Multiple sequence alignment - TraesCS5D01G315800

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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 TraesCS5D01G315800 chr5D 100.000 5564 0 0 1 5564 410000515 410006078 0.000000e+00 10275.0
1 TraesCS5D01G315800 chr5D 78.152 682 131 11 1001 1676 28451259 28450590 8.620000e-113 418.0
2 TraesCS5D01G315800 chr5B 92.751 3904 234 24 1695 5564 491606790 491610678 0.000000e+00 5596.0
3 TraesCS5D01G315800 chr5B 91.495 1505 83 20 4092 5564 491611918 491613409 0.000000e+00 2028.0
4 TraesCS5D01G315800 chr5B 91.926 1189 59 20 4387 5564 491614935 491616097 0.000000e+00 1629.0
5 TraesCS5D01G315800 chr5B 93.504 1093 71 0 3201 4293 491613595 491614687 0.000000e+00 1626.0
6 TraesCS5D01G315800 chr5B 92.659 899 64 2 801 1697 491605858 491606756 0.000000e+00 1293.0
7 TraesCS5D01G315800 chr5B 92.439 820 62 0 3201 4020 491610864 491611683 0.000000e+00 1171.0
8 TraesCS5D01G315800 chr5B 89.270 233 20 3 441 673 491605520 491605747 2.540000e-73 287.0
9 TraesCS5D01G315800 chr5B 86.735 196 19 1 251 439 491603541 491603736 1.570000e-50 211.0
10 TraesCS5D01G315800 chr5A 97.345 1469 37 2 1695 3163 521102839 521104305 0.000000e+00 2495.0
11 TraesCS5D01G315800 chr5A 95.047 848 39 3 532 1376 521092588 521093435 0.000000e+00 1330.0
12 TraesCS5D01G315800 chr5A 94.499 818 42 1 3159 3973 521184665 521185482 0.000000e+00 1258.0
13 TraesCS5D01G315800 chr5A 96.234 717 26 1 3969 4685 521194179 521194894 0.000000e+00 1173.0
14 TraesCS5D01G315800 chr5A 83.398 777 86 23 4811 5564 521226454 521227210 0.000000e+00 680.0
15 TraesCS5D01G315800 chr5A 89.320 515 27 14 24 516 521040729 521041237 6.120000e-174 621.0
16 TraesCS5D01G315800 chr5A 85.688 552 60 12 5016 5564 521245355 521245890 1.050000e-156 564.0
17 TraesCS5D01G315800 chr5A 97.853 326 5 2 1373 1697 521102481 521102805 3.760000e-156 562.0
18 TraesCS5D01G315800 chr5A 77.745 683 144 7 1001 1676 19229384 19230065 4.010000e-111 412.0
19 TraesCS5D01G315800 chr7D 80.117 855 152 16 1718 2562 7750828 7751674 6.120000e-174 621.0
20 TraesCS5D01G315800 chr7D 78.770 862 166 12 1710 2555 7598118 7598978 3.760000e-156 562.0
21 TraesCS5D01G315800 chr7D 78.563 835 149 25 1744 2562 8177884 8178704 1.780000e-144 523.0
22 TraesCS5D01G315800 chr7D 78.755 819 147 20 1751 2551 76920163 76920972 1.780000e-144 523.0
23 TraesCS5D01G315800 chr7D 78.094 703 138 13 1001 1692 76919374 76920071 1.110000e-116 431.0
24 TraesCS5D01G315800 chr7D 76.170 705 131 21 1001 1692 76954651 76955331 2.480000e-88 337.0
25 TraesCS5D01G315800 chr7D 74.490 686 140 25 1001 1674 76971391 76972053 1.190000e-66 265.0
26 TraesCS5D01G315800 chr7D 72.154 729 187 15 2725 3445 7655676 7656396 2.030000e-49 207.0
27 TraesCS5D01G315800 chr7D 72.138 725 170 22 2725 3445 7599148 7599844 2.050000e-44 191.0
28 TraesCS5D01G315800 chr7D 84.810 158 13 9 5341 5492 423334816 423334664 1.250000e-31 148.0
29 TraesCS5D01G315800 chr7D 83.030 165 22 5 5333 5495 260039703 260039543 1.620000e-30 145.0
30 TraesCS5D01G315800 chr7D 73.962 265 44 19 4194 4441 76746408 76746664 3.570000e-12 84.2
31 TraesCS5D01G315800 chr7D 100.000 31 0 0 4194 4224 76632971 76632941 2.170000e-04 58.4
32 TraesCS5D01G315800 chr7A 73.495 1728 398 44 1744 3445 8654584 8656277 2.870000e-167 599.0
33 TraesCS5D01G315800 chr7A 72.951 854 205 20 2728 3568 3430227 3429387 1.970000e-69 274.0
34 TraesCS5D01G315800 chr7B 78.736 823 157 16 1753 2562 23517014 23517831 8.200000e-148 534.0
35 TraesCS5D01G315800 chr7B 76.529 703 149 12 1001 1692 23582376 23583073 2.450000e-98 370.0
36 TraesCS5D01G315800 chr7B 75.836 269 47 13 4194 4447 23936161 23936426 2.720000e-23 121.0
37 TraesCS5D01G315800 chr7B 75.191 262 44 15 4194 4440 23599560 23599815 2.740000e-18 104.0
38 TraesCS5D01G315800 chr1D 83.588 262 37 5 2142 2398 7675473 7675733 2.000000e-59 241.0
39 TraesCS5D01G315800 chr1D 84.472 161 20 4 5338 5495 397053415 397053257 2.680000e-33 154.0
40 TraesCS5D01G315800 chr4A 83.648 159 17 8 5340 5492 722271413 722271568 2.090000e-29 141.0
41 TraesCS5D01G315800 chr4A 92.424 66 5 0 4393 4458 732416158 732416223 1.650000e-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 TraesCS5D01G315800 chr5D 410000515 410006078 5563 False 10275.000 10275 100.000000 1 5564 1 chr5D.!!$F1 5563
1 TraesCS5D01G315800 chr5D 28450590 28451259 669 True 418.000 418 78.152000 1001 1676 1 chr5D.!!$R1 675
2 TraesCS5D01G315800 chr5B 491603541 491616097 12556 False 1730.125 5596 91.347375 251 5564 8 chr5B.!!$F1 5313
3 TraesCS5D01G315800 chr5A 521102481 521104305 1824 False 1528.500 2495 97.599000 1373 3163 2 chr5A.!!$F8 1790
4 TraesCS5D01G315800 chr5A 521092588 521093435 847 False 1330.000 1330 95.047000 532 1376 1 chr5A.!!$F3 844
5 TraesCS5D01G315800 chr5A 521184665 521185482 817 False 1258.000 1258 94.499000 3159 3973 1 chr5A.!!$F4 814
6 TraesCS5D01G315800 chr5A 521194179 521194894 715 False 1173.000 1173 96.234000 3969 4685 1 chr5A.!!$F5 716
7 TraesCS5D01G315800 chr5A 521226454 521227210 756 False 680.000 680 83.398000 4811 5564 1 chr5A.!!$F6 753
8 TraesCS5D01G315800 chr5A 521040729 521041237 508 False 621.000 621 89.320000 24 516 1 chr5A.!!$F2 492
9 TraesCS5D01G315800 chr5A 521245355 521245890 535 False 564.000 564 85.688000 5016 5564 1 chr5A.!!$F7 548
10 TraesCS5D01G315800 chr5A 19229384 19230065 681 False 412.000 412 77.745000 1001 1676 1 chr5A.!!$F1 675
11 TraesCS5D01G315800 chr7D 7750828 7751674 846 False 621.000 621 80.117000 1718 2562 1 chr7D.!!$F2 844
12 TraesCS5D01G315800 chr7D 8177884 8178704 820 False 523.000 523 78.563000 1744 2562 1 chr7D.!!$F3 818
13 TraesCS5D01G315800 chr7D 76919374 76920972 1598 False 477.000 523 78.424500 1001 2551 2 chr7D.!!$F8 1550
14 TraesCS5D01G315800 chr7D 7598118 7599844 1726 False 376.500 562 75.454000 1710 3445 2 chr7D.!!$F7 1735
15 TraesCS5D01G315800 chr7D 76954651 76955331 680 False 337.000 337 76.170000 1001 1692 1 chr7D.!!$F5 691
16 TraesCS5D01G315800 chr7D 76971391 76972053 662 False 265.000 265 74.490000 1001 1674 1 chr7D.!!$F6 673
17 TraesCS5D01G315800 chr7D 7655676 7656396 720 False 207.000 207 72.154000 2725 3445 1 chr7D.!!$F1 720
18 TraesCS5D01G315800 chr7A 8654584 8656277 1693 False 599.000 599 73.495000 1744 3445 1 chr7A.!!$F1 1701
19 TraesCS5D01G315800 chr7A 3429387 3430227 840 True 274.000 274 72.951000 2728 3568 1 chr7A.!!$R1 840
20 TraesCS5D01G315800 chr7B 23517014 23517831 817 False 534.000 534 78.736000 1753 2562 1 chr7B.!!$F1 809
21 TraesCS5D01G315800 chr7B 23582376 23583073 697 False 370.000 370 76.529000 1001 1692 1 chr7B.!!$F2 691

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
721 2580 0.034198 TTAGCCACTACAGCGTTGCA 59.966 50.000 0.00 0.0 34.64 4.08 F
1858 3839 0.108585 GCTCTGTTCTGTTGGTGGGA 59.891 55.000 0.00 0.0 0.00 4.37 F
2249 4237 1.271054 TGCCTTCTGTGCTCTCTTTCC 60.271 52.381 0.00 0.0 0.00 3.13 F
3615 5628 1.217882 CGAAACTTGCGAGTGTTCCT 58.782 50.000 7.56 0.0 35.91 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2040 4024 1.341976 GGAAGCCCCCTGCATTTCTTA 60.342 52.381 0.0 0.0 44.83 2.10 R
3615 5628 0.321671 CTTTCAAGACGGGGCTCTCA 59.678 55.000 0.0 0.0 0.00 3.27 R
3667 5680 1.151668 AGATGTGCAAGCGAACTCAC 58.848 50.000 0.0 0.0 0.00 3.51 R
5288 12775 0.179020 TGGTGGGAGCACAAAGACAG 60.179 55.000 0.0 0.0 0.00 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
17 18 4.368391 CGAGGGATACATGCTGGC 57.632 61.111 0.00 0.00 39.74 4.85
18 19 1.665916 CGAGGGATACATGCTGGCG 60.666 63.158 0.00 0.00 39.74 5.69
19 20 1.963338 GAGGGATACATGCTGGCGC 60.963 63.158 0.00 0.00 39.74 6.53
20 21 3.349006 GGGATACATGCTGGCGCG 61.349 66.667 0.00 0.00 37.34 6.86
21 22 2.588877 GGATACATGCTGGCGCGT 60.589 61.111 8.43 0.00 39.65 6.01
22 23 1.300620 GGATACATGCTGGCGCGTA 60.301 57.895 8.43 0.00 39.65 4.42
23 24 0.878523 GGATACATGCTGGCGCGTAA 60.879 55.000 8.43 0.00 39.65 3.18
24 25 0.232303 GATACATGCTGGCGCGTAAC 59.768 55.000 8.43 0.00 39.65 2.50
25 26 0.461163 ATACATGCTGGCGCGTAACA 60.461 50.000 8.43 3.87 39.65 2.41
26 27 1.081556 TACATGCTGGCGCGTAACAG 61.082 55.000 18.72 18.72 39.65 3.16
30 31 3.545481 CTGGCGCGTAACAGCTCG 61.545 66.667 8.43 0.00 34.40 5.03
114 116 3.726517 CTGGCTCGCCAAACACGG 61.727 66.667 12.29 0.00 46.63 4.94
210 212 1.144708 TGTGGAAATGCCTGAACCTGA 59.855 47.619 0.00 0.00 37.63 3.86
222 224 1.270625 TGAACCTGAACGGGTGTCATC 60.271 52.381 6.06 1.23 39.85 2.92
223 225 0.762418 AACCTGAACGGGTGTCATCA 59.238 50.000 6.06 0.00 39.85 3.07
224 226 0.984230 ACCTGAACGGGTGTCATCAT 59.016 50.000 4.37 0.00 38.30 2.45
225 227 1.339055 ACCTGAACGGGTGTCATCATG 60.339 52.381 4.37 0.00 38.30 3.07
226 228 1.372582 CTGAACGGGTGTCATCATGG 58.627 55.000 0.00 0.00 0.00 3.66
227 229 0.980423 TGAACGGGTGTCATCATGGA 59.020 50.000 0.00 0.00 0.00 3.41
249 251 0.174389 CCAGAGCGCTCGCCATATAT 59.826 55.000 30.39 8.81 43.17 0.86
301 303 2.507484 TGCAGGTCCATTCTTTCACAG 58.493 47.619 0.00 0.00 0.00 3.66
377 387 5.465724 GTGTATACTGTATAACCCTTGCTGC 59.534 44.000 9.01 0.00 0.00 5.25
406 425 4.326766 CACCGTTGGCACGCAAGG 62.327 66.667 0.00 0.00 45.72 3.61
422 441 2.162408 GCAAGGTGGTCAGCTCAAATAC 59.838 50.000 3.02 0.00 38.35 1.89
510 2313 7.559486 AGTAATCAATCATGTCTGCTAGTTCA 58.441 34.615 0.00 0.00 0.00 3.18
516 2319 4.752146 TCATGTCTGCTAGTTCATCAGTG 58.248 43.478 0.00 0.00 0.00 3.66
528 2331 7.201652 GCTAGTTCATCAGTGGTTTCTTATTCC 60.202 40.741 0.00 0.00 0.00 3.01
532 2335 7.119709 TCATCAGTGGTTTCTTATTCCGATA 57.880 36.000 0.00 0.00 0.00 2.92
612 2415 9.921637 GGGTTGAGAAAATGTATTGTGAATTAA 57.078 29.630 0.00 0.00 0.00 1.40
673 2532 9.331282 GAAGTTATCAGTTGGCAGAATATAGTT 57.669 33.333 0.00 0.00 0.00 2.24
674 2533 9.686683 AAGTTATCAGTTGGCAGAATATAGTTT 57.313 29.630 0.00 0.00 0.00 2.66
679 2538 8.718102 TCAGTTGGCAGAATATAGTTTAACTC 57.282 34.615 0.00 0.00 0.00 3.01
680 2539 8.540388 TCAGTTGGCAGAATATAGTTTAACTCT 58.460 33.333 0.00 0.00 0.00 3.24
681 2540 9.167311 CAGTTGGCAGAATATAGTTTAACTCTT 57.833 33.333 0.00 0.00 0.00 2.85
682 2541 9.384764 AGTTGGCAGAATATAGTTTAACTCTTC 57.615 33.333 0.00 4.15 0.00 2.87
683 2542 9.162764 GTTGGCAGAATATAGTTTAACTCTTCA 57.837 33.333 0.00 0.00 0.00 3.02
684 2543 9.905713 TTGGCAGAATATAGTTTAACTCTTCAT 57.094 29.630 0.00 0.00 0.00 2.57
685 2544 9.905713 TGGCAGAATATAGTTTAACTCTTCATT 57.094 29.630 0.00 0.00 0.00 2.57
687 2546 9.657121 GCAGAATATAGTTTAACTCTTCATTGC 57.343 33.333 0.00 7.05 0.00 3.56
694 2553 7.138692 AGTTTAACTCTTCATTGCTCATGAC 57.861 36.000 0.00 0.00 41.98 3.06
695 2554 6.712095 AGTTTAACTCTTCATTGCTCATGACA 59.288 34.615 0.00 0.00 41.98 3.58
696 2555 6.732531 TTAACTCTTCATTGCTCATGACAG 57.267 37.500 0.00 2.23 41.98 3.51
697 2556 3.008330 ACTCTTCATTGCTCATGACAGC 58.992 45.455 0.00 0.00 41.98 4.40
698 2557 3.271729 CTCTTCATTGCTCATGACAGCT 58.728 45.455 8.27 0.00 41.98 4.24
699 2558 3.268330 TCTTCATTGCTCATGACAGCTC 58.732 45.455 8.27 0.00 41.98 4.09
700 2559 2.773993 TCATTGCTCATGACAGCTCA 57.226 45.000 8.27 0.00 40.39 4.26
701 2560 2.353323 TCATTGCTCATGACAGCTCAC 58.647 47.619 8.27 0.00 40.39 3.51
702 2561 2.027469 TCATTGCTCATGACAGCTCACT 60.027 45.455 8.27 0.00 40.39 3.41
703 2562 2.556144 TTGCTCATGACAGCTCACTT 57.444 45.000 8.27 0.00 40.39 3.16
704 2563 3.683365 TTGCTCATGACAGCTCACTTA 57.317 42.857 8.27 0.00 40.39 2.24
705 2564 3.242549 TGCTCATGACAGCTCACTTAG 57.757 47.619 8.27 0.00 40.39 2.18
706 2565 7.423715 CATTGCTCATGACAGCTCACTTAGC 62.424 48.000 8.27 0.00 42.89 3.09
715 2574 1.646189 GCTCACTTAGCCACTACAGC 58.354 55.000 0.00 0.00 46.25 4.40
716 2575 1.914634 CTCACTTAGCCACTACAGCG 58.085 55.000 0.00 0.00 34.64 5.18
717 2576 1.202582 CTCACTTAGCCACTACAGCGT 59.797 52.381 0.00 0.00 34.64 5.07
718 2577 1.616865 TCACTTAGCCACTACAGCGTT 59.383 47.619 0.00 0.00 34.64 4.84
719 2578 1.726791 CACTTAGCCACTACAGCGTTG 59.273 52.381 0.00 0.00 34.64 4.10
720 2579 0.721718 CTTAGCCACTACAGCGTTGC 59.278 55.000 0.00 0.00 34.64 4.17
721 2580 0.034198 TTAGCCACTACAGCGTTGCA 59.966 50.000 0.00 0.00 34.64 4.08
722 2581 0.669318 TAGCCACTACAGCGTTGCAC 60.669 55.000 0.00 0.00 34.64 4.57
723 2582 2.250939 GCCACTACAGCGTTGCACA 61.251 57.895 0.00 0.00 0.00 4.57
724 2583 1.781025 GCCACTACAGCGTTGCACAA 61.781 55.000 0.00 0.00 0.00 3.33
725 2584 0.660488 CCACTACAGCGTTGCACAAA 59.340 50.000 0.00 0.00 0.00 2.83
726 2585 1.334059 CCACTACAGCGTTGCACAAAG 60.334 52.381 0.00 0.00 0.00 2.77
727 2586 1.330521 CACTACAGCGTTGCACAAAGT 59.669 47.619 0.00 0.00 0.00 2.66
728 2587 1.597663 ACTACAGCGTTGCACAAAGTC 59.402 47.619 0.00 0.00 0.00 3.01
729 2588 1.597195 CTACAGCGTTGCACAAAGTCA 59.403 47.619 0.00 0.00 0.00 3.41
730 2589 0.808125 ACAGCGTTGCACAAAGTCAA 59.192 45.000 0.00 0.00 0.00 3.18
731 2590 1.202177 ACAGCGTTGCACAAAGTCAAG 60.202 47.619 0.00 0.00 0.00 3.02
732 2591 1.063912 CAGCGTTGCACAAAGTCAAGA 59.936 47.619 0.00 0.00 0.00 3.02
733 2592 1.949525 AGCGTTGCACAAAGTCAAGAT 59.050 42.857 0.00 0.00 0.00 2.40
734 2593 2.046313 GCGTTGCACAAAGTCAAGATG 58.954 47.619 0.00 0.00 0.00 2.90
735 2594 2.653890 CGTTGCACAAAGTCAAGATGG 58.346 47.619 0.00 0.00 0.00 3.51
738 2597 3.213206 TGCACAAAGTCAAGATGGAGT 57.787 42.857 0.00 0.00 0.00 3.85
753 2612 9.261035 TCAAGATGGAGTTAAGATTAGACTCTT 57.739 33.333 0.00 0.00 39.70 2.85
779 2639 4.972751 ATAAATGGTTTTGTGGGCACTT 57.027 36.364 0.00 0.00 0.00 3.16
789 2649 6.073276 GGTTTTGTGGGCACTTGATATTTTTC 60.073 38.462 0.00 0.00 0.00 2.29
832 2729 5.376625 AGGAGTTGAGCACTTGACATAAAA 58.623 37.500 0.00 0.00 35.01 1.52
1356 3258 5.528320 GCTACTCTTCCGTCTTACTATGAGT 59.472 44.000 0.00 0.00 37.33 3.41
1858 3839 0.108585 GCTCTGTTCTGTTGGTGGGA 59.891 55.000 0.00 0.00 0.00 4.37
2058 4042 2.179427 GTTAAGAAATGCAGGGGGCTT 58.821 47.619 0.00 0.00 45.15 4.35
2131 4115 2.175499 CAGGAATGGGAGGCCATAGAAA 59.825 50.000 5.01 0.00 0.00 2.52
2249 4237 1.271054 TGCCTTCTGTGCTCTCTTTCC 60.271 52.381 0.00 0.00 0.00 3.13
2698 4695 2.792674 TCGTTAAGAGTCTTGTGTTGCG 59.207 45.455 15.90 10.03 0.00 4.85
2826 4829 6.092122 CGTTGTATAACCTGCAATCTTTGAGA 59.908 38.462 0.00 0.00 31.82 3.27
3051 5054 6.208797 GGCACCTTTCAAATAGGTTAGAACTT 59.791 38.462 0.00 0.00 43.45 2.66
3228 5238 5.360144 TCTTATACCTCACAGTAAGCTCCAC 59.640 44.000 0.00 0.00 0.00 4.02
3332 5342 3.448093 TGATATGTCCAACTGCCCAAA 57.552 42.857 0.00 0.00 0.00 3.28
3430 5440 8.536175 TGACCACATTATGTAATAGTCTTGACA 58.464 33.333 0.00 0.00 0.00 3.58
3449 5459 2.774234 ACATGGAAGGTGGAGGATACAG 59.226 50.000 0.00 0.00 41.41 2.74
3522 5532 1.684869 CCCAACTTGGCGATATGGGTT 60.685 52.381 14.20 0.00 44.67 4.11
3572 5585 3.979911 TGGTAATGTTCCCAATGCTCAT 58.020 40.909 0.00 0.00 0.00 2.90
3573 5586 3.700539 TGGTAATGTTCCCAATGCTCATG 59.299 43.478 0.00 0.00 0.00 3.07
3615 5628 1.217882 CGAAACTTGCGAGTGTTCCT 58.782 50.000 7.56 0.00 35.91 3.36
3628 5641 1.985116 GTTCCTGAGAGCCCCGTCT 60.985 63.158 0.00 0.00 0.00 4.18
3667 5680 1.602311 AAACTGCTGCAGTCTTCCAG 58.398 50.000 33.00 15.36 44.62 3.86
3675 5688 1.269778 TGCAGTCTTCCAGTGAGTTCG 60.270 52.381 0.00 0.00 0.00 3.95
3727 5740 5.825532 TCCAATGTGATGGAAAAGGTATCA 58.174 37.500 0.00 0.00 46.36 2.15
3900 5915 4.518970 TGCTTCTTAACAACACCAGGATTC 59.481 41.667 0.00 0.00 0.00 2.52
3966 5981 4.708726 AGAATTGTGGCTTAATCAGTGC 57.291 40.909 0.00 0.00 0.00 4.40
4268 9013 0.727398 GATCGCTGTTGTGGCCTTAC 59.273 55.000 3.32 0.00 0.00 2.34
4351 9096 1.032114 GGAATTCCAGCAGGTTCCCG 61.032 60.000 20.04 0.00 35.17 5.14
4654 12117 3.055094 TCCACTGCTAACCTGGATTTCTC 60.055 47.826 0.00 0.00 0.00 2.87
4698 12161 5.047660 GCATGTTCGAGTTAGGATCCTAGAT 60.048 44.000 20.72 13.67 0.00 1.98
4700 12163 5.691896 TGTTCGAGTTAGGATCCTAGATGA 58.308 41.667 20.72 14.38 0.00 2.92
4741 12204 3.243839 TGCTGACTTTGAGATTTTTGGGC 60.244 43.478 0.00 0.00 0.00 5.36
4776 12239 5.010012 GGACTCCATTTGTCACATTTGTTCT 59.990 40.000 0.00 0.00 36.26 3.01
4778 12241 5.010012 ACTCCATTTGTCACATTTGTTCTCC 59.990 40.000 0.00 0.00 0.00 3.71
4824 12287 4.330074 CCAACACGTTGACCTTATCTCATC 59.670 45.833 11.46 0.00 42.93 2.92
4930 12396 1.022735 GCAGATGCAACTCATGGAGG 58.977 55.000 0.00 0.00 41.59 4.30
5012 12479 2.501223 TTCTGGTAGTCGGCTTGCGG 62.501 60.000 0.00 0.00 0.00 5.69
5050 12534 3.989167 TGGCGATTTCAGATTGCAAAAAG 59.011 39.130 1.71 0.00 0.00 2.27
5107 12591 1.634702 CAAGCTAAGGACGCTCTGAC 58.365 55.000 0.00 0.00 36.56 3.51
5155 12639 3.866651 TCACTTCTCTTCAGCAATAGGC 58.133 45.455 0.00 0.00 45.30 3.93
5179 12663 2.505819 ACTTCCAGTCAGTCCTGTGTTT 59.494 45.455 0.00 0.00 0.00 2.83
5237 12724 3.381983 TCGCCATCAGTCCGTGCT 61.382 61.111 0.00 0.00 0.00 4.40
5238 12725 2.434884 CGCCATCAGTCCGTGCTT 60.435 61.111 0.00 0.00 0.00 3.91
5239 12726 1.153647 CGCCATCAGTCCGTGCTTA 60.154 57.895 0.00 0.00 0.00 3.09
5265 12752 2.452937 GCTACATCCAGGGACCCCC 61.453 68.421 7.00 0.00 45.90 5.40
5278 12765 0.605589 GACCCCCTGTTCCGTTTCAG 60.606 60.000 0.00 0.00 0.00 3.02
5284 12771 2.884639 CCCTGTTCCGTTTCAGACATTT 59.115 45.455 0.00 0.00 34.02 2.32
5288 12775 5.356882 TGTTCCGTTTCAGACATTTCATC 57.643 39.130 0.00 0.00 0.00 2.92
5335 12823 2.685106 TTTGTGGGTGCATTTAGGGA 57.315 45.000 0.00 0.00 0.00 4.20
5343 12832 4.770010 TGGGTGCATTTAGGGACTTTTTAG 59.230 41.667 0.00 0.00 41.75 1.85
5347 12837 7.214381 GGTGCATTTAGGGACTTTTTAGTTTT 58.786 34.615 0.00 0.00 41.75 2.43
5348 12838 7.384115 GGTGCATTTAGGGACTTTTTAGTTTTC 59.616 37.037 0.00 0.00 41.75 2.29
5411 12903 4.201910 GCTATTTGCCTGCGTGATTCTTTA 60.202 41.667 0.00 0.00 35.15 1.85
5419 12911 4.397382 CTGCGTGATTCTTTATGTGTGTG 58.603 43.478 0.00 0.00 0.00 3.82
5486 12978 4.277174 TGTGTGGTCATTGTGTTTGTATCC 59.723 41.667 0.00 0.00 0.00 2.59
5487 12979 3.823873 TGTGGTCATTGTGTTTGTATCCC 59.176 43.478 0.00 0.00 0.00 3.85
5488 12980 4.079253 GTGGTCATTGTGTTTGTATCCCT 58.921 43.478 0.00 0.00 0.00 4.20
5489 12981 4.522789 GTGGTCATTGTGTTTGTATCCCTT 59.477 41.667 0.00 0.00 0.00 3.95
5490 12982 4.522405 TGGTCATTGTGTTTGTATCCCTTG 59.478 41.667 0.00 0.00 0.00 3.61
5491 12983 4.764823 GGTCATTGTGTTTGTATCCCTTGA 59.235 41.667 0.00 0.00 0.00 3.02
5492 12984 5.106157 GGTCATTGTGTTTGTATCCCTTGAG 60.106 44.000 0.00 0.00 0.00 3.02
5493 12985 5.009631 TCATTGTGTTTGTATCCCTTGAGG 58.990 41.667 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.665916 CGCCAGCATGTATCCCTCG 60.666 63.158 0.00 0.00 0.00 4.63
1 2 1.963338 GCGCCAGCATGTATCCCTC 60.963 63.158 0.00 0.00 44.35 4.30
3 4 2.709125 TACGCGCCAGCATGTATCCC 62.709 60.000 5.73 0.00 45.49 3.85
6 7 0.461163 TGTTACGCGCCAGCATGTAT 60.461 50.000 5.73 0.00 45.49 2.29
7 8 1.079750 TGTTACGCGCCAGCATGTA 60.080 52.632 5.73 0.00 45.49 2.29
8 9 2.358125 TGTTACGCGCCAGCATGT 60.358 55.556 5.73 0.00 45.49 3.21
13 14 3.545481 CGAGCTGTTACGCGCCAG 61.545 66.667 5.73 11.51 34.40 4.85
114 116 2.700773 GGAGTTTGGGGTCGCATGC 61.701 63.158 7.91 7.91 0.00 4.06
210 212 1.613255 GGTTCCATGATGACACCCGTT 60.613 52.381 0.00 0.00 0.00 4.44
222 224 1.817099 GAGCGCTCTGGGTTCCATG 60.817 63.158 29.88 0.00 30.82 3.66
223 225 2.586792 GAGCGCTCTGGGTTCCAT 59.413 61.111 29.88 0.00 30.82 3.41
224 226 4.069232 CGAGCGCTCTGGGTTCCA 62.069 66.667 32.88 0.00 0.00 3.53
249 251 2.224523 ACTGGCACGGAAAGAATTGAGA 60.225 45.455 0.00 0.00 38.67 3.27
301 303 5.893897 AACAAAATCAGAAGCTCTCATCC 57.106 39.130 0.00 0.00 0.00 3.51
353 355 5.465724 GCAGCAAGGGTTATACAGTATACAC 59.534 44.000 5.50 2.94 0.00 2.90
398 417 2.281070 AGCTGACCACCTTGCGTG 60.281 61.111 0.00 0.00 42.62 5.34
406 425 2.633488 GAGGGTATTTGAGCTGACCAC 58.367 52.381 0.00 0.00 33.33 4.16
422 441 4.862371 AGTTACAGAGTAGAAGAGGAGGG 58.138 47.826 0.00 0.00 0.00 4.30
510 2313 8.801882 TTTTATCGGAATAAGAAACCACTGAT 57.198 30.769 0.00 0.00 0.00 2.90
516 2319 8.905850 TGGGTTATTTTATCGGAATAAGAAACC 58.094 33.333 0.00 0.00 36.15 3.27
528 2331 4.062293 TGGAGCGATGGGTTATTTTATCG 58.938 43.478 0.00 0.00 43.70 2.92
532 2335 3.644966 TCTGGAGCGATGGGTTATTTT 57.355 42.857 0.00 0.00 0.00 1.82
673 2532 5.122869 GCTGTCATGAGCAATGAAGAGTTAA 59.877 40.000 0.00 0.00 46.90 2.01
674 2533 4.633126 GCTGTCATGAGCAATGAAGAGTTA 59.367 41.667 0.00 0.00 46.90 2.24
676 2535 3.008330 GCTGTCATGAGCAATGAAGAGT 58.992 45.455 0.00 0.00 46.90 3.24
677 2536 3.271729 AGCTGTCATGAGCAATGAAGAG 58.728 45.455 9.38 5.01 46.90 2.85
679 2538 3.007635 TGAGCTGTCATGAGCAATGAAG 58.992 45.455 9.38 5.77 46.90 3.02
680 2539 2.745821 GTGAGCTGTCATGAGCAATGAA 59.254 45.455 9.38 0.00 46.90 2.57
681 2540 2.027469 AGTGAGCTGTCATGAGCAATGA 60.027 45.455 9.38 0.00 43.24 2.57
682 2541 2.357075 AGTGAGCTGTCATGAGCAATG 58.643 47.619 9.38 0.00 41.83 2.82
683 2542 2.783609 AGTGAGCTGTCATGAGCAAT 57.216 45.000 9.38 0.00 41.83 3.56
684 2543 2.556144 AAGTGAGCTGTCATGAGCAA 57.444 45.000 9.38 0.00 41.83 3.91
685 2544 3.242549 CTAAGTGAGCTGTCATGAGCA 57.757 47.619 9.38 4.17 41.83 4.26
697 2556 1.202582 ACGCTGTAGTGGCTAAGTGAG 59.797 52.381 0.00 0.00 0.00 3.51
698 2557 1.254026 ACGCTGTAGTGGCTAAGTGA 58.746 50.000 0.00 0.00 0.00 3.41
699 2558 1.726791 CAACGCTGTAGTGGCTAAGTG 59.273 52.381 0.00 0.00 0.00 3.16
700 2559 1.939838 GCAACGCTGTAGTGGCTAAGT 60.940 52.381 0.00 0.00 38.03 2.24
701 2560 0.721718 GCAACGCTGTAGTGGCTAAG 59.278 55.000 0.00 0.00 38.03 2.18
702 2561 0.034198 TGCAACGCTGTAGTGGCTAA 59.966 50.000 6.40 0.00 41.50 3.09
703 2562 0.669318 GTGCAACGCTGTAGTGGCTA 60.669 55.000 0.00 0.00 41.50 3.93
704 2563 1.961277 GTGCAACGCTGTAGTGGCT 60.961 57.895 0.00 0.00 41.50 4.75
705 2564 1.781025 TTGTGCAACGCTGTAGTGGC 61.781 55.000 0.00 0.00 42.39 5.01
706 2565 0.660488 TTTGTGCAACGCTGTAGTGG 59.340 50.000 0.00 0.00 42.39 4.00
707 2566 1.330521 ACTTTGTGCAACGCTGTAGTG 59.669 47.619 0.00 0.00 42.39 2.74
708 2567 1.597663 GACTTTGTGCAACGCTGTAGT 59.402 47.619 0.00 0.00 42.39 2.73
709 2568 1.597195 TGACTTTGTGCAACGCTGTAG 59.403 47.619 0.00 0.00 42.39 2.74
710 2569 1.657822 TGACTTTGTGCAACGCTGTA 58.342 45.000 0.00 0.00 42.39 2.74
711 2570 0.808125 TTGACTTTGTGCAACGCTGT 59.192 45.000 0.00 0.00 42.39 4.40
712 2571 1.063912 TCTTGACTTTGTGCAACGCTG 59.936 47.619 0.00 0.00 42.39 5.18
713 2572 1.378531 TCTTGACTTTGTGCAACGCT 58.621 45.000 0.00 0.00 42.39 5.07
714 2573 2.046313 CATCTTGACTTTGTGCAACGC 58.954 47.619 0.00 0.00 42.39 4.84
715 2574 2.290367 TCCATCTTGACTTTGTGCAACG 59.710 45.455 0.00 0.00 42.39 4.10
716 2575 3.316308 ACTCCATCTTGACTTTGTGCAAC 59.684 43.478 0.00 0.00 37.35 4.17
717 2576 3.554934 ACTCCATCTTGACTTTGTGCAA 58.445 40.909 0.00 0.00 0.00 4.08
718 2577 3.213206 ACTCCATCTTGACTTTGTGCA 57.787 42.857 0.00 0.00 0.00 4.57
719 2578 5.470098 TCTTAACTCCATCTTGACTTTGTGC 59.530 40.000 0.00 0.00 0.00 4.57
720 2579 7.678947 ATCTTAACTCCATCTTGACTTTGTG 57.321 36.000 0.00 0.00 0.00 3.33
721 2580 9.442047 CTAATCTTAACTCCATCTTGACTTTGT 57.558 33.333 0.00 0.00 0.00 2.83
722 2581 9.658799 TCTAATCTTAACTCCATCTTGACTTTG 57.341 33.333 0.00 0.00 0.00 2.77
723 2582 9.660180 GTCTAATCTTAACTCCATCTTGACTTT 57.340 33.333 0.00 0.00 0.00 2.66
724 2583 9.041354 AGTCTAATCTTAACTCCATCTTGACTT 57.959 33.333 0.00 0.00 0.00 3.01
725 2584 8.602472 AGTCTAATCTTAACTCCATCTTGACT 57.398 34.615 0.00 0.00 0.00 3.41
726 2585 8.691797 AGAGTCTAATCTTAACTCCATCTTGAC 58.308 37.037 0.00 0.00 40.21 3.18
727 2586 8.830915 AGAGTCTAATCTTAACTCCATCTTGA 57.169 34.615 0.00 0.00 40.21 3.02
730 2589 9.702253 TGTAAGAGTCTAATCTTAACTCCATCT 57.298 33.333 1.77 0.00 42.03 2.90
753 2612 5.992217 GTGCCCACAAAACCATTTATTTGTA 59.008 36.000 3.83 0.00 45.31 2.41
1278 3177 3.376078 GTCCTGGACACGCCGGTA 61.376 66.667 21.70 0.00 41.87 4.02
1356 3258 3.131223 CGAGGATGTTTCTCAGCTTCCTA 59.869 47.826 0.00 0.00 38.76 2.94
1455 3363 2.340078 GCTGAGTGTGTCTGCCGA 59.660 61.111 0.00 0.00 42.79 5.54
1858 3839 4.189231 GTGACAACTACAACACTTCCTGT 58.811 43.478 0.00 0.00 32.89 4.00
2040 4024 1.341976 GGAAGCCCCCTGCATTTCTTA 60.342 52.381 0.00 0.00 44.83 2.10
2058 4042 3.307269 CCATTGTCTTCAGAGCAAGAGGA 60.307 47.826 0.00 0.00 32.89 3.71
2249 4237 4.219288 CCTTTTCCATCTCAAAGTCCTTGG 59.781 45.833 0.00 0.00 35.56 3.61
2474 4471 6.824704 TGCATATTCATCTGTGACATCTTTCA 59.175 34.615 0.00 0.00 33.11 2.69
2698 4695 7.445945 CGATTATGGATAATAGAAGGATCCCC 58.554 42.308 8.55 0.14 38.75 4.81
2752 4755 2.642311 TGCCAGACATAGAAAGGTCCAA 59.358 45.455 0.00 0.00 37.11 3.53
2826 4829 3.160679 AGAAGGCTGCAACCATTAAGT 57.839 42.857 9.23 0.00 0.00 2.24
3088 5091 2.089980 CTGGTGGAGATTGGCTTCTTG 58.910 52.381 0.00 0.00 0.00 3.02
3228 5238 2.137810 ATCCATGTACCCCCAAAACG 57.862 50.000 0.00 0.00 0.00 3.60
3332 5342 7.624549 CCATACTATGGGTATATTCTTGCAGT 58.375 38.462 7.16 0.00 46.86 4.40
3430 5440 1.771255 GCTGTATCCTCCACCTTCCAT 59.229 52.381 0.00 0.00 0.00 3.41
3449 5459 1.092348 GAAAATCCGTACAGGGGTGC 58.908 55.000 0.00 0.00 41.52 5.01
3522 5532 4.014406 TCGGCTCTGTTACACTATTCTCA 58.986 43.478 0.00 0.00 0.00 3.27
3572 5585 5.512232 GGGCAATCCTTCATTTTTAACACCA 60.512 40.000 0.00 0.00 0.00 4.17
3573 5586 4.935205 GGGCAATCCTTCATTTTTAACACC 59.065 41.667 0.00 0.00 0.00 4.16
3615 5628 0.321671 CTTTCAAGACGGGGCTCTCA 59.678 55.000 0.00 0.00 0.00 3.27
3628 5641 8.292448 GCAGTTTTCTATGTTCAGATCTTTCAA 58.708 33.333 0.00 0.00 0.00 2.69
3667 5680 1.151668 AGATGTGCAAGCGAACTCAC 58.848 50.000 0.00 0.00 0.00 3.51
3675 5688 5.865552 ACACAATGATTTTAGATGTGCAAGC 59.134 36.000 4.27 0.00 43.89 4.01
3727 5740 5.596836 CCCAAAGGCATATTTGTACACAT 57.403 39.130 0.00 0.00 38.28 3.21
3900 5915 1.270550 AGGCCAAGTTGCGATTTTGAG 59.729 47.619 5.01 0.00 0.00 3.02
3966 5981 2.249535 CCAGCGGGCAAGATCATCG 61.250 63.158 0.00 0.00 0.00 3.84
4268 9013 5.066893 CCATTCATCACACCAGGTAATTCTG 59.933 44.000 0.00 0.00 34.70 3.02
4654 12117 1.128136 CAGAAGAACATGCTGCACTCG 59.872 52.381 3.57 0.00 0.00 4.18
4698 12161 5.305128 AGCAAAGGTGAAGATGGATTTTTCA 59.695 36.000 0.00 0.00 0.00 2.69
4700 12163 5.305128 TCAGCAAAGGTGAAGATGGATTTTT 59.695 36.000 0.00 0.00 37.11 1.94
4741 12204 0.914644 ATGGAGTCCATGTGACCCAG 59.085 55.000 24.27 0.00 43.39 4.45
4776 12239 0.608035 GCCCAAATGTGAACTCCGGA 60.608 55.000 2.93 2.93 0.00 5.14
4778 12241 0.893270 TGGCCCAAATGTGAACTCCG 60.893 55.000 0.00 0.00 0.00 4.63
4804 12267 3.428999 CCGATGAGATAAGGTCAACGTGT 60.429 47.826 0.00 0.00 38.23 4.49
4824 12287 3.119101 ACCTCTGCTAATTACAGTGACCG 60.119 47.826 0.00 5.40 36.50 4.79
4930 12396 7.918643 ACAGTTCGAGTAGCTACTAATAAGAC 58.081 38.462 26.11 17.08 36.50 3.01
5012 12479 1.728490 GCCAATTCCTCATGGGACGC 61.728 60.000 0.00 0.00 45.03 5.19
5050 12534 1.202627 TGAAAGCCATGCCACAAAACC 60.203 47.619 0.00 0.00 0.00 3.27
5107 12591 3.945434 GTCCATCATGCGGCGCTG 61.945 66.667 33.26 25.83 0.00 5.18
5179 12663 8.833734 ACAGGTAGTAGTAGTAGATGGCATATA 58.166 37.037 0.00 0.00 0.00 0.86
5237 12724 4.346709 TCCCTGGATGTAGCGAATGAATAA 59.653 41.667 0.00 0.00 0.00 1.40
5238 12725 3.901222 TCCCTGGATGTAGCGAATGAATA 59.099 43.478 0.00 0.00 0.00 1.75
5239 12726 2.705658 TCCCTGGATGTAGCGAATGAAT 59.294 45.455 0.00 0.00 0.00 2.57
5265 12752 4.811555 TGAAATGTCTGAAACGGAACAG 57.188 40.909 0.00 0.00 35.72 3.16
5278 12765 5.368256 AGCACAAAGACAGATGAAATGTC 57.632 39.130 0.00 0.00 46.01 3.06
5284 12771 1.699083 TGGGAGCACAAAGACAGATGA 59.301 47.619 0.00 0.00 0.00 2.92
5288 12775 0.179020 TGGTGGGAGCACAAAGACAG 60.179 55.000 0.00 0.00 0.00 3.51
5335 12823 6.270815 GCGGAGGAAAAGAAAACTAAAAAGT 58.729 36.000 0.00 0.00 0.00 2.66
5343 12832 2.747989 CCTAGGCGGAGGAAAAGAAAAC 59.252 50.000 0.00 0.00 39.15 2.43
5347 12837 0.907704 TGCCTAGGCGGAGGAAAAGA 60.908 55.000 28.28 4.00 45.51 2.52
5348 12838 0.181350 ATGCCTAGGCGGAGGAAAAG 59.819 55.000 28.28 0.00 45.51 2.27
5352 12842 1.908793 GCTATGCCTAGGCGGAGGA 60.909 63.158 28.28 11.40 45.51 3.71
5411 12903 2.023673 CCAACACCAACTCACACACAT 58.976 47.619 0.00 0.00 0.00 3.21
5419 12911 1.469079 GCACACAACCAACACCAACTC 60.469 52.381 0.00 0.00 0.00 3.01
5469 12961 5.106157 CCTCAAGGGATACAAACACAATGAC 60.106 44.000 0.00 0.00 37.23 3.06
5486 12978 1.101331 GAAGCATCAAGGCCTCAAGG 58.899 55.000 5.23 0.00 38.53 3.61
5487 12979 1.830279 TGAAGCATCAAGGCCTCAAG 58.170 50.000 5.23 0.00 31.62 3.02
5488 12980 2.519771 ATGAAGCATCAAGGCCTCAA 57.480 45.000 5.23 0.00 37.73 3.02
5489 12981 2.519771 AATGAAGCATCAAGGCCTCA 57.480 45.000 5.23 0.00 39.49 3.86
5490 12982 2.756760 TGAAATGAAGCATCAAGGCCTC 59.243 45.455 5.23 0.00 39.49 4.70
5491 12983 2.494870 GTGAAATGAAGCATCAAGGCCT 59.505 45.455 0.00 0.00 39.49 5.19
5492 12984 2.417787 GGTGAAATGAAGCATCAAGGCC 60.418 50.000 0.00 0.00 39.49 5.19
5493 12985 2.417787 GGGTGAAATGAAGCATCAAGGC 60.418 50.000 0.00 0.00 39.49 4.35
5534 13027 5.391449 CAGATCAAAGACAATGACAGCAAG 58.609 41.667 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.