Multiple sequence alignment - TraesCS6B01G111300

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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 TraesCS6B01G111300 chr6B 100.000 3546 0 0 1 3546 93420357 93416812 0.000000e+00 6549.0
1 TraesCS6B01G111300 chr6B 89.916 357 32 4 211 565 636575221 636575575 1.160000e-124 457.0
2 TraesCS6B01G111300 chrUn 92.948 2978 106 49 617 3545 19481293 19484215 0.000000e+00 4241.0
3 TraesCS6B01G111300 chrUn 87.389 563 67 4 1 562 19480739 19481298 0.000000e+00 643.0
4 TraesCS6B01G111300 chrUn 88.889 369 36 4 201 565 331003997 331003630 1.940000e-122 449.0
5 TraesCS6B01G111300 chr6A 90.749 1589 101 22 1327 2883 57669737 57668163 0.000000e+00 2078.0
6 TraesCS6B01G111300 chr6A 93.333 690 25 7 617 1293 57670786 57670105 0.000000e+00 1000.0
7 TraesCS6B01G111300 chr6A 95.703 512 18 3 3036 3546 57667758 57667250 0.000000e+00 821.0
8 TraesCS6B01G111300 chr6A 96.875 64 1 1 617 679 60189355 60189292 4.840000e-19 106.0
9 TraesCS6B01G111300 chr7B 90.028 361 33 3 207 565 640720353 640720712 6.930000e-127 464.0
10 TraesCS6B01G111300 chr5B 90.196 357 31 4 211 565 356369186 356369540 2.490000e-126 462.0
11 TraesCS6B01G111300 chr5B 95.312 64 2 1 617 679 412283880 412283943 2.250000e-17 100.0
12 TraesCS6B01G111300 chr5B 96.000 50 1 1 565 614 674336571 674336619 2.930000e-11 80.5
13 TraesCS6B01G111300 chr5B 94.118 51 2 1 565 615 621798482 621798531 3.800000e-10 76.8
14 TraesCS6B01G111300 chr5B 93.750 48 1 1 568 615 317779168 317779213 1.770000e-08 71.3
15 TraesCS6B01G111300 chr7A 89.944 358 32 4 211 565 689538749 689538393 3.230000e-125 459.0
16 TraesCS6B01G111300 chr7A 96.078 51 1 1 565 615 229838589 229838638 8.160000e-12 82.4
17 TraesCS6B01G111300 chr2D 89.888 356 34 2 211 565 23303664 23303310 1.160000e-124 457.0
18 TraesCS6B01G111300 chr2D 93.023 43 2 1 573 615 603645826 603645867 1.060000e-05 62.1
19 TraesCS6B01G111300 chr1D 89.916 357 33 3 211 565 461344587 461344942 1.160000e-124 457.0
20 TraesCS6B01G111300 chr1D 96.875 64 1 1 617 679 10360075 10360138 4.840000e-19 106.0
21 TraesCS6B01G111300 chr1B 89.916 357 33 3 211 565 437539316 437539671 1.160000e-124 457.0
22 TraesCS6B01G111300 chr6D 96.875 64 1 1 615 677 97129156 97129093 4.840000e-19 106.0
23 TraesCS6B01G111300 chr6D 96.875 64 1 1 617 679 336996389 336996326 4.840000e-19 106.0
24 TraesCS6B01G111300 chr6D 95.312 64 2 1 617 679 22991410 22991347 2.250000e-17 100.0
25 TraesCS6B01G111300 chr7D 95.312 64 2 1 617 679 214358613 214358676 2.250000e-17 100.0
26 TraesCS6B01G111300 chr4D 95.312 64 2 1 617 679 399608245 399608308 2.250000e-17 100.0
27 TraesCS6B01G111300 chr1A 95.312 64 2 1 617 679 552348153 552348090 2.250000e-17 100.0
28 TraesCS6B01G111300 chr1A 93.878 49 2 1 565 613 101382096 101382049 4.910000e-09 73.1
29 TraesCS6B01G111300 chr1A 90.196 51 2 2 566 616 201853516 201853563 2.960000e-06 63.9
30 TraesCS6B01G111300 chr3B 92.727 55 2 2 562 615 593930273 593930326 1.060000e-10 78.7
31 TraesCS6B01G111300 chr5D 97.500 40 1 0 565 604 117941380 117941341 6.350000e-08 69.4


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 TraesCS6B01G111300 chr6B 93416812 93420357 3545 True 6549.000000 6549 100.000000 1 3546 1 chr6B.!!$R1 3545
1 TraesCS6B01G111300 chrUn 19480739 19484215 3476 False 2442.000000 4241 90.168500 1 3545 2 chrUn.!!$F1 3544
2 TraesCS6B01G111300 chr6A 57667250 57670786 3536 True 1299.666667 2078 93.261667 617 3546 3 chr6A.!!$R2 2929

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
142 143 0.033796 CCCCCTTGTGACTCATGCAT 60.034 55.0 0.00 0.0 0.00 3.96 F
1632 2001 0.107361 AGCGTATGCCCCTGTTTACC 60.107 55.0 2.51 0.0 44.31 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2098 2488 0.027455 TGACAAAGTTTCGCTGCACG 59.973 50.0 0.00 2.79 45.62 5.34 R
2883 3283 0.107017 AATGACGGGGCCTTGATGAG 60.107 55.0 0.84 0.00 0.00 2.90 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
22 23 4.610333 GATTTGGGAACTAGGGATTTGGT 58.390 43.478 0.00 0.00 0.00 3.67
56 57 0.262285 GGGAGCTAGTCAGGTAGGGT 59.738 60.000 0.00 0.00 30.99 4.34
77 78 1.606601 GGGGGAGCTGGTTTGGTTC 60.607 63.158 0.00 0.00 0.00 3.62
81 82 1.566018 GGAGCTGGTTTGGTTCGACG 61.566 60.000 0.00 0.00 0.00 5.12
85 86 1.519408 CTGGTTTGGTTCGACGGAAT 58.481 50.000 0.00 0.00 34.05 3.01
95 96 3.165498 GACGGAATCGGTGTGTGC 58.835 61.111 0.00 0.00 41.39 4.57
98 99 0.534203 ACGGAATCGGTGTGTGCTTT 60.534 50.000 0.00 0.00 41.39 3.51
111 112 4.018490 TGTGTGCTTTTGATCTATGGCAT 58.982 39.130 4.88 4.88 32.38 4.40
131 132 2.101640 ATTTGCAAAGACCCCCTTGT 57.898 45.000 18.19 0.00 34.79 3.16
132 133 1.118838 TTTGCAAAGACCCCCTTGTG 58.881 50.000 8.05 0.00 34.79 3.33
137 138 1.142870 CAAAGACCCCCTTGTGACTCA 59.857 52.381 0.00 0.00 34.79 3.41
140 141 0.678048 GACCCCCTTGTGACTCATGC 60.678 60.000 0.00 0.00 0.00 4.06
141 142 1.379916 CCCCCTTGTGACTCATGCA 59.620 57.895 0.00 0.00 0.00 3.96
142 143 0.033796 CCCCCTTGTGACTCATGCAT 60.034 55.000 0.00 0.00 0.00 3.96
146 147 4.446167 CCCCCTTGTGACTCATGCATATTA 60.446 45.833 0.00 0.00 0.00 0.98
148 149 5.240183 CCCCTTGTGACTCATGCATATTAAG 59.760 44.000 0.00 0.00 0.00 1.85
170 171 4.134563 GAGCCATAAACATATTGGACGGT 58.865 43.478 0.00 0.00 31.94 4.83
180 181 0.179004 ATTGGACGGTCAAAGCCACA 60.179 50.000 10.76 0.00 0.00 4.17
187 188 1.172812 GGTCAAAGCCACACTGTCCC 61.173 60.000 0.00 0.00 0.00 4.46
189 190 0.257328 TCAAAGCCACACTGTCCCAA 59.743 50.000 0.00 0.00 0.00 4.12
208 209 0.998928 ATGGACCAAGCCCACATGTA 59.001 50.000 0.00 0.00 36.36 2.29
209 210 0.327924 TGGACCAAGCCCACATGTAG 59.672 55.000 0.00 0.00 0.00 2.74
210 211 0.328258 GGACCAAGCCCACATGTAGT 59.672 55.000 0.00 0.00 0.00 2.73
213 214 3.560453 GGACCAAGCCCACATGTAGTTTA 60.560 47.826 0.00 0.00 0.00 2.01
229 230 9.381027 CATGTAGTTTATTTGCATGGTAATACG 57.619 33.333 0.00 0.00 34.86 3.06
235 236 7.618502 TTATTTGCATGGTAATACGTGTCTT 57.381 32.000 0.00 0.00 0.00 3.01
240 241 8.719560 TTGCATGGTAATACGTGTCTTATTAA 57.280 30.769 0.00 0.00 0.00 1.40
285 286 7.497579 ACAAGCCATGTAAATATCGACATTACA 59.502 33.333 16.93 16.93 41.63 2.41
286 287 7.658179 AGCCATGTAAATATCGACATTACAG 57.342 36.000 18.52 10.99 41.34 2.74
292 293 7.207383 TGTAAATATCGACATTACAGGACTGG 58.793 38.462 12.79 0.00 35.30 4.00
344 346 0.818296 CGTGTCCCTCTCCACTAAGG 59.182 60.000 0.00 0.00 39.47 2.69
357 359 5.165961 TCCACTAAGGAAAAGGAGACATG 57.834 43.478 0.00 0.00 45.65 3.21
361 363 6.176183 CACTAAGGAAAAGGAGACATGTCAT 58.824 40.000 27.02 12.53 0.00 3.06
371 373 3.431486 GGAGACATGTCATCTCTTCACCC 60.431 52.174 27.02 8.39 42.02 4.61
378 380 0.248825 CATCTCTTCACCCGAGCTCG 60.249 60.000 29.06 29.06 39.44 5.03
379 381 0.394488 ATCTCTTCACCCGAGCTCGA 60.394 55.000 36.59 14.79 43.02 4.04
400 402 1.227350 CGGCTCCATCGCTGATCAA 60.227 57.895 0.00 0.00 38.57 2.57
417 419 2.746269 TCAACAGTTTTACGGACCTCG 58.254 47.619 0.00 0.00 45.88 4.63
429 431 1.725164 CGGACCTCGAAAGTAGTTTGC 59.275 52.381 0.00 0.00 42.43 3.68
430 432 2.074576 GGACCTCGAAAGTAGTTTGCC 58.925 52.381 0.00 0.00 0.00 4.52
432 434 3.056322 GGACCTCGAAAGTAGTTTGCCTA 60.056 47.826 0.00 0.00 0.00 3.93
435 437 5.370679 ACCTCGAAAGTAGTTTGCCTAAAA 58.629 37.500 0.00 0.00 0.00 1.52
447 449 5.270083 GTTTGCCTAAAACAAAACCATTGC 58.730 37.500 0.00 0.00 46.30 3.56
449 451 3.118261 TGCCTAAAACAAAACCATTGCCA 60.118 39.130 0.00 0.00 0.00 4.92
460 462 6.546772 ACAAAACCATTGCCATTGAAAGAATT 59.453 30.769 0.00 0.00 0.00 2.17
466 468 4.963276 TGCCATTGAAAGAATTAGACCG 57.037 40.909 0.00 0.00 0.00 4.79
473 475 3.244770 TGAAAGAATTAGACCGGGCAACT 60.245 43.478 11.69 3.84 0.00 3.16
509 511 2.738846 CCATCAAACTCCAGAACTGACG 59.261 50.000 3.19 0.00 0.00 4.35
510 512 3.393800 CATCAAACTCCAGAACTGACGT 58.606 45.455 3.19 0.00 0.00 4.34
525 527 3.524606 CGTCCCCCGCACGACTAT 61.525 66.667 0.00 0.00 39.75 2.12
526 528 2.106332 GTCCCCCGCACGACTATG 59.894 66.667 0.00 0.00 0.00 2.23
562 564 0.397941 CCAGAACTGTCAGCCTCCAA 59.602 55.000 0.00 0.00 0.00 3.53
563 565 1.517242 CAGAACTGTCAGCCTCCAAC 58.483 55.000 0.00 0.00 0.00 3.77
564 566 0.398318 AGAACTGTCAGCCTCCAACC 59.602 55.000 0.00 0.00 0.00 3.77
565 567 0.398318 GAACTGTCAGCCTCCAACCT 59.602 55.000 0.00 0.00 0.00 3.50
566 568 0.398318 AACTGTCAGCCTCCAACCTC 59.602 55.000 0.00 0.00 0.00 3.85
567 569 0.472734 ACTGTCAGCCTCCAACCTCT 60.473 55.000 0.00 0.00 0.00 3.69
568 570 0.248843 CTGTCAGCCTCCAACCTCTC 59.751 60.000 0.00 0.00 0.00 3.20
569 571 0.178921 TGTCAGCCTCCAACCTCTCT 60.179 55.000 0.00 0.00 0.00 3.10
570 572 0.980423 GTCAGCCTCCAACCTCTCTT 59.020 55.000 0.00 0.00 0.00 2.85
571 573 1.066502 GTCAGCCTCCAACCTCTCTTC 60.067 57.143 0.00 0.00 0.00 2.87
572 574 1.203237 TCAGCCTCCAACCTCTCTTCT 60.203 52.381 0.00 0.00 0.00 2.85
573 575 2.043115 TCAGCCTCCAACCTCTCTTCTA 59.957 50.000 0.00 0.00 0.00 2.10
574 576 3.037549 CAGCCTCCAACCTCTCTTCTAT 58.962 50.000 0.00 0.00 0.00 1.98
575 577 4.079154 TCAGCCTCCAACCTCTCTTCTATA 60.079 45.833 0.00 0.00 0.00 1.31
576 578 4.651503 CAGCCTCCAACCTCTCTTCTATAA 59.348 45.833 0.00 0.00 0.00 0.98
577 579 5.129485 CAGCCTCCAACCTCTCTTCTATAAA 59.871 44.000 0.00 0.00 0.00 1.40
578 580 5.365314 AGCCTCCAACCTCTCTTCTATAAAG 59.635 44.000 0.00 0.00 0.00 1.85
579 581 5.129650 GCCTCCAACCTCTCTTCTATAAAGT 59.870 44.000 0.00 0.00 0.00 2.66
580 582 6.352308 GCCTCCAACCTCTCTTCTATAAAGTT 60.352 42.308 0.00 0.00 0.00 2.66
581 583 7.147707 GCCTCCAACCTCTCTTCTATAAAGTTA 60.148 40.741 0.00 0.00 0.00 2.24
582 584 8.759782 CCTCCAACCTCTCTTCTATAAAGTTAA 58.240 37.037 0.00 0.00 0.00 2.01
583 585 9.810545 CTCCAACCTCTCTTCTATAAAGTTAAG 57.189 37.037 0.00 0.00 0.00 1.85
584 586 8.759782 TCCAACCTCTCTTCTATAAAGTTAAGG 58.240 37.037 0.00 0.00 0.00 2.69
585 587 8.541234 CCAACCTCTCTTCTATAAAGTTAAGGT 58.459 37.037 0.00 0.00 0.00 3.50
588 590 8.901793 ACCTCTCTTCTATAAAGTTAAGGTACG 58.098 37.037 0.00 0.00 0.00 3.67
589 591 7.861872 CCTCTCTTCTATAAAGTTAAGGTACGC 59.138 40.741 0.00 0.00 0.00 4.42
590 592 7.710896 TCTCTTCTATAAAGTTAAGGTACGCC 58.289 38.462 0.00 0.00 0.00 5.68
591 593 7.340232 TCTCTTCTATAAAGTTAAGGTACGCCA 59.660 37.037 0.00 0.00 37.19 5.69
592 594 8.015185 TCTTCTATAAAGTTAAGGTACGCCAT 57.985 34.615 0.00 0.00 37.19 4.40
593 595 8.480501 TCTTCTATAAAGTTAAGGTACGCCATT 58.519 33.333 0.00 0.00 37.19 3.16
594 596 8.428186 TTCTATAAAGTTAAGGTACGCCATTG 57.572 34.615 0.00 0.00 37.19 2.82
595 597 6.987992 TCTATAAAGTTAAGGTACGCCATTGG 59.012 38.462 0.00 0.00 37.19 3.16
596 598 1.746470 AGTTAAGGTACGCCATTGGC 58.254 50.000 18.10 18.10 46.75 4.52
605 607 3.706140 GCCATTGGCGTACTCTCG 58.294 61.111 12.82 0.00 39.62 4.04
606 608 1.883084 GCCATTGGCGTACTCTCGG 60.883 63.158 12.82 0.00 39.62 4.63
607 609 1.813859 CCATTGGCGTACTCTCGGA 59.186 57.895 0.00 0.00 0.00 4.55
608 610 0.174845 CCATTGGCGTACTCTCGGAA 59.825 55.000 0.00 0.00 0.00 4.30
609 611 1.404986 CCATTGGCGTACTCTCGGAAA 60.405 52.381 0.00 0.00 0.00 3.13
610 612 2.343101 CATTGGCGTACTCTCGGAAAA 58.657 47.619 0.00 0.00 0.00 2.29
611 613 2.529780 TTGGCGTACTCTCGGAAAAA 57.470 45.000 0.00 0.00 0.00 1.94
652 655 1.154150 GCACAAGATGCGCCACTTC 60.154 57.895 4.18 0.00 46.55 3.01
665 668 1.233019 CCACTTCCAGCTGTCACTTG 58.767 55.000 13.81 2.93 0.00 3.16
675 678 1.192534 GCTGTCACTTGCGTAGACAAC 59.807 52.381 0.00 0.00 41.27 3.32
707 710 6.699575 AAACCGTATATAAGTGACCGTACT 57.300 37.500 0.00 0.00 0.00 2.73
713 716 6.203530 CGTATATAAGTGACCGTACTCTTCCA 59.796 42.308 0.00 0.00 0.00 3.53
715 718 9.224267 GTATATAAGTGACCGTACTCTTCCATA 57.776 37.037 0.00 0.00 0.00 2.74
728 732 5.214293 ACTCTTCCATACCGTATTTAGGGT 58.786 41.667 7.12 7.12 45.51 4.34
746 750 1.743394 GGTATTTTGAAGGGCGGTGAG 59.257 52.381 0.00 0.00 0.00 3.51
893 908 4.675029 CCCAACCTCCGCGTCGTT 62.675 66.667 4.92 0.58 0.00 3.85
1442 1802 2.482864 CTGAAATGGTTGGTTGGTTGC 58.517 47.619 0.00 0.00 0.00 4.17
1578 1938 0.319641 GGTTTCGTGTCGCCTCTCTT 60.320 55.000 0.00 0.00 0.00 2.85
1582 1942 2.507324 GTGTCGCCTCTCTTCGGC 60.507 66.667 0.00 0.00 44.11 5.54
1600 1961 1.202627 GGCTCTCCGCTTCTCATCAAT 60.203 52.381 0.00 0.00 39.13 2.57
1629 1998 0.392998 CAGAGCGTATGCCCCTGTTT 60.393 55.000 15.17 0.00 44.31 2.83
1630 1999 1.134521 CAGAGCGTATGCCCCTGTTTA 60.135 52.381 15.17 0.00 44.31 2.01
1631 2000 1.134491 AGAGCGTATGCCCCTGTTTAC 60.134 52.381 2.51 0.00 44.31 2.01
1632 2001 0.107361 AGCGTATGCCCCTGTTTACC 60.107 55.000 2.51 0.00 44.31 2.85
1633 2002 0.107361 GCGTATGCCCCTGTTTACCT 60.107 55.000 0.00 0.00 33.98 3.08
1634 2003 1.663695 CGTATGCCCCTGTTTACCTG 58.336 55.000 0.00 0.00 0.00 4.00
1635 2004 1.065709 CGTATGCCCCTGTTTACCTGT 60.066 52.381 0.00 0.00 0.00 4.00
1636 2005 2.640184 GTATGCCCCTGTTTACCTGTC 58.360 52.381 0.00 0.00 0.00 3.51
1640 2009 0.953960 CCCCTGTTTACCTGTCGTGC 60.954 60.000 0.00 0.00 0.00 5.34
1642 2011 0.250124 CCTGTTTACCTGTCGTGCCA 60.250 55.000 0.00 0.00 0.00 4.92
1645 2014 1.070914 TGTTTACCTGTCGTGCCATCA 59.929 47.619 0.00 0.00 0.00 3.07
1821 2198 2.488204 TACATGCCAGTTGCTTAGCA 57.512 45.000 1.39 1.39 42.00 3.49
1824 2201 1.746787 CATGCCAGTTGCTTAGCATCA 59.253 47.619 16.31 6.98 43.85 3.07
1842 2219 3.819564 TCACACACTTGCACTAGAAGT 57.180 42.857 0.00 0.00 33.82 3.01
1843 2220 4.929819 TCACACACTTGCACTAGAAGTA 57.070 40.909 0.00 0.00 32.27 2.24
1844 2221 4.871513 TCACACACTTGCACTAGAAGTAG 58.128 43.478 0.00 0.00 32.27 2.57
1845 2222 4.583073 TCACACACTTGCACTAGAAGTAGA 59.417 41.667 0.00 0.00 32.27 2.59
1846 2223 5.068591 TCACACACTTGCACTAGAAGTAGAA 59.931 40.000 0.00 0.00 32.27 2.10
1847 2224 5.403766 CACACACTTGCACTAGAAGTAGAAG 59.596 44.000 0.00 0.00 32.27 2.85
1934 2314 6.897259 ATGCACAAAATCATTAACATCTGC 57.103 33.333 0.00 0.00 0.00 4.26
1942 2322 4.729227 TCATTAACATCTGCGAGTGGTA 57.271 40.909 0.00 0.00 0.00 3.25
1984 2364 1.282157 GGGCAGTGTGTTAGGAAGGAT 59.718 52.381 0.00 0.00 0.00 3.24
2098 2488 8.880878 AGAAGAGAGAAAACAAGTCTACTTTC 57.119 34.615 0.00 0.00 33.11 2.62
2136 2526 6.058827 TGTCACTGTCAATATGTGTTTGTG 57.941 37.500 0.00 0.00 33.82 3.33
2147 2537 7.861872 TCAATATGTGTTTGTGTCTTTGTGATG 59.138 33.333 0.00 0.00 0.00 3.07
2173 2563 2.977772 AGCTCATGAGGCACTAAGTC 57.022 50.000 23.89 4.09 41.55 3.01
2278 2671 2.584835 TGTTTGGAGATGTTCAGGGG 57.415 50.000 0.00 0.00 0.00 4.79
2317 2710 2.158593 TGAAAAATTCCCTGTGGTCCGA 60.159 45.455 0.00 0.00 0.00 4.55
2346 2739 4.081420 CCTTGGTAATCTATCGATCCCCAG 60.081 50.000 0.00 0.00 33.47 4.45
2372 2765 8.451748 GTTCTTACATTGGACATTAGTCTTTCC 58.548 37.037 0.00 0.00 44.36 3.13
2377 2770 1.134907 GGACATTAGTCTTTCCGCGGA 60.135 52.381 27.28 27.28 44.36 5.54
2393 2786 2.541794 CGCGGACATCATATATCCTCGG 60.542 54.545 0.00 0.00 37.14 4.63
2485 2879 6.428385 AAGAAATCAAAGGACACGATCATC 57.572 37.500 0.00 0.00 0.00 2.92
2616 3010 4.422073 AGAATGACTGACAAGTGACCAA 57.578 40.909 0.00 0.00 36.52 3.67
2793 3193 5.850557 TGTTTGGTGAATTGAGATGTTGT 57.149 34.783 0.00 0.00 0.00 3.32
2797 3197 5.850557 TGGTGAATTGAGATGTTGTTTGT 57.149 34.783 0.00 0.00 0.00 2.83
2891 3291 8.906636 CAAATACTTTGTTCCATCTCATCAAG 57.093 34.615 0.00 0.00 35.94 3.02
2895 3295 1.064463 TGTTCCATCTCATCAAGGCCC 60.064 52.381 0.00 0.00 0.00 5.80
2898 3298 1.528824 CATCTCATCAAGGCCCCGT 59.471 57.895 0.00 0.00 0.00 5.28
2900 3300 0.982852 ATCTCATCAAGGCCCCGTCA 60.983 55.000 0.00 0.00 0.00 4.35
2947 3375 3.336468 TGCAAATTCATTTCCATGTGCC 58.664 40.909 0.00 0.00 30.89 5.01
2948 3376 3.008157 TGCAAATTCATTTCCATGTGCCT 59.992 39.130 0.00 0.00 30.89 4.75
2949 3377 4.222366 TGCAAATTCATTTCCATGTGCCTA 59.778 37.500 0.00 0.00 30.89 3.93
2950 3378 5.177326 GCAAATTCATTTCCATGTGCCTAA 58.823 37.500 0.00 0.00 0.00 2.69
2951 3379 5.642919 GCAAATTCATTTCCATGTGCCTAAA 59.357 36.000 0.00 0.00 0.00 1.85
2952 3380 6.183360 GCAAATTCATTTCCATGTGCCTAAAG 60.183 38.462 0.00 0.00 0.00 1.85
2953 3381 5.603170 ATTCATTTCCATGTGCCTAAAGG 57.397 39.130 0.00 0.00 38.53 3.11
3008 3436 5.180810 TCACTCTGTCACTCAGGTAGTAT 57.819 43.478 0.00 0.00 43.76 2.12
3020 3448 5.248477 ACTCAGGTAGTATTTGCCAAAGAGA 59.752 40.000 5.99 0.00 36.36 3.10
3155 3816 7.114388 GCGTTCCCTTTTTACTCTACAAAAATG 59.886 37.037 0.00 0.00 35.09 2.32
3206 3868 1.412343 AGTTTTCACCATTTTGGCGCT 59.588 42.857 7.64 0.00 42.67 5.92
3272 3934 2.105477 AGTTAGCAGCCACATCCTATGG 59.895 50.000 0.00 0.00 40.50 2.74
3362 4024 2.676471 ATCAAGGCCCCAACACGC 60.676 61.111 0.00 0.00 0.00 5.34
3369 4031 3.416382 CCCCAACACGCCGTTACG 61.416 66.667 0.00 0.00 35.52 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 0.262285 ACCCTACCTGACTAGCTCCC 59.738 60.000 0.00 0.00 0.00 4.30
38 39 1.063867 TCACCCTACCTGACTAGCTCC 60.064 57.143 0.00 0.00 0.00 4.70
44 45 1.392534 CCCCTCACCCTACCTGACT 59.607 63.158 0.00 0.00 0.00 3.41
48 49 3.120191 CTCCCCCTCACCCTACCT 58.880 66.667 0.00 0.00 0.00 3.08
52 53 4.748798 CCAGCTCCCCCTCACCCT 62.749 72.222 0.00 0.00 0.00 4.34
56 57 2.538141 CCAAACCAGCTCCCCCTCA 61.538 63.158 0.00 0.00 0.00 3.86
81 82 1.606668 TCAAAAGCACACACCGATTCC 59.393 47.619 0.00 0.00 0.00 3.01
85 86 2.254546 AGATCAAAAGCACACACCGA 57.745 45.000 0.00 0.00 0.00 4.69
87 88 3.428045 GCCATAGATCAAAAGCACACACC 60.428 47.826 0.00 0.00 0.00 4.16
88 89 3.191162 TGCCATAGATCAAAAGCACACAC 59.809 43.478 0.00 0.00 0.00 3.82
91 92 6.964807 AATATGCCATAGATCAAAAGCACA 57.035 33.333 0.00 0.00 32.26 4.57
111 112 2.896685 CACAAGGGGGTCTTTGCAAATA 59.103 45.455 13.23 2.14 32.41 1.40
123 124 0.033796 ATGCATGAGTCACAAGGGGG 60.034 55.000 0.00 0.00 0.00 5.40
128 129 5.528690 GGCTCTTAATATGCATGAGTCACAA 59.471 40.000 10.16 0.00 30.65 3.33
131 132 5.294734 TGGCTCTTAATATGCATGAGTCA 57.705 39.130 12.73 12.73 37.09 3.41
132 133 7.912056 TTATGGCTCTTAATATGCATGAGTC 57.088 36.000 10.16 9.03 0.00 3.36
142 143 9.214957 CGTCCAATATGTTTATGGCTCTTAATA 57.785 33.333 0.00 0.00 0.00 0.98
146 147 4.821805 CCGTCCAATATGTTTATGGCTCTT 59.178 41.667 0.00 0.00 0.00 2.85
148 149 4.134563 ACCGTCCAATATGTTTATGGCTC 58.865 43.478 0.00 0.00 0.00 4.70
170 171 0.257328 TTGGGACAGTGTGGCTTTGA 59.743 50.000 0.00 0.00 42.39 2.69
187 188 0.533491 CATGTGGGCTTGGTCCATTG 59.467 55.000 0.00 0.00 40.40 2.82
189 190 0.998928 TACATGTGGGCTTGGTCCAT 59.001 50.000 9.11 0.00 40.40 3.41
208 209 7.335924 AGACACGTATTACCATGCAAATAAACT 59.664 33.333 0.00 0.00 0.00 2.66
209 210 7.469260 AGACACGTATTACCATGCAAATAAAC 58.531 34.615 0.00 0.00 0.00 2.01
210 211 7.618502 AGACACGTATTACCATGCAAATAAA 57.381 32.000 0.00 0.00 0.00 1.40
213 214 7.801716 ATAAGACACGTATTACCATGCAAAT 57.198 32.000 0.00 0.00 0.00 2.32
267 268 7.068962 TCCAGTCCTGTAATGTCGATATTTACA 59.931 37.037 12.87 13.33 0.00 2.41
285 286 6.943899 GGATTATCCTATCTTTCCAGTCCT 57.056 41.667 3.59 0.00 32.53 3.85
319 320 3.749064 GAGAGGGACACGCGCTGA 61.749 66.667 5.73 0.00 40.28 4.26
344 346 6.091986 GTGAAGAGATGACATGTCTCCTTTTC 59.908 42.308 25.55 25.83 42.41 2.29
357 359 0.820871 AGCTCGGGTGAAGAGATGAC 59.179 55.000 0.00 0.00 37.93 3.06
361 363 1.002502 TCGAGCTCGGGTGAAGAGA 60.003 57.895 33.98 10.31 37.93 3.10
383 385 0.462581 TGTTGATCAGCGATGGAGCC 60.463 55.000 0.00 0.00 38.01 4.70
384 386 0.935898 CTGTTGATCAGCGATGGAGC 59.064 55.000 0.00 0.00 37.36 4.70
400 402 3.181472 ACTTTCGAGGTCCGTAAAACTGT 60.181 43.478 0.00 0.00 39.75 3.55
404 406 4.853924 ACTACTTTCGAGGTCCGTAAAA 57.146 40.909 0.00 0.00 39.75 1.52
417 419 7.546316 TGGTTTTGTTTTAGGCAAACTACTTTC 59.454 33.333 2.66 0.00 44.68 2.62
429 431 5.762218 TCAATGGCAATGGTTTTGTTTTAGG 59.238 36.000 2.15 0.00 0.00 2.69
430 432 6.857777 TCAATGGCAATGGTTTTGTTTTAG 57.142 33.333 2.15 0.00 0.00 1.85
432 434 6.376581 TCTTTCAATGGCAATGGTTTTGTTTT 59.623 30.769 2.15 0.00 0.00 2.43
435 437 5.033589 TCTTTCAATGGCAATGGTTTTGT 57.966 34.783 2.15 0.00 0.00 2.83
447 449 3.066760 GCCCGGTCTAATTCTTTCAATGG 59.933 47.826 0.00 0.00 0.00 3.16
449 451 3.963129 TGCCCGGTCTAATTCTTTCAAT 58.037 40.909 0.00 0.00 0.00 2.57
460 462 1.675219 GGACAAGTTGCCCGGTCTA 59.325 57.895 1.81 0.00 0.00 2.59
493 495 1.070289 GGGACGTCAGTTCTGGAGTTT 59.930 52.381 18.91 0.00 0.00 2.66
509 511 2.106332 CATAGTCGTGCGGGGGAC 59.894 66.667 0.00 0.00 0.00 4.46
510 512 2.043752 TCATAGTCGTGCGGGGGA 60.044 61.111 0.00 0.00 0.00 4.81
525 527 1.530013 GGTTTCCTCCTCCGACGTCA 61.530 60.000 17.16 0.00 0.00 4.35
526 528 1.214853 GGTTTCCTCCTCCGACGTC 59.785 63.158 5.18 5.18 0.00 4.34
562 564 8.901793 CGTACCTTAACTTTATAGAAGAGAGGT 58.098 37.037 12.89 12.89 0.00 3.85
563 565 7.861872 GCGTACCTTAACTTTATAGAAGAGAGG 59.138 40.741 0.00 0.00 0.00 3.69
564 566 7.861872 GGCGTACCTTAACTTTATAGAAGAGAG 59.138 40.741 0.00 0.00 0.00 3.20
565 567 7.340232 TGGCGTACCTTAACTTTATAGAAGAGA 59.660 37.037 0.00 0.00 36.63 3.10
566 568 7.486647 TGGCGTACCTTAACTTTATAGAAGAG 58.513 38.462 0.00 0.00 36.63 2.85
567 569 7.408756 TGGCGTACCTTAACTTTATAGAAGA 57.591 36.000 0.00 0.00 36.63 2.87
568 570 8.548721 CAATGGCGTACCTTAACTTTATAGAAG 58.451 37.037 0.00 0.00 36.63 2.85
569 571 7.496591 CCAATGGCGTACCTTAACTTTATAGAA 59.503 37.037 0.00 0.00 36.63 2.10
570 572 6.987992 CCAATGGCGTACCTTAACTTTATAGA 59.012 38.462 0.00 0.00 36.63 1.98
571 573 6.293244 GCCAATGGCGTACCTTAACTTTATAG 60.293 42.308 9.14 0.00 39.62 1.31
572 574 5.528320 GCCAATGGCGTACCTTAACTTTATA 59.472 40.000 9.14 0.00 39.62 0.98
573 575 4.337274 GCCAATGGCGTACCTTAACTTTAT 59.663 41.667 9.14 0.00 39.62 1.40
574 576 3.690628 GCCAATGGCGTACCTTAACTTTA 59.309 43.478 9.14 0.00 39.62 1.85
575 577 2.490509 GCCAATGGCGTACCTTAACTTT 59.509 45.455 9.14 0.00 39.62 2.66
576 578 2.089201 GCCAATGGCGTACCTTAACTT 58.911 47.619 9.14 0.00 39.62 2.66
577 579 1.746470 GCCAATGGCGTACCTTAACT 58.254 50.000 9.14 0.00 39.62 2.24
588 590 1.883084 CCGAGAGTACGCCAATGGC 60.883 63.158 15.52 15.52 46.75 4.40
589 591 0.174845 TTCCGAGAGTACGCCAATGG 59.825 55.000 0.00 0.00 0.00 3.16
590 592 2.004583 TTTCCGAGAGTACGCCAATG 57.995 50.000 0.00 0.00 0.00 2.82
591 593 2.754946 TTTTCCGAGAGTACGCCAAT 57.245 45.000 0.00 0.00 0.00 3.16
592 594 2.529780 TTTTTCCGAGAGTACGCCAA 57.470 45.000 0.00 0.00 0.00 4.52
611 613 2.237643 GGGTTTGTGGTTGGAGGTTTTT 59.762 45.455 0.00 0.00 0.00 1.94
612 614 1.834896 GGGTTTGTGGTTGGAGGTTTT 59.165 47.619 0.00 0.00 0.00 2.43
613 615 1.273324 TGGGTTTGTGGTTGGAGGTTT 60.273 47.619 0.00 0.00 0.00 3.27
614 616 0.336737 TGGGTTTGTGGTTGGAGGTT 59.663 50.000 0.00 0.00 0.00 3.50
615 617 0.106217 CTGGGTTTGTGGTTGGAGGT 60.106 55.000 0.00 0.00 0.00 3.85
622 624 0.033601 TCTTGTGCTGGGTTTGTGGT 60.034 50.000 0.00 0.00 0.00 4.16
623 625 1.000060 CATCTTGTGCTGGGTTTGTGG 60.000 52.381 0.00 0.00 0.00 4.17
644 646 2.031012 TGACAGCTGGAAGTGGCG 59.969 61.111 19.93 0.00 35.30 5.69
695 698 3.446516 GGTATGGAAGAGTACGGTCACTT 59.553 47.826 0.00 0.00 0.00 3.16
707 710 7.860649 AATACCCTAAATACGGTATGGAAGA 57.139 36.000 0.58 0.00 43.17 2.87
713 716 7.940688 CCCTTCAAAATACCCTAAATACGGTAT 59.059 37.037 0.00 0.00 45.36 2.73
715 718 6.124340 CCCTTCAAAATACCCTAAATACGGT 58.876 40.000 0.00 0.00 36.08 4.83
728 732 1.271652 TGCTCACCGCCCTTCAAAATA 60.272 47.619 0.00 0.00 38.05 1.40
893 908 1.549950 GGAGGAGGATTTGGGTTTGCA 60.550 52.381 0.00 0.00 0.00 4.08
988 1003 4.285149 GTGCATCATCGCCGTCGC 62.285 66.667 0.00 0.00 35.26 5.19
989 1004 3.976375 CGTGCATCATCGCCGTCG 61.976 66.667 0.00 0.00 0.00 5.12
1314 1329 1.595993 CGAGCTTCTGGGAGACGGAA 61.596 60.000 0.00 0.00 42.10 4.30
1582 1942 2.864946 CACATTGATGAGAAGCGGAGAG 59.135 50.000 0.00 0.00 0.00 3.20
1588 1948 3.671928 GCAACAACACATTGATGAGAAGC 59.328 43.478 1.91 0.00 40.18 3.86
1600 1961 1.530720 CATACGCTCTGCAACAACACA 59.469 47.619 0.00 0.00 0.00 3.72
1633 2002 5.771198 GATCAGACTGTGATGGCACGACA 62.771 52.174 1.59 0.00 46.64 4.35
1634 2003 3.304337 GATCAGACTGTGATGGCACGAC 61.304 54.545 1.59 0.00 46.64 4.34
1635 2004 1.134995 GATCAGACTGTGATGGCACGA 60.135 52.381 1.59 0.00 46.64 4.35
1636 2005 1.284657 GATCAGACTGTGATGGCACG 58.715 55.000 1.59 0.00 46.64 5.34
1640 2009 0.873312 CGGCGATCAGACTGTGATGG 60.873 60.000 0.00 0.00 46.64 3.51
1645 2014 1.330655 ATTCCCGGCGATCAGACTGT 61.331 55.000 9.30 0.00 0.00 3.55
1702 2071 1.604378 CCTCTCCCGGAGCAAATGT 59.396 57.895 9.87 0.00 40.57 2.71
1821 2198 4.342862 ACTTCTAGTGCAAGTGTGTGAT 57.657 40.909 0.00 0.00 32.65 3.06
1824 2201 5.509840 CCTTCTACTTCTAGTGCAAGTGTGT 60.510 44.000 5.74 0.00 35.63 3.72
1842 2219 5.970640 ACAAGTCTAAATGGGGATCCTTCTA 59.029 40.000 12.58 0.00 0.00 2.10
1843 2220 4.790790 ACAAGTCTAAATGGGGATCCTTCT 59.209 41.667 12.58 0.00 0.00 2.85
1844 2221 4.884164 CACAAGTCTAAATGGGGATCCTTC 59.116 45.833 12.58 5.20 0.00 3.46
1845 2222 4.540099 TCACAAGTCTAAATGGGGATCCTT 59.460 41.667 12.58 0.00 0.00 3.36
1846 2223 4.111577 TCACAAGTCTAAATGGGGATCCT 58.888 43.478 12.58 0.00 0.00 3.24
1847 2224 4.503714 TCACAAGTCTAAATGGGGATCC 57.496 45.455 1.92 1.92 0.00 3.36
1928 2308 2.602257 TTGGATACCACTCGCAGATG 57.398 50.000 0.00 0.00 33.89 2.90
1934 2314 3.557185 CACATCACATTGGATACCACTCG 59.443 47.826 0.00 0.00 30.78 4.18
1942 2322 3.056393 CCAAGTTGCACATCACATTGGAT 60.056 43.478 0.00 0.00 40.46 3.41
1984 2364 3.844211 ACCCTGTTCTTCCTATTGCTGTA 59.156 43.478 0.00 0.00 0.00 2.74
2020 2400 6.067263 TGTTAGTACAGAAAACATGGTTGC 57.933 37.500 0.00 0.00 0.00 4.17
2098 2488 0.027455 TGACAAAGTTTCGCTGCACG 59.973 50.000 0.00 2.79 45.62 5.34
2136 2526 5.473931 TGAGCTAGAGTTCATCACAAAGAC 58.526 41.667 0.00 0.00 30.24 3.01
2147 2537 2.430332 AGTGCCTCATGAGCTAGAGTTC 59.570 50.000 17.76 1.78 0.00 3.01
2278 2671 2.297701 TCACCCAACTGCTTGACTTTC 58.702 47.619 0.00 0.00 0.00 2.62
2317 2710 2.900546 CGATAGATTACCAAGGAGGCCT 59.099 50.000 3.86 3.86 39.23 5.19
2346 2739 8.451748 GGAAAGACTAATGTCCAATGTAAGAAC 58.548 37.037 0.00 0.00 43.91 3.01
2393 2786 6.630071 AGTGTTGGCATTGGATAAATAACAC 58.370 36.000 0.00 0.00 44.02 3.32
2485 2879 0.652592 CCGCGATTACTGCTGAAAGG 59.347 55.000 8.23 0.00 0.00 3.11
2614 3008 4.393062 AGTCTTTTATCGTGCCATCTGTTG 59.607 41.667 0.00 0.00 0.00 3.33
2615 3009 4.393062 CAGTCTTTTATCGTGCCATCTGTT 59.607 41.667 0.00 0.00 0.00 3.16
2616 3010 3.935203 CAGTCTTTTATCGTGCCATCTGT 59.065 43.478 0.00 0.00 0.00 3.41
2793 3193 7.169476 TGTGTCATCGTATTTACTCGAAACAAA 59.831 33.333 0.00 0.00 39.45 2.83
2797 3197 6.384224 AGTGTGTCATCGTATTTACTCGAAA 58.616 36.000 0.00 0.00 39.45 3.46
2883 3283 0.107017 AATGACGGGGCCTTGATGAG 60.107 55.000 0.84 0.00 0.00 2.90
2884 3284 0.394216 CAATGACGGGGCCTTGATGA 60.394 55.000 0.84 0.00 0.00 2.92
2885 3285 0.394216 TCAATGACGGGGCCTTGATG 60.394 55.000 0.84 0.00 0.00 3.07
2887 3287 1.299648 CTCAATGACGGGGCCTTGA 59.700 57.895 0.84 4.07 0.00 3.02
2888 3288 2.409870 GCTCAATGACGGGGCCTTG 61.410 63.158 0.84 0.00 0.00 3.61
2891 3291 2.825836 CAGCTCAATGACGGGGCC 60.826 66.667 0.00 0.00 0.00 5.80
2895 3295 0.877071 AAGCAACAGCTCAATGACGG 59.123 50.000 0.00 0.00 37.72 4.79
2898 3298 1.001048 GTGCAAGCAACAGCTCAATGA 60.001 47.619 0.00 0.00 37.72 2.57
2900 3300 1.325355 AGTGCAAGCAACAGCTCAAT 58.675 45.000 0.00 0.00 37.72 2.57
2951 3379 9.466497 TGAGATTGACATTTTAATCTTTAGCCT 57.534 29.630 0.92 0.00 42.13 4.58
3008 3436 1.691196 CACAGGGTCTCTTTGGCAAA 58.309 50.000 12.79 12.79 0.00 3.68
3117 3778 2.396157 GGAACGCGGGTGATTGACC 61.396 63.158 12.47 0.00 45.28 4.02
3206 3868 4.074970 GGGATTGAGCTGTTTCTTCTTCA 58.925 43.478 0.00 0.00 0.00 3.02
3223 3885 4.941873 GGTGTTTCTTCTTCATACGGGATT 59.058 41.667 0.00 0.00 0.00 3.01
3272 3934 4.192317 CTGGCTGTAAAGTGGGATAAGAC 58.808 47.826 0.00 0.00 0.00 3.01
3362 4024 1.195900 CATTGTCACCCAACGTAACGG 59.804 52.381 0.00 0.00 35.44 4.44
3369 4031 0.511221 CGACGACATTGTCACCCAAC 59.489 55.000 16.61 1.02 38.84 3.77


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

AutoCloner maintained by Alex Coulton.