Multiple sequence alignment - TraesCS2B01G306300

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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 TraesCS2B01G306300 chr2B 100.000 7398 0 0 1 7398 437007852 437000455 0.000000e+00 13662.0
1 TraesCS2B01G306300 chr2A 94.937 5096 167 35 631 5681 498104573 498099524 0.000000e+00 7897.0
2 TraesCS2B01G306300 chr2A 96.443 984 18 5 5843 6815 498099121 498098144 0.000000e+00 1607.0
3 TraesCS2B01G306300 chr2A 87.656 640 41 19 1 624 498105297 498104680 0.000000e+00 710.0
4 TraesCS2B01G306300 chr2A 93.870 261 16 0 7130 7390 498097590 498097330 1.930000e-105 394.0
5 TraesCS2B01G306300 chr2A 97.714 175 3 1 5681 5854 498099444 498099270 4.340000e-77 300.0
6 TraesCS2B01G306300 chr2A 95.266 169 6 1 6817 6985 498098003 498097837 4.400000e-67 267.0
7 TraesCS2B01G306300 chr2A 92.188 64 3 1 6985 7048 498097790 498097729 1.020000e-13 89.8
8 TraesCS2B01G306300 chr2D 95.732 4850 104 42 631 5431 368008750 368003955 0.000000e+00 7714.0
9 TraesCS2B01G306300 chr2D 98.133 1125 15 2 5423 6544 368003765 368002644 0.000000e+00 1956.0
10 TraesCS2B01G306300 chr2D 87.344 640 46 18 1 624 368009859 368009239 0.000000e+00 701.0
11 TraesCS2B01G306300 chr2D 96.030 403 5 5 6591 6985 368002652 368002253 0.000000e+00 645.0
12 TraesCS2B01G306300 chr2D 93.765 417 18 6 6985 7398 368002206 368001795 2.930000e-173 619.0
13 TraesCS2B01G306300 chr6A 87.356 87 10 1 7279 7365 47883698 47883783 1.700000e-16 99.0


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 TraesCS2B01G306300 chr2B 437000455 437007852 7397 True 13662.000000 13662 100.000000 1 7398 1 chr2B.!!$R1 7397
1 TraesCS2B01G306300 chr2A 498097330 498105297 7967 True 1609.257143 7897 94.010571 1 7390 7 chr2A.!!$R1 7389
2 TraesCS2B01G306300 chr2D 368001795 368009859 8064 True 2327.000000 7714 94.200800 1 7398 5 chr2D.!!$R1 7397

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
441 457 0.688487 TCTGGGACAAACCTTACGGG 59.312 55.000 0.00 0.0 38.70 5.28 F
1154 1687 0.530870 GACCCATCTACTTCTGGCGC 60.531 60.000 0.00 0.0 0.00 6.53 F
2053 2589 0.037512 CTGGTGTGTGCTCTCTCCAG 60.038 60.000 18.80 18.8 40.15 3.86 F
2352 2888 0.389948 GGGTGTAGGCAAGTCAGACG 60.390 60.000 0.00 0.0 0.00 4.18 F
2572 3108 1.882167 GAGAGAGGACAGCATGCGC 60.882 63.158 13.01 0.0 42.53 6.09 F
3745 4281 1.623834 CCCTAGAGAAGCCCTGGAAGT 60.624 57.143 0.00 0.0 0.00 3.01 F
4226 4762 1.960417 TCGTTCAAGTGTCATTGGCA 58.040 45.000 0.00 0.0 0.00 4.92 F
5404 5959 3.214696 AGTCTGGTGGTTGAAGAAAGG 57.785 47.619 0.00 0.0 0.00 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1813 2349 0.318441 TTGAGCTCTACGTTGCTGCT 59.682 50.000 16.19 14.0 39.91 4.24 R
2857 3393 1.065199 TGCTTGGCTAGGGACTTCATG 60.065 52.381 0.00 0.0 41.75 3.07 R
2957 3493 2.817258 TCCAAATAACAAGGACTTGGCG 59.183 45.455 15.72 0.0 44.45 5.69 R
3745 4281 3.382865 TGTGTTAGTTGCTCCAAATGCAA 59.617 39.130 0.00 0.0 46.48 4.08 R
4524 5076 6.150474 GTTACTAAACATAGCAGGAGGCAAAA 59.850 38.462 0.00 0.0 39.25 2.44 R
5363 5918 8.085296 CAGACTACAATATTCTGGACAGGATAC 58.915 40.741 2.50 0.0 32.02 2.24 R
5755 6588 1.021390 GCTGACCACTCCATTGACCG 61.021 60.000 0.00 0.0 0.00 4.79 R
7233 8529 1.191489 TCGTCACATCCAAGGCCTCA 61.191 55.000 5.23 0.0 0.00 3.86 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
116 117 2.680339 GGCAAGCTCAAATCTGTACTCC 59.320 50.000 0.00 0.00 0.00 3.85
149 150 6.539826 TCGATGATAAGTTGTGCATGAAGATT 59.460 34.615 0.00 0.00 0.00 2.40
159 160 1.133853 GCATGAAGATTGGAGAGGGCT 60.134 52.381 0.00 0.00 0.00 5.19
161 162 0.826715 TGAAGATTGGAGAGGGCTCG 59.173 55.000 0.00 0.00 42.25 5.03
215 216 2.224475 GGCATGTGGAGACAGATATGCT 60.224 50.000 0.00 0.00 43.50 3.79
241 255 1.739035 GCACAAGTAGGCATCAGCGTA 60.739 52.381 0.00 0.00 43.41 4.42
249 263 3.045601 AGGCATCAGCGTACCATATTC 57.954 47.619 0.00 0.00 43.41 1.75
263 277 5.643421 ACCATATTCCTGCTGAAGAGAAT 57.357 39.130 0.00 5.18 36.14 2.40
264 278 6.753913 ACCATATTCCTGCTGAAGAGAATA 57.246 37.500 8.24 8.24 36.14 1.75
265 279 6.529220 ACCATATTCCTGCTGAAGAGAATAC 58.471 40.000 8.06 0.00 36.14 1.89
286 302 4.579869 ACATTAGCCTGGTAACTGAAGTG 58.420 43.478 0.00 0.00 37.83 3.16
301 317 3.566261 GTGCACCACACCAGATCG 58.434 61.111 5.22 0.00 44.02 3.69
319 335 1.144057 GCCGCAGCATACCTACACT 59.856 57.895 0.00 0.00 39.53 3.55
324 340 3.318017 CGCAGCATACCTACACTTATCC 58.682 50.000 0.00 0.00 0.00 2.59
328 344 5.765182 GCAGCATACCTACACTTATCCATTT 59.235 40.000 0.00 0.00 0.00 2.32
329 345 6.934645 GCAGCATACCTACACTTATCCATTTA 59.065 38.462 0.00 0.00 0.00 1.40
330 346 7.095187 GCAGCATACCTACACTTATCCATTTAC 60.095 40.741 0.00 0.00 0.00 2.01
355 371 9.330063 ACGAATAATGATATTTCTGCTGAAGAA 57.670 29.630 6.13 0.00 43.37 2.52
367 383 7.559590 TTCTGCTGAAGAAAAGATATTAGCC 57.440 36.000 1.33 0.00 42.09 3.93
368 384 6.893583 TCTGCTGAAGAAAAGATATTAGCCT 58.106 36.000 0.00 0.00 29.54 4.58
369 385 6.765036 TCTGCTGAAGAAAAGATATTAGCCTG 59.235 38.462 0.00 0.00 29.54 4.85
370 386 5.824624 TGCTGAAGAAAAGATATTAGCCTGG 59.175 40.000 0.00 0.00 0.00 4.45
384 400 2.069776 CCTGGTTCCTGAAGAGGCA 58.930 57.895 0.00 0.00 39.57 4.75
403 419 1.521457 CTAATGCCGCGCTTCTCCA 60.521 57.895 5.56 0.00 0.00 3.86
436 452 1.766496 TCGAGTTCTGGGACAAACCTT 59.234 47.619 0.00 0.00 38.70 3.50
441 457 0.688487 TCTGGGACAAACCTTACGGG 59.312 55.000 0.00 0.00 38.70 5.28
471 487 4.873827 AGTTTGTTCGAGTGCTAAACTTCA 59.126 37.500 0.00 0.00 40.07 3.02
475 491 5.806286 TGTTCGAGTGCTAAACTTCAAAAG 58.194 37.500 0.00 0.00 40.07 2.27
478 494 7.064847 TGTTCGAGTGCTAAACTTCAAAAGTAA 59.935 33.333 0.00 0.00 41.91 2.24
504 520 7.775397 ATAAAATTTTATGAGTGCACCATGC 57.225 32.000 20.14 9.55 36.61 4.06
526 542 3.382546 CCACTGCATTTATTTGGCTAGCT 59.617 43.478 15.72 0.00 0.00 3.32
598 614 7.283633 CAGAATGTACATGTATAATGTGACGC 58.716 38.462 9.63 0.00 33.76 5.19
599 615 6.983890 AGAATGTACATGTATAATGTGACGCA 59.016 34.615 9.63 0.00 33.76 5.24
600 616 7.494298 AGAATGTACATGTATAATGTGACGCAA 59.506 33.333 9.63 0.00 33.76 4.85
601 617 6.582437 TGTACATGTATAATGTGACGCAAG 57.418 37.500 9.18 0.00 37.07 4.01
624 640 6.492007 GCACACAGCTGCTTGATTATATAT 57.508 37.500 15.27 0.00 41.15 0.86
625 641 7.601073 GCACACAGCTGCTTGATTATATATA 57.399 36.000 15.27 0.00 41.15 0.86
626 642 8.206325 GCACACAGCTGCTTGATTATATATAT 57.794 34.615 15.27 0.00 41.15 0.86
627 643 8.671921 GCACACAGCTGCTTGATTATATATATT 58.328 33.333 15.27 0.00 41.15 1.28
628 644 9.983804 CACACAGCTGCTTGATTATATATATTG 57.016 33.333 15.27 0.23 0.00 1.90
629 645 9.948964 ACACAGCTGCTTGATTATATATATTGA 57.051 29.630 15.27 0.00 0.00 2.57
653 1152 6.983474 AAAAGGGTTTCATGTTTCAGTTTG 57.017 33.333 0.00 0.00 0.00 2.93
672 1171 2.198406 TGCTCGGTGTTATGTATTCGC 58.802 47.619 0.00 0.00 0.00 4.70
673 1172 2.198406 GCTCGGTGTTATGTATTCGCA 58.802 47.619 0.00 0.00 0.00 5.10
714 1213 4.058124 GTTGAGGCAATTTTCAAAGGTCC 58.942 43.478 0.00 0.00 35.29 4.46
737 1236 3.471354 CTCTCACAGCATCATGGCA 57.529 52.632 0.00 0.00 35.83 4.92
739 1238 0.906775 TCTCACAGCATCATGGCAGA 59.093 50.000 0.00 0.00 35.83 4.26
753 1259 2.747396 GGCAGATTGGCAATGTTGAA 57.253 45.000 19.07 0.00 43.14 2.69
759 1265 5.870978 GCAGATTGGCAATGTTGAATTAACT 59.129 36.000 19.07 1.03 40.05 2.24
763 1269 7.599998 AGATTGGCAATGTTGAATTAACTTGTC 59.400 33.333 19.07 0.00 40.05 3.18
812 1326 4.020617 CCCAGCCAAGGAGTCGCA 62.021 66.667 0.00 0.00 0.00 5.10
813 1327 2.743928 CCAGCCAAGGAGTCGCAC 60.744 66.667 0.00 0.00 0.00 5.34
851 1365 7.182206 ACACAACTCCCTTAGTTCCTGTATATT 59.818 37.037 0.00 0.00 45.64 1.28
856 1370 8.925338 ACTCCCTTAGTTCCTGTATATTTACTG 58.075 37.037 0.00 0.00 33.35 2.74
857 1371 7.732996 TCCCTTAGTTCCTGTATATTTACTGC 58.267 38.462 0.00 0.00 0.00 4.40
858 1372 7.567622 TCCCTTAGTTCCTGTATATTTACTGCT 59.432 37.037 0.00 0.00 0.00 4.24
879 1394 9.593134 ACTGCTAGTTCTTAATCTTCATTACAG 57.407 33.333 0.00 0.00 0.00 2.74
903 1418 2.326428 AGTCCGTTTTCCCTCTCTTCA 58.674 47.619 0.00 0.00 0.00 3.02
908 1423 3.254892 CGTTTTCCCTCTCTTCACTAGC 58.745 50.000 0.00 0.00 0.00 3.42
909 1424 3.306088 CGTTTTCCCTCTCTTCACTAGCA 60.306 47.826 0.00 0.00 0.00 3.49
910 1425 4.621747 CGTTTTCCCTCTCTTCACTAGCAT 60.622 45.833 0.00 0.00 0.00 3.79
912 1427 4.478206 TTCCCTCTCTTCACTAGCATTG 57.522 45.455 0.00 0.00 0.00 2.82
914 1429 2.768527 CCCTCTCTTCACTAGCATTGGA 59.231 50.000 0.00 0.00 0.00 3.53
915 1430 3.390639 CCCTCTCTTCACTAGCATTGGAT 59.609 47.826 0.00 0.00 0.00 3.41
916 1431 4.502950 CCCTCTCTTCACTAGCATTGGATC 60.503 50.000 0.00 0.00 0.00 3.36
917 1432 4.344679 CCTCTCTTCACTAGCATTGGATCT 59.655 45.833 0.00 0.00 0.00 2.75
918 1433 5.163322 CCTCTCTTCACTAGCATTGGATCTT 60.163 44.000 0.00 0.00 0.00 2.40
920 1435 6.810911 TCTCTTCACTAGCATTGGATCTTAC 58.189 40.000 0.00 0.00 0.00 2.34
921 1436 6.609212 TCTCTTCACTAGCATTGGATCTTACT 59.391 38.462 0.00 0.00 0.00 2.24
922 1437 7.780271 TCTCTTCACTAGCATTGGATCTTACTA 59.220 37.037 0.00 0.00 0.00 1.82
923 1438 8.484214 TCTTCACTAGCATTGGATCTTACTAT 57.516 34.615 0.00 0.00 0.00 2.12
924 1439 8.363390 TCTTCACTAGCATTGGATCTTACTATG 58.637 37.037 0.00 0.00 0.00 2.23
925 1440 6.459066 TCACTAGCATTGGATCTTACTATGC 58.541 40.000 8.17 8.17 41.35 3.14
929 1444 4.645535 GCATTGGATCTTACTATGCTGGA 58.354 43.478 8.73 0.00 38.75 3.86
930 1445 4.694509 GCATTGGATCTTACTATGCTGGAG 59.305 45.833 8.73 0.00 38.75 3.86
931 1446 4.963318 TTGGATCTTACTATGCTGGAGG 57.037 45.455 0.00 0.00 0.00 4.30
932 1447 4.199002 TGGATCTTACTATGCTGGAGGA 57.801 45.455 0.00 0.00 0.00 3.71
933 1448 4.155709 TGGATCTTACTATGCTGGAGGAG 58.844 47.826 0.00 0.00 0.00 3.69
934 1449 4.140924 TGGATCTTACTATGCTGGAGGAGA 60.141 45.833 0.00 0.00 0.00 3.71
935 1450 4.462483 GGATCTTACTATGCTGGAGGAGAG 59.538 50.000 0.00 0.00 0.00 3.20
936 1451 4.797912 TCTTACTATGCTGGAGGAGAGA 57.202 45.455 0.00 0.00 0.00 3.10
937 1452 4.724399 TCTTACTATGCTGGAGGAGAGAG 58.276 47.826 0.00 0.00 0.00 3.20
952 1467 3.259625 GGAGAGAGGGGCATATTCTGTAC 59.740 52.174 0.00 0.00 0.00 2.90
956 1471 5.540719 AGAGAGGGGCATATTCTGTACTAAC 59.459 44.000 0.00 0.00 0.00 2.34
985 1500 2.821307 GAGTACGTACTCCGGAACAG 57.179 55.000 35.45 0.00 45.33 3.16
989 1504 3.569701 AGTACGTACTCCGGAACAGAAAA 59.430 43.478 22.45 0.00 42.24 2.29
990 1505 3.672767 ACGTACTCCGGAACAGAAAAT 57.327 42.857 5.23 0.00 42.24 1.82
992 1507 4.383173 ACGTACTCCGGAACAGAAAATTT 58.617 39.130 5.23 0.00 42.24 1.82
993 1508 4.450080 ACGTACTCCGGAACAGAAAATTTC 59.550 41.667 5.23 0.00 42.24 2.17
994 1509 4.449743 CGTACTCCGGAACAGAAAATTTCA 59.550 41.667 5.23 0.00 0.00 2.69
995 1510 5.121768 CGTACTCCGGAACAGAAAATTTCAT 59.878 40.000 5.23 0.00 0.00 2.57
996 1511 5.376854 ACTCCGGAACAGAAAATTTCATG 57.623 39.130 5.23 6.14 0.00 3.07
1030 1563 7.283580 CGGGAACAGGTACAAAATATAAATCCA 59.716 37.037 0.00 0.00 0.00 3.41
1085 1618 0.845102 TTCTCCCCTTCCCAGTTCCC 60.845 60.000 0.00 0.00 0.00 3.97
1154 1687 0.530870 GACCCATCTACTTCTGGCGC 60.531 60.000 0.00 0.00 0.00 6.53
1203 1739 2.103340 GCCGAGTCGCTCTTCCTC 59.897 66.667 7.12 0.00 0.00 3.71
1736 2272 1.799994 GCGGCAACAAGAATGCAATTT 59.200 42.857 0.00 0.00 45.60 1.82
1744 2280 6.795114 GCAACAAGAATGCAATTTTGATCAAG 59.205 34.615 11.68 0.00 43.29 3.02
1759 2295 3.327464 TGATCAAGACAGATTGGGACACA 59.673 43.478 0.00 0.00 39.29 3.72
1782 2318 5.924475 AACCTGATGTTACAAACGAAGAG 57.076 39.130 0.00 0.00 34.69 2.85
1813 2349 2.020720 TGCCTCAAAGAAGCAAACGAA 58.979 42.857 0.00 0.00 32.56 3.85
1821 2357 1.123655 GAAGCAAACGAAGCAGCAAC 58.876 50.000 0.00 0.00 0.00 4.17
1875 2411 2.821366 CAGCATCACACGGAGGGC 60.821 66.667 0.00 0.00 0.00 5.19
1887 2423 1.112315 CGGAGGGCTGCTACTCAGAT 61.112 60.000 20.43 0.00 45.72 2.90
1995 2531 1.490490 CTCCACCCTATTGGCAGCTTA 59.510 52.381 0.00 0.00 37.83 3.09
2053 2589 0.037512 CTGGTGTGTGCTCTCTCCAG 60.038 60.000 18.80 18.80 40.15 3.86
2055 2591 1.257743 GGTGTGTGCTCTCTCCAGTA 58.742 55.000 4.54 0.00 0.00 2.74
2089 2625 5.439721 CCCTTTGTCATGTTGAGATCCATA 58.560 41.667 0.00 0.00 0.00 2.74
2287 2823 3.118920 AGTGTAAGTGGCAACCCAAAAAC 60.119 43.478 0.00 0.00 44.33 2.43
2352 2888 0.389948 GGGTGTAGGCAAGTCAGACG 60.390 60.000 0.00 0.00 0.00 4.18
2363 2899 2.995939 CAAGTCAGACGCAGCATCTTAA 59.004 45.455 0.00 0.00 0.00 1.85
2377 2913 6.532657 GCAGCATCTTAATTTGCAGTATTTGT 59.467 34.615 11.13 0.00 41.35 2.83
2503 3039 5.649831 AGAAGTGATAGCATTTGGAAAGGAC 59.350 40.000 0.00 0.00 0.00 3.85
2572 3108 1.882167 GAGAGAGGACAGCATGCGC 60.882 63.158 13.01 0.00 42.53 6.09
2957 3493 4.081309 TGCTTCAGTACCAGGGTTGTATAC 60.081 45.833 0.00 0.00 0.00 1.47
3169 3705 8.833231 TTGTCCTAACTTCTAGTTCTTCATTG 57.167 34.615 0.00 0.00 39.51 2.82
3172 3708 9.145865 GTCCTAACTTCTAGTTCTTCATTGAAG 57.854 37.037 18.49 18.49 39.51 3.02
3502 4038 6.071616 GGAAGGTACATGCAAACCTCAAAATA 60.072 38.462 16.50 0.00 45.51 1.40
3520 4056 9.341899 CTCAAAATATGTAACTTTTACTGCACC 57.658 33.333 0.00 0.00 0.00 5.01
3538 4074 3.445096 GCACCTTAACTTGCATCCTGATT 59.555 43.478 0.00 0.00 38.68 2.57
3745 4281 1.623834 CCCTAGAGAAGCCCTGGAAGT 60.624 57.143 0.00 0.00 0.00 3.01
4226 4762 1.960417 TCGTTCAAGTGTCATTGGCA 58.040 45.000 0.00 0.00 0.00 4.92
4441 4993 6.255887 CGTTTATTCTTCTTGCCTCTCGTATT 59.744 38.462 0.00 0.00 0.00 1.89
4531 5083 7.173390 GTGACTGTCTAAGTTAATCTTTTGCCT 59.827 37.037 9.51 0.00 40.07 4.75
4550 5102 4.224147 TGCCTCCTGCTATGTTTAGTAACA 59.776 41.667 0.00 0.00 43.86 2.41
4698 5251 8.130671 AGCCAATCATCTTAATATGGGATTTG 57.869 34.615 1.41 2.16 0.00 2.32
5253 5808 3.424703 AGCTGTGCACAATGAAATAGGT 58.575 40.909 21.98 9.13 0.00 3.08
5404 5959 3.214696 AGTCTGGTGGTTGAAGAAAGG 57.785 47.619 0.00 0.00 0.00 3.11
5672 6426 5.658190 GGGAGGATGATGATTCAAGGAAAAA 59.342 40.000 0.00 0.00 34.96 1.94
5755 6588 6.659242 TGAAAATAATTCTCTCACCCTCAACC 59.341 38.462 0.00 0.00 0.00 3.77
6163 7157 0.537143 TTGTCATCCCTGCACCACAC 60.537 55.000 0.00 0.00 0.00 3.82
6328 7325 5.104941 TGACTGTTGTCCTGAAGAGAAAGAA 60.105 40.000 0.00 0.00 42.28 2.52
6471 7468 4.837093 TTGGATAAGAACGTCCAAGGAT 57.163 40.909 2.88 0.00 46.59 3.24
6768 7780 2.437085 TATCGACAGAGCCTGGAAGA 57.563 50.000 0.00 3.97 35.51 2.87
6916 8068 6.732154 CATGAATACCTTTGTAATCCTGCTG 58.268 40.000 0.00 0.00 0.00 4.41
6991 8143 7.678947 ACCTGCATCTTTGATATAATACTGC 57.321 36.000 0.00 0.00 0.00 4.40
7029 8228 7.338449 ACACGTAGATAATTGCAAAACCCTTAT 59.662 33.333 1.71 2.28 0.00 1.73
7030 8229 8.832521 CACGTAGATAATTGCAAAACCCTTATA 58.167 33.333 1.71 0.00 0.00 0.98
7121 8322 4.643784 GTCTGGACCTAGTCGAATCCTTAA 59.356 45.833 0.00 0.00 32.65 1.85
7122 8323 5.302313 GTCTGGACCTAGTCGAATCCTTAAT 59.698 44.000 0.00 0.00 32.65 1.40
7123 8324 5.535406 TCTGGACCTAGTCGAATCCTTAATC 59.465 44.000 0.00 0.00 32.65 1.75
7164 8460 4.437682 TGTTTGAGTATCCATGGGATCC 57.562 45.455 13.02 1.92 42.11 3.36
7233 8529 5.851720 AGCACTATCATGATTGAGATCGTT 58.148 37.500 21.64 2.22 34.73 3.85
7329 8625 4.966787 GCTCAAACCCCACGGCCA 62.967 66.667 2.24 0.00 0.00 5.36
7351 8647 3.383185 ACAAACCACCATCAATGTTTCGT 59.617 39.130 0.00 0.00 0.00 3.85
7366 8662 5.548706 TGTTTCGTCCGAAAAAGAAAAGA 57.451 34.783 15.61 0.00 44.40 2.52
7390 8686 9.965824 AGAAATTTATTTACCTATGGCATTTCG 57.034 29.630 4.78 0.00 34.65 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 6.901615 TTTCCTAATCTCCATCTGGGTAAA 57.098 37.500 0.00 0.00 38.11 2.01
31 32 6.044404 GGATTTCCTAATCTCCATCTGGGTAA 59.956 42.308 0.00 0.00 40.07 2.85
116 117 5.561499 GCACAACTTATCATCGATTATTGCG 59.439 40.000 0.00 0.00 0.00 4.85
149 150 2.997315 CACCACGAGCCCTCTCCA 60.997 66.667 0.00 0.00 35.94 3.86
215 216 0.110295 ATGCCTACTTGTGCCACACA 59.890 50.000 0.00 0.00 43.02 3.72
241 255 5.643421 ATTCTCTTCAGCAGGAATATGGT 57.357 39.130 0.00 0.00 34.32 3.55
249 263 4.754114 GGCTAATGTATTCTCTTCAGCAGG 59.246 45.833 0.00 0.00 0.00 4.85
263 277 5.730550 CACTTCAGTTACCAGGCTAATGTA 58.269 41.667 0.00 0.00 0.00 2.29
264 278 4.579869 CACTTCAGTTACCAGGCTAATGT 58.420 43.478 0.00 0.00 0.00 2.71
265 279 3.375299 GCACTTCAGTTACCAGGCTAATG 59.625 47.826 0.00 0.00 0.00 1.90
286 302 3.127533 GGCGATCTGGTGTGGTGC 61.128 66.667 0.00 0.00 0.00 5.01
300 316 2.106131 TGTAGGTATGCTGCGGCG 59.894 61.111 13.96 0.51 42.25 6.46
301 317 0.462047 AAGTGTAGGTATGCTGCGGC 60.462 55.000 11.65 11.65 39.26 6.53
328 344 9.981114 TCTTCAGCAGAAATATCATTATTCGTA 57.019 29.630 0.00 0.00 32.35 3.43
329 345 8.893219 TCTTCAGCAGAAATATCATTATTCGT 57.107 30.769 0.00 0.00 32.35 3.85
343 359 7.281774 CAGGCTAATATCTTTTCTTCAGCAGAA 59.718 37.037 0.00 0.00 39.99 3.02
345 361 6.017275 CCAGGCTAATATCTTTTCTTCAGCAG 60.017 42.308 0.00 0.00 0.00 4.24
348 364 7.012799 GGAACCAGGCTAATATCTTTTCTTCAG 59.987 40.741 0.00 0.00 0.00 3.02
349 365 6.828785 GGAACCAGGCTAATATCTTTTCTTCA 59.171 38.462 0.00 0.00 0.00 3.02
350 366 7.012799 CAGGAACCAGGCTAATATCTTTTCTTC 59.987 40.741 0.00 0.00 0.00 2.87
351 367 6.830838 CAGGAACCAGGCTAATATCTTTTCTT 59.169 38.462 0.00 0.00 0.00 2.52
352 368 6.158695 TCAGGAACCAGGCTAATATCTTTTCT 59.841 38.462 0.00 0.00 0.00 2.52
353 369 6.357367 TCAGGAACCAGGCTAATATCTTTTC 58.643 40.000 0.00 0.00 0.00 2.29
355 371 5.975988 TCAGGAACCAGGCTAATATCTTT 57.024 39.130 0.00 0.00 0.00 2.52
356 372 5.667626 TCTTCAGGAACCAGGCTAATATCTT 59.332 40.000 0.00 0.00 0.00 2.40
357 373 5.219739 TCTTCAGGAACCAGGCTAATATCT 58.780 41.667 0.00 0.00 0.00 1.98
359 375 4.349342 CCTCTTCAGGAACCAGGCTAATAT 59.651 45.833 0.00 0.00 43.65 1.28
362 378 1.909302 CCTCTTCAGGAACCAGGCTAA 59.091 52.381 0.00 0.00 43.65 3.09
363 379 1.573108 CCTCTTCAGGAACCAGGCTA 58.427 55.000 0.00 0.00 43.65 3.93
364 380 1.846712 GCCTCTTCAGGAACCAGGCT 61.847 60.000 15.47 0.00 43.65 4.58
365 381 1.377856 GCCTCTTCAGGAACCAGGC 60.378 63.158 10.14 10.14 43.65 4.85
366 382 0.322008 GTGCCTCTTCAGGAACCAGG 60.322 60.000 0.00 0.00 42.40 4.45
367 383 3.239861 GTGCCTCTTCAGGAACCAG 57.760 57.895 0.00 0.00 42.40 4.00
384 400 1.521681 GGAGAAGCGCGGCATTAGT 60.522 57.895 8.83 0.00 0.00 2.24
436 452 2.769893 GAACAAACTAAGGTGCCCGTA 58.230 47.619 0.00 0.00 0.00 4.02
441 457 2.349532 GCACTCGAACAAACTAAGGTGC 60.350 50.000 3.79 3.79 41.09 5.01
449 465 5.151632 TGAAGTTTAGCACTCGAACAAAC 57.848 39.130 0.00 0.00 32.94 2.93
453 469 5.807344 ACTTTTGAAGTTTAGCACTCGAAC 58.193 37.500 0.00 0.00 39.04 3.95
478 494 8.667463 GCATGGTGCACTCATAAAATTTTATTT 58.333 29.630 18.72 5.85 44.26 1.40
504 520 3.382546 AGCTAGCCAAATAAATGCAGTGG 59.617 43.478 12.13 0.00 0.00 4.00
514 530 7.182026 TGCCCTCTATTATTAGCTAGCCAAATA 59.818 37.037 12.13 12.97 0.00 1.40
526 542 9.373450 GAGATAGGATGATGCCCTCTATTATTA 57.627 37.037 0.00 0.00 35.30 0.98
571 587 9.458374 CGTCACATTATACATGTACATTCTGTA 57.542 33.333 7.96 7.93 0.00 2.74
572 588 7.042725 GCGTCACATTATACATGTACATTCTGT 60.043 37.037 7.96 5.69 0.00 3.41
585 601 3.124466 TGTGTGCTTGCGTCACATTATAC 59.876 43.478 15.24 0.00 44.96 1.47
601 617 4.825546 ATATAATCAAGCAGCTGTGTGC 57.174 40.909 16.64 0.71 44.35 4.57
624 640 8.482128 ACTGAAACATGAAACCCTTTTTCAATA 58.518 29.630 0.00 0.00 41.16 1.90
625 641 7.337938 ACTGAAACATGAAACCCTTTTTCAAT 58.662 30.769 0.00 0.00 41.16 2.57
626 642 6.706295 ACTGAAACATGAAACCCTTTTTCAA 58.294 32.000 0.00 0.00 41.16 2.69
627 643 6.293004 ACTGAAACATGAAACCCTTTTTCA 57.707 33.333 0.00 1.68 41.91 2.69
628 644 7.463544 CAAACTGAAACATGAAACCCTTTTTC 58.536 34.615 0.00 0.00 0.00 2.29
629 645 6.128035 GCAAACTGAAACATGAAACCCTTTTT 60.128 34.615 0.00 0.00 0.00 1.94
630 646 5.353956 GCAAACTGAAACATGAAACCCTTTT 59.646 36.000 0.00 0.00 0.00 2.27
631 647 4.875536 GCAAACTGAAACATGAAACCCTTT 59.124 37.500 0.00 0.00 0.00 3.11
632 648 4.162131 AGCAAACTGAAACATGAAACCCTT 59.838 37.500 0.00 0.00 0.00 3.95
633 649 3.706086 AGCAAACTGAAACATGAAACCCT 59.294 39.130 0.00 0.00 0.00 4.34
634 650 4.051237 GAGCAAACTGAAACATGAAACCC 58.949 43.478 0.00 0.00 0.00 4.11
647 1146 5.545658 AATACATAACACCGAGCAAACTG 57.454 39.130 0.00 0.00 0.00 3.16
653 1152 2.198406 TGCGAATACATAACACCGAGC 58.802 47.619 0.00 0.00 0.00 5.03
672 1171 4.543590 ACCTGTCCAGATACACTTTCTG 57.456 45.455 0.00 0.00 40.25 3.02
673 1172 4.593206 TCAACCTGTCCAGATACACTTTCT 59.407 41.667 0.00 0.00 0.00 2.52
731 1230 2.093921 TCAACATTGCCAATCTGCCATG 60.094 45.455 0.00 0.00 39.56 3.66
732 1231 2.181125 TCAACATTGCCAATCTGCCAT 58.819 42.857 0.00 0.00 0.00 4.40
735 1234 5.870978 AGTTAATTCAACATTGCCAATCTGC 59.129 36.000 0.00 0.00 39.81 4.26
737 1236 7.444299 ACAAGTTAATTCAACATTGCCAATCT 58.556 30.769 0.00 0.00 39.81 2.40
739 1238 6.365789 CGACAAGTTAATTCAACATTGCCAAT 59.634 34.615 0.00 0.00 39.81 3.16
753 1259 4.331968 TGGAAGATTGCCGACAAGTTAAT 58.668 39.130 0.00 0.00 39.69 1.40
759 1265 1.298157 CGCTGGAAGATTGCCGACAA 61.298 55.000 0.00 0.00 40.87 3.18
763 1269 1.745115 TTCCGCTGGAAGATTGCCG 60.745 57.895 6.01 0.00 36.71 5.69
879 1394 4.268797 AGAGAGGGAAAACGGACTTAAC 57.731 45.455 0.00 0.00 0.00 2.01
908 1423 5.012458 TCCTCCAGCATAGTAAGATCCAATG 59.988 44.000 0.00 0.00 0.00 2.82
909 1424 5.158141 TCCTCCAGCATAGTAAGATCCAAT 58.842 41.667 0.00 0.00 0.00 3.16
910 1425 4.556697 TCCTCCAGCATAGTAAGATCCAA 58.443 43.478 0.00 0.00 0.00 3.53
912 1427 4.411927 TCTCCTCCAGCATAGTAAGATCC 58.588 47.826 0.00 0.00 0.00 3.36
914 1429 5.324409 CTCTCTCCTCCAGCATAGTAAGAT 58.676 45.833 0.00 0.00 0.00 2.40
915 1430 4.447034 CCTCTCTCCTCCAGCATAGTAAGA 60.447 50.000 0.00 0.00 0.00 2.10
916 1431 3.826157 CCTCTCTCCTCCAGCATAGTAAG 59.174 52.174 0.00 0.00 0.00 2.34
917 1432 3.437198 CCCTCTCTCCTCCAGCATAGTAA 60.437 52.174 0.00 0.00 0.00 2.24
918 1433 2.109128 CCCTCTCTCCTCCAGCATAGTA 59.891 54.545 0.00 0.00 0.00 1.82
920 1435 1.631405 CCCTCTCTCCTCCAGCATAG 58.369 60.000 0.00 0.00 0.00 2.23
921 1436 0.189574 CCCCTCTCTCCTCCAGCATA 59.810 60.000 0.00 0.00 0.00 3.14
922 1437 1.074623 CCCCTCTCTCCTCCAGCAT 60.075 63.158 0.00 0.00 0.00 3.79
923 1438 2.366167 CCCCTCTCTCCTCCAGCA 59.634 66.667 0.00 0.00 0.00 4.41
924 1439 3.160748 GCCCCTCTCTCCTCCAGC 61.161 72.222 0.00 0.00 0.00 4.85
925 1440 0.189574 TATGCCCCTCTCTCCTCCAG 59.810 60.000 0.00 0.00 0.00 3.86
926 1441 0.870313 ATATGCCCCTCTCTCCTCCA 59.130 55.000 0.00 0.00 0.00 3.86
927 1442 1.905894 GAATATGCCCCTCTCTCCTCC 59.094 57.143 0.00 0.00 0.00 4.30
928 1443 2.566724 CAGAATATGCCCCTCTCTCCTC 59.433 54.545 0.00 0.00 0.00 3.71
929 1444 2.090267 ACAGAATATGCCCCTCTCTCCT 60.090 50.000 0.00 0.00 0.00 3.69
930 1445 2.334023 ACAGAATATGCCCCTCTCTCC 58.666 52.381 0.00 0.00 0.00 3.71
931 1446 4.156477 AGTACAGAATATGCCCCTCTCTC 58.844 47.826 0.00 0.00 0.00 3.20
932 1447 4.206244 AGTACAGAATATGCCCCTCTCT 57.794 45.455 0.00 0.00 0.00 3.10
933 1448 5.279556 GGTTAGTACAGAATATGCCCCTCTC 60.280 48.000 0.00 0.00 0.00 3.20
934 1449 4.593634 GGTTAGTACAGAATATGCCCCTCT 59.406 45.833 0.00 0.00 0.00 3.69
935 1450 4.347000 TGGTTAGTACAGAATATGCCCCTC 59.653 45.833 0.00 0.00 0.00 4.30
936 1451 4.303794 TGGTTAGTACAGAATATGCCCCT 58.696 43.478 0.00 0.00 0.00 4.79
937 1452 4.699925 TGGTTAGTACAGAATATGCCCC 57.300 45.455 0.00 0.00 0.00 5.80
967 1482 2.479566 TCTGTTCCGGAGTACGTACT 57.520 50.000 27.71 27.71 42.24 2.73
968 1483 3.559238 TTTCTGTTCCGGAGTACGTAC 57.441 47.619 18.10 18.10 42.24 3.67
969 1484 4.789012 ATTTTCTGTTCCGGAGTACGTA 57.211 40.909 3.34 0.00 42.24 3.57
970 1485 3.672767 ATTTTCTGTTCCGGAGTACGT 57.327 42.857 3.34 0.00 42.24 3.57
971 1486 4.449743 TGAAATTTTCTGTTCCGGAGTACG 59.550 41.667 3.34 0.00 43.80 3.67
975 1490 5.376854 ACATGAAATTTTCTGTTCCGGAG 57.623 39.130 3.34 0.00 0.00 4.63
977 1492 7.063308 CCATTTACATGAAATTTTCTGTTCCGG 59.937 37.037 10.33 0.00 35.45 5.14
985 1500 5.415221 TCCCGCCATTTACATGAAATTTTC 58.585 37.500 0.00 2.05 35.45 2.29
989 1504 3.766591 TGTTCCCGCCATTTACATGAAAT 59.233 39.130 0.00 0.00 38.34 2.17
990 1505 3.157881 TGTTCCCGCCATTTACATGAAA 58.842 40.909 0.00 0.00 31.07 2.69
992 1507 2.364632 CTGTTCCCGCCATTTACATGA 58.635 47.619 0.00 0.00 31.07 3.07
993 1508 1.405105 CCTGTTCCCGCCATTTACATG 59.595 52.381 0.00 0.00 0.00 3.21
994 1509 1.005450 ACCTGTTCCCGCCATTTACAT 59.995 47.619 0.00 0.00 0.00 2.29
995 1510 0.402504 ACCTGTTCCCGCCATTTACA 59.597 50.000 0.00 0.00 0.00 2.41
996 1511 2.011947 GTACCTGTTCCCGCCATTTAC 58.988 52.381 0.00 0.00 0.00 2.01
1054 1587 2.124942 GGAGAAGAGCCGCCAAGG 60.125 66.667 0.00 0.00 44.97 3.61
1055 1588 2.124942 GGGAGAAGAGCCGCCAAG 60.125 66.667 0.00 0.00 0.00 3.61
1056 1589 3.717294 GGGGAGAAGAGCCGCCAA 61.717 66.667 0.00 0.00 35.69 4.52
1057 1590 4.722535 AGGGGAGAAGAGCCGCCA 62.723 66.667 0.00 0.00 39.01 5.69
1058 1591 3.393149 GAAGGGGAGAAGAGCCGCC 62.393 68.421 0.00 0.00 39.01 6.13
1059 1592 2.188207 GAAGGGGAGAAGAGCCGC 59.812 66.667 0.00 0.00 38.53 6.53
1085 1618 3.652687 CCATGAGGTGGGAGGGAG 58.347 66.667 0.00 0.00 44.79 4.30
1121 1654 4.922026 GGTCGCCGTGGTGGTTGT 62.922 66.667 0.00 0.00 41.21 3.32
1154 1687 0.761802 GAGATGGAAGTAGCCCAGGG 59.238 60.000 0.00 0.00 37.08 4.45
1190 1726 1.751162 CGGAGGAGGAAGAGCGACT 60.751 63.158 0.00 0.00 0.00 4.18
1736 2272 4.202451 TGTGTCCCAATCTGTCTTGATCAA 60.202 41.667 8.12 8.12 0.00 2.57
1744 2280 2.554032 CAGGTTTGTGTCCCAATCTGTC 59.446 50.000 0.00 0.00 33.57 3.51
1759 2295 6.018180 GTCTCTTCGTTTGTAACATCAGGTTT 60.018 38.462 0.00 0.00 40.96 3.27
1813 2349 0.318441 TTGAGCTCTACGTTGCTGCT 59.682 50.000 16.19 14.00 39.91 4.24
1821 2357 2.200067 CTGCATCCTTTGAGCTCTACG 58.800 52.381 16.19 4.88 0.00 3.51
1875 2411 1.117994 TGCTCCCATCTGAGTAGCAG 58.882 55.000 0.00 0.00 46.31 4.24
1887 2423 1.361204 TCAGGAAGAATGTGCTCCCA 58.639 50.000 0.00 0.00 0.00 4.37
2053 2589 7.386059 ACATGACAAAGGGGAAAATTCAATAC 58.614 34.615 0.00 0.00 0.00 1.89
2055 2591 6.438186 ACATGACAAAGGGGAAAATTCAAT 57.562 33.333 0.00 0.00 0.00 2.57
2287 2823 7.549842 AGCATGAGATATTATAGCTTGCAAGAG 59.450 37.037 30.39 5.73 33.62 2.85
2352 2888 6.532657 ACAAATACTGCAAATTAAGATGCTGC 59.467 34.615 16.82 0.00 42.96 5.25
2363 2899 7.546667 CCATAAAGCTCAACAAATACTGCAAAT 59.453 33.333 0.00 0.00 0.00 2.32
2377 2913 7.994425 TGTTTTGATCTACCATAAAGCTCAA 57.006 32.000 0.00 0.00 29.70 3.02
2456 2992 4.722781 TGGAAATCGGGGGTATCTTAAAGA 59.277 41.667 0.00 0.00 0.00 2.52
2503 3039 3.415212 TGCAACTCCTTGATTCTTCCTG 58.585 45.455 0.00 0.00 0.00 3.86
2572 3108 8.665685 ACCAAGTTAGCTGAAGAAATAATAACG 58.334 33.333 0.00 0.00 0.00 3.18
2772 3308 7.994425 TGCACTAAAAAGACCTGAATAATCA 57.006 32.000 0.00 0.00 0.00 2.57
2857 3393 1.065199 TGCTTGGCTAGGGACTTCATG 60.065 52.381 0.00 0.00 41.75 3.07
2957 3493 2.817258 TCCAAATAACAAGGACTTGGCG 59.183 45.455 15.72 0.00 44.45 5.69
3095 3631 7.742089 GCGAATCATAGATAGCATGTTGTTTAC 59.258 37.037 0.00 0.00 0.00 2.01
3119 3655 4.619760 TGTTTCTACTTGAGAATGTACGCG 59.380 41.667 3.53 3.53 43.84 6.01
3169 3705 5.126707 TCAGGGAATAGGTCGAAACTACTTC 59.873 44.000 0.65 6.29 0.00 3.01
3172 3708 4.441217 GGTCAGGGAATAGGTCGAAACTAC 60.441 50.000 0.65 0.00 0.00 2.73
3502 4038 8.349983 CAAGTTAAGGTGCAGTAAAAGTTACAT 58.650 33.333 0.00 0.00 0.00 2.29
3520 4056 5.320549 AGCAAATCAGGATGCAAGTTAAG 57.679 39.130 0.00 0.00 44.95 1.85
3538 4074 6.201234 CACATGAATCATGAAACACAAAGCAA 59.799 34.615 27.86 0.00 43.81 3.91
3745 4281 3.382865 TGTGTTAGTTGCTCCAAATGCAA 59.617 39.130 0.00 0.00 46.48 4.08
4217 4753 7.417612 ACGATAATTCAACTTATGCCAATGAC 58.582 34.615 0.00 0.00 0.00 3.06
4524 5076 6.150474 GTTACTAAACATAGCAGGAGGCAAAA 59.850 38.462 0.00 0.00 39.25 2.44
4531 5083 7.165485 ACAATGTGTTACTAAACATAGCAGGA 58.835 34.615 0.00 0.00 46.84 3.86
4550 5102 8.743085 ATGCAGATCATAGTTTAAGACAATGT 57.257 30.769 0.00 0.00 32.59 2.71
5363 5918 8.085296 CAGACTACAATATTCTGGACAGGATAC 58.915 40.741 2.50 0.00 32.02 2.24
5755 6588 1.021390 GCTGACCACTCCATTGACCG 61.021 60.000 0.00 0.00 0.00 4.79
6163 7157 4.737946 GCAGGCCTATCACTGTACTTGTAG 60.738 50.000 3.98 0.00 37.07 2.74
6328 7325 4.127171 GAGTCTCTGCGTAGATCTTCTCT 58.873 47.826 2.90 0.00 38.06 3.10
6794 7806 9.511144 AAAGTTAAGTAAAACATTTCGTTCCAG 57.489 29.630 0.00 0.00 36.59 3.86
6985 8137 1.676968 TGGTCAACCAGCGCAGTAT 59.323 52.632 11.47 0.00 42.01 2.12
7071 8270 9.020731 ACCGTTTAACTCCTCAAATTATGAATT 57.979 29.630 0.00 0.00 37.67 2.17
7072 8271 8.458843 CACCGTTTAACTCCTCAAATTATGAAT 58.541 33.333 0.00 0.00 37.67 2.57
7073 8272 7.446013 ACACCGTTTAACTCCTCAAATTATGAA 59.554 33.333 0.00 0.00 37.67 2.57
7164 8460 1.729470 CGGATGTGGAGGAGGTCGAG 61.729 65.000 0.00 0.00 0.00 4.04
7233 8529 1.191489 TCGTCACATCCAAGGCCTCA 61.191 55.000 5.23 0.00 0.00 3.86
7329 8625 3.383185 ACGAAACATTGATGGTGGTTTGT 59.617 39.130 0.00 0.00 36.34 2.83


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

AutoCloner maintained by Alex Coulton.