Multiple sequence alignment - TraesCS4A01G064000

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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 TraesCS4A01G064000 chr4A 100.000 3566 0 0 1 3566 60878984 60882549 0.000000e+00 6586.0
1 TraesCS4A01G064000 chr4A 89.028 1841 164 20 830 2642 60730316 60732146 0.000000e+00 2246.0
2 TraesCS4A01G064000 chr4A 94.026 703 40 2 2781 3482 561152623 561153324 0.000000e+00 1064.0
3 TraesCS4A01G064000 chr4D 92.410 2108 100 20 711 2780 403199476 403201561 0.000000e+00 2952.0
4 TraesCS4A01G064000 chr4D 88.864 1805 149 27 880 2647 403182029 403183818 0.000000e+00 2172.0
5 TraesCS4A01G064000 chr4D 89.157 83 8 1 3479 3560 403201551 403201633 6.300000e-18 102.0
6 TraesCS4A01G064000 chr4B 94.870 1813 78 10 976 2780 500079122 500080927 0.000000e+00 2819.0
7 TraesCS4A01G064000 chr4B 89.251 1842 164 17 830 2647 500052646 500054477 0.000000e+00 2274.0
8 TraesCS4A01G064000 chr4B 83.333 168 10 2 766 933 500078957 500079106 4.800000e-29 139.0
9 TraesCS4A01G064000 chr2D 88.085 1452 150 12 1123 2558 645838270 645839714 0.000000e+00 1701.0
10 TraesCS4A01G064000 chr2D 86.623 613 59 9 91 683 86524632 86525241 0.000000e+00 656.0
11 TraesCS4A01G064000 chr2D 85.691 615 68 6 86 683 7275957 7276568 6.500000e-177 630.0
12 TraesCS4A01G064000 chr2D 85.833 600 69 7 91 683 543290140 543290730 1.090000e-174 623.0
13 TraesCS4A01G064000 chr2D 88.235 68 8 0 5 72 537240752 537240685 8.210000e-12 82.4
14 TraesCS4A01G064000 chr2A 86.381 1564 181 22 996 2552 771538641 771540179 0.000000e+00 1679.0
15 TraesCS4A01G064000 chr2A 93.944 710 38 2 2779 3483 375926798 375926089 0.000000e+00 1068.0
16 TraesCS4A01G064000 chr2A 94.026 703 40 2 2781 3481 671930548 671931250 0.000000e+00 1064.0
17 TraesCS4A01G064000 chr2A 92.898 704 44 3 2781 3481 119765383 119764683 0.000000e+00 1018.0
18 TraesCS4A01G064000 chr2A 91.051 704 59 4 2781 3482 364038323 364039024 0.000000e+00 948.0
19 TraesCS4A01G064000 chr5A 93.892 704 42 1 2781 3483 386649992 386649289 0.000000e+00 1061.0
20 TraesCS4A01G064000 chr5A 90.832 709 62 2 2780 3485 237463826 237464534 0.000000e+00 946.0
21 TraesCS4A01G064000 chr7A 93.608 704 44 1 2779 3481 64440154 64439451 0.000000e+00 1050.0
22 TraesCS4A01G064000 chr7A 92.636 679 49 1 2804 3481 484466083 484466761 0.000000e+00 976.0
23 TraesCS4A01G064000 chr7A 85.774 478 65 3 208 683 64593716 64593240 1.480000e-138 503.0
24 TraesCS4A01G064000 chr7D 86.689 601 69 7 86 683 402316892 402316300 0.000000e+00 656.0
25 TraesCS4A01G064000 chr7D 86.201 616 65 8 86 683 170587347 170586734 0.000000e+00 649.0
26 TraesCS4A01G064000 chr2B 86.678 593 64 8 1123 1715 789672745 789673322 0.000000e+00 643.0
27 TraesCS4A01G064000 chr2B 89.600 250 23 1 2308 2554 789673367 789673616 7.430000e-82 315.0
28 TraesCS4A01G064000 chr3D 86.016 615 64 10 86 683 50542026 50542635 1.080000e-179 640.0
29 TraesCS4A01G064000 chr3D 78.700 554 96 17 1921 2468 438435684 438436221 2.040000e-92 350.0
30 TraesCS4A01G064000 chr3D 74.510 357 71 15 1253 1599 438438380 438438726 1.730000e-28 137.0
31 TraesCS4A01G064000 chr5D 87.956 548 49 10 86 628 510830269 510830804 6.500000e-177 630.0
32 TraesCS4A01G064000 chr3A 85.065 616 67 12 86 683 682247935 682248543 3.940000e-169 604.0
33 TraesCS4A01G064000 chr3A 77.978 554 97 22 1921 2468 576683173 576683707 1.230000e-84 324.0
34 TraesCS4A01G064000 chr3A 75.843 356 68 14 1253 1599 576682526 576682872 7.920000e-37 165.0
35 TraesCS4A01G064000 chr5B 84.288 611 69 10 91 683 263955316 263954715 3.990000e-159 571.0
36 TraesCS4A01G064000 chr5B 80.447 537 54 25 86 606 207154223 207153722 2.620000e-96 363.0
37 TraesCS4A01G064000 chr5B 88.660 291 16 3 86 360 493925804 493926093 4.410000e-89 339.0
38 TraesCS4A01G064000 chr5B 84.451 328 31 14 86 397 80676607 80676930 4.470000e-79 305.0
39 TraesCS4A01G064000 chr5B 84.146 328 32 5 86 397 80271818 80272141 2.080000e-77 300.0
40 TraesCS4A01G064000 chr5B 94.805 77 4 0 1 77 493925514 493925590 1.740000e-23 121.0
41 TraesCS4A01G064000 chr5B 88.732 71 8 0 1 71 222892791 222892861 1.760000e-13 87.9
42 TraesCS4A01G064000 chr3B 82.573 614 70 18 86 683 474004830 474005422 1.140000e-139 507.0
43 TraesCS4A01G064000 chrUn 92.208 77 6 0 1 77 100848195 100848119 3.760000e-20 110.0
44 TraesCS4A01G064000 chr1A 87.209 86 11 0 3 88 540751071 540750986 8.150000e-17 99.0
45 TraesCS4A01G064000 chr6D 100.000 41 0 0 1364 1404 267729391 267729351 3.820000e-10 76.8
46 TraesCS4A01G064000 chr6B 100.000 41 0 0 1364 1404 416101637 416101597 3.820000e-10 76.8
47 TraesCS4A01G064000 chr6A 100.000 41 0 0 1364 1404 381525988 381525948 3.820000e-10 76.8


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 TraesCS4A01G064000 chr4A 60878984 60882549 3565 False 6586.0 6586 100.0000 1 3566 1 chr4A.!!$F2 3565
1 TraesCS4A01G064000 chr4A 60730316 60732146 1830 False 2246.0 2246 89.0280 830 2642 1 chr4A.!!$F1 1812
2 TraesCS4A01G064000 chr4A 561152623 561153324 701 False 1064.0 1064 94.0260 2781 3482 1 chr4A.!!$F3 701
3 TraesCS4A01G064000 chr4D 403182029 403183818 1789 False 2172.0 2172 88.8640 880 2647 1 chr4D.!!$F1 1767
4 TraesCS4A01G064000 chr4D 403199476 403201633 2157 False 1527.0 2952 90.7835 711 3560 2 chr4D.!!$F2 2849
5 TraesCS4A01G064000 chr4B 500052646 500054477 1831 False 2274.0 2274 89.2510 830 2647 1 chr4B.!!$F1 1817
6 TraesCS4A01G064000 chr4B 500078957 500080927 1970 False 1479.0 2819 89.1015 766 2780 2 chr4B.!!$F2 2014
7 TraesCS4A01G064000 chr2D 645838270 645839714 1444 False 1701.0 1701 88.0850 1123 2558 1 chr2D.!!$F4 1435
8 TraesCS4A01G064000 chr2D 86524632 86525241 609 False 656.0 656 86.6230 91 683 1 chr2D.!!$F2 592
9 TraesCS4A01G064000 chr2D 7275957 7276568 611 False 630.0 630 85.6910 86 683 1 chr2D.!!$F1 597
10 TraesCS4A01G064000 chr2D 543290140 543290730 590 False 623.0 623 85.8330 91 683 1 chr2D.!!$F3 592
11 TraesCS4A01G064000 chr2A 771538641 771540179 1538 False 1679.0 1679 86.3810 996 2552 1 chr2A.!!$F3 1556
12 TraesCS4A01G064000 chr2A 375926089 375926798 709 True 1068.0 1068 93.9440 2779 3483 1 chr2A.!!$R2 704
13 TraesCS4A01G064000 chr2A 671930548 671931250 702 False 1064.0 1064 94.0260 2781 3481 1 chr2A.!!$F2 700
14 TraesCS4A01G064000 chr2A 119764683 119765383 700 True 1018.0 1018 92.8980 2781 3481 1 chr2A.!!$R1 700
15 TraesCS4A01G064000 chr2A 364038323 364039024 701 False 948.0 948 91.0510 2781 3482 1 chr2A.!!$F1 701
16 TraesCS4A01G064000 chr5A 386649289 386649992 703 True 1061.0 1061 93.8920 2781 3483 1 chr5A.!!$R1 702
17 TraesCS4A01G064000 chr5A 237463826 237464534 708 False 946.0 946 90.8320 2780 3485 1 chr5A.!!$F1 705
18 TraesCS4A01G064000 chr7A 64439451 64440154 703 True 1050.0 1050 93.6080 2779 3481 1 chr7A.!!$R1 702
19 TraesCS4A01G064000 chr7A 484466083 484466761 678 False 976.0 976 92.6360 2804 3481 1 chr7A.!!$F1 677
20 TraesCS4A01G064000 chr7D 402316300 402316892 592 True 656.0 656 86.6890 86 683 1 chr7D.!!$R2 597
21 TraesCS4A01G064000 chr7D 170586734 170587347 613 True 649.0 649 86.2010 86 683 1 chr7D.!!$R1 597
22 TraesCS4A01G064000 chr2B 789672745 789673616 871 False 479.0 643 88.1390 1123 2554 2 chr2B.!!$F1 1431
23 TraesCS4A01G064000 chr3D 50542026 50542635 609 False 640.0 640 86.0160 86 683 1 chr3D.!!$F1 597
24 TraesCS4A01G064000 chr3D 438435684 438438726 3042 False 243.5 350 76.6050 1253 2468 2 chr3D.!!$F2 1215
25 TraesCS4A01G064000 chr5D 510830269 510830804 535 False 630.0 630 87.9560 86 628 1 chr5D.!!$F1 542
26 TraesCS4A01G064000 chr3A 682247935 682248543 608 False 604.0 604 85.0650 86 683 1 chr3A.!!$F1 597
27 TraesCS4A01G064000 chr3A 576682526 576683707 1181 False 244.5 324 76.9105 1253 2468 2 chr3A.!!$F2 1215
28 TraesCS4A01G064000 chr5B 263954715 263955316 601 True 571.0 571 84.2880 91 683 1 chr5B.!!$R2 592
29 TraesCS4A01G064000 chr5B 207153722 207154223 501 True 363.0 363 80.4470 86 606 1 chr5B.!!$R1 520
30 TraesCS4A01G064000 chr5B 493925514 493926093 579 False 230.0 339 91.7325 1 360 2 chr5B.!!$F4 359
31 TraesCS4A01G064000 chr3B 474004830 474005422 592 False 507.0 507 82.5730 86 683 1 chr3B.!!$F1 597

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
54 55 0.039437 TTCAAGCACGAGGAGACGAC 60.039 55.0 0.00 0.0 37.03 4.34 F
608 888 0.041663 CGCCGATTCAAACACAACGT 60.042 50.0 0.00 0.0 0.00 3.99 F
761 1043 0.109597 GCAGTTCAGTGGAAATGGCG 60.110 55.0 6.96 0.0 46.32 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1022 1346 0.032815 GAGCGGTATCAGGAGGAAGC 59.967 60.0 0.00 0.0 0.0 3.86 R
1777 2167 1.585267 ATGGCAATTGACTCGCGCAA 61.585 50.0 13.62 0.0 0.0 4.85 R
2716 3137 0.734889 CTGTGTTTCCGATCATGGGC 59.265 55.0 0.00 0.0 0.0 5.36 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
19 20 2.649034 GTCGACTCGCCCAACTGA 59.351 61.111 8.70 0.00 0.00 3.41
50 51 1.293498 GCCTTCAAGCACGAGGAGA 59.707 57.895 0.00 0.00 32.11 3.71
54 55 0.039437 TTCAAGCACGAGGAGACGAC 60.039 55.000 0.00 0.00 37.03 4.34
195 400 2.344203 CGACGGAGAAGCAGGAGGT 61.344 63.158 0.00 0.00 0.00 3.85
212 418 2.682494 TGGCCTACCTCGACCACC 60.682 66.667 3.32 0.00 36.63 4.61
262 501 2.354422 CAGATGCTCGAGCGCGAT 60.354 61.111 30.75 19.75 46.80 4.58
376 631 0.888619 GACACTGATCGACCTCACCA 59.111 55.000 0.00 0.00 0.00 4.17
427 682 3.813596 CCTAGGGCAACACATCGC 58.186 61.111 0.00 0.00 39.74 4.58
443 705 7.034685 ACACATCGCCTAGTTTTTAGTTTTT 57.965 32.000 0.00 0.00 0.00 1.94
474 750 7.391148 AATTAATGTAATGTGGACTTTCGCT 57.609 32.000 0.00 0.00 0.00 4.93
573 850 2.359900 GTCGACAAAATGGATCAGGCT 58.640 47.619 11.55 0.00 0.00 4.58
580 857 3.838244 AAATGGATCAGGCTAGCGTTA 57.162 42.857 7.31 0.00 0.00 3.18
608 888 0.041663 CGCCGATTCAAACACAACGT 60.042 50.000 0.00 0.00 0.00 3.99
629 909 2.240230 GACATTTGTGTCCGCCGAA 58.760 52.632 0.00 0.00 32.97 4.30
630 910 0.802494 GACATTTGTGTCCGCCGAAT 59.198 50.000 0.00 0.00 32.97 3.34
641 921 1.519751 CCGCCGAATTGACCCAAACA 61.520 55.000 0.00 0.00 0.00 2.83
673 955 4.033817 ACGAACAAAAACGTCGTCCATTTA 59.966 37.500 0.00 0.00 38.34 1.40
684 966 0.179054 GTCCATTTAGGTCGGCCCTC 60.179 60.000 0.08 0.00 44.81 4.30
685 967 0.326238 TCCATTTAGGTCGGCCCTCT 60.326 55.000 0.08 0.00 44.81 3.69
686 968 1.062734 TCCATTTAGGTCGGCCCTCTA 60.063 52.381 0.08 0.00 44.81 2.43
687 969 1.766496 CCATTTAGGTCGGCCCTCTAA 59.234 52.381 0.08 0.00 44.81 2.10
688 970 2.171870 CCATTTAGGTCGGCCCTCTAAA 59.828 50.000 16.91 16.91 44.81 1.85
689 971 3.203716 CATTTAGGTCGGCCCTCTAAAC 58.796 50.000 16.93 0.00 44.81 2.01
690 972 0.819582 TTAGGTCGGCCCTCTAAACG 59.180 55.000 0.08 0.00 44.81 3.60
691 973 0.323725 TAGGTCGGCCCTCTAAACGT 60.324 55.000 0.08 0.00 44.81 3.99
692 974 1.153686 GGTCGGCCCTCTAAACGTC 60.154 63.158 0.00 0.00 0.00 4.34
693 975 1.153686 GTCGGCCCTCTAAACGTCC 60.154 63.158 0.00 0.00 0.00 4.79
694 976 1.607178 TCGGCCCTCTAAACGTCCA 60.607 57.895 0.00 0.00 0.00 4.02
695 977 1.153628 CGGCCCTCTAAACGTCCAG 60.154 63.158 0.00 0.00 0.00 3.86
696 978 1.885163 CGGCCCTCTAAACGTCCAGT 61.885 60.000 0.00 0.00 0.00 4.00
697 979 0.391263 GGCCCTCTAAACGTCCAGTG 60.391 60.000 0.00 0.00 0.00 3.66
698 980 0.320697 GCCCTCTAAACGTCCAGTGT 59.679 55.000 0.00 0.00 0.00 3.55
699 981 1.270678 GCCCTCTAAACGTCCAGTGTT 60.271 52.381 0.00 0.00 0.00 3.32
700 982 2.413837 CCCTCTAAACGTCCAGTGTTG 58.586 52.381 0.00 0.00 0.00 3.33
701 983 2.036733 CCCTCTAAACGTCCAGTGTTGA 59.963 50.000 0.00 0.00 0.00 3.18
702 984 3.318017 CCTCTAAACGTCCAGTGTTGAG 58.682 50.000 0.00 0.00 38.92 3.02
703 985 3.005472 CCTCTAAACGTCCAGTGTTGAGA 59.995 47.826 0.00 0.00 40.79 3.27
704 986 4.230657 CTCTAAACGTCCAGTGTTGAGAG 58.769 47.826 5.98 5.98 44.47 3.20
705 987 2.981859 AAACGTCCAGTGTTGAGAGT 57.018 45.000 0.00 0.00 0.00 3.24
706 988 2.981859 AACGTCCAGTGTTGAGAGTT 57.018 45.000 0.00 0.00 0.00 3.01
707 989 2.225068 ACGTCCAGTGTTGAGAGTTG 57.775 50.000 0.00 0.00 0.00 3.16
708 990 1.754803 ACGTCCAGTGTTGAGAGTTGA 59.245 47.619 0.00 0.00 0.00 3.18
709 991 2.223829 ACGTCCAGTGTTGAGAGTTGAG 60.224 50.000 0.00 0.00 0.00 3.02
721 1003 7.064016 GTGTTGAGAGTTGAGACAAATATCTCC 59.936 40.741 7.75 0.97 43.94 3.71
722 1004 7.038729 TGTTGAGAGTTGAGACAAATATCTCCT 60.039 37.037 7.75 0.00 43.94 3.69
725 1007 5.068460 AGAGTTGAGACAAATATCTCCTCCG 59.932 44.000 0.53 0.00 43.94 4.63
731 1013 3.231818 ACAAATATCTCCTCCGATCCGT 58.768 45.455 0.00 0.00 0.00 4.69
761 1043 0.109597 GCAGTTCAGTGGAAATGGCG 60.110 55.000 6.96 0.00 46.32 5.69
764 1046 1.228398 TTCAGTGGAAATGGCGGCA 60.228 52.632 16.34 16.34 29.44 5.69
773 1055 0.451783 AAATGGCGGCAGATTCGTTC 59.548 50.000 19.29 0.00 0.00 3.95
792 1074 3.405823 TCCGTACGAAGTTCCCATTTT 57.594 42.857 18.76 0.00 37.78 1.82
794 1076 2.809696 CCGTACGAAGTTCCCATTTTGT 59.190 45.455 18.76 0.00 37.78 2.83
795 1077 3.995705 CCGTACGAAGTTCCCATTTTGTA 59.004 43.478 18.76 0.00 37.78 2.41
796 1078 4.632688 CCGTACGAAGTTCCCATTTTGTAT 59.367 41.667 18.76 0.00 37.78 2.29
801 1091 6.646267 ACGAAGTTCCCATTTTGTATAGCTA 58.354 36.000 0.00 0.00 37.78 3.32
856 1146 3.314331 CTCACCAGTGGCGGAGGT 61.314 66.667 19.18 0.00 35.65 3.85
959 1275 3.031013 CAAACCATGGAGATAAACCCCC 58.969 50.000 21.47 0.00 0.00 5.40
1020 1344 4.487412 GCAATCGCACTGGCAGCC 62.487 66.667 15.89 3.66 41.24 4.85
1021 1345 2.749044 CAATCGCACTGGCAGCCT 60.749 61.111 15.89 0.00 41.24 4.58
1022 1346 2.749044 AATCGCACTGGCAGCCTG 60.749 61.111 15.89 16.57 41.24 4.85
1999 2398 0.109342 CACCTGGTTCTTCTGGCTGT 59.891 55.000 0.00 0.00 0.00 4.40
2472 2885 1.517475 GGAAGAGTTCGAGCTCGCC 60.517 63.158 30.97 22.23 40.26 5.54
2569 2985 6.039616 GTGAAGGCTAGAGTGAATTGAGTAG 58.960 44.000 0.00 0.00 0.00 2.57
2570 2986 5.717178 TGAAGGCTAGAGTGAATTGAGTAGT 59.283 40.000 0.00 0.00 0.00 2.73
2653 3069 8.324306 AGTGAGTGAAAGATGAATTCCAGAATA 58.676 33.333 2.27 0.00 0.00 1.75
2654 3070 8.394121 GTGAGTGAAAGATGAATTCCAGAATAC 58.606 37.037 2.27 0.00 0.00 1.89
2657 3073 7.065085 AGTGAAAGATGAATTCCAGAATACACG 59.935 37.037 2.27 0.00 0.00 4.49
2662 3078 5.895636 TGAATTCCAGAATACACGCAATT 57.104 34.783 2.27 0.00 0.00 2.32
2693 3113 7.613551 TTCTTAGGAGAGTGGTTTTTCTACT 57.386 36.000 0.00 0.00 40.54 2.57
2705 3125 3.328382 TTTTCTACTCCCACGGACATG 57.672 47.619 0.00 0.00 0.00 3.21
2733 3154 1.721487 CGCCCATGATCGGAAACAC 59.279 57.895 0.00 0.00 0.00 3.32
2771 3200 5.893897 AGAATCTGAAACTTGATGGCTTC 57.106 39.130 0.00 0.00 0.00 3.86
2772 3201 5.319453 AGAATCTGAAACTTGATGGCTTCA 58.681 37.500 0.00 0.00 0.00 3.02
2773 3202 5.950549 AGAATCTGAAACTTGATGGCTTCAT 59.049 36.000 3.72 0.00 33.34 2.57
2774 3203 6.436532 AGAATCTGAAACTTGATGGCTTCATT 59.563 34.615 3.72 0.00 33.34 2.57
2775 3204 7.613022 AGAATCTGAAACTTGATGGCTTCATTA 59.387 33.333 3.72 0.00 33.34 1.90
2776 3205 7.893124 ATCTGAAACTTGATGGCTTCATTAT 57.107 32.000 3.72 0.00 33.34 1.28
2777 3206 7.092137 TCTGAAACTTGATGGCTTCATTATG 57.908 36.000 3.72 0.00 33.34 1.90
2788 3217 6.499106 TGGCTTCATTATGACTAAGGATGA 57.501 37.500 0.00 0.00 28.59 2.92
2800 3229 3.591527 ACTAAGGATGACAATGGGTTGGA 59.408 43.478 0.00 0.00 39.70 3.53
2811 3240 0.701731 TGGGTTGGATTTGGATCGGT 59.298 50.000 0.00 0.00 32.84 4.69
2864 3293 2.032681 GACTGTCTTTGCCCGCCT 59.967 61.111 0.00 0.00 0.00 5.52
2906 3337 5.453198 GGAAAATTGTGTCCATGTCCAAACT 60.453 40.000 0.00 0.00 33.79 2.66
2947 3378 1.293763 TGGATATCCACTGGGTCCTCA 59.706 52.381 20.98 0.00 42.01 3.86
3001 3432 4.664688 AACATGAGGTCCTCCATTCTTT 57.335 40.909 16.60 0.00 35.89 2.52
3432 5709 1.999295 TCCAAACCCCATCCATTCAGA 59.001 47.619 0.00 0.00 0.00 3.27
3532 5809 5.913137 AAATTTCGAGGCCAAATGACATA 57.087 34.783 5.01 0.00 0.00 2.29
3533 5810 6.469782 AAATTTCGAGGCCAAATGACATAT 57.530 33.333 5.01 0.00 0.00 1.78
3544 5821 5.591877 GCCAAATGACATATGAGGAGTTCTT 59.408 40.000 10.38 0.00 0.00 2.52
3546 5823 7.283127 GCCAAATGACATATGAGGAGTTCTTTA 59.717 37.037 10.38 0.00 0.00 1.85
3547 5824 9.177608 CCAAATGACATATGAGGAGTTCTTTAA 57.822 33.333 10.38 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 3.847602 CCAGCTCCTCCGGCTCAG 61.848 72.222 0.00 0.00 38.03 3.35
195 400 2.682494 GGTGGTCGAGGTAGGCCA 60.682 66.667 5.01 0.00 44.73 5.36
262 501 2.668212 CACGCCTCCTTTTCGGCA 60.668 61.111 0.00 0.00 46.62 5.69
360 615 1.608717 GGCTGGTGAGGTCGATCAGT 61.609 60.000 0.00 0.00 0.00 3.41
397 652 0.541863 CCCTAGGCGTCCTTGTCATT 59.458 55.000 2.05 0.00 34.61 2.57
398 653 1.972660 GCCCTAGGCGTCCTTGTCAT 61.973 60.000 2.05 0.00 39.62 3.06
399 654 2.656069 GCCCTAGGCGTCCTTGTCA 61.656 63.158 2.05 0.00 39.62 3.58
447 709 9.006215 GCGAAAGTCCACATTACATTAATTAAC 57.994 33.333 0.00 0.00 0.00 2.01
551 828 2.616960 CCTGATCCATTTTGTCGACGA 58.383 47.619 11.62 6.16 0.00 4.20
596 873 1.942677 ATGTCCGACGTTGTGTTTGA 58.057 45.000 1.30 0.00 0.00 2.69
653 935 4.336153 ACCTAAATGGACGACGTTTTTGTT 59.664 37.500 0.13 0.00 39.05 2.83
683 965 3.635373 ACTCTCAACACTGGACGTTTAGA 59.365 43.478 6.96 0.00 0.00 2.10
684 966 3.978687 ACTCTCAACACTGGACGTTTAG 58.021 45.455 0.00 0.00 0.00 1.85
685 967 4.116961 CAACTCTCAACACTGGACGTTTA 58.883 43.478 0.00 0.00 0.00 2.01
686 968 2.936498 CAACTCTCAACACTGGACGTTT 59.064 45.455 0.00 0.00 0.00 3.60
687 969 2.167693 TCAACTCTCAACACTGGACGTT 59.832 45.455 0.00 0.00 0.00 3.99
688 970 1.754803 TCAACTCTCAACACTGGACGT 59.245 47.619 0.00 0.00 0.00 4.34
689 971 2.034685 TCTCAACTCTCAACACTGGACG 59.965 50.000 0.00 0.00 0.00 4.79
690 972 3.181475 TGTCTCAACTCTCAACACTGGAC 60.181 47.826 0.00 0.00 0.00 4.02
691 973 3.031013 TGTCTCAACTCTCAACACTGGA 58.969 45.455 0.00 0.00 0.00 3.86
692 974 3.459232 TGTCTCAACTCTCAACACTGG 57.541 47.619 0.00 0.00 0.00 4.00
693 975 5.998454 ATTTGTCTCAACTCTCAACACTG 57.002 39.130 0.00 0.00 0.00 3.66
694 976 7.675062 AGATATTTGTCTCAACTCTCAACACT 58.325 34.615 0.00 0.00 0.00 3.55
695 977 7.064016 GGAGATATTTGTCTCAACTCTCAACAC 59.936 40.741 6.65 0.00 45.12 3.32
696 978 7.038729 AGGAGATATTTGTCTCAACTCTCAACA 60.039 37.037 6.65 0.00 45.12 3.33
697 979 7.327214 AGGAGATATTTGTCTCAACTCTCAAC 58.673 38.462 6.65 0.00 45.12 3.18
698 980 7.364232 GGAGGAGATATTTGTCTCAACTCTCAA 60.364 40.741 6.65 0.00 45.12 3.02
699 981 6.097554 GGAGGAGATATTTGTCTCAACTCTCA 59.902 42.308 6.65 0.00 45.12 3.27
700 982 6.512297 GGAGGAGATATTTGTCTCAACTCTC 58.488 44.000 6.65 4.08 45.12 3.20
701 983 5.068460 CGGAGGAGATATTTGTCTCAACTCT 59.932 44.000 6.65 0.00 45.12 3.24
702 984 5.067936 TCGGAGGAGATATTTGTCTCAACTC 59.932 44.000 6.65 4.93 45.12 3.01
703 985 4.956700 TCGGAGGAGATATTTGTCTCAACT 59.043 41.667 6.65 0.00 45.12 3.16
704 986 5.263968 TCGGAGGAGATATTTGTCTCAAC 57.736 43.478 6.65 0.78 45.12 3.18
705 987 5.011125 GGATCGGAGGAGATATTTGTCTCAA 59.989 44.000 6.65 0.00 45.12 3.02
706 988 4.524714 GGATCGGAGGAGATATTTGTCTCA 59.475 45.833 6.65 0.00 45.12 3.27
707 989 4.380023 CGGATCGGAGGAGATATTTGTCTC 60.380 50.000 0.00 0.00 43.10 3.36
708 990 3.508012 CGGATCGGAGGAGATATTTGTCT 59.492 47.826 0.00 0.00 0.00 3.41
709 991 3.256136 ACGGATCGGAGGAGATATTTGTC 59.744 47.826 7.35 0.00 0.00 3.18
731 1013 1.269569 ACTGAACTGCGTCACATTCGA 60.270 47.619 0.00 0.00 0.00 3.71
743 1025 0.523072 CCGCCATTTCCACTGAACTG 59.477 55.000 0.00 0.00 32.52 3.16
751 1033 1.375853 CGAATCTGCCGCCATTTCCA 61.376 55.000 0.00 0.00 0.00 3.53
757 1039 2.435938 GGAACGAATCTGCCGCCA 60.436 61.111 0.00 0.00 0.00 5.69
773 1055 2.809696 ACAAAATGGGAACTTCGTACGG 59.190 45.455 16.52 2.32 0.00 4.02
856 1146 2.429930 CCGGTTGGTCTGGAAGCA 59.570 61.111 0.00 0.00 45.09 3.91
890 1192 5.798419 AGATAAGGGAGAGGAGGAAAAGAT 58.202 41.667 0.00 0.00 0.00 2.40
959 1275 0.538118 TACCGTGGGAGGAAATTCGG 59.462 55.000 0.00 0.00 42.94 4.30
1020 1344 0.249657 GCGGTATCAGGAGGAAGCAG 60.250 60.000 0.00 0.00 0.00 4.24
1021 1345 0.687757 AGCGGTATCAGGAGGAAGCA 60.688 55.000 0.00 0.00 0.00 3.91
1022 1346 0.032815 GAGCGGTATCAGGAGGAAGC 59.967 60.000 0.00 0.00 0.00 3.86
1140 1488 3.560251 AGGAACTGCGGCAGGTGT 61.560 61.111 31.38 17.48 37.18 4.16
1777 2167 1.585267 ATGGCAATTGACTCGCGCAA 61.585 50.000 13.62 0.00 0.00 4.85
1929 2328 3.027412 GAGGAGGAAGCTGATCACTACA 58.973 50.000 0.00 0.00 0.00 2.74
2569 2985 3.604875 TTTCCCTCCATCTTGTCGTAC 57.395 47.619 0.00 0.00 0.00 3.67
2570 2986 4.837093 AATTTCCCTCCATCTTGTCGTA 57.163 40.909 0.00 0.00 0.00 3.43
2612 3028 7.392494 TTCACTCACTGACGTTCTTCTATAT 57.608 36.000 0.00 0.00 0.00 0.86
2653 3069 5.298276 TCCTAAGAAAAAGACAATTGCGTGT 59.702 36.000 5.05 0.00 0.00 4.49
2654 3070 5.757886 TCCTAAGAAAAAGACAATTGCGTG 58.242 37.500 5.05 0.00 0.00 5.34
2657 3073 7.080724 CACTCTCCTAAGAAAAAGACAATTGC 58.919 38.462 5.05 0.00 0.00 3.56
2662 3078 5.888982 ACCACTCTCCTAAGAAAAAGACA 57.111 39.130 0.00 0.00 0.00 3.41
2693 3113 4.028490 GGTGCCATGTCCGTGGGA 62.028 66.667 7.61 1.53 39.73 4.37
2716 3137 0.734889 CTGTGTTTCCGATCATGGGC 59.265 55.000 0.00 0.00 0.00 5.36
2742 3165 6.585322 CCATCAAGTTTCAGATTCTTTTGAGC 59.415 38.462 0.00 0.00 0.00 4.26
2750 3179 5.633830 TGAAGCCATCAAGTTTCAGATTC 57.366 39.130 0.00 0.00 34.30 2.52
2751 3180 6.600882 AATGAAGCCATCAAGTTTCAGATT 57.399 33.333 0.00 0.00 42.54 2.40
2771 3200 7.000472 ACCCATTGTCATCCTTAGTCATAATG 59.000 38.462 0.00 0.00 0.00 1.90
2772 3201 7.154191 ACCCATTGTCATCCTTAGTCATAAT 57.846 36.000 0.00 0.00 0.00 1.28
2773 3202 6.575244 ACCCATTGTCATCCTTAGTCATAA 57.425 37.500 0.00 0.00 0.00 1.90
2774 3203 6.356556 CAACCCATTGTCATCCTTAGTCATA 58.643 40.000 0.00 0.00 0.00 2.15
2775 3204 5.195940 CAACCCATTGTCATCCTTAGTCAT 58.804 41.667 0.00 0.00 0.00 3.06
2776 3205 4.567537 CCAACCCATTGTCATCCTTAGTCA 60.568 45.833 0.00 0.00 33.60 3.41
2777 3206 3.947834 CCAACCCATTGTCATCCTTAGTC 59.052 47.826 0.00 0.00 33.60 2.59
2788 3217 2.760092 CGATCCAAATCCAACCCATTGT 59.240 45.455 0.00 0.00 33.60 2.71
2800 3229 7.403312 TGATATTGTTCAAACCGATCCAAAT 57.597 32.000 0.00 0.00 0.00 2.32
2834 3263 6.767902 GGCAAAGACAGTCTTTATGGATATGA 59.232 38.462 25.13 0.00 44.23 2.15
2844 3273 1.172812 GGCGGGCAAAGACAGTCTTT 61.173 55.000 21.03 21.03 46.75 2.52
2878 3307 2.158173 ACATGGACACAATTTTCCCCCT 60.158 45.455 0.00 0.00 0.00 4.79
2882 3312 4.599047 TTGGACATGGACACAATTTTCC 57.401 40.909 0.00 0.00 0.00 3.13
2906 3337 3.038280 AGTGGGTATGAACATCCATCGA 58.962 45.455 0.00 0.00 0.00 3.59
2915 3346 4.974645 TGGATATCCAGTGGGTATGAAC 57.025 45.455 20.06 10.02 42.01 3.18
2978 3409 4.762289 AGAATGGAGGACCTCATGTTAC 57.238 45.455 23.06 5.09 37.04 2.50
3001 3432 2.363795 CTCCCCTGCCACGAGGTA 60.364 66.667 0.00 0.00 37.19 3.08
3154 3602 4.468765 TTCAATCCCCGTCGTAACATAA 57.531 40.909 0.00 0.00 0.00 1.90
3399 5676 3.260632 GGGGTTTGGATATGCTTTTGTGT 59.739 43.478 0.00 0.00 0.00 3.72
3432 5709 4.007581 TGGATACCCATGGATATCCGAT 57.992 45.455 32.06 0.00 46.86 4.18


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

AutoCloner maintained by Alex Coulton.