 bp):
TAATTAAAATGT
Found at i:19606 original size:2 final size:2
Alignment explanation
Indices: 19594--19630 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
19584 CATTATAAAA
*
19594 AT AT CT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19631 CCAAGAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:20720 original size:9 final size:10
Alignment explanation
Indices: 20679--20717 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
20669 AATATTAAGA
20679 TTATTAAATT
1 TTATTAAATT
20689 TTATTAAAACTT
1 TTATT-AAA-TT
*
20701 TTAATAAATT
1 TTATTAAATT
20711 TTATTAA
1 TTATTAA
20718 TTTATAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 13 0.52
11 6 0.24
12 6 0.24
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (10 bp):
TTATTAAATT
Found at i:21033 original size:12 final size:12
Alignment explanation
Indices: 21016--21048 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
21006 TATAATTTAA
*
21016 TAATTAAAATTT
1 TAATTAAAATGT
21028 TAATTAAAATGT
1 TAATTAAAATGT
21040 TAA-TAAAAT
1 TAATTAAAAT
21049 AGTATAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (12 bp):
TAATTAAAATGT
Found at i:22743 original size:2 final size:2
Alignment explanation
Indices: 22738--22768 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
22728 AAAAATATCT
22738 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22769 CCAAGAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23816 original size:10 final size:10
Alignment explanation
Indices: 23801--23835 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
23791 AATATTAAGA
23801 TTATTAAATT
1 TTATTAAATT
23811 TTATTAAACTT
1 TTATTAAA-TT
*
23822 TTAATAAATT
1 TTATTAAATT
23832 TTAT
1 TTAT
23836 AATTTATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (10 bp):
TTATTAAATT
Found at i:24133 original size:12 final size:12
Alignment explanation
Indices: 24116--24148 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
24106 ATATAATTAA
*
24116 TAATTAAAATTT
1 TAATTAAAATGT
24128 TAATTAAAATGT
1 TAATTAAAATGT
24140 TAA-TAAAAT
1 TAATTAAAAT
24149 AGTATAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (12 bp):
TAATTAAAATGT
Found at i:24426 original size:14 final size:15
Alignment explanation
Indices: 24404--24434 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
24394 TAAATTGTCA
24404 TTTCATAAATTCTAT
1 TTTCATAAATTCTAT
24419 TTTC-TAAATTCTAT
1 TTTCATAAATTCTAT
24433 TT
1 TT
24435 ATATTTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTCATAAATTCTAT
Done.