Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003472.1 Hibiscus syriacus cultivar Beakdansim tig00007343_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: 62761
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:12601 original size:54 final size:54
Alignment explanation
Indices: 12535--12644 Score: 166
Period size: 54 Copynumber: 2.0 Consensus size: 54
12525 CGGTTACATC
* *
12535 GGTTAATTGTTACGATTAACAGTAACAGATTAATTTAAACACCCCTAACATGTA
1 GGTTAATAGTTACAATTAACAGTAACAGATTAATTTAAACACCCCTAACATGTA
* * * *
12589 GGTTAATAGTTACAATTAACGGTAGCGGATTAATTTGAACACCCCTAACATGTA
1 GGTTAATAGTTACAATTAACAGTAACAGATTAATTTAAACACCCCTAACATGTA
12643 GG
1 GG
12645 GCTCTTATTA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.30
Consensus pattern (54 bp):
GGTTAATAGTTACAATTAACAGTAACAGATTAATTTAAACACCCCTAACATGTA
Found at i:12873 original size:69 final size:70
Alignment explanation
Indices: 12738--12882 Score: 177
Period size: 69 Copynumber: 2.1 Consensus size: 70
12728 TGGTTTTTCT
* * * * *
12738 TTAATATGTGTCTCTATCGATCACATGTAACATTGATTATGTCGCATGCATATCCAGGTTCCTGG
1 TTAATATGTGTCTCTATCGATCACATGCAACATTGATTATGTCACATACATATCCAGATTCATGG
12803 AATTA
66 AATTA
* * * *
12808 TTAATCTGT-TCTCTATC-AGTCACATGCAACATTGATTATGTCACATATATCTCCATATTCATG
1 TTAATATGTGTCTCTATCGA-TCACATGCAACATTGATTATGTCACATACATATCCAGATTCATG
12871 GAATTA
65 GAATTA
*
12877 GTAATA
1 TTAATA
12883 CAACTTAATT
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
68 1 0.02
69 54 0.86
70 8 0.13
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (70 bp):
TTAATATGTGTCTCTATCGATCACATGCAACATTGATTATGTCACATACATATCCAGATTCATGG
AATTA
Found at i:14101 original size:46 final size:46
Alignment explanation
Indices: 14031--14120 Score: 153
Period size: 46 Copynumber: 2.0 Consensus size: 46
14021 ACAACCGGAG
*
14031 GTCAATGCTAAGCAATATCGTAAATGATGCATGCAAAGTATTAACA
1 GTCAATGCTAAGCAATATCATAAATGATGCATGCAAAGTATTAACA
* *
14077 GTCAATGGTAAGTAATATCATAAATGATGCATGCAAAGTATTAA
1 GTCAATGCTAAGCAATATCATAAATGATGCATGCAAAGTATTAA
14121 AGGTCTGGAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (46 bp):
GTCAATGCTAAGCAATATCATAAATGATGCATGCAAAGTATTAACA
Found at i:20026 original size:199 final size:198
Alignment explanation
Indices: 19687--20080 Score: 623
Period size: 199 Copynumber: 2.0 Consensus size: 198
19677 TGGCACTACA
* *
19687 GTGGTTGTGTCTCTTCTTTTGTTCTTTCATTTGCCTCACATCAAGAGATATTAAACTTACTAGTG
1 GTGGTTGTGTCTCTTCTTTTGTTCTTTCACTTGCCTCACATCAAGAGATATTAAACTTACTAATG
*
19752 AAACATGGTTCTCCAGATACATAAAGGAGCATTGCTGATTCTTTTCCGTTTCTTTATCTTGTTCC
66 AAACATGGTTCTCCAGAAACATAAAGGAGCATTGCTGATTCTTTTCCGTTTCTTTATCTTGTTCC
* * *
19817 TGGAGGTCATAGCG-TATAGATATACATGTACCTTAGT-TGTTTTGCTTTTCCACCTTTGCTCAC
131 TGGAGGTCATAG-GATATAGATACACATATACCTGA-TCTGTTTTGCTTTTCCACCTTTGCTCAC
19880 TTTCG
194 TTTCG
* **
19885 GTGGTTGTGTCTCTTCTTTTGTTCTTTTGTACTT-CCTCATGTCAAGAGATATTAAACTTACTAA
1 GTGGTTGTGTCTCTTCTTTTGTTC-TTT-CACTTGCCTCACATCAAGAGATATTAAACTTACTAA
*
19949 TGAAACGTGGTTCTCCAGAAACATAAAGGAGCATTGCTGATTCTTTTCCGTTTCTTTATCTTGTT
64 TGAAACATGGTTCTCCAGAAACATAAAGGAGCATTGCTGATTCTTTTCCGTTTCTTTATCTTGTT
* *
20014 CCTGGAGGTCATAGGATATATATACACATATATCTGATCTGTTTTGCTTTTCCACCTTTGCTCAC
129 CCTGGAGGTCATAGGATATAGATACACATATACCTGATCTGTTTTGCTTTTCCACCTTTGCTCAC
20079 TT
194 TT
20081 GCAGGATGGA
Statistics
Matches: 180, Mismatches: 12, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
198 26 0.14
199 151 0.84
200 3 0.02
ACGTcount: A:0.21, C:0.20, G:0.17, T:0.42
Consensus pattern (198 bp):
GTGGTTGTGTCTCTTCTTTTGTTCTTTCACTTGCCTCACATCAAGAGATATTAAACTTACTAATG
AAACATGGTTCTCCAGAAACATAAAGGAGCATTGCTGATTCTTTTCCGTTTCTTTATCTTGTTCC
TGGAGGTCATAGGATATAGATACACATATACCTGATCTGTTTTGCTTTTCCACCTTTGCTCACTT
TCG
Found at i:34082 original size:38 final size:34
Alignment explanation
Indices: 34040--34112 Score: 92
Period size: 34 Copynumber: 2.0 Consensus size: 34
34030 TTTAAATTTT
34040 TTTTAAATCATCTTATTTATTTATTTGAAATAATATTA
1 TTTTAAATCATC-TATTTA---ATTTGAAATAATATTA
* *
34078 TTTTAAATTATCTATTTAATTTTAAATAATATTA
1 TTTTAAATCATCTATTTAATTTGAAATAATATTA
34112 T
1 T
34113 ACGGAATCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 16 0.48
37 6 0.18
38 11 0.33
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.56
Consensus pattern (34 bp):
TTTTAAATCATCTATTTAATTTGAAATAATATTA
Found at i:34211 original size:17 final size:17
Alignment explanation
Indices: 34165--34221 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
34155 CCTAAATTTA
*
34165 AATTATTTAAAATTAAAT
1 AATTATTTTAAA-TAAAT
*
34183 AGA-TAATTTAAA-AAAT
1 A-ATTATTTTAAATAAAT
34199 ATATTATTTTAAATAAAT
1 A-ATTATTTTAAATAAAT
34217 AATTA
1 AATTA
34222 ATTGAGTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
16 6 0.19
17 12 0.38
18 13 0.41
19 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
AATTATTTTAAATAAAT
Found at i:37745 original size:28 final size:28
Alignment explanation
Indices: 37711--37766 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
37701 AGTTTTTTTA
37711 TATGTATTTAATATAATTCGAATTTACG
1 TATGTATTTAATATAATTCGAATTTACG
37739 TATGTATTTAATATAATTCGAATTTACG
1 TATGTATTTAATATAATTCGAATTTACG
37767 AGAGTTTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.46
Consensus pattern (28 bp):
TATGTATTTAATATAATTCGAATTTACG
Found at i:45751 original size:34 final size:34
Alignment explanation
Indices: 45713--45780 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
45703 TGATATTTTA
*
45713 TTTTAGTATTTTACGTATAGGTACAAAAATGATC
1 TTTTAGTATTTTACGTATACGTACAAAAATGATC
*
45747 TTTTAGTATTTTACGTATACGTACATAAATGATC
1 TTTTAGTATTTTACGTATACGTACAAAAATGATC
45781 CATTGACTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (34 bp):
TTTTAGTATTTTACGTATACGTACAAAAATGATC
Found at i:46120 original size:29 final size:29
Alignment explanation
Indices: 46086--46153 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 29
46076 AAACATAATA
46086 AATAGTCGAGTGACCAGTTTGTAATTTTT
1 AATAGTCGAGTGACCAGTTTGTAATTTTT
* *
46115 AATAGTAGAGTGATCAGTTTGTAATTTTT
1 AATAGTCGAGTGACCAGTTTGTAATTTTT
46144 AATAGTCGAG
1 AATAGTCGAG
46154 AGACTCAACA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.31, C:0.07, G:0.22, T:0.40
Consensus pattern (29 bp):
AATAGTCGAGTGACCAGTTTGTAATTTTT
Done.