Multiple sequence alignment - TraesCS5A01G268300

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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 TraesCS5A01G268300 chr5A 100.000 3511 0 0 1 3511 479045947 479049457 0.000000e+00 6484
1 TraesCS5A01G268300 chr5A 80.994 805 115 25 2735 3510 364684139 364683344 3.880000e-169 604
2 TraesCS5A01G268300 chr5A 80.769 806 115 27 2735 3510 626088576 626087781 8.390000e-166 593
3 TraesCS5A01G268300 chr5A 83.385 644 98 8 2871 3511 378724687 378725324 3.900000e-164 588
4 TraesCS5A01G268300 chr5A 82.796 465 66 11 1474 1935 479201324 479200871 1.520000e-108 403
5 TraesCS5A01G268300 chr5A 82.796 465 66 11 1474 1935 479227340 479226887 1.520000e-108 403
6 TraesCS5A01G268300 chr5A 74.931 722 151 27 1489 2192 478992186 478991477 1.580000e-78 303
7 TraesCS5A01G268300 chr5A 91.964 112 9 0 1034 1145 478993120 478993009 1.300000e-34 158
8 TraesCS5A01G268300 chr5A 90.826 109 10 0 1039 1147 479204970 479204862 2.820000e-31 147
9 TraesCS5A01G268300 chr5B 88.536 2521 232 39 842 3332 454636311 454638804 0.000000e+00 3001
10 TraesCS5A01G268300 chr5B 89.414 1946 134 33 539 2466 454475944 454477835 0.000000e+00 2386
11 TraesCS5A01G268300 chr5B 80.994 805 115 25 2735 3510 631461255 631460460 3.880000e-169 604
12 TraesCS5A01G268300 chr5B 77.437 1077 173 41 1473 2511 454654528 454653484 2.350000e-161 579
13 TraesCS5A01G268300 chr5B 80.594 505 72 13 2010 2511 454684240 454683759 1.990000e-97 366
14 TraesCS5A01G268300 chr5B 77.978 445 84 13 1759 2192 454403415 454402974 2.080000e-67 267
15 TraesCS5A01G268300 chr5B 77.876 452 71 22 1759 2192 454491493 454491053 1.620000e-63 254
16 TraesCS5A01G268300 chr5B 92.857 112 8 0 1034 1145 454407143 454407032 2.800000e-36 163
17 TraesCS5A01G268300 chr5B 93.519 108 7 0 1039 1146 454657710 454657603 1.010000e-35 161
18 TraesCS5A01G268300 chr5D 90.201 2143 141 35 550 2671 378956178 378958272 0.000000e+00 2730
19 TraesCS5A01G268300 chr5D 90.659 546 47 4 1 542 128586082 128586627 0.000000e+00 723
20 TraesCS5A01G268300 chr5D 90.625 544 44 6 1 541 382082368 382081829 0.000000e+00 715
21 TraesCS5A01G268300 chr5D 78.658 745 110 37 1499 2214 378997234 378996510 1.920000e-122 449
22 TraesCS5A01G268300 chr5D 79.592 441 75 12 1759 2192 378898383 378897951 5.700000e-78 302
23 TraesCS5A01G268300 chr5D 94.231 104 6 0 1042 1145 378899257 378899154 3.630000e-35 159
24 TraesCS5A01G268300 chr5D 91.579 95 8 0 1042 1136 69111195 69111289 7.910000e-27 132
25 TraesCS5A01G268300 chr6D 91.466 539 44 2 1 537 137121755 137122293 0.000000e+00 739
26 TraesCS5A01G268300 chr6D 90.976 543 47 2 1 541 374104204 374103662 0.000000e+00 730
27 TraesCS5A01G268300 chr6D 90.590 542 50 1 1 541 408146610 408146069 0.000000e+00 717
28 TraesCS5A01G268300 chr1D 90.976 543 47 2 1 541 365751773 365751231 0.000000e+00 730
29 TraesCS5A01G268300 chr2D 90.926 540 46 3 4 541 399427938 399427400 0.000000e+00 723
30 TraesCS5A01G268300 chr2D 90.608 543 47 4 1 541 187619773 187619233 0.000000e+00 717
31 TraesCS5A01G268300 chr7D 90.741 540 48 2 4 541 509531569 509531030 0.000000e+00 719
32 TraesCS5A01G268300 chr7B 83.696 644 92 12 2871 3510 720161792 720161158 2.330000e-166 595
33 TraesCS5A01G268300 chr7B 80.549 802 118 25 2735 3507 237913277 237914069 1.820000e-162 582
34 TraesCS5A01G268300 chr2A 80.497 805 119 25 2735 3510 133478220 133477425 1.820000e-162 582
35 TraesCS5A01G268300 chr4A 81.464 642 105 6 2872 3510 676908988 676909618 6.720000e-142 514


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 TraesCS5A01G268300 chr5A 479045947 479049457 3510 False 6484.0 6484 100.0000 1 3511 1 chr5A.!!$F2 3510
1 TraesCS5A01G268300 chr5A 364683344 364684139 795 True 604.0 604 80.9940 2735 3510 1 chr5A.!!$R1 775
2 TraesCS5A01G268300 chr5A 626087781 626088576 795 True 593.0 593 80.7690 2735 3510 1 chr5A.!!$R3 775
3 TraesCS5A01G268300 chr5A 378724687 378725324 637 False 588.0 588 83.3850 2871 3511 1 chr5A.!!$F1 640
4 TraesCS5A01G268300 chr5A 479200871 479204970 4099 True 275.0 403 86.8110 1039 1935 2 chr5A.!!$R5 896
5 TraesCS5A01G268300 chr5A 478991477 478993120 1643 True 230.5 303 83.4475 1034 2192 2 chr5A.!!$R4 1158
6 TraesCS5A01G268300 chr5B 454636311 454638804 2493 False 3001.0 3001 88.5360 842 3332 1 chr5B.!!$F2 2490
7 TraesCS5A01G268300 chr5B 454475944 454477835 1891 False 2386.0 2386 89.4140 539 2466 1 chr5B.!!$F1 1927
8 TraesCS5A01G268300 chr5B 631460460 631461255 795 True 604.0 604 80.9940 2735 3510 1 chr5B.!!$R3 775
9 TraesCS5A01G268300 chr5B 454653484 454657710 4226 True 370.0 579 85.4780 1039 2511 2 chr5B.!!$R5 1472
10 TraesCS5A01G268300 chr5B 454402974 454407143 4169 True 215.0 267 85.4175 1034 2192 2 chr5B.!!$R4 1158
11 TraesCS5A01G268300 chr5D 378956178 378958272 2094 False 2730.0 2730 90.2010 550 2671 1 chr5D.!!$F3 2121
12 TraesCS5A01G268300 chr5D 128586082 128586627 545 False 723.0 723 90.6590 1 542 1 chr5D.!!$F2 541
13 TraesCS5A01G268300 chr5D 382081829 382082368 539 True 715.0 715 90.6250 1 541 1 chr5D.!!$R2 540
14 TraesCS5A01G268300 chr5D 378996510 378997234 724 True 449.0 449 78.6580 1499 2214 1 chr5D.!!$R1 715
15 TraesCS5A01G268300 chr5D 378897951 378899257 1306 True 230.5 302 86.9115 1042 2192 2 chr5D.!!$R3 1150
16 TraesCS5A01G268300 chr6D 137121755 137122293 538 False 739.0 739 91.4660 1 537 1 chr6D.!!$F1 536
17 TraesCS5A01G268300 chr6D 374103662 374104204 542 True 730.0 730 90.9760 1 541 1 chr6D.!!$R1 540
18 TraesCS5A01G268300 chr6D 408146069 408146610 541 True 717.0 717 90.5900 1 541 1 chr6D.!!$R2 540
19 TraesCS5A01G268300 chr1D 365751231 365751773 542 True 730.0 730 90.9760 1 541 1 chr1D.!!$R1 540
20 TraesCS5A01G268300 chr2D 399427400 399427938 538 True 723.0 723 90.9260 4 541 1 chr2D.!!$R2 537
21 TraesCS5A01G268300 chr2D 187619233 187619773 540 True 717.0 717 90.6080 1 541 1 chr2D.!!$R1 540
22 TraesCS5A01G268300 chr7D 509531030 509531569 539 True 719.0 719 90.7410 4 541 1 chr7D.!!$R1 537
23 TraesCS5A01G268300 chr7B 720161158 720161792 634 True 595.0 595 83.6960 2871 3510 1 chr7B.!!$R1 639
24 TraesCS5A01G268300 chr7B 237913277 237914069 792 False 582.0 582 80.5490 2735 3507 1 chr7B.!!$F1 772
25 TraesCS5A01G268300 chr2A 133477425 133478220 795 True 582.0 582 80.4970 2735 3510 1 chr2A.!!$R1 775
26 TraesCS5A01G268300 chr4A 676908988 676909618 630 False 514.0 514 81.4640 2872 3510 1 chr4A.!!$F1 638

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
601 607 0.250295 GTGGCCTGCTGTTACTGTCA 60.250 55.0 3.32 0.0 0.00 3.58 F
1680 8921 0.036306 AACGAGGTAACCTTGGCTGG 59.964 55.0 0.00 0.0 39.29 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2215 9527 0.248907 TCGTCGGGCGATCAGAATTC 60.249 55.0 0.0 0.0 45.68 2.17 R
3098 10454 0.039437 GACGTCGCTTCTCTGTTGGA 60.039 55.0 0.0 0.0 0.00 3.53 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
36 37 1.024271 ACACACATGGCAACTGTGAC 58.976 50.000 26.05 0.00 45.44 3.67
42 43 2.880890 ACATGGCAACTGTGACTCTTTC 59.119 45.455 0.00 0.00 31.93 2.62
73 74 3.399770 GCAGTTGCGCGTACGTGA 61.400 61.111 31.45 14.12 42.83 4.35
80 81 2.587679 GCGCGTACGTGACAACCAA 61.588 57.895 31.45 0.00 42.83 3.67
127 128 9.448438 TGATTAACCATATATGACAACTATGGC 57.552 33.333 14.54 8.99 43.75 4.40
213 215 2.548057 ACTTAATCACACACGGCAACTG 59.452 45.455 0.00 0.00 0.00 3.16
215 217 1.100463 AATCACACACGGCAACTGCA 61.100 50.000 3.76 0.00 44.36 4.41
248 250 5.468746 ACACGCGGCAACTATCATAAATTAT 59.531 36.000 12.47 0.00 0.00 1.28
255 257 8.946085 CGGCAACTATCATAAATTATACATGGT 58.054 33.333 0.00 0.00 0.00 3.55
309 311 5.507315 GCCATGCTTTTACAACTACACTTGT 60.507 40.000 0.00 0.00 38.03 3.16
318 320 3.181458 ACAACTACACTTGTCATTCCGGT 60.181 43.478 0.00 0.00 27.41 5.28
393 397 1.888018 GTAGCTGCACCAGGACGTA 59.112 57.895 1.02 0.00 31.21 3.57
410 415 2.560542 ACGTATGGGCATTTTTGCTTCA 59.439 40.909 0.00 0.00 34.73 3.02
507 513 6.949352 GACAATTCTAATGTCCATCCACAT 57.051 37.500 0.00 0.00 41.02 3.21
542 548 2.513204 CCTCCTGCTCACGCCATG 60.513 66.667 0.00 0.00 34.43 3.66
543 549 2.580815 CTCCTGCTCACGCCATGA 59.419 61.111 0.00 0.00 35.45 3.07
544 550 1.812922 CTCCTGCTCACGCCATGAC 60.813 63.158 0.00 0.00 32.37 3.06
545 551 2.821366 CCTGCTCACGCCATGACC 60.821 66.667 0.00 0.00 32.37 4.02
546 552 2.046988 CTGCTCACGCCATGACCA 60.047 61.111 0.00 0.00 32.37 4.02
552 558 1.131126 CTCACGCCATGACCATGAAAC 59.869 52.381 11.28 0.69 41.20 2.78
573 579 3.702548 ACTTGTAACCATGCATGCATCAT 59.297 39.130 30.07 19.94 33.90 2.45
583 589 4.195225 TGCATGCATCATCAAATGTTGT 57.805 36.364 18.46 0.00 33.57 3.32
601 607 0.250295 GTGGCCTGCTGTTACTGTCA 60.250 55.000 3.32 0.00 0.00 3.58
624 630 1.741770 GAACGTGCTCAAGCCCGAT 60.742 57.895 13.68 1.37 44.47 4.18
634 640 1.026718 CAAGCCCGATGGTGAACTCC 61.027 60.000 0.00 0.00 0.00 3.85
715 721 2.064581 GCTGGGACCGGTAGTGGAT 61.065 63.158 7.34 0.00 0.00 3.41
763 779 2.679092 CCATGGAGGCAAGCAGGA 59.321 61.111 5.56 0.00 0.00 3.86
832 850 3.877450 GGGGCTGGCCGATGATGA 61.877 66.667 14.63 0.00 36.85 2.92
922 949 2.125912 GCATCCGCTCTCGTGTGT 60.126 61.111 0.00 0.00 34.30 3.72
924 951 1.080501 CATCCGCTCTCGTGTGTGT 60.081 57.895 0.26 0.00 0.00 3.72
933 960 2.588596 CGTGTGTGTGGAGCTGCA 60.589 61.111 2.72 2.72 0.00 4.41
1274 3855 1.443802 CGAAAACCTCAGGCTCTTCC 58.556 55.000 0.00 0.00 0.00 3.46
1336 6837 0.486879 TGGGATGCCAGGGAGTTTTT 59.513 50.000 0.00 0.00 0.00 1.94
1397 6902 2.352421 CCAGAGGCAAGCAAGTTTCATG 60.352 50.000 0.00 0.00 0.00 3.07
1401 6906 2.555757 AGGCAAGCAAGTTTCATGACTC 59.444 45.455 0.00 0.00 0.00 3.36
1483 8717 0.806868 CCACAACCATGCAGCTACAG 59.193 55.000 0.00 0.00 0.00 2.74
1497 8731 1.616327 TACAGATGCTGGGCCCTGT 60.616 57.895 27.68 21.58 41.55 4.00
1674 8915 1.002087 CAGGAGCAACGAGGTAACCTT 59.998 52.381 0.00 0.00 31.76 3.50
1675 8916 1.002087 AGGAGCAACGAGGTAACCTTG 59.998 52.381 0.00 0.00 40.74 3.61
1676 8917 1.439679 GAGCAACGAGGTAACCTTGG 58.560 55.000 0.00 0.00 39.29 3.61
1680 8921 0.036306 AACGAGGTAACCTTGGCTGG 59.964 55.000 0.00 0.00 39.29 4.85
1682 8923 0.673644 CGAGGTAACCTTGGCTGGTG 60.674 60.000 3.70 0.00 40.73 4.17
1687 8928 2.224695 GGTAACCTTGGCTGGTGTACTT 60.225 50.000 3.70 0.00 40.73 2.24
1690 8931 3.136009 ACCTTGGCTGGTGTACTTTAC 57.864 47.619 2.15 0.00 39.17 2.01
1703 8961 6.201425 TGGTGTACTTTACGATCTTGTTGAAC 59.799 38.462 0.00 0.00 0.00 3.18
1709 8967 7.712797 ACTTTACGATCTTGTTGAACCAAAAT 58.287 30.769 0.00 0.00 0.00 1.82
1711 8969 9.672086 CTTTACGATCTTGTTGAACCAAAATTA 57.328 29.630 0.00 0.00 0.00 1.40
1715 8973 8.977505 ACGATCTTGTTGAACCAAAATTATTTG 58.022 29.630 0.00 0.00 44.50 2.32
1751 9014 3.003585 TGACTATGCCATTTTGCTATGCG 59.996 43.478 0.00 0.00 0.00 4.73
1752 9015 2.287788 ACTATGCCATTTTGCTATGCGC 60.288 45.455 0.00 0.00 39.77 6.09
1781 9045 1.127567 AGAGCTGGTACCCTGTTGCA 61.128 55.000 10.07 0.00 0.00 4.08
2048 9339 1.001641 GAGGGACAAGCTGTGGCAT 60.002 57.895 0.00 0.00 36.72 4.40
2173 9485 0.892358 CTGCTGGGCTTGCTCAAGAA 60.892 55.000 13.33 0.00 40.79 2.52
2214 9526 2.100916 TGCATAGCCGAGTAAGACTTCC 59.899 50.000 0.00 0.00 0.00 3.46
2215 9527 2.859032 GCATAGCCGAGTAAGACTTCCG 60.859 54.545 0.00 0.00 0.00 4.30
2216 9528 2.408271 TAGCCGAGTAAGACTTCCGA 57.592 50.000 0.00 0.00 0.00 4.55
2217 9529 1.542492 AGCCGAGTAAGACTTCCGAA 58.458 50.000 0.00 0.00 0.00 4.30
2218 9530 2.100989 AGCCGAGTAAGACTTCCGAAT 58.899 47.619 0.00 0.00 0.00 3.34
2220 9532 2.858941 GCCGAGTAAGACTTCCGAATTC 59.141 50.000 0.00 0.00 0.00 2.17
2232 9546 1.215655 CCGAATTCTGATCGCCCGAC 61.216 60.000 3.52 0.00 38.93 4.79
2260 9574 1.858091 GGCGACGATCAATGAGATGT 58.142 50.000 0.00 0.00 37.00 3.06
2262 9576 2.726760 GGCGACGATCAATGAGATGTAC 59.273 50.000 0.00 0.00 37.00 2.90
2264 9578 4.320275 GGCGACGATCAATGAGATGTACTA 60.320 45.833 0.00 0.00 37.00 1.82
2266 9580 5.561145 GCGACGATCAATGAGATGTACTACT 60.561 44.000 0.00 0.00 37.00 2.57
2267 9581 6.347483 GCGACGATCAATGAGATGTACTACTA 60.347 42.308 0.00 0.00 37.00 1.82
2269 9583 7.204496 ACGATCAATGAGATGTACTACTACC 57.796 40.000 0.00 0.00 37.00 3.18
2270 9584 6.771267 ACGATCAATGAGATGTACTACTACCA 59.229 38.462 0.00 0.00 37.00 3.25
2312 9628 5.069119 GGATAATTCCATCCTTTGGGTGTTC 59.931 44.000 0.61 0.00 46.45 3.18
2370 9686 1.306141 ATGACCTCCGGGAAGCTGA 60.306 57.895 0.00 0.00 36.25 4.26
2458 9774 0.955919 GCTGGGTTTCTTGAGGACGG 60.956 60.000 0.00 0.00 0.00 4.79
2513 9829 6.296145 CCCCTCTTCTCAACAAAGTCTAGATT 60.296 42.308 0.00 0.00 0.00 2.40
2514 9830 6.593382 CCCTCTTCTCAACAAAGTCTAGATTG 59.407 42.308 0.00 0.00 0.00 2.67
2562 9878 1.202031 CCACTCGCGAACAAATAAGGC 60.202 52.381 11.33 0.00 0.00 4.35
2563 9879 1.084289 ACTCGCGAACAAATAAGGCC 58.916 50.000 11.33 0.00 0.00 5.19
2656 9973 0.318614 GCCACATGGTTGGTTTCACG 60.319 55.000 0.00 0.00 39.09 4.35
2666 9983 1.008995 GGTTTCACGCGCACAATGT 60.009 52.632 5.73 0.00 0.00 2.71
2674 9991 1.064803 ACGCGCACAATGTTCAAAAGA 59.935 42.857 5.73 0.00 0.00 2.52
2676 9993 2.151736 CGCGCACAATGTTCAAAAGAAG 59.848 45.455 8.75 0.00 0.00 2.85
2679 9996 3.061006 CGCACAATGTTCAAAAGAAGCAC 60.061 43.478 0.00 0.00 0.00 4.40
2680 9997 3.864583 GCACAATGTTCAAAAGAAGCACA 59.135 39.130 0.00 0.00 0.00 4.57
2685 10002 3.843999 TGTTCAAAAGAAGCACAACCAC 58.156 40.909 0.00 0.00 0.00 4.16
2691 10008 6.039616 TCAAAAGAAGCACAACCACAATTAC 58.960 36.000 0.00 0.00 0.00 1.89
2697 10014 7.777095 AGAAGCACAACCACAATTACTAAAAA 58.223 30.769 0.00 0.00 0.00 1.94
2726 10043 7.997773 AAGAGTACGTCTAGGCATATCATAA 57.002 36.000 0.00 0.00 32.65 1.90
2730 10047 7.818642 AGTACGTCTAGGCATATCATAACTTC 58.181 38.462 0.00 0.00 0.00 3.01
2732 10049 7.050970 ACGTCTAGGCATATCATAACTTCAA 57.949 36.000 0.00 0.00 0.00 2.69
2733 10050 7.671302 ACGTCTAGGCATATCATAACTTCAAT 58.329 34.615 0.00 0.00 0.00 2.57
2775 10104 3.410098 TCGATGCGAACAACGATCA 57.590 47.368 0.00 0.00 44.84 2.92
2807 10136 1.410882 CCACAACCGACAAACCCAAAT 59.589 47.619 0.00 0.00 0.00 2.32
2821 10150 5.622346 AACCCAAATACAAACAACACCAT 57.378 34.783 0.00 0.00 0.00 3.55
2834 10163 0.391661 ACACCATCCAGCAAGCTACG 60.392 55.000 0.00 0.00 0.00 3.51
2852 10181 1.067142 ACGACGCAAAAGAGCCTATCA 60.067 47.619 0.00 0.00 0.00 2.15
2858 10187 3.242870 CGCAAAAGAGCCTATCATGAACC 60.243 47.826 0.00 0.00 0.00 3.62
2887 10243 2.158871 AGCACCGAAGACCAACAACTTA 60.159 45.455 0.00 0.00 0.00 2.24
2898 10254 5.761234 AGACCAACAACTTACGCAGAATTTA 59.239 36.000 0.00 0.00 0.00 1.40
2900 10256 6.378582 ACCAACAACTTACGCAGAATTTATG 58.621 36.000 0.00 0.00 0.00 1.90
2904 10260 5.856455 ACAACTTACGCAGAATTTATGTTGC 59.144 36.000 10.49 2.89 35.67 4.17
2917 10273 2.803155 ATGTTGCCGACGCACCATCT 62.803 55.000 0.00 0.00 44.02 2.90
2926 10282 2.351835 CGACGCACCATCTATCCTTAGG 60.352 54.545 0.00 0.00 0.00 2.69
2958 10314 1.064906 AGTGACAGATGAATGGCAGGG 60.065 52.381 0.00 0.00 39.42 4.45
2964 10320 1.153086 ATGAATGGCAGGGCTCGAC 60.153 57.895 0.00 0.00 0.00 4.20
3016 10372 2.100749 CCACCATCAGACGTACATAGCA 59.899 50.000 0.00 0.00 0.00 3.49
3080 10436 0.246635 GCAACGAGGAGTCAGCCTTA 59.753 55.000 0.00 0.00 38.73 2.69
3098 10454 4.082026 GCCTTATCTCCAAACACAATGCTT 60.082 41.667 0.00 0.00 0.00 3.91
3126 10482 2.453773 GAAGCGACGTCGAGGACACA 62.454 60.000 39.74 0.00 43.02 3.72
3128 10484 2.944429 CGACGTCGAGGACACAGT 59.056 61.111 33.35 0.00 43.02 3.55
3151 10507 0.798009 CGTGCCAATCCAAACATCGC 60.798 55.000 0.00 0.00 0.00 4.58
3158 10514 2.602257 ATCCAAACATCGCATCGAGA 57.398 45.000 0.00 0.00 39.91 4.04
3206 10562 2.154462 CAGGAGCGTGAAGAAAATGGT 58.846 47.619 0.00 0.00 0.00 3.55
3219 10575 2.341846 AAATGGTGAACACACTCGGT 57.658 45.000 7.25 0.00 35.21 4.69
3281 10637 3.691342 CCGGACCGACAGAAGCCA 61.691 66.667 17.49 0.00 0.00 4.75
3295 10651 3.924686 CAGAAGCCATGCAAGATTTTCAC 59.075 43.478 0.00 0.00 0.00 3.18
3317 10673 3.621805 ACGTCGCCCATCACACCA 61.622 61.111 0.00 0.00 0.00 4.17
3318 10674 2.815211 CGTCGCCCATCACACCAG 60.815 66.667 0.00 0.00 0.00 4.00
3339 10696 0.249120 TCCATGGACTTGGTAGCACG 59.751 55.000 11.44 0.00 38.01 5.34
3362 10719 1.148273 AAGAAGCTTCACACCGCCA 59.852 52.632 27.57 0.00 0.00 5.69
3392 10752 0.742281 ACTTGCCGATGTAGCTGCAG 60.742 55.000 10.11 10.11 34.81 4.41
3410 10770 1.985116 GAGCCGAGGACCAAGGACT 60.985 63.158 9.21 5.86 0.00 3.85
3413 10773 1.617947 GCCGAGGACCAAGGACTGAT 61.618 60.000 9.21 0.00 0.00 2.90
3416 10776 0.461961 GAGGACCAAGGACTGATCGG 59.538 60.000 0.00 0.00 0.00 4.18
3418 10778 1.617947 GGACCAAGGACTGATCGGCT 61.618 60.000 0.00 0.00 0.00 5.52
3440 10800 3.351416 GGGAAACCGCGACCACAC 61.351 66.667 8.23 0.00 43.64 3.82
3451 10812 1.544825 CGACCACACCATCCACTCCT 61.545 60.000 0.00 0.00 0.00 3.69
3457 10818 1.291033 ACACCATCCACTCCTAGCCTA 59.709 52.381 0.00 0.00 0.00 3.93
3460 10821 2.090494 ACCATCCACTCCTAGCCTACAT 60.090 50.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 2.349886 GCAGTTGCCGTCTATGAAAGAG 59.650 50.000 0.00 0.00 32.36 2.85
42 43 1.442769 AACTGCAGTTGCCGTCTATG 58.557 50.000 30.66 0.00 37.51 2.23
73 74 4.141846 TGCCATGTGTGTTTATTTGGTTGT 60.142 37.500 0.00 0.00 0.00 3.32
80 81 4.340666 TCACAGTTGCCATGTGTGTTTATT 59.659 37.500 11.76 0.00 46.49 1.40
187 189 5.136816 TGCCGTGTGTGATTAAGTACTTA 57.863 39.130 11.38 11.38 0.00 2.24
193 195 2.665519 GCAGTTGCCGTGTGTGATTAAG 60.666 50.000 0.00 0.00 34.31 1.85
213 215 0.793104 GCCGCGTGTAATCAAACTGC 60.793 55.000 4.92 0.00 0.00 4.40
215 217 1.069500 GTTGCCGCGTGTAATCAAACT 60.069 47.619 4.92 0.00 0.00 2.66
309 311 4.439057 GCAGATGTAGTTAACCGGAATGA 58.561 43.478 9.46 0.00 0.00 2.57
318 320 4.037222 TCCTGGATGGCAGATGTAGTTAA 58.963 43.478 0.00 0.00 35.26 2.01
383 387 0.623723 AAATGCCCATACGTCCTGGT 59.376 50.000 14.15 0.00 31.44 4.00
393 397 2.026636 AGCATGAAGCAAAAATGCCCAT 60.027 40.909 0.00 0.00 46.28 4.00
425 430 6.295349 CCCAACAAGTACTACTCATCTTCACT 60.295 42.308 0.00 0.00 0.00 3.41
542 548 4.022416 TGCATGGTTACAAGTTTCATGGTC 60.022 41.667 0.00 0.00 36.62 4.02
543 549 3.894427 TGCATGGTTACAAGTTTCATGGT 59.106 39.130 0.00 0.00 36.62 3.55
544 550 4.517952 TGCATGGTTACAAGTTTCATGG 57.482 40.909 0.00 0.00 36.62 3.66
545 551 4.327898 GCATGCATGGTTACAAGTTTCATG 59.672 41.667 27.34 0.00 38.46 3.07
546 552 4.021280 TGCATGCATGGTTACAAGTTTCAT 60.021 37.500 27.34 0.00 0.00 2.57
552 558 3.786516 TGATGCATGCATGGTTACAAG 57.213 42.857 36.73 0.11 36.70 3.16
573 579 0.675083 CAGCAGGCCACAACATTTGA 59.325 50.000 5.01 0.00 0.00 2.69
583 589 0.250295 GTGACAGTAACAGCAGGCCA 60.250 55.000 5.01 0.00 0.00 5.36
708 714 2.180946 AGATGCAGACCCATCCACTA 57.819 50.000 0.00 0.00 41.98 2.74
715 721 0.833287 GCTTCCTAGATGCAGACCCA 59.167 55.000 0.00 0.00 33.71 4.51
758 774 0.817229 GCCAACTAGCCTGATCCTGC 60.817 60.000 0.00 0.00 0.00 4.85
819 837 0.531532 GGACACTCATCATCGGCCAG 60.532 60.000 2.24 0.00 0.00 4.85
911 936 2.024319 GCTCCACACACACGAGAGC 61.024 63.158 0.00 0.00 42.74 4.09
922 949 3.118629 CCTTAAGTAGATGCAGCTCCACA 60.119 47.826 8.28 0.00 0.00 4.17
924 951 2.158900 GCCTTAAGTAGATGCAGCTCCA 60.159 50.000 8.28 0.00 0.00 3.86
933 960 1.047034 ACGGCCGGCCTTAAGTAGAT 61.047 55.000 41.01 13.37 0.00 1.98
1014 1041 2.045045 CTGCCGGCATTTCCCTCA 60.045 61.111 32.87 2.72 0.00 3.86
1177 3673 4.778143 ATCACTCGTTGCCCGGCC 62.778 66.667 7.03 0.00 37.11 6.13
1178 3674 2.253414 GAAATCACTCGTTGCCCGGC 62.253 60.000 1.04 1.04 37.11 6.13
1336 6837 2.501223 GAACGGGAGTGGCGACATGA 62.501 60.000 0.00 0.00 46.69 3.07
1397 6902 4.424626 TGCATATCGACAGTTCTTGAGTC 58.575 43.478 0.00 0.00 0.00 3.36
1401 6906 5.723492 TTGATGCATATCGACAGTTCTTG 57.277 39.130 0.00 0.00 36.04 3.02
1483 8717 0.323360 TAACAACAGGGCCCAGCATC 60.323 55.000 27.56 0.00 0.00 3.91
1497 8731 1.876799 CATTCGTGGTGCCAGTAACAA 59.123 47.619 0.00 0.00 0.00 2.83
1541 8775 1.064946 CGACCACTCTCTCGGCATC 59.935 63.158 0.00 0.00 0.00 3.91
1674 8915 2.829720 AGATCGTAAAGTACACCAGCCA 59.170 45.455 0.00 0.00 0.00 4.75
1675 8916 3.521947 AGATCGTAAAGTACACCAGCC 57.478 47.619 0.00 0.00 0.00 4.85
1676 8917 4.243270 ACAAGATCGTAAAGTACACCAGC 58.757 43.478 0.00 0.00 0.00 4.85
1680 8921 6.201425 TGGTTCAACAAGATCGTAAAGTACAC 59.799 38.462 0.00 0.00 0.00 2.90
1682 8923 6.774354 TGGTTCAACAAGATCGTAAAGTAC 57.226 37.500 0.00 0.00 0.00 2.73
1690 8931 8.977505 ACAAATAATTTTGGTTCAACAAGATCG 58.022 29.630 3.76 0.00 45.34 3.69
1703 8961 6.070824 AGGTTGGAGCCTACAAATAATTTTGG 60.071 38.462 0.00 0.29 45.34 3.28
1709 8967 5.007682 GTCAAGGTTGGAGCCTACAAATAA 58.992 41.667 0.00 0.00 38.03 1.40
1711 8969 3.074538 AGTCAAGGTTGGAGCCTACAAAT 59.925 43.478 0.00 0.00 38.03 2.32
1715 8973 3.798202 CATAGTCAAGGTTGGAGCCTAC 58.202 50.000 0.00 0.00 38.03 3.18
1752 9015 2.988010 TACCAGCTCTGCAGGTAATG 57.012 50.000 15.13 7.92 46.35 1.90
2048 9339 2.819154 TCGCGGACGTCCACGATA 60.819 61.111 36.53 20.79 44.54 2.92
2214 9526 1.540607 CGTCGGGCGATCAGAATTCG 61.541 60.000 0.00 0.00 44.77 3.34
2215 9527 0.248907 TCGTCGGGCGATCAGAATTC 60.249 55.000 0.00 0.00 45.68 2.17
2216 9528 1.813859 TCGTCGGGCGATCAGAATT 59.186 52.632 0.00 0.00 45.68 2.17
2217 9529 3.521605 TCGTCGGGCGATCAGAAT 58.478 55.556 0.00 0.00 45.68 2.40
2238 9552 2.584970 TCATTGATCGTCGCCGCC 60.585 61.111 0.00 0.00 0.00 6.13
2241 9555 1.858091 ACATCTCATTGATCGTCGCC 58.142 50.000 0.00 0.00 32.05 5.54
2242 9556 3.633235 AGTACATCTCATTGATCGTCGC 58.367 45.455 0.00 0.00 32.05 5.19
2243 9557 5.991568 AGTAGTACATCTCATTGATCGTCG 58.008 41.667 2.52 0.00 32.05 5.12
2244 9558 7.041303 TGGTAGTAGTACATCTCATTGATCGTC 60.041 40.741 9.89 0.00 32.05 4.20
2248 9562 8.484214 ACATGGTAGTAGTACATCTCATTGAT 57.516 34.615 9.89 0.00 35.40 2.57
2249 9563 7.898014 ACATGGTAGTAGTACATCTCATTGA 57.102 36.000 9.89 0.00 0.00 2.57
2251 9565 8.361139 GCTTACATGGTAGTAGTACATCTCATT 58.639 37.037 9.89 0.00 0.00 2.57
2252 9566 7.726291 AGCTTACATGGTAGTAGTACATCTCAT 59.274 37.037 9.89 1.44 0.00 2.90
2253 9567 7.013369 CAGCTTACATGGTAGTAGTACATCTCA 59.987 40.741 9.89 0.00 0.00 3.27
2254 9568 7.364200 CAGCTTACATGGTAGTAGTACATCTC 58.636 42.308 9.89 0.00 0.00 2.75
2255 9569 6.265649 CCAGCTTACATGGTAGTAGTACATCT 59.734 42.308 9.89 0.00 32.85 2.90
2256 9570 6.448006 CCAGCTTACATGGTAGTAGTACATC 58.552 44.000 9.89 0.00 32.85 3.06
2259 9573 4.038883 CCCCAGCTTACATGGTAGTAGTAC 59.961 50.000 0.00 0.00 35.96 2.73
2260 9574 4.220724 CCCCAGCTTACATGGTAGTAGTA 58.779 47.826 0.00 0.00 35.96 1.82
2262 9576 2.224305 GCCCCAGCTTACATGGTAGTAG 60.224 54.545 0.00 0.00 35.96 2.57
2264 9578 0.546598 GCCCCAGCTTACATGGTAGT 59.453 55.000 0.00 0.00 35.96 2.73
2312 9628 2.028190 CGTATGCTCTCCCTGCCG 59.972 66.667 0.00 0.00 0.00 5.69
2343 9659 3.148279 GGAGGTCATCGGAGCCGT 61.148 66.667 8.96 0.00 42.52 5.68
2370 9686 1.849823 AGCTCCACCCCAGCTTCTT 60.850 57.895 0.00 0.00 45.34 2.52
2441 9757 1.758592 CCCGTCCTCAAGAAACCCA 59.241 57.895 0.00 0.00 0.00 4.51
2458 9774 0.321653 GGGCGTATCATCACCATCCC 60.322 60.000 0.00 0.00 0.00 3.85
2513 9829 3.118811 CCAAACTTCTTGGGAAAGTTGCA 60.119 43.478 2.32 0.00 35.96 4.08
2514 9830 3.457234 CCAAACTTCTTGGGAAAGTTGC 58.543 45.455 2.32 0.00 35.96 4.17
2562 9878 3.546002 TTTGCCGTCTTTTATTCGTGG 57.454 42.857 0.00 0.00 0.00 4.94
2563 9879 5.390613 AGAATTTGCCGTCTTTTATTCGTG 58.609 37.500 0.00 0.00 0.00 4.35
2643 9960 2.824489 TGCGCGTGAAACCAACCA 60.824 55.556 8.43 0.00 0.00 3.67
2646 9963 0.593518 CATTGTGCGCGTGAAACCAA 60.594 50.000 8.43 2.42 0.00 3.67
2656 9973 2.097250 GCTTCTTTTGAACATTGTGCGC 60.097 45.455 0.00 0.00 34.31 6.09
2666 9983 4.527509 TTGTGGTTGTGCTTCTTTTGAA 57.472 36.364 0.00 0.00 36.89 2.69
2697 10014 8.857098 TGATATGCCTAGACGTACTCTTAAATT 58.143 33.333 0.00 0.00 0.00 1.82
2698 10015 8.405418 TGATATGCCTAGACGTACTCTTAAAT 57.595 34.615 0.00 0.00 0.00 1.40
2701 10018 8.944029 GTTATGATATGCCTAGACGTACTCTTA 58.056 37.037 0.00 0.00 0.00 2.10
2704 10021 7.380431 AGTTATGATATGCCTAGACGTACTC 57.620 40.000 0.00 0.00 0.00 2.59
2733 10050 8.819974 CGAGTGGTAGTTTTCTTGTAACTAAAA 58.180 33.333 0.00 0.00 39.17 1.52
2749 10078 0.885879 TGTTCGCATCGAGTGGTAGT 59.114 50.000 0.00 0.00 37.14 2.73
2773 10102 0.682292 TTGTGGTGTCCGTGCTATGA 59.318 50.000 0.00 0.00 0.00 2.15
2775 10104 0.321298 GGTTGTGGTGTCCGTGCTAT 60.321 55.000 0.00 0.00 0.00 2.97
2807 10136 2.937519 TGCTGGATGGTGTTGTTTGTA 58.062 42.857 0.00 0.00 0.00 2.41
2821 10150 2.126071 GCGTCGTAGCTTGCTGGA 60.126 61.111 5.26 0.02 0.00 3.86
2834 10163 3.198068 TCATGATAGGCTCTTTTGCGTC 58.802 45.455 0.00 0.00 32.99 5.19
2852 10181 0.951558 GGTGCTTTGTGTCGGTTCAT 59.048 50.000 0.00 0.00 0.00 2.57
2858 10187 0.232303 GTCTTCGGTGCTTTGTGTCG 59.768 55.000 0.00 0.00 0.00 4.35
2887 10243 2.080693 TCGGCAACATAAATTCTGCGT 58.919 42.857 0.00 0.00 35.60 5.24
2904 10260 0.389391 AAGGATAGATGGTGCGTCGG 59.611 55.000 0.00 0.00 0.00 4.79
2917 10273 5.602978 CACTTTCTCTTAGGCCCTAAGGATA 59.397 44.000 26.45 16.84 42.43 2.59
2926 10282 3.963428 TCTGTCACTTTCTCTTAGGCC 57.037 47.619 0.00 0.00 0.00 5.19
2958 10314 3.927163 TTTTCGGAGCGGGTCGAGC 62.927 63.158 5.93 5.93 36.72 5.03
2964 10320 3.431725 GTGCCTTTTCGGAGCGGG 61.432 66.667 0.00 0.00 33.16 6.13
2998 10354 2.100749 TGGTGCTATGTACGTCTGATGG 59.899 50.000 0.00 0.00 0.00 3.51
3000 10356 2.100916 GGTGGTGCTATGTACGTCTGAT 59.899 50.000 0.00 0.00 0.00 2.90
3001 10357 1.475280 GGTGGTGCTATGTACGTCTGA 59.525 52.381 0.00 0.00 0.00 3.27
3016 10372 2.504367 CTGTTTTTGATCCTCGGTGGT 58.496 47.619 0.00 0.00 37.07 4.16
3050 10406 1.153667 CTCGTTGCTCTCCTCCAGC 60.154 63.158 0.00 0.00 37.40 4.85
3052 10408 0.967887 CTCCTCGTTGCTCTCCTCCA 60.968 60.000 0.00 0.00 0.00 3.86
3080 10436 3.499338 TGGAAGCATTGTGTTTGGAGAT 58.501 40.909 0.00 0.00 0.00 2.75
3098 10454 0.039437 GACGTCGCTTCTCTGTTGGA 60.039 55.000 0.00 0.00 0.00 3.53
3126 10482 1.812571 GTTTGGATTGGCACGATGACT 59.187 47.619 0.00 0.00 0.00 3.41
3128 10484 1.902938 TGTTTGGATTGGCACGATGA 58.097 45.000 0.00 0.00 0.00 2.92
3151 10507 2.094700 TCTTCGGGTGAAAGTCTCGATG 60.095 50.000 0.00 0.00 32.66 3.84
3158 10514 1.697432 TGGATGTCTTCGGGTGAAAGT 59.303 47.619 0.00 0.00 32.66 2.66
3206 10562 1.590525 GCGTCACCGAGTGTGTTCA 60.591 57.895 4.33 0.00 45.61 3.18
3228 10584 3.118408 CGTGGATGTCATTCCCCTCTTTA 60.118 47.826 0.00 0.00 34.67 1.85
3272 10628 3.575256 TGAAAATCTTGCATGGCTTCTGT 59.425 39.130 0.00 0.00 0.00 3.41
3281 10637 1.067635 GTGCGGGTGAAAATCTTGCAT 60.068 47.619 0.00 0.00 33.01 3.96
3314 10670 1.136329 ACCAAGTCCATGGAGCTGGT 61.136 55.000 30.15 30.15 43.54 4.00
3317 10673 0.543749 GCTACCAAGTCCATGGAGCT 59.456 55.000 16.81 12.69 43.54 4.09
3318 10674 0.253044 TGCTACCAAGTCCATGGAGC 59.747 55.000 16.81 13.81 43.54 4.70
3339 10696 1.239347 GGTGTGAAGCTTCTTGGACC 58.761 55.000 26.09 20.22 0.00 4.46
3392 10752 1.985116 AGTCCTTGGTCCTCGGCTC 60.985 63.158 0.00 0.00 0.00 4.70
3410 10770 2.601702 TTTCCCTGCCAGCCGATCA 61.602 57.895 0.00 0.00 0.00 2.92
3413 10773 4.344865 GGTTTCCCTGCCAGCCGA 62.345 66.667 0.00 0.00 0.00 5.54
3434 10794 1.573108 CTAGGAGTGGATGGTGTGGT 58.427 55.000 0.00 0.00 0.00 4.16
3440 10800 2.088104 TGTAGGCTAGGAGTGGATGG 57.912 55.000 0.00 0.00 0.00 3.51
3451 10812 0.750850 GCGGTTCCTCATGTAGGCTA 59.249 55.000 6.38 0.00 46.10 3.93
3457 10818 2.045926 GGCTGCGGTTCCTCATGT 60.046 61.111 0.00 0.00 0.00 3.21
3460 10821 2.281484 GTTGGCTGCGGTTCCTCA 60.281 61.111 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.