Multiple sequence alignment - TraesCS2B01G467300

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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 TraesCS2B01G467300 chr2B 100.000 2654 0 0 775 3428 663044778 663047431 0.000000e+00 4902
1 TraesCS2B01G467300 chr2B 91.189 1657 123 10 946 2591 54049020 54050664 0.000000e+00 2230
2 TraesCS2B01G467300 chr2B 92.278 1295 94 5 1299 2591 54034091 54035381 0.000000e+00 1832
3 TraesCS2B01G467300 chr2B 100.000 496 0 0 1 496 663044004 663044499 0.000000e+00 917
4 TraesCS2B01G467300 chr2B 93.952 496 30 0 1 496 690222978 690222483 0.000000e+00 750
5 TraesCS2B01G467300 chr2B 93.750 496 31 0 1 496 71694698 71695193 0.000000e+00 745
6 TraesCS2B01G467300 chr2B 92.430 502 32 2 1 496 5966662 5966161 0.000000e+00 712
7 TraesCS2B01G467300 chr2B 95.238 84 4 0 775 858 717645077 717644994 2.150000e-27 134
8 TraesCS2B01G467300 chr2A 93.016 2520 111 26 927 3425 695469646 695472121 0.000000e+00 3618
9 TraesCS2B01G467300 chr2D 90.275 2581 142 45 912 3425 556049406 556051944 0.000000e+00 3275
10 TraesCS2B01G467300 chr2D 90.833 240 16 2 2723 2962 32609467 32609700 1.990000e-82 316
11 TraesCS2B01G467300 chrUn 91.575 1092 82 5 946 2034 272459305 272458221 0.000000e+00 1498
12 TraesCS2B01G467300 chr7B 93.952 496 29 1 1 496 721586817 721587311 0.000000e+00 749
13 TraesCS2B01G467300 chr7B 92.944 496 35 0 1 496 570273548 570274043 0.000000e+00 723
14 TraesCS2B01G467300 chr7B 91.968 498 37 2 1 496 695313961 695313465 0.000000e+00 695
15 TraesCS2B01G467300 chr7B 91.129 496 44 0 1 496 2236068 2236563 0.000000e+00 673
16 TraesCS2B01G467300 chr7B 96.429 84 3 0 775 858 603300216 603300133 4.610000e-29 139
17 TraesCS2B01G467300 chr5B 93.096 478 33 0 1 478 421608466 421608943 0.000000e+00 701
18 TraesCS2B01G467300 chr5B 92.553 94 6 1 775 868 712447210 712447118 2.150000e-27 134
19 TraesCS2B01G467300 chr5B 96.250 80 3 0 775 854 536889376 536889455 7.720000e-27 132
20 TraesCS2B01G467300 chr5B 91.489 94 7 1 775 867 617044056 617044149 9.990000e-26 128
21 TraesCS2B01G467300 chr1B 91.018 501 36 5 1 493 555296527 555297026 0.000000e+00 667
22 TraesCS2B01G467300 chr3B 96.341 82 3 0 775 856 460181417 460181498 5.970000e-28 135
23 TraesCS2B01G467300 chr3B 95.238 84 4 0 775 858 38815094 38815011 2.150000e-27 134
24 TraesCS2B01G467300 chr3B 95.238 84 4 0 775 858 38831425 38831342 2.150000e-27 134
25 TraesCS2B01G467300 chr3B 93.333 90 5 1 775 863 2155578 2155489 7.720000e-27 132
26 TraesCS2B01G467300 chr7D 92.391 92 5 1 775 866 56544558 56544469 2.780000e-26 130


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 TraesCS2B01G467300 chr2B 663044004 663047431 3427 False 2909.5 4902 100.000 1 3428 2 chr2B.!!$F4 3427
1 TraesCS2B01G467300 chr2B 54049020 54050664 1644 False 2230.0 2230 91.189 946 2591 1 chr2B.!!$F2 1645
2 TraesCS2B01G467300 chr2B 54034091 54035381 1290 False 1832.0 1832 92.278 1299 2591 1 chr2B.!!$F1 1292
3 TraesCS2B01G467300 chr2B 5966161 5966662 501 True 712.0 712 92.430 1 496 1 chr2B.!!$R1 495
4 TraesCS2B01G467300 chr2A 695469646 695472121 2475 False 3618.0 3618 93.016 927 3425 1 chr2A.!!$F1 2498
5 TraesCS2B01G467300 chr2D 556049406 556051944 2538 False 3275.0 3275 90.275 912 3425 1 chr2D.!!$F2 2513
6 TraesCS2B01G467300 chrUn 272458221 272459305 1084 True 1498.0 1498 91.575 946 2034 1 chrUn.!!$R1 1088

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
459 466 0.034059 CCGATCTAGGCCGCTTGATT 59.966 55.0 0.0 0.0 0.0 2.57 F
854 861 0.107945 GAACGGCTGGAGATGCTCTT 60.108 55.0 0.0 0.0 0.0 2.85 F
1628 1644 0.533491 TACCGCCAAATCTACACGCT 59.467 50.0 0.0 0.0 0.0 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1628 1644 0.179012 GTTGGTTCTTGGACCCGGAA 60.179 55.0 0.73 0.0 39.01 4.30 R
1662 1678 0.604578 AGTTAAAGGTCTGCGCCGTA 59.395 50.0 4.18 0.0 0.00 4.02 R
3217 3302 0.108585 TTGCTTCTTCCGCTCTTGGT 59.891 50.0 0.00 0.0 0.00 3.67 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
24 25 3.343788 AAGAGAAGACCGAGGCGCG 62.344 63.158 0.00 0.00 40.47 6.86
46 47 2.126228 TCGGCGTTGATGTCGACC 60.126 61.111 14.12 0.00 41.70 4.79
119 120 2.747855 CCGACCTGGCTTTCCTGC 60.748 66.667 0.00 0.00 0.00 4.85
174 175 1.736645 CGGTCAAGGCGTGGTACAG 60.737 63.158 0.00 0.00 41.80 2.74
184 185 1.019278 CGTGGTACAGGGCACATGTC 61.019 60.000 0.00 0.00 41.80 3.06
218 219 4.117661 AGCTTCCCTCGACGACGC 62.118 66.667 1.48 0.00 39.58 5.19
388 395 2.583593 GACCTCGTCGCCTGATGC 60.584 66.667 0.00 0.00 0.00 3.91
399 406 3.490759 CTGATGCGCGCTTCCGTT 61.491 61.111 34.98 14.23 36.67 4.44
400 407 3.425938 CTGATGCGCGCTTCCGTTC 62.426 63.158 34.98 20.82 36.67 3.95
401 408 3.188786 GATGCGCGCTTCCGTTCT 61.189 61.111 33.29 6.19 36.67 3.01
402 409 2.740714 GATGCGCGCTTCCGTTCTT 61.741 57.895 33.29 5.26 36.67 2.52
403 410 2.240612 GATGCGCGCTTCCGTTCTTT 62.241 55.000 33.29 3.63 36.67 2.52
404 411 2.202184 GCGCGCTTCCGTTCTTTC 60.202 61.111 26.67 0.00 36.67 2.62
405 412 2.474712 CGCGCTTCCGTTCTTTCC 59.525 61.111 5.56 0.00 36.67 3.13
406 413 2.027625 CGCGCTTCCGTTCTTTCCT 61.028 57.895 5.56 0.00 36.67 3.36
407 414 1.497722 GCGCTTCCGTTCTTTCCTG 59.502 57.895 0.00 0.00 36.67 3.86
408 415 1.497722 CGCTTCCGTTCTTTCCTGC 59.502 57.895 0.00 0.00 0.00 4.85
409 416 0.951040 CGCTTCCGTTCTTTCCTGCT 60.951 55.000 0.00 0.00 0.00 4.24
410 417 1.239347 GCTTCCGTTCTTTCCTGCTT 58.761 50.000 0.00 0.00 0.00 3.91
411 418 1.609072 GCTTCCGTTCTTTCCTGCTTT 59.391 47.619 0.00 0.00 0.00 3.51
412 419 2.034685 GCTTCCGTTCTTTCCTGCTTTT 59.965 45.455 0.00 0.00 0.00 2.27
413 420 3.490933 GCTTCCGTTCTTTCCTGCTTTTT 60.491 43.478 0.00 0.00 0.00 1.94
434 441 3.750639 TTTACGCCGAACATTTCATCC 57.249 42.857 0.00 0.00 0.00 3.51
435 442 1.282817 TACGCCGAACATTTCATCCG 58.717 50.000 0.00 0.00 0.00 4.18
436 443 1.351707 CGCCGAACATTTCATCCGG 59.648 57.895 0.00 0.00 42.74 5.14
438 445 1.727467 CCGAACATTTCATCCGGCC 59.273 57.895 0.00 0.00 33.47 6.13
439 446 1.351707 CGAACATTTCATCCGGCCG 59.648 57.895 21.04 21.04 0.00 6.13
440 447 1.064134 GAACATTTCATCCGGCCGC 59.936 57.895 22.85 0.00 0.00 6.53
441 448 2.336400 GAACATTTCATCCGGCCGCC 62.336 60.000 22.85 0.00 0.00 6.13
457 464 3.129300 CCGATCTAGGCCGCTTGA 58.871 61.111 0.00 0.00 0.00 3.02
458 465 1.668294 CCGATCTAGGCCGCTTGAT 59.332 57.895 0.00 0.00 0.00 2.57
459 466 0.034059 CCGATCTAGGCCGCTTGATT 59.966 55.000 0.00 0.00 0.00 2.57
460 467 1.143305 CGATCTAGGCCGCTTGATTG 58.857 55.000 0.00 0.22 0.00 2.67
461 468 0.871057 GATCTAGGCCGCTTGATTGC 59.129 55.000 0.00 0.00 0.00 3.56
462 469 0.536006 ATCTAGGCCGCTTGATTGCC 60.536 55.000 0.00 0.00 45.70 4.52
466 473 3.211963 GCCGCTTGATTGCCGGAT 61.212 61.111 5.05 0.00 0.00 4.18
467 474 2.774799 GCCGCTTGATTGCCGGATT 61.775 57.895 5.05 0.00 0.00 3.01
468 475 1.064621 CCGCTTGATTGCCGGATTG 59.935 57.895 5.05 0.00 0.00 2.67
469 476 1.656818 CCGCTTGATTGCCGGATTGT 61.657 55.000 5.05 0.00 0.00 2.71
470 477 0.523968 CGCTTGATTGCCGGATTGTG 60.524 55.000 5.05 0.00 0.00 3.33
471 478 0.179129 GCTTGATTGCCGGATTGTGG 60.179 55.000 5.05 0.00 0.00 4.17
477 484 2.185867 GCCGGATTGTGGCGTCTA 59.814 61.111 5.05 0.00 43.70 2.59
478 485 1.227556 GCCGGATTGTGGCGTCTAT 60.228 57.895 5.05 0.00 43.70 1.98
479 486 0.814010 GCCGGATTGTGGCGTCTATT 60.814 55.000 5.05 0.00 43.70 1.73
480 487 1.663695 CCGGATTGTGGCGTCTATTT 58.336 50.000 0.00 0.00 0.00 1.40
481 488 2.014128 CCGGATTGTGGCGTCTATTTT 58.986 47.619 0.00 0.00 0.00 1.82
482 489 2.223249 CCGGATTGTGGCGTCTATTTTG 60.223 50.000 0.00 0.00 0.00 2.44
483 490 2.223249 CGGATTGTGGCGTCTATTTTGG 60.223 50.000 0.00 0.00 0.00 3.28
484 491 2.099098 GGATTGTGGCGTCTATTTTGGG 59.901 50.000 0.00 0.00 0.00 4.12
485 492 0.885196 TTGTGGCGTCTATTTTGGGC 59.115 50.000 0.00 0.00 0.00 5.36
486 493 1.302383 TGTGGCGTCTATTTTGGGCG 61.302 55.000 0.00 0.00 0.00 6.13
487 494 2.403378 TGGCGTCTATTTTGGGCGC 61.403 57.895 0.00 0.00 46.24 6.53
488 495 2.022762 GCGTCTATTTTGGGCGCG 59.977 61.111 0.00 0.00 38.75 6.86
489 496 2.707039 CGTCTATTTTGGGCGCGG 59.293 61.111 8.83 0.00 0.00 6.46
490 497 2.819552 CGTCTATTTTGGGCGCGGG 61.820 63.158 8.83 0.00 0.00 6.13
491 498 1.450669 GTCTATTTTGGGCGCGGGA 60.451 57.895 8.83 0.00 0.00 5.14
492 499 1.027792 GTCTATTTTGGGCGCGGGAA 61.028 55.000 8.83 0.00 0.00 3.97
493 500 1.027792 TCTATTTTGGGCGCGGGAAC 61.028 55.000 8.83 0.00 0.00 3.62
816 823 3.002583 CCCCCAGGCCGCATTTTT 61.003 61.111 0.00 0.00 0.00 1.94
830 837 3.863606 TTTTTCAACGCCCTGGGG 58.136 55.556 16.03 7.28 38.57 4.96
850 857 2.892425 CCGAACGGCTGGAGATGC 60.892 66.667 0.00 0.00 0.00 3.91
851 858 2.185350 CGAACGGCTGGAGATGCT 59.815 61.111 0.00 0.00 0.00 3.79
852 859 1.880340 CGAACGGCTGGAGATGCTC 60.880 63.158 0.00 0.00 0.00 4.26
853 860 1.519719 GAACGGCTGGAGATGCTCT 59.480 57.895 0.00 0.00 0.00 4.09
854 861 0.107945 GAACGGCTGGAGATGCTCTT 60.108 55.000 0.00 0.00 0.00 2.85
855 862 1.137086 GAACGGCTGGAGATGCTCTTA 59.863 52.381 0.00 0.00 0.00 2.10
856 863 0.749649 ACGGCTGGAGATGCTCTTAG 59.250 55.000 0.00 0.00 0.00 2.18
857 864 1.035923 CGGCTGGAGATGCTCTTAGA 58.964 55.000 0.00 0.00 0.00 2.10
858 865 1.269517 CGGCTGGAGATGCTCTTAGAC 60.270 57.143 0.00 0.00 0.00 2.59
859 866 2.038659 GGCTGGAGATGCTCTTAGACT 58.961 52.381 0.00 0.00 0.00 3.24
860 867 2.433970 GGCTGGAGATGCTCTTAGACTT 59.566 50.000 0.00 0.00 0.00 3.01
861 868 3.456280 GCTGGAGATGCTCTTAGACTTG 58.544 50.000 0.00 0.00 0.00 3.16
862 869 3.118811 GCTGGAGATGCTCTTAGACTTGT 60.119 47.826 0.00 0.00 0.00 3.16
863 870 4.622695 GCTGGAGATGCTCTTAGACTTGTT 60.623 45.833 0.00 0.00 0.00 2.83
864 871 4.825422 TGGAGATGCTCTTAGACTTGTTG 58.175 43.478 0.00 0.00 0.00 3.33
865 872 4.284490 TGGAGATGCTCTTAGACTTGTTGT 59.716 41.667 0.00 0.00 0.00 3.32
866 873 5.221722 TGGAGATGCTCTTAGACTTGTTGTT 60.222 40.000 0.00 0.00 0.00 2.83
867 874 5.121454 GGAGATGCTCTTAGACTTGTTGTTG 59.879 44.000 0.00 0.00 0.00 3.33
868 875 5.615289 AGATGCTCTTAGACTTGTTGTTGT 58.385 37.500 0.00 0.00 0.00 3.32
869 876 5.468072 AGATGCTCTTAGACTTGTTGTTGTG 59.532 40.000 0.00 0.00 0.00 3.33
870 877 4.513442 TGCTCTTAGACTTGTTGTTGTGT 58.487 39.130 0.00 0.00 0.00 3.72
871 878 4.941263 TGCTCTTAGACTTGTTGTTGTGTT 59.059 37.500 0.00 0.00 0.00 3.32
872 879 5.414454 TGCTCTTAGACTTGTTGTTGTGTTT 59.586 36.000 0.00 0.00 0.00 2.83
873 880 6.072175 TGCTCTTAGACTTGTTGTTGTGTTTT 60.072 34.615 0.00 0.00 0.00 2.43
874 881 6.806739 GCTCTTAGACTTGTTGTTGTGTTTTT 59.193 34.615 0.00 0.00 0.00 1.94
904 911 9.926158 TTGGTTTTACTGTACATAATTAGTCGA 57.074 29.630 0.00 0.00 0.00 4.20
905 912 9.577110 TGGTTTTACTGTACATAATTAGTCGAG 57.423 33.333 0.00 0.00 0.00 4.04
906 913 8.538039 GGTTTTACTGTACATAATTAGTCGAGC 58.462 37.037 0.00 0.00 0.00 5.03
907 914 9.079833 GTTTTACTGTACATAATTAGTCGAGCA 57.920 33.333 0.00 0.00 0.00 4.26
908 915 9.642327 TTTTACTGTACATAATTAGTCGAGCAA 57.358 29.630 0.00 0.00 0.00 3.91
909 916 9.642327 TTTACTGTACATAATTAGTCGAGCAAA 57.358 29.630 0.00 0.00 0.00 3.68
910 917 7.757097 ACTGTACATAATTAGTCGAGCAAAG 57.243 36.000 0.00 0.00 0.00 2.77
931 938 9.967346 GCAAAGAACTTCTTCTATTTTTAACCT 57.033 29.630 4.46 0.00 35.27 3.50
962 969 4.672409 AGAACAAGAAAAAGAAAGCACGG 58.328 39.130 0.00 0.00 0.00 4.94
978 985 1.513586 CGGTAGTGCGTCTCGTTCC 60.514 63.158 0.00 0.00 0.00 3.62
1010 1017 3.264897 CACCTCTATGCACGCCGC 61.265 66.667 0.00 0.00 42.89 6.53
1076 1092 1.061411 CGCCGTACTTCATCGACGA 59.939 57.895 0.00 0.00 38.88 4.20
1297 1313 4.888325 CCCCTCCCCCGCTCATCT 62.888 72.222 0.00 0.00 0.00 2.90
1628 1644 0.533491 TACCGCCAAATCTACACGCT 59.467 50.000 0.00 0.00 0.00 5.07
1983 2001 1.171308 CTGGGATTGAGCCAAGTGTG 58.829 55.000 0.00 0.00 0.00 3.82
2001 2019 5.189928 AGTGTGACAACATTTGAGTGGTTA 58.810 37.500 0.00 0.00 38.92 2.85
2136 2162 4.462483 AGATTGTGTCAGAAGAGGAGAGTC 59.538 45.833 0.00 0.00 0.00 3.36
2320 2346 5.123227 GTGCTGAGGTATACCATGCTTTTA 58.877 41.667 23.87 6.16 38.89 1.52
2388 2414 1.106285 GGAAGGAAATGGCAGCGATT 58.894 50.000 0.00 0.00 0.00 3.34
2421 2447 5.071788 GGATGGAAGTGACCTGGATTGTATA 59.928 44.000 0.00 0.00 0.00 1.47
2442 2468 3.059166 ACAATGATGCGTTTTTCAAGCC 58.941 40.909 0.00 0.00 0.00 4.35
2484 2510 5.334879 GCACACTGGTAAATTCCTGTTGTAG 60.335 44.000 0.00 0.00 37.51 2.74
2495 2521 5.808366 TTCCTGTTGTAGTTGTCTCATCT 57.192 39.130 0.00 0.00 0.00 2.90
2537 2563 8.399425 CAGTCTTTACACTGTACATACTAGAGG 58.601 40.741 0.00 0.00 39.26 3.69
2539 2565 8.397148 GTCTTTACACTGTACATACTAGAGGTC 58.603 40.741 0.00 0.00 0.00 3.85
2540 2566 8.327271 TCTTTACACTGTACATACTAGAGGTCT 58.673 37.037 0.00 0.00 0.00 3.85
2541 2567 9.610705 CTTTACACTGTACATACTAGAGGTCTA 57.389 37.037 0.00 0.00 0.00 2.59
2543 2569 7.434927 ACACTGTACATACTAGAGGTCTAGA 57.565 40.000 18.91 5.17 46.80 2.43
2544 2570 7.859540 ACACTGTACATACTAGAGGTCTAGAA 58.140 38.462 18.91 0.00 46.80 2.10
2545 2571 7.769970 ACACTGTACATACTAGAGGTCTAGAAC 59.230 40.741 18.91 0.00 46.80 3.01
2546 2572 6.985645 ACTGTACATACTAGAGGTCTAGAACG 59.014 42.308 18.91 9.45 46.80 3.95
2549 2575 4.817464 ACATACTAGAGGTCTAGAACGCAG 59.183 45.833 18.91 10.98 46.80 5.18
2556 2587 4.464597 AGAGGTCTAGAACGCAGAAATCTT 59.535 41.667 14.32 0.00 0.00 2.40
2590 2622 7.786030 TCTTTAGAAATGTATGGAGTCTGAGG 58.214 38.462 0.00 0.00 0.00 3.86
2591 2623 7.619698 TCTTTAGAAATGTATGGAGTCTGAGGA 59.380 37.037 0.00 0.00 0.00 3.71
2619 2651 4.080299 GGGTCTTCCACCTCTATTTGTGAT 60.080 45.833 0.00 0.00 45.95 3.06
2657 2689 3.057969 TGACTTCTGGCTGGTTATGTG 57.942 47.619 0.00 0.00 0.00 3.21
2815 2859 6.463995 TTTTGCAGGTTTGTTAAGATCTGT 57.536 33.333 0.00 0.00 0.00 3.41
2862 2906 2.363359 GGCCAGCTCCCTTCATTATTTG 59.637 50.000 0.00 0.00 0.00 2.32
2863 2907 3.290710 GCCAGCTCCCTTCATTATTTGA 58.709 45.455 0.00 0.00 0.00 2.69
2864 2908 3.893813 GCCAGCTCCCTTCATTATTTGAT 59.106 43.478 0.00 0.00 33.34 2.57
2865 2909 4.343239 GCCAGCTCCCTTCATTATTTGATT 59.657 41.667 0.00 0.00 33.34 2.57
2866 2910 5.163374 GCCAGCTCCCTTCATTATTTGATTT 60.163 40.000 0.00 0.00 33.34 2.17
2899 2943 3.949754 CCACATGGACTGCAACTATGAAT 59.050 43.478 18.54 0.99 37.39 2.57
2942 2986 1.990563 GTATGTAGTGTGTGTCGGTGC 59.009 52.381 0.00 0.00 0.00 5.01
2946 2990 0.032952 TAGTGTGTGTCGGTGCTTCC 59.967 55.000 0.00 0.00 0.00 3.46
2981 3042 0.463654 GGTTGGCACCGATGATAGCA 60.464 55.000 0.00 0.00 31.60 3.49
2983 3044 1.064060 GTTGGCACCGATGATAGCAAC 59.936 52.381 0.00 0.00 0.00 4.17
3078 3144 3.278668 AGATCCCTGAGACAATGCAAG 57.721 47.619 0.00 0.00 0.00 4.01
3082 3148 2.027192 TCCCTGAGACAATGCAAGGTAC 60.027 50.000 0.00 0.00 0.00 3.34
3093 3159 0.035739 GCAAGGTACCCGTTCCTGAA 59.964 55.000 8.74 0.00 33.97 3.02
3094 3160 1.339727 GCAAGGTACCCGTTCCTGAAT 60.340 52.381 8.74 0.00 33.97 2.57
3095 3161 2.629051 CAAGGTACCCGTTCCTGAATC 58.371 52.381 8.74 0.00 33.97 2.52
3096 3162 1.201424 AGGTACCCGTTCCTGAATCC 58.799 55.000 8.74 0.00 32.29 3.01
3097 3163 1.201424 GGTACCCGTTCCTGAATCCT 58.799 55.000 0.00 0.00 0.00 3.24
3098 3164 1.134491 GGTACCCGTTCCTGAATCCTG 60.134 57.143 0.00 0.00 0.00 3.86
3099 3165 1.829222 GTACCCGTTCCTGAATCCTGA 59.171 52.381 0.00 0.00 0.00 3.86
3117 3183 1.482182 TGAGCGCATCACCTAACTGAT 59.518 47.619 11.47 0.00 31.12 2.90
3158 3243 5.745312 TGACAGAACTGGATATGACAAGT 57.255 39.130 6.76 0.00 34.19 3.16
3168 3253 4.772100 TGGATATGACAAGTGTGAGAGTGA 59.228 41.667 0.00 0.00 0.00 3.41
3184 3269 7.147915 TGTGAGAGTGAGTGTTATATACATGCA 60.148 37.037 0.00 0.00 39.39 3.96
3217 3302 2.287547 GCAATTGCAAAGGACGAACTCA 60.288 45.455 25.36 0.00 41.59 3.41
3285 3371 0.939577 CCGTGGTCAGTGTTCTGTCG 60.940 60.000 0.00 0.00 41.91 4.35
3346 3433 3.980646 TTGGTGTGATGTGTGTAAAGC 57.019 42.857 0.00 0.00 0.00 3.51
3349 3436 4.905429 TGGTGTGATGTGTGTAAAGCTAT 58.095 39.130 0.00 0.00 0.00 2.97
3401 3513 7.878477 TTTGCTTCTGTCATTCAAATGATTC 57.122 32.000 8.56 0.00 46.17 2.52
3425 3537 6.603201 TCCATGGAAATTTCAGAGGAATGTAC 59.397 38.462 13.46 0.00 31.93 2.90
3426 3538 6.604795 CCATGGAAATTTCAGAGGAATGTACT 59.395 38.462 19.49 0.00 31.93 2.73
3427 3539 7.123247 CCATGGAAATTTCAGAGGAATGTACTT 59.877 37.037 19.49 0.00 31.93 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.740714 GACATCAACGCCGACCAGC 61.741 63.158 0.00 0.00 0.00 4.85
63 64 2.183555 CGTTGGTCCGGAGTAGGC 59.816 66.667 3.06 0.00 0.00 3.93
88 89 2.047830 AGGTCGGTGTTCCTCTTCTTT 58.952 47.619 0.00 0.00 0.00 2.52
151 152 4.680237 CACGCCTTGACCGCCTCA 62.680 66.667 0.00 0.00 0.00 3.86
178 179 1.524002 CAGGATGAGGCCGACATGT 59.476 57.895 19.96 0.00 39.69 3.21
184 185 3.083349 TGGTCCAGGATGAGGCCG 61.083 66.667 0.00 0.00 39.69 6.13
257 264 4.028490 ATCGGTTGGGCTTGGCGA 62.028 61.111 0.00 0.00 0.00 5.54
264 271 3.585990 CGGCATCATCGGTTGGGC 61.586 66.667 0.00 0.00 0.00 5.36
268 275 4.155733 TCGGCGGCATCATCGGTT 62.156 61.111 10.53 0.00 0.00 4.44
273 280 2.107750 CAGTCTCGGCGGCATCAT 59.892 61.111 10.53 0.00 0.00 2.45
371 378 2.583593 GCATCAGGCGACGAGGTC 60.584 66.667 0.00 0.00 0.00 3.85
382 389 3.425938 GAACGGAAGCGCGCATCAG 62.426 63.158 33.66 31.56 0.00 2.90
383 390 3.487202 GAACGGAAGCGCGCATCA 61.487 61.111 33.66 0.00 0.00 3.07
384 391 2.240612 AAAGAACGGAAGCGCGCATC 62.241 55.000 35.10 30.80 0.00 3.91
385 392 2.240612 GAAAGAACGGAAGCGCGCAT 62.241 55.000 35.10 24.08 0.00 4.73
386 393 2.950172 GAAAGAACGGAAGCGCGCA 61.950 57.895 35.10 0.00 0.00 6.09
387 394 2.202184 GAAAGAACGGAAGCGCGC 60.202 61.111 26.66 26.66 0.00 6.86
388 395 2.027625 AGGAAAGAACGGAAGCGCG 61.028 57.895 0.00 0.00 0.00 6.86
389 396 1.497722 CAGGAAAGAACGGAAGCGC 59.502 57.895 0.00 0.00 0.00 5.92
390 397 0.951040 AGCAGGAAAGAACGGAAGCG 60.951 55.000 0.00 0.00 0.00 4.68
391 398 1.239347 AAGCAGGAAAGAACGGAAGC 58.761 50.000 0.00 0.00 0.00 3.86
392 399 3.990318 AAAAGCAGGAAAGAACGGAAG 57.010 42.857 0.00 0.00 0.00 3.46
412 419 4.477780 GGATGAAATGTTCGGCGTAAAAA 58.522 39.130 6.85 0.00 0.00 1.94
413 420 3.425094 CGGATGAAATGTTCGGCGTAAAA 60.425 43.478 6.85 0.00 0.00 1.52
414 421 2.094575 CGGATGAAATGTTCGGCGTAAA 59.905 45.455 6.85 0.00 0.00 2.01
415 422 1.661617 CGGATGAAATGTTCGGCGTAA 59.338 47.619 6.85 0.00 0.00 3.18
416 423 1.282817 CGGATGAAATGTTCGGCGTA 58.717 50.000 6.85 0.00 0.00 4.42
417 424 1.366111 CCGGATGAAATGTTCGGCGT 61.366 55.000 6.85 0.00 34.17 5.68
418 425 1.351707 CCGGATGAAATGTTCGGCG 59.648 57.895 0.00 0.00 34.17 6.46
420 427 1.727467 GGCCGGATGAAATGTTCGG 59.273 57.895 5.05 0.00 43.13 4.30
421 428 1.351707 CGGCCGGATGAAATGTTCG 59.648 57.895 20.10 0.00 0.00 3.95
422 429 1.064134 GCGGCCGGATGAAATGTTC 59.936 57.895 29.38 0.41 0.00 3.18
423 430 2.414785 GGCGGCCGGATGAAATGTT 61.415 57.895 29.38 0.00 0.00 2.71
424 431 2.828549 GGCGGCCGGATGAAATGT 60.829 61.111 29.38 0.00 0.00 2.71
425 432 3.952675 CGGCGGCCGGATGAAATG 61.953 66.667 32.80 1.55 44.15 2.32
440 447 0.034059 AATCAAGCGGCCTAGATCGG 59.966 55.000 0.00 0.00 0.00 4.18
441 448 1.143305 CAATCAAGCGGCCTAGATCG 58.857 55.000 0.00 0.00 0.00 3.69
442 449 0.871057 GCAATCAAGCGGCCTAGATC 59.129 55.000 0.00 0.00 0.00 2.75
443 450 0.536006 GGCAATCAAGCGGCCTAGAT 60.536 55.000 0.00 0.00 44.32 1.98
444 451 1.153168 GGCAATCAAGCGGCCTAGA 60.153 57.895 0.00 0.00 44.32 2.43
445 452 2.537560 CGGCAATCAAGCGGCCTAG 61.538 63.158 0.00 0.00 45.53 3.02
446 453 2.513666 CGGCAATCAAGCGGCCTA 60.514 61.111 0.00 0.00 45.53 3.93
449 456 2.774799 AATCCGGCAATCAAGCGGC 61.775 57.895 0.00 0.00 33.96 6.53
450 457 1.064621 CAATCCGGCAATCAAGCGG 59.935 57.895 0.00 0.00 34.64 5.52
451 458 0.523968 CACAATCCGGCAATCAAGCG 60.524 55.000 0.00 0.00 34.64 4.68
452 459 0.179129 CCACAATCCGGCAATCAAGC 60.179 55.000 0.00 0.00 0.00 4.01
460 467 0.814010 AATAGACGCCACAATCCGGC 60.814 55.000 0.00 0.00 46.62 6.13
461 468 1.663695 AAATAGACGCCACAATCCGG 58.336 50.000 0.00 0.00 0.00 5.14
462 469 2.223249 CCAAAATAGACGCCACAATCCG 60.223 50.000 0.00 0.00 0.00 4.18
463 470 2.099098 CCCAAAATAGACGCCACAATCC 59.901 50.000 0.00 0.00 0.00 3.01
464 471 2.479560 GCCCAAAATAGACGCCACAATC 60.480 50.000 0.00 0.00 0.00 2.67
465 472 1.476488 GCCCAAAATAGACGCCACAAT 59.524 47.619 0.00 0.00 0.00 2.71
466 473 0.885196 GCCCAAAATAGACGCCACAA 59.115 50.000 0.00 0.00 0.00 3.33
467 474 1.302383 CGCCCAAAATAGACGCCACA 61.302 55.000 0.00 0.00 0.00 4.17
468 475 1.427819 CGCCCAAAATAGACGCCAC 59.572 57.895 0.00 0.00 0.00 5.01
469 476 2.403378 GCGCCCAAAATAGACGCCA 61.403 57.895 0.00 0.00 43.58 5.69
470 477 2.407616 GCGCCCAAAATAGACGCC 59.592 61.111 0.00 0.00 43.58 5.68
471 478 2.022762 CGCGCCCAAAATAGACGC 59.977 61.111 0.00 0.00 45.72 5.19
472 479 2.707039 CCGCGCCCAAAATAGACG 59.293 61.111 0.00 0.00 0.00 4.18
473 480 1.027792 TTCCCGCGCCCAAAATAGAC 61.028 55.000 0.00 0.00 0.00 2.59
474 481 1.027792 GTTCCCGCGCCCAAAATAGA 61.028 55.000 0.00 0.00 0.00 1.98
475 482 1.431845 GTTCCCGCGCCCAAAATAG 59.568 57.895 0.00 0.00 0.00 1.73
476 483 2.400158 CGTTCCCGCGCCCAAAATA 61.400 57.895 0.00 0.00 0.00 1.40
477 484 3.743636 CGTTCCCGCGCCCAAAAT 61.744 61.111 0.00 0.00 0.00 1.82
478 485 4.931633 TCGTTCCCGCGCCCAAAA 62.932 61.111 0.00 0.00 0.00 2.44
799 806 3.002583 AAAAATGCGGCCTGGGGG 61.003 61.111 0.00 0.00 0.00 5.40
813 820 1.834822 CCCCCAGGGCGTTGAAAAA 60.835 57.895 0.00 0.00 35.35 1.94
814 821 2.203567 CCCCCAGGGCGTTGAAAA 60.204 61.111 0.00 0.00 35.35 2.29
833 840 2.892425 GCATCTCCAGCCGTTCGG 60.892 66.667 6.90 6.90 0.00 4.30
834 841 1.880340 GAGCATCTCCAGCCGTTCG 60.880 63.158 0.00 0.00 0.00 3.95
835 842 4.116878 GAGCATCTCCAGCCGTTC 57.883 61.111 0.00 0.00 0.00 3.95
846 853 5.237344 ACACAACAACAAGTCTAAGAGCATC 59.763 40.000 0.00 0.00 0.00 3.91
847 854 5.126067 ACACAACAACAAGTCTAAGAGCAT 58.874 37.500 0.00 0.00 0.00 3.79
848 855 4.513442 ACACAACAACAAGTCTAAGAGCA 58.487 39.130 0.00 0.00 0.00 4.26
849 856 5.485662 AACACAACAACAAGTCTAAGAGC 57.514 39.130 0.00 0.00 0.00 4.09
878 885 9.926158 TCGACTAATTATGTACAGTAAAACCAA 57.074 29.630 0.33 0.00 0.00 3.67
879 886 9.577110 CTCGACTAATTATGTACAGTAAAACCA 57.423 33.333 0.33 0.00 0.00 3.67
880 887 8.538039 GCTCGACTAATTATGTACAGTAAAACC 58.462 37.037 0.33 0.00 0.00 3.27
881 888 9.079833 TGCTCGACTAATTATGTACAGTAAAAC 57.920 33.333 0.33 0.00 0.00 2.43
882 889 9.642327 TTGCTCGACTAATTATGTACAGTAAAA 57.358 29.630 0.33 0.00 0.00 1.52
883 890 9.642327 TTTGCTCGACTAATTATGTACAGTAAA 57.358 29.630 0.33 0.00 0.00 2.01
884 891 9.297586 CTTTGCTCGACTAATTATGTACAGTAA 57.702 33.333 0.33 1.27 0.00 2.24
885 892 8.680001 TCTTTGCTCGACTAATTATGTACAGTA 58.320 33.333 0.33 0.00 0.00 2.74
886 893 7.544622 TCTTTGCTCGACTAATTATGTACAGT 58.455 34.615 0.33 0.00 0.00 3.55
887 894 7.987268 TCTTTGCTCGACTAATTATGTACAG 57.013 36.000 0.33 0.00 0.00 2.74
888 895 8.033038 AGTTCTTTGCTCGACTAATTATGTACA 58.967 33.333 0.00 0.00 0.00 2.90
889 896 8.408743 AGTTCTTTGCTCGACTAATTATGTAC 57.591 34.615 0.00 0.00 0.00 2.90
890 897 8.997621 AAGTTCTTTGCTCGACTAATTATGTA 57.002 30.769 0.00 0.00 0.00 2.29
891 898 7.819900 AGAAGTTCTTTGCTCGACTAATTATGT 59.180 33.333 0.00 0.00 0.00 2.29
892 899 8.190888 AGAAGTTCTTTGCTCGACTAATTATG 57.809 34.615 0.00 0.00 0.00 1.90
893 900 8.779354 AAGAAGTTCTTTGCTCGACTAATTAT 57.221 30.769 12.50 0.00 31.57 1.28
894 901 8.088981 AGAAGAAGTTCTTTGCTCGACTAATTA 58.911 33.333 18.96 0.00 40.35 1.40
895 902 6.931840 AGAAGAAGTTCTTTGCTCGACTAATT 59.068 34.615 18.96 0.00 40.35 1.40
896 903 6.459923 AGAAGAAGTTCTTTGCTCGACTAAT 58.540 36.000 18.96 0.00 40.35 1.73
897 904 5.844004 AGAAGAAGTTCTTTGCTCGACTAA 58.156 37.500 18.96 0.00 40.35 2.24
898 905 5.455056 AGAAGAAGTTCTTTGCTCGACTA 57.545 39.130 18.96 0.00 40.35 2.59
899 906 4.329462 AGAAGAAGTTCTTTGCTCGACT 57.671 40.909 18.96 7.18 40.35 4.18
900 907 6.713792 AATAGAAGAAGTTCTTTGCTCGAC 57.286 37.500 18.96 5.01 40.35 4.20
901 908 7.730364 AAAATAGAAGAAGTTCTTTGCTCGA 57.270 32.000 18.96 3.81 40.35 4.04
902 909 9.878599 TTAAAAATAGAAGAAGTTCTTTGCTCG 57.121 29.630 18.96 0.00 40.35 5.03
904 911 9.967346 GGTTAAAAATAGAAGAAGTTCTTTGCT 57.033 29.630 18.96 14.30 40.35 3.91
905 912 9.967346 AGGTTAAAAATAGAAGAAGTTCTTTGC 57.033 29.630 18.96 7.78 40.35 3.68
908 915 9.642343 ACCAGGTTAAAAATAGAAGAAGTTCTT 57.358 29.630 18.05 18.05 40.35 2.52
909 916 9.642343 AACCAGGTTAAAAATAGAAGAAGTTCT 57.358 29.630 1.71 0.00 45.48 3.01
910 917 9.894783 GAACCAGGTTAAAAATAGAAGAAGTTC 57.105 33.333 4.25 0.00 0.00 3.01
974 981 2.046217 GGGGAGTGGCTTCGGAAC 60.046 66.667 0.00 0.00 0.00 3.62
978 985 2.358737 GTGTGGGGAGTGGCTTCG 60.359 66.667 0.00 0.00 0.00 3.79
1027 1034 4.864334 GGTGGCATCTCCGCTGGG 62.864 72.222 0.00 0.00 44.77 4.45
1515 1531 2.890961 GAGGAAAGGTAGCGGCGC 60.891 66.667 26.86 26.86 0.00 6.53
1628 1644 0.179012 GTTGGTTCTTGGACCCGGAA 60.179 55.000 0.73 0.00 39.01 4.30
1662 1678 0.604578 AGTTAAAGGTCTGCGCCGTA 59.395 50.000 4.18 0.00 0.00 4.02
1983 2001 5.758296 TCTGACTAACCACTCAAATGTTGTC 59.242 40.000 0.00 0.00 0.00 3.18
2001 2019 1.834263 GTCCTACAATGCCCTCTGACT 59.166 52.381 0.00 0.00 0.00 3.41
2136 2162 5.641209 CCTCAAAATATCTAATGCCTCCTCG 59.359 44.000 0.00 0.00 0.00 4.63
2320 2346 1.040646 TCCTTCTCATAAGCGCGGAT 58.959 50.000 8.83 0.00 0.00 4.18
2388 2414 1.634973 TCACTTCCATCCTCAATGCCA 59.365 47.619 0.00 0.00 33.71 4.92
2421 2447 3.059166 GGCTTGAAAAACGCATCATTGT 58.941 40.909 0.00 0.00 0.00 2.71
2484 2510 9.766277 GAGATGAACAAAATTAGATGAGACAAC 57.234 33.333 0.00 0.00 0.00 3.32
2495 2521 9.567776 TGTAAAGACTGGAGATGAACAAAATTA 57.432 29.630 0.00 0.00 0.00 1.40
2537 2563 5.164954 ACTCAAGATTTCTGCGTTCTAGAC 58.835 41.667 0.00 0.00 0.00 2.59
2539 2565 5.406780 ACAACTCAAGATTTCTGCGTTCTAG 59.593 40.000 0.00 0.00 0.00 2.43
2540 2566 5.297547 ACAACTCAAGATTTCTGCGTTCTA 58.702 37.500 0.00 0.00 0.00 2.10
2541 2567 4.130118 ACAACTCAAGATTTCTGCGTTCT 58.870 39.130 0.00 0.00 0.00 3.01
2542 2568 4.474226 ACAACTCAAGATTTCTGCGTTC 57.526 40.909 0.00 0.00 0.00 3.95
2543 2569 5.934625 AGATACAACTCAAGATTTCTGCGTT 59.065 36.000 0.00 0.00 0.00 4.84
2544 2570 5.482908 AGATACAACTCAAGATTTCTGCGT 58.517 37.500 0.00 0.00 0.00 5.24
2545 2571 6.414408 AAGATACAACTCAAGATTTCTGCG 57.586 37.500 0.00 0.00 0.00 5.18
2546 2572 9.155975 TCTAAAGATACAACTCAAGATTTCTGC 57.844 33.333 0.00 0.00 0.00 4.26
2632 2664 3.446442 AACCAGCCAGAAGTCATGAAT 57.554 42.857 0.00 0.00 0.00 2.57
2657 2689 7.206687 CCAGGAGATGATCACTAAAGTAGTTC 58.793 42.308 0.00 0.00 36.76 3.01
2715 2747 9.500785 TGACACAAAGATTGATGTAAATCTGTA 57.499 29.630 0.45 0.00 44.35 2.74
2716 2748 8.394971 TGACACAAAGATTGATGTAAATCTGT 57.605 30.769 0.45 0.00 44.35 3.41
2717 2749 9.285770 CATGACACAAAGATTGATGTAAATCTG 57.714 33.333 0.45 0.00 44.35 2.90
2718 2750 7.972277 GCATGACACAAAGATTGATGTAAATCT 59.028 33.333 0.00 0.00 46.52 2.40
2719 2751 7.756272 TGCATGACACAAAGATTGATGTAAATC 59.244 33.333 0.00 0.00 36.91 2.17
2720 2752 7.604549 TGCATGACACAAAGATTGATGTAAAT 58.395 30.769 0.00 0.00 0.00 1.40
2721 2753 6.979465 TGCATGACACAAAGATTGATGTAAA 58.021 32.000 0.00 0.00 0.00 2.01
2775 2815 9.023962 ACCTGCAAAAATCATATTCTCTTTACA 57.976 29.630 0.00 0.00 0.00 2.41
2815 2859 4.634012 AACTCTTTGCCTACATGTACCA 57.366 40.909 0.08 0.00 0.00 3.25
2914 2958 4.163552 ACACACACTACATACATCGAACG 58.836 43.478 0.00 0.00 0.00 3.95
2942 2986 6.586082 CCAACCGAAACATTAGATTTTGGAAG 59.414 38.462 10.13 3.14 41.48 3.46
2946 2990 5.118510 GTGCCAACCGAAACATTAGATTTTG 59.881 40.000 0.00 0.00 0.00 2.44
2998 3059 2.673368 GGCGGAACTGTGACATAAGAAG 59.327 50.000 0.00 0.00 0.00 2.85
3082 3148 0.462759 GCTCAGGATTCAGGAACGGG 60.463 60.000 0.00 0.00 0.00 5.28
3093 3159 1.123077 TTAGGTGATGCGCTCAGGAT 58.877 50.000 9.73 0.00 33.51 3.24
3094 3160 0.175760 GTTAGGTGATGCGCTCAGGA 59.824 55.000 9.73 0.00 33.51 3.86
3095 3161 0.176680 AGTTAGGTGATGCGCTCAGG 59.823 55.000 9.73 0.00 33.51 3.86
3096 3162 1.134995 TCAGTTAGGTGATGCGCTCAG 60.135 52.381 9.73 0.00 33.51 3.35
3097 3163 0.894835 TCAGTTAGGTGATGCGCTCA 59.105 50.000 9.73 7.24 0.00 4.26
3098 3164 2.131183 GATCAGTTAGGTGATGCGCTC 58.869 52.381 9.73 4.27 37.29 5.03
3099 3165 1.759445 AGATCAGTTAGGTGATGCGCT 59.241 47.619 9.73 0.00 37.29 5.92
3117 3183 4.774200 TGTCAAAGTCCTGATCATGAGAGA 59.226 41.667 0.09 0.00 0.00 3.10
3158 3243 7.147915 TGCATGTATATAACACTCACTCTCACA 60.148 37.037 0.00 0.00 42.09 3.58
3168 3253 6.147821 GCTTTCCGATGCATGTATATAACACT 59.852 38.462 2.46 0.00 42.09 3.55
3184 3269 0.174162 GCAATTGCCAGCTTTCCGAT 59.826 50.000 20.06 0.00 34.31 4.18
3217 3302 0.108585 TTGCTTCTTCCGCTCTTGGT 59.891 50.000 0.00 0.00 0.00 3.67
3285 3371 1.008538 CTGCGTGGTTTTGCTGACC 60.009 57.895 0.00 0.00 37.69 4.02
3346 3433 4.762289 AAGGTAAAGAGTGCCAGGATAG 57.238 45.455 0.00 0.00 33.55 2.08
3349 3436 4.986054 TTAAAGGTAAAGAGTGCCAGGA 57.014 40.909 0.00 0.00 33.55 3.86
3401 3513 5.927281 ACATTCCTCTGAAATTTCCATGG 57.073 39.130 15.48 4.97 33.32 3.66


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

AutoCloner maintained by Alex Coulton.