Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001539.1 Hibiscus syriacus cultivar Beakdansim tig00003023_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: 77360
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Found at i:11483 original size:6 final size:6
Alignment explanation
Indices: 11472--11500 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
11462 GAAATTAATC
11472 AGAGAA AGAGAA AGAGAA AGAGAA AGAGA
1 AGAGAA AGAGAA AGAGAA AGAGAA AGAGA
11501 GAAAACCTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (6 bp):
AGAGAA
Found at i:12657 original size:22 final size:22
Alignment explanation
Indices: 12632--12680 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
12622 ATTATATTTA
*
12632 ATAAAAGGCATTCATAACAATT
1 ATAAAAGACATTCATAACAATT
*
12654 ATAAAAGACATTCATAACAGTT
1 ATAAAAGACATTCATAACAATT
12676 ATAAA
1 ATAAA
12681 CCAATTCACC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.53, C:0.12, G:0.08, T:0.27
Consensus pattern (22 bp):
ATAAAAGACATTCATAACAATT
Found at i:14713 original size:15 final size:16
Alignment explanation
Indices: 14693--14733 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
14683 ACCTAACCCA
14693 AACCGTTGACCC-TTT
1 AACCGTTGACCCGTTT
14708 AACCGTTGACCCGTTT
1 AACCGTTGACCCGTTT
*
14724 AACCATTGAC
1 AACCGTTGAC
14734 TTTGACCAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.24, C:0.32, G:0.15, T:0.29
Consensus pattern (16 bp):
AACCGTTGACCCGTTT
Found at i:21035 original size:15 final size:16
Alignment explanation
Indices: 21015--21053 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
21005 TTTGTTCATC
21015 TTTTTTAAAAT-TCAA
1 TTTTTTAAAATGTCAA
*
21030 TTTTTT-AAGTGTCAA
1 TTTTTTAAAATGTCAA
21045 TTTTTTAAA
1 TTTTTTAAA
21054 GTCATTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 3 0.14
15 16 0.76
16 2 0.10
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.56
Consensus pattern (16 bp):
TTTTTTAAAATGTCAA
Found at i:21057 original size:14 final size:14
Alignment explanation
Indices: 21015--21062 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
21005 TTTGTTCATC
*
21015 TTTTTTAAAATTCAA
1 TTTTTT-AAAGTCAA
*
21030 TTTTTTAAGTGTCAA
1 TTTTTTAA-AGTCAA
21045 TTTTTTAAAGTC-A
1 TTTTTTAAAGTCAA
21058 TTTTT
1 TTTTT
21063 AATGCATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 6 0.21
14 5 0.17
15 18 0.62
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.58
Consensus pattern (14 bp):
TTTTTTAAAGTCAA
Found at i:21874 original size:62 final size:62
Alignment explanation
Indices: 21796--21925 Score: 190
Period size: 62 Copynumber: 2.1 Consensus size: 62
21786 AAATAGGTAC
* * *
21796 CGATACCCAAAGGGGTACAAATATTACTTTACATAGTAGTATCAATACCATGAAT-ATAGTAT
1 CGATACCCAAAGGGGTACAAATACTACTTTACACAATAGTATCAATACCATG-ATCATAGTAT
* *
21858 CGATACCCAAAGGGGTACCAATACTACTTTACACAATAGTATCGATACCATGATCATAGTAT
1 CGATACCCAAAGGGGTACAAATACTACTTTACACAATAGTATCAATACCATGATCATAGTAT
*
21920 TGATAC
1 CGATAC
21926 TAGTCAGGCT
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
61 2 0.03
62 59 0.97
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (62 bp):
CGATACCCAAAGGGGTACAAATACTACTTTACACAATAGTATCAATACCATGATCATAGTAT
Found at i:23629 original size:21 final size:21
Alignment explanation
Indices: 23612--23693 Score: 96
Period size: 21 Copynumber: 3.9 Consensus size: 21
23602 GGGAGTATTG
23612 ATACTCCA-CTAAGTAGTATAA
1 ATACTCCATC-AAGTAGTATAA
* *
23633 ATACTTCATCAGGTAGTATAA
1 ATACTCCATCAAGTAGTATAA
* *
23654 ATACTCCA-CTAGGTAGTATAG
1 ATACTCCATC-AAGTAGTATAA
23675 ATACTCCATCAAGTAGTAT
1 ATACTCCATCAAGTAGTAT
23694 TTGTACTCTA
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
20 1 0.02
21 50 0.94
22 2 0.04
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.30
Consensus pattern (21 bp):
ATACTCCATCAAGTAGTATAA
Found at i:23664 original size:42 final size:42
Alignment explanation
Indices: 23612--23693 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
23602 GGGAGTATTG
* *
23612 ATACTCCACTAAGTAGTATAAATACTTCATCAGGTAGTATAA
1 ATACTCCACTAAGTAGTATAAATACTCCATCAAGTAGTATAA
* *
23654 ATACTCCACTAGGTAGTATAGATACTCCATCAAGTAGTAT
1 ATACTCCACTAAGTAGTATAAATACTCCATCAAGTAGTAT
23694 TTGTACTCTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.30
Consensus pattern (42 bp):
ATACTCCACTAAGTAGTATAAATACTCCATCAAGTAGTATAA
Found at i:23701 original size:42 final size:42
Alignment explanation
Indices: 23605--23701 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 42
23595 GATGTTAGGG
* *
23605 AGTA-TTGATACTCCACTAAGTAGTATAAATACTTCATCAGGT
1 AGTATTTG-TACTCCACTAAGTAGTATAAATACTCCATCAAGT
*** * *
23647 AGTATAAATACTCCACTAGGTAGTATAGATACTCCATCAAGT
1 AGTATTTGTACTCCACTAAGTAGTATAAATACTCCATCAAGT
23689 AGTATTTGTACTC
1 AGTATTTGTACTC
23702 TATGGGGTGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (42 bp):
AGTATTTGTACTCCACTAAGTAGTATAAATACTCCATCAAGT
Found at i:31026 original size:21 final size:21
Alignment explanation
Indices: 31000--31054 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
30990 TCTGGGCTAT
31000 GTGCATCGATGCACATTCAAG
1 GTGCATCGATGCACATTCAAG
31021 GTGCATCGATGCACATTCAAG
1 GTGCATCGATGCACATTCAAG
* *
31042 GTACACCGATGCA
1 GTGCATCGATGCA
31055 TCAAGGGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.22
Consensus pattern (21 bp):
GTGCATCGATGCACATTCAAG
Found at i:32833 original size:23 final size:23
Alignment explanation
Indices: 32807--32869 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
32797 AACTTTATAT
*
32807 GGCACTTCGGTGCATTTCTATGC
1 GGCACTTCGGTGCATTTCTACGC
* * * *
32830 GGCACTACGGTGAAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
32853 GGCACTTCGGTGCATTT
1 GGCACTTCGGTGCATTT
32870 ATACAAGCTG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.17, C:0.24, G:0.27, T:0.32
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:36240 original size:21 final size:21
Alignment explanation
Indices: 36214--36268 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
36204 TATGGGCTAT
36214 GTGCATCGATGCACATTCAAG
1 GTGCATCGATGCACATTCAAG
36235 GTGCATCGATGCACATTCAAG
1 GTGCATCGATGCACATTCAAG
*
36256 GTGCACCGATGCA
1 GTGCATCGATGCA
36269 TCAAGGGTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.22
Consensus pattern (21 bp):
GTGCATCGATGCACATTCAAG
Found at i:37621 original size:2 final size:2
Alignment explanation
Indices: 37614--37650 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
37604 GAACATGTGA
37614 AT AT AT 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 AT AT AT A
37651 GGATAAGACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41267 original size:23 final size:23
Alignment explanation
Indices: 41199--41267 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
41189 TAACCTTATA
*
41199 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTATACG
* * * * *
41222 CGGTACTACGGTGCAATTGTACG
1 TGGCACTTCGGTGCATTTATACG
41245 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTATACG
41268 AGCTGTGGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.17, C:0.23, G:0.28, T:0.32
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTATACG
Found at i:42659 original size:7 final size:6
Alignment explanation
Indices: 42640--42666 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
42630 CACAAGATAT
42640 AATAAA AATAAA AATAAA AATAAA AAT
1 AATAAA AATAAA AATAAA AATAAA AAT
42667 TAAATTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
AATAAA
Found at i:42680 original size:7 final size:7
Alignment explanation
Indices: 42670--42696 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
42660 TAAAAATTAA
42670 ATTTATT
1 ATTTATT
42677 ATTTATT
1 ATTTATT
42684 ATTTATT
1 ATTTATT
42691 ATTTAT
1 ATTTAT
42697 GCGCAATCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
ATTTATT
Found at i:46865 original size:41 final size:42
Alignment explanation
Indices: 46784--46868 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
46774 TTTTTAGATA
*
46784 GTTTTACTTTTTAGTTTTCTTATCTTTTTCAGGTTTTTCGCG
1 GTTTTACTTTTTAGTTTCCTTATCTTTTTCAGGTTTTTCGCG
*
46826 GTTTTACTTTTTAGTTTCCTTAT-TTTTTCATGTTTTTCGCG
1 GTTTTACTTTTTAGTTTCCTTATCTTTTTCAGGTTTTTCGCG
46867 GT
1 GT
46869 GTATGACCAG
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 19 0.46
42 22 0.54
ACGTcount: A:0.09, C:0.14, G:0.14, T:0.62
Consensus pattern (42 bp):
GTTTTACTTTTTAGTTTCCTTATCTTTTTCAGGTTTTTCGCG
Found at i:76246 original size:83 final size:83
Alignment explanation
Indices: 76139--76305 Score: 257
Period size: 83 Copynumber: 2.0 Consensus size: 83
76129 GGGTTCGAAT
**
76139 CATCCATGAAAGATTCATAGAAATCATTCGTTCTAACAACCCAAATCAAATGAGAAATAATGTCA
1 CATCCATGAAAGATTCATAGAAATCATTCGTTCTAACAACCCAAATC-AATGAGAAATAACATCA
76204 AA-GGGAGGAGGAAGAAGC
65 AAGGGGAGGAGGAAGAAGC
*
76222 CATCCATGAAAAGATTC-TATAAATCATTCGTTCTAACAACCCAAATCAATGAGAAATAACATCA
1 CATCCATG-AAAGATTCATAGAAATCATTCGTTCTAACAACCCAAATCAATGAGAAATAACATCA
* *
76286 AAGGGGATGAGGAATAAGC
65 AAGGGGAGGAGGAAGAAGC
76305 C
1 C
76306 TTCGAAGCGC
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
82 17 0.22
83 52 0.68
84 8 0.10
ACGTcount: A:0.44, C:0.18, G:0.17, T:0.20
Consensus pattern (83 bp):
CATCCATGAAAGATTCATAGAAATCATTCGTTCTAACAACCCAAATCAATGAGAAATAACATCAA
AGGGGAGGAGGAAGAAGC
Found at i:76371 original size:13 final size:13
Alignment explanation
Indices: 76353--76378 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
76343 GGTTTGCCTT
76353 AGCTCGCTAGCTC
1 AGCTCGCTAGCTC
76366 AGCTCGCTAGCTC
1 AGCTCGCTAGCTC
76379 CTCTAGGTCG
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:0.15, C:0.38, G:0.23, T:0.23
Consensus pattern (13 bp):
AGCTCGCTAGCTC
Done.