Multiple sequence alignment - TraesCS3B01G058800

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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 TraesCS3B01G058800 chr3B 100.000 2711 0 0 1 2711 30493677 30496387 0.000000e+00 5007.0
1 TraesCS3B01G058800 chr3B 81.481 999 166 14 878 1865 29618359 29619349 0.000000e+00 802.0
2 TraesCS3B01G058800 chr3B 80.750 800 144 8 1079 1873 29728680 29729474 1.380000e-172 616.0
3 TraesCS3B01G058800 chr3B 84.161 644 85 10 1233 1865 30506686 30507323 2.310000e-170 608.0
4 TraesCS3B01G058800 chr3B 80.204 783 150 4 1094 1873 29849214 29849994 1.400000e-162 582.0
5 TraesCS3B01G058800 chr3B 87.246 345 31 6 1 342 30463585 30463919 5.480000e-102 381.0
6 TraesCS3B01G058800 chr3B 100.000 31 0 0 422 452 30464086 30464116 1.050000e-04 58.4
7 TraesCS3B01G058800 chr3B 97.059 34 1 0 425 458 30494062 30494095 1.050000e-04 58.4
8 TraesCS3B01G058800 chr3B 97.059 34 1 0 386 419 30494101 30494134 1.050000e-04 58.4
9 TraesCS3B01G058800 chr3B 100.000 28 0 0 428 455 29845231 29845258 5.000000e-03 52.8
10 TraesCS3B01G058800 chr2B 93.284 804 39 6 1921 2711 216856627 216857428 0.000000e+00 1171.0
11 TraesCS3B01G058800 chr2B 89.480 808 68 9 1917 2711 777130327 777131130 0.000000e+00 1005.0
12 TraesCS3B01G058800 chr2B 88.917 803 49 14 1920 2711 96626633 96627406 0.000000e+00 953.0
13 TraesCS3B01G058800 chr2B 81.553 206 34 4 1920 2122 540751086 540750882 1.670000e-37 167.0
14 TraesCS3B01G058800 chr5B 91.551 793 63 4 1920 2711 669510098 669509309 0.000000e+00 1090.0
15 TraesCS3B01G058800 chr1B 91.373 765 53 3 1957 2710 344367032 344366270 0.000000e+00 1035.0
16 TraesCS3B01G058800 chr1B 89.335 797 58 17 1922 2711 266931682 266932458 0.000000e+00 976.0
17 TraesCS3B01G058800 chr1B 86.264 779 96 8 1936 2711 512772926 512773696 0.000000e+00 835.0
18 TraesCS3B01G058800 chr7B 89.428 804 68 9 1920 2711 577130101 577130899 0.000000e+00 998.0
19 TraesCS3B01G058800 chr7B 89.615 780 55 8 1944 2711 583603050 583602285 0.000000e+00 968.0
20 TraesCS3B01G058800 chr7B 87.562 804 88 4 1919 2711 39380666 39381468 0.000000e+00 920.0
21 TraesCS3B01G058800 chr3D 84.038 946 132 10 878 1809 18881018 18881958 0.000000e+00 893.0
22 TraesCS3B01G058800 chr3D 90.728 302 21 5 161 458 18878814 18879112 1.960000e-106 396.0
23 TraesCS3B01G058800 chr3D 79.151 542 90 11 1328 1846 18727992 18728533 1.190000e-93 353.0
24 TraesCS3B01G058800 chr3D 85.215 372 9 8 529 879 18880638 18880984 9.300000e-90 340.0
25 TraesCS3B01G058800 chr3D 94.969 159 3 2 1 159 18878552 18878705 7.500000e-61 244.0
26 TraesCS3B01G058800 chr3D 97.403 77 2 0 386 462 18879079 18879155 6.090000e-27 132.0
27 TraesCS3B01G058800 chr3D 98.113 53 1 0 465 517 18879192 18879244 2.870000e-15 93.5
28 TraesCS3B01G058800 chr3D 92.593 54 1 3 1814 1865 18891890 18891942 1.040000e-09 75.0
29 TraesCS3B01G058800 chr3D 97.059 34 1 0 422 455 18699697 18699730 1.050000e-04 58.4
30 TraesCS3B01G058800 chr4B 85.390 794 103 11 1922 2711 362137906 362137122 0.000000e+00 811.0
31 TraesCS3B01G058800 chr3A 80.677 1004 154 29 878 1865 26451319 26452298 0.000000e+00 743.0
32 TraesCS3B01G058800 chr3A 82.037 874 143 8 878 1742 26415111 26415979 0.000000e+00 732.0
33 TraesCS3B01G058800 chr3A 79.820 555 104 7 1318 1868 26228368 26228918 5.440000e-107 398.0
34 TraesCS3B01G058800 chr3A 80.549 437 85 0 1079 1515 26412912 26413348 1.200000e-88 337.0
35 TraesCS3B01G058800 chr6D 77.311 595 116 13 1090 1673 2051341 2050755 1.560000e-87 333.0
36 TraesCS3B01G058800 chr6A 73.579 598 130 24 1092 1673 812869 813454 1.270000e-48 204.0


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 TraesCS3B01G058800 chr3B 30493677 30496387 2710 False 1707.933333 5007 98.039333 1 2711 3 chr3B.!!$F6 2710
1 TraesCS3B01G058800 chr3B 29618359 29619349 990 False 802.000000 802 81.481000 878 1865 1 chr3B.!!$F1 987
2 TraesCS3B01G058800 chr3B 29728680 29729474 794 False 616.000000 616 80.750000 1079 1873 1 chr3B.!!$F2 794
3 TraesCS3B01G058800 chr3B 30506686 30507323 637 False 608.000000 608 84.161000 1233 1865 1 chr3B.!!$F3 632
4 TraesCS3B01G058800 chr3B 29845231 29849994 4763 False 317.400000 582 90.102000 428 1873 2 chr3B.!!$F4 1445
5 TraesCS3B01G058800 chr3B 30463585 30464116 531 False 219.700000 381 93.623000 1 452 2 chr3B.!!$F5 451
6 TraesCS3B01G058800 chr2B 216856627 216857428 801 False 1171.000000 1171 93.284000 1921 2711 1 chr2B.!!$F2 790
7 TraesCS3B01G058800 chr2B 777130327 777131130 803 False 1005.000000 1005 89.480000 1917 2711 1 chr2B.!!$F3 794
8 TraesCS3B01G058800 chr2B 96626633 96627406 773 False 953.000000 953 88.917000 1920 2711 1 chr2B.!!$F1 791
9 TraesCS3B01G058800 chr5B 669509309 669510098 789 True 1090.000000 1090 91.551000 1920 2711 1 chr5B.!!$R1 791
10 TraesCS3B01G058800 chr1B 344366270 344367032 762 True 1035.000000 1035 91.373000 1957 2710 1 chr1B.!!$R1 753
11 TraesCS3B01G058800 chr1B 266931682 266932458 776 False 976.000000 976 89.335000 1922 2711 1 chr1B.!!$F1 789
12 TraesCS3B01G058800 chr1B 512772926 512773696 770 False 835.000000 835 86.264000 1936 2711 1 chr1B.!!$F2 775
13 TraesCS3B01G058800 chr7B 577130101 577130899 798 False 998.000000 998 89.428000 1920 2711 1 chr7B.!!$F2 791
14 TraesCS3B01G058800 chr7B 583602285 583603050 765 True 968.000000 968 89.615000 1944 2711 1 chr7B.!!$R1 767
15 TraesCS3B01G058800 chr7B 39380666 39381468 802 False 920.000000 920 87.562000 1919 2711 1 chr7B.!!$F1 792
16 TraesCS3B01G058800 chr3D 18727992 18728533 541 False 353.000000 353 79.151000 1328 1846 1 chr3D.!!$F2 518
17 TraesCS3B01G058800 chr3D 18878552 18881958 3406 False 349.750000 893 91.744333 1 1809 6 chr3D.!!$F4 1808
18 TraesCS3B01G058800 chr4B 362137122 362137906 784 True 811.000000 811 85.390000 1922 2711 1 chr4B.!!$R1 789
19 TraesCS3B01G058800 chr3A 26451319 26452298 979 False 743.000000 743 80.677000 878 1865 1 chr3A.!!$F2 987
20 TraesCS3B01G058800 chr3A 26412912 26415979 3067 False 534.500000 732 81.293000 878 1742 2 chr3A.!!$F3 864
21 TraesCS3B01G058800 chr3A 26228368 26228918 550 False 398.000000 398 79.820000 1318 1868 1 chr3A.!!$F1 550
22 TraesCS3B01G058800 chr6D 2050755 2051341 586 True 333.000000 333 77.311000 1090 1673 1 chr6D.!!$R1 583
23 TraesCS3B01G058800 chr6A 812869 813454 585 False 204.000000 204 73.579000 1092 1673 1 chr6A.!!$F1 581

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
760 2448 0.10852 GTTTACCAGTCATCGGCCGA 60.109 55.0 33.12 33.12 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1953 6855 0.236449 AAAGAAGTTTTACCGCGCGG 59.764 50.0 44.88 44.88 42.03 6.46 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
80 81 3.304829 GAAGCAGTCCCCTATTCTCTCT 58.695 50.000 0.00 0.00 0.00 3.10
81 82 2.957474 AGCAGTCCCCTATTCTCTCTC 58.043 52.381 0.00 0.00 0.00 3.20
82 83 2.246067 AGCAGTCCCCTATTCTCTCTCA 59.754 50.000 0.00 0.00 0.00 3.27
83 84 3.034635 GCAGTCCCCTATTCTCTCTCAA 58.965 50.000 0.00 0.00 0.00 3.02
84 85 3.181470 GCAGTCCCCTATTCTCTCTCAAC 60.181 52.174 0.00 0.00 0.00 3.18
85 86 4.026744 CAGTCCCCTATTCTCTCTCAACA 58.973 47.826 0.00 0.00 0.00 3.33
112 117 7.419711 AAAACTCTTCAGGGTAATATCTCGA 57.580 36.000 0.00 0.00 0.00 4.04
159 164 5.973565 GGCACTCATGATTTGCATTAACTAC 59.026 40.000 23.73 6.92 38.04 2.73
232 344 5.163642 TGCCGAGAGAGAAATACAAGACTAC 60.164 44.000 0.00 0.00 0.00 2.73
420 677 6.836007 TCTTAGCCAGATTATTCTCTCACAGA 59.164 38.462 0.00 0.00 0.00 3.41
462 719 4.937620 GCCAGATTATTCTCTCACAACACA 59.062 41.667 0.00 0.00 0.00 3.72
480 771 2.671396 CACAAGTACGTCTAACATGGGC 59.329 50.000 0.00 0.00 0.00 5.36
517 808 0.611896 ATTGACGGGGCAAGGAAAGG 60.612 55.000 0.00 0.00 0.00 3.11
520 811 1.838073 GACGGGGCAAGGAAAGGAGA 61.838 60.000 0.00 0.00 0.00 3.71
523 814 1.379176 GGGCAAGGAAAGGAGAGCC 60.379 63.158 0.00 0.00 41.29 4.70
527 818 1.678425 GCAAGGAAAGGAGAGCCTCTG 60.678 57.143 0.00 0.00 46.28 3.35
600 2288 2.042831 GGTGGCATGCAGAGTGTCC 61.043 63.158 21.36 6.63 0.00 4.02
607 2295 1.134580 CATGCAGAGTGTCCTTCCGAT 60.135 52.381 0.00 0.00 0.00 4.18
619 2307 2.879942 CTTCCGATTTTCCGTGCGCG 62.880 60.000 13.88 13.88 37.95 6.86
737 2425 7.933215 AAACACACTTTATAATACCAGGACC 57.067 36.000 0.00 0.00 0.00 4.46
749 2437 5.952347 ATACCAGGACCTTAGTTTACCAG 57.048 43.478 0.00 0.00 0.00 4.00
750 2438 3.595021 ACCAGGACCTTAGTTTACCAGT 58.405 45.455 0.00 0.00 0.00 4.00
752 2440 3.581332 CCAGGACCTTAGTTTACCAGTCA 59.419 47.826 0.00 0.00 0.00 3.41
753 2441 4.225267 CCAGGACCTTAGTTTACCAGTCAT 59.775 45.833 0.00 0.00 0.00 3.06
754 2442 5.420409 CAGGACCTTAGTTTACCAGTCATC 58.580 45.833 0.00 0.00 0.00 2.92
755 2443 4.159879 AGGACCTTAGTTTACCAGTCATCG 59.840 45.833 0.00 0.00 0.00 3.84
756 2444 4.430908 GACCTTAGTTTACCAGTCATCGG 58.569 47.826 0.00 0.00 0.00 4.18
760 2448 0.108520 GTTTACCAGTCATCGGCCGA 60.109 55.000 33.12 33.12 0.00 5.54
761 2449 0.828022 TTTACCAGTCATCGGCCGAT 59.172 50.000 34.60 34.60 34.81 4.18
763 2451 0.387929 TACCAGTCATCGGCCGATTC 59.612 55.000 37.36 29.64 31.62 2.52
764 2452 1.143838 CCAGTCATCGGCCGATTCA 59.856 57.895 37.36 23.90 31.62 2.57
765 2453 1.154205 CCAGTCATCGGCCGATTCAC 61.154 60.000 37.36 32.17 31.62 3.18
766 2454 1.226974 AGTCATCGGCCGATTCACG 60.227 57.895 37.36 25.40 42.18 4.35
769 2457 4.508128 ATCGGCCGATTCACGCGT 62.508 61.111 34.60 11.74 41.07 6.01
826 2514 4.274950 CGTTCAACCAACTAACTCAACCAT 59.725 41.667 0.00 0.00 32.09 3.55
827 2515 5.467399 CGTTCAACCAACTAACTCAACCATA 59.533 40.000 0.00 0.00 32.09 2.74
828 2516 6.148811 CGTTCAACCAACTAACTCAACCATAT 59.851 38.462 0.00 0.00 32.09 1.78
850 2538 1.160329 GGTCAACAAGAGCGTGCACT 61.160 55.000 16.19 0.00 34.67 4.40
929 4710 1.068472 ACACGACTCGGTCATTGACTC 60.068 52.381 16.02 5.39 32.47 3.36
954 4735 0.933097 CTCCTCGCATACATGTGCAC 59.067 55.000 10.75 10.75 45.30 4.57
996 4779 4.625607 AAATTCTCGACCAAAGTCCTCT 57.374 40.909 0.00 0.00 40.12 3.69
1059 4842 3.070734 CCTTCCTCATCATCTCCACGATT 59.929 47.826 0.00 0.00 0.00 3.34
1062 4845 2.366590 CCTCATCATCTCCACGATTCCA 59.633 50.000 0.00 0.00 0.00 3.53
1063 4846 3.007723 CCTCATCATCTCCACGATTCCAT 59.992 47.826 0.00 0.00 0.00 3.41
1065 4848 3.642848 TCATCATCTCCACGATTCCATCA 59.357 43.478 0.00 0.00 0.00 3.07
1067 4850 2.130395 CATCTCCACGATTCCATCACG 58.870 52.381 0.00 0.00 0.00 4.35
1110 5934 1.417592 CGAGCGATGCGGCAATATC 59.582 57.895 6.82 0.00 34.64 1.63
1113 5937 0.250038 AGCGATGCGGCAATATCACT 60.250 50.000 6.82 0.00 34.64 3.41
1120 5944 3.653344 TGCGGCAATATCACTATCTCAC 58.347 45.455 0.00 0.00 0.00 3.51
1122 5946 3.245797 CGGCAATATCACTATCTCACCG 58.754 50.000 0.00 0.00 0.00 4.94
1141 5965 2.099638 CGTTCGGCATCGTCTCGA 59.900 61.111 0.00 0.00 41.13 4.04
1147 5971 1.944709 TCGGCATCGTCTCGATTTCTA 59.055 47.619 1.82 0.00 44.59 2.10
1148 5972 2.031944 TCGGCATCGTCTCGATTTCTAG 60.032 50.000 1.82 0.00 44.59 2.43
1185 6015 2.982130 CTCGGGTTCCAGGTCCAG 59.018 66.667 0.00 2.55 0.00 3.86
1190 6020 1.198759 GGGTTCCAGGTCCAGTGCTA 61.199 60.000 0.00 0.00 0.00 3.49
1197 6027 0.830444 AGGTCCAGTGCTACAACGGA 60.830 55.000 0.00 0.00 0.00 4.69
1219 6049 1.625511 CCCATACCTCGGGTACTACC 58.374 60.000 5.10 0.00 41.31 3.18
1230 6060 1.907255 GGGTACTACCAGCCTGAGTTT 59.093 52.381 7.57 0.00 41.02 2.66
1274 6104 2.046009 TACAACAACGGCTCCCTGCA 62.046 55.000 0.00 0.00 45.15 4.41
1363 6193 1.077357 AACACCGCCACCAAAGTCA 60.077 52.632 0.00 0.00 0.00 3.41
1473 6327 1.078072 AGTGTGCCGGAACAACACA 60.078 52.632 19.50 12.62 40.69 3.72
1507 6361 2.562912 GGCCGTACAACGAGACGA 59.437 61.111 0.15 0.00 46.05 4.20
1517 6371 2.251040 CAACGAGACGAACGTGATCAT 58.749 47.619 4.19 0.00 43.16 2.45
1580 6446 0.883370 GTGGTTGGGACGACTGGAAC 60.883 60.000 0.00 0.00 32.42 3.62
1602 6468 1.804151 GTGAATGCCAGCGACTACAAA 59.196 47.619 0.00 0.00 0.00 2.83
1683 6555 0.322187 TCACTCATCCTCGTCCGTCA 60.322 55.000 0.00 0.00 0.00 4.35
1693 6568 3.066342 TCCTCGTCCGTCATCAAATACTC 59.934 47.826 0.00 0.00 0.00 2.59
1696 6571 4.421058 TCGTCCGTCATCAAATACTCTTG 58.579 43.478 0.00 0.00 0.00 3.02
1721 6603 4.856801 CAACTAGGCGCCGGGCAT 62.857 66.667 23.20 5.39 46.16 4.40
1724 6606 2.110213 CTAGGCGCCGGGCATTAA 59.890 61.111 23.20 0.15 46.16 1.40
1775 6671 3.795488 GCAACAGTTTTGCCCACTTAGAC 60.795 47.826 2.42 0.00 39.38 2.59
1874 6774 9.300681 AGAAATGAAAATACATTCAAGGTGAGA 57.699 29.630 0.00 0.00 42.22 3.27
1875 6775 9.565213 GAAATGAAAATACATTCAAGGTGAGAG 57.435 33.333 0.00 0.00 42.22 3.20
1876 6776 8.868522 AATGAAAATACATTCAAGGTGAGAGA 57.131 30.769 0.00 0.00 42.22 3.10
1877 6777 9.471702 AATGAAAATACATTCAAGGTGAGAGAT 57.528 29.630 0.00 0.00 42.22 2.75
1878 6778 8.272545 TGAAAATACATTCAAGGTGAGAGATG 57.727 34.615 0.00 0.00 36.42 2.90
1879 6779 6.690194 AAATACATTCAAGGTGAGAGATGC 57.310 37.500 0.00 0.00 0.00 3.91
1880 6780 2.625737 ACATTCAAGGTGAGAGATGCG 58.374 47.619 0.00 0.00 0.00 4.73
1881 6781 2.234661 ACATTCAAGGTGAGAGATGCGA 59.765 45.455 0.00 0.00 0.00 5.10
1882 6782 2.662006 TTCAAGGTGAGAGATGCGAG 57.338 50.000 0.00 0.00 0.00 5.03
1883 6783 1.839424 TCAAGGTGAGAGATGCGAGA 58.161 50.000 0.00 0.00 0.00 4.04
1884 6784 2.382882 TCAAGGTGAGAGATGCGAGAT 58.617 47.619 0.00 0.00 0.00 2.75
1885 6785 2.762887 TCAAGGTGAGAGATGCGAGATT 59.237 45.455 0.00 0.00 0.00 2.40
1886 6786 2.864946 CAAGGTGAGAGATGCGAGATTG 59.135 50.000 0.00 0.00 0.00 2.67
1887 6787 2.382882 AGGTGAGAGATGCGAGATTGA 58.617 47.619 0.00 0.00 0.00 2.57
1888 6788 2.100584 AGGTGAGAGATGCGAGATTGAC 59.899 50.000 0.00 0.00 0.00 3.18
1889 6789 2.100584 GGTGAGAGATGCGAGATTGACT 59.899 50.000 0.00 0.00 0.00 3.41
1890 6790 3.114809 GTGAGAGATGCGAGATTGACTG 58.885 50.000 0.00 0.00 0.00 3.51
1891 6791 2.126467 GAGAGATGCGAGATTGACTGC 58.874 52.381 0.00 0.00 0.00 4.40
1892 6792 0.851495 GAGATGCGAGATTGACTGCG 59.149 55.000 0.00 0.00 0.00 5.18
1893 6793 1.150567 AGATGCGAGATTGACTGCGC 61.151 55.000 0.00 0.00 41.61 6.09
1894 6794 2.048316 TGCGAGATTGACTGCGCA 60.048 55.556 10.98 10.98 45.13 6.09
1895 6795 2.382746 TGCGAGATTGACTGCGCAC 61.383 57.895 5.66 0.00 43.81 5.34
1896 6796 3.084579 CGAGATTGACTGCGCACC 58.915 61.111 5.66 1.22 0.00 5.01
1897 6797 2.792290 CGAGATTGACTGCGCACCG 61.792 63.158 5.66 0.00 0.00 4.94
1898 6798 1.738099 GAGATTGACTGCGCACCGT 60.738 57.895 5.66 3.19 0.00 4.83
1899 6799 1.687494 GAGATTGACTGCGCACCGTC 61.687 60.000 19.72 19.72 0.00 4.79
1900 6800 1.738099 GATTGACTGCGCACCGTCT 60.738 57.895 24.72 10.41 0.00 4.18
1901 6801 1.291877 GATTGACTGCGCACCGTCTT 61.292 55.000 24.72 15.23 0.00 3.01
1902 6802 1.568612 ATTGACTGCGCACCGTCTTG 61.569 55.000 24.72 9.76 0.00 3.02
1903 6803 3.414700 GACTGCGCACCGTCTTGG 61.415 66.667 19.37 5.12 46.41 3.61
1904 6804 3.858868 GACTGCGCACCGTCTTGGA 62.859 63.158 19.37 0.00 42.00 3.53
1905 6805 2.434884 CTGCGCACCGTCTTGGAT 60.435 61.111 5.66 0.00 42.00 3.41
1906 6806 2.031919 TGCGCACCGTCTTGGATT 59.968 55.556 5.66 0.00 42.00 3.01
1907 6807 2.244436 CTGCGCACCGTCTTGGATTG 62.244 60.000 5.66 0.00 42.00 2.67
1908 6808 3.039202 GCGCACCGTCTTGGATTGG 62.039 63.158 0.30 0.00 42.00 3.16
1909 6809 2.398554 CGCACCGTCTTGGATTGGG 61.399 63.158 0.00 0.00 42.00 4.12
1910 6810 2.700773 GCACCGTCTTGGATTGGGC 61.701 63.158 0.00 0.00 42.00 5.36
1911 6811 2.046314 ACCGTCTTGGATTGGGCG 60.046 61.111 0.00 0.00 42.00 6.13
1912 6812 2.824041 CCGTCTTGGATTGGGCGG 60.824 66.667 0.00 0.00 42.00 6.13
1913 6813 2.824041 CGTCTTGGATTGGGCGGG 60.824 66.667 0.00 0.00 0.00 6.13
1914 6814 3.140814 GTCTTGGATTGGGCGGGC 61.141 66.667 0.00 0.00 0.00 6.13
1915 6815 3.656280 TCTTGGATTGGGCGGGCA 61.656 61.111 3.27 0.00 0.00 5.36
1916 6816 3.451894 CTTGGATTGGGCGGGCAC 61.452 66.667 3.27 0.00 0.00 5.01
1917 6817 3.944250 CTTGGATTGGGCGGGCACT 62.944 63.158 3.27 0.00 0.00 4.40
1968 6872 3.729698 GCCCGCGCGGTAAAACTT 61.730 61.111 43.12 0.00 0.00 2.66
2086 7023 2.452813 CGCGTGCTAGATTTGGCGT 61.453 57.895 0.00 0.00 38.90 5.68
2433 7396 1.451387 CTTTCCCGCGGCTTACCAT 60.451 57.895 22.85 0.00 34.57 3.55
2557 7520 5.760253 AGACATCATCAACGAAGAACAGTTT 59.240 36.000 0.00 0.00 0.00 2.66
2630 7593 2.733593 GCGAGGACAAGCGAACGT 60.734 61.111 0.00 0.00 0.00 3.99
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 104 2.805099 AGTCGTCGTCGAGATATTACCC 59.195 50.000 4.68 0.00 46.96 3.69
112 117 5.523188 CCTCTAGTCAGTAATTAGTCGTCGT 59.477 44.000 0.00 0.00 0.00 4.34
159 164 8.717821 TCCAAGTTTCTTCACAAGATAAATACG 58.282 33.333 0.00 0.00 37.38 3.06
232 344 0.954449 GAGATGCCGGGCAGATCATG 60.954 60.000 27.62 0.00 43.65 3.07
376 491 4.640771 AGAATGAAAGGCACTCCACTAA 57.359 40.909 0.00 0.00 38.49 2.24
420 677 6.309357 TCTGGCTAAGAATGAATGGCATATT 58.691 36.000 0.00 0.00 35.78 1.28
462 719 2.565834 AGTGCCCATGTTAGACGTACTT 59.434 45.455 0.00 0.00 0.00 2.24
480 771 5.063438 CGTCAATTGGTATACTTGTGGAGTG 59.937 44.000 5.42 0.00 39.48 3.51
520 811 1.398958 GGAGGAGCGATTCAGAGGCT 61.399 60.000 0.00 0.00 40.29 4.58
523 814 1.361993 CGGGAGGAGCGATTCAGAG 59.638 63.158 0.00 0.00 0.00 3.35
527 818 3.170490 ATGGCGGGAGGAGCGATTC 62.170 63.158 0.00 0.00 35.00 2.52
595 2268 1.463444 CACGGAAAATCGGAAGGACAC 59.537 52.381 0.00 0.00 0.00 3.67
600 2288 1.226018 GCGCACGGAAAATCGGAAG 60.226 57.895 0.30 0.00 0.00 3.46
619 2307 3.477530 AGAAGGCCATAGTTAAATCCGC 58.522 45.455 5.01 0.00 0.00 5.54
620 2308 3.741344 CGAGAAGGCCATAGTTAAATCCG 59.259 47.826 5.01 0.00 0.00 4.18
737 2425 3.195661 GGCCGATGACTGGTAAACTAAG 58.804 50.000 0.00 0.00 0.00 2.18
749 2437 2.871427 GCGTGAATCGGCCGATGAC 61.871 63.158 39.53 33.10 40.26 3.06
750 2438 2.584970 GCGTGAATCGGCCGATGA 60.585 61.111 39.53 26.36 40.26 2.92
752 2440 4.508128 ACGCGTGAATCGGCCGAT 62.508 61.111 34.60 34.60 40.26 4.18
755 2443 2.507547 TACACGCGTGAATCGGCC 60.508 61.111 42.94 0.00 40.26 6.13
756 2444 1.804326 AGTACACGCGTGAATCGGC 60.804 57.895 42.94 23.78 40.26 5.54
760 2448 2.287728 TGTACACAGTACACGCGTGAAT 60.288 45.455 42.94 25.58 34.69 2.57
761 2449 1.065251 TGTACACAGTACACGCGTGAA 59.935 47.619 42.94 15.51 34.69 3.18
763 2451 1.050009 CTGTACACAGTACACGCGTG 58.950 55.000 35.99 35.99 39.09 5.34
764 2452 0.946528 TCTGTACACAGTACACGCGT 59.053 50.000 5.58 5.58 44.12 6.01
765 2453 1.324718 GTCTGTACACAGTACACGCG 58.675 55.000 3.53 3.53 44.12 6.01
766 2454 2.410785 TGTCTGTACACAGTACACGC 57.589 50.000 9.11 3.47 44.12 5.34
826 2514 3.194861 GCACGCTCTTGTTGACCATATA 58.805 45.455 0.00 0.00 0.00 0.86
827 2515 2.009774 GCACGCTCTTGTTGACCATAT 58.990 47.619 0.00 0.00 0.00 1.78
828 2516 1.270571 TGCACGCTCTTGTTGACCATA 60.271 47.619 0.00 0.00 0.00 2.74
850 2538 4.596212 AGATCAGGCTCATCATGTGGATTA 59.404 41.667 0.00 0.00 32.57 1.75
929 4710 0.833834 ATGTATGCGAGGAGAGGGGG 60.834 60.000 0.00 0.00 0.00 5.40
954 4735 5.682943 TTTTTGGTACCAAGTCGATGAAG 57.317 39.130 25.74 0.00 37.24 3.02
1059 4842 2.324330 CGCAAGCAACCGTGATGGA 61.324 57.895 0.00 0.00 42.00 3.41
1062 4845 3.737172 GCCGCAAGCAACCGTGAT 61.737 61.111 0.00 0.00 42.97 3.06
1107 5829 1.977056 ACGGCGGTGAGATAGTGATA 58.023 50.000 13.24 0.00 0.00 2.15
1110 5934 0.866061 CGAACGGCGGTGAGATAGTG 60.866 60.000 13.24 0.00 36.03 2.74
1141 5965 3.535561 CGCATGTGTTCTCCCTAGAAAT 58.464 45.455 0.00 0.00 43.30 2.17
1147 5971 2.045926 GGCGCATGTGTTCTCCCT 60.046 61.111 10.83 0.00 0.00 4.20
1148 5972 3.134127 GGGCGCATGTGTTCTCCC 61.134 66.667 10.83 6.03 0.00 4.30
1185 6015 2.436115 GGGGCTCCGTTGTAGCAC 60.436 66.667 0.00 0.00 42.90 4.40
1190 6020 1.615424 AGGTATGGGGCTCCGTTGT 60.615 57.895 0.44 0.00 35.24 3.32
1230 6060 1.758514 GTCGAGGATCTGGAGCCCA 60.759 63.158 0.91 0.00 37.67 5.36
1274 6104 1.338200 GCTTGTGGACATCGGAGACTT 60.338 52.381 0.00 0.00 42.51 3.01
1341 6171 4.514585 TTGGTGGCGGTGTTGGCT 62.515 61.111 0.00 0.00 35.06 4.75
1363 6193 1.488393 GCTTACTGAGAAGGGATGCCT 59.512 52.381 0.00 0.00 0.00 4.75
1432 6274 2.427245 CCACCAGGTCCTCTAGGCG 61.427 68.421 0.00 0.00 34.44 5.52
1436 6290 0.485543 TGTGTCCACCAGGTCCTCTA 59.514 55.000 0.00 0.00 35.89 2.43
1439 6293 1.074471 ACTGTGTCCACCAGGTCCT 60.074 57.895 0.00 0.00 35.89 3.85
1443 6297 1.893808 GCACACTGTGTCCACCAGG 60.894 63.158 11.12 0.00 35.75 4.45
1473 6327 1.382629 CCCTCCCACCCGAACAAAT 59.617 57.895 0.00 0.00 0.00 2.32
1493 6347 0.693817 CACGTTCGTCTCGTTGTACG 59.306 55.000 0.00 0.00 44.19 3.67
1507 6361 0.671796 TATCCGCCGATGATCACGTT 59.328 50.000 0.00 0.00 0.00 3.99
1564 6430 1.666872 CCGTTCCAGTCGTCCCAAC 60.667 63.158 0.00 0.00 0.00 3.77
1566 6432 2.522436 ACCGTTCCAGTCGTCCCA 60.522 61.111 0.00 0.00 0.00 4.37
1570 6436 0.949105 GCATTCACCGTTCCAGTCGT 60.949 55.000 0.00 0.00 0.00 4.34
1580 6446 1.153647 TAGTCGCTGGCATTCACCG 60.154 57.895 0.00 0.00 0.00 4.94
1602 6468 1.069427 GCCATCGCTGATGAGCTCT 59.931 57.895 16.19 0.00 42.09 4.09
1683 6555 3.019564 GCTGCCCACAAGAGTATTTGAT 58.980 45.455 0.00 0.00 0.00 2.57
1693 6568 1.589716 GCCTAGTTGCTGCCCACAAG 61.590 60.000 0.00 0.00 0.00 3.16
1696 6571 3.127533 CGCCTAGTTGCTGCCCAC 61.128 66.667 0.00 0.00 0.00 4.61
1721 6603 5.199982 TCCAATCCTGGGCACTTATTTAA 57.800 39.130 0.00 0.00 43.71 1.52
1745 6627 2.543653 GGCAAAACTGTTGCATCGAAGT 60.544 45.455 12.66 0.00 46.58 3.01
1752 6634 0.901124 AAGTGGGCAAAACTGTTGCA 59.099 45.000 12.66 0.00 46.58 4.08
1775 6671 1.154205 AAGGCAGGCGATTTCGATCG 61.154 55.000 9.36 9.36 45.99 3.69
1856 6756 5.295292 CGCATCTCTCACCTTGAATGTATTT 59.705 40.000 0.00 0.00 0.00 1.40
1865 6765 2.864946 CAATCTCGCATCTCTCACCTTG 59.135 50.000 0.00 0.00 0.00 3.61
1869 6769 3.114809 CAGTCAATCTCGCATCTCTCAC 58.885 50.000 0.00 0.00 0.00 3.51
1873 6773 0.851495 CGCAGTCAATCTCGCATCTC 59.149 55.000 0.00 0.00 0.00 2.75
1874 6774 1.150567 GCGCAGTCAATCTCGCATCT 61.151 55.000 0.30 0.00 40.03 2.90
1875 6775 1.275066 GCGCAGTCAATCTCGCATC 59.725 57.895 0.30 0.00 40.03 3.91
1876 6776 1.448365 TGCGCAGTCAATCTCGCAT 60.448 52.632 5.66 0.00 42.62 4.73
1877 6777 2.048316 TGCGCAGTCAATCTCGCA 60.048 55.556 5.66 3.97 43.95 5.10
1878 6778 2.397252 GTGCGCAGTCAATCTCGC 59.603 61.111 12.22 0.00 40.38 5.03
1879 6779 2.792290 CGGTGCGCAGTCAATCTCG 61.792 63.158 12.22 0.00 0.00 4.04
1880 6780 1.687494 GACGGTGCGCAGTCAATCTC 61.687 60.000 23.06 3.54 39.18 2.75
1881 6781 1.738099 GACGGTGCGCAGTCAATCT 60.738 57.895 23.06 0.00 39.18 2.40
1882 6782 1.291877 AAGACGGTGCGCAGTCAATC 61.292 55.000 28.09 13.83 41.29 2.67
1883 6783 1.301716 AAGACGGTGCGCAGTCAAT 60.302 52.632 28.09 16.01 41.29 2.57
1884 6784 2.108157 AAGACGGTGCGCAGTCAA 59.892 55.556 28.09 0.00 41.29 3.18
1885 6785 2.661537 CAAGACGGTGCGCAGTCA 60.662 61.111 28.09 0.00 41.29 3.41
1886 6786 3.414700 CCAAGACGGTGCGCAGTC 61.415 66.667 20.95 20.95 39.57 3.51
1887 6787 2.731691 AATCCAAGACGGTGCGCAGT 62.732 55.000 12.22 6.04 35.57 4.40
1888 6788 2.034879 AATCCAAGACGGTGCGCAG 61.035 57.895 12.22 1.57 35.57 5.18
1889 6789 2.031919 AATCCAAGACGGTGCGCA 59.968 55.556 5.66 5.66 35.57 6.09
1890 6790 2.480555 CAATCCAAGACGGTGCGC 59.519 61.111 0.00 0.00 35.57 6.09
1891 6791 2.398554 CCCAATCCAAGACGGTGCG 61.399 63.158 0.00 0.00 35.57 5.34
1892 6792 2.700773 GCCCAATCCAAGACGGTGC 61.701 63.158 0.00 0.00 35.57 5.01
1893 6793 2.398554 CGCCCAATCCAAGACGGTG 61.399 63.158 0.00 0.00 35.57 4.94
1894 6794 2.046314 CGCCCAATCCAAGACGGT 60.046 61.111 0.00 0.00 35.57 4.83
1895 6795 2.824041 CCGCCCAATCCAAGACGG 60.824 66.667 0.00 0.00 0.00 4.79
1896 6796 2.824041 CCCGCCCAATCCAAGACG 60.824 66.667 0.00 0.00 0.00 4.18
1897 6797 3.140814 GCCCGCCCAATCCAAGAC 61.141 66.667 0.00 0.00 0.00 3.01
1898 6798 3.656280 TGCCCGCCCAATCCAAGA 61.656 61.111 0.00 0.00 0.00 3.02
1899 6799 3.451894 GTGCCCGCCCAATCCAAG 61.452 66.667 0.00 0.00 0.00 3.61
1900 6800 3.978193 AGTGCCCGCCCAATCCAA 61.978 61.111 0.00 0.00 0.00 3.53
1901 6801 4.738998 CAGTGCCCGCCCAATCCA 62.739 66.667 0.00 0.00 0.00 3.41
1902 6802 4.424711 TCAGTGCCCGCCCAATCC 62.425 66.667 0.00 0.00 0.00 3.01
1903 6803 2.825836 CTCAGTGCCCGCCCAATC 60.826 66.667 0.00 0.00 0.00 2.67
1904 6804 3.329889 TCTCAGTGCCCGCCCAAT 61.330 61.111 0.00 0.00 0.00 3.16
1905 6805 4.020617 CTCTCAGTGCCCGCCCAA 62.021 66.667 0.00 0.00 0.00 4.12
1908 6808 4.479993 ATGCTCTCAGTGCCCGCC 62.480 66.667 0.00 0.00 0.00 6.13
1909 6809 2.894387 GATGCTCTCAGTGCCCGC 60.894 66.667 0.00 0.00 0.00 6.13
1910 6810 1.227205 GAGATGCTCTCAGTGCCCG 60.227 63.158 0.00 0.00 42.90 6.13
1911 6811 1.145819 GGAGATGCTCTCAGTGCCC 59.854 63.158 13.06 0.00 45.12 5.36
1912 6812 0.251354 TTGGAGATGCTCTCAGTGCC 59.749 55.000 13.06 0.00 45.12 5.01
1913 6813 1.338484 TGTTGGAGATGCTCTCAGTGC 60.338 52.381 13.06 0.00 45.12 4.40
1914 6814 2.619147 CTGTTGGAGATGCTCTCAGTG 58.381 52.381 13.06 0.00 45.12 3.66
1915 6815 1.554160 CCTGTTGGAGATGCTCTCAGT 59.446 52.381 13.06 0.00 45.12 3.41
1916 6816 1.743091 GCCTGTTGGAGATGCTCTCAG 60.743 57.143 13.06 0.00 45.12 3.35
1917 6817 0.251354 GCCTGTTGGAGATGCTCTCA 59.749 55.000 13.06 0.00 45.12 3.27
1953 6855 0.236449 AAAGAAGTTTTACCGCGCGG 59.764 50.000 44.88 44.88 42.03 6.46
2557 7520 3.771160 GCCCTCCTCTCGGCGAAA 61.771 66.667 12.13 0.00 34.94 3.46
2630 7593 0.825410 TATTTAGCGACCGCCTTCCA 59.175 50.000 11.03 0.00 43.17 3.53


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

AutoCloner maintained by Alex Coulton.