Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008021.1 Hibiscus syriacus cultivar Beakdansim tig00110490_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: 84612
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3308 original size:21 final size:22
Alignment explanation
Indices: 3284--3366 Score: 80
Period size: 21 Copynumber: 3.8 Consensus size: 22
3274 TTGGTGCAGA
*
3284 GGGAATCGATTCCCCCCTTGA-
1 GGGAACCGATTCCCCCCTTGAG
* *
3305 GGGAACCGATTCCTCCTTTGAAG
1 GGGAACCGATTCCCCCCTTG-AG
**
3328 GGGAACCGATTCCCCCC-ACAG
1 GGGAACCGATTCCCCCCTTGAG
* *
3349 GGGAATCGATACCCCCCT
1 GGGAACCGATTCCCCCCT
3367 GGGGTTCTGT
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
21 34 0.68
22 1 0.02
23 15 0.30
ACGTcount: A:0.22, C:0.35, G:0.24, T:0.19
Consensus pattern (22 bp):
GGGAACCGATTCCCCCCTTGAG
Found at i:3335 original size:23 final size:21
Alignment explanation
Indices: 3282--3344 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
3272 TTTTGGTGCA
*
3282 GAGGGAATCGATTCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
* *
3303 GAGGGAACCGATTCCTCCTTT
1 GAGGGAACCGATTCCCCCCTT
3324 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
3345 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 19 0.54
22 1 0.03
23 15 0.43
ACGTcount: A:0.21, C:0.33, G:0.25, T:0.21
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:9863 original size:23 final size:24
Alignment explanation
Indices: 9814--9864 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
9804 TTTCTTTTAT
* *
9814 TTTCTTCTTTTTGAGTGCCTGACA
1 TTTCTTCTTTTGGAGTGCCTCACA
*
9838 TTTCTTCTTTTGGAGTGCTTCA-A
1 TTTCTTCTTTTGGAGTGCCTCACA
9861 TTTC
1 TTTC
9865 ATTGCTGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.12, C:0.20, G:0.16, T:0.53
Consensus pattern (24 bp):
TTTCTTCTTTTGGAGTGCCTCACA
Found at i:20151 original size:18 final size:18
Alignment explanation
Indices: 20078--20155 Score: 58
Period size: 18 Copynumber: 4.6 Consensus size: 18
20068 AATTGGAGTG
* *
20078 CAAAAAGAAAGAAAAAGA
1 CAAAAAGAAAAAAAAAGT
*
20096 CAAAAAGAAGAAAATAA-T
1 CAAAAAGAA-AAAAAAAGT
* * *
20114 CAGAAA-ATAAGAAAAG-
1 CAAAAAGAAAAAAAAAGT
20130 --AAAAGAAAAAAAAAGT
1 CAAAAAGAAAAAAAAAGT
20146 CAAAAAGAAA
1 CAAAAAGAAA
20156 GCAAGCCAAG
Statistics
Matches: 44, Mismatches: 10, Indels: 12
0.67 0.15 0.18
Matches are distributed among these distances:
14 3 0.07
15 8 0.18
16 5 0.11
17 1 0.02
18 22 0.50
19 5 0.11
ACGTcount: A:0.76, C:0.05, G:0.14, T:0.05
Consensus pattern (18 bp):
CAAAAAGAAAAAAAAAGT
Found at i:24108 original size:32 final size:32
Alignment explanation
Indices: 24067--24130 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
24057 TATACTTAGT
24067 TTATTTCTTATGTTATGCATGTAGGCACATTC
1 TTATTTCTTATGTTATGCATGTAGGCACATTC
24099 TTATTTCTTATGTTATGCATGTAGGCACATTC
1 TTATTTCTTATGTTATGCATGTAGGCACATTC
24131 GGCCAATACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.47
Consensus pattern (32 bp):
TTATTTCTTATGTTATGCATGTAGGCACATTC
Found at i:25403 original size:61 final size:61
Alignment explanation
Indices: 25328--25457 Score: 233
Period size: 61 Copynumber: 2.1 Consensus size: 61
25318 TATTTATTTC
*
25328 ATTTATTTTCATTTTCAGTGTTTATATTATTATTCATTTCTTAAACCTATAATTAATTCAT
1 ATTTCTTTTCATTTTCAGTGTTTATATTATTATTCATTTCTTAAACCTATAATTAATTCAT
*
25389 ATTTCTTTTCATTTTCAGTGTTTATATTATTATTCATTTCTTAAACCTATCATTAATTCAT
1 ATTTCTTTTCATTTTCAGTGTTTATATTATTATTCATTTCTTAAACCTATAATTAATTCAT
*
25450 TTTTCTTT
1 ATTTCTTT
25458 CTTATTTTAT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.26, C:0.13, G:0.03, T:0.58
Consensus pattern (61 bp):
ATTTCTTTTCATTTTCAGTGTTTATATTATTATTCATTTCTTAAACCTATAATTAATTCAT
Found at i:25901 original size:20 final size:21
Alignment explanation
Indices: 25876--25920 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
25866 ATTCATTAAG
25876 TCATGTCATG-TTAT-TCTAGC
1 TCATGTCATGTTTATAT-TAGC
*
25896 TCATGTTATGTTTATATTAGC
1 TCATGTCATGTTTATATTAGC
25917 TCAT
1 TCAT
25921 TAGCTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 9 0.41
21 12 0.55
22 1 0.05
ACGTcount: A:0.22, C:0.16, G:0.13, T:0.49
Consensus pattern (21 bp):
TCATGTCATGTTTATATTAGC
Found at i:31910 original size:38 final size:38
Alignment explanation
Indices: 31868--31945 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
31858 TAAGGCTATC
* *
31868 TACTCTTTTCACTAGAGCGTGTAGATCACCTTACATCA
1 TACTCTTTTCACCAAAGCGTGTAGATCACCTTACATCA
31906 TACTCTTTTCACCAAAGCGTGTAGATCACCTTACATCA
1 TACTCTTTTCACCAAAGCGTGTAGATCACCTTACATCA
31944 TA
1 TA
31946 TAAAGTCTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.33
Consensus pattern (38 bp):
TACTCTTTTCACCAAAGCGTGTAGATCACCTTACATCA
Found at i:38407 original size:17 final size:16
Alignment explanation
Indices: 38387--38420 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
38377 AAAAGAAAAG
*
38387 AAGAAAATTCAAAGCAA
1 AAGAAAAGTC-AAGCAA
38404 AAGAAAAGTCAAGCAA
1 AAGAAAAGTCAAGCAA
38420 A
1 A
38421 GTTTTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.65, C:0.12, G:0.15, T:0.09
Consensus pattern (16 bp):
AAGAAAAGTCAAGCAA
Found at i:40604 original size:23 final size:24
Alignment explanation
Indices: 40578--40624 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
40568 AAAGTCAACA
40578 AAGAAAATAG-AAGCACTCAAAAG
1 AAGAAAATAGCAAGCACTCAAAAG
* *
40601 AAGAAAATTGCAAGCACTCCAAAG
1 AAGAAAATAGCAAGCACTCAAAAG
40625 GAATAAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.55, C:0.17, G:0.17, T:0.11
Consensus pattern (24 bp):
AAGAAAATAGCAAGCACTCAAAAG
Found at i:47059 original size:21 final size:21
Alignment explanation
Indices: 47033--47072 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
47023 CCCCCTTTGA
*
47033 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
47054 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
47073 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:49374 original size:13 final size:13
Alignment explanation
Indices: 49356--49381 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49346 GAGTAATTAG
49356 TAATTTCTAATTT
1 TAATTTCTAATTT
49369 TAATTTCTAATTT
1 TAATTTCTAATTT
49382 CAAAACTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (13 bp):
TAATTTCTAATTT
Found at i:55658 original size:21 final size:21
Alignment explanation
Indices: 55619--55658 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
55609 TTTGAAAATT
55619 AAAGAAATGAAATGGAAATGG
1 AAAGAAATGAAATGGAAATGG
*
55640 AAAGAATTGAAATGGAAAT
1 AAAGAAATGAAATGGAAAT
55659 AAATGTTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.25, T:0.17
Consensus pattern (21 bp):
AAAGAAATGAAATGGAAATGG
Found at i:55790 original size:11 final size:11
Alignment explanation
Indices: 55755--55783 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
55745 GAATATCTTG
55755 ATGATGATTGA
1 ATGATGATTGA
55766 ATGATGATTGA
1 ATGATGATTGA
55777 ATGATGA
1 ATGATGA
55784 ATAAATGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.28, T:0.34
Consensus pattern (11 bp):
ATGATGATTGA
Found at i:55908 original size:36 final size:35
Alignment explanation
Indices: 55808--55919 Score: 136
Period size: 35 Copynumber: 3.2 Consensus size: 35
55798 ATTGGGGGTT
* * * *
55808 TTATAGGCGTGAAATCGTGATAGAAGATGGTTAGG
1 TTATAGGCGTGAAATAGTGATGGAAGATGGTGATG
* * *
55843 ATATAGGCGTGCAATAGTAATGGAAGATGGTGATG
1 TTATAGGCGTGAAATAGTGATGGAAGATGGTGATG
*
55878 TTATAGGCGTGAAAATGGTGATGGAAGATGGTGATG
1 TTATAGGCGTG-AAATAGTGATGGAAGATGGTGATG
55914 TT-TAGG
1 TTATAGG
55920 TAATATCTTA
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
35 42 0.65
36 23 0.35
ACGTcount: A:0.31, C:0.04, G:0.36, T:0.29
Consensus pattern (35 bp):
TTATAGGCGTGAAATAGTGATGGAAGATGGTGATG
Found at i:61563 original size:36 final size:35
Alignment explanation
Indices: 61464--61574 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 35
61454 TTGGGGGTAA
* * * *
61464 TATAGGCGTGAAATAGTGATAGAAGATGGTTAGGA
1 TATAGGCGTGAAATAGTGATGGAAGATGGTGATGT
* * *
61499 TATAGGTGTGCAATAGTAATGGAAGATGGTGATGT
1 TATAGGCGTGAAATAGTGATGGAAGATGGTGATGT
*
61534 TATAGGCGTGAAAATGGTGATGGAAGATGGTGATGT
1 TATAGGCGTG-AAATAGTGATGGAAGATGGTGATGT
61570 T-TAGG
1 TATAGG
61575 TAGTATCTTA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
35 41 0.64
36 23 0.36
ACGTcount: A:0.32, C:0.03, G:0.36, T:0.29
Consensus pattern (35 bp):
TATAGGCGTGAAATAGTGATGGAAGATGGTGATGT
Found at i:63278 original size:2 final size:2
Alignment explanation
Indices: 63271--63301 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
63261 AGTTATATTC
63271 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
63302 GTTATTATGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:64052 original size:47 final size:46
Alignment explanation
Indices: 63998--64128 Score: 140
Period size: 45 Copynumber: 2.8 Consensus size: 46
63988 TGAGAGCATT
** *
63998 TGGTGCCAACATGAGGAAGCACATCACCATTC-GCCAAGTGGAGAAAA
1 TGGTGCCAACATGAACAAG--CATCACCATTCGGCCAAGGGGAGAAAA
*
64045 TGGTGCCAAGATGAACAAGCATCACCATTCGGCCAAGGGGAGAAAA
1 TGGTGCCAACATGAACAAGCATCACCATTCGGCCAAGGGGAGAAAA
* * * * **
64091 TGGCGCC-ATATTAACAAGAATTGCCATTCGGCCAAGGG
1 TGGTGCCAACATGAACAAGCATCACCATTCGGCCAAGGG
64129 AGATGCCTTC
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
45 37 0.51
46 20 0.27
47 16 0.22
ACGTcount: A:0.34, C:0.23, G:0.27, T:0.16
Consensus pattern (46 bp):
TGGTGCCAACATGAACAAGCATCACCATTCGGCCAAGGGGAGAAAA
Found at i:64107 original size:45 final size:46
Alignment explanation
Indices: 64019--64128 Score: 143
Period size: 45 Copynumber: 2.4 Consensus size: 46
64009 TGAGGAAGCA
* *
64019 CATCACCATTC-GCCAAGTGGAGAAAATGGTGCCAAGATGAACAAG
1 CATCACCATTCGGCCAAGGGGAGAAAATGGCGCCAAGATGAACAAG
* *
64064 CATCACCATTCGGCCAAGGGGAGAAAATGGCGCC-ATATTAACAAG
1 CATCACCATTCGGCCAAGGGGAGAAAATGGCGCCAAGATGAACAAG
* **
64109 AATTGCCATTCGGCCAAGGG
1 CATCACCATTCGGCCAAGGG
64129 AGATGCCTTC
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
45 37 0.65
46 20 0.35
ACGTcount: A:0.35, C:0.24, G:0.25, T:0.16
Consensus pattern (46 bp):
CATCACCATTCGGCCAAGGGGAGAAAATGGCGCCAAGATGAACAAG
Found at i:77596 original size:23 final size:23
Alignment explanation
Indices: 77567--77614 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
77557 CACTTGGATT
77567 TGATGAATGAGTTTGAAAAATAA
1 TGATGAATGAGTTTGAAAAATAA
77590 TGATGAATGAGTTTGAAAAATAA
1 TGATGAATGAGTTTGAAAAATAA
77613 TG
1 TG
77615 CATCCATCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (23 bp):
TGATGAATGAGTTTGAAAAATAA
Found at i:82051 original size:20 final size:20
Alignment explanation
Indices: 82016--82078 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
82006 AGCATTTATC
*
82016 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
82035 TTCATTAAAAATCATGTATT
1 TTCATTAAAAATCATGTATT
*
82055 TTCATTAAAAATCATGTCTT
1 TTCATTAAAAATCATGTATT
82075 TTCA
1 TTCA
82079 AAGGAGTTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
19 6 0.15
20 35 0.85
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.48
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:82853 original size:18 final size:19
Alignment explanation
Indices: 82825--82866 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
82815 AAGTGGGTGC
82825 AAAAAAGAAAAGA-AAGAAG
1 AAAAAAGAAAAGAGAA-AAG
*
82844 AAAAAA-AAAATAGAAAAG
1 AAAAAAGAAAAGAGAAAAG
82862 AAAAA
1 AAAAA
82867 GAACTCCTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.02
Consensus pattern (19 bp):
AAAAAAGAAAAGAGAAAAG
Done.