Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007739.1 Hibiscus syriacus cultivar Beakdansim tig00109999_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: 642700
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:603475 original size:158 final size:157
Alignment explanation
Indices: 603125--603455 Score: 373
Period size: 158 Copynumber: 2.1 Consensus size: 157
603115 TTATTACTCC
* *
603125 CTGAAGCAAGAGAGAGCA-ATCCCGTAGACAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGA
1 CTGAAGCAAGAGAGAG-AGAACCC-TAGATAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGA
* * * * * *
603189 GAGAGAACCCGTAGGCAGAATATTGTTTGAGTTCTTACTCTCTGAAGAAAGAGAGAGCAAACATG
64 GAGAGAACCCGTAGGCAGAAAATTGTTCGAGTTCTCACTCCCTAAAGAAAGAGAGAGCAAACACG
* *
603254 TAGACAAAAGATTGTTTGAGTTCTTACCT
129 TAGACAAAAGATTGTTGGAGTTCTTACAT
*
603283 CTGAAGTAAGAGAGAGAGAACCCCTAGATAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAG
1 CTGAAGCAAGAGAGAGAGAA-CCCTAGATAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAG
* * * *
603348 AGAGCGAACCCGT-GG-ATAAAAGCTTGTTCGAGTTC-CACTCCCTAAAGCAAGAGGGAGCGAAC
65 AGA--GAACCCGTAGGCAGAAAA--TTGTTCGAGTTCTCACTCCCTAAAGAAAGAGAGAGCAAAC
* * * * *
603410 CCGTTGGCAGAAGATTGTTGGAGTTTTATACAT
126 ACGTAGACAAAAGATTGTTGGAGTTCT-TACAT
603443 CCTGAAGCAAGAG
1 -CTGAAGCAAGAG
603456 GCAGCGAACC
Statistics
Matches: 144, Mismatches: 21, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
157 1 0.01
158 63 0.44
159 46 0.32
160 23 0.16
161 11 0.08
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (157 bp):
CTGAAGCAAGAGAGAGAGAACCCTAGATAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGA
GAGAACCCGTAGGCAGAAAATTGTTCGAGTTCTCACTCCCTAAAGAAAGAGAGAGCAAACACGTA
GACAAAAGATTGTTGGAGTTCTTACAT
Found at i:603502 original size:55 final size:54
Alignment explanation
Indices: 603105--603504 Score: 356
Period size: 53 Copynumber: 7.5 Consensus size: 54
603095 CAAGCGATCA
* * *
603105 ATTGTTCGAGTTATTACTCCCTGAAGCAAGAGAGAGC-AATCCCGTAGACAGAAG
1 ATTGTTCGAGTTCTCACTCCCTGAAGCAAGAGAGAGCGAA-CCCGTGGACAGAAG
*
603159 ATTGTTCGAGTTCT-ACTCCCTGAAGCAAGAGAGA--GAACCCGTAGG-CAGAAT
1 ATTGTTCGAGTTCTCACTCCCTGAAGCAAGAGAGAGCGAACCCGT-GGACAGAAG
* * * * * ** * *
603210 ATTGTTTGAGTTCTTACTCTCTGAAGAAAGAGAGAGCAAACATGTAGACAAAAG
1 ATTGTTCGAGTTCTCACTCCCTGAAGCAAGAGAGAGCGAACCCGTGGACAGAAG
* * * * * * * *
603264 ATTGTTTGAGTTCTTAC-CTCTGAAGTAAGAGAGAGAGAACCCCTAGATAGAAG
1 ATTGTTCGAGTTCTCACTCCCTGAAGCAAGAGAGAGCGAACCCGTGGACAGAAG
* *
603317 ATTGTTCGAGTTCT-ACTCCCTGAAGCAAGAGAGAGCGAACCCGTGGATAAAAG
1 ATTGTTCGAGTTCTCACTCCCTGAAGCAAGAGAGAGCGAACCCGTGGACAGAAG
* * *
603370 CTTGTTCGAGTTC-CACTCCCTAAAGCAAGAGGGAGCGAACCCGTTGG-CAGAAG
1 ATTGTTCGAGTTCTCACTCCCTGAAGCAAGAGAGAGCGAACCCG-TGGACAGAAG
* * * *
603423 ATTGTTGGAGTTTTATACAT-CCTGAAGCAAGAG-GCAGCGAACCTGTTGGA-AGAAG
1 ATTGTTCGAGTTCT-CAC-TCCCTGAAGCAAGAGAG-AGCGAACCCG-TGGACAGAAG
**
603478 ATTGTTTAAGTTCTACACTCCCTGAAG
1 ATTGTTCGAGTTCT-CACTCCCTGAAG
603505 TAATAAGAAG
Statistics
Matches: 289, Mismatches: 42, Indels: 29
0.80 0.12 0.08
Matches are distributed among these distances:
51 23 0.08
52 23 0.08
53 145 0.50
54 44 0.15
55 53 0.18
56 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (54 bp):
ATTGTTCGAGTTCTCACTCCCTGAAGCAAGAGAGAGCGAACCCGTGGACAGAAG
Found at i:603824 original size:2 final size:2
Alignment explanation
Indices: 603817--603843 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
603807 GTAATTATTA
603817 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
603844 ATAAGTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:611145 original size:53 final size:53
Alignment explanation
Indices: 611087--611510 Score: 270
Period size: 58 Copynumber: 7.8 Consensus size: 53
611077 GGCTAACGCG
*
611087 ATTTTTTAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATATTTTTAAATGA
1 ATTTTTAAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATATTTTTAAATGA
** * * *
611140 ATTTTTAAAGAAACTAAGTTTGATTTTCAGGGGTTTCTT-ATGTTTTCAAATGA
1 ATTTTT-AAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATATTTTTAAATGA
* * * *
611193 ATTTTGAAAGAATA-GAAGCCTAATTTTTAGGGGTTTCTTGATATTTTCAAATGA
1 ATTTT-TAAGAA-ACTAAGCCTAATTTTCAGGGGTTTCTTGATATTTTTAAATGA
* * * * * * * *
611247 GTTTTTTAGAAACTAAGTCTGATTTTCAGAGGTTTCTTGACA----TGAA-GT
1 ATTTTTAAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATATTTTTAAATGA
* ** * *
611295 ATTTTTAAAGAAGCTAAGCCTGGTTTTTAGGGGTTTCTTGATGATTATTTCCAATGA
1 ATTTTT-AAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGAT-ATT-TTT-AAATGA
* * * * * *
611352 ATTTTCAA-ATAAGTTATGCTTGATTTTTCAGGGGTTTCTTGATGATTATTTCTAATGA
1 ATTTTTAAGA-AA-CTAAGCCT-AATTTTCAGGGGTTTCTTGAT-ATT-TTT-AAATGA
* * * *
611410 ATTTTTAAAAAAATCTAAGCCTAATTTTTAGGGGTTTCTTGATGATAACTGTAAATGAA
1 ATTTTT-AAGAAA-CTAAGCCTAATTTTCAGGGGTTTCTTGAT-AT--TTTTAAATG-A
* * * * *
611469 AGTTTTTAAGAAACTAAACTTGATTTGCAAGGGTTTCTTGAT
1 A-TTTTTAAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGAT
611511 TAGTAAGTCC
Statistics
Matches: 287, Mismatches: 61, Indels: 41
0.74 0.16 0.11
Matches are distributed among these distances:
48 6 0.02
49 30 0.10
50 1 0.00
52 1 0.00
53 75 0.26
54 46 0.16
55 2 0.01
56 5 0.02
57 11 0.04
58 86 0.30
59 18 0.06
60 6 0.02
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (53 bp):
ATTTTTAAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATATTTTTAAATGA
Found at i:611387 original size:160 final size:157
Alignment explanation
Indices: 611088--611451 Score: 365
Period size: 160 Copynumber: 2.2 Consensus size: 157
611078 GCTAACGCGA
* *
611088 TTTTTTAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATATTTTTAAATGAATTTTTAAAGAAA
1 TTTTTTAGAAACTAAGCCTAATTTTCAGAGGTTTCTTGACA---TTAAATGAATTTTTAAAGAAA
** *
611153 CTAAGTTTGATTTTCAGGGGTTTCTTATGTTTTCAAATGAATTTTGAAAGAATAGAAGCCTAATT
63 CTAAGCCTGATTTTCAGGGGTTTCTTATGTTTTCAAATGAATTTTCAAAGAATAGAAGCCTAATT
611218 TTTAGGGGTTTCTTGATATTTTCAAATGAG
128 TTTAGGGGTTTCTTGATATTTTCAAATGAG
* * * * *
611248 TTTTTTAGAAACTAAGTCTGATTTTCAGAGGTTTCTTGACA-TGAA-GTATTTTTAAAGAAGCTA
1 TTTTTTAGAAACTAAGCCTAATTTTCAGAGGTTTCTTGACATTAAATGAATTTTTAAAGAAACTA
* * * * * * * *
611311 AGCCTGGTTTTTAGGGGTTTCTTGATGATTATTTCCAATGAATTTTCAAATAAGT-TATGCTTGA
66 AGCCTGATTTTCAGGGGTTTCTT-ATG--T-TTTCAAATGAATTTTCAAAGAA-TAGAAGCCTAA
* *
611375 TTTTTCAGGGGTTTCTTGATGATTATTTCTAATGAA
126 TTTTT-AGGGGTTTCTTGAT-A-T-TTTCAAATGAG
* * * *
611411 TTTTTAAAAAAATCTAAGCCTAATTTTTAGGGGTTTCTTGA
1 TTTTT-TAGAAA-CTAAGCCTAATTTTCAGAGGTTTCTTGA
611452 TGATAACTGT
Statistics
Matches: 167, Mismatches: 26, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
155 35 0.21
156 6 0.04
158 1 0.01
159 29 0.17
160 52 0.31
161 1 0.01
162 1 0.01
163 14 0.08
164 4 0.02
165 24 0.14
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (157 bp):
TTTTTTAGAAACTAAGCCTAATTTTCAGAGGTTTCTTGACATTAAATGAATTTTTAAAGAAACTA
AGCCTGATTTTCAGGGGTTTCTTATGTTTTCAAATGAATTTTCAAAGAATAGAAGCCTAATTTTT
AGGGGTTTCTTGATATTTTCAAATGAG
Found at i:611620 original size:41 final size:41
Alignment explanation
Indices: 611516--611639 Score: 108
Period size: 42 Copynumber: 3.0 Consensus size: 41
611506 TTGATTAGTA
* *
611516 AGTCCTTCAGGCCATCAATAAGTCTTTTGAGCATGATGTTT
1 AGTCCTTCAGGCCATCAATAAGTCTTTCGAGCAAGATGTTT
* * *
611557 AAATCCTTCAGGTCATCTATAAGTCTTTCGTA-CAAGATGATTT
1 -AGTCCTTCAGGCCATCAATAAGTCTTTCG-AGCAAGATG-TTT
* * * * * *
611600 -GTCCTTCCGGCCATCCATAAGACCTTCGGGCAGGATGTTT
1 AGTCCTTCAGGCCATCAATAAGTCTTTCGAGCAAGATGTTT
611640 TCACATGATT
Statistics
Matches: 66, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
40 3 0.05
41 28 0.42
42 31 0.47
43 4 0.06
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (41 bp):
AGTCCTTCAGGCCATCAATAAGTCTTTCGAGCAAGATGTTT
Found at i:611924 original size:240 final size:239
Alignment explanation
Indices: 611501--612122 Score: 930
Period size: 240 Copynumber: 2.6 Consensus size: 239
611491 ATTTGCAAGG
* *
611501 GTTTCTTGA-TTAGTAAGTCCTTCAGGCCATCAATAAGTCTTTTGAGCATGATGTTTAAATCCTT
1 GTTTCTT-ACTTAGTAAGTCCATCAGGCCATCAATAAGTCTTTTGAGCATGATGTTTAAATCTTT
** *
611565 CAGGTCATCTATAAGTCTTTCGTA-CAAGATGATTTGTCCTTCCGGCCATCCATAAGACCTTCGG
65 CAGGTCATCTATAAGTCTTTCG-AGCAAGATGATAAGTCCTT-AGGCCATCCATAAGACCTTCGG
* *
611629 GCAGGATGTTTTCACATGATTTTCAAACAAAGAGAAAGGGATTTCCAAAGTTTCTCATTTAAATC
128 GCAGGATGTTTTCACATGATTTTCAAACAAAGAAAAAGCGATTTCCAAAGTTTCTCATTTAAATC
611694 TTTTCTGAAAACTGACATTTCTGAAAAGTAAGAAAACGATTTCCAAA
193 TTTTCTGAAAACTGACATTTCTGAAAAGTAAGAAAACGATTTCCAAA
*
611741 GTTTCTTACTTAGTAAGTCCCTCAGGCCATCAATAAGTCTTTTGAGCATGATGTTTAAATCTTTC
1 GTTTCTTACTTAGTAAGTCCATCAGGCCATCAATAAGTCTTTTGAGCATGATGTTTAAATCTTTC
*
611806 GGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCATAAGACCTTCGGGC
66 AGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTA-GGCCATCCATAAGACCTTCGGGC
*
611871 AGGATGTTTTCACATGATTTTCGAAA-AATGAAAAAGCGATTTCCAAAGTTTCTCATTTAAATCT
130 AGGATGTTTTCACATGATTTTC-AAACAAAGAAAAAGCGATTTCCAAAGTTTCTCATTTAAATCT
*
611935 TTTCTGAAAACTGACATTTCTGAAAAGTAAGAAAATGATTTCCAAA
194 TTTCTGAAAACTGACATTTCTGAAAAGTAAGAAAACGATTTCCAAA
* * ** * * *
611981 GTTTCTTACTTAGTAAGTCCATCGGGTCATCTGTAAGCCTTTCGAGCATGACGTTTAAATCCTTT
1 GTTTCTTACTTAGTAAGTCCATCAGGCCATCAATAAGTCTTTTGAGCATGATGTTTAAAT-CTTT
* * * *
612046 -AGGTTATCCA-AACGTCTTTCAAGCAAGATGATAAGTCCTTCAGGCCATCCACAAGACCTTCGG
65 CAGGTCATCTATAA-GTCTTTCGAGCAAGATGATAAGTCCTT-AGGCCATCCATAAGACCTTCGG
*
612109 GTAGGATGTTTTCA
128 GCAGGATGTTTTCA
612123 TATGGTGATA
Statistics
Matches: 351, Mismatches: 24, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
239 4 0.01
240 339 0.97
241 8 0.02
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (239 bp):
GTTTCTTACTTAGTAAGTCCATCAGGCCATCAATAAGTCTTTTGAGCATGATGTTTAAATCTTTC
AGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTAGGCCATCCATAAGACCTTCGGGCA
GGATGTTTTCACATGATTTTCAAACAAAGAAAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTT
TCTGAAAACTGACATTTCTGAAAAGTAAGAAAACGATTTCCAAA
Found at i:622115 original size:20 final size:20
Alignment explanation
Indices: 622089--622138 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
622079 GACTCAAAGA
*
622089 ATTTACAAATTACCTGAAGG
1 ATTTACAAATTACCCGAAGG
* *
622109 CTTTACAAATTACCCGGAGG
1 ATTTACAAATTACCCGAAGG
622129 ATTTACAAAT
1 ATTTACAAAT
622139 GATCCAGAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (20 bp):
ATTTACAAATTACCCGAAGG
Found at i:622148 original size:20 final size:20
Alignment explanation
Indices: 622110--622148 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
622100 ACCTGAAGGC
* *
622110 TTTACAAATTACCCGGAGGA
1 TTTACAAATGACCCAGAGGA
*
622130 TTTACAAATGATCCAGAGG
1 TTTACAAATGACCCAGAGG
622149 CTTTTAATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.26
Consensus pattern (20 bp):
TTTACAAATGACCCAGAGGA
Found at i:638371 original size:8 final size:8
Alignment explanation
Indices: 638358--638385 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
638348 AAATTCTCCC
638358 ATATGTAT
1 ATATGTAT
638366 ATATGTAT
1 ATATGTAT
638374 ATATGTAT
1 ATATGTAT
638382 ATAT
1 ATAT
638386 CTTCTTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (8 bp):
ATATGTAT
Found at i:641872 original size:10 final size:10
Alignment explanation
Indices: 641859--641902 Score: 52
Period size: 11 Copynumber: 4.1 Consensus size: 10
641849 AAAATGAGTG
641859 AAAATGAAAAA
1 AAAAT-AAAAA
*
641870 AAATAAAAAAA
1 AAA-ATAAAAA
641881 AAAATAAAAA
1 AAAATAAAAA
641891 AAAATGAAAAA
1 AAAAT-AAAAA
641902 A
1 A
641903 TGGAAAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 11 0.38
11 17 0.59
12 1 0.03
ACGTcount: A:0.86, C:0.00, G:0.05, T:0.09
Consensus pattern (10 bp):
AAAATAAAAA
Found at i:641880 original size:12 final size:12
Alignment explanation
Indices: 641865--641894 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
641855 AGTGAAAATG
641865 AAAAAAAATAAA
1 AAAAAAAATAAA
641877 AAAAAAAATAAA
1 AAAAAAAATAAA
641889 AAAAAA
1 AAAAAA
641895 TGAAAAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (12 bp):
AAAAAAAATAAA
Found at i:641884 original size:22 final size:22
Alignment explanation
Indices: 641859--641902 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
641849 AAAATGAGTG
*
641859 AAAATGAAAAAAAATAAAAAAA
1 AAAATAAAAAAAAATAAAAAAA
*
641881 AAAATAAAAAAAAATGAAAAAA
1 AAAATAAAAAAAAATAAAAAAA
641903 TGGAAAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.86, C:0.00, G:0.05, T:0.09
Consensus pattern (22 bp):
AAAATAAAAAAAAATAAAAAAA
Done.