Multiple sequence alignment - TraesCS2B01G517100

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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 TraesCS2B01G517100 chr2B 100.000 4047 0 0 1 4047 712001368 712005414 0.000000e+00 7474
1 TraesCS2B01G517100 chr2B 84.630 1633 192 27 1075 2681 689777660 689776061 0.000000e+00 1570
2 TraesCS2B01G517100 chr2B 80.433 971 168 19 1056 2015 712360186 712361145 0.000000e+00 721
3 TraesCS2B01G517100 chr2B 82.861 741 100 17 5 733 712359204 712359929 1.230000e-179 640
4 TraesCS2B01G517100 chr2B 76.349 723 147 18 19 732 712829622 712830329 2.300000e-97 366
5 TraesCS2B01G517100 chr2A 92.550 3208 149 32 1 3190 723100413 723103548 0.000000e+00 4518
6 TraesCS2B01G517100 chr2A 82.511 1115 159 24 1551 2648 712538837 712537742 0.000000e+00 946
7 TraesCS2B01G517100 chr2A 89.032 620 61 5 3272 3888 723126621 723127236 0.000000e+00 761
8 TraesCS2B01G517100 chr2A 80.411 730 100 23 9 733 723511146 723511837 2.160000e-142 516
9 TraesCS2B01G517100 chr2A 88.136 413 47 2 1073 1484 712539279 712538868 1.310000e-134 490
10 TraesCS2B01G517100 chr2A 83.109 521 72 12 994 1501 723511934 723512451 1.020000e-125 460
11 TraesCS2B01G517100 chr2A 84.793 434 64 2 1069 1501 723134379 723134811 6.210000e-118 435
12 TraesCS2B01G517100 chr2A 81.407 398 61 11 385 773 723133761 723134154 3.040000e-81 313
13 TraesCS2B01G517100 chr2A 80.142 282 54 2 5 285 723578383 723578663 4.100000e-50 209
14 TraesCS2B01G517100 chr2A 91.818 110 8 1 3938 4047 723127226 723127334 7.010000e-33 152
15 TraesCS2B01G517100 chr2D 93.590 2730 106 30 1 2693 588497521 588500218 0.000000e+00 4008
16 TraesCS2B01G517100 chr2D 89.304 776 57 7 3272 4045 588537545 588538296 0.000000e+00 950
17 TraesCS2B01G517100 chr2D 85.455 715 104 0 1551 2265 573951932 573951218 0.000000e+00 745
18 TraesCS2B01G517100 chr2D 78.369 1202 222 31 994 2173 588735895 588737080 0.000000e+00 745
19 TraesCS2B01G517100 chr2D 81.351 740 106 22 5 733 588734985 588735703 1.260000e-159 573
20 TraesCS2B01G517100 chr2D 89.930 427 43 0 1075 1501 573952372 573951946 5.910000e-153 551
21 TraesCS2B01G517100 chr2D 83.984 487 38 15 2704 3181 588500356 588500811 8.040000e-117 431


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 TraesCS2B01G517100 chr2B 712001368 712005414 4046 False 7474.0 7474 100.0000 1 4047 1 chr2B.!!$F1 4046
1 TraesCS2B01G517100 chr2B 689776061 689777660 1599 True 1570.0 1570 84.6300 1075 2681 1 chr2B.!!$R1 1606
2 TraesCS2B01G517100 chr2B 712359204 712361145 1941 False 680.5 721 81.6470 5 2015 2 chr2B.!!$F3 2010
3 TraesCS2B01G517100 chr2B 712829622 712830329 707 False 366.0 366 76.3490 19 732 1 chr2B.!!$F2 713
4 TraesCS2B01G517100 chr2A 723100413 723103548 3135 False 4518.0 4518 92.5500 1 3190 1 chr2A.!!$F1 3189
5 TraesCS2B01G517100 chr2A 712537742 712539279 1537 True 718.0 946 85.3235 1073 2648 2 chr2A.!!$R1 1575
6 TraesCS2B01G517100 chr2A 723511146 723512451 1305 False 488.0 516 81.7600 9 1501 2 chr2A.!!$F5 1492
7 TraesCS2B01G517100 chr2A 723126621 723127334 713 False 456.5 761 90.4250 3272 4047 2 chr2A.!!$F3 775
8 TraesCS2B01G517100 chr2A 723133761 723134811 1050 False 374.0 435 83.1000 385 1501 2 chr2A.!!$F4 1116
9 TraesCS2B01G517100 chr2D 588497521 588500811 3290 False 2219.5 4008 88.7870 1 3181 2 chr2D.!!$F2 3180
10 TraesCS2B01G517100 chr2D 588537545 588538296 751 False 950.0 950 89.3040 3272 4045 1 chr2D.!!$F1 773
11 TraesCS2B01G517100 chr2D 588734985 588737080 2095 False 659.0 745 79.8600 5 2173 2 chr2D.!!$F3 2168
12 TraesCS2B01G517100 chr2D 573951218 573952372 1154 True 648.0 745 87.6925 1075 2265 2 chr2D.!!$R1 1190

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
833 915 0.389948 ATGTCACGCTTCCGAGTTCC 60.390 55.000 0.00 0.0 38.29 3.62 F
1042 1247 1.142748 CAAACAACCCTGCGGCAAA 59.857 52.632 3.44 0.0 0.00 3.68 F
1840 2075 1.025812 ACCGCCTGAAGAGAGTATCG 58.974 55.000 0.00 0.0 42.67 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1804 2039 1.269102 CGGTAGATACCTTCCAGCGTG 60.269 57.143 7.42 0.00 44.25 5.34 R
1889 2124 1.461127 GCCGATGTCAACAGACTTCAC 59.539 52.381 10.72 1.12 36.67 3.18 R
3228 3631 0.320508 GGTCGTTGGAGGAGGTGAAC 60.321 60.000 0.00 0.00 0.00 3.18 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
103 104 1.411977 CCGTGATCTCCTTGATGCTCT 59.588 52.381 0.00 0.00 35.14 4.09
201 202 4.504916 CTCCCGAGGCAGAGCGTG 62.505 72.222 0.00 0.00 0.00 5.34
291 292 3.267860 CGGCAGCGGAAGATCAGC 61.268 66.667 0.00 0.00 37.86 4.26
297 298 2.496341 CGGAAGATCAGCCGCTGA 59.504 61.111 24.90 24.90 44.99 4.26
330 331 0.879090 TCTTACTGTCGCTTCGCTCA 59.121 50.000 0.00 0.00 0.00 4.26
331 332 1.472878 TCTTACTGTCGCTTCGCTCAT 59.527 47.619 0.00 0.00 0.00 2.90
572 631 2.169330 GACCTTGAGTCTCCCGTAGTT 58.831 52.381 0.00 0.00 42.69 2.24
771 853 2.943034 GCCATCGTCGTCGTCGTC 60.943 66.667 11.41 0.00 38.33 4.20
772 854 2.643790 CCATCGTCGTCGTCGTCG 60.644 66.667 14.18 14.18 46.06 5.12
786 868 3.312697 TCGTCGTCGAGATCAATCAAGAT 59.687 43.478 0.00 0.00 41.35 2.40
787 869 3.661728 CGTCGTCGAGATCAATCAAGATC 59.338 47.826 0.00 0.00 43.73 2.75
829 911 2.222819 GCTTTTATGTCACGCTTCCGAG 60.223 50.000 0.00 0.00 38.29 4.63
831 913 2.736144 TTATGTCACGCTTCCGAGTT 57.264 45.000 0.00 0.00 38.29 3.01
832 914 2.273370 TATGTCACGCTTCCGAGTTC 57.727 50.000 0.00 0.00 38.29 3.01
833 915 0.389948 ATGTCACGCTTCCGAGTTCC 60.390 55.000 0.00 0.00 38.29 3.62
834 916 2.087009 GTCACGCTTCCGAGTTCCG 61.087 63.158 0.00 0.00 38.29 4.30
835 917 3.479269 CACGCTTCCGAGTTCCGC 61.479 66.667 0.00 0.00 38.29 5.54
836 918 4.736896 ACGCTTCCGAGTTCCGCC 62.737 66.667 0.00 0.00 38.29 6.13
867 949 3.502356 GATCCCTCCTCGACCTCTTAAT 58.498 50.000 0.00 0.00 0.00 1.40
923 1085 3.949754 AGTCGGTTCATATAGTCGGTCAA 59.050 43.478 0.00 0.00 0.00 3.18
934 1096 1.275573 AGTCGGTCAAAAGACTAGGGC 59.724 52.381 0.00 0.00 44.93 5.19
1042 1247 1.142748 CAAACAACCCTGCGGCAAA 59.857 52.632 3.44 0.00 0.00 3.68
1573 1808 3.616721 AGCGGCACCGACAACTCT 61.617 61.111 14.43 0.00 42.83 3.24
1669 1904 2.562489 CATACGGACGCTACGTGTG 58.438 57.895 0.00 9.13 45.20 3.82
1674 1909 2.809601 GACGCTACGTGTGGCCTG 60.810 66.667 3.32 0.00 41.37 4.85
1804 2039 3.917760 CCCCGCCTCATCGACCTC 61.918 72.222 0.00 0.00 0.00 3.85
1815 2050 1.949847 ATCGACCTCACGCTGGAAGG 61.950 60.000 0.00 0.00 0.00 3.46
1840 2075 1.025812 ACCGCCTGAAGAGAGTATCG 58.974 55.000 0.00 0.00 42.67 2.92
1889 2124 1.202568 CTTCGCTGCTGTCACAACG 59.797 57.895 0.00 0.00 0.00 4.10
1908 2143 1.721389 CGTGAAGTCTGTTGACATCGG 59.279 52.381 0.00 0.00 45.20 4.18
1978 2213 1.598130 GCTCTTGTCCTTGCACGGT 60.598 57.895 9.36 0.00 0.00 4.83
2107 2342 3.568093 GCATTTGCACAACCGAAGT 57.432 47.368 0.00 0.00 41.59 3.01
2329 2585 4.753516 ATATGAGGATGACGTTGTGGAA 57.246 40.909 0.00 0.00 0.00 3.53
2362 2618 3.316253 GCAGAGAGCGATGATTTGTTC 57.684 47.619 0.00 0.00 0.00 3.18
2372 2628 3.738281 CGATGATTTGTTCGTAGCTCCCT 60.738 47.826 0.00 0.00 0.00 4.20
2461 2720 1.003839 CATGGTGCACTACGTGGGT 60.004 57.895 17.98 0.00 33.64 4.51
2594 2853 4.657504 AGAATGAGATTGATAGCTGGGTGA 59.342 41.667 0.00 0.00 0.00 4.02
2613 2872 3.309954 GTGATGGCCGATGTAGAAAAGAC 59.690 47.826 0.00 0.00 0.00 3.01
2634 2896 4.899502 ACTTTCTTGTGATCTTCCGTCAT 58.100 39.130 0.00 0.00 0.00 3.06
2651 2913 7.099266 TCCGTCATGCAATCTCAAAATAATT 57.901 32.000 0.00 0.00 0.00 1.40
2693 2955 1.269448 CGTGCCATGTTAGGTTTTGCT 59.731 47.619 0.00 0.00 0.00 3.91
2694 2956 2.676076 GTGCCATGTTAGGTTTTGCTG 58.324 47.619 0.00 0.00 0.00 4.41
2702 3091 5.982465 TGTTAGGTTTTGCTGAAAATTGC 57.018 34.783 0.00 0.00 33.63 3.56
2762 3157 8.798859 AGATGTAAAGAACAGAAGCAATACAT 57.201 30.769 0.00 0.00 42.70 2.29
2774 3169 7.148188 ACAGAAGCAATACATAGGTCATTGTTG 60.148 37.037 9.70 0.00 33.22 3.33
2793 3192 9.241317 CATTGTTGAGATTATAAATGAGTTGGC 57.759 33.333 0.00 0.00 0.00 4.52
2830 3229 6.131544 CTGTAAGCTGTTTTACAGTTTGGT 57.868 37.500 16.05 0.00 46.65 3.67
2840 3239 8.282455 TGTTTTACAGTTTGGTCAGTCAAATA 57.718 30.769 0.00 0.00 38.64 1.40
2934 3334 8.299570 CAGGGTCTATTATGAAATATTTGTGCC 58.700 37.037 5.17 0.00 0.00 5.01
2964 3364 4.392921 AATCTAGATGACTCCCAACACG 57.607 45.455 5.86 0.00 0.00 4.49
2975 3375 2.353839 CAACACGTTGCTGCAGGC 60.354 61.111 17.12 8.54 42.22 4.85
3036 3436 7.960738 CACAATGGAAAATTGAATCATTGAAGC 59.039 33.333 18.39 0.00 44.14 3.86
3039 3439 9.947433 AATGGAAAATTGAATCATTGAAGCTTA 57.053 25.926 0.00 0.00 0.00 3.09
3088 3488 9.827411 GTTCTCATGACTTAAATTTCAAGTACC 57.173 33.333 0.00 0.00 36.38 3.34
3089 3489 9.793259 TTCTCATGACTTAAATTTCAAGTACCT 57.207 29.630 0.00 0.00 36.38 3.08
3090 3490 9.793259 TCTCATGACTTAAATTTCAAGTACCTT 57.207 29.630 0.00 0.00 36.38 3.50
3181 3584 8.058667 TGCAATACATGAAGAAGTTGATCAAT 57.941 30.769 12.12 0.00 0.00 2.57
3190 3593 7.315142 TGAAGAAGTTGATCAATATTGGCAAC 58.685 34.615 28.53 28.53 40.63 4.17
3201 3604 2.032528 TGGCAACAGCTTCCTCGG 59.967 61.111 0.00 0.00 46.17 4.63
3202 3605 2.032681 GGCAACAGCTTCCTCGGT 59.967 61.111 0.00 0.00 0.00 4.69
3203 3606 2.035442 GGCAACAGCTTCCTCGGTC 61.035 63.158 0.00 0.00 0.00 4.79
3204 3607 1.301716 GCAACAGCTTCCTCGGTCA 60.302 57.895 0.00 0.00 0.00 4.02
3205 3608 0.674895 GCAACAGCTTCCTCGGTCAT 60.675 55.000 0.00 0.00 0.00 3.06
3206 3609 1.405526 GCAACAGCTTCCTCGGTCATA 60.406 52.381 0.00 0.00 0.00 2.15
3207 3610 2.743183 GCAACAGCTTCCTCGGTCATAT 60.743 50.000 0.00 0.00 0.00 1.78
3208 3611 3.535561 CAACAGCTTCCTCGGTCATATT 58.464 45.455 0.00 0.00 0.00 1.28
3209 3612 3.460857 ACAGCTTCCTCGGTCATATTC 57.539 47.619 0.00 0.00 0.00 1.75
3210 3613 2.766263 ACAGCTTCCTCGGTCATATTCA 59.234 45.455 0.00 0.00 0.00 2.57
3211 3614 3.389329 ACAGCTTCCTCGGTCATATTCAT 59.611 43.478 0.00 0.00 0.00 2.57
3212 3615 3.993081 CAGCTTCCTCGGTCATATTCATC 59.007 47.826 0.00 0.00 0.00 2.92
3213 3616 3.643320 AGCTTCCTCGGTCATATTCATCA 59.357 43.478 0.00 0.00 0.00 3.07
3214 3617 3.743396 GCTTCCTCGGTCATATTCATCAC 59.257 47.826 0.00 0.00 0.00 3.06
3215 3618 4.740634 GCTTCCTCGGTCATATTCATCACA 60.741 45.833 0.00 0.00 0.00 3.58
3216 3619 5.351948 TTCCTCGGTCATATTCATCACAA 57.648 39.130 0.00 0.00 0.00 3.33
3217 3620 5.351948 TCCTCGGTCATATTCATCACAAA 57.648 39.130 0.00 0.00 0.00 2.83
3218 3621 5.359756 TCCTCGGTCATATTCATCACAAAG 58.640 41.667 0.00 0.00 0.00 2.77
3219 3622 5.104941 TCCTCGGTCATATTCATCACAAAGT 60.105 40.000 0.00 0.00 0.00 2.66
3220 3623 5.586243 CCTCGGTCATATTCATCACAAAGTT 59.414 40.000 0.00 0.00 0.00 2.66
3221 3624 6.094048 CCTCGGTCATATTCATCACAAAGTTT 59.906 38.462 0.00 0.00 0.00 2.66
3222 3625 7.279981 CCTCGGTCATATTCATCACAAAGTTTA 59.720 37.037 0.00 0.00 0.00 2.01
3223 3626 7.970384 TCGGTCATATTCATCACAAAGTTTAC 58.030 34.615 0.00 0.00 0.00 2.01
3224 3627 7.604545 TCGGTCATATTCATCACAAAGTTTACA 59.395 33.333 0.00 0.00 0.00 2.41
3225 3628 8.397906 CGGTCATATTCATCACAAAGTTTACAT 58.602 33.333 0.00 0.00 0.00 2.29
3233 3636 9.891828 TTCATCACAAAGTTTACATATGTTCAC 57.108 29.630 14.77 10.95 0.00 3.18
3234 3637 8.511321 TCATCACAAAGTTTACATATGTTCACC 58.489 33.333 14.77 0.26 0.00 4.02
3235 3638 8.514594 CATCACAAAGTTTACATATGTTCACCT 58.485 33.333 14.77 2.66 0.00 4.00
3236 3639 8.094798 TCACAAAGTTTACATATGTTCACCTC 57.905 34.615 14.77 0.05 0.00 3.85
3237 3640 7.174253 TCACAAAGTTTACATATGTTCACCTCC 59.826 37.037 14.77 0.00 0.00 4.30
3238 3641 7.174946 CACAAAGTTTACATATGTTCACCTCCT 59.825 37.037 14.77 0.00 0.00 3.69
3239 3642 7.390718 ACAAAGTTTACATATGTTCACCTCCTC 59.609 37.037 14.77 0.00 0.00 3.71
3240 3643 5.990668 AGTTTACATATGTTCACCTCCTCC 58.009 41.667 14.77 0.00 0.00 4.30
3241 3644 5.487488 AGTTTACATATGTTCACCTCCTCCA 59.513 40.000 14.77 0.00 0.00 3.86
3242 3645 6.012858 AGTTTACATATGTTCACCTCCTCCAA 60.013 38.462 14.77 0.00 0.00 3.53
3243 3646 4.222124 ACATATGTTCACCTCCTCCAAC 57.778 45.455 1.41 0.00 0.00 3.77
3244 3647 3.198068 CATATGTTCACCTCCTCCAACG 58.802 50.000 0.00 0.00 0.00 4.10
3245 3648 1.348064 ATGTTCACCTCCTCCAACGA 58.652 50.000 0.00 0.00 0.00 3.85
3246 3649 0.391597 TGTTCACCTCCTCCAACGAC 59.608 55.000 0.00 0.00 0.00 4.34
3247 3650 0.320508 GTTCACCTCCTCCAACGACC 60.321 60.000 0.00 0.00 0.00 4.79
3248 3651 0.471211 TTCACCTCCTCCAACGACCT 60.471 55.000 0.00 0.00 0.00 3.85
3249 3652 0.898789 TCACCTCCTCCAACGACCTC 60.899 60.000 0.00 0.00 0.00 3.85
3250 3653 1.609794 ACCTCCTCCAACGACCTCC 60.610 63.158 0.00 0.00 0.00 4.30
3251 3654 1.305381 CCTCCTCCAACGACCTCCT 60.305 63.158 0.00 0.00 0.00 3.69
3252 3655 1.324005 CCTCCTCCAACGACCTCCTC 61.324 65.000 0.00 0.00 0.00 3.71
3253 3656 1.305046 TCCTCCAACGACCTCCTCC 60.305 63.158 0.00 0.00 0.00 4.30
3254 3657 1.609501 CCTCCAACGACCTCCTCCA 60.610 63.158 0.00 0.00 0.00 3.86
3255 3658 1.592223 CTCCAACGACCTCCTCCAC 59.408 63.158 0.00 0.00 0.00 4.02
3256 3659 1.152419 TCCAACGACCTCCTCCACA 60.152 57.895 0.00 0.00 0.00 4.17
3257 3660 0.544357 TCCAACGACCTCCTCCACAT 60.544 55.000 0.00 0.00 0.00 3.21
3258 3661 0.324943 CCAACGACCTCCTCCACATT 59.675 55.000 0.00 0.00 0.00 2.71
3259 3662 1.676014 CCAACGACCTCCTCCACATTC 60.676 57.143 0.00 0.00 0.00 2.67
3260 3663 1.276421 CAACGACCTCCTCCACATTCT 59.724 52.381 0.00 0.00 0.00 2.40
3261 3664 1.187087 ACGACCTCCTCCACATTCTC 58.813 55.000 0.00 0.00 0.00 2.87
3262 3665 1.186200 CGACCTCCTCCACATTCTCA 58.814 55.000 0.00 0.00 0.00 3.27
3263 3666 1.550524 CGACCTCCTCCACATTCTCAA 59.449 52.381 0.00 0.00 0.00 3.02
3264 3667 2.028112 CGACCTCCTCCACATTCTCAAA 60.028 50.000 0.00 0.00 0.00 2.69
3265 3668 3.557054 CGACCTCCTCCACATTCTCAAAA 60.557 47.826 0.00 0.00 0.00 2.44
3266 3669 4.398319 GACCTCCTCCACATTCTCAAAAA 58.602 43.478 0.00 0.00 0.00 1.94
3296 3699 3.731652 TCTCCAACGTACCGAAAAAGA 57.268 42.857 0.00 0.00 0.00 2.52
3297 3700 3.645884 TCTCCAACGTACCGAAAAAGAG 58.354 45.455 0.00 0.00 0.00 2.85
3302 3705 4.271776 CCAACGTACCGAAAAAGAGTTCTT 59.728 41.667 0.00 0.00 37.91 2.52
3303 3706 5.195379 CAACGTACCGAAAAAGAGTTCTTG 58.805 41.667 0.00 0.00 36.12 3.02
3307 3710 3.279434 ACCGAAAAAGAGTTCTTGCACT 58.721 40.909 0.00 0.00 36.12 4.40
3319 3722 5.284079 AGTTCTTGCACTGCTTTGTAAATG 58.716 37.500 1.98 0.00 0.00 2.32
3320 3723 4.241590 TCTTGCACTGCTTTGTAAATGG 57.758 40.909 1.98 0.00 0.00 3.16
3349 3752 3.609853 ACATGATACAGCCACAACGAAT 58.390 40.909 0.00 0.00 0.00 3.34
3354 3757 0.108585 ACAGCCACAACGAATGGAGT 59.891 50.000 8.27 3.68 39.87 3.85
3391 3794 9.607988 AAACAAATAGGTTCGAAAAGGAAAAAT 57.392 25.926 0.00 0.00 0.00 1.82
3416 3821 0.837272 GTACTAGCTGGGGGCATCAA 59.163 55.000 0.85 0.00 44.79 2.57
3463 3868 5.409826 CACAACAAAGTCTCAAGGAGGATAC 59.590 44.000 0.00 0.00 0.00 2.24
3499 3905 1.225704 GGATGCCACCTCCTCCAAG 59.774 63.158 0.00 0.00 0.00 3.61
3516 3922 3.284711 AGGTAGACCTTGTCTCCGG 57.715 57.895 0.00 0.00 46.09 5.14
3517 3923 0.971447 AGGTAGACCTTGTCTCCGGC 60.971 60.000 0.00 0.00 46.09 6.13
3518 3924 1.255667 GGTAGACCTTGTCTCCGGCA 61.256 60.000 0.00 0.00 42.40 5.69
3519 3925 0.606604 GTAGACCTTGTCTCCGGCAA 59.393 55.000 0.00 0.00 42.40 4.52
3573 3979 2.186903 CGGCACATCGTAAGCCCT 59.813 61.111 0.00 0.00 45.56 5.19
3580 3986 0.456221 CATCGTAAGCCCTGTCTCGT 59.544 55.000 0.00 0.00 37.18 4.18
3602 4008 3.726517 CCTTGGCCACACGCTTCG 61.727 66.667 3.88 0.00 37.74 3.79
3614 4020 3.423154 GCTTCGCCTCCAACACCG 61.423 66.667 0.00 0.00 0.00 4.94
3616 4022 2.027625 CTTCGCCTCCAACACCGTC 61.028 63.158 0.00 0.00 0.00 4.79
3648 4054 1.069296 CAGGCGAAGTTGCATCGAAAA 60.069 47.619 12.18 0.00 42.76 2.29
3649 4055 1.606668 AGGCGAAGTTGCATCGAAAAA 59.393 42.857 12.18 0.00 42.76 1.94
3655 4061 4.415735 GAAGTTGCATCGAAAAAGGGATC 58.584 43.478 0.00 0.00 0.00 3.36
3657 4063 2.491693 GTTGCATCGAAAAAGGGATCCA 59.508 45.455 15.23 0.00 0.00 3.41
3788 4194 2.725312 GCTCATCGGTGGAGAGGCA 61.725 63.158 0.00 0.00 34.24 4.75
3819 4225 1.377725 GCAGCCAGCTATGTGTGGT 60.378 57.895 0.00 0.00 41.15 4.16
3896 4302 3.018856 TGTGATGCAAATTCTAGCAGGG 58.981 45.455 0.00 0.00 44.94 4.45
3898 4304 2.025037 TGATGCAAATTCTAGCAGGGGT 60.025 45.455 0.00 0.00 44.94 4.95
3954 4360 8.891671 ACTGTTATTGATGTCAAATTTGCTTT 57.108 26.923 13.54 0.02 39.55 3.51
4028 4434 9.151177 AGTTTAAATGATTATCAGGCATTGGAT 57.849 29.630 0.29 0.00 32.96 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 104 3.695606 GACGCTGGAGGAGTGCCA 61.696 66.667 0.00 0.00 35.37 4.92
201 202 3.188786 GACATGGCGTCGCTGGAC 61.189 66.667 18.11 0.17 39.89 4.02
297 298 3.510360 ACAGTAAGATGTACGCCAAGACT 59.490 43.478 0.00 0.00 0.00 3.24
330 331 2.688507 CTCTGCCCATTACGCGAATAT 58.311 47.619 15.93 0.00 0.00 1.28
331 332 1.872237 GCTCTGCCCATTACGCGAATA 60.872 52.381 15.93 0.00 0.00 1.75
374 415 5.360144 GTCAAGCTCAGATACAAGGGTAGTA 59.640 44.000 0.00 0.00 31.88 1.82
685 744 4.498520 GCTGCAGCGCGTCCTCTA 62.499 66.667 25.23 0.00 0.00 2.43
771 853 6.679843 TCTGATCTGATCTTGATTGATCTCG 58.320 40.000 17.82 13.45 42.30 4.04
772 854 7.117236 GCTTCTGATCTGATCTTGATTGATCTC 59.883 40.741 17.82 0.00 42.30 2.75
773 855 6.932400 GCTTCTGATCTGATCTTGATTGATCT 59.068 38.462 17.82 0.00 42.30 2.75
774 856 6.128769 CGCTTCTGATCTGATCTTGATTGATC 60.129 42.308 17.82 14.58 42.19 2.92
775 857 5.697178 CGCTTCTGATCTGATCTTGATTGAT 59.303 40.000 17.82 0.00 0.00 2.57
786 868 2.903357 GGGCCGCTTCTGATCTGA 59.097 61.111 0.00 0.00 0.00 3.27
787 869 2.587194 CGGGCCGCTTCTGATCTG 60.587 66.667 15.42 0.00 0.00 2.90
838 920 4.924187 AGGAGGGATCGGAGGCGG 62.924 72.222 0.00 0.00 0.00 6.13
839 921 3.299190 GAGGAGGGATCGGAGGCG 61.299 72.222 0.00 0.00 0.00 5.52
840 922 3.299190 CGAGGAGGGATCGGAGGC 61.299 72.222 0.00 0.00 36.54 4.70
841 923 1.899534 GTCGAGGAGGGATCGGAGG 60.900 68.421 0.00 0.00 40.54 4.30
842 924 1.899534 GGTCGAGGAGGGATCGGAG 60.900 68.421 0.00 0.00 40.54 4.63
897 979 4.458295 ACCGACTATATGAACCGACTATGG 59.542 45.833 0.00 0.00 0.00 2.74
923 1085 2.221299 TGCGTGGGCCCTAGTCTTT 61.221 57.895 25.70 0.00 38.85 2.52
934 1096 1.312371 CCAGGGTTTATGTGCGTGGG 61.312 60.000 0.00 0.00 0.00 4.61
1042 1247 2.794910 CGTTGACGAAGCCATATCGATT 59.205 45.455 1.71 0.00 42.76 3.34
1573 1808 0.603065 CACACTCATCCTCGTGGTCA 59.397 55.000 2.99 0.00 35.51 4.02
1674 1909 2.050077 GCAGTTTCAGCCGGCAAC 60.050 61.111 31.54 23.80 0.00 4.17
1711 1946 1.621992 TGCTCAAAGTCTCGAGGAGT 58.378 50.000 13.56 0.00 0.00 3.85
1804 2039 1.269102 CGGTAGATACCTTCCAGCGTG 60.269 57.143 7.42 0.00 44.25 5.34
1815 2050 3.215975 ACTCTCTTCAGGCGGTAGATAC 58.784 50.000 0.00 0.00 0.00 2.24
1840 2075 1.737008 GAGGCGTTTGTCGAGGACC 60.737 63.158 0.00 0.00 42.86 4.46
1889 2124 1.461127 GCCGATGTCAACAGACTTCAC 59.539 52.381 10.72 1.12 36.67 3.18
2329 2585 2.093021 GCTCTCTGCATCCTTCTCCTTT 60.093 50.000 0.00 0.00 42.31 3.11
2372 2628 3.767131 TCATCAGGAACCATGAACTCGTA 59.233 43.478 0.00 0.00 0.00 3.43
2429 2688 3.285484 GCACCATGTTGATCTCCTTCAT 58.715 45.455 0.00 0.00 0.00 2.57
2461 2720 3.588955 CATCATCCTTTGTGTCTCGTCA 58.411 45.455 0.00 0.00 0.00 4.35
2594 2853 3.914426 AGTCTTTTCTACATCGGCCAT 57.086 42.857 2.24 0.00 0.00 4.40
2613 2872 4.436584 GCATGACGGAAGATCACAAGAAAG 60.437 45.833 0.00 0.00 0.00 2.62
2618 2877 2.470983 TGCATGACGGAAGATCACAA 57.529 45.000 0.00 0.00 0.00 3.33
2651 2913 4.377943 CGAAACTAATCATGTCACGGCAAA 60.378 41.667 0.00 0.00 0.00 3.68
2693 2955 6.389830 TGAGTTTAGAAGCTGCAATTTTCA 57.610 33.333 1.02 0.00 0.00 2.69
2694 2956 8.454106 TCTATGAGTTTAGAAGCTGCAATTTTC 58.546 33.333 1.02 0.00 0.00 2.29
2711 3100 7.340232 TCCTTTTGCATATTGCTTCTATGAGTT 59.660 33.333 0.75 0.00 45.31 3.01
2714 3103 7.056006 TCTCCTTTTGCATATTGCTTCTATGA 58.944 34.615 0.75 0.00 45.31 2.15
2774 3169 7.521261 GCAGAAGGCCAACTCATTTATAATCTC 60.521 40.741 5.01 0.00 36.11 2.75
2793 3192 2.413453 GCTTACAGTTTCGAGCAGAAGG 59.587 50.000 0.00 0.00 40.40 3.46
2840 3239 9.295825 TCCATAGTGATTGTCAAACTTACAAAT 57.704 29.630 0.00 0.00 40.05 2.32
2887 3287 9.487442 ACCCTGTAATACCAATTTCACATAATT 57.513 29.630 0.00 0.00 0.00 1.40
2892 3292 6.134535 AGACCCTGTAATACCAATTTCACA 57.865 37.500 0.00 0.00 0.00 3.58
2893 3293 8.747538 AATAGACCCTGTAATACCAATTTCAC 57.252 34.615 0.00 0.00 0.00 3.18
2909 3309 8.004215 TGGCACAAATATTTCATAATAGACCCT 58.996 33.333 0.00 0.00 31.92 4.34
2946 3346 3.254060 CAACGTGTTGGGAGTCATCTAG 58.746 50.000 4.82 0.00 36.95 2.43
2975 3375 4.484236 ACAACATTTTGTATGCGGATGTG 58.516 39.130 0.00 0.00 44.53 3.21
3008 3408 8.766000 TCAATGATTCAATTTTCCATTGTGAG 57.234 30.769 0.00 0.00 42.56 3.51
3084 3484 6.762187 GCCCATCTCTCTAACTTAAAAGGTAC 59.238 42.308 0.00 0.00 0.00 3.34
3085 3485 6.672657 AGCCCATCTCTCTAACTTAAAAGGTA 59.327 38.462 0.00 0.00 0.00 3.08
3086 3486 5.489278 AGCCCATCTCTCTAACTTAAAAGGT 59.511 40.000 0.00 0.00 0.00 3.50
3087 3487 5.995446 AGCCCATCTCTCTAACTTAAAAGG 58.005 41.667 0.00 0.00 0.00 3.11
3088 3488 6.644347 TGAGCCCATCTCTCTAACTTAAAAG 58.356 40.000 0.00 0.00 42.38 2.27
3089 3489 6.620877 TGAGCCCATCTCTCTAACTTAAAA 57.379 37.500 0.00 0.00 42.38 1.52
3090 3490 6.213600 AGTTGAGCCCATCTCTCTAACTTAAA 59.786 38.462 0.00 0.00 42.38 1.52
3091 3491 5.721960 AGTTGAGCCCATCTCTCTAACTTAA 59.278 40.000 0.00 0.00 42.38 1.85
3092 3492 5.127845 CAGTTGAGCCCATCTCTCTAACTTA 59.872 44.000 0.00 0.00 42.38 2.24
3093 3493 4.081198 CAGTTGAGCCCATCTCTCTAACTT 60.081 45.833 0.00 0.00 42.38 2.66
3094 3494 3.450457 CAGTTGAGCCCATCTCTCTAACT 59.550 47.826 0.00 0.00 42.38 2.24
3095 3495 3.449018 TCAGTTGAGCCCATCTCTCTAAC 59.551 47.826 0.00 0.00 42.38 2.34
3096 3496 3.713003 TCAGTTGAGCCCATCTCTCTAA 58.287 45.455 0.00 0.00 42.38 2.10
3097 3497 3.388552 TCAGTTGAGCCCATCTCTCTA 57.611 47.619 0.00 0.00 42.38 2.43
3181 3584 1.678728 CCGAGGAAGCTGTTGCCAATA 60.679 52.381 0.00 0.00 40.80 1.90
3183 3586 1.600636 CCGAGGAAGCTGTTGCCAA 60.601 57.895 0.00 0.00 40.80 4.52
3190 3593 3.459232 TGAATATGACCGAGGAAGCTG 57.541 47.619 0.00 0.00 0.00 4.24
3191 3594 3.643320 TGATGAATATGACCGAGGAAGCT 59.357 43.478 0.00 0.00 0.00 3.74
3192 3595 3.743396 GTGATGAATATGACCGAGGAAGC 59.257 47.826 0.00 0.00 0.00 3.86
3193 3596 4.948847 TGTGATGAATATGACCGAGGAAG 58.051 43.478 0.00 0.00 0.00 3.46
3194 3597 5.351948 TTGTGATGAATATGACCGAGGAA 57.648 39.130 0.00 0.00 0.00 3.36
3195 3598 5.104941 ACTTTGTGATGAATATGACCGAGGA 60.105 40.000 0.00 0.00 0.00 3.71
3196 3599 5.118990 ACTTTGTGATGAATATGACCGAGG 58.881 41.667 0.00 0.00 0.00 4.63
3197 3600 6.668541 AACTTTGTGATGAATATGACCGAG 57.331 37.500 0.00 0.00 0.00 4.63
3198 3601 7.604545 TGTAAACTTTGTGATGAATATGACCGA 59.395 33.333 0.00 0.00 0.00 4.69
3199 3602 7.747888 TGTAAACTTTGTGATGAATATGACCG 58.252 34.615 0.00 0.00 0.00 4.79
3207 3610 9.891828 GTGAACATATGTAAACTTTGTGATGAA 57.108 29.630 9.21 0.00 0.00 2.57
3208 3611 8.511321 GGTGAACATATGTAAACTTTGTGATGA 58.489 33.333 9.21 0.00 0.00 2.92
3209 3612 8.514594 AGGTGAACATATGTAAACTTTGTGATG 58.485 33.333 9.21 0.00 0.00 3.07
3210 3613 8.635765 AGGTGAACATATGTAAACTTTGTGAT 57.364 30.769 9.21 0.00 0.00 3.06
3211 3614 7.174253 GGAGGTGAACATATGTAAACTTTGTGA 59.826 37.037 9.21 0.00 0.00 3.58
3212 3615 7.174946 AGGAGGTGAACATATGTAAACTTTGTG 59.825 37.037 9.21 0.00 0.00 3.33
3213 3616 7.231467 AGGAGGTGAACATATGTAAACTTTGT 58.769 34.615 9.21 0.00 0.00 2.83
3214 3617 7.148239 GGAGGAGGTGAACATATGTAAACTTTG 60.148 40.741 9.21 0.00 0.00 2.77
3215 3618 6.884836 GGAGGAGGTGAACATATGTAAACTTT 59.115 38.462 9.21 2.11 0.00 2.66
3216 3619 6.012858 TGGAGGAGGTGAACATATGTAAACTT 60.013 38.462 9.21 6.96 0.00 2.66
3217 3620 5.487488 TGGAGGAGGTGAACATATGTAAACT 59.513 40.000 9.21 8.73 0.00 2.66
3218 3621 5.741011 TGGAGGAGGTGAACATATGTAAAC 58.259 41.667 9.21 10.22 0.00 2.01
3219 3622 6.177610 GTTGGAGGAGGTGAACATATGTAAA 58.822 40.000 9.21 0.00 0.00 2.01
3220 3623 5.625886 CGTTGGAGGAGGTGAACATATGTAA 60.626 44.000 9.21 0.00 0.00 2.41
3221 3624 4.142026 CGTTGGAGGAGGTGAACATATGTA 60.142 45.833 9.21 0.00 0.00 2.29
3222 3625 3.369471 CGTTGGAGGAGGTGAACATATGT 60.369 47.826 1.41 1.41 0.00 2.29
3223 3626 3.118775 TCGTTGGAGGAGGTGAACATATG 60.119 47.826 0.00 0.00 0.00 1.78
3224 3627 3.104512 TCGTTGGAGGAGGTGAACATAT 58.895 45.455 0.00 0.00 0.00 1.78
3225 3628 2.232941 GTCGTTGGAGGAGGTGAACATA 59.767 50.000 0.00 0.00 0.00 2.29
3226 3629 1.002087 GTCGTTGGAGGAGGTGAACAT 59.998 52.381 0.00 0.00 0.00 2.71
3227 3630 0.391597 GTCGTTGGAGGAGGTGAACA 59.608 55.000 0.00 0.00 0.00 3.18
3228 3631 0.320508 GGTCGTTGGAGGAGGTGAAC 60.321 60.000 0.00 0.00 0.00 3.18
3229 3632 0.471211 AGGTCGTTGGAGGAGGTGAA 60.471 55.000 0.00 0.00 0.00 3.18
3230 3633 0.898789 GAGGTCGTTGGAGGAGGTGA 60.899 60.000 0.00 0.00 0.00 4.02
3231 3634 1.592223 GAGGTCGTTGGAGGAGGTG 59.408 63.158 0.00 0.00 0.00 4.00
3232 3635 1.609794 GGAGGTCGTTGGAGGAGGT 60.610 63.158 0.00 0.00 0.00 3.85
3233 3636 1.305381 AGGAGGTCGTTGGAGGAGG 60.305 63.158 0.00 0.00 0.00 4.30
3234 3637 1.324005 GGAGGAGGTCGTTGGAGGAG 61.324 65.000 0.00 0.00 0.00 3.69
3235 3638 1.305046 GGAGGAGGTCGTTGGAGGA 60.305 63.158 0.00 0.00 0.00 3.71
3236 3639 1.609501 TGGAGGAGGTCGTTGGAGG 60.610 63.158 0.00 0.00 0.00 4.30
3237 3640 1.185618 TGTGGAGGAGGTCGTTGGAG 61.186 60.000 0.00 0.00 0.00 3.86
3238 3641 0.544357 ATGTGGAGGAGGTCGTTGGA 60.544 55.000 0.00 0.00 0.00 3.53
3239 3642 0.324943 AATGTGGAGGAGGTCGTTGG 59.675 55.000 0.00 0.00 0.00 3.77
3240 3643 1.276421 AGAATGTGGAGGAGGTCGTTG 59.724 52.381 0.00 0.00 0.00 4.10
3241 3644 1.550976 GAGAATGTGGAGGAGGTCGTT 59.449 52.381 0.00 0.00 0.00 3.85
3242 3645 1.187087 GAGAATGTGGAGGAGGTCGT 58.813 55.000 0.00 0.00 0.00 4.34
3243 3646 1.186200 TGAGAATGTGGAGGAGGTCG 58.814 55.000 0.00 0.00 0.00 4.79
3244 3647 3.703001 TTTGAGAATGTGGAGGAGGTC 57.297 47.619 0.00 0.00 0.00 3.85
3245 3648 4.453480 TTTTTGAGAATGTGGAGGAGGT 57.547 40.909 0.00 0.00 0.00 3.85
3266 3669 3.628942 GGTACGTTGGAGAAGGTGTTTTT 59.371 43.478 0.00 0.00 32.51 1.94
3267 3670 3.208594 GGTACGTTGGAGAAGGTGTTTT 58.791 45.455 0.00 0.00 32.51 2.43
3268 3671 2.842457 GGTACGTTGGAGAAGGTGTTT 58.158 47.619 0.00 0.00 32.51 2.83
3269 3672 2.538512 GGTACGTTGGAGAAGGTGTT 57.461 50.000 0.00 0.00 32.51 3.32
3276 3679 9.714556 AAGAACTCTTTTTCGGTACGTTGGAGA 62.715 40.741 0.00 0.00 43.40 3.71
3296 3699 4.981806 TTTACAAAGCAGTGCAAGAACT 57.018 36.364 19.20 0.00 0.00 3.01
3297 3700 4.445385 CCATTTACAAAGCAGTGCAAGAAC 59.555 41.667 19.20 0.00 0.00 3.01
3302 3705 2.030007 GCTCCATTTACAAAGCAGTGCA 60.030 45.455 19.20 0.00 34.86 4.57
3303 3706 2.599659 GCTCCATTTACAAAGCAGTGC 58.400 47.619 7.13 7.13 34.86 4.40
3307 3710 2.591923 TGTGGCTCCATTTACAAAGCA 58.408 42.857 0.00 0.00 36.47 3.91
3319 3722 1.672881 GCTGTATCATGTTGTGGCTCC 59.327 52.381 0.00 0.00 0.00 4.70
3320 3723 1.672881 GGCTGTATCATGTTGTGGCTC 59.327 52.381 0.00 0.00 0.00 4.70
3349 3752 3.374042 TGTTTTTCCTGTGGAACTCCA 57.626 42.857 0.00 0.00 41.87 3.86
3354 3757 6.460399 CGAACCTATTTGTTTTTCCTGTGGAA 60.460 38.462 0.00 0.00 40.27 3.53
3391 3794 2.720254 TGCCCCCAGCTAGTACTATCTA 59.280 50.000 5.96 0.00 44.23 1.98
3416 3821 1.272212 CCTTTTGCGGGCTTGTTATGT 59.728 47.619 0.00 0.00 0.00 2.29
3463 3868 5.349817 GGCATCCAGATTACTTATGATCACG 59.650 44.000 0.00 0.00 0.00 4.35
3499 3905 1.255667 TGCCGGAGACAAGGTCTACC 61.256 60.000 5.05 4.45 43.53 3.18
3525 3931 3.461773 CGGCTGAGATGGACCGGT 61.462 66.667 6.92 6.92 41.95 5.28
3555 3961 2.895372 GGGCTTACGATGTGCCGG 60.895 66.667 0.00 0.00 46.97 6.13
3573 3979 1.251527 GGCCAAGGAGAGACGAGACA 61.252 60.000 0.00 0.00 0.00 3.41
3580 3986 3.059982 CGTGTGGCCAAGGAGAGA 58.940 61.111 7.24 0.00 0.00 3.10
3627 4033 1.298157 TTCGATGCAACTTCGCCTGG 61.298 55.000 3.32 0.00 36.56 4.45
3680 4086 1.380515 TCAGAGAAGCGAGAGGGGG 60.381 63.158 0.00 0.00 0.00 5.40
3704 4110 4.655963 AGAATCTTTGAAGCCTACTTGCA 58.344 39.130 0.00 0.00 35.82 4.08
3828 4234 4.414956 TCTCCCTCCACGGCCCAT 62.415 66.667 0.00 0.00 0.00 4.00
3888 4294 1.566298 AAGCTTCCCACCCCTGCTAG 61.566 60.000 0.00 0.00 33.28 3.42
3896 4302 2.033424 GCATATTTCGAAGCTTCCCACC 59.967 50.000 20.62 0.00 0.00 4.61
3898 4304 1.939934 CGCATATTTCGAAGCTTCCCA 59.060 47.619 20.62 4.74 0.00 4.37
3953 4359 8.494433 ACTCTACATGGCAGAAATATTTCCTAA 58.506 33.333 21.86 8.35 37.92 2.69
3954 4360 8.034313 ACTCTACATGGCAGAAATATTTCCTA 57.966 34.615 21.86 8.42 37.92 2.94
3995 4401 7.922278 GCCTGATAATCATTTAAACTGATGCAA 59.078 33.333 11.44 4.67 33.69 4.08
4001 4407 8.415553 TCCAATGCCTGATAATCATTTAAACTG 58.584 33.333 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.