Multiple sequence alignment - TraesCS7B01G148500

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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 TraesCS7B01G148500 chr7B 100.000 4540 0 0 1 4540 196281687 196277148 0.000000e+00 8384.0
1 TraesCS7B01G148500 chr3D 83.333 2166 245 53 866 2951 592871988 592874117 0.000000e+00 1893.0
2 TraesCS7B01G148500 chr3D 83.287 2166 245 54 866 2951 592866248 592868376 0.000000e+00 1886.0
3 TraesCS7B01G148500 chr3D 93.817 372 23 0 2947 3318 592868416 592868787 1.100000e-155 560.0
4 TraesCS7B01G148500 chr3D 93.817 372 23 0 2947 3318 592874157 592874528 1.100000e-155 560.0
5 TraesCS7B01G148500 chr3D 87.671 219 20 4 3313 3525 592868878 592869095 9.750000e-62 248.0
6 TraesCS7B01G148500 chr3D 87.671 219 20 4 3313 3525 592874619 592874836 9.750000e-62 248.0
7 TraesCS7B01G148500 chr7A 93.173 1245 61 11 3313 4540 218263837 218265074 0.000000e+00 1807.0
8 TraesCS7B01G148500 chr7A 88.636 792 59 8 1733 2504 218262256 218263036 0.000000e+00 935.0
9 TraesCS7B01G148500 chr7A 86.483 836 96 8 866 1687 218261424 218262256 0.000000e+00 902.0
10 TraesCS7B01G148500 chr7A 96.053 456 18 0 2499 2954 218263172 218263627 0.000000e+00 743.0
11 TraesCS7B01G148500 chr7A 87.794 467 29 9 382 820 218260876 218261342 5.200000e-144 521.0
12 TraesCS7B01G148500 chr7A 86.387 191 12 8 1 190 218260703 218260880 3.580000e-46 196.0
13 TraesCS7B01G148500 chr7A 76.489 319 73 2 2611 2928 6299823 6300140 6.040000e-39 172.0
14 TraesCS7B01G148500 chr7A 100.000 28 0 0 2948 2975 218263665 218263692 8.000000e-03 52.8
15 TraesCS7B01G148500 chr7D 92.177 1240 70 10 866 2089 205946468 205947696 0.000000e+00 1727.0
16 TraesCS7B01G148500 chr7D 93.049 892 39 11 2073 2951 205949078 205949959 0.000000e+00 1282.0
17 TraesCS7B01G148500 chr7D 94.529 658 25 7 3313 3961 205950461 205951116 0.000000e+00 1005.0
18 TraesCS7B01G148500 chr7D 88.271 827 62 21 1 812 205945566 205946372 0.000000e+00 957.0
19 TraesCS7B01G148500 chr7D 94.286 595 30 2 3947 4540 205952903 205953494 0.000000e+00 907.0
20 TraesCS7B01G148500 chr7D 95.957 371 15 0 2948 3318 205950000 205950370 1.810000e-168 603.0
21 TraesCS7B01G148500 chrUn 83.594 1920 207 58 1107 2951 45771009 45772895 0.000000e+00 1701.0
22 TraesCS7B01G148500 chrUn 81.735 980 113 31 1362 2289 214042654 214043619 0.000000e+00 758.0
23 TraesCS7B01G148500 chrUn 81.735 980 113 30 1362 2289 240302431 240301466 0.000000e+00 758.0
24 TraesCS7B01G148500 chrUn 91.398 558 37 2 2397 2951 214043906 214044455 0.000000e+00 754.0
25 TraesCS7B01G148500 chrUn 91.266 561 38 2 2397 2954 240301179 240300627 0.000000e+00 754.0
26 TraesCS7B01G148500 chrUn 94.879 371 19 0 2948 3318 214044496 214044866 8.470000e-162 580.0
27 TraesCS7B01G148500 chrUn 94.879 371 19 0 2948 3318 240300589 240300219 8.470000e-162 580.0
28 TraesCS7B01G148500 chrUn 93.548 372 24 0 2947 3318 45772935 45773306 5.130000e-154 555.0
29 TraesCS7B01G148500 chrUn 87.671 219 20 4 3313 3525 45773397 45773614 9.750000e-62 248.0
30 TraesCS7B01G148500 chrUn 93.985 133 8 0 3313 3445 214044957 214045089 7.700000e-48 202.0
31 TraesCS7B01G148500 chrUn 93.985 133 8 0 3313 3445 240300128 240299996 7.700000e-48 202.0
32 TraesCS7B01G148500 chrUn 77.311 238 23 11 587 819 45770630 45770841 1.340000e-20 111.0
33 TraesCS7B01G148500 chr2A 81.572 369 62 4 2565 2930 764771385 764771020 2.650000e-77 300.0
34 TraesCS7B01G148500 chr1A 77.224 281 61 3 2946 3224 530516392 530516113 1.310000e-35 161.0
35 TraesCS7B01G148500 chr2D 77.947 263 50 7 2952 3210 602704734 602704992 1.690000e-34 158.0


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 TraesCS7B01G148500 chr7B 196277148 196281687 4539 True 8384.000000 8384 100.000000 1 4540 1 chr7B.!!$R1 4539
1 TraesCS7B01G148500 chr3D 592866248 592874836 8588 False 899.166667 1893 88.266000 866 3525 6 chr3D.!!$F1 2659
2 TraesCS7B01G148500 chr7A 218260703 218265074 4371 False 736.685714 1807 91.218000 1 4540 7 chr7A.!!$F2 4539
3 TraesCS7B01G148500 chr7D 205945566 205953494 7928 False 1080.166667 1727 93.044833 1 4540 6 chr7D.!!$F1 4539
4 TraesCS7B01G148500 chrUn 45770630 45773614 2984 False 653.750000 1701 85.531000 587 3525 4 chrUn.!!$F1 2938
5 TraesCS7B01G148500 chrUn 214042654 214045089 2435 False 573.500000 758 90.499250 1362 3445 4 chrUn.!!$F2 2083
6 TraesCS7B01G148500 chrUn 240299996 240302431 2435 True 573.500000 758 90.466250 1362 3445 4 chrUn.!!$R1 2083

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
883 970 0.476338 TTACCCTGCAAGCACCAAGA 59.524 50.0 0.00 0.00 0.00 3.02 F
1000 1101 0.390866 AGCCATGTCTCTGTTCTGCG 60.391 55.0 0.00 0.00 0.00 5.18 F
1583 1782 0.396435 CCTGCAGGTACCACTTGTCA 59.604 55.0 25.53 5.76 0.00 3.58 F
2470 10030 0.531974 GCCATTGCGGTAGGAATCGA 60.532 55.0 0.00 0.00 36.21 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1955 7903 0.245539 GGTACACAAGGCACTCGCTA 59.754 55.000 0.00 0.0 38.49 4.26 R
2105 9461 1.678101 AGTTTGTGGCTTTGAGCACTC 59.322 47.619 2.04 0.0 44.75 3.51 R
3051 10796 0.036952 TGCCTCGAGAAGCTCCAAAG 60.037 55.000 15.71 0.0 0.00 2.77 R
4087 13746 2.618241 TCAAAGCTCACCATCAACACAC 59.382 45.455 0.00 0.0 0.00 3.82 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
50 51 4.161377 ACCTTCCTTCTCTCTGATAAGCAC 59.839 45.833 0.00 0.00 0.00 4.40
51 52 4.358851 CTTCCTTCTCTCTGATAAGCACG 58.641 47.826 0.00 0.00 0.00 5.34
58 59 6.884280 TCTCTCTGATAAGCACGATTATCA 57.116 37.500 14.94 14.94 45.45 2.15
59 60 6.673106 TCTCTCTGATAAGCACGATTATCAC 58.327 40.000 12.45 0.00 43.74 3.06
60 61 6.488344 TCTCTCTGATAAGCACGATTATCACT 59.512 38.462 12.45 0.00 43.74 3.41
61 62 6.442112 TCTCTGATAAGCACGATTATCACTG 58.558 40.000 12.45 8.96 43.74 3.66
62 63 6.263168 TCTCTGATAAGCACGATTATCACTGA 59.737 38.462 12.45 10.66 43.74 3.41
63 64 6.442112 TCTGATAAGCACGATTATCACTGAG 58.558 40.000 12.45 5.11 43.74 3.35
64 65 6.263168 TCTGATAAGCACGATTATCACTGAGA 59.737 38.462 12.45 7.00 43.74 3.27
65 66 6.442112 TGATAAGCACGATTATCACTGAGAG 58.558 40.000 12.45 0.00 43.74 3.20
66 67 4.727507 AAGCACGATTATCACTGAGAGT 57.272 40.909 0.00 0.00 0.00 3.24
106 107 6.805271 CCATTATTTGAATGATCATCCTTCGC 59.195 38.462 9.06 0.00 34.96 4.70
107 108 6.940831 TTATTTGAATGATCATCCTTCGCA 57.059 33.333 9.06 0.00 34.96 5.10
141 142 5.520632 CCAGCTTCTTTGATTATGCTCATG 58.479 41.667 0.00 0.00 0.00 3.07
209 212 4.819630 TGTCCATGGTTTAACAAGTCACTC 59.180 41.667 12.58 0.00 0.00 3.51
215 218 2.870411 GTTTAACAAGTCACTCGCCACT 59.130 45.455 0.00 0.00 0.00 4.00
222 225 1.474478 AGTCACTCGCCACTGATAGTG 59.526 52.381 2.05 2.05 45.53 2.74
223 226 1.202582 GTCACTCGCCACTGATAGTGT 59.797 52.381 8.04 0.00 44.50 3.55
224 227 1.202348 TCACTCGCCACTGATAGTGTG 59.798 52.381 8.04 0.32 44.50 3.82
225 228 1.202348 CACTCGCCACTGATAGTGTGA 59.798 52.381 8.04 5.01 44.50 3.58
226 229 2.103373 ACTCGCCACTGATAGTGTGAT 58.897 47.619 8.04 0.00 44.50 3.06
227 230 3.066760 CACTCGCCACTGATAGTGTGATA 59.933 47.826 8.04 0.00 44.50 2.15
228 231 3.316588 ACTCGCCACTGATAGTGTGATAG 59.683 47.826 8.04 3.29 44.50 2.08
229 232 3.288092 TCGCCACTGATAGTGTGATAGT 58.712 45.455 8.04 0.00 44.50 2.12
235 238 6.634805 CCACTGATAGTGTGATAGTGTCTTT 58.365 40.000 8.04 0.00 44.50 2.52
302 306 3.509575 TCGGCAAGTCCATTAAATGCTTT 59.490 39.130 0.00 0.00 37.20 3.51
313 317 7.657354 GTCCATTAAATGCTTTCTCTTTTTGGT 59.343 33.333 0.00 0.00 0.00 3.67
316 320 9.654417 CATTAAATGCTTTCTCTTTTTGGTTTG 57.346 29.630 0.00 0.00 0.00 2.93
336 340 9.771534 TGGTTTGGTCTTTTAATCTTATTTTGG 57.228 29.630 0.00 0.00 0.00 3.28
358 362 2.989166 GGCATTAGTCTTTGCAAGCAAC 59.011 45.455 7.03 0.00 40.66 4.17
368 372 5.804979 GTCTTTGCAAGCAACTTCAAAACTA 59.195 36.000 7.03 0.00 35.46 2.24
578 582 2.879026 GTTCTCCATCTTTTATCGGCCC 59.121 50.000 0.00 0.00 0.00 5.80
582 586 0.535102 CATCTTTTATCGGCCCGCCT 60.535 55.000 0.00 0.00 0.00 5.52
689 718 4.060900 TCTGTGCAGAGACAAATGAAGAC 58.939 43.478 9.94 0.00 32.82 3.01
695 724 4.505922 GCAGAGACAAATGAAGACGATAGG 59.494 45.833 0.00 0.00 43.77 2.57
697 726 4.956700 AGAGACAAATGAAGACGATAGGGA 59.043 41.667 0.00 0.00 43.77 4.20
717 747 5.373854 AGGGACTCCTTATTATCAGGCATTT 59.626 40.000 0.00 0.00 41.56 2.32
755 785 1.537202 GGCTTGCAGTTCCTTGTACAG 59.463 52.381 0.00 0.00 0.00 2.74
760 790 3.728845 TGCAGTTCCTTGTACAGAGAAC 58.271 45.455 22.87 22.87 39.09 3.01
763 793 3.996480 AGTTCCTTGTACAGAGAACTGC 58.004 45.455 28.19 12.07 45.39 4.40
764 794 3.388024 AGTTCCTTGTACAGAGAACTGCA 59.612 43.478 28.19 0.86 45.39 4.41
765 795 3.667497 TCCTTGTACAGAGAACTGCAG 57.333 47.619 13.48 13.48 46.95 4.41
766 796 2.300152 TCCTTGTACAGAGAACTGCAGG 59.700 50.000 19.93 0.72 46.95 4.85
767 797 2.300152 CCTTGTACAGAGAACTGCAGGA 59.700 50.000 19.93 0.00 46.95 3.86
768 798 3.055530 CCTTGTACAGAGAACTGCAGGAT 60.056 47.826 19.93 6.29 46.95 3.24
769 799 3.599730 TGTACAGAGAACTGCAGGATG 57.400 47.619 19.93 11.03 46.95 3.51
770 800 2.234661 TGTACAGAGAACTGCAGGATGG 59.765 50.000 19.93 4.79 46.95 3.51
771 801 1.356124 ACAGAGAACTGCAGGATGGT 58.644 50.000 19.93 5.45 46.95 3.55
777 809 1.771255 GAACTGCAGGATGGTAGGGAT 59.229 52.381 19.93 0.00 35.86 3.85
785 817 3.008813 CAGGATGGTAGGGATTCCTCATG 59.991 52.174 0.00 0.00 43.66 3.07
788 820 1.345422 TGGTAGGGATTCCTCATGGCT 60.345 52.381 0.00 0.00 43.66 4.75
808 840 3.385755 GCTAGGCATTTGGACAATTGGAT 59.614 43.478 10.83 0.00 0.00 3.41
815 854 5.469421 GCATTTGGACAATTGGATTTGACAA 59.531 36.000 10.83 1.64 0.00 3.18
820 859 8.517062 TTGGACAATTGGATTTGACAAATTTT 57.483 26.923 14.46 4.67 30.35 1.82
821 860 8.517062 TGGACAATTGGATTTGACAAATTTTT 57.483 26.923 14.46 4.36 0.00 1.94
828 867 9.829507 ATTGGATTTGACAAATTTTTAGTCACA 57.170 25.926 14.46 4.44 41.53 3.58
829 868 8.870160 TGGATTTGACAAATTTTTAGTCACAG 57.130 30.769 14.46 0.00 41.53 3.66
830 869 8.690884 TGGATTTGACAAATTTTTAGTCACAGA 58.309 29.630 14.46 1.33 41.53 3.41
839 925 3.364889 TTTAGTCACAGAGTCCACACG 57.635 47.619 0.00 0.00 0.00 4.49
840 926 0.596577 TAGTCACAGAGTCCACACGC 59.403 55.000 0.00 0.00 0.00 5.34
855 942 2.550606 CACACGCAAGGCTTTTACCTAA 59.449 45.455 0.00 0.00 39.93 2.69
856 943 3.003897 CACACGCAAGGCTTTTACCTAAA 59.996 43.478 0.00 0.00 39.93 1.85
857 944 3.824443 ACACGCAAGGCTTTTACCTAAAT 59.176 39.130 0.00 0.00 39.93 1.40
858 945 4.165779 CACGCAAGGCTTTTACCTAAATG 58.834 43.478 0.00 0.00 39.93 2.32
859 946 4.076394 ACGCAAGGCTTTTACCTAAATGA 58.924 39.130 0.00 0.00 39.93 2.57
860 947 4.705023 ACGCAAGGCTTTTACCTAAATGAT 59.295 37.500 0.00 0.00 39.93 2.45
861 948 5.185056 ACGCAAGGCTTTTACCTAAATGATT 59.815 36.000 0.00 0.00 39.93 2.57
862 949 5.743872 CGCAAGGCTTTTACCTAAATGATTC 59.256 40.000 0.00 0.00 39.93 2.52
863 950 6.624861 CGCAAGGCTTTTACCTAAATGATTCA 60.625 38.462 0.00 0.00 39.93 2.57
864 951 7.267857 GCAAGGCTTTTACCTAAATGATTCAT 58.732 34.615 0.00 0.00 39.93 2.57
865 952 7.765819 GCAAGGCTTTTACCTAAATGATTCATT 59.234 33.333 6.06 6.06 39.93 2.57
876 963 4.660789 AATGATTCATTACCCTGCAAGC 57.339 40.909 10.16 0.00 31.77 4.01
877 964 3.084536 TGATTCATTACCCTGCAAGCA 57.915 42.857 0.00 0.00 0.00 3.91
882 969 1.203052 CATTACCCTGCAAGCACCAAG 59.797 52.381 0.00 0.00 0.00 3.61
883 970 0.476338 TTACCCTGCAAGCACCAAGA 59.524 50.000 0.00 0.00 0.00 3.02
884 971 0.476338 TACCCTGCAAGCACCAAGAA 59.524 50.000 0.00 0.00 0.00 2.52
909 996 8.641498 ATCTTGTGAAGGTAAACTTGATGATT 57.359 30.769 0.00 0.00 40.21 2.57
929 1024 5.639506 TGATTGCTTAGAACAGTCAGTAAGC 59.360 40.000 11.90 11.90 45.04 3.09
930 1025 3.575630 TGCTTAGAACAGTCAGTAAGCG 58.424 45.455 13.15 0.00 46.87 4.68
946 1043 1.443802 AGCGAGGAAAAGTAAGCAGC 58.556 50.000 0.00 0.00 0.00 5.25
955 1052 7.307455 CGAGGAAAAGTAAGCAGCTATTAATCC 60.307 40.741 0.00 0.00 0.00 3.01
985 1086 3.007940 AGTTAGCGCCATATGATAAGCCA 59.992 43.478 2.29 0.00 0.00 4.75
991 1092 3.620374 CGCCATATGATAAGCCATGTCTC 59.380 47.826 3.65 0.00 0.00 3.36
992 1093 4.622457 CGCCATATGATAAGCCATGTCTCT 60.622 45.833 3.65 0.00 0.00 3.10
993 1094 4.634883 GCCATATGATAAGCCATGTCTCTG 59.365 45.833 3.65 0.00 0.00 3.35
1000 1101 0.390866 AGCCATGTCTCTGTTCTGCG 60.391 55.000 0.00 0.00 0.00 5.18
1006 1107 5.109210 CCATGTCTCTGTTCTGCGTATAAA 58.891 41.667 0.00 0.00 0.00 1.40
1031 1134 4.216257 GGCACATAACACAGAACATCTTGT 59.784 41.667 0.00 0.00 0.00 3.16
1032 1135 5.149273 GCACATAACACAGAACATCTTGTG 58.851 41.667 3.29 3.29 33.33 3.33
1096 1209 2.632996 AGTTAGCACTTCTGTGTGGCTA 59.367 45.455 0.00 0.00 45.44 3.93
1102 1215 1.417890 ACTTCTGTGTGGCTAAGCTGT 59.582 47.619 0.00 0.00 0.00 4.40
1103 1216 1.802960 CTTCTGTGTGGCTAAGCTGTG 59.197 52.381 0.00 0.00 0.00 3.66
1133 1300 3.374988 ACATCACACAAATGAGTATGGCG 59.625 43.478 0.00 0.00 30.46 5.69
1145 1315 0.608640 GTATGGCGGGTATAGCAGCT 59.391 55.000 23.04 9.87 36.08 4.24
1174 1344 1.836166 TCTTCTGCAGCTTCTAGCCAT 59.164 47.619 9.47 0.00 43.77 4.40
1245 1417 3.927555 TGCGGCTATAAGCATACCC 57.072 52.632 0.00 0.00 44.75 3.69
1299 1471 1.905354 GGGCTTCAAGCTTGCCTGT 60.905 57.895 21.99 0.00 45.45 4.00
1303 1475 1.608590 GCTTCAAGCTTGCCTGTAACA 59.391 47.619 21.99 0.00 38.45 2.41
1514 1692 6.027749 CAGGCAGGAATAAAATCGTTGTTAC 58.972 40.000 0.00 0.00 0.00 2.50
1583 1782 0.396435 CCTGCAGGTACCACTTGTCA 59.604 55.000 25.53 5.76 0.00 3.58
1695 7637 7.972277 CCTGACTCAAATATGTTTTCCATCAAG 59.028 37.037 0.00 0.00 34.86 3.02
1696 7638 8.408043 TGACTCAAATATGTTTTCCATCAAGT 57.592 30.769 0.00 0.00 34.86 3.16
1697 7639 9.513906 TGACTCAAATATGTTTTCCATCAAGTA 57.486 29.630 0.00 0.00 34.86 2.24
1698 7640 9.774742 GACTCAAATATGTTTTCCATCAAGTAC 57.225 33.333 0.00 0.00 34.86 2.73
1699 7641 9.295825 ACTCAAATATGTTTTCCATCAAGTACA 57.704 29.630 0.00 0.00 34.86 2.90
1700 7642 9.559958 CTCAAATATGTTTTCCATCAAGTACAC 57.440 33.333 0.00 0.00 34.86 2.90
1701 7643 9.295825 TCAAATATGTTTTCCATCAAGTACACT 57.704 29.630 0.00 0.00 34.86 3.55
1793 7738 3.696051 GCAAGAAGAAGAATGCCATGGTA 59.304 43.478 14.67 9.89 32.73 3.25
1921 7866 2.038952 ACTTGTCATGTGCTGAGGCTAA 59.961 45.455 0.00 0.00 39.59 3.09
1934 7882 4.397417 GCTGAGGCTAACAATTCAAGTGAT 59.603 41.667 0.00 0.00 35.22 3.06
1943 7891 7.814107 GCTAACAATTCAAGTGATTTTGGATGA 59.186 33.333 0.00 0.00 0.00 2.92
1955 7903 6.005823 TGATTTTGGATGACTCAGTGACAAT 58.994 36.000 0.00 0.00 0.00 2.71
2094 9450 8.845413 ACTAGACTCCCTGTATAATTAGTACG 57.155 38.462 0.00 0.00 0.00 3.67
2111 9467 4.017808 AGTACGATTACTTCAGGAGTGCT 58.982 43.478 0.00 0.00 39.48 4.40
2256 9692 0.618458 GGCACCACTGGTAATCCTCA 59.382 55.000 0.00 0.00 32.11 3.86
2257 9693 1.004277 GGCACCACTGGTAATCCTCAA 59.996 52.381 0.00 0.00 32.11 3.02
2261 9697 4.558697 GCACCACTGGTAATCCTCAAAAAC 60.559 45.833 0.00 0.00 32.11 2.43
2295 9731 5.115480 GTTCTTCAACCAAATCAGCCAAAA 58.885 37.500 0.00 0.00 0.00 2.44
2349 9793 9.490663 GGAAAATACTGATCTTTGTTGATAACG 57.509 33.333 0.00 0.00 0.00 3.18
2357 9801 5.505165 TCTTTGTTGATAACGTCGTAAGC 57.495 39.130 0.00 0.00 37.18 3.09
2424 9984 4.917906 ACTCAAAATCTAGACCCAAGCT 57.082 40.909 0.00 0.00 0.00 3.74
2470 10030 0.531974 GCCATTGCGGTAGGAATCGA 60.532 55.000 0.00 0.00 36.21 3.59
2588 10289 6.887545 TCTTCAAAAAGAACAGAGGGTTGTTA 59.112 34.615 0.00 0.00 41.66 2.41
2589 10290 7.394923 TCTTCAAAAAGAACAGAGGGTTGTTAA 59.605 33.333 0.00 0.00 41.66 2.01
2735 10436 9.178758 GTCTACAAAGGGATTTTATCTGACAAT 57.821 33.333 0.00 0.00 0.00 2.71
2879 10580 5.312120 GTCTCGAGACAGAAGTTCCATTA 57.688 43.478 34.97 0.00 44.18 1.90
2939 10640 1.931841 CATCTTCATGTCAGCACTCCG 59.068 52.381 0.00 0.00 0.00 4.63
3051 10796 3.126000 GCCTCACAGCAAAAGTATCAGAC 59.874 47.826 0.00 0.00 0.00 3.51
3087 10832 2.109774 GGCATCCCCATTGATCAAACA 58.890 47.619 13.09 0.00 0.00 2.83
3147 10892 2.652590 GATCCGGAGTACTACCACACT 58.347 52.381 11.34 0.00 0.00 3.55
3354 11195 4.942761 AGTGATGCAAACTGTGGAAAAT 57.057 36.364 4.71 0.00 0.00 1.82
3424 11265 4.882427 TCAGTAGGCGATATAGTATGGAGC 59.118 45.833 0.00 0.00 0.00 4.70
3469 11311 1.066430 TGCCTCGGTAACCTGATTGAC 60.066 52.381 0.00 0.00 0.00 3.18
3534 11381 6.658849 TCCTGCCTCAGTAAAAATTGCTATA 58.341 36.000 0.00 0.00 0.00 1.31
3613 11461 9.174166 ACGTCCTTTTTAAATATGCTTACAGAT 57.826 29.630 0.00 0.00 0.00 2.90
3623 11471 7.736447 AATATGCTTACAGATAGGTTTCAGC 57.264 36.000 0.00 0.00 0.00 4.26
3627 11475 5.945784 TGCTTACAGATAGGTTTCAGCAATT 59.054 36.000 0.00 0.00 33.18 2.32
3682 11530 9.804758 AGGTTTCGACTATATTCAGAAGTAAAG 57.195 33.333 0.00 0.00 0.00 1.85
3774 11622 5.298197 GCATCATCAGCCATATCTTTCAG 57.702 43.478 0.00 0.00 0.00 3.02
3821 11669 4.363138 CAGAGATTTATCGTGTAGCTGCA 58.637 43.478 0.00 0.00 0.00 4.41
3917 11773 5.754890 CCCATTGATTTTAGCCTTAATGCAC 59.245 40.000 5.50 0.00 0.00 4.57
3956 13613 3.011566 TGGACACAGAAAAAGCAAGGA 57.988 42.857 0.00 0.00 0.00 3.36
3961 13618 6.095377 GGACACAGAAAAAGCAAGGAATATG 58.905 40.000 0.00 0.00 0.00 1.78
4049 13708 3.135348 AGTGTCATATCACAGGTCCATGG 59.865 47.826 4.97 4.97 40.37 3.66
4087 13746 5.886960 ATAGCAAGTTGGCAACTCTAAAG 57.113 39.130 31.24 19.12 41.91 1.85
4102 13761 5.300752 ACTCTAAAGTGTGTTGATGGTGAG 58.699 41.667 0.00 0.00 33.32 3.51
4105 13764 2.645838 AGTGTGTTGATGGTGAGCTT 57.354 45.000 0.00 0.00 0.00 3.74
4317 13976 4.437967 TCCTAGATGGCAATGGATATCCA 58.562 43.478 26.49 26.49 42.68 3.41
4375 14034 3.817647 AGACAACAGCAGAACTTCCATTC 59.182 43.478 0.00 0.00 0.00 2.67
4426 14085 4.992951 TCTTATATGCACTGCTAGCACATG 59.007 41.667 22.84 19.86 45.95 3.21
4521 14194 7.801716 ATTGAAGTAACAAGTGCTAGTTTCA 57.198 32.000 0.00 0.00 33.22 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 6.047870 CAGAGAGAAGGAAGGTCACAATATG 58.952 44.000 0.00 0.00 0.00 1.78
23 24 3.244887 TCAGAGAGAAGGAAGGTCACA 57.755 47.619 0.00 0.00 0.00 3.58
24 25 5.681179 GCTTATCAGAGAGAAGGAAGGTCAC 60.681 48.000 3.89 0.00 32.30 3.67
29 30 4.097135 TCGTGCTTATCAGAGAGAAGGAAG 59.903 45.833 3.89 3.60 33.50 3.46
58 59 6.440647 TGGAACCTAATACATTCACTCTCAGT 59.559 38.462 0.00 0.00 0.00 3.41
59 60 6.878317 TGGAACCTAATACATTCACTCTCAG 58.122 40.000 0.00 0.00 0.00 3.35
60 61 6.867519 TGGAACCTAATACATTCACTCTCA 57.132 37.500 0.00 0.00 0.00 3.27
90 91 2.547211 CCTGTGCGAAGGATGATCATTC 59.453 50.000 10.14 7.94 40.02 2.67
94 95 1.863267 CTCCTGTGCGAAGGATGATC 58.137 55.000 7.59 0.00 45.41 2.92
106 107 3.564345 AAGCTGGCCTGCTCCTGTG 62.564 63.158 34.08 0.82 43.24 3.66
107 108 3.255397 AAGCTGGCCTGCTCCTGT 61.255 61.111 34.08 18.16 43.24 4.00
179 182 3.067461 TGTTAAACCATGGACAGTTGCAC 59.933 43.478 21.47 8.57 0.00 4.57
215 218 5.958380 AGGGAAAGACACTATCACACTATCA 59.042 40.000 0.00 0.00 0.00 2.15
222 225 3.265791 CAGCAGGGAAAGACACTATCAC 58.734 50.000 0.00 0.00 0.00 3.06
223 226 2.237143 CCAGCAGGGAAAGACACTATCA 59.763 50.000 0.00 0.00 40.01 2.15
224 227 2.501723 TCCAGCAGGGAAAGACACTATC 59.498 50.000 0.00 0.00 44.80 2.08
225 228 2.551270 TCCAGCAGGGAAAGACACTAT 58.449 47.619 0.00 0.00 44.80 2.12
226 229 2.024176 TCCAGCAGGGAAAGACACTA 57.976 50.000 0.00 0.00 44.80 2.74
227 230 2.854253 TCCAGCAGGGAAAGACACT 58.146 52.632 0.00 0.00 44.80 3.55
235 238 2.742348 TCGTAGTATTTCCAGCAGGGA 58.258 47.619 0.00 0.00 46.61 4.20
277 281 4.887071 AGCATTTAATGGACTTGCCGAATA 59.113 37.500 7.08 0.00 40.66 1.75
282 286 5.077134 AGAAAGCATTTAATGGACTTGCC 57.923 39.130 7.08 0.23 39.27 4.52
302 306 8.977412 AGATTAAAAGACCAAACCAAAAAGAGA 58.023 29.630 0.00 0.00 0.00 3.10
313 317 7.880713 GCCCCAAAATAAGATTAAAAGACCAAA 59.119 33.333 0.00 0.00 0.00 3.28
316 320 6.941857 TGCCCCAAAATAAGATTAAAAGACC 58.058 36.000 0.00 0.00 0.00 3.85
368 372 7.308589 GCGACTAATGGCAGGTTTTATTGATAT 60.309 37.037 0.00 0.00 0.00 1.63
397 401 5.045215 TGAGCTTCTTGTTTTTCTGCAATG 58.955 37.500 0.00 0.00 0.00 2.82
471 475 1.614996 AACCACAATGGCATTCGACA 58.385 45.000 10.36 0.00 42.67 4.35
578 582 0.601046 TGAAGCAGTCAAGTCAGGCG 60.601 55.000 0.00 0.00 31.51 5.52
582 586 4.060900 GACTTCATGAAGCAGTCAAGTCA 58.939 43.478 30.95 0.00 39.74 3.41
689 718 5.163499 GCCTGATAATAAGGAGTCCCTATCG 60.163 48.000 5.25 4.86 43.48 2.92
695 724 5.474876 CCAAATGCCTGATAATAAGGAGTCC 59.525 44.000 0.00 0.00 36.91 3.85
697 726 6.064717 GTCCAAATGCCTGATAATAAGGAGT 58.935 40.000 0.00 0.00 36.91 3.85
717 747 1.475034 GCCTGTCAAGTCTGTTGTCCA 60.475 52.381 0.00 0.00 0.00 4.02
755 785 1.139853 CCCTACCATCCTGCAGTTCTC 59.860 57.143 13.81 0.00 0.00 2.87
760 790 1.072965 GGAATCCCTACCATCCTGCAG 59.927 57.143 6.78 6.78 0.00 4.41
761 791 1.140312 GGAATCCCTACCATCCTGCA 58.860 55.000 0.00 0.00 0.00 4.41
762 792 1.349357 GAGGAATCCCTACCATCCTGC 59.651 57.143 0.00 0.00 44.53 4.85
763 793 2.694397 TGAGGAATCCCTACCATCCTG 58.306 52.381 0.00 0.00 44.53 3.86
764 794 3.254960 CATGAGGAATCCCTACCATCCT 58.745 50.000 0.00 0.00 44.53 3.24
765 795 2.307098 CCATGAGGAATCCCTACCATCC 59.693 54.545 0.00 0.00 44.53 3.51
766 796 2.290577 GCCATGAGGAATCCCTACCATC 60.291 54.545 0.00 0.00 44.53 3.51
767 797 1.707427 GCCATGAGGAATCCCTACCAT 59.293 52.381 0.00 0.00 44.53 3.55
768 798 1.140312 GCCATGAGGAATCCCTACCA 58.860 55.000 0.00 0.00 44.53 3.25
769 799 1.439543 AGCCATGAGGAATCCCTACC 58.560 55.000 0.00 0.00 44.53 3.18
770 800 2.569404 CCTAGCCATGAGGAATCCCTAC 59.431 54.545 0.00 0.00 44.53 3.18
771 801 2.907892 CCTAGCCATGAGGAATCCCTA 58.092 52.381 0.00 0.00 44.53 3.53
777 809 2.658285 CAAATGCCTAGCCATGAGGAA 58.342 47.619 3.14 0.00 35.99 3.36
785 817 2.159057 CCAATTGTCCAAATGCCTAGCC 60.159 50.000 4.43 0.00 0.00 3.93
788 820 5.483231 TCAAATCCAATTGTCCAAATGCCTA 59.517 36.000 4.43 0.00 0.00 3.93
808 840 8.188139 GGACTCTGTGACTAAAAATTTGTCAAA 58.812 33.333 10.44 0.00 41.52 2.69
815 854 5.236478 CGTGTGGACTCTGTGACTAAAAATT 59.764 40.000 0.00 0.00 0.00 1.82
820 859 1.000607 GCGTGTGGACTCTGTGACTAA 60.001 52.381 0.00 0.00 0.00 2.24
821 860 0.596577 GCGTGTGGACTCTGTGACTA 59.403 55.000 0.00 0.00 0.00 2.59
825 864 1.224069 CCTTGCGTGTGGACTCTGTG 61.224 60.000 0.00 0.00 0.00 3.66
826 865 1.069765 CCTTGCGTGTGGACTCTGT 59.930 57.895 0.00 0.00 0.00 3.41
828 867 2.031163 GCCTTGCGTGTGGACTCT 59.969 61.111 0.00 0.00 0.00 3.24
829 868 1.166531 AAAGCCTTGCGTGTGGACTC 61.167 55.000 0.00 0.00 0.00 3.36
830 869 0.751643 AAAAGCCTTGCGTGTGGACT 60.752 50.000 0.00 0.00 0.00 3.85
839 925 6.630071 TGAATCATTTAGGTAAAAGCCTTGC 58.370 36.000 0.00 0.00 39.94 4.01
855 942 4.025360 TGCTTGCAGGGTAATGAATCATT 58.975 39.130 13.43 13.43 37.80 2.57
856 943 3.382546 GTGCTTGCAGGGTAATGAATCAT 59.617 43.478 0.00 0.00 0.00 2.45
857 944 2.754552 GTGCTTGCAGGGTAATGAATCA 59.245 45.455 0.00 0.00 0.00 2.57
858 945 2.099756 GGTGCTTGCAGGGTAATGAATC 59.900 50.000 0.00 0.00 0.00 2.52
859 946 2.102578 GGTGCTTGCAGGGTAATGAAT 58.897 47.619 0.00 0.00 0.00 2.57
860 947 1.202989 TGGTGCTTGCAGGGTAATGAA 60.203 47.619 0.00 0.00 0.00 2.57
861 948 0.403655 TGGTGCTTGCAGGGTAATGA 59.596 50.000 0.00 0.00 0.00 2.57
862 949 1.203052 CTTGGTGCTTGCAGGGTAATG 59.797 52.381 0.00 0.00 0.00 1.90
863 950 1.075374 TCTTGGTGCTTGCAGGGTAAT 59.925 47.619 0.00 0.00 0.00 1.89
864 951 0.476338 TCTTGGTGCTTGCAGGGTAA 59.524 50.000 0.00 0.00 0.00 2.85
865 952 0.476338 TTCTTGGTGCTTGCAGGGTA 59.524 50.000 0.00 0.00 0.00 3.69
866 953 0.178953 ATTCTTGGTGCTTGCAGGGT 60.179 50.000 0.00 0.00 0.00 4.34
867 954 0.529378 GATTCTTGGTGCTTGCAGGG 59.471 55.000 0.00 0.00 0.00 4.45
876 963 6.263168 AGTTTACCTTCACAAGATTCTTGGTG 59.737 38.462 25.94 20.60 0.00 4.17
877 964 6.365520 AGTTTACCTTCACAAGATTCTTGGT 58.634 36.000 25.94 17.49 0.00 3.67
882 969 8.099364 TCATCAAGTTTACCTTCACAAGATTC 57.901 34.615 0.00 0.00 0.00 2.52
883 970 8.641498 ATCATCAAGTTTACCTTCACAAGATT 57.359 30.769 0.00 0.00 0.00 2.40
884 971 8.517878 CAATCATCAAGTTTACCTTCACAAGAT 58.482 33.333 0.00 0.00 0.00 2.40
909 996 3.254903 TCGCTTACTGACTGTTCTAAGCA 59.745 43.478 17.70 8.26 37.52 3.91
929 1024 6.903883 TTAATAGCTGCTTACTTTTCCTCG 57.096 37.500 7.79 0.00 0.00 4.63
930 1025 7.717436 AGGATTAATAGCTGCTTACTTTTCCTC 59.283 37.037 7.79 0.00 0.00 3.71
968 1069 2.086869 ACATGGCTTATCATATGGCGC 58.913 47.619 0.00 0.00 0.00 6.53
985 1086 5.755375 CCATTTATACGCAGAACAGAGACAT 59.245 40.000 0.00 0.00 0.00 3.06
991 1092 3.373748 TGTGCCATTTATACGCAGAACAG 59.626 43.478 0.00 0.00 32.08 3.16
992 1093 3.339141 TGTGCCATTTATACGCAGAACA 58.661 40.909 0.00 0.00 32.08 3.18
993 1094 4.552166 ATGTGCCATTTATACGCAGAAC 57.448 40.909 0.00 0.00 32.08 3.01
1000 1101 7.757526 TGTTCTGTGTTATGTGCCATTTATAC 58.242 34.615 0.00 0.00 0.00 1.47
1006 1107 4.592942 AGATGTTCTGTGTTATGTGCCAT 58.407 39.130 0.00 0.00 0.00 4.40
1023 1124 3.807622 CGTAGTGTGAAACCACAAGATGT 59.192 43.478 0.00 0.00 45.11 3.06
1024 1125 4.055360 TCGTAGTGTGAAACCACAAGATG 58.945 43.478 0.00 0.00 45.11 2.90
1026 1127 3.804786 TCGTAGTGTGAAACCACAAGA 57.195 42.857 0.00 0.00 45.11 3.02
1031 1134 1.346395 AGCCATCGTAGTGTGAAACCA 59.654 47.619 0.00 0.00 34.36 3.67
1032 1135 2.094762 AGCCATCGTAGTGTGAAACC 57.905 50.000 0.00 0.00 34.36 3.27
1045 1152 8.730680 CCTTTGTTTGGTGTATATATAGCCATC 58.269 37.037 13.68 11.29 0.00 3.51
1087 1200 1.414550 TGTACACAGCTTAGCCACACA 59.585 47.619 0.00 0.00 0.00 3.72
1102 1215 4.884164 TCATTTGTGTGATGTGGTTGTACA 59.116 37.500 0.00 0.00 34.63 2.90
1103 1216 5.008613 ACTCATTTGTGTGATGTGGTTGTAC 59.991 40.000 0.00 0.00 0.00 2.90
1174 1344 1.736126 CCGAGACTAGCACTAACACGA 59.264 52.381 0.00 0.00 0.00 4.35
1225 1395 3.104512 AGGGTATGCTTATAGCCGCATA 58.895 45.455 9.20 8.50 46.34 3.14
1245 1417 1.586422 CACTGATGCCGAATGGGTAG 58.414 55.000 0.00 0.00 38.44 3.18
1299 1471 5.985175 TTGGGGGATGATATGTCTTGTTA 57.015 39.130 0.00 0.00 0.00 2.41
1303 1475 3.464833 AGCTTTGGGGGATGATATGTCTT 59.535 43.478 0.00 0.00 0.00 3.01
1514 1692 0.810648 CACAATGATTCCACACCCCG 59.189 55.000 0.00 0.00 0.00 5.73
1583 1782 4.511246 CCGGCATGCATCCTGGGT 62.511 66.667 21.36 0.00 0.00 4.51
1698 7640 3.190744 TCTTTCTCCACGCTGTACTAGTG 59.809 47.826 5.39 1.87 42.68 2.74
1699 7641 3.418995 TCTTTCTCCACGCTGTACTAGT 58.581 45.455 0.00 0.00 0.00 2.57
1700 7642 3.690139 TCTCTTTCTCCACGCTGTACTAG 59.310 47.826 0.00 0.00 0.00 2.57
1701 7643 3.682696 TCTCTTTCTCCACGCTGTACTA 58.317 45.455 0.00 0.00 0.00 1.82
1702 7644 2.515854 TCTCTTTCTCCACGCTGTACT 58.484 47.619 0.00 0.00 0.00 2.73
1793 7738 0.833287 ATGATACCGCCTTCTGCAGT 59.167 50.000 14.67 0.00 41.33 4.40
1921 7866 7.014518 TGAGTCATCCAAAATCACTTGAATTGT 59.985 33.333 0.00 0.00 0.00 2.71
1934 7882 5.412594 GCTATTGTCACTGAGTCATCCAAAA 59.587 40.000 0.00 0.00 0.00 2.44
1943 7891 2.672478 GCACTCGCTATTGTCACTGAGT 60.672 50.000 0.00 0.00 37.17 3.41
1955 7903 0.245539 GGTACACAAGGCACTCGCTA 59.754 55.000 0.00 0.00 38.49 4.26
2094 9450 4.094146 GCTTTGAGCACTCCTGAAGTAATC 59.906 45.833 0.00 0.00 41.89 1.75
2105 9461 1.678101 AGTTTGTGGCTTTGAGCACTC 59.322 47.619 2.04 0.00 44.75 3.51
2111 9467 3.287222 AGCAAGTAGTTTGTGGCTTTGA 58.713 40.909 0.00 0.00 39.08 2.69
2256 9692 8.458052 GGTTGAAGAACATCCATTTTTGTTTTT 58.542 29.630 0.00 0.00 36.25 1.94
2257 9693 7.609532 TGGTTGAAGAACATCCATTTTTGTTTT 59.390 29.630 0.00 0.00 41.66 2.43
2261 9697 7.551035 TTTGGTTGAAGAACATCCATTTTTG 57.449 32.000 0.00 0.00 44.61 2.44
2424 9984 5.944135 TCCTGGAGAATGCATAATCAATCA 58.056 37.500 0.00 0.00 34.26 2.57
2588 10289 2.566833 TGTCCACAAGCTGCTGTATT 57.433 45.000 1.35 0.00 0.00 1.89
2589 10290 2.430465 CTTGTCCACAAGCTGCTGTAT 58.570 47.619 1.35 0.00 45.59 2.29
2807 10508 5.513094 CCTGTGGTTCACTTGAGAAAGGATA 60.513 44.000 0.00 0.00 35.11 2.59
2879 10580 7.975616 CCATTTGAAATGAATTCGTAGACCAAT 59.024 33.333 18.82 0.00 41.18 3.16
2939 10640 3.497640 CAGATAAGCAAGGCACTGATAGC 59.502 47.826 0.00 0.00 40.86 2.97
3051 10796 0.036952 TGCCTCGAGAAGCTCCAAAG 60.037 55.000 15.71 0.00 0.00 2.77
3087 10832 1.414919 TGAACCGCAGTTGTAACTCCT 59.585 47.619 0.00 0.00 37.08 3.69
3102 10847 6.873605 CCAAATATCCAAAAGTTCCTTGAACC 59.126 38.462 3.47 0.00 42.85 3.62
3354 11195 7.576666 GCATTGTTCTGTTCCATTGGTGTATTA 60.577 37.037 1.86 0.00 0.00 0.98
3424 11265 6.862711 ACTCATAGATGACATGCATTCTTG 57.137 37.500 0.00 0.00 37.34 3.02
3579 11427 8.372521 GCATATTTAAAAAGGACGTGACAATTG 58.627 33.333 3.24 3.24 0.00 2.32
3613 11461 9.995003 AAAATAATTGTCAATTGCTGAAACCTA 57.005 25.926 19.10 0.00 35.22 3.08
3627 11475 9.770097 TTCCATGCAAACTAAAAATAATTGTCA 57.230 25.926 0.00 0.00 0.00 3.58
3917 11773 9.987272 TGTGTCCATATGAATTCTAACTATGAG 57.013 33.333 3.65 4.43 0.00 2.90
3956 13613 5.248020 TGGGTTTTTCCTTGTCATGCATATT 59.752 36.000 0.00 0.00 36.25 1.28
3961 13618 2.754472 GTGGGTTTTTCCTTGTCATGC 58.246 47.619 0.00 0.00 36.25 4.06
4025 13682 4.471904 TGGACCTGTGATATGACACTTC 57.528 45.455 0.00 0.00 40.87 3.01
4027 13684 3.135348 CCATGGACCTGTGATATGACACT 59.865 47.826 5.56 0.00 40.87 3.55
4034 13693 4.860802 AACATTCCATGGACCTGTGATA 57.139 40.909 23.42 5.55 33.60 2.15
4049 13708 9.294030 CAACTTGCTATTAATGGAGAAACATTC 57.706 33.333 2.52 0.00 41.12 2.67
4063 13722 6.940298 ACTTTAGAGTTGCCAACTTGCTATTA 59.060 34.615 12.09 1.23 43.03 0.98
4087 13746 2.618241 TCAAAGCTCACCATCAACACAC 59.382 45.455 0.00 0.00 0.00 3.82
4102 13761 4.309933 AGCTGGCATAACTTTTTCAAAGC 58.690 39.130 0.00 0.00 0.00 3.51
4105 13764 5.007528 GCAAAAGCTGGCATAACTTTTTCAA 59.992 36.000 15.97 0.00 40.63 2.69
4220 13879 5.941555 TGTTTACACCATCCCTTGTTTTT 57.058 34.783 0.00 0.00 0.00 1.94
4221 13880 5.187967 TGTTGTTTACACCATCCCTTGTTTT 59.812 36.000 0.00 0.00 0.00 2.43
4222 13881 4.712337 TGTTGTTTACACCATCCCTTGTTT 59.288 37.500 0.00 0.00 0.00 2.83
4223 13882 4.282496 TGTTGTTTACACCATCCCTTGTT 58.718 39.130 0.00 0.00 0.00 2.83
4261 13920 8.023050 AGAAACTCAAAATATGACTCTGTTCG 57.977 34.615 0.00 0.00 33.47 3.95
4375 14034 8.770828 AGTGATATTTTTCAACGGATATTACGG 58.229 33.333 5.86 0.00 35.23 4.02
4426 14085 6.926272 CCTAGACTATGTCTGGACTTTATTGC 59.074 42.308 11.71 0.00 42.49 3.56


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

AutoCloner maintained by Alex Coulton.