Multiple sequence alignment - TraesCS7A01G037100

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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 TraesCS7A01G037100 chr7A 100.000 5715 0 0 1 5715 16648190 16653904 0.000000e+00 10554.0
1 TraesCS7A01G037100 chr7A 78.329 826 149 16 53 866 678592607 678593414 1.840000e-139 507.0
2 TraesCS7A01G037100 chr7A 77.053 828 163 14 51 866 42799422 42800234 8.730000e-123 451.0
3 TraesCS7A01G037100 chr7D 97.363 4210 80 14 1001 5198 17257029 17261219 0.000000e+00 7131.0
4 TraesCS7A01G037100 chr7D 93.030 990 53 7 1 988 17255999 17256974 0.000000e+00 1432.0
5 TraesCS7A01G037100 chr7D 96.094 256 9 1 5195 5450 17262765 17263019 3.190000e-112 416.0
6 TraesCS7A01G037100 chr7D 80.258 542 84 15 56 585 503088805 503088275 2.500000e-103 387.0
7 TraesCS7A01G037100 chr7D 97.674 86 2 0 5540 5625 17263055 17263140 1.280000e-31 148.0
8 TraesCS7A01G037100 chr7D 84.127 126 12 3 5574 5691 17210299 17210424 1.300000e-21 115.0
9 TraesCS7A01G037100 chr7D 100.000 37 0 0 5468 5504 17263020 17263056 1.030000e-07 69.4
10 TraesCS7A01G037100 chr4A 93.227 1447 90 4 3425 4871 716997197 716995759 0.000000e+00 2122.0
11 TraesCS7A01G037100 chr4A 84.572 1238 157 16 3444 4664 676544657 676545877 0.000000e+00 1197.0
12 TraesCS7A01G037100 chr4A 86.458 1056 127 12 2424 3471 716998390 716997343 0.000000e+00 1144.0
13 TraesCS7A01G037100 chr4A 89.136 718 55 10 1735 2430 716999175 716998459 0.000000e+00 872.0
14 TraesCS7A01G037100 chr4A 85.480 792 97 9 1521 2305 676542565 676543345 0.000000e+00 809.0
15 TraesCS7A01G037100 chr4A 88.247 485 51 2 2585 3063 676543682 676544166 4.970000e-160 575.0
16 TraesCS7A01G037100 chr4A 77.570 642 126 11 59 693 662435948 662435318 6.990000e-99 372.0
17 TraesCS7A01G037100 chr4A 83.761 351 36 10 3108 3457 676544283 676544613 4.300000e-81 313.0
18 TraesCS7A01G037100 chr4A 86.102 295 18 6 5238 5515 716995742 716995454 4.330000e-76 296.0
19 TraesCS7A01G037100 chr4A 92.366 131 6 2 5510 5639 716995271 716995144 3.520000e-42 183.0
20 TraesCS7A01G037100 chr4A 77.523 218 33 12 1112 1324 676542225 676542431 3.620000e-22 117.0
21 TraesCS7A01G037100 chr5B 83.684 1379 190 17 3327 4684 406949842 406951206 0.000000e+00 1267.0
22 TraesCS7A01G037100 chr5B 83.592 1030 123 32 1403 2424 406947841 406948832 0.000000e+00 924.0
23 TraesCS7A01G037100 chr5B 86.207 783 93 12 2579 3351 406949014 406949791 0.000000e+00 833.0
24 TraesCS7A01G037100 chr5B 78.934 807 134 21 56 846 450768633 450767847 3.050000e-142 516.0
25 TraesCS7A01G037100 chr5B 76.908 524 98 13 349 867 598525095 598525600 5.640000e-70 276.0
26 TraesCS7A01G037100 chr5D 80.789 1192 167 43 1255 2422 344809938 344808785 0.000000e+00 876.0
27 TraesCS7A01G037100 chr5D 86.590 783 94 8 2579 3351 344808601 344807820 0.000000e+00 854.0
28 TraesCS7A01G037100 chr5D 77.343 843 157 19 53 882 434613631 434614452 8.670000e-128 468.0
29 TraesCS7A01G037100 chr5D 77.356 764 141 17 53 802 487310813 487310068 1.900000e-114 424.0
30 TraesCS7A01G037100 chr5D 78.331 623 97 25 53 651 464993831 464994439 9.050000e-98 368.0
31 TraesCS7A01G037100 chr5D 76.821 151 21 10 1112 1261 344810101 344809964 7.940000e-09 73.1
32 TraesCS7A01G037100 chr4B 82.603 707 111 9 174 874 95705576 95704876 1.050000e-171 614.0
33 TraesCS7A01G037100 chr7B 79.953 848 138 16 51 879 366042501 366043335 3.810000e-166 595.0
34 TraesCS7A01G037100 chr7B 78.323 835 127 24 53 874 158374664 158375457 1.850000e-134 490.0
35 TraesCS7A01G037100 chr1B 81.543 363 64 3 356 717 111916346 111915986 4.330000e-76 296.0
36 TraesCS7A01G037100 chrUn 79.695 394 62 15 489 874 68882603 68882986 9.440000e-68 268.0
37 TraesCS7A01G037100 chr1D 73.764 728 163 25 2579 3292 486755903 486756616 1.580000e-65 261.0
38 TraesCS7A01G037100 chr3D 73.324 746 164 16 57 787 388820650 388819925 5.720000e-60 243.0
39 TraesCS7A01G037100 chr2D 80.117 342 55 9 53 385 205587845 205588182 5.720000e-60 243.0
40 TraesCS7A01G037100 chr3B 74.276 587 117 18 183 754 506495520 506494953 3.470000e-52 217.0
41 TraesCS7A01G037100 chr6A 100.000 28 0 0 2974 3001 213783577 213783604 1.000000e-02 52.8


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 TraesCS7A01G037100 chr7A 16648190 16653904 5714 False 10554.000000 10554 100.000000 1 5715 1 chr7A.!!$F1 5714
1 TraesCS7A01G037100 chr7A 678592607 678593414 807 False 507.000000 507 78.329000 53 866 1 chr7A.!!$F3 813
2 TraesCS7A01G037100 chr7A 42799422 42800234 812 False 451.000000 451 77.053000 51 866 1 chr7A.!!$F2 815
3 TraesCS7A01G037100 chr7D 17255999 17263140 7141 False 1839.280000 7131 96.832200 1 5625 5 chr7D.!!$F2 5624
4 TraesCS7A01G037100 chr7D 503088275 503088805 530 True 387.000000 387 80.258000 56 585 1 chr7D.!!$R1 529
5 TraesCS7A01G037100 chr4A 716995144 716999175 4031 True 923.400000 2122 89.457800 1735 5639 5 chr4A.!!$R2 3904
6 TraesCS7A01G037100 chr4A 676542225 676545877 3652 False 602.200000 1197 83.916600 1112 4664 5 chr4A.!!$F1 3552
7 TraesCS7A01G037100 chr4A 662435318 662435948 630 True 372.000000 372 77.570000 59 693 1 chr4A.!!$R1 634
8 TraesCS7A01G037100 chr5B 406947841 406951206 3365 False 1008.000000 1267 84.494333 1403 4684 3 chr5B.!!$F2 3281
9 TraesCS7A01G037100 chr5B 450767847 450768633 786 True 516.000000 516 78.934000 56 846 1 chr5B.!!$R1 790
10 TraesCS7A01G037100 chr5B 598525095 598525600 505 False 276.000000 276 76.908000 349 867 1 chr5B.!!$F1 518
11 TraesCS7A01G037100 chr5D 344807820 344810101 2281 True 601.033333 876 81.400000 1112 3351 3 chr5D.!!$R2 2239
12 TraesCS7A01G037100 chr5D 434613631 434614452 821 False 468.000000 468 77.343000 53 882 1 chr5D.!!$F1 829
13 TraesCS7A01G037100 chr5D 487310068 487310813 745 True 424.000000 424 77.356000 53 802 1 chr5D.!!$R1 749
14 TraesCS7A01G037100 chr5D 464993831 464994439 608 False 368.000000 368 78.331000 53 651 1 chr5D.!!$F2 598
15 TraesCS7A01G037100 chr4B 95704876 95705576 700 True 614.000000 614 82.603000 174 874 1 chr4B.!!$R1 700
16 TraesCS7A01G037100 chr7B 366042501 366043335 834 False 595.000000 595 79.953000 51 879 1 chr7B.!!$F2 828
17 TraesCS7A01G037100 chr7B 158374664 158375457 793 False 490.000000 490 78.323000 53 874 1 chr7B.!!$F1 821
18 TraesCS7A01G037100 chr1D 486755903 486756616 713 False 261.000000 261 73.764000 2579 3292 1 chr1D.!!$F1 713
19 TraesCS7A01G037100 chr3D 388819925 388820650 725 True 243.000000 243 73.324000 57 787 1 chr3D.!!$R1 730
20 TraesCS7A01G037100 chr3B 506494953 506495520 567 True 217.000000 217 74.276000 183 754 1 chr3B.!!$R1 571

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
993 1035 0.106708 TTGCCTATCGAGGTGGATGC 59.893 55.000 5.46 0.0 45.78 3.91 F
1305 1431 0.396811 AAAGCGCAGGTACAGTTCCT 59.603 50.000 11.47 0.0 37.06 3.36 F
2163 2313 0.460109 CGCGTGGATCCAGATTCACA 60.460 55.000 16.81 0.0 45.50 3.58 F
2574 2890 1.068741 GGCGATACACCTACCCAGAAG 59.931 57.143 0.00 0.0 0.00 2.85 F
4157 4864 0.313672 TGGCCAAATGAAGTTGCGAC 59.686 50.000 0.61 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2574 2890 1.687660 GGGAGATCCTTTAGGTCGGTC 59.312 57.143 0.00 0.00 36.34 4.79 R
3321 3755 5.601313 ACTACAACCTTGTTCTTCCTCTACA 59.399 40.000 0.00 0.00 42.35 2.74 R
3939 4640 1.298859 GCAGTTCCTTACCCAGCACG 61.299 60.000 0.00 0.00 0.00 5.34 R
4408 5121 1.133853 GCCAGCCATTCCTCTCTGAAT 60.134 52.381 0.00 0.00 35.36 2.57 R
5538 8032 0.034767 ATCTGGCCATATGGATGCCG 60.035 55.000 26.47 14.38 37.39 5.69 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
417 443 1.810755 ACAGTATCAACGACAGCGAGA 59.189 47.619 0.00 0.00 41.64 4.04
656 694 4.350441 GCTCCTAGCTAGCCGGCG 62.350 72.222 23.20 9.22 38.45 6.46
702 743 0.478072 TCTTGGTGTGTGGGCTTGAT 59.522 50.000 0.00 0.00 0.00 2.57
805 846 9.646427 TTATATTGTATGGCCTTGTTGAAAAAC 57.354 29.630 3.32 0.00 0.00 2.43
837 878 1.237285 ATGGTTGTGTGCTTCGCTCC 61.237 55.000 0.00 0.00 0.00 4.70
851 892 1.377202 GCTCCATGCAAAGACCGGA 60.377 57.895 9.46 0.00 42.31 5.14
930 972 1.284297 TTGTCAGACACGCATGCTCG 61.284 55.000 17.13 8.93 0.00 5.03
939 981 0.249238 ACGCATGCTCGGATCTTCTC 60.249 55.000 17.13 0.00 0.00 2.87
940 982 0.249197 CGCATGCTCGGATCTTCTCA 60.249 55.000 17.13 0.00 0.00 3.27
941 983 1.500108 GCATGCTCGGATCTTCTCAG 58.500 55.000 11.37 0.00 0.00 3.35
942 984 1.202510 GCATGCTCGGATCTTCTCAGT 60.203 52.381 11.37 0.00 0.00 3.41
943 985 2.741612 CATGCTCGGATCTTCTCAGTC 58.258 52.381 0.00 0.00 0.00 3.51
944 986 1.107114 TGCTCGGATCTTCTCAGTCC 58.893 55.000 0.00 0.00 0.00 3.85
945 987 0.387565 GCTCGGATCTTCTCAGTCCC 59.612 60.000 0.00 0.00 0.00 4.46
946 988 1.769026 CTCGGATCTTCTCAGTCCCA 58.231 55.000 0.00 0.00 0.00 4.37
947 989 1.407258 CTCGGATCTTCTCAGTCCCAC 59.593 57.143 0.00 0.00 0.00 4.61
948 990 1.186200 CGGATCTTCTCAGTCCCACA 58.814 55.000 0.00 0.00 0.00 4.17
951 993 2.093235 GGATCTTCTCAGTCCCACAAGG 60.093 54.545 0.00 0.00 0.00 3.61
959 1001 2.203480 TCCCACAAGGCCACAAGC 60.203 61.111 5.01 0.00 42.60 4.01
988 1030 8.035394 ACAAAGTATATATTGCCTATCGAGGTG 58.965 37.037 0.00 0.00 45.78 4.00
991 1033 7.069986 AGTATATATTGCCTATCGAGGTGGAT 58.930 38.462 5.46 0.00 45.78 3.41
993 1035 0.106708 TTGCCTATCGAGGTGGATGC 59.893 55.000 5.46 0.00 45.78 3.91
994 1036 1.373497 GCCTATCGAGGTGGATGCG 60.373 63.158 5.46 0.00 45.78 4.73
995 1037 1.290324 CCTATCGAGGTGGATGCGG 59.710 63.158 0.00 0.00 38.16 5.69
996 1038 1.373497 CTATCGAGGTGGATGCGGC 60.373 63.158 0.00 0.00 0.00 6.53
997 1039 2.087462 CTATCGAGGTGGATGCGGCA 62.087 60.000 4.58 4.58 0.00 5.69
998 1040 2.087462 TATCGAGGTGGATGCGGCAG 62.087 60.000 9.25 0.00 0.00 4.85
1042 1126 0.824109 CAGAGCCGTTACTCCATGGA 59.176 55.000 15.27 15.27 37.39 3.41
1087 1171 0.611062 TTCGGGTGTCGTCTCTCCAT 60.611 55.000 0.00 0.00 40.32 3.41
1153 1243 0.744414 CCCAGGTACCGACAATGCAG 60.744 60.000 6.18 0.00 0.00 4.41
1305 1431 0.396811 AAAGCGCAGGTACAGTTCCT 59.603 50.000 11.47 0.00 37.06 3.36
1546 1680 3.220110 CATAGAAACAGCATGCCTCCAT 58.780 45.455 15.66 0.00 42.53 3.41
1609 1744 3.556365 GGTTAAGACTTAAGCGCCTCATC 59.444 47.826 18.53 0.00 34.42 2.92
2163 2313 0.460109 CGCGTGGATCCAGATTCACA 60.460 55.000 16.81 0.00 45.50 3.58
2515 2831 3.589654 TACAGCAGCACCAGGTCGC 62.590 63.158 0.00 6.02 0.00 5.19
2549 2865 1.745141 GCTGGACAAGGTCTGGCTATG 60.745 57.143 0.00 0.00 31.36 2.23
2574 2890 1.068741 GGCGATACACCTACCCAGAAG 59.931 57.143 0.00 0.00 0.00 2.85
3321 3755 4.815533 TCTAGAGAAGCTCAGCACAATT 57.184 40.909 0.00 0.00 32.06 2.32
3422 3931 1.726791 CTACAAGGCTTACAGTGCACG 59.273 52.381 12.01 9.15 0.00 5.34
3939 4640 5.391312 AAGATGTATTGAAACAAGGTGCC 57.609 39.130 0.00 0.00 32.02 5.01
4157 4864 0.313672 TGGCCAAATGAAGTTGCGAC 59.686 50.000 0.61 0.00 0.00 5.19
4207 4914 6.093495 TCAGAATAATGGTGTCGGAAATGAAC 59.907 38.462 0.00 0.00 0.00 3.18
4585 5305 5.541868 GGATCTGTTGATCTTCTATCTGGGA 59.458 44.000 6.08 0.00 46.18 4.37
4942 5678 7.639113 TCCGGCATTTTAATTATGGATATCC 57.361 36.000 15.39 15.39 0.00 2.59
4980 5716 9.690434 GAAATTTGAAGTACTAAGTAGCAATCG 57.310 33.333 0.00 0.00 0.00 3.34
4981 5717 7.772332 ATTTGAAGTACTAAGTAGCAATCGG 57.228 36.000 0.00 0.00 0.00 4.18
5074 5810 7.658575 ACCTTCTAACGCTTTATGTGTTCTTAA 59.341 33.333 0.36 0.00 45.18 1.85
5170 5910 4.906618 TCCTCCAGTTTCCAATGTTAGTC 58.093 43.478 0.00 0.00 0.00 2.59
5190 5930 5.941788 AGTCTGTTCTAAGGATTTGTGGTT 58.058 37.500 0.00 0.00 0.00 3.67
5214 7503 2.113986 GGAGTGCTTGCAGTGGGT 59.886 61.111 7.75 0.00 0.00 4.51
5218 7507 2.591429 TGCTTGCAGTGGGTGACG 60.591 61.111 0.00 0.00 0.00 4.35
5268 7557 3.483922 CGTTTGTTTCAGTTTATTGCGCA 59.516 39.130 5.66 5.66 0.00 6.09
5270 7559 5.340932 CGTTTGTTTCAGTTTATTGCGCATA 59.659 36.000 12.75 2.21 0.00 3.14
5368 7674 1.597578 GCACGGGGGTTAAACGACA 60.598 57.895 0.00 0.00 0.00 4.35
5402 7708 1.727335 GGTCGTTGCTAGCTTTCTGTC 59.273 52.381 17.23 0.77 0.00 3.51
5453 7759 3.052745 GCTTACAAGAAACCAAGCTTGC 58.947 45.455 21.43 7.31 43.99 4.01
5465 7771 3.076621 CCAAGCTTGCTGTCATCACTAA 58.923 45.455 21.43 0.00 0.00 2.24
5504 7810 1.708551 CTTGGGTCCTAAGTTTGGGGA 59.291 52.381 6.82 0.00 0.00 4.81
5519 8013 1.004277 TGGGGACAACTACATTCAGGC 59.996 52.381 0.00 0.00 37.44 4.85
5524 8018 2.928116 GACAACTACATTCAGGCGTACC 59.072 50.000 0.00 0.00 0.00 3.34
5536 8030 2.202650 CGTACCGCAACCCCTACG 60.203 66.667 0.00 0.00 0.00 3.51
5629 8124 8.770438 TTAATAAAACATTTCCCTGAACATGC 57.230 30.769 0.00 0.00 0.00 4.06
5645 8140 3.961582 TGCCTTGCATGACAGATGA 57.038 47.368 0.00 0.00 31.71 2.92
5646 8141 2.203470 TGCCTTGCATGACAGATGAA 57.797 45.000 0.00 0.00 31.71 2.57
5647 8142 2.516906 TGCCTTGCATGACAGATGAAA 58.483 42.857 0.00 0.00 31.71 2.69
5648 8143 3.093814 TGCCTTGCATGACAGATGAAAT 58.906 40.909 0.00 0.00 31.71 2.17
5649 8144 3.129813 TGCCTTGCATGACAGATGAAATC 59.870 43.478 0.00 0.00 37.32 2.17
5650 8145 5.111148 TGCCTTGCATGACAGATGAAATCT 61.111 41.667 0.00 0.00 44.82 2.40
5651 8146 5.862490 TGCCTTGCATGACAGATGAAATCTA 60.862 40.000 0.00 0.00 42.95 1.98
5652 8147 7.303809 TGCCTTGCATGACAGATGAAATCTAA 61.304 38.462 0.00 0.00 42.95 2.10
5653 8148 9.019222 TGCCTTGCATGACAGATGAAATCTAAG 62.019 40.741 0.00 0.00 42.95 2.18
5664 8159 6.209129 GATGAAATCTAAGACGCATCTGAC 57.791 41.667 0.00 0.00 41.17 3.51
5665 8160 5.330455 TGAAATCTAAGACGCATCTGACT 57.670 39.130 0.00 0.00 34.48 3.41
5666 8161 5.105063 TGAAATCTAAGACGCATCTGACTG 58.895 41.667 0.00 0.00 34.48 3.51
5667 8162 4.991153 AATCTAAGACGCATCTGACTGA 57.009 40.909 0.00 0.00 34.48 3.41
5668 8163 4.991153 ATCTAAGACGCATCTGACTGAA 57.009 40.909 0.00 0.00 34.48 3.02
5669 8164 4.098055 TCTAAGACGCATCTGACTGAAC 57.902 45.455 0.00 0.00 34.48 3.18
5670 8165 3.759086 TCTAAGACGCATCTGACTGAACT 59.241 43.478 0.00 0.00 34.48 3.01
5671 8166 2.360553 AGACGCATCTGACTGAACTG 57.639 50.000 0.00 0.00 32.29 3.16
5672 8167 1.889170 AGACGCATCTGACTGAACTGA 59.111 47.619 0.00 0.00 32.29 3.41
5673 8168 2.297315 AGACGCATCTGACTGAACTGAA 59.703 45.455 0.00 0.00 32.29 3.02
5674 8169 2.408050 ACGCATCTGACTGAACTGAAC 58.592 47.619 0.00 0.00 0.00 3.18
5675 8170 1.728971 CGCATCTGACTGAACTGAACC 59.271 52.381 0.00 0.00 0.00 3.62
5676 8171 2.771089 GCATCTGACTGAACTGAACCA 58.229 47.619 0.00 0.00 0.00 3.67
5677 8172 3.341823 GCATCTGACTGAACTGAACCAT 58.658 45.455 0.00 0.00 0.00 3.55
5678 8173 3.373439 GCATCTGACTGAACTGAACCATC 59.627 47.826 0.00 0.00 0.00 3.51
5679 8174 4.572909 CATCTGACTGAACTGAACCATCA 58.427 43.478 0.00 0.00 0.00 3.07
5680 8175 4.687901 TCTGACTGAACTGAACCATCAA 57.312 40.909 0.00 0.00 34.49 2.57
5681 8176 4.380531 TCTGACTGAACTGAACCATCAAC 58.619 43.478 0.00 0.00 34.49 3.18
5682 8177 3.130633 TGACTGAACTGAACCATCAACG 58.869 45.455 0.00 0.00 34.49 4.10
5683 8178 3.131396 GACTGAACTGAACCATCAACGT 58.869 45.455 0.00 0.00 34.49 3.99
5684 8179 4.202172 TGACTGAACTGAACCATCAACGTA 60.202 41.667 0.00 0.00 34.49 3.57
5685 8180 4.056050 ACTGAACTGAACCATCAACGTAC 58.944 43.478 0.00 0.00 34.49 3.67
5686 8181 4.202223 ACTGAACTGAACCATCAACGTACT 60.202 41.667 0.00 0.00 34.49 2.73
5687 8182 4.304110 TGAACTGAACCATCAACGTACTC 58.696 43.478 0.00 0.00 34.49 2.59
5688 8183 4.038763 TGAACTGAACCATCAACGTACTCT 59.961 41.667 0.00 0.00 34.49 3.24
5689 8184 3.914312 ACTGAACCATCAACGTACTCTG 58.086 45.455 0.00 0.00 34.49 3.35
5690 8185 3.321111 ACTGAACCATCAACGTACTCTGT 59.679 43.478 0.00 0.00 34.49 3.41
5691 8186 4.521639 ACTGAACCATCAACGTACTCTGTA 59.478 41.667 0.00 0.00 34.49 2.74
5692 8187 5.185249 ACTGAACCATCAACGTACTCTGTAT 59.815 40.000 0.00 0.00 34.49 2.29
5693 8188 6.376299 ACTGAACCATCAACGTACTCTGTATA 59.624 38.462 0.00 0.00 34.49 1.47
5694 8189 6.558009 TGAACCATCAACGTACTCTGTATAC 58.442 40.000 0.00 0.00 30.99 1.47
5695 8190 5.511234 ACCATCAACGTACTCTGTATACC 57.489 43.478 0.00 0.00 0.00 2.73
5696 8191 5.198965 ACCATCAACGTACTCTGTATACCT 58.801 41.667 0.00 0.00 0.00 3.08
5697 8192 5.655532 ACCATCAACGTACTCTGTATACCTT 59.344 40.000 0.00 0.00 0.00 3.50
5698 8193 6.183360 ACCATCAACGTACTCTGTATACCTTC 60.183 42.308 0.00 0.00 0.00 3.46
5699 8194 5.824904 TCAACGTACTCTGTATACCTTCC 57.175 43.478 0.00 0.00 0.00 3.46
5700 8195 5.503927 TCAACGTACTCTGTATACCTTCCT 58.496 41.667 0.00 0.00 0.00 3.36
5701 8196 5.948162 TCAACGTACTCTGTATACCTTCCTT 59.052 40.000 0.00 0.00 0.00 3.36
5702 8197 6.435277 TCAACGTACTCTGTATACCTTCCTTT 59.565 38.462 0.00 0.00 0.00 3.11
5703 8198 7.611467 TCAACGTACTCTGTATACCTTCCTTTA 59.389 37.037 0.00 0.00 0.00 1.85
5704 8199 7.944729 ACGTACTCTGTATACCTTCCTTTAA 57.055 36.000 0.00 0.00 0.00 1.52
5705 8200 7.766283 ACGTACTCTGTATACCTTCCTTTAAC 58.234 38.462 0.00 0.00 0.00 2.01
5706 8201 6.909357 CGTACTCTGTATACCTTCCTTTAACG 59.091 42.308 0.00 0.00 0.00 3.18
5707 8202 7.201644 CGTACTCTGTATACCTTCCTTTAACGA 60.202 40.741 0.00 0.00 0.00 3.85
5708 8203 7.472334 ACTCTGTATACCTTCCTTTAACGAA 57.528 36.000 0.00 0.00 0.00 3.85
5709 8204 7.899973 ACTCTGTATACCTTCCTTTAACGAAA 58.100 34.615 0.00 0.00 0.00 3.46
5710 8205 8.370182 ACTCTGTATACCTTCCTTTAACGAAAA 58.630 33.333 0.00 0.00 0.00 2.29
5711 8206 8.767478 TCTGTATACCTTCCTTTAACGAAAAG 57.233 34.615 0.00 0.00 43.66 2.27
5712 8207 8.370182 TCTGTATACCTTCCTTTAACGAAAAGT 58.630 33.333 0.00 0.58 42.68 2.66
5713 8208 8.907222 TGTATACCTTCCTTTAACGAAAAGTT 57.093 30.769 0.00 0.00 42.68 2.66
5714 8209 8.992073 TGTATACCTTCCTTTAACGAAAAGTTC 58.008 33.333 0.00 0.00 42.68 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
344 364 5.633601 CACACAAGAAGCATACGAAGACTTA 59.366 40.000 0.00 0.00 0.00 2.24
417 443 1.302511 CTACACCTTGCCGCCAAGT 60.303 57.895 5.31 0.00 45.57 3.16
517 552 2.769095 ACTGATCTTGCTAGACCCTTCC 59.231 50.000 0.00 0.00 31.99 3.46
702 743 0.908910 ATTAGTGATGTGCCCGGACA 59.091 50.000 0.73 0.00 0.00 4.02
802 843 9.044150 CACACAACCATCTTTATTCAATTGTTT 57.956 29.630 5.13 0.00 0.00 2.83
805 846 6.869913 AGCACACAACCATCTTTATTCAATTG 59.130 34.615 0.00 0.00 0.00 2.32
837 878 2.614057 GGATTACTCCGGTCTTTGCATG 59.386 50.000 0.00 0.00 0.00 4.06
904 946 0.671781 GCGTGTCTGACAAGGCATCT 60.672 55.000 21.99 0.00 40.95 2.90
930 972 2.093235 CCTTGTGGGACTGAGAAGATCC 60.093 54.545 0.00 0.00 37.23 3.36
939 981 1.152777 TTGTGGCCTTGTGGGACTG 60.153 57.895 3.32 0.00 45.52 3.51
940 982 1.151450 CTTGTGGCCTTGTGGGACT 59.849 57.895 3.32 0.00 45.52 3.85
941 983 2.564721 GCTTGTGGCCTTGTGGGAC 61.565 63.158 3.32 0.00 45.52 4.46
942 984 2.203480 GCTTGTGGCCTTGTGGGA 60.203 61.111 3.32 0.00 37.23 4.37
951 993 1.256812 ATACTTTGTGGGCTTGTGGC 58.743 50.000 0.00 0.00 40.90 5.01
959 1001 7.327975 TCGATAGGCAATATATACTTTGTGGG 58.672 38.462 0.00 0.00 0.00 4.61
988 1030 4.802051 TTCTGCCCTGCCGCATCC 62.802 66.667 0.00 0.00 38.30 3.51
993 1035 3.694058 ATCTGCTTCTGCCCTGCCG 62.694 63.158 0.00 0.00 38.71 5.69
994 1036 2.119655 CATCTGCTTCTGCCCTGCC 61.120 63.158 0.00 0.00 38.71 4.85
995 1037 2.772691 GCATCTGCTTCTGCCCTGC 61.773 63.158 0.00 0.00 38.71 4.85
996 1038 3.510846 GCATCTGCTTCTGCCCTG 58.489 61.111 0.00 0.00 38.71 4.45
1042 1126 7.483018 AGGTGAGATCTATGATAACTGGGTAT 58.517 38.462 0.00 0.00 0.00 2.73
1087 1171 0.108585 ACCAGCCTCGCTTCTTCAAA 59.891 50.000 0.00 0.00 36.40 2.69
1153 1243 6.284459 ACTATGTATGAAAGAGTAAGCAGCC 58.716 40.000 0.00 0.00 0.00 4.85
1305 1431 6.306199 AGCCAATTTGTGCATCCTGTATATA 58.694 36.000 10.96 0.00 0.00 0.86
1476 1609 2.622064 ATAGCCGAGGAATTGTGGAC 57.378 50.000 0.00 0.00 0.00 4.02
2549 2865 2.011947 GGGTAGGTGTATCGCCAAAAC 58.988 52.381 2.23 0.00 36.32 2.43
2574 2890 1.687660 GGGAGATCCTTTAGGTCGGTC 59.312 57.143 0.00 0.00 36.34 4.79
3321 3755 5.601313 ACTACAACCTTGTTCTTCCTCTACA 59.399 40.000 0.00 0.00 42.35 2.74
3422 3931 2.615262 GATCTGGGTGCTCGTCGGTC 62.615 65.000 0.00 0.00 0.00 4.79
3939 4640 1.298859 GCAGTTCCTTACCCAGCACG 61.299 60.000 0.00 0.00 0.00 5.34
4177 4884 3.470709 CGACACCATTATTCTGAGGCAT 58.529 45.455 0.00 0.00 0.00 4.40
4178 4885 2.419990 CCGACACCATTATTCTGAGGCA 60.420 50.000 0.00 0.00 0.00 4.75
4207 4914 2.826428 CCCTGTCTCGTCCATATTGTG 58.174 52.381 0.00 0.00 0.00 3.33
4408 5121 1.133853 GCCAGCCATTCCTCTCTGAAT 60.134 52.381 0.00 0.00 35.36 2.57
4557 5277 7.015487 CCAGATAGAAGATCAACAGATCCTCTT 59.985 40.741 10.77 0.00 39.28 2.85
4585 5305 7.722949 AACATCCATATGAACAAATCAGGTT 57.277 32.000 3.65 0.00 42.53 3.50
4649 5378 9.396022 GAGAGTCCAATAAAGGATATCACAAAA 57.604 33.333 4.83 0.00 40.42 2.44
4942 5678 8.458843 AGTACTTCAAATTTCACCCATTAATCG 58.541 33.333 0.00 0.00 0.00 3.34
4980 5716 7.483307 TCTCATAAGCAAAAATAGCATTCACC 58.517 34.615 0.00 0.00 0.00 4.02
4981 5717 8.965172 CATCTCATAAGCAAAAATAGCATTCAC 58.035 33.333 0.00 0.00 0.00 3.18
5139 5879 2.305927 GGAAACTGGAGGAGGAATGTGA 59.694 50.000 0.00 0.00 0.00 3.58
5141 5881 2.348472 TGGAAACTGGAGGAGGAATGT 58.652 47.619 0.00 0.00 0.00 2.71
5150 5890 5.308825 ACAGACTAACATTGGAAACTGGAG 58.691 41.667 0.00 0.00 0.00 3.86
5170 5910 5.070001 TCCAACCACAAATCCTTAGAACAG 58.930 41.667 0.00 0.00 0.00 3.16
5190 5930 2.401699 CTGCAAGCACTCCACCTCCA 62.402 60.000 0.00 0.00 0.00 3.86
5232 7521 7.012044 ACTGAAACAAACGACAGCTAATTAAGT 59.988 33.333 0.00 0.00 34.25 2.24
5268 7557 5.419155 TGAACCGAAGAACAGAGTGAGATAT 59.581 40.000 0.00 0.00 0.00 1.63
5270 7559 3.574396 TGAACCGAAGAACAGAGTGAGAT 59.426 43.478 0.00 0.00 0.00 2.75
5368 7674 0.759436 ACGACCCTCCTCTTGTGTGT 60.759 55.000 0.00 0.00 0.00 3.72
5402 7708 1.202687 TGCAACCCTTGTCAGAGTCAG 60.203 52.381 0.00 0.00 0.00 3.51
5453 7759 4.331992 CCACAATCTGCTTAGTGATGACAG 59.668 45.833 0.00 0.00 33.99 3.51
5465 7771 2.106566 AGATCTCGACCACAATCTGCT 58.893 47.619 0.00 0.00 0.00 4.24
5504 7810 2.968675 GGTACGCCTGAATGTAGTTGT 58.031 47.619 0.00 0.00 0.00 3.32
5532 8026 0.740868 CCATATGGATGCCGCCGTAG 60.741 60.000 17.49 0.00 37.39 3.51
5536 8030 3.064324 GGCCATATGGATGCCGCC 61.064 66.667 26.47 13.90 34.50 6.13
5537 8031 2.282391 TGGCCATATGGATGCCGC 60.282 61.111 26.47 8.36 37.39 6.53
5538 8032 0.034767 ATCTGGCCATATGGATGCCG 60.035 55.000 26.47 14.38 37.39 5.69
5627 8122 2.203470 TTCATCTGTCATGCAAGGCA 57.797 45.000 0.00 0.00 44.86 4.75
5629 8124 6.541278 TCTTAGATTTCATCTGTCATGCAAGG 59.459 38.462 0.00 0.00 40.51 3.61
5639 8134 6.212934 CAGATGCGTCTTAGATTTCATCTG 57.787 41.667 23.10 23.10 46.07 2.90
5640 8135 5.982516 GTCAGATGCGTCTTAGATTTCATCT 59.017 40.000 5.46 13.82 40.64 2.90
5641 8136 5.982516 AGTCAGATGCGTCTTAGATTTCATC 59.017 40.000 5.46 10.89 30.42 2.92
5642 8137 5.752472 CAGTCAGATGCGTCTTAGATTTCAT 59.248 40.000 5.46 0.00 30.42 2.57
5643 8138 5.105063 CAGTCAGATGCGTCTTAGATTTCA 58.895 41.667 5.46 0.00 30.42 2.69
5644 8139 5.344066 TCAGTCAGATGCGTCTTAGATTTC 58.656 41.667 5.46 0.00 30.42 2.17
5645 8140 5.330455 TCAGTCAGATGCGTCTTAGATTT 57.670 39.130 5.46 0.00 30.42 2.17
5646 8141 4.991153 TCAGTCAGATGCGTCTTAGATT 57.009 40.909 5.46 0.00 30.42 2.40
5647 8142 4.400884 AGTTCAGTCAGATGCGTCTTAGAT 59.599 41.667 5.46 0.00 30.42 1.98
5648 8143 3.759086 AGTTCAGTCAGATGCGTCTTAGA 59.241 43.478 5.46 0.00 30.42 2.10
5649 8144 3.856521 CAGTTCAGTCAGATGCGTCTTAG 59.143 47.826 5.46 0.00 30.42 2.18
5650 8145 3.506067 TCAGTTCAGTCAGATGCGTCTTA 59.494 43.478 5.46 0.00 30.42 2.10
5651 8146 2.297315 TCAGTTCAGTCAGATGCGTCTT 59.703 45.455 5.46 0.00 30.42 3.01
5652 8147 1.889170 TCAGTTCAGTCAGATGCGTCT 59.111 47.619 1.48 1.48 34.14 4.18
5653 8148 2.354109 TCAGTTCAGTCAGATGCGTC 57.646 50.000 0.00 0.00 0.00 5.19
5654 8149 2.408050 GTTCAGTTCAGTCAGATGCGT 58.592 47.619 0.00 0.00 0.00 5.24
5655 8150 1.728971 GGTTCAGTTCAGTCAGATGCG 59.271 52.381 0.00 0.00 0.00 4.73
5656 8151 2.771089 TGGTTCAGTTCAGTCAGATGC 58.229 47.619 0.00 0.00 0.00 3.91
5657 8152 4.572909 TGATGGTTCAGTTCAGTCAGATG 58.427 43.478 0.00 0.00 0.00 2.90
5658 8153 4.897509 TGATGGTTCAGTTCAGTCAGAT 57.102 40.909 0.00 0.00 0.00 2.90
5659 8154 4.380531 GTTGATGGTTCAGTTCAGTCAGA 58.619 43.478 0.00 0.00 32.27 3.27
5660 8155 3.185188 CGTTGATGGTTCAGTTCAGTCAG 59.815 47.826 0.00 0.00 32.27 3.51
5661 8156 3.130633 CGTTGATGGTTCAGTTCAGTCA 58.869 45.455 0.00 0.00 32.27 3.41
5662 8157 3.131396 ACGTTGATGGTTCAGTTCAGTC 58.869 45.455 0.00 0.00 32.27 3.51
5663 8158 3.194005 ACGTTGATGGTTCAGTTCAGT 57.806 42.857 0.00 0.00 32.27 3.41
5664 8159 4.307432 AGTACGTTGATGGTTCAGTTCAG 58.693 43.478 0.00 0.00 32.27 3.02
5665 8160 4.038763 AGAGTACGTTGATGGTTCAGTTCA 59.961 41.667 0.00 0.00 32.27 3.18
5666 8161 4.386049 CAGAGTACGTTGATGGTTCAGTTC 59.614 45.833 0.00 0.00 32.27 3.01
5667 8162 4.202223 ACAGAGTACGTTGATGGTTCAGTT 60.202 41.667 0.00 0.00 32.27 3.16
5668 8163 3.321111 ACAGAGTACGTTGATGGTTCAGT 59.679 43.478 0.00 0.00 32.27 3.41
5669 8164 3.914312 ACAGAGTACGTTGATGGTTCAG 58.086 45.455 0.00 0.00 32.27 3.02
5670 8165 5.654603 ATACAGAGTACGTTGATGGTTCA 57.345 39.130 0.00 0.00 0.00 3.18
5671 8166 5.975939 GGTATACAGAGTACGTTGATGGTTC 59.024 44.000 5.01 0.00 0.00 3.62
5672 8167 5.655532 AGGTATACAGAGTACGTTGATGGTT 59.344 40.000 5.01 0.00 0.00 3.67
5673 8168 5.198965 AGGTATACAGAGTACGTTGATGGT 58.801 41.667 5.01 0.00 0.00 3.55
5674 8169 5.769484 AGGTATACAGAGTACGTTGATGG 57.231 43.478 5.01 0.00 0.00 3.51
5675 8170 6.039493 AGGAAGGTATACAGAGTACGTTGATG 59.961 42.308 5.01 0.00 32.25 3.07
5676 8171 6.127793 AGGAAGGTATACAGAGTACGTTGAT 58.872 40.000 5.01 0.00 32.25 2.57
5677 8172 5.503927 AGGAAGGTATACAGAGTACGTTGA 58.496 41.667 5.01 0.00 32.25 3.18
5678 8173 5.831702 AGGAAGGTATACAGAGTACGTTG 57.168 43.478 5.01 0.00 32.25 4.10
5679 8174 6.847421 AAAGGAAGGTATACAGAGTACGTT 57.153 37.500 5.01 0.00 34.09 3.99
5680 8175 7.414540 CGTTAAAGGAAGGTATACAGAGTACGT 60.415 40.741 5.01 0.00 0.00 3.57
5681 8176 6.909357 CGTTAAAGGAAGGTATACAGAGTACG 59.091 42.308 5.01 0.00 0.00 3.67
5682 8177 7.989826 TCGTTAAAGGAAGGTATACAGAGTAC 58.010 38.462 5.01 0.00 0.00 2.73
5683 8178 8.579850 TTCGTTAAAGGAAGGTATACAGAGTA 57.420 34.615 5.01 0.00 0.00 2.59
5684 8179 7.472334 TTCGTTAAAGGAAGGTATACAGAGT 57.528 36.000 5.01 0.00 0.00 3.24
5685 8180 8.767478 TTTTCGTTAAAGGAAGGTATACAGAG 57.233 34.615 5.01 0.00 0.00 3.35
5686 8181 8.370182 ACTTTTCGTTAAAGGAAGGTATACAGA 58.630 33.333 5.01 0.00 46.16 3.41
5687 8182 8.543862 ACTTTTCGTTAAAGGAAGGTATACAG 57.456 34.615 5.01 0.00 46.16 2.74
5688 8183 8.907222 AACTTTTCGTTAAAGGAAGGTATACA 57.093 30.769 5.01 0.00 46.16 2.29


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

AutoCloner maintained by Alex Coulton.