Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000324.1 Hibiscus syriacus cultivar Beakdansim tig00000606_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: 61221
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1820 original size:26 final size:26
Alignment explanation
Indices: 1743--1807 Score: 121
Period size: 26 Copynumber: 2.5 Consensus size: 26
1733 AAGGAAGAAA
*
1743 TTATAAAATTTTAAGGGACGATAAAC
1 TTATAAAATTTTAAGGGACGATAAAT
1769 TTATAAAATTTTAAGGGACGATAAAT
1 TTATAAAATTTTAAGGGACGATAAAT
1795 TTATAAAATTTTA
1 TTATAAAATTTTA
1808 CATGAACAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.37
Consensus pattern (26 bp):
TTATAAAATTTTAAGGGACGATAAAT
Found at i:2150 original size:8 final size:9
Alignment explanation
Indices: 2122--2165 Score: 54
Period size: 10 Copynumber: 4.7 Consensus size: 9
2112 ATTTAGAATA
2122 AAAATATTT
1 AAAATATTT
2131 AAAAATATTT
1 -AAAATATTT
2141 AAAA-ATTT
1 AAAATATTT
2149 AAAATCAATTT
1 AAAAT--ATTT
2160 AAAATA
1 AAAATA
2166 AAAACATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 8 0.26
9 5 0.16
10 9 0.29
11 9 0.29
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (9 bp):
AAAATATTT
Found at i:29393 original size:24 final size:25
Alignment explanation
Indices: 29366--29420 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
29356 CGTTCATTTA
29366 CGTTCGTG-AACGTTCGGTTATGTT
1 CGTTCGTGTAACGTTCGGTTATGTT
* * * *
29390 CGTTTG-GTTATGTTCGTTTATGTT
1 CGTTCGTGTAACGTTCGGTTATGTT
29414 CGTTCGT
1 CGTTCGT
29421 TTATGTTCAT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.09, C:0.15, G:0.27, T:0.49
Consensus pattern (25 bp):
CGTTCGTGTAACGTTCGGTTATGTT
Found at i:29398 original size:14 final size:14
Alignment explanation
Indices: 29376--29408 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
29366 CGTTCGTGAA
*
29376 CGTTCGGTTATGTT
1 CGTTTGGTTATGTT
29390 CGTTTGGTTATGTT
1 CGTTTGGTTATGTT
29404 CGTTT
1 CGTTT
29409 ATGTTCGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.12, G:0.27, T:0.55
Consensus pattern (14 bp):
CGTTTGGTTATGTT
Found at i:29418 original size:14 final size:14
Alignment explanation
Indices: 29401--29441 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
29391 GTTTGGTTAT
29401 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
29415 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
* *
29429 ATTCATTTATGTT
1 GTTCGTTTATGTT
29442 TAATACAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.12, C:0.12, G:0.17, T:0.59
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:29424 original size:24 final size:24
Alignment explanation
Indices: 29377--29428 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
29367 GTTCGTGAAC
*
29377 GTTCGGTTATGTTCGTTTGGTTAT
1 GTTCGGTTATGTTCGTTCGGTTAT
* *
29401 GTTCGTTTATGTTCGTTCGTTTAT
1 GTTCGGTTATGTTCGTTCGGTTAT
29425 GTTC
1 GTTC
29429 ATTCATTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.08, C:0.12, G:0.25, T:0.56
Consensus pattern (24 bp):
GTTCGGTTATGTTCGTTCGGTTAT
Found at i:30196 original size:16 final size:16
Alignment explanation
Indices: 30177--30243 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
30167 TTTATGTTCG
* *
30177 TTTATATTCGTGTTCA
1 TTTATGTTCGTATTCA
30193 TTTATGTTCGTATTCA
1 TTTATGTTCGTATTCA
*
30209 TTTATGTTCGTATTCG
1 TTTATGTTCGTATTCA
30225 TTTATGTTCGT-TT-A
1 TTTATGTTCGTATTCA
30239 TTTAT
1 TTTAT
30244 TAAATGAACG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
14 5 0.11
15 2 0.04
16 40 0.85
ACGTcount: A:0.16, C:0.10, G:0.13, T:0.60
Consensus pattern (16 bp):
TTTATGTTCGTATTCA
Found at i:30203 original size:26 final size:27
Alignment explanation
Indices: 30167--30239 Score: 76
Period size: 32 Copynumber: 2.6 Consensus size: 27
30157 GCCTCCAACG
*
30167 TTTATGTTCGTTTATA-TTCGTGTTCA
1 TTTATGTTCGTTTATAGTTCGTATTCA
*
30193 TTTATGTTCGTATTCATTTATGTTCGTATTCG
1 TTTATGTTCGT-TT-A--TA-GTTCGTATTCA
30225 TTTATGTTCGTTTAT
1 TTTATGTTCGTTTAT
30240 TTATTAAATG
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
26 11 0.28
27 2 0.05
28 2 0.05
30 3 0.08
31 2 0.05
32 19 0.49
ACGTcount: A:0.15, C:0.11, G:0.15, T:0.59
Consensus pattern (27 bp):
TTTATGTTCGTTTATAGTTCGTATTCA
Found at i:32429 original size:28 final size:28
Alignment explanation
Indices: 32390--32465 Score: 127
Period size: 28 Copynumber: 2.7 Consensus size: 28
32380 TAACCCATAG
32390 AATT-AAATATATTAATTTTTTTAAATA
1 AATTAAAATATATTAATTTTTTTAAATA
32417 AATTAAAATATATTAATTTTTTTAAATA
1 AATTAAAATATATTAATTTTTTTAAATA
*
32445 AAATAAAATATATTATATTTT
1 AATTAAAATATATTA-ATTTT
32466 CAAGATAAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
27 4 0.09
28 37 0.80
29 5 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
AATTAAAATATATTAATTTTTTTAAATA
Found at i:32554 original size:27 final size:28
Alignment explanation
Indices: 32524--32580 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
32514 GATATCAATT
32524 AAATATATTA-A-ATTTTATTATGTTTAA
1 AAATATATTATATATTTTA-TATGTTTAA
* *
32551 AAATATTTTATATATTTTATATTTTTAA
1 AAATATATTATATATTTTATATGTTTAA
32579 AA
1 AA
32581 TTTTGTTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 9 0.35
28 11 0.42
29 6 0.23
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (28 bp):
AAATATATTATATATTTTATATGTTTAA
Found at i:37539 original size:20 final size:20
Alignment explanation
Indices: 37514--37567 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
37504 TATTCCCTGA
37514 TAATCTTACATTTCCACTGG
1 TAATCTTACATTTCCACTGG
*
37534 TAATCTTACATTCCCACTGG
1 TAATCTTACATTTCCACTGG
37554 TAATCTTACATTTC
1 TAATCTTACATTTC
37568 GTGAACCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.26, C:0.26, G:0.07, T:0.41
Consensus pattern (20 bp):
TAATCTTACATTTCCACTGG
Found at i:38202 original size:677 final size:680
Alignment explanation
Indices: 36924--38202 Score: 1972
Period size: 677 Copynumber: 1.9 Consensus size: 680
36914 TTGGATCAAA
* * *
36924 GAATATGAGACTCCCATAGGAATGAAATTCACATTCTCATGTTTGGTTGGCCGGGAATCTCATTC
1 GAATATGAGACTCCCATAGGAATGAAATCCACATTCTCACGTTTGGTTAGCCGGGAATCTCATTC
* ** * *
36989 CCGGTAATGTTTTATTACCAATAGTAGATTTTTTGAGGTATATTACCGGGAATGTCATTATCTCC
66 CCGGTAATCTTACATTACCAATAGTAGATTTTTTGAGGTATATTACCGGAAATGTCATTACCTCC
* * * **
37054 ATTTCCTTAGGTATTGTTGGATTACCGGCGTTTTAGACTAAAATACCTAAAATTTTTATTTTTTT
131 ATTTCCTTAAGTATTATTGGATTACCGGCGCTTTAGACTAAAATACCTAAAA-TTTTATTTCCTT
*
37119 CCAAAAATATTCTTCTTCTGTCATTGAATAATAAAAATTCTACGAAGGTTAAATTACAAATTTAT
195 CCAAAAATATTCTTATTCTGTCATTGAATAATAAAAATTCTACGAAGGTTAAATTACAAATTTAT
37184 CCTTAAACTATTTTAGATTTACAAAAAAAAGTCTATAATTAAAATTTTATATGAAGTTCAGGGGT
260 CCTTAAACTATTTTAGATTTACAAAAAAAAGTCTATAATTAAAATTTTATATGAAGTTCAGGGGT
*
37249 TAAAATAAAATTTTACCCTTTCATTAAATATTTTTATATTTTCAATTTTGTAAAAAAATATATAA
325 TAAAATAAAATTTTACCCTTTCATTAAACATTTTTATATTTTCAATTTTGTAAAAAAATATATAA
*
37314 ATTTTATGAATTTAAATTTTTTTAAAGAAAAATATATAAATATTTTCCTACTTGGTAAAAAACAA
390 ATTTTATGAATTTAAATTTTTTTAAAGAAAAATATATAAATATTTTCCAACTTGGTAAAAAACAA
*
37379 ATATATAATAAGAAAAATTTGGTCAAATATACATTCCAATAATATTTTATTCCTTTAACCAAACA
455 AAATATAATAAGAAAAATTTGGTCAAATATACATTCCAATAATATTTTATTCCTTTAACCAAACA
* *
37444 CGAGAATCTTACATTTCTGCTAAACCAACCAAACACAAAATACAACATTCCCAGTAATCTTATTC
520 CGAGAATCTTACATTTCTACTAAACCAACCAAACACAAAATACAACATTCCCAGTAATCCTATTC
37509 CCTGATAATCTTACATTTCCACTGGTAATCTTACATTCCCACTGGTAATCTTACATTTCGTGAAC
585 CCTGATAATCTTACATTTCCACTGGTAATCTTACATTCCCACTGGTAATCTTACATTTCGTGAAC
37574 CAAACGCACCCTAAGGGTGTGTTTGGTTGGG
650 CAAACGCACCCTAAGGGTGTGTTTGGTTGGG
* * * * *
37605 GAATGTGAGATTCCCATGGGAAT-AGAATCCACATTC-CCCGTTTGGTTAGCCGGGAATGTCATT
1 GAATATGAGACTCCCATAGGAATGA-AATCCACATTCTCACGTTTGGTTAGCCGGGAATCTCATT
* * *
37668 TCCGGTAATCTTACATTACCAATAGT-GAATTTTTTGGGGTATATTATCGGAAATGTCATTACCT
65 CCCGGTAATCTTACATTACCAATAGTAG-ATTTTTTGAGGTATATTACCGGAAATGTCATTACCT
* * * *
37732 CCCTTTCCTTAAGTATTATTGGATTACCGGCGCTTTGGACTAAAATACCCTTACA-TTT-TTTCC
129 CCATTTCCTTAAGTATTATTGGATTACCGGCGCTTTAGACTAAAATA-CCTAAAATTTTATTTCC
* * *
37795 TT-CAAAAATA-TCATTATTTTGTCATTGAATAATAAAAATTCTACGAATGTTAATTTACAAATT
193 TTCCAAAAATATTC-TTATTCTGTCATTGAATAATAAAAATTCTACGAAGGTTAAATTACAAATT
37858 TATCCTTAAACTATTTTAGATTTAC-AAAAAAAGTCTATAATTAAAATTTTATATGAAGTTCAGG
257 TATCCTTAAACTATTTTAGATTTACAAAAAAAAGTCTATAATTAAAATTTTATATGAAGTTCAGG
* *
37922 GGTTGAAATAAAATTTTACCCTTTCATTAAACCTTTTTATATTTTCAATTTTGTAAAAAATATAT
322 GGTTAAAATAAAATTTTACCCTTTCATTAAACATTTTTATATTTTCAATTTTGT-AAAAA-A-AT
*
37987 ATATAAATTTTATGAATTT-AATTTTTTTAAAG-AAAATATATAAATATTTTCCAACTTGTTAAA
384 ATATAAATTTTATGAATTTAAATTTTTTTAAAGAAAAATATATAAATATTTTCCAACTTGGTAAA
* * *
38050 AAA-AATAAATATAATAAGGATAATTTGGTCAAATATACATTCCAATAATCTTTTATTCCTTTAA
449 AAACAA-AAATATAATAAGAAAAATTTGGTCAAATATACATTCCAATAATATTTTATTCCTTTAA
* *
38114 CCAAACACG-GTAATCTTACA-TTCTTACTAAACCAACCAAACACAAAATACAACATTTCTAGTA
513 CCAAACACGAG-AATCTTACATTTC-TACTAAACCAACCAAACACAAAATACAACATTCCCAGTA
* *
38177 ATCCTATTCTCTGGTAATCTTACATT
576 ATCCTATTCCCTGATAATCTTACATT
38203 CTGTGAACCA
Statistics
Matches: 544, Mismatches: 44, Indels: 24
0.89 0.07 0.04
Matches are distributed among these distances:
676 98 0.18
677 247 0.45
678 19 0.03
679 25 0.05
680 120 0.22
681 35 0.06
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (680 bp):
GAATATGAGACTCCCATAGGAATGAAATCCACATTCTCACGTTTGGTTAGCCGGGAATCTCATTC
CCGGTAATCTTACATTACCAATAGTAGATTTTTTGAGGTATATTACCGGAAATGTCATTACCTCC
ATTTCCTTAAGTATTATTGGATTACCGGCGCTTTAGACTAAAATACCTAAAATTTTATTTCCTTC
CAAAAATATTCTTATTCTGTCATTGAATAATAAAAATTCTACGAAGGTTAAATTACAAATTTATC
CTTAAACTATTTTAGATTTACAAAAAAAAGTCTATAATTAAAATTTTATATGAAGTTCAGGGGTT
AAAATAAAATTTTACCCTTTCATTAAACATTTTTATATTTTCAATTTTGTAAAAAAATATATAAA
TTTTATGAATTTAAATTTTTTTAAAGAAAAATATATAAATATTTTCCAACTTGGTAAAAAACAAA
AATATAATAAGAAAAATTTGGTCAAATATACATTCCAATAATATTTTATTCCTTTAACCAAACAC
GAGAATCTTACATTTCTACTAAACCAACCAAACACAAAATACAACATTCCCAGTAATCCTATTCC
CTGATAATCTTACATTTCCACTGGTAATCTTACATTCCCACTGGTAATCTTACATTTCGTGAACC
AAACGCACCCTAAGGGTGTGTTTGGTTGGG
Found at i:53404 original size:34 final size:34
Alignment explanation
Indices: 53366--53454 Score: 97
Period size: 34 Copynumber: 2.5 Consensus size: 34
53356 AACACGCTGG
* *
53366 GCATCTGAGGCCATCCGAACGAGGCCATCCGAGA
1 GCATCCGAGGCCATCCGAACGAGGCAATCCGAGA
* *
53400 GCATCCGAGGTCATCCGACCGAGGCAATCCGAACGA
1 GCATCCGAGGCCATCCGAACGAGGCAATCCG-A-GA
* *
53436 GCTATGCGAGGGCATCCGA
1 GC-ATCCGAGGCCATCCGA
53455 GGGCAACCGA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
34 27 0.59
35 1 0.02
36 4 0.09
37 14 0.30
ACGTcount: A:0.26, C:0.31, G:0.30, T:0.12
Consensus pattern (34 bp):
GCATCCGAGGCCATCCGAACGAGGCAATCCGAGA
Found at i:53470 original size:33 final size:34
Alignment explanation
Indices: 53418--53502 Score: 122
Period size: 33 Copynumber: 2.6 Consensus size: 34
53408 GGTCATCCGA
* * *
53418 CCGA-GGCAATCCGAACGAGCTATGCGAGGGCAT
1 CCGAGGGCAAGCCGAGCGAGCTATGCGAGGGAAT
53451 CCGAGGGCAA-CCGAGCGAGCTATGCGAGGGAAT
1 CCGAGGGCAAGCCGAGCGAGCTATGCGAGGGAAT
53484 CCGAGGG-AAGCCGAGCGAG
1 CCGAGGGCAAGCCGAGCGAG
53503 GGTAGGTCGC
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
32 2 0.04
33 41 0.85
34 5 0.10
ACGTcount: A:0.27, C:0.26, G:0.39, T:0.08
Consensus pattern (34 bp):
CCGAGGGCAAGCCGAGCGAGCTATGCGAGGGAAT
Found at i:53539 original size:29 final size:29
Alignment explanation
Indices: 53506--53562 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
53496 GAGCGAGGGT
*
53506 AGGTCGCCCGGAGTGCATGGCGACCTATA
1 AGGTCGCCCGGAGAGCATGGCGACCTATA
*
53535 AGGTCGCCCGGAGAGCATGTCGACCTAT
1 AGGTCGCCCGGAGAGCATGGCGACCTAT
53563 GTGTTGGGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.28, G:0.33, T:0.18
Consensus pattern (29 bp):
AGGTCGCCCGGAGAGCATGGCGACCTATA
Found at i:53662 original size:29 final size:29
Alignment explanation
Indices: 53620--53675 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
53610 GAGCAAGGGT
53620 AGGTCGCCCAGAGTGCATGGCGACCTACA
1 AGGTCGCCCAGAGTGCATGGCGACCTACA
53649 AGGTCG-CCATGAGTGCATGGCGACCTA
1 AGGTCGCCCA-GAGTGCATGGCGACCTA
53676 TGGCGACCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 3 0.12
29 23 0.88
ACGTcount: A:0.23, C:0.29, G:0.32, T:0.16
Consensus pattern (29 bp):
AGGTCGCCCAGAGTGCATGGCGACCTACA
Done.