Multiple sequence alignment - TraesCS2B01G538100

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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 TraesCS2B01G538100 chr2B 100.000 5331 0 0 1 5331 733646793 733641463 0.000000e+00 9845.0
1 TraesCS2B01G538100 chr2B 84.928 2289 278 31 854 3096 733715779 733713512 0.000000e+00 2254.0
2 TraesCS2B01G538100 chr2B 88.402 1233 130 6 891 2111 733733054 733731823 0.000000e+00 1472.0
3 TraesCS2B01G538100 chr2B 90.151 1127 99 4 912 2026 733472858 733471732 0.000000e+00 1456.0
4 TraesCS2B01G538100 chr2B 88.391 1206 120 9 843 2030 733458610 733457407 0.000000e+00 1434.0
5 TraesCS2B01G538100 chr2B 87.646 1198 134 7 903 2087 733746719 733745523 0.000000e+00 1380.0
6 TraesCS2B01G538100 chr2B 84.548 1139 134 19 1993 3099 733471699 733470571 0.000000e+00 1090.0
7 TraesCS2B01G538100 chr2B 83.422 1128 178 8 2131 3252 733745449 733744325 0.000000e+00 1038.0
8 TraesCS2B01G538100 chr2B 82.636 1123 166 17 3274 4381 733471620 733470512 0.000000e+00 966.0
9 TraesCS2B01G538100 chr2B 81.036 1197 193 20 3274 4442 733731739 733730549 0.000000e+00 922.0
10 TraesCS2B01G538100 chr2B 83.027 978 155 8 2129 3099 733643445 733642472 0.000000e+00 876.0
11 TraesCS2B01G538100 chr2B 83.027 978 155 8 3349 4322 733644665 733643695 0.000000e+00 876.0
12 TraesCS2B01G538100 chr2B 82.688 982 160 7 2120 3096 733744303 733743327 0.000000e+00 863.0
13 TraesCS2B01G538100 chr2B 82.316 967 153 15 2138 3089 733731643 733730680 0.000000e+00 822.0
14 TraesCS2B01G538100 chr2B 80.532 1053 186 9 3387 4430 733843577 733842535 0.000000e+00 791.0
15 TraesCS2B01G538100 chr2B 83.636 330 41 11 1 326 733747509 733747189 1.120000e-76 298.0
16 TraesCS2B01G538100 chr2B 76.399 411 40 28 4674 5042 733730423 733730028 9.180000e-38 169.0
17 TraesCS2B01G538100 chr2B 86.000 150 17 4 183 331 733716436 733716290 1.990000e-34 158.0
18 TraesCS2B01G538100 chr2B 79.221 231 33 12 5050 5271 733729991 733729767 4.300000e-31 147.0
19 TraesCS2B01G538100 chr2B 88.281 128 5 4 5144 5271 733199655 733199538 1.550000e-30 145.0
20 TraesCS2B01G538100 chr2B 81.714 175 27 3 404 574 733845105 733844932 2.000000e-29 141.0
21 TraesCS2B01G538100 chr2B 78.656 253 22 12 4820 5042 733841795 733841545 7.200000e-29 139.0
22 TraesCS2B01G538100 chr2B 76.174 298 45 14 4839 5117 733712667 733712377 3.350000e-27 134.0
23 TraesCS2B01G538100 chr2B 98.571 70 1 0 5050 5119 733841508 733841439 2.020000e-24 124.0
24 TraesCS2B01G538100 chr2B 94.595 74 4 0 3196 3269 733643520 733643447 1.210000e-21 115.0
25 TraesCS2B01G538100 chr2B 94.595 74 4 0 3274 3347 733643598 733643525 1.210000e-21 115.0
26 TraesCS2B01G538100 chr2B 93.750 64 4 0 5208 5271 733209537 733209474 4.390000e-16 97.1
27 TraesCS2B01G538100 chr2B 96.078 51 2 0 629 679 733646073 733646023 3.420000e-12 84.2
28 TraesCS2B01G538100 chr2B 96.078 51 2 0 721 771 733646165 733646115 3.420000e-12 84.2
29 TraesCS2B01G538100 chr2B 92.593 54 4 0 4377 4430 733281605 733281552 1.590000e-10 78.7
30 TraesCS2B01G538100 chr2B 96.875 32 1 0 493 524 733733338 733733307 3.000000e-03 54.7
31 TraesCS2B01G538100 chr2A 92.093 1328 83 10 3274 4587 735401584 735400265 0.000000e+00 1851.0
32 TraesCS2B01G538100 chr2A 90.576 1337 104 10 3264 4587 735565576 735564249 0.000000e+00 1751.0
33 TraesCS2B01G538100 chr2A 90.833 1200 95 7 919 2105 735566731 735565534 0.000000e+00 1592.0
34 TraesCS2B01G538100 chr2A 88.932 1274 121 12 849 2105 735446773 735445503 0.000000e+00 1554.0
35 TraesCS2B01G538100 chr2A 89.182 1137 117 5 970 2103 735402686 735401553 0.000000e+00 1413.0
36 TraesCS2B01G538100 chr2A 81.727 1193 192 17 3274 4446 735445413 735444227 0.000000e+00 972.0
37 TraesCS2B01G538100 chr2A 83.640 978 148 8 2129 3099 735565480 735564508 0.000000e+00 909.0
38 TraesCS2B01G538100 chr2A 83.368 968 148 13 2138 3096 735445317 735444354 0.000000e+00 883.0
39 TraesCS2B01G538100 chr2A 82.702 977 161 6 2129 3099 735401497 735400523 0.000000e+00 861.0
40 TraesCS2B01G538100 chr2A 80.874 1030 183 7 3351 4370 735583751 735582726 0.000000e+00 798.0
41 TraesCS2B01G538100 chr2A 90.566 371 26 5 4553 4921 735564242 735563879 2.890000e-132 483.0
42 TraesCS2B01G538100 chr2A 80.299 335 34 21 16 322 735447501 735447171 1.930000e-54 224.0
43 TraesCS2B01G538100 chr2A 84.324 185 27 1 390 574 735413005 735412823 4.240000e-41 180.0
44 TraesCS2B01G538100 chr2A 76.528 409 41 26 4674 5042 735582540 735582147 7.100000e-39 172.0
45 TraesCS2B01G538100 chr2A 86.667 135 18 0 3104 3238 735445628 735445494 3.330000e-32 150.0
46 TraesCS2B01G538100 chr2A 94.872 78 3 1 5194 5271 735576488 735576412 2.610000e-23 121.0
47 TraesCS2B01G538100 chr2A 95.714 70 3 0 5050 5119 735582110 735582041 4.360000e-21 113.0
48 TraesCS2B01G538100 chr2A 91.549 71 6 0 5049 5119 735563696 735563626 1.220000e-16 99.0
49 TraesCS2B01G538100 chr2D 91.108 1237 104 2 3351 4587 602782154 602780924 0.000000e+00 1670.0
50 TraesCS2B01G538100 chr2D 90.403 1167 97 5 855 2006 602783377 602782211 0.000000e+00 1520.0
51 TraesCS2B01G538100 chr2D 88.889 1188 113 8 861 2030 603129569 603128383 0.000000e+00 1445.0
52 TraesCS2B01G538100 chr2D 82.650 1049 162 10 3349 4396 603128380 603127351 0.000000e+00 911.0
53 TraesCS2B01G538100 chr2D 83.114 989 152 10 2120 3099 602782165 602781183 0.000000e+00 887.0
54 TraesCS2B01G538100 chr2D 84.695 771 55 32 4553 5271 602780917 602780158 0.000000e+00 712.0
55 TraesCS2B01G538100 chr2D 81.503 346 31 13 16 331 602784107 602783765 2.460000e-63 254.0
56 TraesCS2B01G538100 chr5B 87.719 57 7 0 2907 2963 243361527 243361583 3.450000e-07 67.6


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G538100 chr2B 733641463 733646793 5330 True 9845.000000 9845 100.000000 1 5331 1 chr2B.!!$R5 5330
1 TraesCS2B01G538100 chr2B 733457407 733458610 1203 True 1434.000000 1434 88.391000 843 2030 1 chr2B.!!$R4 1187
2 TraesCS2B01G538100 chr2B 733470512 733472858 2346 True 1170.666667 1456 85.778333 912 4381 3 chr2B.!!$R6 3469
3 TraesCS2B01G538100 chr2B 733743327 733747509 4182 True 894.750000 1380 84.348000 1 3252 4 chr2B.!!$R10 3251
4 TraesCS2B01G538100 chr2B 733712377 733716436 4059 True 848.666667 2254 82.367333 183 5117 3 chr2B.!!$R8 4934
5 TraesCS2B01G538100 chr2B 733729767 733733338 3571 True 597.783333 1472 84.041500 493 5271 6 chr2B.!!$R9 4778
6 TraesCS2B01G538100 chr2B 733642472 733646165 3693 True 358.400000 876 91.233333 629 4322 6 chr2B.!!$R7 3693
7 TraesCS2B01G538100 chr2B 733841439 733845105 3666 True 298.750000 791 84.868250 404 5119 4 chr2B.!!$R11 4715
8 TraesCS2B01G538100 chr2A 735400265 735402686 2421 True 1375.000000 1851 87.992333 970 4587 3 chr2A.!!$R3 3617
9 TraesCS2B01G538100 chr2A 735563626 735566731 3105 True 966.800000 1751 89.432800 919 5119 5 chr2A.!!$R5 4200
10 TraesCS2B01G538100 chr2A 735444227 735447501 3274 True 756.600000 1554 84.198600 16 4446 5 chr2A.!!$R4 4430
11 TraesCS2B01G538100 chr2A 735582041 735583751 1710 True 361.000000 798 84.372000 3351 5119 3 chr2A.!!$R6 1768
12 TraesCS2B01G538100 chr2D 603127351 603129569 2218 True 1178.000000 1445 85.769500 861 4396 2 chr2D.!!$R2 3535
13 TraesCS2B01G538100 chr2D 602780158 602784107 3949 True 1008.600000 1670 86.164600 16 5271 5 chr2D.!!$R1 5255

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
236 274 1.001378 CCACCAACAAAAGAAGGCTCG 60.001 52.381 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
4465 6381 8.035448 TCAGGATAGTAGTTCTCTGAGATACA 57.965 38.462 16.62 6.95 0.0 2.29 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
99 107 4.002982 TGGTAGCAGTTGTCATTAAGCAG 58.997 43.478 0.00 0.00 0.00 4.24
114 135 2.927056 CAGGATAAGGCCACCCCC 59.073 66.667 5.01 0.00 0.00 5.40
127 148 1.768888 ACCCCCTTCGTGTTCTGGT 60.769 57.895 0.00 0.00 0.00 4.00
170 208 5.335897 GCAATTCATGAAAGAAGGCTACACA 60.336 40.000 13.09 0.00 32.34 3.72
176 214 3.072330 TGAAAGAAGGCTACACACCATCA 59.928 43.478 0.00 0.00 0.00 3.07
220 258 3.188786 GCGATCTGTGCGACCACC 61.189 66.667 0.00 0.00 41.35 4.61
236 274 1.001378 CCACCAACAAAAGAAGGCTCG 60.001 52.381 0.00 0.00 0.00 5.03
281 320 6.708285 ACGTCCATCTTAAGAGGTATGTTTT 58.292 36.000 15.47 0.00 29.82 2.43
282 321 7.844009 ACGTCCATCTTAAGAGGTATGTTTTA 58.156 34.615 15.47 0.00 29.82 1.52
283 322 7.980099 ACGTCCATCTTAAGAGGTATGTTTTAG 59.020 37.037 15.47 0.00 29.82 1.85
285 324 9.668497 GTCCATCTTAAGAGGTATGTTTTAGTT 57.332 33.333 15.47 0.00 0.00 2.24
286 325 9.886132 TCCATCTTAAGAGGTATGTTTTAGTTC 57.114 33.333 15.47 0.00 0.00 3.01
318 360 3.559811 CCATCTCCATGTCTTCACCACAA 60.560 47.826 0.00 0.00 0.00 3.33
321 363 4.728772 TCTCCATGTCTTCACCACAATTT 58.271 39.130 0.00 0.00 0.00 1.82
360 464 9.688592 ATTTCAATCTCTTCACATCTTTGTTTC 57.311 29.630 0.00 0.00 32.34 2.78
364 468 3.476552 TCTTCACATCTTTGTTTCGCCT 58.523 40.909 0.00 0.00 32.34 5.52
365 469 3.250762 TCTTCACATCTTTGTTTCGCCTG 59.749 43.478 0.00 0.00 32.34 4.85
366 470 1.266718 TCACATCTTTGTTTCGCCTGC 59.733 47.619 0.00 0.00 32.34 4.85
388 536 5.289675 TGCAAGGAAACAAACATGTAAAACG 59.710 36.000 0.00 0.00 0.00 3.60
398 546 4.553330 ACATGTAAAACGACCCAGATCT 57.447 40.909 0.00 0.00 0.00 2.75
408 556 2.726821 GACCCAGATCTTGCCATGAAA 58.273 47.619 0.00 0.00 0.00 2.69
409 557 3.294214 GACCCAGATCTTGCCATGAAAT 58.706 45.455 0.00 0.00 0.00 2.17
413 561 4.441079 CCCAGATCTTGCCATGAAATTGTC 60.441 45.833 0.00 0.00 0.00 3.18
426 577 7.066525 GCCATGAAATTGTCATTCAAAATCCAT 59.933 33.333 0.00 0.00 45.13 3.41
427 578 8.394877 CCATGAAATTGTCATTCAAAATCCATG 58.605 33.333 0.00 0.00 45.13 3.66
436 588 4.789012 TTCAAAATCCATGGCAGAACTC 57.211 40.909 6.96 0.00 0.00 3.01
490 646 4.498345 GGTTCTACTTCCTCTAGCGATGTG 60.498 50.000 0.00 0.00 0.00 3.21
521 685 4.874970 ACAAACACAAATGATTCTCTGCC 58.125 39.130 0.00 0.00 0.00 4.85
543 707 7.649973 TGCCGTGTTGTGTAAATAACTAAAAT 58.350 30.769 0.00 0.00 0.00 1.82
581 851 9.694137 AATCTAGACTGGTTATATTTTACTCGC 57.306 33.333 0.00 0.00 0.00 5.03
582 852 8.229253 TCTAGACTGGTTATATTTTACTCGCA 57.771 34.615 0.00 0.00 0.00 5.10
583 853 8.350722 TCTAGACTGGTTATATTTTACTCGCAG 58.649 37.037 0.00 0.00 0.00 5.18
584 854 7.108841 AGACTGGTTATATTTTACTCGCAGA 57.891 36.000 0.00 0.00 0.00 4.26
585 855 7.553334 AGACTGGTTATATTTTACTCGCAGAA 58.447 34.615 0.00 0.00 34.09 3.02
586 856 8.038944 AGACTGGTTATATTTTACTCGCAGAAA 58.961 33.333 0.00 0.00 34.09 2.52
587 857 8.556213 ACTGGTTATATTTTACTCGCAGAAAA 57.444 30.769 0.00 0.00 34.09 2.29
588 858 9.005777 ACTGGTTATATTTTACTCGCAGAAAAA 57.994 29.630 0.00 0.00 34.09 1.94
623 893 3.584733 TCAGCAGCTAGAGGAGATGTA 57.415 47.619 0.00 0.00 43.87 2.29
624 894 4.111255 TCAGCAGCTAGAGGAGATGTAT 57.889 45.455 0.00 0.00 43.87 2.29
625 895 3.825585 TCAGCAGCTAGAGGAGATGTATG 59.174 47.826 0.00 0.00 43.87 2.39
626 896 3.056678 CAGCAGCTAGAGGAGATGTATGG 60.057 52.174 0.00 0.00 43.87 2.74
792 1063 6.029492 TCCAAATGGACATATGAAATCCCT 57.971 37.500 10.38 0.00 39.78 4.20
793 1064 7.160457 TCCAAATGGACATATGAAATCCCTA 57.840 36.000 10.38 0.00 39.78 3.53
794 1065 7.004086 TCCAAATGGACATATGAAATCCCTAC 58.996 38.462 10.38 0.00 39.78 3.18
795 1066 7.006509 CCAAATGGACATATGAAATCCCTACT 58.993 38.462 10.38 0.00 37.39 2.57
802 1073 9.660180 GGACATATGAAATCCCTACTAATTCTC 57.340 37.037 10.38 0.00 0.00 2.87
803 1074 9.360093 GACATATGAAATCCCTACTAATTCTCG 57.640 37.037 10.38 0.00 0.00 4.04
4583 6540 8.641541 CATATATACCCTGCACTTTTCCAAATT 58.358 33.333 0.00 0.00 0.00 1.82
4587 6544 6.186420 ACCCTGCACTTTTCCAAATTAAAT 57.814 33.333 0.00 0.00 0.00 1.40
4588 6545 5.997129 ACCCTGCACTTTTCCAAATTAAATG 59.003 36.000 0.00 0.00 0.00 2.32
4589 6546 5.412286 CCCTGCACTTTTCCAAATTAAATGG 59.588 40.000 4.64 4.64 39.41 3.16
4614 6612 5.045213 TGGGTTCATGATTCTACCAGCTAAA 60.045 40.000 14.71 0.00 32.20 1.85
4877 7609 3.329386 ACGGATGAACAGAACACATCAG 58.671 45.455 0.00 0.00 41.17 2.90
4883 7615 2.592102 ACAGAACACATCAGGCCAAT 57.408 45.000 5.01 0.00 0.00 3.16
4911 7653 3.678056 ATGTTCAGTACCTTGCTCGAA 57.322 42.857 0.00 0.00 0.00 3.71
4926 7676 1.447489 CGAACAGGAGCAGGAGCAG 60.447 63.158 0.00 0.00 45.49 4.24
4928 7678 3.602513 AACAGGAGCAGGAGCAGCG 62.603 63.158 0.00 0.00 45.49 5.18
4929 7679 4.079850 CAGGAGCAGGAGCAGCGT 62.080 66.667 0.00 0.00 45.49 5.07
4930 7680 3.768922 AGGAGCAGGAGCAGCGTC 61.769 66.667 0.00 0.00 45.49 5.19
4931 7681 4.074526 GGAGCAGGAGCAGCGTCA 62.075 66.667 0.00 0.00 45.49 4.35
4932 7682 2.047844 GAGCAGGAGCAGCGTCAA 60.048 61.111 0.00 0.00 45.49 3.18
4933 7683 2.358003 AGCAGGAGCAGCGTCAAC 60.358 61.111 0.00 0.00 45.49 3.18
4935 7685 3.114616 CAGGAGCAGCGTCAACCG 61.115 66.667 0.00 0.00 40.40 4.44
4936 7686 3.303135 AGGAGCAGCGTCAACCGA 61.303 61.111 0.00 0.00 39.56 4.69
4985 7757 1.299468 GCCTCGTGTATCAGCTCCG 60.299 63.158 0.00 0.00 0.00 4.63
4993 7765 2.203082 TATCAGCTCCGCCGATGCT 61.203 57.895 0.00 0.00 37.56 3.79
5039 7811 2.359230 GCGCTGGAGCAGAAGGTT 60.359 61.111 0.00 0.00 42.21 3.50
5135 8007 1.412074 GGGATTGGGATTCAGGCATGT 60.412 52.381 0.00 0.00 0.00 3.21
5178 8051 5.004922 CTTTTGGAGCTCGAGAAGTATCT 57.995 43.478 18.75 1.48 39.10 1.98
5179 8052 4.377839 TTTGGAGCTCGAGAAGTATCTG 57.622 45.455 18.75 0.00 35.54 2.90
5180 8053 3.006112 TGGAGCTCGAGAAGTATCTGT 57.994 47.619 18.75 0.00 35.54 3.41
5181 8054 2.946329 TGGAGCTCGAGAAGTATCTGTC 59.054 50.000 18.75 0.00 35.54 3.51
5182 8055 3.211045 GGAGCTCGAGAAGTATCTGTCT 58.789 50.000 18.75 0.00 35.54 3.41
5183 8056 3.003275 GGAGCTCGAGAAGTATCTGTCTG 59.997 52.174 18.75 0.00 35.54 3.51
5184 8057 2.948979 AGCTCGAGAAGTATCTGTCTGG 59.051 50.000 18.75 0.00 35.54 3.86
5185 8058 2.542824 GCTCGAGAAGTATCTGTCTGGC 60.543 54.545 18.75 0.00 35.54 4.85
5186 8059 2.685388 CTCGAGAAGTATCTGTCTGGCA 59.315 50.000 6.58 0.00 35.54 4.92
5187 8060 3.089284 TCGAGAAGTATCTGTCTGGCAA 58.911 45.455 0.00 0.00 35.54 4.52
5188 8061 3.129462 TCGAGAAGTATCTGTCTGGCAAG 59.871 47.826 0.00 0.00 35.54 4.01
5253 8144 1.291132 GCTCGAATGTCTGGGCTTAC 58.709 55.000 0.00 0.00 0.00 2.34
5268 8159 2.170607 GGCTTACTCATGAGTGGGCTTA 59.829 50.000 33.10 17.84 42.52 3.09
5271 8162 4.443457 GCTTACTCATGAGTGGGCTTATGA 60.443 45.833 33.76 11.47 42.89 2.15
5272 8163 5.744300 GCTTACTCATGAGTGGGCTTATGAT 60.744 44.000 33.76 8.74 43.68 2.45
5273 8164 6.519043 GCTTACTCATGAGTGGGCTTATGATA 60.519 42.308 33.76 10.23 43.68 2.15
5274 8165 5.220710 ACTCATGAGTGGGCTTATGATAC 57.779 43.478 27.37 0.00 43.68 2.24
5275 8166 4.904251 ACTCATGAGTGGGCTTATGATACT 59.096 41.667 27.37 0.00 43.68 2.12
5276 8167 5.219343 TCATGAGTGGGCTTATGATACTG 57.781 43.478 0.00 0.00 41.09 2.74
5277 8168 3.475566 TGAGTGGGCTTATGATACTGC 57.524 47.619 0.00 0.00 0.00 4.40
5278 8169 2.104792 TGAGTGGGCTTATGATACTGCC 59.895 50.000 7.02 7.02 44.22 4.85
5279 8170 2.370189 GAGTGGGCTTATGATACTGCCT 59.630 50.000 13.14 0.00 44.36 4.75
5280 8171 3.578716 GAGTGGGCTTATGATACTGCCTA 59.421 47.826 13.14 6.62 44.36 3.93
5281 8172 3.580458 AGTGGGCTTATGATACTGCCTAG 59.420 47.826 13.14 0.00 44.36 3.02
5282 8173 2.303022 TGGGCTTATGATACTGCCTAGC 59.697 50.000 13.14 0.45 44.36 3.42
5283 8174 2.569404 GGGCTTATGATACTGCCTAGCT 59.431 50.000 13.14 0.00 44.36 3.32
5284 8175 3.008485 GGGCTTATGATACTGCCTAGCTT 59.992 47.826 13.14 0.00 44.36 3.74
5285 8176 4.505742 GGGCTTATGATACTGCCTAGCTTT 60.506 45.833 13.14 0.00 44.36 3.51
5286 8177 5.066593 GGCTTATGATACTGCCTAGCTTTT 58.933 41.667 0.00 0.00 41.92 2.27
5287 8178 5.532779 GGCTTATGATACTGCCTAGCTTTTT 59.467 40.000 0.00 0.00 41.92 1.94
5313 8204 7.759489 TTTTGAACTTATTATGACACAGCCT 57.241 32.000 0.00 0.00 0.00 4.58
5314 8205 8.856153 TTTTGAACTTATTATGACACAGCCTA 57.144 30.769 0.00 0.00 0.00 3.93
5315 8206 8.492673 TTTGAACTTATTATGACACAGCCTAG 57.507 34.615 0.00 0.00 0.00 3.02
5316 8207 6.049149 TGAACTTATTATGACACAGCCTAGC 58.951 40.000 0.00 0.00 0.00 3.42
5317 8208 5.878406 ACTTATTATGACACAGCCTAGCT 57.122 39.130 0.00 0.00 40.77 3.32
5318 8209 6.240549 ACTTATTATGACACAGCCTAGCTT 57.759 37.500 0.00 0.00 36.40 3.74
5319 8210 7.361457 ACTTATTATGACACAGCCTAGCTTA 57.639 36.000 0.00 0.00 36.40 3.09
5320 8211 7.967908 ACTTATTATGACACAGCCTAGCTTAT 58.032 34.615 0.00 0.00 36.40 1.73
5321 8212 8.091449 ACTTATTATGACACAGCCTAGCTTATC 58.909 37.037 0.00 0.00 36.40 1.75
5322 8213 3.760580 ATGACACAGCCTAGCTTATCC 57.239 47.619 0.00 0.00 36.40 2.59
5323 8214 2.466846 TGACACAGCCTAGCTTATCCA 58.533 47.619 0.00 0.00 36.40 3.41
5324 8215 2.837591 TGACACAGCCTAGCTTATCCAA 59.162 45.455 0.00 0.00 36.40 3.53
5325 8216 3.198872 GACACAGCCTAGCTTATCCAAC 58.801 50.000 0.00 0.00 36.40 3.77
5326 8217 2.205074 CACAGCCTAGCTTATCCAACG 58.795 52.381 0.00 0.00 36.40 4.10
5327 8218 2.108168 ACAGCCTAGCTTATCCAACGA 58.892 47.619 0.00 0.00 36.40 3.85
5328 8219 2.101582 ACAGCCTAGCTTATCCAACGAG 59.898 50.000 0.00 0.00 36.40 4.18
5329 8220 2.362397 CAGCCTAGCTTATCCAACGAGA 59.638 50.000 0.00 0.00 36.40 4.04
5330 8221 3.006323 CAGCCTAGCTTATCCAACGAGAT 59.994 47.826 0.00 0.00 36.40 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.106439 TCCAAAGATTGCACTAGAAAACAAA 57.894 32.000 0.00 0.00 0.00 2.83
99 107 1.537172 GAAGGGGGTGGCCTTATCC 59.463 63.158 3.32 0.47 0.00 2.59
170 208 6.441924 TGGATCTAGAAGAAAGAACTGATGGT 59.558 38.462 0.00 0.00 0.00 3.55
176 214 7.502060 TGGAATGGATCTAGAAGAAAGAACT 57.498 36.000 0.00 0.00 0.00 3.01
220 258 4.488126 TCAATCGAGCCTTCTTTTGTTG 57.512 40.909 0.00 0.00 0.00 3.33
257 295 5.934402 AACATACCTCTTAAGATGGACGT 57.066 39.130 20.98 6.87 0.00 4.34
259 297 9.668497 AACTAAAACATACCTCTTAAGATGGAC 57.332 33.333 20.98 0.00 0.00 4.02
281 320 4.411869 TGGAGATGGCCATATGTTGAACTA 59.588 41.667 19.70 0.00 31.66 2.24
282 321 3.202818 TGGAGATGGCCATATGTTGAACT 59.797 43.478 19.70 8.43 31.66 3.01
283 322 3.554934 TGGAGATGGCCATATGTTGAAC 58.445 45.455 19.70 2.78 31.66 3.18
285 324 3.138839 ACATGGAGATGGCCATATGTTGA 59.861 43.478 19.70 0.54 46.70 3.18
286 325 3.493334 ACATGGAGATGGCCATATGTTG 58.507 45.455 19.70 14.03 46.70 3.33
288 327 2.984604 AGACATGGAGATGGCCATATGT 59.015 45.455 25.27 25.27 46.70 2.29
290 329 3.654321 TGAAGACATGGAGATGGCCATAT 59.346 43.478 20.84 17.43 46.70 1.78
291 330 3.047857 TGAAGACATGGAGATGGCCATA 58.952 45.455 20.84 2.55 46.70 2.74
342 446 3.499918 AGGCGAAACAAAGATGTGAAGAG 59.500 43.478 0.00 0.00 40.46 2.85
360 464 0.102120 TGTTTGTTTCCTTGCAGGCG 59.898 50.000 0.00 0.00 34.61 5.52
364 468 5.289675 CGTTTTACATGTTTGTTTCCTTGCA 59.710 36.000 2.30 0.00 37.28 4.08
365 469 5.517054 TCGTTTTACATGTTTGTTTCCTTGC 59.483 36.000 2.30 0.00 37.28 4.01
366 470 6.020201 GGTCGTTTTACATGTTTGTTTCCTTG 60.020 38.462 2.30 0.00 37.28 3.61
373 521 4.200874 TCTGGGTCGTTTTACATGTTTGT 58.799 39.130 2.30 0.00 39.98 2.83
384 532 0.400213 TGGCAAGATCTGGGTCGTTT 59.600 50.000 0.00 0.00 0.00 3.60
388 536 2.425143 TTCATGGCAAGATCTGGGTC 57.575 50.000 0.00 0.00 0.00 4.46
398 546 7.094720 GGATTTTGAATGACAATTTCATGGCAA 60.095 33.333 0.00 8.38 44.86 4.52
408 556 5.188163 TCTGCCATGGATTTTGAATGACAAT 59.812 36.000 18.40 0.00 38.36 2.71
409 557 4.527427 TCTGCCATGGATTTTGAATGACAA 59.473 37.500 18.40 0.00 36.65 3.18
413 561 5.080969 AGTTCTGCCATGGATTTTGAATG 57.919 39.130 18.40 0.00 0.00 2.67
455 608 4.885325 GGAAGTAGAACCTAGGAGAGAGTG 59.115 50.000 17.98 0.00 0.00 3.51
467 623 3.633065 ACATCGCTAGAGGAAGTAGAACC 59.367 47.826 0.00 0.00 31.71 3.62
471 627 2.952978 ACCACATCGCTAGAGGAAGTAG 59.047 50.000 0.00 0.00 31.71 2.57
490 646 4.942852 TCATTTGTGTTTGTTCATGGACC 58.057 39.130 0.46 0.00 0.00 4.46
589 859 9.664332 CTCTAGCTGCTGAATATAACCAATATT 57.336 33.333 13.43 0.00 42.36 1.28
590 860 8.263640 CCTCTAGCTGCTGAATATAACCAATAT 58.736 37.037 13.43 0.00 31.75 1.28
591 861 7.454694 TCCTCTAGCTGCTGAATATAACCAATA 59.545 37.037 13.43 0.00 0.00 1.90
601 871 3.307506 ACATCTCCTCTAGCTGCTGAAT 58.692 45.455 13.43 0.00 0.00 2.57
623 893 6.937436 AGAGTTCGTTTAGAAACAAACCAT 57.063 33.333 5.54 0.00 36.68 3.55
624 894 7.846644 TTAGAGTTCGTTTAGAAACAAACCA 57.153 32.000 5.54 0.00 36.68 3.67
625 895 8.553696 TCATTAGAGTTCGTTTAGAAACAAACC 58.446 33.333 5.54 0.00 36.68 3.27
626 896 9.582223 CTCATTAGAGTTCGTTTAGAAACAAAC 57.418 33.333 6.00 3.72 41.10 2.93
4465 6381 8.035448 TCAGGATAGTAGTTCTCTGAGATACA 57.965 38.462 16.62 6.95 0.00 2.29
4466 6382 8.911918 TTCAGGATAGTAGTTCTCTGAGATAC 57.088 38.462 8.42 9.02 33.58 2.24
4527 6443 6.465439 ACATGTAGAACAGGTGATCGATTA 57.535 37.500 0.00 0.00 41.98 1.75
4528 6444 5.344743 ACATGTAGAACAGGTGATCGATT 57.655 39.130 0.00 0.00 41.98 3.34
4583 6540 6.126409 GGTAGAATCATGAACCCACCATTTA 58.874 40.000 0.00 0.00 0.00 1.40
4587 6544 2.916269 TGGTAGAATCATGAACCCACCA 59.084 45.455 14.99 14.99 32.58 4.17
4588 6545 3.545703 CTGGTAGAATCATGAACCCACC 58.454 50.000 11.03 11.10 0.00 4.61
4589 6546 2.945668 GCTGGTAGAATCATGAACCCAC 59.054 50.000 11.03 2.81 0.00 4.61
4614 6612 8.152898 TCTTCACATATATCTAAGCATTGCAGT 58.847 33.333 11.91 0.54 0.00 4.40
4646 6644 8.313944 TCTGTAAAGGAAACATATAGCAGGTA 57.686 34.615 0.00 0.00 0.00 3.08
4718 6969 5.984725 TCCGGAAATATGAGTCTAAAAGCA 58.015 37.500 0.00 0.00 0.00 3.91
4846 7578 5.515797 TCTGTTCATCCGTAATCTGTAGG 57.484 43.478 0.00 0.00 0.00 3.18
4877 7609 7.068226 AGGTACTGAACATTGTAATTATTGGCC 59.932 37.037 0.00 0.00 37.18 5.36
4911 7653 4.079850 CGCTGCTCCTGCTCCTGT 62.080 66.667 0.00 0.00 40.48 4.00
4928 7678 4.349871 GCGTGCGTGTCGGTTGAC 62.350 66.667 0.00 0.00 45.71 3.18
4929 7679 4.578898 AGCGTGCGTGTCGGTTGA 62.579 61.111 0.00 0.00 35.53 3.18
4930 7680 4.059459 GAGCGTGCGTGTCGGTTG 62.059 66.667 0.00 0.00 39.08 3.77
4931 7681 4.280494 AGAGCGTGCGTGTCGGTT 62.280 61.111 0.00 0.00 39.08 4.44
4932 7682 4.702081 GAGAGCGTGCGTGTCGGT 62.702 66.667 1.22 1.22 41.60 4.69
4935 7685 4.357947 TGGGAGAGCGTGCGTGTC 62.358 66.667 0.00 0.00 0.00 3.67
4936 7686 4.363990 CTGGGAGAGCGTGCGTGT 62.364 66.667 0.00 0.00 0.00 4.49
4993 7765 2.669569 GCAAGCTCTTCCACGCCA 60.670 61.111 0.00 0.00 0.00 5.69
5156 8029 4.803088 CAGATACTTCTCGAGCTCCAAAAG 59.197 45.833 7.81 11.08 0.00 2.27
5157 8030 4.220821 ACAGATACTTCTCGAGCTCCAAAA 59.779 41.667 7.81 0.00 0.00 2.44
5158 8031 3.764434 ACAGATACTTCTCGAGCTCCAAA 59.236 43.478 7.81 0.00 0.00 3.28
5161 8034 3.003275 CAGACAGATACTTCTCGAGCTCC 59.997 52.174 7.81 0.00 0.00 4.70
5172 8045 3.435275 TGTCTCTTGCCAGACAGATACT 58.565 45.455 6.23 0.00 46.43 2.12
5173 8046 3.876274 TGTCTCTTGCCAGACAGATAC 57.124 47.619 6.23 0.00 46.43 2.24
5179 8052 0.389166 CGTCCTGTCTCTTGCCAGAC 60.389 60.000 1.49 1.49 42.90 3.51
5180 8053 0.539669 TCGTCCTGTCTCTTGCCAGA 60.540 55.000 0.00 0.00 0.00 3.86
5181 8054 0.389166 GTCGTCCTGTCTCTTGCCAG 60.389 60.000 0.00 0.00 0.00 4.85
5182 8055 1.666011 GTCGTCCTGTCTCTTGCCA 59.334 57.895 0.00 0.00 0.00 4.92
5183 8056 1.079750 GGTCGTCCTGTCTCTTGCC 60.080 63.158 0.00 0.00 0.00 4.52
5184 8057 1.968310 AGGTCGTCCTGTCTCTTGC 59.032 57.895 0.00 0.00 43.33 4.01
5253 8144 5.236282 CAGTATCATAAGCCCACTCATGAG 58.764 45.833 21.37 21.37 31.35 2.90
5288 8179 8.177119 AGGCTGTGTCATAATAAGTTCAAAAA 57.823 30.769 0.00 0.00 0.00 1.94
5289 8180 7.759489 AGGCTGTGTCATAATAAGTTCAAAA 57.241 32.000 0.00 0.00 0.00 2.44
5290 8181 7.065803 GCTAGGCTGTGTCATAATAAGTTCAAA 59.934 37.037 0.00 0.00 0.00 2.69
5291 8182 6.538742 GCTAGGCTGTGTCATAATAAGTTCAA 59.461 38.462 0.00 0.00 0.00 2.69
5292 8183 6.049149 GCTAGGCTGTGTCATAATAAGTTCA 58.951 40.000 0.00 0.00 0.00 3.18
5293 8184 6.284459 AGCTAGGCTGTGTCATAATAAGTTC 58.716 40.000 0.00 0.00 37.57 3.01
5294 8185 6.240549 AGCTAGGCTGTGTCATAATAAGTT 57.759 37.500 0.00 0.00 37.57 2.66
5295 8186 5.878406 AGCTAGGCTGTGTCATAATAAGT 57.122 39.130 0.00 0.00 37.57 2.24
5296 8187 7.547370 GGATAAGCTAGGCTGTGTCATAATAAG 59.453 40.741 0.00 0.00 39.62 1.73
5297 8188 7.016170 TGGATAAGCTAGGCTGTGTCATAATAA 59.984 37.037 0.00 0.00 39.62 1.40
5298 8189 6.496911 TGGATAAGCTAGGCTGTGTCATAATA 59.503 38.462 0.00 0.00 39.62 0.98
5299 8190 5.307976 TGGATAAGCTAGGCTGTGTCATAAT 59.692 40.000 0.00 0.00 39.62 1.28
5300 8191 4.653801 TGGATAAGCTAGGCTGTGTCATAA 59.346 41.667 0.00 0.00 39.62 1.90
5301 8192 4.223144 TGGATAAGCTAGGCTGTGTCATA 58.777 43.478 0.00 0.00 39.62 2.15
5302 8193 3.041211 TGGATAAGCTAGGCTGTGTCAT 58.959 45.455 0.00 0.00 39.62 3.06
5303 8194 2.466846 TGGATAAGCTAGGCTGTGTCA 58.533 47.619 0.00 0.00 39.62 3.58
5304 8195 3.198872 GTTGGATAAGCTAGGCTGTGTC 58.801 50.000 0.00 0.00 39.62 3.67
5305 8196 2.418746 CGTTGGATAAGCTAGGCTGTGT 60.419 50.000 0.00 0.00 39.62 3.72
5306 8197 2.159099 TCGTTGGATAAGCTAGGCTGTG 60.159 50.000 0.00 0.00 39.62 3.66
5307 8198 2.101582 CTCGTTGGATAAGCTAGGCTGT 59.898 50.000 0.00 0.00 39.62 4.40
5308 8199 2.362397 TCTCGTTGGATAAGCTAGGCTG 59.638 50.000 0.00 0.00 39.62 4.85
5309 8200 2.667470 TCTCGTTGGATAAGCTAGGCT 58.333 47.619 0.00 0.00 42.56 4.58
5310 8201 3.669251 ATCTCGTTGGATAAGCTAGGC 57.331 47.619 0.00 0.00 0.00 3.93


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

AutoCloner maintained by Alex Coulton.