Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004927.1 Hibiscus syriacus cultivar Beakdansim tig00011091_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: 36518
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Found at i:2168 original size:2 final size:2
Alignment explanation
Indices: 2161--2189 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2151 AAAAGGAAAT
2161 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2190 GGTTGGATGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3482 original size:23 final size:23
Alignment explanation
Indices: 3452--3531 Score: 133
Period size: 23 Copynumber: 3.5 Consensus size: 23
3442 ACATCTTATA
*
3452 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
3475 TGGCACTTAGGTGTAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
3498 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
3521 TGGCACTTCGG
1 TGGCACTTCGG
3532 CATTTATACG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.16, C:0.24, G:0.28, T:0.33
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:5271 original size:23 final size:24
Alignment explanation
Indices: 5241--5299 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 24
5231 ATGGCATTTT
5241 GGTG-AATTTCTACG-CGCACTTA
1 GGTGCAATTTCTACGTCGCACTTA
* *
5263 GGTGCAA-TTCTACGTGGCACTTC
1 GGTGCAATTTCTACGTCGCACTTA
*
5286 GGTGC-ATTTATACG
1 GGTGCAATTTCTACG
5300 AGCTGTGGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 12 0.39
23 19 0.61
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.32
Consensus pattern (24 bp):
GGTGCAATTTCTACGTCGCACTTA
Found at i:10456 original size:23 final size:22
Alignment explanation
Indices: 10423--10484 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 22
10413 ATCTTATATG
10423 GCACTTCGGTGCATTTTAACGTA
1 GCACTTCGGTGCATTTT-ACGTA
* * *
10446 GCACTTAGGTGCAATTCTACGTG
1 GCACTTCGGTGC-ATTTTACGTA
*
10469 GCGCTTCGGTGCATTT
1 GCACTTCGGTGCATTT
10485 ATATGGTGAC
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
22 3 0.09
23 25 0.78
24 4 0.12
ACGTcount: A:0.18, C:0.23, G:0.26, T:0.34
Consensus pattern (22 bp):
GCACTTCGGTGCATTTTACGTA
Found at i:16009 original size:68 final size:68
Alignment explanation
Indices: 15936--16072 Score: 229
Period size: 68 Copynumber: 2.0 Consensus size: 68
15926 TAGTCTTTTA
* * * *
15936 CTCAAAGGCATTTAGCCTTTCATCTAACTGACATAATTGACATCTTTCTGTCAAATGCACAGCTA
1 CTCAAAGACACTTAGCCTTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGCACAACTA
16001 GGC
66 GGC
*
16004 CTCAAAGACACTTAGCCTTTCATCTAACTGACATAATTGACACCTTTTTGTCAAATGCACAACTA
1 CTCAAAGACACTTAGCCTTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGCACAACTA
16069 GGC
66 GGC
16072 C
1 C
16073 ATTAATCTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.30
Consensus pattern (68 bp):
CTCAAAGACACTTAGCCTTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGCACAACTA
GGC
Found at i:16490 original size:55 final size:55
Alignment explanation
Indices: 16282--16949 Score: 852
Period size: 55 Copynumber: 12.3 Consensus size: 55
16272 TTTATTAAGA
* * * *
16282 TGCACACATAGTGCCTATACGG-TAGTTCATCAACTCATAATGAATT-TCGTGG-GT
1 TGCACACATAGTGCATGTACGGTTA-TTCATCAACTCATGATGAATTCT-GTGGATT
* * * * *
16336 TGCACACATCGTGCATGTACGGTTATTCATCAACTCGTAATGAATTCCGTGAATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
* * * * *
16391 TGGACACATAGTGCTTGTAC-GTTATTCATCAACTCGTAATGAATTCTATGGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
* * *
16445 TGCACACATAGTGTATGTATGGTTATTCATCAACTCATGATGAATTCT-TTGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
* *
16499 TGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATAAATTC-GTGGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
* * * *
16553 TGTACACATAGTGCCTGTATGGTTATTCATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
* * * *
16608 TGCATACATAGTGCCTCTACGGTTATTCATCCACTCATGATGAATTCAT-TGGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTC-TGTGGATT
*
16663 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
* * *
16718 TGTACACATAGTGCATGTACGGTTATTCATCAATTCATGATGAATTTTGTGGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
* *
16773 TGCACACATAGTGCCTGTAAGGTTATTCATCAACTCATGATGAATT-TCGTGGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCT-GTGGATT
* * *
16828 TTCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCTGCGGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
* ** * **
16883 TGCACACTTAGTGTTTGTAC-GTTA-TCATCAACTCAAGATGAATTCCATGGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
16936 TGCACACATAGTGC
1 TGCACACATAGTGC
16950 CTATTTGGTA
Statistics
Matches: 543, Mismatches: 61, Indels: 21
0.87 0.10 0.03
Matches are distributed among these distances:
53 37 0.07
54 190 0.35
55 315 0.58
56 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (55 bp):
TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
Found at i:16580 original size:163 final size:163
Alignment explanation
Indices: 16282--16951 Score: 882
Period size: 163 Copynumber: 4.1 Consensus size: 163
16272 TTTATTAAGA
* * * * *
16282 TGCACACATAGTGCCTATACGG-TAGTTCATCAACTCATAATGAATTTCGTGG-GTTGCACACAT
1 TGCACACATAGTGCCTGTAAGGTTA-TTCATCAACTCATGATGAA-TTCTTGGATTTGCACACAT
* * * * *
16345 CGTGCATGTACGGTTATTCATCAACTCGTAATGAATTCCGTGAATTTGGACACATAGTGCTTGTA
64 AGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGTACACATAGTGCTTGTA
* *
16410 CGTTATTCATCAACTCGTAATGAATTCTATGGATT
129 CGTTATTCATCAACTCATAATGAATTCCATGGATT
** * *
16445 TGCACACATAGTGTATGTATGGTTATTCATCAACTCATGATGAATTCTTTGATTTGCACACATAG
1 TGCACACATAGTGCCTGTAAGGTTATTCATCAACTCATGATGAATTCTTGGATTTGCACACATAG
* * * *
16510 TGCTTGTACGGTTATTCATCAACTCATGATAAATT-CGTGGATTTGTACACATAGTGCCTGTATG
66 TGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGTACACATAGTGCTTGTA-C
* *
16574 GTTATTCATCAACTCATGATGAATTCCGTGGATT
130 GTTATTCATCAACTCATAATGAATTCCATGGATT
* * * *
16608 TGCATACATAGTGCCTCTACGGTTATTCATCCACTCATGATGAATTCATTGGATTTGCACACATA
1 TGCACACATAGTGCCTGTAAGGTTATTCATCAACTCATGATGAATTC-TTGGATTTGCACACATA
*
16673 GTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGTACACATAGTGCATGTAC
65 GTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGTACACATAGTGCTTGTAC
* * ***
16738 GGTTATTCATCAATTCATGATGAATTTTGTGGATT
130 -GTTATTCATCAACTCATAATGAATTCCATGGATT
* *
16773 TGCACACATAGTGCCTGTAAGGTTATTCATCAACTCATGATGAATTTCGTGGATTTTCACACATA
1 TGCACACATAGTGCCTGTAAGGTTATTCATCAACTCATGATGAA-TTCTTGGATTTGCACACATA
* * * * * *
16838 GTGCTTGTACGGTTATTCATCAACTCATGATGAATTCTGCGGATTTGCACACTTAGTGTTTGTAC
65 GTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGTACACATAGTGCTTGTAC
16903 GTTA-TCATCAACTCA-AGATGAATTCCATGGATT
130 GTTATTCATCAACTCATA-ATGAATTCCATGGATT
16936 TGCACACATAGTGCCT
1 TGCACACATAGTGCCT
16952 ATTTGGTAAT
Statistics
Matches: 446, Mismatches: 53, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
162 29 0.07
163 188 0.42
164 56 0.13
165 170 0.38
166 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (163 bp):
TGCACACATAGTGCCTGTAAGGTTATTCATCAACTCATGATGAATTCTTGGATTTGCACACATAG
TGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGTACACATAGTGCTTGTACG
TTATTCATCAACTCATAATGAATTCCATGGATT
Found at i:17384 original size:20 final size:20
Alignment explanation
Indices: 17361--17432 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
17351 CATCTTTATA
*
17361 GTATCGACACTCCCCTCTTG
1 GTATCGATACTCCCCTCTTG
* * * *
17381 GTATCGATAC-CACTTGAATCG
1 GTATCGATACTCCCCT--CTTG
17402 GTATCGATACTCCCCTCTTG
1 GTATCGATACTCCCCTCTTG
17422 GTATCGATACT
1 GTATCGATACT
17433 ACTTGAATCG
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
19 3 0.08
20 22 0.55
21 12 0.30
22 3 0.08
ACGTcount: A:0.21, C:0.31, G:0.17, T:0.32
Consensus pattern (20 bp):
GTATCGATACTCCCCTCTTG
Found at i:17416 original size:41 final size:41
Alignment explanation
Indices: 17339--17453 Score: 171
Period size: 41 Copynumber: 2.8 Consensus size: 41
17329 TTTTTAACAA
* * *
17339 TGGTATCGATACCATCTT-TAT-AGTATCGACACTCCCCTCT
1 TGGTATCGATACCA-CTTGAATCGGTATCGATACTCCCCTCT
17379 TGGTATCGATACCACTTGAATCGGTATCGATACTCCCCTCT
1 TGGTATCGATACCACTTGAATCGGTATCGATACTCCCCTCT
*
17420 TGGTATCGATACTACTTGAATCGGTATCGATACT
1 TGGTATCGATACCACTTGAATCGGTATCGATACT
17454 ACTGAGCAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
39 3 0.04
40 16 0.23
41 50 0.72
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (41 bp):
TGGTATCGATACCACTTGAATCGGTATCGATACTCCCCTCT
Found at i:17453 original size:21 final size:21
Alignment explanation
Indices: 17380--17456 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
17370 CTCCCCTCTT
*
17380 GGTATCGATACCACTTGAATC
1 GGTATCGATACTACTTGAATC
* * * *
17401 GGTATCGATACTCCCCT--CTT
1 GGTATCGATACT-ACTTGAATC
17421 GGTATCGATACTACTTGAATC
1 GGTATCGATACTACTTGAATC
17442 GGTATCGATACTACT
1 GGTATCGATACTACT
17457 GAGCAAATTC
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
19 2 0.05
20 13 0.30
21 27 0.61
22 2 0.05
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (21 bp):
GGTATCGATACTACTTGAATC
Found at i:19808 original size:65 final size:66
Alignment explanation
Indices: 19717--19852 Score: 256
Period size: 65 Copynumber: 2.1 Consensus size: 66
19707 AAGCTTTGAA
19717 ACATAATATGTGTGGTAAAATGGGTTTAGGTAAGCGGTTAACAGACCAATTCAACTTTTCGTCAC
1 ACATAATA-GTGTGGTAAAATGGGTTTAGGTAAGCGGTTAACAGACCAATTCAACTTTTCGTCAC
19782 CC
65 CC
19784 ACATAATA-TGTGGTAAAATGGGTTTAGGTAAGCGGTTAACAGACCAATTCAACTTTTCGTCACC
1 ACATAATAGTGTGGTAAAATGGGTTTAGGTAAGCGGTTAACAGACCAATTCAACTTTTCGTCACC
19848 C
66 C
19849 ACAT
1 ACAT
19853 TAAAGGTGAT
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
65 61 0.88
67 8 0.12
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (66 bp):
ACATAATAGTGTGGTAAAATGGGTTTAGGTAAGCGGTTAACAGACCAATTCAACTTTTCGTCACC
C
Found at i:21088 original size:24 final size:24
Alignment explanation
Indices: 21061--21129 Score: 104
Period size: 24 Copynumber: 2.9 Consensus size: 24
21051 TAAAGTTGAA
*
21061 TTATAAATTAGGGTAATTCAACTG
1 TTATGAATTAGGGTAATTCAACTG
21085 TTATGAATTAGGGTAATTCAACTG
1 TTATGAATTAGGGTAATTCAACTG
*
21109 TT-TCGAATTAGGATAATTCAA
1 TTAT-GAATTAGGGTAATTCAA
21130 TGCTGCGTGT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
23 1 0.02
24 41 0.98
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (24 bp):
TTATGAATTAGGGTAATTCAACTG
Found at i:21331 original size:2 final size:2
Alignment explanation
Indices: 21324--21362 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
21314 TCATCTTTAG
21324 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21363 TTCTAGTAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:23318 original size:26 final size:26
Alignment explanation
Indices: 23282--23344 Score: 126
Period size: 26 Copynumber: 2.4 Consensus size: 26
23272 CTAGTGGTCA
23282 TGAAAAGATTACTAAGGCACATAATC
1 TGAAAAGATTACTAAGGCACATAATC
23308 TGAAAAGATTACTAAGGCACATAATC
1 TGAAAAGATTACTAAGGCACATAATC
23334 TGAAAAGATTA
1 TGAAAAGATTA
23345 TCAAGATCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.48, C:0.13, G:0.16, T:0.24
Consensus pattern (26 bp):
TGAAAAGATTACTAAGGCACATAATC
Done.