Multiple sequence alignment - TraesCS2A01G087300

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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 TraesCS2A01G087300 chr2A 100.000 2769 0 0 1 2769 40831289 40828521 0.000000e+00 5114.0
1 TraesCS2A01G087300 chr2A 82.808 634 55 17 1953 2544 179296849 179297470 4.090000e-143 518.0
2 TraesCS2A01G087300 chr2A 87.798 336 40 1 1406 1741 179270271 179269937 2.590000e-105 392.0
3 TraesCS2A01G087300 chr2A 88.525 122 11 3 100 219 427338845 427338725 7.990000e-31 145.0
4 TraesCS2A01G087300 chr2A 85.294 136 12 5 2630 2765 179297474 179297601 1.730000e-27 134.0
5 TraesCS2A01G087300 chr1B 93.813 1972 85 13 602 2544 548976597 548974634 0.000000e+00 2931.0
6 TraesCS2A01G087300 chr1B 93.793 145 9 0 2625 2769 548974636 548974492 4.640000e-53 219.0
7 TraesCS2A01G087300 chr1B 94.444 36 0 2 93 128 665285151 665285184 1.000000e-03 54.7
8 TraesCS2A01G087300 chr1A 95.819 1435 50 4 586 2010 504251755 504250321 0.000000e+00 2309.0
9 TraesCS2A01G087300 chr1A 85.289 605 31 10 1997 2544 504250303 504249700 3.090000e-159 571.0
10 TraesCS2A01G087300 chr1A 96.552 145 5 0 2625 2769 504249702 504249558 9.910000e-60 241.0
11 TraesCS2A01G087300 chr1D 94.118 1530 57 11 1046 2544 408250319 408248792 0.000000e+00 2296.0
12 TraesCS2A01G087300 chr1D 91.787 414 21 3 586 986 408250731 408250318 5.180000e-157 564.0
13 TraesCS2A01G087300 chr1D 93.333 150 4 3 2625 2769 408248794 408248646 1.670000e-52 217.0
14 TraesCS2A01G087300 chr2B 83.434 664 85 17 1094 1741 226686576 226685922 6.600000e-166 593.0
15 TraesCS2A01G087300 chr2B 82.344 657 59 21 1930 2544 226700489 226701130 4.090000e-143 518.0
16 TraesCS2A01G087300 chr2B 95.455 88 4 0 2543 2630 706831465 706831378 1.030000e-29 141.0
17 TraesCS2A01G087300 chr2B 80.100 201 31 8 357 552 735941452 735941648 1.030000e-29 141.0
18 TraesCS2A01G087300 chr2D 82.344 657 61 22 1930 2544 170613360 170612717 1.140000e-143 520.0
19 TraesCS2A01G087300 chr2D 87.941 340 30 4 1377 1705 170626830 170627169 9.300000e-105 390.0
20 TraesCS2A01G087300 chr2D 92.632 95 6 1 2539 2633 341665856 341665949 4.810000e-28 135.0
21 TraesCS2A01G087300 chr2D 84.559 136 12 5 2630 2765 170612713 170612587 2.900000e-25 126.0
22 TraesCS2A01G087300 chr2D 86.364 110 11 2 115 220 155563931 155563822 1.740000e-22 117.0
23 TraesCS2A01G087300 chr7D 93.452 336 19 3 219 552 637322858 637322524 1.920000e-136 496.0
24 TraesCS2A01G087300 chr7D 97.143 105 2 1 115 218 47460671 47460775 2.830000e-40 176.0
25 TraesCS2A01G087300 chr7D 93.478 92 5 1 2542 2633 22964256 22964346 4.810000e-28 135.0
26 TraesCS2A01G087300 chr7D 92.473 93 7 0 2536 2628 79628337 79628429 1.730000e-27 134.0
27 TraesCS2A01G087300 chr7D 93.407 91 5 1 2542 2631 426558898 426558988 1.730000e-27 134.0
28 TraesCS2A01G087300 chr7D 95.556 45 1 1 545 589 637322546 637322589 1.380000e-08 71.3
29 TraesCS2A01G087300 chr6D 87.088 364 23 10 212 552 397626454 397626816 9.300000e-105 390.0
30 TraesCS2A01G087300 chr6D 94.915 118 1 4 99 215 397626295 397626408 2.190000e-41 180.0
31 TraesCS2A01G087300 chr6D 93.684 95 6 0 2543 2637 78083079 78083173 2.870000e-30 143.0
32 TraesCS2A01G087300 chr6D 95.556 45 1 1 545 589 397626794 397626751 1.380000e-08 71.3
33 TraesCS2A01G087300 chr3A 87.429 350 21 9 219 547 340975938 340976285 5.600000e-102 381.0
34 TraesCS2A01G087300 chr3A 94.231 104 5 1 115 218 340975787 340975889 1.030000e-34 158.0
35 TraesCS2A01G087300 chr3A 94.382 89 4 1 2542 2630 416192254 416192341 4.810000e-28 135.0
36 TraesCS2A01G087300 chr6A 84.831 356 29 13 219 552 358154851 358155203 4.420000e-88 335.0
37 TraesCS2A01G087300 chr6A 92.381 105 7 1 115 218 358154697 358154801 6.180000e-32 148.0
38 TraesCS2A01G087300 chr6A 94.872 39 2 0 551 589 358155176 358155138 8.280000e-06 62.1
39 TraesCS2A01G087300 chr3D 82.535 355 19 15 219 552 59930725 59931057 3.510000e-69 272.0
40 TraesCS2A01G087300 chr3D 95.146 103 4 1 115 216 59930572 59930674 7.940000e-36 161.0
41 TraesCS2A01G087300 chr3D 92.632 95 5 1 2543 2635 54370497 54370403 4.810000e-28 135.0
42 TraesCS2A01G087300 chr4A 80.693 202 29 8 357 552 647335690 647335887 6.180000e-32 148.0
43 TraesCS2A01G087300 chr4A 81.977 172 24 5 357 526 477592762 477592928 3.720000e-29 139.0
44 TraesCS2A01G087300 chr5B 89.286 112 12 0 99 210 704398132 704398243 1.030000e-29 141.0
45 TraesCS2A01G087300 chr4D 87.402 127 10 3 100 220 465968458 465968332 1.030000e-29 141.0
46 TraesCS2A01G087300 chr4D 94.186 86 5 0 2543 2628 333063273 333063358 6.220000e-27 132.0
47 TraesCS2A01G087300 chr4D 77.333 225 34 13 310 526 298903206 298902991 1.740000e-22 117.0
48 TraesCS2A01G087300 chr3B 79.104 201 33 9 357 552 634150917 634151113 2.240000e-26 130.0


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 TraesCS2A01G087300 chr2A 40828521 40831289 2768 True 5114.000000 5114 100.000000 1 2769 1 chr2A.!!$R1 2768
1 TraesCS2A01G087300 chr2A 179296849 179297601 752 False 326.000000 518 84.051000 1953 2765 2 chr2A.!!$F1 812
2 TraesCS2A01G087300 chr1B 548974492 548976597 2105 True 1575.000000 2931 93.803000 602 2769 2 chr1B.!!$R1 2167
3 TraesCS2A01G087300 chr1A 504249558 504251755 2197 True 1040.333333 2309 92.553333 586 2769 3 chr1A.!!$R1 2183
4 TraesCS2A01G087300 chr1D 408248646 408250731 2085 True 1025.666667 2296 93.079333 586 2769 3 chr1D.!!$R1 2183
5 TraesCS2A01G087300 chr2B 226685922 226686576 654 True 593.000000 593 83.434000 1094 1741 1 chr2B.!!$R1 647
6 TraesCS2A01G087300 chr2B 226700489 226701130 641 False 518.000000 518 82.344000 1930 2544 1 chr2B.!!$F1 614
7 TraesCS2A01G087300 chr2D 170612587 170613360 773 True 323.000000 520 83.451500 1930 2765 2 chr2D.!!$R2 835
8 TraesCS2A01G087300 chr6D 397626295 397626816 521 False 285.000000 390 91.001500 99 552 2 chr6D.!!$F2 453
9 TraesCS2A01G087300 chr6A 358154697 358155203 506 False 241.500000 335 88.606000 115 552 2 chr6A.!!$F1 437

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
75 76 0.242286 AGAGGCGCTGCTATGTATCG 59.758 55.0 7.64 0.0 0.0 2.92 F
786 867 0.338814 AGGGGGAGGAGTCGTGTATT 59.661 55.0 0.00 0.0 0.0 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1083 1174 0.608130 CACCTTGTGGTCATCCGAGA 59.392 55.000 0.0 0.0 46.6 4.04 R
2185 2343 1.933853 CGAATACTGCGAAAGGAAGGG 59.066 52.381 0.0 0.0 0.0 3.95 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
26 27 7.888250 TTTTTAGGCAAATGGATTTTGGTTT 57.112 28.000 0.79 0.00 44.10 3.27
27 28 7.888250 TTTTAGGCAAATGGATTTTGGTTTT 57.112 28.000 0.79 0.00 44.10 2.43
28 29 7.888250 TTTAGGCAAATGGATTTTGGTTTTT 57.112 28.000 0.79 0.00 44.10 1.94
29 30 5.771153 AGGCAAATGGATTTTGGTTTTTG 57.229 34.783 0.79 0.00 44.10 2.44
30 31 5.199723 AGGCAAATGGATTTTGGTTTTTGT 58.800 33.333 0.79 0.00 44.10 2.83
31 32 5.299028 AGGCAAATGGATTTTGGTTTTTGTC 59.701 36.000 0.79 0.00 44.10 3.18
32 33 5.507149 GGCAAATGGATTTTGGTTTTTGTCC 60.507 40.000 0.79 0.00 44.10 4.02
33 34 5.299028 GCAAATGGATTTTGGTTTTTGTCCT 59.701 36.000 0.79 0.00 44.10 3.85
34 35 6.513230 GCAAATGGATTTTGGTTTTTGTCCTC 60.513 38.462 0.79 0.00 44.10 3.71
35 36 4.314740 TGGATTTTGGTTTTTGTCCTCG 57.685 40.909 0.00 0.00 0.00 4.63
36 37 3.057019 GGATTTTGGTTTTTGTCCTCGC 58.943 45.455 0.00 0.00 0.00 5.03
37 38 3.243737 GGATTTTGGTTTTTGTCCTCGCT 60.244 43.478 0.00 0.00 0.00 4.93
38 39 3.430333 TTTTGGTTTTTGTCCTCGCTC 57.570 42.857 0.00 0.00 0.00 5.03
39 40 2.341846 TTGGTTTTTGTCCTCGCTCT 57.658 45.000 0.00 0.00 0.00 4.09
40 41 1.593196 TGGTTTTTGTCCTCGCTCTG 58.407 50.000 0.00 0.00 0.00 3.35
41 42 0.875059 GGTTTTTGTCCTCGCTCTGG 59.125 55.000 0.00 0.00 0.00 3.86
42 43 1.542547 GGTTTTTGTCCTCGCTCTGGA 60.543 52.381 0.00 0.00 0.00 3.86
43 44 1.801178 GTTTTTGTCCTCGCTCTGGAG 59.199 52.381 0.00 0.00 33.78 3.86
56 57 3.251509 TGGAGCTTGCCAGGCAGA 61.252 61.111 15.50 5.19 40.61 4.26
57 58 2.438075 GGAGCTTGCCAGGCAGAG 60.438 66.667 15.50 15.57 40.61 3.35
58 59 2.667418 GAGCTTGCCAGGCAGAGA 59.333 61.111 15.50 0.00 40.61 3.10
59 60 1.449956 GAGCTTGCCAGGCAGAGAG 60.450 63.158 15.50 10.88 40.61 3.20
60 61 2.438075 GCTTGCCAGGCAGAGAGG 60.438 66.667 15.50 5.26 40.61 3.69
70 71 4.340076 CAGAGAGGCGCTGCTATG 57.660 61.111 7.64 8.83 0.00 2.23
71 72 1.440893 CAGAGAGGCGCTGCTATGT 59.559 57.895 7.64 0.00 0.00 2.29
72 73 0.670706 CAGAGAGGCGCTGCTATGTA 59.329 55.000 7.64 0.00 0.00 2.29
73 74 1.271934 CAGAGAGGCGCTGCTATGTAT 59.728 52.381 7.64 0.00 0.00 2.29
74 75 1.543802 AGAGAGGCGCTGCTATGTATC 59.456 52.381 7.64 0.00 0.00 2.24
75 76 0.242286 AGAGGCGCTGCTATGTATCG 59.758 55.000 7.64 0.00 0.00 2.92
76 77 1.347817 GAGGCGCTGCTATGTATCGC 61.348 60.000 7.64 0.00 44.39 4.58
77 78 2.720758 GGCGCTGCTATGTATCGCG 61.721 63.158 7.64 0.00 45.85 5.87
78 79 2.765785 CGCTGCTATGTATCGCGC 59.234 61.111 0.00 0.00 37.29 6.86
79 80 2.016165 CGCTGCTATGTATCGCGCA 61.016 57.895 8.75 0.00 37.29 6.09
80 81 1.488957 GCTGCTATGTATCGCGCAC 59.511 57.895 8.75 1.84 0.00 5.34
81 82 1.215014 GCTGCTATGTATCGCGCACA 61.215 55.000 8.75 14.40 0.00 4.57
82 83 0.504384 CTGCTATGTATCGCGCACAC 59.496 55.000 14.34 1.62 0.00 3.82
83 84 1.206115 TGCTATGTATCGCGCACACG 61.206 55.000 14.34 10.25 44.07 4.49
92 93 3.960998 GCGCACACGATCGCTACG 61.961 66.667 16.60 14.90 46.92 3.51
93 94 3.960998 CGCACACGATCGCTACGC 61.961 66.667 16.60 11.91 43.93 4.42
94 95 2.579787 GCACACGATCGCTACGCT 60.580 61.111 16.60 0.00 0.00 5.07
95 96 2.568912 GCACACGATCGCTACGCTC 61.569 63.158 16.60 0.00 0.00 5.03
97 98 3.379625 CACGATCGCTACGCTCGC 61.380 66.667 16.60 0.00 46.83 5.03
255 307 2.037641 TGATCCACTTGGTGTCTGTCAG 59.962 50.000 0.00 0.00 36.34 3.51
288 340 5.360999 CCTTCTTTTCTTGTTTCTCCAGGTT 59.639 40.000 0.00 0.00 0.00 3.50
321 373 7.938140 TTCTTCTTCTTCTTTTTCCTGTTCA 57.062 32.000 0.00 0.00 0.00 3.18
353 423 6.612247 TTTTCTTTTCTTCGTAGATGTGCA 57.388 33.333 0.00 0.00 35.04 4.57
354 424 6.801539 TTTCTTTTCTTCGTAGATGTGCAT 57.198 33.333 0.00 0.00 35.04 3.96
384 454 6.491714 TCCCAAATTCAATGAACCTTTTCA 57.508 33.333 0.00 0.00 45.93 2.69
540 615 6.390721 TGAACTTTTTCAAAACCGATGAACA 58.609 32.000 0.00 0.00 38.87 3.18
547 622 6.639671 TTCAAAACCGATGAACACTTTTTG 57.360 33.333 0.00 0.00 35.97 2.44
552 627 7.659652 AAACCGATGAACACTTTTTGAAAAA 57.340 28.000 2.83 2.83 0.00 1.94
784 865 1.000019 CAGGGGGAGGAGTCGTGTA 60.000 63.158 0.00 0.00 0.00 2.90
786 867 0.338814 AGGGGGAGGAGTCGTGTATT 59.661 55.000 0.00 0.00 0.00 1.89
857 945 4.906618 ACAAGGTCGGACAAAATGAGTAT 58.093 39.130 10.76 0.00 0.00 2.12
860 948 2.864343 GGTCGGACAAAATGAGTATCGG 59.136 50.000 10.76 0.00 38.61 4.18
909 997 1.967066 CACCAACCCAAACATAAGGCA 59.033 47.619 0.00 0.00 0.00 4.75
1018 1106 1.533625 CAAAAGGGACAAGATCGCCA 58.466 50.000 0.00 0.00 41.22 5.69
1026 1114 2.293399 GGACAAGATCGCCACACTTTTT 59.707 45.455 0.00 0.00 0.00 1.94
1082 1173 3.628008 TGGACGCTGGTCTAGAGATTTA 58.372 45.455 0.00 0.00 42.97 1.40
1083 1174 4.215908 TGGACGCTGGTCTAGAGATTTAT 58.784 43.478 0.00 0.00 42.97 1.40
1186 1277 4.219944 AGATGCAGTGAGGTCGTACTTTTA 59.780 41.667 0.00 0.00 0.00 1.52
1232 1326 3.871594 GCGCACTTACTCTGGTTATCAAT 59.128 43.478 0.30 0.00 0.00 2.57
1255 1349 0.603707 TCTGTTGCAGGCCGAAGAAG 60.604 55.000 0.00 0.00 31.51 2.85
1512 1606 2.604046 ATGGCATCTTCTCGTACCAC 57.396 50.000 0.00 0.00 0.00 4.16
1967 2077 4.898861 TGTAGCTTTTCCCCTGAAATGTTT 59.101 37.500 0.00 0.00 40.08 2.83
1974 2084 9.278978 GCTTTTCCCCTGAAATGTTTAAAATAA 57.721 29.630 0.00 0.00 40.08 1.40
2073 2216 9.726232 CTGTTGGTCTCATAATTTGATTACATG 57.274 33.333 0.00 0.00 32.72 3.21
2110 2253 6.015688 ACTGAAATGCACTGAAATTCTGATGT 60.016 34.615 6.87 0.00 0.00 3.06
2148 2291 2.329267 TCCTTCTTGGCAGAGTTCAGA 58.671 47.619 0.00 0.00 35.26 3.27
2149 2292 2.301296 TCCTTCTTGGCAGAGTTCAGAG 59.699 50.000 0.00 0.00 35.26 3.35
2153 2311 2.700371 TCTTGGCAGAGTTCAGAGTTCA 59.300 45.455 0.00 0.00 0.00 3.18
2154 2312 2.827800 TGGCAGAGTTCAGAGTTCAG 57.172 50.000 0.00 0.00 0.00 3.02
2164 2322 2.837947 TCAGAGTTCAGGTCCATGGAT 58.162 47.619 19.62 0.00 0.00 3.41
2185 2343 4.430137 TGATACTCACACAACCGTACTC 57.570 45.455 0.00 0.00 0.00 2.59
2277 2479 5.924475 AACAAAGTCACGAGTCCTTATTG 57.076 39.130 0.00 0.00 0.00 1.90
2290 2500 3.557595 GTCCTTATTGCACCTTCAGATCG 59.442 47.826 0.00 0.00 0.00 3.69
2393 2612 5.529014 TGCAGTTTTTCTTTTGTTTCAGC 57.471 34.783 0.00 0.00 0.00 4.26
2398 2617 9.030301 GCAGTTTTTCTTTTGTTTCAGCTATTA 57.970 29.630 0.00 0.00 0.00 0.98
2469 2697 3.623510 GCATTCCTGTTCTAACTACTGCC 59.376 47.826 0.00 0.00 0.00 4.85
2543 2772 3.403624 CTGCCAGGCTGGAAGGTA 58.596 61.111 37.07 15.02 39.67 3.08
2544 2773 1.078143 CTGCCAGGCTGGAAGGTAC 60.078 63.158 37.07 18.05 39.67 3.34
2545 2774 1.538876 TGCCAGGCTGGAAGGTACT 60.539 57.895 37.07 0.00 40.96 2.73
2556 2785 4.781264 AGGTACTTCCTCCGTCCC 57.219 61.111 0.00 0.00 44.42 4.46
2557 2786 1.778981 AGGTACTTCCTCCGTCCCA 59.221 57.895 0.00 0.00 44.42 4.37
2558 2787 0.338814 AGGTACTTCCTCCGTCCCAT 59.661 55.000 0.00 0.00 44.42 4.00
2559 2788 1.572415 AGGTACTTCCTCCGTCCCATA 59.428 52.381 0.00 0.00 44.42 2.74
2560 2789 2.023695 AGGTACTTCCTCCGTCCCATAA 60.024 50.000 0.00 0.00 44.42 1.90
2561 2790 2.970640 GGTACTTCCTCCGTCCCATAAT 59.029 50.000 0.00 0.00 0.00 1.28
2562 2791 4.140853 AGGTACTTCCTCCGTCCCATAATA 60.141 45.833 0.00 0.00 44.42 0.98
2563 2792 4.776308 GGTACTTCCTCCGTCCCATAATAT 59.224 45.833 0.00 0.00 0.00 1.28
2564 2793 5.954150 GGTACTTCCTCCGTCCCATAATATA 59.046 44.000 0.00 0.00 0.00 0.86
2565 2794 6.438425 GGTACTTCCTCCGTCCCATAATATAA 59.562 42.308 0.00 0.00 0.00 0.98
2566 2795 6.607004 ACTTCCTCCGTCCCATAATATAAG 57.393 41.667 0.00 0.00 0.00 1.73
2567 2796 6.320518 ACTTCCTCCGTCCCATAATATAAGA 58.679 40.000 0.00 0.00 0.00 2.10
2568 2797 6.437793 ACTTCCTCCGTCCCATAATATAAGAG 59.562 42.308 0.00 0.00 0.00 2.85
2569 2798 4.710375 TCCTCCGTCCCATAATATAAGAGC 59.290 45.833 0.00 0.00 0.00 4.09
2570 2799 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
2571 2800 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
2572 2801 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
2573 2802 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
2574 2803 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
2575 2804 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
2600 2829 4.684703 ACACTAGTGTAATGTCAAGAACGC 59.315 41.667 26.91 0.00 42.90 4.84
2601 2830 4.923871 CACTAGTGTAATGTCAAGAACGCT 59.076 41.667 15.06 0.00 36.68 5.07
2602 2831 5.061064 CACTAGTGTAATGTCAAGAACGCTC 59.939 44.000 15.06 0.00 34.68 5.03
2603 2832 4.258702 AGTGTAATGTCAAGAACGCTCT 57.741 40.909 0.00 0.00 0.00 4.09
2604 2833 4.632153 AGTGTAATGTCAAGAACGCTCTT 58.368 39.130 0.00 0.00 42.96 2.85
2605 2834 5.779922 AGTGTAATGTCAAGAACGCTCTTA 58.220 37.500 0.00 0.00 40.05 2.10
2606 2835 5.634020 AGTGTAATGTCAAGAACGCTCTTAC 59.366 40.000 0.00 1.78 40.05 2.34
2607 2836 5.404366 GTGTAATGTCAAGAACGCTCTTACA 59.596 40.000 0.00 6.96 40.05 2.41
2608 2837 6.090898 GTGTAATGTCAAGAACGCTCTTACAT 59.909 38.462 0.00 8.73 40.05 2.29
2609 2838 6.649141 TGTAATGTCAAGAACGCTCTTACATT 59.351 34.615 23.80 23.80 40.05 2.71
2610 2839 7.815549 TGTAATGTCAAGAACGCTCTTACATTA 59.184 33.333 22.63 22.63 40.05 1.90
2611 2840 7.849804 AATGTCAAGAACGCTCTTACATTAT 57.150 32.000 21.55 9.71 40.05 1.28
2612 2841 6.647212 TGTCAAGAACGCTCTTACATTATG 57.353 37.500 0.00 0.00 40.05 1.90
2613 2842 5.580691 TGTCAAGAACGCTCTTACATTATGG 59.419 40.000 0.00 0.00 40.05 2.74
2614 2843 5.006746 GTCAAGAACGCTCTTACATTATGGG 59.993 44.000 0.00 0.00 40.05 4.00
2615 2844 5.105106 TCAAGAACGCTCTTACATTATGGGA 60.105 40.000 0.00 0.00 40.05 4.37
2616 2845 4.694339 AGAACGCTCTTACATTATGGGAC 58.306 43.478 0.00 0.00 0.00 4.46
2617 2846 3.093717 ACGCTCTTACATTATGGGACG 57.906 47.619 0.00 2.61 0.00 4.79
2618 2847 2.223971 ACGCTCTTACATTATGGGACGG 60.224 50.000 0.00 0.00 0.00 4.79
2619 2848 2.035449 CGCTCTTACATTATGGGACGGA 59.965 50.000 0.00 0.00 0.00 4.69
2620 2849 3.654414 GCTCTTACATTATGGGACGGAG 58.346 50.000 0.00 0.00 0.00 4.63
2621 2850 3.555168 GCTCTTACATTATGGGACGGAGG 60.555 52.174 0.00 0.00 0.00 4.30
2622 2851 3.641906 CTCTTACATTATGGGACGGAGGT 59.358 47.826 0.00 0.00 0.00 3.85
2623 2852 4.806892 TCTTACATTATGGGACGGAGGTA 58.193 43.478 0.00 0.00 0.00 3.08
2681 2911 9.445878 CAGCATCCATATGTTCTATATGTTCTT 57.554 33.333 1.24 0.00 35.38 2.52
2754 2989 9.853555 CAAATTTGTGTTGCCTTCACTAATATA 57.146 29.630 10.15 0.00 39.10 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 7.888250 AAACCAAAATCCATTTGCCTAAAAA 57.112 28.000 0.00 0.00 45.79 1.94
3 4 7.888250 AAAACCAAAATCCATTTGCCTAAAA 57.112 28.000 0.00 0.00 45.79 1.52
5 6 6.830838 ACAAAAACCAAAATCCATTTGCCTAA 59.169 30.769 0.00 0.00 45.79 2.69
6 7 6.360618 ACAAAAACCAAAATCCATTTGCCTA 58.639 32.000 0.00 0.00 45.79 3.93
7 8 5.199723 ACAAAAACCAAAATCCATTTGCCT 58.800 33.333 0.00 0.00 45.79 4.75
8 9 5.507149 GGACAAAAACCAAAATCCATTTGCC 60.507 40.000 0.00 0.00 45.79 4.52
9 10 5.299028 AGGACAAAAACCAAAATCCATTTGC 59.701 36.000 0.00 0.00 45.79 3.68
10 11 6.292811 CGAGGACAAAAACCAAAATCCATTTG 60.293 38.462 0.00 0.00 46.54 2.32
11 12 5.757808 CGAGGACAAAAACCAAAATCCATTT 59.242 36.000 0.00 0.00 0.00 2.32
12 13 5.296748 CGAGGACAAAAACCAAAATCCATT 58.703 37.500 0.00 0.00 0.00 3.16
13 14 4.799255 GCGAGGACAAAAACCAAAATCCAT 60.799 41.667 0.00 0.00 0.00 3.41
14 15 3.491792 GCGAGGACAAAAACCAAAATCCA 60.492 43.478 0.00 0.00 0.00 3.41
15 16 3.057019 GCGAGGACAAAAACCAAAATCC 58.943 45.455 0.00 0.00 0.00 3.01
16 17 3.977427 AGCGAGGACAAAAACCAAAATC 58.023 40.909 0.00 0.00 0.00 2.17
17 18 3.636764 AGAGCGAGGACAAAAACCAAAAT 59.363 39.130 0.00 0.00 0.00 1.82
18 19 3.020984 AGAGCGAGGACAAAAACCAAAA 58.979 40.909 0.00 0.00 0.00 2.44
19 20 2.357637 CAGAGCGAGGACAAAAACCAAA 59.642 45.455 0.00 0.00 0.00 3.28
20 21 1.946768 CAGAGCGAGGACAAAAACCAA 59.053 47.619 0.00 0.00 0.00 3.67
21 22 1.593196 CAGAGCGAGGACAAAAACCA 58.407 50.000 0.00 0.00 0.00 3.67
22 23 0.875059 CCAGAGCGAGGACAAAAACC 59.125 55.000 0.00 0.00 0.00 3.27
23 24 1.801178 CTCCAGAGCGAGGACAAAAAC 59.199 52.381 0.00 0.00 0.00 2.43
24 25 1.878102 GCTCCAGAGCGAGGACAAAAA 60.878 52.381 3.49 0.00 45.29 1.94
25 26 0.320771 GCTCCAGAGCGAGGACAAAA 60.321 55.000 3.49 0.00 45.29 2.44
26 27 1.293498 GCTCCAGAGCGAGGACAAA 59.707 57.895 3.49 0.00 45.29 2.83
27 28 2.973899 GCTCCAGAGCGAGGACAA 59.026 61.111 3.49 0.00 45.29 3.18
39 40 3.251509 TCTGCCTGGCAAGCTCCA 61.252 61.111 23.51 0.00 38.41 3.86
40 41 2.438075 CTCTGCCTGGCAAGCTCC 60.438 66.667 23.51 0.00 38.41 4.70
41 42 1.449956 CTCTCTGCCTGGCAAGCTC 60.450 63.158 23.51 0.00 38.41 4.09
42 43 2.669849 CTCTCTGCCTGGCAAGCT 59.330 61.111 23.51 0.00 38.41 3.74
43 44 2.438075 CCTCTCTGCCTGGCAAGC 60.438 66.667 23.51 0.00 38.41 4.01
44 45 2.438075 GCCTCTCTGCCTGGCAAG 60.438 66.667 23.51 20.62 45.46 4.01
45 46 4.399395 CGCCTCTCTGCCTGGCAA 62.399 66.667 23.51 12.48 46.39 4.52
48 49 4.834453 CAGCGCCTCTCTGCCTGG 62.834 72.222 2.29 0.00 0.00 4.45
53 54 0.670706 TACATAGCAGCGCCTCTCTG 59.329 55.000 2.29 7.06 34.79 3.35
54 55 1.543802 GATACATAGCAGCGCCTCTCT 59.456 52.381 2.29 0.00 0.00 3.10
55 56 1.730772 CGATACATAGCAGCGCCTCTC 60.731 57.143 2.29 0.00 0.00 3.20
56 57 0.242286 CGATACATAGCAGCGCCTCT 59.758 55.000 2.29 3.60 0.00 3.69
57 58 1.347817 GCGATACATAGCAGCGCCTC 61.348 60.000 2.29 0.00 41.65 4.70
58 59 1.373497 GCGATACATAGCAGCGCCT 60.373 57.895 2.29 0.00 41.65 5.52
59 60 2.720758 CGCGATACATAGCAGCGCC 61.721 63.158 2.29 0.00 44.31 6.53
60 61 2.765785 CGCGATACATAGCAGCGC 59.234 61.111 0.00 0.00 44.19 5.92
62 63 1.215014 TGTGCGCGATACATAGCAGC 61.215 55.000 12.10 0.00 40.53 5.25
63 64 0.504384 GTGTGCGCGATACATAGCAG 59.496 55.000 12.10 0.00 40.53 4.24
64 65 1.206115 CGTGTGCGCGATACATAGCA 61.206 55.000 12.10 0.00 37.26 3.49
65 66 0.933047 TCGTGTGCGCGATACATAGC 60.933 55.000 12.10 1.63 35.83 2.97
66 67 3.157922 TCGTGTGCGCGATACATAG 57.842 52.632 12.10 12.38 35.83 2.23
88 89 2.871427 GATTTGCCCGCGAGCGTAG 61.871 63.158 8.23 8.40 37.81 3.51
89 90 2.888534 GATTTGCCCGCGAGCGTA 60.889 61.111 8.23 0.00 37.81 4.42
92 93 1.373590 TTTAGGATTTGCCCGCGAGC 61.374 55.000 8.23 6.70 37.37 5.03
93 94 0.377203 GTTTAGGATTTGCCCGCGAG 59.623 55.000 8.23 0.00 37.37 5.03
94 95 1.363145 CGTTTAGGATTTGCCCGCGA 61.363 55.000 8.23 0.00 37.37 5.87
95 96 1.061887 CGTTTAGGATTTGCCCGCG 59.938 57.895 0.00 0.00 37.37 6.46
96 97 1.431845 CCGTTTAGGATTTGCCCGC 59.568 57.895 0.00 0.00 45.00 6.13
97 98 1.431845 GCCGTTTAGGATTTGCCCG 59.568 57.895 0.00 0.00 45.00 6.13
230 282 3.181440 ACAGACACCAAGTGGATCATTGT 60.181 43.478 3.83 0.00 37.94 2.71
236 288 1.271054 GCTGACAGACACCAAGTGGAT 60.271 52.381 6.65 0.00 37.94 3.41
255 307 5.521906 ACAAGAAAAGAAGGAAAAGAGGC 57.478 39.130 0.00 0.00 0.00 4.70
288 340 6.867662 AAAGAAGAAGAAGAAAATCTCGCA 57.132 33.333 0.00 0.00 0.00 5.10
362 432 7.565323 TTTGAAAAGGTTCATTGAATTTGGG 57.435 32.000 1.78 0.00 43.29 4.12
570 645 5.469479 CATACCCAAATCGCTGAACTTTTT 58.531 37.500 0.00 0.00 0.00 1.94
571 646 4.082245 CCATACCCAAATCGCTGAACTTTT 60.082 41.667 0.00 0.00 0.00 2.27
572 647 3.443681 CCATACCCAAATCGCTGAACTTT 59.556 43.478 0.00 0.00 0.00 2.66
573 648 3.016736 CCATACCCAAATCGCTGAACTT 58.983 45.455 0.00 0.00 0.00 2.66
574 649 2.026262 ACCATACCCAAATCGCTGAACT 60.026 45.455 0.00 0.00 0.00 3.01
575 650 2.365582 ACCATACCCAAATCGCTGAAC 58.634 47.619 0.00 0.00 0.00 3.18
576 651 2.799126 ACCATACCCAAATCGCTGAA 57.201 45.000 0.00 0.00 0.00 3.02
577 652 3.035363 TCTACCATACCCAAATCGCTGA 58.965 45.455 0.00 0.00 0.00 4.26
578 653 3.469008 TCTACCATACCCAAATCGCTG 57.531 47.619 0.00 0.00 0.00 5.18
579 654 3.646162 TGATCTACCATACCCAAATCGCT 59.354 43.478 0.00 0.00 0.00 4.93
580 655 4.002906 TGATCTACCATACCCAAATCGC 57.997 45.455 0.00 0.00 0.00 4.58
581 656 5.412594 CCAATGATCTACCATACCCAAATCG 59.587 44.000 0.00 0.00 0.00 3.34
582 657 6.306987 ACCAATGATCTACCATACCCAAATC 58.693 40.000 0.00 0.00 0.00 2.17
583 658 6.279813 ACCAATGATCTACCATACCCAAAT 57.720 37.500 0.00 0.00 0.00 2.32
584 659 5.725551 ACCAATGATCTACCATACCCAAA 57.274 39.130 0.00 0.00 0.00 3.28
784 865 2.057922 CACCCCATACTCTAGCCCAAT 58.942 52.381 0.00 0.00 0.00 3.16
786 867 0.399949 CCACCCCATACTCTAGCCCA 60.400 60.000 0.00 0.00 0.00 5.36
860 948 0.179156 CATGTTGATTGCGGCAGGAC 60.179 55.000 1.67 1.73 0.00 3.85
888 976 1.967779 GCCTTATGTTTGGGTTGGTGT 59.032 47.619 0.00 0.00 0.00 4.16
895 983 1.747355 CTGCTCTGCCTTATGTTTGGG 59.253 52.381 0.00 0.00 0.00 4.12
1026 1114 5.277974 CCAAACGCATGAGAAAGAGAAGAAA 60.278 40.000 2.50 0.00 0.00 2.52
1031 1122 3.126001 ACCAAACGCATGAGAAAGAGA 57.874 42.857 2.50 0.00 0.00 3.10
1082 1173 1.208052 CACCTTGTGGTCATCCGAGAT 59.792 52.381 0.00 0.00 46.60 2.75
1083 1174 0.608130 CACCTTGTGGTCATCCGAGA 59.392 55.000 0.00 0.00 46.60 4.04
1171 1262 5.079689 TGCATCATAAAAGTACGACCTCA 57.920 39.130 0.00 0.00 0.00 3.86
1186 1277 6.514541 GCATGAACTAGCTACATTTGCATCAT 60.515 38.462 0.00 0.00 0.00 2.45
1232 1326 2.083774 CTTCGGCCTGCAACAGATTTA 58.916 47.619 0.00 0.00 32.44 1.40
1255 1349 0.905337 ATCCTCCCGCCACCTATAGC 60.905 60.000 0.00 0.00 0.00 2.97
1493 1587 1.831106 TGTGGTACGAGAAGATGCCAT 59.169 47.619 0.00 0.00 0.00 4.40
1881 1991 5.990996 GCTTGCTAAATCTTCTATGAGCTCT 59.009 40.000 16.19 3.04 0.00 4.09
1948 2058 7.744087 ATTTTAAACATTTCAGGGGAAAAGC 57.256 32.000 0.00 0.00 45.52 3.51
1967 2077 7.113658 TGCCCACAACTTCAGTTTTATTTTA 57.886 32.000 0.00 0.00 35.83 1.52
1974 2084 2.689983 CTCTTGCCCACAACTTCAGTTT 59.310 45.455 0.00 0.00 35.83 2.66
2020 2163 9.985318 TTGAGCAATTTCATAAAACACAAAAAG 57.015 25.926 0.00 0.00 0.00 2.27
2073 2216 4.445385 GTGCATTTCAGTGTTTCAACCATC 59.555 41.667 0.00 0.00 0.00 3.51
2148 2291 4.302067 AGTATCATCCATGGACCTGAACT 58.698 43.478 18.99 18.33 0.00 3.01
2149 2292 4.101585 TGAGTATCATCCATGGACCTGAAC 59.898 45.833 18.99 16.65 42.56 3.18
2185 2343 1.933853 CGAATACTGCGAAAGGAAGGG 59.066 52.381 0.00 0.00 0.00 3.95
2251 2433 3.606687 AGGACTCGTGACTTTGTTTGTT 58.393 40.909 0.00 0.00 0.00 2.83
2277 2479 9.239002 GATATTACATATACGATCTGAAGGTGC 57.761 37.037 0.00 0.00 0.00 5.01
2357 2575 6.982141 AGAAAAACTGCATGCATACAATATGG 59.018 34.615 22.97 8.59 0.00 2.74
2398 2617 7.272037 ACTGAATTGAATAAACTTGTTCGGT 57.728 32.000 0.00 0.00 31.81 4.69
2469 2697 6.886459 TCTTTTCAGATAAATCCTTGTCCAGG 59.114 38.462 0.00 0.00 45.64 4.45
2541 2770 5.997384 ATATTATGGGACGGAGGAAGTAC 57.003 43.478 0.00 0.00 0.00 2.73
2542 2771 7.472741 TCTTATATTATGGGACGGAGGAAGTA 58.527 38.462 0.00 0.00 0.00 2.24
2543 2772 6.320518 TCTTATATTATGGGACGGAGGAAGT 58.679 40.000 0.00 0.00 0.00 3.01
2544 2773 6.628398 GCTCTTATATTATGGGACGGAGGAAG 60.628 46.154 0.00 0.00 0.00 3.46
2545 2774 5.187186 GCTCTTATATTATGGGACGGAGGAA 59.813 44.000 0.00 0.00 0.00 3.36
2546 2775 4.710375 GCTCTTATATTATGGGACGGAGGA 59.290 45.833 0.00 0.00 0.00 3.71
2547 2776 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
2548 2777 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
2549 2778 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
2550 2779 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
2551 2780 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
2576 2805 5.860182 GCGTTCTTGACATTACACTAGTGTA 59.140 40.000 27.99 27.99 44.42 2.90
2577 2806 4.684703 GCGTTCTTGACATTACACTAGTGT 59.315 41.667 30.13 30.13 46.87 3.55
2578 2807 4.923871 AGCGTTCTTGACATTACACTAGTG 59.076 41.667 21.44 21.44 0.00 2.74
2579 2808 5.047943 AGAGCGTTCTTGACATTACACTAGT 60.048 40.000 0.00 0.00 0.00 2.57
2580 2809 5.403246 AGAGCGTTCTTGACATTACACTAG 58.597 41.667 0.00 0.00 0.00 2.57
2581 2810 5.386958 AGAGCGTTCTTGACATTACACTA 57.613 39.130 0.00 0.00 0.00 2.74
2582 2811 4.258702 AGAGCGTTCTTGACATTACACT 57.741 40.909 0.00 0.00 0.00 3.55
2583 2812 4.992381 AAGAGCGTTCTTGACATTACAC 57.008 40.909 14.17 0.00 42.04 2.90
2584 2813 5.534407 TGTAAGAGCGTTCTTGACATTACA 58.466 37.500 22.97 15.16 43.41 2.41
2585 2814 6.648725 ATGTAAGAGCGTTCTTGACATTAC 57.351 37.500 22.97 12.91 43.41 1.89
2586 2815 8.817100 CATAATGTAAGAGCGTTCTTGACATTA 58.183 33.333 30.42 30.42 43.41 1.90
2587 2816 7.201644 CCATAATGTAAGAGCGTTCTTGACATT 60.202 37.037 29.25 29.25 43.41 2.71
2588 2817 6.258727 CCATAATGTAAGAGCGTTCTTGACAT 59.741 38.462 22.97 21.45 43.41 3.06
2589 2818 5.580691 CCATAATGTAAGAGCGTTCTTGACA 59.419 40.000 22.97 20.43 43.41 3.58
2590 2819 5.006746 CCCATAATGTAAGAGCGTTCTTGAC 59.993 44.000 22.97 16.37 43.41 3.18
2591 2820 5.105106 TCCCATAATGTAAGAGCGTTCTTGA 60.105 40.000 22.97 10.78 43.41 3.02
2592 2821 5.006746 GTCCCATAATGTAAGAGCGTTCTTG 59.993 44.000 22.97 6.36 43.41 3.02
2593 2822 5.116882 GTCCCATAATGTAAGAGCGTTCTT 58.883 41.667 18.78 18.78 45.45 2.52
2594 2823 4.694339 GTCCCATAATGTAAGAGCGTTCT 58.306 43.478 0.00 0.00 34.29 3.01
2595 2824 3.489785 CGTCCCATAATGTAAGAGCGTTC 59.510 47.826 0.00 0.00 0.00 3.95
2596 2825 3.454375 CGTCCCATAATGTAAGAGCGTT 58.546 45.455 0.00 0.00 0.00 4.84
2597 2826 2.223971 CCGTCCCATAATGTAAGAGCGT 60.224 50.000 0.00 0.00 0.00 5.07
2598 2827 2.035449 TCCGTCCCATAATGTAAGAGCG 59.965 50.000 0.00 0.00 0.00 5.03
2599 2828 3.555168 CCTCCGTCCCATAATGTAAGAGC 60.555 52.174 0.00 0.00 0.00 4.09
2600 2829 3.641906 ACCTCCGTCCCATAATGTAAGAG 59.358 47.826 0.00 0.00 0.00 2.85
2601 2830 3.649843 ACCTCCGTCCCATAATGTAAGA 58.350 45.455 0.00 0.00 0.00 2.10
2602 2831 4.587684 ACTACCTCCGTCCCATAATGTAAG 59.412 45.833 0.00 0.00 0.00 2.34
2603 2832 4.549668 ACTACCTCCGTCCCATAATGTAA 58.450 43.478 0.00 0.00 0.00 2.41
2604 2833 4.188937 ACTACCTCCGTCCCATAATGTA 57.811 45.455 0.00 0.00 0.00 2.29
2605 2834 3.042059 ACTACCTCCGTCCCATAATGT 57.958 47.619 0.00 0.00 0.00 2.71
2606 2835 4.404640 TCTACTACCTCCGTCCCATAATG 58.595 47.826 0.00 0.00 0.00 1.90
2607 2836 4.736611 TCTACTACCTCCGTCCCATAAT 57.263 45.455 0.00 0.00 0.00 1.28
2608 2837 4.736611 ATCTACTACCTCCGTCCCATAA 57.263 45.455 0.00 0.00 0.00 1.90
2609 2838 4.736611 AATCTACTACCTCCGTCCCATA 57.263 45.455 0.00 0.00 0.00 2.74
2610 2839 3.614568 AATCTACTACCTCCGTCCCAT 57.385 47.619 0.00 0.00 0.00 4.00
2611 2840 4.736611 ATAATCTACTACCTCCGTCCCA 57.263 45.455 0.00 0.00 0.00 4.37
2612 2841 6.661777 AGATATAATCTACTACCTCCGTCCC 58.338 44.000 0.00 0.00 38.00 4.46
2613 2842 6.767423 GGAGATATAATCTACTACCTCCGTCC 59.233 46.154 0.00 0.00 40.38 4.79
2614 2843 7.790823 GGAGATATAATCTACTACCTCCGTC 57.209 44.000 0.00 0.00 40.38 4.79
2731 2961 8.137437 GCATATATTAGTGAAGGCAACACAAAT 58.863 33.333 14.38 6.39 40.25 2.32


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

AutoCloner maintained by Alex Coulton.