Multiple sequence alignment - TraesCS5B01G142100

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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 TraesCS5B01G142100 chr5B 100.000 3349 0 0 1 3349 267780316 267776968 0.000000e+00 6185.0
1 TraesCS5B01G142100 chr5B 77.124 153 21 10 1033 1178 461141441 461141296 3.580000e-10 76.8
2 TraesCS5B01G142100 chr5D 92.351 3216 141 42 136 3290 238065285 238068456 0.000000e+00 4479.0
3 TraesCS5B01G142100 chr5D 77.124 153 21 10 1033 1178 384348078 384347933 3.580000e-10 76.8
4 TraesCS5B01G142100 chr5D 85.333 75 3 2 34 108 238065219 238065285 1.670000e-08 71.3
5 TraesCS5B01G142100 chr5A 91.648 2730 132 44 601 3290 317248598 317245925 0.000000e+00 3690.0
6 TraesCS5B01G142100 chr5A 87.891 512 33 18 35 542 317249508 317249022 2.900000e-160 575.0
7 TraesCS5B01G142100 chr5A 100.000 60 0 0 3290 3349 350085412 350085471 9.820000e-21 111.0
8 TraesCS5B01G142100 chr2B 78.706 479 82 14 1046 1516 85177897 85177431 5.430000e-78 302.0
9 TraesCS5B01G142100 chr2B 78.068 497 81 19 1034 1516 85074019 85074501 4.230000e-74 289.0
10 TraesCS5B01G142100 chr2B 93.243 74 3 2 3276 3349 133122938 133123009 1.270000e-19 108.0
11 TraesCS5B01G142100 chr2B 87.500 48 6 0 1043 1090 83955340 83955293 4.670000e-04 56.5
12 TraesCS5B01G142100 chr2D 78.423 482 80 18 1043 1516 54317534 54317999 3.270000e-75 292.0
13 TraesCS5B01G142100 chr2D 84.100 239 33 4 1281 1515 175331629 175331866 3.360000e-55 226.0
14 TraesCS5B01G142100 chr2D 85.965 57 8 0 1034 1090 52647005 52647061 1.000000e-05 62.1
15 TraesCS5B01G142100 chr2D 85.000 60 9 0 1031 1090 52852077 52852136 1.000000e-05 62.1
16 TraesCS5B01G142100 chr2A 77.172 495 85 19 1034 1516 54882383 54882861 2.560000e-66 263.0
17 TraesCS5B01G142100 chr2A 86.667 225 28 2 1293 1516 54955222 54954999 7.180000e-62 248.0
18 TraesCS5B01G142100 chr2A 95.714 70 3 0 3280 3349 237315634 237315703 2.730000e-21 113.0
19 TraesCS5B01G142100 chr4B 83.077 260 42 2 1265 1523 380653772 380654030 5.590000e-58 235.0
20 TraesCS5B01G142100 chr4B 100.000 60 0 0 3290 3349 124883024 124883083 9.820000e-21 111.0
21 TraesCS5B01G142100 chr4B 100.000 60 0 0 3290 3349 505207611 505207670 9.820000e-21 111.0
22 TraesCS5B01G142100 chr1B 100.000 60 0 0 3290 3349 593410885 593410944 9.820000e-21 111.0
23 TraesCS5B01G142100 chr3D 95.455 66 3 0 3284 3349 164901723 164901658 4.570000e-19 106.0
24 TraesCS5B01G142100 chr7A 96.825 63 1 1 3287 3349 659641044 659640983 1.640000e-18 104.0
25 TraesCS5B01G142100 chr7A 89.796 49 5 0 1042 1090 410727038 410727086 2.790000e-06 63.9
26 TraesCS5B01G142100 chr1A 90.123 81 4 3 3273 3349 204991554 204991634 5.910000e-18 102.0
27 TraesCS5B01G142100 chr7B 89.796 49 5 0 1042 1090 316006655 316006607 2.790000e-06 63.9


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 TraesCS5B01G142100 chr5B 267776968 267780316 3348 True 6185.00 6185 100.0000 1 3349 1 chr5B.!!$R1 3348
1 TraesCS5B01G142100 chr5D 238065219 238068456 3237 False 2275.15 4479 88.8420 34 3290 2 chr5D.!!$F1 3256
2 TraesCS5B01G142100 chr5A 317245925 317249508 3583 True 2132.50 3690 89.7695 35 3290 2 chr5A.!!$R1 3255

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
808 1205 0.395312 ACCTATAAATCCACGCCCCG 59.605 55.0 0.00 0.0 0.0 5.73 F
1276 1692 0.327259 TGATCTCTGCAGGCAAAGCT 59.673 50.0 15.13 0.0 0.0 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1742 2164 0.818445 CCCAGTCATCCAGCTGCATC 60.818 60.0 8.66 0.0 0.0 3.91 R
2821 3256 0.958822 GGTTTCCGGTGACAAATGCT 59.041 50.0 0.00 0.0 0.0 3.79 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
19 20 2.278332 GCACCCCATTCTCCCTTATC 57.722 55.000 0.00 0.00 0.00 1.75
20 21 1.777272 GCACCCCATTCTCCCTTATCT 59.223 52.381 0.00 0.00 0.00 1.98
21 22 2.487986 GCACCCCATTCTCCCTTATCTG 60.488 54.545 0.00 0.00 0.00 2.90
22 23 3.048600 CACCCCATTCTCCCTTATCTGA 58.951 50.000 0.00 0.00 0.00 3.27
23 24 3.459598 CACCCCATTCTCCCTTATCTGAA 59.540 47.826 0.00 0.00 0.00 3.02
24 25 3.718956 ACCCCATTCTCCCTTATCTGAAG 59.281 47.826 0.00 0.00 0.00 3.02
25 26 3.718956 CCCCATTCTCCCTTATCTGAAGT 59.281 47.826 0.00 0.00 0.00 3.01
26 27 4.166919 CCCCATTCTCCCTTATCTGAAGTT 59.833 45.833 0.00 0.00 0.00 2.66
27 28 5.372373 CCCATTCTCCCTTATCTGAAGTTC 58.628 45.833 0.00 0.00 0.00 3.01
28 29 5.131809 CCCATTCTCCCTTATCTGAAGTTCT 59.868 44.000 4.17 0.00 0.00 3.01
29 30 6.287525 CCATTCTCCCTTATCTGAAGTTCTC 58.712 44.000 4.17 0.00 0.00 2.87
30 31 5.941555 TTCTCCCTTATCTGAAGTTCTCC 57.058 43.478 4.17 0.00 0.00 3.71
31 32 4.947883 TCTCCCTTATCTGAAGTTCTCCA 58.052 43.478 4.17 0.00 0.00 3.86
32 33 5.533112 TCTCCCTTATCTGAAGTTCTCCAT 58.467 41.667 4.17 0.00 0.00 3.41
33 34 5.365025 TCTCCCTTATCTGAAGTTCTCCATG 59.635 44.000 4.17 0.00 0.00 3.66
108 110 1.747355 GGCCATTGATCAACTCCACAG 59.253 52.381 11.07 0.00 0.00 3.66
110 112 2.681848 GCCATTGATCAACTCCACAGAG 59.318 50.000 11.07 0.00 46.36 3.35
112 114 3.276857 CATTGATCAACTCCACAGAGGG 58.723 50.000 11.07 0.00 45.11 4.30
113 115 2.325661 TGATCAACTCCACAGAGGGA 57.674 50.000 0.00 0.00 45.11 4.20
115 117 2.978978 TGATCAACTCCACAGAGGGAAA 59.021 45.455 0.00 0.00 45.11 3.13
117 119 4.043310 TGATCAACTCCACAGAGGGAAATT 59.957 41.667 0.00 0.00 45.11 1.82
118 120 4.021102 TCAACTCCACAGAGGGAAATTC 57.979 45.455 0.00 0.00 45.11 2.17
119 121 3.084786 CAACTCCACAGAGGGAAATTCC 58.915 50.000 2.79 2.79 45.11 3.01
209 211 3.655810 GACAGAGGCAGGCACGAGG 62.656 68.421 0.00 0.00 0.00 4.63
258 260 0.669619 TGCATATCATTGGCGGCAAG 59.330 50.000 28.83 19.88 0.00 4.01
335 340 7.329471 GCTATTGCTAACCAAAAGAAAAGAAGG 59.671 37.037 0.00 0.00 36.92 3.46
343 348 6.194967 ACCAAAAGAAAAGAAGGGAAGAGAA 58.805 36.000 0.00 0.00 0.00 2.87
344 349 6.322456 ACCAAAAGAAAAGAAGGGAAGAGAAG 59.678 38.462 0.00 0.00 0.00 2.85
345 350 6.547510 CCAAAAGAAAAGAAGGGAAGAGAAGA 59.452 38.462 0.00 0.00 0.00 2.87
346 351 7.068716 CCAAAAGAAAAGAAGGGAAGAGAAGAA 59.931 37.037 0.00 0.00 0.00 2.52
449 454 0.596859 GATTAGCTCACCCGTACGCC 60.597 60.000 10.49 0.00 0.00 5.68
452 457 4.814294 GCTCACCCGTACGCCCAG 62.814 72.222 10.49 3.64 0.00 4.45
481 486 0.523966 TTAGCCATTTGCCCGTTTCG 59.476 50.000 0.00 0.00 42.71 3.46
501 506 1.156736 CTTTCACCGCGGTCAGAAAT 58.843 50.000 31.84 10.00 30.51 2.17
515 520 5.406175 CGGTCAGAAATTTGTGCATTTGATT 59.594 36.000 10.37 0.00 0.00 2.57
532 537 4.214327 TGCACTCGCACGTGTCCA 62.214 61.111 18.38 2.89 45.36 4.02
558 563 1.724082 GTTTGCACTTGTGTTTTGCGT 59.276 42.857 2.61 0.00 39.22 5.24
560 565 2.921634 TGCACTTGTGTTTTGCGTTA 57.078 40.000 2.61 0.00 39.22 3.18
572 577 6.858993 TGTGTTTTGCGTTACAAGGATTAATC 59.141 34.615 6.93 6.93 40.06 1.75
594 599 3.307691 CCTGGTGTGAATCTAGGCTTGAA 60.308 47.826 2.10 0.00 0.00 2.69
596 601 4.264253 TGGTGTGAATCTAGGCTTGAATG 58.736 43.478 2.10 0.00 0.00 2.67
635 1022 6.459670 TCGTGAGGCAGAATATAACTACAA 57.540 37.500 0.00 0.00 0.00 2.41
655 1049 4.022589 ACAATCCACTGATGCAAGAAGTTG 60.023 41.667 0.00 0.00 36.67 3.16
659 1053 4.216902 TCCACTGATGCAAGAAGTTGATTG 59.783 41.667 0.00 0.00 35.46 2.67
712 1109 9.615779 GTGATGACGTAAATAAACGAAGTAATC 57.384 33.333 3.10 0.60 45.00 1.75
808 1205 0.395312 ACCTATAAATCCACGCCCCG 59.605 55.000 0.00 0.00 0.00 5.73
840 1241 4.482990 TCTGAAAAATTTCAAGCCTCCCT 58.517 39.130 9.63 0.00 45.61 4.20
841 1242 4.524328 TCTGAAAAATTTCAAGCCTCCCTC 59.476 41.667 9.63 0.00 45.61 4.30
843 1244 2.238084 AAATTTCAAGCCTCCCTCCC 57.762 50.000 0.00 0.00 0.00 4.30
844 1245 1.084018 AATTTCAAGCCTCCCTCCCA 58.916 50.000 0.00 0.00 0.00 4.37
845 1246 1.312884 ATTTCAAGCCTCCCTCCCAT 58.687 50.000 0.00 0.00 0.00 4.00
846 1247 1.979809 TTTCAAGCCTCCCTCCCATA 58.020 50.000 0.00 0.00 0.00 2.74
901 1305 1.715785 CATCTTCTCCTCCTCCTCCC 58.284 60.000 0.00 0.00 0.00 4.30
1090 1497 0.386113 GCTCATCGTCCACTACCTCC 59.614 60.000 0.00 0.00 0.00 4.30
1231 1638 2.315925 TCGATCAATCAGCTCCAACC 57.684 50.000 0.00 0.00 0.00 3.77
1244 1651 2.158696 GCTCCAACCCTGCTCTGATTAT 60.159 50.000 0.00 0.00 0.00 1.28
1273 1689 2.275134 TGTTGATCTCTGCAGGCAAA 57.725 45.000 15.13 0.00 0.00 3.68
1276 1692 0.327259 TGATCTCTGCAGGCAAAGCT 59.673 50.000 15.13 0.00 0.00 3.74
1516 1932 3.755628 GAGTACCGCCTCACCGCA 61.756 66.667 0.00 0.00 0.00 5.69
1564 1980 1.055040 GATCCTCCATGAGGGTGAGG 58.945 60.000 10.13 8.28 44.18 3.86
1634 2053 9.787435 ATACTGTATTGTCTTCACTTTGGTAAA 57.213 29.630 0.00 0.00 0.00 2.01
1669 2091 7.470935 TGTACCATAAGCTACAACTTACTCA 57.529 36.000 0.00 0.00 35.05 3.41
1680 2102 8.989980 AGCTACAACTTACTCAACTTAATTGTC 58.010 33.333 0.00 0.00 39.54 3.18
1701 2123 7.375106 TGTCTGCATTTGAAATGTTTGTTTT 57.625 28.000 18.12 0.00 0.00 2.43
1702 2124 7.242079 TGTCTGCATTTGAAATGTTTGTTTTG 58.758 30.769 18.12 2.33 0.00 2.44
1704 2126 7.216693 GTCTGCATTTGAAATGTTTGTTTTGTG 59.783 33.333 18.12 0.00 0.00 3.33
1721 2143 8.430801 TGTTTTGTGAGTGAATTAATTTTGGG 57.569 30.769 1.43 0.00 0.00 4.12
1722 2144 7.497249 TGTTTTGTGAGTGAATTAATTTTGGGG 59.503 33.333 1.43 0.00 0.00 4.96
1725 2147 6.754193 TGTGAGTGAATTAATTTTGGGGTTC 58.246 36.000 1.43 0.00 0.00 3.62
1727 2149 7.090808 GTGAGTGAATTAATTTTGGGGTTCTC 58.909 38.462 1.43 3.53 0.00 2.87
1728 2150 6.210584 TGAGTGAATTAATTTTGGGGTTCTCC 59.789 38.462 1.43 0.00 0.00 3.71
1731 2153 7.292356 AGTGAATTAATTTTGGGGTTCTCCTTT 59.708 33.333 1.43 0.00 35.33 3.11
1732 2154 7.387673 GTGAATTAATTTTGGGGTTCTCCTTTG 59.612 37.037 1.43 0.00 35.33 2.77
1733 2155 7.071824 TGAATTAATTTTGGGGTTCTCCTTTGT 59.928 33.333 1.43 0.00 35.33 2.83
1734 2156 6.816616 TTAATTTTGGGGTTCTCCTTTGTT 57.183 33.333 0.00 0.00 35.33 2.83
1735 2157 5.708736 AATTTTGGGGTTCTCCTTTGTTT 57.291 34.783 0.00 0.00 35.33 2.83
1895 2320 2.737376 GTGTCGTCGCCCAAGTCC 60.737 66.667 0.00 0.00 0.00 3.85
1932 2357 3.681835 GCGACGACCACCTCCAGT 61.682 66.667 0.00 0.00 0.00 4.00
2081 2512 1.687493 AGACTACCAGCTGCCTCCC 60.687 63.158 8.66 0.00 0.00 4.30
2412 2846 4.783764 TTGAACTTGCTGTAGATCGAGA 57.216 40.909 0.00 0.00 0.00 4.04
2450 2884 3.879718 GCAGATAGGCAGGGATCTAGCTA 60.880 52.174 0.00 0.00 31.88 3.32
2612 3047 9.322769 TGATGATCATCATATATATGCTAGGCT 57.677 33.333 30.27 0.00 42.42 4.58
2615 3050 9.377238 TGATCATCATATATATGCTAGGCTTCT 57.623 33.333 16.59 0.00 33.76 2.85
2635 3070 9.917872 GGCTTCTTAATTAGTTAATTCGAGAAC 57.082 33.333 13.62 11.71 35.45 3.01
2680 3115 2.899838 GGTTGACACACGCAGCCA 60.900 61.111 0.00 0.00 36.72 4.75
2722 3157 3.528532 GCGTACCCAGCACTAGTTAATT 58.471 45.455 0.00 0.00 34.19 1.40
2732 3167 4.120589 GCACTAGTTAATTAGCGAGGCTT 58.879 43.478 12.67 0.00 40.44 4.35
2779 3214 1.071071 CTTCCCTTGTCCACCGTACAA 59.929 52.381 0.00 0.00 35.61 2.41
2780 3215 1.354101 TCCCTTGTCCACCGTACAAT 58.646 50.000 0.00 0.00 36.33 2.71
2794 3229 4.876107 ACCGTACAATCAGGAGCAATTAAG 59.124 41.667 0.00 0.00 0.00 1.85
2815 3250 0.101399 AACGCTCGCTCGAATGATCT 59.899 50.000 3.28 0.00 0.00 2.75
2819 3254 3.095016 CGCTCGCTCGAATGATCTATAC 58.905 50.000 0.00 0.00 0.00 1.47
2820 3255 3.181515 CGCTCGCTCGAATGATCTATACT 60.182 47.826 0.00 0.00 0.00 2.12
2821 3256 4.033014 CGCTCGCTCGAATGATCTATACTA 59.967 45.833 0.00 0.00 0.00 1.82
2862 3297 1.813513 AGCCCGAATCAAAGACACAG 58.186 50.000 0.00 0.00 0.00 3.66
2996 3432 3.485431 CGCTCAACTGCTGCCGAG 61.485 66.667 0.00 5.73 0.00 4.63
3013 3449 2.334838 CGAGCTTACTTTAGTTGCCGT 58.665 47.619 0.00 0.00 0.00 5.68
3046 3482 7.815549 TGGTATATATCACACGTTGCGAATTAT 59.184 33.333 0.00 0.00 0.00 1.28
3047 3483 9.292846 GGTATATATCACACGTTGCGAATTATA 57.707 33.333 0.00 0.00 0.00 0.98
3060 3496 5.641709 TGCGAATTATAGATAGGCTCGAAG 58.358 41.667 0.00 0.00 0.00 3.79
3072 3509 1.406069 GGCTCGAAGCTGAATCTTCCA 60.406 52.381 6.78 0.00 41.99 3.53
3093 3530 5.917087 TCCATCCTCCTCCATTAGGTTAATT 59.083 40.000 0.00 0.00 46.62 1.40
3095 3532 7.574750 TCCATCCTCCTCCATTAGGTTAATTAA 59.425 37.037 0.00 0.00 46.62 1.40
3096 3533 8.394040 CCATCCTCCTCCATTAGGTTAATTAAT 58.606 37.037 0.31 0.00 46.62 1.40
3097 3534 9.813826 CATCCTCCTCCATTAGGTTAATTAATT 57.186 33.333 5.89 5.89 46.62 1.40
3147 3590 6.372659 TGGAGACAGAGATTTGTTTATGCTTC 59.627 38.462 0.00 0.00 35.01 3.86
3290 3740 4.213482 AGCGATCACACCAAAGAAACTTAC 59.787 41.667 0.00 0.00 0.00 2.34
3291 3741 4.213482 GCGATCACACCAAAGAAACTTACT 59.787 41.667 0.00 0.00 0.00 2.24
3292 3742 5.407387 GCGATCACACCAAAGAAACTTACTA 59.593 40.000 0.00 0.00 0.00 1.82
3293 3743 6.073440 GCGATCACACCAAAGAAACTTACTAA 60.073 38.462 0.00 0.00 0.00 2.24
3294 3744 7.510630 CGATCACACCAAAGAAACTTACTAAG 58.489 38.462 0.00 0.00 0.00 2.18
3295 3745 7.360101 CGATCACACCAAAGAAACTTACTAAGG 60.360 40.741 0.88 0.00 0.00 2.69
3296 3746 5.529800 TCACACCAAAGAAACTTACTAAGGC 59.470 40.000 0.88 0.00 0.00 4.35
3297 3747 5.531287 CACACCAAAGAAACTTACTAAGGCT 59.469 40.000 0.88 0.00 0.00 4.58
3298 3748 5.531287 ACACCAAAGAAACTTACTAAGGCTG 59.469 40.000 0.88 0.00 0.00 4.85
3299 3749 5.048713 CACCAAAGAAACTTACTAAGGCTGG 60.049 44.000 0.88 0.00 0.00 4.85
3300 3750 5.070685 CCAAAGAAACTTACTAAGGCTGGT 58.929 41.667 0.88 0.00 0.00 4.00
3301 3751 5.181433 CCAAAGAAACTTACTAAGGCTGGTC 59.819 44.000 0.88 0.00 0.00 4.02
3302 3752 4.189639 AGAAACTTACTAAGGCTGGTCG 57.810 45.455 0.88 0.00 0.00 4.79
3303 3753 3.577415 AGAAACTTACTAAGGCTGGTCGT 59.423 43.478 0.88 0.00 0.00 4.34
3304 3754 4.768968 AGAAACTTACTAAGGCTGGTCGTA 59.231 41.667 0.88 0.00 0.00 3.43
3305 3755 5.244626 AGAAACTTACTAAGGCTGGTCGTAA 59.755 40.000 0.88 0.00 0.00 3.18
3306 3756 5.672421 AACTTACTAAGGCTGGTCGTAAT 57.328 39.130 0.88 0.00 0.00 1.89
3307 3757 5.007385 ACTTACTAAGGCTGGTCGTAATG 57.993 43.478 0.88 0.00 0.00 1.90
3308 3758 2.981859 ACTAAGGCTGGTCGTAATGG 57.018 50.000 0.00 0.00 0.00 3.16
3309 3759 2.185387 ACTAAGGCTGGTCGTAATGGT 58.815 47.619 0.00 0.00 0.00 3.55
3310 3760 3.368248 ACTAAGGCTGGTCGTAATGGTA 58.632 45.455 0.00 0.00 0.00 3.25
3311 3761 2.981859 AAGGCTGGTCGTAATGGTAG 57.018 50.000 0.00 0.00 0.00 3.18
3312 3762 1.861982 AGGCTGGTCGTAATGGTAGT 58.138 50.000 0.00 0.00 0.00 2.73
3313 3763 3.022557 AGGCTGGTCGTAATGGTAGTA 57.977 47.619 0.00 0.00 0.00 1.82
3314 3764 3.573695 AGGCTGGTCGTAATGGTAGTAT 58.426 45.455 0.00 0.00 0.00 2.12
3315 3765 3.573110 AGGCTGGTCGTAATGGTAGTATC 59.427 47.826 0.00 0.00 0.00 2.24
3316 3766 3.319972 GGCTGGTCGTAATGGTAGTATCA 59.680 47.826 0.00 0.00 0.00 2.15
3317 3767 4.021368 GGCTGGTCGTAATGGTAGTATCAT 60.021 45.833 0.00 0.00 0.00 2.45
3318 3768 5.184479 GGCTGGTCGTAATGGTAGTATCATA 59.816 44.000 0.00 0.00 0.00 2.15
3319 3769 6.323266 GCTGGTCGTAATGGTAGTATCATAG 58.677 44.000 0.00 0.00 0.00 2.23
3320 3770 6.263516 TGGTCGTAATGGTAGTATCATAGC 57.736 41.667 0.00 0.00 0.00 2.97
3321 3771 6.008331 TGGTCGTAATGGTAGTATCATAGCT 58.992 40.000 0.00 0.00 0.00 3.32
3322 3772 7.170277 TGGTCGTAATGGTAGTATCATAGCTA 58.830 38.462 0.00 0.00 0.00 3.32
3323 3773 7.336176 TGGTCGTAATGGTAGTATCATAGCTAG 59.664 40.741 0.00 0.00 0.00 3.42
3324 3774 7.336427 GGTCGTAATGGTAGTATCATAGCTAGT 59.664 40.741 0.00 0.00 0.00 2.57
3325 3775 9.376075 GTCGTAATGGTAGTATCATAGCTAGTA 57.624 37.037 0.00 0.00 0.00 1.82
3331 3781 8.226819 TGGTAGTATCATAGCTAGTATCATGC 57.773 38.462 0.00 0.00 0.00 4.06
3332 3782 7.834181 TGGTAGTATCATAGCTAGTATCATGCA 59.166 37.037 0.00 0.00 0.00 3.96
3333 3783 8.855110 GGTAGTATCATAGCTAGTATCATGCAT 58.145 37.037 0.00 0.00 0.00 3.96
3334 3784 9.676195 GTAGTATCATAGCTAGTATCATGCATG 57.324 37.037 21.07 21.07 0.00 4.06
3335 3785 7.208777 AGTATCATAGCTAGTATCATGCATGC 58.791 38.462 22.25 11.82 0.00 4.06
3336 3786 4.763073 TCATAGCTAGTATCATGCATGCC 58.237 43.478 22.25 11.72 0.00 4.40
3337 3787 4.223477 TCATAGCTAGTATCATGCATGCCA 59.777 41.667 22.25 8.84 0.00 4.92
3338 3788 3.497103 AGCTAGTATCATGCATGCCAA 57.503 42.857 22.25 5.34 0.00 4.52
3339 3789 3.144506 AGCTAGTATCATGCATGCCAAC 58.855 45.455 22.25 17.59 0.00 3.77
3340 3790 3.144506 GCTAGTATCATGCATGCCAACT 58.855 45.455 22.25 22.78 0.00 3.16
3341 3791 4.040829 AGCTAGTATCATGCATGCCAACTA 59.959 41.667 22.25 22.70 0.00 2.24
3342 3792 4.391216 GCTAGTATCATGCATGCCAACTAG 59.609 45.833 32.38 32.38 37.27 2.57
3343 3793 3.748083 AGTATCATGCATGCCAACTAGG 58.252 45.455 22.25 0.00 41.84 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.048600 TCAGATAAGGGAGAATGGGGTG 58.951 50.000 0.00 0.00 0.00 4.61
2 3 3.438131 TCAGATAAGGGAGAATGGGGT 57.562 47.619 0.00 0.00 0.00 4.95
4 5 5.131809 AGAACTTCAGATAAGGGAGAATGGG 59.868 44.000 0.00 0.00 0.00 4.00
5 6 6.245890 AGAACTTCAGATAAGGGAGAATGG 57.754 41.667 0.00 0.00 0.00 3.16
6 7 6.126940 TGGAGAACTTCAGATAAGGGAGAATG 60.127 42.308 0.00 0.00 0.00 2.67
7 8 5.966935 TGGAGAACTTCAGATAAGGGAGAAT 59.033 40.000 0.00 0.00 0.00 2.40
8 9 5.342017 TGGAGAACTTCAGATAAGGGAGAA 58.658 41.667 0.00 0.00 0.00 2.87
9 10 4.947883 TGGAGAACTTCAGATAAGGGAGA 58.052 43.478 0.00 0.00 0.00 3.71
10 11 5.454471 CCATGGAGAACTTCAGATAAGGGAG 60.454 48.000 5.56 0.00 0.00 4.30
11 12 4.410228 CCATGGAGAACTTCAGATAAGGGA 59.590 45.833 5.56 0.00 0.00 4.20
12 13 4.712476 CCATGGAGAACTTCAGATAAGGG 58.288 47.826 5.56 0.00 0.00 3.95
13 14 4.133078 GCCATGGAGAACTTCAGATAAGG 58.867 47.826 18.40 0.00 0.00 2.69
14 15 4.133078 GGCCATGGAGAACTTCAGATAAG 58.867 47.826 18.40 0.00 0.00 1.73
15 16 3.523157 TGGCCATGGAGAACTTCAGATAA 59.477 43.478 18.40 0.00 0.00 1.75
16 17 3.114606 TGGCCATGGAGAACTTCAGATA 58.885 45.455 18.40 0.00 0.00 1.98
17 18 1.918262 TGGCCATGGAGAACTTCAGAT 59.082 47.619 18.40 0.00 0.00 2.90
18 19 1.361204 TGGCCATGGAGAACTTCAGA 58.639 50.000 18.40 0.00 0.00 3.27
19 20 2.022195 CATGGCCATGGAGAACTTCAG 58.978 52.381 34.31 7.35 35.24 3.02
20 21 1.956636 GCATGGCCATGGAGAACTTCA 60.957 52.381 39.72 0.00 39.16 3.02
21 22 0.743097 GCATGGCCATGGAGAACTTC 59.257 55.000 39.72 21.08 39.16 3.01
22 23 0.333993 AGCATGGCCATGGAGAACTT 59.666 50.000 39.72 14.69 39.16 2.66
23 24 1.216064 TAGCATGGCCATGGAGAACT 58.784 50.000 39.72 30.10 39.16 3.01
24 25 1.952296 CTTAGCATGGCCATGGAGAAC 59.048 52.381 39.72 25.65 39.16 3.01
25 26 1.751733 GCTTAGCATGGCCATGGAGAA 60.752 52.381 39.72 19.38 39.16 2.87
26 27 0.179009 GCTTAGCATGGCCATGGAGA 60.179 55.000 39.72 14.40 39.16 3.71
27 28 0.178998 AGCTTAGCATGGCCATGGAG 60.179 55.000 39.72 20.87 39.16 3.86
28 29 1.139439 TAGCTTAGCATGGCCATGGA 58.861 50.000 39.72 11.59 39.16 3.41
29 30 1.816835 CATAGCTTAGCATGGCCATGG 59.183 52.381 39.72 26.68 39.16 3.66
30 31 1.816835 CCATAGCTTAGCATGGCCATG 59.183 52.381 36.80 36.80 41.60 3.66
31 32 1.426598 ACCATAGCTTAGCATGGCCAT 59.573 47.619 24.80 14.09 39.22 4.40
32 33 0.846015 ACCATAGCTTAGCATGGCCA 59.154 50.000 24.80 8.56 39.22 5.36
33 34 1.528129 GACCATAGCTTAGCATGGCC 58.472 55.000 24.80 16.28 39.22 5.36
95 97 3.703001 TTTCCCTCTGTGGAGTTGATC 57.297 47.619 0.00 0.00 37.86 2.92
258 260 3.357079 CACCTGTCCGCCTTGTGC 61.357 66.667 0.00 0.00 0.00 4.57
299 301 3.065925 GGTTAGCAATAGCAAGCAGGAAG 59.934 47.826 0.00 0.00 45.49 3.46
361 366 3.004944 TGGATAACCAACGCAAAAGAACC 59.995 43.478 0.00 0.00 43.91 3.62
449 454 1.453669 GGCTAATCTGCCCCTCTGG 59.546 63.158 0.00 0.00 46.82 3.86
481 486 1.503818 TTTCTGACCGCGGTGAAAGC 61.504 55.000 39.65 21.87 0.00 3.51
518 523 3.224324 AGGTGGACACGTGCGAGT 61.224 61.111 17.22 0.00 0.00 4.18
572 577 2.237143 TCAAGCCTAGATTCACACCAGG 59.763 50.000 0.00 0.00 0.00 4.45
594 599 3.005367 CACGAGGGCAAAACTAAAACCAT 59.995 43.478 0.00 0.00 0.00 3.55
596 601 2.619646 TCACGAGGGCAAAACTAAAACC 59.380 45.455 0.00 0.00 0.00 3.27
635 1022 4.025040 TCAACTTCTTGCATCAGTGGAT 57.975 40.909 0.00 0.00 0.00 3.41
704 1101 4.972440 GCAGAATCGGCAATTGATTACTTC 59.028 41.667 10.34 5.04 36.24 3.01
712 1109 1.039233 AGGGGCAGAATCGGCAATTG 61.039 55.000 7.78 0.00 0.00 2.32
714 1111 1.152881 GAGGGGCAGAATCGGCAAT 60.153 57.895 7.78 0.00 0.00 3.56
808 1205 3.881937 AATTTTTCAGATGCAGGGAGC 57.118 42.857 0.00 0.00 45.96 4.70
840 1241 1.495148 TGTGGTGTGGTGTTTATGGGA 59.505 47.619 0.00 0.00 0.00 4.37
841 1242 1.611491 GTGTGGTGTGGTGTTTATGGG 59.389 52.381 0.00 0.00 0.00 4.00
843 1244 2.287547 GCTGTGTGGTGTGGTGTTTATG 60.288 50.000 0.00 0.00 0.00 1.90
844 1245 1.953686 GCTGTGTGGTGTGGTGTTTAT 59.046 47.619 0.00 0.00 0.00 1.40
845 1246 1.340114 TGCTGTGTGGTGTGGTGTTTA 60.340 47.619 0.00 0.00 0.00 2.01
846 1247 0.610509 TGCTGTGTGGTGTGGTGTTT 60.611 50.000 0.00 0.00 0.00 2.83
901 1305 4.554036 GCTAGCTGGAAGGCGGGG 62.554 72.222 7.70 0.00 37.29 5.73
1184 1591 8.019669 GGATGACGTCGATTAGTTTTAGCTATA 58.980 37.037 11.62 0.00 0.00 1.31
1188 1595 4.802039 TGGATGACGTCGATTAGTTTTAGC 59.198 41.667 11.62 0.00 0.00 3.09
1204 1611 3.661944 AGCTGATTGATCGATGGATGAC 58.338 45.455 0.54 0.00 31.51 3.06
1205 1612 3.306571 GGAGCTGATTGATCGATGGATGA 60.307 47.826 0.54 0.00 31.51 2.92
1231 1638 8.674263 ACAAGAAGATTAATAATCAGAGCAGG 57.326 34.615 14.63 1.93 40.42 4.85
1244 1651 6.596888 CCTGCAGAGATCAACAAGAAGATTAA 59.403 38.462 17.39 0.00 0.00 1.40
1260 1676 0.956633 CAAAGCTTTGCCTGCAGAGA 59.043 50.000 25.26 0.00 30.72 3.10
1263 1679 1.494824 GAACAAAGCTTTGCCTGCAG 58.505 50.000 33.72 13.19 41.79 4.41
1273 1689 1.351017 TCATTCTCCCCGAACAAAGCT 59.649 47.619 0.00 0.00 33.72 3.74
1276 1692 2.552155 CCACTCATTCTCCCCGAACAAA 60.552 50.000 0.00 0.00 33.72 2.83
1429 1845 2.048127 ACGAGCGCCTTCTTGACC 60.048 61.111 2.29 0.00 0.00 4.02
1605 2024 8.041323 ACCAAAGTGAAGACAATACAGTATAGG 58.959 37.037 0.00 0.00 0.00 2.57
1608 2027 9.787435 TTTACCAAAGTGAAGACAATACAGTAT 57.213 29.630 0.00 0.00 0.00 2.12
1609 2028 9.616156 TTTTACCAAAGTGAAGACAATACAGTA 57.384 29.630 0.00 0.00 0.00 2.74
1610 2029 8.514330 TTTTACCAAAGTGAAGACAATACAGT 57.486 30.769 0.00 0.00 0.00 3.55
1611 2030 7.591426 GCTTTTACCAAAGTGAAGACAATACAG 59.409 37.037 0.00 0.00 41.51 2.74
1612 2031 7.067615 TGCTTTTACCAAAGTGAAGACAATACA 59.932 33.333 0.00 0.00 41.51 2.29
1618 2037 5.500645 ACTGCTTTTACCAAAGTGAAGAC 57.499 39.130 0.00 0.00 41.51 3.01
1669 2091 8.891671 ACATTTCAAATGCAGACAATTAAGTT 57.108 26.923 10.21 0.00 0.00 2.66
1680 2102 7.242079 TCACAAAACAAACATTTCAAATGCAG 58.758 30.769 10.21 3.07 0.00 4.41
1701 2123 6.553100 AGAACCCCAAAATTAATTCACTCACA 59.447 34.615 0.10 0.00 0.00 3.58
1702 2124 6.993079 AGAACCCCAAAATTAATTCACTCAC 58.007 36.000 0.10 0.00 0.00 3.51
1704 2126 6.437477 AGGAGAACCCCAAAATTAATTCACTC 59.563 38.462 0.10 0.00 36.73 3.51
1734 2156 3.321396 TCATCCAGCTGCATCAACAAAAA 59.679 39.130 8.66 0.00 0.00 1.94
1735 2157 2.892215 TCATCCAGCTGCATCAACAAAA 59.108 40.909 8.66 0.00 0.00 2.44
1742 2164 0.818445 CCCAGTCATCCAGCTGCATC 60.818 60.000 8.66 0.00 0.00 3.91
1925 2350 1.239968 GGAACTGCTGCAACTGGAGG 61.240 60.000 3.02 0.00 33.79 4.30
2078 2509 1.358152 AGATGAGTGGGTTTTCGGGA 58.642 50.000 0.00 0.00 0.00 5.14
2081 2512 3.179830 CGAGTAGATGAGTGGGTTTTCG 58.820 50.000 0.00 0.00 0.00 3.46
2162 2596 1.517257 CTGAGGCACGTCGATGGTC 60.517 63.158 9.90 0.00 0.00 4.02
2224 2658 4.649674 TCTTCCTCTTCATGCCGTTATACT 59.350 41.667 0.00 0.00 0.00 2.12
2288 2722 2.808315 CCGCTGTACTGATCCGCT 59.192 61.111 3.61 0.00 0.00 5.52
2450 2884 1.490693 CGTTCACGACACAGCAAGCT 61.491 55.000 0.00 0.00 43.02 3.74
2604 3039 9.042008 CGAATTAACTAATTAAGAAGCCTAGCA 57.958 33.333 0.00 0.00 36.13 3.49
2605 3040 9.257651 TCGAATTAACTAATTAAGAAGCCTAGC 57.742 33.333 0.00 0.00 36.13 3.42
2609 3044 9.917872 GTTCTCGAATTAACTAATTAAGAAGCC 57.082 33.333 14.14 6.10 37.74 4.35
2610 3045 9.621046 CGTTCTCGAATTAACTAATTAAGAAGC 57.379 33.333 14.14 10.63 37.74 3.86
2618 3053 9.206870 TGGTTTTACGTTCTCGAATTAACTAAT 57.793 29.630 0.00 0.00 40.62 1.73
2635 3070 1.462869 GGATGCGTCGTTGGTTTTACG 60.463 52.381 0.00 0.00 40.23 3.18
2637 3072 1.880271 TGGATGCGTCGTTGGTTTTA 58.120 45.000 0.00 0.00 0.00 1.52
2666 3101 2.280119 GTCTGGCTGCGTGTGTCA 60.280 61.111 0.00 0.00 0.00 3.58
2680 3115 4.154195 CGCCAGCAGTTAATTAACAAGTCT 59.846 41.667 26.06 16.47 38.62 3.24
2722 3157 2.007049 GCTAGCAACAAAGCCTCGCTA 61.007 52.381 10.63 0.00 38.25 4.26
2732 3167 2.603247 CCGCACACGCTAGCAACAA 61.603 57.895 16.45 0.00 38.22 2.83
2779 3214 4.770795 AGCGTTACTTAATTGCTCCTGAT 58.229 39.130 0.00 0.00 0.00 2.90
2780 3215 4.181578 GAGCGTTACTTAATTGCTCCTGA 58.818 43.478 12.04 0.00 44.76 3.86
2794 3229 1.448677 GATCATTCGAGCGAGCGTTAC 59.551 52.381 0.00 0.00 0.00 2.50
2815 3250 5.601583 TTCCGGTGACAAATGCTAGTATA 57.398 39.130 0.00 0.00 0.00 1.47
2819 3254 2.161609 GGTTTCCGGTGACAAATGCTAG 59.838 50.000 0.00 0.00 0.00 3.42
2820 3255 2.156098 GGTTTCCGGTGACAAATGCTA 58.844 47.619 0.00 0.00 0.00 3.49
2821 3256 0.958822 GGTTTCCGGTGACAAATGCT 59.041 50.000 0.00 0.00 0.00 3.79
2862 3297 2.952310 CCCTGGAGCCTTAGTTAAATGC 59.048 50.000 0.00 0.00 0.00 3.56
2893 3328 2.892334 GCGAGCTGACGTTTTGCCA 61.892 57.895 0.00 0.00 35.59 4.92
2993 3429 2.092211 CACGGCAACTAAAGTAAGCTCG 59.908 50.000 0.00 10.14 33.64 5.03
2996 3432 1.533731 TGCACGGCAACTAAAGTAAGC 59.466 47.619 0.00 0.27 34.76 3.09
3013 3449 4.244862 CGTGTGATATATACCAGCATGCA 58.755 43.478 21.98 0.00 31.97 3.96
3046 3482 4.402829 AGATTCAGCTTCGAGCCTATCTA 58.597 43.478 3.66 0.00 43.77 1.98
3047 3483 3.230134 AGATTCAGCTTCGAGCCTATCT 58.770 45.455 3.66 6.67 43.77 1.98
3060 3496 2.224499 GGAGGAGGATGGAAGATTCAGC 60.224 54.545 0.00 0.00 0.00 4.26
3093 3530 9.841295 AGGGAGACGCTGTTAATTAATTAATTA 57.159 29.630 21.49 21.49 37.16 1.40
3096 3533 9.841295 AATAGGGAGACGCTGTTAATTAATTAA 57.159 29.630 15.19 15.19 0.00 1.40
3097 3534 9.268268 CAATAGGGAGACGCTGTTAATTAATTA 57.732 33.333 3.71 3.71 0.00 1.40
3098 3535 7.228706 CCAATAGGGAGACGCTGTTAATTAATT 59.771 37.037 5.89 5.89 40.01 1.40
3099 3536 6.710744 CCAATAGGGAGACGCTGTTAATTAAT 59.289 38.462 0.31 0.00 40.01 1.40
3100 3537 6.053005 CCAATAGGGAGACGCTGTTAATTAA 58.947 40.000 0.00 0.00 40.01 1.40
3101 3538 5.364446 TCCAATAGGGAGACGCTGTTAATTA 59.636 40.000 0.00 0.00 42.15 1.40
3102 3539 4.163458 TCCAATAGGGAGACGCTGTTAATT 59.837 41.667 0.00 0.00 42.15 1.40
3103 3540 3.709653 TCCAATAGGGAGACGCTGTTAAT 59.290 43.478 0.00 0.00 42.15 1.40
3104 3541 3.101437 TCCAATAGGGAGACGCTGTTAA 58.899 45.455 0.00 0.00 42.15 2.01
3105 3542 2.742348 TCCAATAGGGAGACGCTGTTA 58.258 47.619 0.00 0.00 42.15 2.41
3106 3543 1.568504 TCCAATAGGGAGACGCTGTT 58.431 50.000 0.00 0.00 42.15 3.16
3107 3544 3.300032 TCCAATAGGGAGACGCTGT 57.700 52.632 0.00 0.00 42.15 4.40
3147 3590 2.045340 ATGGTTCGAAAGGGCCGG 60.045 61.111 0.00 0.00 0.00 6.13
3173 3616 4.197750 ACTCTGCATTATCTTCTTGGCTG 58.802 43.478 0.00 0.00 0.00 4.85
3210 3659 2.467880 AGACCAGATCGGAAAGGCTAA 58.532 47.619 10.05 0.00 38.63 3.09
3211 3660 2.160721 AGACCAGATCGGAAAGGCTA 57.839 50.000 10.05 0.00 38.63 3.93
3212 3661 1.757699 GTAGACCAGATCGGAAAGGCT 59.242 52.381 10.05 0.00 38.63 4.58
3290 3740 2.981859 ACCATTACGACCAGCCTTAG 57.018 50.000 0.00 0.00 0.00 2.18
3291 3741 3.368248 ACTACCATTACGACCAGCCTTA 58.632 45.455 0.00 0.00 0.00 2.69
3292 3742 2.185387 ACTACCATTACGACCAGCCTT 58.815 47.619 0.00 0.00 0.00 4.35
3293 3743 1.861982 ACTACCATTACGACCAGCCT 58.138 50.000 0.00 0.00 0.00 4.58
3294 3744 3.319972 TGATACTACCATTACGACCAGCC 59.680 47.826 0.00 0.00 0.00 4.85
3295 3745 4.579454 TGATACTACCATTACGACCAGC 57.421 45.455 0.00 0.00 0.00 4.85
3296 3746 6.151312 AGCTATGATACTACCATTACGACCAG 59.849 42.308 0.00 0.00 0.00 4.00
3297 3747 6.008331 AGCTATGATACTACCATTACGACCA 58.992 40.000 0.00 0.00 0.00 4.02
3298 3748 6.512342 AGCTATGATACTACCATTACGACC 57.488 41.667 0.00 0.00 0.00 4.79
3299 3749 8.266392 ACTAGCTATGATACTACCATTACGAC 57.734 38.462 0.00 0.00 0.00 4.34
3305 3755 8.855110 GCATGATACTAGCTATGATACTACCAT 58.145 37.037 0.00 0.00 0.00 3.55
3306 3756 7.834181 TGCATGATACTAGCTATGATACTACCA 59.166 37.037 0.00 0.00 0.00 3.25
3307 3757 8.226819 TGCATGATACTAGCTATGATACTACC 57.773 38.462 0.00 0.00 0.00 3.18
3308 3758 9.676195 CATGCATGATACTAGCTATGATACTAC 57.324 37.037 22.59 0.00 0.00 2.73
3309 3759 8.355913 GCATGCATGATACTAGCTATGATACTA 58.644 37.037 30.64 0.00 0.00 1.82
3310 3760 7.208777 GCATGCATGATACTAGCTATGATACT 58.791 38.462 30.64 0.00 0.00 2.12
3311 3761 6.423302 GGCATGCATGATACTAGCTATGATAC 59.577 42.308 30.64 5.71 0.00 2.24
3312 3762 6.098695 TGGCATGCATGATACTAGCTATGATA 59.901 38.462 30.64 0.00 0.00 2.15
3313 3763 5.104652 TGGCATGCATGATACTAGCTATGAT 60.105 40.000 30.64 0.00 0.00 2.45
3314 3764 4.223477 TGGCATGCATGATACTAGCTATGA 59.777 41.667 30.64 0.00 0.00 2.15
3315 3765 4.510571 TGGCATGCATGATACTAGCTATG 58.489 43.478 30.64 0.23 0.00 2.23
3316 3766 4.831674 TGGCATGCATGATACTAGCTAT 57.168 40.909 30.64 0.00 0.00 2.97
3317 3767 4.040829 AGTTGGCATGCATGATACTAGCTA 59.959 41.667 30.64 7.90 0.00 3.32
3318 3768 3.144506 GTTGGCATGCATGATACTAGCT 58.855 45.455 30.64 0.00 0.00 3.32
3319 3769 3.144506 AGTTGGCATGCATGATACTAGC 58.855 45.455 30.64 12.56 0.00 3.42
3320 3770 4.934001 CCTAGTTGGCATGCATGATACTAG 59.066 45.833 31.40 31.40 36.03 2.57
3321 3771 4.898320 CCTAGTTGGCATGCATGATACTA 58.102 43.478 30.64 25.87 0.00 1.82
3322 3772 3.748083 CCTAGTTGGCATGCATGATACT 58.252 45.455 30.64 26.11 0.00 2.12


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

AutoCloner maintained by Alex Coulton.