Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000875.1 Hibiscus syriacus cultivar Beakdansim tig00001694_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: 60045
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:6936 original size:137 final size:138
Alignment explanation
Indices: 6708--6962 Score: 390
Period size: 137 Copynumber: 1.9 Consensus size: 138
6698 GTATGTAATG
* * *
6708 GTTATTGATTGATTTTGTGTAATACATAATGGTGCATTTTCGTATCAGTACTATGTGTACTTTCG
1 GTTATCGATTGATTTTGTGTAATACATAACGGTGCATTTTCGTATCAGTACTAAGTGTACTTTCG
* *
6773 GCACTAGATATTCAACTATGGTATTCATAATGAGTTTGTGAATTACCATTTCGATATACAATTAT
66 GCACTAGATATTCAACCATGGAATTCATAATGAGTTTGTGAATTACCATTTCGATATACAATTAT
6838 GTATGAAA
131 GTATGAAA
* *
6846 GTTATCGATTGATTTTGTTTAATGCATAACGGTGCATTTT-GTATCAGTACTAAGTGTACTTTCG
1 GTTATCGATTGATTTTGTGTAATACATAACGGTGCATTTTCGTATCAGTACTAAGTGTACTTTCG
* *
6910 GCACTATG-T-TTGCATCCATGGAATTCATAATGAGTTTGTGAATTTCCATTTCG
66 GCACTA-GATATT-CAACCATGGAATTCATAATGAGTTTGTGAATTACCATTTCG
6963 GCACTTCGGT
Statistics
Matches: 106, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
136 2 0.02
137 67 0.63
138 37 0.35
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (138 bp):
GTTATCGATTGATTTTGTGTAATACATAACGGTGCATTTTCGTATCAGTACTAAGTGTACTTTCG
GCACTAGATATTCAACCATGGAATTCATAATGAGTTTGTGAATTACCATTTCGATATACAATTAT
GTATGAAA
Found at i:14245 original size:17 final size:16
Alignment explanation
Indices: 14223--14256 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
14213 TAAAGACAGT
14223 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
14240 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
14256 A
1 A
14257 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:23888 original size:16 final size:16
Alignment explanation
Indices: 23867--23905 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
23857 TAAACTATAC
23867 AAAAAAAAATGCAAAA
1 AAAAAAAAATGCAAAA
23883 AAAAAAAAATGCAAAA
1 AAAAAAAAATGCAAAA
23899 AAAAAAA
1 AAAAAAA
23906 TGCTCTGGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.85, C:0.05, G:0.05, T:0.05
Consensus pattern (16 bp):
AAAAAAAAATGCAAAA
Found at i:24306 original size:17 final size:16
Alignment explanation
Indices: 24284--24317 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
24274 GTAAAGACAT
24284 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
24301 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
24317 A
1 A
24318 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:35021 original size:24 final size:19
Alignment explanation
Indices: 34959--35008 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
34949 CATCCTTCAT
*
34959 TATATAAA-AAATTATCTAA
1 TATATAAATAAATAAT-TAA
34978 TATATAAATAAATAATTAA
1 TATATAAATAAATAATTAA
34997 TATATAATATAA
1 TATATAA-ATAA
35009 TTATAATAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 18 0.64
20 10 0.36
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
TATATAAATAAATAATTAA
Found at i:35454 original size:20 final size:21
Alignment explanation
Indices: 35429--35469 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
35419 GTCATCAAGT
*
35429 CTGTCAGATG-ATGTTGAAGA
1 CTGTCAGAGGAATGTTGAAGA
35449 CTGTCAGAGGAATGTTGAAGA
1 CTGTCAGAGGAATGTTGAAGA
35470 GTGCGAAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.32, C:0.10, G:0.32, T:0.27
Consensus pattern (21 bp):
CTGTCAGAGGAATGTTGAAGA
Found at i:44386 original size:64 final size:63
Alignment explanation
Indices: 44314--44433 Score: 168
Period size: 64 Copynumber: 1.9 Consensus size: 63
44304 ATTGTTCAAG
* * * *
44314 GTGTATCGATGCACATGAAGTGCATCGATGCACTACTTTAAAATAAAAACATCGAATGCCATCA
1 GTGTATCGATGCACAAGAAGTGCATCAATGCACCACCTT-AAATAAAAACATCGAATGCCATCA
* * *
44378 GTGTATCGATGCACAAGTAGTGCATCAATGCACCCCCTTAAATACAAACATCGAAT
1 GTGTATCGATGCACAAGAAGTGCATCAATGCACCACCTTAAATAAAAACATCGAAT
44434 AGGATTTATG
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
63 16 0.33
64 33 0.67
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.24
Consensus pattern (63 bp):
GTGTATCGATGCACAAGAAGTGCATCAATGCACCACCTTAAATAAAAACATCGAATGCCATCA
Found at i:44453 original size:63 final size:64
Alignment explanation
Indices: 44314--44475 Score: 170
Period size: 63 Copynumber: 2.5 Consensus size: 64
44304 ATTGTTCAAG
* * ** *
44314 GTGTATCGATGCACATGAAGTGCATCGATGCACTACTTTAAAATAAAAACATCGAATGCCATCA
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATCA
* * * *
44378 GTGTATCGATGCACAAGTAGTGCATCAATGCACCCCCTT-AAATACAAACATCGAATAG-GATTT
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAAT-GCCA-TC
44441 A
64 A
* *
44442 -TGTATCGATGCA-TAGATAGTACATCGATGCACCC
1 GTGTATCGATGCACAAG-TAGTGCATCGATGCACCC
44476 GTCAAGGGAT
Statistics
Matches: 83, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
62 2 0.02
63 45 0.54
64 36 0.43
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (64 bp):
GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATCA
Found at i:45696 original size:11 final size:11
Alignment explanation
Indices: 45680--45705 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
45670 ACTCGTATCC
45680 GGGTCGGATAT
1 GGGTCGGATAT
45691 GGGTCGGATAT
1 GGGTCGGATAT
45702 GGGT
1 GGGT
45706 TGAGAGTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.08, G:0.50, T:0.27
Consensus pattern (11 bp):
GGGTCGGATAT
Found at i:54060 original size:3 final size:3
Alignment explanation
Indices: 54046--54103 Score: 73
Period size: 3 Copynumber: 19.0 Consensus size: 3
54036 CTACAAAAAC
*
54046 ATT ATAT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AAT -TT ATAT
1 ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
*
54092 ATT ATA ATT ATT
1 ATT ATT ATT ATT
54104 TTACGGGCCC
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 1 0.02
3 41 0.85
4 6 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:56398 original size:26 final size:26
Alignment explanation
Indices: 56359--56409 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
56349 TAGTCTCTCG
56359 ACTATAGCACACTATTTTATTAAGTC
1 ACTATAGCACACTATTTTATTAAGTC
*
56385 ACTATAGCATACTATTTTATTAAGT
1 ACTATAGCACACTATTTTATTAAGT
56410 ATCATGATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (26 bp):
ACTATAGCACACTATTTTATTAAGTC
Done.