Multiple sequence alignment - TraesCS2B01G577300

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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 TraesCS2B01G577300 chr2B 100.000 3410 0 0 1 3410 765585453 765588862 0.000000e+00 6298.0
1 TraesCS2B01G577300 chr2B 93.025 1448 94 5 992 2436 765792944 765791501 0.000000e+00 2108.0
2 TraesCS2B01G577300 chr2A 93.388 1815 89 11 614 2410 755118128 755119929 0.000000e+00 2658.0
3 TraesCS2B01G577300 chr2A 93.333 1440 87 6 988 2425 755340929 755339497 0.000000e+00 2119.0
4 TraesCS2B01G577300 chr2A 93.766 401 25 0 176 576 755116417 755116817 1.350000e-168 603.0
5 TraesCS2B01G577300 chr2A 94.565 276 9 4 2930 3204 755120287 755120557 4.070000e-114 422.0
6 TraesCS2B01G577300 chr2A 87.546 273 16 5 2841 3113 755339170 755338916 1.990000e-77 300.0
7 TraesCS2B01G577300 chr2A 90.909 198 14 3 2511 2706 755119967 755120162 2.610000e-66 263.0
8 TraesCS2B01G577300 chr2A 94.531 128 6 1 3284 3410 755121955 755122082 2.680000e-46 196.0
9 TraesCS2B01G577300 chr2A 85.271 129 17 2 3284 3410 577214506 577214634 7.680000e-27 132.0
10 TraesCS2B01G577300 chr2A 100.000 48 0 0 2800 2847 755339241 755339194 4.690000e-14 89.8
11 TraesCS2B01G577300 chr2A 92.727 55 3 1 2841 2894 755120233 755120287 1.010000e-10 78.7
12 TraesCS2B01G577300 chr2D 94.337 1395 76 1 1016 2410 623947752 623949143 0.000000e+00 2135.0
13 TraesCS2B01G577300 chr2D 92.872 1459 96 6 982 2436 624054186 624052732 0.000000e+00 2111.0
14 TraesCS2B01G577300 chr2D 90.586 563 35 12 2850 3410 623952013 623952559 0.000000e+00 730.0
15 TraesCS2B01G577300 chr2D 88.914 451 18 9 570 1004 623947342 623947776 8.380000e-146 527.0
16 TraesCS2B01G577300 chr2D 92.523 107 4 3 2707 2812 488233726 488233623 2.120000e-32 150.0
17 TraesCS2B01G577300 chr2D 79.556 225 31 8 3188 3410 448909636 448909425 2.740000e-31 147.0
18 TraesCS2B01G577300 chr2D 78.302 212 30 9 3201 3410 459573509 459573706 4.620000e-24 122.0
19 TraesCS2B01G577300 chr5D 82.816 1193 162 28 1133 2308 238670462 238669296 0.000000e+00 1027.0
20 TraesCS2B01G577300 chr5D 95.833 96 2 1 2708 2803 557210943 557211036 1.640000e-33 154.0
21 TraesCS2B01G577300 chr4A 85.138 1016 128 16 944 1943 677272480 677273488 0.000000e+00 1018.0
22 TraesCS2B01G577300 chr4A 82.443 131 19 3 3284 3410 620851580 620851710 1.000000e-20 111.0
23 TraesCS2B01G577300 chr7A 82.441 1196 164 31 1130 2302 262852443 262853615 0.000000e+00 1003.0
24 TraesCS2B01G577300 chr7B 82.358 1196 165 29 1130 2302 222553192 222554364 0.000000e+00 998.0
25 TraesCS2B01G577300 chr7B 93.204 103 5 1 2701 2803 230028188 230028288 2.120000e-32 150.0
26 TraesCS2B01G577300 chr7B 92.233 103 6 1 2701 2803 203549587 203549687 9.860000e-31 145.0
27 TraesCS2B01G577300 chr7D 92.042 578 39 5 1 576 534358752 534358180 0.000000e+00 806.0
28 TraesCS2B01G577300 chr7D 92.326 430 23 5 2841 3269 534447498 534447078 1.350000e-168 603.0
29 TraesCS2B01G577300 chr7D 91.501 353 30 0 970 1322 534357812 534357460 1.420000e-133 486.0
30 TraesCS2B01G577300 chr7D 84.327 453 60 11 1130 1578 246373949 246374394 1.880000e-117 433.0
31 TraesCS2B01G577300 chr7D 89.231 260 19 8 600 857 534449707 534449455 1.970000e-82 316.0
32 TraesCS2B01G577300 chr7D 82.796 372 24 23 570 925 534358155 534357808 2.570000e-76 296.0
33 TraesCS2B01G577300 chr7D 89.450 218 18 3 2490 2706 534447786 534447573 1.560000e-68 270.0
34 TraesCS2B01G577300 chr7D 97.561 41 1 0 570 610 534455522 534455482 1.700000e-08 71.3
35 TraesCS2B01G577300 chr6D 83.111 225 23 7 3188 3410 374123974 374123763 1.250000e-44 191.0
36 TraesCS2B01G577300 chr6B 80.603 232 23 11 3188 3410 561288550 561288332 3.520000e-35 159.0
37 TraesCS2B01G577300 chr6B 95.918 98 2 1 2707 2804 38619599 38619694 1.270000e-34 158.0
38 TraesCS2B01G577300 chr5B 93.269 104 5 1 2707 2810 539328255 539328154 5.890000e-33 152.0
39 TraesCS2B01G577300 chr5B 94.898 98 3 1 2707 2804 704989274 704989369 5.890000e-33 152.0
40 TraesCS2B01G577300 chr5B 93.204 103 5 1 2701 2803 223038240 223038340 2.120000e-32 150.0
41 TraesCS2B01G577300 chr3A 94.898 98 3 1 2707 2804 523554212 523554117 5.890000e-33 152.0
42 TraesCS2B01G577300 chr3B 86.555 119 14 2 3294 3410 746798750 746798868 2.760000e-26 130.0
43 TraesCS2B01G577300 chr6A 89.474 76 6 2 3188 3263 384087918 384087845 1.010000e-15 95.3


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 TraesCS2B01G577300 chr2B 765585453 765588862 3409 False 6298.000000 6298 100.000000 1 3410 1 chr2B.!!$F1 3409
1 TraesCS2B01G577300 chr2B 765791501 765792944 1443 True 2108.000000 2108 93.025000 992 2436 1 chr2B.!!$R1 1444
2 TraesCS2B01G577300 chr2A 755338916 755340929 2013 True 836.266667 2119 93.626333 988 3113 3 chr2A.!!$R1 2125
3 TraesCS2B01G577300 chr2A 755116417 755122082 5665 False 703.450000 2658 93.314333 176 3410 6 chr2A.!!$F2 3234
4 TraesCS2B01G577300 chr2D 624052732 624054186 1454 True 2111.000000 2111 92.872000 982 2436 1 chr2D.!!$R3 1454
5 TraesCS2B01G577300 chr2D 623947342 623952559 5217 False 1130.666667 2135 91.279000 570 3410 3 chr2D.!!$F2 2840
6 TraesCS2B01G577300 chr5D 238669296 238670462 1166 True 1027.000000 1027 82.816000 1133 2308 1 chr5D.!!$R1 1175
7 TraesCS2B01G577300 chr4A 677272480 677273488 1008 False 1018.000000 1018 85.138000 944 1943 1 chr4A.!!$F2 999
8 TraesCS2B01G577300 chr7A 262852443 262853615 1172 False 1003.000000 1003 82.441000 1130 2302 1 chr7A.!!$F1 1172
9 TraesCS2B01G577300 chr7B 222553192 222554364 1172 False 998.000000 998 82.358000 1130 2302 1 chr7B.!!$F2 1172
10 TraesCS2B01G577300 chr7D 534357460 534358752 1292 True 529.333333 806 88.779667 1 1322 3 chr7D.!!$R2 1321
11 TraesCS2B01G577300 chr7D 534447078 534449707 2629 True 396.333333 603 90.335667 600 3269 3 chr7D.!!$R3 2669

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
118 119 0.322546 AGAAATGGACGAGGGGTTGC 60.323 55.0 0.0 0.0 0.0 4.17 F
937 2561 1.030457 ATGATCCCTGGTACGACGAC 58.970 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
1039 3646 1.341606 GCGAAGAAGACGAGGAACAG 58.658 55.0 0.0 0.0 0.0 3.16 R
2447 5082 0.037605 ACCTAAAACGCCGTCCTCTG 60.038 55.0 0.0 0.0 0.0 3.35 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
21 22 1.546961 GTTCCCGGAGAAGAGAGACA 58.453 55.000 0.73 0.00 34.29 3.41
28 29 3.078097 CGGAGAAGAGAGACAGTGAGAA 58.922 50.000 0.00 0.00 0.00 2.87
34 35 5.241506 AGAAGAGAGACAGTGAGAACTCAAG 59.758 44.000 6.08 5.27 41.85 3.02
36 37 3.823873 GAGAGACAGTGAGAACTCAAGGA 59.176 47.826 6.08 0.00 41.85 3.36
45 46 4.278669 GTGAGAACTCAAGGATATAGCCGA 59.721 45.833 6.08 0.00 41.85 5.54
49 50 3.158676 ACTCAAGGATATAGCCGAGTCC 58.841 50.000 10.69 0.00 26.75 3.85
68 69 2.192979 GGGCATGCGAGATGGGAA 59.807 61.111 12.44 0.00 0.00 3.97
69 70 1.228367 GGGCATGCGAGATGGGAAT 60.228 57.895 12.44 0.00 0.00 3.01
70 71 1.521450 GGGCATGCGAGATGGGAATG 61.521 60.000 12.44 0.00 0.00 2.67
76 77 0.607489 GCGAGATGGGAATGGGGATG 60.607 60.000 0.00 0.00 0.00 3.51
90 91 0.621862 GGGATGGGGAAGGTGAGACT 60.622 60.000 0.00 0.00 0.00 3.24
95 96 2.915869 TGGGGAAGGTGAGACTAATGT 58.084 47.619 0.00 0.00 0.00 2.71
118 119 0.322546 AGAAATGGACGAGGGGTTGC 60.323 55.000 0.00 0.00 0.00 4.17
122 124 3.637273 GGACGAGGGGTTGCTGGT 61.637 66.667 0.00 0.00 0.00 4.00
172 174 4.293415 GCTTGATTGGTTTGTTCAGTGAG 58.707 43.478 0.00 0.00 0.00 3.51
223 225 5.635417 TGAAAAATGTATTGGCGTCATGA 57.365 34.783 0.00 0.00 0.00 3.07
387 390 9.142014 TCTGGAGTTTGATTTTTCTTCCAAATA 57.858 29.630 0.00 0.00 32.16 1.40
429 432 8.862550 AACTTGAATTTCTGAAACTTCATGAC 57.137 30.769 25.71 10.14 36.46 3.06
491 494 5.630121 TCAAATTCTGAAAACTAGGCCTGA 58.370 37.500 17.99 0.00 0.00 3.86
534 537 8.845942 ACTGTACTCGAAAATTTACCAAAAAC 57.154 30.769 0.00 0.00 0.00 2.43
541 544 7.901002 TCGAAAATTTACCAAAAACTTGAAGC 58.099 30.769 0.00 0.00 0.00 3.86
556 559 8.648557 AAACTTGAAGCTCCAAAAATAGAAAC 57.351 30.769 0.00 0.00 0.00 2.78
643 1919 1.669049 TACTACGTGGTGGATGGCGG 61.669 60.000 15.58 0.00 0.00 6.13
692 1968 1.095807 TCTCGACCGTGCGATCTGAT 61.096 55.000 0.00 0.00 39.85 2.90
756 2039 3.131223 GGATCAGATCACAGAGGTCGAAA 59.869 47.826 12.66 0.00 0.00 3.46
880 2504 8.848474 AGACCAATATAAAATAAGATCACCGG 57.152 34.615 0.00 0.00 0.00 5.28
881 2505 7.390718 AGACCAATATAAAATAAGATCACCGGC 59.609 37.037 0.00 0.00 0.00 6.13
882 2506 6.433093 ACCAATATAAAATAAGATCACCGGCC 59.567 38.462 0.00 0.00 0.00 6.13
927 2551 2.545526 CGATCGAAACCAATGATCCCTG 59.454 50.000 10.26 0.00 36.08 4.45
933 2557 1.874129 ACCAATGATCCCTGGTACGA 58.126 50.000 12.89 0.00 44.28 3.43
934 2558 1.485066 ACCAATGATCCCTGGTACGAC 59.515 52.381 12.89 0.00 44.28 4.34
936 2560 1.407618 CAATGATCCCTGGTACGACGA 59.592 52.381 0.00 0.00 0.00 4.20
937 2561 1.030457 ATGATCCCTGGTACGACGAC 58.970 55.000 0.00 0.00 0.00 4.34
938 2562 1.033746 TGATCCCTGGTACGACGACC 61.034 60.000 0.00 5.67 40.21 4.79
940 2564 1.318158 ATCCCTGGTACGACGACCAC 61.318 60.000 13.06 3.48 44.79 4.16
941 2565 2.177531 CCTGGTACGACGACCACG 59.822 66.667 13.06 7.66 44.79 4.94
942 2566 2.327343 CCTGGTACGACGACCACGA 61.327 63.158 13.06 0.82 44.79 4.35
943 2567 1.154338 CTGGTACGACGACCACGAC 60.154 63.158 13.06 0.00 44.79 4.34
944 2568 2.176792 GGTACGACGACCACGACC 59.823 66.667 0.00 0.00 42.66 4.79
959 2589 3.185082 GACCACGACCACGACGACA 62.185 63.158 0.00 0.00 42.66 4.35
1097 3707 3.762992 CGCGCACGTCGACAATGT 61.763 61.111 17.16 2.20 41.67 2.71
1607 4220 2.515057 ACGCAACGGGCAGAACAA 60.515 55.556 2.26 0.00 45.17 2.83
1733 4346 1.612442 ACCTCGCTAAGAAGGCCCA 60.612 57.895 0.00 0.00 0.00 5.36
1872 4493 1.153086 GCTCTACGAGTCCGGGGTA 60.153 63.158 0.00 0.00 40.78 3.69
1911 4532 2.260434 GAGCTTGACCACGCCGTA 59.740 61.111 0.00 0.00 0.00 4.02
2088 4711 1.980772 CTACCCCGTCAAGACCGGT 60.981 63.158 6.92 6.92 43.98 5.28
2139 4774 1.268352 GAGGAGAAGTGCGATCGCTAT 59.732 52.381 37.01 24.10 42.51 2.97
2140 4775 1.683917 AGGAGAAGTGCGATCGCTATT 59.316 47.619 37.01 29.94 42.51 1.73
2303 4938 2.281208 TGGGAAACGAACCTGCGG 60.281 61.111 0.00 0.00 35.12 5.69
2327 4962 0.608640 AGCAAGGGAAGTCCGTACAG 59.391 55.000 0.00 0.00 41.52 2.74
2422 5057 9.629878 TCTTTTCGATCTAGATCTACTTTAGGT 57.370 33.333 26.29 0.00 35.72 3.08
2451 5086 6.771188 ACGTTACAACTTTCATTCTCAGAG 57.229 37.500 0.00 0.00 0.00 3.35
2452 5087 5.696724 ACGTTACAACTTTCATTCTCAGAGG 59.303 40.000 0.00 0.00 0.00 3.69
2453 5088 5.926542 CGTTACAACTTTCATTCTCAGAGGA 59.073 40.000 0.00 0.00 0.00 3.71
2454 5089 6.128795 CGTTACAACTTTCATTCTCAGAGGAC 60.129 42.308 0.00 0.00 0.00 3.85
2455 5090 4.310769 ACAACTTTCATTCTCAGAGGACG 58.689 43.478 0.00 0.00 0.00 4.79
2476 5111 3.666111 CGGCGTTTTAGGTTACAGCTTTC 60.666 47.826 0.00 0.00 0.00 2.62
2496 5151 2.751259 TCGGTTCTCATAACGTAGCAGT 59.249 45.455 0.00 0.00 0.00 4.40
2497 5152 3.106672 CGGTTCTCATAACGTAGCAGTC 58.893 50.000 0.00 0.00 0.00 3.51
2498 5153 3.181499 CGGTTCTCATAACGTAGCAGTCT 60.181 47.826 0.00 0.00 0.00 3.24
2499 5154 4.674623 CGGTTCTCATAACGTAGCAGTCTT 60.675 45.833 0.00 0.00 0.00 3.01
2500 5155 5.169295 GGTTCTCATAACGTAGCAGTCTTT 58.831 41.667 0.00 0.00 0.00 2.52
2501 5156 5.288952 GGTTCTCATAACGTAGCAGTCTTTC 59.711 44.000 0.00 0.00 0.00 2.62
2502 5157 5.899120 TCTCATAACGTAGCAGTCTTTCT 57.101 39.130 0.00 0.00 0.00 2.52
2503 5158 6.268825 TCTCATAACGTAGCAGTCTTTCTT 57.731 37.500 0.00 0.00 0.00 2.52
2504 5159 6.688578 TCTCATAACGTAGCAGTCTTTCTTT 58.311 36.000 0.00 0.00 0.00 2.52
2505 5160 7.152645 TCTCATAACGTAGCAGTCTTTCTTTT 58.847 34.615 0.00 0.00 0.00 2.27
2506 5161 7.656137 TCTCATAACGTAGCAGTCTTTCTTTTT 59.344 33.333 0.00 0.00 0.00 1.94
2561 5244 5.541484 AGCAGGAGTCATTCTTTTTCCAATT 59.459 36.000 0.00 0.00 0.00 2.32
2706 6467 5.721960 TCCTAATATGATCCAGGGTAAGAGC 59.278 44.000 0.00 0.00 0.00 4.09
2707 6468 5.723887 CCTAATATGATCCAGGGTAAGAGCT 59.276 44.000 0.00 0.00 0.00 4.09
2708 6469 5.753721 AATATGATCCAGGGTAAGAGCTC 57.246 43.478 5.27 5.27 0.00 4.09
2709 6470 1.794714 TGATCCAGGGTAAGAGCTCC 58.205 55.000 10.93 0.00 0.00 4.70
2710 6471 1.052617 GATCCAGGGTAAGAGCTCCC 58.947 60.000 10.93 4.88 43.71 4.30
2714 6475 3.539842 GGGTAAGAGCTCCCTCCG 58.460 66.667 10.93 0.00 40.48 4.63
2715 6476 1.381463 GGGTAAGAGCTCCCTCCGT 60.381 63.158 10.93 0.00 40.48 4.69
2716 6477 0.976590 GGGTAAGAGCTCCCTCCGTT 60.977 60.000 10.93 0.00 40.48 4.44
2717 6478 0.460722 GGTAAGAGCTCCCTCCGTTC 59.539 60.000 10.93 0.00 38.96 3.95
2718 6479 0.460722 GTAAGAGCTCCCTCCGTTCC 59.539 60.000 10.93 0.00 38.96 3.62
2719 6480 0.040646 TAAGAGCTCCCTCCGTTCCA 59.959 55.000 10.93 0.00 38.96 3.53
2720 6481 0.836400 AAGAGCTCCCTCCGTTCCAA 60.836 55.000 10.93 0.00 38.96 3.53
2721 6482 0.836400 AGAGCTCCCTCCGTTCCAAA 60.836 55.000 10.93 0.00 38.96 3.28
2722 6483 0.036306 GAGCTCCCTCCGTTCCAAAA 59.964 55.000 0.87 0.00 31.68 2.44
2723 6484 0.698818 AGCTCCCTCCGTTCCAAAAT 59.301 50.000 0.00 0.00 0.00 1.82
2724 6485 1.913419 AGCTCCCTCCGTTCCAAAATA 59.087 47.619 0.00 0.00 0.00 1.40
2725 6486 2.092914 AGCTCCCTCCGTTCCAAAATAG 60.093 50.000 0.00 0.00 0.00 1.73
2726 6487 2.355818 GCTCCCTCCGTTCCAAAATAGT 60.356 50.000 0.00 0.00 0.00 2.12
2727 6488 3.872630 GCTCCCTCCGTTCCAAAATAGTT 60.873 47.826 0.00 0.00 0.00 2.24
2728 6489 3.681593 TCCCTCCGTTCCAAAATAGTTG 58.318 45.455 0.00 0.00 0.00 3.16
2729 6490 3.328343 TCCCTCCGTTCCAAAATAGTTGA 59.672 43.478 0.00 0.00 0.00 3.18
2730 6491 3.439129 CCCTCCGTTCCAAAATAGTTGAC 59.561 47.826 0.00 0.00 0.00 3.18
2731 6492 3.439129 CCTCCGTTCCAAAATAGTTGACC 59.561 47.826 0.00 0.00 0.00 4.02
2732 6493 3.414269 TCCGTTCCAAAATAGTTGACCC 58.586 45.455 0.00 0.00 0.00 4.46
2733 6494 3.150767 CCGTTCCAAAATAGTTGACCCA 58.849 45.455 0.00 0.00 0.00 4.51
2734 6495 3.570550 CCGTTCCAAAATAGTTGACCCAA 59.429 43.478 0.00 0.00 0.00 4.12
2735 6496 4.542735 CGTTCCAAAATAGTTGACCCAAC 58.457 43.478 1.86 1.86 43.83 3.77
2748 6509 6.688637 GTTGACCCAACTTTGTACTAACTT 57.311 37.500 2.85 0.00 40.73 2.66
2749 6510 7.092137 GTTGACCCAACTTTGTACTAACTTT 57.908 36.000 2.85 0.00 40.73 2.66
2750 6511 6.687081 TGACCCAACTTTGTACTAACTTTG 57.313 37.500 0.00 0.00 0.00 2.77
2751 6512 6.181908 TGACCCAACTTTGTACTAACTTTGT 58.818 36.000 0.00 0.00 0.00 2.83
2752 6513 7.337167 TGACCCAACTTTGTACTAACTTTGTA 58.663 34.615 0.00 0.00 0.00 2.41
2753 6514 7.280652 TGACCCAACTTTGTACTAACTTTGTAC 59.719 37.037 6.58 6.58 40.27 2.90
2754 6515 7.341030 ACCCAACTTTGTACTAACTTTGTACT 58.659 34.615 12.73 0.00 40.44 2.73
2755 6516 8.485392 ACCCAACTTTGTACTAACTTTGTACTA 58.515 33.333 12.73 4.86 40.44 1.82
2756 6517 9.328845 CCCAACTTTGTACTAACTTTGTACTAA 57.671 33.333 12.73 10.75 40.44 2.24
2793 6554 9.746711 CAAAGTTGAGTCATCTATTTTAGAACG 57.253 33.333 4.14 0.00 38.50 3.95
2794 6555 8.480643 AAGTTGAGTCATCTATTTTAGAACGG 57.519 34.615 4.14 0.00 38.50 4.44
2795 6556 7.837863 AGTTGAGTCATCTATTTTAGAACGGA 58.162 34.615 1.70 0.00 38.50 4.69
2796 6557 7.976734 AGTTGAGTCATCTATTTTAGAACGGAG 59.023 37.037 1.70 0.00 38.50 4.63
2797 6558 7.640597 TGAGTCATCTATTTTAGAACGGAGA 57.359 36.000 0.00 0.00 38.50 3.71
2798 6559 7.708051 TGAGTCATCTATTTTAGAACGGAGAG 58.292 38.462 0.00 0.00 38.50 3.20
2799 6560 7.556635 TGAGTCATCTATTTTAGAACGGAGAGA 59.443 37.037 0.00 0.00 38.50 3.10
2800 6561 7.936584 AGTCATCTATTTTAGAACGGAGAGAG 58.063 38.462 0.00 0.00 38.50 3.20
2912 8197 5.381174 TGGCAAAATCTGAAGTCATGAAG 57.619 39.130 0.00 0.00 0.00 3.02
2934 8219 5.475719 AGTAACAATCGTTAAGCACTGCTA 58.524 37.500 3.33 0.00 39.29 3.49
2987 8272 1.985473 TCAGCAAGCAACAGTCCATT 58.015 45.000 0.00 0.00 0.00 3.16
3017 8302 3.552294 GCCATAGCTTCTACTGAAACGAC 59.448 47.826 0.00 0.00 35.50 4.34
3018 8303 4.744570 CCATAGCTTCTACTGAAACGACA 58.255 43.478 0.00 0.00 0.00 4.35
3019 8304 5.352284 CCATAGCTTCTACTGAAACGACAT 58.648 41.667 0.00 0.00 0.00 3.06
3023 8308 6.208988 AGCTTCTACTGAAACGACATCATA 57.791 37.500 0.00 0.00 0.00 2.15
3205 8495 3.279434 CATTCCTTCCGGTCCCTTTTAG 58.721 50.000 0.00 0.00 0.00 1.85
3269 8559 9.892130 AATTTGACTAGAAACTTATACTCCCTG 57.108 33.333 0.00 0.00 0.00 4.45
3270 8560 8.660295 TTTGACTAGAAACTTATACTCCCTGA 57.340 34.615 0.00 0.00 0.00 3.86
3271 8561 8.660295 TTGACTAGAAACTTATACTCCCTGAA 57.340 34.615 0.00 0.00 0.00 3.02
3277 8567 8.581253 AGAAACTTATACTCCCTGAATTTTGG 57.419 34.615 0.00 0.00 0.00 3.28
3278 8568 8.170730 AGAAACTTATACTCCCTGAATTTTGGT 58.829 33.333 0.00 0.00 0.00 3.67
3280 8570 8.803397 AACTTATACTCCCTGAATTTTGGTAC 57.197 34.615 0.00 0.00 0.00 3.34
3281 8571 7.344134 ACTTATACTCCCTGAATTTTGGTACC 58.656 38.462 4.43 4.43 0.00 3.34
3288 9942 6.022315 TCCCTGAATTTTGGTACCAATCAAT 58.978 36.000 27.57 20.99 35.70 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.079253 AGTTCTCACTGTCTCTCTTCTCC 58.921 47.826 0.00 0.00 0.00 3.71
9 10 4.759693 TGAGTTCTCACTGTCTCTCTTCTC 59.240 45.833 0.00 0.00 31.22 2.87
21 22 4.279671 CGGCTATATCCTTGAGTTCTCACT 59.720 45.833 1.72 0.00 35.17 3.41
28 29 3.158676 GGACTCGGCTATATCCTTGAGT 58.841 50.000 3.62 3.62 39.24 3.41
68 69 0.995675 CTCACCTTCCCCATCCCCAT 60.996 60.000 0.00 0.00 0.00 4.00
69 70 1.619363 CTCACCTTCCCCATCCCCA 60.619 63.158 0.00 0.00 0.00 4.96
70 71 1.307866 TCTCACCTTCCCCATCCCC 60.308 63.158 0.00 0.00 0.00 4.81
76 77 2.170817 GGACATTAGTCTCACCTTCCCC 59.829 54.545 0.00 0.00 44.36 4.81
95 96 1.327690 CCCCTCGTCCATTTCTCGGA 61.328 60.000 0.00 0.00 0.00 4.55
132 134 0.940833 GCCCTATTTTCTCTCTGCGC 59.059 55.000 0.00 0.00 0.00 6.09
136 138 5.044550 ACCAATCAAGCCCTATTTTCTCTCT 60.045 40.000 0.00 0.00 0.00 3.10
172 174 7.809806 CCATAGTTGAGATTCTTTCAAAACCAC 59.190 37.037 0.00 0.00 36.41 4.16
215 217 1.812922 CAGGCCACTCTCATGACGC 60.813 63.158 5.01 0.00 0.00 5.19
223 225 0.917533 AGCATTCATCAGGCCACTCT 59.082 50.000 5.01 0.00 0.00 3.24
362 365 9.933723 ATATTTGGAAGAAAAATCAAACTCCAG 57.066 29.630 0.00 0.00 32.87 3.86
456 459 6.391227 TTCAGAATTTGAAACTTCCTGGAC 57.609 37.500 0.00 0.00 42.69 4.02
491 494 6.759827 AGTACAGTACTGACGTTCACAAATTT 59.240 34.615 29.30 4.06 37.69 1.82
534 537 6.865205 CAGGTTTCTATTTTTGGAGCTTCAAG 59.135 38.462 7.67 0.00 0.00 3.02
541 544 7.093322 CCTGATCAGGTTTCTATTTTTGGAG 57.907 40.000 30.55 1.70 43.61 3.86
604 639 2.478335 TAGGAAACTTGCAGCCGGGG 62.478 60.000 2.18 0.00 43.67 5.73
652 1928 1.006220 AGCACGATGACAACTGCGA 60.006 52.632 0.00 0.00 34.69 5.10
738 2014 2.095212 TCGTTTCGACCTCTGTGATCTG 60.095 50.000 0.00 0.00 0.00 2.90
739 2015 2.160205 TCGTTTCGACCTCTGTGATCT 58.840 47.619 0.00 0.00 0.00 2.75
740 2016 2.631418 TCGTTTCGACCTCTGTGATC 57.369 50.000 0.00 0.00 0.00 2.92
756 2039 1.623811 AGGTAGATTGGTGCAAGTCGT 59.376 47.619 0.00 0.00 0.00 4.34
800 2091 2.807967 CCTTGTGATTGACGTGTGTGAT 59.192 45.455 0.00 0.00 0.00 3.06
803 2094 2.612212 GTTCCTTGTGATTGACGTGTGT 59.388 45.455 0.00 0.00 0.00 3.72
857 2150 6.433093 GGCCGGTGATCTTATTTTATATTGGT 59.567 38.462 1.90 0.00 0.00 3.67
880 2504 2.666098 TTCTGGGTAGAAGGCCGGC 61.666 63.158 21.18 21.18 37.99 6.13
881 2505 1.221021 GTTCTGGGTAGAAGGCCGG 59.779 63.158 0.00 0.00 43.29 6.13
882 2506 1.221021 GGTTCTGGGTAGAAGGCCG 59.779 63.158 0.00 0.00 43.29 6.13
927 2551 2.176792 GGTCGTGGTCGTCGTACC 59.823 66.667 6.85 6.85 40.19 3.34
933 2557 3.969802 GGTCGTGGTCGTGGTCGT 61.970 66.667 0.00 0.00 38.33 4.34
934 2558 3.968568 TGGTCGTGGTCGTGGTCG 61.969 66.667 0.00 0.00 38.33 4.79
936 2560 4.274700 CGTGGTCGTGGTCGTGGT 62.275 66.667 0.00 0.00 38.33 4.16
937 2561 3.968568 TCGTGGTCGTGGTCGTGG 61.969 66.667 0.00 0.00 38.33 4.94
938 2562 2.728383 GTCGTGGTCGTGGTCGTG 60.728 66.667 0.00 0.00 38.33 4.35
940 2564 4.016629 TCGTCGTGGTCGTGGTCG 62.017 66.667 0.00 0.00 38.33 4.79
941 2565 2.428071 GTCGTCGTGGTCGTGGTC 60.428 66.667 0.00 0.00 38.33 4.02
942 2566 3.190323 CTGTCGTCGTGGTCGTGGT 62.190 63.158 0.00 0.00 38.33 4.16
943 2567 2.428569 CTGTCGTCGTGGTCGTGG 60.429 66.667 0.00 0.00 38.33 4.94
944 2568 3.097728 GCTGTCGTCGTGGTCGTG 61.098 66.667 0.00 0.00 38.33 4.35
959 2589 0.105964 TCTCTGGATCGGCTTAGGCT 60.106 55.000 3.89 0.00 38.73 4.58
1031 3635 3.121030 CGAGGAACAGCAAGGCCG 61.121 66.667 0.00 0.00 0.00 6.13
1039 3646 1.341606 GCGAAGAAGACGAGGAACAG 58.658 55.000 0.00 0.00 0.00 3.16
1093 3703 1.745115 CACCATGGTCCGCGACATT 60.745 57.895 16.53 0.00 33.68 2.71
1383 3996 4.180946 CTGTAGCGCTCGCCGACT 62.181 66.667 16.34 0.00 43.17 4.18
1461 4074 3.157680 CCCTGGTTCTTGACGGGT 58.842 61.111 0.00 0.00 0.00 5.28
1733 4346 1.673337 TCGATGGAGACGACCGTGT 60.673 57.895 0.00 0.00 34.85 4.49
1788 4401 2.045926 GCCACGGCCTTCATCAGT 60.046 61.111 0.00 0.00 34.56 3.41
1899 4520 4.409218 GCGAGTACGGCGTGGTCA 62.409 66.667 24.86 0.00 40.15 4.02
1941 4564 3.766691 TAGTCCTTGCCGCCGTCC 61.767 66.667 0.00 0.00 0.00 4.79
1942 4565 2.508663 GTAGTCCTTGCCGCCGTC 60.509 66.667 0.00 0.00 0.00 4.79
2303 4938 1.301677 CGGACTTCCCTTGCTCTTGC 61.302 60.000 0.00 0.00 40.20 4.01
2425 5060 9.569167 CTCTGAGAATGAAAGTTGTAACGTATA 57.431 33.333 0.00 0.00 0.00 1.47
2426 5061 7.545965 CCTCTGAGAATGAAAGTTGTAACGTAT 59.454 37.037 6.17 0.00 0.00 3.06
2427 5062 6.866770 CCTCTGAGAATGAAAGTTGTAACGTA 59.133 38.462 6.17 0.00 0.00 3.57
2428 5063 5.696724 CCTCTGAGAATGAAAGTTGTAACGT 59.303 40.000 6.17 0.00 0.00 3.99
2429 5064 5.926542 TCCTCTGAGAATGAAAGTTGTAACG 59.073 40.000 6.17 0.00 0.00 3.18
2430 5065 6.128795 CGTCCTCTGAGAATGAAAGTTGTAAC 60.129 42.308 6.17 0.00 0.00 2.50
2431 5066 5.926542 CGTCCTCTGAGAATGAAAGTTGTAA 59.073 40.000 6.17 0.00 0.00 2.41
2432 5067 5.470368 CGTCCTCTGAGAATGAAAGTTGTA 58.530 41.667 6.17 0.00 0.00 2.41
2433 5068 4.310769 CGTCCTCTGAGAATGAAAGTTGT 58.689 43.478 6.17 0.00 0.00 3.32
2434 5069 3.681897 CCGTCCTCTGAGAATGAAAGTTG 59.318 47.826 6.17 0.00 0.00 3.16
2435 5070 3.866449 GCCGTCCTCTGAGAATGAAAGTT 60.866 47.826 6.17 0.00 0.00 2.66
2436 5071 2.354203 GCCGTCCTCTGAGAATGAAAGT 60.354 50.000 6.17 0.00 0.00 2.66
2437 5072 2.275318 GCCGTCCTCTGAGAATGAAAG 58.725 52.381 6.17 0.00 0.00 2.62
2438 5073 1.404181 CGCCGTCCTCTGAGAATGAAA 60.404 52.381 6.17 0.00 0.00 2.69
2439 5074 0.173481 CGCCGTCCTCTGAGAATGAA 59.827 55.000 6.17 0.00 0.00 2.57
2440 5075 0.965866 ACGCCGTCCTCTGAGAATGA 60.966 55.000 6.17 0.00 0.00 2.57
2441 5076 0.108615 AACGCCGTCCTCTGAGAATG 60.109 55.000 6.17 0.00 0.00 2.67
2442 5077 0.608640 AAACGCCGTCCTCTGAGAAT 59.391 50.000 6.17 0.00 0.00 2.40
2443 5078 0.391597 AAAACGCCGTCCTCTGAGAA 59.608 50.000 6.17 0.00 0.00 2.87
2444 5079 1.201647 CTAAAACGCCGTCCTCTGAGA 59.798 52.381 6.17 0.00 0.00 3.27
2445 5080 1.630148 CTAAAACGCCGTCCTCTGAG 58.370 55.000 0.00 0.00 0.00 3.35
2446 5081 0.245539 CCTAAAACGCCGTCCTCTGA 59.754 55.000 0.00 0.00 0.00 3.27
2447 5082 0.037605 ACCTAAAACGCCGTCCTCTG 60.038 55.000 0.00 0.00 0.00 3.35
2448 5083 0.683412 AACCTAAAACGCCGTCCTCT 59.317 50.000 0.00 0.00 0.00 3.69
2449 5084 1.995484 GTAACCTAAAACGCCGTCCTC 59.005 52.381 0.00 0.00 0.00 3.71
2450 5085 1.344114 TGTAACCTAAAACGCCGTCCT 59.656 47.619 0.00 0.00 0.00 3.85
2451 5086 1.728425 CTGTAACCTAAAACGCCGTCC 59.272 52.381 0.00 0.00 0.00 4.79
2452 5087 1.127397 GCTGTAACCTAAAACGCCGTC 59.873 52.381 0.00 0.00 0.00 4.79
2453 5088 1.150827 GCTGTAACCTAAAACGCCGT 58.849 50.000 0.00 0.00 0.00 5.68
2454 5089 1.435577 AGCTGTAACCTAAAACGCCG 58.564 50.000 0.00 0.00 0.00 6.46
2455 5090 3.666111 CGAAAGCTGTAACCTAAAACGCC 60.666 47.826 0.00 0.00 0.00 5.68
2476 5111 3.106672 GACTGCTACGTTATGAGAACCG 58.893 50.000 0.00 0.00 0.00 4.44
2503 5158 7.199766 ACAAGTATTTGCAATGACTCGAAAAA 58.800 30.769 12.68 0.00 37.85 1.94
2504 5159 6.734137 ACAAGTATTTGCAATGACTCGAAAA 58.266 32.000 12.68 0.00 37.85 2.29
2505 5160 6.312399 ACAAGTATTTGCAATGACTCGAAA 57.688 33.333 12.68 0.00 37.85 3.46
2506 5161 5.940192 ACAAGTATTTGCAATGACTCGAA 57.060 34.783 12.68 0.00 37.85 3.71
2507 5162 8.887036 ATATACAAGTATTTGCAATGACTCGA 57.113 30.769 12.68 4.11 37.85 4.04
2539 5219 6.752168 ACAATTGGAAAAAGAATGACTCCTG 58.248 36.000 10.83 0.00 0.00 3.86
2674 6435 7.908917 ACCCTGGATCATATTAGGAACTATGAT 59.091 37.037 0.00 5.06 44.06 2.45
2697 6458 0.976590 AACGGAGGGAGCTCTTACCC 60.977 60.000 14.64 6.92 45.88 3.69
2706 6467 3.629142 ACTATTTTGGAACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
2707 6468 3.328343 TCAACTATTTTGGAACGGAGGGA 59.672 43.478 0.00 0.00 0.00 4.20
2708 6469 3.439129 GTCAACTATTTTGGAACGGAGGG 59.561 47.826 0.00 0.00 0.00 4.30
2709 6470 3.439129 GGTCAACTATTTTGGAACGGAGG 59.561 47.826 0.00 0.00 0.00 4.30
2710 6471 3.439129 GGGTCAACTATTTTGGAACGGAG 59.561 47.826 0.00 0.00 0.00 4.63
2711 6472 3.181442 TGGGTCAACTATTTTGGAACGGA 60.181 43.478 0.00 0.00 0.00 4.69
2712 6473 3.150767 TGGGTCAACTATTTTGGAACGG 58.849 45.455 0.00 0.00 0.00 4.44
2713 6474 4.542735 GTTGGGTCAACTATTTTGGAACG 58.457 43.478 3.78 0.00 40.73 3.95
2725 6486 6.688637 AAGTTAGTACAAAGTTGGGTCAAC 57.311 37.500 0.00 2.85 43.83 3.18
2726 6487 6.660094 ACAAAGTTAGTACAAAGTTGGGTCAA 59.340 34.615 0.00 0.00 0.00 3.18
2727 6488 6.181908 ACAAAGTTAGTACAAAGTTGGGTCA 58.818 36.000 0.00 0.00 0.00 4.02
2728 6489 6.688637 ACAAAGTTAGTACAAAGTTGGGTC 57.311 37.500 0.00 0.00 0.00 4.46
2729 6490 7.341030 AGTACAAAGTTAGTACAAAGTTGGGT 58.659 34.615 6.30 0.00 43.24 4.51
2730 6491 7.797038 AGTACAAAGTTAGTACAAAGTTGGG 57.203 36.000 6.30 0.00 43.24 4.12
2767 6528 9.746711 CGTTCTAAAATAGATGACTCAACTTTG 57.253 33.333 0.00 0.00 34.22 2.77
2768 6529 8.936864 CCGTTCTAAAATAGATGACTCAACTTT 58.063 33.333 0.00 0.00 34.22 2.66
2769 6530 8.311836 TCCGTTCTAAAATAGATGACTCAACTT 58.688 33.333 0.00 0.00 34.22 2.66
2770 6531 7.837863 TCCGTTCTAAAATAGATGACTCAACT 58.162 34.615 0.00 0.00 34.22 3.16
2771 6532 7.974501 TCTCCGTTCTAAAATAGATGACTCAAC 59.025 37.037 0.00 0.00 34.22 3.18
2772 6533 8.063200 TCTCCGTTCTAAAATAGATGACTCAA 57.937 34.615 0.00 0.00 34.22 3.02
2773 6534 7.556635 TCTCTCCGTTCTAAAATAGATGACTCA 59.443 37.037 0.00 0.00 34.22 3.41
2774 6535 7.932335 TCTCTCCGTTCTAAAATAGATGACTC 58.068 38.462 0.00 0.00 34.22 3.36
2775 6536 7.558444 ACTCTCTCCGTTCTAAAATAGATGACT 59.442 37.037 0.00 0.00 34.22 3.41
2776 6537 7.708998 ACTCTCTCCGTTCTAAAATAGATGAC 58.291 38.462 0.00 0.00 34.22 3.06
2777 6538 7.883391 ACTCTCTCCGTTCTAAAATAGATGA 57.117 36.000 0.00 0.00 34.22 2.92
2778 6539 9.058174 TCTACTCTCTCCGTTCTAAAATAGATG 57.942 37.037 0.00 0.00 34.22 2.90
2779 6540 9.629878 TTCTACTCTCTCCGTTCTAAAATAGAT 57.370 33.333 0.00 0.00 34.22 1.98
2780 6541 9.629878 ATTCTACTCTCTCCGTTCTAAAATAGA 57.370 33.333 0.00 0.00 0.00 1.98
2783 6544 8.750298 TCAATTCTACTCTCTCCGTTCTAAAAT 58.250 33.333 0.00 0.00 0.00 1.82
2784 6545 8.118976 TCAATTCTACTCTCTCCGTTCTAAAA 57.881 34.615 0.00 0.00 0.00 1.52
2785 6546 7.148052 CCTCAATTCTACTCTCTCCGTTCTAAA 60.148 40.741 0.00 0.00 0.00 1.85
2786 6547 6.319152 CCTCAATTCTACTCTCTCCGTTCTAA 59.681 42.308 0.00 0.00 0.00 2.10
2787 6548 5.823570 CCTCAATTCTACTCTCTCCGTTCTA 59.176 44.000 0.00 0.00 0.00 2.10
2788 6549 4.642885 CCTCAATTCTACTCTCTCCGTTCT 59.357 45.833 0.00 0.00 0.00 3.01
2789 6550 4.202070 CCCTCAATTCTACTCTCTCCGTTC 60.202 50.000 0.00 0.00 0.00 3.95
2790 6551 3.702045 CCCTCAATTCTACTCTCTCCGTT 59.298 47.826 0.00 0.00 0.00 4.44
2791 6552 3.053544 TCCCTCAATTCTACTCTCTCCGT 60.054 47.826 0.00 0.00 0.00 4.69
2792 6553 3.556999 TCCCTCAATTCTACTCTCTCCG 58.443 50.000 0.00 0.00 0.00 4.63
2793 6554 3.895041 CCTCCCTCAATTCTACTCTCTCC 59.105 52.174 0.00 0.00 0.00 3.71
2794 6555 4.340950 CACCTCCCTCAATTCTACTCTCTC 59.659 50.000 0.00 0.00 0.00 3.20
2795 6556 4.017037 TCACCTCCCTCAATTCTACTCTCT 60.017 45.833 0.00 0.00 0.00 3.10
2796 6557 4.282496 TCACCTCCCTCAATTCTACTCTC 58.718 47.826 0.00 0.00 0.00 3.20
2797 6558 4.338795 TCACCTCCCTCAATTCTACTCT 57.661 45.455 0.00 0.00 0.00 3.24
2798 6559 5.046231 AGTTTCACCTCCCTCAATTCTACTC 60.046 44.000 0.00 0.00 0.00 2.59
2799 6560 4.846940 AGTTTCACCTCCCTCAATTCTACT 59.153 41.667 0.00 0.00 0.00 2.57
2800 6561 5.167303 AGTTTCACCTCCCTCAATTCTAC 57.833 43.478 0.00 0.00 0.00 2.59
2881 8164 5.362430 ACTTCAGATTTTGCCAAAGTGGTTA 59.638 36.000 0.00 0.00 40.46 2.85
2912 8197 4.663636 AGCAGTGCTTAACGATTGTTAC 57.336 40.909 13.14 0.00 40.19 2.50
2934 8219 4.851639 AAATAGATTGAGGAGGTGCAGT 57.148 40.909 0.00 0.00 0.00 4.40
3039 8327 4.689612 TCTTGTTGCCACTAGAAACTCT 57.310 40.909 0.00 0.00 32.57 3.24
3059 8347 3.692370 ATTAGTGGGCCGGCCGTTC 62.692 63.158 38.22 28.31 36.85 3.95
3060 8348 3.692370 GATTAGTGGGCCGGCCGTT 62.692 63.158 38.22 26.95 36.85 4.44
3251 8541 9.681062 CCAAAATTCAGGGAGTATAAGTTTCTA 57.319 33.333 0.00 0.00 0.00 2.10
3252 8542 8.170730 ACCAAAATTCAGGGAGTATAAGTTTCT 58.829 33.333 1.71 0.00 0.00 2.52
3253 8543 8.349568 ACCAAAATTCAGGGAGTATAAGTTTC 57.650 34.615 1.71 0.00 0.00 2.78
3260 8550 5.789574 TGGTACCAAAATTCAGGGAGTAT 57.210 39.130 13.60 0.00 0.00 2.12
3269 8559 9.868277 TGTGAATATTGATTGGTACCAAAATTC 57.132 29.630 30.31 26.77 39.55 2.17
3275 8565 8.055790 TGGTATTGTGAATATTGATTGGTACCA 58.944 33.333 11.60 11.60 35.60 3.25
3276 8566 8.458573 TGGTATTGTGAATATTGATTGGTACC 57.541 34.615 4.43 4.43 0.00 3.34


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

AutoCloner maintained by Alex Coulton.