Multiple sequence alignment - TraesCS3B01G461100

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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 TraesCS3B01G461100 chr3B 100.000 3410 0 0 1 3410 704322834 704326243 0.000000e+00 6298
1 TraesCS3B01G461100 chr3B 78.837 808 94 41 1526 2311 704311620 704312372 1.110000e-129 473
2 TraesCS3B01G461100 chr3B 83.588 262 41 2 1911 2171 704025597 704025857 9.450000e-61 244
3 TraesCS3B01G461100 chr3B 82.213 253 41 4 1911 2161 704109725 704109975 7.410000e-52 215
4 TraesCS3B01G461100 chr3B 82.178 202 33 2 19 220 147776514 147776316 1.630000e-38 171
5 TraesCS3B01G461100 chr3A 90.699 1903 100 42 1532 3410 667353727 667355576 0.000000e+00 2462
6 TraesCS3B01G461100 chr3A 90.312 640 43 13 800 1430 667353070 667353699 0.000000e+00 821
7 TraesCS3B01G461100 chr3A 81.017 806 91 38 1526 2308 667345283 667346049 4.900000e-163 584
8 TraesCS3B01G461100 chr3A 92.708 384 11 5 1 370 667350867 667351247 3.870000e-149 538
9 TraesCS3B01G461100 chr3A 76.407 551 96 26 1924 2447 667132900 667133443 2.020000e-67 267
10 TraesCS3B01G461100 chr3A 85.845 219 25 5 15 233 114544915 114544703 9.520000e-56 228
11 TraesCS3B01G461100 chr3A 85.345 116 17 0 2 117 112915785 112915900 1.660000e-23 121
12 TraesCS3B01G461100 chr3D 88.506 1392 93 25 1691 3065 532170362 532171703 0.000000e+00 1622
13 TraesCS3B01G461100 chr3D 91.575 724 38 13 800 1502 532169370 532170091 0.000000e+00 977
14 TraesCS3B01G461100 chr3D 86.762 491 34 14 1 491 532168465 532168924 5.040000e-143 518
15 TraesCS3B01G461100 chr3D 78.810 807 93 41 1526 2311 532155754 532156503 3.980000e-129 472
16 TraesCS3B01G461100 chr3D 92.720 261 12 5 3151 3410 532172093 532172347 1.490000e-98 370
17 TraesCS3B01G461100 chr3D 76.693 502 94 17 1924 2411 532105487 532105979 1.210000e-64 257
18 TraesCS3B01G461100 chr3D 85.185 216 28 3 9 223 96677452 96677240 5.730000e-53 219
19 TraesCS3B01G461100 chr3D 87.302 126 5 5 3030 3152 532171718 532171835 2.130000e-27 134
20 TraesCS3B01G461100 chr2B 87.374 198 22 2 13 210 158650730 158650536 1.230000e-54 224
21 TraesCS3B01G461100 chr2D 86.869 198 23 2 13 210 109076686 109076492 5.730000e-53 219
22 TraesCS3B01G461100 chr2A 85.561 187 24 3 22 208 104978351 104978168 3.470000e-45 193


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 TraesCS3B01G461100 chr3B 704322834 704326243 3409 False 6298.000000 6298 100.000000 1 3410 1 chr3B.!!$F4 3409
1 TraesCS3B01G461100 chr3B 704311620 704312372 752 False 473.000000 473 78.837000 1526 2311 1 chr3B.!!$F3 785
2 TraesCS3B01G461100 chr3A 667350867 667355576 4709 False 1273.666667 2462 91.239667 1 3410 3 chr3A.!!$F4 3409
3 TraesCS3B01G461100 chr3A 667345283 667346049 766 False 584.000000 584 81.017000 1526 2308 1 chr3A.!!$F3 782
4 TraesCS3B01G461100 chr3A 667132900 667133443 543 False 267.000000 267 76.407000 1924 2447 1 chr3A.!!$F2 523
5 TraesCS3B01G461100 chr3D 532168465 532172347 3882 False 724.200000 1622 89.373000 1 3410 5 chr3D.!!$F3 3409
6 TraesCS3B01G461100 chr3D 532155754 532156503 749 False 472.000000 472 78.810000 1526 2311 1 chr3D.!!$F2 785

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
724 2325 0.179032 ATGTGTGAGTTCACCCGCAA 60.179 50.0 9.6 0.0 45.88 4.85 F
1171 2807 0.037326 CCGCCTCAACAGCTACTTCA 60.037 55.0 0.0 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 3577 0.179103 GCAGCTTTGCCACAAGTGTT 60.179 50.000 0.00 0.00 0.0 3.32 R
3017 4840 2.111384 TGGAGGGAGTACTGCTGAATC 58.889 52.381 14.52 7.46 0.0 2.52 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
60 61 1.446272 GGGTCGTAGCAGTGCAGTC 60.446 63.158 19.20 6.03 0.00 3.51
320 338 5.187186 AGGATTTTAGGAAGCGTTCTCTACA 59.813 40.000 0.00 0.00 0.00 2.74
321 339 6.049790 GGATTTTAGGAAGCGTTCTCTACAT 58.950 40.000 0.00 0.00 0.00 2.29
325 343 3.626930 AGGAAGCGTTCTCTACATCTCT 58.373 45.455 0.00 0.00 0.00 3.10
349 367 2.735663 AGAGAGACCGCGTACGTATATG 59.264 50.000 17.90 3.80 37.70 1.78
376 394 3.105659 GCCAAAGCCTGATCGAGC 58.894 61.111 0.00 0.00 0.00 5.03
400 451 3.551890 GTGTACGTGCTGGATTACATCAG 59.448 47.826 4.97 0.00 0.00 2.90
420 471 7.493320 ACATCAGCGATTCGGTTTATAACTTAA 59.507 33.333 8.24 0.00 34.62 1.85
486 537 1.226239 GCTGCAGCGAGCTTTAAGC 60.226 57.895 25.23 9.18 45.94 3.09
491 542 1.168714 CAGCGAGCTTTAAGCCCTTT 58.831 50.000 13.84 0.00 43.77 3.11
493 544 1.541588 AGCGAGCTTTAAGCCCTTTTG 59.458 47.619 13.84 0.12 43.77 2.44
602 844 6.045955 TCAATAGCTGTTCACGCACATATAA 58.954 36.000 0.00 0.00 0.00 0.98
607 849 4.581493 CTGTTCACGCACATATAAAGCTG 58.419 43.478 0.00 0.00 0.00 4.24
670 915 8.931385 ATTTAGAAAGCGTTCAATATTTGCAT 57.069 26.923 14.88 0.00 36.09 3.96
678 1737 8.532977 AGCGTTCAATATTTGCATTAAGTTTT 57.467 26.923 0.00 0.00 0.00 2.43
717 2318 7.503521 TTTGCATTAAGTATGTGTGAGTTCA 57.496 32.000 0.00 0.00 36.57 3.18
718 2319 6.480524 TGCATTAAGTATGTGTGAGTTCAC 57.519 37.500 5.33 5.33 39.68 3.18
719 2320 5.411361 TGCATTAAGTATGTGTGAGTTCACC 59.589 40.000 9.60 2.54 39.10 4.02
720 2321 5.163754 GCATTAAGTATGTGTGAGTTCACCC 60.164 44.000 9.60 0.00 39.10 4.61
721 2322 2.743636 AGTATGTGTGAGTTCACCCG 57.256 50.000 9.60 0.00 45.88 5.28
722 2323 1.076332 GTATGTGTGAGTTCACCCGC 58.924 55.000 9.60 1.71 45.88 6.13
723 2324 0.682292 TATGTGTGAGTTCACCCGCA 59.318 50.000 9.60 6.74 45.88 5.69
724 2325 0.179032 ATGTGTGAGTTCACCCGCAA 60.179 50.000 9.60 0.00 45.88 4.85
725 2326 0.393132 TGTGTGAGTTCACCCGCAAA 60.393 50.000 9.60 0.00 45.88 3.68
726 2327 0.736053 GTGTGAGTTCACCCGCAAAA 59.264 50.000 9.60 0.00 45.88 2.44
727 2328 1.133407 GTGTGAGTTCACCCGCAAAAA 59.867 47.619 9.60 0.00 45.88 1.94
760 2361 4.041567 CCTATGTGTGAGTATAATGGGCCA 59.958 45.833 9.61 9.61 0.00 5.36
775 2376 2.735772 GCCAAGATGAGAGCGGGGA 61.736 63.158 0.00 0.00 0.00 4.81
874 2503 1.808411 GGCGACACTTCCAGAAATCA 58.192 50.000 0.00 0.00 0.00 2.57
937 2566 2.954753 GCAACCAGAGTGTTCGCCG 61.955 63.158 0.00 0.00 0.00 6.46
949 2578 0.319641 GTTCGCCGTTGTTCCTCTCT 60.320 55.000 0.00 0.00 0.00 3.10
972 2608 2.102357 CGATCGTACCAGCTGCGT 59.898 61.111 8.66 10.58 0.00 5.24
973 2609 1.354155 CGATCGTACCAGCTGCGTA 59.646 57.895 8.66 9.51 0.00 4.42
974 2610 0.928908 CGATCGTACCAGCTGCGTAC 60.929 60.000 24.33 24.33 34.08 3.67
997 2633 3.539604 AGCATCCAAGAAGAATCGAAGG 58.460 45.455 0.00 0.00 0.00 3.46
1162 2798 4.680237 CCAGCGTCCGCCTCAACA 62.680 66.667 8.23 0.00 43.17 3.33
1171 2807 0.037326 CCGCCTCAACAGCTACTTCA 60.037 55.000 0.00 0.00 0.00 3.02
1332 2968 2.125350 CCAGGTGCGCCTCTCTTC 60.125 66.667 18.11 0.00 44.97 2.87
1333 2969 2.654079 CCAGGTGCGCCTCTCTTCT 61.654 63.158 18.11 0.00 44.97 2.85
1334 2970 1.294780 CAGGTGCGCCTCTCTTCTT 59.705 57.895 18.11 0.00 44.97 2.52
1335 2971 0.532573 CAGGTGCGCCTCTCTTCTTA 59.467 55.000 18.11 0.00 44.97 2.10
1338 2974 2.625790 AGGTGCGCCTCTCTTCTTATAG 59.374 50.000 14.67 0.00 42.67 1.31
1339 2975 2.362717 GGTGCGCCTCTCTTCTTATAGT 59.637 50.000 9.68 0.00 0.00 2.12
1341 2977 4.538917 GTGCGCCTCTCTTCTTATAGTAC 58.461 47.826 4.18 0.00 0.00 2.73
1342 2978 4.276431 GTGCGCCTCTCTTCTTATAGTACT 59.724 45.833 4.18 0.00 0.00 2.73
1343 2979 5.469421 GTGCGCCTCTCTTCTTATAGTACTA 59.531 44.000 4.18 4.77 0.00 1.82
1344 2980 5.469421 TGCGCCTCTCTTCTTATAGTACTAC 59.531 44.000 4.18 0.00 0.00 2.73
1345 2981 5.702209 GCGCCTCTCTTCTTATAGTACTACT 59.298 44.000 4.31 0.00 0.00 2.57
1367 3003 6.349300 ACTACTATTCAATGATTCTTGCGGT 58.651 36.000 0.00 0.00 0.00 5.68
1370 3006 1.825090 TCAATGATTCTTGCGGTGCT 58.175 45.000 0.00 0.00 0.00 4.40
1382 3018 2.639286 GGTGCTGCCGTGTTCTTG 59.361 61.111 0.00 0.00 0.00 3.02
1383 3019 1.891919 GGTGCTGCCGTGTTCTTGA 60.892 57.895 0.00 0.00 0.00 3.02
1384 3020 1.571460 GTGCTGCCGTGTTCTTGAG 59.429 57.895 0.00 0.00 0.00 3.02
1393 3031 4.716003 GTTCTTGAGGAACCCCGG 57.284 61.111 0.00 0.00 46.17 5.73
1398 3036 2.124507 CTTGAGGAACCCCGGCTTCA 62.125 60.000 11.14 0.70 37.58 3.02
1410 3048 1.026584 CGGCTTCATGATTCATGGCA 58.973 50.000 23.07 11.62 41.66 4.92
1416 3054 4.337555 GCTTCATGATTCATGGCACTACTT 59.662 41.667 23.07 0.00 41.66 2.24
1423 3061 6.888105 TGATTCATGGCACTACTTGAGATAA 58.112 36.000 0.00 0.00 0.00 1.75
1429 3074 4.222810 TGGCACTACTTGAGATAAAGAGCA 59.777 41.667 0.00 0.00 0.00 4.26
1453 3099 4.576463 GGATGGAAGATACATGTTCGCTTT 59.424 41.667 2.30 0.00 31.43 3.51
1463 3109 5.431420 ACATGTTCGCTTTGTGACATTTA 57.569 34.783 0.00 0.00 0.00 1.40
1464 3110 5.826586 ACATGTTCGCTTTGTGACATTTAA 58.173 33.333 0.00 0.00 0.00 1.52
1466 3112 6.582295 ACATGTTCGCTTTGTGACATTTAATC 59.418 34.615 0.00 0.00 0.00 1.75
1467 3113 6.312399 TGTTCGCTTTGTGACATTTAATCT 57.688 33.333 0.00 0.00 0.00 2.40
1468 3114 6.142139 TGTTCGCTTTGTGACATTTAATCTG 58.858 36.000 0.00 0.00 0.00 2.90
1471 3117 5.088739 CGCTTTGTGACATTTAATCTGTCC 58.911 41.667 13.29 7.65 41.87 4.02
1472 3118 5.334802 CGCTTTGTGACATTTAATCTGTCCA 60.335 40.000 13.29 9.42 41.87 4.02
1493 3145 0.391130 TGCGGCTGTGGAAGTACATC 60.391 55.000 0.00 0.00 0.00 3.06
1508 3179 0.037326 ACATCGTGCGACCTGTTGAT 60.037 50.000 0.00 0.00 0.00 2.57
1514 3185 1.067565 GTGCGACCTGTTGATCTCTGA 60.068 52.381 0.00 0.00 0.00 3.27
1521 3192 5.298026 CGACCTGTTGATCTCTGATTCTCTA 59.702 44.000 0.00 0.00 0.00 2.43
1522 3193 6.016360 CGACCTGTTGATCTCTGATTCTCTAT 60.016 42.308 0.00 0.00 0.00 1.98
1524 3195 8.954834 ACCTGTTGATCTCTGATTCTCTATAT 57.045 34.615 0.00 0.00 0.00 0.86
1543 3249 9.613428 CTCTATATATGTTGTTCAGGTTCCAAA 57.387 33.333 0.00 0.00 0.00 3.28
1560 3266 5.850557 TCCAAAGCTTGATTGAGTTTTGA 57.149 34.783 13.42 1.18 45.20 2.69
1579 3285 8.370182 AGTTTTGAGCCAGTTTCATCAAATATT 58.630 29.630 0.56 0.00 40.32 1.28
1580 3286 9.638239 GTTTTGAGCCAGTTTCATCAAATATTA 57.362 29.630 0.56 0.00 40.32 0.98
1581 3287 9.859427 TTTTGAGCCAGTTTCATCAAATATTAG 57.141 29.630 0.56 0.00 40.32 1.73
1582 3288 7.031226 TGAGCCAGTTTCATCAAATATTAGC 57.969 36.000 0.00 0.00 0.00 3.09
1583 3289 6.602803 TGAGCCAGTTTCATCAAATATTAGCA 59.397 34.615 0.00 0.00 0.00 3.49
1584 3290 7.035840 AGCCAGTTTCATCAAATATTAGCAG 57.964 36.000 0.00 0.00 0.00 4.24
1608 3314 3.637229 AGTACACGATAATGAGGGTCCAG 59.363 47.826 0.00 0.00 0.00 3.86
1622 3328 4.668636 AGGGTCCAGAGATATAGTAGCAC 58.331 47.826 0.00 0.00 0.00 4.40
1702 3455 5.075493 CCTGATATTCTAGCAAGGGCATTT 58.925 41.667 0.00 0.00 44.61 2.32
1705 3459 5.766670 TGATATTCTAGCAAGGGCATTTGAG 59.233 40.000 5.31 0.00 44.61 3.02
1708 3462 5.372343 TTCTAGCAAGGGCATTTGAGATA 57.628 39.130 5.31 0.00 44.61 1.98
1709 3463 4.708177 TCTAGCAAGGGCATTTGAGATAC 58.292 43.478 5.31 0.00 44.61 2.24
1723 3477 5.957771 TTGAGATACTATTGAACTGCCCT 57.042 39.130 0.00 0.00 0.00 5.19
1725 3479 7.432148 TTGAGATACTATTGAACTGCCCTAA 57.568 36.000 0.00 0.00 0.00 2.69
1729 3483 4.235079 ACTATTGAACTGCCCTAATGCA 57.765 40.909 0.00 0.00 39.37 3.96
1735 3494 4.643795 TGCCCTAATGCAGTCTGC 57.356 55.556 18.32 18.32 45.29 4.26
1784 3543 3.702330 TGATTTCGGTACTATGCGTCTG 58.298 45.455 0.00 0.00 0.00 3.51
1796 3555 4.692625 ACTATGCGTCTGATATTTGGCATC 59.307 41.667 0.00 0.00 41.03 3.91
1797 3556 3.198409 TGCGTCTGATATTTGGCATCT 57.802 42.857 0.00 0.00 0.00 2.90
1798 3557 2.874086 TGCGTCTGATATTTGGCATCTG 59.126 45.455 0.00 0.00 0.00 2.90
1799 3558 2.874701 GCGTCTGATATTTGGCATCTGT 59.125 45.455 0.00 0.00 0.00 3.41
1800 3559 3.303593 GCGTCTGATATTTGGCATCTGTG 60.304 47.826 0.00 0.00 0.00 3.66
1801 3560 3.249320 CGTCTGATATTTGGCATCTGTGG 59.751 47.826 0.00 0.00 0.00 4.17
1802 3561 3.567164 GTCTGATATTTGGCATCTGTGGG 59.433 47.826 0.00 0.00 0.00 4.61
1803 3562 2.295349 CTGATATTTGGCATCTGTGGGC 59.705 50.000 0.00 0.00 0.00 5.36
1805 3564 3.138098 TGATATTTGGCATCTGTGGGCTA 59.862 43.478 0.00 0.00 0.00 3.93
1806 3565 2.761786 ATTTGGCATCTGTGGGCTAT 57.238 45.000 0.00 0.00 0.00 2.97
1808 3567 2.638480 TTGGCATCTGTGGGCTATAC 57.362 50.000 0.00 0.00 0.00 1.47
1809 3568 0.392706 TGGCATCTGTGGGCTATACG 59.607 55.000 0.00 0.00 0.00 3.06
1811 3570 0.679505 GCATCTGTGGGCTATACGGA 59.320 55.000 0.00 0.00 37.79 4.69
1812 3571 1.337260 GCATCTGTGGGCTATACGGAG 60.337 57.143 0.00 0.00 36.91 4.63
1814 3573 2.154567 TCTGTGGGCTATACGGAGTT 57.845 50.000 0.00 0.00 37.78 3.01
1815 3574 2.463752 TCTGTGGGCTATACGGAGTTT 58.536 47.619 0.00 0.00 37.78 2.66
1817 3576 1.483415 TGTGGGCTATACGGAGTTTCC 59.517 52.381 0.00 0.00 37.78 3.13
1818 3577 1.483415 GTGGGCTATACGGAGTTTCCA 59.517 52.381 0.00 0.00 37.78 3.53
1819 3578 2.093341 GTGGGCTATACGGAGTTTCCAA 60.093 50.000 0.00 0.00 37.78 3.53
1820 3579 2.093341 TGGGCTATACGGAGTTTCCAAC 60.093 50.000 0.00 0.00 37.78 3.77
1827 3603 2.014128 ACGGAGTTTCCAACACTTGTG 58.986 47.619 0.00 0.00 37.78 3.33
1890 3677 3.855858 TGTTGTTATGCTGCACTCGATA 58.144 40.909 3.57 0.00 0.00 2.92
1918 3705 9.798994 AAAAGCTTAATGCAAAGAGATATTCTG 57.201 29.630 0.00 0.00 45.94 3.02
1920 3707 8.152309 AGCTTAATGCAAAGAGATATTCTGAC 57.848 34.615 2.23 0.00 45.94 3.51
1922 3709 8.566260 GCTTAATGCAAAGAGATATTCTGACAT 58.434 33.333 2.23 0.00 42.31 3.06
2048 3835 0.882042 AGCTCCAACACAACAGCTCG 60.882 55.000 0.00 0.00 37.72 5.03
2137 3927 3.070159 AGGTTGGACGATATGACTCCATG 59.930 47.826 0.00 0.00 33.99 3.66
2206 4012 4.150804 GCCGAAGTTCAGTCTCTTAACTTG 59.849 45.833 11.94 6.49 42.06 3.16
2505 4320 6.763135 GCTAAGATTATGTGAACTGACATGGA 59.237 38.462 0.00 0.00 37.16 3.41
2684 4501 7.984422 AGATGATATAATCGGTGCAAAATGA 57.016 32.000 0.00 0.00 0.00 2.57
2686 4503 8.456471 AGATGATATAATCGGTGCAAAATGATG 58.544 33.333 0.00 0.00 0.00 3.07
2687 4504 7.509141 TGATATAATCGGTGCAAAATGATGT 57.491 32.000 0.00 0.00 0.00 3.06
2688 4505 8.614469 TGATATAATCGGTGCAAAATGATGTA 57.386 30.769 0.00 0.00 0.00 2.29
2692 4509 6.455360 AATCGGTGCAAAATGATGTAATCT 57.545 33.333 0.00 0.00 45.81 2.40
2694 4511 3.792956 CGGTGCAAAATGATGTAATCTGC 59.207 43.478 0.00 0.00 45.81 4.26
2695 4512 4.439153 CGGTGCAAAATGATGTAATCTGCT 60.439 41.667 0.00 0.00 45.81 4.24
2696 4513 5.220835 CGGTGCAAAATGATGTAATCTGCTA 60.221 40.000 0.00 0.00 45.81 3.49
2697 4514 6.563422 GGTGCAAAATGATGTAATCTGCTAA 58.437 36.000 0.00 0.00 45.81 3.09
2698 4515 7.205297 GGTGCAAAATGATGTAATCTGCTAAT 58.795 34.615 0.00 0.00 45.81 1.73
2699 4516 7.168637 GGTGCAAAATGATGTAATCTGCTAATG 59.831 37.037 0.00 0.00 45.81 1.90
2700 4517 7.168637 GTGCAAAATGATGTAATCTGCTAATGG 59.831 37.037 0.00 0.00 45.81 3.16
2701 4518 7.147863 TGCAAAATGATGTAATCTGCTAATGGT 60.148 33.333 0.00 0.00 45.81 3.55
2702 4519 7.168637 GCAAAATGATGTAATCTGCTAATGGTG 59.831 37.037 0.00 0.00 45.81 4.17
2756 4573 5.913137 TCCCAAAATATGTCATGTTGGTC 57.087 39.130 17.10 0.00 37.60 4.02
2903 4725 8.628882 AAACTTGGTCGACTTTTTAAAATGAG 57.371 30.769 16.46 8.98 0.00 2.90
3010 4833 5.434408 ACTGCTGCATCTTTATGAGATCAA 58.566 37.500 1.31 0.00 43.32 2.57
3037 4910 2.111384 GATTCAGCAGTACTCCCTCCA 58.889 52.381 0.00 0.00 0.00 3.86
3190 5325 4.698201 TTGTGTACATGAGTGGGAGAAA 57.302 40.909 0.00 0.00 0.00 2.52
3396 5531 8.922237 ACTACATCTCTTGATATTGACAGTGAT 58.078 33.333 0.00 0.00 0.00 3.06
3397 5532 9.194271 CTACATCTCTTGATATTGACAGTGATG 57.806 37.037 0.00 8.00 35.23 3.07
3398 5533 7.789026 ACATCTCTTGATATTGACAGTGATGA 58.211 34.615 14.02 0.00 33.85 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 1.687493 GGAGGAGGTGGTGGAGGAG 60.687 68.421 0.00 0.00 0.00 3.69
78 79 2.169590 GAGGAGGAGGTGGTGGAGGA 62.170 65.000 0.00 0.00 0.00 3.71
79 80 1.687493 GAGGAGGAGGTGGTGGAGG 60.687 68.421 0.00 0.00 0.00 4.30
172 176 1.154580 GAGACAAACGCGCAGAAGC 60.155 57.895 5.73 0.00 37.42 3.86
325 343 2.104859 CGTACGCGGTCTCTCTCCA 61.105 63.158 12.47 0.00 0.00 3.86
334 352 3.558505 GATCAACATATACGTACGCGGT 58.441 45.455 16.72 0.39 43.45 5.68
370 388 2.202570 GCACGTACACGGCTCGAT 60.203 61.111 6.72 0.00 44.95 3.59
371 389 3.359523 AGCACGTACACGGCTCGA 61.360 61.111 6.72 0.00 44.95 4.04
374 392 2.167398 AATCCAGCACGTACACGGCT 62.167 55.000 6.72 8.98 43.15 5.52
376 394 1.274596 GTAATCCAGCACGTACACGG 58.725 55.000 6.72 0.00 44.95 4.94
400 451 7.216881 GGTTTGTTAAGTTATAAACCGAATCGC 59.783 37.037 18.75 3.82 41.60 4.58
420 471 2.036217 TCCAGAATCGTACACGGTTTGT 59.964 45.455 1.27 0.00 43.48 2.83
566 808 7.693951 GTGAACAGCTATTGAACATGTGAATAC 59.306 37.037 0.00 1.78 0.00 1.89
579 821 4.801147 ATATGTGCGTGAACAGCTATTG 57.199 40.909 0.00 0.00 32.52 1.90
582 824 4.270084 GCTTTATATGTGCGTGAACAGCTA 59.730 41.667 0.00 0.00 32.52 3.32
584 826 3.063997 AGCTTTATATGTGCGTGAACAGC 59.936 43.478 0.00 0.00 32.52 4.40
730 2331 9.516546 CCATTATACTCACACATAGGAGTACTA 57.483 37.037 0.00 0.00 46.17 1.82
731 2332 7.451877 CCCATTATACTCACACATAGGAGTACT 59.548 40.741 0.00 0.00 46.17 2.73
732 2333 7.603651 CCCATTATACTCACACATAGGAGTAC 58.396 42.308 3.85 0.00 46.17 2.73
734 2335 5.012148 GCCCATTATACTCACACATAGGAGT 59.988 44.000 0.00 0.00 45.72 3.85
735 2336 5.482908 GCCCATTATACTCACACATAGGAG 58.517 45.833 0.00 0.00 37.18 3.69
736 2337 4.286032 GGCCCATTATACTCACACATAGGA 59.714 45.833 0.00 0.00 0.00 2.94
737 2338 4.041567 TGGCCCATTATACTCACACATAGG 59.958 45.833 0.00 0.00 0.00 2.57
738 2339 5.227569 TGGCCCATTATACTCACACATAG 57.772 43.478 0.00 0.00 0.00 2.23
739 2340 5.368230 TCTTGGCCCATTATACTCACACATA 59.632 40.000 0.00 0.00 0.00 2.29
740 2341 4.165950 TCTTGGCCCATTATACTCACACAT 59.834 41.667 0.00 0.00 0.00 3.21
741 2342 3.521531 TCTTGGCCCATTATACTCACACA 59.478 43.478 0.00 0.00 0.00 3.72
742 2343 4.150897 TCTTGGCCCATTATACTCACAC 57.849 45.455 0.00 0.00 0.00 3.82
743 2344 4.411869 TCATCTTGGCCCATTATACTCACA 59.588 41.667 0.00 0.00 0.00 3.58
744 2345 4.973168 TCATCTTGGCCCATTATACTCAC 58.027 43.478 0.00 0.00 0.00 3.51
745 2346 4.907269 TCTCATCTTGGCCCATTATACTCA 59.093 41.667 0.00 0.00 0.00 3.41
746 2347 5.486526 CTCTCATCTTGGCCCATTATACTC 58.513 45.833 0.00 0.00 0.00 2.59
747 2348 4.263243 GCTCTCATCTTGGCCCATTATACT 60.263 45.833 0.00 0.00 0.00 2.12
748 2349 4.006319 GCTCTCATCTTGGCCCATTATAC 58.994 47.826 0.00 0.00 0.00 1.47
749 2350 3.306989 CGCTCTCATCTTGGCCCATTATA 60.307 47.826 0.00 0.00 0.00 0.98
750 2351 2.551721 CGCTCTCATCTTGGCCCATTAT 60.552 50.000 0.00 0.00 0.00 1.28
751 2352 1.202687 CGCTCTCATCTTGGCCCATTA 60.203 52.381 0.00 0.00 0.00 1.90
760 2361 0.909610 TTGGTCCCCGCTCTCATCTT 60.910 55.000 0.00 0.00 0.00 2.40
813 2442 2.338381 GGATACGGGCTCTCGCTAA 58.662 57.895 0.00 0.00 36.09 3.09
814 2443 4.076244 GGATACGGGCTCTCGCTA 57.924 61.111 0.00 0.00 36.09 4.26
937 2566 0.533032 CGGGGAGAGAGAGGAACAAC 59.467 60.000 0.00 0.00 0.00 3.32
949 2578 1.826921 GCTGGTACGATCGGGGAGA 60.827 63.158 20.98 0.00 0.00 3.71
972 2608 3.380320 TCGATTCTTCTTGGATGCTCGTA 59.620 43.478 0.00 0.00 0.00 3.43
973 2609 2.166459 TCGATTCTTCTTGGATGCTCGT 59.834 45.455 0.00 0.00 0.00 4.18
974 2610 2.814269 TCGATTCTTCTTGGATGCTCG 58.186 47.619 0.00 0.00 0.00 5.03
975 2611 3.559242 CCTTCGATTCTTCTTGGATGCTC 59.441 47.826 0.00 0.00 0.00 4.26
1162 2798 1.227089 CGCGGCTGATGAAGTAGCT 60.227 57.895 0.00 0.00 39.80 3.32
1339 2975 9.678941 CGCAAGAATCATTGAATAGTAGTAGTA 57.321 33.333 0.00 0.00 43.02 1.82
1341 2977 7.653713 ACCGCAAGAATCATTGAATAGTAGTAG 59.346 37.037 0.00 0.00 43.02 2.57
1342 2978 7.438160 CACCGCAAGAATCATTGAATAGTAGTA 59.562 37.037 0.00 0.00 43.02 1.82
1343 2979 6.258727 CACCGCAAGAATCATTGAATAGTAGT 59.741 38.462 0.00 0.00 43.02 2.73
1344 2980 6.653183 CACCGCAAGAATCATTGAATAGTAG 58.347 40.000 0.00 0.00 43.02 2.57
1345 2981 5.007626 GCACCGCAAGAATCATTGAATAGTA 59.992 40.000 0.00 0.00 43.02 1.82
1352 2988 1.904144 CAGCACCGCAAGAATCATTG 58.096 50.000 0.00 0.00 43.02 2.82
1355 2991 2.334946 GGCAGCACCGCAAGAATCA 61.335 57.895 0.00 0.00 43.02 2.57
1367 3003 1.597854 CCTCAAGAACACGGCAGCA 60.598 57.895 0.00 0.00 0.00 4.41
1382 3018 1.452108 CATGAAGCCGGGGTTCCTC 60.452 63.158 30.13 12.25 39.02 3.71
1383 3019 1.281925 ATCATGAAGCCGGGGTTCCT 61.282 55.000 30.13 20.87 39.02 3.36
1384 3020 0.395724 AATCATGAAGCCGGGGTTCC 60.396 55.000 30.13 16.17 39.02 3.62
1393 3031 3.881688 AGTAGTGCCATGAATCATGAAGC 59.118 43.478 23.55 18.63 43.81 3.86
1398 3036 5.363562 TCTCAAGTAGTGCCATGAATCAT 57.636 39.130 0.00 0.00 0.00 2.45
1410 3048 6.183360 CCATCCTGCTCTTTATCTCAAGTAGT 60.183 42.308 0.00 0.00 0.00 2.73
1416 3054 4.964897 TCTTCCATCCTGCTCTTTATCTCA 59.035 41.667 0.00 0.00 0.00 3.27
1423 3061 4.411540 ACATGTATCTTCCATCCTGCTCTT 59.588 41.667 0.00 0.00 0.00 2.85
1429 3074 3.389329 AGCGAACATGTATCTTCCATCCT 59.611 43.478 0.00 0.00 0.00 3.24
1463 3109 0.322816 ACAGCCGCAATGGACAGATT 60.323 50.000 0.00 0.00 42.00 2.40
1464 3110 1.028330 CACAGCCGCAATGGACAGAT 61.028 55.000 0.00 0.00 42.00 2.90
1466 3112 2.693762 CCACAGCCGCAATGGACAG 61.694 63.158 7.04 0.00 42.00 3.51
1467 3113 2.672651 CCACAGCCGCAATGGACA 60.673 61.111 7.04 0.00 42.00 4.02
1468 3114 1.926511 CTTCCACAGCCGCAATGGAC 61.927 60.000 13.69 0.00 42.26 4.02
1471 3117 0.447801 GTACTTCCACAGCCGCAATG 59.552 55.000 0.00 0.00 0.00 2.82
1472 3118 0.036164 TGTACTTCCACAGCCGCAAT 59.964 50.000 0.00 0.00 0.00 3.56
1493 3145 0.109086 AGAGATCAACAGGTCGCACG 60.109 55.000 0.00 0.00 0.00 5.34
1521 3192 6.891908 AGCTTTGGAACCTGAACAACATATAT 59.108 34.615 0.00 0.00 0.00 0.86
1522 3193 6.245408 AGCTTTGGAACCTGAACAACATATA 58.755 36.000 0.00 0.00 0.00 0.86
1524 3195 4.469657 AGCTTTGGAACCTGAACAACATA 58.530 39.130 0.00 0.00 0.00 2.29
1537 3243 6.219417 TCAAAACTCAATCAAGCTTTGGAA 57.781 33.333 0.00 0.00 34.56 3.53
1543 3249 3.225104 TGGCTCAAAACTCAATCAAGCT 58.775 40.909 0.00 0.00 0.00 3.74
1560 3266 6.604795 ACTGCTAATATTTGATGAAACTGGCT 59.395 34.615 0.77 0.00 0.00 4.75
1579 3285 5.472478 CCCTCATTATCGTGTACTACTGCTA 59.528 44.000 0.00 0.00 0.00 3.49
1580 3286 4.278669 CCCTCATTATCGTGTACTACTGCT 59.721 45.833 0.00 0.00 0.00 4.24
1581 3287 4.037684 ACCCTCATTATCGTGTACTACTGC 59.962 45.833 0.00 0.00 0.00 4.40
1582 3288 5.278364 GGACCCTCATTATCGTGTACTACTG 60.278 48.000 0.00 0.00 0.00 2.74
1583 3289 4.826183 GGACCCTCATTATCGTGTACTACT 59.174 45.833 0.00 0.00 0.00 2.57
1584 3290 4.581824 TGGACCCTCATTATCGTGTACTAC 59.418 45.833 0.00 0.00 0.00 2.73
1597 3303 5.015710 TGCTACTATATCTCTGGACCCTCAT 59.984 44.000 0.00 0.00 0.00 2.90
1599 3305 4.703093 GTGCTACTATATCTCTGGACCCTC 59.297 50.000 0.00 0.00 0.00 4.30
1608 3314 8.307483 TGCTCAAATAAGGTGCTACTATATCTC 58.693 37.037 0.00 0.00 0.00 2.75
1622 3328 4.022068 TGCTTCCAACTTGCTCAAATAAGG 60.022 41.667 0.00 0.00 0.00 2.69
1689 3442 4.778213 AGTATCTCAAATGCCCTTGCTA 57.222 40.909 0.00 0.00 38.71 3.49
1702 3455 7.445121 CATTAGGGCAGTTCAATAGTATCTCA 58.555 38.462 0.00 0.00 0.00 3.27
1705 3459 5.997746 TGCATTAGGGCAGTTCAATAGTATC 59.002 40.000 0.00 0.00 39.25 2.24
1708 3462 4.235079 TGCATTAGGGCAGTTCAATAGT 57.765 40.909 0.00 0.00 39.25 2.12
1729 3483 5.625150 AGTTGAGTTGGAAAATAGCAGACT 58.375 37.500 0.00 0.00 0.00 3.24
1735 3494 7.616313 AGGAGTAGAGTTGAGTTGGAAAATAG 58.384 38.462 0.00 0.00 0.00 1.73
1784 3543 2.590821 AGCCCACAGATGCCAAATATC 58.409 47.619 0.00 0.00 0.00 1.63
1796 3555 2.483188 GGAAACTCCGTATAGCCCACAG 60.483 54.545 0.00 0.00 0.00 3.66
1797 3556 1.483415 GGAAACTCCGTATAGCCCACA 59.517 52.381 0.00 0.00 0.00 4.17
1798 3557 1.483415 TGGAAACTCCGTATAGCCCAC 59.517 52.381 0.00 0.00 40.17 4.61
1799 3558 1.868713 TGGAAACTCCGTATAGCCCA 58.131 50.000 0.00 0.00 40.17 5.36
1800 3559 2.558378 GTTGGAAACTCCGTATAGCCC 58.442 52.381 0.00 0.00 45.32 5.19
1814 3573 1.134848 GCTTTGCCACAAGTGTTGGAA 60.135 47.619 0.00 0.00 34.12 3.53
1815 3574 0.459489 GCTTTGCCACAAGTGTTGGA 59.541 50.000 0.00 0.00 34.12 3.53
1817 3576 1.563111 CAGCTTTGCCACAAGTGTTG 58.437 50.000 0.00 0.00 0.00 3.33
1818 3577 0.179103 GCAGCTTTGCCACAAGTGTT 60.179 50.000 0.00 0.00 0.00 3.32
1819 3578 1.438814 GCAGCTTTGCCACAAGTGT 59.561 52.632 0.00 0.00 0.00 3.55
1820 3579 1.659335 CGCAGCTTTGCCACAAGTG 60.659 57.895 0.00 0.00 0.00 3.16
1827 3603 1.737793 ACTATGTAACGCAGCTTTGCC 59.262 47.619 0.00 0.00 0.00 4.52
1837 3614 6.140896 GCACTATGCACATACTATGTAACG 57.859 41.667 1.19 0.00 44.26 3.18
1917 3704 7.857389 GCGCAGATTCAGATTAAAATTATGTCA 59.143 33.333 0.30 0.00 0.00 3.58
1918 3705 7.857389 TGCGCAGATTCAGATTAAAATTATGTC 59.143 33.333 5.66 0.00 0.00 3.06
1920 3707 8.635983 CATGCGCAGATTCAGATTAAAATTATG 58.364 33.333 18.32 0.00 0.00 1.90
1922 3709 7.929159 TCATGCGCAGATTCAGATTAAAATTA 58.071 30.769 18.32 0.00 0.00 1.40
1929 3716 6.430308 AGAAATATCATGCGCAGATTCAGATT 59.570 34.615 18.32 11.75 0.00 2.40
2048 3835 5.491982 TCCTCACTAGATTTTGAAAGAGCC 58.508 41.667 0.00 0.00 0.00 4.70
2137 3927 8.521176 TGTAGTCTACTTGTTTGATCCTCTTAC 58.479 37.037 11.28 0.00 0.00 2.34
2416 4231 4.584325 AGTCTCAGTCTGCAGGATAGATTC 59.416 45.833 15.13 2.09 0.00 2.52
2422 4237 3.072184 ACAAAAGTCTCAGTCTGCAGGAT 59.928 43.478 15.13 0.00 0.00 3.24
2505 4320 8.432805 ACATCTACACATAGCTTTAAGCCTTAT 58.567 33.333 13.84 3.19 43.77 1.73
2667 4484 8.077991 CAGATTACATCATTTTGCACCGATTAT 58.922 33.333 0.00 0.00 0.00 1.28
2684 4501 5.372343 TGACCACCATTAGCAGATTACAT 57.628 39.130 0.00 0.00 0.00 2.29
2686 4503 6.318648 TGATTTGACCACCATTAGCAGATTAC 59.681 38.462 0.00 0.00 0.00 1.89
2687 4504 6.422333 TGATTTGACCACCATTAGCAGATTA 58.578 36.000 0.00 0.00 0.00 1.75
2688 4505 5.263599 TGATTTGACCACCATTAGCAGATT 58.736 37.500 0.00 0.00 0.00 2.40
2692 4509 4.032960 ACTGATTTGACCACCATTAGCA 57.967 40.909 0.00 0.00 0.00 3.49
2694 4511 5.943416 TGGTTACTGATTTGACCACCATTAG 59.057 40.000 0.00 0.00 37.26 1.73
2695 4512 5.882040 TGGTTACTGATTTGACCACCATTA 58.118 37.500 0.00 0.00 37.26 1.90
2696 4513 4.735369 TGGTTACTGATTTGACCACCATT 58.265 39.130 0.00 0.00 37.26 3.16
2697 4514 4.202567 ACTGGTTACTGATTTGACCACCAT 60.203 41.667 0.00 0.00 37.26 3.55
2698 4515 3.137544 ACTGGTTACTGATTTGACCACCA 59.862 43.478 0.00 0.00 37.26 4.17
2699 4516 3.502211 CACTGGTTACTGATTTGACCACC 59.498 47.826 0.00 0.00 37.26 4.61
2700 4517 3.058224 GCACTGGTTACTGATTTGACCAC 60.058 47.826 0.00 0.00 37.26 4.16
2701 4518 3.146066 GCACTGGTTACTGATTTGACCA 58.854 45.455 0.00 0.00 39.72 4.02
2702 4519 3.146066 TGCACTGGTTACTGATTTGACC 58.854 45.455 0.00 0.00 0.00 4.02
2756 4573 8.219105 GCTTTTTCTATGAAATTGCTCAACAAG 58.781 33.333 0.00 0.00 42.87 3.16
2968 4791 6.646653 CAGCAGTTGATGTAGTACTTGAGAAA 59.353 38.462 0.00 0.00 0.00 2.52
2976 4799 4.437239 AGATGCAGCAGTTGATGTAGTAC 58.563 43.478 4.07 0.00 33.30 2.73
2977 4800 4.743057 AGATGCAGCAGTTGATGTAGTA 57.257 40.909 4.07 0.00 33.30 1.82
2978 4801 3.623906 AGATGCAGCAGTTGATGTAGT 57.376 42.857 4.07 0.00 33.30 2.73
2979 4802 4.959596 AAAGATGCAGCAGTTGATGTAG 57.040 40.909 4.07 0.00 33.30 2.74
3010 4833 4.323104 GGGAGTACTGCTGAATCTTTGAGT 60.323 45.833 14.52 0.00 0.00 3.41
3017 4840 2.111384 TGGAGGGAGTACTGCTGAATC 58.889 52.381 14.52 7.46 0.00 2.52
3024 4847 8.190326 TGTATTATGTTATGGAGGGAGTACTG 57.810 38.462 0.00 0.00 0.00 2.74
3156 5291 5.475220 TCATGTACACAATTGTTAACCCCAG 59.525 40.000 8.77 0.00 37.15 4.45


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

AutoCloner maintained by Alex Coulton.