Multiple sequence alignment - TraesCS6A01G359200

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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 TraesCS6A01G359200 chr6A 100.000 6452 0 0 1 6452 590080159 590073708 0.000000e+00 11915
1 TraesCS6A01G359200 chr6A 88.670 203 18 3 1775 1975 196314597 196314796 6.460000e-60 243
2 TraesCS6A01G359200 chr6D 97.220 3705 76 15 2208 5903 441622922 441619236 0.000000e+00 6246
3 TraesCS6A01G359200 chr6D 91.008 1379 61 35 1 1359 441624245 441622910 0.000000e+00 1801
4 TraesCS6A01G359200 chr6D 90.631 523 22 11 5903 6424 441619137 441618641 0.000000e+00 669
5 TraesCS6A01G359200 chr6D 87.162 296 31 4 1070 1359 460156751 460157045 4.820000e-86 329
6 TraesCS6A01G359200 chr6B 94.628 1396 71 2 3906 5300 667072922 667071530 0.000000e+00 2159
7 TraesCS6A01G359200 chr6B 92.609 1353 66 20 25 1359 667075955 667074619 0.000000e+00 1914
8 TraesCS6A01G359200 chr6B 90.038 1315 99 12 2208 3495 667074631 667073322 0.000000e+00 1674
9 TraesCS6A01G359200 chr6B 89.300 486 29 14 5274 5754 667071493 667071026 7.210000e-164 588
10 TraesCS6A01G359200 chr6B 87.316 339 35 4 3173 3503 117907752 117907414 1.310000e-101 381
11 TraesCS6A01G359200 chr6B 90.947 243 22 0 2702 2944 117907986 117907744 1.730000e-85 327
12 TraesCS6A01G359200 chr6B 91.304 184 13 2 2208 2389 101435780 101435962 1.390000e-61 248
13 TraesCS6A01G359200 chr6B 88.947 190 12 2 6237 6424 667070885 667070703 6.510000e-55 226
14 TraesCS6A01G359200 chr5A 97.892 854 17 1 1357 2210 48180007 48180859 0.000000e+00 1476
15 TraesCS6A01G359200 chr5A 85.312 320 27 6 3192 3503 544168577 544168884 4.860000e-81 313
16 TraesCS6A01G359200 chr7A 96.977 860 16 3 1358 2208 17437525 17436667 0.000000e+00 1435
17 TraesCS6A01G359200 chr7A 88.162 321 29 4 3192 3503 59609400 59609080 2.200000e-99 374
18 TraesCS6A01G359200 chr7A 89.189 111 11 1 1036 1145 98545382 98545492 3.140000e-28 137
19 TraesCS6A01G359200 chr7A 89.091 110 11 1 1036 1144 98736029 98735920 1.130000e-27 135
20 TraesCS6A01G359200 chrUn 100.000 415 0 0 2800 3214 477231703 477231289 0.000000e+00 767
21 TraesCS6A01G359200 chrUn 86.420 243 23 3 2436 2678 8489226 8489458 2.310000e-64 257
22 TraesCS6A01G359200 chr2A 90.891 494 43 2 2449 2941 736738636 736739128 0.000000e+00 662
23 TraesCS6A01G359200 chr2A 86.726 339 37 1 3173 3503 736739123 736739461 2.840000e-98 370
24 TraesCS6A01G359200 chr1A 94.774 421 19 1 1358 1775 570245383 570245803 0.000000e+00 652
25 TraesCS6A01G359200 chr1A 93.396 424 22 4 1357 1775 480744984 480745406 1.980000e-174 623
26 TraesCS6A01G359200 chr1A 86.301 438 25 9 1775 2212 480745442 480745844 1.650000e-120 444
27 TraesCS6A01G359200 chr1A 84.404 436 33 10 1775 2210 570245839 570246239 4.690000e-106 396
28 TraesCS6A01G359200 chr2B 93.412 425 23 3 1355 1775 321737732 321737309 5.490000e-175 625
29 TraesCS6A01G359200 chr2B 92.333 300 22 1 1358 1656 564861559 564861260 5.980000e-115 425
30 TraesCS6A01G359200 chr2B 92.793 222 16 0 1775 1996 564860986 564860765 8.070000e-84 322
31 TraesCS6A01G359200 chr2B 92.377 223 16 1 2434 2655 764523887 764524109 3.750000e-82 316
32 TraesCS6A01G359200 chr2B 88.571 175 15 3 2211 2385 764523730 764523899 2.360000e-49 207
33 TraesCS6A01G359200 chr3A 92.584 418 30 1 1358 1775 192824574 192824158 3.330000e-167 599
34 TraesCS6A01G359200 chr7B 90.802 424 36 2 1358 1778 88858413 88858836 1.210000e-156 564
35 TraesCS6A01G359200 chr7B 90.547 201 19 0 1775 1975 701065566 701065366 3.840000e-67 267
36 TraesCS6A01G359200 chr7B 83.658 257 29 4 2434 2690 68749756 68749513 5.030000e-56 230
37 TraesCS6A01G359200 chr7B 90.909 110 9 1 1036 1144 49189200 49189091 5.210000e-31 147
38 TraesCS6A01G359200 chr7B 90.385 104 10 0 1893 1996 88859239 88859136 3.140000e-28 137
39 TraesCS6A01G359200 chr7B 89.720 107 10 1 1036 1141 49026489 49026595 1.130000e-27 135
40 TraesCS6A01G359200 chr5D 91.148 418 33 2 1358 1775 396832137 396832550 1.210000e-156 564
41 TraesCS6A01G359200 chr5D 82.452 473 39 11 1775 2209 396832586 396833052 2.200000e-99 374
42 TraesCS6A01G359200 chr5D 85.163 337 36 9 3497 3831 461620779 461621103 3.730000e-87 333
43 TraesCS6A01G359200 chr5D 92.754 207 12 2 3297 3502 461620547 461620751 4.890000e-76 296
44 TraesCS6A01G359200 chr3D 89.822 393 36 4 2551 2941 156977500 156977890 9.660000e-138 501
45 TraesCS6A01G359200 chr3D 84.570 337 38 9 3497 3831 477825804 477826128 8.070000e-84 322
46 TraesCS6A01G359200 chr3D 91.304 207 17 1 3297 3502 477825570 477825776 1.370000e-71 281
47 TraesCS6A01G359200 chr3D 84.588 279 21 5 3173 3443 156977885 156978149 2.310000e-64 257
48 TraesCS6A01G359200 chr4D 86.607 448 34 12 1775 2210 494856965 494857398 7.570000e-129 472
49 TraesCS6A01G359200 chr4D 85.629 334 40 6 3497 3830 430852759 430852434 1.720000e-90 344
50 TraesCS6A01G359200 chr4D 88.060 201 22 2 1576 1775 494856724 494856923 3.010000e-58 237
51 TraesCS6A01G359200 chr4D 91.304 138 12 0 3306 3443 49768239 49768376 8.540000e-44 189
52 TraesCS6A01G359200 chr4B 91.667 240 20 0 2702 2941 97058637 97058398 3.730000e-87 333
53 TraesCS6A01G359200 chr4B 85.088 342 31 7 3173 3503 97058403 97058071 1.340000e-86 331
54 TraesCS6A01G359200 chr4B 90.608 181 16 1 2208 2388 580716569 580716390 8.360000e-59 239
55 TraesCS6A01G359200 chr1B 92.576 229 15 2 2434 2661 45380582 45380355 1.730000e-85 327
56 TraesCS6A01G359200 chr1B 86.381 257 25 2 2434 2690 635879227 635878981 8.240000e-69 272
57 TraesCS6A01G359200 chr1B 88.166 169 15 3 2220 2388 45380730 45380567 5.100000e-46 196
58 TraesCS6A01G359200 chr5B 84.825 257 29 2 2434 2690 22357054 22356808 3.860000e-62 250
59 TraesCS6A01G359200 chr5B 91.892 148 11 1 3297 3443 441695016 441694869 8.480000e-49 206
60 TraesCS6A01G359200 chr4A 90.217 184 14 3 2208 2389 56472980 56472799 3.010000e-58 237
61 TraesCS6A01G359200 chr7D 88.288 111 12 1 1036 1145 94936622 94936732 1.460000e-26 132


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 TraesCS6A01G359200 chr6A 590073708 590080159 6451 True 11915.000000 11915 100.0000 1 6452 1 chr6A.!!$R1 6451
1 TraesCS6A01G359200 chr6D 441618641 441624245 5604 True 2905.333333 6246 92.9530 1 6424 3 chr6D.!!$R1 6423
2 TraesCS6A01G359200 chr6B 667070703 667075955 5252 True 1312.200000 2159 91.1044 25 6424 5 chr6B.!!$R2 6399
3 TraesCS6A01G359200 chr6B 117907414 117907986 572 True 354.000000 381 89.1315 2702 3503 2 chr6B.!!$R1 801
4 TraesCS6A01G359200 chr5A 48180007 48180859 852 False 1476.000000 1476 97.8920 1357 2210 1 chr5A.!!$F1 853
5 TraesCS6A01G359200 chr7A 17436667 17437525 858 True 1435.000000 1435 96.9770 1358 2208 1 chr7A.!!$R1 850
6 TraesCS6A01G359200 chr2A 736738636 736739461 825 False 516.000000 662 88.8085 2449 3503 2 chr2A.!!$F1 1054
7 TraesCS6A01G359200 chr1A 480744984 480745844 860 False 533.500000 623 89.8485 1357 2212 2 chr1A.!!$F1 855
8 TraesCS6A01G359200 chr1A 570245383 570246239 856 False 524.000000 652 89.5890 1358 2210 2 chr1A.!!$F2 852
9 TraesCS6A01G359200 chr2B 564860765 564861559 794 True 373.500000 425 92.5630 1358 1996 2 chr2B.!!$R2 638
10 TraesCS6A01G359200 chr5D 396832137 396833052 915 False 469.000000 564 86.8000 1358 2209 2 chr5D.!!$F1 851
11 TraesCS6A01G359200 chr5D 461620547 461621103 556 False 314.500000 333 88.9585 3297 3831 2 chr5D.!!$F2 534
12 TraesCS6A01G359200 chr3D 156977500 156978149 649 False 379.000000 501 87.2050 2551 3443 2 chr3D.!!$F1 892
13 TraesCS6A01G359200 chr3D 477825570 477826128 558 False 301.500000 322 87.9370 3297 3831 2 chr3D.!!$F2 534
14 TraesCS6A01G359200 chr4D 494856724 494857398 674 False 354.500000 472 87.3335 1576 2210 2 chr4D.!!$F2 634
15 TraesCS6A01G359200 chr4B 97058071 97058637 566 True 332.000000 333 88.3775 2702 3503 2 chr4B.!!$R2 801

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
223 224 0.182775 ACGCCACTCTTTTGACCCTT 59.817 50.000 0.00 0.00 0.00 3.95 F
351 360 0.392595 GCTCCCTCCAACTAAACCCG 60.393 60.000 0.00 0.00 0.00 5.28 F
2213 2511 0.321653 GGTATAATCGCCCCTGCCTG 60.322 60.000 0.00 0.00 0.00 4.85 F
2413 2718 2.000447 GCGGTCTGTTTGGTAAGCTAG 59.000 52.381 0.00 0.00 0.00 3.42 F
2798 3105 2.158219 TGAGGAGGGGAAAGTGTCAGTA 60.158 50.000 0.00 0.00 0.00 2.74 F
4686 5127 1.135199 GCCTGTGCATGGTTCATTCAG 60.135 52.381 9.89 0.15 37.47 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1184 1223 0.104487 GGAGTAGCCGGCTCCTAAAC 59.896 60.000 36.73 25.44 46.71 2.01 R
2298 2596 1.244019 AAAACCAGATGCCTCGTGCC 61.244 55.000 0.00 0.00 40.16 5.01 R
4201 4642 0.798776 CCTGAATCACAACCGCTGTC 59.201 55.000 0.00 0.00 35.47 3.51 R
4686 5127 3.800506 GCTGAATGAAGCACCATTATTGC 59.199 43.478 3.96 5.56 43.01 3.56 R
4853 5294 5.241662 ACTATCTGAACTTCCAAAGCTCAC 58.758 41.667 0.00 0.00 30.92 3.51 R
6175 6792 0.111061 AAGGTGCTCAGCATGTGGAA 59.889 50.000 0.54 0.00 41.91 3.53 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
86 87 6.547141 TCCTCAAACAAATCACAAGAATCACT 59.453 34.615 0.00 0.00 0.00 3.41
87 88 7.068593 TCCTCAAACAAATCACAAGAATCACTT 59.931 33.333 0.00 0.00 39.70 3.16
114 115 3.341823 GTGTTGAGCCACAGAGAATCAT 58.658 45.455 0.00 0.00 37.82 2.45
130 131 5.549347 AGAATCATATTCCTGCAGCAGTAG 58.451 41.667 21.26 6.99 0.00 2.57
131 132 4.970860 ATCATATTCCTGCAGCAGTAGT 57.029 40.909 21.26 4.86 0.00 2.73
132 133 6.268617 AGAATCATATTCCTGCAGCAGTAGTA 59.731 38.462 21.26 7.17 0.00 1.82
223 224 0.182775 ACGCCACTCTTTTGACCCTT 59.817 50.000 0.00 0.00 0.00 3.95
309 310 0.771127 CTCTTCCTCCCCAACACCAA 59.229 55.000 0.00 0.00 0.00 3.67
310 311 1.144913 CTCTTCCTCCCCAACACCAAA 59.855 52.381 0.00 0.00 0.00 3.28
311 312 1.144913 TCTTCCTCCCCAACACCAAAG 59.855 52.381 0.00 0.00 0.00 2.77
344 353 2.685380 CCTCCGCTCCCTCCAACT 60.685 66.667 0.00 0.00 0.00 3.16
351 360 0.392595 GCTCCCTCCAACTAAACCCG 60.393 60.000 0.00 0.00 0.00 5.28
486 498 2.749839 CATCGGCGCCCTTTTCCA 60.750 61.111 23.46 0.00 0.00 3.53
498 510 3.563479 GCCCTTTTCCACCCATCTCTTTA 60.563 47.826 0.00 0.00 0.00 1.85
547 564 1.856265 CGCCTCTTGCTTTCCCACAC 61.856 60.000 0.00 0.00 38.05 3.82
551 568 1.153756 CTTGCTTTCCCACACCCCT 59.846 57.895 0.00 0.00 0.00 4.79
733 762 2.204448 TGGGGATTGGGAGGCCTT 60.204 61.111 6.77 0.00 0.00 4.35
883 912 1.397945 CCCGTGTGAAATTCGTGTTCG 60.398 52.381 0.00 0.00 38.55 3.95
899 933 4.056125 CGTGCTCCGAGCCTGTCA 62.056 66.667 17.81 0.00 41.51 3.58
901 935 2.601666 TGCTCCGAGCCTGTCAGT 60.602 61.111 17.81 0.00 41.51 3.41
955 989 1.175983 TGCTTCCGGCGAATTGGTTT 61.176 50.000 9.30 0.00 45.43 3.27
980 1019 1.134371 CGAGTGAGGGAGGGGATTTTC 60.134 57.143 0.00 0.00 0.00 2.29
989 1028 1.492599 GAGGGGATTTTCTCTGGAGGG 59.507 57.143 0.00 0.00 0.00 4.30
1092 1131 4.712425 GTGGACGACGACCCGGTG 62.712 72.222 13.72 0.00 0.00 4.94
1145 1184 1.204704 CTGCCAGTATCACGGTGAGAA 59.795 52.381 16.84 4.49 0.00 2.87
1148 1187 2.353803 GCCAGTATCACGGTGAGAACTT 60.354 50.000 20.28 6.36 27.90 2.66
1150 1189 3.679980 CCAGTATCACGGTGAGAACTTTG 59.320 47.826 20.28 13.68 27.90 2.77
1152 1191 4.750098 CAGTATCACGGTGAGAACTTTGTT 59.250 41.667 20.28 3.86 27.90 2.83
1155 1194 4.349663 TCACGGTGAGAACTTTGTTTTG 57.650 40.909 6.76 0.00 0.00 2.44
1156 1195 2.851824 CACGGTGAGAACTTTGTTTTGC 59.148 45.455 0.74 0.00 0.00 3.68
1158 1197 3.108144 CGGTGAGAACTTTGTTTTGCTG 58.892 45.455 0.00 0.00 0.00 4.41
1163 1202 6.588373 GGTGAGAACTTTGTTTTGCTGTTTTA 59.412 34.615 0.00 0.00 0.00 1.52
1180 1219 7.272037 CTGTTTTACAGTTCAGGGTTGTAAT 57.728 36.000 0.00 0.00 41.19 1.89
1184 1223 8.813282 GTTTTACAGTTCAGGGTTGTAATTTTG 58.187 33.333 0.00 0.00 37.21 2.44
1196 1235 5.158494 GTTGTAATTTTGTTTAGGAGCCGG 58.842 41.667 0.00 0.00 0.00 6.13
1202 1241 0.822164 TGTTTAGGAGCCGGCTACTC 59.178 55.000 44.21 29.64 38.39 2.59
1213 1252 4.129737 GCTACTCCGTCAGGCGCA 62.130 66.667 10.83 0.00 39.71 6.09
1277 1323 2.303022 CAGTGTCCAGGACAACCACTAT 59.697 50.000 24.65 1.81 44.49 2.12
1353 1399 6.446781 ACATCATATATAAATGCTGCCTGC 57.553 37.500 0.00 0.00 43.25 4.85
1415 1461 6.574462 GCACGACGCAAACTAAAATTTACTTA 59.426 34.615 0.00 0.00 41.79 2.24
1797 2054 1.971505 CTGATTAGGCCCAGGCGTGA 61.972 60.000 13.96 6.21 43.06 4.35
2212 2510 1.827399 CGGTATAATCGCCCCTGCCT 61.827 60.000 0.00 0.00 0.00 4.75
2213 2511 0.321653 GGTATAATCGCCCCTGCCTG 60.322 60.000 0.00 0.00 0.00 4.85
2253 2551 8.110271 AGTACCTCTCGATGGATAGATTCATTA 58.890 37.037 11.00 0.00 0.00 1.90
2334 2632 6.036953 TCTGGTTTTTGTCATGAAAAATGCAC 59.963 34.615 11.86 9.01 37.20 4.57
2370 2675 6.943718 CCCTTTTCTTGTATTGTTACCCACTA 59.056 38.462 0.00 0.00 0.00 2.74
2413 2718 2.000447 GCGGTCTGTTTGGTAAGCTAG 59.000 52.381 0.00 0.00 0.00 3.42
2420 2725 4.515191 TCTGTTTGGTAAGCTAGCAACAAG 59.485 41.667 18.83 10.79 44.80 3.16
2610 2915 2.819348 GCTTGAAATGGACCTCCCTGTT 60.819 50.000 0.00 0.00 35.38 3.16
2661 2967 2.228822 ACAGCTGCCCAATTTTCTTACG 59.771 45.455 15.27 0.00 0.00 3.18
2680 2986 3.175594 ACGGGTCTTGGTAATAGGAACA 58.824 45.455 0.00 0.00 0.00 3.18
2752 3059 6.457355 TGCAAAATATCAATTCAGCACAGTT 58.543 32.000 0.00 0.00 32.85 3.16
2790 3097 3.265479 ACTTCTGATTGAGGAGGGGAAAG 59.735 47.826 0.00 0.00 30.13 2.62
2798 3105 2.158219 TGAGGAGGGGAAAGTGTCAGTA 60.158 50.000 0.00 0.00 0.00 2.74
3796 4237 9.654663 GTAAATGAGTAATCTGGTAAGAACTGT 57.345 33.333 0.00 0.00 35.59 3.55
3880 4321 8.283291 GCATGTAGTATATGCTAAACCAGAAAC 58.717 37.037 20.98 0.00 45.64 2.78
4156 4597 3.888079 CTCTCCCGCAGCGCTATCG 62.888 68.421 10.99 17.02 39.07 2.92
4201 4642 7.103641 TGCTAAATAGTCCTAGAAACAACCAG 58.896 38.462 0.00 0.00 0.00 4.00
4686 5127 1.135199 GCCTGTGCATGGTTCATTCAG 60.135 52.381 9.89 0.15 37.47 3.02
4853 5294 2.287069 CCAGATACCGAGCAGAAGTACG 60.287 54.545 0.00 0.00 0.00 3.67
5074 5515 2.980246 TCCTCTTCTCAGGAGACACA 57.020 50.000 0.00 0.00 37.68 3.72
5315 5818 3.932545 AATCAGCCTAGTAGAGCGATG 57.067 47.619 0.00 0.00 0.00 3.84
5341 5844 4.379243 CTCAGCGCCACCCGAACT 62.379 66.667 2.29 0.00 40.02 3.01
5342 5845 3.883744 CTCAGCGCCACCCGAACTT 62.884 63.158 2.29 0.00 40.02 2.66
5358 5861 7.657354 CACCCGAACTTGATTGATCTAATGATA 59.343 37.037 0.00 0.00 32.19 2.15
5512 6016 1.134340 TGTGTATACGCATGTTCCCCC 60.134 52.381 15.05 0.00 0.00 5.40
5557 6061 4.167268 GTGTAGTGTAGCTAGTGTTGCTC 58.833 47.826 0.00 0.00 41.46 4.26
5579 6083 4.962995 TCATCTTTAGTAGGCCTAGTGCTT 59.037 41.667 27.54 7.93 40.92 3.91
5606 6110 7.597743 GGGCTGTATGTGTATGTATTGTAGTAC 59.402 40.741 0.00 0.00 0.00 2.73
5607 6111 8.358148 GGCTGTATGTGTATGTATTGTAGTACT 58.642 37.037 0.00 0.00 0.00 2.73
5646 6150 5.305585 TGTTGGAGAAACAAGTAGGATGAC 58.694 41.667 0.00 0.00 45.85 3.06
5758 6274 6.294342 CCTGGAATTTGTATGTCATGCATAGG 60.294 42.308 4.31 0.00 40.42 2.57
5765 6285 0.107066 TGTCATGCATAGGCCAGGTG 60.107 55.000 5.01 0.88 40.13 4.00
5795 6315 2.513753 TCGAAATGTGGCTGGTGAAAT 58.486 42.857 0.00 0.00 0.00 2.17
5796 6316 2.228582 TCGAAATGTGGCTGGTGAAATG 59.771 45.455 0.00 0.00 0.00 2.32
5797 6317 2.340337 GAAATGTGGCTGGTGAAATGC 58.660 47.619 0.00 0.00 0.00 3.56
5798 6318 1.340088 AATGTGGCTGGTGAAATGCA 58.660 45.000 0.00 0.00 0.00 3.96
5822 6342 1.630223 TCCAAAACCTGATGCATGCA 58.370 45.000 25.04 25.04 0.00 3.96
5844 6364 5.756833 GCAGGAATGGATTTGGATTTGAATC 59.243 40.000 0.00 0.00 34.66 2.52
5857 6377 4.497006 GGATTTGAATCTGAATGGCTCGTG 60.497 45.833 3.94 0.00 35.73 4.35
5888 6408 6.988580 TCCATGAATTAGCTGTCTGTTCATAG 59.011 38.462 0.00 0.00 37.12 2.23
5904 6424 9.087424 TCTGTTCATAGATAAACTTCAATCACG 57.913 33.333 0.00 0.00 0.00 4.35
5905 6425 7.684670 TGTTCATAGATAAACTTCAATCACGC 58.315 34.615 0.00 0.00 0.00 5.34
5907 6427 7.468922 TCATAGATAAACTTCAATCACGCAG 57.531 36.000 0.00 0.00 0.00 5.18
5908 6428 4.606457 AGATAAACTTCAATCACGCAGC 57.394 40.909 0.00 0.00 0.00 5.25
5909 6429 3.375299 AGATAAACTTCAATCACGCAGCC 59.625 43.478 0.00 0.00 0.00 4.85
5913 6433 0.169672 CTTCAATCACGCAGCCAAGG 59.830 55.000 0.00 0.00 0.00 3.61
5914 6434 0.537143 TTCAATCACGCAGCCAAGGT 60.537 50.000 0.00 0.00 0.00 3.50
5915 6435 0.323302 TCAATCACGCAGCCAAGGTA 59.677 50.000 0.00 0.00 0.00 3.08
5916 6436 1.065491 TCAATCACGCAGCCAAGGTAT 60.065 47.619 0.00 0.00 0.00 2.73
5917 6437 1.745087 CAATCACGCAGCCAAGGTATT 59.255 47.619 0.00 0.00 0.00 1.89
5924 6540 2.364324 CGCAGCCAAGGTATTCCTACTA 59.636 50.000 0.00 0.00 44.35 1.82
5934 6550 3.390311 GGTATTCCTACTACCCACCCTTG 59.610 52.174 0.00 0.00 33.84 3.61
5955 6572 3.518998 ATCCAGACCTCGTCCGCG 61.519 66.667 0.00 0.00 39.92 6.46
5957 6574 4.052229 CCAGACCTCGTCCGCGTT 62.052 66.667 4.92 0.00 39.49 4.84
5972 6589 2.110967 CGTTGAGCAGCATCAGGGG 61.111 63.158 0.00 0.00 0.00 4.79
6052 6669 1.503818 TTGTTTCCAGCTCGTTCGCC 61.504 55.000 0.00 0.00 0.00 5.54
6212 6829 3.499406 TCAGCAGCCCTGACCAAT 58.501 55.556 0.00 0.00 45.44 3.16
6223 6840 3.860754 GCCCTGACCAATACAGCAAAAAC 60.861 47.826 0.00 0.00 34.47 2.43
6226 6843 4.549458 CTGACCAATACAGCAAAAACCTG 58.451 43.478 0.00 0.00 36.41 4.00
6230 6847 3.680937 CCAATACAGCAAAAACCTGCATG 59.319 43.478 0.00 0.00 45.18 4.06
6274 6891 2.878406 AGACCTCACCACATGTTTTTCG 59.122 45.455 0.00 0.00 0.00 3.46
6303 6920 7.536281 GGTAATCTTGTTACGAACATTCCAAAC 59.464 37.037 0.00 0.00 41.79 2.93
6322 6939 1.680651 CCCCCAAATAACCGCAGCA 60.681 57.895 0.00 0.00 0.00 4.41
6393 7010 1.666189 GTTACTCTGCCGAGCATTTCC 59.334 52.381 4.89 0.00 41.09 3.13
6424 7041 3.215587 AACAGGCAGCCCCCAGAAG 62.216 63.158 8.22 0.00 0.00 2.85
6425 7042 4.437587 CAGGCAGCCCCCAGAAGG 62.438 72.222 8.22 0.00 0.00 3.46
6431 7048 3.661648 GCCCCCAGAAGGCCAGAA 61.662 66.667 5.01 0.00 45.16 3.02
6432 7049 3.001358 GCCCCCAGAAGGCCAGAAT 62.001 63.158 5.01 0.00 45.16 2.40
6433 7050 1.645402 GCCCCCAGAAGGCCAGAATA 61.645 60.000 5.01 0.00 45.16 1.75
6434 7051 1.152649 CCCCCAGAAGGCCAGAATAT 58.847 55.000 5.01 0.00 0.00 1.28
6435 7052 1.500736 CCCCCAGAAGGCCAGAATATT 59.499 52.381 5.01 0.00 0.00 1.28
6436 7053 2.590821 CCCCAGAAGGCCAGAATATTG 58.409 52.381 5.01 0.00 0.00 1.90
6437 7054 2.590821 CCCAGAAGGCCAGAATATTGG 58.409 52.381 5.01 2.40 41.35 3.16
6438 7055 2.175499 CCCAGAAGGCCAGAATATTGGA 59.825 50.000 5.01 0.00 40.87 3.53
6439 7056 3.373001 CCCAGAAGGCCAGAATATTGGAA 60.373 47.826 5.01 0.00 40.87 3.53
6440 7057 4.477249 CCAGAAGGCCAGAATATTGGAAT 58.523 43.478 5.01 0.00 40.87 3.01
6441 7058 4.897670 CCAGAAGGCCAGAATATTGGAATT 59.102 41.667 5.01 0.00 40.87 2.17
6442 7059 5.221382 CCAGAAGGCCAGAATATTGGAATTG 60.221 44.000 5.01 0.00 40.87 2.32
6443 7060 4.343239 AGAAGGCCAGAATATTGGAATTGC 59.657 41.667 5.01 0.00 40.87 3.56
6444 7061 3.645434 AGGCCAGAATATTGGAATTGCA 58.355 40.909 5.01 0.00 40.87 4.08
6445 7062 3.385755 AGGCCAGAATATTGGAATTGCAC 59.614 43.478 5.01 0.00 40.87 4.57
6446 7063 3.493176 GGCCAGAATATTGGAATTGCACC 60.493 47.826 0.00 0.00 40.87 5.01
6447 7064 3.493176 GCCAGAATATTGGAATTGCACCC 60.493 47.826 0.00 0.00 40.87 4.61
6448 7065 3.070015 CCAGAATATTGGAATTGCACCCC 59.930 47.826 0.00 0.00 40.87 4.95
6449 7066 3.070015 CAGAATATTGGAATTGCACCCCC 59.930 47.826 0.00 0.00 0.00 5.40
6450 7067 2.864885 ATATTGGAATTGCACCCCCA 57.135 45.000 0.00 0.00 0.00 4.96
6451 7068 2.630889 TATTGGAATTGCACCCCCAA 57.369 45.000 13.26 13.26 42.16 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.822990 ACCGTGATATCTGTGGAACGT 59.177 47.619 13.23 0.00 42.39 3.99
86 87 2.023673 CTGTGGCTCAACACCAAAGAA 58.976 47.619 0.00 0.00 44.23 2.52
87 88 1.679139 CTGTGGCTCAACACCAAAGA 58.321 50.000 0.00 0.00 44.23 2.52
96 97 5.131642 AGGAATATGATTCTCTGTGGCTCAA 59.868 40.000 0.00 0.00 0.00 3.02
114 115 6.549736 TCATTACTACTACTGCTGCAGGAATA 59.450 38.462 31.00 18.11 35.51 1.75
130 131 6.284459 CCTCCTCCAAACTGATCATTACTAC 58.716 44.000 0.00 0.00 0.00 2.73
131 132 5.163301 GCCTCCTCCAAACTGATCATTACTA 60.163 44.000 0.00 0.00 0.00 1.82
132 133 4.384647 GCCTCCTCCAAACTGATCATTACT 60.385 45.833 0.00 0.00 0.00 2.24
223 224 3.567441 CCATGGATATAGAGGAGGGAGCA 60.567 52.174 5.56 0.00 0.00 4.26
259 260 1.625818 AGTGAATGTGTGAGAGGGGAC 59.374 52.381 0.00 0.00 0.00 4.46
309 310 0.755327 GGTGTGGTGGTTCTTGGCTT 60.755 55.000 0.00 0.00 0.00 4.35
310 311 1.152756 GGTGTGGTGGTTCTTGGCT 60.153 57.895 0.00 0.00 0.00 4.75
311 312 1.152756 AGGTGTGGTGGTTCTTGGC 60.153 57.895 0.00 0.00 0.00 4.52
344 353 2.737881 CGGAGGGGATGCGGGTTTA 61.738 63.158 0.00 0.00 39.39 2.01
424 435 4.740822 AATCCCGCACTGCACCCC 62.741 66.667 1.11 0.00 0.00 4.95
486 498 0.831307 GGACGCCTAAAGAGATGGGT 59.169 55.000 0.00 0.00 0.00 4.51
529 546 1.527433 GGTGTGGGAAAGCAAGAGGC 61.527 60.000 0.00 0.00 45.30 4.70
530 547 0.895559 GGGTGTGGGAAAGCAAGAGG 60.896 60.000 0.00 0.00 0.00 3.69
531 548 0.895559 GGGGTGTGGGAAAGCAAGAG 60.896 60.000 0.00 0.00 0.00 2.85
532 549 1.152830 GGGGTGTGGGAAAGCAAGA 59.847 57.895 0.00 0.00 0.00 3.02
533 550 1.153756 AGGGGTGTGGGAAAGCAAG 59.846 57.895 0.00 0.00 0.00 4.01
547 564 1.961394 CCATCATCATTGAAGCAGGGG 59.039 52.381 0.00 0.00 34.96 4.79
551 568 1.405872 GCCCCATCATCATTGAAGCA 58.594 50.000 0.00 0.00 34.96 3.91
701 730 1.219213 TCCCCAGCAAGGAAAGGAAAA 59.781 47.619 0.00 0.00 41.22 2.29
733 762 2.283529 GGGAGGTGGCTTCGACTCA 61.284 63.158 1.52 0.00 0.00 3.41
883 912 1.595993 TACTGACAGGCTCGGAGCAC 61.596 60.000 29.33 18.89 44.75 4.40
899 933 3.074999 GCAGAGGCAGCTCGCTACT 62.075 63.158 7.85 0.00 41.91 2.57
901 935 2.757508 AGCAGAGGCAGCTCGCTA 60.758 61.111 7.85 0.00 44.61 4.26
955 989 1.000486 CCCTCCCTCACTCGAAGGA 60.000 63.158 3.07 0.00 30.67 3.36
980 1019 0.610687 GAGGACAACACCCTCCAGAG 59.389 60.000 0.00 0.00 43.37 3.35
1092 1131 1.739562 CTCGAGCACCTTGAGGCAC 60.740 63.158 0.00 0.00 38.11 5.01
1158 1197 8.813282 CAAAATTACAACCCTGAACTGTAAAAC 58.187 33.333 0.00 0.00 38.61 2.43
1163 1202 6.538945 AACAAAATTACAACCCTGAACTGT 57.461 33.333 0.00 0.00 0.00 3.55
1167 1206 7.470841 GCTCCTAAACAAAATTACAACCCTGAA 60.471 37.037 0.00 0.00 0.00 3.02
1173 1212 5.158494 CCGGCTCCTAAACAAAATTACAAC 58.842 41.667 0.00 0.00 0.00 3.32
1174 1213 4.321378 GCCGGCTCCTAAACAAAATTACAA 60.321 41.667 22.15 0.00 0.00 2.41
1178 1217 2.525368 AGCCGGCTCCTAAACAAAATT 58.475 42.857 27.08 0.00 0.00 1.82
1180 1219 2.039348 AGTAGCCGGCTCCTAAACAAAA 59.961 45.455 36.73 8.49 0.00 2.44
1184 1223 0.104487 GGAGTAGCCGGCTCCTAAAC 59.896 60.000 36.73 25.44 46.71 2.01
1202 1241 1.577328 AAATTGACTGCGCCTGACGG 61.577 55.000 4.18 0.00 43.93 4.79
1210 1249 4.153986 CAGAGCAACTAAAATTGACTGCG 58.846 43.478 0.00 0.00 35.00 5.18
1213 1252 7.283127 TCTGAAACAGAGCAACTAAAATTGACT 59.717 33.333 0.00 0.00 35.39 3.41
1277 1323 6.975772 GTGACAACTACCAACAGCAATTTTTA 59.024 34.615 0.00 0.00 0.00 1.52
1312 1358 9.770097 ATATGATGTTCAGTACACCAAATCTAG 57.230 33.333 0.00 0.00 40.19 2.43
1415 1461 5.958380 TGATACTTCTGGTGTTGATAGACCT 59.042 40.000 0.00 0.00 38.50 3.85
1797 2054 2.012673 GCAAGACCGCAAGAGATGATT 58.987 47.619 0.00 0.00 43.02 2.57
2065 2331 3.571590 TCACAAATTGGGCTACTTTGGT 58.428 40.909 15.97 2.09 34.86 3.67
2212 2510 2.040278 AGGTACTCAATCTTTGGCTGCA 59.960 45.455 0.50 0.00 0.00 4.41
2213 2511 2.716217 AGGTACTCAATCTTTGGCTGC 58.284 47.619 0.00 0.00 0.00 5.25
2253 2551 5.185454 TCATAAATTCAGGTCACGCAATCT 58.815 37.500 0.00 0.00 0.00 2.40
2295 2593 2.184830 CCAGATGCCTCGTGCCATG 61.185 63.158 0.00 0.00 40.16 3.66
2298 2596 1.244019 AAAACCAGATGCCTCGTGCC 61.244 55.000 0.00 0.00 40.16 5.01
2334 2632 3.897505 ACAAGAAAAGGGAAATGGTCCTG 59.102 43.478 0.00 0.00 46.92 3.86
2661 2967 5.605488 TCCTATGTTCCTATTACCAAGACCC 59.395 44.000 0.00 0.00 0.00 4.46
2790 3097 9.005777 TGGAAAATAATTGGTTAGTACTGACAC 57.994 33.333 18.44 9.15 0.00 3.67
2798 3105 7.039082 ACACTGCATGGAAAATAATTGGTTAGT 60.039 33.333 0.00 0.00 0.00 2.24
3725 4166 7.639039 TGAAACTGCAGTGTTTAATAGTGAAG 58.361 34.615 22.49 3.37 39.86 3.02
3796 4237 3.332485 ACAGACAAGTGCCCCCTTTTATA 59.668 43.478 0.00 0.00 0.00 0.98
4201 4642 0.798776 CCTGAATCACAACCGCTGTC 59.201 55.000 0.00 0.00 35.47 3.51
4686 5127 3.800506 GCTGAATGAAGCACCATTATTGC 59.199 43.478 3.96 5.56 43.01 3.56
4853 5294 5.241662 ACTATCTGAACTTCCAAAGCTCAC 58.758 41.667 0.00 0.00 30.92 3.51
5105 5546 2.876219 GCTCTGCAGCCTTTGAGC 59.124 61.111 9.47 8.32 43.75 4.26
5315 5818 1.363744 GTGGCGCTGAGGATATATGC 58.636 55.000 7.64 0.00 0.00 3.14
5512 6016 3.064820 GGCATACCATACACAAAAGGTCG 59.935 47.826 0.00 0.00 35.62 4.79
5557 6061 4.946478 AGCACTAGGCCTACTAAAGATG 57.054 45.455 8.91 0.00 46.50 2.90
5579 6083 5.366482 ACAATACATACACATACAGCCCA 57.634 39.130 0.00 0.00 0.00 5.36
5606 6110 3.443037 CAACAGCTGCTACTGCTACTAG 58.557 50.000 15.27 0.00 41.60 2.57
5607 6111 2.166459 CCAACAGCTGCTACTGCTACTA 59.834 50.000 15.27 0.00 41.60 1.82
5638 6142 1.837439 AGCAATCAACCCGTCATCCTA 59.163 47.619 0.00 0.00 0.00 2.94
5646 6150 2.009774 CTCAGGTTAGCAATCAACCCG 58.990 52.381 0.72 0.00 45.55 5.28
5758 6274 2.091541 TCGATTCAAATTCCACCTGGC 58.908 47.619 0.00 0.00 34.44 4.85
5765 6285 4.563976 CAGCCACATTTCGATTCAAATTCC 59.436 41.667 0.00 0.00 0.00 3.01
5795 6315 2.601240 TCAGGTTTTGGATGGATGCA 57.399 45.000 0.00 0.00 0.00 3.96
5796 6316 3.447918 CATCAGGTTTTGGATGGATGC 57.552 47.619 0.00 0.00 37.77 3.91
5797 6317 2.761767 TGCATCAGGTTTTGGATGGATG 59.238 45.455 0.00 0.00 40.91 3.51
5798 6318 3.104519 TGCATCAGGTTTTGGATGGAT 57.895 42.857 0.00 0.00 40.91 3.41
5822 6342 6.899075 TCAGATTCAAATCCAAATCCATTCCT 59.101 34.615 0.00 0.00 36.04 3.36
5825 6345 7.990886 CCATTCAGATTCAAATCCAAATCCATT 59.009 33.333 0.00 0.00 36.04 3.16
5829 6349 6.579865 AGCCATTCAGATTCAAATCCAAATC 58.420 36.000 0.00 0.00 36.04 2.17
5844 6364 3.805267 GCCTCACGAGCCATTCAG 58.195 61.111 0.00 0.00 0.00 3.02
5857 6377 2.158696 ACAGCTAATTCATGGAGGCCTC 60.159 50.000 25.59 25.59 0.00 4.70
5888 6408 3.126858 TGGCTGCGTGATTGAAGTTTATC 59.873 43.478 0.00 0.00 0.00 1.75
5903 6423 1.139058 AGTAGGAATACCTTGGCTGCG 59.861 52.381 0.00 0.00 45.36 5.18
5904 6424 3.494573 GGTAGTAGGAATACCTTGGCTGC 60.495 52.174 0.00 0.00 45.36 5.25
5905 6425 3.071167 GGGTAGTAGGAATACCTTGGCTG 59.929 52.174 3.39 0.00 45.36 4.85
5907 6427 3.043418 TGGGTAGTAGGAATACCTTGGC 58.957 50.000 3.39 0.00 45.36 4.52
5908 6428 3.390311 GGTGGGTAGTAGGAATACCTTGG 59.610 52.174 3.39 0.00 45.36 3.61
5909 6429 3.390311 GGGTGGGTAGTAGGAATACCTTG 59.610 52.174 3.39 0.00 45.36 3.61
5913 6433 3.390311 CCAAGGGTGGGTAGTAGGAATAC 59.610 52.174 0.00 0.00 41.77 1.89
5914 6434 3.660959 CCAAGGGTGGGTAGTAGGAATA 58.339 50.000 0.00 0.00 41.77 1.75
5915 6435 2.488836 CCAAGGGTGGGTAGTAGGAAT 58.511 52.381 0.00 0.00 41.77 3.01
5916 6436 1.961133 CCAAGGGTGGGTAGTAGGAA 58.039 55.000 0.00 0.00 41.77 3.36
5917 6437 0.619543 GCCAAGGGTGGGTAGTAGGA 60.620 60.000 0.00 0.00 46.09 2.94
5924 6540 3.672503 GGATGGCCAAGGGTGGGT 61.673 66.667 10.96 0.00 46.09 4.51
5934 6550 2.501610 GACGAGGTCTGGATGGCC 59.498 66.667 0.00 0.00 41.82 5.36
5955 6572 1.001641 ACCCCTGATGCTGCTCAAC 60.002 57.895 0.00 0.00 0.00 3.18
5957 6574 2.672908 CACCCCTGATGCTGCTCA 59.327 61.111 0.00 1.50 0.00 4.26
6164 6781 3.605749 ATGTGGAACCAGGCGACGG 62.606 63.158 0.00 0.00 34.36 4.79
6165 6782 2.047274 ATGTGGAACCAGGCGACG 60.047 61.111 0.00 0.00 34.36 5.12
6166 6783 2.690778 GCATGTGGAACCAGGCGAC 61.691 63.158 0.00 0.00 32.01 5.19
6167 6784 2.359850 GCATGTGGAACCAGGCGA 60.360 61.111 0.00 0.00 32.01 5.54
6168 6785 2.360350 AGCATGTGGAACCAGGCG 60.360 61.111 0.00 0.00 46.14 5.52
6175 6792 0.111061 AAGGTGCTCAGCATGTGGAA 59.889 50.000 0.54 0.00 41.91 3.53
6212 6829 2.031245 CGACATGCAGGTTTTTGCTGTA 60.031 45.455 5.07 0.00 44.38 2.74
6223 6840 5.123186 TGAGGTTATTTTTACGACATGCAGG 59.877 40.000 0.00 0.00 0.00 4.85
6226 6843 7.855904 CCTATTGAGGTTATTTTTACGACATGC 59.144 37.037 0.00 0.00 38.16 4.06
6230 6847 8.815189 GTCTCCTATTGAGGTTATTTTTACGAC 58.185 37.037 0.00 0.00 44.19 4.34
6274 6891 7.118680 TGGAATGTTCGTAACAAGATTACCTTC 59.881 37.037 4.87 2.83 45.86 3.46
6393 7010 3.119708 GCTGCCTGTTGTCCTAGAAATTG 60.120 47.826 0.00 0.00 0.00 2.32
6424 7041 3.493176 GGTGCAATTCCAATATTCTGGCC 60.493 47.826 0.00 0.00 36.32 5.36
6425 7042 3.493176 GGGTGCAATTCCAATATTCTGGC 60.493 47.826 0.00 0.00 36.32 4.85
6426 7043 3.070015 GGGGTGCAATTCCAATATTCTGG 59.930 47.826 0.00 0.00 37.87 3.86
6427 7044 3.070015 GGGGGTGCAATTCCAATATTCTG 59.930 47.826 0.00 0.00 0.00 3.02
6428 7045 3.308401 GGGGGTGCAATTCCAATATTCT 58.692 45.455 0.00 0.00 0.00 2.40
6429 7046 3.037549 TGGGGGTGCAATTCCAATATTC 58.962 45.455 0.00 0.00 0.00 1.75
6430 7047 3.127791 TGGGGGTGCAATTCCAATATT 57.872 42.857 0.00 0.00 0.00 1.28
6431 7048 2.864885 TGGGGGTGCAATTCCAATAT 57.135 45.000 0.00 0.00 0.00 1.28
6432 7049 2.630889 TTGGGGGTGCAATTCCAATA 57.369 45.000 10.64 0.00 34.71 1.90
6433 7050 3.490814 TTGGGGGTGCAATTCCAAT 57.509 47.368 10.64 0.00 34.71 3.16


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

AutoCloner maintained by Alex Coulton.