Multiple sequence alignment - TraesCS3B01G334600

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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 TraesCS3B01G334600 chr3B 100.000 4803 0 0 1 4803 540726863 540731665 0.000000e+00 8870.0
1 TraesCS3B01G334600 chr3B 91.856 749 57 1 2 746 774795885 774795137 0.000000e+00 1042.0
2 TraesCS3B01G334600 chr3B 91.322 749 61 1 2 746 763274970 763274222 0.000000e+00 1020.0
3 TraesCS3B01G334600 chr3B 90.763 498 38 4 2307 2804 367487951 367487462 0.000000e+00 658.0
4 TraesCS3B01G334600 chr3B 83.677 631 78 13 1526 2148 367489334 367488721 5.390000e-159 571.0
5 TraesCS3B01G334600 chr3B 81.800 489 56 29 1736 2206 672673786 672673313 3.510000e-101 379.0
6 TraesCS3B01G334600 chr3B 84.880 291 29 12 3219 3497 770094536 770094823 3.660000e-71 279.0
7 TraesCS3B01G334600 chr3B 85.560 277 27 8 3219 3491 545011180 545010913 1.320000e-70 278.0
8 TraesCS3B01G334600 chr3B 84.536 291 30 12 3219 3497 770091126 770091413 1.700000e-69 274.0
9 TraesCS3B01G334600 chr3B 92.941 85 6 0 947 1031 367489856 367489772 1.810000e-24 124.0
10 TraesCS3B01G334600 chr3D 92.969 2617 108 25 2203 4803 414906269 414908825 0.000000e+00 3744.0
11 TraesCS3B01G334600 chr3D 95.471 1391 41 13 744 2120 414904507 414905889 0.000000e+00 2200.0
12 TraesCS3B01G334600 chr3D 80.844 308 29 16 3219 3497 380384973 380384667 1.050000e-51 215.0
13 TraesCS3B01G334600 chr3A 93.092 1766 74 19 3055 4803 535225213 535223479 0.000000e+00 2542.0
14 TraesCS3B01G334600 chr3A 95.022 1366 47 9 756 2120 535228084 535226739 0.000000e+00 2126.0
15 TraesCS3B01G334600 chr3A 93.586 686 28 4 2201 2873 535226419 535225737 0.000000e+00 1009.0
16 TraesCS3B01G334600 chr3A 94.737 190 10 0 2868 3057 535225525 535225336 3.630000e-76 296.0
17 TraesCS3B01G334600 chr3A 85.106 94 14 0 2815 2908 164625395 164625488 3.960000e-16 97.1
18 TraesCS3B01G334600 chr2B 92.267 750 53 2 1 746 541916886 541916138 0.000000e+00 1059.0
19 TraesCS3B01G334600 chr2B 89.006 473 37 7 2341 2813 1849585 1849128 5.390000e-159 571.0
20 TraesCS3B01G334600 chr5B 91.055 749 63 2 2 746 623559765 623559017 0.000000e+00 1009.0
21 TraesCS3B01G334600 chr5B 90.921 749 64 1 2 746 627157999 627157251 0.000000e+00 1003.0
22 TraesCS3B01G334600 chr5B 89.423 520 40 9 2294 2813 693117822 693118326 4.050000e-180 641.0
23 TraesCS3B01G334600 chr5B 80.491 692 79 28 1523 2206 693117138 693117781 3.360000e-131 479.0
24 TraesCS3B01G334600 chr5B 95.122 41 2 0 2811 2851 621208858 621208818 1.120000e-06 65.8
25 TraesCS3B01G334600 chr7B 88.385 749 83 3 2 746 639866763 639867511 0.000000e+00 898.0
26 TraesCS3B01G334600 chr7B 80.800 750 132 7 2 743 630545626 630546371 1.160000e-160 577.0
27 TraesCS3B01G334600 chr7B 79.568 695 86 32 1520 2206 382731035 382731681 3.410000e-121 446.0
28 TraesCS3B01G334600 chr7B 85.932 263 32 4 1174 1435 82145036 82145294 4.740000e-70 276.0
29 TraesCS3B01G334600 chr7A 83.665 753 117 4 2 750 598357519 598356769 0.000000e+00 704.0
30 TraesCS3B01G334600 chr7A 80.734 109 19 2 2801 2907 112339587 112339479 3.080000e-12 84.2
31 TraesCS3B01G334600 chr7A 82.000 100 14 4 2811 2908 654781584 654781681 1.110000e-11 82.4
32 TraesCS3B01G334600 chr2A 90.962 520 32 8 2294 2813 665835724 665836228 0.000000e+00 686.0
33 TraesCS3B01G334600 chr2A 85.468 406 46 7 2906 3305 665836226 665836624 1.240000e-110 411.0
34 TraesCS3B01G334600 chr2A 86.053 380 45 6 1119 1494 665834606 665834981 7.490000e-108 401.0
35 TraesCS3B01G334600 chr2A 85.411 377 44 7 1119 1494 665833527 665833893 9.750000e-102 381.0
36 TraesCS3B01G334600 chr2A 86.411 287 36 1 1518 1804 665834977 665835260 1.300000e-80 311.0
37 TraesCS3B01G334600 chr2A 77.946 331 44 15 1886 2206 665835364 665835675 3.820000e-41 180.0
38 TraesCS3B01G334600 chr6A 90.769 520 32 8 2294 2813 102112237 102112740 0.000000e+00 680.0
39 TraesCS3B01G334600 chr6A 81.392 747 129 5 2 741 607049065 607049808 6.880000e-168 601.0
40 TraesCS3B01G334600 chr6A 79.196 721 96 37 1518 2206 3276791 3277489 7.330000e-123 451.0
41 TraesCS3B01G334600 chr6A 85.942 377 42 7 1119 1494 102111128 102111494 4.510000e-105 392.0
42 TraesCS3B01G334600 chr6A 85.484 372 46 7 1127 1494 3276428 3276795 9.750000e-102 381.0
43 TraesCS3B01G334600 chr6A 86.760 287 35 1 1518 1804 102111490 102111773 2.790000e-82 316.0
44 TraesCS3B01G334600 chr6A 82.938 211 23 7 1886 2087 102111877 102112083 1.370000e-40 178.0
45 TraesCS3B01G334600 chr5D 88.091 571 51 7 2245 2813 127880043 127880598 0.000000e+00 662.0
46 TraesCS3B01G334600 chr5D 83.967 605 62 19 2906 3490 127880596 127881185 9.090000e-152 547.0
47 TraesCS3B01G334600 chr5D 88.010 417 45 4 1518 1933 127879198 127879610 5.590000e-134 488.0
48 TraesCS3B01G334600 chr1B 91.131 451 35 4 2294 2741 319969958 319970406 1.480000e-169 606.0
49 TraesCS3B01G334600 chr1B 80.363 331 40 12 1886 2206 319969602 319969917 1.340000e-55 228.0
50 TraesCS3B01G334600 chr1B 90.476 63 4 2 2846 2907 486974393 486974454 1.110000e-11 82.4
51 TraesCS3B01G334600 chr6D 87.072 263 29 4 1174 1435 231083423 231083165 4.700000e-75 292.0
52 TraesCS3B01G334600 chr6B 86.920 237 28 3 1186 1420 660668999 660668764 3.690000e-66 263.0
53 TraesCS3B01G334600 chr6B 91.860 86 6 1 997 1082 660669146 660669062 8.440000e-23 119.0
54 TraesCS3B01G334600 chr1A 83.904 292 30 15 3219 3497 50705071 50705358 3.690000e-66 263.0
55 TraesCS3B01G334600 chr1A 82.828 99 10 6 2813 2905 50930707 50930610 1.110000e-11 82.4
56 TraesCS3B01G334600 chr4B 90.116 172 16 1 3468 3638 355507079 355507250 6.260000e-54 222.0
57 TraesCS3B01G334600 chr4B 81.132 106 15 2 2811 2911 131353626 131353521 3.980000e-11 80.5
58 TraesCS3B01G334600 chr7D 91.089 101 9 0 2807 2907 29877476 29877576 2.330000e-28 137.0
59 TraesCS3B01G334600 chr2D 80.556 180 23 9 1009 1187 604702154 604701986 1.400000e-25 128.0


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 TraesCS3B01G334600 chr3B 540726863 540731665 4802 False 8870.000000 8870 100.000000 1 4803 1 chr3B.!!$F1 4802
1 TraesCS3B01G334600 chr3B 774795137 774795885 748 True 1042.000000 1042 91.856000 2 746 1 chr3B.!!$R4 744
2 TraesCS3B01G334600 chr3B 763274222 763274970 748 True 1020.000000 1020 91.322000 2 746 1 chr3B.!!$R3 744
3 TraesCS3B01G334600 chr3B 367487462 367489856 2394 True 451.000000 658 89.127000 947 2804 3 chr3B.!!$R5 1857
4 TraesCS3B01G334600 chr3B 770091126 770094823 3697 False 276.500000 279 84.708000 3219 3497 2 chr3B.!!$F2 278
5 TraesCS3B01G334600 chr3D 414904507 414908825 4318 False 2972.000000 3744 94.220000 744 4803 2 chr3D.!!$F1 4059
6 TraesCS3B01G334600 chr3A 535223479 535228084 4605 True 1493.250000 2542 94.109250 756 4803 4 chr3A.!!$R1 4047
7 TraesCS3B01G334600 chr2B 541916138 541916886 748 True 1059.000000 1059 92.267000 1 746 1 chr2B.!!$R2 745
8 TraesCS3B01G334600 chr5B 623559017 623559765 748 True 1009.000000 1009 91.055000 2 746 1 chr5B.!!$R2 744
9 TraesCS3B01G334600 chr5B 627157251 627157999 748 True 1003.000000 1003 90.921000 2 746 1 chr5B.!!$R3 744
10 TraesCS3B01G334600 chr5B 693117138 693118326 1188 False 560.000000 641 84.957000 1523 2813 2 chr5B.!!$F1 1290
11 TraesCS3B01G334600 chr7B 639866763 639867511 748 False 898.000000 898 88.385000 2 746 1 chr7B.!!$F4 744
12 TraesCS3B01G334600 chr7B 630545626 630546371 745 False 577.000000 577 80.800000 2 743 1 chr7B.!!$F3 741
13 TraesCS3B01G334600 chr7B 382731035 382731681 646 False 446.000000 446 79.568000 1520 2206 1 chr7B.!!$F2 686
14 TraesCS3B01G334600 chr7A 598356769 598357519 750 True 704.000000 704 83.665000 2 750 1 chr7A.!!$R2 748
15 TraesCS3B01G334600 chr2A 665833527 665836624 3097 False 395.000000 686 85.375167 1119 3305 6 chr2A.!!$F1 2186
16 TraesCS3B01G334600 chr6A 607049065 607049808 743 False 601.000000 601 81.392000 2 741 1 chr6A.!!$F1 739
17 TraesCS3B01G334600 chr6A 3276428 3277489 1061 False 416.000000 451 82.340000 1127 2206 2 chr6A.!!$F2 1079
18 TraesCS3B01G334600 chr6A 102111128 102112740 1612 False 391.500000 680 86.602250 1119 2813 4 chr6A.!!$F3 1694
19 TraesCS3B01G334600 chr5D 127879198 127881185 1987 False 565.666667 662 86.689333 1518 3490 3 chr5D.!!$F1 1972
20 TraesCS3B01G334600 chr1B 319969602 319970406 804 False 417.000000 606 85.747000 1886 2741 2 chr1B.!!$F2 855

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
667 672 0.898326 TGACGAGCTAGGAGTGCCAA 60.898 55.000 0.00 0.0 36.29 4.52 F
1310 2401 0.687354 TTCCTCTCAACCAGGTGAGC 59.313 55.000 7.87 0.0 44.01 4.26 F
1921 3077 1.003118 TCACGAGCTGGCCTGTTATTT 59.997 47.619 11.69 0.0 0.00 1.40 F
1922 3078 1.398390 CACGAGCTGGCCTGTTATTTC 59.602 52.381 11.69 1.7 0.00 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2166 3401 1.407434 ACAATGTTGCGCATGTTTCG 58.593 45.000 12.75 0.75 37.96 3.46 R
2743 4774 2.159382 ACATACCTGTCAAAAAGGCCG 58.841 47.619 0.00 0.00 38.48 6.13 R
3706 6101 2.084546 CCCCACTCCAGAAAATTCGAC 58.915 52.381 0.00 0.00 0.00 4.20 R
3891 6286 5.869579 TGCTTTCAACTGAGGTTAGAGATT 58.130 37.500 0.00 0.00 33.88 2.40 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
27 28 2.036346 TGCCATATGTCTCTCATGTCGG 59.964 50.000 1.24 0.00 37.91 4.79
48 49 1.637553 ACTGAGCCAGTTGGGATTGAT 59.362 47.619 0.00 0.00 42.59 2.57
267 268 1.846712 AAGCCCAGAAGTCCTCCTGC 61.847 60.000 0.00 0.00 0.00 4.85
291 292 3.947834 GCCTTGTGCTGAGTGGTATATTT 59.052 43.478 0.00 0.00 36.87 1.40
344 345 5.269505 TGTTCTTCTAGAGCTGGCTTATC 57.730 43.478 0.00 0.00 0.00 1.75
354 355 1.002430 GCTGGCTTATCCCATGATCGA 59.998 52.381 0.00 0.00 33.64 3.59
397 398 2.348243 CCAACTCCGGCGGGTTTA 59.652 61.111 27.98 5.30 33.83 2.01
405 406 1.493134 CCGGCGGGTTTACTAATCGC 61.493 60.000 20.56 0.00 44.80 4.58
450 451 3.162147 TCTCTCAGTAGCCAGTTGTCT 57.838 47.619 0.00 0.00 0.00 3.41
473 478 6.888088 TCTGACCAAATGCTAGTAGTACTGTA 59.112 38.462 13.29 3.40 0.00 2.74
491 496 6.651975 ACTGTACCGATCCTCTTAATAAGG 57.348 41.667 0.00 0.00 35.05 2.69
590 595 4.593206 AGCAGATCAGTATCCGGGAAATAA 59.407 41.667 0.00 0.00 31.98 1.40
667 672 0.898326 TGACGAGCTAGGAGTGCCAA 60.898 55.000 0.00 0.00 36.29 4.52
794 799 2.223994 GGACGGCCCAGATAAACTAGAC 60.224 54.545 0.00 0.00 34.14 2.59
806 811 0.916358 AACTAGACCATGCCAGGCCT 60.916 55.000 9.64 0.00 0.00 5.19
846 851 2.101750 TGAGCCCAAATCTACGCGATAA 59.898 45.455 15.93 0.00 0.00 1.75
856 861 1.792949 CTACGCGATAAAGCCCATGTC 59.207 52.381 15.93 0.00 0.00 3.06
1116 1122 2.027625 CACCCGCGTGTCTCCTTTC 61.028 63.158 4.92 0.00 35.10 2.62
1299 2390 2.180276 GTCAAGGCCTACTTCCTCTCA 58.820 52.381 5.16 0.00 37.29 3.27
1310 2401 0.687354 TTCCTCTCAACCAGGTGAGC 59.313 55.000 7.87 0.00 44.01 4.26
1449 2548 5.246656 TGATTTGGTGCAGAGGAATGAAAAT 59.753 36.000 0.00 0.00 0.00 1.82
1668 2771 7.681903 AGAATTATATTCGTGTTTGACCGTTC 58.318 34.615 0.00 0.00 0.00 3.95
1836 2940 4.541973 TGAAGCTGAGCACTATCTTGAA 57.458 40.909 7.39 0.00 0.00 2.69
1921 3077 1.003118 TCACGAGCTGGCCTGTTATTT 59.997 47.619 11.69 0.00 0.00 1.40
1922 3078 1.398390 CACGAGCTGGCCTGTTATTTC 59.602 52.381 11.69 1.70 0.00 2.17
1951 3107 8.919777 AACTGCTAAATAGTGTACTTTTCCTT 57.080 30.769 0.00 0.00 0.00 3.36
1952 3108 8.324163 ACTGCTAAATAGTGTACTTTTCCTTG 57.676 34.615 0.00 0.00 0.00 3.61
2021 3188 8.201464 TGATCAATCCAATTTCCTTTGATGATG 58.799 33.333 0.00 0.00 37.20 3.07
2150 3354 6.372981 CCTTCTTAATTGTTTGCAAAATGCC 58.627 36.000 14.67 1.68 44.23 4.40
2155 3359 8.127954 TCTTAATTGTTTGCAAAATGCCTTTTC 58.872 29.630 14.67 0.00 44.23 2.29
2166 3401 8.555361 TGCAAAATGCCTTTTCAAATTTACTAC 58.445 29.630 0.00 0.00 44.23 2.73
2232 4231 3.464833 ACCCAATCATGCCTAAGATTCCT 59.535 43.478 0.00 0.00 32.43 3.36
2309 4339 2.413112 CAGAAATATGGCACCTATCGCG 59.587 50.000 0.00 0.00 0.00 5.87
2400 4430 5.046529 AGATTATGCAGTAGTTGAGAAGCG 58.953 41.667 0.00 0.00 0.00 4.68
2557 4587 5.684626 GTGATTGAGCAAAGTCAAGAAACTG 59.315 40.000 0.00 0.00 39.78 3.16
2567 4597 9.296400 GCAAAGTCAAGAAACTGTTTTAATGTA 57.704 29.630 7.28 0.00 0.00 2.29
2743 4774 8.830201 ATCTTGCAGATGTTATCATTAGACTC 57.170 34.615 0.00 0.00 32.80 3.36
2789 4820 1.428869 AGTGTTGCACTCCCTTCTCT 58.571 50.000 0.00 0.00 41.21 3.10
2800 4831 6.043127 TGCACTCCCTTCTCTTGCATATTATA 59.957 38.462 0.00 0.00 38.25 0.98
2801 4832 7.108847 GCACTCCCTTCTCTTGCATATTATAT 58.891 38.462 0.00 0.00 33.24 0.86
2828 4859 9.821240 ATATCATATACTCCCTCTGATCCATAC 57.179 37.037 0.00 0.00 0.00 2.39
2856 4887 4.449743 TGACGCACACTTAATACACCTTTC 59.550 41.667 0.00 0.00 0.00 2.62
2880 5129 9.767228 TTCTACTAAAGTTGTACTAAATGTGCA 57.233 29.630 0.00 0.00 39.46 4.57
2942 5191 4.917415 GCAGTGTATGTGTTGTCATTTTCC 59.083 41.667 0.00 0.00 0.00 3.13
3427 5809 6.128063 GCATAACATGGATGCTAGAATCTTCC 60.128 42.308 21.41 0.00 45.14 3.46
3441 5827 8.491950 GCTAGAATCTTCCTTTTCATCGTATTC 58.508 37.037 0.00 0.00 0.00 1.75
3444 5830 7.497249 AGAATCTTCCTTTTCATCGTATTCTGG 59.503 37.037 0.00 0.00 31.75 3.86
3596 5991 5.232463 GTGGAGGTATTGTGTTCGTTCTTA 58.768 41.667 0.00 0.00 0.00 2.10
3632 6027 6.008960 AGCTGATTTCATCCATCCTATTTCC 58.991 40.000 0.00 0.00 0.00 3.13
3706 6101 3.600388 AGAAGTGCTCCAAAATAGACGG 58.400 45.455 0.00 0.00 0.00 4.79
3891 6286 2.447408 TCTGTCGCCATTCCCTACTA 57.553 50.000 0.00 0.00 0.00 1.82
3997 6395 8.214364 AGTGCATTTTTGGGTTTTATCCTTTTA 58.786 29.630 0.00 0.00 0.00 1.52
4055 6457 1.909302 TCCTTCACTCTCCAATGACCC 59.091 52.381 0.00 0.00 0.00 4.46
4062 6465 2.644299 ACTCTCCAATGACCCAATGACA 59.356 45.455 0.00 0.00 0.00 3.58
4152 6555 4.362279 TCTCTTTTCAACAACAATGCTGC 58.638 39.130 0.00 0.00 0.00 5.25
4175 6578 8.006298 TGCCAGGGTTCAGTTATATTATTTTG 57.994 34.615 0.00 0.00 0.00 2.44
4197 6600 1.940613 GCTTATGTTAGGTTCTGCCCG 59.059 52.381 0.00 0.00 38.26 6.13
4202 6605 1.141254 TGTTAGGTTCTGCCCGTTTGA 59.859 47.619 0.00 0.00 38.26 2.69
4204 6607 2.817844 GTTAGGTTCTGCCCGTTTGATT 59.182 45.455 0.00 0.00 38.26 2.57
4209 6613 3.561503 GTTCTGCCCGTTTGATTACAAC 58.438 45.455 0.00 0.00 35.63 3.32
4214 6618 4.363999 TGCCCGTTTGATTACAACAAAAG 58.636 39.130 0.00 0.00 38.63 2.27
4230 6634 4.074970 ACAAAAGAGGCTCACCATTACTG 58.925 43.478 18.26 6.08 39.06 2.74
4273 6677 7.448469 ACTTTGCACTAGTATTCCTCACATTTT 59.552 33.333 0.00 0.00 0.00 1.82
4336 6740 5.980116 CAGCAGTAGTGTATATGGTTCTGAC 59.020 44.000 0.00 0.00 0.00 3.51
4377 6782 0.745468 GTTTGCCAACGGGGTAACAA 59.255 50.000 0.00 0.00 41.33 2.83
4384 6789 3.414269 CCAACGGGGTAACAATGTTACT 58.586 45.455 28.49 11.87 39.74 2.24
4394 6799 7.229907 GGGGTAACAATGTTACTATGGGTATTG 59.770 40.741 28.49 0.00 39.74 1.90
4442 6847 1.273327 GTGCCTCAAATCCCTGGTTTG 59.727 52.381 3.95 3.95 37.79 2.93
4450 6855 1.072266 ATCCCTGGTTTGTGCAGGTA 58.928 50.000 0.00 0.00 34.42 3.08
4496 6901 8.074370 AGTCGCAAAAGGATTTAAAAGTAACTC 58.926 33.333 0.00 0.00 37.28 3.01
4526 6931 7.578458 ACCTAGGGTTCCTTTAGACAATTTA 57.422 36.000 14.81 0.00 34.61 1.40
4566 6990 0.178992 TTCAAAGGTGCACCCAGGAG 60.179 55.000 32.29 17.39 36.42 3.69
4567 6991 1.059584 TCAAAGGTGCACCCAGGAGA 61.060 55.000 32.29 19.35 36.42 3.71
4568 6992 0.178992 CAAAGGTGCACCCAGGAGAA 60.179 55.000 32.29 0.00 36.42 2.87
4569 6993 0.779997 AAAGGTGCACCCAGGAGAAT 59.220 50.000 32.29 8.36 36.42 2.40
4570 6994 0.038744 AAGGTGCACCCAGGAGAATG 59.961 55.000 32.29 0.00 36.42 2.67
4571 6995 1.379044 GGTGCACCCAGGAGAATGG 60.379 63.158 26.31 0.00 40.29 3.16
4577 7001 4.972875 CCAGGAGAATGGGCACTC 57.027 61.111 0.00 0.00 36.64 3.51
4578 7002 1.153289 CCAGGAGAATGGGCACTCG 60.153 63.158 0.00 0.00 36.64 4.18
4579 7003 1.153289 CAGGAGAATGGGCACTCGG 60.153 63.158 0.00 0.00 34.40 4.63
4580 7004 1.613630 AGGAGAATGGGCACTCGGT 60.614 57.895 0.00 0.00 34.40 4.69
4581 7005 1.201429 AGGAGAATGGGCACTCGGTT 61.201 55.000 0.00 0.00 34.40 4.44
4582 7006 1.026718 GGAGAATGGGCACTCGGTTG 61.027 60.000 0.00 0.00 34.40 3.77
4583 7007 1.648467 GAGAATGGGCACTCGGTTGC 61.648 60.000 0.91 0.91 42.18 4.17
4584 7008 1.971167 GAATGGGCACTCGGTTGCA 60.971 57.895 10.71 0.00 44.94 4.08
4597 7021 4.165779 CTCGGTTGCAAAATGTAATGTCC 58.834 43.478 0.00 0.00 0.00 4.02
4605 7029 4.381505 GCAAAATGTAATGTCCCGAATGGT 60.382 41.667 0.00 0.00 34.77 3.55
4661 7085 4.141274 TGACCAATTCCTTTCTGGACTCAA 60.141 41.667 0.00 0.00 46.14 3.02
4741 7165 6.314896 CCAAACTTTTACTCCATGTGCAAAAA 59.685 34.615 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 0.179116 CTGGCTCAGTCCGACATGAG 60.179 60.000 17.13 17.13 44.70 2.90
27 28 1.003580 TCAATCCCAACTGGCTCAGTC 59.996 52.381 8.09 0.00 44.62 3.51
231 232 2.554032 GGCTTGGCATTATGATAAGCGT 59.446 45.455 19.62 0.00 43.38 5.07
291 292 3.562182 TGCTGATGTCGAGGTTATCCTA 58.438 45.455 0.00 0.00 45.24 2.94
344 345 1.227764 CCTGCCACTCGATCATGGG 60.228 63.158 11.31 0.00 36.41 4.00
354 355 0.995024 AGCTAATCAACCCTGCCACT 59.005 50.000 0.00 0.00 0.00 4.00
397 398 1.597663 GCCTATTTGTGCGCGATTAGT 59.402 47.619 12.10 0.00 0.00 2.24
405 406 0.745845 AGCTCAGGCCTATTTGTGCG 60.746 55.000 3.98 0.00 38.46 5.34
450 451 5.995565 ACAGTACTACTAGCATTTGGTCA 57.004 39.130 0.00 0.00 0.00 4.02
473 478 2.638363 GGGCCTTATTAAGAGGATCGGT 59.362 50.000 0.84 0.00 42.67 4.69
491 496 1.450312 CGATGTTCTGTCCCTGGGC 60.450 63.158 8.22 3.87 0.00 5.36
590 595 3.656045 CGCGTTTTGAAGGCCCGT 61.656 61.111 0.00 0.00 38.99 5.28
593 598 2.126850 GCTCGCGTTTTGAAGGCC 60.127 61.111 5.77 0.00 38.99 5.19
667 672 5.562506 TCGAGATATCGAACTGTTCAACT 57.437 39.130 19.56 10.41 39.34 3.16
813 818 2.598394 GGCTCACTGGGCTTGCAA 60.598 61.111 0.00 0.00 0.00 4.08
816 821 0.901580 ATTTGGGCTCACTGGGCTTG 60.902 55.000 0.00 0.00 0.00 4.01
846 851 4.778143 GGACGGCGACATGGGCTT 62.778 66.667 16.62 0.00 0.00 4.35
856 861 1.090052 GGAGAAAGGAATGGACGGCG 61.090 60.000 4.80 4.80 0.00 6.46
935 940 2.282462 CAAAGCTCCGGTTGGCCT 60.282 61.111 3.32 0.00 34.14 5.19
1099 1105 2.156051 GAGAAAGGAGACACGCGGGT 62.156 60.000 17.23 17.23 0.00 5.28
1668 2771 3.300328 CACACACAACAACATGTTCAACG 59.700 43.478 8.48 0.00 38.77 4.10
1921 3077 9.480053 AAAAGTACACTATTTAGCAGTTTACGA 57.520 29.630 0.00 0.00 35.36 3.43
1922 3078 9.737025 GAAAAGTACACTATTTAGCAGTTTACG 57.263 33.333 0.00 0.00 35.36 3.18
2021 3188 7.185453 GTCTTTATCAAATGTCAGCAGTCATC 58.815 38.462 0.00 0.00 0.00 2.92
2150 3354 8.147172 CGCATGTTTCGTAGTAAATTTGAAAAG 58.853 33.333 0.00 0.00 31.10 2.27
2155 3359 4.848841 TGCGCATGTTTCGTAGTAAATTTG 59.151 37.500 5.66 0.00 0.00 2.32
2166 3401 1.407434 ACAATGTTGCGCATGTTTCG 58.593 45.000 12.75 0.75 37.96 3.46
2275 4286 6.038603 TGCCATATTTCTGCTGTTATTCTGTC 59.961 38.462 0.00 0.00 0.00 3.51
2309 4339 7.065443 AGGTTCAGTGTTATAAAAGCGGATTAC 59.935 37.037 0.00 0.00 0.00 1.89
2567 4597 7.466860 CGTCTTAGAACTTTAAACCTTGCAACT 60.467 37.037 0.00 0.00 0.00 3.16
2743 4774 2.159382 ACATACCTGTCAAAAAGGCCG 58.841 47.619 0.00 0.00 38.48 6.13
2819 4850 4.808895 GTGTGCGTCAATTAGTATGGATCA 59.191 41.667 0.00 0.00 0.00 2.92
2828 4859 6.312918 AGGTGTATTAAGTGTGCGTCAATTAG 59.687 38.462 2.90 0.00 37.77 1.73
2880 5129 6.445139 ACTCCCTCCGATCCATATTAATTGAT 59.555 38.462 0.00 0.00 0.00 2.57
2942 5191 5.067674 TGCATAATGAAATTCCTTCCTTCCG 59.932 40.000 0.00 0.00 37.87 4.30
3147 5523 5.049680 TGAAAGCACGAGGAAAGTTATTCAC 60.050 40.000 0.00 0.00 0.00 3.18
3217 5594 6.903419 AGACTAAAAACATAAAGAGCTGTGC 58.097 36.000 0.00 0.00 0.00 4.57
3427 5809 6.480524 TGTTGTCCAGAATACGATGAAAAG 57.519 37.500 0.00 0.00 0.00 2.27
3649 6044 8.240682 TGAATATTGTGCTGTTACCAACAATAC 58.759 33.333 13.14 6.34 41.61 1.89
3671 6066 6.266103 TGGAGCACTTCTTGAAGAAAATGAAT 59.734 34.615 18.09 8.85 33.19 2.57
3706 6101 2.084546 CCCCACTCCAGAAAATTCGAC 58.915 52.381 0.00 0.00 0.00 4.20
3891 6286 5.869579 TGCTTTCAACTGAGGTTAGAGATT 58.130 37.500 0.00 0.00 33.88 2.40
4021 6419 6.494952 AGAGTGAAGGAACTATCTGACCTAA 58.505 40.000 0.00 0.00 38.49 2.69
4055 6457 2.094390 CCCTGGATGTTGCTTGTCATTG 60.094 50.000 0.00 0.00 0.00 2.82
4062 6465 1.228552 AACGCCCTGGATGTTGCTT 60.229 52.632 0.00 0.00 0.00 3.91
4152 6555 7.471399 GCCCAAAATAATATAACTGAACCCTGG 60.471 40.741 0.00 0.00 0.00 4.45
4175 6578 2.298610 GGCAGAACCTAACATAAGCCC 58.701 52.381 0.00 0.00 34.94 5.19
4197 6600 6.417930 GTGAGCCTCTTTTGTTGTAATCAAAC 59.582 38.462 0.00 0.00 35.05 2.93
4202 6605 4.469657 TGGTGAGCCTCTTTTGTTGTAAT 58.530 39.130 0.00 0.00 35.27 1.89
4204 6607 3.569194 TGGTGAGCCTCTTTTGTTGTA 57.431 42.857 0.00 0.00 35.27 2.41
4209 6613 4.326826 TCAGTAATGGTGAGCCTCTTTTG 58.673 43.478 0.00 0.00 35.27 2.44
4230 6634 7.017055 GTGCAAAGTAATTGAAAATGCCATTC 58.983 34.615 0.00 0.00 41.85 2.67
4394 6799 1.315690 CATGCACCATCATCAGGTCC 58.684 55.000 0.00 0.00 37.23 4.46
4403 6808 3.794475 GCACTGATTTAGCATGCACCATC 60.794 47.826 21.98 16.77 36.30 3.51
4442 6847 4.968259 TGGGTACATATTGATACCTGCAC 58.032 43.478 0.00 0.00 40.71 4.57
4496 6901 8.258850 TGTCTAAAGGAACCCTAGGTATATTG 57.741 38.462 8.29 0.00 33.12 1.90
4566 6990 1.523154 TTGCAACCGAGTGCCCATTC 61.523 55.000 0.00 0.00 44.26 2.67
4567 6991 1.112315 TTTGCAACCGAGTGCCCATT 61.112 50.000 0.00 0.00 44.26 3.16
4568 6992 1.112315 TTTTGCAACCGAGTGCCCAT 61.112 50.000 0.00 0.00 44.26 4.00
4569 6993 1.112315 ATTTTGCAACCGAGTGCCCA 61.112 50.000 0.00 0.00 44.26 5.36
4570 6994 0.667184 CATTTTGCAACCGAGTGCCC 60.667 55.000 0.00 0.00 44.26 5.36
4571 6995 0.031994 ACATTTTGCAACCGAGTGCC 59.968 50.000 0.00 0.00 44.26 5.01
4572 6996 2.697431 TACATTTTGCAACCGAGTGC 57.303 45.000 0.00 3.58 45.15 4.40
4573 6997 4.545610 ACATTACATTTTGCAACCGAGTG 58.454 39.130 0.00 0.00 0.00 3.51
4574 6998 4.320935 GGACATTACATTTTGCAACCGAGT 60.321 41.667 0.00 0.00 0.00 4.18
4575 6999 4.165779 GGACATTACATTTTGCAACCGAG 58.834 43.478 0.00 0.00 0.00 4.63
4576 7000 3.057174 GGGACATTACATTTTGCAACCGA 60.057 43.478 0.00 0.00 0.00 4.69
4577 7001 3.249917 GGGACATTACATTTTGCAACCG 58.750 45.455 0.00 0.00 0.00 4.44
4578 7002 3.057174 TCGGGACATTACATTTTGCAACC 60.057 43.478 0.00 0.00 0.00 3.77
4579 7003 4.167554 TCGGGACATTACATTTTGCAAC 57.832 40.909 0.00 0.00 0.00 4.17
4580 7004 4.855715 TTCGGGACATTACATTTTGCAA 57.144 36.364 0.00 0.00 0.00 4.08
4581 7005 4.381398 CCATTCGGGACATTACATTTTGCA 60.381 41.667 0.00 0.00 40.01 4.08
4582 7006 4.111916 CCATTCGGGACATTACATTTTGC 58.888 43.478 0.00 0.00 40.01 3.68
4583 7007 5.323371 ACCATTCGGGACATTACATTTTG 57.677 39.130 0.00 0.00 41.15 2.44
4584 7008 7.469537 TTTACCATTCGGGACATTACATTTT 57.530 32.000 0.00 0.00 41.15 1.82
4766 7191 9.661954 AGGAAGGAAACATATCTCAATACTCTA 57.338 33.333 0.00 0.00 0.00 2.43
4767 7192 8.560124 AGGAAGGAAACATATCTCAATACTCT 57.440 34.615 0.00 0.00 0.00 3.24
4768 7193 7.875554 GGAGGAAGGAAACATATCTCAATACTC 59.124 40.741 0.00 0.00 0.00 2.59
4769 7194 7.570607 AGGAGGAAGGAAACATATCTCAATACT 59.429 37.037 0.00 0.00 0.00 2.12
4770 7195 7.659390 CAGGAGGAAGGAAACATATCTCAATAC 59.341 40.741 0.00 0.00 0.00 1.89
4771 7196 7.202130 CCAGGAGGAAGGAAACATATCTCAATA 60.202 40.741 0.00 0.00 36.89 1.90
4772 7197 6.410157 CCAGGAGGAAGGAAACATATCTCAAT 60.410 42.308 0.00 0.00 36.89 2.57
4773 7198 5.104360 CCAGGAGGAAGGAAACATATCTCAA 60.104 44.000 0.00 0.00 36.89 3.02
4774 7199 4.410228 CCAGGAGGAAGGAAACATATCTCA 59.590 45.833 0.00 0.00 36.89 3.27


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

AutoCloner maintained by Alex Coulton.