Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008850.1 Hibiscus syriacus cultivar Beakdansim tig00112060_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: 71152
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:8815 original size:42 final size:42
Alignment explanation
Indices: 8736--8815 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
8726 TGGATGGAGG
*** * *
8736 TGGTGCATTGATTGATGTGGTCTTGGGAGGTGGTGGTGATGC
1 TGGTGCATTGATTGATACAGTCTTGGGAGGAGATGGTGATGC
8778 TGGTGCATTGATTGATACAGTCTT-GGATGGAGATGGTG
1 TGGTGCATTGATTGATACAGTCTTGGGA-GGAGATGGTG
8816 CATTGTTGCT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 3 0.09
42 29 0.91
ACGTcount: A:0.16, C:0.07, G:0.41, T:0.35
Consensus pattern (42 bp):
TGGTGCATTGATTGATACAGTCTTGGGAGGAGATGGTGATGC
Found at i:16997 original size:48 final size:48
Alignment explanation
Indices: 16929--17224 Score: 295
Period size: 48 Copynumber: 6.3 Consensus size: 48
16919 CCGCTGTCAC
* * * *
16929 AGGGAATACCAAACCTTGGAAAAAAGAGATATGTTCCGCTT-CTTCTGA
1 AGGGAATATCAAATCTTGGAAAAAAGAGACATGTTCCACTTAC-TCTGA
*
16977 AGGGAATATCAAATCATGG-AAAAAGAGACATGTTCCACTTACTCTGA
1 AGGGAATATCAAATCTTGGAAAAAAGAGACATGTTCCACTTACTCTGA
* * * * * **
17024 AGGAAATATCAGATCTTGGAGAAGATAGATTTGTTCCACTTACTCTGA
1 AGGGAATATCAAATCTTGGAAAAAAGAGACATGTTCCACTTACTCTGA
* * * * *
17072 AGGGAATATCAAATCTTTGAGAAGAGAGACCTGTTCCGCTTACTCTGA
1 AGGGAATATCAAATCTTGGAAAAAAGAGACATGTTCCACTTACTCTGA
* * * *
17120 AGGGAATATCAGATC-TGG------CAGACTTGTTCCACTTACTCTAA
1 AGGGAATATCAAATCTTGGAAAAAAGAGACATGTTCCACTTACTCTGA
* * *
17161 AGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGA
1 AGGGAATATCAAATCTTGGAAAAAAGAGACATGTTCCACTTACTCTGA
*
17209 AGGGAATATCAGATCT
1 AGGGAATATCAAATCT
17225 GGGGGAGTTG
Statistics
Matches: 208, Mismatches: 31, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
41 33 0.16
42 3 0.01
47 42 0.20
48 130 0.62
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (48 bp):
AGGGAATATCAAATCTTGGAAAAAAGAGACATGTTCCACTTACTCTGA
Found at i:17164 original size:89 final size:89
Alignment explanation
Indices: 17054--17226 Score: 319
Period size: 89 Copynumber: 1.9 Consensus size: 89
17044 GAAGATAGAT
* * *
17054 TTGTTCCACTTACTCTGAAGGGAATATCAAATCTTTGAGAAGAGAGACCTGTTCCGCTTACTCTG
1 TTGTTCCACTTACTCTAAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTG
17119 AAGGGAATATCAGATCTGGCAGAC
66 AAGGGAATATCAGATCTGGCAGAC
17143 TTGTTCCACTTACTCTAAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTG
1 TTGTTCCACTTACTCTAAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTG
17208 AAGGGAATATCAGATCTGG
66 AAGGGAATATCAGATCTGG
17227 GGGAGTTGAT
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 81 1.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (89 bp):
TTGTTCCACTTACTCTAAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTG
AAGGGAATATCAGATCTGGCAGAC
Found at i:18385 original size:26 final size:25
Alignment explanation
Indices: 18354--18413 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
18344 CCCTCCTTTA
*
18354 TTTTTTTC-TTTTCTT-TCTCTTTCTT
1 TTTTTTTCATTTT-TTGTCT-TTTCAT
18379 TTATTTTTCATTTTTTGTCTTTTCAT
1 TT-TTTTTCATTTTTTGTCTTTTCAT
18405 TTTTTTTCA
1 TTTTTTTCA
18414 AGCAAAATAC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
25 9 0.29
26 15 0.48
27 7 0.23
ACGTcount: A:0.07, C:0.15, G:0.02, T:0.77
Consensus pattern (25 bp):
TTTTTTTCATTTTTTGTCTTTTCAT
Found at i:25315 original size:21 final size:21
Alignment explanation
Indices: 25289--25328 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
25279 CAGAACCCCA
*
25289 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
25310 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
25329 TCAAAGGGGG
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:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:25364 original size:21 final size:21
Alignment explanation
Indices: 25310--25372 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
25300 ATTCCCCTGT
25310 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTT-CCC-TCAA
* *
25333 AGGGGGAATCGGTTCCCTCAG
1 GGGGGGAATCGGTTCCCTCAA
* *
25354 GGGGGGGATCGATTCCCTC
1 GGGGGGAATCGGTTCCCTC
25373 TGCACAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 19 0.54
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.25, G:0.38, T:0.21
Consensus pattern (21 bp):
GGGGGGAATCGGTTCCCTCAA
Found at i:41264 original size:3 final size:3
Alignment explanation
Indices: 41250--41290 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
41240 AAATATGTAA
*
41250 AAT AAT ATT AAT AAT AAT AAT AAT ACAT -AT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AA
41291 GAACGAGATG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.88
4 2 0.06
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:44286 original size:45 final size:47
Alignment explanation
Indices: 44228--44317 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 47
44218 TCAAAATTTT
*
44228 ATATATTACATTTATT-AACGATCTAAATGAT-AAAAAATAATTATA
1 ATATATTAAATTTATTAAACGATCTAAATGATAAAAAAATAATTATA
* *
44273 ATATGTTAAATTTATTAAACGGTCTAAATGATAAAAAAATAATTA
1 ATATATTAAATTTATTAAACGATCTAAATGATAAAAAAATAATTA
44318 CTCTCTTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
45 14 0.35
46 14 0.35
47 12 0.30
ACGTcount: A:0.51, C:0.06, G:0.07, T:0.37
Consensus pattern (47 bp):
ATATATTAAATTTATTAAACGATCTAAATGATAAAAAAATAATTATA
Found at i:47068 original size:22 final size:24
Alignment explanation
Indices: 47041--47091 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
47031 AAAATATTAC
*
47041 TAAAAT-TATACTTA-TTTATAAT
1 TAAAATATATACGTATTTTATAAT
*
47063 TAAAATATTTACGTATTTTATAAT
1 TAAAATATATACGTATTTTATAAT
*
47087 AAAAA
1 TAAAA
47092 ATTTAAAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 6 0.25
23 6 0.25
24 12 0.50
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (24 bp):
TAAAATATATACGTATTTTATAAT
Found at i:48026 original size:43 final size:44
Alignment explanation
Indices: 47948--48034 Score: 149
Period size: 43 Copynumber: 2.0 Consensus size: 44
47938 GAATGACAAG
*
47948 CCTTTGAAAATTAGTATTTTTTTTTAATTTTATTAAATGAGGTT
1 CCTTTGAAAATTAGTATTTTTTTTAAATTTTATTAAATGAGGTT
*
47992 CCTTTGGAAATTAGTA-TTTTTTTAAATTTTATTAAATGAGGTT
1 CCTTTGAAAATTAGTATTTTTTTTAAATTTTATTAAATGAGGTT
48035 TTCATTATTC
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 26 0.63
44 15 0.37
ACGTcount: A:0.30, C:0.05, G:0.13, T:0.53
Consensus pattern (44 bp):
CCTTTGAAAATTAGTATTTTTTTTAAATTTTATTAAATGAGGTT
Found at i:51269 original size:4 final size:4
Alignment explanation
Indices: 51260--51286 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
51250 CAATGCATGT
51260 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
51287 TATAGTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:67780 original size:56 final size:56
Alignment explanation
Indices: 67684--67792 Score: 134
Period size: 56 Copynumber: 1.9 Consensus size: 56
67674 TTTGAAGATG
** *
67684 AAATTAAAATATTCAAAAGTTTAAGAATTGATTTAGAAT-AAAAATCATATTTAGAA
1 AAATTAAAATATTCAAAAGTTTAAGAATAAATTGAGAATAAAAAATCAT-TTTAGAA
*
67740 AAATTAAAATATTTAAAAGTTTAA-AGATCAAATTGA-AATAAAAAATCATTTTA
1 AAATTAAAATATTCAAAAGTTTAAGA-AT-AAATTGAGAATAAAAAATCATTTTA
67793 CCTGTAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
55 1 0.02
56 32 0.70
57 13 0.28
ACGTcount: A:0.55, C:0.04, G:0.07, T:0.34
Consensus pattern (56 bp):
AAATTAAAATATTCAAAAGTTTAAGAATAAATTGAGAATAAAAAATCATTTTAGAA
Done.