Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009166.1 Hibiscus syriacus cultivar Beakdansim tig00112701_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: 61725
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:2731 original size:13 final size:13
Alignment explanation
Indices: 2698--2742 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
2688 AGTGGCGAGG
2698 AGAAG-AAAGTGA
1 AGAAGAAAAGTGA
*
2710 A-AAGAAAAAATGA
1 AGAAG-AAAAGTGA
2723 AGAAGAAAAGTGA
1 AGAAGAAAAGTGA
2736 AGAAGAA
1 AGAAGAA
2743 TGGGAACGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 3 0.11
12 1 0.04
13 21 0.75
14 3 0.11
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (13 bp):
AGAAGAAAAGTGA
Found at i:8457 original size:83 final size:83
Alignment explanation
Indices: 8250--8462 Score: 272
Period size: 82 Copynumber: 2.6 Consensus size: 83
8240 GAGTTTCTTA
* * *
8250 AACAAACGCCGTGATAGAGTAGTACTTTAGCT-GCGTTTTTATACAAA-TGCCAGAATAGGGATC
1 AACAAACGCCGCGATAGAGTAGTACTTTA-ATGGCGTTTTTATACAAACTGCCACAATAGGGATC
*
8313 GTTTATAGTGGCATTTTCT
65 GTTTATAGTGGCATTTTCC
* *
8332 AATAAACGCCGCGATAGAGTAGTACTTT-ATCGGCGTTTTTATACAAACT-CCTCAATAGGGATC
1 AACAAACGCCGCGATAGAGTAGTACTTTAAT-GGCGTTTTTATACAAACTGCCACAATAGGGATC
* *
8395 GTTTATATTGGTATTTTTCC
65 GTTTATAGTGGCA-TTTTCC
* * *
8415 AACAAATGTCGCGATAGAGTAGTACTTTAATGGCGTTTTTATATAAAC
1 AACAAACGCCGCGATAGAGTAGTACTTTAATGGCGTTTTTATACAAAC
8463 ACTGTAATAG
Statistics
Matches: 114, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
80 1 0.01
82 64 0.56
83 47 0.41
84 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (83 bp):
AACAAACGCCGCGATAGAGTAGTACTTTAATGGCGTTTTTATACAAACTGCCACAATAGGGATCG
TTTATAGTGGCATTTTCC
Found at i:8495 original size:83 final size:83
Alignment explanation
Indices: 8262--8487 Score: 212
Period size: 82 Copynumber: 2.7 Consensus size: 83
8252 CAAACGCCGT
* * * * * *
8262 GATAGAGTAGTACTTTAGCTGCGTTTTTATACAAA-TGC-CAGAATAGGGATCGTTTATAGTGGC
1 GATAGAGTAGTACTTTATCGGCGTTTTTATACAAACTACTC--AATAGGGATCGTTTACAGCGGT
* * * *
8325 A-TTTTCTAATAAACGCCGC
64 ATTTTTCCAACAAATGTCGC
* * **
8344 GATAGAGTAGTACTTTATCGGCGTTTTTATACAAACTCCTCAATAGGGATCGTTTATATTGGTAT
1 GATAGAGTAGTACTTTATCGGCGTTTTTATACAAACTACTCAATAGGGATCGTTTACAGCGGTAT
8409 TTTTCCAACAAATGTCGC
66 TTTTCCAACAAATGTCGC
* * *
8427 GATAGAGTAGTACTTTAAT-GGCGTTTTTATATAAAC-ACTGTAATAGGGTTC-TTTAGCAGCG
1 GATAGAGTAGTACTTT-ATCGGCGTTTTTATACAAACTACT-CAATAGGGATCGTTTA-CAGCG
8488 TTTTTTTTTA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
82 60 0.49
83 59 0.48
84 3 0.02
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (83 bp):
GATAGAGTAGTACTTTATCGGCGTTTTTATACAAACTACTCAATAGGGATCGTTTACAGCGGTAT
TTTTCCAACAAATGTCGC
Found at i:8806 original size:38 final size:40
Alignment explanation
Indices: 8717--8807 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 40
8707 TTGTCTTTTA
8717 TGGCGTTTTT-AACAAACGCCGCAATAAATCAGTGCAGTAG
1 TGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGCAG-AG
* *
8757 TGGCGTTTTTAAACAAACGCCGCAATAAGTTAGTG-A-AG
1 TGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGCAGAG
*
8795 TGGTGTTTTTAAA
1 TGGCGTTTTTAAA
8808 TACAAACACC
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
38 14 0.30
40 11 0.23
41 22 0.47
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (40 bp):
TGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGCAGAG
Found at i:10269 original size:22 final size:22
Alignment explanation
Indices: 10244--10298 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
10234 TTTGTAAAGC
10244 CTTCTTGATCCTTGAATGTTTA
1 CTTCTTGATCCTTGAATGTTTA
10266 CTTCTTGATCCTTGAATGTTTA
1 CTTCTTGATCCTTGAATGTTTA
10288 CTTCTTGATCC
1 CTTCTTGATCC
10299 GTCTATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.16, C:0.22, G:0.13, T:0.49
Consensus pattern (22 bp):
CTTCTTGATCCTTGAATGTTTA
Found at i:13069 original size:62 final size:62
Alignment explanation
Indices: 12967--13092 Score: 243
Period size: 62 Copynumber: 2.0 Consensus size: 62
12957 ACCCGTTTTT
*
12967 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATTATGTATTTATGTTAATGCATTTCCTA
1 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATAATGTATTTATGTTAATGCATTTCCTA
13029 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATAATGTATTTATGTTAATGCATTTCCTA
1 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATAATGTATTTATGTTAATGCATTTCCTA
13091 AT
1 AT
13093 GATACGTAAG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.27, C:0.16, G:0.08, T:0.49
Consensus pattern (62 bp):
ATAGTTTACACACTTTTGTATTACCTCTTCTTAATAATGTATTTATGTTAATGCATTTCCTA
Found at i:18211 original size:14 final size:14
Alignment explanation
Indices: 18192--18224 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
18182 AGACCCTTGA
18192 ATCACGGATGCTTC
1 ATCACGGATGCTTC
18206 ATCACGGATGCTTC
1 ATCACGGATGCTTC
18220 ATCAC
1 ATCAC
18225 TATCATTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.27
Consensus pattern (14 bp):
ATCACGGATGCTTC
Found at i:24373 original size:14 final size:14
Alignment explanation
Indices: 24354--24386 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
24344 AGACCCTTGA
24354 ATCACGGATGCTTC
1 ATCACGGATGCTTC
24368 ATCACGGATGCTTC
1 ATCACGGATGCTTC
24382 ATCAC
1 ATCAC
24387 TATCATTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.27
Consensus pattern (14 bp):
ATCACGGATGCTTC
Found at i:34439 original size:13 final size:14
Alignment explanation
Indices: 34418--34462 Score: 60
Period size: 13 Copynumber: 3.4 Consensus size: 14
34408 AGTGGTGAGG
34418 AGAAG-AAAAGTGA
1 AGAAGAAAAAGTGA
*
34431 A-AAGAAAAAATGA
1 AGAAGAAAAAGTGA
34444 AGAAG-AAAAGTGA
1 AGAAGAAAAAGTGA
34457 AGAAGA
1 AGAAGA
34463 TGATGGGAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 3 0.11
13 21 0.78
14 3 0.11
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (14 bp):
AGAAGAAAAAGTGA
Found at i:40096 original size:83 final size:82
Alignment explanation
Indices: 39997--40210 Score: 277
Period size: 83 Copynumber: 2.6 Consensus size: 82
39987 GAGTTTCTTA
* * *
39997 AACAAACGCCGTGATAGAGTAGTACTTTAGCTGCGTTTTTATACAAA-TGCCAGAATAGGGATCG
1 AACAAACGTCGCGATAGAGTAGTACTTTA-CTGCGTTTTTATACAAACT-CCACAATAGGGATCG
*
40061 TTTATAGTGGCATTTTTCT
64 TTTATAGTGGCATTTTTCC
* * *
40080 AATAAACGTCGCGATAGAGTAGTACTTTATCGGCGTTTTTATACAAACTCCTCAATAGGGATCGT
1 AACAAACGTCGCGATAGAGTAGTACTTTA-CTGCGTTTTTATACAAACTCCACAATAGGGATCGT
* *
40145 TTATATTGGTATTTTTCC
65 TTATAGTGGCATTTTTCC
* * *
40163 AACAAATGTCGCGATAGAGTAGTACTTTAATGGCGTTTTTATATAAAC
1 AACAAACGTCGCGATAGAGTAGTACTTTACT-GCGTTTTTATACAAAC
40211 ACTGTAATAG
Statistics
Matches: 114, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
83 113 0.99
84 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (82 bp):
AACAAACGTCGCGATAGAGTAGTACTTTACTGCGTTTTTATACAAACTCCACAATAGGGATCGTT
TATAGTGGCATTTTTCC
Found at i:40553 original size:38 final size:40
Alignment explanation
Indices: 40463--40554 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 40
40453 TTGTCTTTTA
*
40463 TGGCGTTTTTTAACAAACGCCGCAATAAATCAGTGCAGTAG
1 TGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGCAG-AG
* *
40504 TGGCGTTTTTAAACAAACGCCGCAATAAGTTAGTG-A-AG
1 TGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGCAGAG
*
40542 TGGTGTTTTTAAA
1 TGGCGTTTTTAAA
40555 TACAAACACC
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
38 14 0.30
40 1 0.02
41 32 0.68
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (40 bp):
TGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGCAGAG
Found at i:42018 original size:22 final size:22
Alignment explanation
Indices: 41993--42047 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
41983 TTTGTAAAGC
41993 CTTCTTGATCCTTGAATGTTTA
1 CTTCTTGATCCTTGAATGTTTA
42015 CTTCTTGATCCTTGAATGTTTA
1 CTTCTTGATCCTTGAATGTTTA
42037 CTTCTTGATCC
1 CTTCTTGATCC
42048 GTCTATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.16, C:0.22, G:0.13, T:0.49
Consensus pattern (22 bp):
CTTCTTGATCCTTGAATGTTTA
Found at i:44824 original size:62 final size:62
Alignment explanation
Indices: 44722--44847 Score: 243
Period size: 62 Copynumber: 2.0 Consensus size: 62
44712 ACCCGTTTTT
*
44722 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATTATGTATTTATGTTAATGCATTTCCTA
1 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATAATGTATTTATGTTAATGCATTTCCTA
44784 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATAATGTATTTATGTTAATGCATTTCCTA
1 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATAATGTATTTATGTTAATGCATTTCCTA
44846 AT
1 AT
44848 GATACGTAAG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.27, C:0.16, G:0.08, T:0.49
Consensus pattern (62 bp):
ATAGTTTACACACTTTTGTATTACCTCTTCTTAATAATGTATTTATGTTAATGCATTTCCTA
Found at i:59367 original size:81 final size:82
Alignment explanation
Indices: 59193--59388 Score: 206
Period size: 81 Copynumber: 2.4 Consensus size: 82
59183 TAAACAAACG
* * * *
59193 CCGCGATAGAGTAGTAC-TTAACTGCGTTTTTATACAAATGCCAAAATAGGGATCGTTTATGGTG
1 CCGCGATAGAGTAGTACTTTATCGGCGTTTTTATACAAATGCCAAAATAGGGATCATTTATAGTG
* * *
59257 GTACTTTTCTAATAACT
66 GCACTTTTCCAATAAAT
* ** *
59274 CCGTGATAGAGTAGTACTTTATCGGCGTTTTTATACAAACT-CCTCAATAGGGATCATTTATATT
1 CCGCGATAGAGTAGTACTTTATCGGCGTTTTTATACAAA-TGCCAAAATAGGGATCATTTATAGT
59338 GGCA-TTTTCCAGCA-AAAT
65 GGCACTTTTCCA--ATAAAT
*
59356 -CGCGATAGAGTAGTACTTTAAT-GGTGTTTTTAT
1 CCGCGATAGAGTAGTACTTT-ATCGGCGTTTTTAT
59389 TAAACACCGT
Statistics
Matches: 97, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
81 50 0.52
82 45 0.46
83 2 0.02
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (82 bp):
CCGCGATAGAGTAGTACTTTATCGGCGTTTTTATACAAATGCCAAAATAGGGATCATTTATAGTG
GCACTTTTCCAATAAAT
Found at i:61176 original size:22 final size:22
Alignment explanation
Indices: 61151--61204 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
61141 TTTGTAAAGC
61151 CTTCTTGATCCTTGAATGTTTA
1 CTTCTTGATCCTTGAATGTTTA
61173 CTTCTTGATCCTTGAATGTTTA
1 CTTCTTGATCCTTGAATGTTTA
61195 CTTC-TGATCC
1 CTTCTTGATCC
61205 GTCTATTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 6 0.19
22 26 0.81
ACGTcount: A:0.17, C:0.22, G:0.13, T:0.48
Consensus pattern (22 bp):
CTTCTTGATCCTTGAATGTTTA
Done.