Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007285.1 Hibiscus syriacus cultivar Beakdansim tig00019337_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: 59108
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:2595 original size:2 final size:2
Alignment explanation
Indices: 2588--2635 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
2578 CTCTCAAGCT
*
2588 TA TA TA TA TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2630 TA TA TA
1 TA TA TA
2636 ATTCATACAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5421 original size:29 final size:29
Alignment explanation
Indices: 5376--5433 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
5366 ATTTTATGTT
* * **
5376 AGGGGTGAACTTTAACTTTTAAAATTTTA
1 AGGGGTAAACTTAAACTCATAAAATTTTA
5405 AGGGGTAAACTTAAACTCATAAAATTTTA
1 AGGGGTAAACTTAAACTCATAAAATTTTA
5434 GGAGGGCGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (29 bp):
AGGGGTAAACTTAAACTCATAAAATTTTA
Found at i:5651 original size:31 final size:31
Alignment explanation
Indices: 5576--5643 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
5566 TTGCAATACA
*
5576 GTCCTCCAACATTTAGTCCGTTTGTAAAATG
1 GTCCCCCAACATTTAGTCCGTTTGTAAAATG
* *
5607 GTCCCCCAACATTTAGTCTGTTTGTAATATG
1 GTCCCCCAACATTTAGTCCGTTTGTAAAATG
5638 GTCCCC
1 GTCCCC
5644 GACCATTTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.35
Consensus pattern (31 bp):
GTCCCCCAACATTTAGTCCGTTTGTAAAATG
Found at i:13093 original size:2 final size:2
Alignment explanation
Indices: 13086--13111 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13076 TGTAAATCAA
13086 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
13112 TTGATTGTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16632 original size:14 final size:14
Alignment explanation
Indices: 16613--16644 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
16603 CGTTCGTGAA
16613 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
16627 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
16641 CGTT
1 CGTT
16645 TATGTTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.28, T:0.50
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:16661 original size:24 final size:24
Alignment explanation
Indices: 16614--16664 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
16604 GTTCGTGAAC
* *
16614 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGGTTATGTTCATTCAGTTAT
* *
16638 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGGTTATGTTCATTCAGTTAT
16662 GTT
1 GTT
16665 TAACCCAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.12, G:0.22, T:0.55
Consensus pattern (24 bp):
GTTCGGTTATGTTCATTCAGTTAT
Found at i:17188 original size:11 final size:11
Alignment explanation
Indices: 17172--17237 Score: 96
Period size: 11 Copynumber: 5.9 Consensus size: 11
17162 GTCGAGCTCA
17172 GAATCGAGCTT
1 GAATCGAGCTT
*
17183 GAATCGAGCAT
1 GAATCGAGCTT
17194 GAATCGAGCTT
1 GAATCGAGCTT
*
17205 GAATTGAGCTT
1 GAATCGAGCTT
17216 AGAATCGAGCTT
1 -GAATCGAGCTT
*
17228 CAATCGAGCT
1 GAATCGAGCT
17238 CGAGTCTCGA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
11 39 0.80
12 10 0.20
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (11 bp):
GAATCGAGCTT
Found at i:17199 original size:22 final size:23
Alignment explanation
Indices: 17163--17236 Score: 98
Period size: 23 Copynumber: 3.3 Consensus size: 23
17153 TGGGGCAATG
17163 TCGAGC-TCAGAATCGAGCTTGAA
1 TCGAGCAT-AGAATCGAGCTTGAA
17186 TCGAGCAT-GAATCGAGCTTGAA
1 TCGAGCATAGAATCGAGCTTGAA
* * *
17208 TTGAGCTTAGAATCGAGCTTCAA
1 TCGAGCATAGAATCGAGCTTGAA
17231 TCGAGC
1 TCGAGC
17237 TCGAGTCTCG
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
22 20 0.44
23 24 0.53
24 1 0.02
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (23 bp):
TCGAGCATAGAATCGAGCTTGAA
Found at i:17470 original size:16 final size:15
Alignment explanation
Indices: 17449--17499 Score: 68
Period size: 16 Copynumber: 3.3 Consensus size: 15
17439 GTCTCCAACG
17449 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTT-A
*
17465 TTTATGTTCGTGTTTG
1 TTTATGTTCGTG-TTA
17481 TTTATGTTCGT-TTA
1 TTTATGTTCGTGTTA
17495 TTTAT
1 TTTAT
17500 TAAATGAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 7 0.22
16 23 0.72
17 2 0.06
ACGTcount: A:0.12, C:0.08, G:0.18, T:0.63
Consensus pattern (15 bp):
TTTATGTTCGTGTTA
Found at i:25016 original size:16 final size:16
Alignment explanation
Indices: 24995--25025 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
24985 CCACGGTGCT
24995 CCCGGAATCCTGCGCC
1 CCCGGAATCCTGCGCC
25011 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
25026 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.48, G:0.26, T:0.13
Consensus pattern (16 bp):
CCCGGAATCCTGCGCC
Found at i:26161 original size:26 final size:26
Alignment explanation
Indices: 26125--26177 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
26115 GTTCTGAGGG
26125 TATGAAACTAGTGTGGGATAAAACTA
1 TATGAAACTAGTGTGGGATAAAACTA
26151 TATGAAACTAGTGTGGGATAAAACTA
1 TATGAAACTAGTGTGGGATAAAACTA
26177 T
1 T
26178 CTTCTTGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.28
Consensus pattern (26 bp):
TATGAAACTAGTGTGGGATAAAACTA
Found at i:38195 original size:60 final size:60
Alignment explanation
Indices: 38130--38285 Score: 206
Period size: 60 Copynumber: 2.6 Consensus size: 60
38120 TTATATCAGC
* * * *
38130 CCTTAAACTTTTGAATATTTTAATTTTATCCCCAAACTATGACTCTCATTCTAAATTAGT
1 CCTTAAACTTTTGAATATTCTAATTTCATCCCCAAACCATGACCCTCATTCTAAATTAGT
* * * * *
38190 CCTTAAACTTTTAAACATTCTAATTTCATCCCTAAACCATGACCCTCTTTCTAAATTGGT
1 CCTTAAACTTTTGAATATTCTAATTTCATCCCCAAACCATGACCCTCATTCTAAATTAGT
*
38250 CAC-TAAACTTTTGAATATTCCAATTTCATCCCCAAA
1 C-CTTAAACTTTTGAATATTCTAATTTCATCCCCAAA
38286 TTCATCCAAA
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
60 81 0.99
61 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.39
Consensus pattern (60 bp):
CCTTAAACTTTTGAATATTCTAATTTCATCCCCAAACCATGACCCTCATTCTAAATTAGT
Found at i:38517 original size:60 final size:61
Alignment explanation
Indices: 38408--38551 Score: 177
Period size: 60 Copynumber: 2.4 Consensus size: 61
38398 GTAGATACAT
* * *
38408 ATAGTTTGGGG-TGAAATTGGAATGTTCAAAAAACTTGGGGACCAATTTAGAATGA-AGATC
1 ATAGTTTGGGGATGAAATTGAAATGTTCAAAAAACTTGAGAACCAATTTAGAATGACAG-TC
* * *
38468 ATAGTTTGGGGATGAAATTGAAATGTTC-AAAAATTTGAGAACTAGTTTAGAATGACAGTC
1 ATAGTTTGGGGATGAAATTGAAATGTTCAAAAAACTTGAGAACCAATTTAGAATGACAGTC
* **
38528 ACAGTTTAAGGATGAAATTGAAAT
1 ATAGTTTGGGGATGAAATTGAAAT
38552 ATTTAAAATT
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
60 56 0.77
61 17 0.23
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.30
Consensus pattern (61 bp):
ATAGTTTGGGGATGAAATTGAAATGTTCAAAAAACTTGAGAACCAATTTAGAATGACAGTC
Found at i:39452 original size:30 final size:30
Alignment explanation
Indices: 39418--39479 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
39408 GGTTTAGGTG
*
39418 AAAATACCAACCAGACCTGACTCACAAAAA
1 AAAATACCAACCAGACCTGACCCACAAAAA
*
39448 AAAATACCAACCAGACCTGACCCAGAAAAA
1 AAAATACCAACCAGACCTGACCCACAAAAA
39478 AA
1 AA
39480 TAATTTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.55, C:0.29, G:0.08, T:0.08
Consensus pattern (30 bp):
AAAATACCAACCAGACCTGACCCACAAAAA
Found at i:39610 original size:25 final size:22
Alignment explanation
Indices: 39554--39607 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
39544 ATTAAGTCAT
39554 TGTTTTTATTGAATAAAAATAA
1 TGTTTTTATTGAATAAAAATAA
39576 TGTTTTTATTGAATAAAAATAA
1 TGTTTTTATTGAATAAAAATAA
*
39598 TATTTTTATT
1 TGTTTTTATT
39608 ATTATTTAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (22 bp):
TGTTTTTATTGAATAAAAATAA
Found at i:40883 original size:2 final size:2
Alignment explanation
Indices: 40878--40905 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
40868 AAAATGAGTT
40878 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40906 ACTTTTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:44960 original size:27 final size:27
Alignment explanation
Indices: 44930--44989 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
44920 ATATAAAAAC
*
44930 AATTTATTAATCTAA-TAATCATAATTA
1 AATTTATTAATCTAACAAAT-ATAATTA
*
44957 AATTTATTAGTCTAACAAATATAATTA
1 AATTTATTAATCTAACAAATATAATTA
44984 ATATTT
1 A-ATTT
44990 TCCTTTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 22 0.76
28 7 0.24
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.45
Consensus pattern (27 bp):
AATTTATTAATCTAACAAATATAATTA
Found at i:47272 original size:3 final size:3
Alignment explanation
Indices: 47264--47345 Score: 130
Period size: 3 Copynumber: 27.7 Consensus size: 3
47254 TTTTTATCCA
* *
47264 TAT TAT TAT TA- TAA TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
47311 TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
47346 AATATATTAA
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
2 2 0.03
3 71 0.97
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:48748 original size:20 final size:20
Alignment explanation
Indices: 48725--48765 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
48715 TTTATTGTTA
48725 TTTTATTATATT-ATTAAATAT
1 TTTTA-TATATTCA-TAAATAT
48746 TTTTATATATTCATAAATAT
1 TTTTATATATTCATAAATAT
48766 ATATATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTATATATTCATAAATAT
Found at i:49429 original size:6 final size:7
Alignment explanation
Indices: 49408--49432 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
49398 TGTCTCTATT
49408 AATTAAA
1 AATTAAA
49415 AATTAAA
1 AATTAAA
49422 AATTAAA
1 AATTAAA
49429 AATT
1 AATT
49433 TATATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AATTAAA
Done.