Multiple sequence alignment - TraesCS3B01G379000

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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 TraesCS3B01G379000 chr3B 100.000 3545 0 0 1 3545 597045036 597048580 0.000000e+00 6547.0
1 TraesCS3B01G379000 chr3A 92.413 2122 104 17 704 2795 596499390 596501484 0.000000e+00 2974.0
2 TraesCS3B01G379000 chr3A 88.390 801 44 19 2780 3545 596501538 596502324 0.000000e+00 918.0
3 TraesCS3B01G379000 chr3A 90.379 343 17 6 37 366 596498695 596499034 1.510000e-118 436.0
4 TraesCS3B01G379000 chr3D 91.577 2149 153 20 751 2882 454497791 454499928 0.000000e+00 2940.0
5 TraesCS3B01G379000 chr3D 91.259 675 42 9 2880 3545 454500249 454500915 0.000000e+00 904.0
6 TraesCS3B01G379000 chr3D 86.572 633 53 13 1 612 454497001 454497622 0.000000e+00 669.0
7 TraesCS3B01G379000 chr3D 84.507 71 10 1 1439 1508 613590376 613590306 6.350000e-08 69.4
8 TraesCS3B01G379000 chr6A 86.364 110 13 2 1448 1556 100653182 100653074 6.220000e-23 119.0


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 TraesCS3B01G379000 chr3B 597045036 597048580 3544 False 6547.000000 6547 100.000000 1 3545 1 chr3B.!!$F1 3544
1 TraesCS3B01G379000 chr3A 596498695 596502324 3629 False 1442.666667 2974 90.394000 37 3545 3 chr3A.!!$F1 3508
2 TraesCS3B01G379000 chr3D 454497001 454500915 3914 False 1504.333333 2940 89.802667 1 3545 3 chr3D.!!$F1 3544

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
438 449 0.031449 CTTCGATCGGCTTCTCCTCC 59.969 60.0 16.41 0.0 0.0 4.30 F
552 572 0.684805 TTTGGTGCGGGTCCTTTTGT 60.685 50.0 0.00 0.0 0.0 2.83 F
1323 1433 0.329596 AGAACCACCTCAAGCATCCC 59.670 55.0 0.00 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1323 1433 0.824109 TGAGTAGGGCGATGTTGAGG 59.176 55.0 0.0 0.0 0.0 3.86 R
2329 2451 0.970937 TCCACCAGCTTCCCGTAGAG 60.971 60.0 0.0 0.0 0.0 2.43 R
3186 3715 0.608640 AGCCACCACTTACTTCTCGG 59.391 55.0 0.0 0.0 0.0 4.63 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
48 49 5.011090 AGCATATTATGTCGTATCGCCAT 57.989 39.130 5.60 0.00 0.00 4.40
71 72 1.202806 CCTCCAAGCTTGACTGGTTCA 60.203 52.381 28.05 0.00 0.00 3.18
149 150 2.031857 ACGACGAGTCAAGAGTCAAGAC 60.032 50.000 0.00 6.83 34.80 3.01
172 173 4.723248 TGACTGCTATACTATTCGCGATG 58.277 43.478 10.88 6.16 0.00 3.84
182 183 4.504858 ACTATTCGCGATGAAGTCCTTTT 58.495 39.130 10.88 0.00 40.65 2.27
183 184 4.935808 ACTATTCGCGATGAAGTCCTTTTT 59.064 37.500 10.88 0.00 40.65 1.94
184 185 3.536158 TTCGCGATGAAGTCCTTTTTG 57.464 42.857 10.88 0.00 31.44 2.44
186 187 1.197721 CGCGATGAAGTCCTTTTTGCT 59.802 47.619 0.00 0.00 0.00 3.91
188 189 2.726066 GCGATGAAGTCCTTTTTGCTCG 60.726 50.000 0.00 0.00 0.00 5.03
189 190 2.726066 CGATGAAGTCCTTTTTGCTCGC 60.726 50.000 0.00 0.00 0.00 5.03
190 191 1.674359 TGAAGTCCTTTTTGCTCGCA 58.326 45.000 0.00 0.00 0.00 5.10
191 192 2.020720 TGAAGTCCTTTTTGCTCGCAA 58.979 42.857 0.00 0.00 0.00 4.85
192 193 2.425312 TGAAGTCCTTTTTGCTCGCAAA 59.575 40.909 12.62 12.62 43.23 3.68
195 196 0.387565 TCCTTTTTGCTCGCAAACCC 59.612 50.000 15.89 0.00 44.39 4.11
221 222 0.464916 GACCTTTGTCCCGTTGGTGT 60.465 55.000 0.00 0.00 35.34 4.16
256 257 2.352030 CGTACTTCAACTAACCTGCCGA 60.352 50.000 0.00 0.00 0.00 5.54
297 298 1.276421 CAGAACCAGTTCATCGGAGGT 59.724 52.381 12.76 0.00 41.84 3.85
300 301 1.265454 ACCAGTTCATCGGAGGTCCC 61.265 60.000 0.00 0.00 0.00 4.46
367 378 1.770957 TTCGGATGATCAATCGAGCG 58.229 50.000 18.51 8.80 35.99 5.03
374 385 2.083774 TGATCAATCGAGCGGCTTTTT 58.916 42.857 2.97 0.00 0.00 1.94
379 390 0.605319 ATCGAGCGGCTTTTTGTCCA 60.605 50.000 2.97 0.00 0.00 4.02
404 415 2.704190 TCCTGGGTGATCCTCTATCC 57.296 55.000 0.00 0.00 36.20 2.59
418 429 3.477530 CTCTATCCGGTTGGGGATTTTC 58.522 50.000 0.00 0.00 44.44 2.29
438 449 0.031449 CTTCGATCGGCTTCTCCTCC 59.969 60.000 16.41 0.00 0.00 4.30
462 473 7.038587 TCCTAAGAGGTATGTTCAGTTTTGCTA 60.039 37.037 0.00 0.00 36.53 3.49
463 474 7.770897 CCTAAGAGGTATGTTCAGTTTTGCTAT 59.229 37.037 0.00 0.00 0.00 2.97
472 483 7.197071 TGTTCAGTTTTGCTATAATTCGTGT 57.803 32.000 0.00 0.00 0.00 4.49
476 487 5.734498 CAGTTTTGCTATAATTCGTGTGCTC 59.266 40.000 0.00 0.00 0.00 4.26
487 503 2.235891 TCGTGTGCTCCTCTGTTCTTA 58.764 47.619 0.00 0.00 0.00 2.10
488 504 2.229062 TCGTGTGCTCCTCTGTTCTTAG 59.771 50.000 0.00 0.00 0.00 2.18
489 505 2.672478 CGTGTGCTCCTCTGTTCTTAGG 60.672 54.545 0.00 0.00 0.00 2.69
490 506 1.902508 TGTGCTCCTCTGTTCTTAGGG 59.097 52.381 0.00 0.00 33.40 3.53
491 507 1.208293 GTGCTCCTCTGTTCTTAGGGG 59.792 57.143 0.00 0.00 39.85 4.79
493 509 1.483004 GCTCCTCTGTTCTTAGGGGAC 59.517 57.143 0.00 0.00 42.43 4.46
511 527 3.131396 GGACGCTTATGAATTGGACGAT 58.869 45.455 0.00 0.00 0.00 3.73
517 537 6.481976 ACGCTTATGAATTGGACGATCATTTA 59.518 34.615 0.00 0.00 35.53 1.40
519 539 6.798959 GCTTATGAATTGGACGATCATTTAGC 59.201 38.462 0.00 0.00 35.53 3.09
520 540 4.794248 TGAATTGGACGATCATTTAGCG 57.206 40.909 0.00 0.00 44.31 4.26
521 541 3.559655 TGAATTGGACGATCATTTAGCGG 59.440 43.478 0.00 0.00 42.62 5.52
552 572 0.684805 TTTGGTGCGGGTCCTTTTGT 60.685 50.000 0.00 0.00 0.00 2.83
583 608 5.506483 GCTTTTGAGGTTCAGAAGAGGAAAC 60.506 44.000 12.03 0.00 39.99 2.78
585 610 4.982241 TGAGGTTCAGAAGAGGAAACAT 57.018 40.909 0.00 0.00 34.40 2.71
586 611 5.310409 TGAGGTTCAGAAGAGGAAACATT 57.690 39.130 0.00 0.00 34.40 2.71
588 613 6.129179 TGAGGTTCAGAAGAGGAAACATTTT 58.871 36.000 0.00 0.00 34.40 1.82
617 645 7.011109 CGTTAAAGAAATCTCATACATTCCGGT 59.989 37.037 0.00 0.00 0.00 5.28
625 653 3.815401 CTCATACATTCCGGTGATTTCCC 59.185 47.826 0.00 0.00 0.00 3.97
632 660 3.343941 TCCGGTGATTTCCCTAGTTTG 57.656 47.619 0.00 0.00 0.00 2.93
637 665 3.191371 GGTGATTTCCCTAGTTTGTGCAG 59.809 47.826 0.00 0.00 0.00 4.41
644 672 2.808543 CCCTAGTTTGTGCAGAACTGAC 59.191 50.000 20.24 7.13 37.84 3.51
648 697 5.406780 CCTAGTTTGTGCAGAACTGACTAAG 59.593 44.000 20.24 11.77 37.84 2.18
663 712 4.637276 TGACTAAGGATTTCTGAAACGCA 58.363 39.130 4.73 0.00 0.00 5.24
671 720 5.402270 AGGATTTCTGAAACGCAAAATTTCG 59.598 36.000 4.73 0.00 38.64 3.46
679 728 2.384382 ACGCAAAATTTCGCACTTCTG 58.616 42.857 1.46 0.00 0.00 3.02
682 731 3.578688 GCAAAATTTCGCACTTCTGGAT 58.421 40.909 0.00 0.00 0.00 3.41
687 736 5.998454 AATTTCGCACTTCTGGATCATAG 57.002 39.130 0.00 0.00 0.00 2.23
688 737 4.471904 TTTCGCACTTCTGGATCATAGT 57.528 40.909 0.00 0.00 0.00 2.12
689 738 3.443099 TCGCACTTCTGGATCATAGTG 57.557 47.619 9.89 9.89 40.65 2.74
691 740 3.119291 CGCACTTCTGGATCATAGTGTC 58.881 50.000 13.64 7.96 40.02 3.67
692 741 3.462021 GCACTTCTGGATCATAGTGTCC 58.538 50.000 13.64 0.00 40.02 4.02
693 742 3.118629 GCACTTCTGGATCATAGTGTCCA 60.119 47.826 13.64 0.00 42.03 4.02
699 748 4.471904 TGGATCATAGTGTCCAGTGAAC 57.528 45.455 0.00 0.00 39.51 3.18
701 750 4.471025 TGGATCATAGTGTCCAGTGAACAT 59.529 41.667 0.00 0.00 39.51 2.71
710 789 2.676839 GTCCAGTGAACATGCTCTGATG 59.323 50.000 0.00 0.00 32.62 3.07
712 791 3.199289 TCCAGTGAACATGCTCTGATGAT 59.801 43.478 0.00 0.00 32.62 2.45
713 792 3.945921 CCAGTGAACATGCTCTGATGATT 59.054 43.478 0.00 0.00 32.62 2.57
719 798 7.989170 AGTGAACATGCTCTGATGATTAACATA 59.011 33.333 0.00 0.00 39.56 2.29
721 800 9.346005 TGAACATGCTCTGATGATTAACATATT 57.654 29.630 0.00 0.00 39.56 1.28
744 823 4.799564 TTCCAGAACAATATTTGTGGCC 57.200 40.909 0.00 0.00 44.59 5.36
745 824 4.046286 TCCAGAACAATATTTGTGGCCT 57.954 40.909 3.32 0.00 44.59 5.19
746 825 5.186256 TCCAGAACAATATTTGTGGCCTA 57.814 39.130 3.32 0.00 44.59 3.93
776 855 7.440523 ACTGTACTTTTGGAGAATTTGCTAG 57.559 36.000 0.00 0.00 0.00 3.42
777 856 7.224297 ACTGTACTTTTGGAGAATTTGCTAGA 58.776 34.615 0.00 0.00 0.00 2.43
778 857 7.389053 ACTGTACTTTTGGAGAATTTGCTAGAG 59.611 37.037 0.00 0.00 0.00 2.43
791 870 9.453572 AGAATTTGCTAGAGTACATTGAAATGA 57.546 29.630 9.94 0.00 39.67 2.57
849 941 7.136822 TGCATATTTCAGGTTCCACTAGTAT 57.863 36.000 0.00 0.00 0.00 2.12
850 942 6.992123 TGCATATTTCAGGTTCCACTAGTATG 59.008 38.462 0.00 0.00 0.00 2.39
851 943 6.073003 GCATATTTCAGGTTCCACTAGTATGC 60.073 42.308 0.00 0.00 35.52 3.14
852 944 5.700402 ATTTCAGGTTCCACTAGTATGCT 57.300 39.130 0.00 0.00 0.00 3.79
853 945 4.737855 TTCAGGTTCCACTAGTATGCTC 57.262 45.455 0.00 0.00 0.00 4.26
854 946 3.708451 TCAGGTTCCACTAGTATGCTCA 58.292 45.455 0.00 0.00 0.00 4.26
855 947 4.290093 TCAGGTTCCACTAGTATGCTCAT 58.710 43.478 0.00 0.00 0.00 2.90
856 948 4.342378 TCAGGTTCCACTAGTATGCTCATC 59.658 45.833 0.00 0.00 0.00 2.92
857 949 3.643792 AGGTTCCACTAGTATGCTCATCC 59.356 47.826 0.00 0.00 0.00 3.51
858 950 3.643792 GGTTCCACTAGTATGCTCATCCT 59.356 47.826 0.00 0.00 0.00 3.24
859 951 4.833380 GGTTCCACTAGTATGCTCATCCTA 59.167 45.833 0.00 0.00 0.00 2.94
879 971 3.726557 ACTTGATGCCAGAAATCCAGA 57.273 42.857 0.00 0.00 0.00 3.86
883 986 2.573009 TGATGCCAGAAATCCAGAGTCA 59.427 45.455 0.00 0.00 0.00 3.41
888 991 5.569355 TGCCAGAAATCCAGAGTCATTTTA 58.431 37.500 0.00 0.00 0.00 1.52
889 992 6.009589 TGCCAGAAATCCAGAGTCATTTTAA 58.990 36.000 0.00 0.00 0.00 1.52
890 993 6.071952 TGCCAGAAATCCAGAGTCATTTTAAC 60.072 38.462 0.00 0.00 0.00 2.01
915 1018 9.780186 ACTACTTTTATAGCAGAAAGAACACTT 57.220 29.630 3.14 0.00 36.58 3.16
923 1026 4.889409 AGCAGAAAGAACACTTCAATTCCA 59.111 37.500 0.00 0.00 31.85 3.53
926 1029 7.231317 AGCAGAAAGAACACTTCAATTCCATTA 59.769 33.333 0.00 0.00 31.85 1.90
929 1032 9.136323 AGAAAGAACACTTCAATTCCATTAACT 57.864 29.630 0.00 0.00 31.85 2.24
934 1037 7.206981 ACACTTCAATTCCATTAACTCACAG 57.793 36.000 0.00 0.00 0.00 3.66
1006 1110 5.247337 TCAGTCACACATACAGAAATGGGTA 59.753 40.000 0.00 0.00 41.59 3.69
1023 1133 1.541670 GGTAACACTGTTGCCGAGGAA 60.542 52.381 12.66 0.00 0.00 3.36
1043 1153 7.496346 AGGAAGACATAGAAGACATACCAAA 57.504 36.000 0.00 0.00 0.00 3.28
1057 1167 7.486647 AGACATACCAAATTCAGATGCAAATC 58.513 34.615 0.00 0.00 0.00 2.17
1066 1176 5.486735 TTCAGATGCAAATCCACCAATTT 57.513 34.783 0.00 0.00 0.00 1.82
1138 1248 1.202604 GGGAACACCAACACGAGAGAA 60.203 52.381 0.00 0.00 39.85 2.87
1216 1326 3.747976 GCGCGCCACTGGGAAAAT 61.748 61.111 23.24 0.00 35.59 1.82
1272 1382 3.584406 TCCATGTCCACTTCATCAGAACT 59.416 43.478 0.00 0.00 0.00 3.01
1323 1433 0.329596 AGAACCACCTCAAGCATCCC 59.670 55.000 0.00 0.00 0.00 3.85
1407 1517 1.975407 CCTGTTGGGGCTGCTGAAG 60.975 63.158 0.00 0.00 0.00 3.02
1473 1583 0.670546 ACAACCAGATCCTCAACGCG 60.671 55.000 3.53 3.53 0.00 6.01
1569 1679 3.818787 GACGCCGCCGAGGTAAGA 61.819 66.667 0.00 0.00 43.70 2.10
1650 1760 0.548926 TGGCCCTCCTCCACATTACA 60.549 55.000 0.00 0.00 0.00 2.41
1719 1829 4.415332 TCACGCTCCGAGTTCGCC 62.415 66.667 0.00 0.00 38.18 5.54
1846 1959 3.255397 AGGCCAAGCAGCTCCACT 61.255 61.111 5.01 0.00 0.00 4.00
1877 1999 1.060698 CGAAGAATCGCCGGAAGAAAC 59.939 52.381 5.05 2.46 42.96 2.78
1884 2006 2.048503 CCGGAAGAAACGACGGCT 60.049 61.111 0.00 0.00 39.85 5.52
2256 2378 3.181967 GACTACGCGCAGTGGCTG 61.182 66.667 18.44 0.00 45.78 4.85
2553 2675 0.394938 TCCAAAGTTGACCGCAGCTA 59.605 50.000 0.00 0.00 34.21 3.32
2578 2700 4.202253 TGGATGGTGACTGATGCTGTATAC 60.202 45.833 0.00 0.00 0.00 1.47
2579 2701 4.039730 GGATGGTGACTGATGCTGTATACT 59.960 45.833 4.17 0.00 0.00 2.12
2607 2733 4.208047 CGAAAGCTGACGGATAGATTCTTG 59.792 45.833 5.12 0.00 0.00 3.02
2615 2743 4.504858 ACGGATAGATTCTTGCTTTTCGT 58.495 39.130 0.00 0.00 0.00 3.85
2662 2790 2.592102 ATGCTCCTGGTTTGTCATGT 57.408 45.000 0.00 0.00 0.00 3.21
2694 2825 5.100943 GGACTTTAGGTCGTCAGTCATTAC 58.899 45.833 0.00 0.00 45.35 1.89
2753 2884 6.150641 CACTCCAACAGATGTCATCTTTCATT 59.849 38.462 12.88 3.08 37.58 2.57
2803 3003 7.839680 AGAAGAAGAAGAAGAAAGTCTCTCT 57.160 36.000 0.00 0.00 31.02 3.10
2821 3021 6.950842 TCTCTCTTGATTATTTTGAGAGGCA 58.049 36.000 15.41 0.00 46.20 4.75
2947 3470 1.000938 GCTGGAGCCAGTTCAAAAGTG 60.001 52.381 17.23 0.00 45.24 3.16
2999 3522 1.383963 ACCTGTAGAGTCCCTCTCCA 58.616 55.000 0.00 0.00 43.71 3.86
3063 3586 2.774007 CTTTAAAGCGAACCGATGCTG 58.226 47.619 1.47 0.00 41.46 4.41
3111 3634 3.182967 CAAAAGTTTGCCGTTGCTTGTA 58.817 40.909 0.00 0.00 38.71 2.41
3116 3639 3.317993 AGTTTGCCGTTGCTTGTAGAAAT 59.682 39.130 0.00 0.00 38.71 2.17
3126 3649 6.147164 CGTTGCTTGTAGAAATGAGAAAGGTA 59.853 38.462 0.00 0.00 0.00 3.08
3135 3658 3.895232 ATGAGAAAGGTACAGACGCAT 57.105 42.857 0.00 0.00 0.00 4.73
3176 3705 5.007682 ACAGAGACTGAAACCTCTCTACTC 58.992 45.833 5.76 0.00 41.15 2.59
3178 3707 3.697542 GAGACTGAAACCTCTCTACTCCC 59.302 52.174 0.00 0.00 31.74 4.30
3181 3710 2.685897 CTGAAACCTCTCTACTCCCGAG 59.314 54.545 0.00 0.00 0.00 4.63
3182 3711 1.406180 GAAACCTCTCTACTCCCGAGC 59.594 57.143 0.00 0.00 0.00 5.03
3186 3715 1.305201 CTCTCTACTCCCGAGCTCAC 58.695 60.000 15.40 0.00 0.00 3.51
3187 3716 0.107116 TCTCTACTCCCGAGCTCACC 60.107 60.000 15.40 0.00 0.00 4.02
3189 3718 1.451567 CTACTCCCGAGCTCACCGA 60.452 63.158 15.40 4.40 0.00 4.69
3190 3719 1.440938 CTACTCCCGAGCTCACCGAG 61.441 65.000 15.40 15.94 0.00 4.63
3191 3720 1.907222 TACTCCCGAGCTCACCGAGA 61.907 60.000 22.03 7.94 0.00 4.04
3192 3721 2.035155 TCCCGAGCTCACCGAGAA 59.965 61.111 15.40 0.00 0.00 2.87
3193 3722 1.999071 CTCCCGAGCTCACCGAGAAG 61.999 65.000 15.40 0.00 0.00 2.85
3212 3744 0.955919 GTAAGTGGTGGCTGCACCTC 60.956 60.000 17.81 15.03 45.21 3.85
3334 3890 2.674796 ATCCGAAGAACTACTGTGCC 57.325 50.000 0.00 0.00 0.00 5.01
3341 3897 4.434520 GAAGAACTACTGTGCCTATGGAC 58.565 47.826 0.00 0.00 0.00 4.02
3357 3913 6.351286 GCCTATGGACATGGAAAGTTGATTTT 60.351 38.462 0.00 0.00 0.00 1.82
3371 3927 6.401047 AGTTGATTTTATGGATGGATGCTG 57.599 37.500 0.00 0.00 0.00 4.41
3387 3943 3.618780 CTGGCAGGTGGTGGAGCTC 62.619 68.421 6.61 4.71 0.00 4.09
3468 4027 2.541556 GATGGTACGAAAGCCTCTGAC 58.458 52.381 0.00 0.00 0.00 3.51
3482 4041 2.408050 CTCTGACCCACTCGACAAAAG 58.592 52.381 0.00 0.00 0.00 2.27
3504 4063 5.788450 AGACAGTCTCACTTTCCATACTTG 58.212 41.667 0.00 0.00 0.00 3.16
3505 4064 4.319177 ACAGTCTCACTTTCCATACTTGC 58.681 43.478 0.00 0.00 0.00 4.01
3506 4065 4.202357 ACAGTCTCACTTTCCATACTTGCA 60.202 41.667 0.00 0.00 0.00 4.08
3507 4066 4.391216 CAGTCTCACTTTCCATACTTGCAG 59.609 45.833 0.00 0.00 0.00 4.41
3508 4067 4.040952 AGTCTCACTTTCCATACTTGCAGT 59.959 41.667 0.00 0.00 0.00 4.40
3509 4068 5.246203 AGTCTCACTTTCCATACTTGCAGTA 59.754 40.000 0.00 0.00 34.82 2.74
3510 4069 6.070538 AGTCTCACTTTCCATACTTGCAGTAT 60.071 38.462 3.78 3.78 41.82 2.12
3511 4070 7.124298 AGTCTCACTTTCCATACTTGCAGTATA 59.876 37.037 8.03 0.00 39.26 1.47
3512 4071 7.928706 GTCTCACTTTCCATACTTGCAGTATAT 59.071 37.037 8.03 0.00 39.26 0.86
3513 4072 8.144478 TCTCACTTTCCATACTTGCAGTATATC 58.856 37.037 8.03 0.00 39.26 1.63
3514 4073 8.023021 TCACTTTCCATACTTGCAGTATATCT 57.977 34.615 8.03 0.00 39.26 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.941999 GCTCCCATGCTGGTTGAAGC 61.942 60.000 0.00 0.00 43.82 3.86
48 49 0.538057 CCAGTCAAGCTTGGAGGCAA 60.538 55.000 25.73 2.68 34.17 4.52
149 150 4.406001 TCGCGAATAGTATAGCAGTCAG 57.594 45.455 6.20 0.00 0.00 3.51
162 163 4.436852 GCAAAAAGGACTTCATCGCGAATA 60.437 41.667 15.24 0.00 31.69 1.75
172 173 2.774439 TTGCGAGCAAAAAGGACTTC 57.226 45.000 8.17 0.00 32.44 3.01
182 183 0.753479 TTTCCTGGGTTTGCGAGCAA 60.753 50.000 6.39 6.39 0.00 3.91
183 184 1.152860 TTTCCTGGGTTTGCGAGCA 60.153 52.632 0.00 0.00 0.00 4.26
184 185 0.889186 TCTTTCCTGGGTTTGCGAGC 60.889 55.000 0.00 0.00 0.00 5.03
186 187 0.536460 GGTCTTTCCTGGGTTTGCGA 60.536 55.000 0.00 0.00 0.00 5.10
188 189 3.439440 AGGTCTTTCCTGGGTTTGC 57.561 52.632 0.00 0.00 46.19 3.68
256 257 0.834687 TGAGTGTAGGGGAAAGCGGT 60.835 55.000 0.00 0.00 0.00 5.68
367 378 2.959030 AGGAAGAACTGGACAAAAAGCC 59.041 45.455 0.00 0.00 0.00 4.35
379 390 2.192263 GAGGATCACCCAGGAAGAACT 58.808 52.381 0.00 0.00 37.41 3.01
404 415 0.808755 CGAAGGAAAATCCCCAACCG 59.191 55.000 0.00 0.00 37.19 4.44
418 429 0.031449 GAGGAGAAGCCGATCGAAGG 59.969 60.000 18.66 0.27 43.43 3.46
438 449 8.723942 ATAGCAAAACTGAACATACCTCTTAG 57.276 34.615 0.00 0.00 0.00 2.18
457 468 4.119862 GAGGAGCACACGAATTATAGCAA 58.880 43.478 0.00 0.00 0.00 3.91
462 473 3.895232 ACAGAGGAGCACACGAATTAT 57.105 42.857 0.00 0.00 0.00 1.28
463 474 3.258372 AGAACAGAGGAGCACACGAATTA 59.742 43.478 0.00 0.00 0.00 1.40
472 483 1.078823 TCCCCTAAGAACAGAGGAGCA 59.921 52.381 0.00 0.00 34.46 4.26
476 487 0.175989 GCGTCCCCTAAGAACAGAGG 59.824 60.000 0.00 0.00 0.00 3.69
487 503 1.843851 TCCAATTCATAAGCGTCCCCT 59.156 47.619 0.00 0.00 0.00 4.79
488 504 1.947456 GTCCAATTCATAAGCGTCCCC 59.053 52.381 0.00 0.00 0.00 4.81
489 505 1.597663 CGTCCAATTCATAAGCGTCCC 59.402 52.381 0.00 0.00 0.00 4.46
490 506 2.546778 TCGTCCAATTCATAAGCGTCC 58.453 47.619 0.00 0.00 0.00 4.79
491 507 3.802139 TGATCGTCCAATTCATAAGCGTC 59.198 43.478 0.00 0.00 0.00 5.19
493 509 4.997905 ATGATCGTCCAATTCATAAGCG 57.002 40.909 0.00 0.00 0.00 4.68
511 527 0.958382 AAACAGCCGCCGCTAAATGA 60.958 50.000 0.00 0.00 46.25 2.57
519 539 1.444212 CCAAATCAAACAGCCGCCG 60.444 57.895 0.00 0.00 0.00 6.46
520 540 0.667184 CACCAAATCAAACAGCCGCC 60.667 55.000 0.00 0.00 0.00 6.13
521 541 1.284297 GCACCAAATCAAACAGCCGC 61.284 55.000 0.00 0.00 0.00 6.53
552 572 3.084039 CTGAACCTCAAAAGCATAGGCA 58.916 45.455 0.67 0.00 44.61 4.75
590 615 7.223971 CCGGAATGTATGAGATTTCTTTAACGA 59.776 37.037 0.00 0.00 0.00 3.85
592 617 8.122952 CACCGGAATGTATGAGATTTCTTTAAC 58.877 37.037 9.46 0.00 0.00 2.01
593 618 8.044309 TCACCGGAATGTATGAGATTTCTTTAA 58.956 33.333 9.46 0.00 0.00 1.52
612 640 2.640826 ACAAACTAGGGAAATCACCGGA 59.359 45.455 9.46 0.00 0.00 5.14
613 641 2.747446 CACAAACTAGGGAAATCACCGG 59.253 50.000 0.00 0.00 0.00 5.28
614 642 2.161609 GCACAAACTAGGGAAATCACCG 59.838 50.000 0.00 0.00 0.00 4.94
617 645 4.365514 TCTGCACAAACTAGGGAAATCA 57.634 40.909 0.00 0.00 0.00 2.57
625 653 5.406780 CCTTAGTCAGTTCTGCACAAACTAG 59.593 44.000 8.93 4.08 35.25 2.57
632 660 5.121454 CAGAAATCCTTAGTCAGTTCTGCAC 59.879 44.000 5.93 0.00 36.59 4.57
637 665 6.618805 GCGTTTCAGAAATCCTTAGTCAGTTC 60.619 42.308 0.00 0.00 0.00 3.01
644 672 7.873739 AATTTTGCGTTTCAGAAATCCTTAG 57.126 32.000 0.00 0.00 0.00 2.18
648 697 5.598783 CGAAATTTTGCGTTTCAGAAATCC 58.401 37.500 0.00 0.00 35.77 3.01
663 712 5.649782 ATGATCCAGAAGTGCGAAATTTT 57.350 34.783 0.00 0.00 0.00 1.82
671 720 3.118629 TGGACACTATGATCCAGAAGTGC 60.119 47.826 11.55 8.82 42.44 4.40
679 728 4.471904 TGTTCACTGGACACTATGATCC 57.528 45.455 0.00 0.00 35.37 3.36
682 731 3.261643 AGCATGTTCACTGGACACTATGA 59.738 43.478 0.00 0.00 0.00 2.15
687 736 1.802960 CAGAGCATGTTCACTGGACAC 59.197 52.381 12.41 0.00 0.00 3.67
688 737 1.693606 TCAGAGCATGTTCACTGGACA 59.306 47.619 12.41 0.00 0.00 4.02
689 738 2.462456 TCAGAGCATGTTCACTGGAC 57.538 50.000 12.41 0.00 0.00 4.02
691 740 2.981898 TCATCAGAGCATGTTCACTGG 58.018 47.619 12.41 0.00 0.00 4.00
692 741 6.093082 TGTTAATCATCAGAGCATGTTCACTG 59.907 38.462 12.41 2.52 0.00 3.66
693 742 6.175471 TGTTAATCATCAGAGCATGTTCACT 58.825 36.000 12.41 0.00 0.00 3.41
694 743 6.426980 TGTTAATCATCAGAGCATGTTCAC 57.573 37.500 12.41 0.00 0.00 3.18
719 798 7.345392 AGGCCACAAATATTGTTCTGGAATAAT 59.655 33.333 5.01 9.53 43.23 1.28
721 800 6.194235 AGGCCACAAATATTGTTCTGGAATA 58.806 36.000 5.01 0.00 43.23 1.75
742 821 3.939592 CCAAAAGTACAGTTAGGCTAGGC 59.060 47.826 8.55 8.55 0.00 3.93
743 822 5.187186 TCTCCAAAAGTACAGTTAGGCTAGG 59.813 44.000 0.00 0.00 0.00 3.02
744 823 6.282199 TCTCCAAAAGTACAGTTAGGCTAG 57.718 41.667 0.00 0.00 0.00 3.42
745 824 6.675413 TTCTCCAAAAGTACAGTTAGGCTA 57.325 37.500 0.00 0.00 0.00 3.93
746 825 5.562298 TTCTCCAAAAGTACAGTTAGGCT 57.438 39.130 0.00 0.00 0.00 4.58
758 837 7.672983 TGTACTCTAGCAAATTCTCCAAAAG 57.327 36.000 0.00 0.00 0.00 2.27
759 838 8.514594 CAATGTACTCTAGCAAATTCTCCAAAA 58.485 33.333 0.00 0.00 0.00 2.44
776 855 7.798596 ATCCAGTGATCATTTCAATGTACTC 57.201 36.000 0.00 0.00 46.48 2.59
777 856 8.585471 AAATCCAGTGATCATTTCAATGTACT 57.415 30.769 0.00 1.57 46.48 2.73
822 903 3.382546 AGTGGAACCTGAAATATGCATGC 59.617 43.478 11.82 11.82 37.80 4.06
849 941 1.839354 TGGCATCAAGTAGGATGAGCA 59.161 47.619 7.30 0.00 46.00 4.26
850 942 2.103771 TCTGGCATCAAGTAGGATGAGC 59.896 50.000 7.30 0.00 46.00 4.26
851 943 4.412796 TTCTGGCATCAAGTAGGATGAG 57.587 45.455 7.30 0.00 46.00 2.90
852 944 4.842531 TTTCTGGCATCAAGTAGGATGA 57.157 40.909 7.30 0.00 46.00 2.92
853 945 4.518211 GGATTTCTGGCATCAAGTAGGATG 59.482 45.833 0.00 0.00 45.89 3.51
854 946 4.166725 TGGATTTCTGGCATCAAGTAGGAT 59.833 41.667 0.00 0.00 0.00 3.24
855 947 3.523157 TGGATTTCTGGCATCAAGTAGGA 59.477 43.478 0.00 0.00 0.00 2.94
856 948 3.881688 CTGGATTTCTGGCATCAAGTAGG 59.118 47.826 0.00 0.00 0.00 3.18
857 949 4.774124 TCTGGATTTCTGGCATCAAGTAG 58.226 43.478 0.00 0.00 0.00 2.57
858 950 4.225942 ACTCTGGATTTCTGGCATCAAGTA 59.774 41.667 0.00 0.00 0.00 2.24
859 951 3.009916 ACTCTGGATTTCTGGCATCAAGT 59.990 43.478 0.00 0.00 0.00 3.16
888 991 9.780186 AGTGTTCTTTCTGCTATAAAAGTAGTT 57.220 29.630 0.00 0.00 38.90 2.24
889 992 9.780186 AAGTGTTCTTTCTGCTATAAAAGTAGT 57.220 29.630 0.00 0.00 38.90 2.73
915 1018 6.003326 TGAAGCTGTGAGTTAATGGAATTGA 58.997 36.000 0.00 0.00 36.99 2.57
923 1026 6.712095 TGATGAACTTGAAGCTGTGAGTTAAT 59.288 34.615 8.36 7.19 32.85 1.40
926 1029 4.454678 TGATGAACTTGAAGCTGTGAGTT 58.545 39.130 8.17 8.17 35.22 3.01
929 1032 4.005650 GGATGATGAACTTGAAGCTGTGA 58.994 43.478 0.00 0.00 0.00 3.58
934 1037 4.260170 ACAGAGGATGATGAACTTGAAGC 58.740 43.478 0.00 0.00 0.00 3.86
995 1099 3.305335 GGCAACAGTGTTACCCATTTCTG 60.305 47.826 13.61 0.00 0.00 3.02
1006 1110 0.468226 TCTTCCTCGGCAACAGTGTT 59.532 50.000 1.64 1.64 0.00 3.32
1023 1133 8.762645 TCTGAATTTGGTATGTCTTCTATGTCT 58.237 33.333 0.00 0.00 0.00 3.41
1043 1153 5.687166 AATTGGTGGATTTGCATCTGAAT 57.313 34.783 0.00 0.00 0.00 2.57
1057 1167 6.923012 TGTGATATTCAGTCAAAATTGGTGG 58.077 36.000 0.00 0.00 0.00 4.61
1138 1248 3.694926 CTTTCAGGAAATCCAGAAGCCT 58.305 45.455 7.27 0.00 41.55 4.58
1216 1326 0.811219 CCGATCGATGGCAGCTGAAA 60.811 55.000 20.43 4.25 0.00 2.69
1272 1382 1.959848 CAGTGAGCTCCAGTCGACA 59.040 57.895 19.50 0.00 0.00 4.35
1323 1433 0.824109 TGAGTAGGGCGATGTTGAGG 59.176 55.000 0.00 0.00 0.00 3.86
1380 1490 3.970410 CCCAACAGGAGCAGCCCA 61.970 66.667 3.08 0.00 38.24 5.36
1383 1493 4.357279 AGCCCCAACAGGAGCAGC 62.357 66.667 0.00 0.00 38.24 5.25
1428 1538 1.198713 CTATCCAGTGGTGCCTCAGT 58.801 55.000 9.54 0.00 0.00 3.41
1429 1539 1.411977 CTCTATCCAGTGGTGCCTCAG 59.588 57.143 9.54 0.00 0.00 3.35
1473 1583 2.005220 GCTCATGAGCGTGAAGAGC 58.995 57.895 30.64 7.00 45.29 4.09
1561 1671 4.267349 TGCAGTACACCTTTCTTACCTC 57.733 45.455 0.00 0.00 0.00 3.85
1564 1674 6.348540 CCATTCTTGCAGTACACCTTTCTTAC 60.349 42.308 0.00 0.00 0.00 2.34
1569 1679 2.558359 GCCATTCTTGCAGTACACCTTT 59.442 45.455 0.00 0.00 0.00 3.11
1719 1829 4.101942 CGAGGATGAAGAAGAAGTTCTCG 58.898 47.826 5.70 0.00 42.59 4.04
1773 1883 2.958818 CCTAGAGGGCTGTACACCATA 58.041 52.381 14.03 3.26 0.00 2.74
1831 1944 2.033141 TGAGTGGAGCTGCTTGGC 59.967 61.111 6.82 0.00 0.00 4.52
1884 2006 2.358125 CACATCGGGTTGCCGACA 60.358 61.111 0.00 0.00 45.06 4.35
2058 2180 1.639534 CGTGACGTTGAACACCCAC 59.360 57.895 0.00 0.00 34.05 4.61
2329 2451 0.970937 TCCACCAGCTTCCCGTAGAG 60.971 60.000 0.00 0.00 0.00 2.43
2387 2509 3.499737 CCTCGTGCATCCCAACGC 61.500 66.667 0.00 0.00 0.00 4.84
2498 2620 3.120580 GCCATTTGCAACAATTTCTTCGG 60.121 43.478 0.00 0.00 40.77 4.30
2536 2658 2.414559 CCAATAGCTGCGGTCAACTTTG 60.415 50.000 0.00 0.00 0.00 2.77
2553 2675 2.025605 ACAGCATCAGTCACCATCCAAT 60.026 45.455 0.00 0.00 0.00 3.16
2578 2700 1.640428 TCCGTCAGCTTTCGCATAAG 58.360 50.000 2.24 0.00 39.10 1.73
2579 2701 2.309528 ATCCGTCAGCTTTCGCATAA 57.690 45.000 2.24 0.00 39.10 1.90
2662 2790 2.288825 CGACCTAAAGTCCTGTGCAGAA 60.289 50.000 0.02 0.00 43.08 3.02
2694 2825 9.829507 AGATGATCTGAATAAAACTGGACTAAG 57.170 33.333 0.00 0.00 0.00 2.18
2718 2849 3.572642 TCTGTTGGAGTGTCAAGGTAGA 58.427 45.455 0.00 0.00 0.00 2.59
2753 2884 7.644490 AGTAACGTGCAATACAAAAAGAATCA 58.356 30.769 0.00 0.00 0.00 2.57
2763 2894 6.916440 TCTTCTTCTAGTAACGTGCAATACA 58.084 36.000 0.00 0.00 0.00 2.29
2803 3003 6.721318 AGTAGGTGCCTCTCAAAATAATCAA 58.279 36.000 0.00 0.00 0.00 2.57
2821 3021 6.901081 TTCATCATCATCGTCATAGTAGGT 57.099 37.500 0.00 0.00 0.00 3.08
2849 3049 4.265073 ACCAGAGGCTTACACATGATTTC 58.735 43.478 0.00 0.00 0.00 2.17
2947 3470 1.538276 CATGAAACGCGCAAGAATCC 58.462 50.000 5.73 0.00 43.02 3.01
2999 3522 5.535333 CATTGGAGCATTTCTTTCACACTT 58.465 37.500 0.00 0.00 0.00 3.16
3063 3586 1.333619 ACCGTGAATGACAAAGCACAC 59.666 47.619 0.00 0.00 0.00 3.82
3111 3634 4.246458 GCGTCTGTACCTTTCTCATTTCT 58.754 43.478 0.00 0.00 0.00 2.52
3116 3639 3.678056 AATGCGTCTGTACCTTTCTCA 57.322 42.857 0.00 0.00 0.00 3.27
3126 3649 5.468540 TGGAGCTTATATAATGCGTCTGT 57.531 39.130 0.00 0.00 0.00 3.41
3135 3658 8.394822 AGTCTCTGTATCCTGGAGCTTATATAA 58.605 37.037 1.52 0.00 0.00 0.98
3176 3705 1.030488 TACTTCTCGGTGAGCTCGGG 61.030 60.000 9.64 0.00 0.00 5.14
3178 3707 1.469308 ACTTACTTCTCGGTGAGCTCG 59.531 52.381 9.64 0.00 0.00 5.03
3181 3710 1.272769 ACCACTTACTTCTCGGTGAGC 59.727 52.381 0.00 0.00 32.12 4.26
3186 3715 0.608640 AGCCACCACTTACTTCTCGG 59.391 55.000 0.00 0.00 0.00 4.63
3187 3716 1.714794 CAGCCACCACTTACTTCTCG 58.285 55.000 0.00 0.00 0.00 4.04
3189 3718 0.764890 TGCAGCCACCACTTACTTCT 59.235 50.000 0.00 0.00 0.00 2.85
3190 3719 0.875059 GTGCAGCCACCACTTACTTC 59.125 55.000 0.00 0.00 35.92 3.01
3191 3720 3.021451 GTGCAGCCACCACTTACTT 57.979 52.632 0.00 0.00 35.92 2.24
3192 3721 4.800554 GTGCAGCCACCACTTACT 57.199 55.556 0.00 0.00 35.92 2.24
3317 3849 3.448686 CATAGGCACAGTAGTTCTTCGG 58.551 50.000 0.00 0.00 0.00 4.30
3318 3850 3.130516 TCCATAGGCACAGTAGTTCTTCG 59.869 47.826 0.00 0.00 0.00 3.79
3334 3890 9.740239 CATAAAATCAACTTTCCATGTCCATAG 57.260 33.333 0.00 0.00 0.00 2.23
3341 3897 7.784037 TCCATCCATAAAATCAACTTTCCATG 58.216 34.615 0.00 0.00 0.00 3.66
3357 3913 0.402887 CCTGCCAGCATCCATCCATA 59.597 55.000 0.00 0.00 0.00 2.74
3371 3927 3.196207 TTGAGCTCCACCACCTGCC 62.196 63.158 12.15 0.00 0.00 4.85
3387 3943 2.401766 GCAGTGCATCCCGACCTTG 61.402 63.158 11.09 0.00 0.00 3.61
3468 4027 2.135933 GACTGTCTTTTGTCGAGTGGG 58.864 52.381 0.00 0.00 0.00 4.61
3482 4041 4.390297 GCAAGTATGGAAAGTGAGACTGTC 59.610 45.833 0.00 0.00 31.57 3.51


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

AutoCloner maintained by Alex Coulton.