Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004181.1 Hibiscus syriacus cultivar Beakdansim tig00009145_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: 61897
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:10662 original size:29 final size:30
Alignment explanation
Indices: 10620--10683 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
10610 ACAAGCCTCA
* *
10620 GAAAAATTGGGGATCATTTCGT-AAGTTTG
1 GAAAAATTGGGGATAAATTCGTAAAGTTTG
* *
10649 GAAAAGTTGGGGATAAATTCGTAAATTTTG
1 GAAAAATTGGGGATAAATTCGTAAAGTTTG
10679 GAAAA
1 GAAAA
10684 TTGATGAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 19 0.63
30 11 0.37
ACGTcount: A:0.38, C:0.05, G:0.27, T:0.31
Consensus pattern (30 bp):
GAAAAATTGGGGATAAATTCGTAAAGTTTG
Found at i:12191 original size:47 final size:44
Alignment explanation
Indices: 12094--12207 Score: 149
Period size: 47 Copynumber: 2.5 Consensus size: 44
12084 GTAAGTATGC
12094 AAATAAGCTTACGAGCTTAT-GAATAATGACAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGGAATAATGACAAGTATATTGATA
* ** * *
12137 AAATAAGCTTACAAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--T-AATGACAAGTATATTGATA
12184 AAATAAGCTTACGAGCTTATGGAA
1 AAATAAGCTTACGAGCTTATGGAA
12208 AAAAAGGTAA
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
43 19 0.31
44 3 0.05
46 1 0.02
47 38 0.62
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGGAATAATGACAAGTATATTGATA
Found at i:13064 original size:17 final size:18
Alignment explanation
Indices: 13028--13083 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
13018 TGGTACAGTG
* *
13028 AAAGTAACATTATAAGAA
1 AAAGGAACAATATAAGAA
13046 AAAGGAACAATAT-AGAA
1 AAAGGAACAATATAAGAA
** *
13063 AATAAAAACAATAAAAGAA
1 AA-AGGAACAATATAAGAA
13082 AA
1 AA
13084 GAAATAGTCC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
17 6 0.19
18 19 0.61
19 6 0.19
ACGTcount: A:0.70, C:0.05, G:0.11, T:0.14
Consensus pattern (18 bp):
AAAGGAACAATATAAGAA
Found at i:17309 original size:13 final size:13
Alignment explanation
Indices: 17291--17324 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
17281 ATGGGCAAAT
*
17291 TTTGAAAACTATG
1 TTTGAAAACGATG
17304 TTTGAAAACGATG
1 TTTGAAAACGATG
17317 TTTGAAAA
1 TTTGAAAA
17325 ATTATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (13 bp):
TTTGAAAACGATG
Found at i:21170 original size:12 final size:12
Alignment explanation
Indices: 21153--21177 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21143 CCAACGTTTT
21153 TCTCCTTCTTTG
1 TCTCCTTCTTTG
21165 TCTCCTTCTTTG
1 TCTCCTTCTTTG
21177 T
1 T
21178 TTCGTCCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.32, G:0.08, T:0.60
Consensus pattern (12 bp):
TCTCCTTCTTTG
Found at i:22719 original size:35 final size:35
Alignment explanation
Indices: 22672--22756 Score: 125
Period size: 35 Copynumber: 2.4 Consensus size: 35
22662 AATGCATGGC
* *
22672 TGTGCATCGGTACACAAAATAGCTTTGATGTTGGG
1 TGTGCATCGGTACACAAAACAGATTTGATGTTGGG
* *
22707 TGTGCATTGGTACACAAAACATATTTGATGTTGGG
1 TGTGCATCGGTACACAAAACAGATTTGATGTTGGG
*
22742 TGTGCATCGATACAC
1 TGTGCATCGGTACAC
22757 TAAAGAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (35 bp):
TGTGCATCGGTACACAAAACAGATTTGATGTTGGG
Found at i:36946 original size:21 final size:19
Alignment explanation
Indices: 36922--36966 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
36912 GATAAACTAT
36922 AAAAATAACATAATAATTAAA
1 AAAAATAA-A-AATAATTAAA
* *
36943 AAAAATAAAATTTATTAAA
1 AAAAATAAAAATAATTAAA
36962 AAAAA
1 AAAAA
36967 ATTAAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 13 0.59
20 1 0.05
21 8 0.36
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAAATAAAAATAATTAAA
Found at i:41961 original size:16 final size:17
Alignment explanation
Indices: 41929--41961 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
41919 ACTGAAGATA
41929 TAACAATAATCCTCTAT
1 TAACAATAATCCTCTAT
*
41946 TAACATTAAT-CTCTAT
1 TAACAATAATCCTCTAT
41962 GCGTCTACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (17 bp):
TAACAATAATCCTCTAT
Found at i:51849 original size:25 final size:26
Alignment explanation
Indices: 51815--51864 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 26
51805 CGAAGTGCTA
51815 ATACACATAAGGTCGTG-CCACCATC
1 ATACACATAAGGTCGTGCCCACCATC
51840 ATACACATAAGGTCGTGCCCACCAT
1 ATACACATAAGGTCGTGCCCACCAT
51865 ATGCACGTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.20
Consensus pattern (26 bp):
ATACACATAAGGTCGTGCCCACCATC
Found at i:58767 original size:18 final size:17
Alignment explanation
Indices: 58741--58774 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
58731 AACAATAGAA
58741 ACAAAAAGAAAAAGAAAT
1 ACAAAAAG-AAAAGAAAT
*
58759 ACAAGAAGAAAAGAAA
1 ACAAAAAGAAAAGAAA
58775 GTCTCCTACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.03
Consensus pattern (17 bp):
ACAAAAAGAAAAGAAAT
Done.