Multiple sequence alignment - TraesCS7B01G299500

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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 TraesCS7B01G299500 chr7B 100.000 3168 0 0 1 3168 536638243 536641410 0.000000e+00 5851.0
1 TraesCS7B01G299500 chr7B 100.000 87 0 0 3513 3599 536641755 536641841 1.030000e-35 161.0
2 TraesCS7B01G299500 chr7B 90.476 84 8 0 3516 3599 580948407 580948324 1.060000e-20 111.0
3 TraesCS7B01G299500 chr7A 93.342 2448 97 27 494 2934 578716916 578719304 0.000000e+00 3557.0
4 TraesCS7B01G299500 chr7A 94.343 495 21 4 5 496 578714793 578715283 0.000000e+00 752.0
5 TraesCS7B01G299500 chr2B 91.859 2297 107 32 575 2852 157372338 157374573 0.000000e+00 3133.0
6 TraesCS7B01G299500 chr2B 89.394 396 35 4 84 476 157374939 157374548 3.230000e-135 492.0
7 TraesCS7B01G299500 chr7D 93.840 2078 76 18 565 2626 508334158 508332117 0.000000e+00 3081.0
8 TraesCS7B01G299500 chr7D 93.474 475 23 5 6 476 508327297 508327767 0.000000e+00 699.0
9 TraesCS7B01G299500 chr7D 88.936 235 17 1 2930 3164 102942862 102943087 7.610000e-72 281.0
10 TraesCS7B01G299500 chr7D 91.803 183 14 1 2930 3112 565389609 565389790 1.660000e-63 254.0
11 TraesCS7B01G299500 chr7D 90.476 84 8 0 3516 3599 626477522 626477605 1.060000e-20 111.0
12 TraesCS7B01G299500 chr2D 94.723 1876 73 14 725 2590 107027364 107029223 0.000000e+00 2892.0
13 TraesCS7B01G299500 chr2D 83.900 441 28 10 2419 2855 107133596 107133997 7.290000e-102 381.0
14 TraesCS7B01G299500 chr2D 76.471 612 124 17 1190 1791 382380402 382381003 7.500000e-82 315.0
15 TraesCS7B01G299500 chr2D 83.660 153 13 5 496 646 107027193 107027335 2.250000e-27 134.0
16 TraesCS7B01G299500 chr2D 87.500 112 12 1 537 646 107136569 107136680 1.050000e-25 128.0
17 TraesCS7B01G299500 chr2A 90.410 1074 82 7 1700 2769 103380998 103382054 0.000000e+00 1393.0
18 TraesCS7B01G299500 chr2A 91.076 381 18 4 2333 2711 103366020 103366386 5.360000e-138 501.0
19 TraesCS7B01G299500 chr3D 79.700 601 102 16 1199 1789 448497005 448496415 2.000000e-112 416.0
20 TraesCS7B01G299500 chr3D 89.899 198 19 1 2930 3126 81723900 81723703 1.660000e-63 254.0
21 TraesCS7B01G299500 chr3D 89.655 87 8 1 3513 3599 471822062 471822147 3.800000e-20 110.0
22 TraesCS7B01G299500 chr3D 83.146 89 15 0 1901 1989 95563820 95563908 8.280000e-12 82.4
23 TraesCS7B01G299500 chr3A 79.700 601 102 16 1199 1789 589826413 589825823 2.000000e-112 416.0
24 TraesCS7B01G299500 chr3A 80.172 116 17 5 1876 1989 113712985 113713096 8.280000e-12 82.4
25 TraesCS7B01G299500 chr3B 79.070 602 106 16 1199 1790 588696522 588695931 2.600000e-106 396.0
26 TraesCS7B01G299500 chr3B 94.000 150 5 2 283 432 201510305 201510160 1.300000e-54 224.0
27 TraesCS7B01G299500 chr3B 89.286 84 9 0 3516 3599 437508470 437508553 4.910000e-19 106.0
28 TraesCS7B01G299500 chr3B 83.146 89 15 0 1901 1989 146552919 146553007 8.280000e-12 82.4
29 TraesCS7B01G299500 chr5D 90.756 238 21 1 2930 3167 371026245 371026481 2.090000e-82 316.0
30 TraesCS7B01G299500 chr5D 89.500 200 20 1 2930 3129 541576855 541577053 5.970000e-63 252.0
31 TraesCS7B01G299500 chr5D 94.000 150 5 2 283 432 240134882 240134737 1.300000e-54 224.0
32 TraesCS7B01G299500 chr5D 93.464 153 6 2 280 432 449151973 449152121 1.300000e-54 224.0
33 TraesCS7B01G299500 chr6D 90.521 211 19 1 2919 3128 427338318 427338108 9.840000e-71 278.0
34 TraesCS7B01G299500 chr4D 88.991 218 20 3 2924 3138 483487625 483487841 2.130000e-67 267.0
35 TraesCS7B01G299500 chr4D 90.361 83 8 0 3516 3598 465071801 465071883 3.800000e-20 110.0
36 TraesCS7B01G299500 chr4D 89.286 84 9 0 3516 3599 8142932 8142849 4.910000e-19 106.0
37 TraesCS7B01G299500 chr5B 86.842 228 28 2 2933 3160 705255694 705255469 1.660000e-63 254.0
38 TraesCS7B01G299500 chr5B 89.286 84 9 0 3516 3599 575070255 575070172 4.910000e-19 106.0
39 TraesCS7B01G299500 chr1D 86.404 228 24 5 2933 3160 377953221 377953441 3.590000e-60 243.0
40 TraesCS7B01G299500 chr1D 93.464 153 6 2 280 432 483917423 483917571 1.300000e-54 224.0
41 TraesCS7B01G299500 chr1D 93.333 150 6 2 283 432 254495189 254495044 6.050000e-53 219.0
42 TraesCS7B01G299500 chrUn 93.464 153 6 2 280 432 441827328 441827476 1.300000e-54 224.0
43 TraesCS7B01G299500 chr6B 91.667 84 7 0 3516 3599 686507381 686507464 2.270000e-22 117.0
44 TraesCS7B01G299500 chr6A 91.667 84 7 0 3516 3599 85578350 85578433 2.270000e-22 117.0


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 TraesCS7B01G299500 chr7B 536638243 536641841 3598 False 3006.0 5851 100.0000 1 3599 2 chr7B.!!$F1 3598
1 TraesCS7B01G299500 chr7A 578714793 578719304 4511 False 2154.5 3557 93.8425 5 2934 2 chr7A.!!$F1 2929
2 TraesCS7B01G299500 chr2B 157372338 157374573 2235 False 3133.0 3133 91.8590 575 2852 1 chr2B.!!$F1 2277
3 TraesCS7B01G299500 chr7D 508332117 508334158 2041 True 3081.0 3081 93.8400 565 2626 1 chr7D.!!$R1 2061
4 TraesCS7B01G299500 chr2D 107027193 107029223 2030 False 1513.0 2892 89.1915 496 2590 2 chr2D.!!$F2 2094
5 TraesCS7B01G299500 chr2D 382380402 382381003 601 False 315.0 315 76.4710 1190 1791 1 chr2D.!!$F1 601
6 TraesCS7B01G299500 chr2D 107133596 107136680 3084 False 254.5 381 85.7000 537 2855 2 chr2D.!!$F3 2318
7 TraesCS7B01G299500 chr2A 103380998 103382054 1056 False 1393.0 1393 90.4100 1700 2769 1 chr2A.!!$F2 1069
8 TraesCS7B01G299500 chr3D 448496415 448497005 590 True 416.0 416 79.7000 1199 1789 1 chr3D.!!$R2 590
9 TraesCS7B01G299500 chr3A 589825823 589826413 590 True 416.0 416 79.7000 1199 1789 1 chr3A.!!$R1 590
10 TraesCS7B01G299500 chr3B 588695931 588696522 591 True 396.0 396 79.0700 1199 1790 1 chr3B.!!$R2 591

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
650 2291 0.107831 ACCAACCAGCGCAGTCTAAA 59.892 50.0 11.47 0.0 0.0 1.85 F
1794 3475 0.179043 TGCGTGGCTACCTCAACAAA 60.179 50.0 0.00 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2320 4004 2.592993 CCAAGAACCTCTCCGGGCA 61.593 63.158 0.00 0.0 36.97 5.36 R
2860 4563 0.532115 AGCATTTCGATTTGCACCCC 59.468 50.000 18.76 0.0 41.35 4.95 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
25 26 4.832248 TGCAAGGAGTAGAGTTTACCATG 58.168 43.478 0.00 0.00 0.00 3.66
46 47 0.176680 AGTTAGGCTGCACATCGAGG 59.823 55.000 0.50 0.00 0.00 4.63
54 55 2.222678 GCTGCACATCGAGGTATGAATG 59.777 50.000 0.77 0.00 0.00 2.67
110 113 1.133598 TCGTATGAACTAGTGGGTGCG 59.866 52.381 0.00 0.97 0.00 5.34
145 149 5.380043 TGAAAACCTGAAGCTCTTTGAGAT 58.620 37.500 0.00 0.00 0.00 2.75
227 231 1.205460 AGGCATGTACCCCGGTTTCT 61.205 55.000 0.00 0.00 0.00 2.52
233 237 4.201980 GCATGTACCCCGGTTTCTATTTTC 60.202 45.833 0.00 0.00 0.00 2.29
241 245 5.193679 CCCGGTTTCTATTTTCAGAAGGAT 58.806 41.667 0.00 0.00 35.99 3.24
297 301 6.624423 CCACATTTGTTAATGAGAAAGAGGG 58.376 40.000 4.99 0.00 43.12 4.30
307 311 4.021102 TGAGAAAGAGGGTGGCTAAAAG 57.979 45.455 0.00 0.00 0.00 2.27
384 388 0.311165 CGCGAGGATATATAGCCCGG 59.689 60.000 21.48 12.88 30.36 5.73
445 449 5.512942 TTAGAGGGGTGAATGAATGACAA 57.487 39.130 0.00 0.00 0.00 3.18
447 451 4.275810 AGAGGGGTGAATGAATGACAATG 58.724 43.478 0.00 0.00 0.00 2.82
486 490 7.653713 GCAGAATACATACATTGTGCTAGTAGT 59.346 37.037 9.85 0.00 46.32 2.73
487 491 9.186323 CAGAATACATACATTGTGCTAGTAGTC 57.814 37.037 0.00 5.99 39.48 2.59
521 2160 0.597637 CTGTTTCTGGTCGAGCACGT 60.598 55.000 14.39 0.00 40.69 4.49
522 2161 0.669619 TGTTTCTGGTCGAGCACGTA 59.330 50.000 14.39 0.00 40.69 3.57
523 2162 1.058404 GTTTCTGGTCGAGCACGTAC 58.942 55.000 14.39 7.76 40.69 3.67
526 2165 2.974489 CTGGTCGAGCACGTACGGT 61.974 63.158 21.06 3.20 40.69 4.83
527 2166 2.256461 GGTCGAGCACGTACGGTT 59.744 61.111 21.06 6.51 40.69 4.44
528 2167 2.084681 GGTCGAGCACGTACGGTTG 61.085 63.158 21.06 10.89 40.69 3.77
529 2168 1.081906 GTCGAGCACGTACGGTTGA 60.082 57.895 21.06 10.02 40.69 3.18
648 2289 1.005037 CACCAACCAGCGCAGTCTA 60.005 57.895 11.47 0.00 0.00 2.59
649 2290 0.602638 CACCAACCAGCGCAGTCTAA 60.603 55.000 11.47 0.00 0.00 2.10
650 2291 0.107831 ACCAACCAGCGCAGTCTAAA 59.892 50.000 11.47 0.00 0.00 1.85
652 2293 1.812571 CCAACCAGCGCAGTCTAAATT 59.187 47.619 11.47 0.00 0.00 1.82
653 2294 2.159517 CCAACCAGCGCAGTCTAAATTC 60.160 50.000 11.47 0.00 0.00 2.17
654 2295 2.744202 CAACCAGCGCAGTCTAAATTCT 59.256 45.455 11.47 0.00 0.00 2.40
927 2589 2.373224 TCACAGCAACCAACAACATCA 58.627 42.857 0.00 0.00 0.00 3.07
928 2590 2.957680 TCACAGCAACCAACAACATCAT 59.042 40.909 0.00 0.00 0.00 2.45
935 2597 4.675510 CAACCAACAACATCATAGCATCC 58.324 43.478 0.00 0.00 0.00 3.51
957 2627 2.095567 GCACCAGCTCAAACACACATAG 60.096 50.000 0.00 0.00 37.91 2.23
959 2629 4.314961 CACCAGCTCAAACACACATAGTA 58.685 43.478 0.00 0.00 0.00 1.82
960 2630 4.152402 CACCAGCTCAAACACACATAGTAC 59.848 45.833 0.00 0.00 0.00 2.73
962 2632 4.152402 CCAGCTCAAACACACATAGTACAC 59.848 45.833 0.00 0.00 0.00 2.90
1080 2758 2.420687 GCTCCTCAAATCGTTCCTCCAT 60.421 50.000 0.00 0.00 0.00 3.41
1488 3169 1.301716 GACGCTGCCCTTCTTCACA 60.302 57.895 0.00 0.00 0.00 3.58
1794 3475 0.179043 TGCGTGGCTACCTCAACAAA 60.179 50.000 0.00 0.00 0.00 2.83
1845 3526 1.493772 TCTTCAACGCCAACTACGTG 58.506 50.000 0.00 0.00 44.30 4.49
1869 3550 3.774216 AGAAGAGAAGGAAGGTGATGGAG 59.226 47.826 0.00 0.00 0.00 3.86
1872 3553 3.103742 GAGAAGGAAGGTGATGGAGACT 58.896 50.000 0.00 0.00 0.00 3.24
1875 3556 1.364328 AGGAAGGTGATGGAGACTCCT 59.636 52.381 22.14 8.03 37.46 3.69
1879 3560 1.118838 GGTGATGGAGACTCCTGGAG 58.881 60.000 22.00 22.00 37.46 3.86
2593 4283 1.225704 GCCTTCCACCCCATCTCAG 59.774 63.158 0.00 0.00 0.00 3.35
2667 4359 9.793252 TTACTCTTCGGATTACAAATACAGTAC 57.207 33.333 0.00 0.00 0.00 2.73
2668 4360 8.064336 ACTCTTCGGATTACAAATACAGTACT 57.936 34.615 0.00 0.00 0.00 2.73
2669 4361 9.182214 ACTCTTCGGATTACAAATACAGTACTA 57.818 33.333 0.00 0.00 0.00 1.82
2670 4362 9.448294 CTCTTCGGATTACAAATACAGTACTAC 57.552 37.037 0.00 0.00 0.00 2.73
2671 4363 9.182214 TCTTCGGATTACAAATACAGTACTACT 57.818 33.333 0.00 0.00 0.00 2.57
2702 4394 8.918202 ACAGGAAAGTATGTCAGTTGATTTAA 57.082 30.769 0.00 0.00 0.00 1.52
2827 4530 6.856426 ACGCTTTTCAGCTTTAAGAAATGTAC 59.144 34.615 0.00 0.00 44.85 2.90
2828 4531 6.855914 CGCTTTTCAGCTTTAAGAAATGTACA 59.144 34.615 0.00 0.00 44.85 2.90
2829 4532 7.059945 CGCTTTTCAGCTTTAAGAAATGTACAG 59.940 37.037 0.33 2.25 44.85 2.74
2830 4533 7.327032 GCTTTTCAGCTTTAAGAAATGTACAGG 59.673 37.037 0.33 0.00 43.51 4.00
2831 4534 6.817765 TTCAGCTTTAAGAAATGTACAGGG 57.182 37.500 0.33 0.00 0.00 4.45
2858 4561 9.643652 TGTATTTTGCAAATCGAAATGTTTTTC 57.356 25.926 13.65 0.00 38.79 2.29
2860 4563 8.770850 ATTTTGCAAATCGAAATGTTTTTCTG 57.229 26.923 13.65 0.00 39.30 3.02
2871 4575 3.467374 TGTTTTTCTGGGGTGCAAATC 57.533 42.857 0.00 0.00 0.00 2.17
2878 4582 0.246086 TGGGGTGCAAATCGAAATGC 59.754 50.000 16.38 16.38 42.86 3.56
2894 4598 4.682860 CGAAATGCTATTGCCATTCATTCC 59.317 41.667 12.09 0.00 38.71 3.01
2920 4625 0.175760 TGAAGTATGGTGCTCCGCTC 59.824 55.000 0.00 0.00 36.30 5.03
2934 4639 0.169672 CCGCTCGGTTCGTTCTTAGA 59.830 55.000 0.00 0.00 0.00 2.10
2935 4640 1.536149 CGCTCGGTTCGTTCTTAGAG 58.464 55.000 0.00 0.00 0.00 2.43
2936 4641 1.270068 GCTCGGTTCGTTCTTAGAGC 58.730 55.000 0.00 0.00 43.11 4.09
2937 4642 2.631418 CTCGGTTCGTTCTTAGAGCA 57.369 50.000 0.00 0.00 0.00 4.26
2938 4643 2.942710 CTCGGTTCGTTCTTAGAGCAA 58.057 47.619 0.00 0.00 0.00 3.91
2939 4644 2.662156 CTCGGTTCGTTCTTAGAGCAAC 59.338 50.000 0.00 0.93 0.00 4.17
2942 4647 3.612004 CGGTTCGTTCTTAGAGCAACTCT 60.612 47.826 2.23 2.23 43.83 3.24
2945 4650 4.358494 TCGTTCTTAGAGCAACTCTAGC 57.642 45.455 4.64 0.00 42.92 3.42
2946 4651 3.756963 TCGTTCTTAGAGCAACTCTAGCA 59.243 43.478 4.64 0.00 42.92 3.49
2947 4652 4.101942 CGTTCTTAGAGCAACTCTAGCAG 58.898 47.826 4.64 1.69 42.92 4.24
2949 4654 4.974368 TCTTAGAGCAACTCTAGCAGAC 57.026 45.455 4.64 0.00 42.92 3.51
2950 4655 3.697045 TCTTAGAGCAACTCTAGCAGACC 59.303 47.826 4.64 0.00 42.92 3.85
2951 4656 1.190643 AGAGCAACTCTAGCAGACCC 58.809 55.000 0.00 0.00 39.28 4.46
2952 4657 0.176910 GAGCAACTCTAGCAGACCCC 59.823 60.000 0.00 0.00 0.00 4.95
2953 4658 1.153549 GCAACTCTAGCAGACCCCG 60.154 63.158 0.00 0.00 0.00 5.73
2955 4660 1.609501 AACTCTAGCAGACCCCGCA 60.610 57.895 0.00 0.00 0.00 5.69
2957 4662 1.365633 CTCTAGCAGACCCCGCATC 59.634 63.158 0.00 0.00 0.00 3.91
2958 4663 2.093537 CTCTAGCAGACCCCGCATCC 62.094 65.000 0.00 0.00 0.00 3.51
2959 4664 3.161450 TAGCAGACCCCGCATCCC 61.161 66.667 0.00 0.00 0.00 3.85
2989 4694 1.441725 CAAAACGCGTTTACAGTTCGC 59.558 47.619 34.89 0.00 45.28 4.70
2992 4697 2.547305 GCGTTTACAGTTCGCGCA 59.453 55.556 8.75 0.00 46.23 6.09
2996 4701 2.303537 CGTTTACAGTTCGCGCAAAAT 58.696 42.857 8.75 0.00 0.00 1.82
2997 4702 2.334454 CGTTTACAGTTCGCGCAAAATC 59.666 45.455 8.75 0.00 0.00 2.17
2998 4703 2.220315 TTACAGTTCGCGCAAAATCG 57.780 45.000 8.75 0.00 0.00 3.34
3008 4713 1.255767 CGCAAAATCGCTTTTACGGG 58.744 50.000 8.79 0.00 37.43 5.28
3009 4714 0.989164 GCAAAATCGCTTTTACGGGC 59.011 50.000 0.00 0.00 32.81 6.13
3010 4715 1.402325 GCAAAATCGCTTTTACGGGCT 60.402 47.619 0.00 0.00 32.81 5.19
3011 4716 2.250188 CAAAATCGCTTTTACGGGCTG 58.750 47.619 0.00 0.00 32.81 4.85
3012 4717 0.808755 AAATCGCTTTTACGGGCTGG 59.191 50.000 0.00 0.00 0.00 4.85
3013 4718 1.654023 AATCGCTTTTACGGGCTGGC 61.654 55.000 0.00 0.00 0.00 4.85
3014 4719 2.536997 ATCGCTTTTACGGGCTGGCT 62.537 55.000 0.00 0.00 0.00 4.75
3015 4720 2.750888 CGCTTTTACGGGCTGGCTC 61.751 63.158 0.00 0.00 0.00 4.70
3016 4721 2.750888 GCTTTTACGGGCTGGCTCG 61.751 63.158 13.54 13.54 46.76 5.03
3017 4722 2.046700 TTTTACGGGCTGGCTCGG 60.047 61.111 19.04 1.62 45.45 4.63
3018 4723 2.515996 CTTTTACGGGCTGGCTCGGA 62.516 60.000 19.04 7.87 45.45 4.55
3019 4724 2.791501 TTTTACGGGCTGGCTCGGAC 62.792 60.000 19.04 0.00 45.45 4.79
3020 4725 4.753662 TACGGGCTGGCTCGGACT 62.754 66.667 19.04 0.82 45.45 3.85
3026 4731 4.007644 CTGGCTCGGACTGGCACA 62.008 66.667 0.00 0.00 36.06 4.57
3057 4762 4.810191 CCCCCAAATGGATTCGTAAAAA 57.190 40.909 0.00 0.00 37.39 1.94
3058 4763 5.351948 CCCCCAAATGGATTCGTAAAAAT 57.648 39.130 0.00 0.00 37.39 1.82
3059 4764 5.115480 CCCCCAAATGGATTCGTAAAAATG 58.885 41.667 0.00 0.00 37.39 2.32
3060 4765 5.337975 CCCCCAAATGGATTCGTAAAAATGT 60.338 40.000 0.00 0.00 37.39 2.71
3062 4767 7.418483 CCCCCAAATGGATTCGTAAAAATGTAT 60.418 37.037 0.00 0.00 37.39 2.29
3070 4775 8.552865 TGGATTCGTAAAAATGTATATTCGTGG 58.447 33.333 0.00 0.00 0.00 4.94
3071 4776 7.532884 GGATTCGTAAAAATGTATATTCGTGGC 59.467 37.037 0.00 0.00 0.00 5.01
3072 4777 6.289745 TCGTAAAAATGTATATTCGTGGCC 57.710 37.500 0.00 0.00 0.00 5.36
3074 4779 6.018588 TCGTAAAAATGTATATTCGTGGCCAG 60.019 38.462 5.11 0.00 0.00 4.85
3075 4780 4.568152 AAAATGTATATTCGTGGCCAGC 57.432 40.909 5.11 0.00 0.00 4.85
3076 4781 2.185004 ATGTATATTCGTGGCCAGCC 57.815 50.000 5.11 0.38 0.00 4.85
3077 4782 1.128200 TGTATATTCGTGGCCAGCCT 58.872 50.000 5.11 0.00 36.94 4.58
3078 4783 1.070134 TGTATATTCGTGGCCAGCCTC 59.930 52.381 5.11 5.38 36.94 4.70
3079 4784 0.685097 TATATTCGTGGCCAGCCTCC 59.315 55.000 5.11 0.00 36.94 4.30
3081 4786 1.971505 TATTCGTGGCCAGCCTCCAG 61.972 60.000 5.11 0.00 36.94 3.86
3083 4788 4.767255 CGTGGCCAGCCTCCAGTC 62.767 72.222 5.11 0.00 36.94 3.51
3084 4789 4.416738 GTGGCCAGCCTCCAGTCC 62.417 72.222 5.11 0.00 36.94 3.85
3105 4810 2.182030 CGCTGTCGTCCCTTCCTC 59.818 66.667 0.00 0.00 0.00 3.71
3106 4811 2.579738 GCTGTCGTCCCTTCCTCC 59.420 66.667 0.00 0.00 0.00 4.30
3108 4813 1.893786 CTGTCGTCCCTTCCTCCAG 59.106 63.158 0.00 0.00 0.00 3.86
3109 4814 2.232298 CTGTCGTCCCTTCCTCCAGC 62.232 65.000 0.00 0.00 0.00 4.85
3110 4815 2.683933 TCGTCCCTTCCTCCAGCC 60.684 66.667 0.00 0.00 0.00 4.85
3111 4816 4.148825 CGTCCCTTCCTCCAGCCG 62.149 72.222 0.00 0.00 0.00 5.52
3112 4817 3.787001 GTCCCTTCCTCCAGCCGG 61.787 72.222 0.00 0.00 0.00 6.13
3116 4821 4.785453 CTTCCTCCAGCCGGCCAC 62.785 72.222 26.15 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.614694 TGGTAAACTCTACTCCTTGCATTA 57.385 37.500 0.00 0.00 0.00 1.90
1 2 5.499004 TGGTAAACTCTACTCCTTGCATT 57.501 39.130 0.00 0.00 0.00 3.56
2 3 5.045578 ACATGGTAAACTCTACTCCTTGCAT 60.046 40.000 0.00 0.00 0.00 3.96
3 4 4.286032 ACATGGTAAACTCTACTCCTTGCA 59.714 41.667 0.00 0.00 0.00 4.08
25 26 2.464865 CTCGATGTGCAGCCTAACTAC 58.535 52.381 0.00 0.00 0.00 2.73
46 47 6.734104 ACAAGAGCTTTCACTCATTCATAC 57.266 37.500 0.00 0.00 39.26 2.39
80 81 5.972382 CACTAGTTCATACGAGAGCTTTACC 59.028 44.000 0.00 0.00 32.09 2.85
110 113 6.420903 GCTTCAGGTTTTCAAGTAAATTGGAC 59.579 38.462 0.00 0.00 39.54 4.02
145 149 6.809196 GGTTTGCATATTTTAACGATGAACCA 59.191 34.615 0.00 0.00 32.04 3.67
180 184 3.206150 ACTTTGGTCGGCACATCATATC 58.794 45.455 0.00 0.00 0.00 1.63
227 231 6.876789 TCGTTGTTAGCATCCTTCTGAAAATA 59.123 34.615 0.00 0.00 0.00 1.40
233 237 3.125316 GGTTCGTTGTTAGCATCCTTCTG 59.875 47.826 0.00 0.00 0.00 3.02
241 245 0.249531 TGCTCGGTTCGTTGTTAGCA 60.250 50.000 0.00 0.00 37.62 3.49
297 301 5.966742 ATGGTTTCTCTTCTTTTAGCCAC 57.033 39.130 0.00 0.00 0.00 5.01
359 363 3.243134 GGCTATATATCCTCGCGGAACTC 60.243 52.174 6.13 0.00 44.02 3.01
400 404 3.569701 AGTTCGAGGCAAATGAACACATT 59.430 39.130 11.30 0.00 43.36 2.71
429 433 3.440173 ACGTCATTGTCATTCATTCACCC 59.560 43.478 0.00 0.00 0.00 4.61
445 449 4.685169 ATTCTGCAAATCGAAACGTCAT 57.315 36.364 0.00 0.00 0.00 3.06
447 451 4.953269 TGTATTCTGCAAATCGAAACGTC 58.047 39.130 0.00 0.00 0.00 4.34
486 490 6.486657 CCAGAAACAGTTTCCTTAATCACTGA 59.513 38.462 20.47 0.00 39.25 3.41
487 491 6.263168 ACCAGAAACAGTTTCCTTAATCACTG 59.737 38.462 20.47 9.95 42.08 3.66
521 2160 7.283580 TCCTTTTCTTTCTTTCAATCAACCGTA 59.716 33.333 0.00 0.00 0.00 4.02
522 2161 6.096282 TCCTTTTCTTTCTTTCAATCAACCGT 59.904 34.615 0.00 0.00 0.00 4.83
523 2162 6.503524 TCCTTTTCTTTCTTTCAATCAACCG 58.496 36.000 0.00 0.00 0.00 4.44
526 2165 8.292448 CGAGATCCTTTTCTTTCTTTCAATCAA 58.708 33.333 0.00 0.00 0.00 2.57
527 2166 7.573843 GCGAGATCCTTTTCTTTCTTTCAATCA 60.574 37.037 0.00 0.00 0.00 2.57
528 2167 6.744993 GCGAGATCCTTTTCTTTCTTTCAATC 59.255 38.462 0.00 0.00 0.00 2.67
529 2168 6.349694 GGCGAGATCCTTTTCTTTCTTTCAAT 60.350 38.462 0.00 0.00 0.00 2.57
648 2289 5.242393 CCTGTGTGGTCAGAATTGAGAATTT 59.758 40.000 0.00 0.00 37.61 1.82
649 2290 4.763793 CCTGTGTGGTCAGAATTGAGAATT 59.236 41.667 0.00 0.00 37.61 2.17
650 2291 4.042062 TCCTGTGTGGTCAGAATTGAGAAT 59.958 41.667 0.00 0.00 37.61 2.40
652 2293 2.972021 TCCTGTGTGGTCAGAATTGAGA 59.028 45.455 0.00 0.00 37.61 3.27
653 2294 3.332919 CTCCTGTGTGGTCAGAATTGAG 58.667 50.000 0.00 0.00 37.61 3.02
654 2295 2.550855 GCTCCTGTGTGGTCAGAATTGA 60.551 50.000 0.00 0.00 37.61 2.57
927 2589 1.070445 GAGCTGGTGCGGATGCTAT 59.930 57.895 0.00 0.00 45.42 2.97
928 2590 1.898330 TTGAGCTGGTGCGGATGCTA 61.898 55.000 0.00 0.00 45.42 3.49
935 2597 1.009675 GTGTGTTTGAGCTGGTGCG 60.010 57.895 0.00 0.00 45.42 5.34
957 2627 1.202031 GCTTGGCGTGCAATAGTGTAC 60.202 52.381 0.96 0.96 37.04 2.90
959 2629 0.606401 AGCTTGGCGTGCAATAGTGT 60.606 50.000 0.00 0.00 0.00 3.55
960 2630 1.328680 CTAGCTTGGCGTGCAATAGTG 59.671 52.381 0.00 0.00 0.00 2.74
962 2632 0.305922 GCTAGCTTGGCGTGCAATAG 59.694 55.000 7.70 0.27 33.60 1.73
1845 3526 3.118445 CCATCACCTTCCTTCTCTTCTCC 60.118 52.174 0.00 0.00 0.00 3.71
1869 3550 3.322254 TGTTCTTGTCTTCTCCAGGAGTC 59.678 47.826 16.65 6.57 0.00 3.36
1872 3553 3.495100 GCTTGTTCTTGTCTTCTCCAGGA 60.495 47.826 0.00 0.00 0.00 3.86
1875 3556 3.495100 GGAGCTTGTTCTTGTCTTCTCCA 60.495 47.826 0.00 0.00 38.85 3.86
1879 3560 2.755650 TCGGAGCTTGTTCTTGTCTTC 58.244 47.619 0.00 0.00 0.00 2.87
2320 4004 2.592993 CCAAGAACCTCTCCGGGCA 61.593 63.158 0.00 0.00 36.97 5.36
2322 4006 2.990479 CCCAAGAACCTCTCCGGG 59.010 66.667 0.00 0.00 34.15 5.73
2593 4283 5.098211 GGTTGAAGAAGTAATTGCTCATGC 58.902 41.667 0.00 0.00 40.20 4.06
2668 4360 9.696572 ACTGACATACTTTCCTGTAATCTAGTA 57.303 33.333 0.00 0.00 0.00 1.82
2669 4361 8.596781 ACTGACATACTTTCCTGTAATCTAGT 57.403 34.615 0.00 0.00 0.00 2.57
2670 4362 9.307121 CAACTGACATACTTTCCTGTAATCTAG 57.693 37.037 0.00 0.00 0.00 2.43
2671 4363 9.031537 TCAACTGACATACTTTCCTGTAATCTA 57.968 33.333 0.00 0.00 0.00 1.98
2672 4364 7.907389 TCAACTGACATACTTTCCTGTAATCT 58.093 34.615 0.00 0.00 0.00 2.40
2753 4456 7.832769 TGAAAAGCATTATGTAAACCCCTTAC 58.167 34.615 0.00 0.00 40.42 2.34
2827 4530 4.433186 TCGATTTGCAAAATACACCCTG 57.567 40.909 17.19 0.00 0.00 4.45
2828 4531 5.461032 TTTCGATTTGCAAAATACACCCT 57.539 34.783 17.19 0.00 0.00 4.34
2829 4532 5.637387 ACATTTCGATTTGCAAAATACACCC 59.363 36.000 17.19 0.00 0.00 4.61
2830 4533 6.704512 ACATTTCGATTTGCAAAATACACC 57.295 33.333 17.19 1.06 0.00 4.16
2831 4534 8.986039 AAAACATTTCGATTTGCAAAATACAC 57.014 26.923 17.19 5.00 0.00 2.90
2858 4561 1.736696 GCATTTCGATTTGCACCCCAG 60.737 52.381 13.48 0.00 38.72 4.45
2860 4563 0.532115 AGCATTTCGATTTGCACCCC 59.468 50.000 18.76 0.00 41.35 4.95
2871 4575 4.682860 GGAATGAATGGCAATAGCATTTCG 59.317 41.667 0.00 0.00 44.61 3.46
2878 4582 5.751509 CACATTGTGGAATGAATGGCAATAG 59.248 40.000 9.00 0.00 41.49 1.73
2894 4598 3.127548 GGAGCACCATACTTCACATTGTG 59.872 47.826 10.64 10.64 35.97 3.33
2920 4625 2.662156 GAGTTGCTCTAAGAACGAACCG 59.338 50.000 0.00 0.00 0.00 4.44
2934 4639 1.608717 CGGGGTCTGCTAGAGTTGCT 61.609 60.000 0.00 0.00 0.00 3.91
2935 4640 1.153549 CGGGGTCTGCTAGAGTTGC 60.154 63.158 0.00 0.00 0.00 4.17
2936 4641 1.153549 GCGGGGTCTGCTAGAGTTG 60.154 63.158 0.00 0.00 0.00 3.16
2937 4642 0.978146 ATGCGGGGTCTGCTAGAGTT 60.978 55.000 0.00 0.00 0.00 3.01
2938 4643 1.381872 ATGCGGGGTCTGCTAGAGT 60.382 57.895 0.00 0.00 0.00 3.24
2939 4644 1.365633 GATGCGGGGTCTGCTAGAG 59.634 63.158 0.00 0.00 0.00 2.43
2942 4647 3.161450 GGGATGCGGGGTCTGCTA 61.161 66.667 0.30 0.00 0.00 3.49
2968 4673 1.441725 CGAACTGTAAACGCGTTTTGC 59.558 47.619 38.53 29.69 41.47 3.68
2969 4674 1.441725 GCGAACTGTAAACGCGTTTTG 59.558 47.619 38.53 28.67 42.65 2.44
2971 4676 3.426008 GCGAACTGTAAACGCGTTT 57.574 47.368 36.15 36.15 42.65 3.60
2976 4681 1.732528 TTTTGCGCGAACTGTAAACG 58.267 45.000 12.10 0.00 0.00 3.60
2978 4683 2.566036 CGATTTTGCGCGAACTGTAAA 58.434 42.857 12.10 0.00 0.00 2.01
2979 4684 2.220315 CGATTTTGCGCGAACTGTAA 57.780 45.000 12.10 0.00 0.00 2.41
2980 4685 3.939171 CGATTTTGCGCGAACTGTA 57.061 47.368 12.10 0.00 0.00 2.74
2981 4686 4.818417 CGATTTTGCGCGAACTGT 57.182 50.000 12.10 0.00 0.00 3.55
2989 4694 1.255767 CCCGTAAAAGCGATTTTGCG 58.744 50.000 32.59 32.59 45.21 4.85
2990 4695 0.989164 GCCCGTAAAAGCGATTTTGC 59.011 50.000 20.90 18.19 32.27 3.68
2991 4696 2.250188 CAGCCCGTAAAAGCGATTTTG 58.750 47.619 20.90 5.49 32.27 2.44
2992 4697 1.201414 CCAGCCCGTAAAAGCGATTTT 59.799 47.619 16.41 16.41 32.27 1.82
2996 4701 2.744709 GCCAGCCCGTAAAAGCGA 60.745 61.111 0.00 0.00 0.00 4.93
2997 4702 2.746277 AGCCAGCCCGTAAAAGCG 60.746 61.111 0.00 0.00 0.00 4.68
2998 4703 2.750888 CGAGCCAGCCCGTAAAAGC 61.751 63.158 0.00 0.00 0.00 3.51
2999 4704 2.106683 CCGAGCCAGCCCGTAAAAG 61.107 63.158 0.00 0.00 0.00 2.27
3001 4706 2.998480 TCCGAGCCAGCCCGTAAA 60.998 61.111 0.00 0.00 0.00 2.01
3002 4707 3.766691 GTCCGAGCCAGCCCGTAA 61.767 66.667 0.00 0.00 0.00 3.18
3003 4708 4.753662 AGTCCGAGCCAGCCCGTA 62.754 66.667 0.00 0.00 0.00 4.02
3009 4714 3.947132 CTGTGCCAGTCCGAGCCAG 62.947 68.421 0.00 0.00 0.00 4.85
3010 4715 4.007644 CTGTGCCAGTCCGAGCCA 62.008 66.667 0.00 0.00 0.00 4.75
3011 4716 3.023949 ATCTGTGCCAGTCCGAGCC 62.024 63.158 2.68 0.00 32.61 4.70
3012 4717 1.812922 CATCTGTGCCAGTCCGAGC 60.813 63.158 2.68 0.00 32.61 5.03
3013 4718 1.812922 GCATCTGTGCCAGTCCGAG 60.813 63.158 2.68 0.00 45.76 4.63
3014 4719 2.265739 GCATCTGTGCCAGTCCGA 59.734 61.111 2.68 0.00 45.76 4.55
3036 4741 4.810191 TTTTTACGAATCCATTTGGGGG 57.190 40.909 0.00 0.00 37.22 5.40
3037 4742 5.729510 ACATTTTTACGAATCCATTTGGGG 58.270 37.500 0.00 0.00 37.22 4.96
3045 4750 7.532884 GCCACGAATATACATTTTTACGAATCC 59.467 37.037 0.00 0.00 0.00 3.01
3046 4751 7.532884 GGCCACGAATATACATTTTTACGAATC 59.467 37.037 0.00 0.00 0.00 2.52
3047 4752 7.012515 TGGCCACGAATATACATTTTTACGAAT 59.987 33.333 0.00 0.00 0.00 3.34
3049 4754 5.816258 TGGCCACGAATATACATTTTTACGA 59.184 36.000 0.00 0.00 0.00 3.43
3051 4756 5.912955 GCTGGCCACGAATATACATTTTTAC 59.087 40.000 0.00 0.00 0.00 2.01
3052 4757 5.009210 GGCTGGCCACGAATATACATTTTTA 59.991 40.000 0.00 0.00 35.81 1.52
3053 4758 4.202111 GGCTGGCCACGAATATACATTTTT 60.202 41.667 0.00 0.00 35.81 1.94
3054 4759 3.317993 GGCTGGCCACGAATATACATTTT 59.682 43.478 0.00 0.00 35.81 1.82
3055 4760 2.884639 GGCTGGCCACGAATATACATTT 59.115 45.455 0.00 0.00 35.81 2.32
3056 4761 2.106511 AGGCTGGCCACGAATATACATT 59.893 45.455 14.39 0.00 38.92 2.71
3057 4762 1.699634 AGGCTGGCCACGAATATACAT 59.300 47.619 14.39 0.00 38.92 2.29
3058 4763 1.070134 GAGGCTGGCCACGAATATACA 59.930 52.381 14.39 0.00 38.92 2.29
3059 4764 1.608283 GGAGGCTGGCCACGAATATAC 60.608 57.143 14.39 0.00 38.92 1.47
3060 4765 0.685097 GGAGGCTGGCCACGAATATA 59.315 55.000 14.39 0.00 38.92 0.86
3062 4767 1.971505 CTGGAGGCTGGCCACGAATA 61.972 60.000 14.39 0.00 38.92 1.75
3066 4771 4.767255 GACTGGAGGCTGGCCACG 62.767 72.222 14.39 0.00 38.92 4.94
3067 4772 4.416738 GGACTGGAGGCTGGCCAC 62.417 72.222 14.39 7.45 38.92 5.01
3087 4792 3.358076 GAGGAAGGGACGACAGCGG 62.358 68.421 0.00 0.00 43.17 5.52
3089 4794 2.232298 CTGGAGGAAGGGACGACAGC 62.232 65.000 0.00 0.00 0.00 4.40
3091 4796 2.283529 GCTGGAGGAAGGGACGACA 61.284 63.158 0.00 0.00 0.00 4.35
3092 4797 2.579738 GCTGGAGGAAGGGACGAC 59.420 66.667 0.00 0.00 0.00 4.34
3099 4804 4.785453 GTGGCCGGCTGGAGGAAG 62.785 72.222 28.56 0.00 37.49 3.46


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

AutoCloner maintained by Alex Coulton.