Multiple sequence alignment - TraesCS1D01G315100

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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 TraesCS1D01G315100 chr1D 100.000 2031 0 0 634 2664 410483260 410481230 0.000000e+00 3714.0
1 TraesCS1D01G315100 chr1D 97.848 883 7 8 863 1737 410472401 410471523 0.000000e+00 1515.0
2 TraesCS1D01G315100 chr1D 86.552 1279 106 31 863 2117 410491238 410490002 0.000000e+00 1349.0
3 TraesCS1D01G315100 chr1D 100.000 427 0 0 1 427 410483893 410483467 0.000000e+00 789.0
4 TraesCS1D01G315100 chr1D 100.000 222 0 0 1 222 410473241 410473020 6.860000e-111 411.0
5 TraesCS1D01G315100 chr1D 100.000 219 0 0 634 852 410472779 410472561 3.190000e-109 405.0
6 TraesCS1D01G315100 chr1D 81.782 505 58 17 2179 2660 410489986 410489493 2.490000e-105 392.0
7 TraesCS1D01G315100 chr1D 80.663 181 25 5 2491 2662 50287513 50287334 5.980000e-27 132.0
8 TraesCS1D01G315100 chr1B 85.579 1685 177 37 863 2523 553136318 553134676 0.000000e+00 1705.0
9 TraesCS1D01G315100 chr1B 93.679 886 44 7 863 1737 553025385 553024501 0.000000e+00 1315.0
10 TraesCS1D01G315100 chr1B 80.046 431 69 12 1 425 474842160 474841741 1.200000e-78 303.0
11 TraesCS1D01G315100 chr1B 78.740 127 19 5 2039 2165 646200075 646199957 7.910000e-11 78.7
12 TraesCS1D01G315100 chr1A 89.513 1068 82 14 863 1911 506493801 506492745 0.000000e+00 1325.0
13 TraesCS1D01G315100 chr1A 89.286 1064 77 14 863 1906 506474323 506473277 0.000000e+00 1299.0
14 TraesCS1D01G315100 chr1A 90.755 887 45 8 863 1737 506308996 506308135 0.000000e+00 1149.0
15 TraesCS1D01G315100 chr1A 91.826 783 52 7 1047 1818 506481145 506480364 0.000000e+00 1081.0
16 TraesCS1D01G315100 chr1A 84.752 1069 101 31 885 1911 506489450 506488402 0.000000e+00 1014.0
17 TraesCS1D01G315100 chr1A 92.473 558 30 6 1192 1737 506288731 506288174 0.000000e+00 787.0
18 TraesCS1D01G315100 chr1A 89.820 334 14 2 863 1195 506294397 506294083 6.860000e-111 411.0
19 TraesCS1D01G315100 chr1A 81.383 188 21 11 2485 2662 532474510 532474693 9.940000e-30 141.0
20 TraesCS1D01G315100 chr1A 92.473 93 7 0 1764 1856 506477616 506477524 1.660000e-27 134.0
21 TraesCS1D01G315100 chr1A 90.323 93 9 0 1764 1856 506491618 506491526 3.600000e-24 122.0
22 TraesCS1D01G315100 chr1A 89.247 93 10 0 1764 1856 506481358 506481266 1.680000e-22 117.0
23 TraesCS1D01G315100 chr1A 86.598 97 4 5 1816 1911 506478622 506478534 6.070000e-17 99.0
24 TraesCS1D01G315100 chrUn 99.532 427 2 0 1 427 445057915 445057489 0.000000e+00 778.0
25 TraesCS1D01G315100 chr3D 91.163 430 34 2 1 427 309692155 309691727 4.940000e-162 580.0
26 TraesCS1D01G315100 chr3D 90.083 121 11 1 2542 2662 373598238 373598357 3.550000e-34 156.0
27 TraesCS1D01G315100 chr2D 90.465 430 37 2 1 427 32773100 32773528 4.980000e-157 564.0
28 TraesCS1D01G315100 chr7A 87.413 429 41 8 3 427 162874463 162874882 5.160000e-132 481.0
29 TraesCS1D01G315100 chr7A 83.251 406 54 10 12 413 28172692 28173087 7.010000e-96 361.0
30 TraesCS1D01G315100 chr7A 83.471 121 20 0 2045 2165 681972661 681972781 2.170000e-21 113.0
31 TraesCS1D01G315100 chr3B 78.165 316 48 12 2 310 7331359 7331660 5.860000e-42 182.0
32 TraesCS1D01G315100 chr6A 75.692 325 70 8 2 319 382506813 382507135 1.280000e-33 154.0
33 TraesCS1D01G315100 chr5B 87.603 121 15 0 2542 2662 352142964 352142844 9.940000e-30 141.0
34 TraesCS1D01G315100 chr3A 87.603 121 14 1 2542 2662 552564088 552564207 3.580000e-29 139.0
35 TraesCS1D01G315100 chr3A 94.595 37 2 0 2129 2165 467120230 467120194 1.030000e-04 58.4
36 TraesCS1D01G315100 chr5D 87.826 115 13 1 2542 2656 378954353 378954466 1.660000e-27 134.0
37 TraesCS1D01G315100 chr2A 85.950 121 16 1 2542 2662 58397432 58397313 7.740000e-26 128.0
38 TraesCS1D01G315100 chr4B 85.246 122 18 0 2044 2165 71565303 71565182 2.780000e-25 126.0
39 TraesCS1D01G315100 chr7D 81.457 151 25 3 2508 2656 71581074 71581223 1.300000e-23 121.0
40 TraesCS1D01G315100 chr7D 82.400 125 20 2 2041 2165 212094966 212095088 1.010000e-19 108.0
41 TraesCS1D01G315100 chr7D 81.319 91 14 3 2074 2163 579140864 579140952 1.320000e-08 71.3
42 TraesCS1D01G315100 chr4D 82.119 151 18 8 2022 2165 62483699 62483551 1.300000e-23 121.0
43 TraesCS1D01G315100 chr2B 82.114 123 19 3 2044 2165 29864419 29864539 4.690000e-18 102.0
44 TraesCS1D01G315100 chr6B 81.897 116 19 2 2 115 416605778 416605663 2.180000e-16 97.1
45 TraesCS1D01G315100 chr6D 81.818 99 12 5 2022 2115 414451962 414452059 7.910000e-11 78.7
46 TraesCS1D01G315100 chr6D 78.151 119 22 3 2049 2165 82215602 82215718 3.680000e-09 73.1


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 TraesCS1D01G315100 chr1D 410481230 410483893 2663 True 2251.500000 3714 100.000000 1 2664 2 chr1D.!!$R3 2663
1 TraesCS1D01G315100 chr1D 410489493 410491238 1745 True 870.500000 1349 84.167000 863 2660 2 chr1D.!!$R4 1797
2 TraesCS1D01G315100 chr1D 410471523 410473241 1718 True 777.000000 1515 99.282667 1 1737 3 chr1D.!!$R2 1736
3 TraesCS1D01G315100 chr1B 553134676 553136318 1642 True 1705.000000 1705 85.579000 863 2523 1 chr1B.!!$R3 1660
4 TraesCS1D01G315100 chr1B 553024501 553025385 884 True 1315.000000 1315 93.679000 863 1737 1 chr1B.!!$R2 874
5 TraesCS1D01G315100 chr1A 506308135 506308996 861 True 1149.000000 1149 90.755000 863 1737 1 chr1A.!!$R3 874
6 TraesCS1D01G315100 chr1A 506488402 506493801 5399 True 820.333333 1325 88.196000 863 1911 3 chr1A.!!$R5 1048
7 TraesCS1D01G315100 chr1A 506288174 506288731 557 True 787.000000 787 92.473000 1192 1737 1 chr1A.!!$R1 545
8 TraesCS1D01G315100 chr1A 506473277 506481358 8081 True 546.000000 1299 89.886000 863 1911 5 chr1A.!!$R4 1048

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
297 298 0.029567 CGCAACTACTCCTAGCCGAG 59.97 60.0 0.0 0.0 35.88 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2120 9718 0.322816 TCCAGGCCTTTCAGTGATGC 60.323 55.0 0.0 0.0 0.0 3.91 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
222 223 2.430244 CCACGACCACGAAGACCG 60.430 66.667 0.00 0.00 42.66 4.79
223 224 2.430244 CACGACCACGAAGACCGG 60.430 66.667 0.00 0.00 43.93 5.28
224 225 3.677648 ACGACCACGAAGACCGGG 61.678 66.667 6.32 0.00 43.93 5.73
225 226 3.367743 CGACCACGAAGACCGGGA 61.368 66.667 6.32 0.00 46.66 5.14
226 227 2.572284 GACCACGAAGACCGGGAG 59.428 66.667 6.32 0.00 46.66 4.30
245 246 3.403624 GGGACCATGACAGAGGCA 58.596 61.111 0.00 0.00 0.00 4.75
246 247 1.078143 GGGACCATGACAGAGGCAC 60.078 63.158 0.00 0.00 0.00 5.01
247 248 1.448540 GGACCATGACAGAGGCACG 60.449 63.158 0.00 0.00 0.00 5.34
248 249 1.591703 GACCATGACAGAGGCACGA 59.408 57.895 0.00 0.00 0.00 4.35
249 250 0.459237 GACCATGACAGAGGCACGAG 60.459 60.000 0.00 0.00 0.00 4.18
250 251 1.153489 CCATGACAGAGGCACGAGG 60.153 63.158 0.00 0.00 0.00 4.63
251 252 1.607801 CCATGACAGAGGCACGAGGA 61.608 60.000 0.00 0.00 0.00 3.71
252 253 0.459237 CATGACAGAGGCACGAGGAC 60.459 60.000 0.00 0.00 0.00 3.85
253 254 1.608717 ATGACAGAGGCACGAGGACC 61.609 60.000 0.00 0.00 0.00 4.46
254 255 2.997897 ACAGAGGCACGAGGACCC 60.998 66.667 0.00 0.00 0.00 4.46
255 256 3.775654 CAGAGGCACGAGGACCCC 61.776 72.222 0.00 0.00 0.00 4.95
261 262 4.415332 CACGAGGACCCCGACGTG 62.415 72.222 0.95 17.82 45.34 4.49
264 265 4.131088 GAGGACCCCGACGTGCTC 62.131 72.222 0.00 7.41 42.84 4.26
287 288 3.423154 GCCGCAAGCGCAACTACT 61.423 61.111 11.47 0.00 38.40 2.57
288 289 2.778679 CCGCAAGCGCAACTACTC 59.221 61.111 11.47 0.00 38.40 2.59
289 290 2.740714 CCGCAAGCGCAACTACTCC 61.741 63.158 11.47 0.00 38.40 3.85
290 291 1.738099 CGCAAGCGCAACTACTCCT 60.738 57.895 11.47 0.00 38.40 3.69
291 292 0.457853 CGCAAGCGCAACTACTCCTA 60.458 55.000 11.47 0.00 38.40 2.94
292 293 1.281899 GCAAGCGCAACTACTCCTAG 58.718 55.000 11.47 0.00 38.36 3.02
293 294 1.281899 CAAGCGCAACTACTCCTAGC 58.718 55.000 11.47 0.00 0.00 3.42
294 295 0.175989 AAGCGCAACTACTCCTAGCC 59.824 55.000 11.47 0.00 0.00 3.93
295 296 1.589196 GCGCAACTACTCCTAGCCG 60.589 63.158 0.30 0.00 0.00 5.52
296 297 2.001361 GCGCAACTACTCCTAGCCGA 62.001 60.000 0.30 0.00 0.00 5.54
297 298 0.029567 CGCAACTACTCCTAGCCGAG 59.970 60.000 0.00 0.00 35.88 4.63
298 299 0.249114 GCAACTACTCCTAGCCGAGC 60.249 60.000 0.00 0.00 32.79 5.03
299 300 1.103803 CAACTACTCCTAGCCGAGCA 58.896 55.000 0.00 0.00 32.79 4.26
300 301 1.104630 AACTACTCCTAGCCGAGCAC 58.895 55.000 0.00 0.00 32.79 4.40
301 302 0.752376 ACTACTCCTAGCCGAGCACC 60.752 60.000 0.00 0.00 32.79 5.01
302 303 0.752009 CTACTCCTAGCCGAGCACCA 60.752 60.000 0.00 0.00 32.79 4.17
303 304 1.035932 TACTCCTAGCCGAGCACCAC 61.036 60.000 0.00 0.00 32.79 4.16
304 305 3.075005 TCCTAGCCGAGCACCACC 61.075 66.667 0.00 0.00 0.00 4.61
305 306 3.390521 CCTAGCCGAGCACCACCA 61.391 66.667 0.00 0.00 0.00 4.17
306 307 2.125512 CTAGCCGAGCACCACCAC 60.126 66.667 0.00 0.00 0.00 4.16
307 308 3.989698 CTAGCCGAGCACCACCACG 62.990 68.421 0.00 0.00 0.00 4.94
315 316 3.364441 CACCACCACGCCACCATG 61.364 66.667 0.00 0.00 0.00 3.66
316 317 4.659172 ACCACCACGCCACCATGG 62.659 66.667 11.19 11.19 41.55 3.66
349 350 3.056328 GCCTTGACCCGCCAAGTC 61.056 66.667 0.00 0.00 41.34 3.01
350 351 2.359975 CCTTGACCCGCCAAGTCC 60.360 66.667 0.00 0.00 41.34 3.85
351 352 2.359975 CTTGACCCGCCAAGTCCC 60.360 66.667 0.00 0.00 38.87 4.46
352 353 4.323477 TTGACCCGCCAAGTCCCG 62.323 66.667 0.00 0.00 33.09 5.14
358 359 4.657824 CGCCAAGTCCCGTGTCGT 62.658 66.667 0.00 0.00 0.00 4.34
359 360 2.737376 GCCAAGTCCCGTGTCGTC 60.737 66.667 0.00 0.00 0.00 4.20
360 361 2.430244 CCAAGTCCCGTGTCGTCG 60.430 66.667 0.00 0.00 0.00 5.12
361 362 3.103911 CAAGTCCCGTGTCGTCGC 61.104 66.667 0.00 0.00 0.00 5.19
362 363 4.353437 AAGTCCCGTGTCGTCGCC 62.353 66.667 0.00 0.00 0.00 5.54
364 365 4.773117 GTCCCGTGTCGTCGCCTC 62.773 72.222 0.00 0.00 0.00 4.70
366 367 3.129502 CCCGTGTCGTCGCCTCTA 61.130 66.667 0.00 0.00 0.00 2.43
367 368 2.403987 CCGTGTCGTCGCCTCTAG 59.596 66.667 0.00 0.00 0.00 2.43
368 369 2.403987 CGTGTCGTCGCCTCTAGG 59.596 66.667 0.00 0.00 38.53 3.02
369 370 2.104859 CGTGTCGTCGCCTCTAGGA 61.105 63.158 0.00 0.00 37.39 2.94
370 371 1.722677 GTGTCGTCGCCTCTAGGAG 59.277 63.158 0.00 0.00 37.39 3.69
378 379 2.446802 CCTCTAGGAGGGGCCACC 60.447 72.222 0.00 8.53 45.43 4.61
379 380 2.840102 CTCTAGGAGGGGCCACCG 60.840 72.222 0.00 0.00 46.96 4.94
399 400 3.966543 CCGCAACCAACTCCCCCT 61.967 66.667 0.00 0.00 0.00 4.79
400 401 2.672996 CGCAACCAACTCCCCCTG 60.673 66.667 0.00 0.00 0.00 4.45
401 402 2.991540 GCAACCAACTCCCCCTGC 60.992 66.667 0.00 0.00 0.00 4.85
402 403 2.672996 CAACCAACTCCCCCTGCG 60.673 66.667 0.00 0.00 0.00 5.18
403 404 2.852075 AACCAACTCCCCCTGCGA 60.852 61.111 0.00 0.00 0.00 5.10
404 405 2.895424 AACCAACTCCCCCTGCGAG 61.895 63.158 0.00 0.00 0.00 5.03
405 406 4.785453 CCAACTCCCCCTGCGAGC 62.785 72.222 0.00 0.00 0.00 5.03
406 407 4.785453 CAACTCCCCCTGCGAGCC 62.785 72.222 0.00 0.00 0.00 4.70
422 423 4.864334 CCCCAGCCACGCATCTCC 62.864 72.222 0.00 0.00 0.00 3.71
423 424 4.100084 CCCAGCCACGCATCTCCA 62.100 66.667 0.00 0.00 0.00 3.86
424 425 2.821366 CCAGCCACGCATCTCCAC 60.821 66.667 0.00 0.00 0.00 4.02
425 426 2.821366 CAGCCACGCATCTCCACC 60.821 66.667 0.00 0.00 0.00 4.61
426 427 4.101448 AGCCACGCATCTCCACCC 62.101 66.667 0.00 0.00 0.00 4.61
1757 8955 7.163520 CACGTTGCAATTTTGTATTACTATCGG 59.836 37.037 0.59 0.00 0.00 4.18
1814 9012 4.989279 TTCATGGCTTCTTATCCTTTGC 57.011 40.909 0.00 0.00 0.00 3.68
1914 9503 9.803315 CTCTTGCGGCTAACTATATATTTGATA 57.197 33.333 0.00 0.00 0.00 2.15
1918 9507 7.009815 TGCGGCTAACTATATATTTGATAACGC 59.990 37.037 0.00 0.00 38.84 4.84
1974 9565 7.982224 ACGCTCATACGTACATACACATATAT 58.018 34.615 0.00 0.00 46.19 0.86
1983 9574 9.498176 ACGTACATACACATATATACTCACTCA 57.502 33.333 0.00 0.00 0.00 3.41
2002 9594 8.907222 TCACTCATATATAAATGCACACATGT 57.093 30.769 0.00 0.00 36.36 3.21
2005 9597 9.777297 ACTCATATATAAATGCACACATGTACA 57.223 29.630 0.00 0.00 36.36 2.90
2009 9601 7.728847 ATATAAATGCACACATGTACATCGT 57.271 32.000 5.07 3.40 36.36 3.73
2010 9602 3.745332 AATGCACACATGTACATCGTG 57.255 42.857 24.54 24.54 36.36 4.35
2011 9603 2.162319 TGCACACATGTACATCGTGT 57.838 45.000 25.44 25.44 45.91 4.49
2012 9604 2.065512 TGCACACATGTACATCGTGTC 58.934 47.619 27.01 22.70 43.52 3.67
2013 9605 2.288763 TGCACACATGTACATCGTGTCT 60.289 45.455 27.01 13.98 43.52 3.41
2014 9606 2.345641 GCACACATGTACATCGTGTCTC 59.654 50.000 27.01 20.96 43.52 3.36
2015 9607 3.838120 CACACATGTACATCGTGTCTCT 58.162 45.455 27.01 13.25 43.52 3.10
2016 9608 4.674362 GCACACATGTACATCGTGTCTCTA 60.674 45.833 27.01 0.00 43.52 2.43
2017 9609 5.030936 CACACATGTACATCGTGTCTCTAG 58.969 45.833 27.01 17.95 43.52 2.43
2033 9625 5.820423 TGTCTCTAGTCTCTATGAGCACTTC 59.180 44.000 0.00 0.00 0.00 3.01
2042 9634 0.453793 ATGAGCACTTCCGAGAGACG 59.546 55.000 0.00 0.00 42.18 4.18
2054 9651 0.749649 GAGAGACGGGCACATCATCT 59.250 55.000 0.00 0.00 0.00 2.90
2110 9708 1.605710 TCGACGAAAACGTCTTCTCCT 59.394 47.619 17.92 0.00 36.81 3.69
2118 9716 4.931661 AAACGTCTTCTCCTACTGAACA 57.068 40.909 0.00 0.00 0.00 3.18
2119 9717 5.470047 AAACGTCTTCTCCTACTGAACAT 57.530 39.130 0.00 0.00 0.00 2.71
2120 9718 4.442375 ACGTCTTCTCCTACTGAACATG 57.558 45.455 0.00 0.00 0.00 3.21
2127 9725 3.771479 TCTCCTACTGAACATGCATCACT 59.229 43.478 0.00 0.00 0.00 3.41
2137 9735 1.134367 CATGCATCACTGAAAGGCCTG 59.866 52.381 5.69 0.00 39.30 4.85
2138 9736 0.609957 TGCATCACTGAAAGGCCTGG 60.610 55.000 5.69 0.00 39.30 4.45
2147 9745 4.952335 CACTGAAAGGCCTGGAATAAATCT 59.048 41.667 5.69 0.00 39.30 2.40
2148 9746 6.069673 TCACTGAAAGGCCTGGAATAAATCTA 60.070 38.462 5.69 0.00 39.30 1.98
2182 9780 0.315568 CCCTCGTATCTGTGGCTAGC 59.684 60.000 6.04 6.04 0.00 3.42
2209 9807 7.275183 TGTGCTACATGTTTATCTGCTAATCT 58.725 34.615 2.30 0.00 0.00 2.40
2215 9813 6.256539 ACATGTTTATCTGCTAATCTGTCACG 59.743 38.462 0.00 0.00 0.00 4.35
2227 9825 6.918569 GCTAATCTGTCACGTACTCATATGTT 59.081 38.462 1.90 0.00 0.00 2.71
2287 9885 8.736244 TCACATTAGCTATATACATAAGTCGCA 58.264 33.333 0.00 0.00 0.00 5.10
2347 9946 7.591057 CGTTGATTTCTGCTTTAAGATTTGTGA 59.409 33.333 0.00 0.00 0.00 3.58
2349 9948 9.814899 TTGATTTCTGCTTTAAGATTTGTGAAA 57.185 25.926 0.00 0.00 0.00 2.69
2350 9949 9.248291 TGATTTCTGCTTTAAGATTTGTGAAAC 57.752 29.630 0.00 0.00 37.35 2.78
2381 9980 7.747155 TTTCCGGATTAATCTGTGTGTTTTA 57.253 32.000 20.41 0.00 0.00 1.52
2387 9986 7.148154 CGGATTAATCTGTGTGTTTTATTGGGA 60.148 37.037 15.10 0.00 0.00 4.37
2392 9991 8.831715 AATCTGTGTGTTTTATTGGGATTTTC 57.168 30.769 0.00 0.00 0.00 2.29
2396 9995 7.512992 TGTGTGTTTTATTGGGATTTTCCATT 58.487 30.769 0.00 0.00 38.64 3.16
2397 9996 7.995488 TGTGTGTTTTATTGGGATTTTCCATTT 59.005 29.630 0.00 0.00 38.64 2.32
2399 9998 9.413734 TGTGTTTTATTGGGATTTTCCATTTTT 57.586 25.926 0.00 0.00 38.64 1.94
2400 9999 9.891828 GTGTTTTATTGGGATTTTCCATTTTTC 57.108 29.630 0.00 0.00 38.64 2.29
2401 10000 8.778358 TGTTTTATTGGGATTTTCCATTTTTCG 58.222 29.630 0.00 0.00 38.64 3.46
2402 10001 8.994170 GTTTTATTGGGATTTTCCATTTTTCGA 58.006 29.630 0.00 0.00 38.64 3.71
2404 10003 5.537300 TTGGGATTTTCCATTTTTCGACA 57.463 34.783 0.00 0.00 38.64 4.35
2405 10004 5.132897 TGGGATTTTCCATTTTTCGACAG 57.867 39.130 0.00 0.00 38.64 3.51
2406 10005 4.830046 TGGGATTTTCCATTTTTCGACAGA 59.170 37.500 0.00 0.00 38.64 3.41
2407 10006 5.303078 TGGGATTTTCCATTTTTCGACAGAA 59.697 36.000 0.00 0.00 38.64 3.02
2408 10007 5.633601 GGGATTTTCCATTTTTCGACAGAAC 59.366 40.000 0.00 0.00 38.64 3.01
2409 10008 5.633601 GGATTTTCCATTTTTCGACAGAACC 59.366 40.000 0.00 0.00 36.28 3.62
2410 10009 5.584253 TTTTCCATTTTTCGACAGAACCA 57.416 34.783 0.00 0.00 35.86 3.67
2455 10054 3.830192 GCCGAAGCCCATTGCAGG 61.830 66.667 0.00 0.00 44.83 4.85
2481 10083 7.066404 GGCATAACCTTCTTCTTTCTCCTTTAG 59.934 40.741 0.00 0.00 34.51 1.85
2600 10220 7.878477 ATAATTTGCGCCATAATTTCATGAG 57.122 32.000 4.18 0.00 0.00 2.90
2604 10224 5.361135 TGCGCCATAATTTCATGAGTATG 57.639 39.130 4.18 12.73 35.57 2.39
2651 10272 2.368655 ATGCAATTTCGGTGGAAAGC 57.631 45.000 0.00 0.00 44.81 3.51
2660 10281 1.723608 CGGTGGAAAGCTGTGTGCAA 61.724 55.000 0.00 0.00 45.94 4.08
2661 10282 0.031178 GGTGGAAAGCTGTGTGCAAG 59.969 55.000 0.00 0.00 45.94 4.01
2662 10283 0.031178 GTGGAAAGCTGTGTGCAAGG 59.969 55.000 0.00 0.00 45.94 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
222 223 2.286121 TGTCATGGTCCCCCTCCC 60.286 66.667 0.00 0.00 0.00 4.30
223 224 1.306997 TCTGTCATGGTCCCCCTCC 60.307 63.158 0.00 0.00 0.00 4.30
224 225 1.341156 CCTCTGTCATGGTCCCCCTC 61.341 65.000 0.00 0.00 0.00 4.30
225 226 1.307343 CCTCTGTCATGGTCCCCCT 60.307 63.158 0.00 0.00 0.00 4.79
226 227 3.049080 GCCTCTGTCATGGTCCCCC 62.049 68.421 0.00 0.00 0.00 5.40
227 228 2.300967 TGCCTCTGTCATGGTCCCC 61.301 63.158 0.00 0.00 0.00 4.81
228 229 1.078143 GTGCCTCTGTCATGGTCCC 60.078 63.158 0.00 0.00 0.00 4.46
229 230 1.448540 CGTGCCTCTGTCATGGTCC 60.449 63.158 0.00 0.00 0.00 4.46
230 231 0.459237 CTCGTGCCTCTGTCATGGTC 60.459 60.000 0.00 0.00 0.00 4.02
231 232 1.593787 CTCGTGCCTCTGTCATGGT 59.406 57.895 0.00 0.00 0.00 3.55
232 233 1.153489 CCTCGTGCCTCTGTCATGG 60.153 63.158 0.00 0.00 0.00 3.66
233 234 0.459237 GTCCTCGTGCCTCTGTCATG 60.459 60.000 0.00 0.00 0.00 3.07
234 235 1.608717 GGTCCTCGTGCCTCTGTCAT 61.609 60.000 0.00 0.00 0.00 3.06
235 236 2.276116 GGTCCTCGTGCCTCTGTCA 61.276 63.158 0.00 0.00 0.00 3.58
236 237 2.574399 GGTCCTCGTGCCTCTGTC 59.426 66.667 0.00 0.00 0.00 3.51
237 238 2.997897 GGGTCCTCGTGCCTCTGT 60.998 66.667 0.00 0.00 0.00 3.41
238 239 3.775654 GGGGTCCTCGTGCCTCTG 61.776 72.222 0.00 0.00 0.00 3.35
244 245 4.415332 CACGTCGGGGTCCTCGTG 62.415 72.222 11.82 12.01 40.48 4.35
247 248 4.131088 GAGCACGTCGGGGTCCTC 62.131 72.222 15.77 0.00 0.00 3.71
270 271 3.368455 GAGTAGTTGCGCTTGCGGC 62.368 63.158 16.79 9.40 43.34 6.53
271 272 2.740714 GGAGTAGTTGCGCTTGCGG 61.741 63.158 16.79 0.00 43.34 5.69
272 273 0.457853 TAGGAGTAGTTGCGCTTGCG 60.458 55.000 9.73 10.90 43.34 4.85
273 274 1.281899 CTAGGAGTAGTTGCGCTTGC 58.718 55.000 9.73 0.00 39.78 4.01
274 275 1.281899 GCTAGGAGTAGTTGCGCTTG 58.718 55.000 9.73 0.00 0.00 4.01
275 276 0.175989 GGCTAGGAGTAGTTGCGCTT 59.824 55.000 9.73 0.00 0.00 4.68
276 277 1.817209 GGCTAGGAGTAGTTGCGCT 59.183 57.895 9.73 0.00 0.00 5.92
277 278 1.589196 CGGCTAGGAGTAGTTGCGC 60.589 63.158 0.00 0.00 0.00 6.09
278 279 0.029567 CTCGGCTAGGAGTAGTTGCG 59.970 60.000 0.00 0.00 0.00 4.85
279 280 0.249114 GCTCGGCTAGGAGTAGTTGC 60.249 60.000 0.00 0.00 36.41 4.17
280 281 1.103803 TGCTCGGCTAGGAGTAGTTG 58.896 55.000 0.00 0.00 36.41 3.16
281 282 1.104630 GTGCTCGGCTAGGAGTAGTT 58.895 55.000 0.00 0.00 36.41 2.24
282 283 0.752376 GGTGCTCGGCTAGGAGTAGT 60.752 60.000 0.00 0.00 36.41 2.73
283 284 0.752009 TGGTGCTCGGCTAGGAGTAG 60.752 60.000 0.00 0.00 36.41 2.57
284 285 1.035932 GTGGTGCTCGGCTAGGAGTA 61.036 60.000 0.00 0.00 36.41 2.59
285 286 2.037367 TGGTGCTCGGCTAGGAGT 59.963 61.111 0.00 0.00 36.41 3.85
286 287 2.496817 GTGGTGCTCGGCTAGGAG 59.503 66.667 0.00 0.00 37.11 3.69
287 288 3.075005 GGTGGTGCTCGGCTAGGA 61.075 66.667 0.00 0.00 0.00 2.94
288 289 3.390521 TGGTGGTGCTCGGCTAGG 61.391 66.667 0.00 0.00 0.00 3.02
289 290 2.125512 GTGGTGGTGCTCGGCTAG 60.126 66.667 0.00 0.00 0.00 3.42
290 291 4.063967 CGTGGTGGTGCTCGGCTA 62.064 66.667 0.00 0.00 0.00 3.93
298 299 3.364441 CATGGTGGCGTGGTGGTG 61.364 66.667 0.00 0.00 0.00 4.17
299 300 4.659172 CCATGGTGGCGTGGTGGT 62.659 66.667 2.57 0.00 0.00 4.16
332 333 3.056328 GACTTGGCGGGTCAAGGC 61.056 66.667 16.52 10.47 46.04 4.35
333 334 2.359975 GGACTTGGCGGGTCAAGG 60.360 66.667 16.52 0.40 46.04 3.61
334 335 2.359975 GGGACTTGGCGGGTCAAG 60.360 66.667 11.24 11.24 46.86 3.02
335 336 4.323477 CGGGACTTGGCGGGTCAA 62.323 66.667 10.83 0.00 35.61 3.18
342 343 2.737376 GACGACACGGGACTTGGC 60.737 66.667 0.00 0.00 29.34 4.52
343 344 2.430244 CGACGACACGGGACTTGG 60.430 66.667 0.00 0.00 0.00 3.61
344 345 3.103911 GCGACGACACGGGACTTG 61.104 66.667 0.00 0.00 0.00 3.16
345 346 4.353437 GGCGACGACACGGGACTT 62.353 66.667 0.00 0.00 0.00 3.01
347 348 4.773117 GAGGCGACGACACGGGAC 62.773 72.222 2.19 0.00 0.00 4.46
348 349 3.610619 TAGAGGCGACGACACGGGA 62.611 63.158 2.19 0.00 0.00 5.14
349 350 3.109612 CTAGAGGCGACGACACGGG 62.110 68.421 2.19 0.00 0.00 5.28
350 351 2.403987 CTAGAGGCGACGACACGG 59.596 66.667 2.19 0.00 0.00 4.94
351 352 2.037913 CTCCTAGAGGCGACGACACG 62.038 65.000 2.19 0.00 34.44 4.49
352 353 1.716826 CCTCCTAGAGGCGACGACAC 61.717 65.000 2.19 0.00 43.29 3.67
353 354 1.451567 CCTCCTAGAGGCGACGACA 60.452 63.158 2.19 0.00 43.29 4.35
354 355 3.423179 CCTCCTAGAGGCGACGAC 58.577 66.667 0.00 0.00 43.29 4.34
362 363 2.840102 CGGTGGCCCCTCCTAGAG 60.840 72.222 0.00 0.00 35.26 2.43
382 383 3.966543 AGGGGGAGTTGGTTGCGG 61.967 66.667 0.00 0.00 0.00 5.69
383 384 2.672996 CAGGGGGAGTTGGTTGCG 60.673 66.667 0.00 0.00 0.00 4.85
384 385 2.991540 GCAGGGGGAGTTGGTTGC 60.992 66.667 0.00 0.00 0.00 4.17
385 386 2.672996 CGCAGGGGGAGTTGGTTG 60.673 66.667 0.00 0.00 0.00 3.77
386 387 2.852075 TCGCAGGGGGAGTTGGTT 60.852 61.111 0.00 0.00 0.00 3.67
387 388 3.322466 CTCGCAGGGGGAGTTGGT 61.322 66.667 2.47 0.00 37.75 3.67
388 389 4.785453 GCTCGCAGGGGGAGTTGG 62.785 72.222 11.25 0.00 43.22 3.77
389 390 4.785453 GGCTCGCAGGGGGAGTTG 62.785 72.222 11.25 0.00 43.22 3.16
405 406 4.864334 GGAGATGCGTGGCTGGGG 62.864 72.222 0.00 0.00 0.00 4.96
406 407 4.100084 TGGAGATGCGTGGCTGGG 62.100 66.667 0.00 0.00 0.00 4.45
407 408 2.821366 GTGGAGATGCGTGGCTGG 60.821 66.667 0.00 0.00 0.00 4.85
408 409 2.821366 GGTGGAGATGCGTGGCTG 60.821 66.667 0.00 0.00 0.00 4.85
409 410 4.101448 GGGTGGAGATGCGTGGCT 62.101 66.667 0.00 0.00 0.00 4.75
1618 8804 2.862674 TAATGAACTCGGTGGCGGCC 62.863 60.000 13.32 13.32 0.00 6.13
1673 8859 1.726853 AAGAATCCACAGCGCTACAC 58.273 50.000 10.99 0.00 0.00 2.90
1784 8982 6.377146 GGATAAGAAGCCATGAAAACAACCTA 59.623 38.462 0.00 0.00 0.00 3.08
1814 9012 4.280101 CACACTCGTGGACTCATACTAG 57.720 50.000 1.77 0.00 39.64 2.57
1935 9526 5.628193 CGTATGAGCGTTTCCGTCTATATTT 59.372 40.000 0.00 0.00 36.15 1.40
1940 9531 1.739466 ACGTATGAGCGTTTCCGTCTA 59.261 47.619 0.00 0.00 43.04 2.59
1946 9537 4.794762 TGTGTATGTACGTATGAGCGTTTC 59.205 41.667 0.00 0.00 43.04 2.78
2002 9594 7.052142 TCATAGAGACTAGAGACACGATGTA 57.948 40.000 0.00 0.00 0.00 2.29
2005 9597 4.994852 GCTCATAGAGACTAGAGACACGAT 59.005 45.833 0.00 0.00 0.00 3.73
2006 9598 4.141914 TGCTCATAGAGACTAGAGACACGA 60.142 45.833 0.00 0.00 0.00 4.35
2007 9599 4.025229 GTGCTCATAGAGACTAGAGACACG 60.025 50.000 0.00 0.00 31.16 4.49
2009 9601 5.366482 AGTGCTCATAGAGACTAGAGACA 57.634 43.478 0.00 0.00 0.00 3.41
2010 9602 5.238650 GGAAGTGCTCATAGAGACTAGAGAC 59.761 48.000 0.00 0.00 0.00 3.36
2011 9603 5.373222 GGAAGTGCTCATAGAGACTAGAGA 58.627 45.833 0.00 0.00 0.00 3.10
2012 9604 4.213270 CGGAAGTGCTCATAGAGACTAGAG 59.787 50.000 0.00 0.00 0.00 2.43
2013 9605 4.130857 CGGAAGTGCTCATAGAGACTAGA 58.869 47.826 0.00 0.00 0.00 2.43
2014 9606 4.130857 TCGGAAGTGCTCATAGAGACTAG 58.869 47.826 0.00 0.00 0.00 2.57
2015 9607 4.130857 CTCGGAAGTGCTCATAGAGACTA 58.869 47.826 0.00 0.00 0.00 2.59
2016 9608 2.948979 CTCGGAAGTGCTCATAGAGACT 59.051 50.000 0.00 0.00 0.00 3.24
2017 9609 2.946329 TCTCGGAAGTGCTCATAGAGAC 59.054 50.000 0.00 0.00 30.56 3.36
2042 9634 3.548770 TCAATCTCAAGATGATGTGCCC 58.451 45.455 0.00 0.00 34.49 5.36
2054 9651 0.392998 GGCGGCTTCCTCAATCTCAA 60.393 55.000 0.00 0.00 0.00 3.02
2097 9695 4.931661 TGTTCAGTAGGAGAAGACGTTT 57.068 40.909 0.00 0.00 0.00 3.60
2110 9708 4.696877 CCTTTCAGTGATGCATGTTCAGTA 59.303 41.667 2.46 0.00 0.00 2.74
2118 9716 1.471119 CAGGCCTTTCAGTGATGCAT 58.529 50.000 0.00 0.00 0.00 3.96
2119 9717 0.609957 CCAGGCCTTTCAGTGATGCA 60.610 55.000 0.00 0.00 0.00 3.96
2120 9718 0.322816 TCCAGGCCTTTCAGTGATGC 60.323 55.000 0.00 0.00 0.00 3.91
2127 9725 6.575244 TCTAGATTTATTCCAGGCCTTTCA 57.425 37.500 0.00 0.00 0.00 2.69
2137 9735 7.377131 GTGCTCGCATTTTTCTAGATTTATTCC 59.623 37.037 0.00 0.00 0.00 3.01
2138 9736 7.377131 GGTGCTCGCATTTTTCTAGATTTATTC 59.623 37.037 0.00 0.00 0.00 1.75
2147 9745 2.356135 GAGGGTGCTCGCATTTTTCTA 58.644 47.619 5.59 0.00 0.00 2.10
2148 9746 1.168714 GAGGGTGCTCGCATTTTTCT 58.831 50.000 5.59 0.00 0.00 2.52
2170 9768 3.091318 GCACATGCTAGCCACAGAT 57.909 52.632 13.29 0.00 38.21 2.90
2209 9807 8.083462 TCAAAGTAAACATATGAGTACGTGACA 58.917 33.333 10.38 0.00 0.00 3.58
2277 9875 9.904647 CCAAATTTAATTTTCATGCGACTTATG 57.095 29.630 0.00 0.00 0.00 1.90
2278 9876 9.097257 CCCAAATTTAATTTTCATGCGACTTAT 57.903 29.630 0.00 0.00 0.00 1.73
2287 9885 6.777782 TGACTGGCCCAAATTTAATTTTCAT 58.222 32.000 0.00 0.00 0.00 2.57
2359 9958 7.148154 CCAATAAAACACACAGATTAATCCGGA 60.148 37.037 6.61 6.61 0.00 5.14
2360 9959 6.972328 CCAATAAAACACACAGATTAATCCGG 59.028 38.462 11.92 7.43 0.00 5.14
2381 9980 6.014669 TCTGTCGAAAAATGGAAAATCCCAAT 60.015 34.615 0.00 0.00 40.04 3.16
2387 9986 6.155475 TGGTTCTGTCGAAAAATGGAAAAT 57.845 33.333 0.00 0.00 0.00 1.82
2392 9991 7.063308 CCAAATATTGGTTCTGTCGAAAAATGG 59.937 37.037 0.87 0.00 45.93 3.16
2423 10022 3.802675 GCTTCGGCCCGTTAAGAATAGAT 60.803 47.826 8.62 0.00 34.32 1.98
2426 10025 1.944032 GCTTCGGCCCGTTAAGAATA 58.056 50.000 8.62 0.00 34.32 1.75
2451 10050 2.426842 AGAAGAAGGTTATGCCCTGC 57.573 50.000 0.00 0.00 38.26 4.85
2455 10054 4.849518 AGGAGAAAGAAGAAGGTTATGCC 58.150 43.478 0.00 0.00 37.58 4.40
2526 10128 8.109634 ACACTCATCCAACATCCTAAAAATACT 58.890 33.333 0.00 0.00 0.00 2.12
2577 10197 6.804677 ACTCATGAAATTATGGCGCAAATTA 58.195 32.000 10.83 0.00 0.00 1.40
2582 10202 4.821260 ACATACTCATGAAATTATGGCGCA 59.179 37.500 10.83 0.00 35.96 6.09
2583 10203 5.049474 TCACATACTCATGAAATTATGGCGC 60.049 40.000 17.03 0.00 35.96 6.53
2584 10204 6.544038 TCACATACTCATGAAATTATGGCG 57.456 37.500 17.03 10.89 35.96 5.69
2642 10263 0.031178 CTTGCACACAGCTTTCCACC 59.969 55.000 0.00 0.00 45.94 4.61


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

AutoCloner maintained by Alex Coulton.