Multiple sequence alignment - TraesCS7B01G084300

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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 TraesCS7B01G084300 chr7B 100.000 2972 0 0 1 2972 95047429 95044458 0.000000e+00 5489.0
1 TraesCS7B01G084300 chr7B 94.939 1225 60 2 859 2082 94811074 94809851 0.000000e+00 1917.0
2 TraesCS7B01G084300 chr7B 95.783 498 21 0 2475 2972 713549361 713548864 0.000000e+00 804.0
3 TraesCS7B01G084300 chr7B 83.361 607 89 6 3 598 6005222 6004617 4.330000e-153 551.0
4 TraesCS7B01G084300 chr7B 92.946 241 17 0 2204 2444 94808823 94808583 4.710000e-93 351.0
5 TraesCS7B01G084300 chr7B 90.204 245 21 3 908 1150 94922136 94921893 1.720000e-82 316.0
6 TraesCS7B01G084300 chr7B 94.203 69 2 1 2082 2148 94809322 94809254 1.460000e-18 104.0
7 TraesCS7B01G084300 chr7A 93.554 1722 81 14 739 2441 132618771 132620481 0.000000e+00 2538.0
8 TraesCS7B01G084300 chr7A 93.992 1315 65 5 861 2172 132411778 132410475 0.000000e+00 1978.0
9 TraesCS7B01G084300 chr7A 97.436 117 3 0 1189 1305 216416045 216416161 1.810000e-47 200.0
10 TraesCS7B01G084300 chr7D 92.741 1722 82 18 739 2444 133826991 133828685 0.000000e+00 2447.0
11 TraesCS7B01G084300 chr7D 94.100 1322 64 8 859 2176 133491999 133493310 0.000000e+00 1997.0
12 TraesCS7B01G084300 chr7D 93.797 1322 68 8 859 2176 133612500 133611189 0.000000e+00 1975.0
13 TraesCS7B01G084300 chr7D 80.854 726 102 23 3 693 513205382 513204659 1.210000e-148 536.0
14 TraesCS7B01G084300 chr7D 94.444 144 8 0 2301 2444 133500173 133500316 3.860000e-54 222.0
15 TraesCS7B01G084300 chr7D 94.444 144 8 0 2301 2444 133604328 133604185 3.860000e-54 222.0
16 TraesCS7B01G084300 chrUn 95.004 1121 44 6 1058 2176 429907488 429906378 0.000000e+00 1749.0
17 TraesCS7B01G084300 chrUn 95.817 502 19 2 2473 2972 17578534 17579035 0.000000e+00 809.0
18 TraesCS7B01G084300 chrUn 84.022 557 83 6 3 555 28739735 28740289 5.640000e-147 531.0
19 TraesCS7B01G084300 chr4B 96.614 502 15 1 2473 2972 659570552 659571053 0.000000e+00 832.0
20 TraesCS7B01G084300 chr5B 96.579 497 17 0 2476 2972 548569810 548569314 0.000000e+00 824.0
21 TraesCS7B01G084300 chr5B 96.185 498 18 1 2476 2972 658081085 658081582 0.000000e+00 813.0
22 TraesCS7B01G084300 chr6B 96.386 498 17 1 2476 2972 650649743 650649246 0.000000e+00 819.0
23 TraesCS7B01G084300 chr6B 82.564 866 119 20 1106 1971 611500178 611501011 0.000000e+00 734.0
24 TraesCS7B01G084300 chr6B 84.615 546 81 3 11 554 576038123 576037579 9.370000e-150 540.0
25 TraesCS7B01G084300 chr1B 96.378 497 17 1 2476 2972 612404893 612405388 0.000000e+00 817.0
26 TraesCS7B01G084300 chr1B 95.992 499 17 3 2476 2972 357905209 357904712 0.000000e+00 808.0
27 TraesCS7B01G084300 chr3B 96.185 498 17 2 2476 2972 393326364 393326860 0.000000e+00 813.0
28 TraesCS7B01G084300 chr6A 82.069 870 116 25 1106 1971 553055006 553055839 0.000000e+00 706.0
29 TraesCS7B01G084300 chr1D 81.956 726 98 16 3 695 228825664 228824939 4.270000e-163 584.0
30 TraesCS7B01G084300 chr3D 85.821 536 75 1 11 545 8383115 8383650 4.300000e-158 568.0
31 TraesCS7B01G084300 chr5D 84.545 550 82 3 3 550 29876904 29877452 2.610000e-150 542.0
32 TraesCS7B01G084300 chr4A 84.278 547 82 4 11 555 631493320 631493864 5.640000e-147 531.0
33 TraesCS7B01G084300 chr2B 84.066 546 83 4 11 554 28213625 28213082 9.440000e-145 523.0
34 TraesCS7B01G084300 chr2B 81.878 607 89 12 3 594 737932828 737933428 2.660000e-135 492.0
35 TraesCS7B01G084300 chr2A 88.060 67 5 2 588 651 717737172 717737106 3.180000e-10 76.8


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 TraesCS7B01G084300 chr7B 95044458 95047429 2971 True 5489.000000 5489 100.000000 1 2972 1 chr7B.!!$R3 2971
1 TraesCS7B01G084300 chr7B 94808583 94811074 2491 True 790.666667 1917 94.029333 859 2444 3 chr7B.!!$R5 1585
2 TraesCS7B01G084300 chr7B 6004617 6005222 605 True 551.000000 551 83.361000 3 598 1 chr7B.!!$R1 595
3 TraesCS7B01G084300 chr7A 132618771 132620481 1710 False 2538.000000 2538 93.554000 739 2441 1 chr7A.!!$F1 1702
4 TraesCS7B01G084300 chr7A 132410475 132411778 1303 True 1978.000000 1978 93.992000 861 2172 1 chr7A.!!$R1 1311
5 TraesCS7B01G084300 chr7D 133826991 133828685 1694 False 2447.000000 2447 92.741000 739 2444 1 chr7D.!!$F3 1705
6 TraesCS7B01G084300 chr7D 133491999 133493310 1311 False 1997.000000 1997 94.100000 859 2176 1 chr7D.!!$F1 1317
7 TraesCS7B01G084300 chr7D 133611189 133612500 1311 True 1975.000000 1975 93.797000 859 2176 1 chr7D.!!$R2 1317
8 TraesCS7B01G084300 chr7D 513204659 513205382 723 True 536.000000 536 80.854000 3 693 1 chr7D.!!$R3 690
9 TraesCS7B01G084300 chrUn 429906378 429907488 1110 True 1749.000000 1749 95.004000 1058 2176 1 chrUn.!!$R1 1118
10 TraesCS7B01G084300 chrUn 17578534 17579035 501 False 809.000000 809 95.817000 2473 2972 1 chrUn.!!$F1 499
11 TraesCS7B01G084300 chrUn 28739735 28740289 554 False 531.000000 531 84.022000 3 555 1 chrUn.!!$F2 552
12 TraesCS7B01G084300 chr4B 659570552 659571053 501 False 832.000000 832 96.614000 2473 2972 1 chr4B.!!$F1 499
13 TraesCS7B01G084300 chr6B 611500178 611501011 833 False 734.000000 734 82.564000 1106 1971 1 chr6B.!!$F1 865
14 TraesCS7B01G084300 chr6B 576037579 576038123 544 True 540.000000 540 84.615000 11 554 1 chr6B.!!$R1 543
15 TraesCS7B01G084300 chr6A 553055006 553055839 833 False 706.000000 706 82.069000 1106 1971 1 chr6A.!!$F1 865
16 TraesCS7B01G084300 chr1D 228824939 228825664 725 True 584.000000 584 81.956000 3 695 1 chr1D.!!$R1 692
17 TraesCS7B01G084300 chr3D 8383115 8383650 535 False 568.000000 568 85.821000 11 545 1 chr3D.!!$F1 534
18 TraesCS7B01G084300 chr5D 29876904 29877452 548 False 542.000000 542 84.545000 3 550 1 chr5D.!!$F1 547
19 TraesCS7B01G084300 chr4A 631493320 631493864 544 False 531.000000 531 84.278000 11 555 1 chr4A.!!$F1 544
20 TraesCS7B01G084300 chr2B 28213082 28213625 543 True 523.000000 523 84.066000 11 554 1 chr2B.!!$R1 543
21 TraesCS7B01G084300 chr2B 737932828 737933428 600 False 492.000000 492 81.878000 3 594 1 chr2B.!!$F1 591

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
854 891 0.168128 GTAACACACGCTCAATGGCC 59.832 55.0 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2446 3452 0.179089 CTCTCGGGGAATGCAGACAG 60.179 60.0 0.0 0.0 0.0 3.51 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
44 45 2.615869 GAATGCTCCGCCAGATATCTC 58.384 52.381 1.03 0.00 0.00 2.75
49 50 2.289945 GCTCCGCCAGATATCTCCATTT 60.290 50.000 1.03 0.00 0.00 2.32
89 90 4.599241 AGATTACTGGATCGGATGGGATTT 59.401 41.667 0.00 0.00 0.00 2.17
120 121 1.343681 ACCCCTATTTCAGCCCGAGTA 60.344 52.381 0.00 0.00 0.00 2.59
125 126 2.789409 ATTTCAGCCCGAGTAGCTTT 57.211 45.000 0.00 0.00 38.95 3.51
159 160 3.190535 ACGTGAAGCTTTGTTGTCTGTTT 59.809 39.130 0.00 0.00 0.00 2.83
168 169 7.940850 AGCTTTGTTGTCTGTTTACATTATGT 58.059 30.769 2.58 2.58 0.00 2.29
215 216 2.271800 GTGAATACAGTGGCGGAGAAG 58.728 52.381 0.00 0.00 0.00 2.85
221 222 1.837051 AGTGGCGGAGAAGGTCACA 60.837 57.895 0.00 0.00 0.00 3.58
257 258 1.366366 CCTAGTAATGGCGGGTCGG 59.634 63.158 0.00 0.00 0.00 4.79
293 294 1.625818 AGGACTTCGCTTGGTGATTCT 59.374 47.619 0.00 0.00 0.00 2.40
321 322 2.395360 GCAACGGCATCGGCAAGTA 61.395 57.895 0.00 0.00 43.71 2.24
325 326 2.908015 GGCATCGGCAAGTAGGGA 59.092 61.111 0.00 0.00 43.71 4.20
329 330 1.684734 ATCGGCAAGTAGGGACGGT 60.685 57.895 0.00 0.00 37.38 4.83
441 444 0.517316 ATTGTTTTGAGAGCGCGGAC 59.483 50.000 8.83 0.00 0.00 4.79
471 475 5.594317 CCAGGGTGAAAACCTAAGATTATGG 59.406 44.000 0.00 0.00 36.32 2.74
479 483 2.368875 ACCTAAGATTATGGTCAGGCGG 59.631 50.000 0.00 0.00 0.00 6.13
507 511 0.998727 CTTGCGCGCTGTTTCCTTTC 60.999 55.000 33.29 0.00 0.00 2.62
513 517 1.876664 GCTGTTTCCTTTCCGGAGC 59.123 57.895 3.34 0.00 44.28 4.70
530 534 0.586802 AGCCGTCGCTTTTGAAGAAC 59.413 50.000 0.00 0.00 45.55 3.01
534 538 2.286833 CCGTCGCTTTTGAAGAACTTGA 59.713 45.455 0.00 0.00 0.00 3.02
547 551 3.617284 AGAACTTGAACTTCGGGTGTTT 58.383 40.909 0.00 0.00 0.00 2.83
548 552 3.626217 AGAACTTGAACTTCGGGTGTTTC 59.374 43.478 0.00 0.00 0.00 2.78
549 553 3.277142 ACTTGAACTTCGGGTGTTTCT 57.723 42.857 0.00 0.00 0.00 2.52
551 555 3.377172 ACTTGAACTTCGGGTGTTTCTTG 59.623 43.478 0.00 0.00 0.00 3.02
625 651 1.208293 TGGCTGTGTGCATCCGTAATA 59.792 47.619 0.00 0.00 45.15 0.98
632 658 6.147821 GCTGTGTGCATCCGTAATATCTTTAT 59.852 38.462 0.00 0.00 42.31 1.40
635 661 7.384932 TGTGTGCATCCGTAATATCTTTATGAG 59.615 37.037 0.00 0.00 0.00 2.90
639 665 9.725019 TGCATCCGTAATATCTTTATGAGATTT 57.275 29.630 0.00 0.00 42.55 2.17
653 679 2.224079 TGAGATTTTGTCGTTGCAGAGC 59.776 45.455 0.00 0.00 0.00 4.09
654 680 2.481952 GAGATTTTGTCGTTGCAGAGCT 59.518 45.455 0.00 0.00 0.00 4.09
655 681 2.880890 AGATTTTGTCGTTGCAGAGCTT 59.119 40.909 0.00 0.00 0.00 3.74
658 684 0.179059 TTGTCGTTGCAGAGCTTGGA 60.179 50.000 0.00 0.00 0.00 3.53
719 754 6.737254 ATAAATGAAGGTGGTTTCAGTACG 57.263 37.500 0.00 0.00 40.16 3.67
720 755 3.764237 ATGAAGGTGGTTTCAGTACGT 57.236 42.857 0.00 0.00 40.16 3.57
721 756 3.547054 TGAAGGTGGTTTCAGTACGTT 57.453 42.857 0.00 0.00 32.39 3.99
722 757 3.876341 TGAAGGTGGTTTCAGTACGTTT 58.124 40.909 0.00 0.00 32.39 3.60
723 758 4.263435 TGAAGGTGGTTTCAGTACGTTTT 58.737 39.130 0.00 0.00 32.39 2.43
724 759 4.333372 TGAAGGTGGTTTCAGTACGTTTTC 59.667 41.667 0.00 0.00 32.39 2.29
725 760 3.876341 AGGTGGTTTCAGTACGTTTTCA 58.124 40.909 0.00 0.00 0.00 2.69
726 761 3.875134 AGGTGGTTTCAGTACGTTTTCAG 59.125 43.478 0.00 0.00 0.00 3.02
727 762 3.872771 GGTGGTTTCAGTACGTTTTCAGA 59.127 43.478 0.00 0.00 0.00 3.27
728 763 4.514066 GGTGGTTTCAGTACGTTTTCAGAT 59.486 41.667 0.00 0.00 0.00 2.90
729 764 5.697633 GGTGGTTTCAGTACGTTTTCAGATA 59.302 40.000 0.00 0.00 0.00 1.98
730 765 6.203338 GGTGGTTTCAGTACGTTTTCAGATAA 59.797 38.462 0.00 0.00 0.00 1.75
731 766 7.254863 GGTGGTTTCAGTACGTTTTCAGATAAA 60.255 37.037 0.00 0.00 0.00 1.40
732 767 7.797123 GTGGTTTCAGTACGTTTTCAGATAAAG 59.203 37.037 0.00 0.00 0.00 1.85
733 768 6.795593 GGTTTCAGTACGTTTTCAGATAAAGC 59.204 38.462 0.00 0.00 0.00 3.51
734 769 7.349711 GTTTCAGTACGTTTTCAGATAAAGCA 58.650 34.615 0.00 0.00 0.00 3.91
735 770 7.485418 TTCAGTACGTTTTCAGATAAAGCAA 57.515 32.000 0.00 0.00 0.00 3.91
736 771 6.884187 TCAGTACGTTTTCAGATAAAGCAAC 58.116 36.000 0.00 0.00 0.00 4.17
737 772 6.704493 TCAGTACGTTTTCAGATAAAGCAACT 59.296 34.615 0.00 0.00 0.00 3.16
738 773 7.868922 TCAGTACGTTTTCAGATAAAGCAACTA 59.131 33.333 0.00 0.00 0.00 2.24
739 774 8.492748 CAGTACGTTTTCAGATAAAGCAACTAA 58.507 33.333 0.00 0.00 0.00 2.24
740 775 8.709646 AGTACGTTTTCAGATAAAGCAACTAAG 58.290 33.333 0.00 0.00 0.00 2.18
741 776 7.492352 ACGTTTTCAGATAAAGCAACTAAGT 57.508 32.000 0.00 0.00 0.00 2.24
742 777 8.597662 ACGTTTTCAGATAAAGCAACTAAGTA 57.402 30.769 0.00 0.00 0.00 2.24
743 778 8.493547 ACGTTTTCAGATAAAGCAACTAAGTAC 58.506 33.333 0.00 0.00 0.00 2.73
774 809 0.385473 ATTAGTGCACACGCGTTTGC 60.385 50.000 36.29 36.29 42.97 3.68
780 815 0.702383 GCACACGCGTTTGCATTAAG 59.298 50.000 37.40 14.93 42.97 1.85
782 817 1.069568 CACACGCGTTTGCATTAAGGA 60.070 47.619 10.22 0.00 42.97 3.36
784 819 1.976045 CACGCGTTTGCATTAAGGAAC 59.024 47.619 10.22 0.00 42.97 3.62
785 820 1.877443 ACGCGTTTGCATTAAGGAACT 59.123 42.857 5.58 0.00 41.55 3.01
786 821 3.068560 ACGCGTTTGCATTAAGGAACTA 58.931 40.909 5.58 0.00 38.78 2.24
800 837 2.490718 AGGAACTATTGGCTGGCAACAA 60.491 45.455 19.40 9.48 43.87 2.83
815 852 4.824289 GGCAACAACCTGATCATTTTGAT 58.176 39.130 18.63 7.97 40.34 2.57
816 853 5.240121 GGCAACAACCTGATCATTTTGATT 58.760 37.500 18.63 9.44 37.20 2.57
819 856 6.867816 GCAACAACCTGATCATTTTGATTACA 59.132 34.615 18.63 0.00 37.20 2.41
820 857 7.148755 GCAACAACCTGATCATTTTGATTACAC 60.149 37.037 18.63 3.68 37.20 2.90
821 858 6.611381 ACAACCTGATCATTTTGATTACACG 58.389 36.000 18.63 0.00 37.20 4.49
822 859 6.429692 ACAACCTGATCATTTTGATTACACGA 59.570 34.615 18.63 0.00 37.20 4.35
824 861 6.406370 ACCTGATCATTTTGATTACACGAGA 58.594 36.000 0.00 0.00 37.20 4.04
831 868 9.682092 ATCATTTTGATTACACGAGAAACGGCC 62.682 40.741 0.00 0.00 39.13 6.13
838 875 3.204505 CGAGAAACGGCCTGTGTAA 57.795 52.632 0.00 0.00 38.46 2.41
841 878 1.529865 GAGAAACGGCCTGTGTAACAC 59.470 52.381 0.00 0.00 45.67 3.32
843 880 1.003223 GAAACGGCCTGTGTAACACAC 60.003 52.381 0.00 6.40 45.67 3.82
852 889 2.594529 GTGTAACACACGCTCAATGG 57.405 50.000 0.00 0.00 39.53 3.16
853 890 0.871722 TGTAACACACGCTCAATGGC 59.128 50.000 0.00 0.00 0.00 4.40
854 891 0.168128 GTAACACACGCTCAATGGCC 59.832 55.000 0.00 0.00 0.00 5.36
855 892 0.250510 TAACACACGCTCAATGGCCA 60.251 50.000 8.56 8.56 0.00 5.36
856 893 1.106351 AACACACGCTCAATGGCCAA 61.106 50.000 10.96 0.00 0.00 4.52
857 894 0.895100 ACACACGCTCAATGGCCAAT 60.895 50.000 10.96 0.00 0.00 3.16
879 916 4.193334 CTCGCATCTCGCACCGGA 62.193 66.667 9.46 0.00 42.60 5.14
894 931 3.834610 CACCGGACTCCGCTATATAAAG 58.165 50.000 9.46 0.00 46.86 1.85
895 932 2.824341 ACCGGACTCCGCTATATAAAGG 59.176 50.000 9.46 0.00 46.86 3.11
972 1017 0.939419 ACACGTACGCAAAACCTTCC 59.061 50.000 16.72 0.00 0.00 3.46
998 1045 1.036092 ATCTAAACCCCTCCTCCCCT 58.964 55.000 0.00 0.00 0.00 4.79
1982 2033 1.303561 TGGTGTAGGAGTACGGCGT 60.304 57.895 19.64 19.64 30.95 5.68
2029 2080 2.190313 CAATCCGCTAGCTGCCCA 59.810 61.111 13.93 0.00 38.78 5.36
2049 2100 3.812053 CCATCTAGCCAAGAGTGTATTGC 59.188 47.826 0.00 0.00 37.74 3.56
2186 3188 5.001232 TGGAGTGCTAGTGGTAATTTTGTC 58.999 41.667 0.00 0.00 0.00 3.18
2246 3252 4.859629 ACGAATTAATCTCGAACTTGGC 57.140 40.909 19.76 0.00 39.60 4.52
2354 3360 2.928361 CGTGTCCGTGCTTCACAC 59.072 61.111 0.00 0.00 46.45 3.82
2419 3425 4.977741 CGTAACACACGTTTCTATGGTT 57.022 40.909 0.00 0.00 45.82 3.67
2445 3451 4.359475 CAGCATGTGTGACCGACA 57.641 55.556 0.00 0.00 0.00 4.35
2453 3459 3.938112 GTGACCGACACTGTCTGC 58.062 61.111 7.58 0.00 45.13 4.26
2454 3460 1.067416 GTGACCGACACTGTCTGCA 59.933 57.895 7.58 1.60 45.13 4.41
2455 3461 0.319900 GTGACCGACACTGTCTGCAT 60.320 55.000 7.58 0.00 45.13 3.96
2456 3462 0.392706 TGACCGACACTGTCTGCATT 59.607 50.000 7.58 0.00 33.83 3.56
2457 3463 1.071605 GACCGACACTGTCTGCATTC 58.928 55.000 7.58 0.00 0.00 2.67
2458 3464 0.320771 ACCGACACTGTCTGCATTCC 60.321 55.000 7.58 0.00 0.00 3.01
2459 3465 1.021390 CCGACACTGTCTGCATTCCC 61.021 60.000 7.58 0.00 0.00 3.97
2460 3466 1.021390 CGACACTGTCTGCATTCCCC 61.021 60.000 7.58 0.00 0.00 4.81
2461 3467 1.003355 ACACTGTCTGCATTCCCCG 60.003 57.895 0.00 0.00 0.00 5.73
2462 3468 1.296392 CACTGTCTGCATTCCCCGA 59.704 57.895 0.00 0.00 0.00 5.14
2463 3469 0.742281 CACTGTCTGCATTCCCCGAG 60.742 60.000 0.00 0.00 0.00 4.63
2464 3470 0.904865 ACTGTCTGCATTCCCCGAGA 60.905 55.000 0.00 0.00 0.00 4.04
2465 3471 0.179089 CTGTCTGCATTCCCCGAGAG 60.179 60.000 0.00 0.00 0.00 3.20
2466 3472 0.614697 TGTCTGCATTCCCCGAGAGA 60.615 55.000 0.00 0.00 0.00 3.10
2467 3473 0.179097 GTCTGCATTCCCCGAGAGAC 60.179 60.000 0.00 0.00 0.00 3.36
2468 3474 0.614697 TCTGCATTCCCCGAGAGACA 60.615 55.000 0.00 0.00 0.00 3.41
2469 3475 0.467384 CTGCATTCCCCGAGAGACAT 59.533 55.000 0.00 0.00 0.00 3.06
2470 3476 0.465705 TGCATTCCCCGAGAGACATC 59.534 55.000 0.00 0.00 0.00 3.06
2471 3477 0.465705 GCATTCCCCGAGAGACATCA 59.534 55.000 0.00 0.00 0.00 3.07
2474 3480 3.616076 GCATTCCCCGAGAGACATCATAG 60.616 52.174 0.00 0.00 0.00 2.23
2527 3533 5.336451 GCTAACAAAATCCCGATTTGACCTT 60.336 40.000 3.51 0.00 40.57 3.50
2964 3972 7.834803 TGATTGCATTTTATACATGTTGGTGA 58.165 30.769 2.30 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.181490 CGGAACTCGTCAATCACCAGATA 60.181 47.826 0.00 0.00 33.08 1.98
9 10 1.327764 GCATTCCGGAACTCGTCAATC 59.672 52.381 21.56 0.00 37.11 2.67
39 40 3.270027 CGTCAAGCACCAAATGGAGATA 58.730 45.455 6.42 0.00 38.94 1.98
89 90 1.485294 AATAGGGGTGCACACGACCA 61.485 55.000 20.43 0.69 34.89 4.02
120 121 1.692519 ACGTCACACCCTCTTAAAGCT 59.307 47.619 0.00 0.00 0.00 3.74
125 126 1.000506 GCTTCACGTCACACCCTCTTA 59.999 52.381 0.00 0.00 0.00 2.10
159 160 8.608317 CAAAATACCGACATGTCACATAATGTA 58.392 33.333 24.93 13.21 37.15 2.29
168 169 5.707764 TGGAAATCAAAATACCGACATGTCA 59.292 36.000 24.93 6.74 0.00 3.58
215 216 1.004440 GACCTCAGCCACTGTGACC 60.004 63.158 9.86 0.00 32.61 4.02
221 222 2.289532 GCCTCAGACCTCAGCCACT 61.290 63.158 0.00 0.00 0.00 4.00
253 254 0.179134 CATCACCTCGAAGACCCGAC 60.179 60.000 0.00 0.00 34.56 4.79
257 258 1.135333 GTCCTCATCACCTCGAAGACC 59.865 57.143 0.00 0.00 0.00 3.85
321 322 2.584608 GCATGTGCTACCGTCCCT 59.415 61.111 0.00 0.00 38.21 4.20
325 326 1.317431 TACTCCGCATGTGCTACCGT 61.317 55.000 0.00 0.00 39.32 4.83
329 330 1.950216 CTCTCTACTCCGCATGTGCTA 59.050 52.381 0.00 0.00 39.32 3.49
345 346 3.511934 TCACCCTGAAAGCTAAGACTCTC 59.488 47.826 0.00 0.00 0.00 3.20
379 382 1.554617 GGCACAACCAATTAAGGCCAT 59.445 47.619 5.01 0.00 39.66 4.40
441 444 3.229697 AGGTTTTCACCCTGGAGAAAG 57.770 47.619 8.46 0.00 45.63 2.62
471 475 3.188786 GCGTCATCACCGCCTGAC 61.189 66.667 0.00 0.00 45.20 3.51
492 496 2.173382 CGGAAAGGAAACAGCGCG 59.827 61.111 0.00 0.00 0.00 6.86
513 517 2.286833 TCAAGTTCTTCAAAAGCGACGG 59.713 45.455 0.00 0.00 0.00 4.79
530 534 3.243068 CCAAGAAACACCCGAAGTTCAAG 60.243 47.826 3.32 0.00 0.00 3.02
534 538 2.021457 CACCAAGAAACACCCGAAGTT 58.979 47.619 0.00 0.00 0.00 2.66
547 551 2.221169 CTTGTAGTTGCAGCACCAAGA 58.779 47.619 20.22 0.00 32.96 3.02
548 552 1.267806 CCTTGTAGTTGCAGCACCAAG 59.732 52.381 18.82 18.82 0.00 3.61
549 553 1.133945 TCCTTGTAGTTGCAGCACCAA 60.134 47.619 2.55 4.15 0.00 3.67
551 555 1.604604 TTCCTTGTAGTTGCAGCACC 58.395 50.000 2.55 0.00 0.00 5.01
599 614 2.056094 GATGCACACAGCCAAAAGAC 57.944 50.000 0.00 0.00 44.83 3.01
632 658 2.224079 GCTCTGCAACGACAAAATCTCA 59.776 45.455 0.00 0.00 0.00 3.27
635 661 2.975851 CAAGCTCTGCAACGACAAAATC 59.024 45.455 0.00 0.00 0.00 2.17
639 665 0.179059 TCCAAGCTCTGCAACGACAA 60.179 50.000 0.00 0.00 0.00 3.18
640 666 0.035317 ATCCAAGCTCTGCAACGACA 59.965 50.000 0.00 0.00 0.00 4.35
643 669 1.725641 TACATCCAAGCTCTGCAACG 58.274 50.000 0.00 0.00 0.00 4.10
695 730 7.388437 ACGTACTGAAACCACCTTCATTTATA 58.612 34.615 0.00 0.00 34.86 0.98
696 731 6.235664 ACGTACTGAAACCACCTTCATTTAT 58.764 36.000 0.00 0.00 34.86 1.40
697 732 5.613329 ACGTACTGAAACCACCTTCATTTA 58.387 37.500 0.00 0.00 34.86 1.40
698 733 4.457466 ACGTACTGAAACCACCTTCATTT 58.543 39.130 0.00 0.00 34.86 2.32
699 734 4.081322 ACGTACTGAAACCACCTTCATT 57.919 40.909 0.00 0.00 34.86 2.57
700 735 3.764237 ACGTACTGAAACCACCTTCAT 57.236 42.857 0.00 0.00 34.86 2.57
701 736 3.547054 AACGTACTGAAACCACCTTCA 57.453 42.857 0.00 0.00 34.22 3.02
702 737 4.333372 TGAAAACGTACTGAAACCACCTTC 59.667 41.667 0.00 0.00 0.00 3.46
703 738 4.263435 TGAAAACGTACTGAAACCACCTT 58.737 39.130 0.00 0.00 0.00 3.50
704 739 3.875134 CTGAAAACGTACTGAAACCACCT 59.125 43.478 0.00 0.00 0.00 4.00
705 740 3.872771 TCTGAAAACGTACTGAAACCACC 59.127 43.478 0.00 0.00 0.00 4.61
706 741 5.668558 ATCTGAAAACGTACTGAAACCAC 57.331 39.130 0.00 0.00 0.00 4.16
707 742 7.519328 GCTTTATCTGAAAACGTACTGAAACCA 60.519 37.037 0.00 0.00 0.00 3.67
708 743 6.795593 GCTTTATCTGAAAACGTACTGAAACC 59.204 38.462 0.00 0.00 0.00 3.27
709 744 7.349711 TGCTTTATCTGAAAACGTACTGAAAC 58.650 34.615 0.00 0.00 0.00 2.78
710 745 7.485418 TGCTTTATCTGAAAACGTACTGAAA 57.515 32.000 0.00 0.00 0.00 2.69
711 746 7.225931 AGTTGCTTTATCTGAAAACGTACTGAA 59.774 33.333 0.00 0.00 0.00 3.02
712 747 6.704493 AGTTGCTTTATCTGAAAACGTACTGA 59.296 34.615 0.00 0.00 0.00 3.41
713 748 6.888430 AGTTGCTTTATCTGAAAACGTACTG 58.112 36.000 0.00 0.00 0.00 2.74
714 749 8.597662 TTAGTTGCTTTATCTGAAAACGTACT 57.402 30.769 0.00 0.00 0.00 2.73
715 750 8.493547 ACTTAGTTGCTTTATCTGAAAACGTAC 58.506 33.333 0.00 0.00 0.00 3.67
716 751 8.597662 ACTTAGTTGCTTTATCTGAAAACGTA 57.402 30.769 0.00 0.00 0.00 3.57
717 752 7.492352 ACTTAGTTGCTTTATCTGAAAACGT 57.508 32.000 0.00 0.00 0.00 3.99
718 753 8.709646 AGTACTTAGTTGCTTTATCTGAAAACG 58.290 33.333 0.00 0.00 0.00 3.60
728 763 9.415544 GCAGTTACTTAGTACTTAGTTGCTTTA 57.584 33.333 21.46 3.69 0.00 1.85
729 764 7.929785 TGCAGTTACTTAGTACTTAGTTGCTTT 59.070 33.333 25.65 5.94 30.68 3.51
730 765 7.439381 TGCAGTTACTTAGTACTTAGTTGCTT 58.561 34.615 25.65 9.20 30.68 3.91
731 766 6.989659 TGCAGTTACTTAGTACTTAGTTGCT 58.010 36.000 25.65 18.45 30.68 3.91
732 767 7.829378 ATGCAGTTACTTAGTACTTAGTTGC 57.171 36.000 21.75 21.75 0.00 4.17
762 797 1.069568 TCCTTAATGCAAACGCGTGTG 60.070 47.619 25.16 25.16 0.00 3.82
774 809 3.953612 TGCCAGCCAATAGTTCCTTAATG 59.046 43.478 0.00 0.00 0.00 1.90
780 815 1.544724 TGTTGCCAGCCAATAGTTCC 58.455 50.000 0.00 0.00 35.55 3.62
782 817 1.618343 GGTTGTTGCCAGCCAATAGTT 59.382 47.619 0.00 0.00 41.34 2.24
784 819 1.203052 CAGGTTGTTGCCAGCCAATAG 59.797 52.381 0.00 0.00 43.95 1.73
785 820 1.202989 TCAGGTTGTTGCCAGCCAATA 60.203 47.619 0.00 0.00 43.95 1.90
786 821 0.469705 TCAGGTTGTTGCCAGCCAAT 60.470 50.000 0.00 0.00 43.95 3.16
800 837 6.406370 TCTCGTGTAATCAAAATGATCAGGT 58.594 36.000 0.09 0.00 35.76 4.00
807 844 4.553429 GCCGTTTCTCGTGTAATCAAAATG 59.447 41.667 0.00 0.00 37.94 2.32
809 846 3.058777 GGCCGTTTCTCGTGTAATCAAAA 60.059 43.478 0.00 0.00 37.94 2.44
812 849 1.274167 AGGCCGTTTCTCGTGTAATCA 59.726 47.619 0.00 0.00 37.94 2.57
815 852 0.390124 ACAGGCCGTTTCTCGTGTAA 59.610 50.000 0.00 0.00 37.94 2.41
816 853 0.319211 CACAGGCCGTTTCTCGTGTA 60.319 55.000 0.00 0.00 37.94 2.90
819 856 0.390124 TTACACAGGCCGTTTCTCGT 59.610 50.000 0.00 0.00 37.94 4.18
820 857 0.788391 GTTACACAGGCCGTTTCTCG 59.212 55.000 0.00 0.00 39.52 4.04
821 858 1.529865 GTGTTACACAGGCCGTTTCTC 59.470 52.381 10.96 0.00 34.08 2.87
822 859 1.134340 TGTGTTACACAGGCCGTTTCT 60.134 47.619 14.73 0.00 39.62 2.52
824 861 3.480342 TGTGTTACACAGGCCGTTT 57.520 47.368 14.73 0.00 39.62 3.60
835 872 0.168128 GGCCATTGAGCGTGTGTTAC 59.832 55.000 0.00 0.00 0.00 2.50
838 875 0.895100 ATTGGCCATTGAGCGTGTGT 60.895 50.000 6.09 0.00 0.00 3.72
841 878 1.140161 CCATTGGCCATTGAGCGTG 59.860 57.895 25.72 7.65 0.00 5.34
843 880 2.105528 GCCATTGGCCATTGAGCG 59.894 61.111 25.72 12.36 44.06 5.03
853 890 1.769098 CGAGATGCGAGTGCCATTGG 61.769 60.000 0.00 0.00 44.57 3.16
854 891 1.640069 CGAGATGCGAGTGCCATTG 59.360 57.895 0.00 0.00 44.57 2.82
855 892 2.176273 GCGAGATGCGAGTGCCATT 61.176 57.895 0.00 0.00 44.57 3.16
856 893 2.587194 GCGAGATGCGAGTGCCAT 60.587 61.111 0.00 0.00 44.57 4.40
865 902 2.583593 GAGTCCGGTGCGAGATGC 60.584 66.667 0.00 0.00 46.70 3.91
879 916 4.031611 GGGATCCCTTTATATAGCGGAGT 58.968 47.826 24.69 0.00 0.00 3.85
884 921 2.772515 AGCGGGGATCCCTTTATATAGC 59.227 50.000 30.08 19.76 42.67 2.97
894 931 3.738745 AATGGCAAGCGGGGATCCC 62.739 63.158 23.95 23.95 41.09 3.85
895 932 2.123726 AATGGCAAGCGGGGATCC 60.124 61.111 1.92 1.92 0.00 3.36
972 1017 2.853077 AGGAGGGGTTTAGATTTGGGAG 59.147 50.000 0.00 0.00 0.00 4.30
998 1045 2.919602 AGGAGGTTTCTCTTGGCCATTA 59.080 45.455 6.09 0.00 39.86 1.90
1069 1120 2.811317 CTTCCTCGTGCTCGTGGC 60.811 66.667 21.08 0.00 46.27 5.01
1362 1413 2.432456 GACATGACCACTCGCGCA 60.432 61.111 8.75 0.00 0.00 6.09
1368 1419 2.927856 TGGCCGGACATGACCACT 60.928 61.111 5.41 0.00 0.00 4.00
1375 1426 3.083997 GGAGACCTGGCCGGACAT 61.084 66.667 12.52 0.00 36.31 3.06
1982 2033 1.037493 ACTTGTCGCTACCACTGTGA 58.963 50.000 9.86 0.00 0.00 3.58
2029 2080 3.133003 ACGCAATACACTCTTGGCTAGAT 59.867 43.478 0.00 0.00 30.92 1.98
2246 3252 4.054671 GGAAGATGAGATAAGCTTCACCG 58.945 47.826 0.00 0.00 38.72 4.94
2281 3287 2.003548 AGGCATCCCCTTGTCCTCC 61.004 63.158 0.00 0.00 43.06 4.30
2349 3355 1.110518 TGTCCAGTACGGCAGTGTGA 61.111 55.000 0.00 0.00 33.14 3.58
2354 3360 0.317160 TCTGTTGTCCAGTACGGCAG 59.683 55.000 0.00 0.00 42.19 4.85
2444 3450 0.742281 CTCGGGGAATGCAGACAGTG 60.742 60.000 0.00 0.00 0.00 3.66
2445 3451 0.904865 TCTCGGGGAATGCAGACAGT 60.905 55.000 0.00 0.00 0.00 3.55
2446 3452 0.179089 CTCTCGGGGAATGCAGACAG 60.179 60.000 0.00 0.00 0.00 3.51
2447 3453 0.614697 TCTCTCGGGGAATGCAGACA 60.615 55.000 0.00 0.00 0.00 3.41
2448 3454 0.179097 GTCTCTCGGGGAATGCAGAC 60.179 60.000 0.00 0.00 0.00 3.51
2449 3455 0.614697 TGTCTCTCGGGGAATGCAGA 60.615 55.000 0.00 0.00 0.00 4.26
2450 3456 0.467384 ATGTCTCTCGGGGAATGCAG 59.533 55.000 0.00 0.00 0.00 4.41
2451 3457 0.465705 GATGTCTCTCGGGGAATGCA 59.534 55.000 0.00 0.00 0.00 3.96
2452 3458 0.465705 TGATGTCTCTCGGGGAATGC 59.534 55.000 0.00 0.00 0.00 3.56
2453 3459 3.056250 CCTATGATGTCTCTCGGGGAATG 60.056 52.174 0.00 0.00 0.00 2.67
2454 3460 3.169099 CCTATGATGTCTCTCGGGGAAT 58.831 50.000 0.00 0.00 0.00 3.01
2455 3461 2.598565 CCTATGATGTCTCTCGGGGAA 58.401 52.381 0.00 0.00 0.00 3.97
2456 3462 1.203063 CCCTATGATGTCTCTCGGGGA 60.203 57.143 0.00 0.00 34.94 4.81
2457 3463 1.203063 TCCCTATGATGTCTCTCGGGG 60.203 57.143 0.00 0.00 0.00 5.73
2458 3464 1.889829 GTCCCTATGATGTCTCTCGGG 59.110 57.143 0.00 0.00 0.00 5.14
2459 3465 2.587522 TGTCCCTATGATGTCTCTCGG 58.412 52.381 0.00 0.00 0.00 4.63
2460 3466 4.655762 TTTGTCCCTATGATGTCTCTCG 57.344 45.455 0.00 0.00 0.00 4.04
2461 3467 8.207545 AGTAATTTTGTCCCTATGATGTCTCTC 58.792 37.037 0.00 0.00 0.00 3.20
2462 3468 7.989741 CAGTAATTTTGTCCCTATGATGTCTCT 59.010 37.037 0.00 0.00 0.00 3.10
2463 3469 7.770897 ACAGTAATTTTGTCCCTATGATGTCTC 59.229 37.037 0.00 0.00 0.00 3.36
2464 3470 7.633789 ACAGTAATTTTGTCCCTATGATGTCT 58.366 34.615 0.00 0.00 0.00 3.41
2465 3471 7.865706 ACAGTAATTTTGTCCCTATGATGTC 57.134 36.000 0.00 0.00 0.00 3.06
2466 3472 9.920946 ATAACAGTAATTTTGTCCCTATGATGT 57.079 29.630 0.00 0.00 0.00 3.06
2474 3480 8.803397 AGAGGTAATAACAGTAATTTTGTCCC 57.197 34.615 0.00 0.00 0.00 4.46
2493 3499 4.080526 GGGATTTTGTTAGCCAGAGAGGTA 60.081 45.833 0.00 0.00 40.61 3.08
2544 3552 6.208599 TGGCGTCTCCTAAAAAGATCAAAAAT 59.791 34.615 0.00 0.00 35.26 1.82
2552 3560 3.478857 TGTTGGCGTCTCCTAAAAAGA 57.521 42.857 0.00 0.00 35.26 2.52
2581 3589 0.674895 GTCTGCTTCGCAACCCAGAT 60.675 55.000 0.00 0.00 38.41 2.90
2605 3613 3.785859 GCCAGACGCCAGGATCCA 61.786 66.667 15.82 0.00 0.00 3.41
2638 3646 3.998672 GGTCAACGGGCAGACGGA 61.999 66.667 0.00 0.00 38.39 4.69
2642 3650 3.241530 AGCAGGTCAACGGGCAGA 61.242 61.111 0.00 0.00 0.00 4.26
2941 3949 8.934825 GTTTCACCAACATGTATAAAATGCAAT 58.065 29.630 0.00 0.00 35.18 3.56


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

AutoCloner maintained by Alex Coulton.