Multiple sequence alignment - TraesCS3A01G220800

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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 TraesCS3A01G220800 chr3A 100.000 3737 0 0 1 3737 408950534 408946798 0.000000e+00 6902
1 TraesCS3A01G220800 chr3A 98.281 2734 22 5 1027 3737 447277495 447274764 0.000000e+00 4765
2 TraesCS3A01G220800 chr3A 93.948 727 40 3 1 723 447278217 447277491 0.000000e+00 1096
3 TraesCS3A01G220800 chr3A 92.050 478 35 3 1 476 447287089 447286613 0.000000e+00 669
4 TraesCS3A01G220800 chr3A 91.423 478 37 4 1 476 430932755 430932280 0.000000e+00 652
5 TraesCS3A01G220800 chr3A 75.913 876 148 42 1669 2505 683449635 683448784 1.260000e-104 390
6 TraesCS3A01G220800 chr3A 82.857 175 29 1 477 651 589544406 589544233 5.000000e-34 156
7 TraesCS3A01G220800 chr3D 95.045 2099 55 12 1036 3102 317550960 317553041 0.000000e+00 3254
8 TraesCS3A01G220800 chr3D 97.468 395 10 0 3144 3538 317553039 317553433 0.000000e+00 675
9 TraesCS3A01G220800 chr3D 98.182 110 1 1 3629 3737 317553430 317553539 1.370000e-44 191
10 TraesCS3A01G220800 chr3D 95.098 102 2 2 3537 3635 57354676 57354575 1.390000e-34 158
11 TraesCS3A01G220800 chr3D 95.918 98 3 1 3537 3633 582796959 582796862 1.390000e-34 158
12 TraesCS3A01G220800 chr3D 95.876 97 3 1 3537 3632 613073452 613073356 5.000000e-34 156
13 TraesCS3A01G220800 chr3D 92.208 77 6 0 647 723 317550882 317550958 3.950000e-20 110
14 TraesCS3A01G220800 chr3B 94.385 2048 56 15 1027 3041 401413765 401411744 0.000000e+00 3090
15 TraesCS3A01G220800 chr3B 95.016 321 10 1 3032 3346 401411473 401411153 2.000000e-137 499
16 TraesCS3A01G220800 chr3B 98.485 198 3 0 3341 3538 401411043 401410846 2.140000e-92 350
17 TraesCS3A01G220800 chr3B 97.248 109 3 0 3629 3737 401410849 401410741 6.370000e-43 185
18 TraesCS3A01G220800 chr3B 95.283 106 3 2 3535 3639 12406770 12406666 2.310000e-37 167
19 TraesCS3A01G220800 chr3B 94.444 108 4 2 3530 3636 220754733 220754839 8.300000e-37 165
20 TraesCS3A01G220800 chr3B 93.519 108 5 2 3530 3636 219440235 219440341 3.860000e-35 159
21 TraesCS3A01G220800 chr7A 92.389 473 34 2 1 471 251185959 251185487 0.000000e+00 673
22 TraesCS3A01G220800 chr7A 92.034 477 36 2 1 476 251159526 251159051 0.000000e+00 669
23 TraesCS3A01G220800 chr7A 96.393 305 11 0 723 1027 215187672 215187976 1.550000e-138 503
24 TraesCS3A01G220800 chr5A 90.985 477 40 3 1 476 287118041 287118515 1.130000e-179 640
25 TraesCS3A01G220800 chr5A 91.083 471 38 4 2 471 287123747 287124214 5.270000e-178 634
26 TraesCS3A01G220800 chr5A 95.161 310 15 0 720 1029 1838640 1838949 1.210000e-134 490
27 TraesCS3A01G220800 chr2A 90.776 477 42 2 2 476 223500979 223501455 1.460000e-178 636
28 TraesCS3A01G220800 chr2A 96.104 308 12 0 724 1031 306176196 306176503 1.550000e-138 503
29 TraesCS3A01G220800 chr2A 94.357 319 17 1 712 1029 612663075 612663393 4.340000e-134 488
30 TraesCS3A01G220800 chr2A 94.340 318 18 0 712 1029 612669687 612670004 4.340000e-134 488
31 TraesCS3A01G220800 chr2A 95.050 101 4 1 3533 3632 240459567 240459667 1.390000e-34 158
32 TraesCS3A01G220800 chr6A 90.566 477 43 2 2 476 351162467 351162943 6.810000e-177 630
33 TraesCS3A01G220800 chr6A 94.231 104 4 2 3537 3639 11165056 11165158 1.390000e-34 158
34 TraesCS3A01G220800 chr1A 95.806 310 13 0 720 1029 354954298 354954607 5.570000e-138 501
35 TraesCS3A01G220800 chr1A 95.000 100 4 1 3534 3632 176413054 176412955 5.000000e-34 156
36 TraesCS3A01G220800 chr1A 95.876 97 3 1 3537 3632 423909782 423909878 5.000000e-34 156
37 TraesCS3A01G220800 chr1A 93.333 105 5 2 3534 3636 324495831 324495727 1.800000e-33 154
38 TraesCS3A01G220800 chr4A 95.192 312 15 0 720 1031 681903601 681903912 9.320000e-136 494
39 TraesCS3A01G220800 chr4A 95.440 307 14 0 723 1029 17247791 17248097 1.210000e-134 490
40 TraesCS3A01G220800 chr4A 95.177 311 14 1 720 1029 146758262 146758572 1.210000e-134 490
41 TraesCS3A01G220800 chr4A 93.396 106 5 2 3537 3641 710665614 710665510 5.000000e-34 156
42 TraesCS3A01G220800 chr4B 85.747 435 51 7 1114 1538 825924 825491 2.050000e-122 449
43 TraesCS3A01G220800 chr4B 75.887 846 178 20 1661 2493 825411 824579 3.470000e-110 409
44 TraesCS3A01G220800 chr4D 85.847 431 47 8 1114 1537 1197805 1198228 2.650000e-121 446
45 TraesCS3A01G220800 chr4D 76.303 844 176 20 1655 2486 1198323 1199154 2.670000e-116 429
46 TraesCS3A01G220800 chr4D 95.000 100 4 1 3537 3635 54727324 54727225 5.000000e-34 156
47 TraesCS3A01G220800 chr4D 94.845 97 4 1 3537 3632 179707435 179707531 2.330000e-32 150
48 TraesCS3A01G220800 chr4D 93.204 103 6 1 3534 3635 213702959 213702857 2.330000e-32 150
49 TraesCS3A01G220800 chr4D 93.137 102 6 1 3533 3633 265367330 265367229 8.360000e-32 148
50 TraesCS3A01G220800 chr2B 94.393 107 4 2 3531 3636 683271070 683270965 2.990000e-36 163
51 TraesCS3A01G220800 chr6B 95.146 103 4 1 3536 3637 475446752 475446854 1.070000e-35 161
52 TraesCS3A01G220800 chr5D 95.146 103 3 2 3537 3638 29498209 29498108 1.070000e-35 161
53 TraesCS3A01G220800 chr5D 95.918 98 3 1 3537 3633 266749356 266749453 1.390000e-34 158
54 TraesCS3A01G220800 chr5D 93.333 105 6 1 3530 3633 507553610 507553714 1.800000e-33 154
55 TraesCS3A01G220800 chr5D 89.655 116 8 4 3537 3650 110786710 110786597 1.080000e-30 145
56 TraesCS3A01G220800 chr2D 95.098 102 4 1 3537 3637 442441937 442441836 3.860000e-35 159
57 TraesCS3A01G220800 chr2D 94.231 104 5 1 3535 3637 609331812 609331915 1.390000e-34 158
58 TraesCS3A01G220800 chr7D 92.793 111 5 3 3528 3635 119737458 119737348 1.390000e-34 158
59 TraesCS3A01G220800 chr6D 95.918 98 3 1 3537 3633 356602723 356602626 1.390000e-34 158
60 TraesCS3A01G220800 chr6D 95.000 100 4 1 3534 3632 73831590 73831491 5.000000e-34 156
61 TraesCS3A01G220800 chr6D 93.269 104 6 1 3530 3632 320709236 320709339 6.460000e-33 152
62 TraesCS3A01G220800 chr6D 94.898 98 4 1 3536 3632 439506381 439506478 6.460000e-33 152
63 TraesCS3A01G220800 chr6D 92.453 106 5 3 3535 3638 27764386 27764490 8.360000e-32 148
64 TraesCS3A01G220800 chr6D 93.069 101 5 2 3537 3636 217918864 217918765 3.010000e-31 147
65 TraesCS3A01G220800 chr6D 93.069 101 5 2 3537 3635 467773574 467773474 3.010000e-31 147
66 TraesCS3A01G220800 chr6D 93.000 100 6 1 3534 3632 256247074 256246975 1.080000e-30 145
67 TraesCS3A01G220800 chr6D 92.308 104 5 3 3534 3635 320709342 320709240 1.080000e-30 145
68 TraesCS3A01G220800 chr1D 95.876 97 3 1 3537 3632 275529201 275529297 5.000000e-34 156
69 TraesCS3A01G220800 chr1D 94.118 102 5 1 3534 3634 12070095 12070196 1.800000e-33 154
70 TraesCS3A01G220800 chr5B 91.743 109 7 2 3526 3633 428958892 428958999 2.330000e-32 150


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 TraesCS3A01G220800 chr3A 408946798 408950534 3736 True 6902.0 6902 100.00000 1 3737 1 chr3A.!!$R1 3736
1 TraesCS3A01G220800 chr3A 447274764 447278217 3453 True 2930.5 4765 96.11450 1 3737 2 chr3A.!!$R6 3736
2 TraesCS3A01G220800 chr3A 683448784 683449635 851 True 390.0 390 75.91300 1669 2505 1 chr3A.!!$R5 836
3 TraesCS3A01G220800 chr3D 317550882 317553539 2657 False 1057.5 3254 95.72575 647 3737 4 chr3D.!!$F1 3090
4 TraesCS3A01G220800 chr3B 401410741 401413765 3024 True 1031.0 3090 96.28350 1027 3737 4 chr3B.!!$R2 2710
5 TraesCS3A01G220800 chr4B 824579 825924 1345 True 429.0 449 80.81700 1114 2493 2 chr4B.!!$R1 1379
6 TraesCS3A01G220800 chr4D 1197805 1199154 1349 False 437.5 446 81.07500 1114 2486 2 chr4D.!!$F2 1372

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
55 56 0.040067 GCAGGCGAAGACCACTTTTG 60.040 55.0 0.0 0.0 31.70 2.44 F
383 385 0.456628 GTCGAGTTAGGCCCTGAGAC 59.543 60.0 0.0 0.0 0.00 3.36 F
723 728 0.532862 ACTGACGGCAACAACCTCAG 60.533 55.0 0.0 0.0 39.19 3.35 F
730 735 0.538287 GCAACAACCTCAGGCCTCTT 60.538 55.0 0.0 0.0 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1022 1027 0.031616 ATGGAGGAGGGTGAGGACTC 60.032 60.000 0.00 0.0 0.0 3.36 R
1286 1310 2.435938 GAACCCTTGGCGCATCGA 60.436 61.111 10.83 0.0 0.0 3.59 R
2520 2606 1.831106 AGAACATGTACTCGGCCATGA 59.169 47.619 2.24 0.0 40.7 3.07 R
3621 4111 3.010361 ACCTGGTCTATATACTCCCTCCG 59.990 52.174 0.00 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
55 56 0.040067 GCAGGCGAAGACCACTTTTG 60.040 55.000 0.00 0.00 31.70 2.44
60 61 0.865769 CGAAGACCACTTTTGTCCGG 59.134 55.000 0.00 0.00 36.39 5.14
86 87 4.593634 AGCTTGTACTAGTTGTCTCCCTTT 59.406 41.667 0.00 0.00 0.00 3.11
87 88 5.778750 AGCTTGTACTAGTTGTCTCCCTTTA 59.221 40.000 0.00 0.00 0.00 1.85
136 137 3.561725 CGCTCAATATTTGGGAAGAGGAC 59.438 47.826 0.00 0.00 30.85 3.85
167 168 6.722129 CCTCTATAAGTAGAACTAGCCACCAT 59.278 42.308 0.00 0.00 36.54 3.55
169 170 3.802948 AAGTAGAACTAGCCACCATCG 57.197 47.619 0.00 0.00 0.00 3.84
245 246 3.187211 CCTCGCGAGGCTATTCTTC 57.813 57.895 39.83 0.00 42.44 2.87
255 256 4.141914 CGAGGCTATTCTTCCCTTGTACTT 60.142 45.833 0.00 0.00 0.00 2.24
313 315 9.275660 CCACATTGGAGTAGGGTATTACACCAT 62.276 44.444 3.74 0.00 44.83 3.55
347 349 6.432783 CCCAAACCAGTATAAATCTTGTGTCA 59.567 38.462 0.00 0.00 0.00 3.58
383 385 0.456628 GTCGAGTTAGGCCCTGAGAC 59.543 60.000 0.00 0.00 0.00 3.36
388 390 0.745468 GTTAGGCCCTGAGACCGTAG 59.255 60.000 0.00 0.00 0.00 3.51
483 485 1.472878 CCGAAATCTGACAGGTCTCGA 59.527 52.381 13.03 3.00 0.00 4.04
504 506 1.536284 CGGTGTCGGAGCTTTAGATCC 60.536 57.143 3.95 3.95 46.58 3.36
515 517 6.773080 GGAGCTTTAGATCCTTTTACGAAAC 58.227 40.000 6.79 0.00 46.53 2.78
521 523 9.635520 CTTTAGATCCTTTTACGAAACAGTAGA 57.364 33.333 0.00 0.00 0.00 2.59
553 555 5.823312 TCTAAGATGTAGGAGTGGTGTGTA 58.177 41.667 0.00 0.00 0.00 2.90
560 562 0.831307 GGAGTGGTGTGTATCCCTCC 59.169 60.000 0.00 0.00 36.26 4.30
564 566 2.091499 AGTGGTGTGTATCCCTCCGATA 60.091 50.000 0.00 0.00 31.92 2.92
574 576 8.602424 TGTGTATCCCTCCGATATTTTATTCAT 58.398 33.333 0.00 0.00 35.87 2.57
585 587 9.973246 CCGATATTTTATTCATATCTTGTTCGG 57.027 33.333 0.00 0.00 33.17 4.30
609 611 6.206829 GGACTTTTGTACATAAACTTCTGCCT 59.793 38.462 0.00 0.00 32.22 4.75
628 631 6.036735 TCTGCCTTCTATAAAACAACGTATGC 59.963 38.462 0.00 0.00 0.00 3.14
723 728 0.532862 ACTGACGGCAACAACCTCAG 60.533 55.000 0.00 0.00 39.19 3.35
724 729 1.227823 TGACGGCAACAACCTCAGG 60.228 57.895 0.00 0.00 0.00 3.86
725 730 2.594592 ACGGCAACAACCTCAGGC 60.595 61.111 0.00 0.00 0.00 4.85
726 731 3.365265 CGGCAACAACCTCAGGCC 61.365 66.667 0.00 0.00 41.20 5.19
727 732 2.116125 GGCAACAACCTCAGGCCT 59.884 61.111 0.00 0.00 41.39 5.19
728 733 1.973812 GGCAACAACCTCAGGCCTC 60.974 63.158 0.00 0.00 41.39 4.70
729 734 1.073897 GCAACAACCTCAGGCCTCT 59.926 57.895 0.00 0.00 0.00 3.69
730 735 0.538287 GCAACAACCTCAGGCCTCTT 60.538 55.000 0.00 0.00 0.00 2.85
731 736 1.986882 CAACAACCTCAGGCCTCTTT 58.013 50.000 0.00 0.00 0.00 2.52
732 737 2.310538 CAACAACCTCAGGCCTCTTTT 58.689 47.619 0.00 0.00 0.00 2.27
733 738 1.986882 ACAACCTCAGGCCTCTTTTG 58.013 50.000 0.00 6.83 0.00 2.44
734 739 1.251251 CAACCTCAGGCCTCTTTTGG 58.749 55.000 0.00 3.15 0.00 3.28
735 740 0.853530 AACCTCAGGCCTCTTTTGGT 59.146 50.000 0.00 3.87 0.00 3.67
736 741 0.853530 ACCTCAGGCCTCTTTTGGTT 59.146 50.000 0.00 0.00 0.00 3.67
737 742 1.202940 ACCTCAGGCCTCTTTTGGTTC 60.203 52.381 0.00 0.00 0.00 3.62
738 743 1.202927 CCTCAGGCCTCTTTTGGTTCA 60.203 52.381 0.00 0.00 0.00 3.18
739 744 2.556114 CCTCAGGCCTCTTTTGGTTCAT 60.556 50.000 0.00 0.00 0.00 2.57
740 745 3.308402 CCTCAGGCCTCTTTTGGTTCATA 60.308 47.826 0.00 0.00 0.00 2.15
741 746 3.944015 CTCAGGCCTCTTTTGGTTCATAG 59.056 47.826 0.00 0.00 0.00 2.23
742 747 3.019564 CAGGCCTCTTTTGGTTCATAGG 58.980 50.000 0.00 0.00 0.00 2.57
743 748 2.919602 AGGCCTCTTTTGGTTCATAGGA 59.080 45.455 0.00 0.00 0.00 2.94
744 749 3.529319 AGGCCTCTTTTGGTTCATAGGAT 59.471 43.478 0.00 0.00 0.00 3.24
745 750 4.726825 AGGCCTCTTTTGGTTCATAGGATA 59.273 41.667 0.00 0.00 0.00 2.59
746 751 5.066593 GGCCTCTTTTGGTTCATAGGATAG 58.933 45.833 0.00 0.00 0.00 2.08
747 752 5.066593 GCCTCTTTTGGTTCATAGGATAGG 58.933 45.833 0.00 0.00 0.00 2.57
748 753 5.163195 GCCTCTTTTGGTTCATAGGATAGGA 60.163 44.000 0.00 0.00 0.00 2.94
749 754 6.466470 GCCTCTTTTGGTTCATAGGATAGGAT 60.466 42.308 0.00 0.00 28.27 3.24
750 755 7.521669 CCTCTTTTGGTTCATAGGATAGGATT 58.478 38.462 0.00 0.00 28.27 3.01
751 756 8.660435 CCTCTTTTGGTTCATAGGATAGGATTA 58.340 37.037 0.00 0.00 28.27 1.75
758 763 9.439461 TGGTTCATAGGATAGGATTATCATAGG 57.561 37.037 0.00 0.00 36.37 2.57
759 764 9.661954 GGTTCATAGGATAGGATTATCATAGGA 57.338 37.037 0.00 1.09 39.88 2.94
782 787 9.413734 AGGAATAGGAATTTTGTAGGAAATGAG 57.586 33.333 0.00 0.00 30.06 2.90
783 788 9.408648 GGAATAGGAATTTTGTAGGAAATGAGA 57.591 33.333 0.00 0.00 30.06 3.27
786 791 7.651027 AGGAATTTTGTAGGAAATGAGATGG 57.349 36.000 0.00 0.00 30.06 3.51
787 792 6.097412 AGGAATTTTGTAGGAAATGAGATGGC 59.903 38.462 0.00 0.00 30.06 4.40
788 793 6.127366 GGAATTTTGTAGGAAATGAGATGGCA 60.127 38.462 0.00 0.00 30.06 4.92
789 794 7.418254 GGAATTTTGTAGGAAATGAGATGGCAT 60.418 37.037 0.00 0.00 30.06 4.40
790 795 5.840243 TTTGTAGGAAATGAGATGGCATG 57.160 39.130 3.81 0.00 0.00 4.06
791 796 4.508551 TGTAGGAAATGAGATGGCATGT 57.491 40.909 3.81 0.00 0.00 3.21
792 797 5.628797 TGTAGGAAATGAGATGGCATGTA 57.371 39.130 3.81 0.00 0.00 2.29
793 798 6.191657 TGTAGGAAATGAGATGGCATGTAT 57.808 37.500 3.81 0.00 0.00 2.29
794 799 6.233434 TGTAGGAAATGAGATGGCATGTATC 58.767 40.000 3.81 0.45 0.00 2.24
795 800 5.579753 AGGAAATGAGATGGCATGTATCT 57.420 39.130 3.81 12.53 37.59 1.98
796 801 5.558818 AGGAAATGAGATGGCATGTATCTC 58.441 41.667 23.83 23.83 46.82 2.75
802 807 5.876612 GAGATGGCATGTATCTCAAATCC 57.123 43.478 24.83 4.94 46.22 3.01
803 808 5.558818 GAGATGGCATGTATCTCAAATCCT 58.441 41.667 24.83 0.00 46.22 3.24
804 809 6.692849 AGATGGCATGTATCTCAAATCCTA 57.307 37.500 3.81 0.00 29.05 2.94
805 810 7.268212 AGATGGCATGTATCTCAAATCCTAT 57.732 36.000 3.81 0.00 29.05 2.57
806 811 7.110810 AGATGGCATGTATCTCAAATCCTATG 58.889 38.462 3.81 0.00 29.05 2.23
807 812 6.438186 TGGCATGTATCTCAAATCCTATGA 57.562 37.500 0.00 0.00 0.00 2.15
808 813 6.470278 TGGCATGTATCTCAAATCCTATGAG 58.530 40.000 0.00 0.00 44.53 2.90
809 814 6.043590 TGGCATGTATCTCAAATCCTATGAGT 59.956 38.462 3.72 0.00 43.77 3.41
810 815 7.235399 TGGCATGTATCTCAAATCCTATGAGTA 59.765 37.037 3.72 0.00 43.77 2.59
811 816 7.763528 GGCATGTATCTCAAATCCTATGAGTAG 59.236 40.741 3.72 0.00 43.77 2.57
830 835 9.606631 ATGAGTAGGAATAAGAAACAAGATGTC 57.393 33.333 0.00 0.00 0.00 3.06
831 836 8.593679 TGAGTAGGAATAAGAAACAAGATGTCA 58.406 33.333 0.00 0.00 0.00 3.58
832 837 9.606631 GAGTAGGAATAAGAAACAAGATGTCAT 57.393 33.333 0.00 0.00 0.00 3.06
833 838 9.965902 AGTAGGAATAAGAAACAAGATGTCATT 57.034 29.630 0.00 0.00 0.00 2.57
836 841 8.526147 AGGAATAAGAAACAAGATGTCATTTGG 58.474 33.333 10.50 0.00 0.00 3.28
837 842 8.306761 GGAATAAGAAACAAGATGTCATTTGGT 58.693 33.333 10.50 3.75 0.00 3.67
838 843 9.696917 GAATAAGAAACAAGATGTCATTTGGTT 57.303 29.630 9.41 9.41 36.95 3.67
839 844 9.480053 AATAAGAAACAAGATGTCATTTGGTTG 57.520 29.630 12.70 6.32 34.55 3.77
840 845 6.713762 AGAAACAAGATGTCATTTGGTTGA 57.286 33.333 12.70 0.00 34.55 3.18
841 846 6.507023 AGAAACAAGATGTCATTTGGTTGAC 58.493 36.000 12.70 0.00 45.05 3.18
877 882 7.765695 TTTTTCATTGAGTCTAGGCTCATTT 57.234 32.000 26.91 15.12 43.99 2.32
878 883 7.765695 TTTTCATTGAGTCTAGGCTCATTTT 57.234 32.000 26.91 12.69 43.99 1.82
879 884 7.765695 TTTCATTGAGTCTAGGCTCATTTTT 57.234 32.000 26.91 10.30 43.99 1.94
880 885 8.862325 TTTCATTGAGTCTAGGCTCATTTTTA 57.138 30.769 26.91 12.75 43.99 1.52
881 886 9.466497 TTTCATTGAGTCTAGGCTCATTTTTAT 57.534 29.630 26.91 14.49 43.99 1.40
882 887 9.466497 TTCATTGAGTCTAGGCTCATTTTTATT 57.534 29.630 26.91 4.66 43.99 1.40
883 888 9.466497 TCATTGAGTCTAGGCTCATTTTTATTT 57.534 29.630 26.91 3.37 43.99 1.40
886 891 8.281212 TGAGTCTAGGCTCATTTTTATTTTCC 57.719 34.615 23.07 0.00 40.23 3.13
887 892 8.109634 TGAGTCTAGGCTCATTTTTATTTTCCT 58.890 33.333 23.07 0.00 40.23 3.36
888 893 9.614792 GAGTCTAGGCTCATTTTTATTTTCCTA 57.385 33.333 19.57 0.00 35.67 2.94
910 915 8.826765 TCCTATGAAATATGGAAGATAGGAACC 58.173 37.037 0.00 0.00 38.86 3.62
911 916 8.605947 CCTATGAAATATGGAAGATAGGAACCA 58.394 37.037 0.00 0.00 36.16 3.67
914 919 8.924511 TGAAATATGGAAGATAGGAACCAATC 57.075 34.615 0.00 0.00 36.00 2.67
955 960 8.829373 AATCTATTCCTATGAACAAAAAGGCT 57.171 30.769 0.00 0.00 32.13 4.58
956 961 8.829373 ATCTATTCCTATGAACAAAAAGGCTT 57.171 30.769 0.00 0.00 32.13 4.35
957 962 8.650143 TCTATTCCTATGAACAAAAAGGCTTT 57.350 30.769 6.68 6.68 32.13 3.51
958 963 9.747898 TCTATTCCTATGAACAAAAAGGCTTTA 57.252 29.630 13.77 0.00 32.13 1.85
961 966 9.710900 ATTCCTATGAACAAAAAGGCTTTAAAG 57.289 29.630 13.77 11.02 32.13 1.85
962 967 7.666623 TCCTATGAACAAAAAGGCTTTAAAGG 58.333 34.615 13.77 10.67 0.00 3.11
963 968 7.507616 TCCTATGAACAAAAAGGCTTTAAAGGA 59.492 33.333 13.77 12.54 0.00 3.36
964 969 8.147704 CCTATGAACAAAAAGGCTTTAAAGGAA 58.852 33.333 13.77 0.00 0.00 3.36
965 970 9.541143 CTATGAACAAAAAGGCTTTAAAGGAAA 57.459 29.630 13.77 0.00 0.00 3.13
966 971 8.800370 ATGAACAAAAAGGCTTTAAAGGAAAA 57.200 26.923 13.77 0.00 0.00 2.29
967 972 8.622948 TGAACAAAAAGGCTTTAAAGGAAAAA 57.377 26.923 13.77 0.00 0.00 1.94
1011 1016 9.853177 TCCTCTAAAATTCCTATGAAATTCCTC 57.147 33.333 0.00 0.00 33.32 3.71
1012 1017 9.072375 CCTCTAAAATTCCTATGAAATTCCTCC 57.928 37.037 0.00 0.00 33.32 4.30
1013 1018 9.632638 CTCTAAAATTCCTATGAAATTCCTCCA 57.367 33.333 0.00 0.00 33.32 3.86
1014 1019 9.989296 TCTAAAATTCCTATGAAATTCCTCCAA 57.011 29.630 0.00 0.00 33.32 3.53
1017 1022 7.423844 AATTCCTATGAAATTCCTCCAAACC 57.576 36.000 0.00 0.00 33.32 3.27
1018 1023 5.528600 TCCTATGAAATTCCTCCAAACCA 57.471 39.130 0.00 0.00 0.00 3.67
1019 1024 5.898120 TCCTATGAAATTCCTCCAAACCAA 58.102 37.500 0.00 0.00 0.00 3.67
1020 1025 6.318913 TCCTATGAAATTCCTCCAAACCAAA 58.681 36.000 0.00 0.00 0.00 3.28
1021 1026 6.437162 TCCTATGAAATTCCTCCAAACCAAAG 59.563 38.462 0.00 0.00 0.00 2.77
1022 1027 4.953940 TGAAATTCCTCCAAACCAAAGG 57.046 40.909 0.00 0.00 0.00 3.11
1023 1028 4.551671 TGAAATTCCTCCAAACCAAAGGA 58.448 39.130 0.00 0.00 37.42 3.36
1031 1036 2.158667 TCCAAACCAAAGGAGTCCTCAC 60.159 50.000 13.43 0.00 30.89 3.51
1074 1079 2.733945 GGGAAGCGCCAAAGCAAA 59.266 55.556 2.29 0.00 39.83 3.68
1582 1631 3.055591 CTCATCTCGATCCAATCCAACG 58.944 50.000 0.00 0.00 0.00 4.10
2520 2606 0.964358 GCTGGATGCTGCTTCTTGGT 60.964 55.000 14.20 0.00 38.95 3.67
3174 3546 5.925397 CAGCTATCTGTCACTATTCACCATC 59.075 44.000 0.00 0.00 35.61 3.51
3201 3573 7.555306 GGTATTCACCTTTATCTTCTTCACC 57.445 40.000 0.00 0.00 42.11 4.02
3621 4111 7.433680 ACAAATTGAGTCACTTATTTTGGGAC 58.566 34.615 16.81 0.00 30.25 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.770110 AAGGGCTCTGGTGGTGACA 60.770 57.895 0.00 0.00 38.70 3.58
55 56 4.097589 ACAACTAGTACAAGCTATCCGGAC 59.902 45.833 6.12 0.00 0.00 4.79
60 61 5.595133 AGGGAGACAACTAGTACAAGCTATC 59.405 44.000 0.00 0.00 0.00 2.08
86 87 1.996798 TCCCACAACGGCCAAATTTA 58.003 45.000 2.24 0.00 0.00 1.40
87 88 1.275010 GATCCCACAACGGCCAAATTT 59.725 47.619 2.24 0.00 0.00 1.82
136 137 4.484912 AGTTCTACTTATAGAGGCCCTGG 58.515 47.826 0.00 0.00 38.69 4.45
167 168 0.340558 TTGGAATCCCCCTCCTACGA 59.659 55.000 0.00 0.00 33.77 3.43
169 170 2.707554 AGATTGGAATCCCCCTCCTAC 58.292 52.381 0.00 0.00 36.04 3.18
239 240 5.953571 AGGACAAAAGTACAAGGGAAGAAT 58.046 37.500 0.00 0.00 0.00 2.40
245 246 2.814336 GCTGAGGACAAAAGTACAAGGG 59.186 50.000 0.00 0.00 0.00 3.95
317 319 5.506708 AGATTTATACTGGTTTGGGTCACC 58.493 41.667 0.00 0.00 34.52 4.02
325 327 8.514594 CATGTGACACAAGATTTATACTGGTTT 58.485 33.333 13.23 0.00 0.00 3.27
347 349 1.871039 CGACGAACCCAAAGAACATGT 59.129 47.619 0.00 0.00 0.00 3.21
383 385 2.703425 CTAGCTCGCGCACTCTACGG 62.703 65.000 8.75 0.00 39.10 4.02
388 390 1.585002 CACTCTAGCTCGCGCACTC 60.585 63.158 8.75 0.00 39.10 3.51
405 407 1.330655 GCACGAAGATCTCTCCCCCA 61.331 60.000 0.00 0.00 0.00 4.96
408 410 1.590259 GCGCACGAAGATCTCTCCC 60.590 63.158 0.30 0.00 0.00 4.30
471 473 1.512996 GACACCGTCGAGACCTGTCA 61.513 60.000 17.20 0.00 36.37 3.58
483 485 1.134560 GATCTAAAGCTCCGACACCGT 59.865 52.381 0.00 0.00 0.00 4.83
504 506 9.460906 AAGACTTAGTCTACTGTTTCGTAAAAG 57.539 33.333 15.83 0.00 42.59 2.27
513 515 9.523168 ACATCTTAGAAGACTTAGTCTACTGTT 57.477 33.333 15.83 0.00 42.59 3.16
521 523 7.558444 CCACTCCTACATCTTAGAAGACTTAGT 59.442 40.741 0.00 0.00 37.98 2.24
538 540 2.694109 GAGGGATACACACCACTCCTAC 59.306 54.545 0.00 0.00 39.74 3.18
541 543 0.831307 GGAGGGATACACACCACTCC 59.169 60.000 0.00 0.00 37.54 3.85
574 576 9.491675 TTTATGTACAAAAGTCCGAACAAGATA 57.508 29.630 0.00 0.00 0.00 1.98
585 587 7.203255 AGGCAGAAGTTTATGTACAAAAGTC 57.797 36.000 0.00 3.55 0.00 3.01
609 611 7.476667 CCAATGGCATACGTTGTTTTATAGAA 58.523 34.615 0.00 0.00 43.17 2.10
655 660 5.502079 TCACTTCTGGTTTGAAAGTGGTTA 58.498 37.500 12.89 0.00 31.94 2.85
703 708 0.753867 TGAGGTTGTTGCCGTCAGTA 59.246 50.000 0.00 0.00 0.00 2.74
723 728 3.366052 TCCTATGAACCAAAAGAGGCC 57.634 47.619 0.00 0.00 0.00 5.19
724 729 5.066593 CCTATCCTATGAACCAAAAGAGGC 58.933 45.833 0.00 0.00 0.00 4.70
725 730 6.500589 TCCTATCCTATGAACCAAAAGAGG 57.499 41.667 0.00 0.00 0.00 3.69
732 737 9.439461 CCTATGATAATCCTATCCTATGAACCA 57.561 37.037 0.00 0.00 34.10 3.67
733 738 9.661954 TCCTATGATAATCCTATCCTATGAACC 57.338 37.037 0.00 0.00 34.10 3.62
756 761 9.413734 CTCATTTCCTACAAAATTCCTATTCCT 57.586 33.333 0.00 0.00 0.00 3.36
757 762 9.408648 TCTCATTTCCTACAAAATTCCTATTCC 57.591 33.333 0.00 0.00 0.00 3.01
760 765 9.359653 CCATCTCATTTCCTACAAAATTCCTAT 57.640 33.333 0.00 0.00 0.00 2.57
761 766 7.285401 GCCATCTCATTTCCTACAAAATTCCTA 59.715 37.037 0.00 0.00 0.00 2.94
762 767 6.097412 GCCATCTCATTTCCTACAAAATTCCT 59.903 38.462 0.00 0.00 0.00 3.36
763 768 6.127366 TGCCATCTCATTTCCTACAAAATTCC 60.127 38.462 0.00 0.00 0.00 3.01
764 769 6.866480 TGCCATCTCATTTCCTACAAAATTC 58.134 36.000 0.00 0.00 0.00 2.17
765 770 6.855763 TGCCATCTCATTTCCTACAAAATT 57.144 33.333 0.00 0.00 0.00 1.82
766 771 6.381994 ACATGCCATCTCATTTCCTACAAAAT 59.618 34.615 0.00 0.00 0.00 1.82
767 772 5.716228 ACATGCCATCTCATTTCCTACAAAA 59.284 36.000 0.00 0.00 0.00 2.44
768 773 5.263599 ACATGCCATCTCATTTCCTACAAA 58.736 37.500 0.00 0.00 0.00 2.83
769 774 4.858850 ACATGCCATCTCATTTCCTACAA 58.141 39.130 0.00 0.00 0.00 2.41
770 775 4.508551 ACATGCCATCTCATTTCCTACA 57.491 40.909 0.00 0.00 0.00 2.74
771 776 6.471146 AGATACATGCCATCTCATTTCCTAC 58.529 40.000 4.89 0.00 0.00 3.18
772 777 6.692849 AGATACATGCCATCTCATTTCCTA 57.307 37.500 4.89 0.00 0.00 2.94
773 778 5.558818 GAGATACATGCCATCTCATTTCCT 58.441 41.667 23.49 0.00 45.17 3.36
774 779 5.876612 GAGATACATGCCATCTCATTTCC 57.123 43.478 23.49 5.23 45.17 3.13
780 785 5.558818 AGGATTTGAGATACATGCCATCTC 58.441 41.667 22.40 22.40 45.76 2.75
781 786 5.579753 AGGATTTGAGATACATGCCATCT 57.420 39.130 9.57 9.57 35.43 2.90
782 787 7.108194 TCATAGGATTTGAGATACATGCCATC 58.892 38.462 0.00 0.00 0.00 3.51
783 788 7.024345 TCATAGGATTTGAGATACATGCCAT 57.976 36.000 0.00 0.00 0.00 4.40
784 789 6.043590 ACTCATAGGATTTGAGATACATGCCA 59.956 38.462 7.63 0.00 42.63 4.92
785 790 6.471146 ACTCATAGGATTTGAGATACATGCC 58.529 40.000 7.63 0.00 42.63 4.40
786 791 8.700722 CTACTCATAGGATTTGAGATACATGC 57.299 38.462 7.63 0.00 42.63 4.06
804 809 9.606631 GACATCTTGTTTCTTATTCCTACTCAT 57.393 33.333 0.00 0.00 0.00 2.90
805 810 8.593679 TGACATCTTGTTTCTTATTCCTACTCA 58.406 33.333 0.00 0.00 0.00 3.41
806 811 9.606631 ATGACATCTTGTTTCTTATTCCTACTC 57.393 33.333 0.00 0.00 0.00 2.59
807 812 9.965902 AATGACATCTTGTTTCTTATTCCTACT 57.034 29.630 0.00 0.00 0.00 2.57
810 815 8.526147 CCAAATGACATCTTGTTTCTTATTCCT 58.474 33.333 0.00 0.00 0.00 3.36
811 816 8.306761 ACCAAATGACATCTTGTTTCTTATTCC 58.693 33.333 0.00 0.00 0.00 3.01
812 817 9.696917 AACCAAATGACATCTTGTTTCTTATTC 57.303 29.630 0.00 0.00 0.00 1.75
813 818 9.480053 CAACCAAATGACATCTTGTTTCTTATT 57.520 29.630 0.00 0.00 0.00 1.40
814 819 8.859090 TCAACCAAATGACATCTTGTTTCTTAT 58.141 29.630 0.00 0.00 0.00 1.73
815 820 8.231692 TCAACCAAATGACATCTTGTTTCTTA 57.768 30.769 0.00 0.00 0.00 2.10
816 821 7.111247 TCAACCAAATGACATCTTGTTTCTT 57.889 32.000 0.00 0.00 0.00 2.52
817 822 6.713762 TCAACCAAATGACATCTTGTTTCT 57.286 33.333 0.00 0.00 0.00 2.52
862 867 8.512966 AGGAAAATAAAAATGAGCCTAGACTC 57.487 34.615 0.00 0.00 37.19 3.36
884 889 8.826765 GGTTCCTATCTTCCATATTTCATAGGA 58.173 37.037 2.01 2.01 39.98 2.94
885 890 8.605947 TGGTTCCTATCTTCCATATTTCATAGG 58.394 37.037 0.00 0.00 35.93 2.57
888 893 9.525826 GATTGGTTCCTATCTTCCATATTTCAT 57.474 33.333 6.14 0.00 0.00 2.57
889 894 7.944554 GGATTGGTTCCTATCTTCCATATTTCA 59.055 37.037 11.60 0.00 41.78 2.69
890 895 8.341892 GGATTGGTTCCTATCTTCCATATTTC 57.658 38.462 11.60 0.00 41.78 2.17
905 910 7.974504 TCCTATTTCTACATAGGATTGGTTCC 58.025 38.462 5.49 0.00 46.83 3.62
929 934 8.907885 AGCCTTTTTGTTCATAGGAATAGATTC 58.092 33.333 0.00 0.00 35.05 2.52
930 935 8.829373 AGCCTTTTTGTTCATAGGAATAGATT 57.171 30.769 0.00 0.00 35.05 2.40
931 936 8.829373 AAGCCTTTTTGTTCATAGGAATAGAT 57.171 30.769 0.00 0.00 35.05 1.98
932 937 8.650143 AAAGCCTTTTTGTTCATAGGAATAGA 57.350 30.769 0.00 0.00 35.05 1.98
935 940 9.710900 CTTTAAAGCCTTTTTGTTCATAGGAAT 57.289 29.630 1.47 0.00 35.05 3.01
936 941 8.147704 CCTTTAAAGCCTTTTTGTTCATAGGAA 58.852 33.333 9.86 0.00 0.00 3.36
937 942 7.507616 TCCTTTAAAGCCTTTTTGTTCATAGGA 59.492 33.333 9.86 0.00 0.00 2.94
938 943 7.666623 TCCTTTAAAGCCTTTTTGTTCATAGG 58.333 34.615 9.86 0.00 0.00 2.57
939 944 9.541143 TTTCCTTTAAAGCCTTTTTGTTCATAG 57.459 29.630 9.86 0.00 0.00 2.23
940 945 9.892130 TTTTCCTTTAAAGCCTTTTTGTTCATA 57.108 25.926 9.86 0.00 0.00 2.15
941 946 8.800370 TTTTCCTTTAAAGCCTTTTTGTTCAT 57.200 26.923 9.86 0.00 0.00 2.57
942 947 8.622948 TTTTTCCTTTAAAGCCTTTTTGTTCA 57.377 26.923 9.86 0.00 0.00 3.18
985 990 9.853177 GAGGAATTTCATAGGAATTTTAGAGGA 57.147 33.333 0.00 0.00 31.93 3.71
986 991 9.072375 GGAGGAATTTCATAGGAATTTTAGAGG 57.928 37.037 0.00 0.00 31.93 3.69
987 992 9.632638 TGGAGGAATTTCATAGGAATTTTAGAG 57.367 33.333 0.00 0.00 31.93 2.43
988 993 9.989296 TTGGAGGAATTTCATAGGAATTTTAGA 57.011 29.630 0.00 0.00 31.93 2.10
991 996 8.321353 GGTTTGGAGGAATTTCATAGGAATTTT 58.679 33.333 0.00 0.00 31.93 1.82
992 997 7.457535 TGGTTTGGAGGAATTTCATAGGAATTT 59.542 33.333 0.00 0.00 31.93 1.82
993 998 6.959366 TGGTTTGGAGGAATTTCATAGGAATT 59.041 34.615 0.00 0.00 31.93 2.17
994 999 6.502138 TGGTTTGGAGGAATTTCATAGGAAT 58.498 36.000 0.00 0.00 31.93 3.01
995 1000 5.898120 TGGTTTGGAGGAATTTCATAGGAA 58.102 37.500 0.00 0.00 0.00 3.36
996 1001 5.528600 TGGTTTGGAGGAATTTCATAGGA 57.471 39.130 0.00 0.00 0.00 2.94
997 1002 6.351286 CCTTTGGTTTGGAGGAATTTCATAGG 60.351 42.308 0.00 0.00 32.11 2.57
998 1003 6.437162 TCCTTTGGTTTGGAGGAATTTCATAG 59.563 38.462 0.00 0.00 36.67 2.23
999 1004 6.318913 TCCTTTGGTTTGGAGGAATTTCATA 58.681 36.000 0.00 0.00 36.67 2.15
1000 1005 5.154418 TCCTTTGGTTTGGAGGAATTTCAT 58.846 37.500 0.00 0.00 36.67 2.57
1001 1006 4.551671 TCCTTTGGTTTGGAGGAATTTCA 58.448 39.130 0.00 0.00 36.67 2.69
1002 1007 5.139435 CTCCTTTGGTTTGGAGGAATTTC 57.861 43.478 0.00 0.00 44.44 2.17
1010 1015 2.131854 TGAGGACTCCTTTGGTTTGGA 58.868 47.619 0.00 0.00 31.76 3.53
1011 1016 2.230660 GTGAGGACTCCTTTGGTTTGG 58.769 52.381 0.00 0.00 31.76 3.28
1012 1017 2.230660 GGTGAGGACTCCTTTGGTTTG 58.769 52.381 0.00 0.00 31.76 2.93
1013 1018 1.145119 GGGTGAGGACTCCTTTGGTTT 59.855 52.381 0.00 0.00 31.76 3.27
1014 1019 0.771755 GGGTGAGGACTCCTTTGGTT 59.228 55.000 0.00 0.00 31.76 3.67
1015 1020 0.104409 AGGGTGAGGACTCCTTTGGT 60.104 55.000 0.00 0.00 31.76 3.67
1016 1021 0.615850 GAGGGTGAGGACTCCTTTGG 59.384 60.000 0.00 0.00 31.76 3.28
1022 1027 0.031616 ATGGAGGAGGGTGAGGACTC 60.032 60.000 0.00 0.00 0.00 3.36
1023 1028 0.419459 AATGGAGGAGGGTGAGGACT 59.581 55.000 0.00 0.00 0.00 3.85
1024 1029 0.833949 GAATGGAGGAGGGTGAGGAC 59.166 60.000 0.00 0.00 0.00 3.85
1025 1030 0.417437 TGAATGGAGGAGGGTGAGGA 59.583 55.000 0.00 0.00 0.00 3.71
1031 1036 2.715336 AGGAATGATGAATGGAGGAGGG 59.285 50.000 0.00 0.00 0.00 4.30
1286 1310 2.435938 GAACCCTTGGCGCATCGA 60.436 61.111 10.83 0.00 0.00 3.59
1582 1631 3.495001 CGTCTGGGTCTTGTTTCTCTTTC 59.505 47.826 0.00 0.00 0.00 2.62
2520 2606 1.831106 AGAACATGTACTCGGCCATGA 59.169 47.619 2.24 0.00 40.70 3.07
3621 4111 3.010361 ACCTGGTCTATATACTCCCTCCG 59.990 52.174 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.