Multiple sequence alignment - TraesCS5A01G233900

Loading Multiple Alignment...

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 TraesCS5A01G233900 chr5A 100.000 5829 0 0 1 5829 450169240 450163412 0.000000e+00 10765.0
1 TraesCS5A01G233900 chr5A 100.000 36 0 0 210 245 703349465 703349500 3.770000e-07 67.6
2 TraesCS5A01G233900 chr5D 92.838 5306 214 73 633 5829 349869019 349863771 0.000000e+00 7540.0
3 TraesCS5A01G233900 chr5D 90.306 196 6 4 326 521 349869257 349869075 1.620000e-60 244.0
4 TraesCS5A01G233900 chr5D 88.263 213 4 9 1 192 349869651 349869439 9.770000e-58 235.0
5 TraesCS5A01G233900 chr5D 98.333 60 1 0 252 311 349869304 349869245 7.990000e-19 106.0
6 TraesCS5A01G233900 chr5B 95.638 3026 112 10 2812 5828 410533453 410530439 0.000000e+00 4839.0
7 TraesCS5A01G233900 chr5B 92.795 1388 57 17 1444 2811 410534848 410533484 0.000000e+00 1969.0
8 TraesCS5A01G233900 chr5B 84.914 1160 83 40 326 1413 410536134 410534995 0.000000e+00 1088.0
9 TraesCS5A01G233900 chr5B 92.405 158 11 1 1 157 410536624 410536467 2.110000e-54 224.0
10 TraesCS5A01G233900 chr5B 95.238 63 3 0 249 311 410536184 410536122 3.720000e-17 100.0
11 TraesCS5A01G233900 chr5B 97.368 38 0 1 211 247 328245585 328245548 4.880000e-06 63.9
12 TraesCS5A01G233900 chr1D 89.372 1195 102 15 2892 4082 455130759 455129586 0.000000e+00 1480.0
13 TraesCS5A01G233900 chr1D 85.052 669 84 9 2240 2897 455143411 455142748 0.000000e+00 667.0
14 TraesCS5A01G233900 chr1D 88.743 382 34 2 1850 2222 455143881 455143500 5.320000e-125 459.0
15 TraesCS5A01G233900 chr1D 88.690 168 13 2 4160 4327 455129555 455129394 3.560000e-47 200.0
16 TraesCS5A01G233900 chr7B 86.532 1188 97 27 2217 3376 646036025 646034873 0.000000e+00 1249.0
17 TraesCS5A01G233900 chr7B 83.113 302 32 6 351 637 227819050 227818753 2.080000e-64 257.0
18 TraesCS5A01G233900 chr7B 89.516 124 12 1 3321 3444 646034869 646034747 7.820000e-34 156.0
19 TraesCS5A01G233900 chr6B 86.532 1188 94 28 2217 3376 124630925 124629776 0.000000e+00 1247.0
20 TraesCS5A01G233900 chr6B 85.392 753 71 20 3586 4327 481663763 481663039 0.000000e+00 745.0
21 TraesCS5A01G233900 chr6B 85.498 331 29 8 323 637 457271665 457271992 1.570000e-85 327.0
22 TraesCS5A01G233900 chr6B 88.710 124 13 1 3321 3444 124629772 124629650 3.640000e-32 150.0
23 TraesCS5A01G233900 chr3D 87.062 657 64 10 1850 2490 380254352 380255003 0.000000e+00 723.0
24 TraesCS5A01G233900 chr3D 90.833 120 9 1 2514 2633 501136391 501136274 6.050000e-35 159.0
25 TraesCS5A01G233900 chr2A 81.603 761 118 20 2637 3388 753425559 753426306 1.390000e-170 610.0
26 TraesCS5A01G233900 chr2A 100.000 36 0 0 209 244 739473100 739473135 3.770000e-07 67.6
27 TraesCS5A01G233900 chr1A 91.451 386 31 2 1850 2233 549126181 549125796 4.000000e-146 529.0
28 TraesCS5A01G233900 chr1A 91.818 110 7 2 2654 2761 549119559 549119450 1.010000e-32 152.0
29 TraesCS5A01G233900 chr4D 88.702 416 28 5 323 724 331661785 331661375 1.890000e-134 490.0
30 TraesCS5A01G233900 chr4D 91.667 60 4 1 253 311 331661829 331661770 1.350000e-11 82.4
31 TraesCS5A01G233900 chr4D 97.500 40 1 0 213 252 35523352 35523313 1.050000e-07 69.4
32 TraesCS5A01G233900 chr4D 100.000 36 0 0 210 245 506898075 506898110 3.770000e-07 67.6
33 TraesCS5A01G233900 chr2B 84.969 326 33 8 326 637 516320867 516320544 3.390000e-82 316.0
34 TraesCS5A01G233900 chr1B 85.660 265 25 4 384 637 121743460 121743722 3.460000e-67 267.0
35 TraesCS5A01G233900 chr4B 95.238 42 2 0 210 251 664320999 664320958 3.770000e-07 67.6
36 TraesCS5A01G233900 chr4B 97.222 36 1 0 209 244 41700707 41700672 1.750000e-05 62.1
37 TraesCS5A01G233900 chr7D 97.297 37 1 0 209 245 423458614 423458578 4.880000e-06 63.9
38 TraesCS5A01G233900 chr4A 91.304 46 3 1 203 247 424369474 424369519 1.750000e-05 62.1


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 TraesCS5A01G233900 chr5A 450163412 450169240 5828 True 10765.00 10765 100.0000 1 5829 1 chr5A.!!$R1 5828
1 TraesCS5A01G233900 chr5D 349863771 349869651 5880 True 2031.25 7540 92.4350 1 5829 4 chr5D.!!$R1 5828
2 TraesCS5A01G233900 chr5B 410530439 410536624 6185 True 1644.00 4839 92.1980 1 5828 5 chr5B.!!$R2 5827
3 TraesCS5A01G233900 chr1D 455129394 455130759 1365 True 840.00 1480 89.0310 2892 4327 2 chr1D.!!$R1 1435
4 TraesCS5A01G233900 chr1D 455142748 455143881 1133 True 563.00 667 86.8975 1850 2897 2 chr1D.!!$R2 1047
5 TraesCS5A01G233900 chr7B 646034747 646036025 1278 True 702.50 1249 88.0240 2217 3444 2 chr7B.!!$R2 1227
6 TraesCS5A01G233900 chr6B 481663039 481663763 724 True 745.00 745 85.3920 3586 4327 1 chr6B.!!$R1 741
7 TraesCS5A01G233900 chr6B 124629650 124630925 1275 True 698.50 1247 87.6210 2217 3444 2 chr6B.!!$R2 1227
8 TraesCS5A01G233900 chr3D 380254352 380255003 651 False 723.00 723 87.0620 1850 2490 1 chr3D.!!$F1 640
9 TraesCS5A01G233900 chr2A 753425559 753426306 747 False 610.00 610 81.6030 2637 3388 1 chr2A.!!$F2 751

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
299 499 0.035176 GGGGTACGGTGCAGTAACAA 59.965 55.0 3.82 0.0 36.08 2.83 F
533 733 0.187606 ACCTCCCCAAAGTCCCAAAC 59.812 55.0 0.00 0.0 0.00 2.93 F
2140 2578 0.257328 TGGTTGTCTGTTGGCTTCCA 59.743 50.0 0.00 0.0 0.00 3.53 F
2395 2915 0.884704 GCTCAAGGAACAACTCGCCA 60.885 55.0 0.00 0.0 0.00 5.69 F
3611 4238 1.305930 CCCCTGAGCAAACTAACGCC 61.306 60.0 0.00 0.0 0.00 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2006 2438 0.038744 CTTCCTTGGTGGCCACAGAT 59.961 55.0 35.78 0.0 30.78 2.90 R
2395 2915 0.035881 TCGAGTACAGGGACGACAGT 59.964 55.0 0.00 0.0 0.00 3.55 R
3831 4461 0.731417 CAAGCCAAGCCTCTTCATCG 59.269 55.0 0.00 0.0 0.00 3.84 R
4377 5016 2.030185 GCCGTTTTTCCTCCTCCTTTTC 60.030 50.0 0.00 0.0 0.00 2.29 R
5379 6018 0.688087 GGATGGTCGGAGGGAGAAGT 60.688 60.0 0.00 0.0 0.00 3.01 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
30 31 1.975680 TGTTCCAGTTCAGGTACCCTC 59.024 52.381 8.74 0.00 0.00 4.30
103 112 1.572085 CTTGGCAGCTCACGACAAGG 61.572 60.000 9.74 0.00 35.96 3.61
186 208 3.387050 ACCTCACTCGGTTAAAAGTGACT 59.613 43.478 10.84 0.00 45.18 3.41
192 225 8.114331 TCACTCGGTTAAAAGTGACTATCTAA 57.886 34.615 10.84 0.00 45.18 2.10
221 254 8.750515 ACTAGTACTCCCTTAGTGATCTAAAC 57.249 38.462 0.00 0.00 39.39 2.01
222 255 6.696441 AGTACTCCCTTAGTGATCTAAACG 57.304 41.667 0.00 0.00 39.39 3.60
225 258 6.793505 ACTCCCTTAGTGATCTAAACGATT 57.206 37.500 0.00 0.00 36.93 3.34
226 259 7.184067 ACTCCCTTAGTGATCTAAACGATTT 57.816 36.000 0.00 0.00 36.93 2.17
228 261 8.755977 ACTCCCTTAGTGATCTAAACGATTTTA 58.244 33.333 0.00 0.00 36.93 1.52
229 262 9.765795 CTCCCTTAGTGATCTAAACGATTTTAT 57.234 33.333 0.00 0.00 35.98 1.40
295 495 3.762247 GCGGGGTACGGTGCAGTA 61.762 66.667 0.00 0.00 44.51 2.74
296 496 2.972267 CGGGGTACGGTGCAGTAA 59.028 61.111 0.00 0.00 39.42 2.24
297 497 1.446618 CGGGGTACGGTGCAGTAAC 60.447 63.158 0.00 0.00 39.42 2.50
298 498 1.672898 GGGGTACGGTGCAGTAACA 59.327 57.895 3.82 0.00 36.08 2.41
299 499 0.035176 GGGGTACGGTGCAGTAACAA 59.965 55.000 3.82 0.00 36.08 2.83
300 500 1.150827 GGGTACGGTGCAGTAACAAC 58.849 55.000 3.82 0.00 36.08 3.32
301 501 1.150827 GGTACGGTGCAGTAACAACC 58.849 55.000 0.00 0.00 34.59 3.77
302 502 1.270465 GGTACGGTGCAGTAACAACCT 60.270 52.381 0.00 0.00 34.59 3.50
303 503 2.486918 GTACGGTGCAGTAACAACCTT 58.513 47.619 0.00 0.00 0.00 3.50
304 504 2.047002 ACGGTGCAGTAACAACCTTT 57.953 45.000 0.00 0.00 0.00 3.11
305 505 2.371306 ACGGTGCAGTAACAACCTTTT 58.629 42.857 0.00 0.00 0.00 2.27
306 506 2.098443 ACGGTGCAGTAACAACCTTTTG 59.902 45.455 0.00 0.00 38.83 2.44
376 576 1.279496 TGGCACCAGCTAGACTCAAT 58.721 50.000 0.00 0.00 41.70 2.57
533 733 0.187606 ACCTCCCCAAAGTCCCAAAC 59.812 55.000 0.00 0.00 0.00 2.93
578 782 3.467776 GCAACTGGCAAAAACCCAA 57.532 47.368 0.00 0.00 43.97 4.12
590 794 4.518249 CAAAAACCCAACCAGCCTAAAAA 58.482 39.130 0.00 0.00 0.00 1.94
592 796 2.009681 ACCCAACCAGCCTAAAAAGG 57.990 50.000 0.00 0.00 0.00 3.11
604 808 4.772624 AGCCTAAAAAGGTCCCAAATTCTC 59.227 41.667 0.00 0.00 0.00 2.87
671 876 1.195115 CGATCAACAGAAGGGGAGGA 58.805 55.000 0.00 0.00 0.00 3.71
679 884 4.576330 ACAGAAGGGGAGGAAAACATAG 57.424 45.455 0.00 0.00 0.00 2.23
682 887 1.681229 AGGGGAGGAAAACATAGCCA 58.319 50.000 0.00 0.00 0.00 4.75
719 929 3.560025 CCAGGAAAAGAGCTTAGCTTCCA 60.560 47.826 20.66 0.00 39.88 3.53
736 946 1.362237 TCCATTGATCCCAAAGGGCTT 59.638 47.619 0.00 0.00 43.94 4.35
790 1003 4.862641 TCTTTTCCTAATCCCAAGGAGG 57.137 45.455 0.00 0.00 43.90 4.30
918 1141 1.692762 GGGGTGGATAAGAGCCTGAGA 60.693 57.143 0.00 0.00 0.00 3.27
929 1152 1.276421 GAGCCTGAGACTTTGCTACCA 59.724 52.381 0.00 0.00 33.41 3.25
944 1167 1.614241 TACCAGCCTTTCCTCGCCTC 61.614 60.000 0.00 0.00 0.00 4.70
946 1169 2.284995 AGCCTTTCCTCGCCTCCT 60.285 61.111 0.00 0.00 0.00 3.69
948 1171 1.746991 GCCTTTCCTCGCCTCCTTG 60.747 63.158 0.00 0.00 0.00 3.61
953 1200 1.258445 TTCCTCGCCTCCTTGTCTCC 61.258 60.000 0.00 0.00 0.00 3.71
954 1201 1.684049 CCTCGCCTCCTTGTCTCCT 60.684 63.158 0.00 0.00 0.00 3.69
970 1217 1.194781 TCCTCTTTGAGCCGCTCCTT 61.195 55.000 17.81 0.00 0.00 3.36
1056 1310 2.297701 CTCAGAGAGCTCCAGGTACTC 58.702 57.143 10.93 0.00 34.60 2.59
1071 1326 0.966179 TACTCGCTGCTCACCTTTGA 59.034 50.000 0.00 0.00 0.00 2.69
1088 1343 0.740868 TGATTCGTGCCACTGCTAGC 60.741 55.000 8.10 8.10 38.71 3.42
1111 1366 5.587289 CAGTATTGAGTGAAGTAGAGCTCC 58.413 45.833 10.93 0.00 0.00 4.70
1130 1386 5.763204 AGCTCCGTTCTCTGAAAACAAATTA 59.237 36.000 0.00 0.00 0.00 1.40
1134 1390 6.206634 TCCGTTCTCTGAAAACAAATTATGCT 59.793 34.615 0.00 0.00 0.00 3.79
1159 1418 2.796227 CGTTTTGCCGCCTTCTTTC 58.204 52.632 0.00 0.00 0.00 2.62
1163 1422 2.507339 TTTGCCGCCTTCTTTCTTTG 57.493 45.000 0.00 0.00 0.00 2.77
1165 1424 0.823356 TGCCGCCTTCTTTCTTTGCT 60.823 50.000 0.00 0.00 0.00 3.91
1229 1506 0.527565 ACCCAATTCGCATGCTTCAC 59.472 50.000 17.13 0.00 0.00 3.18
1242 1519 4.678742 GCATGCTTCACTTCAGAAGAAAAC 59.321 41.667 17.56 6.80 46.18 2.43
1246 1524 5.647658 TGCTTCACTTCAGAAGAAAACTTCA 59.352 36.000 17.56 3.28 46.18 3.02
1251 1529 6.375455 TCACTTCAGAAGAAAACTTCAGCTTT 59.625 34.615 17.56 0.00 35.91 3.51
1258 1536 5.956068 AGAAAACTTCAGCTTTCATCTCC 57.044 39.130 5.68 0.00 33.77 3.71
1261 1539 4.906747 AACTTCAGCTTTCATCTCCTCT 57.093 40.909 0.00 0.00 0.00 3.69
1266 1544 6.665680 ACTTCAGCTTTCATCTCCTCTAGTAA 59.334 38.462 0.00 0.00 0.00 2.24
1287 1567 8.986477 AGTAATAGGTGAAAAATCATTGTTGC 57.014 30.769 0.00 0.00 0.00 4.17
1293 1573 5.294060 GGTGAAAAATCATTGTTGCAACTGT 59.706 36.000 28.61 15.21 0.00 3.55
1321 1611 4.576053 TGTTTGAGTGTCCTCTGTGATTTG 59.424 41.667 0.00 0.00 38.61 2.32
1322 1612 4.687901 TTGAGTGTCCTCTGTGATTTGA 57.312 40.909 0.00 0.00 38.61 2.69
1347 1637 6.039941 AGAGACTAGAGAATCGGGTGTTATTG 59.960 42.308 0.00 0.00 42.67 1.90
1353 1643 7.787725 AGAGAATCGGGTGTTATTGTATTTC 57.212 36.000 0.00 0.00 42.67 2.17
1406 1697 2.813908 GTTACACGGGCTGCGGAG 60.814 66.667 0.00 0.00 0.00 4.63
1629 2041 2.365293 GCAGTTGAGGTGGGACAAATTT 59.635 45.455 0.00 0.00 44.16 1.82
1631 2043 4.558697 GCAGTTGAGGTGGGACAAATTTAC 60.559 45.833 0.00 0.00 44.16 2.01
1633 2045 4.141018 AGTTGAGGTGGGACAAATTTACCT 60.141 41.667 8.96 8.96 44.16 3.08
1799 2220 5.898174 TGCATTCTTGAATCTATTGCCTTG 58.102 37.500 4.22 0.00 0.00 3.61
1816 2237 3.272581 CCTTGGCCTTGCATTTATTTGG 58.727 45.455 3.32 0.00 0.00 3.28
2006 2438 3.177884 AGGGTCCAGCTGCACCAA 61.178 61.111 27.91 0.00 33.91 3.67
2140 2578 0.257328 TGGTTGTCTGTTGGCTTCCA 59.743 50.000 0.00 0.00 0.00 3.53
2234 2739 7.048512 GTGGATTGCTACTAAATAGGACTTGT 58.951 38.462 0.00 0.00 29.57 3.16
2235 2740 7.553044 GTGGATTGCTACTAAATAGGACTTGTT 59.447 37.037 0.00 0.00 29.57 2.83
2294 2810 7.039363 ACTGGCTTATAGTAAATCTCTAGGCAG 60.039 40.741 17.29 17.29 45.54 4.85
2305 2821 1.555075 CTCTAGGCAGCACCACCTTAA 59.445 52.381 0.00 0.00 43.14 1.85
2312 2828 5.515106 AGGCAGCACCACCTTAATTTAATA 58.485 37.500 0.00 0.00 43.14 0.98
2371 2891 1.454201 GCAGAAAGACAAGGGCTACC 58.546 55.000 0.00 0.00 0.00 3.18
2395 2915 0.884704 GCTCAAGGAACAACTCGCCA 60.885 55.000 0.00 0.00 0.00 5.69
2451 2971 6.736794 GCAAGAAAGAAGAAAGGATCAAGCAA 60.737 38.462 0.00 0.00 0.00 3.91
2504 3024 2.654939 GCTCCGAGTTAAGTGAGCG 58.345 57.895 6.82 0.00 40.61 5.03
2507 3027 2.791849 GCTCCGAGTTAAGTGAGCGTAG 60.792 54.545 6.82 0.00 40.61 3.51
2556 3076 6.261603 GTCCAGCTGATGATGAACATGATTTA 59.738 38.462 17.39 0.00 39.56 1.40
2840 3394 2.500098 TGTGTATCAACTGTCTAGGGCC 59.500 50.000 0.00 0.00 0.00 5.80
2886 3440 2.191128 AGGATTGAGTGTTGACTGGC 57.809 50.000 0.00 0.00 30.16 4.85
2906 3461 4.142730 TGGCAATGTTTTCTTGTTTGCAAC 60.143 37.500 0.00 0.00 43.35 4.17
3181 3744 7.307751 CGGTGTTTTGTTATATGAGTTCTGTGT 60.308 37.037 0.00 0.00 0.00 3.72
3182 3745 8.995220 GGTGTTTTGTTATATGAGTTCTGTGTA 58.005 33.333 0.00 0.00 0.00 2.90
3224 3787 6.698008 ATCGATTGCCTATAGATGAGAGAG 57.302 41.667 0.00 0.00 28.75 3.20
3488 4114 2.421619 GAAGCTGAGGTTGAGAGGTTG 58.578 52.381 0.00 0.00 0.00 3.77
3611 4238 1.305930 CCCCTGAGCAAACTAACGCC 61.306 60.000 0.00 0.00 0.00 5.68
3632 4259 4.588899 CCCTGATTGATTCTGGTTGTACA 58.411 43.478 0.00 0.00 40.85 2.90
3831 4461 3.464111 AATAAATGGATTGCTGCCTGC 57.536 42.857 0.00 0.00 43.25 4.85
3872 4502 8.613482 GCTTGAAGAATATAACCAGGTAGTTTC 58.387 37.037 0.00 0.00 0.00 2.78
3976 4607 6.203530 CGCATGCCTTTTCTAGATAATTCTGA 59.796 38.462 13.15 0.00 33.17 3.27
4085 4716 3.485346 AAGGGCGGAAAAGGCACGA 62.485 57.895 0.00 0.00 39.29 4.35
4094 4725 3.462982 GGAAAAGGCACGAATTTTGGTT 58.537 40.909 0.00 0.00 0.00 3.67
4163 4802 4.446385 TCAGTTTAGTTCAACGAATGACCG 59.554 41.667 0.00 0.00 37.92 4.79
4258 4897 7.056635 CCATTCTTATATGATGGGGTATGTCC 58.943 42.308 0.00 0.00 0.00 4.02
4822 5461 4.656112 TCTGAACCAGAATCCCCTTCTATC 59.344 45.833 0.00 0.00 42.48 2.08
5087 5726 2.021723 GCACTGGGTTGGTTGACTTGA 61.022 52.381 0.00 0.00 0.00 3.02
5337 5976 9.357652 CATGTGAATTTCAGTACCCTTATTTTG 57.642 33.333 0.00 0.00 0.00 2.44
5375 6014 4.280174 AGAGTCCATGCCATAAAATGCATC 59.720 41.667 0.00 0.00 45.98 3.91
5379 6018 5.009911 GTCCATGCCATAAAATGCATCTGTA 59.990 40.000 0.00 0.00 45.98 2.74
5391 6031 1.067821 GCATCTGTACTTCTCCCTCCG 59.932 57.143 0.00 0.00 0.00 4.63
5399 6039 0.397816 CTTCTCCCTCCGACCATCCT 60.398 60.000 0.00 0.00 0.00 3.24
5400 6040 0.687757 TTCTCCCTCCGACCATCCTG 60.688 60.000 0.00 0.00 0.00 3.86
5414 6054 3.009916 ACCATCCTGTGCTTCTCAATTCT 59.990 43.478 0.00 0.00 0.00 2.40
5495 6136 2.143122 GCTCTTTCGGACAACATGACA 58.857 47.619 0.00 0.00 0.00 3.58
5551 6192 4.840271 TCATCACAGTGCATCAGATTCTT 58.160 39.130 0.00 0.00 0.00 2.52
5592 6233 2.094894 CCATGAGTTGTGTCAATCGAGC 59.905 50.000 0.00 0.00 0.00 5.03
5723 6367 1.213678 CCTGGAGGAAGATGAATGCCA 59.786 52.381 0.00 0.00 37.39 4.92
5746 6390 1.680651 CTCGCTCTGGTGAGGACCT 60.681 63.158 0.00 0.00 43.95 3.85
5759 6403 2.258591 GACCTGAGCGCTTCGTCA 59.741 61.111 13.26 3.70 0.00 4.35
5761 6405 2.259818 CCTGAGCGCTTCGTCACT 59.740 61.111 13.26 0.00 0.00 3.41
5806 6450 3.876274 TCGTCTCCTCATTTCTCCAAG 57.124 47.619 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.609208 ACCTGAACTGGAACATGCAC 58.391 50.000 0.00 0.00 38.20 4.57
30 31 4.087892 CCTGACCGTCCTGCCCAG 62.088 72.222 0.00 0.00 0.00 4.45
103 112 1.811645 GCAGCTCGATCTCCCCTACC 61.812 65.000 0.00 0.00 0.00 3.18
150 159 1.523938 GAGGTGGTTCCGGCTATGC 60.524 63.158 0.00 0.00 41.99 3.14
154 163 2.526873 AGTGAGGTGGTTCCGGCT 60.527 61.111 0.00 0.00 41.99 5.52
195 228 9.844257 GTTTAGATCACTAAGGGAGTACTAGTA 57.156 37.037 0.00 0.00 39.36 1.82
196 229 7.498570 CGTTTAGATCACTAAGGGAGTACTAGT 59.501 40.741 0.00 0.00 39.36 2.57
197 230 7.714377 TCGTTTAGATCACTAAGGGAGTACTAG 59.286 40.741 0.00 0.00 39.36 2.57
198 231 7.568349 TCGTTTAGATCACTAAGGGAGTACTA 58.432 38.462 0.00 0.00 39.36 1.82
199 232 6.421485 TCGTTTAGATCACTAAGGGAGTACT 58.579 40.000 0.00 0.00 39.36 2.73
202 235 6.793505 AATCGTTTAGATCACTAAGGGAGT 57.206 37.500 0.00 0.00 38.98 3.85
231 264 9.584008 CCATATAGTACCTCCTCTGTAAACTAA 57.416 37.037 0.00 0.00 0.00 2.24
232 265 7.668886 GCCATATAGTACCTCCTCTGTAAACTA 59.331 40.741 0.00 0.00 0.00 2.24
233 266 6.494146 GCCATATAGTACCTCCTCTGTAAACT 59.506 42.308 0.00 0.00 0.00 2.66
234 267 6.569994 CGCCATATAGTACCTCCTCTGTAAAC 60.570 46.154 0.00 0.00 0.00 2.01
236 269 5.008331 CGCCATATAGTACCTCCTCTGTAA 58.992 45.833 0.00 0.00 0.00 2.41
237 270 4.287845 TCGCCATATAGTACCTCCTCTGTA 59.712 45.833 0.00 0.00 0.00 2.74
240 273 4.594675 ATCGCCATATAGTACCTCCTCT 57.405 45.455 0.00 0.00 0.00 3.69
241 274 4.678309 GCAATCGCCATATAGTACCTCCTC 60.678 50.000 0.00 0.00 0.00 3.71
243 276 3.522553 GCAATCGCCATATAGTACCTCC 58.477 50.000 0.00 0.00 0.00 4.30
376 576 6.200665 CGGAATTTTGTTCAAGCTGAAATGAA 59.799 34.615 0.00 0.00 38.22 2.57
424 624 4.759096 GGCGTCGCAATGGTGTGC 62.759 66.667 20.50 0.00 41.32 4.57
436 636 7.309920 TGTCTTTCCTTTTATTTAATGGCGTC 58.690 34.615 0.00 0.00 32.43 5.19
533 733 2.419436 GGGAGGGTGGTTTGTTTGTTTG 60.419 50.000 0.00 0.00 0.00 2.93
578 782 1.154430 TGGGACCTTTTTAGGCTGGT 58.846 50.000 0.00 0.00 35.23 4.00
590 794 2.450476 GTGCATGAGAATTTGGGACCT 58.550 47.619 0.00 0.00 0.00 3.85
592 796 1.478105 GGGTGCATGAGAATTTGGGAC 59.522 52.381 0.00 0.00 0.00 4.46
604 808 2.825836 GAAGGGCGAGGGTGCATG 60.826 66.667 0.00 0.00 36.28 4.06
719 929 2.625087 CCAGAAGCCCTTTGGGATCAAT 60.625 50.000 6.85 0.00 42.68 2.57
751 961 5.764487 AAAGAAGAGGAGAAAAAGCACAG 57.236 39.130 0.00 0.00 0.00 3.66
790 1003 1.997256 TAGCCTCGTCCTCCTCTCCC 61.997 65.000 0.00 0.00 0.00 4.30
918 1141 1.425448 AGGAAAGGCTGGTAGCAAAGT 59.575 47.619 2.99 0.00 44.75 2.66
944 1167 1.674221 CGGCTCAAAGAGGAGACAAGG 60.674 57.143 0.00 0.00 43.43 3.61
946 1169 0.320771 GCGGCTCAAAGAGGAGACAA 60.321 55.000 0.00 0.00 43.43 3.18
948 1171 0.459411 GAGCGGCTCAAAGAGGAGAC 60.459 60.000 24.42 0.00 39.67 3.36
953 1200 0.801251 CAAAGGAGCGGCTCAAAGAG 59.199 55.000 29.33 12.31 31.08 2.85
954 1201 0.606401 CCAAAGGAGCGGCTCAAAGA 60.606 55.000 29.33 0.00 31.08 2.52
970 1217 2.818169 AAGCAGAGGACACCGCCAA 61.818 57.895 0.00 0.00 0.00 4.52
974 1227 0.951040 GAACCAAGCAGAGGACACCG 60.951 60.000 0.00 0.00 0.00 4.94
1047 1301 1.153745 GTGAGCAGCGAGTACCTGG 60.154 63.158 0.00 0.00 0.00 4.45
1056 1310 0.095935 CGAATCAAAGGTGAGCAGCG 59.904 55.000 0.00 0.00 37.14 5.18
1071 1326 0.742281 CTGCTAGCAGTGGCACGAAT 60.742 55.000 32.46 4.37 44.61 3.34
1088 1343 5.587289 GGAGCTCTACTTCACTCAATACTG 58.413 45.833 14.64 0.00 0.00 2.74
1111 1366 7.201182 CGAAGCATAATTTGTTTTCAGAGAACG 60.201 37.037 0.00 0.00 0.00 3.95
1159 1418 4.377839 TCACCGAGAGAAGATAGCAAAG 57.622 45.455 0.00 0.00 0.00 2.77
1163 1422 5.112686 ACAAATTCACCGAGAGAAGATAGC 58.887 41.667 0.00 0.00 0.00 2.97
1165 1424 6.936279 AGAACAAATTCACCGAGAGAAGATA 58.064 36.000 0.00 0.00 37.29 1.98
1242 1519 5.596836 ACTAGAGGAGATGAAAGCTGAAG 57.403 43.478 0.00 0.00 22.26 3.02
1246 1524 7.232534 CACCTATTACTAGAGGAGATGAAAGCT 59.767 40.741 0.00 0.00 36.23 3.74
1251 1529 9.488762 TTTTTCACCTATTACTAGAGGAGATGA 57.511 33.333 0.00 0.00 36.23 2.92
1266 1544 7.385752 CAGTTGCAACAATGATTTTTCACCTAT 59.614 33.333 30.11 0.88 0.00 2.57
1287 1567 4.034048 GGACACTCAAACACAGTACAGTTG 59.966 45.833 0.00 0.00 0.00 3.16
1293 1573 3.704566 ACAGAGGACACTCAAACACAGTA 59.295 43.478 0.00 0.00 46.44 2.74
1321 1611 3.547746 ACACCCGATTCTCTAGTCTCTC 58.452 50.000 0.00 0.00 0.00 3.20
1322 1612 3.655615 ACACCCGATTCTCTAGTCTCT 57.344 47.619 0.00 0.00 0.00 3.10
1347 1637 6.747280 CCTCGTTCCATGTCAAAATGAAATAC 59.253 38.462 0.00 0.00 0.00 1.89
1353 1643 2.819608 ACCCTCGTTCCATGTCAAAATG 59.180 45.455 0.00 0.00 0.00 2.32
1406 1697 0.168348 TACTCGCTCACGCTGACTTC 59.832 55.000 0.00 0.00 39.84 3.01
1572 1981 4.276926 GCCGAATAGAATCAAGGAAATGCT 59.723 41.667 0.00 0.00 0.00 3.79
1642 2054 4.608948 AACAGAGTGTTAGTTGAGAGGG 57.391 45.455 0.00 0.00 39.09 4.30
1643 2055 6.538742 TGAAAAACAGAGTGTTAGTTGAGAGG 59.461 38.462 0.00 0.00 40.14 3.69
1644 2056 7.402640 GTGAAAAACAGAGTGTTAGTTGAGAG 58.597 38.462 0.00 0.00 40.14 3.20
1645 2057 6.315393 GGTGAAAAACAGAGTGTTAGTTGAGA 59.685 38.462 0.00 0.00 40.14 3.27
1646 2058 6.316390 AGGTGAAAAACAGAGTGTTAGTTGAG 59.684 38.462 0.00 0.00 40.14 3.02
1655 2067 5.215160 GCATTACAGGTGAAAAACAGAGTG 58.785 41.667 0.00 0.00 0.00 3.51
1735 2148 2.774234 CTGATTCATGTACTCCCCAGGT 59.226 50.000 0.00 0.00 0.00 4.00
1738 2151 1.490490 GCCTGATTCATGTACTCCCCA 59.510 52.381 0.00 0.00 0.00 4.96
1787 2200 1.342275 TGCAAGGCCAAGGCAATAGAT 60.342 47.619 13.87 0.00 44.11 1.98
1816 2237 1.477700 TGCTTCAACCTTATGCATGGC 59.522 47.619 10.16 0.69 0.00 4.40
2006 2438 0.038744 CTTCCTTGGTGGCCACAGAT 59.961 55.000 35.78 0.00 30.78 2.90
2140 2578 3.421567 GGAACCAAGCAACCACTCT 57.578 52.632 0.00 0.00 0.00 3.24
2342 2858 1.525765 TCTTTCTGCGCAAGTGCCA 60.526 52.632 13.05 0.00 41.68 4.92
2371 2891 1.795286 GAGTTGTTCCTTGAGCGACAG 59.205 52.381 0.00 0.00 31.02 3.51
2395 2915 0.035881 TCGAGTACAGGGACGACAGT 59.964 55.000 0.00 0.00 0.00 3.55
2451 2971 8.947115 TCAATCTGTGATCGAATATCGTAGTAT 58.053 33.333 0.00 0.00 41.35 2.12
2504 3024 7.985184 TGTTTACATGATCACCCTTATCACTAC 59.015 37.037 0.00 0.00 36.24 2.73
2507 3027 6.823689 ACTGTTTACATGATCACCCTTATCAC 59.176 38.462 0.00 0.00 36.24 3.06
2540 3060 7.716560 TCCTTGTCGATAAATCATGTTCATCAT 59.283 33.333 0.00 0.00 37.22 2.45
2840 3394 7.772332 AGTAACTTAAATTAGATGACCAGCG 57.228 36.000 0.00 0.00 0.00 5.18
3018 3573 5.121811 GCTCAACACCATTCTGATGTAGAT 58.878 41.667 0.00 0.00 34.80 1.98
3182 3745 9.888878 CAATCGATTGCTTGAGAATGTATTATT 57.111 29.630 24.15 0.00 0.00 1.40
3224 3787 5.431765 AGGTGACATAATGACTCCATTGTC 58.568 41.667 0.00 0.00 42.55 3.18
3488 4114 7.703328 TCAATCTGTTGGTTTTAAGTTCTGTC 58.297 34.615 0.00 0.00 35.99 3.51
3573 4199 1.085091 GCTGTGCTGAGATCAGGTTG 58.915 55.000 11.63 0.00 43.94 3.77
3611 4238 6.764308 AATGTACAACCAGAATCAATCAGG 57.236 37.500 0.00 0.00 40.45 3.86
3831 4461 0.731417 CAAGCCAAGCCTCTTCATCG 59.269 55.000 0.00 0.00 0.00 3.84
3936 4567 4.484872 GCGGGGGCAGGTTAGTCC 62.485 72.222 0.00 0.00 0.00 3.85
4094 4725 9.238368 CATCAAAACCTACCTGGAATTTTAGTA 57.762 33.333 0.00 0.00 39.71 1.82
4163 4802 7.609960 TGTCCATCATAGCTGAGAAAGATATC 58.390 38.462 0.00 0.00 35.25 1.63
4258 4897 5.053145 GCTTACCCTACTGATCAGATTGTG 58.947 45.833 29.27 14.48 0.00 3.33
4377 5016 2.030185 GCCGTTTTTCCTCCTCCTTTTC 60.030 50.000 0.00 0.00 0.00 2.29
4519 5158 1.151668 TCGCTTCTTTCTCTGCAAGC 58.848 50.000 0.00 0.00 38.31 4.01
5087 5726 6.145371 CGAAACATCAATTTCAAACCCGAAAT 59.855 34.615 0.00 0.00 45.35 2.17
5132 5771 8.258007 CCACTCACTACATCTTTCACCTAATTA 58.742 37.037 0.00 0.00 0.00 1.40
5133 5772 7.106239 CCACTCACTACATCTTTCACCTAATT 58.894 38.462 0.00 0.00 0.00 1.40
5248 5887 9.687210 GAAGTATGATATGTTACATCCGTACAA 57.313 33.333 21.02 0.31 0.00 2.41
5317 5956 7.232534 TGCTCACAAAATAAGGGTACTGAAATT 59.767 33.333 0.00 0.00 0.00 1.82
5337 5976 1.803555 GACTCTGCCTTTTCTGCTCAC 59.196 52.381 0.00 0.00 0.00 3.51
5375 6014 1.104630 GGTCGGAGGGAGAAGTACAG 58.895 60.000 0.00 0.00 0.00 2.74
5379 6018 0.688087 GGATGGTCGGAGGGAGAAGT 60.688 60.000 0.00 0.00 0.00 3.01
5391 6031 2.479566 TTGAGAAGCACAGGATGGTC 57.520 50.000 0.00 0.00 43.62 4.02
5399 6039 2.555325 CCAAGCAGAATTGAGAAGCACA 59.445 45.455 0.00 0.00 31.55 4.57
5400 6040 2.816087 TCCAAGCAGAATTGAGAAGCAC 59.184 45.455 0.00 0.00 31.55 4.40
5480 6121 2.143122 GCTTCTGTCATGTTGTCCGAA 58.857 47.619 0.00 0.00 0.00 4.30
5487 6128 8.114331 TCTAATCAATTTGCTTCTGTCATGTT 57.886 30.769 0.00 0.00 0.00 2.71
5495 6136 8.804912 AGTTCTCATCTAATCAATTTGCTTCT 57.195 30.769 0.00 0.00 0.00 2.85
5522 6163 5.761726 TCTGATGCACTGTGATGATTATTCC 59.238 40.000 12.86 0.00 0.00 3.01
5551 6192 1.271871 GGATGGGACCACACATGACAA 60.272 52.381 0.00 0.00 40.57 3.18
5735 6379 3.695606 GCGCTCAGGTCCTCACCA 61.696 66.667 0.00 0.00 46.68 4.17
5736 6380 2.844072 GAAGCGCTCAGGTCCTCACC 62.844 65.000 12.06 0.00 44.19 4.02
5746 6390 2.049156 CCAGTGACGAAGCGCTCA 60.049 61.111 12.06 0.32 0.00 4.26
5759 6403 1.625818 AGGAGATCGAGTTTTGCCAGT 59.374 47.619 0.00 0.00 0.00 4.00
5761 6405 1.066143 GGAGGAGATCGAGTTTTGCCA 60.066 52.381 0.00 0.00 0.00 4.92


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

AutoCloner maintained by Alex Coulton.