Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008251.1 Hibiscus syriacus cultivar Beakdansim tig00110903_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: 521115
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 3 of 3
Found at i:476183 original size:42 final size:41
Alignment explanation
Indices: 476070--476184 Score: 124
Period size: 42 Copynumber: 2.8 Consensus size: 41
476060 GCCCAAAGGT
* * ** *
476070 CTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
1 CTTATAGATGACCCGAAGGACTTATCATCAAGCTCAAAAGA
* * *
476111 CTTATAGATGACCCGAAAGATTTAAGCATCAAGCTCAAAAGA
1 CTTATAGATGACCCGAAGGACTT-ATCATCAAGCTCAAAAGA
476153 CTTACT-GATGACCCGAAGGACTTACTCATCAA
1 CTTA-TAGATGACCCGAAGGACTTA-TCATCAA
476185 TAAACCCTTG
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
41 20 0.33
42 39 0.65
43 1 0.02
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (41 bp):
CTTATAGATGACCCGAAGGACTTATCATCAAGCTCAAAAGA
Found at i:478337 original size:17 final size:16
Alignment explanation
Indices: 478312--478368 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
478302 ATTGGATTTG
*
478312 TTTTCTTTCTTC-TTTC
1 TTTTCTTT-TTCTTTTT
478328 TTTT-TTTTTC-TTTT
1 TTTTCTTTTTCTTTTT
*
478342 TTCTCTTTTTCTCTTTT
1 TTTTCTTTTTCT-TTTT
478359 TTTTCTTTTT
1 TTTTCTTTTT
478369 TCCCTATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 9 0.26
15 9 0.26
16 4 0.11
17 13 0.37
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTCTTTTTCTTTTT
Found at i:478348 original size:26 final size:26
Alignment explanation
Indices: 478319--478370 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
478309 TTGTTTTCTT
478319 TCTTCTTTCT-TTTTTTTTCTTTTTTC
1 TCTT-TTTCTCTTTTTTTTCTTTTTTC
478345 TCTTTTTCTCTTTTTTTTCTTTTTTC
1 TCTTTTTCTCTTTTTTTTCTTTTTTC
478371 CCTATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (26 bp):
TCTTTTTCTCTTTTTTTTCTTTTTTC
Found at i:478367 original size:7 final size:7
Alignment explanation
Indices: 478312--478370 Score: 54
Period size: 7 Copynumber: 8.7 Consensus size: 7
478302 ATTGGATTTG
478312 TTTTCTT
1 TTTTCTT
*
478319 TCTTCTT
1 TTTTCTT
478326 TCTTT-TT
1 T-TTTCTT
478333 TTTTCTT
1 TTTTCTT
478340 TTTTCTCT
1 TTTTCT-T
478348 TTTTC--
1 TTTTCTT
*
478353 TCTT-TT
1 TTTTCTT
478359 TTTTCTT
1 TTTTCTT
478366 TTTTC
1 TTTTC
478371 CCTATTTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
5 3 0.07
6 6 0.14
7 25 0.60
8 8 0.19
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTCTT
Found at i:478388 original size:26 final size:26
Alignment explanation
Indices: 478324--478378 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 26
478314 TTCTTTCTTC
*
478324 TTTCT-TTTTTTTTCTTTTTTCTCTT
1 TTTCTCTTTTTTTTCTTTTTTCCCTT
478349 TTTCTCTTTTTTTTCTTTTTTCCCTAT
1 TTTCTCTTTTTTTTCTTTTTTCCCT-T
478376 TTT
1 TTT
478379 TTTGTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 5 0.19
26 18 0.67
27 4 0.15
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (26 bp):
TTTCTCTTTTTTTTCTTTTTTCCCTT
Found at i:484097 original size:9 final size:9
Alignment explanation
Indices: 484068--484096 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
484058 TAATAAACTT
484068 AAATAACAA
1 AAATAACAA
484077 AAATAACAA
1 AAATAACAA
484086 AAATAA-AA
1 AAATAACAA
484094 AAA
1 AAA
484097 AGTGAAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 5 0.25
9 15 0.75
ACGTcount: A:0.83, C:0.07, G:0.00, T:0.10
Consensus pattern (9 bp):
AAATAACAA
Found at i:489315 original size:13 final size:13
Alignment explanation
Indices: 489297--489323 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
489287 TAGAGCCATG
489297 ATGATTATTTGTA
1 ATGATTATTTGTA
489310 ATGATTATTTGTA
1 ATGATTATTTGTA
489323 A
1 A
489324 GTTGGTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (13 bp):
ATGATTATTTGTA
Found at i:493517 original size:313 final size:313
Alignment explanation
Indices: 492879--494128 Score: 2418
Period size: 312 Copynumber: 4.0 Consensus size: 313
492869 CTGTTGAGTC
* * *
492879 GTACACTTCTTTTTCAGGTTAATGAAATCGCTTGGAACATGACCGGAGATATGTTCTTTTTGACA
1 GTACACTTTTTTTTCAGGTAAATGAAATTGCTTGGAACATGACCGGAGATATGTTCTTTTTGACA
492944 ACAGGAAATGGTTGGATCAATTTCTTTCTTAGCAATTATGCTTCTCTCCGATTCAAAAACTGTTT
66 ACAGGAAATGGTTGGATCAATTTCTTTCTTAGCAATTATGCTTCTCTCCGATTCAAAAACTGTTT
* *
493009 ATTCTCCTTGATTGTTTTTCTTCTCAGGTACTGTTGAAGTACTTGGATACCCAATACTTAAACCT
131 ATTCTCCTTGATTGTTTTTCTTCTCAGGTACTGTTGAAGTACTTGCATACCCATTACTTAAACCT
*
493074 GTTGACACCCTCATGGCACAAACAGCTGGCTGCTACTGTATTGCAATTGATCCAACAGGAAGGTA
196 GTTGACACCCTCATGGCACATACAGCTGGCTGCTACTGTATTGCAATTGATCCAACAGGAAGGTA
493139 AGGTTTGGCCTAAATCTCTCCTAATTTCCAAGCTCTGTTGCATCTTGACTTTG
261 AGGTTTGGCCTAAATCTCTCCTAATTTCCAAGCTCTGTTGCATCTTGACTTTG
493192 GTACACTTTTTTTTCAGGTAAATGAAATTGCTTGGAACATGACCGGAGATATGTTCTTTTTGACA
1 GTACACTTTTTTTTCAGGTAAATGAAATTGCTTGGAACATGACCGGAGATATGTTCTTTTTGACA
493257 ACAGGAAATGGTTGGATCAATTTCTTTCTTAGCAATTATGCTTCTCTCCGATTCAAAAACTGTTT
66 ACAGGAAATGGTTGGATCAATTTCTTTCTTAGCAATTATGCTTCTCTCCGATTCAAAAACTGTTT
493322 ATTCTCCTTGATTG-TTTTCTTCTCAGGTACTGTTGAAGTACTTGCATACCCATTACTTAAACCT
131 ATTCTCCTTGATTGTTTTTCTTCTCAGGTACTGTTGAAGTACTTGCATACCCATTACTTAAACCT
493386 GTTGACACCCTCATGGCACATACAGCTGGCTGCTACTGTATTGCAATTGATCCAACAGGAAGGTA
196 GTTGACACCCTCATGGCACATACAGCTGGCTGCTACTGTATTGCAATTGATCCAACAGGAAGGTA
493451 AGGTTTGGCCTAAATCTCTCCTAATTTCCAAGCTCTGTTGCATCTTGACTTTG
261 AGGTTTGGCCTAAATCTCTCCTAATTTCCAAGCTCTGTTGCATCTTGACTTTG
493504 GTACACTTTTTTTTCAGGTAAATGAAATTGCTTGGAACATGACCGGAGATATGTTCTTTTTGACA
1 GTACACTTTTTTTTCAGGTAAATGAAATTGCTTGGAACATGACCGGAGATATGTTCTTTTTGACA
493569 ACAGGAAATGGTTGGATCAATTTCTTTCTTAGCAATTATGCTTCTCTCCGATTCAAAAACTGTTT
66 ACAGGAAATGGTTGGATCAATTTCTTTCTTAGCAATTATGCTTCTCTCCGATTCAAAAACTGTTT
493634 ATTCTCCTTGATTGTTTTTCTTCTCAGGTACTGTTGAAGTACTTGCATACCCATTACTTAAACCT
131 ATTCTCCTTGATTGTTTTTCTTCTCAGGTACTGTTGAAGTACTTGCATACCCATTACTTAAACCT
493699 GTTGACACCCTCATGGCACATACAGCTGGCTGCTACTGTATTGCAATTGATCCAACAGGAAGGTA
196 GTTGACACCCTCATGGCACATACAGCTGGCTGCTACTGTATTGCAATTGATCCAACAGGAAGGTA
493764 AGGTTTGGCCTAAATCTCTCCTAATTTCCAAGCTCTGTTGCATCTTGACTTTG
261 AGGTTTGGCCTAAATCTCTCCTAATTTCCAAGCTCTGTTGCATCTTGACTTTG
493817 GTACAC-TTTTTTTCAGGTAAATGAAATTGCTTGGAACATGACCGGAGATATGTTCTTTTTGACA
1 GTACACTTTTTTTTCAGGTAAATGAAATTGCTTGGAACATGACCGGAGATATGTTCTTTTTGACA
493881 ACAGGAAATGGTTGGATCAATTTC-TTCTTAGCAATTATGCTTCTCTCCGATTCAAAAACTGTTT
66 ACAGGAAATGGTTGGATCAATTTCTTTCTTAGCAATTATGCTTCTCTCCGATTCAAAAACTGTTT
493945 ATTCTCCTTGATTGTTTTT-TTCTCAGGTACTGTTGAAGTACTTGCATACCCATTACTTAAACCT
131 ATTCTCCTTGATTGTTTTTCTTCTCAGGTACTGTTGAAGTACTTGCATACCCATTACTTAAACCT
494009 GTTGACACCCTCATGGCACATACAGCTGGCTGCTACTGTATTGCAATTGATCCAACAGGAAGGTA
196 GTTGACACCCTCATGGCACATACAGCTGGCTGCTACTGTATTGCAATTGATCCAACAGGAAGGTA
494074 AGGTTTGGCCTAAATCTCTCCTAATTTCCAAGCTCTGTTGCATCTTGACTTTG
261 AGGTTTGGCCTAAATCTCTCCTAATTTCCAAGCTCTGTTGCATCTTGACTTTG
494127 GT
1 GT
494129 TGCCATCTTC
Statistics
Matches: 930, Mismatches: 6, Indels: 5
0.99 0.01 0.01
Matches are distributed among these distances:
310 165 0.18
311 59 0.06
312 391 0.42
313 315 0.34
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (313 bp):
GTACACTTTTTTTTCAGGTAAATGAAATTGCTTGGAACATGACCGGAGATATGTTCTTTTTGACA
ACAGGAAATGGTTGGATCAATTTCTTTCTTAGCAATTATGCTTCTCTCCGATTCAAAAACTGTTT
ATTCTCCTTGATTGTTTTTCTTCTCAGGTACTGTTGAAGTACTTGCATACCCATTACTTAAACCT
GTTGACACCCTCATGGCACATACAGCTGGCTGCTACTGTATTGCAATTGATCCAACAGGAAGGTA
AGGTTTGGCCTAAATCTCTCCTAATTTCCAAGCTCTGTTGCATCTTGACTTTG
Found at i:497758 original size:19 final size:19
Alignment explanation
Indices: 497711--497764 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
497701 AGACTTATAA
497711 AATTT-TTAAAAAAATTAT
1 AATTTATTAAAAAAATTAT
*
497729 --TTTGAAATAAAAAAATTAT
1 AATTT--ATTAAAAAAATTAT
497748 AATTTATTAAAAAAATT
1 AATTTATTAAAAAAATT
497765 CTTTATAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
16 3 0.10
19 23 0.79
21 3 0.10
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
AATTTATTAAAAAAATTAT
Found at i:502986 original size:25 final size:26
Alignment explanation
Indices: 502945--503002 Score: 91
Period size: 25 Copynumber: 2.3 Consensus size: 26
502935 ATTAGCGAAG
*
502945 GAGAATAGAAGAACGAAGATAAAGAA
1 GAGAAGAGAAGAACGAAGATAAAGAA
*
502971 GAGAAGAG-AGAACGAATATAAAGAA
1 GAGAAGAGAAGAACGAAGATAAAGAA
502996 GAGAAGA
1 GAGAAGA
503003 AATATTCAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 23 0.77
26 7 0.23
ACGTcount: A:0.60, C:0.03, G:0.29, T:0.07
Consensus pattern (26 bp):
GAGAAGAGAAGAACGAAGATAAAGAA
Found at i:505952 original size:25 final size:24
Alignment explanation
Indices: 505916--505964 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 24
505906 AGAGAATAGG
505916 GAATGAGATAAAGAAAAGAAGAGA
1 GAATGAGATAAAGAAAAGAAGAGA
*
505940 GAATAGAGATAAAGAAGAGAAGAGA
1 GAAT-GAGATAAAGAAAAGAAGAGA
505965 TGTTTAAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.61, C:0.00, G:0.31, T:0.08
Consensus pattern (24 bp):
GAATGAGATAAAGAAAAGAAGAGA
Found at i:513856 original size:17 final size:19
Alignment explanation
Indices: 513820--513857 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
513810 TTAGTTAGGT
513820 AACTCATTTTATATCTTTC
1 AACTCATTTTATATCTTTC
*
513839 AACT-ATTTTTTA-CTTTC
1 AACTCATTTTATATCTTTC
513856 AA
1 AA
513858 TTTCACCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 7 0.39
19 4 0.22
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (19 bp):
AACTCATTTTATATCTTTC
Found at i:516165 original size:22 final size:22
Alignment explanation
Indices: 516137--516203 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
516127 TTAGTTGCAG
*
516137 TTTCATCTGATTCAGACTTGGA
1 TTTCATCTGATTCAGACTTAGA
516159 TTTCATCTGATTCAGACTTAGA
1 TTTCATCTGATTCAGACTTAGA
516181 TTTCATCTGATTCAGACTTAGA
1 TTTCATCTGATTCAGACTTAGA
516203 T
1 T
516204 AGATCCTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.42
Consensus pattern (22 bp):
TTTCATCTGATTCAGACTTAGA
Done.