Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004820.1 Hibiscus syriacus cultivar Beakdansim tig00010863_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: 79710
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1482 original size:14 final size:14
Alignment explanation
Indices: 1448--1476 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1438 AATTATATAG
1448 AAGAAA-AATACAT
1 AAGAAATAATACAT
1461 AAGAAATAATACAT
1 AAGAAATAATACAT
1475 AA
1 AA
1477 CGAATATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.69, C:0.07, G:0.07, T:0.17
Consensus pattern (14 bp):
AAGAAATAATACAT
Found at i:6655 original size:42 final size:42
Alignment explanation
Indices: 6608--6703 Score: 192
Period size: 42 Copynumber: 2.3 Consensus size: 42
6598 TTACATGGGC
6608 TCAACAGCAGCAACTTCAGCAGTTATTGCAGACTCCTTTAAA
1 TCAACAGCAGCAACTTCAGCAGTTATTGCAGACTCCTTTAAA
6650 TCAACAGCAGCAACTTCAGCAGTTATTGCAGACTCCTTTAAA
1 TCAACAGCAGCAACTTCAGCAGTTATTGCAGACTCCTTTAAA
6692 TCAACAGCAGCA
1 TCAACAGCAGCA
6704 GCAATCCCTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (42 bp):
TCAACAGCAGCAACTTCAGCAGTTATTGCAGACTCCTTTAAA
Found at i:6723 original size:45 final size:42
Alignment explanation
Indices: 6608--6725 Score: 121
Period size: 42 Copynumber: 2.7 Consensus size: 42
6598 TTACATGGGC
* * **
6608 TCAACAGCAGCAACTTCAGCAGTTATTGCAGACTCCTTTAAA
1 TCAACAGCAGCAAATCCAGCAGCAATTGCAGACTCCTTTAAA
* * **
6650 TCAACAGCAGCAACTTCAGCAGTTATTGCAGACTCCTTTAAA
1 TCAACAGCAGCAAATCCAGCAGCAATTGCAGACTCCTTTAAA
6692 TCAACAGCAGCAGCAATCCCTA-CAGCAATTGCAG
1 TCAACAGCAGCA--AAT-CC-AGCAGCAATTGCAG
6726 CGACATCAAC
Statistics
Matches: 68, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
42 54 0.79
44 2 0.03
45 11 0.16
46 1 0.01
ACGTcount: A:0.34, C:0.28, G:0.15, T:0.23
Consensus pattern (42 bp):
TCAACAGCAGCAAATCCAGCAGCAATTGCAGACTCCTTTAAA
Found at i:9718 original size:2 final size:2
Alignment explanation
Indices: 9711--9746 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
9701 AATTCAATTA
9711 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
9747 GTCATGTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17664 original size:19 final size:16
Alignment explanation
Indices: 17628--17661 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
17618 TGCAATTTTT
17628 CATCTATGAGAACCAC
1 CATCTATGAGAACCAC
17644 CATCTATGAGAACCAC
1 CATCTATGAGAACCAC
17660 CA
1 CA
17662 CCACCAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.32, G:0.12, T:0.18
Consensus pattern (16 bp):
CATCTATGAGAACCAC
Found at i:21329 original size:20 final size:20
Alignment explanation
Indices: 21284--21334 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
21274 TATTCATTAA
*
21284 AGTTTTAAAATTTACAAAAT
1 AGTTATAAAATTTACAAAAT
* *
21304 AGTTATTAAATTTATCAAATT
1 AGTTATAAAATTTA-CAAAAT
21325 A-TTATAAAAT
1 AGTTATAAAAT
21335 GATCATTGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 20 0.77
21 6 0.23
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (20 bp):
AGTTATAAAATTTACAAAAT
Found at i:38924 original size:23 final size:23
Alignment explanation
Indices: 38897--38973 Score: 68
Period size: 23 Copynumber: 3.2 Consensus size: 23
38887 AAAAGATTAT
38897 AAATAATTTAAGTATTGTATAGAA
1 AAATAATTTAAGTATTGTATAG-A
* *
38921 AATACTAATTATAA-TATATATATA-T
1 AA-A-TAATT-TAAGTAT-TGTATAGA
*
38946 ATATAATTTAAGTATTGTATAGA
1 AAATAATTTAAGTATTGTATAGA
38969 AAATA
1 AAATA
38974 CTAATTATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
22 8 0.20
23 12 0.29
24 3 0.07
25 2 0.05
26 8 0.20
27 8 0.20
ACGTcount: A:0.51, C:0.01, G:0.08, T:0.40
Consensus pattern (23 bp):
AAATAATTTAAGTATTGTATAGA
Found at i:38930 original size:26 final size:26
Alignment explanation
Indices: 38900--38979 Score: 96
Period size: 26 Copynumber: 3.2 Consensus size: 26
38890 AGATTATAAA
38900 TAATTTAAGTATTGTATAGAAAATAC
1 TAATTTAAGTATTGTATAGAAAATAC
* * *
38926 TAATTATAA-TA-TATATA-TATATA-
1 TAATT-TAAGTATTGTATAGAAAATAC
38949 TAATTTAAGTATTGTATAGAAAATAC
1 TAATTTAAGTATTGTATAGAAAATAC
38975 TAATT
1 TAATT
38980 ATAATATATA
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
22 3 0.07
23 7 0.16
24 9 0.21
25 9 0.21
26 12 0.28
27 3 0.07
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (26 bp):
TAATTTAAGTATTGTATAGAAAATAC
Found at i:38956 original size:49 final size:49
Alignment explanation
Indices: 38894--38999 Score: 203
Period size: 49 Copynumber: 2.2 Consensus size: 49
38884 TAAAAAAGAT
*
38894 TATAAATAATTTAAGTATTGTATAGAAAATACTAATTATAATATATATA
1 TATATATAATTTAAGTATTGTATAGAAAATACTAATTATAATATATATA
38943 TATATATAATTTAAGTATTGTATAGAAAATACTAATTATAATATATATA
1 TATATATAATTTAAGTATTGTATAGAAAATACTAATTATAATATATATA
38992 TATATATA
1 TATATATA
39000 TAGATACATA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 56 1.00
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (49 bp):
TATATATAATTTAAGTATTGTATAGAAAATACTAATTATAATATATATA
Found at i:41735 original size:2 final size:2
Alignment explanation
Indices: 41728--41755 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
41718 CTAAATGTAC
41728 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
41756 GGCATAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:45686 original size:21 final size:20
Alignment explanation
Indices: 45662--45703 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
45652 ATTTATATCC
45662 ATATATAAAAATATACTATTT
1 ATATATAAAAATATA-TATTT
**
45683 ATATATATTAATATATATTT
1 ATATATAAAAATATATATTT
45703 A
1 A
45704 ATAAAATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
ATATATAAAAATATATATTT
Found at i:49250 original size:126 final size:128
Alignment explanation
Indices: 49024--49254 Score: 281
Period size: 126 Copynumber: 1.8 Consensus size: 128
49014 ACACACTATT
* * ** * *
49024 GATGTGGATTTGAAAACAGCCTAGTAGGGGGTTGTCCAGACATGTGGAACGCACCACAGACATGT
1 GATGTGGATTTGAAAACAACCTACTAGGGGGTTGTCCAGACATGCAGAAAGCACCACACACATGT
* *
49089 ATTTATCTTATTAGCCAAATGGCACACAAGTAGTTAAAAGACCTATAAGAAACTCACATTGTC
66 ATTTATCTTATTAGCCAAAGGGCACACAAGCAGTTAAAAGACCTATAAGAAACTCACATTGTC
* *
49152 GATGTGGATTTGAAAA-AATCT-CTAGGGGGTTGTCCGGACATGCAGAAAGCACCACACACATGT
1 GATGTGGATTTGAAAACAACCTACTAGGGGGTTGTCCAGACATGCAGAAAGCACCACACACATGT
* * * * *
49215 TTTTACTTTTTTTA-CCAAAGGGACACGCTA-CAGTTAAAAG
66 ATTTA-TCTTATTAGCCAAAGGG-CACACAAGCAGTTAAAAG
49255 CTAGCTTGCT
Statistics
Matches: 86, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
126 56 0.65
127 14 0.16
128 16 0.19
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (128 bp):
GATGTGGATTTGAAAACAACCTACTAGGGGGTTGTCCAGACATGCAGAAAGCACCACACACATGT
ATTTATCTTATTAGCCAAAGGGCACACAAGCAGTTAAAAGACCTATAAGAAACTCACATTGTC
Found at i:52812 original size:13 final size:15
Alignment explanation
Indices: 52794--52826 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
52784 TTTTTTATCA
52794 TAAAAT-AAAAT-GT
1 TAAAATCAAAATAGT
52807 TAAAATCAAAATAGT
1 TAAAATCAAAATAGT
52822 TAAAA
1 TAAAA
52827 ATAATCAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 5 0.28
15 7 0.39
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.27
Consensus pattern (15 bp):
TAAAATCAAAATAGT
Found at i:53946 original size:31 final size:31
Alignment explanation
Indices: 53911--53981 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
53901 AAAATTGAAG
*
53911 GACCATTTTGTAAAAATTTCATAGATTTATT
1 GACCATTTTGTAAAAATTTCATAAATTTATT
* *
53942 GACCATTTTGTAATAATTTCTTAAATTTATT
1 GACCATTTTGTAAAAATTTCATAAATTTATT
*
53973 GACTATTTT
1 GACCATTTT
53982 ATATTACTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.32, C:0.10, G:0.08, T:0.49
Consensus pattern (31 bp):
GACCATTTTGTAAAAATTTCATAAATTTATT
Done.