Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009411.1 Hibiscus syriacus cultivar Beakdansim tig00113348_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: 25125
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:186 original size:29 final size:30
Alignment explanation
Indices: 148--205 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
138 TAAAATTTTT
* *
148 AAGGACTAAATTG-AATTTTGATTAAATTC
1 AAGGACTAAAGTGAAATTTTGAATAAATTC
*
177 AAGGATTAAAGTGAAATTTTGAATAAATT
1 AAGGACTAAAGTGAAATTTTGAATAAATT
206 TGGATCCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.45, C:0.03, G:0.16, T:0.36
Consensus pattern (30 bp):
AAGGACTAAAGTGAAATTTTGAATAAATTC
Found at i:779 original size:18 final size:18
Alignment explanation
Indices: 746--780 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
736 GGTCCAACAT
* *
746 TGACCATTGACTGTTGAC
1 TGACCATTAACCGTTGAC
764 TGACCATTAACCGTTGA
1 TGACCATTAACCGTTGA
781 TCATTGACTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (18 bp):
TGACCATTAACCGTTGAC
Found at i:1317 original size:15 final size:15
Alignment explanation
Indices: 1291--1326 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1281 ACACAATGCT
1291 TGATTT-TCTGAACA
1 TGATTTATCTGAACA
*
1305 TGATTTATCTGAATA
1 TGATTTATCTGAACA
1320 TGATTTA
1 TGATTTA
1327 CTGTATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.31, C:0.08, G:0.14, T:0.47
Consensus pattern (15 bp):
TGATTTATCTGAACA
Found at i:1577 original size:39 final size:39
Alignment explanation
Indices: 1534--1618 Score: 125
Period size: 39 Copynumber: 2.2 Consensus size: 39
1524 GGCTCCTCAA
* *
1534 CTTTGTGCTCATGGTAAGACCTTACCGTAGGCTCCTAGG
1 CTTTGTGCTCAGGGTAAGACCTTACCGCAGGCTCCTAGG
* * *
1573 CTTTGTGCTCAGGGTAAGTCCTTACTGCAGGCTCCTTGG
1 CTTTGTGCTCAGGGTAAGACCTTACCGCAGGCTCCTAGG
1612 CTTTGTG
1 CTTTGTG
1619 GGTAAGTCCT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.14, C:0.25, G:0.27, T:0.34
Consensus pattern (39 bp):
CTTTGTGCTCAGGGTAAGACCTTACCGCAGGCTCCTAGG
Found at i:2878 original size:59 final size:59
Alignment explanation
Indices: 2806--3215 Score: 569
Period size: 59 Copynumber: 7.0 Consensus size: 59
2796 CACTATTTTT
* * * *
2806 ATCTAACTTGCATTAGTGGCACCTTTATGCCAAATGCACATTTAGGCATTTAACCATTC
1 ATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACCTTTC
* * *
2865 ATCTAACTTGCATTATTGGCACCTTTCTTCCAAATGAACAGTTAGGCATTTAACTTTTC
1 ATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACCTTTC
* * *
2924 ATCTAACTTGAATTATTGG--CCTTTCTACCAAATGCATAGTTAGGCATTTAACCTTTC
1 ATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACCTTTC
* * ** *
2981 ATCTAAATTGCATTATT-GCACCTTTCTGCCAAATACACAGTTATACATTTAACATTTC
1 ATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACCTTTC
* * * *
3039 ATCTAACATGCATTATTGGCACCTTTCTTCCAAATGCACAGTTAGGCA-TGAACTTTTC
1 ATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACCTTTC
* * *
3097 ATCTAACTTGCATTA-TGTCACCTTTCTGCCAAATGCACAATTAGGTATTTAACCTTTC
1 ATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACCTTTC
* *
3155 ATCTAACTTGCATTATTGGCACCTTTCTTCCAAATGCACAATTAGGCATTTAACCTTTC
1 ATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACCTTTC
3214 AT
1 AT
3216 TTTAGAGAAA
Statistics
Matches: 308, Mismatches: 38, Indels: 10
0.87 0.11 0.03
Matches are distributed among these distances:
56 1 0.00
57 77 0.25
58 92 0.30
59 138 0.45
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (59 bp):
ATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACCTTTC
Found at i:3123 original size:174 final size:174
Alignment explanation
Indices: 2806--3215 Score: 590
Period size: 174 Copynumber: 2.3 Consensus size: 174
2796 CACTATTTTT
* * *
2806 ATCTAACTTGCATTAGTGGCACCTTTATGCCAAATGCACATTTAGGCATTTAACCA-TTCATCTA
1 ATCTAACTTGCATTA-TTGCACCTTTCTGCCAAATGCACAATTAGGCATTTAA-CATTTCATCTA
* *
2870 ACTTGCATTATTGGCACCTTTCTTCCAAATGAACAGTTAGGCATTTAACTTTTCATCTAACTTGA
64 ACATGCATTATTGGCACCTTTCTTCCAAATGAACAGTTAGGCATTGAACTTTTCATCTAACTTGA
** * *
2935 ATTATTGGCCTTTCTACCAAATGCATAGTTAGGCATTTAACCTTTC
129 ATTATTCACCTTTCTACCAAATGCACAATTAGGCATTTAACCTTTC
* * * **
2981 ATCTAAATTGCATTATTGCACCTTTCTGCCAAATACACAGTTATACATTTAACATTTCATCTAAC
1 ATCTAACTTGCATTATTGCACCTTTCTGCCAAATGCACAATTAGGCATTTAACATTTCATCTAAC
* *
3046 ATGCATTATTGGCACCTTTCTTCCAAATGCACAGTTAGGCA-TGAACTTTTCATCTAACTTGCAT
66 ATGCATTATTGGCACCTTTCTTCCAAATGAACAGTTAGGCATTGAACTTTTCATCTAACTTGAAT
* *
3110 TATGTCACCTTTCTGCCAAATGCACAATTAGGTATTTAACCTTTC
131 TAT-TCACCTTTCTACCAAATGCACAATTAGGCATTTAACCTTTC
* *
3155 ATCTAACTTGCATTATTGGCACCTTTCTTCCAAATGCACAATTAGGCATTTAACCTTTCAT
1 ATCTAACTTGCATTATT-GCACCTTTCTGCCAAATGCACAATTAGGCATTTAACATTTCAT
3216 TTTAGAGAAA
Statistics
Matches: 208, Mismatches: 24, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
173 26 0.12
174 131 0.63
175 51 0.25
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (174 bp):
ATCTAACTTGCATTATTGCACCTTTCTGCCAAATGCACAATTAGGCATTTAACATTTCATCTAAC
ATGCATTATTGGCACCTTTCTTCCAAATGAACAGTTAGGCATTGAACTTTTCATCTAACTTGAAT
TATTCACCTTTCTACCAAATGCACAATTAGGCATTTAACCTTTC
Found at i:3130 original size:116 final size:117
Alignment explanation
Indices: 2806--3215 Score: 560
Period size: 116 Copynumber: 3.5 Consensus size: 117
2796 CACTATTTTT
* * * * *
2806 ATCTAACTTGCATTAGTGGCACCTTTATGCCAAATGCACATTTAGGCATTTAACCATTCATCTAA
1 ATCTAACTTGCATTATTGGCACCTTTCTTCCAAATGCACAGTTAGGCATTTAACCTTTCATCTAA
* * *
2871 CTTGCATTATTGGCACCTTTCTTCCAAATGA-ACAGTTAGGCATTTAACTTTTC
66 CTTGCATTA-TGTCACCTTTCTGCCAAAT-ACACAGTTAGGCATTTAACATTTC
* * *
2924 ATCTAACTTGAATTATTGG--CCTTTCTACCAAATGCATAGTTAGGCATTTAACCTTTCATCTAA
1 ATCTAACTTGCATTATTGGCACCTTTCTTCCAAATGCACAGTTAGGCATTTAACCTTTCATCTAA
* **
2987 ATTGCATTAT-TGCACCTTTCTGCCAAATACACAGTTATACATTTAACATTTC
66 CTTGCATTATGT-CACCTTTCTGCCAAATACACAGTTAGGCATTTAACATTTC
* * *
3039 ATCTAACATGCATTATTGGCACCTTTCTTCCAAATGCACAGTTAGGCA-TGAACTTTTCATCTAA
1 ATCTAACTTGCATTATTGGCACCTTTCTTCCAAATGCACAGTTAGGCATTTAACCTTTCATCTAA
* * * *
3103 CTTGCATTATGTCACCTTTCTGCCAAATGCACAATTAGGTATTTAACCTTTC
66 CTTGCATTATGTCACCTTTCTGCCAAATACACAGTTAGGCATTTAACATTTC
*
3155 ATCTAACTTGCATTATTGGCACCTTTCTTCCAAATGCACAATTAGGCATTTAACCTTTCAT
1 ATCTAACTTGCATTATTGGCACCTTTCTTCCAAATGCACAGTTAGGCATTTAACCTTTCAT
3216 TTTAGAGAAA
Statistics
Matches: 256, Mismatches: 30, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
114 1 0.00
115 52 0.20
116 150 0.59
117 36 0.14
118 17 0.07
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (117 bp):
ATCTAACTTGCATTATTGGCACCTTTCTTCCAAATGCACAGTTAGGCATTTAACCTTTCATCTAA
CTTGCATTATGTCACCTTTCTGCCAAATACACAGTTAGGCATTTAACATTTC
Found at i:3211 original size:32 final size:32
Alignment explanation
Indices: 3116--3213 Score: 82
Period size: 32 Copynumber: 3.2 Consensus size: 32
3106 GCATTATGTC
* *
3116 ACCTTTCTGCCAAATGCACAATTAGGTATTTA
1 ACCTTTCTTCCAAATGCACAATTAGGCATTTA
* * * **
3148 ACCTTTCATCTAACTTGCATTATT-GGC-----
1 ACCTTTCTTCCAA-ATGCACAATTAGGCATTTA
3175 ACCTTTCTTCCAAATGCACAATTAGGCATTTA
1 ACCTTTCTTCCAAATGCACAATTAGGCATTTA
3207 ACCTTTC
1 ACCTTTC
3214 ATTTTAGAGA
Statistics
Matches: 47, Mismatches: 12, Indels: 14
0.64 0.16 0.19
Matches are distributed among these distances:
26 7 0.15
27 14 0.30
32 19 0.40
33 7 0.15
ACGTcount: A:0.28, C:0.26, G:0.10, T:0.37
Consensus pattern (32 bp):
ACCTTTCTTCCAAATGCACAATTAGGCATTTA
Found at i:9843 original size:59 final size:59
Alignment explanation
Indices: 9751--10166 Score: 631
Period size: 59 Copynumber: 7.1 Consensus size: 59
9741 ATACATTGTT
* * * **
9751 TTTCATCCAACTTGCATTAATGGCACTTTTCTGCCAAATGCACTGTTAGGCATTTAACC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAATTAGGCATTTAACC
* * * *
9810 TTTCATCTAACTTGCATTATTAGAACCTTTCTGCCAAATGCACATTTAGGAATTTAACC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAATTAGGCATTTAACC
* * * *
9869 TTTCATCTAACTTGCATTATTGGAACCTTTCTTCCAAATGCACAGTTAGACATTTAACC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAATTAGGCATTTAACC
* *
9928 TTTCATCTAACTTGCACTATTGGCACCTTTCTGCCAAATGCACAATTAGACATTTAACC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAATTAGGCATTTAACC
*
9987 TTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCATAATTAGGCATTTAACC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAATTAGGCATTTAACC
* *
10046 TTTCATCTAACTTGCATTATTGGCACCTTTCTTCCAAGTGCAC-ATTAGGCATTTAACC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAATTAGGCATTTAACC
* *
10104 TTTCATCTAACTTGCA-T-TTGGCACCTTTCTGCCAAATGCACAGTTAGGCTTTTAACC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAATTAGGCATTTAACC
10161 TTTCAT
1 TTTCAT
10167 TTTAGAGAAA
Statistics
Matches: 329, Mismatches: 27, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
56 22 0.07
57 20 0.06
58 31 0.09
59 256 0.78
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.37
Consensus pattern (59 bp):
TTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAATTAGGCATTTAACC
Found at i:17391 original size:63 final size:62
Alignment explanation
Indices: 17314--17471 Score: 201
Period size: 63 Copynumber: 2.5 Consensus size: 62
17304 AATTAAATTG
* *
17314 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCATAGATGCACTGAGG-ATTATGAA
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCATAGATGCACTCAGGCATTATG-A
* * * *
17377 AACATCGAATGCATTTGATGAATCGATGCAACAACCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGC-ACAACCATGCATAGATGCACTCAGGC-ATTATGA
* *
17441 AACCTCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
17472 TCTTAGTGCA
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
63 48 0.58
64 30 0.36
65 5 0.06
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (62 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCATAGATGCACTCAGGCATTATGA
Found at i:17469 original size:64 final size:62
Alignment explanation
Indices: 17264--17470 Score: 213
Period size: 64 Copynumber: 3.2 Consensus size: 62
17254 TTTTTCAGAG
* * *
17264 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CTTGAATTAAATTG-AACATCGAATGCA
1 TGATGCATCGATGCAACAA-CCATGCATCGATGCACTC-TGGATT---TTGAAACATCGAATGCA
17327 TT
61 TT
* * ** *
17329 TCATGCATCGATGC-ACATACCATGCATAGATGCACTGAGGATTATGAAAACATCGAATGCATT
1 TGATGCATCGATGCAACA-ACCATGCATCGATGCACTCTGGATTTTG-AAACATCGAATGCATT
* * *
17392 TGATGAATCGATGCAACAACCATGCATCGATGCACTCTGGCTATTTTGAAACCTCGAATGCACT
1 TGATGCATCGATGCAACAACCATGCATCGATGCACTCTGG--ATTTTGAAACATCGAATGCATT
17456 TGATGCATCGATGCA
1 TGATGCATCGATGCA
17471 CTCTTAGTGC
Statistics
Matches: 118, Mismatches: 17, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
61 2 0.02
63 46 0.39
64 52 0.44
65 18 0.15
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (62 bp):
TGATGCATCGATGCAACAACCATGCATCGATGCACTCTGGATTTTGAAACATCGAATGCATT
Found at i:20918 original size:14 final size:14
Alignment explanation
Indices: 20899--20933 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
20889 AATATTGAAT
20899 TATTATAGAGTATC
1 TATTATAGAGTATC
20913 TATTATAGAGTATC
1 TATTATAGAGTATC
20927 TATTATA
1 TATTATA
20934 ATGACATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (14 bp):
TATTATAGAGTATC
Done.