Multiple sequence alignment - TraesCS3B01G456400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G456400 chr3B 100.000 2867 0 0 1 2867 697912063 697909197 0.000000e+00 5295
1 TraesCS3B01G456400 chr3A 88.802 1795 116 43 667 2426 662413954 662412210 0.000000e+00 2122
2 TraesCS3B01G456400 chr3A 87.500 240 16 6 2632 2867 662411092 662410863 6.090000e-67 265
3 TraesCS3B01G456400 chr3D 94.204 1225 42 12 667 1866 527675911 527674691 0.000000e+00 1842
4 TraesCS3B01G456400 chr3D 82.770 592 51 26 1929 2507 527674669 527674116 5.560000e-132 481
5 TraesCS3B01G456400 chr3D 80.882 612 60 26 6 590 527676518 527675937 2.040000e-116 429
6 TraesCS3B01G456400 chr3D 89.259 270 11 9 2612 2867 527674138 527673873 3.560000e-84 322
7 TraesCS3B01G456400 chr4B 91.463 82 7 0 2509 2590 568662298 568662217 2.330000e-21 113
8 TraesCS3B01G456400 chr5B 91.358 81 7 0 2510 2590 360936599 360936519 8.400000e-21 111
9 TraesCS3B01G456400 chr5B 91.358 81 7 0 2509 2589 529277066 529277146 8.400000e-21 111
10 TraesCS3B01G456400 chr2B 90.244 82 8 0 2509 2590 736908209 736908290 1.090000e-19 108
11 TraesCS3B01G456400 chr2B 89.157 83 9 0 2508 2590 245302046 245301964 1.410000e-18 104
12 TraesCS3B01G456400 chr2B 86.170 94 10 3 2502 2595 468551196 468551106 6.540000e-17 99
13 TraesCS3B01G456400 chr6B 87.912 91 9 2 2500 2590 561645366 561645278 3.910000e-19 106
14 TraesCS3B01G456400 chr2A 90.123 81 8 0 2510 2590 768200847 768200767 3.910000e-19 106
15 TraesCS3B01G456400 chrUn 87.356 87 11 0 2509 2595 31719449 31719363 1.820000e-17 100


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G456400 chr3B 697909197 697912063 2866 True 5295.0 5295 100.00000 1 2867 1 chr3B.!!$R1 2866
1 TraesCS3B01G456400 chr3A 662410863 662413954 3091 True 1193.5 2122 88.15100 667 2867 2 chr3A.!!$R1 2200
2 TraesCS3B01G456400 chr3D 527673873 527676518 2645 True 768.5 1842 86.77875 6 2867 4 chr3D.!!$R1 2861

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
355 366 0.032912 TACCCCCACTGCTATCACGA 60.033 55.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2058 2131 0.040067 GCTGCTTGAAAGGTTGACGG 60.04 55.0 0.0 0.0 0.0 4.79 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 95 1.096416 CTCGCCTCGGGTATATCCTC 58.904 60.000 0.00 0.00 36.25 3.71
88 96 0.323178 TCGCCTCGGGTATATCCTCC 60.323 60.000 0.00 0.00 36.25 4.30
89 97 0.323542 CGCCTCGGGTATATCCTCCT 60.324 60.000 0.00 0.00 36.25 3.69
90 98 1.187087 GCCTCGGGTATATCCTCCTG 58.813 60.000 0.00 0.00 36.25 3.86
91 99 1.187087 CCTCGGGTATATCCTCCTGC 58.813 60.000 0.00 0.00 36.25 4.85
92 100 1.187087 CTCGGGTATATCCTCCTGCC 58.813 60.000 0.00 0.00 36.25 4.85
93 101 0.784495 TCGGGTATATCCTCCTGCCT 59.216 55.000 0.00 0.00 36.25 4.75
94 102 1.187087 CGGGTATATCCTCCTGCCTC 58.813 60.000 0.00 0.00 36.25 4.70
95 103 1.574263 GGGTATATCCTCCTGCCTCC 58.426 60.000 0.00 0.00 36.25 4.30
96 104 1.574263 GGTATATCCTCCTGCCTCCC 58.426 60.000 0.00 0.00 0.00 4.30
97 105 1.079658 GGTATATCCTCCTGCCTCCCT 59.920 57.143 0.00 0.00 0.00 4.20
121 129 1.221840 CTGCTACGTTGATGCCCCT 59.778 57.895 0.00 0.00 0.00 4.79
140 148 3.510459 CCTCCCCAACTCCAATTCTTTT 58.490 45.455 0.00 0.00 0.00 2.27
141 149 3.511540 CCTCCCCAACTCCAATTCTTTTC 59.488 47.826 0.00 0.00 0.00 2.29
148 156 2.814336 ACTCCAATTCTTTTCAGGACGC 59.186 45.455 0.00 0.00 0.00 5.19
151 159 1.069296 CAATTCTTTTCAGGACGCGCA 60.069 47.619 5.73 0.00 0.00 6.09
153 161 0.812014 TTCTTTTCAGGACGCGCACA 60.812 50.000 5.73 0.00 0.00 4.57
171 182 2.740055 GCACAGGGCACTCACTCG 60.740 66.667 0.00 0.00 43.97 4.18
172 183 2.737180 CACAGGGCACTCACTCGT 59.263 61.111 0.00 0.00 0.00 4.18
173 184 1.665916 CACAGGGCACTCACTCGTG 60.666 63.158 0.00 0.00 37.94 4.35
174 185 1.832608 ACAGGGCACTCACTCGTGA 60.833 57.895 0.00 0.00 37.06 4.35
175 186 1.367471 CAGGGCACTCACTCGTGAA 59.633 57.895 1.02 0.00 39.39 3.18
189 200 4.666176 CACTCGTGAATGAAAGTTTCAACG 59.334 41.667 25.06 25.06 43.95 4.10
192 203 4.025229 TCGTGAATGAAAGTTTCAACGAGG 60.025 41.667 27.69 17.48 43.95 4.63
220 231 4.779475 CCTAATCGGCCAGCGAAT 57.221 55.556 2.24 0.00 0.00 3.34
221 232 3.906660 CCTAATCGGCCAGCGAATA 57.093 52.632 2.24 0.00 0.00 1.75
222 233 2.386661 CCTAATCGGCCAGCGAATAT 57.613 50.000 2.24 0.00 0.00 1.28
223 234 2.002586 CCTAATCGGCCAGCGAATATG 58.997 52.381 2.24 0.00 0.00 1.78
224 235 1.394917 CTAATCGGCCAGCGAATATGC 59.605 52.381 2.24 0.00 0.00 3.14
225 236 1.237285 AATCGGCCAGCGAATATGCC 61.237 55.000 2.24 0.00 40.54 4.40
226 237 2.395988 ATCGGCCAGCGAATATGCCA 62.396 55.000 2.24 0.00 44.22 4.92
227 238 1.968017 CGGCCAGCGAATATGCCAT 60.968 57.895 2.24 0.00 44.22 4.40
228 239 1.582968 GGCCAGCGAATATGCCATG 59.417 57.895 0.00 0.00 43.46 3.66
229 240 1.080974 GCCAGCGAATATGCCATGC 60.081 57.895 0.00 0.00 34.65 4.06
230 241 1.208358 CCAGCGAATATGCCATGCG 59.792 57.895 0.00 0.00 34.65 4.73
231 242 1.229975 CCAGCGAATATGCCATGCGA 61.230 55.000 0.10 0.00 34.65 5.10
232 243 0.800631 CAGCGAATATGCCATGCGAT 59.199 50.000 0.10 0.00 34.65 4.58
233 244 2.001872 CAGCGAATATGCCATGCGATA 58.998 47.619 0.10 0.00 34.65 2.92
236 247 2.222886 GCGAATATGCCATGCGATAGTG 60.223 50.000 0.10 0.00 39.35 2.74
240 251 1.168407 ATGCCATGCGATAGTGCCAC 61.168 55.000 0.00 0.00 39.35 5.01
241 252 1.819208 GCCATGCGATAGTGCCACA 60.819 57.895 0.00 0.00 39.35 4.17
253 264 4.922026 GCCACACCGTGAACCCGT 62.922 66.667 5.28 0.00 35.23 5.28
256 267 2.279650 ACACCGTGAACCCGTTCG 60.280 61.111 5.28 0.00 42.28 3.95
257 268 3.708734 CACCGTGAACCCGTTCGC 61.709 66.667 10.43 10.43 44.25 4.70
340 351 5.473504 ACTGATAATCCGATGCAAATTACCC 59.526 40.000 0.00 0.00 0.00 3.69
355 366 0.032912 TACCCCCACTGCTATCACGA 60.033 55.000 0.00 0.00 0.00 4.35
357 368 1.330655 CCCCCACTGCTATCACGACT 61.331 60.000 0.00 0.00 0.00 4.18
389 400 2.052157 GATCGTTATCGCAGCAGTACC 58.948 52.381 0.00 0.00 36.96 3.34
391 402 1.407618 TCGTTATCGCAGCAGTACCAT 59.592 47.619 0.00 0.00 36.96 3.55
392 403 1.522676 CGTTATCGCAGCAGTACCATG 59.477 52.381 0.00 0.00 0.00 3.66
402 417 2.031157 AGCAGTACCATGTTTTCAACGC 60.031 45.455 0.00 0.00 0.00 4.84
403 418 2.920647 GCAGTACCATGTTTTCAACGCC 60.921 50.000 0.00 0.00 0.00 5.68
440 455 4.936823 ACGTCGCGTTCGTTGGCT 62.937 61.111 21.14 4.16 36.35 4.75
442 457 4.117372 GTCGCGTTCGTTGGCTCG 62.117 66.667 5.77 0.00 36.96 5.03
459 474 0.528924 TCGATCGGATCCACGTGTTT 59.471 50.000 16.41 0.29 34.94 2.83
461 476 2.359848 TCGATCGGATCCACGTGTTTAT 59.640 45.455 16.41 4.87 34.94 1.40
462 477 2.471370 CGATCGGATCCACGTGTTTATG 59.529 50.000 15.65 0.00 34.94 1.90
463 478 3.713288 GATCGGATCCACGTGTTTATGA 58.287 45.455 15.65 4.23 34.94 2.15
464 479 3.812156 TCGGATCCACGTGTTTATGAT 57.188 42.857 15.65 9.35 34.94 2.45
465 480 4.922471 TCGGATCCACGTGTTTATGATA 57.078 40.909 15.65 0.00 34.94 2.15
466 481 5.462530 TCGGATCCACGTGTTTATGATAT 57.537 39.130 15.65 0.00 34.94 1.63
467 482 5.466819 TCGGATCCACGTGTTTATGATATC 58.533 41.667 15.65 0.00 34.94 1.63
468 483 5.010213 TCGGATCCACGTGTTTATGATATCA 59.990 40.000 15.65 8.10 34.94 2.15
469 484 5.869344 CGGATCCACGTGTTTATGATATCAT 59.131 40.000 21.50 21.50 40.22 2.45
470 485 6.183360 CGGATCCACGTGTTTATGATATCATG 60.183 42.308 25.44 11.75 37.15 3.07
471 486 6.873605 GGATCCACGTGTTTATGATATCATGA 59.126 38.462 25.44 16.36 37.15 3.07
491 506 2.821366 CCACGGCTCTGGCATGTC 60.821 66.667 0.00 0.00 40.87 3.06
492 507 2.821366 CACGGCTCTGGCATGTCC 60.821 66.667 0.00 0.00 40.87 4.02
493 508 3.321648 ACGGCTCTGGCATGTCCA 61.322 61.111 8.33 8.33 44.18 4.02
511 545 2.203451 GAGCATGGATGGGGCTGG 60.203 66.667 0.00 0.00 38.15 4.85
514 548 2.129785 GCATGGATGGGGCTGGAAC 61.130 63.158 0.00 0.00 0.00 3.62
516 550 0.105862 CATGGATGGGGCTGGAACAT 60.106 55.000 0.00 0.00 38.20 2.71
517 551 0.105862 ATGGATGGGGCTGGAACATG 60.106 55.000 0.00 0.00 38.20 3.21
519 553 0.466922 GGATGGGGCTGGAACATGAG 60.467 60.000 0.00 0.00 38.20 2.90
521 555 1.144503 GATGGGGCTGGAACATGAGAT 59.855 52.381 0.00 0.00 38.20 2.75
529 564 3.181467 GCTGGAACATGAGATGAGCTACT 60.181 47.826 0.00 0.00 38.20 2.57
544 579 5.947443 TGAGCTACTAGTAAACGTTTCTCC 58.053 41.667 18.42 6.97 0.00 3.71
546 581 6.208204 TGAGCTACTAGTAAACGTTTCTCCTT 59.792 38.462 18.42 3.31 0.00 3.36
563 598 3.270027 TCCTTAACATTGTCAGCCATCG 58.730 45.455 0.00 0.00 0.00 3.84
570 605 1.737838 TTGTCAGCCATCGGTCAATC 58.262 50.000 0.00 0.00 0.00 2.67
571 606 0.612744 TGTCAGCCATCGGTCAATCA 59.387 50.000 0.00 0.00 0.00 2.57
574 609 0.734889 CAGCCATCGGTCAATCAACC 59.265 55.000 0.00 0.00 35.86 3.77
580 615 2.350057 TCGGTCAATCAACCCACAAA 57.650 45.000 0.00 0.00 35.79 2.83
583 618 2.099921 CGGTCAATCAACCCACAAACAA 59.900 45.455 0.00 0.00 35.79 2.83
594 629 1.826327 CACAAACAAACGTGGAGCTG 58.174 50.000 0.00 0.00 0.00 4.24
595 630 0.738389 ACAAACAAACGTGGAGCTGG 59.262 50.000 0.00 0.00 0.00 4.85
596 631 0.738389 CAAACAAACGTGGAGCTGGT 59.262 50.000 0.00 0.00 0.00 4.00
597 632 1.134175 CAAACAAACGTGGAGCTGGTT 59.866 47.619 0.00 0.00 0.00 3.67
598 633 2.335316 AACAAACGTGGAGCTGGTTA 57.665 45.000 0.00 0.00 0.00 2.85
599 634 2.335316 ACAAACGTGGAGCTGGTTAA 57.665 45.000 0.00 0.00 0.00 2.01
600 635 2.858745 ACAAACGTGGAGCTGGTTAAT 58.141 42.857 0.00 0.00 0.00 1.40
601 636 2.812011 ACAAACGTGGAGCTGGTTAATC 59.188 45.455 0.00 0.00 0.00 1.75
602 637 2.109425 AACGTGGAGCTGGTTAATCC 57.891 50.000 0.00 0.00 0.00 3.01
603 638 0.981183 ACGTGGAGCTGGTTAATCCA 59.019 50.000 0.00 0.00 45.01 3.41
610 645 3.883462 TGGTTAATCCAGTGCGCG 58.117 55.556 0.00 0.00 41.93 6.86
611 646 1.743623 TGGTTAATCCAGTGCGCGG 60.744 57.895 8.83 0.00 41.93 6.46
612 647 2.469516 GGTTAATCCAGTGCGCGGG 61.470 63.158 10.51 10.51 35.97 6.13
613 648 2.822255 TTAATCCAGTGCGCGGGC 60.822 61.111 18.81 18.81 40.52 6.13
633 668 2.869233 GTGGCATGGCACGATTAAAT 57.131 45.000 33.16 0.00 0.00 1.40
645 680 6.764085 TGGCACGATTAAATTAGCTTAGCTTA 59.236 34.615 13.44 3.00 40.44 3.09
647 682 6.792726 GCACGATTAAATTAGCTTAGCTTAGC 59.207 38.462 16.83 16.83 40.44 3.09
661 696 2.347731 GCTTAGCTTAGCTTTGGACGT 58.652 47.619 17.24 0.00 40.44 4.34
662 697 2.094417 GCTTAGCTTAGCTTTGGACGTG 59.906 50.000 17.24 0.00 40.44 4.49
663 698 3.585862 CTTAGCTTAGCTTTGGACGTGA 58.414 45.455 13.44 0.00 40.44 4.35
664 699 2.086054 AGCTTAGCTTTGGACGTGAG 57.914 50.000 0.00 0.00 33.89 3.51
665 700 1.344763 AGCTTAGCTTTGGACGTGAGT 59.655 47.619 0.00 0.00 42.37 3.41
751 801 0.826715 TCCAGGGCTCAATTCTCTCG 59.173 55.000 0.00 0.00 0.00 4.04
792 842 6.947733 AGAAGACAACAATGGTAATCAATCCA 59.052 34.615 0.00 0.00 38.14 3.41
793 843 7.451255 AGAAGACAACAATGGTAATCAATCCAA 59.549 33.333 0.00 0.00 37.27 3.53
920 970 4.988598 CCGCACACCGCAACCTCT 62.989 66.667 0.00 0.00 42.60 3.69
924 974 1.912371 GCACACCGCAACCTCTAAGC 61.912 60.000 0.00 0.00 41.79 3.09
937 987 2.480419 CCTCTAAGCTCAAACCACAACG 59.520 50.000 0.00 0.00 0.00 4.10
941 991 2.712539 CTCAAACCACAACGCGCA 59.287 55.556 5.73 0.00 0.00 6.09
942 992 1.654137 CTCAAACCACAACGCGCAC 60.654 57.895 5.73 0.00 0.00 5.34
1020 1076 2.890474 GCCGTGTACATCCGCCTG 60.890 66.667 0.00 0.00 0.00 4.85
1753 1821 1.455773 TCGCCGTCCTCCTCATCAT 60.456 57.895 0.00 0.00 0.00 2.45
1866 1934 1.143183 GGCGGCGAGGATCAAGTAA 59.857 57.895 12.98 0.00 33.17 2.24
1867 1935 0.461339 GGCGGCGAGGATCAAGTAAA 60.461 55.000 12.98 0.00 33.17 2.01
1868 1936 1.365699 GCGGCGAGGATCAAGTAAAA 58.634 50.000 12.98 0.00 33.17 1.52
1896 1964 2.585247 ACCGCTAATTCTCCGCGC 60.585 61.111 0.00 0.00 45.02 6.86
1897 1965 3.692367 CCGCTAATTCTCCGCGCG 61.692 66.667 25.67 25.67 45.02 6.86
1899 1967 4.341240 GCTAATTCTCCGCGCGCG 62.341 66.667 43.73 43.73 39.44 6.86
1900 1968 2.954868 CTAATTCTCCGCGCGCGT 60.955 61.111 45.51 31.22 37.81 6.01
1901 1969 2.917656 CTAATTCTCCGCGCGCGTC 61.918 63.158 45.51 21.85 37.81 5.19
1902 1970 3.405592 TAATTCTCCGCGCGCGTCT 62.406 57.895 45.51 26.72 37.81 4.18
1916 1984 1.202348 CGCGTCTCTGGAAGATGTCAT 60.202 52.381 0.00 0.00 45.62 3.06
1917 1985 2.033424 CGCGTCTCTGGAAGATGTCATA 59.967 50.000 0.00 0.00 45.62 2.15
1918 1986 3.637432 GCGTCTCTGGAAGATGTCATAG 58.363 50.000 0.00 0.00 45.62 2.23
1919 1987 3.067461 GCGTCTCTGGAAGATGTCATAGT 59.933 47.826 0.00 0.00 45.62 2.12
1920 1988 4.791411 GCGTCTCTGGAAGATGTCATAGTC 60.791 50.000 0.00 0.00 45.62 2.59
1921 1989 4.578516 CGTCTCTGGAAGATGTCATAGTCT 59.421 45.833 0.00 0.00 45.62 3.24
1922 1990 5.505489 CGTCTCTGGAAGATGTCATAGTCTG 60.505 48.000 0.00 0.00 45.62 3.51
1923 1991 5.592282 GTCTCTGGAAGATGTCATAGTCTGA 59.408 44.000 0.00 0.00 45.62 3.27
1924 1992 6.265196 GTCTCTGGAAGATGTCATAGTCTGAT 59.735 42.308 0.00 0.00 45.62 2.90
1925 1993 7.446931 GTCTCTGGAAGATGTCATAGTCTGATA 59.553 40.741 0.00 0.00 45.62 2.15
1926 1994 8.001292 TCTCTGGAAGATGTCATAGTCTGATAA 58.999 37.037 0.00 0.00 45.62 1.75
1927 1995 8.175925 TCTGGAAGATGTCATAGTCTGATAAG 57.824 38.462 0.00 0.00 38.67 1.73
1950 2018 7.848223 AGTAGATGTAGAGAGATGATCGATG 57.152 40.000 0.54 0.00 0.00 3.84
1955 2023 6.311055 TGTAGAGAGATGATCGATGAGTTG 57.689 41.667 0.54 0.00 0.00 3.16
1999 2068 9.961266 GTTTTTGTACAAACATTTTTGGTCTAC 57.039 29.630 20.43 3.66 45.65 2.59
2000 2069 8.705048 TTTTGTACAAACATTTTTGGTCTACC 57.295 30.769 20.43 0.00 45.65 3.18
2002 2071 8.749026 TTGTACAAACATTTTTGGTCTACCTA 57.251 30.769 5.64 0.00 45.65 3.08
2003 2072 8.385898 TGTACAAACATTTTTGGTCTACCTAG 57.614 34.615 9.06 0.00 45.65 3.02
2004 2073 8.212312 TGTACAAACATTTTTGGTCTACCTAGA 58.788 33.333 9.06 0.00 45.65 2.43
2035 2108 2.607499 AGCAAATTGTTGGTCCATCCA 58.393 42.857 0.00 0.00 41.63 3.41
2058 2131 3.549423 CCATCCACATGCATGATCGAAAC 60.549 47.826 32.75 0.00 0.00 2.78
2069 2142 2.841215 TGATCGAAACCGTCAACCTTT 58.159 42.857 0.00 0.00 0.00 3.11
2070 2143 2.803956 TGATCGAAACCGTCAACCTTTC 59.196 45.455 0.00 0.00 0.00 2.62
2107 2182 6.511767 GCACGATTAAACTATGGATCTTGGTG 60.512 42.308 0.00 0.00 0.00 4.17
2133 2208 0.525761 AAACATAAAGGCGTGCGCAT 59.474 45.000 15.91 8.56 44.11 4.73
2135 2210 1.374560 ACATAAAGGCGTGCGCATAA 58.625 45.000 15.91 3.94 44.11 1.90
2136 2211 1.330521 ACATAAAGGCGTGCGCATAAG 59.669 47.619 15.91 9.94 44.11 1.73
2137 2212 1.597195 CATAAAGGCGTGCGCATAAGA 59.403 47.619 15.91 0.00 44.11 2.10
2139 2214 1.094785 AAAGGCGTGCGCATAAGATT 58.905 45.000 15.91 3.93 44.11 2.40
2140 2215 1.094785 AAGGCGTGCGCATAAGATTT 58.905 45.000 15.91 0.83 44.11 2.17
2141 2216 1.948104 AGGCGTGCGCATAAGATTTA 58.052 45.000 15.91 0.00 44.11 1.40
2142 2217 2.285083 AGGCGTGCGCATAAGATTTAA 58.715 42.857 15.91 0.00 44.11 1.52
2143 2218 2.878406 AGGCGTGCGCATAAGATTTAAT 59.122 40.909 15.91 0.00 44.11 1.40
2144 2219 4.062293 AGGCGTGCGCATAAGATTTAATA 58.938 39.130 15.91 0.00 44.11 0.98
2145 2220 4.152402 AGGCGTGCGCATAAGATTTAATAG 59.848 41.667 15.91 0.00 44.11 1.73
2243 2322 2.494059 CGGATTAGCATGGGTCGAATT 58.506 47.619 0.00 0.00 0.00 2.17
2245 2324 3.432252 CGGATTAGCATGGGTCGAATTAC 59.568 47.826 0.00 0.00 0.00 1.89
2262 2341 8.117988 GTCGAATTACGGCATTACTTTTATCAA 58.882 33.333 0.00 0.00 46.56 2.57
2339 2425 6.432783 ACCAAGCAAGCAACATATGTTTAGTA 59.567 34.615 18.50 0.00 35.83 1.82
2364 2450 1.134788 CCTAAACGAATCAGGCGAGGT 60.135 52.381 0.00 0.00 0.00 3.85
2376 2462 1.299976 GCGAGGTGGAATTCTGGGT 59.700 57.895 5.23 0.00 0.00 4.51
2390 2476 4.819105 TTCTGGGTGTGATCTTTCGTAT 57.181 40.909 0.00 0.00 0.00 3.06
2402 2488 8.539674 TGTGATCTTTCGTATGATATTTTGTCG 58.460 33.333 0.00 0.00 0.00 4.35
2403 2489 7.527516 GTGATCTTTCGTATGATATTTTGTCGC 59.472 37.037 0.00 0.00 0.00 5.19
2404 2490 6.281848 TCTTTCGTATGATATTTTGTCGCC 57.718 37.500 0.00 0.00 0.00 5.54
2424 2510 2.358957 CGCAAGGATCCTGATGAAACA 58.641 47.619 17.02 0.00 0.00 2.83
2425 2511 2.096496 CGCAAGGATCCTGATGAAACAC 59.904 50.000 17.02 0.00 0.00 3.32
2428 2514 2.996631 AGGATCCTGATGAAACACTGC 58.003 47.619 15.29 0.00 0.00 4.40
2430 2516 2.019984 GATCCTGATGAAACACTGCCC 58.980 52.381 0.00 0.00 0.00 5.36
2432 2518 1.003580 TCCTGATGAAACACTGCCCTC 59.996 52.381 0.00 0.00 0.00 4.30
2433 2519 1.271543 CCTGATGAAACACTGCCCTCA 60.272 52.381 0.00 0.00 0.00 3.86
2434 2520 2.507484 CTGATGAAACACTGCCCTCAA 58.493 47.619 0.00 0.00 0.00 3.02
2438 2933 0.178990 GAAACACTGCCCTCAACCCT 60.179 55.000 0.00 0.00 0.00 4.34
2446 2941 1.394151 CCCTCAACCCTCCTCCTCT 59.606 63.158 0.00 0.00 0.00 3.69
2452 2947 1.287739 CAACCCTCCTCCTCTCTCTCT 59.712 57.143 0.00 0.00 0.00 3.10
2454 2949 1.275002 ACCCTCCTCCTCTCTCTCTCT 60.275 57.143 0.00 0.00 0.00 3.10
2455 2950 1.852965 CCCTCCTCCTCTCTCTCTCTT 59.147 57.143 0.00 0.00 0.00 2.85
2456 2951 2.423373 CCCTCCTCCTCTCTCTCTCTTG 60.423 59.091 0.00 0.00 0.00 3.02
2458 2953 1.024271 CCTCCTCTCTCTCTCTTGCG 58.976 60.000 0.00 0.00 0.00 4.85
2459 2954 1.681780 CCTCCTCTCTCTCTCTTGCGT 60.682 57.143 0.00 0.00 0.00 5.24
2461 2956 1.173043 CCTCTCTCTCTCTTGCGTGT 58.827 55.000 0.00 0.00 0.00 4.49
2462 2957 2.027100 TCCTCTCTCTCTCTTGCGTGTA 60.027 50.000 0.00 0.00 0.00 2.90
2464 2959 2.744741 CTCTCTCTCTCTTGCGTGTACA 59.255 50.000 0.00 0.00 0.00 2.90
2465 2960 3.348119 TCTCTCTCTCTTGCGTGTACAT 58.652 45.455 0.00 0.00 0.00 2.29
2508 3003 5.889289 ACTGTAGGAGCACCAAAAAGTAAAA 59.111 36.000 2.07 0.00 38.94 1.52
2509 3004 6.378848 ACTGTAGGAGCACCAAAAAGTAAAAA 59.621 34.615 2.07 0.00 38.94 1.94
2538 3033 4.750952 GAGACCAACTCAAAAGCTAACC 57.249 45.455 0.00 0.00 44.36 2.85
2541 3036 3.487372 ACCAACTCAAAAGCTAACCCTC 58.513 45.455 0.00 0.00 0.00 4.30
2542 3037 2.484264 CCAACTCAAAAGCTAACCCTCG 59.516 50.000 0.00 0.00 0.00 4.63
2543 3038 3.139077 CAACTCAAAAGCTAACCCTCGT 58.861 45.455 0.00 0.00 0.00 4.18
2544 3039 3.487120 ACTCAAAAGCTAACCCTCGTT 57.513 42.857 0.00 0.00 35.90 3.85
2546 3041 2.484264 CTCAAAAGCTAACCCTCGTTGG 59.516 50.000 0.00 0.00 33.17 3.77
2555 3050 5.576447 CTAACCCTCGTTGGCATTTATTT 57.424 39.130 0.00 0.00 33.17 1.40
2556 3051 6.687081 CTAACCCTCGTTGGCATTTATTTA 57.313 37.500 0.00 0.00 33.17 1.40
2557 3052 7.272037 CTAACCCTCGTTGGCATTTATTTAT 57.728 36.000 0.00 0.00 33.17 1.40
2559 3054 6.877611 ACCCTCGTTGGCATTTATTTATAG 57.122 37.500 0.00 0.00 0.00 1.31
2560 3055 6.597562 ACCCTCGTTGGCATTTATTTATAGA 58.402 36.000 0.00 0.00 0.00 1.98
2561 3056 7.057894 ACCCTCGTTGGCATTTATTTATAGAA 58.942 34.615 0.00 0.00 0.00 2.10
2562 3057 7.228706 ACCCTCGTTGGCATTTATTTATAGAAG 59.771 37.037 0.00 0.00 0.00 2.85
2563 3058 7.444183 CCCTCGTTGGCATTTATTTATAGAAGA 59.556 37.037 0.00 0.00 0.00 2.87
2564 3059 8.836413 CCTCGTTGGCATTTATTTATAGAAGAA 58.164 33.333 0.00 0.00 0.00 2.52
2566 3061 9.997482 TCGTTGGCATTTATTTATAGAAGAAAC 57.003 29.630 0.00 0.00 0.00 2.78
2571 3066 9.967346 GGCATTTATTTATAGAAGAAACTTCCC 57.033 33.333 7.72 0.00 0.00 3.97
2576 3071 5.670792 TTATAGAAGAAACTTCCCGAGCA 57.329 39.130 7.72 0.00 0.00 4.26
2578 3073 1.157585 GAAGAAACTTCCCGAGCACC 58.842 55.000 0.00 0.00 0.00 5.01
2580 3075 1.674651 GAAACTTCCCGAGCACCCC 60.675 63.158 0.00 0.00 0.00 4.95
2581 3076 2.406002 GAAACTTCCCGAGCACCCCA 62.406 60.000 0.00 0.00 0.00 4.96
2582 3077 2.692273 AAACTTCCCGAGCACCCCAC 62.692 60.000 0.00 0.00 0.00 4.61
2583 3078 4.760047 CTTCCCGAGCACCCCACG 62.760 72.222 0.00 0.00 0.00 4.94
2588 3083 4.308458 CGAGCACCCCACGTCCAA 62.308 66.667 0.00 0.00 0.00 3.53
2590 3085 3.168528 AGCACCCCACGTCCAAGT 61.169 61.111 0.00 0.00 0.00 3.16
2592 3087 1.375523 GCACCCCACGTCCAAGTAG 60.376 63.158 0.00 0.00 0.00 2.57
2593 3088 1.295423 CACCCCACGTCCAAGTAGG 59.705 63.158 0.00 0.00 39.47 3.18
2595 3090 1.916777 CCCCACGTCCAAGTAGGGT 60.917 63.158 4.36 0.00 38.11 4.34
2596 3091 1.295423 CCCACGTCCAAGTAGGGTG 59.705 63.158 0.00 0.00 38.24 4.61
2598 3093 1.295423 CACGTCCAAGTAGGGTGGG 59.705 63.158 0.00 0.00 36.73 4.61
2600 3095 2.291043 CGTCCAAGTAGGGTGGGCT 61.291 63.158 0.00 0.00 38.70 5.19
2604 3099 2.531685 AAGTAGGGTGGGCTGGCA 60.532 61.111 2.88 0.00 0.00 4.92
2605 3100 2.606587 AAGTAGGGTGGGCTGGCAG 61.607 63.158 10.94 10.94 0.00 4.85
2613 3108 4.982701 GGGCTGGCAGCAACCACT 62.983 66.667 37.49 0.00 44.75 4.00
2614 3109 3.677648 GGCTGGCAGCAACCACTG 61.678 66.667 37.49 0.50 44.75 3.66
2616 3111 1.600636 GCTGGCAGCAACCACTGTA 60.601 57.895 33.33 0.00 41.89 2.74
2618 3113 0.957395 CTGGCAGCAACCACTGTAGG 60.957 60.000 0.00 0.00 39.96 3.18
2619 3114 1.374947 GGCAGCAACCACTGTAGGA 59.625 57.895 0.00 0.00 39.96 2.94
2621 3116 1.301677 GCAGCAACCACTGTAGGAGC 61.302 60.000 3.76 6.76 39.96 4.70
2623 3118 0.035458 AGCAACCACTGTAGGAGCAC 59.965 55.000 14.69 0.00 36.29 4.40
2625 3120 0.396435 CAACCACTGTAGGAGCACCA 59.604 55.000 2.07 0.00 38.94 4.17
2626 3121 1.136828 AACCACTGTAGGAGCACCAA 58.863 50.000 2.07 0.00 38.94 3.67
2627 3122 1.136828 ACCACTGTAGGAGCACCAAA 58.863 50.000 2.07 0.00 38.94 3.28
2629 3124 2.092103 ACCACTGTAGGAGCACCAAAAA 60.092 45.455 2.07 0.00 38.94 1.94
2634 3631 5.473504 CACTGTAGGAGCACCAAAAAGTAAT 59.526 40.000 2.07 0.00 38.94 1.89
2699 3696 7.634671 TCGGTAGATGATCAAACAGTAGTTA 57.365 36.000 0.00 0.00 36.84 2.24
2703 3700 9.871238 GGTAGATGATCAAACAGTAGTTAGAAA 57.129 33.333 0.00 0.00 36.84 2.52
2739 3741 0.251787 AAAGGTGATGGAGTTGGGGC 60.252 55.000 0.00 0.00 0.00 5.80
2778 3780 2.238646 GGTGTGGTCCATGGTTAGATGA 59.761 50.000 12.58 0.00 0.00 2.92
2790 3792 5.540400 TGGTTAGATGAATAACGGGGTAG 57.460 43.478 0.00 0.00 36.66 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 96 4.798344 CAGGCAGCAGGGAGGCAG 62.798 72.222 0.00 0.00 35.83 4.85
121 129 4.151883 CTGAAAAGAATTGGAGTTGGGGA 58.848 43.478 0.00 0.00 0.00 4.81
151 159 2.111878 GTGAGTGCCCTGTGCTGT 59.888 61.111 0.00 0.00 42.00 4.40
153 161 2.746359 GAGTGAGTGCCCTGTGCT 59.254 61.111 0.00 0.00 42.00 4.40
167 178 4.569162 TCGTTGAAACTTTCATTCACGAGT 59.431 37.500 19.11 0.00 39.84 4.18
168 179 5.078153 TCGTTGAAACTTTCATTCACGAG 57.922 39.130 19.11 1.74 39.84 4.18
169 180 4.025229 CCTCGTTGAAACTTTCATTCACGA 60.025 41.667 20.66 20.66 39.84 4.35
170 181 4.025229 TCCTCGTTGAAACTTTCATTCACG 60.025 41.667 16.16 16.16 39.84 4.35
171 182 5.236478 TCTCCTCGTTGAAACTTTCATTCAC 59.764 40.000 5.03 0.67 39.84 3.18
172 183 5.236478 GTCTCCTCGTTGAAACTTTCATTCA 59.764 40.000 5.03 0.00 39.84 2.57
173 184 5.612709 CGTCTCCTCGTTGAAACTTTCATTC 60.613 44.000 5.03 2.06 39.84 2.67
174 185 4.211374 CGTCTCCTCGTTGAAACTTTCATT 59.789 41.667 5.03 0.00 39.84 2.57
175 186 3.741344 CGTCTCCTCGTTGAAACTTTCAT 59.259 43.478 5.03 0.00 39.84 2.57
211 222 1.080974 GCATGGCATATTCGCTGGC 60.081 57.895 0.00 0.00 39.47 4.85
212 223 1.208358 CGCATGGCATATTCGCTGG 59.792 57.895 0.00 0.00 0.00 4.85
213 224 0.800631 ATCGCATGGCATATTCGCTG 59.199 50.000 0.00 0.00 0.00 5.18
214 225 2.274437 CTATCGCATGGCATATTCGCT 58.726 47.619 0.00 0.00 0.00 4.93
215 226 2.002586 ACTATCGCATGGCATATTCGC 58.997 47.619 0.00 0.00 0.00 4.70
216 227 2.222886 GCACTATCGCATGGCATATTCG 60.223 50.000 0.00 4.63 0.00 3.34
217 228 2.096496 GGCACTATCGCATGGCATATTC 59.904 50.000 0.00 0.00 40.91 1.75
219 230 1.003464 TGGCACTATCGCATGGCATAT 59.997 47.619 0.00 0.00 45.49 1.78
220 231 0.396060 TGGCACTATCGCATGGCATA 59.604 50.000 0.00 0.00 45.49 3.14
221 232 1.148949 TGGCACTATCGCATGGCAT 59.851 52.632 0.00 0.00 45.49 4.40
223 234 1.819208 TGTGGCACTATCGCATGGC 60.819 57.895 19.83 0.00 41.57 4.40
224 235 1.439353 GGTGTGGCACTATCGCATGG 61.439 60.000 19.83 0.00 34.40 3.66
225 236 1.765161 CGGTGTGGCACTATCGCATG 61.765 60.000 19.83 0.00 34.40 4.06
226 237 1.521457 CGGTGTGGCACTATCGCAT 60.521 57.895 19.83 0.00 34.40 4.73
227 238 2.125713 CGGTGTGGCACTATCGCA 60.126 61.111 19.83 0.00 34.40 5.10
228 239 2.125673 ACGGTGTGGCACTATCGC 60.126 61.111 19.83 0.00 34.40 4.58
229 240 0.389296 TTCACGGTGTGGCACTATCG 60.389 55.000 19.83 19.83 34.40 2.92
230 241 1.076332 GTTCACGGTGTGGCACTATC 58.924 55.000 19.83 9.10 34.40 2.08
231 242 0.321298 GGTTCACGGTGTGGCACTAT 60.321 55.000 19.83 0.00 34.40 2.12
232 243 1.070105 GGTTCACGGTGTGGCACTA 59.930 57.895 19.83 2.23 34.40 2.74
233 244 2.203153 GGTTCACGGTGTGGCACT 60.203 61.111 19.83 0.00 34.40 4.40
236 247 4.922026 ACGGGTTCACGGTGTGGC 62.922 66.667 8.17 0.00 38.39 5.01
240 251 3.708734 GCGAACGGGTTCACGGTG 61.709 66.667 11.69 0.56 39.46 4.94
253 264 2.920912 ACCCTCCTTGACCGCGAA 60.921 61.111 8.23 0.00 0.00 4.70
256 267 2.047179 GTGACCCTCCTTGACCGC 60.047 66.667 0.00 0.00 0.00 5.68
257 268 0.613853 TAGGTGACCCTCCTTGACCG 60.614 60.000 0.00 0.00 41.45 4.79
340 351 1.269309 GCTAGTCGTGATAGCAGTGGG 60.269 57.143 10.12 0.00 44.14 4.61
355 366 1.093159 ACGATCGAGGAAACGCTAGT 58.907 50.000 24.34 0.00 0.00 2.57
357 368 3.881795 GATAACGATCGAGGAAACGCTA 58.118 45.455 24.34 0.00 0.00 4.26
379 390 3.641437 TTGAAAACATGGTACTGCTGC 57.359 42.857 0.00 0.00 0.00 5.25
392 403 2.710460 CGTTTACTTCGGCGTTGAAAAC 59.290 45.455 6.85 12.62 45.31 2.43
440 455 0.528924 AAACACGTGGATCCGATCGA 59.471 50.000 21.57 2.91 0.00 3.59
442 457 3.713288 TCATAAACACGTGGATCCGATC 58.287 45.455 21.57 0.00 0.00 3.69
459 474 2.093500 GCCGTGGCCTCATGATATCATA 60.093 50.000 17.77 6.34 33.12 2.15
461 476 0.035317 GCCGTGGCCTCATGATATCA 59.965 55.000 8.10 8.10 34.56 2.15
462 477 0.322975 AGCCGTGGCCTCATGATATC 59.677 55.000 7.39 0.00 43.17 1.63
463 478 0.322975 GAGCCGTGGCCTCATGATAT 59.677 55.000 7.39 0.00 43.17 1.63
464 479 0.760567 AGAGCCGTGGCCTCATGATA 60.761 55.000 7.39 0.00 43.17 2.15
465 480 2.068821 AGAGCCGTGGCCTCATGAT 61.069 57.895 7.39 0.00 43.17 2.45
466 481 2.685017 AGAGCCGTGGCCTCATGA 60.685 61.111 7.39 0.00 43.17 3.07
467 482 2.513204 CAGAGCCGTGGCCTCATG 60.513 66.667 7.39 0.00 43.17 3.07
468 483 3.790437 CCAGAGCCGTGGCCTCAT 61.790 66.667 7.39 0.00 43.17 2.90
492 507 1.528542 CAGCCCCATCCATGCTCTG 60.529 63.158 0.00 0.00 31.77 3.35
493 508 2.764737 CCAGCCCCATCCATGCTCT 61.765 63.158 0.00 0.00 31.77 4.09
495 510 2.318966 TTCCAGCCCCATCCATGCT 61.319 57.895 0.00 0.00 35.25 3.79
496 511 2.129785 GTTCCAGCCCCATCCATGC 61.130 63.158 0.00 0.00 0.00 4.06
499 533 1.213619 TCATGTTCCAGCCCCATCCA 61.214 55.000 0.00 0.00 0.00 3.41
502 536 1.133575 CATCTCATGTTCCAGCCCCAT 60.134 52.381 0.00 0.00 0.00 4.00
511 545 7.377397 CGTTTACTAGTAGCTCATCTCATGTTC 59.623 40.741 2.23 0.00 0.00 3.18
514 548 6.730175 ACGTTTACTAGTAGCTCATCTCATG 58.270 40.000 2.23 0.00 0.00 3.07
516 550 6.754702 AACGTTTACTAGTAGCTCATCTCA 57.245 37.500 2.23 0.00 0.00 3.27
517 551 7.474190 AGAAACGTTTACTAGTAGCTCATCTC 58.526 38.462 14.65 0.00 0.00 2.75
519 553 6.692249 GGAGAAACGTTTACTAGTAGCTCATC 59.308 42.308 14.65 0.00 0.00 2.92
521 555 5.709164 AGGAGAAACGTTTACTAGTAGCTCA 59.291 40.000 14.65 0.00 0.00 4.26
529 564 8.891671 ACAATGTTAAGGAGAAACGTTTACTA 57.108 30.769 14.65 0.00 34.61 1.82
544 579 3.009723 ACCGATGGCTGACAATGTTAAG 58.990 45.455 0.00 0.00 0.00 1.85
546 581 2.027653 TGACCGATGGCTGACAATGTTA 60.028 45.455 0.00 0.00 0.00 2.41
563 598 3.810310 TTGTTTGTGGGTTGATTGACC 57.190 42.857 0.00 0.00 39.04 4.02
580 615 2.335316 TTAACCAGCTCCACGTTTGT 57.665 45.000 0.00 0.00 0.00 2.83
583 618 1.349688 TGGATTAACCAGCTCCACGTT 59.650 47.619 0.00 0.00 44.64 3.99
594 629 2.469516 CCCGCGCACTGGATTAACC 61.470 63.158 8.75 0.00 39.54 2.85
595 630 3.098555 CCCGCGCACTGGATTAAC 58.901 61.111 8.75 0.00 0.00 2.01
596 631 2.822255 GCCCGCGCACTGGATTAA 60.822 61.111 8.75 0.00 34.03 1.40
614 649 2.869233 ATTTAATCGTGCCATGCCAC 57.131 45.000 0.00 0.00 0.00 5.01
615 650 3.243367 GCTAATTTAATCGTGCCATGCCA 60.243 43.478 0.00 0.00 0.00 4.92
616 651 3.004734 AGCTAATTTAATCGTGCCATGCC 59.995 43.478 0.00 0.00 0.00 4.40
617 652 4.228912 AGCTAATTTAATCGTGCCATGC 57.771 40.909 0.00 0.00 0.00 4.06
618 653 5.853282 GCTAAGCTAATTTAATCGTGCCATG 59.147 40.000 0.00 0.00 0.00 3.66
619 654 5.765182 AGCTAAGCTAATTTAATCGTGCCAT 59.235 36.000 0.00 0.00 36.99 4.40
620 655 5.123227 AGCTAAGCTAATTTAATCGTGCCA 58.877 37.500 0.00 0.00 36.99 4.92
621 656 5.674933 AGCTAAGCTAATTTAATCGTGCC 57.325 39.130 0.00 0.00 36.99 5.01
645 680 1.344763 ACTCACGTCCAAAGCTAAGCT 59.655 47.619 0.00 0.00 42.56 3.74
647 682 2.915463 CGTACTCACGTCCAAAGCTAAG 59.085 50.000 0.00 0.00 43.31 2.18
648 683 2.937591 CGTACTCACGTCCAAAGCTAA 58.062 47.619 0.00 0.00 43.31 3.09
649 684 2.624316 CGTACTCACGTCCAAAGCTA 57.376 50.000 0.00 0.00 43.31 3.32
650 685 3.491581 CGTACTCACGTCCAAAGCT 57.508 52.632 0.00 0.00 43.31 3.74
660 695 4.202080 TGCCCATAATAGTCACGTACTCAC 60.202 45.833 0.00 0.00 39.80 3.51
661 696 3.955551 TGCCCATAATAGTCACGTACTCA 59.044 43.478 0.00 0.00 39.80 3.41
662 697 4.296690 GTGCCCATAATAGTCACGTACTC 58.703 47.826 0.00 0.00 39.80 2.59
663 698 3.069158 GGTGCCCATAATAGTCACGTACT 59.931 47.826 0.00 0.00 42.62 2.73
664 699 3.069158 AGGTGCCCATAATAGTCACGTAC 59.931 47.826 0.00 0.00 0.00 3.67
665 700 3.302161 AGGTGCCCATAATAGTCACGTA 58.698 45.455 0.00 0.00 0.00 3.57
724 764 0.185901 TTGAGCCCTGGAATATGCCC 59.814 55.000 0.00 0.00 0.00 5.36
764 814 5.009631 TGATTACCATTGTTGTCTTCTGGG 58.990 41.667 0.00 0.00 0.00 4.45
880 930 1.592223 GGGAGGACAGAGGTTGACG 59.408 63.158 0.00 0.00 0.00 4.35
920 970 0.584396 CGCGTTGTGGTTTGAGCTTA 59.416 50.000 0.00 0.00 0.00 3.09
924 974 1.654137 GTGCGCGTTGTGGTTTGAG 60.654 57.895 8.43 0.00 0.00 3.02
937 987 4.645921 GGCTTTGTGTGGGTGCGC 62.646 66.667 0.00 0.00 0.00 6.09
941 991 1.071471 CTCTCGGCTTTGTGTGGGT 59.929 57.895 0.00 0.00 0.00 4.51
942 992 2.328099 GCTCTCGGCTTTGTGTGGG 61.328 63.158 0.00 0.00 38.06 4.61
1179 1241 2.328099 GGAGTCGTACCCGTCACGT 61.328 63.158 0.00 0.00 40.27 4.49
1698 1763 2.089854 CCACTTGGCGAGCATGTAC 58.910 57.895 0.37 0.00 0.00 2.90
1719 1784 4.484872 GACCGCTTGTAGGGCCCC 62.485 72.222 21.43 4.15 0.00 5.80
1784 1852 2.754664 GATGATGTCCATCCCGGGGC 62.755 65.000 23.50 6.81 44.59 5.80
1798 1866 3.204827 GGCGCGGCACTTGATGAT 61.205 61.111 29.32 0.00 0.00 2.45
1896 1964 0.171231 TGACATCTTCCAGAGACGCG 59.829 55.000 3.53 3.53 37.17 6.01
1897 1965 2.593346 ATGACATCTTCCAGAGACGC 57.407 50.000 0.00 0.00 37.17 5.19
1899 1967 5.592282 TCAGACTATGACATCTTCCAGAGAC 59.408 44.000 0.00 0.00 32.57 3.36
1900 1968 5.760131 TCAGACTATGACATCTTCCAGAGA 58.240 41.667 0.00 0.00 33.74 3.10
1901 1969 6.653526 ATCAGACTATGACATCTTCCAGAG 57.346 41.667 0.00 0.00 41.91 3.35
1902 1970 7.782168 ACTTATCAGACTATGACATCTTCCAGA 59.218 37.037 0.00 0.00 41.91 3.86
1903 1971 7.950512 ACTTATCAGACTATGACATCTTCCAG 58.049 38.462 0.00 0.00 41.91 3.86
1904 1972 7.904558 ACTTATCAGACTATGACATCTTCCA 57.095 36.000 0.00 0.00 41.91 3.53
1908 1976 9.806448 ACATCTACTTATCAGACTATGACATCT 57.194 33.333 0.00 0.00 41.91 2.90
1917 1985 9.725019 CATCTCTCTACATCTACTTATCAGACT 57.275 37.037 0.00 0.00 0.00 3.24
1918 1986 9.719355 TCATCTCTCTACATCTACTTATCAGAC 57.281 37.037 0.00 0.00 0.00 3.51
1921 1989 9.377312 CGATCATCTCTCTACATCTACTTATCA 57.623 37.037 0.00 0.00 0.00 2.15
1922 1990 9.594478 TCGATCATCTCTCTACATCTACTTATC 57.406 37.037 0.00 0.00 0.00 1.75
1924 1992 9.377312 CATCGATCATCTCTCTACATCTACTTA 57.623 37.037 0.00 0.00 0.00 2.24
1925 1993 8.100164 TCATCGATCATCTCTCTACATCTACTT 58.900 37.037 0.00 0.00 0.00 2.24
1926 1994 7.619965 TCATCGATCATCTCTCTACATCTACT 58.380 38.462 0.00 0.00 0.00 2.57
1927 1995 7.549134 ACTCATCGATCATCTCTCTACATCTAC 59.451 40.741 0.00 0.00 0.00 2.59
1950 2018 2.765250 TTCGAGGCACGCTCCAACTC 62.765 60.000 0.00 0.00 42.26 3.01
1955 2023 2.517450 CGAATTCGAGGCACGCTCC 61.517 63.158 23.29 0.00 43.02 4.70
1999 2068 6.825721 ACAATTTGCTCCTTTCATAGTCTAGG 59.174 38.462 0.00 0.00 0.00 3.02
2000 2069 7.856145 ACAATTTGCTCCTTTCATAGTCTAG 57.144 36.000 0.00 0.00 0.00 2.43
2002 2071 6.071728 CCAACAATTTGCTCCTTTCATAGTCT 60.072 38.462 0.00 0.00 0.00 3.24
2003 2072 6.095377 CCAACAATTTGCTCCTTTCATAGTC 58.905 40.000 0.00 0.00 0.00 2.59
2004 2073 5.539955 ACCAACAATTTGCTCCTTTCATAGT 59.460 36.000 0.00 0.00 0.00 2.12
2005 2074 6.029346 ACCAACAATTTGCTCCTTTCATAG 57.971 37.500 0.00 0.00 0.00 2.23
2009 2078 3.069443 TGGACCAACAATTTGCTCCTTTC 59.931 43.478 0.00 0.00 38.06 2.62
2013 2086 2.094026 GGATGGACCAACAATTTGCTCC 60.094 50.000 0.00 0.00 37.81 4.70
2029 2102 0.396001 TGCATGTGGATGGTGGATGG 60.396 55.000 0.00 0.00 0.00 3.51
2030 2103 1.339929 CATGCATGTGGATGGTGGATG 59.660 52.381 18.91 0.00 39.75 3.51
2031 2104 1.215924 TCATGCATGTGGATGGTGGAT 59.784 47.619 25.43 0.00 43.03 3.41
2032 2105 0.624785 TCATGCATGTGGATGGTGGA 59.375 50.000 25.43 0.00 43.03 4.02
2033 2106 1.611977 GATCATGCATGTGGATGGTGG 59.388 52.381 25.43 0.00 43.03 4.61
2034 2107 1.265905 CGATCATGCATGTGGATGGTG 59.734 52.381 25.43 0.00 43.03 4.17
2035 2108 1.141455 TCGATCATGCATGTGGATGGT 59.859 47.619 25.43 7.28 43.03 3.55
2058 2131 0.040067 GCTGCTTGAAAGGTTGACGG 60.040 55.000 0.00 0.00 0.00 4.79
2069 2142 2.825075 ATCGTGCCATGGCTGCTTGA 62.825 55.000 35.53 24.24 42.51 3.02
2070 2143 1.940883 AATCGTGCCATGGCTGCTTG 61.941 55.000 35.53 20.27 42.51 4.01
2107 2182 2.084546 ACGCCTTTATGTTTCCAGCTC 58.915 47.619 0.00 0.00 0.00 4.09
2211 2290 2.710724 CTAATCCGCCTACACCCGCC 62.711 65.000 0.00 0.00 0.00 6.13
2212 2291 1.300697 CTAATCCGCCTACACCCGC 60.301 63.158 0.00 0.00 0.00 6.13
2213 2292 1.300697 GCTAATCCGCCTACACCCG 60.301 63.158 0.00 0.00 0.00 5.28
2214 2293 0.396811 ATGCTAATCCGCCTACACCC 59.603 55.000 0.00 0.00 0.00 4.61
2222 2301 0.531974 TTCGACCCATGCTAATCCGC 60.532 55.000 0.00 0.00 0.00 5.54
2243 2322 6.292649 CGCAGATTGATAAAAGTAATGCCGTA 60.293 38.462 0.00 0.00 0.00 4.02
2245 2324 4.905866 CGCAGATTGATAAAAGTAATGCCG 59.094 41.667 0.00 0.00 0.00 5.69
2254 2333 3.823873 ACAACCACCGCAGATTGATAAAA 59.176 39.130 0.00 0.00 0.00 1.52
2262 2341 2.047274 CCGACAACCACCGCAGAT 60.047 61.111 0.00 0.00 0.00 2.90
2296 2382 9.778741 TTGCTTGGTTGATCCTTATATTACTAG 57.221 33.333 0.00 0.00 37.07 2.57
2299 2385 7.013274 TGCTTGCTTGGTTGATCCTTATATTAC 59.987 37.037 0.00 0.00 37.07 1.89
2303 2389 4.854173 TGCTTGCTTGGTTGATCCTTATA 58.146 39.130 0.00 0.00 37.07 0.98
2304 2390 3.700538 TGCTTGCTTGGTTGATCCTTAT 58.299 40.909 0.00 0.00 37.07 1.73
2306 2392 1.999648 TGCTTGCTTGGTTGATCCTT 58.000 45.000 0.00 0.00 37.07 3.36
2307 2393 1.615392 GTTGCTTGCTTGGTTGATCCT 59.385 47.619 0.00 0.00 37.07 3.24
2308 2394 1.340889 TGTTGCTTGCTTGGTTGATCC 59.659 47.619 0.00 0.00 0.00 3.36
2309 2395 2.798976 TGTTGCTTGCTTGGTTGATC 57.201 45.000 0.00 0.00 0.00 2.92
2310 2396 4.221262 ACATATGTTGCTTGCTTGGTTGAT 59.779 37.500 1.41 0.00 0.00 2.57
2311 2397 3.573538 ACATATGTTGCTTGCTTGGTTGA 59.426 39.130 1.41 0.00 0.00 3.18
2312 2398 3.916761 ACATATGTTGCTTGCTTGGTTG 58.083 40.909 1.41 0.00 0.00 3.77
2313 2399 4.605640 AACATATGTTGCTTGCTTGGTT 57.394 36.364 20.19 0.00 36.80 3.67
2314 2400 4.605640 AAACATATGTTGCTTGCTTGGT 57.394 36.364 21.46 0.00 38.44 3.67
2339 2425 5.209818 TCGCCTGATTCGTTTAGGATAAT 57.790 39.130 0.00 0.00 33.33 1.28
2364 2450 4.335416 GAAAGATCACACCCAGAATTCCA 58.665 43.478 0.65 0.00 0.00 3.53
2376 2462 8.539674 CGACAAAATATCATACGAAAGATCACA 58.460 33.333 0.00 0.00 0.00 3.58
2390 2476 1.400142 CCTTGCGGCGACAAAATATCA 59.600 47.619 12.98 0.00 0.00 2.15
2402 2488 0.464373 TTCATCAGGATCCTTGCGGC 60.464 55.000 13.00 0.00 0.00 6.53
2403 2489 1.672881 GTTTCATCAGGATCCTTGCGG 59.327 52.381 13.00 0.07 0.00 5.69
2404 2490 2.096496 GTGTTTCATCAGGATCCTTGCG 59.904 50.000 13.00 0.51 0.00 4.85
2419 2505 0.178990 AGGGTTGAGGGCAGTGTTTC 60.179 55.000 0.00 0.00 0.00 2.78
2421 2507 1.456287 GAGGGTTGAGGGCAGTGTT 59.544 57.895 0.00 0.00 0.00 3.32
2422 2508 2.529744 GGAGGGTTGAGGGCAGTGT 61.530 63.158 0.00 0.00 0.00 3.55
2423 2509 2.190488 GAGGAGGGTTGAGGGCAGTG 62.190 65.000 0.00 0.00 0.00 3.66
2424 2510 1.920835 GAGGAGGGTTGAGGGCAGT 60.921 63.158 0.00 0.00 0.00 4.40
2425 2511 2.674220 GGAGGAGGGTTGAGGGCAG 61.674 68.421 0.00 0.00 0.00 4.85
2428 2514 0.689412 GAGAGGAGGAGGGTTGAGGG 60.689 65.000 0.00 0.00 0.00 4.30
2430 2516 1.287739 AGAGAGAGGAGGAGGGTTGAG 59.712 57.143 0.00 0.00 0.00 3.02
2432 2518 1.287739 AGAGAGAGAGGAGGAGGGTTG 59.712 57.143 0.00 0.00 0.00 3.77
2433 2519 1.569072 GAGAGAGAGAGGAGGAGGGTT 59.431 57.143 0.00 0.00 0.00 4.11
2434 2520 1.222567 GAGAGAGAGAGGAGGAGGGT 58.777 60.000 0.00 0.00 0.00 4.34
2438 2933 1.408127 CGCAAGAGAGAGAGAGGAGGA 60.408 57.143 0.00 0.00 43.02 3.71
2446 2941 4.521130 AAATGTACACGCAAGAGAGAGA 57.479 40.909 0.00 0.00 43.62 3.10
2452 2947 3.304391 GCCTGAAAAATGTACACGCAAGA 60.304 43.478 0.00 0.00 43.62 3.02
2454 2949 2.621055 AGCCTGAAAAATGTACACGCAA 59.379 40.909 0.00 0.00 0.00 4.85
2455 2950 2.226330 AGCCTGAAAAATGTACACGCA 58.774 42.857 0.00 0.00 0.00 5.24
2456 2951 2.989422 AGCCTGAAAAATGTACACGC 57.011 45.000 0.00 0.00 0.00 5.34
2458 2953 7.918562 TCTTGTTTAAGCCTGAAAAATGTACAC 59.081 33.333 0.00 0.00 33.82 2.90
2459 2954 7.918562 GTCTTGTTTAAGCCTGAAAAATGTACA 59.081 33.333 0.00 0.00 33.82 2.90
2461 2956 8.134895 CAGTCTTGTTTAAGCCTGAAAAATGTA 58.865 33.333 0.00 0.00 41.26 2.29
2462 2957 6.980397 CAGTCTTGTTTAAGCCTGAAAAATGT 59.020 34.615 0.00 0.00 41.26 2.71
2464 2959 7.112452 ACAGTCTTGTTTAAGCCTGAAAAAT 57.888 32.000 5.24 0.00 41.26 1.82
2465 2960 6.524101 ACAGTCTTGTTTAAGCCTGAAAAA 57.476 33.333 5.24 0.00 41.26 1.94
2517 3012 3.502595 GGGTTAGCTTTTGAGTTGGTCTC 59.497 47.826 0.00 0.00 43.03 3.36
2518 3013 3.138468 AGGGTTAGCTTTTGAGTTGGTCT 59.862 43.478 0.00 0.00 0.00 3.85
2519 3014 3.487372 AGGGTTAGCTTTTGAGTTGGTC 58.513 45.455 0.00 0.00 0.00 4.02
2520 3015 3.487372 GAGGGTTAGCTTTTGAGTTGGT 58.513 45.455 0.00 0.00 0.00 3.67
2521 3016 2.484264 CGAGGGTTAGCTTTTGAGTTGG 59.516 50.000 0.00 0.00 0.00 3.77
2523 3018 3.487120 ACGAGGGTTAGCTTTTGAGTT 57.513 42.857 0.00 0.00 0.00 3.01
2525 3020 2.484264 CCAACGAGGGTTAGCTTTTGAG 59.516 50.000 0.00 0.00 33.72 3.02
2526 3021 2.500229 CCAACGAGGGTTAGCTTTTGA 58.500 47.619 0.00 0.00 33.72 2.69
2527 3022 1.068541 GCCAACGAGGGTTAGCTTTTG 60.069 52.381 0.00 0.00 37.72 2.44
2528 3023 1.244816 GCCAACGAGGGTTAGCTTTT 58.755 50.000 0.00 0.00 37.72 2.27
2529 3024 0.109723 TGCCAACGAGGGTTAGCTTT 59.890 50.000 0.00 0.00 40.75 3.51
2530 3025 0.328258 ATGCCAACGAGGGTTAGCTT 59.672 50.000 0.00 0.00 40.75 3.74
2531 3026 0.328258 AATGCCAACGAGGGTTAGCT 59.672 50.000 0.00 0.00 40.75 3.32
2532 3027 1.173913 AAATGCCAACGAGGGTTAGC 58.826 50.000 0.00 0.00 40.57 3.09
2533 3028 5.576447 AAATAAATGCCAACGAGGGTTAG 57.424 39.130 0.00 0.00 38.09 2.34
2534 3029 8.212312 TCTATAAATAAATGCCAACGAGGGTTA 58.788 33.333 0.00 0.00 38.09 2.85
2536 3031 6.597562 TCTATAAATAAATGCCAACGAGGGT 58.402 36.000 0.00 0.00 38.09 4.34
2537 3032 7.444183 TCTTCTATAAATAAATGCCAACGAGGG 59.556 37.037 0.00 0.00 38.09 4.30
2538 3033 8.378172 TCTTCTATAAATAAATGCCAACGAGG 57.622 34.615 0.00 0.00 41.84 4.63
2546 3041 9.665264 CGGGAAGTTTCTTCTATAAATAAATGC 57.335 33.333 8.96 0.00 0.00 3.56
2549 3044 9.106070 GCTCGGGAAGTTTCTTCTATAAATAAA 57.894 33.333 8.96 0.00 0.00 1.40
2550 3045 8.262227 TGCTCGGGAAGTTTCTTCTATAAATAA 58.738 33.333 8.96 0.00 0.00 1.40
2551 3046 7.709613 GTGCTCGGGAAGTTTCTTCTATAAATA 59.290 37.037 8.96 0.00 0.00 1.40
2552 3047 6.539103 GTGCTCGGGAAGTTTCTTCTATAAAT 59.461 38.462 8.96 0.00 0.00 1.40
2553 3048 5.873164 GTGCTCGGGAAGTTTCTTCTATAAA 59.127 40.000 8.96 0.00 0.00 1.40
2554 3049 5.416947 GTGCTCGGGAAGTTTCTTCTATAA 58.583 41.667 8.96 0.00 0.00 0.98
2555 3050 4.142004 GGTGCTCGGGAAGTTTCTTCTATA 60.142 45.833 8.96 0.00 0.00 1.31
2556 3051 3.369576 GGTGCTCGGGAAGTTTCTTCTAT 60.370 47.826 8.96 0.00 0.00 1.98
2557 3052 2.028385 GGTGCTCGGGAAGTTTCTTCTA 60.028 50.000 8.96 0.00 0.00 2.10
2559 3054 1.157585 GGTGCTCGGGAAGTTTCTTC 58.842 55.000 0.00 1.39 0.00 2.87
2560 3055 0.250770 GGGTGCTCGGGAAGTTTCTT 60.251 55.000 0.00 0.00 0.00 2.52
2561 3056 1.375326 GGGTGCTCGGGAAGTTTCT 59.625 57.895 0.00 0.00 0.00 2.52
2562 3057 1.674651 GGGGTGCTCGGGAAGTTTC 60.675 63.158 0.00 0.00 0.00 2.78
2563 3058 2.434774 GGGGTGCTCGGGAAGTTT 59.565 61.111 0.00 0.00 0.00 2.66
2564 3059 2.852075 TGGGGTGCTCGGGAAGTT 60.852 61.111 0.00 0.00 0.00 2.66
2565 3060 3.637273 GTGGGGTGCTCGGGAAGT 61.637 66.667 0.00 0.00 0.00 3.01
2566 3061 4.760047 CGTGGGGTGCTCGGGAAG 62.760 72.222 0.00 0.00 0.00 3.46
2571 3066 4.308458 TTGGACGTGGGGTGCTCG 62.308 66.667 0.00 0.00 37.93 5.03
2573 3068 1.827399 CTACTTGGACGTGGGGTGCT 61.827 60.000 0.00 0.00 37.93 4.40
2574 3069 1.375523 CTACTTGGACGTGGGGTGC 60.376 63.158 0.00 0.00 37.52 5.01
2576 3071 3.801620 CCTACTTGGACGTGGGGT 58.198 61.111 0.00 0.00 38.35 4.95
2578 3073 1.295423 CACCCTACTTGGACGTGGG 59.705 63.158 0.00 0.00 43.26 4.61
2580 3075 1.295423 CCCACCCTACTTGGACGTG 59.705 63.158 0.00 0.00 36.02 4.49
2581 3076 2.590114 GCCCACCCTACTTGGACGT 61.590 63.158 0.00 0.00 36.02 4.34
2582 3077 2.267961 GCCCACCCTACTTGGACG 59.732 66.667 0.00 0.00 36.02 4.79
2583 3078 1.299976 CAGCCCACCCTACTTGGAC 59.700 63.158 0.00 0.00 36.02 4.02
2584 3079 1.923395 CCAGCCCACCCTACTTGGA 60.923 63.158 0.00 0.00 36.02 3.53
2585 3080 2.677228 CCAGCCCACCCTACTTGG 59.323 66.667 0.00 0.00 0.00 3.61
2587 3082 2.531685 TGCCAGCCCACCCTACTT 60.532 61.111 0.00 0.00 0.00 2.24
2588 3083 3.011517 CTGCCAGCCCACCCTACT 61.012 66.667 0.00 0.00 0.00 2.57
2596 3091 4.982701 AGTGGTTGCTGCCAGCCC 62.983 66.667 15.29 9.71 41.51 5.19
2598 3093 1.580845 CTACAGTGGTTGCTGCCAGC 61.581 60.000 10.45 10.45 42.82 4.85
2600 3095 1.073025 CCTACAGTGGTTGCTGCCA 59.927 57.895 0.00 0.00 39.96 4.92
2604 3099 0.035458 GTGCTCCTACAGTGGTTGCT 59.965 55.000 0.00 0.00 0.00 3.91
2605 3100 0.955919 GGTGCTCCTACAGTGGTTGC 60.956 60.000 0.00 0.00 0.00 4.17
2607 3102 1.136828 TTGGTGCTCCTACAGTGGTT 58.863 50.000 6.34 0.00 34.23 3.67
2608 3103 1.136828 TTTGGTGCTCCTACAGTGGT 58.863 50.000 6.34 0.00 34.23 4.16
2612 3107 6.381801 CAATTACTTTTTGGTGCTCCTACAG 58.618 40.000 6.34 0.32 34.23 2.74
2613 3108 5.278758 GCAATTACTTTTTGGTGCTCCTACA 60.279 40.000 6.34 0.00 34.23 2.74
2614 3109 5.161358 GCAATTACTTTTTGGTGCTCCTAC 58.839 41.667 6.34 0.00 34.23 3.18
2616 3111 3.640967 TGCAATTACTTTTTGGTGCTCCT 59.359 39.130 6.34 0.00 33.19 3.69
2618 3113 4.143052 GCATGCAATTACTTTTTGGTGCTC 60.143 41.667 14.21 0.00 33.19 4.26
2619 3114 3.747529 GCATGCAATTACTTTTTGGTGCT 59.252 39.130 14.21 0.00 33.19 4.40
2621 3116 3.436359 GGGCATGCAATTACTTTTTGGTG 59.564 43.478 21.36 0.00 0.00 4.17
2623 3118 2.672381 CGGGCATGCAATTACTTTTTGG 59.328 45.455 21.36 0.00 0.00 3.28
2625 3120 3.676291 ACGGGCATGCAATTACTTTTT 57.324 38.095 21.36 0.00 0.00 1.94
2626 3121 3.428862 GCTACGGGCATGCAATTACTTTT 60.429 43.478 21.36 0.00 41.35 2.27
2627 3122 2.099098 GCTACGGGCATGCAATTACTTT 59.901 45.455 21.36 0.00 41.35 2.66
2629 3124 1.308998 GCTACGGGCATGCAATTACT 58.691 50.000 21.36 0.00 41.35 2.24
2650 3647 1.336795 GCAATCCCGTTGTTTCCTTGG 60.337 52.381 0.00 0.00 40.07 3.61
2699 3696 6.408662 CCTTTTCCTTATCCTCTCCGATTTCT 60.409 42.308 0.00 0.00 0.00 2.52
2703 3700 4.101741 CACCTTTTCCTTATCCTCTCCGAT 59.898 45.833 0.00 0.00 0.00 4.18
2704 3701 3.451178 CACCTTTTCCTTATCCTCTCCGA 59.549 47.826 0.00 0.00 0.00 4.55
2705 3702 3.451178 TCACCTTTTCCTTATCCTCTCCG 59.549 47.826 0.00 0.00 0.00 4.63
2778 3780 1.638679 GGCCCCACTACCCCGTTATT 61.639 60.000 0.00 0.00 0.00 1.40
2832 3838 2.017752 GCATGGGCGAAGAAGCTAC 58.982 57.895 0.00 0.00 37.29 3.58


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.