Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008527.1 Hibiscus syriacus cultivar Beakdansim tig00111402_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: 9057482
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 37 of 37
Found at i:9026821 original size:20 final size:20
Alignment explanation
Indices: 9026796--9026841 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
9026786 TCTGAAACTT
* *
9026796 AAAATCACAACGCGGAAATG
1 AAAATCACAACGCGAAAATA
**
9026816 AAAATCGTAACGCGAAAATA
1 AAAATCACAACGCGAAAATA
9026836 AAAATC
1 AAAATC
9026842 GATCGCGTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.54, C:0.17, G:0.15, T:0.13
Consensus pattern (20 bp):
AAAATCACAACGCGAAAATA
Found at i:9026848 original size:19 final size:20
Alignment explanation
Indices: 9026804--9026842 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9026794 TTAAAATCAC
* *
9026804 AACGCGGAAATGAAAATCGT
1 AACGCGAAAATAAAAATCGT
9026824 AACGCGAAAATAAAAATCG
1 AACGCGAAAATAAAAATCG
9026843 ATCGCGTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.15, G:0.21, T:0.13
Consensus pattern (20 bp):
AACGCGAAAATAAAAATCGT
Found at i:9027381 original size:20 final size:20
Alignment explanation
Indices: 9027358--9027404 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
9027348 TAAAATTCGC
9027358 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTCTGT
9027378 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTCTGT
9027398 GTTGCGA
1 GTTGCGA
9027405 TTTACAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.15, C:0.15, G:0.28, T:0.43
Consensus pattern (20 bp):
GTTGCGAATTTGACTTCTGT
Found at i:9027418 original size:20 final size:20
Alignment explanation
Indices: 9027395--9027453 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
9027385 ATTTGACTTC
9027395 TGTGTTGCGATTTACAAATT
1 TGTGTTGCGATTTACAAATT
9027415 TGTGTTGC-ATTTACAAATT
1 TGTGTTGCGATTTACAAATT
* * *
9027434 CGCGTTGTGATTTACAAATT
1 TGTGTTGCGATTTACAAATT
9027454 CGCGTTACGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
19 16 0.46
20 19 0.54
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (20 bp):
TGTGTTGCGATTTACAAATT
Found at i:9027897 original size:18 final size:19
Alignment explanation
Indices: 9027863--9027900 Score: 60
Period size: 18 Copynumber: 2.0 Consensus size: 19
9027853 TTTAATTTAA
9027863 AAATAAAAATTTATTAAAAT
1 AAATAAAAA-TTATTAAAAT
9027883 AAATAAAAA-TATTAAAAT
1 AAATAAAAATTATTAAAAT
9027901 TTATAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
20 9 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AAATAAAAATTATTAAAAT
Found at i:9027907 original size:27 final size:25
Alignment explanation
Indices: 9027860--9027922 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 25
9027850 CTATTTAATT
9027860 TAAAAATAAAAATTTATTAAAATAAA
1 TAAAAATAAAAATTTATTAAAAT-AA
9027886 TAAAAATATTAAAATTTA-TAAAATAA
1 TAAAAATA--AAAATTTATTAAAATAA
9027912 TAAACAATAAA
1 TAAA-AATAAA
9027923 TTATTTAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
25 2 0.06
26 14 0.41
27 10 0.29
28 8 0.24
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (25 bp):
TAAAAATAAAAATTTATTAAAATAA
Found at i:9032875 original size:21 final size:22
Alignment explanation
Indices: 9032836--9032879 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
9032826 AAAAACTTAG
9032836 AATTAAAAACAAGTTATAAATT
1 AATTAAAAACAAGTTATAAATT
9032858 AATTCAAAAA-AA-TTATAAATT
1 AATT-AAAAACAAGTTATAAATT
9032879 A
1 A
9032880 CATGTGATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.48
22 6 0.29
23 5 0.24
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (22 bp):
AATTAAAAACAAGTTATAAATT
Found at i:9046209 original size:23 final size:23
Alignment explanation
Indices: 9046183--9046227 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
9046173 CACCACATCT
*
9046183 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
* *
9046206 CGTAGAATTGCGCCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
9046228 ATATAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.27, G:0.29, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:9046445 original size:149 final size:149
Alignment explanation
Indices: 9046195--9046509 Score: 542
Period size: 149 Copynumber: 2.1 Consensus size: 149
9046185 TATAATTGCA
*
9046195 CCGAAGTG-CCGCGTAGAATTGCGCCGTAGTGCCATATAAAAATGTCCATAAGGACCACATATTA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAAAAATGTCCATAAGGACCACATATTA
*
9046259 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATATGTCTTTCAAGACTTCACACATGTT
* *
9046324 CCACAGAATATATATATATC
130 CCAAAGAATATACATATATC
* **
9046344 CCGAAGGACTGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAAAAATGTCCATAAGGACCACATATTAT
9046409 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATATGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATATGTCTTTCAAGACTTCACACATGTTC
*
9046474 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
9046493 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
9046510 CCCTCGACTC
Statistics
Matches: 156, Mismatches: 9, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
148 1 0.01
149 155 0.99
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAAAAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATATGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:9046629 original size:14 final size:14
Alignment explanation
Indices: 9046610--9046637 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
9046600 AACTTGTAAT
9046610 TCACGTATCACATA
1 TCACGTATCACATA
9046624 TCACGTATCACATA
1 TCACGTATCACATA
9046638 GCTTCTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (14 bp):
TCACGTATCACATA
Found at i:9048034 original size:21 final size:21
Alignment explanation
Indices: 9048010--9048054 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
9048000 TGTTGTTCGT
* * *
9048010 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGAACCGATTCCCC
*
9048031 TTGAATGGGAACCGATTCCCC
1 TTGAAGGGGAACCGATTCCCC
9048052 TTG
1 TTG
9048055 CCCAGAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGAACCGATTCCCC
Found at i:9051343 original size:23 final size:23
Alignment explanation
Indices: 9051317--9051361 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
9051307 CACCACAGCT
*
9051317 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
* *
9051340 CGTAGAATTGCGCCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
9051362 ATATAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.27, G:0.29, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:9051579 original size:149 final size:148
Alignment explanation
Indices: 9051329--9051642 Score: 522
Period size: 149 Copynumber: 2.1 Consensus size: 148
9051319 TATAATTGCA
*
9051329 CCGAAGTG-CCGCGTAGAATTGCGCCGTAGTGCCATATAAAAATGTCCATAAGGACCACATATTA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAAAAATGTCCATAAGGACCACATATTA
*
9051393 TTCCTTAATAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
* * *
9051458 CCACATAATATATATATAT
130 CCAAAGAATATACATATAT
**
9051477 CCCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATTA
1 -CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAAAAATGTCCATAAGGACCACATATTA
*
9051542 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTTACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
*
9051607 CCAAAGAATATACATATGT
130 CCAAAGAATATACATATAT
9051626 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
9051643 CCCTCGACTC
Statistics
Matches: 155, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
148 18 0.12
149 137 0.88
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (148 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAAAAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATAT
Found at i:9051762 original size:14 final size:14
Alignment explanation
Indices: 9051743--9051770 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
9051733 AACTTGTAAT
9051743 TCACGTATCACATA
1 TCACGTATCACATA
9051757 TCACGTATCACATA
1 TCACGTATCACATA
9051771 GCTTCTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (14 bp):
TCACGTATCACATA
Found at i:9053165 original size:21 final size:21
Alignment explanation
Indices: 9053141--9053185 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
9053131 TGTTGTTCGT
* *
9053141 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
9053162 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
9053183 TTG
1 TTG
9053186 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:9056683 original size:12 final size:12
Alignment explanation
Indices: 9056666--9056690 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9056656 ACACATTTTT
9056666 CACTCACATTTC
1 CACTCACATTTC
9056678 CACTCACATTTC
1 CACTCACATTTC
9056690 C
1 C
9056691 CCCTGCTAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.44, G:0.00, T:0.32
Consensus pattern (12 bp):
CACTCACATTTC
Done.