Multiple sequence alignment - TraesCS5B01G100500

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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 TraesCS5B01G100500 chr5B 100.000 7129 0 0 1 7129 133600587 133593459 0.000000e+00 13165.0
1 TraesCS5B01G100500 chr5B 91.667 60 4 1 5810 5868 406172716 406172775 1.650000e-11 82.4
2 TraesCS5B01G100500 chr5D 94.442 7161 270 55 19 7129 120347311 120340229 0.000000e+00 10901.0
3 TraesCS5B01G100500 chr5D 87.324 71 8 1 5796 5865 522111452 522111522 5.930000e-11 80.5
4 TraesCS5B01G100500 chr5A 93.924 5201 213 29 1309 6472 130541710 130536576 0.000000e+00 7758.0
5 TraesCS5B01G100500 chr5A 90.699 1301 53 20 37 1311 130543077 130541819 0.000000e+00 1670.0
6 TraesCS5B01G100500 chr5A 94.400 625 26 4 6508 7129 130536577 130535959 0.000000e+00 952.0
7 TraesCS5B01G100500 chr5A 89.394 66 7 0 5796 5861 536863554 536863619 4.580000e-12 84.2
8 TraesCS5B01G100500 chr7D 92.857 154 10 1 2361 2514 34756866 34757018 9.310000e-54 222.0
9 TraesCS5B01G100500 chr7D 90.909 165 15 0 2350 2514 454079241 454079077 9.310000e-54 222.0
10 TraesCS5B01G100500 chr6A 92.357 157 11 1 2359 2515 411770407 411770252 9.310000e-54 222.0
11 TraesCS5B01G100500 chr6A 90.226 133 10 1 1367 1499 84434888 84434759 3.420000e-38 171.0
12 TraesCS5B01G100500 chr7B 92.208 154 11 1 2361 2514 369872871 369872719 4.330000e-52 217.0
13 TraesCS5B01G100500 chr7A 91.613 155 11 2 2361 2514 579808527 579808374 5.600000e-51 213.0
14 TraesCS5B01G100500 chr6D 91.139 158 13 1 2359 2515 303060009 303059852 5.600000e-51 213.0
15 TraesCS5B01G100500 chr4D 91.558 154 13 0 2361 2514 74079504 74079351 5.600000e-51 213.0
16 TraesCS5B01G100500 chr4D 85.549 173 12 2 1337 1499 123424498 123424329 1.230000e-37 169.0
17 TraesCS5B01G100500 chr4D 87.037 108 14 0 4340 4447 138280230 138280123 9.710000e-24 122.0
18 TraesCS5B01G100500 chrUn 85.882 170 11 2 1337 1496 86509228 86509394 1.230000e-37 169.0
19 TraesCS5B01G100500 chrUn 85.882 170 11 2 1337 1496 260202943 260203109 1.230000e-37 169.0
20 TraesCS5B01G100500 chrUn 85.882 170 11 2 1337 1496 270908438 270908604 1.230000e-37 169.0
21 TraesCS5B01G100500 chrUn 85.882 170 11 2 1337 1496 282363912 282364078 1.230000e-37 169.0
22 TraesCS5B01G100500 chrUn 85.882 170 11 2 1337 1496 397470688 397470854 1.230000e-37 169.0
23 TraesCS5B01G100500 chrUn 87.963 108 13 0 4340 4447 55797786 55797679 2.090000e-25 128.0
24 TraesCS5B01G100500 chr4A 86.111 108 15 0 4340 4447 418077438 418077545 4.520000e-22 117.0
25 TraesCS5B01G100500 chr4A 88.889 63 7 0 5796 5858 464687303 464687365 2.130000e-10 78.7
26 TraesCS5B01G100500 chr3D 87.500 72 6 3 5791 5861 471968512 471968443 5.930000e-11 80.5
27 TraesCS5B01G100500 chr3B 88.889 63 7 0 5796 5858 422317363 422317425 2.130000e-10 78.7
28 TraesCS5B01G100500 chr1B 92.453 53 4 0 5808 5860 322104596 322104544 7.670000e-10 76.8
29 TraesCS5B01G100500 chr1B 87.692 65 8 0 5796 5860 484361133 484361197 7.670000e-10 76.8


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 TraesCS5B01G100500 chr5B 133593459 133600587 7128 True 13165 13165 100.000000 1 7129 1 chr5B.!!$R1 7128
1 TraesCS5B01G100500 chr5D 120340229 120347311 7082 True 10901 10901 94.442000 19 7129 1 chr5D.!!$R1 7110
2 TraesCS5B01G100500 chr5A 130535959 130543077 7118 True 3460 7758 93.007667 37 7129 3 chr5A.!!$R1 7092

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
812 832 0.033504 TCCTTCTTGGTCTCGTGTGC 59.966 55.000 0.00 0.0 37.07 4.57 F
1459 1593 0.107456 ATGGTGGCCGAGTCATGATC 59.893 55.000 0.00 0.0 0.00 2.92 F
1911 2046 0.110056 GCCTGTCAAATGTGAGTGCG 60.110 55.000 0.00 0.0 33.27 5.34 F
3251 3388 0.106149 ACACGAAAGGGAAGAAGCGT 59.894 50.000 0.00 0.0 38.45 5.07 F
3649 3787 2.750948 TGAGACAGTAAGTTTCGTGGC 58.249 47.619 0.00 0.0 34.21 5.01 F
4948 5110 1.416030 TCTGTTGCAAGGCACAGTCTA 59.584 47.619 14.32 0.0 38.71 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2772 2909 0.319813 CAAAAAGCGGCCCAAAGGAG 60.320 55.0 0.00 0.00 33.47 3.69 R
3234 3371 0.391597 TGACGCTTCTTCCCTTTCGT 59.608 50.0 0.00 0.00 0.00 3.85 R
3818 3956 0.179020 TCTTGCTTCCACCACCAGTG 60.179 55.0 0.00 0.00 46.83 3.66 R
4607 4766 0.105964 TCAGGGGATTCGGGAGAGAG 60.106 60.0 0.00 0.00 41.75 3.20 R
5194 5360 0.169009 GGTGATCTTTCGGCTGCAAC 59.831 55.0 0.50 0.00 0.00 4.17 R
6743 6925 0.026414 ATGACGACGACGACGATGAG 59.974 55.0 25.15 4.59 42.66 2.90 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
50 51 1.860676 GTGTGTTTGGAGCGTGTAGA 58.139 50.000 0.00 0.00 0.00 2.59
67 68 1.745115 GACAGCCAGCGCAATGGTA 60.745 57.895 16.24 0.00 42.75 3.25
68 69 1.982073 GACAGCCAGCGCAATGGTAC 61.982 60.000 16.24 1.87 42.75 3.34
69 70 2.819595 AGCCAGCGCAATGGTACG 60.820 61.111 16.24 0.00 42.75 3.67
70 71 3.124921 GCCAGCGCAATGGTACGT 61.125 61.111 16.24 0.00 42.75 3.57
76 77 3.496884 CCAGCGCAATGGTACGTATTTAT 59.503 43.478 11.47 0.00 35.47 1.40
95 96 6.371809 TTTATTTAGCAGCATTTAGGACGG 57.628 37.500 0.00 0.00 0.00 4.79
104 105 2.629051 CATTTAGGACGGGACAGGTTC 58.371 52.381 0.00 0.00 0.00 3.62
305 306 4.644288 TCCCCCGACCCGTTTCCT 62.644 66.667 0.00 0.00 0.00 3.36
306 307 4.091939 CCCCCGACCCGTTTCCTC 62.092 72.222 0.00 0.00 0.00 3.71
407 409 0.773644 TTTTGCTTCCTGCTCCTCCT 59.226 50.000 0.00 0.00 43.37 3.69
461 463 2.726351 CCTTCTCCCTCGGTGAGCC 61.726 68.421 0.00 0.00 0.00 4.70
462 464 1.984570 CTTCTCCCTCGGTGAGCCA 60.985 63.158 0.00 0.00 34.09 4.75
463 465 1.535444 TTCTCCCTCGGTGAGCCAA 60.535 57.895 0.00 0.00 34.09 4.52
464 466 1.544825 TTCTCCCTCGGTGAGCCAAG 61.545 60.000 0.00 0.00 34.09 3.61
563 569 3.126514 ACAGCAATGCATCTTCTTCTTCG 59.873 43.478 8.35 0.00 0.00 3.79
564 570 2.681848 AGCAATGCATCTTCTTCTTCGG 59.318 45.455 8.35 0.00 0.00 4.30
565 571 2.679837 GCAATGCATCTTCTTCTTCGGA 59.320 45.455 0.00 0.00 0.00 4.55
566 572 3.242673 GCAATGCATCTTCTTCTTCGGAG 60.243 47.826 0.00 0.00 0.00 4.63
567 573 2.680312 TGCATCTTCTTCTTCGGAGG 57.320 50.000 0.00 0.00 0.00 4.30
568 574 2.179427 TGCATCTTCTTCTTCGGAGGA 58.821 47.619 0.00 0.00 0.00 3.71
569 575 2.167281 TGCATCTTCTTCTTCGGAGGAG 59.833 50.000 0.00 0.00 31.74 3.69
570 576 2.482839 GCATCTTCTTCTTCGGAGGAGG 60.483 54.545 0.00 0.00 31.74 4.30
571 577 2.606751 TCTTCTTCTTCGGAGGAGGT 57.393 50.000 0.00 0.00 31.74 3.85
572 578 3.733883 TCTTCTTCTTCGGAGGAGGTA 57.266 47.619 0.00 0.00 31.74 3.08
573 579 4.043608 TCTTCTTCTTCGGAGGAGGTAA 57.956 45.455 0.00 0.00 31.74 2.85
574 580 4.413760 TCTTCTTCTTCGGAGGAGGTAAA 58.586 43.478 0.00 0.00 31.74 2.01
575 581 4.463186 TCTTCTTCTTCGGAGGAGGTAAAG 59.537 45.833 0.00 0.00 31.74 1.85
576 582 3.775910 TCTTCTTCGGAGGAGGTAAAGT 58.224 45.455 0.00 0.00 0.00 2.66
664 684 2.915604 TCTTCTTCTCTTCCTGCCCAAT 59.084 45.455 0.00 0.00 0.00 3.16
665 685 3.054802 TCTTCTTCTCTTCCTGCCCAATC 60.055 47.826 0.00 0.00 0.00 2.67
699 719 1.102978 CGTGGATGATTTTCACCCCC 58.897 55.000 0.00 0.00 24.64 5.40
812 832 0.033504 TCCTTCTTGGTCTCGTGTGC 59.966 55.000 0.00 0.00 37.07 4.57
888 908 3.440127 CACCAAATCCCCATTTACCACT 58.560 45.455 0.00 0.00 30.51 4.00
890 910 4.401202 CACCAAATCCCCATTTACCACTAC 59.599 45.833 0.00 0.00 30.51 2.73
957 977 2.124507 ATATAATGTGCGGCCCGGCT 62.125 55.000 9.86 0.00 0.00 5.52
1005 1025 6.272822 AGAAATAGGAAGCCAAACATGTTC 57.727 37.500 12.39 0.00 0.00 3.18
1088 1108 3.643763 CTCCTGGACCTTATTCGATTCG 58.356 50.000 0.00 0.00 0.00 3.34
1150 1170 2.620251 TGCATATGGTACTGGAGTGC 57.380 50.000 4.56 0.00 0.00 4.40
1158 1178 1.610886 GGTACTGGAGTGCTGGTTTCC 60.611 57.143 0.00 0.00 0.00 3.13
1190 1214 5.047731 AGCTGCTTCTTTCTTTTAATGGACC 60.048 40.000 0.00 0.00 0.00 4.46
1209 1233 2.367567 ACCGTACCATGTTCAGACAAGT 59.632 45.455 0.00 0.00 39.66 3.16
1317 1451 8.664211 TTAAATTTGGCGAAATGTACCTTTTT 57.336 26.923 7.50 0.00 31.83 1.94
1335 1469 6.949463 ACCTTTTTATCCAAAAACTCCGGATA 59.051 34.615 3.57 0.00 38.42 2.59
1336 1470 7.094075 ACCTTTTTATCCAAAAACTCCGGATAC 60.094 37.037 3.57 0.00 40.63 2.24
1337 1471 6.762702 TTTTATCCAAAAACTCCGGATACC 57.237 37.500 3.57 0.00 40.63 2.73
1338 1472 5.354792 TTTTATCCAAAAACTCCGGATACCG 59.645 40.000 3.57 3.03 40.63 4.02
1447 1581 1.405933 GCAATTCCCTTTCATGGTGGC 60.406 52.381 0.00 0.00 0.00 5.01
1459 1593 0.107456 ATGGTGGCCGAGTCATGATC 59.893 55.000 0.00 0.00 0.00 2.92
1805 1940 0.396435 TCTCTCGCAAAGGAAAGCCA 59.604 50.000 0.00 0.00 36.29 4.75
1818 1953 2.948315 GGAAAGCCAAGAGTGATGATCC 59.052 50.000 0.00 0.00 0.00 3.36
1911 2046 0.110056 GCCTGTCAAATGTGAGTGCG 60.110 55.000 0.00 0.00 33.27 5.34
2112 2249 1.346068 GATAGCTCGGAGAATTGGGCT 59.654 52.381 9.69 0.00 36.93 5.19
2179 2316 8.630054 TGTAAGCAACAACCTAAACTATGAAT 57.370 30.769 0.00 0.00 34.29 2.57
2351 2488 3.417069 TGTGTTGTTATGGACTCCCTG 57.583 47.619 0.00 0.00 0.00 4.45
2451 2588 6.879993 TGAGTGAACAAACACACTAAAAGGTA 59.120 34.615 0.00 0.00 45.54 3.08
2533 2670 5.297547 AGTATCATGTTATTCGGCGATTGT 58.702 37.500 11.76 2.50 0.00 2.71
2802 2939 1.669795 CCGCTTTTTGCAATGGACCTC 60.670 52.381 0.00 0.00 43.06 3.85
2832 2969 6.757237 TGAACAAATACATGAATGTGGCTTT 58.243 32.000 0.00 1.52 41.89 3.51
2852 2989 8.091449 TGGCTTTATAGAGAAATAGCTAAGCTC 58.909 37.037 0.00 5.19 40.44 4.09
2952 3089 2.751166 ATCAGGTTCTCACACTTCCG 57.249 50.000 0.00 0.00 0.00 4.30
2975 3112 5.707298 CGAAGCCCTTGGATTTATATGATGT 59.293 40.000 0.00 0.00 28.48 3.06
3125 3262 3.016736 AGTGCTATGCTGCGGTTAAATT 58.983 40.909 0.00 0.00 35.36 1.82
3148 3285 6.377327 TTTCATTTGACCTGACAGAGTTTC 57.623 37.500 3.32 0.00 0.00 2.78
3208 3345 3.866582 GACCAGGGCAGGCGCTAT 61.867 66.667 7.64 2.43 37.46 2.97
3216 3353 1.018226 GGCAGGCGCTATGCTGATAG 61.018 60.000 28.37 1.14 45.43 2.08
3234 3371 2.818751 AGTTTTTGGTGGTGAGGACA 57.181 45.000 0.00 0.00 0.00 4.02
3242 3379 0.602905 GTGGTGAGGACACGAAAGGG 60.603 60.000 0.00 0.00 46.77 3.95
3251 3388 0.106149 ACACGAAAGGGAAGAAGCGT 59.894 50.000 0.00 0.00 38.45 5.07
3284 3421 4.866486 CACATGTTCGATCTCAAGTCATCA 59.134 41.667 0.00 0.00 0.00 3.07
3540 3678 6.019748 GGACCTTCTCCTAGATCCAATCATA 58.980 44.000 0.00 0.00 35.89 2.15
3648 3786 5.728351 TTTTGAGACAGTAAGTTTCGTGG 57.272 39.130 0.00 0.00 34.21 4.94
3649 3787 2.750948 TGAGACAGTAAGTTTCGTGGC 58.249 47.619 0.00 0.00 34.21 5.01
3681 3819 8.212317 TGATTACATCACCAATTATGTCACTG 57.788 34.615 0.00 0.00 37.50 3.66
3707 3845 7.308589 GGGTATGATGCATGTTAATGGTTACTC 60.309 40.741 2.46 0.00 34.09 2.59
3782 3920 4.598894 CCATCGCCTCGAGCAGGG 62.599 72.222 6.99 2.98 43.70 4.45
3809 3947 4.777896 AGTGGAGCTCTATGTGGAACTAAA 59.222 41.667 14.64 0.00 38.04 1.85
3818 3956 7.171678 GCTCTATGTGGAACTAAATGGTACATC 59.828 40.741 0.00 0.00 40.66 3.06
4094 4232 7.380423 AGAAAGTAAGCCACCAGATATATGT 57.620 36.000 0.00 0.00 0.00 2.29
4265 4405 3.347958 ACAAACCATGTACAAAGTGCG 57.652 42.857 0.00 0.00 41.63 5.34
4458 4598 5.008217 CGACAAGGTGAAACTTTTACCATCA 59.992 40.000 15.81 0.00 31.80 3.07
4554 4694 5.522460 CCTCGTGTTCTAAAGACTTTCAACA 59.478 40.000 16.21 16.21 0.00 3.33
4556 4696 7.367159 TCGTGTTCTAAAGACTTTCAACAAA 57.633 32.000 19.60 12.27 31.32 2.83
4567 4726 8.926715 AAGACTTTCAACAAACAACTTTATCC 57.073 30.769 0.00 0.00 0.00 2.59
4623 4783 1.497161 TTTCTCTCTCCCGAATCCCC 58.503 55.000 0.00 0.00 0.00 4.81
4720 4880 8.800370 TGCACCTGAATATACTGAAACATTTA 57.200 30.769 0.00 0.00 0.00 1.40
4764 4924 4.959596 ATTGAGATGCATCACTGAACAC 57.040 40.909 27.81 9.17 0.00 3.32
4798 4960 7.549147 TCTGTAGGTTGAAGTATTAGTGGTT 57.451 36.000 0.00 0.00 0.00 3.67
4818 4980 4.359706 GTTCTGCAAAACGACCATTCTTT 58.640 39.130 0.00 0.00 0.00 2.52
4853 5015 1.846439 CCCCAGATGTAGACCCATTGT 59.154 52.381 0.00 0.00 0.00 2.71
4948 5110 1.416030 TCTGTTGCAAGGCACAGTCTA 59.584 47.619 14.32 0.00 38.71 2.59
4982 5144 2.018544 CGTGCGTCTAGAGAGGAGG 58.981 63.158 3.47 0.00 32.08 4.30
5061 5226 1.688735 AGCCCAAAAGCTTGAGAAACC 59.311 47.619 0.00 0.00 41.41 3.27
5083 5248 4.088638 CCGATCGATGATGACAAATACGAC 59.911 45.833 18.66 0.00 0.00 4.34
5088 5253 4.661649 CGATGATGACAAATACGACGATGC 60.662 45.833 0.00 0.00 0.00 3.91
5104 5269 2.347939 CGATGCCGATGATTGTTCTTCG 60.348 50.000 4.77 4.77 44.67 3.79
5110 5275 2.028045 CGATGATTGTTCTTCGTGTCCG 59.972 50.000 3.84 0.00 41.86 4.79
5160 5326 4.700596 GTCAATAGACAAGCGCATACTC 57.299 45.455 11.47 0.00 44.34 2.59
5161 5327 3.491267 GTCAATAGACAAGCGCATACTCC 59.509 47.826 11.47 0.00 44.34 3.85
5177 5343 2.162681 ACTCCTACTTTGTTGCCATGC 58.837 47.619 0.00 0.00 0.00 4.06
5186 5352 3.994204 TTGTTGCCATGCATATAGCTG 57.006 42.857 14.44 0.00 45.94 4.24
5187 5353 3.211718 TGTTGCCATGCATATAGCTGA 57.788 42.857 14.44 3.63 45.94 4.26
5194 5360 4.921515 GCCATGCATATAGCTGATTGTTTG 59.078 41.667 0.00 0.00 45.94 2.93
5241 5407 1.760875 GGACAGGGGCCGATACTCA 60.761 63.158 0.00 0.00 0.00 3.41
5308 5474 1.518367 ACCAAGGACCAAGTGGAAGA 58.482 50.000 14.11 0.00 38.94 2.87
5403 5569 1.302033 CGCTTGAGGACCAGCTTGT 60.302 57.895 0.00 0.00 0.00 3.16
5404 5570 1.572085 CGCTTGAGGACCAGCTTGTG 61.572 60.000 0.00 0.00 0.00 3.33
5677 5843 2.265904 CCCCTGGCGCATGATGATG 61.266 63.158 10.83 0.00 0.00 3.07
5690 5856 1.546923 TGATGATGTTGGCTGCCTTTG 59.453 47.619 21.03 0.00 0.00 2.77
5725 5894 4.022849 GTGAGTTTATTTTGCTGCTCCTGT 60.023 41.667 0.00 0.00 0.00 4.00
5769 5938 2.050836 TTTTGGCGGGAGAGCAGTCA 62.051 55.000 0.00 0.00 39.27 3.41
5781 5950 1.593209 GCAGTCACGGACGTTCCAA 60.593 57.895 0.00 0.00 35.91 3.53
5799 5968 6.228258 GTTCCAACTACAGGTATTTGAGACA 58.772 40.000 10.12 0.00 30.22 3.41
5803 5972 6.094048 CCAACTACAGGTATTTGAGACATTGG 59.906 42.308 10.12 0.00 30.22 3.16
5804 5973 6.374417 ACTACAGGTATTTGAGACATTGGT 57.626 37.500 0.00 0.00 0.00 3.67
5805 5974 6.779860 ACTACAGGTATTTGAGACATTGGTT 58.220 36.000 0.00 0.00 0.00 3.67
5806 5975 6.879458 ACTACAGGTATTTGAGACATTGGTTC 59.121 38.462 0.00 0.00 0.00 3.62
5807 5976 5.630121 ACAGGTATTTGAGACATTGGTTCA 58.370 37.500 0.00 0.00 0.00 3.18
5808 5977 5.473504 ACAGGTATTTGAGACATTGGTTCAC 59.526 40.000 0.00 0.00 0.00 3.18
5809 5978 5.473162 CAGGTATTTGAGACATTGGTTCACA 59.527 40.000 0.00 0.00 0.00 3.58
5810 5979 5.473504 AGGTATTTGAGACATTGGTTCACAC 59.526 40.000 0.00 0.00 0.00 3.82
5811 5980 5.473504 GGTATTTGAGACATTGGTTCACACT 59.526 40.000 0.00 0.00 0.00 3.55
5812 5981 6.653320 GGTATTTGAGACATTGGTTCACACTA 59.347 38.462 0.00 0.00 0.00 2.74
5850 6019 4.182693 CGTCTTATATTATGGGACGGCA 57.817 45.455 17.59 0.00 43.69 5.69
5882 6051 4.698575 AGAATAGAATTCCGGTGCTTCTC 58.301 43.478 15.72 6.27 31.89 2.87
5904 6073 1.106285 GCCAGCATAGGTTTTCAGGG 58.894 55.000 0.00 0.00 0.00 4.45
5915 6084 1.541588 GTTTTCAGGGTGCATCAGACC 59.458 52.381 0.00 0.00 0.00 3.85
5935 6104 7.602644 TCAGACCCTTATTCGTCATAATAATGC 59.397 37.037 0.00 0.00 32.39 3.56
5954 6123 3.745799 TGCGTAAAGTCTCCCAAAATCA 58.254 40.909 0.00 0.00 0.00 2.57
6098 6272 2.076863 CAAACGGCGAAAGGAAGATCT 58.923 47.619 16.62 0.00 0.00 2.75
6147 6324 0.608308 GTAGCCAAAAGAAGCGGGGT 60.608 55.000 0.00 0.00 35.02 4.95
6168 6345 5.295292 GGGTGAGTTCATGATCATGTACTTG 59.705 44.000 34.63 15.39 45.38 3.16
6177 6354 9.612066 TTCATGATCATGTACTTGTGCTAAATA 57.388 29.630 30.01 6.98 39.72 1.40
6272 6449 5.472820 TGTGTGTGAATCATTGTGCTTCATA 59.527 36.000 0.36 0.00 35.36 2.15
6321 6499 0.038709 AGTCGACTGAGAGCAACTGC 60.039 55.000 19.30 0.00 42.49 4.40
6408 6586 5.003804 GTGAGCTGATTTTCTTCCCTTGTA 58.996 41.667 0.00 0.00 0.00 2.41
6457 6635 1.463674 AAATCAAGTCGGCCCATCAC 58.536 50.000 0.00 0.00 0.00 3.06
6497 6675 0.598065 GGTGCAGACCATGGAAACAC 59.402 55.000 21.47 19.02 42.59 3.32
6526 6704 5.417580 TGGGCCAAGTTACTTGAAATGATAC 59.582 40.000 24.79 7.77 43.42 2.24
6528 6706 6.096846 GGGCCAAGTTACTTGAAATGATACAT 59.903 38.462 24.79 0.00 43.42 2.29
6529 6707 7.284489 GGGCCAAGTTACTTGAAATGATACATA 59.716 37.037 24.79 0.00 43.42 2.29
6530 6708 8.682710 GGCCAAGTTACTTGAAATGATACATAA 58.317 33.333 24.79 0.00 43.42 1.90
6605 6783 7.961326 AGTCTTGGCATCCATAAATAACTTT 57.039 32.000 0.00 0.00 31.53 2.66
6634 6812 0.250124 TGGCCACCTTTGTCTACACG 60.250 55.000 0.00 0.00 0.00 4.49
6704 6886 6.888088 CCATGATTGGATAAATGATGCTAGGA 59.112 38.462 0.00 0.00 46.92 2.94
6736 6918 5.036737 AGATGAAAGTGAAGCAAAAACACG 58.963 37.500 0.00 0.00 39.19 4.49
6743 6925 5.329493 AGTGAAGCAAAAACACGTTACTTC 58.671 37.500 0.00 0.00 39.19 3.01
6755 6937 2.092151 CGTTACTTCTCATCGTCGTCG 58.908 52.381 0.00 0.00 38.55 5.12
6761 6946 1.010419 TCTCATCGTCGTCGTCGTCA 61.010 55.000 11.41 0.00 38.33 4.35
6779 6964 3.608008 CGTCATCATCATCATCGTCGTCT 60.608 47.826 0.00 0.00 0.00 4.18
6780 6965 3.667726 GTCATCATCATCATCGTCGTCTG 59.332 47.826 0.00 0.00 0.00 3.51
6781 6966 2.781945 TCATCATCATCGTCGTCTGG 57.218 50.000 0.00 0.00 0.00 3.86
6872 7057 1.534595 GCACTCAGCTTCTCAACCTTG 59.465 52.381 0.00 0.00 41.15 3.61
6889 7074 0.106268 TTGCTTTGCTCCTGTCCCAA 60.106 50.000 0.00 0.00 0.00 4.12
6971 7156 3.062234 GCGCTTTTATTGCTTCTACGTCT 59.938 43.478 0.00 0.00 0.00 4.18
7070 7255 2.795231 AAGCATCTGCCAAGCTCTTA 57.205 45.000 0.00 0.00 43.38 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.741528 ACACACGTCCTTCCGTTTTT 58.258 45.000 0.00 0.00 39.45 1.94
27 28 1.885850 ACGCTCCAAACACACGTCC 60.886 57.895 0.00 0.00 29.64 4.79
50 51 2.040544 GTACCATTGCGCTGGCTGT 61.041 57.895 15.15 5.61 40.15 4.40
67 68 8.557029 GTCCTAAATGCTGCTAAATAAATACGT 58.443 33.333 0.00 0.00 0.00 3.57
68 69 7.740346 CGTCCTAAATGCTGCTAAATAAATACG 59.260 37.037 0.00 0.00 0.00 3.06
69 70 8.015658 CCGTCCTAAATGCTGCTAAATAAATAC 58.984 37.037 0.00 0.00 0.00 1.89
70 71 7.174253 CCCGTCCTAAATGCTGCTAAATAAATA 59.826 37.037 0.00 0.00 0.00 1.40
76 77 2.237643 TCCCGTCCTAAATGCTGCTAAA 59.762 45.455 0.00 0.00 0.00 1.85
95 96 1.993391 TGGGATCCGGAACCTGTCC 60.993 63.158 27.91 20.03 43.90 4.02
104 105 0.249911 GGAAATCTCGTGGGATCCGG 60.250 60.000 5.45 0.00 0.00 5.14
305 306 0.252742 GTGGAAGGGAAGGGGAGAGA 60.253 60.000 0.00 0.00 0.00 3.10
306 307 1.275421 GGTGGAAGGGAAGGGGAGAG 61.275 65.000 0.00 0.00 0.00 3.20
350 351 3.315142 GATCCACTGGCACTGGCGA 62.315 63.158 8.17 0.00 42.47 5.54
407 409 2.218037 CTGCACGAGCTACCTCTGCA 62.218 60.000 6.36 13.24 43.44 4.41
461 463 2.425124 CAACCGAACGCACGCTTG 60.425 61.111 0.00 0.00 0.00 4.01
462 464 2.586635 TCAACCGAACGCACGCTT 60.587 55.556 0.00 0.00 0.00 4.68
463 465 3.036084 CTCAACCGAACGCACGCT 61.036 61.111 0.00 0.00 0.00 5.07
464 466 4.719616 GCTCAACCGAACGCACGC 62.720 66.667 0.00 0.00 0.00 5.34
812 832 2.536997 AAATCAGGGGAACGAGGCGG 62.537 60.000 0.00 0.00 0.00 6.13
903 923 3.803555 CAGACAAGTCAATGCGAGAAAC 58.196 45.455 2.72 0.00 0.00 2.78
909 929 0.167470 CCTGCAGACAAGTCAATGCG 59.833 55.000 17.39 2.29 41.58 4.73
957 977 4.245660 CAAATTCGTCCTAGAAGCAGACA 58.754 43.478 0.00 0.00 33.19 3.41
1088 1108 2.984562 CCAAAATGGGCAATTGGTACC 58.015 47.619 4.43 4.43 38.99 3.34
1150 1170 2.391389 GCTTCTCGCCGGAAACCAG 61.391 63.158 5.05 0.00 0.00 4.00
1158 1178 2.125753 AGAAGCAGCTTCTCGCCG 60.126 61.111 29.05 0.00 46.42 6.46
1170 1193 5.372547 ACGGTCCATTAAAAGAAAGAAGC 57.627 39.130 0.00 0.00 0.00 3.86
1190 1214 4.621460 CACTACTTGTCTGAACATGGTACG 59.379 45.833 0.00 0.00 35.43 3.67
1250 1274 9.190858 CGTTTCCTCATCAATTTCACAATAAAA 57.809 29.630 0.00 0.00 0.00 1.52
1260 1284 5.782893 TTTCACCGTTTCCTCATCAATTT 57.217 34.783 0.00 0.00 0.00 1.82
1263 1287 5.070001 AGATTTTCACCGTTTCCTCATCAA 58.930 37.500 0.00 0.00 0.00 2.57
1264 1288 4.651778 AGATTTTCACCGTTTCCTCATCA 58.348 39.130 0.00 0.00 0.00 3.07
1302 1353 9.471084 AGTTTTTGGATAAAAAGGTACATTTCG 57.529 29.630 5.89 0.00 44.07 3.46
1317 1451 4.062677 CGGTATCCGGAGTTTTTGGATA 57.937 45.455 11.34 0.00 44.15 2.59
1338 1472 5.294552 CCATCTTCAAAACTTCTCGGTATCC 59.705 44.000 0.00 0.00 0.00 2.59
1339 1473 5.875359 ACCATCTTCAAAACTTCTCGGTATC 59.125 40.000 0.00 0.00 0.00 2.24
1340 1474 5.643777 CACCATCTTCAAAACTTCTCGGTAT 59.356 40.000 0.00 0.00 0.00 2.73
1341 1475 4.994852 CACCATCTTCAAAACTTCTCGGTA 59.005 41.667 0.00 0.00 0.00 4.02
1342 1476 3.815401 CACCATCTTCAAAACTTCTCGGT 59.185 43.478 0.00 0.00 0.00 4.69
1447 1581 6.703165 TCACAATATTTCTGATCATGACTCGG 59.297 38.462 0.00 2.67 0.00 4.63
1661 1796 9.048446 CAGACCTCAAATGTGAAATTTGATTTT 57.952 29.630 10.95 0.00 44.14 1.82
1714 1849 8.572855 AGAGCAAAAGAATAACAAGAAGCTAT 57.427 30.769 0.00 0.00 0.00 2.97
1780 1915 4.572389 GCTTTCCTTTGCGAGAGAATCATA 59.428 41.667 0.00 0.00 37.82 2.15
1805 1940 6.590068 CATAAGTCTTGGGATCATCACTCTT 58.410 40.000 0.00 0.90 0.00 2.85
1818 1953 2.787473 TGGACCTGCATAAGTCTTGG 57.213 50.000 10.43 0.00 33.39 3.61
1888 2023 2.483106 CACTCACATTTGACAGGCTGAG 59.517 50.000 23.66 7.29 32.94 3.35
2022 2159 1.672356 GTCATCTGCACGGCCACTT 60.672 57.895 2.24 0.00 0.00 3.16
2297 2434 8.522830 ACAATTACCTTTGTATCATCCAACAAG 58.477 33.333 0.00 0.00 38.04 3.16
2404 2541 4.445452 TTTCAGTCCGTATGTAGTCCAC 57.555 45.455 0.00 0.00 0.00 4.02
2604 2741 4.615912 CGAATTGGCGATGGAAGAACTTTT 60.616 41.667 0.00 0.00 0.00 2.27
2772 2909 0.319813 CAAAAAGCGGCCCAAAGGAG 60.320 55.000 0.00 0.00 33.47 3.69
2802 2939 7.115236 CCACATTCATGTATTTGTTCAGTTGTG 59.885 37.037 0.00 0.00 39.39 3.33
2832 2969 8.050325 AGGATCGAGCTTAGCTATTTCTCTATA 58.950 37.037 6.75 0.00 39.88 1.31
2852 2989 5.445939 CGAAACCTGTACATCAAAAGGATCG 60.446 44.000 0.00 5.72 36.83 3.69
2952 3089 7.530426 AACATCATATAAATCCAAGGGCTTC 57.470 36.000 0.00 0.00 0.00 3.86
2975 3112 2.091499 TCTATCGGGCAGAGGAGGTTAA 60.091 50.000 0.00 0.00 0.00 2.01
3090 3227 8.725148 GCAGCATAGCACTCAATACTTAATAAT 58.275 33.333 0.00 0.00 0.00 1.28
3091 3228 7.095649 CGCAGCATAGCACTCAATACTTAATAA 60.096 37.037 0.00 0.00 0.00 1.40
3125 3262 6.122277 AGAAACTCTGTCAGGTCAAATGAAA 58.878 36.000 0.00 0.00 0.00 2.69
3148 3285 3.254657 TGCCTAAAATCCGAACCACAAAG 59.745 43.478 0.00 0.00 0.00 2.77
3208 3345 3.820467 CTCACCACCAAAAACTATCAGCA 59.180 43.478 0.00 0.00 0.00 4.41
3210 3347 4.455877 GTCCTCACCACCAAAAACTATCAG 59.544 45.833 0.00 0.00 0.00 2.90
3216 3353 1.064952 CGTGTCCTCACCACCAAAAAC 59.935 52.381 0.00 0.00 41.09 2.43
3234 3371 0.391597 TGACGCTTCTTCCCTTTCGT 59.608 50.000 0.00 0.00 0.00 3.85
3242 3379 3.928992 TGTGAAGATCATGACGCTTCTTC 59.071 43.478 27.25 24.74 42.74 2.87
3251 3388 5.910614 AGATCGAACATGTGAAGATCATGA 58.089 37.500 26.35 0.00 43.47 3.07
3284 3421 6.948309 ACTTATAGTTCAAAGGAAGCCATGTT 59.052 34.615 0.00 0.00 32.62 2.71
3367 3504 7.200434 ACATCCTAGAATGTAACCATGAAGT 57.800 36.000 0.00 0.00 38.09 3.01
3411 3549 8.950208 AAGAGTATTAGGCAGTGAAAGATTAC 57.050 34.615 0.00 0.00 0.00 1.89
3540 3678 5.417894 CCCTATCATCATACAATGCAGCAAT 59.582 40.000 0.00 0.00 0.00 3.56
3681 3819 5.789643 AACCATTAACATGCATCATACCC 57.210 39.130 0.00 0.00 0.00 3.69
3707 3845 8.420222 ACCATCTGACAAGAAGATAGATACTTG 58.580 37.037 0.00 0.00 43.30 3.16
3782 3920 3.024547 TCCACATAGAGCTCCACTACAC 58.975 50.000 10.93 0.00 0.00 2.90
3818 3956 0.179020 TCTTGCTTCCACCACCAGTG 60.179 55.000 0.00 0.00 46.83 3.66
4094 4232 5.957771 AGTACCATCATAAGAGAGGCAAA 57.042 39.130 0.00 0.00 0.00 3.68
4181 4319 1.895798 TGAGCGAGAAGTCCAGAACAT 59.104 47.619 0.00 0.00 0.00 2.71
4265 4405 8.142551 CCTGTGGAAGTATTATACACTAGAACC 58.857 40.741 5.11 0.00 31.29 3.62
4341 4481 3.057596 TGAAACCCTGCATGAATCGTTTC 60.058 43.478 14.69 14.69 39.51 2.78
4343 4483 2.489329 CTGAAACCCTGCATGAATCGTT 59.511 45.455 0.00 0.00 0.00 3.85
4458 4598 5.807011 GTCAAAGTGACACAAGAAAATGCTT 59.193 36.000 8.59 0.00 46.22 3.91
4567 4726 0.790207 AATGTCAGCACTACAACGCG 59.210 50.000 3.53 3.53 0.00 6.01
4607 4766 0.105964 TCAGGGGATTCGGGAGAGAG 60.106 60.000 0.00 0.00 41.75 3.20
4614 4774 4.579869 CCAAATATACTCAGGGGATTCGG 58.420 47.826 0.00 0.00 0.00 4.30
4616 4776 4.762251 GTGCCAAATATACTCAGGGGATTC 59.238 45.833 0.00 0.00 0.00 2.52
4623 4783 9.167311 AGAAAGTAAAGTGCCAAATATACTCAG 57.833 33.333 0.00 0.00 0.00 3.35
4655 4815 6.019881 TGACGAGACAATTACGCATAATTCAG 60.020 38.462 0.00 0.00 38.67 3.02
4764 4924 4.713824 TCAACCTACAGATAACCAGACG 57.286 45.455 0.00 0.00 0.00 4.18
4798 4960 4.647424 AAAAGAATGGTCGTTTTGCAGA 57.353 36.364 0.00 0.00 32.35 4.26
4853 5015 6.422333 TGGTGCTTGGAGAATATTCATACAA 58.578 36.000 17.56 15.78 0.00 2.41
4982 5144 0.463474 GAAGTGCCCAGAGCTCCATC 60.463 60.000 10.93 0.00 44.23 3.51
5061 5226 4.201307 CGTCGTATTTGTCATCATCGATCG 60.201 45.833 9.36 9.36 0.00 3.69
5083 5248 2.347939 CGAAGAACAATCATCGGCATCG 60.348 50.000 0.00 0.00 41.68 3.84
5110 5275 1.866925 GTCACTTACGGTGCTTGCC 59.133 57.895 0.00 0.00 44.98 4.52
5131 5296 3.935203 CGCTTGTCTATTGACTTGGATGT 59.065 43.478 8.74 0.00 43.29 3.06
5159 5325 9.751630 AGCTATATGCATGGCAACAAAGTAGGA 62.752 40.741 10.16 0.00 46.22 2.94
5160 5326 7.687120 AGCTATATGCATGGCAACAAAGTAGG 61.687 42.308 10.16 0.00 46.22 3.18
5161 5327 5.240183 AGCTATATGCATGGCAACAAAGTAG 59.760 40.000 10.16 0.00 46.22 2.57
5177 5343 5.457799 GCTGCAACAAACAATCAGCTATATG 59.542 40.000 5.40 0.00 44.71 1.78
5186 5352 2.132740 TTCGGCTGCAACAAACAATC 57.867 45.000 0.50 0.00 0.00 2.67
5187 5353 2.100584 TCTTTCGGCTGCAACAAACAAT 59.899 40.909 0.50 0.00 0.00 2.71
5194 5360 0.169009 GGTGATCTTTCGGCTGCAAC 59.831 55.000 0.50 0.00 0.00 4.17
5241 5407 1.002888 CAGTTCTGGCCATGTCAGTCT 59.997 52.381 5.51 0.00 36.55 3.24
5548 5714 2.042433 AGACAGGCTGTTAGACTCCTCT 59.958 50.000 22.98 7.75 24.26 3.69
5649 5815 2.131709 CGCCAGGGGATCGTCCTTA 61.132 63.158 0.00 0.00 36.57 2.69
5702 5871 4.022849 ACAGGAGCAGCAAAATAAACTCAC 60.023 41.667 0.00 0.00 0.00 3.51
5725 5894 0.758734 CGGGTGGAATGCATCTCCTA 59.241 55.000 21.12 10.48 33.77 2.94
5769 5938 0.316204 CCTGTAGTTGGAACGTCCGT 59.684 55.000 0.00 0.00 40.17 4.69
5781 5950 6.374417 ACCAATGTCTCAAATACCTGTAGT 57.626 37.500 0.00 0.00 0.00 2.73
5799 5968 5.069914 TGACAGTACACTAGTGTGAACCAAT 59.930 40.000 33.77 13.64 46.55 3.16
5803 5972 6.897259 TTTTGACAGTACACTAGTGTGAAC 57.103 37.500 33.77 25.34 46.55 3.18
5849 6018 7.014422 ACCGGAATTCTATTCTAAGTACTCCTG 59.986 40.741 9.46 0.00 0.00 3.86
5850 6019 7.014422 CACCGGAATTCTATTCTAAGTACTCCT 59.986 40.741 9.46 0.00 0.00 3.69
5882 6051 1.747355 CTGAAAACCTATGCTGGCCTG 59.253 52.381 3.32 4.26 0.00 4.85
5904 6073 2.866762 GACGAATAAGGGTCTGATGCAC 59.133 50.000 0.00 0.00 0.00 4.57
5915 6084 9.741168 CTTTACGCATTATTATGACGAATAAGG 57.259 33.333 12.94 0.00 35.34 2.69
5935 6104 4.034048 CGGATGATTTTGGGAGACTTTACG 59.966 45.833 0.00 0.00 0.00 3.18
5954 6123 4.929808 GTCAAAGTGTATGAAGTGTCGGAT 59.070 41.667 0.00 0.00 0.00 4.18
5988 6158 5.590259 ACAGAGTTCATTTGTGTTACAGCTT 59.410 36.000 0.00 0.00 0.00 3.74
6080 6254 1.676014 CCAGATCTTCCTTTCGCCGTT 60.676 52.381 0.00 0.00 0.00 4.44
6087 6261 1.351017 TGGCGTTCCAGATCTTCCTTT 59.649 47.619 0.00 0.00 37.47 3.11
6098 6272 2.282180 GGCTTCCTTGGCGTTCCA 60.282 61.111 0.00 0.00 41.55 3.53
6147 6324 5.352293 GCACAAGTACATGATCATGAACTCA 59.648 40.000 36.37 15.91 41.20 3.41
6168 6345 4.398319 ACCACAGCCCATATATTTAGCAC 58.602 43.478 0.00 0.00 0.00 4.40
6177 6354 5.104982 CCAATTTACAAACCACAGCCCATAT 60.105 40.000 0.00 0.00 0.00 1.78
6433 6611 2.285083 TGGGCCGACTTGATTTAATCG 58.715 47.619 0.00 0.00 0.00 3.34
6457 6635 7.148086 TGCACCTAATAATGTAGCCTTTTCAAG 60.148 37.037 0.00 0.00 0.00 3.02
6497 6675 3.420893 TCAAGTAACTTGGCCCATCTTG 58.579 45.455 0.00 7.04 41.33 3.02
6556 6734 1.623811 TGCTGACCCACCTTCTAGTTC 59.376 52.381 0.00 0.00 0.00 3.01
6605 6783 3.390639 ACAAAGGTGGCCATTTCATTTCA 59.609 39.130 9.72 0.00 0.00 2.69
6634 6812 3.472652 TGTACAGTGGAATGTTGGTGAC 58.527 45.455 0.00 0.00 34.56 3.67
6688 6870 9.539825 CTATGGTGTATCCTAGCATCATTTATC 57.460 37.037 0.02 0.00 37.57 1.75
6704 6886 6.653020 TGCTTCACTTTCATCTATGGTGTAT 58.347 36.000 0.00 0.00 0.00 2.29
6736 6918 3.089982 GACGACGACGATGAGAAGTAAC 58.910 50.000 15.32 0.00 42.66 2.50
6743 6925 0.026414 ATGACGACGACGACGATGAG 59.974 55.000 25.15 4.59 42.66 2.90
6755 6937 2.654056 CGACGATGATGATGATGACGAC 59.346 50.000 0.00 0.00 0.00 4.34
6761 6946 2.625314 ACCAGACGACGATGATGATGAT 59.375 45.455 0.00 0.00 0.00 2.45
6779 6964 2.677524 GATGCTGCCTTGCCACCA 60.678 61.111 0.00 0.00 0.00 4.17
6780 6965 2.012902 GATGATGCTGCCTTGCCACC 62.013 60.000 0.00 0.00 0.00 4.61
6781 6966 1.436336 GATGATGCTGCCTTGCCAC 59.564 57.895 0.00 0.00 0.00 5.01
6872 7057 1.871126 GCTTGGGACAGGAGCAAAGC 61.871 60.000 0.00 0.00 41.43 3.51
6971 7156 3.009115 GGCAGTGCTCCCTACCCA 61.009 66.667 16.11 0.00 0.00 4.51
7070 7255 7.750229 TGCAGTAAAACTTGAATCTGATCTT 57.250 32.000 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.