Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001171.1 Hibiscus syriacus cultivar Beakdansim tig00002334_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: 57319
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:1326 original size:24 final size:25
Alignment explanation
Indices: 1286--1336 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
1276 AGTACTAATC
1286 TTTAAAAAATCATCATAATTTAAAA
1 TTTAAAAAATCATCATAATTTAAAA
*
1311 TTTAAAATAAT-A-CATAATTTGAAA
1 TTTAAAA-AATCATCATAATTTAAAA
1335 TT
1 TT
1337 ATAATTTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 13 0.54
25 8 0.33
26 3 0.12
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (25 bp):
TTTAAAAAATCATCATAATTTAAAA
Found at i:6175 original size:19 final size:19
Alignment explanation
Indices: 6153--6190 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
6143 ATAATTTGAT
6153 AAATTTAAAATAA-ATTTTA
1 AAATTT-AAATAATATTTTA
*
6172 AAATTTTAATAATATTTTA
1 AAATTTAAATAATATTTTA
6191 TAATATTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAATTTAAATAATATTTTA
Found at i:6179 original size:20 final size:21
Alignment explanation
Indices: 6135--6185 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
6125 TTCAAATATT
*
6135 ATTTTATAAT-AATTTGATAA
1 ATTTTAAAATAAATTTGATAA
*
6155 A-TTTAAAATAAATTTTA-AA
1 ATTTTAAAATAAATTTGATAA
6174 ATTTTAATAATA
1 ATTTTAA-AATA
6186 TTTTATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 10 0.38
20 12 0.46
21 4 0.15
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
ATTTTAAAATAAATTTGATAA
Found at i:23519 original size:104 final size:101
Alignment explanation
Indices: 23324--23525 Score: 302
Period size: 98 Copynumber: 2.0 Consensus size: 101
23314 CGAGTATGAA
* *
23324 GTAGTTCGTTTCTACTTGTTAAGAACTCGAATCAAGCTTGAGTTCGAGTCCGAGCTCAAGTCGAA
1 GTAGCTCGTTTCTACTTGTTAAAAACTCGAATCAAGCTTGAGTT---GTCCGAGCTCAAGTCGAA
* *
23389 TATTTATCAAGCTTTGATCGAGTCAAACTCAAATAACTT
63 TATTTATAAAACTTTGATCGAGTCAAACTCAAATAACTT
* *
23428 GTAGCTCGTTTCTACTTGTTAAAAACTCGAATCGAGCTTGAG-T-T-CGAGCTCGAGTCGAATAT
1 GTAGCTCGTTTCTACTTGTTAAAAACTCGAATCAAGCTTGAGTTGTCCGAGCTCAAGTCGAATAT
23490 TTATAAAACTTTGATCGAGTCAAACTCAAATAACTT
66 TTATAAAACTTTGATCGAGTCAAACTCAAATAACTT
23526 ACAATCTGAT
Statistics
Matches: 92, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
98 51 0.55
99 1 0.01
103 1 0.01
104 39 0.42
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Consensus pattern (101 bp):
GTAGCTCGTTTCTACTTGTTAAAAACTCGAATCAAGCTTGAGTTGTCCGAGCTCAAGTCGAATAT
TTATAAAACTTTGATCGAGTCAAACTCAAATAACTT
Found at i:32524 original size:80 final size:80
Alignment explanation
Indices: 32391--32551 Score: 304
Period size: 80 Copynumber: 2.0 Consensus size: 80
32381 ATTATTGTTC
*
32391 AACTATGGTTGACATCAGACACTCCATATAGTTTAGGTAAACTAACCTTGAAATTAAAACGAGCA
1 AACTATGGTTAACATCAGACACTCCATATAGTTTAGGTAAACTAACCTTGAAATTAAAACGAGCA
32456 AGAGTCTGCAAAGCA
66 AGAGTCTGCAAAGCA
*
32471 AACTATGGTTAACATCAGACACTCCATATAGTTTCGGTAAACTAACCTTGAAATTAAAACGAGCA
1 AACTATGGTTAACATCAGACACTCCATATAGTTTAGGTAAACTAACCTTGAAATTAAAACGAGCA
32536 AGAGTCTGCAAAGCA
66 AGAGTCTGCAAAGCA
32551 A
1 A
32552 GCTGAACAAG
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (80 bp):
AACTATGGTTAACATCAGACACTCCATATAGTTTAGGTAAACTAACCTTGAAATTAAAACGAGCA
AGAGTCTGCAAAGCA
Found at i:49779 original size:19 final size:19
Alignment explanation
Indices: 49757--49794 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
49747 ATAATTTGAT
49757 AAATTTAAAATAA-ATTTTA
1 AAATTT-AAATAATATTTTA
*
49776 AAATTTTAATAATATTTTA
1 AAATTTAAATAATATTTTA
49795 TAATATTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAATTTAAATAATATTTTA
Found at i:49783 original size:20 final size:21
Alignment explanation
Indices: 49739--49789 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
49729 TTCAAATATT
*
49739 ATTTTATAAT-AATTTGATAA
1 ATTTTAAAATAAATTTGATAA
*
49759 A-TTTAAAATAAATTTTA-AA
1 ATTTTAAAATAAATTTGATAA
49778 ATTTTAATAATA
1 ATTTTAA-AATA
49790 TTTTATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 10 0.38
20 12 0.46
21 4 0.15
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
ATTTTAAAATAAATTTGATAA
Done.