Multiple sequence alignment - TraesCS3B01G508200

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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 TraesCS3B01G508200 chr3B 100.000 3041 0 0 1 3041 752179746 752176706 0.000000e+00 5616.0
1 TraesCS3B01G508200 chr3B 78.375 2104 297 85 981 3041 752122936 752120948 0.000000e+00 1219.0
2 TraesCS3B01G508200 chr3B 74.912 1419 259 54 1031 2392 752920196 752918818 2.650000e-155 558.0
3 TraesCS3B01G508200 chr3B 73.851 1197 230 58 1539 2693 754982166 754983321 1.700000e-107 399.0
4 TraesCS3B01G508200 chr3B 82.848 309 45 5 966 1270 752809632 752809328 1.390000e-68 270.0
5 TraesCS3B01G508200 chr3B 87.204 211 26 1 966 1175 753964669 753964459 3.920000e-59 239.0
6 TraesCS3B01G508200 chr3B 80.783 281 47 6 992 1267 752377134 752376856 2.380000e-51 213.0
7 TraesCS3B01G508200 chr3B 73.514 370 76 14 1463 1812 756252543 756252176 1.480000e-23 121.0
8 TraesCS3B01G508200 chr3B 78.761 113 23 1 2088 2199 754303367 754303479 1.170000e-09 75.0
9 TraesCS3B01G508200 chr3A 90.038 1325 107 17 1510 2815 699251542 699250224 0.000000e+00 1692.0
10 TraesCS3B01G508200 chr3A 94.444 342 16 2 2 340 671756153 671755812 9.660000e-145 523.0
11 TraesCS3B01G508200 chr3A 95.294 255 9 2 330 584 671755789 671755538 4.720000e-108 401.0
12 TraesCS3B01G508200 chr3A 72.979 1410 276 61 1024 2385 698739719 698741071 2.200000e-106 396.0
13 TraesCS3B01G508200 chr3A 97.403 231 6 0 2811 3041 699244525 699244295 7.900000e-106 394.0
14 TraesCS3B01G508200 chr3A 72.875 800 163 36 1045 1826 700631937 700631174 3.050000e-55 226.0
15 TraesCS3B01G508200 chr3A 80.198 303 51 5 972 1270 700025608 700025311 5.100000e-53 219.0
16 TraesCS3B01G508200 chr3A 90.000 90 9 0 1721 1810 701834608 701834697 1.920000e-22 117.0
17 TraesCS3B01G508200 chr3A 78.049 123 21 5 1553 1672 701239043 701238924 4.210000e-09 73.1
18 TraesCS3B01G508200 chr3D 96.853 985 28 2 777 1758 564513544 564512560 0.000000e+00 1644.0
19 TraesCS3B01G508200 chr3D 95.824 431 14 2 2075 2504 564512562 564512135 0.000000e+00 693.0
20 TraesCS3B01G508200 chr3D 76.414 1361 233 49 992 2303 564905433 564904112 0.000000e+00 654.0
21 TraesCS3B01G508200 chr3D 73.959 1225 231 55 1539 2725 567223624 567222450 6.070000e-112 414.0
22 TraesCS3B01G508200 chr3D 95.294 255 12 0 330 584 566000919 566000665 3.650000e-109 405.0
23 TraesCS3B01G508200 chr3D 85.641 390 25 8 2501 2890 564496872 564496514 6.150000e-102 381.0
24 TraesCS3B01G508200 chr3D 74.808 782 130 36 1024 1781 564150942 564151680 1.070000e-74 291.0
25 TraesCS3B01G508200 chr3D 83.654 312 37 9 963 1267 565258613 565258917 6.420000e-72 281.0
26 TraesCS3B01G508200 chr3D 87.712 236 29 0 960 1195 565162744 565162979 2.990000e-70 276.0
27 TraesCS3B01G508200 chr3D 90.686 204 17 1 567 770 91821970 91822171 1.390000e-68 270.0
28 TraesCS3B01G508200 chr3D 92.432 185 14 0 567 751 566000715 566000531 6.460000e-67 265.0
29 TraesCS3B01G508200 chr3D 96.815 157 4 1 2878 3034 564496484 564496329 8.360000e-66 261.0
30 TraesCS3B01G508200 chr3D 85.268 224 27 5 982 1201 567220215 567219994 3.050000e-55 226.0
31 TraesCS3B01G508200 chr3D 75.090 558 91 28 2064 2605 569577900 569577375 1.840000e-52 217.0
32 TraesCS3B01G508200 chr3D 75.262 477 78 23 1045 1513 561098370 561097926 1.110000e-44 191.0
33 TraesCS3B01G508200 chr3D 82.609 207 28 7 995 1197 567137872 567138074 3.120000e-40 176.0
34 TraesCS3B01G508200 chr3D 81.592 201 35 2 998 1197 569676766 569676567 6.750000e-37 165.0
35 TraesCS3B01G508200 chr3D 82.353 170 28 2 996 1164 565675381 565675549 2.440000e-31 147.0
36 TraesCS3B01G508200 chr3D 87.619 105 13 0 1708 1812 569517284 569517388 4.120000e-24 122.0
37 TraesCS3B01G508200 chr3D 97.222 36 1 0 1232 1267 567138091 567138126 9.100000e-06 62.1
38 TraesCS3B01G508200 chr5D 90.355 591 47 9 1 584 524593640 524593053 0.000000e+00 767.0
39 TraesCS3B01G508200 chr5D 93.623 345 17 4 1 340 370953994 370953650 7.520000e-141 510.0
40 TraesCS3B01G508200 chr5D 93.725 255 16 0 330 584 288161992 288161738 1.710000e-102 383.0
41 TraesCS3B01G508200 chr5D 93.725 255 16 0 330 584 370953627 370953373 1.710000e-102 383.0
42 TraesCS3B01G508200 chr5D 90.367 218 15 5 558 770 524593114 524592898 6.420000e-72 281.0
43 TraesCS3B01G508200 chr5D 90.865 208 15 2 567 770 288161788 288161581 2.990000e-70 276.0
44 TraesCS3B01G508200 chr5D 89.320 206 20 1 567 770 14530940 14530735 1.080000e-64 257.0
45 TraesCS3B01G508200 chr1D 95.000 340 15 1 1 338 467601168 467601507 1.610000e-147 532.0
46 TraesCS3B01G508200 chr1D 94.048 252 15 0 330 581 467601532 467601783 1.710000e-102 383.0
47 TraesCS3B01G508200 chr1D 90.385 208 15 3 567 770 467601736 467601942 5.000000e-68 268.0
48 TraesCS3B01G508200 chr4A 94.721 341 16 1 1 339 589784375 589784035 2.080000e-146 529.0
49 TraesCS3B01G508200 chr7A 94.152 342 18 1 1 340 679828815 679829156 1.250000e-143 520.0
50 TraesCS3B01G508200 chr7A 93.043 345 19 2 1 340 15255841 15255497 1.630000e-137 499.0
51 TraesCS3B01G508200 chr7A 94.118 255 15 0 330 584 15255474 15255220 3.680000e-104 388.0
52 TraesCS3B01G508200 chr2A 93.567 342 17 2 1 340 744776655 744776993 3.500000e-139 505.0
53 TraesCS3B01G508200 chr2A 94.048 252 15 0 330 581 744777016 744777267 1.710000e-102 383.0
54 TraesCS3B01G508200 chr2A 90.338 207 14 4 567 767 744777220 744777426 1.800000e-67 267.0
55 TraesCS3B01G508200 chr4D 93.043 345 19 2 1 340 53420137 53419793 1.630000e-137 499.0
56 TraesCS3B01G508200 chrUn 73.906 1234 236 59 1539 2725 41110460 41109266 1.690000e-112 416.0
57 TraesCS3B01G508200 chrUn 88.177 203 22 1 567 767 35823987 35824189 1.090000e-59 241.0
58 TraesCS3B01G508200 chrUn 84.848 231 30 4 975 1201 41107077 41106848 8.480000e-56 228.0
59 TraesCS3B01G508200 chrUn 81.319 182 33 1 1030 1211 279459077 279458897 2.440000e-31 147.0
60 TraesCS3B01G508200 chrUn 82.069 145 14 4 1051 1195 286487385 286487517 2.480000e-21 113.0
61 TraesCS3B01G508200 chrUn 82.069 145 14 4 1051 1195 293133130 293133262 2.480000e-21 113.0
62 TraesCS3B01G508200 chrUn 87.000 100 11 2 1017 1115 39287320 39287418 8.910000e-21 111.0
63 TraesCS3B01G508200 chr5A 94.531 256 12 2 330 584 709280171 709279917 7.900000e-106 394.0
64 TraesCS3B01G508200 chr5A 89.806 206 19 1 567 770 709279967 709279762 2.330000e-66 263.0
65 TraesCS3B01G508200 chr5A 88.780 205 17 3 570 770 631680364 631680162 2.340000e-61 246.0
66 TraesCS3B01G508200 chr7D 93.725 255 16 0 330 584 422153264 422153010 1.710000e-102 383.0


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 TraesCS3B01G508200 chr3B 752176706 752179746 3040 True 5616.000000 5616 100.000000 1 3041 1 chr3B.!!$R2 3040
1 TraesCS3B01G508200 chr3B 752120948 752122936 1988 True 1219.000000 1219 78.375000 981 3041 1 chr3B.!!$R1 2060
2 TraesCS3B01G508200 chr3B 752918818 752920196 1378 True 558.000000 558 74.912000 1031 2392 1 chr3B.!!$R5 1361
3 TraesCS3B01G508200 chr3B 754982166 754983321 1155 False 399.000000 399 73.851000 1539 2693 1 chr3B.!!$F2 1154
4 TraesCS3B01G508200 chr3A 699250224 699251542 1318 True 1692.000000 1692 90.038000 1510 2815 1 chr3A.!!$R2 1305
5 TraesCS3B01G508200 chr3A 671755538 671756153 615 True 462.000000 523 94.869000 2 584 2 chr3A.!!$R6 582
6 TraesCS3B01G508200 chr3A 698739719 698741071 1352 False 396.000000 396 72.979000 1024 2385 1 chr3A.!!$F1 1361
7 TraesCS3B01G508200 chr3A 700631174 700631937 763 True 226.000000 226 72.875000 1045 1826 1 chr3A.!!$R4 781
8 TraesCS3B01G508200 chr3D 564512135 564513544 1409 True 1168.500000 1644 96.338500 777 2504 2 chr3D.!!$R6 1727
9 TraesCS3B01G508200 chr3D 564904112 564905433 1321 True 654.000000 654 76.414000 992 2303 1 chr3D.!!$R2 1311
10 TraesCS3B01G508200 chr3D 564496329 564496872 543 True 321.000000 381 91.228000 2501 3034 2 chr3D.!!$R5 533
11 TraesCS3B01G508200 chr3D 567219994 567223624 3630 True 320.000000 414 79.613500 982 2725 2 chr3D.!!$R8 1743
12 TraesCS3B01G508200 chr3D 564150942 564151680 738 False 291.000000 291 74.808000 1024 1781 1 chr3D.!!$F2 757
13 TraesCS3B01G508200 chr3D 569577375 569577900 525 True 217.000000 217 75.090000 2064 2605 1 chr3D.!!$R3 541
14 TraesCS3B01G508200 chr5D 524592898 524593640 742 True 524.000000 767 90.361000 1 770 2 chr5D.!!$R4 769
15 TraesCS3B01G508200 chr5D 370953373 370953994 621 True 446.500000 510 93.674000 1 584 2 chr5D.!!$R3 583
16 TraesCS3B01G508200 chr1D 467601168 467601942 774 False 394.333333 532 93.144333 1 770 3 chr1D.!!$F1 769
17 TraesCS3B01G508200 chr7A 15255220 15255841 621 True 443.500000 499 93.580500 1 584 2 chr7A.!!$R1 583
18 TraesCS3B01G508200 chr2A 744776655 744777426 771 False 385.000000 505 92.651000 1 767 3 chr2A.!!$F1 766
19 TraesCS3B01G508200 chrUn 41106848 41110460 3612 True 322.000000 416 79.377000 975 2725 2 chrUn.!!$R2 1750

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
913 958 0.036306 CAGCCCGTTTTAGACCCACT 59.964 55.0 0.0 0.0 0.0 4.00 F
1410 1460 1.127343 GCCTCTCTATCTGCAACCCT 58.873 55.0 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 1991 0.180171 TATGGTTGTGGATGCCGAGG 59.82 55.000 0.0 0.0 0.0 4.63 R
2480 2774 2.559668 TCAATTGCTCAGCCCAAGAAAG 59.44 45.455 0.0 0.0 0.0 2.62 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
33 34 1.198713 ATCGAGCCACATGTCTTCCT 58.801 50.000 0.00 0.00 0.00 3.36
37 38 2.353704 CGAGCCACATGTCTTCCTAACA 60.354 50.000 0.00 0.00 0.00 2.41
406 449 0.172803 GTGCGAGGTCTGGAACGTAT 59.827 55.000 0.00 0.00 0.00 3.06
450 493 4.610844 CGAATCTCGGCGGAGTAC 57.389 61.111 19.51 11.52 41.26 2.73
451 494 2.023318 CGAATCTCGGCGGAGTACT 58.977 57.895 19.51 0.00 41.26 2.73
452 495 1.224075 CGAATCTCGGCGGAGTACTA 58.776 55.000 19.51 2.23 41.26 1.82
453 496 1.194997 CGAATCTCGGCGGAGTACTAG 59.805 57.143 19.51 6.65 41.26 2.57
454 497 0.953003 AATCTCGGCGGAGTACTAGC 59.047 55.000 19.51 12.85 41.26 3.42
455 498 0.890090 ATCTCGGCGGAGTACTAGCC 60.890 60.000 24.47 24.47 46.88 3.93
461 504 1.436336 CGGAGTACTAGCCGTTGGG 59.564 63.158 13.49 0.00 42.49 4.12
462 505 1.821258 GGAGTACTAGCCGTTGGGG 59.179 63.158 0.00 0.00 39.58 4.96
553 596 3.898509 CTGGAGCGGCGAGGAGAG 61.899 72.222 12.98 0.00 0.00 3.20
556 599 3.141488 GAGCGGCGAGGAGAGGAA 61.141 66.667 12.98 0.00 0.00 3.36
557 600 3.132481 GAGCGGCGAGGAGAGGAAG 62.132 68.421 12.98 0.00 0.00 3.46
558 601 4.882396 GCGGCGAGGAGAGGAAGC 62.882 72.222 12.98 0.00 0.00 3.86
559 602 4.560856 CGGCGAGGAGAGGAAGCG 62.561 72.222 0.00 0.00 0.00 4.68
560 603 4.214327 GGCGAGGAGAGGAAGCGG 62.214 72.222 0.00 0.00 0.00 5.52
561 604 3.453679 GCGAGGAGAGGAAGCGGT 61.454 66.667 0.00 0.00 0.00 5.68
562 605 2.492090 CGAGGAGAGGAAGCGGTG 59.508 66.667 0.00 0.00 0.00 4.94
563 606 2.896443 GAGGAGAGGAAGCGGTGG 59.104 66.667 0.00 0.00 0.00 4.61
564 607 1.682684 GAGGAGAGGAAGCGGTGGA 60.683 63.158 0.00 0.00 0.00 4.02
565 608 1.950973 GAGGAGAGGAAGCGGTGGAC 61.951 65.000 0.00 0.00 0.00 4.02
586 629 3.898509 CTGGAGCGGCGAGGAGAG 61.899 72.222 12.98 0.00 0.00 3.20
589 632 3.141488 GAGCGGCGAGGAGAGGAA 61.141 66.667 12.98 0.00 0.00 3.36
590 633 3.132481 GAGCGGCGAGGAGAGGAAG 62.132 68.421 12.98 0.00 0.00 3.46
591 634 4.882396 GCGGCGAGGAGAGGAAGC 62.882 72.222 12.98 0.00 0.00 3.86
592 635 4.560856 CGGCGAGGAGAGGAAGCG 62.561 72.222 0.00 0.00 0.00 4.68
593 636 4.214327 GGCGAGGAGAGGAAGCGG 62.214 72.222 0.00 0.00 0.00 5.52
594 637 3.453679 GCGAGGAGAGGAAGCGGT 61.454 66.667 0.00 0.00 0.00 5.68
595 638 2.492090 CGAGGAGAGGAAGCGGTG 59.508 66.667 0.00 0.00 0.00 4.94
596 639 2.896443 GAGGAGAGGAAGCGGTGG 59.104 66.667 0.00 0.00 0.00 4.61
597 640 1.682684 GAGGAGAGGAAGCGGTGGA 60.683 63.158 0.00 0.00 0.00 4.02
598 641 1.950973 GAGGAGAGGAAGCGGTGGAC 61.951 65.000 0.00 0.00 0.00 4.02
618 661 2.796651 GCTGGAGCGGCAAAGATG 59.203 61.111 1.45 0.00 35.55 2.90
629 672 1.638467 CAAAGATGCTACGAGGCGC 59.362 57.895 0.00 0.00 34.52 6.53
631 674 4.933064 AGATGCTACGAGGCGCGC 62.933 66.667 25.94 25.94 46.04 6.86
646 689 2.125713 CGCGTGGCAGTGTGGATA 60.126 61.111 0.00 0.00 0.00 2.59
647 690 2.167219 CGCGTGGCAGTGTGGATAG 61.167 63.158 0.00 0.00 0.00 2.08
648 691 1.815421 GCGTGGCAGTGTGGATAGG 60.815 63.158 0.00 0.00 0.00 2.57
649 692 1.815421 CGTGGCAGTGTGGATAGGC 60.815 63.158 0.00 0.00 0.00 3.93
650 693 1.815421 GTGGCAGTGTGGATAGGCG 60.815 63.158 0.00 0.00 0.00 5.52
651 694 2.897350 GGCAGTGTGGATAGGCGC 60.897 66.667 0.00 0.00 0.00 6.53
652 695 3.264897 GCAGTGTGGATAGGCGCG 61.265 66.667 0.00 0.00 0.00 6.86
653 696 2.184322 CAGTGTGGATAGGCGCGT 59.816 61.111 8.43 8.08 0.00 6.01
654 697 2.167219 CAGTGTGGATAGGCGCGTG 61.167 63.158 13.84 0.00 0.00 5.34
655 698 2.890474 GTGTGGATAGGCGCGTGG 60.890 66.667 13.84 0.00 0.00 4.94
656 699 4.830765 TGTGGATAGGCGCGTGGC 62.831 66.667 15.67 15.67 42.51 5.01
676 719 3.404550 CGAGCGTCGCAATTTATAGAC 57.595 47.619 21.09 0.00 31.14 2.59
680 723 1.920553 GTCGCAATTTATAGACGCGC 58.079 50.000 5.73 0.00 45.27 6.86
681 724 0.501015 TCGCAATTTATAGACGCGCG 59.499 50.000 30.96 30.96 45.27 6.86
682 725 0.501015 CGCAATTTATAGACGCGCGA 59.499 50.000 39.36 15.84 43.64 5.87
683 726 1.458665 CGCAATTTATAGACGCGCGAG 60.459 52.381 39.36 10.29 43.64 5.03
684 727 1.784856 GCAATTTATAGACGCGCGAGA 59.215 47.619 39.36 20.98 0.00 4.04
685 728 2.217847 GCAATTTATAGACGCGCGAGAA 59.782 45.455 39.36 20.70 0.00 2.87
686 729 3.659364 GCAATTTATAGACGCGCGAGAAG 60.659 47.826 39.36 14.52 0.00 2.85
687 730 1.474017 TTTATAGACGCGCGAGAAGC 58.526 50.000 39.36 18.85 43.95 3.86
710 753 3.784412 GCCAAAAGTAGCGCGCGA 61.784 61.111 37.18 19.65 0.00 5.87
711 754 2.395690 CCAAAAGTAGCGCGCGAG 59.604 61.111 37.18 8.39 0.00 5.03
737 780 4.101790 CTTTCCCGCACGCGCAAT 62.102 61.111 5.73 0.00 38.40 3.56
738 781 3.609214 CTTTCCCGCACGCGCAATT 62.609 57.895 5.73 0.00 38.40 2.32
739 782 3.888079 TTTCCCGCACGCGCAATTG 62.888 57.895 5.73 0.00 38.40 2.32
741 784 4.698651 CCCGCACGCGCAATTGTT 62.699 61.111 5.73 0.00 38.40 2.83
742 785 3.460278 CCGCACGCGCAATTGTTG 61.460 61.111 5.73 0.00 38.40 3.33
751 794 4.698651 CAATTGTTGCCCGCGCGT 62.699 61.111 29.95 3.84 38.08 6.01
752 795 3.972276 AATTGTTGCCCGCGCGTT 61.972 55.556 29.95 10.85 38.08 4.84
753 796 3.492311 AATTGTTGCCCGCGCGTTT 62.492 52.632 29.95 5.91 38.08 3.60
754 797 4.914420 TTGTTGCCCGCGCGTTTG 62.914 61.111 29.95 17.53 38.08 2.93
756 799 4.916273 GTTGCCCGCGCGTTTGTT 62.916 61.111 29.95 0.00 38.08 2.83
757 800 4.194720 TTGCCCGCGCGTTTGTTT 62.195 55.556 29.95 0.00 38.08 2.83
758 801 3.701604 TTGCCCGCGCGTTTGTTTT 62.702 52.632 29.95 0.00 38.08 2.43
759 802 3.391631 GCCCGCGCGTTTGTTTTC 61.392 61.111 29.95 4.16 0.00 2.29
760 803 2.728015 CCCGCGCGTTTGTTTTCC 60.728 61.111 29.95 0.00 0.00 3.13
761 804 3.088608 CCGCGCGTTTGTTTTCCG 61.089 61.111 29.95 4.86 0.00 4.30
762 805 3.738032 CGCGCGTTTGTTTTCCGC 61.738 61.111 24.19 0.00 43.74 5.54
763 806 3.391631 GCGCGTTTGTTTTCCGCC 61.392 61.111 8.43 0.00 44.29 6.13
764 807 2.024871 CGCGTTTGTTTTCCGCCA 59.975 55.556 0.00 0.00 44.29 5.69
765 808 2.290082 CGCGTTTGTTTTCCGCCAC 61.290 57.895 0.00 0.00 44.29 5.01
766 809 1.947146 GCGTTTGTTTTCCGCCACC 60.947 57.895 0.00 0.00 41.50 4.61
767 810 1.655959 CGTTTGTTTTCCGCCACCG 60.656 57.895 0.00 0.00 0.00 4.94
768 811 1.947146 GTTTGTTTTCCGCCACCGC 60.947 57.895 0.00 0.00 0.00 5.68
769 812 2.122167 TTTGTTTTCCGCCACCGCT 61.122 52.632 0.00 0.00 0.00 5.52
770 813 2.065906 TTTGTTTTCCGCCACCGCTC 62.066 55.000 0.00 0.00 0.00 5.03
771 814 2.975799 GTTTTCCGCCACCGCTCA 60.976 61.111 0.00 0.00 0.00 4.26
772 815 2.203224 TTTTCCGCCACCGCTCAA 60.203 55.556 0.00 0.00 0.00 3.02
773 816 2.258013 TTTTCCGCCACCGCTCAAG 61.258 57.895 0.00 0.00 0.00 3.02
774 817 2.668185 TTTTCCGCCACCGCTCAAGA 62.668 55.000 0.00 0.00 0.00 3.02
775 818 2.668185 TTTCCGCCACCGCTCAAGAA 62.668 55.000 0.00 0.00 0.00 2.52
784 827 3.441572 CCACCGCTCAAGAATCAAGAATT 59.558 43.478 0.00 0.00 0.00 2.17
845 890 7.012894 AGAGAAGAGTCGTTGGAACATATAGAG 59.987 40.741 0.00 0.00 39.30 2.43
913 958 0.036306 CAGCCCGTTTTAGACCCACT 59.964 55.000 0.00 0.00 0.00 4.00
929 974 3.910627 ACCCACTCCAATCCATACCTATC 59.089 47.826 0.00 0.00 0.00 2.08
938 983 5.365605 CCAATCCATACCTATCCGGCTATAA 59.634 44.000 0.00 0.00 35.61 0.98
939 984 6.281405 CAATCCATACCTATCCGGCTATAAC 58.719 44.000 0.00 0.00 35.61 1.89
1101 1146 1.963464 GCCTCGACCCCAAATCCGTA 61.963 60.000 0.00 0.00 0.00 4.02
1218 1265 1.529226 TCGACACCGGCAAATTCATT 58.471 45.000 0.00 0.00 36.24 2.57
1220 1267 1.732077 CGACACCGGCAAATTCATTGG 60.732 52.381 0.00 0.00 39.54 3.16
1300 1347 3.687698 GCGTAACAAGGGCTTAAATCTGA 59.312 43.478 0.00 0.00 0.00 3.27
1410 1460 1.127343 GCCTCTCTATCTGCAACCCT 58.873 55.000 0.00 0.00 0.00 4.34
1812 1991 2.425143 TCTTTGAGATGGATGGCACC 57.575 50.000 0.00 0.00 0.00 5.01
1911 2096 7.880160 TTGGGATTTCAAGTACCATATCAAG 57.120 36.000 0.00 0.00 0.00 3.02
1929 2114 4.854399 TCAAGTTGCCGTTTACAGAAATG 58.146 39.130 0.00 0.00 0.00 2.32
1934 2122 2.225491 TGCCGTTTACAGAAATGAGCAC 59.775 45.455 0.00 0.00 35.05 4.40
1935 2123 2.225491 GCCGTTTACAGAAATGAGCACA 59.775 45.455 0.00 0.00 34.00 4.57
1945 2133 1.927487 AATGAGCACATTTGGAGGCA 58.073 45.000 3.28 0.00 43.17 4.75
1968 2177 3.956199 GTGATGAACATTGGGATGTGGAT 59.044 43.478 0.00 0.00 45.58 3.41
1998 2207 0.179034 GGGATGGCGATCTGCTCTTT 60.179 55.000 8.71 0.00 45.43 2.52
2020 2229 1.340211 TGGTCAGTTTTGGTCGGTGTT 60.340 47.619 0.00 0.00 0.00 3.32
2089 2308 3.087031 CCCTCTGCATGTTCAAATGTCT 58.913 45.455 0.00 0.00 0.00 3.41
2194 2426 1.071699 GTTGGTGAGGTGGTGCTTCTA 59.928 52.381 0.00 0.00 0.00 2.10
2285 2540 5.541953 AGCCTCTTCTTCTTTTTGCATTT 57.458 34.783 0.00 0.00 0.00 2.32
2359 2628 2.868839 GCGTGCTTGTCTTGGTACCTTA 60.869 50.000 14.36 0.00 0.00 2.69
2370 2639 4.469945 TCTTGGTACCTTATGGACTGAAGG 59.530 45.833 14.36 0.00 46.56 3.46
2406 2678 7.148154 TGTGTTATTGCTAAAATGCCGAAGTAT 60.148 33.333 0.00 0.00 0.00 2.12
2407 2679 7.700656 GTGTTATTGCTAAAATGCCGAAGTATT 59.299 33.333 0.00 0.00 0.00 1.89
2408 2680 8.247562 TGTTATTGCTAAAATGCCGAAGTATTT 58.752 29.630 0.00 0.00 39.64 1.40
2480 2774 1.409064 TGATCCGCCTCATGTGTCTAC 59.591 52.381 0.00 0.00 0.00 2.59
2509 2803 3.338249 GGCTGAGCAATTGACTTCACTA 58.662 45.455 10.34 0.00 0.00 2.74
2597 2902 7.449395 TCTTCCTTGAACTGATGAATTGACATT 59.551 33.333 0.00 0.00 0.00 2.71
2619 3276 4.755411 TCCTTTTTATCTAGTGGTCTGCG 58.245 43.478 0.00 0.00 0.00 5.18
2633 3290 5.069914 AGTGGTCTGCGTAATGGTCAATATA 59.930 40.000 0.00 0.00 0.00 0.86
2635 3292 4.389077 GGTCTGCGTAATGGTCAATATAGC 59.611 45.833 0.00 0.00 0.00 2.97
2636 3293 4.988540 GTCTGCGTAATGGTCAATATAGCA 59.011 41.667 0.00 0.00 0.00 3.49
2656 3313 2.702748 AGGTGTTCCCTGTTTCTACCT 58.297 47.619 0.00 0.00 44.08 3.08
2660 3317 3.007614 GTGTTCCCTGTTTCTACCTGCTA 59.992 47.826 0.00 0.00 0.00 3.49
2666 3323 5.486063 TCCCTGTTTCTACCTGCTATTGTAA 59.514 40.000 0.00 0.00 0.00 2.41
2667 3324 6.157994 TCCCTGTTTCTACCTGCTATTGTAAT 59.842 38.462 0.00 0.00 0.00 1.89
2678 3335 8.701908 ACCTGCTATTGTAATTGATGATGAAT 57.298 30.769 0.00 0.00 0.00 2.57
2726 3388 7.660112 TGCAAGCTGAATCTGATTTTTAGAAA 58.340 30.769 4.11 0.00 0.00 2.52
2735 3397 8.491045 AATCTGATTTTTAGAAAACCCTGGAA 57.509 30.769 0.00 0.00 0.00 3.53
2740 3402 9.374711 TGATTTTTAGAAAACCCTGGAATACTT 57.625 29.630 0.00 0.00 0.00 2.24
2791 3453 6.477688 ACTCAACTGCTCAATGAAATGTTTTG 59.522 34.615 0.00 0.00 0.00 2.44
2795 3525 5.981315 ACTGCTCAATGAAATGTTTTGTCAG 59.019 36.000 0.00 0.00 33.11 3.51
2826 3556 9.104965 CATTTTTCTTCATGCATCCATTGTTAT 57.895 29.630 0.00 0.00 0.00 1.89
2827 3557 9.675464 ATTTTTCTTCATGCATCCATTGTTATT 57.325 25.926 0.00 0.00 0.00 1.40
2836 3566 5.105146 TGCATCCATTGTTATTGGGTTAACC 60.105 40.000 16.85 16.85 40.81 2.85
2841 3571 4.506886 TTGTTATTGGGTTAACCTTGCG 57.493 40.909 23.69 0.00 41.11 4.85
2848 3578 6.837471 ATTGGGTTAACCTTGCGTTATTTA 57.163 33.333 23.69 0.00 41.11 1.40
2849 3579 6.837471 TTGGGTTAACCTTGCGTTATTTAT 57.163 33.333 23.69 0.00 41.11 1.40
2852 3582 7.668492 TGGGTTAACCTTGCGTTATTTATTTT 58.332 30.769 23.69 0.00 41.11 1.82
2898 3628 9.909644 TCTTAGTACTCAAAAAGTAGACATGAC 57.090 33.333 0.00 0.00 41.17 3.06
2926 3656 7.940850 TGCTTTATATTATTTGGCTGAGGAAC 58.059 34.615 0.00 0.00 0.00 3.62
2997 4131 1.993370 GTTGTAGGCTTGTAGCTGACG 59.007 52.381 0.00 0.00 41.99 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 6.403049 TCTTTTCGGCTAATGATGACTGTTA 58.597 36.000 0.00 0.00 0.00 2.41
37 38 4.747108 CGATCTTTTCGGCTAATGATGACT 59.253 41.667 0.00 0.00 44.28 3.41
171 180 0.391597 TCGTCAACGAGGAAGCCTTT 59.608 50.000 0.22 0.00 44.22 3.11
435 478 0.953003 GCTAGTACTCCGCCGAGATT 59.047 55.000 9.16 0.00 38.52 2.40
536 579 3.898509 CTCTCCTCGCCGCTCCAG 61.899 72.222 0.00 0.00 0.00 3.86
539 582 3.132481 CTTCCTCTCCTCGCCGCTC 62.132 68.421 0.00 0.00 0.00 5.03
540 583 3.144193 CTTCCTCTCCTCGCCGCT 61.144 66.667 0.00 0.00 0.00 5.52
541 584 4.882396 GCTTCCTCTCCTCGCCGC 62.882 72.222 0.00 0.00 0.00 6.53
542 585 4.560856 CGCTTCCTCTCCTCGCCG 62.561 72.222 0.00 0.00 0.00 6.46
543 586 4.214327 CCGCTTCCTCTCCTCGCC 62.214 72.222 0.00 0.00 0.00 5.54
544 587 3.453679 ACCGCTTCCTCTCCTCGC 61.454 66.667 0.00 0.00 0.00 5.03
545 588 2.492090 CACCGCTTCCTCTCCTCG 59.508 66.667 0.00 0.00 0.00 4.63
546 589 1.682684 TCCACCGCTTCCTCTCCTC 60.683 63.158 0.00 0.00 0.00 3.71
547 590 1.985116 GTCCACCGCTTCCTCTCCT 60.985 63.158 0.00 0.00 0.00 3.69
548 591 2.579738 GTCCACCGCTTCCTCTCC 59.420 66.667 0.00 0.00 0.00 3.71
549 592 2.182030 CGTCCACCGCTTCCTCTC 59.818 66.667 0.00 0.00 0.00 3.20
569 612 3.898509 CTCTCCTCGCCGCTCCAG 61.899 72.222 0.00 0.00 0.00 3.86
572 615 3.132481 CTTCCTCTCCTCGCCGCTC 62.132 68.421 0.00 0.00 0.00 5.03
573 616 3.144193 CTTCCTCTCCTCGCCGCT 61.144 66.667 0.00 0.00 0.00 5.52
574 617 4.882396 GCTTCCTCTCCTCGCCGC 62.882 72.222 0.00 0.00 0.00 6.53
575 618 4.560856 CGCTTCCTCTCCTCGCCG 62.561 72.222 0.00 0.00 0.00 6.46
576 619 4.214327 CCGCTTCCTCTCCTCGCC 62.214 72.222 0.00 0.00 0.00 5.54
577 620 3.453679 ACCGCTTCCTCTCCTCGC 61.454 66.667 0.00 0.00 0.00 5.03
578 621 2.492090 CACCGCTTCCTCTCCTCG 59.508 66.667 0.00 0.00 0.00 4.63
579 622 1.682684 TCCACCGCTTCCTCTCCTC 60.683 63.158 0.00 0.00 0.00 3.71
580 623 1.985116 GTCCACCGCTTCCTCTCCT 60.985 63.158 0.00 0.00 0.00 3.69
581 624 2.579738 GTCCACCGCTTCCTCTCC 59.420 66.667 0.00 0.00 0.00 3.71
582 625 2.182030 CGTCCACCGCTTCCTCTC 59.818 66.667 0.00 0.00 0.00 3.20
601 644 2.796651 CATCTTTGCCGCTCCAGC 59.203 61.111 0.00 0.00 37.78 4.85
602 645 2.796651 GCATCTTTGCCGCTCCAG 59.203 61.111 0.00 0.00 43.38 3.86
611 654 1.638467 GCGCCTCGTAGCATCTTTG 59.362 57.895 0.00 0.00 0.00 2.77
612 655 1.878522 CGCGCCTCGTAGCATCTTT 60.879 57.895 0.00 0.00 0.00 2.52
613 656 2.278857 CGCGCCTCGTAGCATCTT 60.279 61.111 0.00 0.00 0.00 2.40
614 657 4.933064 GCGCGCCTCGTAGCATCT 62.933 66.667 23.24 0.00 41.07 2.90
629 672 2.125713 TATCCACACTGCCACGCG 60.126 61.111 3.53 3.53 0.00 6.01
630 673 1.815421 CCTATCCACACTGCCACGC 60.815 63.158 0.00 0.00 0.00 5.34
631 674 1.815421 GCCTATCCACACTGCCACG 60.815 63.158 0.00 0.00 0.00 4.94
632 675 1.815421 CGCCTATCCACACTGCCAC 60.815 63.158 0.00 0.00 0.00 5.01
633 676 2.584064 CGCCTATCCACACTGCCA 59.416 61.111 0.00 0.00 0.00 4.92
634 677 2.897350 GCGCCTATCCACACTGCC 60.897 66.667 0.00 0.00 0.00 4.85
635 678 3.264897 CGCGCCTATCCACACTGC 61.265 66.667 0.00 0.00 0.00 4.40
636 679 2.167219 CACGCGCCTATCCACACTG 61.167 63.158 5.73 0.00 0.00 3.66
637 680 2.184322 CACGCGCCTATCCACACT 59.816 61.111 5.73 0.00 0.00 3.55
638 681 2.890474 CCACGCGCCTATCCACAC 60.890 66.667 5.73 0.00 0.00 3.82
639 682 4.830765 GCCACGCGCCTATCCACA 62.831 66.667 5.73 0.00 0.00 4.17
656 699 2.160272 CGTCTATAAATTGCGACGCTCG 60.160 50.000 22.08 0.00 41.97 5.03
657 700 3.404550 CGTCTATAAATTGCGACGCTC 57.595 47.619 22.08 0.00 41.97 5.03
664 707 1.784856 TCTCGCGCGTCTATAAATTGC 59.215 47.619 30.98 0.00 0.00 3.56
665 708 3.659364 GCTTCTCGCGCGTCTATAAATTG 60.659 47.826 30.98 10.63 0.00 2.32
666 709 2.471743 GCTTCTCGCGCGTCTATAAATT 59.528 45.455 30.98 0.00 0.00 1.82
667 710 2.052157 GCTTCTCGCGCGTCTATAAAT 58.948 47.619 30.98 0.00 0.00 1.40
668 711 1.474017 GCTTCTCGCGCGTCTATAAA 58.526 50.000 30.98 14.10 0.00 1.40
669 712 3.159446 GCTTCTCGCGCGTCTATAA 57.841 52.632 30.98 15.79 0.00 0.98
670 713 4.916412 GCTTCTCGCGCGTCTATA 57.084 55.556 30.98 9.10 0.00 1.31
687 730 2.175811 GCTACTTTTGGCGTGCCG 59.824 61.111 6.37 0.00 39.42 5.69
688 731 2.175811 CGCTACTTTTGGCGTGCC 59.824 61.111 3.30 3.30 45.34 5.01
693 736 3.702334 CTCGCGCGCTACTTTTGGC 62.702 63.158 30.48 0.00 0.00 4.52
694 737 2.395690 CTCGCGCGCTACTTTTGG 59.604 61.111 30.48 11.00 0.00 3.28
695 738 2.276058 GCTCGCGCGCTACTTTTG 60.276 61.111 30.48 11.83 0.00 2.44
696 739 2.432628 AGCTCGCGCGCTACTTTT 60.433 55.556 30.48 6.70 42.32 2.27
697 740 3.181967 CAGCTCGCGCGCTACTTT 61.182 61.111 30.48 7.88 42.32 2.66
734 777 4.698651 ACGCGCGGGCAACAATTG 62.699 61.111 35.22 3.24 39.92 2.32
735 778 3.492311 AAACGCGCGGGCAACAATT 62.492 52.632 35.22 13.77 39.92 2.32
736 779 3.972276 AAACGCGCGGGCAACAAT 61.972 55.556 35.22 7.19 39.92 2.71
737 780 4.914420 CAAACGCGCGGGCAACAA 62.914 61.111 35.22 0.00 39.92 2.83
739 782 4.916273 AACAAACGCGCGGGCAAC 62.916 61.111 35.22 0.00 39.92 4.17
740 783 3.701604 AAAACAAACGCGCGGGCAA 62.702 52.632 35.22 0.00 39.92 4.52
741 784 4.194720 AAAACAAACGCGCGGGCA 62.195 55.556 35.22 0.00 39.92 5.36
742 785 3.391631 GAAAACAAACGCGCGGGC 61.392 61.111 35.22 15.47 0.00 6.13
743 786 2.728015 GGAAAACAAACGCGCGGG 60.728 61.111 35.22 24.28 0.00 6.13
744 787 3.088608 CGGAAAACAAACGCGCGG 61.089 61.111 35.22 19.11 0.00 6.46
745 788 3.738032 GCGGAAAACAAACGCGCG 61.738 61.111 30.96 30.96 43.98 6.86
749 792 1.655959 CGGTGGCGGAAAACAAACG 60.656 57.895 0.00 0.00 0.00 3.60
750 793 1.947146 GCGGTGGCGGAAAACAAAC 60.947 57.895 0.00 0.00 0.00 2.93
751 794 2.065906 GAGCGGTGGCGGAAAACAAA 62.066 55.000 0.00 0.00 46.35 2.83
752 795 2.517402 AGCGGTGGCGGAAAACAA 60.517 55.556 0.00 0.00 46.35 2.83
753 796 2.975799 GAGCGGTGGCGGAAAACA 60.976 61.111 0.00 0.00 46.35 2.83
754 797 2.458006 CTTGAGCGGTGGCGGAAAAC 62.458 60.000 0.00 0.00 46.35 2.43
755 798 2.203224 TTGAGCGGTGGCGGAAAA 60.203 55.556 0.00 0.00 46.35 2.29
756 799 2.668185 TTCTTGAGCGGTGGCGGAAA 62.668 55.000 0.00 0.00 46.35 3.13
757 800 2.463589 ATTCTTGAGCGGTGGCGGAA 62.464 55.000 0.00 0.00 46.35 4.30
758 801 2.852495 GATTCTTGAGCGGTGGCGGA 62.852 60.000 0.00 0.00 46.35 5.54
759 802 2.436646 ATTCTTGAGCGGTGGCGG 60.437 61.111 0.00 0.00 46.35 6.13
760 803 1.298157 TTGATTCTTGAGCGGTGGCG 61.298 55.000 0.00 0.00 46.35 5.69
761 804 0.449388 CTTGATTCTTGAGCGGTGGC 59.551 55.000 0.00 0.00 40.37 5.01
762 805 2.099141 TCTTGATTCTTGAGCGGTGG 57.901 50.000 0.00 0.00 0.00 4.61
763 806 4.691860 AATTCTTGATTCTTGAGCGGTG 57.308 40.909 0.00 0.00 0.00 4.94
764 807 6.173339 TCTTAATTCTTGATTCTTGAGCGGT 58.827 36.000 0.00 0.00 0.00 5.68
765 808 6.668541 TCTTAATTCTTGATTCTTGAGCGG 57.331 37.500 0.00 0.00 0.00 5.52
766 809 7.746929 AGTTCTTAATTCTTGATTCTTGAGCG 58.253 34.615 0.00 0.00 0.00 5.03
767 810 8.725148 TGAGTTCTTAATTCTTGATTCTTGAGC 58.275 33.333 0.00 0.00 0.00 4.26
784 827 6.524734 TGCAGAGTTCAGATTTGAGTTCTTA 58.475 36.000 0.00 0.00 34.15 2.10
800 843 1.806542 CTTACCGTGCATTGCAGAGTT 59.193 47.619 12.53 0.36 40.08 3.01
845 890 0.540923 AGACCCAATGCTCTCTCTGC 59.459 55.000 0.00 0.00 0.00 4.26
913 958 1.906574 GCCGGATAGGTATGGATTGGA 59.093 52.381 5.05 0.00 43.70 3.53
1017 1062 3.468326 GAGAGGATTCGCCCCTGCC 62.468 68.421 0.00 0.00 37.37 4.85
1220 1267 2.995881 GATACGGTAGTGGACGCGGC 62.996 65.000 12.47 7.53 0.00 6.53
1300 1347 2.357517 CTTGTCAAGCCGAGCCGT 60.358 61.111 0.00 0.00 0.00 5.68
1812 1991 0.180171 TATGGTTGTGGATGCCGAGG 59.820 55.000 0.00 0.00 0.00 4.63
1911 2096 3.234386 GCTCATTTCTGTAAACGGCAAC 58.766 45.455 0.00 0.00 0.00 4.17
1929 2114 0.524862 CACTGCCTCCAAATGTGCTC 59.475 55.000 0.00 0.00 0.00 4.26
1934 2122 2.821378 TGTTCATCACTGCCTCCAAATG 59.179 45.455 0.00 0.00 0.00 2.32
1935 2123 3.159213 TGTTCATCACTGCCTCCAAAT 57.841 42.857 0.00 0.00 0.00 2.32
1940 2128 1.747355 CCCAATGTTCATCACTGCCTC 59.253 52.381 0.00 0.00 0.00 4.70
1945 2133 3.010472 TCCACATCCCAATGTTCATCACT 59.990 43.478 0.00 0.00 43.74 3.41
1968 2177 0.958091 CGCCATCCCTTGAAACAACA 59.042 50.000 0.00 0.00 0.00 3.33
1998 2207 0.834612 ACCGACCAAAACTGACCAGA 59.165 50.000 3.76 0.00 0.00 3.86
2020 2229 1.406898 TCAATTTGCCACGTGAAGCAA 59.593 42.857 22.92 22.92 46.74 3.91
2047 2266 8.898728 AGAGGGTTTCATAATCATGATAGGAAT 58.101 33.333 9.04 0.00 40.85 3.01
2194 2426 2.357154 GGACATGACAGGTAGGGCATTT 60.357 50.000 0.00 0.00 0.00 2.32
2359 2628 4.289672 ACAACATTAGTCCCTTCAGTCCAT 59.710 41.667 0.00 0.00 0.00 3.41
2370 2639 9.855021 ATTTTAGCAATAACACAACATTAGTCC 57.145 29.630 0.00 0.00 0.00 3.85
2480 2774 2.559668 TCAATTGCTCAGCCCAAGAAAG 59.440 45.455 0.00 0.00 0.00 2.62
2597 2902 4.222145 ACGCAGACCACTAGATAAAAAGGA 59.778 41.667 0.00 0.00 0.00 3.36
2619 3276 6.204882 GGAACACCTGCTATATTGACCATTAC 59.795 42.308 0.00 0.00 0.00 1.89
2700 3362 6.849502 TCTAAAAATCAGATTCAGCTTGCAG 58.150 36.000 0.00 0.00 0.00 4.41
2791 3453 7.878477 TGCATGAAGAAAAATGAATTCTGAC 57.122 32.000 7.05 0.00 37.22 3.51
2795 3525 7.837202 TGGATGCATGAAGAAAAATGAATTC 57.163 32.000 2.46 0.00 0.00 2.17
2805 3535 6.407187 CCCAATAACAATGGATGCATGAAGAA 60.407 38.462 2.46 0.00 40.56 2.52
2813 3543 5.128663 AGGTTAACCCAATAACAATGGATGC 59.871 40.000 21.30 0.00 40.56 3.91
2826 3556 6.837471 ATAAATAACGCAAGGTTAACCCAA 57.163 33.333 21.30 0.00 43.93 4.12
2827 3557 6.837471 AATAAATAACGCAAGGTTAACCCA 57.163 33.333 21.30 0.00 43.93 4.51
2873 3603 9.915629 AGTCATGTCTACTTTTTGAGTACTAAG 57.084 33.333 0.00 0.00 39.86 2.18
2882 3612 7.992180 AAAGCAAAGTCATGTCTACTTTTTG 57.008 32.000 7.98 3.42 42.97 2.44
2898 3628 8.632679 TCCTCAGCCAAATAATATAAAGCAAAG 58.367 33.333 0.00 0.00 0.00 2.77
2961 4095 6.436218 AGCCTACAACAAAGGGTAAAAATAGG 59.564 38.462 0.00 0.00 42.95 2.57
2964 4098 6.099125 ACAAGCCTACAACAAAGGGTAAAAAT 59.901 34.615 0.00 0.00 43.96 1.82
2968 4102 4.173290 ACAAGCCTACAACAAAGGGTAA 57.827 40.909 0.00 0.00 43.96 2.85
2997 4131 5.911378 AGGAAAATCTGCCTCTTTTCATC 57.089 39.130 13.40 2.19 41.15 2.92


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

AutoCloner maintained by Alex Coulton.