Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004879.1 Hibiscus syriacus cultivar Beakdansim tig00010994_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: 30998
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:1112 original size:18 final size:19
Alignment explanation
Indices: 1067--1113 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
1057 CCCTATGGTA
*
1067 AGTATCGATACTCTACCCTG
1 AGTATCGATACTC-ACCATG
1087 -GTTATCGATACTC-CCATG
1 AG-TATCGATACTCACCATG
1105 AGTATCGAT
1 AGTATCGAT
1114 GCCAAAATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 11 0.46
19 2 0.08
20 11 0.46
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.32
Consensus pattern (19 bp):
AGTATCGATACTCACCATG
Found at i:1159 original size:103 final size:104
Alignment explanation
Indices: 963--1159 Score: 220
Period size: 103 Copynumber: 1.9 Consensus size: 104
953 CTATACCAAC
* * * * **
963 AGTATCGATACTGGACCCTTGGGTATCGATACTTACTTGAGTATCGATACCAAATTTTGCTTCGA
1 AGTATCGATACTCGACCCTTGGGTATCGATACTCACATGAGTATCGATACCAAAATCAGCTTCGA
* * * *
1028 TTTTTTGGAAAATATCTCGGTATCGATACCCCTATGGTA
66 TATTTTGCAAAATATCTCAGTATAGATACCCCTATGGTA
* * * * *
1067 AGTATCGATACTCTACCC-TGGTTATCGATACTCCCATGAGTATCGATGCCAAAATCAGGTTCGA
1 AGTATCGATACTCGACCCTTGGGTATCGATACTCACATGAGTATCGATACCAAAATCAGCTTCGA
1131 TATTTT-CAAAAT-TGCCTCAGTATAGATAC
66 TATTTTGCAAAATAT--CTCAGTATAGATAC
1160 TGACCAATTG
Statistics
Matches: 76, Mismatches: 15, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
101 1 0.01
102 5 0.07
103 54 0.71
104 16 0.21
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.34
Consensus pattern (104 bp):
AGTATCGATACTCGACCCTTGGGTATCGATACTCACATGAGTATCGATACCAAAATCAGCTTCGA
TATTTTGCAAAATATCTCAGTATAGATACCCCTATGGTA
Found at i:9369 original size:19 final size:19
Alignment explanation
Indices: 9347--9386 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
9337 GACTTGTTGG
*
9347 CACACTAAGCACTTGGTAA
1 CACACAAAGCACTTGGTAA
9366 CACACAAAGCACTTGGTAA
1 CACACAAAGCACTTGGTAA
9385 CA
1 CA
9387 AATTCAGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.28, G:0.15, T:0.17
Consensus pattern (19 bp):
CACACAAAGCACTTGGTAA
Found at i:11293 original size:37 final size:37
Alignment explanation
Indices: 11243--11320 Score: 120
Period size: 37 Copynumber: 2.1 Consensus size: 37
11233 TTTAAAATGG
11243 TCTAAGTTTCTATGTCACACTTCCTCGACAAAGTTCA
1 TCTAAGTTTCTATGTCACACTTCCTCGACAAAGTTCA
* ** *
11280 TCTAAGTTTCTATGTCTCACTTGTTCGACAGAGTTCA
1 TCTAAGTTTCTATGTCACACTTCCTCGACAAAGTTCA
11317 TCTA
1 TCTA
11321 GAGTATCCCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.38
Consensus pattern (37 bp):
TCTAAGTTTCTATGTCACACTTCCTCGACAAAGTTCA
Found at i:14517 original size:22 final size:22
Alignment explanation
Indices: 14491--14534 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
14481 GCAGAATTAT
14491 GAAGATGTTGATGGCCTTGATG
1 GAAGATGTTGATGGCCTTGATG
*
14513 GAAGATGTTGATGGCGTTGATG
1 GAAGATGTTGATGGCCTTGATG
14535 TTGATGTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.07, G:0.39, T:0.32
Consensus pattern (22 bp):
GAAGATGTTGATGGCCTTGATG
Found at i:21089 original size:19 final size:20
Alignment explanation
Indices: 21039--21081 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
21029 GAAACCCCTG
21039 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
21059 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
21078 TGAA
1 TGAA
21082 GATGCATGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:22029 original size:21 final size:21
Alignment explanation
Indices: 21995--22045 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 21
21985 GCCATGATAT
21995 GTAAATGATA-TGCA-AACATAA
1 GTAAAT-ATAGTGCATAA-ATAA
22016 -TAATATATAGTGCATAAATAA
1 GTAA-ATATAGTGCATAAATAA
22037 GTAAATATA
1 GTAAATATA
22046 AGATAAAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
20 6 0.23
21 15 0.58
22 5 0.19
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.29
Consensus pattern (21 bp):
GTAAATATAGTGCATAAATAA
Found at i:23032 original size:21 final size:20
Alignment explanation
Indices: 22999--23037 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
22989 TATGTACTTC
*
22999 ATTCTCCTCTTTATCTCTAA
1 ATTCTCCTCTTTAACTCTAA
*
23019 ATTCATCCTTTTTAACTCT
1 ATTC-TCCTCTTTAACTCT
23038 CTCATTTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.21, C:0.28, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTCTCCTCTTTAACTCTAA
Found at i:25068 original size:19 final size:20
Alignment explanation
Indices: 25029--25080 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
25019 GAAACCCCCT
25029 TGAAAATACATGATTTTTTAA
1 TGAAAATACATGA-TTTTTAA
25050 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
25069 TGAAGATACATG
1 TGAAAATACATG
25081 CTCTTGGCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 17 0.57
21 13 0.43
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:26979 original size:24 final size:23
Alignment explanation
Indices: 26911--26980 Score: 56
Period size: 24 Copynumber: 3.0 Consensus size: 23
26901 TAATCTGCAC
*
26911 AATGAAATGAAAGAAATGAATA-A
1 AATGAAATGAAATAAATGAA-AGA
*
26934 AATGGAAT-AAGA-AAATAAGAAAGA
1 AATGAAATGAA-ATAAAT--GAAAGA
26958 AATGAAATGATAATAAATGAAAG
1 AATGAAATGA-AATAAATGAAAG
26981 GGATAGAGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 13
0.72 0.04 0.25
Matches are distributed among these distances:
22 6 0.16
23 9 0.24
24 16 0.42
25 2 0.05
26 5 0.13
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.17
Consensus pattern (23 bp):
AATGAAATGAAATAAATGAAAGA
Done.