Multiple sequence alignment - TraesCS5A01G235100

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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 TraesCS5A01G235100 chr5A 100.000 3547 0 0 1 3547 451255978 451252432 0.000000e+00 6551.0
1 TraesCS5A01G235100 chr5A 83.780 1455 209 21 1108 2548 709519966 709518525 0.000000e+00 1354.0
2 TraesCS5A01G235100 chr5A 84.889 675 93 7 12 682 472499829 472499160 0.000000e+00 673.0
3 TraesCS5A01G235100 chr5A 80.380 158 31 0 1157 1314 697706265 697706108 1.730000e-23 121.0
4 TraesCS5A01G235100 chr5D 94.049 1714 87 12 990 2699 350734838 350733136 0.000000e+00 2586.0
5 TraesCS5A01G235100 chr5D 92.697 178 9 4 803 978 350734993 350734818 1.630000e-63 254.0
6 TraesCS5A01G235100 chr5D 78.481 395 73 9 1161 1545 456066453 456066845 7.600000e-62 248.0
7 TraesCS5A01G235100 chr1D 85.010 1481 199 16 1081 2548 485942687 485944157 0.000000e+00 1483.0
8 TraesCS5A01G235100 chr1D 80.476 210 37 4 1120 1329 485963936 485964141 1.320000e-34 158.0
9 TraesCS5A01G235100 chr1B 97.512 844 18 1 2703 3546 45813259 45814099 0.000000e+00 1439.0
10 TraesCS5A01G235100 chr1B 96.923 845 22 2 2703 3547 68292386 68291546 0.000000e+00 1413.0
11 TraesCS5A01G235100 chr1B 83.144 706 110 8 6 707 419401203 419401903 1.390000e-178 636.0
12 TraesCS5A01G235100 chr1B 90.698 43 3 1 1815 1857 424594777 424594818 4.950000e-04 56.5
13 TraesCS5A01G235100 chr4B 84.394 1493 195 26 1081 2548 671854938 671853459 0.000000e+00 1432.0
14 TraesCS5A01G235100 chr4B 87.850 214 19 1 1082 1295 671902628 671902422 9.840000e-61 244.0
15 TraesCS5A01G235100 chr5B 97.160 845 20 2 2703 3547 87915512 87916352 0.000000e+00 1424.0
16 TraesCS5A01G235100 chr5B 97.045 846 22 1 2702 3547 441101185 441102027 0.000000e+00 1421.0
17 TraesCS5A01G235100 chr5B 79.762 1428 250 25 1142 2548 525525243 525523834 0.000000e+00 1000.0
18 TraesCS5A01G235100 chr4A 96.927 846 22 2 2703 3547 125382347 125381505 0.000000e+00 1415.0
19 TraesCS5A01G235100 chr6B 96.923 845 23 1 2703 3547 54412333 54411492 0.000000e+00 1413.0
20 TraesCS5A01G235100 chr6B 100.000 28 0 0 1815 1842 29693703 29693676 6.000000e-03 52.8
21 TraesCS5A01G235100 chr6A 96.809 846 24 1 2702 3547 74227414 74226572 0.000000e+00 1410.0
22 TraesCS5A01G235100 chr6A 83.122 711 106 12 2 705 610789885 610789182 1.390000e-178 636.0
23 TraesCS5A01G235100 chr4D 96.479 852 24 3 2696 3547 489335021 489334176 0.000000e+00 1402.0
24 TraesCS5A01G235100 chr4D 84.831 712 96 12 1 707 8133829 8133125 0.000000e+00 706.0
25 TraesCS5A01G235100 chr2D 96.270 858 27 3 2691 3547 38674435 38675288 0.000000e+00 1402.0
26 TraesCS5A01G235100 chr7A 79.293 1415 262 18 1142 2548 150730345 150728954 0.000000e+00 961.0
27 TraesCS5A01G235100 chr7A 80.837 454 72 8 2125 2572 150785833 150786277 3.390000e-90 342.0
28 TraesCS5A01G235100 chr3B 84.348 690 95 12 24 708 20748084 20747403 0.000000e+00 664.0
29 TraesCS5A01G235100 chr3B 83.286 706 103 11 6 705 614910718 614911414 1.390000e-178 636.0
30 TraesCS5A01G235100 chr3D 83.826 711 100 12 1 707 406137540 406138239 0.000000e+00 662.0
31 TraesCS5A01G235100 chr3D 84.157 688 96 10 24 705 576318612 576319292 0.000000e+00 654.0
32 TraesCS5A01G235100 chr7B 82.825 722 113 8 1 719 592179498 592180211 1.390000e-178 636.0
33 TraesCS5A01G235100 chr7B 100.000 28 0 0 1815 1842 735025900 735025873 6.000000e-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 TraesCS5A01G235100 chr5A 451252432 451255978 3546 True 6551 6551 100.000 1 3547 1 chr5A.!!$R1 3546
1 TraesCS5A01G235100 chr5A 709518525 709519966 1441 True 1354 1354 83.780 1108 2548 1 chr5A.!!$R4 1440
2 TraesCS5A01G235100 chr5A 472499160 472499829 669 True 673 673 84.889 12 682 1 chr5A.!!$R2 670
3 TraesCS5A01G235100 chr5D 350733136 350734993 1857 True 1420 2586 93.373 803 2699 2 chr5D.!!$R1 1896
4 TraesCS5A01G235100 chr1D 485942687 485944157 1470 False 1483 1483 85.010 1081 2548 1 chr1D.!!$F1 1467
5 TraesCS5A01G235100 chr1B 45813259 45814099 840 False 1439 1439 97.512 2703 3546 1 chr1B.!!$F1 843
6 TraesCS5A01G235100 chr1B 68291546 68292386 840 True 1413 1413 96.923 2703 3547 1 chr1B.!!$R1 844
7 TraesCS5A01G235100 chr1B 419401203 419401903 700 False 636 636 83.144 6 707 1 chr1B.!!$F2 701
8 TraesCS5A01G235100 chr4B 671853459 671854938 1479 True 1432 1432 84.394 1081 2548 1 chr4B.!!$R1 1467
9 TraesCS5A01G235100 chr5B 87915512 87916352 840 False 1424 1424 97.160 2703 3547 1 chr5B.!!$F1 844
10 TraesCS5A01G235100 chr5B 441101185 441102027 842 False 1421 1421 97.045 2702 3547 1 chr5B.!!$F2 845
11 TraesCS5A01G235100 chr5B 525523834 525525243 1409 True 1000 1000 79.762 1142 2548 1 chr5B.!!$R1 1406
12 TraesCS5A01G235100 chr4A 125381505 125382347 842 True 1415 1415 96.927 2703 3547 1 chr4A.!!$R1 844
13 TraesCS5A01G235100 chr6B 54411492 54412333 841 True 1413 1413 96.923 2703 3547 1 chr6B.!!$R2 844
14 TraesCS5A01G235100 chr6A 74226572 74227414 842 True 1410 1410 96.809 2702 3547 1 chr6A.!!$R1 845
15 TraesCS5A01G235100 chr6A 610789182 610789885 703 True 636 636 83.122 2 705 1 chr6A.!!$R2 703
16 TraesCS5A01G235100 chr4D 489334176 489335021 845 True 1402 1402 96.479 2696 3547 1 chr4D.!!$R2 851
17 TraesCS5A01G235100 chr4D 8133125 8133829 704 True 706 706 84.831 1 707 1 chr4D.!!$R1 706
18 TraesCS5A01G235100 chr2D 38674435 38675288 853 False 1402 1402 96.270 2691 3547 1 chr2D.!!$F1 856
19 TraesCS5A01G235100 chr7A 150728954 150730345 1391 True 961 961 79.293 1142 2548 1 chr7A.!!$R1 1406
20 TraesCS5A01G235100 chr3B 20747403 20748084 681 True 664 664 84.348 24 708 1 chr3B.!!$R1 684
21 TraesCS5A01G235100 chr3B 614910718 614911414 696 False 636 636 83.286 6 705 1 chr3B.!!$F1 699
22 TraesCS5A01G235100 chr3D 406137540 406138239 699 False 662 662 83.826 1 707 1 chr3D.!!$F1 706
23 TraesCS5A01G235100 chr3D 576318612 576319292 680 False 654 654 84.157 24 705 1 chr3D.!!$F2 681
24 TraesCS5A01G235100 chr7B 592179498 592180211 713 False 636 636 82.825 1 719 1 chr7B.!!$F1 718

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
773 786 0.038983 TGTAACGTGCTCGCTTGCTA 60.039 50.0 8.29 0.00 41.18 3.49 F
2333 2382 0.179234 TGGAGGCAGACGTCAAAACA 59.821 50.0 19.50 5.98 32.18 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2507 2556 0.883370 GGAAGAACCACGTCGGCTTT 60.883 55.000 0.0 0.0 39.03 3.51 R
3497 3547 1.272212 GACATGGTTGCCGGTGAAAAT 59.728 47.619 1.9 0.0 0.00 1.82 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
64 66 2.910479 ATCGCGATACGGGCCTCA 60.910 61.111 22.33 0.00 43.89 3.86
125 127 2.856864 TCCTGGTGGGACTCATAGTCTA 59.143 50.000 6.99 0.00 44.46 2.59
135 137 0.820891 TCATAGTCTACCCGACCGGC 60.821 60.000 0.00 0.00 43.91 6.13
349 356 2.105128 CGACAGATCCGGACTGGC 59.895 66.667 26.99 24.98 39.72 4.85
362 369 1.000993 ACTGGCCAGAGTCCGATCT 59.999 57.895 39.19 10.61 0.00 2.75
488 497 4.978099 AGACGAATATAAGTAGGGTCGGA 58.022 43.478 0.00 0.00 32.96 4.55
516 525 1.105457 CATAGGTTGGGTCCGACGTA 58.895 55.000 10.99 10.99 35.83 3.57
518 527 1.626686 TAGGTTGGGTCCGACGTAAA 58.373 50.000 7.19 0.00 30.54 2.01
522 531 1.120795 TTGGGTCCGACGTAAAGGGT 61.121 55.000 0.00 0.00 0.00 4.34
527 536 1.301087 CCGACGTAAAGGGTGTGCA 60.301 57.895 0.00 0.00 0.00 4.57
534 543 2.030490 TAAAGGGTGTGCACGGACGT 62.030 55.000 13.13 3.51 0.00 4.34
543 552 1.300697 GCACGGACGTCCCCATATC 60.301 63.158 28.52 8.41 0.00 1.63
593 603 2.027625 CCAGTCAGCCCGAACGTTC 61.028 63.158 18.47 18.47 0.00 3.95
708 721 1.336424 GGCGGAGTAGATGCTCTTAGC 60.336 57.143 0.00 0.00 42.82 3.09
722 735 3.972950 TCTTAGCAGAGAGACGCATAC 57.027 47.619 0.00 0.00 0.00 2.39
724 737 0.308068 TAGCAGAGAGACGCATACGC 59.692 55.000 0.00 0.00 45.53 4.42
725 738 1.946650 GCAGAGAGACGCATACGCC 60.947 63.158 0.00 0.00 45.53 5.68
726 739 1.730487 CAGAGAGACGCATACGCCT 59.270 57.895 0.00 0.00 45.53 5.52
729 742 4.618513 GAGACGCATACGCCTCTC 57.381 61.111 0.00 0.00 44.42 3.20
730 743 1.369448 GAGACGCATACGCCTCTCG 60.369 63.158 0.00 0.00 44.42 4.04
731 744 3.025176 GACGCATACGCCTCTCGC 61.025 66.667 0.00 0.00 45.53 5.03
732 745 3.751401 GACGCATACGCCTCTCGCA 62.751 63.158 0.00 0.00 45.53 5.10
733 746 2.582226 CGCATACGCCTCTCGCAA 60.582 61.111 0.00 0.00 43.23 4.85
734 747 2.164663 CGCATACGCCTCTCGCAAA 61.165 57.895 0.00 0.00 43.23 3.68
735 748 1.692148 CGCATACGCCTCTCGCAAAA 61.692 55.000 0.00 0.00 43.23 2.44
736 749 0.446222 GCATACGCCTCTCGCAAAAA 59.554 50.000 0.00 0.00 43.23 1.94
755 768 2.468532 AAAAGAACGAAACGCAGGTG 57.531 45.000 0.00 0.00 0.00 4.00
756 769 1.375551 AAAGAACGAAACGCAGGTGT 58.624 45.000 0.00 0.00 0.00 4.16
757 770 2.228138 AAGAACGAAACGCAGGTGTA 57.772 45.000 0.00 0.00 0.00 2.90
758 771 2.228138 AGAACGAAACGCAGGTGTAA 57.772 45.000 0.00 0.00 0.00 2.41
759 772 1.862827 AGAACGAAACGCAGGTGTAAC 59.137 47.619 0.00 0.00 0.00 2.50
760 773 0.578211 AACGAAACGCAGGTGTAACG 59.422 50.000 0.00 9.08 38.12 3.18
761 774 0.528249 ACGAAACGCAGGTGTAACGT 60.528 50.000 10.05 10.05 42.81 3.99
767 780 3.156334 CAGGTGTAACGTGCTCGC 58.844 61.111 8.29 0.00 46.32 5.03
768 781 1.372997 CAGGTGTAACGTGCTCGCT 60.373 57.895 8.29 0.00 46.32 4.93
769 782 0.944311 CAGGTGTAACGTGCTCGCTT 60.944 55.000 8.29 4.85 46.32 4.68
770 783 0.944311 AGGTGTAACGTGCTCGCTTG 60.944 55.000 8.29 0.00 41.18 4.01
771 784 1.154654 GTGTAACGTGCTCGCTTGC 60.155 57.895 8.29 6.40 41.18 4.01
772 785 1.300620 TGTAACGTGCTCGCTTGCT 60.301 52.632 8.29 0.00 41.18 3.91
773 786 0.038983 TGTAACGTGCTCGCTTGCTA 60.039 50.000 8.29 0.00 41.18 3.49
774 787 0.365859 GTAACGTGCTCGCTTGCTAC 59.634 55.000 8.29 0.00 41.18 3.58
775 788 0.038983 TAACGTGCTCGCTTGCTACA 60.039 50.000 8.29 0.00 41.18 2.74
776 789 0.878523 AACGTGCTCGCTTGCTACAA 60.879 50.000 8.29 0.00 41.18 2.41
777 790 0.878523 ACGTGCTCGCTTGCTACAAA 60.879 50.000 8.29 0.00 41.18 2.83
778 791 0.443869 CGTGCTCGCTTGCTACAAAT 59.556 50.000 0.00 0.00 0.00 2.32
779 792 1.135972 CGTGCTCGCTTGCTACAAATT 60.136 47.619 0.00 0.00 0.00 1.82
780 793 2.665519 CGTGCTCGCTTGCTACAAATTT 60.666 45.455 0.00 0.00 0.00 1.82
781 794 2.658325 GTGCTCGCTTGCTACAAATTTG 59.342 45.455 16.67 16.67 0.00 2.32
782 795 2.551887 TGCTCGCTTGCTACAAATTTGA 59.448 40.909 24.64 7.56 0.00 2.69
783 796 3.166657 GCTCGCTTGCTACAAATTTGAG 58.833 45.455 24.64 16.76 0.00 3.02
784 797 3.751621 CTCGCTTGCTACAAATTTGAGG 58.248 45.455 24.64 15.88 0.00 3.86
785 798 3.407698 TCGCTTGCTACAAATTTGAGGA 58.592 40.909 24.64 14.76 0.00 3.71
786 799 4.009675 TCGCTTGCTACAAATTTGAGGAT 58.990 39.130 24.64 4.75 0.00 3.24
787 800 5.182487 TCGCTTGCTACAAATTTGAGGATA 58.818 37.500 24.64 5.70 0.00 2.59
788 801 5.064707 TCGCTTGCTACAAATTTGAGGATAC 59.935 40.000 24.64 11.55 0.00 2.24
812 825 0.856641 TTTTTCTCCGTTCTCGTGCG 59.143 50.000 0.00 0.00 35.01 5.34
813 826 1.554042 TTTTCTCCGTTCTCGTGCGC 61.554 55.000 0.00 0.00 35.01 6.09
820 833 3.399770 TTCTCGTGCGCCGAAACG 61.400 61.111 18.95 15.50 46.75 3.60
833 846 1.262151 CCGAAACGACGTGGTTGAAAT 59.738 47.619 16.97 0.56 0.00 2.17
842 855 1.194547 CGTGGTTGAAATCGTGTCCTG 59.805 52.381 0.00 0.00 0.00 3.86
845 858 1.804748 GGTTGAAATCGTGTCCTGTCC 59.195 52.381 0.00 0.00 0.00 4.02
915 928 2.995283 TCCTTTCTGTATCGAGTCGGA 58.005 47.619 13.54 0.00 0.00 4.55
929 942 1.205055 GTCGGATTTCCTTCCCCTCT 58.795 55.000 0.00 0.00 31.61 3.69
935 948 1.073098 TTTCCTTCCCCTCTTCCACC 58.927 55.000 0.00 0.00 0.00 4.61
962 976 2.158667 CCCCCTTGACGCACCTATTATT 60.159 50.000 0.00 0.00 0.00 1.40
963 977 3.071892 CCCCCTTGACGCACCTATTATTA 59.928 47.826 0.00 0.00 0.00 0.98
964 978 4.263331 CCCCCTTGACGCACCTATTATTAT 60.263 45.833 0.00 0.00 0.00 1.28
965 979 5.046159 CCCCCTTGACGCACCTATTATTATA 60.046 44.000 0.00 0.00 0.00 0.98
966 980 6.352737 CCCCCTTGACGCACCTATTATTATAT 60.353 42.308 0.00 0.00 0.00 0.86
967 981 7.147620 CCCCCTTGACGCACCTATTATTATATA 60.148 40.741 0.00 0.00 0.00 0.86
968 982 7.709613 CCCCTTGACGCACCTATTATTATATAC 59.290 40.741 0.00 0.00 0.00 1.47
969 983 8.475639 CCCTTGACGCACCTATTATTATATACT 58.524 37.037 0.00 0.00 0.00 2.12
970 984 9.517609 CCTTGACGCACCTATTATTATATACTC 57.482 37.037 0.00 0.00 0.00 2.59
1045 1059 0.584054 CGTGCGACGCAGCTTTTATC 60.584 55.000 25.21 7.80 40.08 1.75
1058 1072 6.608610 GCAGCTTTTATCTTCGAAGGTTTTA 58.391 36.000 24.37 5.63 0.00 1.52
1068 1082 7.979444 TCTTCGAAGGTTTTATGAAAGTCAT 57.021 32.000 24.37 0.00 40.72 3.06
1069 1083 9.667107 ATCTTCGAAGGTTTTATGAAAGTCATA 57.333 29.630 24.37 0.00 38.26 2.15
1101 1116 2.076100 CGCAGCTTTTATCTGTGGACA 58.924 47.619 0.00 0.00 38.14 4.02
1299 1322 1.154205 GCATAATCGTCCGCAGCTGT 61.154 55.000 16.64 0.00 0.00 4.40
1372 1395 1.043816 CATCACGGGCTATCACTCCT 58.956 55.000 0.00 0.00 0.00 3.69
1374 1397 0.755698 TCACGGGCTATCACTCCTCC 60.756 60.000 0.00 0.00 0.00 4.30
1401 1425 0.454600 GACCTTCATCGGCGTCTGTA 59.545 55.000 6.85 0.00 0.00 2.74
1411 1435 1.574702 GGCGTCTGTAACAACTGGCC 61.575 60.000 0.00 0.00 0.00 5.36
1424 1448 1.743995 CTGGCCCGTCTTTTACCGG 60.744 63.158 0.00 0.00 43.82 5.28
1470 1497 4.326826 TCTCTTGCATAACCCTTTCACAG 58.673 43.478 0.00 0.00 0.00 3.66
1511 1538 1.649815 GCTCGACTCCGTCATCGAT 59.350 57.895 0.00 0.00 45.63 3.59
1521 1548 2.814336 TCCGTCATCGATGATACCTCTG 59.186 50.000 29.53 13.46 39.30 3.35
1572 1599 2.225727 CCGTCGACCGAAGATGATATCA 59.774 50.000 10.58 8.10 39.56 2.15
1574 1602 4.476862 CGTCGACCGAAGATGATATCATT 58.523 43.478 19.11 5.46 39.56 2.57
1609 1637 3.115554 GCAATTGCAATTACCCGATCAC 58.884 45.455 25.36 2.74 41.59 3.06
1621 1649 1.079819 CGATCACCTTGTGTCGCCT 60.080 57.895 0.00 0.00 33.43 5.52
1694 1722 8.123575 GCGTCTATATATGATGTCGTGTTCTAT 58.876 37.037 0.00 0.00 0.00 1.98
1760 1788 6.425735 TGTGATGGATATTGGTGAAGACAAT 58.574 36.000 0.00 0.00 41.17 2.71
1772 1800 2.571653 TGAAGACAATGACGGAATCCCT 59.428 45.455 0.00 0.00 0.00 4.20
1904 1950 1.732259 GAGGTGGTGTACAATGAAGCG 59.268 52.381 0.00 0.00 0.00 4.68
2063 2112 5.169992 TGAGCAATGAGGATGAAGAAGAA 57.830 39.130 0.00 0.00 0.00 2.52
2181 2230 1.069364 GCACTGAGCAGCTCTTTTGTC 60.069 52.381 23.15 9.59 44.79 3.18
2203 2252 1.751924 ACACGGAGAAGACCTAGATGC 59.248 52.381 0.00 0.00 0.00 3.91
2210 2259 4.774726 GGAGAAGACCTAGATGCCATCATA 59.225 45.833 7.56 0.00 31.96 2.15
2233 2282 3.322254 ACCAGTCGACATCTCTTTGAGTT 59.678 43.478 19.50 0.00 0.00 3.01
2275 2324 0.964860 AGGCGGCAACAATATGTGCA 60.965 50.000 13.08 0.00 0.00 4.57
2333 2382 0.179234 TGGAGGCAGACGTCAAAACA 59.821 50.000 19.50 5.98 32.18 2.83
2385 2434 0.674895 AGGTGCATTCTTCGTGAGCC 60.675 55.000 0.00 0.00 0.00 4.70
2424 2473 0.331278 CCCCACATACCAAGAGGCAA 59.669 55.000 0.00 0.00 39.06 4.52
2507 2556 3.649843 ACGGTTTACTCTATGGGATGGA 58.350 45.455 0.00 0.00 0.00 3.41
2612 2661 1.270274 TGAACCATTGTGCATGTGCTC 59.730 47.619 6.55 3.34 42.66 4.26
2616 2665 1.202371 CCATTGTGCATGTGCTCCATC 60.202 52.381 6.55 0.00 42.66 3.51
2625 2674 1.808411 TGTGCTCCATCCGTTTCTTC 58.192 50.000 0.00 0.00 0.00 2.87
2681 2730 9.511144 AATTTCTCGTAAAGTTTTACCAAGTTG 57.489 29.630 8.69 0.00 39.81 3.16
2829 2879 0.739561 AGACTAAAGCCGCCGTCTAG 59.260 55.000 0.00 0.00 35.15 2.43
3025 3075 7.631594 GCTCCATCTTTAGAACTGTACTGATGA 60.632 40.741 6.77 0.00 33.92 2.92
3282 3332 1.448540 CCGAAGCTCCGTGCAAGAT 60.449 57.895 0.00 0.00 45.94 2.40
3423 3473 4.056125 CGGAGCAGCACGAGTGGA 62.056 66.667 5.32 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 49 2.910479 TGAGGCCCGTATCGCGAT 60.910 61.111 26.78 26.78 44.77 4.58
64 66 1.839296 GGAGAGGATAAGGGCCGCT 60.839 63.158 0.00 0.00 38.31 5.52
135 137 0.978146 ACACCTCTCCTTCCCCATCG 60.978 60.000 0.00 0.00 0.00 3.84
278 284 3.364441 GGCAGTCCGCATTGCACA 61.364 61.111 9.69 0.00 45.17 4.57
308 314 1.671054 GTGTCACCCCGTGTGGATG 60.671 63.158 2.89 0.00 45.48 3.51
310 316 3.552384 GGTGTCACCCCGTGTGGA 61.552 66.667 11.30 0.00 45.48 4.02
320 326 0.603569 ATCTGTCGACTGGGTGTCAC 59.396 55.000 20.57 0.00 45.60 3.67
349 356 1.227205 GCTGCAGATCGGACTCTGG 60.227 63.158 20.43 0.00 42.42 3.86
488 497 1.231068 CCAACCTATGCTGGCCCAT 59.769 57.895 0.00 0.00 0.00 4.00
516 525 2.590575 CGTCCGTGCACACCCTTT 60.591 61.111 18.64 0.00 0.00 3.11
518 527 4.295119 GACGTCCGTGCACACCCT 62.295 66.667 18.64 0.00 0.00 4.34
527 536 1.835712 GGGATATGGGGACGTCCGT 60.836 63.158 27.68 18.09 36.71 4.69
534 543 2.126375 TATGGGGCGGGATATGGGGA 62.126 60.000 0.00 0.00 0.00 4.81
543 552 1.151450 AGCTCAAATATGGGGCGGG 59.849 57.895 0.00 0.00 33.29 6.13
564 573 1.224592 CTGACTGGCACCCCCATAC 59.775 63.158 0.00 0.00 44.33 2.39
593 603 2.809601 CGCCTCAAACGGGTCTCG 60.810 66.667 0.00 0.00 45.88 4.04
626 636 1.499049 GTCACTGACCGGTCACTTTC 58.501 55.000 33.23 18.94 35.46 2.62
660 673 3.569548 CTCAATCCCGTCTCATATGTCG 58.430 50.000 1.90 6.66 0.00 4.35
708 721 4.310672 GGCGTATGCGTCTCTCTG 57.689 61.111 4.81 0.00 44.10 3.35
735 748 2.162809 ACACCTGCGTTTCGTTCTTTTT 59.837 40.909 0.00 0.00 0.00 1.94
736 749 1.741145 ACACCTGCGTTTCGTTCTTTT 59.259 42.857 0.00 0.00 0.00 2.27
737 750 1.375551 ACACCTGCGTTTCGTTCTTT 58.624 45.000 0.00 0.00 0.00 2.52
738 751 2.228138 TACACCTGCGTTTCGTTCTT 57.772 45.000 0.00 0.00 0.00 2.52
739 752 1.862827 GTTACACCTGCGTTTCGTTCT 59.137 47.619 0.00 0.00 0.00 3.01
740 753 1.396316 CGTTACACCTGCGTTTCGTTC 60.396 52.381 0.00 0.00 0.00 3.95
741 754 0.578211 CGTTACACCTGCGTTTCGTT 59.422 50.000 0.00 0.00 0.00 3.85
742 755 0.528249 ACGTTACACCTGCGTTTCGT 60.528 50.000 0.00 0.00 35.11 3.85
743 756 0.111442 CACGTTACACCTGCGTTTCG 60.111 55.000 0.00 0.00 36.67 3.46
744 757 0.383860 GCACGTTACACCTGCGTTTC 60.384 55.000 0.00 0.00 36.67 2.78
745 758 0.812412 AGCACGTTACACCTGCGTTT 60.812 50.000 0.00 0.00 35.70 3.60
746 759 1.219522 GAGCACGTTACACCTGCGTT 61.220 55.000 0.00 0.00 35.70 4.84
747 760 1.663702 GAGCACGTTACACCTGCGT 60.664 57.895 0.00 0.00 35.70 5.24
748 761 2.716828 CGAGCACGTTACACCTGCG 61.717 63.158 0.00 0.00 35.70 5.18
749 762 3.011760 GCGAGCACGTTACACCTGC 62.012 63.158 5.23 0.00 41.98 4.85
750 763 0.944311 AAGCGAGCACGTTACACCTG 60.944 55.000 5.23 0.00 41.98 4.00
751 764 0.944311 CAAGCGAGCACGTTACACCT 60.944 55.000 5.23 0.00 41.98 4.00
752 765 1.491563 CAAGCGAGCACGTTACACC 59.508 57.895 5.23 0.00 41.98 4.16
753 766 1.154654 GCAAGCGAGCACGTTACAC 60.155 57.895 5.23 0.00 41.98 2.90
754 767 0.038983 TAGCAAGCGAGCACGTTACA 60.039 50.000 5.23 0.00 41.98 2.41
755 768 0.365859 GTAGCAAGCGAGCACGTTAC 59.634 55.000 5.23 0.00 41.98 2.50
756 769 0.038983 TGTAGCAAGCGAGCACGTTA 60.039 50.000 5.23 0.00 41.98 3.18
757 770 0.878523 TTGTAGCAAGCGAGCACGTT 60.879 50.000 5.23 0.00 41.98 3.99
758 771 0.878523 TTTGTAGCAAGCGAGCACGT 60.879 50.000 5.23 0.00 41.98 4.49
759 772 0.443869 ATTTGTAGCAAGCGAGCACG 59.556 50.000 0.00 0.00 42.93 5.34
760 773 2.619013 AATTTGTAGCAAGCGAGCAC 57.381 45.000 6.21 3.41 36.85 4.40
761 774 2.551887 TCAAATTTGTAGCAAGCGAGCA 59.448 40.909 17.47 0.00 36.85 4.26
762 775 3.166657 CTCAAATTTGTAGCAAGCGAGC 58.833 45.455 17.47 0.00 0.00 5.03
763 776 3.436704 TCCTCAAATTTGTAGCAAGCGAG 59.563 43.478 17.47 4.67 0.00 5.03
764 777 3.407698 TCCTCAAATTTGTAGCAAGCGA 58.592 40.909 17.47 4.95 0.00 4.93
765 778 3.829886 TCCTCAAATTTGTAGCAAGCG 57.170 42.857 17.47 2.95 0.00 4.68
766 779 6.442513 AGTATCCTCAAATTTGTAGCAAGC 57.557 37.500 17.47 5.00 0.00 4.01
767 780 9.696917 AAAAAGTATCCTCAAATTTGTAGCAAG 57.303 29.630 17.47 7.37 0.00 4.01
793 806 0.856641 CGCACGAGAACGGAGAAAAA 59.143 50.000 0.00 0.00 44.46 1.94
794 807 1.554042 GCGCACGAGAACGGAGAAAA 61.554 55.000 0.30 0.00 44.46 2.29
795 808 2.019951 GCGCACGAGAACGGAGAAA 61.020 57.895 0.30 0.00 44.46 2.52
796 809 2.430244 GCGCACGAGAACGGAGAA 60.430 61.111 0.30 0.00 44.46 2.87
797 810 4.415332 GGCGCACGAGAACGGAGA 62.415 66.667 10.83 0.00 44.46 3.71
812 825 1.764180 TTCAACCACGTCGTTTCGGC 61.764 55.000 0.00 0.00 34.94 5.54
813 826 0.651551 TTTCAACCACGTCGTTTCGG 59.348 50.000 0.00 0.00 34.94 4.30
820 833 1.193874 GGACACGATTTCAACCACGTC 59.806 52.381 0.00 0.00 36.86 4.34
833 846 0.391528 TCGATACGGACAGGACACGA 60.392 55.000 0.00 0.00 0.00 4.35
862 875 5.537300 ATCTCATATGTAAAGGACGCACT 57.463 39.130 1.90 0.00 0.00 4.40
915 928 1.641192 GGTGGAAGAGGGGAAGGAAAT 59.359 52.381 0.00 0.00 0.00 2.17
929 942 0.116143 CAAGGGGGATTTGGGTGGAA 59.884 55.000 0.00 0.00 0.00 3.53
935 948 1.304052 TGCGTCAAGGGGGATTTGG 60.304 57.895 0.00 0.00 0.00 3.28
1017 1031 1.226491 GCGTCGCACGTGTACCTAT 60.226 57.895 18.38 0.00 44.73 2.57
1029 1043 1.589968 CGAAGATAAAAGCTGCGTCGC 60.590 52.381 11.10 11.10 29.78 5.19
1037 1051 9.620660 TTTCATAAAACCTTCGAAGATAAAAGC 57.379 29.630 26.61 0.00 35.04 3.51
1058 1072 6.018994 GCGTTACCTTCGAATATGACTTTCAT 60.019 38.462 0.00 0.00 40.72 2.57
1068 1082 2.953466 AGCTGCGTTACCTTCGAATA 57.047 45.000 0.00 0.00 0.00 1.75
1069 1083 2.094762 AAGCTGCGTTACCTTCGAAT 57.905 45.000 0.00 0.00 0.00 3.34
1101 1116 0.391661 CTACTGTGGTGCCGATGCTT 60.392 55.000 0.00 0.00 38.71 3.91
1299 1322 3.321968 CCATCCAAGTAGATGATCCACGA 59.678 47.826 3.14 0.00 45.43 4.35
1372 1395 0.242825 GATGAAGGTCGTGTCGTGGA 59.757 55.000 0.00 0.00 0.00 4.02
1374 1397 1.071019 CCGATGAAGGTCGTGTCGTG 61.071 60.000 0.00 0.00 39.89 4.35
1401 1425 1.951602 GTAAAAGACGGGCCAGTTGTT 59.048 47.619 10.75 4.30 0.00 2.83
1470 1497 2.750888 GGAGCGGCACCGTTGATTC 61.751 63.158 11.27 1.73 42.09 2.52
1511 1538 3.017442 CTCGAACAGGTCAGAGGTATCA 58.983 50.000 0.00 0.00 0.00 2.15
1521 1548 2.531206 CTTCCGAATCTCGAACAGGTC 58.469 52.381 0.00 0.00 43.74 3.85
1609 1637 1.228124 TTCCCAAGGCGACACAAGG 60.228 57.895 0.00 0.00 0.00 3.61
1678 1706 4.584743 TGCCTCTATAGAACACGACATCAT 59.415 41.667 3.57 0.00 0.00 2.45
1694 1722 4.037222 TGATCCCACATAGTTTGCCTCTA 58.963 43.478 0.00 0.00 0.00 2.43
1760 1788 3.773418 TTAACAACAGGGATTCCGTCA 57.227 42.857 0.00 0.00 38.33 4.35
1904 1950 1.134530 CGTCCTCGTCGATGCTTGAC 61.135 60.000 0.00 5.49 0.00 3.18
2063 2112 6.947376 TCATCATAATCTCCATCATCCACT 57.053 37.500 0.00 0.00 0.00 4.00
2176 2225 1.202604 GGTCTTCTCCGTGTGGACAAA 60.203 52.381 0.00 0.00 40.17 2.83
2181 2230 1.835494 TCTAGGTCTTCTCCGTGTGG 58.165 55.000 0.00 0.00 0.00 4.17
2203 2252 4.038522 AGAGATGTCGACTGGTTATGATGG 59.961 45.833 17.92 0.00 0.00 3.51
2210 2259 3.322254 ACTCAAAGAGATGTCGACTGGTT 59.678 43.478 17.92 0.00 33.32 3.67
2233 2282 4.705991 TGAGCATGAATAACTTGCCATTCA 59.294 37.500 0.00 0.00 46.43 2.57
2275 2324 4.895224 TTGTAGCGACGAGAGAATACAT 57.105 40.909 0.00 0.00 0.00 2.29
2333 2382 1.069765 CCGCAGAATCCATACGCCT 59.930 57.895 0.00 0.00 0.00 5.52
2385 2434 5.010516 TGGGGACATGTTTTGAGTAATGTTG 59.989 40.000 0.00 0.00 33.51 3.33
2424 2473 6.833933 ACAAAGTGGTGGATAAACTTCTTTCT 59.166 34.615 0.00 0.00 33.09 2.52
2507 2556 0.883370 GGAAGAACCACGTCGGCTTT 60.883 55.000 0.00 0.00 39.03 3.51
2586 2635 3.247442 CATGCACAATGGTTCACATCAC 58.753 45.455 0.00 0.00 39.40 3.06
2612 2661 3.619038 GCAGAGTTAGAAGAAACGGATGG 59.381 47.826 0.00 0.00 34.46 3.51
2616 2665 7.653713 ACATATATGCAGAGTTAGAAGAAACGG 59.346 37.037 12.79 0.00 34.46 4.44
2709 2759 2.426842 GGGGTCATCCTCCTTTTCTG 57.573 55.000 0.00 0.00 35.33 3.02
2732 2782 4.201122 GCCCAGATGCAGAGGGGG 62.201 72.222 19.17 14.90 43.04 5.40
2733 2783 4.559063 CGCCCAGATGCAGAGGGG 62.559 72.222 19.17 16.48 43.04 4.79
2734 2784 2.815945 ATCGCCCAGATGCAGAGGG 61.816 63.158 14.79 14.79 45.68 4.30
2805 2855 2.094675 ACGGCGGCTTTAGTCTTACTA 58.905 47.619 13.24 0.00 0.00 1.82
2829 2879 1.055040 ATCAGCTGGATAGAGGTGCC 58.945 55.000 15.13 0.00 40.58 5.01
3025 3075 2.678190 GCTAGACCGAGCAAGGTTGATT 60.678 50.000 4.58 0.00 46.09 2.57
3282 3332 3.706373 GGAGGTGGAGCGGCTTCA 61.706 66.667 6.94 6.94 0.00 3.02
3423 3473 4.604843 TCGTCGTGTAACTATTGTCGAT 57.395 40.909 0.00 0.00 31.75 3.59
3497 3547 1.272212 GACATGGTTGCCGGTGAAAAT 59.728 47.619 1.90 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.