Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008721.1 Hibiscus syriacus cultivar Beakdansim tig00111779_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: 2464137
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 12
Found at i:2408155 original size:12 final size:12
Alignment explanation
Indices: 2408140--2408195 Score: 58
Period size: 12 Copynumber: 4.4 Consensus size: 12
2408130 TGAAGCTGAA
2408140 GATGACGATGAT
1 GATGACGATGAT
* *
2408152 GATGGCGATGAA
1 GATGACGATGAT
*
2408164 GCTGACGATGAAGAT
1 GATGACGAT---GAT
2408179 GATGACGATGAT
1 GATGACGATGAT
2408191 GATGA
1 GATGA
2408196 TGATCCAAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
12 25 0.71
15 10 0.29
ACGTcount: A:0.34, C:0.09, G:0.36, T:0.21
Consensus pattern (12 bp):
GATGACGATGAT
Found at i:2408155 original size:24 final size:24
Alignment explanation
Indices: 2408123--2408198 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 24
2408113 CAAGCGGTCA
*
2408123 ATGAAGATGAAGCTGAAGATGACG
1 ATGAAGATGAAGATGAAGATGACG
* ** *
2408147 ATGATGATGGCGATGAAGCTGACG
1 ATGAAGATGAAGATGAAGATGACG
* * * *
2408171 ATGAAGATGATGACGATGATGATG
1 ATGAAGATGAAGATGAAGATGACG
2408195 ATGA
1 ATGA
2408199 TCCAAACAAG
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.37, C:0.08, G:0.34, T:0.21
Consensus pattern (24 bp):
ATGAAGATGAAGATGAAGATGACG
Found at i:2408186 original size:15 final size:15
Alignment explanation
Indices: 2408166--2408198 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2408156 GCGATGAAGC
2408166 TGACGATGAAGATGA
1 TGACGATGAAGATGA
*
2408181 TGACGATGATGATGA
1 TGACGATGAAGATGA
2408196 TGA
1 TGA
2408199 TCCAAACAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.33, T:0.24
Consensus pattern (15 bp):
TGACGATGAAGATGA
Found at i:2408192 original size:30 final size:30
Alignment explanation
Indices: 2408128--2408192 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
2408118 GGTCAATGAA
* * *
2408128 GATGAAGCTGAAGATGACGATGATGATGGC
1 GATGAAGCTGAAGATGAAGATGATGACGAC
* *
2408158 GATGAAGCTGACGATGAAGATGATGACGAT
1 GATGAAGCTGAAGATGAAGATGATGACGAC
2408188 GATGA
1 GATGA
2408193 TGATGATCCA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.35, C:0.09, G:0.35, T:0.20
Consensus pattern (30 bp):
GATGAAGCTGAAGATGAAGATGATGACGAC
Found at i:2409728 original size:23 final size:23
Alignment explanation
Indices: 2409702--2409768 Score: 107
Period size: 23 Copynumber: 2.9 Consensus size: 23
2409692 AGATTTATGG
2409702 TGTAATAGGTAGCGCTTATATAA
1 TGTAATAGGTAGCGCTTATATAA
* *
2409725 TGTAATAGGTATCGTTTATATAA
1 TGTAATAGGTAGCGCTTATATAA
*
2409748 TGTAATAGGTAGTGCTTATAT
1 TGTAATAGGTAGCGCTTATAT
2409769 TGTAAAGTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (23 bp):
TGTAATAGGTAGCGCTTATATAA
Found at i:2409793 original size:46 final size:45
Alignment explanation
Indices: 2409702--2409793 Score: 105
Period size: 46 Copynumber: 2.0 Consensus size: 45
2409692 AGATTTATGG
* *
2409702 TGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAA
1 TGTAATAGGTAGCGCTTATAT-ATGTAATAGCTATCCTTTATATAA
* * *
2409748 TGTAATAGGTAGTGCTTATAT-TGTAAAGTATCTATCCTTTTTATAA
1 TGTAATAGGTAGCGCTTATATATGT-AA-TAGCTATCCTTTATATAA
2409794 AAATGTCCAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
44 3 0.08
45 2 0.05
46 34 0.87
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (45 bp):
TGTAATAGGTAGCGCTTATATATGTAATAGCTATCCTTTATATAA
Found at i:2410215 original size:23 final size:23
Alignment explanation
Indices: 2410184--2410256 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
2410174 ATAGGTAAAA
*
2410184 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
2410207 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
2410230 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
2410253 ATAT
1 ATAT
2410257 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:2410281 original size:46 final size:45
Alignment explanation
Indices: 2410184--2410281 Score: 108
Period size: 46 Copynumber: 2.1 Consensus size: 45
2410174 ATAGGTAAAA
* * *
2410184 ATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTTATAT-ATGTAATAGCTATCCTTT
* *
2410230 ATATAATGTAATAGGTAGTGCTTATAT-TGTAAAGTATCTATCCTTT
1 ATATAATGTAATAGGTAGCGCTTATATATGT-AA-TAGCTATCCTTT
*
2410276 GTATAA
1 ATATAA
2410282 AAGTGTCCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
44 3 0.07
45 2 0.05
46 39 0.89
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.41
Consensus pattern (45 bp):
ATATAATGTAATAGGTAGCGCTTATATATGTAATAGCTATCCTTT
Found at i:2411333 original size:21 final size:21
Alignment explanation
Indices: 2411309--2411377 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
2411299 CTTATTTGTG
*
2411309 TATAGGGTTAGAATCTAATTA
1 TATAGGGTTAAAATCTAATTA
*
2411330 TATAGTG-TAAAAT-TGATGATATA
1 TATAGGGTTAAAATCT-A--AT-TA
* *
2411353 TATTGGGTTATAATCTAATTA
1 TATAGGGTTAAAATCTAATTA
2411374 TATA
1 TATA
2411378 ATATAAAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
19 1 0.03
20 6 0.17
21 11 0.31
22 4 0.11
23 7 0.19
24 6 0.17
25 1 0.03
ACGTcount: A:0.39, C:0.03, G:0.16, T:0.42
Consensus pattern (21 bp):
TATAGGGTTAAAATCTAATTA
Found at i:2419658 original size:31 final size:31
Alignment explanation
Indices: 2419621--2419695 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
2419611 ATTTATTAAC
*
2419621 ATTAATTTATTATAAATTAATAATATTAATA
1 ATTAATTTATTATAAATTAATAACATTAATA
* * * *
2419652 ATTAATTTGTTCTAAATTAATAACGTTAATG
1 ATTAATTTATTATAAATTAATAACATTAATA
2419683 ATTAATTTTATTA
1 ATTAA-TTTATTA
2419696 ATTTTAAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 31 0.86
32 5 0.14
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (31 bp):
ATTAATTTATTATAAATTAATAACATTAATA
Found at i:2420869 original size:15 final size:15
Alignment explanation
Indices: 2420851--2420892 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
2420841 CTACTGTCTT
*
2420851 CTTCTCCTCAGCGGG
1 CTTCTTCTCAGCGGG
* *
2420866 CTTCTTCTCCGCTGG
1 CTTCTTCTCAGCGGG
2420881 CTTCTTCTCAGC
1 CTTCTTCTCAGC
2420893 TTTTGGTGCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.05, C:0.40, G:0.19, T:0.36
Consensus pattern (15 bp):
CTTCTTCTCAGCGGG
Found at i:2421334 original size:28 final size:27
Alignment explanation
Indices: 2421251--2421347 Score: 97
Period size: 28 Copynumber: 3.5 Consensus size: 27
2421241 ATATTTACAA
* *
2421251 TTATATTTATAATTGAAGGCCTAATTT
1 TTATATTTATAATTGAAGTCTTAATTT
* * *
2421278 CTATATTTATAAATG-AGTCCCTTGATTT
1 TTATATTTATAATTGAAGT--CTTAATTT
*
2421306 TTATATTTATAATTGAAATCTTAATTT
1 TTATATTTATAATTGAAGTCTTAATTT
*
2421333 TTTTATTTTATAATT
1 TTATA-TTTATAATT
2421348 TTTTTAATTT
Statistics
Matches: 56, Mismatches: 10, Indels: 7
0.77 0.14 0.10
Matches are distributed among these distances:
26 2 0.04
27 24 0.43
28 28 0.50
29 2 0.04
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.54
Consensus pattern (27 bp):
TTATATTTATAATTGAAGTCTTAATTT
Found at i:2421348 original size:16 final size:17
Alignment explanation
Indices: 2421327--2421358 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2421317 ATTGAAATCT
2421327 TAATTTTTTT-ATTTTA
1 TAATTTTTTTAATTTTA
2421343 TAATTTTTTTAATTTT
1 TAATTTTTTTAATTTT
2421359 TGACCTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (17 bp):
TAATTTTTTTAATTTTA
Found at i:2422830 original size:23 final size:22
Alignment explanation
Indices: 2422784--2422838 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
2422774 TTGGGGCATT
* *
2422784 ATATTTTTTATTATTTTGTAAC
1 ATATTTTCTATTATTATGTAAC
2422806 ATAATTTTCTATTATTATG-ATAC
1 AT-ATTTTCTATTATTATGTA-AC
*
2422829 ATTTTTTCTA
1 ATATTTTCTA
2422839 GAGTTGAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.60
Consensus pattern (22 bp):
ATATTTTCTATTATTATGTAAC
Found at i:2429365 original size:60 final size:60
Alignment explanation
Indices: 2429267--2429381 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
2429257 TGTCCCCATT
* ** * * *
2429267 CTATAACCCTCATTTTAAATTGGTTCCTCATCTTTTGAATATTCTAATTTTATCCCTAAA
1 CTATAACCCTCATTTTAAATTGGTCCCAAAACTTTTGAATATTCCAATTTCATCCCTAAA
*
2429327 CTATGACCCTC-TTTCTAAATTGGTCCCAAAACTTTTGAATATTCCAATTTCATCC
1 CTATAACCCTCATTT-TAAATTGGTCCCAAAACTTTTGAATATTCCAATTTCATCC
2429382 TCAAATTCAT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
59 3 0.06
60 44 0.94
ACGTcount: A:0.28, C:0.24, G:0.06, T:0.42
Consensus pattern (60 bp):
CTATAACCCTCATTTTAAATTGGTCCCAAAACTTTTGAATATTCCAATTTCATCCCTAAA
Found at i:2429602 original size:60 final size:60
Alignment explanation
Indices: 2429509--2429635 Score: 152
Period size: 60 Copynumber: 2.1 Consensus size: 60
2429499 GTATATACGT
* * * *
2429509 ATAGTTTGGGTTGAAATTGGAATGTTCAAAAAGTTT-GGAGACCAATTTAGAATGAATA-TC
1 ATAGTTTGGGATGAAATTGAAATATTCAAAAAGTTTAAG-GACCAATTTAGAATG-ATAGTC
**
2429569 ATAGTTTGGGGATGAAATTGAAATATTC-AAAAGTTTAAGGACTTATTTAGAATGATAGTC
1 ATAGTTT-GGGATGAAATTGAAATATTCAAAAAGTTTAAGGACCAATTTAGAATGATAGTC
2429629 ATAGTTT
1 ATAGTTT
2429636 ACGGATGTAG
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
59 3 0.05
60 37 0.64
61 18 0.31
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.35
Consensus pattern (60 bp):
ATAGTTTGGGATGAAATTGAAATATTCAAAAAGTTTAAGGACCAATTTAGAATGATAGTC
Found at i:2429677 original size:60 final size:59
Alignment explanation
Indices: 2429537--2429683 Score: 154
Period size: 60 Copynumber: 2.5 Consensus size: 59
2429527 GGAATGTTCA
* * ** *
2429537 AAAAGTTTGGAGACCAATTTAGAATGAATATCATAGTTTGGGGATGAAATTGAAATATTC
1 AAAAGTTTAGAGACTAATTTAGAATG-ATATCATAGTTTACGGATGAAATTGAAACATTC
* * *
2429597 AAAAGTTTA-AGGACTTATTTAGAATGATAGTCATAGTTTACGGATGTAGTTGAAACATAT-
1 AAAAGTTTAGA-GACTAATTTAGAATGATA-TCATAGTTTACGGATGAAATTGAAACAT-TC
* *
2429657 AAAAGTTTAGAAACTAATTTAAAATGA
1 AAAAGTTTAGAGACTAATTTAGAATGA
2429684 GGGTCATACT
Statistics
Matches: 72, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
59 4 0.06
60 66 0.92
61 2 0.03
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (59 bp):
AAAAGTTTAGAGACTAATTTAGAATGATATCATAGTTTACGGATGAAATTGAAACATTC
Found at i:2431011 original size:2 final size:2
Alignment explanation
Indices: 2431004--2431040 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2430994 AGGAGGCTGA
2431004 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2431041 TCTAATTTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2431066 original size:24 final size:23
Alignment explanation
Indices: 2431026--2431070 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
2431016 ATATATATAT
2431026 ATATATATATTATATTCTAATTTC
1 ATATATATATTATATTC-AATTTC
*
2431050 ATATATTTACTTA-ATTCAATT
1 ATATATATA-TTATATTCAATT
2431071 ATCAATGTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 4 0.21
24 12 0.63
25 3 0.16
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (23 bp):
ATATATATATTATATTCAATTTC
Found at i:2461309 original size:16 final size:17
Alignment explanation
Indices: 2461290--2461321 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2461280 ATTTTGGAAT
2461290 TTAAAA-TTTAAATTTC
1 TTAAAATTTTAAATTTC
2461306 TTAAAATTTTAAATTT
1 TTAAAATTTTAAATTT
2461322 AAATCTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAAAATTTTAAATTTC
Found at i:2462541 original size:15 final size:15
Alignment explanation
Indices: 2462518--2462549 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2462508 TTCTCAGGTA
*
2462518 TCTCTCTTTTCATCT
1 TCTCCCTTTTCATCT
2462533 TCTCCCTTTTCATCT
1 TCTCCCTTTTCATCT
2462548 TC
1 TC
2462550 CTTGACCTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.38, G:0.00, T:0.56
Consensus pattern (15 bp):
TCTCCCTTTTCATCT
Found at i:2462600 original size:28 final size:26
Alignment explanation
Indices: 2462538--2462600 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 26
2462528 CATCTTCTCC
*
2462538 CTTTTCATCTTCCTTGACCTCCTTTT
1 CTTTTCATCTTCCTTGACCTCATTTT
*
2462564 CTTGATTCATCTTTCTTGACCTCTATTTT
1 CTT--TTCATCTTCCTTGACCTC-ATTTT
2462593 CATTTTCA
1 C-TTTTCA
2462601 CCGACGAGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
26 3 0.10
28 21 0.68
29 5 0.16
30 2 0.06
ACGTcount: A:0.13, C:0.29, G:0.05, T:0.54
Consensus pattern (26 bp):
CTTTTCATCTTCCTTGACCTCATTTT
Done.