Multiple sequence alignment - TraesCS2A01G132500

Loading Multiple Alignment...

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 TraesCS2A01G132500 chr2A 100.000 3706 0 0 1 3706 79356481 79352776 0.000000e+00 6844.0
1 TraesCS2A01G132500 chr2D 95.932 1647 48 7 2076 3706 79094865 79093222 0.000000e+00 2652.0
2 TraesCS2A01G132500 chr2D 95.440 614 23 4 1 610 79097314 79096702 0.000000e+00 974.0
3 TraesCS2A01G132500 chr2D 92.701 548 29 5 1538 2079 79095565 79095023 0.000000e+00 780.0
4 TraesCS2A01G132500 chr2D 84.699 830 45 34 720 1494 79096372 79095570 0.000000e+00 754.0
5 TraesCS2A01G132500 chr2B 87.147 1097 71 26 720 1777 123064479 123063414 0.000000e+00 1181.0
6 TraesCS2A01G132500 chr2B 91.007 834 34 15 2898 3706 123062179 123061362 0.000000e+00 1086.0
7 TraesCS2A01G132500 chr2B 91.162 611 41 3 2295 2905 123062819 123062222 0.000000e+00 817.0
8 TraesCS2A01G132500 chr2B 92.698 493 26 6 1775 2259 123063311 123062821 0.000000e+00 702.0
9 TraesCS2A01G132500 chr1A 88.027 593 54 12 30 610 223989446 223988859 0.000000e+00 686.0
10 TraesCS2A01G132500 chr1A 86.371 631 57 17 1 610 449329324 449328702 0.000000e+00 662.0
11 TraesCS2A01G132500 chr1A 96.000 50 2 0 607 656 323895611 323895562 8.530000e-12 82.4
12 TraesCS2A01G132500 chr3A 86.984 630 55 15 1 610 552252794 552252172 0.000000e+00 684.0
13 TraesCS2A01G132500 chr3A 91.045 67 6 0 607 673 17734875 17734809 1.420000e-14 91.6
14 TraesCS2A01G132500 chr4A 90.476 273 21 3 1 270 395092149 395091879 4.550000e-94 355.0
15 TraesCS2A01G132500 chr4A 88.079 302 28 6 309 609 395091870 395091576 5.890000e-93 351.0
16 TraesCS2A01G132500 chr4A 91.954 87 7 0 607 693 478751885 478751971 5.030000e-24 122.0
17 TraesCS2A01G132500 chrUn 85.714 133 15 3 14 143 479443337 479443468 1.800000e-28 137.0
18 TraesCS2A01G132500 chr5B 85.714 133 15 3 14 143 393839560 393839429 1.800000e-28 137.0
19 TraesCS2A01G132500 chr5B 85.714 133 15 3 14 143 670802814 670802683 1.800000e-28 137.0
20 TraesCS2A01G132500 chr5B 80.000 110 17 5 1026 1134 433548424 433548529 3.970000e-10 76.8
21 TraesCS2A01G132500 chr3D 90.000 90 8 1 607 696 104029037 104029125 8.410000e-22 115.0
22 TraesCS2A01G132500 chr1B 89.655 87 9 0 607 693 626146901 626146987 1.090000e-20 111.0
23 TraesCS2A01G132500 chr1B 100.000 28 0 0 1004 1031 310552812 310552785 7.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G132500 chr2A 79352776 79356481 3705 True 6844.0 6844 100.0000 1 3706 1 chr2A.!!$R1 3705
1 TraesCS2A01G132500 chr2D 79093222 79097314 4092 True 1290.0 2652 92.1930 1 3706 4 chr2D.!!$R1 3705
2 TraesCS2A01G132500 chr2B 123061362 123064479 3117 True 946.5 1181 90.5035 720 3706 4 chr2B.!!$R1 2986
3 TraesCS2A01G132500 chr1A 223988859 223989446 587 True 686.0 686 88.0270 30 610 1 chr1A.!!$R1 580
4 TraesCS2A01G132500 chr1A 449328702 449329324 622 True 662.0 662 86.3710 1 610 1 chr1A.!!$R3 609
5 TraesCS2A01G132500 chr3A 552252172 552252794 622 True 684.0 684 86.9840 1 610 1 chr3A.!!$R2 609
6 TraesCS2A01G132500 chr4A 395091576 395092149 573 True 353.0 355 89.2775 1 609 2 chr4A.!!$R1 608

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
610 639 0.036164 TTGATGTCTCACCGGTTGGG 59.964 55.0 2.97 0.0 40.75 4.12 F
1091 1380 0.040692 CGTCGGTCGTCTGTTTCTCA 60.041 55.0 0.00 0.0 34.52 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1630 1938 0.738975 TACCGTAGTGCTGCAGCTAG 59.261 55.0 36.61 22.19 42.66 3.42 R
2861 3457 0.953727 TGTGAGGCACAGCACATTTC 59.046 50.0 0.00 0.00 39.62 2.17 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
59 62 7.272244 TGTGTGATGATCACCGAATAACTTAT 58.728 34.615 21.68 0.00 46.40 1.73
170 173 4.526262 CACAAGTGGATTTATTGGGTTGGA 59.474 41.667 0.00 0.00 0.00 3.53
220 226 8.451748 GTTCTTGTATTCTCTTTCCAATGTACC 58.548 37.037 0.00 0.00 0.00 3.34
296 308 9.738832 TGAACTTCGATACGTTTCATAATATGA 57.261 29.630 6.81 0.00 37.55 2.15
307 319 9.567776 ACGTTTCATAATATGATTGGGTATTCA 57.432 29.630 3.54 0.00 39.39 2.57
358 371 7.962995 TCCACAATTATGCACCCTTAATTTA 57.037 32.000 0.00 0.00 32.23 1.40
472 493 9.866655 TTAATAGCTTTCCATGGATAATGAACT 57.133 29.630 17.06 8.94 38.72 3.01
503 531 6.380846 TGGTGGCTTTATTAATCTTCAAGCAT 59.619 34.615 16.99 0.00 41.42 3.79
573 602 0.036765 GTGCGTGATTGGGAGTGGTA 60.037 55.000 0.00 0.00 0.00 3.25
604 633 8.236586 TCAGAAAATAAAATTGATGTCTCACCG 58.763 33.333 0.00 0.00 0.00 4.94
610 639 0.036164 TTGATGTCTCACCGGTTGGG 59.964 55.000 2.97 0.00 40.75 4.12
619 648 2.825982 CCGGTTGGGTCACTGACA 59.174 61.111 11.34 0.00 33.68 3.58
620 649 1.374947 CCGGTTGGGTCACTGACAT 59.625 57.895 11.34 0.00 33.68 3.06
621 650 0.955428 CCGGTTGGGTCACTGACATG 60.955 60.000 11.34 0.00 33.68 3.21
622 651 0.250295 CGGTTGGGTCACTGACATGT 60.250 55.000 11.34 0.00 33.68 3.21
623 652 1.238439 GGTTGGGTCACTGACATGTG 58.762 55.000 1.15 0.00 39.15 3.21
624 653 1.238439 GTTGGGTCACTGACATGTGG 58.762 55.000 1.15 0.00 38.40 4.17
625 654 0.110295 TTGGGTCACTGACATGTGGG 59.890 55.000 1.15 0.00 38.40 4.61
627 656 0.321653 GGGTCACTGACATGTGGGTC 60.322 60.000 1.15 0.00 38.40 4.46
628 657 0.396435 GGTCACTGACATGTGGGTCA 59.604 55.000 1.15 0.00 45.06 4.02
634 663 0.396435 TGACATGTGGGTCAGTCACC 59.604 55.000 1.15 0.00 42.56 4.02
636 665 0.397941 ACATGTGGGTCAGTCACCTG 59.602 55.000 0.00 0.00 45.95 4.00
637 666 0.397941 CATGTGGGTCAGTCACCTGT 59.602 55.000 0.00 0.00 45.95 4.00
639 668 0.180171 TGTGGGTCAGTCACCTGTTG 59.820 55.000 0.00 0.00 45.95 3.33
640 669 0.535102 GTGGGTCAGTCACCTGTTGG 60.535 60.000 0.00 0.00 45.95 3.77
642 671 0.250338 GGGTCAGTCACCTGTTGGAC 60.250 60.000 0.00 0.00 45.95 4.02
643 672 0.759346 GGTCAGTCACCTGTTGGACT 59.241 55.000 0.00 0.00 44.84 3.85
645 674 1.412710 GTCAGTCACCTGTTGGACTCA 59.587 52.381 0.00 0.00 42.22 3.41
646 675 1.412710 TCAGTCACCTGTTGGACTCAC 59.587 52.381 0.00 0.00 42.22 3.51
647 676 1.138859 CAGTCACCTGTTGGACTCACA 59.861 52.381 0.00 0.00 42.22 3.58
648 677 2.050144 AGTCACCTGTTGGACTCACAT 58.950 47.619 0.00 0.00 40.18 3.21
649 678 2.146342 GTCACCTGTTGGACTCACATG 58.854 52.381 0.00 0.00 37.04 3.21
651 680 2.146342 CACCTGTTGGACTCACATGTC 58.854 52.381 0.00 0.00 37.04 3.06
652 681 1.768275 ACCTGTTGGACTCACATGTCA 59.232 47.619 0.00 0.00 38.61 3.58
653 682 2.373169 ACCTGTTGGACTCACATGTCAT 59.627 45.455 0.00 0.00 38.61 3.06
655 684 4.186926 CCTGTTGGACTCACATGTCATAG 58.813 47.826 0.00 0.00 38.61 2.23
656 685 4.081476 CCTGTTGGACTCACATGTCATAGA 60.081 45.833 0.00 0.00 38.61 1.98
658 687 6.183360 CCTGTTGGACTCACATGTCATAGATA 60.183 42.308 0.00 0.00 38.61 1.98
662 691 7.181569 TGGACTCACATGTCATAGATACAAA 57.818 36.000 0.00 0.00 38.61 2.83
663 692 7.267857 TGGACTCACATGTCATAGATACAAAG 58.732 38.462 0.00 0.00 38.61 2.77
664 693 7.124147 TGGACTCACATGTCATAGATACAAAGA 59.876 37.037 0.00 0.00 38.61 2.52
668 697 9.636879 CTCACATGTCATAGATACAAAGATAGG 57.363 37.037 0.00 0.00 0.00 2.57
669 698 9.147732 TCACATGTCATAGATACAAAGATAGGT 57.852 33.333 0.00 0.00 0.00 3.08
671 700 7.875041 ACATGTCATAGATACAAAGATAGGTGC 59.125 37.037 0.00 0.00 0.00 5.01
672 701 6.759272 TGTCATAGATACAAAGATAGGTGCC 58.241 40.000 0.00 0.00 0.00 5.01
673 702 6.554982 TGTCATAGATACAAAGATAGGTGCCT 59.445 38.462 0.00 0.00 0.00 4.75
674 703 7.071196 TGTCATAGATACAAAGATAGGTGCCTT 59.929 37.037 0.00 0.00 0.00 4.35
675 704 8.585881 GTCATAGATACAAAGATAGGTGCCTTA 58.414 37.037 0.00 0.00 0.00 2.69
676 705 9.154632 TCATAGATACAAAGATAGGTGCCTTAA 57.845 33.333 0.00 0.00 0.00 1.85
677 706 9.778741 CATAGATACAAAGATAGGTGCCTTAAA 57.221 33.333 0.00 0.00 0.00 1.52
679 708 6.768381 AGATACAAAGATAGGTGCCTTAAAGC 59.232 38.462 0.00 0.00 0.00 3.51
680 709 4.662278 ACAAAGATAGGTGCCTTAAAGCA 58.338 39.130 0.00 0.00 41.46 3.91
687 716 2.253513 TGCCTTAAAGCACCGAAGC 58.746 52.632 0.00 0.00 38.00 3.86
690 719 1.202188 GCCTTAAAGCACCGAAGCATC 60.202 52.381 2.02 0.00 36.85 3.91
699 728 2.885644 CGAAGCATCGTCCGGTGG 60.886 66.667 0.00 0.00 44.06 4.61
700 729 3.195698 GAAGCATCGTCCGGTGGC 61.196 66.667 0.00 0.00 0.00 5.01
712 741 3.480133 GGTGGCGCCCTAGTCCAT 61.480 66.667 26.77 0.00 31.83 3.41
713 742 2.203070 GTGGCGCCCTAGTCCATG 60.203 66.667 26.77 0.00 31.83 3.66
715 744 3.161450 GGCGCCCTAGTCCATGGA 61.161 66.667 18.11 11.44 0.00 3.41
716 745 2.742116 GGCGCCCTAGTCCATGGAA 61.742 63.158 18.20 0.00 0.00 3.53
717 746 1.451936 GCGCCCTAGTCCATGGAAT 59.548 57.895 20.09 20.09 0.00 3.01
718 747 0.603975 GCGCCCTAGTCCATGGAATC 60.604 60.000 19.79 6.06 0.00 2.52
723 972 1.336332 CCTAGTCCATGGAATCGAGCG 60.336 57.143 19.79 2.39 0.00 5.03
748 997 3.249189 GGACAGACAGGTGGGCCA 61.249 66.667 0.00 0.00 37.19 5.36
751 1000 2.930019 CAGACAGGTGGGCCAGGA 60.930 66.667 6.40 0.00 37.19 3.86
783 1032 1.675219 GGTGAAACTACCGCTCCCA 59.325 57.895 0.00 0.00 36.74 4.37
878 1136 2.620367 CCCTCGATATCTCCTCCTCCAG 60.620 59.091 0.34 0.00 0.00 3.86
908 1166 2.037620 CTTCTCGCCTCCATCCCCAG 62.038 65.000 0.00 0.00 0.00 4.45
909 1167 2.444706 CTCGCCTCCATCCCCAGA 60.445 66.667 0.00 0.00 0.00 3.86
910 1168 2.040442 TCGCCTCCATCCCCAGAA 59.960 61.111 0.00 0.00 0.00 3.02
1064 1353 1.262640 TGGTAACCTTCCGGCCTCTC 61.263 60.000 0.00 0.00 0.00 3.20
1086 1375 4.695231 CGCCGTCGGTCGTCTGTT 62.695 66.667 13.94 0.00 37.94 3.16
1090 1379 0.728466 CCGTCGGTCGTCTGTTTCTC 60.728 60.000 2.08 0.00 37.94 2.87
1091 1380 0.040692 CGTCGGTCGTCTGTTTCTCA 60.041 55.000 0.00 0.00 34.52 3.27
1092 1381 1.406447 GTCGGTCGTCTGTTTCTCAC 58.594 55.000 0.00 0.00 0.00 3.51
1093 1382 1.001597 GTCGGTCGTCTGTTTCTCACT 60.002 52.381 0.00 0.00 0.00 3.41
1094 1383 2.225019 GTCGGTCGTCTGTTTCTCACTA 59.775 50.000 0.00 0.00 0.00 2.74
1095 1384 3.079578 TCGGTCGTCTGTTTCTCACTAT 58.920 45.455 0.00 0.00 0.00 2.12
1096 1385 3.126514 TCGGTCGTCTGTTTCTCACTATC 59.873 47.826 0.00 0.00 0.00 2.08
1097 1386 3.127203 CGGTCGTCTGTTTCTCACTATCT 59.873 47.826 0.00 0.00 0.00 1.98
1098 1387 4.416620 GGTCGTCTGTTTCTCACTATCTG 58.583 47.826 0.00 0.00 0.00 2.90
1099 1388 3.854809 GTCGTCTGTTTCTCACTATCTGC 59.145 47.826 0.00 0.00 0.00 4.26
1100 1389 3.759086 TCGTCTGTTTCTCACTATCTGCT 59.241 43.478 0.00 0.00 0.00 4.24
1101 1390 3.856521 CGTCTGTTTCTCACTATCTGCTG 59.143 47.826 0.00 0.00 0.00 4.41
1104 1393 3.593096 TGTTTCTCACTATCTGCTGCTG 58.407 45.455 0.00 0.00 0.00 4.41
1105 1394 2.935201 GTTTCTCACTATCTGCTGCTGG 59.065 50.000 6.69 0.00 0.00 4.85
1109 1398 1.410517 TCACTATCTGCTGCTGGCTAC 59.589 52.381 6.69 0.00 42.39 3.58
1110 1399 0.387202 ACTATCTGCTGCTGGCTACG 59.613 55.000 6.69 0.00 42.39 3.51
1113 1402 2.641439 ATCTGCTGCTGGCTACGAGC 62.641 60.000 6.69 0.00 42.39 5.03
1132 1421 6.214399 ACGAGCTGCCAAATAATAGTAGTAC 58.786 40.000 0.00 0.00 0.00 2.73
1135 1424 8.244802 CGAGCTGCCAAATAATAGTAGTACTAT 58.755 37.037 15.79 15.79 42.86 2.12
1151 1440 6.374417 AGTACTATTGCTTTCCTCTTTCCA 57.626 37.500 0.00 0.00 0.00 3.53
1152 1441 6.174049 AGTACTATTGCTTTCCTCTTTCCAC 58.826 40.000 0.00 0.00 0.00 4.02
1168 1457 4.722361 TTCCACCCGGCAATATTTTTAC 57.278 40.909 0.00 0.00 0.00 2.01
1210 1499 5.044451 AGTTATTAGTAGCCTTTTCCCCCT 58.956 41.667 0.00 0.00 0.00 4.79
1211 1500 5.132312 AGTTATTAGTAGCCTTTTCCCCCTC 59.868 44.000 0.00 0.00 0.00 4.30
1270 1578 1.607178 TGCTTGGGGGCATGTCTTG 60.607 57.895 0.00 0.00 37.29 3.02
1277 1585 1.080298 GGGCATGTCTTGTGCTTGC 60.080 57.895 0.00 0.00 42.16 4.01
1278 1586 1.080298 GGCATGTCTTGTGCTTGCC 60.080 57.895 6.48 6.48 45.45 4.52
1290 1598 0.739462 TGCTTGCCGATTACTGACCG 60.739 55.000 0.00 0.00 0.00 4.79
1296 1604 2.190981 GCCGATTACTGACCGTACTTG 58.809 52.381 0.00 0.00 0.00 3.16
1336 1644 3.198582 CGAGAGGTTCCGTCTCCC 58.801 66.667 8.01 0.00 40.83 4.30
1458 1766 2.394632 TGATAACCATGCTCCGGTACT 58.605 47.619 0.00 0.00 34.99 2.73
1529 1837 6.883756 TGTATGCACACATTTTCATTCTCCTA 59.116 34.615 0.00 0.00 37.74 2.94
1530 1838 5.885230 TGCACACATTTTCATTCTCCTAG 57.115 39.130 0.00 0.00 0.00 3.02
1532 1840 4.728882 GCACACATTTTCATTCTCCTAGCG 60.729 45.833 0.00 0.00 0.00 4.26
1535 1843 4.396166 CACATTTTCATTCTCCTAGCGGTT 59.604 41.667 0.00 0.00 0.00 4.44
1536 1844 5.584649 CACATTTTCATTCTCCTAGCGGTTA 59.415 40.000 0.00 0.00 0.00 2.85
1630 1938 6.920758 ACAGCTAAGATCGTTCTGACATAATC 59.079 38.462 14.20 0.00 30.72 1.75
1633 1941 8.511321 AGCTAAGATCGTTCTGACATAATCTAG 58.489 37.037 0.00 0.00 30.72 2.43
1635 1943 6.892658 AGATCGTTCTGACATAATCTAGCT 57.107 37.500 0.00 0.00 0.00 3.32
1650 1958 0.738975 TAGCTGCAGCACTACGGTAG 59.261 55.000 38.24 13.49 45.16 3.18
1715 2024 6.175471 TCATCATGTCAGTGTCTTATGCTTT 58.825 36.000 0.00 0.00 0.00 3.51
1729 2038 6.144402 GTCTTATGCTTTGTGTGGAAAACATG 59.856 38.462 0.00 0.00 41.97 3.21
1841 2255 7.251704 ACACCGCTAATCAGATTCTTATTTG 57.748 36.000 0.00 0.00 0.00 2.32
1848 2262 8.887717 GCTAATCAGATTCTTATTTGCGGATAT 58.112 33.333 9.98 0.00 0.00 1.63
1864 2278 3.244561 CGGATATAGGTGAATTGCCCACT 60.245 47.826 0.00 0.00 35.05 4.00
1943 2357 1.870055 AAAGGATGCTTGCGTGCCAG 61.870 55.000 0.00 0.00 0.00 4.85
1964 2378 5.473504 CCAGTATTGCAAGTTTGAACTACCT 59.526 40.000 4.94 0.00 38.57 3.08
2005 2419 6.707608 GAGCATCAGGTGTGAATGTATTCATA 59.292 38.462 10.20 5.39 41.28 2.15
2006 2420 7.307632 GAGCATCAGGTGTGAATGTATTCATAC 60.308 40.741 19.85 19.85 44.36 2.39
2043 2463 6.544928 AAACTGGACAACATTCTTTTCCTT 57.455 33.333 0.00 0.00 0.00 3.36
2051 2471 9.325198 GGACAACATTCTTTTCCTTAAAACATT 57.675 29.630 0.00 0.00 31.37 2.71
2097 2678 9.647918 TCCATCTCTGTCTAACTATATGAGTTT 57.352 33.333 0.70 0.00 46.79 2.66
2102 2683 9.243637 CTCTGTCTAACTATATGAGTTTTGCTC 57.756 37.037 0.70 0.00 46.79 4.26
2259 2842 6.639632 ACATGGAACCTTATATTGATGCAC 57.360 37.500 0.00 0.00 0.00 4.57
2289 2872 8.939929 ACTTGTTTATGTAGACATGATTCAGTG 58.060 33.333 0.00 0.00 37.15 3.66
2421 3004 9.914131 AGTTGCAGTTTTTAGATAAAAATCCTC 57.086 29.630 12.29 2.26 44.16 3.71
2500 3083 8.414003 TGTATTTCTATCGTCACAGCTAATTCT 58.586 33.333 0.00 0.00 0.00 2.40
2522 3105 2.698855 TTGAGCCTGCCTTCTGATAC 57.301 50.000 0.00 0.00 0.00 2.24
2584 3167 1.279840 GTGGTCGTCACAAGCAAGC 59.720 57.895 6.75 0.00 45.39 4.01
2591 3174 4.347453 CACAAGCAAGCACGCCCC 62.347 66.667 0.00 0.00 0.00 5.80
2728 3311 3.436704 AGTTGTAATGATGTTCACCGCAG 59.563 43.478 0.00 0.00 0.00 5.18
2826 3409 9.567776 TTATTCCTTGAGTAATGTTCAGAACAA 57.432 29.630 19.92 1.62 45.86 2.83
2854 3450 6.931281 ACCATGTAGAATATCAGAAATCACCG 59.069 38.462 0.00 0.00 0.00 4.94
2861 3457 2.871182 TCAGAAATCACCGGATCGAG 57.129 50.000 9.46 0.00 31.88 4.04
2868 3464 2.293677 TCACCGGATCGAGAAATGTG 57.706 50.000 9.46 0.00 0.00 3.21
3001 3647 7.334921 TGTTGTTAATGATAGACCTTTTACGGG 59.665 37.037 0.00 0.00 0.00 5.28
3054 3704 6.699204 TCATTTCAACAAATTGCGCTCTTTAA 59.301 30.769 9.73 0.00 35.63 1.52
3117 3771 9.959721 AATTGAAGTACCTGATAACACATTAGT 57.040 29.630 0.00 0.00 0.00 2.24
3169 3823 2.355209 GCAGGACTCTGTTCCCCTAAAG 60.355 54.545 0.00 0.00 42.78 1.85
3205 3859 3.553828 TGAAGGGGAAAATAGGCTACG 57.446 47.619 0.00 0.00 0.00 3.51
3246 3916 2.816087 CAGGCAGCAACTACAACAATCT 59.184 45.455 0.00 0.00 0.00 2.40
3284 3954 2.298729 TGTAAGTTGATTTTGGCAGGGC 59.701 45.455 0.00 0.00 0.00 5.19
3484 4155 5.945191 TGTCAGCATGTCAAAAGGATGATAA 59.055 36.000 0.00 0.00 37.40 1.75
3502 4173 6.741992 TGATAAACTAAATGCCAGTGTCAG 57.258 37.500 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 62 8.603898 TCCAGAGTCATTACTGAAAAGGTATA 57.396 34.615 0.00 0.00 35.56 1.47
220 226 8.472683 TTCCATGCCGAAAATACATTAAAAAG 57.527 30.769 0.00 0.00 0.00 2.27
358 371 8.276252 ACAAGTTATAAAGGCAATACGAACAT 57.724 30.769 0.00 0.00 0.00 2.71
405 420 7.347252 TCACATAATAGACTGTGAGTAGGAGT 58.653 38.462 1.47 0.00 45.01 3.85
406 421 7.809546 TCACATAATAGACTGTGAGTAGGAG 57.190 40.000 1.47 0.00 45.01 3.69
472 493 7.831690 TGAAGATTAATAAAGCCACCATACACA 59.168 33.333 0.00 0.00 0.00 3.72
604 633 1.238439 CACATGTCAGTGACCCAACC 58.762 55.000 20.43 0.00 42.05 3.77
616 645 3.233355 GGTGACTGACCCACATGTC 57.767 57.895 0.00 0.00 39.10 3.06
628 657 1.496060 TGTGAGTCCAACAGGTGACT 58.504 50.000 0.00 0.00 44.25 3.41
631 660 2.146342 GACATGTGAGTCCAACAGGTG 58.854 52.381 1.15 0.00 32.36 4.00
632 661 1.768275 TGACATGTGAGTCCAACAGGT 59.232 47.619 1.15 1.00 37.73 4.00
633 662 2.549064 TGACATGTGAGTCCAACAGG 57.451 50.000 1.15 0.00 37.73 4.00
634 663 5.077134 TCTATGACATGTGAGTCCAACAG 57.923 43.478 1.15 0.00 37.73 3.16
636 665 6.573434 TGTATCTATGACATGTGAGTCCAAC 58.427 40.000 1.15 0.00 37.73 3.77
637 666 6.790232 TGTATCTATGACATGTGAGTCCAA 57.210 37.500 1.15 0.00 37.73 3.53
639 668 7.492524 TCTTTGTATCTATGACATGTGAGTCC 58.507 38.462 1.15 0.00 37.73 3.85
642 671 9.636879 CCTATCTTTGTATCTATGACATGTGAG 57.363 37.037 1.15 0.00 0.00 3.51
643 672 9.147732 ACCTATCTTTGTATCTATGACATGTGA 57.852 33.333 1.15 0.00 0.00 3.58
645 674 7.875041 GCACCTATCTTTGTATCTATGACATGT 59.125 37.037 0.00 0.00 0.00 3.21
646 675 7.332926 GGCACCTATCTTTGTATCTATGACATG 59.667 40.741 0.00 0.00 0.00 3.21
647 676 7.236432 AGGCACCTATCTTTGTATCTATGACAT 59.764 37.037 0.00 0.00 0.00 3.06
648 677 6.554982 AGGCACCTATCTTTGTATCTATGACA 59.445 38.462 0.00 0.00 0.00 3.58
649 678 6.998802 AGGCACCTATCTTTGTATCTATGAC 58.001 40.000 0.00 0.00 0.00 3.06
651 680 9.778741 TTTAAGGCACCTATCTTTGTATCTATG 57.221 33.333 0.00 0.00 0.00 2.23
653 682 7.931948 GCTTTAAGGCACCTATCTTTGTATCTA 59.068 37.037 4.44 0.00 0.00 1.98
655 684 6.542370 TGCTTTAAGGCACCTATCTTTGTATC 59.458 38.462 8.37 0.00 37.29 2.24
656 685 6.423182 TGCTTTAAGGCACCTATCTTTGTAT 58.577 36.000 8.37 0.00 37.29 2.29
658 687 4.662278 TGCTTTAAGGCACCTATCTTTGT 58.338 39.130 8.37 0.00 37.29 2.83
669 698 0.536233 TGCTTCGGTGCTTTAAGGCA 60.536 50.000 8.37 8.37 40.15 4.75
671 700 1.062587 CGATGCTTCGGTGCTTTAAGG 59.937 52.381 13.82 0.00 41.74 2.69
672 701 2.442189 CGATGCTTCGGTGCTTTAAG 57.558 50.000 13.82 0.00 41.74 1.85
683 712 3.195698 GCCACCGGACGATGCTTC 61.196 66.667 9.46 0.00 0.00 3.86
695 724 3.480133 ATGGACTAGGGCGCCACC 61.480 66.667 30.85 21.47 33.93 4.61
698 727 2.056906 ATTCCATGGACTAGGGCGCC 62.057 60.000 21.18 21.18 0.00 6.53
699 728 0.603975 GATTCCATGGACTAGGGCGC 60.604 60.000 15.91 0.00 0.00 6.53
700 729 0.319900 CGATTCCATGGACTAGGGCG 60.320 60.000 15.91 5.20 0.00 6.13
701 730 1.001406 CTCGATTCCATGGACTAGGGC 59.999 57.143 15.91 0.00 0.00 5.19
702 731 1.001406 GCTCGATTCCATGGACTAGGG 59.999 57.143 15.91 11.07 0.00 3.53
703 732 1.336332 CGCTCGATTCCATGGACTAGG 60.336 57.143 15.91 5.11 0.00 3.02
704 733 1.338337 ACGCTCGATTCCATGGACTAG 59.662 52.381 15.91 10.12 0.00 2.57
705 734 1.337071 GACGCTCGATTCCATGGACTA 59.663 52.381 15.91 0.00 0.00 2.59
706 735 0.103208 GACGCTCGATTCCATGGACT 59.897 55.000 15.91 9.69 0.00 3.85
707 736 0.103208 AGACGCTCGATTCCATGGAC 59.897 55.000 15.91 2.61 0.00 4.02
708 737 1.687563 TAGACGCTCGATTCCATGGA 58.312 50.000 11.44 11.44 0.00 3.41
709 738 2.029918 TGATAGACGCTCGATTCCATGG 60.030 50.000 4.97 4.97 0.00 3.66
710 739 3.240884 CTGATAGACGCTCGATTCCATG 58.759 50.000 0.00 0.00 0.00 3.66
711 740 2.230025 CCTGATAGACGCTCGATTCCAT 59.770 50.000 0.00 0.00 0.00 3.41
712 741 1.609072 CCTGATAGACGCTCGATTCCA 59.391 52.381 0.00 0.00 0.00 3.53
713 742 1.880675 TCCTGATAGACGCTCGATTCC 59.119 52.381 0.00 0.00 0.00 3.01
715 744 2.292016 CTGTCCTGATAGACGCTCGATT 59.708 50.000 0.00 0.00 39.77 3.34
716 745 1.876799 CTGTCCTGATAGACGCTCGAT 59.123 52.381 0.00 0.00 39.77 3.59
717 746 1.134491 TCTGTCCTGATAGACGCTCGA 60.134 52.381 0.00 0.00 39.77 4.04
718 747 1.003331 GTCTGTCCTGATAGACGCTCG 60.003 57.143 8.07 0.00 39.22 5.03
723 972 2.428890 CCACCTGTCTGTCCTGATAGAC 59.571 54.545 14.86 14.86 45.94 2.59
837 1095 2.262915 CTCGTGGTGAGGTGAGGC 59.737 66.667 0.00 0.00 41.29 4.70
878 1136 2.498726 CGAGAAGAGCAGAGGGGC 59.501 66.667 0.00 0.00 0.00 5.80
908 1166 1.153147 GCCGAATCAGGGGGTCTTC 60.153 63.158 0.00 0.00 0.00 2.87
909 1167 2.998949 GCCGAATCAGGGGGTCTT 59.001 61.111 0.00 0.00 0.00 3.01
910 1168 3.470888 CGCCGAATCAGGGGGTCT 61.471 66.667 0.00 0.00 40.16 3.85
1077 1366 3.854809 GCAGATAGTGAGAAACAGACGAC 59.145 47.826 0.00 0.00 0.00 4.34
1079 1368 3.856521 CAGCAGATAGTGAGAAACAGACG 59.143 47.826 0.00 0.00 0.00 4.18
1086 1375 1.134580 GCCAGCAGCAGATAGTGAGAA 60.135 52.381 0.00 0.00 42.97 2.87
1098 1387 2.889503 CAGCTCGTAGCCAGCAGC 60.890 66.667 3.66 0.00 43.77 5.25
1099 1388 2.889503 GCAGCTCGTAGCCAGCAG 60.890 66.667 13.16 0.60 43.77 4.24
1105 1394 4.058817 ACTATTATTTGGCAGCTCGTAGC 58.941 43.478 0.00 0.00 42.84 3.58
1109 1398 6.448006 AGTACTACTATTATTTGGCAGCTCG 58.552 40.000 0.00 0.00 0.00 5.03
1110 1399 9.930693 AATAGTACTACTATTATTTGGCAGCTC 57.069 33.333 16.75 0.00 46.38 4.09
1113 1402 9.712305 AGCAATAGTACTACTATTATTTGGCAG 57.288 33.333 17.52 7.39 46.48 4.85
1124 1413 8.693625 GGAAAGAGGAAAGCAATAGTACTACTA 58.306 37.037 4.31 0.00 34.82 1.82
1132 1421 3.696548 GGGTGGAAAGAGGAAAGCAATAG 59.303 47.826 0.00 0.00 0.00 1.73
1135 1424 1.817740 CGGGTGGAAAGAGGAAAGCAA 60.818 52.381 0.00 0.00 0.00 3.91
1151 1440 7.111466 TGTAGTAAGTAAAAATATTGCCGGGT 58.889 34.615 2.18 0.00 0.00 5.28
1152 1441 7.281549 ACTGTAGTAAGTAAAAATATTGCCGGG 59.718 37.037 2.18 0.00 0.00 5.73
1190 1479 4.658901 CAGAGGGGGAAAAGGCTACTAATA 59.341 45.833 0.00 0.00 0.00 0.98
1191 1480 3.459969 CAGAGGGGGAAAAGGCTACTAAT 59.540 47.826 0.00 0.00 0.00 1.73
1192 1481 2.844348 CAGAGGGGGAAAAGGCTACTAA 59.156 50.000 0.00 0.00 0.00 2.24
1193 1482 2.478292 CAGAGGGGGAAAAGGCTACTA 58.522 52.381 0.00 0.00 0.00 1.82
1241 1549 2.375509 GCCCCCAAGCACTACCTATATT 59.624 50.000 0.00 0.00 0.00 1.28
1270 1578 0.727398 GGTCAGTAATCGGCAAGCAC 59.273 55.000 0.00 0.00 0.00 4.40
1277 1585 3.128242 AGACAAGTACGGTCAGTAATCGG 59.872 47.826 18.73 0.00 37.02 4.18
1278 1586 4.096311 CAGACAAGTACGGTCAGTAATCG 58.904 47.826 18.73 0.00 37.02 3.34
1290 1598 5.985781 TGAAGAAAATTCGCAGACAAGTAC 58.014 37.500 0.00 0.00 34.32 2.73
1296 1604 5.383130 GGTTACTGAAGAAAATTCGCAGAC 58.617 41.667 19.01 11.26 37.66 3.51
1325 1633 1.359459 GCGATGTTGGGAGACGGAAC 61.359 60.000 0.00 0.00 0.00 3.62
1336 1644 0.860203 CAGAATGCAGCGCGATGTTG 60.860 55.000 26.61 12.51 0.00 3.33
1458 1766 8.025270 TCTGGATACGGTTATAATTTGGAGAA 57.975 34.615 0.00 0.00 45.94 2.87
1532 1840 3.248602 CACAGGCTATGCGAAGAATAACC 59.751 47.826 0.00 0.00 0.00 2.85
1535 1843 4.309933 CATCACAGGCTATGCGAAGAATA 58.690 43.478 0.00 0.00 0.00 1.75
1536 1844 2.988010 TCACAGGCTATGCGAAGAAT 57.012 45.000 0.00 0.00 0.00 2.40
1630 1938 0.738975 TACCGTAGTGCTGCAGCTAG 59.261 55.000 36.61 22.19 42.66 3.42
1633 1941 2.167861 GCTACCGTAGTGCTGCAGC 61.168 63.158 31.89 31.89 42.50 5.25
1635 1943 1.822114 TTGGCTACCGTAGTGCTGCA 61.822 55.000 0.00 0.00 0.00 4.41
1650 1958 1.153842 GGCACGCAGGTTATTTGGC 60.154 57.895 0.00 0.00 0.00 4.52
1671 1979 5.862924 TGATCAAATCACCGAGTCTTTTC 57.137 39.130 0.00 0.00 33.59 2.29
1715 2024 4.603989 ATGAATGCATGTTTTCCACACA 57.396 36.364 0.00 0.00 38.61 3.72
1729 2038 8.798859 AATCTATCCAGTGGTTATATGAATGC 57.201 34.615 9.54 0.00 0.00 3.56
1757 2066 7.976135 AAGATGTATATCTGTTGCCATCTTC 57.024 36.000 2.35 0.00 42.78 2.87
1791 2205 9.592196 TTAGGATTAGTAATACCGGAAGTACAT 57.408 33.333 9.46 0.00 32.46 2.29
1814 2228 8.594881 AATAAGAATCTGATTAGCGGTGTTAG 57.405 34.615 2.28 0.00 0.00 2.34
1841 2255 2.084546 GGGCAATTCACCTATATCCGC 58.915 52.381 0.00 0.00 0.00 5.54
1848 2262 1.340017 GCAGAGTGGGCAATTCACCTA 60.340 52.381 0.00 0.00 35.87 3.08
1864 2278 1.581934 CTCCACAGTTTGTTCGCAGA 58.418 50.000 0.00 0.00 0.00 4.26
1943 2357 5.154222 GCAGGTAGTTCAAACTTGCAATAC 58.846 41.667 0.00 0.00 39.12 1.89
1964 2378 1.682323 TGCTCAAAAATGTCAGCTGCA 59.318 42.857 9.47 11.14 32.76 4.41
2018 2438 6.946340 AGGAAAAGAATGTTGTCCAGTTTTT 58.054 32.000 1.98 0.00 27.98 1.94
2051 2471 9.715119 AGATGGACTATATATGTGTGGCTTATA 57.285 33.333 0.00 0.00 0.00 0.98
2052 2472 8.615360 AGATGGACTATATATGTGTGGCTTAT 57.385 34.615 0.00 0.00 0.00 1.73
2097 2678 4.030216 TCCACATACATCCTGTAGAGCAA 58.970 43.478 0.00 0.00 36.14 3.91
2102 2683 5.842907 TCGATTTCCACATACATCCTGTAG 58.157 41.667 0.00 0.00 36.14 2.74
2259 2842 6.944557 TCATGTCTACATAAACAAGTCACG 57.055 37.500 0.00 0.00 34.26 4.35
2289 2872 6.578919 GCAGCATTGTTCTAACTGAAACTTAC 59.421 38.462 0.00 0.00 36.30 2.34
2421 3004 4.617067 CGATAGGCTGAGGCACTGTATTAG 60.617 50.000 9.23 0.00 41.55 1.73
2500 3083 3.939740 ATCAGAAGGCAGGCTCAAATA 57.060 42.857 0.00 0.00 0.00 1.40
2522 3105 7.372714 TGGATCTGTCACAAGAATTTGAATTG 58.627 34.615 0.00 0.00 37.73 2.32
2584 3167 3.145422 AAACCAAAAGCGGGGCGTG 62.145 57.895 0.00 0.00 0.00 5.34
2591 3174 3.483411 GCTTGTGTTTCAAACCAAAAGCG 60.483 43.478 13.01 2.07 35.48 4.68
2757 3340 8.514594 TGGAAGAACTTGTGCATTAAGATTTAG 58.485 33.333 17.37 0.00 0.00 1.85
2854 3450 1.063174 GCACAGCACATTTCTCGATCC 59.937 52.381 0.00 0.00 0.00 3.36
2861 3457 0.953727 TGTGAGGCACAGCACATTTC 59.046 50.000 0.00 0.00 39.62 2.17
2868 3464 1.202222 GCATACATTGTGAGGCACAGC 60.202 52.381 0.00 0.00 45.39 4.40
3101 3755 6.536582 CCAGACTGAACTAATGTGTTATCAGG 59.463 42.308 3.32 0.00 30.69 3.86
3117 3771 4.973168 AGTTTGTAGCATTCCAGACTGAA 58.027 39.130 3.32 0.00 0.00 3.02
3169 3823 4.458295 CCCCTTCATGAATGCATCTCATAC 59.542 45.833 18.05 2.14 34.33 2.39
3205 3859 5.172205 CCTGTTCTAGTAAGCAGAAAGTCC 58.828 45.833 0.00 0.00 33.95 3.85
3246 3916 9.567776 TCAACTTACAACATAGAGGAATTTTGA 57.432 29.630 0.00 0.00 0.00 2.69
3387 4057 3.191162 TGACAAGCAATTTGGGAAGATCG 59.809 43.478 0.00 0.00 41.25 3.69
3484 4155 6.463995 TTTTTCTGACACTGGCATTTAGTT 57.536 33.333 0.00 0.00 0.00 2.24
3509 4180 8.100791 TCAGTTCTTAGCATACTGGTATGTTTT 58.899 33.333 18.24 9.70 43.57 2.43
3510 4181 7.620880 TCAGTTCTTAGCATACTGGTATGTTT 58.379 34.615 18.24 11.54 43.57 2.83
3511 4182 7.182817 TCAGTTCTTAGCATACTGGTATGTT 57.817 36.000 18.24 15.65 43.57 2.71


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

AutoCloner maintained by Alex Coulton.