Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008341.1 Hibiscus syriacus cultivar Beakdansim tig00111067_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: 1248125
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1199842 original size:12 final size:12
Alignment explanation
Indices: 1199825--1199851 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1199815 TTGCACTGAT
1199825 ACGGATACGGGG
1 ACGGATACGGGG
1199837 ACGGATACGGGG
1 ACGGATACGGGG
1199849 ACG
1 ACG
1199852 AGAAATGGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.19, G:0.48, T:0.07
Consensus pattern (12 bp):
ACGGATACGGGG
Found at i:1207035 original size:19 final size:18
Alignment explanation
Indices: 1207013--1207051 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1207003 TTATACATTT
1207013 TTATATTCTTTATAATTCA
1 TTATATTCTTT-TAATTCA
* *
1207032 TTATTTTCTTTTATTTCA
1 TTATATTCTTTTAATTCA
1207050 TT
1 TT
1207052 TTTGACATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATATTCTTTTAATTCA
Found at i:1207073 original size:26 final size:26
Alignment explanation
Indices: 1207042--1207103 Score: 124
Period size: 26 Copynumber: 2.4 Consensus size: 26
1207032 TTATTTTCTT
1207042 TTATTTCATTTTTGACATTTTTGTTA
1 TTATTTCATTTTTGACATTTTTGTTA
1207068 TTATTTCATTTTTGACATTTTTGTTA
1 TTATTTCATTTTTGACATTTTTGTTA
1207094 TTATTTCATT
1 TTATTTCATT
1207104 CATTCCATAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.19, C:0.08, G:0.06, T:0.66
Consensus pattern (26 bp):
TTATTTCATTTTTGACATTTTTGTTA
Found at i:1208642 original size:8 final size:8
Alignment explanation
Indices: 1208629--1208765 Score: 60
Period size: 8 Copynumber: 17.4 Consensus size: 8
1208619 AATTACACCT
1208629 GAAGAAAA
1 GAAGAAAA
1208637 GAAGAAAA
1 GAAGAAAA
*
1208645 GAAAAAAA
1 GAAGAAAA
1208653 TGAA-AAATA
1 -GAAGAAA-A
*
1208662 -AAAAAAA
1 GAAGAAAA
**
1208669 TTA-AAAA
1 GAAGAAAA
1208676 GAGAGAAAA
1 GA-AGAAAA
1208685 -AAGAAGAGA
1 GAAGAA-A-A
1208694 GAAAGAAAA
1 G-AAGAAAA
1208703 -AAGAAAA
1 GAAGAAAA
* *
1208710 AAATAAAA
1 GAAGAAAA
1208718 -AAGAAAAA
1 GAAG-AAAA
1208726 GAA-AAAA
1 GAAGAAAA
*
1208733 GAAAAAAA
1 GAAGAAAA
1208741 G-AGAAAAA
1 GAAG-AAAA
1208749 GAA-AAAA
1 GAAGAAAA
*
1208756 GTA-AAAA
1 GAAGAAAA
1208763 GAA
1 GAA
1208766 AACTGAATGA
Statistics
Matches: 104, Mismatches: 9, Indels: 33
0.71 0.06 0.23
Matches are distributed among these distances:
7 40 0.38
8 45 0.43
9 13 0.12
10 1 0.01
11 5 0.05
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (8 bp):
GAAGAAAA
Found at i:1208659 original size:15 final size:14
Alignment explanation
Indices: 1208641--1208767 Score: 89
Period size: 15 Copynumber: 8.6 Consensus size: 14
1208631 AGAAAAGAAG
1208641 AAAAGAAAAAAATGA
1 AAAAGAAAAAAAT-A
*
1208656 AAAATAAAAAAAATTA
1 AAAA-GAAAAAAA-TA
1208672 AAAAGAGAGAAAAA-A
1 AAAAGA-A-AAAAATA
* * *
1208687 GAAGAGAGAAAGA-A
1 -AAAAGAAAAAAATA
1208701 AAAAGAAAAAAATAA
1 AAAAGAAAAAAAT-A
*
1208716 AAAAGAAAAAGA-A
1 AAAAGAAAAAAATA
*
1208729 AAAAGAAAAAAAGAGA
1 AAAAG-AAAAAA-ATA
*
1208745 AAAAGAAAAAAGTA
1 AAAAGAAAAAAATA
1208759 AAAAGAAAA
1 AAAAGAAAA
1208768 CTGAATGAAG
Statistics
Matches: 90, Mismatches: 12, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
13 15 0.17
14 20 0.22
15 25 0.28
16 24 0.27
17 6 0.07
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (14 bp):
AAAAGAAAAAAATA
Found at i:1208689 original size:7 final size:7
Alignment explanation
Indices: 1208679--1208767 Score: 90
Period size: 7 Copynumber: 11.9 Consensus size: 7
1208669 TTAAAAAGAG
1208679 AGAAAAA
1 AGAAAAA
1208686 AGAAGAGAGA
1 AGAA-A-A-A
1208696 AAGAAAAA
1 A-GAAAAA
1208704 AGAAAAAA
1 AG-AAAAA
*
1208712 ATAAAAA
1 AGAAAAA
1208719 AG-AAAA
1 AGAAAAA
1208725 AGAAAAA
1 AGAAAAA
1208732 AGAAAAAA
1 AG-AAAAA
1208740 AGAGAAAA
1 AGA-AAAA
1208748 AGAAAAA
1 AGAAAAA
*
1208755 AGTAAAA
1 AGAAAAA
1208762 AGAAAA
1 AGAAAA
1208768 CTGAATGAAG
Statistics
Matches: 70, Mismatches: 4, Indels: 16
0.78 0.04 0.18
Matches are distributed among these distances:
6 6 0.09
7 33 0.47
8 23 0.33
9 2 0.03
10 3 0.04
11 3 0.04
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (7 bp):
AGAAAAA
Found at i:1208710 original size:51 final size:50
Alignment explanation
Indices: 1208633--1208767 Score: 139
Period size: 51 Copynumber: 2.6 Consensus size: 50
1208623 ACACCTGAAG
* * *
1208633 AAAAGA-AGAAAAGAAAAAAATGAAAAATAAAAAAAATTAAAAAGAGAGAA-AAA
1 AAAAGAGA-AAAAG-AAAAAA-GAAAAA-AAAAAAAA-GAAAAAGAAAAAAGAAA
* *
1208686 AGAAGAGAGAAAGAAAAAAGAAAAAAATAAAAAAGAAAAAGAAAAAAGAAA
1 AAAAGAGAAAAAGAAAAAAGAAAAAAA-AAAAAAGAAAAAGAAAAAAGAAA
* *
1208737 AAAAGAGAAAAAGAAAAAAGTAAAAAGAAAA
1 AAAAGAGAAAAAGAAAAAAGAAAAAAAAAAA
1208768 CTGAATGAAG
Statistics
Matches: 70, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
50 16 0.23
51 38 0.54
52 6 0.09
53 9 0.13
54 1 0.01
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (50 bp):
AAAAGAGAAAAAGAAAAAAGAAAAAAAAAAAAAGAAAAAGAAAAAAGAAA
Found at i:1208711 original size:44 final size:41
Alignment explanation
Indices: 1208634--1208766 Score: 144
Period size: 44 Copynumber: 3.1 Consensus size: 41
1208624 CACCTGAAGA
1208634 AAAGAAGAAAAGAAAAAAATGAAAAATA-AAAAAAATTAAAAAG
1 AAAGAA-AAAAGAAAAAAA-GAAAAA-AGAAAAAAATTAAAAAG
* *
1208677 AGAGAAAAAAGAAGAGAGAAAGAAAAAAGAAAAAAATAAAAAAG
1 AAAGAAAAAAGAA-A-A-AAAGAAAAAAGAAAAAAATTAAAAAG
*
1208721 AAAAAGAAAAAAGAAAAAAAGAGAAAAAG-AAAAAAGTAAAAAG
1 --AAAGAAAAAAGAAAAAAAGA-AAAAAGAAAAAAATTAAAAAG
1208764 AAA
1 AAA
1208767 ACTGAATGAA
Statistics
Matches: 78, Mismatches: 5, Indels: 16
0.79 0.05 0.16
Matches are distributed among these distances:
41 3 0.04
42 7 0.09
43 24 0.31
44 28 0.36
45 4 0.05
46 12 0.15
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.05
Consensus pattern (41 bp):
AAAGAAAAAAGAAAAAAAGAAAAAAGAAAAAAATTAAAAAG
Found at i:1208764 original size:65 final size:65
Alignment explanation
Indices: 1208630--1208767 Score: 158
Period size: 65 Copynumber: 2.1 Consensus size: 65
1208620 ATTACACCTG
* * * * *
1208630 AAGAAAAGAAGAAAAGAAAAAAATGAAAAATAAAAAAAATTAAAAAGAGAGAAAAAAGAAGAGAG
1 AAGAAAAGAAGAAAAAAAAAAAAAGAAAAAGAAAAAAAA-TAAAAAGAGAGAAAAAAGAAAAGAA
1208695 A
65 A
1208696 AAGAAAA-AAGAAAAAAATAAAAAAGAAAAAGAAAAAAGAA-AAAAAGAGA-AAAAGAA-AAAAG
1 AAGAAAAGAAGAAAAAAA-AAAAAAGAAAAAGAAAAAA-AATAAAAAGAGAGAAAA-AAGAAAAG
1208757 TAAA
63 -AAA
1208761 AAGAAAA
1 AAGAAAA
1208768 CTGAATGAAG
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
64 8 0.13
65 29 0.46
66 24 0.38
67 2 0.03
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (65 bp):
AAGAAAAGAAGAAAAAAAAAAAAAGAAAAAGAAAAAAAATAAAAAGAGAGAAAAAAGAAAAGAAA
Found at i:1210788 original size:36 final size:36
Alignment explanation
Indices: 1210703--1210788 Score: 84
Period size: 37 Copynumber: 2.4 Consensus size: 36
1210693 TGTGTCACCT
* * *
1210703 TTGAGATTGTTTCTCTCGAAACAAAGTTTCATCTCG
1 TTGAGATTGTTTTTCTCGAAACAAAGATTCATCTCC
* * * *
1210739 TTATAGATAGTTTTTCTTGAAACAAA-ATTGATCTCAC
1 TT-GAGATTGTTTTTCTCGAAACAAAGATTCATCTC-C
1210776 TTGAGATTGTTTT
1 TTGAGATTGTTTT
1210789 CCTAAAAACA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
36 18 0.46
37 21 0.54
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.43
Consensus pattern (36 bp):
TTGAGATTGTTTTTCTCGAAACAAAGATTCATCTCC
Found at i:1210798 original size:36 final size:36
Alignment explanation
Indices: 1210743--1210826 Score: 89
Period size: 36 Copynumber: 2.3 Consensus size: 36
1210733 ATCTCGTTAT
* ** *
1210743 AGATAGTTTTTCTTGAAACAA-AATTGATCTCACTTG
1 AGATAGTTTTCCTAAAAACAAGAATCG-TCTCACTTG
* * *
1210779 AGATTGTTTTCCTAAAAACAAGTATCGTCTCGCTTG
1 AGATAGTTTTCCTAAAAACAAGAATCGTCTCACTTG
1210815 AGATAGTTTTCC
1 AGATAGTTTTCC
1210827 CTTGAAACGT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
36 36 0.92
37 3 0.08
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (36 bp):
AGATAGTTTTCCTAAAAACAAGAATCGTCTCACTTG
Found at i:1211991 original size:115 final size:116
Alignment explanation
Indices: 1211774--1212007 Score: 260
Period size: 115 Copynumber: 2.0 Consensus size: 116
1211764 TGACAAGGAA
* * * * * *
1211774 CATTTTCATATGAAAGCGGCTATAACTCTTCAACATGAATGAGTAGTGTCGTCTTCAACATCAGA
1 CATTTTAATATGAAAGCGGCTAGAACTCTTCAACATGAATGAGCAGTGTCGTCATCAACAACAAA
* * * * * * *
1211839 TTATCTCTAGATTGACTCGACTTCCTCAGAGATAAGGAATAATGTCATATT
66 TTATATCCAAATTGACTCGACTTCCTCAGAAAGAAGGAACAACGTCATATT
* *
1211890 CATTTTAAT-TGAAAGCGGCTAGAACTCTTCAACATGGATGAGCAGTGTTGTCATCAACAACAAA
1 CATTTTAATATGAAAGCGGCTAGAACTCTTCAACATGAATGAGCAGTGTCGTCATCAACAACAAA
* *
1211954 TTATATCCAAATAT-ACAT-GACTTTCTCA-ACAAGAAGGAACAACGTCATTTT
66 TTATATCCAAAT-TGAC-TCGACTTCCTCAGA-AAGAAGGAACAACGTCATATT
1212005 CAT
1 CAT
1212008 CAAATAATTT
Statistics
Matches: 98, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
114 1 0.01
115 87 0.89
116 10 0.10
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (116 bp):
CATTTTAATATGAAAGCGGCTAGAACTCTTCAACATGAATGAGCAGTGTCGTCATCAACAACAAA
TTATATCCAAATTGACTCGACTTCCTCAGAAAGAAGGAACAACGTCATATT
Found at i:1212399 original size:15 final size:15
Alignment explanation
Indices: 1212379--1212410 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1212369 TATTGTCATC
1212379 CACCATACCCTGTTG
1 CACCATACCCTGTTG
*
1212394 CACCATGCCCTGTTG
1 CACCATACCCTGTTG
1212409 CA
1 CA
1212411 GCAACAAGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.41, G:0.16, T:0.25
Consensus pattern (15 bp):
CACCATACCCTGTTG
Found at i:1223281 original size:23 final size:24
Alignment explanation
Indices: 1223241--1223288 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1223231 GTCATACCGA
* *
1223241 TCAAAGTTCAACGGGTTGACTCAG
1 TCAAAGTTCAACGAGTTGAATCAG
*
1223265 TCAAAG-TGAACGAGTTGAATCAG
1 TCAAAGTTCAACGAGTTGAATCAG
1223288 T
1 T
1223289 GACTGGGCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (24 bp):
TCAAAGTTCAACGAGTTGAATCAG
Found at i:1230376 original size:327 final size:327
Alignment explanation
Indices: 1229782--1230762 Score: 1854
Period size: 327 Copynumber: 3.0 Consensus size: 327
1229772 GACCTATGAT
1229782 CCAACCTAAGGGAGTATGATAACTCTGTAAAAGACTTTGTTTTGCGTCTTTTTACTTAGGTTATT
1 CCAACCTAAGGGAGTATGATAACTCTGTAAAAGACTTTGTTTTGCGTCTTTTTACTTAGGTTATT
1229847 GTTTGTCTAAAAGCCATTTGTCATAGCATTTTAGTTGCATATAGTTCAATTTAGGGCATATTTGT
66 GTTTGTCTAAAAGCCATTTGTCATAGCATTTTAGTTGCATATAGTTCAATTTAGGGCATATTTGT
1229912 ATGTGGTGGATAAGTTTTCCAGAGACAAACTTTATTTGGTCTAACTGATGCTGTTGAGGAGGAAG
131 ATGTGGTGGATAAGTTTTCCAGAGACAAACTTTATTTGGTCTAACTGATGCTGTTGAGGAGGAAG
* *
1229977 GTTGTTTACTGGTTGTGTTGATGGAGGAAATGACGAAGGAAGAATTCATTTATCGAGACAAACCA
196 GTTGTTTGCTGGTTGTGTTGATGGAGGAAATGACGAAGGAAGAATTCATTTGTCGAGACAAACCA
1230042 ATTTGCTAGGGCCCGTAGAGCATAAGAAGATGACAGTGAGGAACATATTTTCTTGCCTAGGTGAG
261 ATTTGCTAGGGCCCGTAGAGCATAAGAAGATGACAGTGAGGAACATATTTTCTTGCCTAGGTGAG
1230107 AG
326 AG
1230109 CCAACCTAAGGGAGTATGATAACTCTGTAAAAGACTTTGTTTTGCGTCTTTTTACTTAGGTTATT
1 CCAACCTAAGGGAGTATGATAACTCTGTAAAAGACTTTGTTTTGCGTCTTTTTACTTAGGTTATT
1230174 GTTTGTCTAAAAGCCATTTGTCATAGCATTTTAGTTGCATATAGTTCAATTTAGGGCATATTTGT
66 GTTTGTCTAAAAGCCATTTGTCATAGCATTTTAGTTGCATATAGTTCAATTTAGGGCATATTTGT
1230239 ATGTGGTGGATAAGTTTTCCAGAGACAAACTTTATTTGGTCTAACTGATGCTGTTGAGGAGGAAG
131 ATGTGGTGGATAAGTTTTCCAGAGACAAACTTTATTTGGTCTAACTGATGCTGTTGAGGAGGAAG
*
1230304 GTTGTTTGCTGGTTGTGTTGATGGAGGAAATAACGAAGGAAGAATTCATTTGTCGAGACAAACCA
196 GTTGTTTGCTGGTTGTGTTGATGGAGGAAATGACGAAGGAAGAATTCATTTGTCGAGACAAACCA
*
1230369 ATTTGCTAGGGCCCGTAGAGCATAAGAAGATGACAGTGAGGAACATATTTTCTTTCCTAGGTGAG
261 ATTTGCTAGGGCCCGTAGAGCATAAGAAGATGACAGTGAGGAACATATTTTCTTGCCTAGGTGAG
1230434 AG
326 AG
1230436 CCAACCTAAGGGAGTATGATAACTCTGTAAAAGACTTTGTTTTGCGTCTTTTTACTTAGGTTATT
1 CCAACCTAAGGGAGTATGATAACTCTGTAAAAGACTTTGTTTTGCGTCTTTTTACTTAGGTTATT
* *
1230501 GTTTGTCTAAAAGCAATTTTTCATAGCATTTTAGTTGCATATAGTTCAATTTAGGGCATATTTGT
66 GTTTGTCTAAAAGCCATTTGTCATAGCATTTTAGTTGCATATAGTTCAATTTAGGGCATATTTGT
1230566 ATGTGGTGGATAAGTTTTCCAGAGACAAACTTTATTTGGTCTAACTGATGCTGTTGAGGAGGAAG
131 ATGTGGTGGATAAGTTTTCCAGAGACAAACTTTATTTGGTCTAACTGATGCTGTTGAGGAGGAAG
* *
1230631 GTTATTTGCTGGTTGTGTTGATGGAGGAAATGACGAAGGAAGAATTCATTTGTCAAGACAAACCA
196 GTTGTTTGCTGGTTGTGTTGATGGAGGAAATGACGAAGGAAGAATTCATTTGTCGAGACAAACCA
* * * *
1230696 ATTTGCTAGGGTCTGTAGAGTATAAGAAGATGACAGTGAGGAACATATTTTCTTGCCTAAGTGAG
261 ATTTGCTAGGGCCCGTAGAGCATAAGAAGATGACAGTGAGGAACATATTTTCTTGCCTAGGTGAG
1230761 AG
326 AG
1230763 ATATCTTGCA
Statistics
Matches: 640, Mismatches: 14, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
327 640 1.00
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (327 bp):
CCAACCTAAGGGAGTATGATAACTCTGTAAAAGACTTTGTTTTGCGTCTTTTTACTTAGGTTATT
GTTTGTCTAAAAGCCATTTGTCATAGCATTTTAGTTGCATATAGTTCAATTTAGGGCATATTTGT
ATGTGGTGGATAAGTTTTCCAGAGACAAACTTTATTTGGTCTAACTGATGCTGTTGAGGAGGAAG
GTTGTTTGCTGGTTGTGTTGATGGAGGAAATGACGAAGGAAGAATTCATTTGTCGAGACAAACCA
ATTTGCTAGGGCCCGTAGAGCATAAGAAGATGACAGTGAGGAACATATTTTCTTGCCTAGGTGAG
AG
Found at i:1231918 original size:34 final size:34
Alignment explanation
Indices: 1231873--1231945 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
1231863 GACGATAACT
* *
1231873 CACTTTATACTATATTACTTGCATCGATTGTGTA
1 CACTTTATACTATATTACCTACATCGATTGTGTA
* *
1231907 CACTTTCTACTATATTACCTACATTGATTGTGTA
1 CACTTTATACTATATTACCTACATCGATTGTGTA
1231941 CACTT
1 CACTT
1231946 GCACAAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.44
Consensus pattern (34 bp):
CACTTTATACTATATTACCTACATCGATTGTGTA
Found at i:1234125 original size:2 final size:2
Alignment explanation
Indices: 1234118--1234158 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
1234108 TGTCGTAAAT
*
1234118 TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1234159 GATTGACAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Done.