Multiple sequence alignment - TraesCS5D01G440800

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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 TraesCS5D01G440800 chr5D 100.000 2694 0 0 1 2694 493836717 493834024 0.000000e+00 4975.0
1 TraesCS5D01G440800 chr5D 92.857 294 21 0 1391 1684 494053048 494053341 6.890000e-116 427.0
2 TraesCS5D01G440800 chr5D 96.842 190 4 2 1223 1410 412360961 412360772 1.560000e-82 316.0
3 TraesCS5D01G440800 chr5D 78.990 495 59 24 748 1224 494052589 494053056 2.030000e-76 296.0
4 TraesCS5D01G440800 chr5D 90.431 209 19 1 1024 1231 494042030 494042238 9.500000e-70 274.0
5 TraesCS5D01G440800 chr5D 92.742 124 9 0 1391 1514 494042222 494042345 2.130000e-41 180.0
6 TraesCS5D01G440800 chr5D 80.172 116 19 3 838 952 494033067 494033179 1.720000e-12 84.2
7 TraesCS5D01G440800 chr6D 97.651 596 13 1 1 596 178864042 178863448 0.000000e+00 1022.0
8 TraesCS5D01G440800 chr6D 97.643 594 13 1 3 596 9824749 9825341 0.000000e+00 1018.0
9 TraesCS5D01G440800 chr6D 96.980 596 17 1 1 596 17163835 17163241 0.000000e+00 1000.0
10 TraesCS5D01G440800 chr2D 97.651 596 13 1 1 596 498000553 498001147 0.000000e+00 1022.0
11 TraesCS5D01G440800 chr2D 98.343 181 1 2 1216 1395 33774627 33774448 1.560000e-82 316.0
12 TraesCS5D01G440800 chr2D 80.000 200 40 0 2285 2484 15967247 15967048 6.010000e-32 148.0
13 TraesCS5D01G440800 chr7B 94.631 596 31 1 1 596 15030141 15029547 0.000000e+00 922.0
14 TraesCS5D01G440800 chr7B 93.686 586 33 3 11 596 495027728 495027147 0.000000e+00 874.0
15 TraesCS5D01G440800 chr5A 93.126 611 29 2 2078 2688 616879674 616879077 0.000000e+00 883.0
16 TraesCS5D01G440800 chr5A 92.776 526 29 2 1391 1916 616880348 616879832 0.000000e+00 752.0
17 TraesCS5D01G440800 chr5A 87.581 620 44 9 628 1224 616880949 616880340 0.000000e+00 688.0
18 TraesCS5D01G440800 chr5A 87.151 537 44 13 1391 1917 616909579 616909058 1.070000e-163 586.0
19 TraesCS5D01G440800 chr5A 83.562 511 57 15 739 1224 616914835 616914327 1.140000e-123 453.0
20 TraesCS5D01G440800 chr5A 93.537 294 19 0 1391 1684 616914335 616914042 3.180000e-119 438.0
21 TraesCS5D01G440800 chr5A 83.004 506 62 12 739 1224 616910072 616909571 1.150000e-118 436.0
22 TraesCS5D01G440800 chr5A 91.186 295 24 2 1391 1684 616919697 616919404 1.500000e-107 399.0
23 TraesCS5D01G440800 chr5A 98.883 179 2 0 1216 1394 702454312 702454490 1.200000e-83 320.0
24 TraesCS5D01G440800 chr5A 98.333 180 1 2 1222 1401 32840116 32839939 5.600000e-82 315.0
25 TraesCS5D01G440800 chr5A 99.419 172 1 0 1224 1395 476123812 476123641 2.010000e-81 313.0
26 TraesCS5D01G440800 chr5A 80.042 476 50 22 768 1224 616920138 616919689 7.240000e-81 311.0
27 TraesCS5D01G440800 chr5A 98.305 59 1 0 749 807 616908313 616908255 1.320000e-18 104.0
28 TraesCS5D01G440800 chr7D 97.149 456 12 1 1 456 47986186 47986640 0.000000e+00 769.0
29 TraesCS5D01G440800 chr5B 94.856 486 25 0 2209 2694 609599617 609599132 0.000000e+00 760.0
30 TraesCS5D01G440800 chr5B 87.544 562 32 11 692 1224 609600845 609600293 1.370000e-172 616.0
31 TraesCS5D01G440800 chr5B 85.283 530 47 17 1391 1917 609927632 609927131 3.980000e-143 518.0
32 TraesCS5D01G440800 chr5B 88.189 381 31 4 1525 1901 609600270 609599900 2.460000e-120 442.0
33 TraesCS5D01G440800 chr5B 92.177 294 23 0 1391 1684 609935538 609935245 1.490000e-112 416.0
34 TraesCS5D01G440800 chr5B 81.855 496 59 13 749 1224 609928108 609927624 3.250000e-104 388.0
35 TraesCS5D01G440800 chr5B 89.508 305 21 4 667 971 609855788 609855495 2.530000e-100 375.0
36 TraesCS5D01G440800 chr5B 87.543 289 26 5 1391 1678 609848417 609848138 2.590000e-85 326.0
37 TraesCS5D01G440800 chr5B 90.050 201 20 0 1024 1224 610007727 610007527 7.400000e-66 261.0
38 TraesCS5D01G440800 chr5B 79.200 250 39 7 1566 1812 610085284 610085045 7.720000e-36 161.0
39 TraesCS5D01G440800 chr5B 83.077 130 9 6 2001 2129 609599861 609599744 3.670000e-19 106.0
40 TraesCS5D01G440800 chr5B 100.000 56 0 0 628 683 609857246 609857191 1.320000e-18 104.0
41 TraesCS5D01G440800 chr5B 97.872 47 1 0 2001 2047 609604671 609604625 6.180000e-12 82.4
42 TraesCS5D01G440800 chr5B 97.872 47 1 0 2001 2047 609926897 609926851 6.180000e-12 82.4
43 TraesCS5D01G440800 chr3A 88.702 593 61 5 4 594 583743963 583743375 0.000000e+00 719.0
44 TraesCS5D01G440800 chr3B 88.423 596 65 4 1 595 101424788 101425380 0.000000e+00 715.0
45 TraesCS5D01G440800 chr3B 97.283 184 3 2 1217 1399 242488272 242488454 7.240000e-81 311.0
46 TraesCS5D01G440800 chr2A 100.000 171 0 0 1224 1394 2261190 2261360 1.560000e-82 316.0
47 TraesCS5D01G440800 chr1D 99.419 172 1 0 1223 1394 469836257 469836086 2.010000e-81 313.0
48 TraesCS5D01G440800 chrUn 98.276 174 1 2 1224 1395 108724779 108724606 1.210000e-78 303.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G440800 chr5D 493834024 493836717 2693 True 4975.000000 4975 100.000000 1 2694 1 chr5D.!!$R2 2693
1 TraesCS5D01G440800 chr5D 494052589 494053341 752 False 361.500000 427 85.923500 748 1684 2 chr5D.!!$F3 936
2 TraesCS5D01G440800 chr6D 178863448 178864042 594 True 1022.000000 1022 97.651000 1 596 1 chr6D.!!$R2 595
3 TraesCS5D01G440800 chr6D 9824749 9825341 592 False 1018.000000 1018 97.643000 3 596 1 chr6D.!!$F1 593
4 TraesCS5D01G440800 chr6D 17163241 17163835 594 True 1000.000000 1000 96.980000 1 596 1 chr6D.!!$R1 595
5 TraesCS5D01G440800 chr2D 498000553 498001147 594 False 1022.000000 1022 97.651000 1 596 1 chr2D.!!$F1 595
6 TraesCS5D01G440800 chr7B 15029547 15030141 594 True 922.000000 922 94.631000 1 596 1 chr7B.!!$R1 595
7 TraesCS5D01G440800 chr7B 495027147 495027728 581 True 874.000000 874 93.686000 11 596 1 chr7B.!!$R2 585
8 TraesCS5D01G440800 chr5A 616879077 616880949 1872 True 774.333333 883 91.161000 628 2688 3 chr5A.!!$R3 2060
9 TraesCS5D01G440800 chr5A 616908255 616914835 6580 True 403.400000 586 89.111800 739 1917 5 chr5A.!!$R4 1178
10 TraesCS5D01G440800 chr5A 616919404 616920138 734 True 355.000000 399 85.614000 768 1684 2 chr5A.!!$R5 916
11 TraesCS5D01G440800 chr5B 609599132 609604671 5539 True 401.280000 760 90.307600 692 2694 5 chr5B.!!$R5 2002
12 TraesCS5D01G440800 chr5B 609926851 609928108 1257 True 329.466667 518 88.336667 749 2047 3 chr5B.!!$R7 1298
13 TraesCS5D01G440800 chr5B 609855495 609857246 1751 True 239.500000 375 94.754000 628 971 2 chr5B.!!$R6 343
14 TraesCS5D01G440800 chr3A 583743375 583743963 588 True 719.000000 719 88.702000 4 594 1 chr3A.!!$R1 590
15 TraesCS5D01G440800 chr3B 101424788 101425380 592 False 715.000000 715 88.423000 1 595 1 chr3B.!!$F1 594

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
621 623 1.072331 CAGGGTCACTGGCTAACAACT 59.928 52.381 0.0 0.0 43.7 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2353 10523 1.920835 GGACCTCAGCCACTTCCCT 60.921 63.158 0.0 0.0 0.0 4.2 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
604 606 4.814294 GACGCGGGGCTGTACAGG 62.814 72.222 23.95 8.63 0.00 4.00
607 609 4.468689 GCGGGGCTGTACAGGGTC 62.469 72.222 23.95 7.67 0.00 4.46
608 610 3.000819 CGGGGCTGTACAGGGTCA 61.001 66.667 23.95 0.00 0.00 4.02
609 611 2.669240 GGGGCTGTACAGGGTCAC 59.331 66.667 23.95 8.75 0.00 3.67
620 622 1.523758 CAGGGTCACTGGCTAACAAC 58.476 55.000 0.00 0.00 43.70 3.32
621 623 1.072331 CAGGGTCACTGGCTAACAACT 59.928 52.381 0.00 0.00 43.70 3.16
622 624 1.348036 AGGGTCACTGGCTAACAACTC 59.652 52.381 0.00 0.00 0.00 3.01
624 626 2.486548 GGGTCACTGGCTAACAACTCAA 60.487 50.000 0.00 0.00 0.00 3.02
625 627 2.808543 GGTCACTGGCTAACAACTCAAG 59.191 50.000 0.00 0.00 0.00 3.02
626 628 3.467803 GTCACTGGCTAACAACTCAAGT 58.532 45.455 0.00 0.00 0.00 3.16
737 3873 4.005650 CCTGGTTATAGCAGCCACATATG 58.994 47.826 0.00 0.00 42.05 1.78
738 3874 4.263025 CCTGGTTATAGCAGCCACATATGA 60.263 45.833 10.38 0.00 42.05 2.15
739 3875 4.641396 TGGTTATAGCAGCCACATATGAC 58.359 43.478 10.38 0.00 31.56 3.06
740 3876 4.102367 TGGTTATAGCAGCCACATATGACA 59.898 41.667 10.38 0.00 31.56 3.58
741 3877 5.221904 TGGTTATAGCAGCCACATATGACAT 60.222 40.000 10.38 0.00 31.56 3.06
742 3878 5.122869 GGTTATAGCAGCCACATATGACATG 59.877 44.000 10.38 3.89 0.00 3.21
743 3879 2.723322 AGCAGCCACATATGACATGT 57.277 45.000 10.38 0.00 0.00 3.21
744 3880 2.569059 AGCAGCCACATATGACATGTC 58.431 47.619 19.27 19.27 0.00 3.06
745 3881 1.605710 GCAGCCACATATGACATGTCC 59.394 52.381 22.85 4.95 0.00 4.02
746 3882 2.921821 CAGCCACATATGACATGTCCA 58.078 47.619 22.85 11.29 0.00 4.02
785 3921 2.578786 TCAGTGTACGACAACTCCAGA 58.421 47.619 0.00 0.00 0.00 3.86
916 4054 3.340034 TCACGCTAACCCGAATTTCAAT 58.660 40.909 0.00 0.00 0.00 2.57
926 4064 3.851403 CCCGAATTTCAATAGCACAAACG 59.149 43.478 0.00 0.00 0.00 3.60
1033 4226 0.686789 TATGTCCGGCAGCAGCATAT 59.313 50.000 2.65 0.00 44.61 1.78
1240 9189 1.367840 GCAGTGGCGTATCTAGGGG 59.632 63.158 0.00 0.00 0.00 4.79
1241 9190 2.050269 CAGTGGCGTATCTAGGGGG 58.950 63.158 0.00 0.00 0.00 5.40
1242 9191 0.759436 CAGTGGCGTATCTAGGGGGT 60.759 60.000 0.00 0.00 0.00 4.95
1243 9192 0.759436 AGTGGCGTATCTAGGGGGTG 60.759 60.000 0.00 0.00 0.00 4.61
1244 9193 1.458777 TGGCGTATCTAGGGGGTGG 60.459 63.158 0.00 0.00 0.00 4.61
1245 9194 1.152398 GGCGTATCTAGGGGGTGGA 60.152 63.158 0.00 0.00 0.00 4.02
1246 9195 1.470165 GGCGTATCTAGGGGGTGGAC 61.470 65.000 0.00 0.00 0.00 4.02
1247 9196 0.757935 GCGTATCTAGGGGGTGGACA 60.758 60.000 0.00 0.00 0.00 4.02
1248 9197 1.329256 CGTATCTAGGGGGTGGACAG 58.671 60.000 0.00 0.00 0.00 3.51
1249 9198 1.718280 GTATCTAGGGGGTGGACAGG 58.282 60.000 0.00 0.00 0.00 4.00
1250 9199 0.566176 TATCTAGGGGGTGGACAGGG 59.434 60.000 0.00 0.00 0.00 4.45
1251 9200 1.537478 ATCTAGGGGGTGGACAGGGT 61.537 60.000 0.00 0.00 0.00 4.34
1252 9201 1.995626 CTAGGGGGTGGACAGGGTG 60.996 68.421 0.00 0.00 0.00 4.61
1253 9202 3.572715 TAGGGGGTGGACAGGGTGG 62.573 68.421 0.00 0.00 0.00 4.61
1255 9204 3.647771 GGGGTGGACAGGGTGGTC 61.648 72.222 0.00 0.00 37.06 4.02
1275 9224 2.236489 CATGGACCACCCTGGAATTT 57.764 50.000 0.00 0.00 40.96 1.82
1276 9225 2.102578 CATGGACCACCCTGGAATTTC 58.897 52.381 0.00 0.00 40.96 2.17
1277 9226 0.407918 TGGACCACCCTGGAATTTCC 59.592 55.000 8.59 8.59 40.96 3.13
1278 9227 0.324368 GGACCACCCTGGAATTTCCC 60.324 60.000 12.90 0.00 40.96 3.97
1279 9228 0.324368 GACCACCCTGGAATTTCCCC 60.324 60.000 12.90 0.00 40.96 4.81
1280 9229 1.077298 ACCACCCTGGAATTTCCCCA 61.077 55.000 12.90 0.00 40.96 4.96
1281 9230 0.339510 CCACCCTGGAATTTCCCCAT 59.660 55.000 12.90 0.00 40.96 4.00
1282 9231 1.573376 CCACCCTGGAATTTCCCCATA 59.427 52.381 12.90 0.00 40.96 2.74
1283 9232 2.023501 CCACCCTGGAATTTCCCCATAA 60.024 50.000 12.90 0.00 40.96 1.90
1284 9233 3.375207 CCACCCTGGAATTTCCCCATAAT 60.375 47.826 12.90 0.00 40.96 1.28
1285 9234 4.140805 CCACCCTGGAATTTCCCCATAATA 60.141 45.833 12.90 0.00 40.96 0.98
1286 9235 5.461018 CCACCCTGGAATTTCCCCATAATAT 60.461 44.000 12.90 0.00 40.96 1.28
1287 9236 6.240733 CCACCCTGGAATTTCCCCATAATATA 60.241 42.308 12.90 0.00 40.96 0.86
1288 9237 7.421684 CACCCTGGAATTTCCCCATAATATAT 58.578 38.462 12.90 0.00 35.03 0.86
1289 9238 8.565239 CACCCTGGAATTTCCCCATAATATATA 58.435 37.037 12.90 0.00 35.03 0.86
1290 9239 9.321500 ACCCTGGAATTTCCCCATAATATATAT 57.678 33.333 12.90 0.00 35.03 0.86
1355 9304 8.489990 TTTATGTGAATATTTTGCATTGGTGG 57.510 30.769 0.00 0.00 0.00 4.61
1356 9305 5.735285 TGTGAATATTTTGCATTGGTGGA 57.265 34.783 0.00 0.00 0.00 4.02
1357 9306 5.477510 TGTGAATATTTTGCATTGGTGGAC 58.522 37.500 0.00 0.00 0.00 4.02
1358 9307 4.869861 GTGAATATTTTGCATTGGTGGACC 59.130 41.667 0.00 0.00 0.00 4.46
1359 9308 4.529769 TGAATATTTTGCATTGGTGGACCA 59.470 37.500 0.00 0.00 45.94 4.02
1369 9318 2.361610 GTGGACCACCCTGGCATG 60.362 66.667 14.16 0.00 42.67 4.06
1370 9319 2.858476 TGGACCACCCTGGCATGT 60.858 61.111 0.00 0.00 42.67 3.21
1371 9320 2.440599 GGACCACCCTGGCATGTT 59.559 61.111 0.00 0.00 42.67 2.71
1372 9321 1.978617 GGACCACCCTGGCATGTTG 60.979 63.158 0.00 0.00 42.67 3.33
1373 9322 1.978617 GACCACCCTGGCATGTTGG 60.979 63.158 4.83 4.83 42.67 3.77
1374 9323 2.681064 CCACCCTGGCATGTTGGG 60.681 66.667 15.17 15.17 46.07 4.12
1375 9324 3.384532 CACCCTGGCATGTTGGGC 61.385 66.667 16.24 0.00 44.56 5.36
1376 9325 3.593680 ACCCTGGCATGTTGGGCT 61.594 61.111 16.24 5.04 44.56 5.19
1377 9326 2.237965 ACCCTGGCATGTTGGGCTA 61.238 57.895 16.24 0.00 44.56 3.93
1378 9327 1.454479 CCCTGGCATGTTGGGCTAG 60.454 63.158 6.83 0.00 39.31 3.42
1379 9328 2.123428 CCTGGCATGTTGGGCTAGC 61.123 63.158 6.04 6.04 38.40 3.42
1380 9329 1.077212 CTGGCATGTTGGGCTAGCT 60.077 57.895 15.72 0.00 33.06 3.32
1381 9330 0.181114 CTGGCATGTTGGGCTAGCTA 59.819 55.000 15.72 0.96 33.06 3.32
1382 9331 0.107214 TGGCATGTTGGGCTAGCTAC 60.107 55.000 15.72 10.98 0.00 3.58
1383 9332 1.160329 GGCATGTTGGGCTAGCTACG 61.160 60.000 15.72 1.04 0.00 3.51
1384 9333 1.776034 GCATGTTGGGCTAGCTACGC 61.776 60.000 15.72 6.93 0.00 4.42
1385 9334 1.146263 ATGTTGGGCTAGCTACGCC 59.854 57.895 15.72 19.98 46.83 5.68
1390 9339 2.586357 GGCTAGCTACGCCACTGC 60.586 66.667 22.05 9.22 46.77 4.40
1391 9340 2.496817 GCTAGCTACGCCACTGCT 59.503 61.111 7.70 0.00 40.43 4.24
1392 9341 1.880340 GCTAGCTACGCCACTGCTG 60.880 63.158 7.70 0.00 37.62 4.41
1393 9342 1.880340 CTAGCTACGCCACTGCTGC 60.880 63.158 0.00 0.00 37.62 5.25
1394 9343 2.563050 CTAGCTACGCCACTGCTGCA 62.563 60.000 0.88 0.88 37.62 4.41
1395 9344 2.563050 TAGCTACGCCACTGCTGCAG 62.563 60.000 27.02 27.02 37.62 4.41
1396 9345 3.494336 CTACGCCACTGCTGCAGC 61.494 66.667 31.89 31.89 42.50 5.25
1651 9603 3.868985 ACGGCGGGTCTGGTGTTT 61.869 61.111 13.24 0.00 0.00 2.83
1703 9662 2.577112 CCGTGTAGTGAGCGAGCG 60.577 66.667 0.00 0.00 0.00 5.03
1778 9741 4.213270 TCCTGTGTGACACGATTTGATTTC 59.787 41.667 11.51 0.00 37.14 2.17
1821 9784 2.670148 GGCGAGGAGGGTTGGTCAT 61.670 63.158 0.00 0.00 0.00 3.06
1891 9854 4.268884 CAGTCGAAATAAAGAGCTACTGGC 59.731 45.833 0.00 0.00 42.19 4.85
1927 9965 4.908601 TCCCATTGATGCCTATTATCGT 57.091 40.909 0.00 0.00 0.00 3.73
1943 9981 0.462759 TCGTTGTGTCATGTGTGCCA 60.463 50.000 0.00 0.00 0.00 4.92
2048 10171 2.604046 ACTCAGAAAACAGAGCACGT 57.396 45.000 0.00 0.00 35.28 4.49
2050 10173 2.609459 ACTCAGAAAACAGAGCACGTTG 59.391 45.455 0.00 0.00 35.28 4.10
2052 10175 2.607635 TCAGAAAACAGAGCACGTTGAC 59.392 45.455 0.00 0.00 0.00 3.18
2055 10178 3.063997 AGAAAACAGAGCACGTTGACAAG 59.936 43.478 0.00 0.00 0.00 3.16
2056 10179 2.024176 AACAGAGCACGTTGACAAGT 57.976 45.000 0.00 0.00 0.00 3.16
2057 10180 2.024176 ACAGAGCACGTTGACAAGTT 57.976 45.000 0.00 0.00 0.00 2.66
2058 10181 3.173668 ACAGAGCACGTTGACAAGTTA 57.826 42.857 0.00 0.00 0.00 2.24
2059 10182 3.728845 ACAGAGCACGTTGACAAGTTAT 58.271 40.909 0.00 0.00 0.00 1.89
2060 10183 3.741344 ACAGAGCACGTTGACAAGTTATC 59.259 43.478 0.00 0.00 0.00 1.75
2061 10184 3.740832 CAGAGCACGTTGACAAGTTATCA 59.259 43.478 0.00 0.00 0.00 2.15
2063 10186 4.814234 AGAGCACGTTGACAAGTTATCAAA 59.186 37.500 0.00 0.00 37.80 2.69
2076 10199 6.373216 ACAAGTTATCAAATAGTAGCGGCAAA 59.627 34.615 1.45 0.00 0.00 3.68
2081 10204 8.436200 GTTATCAAATAGTAGCGGCAAATCTAG 58.564 37.037 1.45 0.00 0.00 2.43
2129 10252 9.803315 GAGATGTAAAGACAATACATACAGTCA 57.197 33.333 0.00 0.00 42.48 3.41
2149 10286 5.882557 AGTCAACCTTGGTCTTATTGCATAG 59.117 40.000 0.00 0.00 0.00 2.23
2186 10324 5.097742 TCTCACCACATAATGTAACCTGG 57.902 43.478 0.00 0.00 0.00 4.45
2193 10331 0.906066 TAATGTAACCTGGCAGGCGA 59.094 50.000 33.04 18.48 39.63 5.54
2266 10436 4.697756 TTCTTGACGGCGGGCCTG 62.698 66.667 13.24 7.41 0.00 4.85
2281 10451 1.153939 CCTGTCGAACAGCTCCTCG 60.154 63.158 7.51 7.51 44.63 4.63
2353 10523 1.204704 CCCATGAAGTAGTGCGTCTCA 59.795 52.381 0.00 0.00 0.00 3.27
2684 11001 1.803943 CGGGACTCTGAGAAGACGG 59.196 63.158 12.44 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 1.077828 ACTGGATCTCCACTCTGGTCA 59.922 52.381 0.00 0.00 42.01 4.02
596 598 1.557099 TAGCCAGTGACCCTGTACAG 58.443 55.000 16.34 16.34 39.74 2.74
598 600 1.621814 TGTTAGCCAGTGACCCTGTAC 59.378 52.381 0.00 0.00 39.74 2.90
600 602 1.136828 TTGTTAGCCAGTGACCCTGT 58.863 50.000 0.00 0.00 39.74 4.00
602 604 1.348036 GAGTTGTTAGCCAGTGACCCT 59.652 52.381 0.00 0.00 0.00 4.34
603 605 1.071699 TGAGTTGTTAGCCAGTGACCC 59.928 52.381 0.00 0.00 0.00 4.46
604 606 2.543777 TGAGTTGTTAGCCAGTGACC 57.456 50.000 0.00 0.00 0.00 4.02
605 607 3.467803 ACTTGAGTTGTTAGCCAGTGAC 58.532 45.455 0.00 0.00 0.00 3.67
607 609 2.808543 GGACTTGAGTTGTTAGCCAGTG 59.191 50.000 0.00 0.00 0.00 3.66
608 610 2.548067 CGGACTTGAGTTGTTAGCCAGT 60.548 50.000 0.00 0.00 0.00 4.00
609 611 2.069273 CGGACTTGAGTTGTTAGCCAG 58.931 52.381 0.00 0.00 0.00 4.85
611 613 1.439679 CCGGACTTGAGTTGTTAGCC 58.560 55.000 0.00 0.00 0.00 3.93
612 614 1.001633 TCCCGGACTTGAGTTGTTAGC 59.998 52.381 0.73 0.00 0.00 3.09
613 615 3.396260 TTCCCGGACTTGAGTTGTTAG 57.604 47.619 0.73 0.00 0.00 2.34
617 619 1.235724 GGTTTCCCGGACTTGAGTTG 58.764 55.000 0.73 0.00 0.00 3.16
618 620 0.109913 GGGTTTCCCGGACTTGAGTT 59.890 55.000 0.73 0.00 32.13 3.01
619 621 1.759236 GGGTTTCCCGGACTTGAGT 59.241 57.895 0.73 0.00 32.13 3.41
620 622 4.716003 GGGTTTCCCGGACTTGAG 57.284 61.111 0.73 0.00 32.13 3.02
737 3873 8.299570 AGTTCAGACAAATATTTTGGACATGTC 58.700 33.333 17.91 17.91 36.77 3.06
738 3874 8.181904 AGTTCAGACAAATATTTTGGACATGT 57.818 30.769 0.00 0.00 0.00 3.21
741 3877 9.513906 TGATAGTTCAGACAAATATTTTGGACA 57.486 29.630 10.89 0.93 0.00 4.02
952 4101 2.616842 GCTTTTTCTTGGGTTCGACTCA 59.383 45.455 0.00 0.00 0.00 3.41
1224 9173 0.759436 CACCCCCTAGATACGCCACT 60.759 60.000 0.00 0.00 0.00 4.00
1225 9174 1.746517 CACCCCCTAGATACGCCAC 59.253 63.158 0.00 0.00 0.00 5.01
1226 9175 1.458777 CCACCCCCTAGATACGCCA 60.459 63.158 0.00 0.00 0.00 5.69
1227 9176 1.152398 TCCACCCCCTAGATACGCC 60.152 63.158 0.00 0.00 0.00 5.68
1228 9177 0.757935 TGTCCACCCCCTAGATACGC 60.758 60.000 0.00 0.00 0.00 4.42
1229 9178 1.329256 CTGTCCACCCCCTAGATACG 58.671 60.000 0.00 0.00 0.00 3.06
1230 9179 1.718280 CCTGTCCACCCCCTAGATAC 58.282 60.000 0.00 0.00 0.00 2.24
1231 9180 0.566176 CCCTGTCCACCCCCTAGATA 59.434 60.000 0.00 0.00 0.00 1.98
1232 9181 1.318380 CCCTGTCCACCCCCTAGAT 59.682 63.158 0.00 0.00 0.00 1.98
1233 9182 2.181773 ACCCTGTCCACCCCCTAGA 61.182 63.158 0.00 0.00 0.00 2.43
1234 9183 1.995626 CACCCTGTCCACCCCCTAG 60.996 68.421 0.00 0.00 0.00 3.02
1235 9184 2.124085 CACCCTGTCCACCCCCTA 59.876 66.667 0.00 0.00 0.00 3.53
1238 9187 3.647771 GACCACCCTGTCCACCCC 61.648 72.222 0.00 0.00 0.00 4.95
1244 9193 1.299976 GTCCATGGACCACCCTGTC 59.700 63.158 31.37 5.53 39.08 3.51
1245 9194 3.495729 GTCCATGGACCACCCTGT 58.504 61.111 31.37 0.00 39.08 4.00
1256 9205 2.102578 GAAATTCCAGGGTGGTCCATG 58.897 52.381 0.00 0.00 44.12 3.66
1257 9206 1.007118 GGAAATTCCAGGGTGGTCCAT 59.993 52.381 7.23 0.00 39.03 3.41
1258 9207 0.407918 GGAAATTCCAGGGTGGTCCA 59.592 55.000 7.23 0.00 39.03 4.02
1259 9208 0.324368 GGGAAATTCCAGGGTGGTCC 60.324 60.000 14.68 0.00 38.64 4.46
1260 9209 0.324368 GGGGAAATTCCAGGGTGGTC 60.324 60.000 14.68 0.00 38.64 4.02
1261 9210 1.077298 TGGGGAAATTCCAGGGTGGT 61.077 55.000 14.68 0.00 38.64 4.16
1262 9211 0.339510 ATGGGGAAATTCCAGGGTGG 59.660 55.000 14.68 0.00 38.64 4.61
1263 9212 3.396685 TTATGGGGAAATTCCAGGGTG 57.603 47.619 14.68 0.00 38.64 4.61
1264 9213 5.966968 ATATTATGGGGAAATTCCAGGGT 57.033 39.130 14.68 0.00 38.64 4.34
1329 9278 9.111613 CCACCAATGCAAAATATTCACATAAAT 57.888 29.630 0.00 0.00 0.00 1.40
1330 9279 8.316946 TCCACCAATGCAAAATATTCACATAAA 58.683 29.630 0.00 0.00 0.00 1.40
1331 9280 7.763528 GTCCACCAATGCAAAATATTCACATAA 59.236 33.333 0.00 0.00 0.00 1.90
1332 9281 7.264221 GTCCACCAATGCAAAATATTCACATA 58.736 34.615 0.00 0.00 0.00 2.29
1333 9282 6.108015 GTCCACCAATGCAAAATATTCACAT 58.892 36.000 0.00 0.00 0.00 3.21
1334 9283 5.477510 GTCCACCAATGCAAAATATTCACA 58.522 37.500 0.00 0.00 0.00 3.58
1335 9284 4.869861 GGTCCACCAATGCAAAATATTCAC 59.130 41.667 0.00 0.00 35.64 3.18
1336 9285 4.529769 TGGTCCACCAATGCAAAATATTCA 59.470 37.500 0.00 0.00 44.35 2.57
1337 9286 5.083533 TGGTCCACCAATGCAAAATATTC 57.916 39.130 0.00 0.00 44.35 1.75
1352 9301 2.361610 CATGCCAGGGTGGTCCAC 60.362 66.667 14.13 14.13 40.46 4.02
1353 9302 2.468868 AACATGCCAGGGTGGTCCA 61.469 57.895 0.00 0.00 40.46 4.02
1354 9303 1.978617 CAACATGCCAGGGTGGTCC 60.979 63.158 0.00 0.00 40.46 4.46
1355 9304 1.978617 CCAACATGCCAGGGTGGTC 60.979 63.158 4.99 0.00 40.46 4.02
1356 9305 2.118076 CCAACATGCCAGGGTGGT 59.882 61.111 4.99 0.00 40.46 4.16
1357 9306 2.681064 CCCAACATGCCAGGGTGG 60.681 66.667 6.42 6.42 41.55 4.61
1358 9307 2.497792 TAGCCCAACATGCCAGGGTG 62.498 60.000 16.46 0.00 44.69 4.61
1359 9308 2.215451 CTAGCCCAACATGCCAGGGT 62.215 60.000 16.46 11.28 44.69 4.34
1360 9309 1.454479 CTAGCCCAACATGCCAGGG 60.454 63.158 12.20 12.20 45.68 4.45
1361 9310 2.123428 GCTAGCCCAACATGCCAGG 61.123 63.158 2.29 0.00 0.00 4.45
1362 9311 0.181114 TAGCTAGCCCAACATGCCAG 59.819 55.000 12.13 0.00 0.00 4.85
1363 9312 0.107214 GTAGCTAGCCCAACATGCCA 60.107 55.000 12.13 0.00 0.00 4.92
1364 9313 1.160329 CGTAGCTAGCCCAACATGCC 61.160 60.000 12.13 0.00 0.00 4.40
1365 9314 2.311294 CGTAGCTAGCCCAACATGC 58.689 57.895 12.13 0.00 0.00 4.06
1474 9423 4.382320 GGCGGGGTCTGCACGTTA 62.382 66.667 1.01 0.00 0.00 3.18
1591 9543 2.758327 TCCTGCAGGTACGCCGAT 60.758 61.111 31.58 0.00 40.50 4.18
1642 9594 3.345808 GCGAGCGCAAACACCAGA 61.346 61.111 11.47 0.00 41.49 3.86
1703 9662 4.803426 CAGTCCAGCGGCCGAGAC 62.803 72.222 33.48 29.17 0.00 3.36
1778 9741 5.518848 TGCTCAATGCTAAACCAATATGG 57.481 39.130 0.00 0.00 42.60 2.74
1813 9776 3.791973 TGGAACACAACAATGACCAAC 57.208 42.857 0.00 0.00 31.00 3.77
1943 9981 3.385755 ACCAACTGAGCTTTCTTTGCAAT 59.614 39.130 0.00 0.00 0.00 3.56
1995 10062 6.480651 TCTGTTTTATGCTCTGTTTTCGTACA 59.519 34.615 0.00 0.00 0.00 2.90
1999 10066 5.990408 ACTCTGTTTTATGCTCTGTTTTCG 58.010 37.500 0.00 0.00 0.00 3.46
2048 10171 6.036735 GCCGCTACTATTTGATAACTTGTCAA 59.963 38.462 0.00 0.00 34.01 3.18
2050 10173 5.522460 TGCCGCTACTATTTGATAACTTGTC 59.478 40.000 0.00 0.00 0.00 3.18
2052 10175 5.984233 TGCCGCTACTATTTGATAACTTG 57.016 39.130 0.00 0.00 0.00 3.16
2055 10178 7.190920 AGATTTGCCGCTACTATTTGATAAC 57.809 36.000 0.00 0.00 0.00 1.89
2056 10179 8.364894 TCTAGATTTGCCGCTACTATTTGATAA 58.635 33.333 0.00 0.00 0.00 1.75
2057 10180 7.892609 TCTAGATTTGCCGCTACTATTTGATA 58.107 34.615 0.00 0.00 0.00 2.15
2058 10181 6.759272 TCTAGATTTGCCGCTACTATTTGAT 58.241 36.000 0.00 0.00 0.00 2.57
2059 10182 6.156748 TCTAGATTTGCCGCTACTATTTGA 57.843 37.500 0.00 0.00 0.00 2.69
2060 10183 7.171508 TCAATCTAGATTTGCCGCTACTATTTG 59.828 37.037 15.49 0.61 0.00 2.32
2061 10184 7.217200 TCAATCTAGATTTGCCGCTACTATTT 58.783 34.615 15.49 0.00 0.00 1.40
2063 10186 6.346477 TCAATCTAGATTTGCCGCTACTAT 57.654 37.500 15.49 0.00 0.00 2.12
2076 10199 8.986991 ACCACAGACTTTCTTATCAATCTAGAT 58.013 33.333 0.00 0.00 0.00 1.98
2081 10204 7.099764 TCTCACCACAGACTTTCTTATCAATC 58.900 38.462 0.00 0.00 0.00 2.67
2129 10252 4.536765 CCCTATGCAATAAGACCAAGGTT 58.463 43.478 0.00 0.00 0.00 3.50
2149 10286 2.656002 GTGAGAAATAAGAAGGGGCCC 58.344 52.381 17.12 17.12 0.00 5.80
2266 10436 4.775746 CTCGAGGAGCTGTTCGAC 57.224 61.111 13.46 0.00 40.55 4.20
2281 10451 2.813908 CGTGTTAGGGCGTGGCTC 60.814 66.667 0.00 0.00 0.00 4.70
2353 10523 1.920835 GGACCTCAGCCACTTCCCT 60.921 63.158 0.00 0.00 0.00 4.20
2590 10907 2.269241 GAAGGCGACCCCAAGGAG 59.731 66.667 0.00 0.00 36.73 3.69


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

AutoCloner maintained by Alex Coulton.