Multiple sequence alignment - TraesCS3A01G523500

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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 TraesCS3A01G523500 chr3A 100.000 3523 0 0 1 3523 738920713 738917191 0.000000e+00 6506.0
1 TraesCS3A01G523500 chr3A 91.649 1880 150 2 1398 3277 738245398 738243526 0.000000e+00 2595.0
2 TraesCS3A01G523500 chr3A 95.354 1485 58 5 56 1536 738865970 738864493 0.000000e+00 2350.0
3 TraesCS3A01G523500 chr3A 86.130 2235 243 35 1234 3436 738678059 738675860 0.000000e+00 2348.0
4 TraesCS3A01G523500 chr3A 86.336 2159 241 29 1234 3372 738503388 738501264 0.000000e+00 2303.0
5 TraesCS3A01G523500 chr3A 86.796 1810 219 12 925 2730 738692201 738690408 0.000000e+00 2001.0
6 TraesCS3A01G523500 chr3A 89.196 1518 155 6 1067 2579 738708884 738707371 0.000000e+00 1886.0
7 TraesCS3A01G523500 chr3A 85.949 1701 209 18 1064 2741 738223670 738221977 0.000000e+00 1790.0
8 TraesCS3A01G523500 chr3A 94.892 744 22 3 207 949 738320202 738319474 0.000000e+00 1149.0
9 TraesCS3A01G523500 chr3A 80.918 828 101 29 2631 3436 738707370 738706578 5.030000e-168 601.0
10 TraesCS3A01G523500 chr3A 81.647 692 103 18 115 797 738856547 738855871 1.430000e-153 553.0
11 TraesCS3A01G523500 chr3A 77.574 709 111 20 115 805 738693194 738692516 5.520000e-103 385.0
12 TraesCS3A01G523500 chr3A 77.458 661 108 22 134 782 738306657 738306026 1.200000e-94 357.0
13 TraesCS3A01G523500 chr3A 96.795 156 5 0 56 211 738325223 738325068 9.700000e-66 261.0
14 TraesCS3A01G523500 chr3A 92.857 56 4 0 2 57 738504193 738504138 8.110000e-12 82.4
15 TraesCS3A01G523500 chr3A 92.857 56 4 0 2 57 738600526 738600471 8.110000e-12 82.4
16 TraesCS3A01G523500 chr3A 92.857 56 4 0 2 57 738679493 738679438 8.110000e-12 82.4
17 TraesCS3A01G523500 chr3A 87.931 58 5 2 1 57 738584158 738584102 2.270000e-07 67.6
18 TraesCS3A01G523500 chr3A 87.931 58 5 2 1 57 738662650 738662594 2.270000e-07 67.6
19 TraesCS3A01G523500 chr3D 89.455 1925 189 10 1055 2973 605676376 605678292 0.000000e+00 2418.0
20 TraesCS3A01G523500 chr3D 88.450 1671 164 12 1055 2718 605973367 605975015 0.000000e+00 1989.0
21 TraesCS3A01G523500 chr3D 87.871 371 37 4 2751 3119 605975008 605975372 2.510000e-116 429.0
22 TraesCS3A01G523500 chr3D 76.758 697 107 32 140 826 605972265 605972916 4.360000e-89 339.0
23 TraesCS3A01G523500 chr3D 81.220 410 60 13 120 524 606775127 606774730 7.340000e-82 315.0
24 TraesCS3A01G523500 chr3D 77.606 518 82 22 285 797 606001482 606001970 2.070000e-72 283.0
25 TraesCS3A01G523500 chr3D 75.388 451 78 17 2769 3217 605636476 605636895 1.670000e-43 187.0
26 TraesCS3A01G523500 chr3D 81.579 228 41 1 259 486 605954226 605954452 1.670000e-43 187.0
27 TraesCS3A01G523500 chr3D 82.390 159 18 5 3242 3390 605636879 605637037 2.850000e-26 130.0
28 TraesCS3A01G523500 chr3D 91.379 58 3 2 1 57 605953630 605953686 1.050000e-10 78.7
29 TraesCS3A01G523500 chr3B 85.946 1544 176 25 1759 3278 816039922 816038396 0.000000e+00 1611.0
30 TraesCS3A01G523500 chr3B 85.266 1561 198 21 1028 2561 816172339 816170784 0.000000e+00 1580.0
31 TraesCS3A01G523500 chr3B 86.797 409 47 4 2537 2942 816097988 816097584 1.930000e-122 449.0
32 TraesCS3A01G523500 chr5A 77.185 675 105 27 147 807 624725019 624724380 7.240000e-92 348.0
33 TraesCS3A01G523500 chr5A 74.091 660 116 29 165 797 624713086 624712455 1.650000e-53 220.0
34 TraesCS3A01G523500 chr5A 94.253 87 5 0 3437 3523 468360541 468360455 2.210000e-27 134.0
35 TraesCS3A01G523500 chr5D 76.723 653 99 26 165 797 500134335 500133716 7.340000e-82 315.0
36 TraesCS3A01G523500 chr5B 74.848 660 111 29 165 797 621470389 621469758 7.550000e-62 248.0
37 TraesCS3A01G523500 chr7A 97.727 88 2 0 3436 3523 736672269 736672356 6.090000e-33 152.0
38 TraesCS3A01G523500 chr7A 96.591 88 2 1 3436 3523 690431341 690431255 1.020000e-30 145.0
39 TraesCS3A01G523500 chr1A 93.684 95 6 0 3429 3523 539730560 539730654 3.670000e-30 143.0
40 TraesCS3A01G523500 chr1A 94.318 88 5 0 3436 3523 555966923 555966836 6.130000e-28 135.0
41 TraesCS3A01G523500 chr2A 94.318 88 5 0 3436 3523 169356970 169356883 6.130000e-28 135.0
42 TraesCS3A01G523500 chr2A 93.407 91 3 3 3436 3523 72695600 72695690 7.940000e-27 132.0
43 TraesCS3A01G523500 chr7B 93.258 89 6 0 3435 3523 581407467 581407555 7.940000e-27 132.0
44 TraesCS3A01G523500 chr6D 93.258 89 4 1 3435 3523 58247994 58248080 2.850000e-26 130.0
45 TraesCS3A01G523500 chrUn 92.857 56 4 0 2 57 344271535 344271480 8.110000e-12 82.4
46 TraesCS3A01G523500 chrUn 87.931 58 5 2 1 57 259684598 259684542 2.270000e-07 67.6
47 TraesCS3A01G523500 chrUn 91.837 49 2 2 1 48 388556773 388556820 2.270000e-07 67.6


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 TraesCS3A01G523500 chr3A 738917191 738920713 3522 True 6506.0 6506 100.000000 1 3523 1 chr3A.!!$R11 3522
1 TraesCS3A01G523500 chr3A 738243526 738245398 1872 True 2595.0 2595 91.649000 1398 3277 1 chr3A.!!$R2 1879
2 TraesCS3A01G523500 chr3A 738864493 738865970 1477 True 2350.0 2350 95.354000 56 1536 1 chr3A.!!$R10 1480
3 TraesCS3A01G523500 chr3A 738221977 738223670 1693 True 1790.0 1790 85.949000 1064 2741 1 chr3A.!!$R1 1677
4 TraesCS3A01G523500 chr3A 738706578 738708884 2306 True 1243.5 1886 85.057000 1067 3436 2 chr3A.!!$R15 2369
5 TraesCS3A01G523500 chr3A 738675860 738679493 3633 True 1215.2 2348 89.493500 2 3436 2 chr3A.!!$R13 3434
6 TraesCS3A01G523500 chr3A 738690408 738693194 2786 True 1193.0 2001 82.185000 115 2730 2 chr3A.!!$R14 2615
7 TraesCS3A01G523500 chr3A 738501264 738504193 2929 True 1192.7 2303 89.596500 2 3372 2 chr3A.!!$R12 3370
8 TraesCS3A01G523500 chr3A 738319474 738320202 728 True 1149.0 1149 94.892000 207 949 1 chr3A.!!$R4 742
9 TraesCS3A01G523500 chr3A 738855871 738856547 676 True 553.0 553 81.647000 115 797 1 chr3A.!!$R9 682
10 TraesCS3A01G523500 chr3A 738306026 738306657 631 True 357.0 357 77.458000 134 782 1 chr3A.!!$R3 648
11 TraesCS3A01G523500 chr3D 605676376 605678292 1916 False 2418.0 2418 89.455000 1055 2973 1 chr3D.!!$F1 1918
12 TraesCS3A01G523500 chr3D 605972265 605975372 3107 False 919.0 1989 84.359667 140 3119 3 chr3D.!!$F5 2979
13 TraesCS3A01G523500 chr3B 816038396 816039922 1526 True 1611.0 1611 85.946000 1759 3278 1 chr3B.!!$R1 1519
14 TraesCS3A01G523500 chr3B 816170784 816172339 1555 True 1580.0 1580 85.266000 1028 2561 1 chr3B.!!$R3 1533
15 TraesCS3A01G523500 chr5A 624724380 624725019 639 True 348.0 348 77.185000 147 807 1 chr5A.!!$R3 660
16 TraesCS3A01G523500 chr5A 624712455 624713086 631 True 220.0 220 74.091000 165 797 1 chr5A.!!$R2 632
17 TraesCS3A01G523500 chr5D 500133716 500134335 619 True 315.0 315 76.723000 165 797 1 chr5D.!!$R1 632
18 TraesCS3A01G523500 chr5B 621469758 621470389 631 True 248.0 248 74.848000 165 797 1 chr5B.!!$R1 632

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
53 54 6.879458 AGTGTCTACAACTTGTCTTTGAAACT 59.121 34.615 0.00 1.88 0.00 2.66 F
1124 1951 2.223572 GCAAATGTAAAGGGATCTGCCG 60.224 50.000 0.00 0.00 37.63 5.69 F
1835 2679 1.405105 GGCGATTGCTTAAGGATTGCA 59.595 47.619 4.59 0.96 42.25 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1556 2400 0.033228 TGCCTTTGAAAACCATGCCG 59.967 50.0 0.0 0.0 0.00 5.69 R
2253 3097 0.166814 GCCAAAGATGCGACACTGTC 59.833 55.0 0.0 0.0 0.00 3.51 R
3031 3961 0.236711 CTTCAGACGCCTTTGCTGTG 59.763 55.0 0.0 0.0 34.43 3.66 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
53 54 6.879458 AGTGTCTACAACTTGTCTTTGAAACT 59.121 34.615 0.00 1.88 0.00 2.66
306 696 7.986085 AGTACATGCTAACTTTTGACTGATT 57.014 32.000 0.00 0.00 0.00 2.57
720 1146 9.220767 GTTAAAGACCTTGATTCTGTTGATAGT 57.779 33.333 0.00 0.00 0.00 2.12
1050 1877 7.095187 GGTTTCCATGTCATAGATTTATCGACC 60.095 40.741 0.00 0.00 0.00 4.79
1097 1924 8.707796 ATTTCAGATATCAATGAATGCCTTCT 57.292 30.769 5.32 0.00 35.47 2.85
1124 1951 2.223572 GCAAATGTAAAGGGATCTGCCG 60.224 50.000 0.00 0.00 37.63 5.69
1131 1958 5.547465 TGTAAAGGGATCTGCCGTAATATG 58.453 41.667 0.00 0.00 37.63 1.78
1193 2020 8.757982 ACTGAGTATGATCCAATTAAAATGCT 57.242 30.769 0.00 0.00 0.00 3.79
1296 2140 7.996098 ACTTAAAAGAGCTTAATGCCTACAA 57.004 32.000 0.00 0.00 44.23 2.41
1314 2158 7.504238 TGCCTACAAGTATAATTATTGGGTTGG 59.496 37.037 2.68 8.68 0.00 3.77
1449 2293 8.345724 AGGTCTTCTACTAGAAACGTTGATAA 57.654 34.615 0.00 0.00 33.19 1.75
1450 2294 8.968969 AGGTCTTCTACTAGAAACGTTGATAAT 58.031 33.333 0.00 0.00 33.19 1.28
1542 2386 6.465439 ACTTTGATCCTACACGTATCATCA 57.535 37.500 0.00 0.00 30.17 3.07
1546 2390 5.130350 TGATCCTACACGTATCATCAGACA 58.870 41.667 0.00 0.00 0.00 3.41
1556 2400 1.454479 CATCAGACATGGGGGCCAC 60.454 63.158 4.39 0.17 35.80 5.01
1588 2432 5.739752 TTCAAAGGCATATTGTCTGATCG 57.260 39.130 0.00 0.00 29.54 3.69
1591 2435 1.417517 AGGCATATTGTCTGATCGGCA 59.582 47.619 0.00 0.00 26.79 5.69
1715 2559 2.299326 AGCTCTTTGGATGTTGCCTT 57.701 45.000 0.00 0.00 0.00 4.35
1771 2615 1.669115 CCAACGGCTCACTGTCTGG 60.669 63.158 0.00 0.00 32.87 3.86
1817 2661 3.169908 TGGTTTTTCTTTATCCTGGGGC 58.830 45.455 0.00 0.00 0.00 5.80
1822 2666 2.638480 TCTTTATCCTGGGGCGATTG 57.362 50.000 0.00 0.00 0.00 2.67
1835 2679 1.405105 GGCGATTGCTTAAGGATTGCA 59.595 47.619 4.59 0.96 42.25 4.08
2049 2893 8.652290 GGTACTTAGATCCAGAGTATTTCCATT 58.348 37.037 0.00 0.00 0.00 3.16
2211 3055 8.277197 TCAATGAGGGAAGAATCACAGATATTT 58.723 33.333 0.00 0.00 0.00 1.40
2253 3097 1.933247 GGCAACTGAGGAAGAGATCG 58.067 55.000 0.00 0.00 0.00 3.69
2276 3120 0.166814 GTGTCGCATCTTTGGCAGAC 59.833 55.000 0.00 0.00 32.83 3.51
2289 3133 2.743718 CAGACCGGTGCTTGAGGT 59.256 61.111 14.63 0.00 41.63 3.85
2438 3282 1.944024 CGAAGGACTAGATCTGCTCGT 59.056 52.381 5.18 0.00 0.00 4.18
2446 3290 2.949451 AGATCTGCTCGTCAATCGTT 57.051 45.000 0.00 0.00 40.80 3.85
2455 3326 0.041400 CGTCAATCGTTTGCACAGCA 60.041 50.000 1.18 0.00 33.71 4.41
2481 3352 1.026584 TAGCCAACGACGCTATAGCA 58.973 50.000 23.99 0.00 42.21 3.49
2588 3460 6.769512 TCTTTTATGAACTGTTGCTAGGACT 58.230 36.000 0.00 0.00 0.00 3.85
2610 3483 7.110043 ACTTGTATTACAGGCTAGTTAGGTC 57.890 40.000 5.90 0.00 0.00 3.85
2625 3498 6.141560 AGTTAGGTCGGTACTGTAATAAGC 57.858 41.667 0.64 0.00 0.00 3.09
2684 3590 5.523369 GGTTGGAATTATGCTTGCTGATAC 58.477 41.667 0.00 0.00 0.00 2.24
2688 3594 9.219603 GTTGGAATTATGCTTGCTGATACTATA 57.780 33.333 0.00 0.00 0.00 1.31
2759 3674 3.264947 TGCATAGTGTTGCTGAGATGTC 58.735 45.455 0.00 0.00 43.18 3.06
2904 3824 2.330231 TTTTTCTCTCGGCGCAAATG 57.670 45.000 10.83 0.00 0.00 2.32
2915 3835 0.451383 GCGCAAATGTGACAGGCATA 59.549 50.000 0.30 0.00 0.00 3.14
2916 3836 1.135431 GCGCAAATGTGACAGGCATAA 60.135 47.619 0.30 0.00 0.00 1.90
2923 3843 6.183360 GCAAATGTGACAGGCATAAAGATACT 60.183 38.462 0.00 0.00 0.00 2.12
2957 3877 9.202273 GAAACAGAAGGAGAATGCACTATATAG 57.798 37.037 8.27 8.27 0.00 1.31
2963 3885 4.323028 GGAGAATGCACTATATAGCCAGCA 60.323 45.833 20.53 20.53 34.82 4.41
2968 3890 5.745312 TGCACTATATAGCCAGCACTAAT 57.255 39.130 16.61 0.00 0.00 1.73
2973 3895 7.981789 GCACTATATAGCCAGCACTAATATTCA 59.018 37.037 9.78 0.00 0.00 2.57
3012 3942 1.003580 CTGCTGCCCTTCTCCAACTTA 59.996 52.381 0.00 0.00 0.00 2.24
3013 3943 1.423541 TGCTGCCCTTCTCCAACTTAA 59.576 47.619 0.00 0.00 0.00 1.85
3014 3944 2.041620 TGCTGCCCTTCTCCAACTTAAT 59.958 45.455 0.00 0.00 0.00 1.40
3015 3945 3.092301 GCTGCCCTTCTCCAACTTAATT 58.908 45.455 0.00 0.00 0.00 1.40
3031 3961 5.548406 ACTTAATTGTACCTCCAGTGTCAC 58.452 41.667 0.00 0.00 0.00 3.67
3074 4004 4.981389 TTGAATGCGTATTTTGTTTGCC 57.019 36.364 0.00 0.00 0.00 4.52
3228 4162 9.781633 GTATCTACTTTATCTCCAGTAGTGAGA 57.218 37.037 0.00 0.93 42.20 3.27
3300 4235 3.087031 AGGATGGATTCAGTTGCTGTTG 58.913 45.455 0.00 0.00 32.61 3.33
3302 4237 0.961019 TGGATTCAGTTGCTGTTGGC 59.039 50.000 0.00 0.00 42.22 4.52
3305 4240 1.470098 GATTCAGTTGCTGTTGGCGAT 59.530 47.619 0.00 0.00 45.43 4.58
3357 4301 2.029904 GACTGAAGATCGCAAGCCGC 62.030 60.000 0.00 0.00 36.73 6.53
3419 4375 1.284111 TGCATTCTCCTGATGCCCCT 61.284 55.000 6.62 0.00 40.34 4.79
3457 4413 0.667453 TTTTTGAACCGGGCGTTACC 59.333 50.000 6.32 0.00 33.74 2.85
3468 4424 2.647529 GGCGTTACCCCTTTTCATTG 57.352 50.000 0.00 0.00 0.00 2.82
3469 4425 1.403647 GGCGTTACCCCTTTTCATTGC 60.404 52.381 0.00 0.00 0.00 3.56
3470 4426 1.271102 GCGTTACCCCTTTTCATTGCA 59.729 47.619 0.00 0.00 0.00 4.08
3471 4427 2.288518 GCGTTACCCCTTTTCATTGCAA 60.289 45.455 0.00 0.00 0.00 4.08
3472 4428 3.800604 GCGTTACCCCTTTTCATTGCAAA 60.801 43.478 1.71 0.00 0.00 3.68
3473 4429 3.738791 CGTTACCCCTTTTCATTGCAAAC 59.261 43.478 1.71 0.00 0.00 2.93
3474 4430 4.698575 GTTACCCCTTTTCATTGCAAACA 58.301 39.130 1.71 0.00 0.00 2.83
3475 4431 3.922171 ACCCCTTTTCATTGCAAACAA 57.078 38.095 1.71 0.00 40.87 2.83
3476 4432 3.540617 ACCCCTTTTCATTGCAAACAAC 58.459 40.909 1.71 0.00 38.99 3.32
3477 4433 2.543430 CCCCTTTTCATTGCAAACAACG 59.457 45.455 1.71 0.00 38.99 4.10
3478 4434 2.543430 CCCTTTTCATTGCAAACAACGG 59.457 45.455 1.71 3.83 38.99 4.44
3479 4435 3.452474 CCTTTTCATTGCAAACAACGGA 58.548 40.909 1.71 0.00 38.99 4.69
3480 4436 3.868077 CCTTTTCATTGCAAACAACGGAA 59.132 39.130 1.71 0.00 38.99 4.30
3481 4437 4.331168 CCTTTTCATTGCAAACAACGGAAA 59.669 37.500 1.71 4.65 39.09 3.13
3482 4438 5.007528 CCTTTTCATTGCAAACAACGGAAAT 59.992 36.000 1.71 0.00 39.84 2.17
3483 4439 6.201806 CCTTTTCATTGCAAACAACGGAAATA 59.798 34.615 1.71 0.00 39.84 1.40
3484 4440 6.517914 TTTCATTGCAAACAACGGAAATAC 57.482 33.333 1.71 0.00 38.99 1.89
3485 4441 5.188327 TCATTGCAAACAACGGAAATACA 57.812 34.783 1.71 0.00 38.99 2.29
3486 4442 5.592054 TCATTGCAAACAACGGAAATACAA 58.408 33.333 1.71 0.00 38.99 2.41
3487 4443 5.460419 TCATTGCAAACAACGGAAATACAAC 59.540 36.000 1.71 0.00 38.99 3.32
3488 4444 3.707793 TGCAAACAACGGAAATACAACC 58.292 40.909 0.00 0.00 0.00 3.77
3489 4445 3.130516 TGCAAACAACGGAAATACAACCA 59.869 39.130 0.00 0.00 0.00 3.67
3490 4446 3.733727 GCAAACAACGGAAATACAACCAG 59.266 43.478 0.00 0.00 0.00 4.00
3491 4447 4.735283 GCAAACAACGGAAATACAACCAGT 60.735 41.667 0.00 0.00 0.00 4.00
3492 4448 5.344884 CAAACAACGGAAATACAACCAGTT 58.655 37.500 0.00 0.00 0.00 3.16
3493 4449 5.585820 AACAACGGAAATACAACCAGTTT 57.414 34.783 0.00 0.00 0.00 2.66
3494 4450 5.177725 ACAACGGAAATACAACCAGTTTC 57.822 39.130 0.00 0.00 0.00 2.78
3495 4451 4.215965 CAACGGAAATACAACCAGTTTCG 58.784 43.478 0.00 0.00 33.72 3.46
3496 4452 3.731089 ACGGAAATACAACCAGTTTCGA 58.269 40.909 0.00 0.00 33.72 3.71
3497 4453 4.128643 ACGGAAATACAACCAGTTTCGAA 58.871 39.130 0.00 0.00 33.72 3.71
3498 4454 4.758165 ACGGAAATACAACCAGTTTCGAAT 59.242 37.500 0.00 0.00 33.72 3.34
3499 4455 5.933463 ACGGAAATACAACCAGTTTCGAATA 59.067 36.000 0.00 0.00 33.72 1.75
3500 4456 6.128472 ACGGAAATACAACCAGTTTCGAATAC 60.128 38.462 0.00 0.36 33.72 1.89
3501 4457 6.128499 CGGAAATACAACCAGTTTCGAATACA 60.128 38.462 0.00 0.00 33.72 2.29
3502 4458 7.241376 GGAAATACAACCAGTTTCGAATACAG 58.759 38.462 0.00 0.00 33.72 2.74
3503 4459 7.118680 GGAAATACAACCAGTTTCGAATACAGA 59.881 37.037 0.00 0.00 33.72 3.41
3504 4460 7.596749 AATACAACCAGTTTCGAATACAGAG 57.403 36.000 0.00 0.00 0.00 3.35
3505 4461 4.957296 ACAACCAGTTTCGAATACAGAGT 58.043 39.130 0.00 0.00 0.00 3.24
3506 4462 4.989168 ACAACCAGTTTCGAATACAGAGTC 59.011 41.667 0.00 0.00 0.00 3.36
3507 4463 4.866508 ACCAGTTTCGAATACAGAGTCA 57.133 40.909 0.00 0.00 0.00 3.41
3508 4464 4.810790 ACCAGTTTCGAATACAGAGTCAG 58.189 43.478 0.00 0.00 0.00 3.51
3509 4465 4.177026 CCAGTTTCGAATACAGAGTCAGG 58.823 47.826 0.00 0.00 0.00 3.86
3510 4466 4.177026 CAGTTTCGAATACAGAGTCAGGG 58.823 47.826 0.00 0.00 0.00 4.45
3511 4467 3.195825 AGTTTCGAATACAGAGTCAGGGG 59.804 47.826 0.00 0.00 0.00 4.79
3512 4468 1.776662 TCGAATACAGAGTCAGGGGG 58.223 55.000 0.00 0.00 0.00 5.40
3513 4469 1.286849 TCGAATACAGAGTCAGGGGGA 59.713 52.381 0.00 0.00 0.00 4.81
3514 4470 1.683917 CGAATACAGAGTCAGGGGGAG 59.316 57.143 0.00 0.00 0.00 4.30
3515 4471 2.043227 GAATACAGAGTCAGGGGGAGG 58.957 57.143 0.00 0.00 0.00 4.30
3516 4472 0.266152 ATACAGAGTCAGGGGGAGGG 59.734 60.000 0.00 0.00 0.00 4.30
3517 4473 0.854039 TACAGAGTCAGGGGGAGGGA 60.854 60.000 0.00 0.00 0.00 4.20
3518 4474 1.081092 CAGAGTCAGGGGGAGGGAA 59.919 63.158 0.00 0.00 0.00 3.97
3519 4475 0.547712 CAGAGTCAGGGGGAGGGAAA 60.548 60.000 0.00 0.00 0.00 3.13
3520 4476 0.252927 AGAGTCAGGGGGAGGGAAAG 60.253 60.000 0.00 0.00 0.00 2.62
3521 4477 0.252742 GAGTCAGGGGGAGGGAAAGA 60.253 60.000 0.00 0.00 0.00 2.52
3522 4478 0.252927 AGTCAGGGGGAGGGAAAGAG 60.253 60.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 0.322456 TGACACCAGGTTGCATAGGC 60.322 55.000 0.00 0.00 41.68 3.93
12 13 1.419762 ACACTGACACCAGGTTGCATA 59.580 47.619 0.00 0.00 44.60 3.14
15 16 0.179045 AGACACTGACACCAGGTTGC 60.179 55.000 0.00 0.00 44.60 4.17
53 54 0.388659 GCAACACAGTTGGATTGGCA 59.611 50.000 11.39 0.00 0.00 4.92
306 696 8.495160 TCGGAATTGGATTATACCCTAGTTTA 57.505 34.615 0.00 0.00 0.00 2.01
368 758 1.276989 AGCCAAATGGGAATTGCACAG 59.723 47.619 0.00 0.00 40.01 3.66
672 1098 0.883153 TTACTTCCACGCACTCGCTA 59.117 50.000 0.00 0.00 39.84 4.26
676 1102 2.150397 ACACTTACTTCCACGCACTC 57.850 50.000 0.00 0.00 0.00 3.51
720 1146 3.068560 GCAACGGTAACCAACATAGACA 58.931 45.455 0.00 0.00 0.00 3.41
1000 1668 6.148811 CCGGAAGACTGTACAACATTTAACAT 59.851 38.462 0.00 0.00 0.00 2.71
1097 1924 3.985019 TCCCTTTACATTTGCTCGGTA 57.015 42.857 0.00 0.00 0.00 4.02
1124 1951 8.507524 ACAACTAAAGCTTCCTTCCATATTAC 57.492 34.615 0.00 0.00 0.00 1.89
1131 1958 5.548406 TCAGTACAACTAAAGCTTCCTTCC 58.452 41.667 0.00 0.00 0.00 3.46
1193 2020 3.389983 AGGTTGTTGCCTCTTAGTACACA 59.610 43.478 0.00 0.00 32.39 3.72
1261 2104 7.797038 AAGCTCTTTTAAGTTTCCGTTCTAA 57.203 32.000 0.00 0.00 0.00 2.10
1296 2140 6.323739 CCACAAGCCAACCCAATAATTATACT 59.676 38.462 0.00 0.00 0.00 2.12
1314 2158 0.598065 AGAATGCCGAAACCACAAGC 59.402 50.000 0.00 0.00 0.00 4.01
1449 2293 6.057533 TCTCATTTGCAGTTTCATCCGATAT 58.942 36.000 0.00 0.00 0.00 1.63
1450 2294 5.427378 TCTCATTTGCAGTTTCATCCGATA 58.573 37.500 0.00 0.00 0.00 2.92
1481 2325 6.443849 TCTCCAGCTCTTCTAAAGGGAAAATA 59.556 38.462 0.00 0.00 0.00 1.40
1490 2334 2.906389 TGCCTTCTCCAGCTCTTCTAAA 59.094 45.455 0.00 0.00 0.00 1.85
1556 2400 0.033228 TGCCTTTGAAAACCATGCCG 59.967 50.000 0.00 0.00 0.00 5.69
1567 2411 4.129380 CCGATCAGACAATATGCCTTTGA 58.871 43.478 0.00 0.00 0.00 2.69
1623 2467 1.637338 TGACTGATCTCACACTGCCT 58.363 50.000 0.00 0.00 0.00 4.75
1624 2468 2.462456 TTGACTGATCTCACACTGCC 57.538 50.000 0.00 0.00 0.00 4.85
1715 2559 2.036733 CAGTAGTGGAACCTCGGTTTCA 59.963 50.000 5.70 5.70 40.93 2.69
1822 2666 4.732784 TGTTTCGATTGCAATCCTTAAGC 58.267 39.130 29.10 21.96 31.68 3.09
2049 2893 4.020617 CCCGTTCAGCTGCCTGGA 62.021 66.667 9.47 0.00 39.61 3.86
2211 3055 6.054860 CTCCTCAAGGACCTGAGAATTAAA 57.945 41.667 17.62 1.93 44.82 1.52
2253 3097 0.166814 GCCAAAGATGCGACACTGTC 59.833 55.000 0.00 0.00 0.00 3.51
2264 3108 1.675641 GCACCGGTCTGCCAAAGAT 60.676 57.895 2.59 0.00 37.23 2.40
2276 3120 1.086696 CATGTAACCTCAAGCACCGG 58.913 55.000 0.00 0.00 0.00 5.28
2289 3133 3.410631 TGGTCTTTCTTCGCCATGTAA 57.589 42.857 0.00 0.00 0.00 2.41
2446 3290 0.606401 GCTACCTCCTTGCTGTGCAA 60.606 55.000 4.87 4.87 46.80 4.08
2455 3326 1.590147 CGTCGTTGGCTACCTCCTT 59.410 57.895 0.00 0.00 0.00 3.36
2481 3352 1.980765 TGACAAGAACTCTGCCTCCAT 59.019 47.619 0.00 0.00 0.00 3.41
2588 3460 5.068198 CCGACCTAACTAGCCTGTAATACAA 59.932 44.000 0.00 0.00 0.00 2.41
2610 3483 6.481976 TGAAATCATGGCTTATTACAGTACCG 59.518 38.462 0.00 0.00 0.00 4.02
2648 3537 7.041098 GCATAATTCCAACCGAGAAACTGATAT 60.041 37.037 0.00 0.00 0.00 1.63
2688 3594 7.458397 TCAGGGTAACAAAATTCAGTCTACAT 58.542 34.615 0.00 0.00 39.74 2.29
2904 3824 6.403636 CCAACAAGTATCTTTATGCCTGTCAC 60.404 42.308 0.00 0.00 0.00 3.67
2915 3835 5.701224 TCTGTTTCCCCAACAAGTATCTTT 58.299 37.500 0.00 0.00 45.11 2.52
2916 3836 5.319043 TCTGTTTCCCCAACAAGTATCTT 57.681 39.130 0.00 0.00 45.11 2.40
2923 3843 2.512056 TCTCCTTCTGTTTCCCCAACAA 59.488 45.455 0.00 0.00 45.11 2.83
2957 3877 3.256631 CCCCAATGAATATTAGTGCTGGC 59.743 47.826 0.00 0.00 0.00 4.85
2963 3885 5.536161 GTGATGTGCCCCAATGAATATTAGT 59.464 40.000 0.00 0.00 0.00 2.24
2968 3890 3.023119 GTGTGATGTGCCCCAATGAATA 58.977 45.455 0.00 0.00 0.00 1.75
2973 3895 1.678635 CGGTGTGATGTGCCCCAAT 60.679 57.895 0.00 0.00 0.00 3.16
2981 3903 3.052082 GCAGCAGCGGTGTGATGT 61.052 61.111 17.07 0.00 36.19 3.06
3012 3942 3.135712 TGTGTGACACTGGAGGTACAATT 59.864 43.478 17.47 0.00 35.11 2.32
3013 3943 2.703536 TGTGTGACACTGGAGGTACAAT 59.296 45.455 17.47 0.00 35.11 2.71
3014 3944 2.102420 CTGTGTGACACTGGAGGTACAA 59.898 50.000 17.47 0.00 35.11 2.41
3015 3945 1.686587 CTGTGTGACACTGGAGGTACA 59.313 52.381 17.47 0.00 35.11 2.90
3031 3961 0.236711 CTTCAGACGCCTTTGCTGTG 59.763 55.000 0.00 0.00 34.43 3.66
3147 4080 8.169839 CAGAAATGAGCATCTGTACATTTTTG 57.830 34.615 0.00 0.00 41.11 2.44
3278 4212 2.719739 ACAGCAACTGAATCCATCCTG 58.280 47.619 0.78 0.00 35.18 3.86
3300 4235 1.407258 AGCTAACTGACTGAGATCGCC 59.593 52.381 0.00 0.00 0.00 5.54
3302 4237 6.312399 AGATAAGCTAACTGACTGAGATCG 57.688 41.667 0.00 0.00 0.00 3.69
3305 4240 5.952347 TGGAAGATAAGCTAACTGACTGAGA 59.048 40.000 0.00 0.00 0.00 3.27
3357 4301 2.926200 CCTACTCATCAACAGCGACAAG 59.074 50.000 0.00 0.00 0.00 3.16
3390 4334 6.348295 GCATCAGGAGAATGCATAACTGTATG 60.348 42.308 0.00 11.75 40.72 2.39
3395 4351 3.484407 GGCATCAGGAGAATGCATAACT 58.516 45.455 0.00 2.40 42.65 2.24
3438 4394 0.667453 GGTAACGCCCGGTTCAAAAA 59.333 50.000 0.00 0.00 40.09 1.94
3439 4395 2.329244 GGTAACGCCCGGTTCAAAA 58.671 52.632 0.00 0.00 40.09 2.44
3440 4396 4.061949 GGTAACGCCCGGTTCAAA 57.938 55.556 0.00 0.00 40.09 2.69
3451 4407 3.651803 TTGCAATGAAAAGGGGTAACG 57.348 42.857 0.00 0.00 37.60 3.18
3452 4408 4.698575 TGTTTGCAATGAAAAGGGGTAAC 58.301 39.130 0.00 0.00 0.00 2.50
3453 4409 5.119694 GTTGTTTGCAATGAAAAGGGGTAA 58.880 37.500 0.00 0.00 36.92 2.85
3454 4410 4.698575 GTTGTTTGCAATGAAAAGGGGTA 58.301 39.130 0.00 0.00 36.92 3.69
3455 4411 3.540617 GTTGTTTGCAATGAAAAGGGGT 58.459 40.909 0.00 0.00 36.92 4.95
3456 4412 2.543430 CGTTGTTTGCAATGAAAAGGGG 59.457 45.455 0.00 0.00 42.61 4.79
3457 4413 2.543430 CCGTTGTTTGCAATGAAAAGGG 59.457 45.455 0.00 0.00 42.61 3.95
3458 4414 3.452474 TCCGTTGTTTGCAATGAAAAGG 58.548 40.909 0.00 7.37 42.61 3.11
3459 4415 5.462034 TTTCCGTTGTTTGCAATGAAAAG 57.538 34.783 0.00 0.00 42.61 2.27
3460 4416 6.535150 TGTATTTCCGTTGTTTGCAATGAAAA 59.465 30.769 0.00 0.00 42.61 2.29
3461 4417 6.042777 TGTATTTCCGTTGTTTGCAATGAAA 58.957 32.000 0.00 3.91 42.61 2.69
3462 4418 5.592054 TGTATTTCCGTTGTTTGCAATGAA 58.408 33.333 0.00 0.00 42.61 2.57
3463 4419 5.188327 TGTATTTCCGTTGTTTGCAATGA 57.812 34.783 0.00 0.00 42.61 2.57
3464 4420 5.332959 GGTTGTATTTCCGTTGTTTGCAATG 60.333 40.000 0.00 0.00 40.38 2.82
3465 4421 4.747605 GGTTGTATTTCCGTTGTTTGCAAT 59.252 37.500 0.00 0.00 36.92 3.56
3466 4422 4.113354 GGTTGTATTTCCGTTGTTTGCAA 58.887 39.130 0.00 0.00 0.00 4.08
3467 4423 3.130516 TGGTTGTATTTCCGTTGTTTGCA 59.869 39.130 0.00 0.00 0.00 4.08
3468 4424 3.707793 TGGTTGTATTTCCGTTGTTTGC 58.292 40.909 0.00 0.00 0.00 3.68
3469 4425 4.927422 ACTGGTTGTATTTCCGTTGTTTG 58.073 39.130 0.00 0.00 0.00 2.93
3470 4426 5.585820 AACTGGTTGTATTTCCGTTGTTT 57.414 34.783 0.00 0.00 0.00 2.83
3471 4427 5.584442 GAAACTGGTTGTATTTCCGTTGTT 58.416 37.500 0.00 0.00 0.00 2.83
3472 4428 4.260866 CGAAACTGGTTGTATTTCCGTTGT 60.261 41.667 0.00 0.00 0.00 3.32
3473 4429 4.024725 TCGAAACTGGTTGTATTTCCGTTG 60.025 41.667 0.00 0.00 0.00 4.10
3474 4430 4.128643 TCGAAACTGGTTGTATTTCCGTT 58.871 39.130 0.00 0.00 0.00 4.44
3475 4431 3.731089 TCGAAACTGGTTGTATTTCCGT 58.269 40.909 0.00 0.00 0.00 4.69
3476 4432 4.735662 TTCGAAACTGGTTGTATTTCCG 57.264 40.909 0.00 0.00 0.00 4.30
3477 4433 7.118680 TCTGTATTCGAAACTGGTTGTATTTCC 59.881 37.037 0.00 0.00 0.00 3.13
3478 4434 8.025243 TCTGTATTCGAAACTGGTTGTATTTC 57.975 34.615 0.00 0.00 0.00 2.17
3479 4435 7.660208 ACTCTGTATTCGAAACTGGTTGTATTT 59.340 33.333 0.00 0.00 0.00 1.40
3480 4436 7.159372 ACTCTGTATTCGAAACTGGTTGTATT 58.841 34.615 0.00 0.00 0.00 1.89
3481 4437 6.698380 ACTCTGTATTCGAAACTGGTTGTAT 58.302 36.000 0.00 0.00 0.00 2.29
3482 4438 6.092955 ACTCTGTATTCGAAACTGGTTGTA 57.907 37.500 0.00 0.00 0.00 2.41
3483 4439 4.957296 ACTCTGTATTCGAAACTGGTTGT 58.043 39.130 0.00 4.55 0.00 3.32
3484 4440 4.988540 TGACTCTGTATTCGAAACTGGTTG 59.011 41.667 0.00 4.05 0.00 3.77
3485 4441 5.209818 TGACTCTGTATTCGAAACTGGTT 57.790 39.130 0.00 0.00 0.00 3.67
3486 4442 4.322049 CCTGACTCTGTATTCGAAACTGGT 60.322 45.833 0.00 6.58 0.00 4.00
3487 4443 4.177026 CCTGACTCTGTATTCGAAACTGG 58.823 47.826 0.00 3.90 0.00 4.00
3488 4444 4.177026 CCCTGACTCTGTATTCGAAACTG 58.823 47.826 0.00 6.50 0.00 3.16
3489 4445 3.195825 CCCCTGACTCTGTATTCGAAACT 59.804 47.826 0.00 0.00 0.00 2.66
3490 4446 3.522553 CCCCTGACTCTGTATTCGAAAC 58.477 50.000 0.00 2.73 0.00 2.78
3491 4447 2.500098 CCCCCTGACTCTGTATTCGAAA 59.500 50.000 0.00 0.00 0.00 3.46
3492 4448 2.108168 CCCCCTGACTCTGTATTCGAA 58.892 52.381 0.00 0.00 0.00 3.71
3493 4449 1.286849 TCCCCCTGACTCTGTATTCGA 59.713 52.381 0.00 0.00 0.00 3.71
3494 4450 1.683917 CTCCCCCTGACTCTGTATTCG 59.316 57.143 0.00 0.00 0.00 3.34
3495 4451 2.043227 CCTCCCCCTGACTCTGTATTC 58.957 57.143 0.00 0.00 0.00 1.75
3496 4452 1.344496 CCCTCCCCCTGACTCTGTATT 60.344 57.143 0.00 0.00 0.00 1.89
3497 4453 0.266152 CCCTCCCCCTGACTCTGTAT 59.734 60.000 0.00 0.00 0.00 2.29
3498 4454 0.854039 TCCCTCCCCCTGACTCTGTA 60.854 60.000 0.00 0.00 0.00 2.74
3499 4455 1.751143 TTCCCTCCCCCTGACTCTGT 61.751 60.000 0.00 0.00 0.00 3.41
3500 4456 0.547712 TTTCCCTCCCCCTGACTCTG 60.548 60.000 0.00 0.00 0.00 3.35
3501 4457 0.252927 CTTTCCCTCCCCCTGACTCT 60.253 60.000 0.00 0.00 0.00 3.24
3502 4458 0.252742 TCTTTCCCTCCCCCTGACTC 60.253 60.000 0.00 0.00 0.00 3.36
3503 4459 0.252927 CTCTTTCCCTCCCCCTGACT 60.253 60.000 0.00 0.00 0.00 3.41
3504 4460 2.302019 CTCTTTCCCTCCCCCTGAC 58.698 63.158 0.00 0.00 0.00 3.51
3505 4461 4.919770 CTCTTTCCCTCCCCCTGA 57.080 61.111 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.