Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006038.1 Hibiscus syriacus cultivar Beakdansim tig00014258_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: 87292
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:10467 original size:20 final size:21
Alignment explanation
Indices: 10415--10467 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
10405 CGATACTCAG
10415 GAAGTATCGATACCAAAAACCA
1 GAAGTATCGATACCAAAAA-CA
*
10437 GAAGTACCGATACTCAAAAA-A
1 GAAGTATCGATAC-CAAAAACA
10458 G-AGTATCGAT
1 GAAGTATCGAT
10468 GTCAGTCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 8 0.29
21 2 0.07
22 12 0.43
23 6 0.21
ACGTcount: A:0.47, C:0.19, G:0.17, T:0.17
Consensus pattern (21 bp):
GAAGTATCGATACCAAAAACA
Found at i:10546 original size:20 final size:20
Alignment explanation
Indices: 10505--10552 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
10495 AAGTTAGTAC
**
10505 TATCAATACCCAGAGGTTAG
1 TATCAATACCCAGAGGACAG
*
10525 TATCGATACCCAGAGGACAG
1 TATCAATACCCAGAGGACAG
10545 TATCAATA
1 TATCAATA
10553 ATAAAAAGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.23
Consensus pattern (20 bp):
TATCAATACCCAGAGGACAG
Found at i:17675 original size:44 final size:44
Alignment explanation
Indices: 17625--17794 Score: 268
Period size: 44 Copynumber: 3.9 Consensus size: 44
17615 GAGTGGAACC
* *
17625 TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCATA
1 TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGACACA
* * * *
17669 TTTCTGCCAATAATACAGCATTATGCATTTTCATTTATGACACC
1 TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGACACA
*
17713 TTTCTGCCAATAATGCACCGTTATGGATTTTCATTTATGACACA
1 TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGACACA
*
17757 TTTATGCCAATAATGCACCGTTATGCATTTTCATTTAT
1 TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTAT
17795 TTCGATAACA
Statistics
Matches: 113, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 113 1.00
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.41
Consensus pattern (44 bp):
TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGACACA
Found at i:21605 original size:44 final size:44
Alignment explanation
Indices: 21542--21718 Score: 246
Period size: 44 Copynumber: 4.0 Consensus size: 44
21532 ATACCATGAG
* *
21542 TGGCACATTTCTGCCAATAATGCACCGTTAAGCATTTTCATTTA
1 TGGCACATTTCTACCAATAATGCACCGTTATGCATTTTCATTTA
* *
21586 TGGCACTTTTCTACCAATAATGCACAGTTATGCATTTTCATTTA
1 TGGCACATTTCTACCAATAATGCACCGTTATGCATTTTCATTTA
* *
21630 TGGCACATTTCTACCAATAATACATCGTTATGCATTTTCATTTA
1 TGGCACATTTCTACCAATAATGCACCGTTATGCATTTTCATTTA
* * * * * *
21674 TGACATATTTATGCTAATAATGCATCGTTATGCATTTTCATTTA
1 TGGCACATTTCTACCAATAATGCACCGTTATGCATTTTCATTTA
21718 T
1 T
21719 TTCGGTAACA
Statistics
Matches: 119, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 119 1.00
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.41
Consensus pattern (44 bp):
TGGCACATTTCTACCAATAATGCACCGTTATGCATTTTCATTTA
Found at i:35275 original size:6 final size:6
Alignment explanation
Indices: 35261--35309 Score: 80
Period size: 6 Copynumber: 8.2 Consensus size: 6
35251 TCGGCTCGGC
* *
35261 TCGTTG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTAG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
35309 T
1 T
35310 AATACGTGTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.02, C:0.16, G:0.45, T:0.37
Consensus pattern (6 bp):
TCGTGG
Found at i:54033 original size:10 final size:10
Alignment explanation
Indices: 54012--54049 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
54002 ATGAAAAATG
54012 AAAAAAGA-A
1 AAAAAAGAGA
54021 AAAAAAGAGA
1 AAAAAAGAGA
*
54031 AAAAGAGAGA
1 AAAAAAGAGA
54041 AAACAAAGA
1 AAA-AAAGA
54050 AAGAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 8 0.32
10 13 0.52
11 4 0.16
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAAAAGAGA
Found at i:55129 original size:56 final size:56
Alignment explanation
Indices: 55086--55415 Score: 489
Period size: 56 Copynumber: 5.9 Consensus size: 56
55076 CCCACTACCA
* ** * *
55086 ATACGGAAATTCATATACTTATTATGAATTTAATAGTTATTGCACACAAAGTGTCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
* *
55142 ATACGGAAATTCATAAACTCATTATAAATTTCTTAGTTTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
* * * *
55198 ATACGGAAATTTATAAACTCATTATGAATTTCTTAATTTTTGCACACAAAGTGCTC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
* *
55254 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTTCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
*
55310 ATACGGAAATTCATAAAGTTATTATGAATTTCTTAGTTTTTGCACACACACAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACA-A-AGTGCCC
* * *
55368 ATACAGAAATTCATCAACTTATTATGAATTTCTTAGTTTTTGAACACA
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACA
55416 CACAGAAATG
Statistics
Matches: 248, Mismatches: 24, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
56 197 0.79
57 1 0.00
58 50 0.20
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.36
Consensus pattern (56 bp):
ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
Found at i:62787 original size:135 final size:135
Alignment explanation
Indices: 62481--63183 Score: 779
Period size: 135 Copynumber: 5.2 Consensus size: 135
62471 AACTCAATTT
* *
62481 AATCTTCCCTCAAGAACAGTGGAATGAATCAACGTCCCCAGAGT-TGATTTTCCCTGAAGAAATA
1 AATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAGA-TCTGATTTTCCCTGAAGAAACA
* * * * ** *
62545 ACAGAACAGATCCCCTCTCTTTCCAGATTTGATCTTCTCTTAGT-GGCATGGAACAAGTCTGCCT
65 ACAGAATAGATCCCCTCTCTTTCTAGATTTGATCTTCCCTGAGTAGTAATGGAACAAGTATGCCT
62609 CGATTC
130 CGATTC
* * * * *
62615 AATCTTCCCTAAAGAATAATGGAATGAATCAACGTCCCCGGATCTGATTTTCCCTGAAGAAACCA
1 AATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTGAAGAAACAA
* * ** *
62680 CATAATATATCCTTTCTCTTTCTAGATTTGATCTTCCCTGAGTAGTAATGGAACAAGTCTGCCTC
66 CAGAATAGATCCCCTCTCTTTCTAGATTTGATCTTCCCTGAGTAGTAATGGAACAAGTATGCCTC
62745 GATTC
131 GATTC
* * * *
62750 AGTCTTCACTGAAGAATAGTAGAATGAATCAACGTCCCCAGATCTGATTTTCCCTGAAGAAACAA
1 AATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTGAAGAAACAA
** ** * *
62815 TGGAATAGATCCCCTCTCTTTTCT-GATTTGATCTTCTTTGAGTAGCAGTGGAACAAGTATGCCT
66 CAGAATAGATCCCCTCTC-TTTCTAGATTTGATCTTCCCTGAGTAGTAATGGAACAAGTATGCCT
62879 CGATTC
130 CGATTC
* *
62885 AATCTTCCCTGAAGAACAGTGAAATGAATCAACGTCCCCAGATCTGGTTTTCCCTGAAGAAACAA
1 AATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTGAAGAAACAA
* * * * * * * *
62950 CAGAAAATATCCCCTCCCTATCTGGATTTGATCTTCCCTGAGTAGTAGTGGAACAAATATACCTC
66 CAGAATAGATCCCCTCTCTTTCTAGATTTGATCTTCCCTGAGTAGTAATGGAACAAGTATGCCTC
*
63015 TATTC
131 GATTC
* * * * * * * * * *
63020 AATCTTCCCTGAAGAACATTGGAGTAAATCAATGTCTCCATATATGATTTTCCCCGAAGAAGCAG
1 AATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTGAAGAAACAA
* * * * * * ** ** * * *
63085 CGGAACAGAT--CATCTCTTTCCAGATTTGATCTTTCTTGAACAACAGTGTAACAAGTCT-CCTC
66 CAGAATAGATCCCCTCTCTTTCTAGATTTGATCTTCCCTGAGTAGTAATGGAACAAGTATGCCTC
63147 GATTC
131 GATTC
63152 AATCTTCCCTGAAGAACAGTGGAATGAATCAA
1 AATCTTCCCTGAAGAACAGTGGAATGAATCAA
63184 AGCTTCTCGA
Statistics
Matches: 480, Mismatches: 85, Indels: 10
0.83 0.15 0.02
Matches are distributed among these distances:
132 37 0.08
133 35 0.07
134 96 0.20
135 307 0.64
136 5 0.01
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (135 bp):
AATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTGAAGAAACAA
CAGAATAGATCCCCTCTCTTTCTAGATTTGATCTTCCCTGAGTAGTAATGGAACAAGTATGCCTC
GATTC
Found at i:62982 original size:270 final size:270
Alignment explanation
Indices: 62481--63183 Score: 916
Period size: 270 Copynumber: 2.6 Consensus size: 270
62471 AACTCAATTT
* *
62481 AATCTTCCCTCAAGAACAGTGGAATGAATCAACGTCCCCAGAGTTGATTTTCCCTGAAGAAATAA
1 AATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAGA-TTGATTTTCCCTGAAGAAACAA
* *
62546 CAGAACAGATCCCCTCTCTTTCCAGATTTGATCTTCTCTT-AGTGGCA-TGGAACAAGTCTGCCT
65 CGGAACAGATCCCCTCTCTTTCCAGATTTGATCTTCTCTTGAGTAGCAGTGGAACAAGTCTGCCT
* * * *
62609 CGATTCAATCTTCCCTAAAGAATAATGGAATGAATCAACGTCCCCGGATCTGATTTTCCCTGAAG
130 CGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTGAAG
* * * ** * * * *
62674 AAACCACATAATATATCCTTTCTCTTTCTAGATTTGATCTTCCCTGAGTAGTAATGGAACAAGTC
195 AAACAACAGAAAATATCCCCTCCCTATCTAGATTTGATCTTCCCTGAGTAGTAATGGAACAAATA
*
62739 TGCCTCGATTC
260 TACCTCGATTC
* * * *
62750 AGTCTTCACTGAAGAATAGTAGAATGAATCAACGTCCCCAGATCTGATTTTCCCTGAAGAAACAA
1 AATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAGAT-TGATTTTCCCTGAAGAAACAA
* * * * *
62815 TGGAATAGATCCCCTCTCTTTTCTGATTTGATCTTCT-TTGAGTAGCAGTGGAACAAGTATGCCT
65 CGGAACAGATCCCCTCTCTTTCCAGATTTGATCTTCTCTTGAGTAGCAGTGGAACAAGTCTGCCT
* *
62879 CGATTCAATCTTCCCTGAAGAACAGTGAAATGAATCAACGTCCCCAGATCTGGTTTTCCCTGAAG
130 CGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTGAAG
* *
62944 AAACAACAGAAAATATCCCCTCCCTATCTGGATTTGATCTTCCCTGAGTAGTAGTGGAACAAATA
195 AAACAACAGAAAATATCCCCTCCCTATCTAGATTTGATCTTCCCTGAGTAGTAATGGAACAAATA
*
63009 TACCTCTATTC
260 TACCTCGATTC
* * * * * * * * *
63020 AATCTTCCCTGAAGAACATTGGAGTAAATCAATGTCTCCATATATGATTTTCCCCGAAGAAGCAG
1 AATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAGAT-TGATTTTCCCTGAAGAAACAA
* ** * *
63085 CGGAACAGAT--CATCTCTTTCCAGATTTGATCTT-TCTTGAACAACAGTGTAACAAGTCT-CCT
65 CGGAACAGATCCCCTCTCTTTCCAGATTTGATCTTCTCTTGAGTAGCAGTGGAACAAGTCTGCCT
63146 CGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAA
130 CGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAA
63184 AGCTTCTCGA
Statistics
Matches: 373, Mismatches: 57, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
267 41 0.11
268 41 0.11
269 95 0.25
270 196 0.53
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (270 bp):
AATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATTGATTTTCCCTGAAGAAACAAC
GGAACAGATCCCCTCTCTTTCCAGATTTGATCTTCTCTTGAGTAGCAGTGGAACAAGTCTGCCTC
GATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTGAAGA
AACAACAGAAAATATCCCCTCCCTATCTAGATTTGATCTTCCCTGAGTAGTAATGGAACAAATAT
ACCTCGATTC
Found at i:63360 original size:3 final size:3
Alignment explanation
Indices: 63352--63437 Score: 165
Period size: 3 Copynumber: 29.0 Consensus size: 3
63342 TTCTTATCCC
63352 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
63399 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
63438 CCAGCCTTTA
Statistics
Matches: 82, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 80 0.98
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:68137 original size:31 final size:32
Alignment explanation
Indices: 68055--68138 Score: 82
Period size: 31 Copynumber: 2.7 Consensus size: 32
68045 GACCTAAACA
* * * *
68055 AAAAACAATTGATCTCATATTGACTCGACCCG
1 AAAATCAACTGATCTGATATTGACGCGACCCG
* *
68087 AAAATCAACTAAT-TCGATATTGA-GCGACTCG
1 AAAATCAACTGATCT-GATATTGACGCGACCCG
*
68118 AAAATCAAGTGATCTGATATT
1 AAAATCAACTGATCTGATATT
68139 AACCCAAACT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
31 24 0.57
32 18 0.43
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.27
Consensus pattern (32 bp):
AAAATCAACTGATCTGATATTGACGCGACCCG
Found at i:69144 original size:18 final size:18
Alignment explanation
Indices: 69121--69167 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
69111 ATTATTGTAA
*
69121 AATCATAATACT-TACAAT
1 AATCATAATAATAT-CAAT
* *
69139 AATCATGATAATATCTAT
1 AATCATAATAATATCAAT
69157 AATCATAATAA
1 AATCATAATAA
69168 ATATAATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 23 0.96
19 1 0.04
ACGTcount: A:0.51, C:0.13, G:0.02, T:0.34
Consensus pattern (18 bp):
AATCATAATAATATCAAT
Found at i:70242 original size:2 final size:2
Alignment explanation
Indices: 70235--70278 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
70225 TCATTTAGGA
70235 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
70277 AT
1 AT
70279 TTACATGTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:73711 original size:43 final size:43
Alignment explanation
Indices: 73650--73732 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
73640 TCCTTGATTA
*
73650 CAAGCAGAGAAATGGTTGAAAAGCATACCAAATGGCTCACTCG
1 CAAGCAGAGAAATGGTTGAAAAGCATACCAAAAGGCTCACTCG
* * *
73693 CAAGCAGAGAAATGGTTGAATATCATATCAAAAGGCTCAC
1 CAAGCAGAGAAATGGTTGAAAAGCATACCAAAAGGCTCAC
73733 CAATTATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.18
Consensus pattern (43 bp):
CAAGCAGAGAAATGGTTGAAAAGCATACCAAAAGGCTCACTCG
Found at i:83563 original size:11 final size:11
Alignment explanation
Indices: 83547--83572 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
83537 TAACAAGTTG
83547 AATTTTACTAT
1 AATTTTACTAT
83558 AATTTTACTAT
1 AATTTTACTAT
83569 AATT
1 AATT
83573 AATTTATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
AATTTTACTAT
Done.