Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003224.1 Hibiscus syriacus cultivar Beakdansim tig00006790_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: 30226
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:9075 original size:112 final size:112
Alignment explanation
Indices: 8782--9135 Score: 510
Period size: 112 Copynumber: 3.1 Consensus size: 112
8772 ATATGTACAA
*
8782 AAAGTATCTATACTTTCAACATATCAGGTAACTCTTTACCGATTTTATCATAATGAAACTGGTTT
1 AAAGTATCGATACTTTCAACATATCAGGTAACTCTTTACCGATTTTATCATAATGAAACTGGTTT
* * *
8847 TGTCATATTTTTACCTATTATATTGTAAAGTATTGATACATTTTTAT
66 TGTCATATTTTTACATGTTATATTGTAAAGTATCGATACATTTTTAT
* * * * * *
8894 AAAAAGAATCGATACTTTCAACATATCAGGTAGCTCTTTACCGGTTTTGTCATAATGAAATTGGC
1 --AAAGTATCGATACTTTCAACATATCAGGTAACTCTTTACCGATTTTATCATAATGAAACTGGT
* * *
8959 TTTGTCATGTTTTTACATGTTATATTGTAAAGCATCGATACATTCTTAT
64 TTTGTCATATTTTTACATGTTATATTGTAAAGTATCGATACATTTTTAT
* * ** * *
9008 AAAGTATCGATACTTTCAACATATTATGTATTTCTTTACCGATTTTTTCATAATGAAACTGATTT
1 AAAGTATCGATACTTTCAACATATCAGGTAACTCTTTACCGATTTTATCATAATGAAACTGGTTT
*
9073 TGTTATATTTTTACATGTTATATTGTAAAGTATCGATACATTTTTAT
66 TGTCATATTTTTACATGTTATATTGTAAAGTATCGATACATTTTTAT
9120 AAAGTATCGATACTTT
1 AAAGTATCGATACTTT
9136 ATAGGCGTTA
Statistics
Matches: 213, Mismatches: 27, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
112 114 0.54
114 99 0.46
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.44
Consensus pattern (112 bp):
AAAGTATCGATACTTTCAACATATCAGGTAACTCTTTACCGATTTTATCATAATGAAACTGGTTT
TGTCATATTTTTACATGTTATATTGTAAAGTATCGATACATTTTTAT
Found at i:9355 original size:72 final size:73
Alignment explanation
Indices: 9226--9464 Score: 347
Period size: 73 Copynumber: 3.2 Consensus size: 73
9216 CGGTAAGTAG
9226 TTTAATGTAATAGGTAGCACCTATTTTTTTTTTACCGTTTACATTATTAGCAACCTTCAAAAAAA
1 TTTAATGTAATAGGTAGCA-CTA--TTTTTTTTACCGTTTACATTATTAGCAACCTTCAAAAAAA
9291 TCGATAGGTAT
63 TCGATAGGTAT
* *
9302 TTTAATGTAATAGGTAGCACTA-TTTTTTTACCATTTACATTATTAGCAACCTTCAAAAAAAACT
1 TTTAATGTAATAGGTAGCACTATTTTTTTTACCGTTTACATTATTAGCAACCTTCAAAAAAATC-
9366 GATAGGTAT
65 GATAGGTAT
* * * * *
9375 TTTTATGTAATAGGTAGCGTCTATTTTTTTTACCGTTTATATTATTAACAACCTTC-AAAAAATT
1 TTTAATGTAATAGGTAGC-ACTATTTTTTTTACCGTTTACATTATTAGCAACCTTCAAAAAAATC
*
9439 GATAGATAT
65 GATAGGTAT
9448 TTTAATGTAATAGGTAG
1 TTTAATGTAATAGGTAG
9465 TTTAAATTTT
Statistics
Matches: 149, Mismatches: 11, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
72 39 0.26
73 50 0.34
74 9 0.06
75 32 0.21
76 19 0.13
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (73 bp):
TTTAATGTAATAGGTAGCACTATTTTTTTTACCGTTTACATTATTAGCAACCTTCAAAAAAATCG
ATAGGTAT
Found at i:9727 original size:23 final size:23
Alignment explanation
Indices: 9678--9721 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
9668 ACATATTTTA
* *
9678 TTATATAAGCACTACCTATTACG
1 TTATATAAACACTACCTAATACG
*
9701 TTATATAAACGCTACCTAATA
1 TTATATAAACACTACCTAATA
9722 TTTTATTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (23 bp):
TTATATAAACACTACCTAATACG
Found at i:9823 original size:157 final size:157
Alignment explanation
Indices: 9533--10041 Score: 747
Period size: 156 Copynumber: 3.2 Consensus size: 157
9523 AGTAAGTAAT
** *
9533 TACCTATTTTGTTACATAAACGCTACCTAATATGTTATTATGCTTGATAATGTTTCTAGTAATTA
1 TACCTATTACGTTATATAAACGCTACCTAATATGTTATTATGCTTGATAATGTTTC-AGTAATTA
*
9598 ACCGGTTATGTTATCCTTGGTAACA-TTTAAGCGTTTACCTAATATGTTGTAATAACAAATTAAG
65 ACCGGTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAG
*
9662 TAATTAACATATTTTATTATATAAGCAC
130 TAATTAACATATTTTATTATATAAGCGC
*
9690 TACCTATTACGTTATATAAACGCTACCTAATATTTTATTATTG-TTGATAATGTTTCAGTAATTA
1 TACCTATTACGTTATATAAACGCTACCTAATATGTTATTA-TGCTTGATAATGTTTCAGTAATTA
* *
9754 ACCGGTTATGTTATCCTTGGTAATATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAA
65 ACCGGTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAG
9819 TAATT-A-ATATTTTATTATATAAGCGC
130 TAATTAACATATTTTATTATATAAGCGC
** * * * *
9845 TACCTATTACGTTATATAAGTGCTACCTAATATGTTATTGTGCTTGATAATATTTCCAATAAATA
1 TACCTATTACGTTATATAAACGCTACCTAATATGTTATTATGCTTGATAATGTTT-CAGTAATTA
* * *
9910 ACCGATTATATTATCATTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAG
65 ACCGGTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAG
* *
9975 TAATTAACCTATTTTATTATATAAGCGT
130 TAATTAACATATTTTATTATATAAGCGC
* ** * *
10003 TACCTATTACATTATATAATTGTTACATAATATGTTATT
1 TACCTATTACGTTATATAAACGCTACCTAATATGTTATT
10042 GTATTTGATA
Statistics
Matches: 320, Mismatches: 26, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
154 2 0.01
155 66 0.21
156 105 0.33
157 92 0.29
158 55 0.17
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.42
Consensus pattern (157 bp):
TACCTATTACGTTATATAAACGCTACCTAATATGTTATTATGCTTGATAATGTTTCAGTAATTAA
CCGGTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGT
AATTAACATATTTTATTATATAAGCGC
Found at i:9859 original size:23 final size:23
Alignment explanation
Indices: 9833--9882 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
9823 TAATATTTTA
*
9833 TTATATAAGCGCTACCTATTACG
1 TTATATAAGCGCTACCTAATACG
* *
9856 TTATATAAGTGCTACCTAATATG
1 TTATATAAGCGCTACCTAATACG
9879 TTAT
1 TTAT
9883 TGTGCTTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (23 bp):
TTATATAAGCGCTACCTAATACG
Found at i:10580 original size:55 final size:55
Alignment explanation
Indices: 10478--10614 Score: 179
Period size: 56 Copynumber: 2.5 Consensus size: 55
10468 AGACGCGGAT
* *
10478 CACCTACTCTTCCCCTAAAAATACCTCCAACCGTCTGTCGCTCCCCCTTAATTAC
1 CACCTACTCTTCCCCTATAAATACCCCCAACCGTCTGTCGCTCCCCCTTAATTAC
* * *
10533 CACCTACTCCTCCCCCTATAAATACCCCCAATCGT-TCGTCGCT-CCCCTTAATTAT
1 CACCTACT-CTTCCCCTATAAATACCCCCAACCGTCT-GTCGCTCCCCCTTAATTAC
* *
10588 CATCTACTCTTCCCCTATTAATACCCC
1 CACCTACTCTTCCCCTATAAATACCCC
10615 TTATACAACT
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
54 17 0.24
55 27 0.38
56 28 0.39
ACGTcount: A:0.23, C:0.44, G:0.04, T:0.29
Consensus pattern (55 bp):
CACCTACTCTTCCCCTATAAATACCCCCAACCGTCTGTCGCTCCCCCTTAATTAC
Found at i:13138 original size:59 final size:59
Alignment explanation
Indices: 13063--13175 Score: 190
Period size: 59 Copynumber: 1.9 Consensus size: 59
13053 ACAAATATTT
* * *
13063 AAAATTATAACAGTAAAATTAACCCAAAAATAAAATTTTAAAAGTGATTATTATGATTA
1 AAAATTACAACAGTAAAAATAACCCAAAAATAAAATTTTAAAAGTGAATATTATGATTA
*
13122 AAAATTACAACCGTAAAAATAACCCAAAAATAAAATTTTAAAAGTGAATATTAT
1 AAAATTACAACAGTAAAAATAACCCAAAAATAAAATTTTAAAAGTGAATATTAT
13176 TTCAATTTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 50 1.00
ACGTcount: A:0.56, C:0.09, G:0.06, T:0.29
Consensus pattern (59 bp):
AAAATTACAACAGTAAAAATAACCCAAAAATAAAATTTTAAAAGTGAATATTATGATTA
Found at i:24132 original size:71 final size:71
Alignment explanation
Indices: 24030--24164 Score: 191
Period size: 71 Copynumber: 1.9 Consensus size: 71
24020 TTACGCTCAG
* * * *
24030 AATTCATCCTTCAATGCTCTAATTCTATCAAAAGTCAATTACTTCTTACCATTG-TGAGTTATTA
1 AATTCATCCTCCAATGCTCTAATTCCATCAAAAGACAATTACTTCCTACCATTGTTG-GTTATTA
24094 TGCCCCT
65 TGCCCCT
* * *
24101 AATTCATCCTCCAATTCTCTAATTCCATCAAAAGACATTTGCTTCCTACCATTGTTGGTTATTA
1 AATTCATCCTCCAATGCTCTAATTCCATCAAAAGACAATTACTTCCTACCATTGTTGGTTATTA
24165 CGTCCAGAGC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
71 54 0.96
72 2 0.04
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.39
Consensus pattern (71 bp):
AATTCATCCTCCAATGCTCTAATTCCATCAAAAGACAATTACTTCCTACCATTGTTGGTTATTAT
GCCCCT
Done.