Multiple sequence alignment - TraesCS2A01G003300

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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 TraesCS2A01G003300 chr2A 100.000 2972 0 0 1 2972 2261928 2258957 0.000000e+00 5489.0
1 TraesCS2A01G003300 chr2A 98.930 2244 15 3 738 2972 2219055 2216812 0.000000e+00 4002.0
2 TraesCS2A01G003300 chr2A 99.130 460 4 0 115 574 2219503 2219044 0.000000e+00 828.0
3 TraesCS2A01G003300 chr2A 80.403 944 174 9 1041 1978 2876791 2877729 0.000000e+00 708.0
4 TraesCS2A01G003300 chr2A 82.787 366 63 0 208 573 1883809 1884174 7.940000e-86 327.0
5 TraesCS2A01G003300 chr2A 98.246 171 2 1 573 743 111432902 111432733 6.230000e-77 298.0
6 TraesCS2A01G003300 chr2B 80.234 941 180 4 1041 1977 9198466 9197528 0.000000e+00 702.0
7 TraesCS2A01G003300 chr2B 80.126 951 171 14 1035 1978 31048427 31049366 0.000000e+00 693.0
8 TraesCS2A01G003300 chr2B 79.958 958 158 19 1049 1983 477814 478760 0.000000e+00 675.0
9 TraesCS2A01G003300 chr2B 81.596 777 129 11 1208 1983 64731 65494 5.410000e-177 630.0
10 TraesCS2A01G003300 chr2B 82.921 404 68 1 171 573 6827355 6826952 2.180000e-96 363.0
11 TraesCS2A01G003300 chr2B 82.673 404 69 1 171 573 6779377 6778974 1.010000e-94 357.0
12 TraesCS2A01G003300 chr2B 82.673 404 69 1 171 573 6914817 6914414 1.010000e-94 357.0
13 TraesCS2A01G003300 chr2B 82.164 342 57 4 2048 2386 481052345 481052005 1.040000e-74 291.0
14 TraesCS2A01G003300 chr2B 81.455 275 51 0 743 1017 9198718 9198444 2.980000e-55 226.0
15 TraesCS2A01G003300 chr2B 78.149 389 58 14 2001 2386 15418378 15418742 3.860000e-54 222.0
16 TraesCS2A01G003300 chr2B 77.492 311 63 5 2045 2351 105478779 105479086 2.350000e-41 180.0
17 TraesCS2A01G003300 chr2B 79.144 187 30 8 567 749 94166342 94166161 1.450000e-23 121.0
18 TraesCS2A01G003300 chrUn 79.957 938 184 2 1035 1970 15865524 15866459 0.000000e+00 688.0
19 TraesCS2A01G003300 chrUn 80.052 772 152 2 1035 1805 15759862 15759092 3.320000e-159 571.0
20 TraesCS2A01G003300 chrUn 83.240 358 59 1 171 527 339338646 339338289 7.940000e-86 327.0
21 TraesCS2A01G003300 chrUn 85.015 327 41 5 255 574 15864958 15865283 2.860000e-85 326.0
22 TraesCS2A01G003300 chrUn 98.830 171 1 1 572 741 74769938 74769768 1.340000e-78 303.0
23 TraesCS2A01G003300 chr2D 79.894 940 185 2 1041 1978 2511675 2510738 0.000000e+00 686.0
24 TraesCS2A01G003300 chr2D 84.049 326 44 6 255 573 7588435 7588111 1.030000e-79 307.0
25 TraesCS2A01G003300 chr2D 84.227 317 42 5 255 564 2512247 2511932 4.810000e-78 302.0
26 TraesCS2A01G003300 chr2D 79.747 395 68 12 1999 2386 405419766 405419377 2.920000e-70 276.0
27 TraesCS2A01G003300 chr3D 90.845 284 26 0 2689 2972 573140809 573140526 6.010000e-102 381.0
28 TraesCS2A01G003300 chr6B 90.493 284 26 1 2689 2972 74763406 74763688 1.010000e-99 374.0
29 TraesCS2A01G003300 chr3B 89.362 282 30 0 2691 2972 612717512 612717793 3.640000e-94 355.0
30 TraesCS2A01G003300 chr3B 81.356 177 26 6 573 746 228805411 228805239 1.440000e-28 137.0
31 TraesCS2A01G003300 chr5A 97.826 184 4 0 568 751 702454491 702454308 4.780000e-83 318.0
32 TraesCS2A01G003300 chr5A 81.235 405 57 11 1999 2386 445152514 445152916 2.880000e-80 309.0
33 TraesCS2A01G003300 chr5A 97.238 181 3 2 567 746 492636192 492636013 3.720000e-79 305.0
34 TraesCS2A01G003300 chr4A 98.876 178 2 0 564 741 445074538 445074715 4.780000e-83 318.0
35 TraesCS2A01G003300 chr4A 83.784 185 23 7 563 744 556631201 556631381 5.090000e-38 169.0
36 TraesCS2A01G003300 chr5D 100.000 171 0 0 569 739 493835324 493835494 1.720000e-82 316.0
37 TraesCS2A01G003300 chr5D 100.000 170 0 0 571 740 451571695 451571526 6.180000e-82 315.0
38 TraesCS2A01G003300 chr6D 97.802 182 3 1 567 747 455497378 455497559 2.220000e-81 313.0
39 TraesCS2A01G003300 chr1D 99.419 172 1 0 568 739 469836085 469836256 2.220000e-81 313.0
40 TraesCS2A01G003300 chr1D 99.422 173 0 1 568 740 475110999 475111170 2.220000e-81 313.0
41 TraesCS2A01G003300 chr5B 78.497 386 71 10 2014 2395 678489282 678488905 2.960000e-60 243.0
42 TraesCS2A01G003300 chr7B 78.386 347 65 10 2048 2386 681738754 681739098 1.790000e-52 217.0
43 TraesCS2A01G003300 chr7B 78.485 330 58 10 2025 2349 121502330 121502009 1.400000e-48 204.0
44 TraesCS2A01G003300 chr3A 92.188 64 4 1 680 743 671287603 671287541 4.080000e-14 89.8


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 TraesCS2A01G003300 chr2A 2258957 2261928 2971 True 5489 5489 100.0000 1 2972 1 chr2A.!!$R1 2971
1 TraesCS2A01G003300 chr2A 2216812 2219503 2691 True 2415 4002 99.0300 115 2972 2 chr2A.!!$R3 2857
2 TraesCS2A01G003300 chr2A 2876791 2877729 938 False 708 708 80.4030 1041 1978 1 chr2A.!!$F2 937
3 TraesCS2A01G003300 chr2B 31048427 31049366 939 False 693 693 80.1260 1035 1978 1 chr2B.!!$F4 943
4 TraesCS2A01G003300 chr2B 477814 478760 946 False 675 675 79.9580 1049 1983 1 chr2B.!!$F2 934
5 TraesCS2A01G003300 chr2B 64731 65494 763 False 630 630 81.5960 1208 1983 1 chr2B.!!$F1 775
6 TraesCS2A01G003300 chr2B 9197528 9198718 1190 True 464 702 80.8445 743 1977 2 chr2B.!!$R6 1234
7 TraesCS2A01G003300 chrUn 15759092 15759862 770 True 571 571 80.0520 1035 1805 1 chrUn.!!$R1 770
8 TraesCS2A01G003300 chrUn 15864958 15866459 1501 False 507 688 82.4860 255 1970 2 chrUn.!!$F1 1715
9 TraesCS2A01G003300 chr2D 2510738 2512247 1509 True 494 686 82.0605 255 1978 2 chr2D.!!$R3 1723

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
80 81 0.032416 TACCAGTCTACCAGAGGGGC 60.032 60.0 0.00 0.0 42.05 5.80 F
598 605 0.107214 GTAGCTAGCCCAACATGCCA 60.107 55.0 12.13 0.0 0.00 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1560 1589 0.251165 GTGGTGCAGGTGGGTACAAT 60.251 55.000 0.0 0.0 0.0 2.71 R
2028 2057 6.017109 GCAAACTGAACAAACAAGATAGAGGA 60.017 38.462 0.0 0.0 0.0 3.71 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 3.135457 TGTGATAGGCGCCGACGA 61.135 61.111 23.20 8.45 43.93 4.20
18 19 2.335369 GTGATAGGCGCCGACGAT 59.665 61.111 23.20 13.40 43.93 3.73
19 20 2.016704 GTGATAGGCGCCGACGATG 61.017 63.158 23.20 0.00 43.93 3.84
20 21 2.430921 GATAGGCGCCGACGATGG 60.431 66.667 23.20 0.00 43.93 3.51
28 29 3.786101 CCGACGATGGCAGTCTTG 58.214 61.111 0.00 0.00 36.53 3.02
37 38 3.741476 GCAGTCTTGCTTGCCCGG 61.741 66.667 0.00 0.00 46.95 5.73
38 39 2.032528 CAGTCTTGCTTGCCCGGA 59.967 61.111 0.73 0.00 0.00 5.14
39 40 1.600636 CAGTCTTGCTTGCCCGGAA 60.601 57.895 0.73 0.00 0.00 4.30
40 41 1.150536 AGTCTTGCTTGCCCGGAAA 59.849 52.632 0.73 0.00 0.00 3.13
41 42 0.251341 AGTCTTGCTTGCCCGGAAAT 60.251 50.000 0.73 0.00 0.00 2.17
42 43 0.603065 GTCTTGCTTGCCCGGAAATT 59.397 50.000 0.73 0.00 0.00 1.82
43 44 1.816224 GTCTTGCTTGCCCGGAAATTA 59.184 47.619 0.73 0.00 0.00 1.40
44 45 2.230266 GTCTTGCTTGCCCGGAAATTAA 59.770 45.455 0.73 0.00 0.00 1.40
45 46 3.096092 TCTTGCTTGCCCGGAAATTAAT 58.904 40.909 0.73 0.00 0.00 1.40
46 47 4.097286 GTCTTGCTTGCCCGGAAATTAATA 59.903 41.667 0.73 0.00 0.00 0.98
47 48 4.892934 TCTTGCTTGCCCGGAAATTAATAT 59.107 37.500 0.73 0.00 0.00 1.28
48 49 4.846779 TGCTTGCCCGGAAATTAATATC 57.153 40.909 0.73 0.00 0.00 1.63
49 50 3.252215 TGCTTGCCCGGAAATTAATATCG 59.748 43.478 0.73 0.00 0.00 2.92
50 51 3.500680 GCTTGCCCGGAAATTAATATCGA 59.499 43.478 0.73 0.00 0.00 3.59
51 52 4.156008 GCTTGCCCGGAAATTAATATCGAT 59.844 41.667 0.73 2.16 0.00 3.59
52 53 5.621197 TTGCCCGGAAATTAATATCGATG 57.379 39.130 8.54 0.00 0.00 3.84
53 54 4.006989 TGCCCGGAAATTAATATCGATGG 58.993 43.478 8.54 0.00 0.00 3.51
54 55 4.007659 GCCCGGAAATTAATATCGATGGT 58.992 43.478 8.54 0.00 0.00 3.55
55 56 5.180271 GCCCGGAAATTAATATCGATGGTA 58.820 41.667 8.54 0.00 0.00 3.25
56 57 5.293569 GCCCGGAAATTAATATCGATGGTAG 59.706 44.000 8.54 0.00 0.00 3.18
57 58 6.403878 CCCGGAAATTAATATCGATGGTAGT 58.596 40.000 8.54 0.00 0.00 2.73
58 59 6.534079 CCCGGAAATTAATATCGATGGTAGTC 59.466 42.308 8.54 0.00 0.00 2.59
59 60 7.094631 CCGGAAATTAATATCGATGGTAGTCA 58.905 38.462 8.54 0.00 0.00 3.41
60 61 7.275779 CCGGAAATTAATATCGATGGTAGTCAG 59.724 40.741 8.54 0.00 0.00 3.51
61 62 7.813148 CGGAAATTAATATCGATGGTAGTCAGT 59.187 37.037 8.54 0.00 0.00 3.41
75 76 4.841422 GTAGTCAGTACCAGTCTACCAGA 58.159 47.826 8.27 0.00 0.00 3.86
76 77 3.958018 AGTCAGTACCAGTCTACCAGAG 58.042 50.000 0.00 0.00 0.00 3.35
77 78 3.018149 GTCAGTACCAGTCTACCAGAGG 58.982 54.545 0.00 0.00 0.00 3.69
78 79 2.025226 TCAGTACCAGTCTACCAGAGGG 60.025 54.545 0.00 0.00 41.29 4.30
79 80 1.288335 AGTACCAGTCTACCAGAGGGG 59.712 57.143 0.00 0.00 44.81 4.79
80 81 0.032416 TACCAGTCTACCAGAGGGGC 60.032 60.000 0.00 0.00 42.05 5.80
81 82 2.427245 CCAGTCTACCAGAGGGGCG 61.427 68.421 0.00 0.00 42.05 6.13
82 83 1.379977 CAGTCTACCAGAGGGGCGA 60.380 63.158 0.00 0.00 42.05 5.54
83 84 0.970937 CAGTCTACCAGAGGGGCGAA 60.971 60.000 0.00 0.00 42.05 4.70
84 85 0.252103 AGTCTACCAGAGGGGCGAAA 60.252 55.000 0.00 0.00 42.05 3.46
85 86 0.611714 GTCTACCAGAGGGGCGAAAA 59.388 55.000 0.00 0.00 42.05 2.29
86 87 1.209747 GTCTACCAGAGGGGCGAAAAT 59.790 52.381 0.00 0.00 42.05 1.82
87 88 1.209504 TCTACCAGAGGGGCGAAAATG 59.790 52.381 0.00 0.00 42.05 2.32
88 89 0.988832 TACCAGAGGGGCGAAAATGT 59.011 50.000 0.00 0.00 42.05 2.71
89 90 0.988832 ACCAGAGGGGCGAAAATGTA 59.011 50.000 0.00 0.00 42.05 2.29
90 91 1.339727 ACCAGAGGGGCGAAAATGTAC 60.340 52.381 0.00 0.00 42.05 2.90
91 92 1.339631 CCAGAGGGGCGAAAATGTACA 60.340 52.381 0.00 0.00 0.00 2.90
92 93 2.643551 CAGAGGGGCGAAAATGTACAT 58.356 47.619 1.41 1.41 0.00 2.29
93 94 2.355756 CAGAGGGGCGAAAATGTACATG 59.644 50.000 9.63 0.00 0.00 3.21
94 95 2.026262 AGAGGGGCGAAAATGTACATGT 60.026 45.455 9.63 2.69 0.00 3.21
95 96 2.091541 AGGGGCGAAAATGTACATGTG 58.908 47.619 9.63 0.99 0.00 3.21
96 97 1.469079 GGGGCGAAAATGTACATGTGC 60.469 52.381 9.63 8.01 0.00 4.57
97 98 1.201181 GGGCGAAAATGTACATGTGCA 59.799 47.619 19.24 19.24 0.00 4.57
98 99 2.250188 GGCGAAAATGTACATGTGCAC 58.750 47.619 19.33 10.75 0.00 4.57
99 100 2.351253 GGCGAAAATGTACATGTGCACA 60.351 45.455 24.08 24.08 0.00 4.57
100 101 3.500982 GCGAAAATGTACATGTGCACAT 58.499 40.909 26.61 26.61 36.96 3.21
101 102 3.543494 GCGAAAATGTACATGTGCACATC 59.457 43.478 29.23 18.47 34.32 3.06
102 103 3.780279 CGAAAATGTACATGTGCACATCG 59.220 43.478 29.23 24.07 34.32 3.84
103 104 2.830772 AATGTACATGTGCACATCGC 57.169 45.000 29.23 20.50 42.89 4.58
104 105 2.028420 ATGTACATGTGCACATCGCT 57.972 45.000 29.23 16.39 43.06 4.93
105 106 1.077915 TGTACATGTGCACATCGCTG 58.922 50.000 29.23 21.50 43.06 5.18
106 107 0.374758 GTACATGTGCACATCGCTGG 59.625 55.000 29.23 19.41 43.06 4.85
107 108 1.368345 TACATGTGCACATCGCTGGC 61.368 55.000 29.23 0.00 43.06 4.85
108 109 2.045634 ATGTGCACATCGCTGGCT 60.046 55.556 26.61 2.62 43.06 4.75
109 110 2.404186 ATGTGCACATCGCTGGCTG 61.404 57.895 26.61 0.00 43.06 4.85
110 111 3.807538 GTGCACATCGCTGGCTGG 61.808 66.667 13.17 0.00 43.06 4.85
111 112 4.334118 TGCACATCGCTGGCTGGT 62.334 61.111 0.00 0.00 43.06 4.00
112 113 2.125147 GCACATCGCTGGCTGGTA 60.125 61.111 0.00 0.00 37.77 3.25
113 114 2.176273 GCACATCGCTGGCTGGTAG 61.176 63.158 0.00 0.00 37.77 3.18
134 135 6.041751 GGTAGCTTATACAGTACCAATGGACT 59.958 42.308 6.16 2.15 35.86 3.85
566 573 2.983136 CGCTATCTTCGACATCATGGAC 59.017 50.000 0.00 0.00 0.00 4.02
567 574 2.983136 GCTATCTTCGACATCATGGACG 59.017 50.000 0.00 0.00 0.00 4.79
568 575 2.515926 ATCTTCGACATCATGGACGG 57.484 50.000 6.65 0.00 0.00 4.79
569 576 0.179111 TCTTCGACATCATGGACGGC 60.179 55.000 6.65 0.00 0.00 5.68
570 577 0.460109 CTTCGACATCATGGACGGCA 60.460 55.000 0.00 0.00 0.00 5.69
571 578 0.460109 TTCGACATCATGGACGGCAG 60.460 55.000 0.00 0.00 0.00 4.85
572 579 2.528743 CGACATCATGGACGGCAGC 61.529 63.158 0.00 0.00 0.00 5.25
573 580 1.450134 GACATCATGGACGGCAGCA 60.450 57.895 0.00 0.00 0.00 4.41
574 581 1.434622 GACATCATGGACGGCAGCAG 61.435 60.000 0.00 0.00 0.00 4.24
575 582 1.450848 CATCATGGACGGCAGCAGT 60.451 57.895 0.00 0.00 0.00 4.40
576 583 1.450848 ATCATGGACGGCAGCAGTG 60.451 57.895 1.66 0.00 0.00 3.66
577 584 2.881539 ATCATGGACGGCAGCAGTGG 62.882 60.000 1.66 0.00 0.00 4.00
596 603 2.311294 CGTAGCTAGCCCAACATGC 58.689 57.895 12.13 0.00 0.00 4.06
597 604 1.160329 CGTAGCTAGCCCAACATGCC 61.160 60.000 12.13 0.00 0.00 4.40
598 605 0.107214 GTAGCTAGCCCAACATGCCA 60.107 55.000 12.13 0.00 0.00 4.92
599 606 0.181114 TAGCTAGCCCAACATGCCAG 59.819 55.000 12.13 0.00 0.00 4.85
600 607 2.123428 GCTAGCCCAACATGCCAGG 61.123 63.158 2.29 0.00 0.00 4.45
601 608 1.454479 CTAGCCCAACATGCCAGGG 60.454 63.158 12.20 12.20 45.68 4.45
602 609 2.215451 CTAGCCCAACATGCCAGGGT 62.215 60.000 16.46 11.28 44.69 4.34
603 610 2.497792 TAGCCCAACATGCCAGGGTG 62.498 60.000 16.46 0.00 44.69 4.61
604 611 2.681064 CCCAACATGCCAGGGTGG 60.681 66.667 6.42 6.42 41.55 4.61
605 612 2.118076 CCAACATGCCAGGGTGGT 59.882 61.111 4.99 0.00 40.46 4.16
606 613 1.978617 CCAACATGCCAGGGTGGTC 60.979 63.158 4.99 0.00 40.46 4.02
607 614 1.978617 CAACATGCCAGGGTGGTCC 60.979 63.158 0.00 0.00 40.46 4.46
608 615 2.468868 AACATGCCAGGGTGGTCCA 61.469 57.895 0.00 0.00 40.46 4.02
609 616 2.361610 CATGCCAGGGTGGTCCAC 60.362 66.667 14.13 14.13 40.46 4.02
624 631 5.083533 TGGTCCACCAATGCAAAATATTC 57.916 39.130 0.00 0.00 44.35 1.75
625 632 4.529769 TGGTCCACCAATGCAAAATATTCA 59.470 37.500 0.00 0.00 44.35 2.57
626 633 4.869861 GGTCCACCAATGCAAAATATTCAC 59.130 41.667 0.00 0.00 35.64 3.18
627 634 5.477510 GTCCACCAATGCAAAATATTCACA 58.522 37.500 0.00 0.00 0.00 3.58
628 635 6.108015 GTCCACCAATGCAAAATATTCACAT 58.892 36.000 0.00 0.00 0.00 3.21
629 636 7.264221 GTCCACCAATGCAAAATATTCACATA 58.736 34.615 0.00 0.00 0.00 2.29
630 637 7.763528 GTCCACCAATGCAAAATATTCACATAA 59.236 33.333 0.00 0.00 0.00 1.90
631 638 8.316946 TCCACCAATGCAAAATATTCACATAAA 58.683 29.630 0.00 0.00 0.00 1.40
632 639 9.111613 CCACCAATGCAAAATATTCACATAAAT 57.888 29.630 0.00 0.00 0.00 1.40
697 704 5.966968 ATATTATGGGGAAATTCCAGGGT 57.033 39.130 14.68 0.00 38.64 4.34
698 705 3.396685 TTATGGGGAAATTCCAGGGTG 57.603 47.619 14.68 0.00 38.64 4.61
699 706 0.339510 ATGGGGAAATTCCAGGGTGG 59.660 55.000 14.68 0.00 38.64 4.61
700 707 1.077298 TGGGGAAATTCCAGGGTGGT 61.077 55.000 14.68 0.00 38.64 4.16
701 708 0.324368 GGGGAAATTCCAGGGTGGTC 60.324 60.000 14.68 0.00 38.64 4.02
702 709 0.324368 GGGAAATTCCAGGGTGGTCC 60.324 60.000 14.68 0.00 38.64 4.46
703 710 0.407918 GGAAATTCCAGGGTGGTCCA 59.592 55.000 7.23 0.00 39.03 4.02
704 711 1.007118 GGAAATTCCAGGGTGGTCCAT 59.993 52.381 7.23 0.00 39.03 3.41
705 712 2.102578 GAAATTCCAGGGTGGTCCATG 58.897 52.381 0.00 0.00 44.12 3.66
716 723 3.495729 GTCCATGGACCACCCTGT 58.504 61.111 31.37 0.00 39.08 4.00
717 724 1.299976 GTCCATGGACCACCCTGTC 59.700 63.158 31.37 5.53 39.08 3.51
723 730 3.647771 GACCACCCTGTCCACCCC 61.648 72.222 0.00 0.00 0.00 4.95
726 733 2.124085 CACCCTGTCCACCCCCTA 59.876 66.667 0.00 0.00 0.00 3.53
727 734 1.995626 CACCCTGTCCACCCCCTAG 60.996 68.421 0.00 0.00 0.00 3.02
728 735 2.181773 ACCCTGTCCACCCCCTAGA 61.182 63.158 0.00 0.00 0.00 2.43
729 736 1.318380 CCCTGTCCACCCCCTAGAT 59.682 63.158 0.00 0.00 0.00 1.98
730 737 0.566176 CCCTGTCCACCCCCTAGATA 59.434 60.000 0.00 0.00 0.00 1.98
731 738 1.718280 CCTGTCCACCCCCTAGATAC 58.282 60.000 0.00 0.00 0.00 2.24
732 739 1.329256 CTGTCCACCCCCTAGATACG 58.671 60.000 0.00 0.00 0.00 3.06
733 740 0.757935 TGTCCACCCCCTAGATACGC 60.758 60.000 0.00 0.00 0.00 4.42
734 741 1.152398 TCCACCCCCTAGATACGCC 60.152 63.158 0.00 0.00 0.00 5.68
735 742 1.458777 CCACCCCCTAGATACGCCA 60.459 63.158 0.00 0.00 0.00 5.69
736 743 1.746517 CACCCCCTAGATACGCCAC 59.253 63.158 0.00 0.00 0.00 5.01
737 744 0.759436 CACCCCCTAGATACGCCACT 60.759 60.000 0.00 0.00 0.00 4.00
738 745 0.759436 ACCCCCTAGATACGCCACTG 60.759 60.000 0.00 0.00 0.00 3.66
739 746 1.472662 CCCCCTAGATACGCCACTGG 61.473 65.000 0.00 0.00 0.00 4.00
740 747 0.469331 CCCCTAGATACGCCACTGGA 60.469 60.000 0.00 0.00 0.00 3.86
908 915 4.626081 GGCGAGCACCACCACTGT 62.626 66.667 0.00 0.00 0.00 3.55
2073 2102 4.383173 TGCATCATGATTCGTGCTATTCT 58.617 39.130 17.44 0.00 38.37 2.40
2636 2673 5.249163 TGGATGATAGAGAGAGAGAGAGAGG 59.751 48.000 0.00 0.00 0.00 3.69
2968 3005 1.064017 AGGAAAACAACAGAGCCCACA 60.064 47.619 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.486663 ATCGTCGGCGCCTATCACA 61.487 57.895 26.68 3.26 38.14 3.58
1 2 2.016704 CATCGTCGGCGCCTATCAC 61.017 63.158 26.68 14.25 38.14 3.06
2 3 2.335011 CATCGTCGGCGCCTATCA 59.665 61.111 26.68 6.13 38.14 2.15
3 4 2.430921 CCATCGTCGGCGCCTATC 60.431 66.667 26.68 13.30 38.14 2.08
4 5 4.664677 GCCATCGTCGGCGCCTAT 62.665 66.667 26.68 9.76 43.52 2.57
11 12 2.456119 GCAAGACTGCCATCGTCGG 61.456 63.158 0.00 0.00 43.26 4.79
12 13 3.084579 GCAAGACTGCCATCGTCG 58.915 61.111 0.00 0.00 43.26 5.12
21 22 1.172180 TTTCCGGGCAAGCAAGACTG 61.172 55.000 0.00 0.00 0.00 3.51
22 23 0.251341 ATTTCCGGGCAAGCAAGACT 60.251 50.000 0.00 0.00 0.00 3.24
23 24 0.603065 AATTTCCGGGCAAGCAAGAC 59.397 50.000 0.00 0.00 0.00 3.01
24 25 2.208132 TAATTTCCGGGCAAGCAAGA 57.792 45.000 0.00 0.00 0.00 3.02
25 26 3.525268 ATTAATTTCCGGGCAAGCAAG 57.475 42.857 0.00 0.00 0.00 4.01
26 27 4.261405 CGATATTAATTTCCGGGCAAGCAA 60.261 41.667 0.00 0.00 0.00 3.91
27 28 3.252215 CGATATTAATTTCCGGGCAAGCA 59.748 43.478 0.00 0.00 0.00 3.91
28 29 3.500680 TCGATATTAATTTCCGGGCAAGC 59.499 43.478 0.00 0.00 0.00 4.01
29 30 5.391950 CCATCGATATTAATTTCCGGGCAAG 60.392 44.000 0.00 0.00 0.00 4.01
30 31 4.457603 CCATCGATATTAATTTCCGGGCAA 59.542 41.667 0.00 0.00 0.00 4.52
31 32 4.006989 CCATCGATATTAATTTCCGGGCA 58.993 43.478 0.00 0.00 0.00 5.36
32 33 4.007659 ACCATCGATATTAATTTCCGGGC 58.992 43.478 0.00 0.00 0.00 6.13
33 34 6.403878 ACTACCATCGATATTAATTTCCGGG 58.596 40.000 0.00 0.00 0.00 5.73
34 35 7.094631 TGACTACCATCGATATTAATTTCCGG 58.905 38.462 0.00 0.00 0.00 5.14
35 36 7.813148 ACTGACTACCATCGATATTAATTTCCG 59.187 37.037 0.00 0.00 0.00 4.30
38 39 9.924650 GGTACTGACTACCATCGATATTAATTT 57.075 33.333 0.00 0.00 44.32 1.82
54 55 4.080469 CCTCTGGTAGACTGGTACTGACTA 60.080 50.000 0.00 0.00 34.22 2.59
55 56 3.308545 CCTCTGGTAGACTGGTACTGACT 60.309 52.174 0.00 0.00 36.31 3.41
56 57 3.018149 CCTCTGGTAGACTGGTACTGAC 58.982 54.545 0.00 0.00 0.00 3.51
57 58 2.025226 CCCTCTGGTAGACTGGTACTGA 60.025 54.545 0.00 0.00 0.00 3.41
58 59 2.379972 CCCTCTGGTAGACTGGTACTG 58.620 57.143 0.00 0.00 0.00 2.74
59 60 1.288335 CCCCTCTGGTAGACTGGTACT 59.712 57.143 0.00 0.00 0.00 2.73
60 61 1.777941 CCCCTCTGGTAGACTGGTAC 58.222 60.000 0.00 0.00 0.00 3.34
61 62 0.032416 GCCCCTCTGGTAGACTGGTA 60.032 60.000 0.00 0.00 36.04 3.25
62 63 1.306226 GCCCCTCTGGTAGACTGGT 60.306 63.158 0.00 0.00 36.04 4.00
63 64 2.427245 CGCCCCTCTGGTAGACTGG 61.427 68.421 0.00 0.00 36.04 4.00
64 65 0.970937 TTCGCCCCTCTGGTAGACTG 60.971 60.000 0.00 0.00 36.04 3.51
65 66 0.252103 TTTCGCCCCTCTGGTAGACT 60.252 55.000 0.00 0.00 36.04 3.24
66 67 0.611714 TTTTCGCCCCTCTGGTAGAC 59.388 55.000 0.00 0.00 36.04 2.59
67 68 1.209504 CATTTTCGCCCCTCTGGTAGA 59.790 52.381 0.00 0.00 36.04 2.59
68 69 1.065418 ACATTTTCGCCCCTCTGGTAG 60.065 52.381 0.00 0.00 36.04 3.18
69 70 0.988832 ACATTTTCGCCCCTCTGGTA 59.011 50.000 0.00 0.00 36.04 3.25
70 71 0.988832 TACATTTTCGCCCCTCTGGT 59.011 50.000 0.00 0.00 36.04 4.00
71 72 1.339631 TGTACATTTTCGCCCCTCTGG 60.340 52.381 0.00 0.00 37.09 3.86
72 73 2.107950 TGTACATTTTCGCCCCTCTG 57.892 50.000 0.00 0.00 0.00 3.35
73 74 2.026262 ACATGTACATTTTCGCCCCTCT 60.026 45.455 5.37 0.00 0.00 3.69
74 75 2.097466 CACATGTACATTTTCGCCCCTC 59.903 50.000 5.37 0.00 0.00 4.30
75 76 2.091541 CACATGTACATTTTCGCCCCT 58.908 47.619 5.37 0.00 0.00 4.79
76 77 1.469079 GCACATGTACATTTTCGCCCC 60.469 52.381 5.37 0.00 0.00 5.80
77 78 1.201181 TGCACATGTACATTTTCGCCC 59.799 47.619 5.37 0.00 0.00 6.13
78 79 2.250188 GTGCACATGTACATTTTCGCC 58.750 47.619 13.17 0.00 0.00 5.54
79 80 2.927429 TGTGCACATGTACATTTTCGC 58.073 42.857 17.42 7.07 35.76 4.70
95 96 2.125147 TACCAGCCAGCGATGTGC 60.125 61.111 0.00 2.68 46.98 4.57
96 97 2.176273 GCTACCAGCCAGCGATGTG 61.176 63.158 0.00 0.00 34.48 3.21
97 98 1.903877 AAGCTACCAGCCAGCGATGT 61.904 55.000 0.00 0.00 43.77 3.06
98 99 0.104855 TAAGCTACCAGCCAGCGATG 59.895 55.000 0.00 0.00 43.77 3.84
99 100 1.051812 ATAAGCTACCAGCCAGCGAT 58.948 50.000 0.00 0.00 43.77 4.58
100 101 1.340248 GTATAAGCTACCAGCCAGCGA 59.660 52.381 0.00 0.00 43.77 4.93
101 102 1.068588 TGTATAAGCTACCAGCCAGCG 59.931 52.381 0.00 0.00 43.77 5.18
102 103 2.103263 ACTGTATAAGCTACCAGCCAGC 59.897 50.000 0.00 0.00 43.77 4.85
103 104 4.262079 GGTACTGTATAAGCTACCAGCCAG 60.262 50.000 0.00 0.00 43.77 4.85
104 105 3.640029 GGTACTGTATAAGCTACCAGCCA 59.360 47.826 0.00 0.00 43.77 4.75
105 106 3.640029 TGGTACTGTATAAGCTACCAGCC 59.360 47.826 0.00 0.00 43.77 4.85
106 107 4.931661 TGGTACTGTATAAGCTACCAGC 57.068 45.455 0.00 0.00 42.84 4.85
107 108 6.041637 TCCATTGGTACTGTATAAGCTACCAG 59.958 42.308 1.86 1.45 40.52 4.00
108 109 5.900699 TCCATTGGTACTGTATAAGCTACCA 59.099 40.000 1.86 0.00 39.11 3.25
109 110 6.041751 AGTCCATTGGTACTGTATAAGCTACC 59.958 42.308 1.86 0.00 35.11 3.18
110 111 6.924060 CAGTCCATTGGTACTGTATAAGCTAC 59.076 42.308 19.16 1.74 38.62 3.58
111 112 6.837048 TCAGTCCATTGGTACTGTATAAGCTA 59.163 38.462 23.15 8.74 42.96 3.32
112 113 5.661312 TCAGTCCATTGGTACTGTATAAGCT 59.339 40.000 23.15 0.00 42.96 3.74
113 114 5.914033 TCAGTCCATTGGTACTGTATAAGC 58.086 41.667 23.15 0.00 42.96 3.09
134 135 4.103153 GGAAGTTCCCACCATGATATCTCA 59.897 45.833 11.17 0.00 35.41 3.27
165 166 4.079844 TCCTTCAATGGACATGGCTTCATA 60.080 41.667 0.00 0.00 0.00 2.15
567 574 3.371097 TAGCTACGCCACTGCTGCC 62.371 63.158 0.00 0.00 37.62 4.85
568 575 1.880340 CTAGCTACGCCACTGCTGC 60.880 63.158 0.00 0.00 37.62 5.25
569 576 1.880340 GCTAGCTACGCCACTGCTG 60.880 63.158 7.70 0.00 37.62 4.41
570 577 2.496817 GCTAGCTACGCCACTGCT 59.503 61.111 7.70 0.00 40.43 4.24
571 578 2.586357 GGCTAGCTACGCCACTGC 60.586 66.667 22.05 9.22 46.77 4.40
576 583 1.146263 ATGTTGGGCTAGCTACGCC 59.854 57.895 15.72 19.98 46.83 5.68
577 584 1.776034 GCATGTTGGGCTAGCTACGC 61.776 60.000 15.72 6.93 0.00 4.42
578 585 1.160329 GGCATGTTGGGCTAGCTACG 61.160 60.000 15.72 1.04 0.00 3.51
579 586 0.107214 TGGCATGTTGGGCTAGCTAC 60.107 55.000 15.72 10.98 0.00 3.58
580 587 0.181114 CTGGCATGTTGGGCTAGCTA 59.819 55.000 15.72 0.96 33.06 3.32
581 588 1.077212 CTGGCATGTTGGGCTAGCT 60.077 57.895 15.72 0.00 33.06 3.32
582 589 2.123428 CCTGGCATGTTGGGCTAGC 61.123 63.158 6.04 6.04 38.40 3.42
583 590 1.454479 CCCTGGCATGTTGGGCTAG 60.454 63.158 6.83 0.00 39.31 3.42
584 591 2.237965 ACCCTGGCATGTTGGGCTA 61.238 57.895 16.24 0.00 44.56 3.93
585 592 3.593680 ACCCTGGCATGTTGGGCT 61.594 61.111 16.24 5.04 44.56 5.19
586 593 3.384532 CACCCTGGCATGTTGGGC 61.385 66.667 16.24 0.00 44.56 5.36
587 594 2.681064 CCACCCTGGCATGTTGGG 60.681 66.667 15.17 15.17 46.07 4.12
588 595 1.978617 GACCACCCTGGCATGTTGG 60.979 63.158 4.83 4.83 42.67 3.77
589 596 1.978617 GGACCACCCTGGCATGTTG 60.979 63.158 0.00 0.00 42.67 3.33
590 597 2.440599 GGACCACCCTGGCATGTT 59.559 61.111 0.00 0.00 42.67 2.71
591 598 2.858476 TGGACCACCCTGGCATGT 60.858 61.111 0.00 0.00 42.67 3.21
592 599 2.361610 GTGGACCACCCTGGCATG 60.362 66.667 14.16 0.00 42.67 4.06
602 609 4.529769 TGAATATTTTGCATTGGTGGACCA 59.470 37.500 0.00 0.00 45.94 4.02
603 610 4.869861 GTGAATATTTTGCATTGGTGGACC 59.130 41.667 0.00 0.00 0.00 4.46
604 611 5.477510 TGTGAATATTTTGCATTGGTGGAC 58.522 37.500 0.00 0.00 0.00 4.02
605 612 5.735285 TGTGAATATTTTGCATTGGTGGA 57.265 34.783 0.00 0.00 0.00 4.02
606 613 8.489990 TTTATGTGAATATTTTGCATTGGTGG 57.510 30.769 0.00 0.00 0.00 4.61
671 678 9.321500 ACCCTGGAATTTCCCCATAATATATAT 57.678 33.333 12.90 0.00 35.03 0.86
672 679 8.565239 CACCCTGGAATTTCCCCATAATATATA 58.435 37.037 12.90 0.00 35.03 0.86
673 680 7.421684 CACCCTGGAATTTCCCCATAATATAT 58.578 38.462 12.90 0.00 35.03 0.86
674 681 6.240733 CCACCCTGGAATTTCCCCATAATATA 60.241 42.308 12.90 0.00 40.96 0.86
675 682 5.461018 CCACCCTGGAATTTCCCCATAATAT 60.461 44.000 12.90 0.00 40.96 1.28
676 683 4.140805 CCACCCTGGAATTTCCCCATAATA 60.141 45.833 12.90 0.00 40.96 0.98
677 684 3.375207 CCACCCTGGAATTTCCCCATAAT 60.375 47.826 12.90 0.00 40.96 1.28
678 685 2.023501 CCACCCTGGAATTTCCCCATAA 60.024 50.000 12.90 0.00 40.96 1.90
679 686 1.573376 CCACCCTGGAATTTCCCCATA 59.427 52.381 12.90 0.00 40.96 2.74
680 687 0.339510 CCACCCTGGAATTTCCCCAT 59.660 55.000 12.90 0.00 40.96 4.00
681 688 1.077298 ACCACCCTGGAATTTCCCCA 61.077 55.000 12.90 0.00 40.96 4.96
682 689 0.324368 GACCACCCTGGAATTTCCCC 60.324 60.000 12.90 0.00 40.96 4.81
683 690 0.324368 GGACCACCCTGGAATTTCCC 60.324 60.000 12.90 0.00 40.96 3.97
684 691 0.407918 TGGACCACCCTGGAATTTCC 59.592 55.000 8.59 8.59 40.96 3.13
685 692 2.102578 CATGGACCACCCTGGAATTTC 58.897 52.381 0.00 0.00 40.96 2.17
686 693 2.236489 CATGGACCACCCTGGAATTT 57.764 50.000 0.00 0.00 40.96 1.82
706 713 3.647771 GGGGTGGACAGGGTGGTC 61.648 72.222 0.00 0.00 37.06 4.02
708 715 3.572715 TAGGGGGTGGACAGGGTGG 62.573 68.421 0.00 0.00 0.00 4.61
709 716 1.995626 CTAGGGGGTGGACAGGGTG 60.996 68.421 0.00 0.00 0.00 4.61
710 717 1.537478 ATCTAGGGGGTGGACAGGGT 61.537 60.000 0.00 0.00 0.00 4.34
711 718 0.566176 TATCTAGGGGGTGGACAGGG 59.434 60.000 0.00 0.00 0.00 4.45
712 719 1.718280 GTATCTAGGGGGTGGACAGG 58.282 60.000 0.00 0.00 0.00 4.00
713 720 1.329256 CGTATCTAGGGGGTGGACAG 58.671 60.000 0.00 0.00 0.00 3.51
714 721 0.757935 GCGTATCTAGGGGGTGGACA 60.758 60.000 0.00 0.00 0.00 4.02
715 722 1.470165 GGCGTATCTAGGGGGTGGAC 61.470 65.000 0.00 0.00 0.00 4.02
716 723 1.152398 GGCGTATCTAGGGGGTGGA 60.152 63.158 0.00 0.00 0.00 4.02
717 724 1.458777 TGGCGTATCTAGGGGGTGG 60.459 63.158 0.00 0.00 0.00 4.61
718 725 0.759436 AGTGGCGTATCTAGGGGGTG 60.759 60.000 0.00 0.00 0.00 4.61
719 726 0.759436 CAGTGGCGTATCTAGGGGGT 60.759 60.000 0.00 0.00 0.00 4.95
720 727 1.472662 CCAGTGGCGTATCTAGGGGG 61.473 65.000 0.00 0.00 0.00 5.40
721 728 0.469331 TCCAGTGGCGTATCTAGGGG 60.469 60.000 3.51 0.00 0.00 4.79
722 729 0.674534 GTCCAGTGGCGTATCTAGGG 59.325 60.000 3.51 0.00 0.00 3.53
723 730 0.311165 CGTCCAGTGGCGTATCTAGG 59.689 60.000 15.23 0.00 0.00 3.02
724 731 0.311165 CCGTCCAGTGGCGTATCTAG 59.689 60.000 19.84 4.87 0.00 2.43
725 732 1.731433 GCCGTCCAGTGGCGTATCTA 61.731 60.000 19.84 0.00 43.70 1.98
726 733 3.077519 GCCGTCCAGTGGCGTATCT 62.078 63.158 19.84 0.00 43.70 1.98
727 734 2.585247 GCCGTCCAGTGGCGTATC 60.585 66.667 19.84 8.82 43.70 2.24
733 740 2.809861 AAGATGCTGCCGTCCAGTGG 62.810 60.000 1.40 1.40 43.71 4.00
734 741 1.364626 GAAGATGCTGCCGTCCAGTG 61.365 60.000 0.00 0.00 43.71 3.66
735 742 1.078848 GAAGATGCTGCCGTCCAGT 60.079 57.895 0.00 0.00 43.71 4.00
736 743 1.078918 TGAAGATGCTGCCGTCCAG 60.079 57.895 0.00 0.00 44.67 3.86
737 744 1.375908 GTGAAGATGCTGCCGTCCA 60.376 57.895 0.00 0.00 0.00 4.02
738 745 0.175760 TAGTGAAGATGCTGCCGTCC 59.824 55.000 0.00 0.00 0.00 4.79
739 746 2.131183 GATAGTGAAGATGCTGCCGTC 58.869 52.381 0.00 0.00 0.00 4.79
740 747 1.536922 CGATAGTGAAGATGCTGCCGT 60.537 52.381 0.00 0.00 0.00 5.68
908 915 4.281435 ACATCAATTCCTGCATGTCAAACA 59.719 37.500 0.00 0.00 0.00 2.83
1560 1589 0.251165 GTGGTGCAGGTGGGTACAAT 60.251 55.000 0.00 0.00 0.00 2.71
2028 2057 6.017109 GCAAACTGAACAAACAAGATAGAGGA 60.017 38.462 0.00 0.00 0.00 3.71
2636 2673 3.072038 GGTCTAGTCTACTCTCTCTCCCC 59.928 56.522 0.00 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.