Multiple sequence alignment - TraesCS7A01G390700

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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 TraesCS7A01G390700 chr7A 100.000 3435 0 0 1 3435 566789509 566792943 0.000000e+00 6344
1 TraesCS7A01G390700 chr7A 87.488 2062 177 27 1309 3339 566910754 566912765 0.000000e+00 2303
2 TraesCS7A01G390700 chr7A 85.840 1483 143 46 1318 2783 566990033 566991465 0.000000e+00 1513
3 TraesCS7A01G390700 chr7A 86.462 1300 125 21 1267 2541 619305129 619306402 0.000000e+00 1378
4 TraesCS7A01G390700 chr7A 94.955 337 16 1 991 1327 566989673 566990008 8.440000e-146 527
5 TraesCS7A01G390700 chr7A 94.801 327 14 1 991 1314 566910398 566910724 1.100000e-139 507
6 TraesCS7A01G390700 chr7A 78.545 536 43 39 472 974 566909830 566910326 1.560000e-73 287
7 TraesCS7A01G390700 chr7A 82.517 286 24 14 168 443 566988828 566989097 9.590000e-56 228
8 TraesCS7A01G390700 chr7A 81.496 254 19 12 480 718 566989086 566989326 2.110000e-42 183
9 TraesCS7A01G390700 chr7A 89.831 118 9 2 218 333 566909654 566909770 7.680000e-32 148
10 TraesCS7A01G390700 chr7A 83.871 124 16 2 3 122 566912498 566912621 7.790000e-22 115
11 TraesCS7A01G390700 chr7B 87.433 1870 159 26 991 2817 528873874 528875710 0.000000e+00 2082
12 TraesCS7A01G390700 chr7B 84.248 2241 177 84 474 2584 664399451 664397257 0.000000e+00 2021
13 TraesCS7A01G390700 chr7B 87.525 1523 137 24 1046 2541 73176689 73178185 0.000000e+00 1711
14 TraesCS7A01G390700 chr7B 91.515 1096 43 23 1 1055 73175437 73176523 0.000000e+00 1463
15 TraesCS7A01G390700 chr7B 88.841 932 85 10 1667 2581 528876816 528877745 0.000000e+00 1127
16 TraesCS7A01G390700 chr7B 95.970 397 16 0 1 397 528872908 528873304 0.000000e+00 645
17 TraesCS7A01G390700 chr7B 85.000 560 34 21 455 991 528873308 528873840 1.090000e-144 523
18 TraesCS7A01G390700 chr7B 89.558 249 17 6 2486 2727 73178185 73178431 1.200000e-79 307
19 TraesCS7A01G390700 chr7B 87.218 133 9 3 1 125 557490337 557490205 9.940000e-31 145
20 TraesCS7A01G390700 chr7D 88.285 1784 145 25 790 2541 113582861 113584612 0.000000e+00 2078
21 TraesCS7A01G390700 chr7D 86.424 1893 149 67 991 2830 500776216 500778053 0.000000e+00 1973
22 TraesCS7A01G390700 chr7D 90.459 566 27 8 453 991 500775617 500776182 0.000000e+00 721
23 TraesCS7A01G390700 chr7D 91.904 457 21 4 1 452 500775013 500775458 2.910000e-175 625
24 TraesCS7A01G390700 chr7D 91.532 248 13 6 2486 2727 113584612 113584857 5.490000e-88 335
25 TraesCS7A01G390700 chr7D 93.182 88 6 0 1 88 523132544 523132457 2.780000e-26 130
26 TraesCS7A01G390700 chrUn 85.531 1873 177 57 991 2827 86612154 86613968 0.000000e+00 1871
27 TraesCS7A01G390700 chrUn 84.645 521 31 20 472 969 86611602 86612096 1.120000e-129 473
28 TraesCS7A01G390700 chrUn 89.216 102 6 2 168 269 86611297 86611393 4.660000e-24 122
29 TraesCS7A01G390700 chr3A 87.523 1643 125 30 992 2584 732404542 732402930 0.000000e+00 1825
30 TraesCS7A01G390700 chr3A 82.224 1052 135 30 1103 2128 728915280 728914255 0.000000e+00 859
31 TraesCS7A01G390700 chr3A 87.534 369 38 7 3069 3435 728985681 728985319 1.470000e-113 420
32 TraesCS7A01G390700 chr3A 77.823 487 53 35 520 975 732405069 732404607 2.050000e-62 250
33 TraesCS7A01G390700 chr3B 87.558 1286 109 21 1319 2584 810193861 810192607 0.000000e+00 1441
34 TraesCS7A01G390700 chr3B 89.766 342 33 2 3045 3385 806037913 806037573 1.460000e-118 436
35 TraesCS7A01G390700 chr3B 88.393 336 37 2 3049 3383 806049234 806048900 1.480000e-108 403
36 TraesCS7A01G390700 chr3B 86.784 227 21 4 168 386 806016605 806016380 9.520000e-61 244
37 TraesCS7A01G390700 chr3B 77.640 483 44 40 520 975 810195314 810194869 5.730000e-58 235
38 TraesCS7A01G390700 chr3B 88.119 202 17 5 168 365 805979808 805979610 2.060000e-57 233
39 TraesCS7A01G390700 chr3B 80.564 319 47 8 2471 2780 805931909 805931597 7.410000e-57 231
40 TraesCS7A01G390700 chr3B 87.222 180 18 3 229 403 805812637 805812458 2.090000e-47 200
41 TraesCS7A01G390700 chr3B 80.952 252 21 12 480 717 805977934 805977696 1.270000e-39 174
42 TraesCS7A01G390700 chr3B 80.237 253 23 12 480 718 805812446 805812207 7.630000e-37 165
43 TraesCS7A01G390700 chr3B 86.047 129 14 2 1 125 806037895 806037767 5.980000e-28 135
44 TraesCS7A01G390700 chr3B 86.667 120 12 2 6 121 806064575 806064456 2.780000e-26 130
45 TraesCS7A01G390700 chr3B 82.069 145 6 2 294 438 810195482 810195358 4.690000e-19 106
46 TraesCS7A01G390700 chr3D 83.607 1159 143 29 991 2127 598726091 598724958 0.000000e+00 1044
47 TraesCS7A01G390700 chr3D 86.344 227 22 4 168 386 598726927 598726702 4.430000e-59 239
48 TraesCS7A01G390700 chr3D 95.946 148 3 1 1 145 603683606 603683753 1.590000e-58 237
49 TraesCS7A01G390700 chr3D 80.233 258 19 14 480 718 598726670 598726426 7.630000e-37 165
50 TraesCS7A01G390700 chr3D 83.429 175 17 8 3044 3218 603683587 603683749 5.940000e-33 152
51 TraesCS7A01G390700 chr5D 83.184 1118 147 25 1675 2774 483769564 483768470 0.000000e+00 985


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 TraesCS7A01G390700 chr7A 566789509 566792943 3434 False 6344.000000 6344 100.000000 1 3435 1 chr7A.!!$F1 3434
1 TraesCS7A01G390700 chr7A 619305129 619306402 1273 False 1378.000000 1378 86.462000 1267 2541 1 chr7A.!!$F2 1274
2 TraesCS7A01G390700 chr7A 566909654 566912765 3111 False 672.000000 2303 86.907200 3 3339 5 chr7A.!!$F3 3336
3 TraesCS7A01G390700 chr7A 566988828 566991465 2637 False 612.750000 1513 86.202000 168 2783 4 chr7A.!!$F4 2615
4 TraesCS7A01G390700 chr7B 664397257 664399451 2194 True 2021.000000 2021 84.248000 474 2584 1 chr7B.!!$R2 2110
5 TraesCS7A01G390700 chr7B 73175437 73178431 2994 False 1160.333333 1711 89.532667 1 2727 3 chr7B.!!$F1 2726
6 TraesCS7A01G390700 chr7B 528872908 528877745 4837 False 1094.250000 2082 89.311000 1 2817 4 chr7B.!!$F2 2816
7 TraesCS7A01G390700 chr7D 113582861 113584857 1996 False 1206.500000 2078 89.908500 790 2727 2 chr7D.!!$F1 1937
8 TraesCS7A01G390700 chr7D 500775013 500778053 3040 False 1106.333333 1973 89.595667 1 2830 3 chr7D.!!$F2 2829
9 TraesCS7A01G390700 chrUn 86611297 86613968 2671 False 822.000000 1871 86.464000 168 2827 3 chrUn.!!$F1 2659
10 TraesCS7A01G390700 chr3A 732402930 732405069 2139 True 1037.500000 1825 82.673000 520 2584 2 chr3A.!!$R3 2064
11 TraesCS7A01G390700 chr3A 728914255 728915280 1025 True 859.000000 859 82.224000 1103 2128 1 chr3A.!!$R1 1025
12 TraesCS7A01G390700 chr3B 810192607 810195482 2875 True 594.000000 1441 82.422333 294 2584 3 chr3B.!!$R8 2290
13 TraesCS7A01G390700 chr3B 805977696 805979808 2112 True 203.500000 233 84.535500 168 717 2 chr3B.!!$R6 549
14 TraesCS7A01G390700 chr3D 598724958 598726927 1969 True 482.666667 1044 83.394667 168 2127 3 chr3D.!!$R1 1959
15 TraesCS7A01G390700 chr5D 483768470 483769564 1094 True 985.000000 985 83.184000 1675 2774 1 chr5D.!!$R1 1099

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
807 2896 0.040336 CCCGTCCATGACTCGTATCG 60.040 60.0 0.0 0.0 0.0 2.92 F
1583 4623 0.541863 GTCAAGGACGGGACCATCAT 59.458 55.0 0.0 0.0 0.0 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1656 4696 0.107214 GCCAGTGCCTACTTATGCCA 60.107 55.0 0.0 0.0 34.07 4.92 R
3346 8160 0.169672 AACATGCATCGCTTGACTGC 59.830 50.0 0.0 0.0 37.20 4.40 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
340 450 6.289064 AGTCACTTGGTTCTACTTTGTAAGG 58.711 40.000 0.00 0.00 0.00 2.69
427 2163 7.351223 GCATGAGCATCTTTCTATTCAAGTAC 58.649 38.462 0.00 0.00 41.58 2.73
504 2429 1.172812 ACTGCGGTTTTGAAGAGCCC 61.173 55.000 0.00 0.00 0.00 5.19
650 2625 2.427320 CCATGGCATCGATCCGGT 59.573 61.111 0.00 0.00 0.00 5.28
807 2896 0.040336 CCCGTCCATGACTCGTATCG 60.040 60.000 0.00 0.00 0.00 2.92
1184 4170 2.159819 CTGACCGACCCAGTCACCAG 62.160 65.000 0.00 0.00 39.29 4.00
1316 4306 6.017605 TCGGATTTCATCGGTAAGTACTACTC 60.018 42.308 0.00 0.00 0.00 2.59
1364 4394 8.922931 TGTAATCTATGGTGCATCACAATTAT 57.077 30.769 0.00 0.00 35.86 1.28
1368 4398 7.744087 TCTATGGTGCATCACAATTATAACC 57.256 36.000 0.00 0.00 35.86 2.85
1371 4401 9.230122 CTATGGTGCATCACAATTATAACCATA 57.770 33.333 0.00 2.70 43.54 2.74
1374 4404 7.228507 TGGTGCATCACAATTATAACCATACTC 59.771 37.037 0.00 0.00 35.86 2.59
1375 4405 7.290842 GTGCATCACAATTATAACCATACTCG 58.709 38.462 0.00 0.00 34.08 4.18
1378 4418 7.798516 GCATCACAATTATAACCATACTCGTTG 59.201 37.037 0.00 0.00 0.00 4.10
1583 4623 0.541863 GTCAAGGACGGGACCATCAT 59.458 55.000 0.00 0.00 0.00 2.45
1647 4687 1.386533 GCAATGACTATGCAGGCACT 58.613 50.000 0.00 0.00 44.69 4.40
1658 4698 2.360350 AGGCACTGGCGTCATTGG 60.360 61.111 9.54 0.00 42.47 3.16
1659 4699 4.120331 GGCACTGGCGTCATTGGC 62.120 66.667 17.69 17.69 40.64 4.52
1660 4700 3.364441 GCACTGGCGTCATTGGCA 61.364 61.111 9.54 0.00 42.76 4.92
1661 4701 2.703798 GCACTGGCGTCATTGGCAT 61.704 57.895 9.54 0.00 44.06 4.40
1662 4702 1.375853 GCACTGGCGTCATTGGCATA 61.376 55.000 9.54 0.00 44.06 3.14
1663 4703 1.093972 CACTGGCGTCATTGGCATAA 58.906 50.000 0.00 0.00 44.06 1.90
1664 4704 1.064505 CACTGGCGTCATTGGCATAAG 59.935 52.381 0.00 0.00 44.06 1.73
1665 4705 1.340017 ACTGGCGTCATTGGCATAAGT 60.340 47.619 0.00 0.00 44.06 2.24
1666 4706 2.093181 ACTGGCGTCATTGGCATAAGTA 60.093 45.455 0.00 0.00 44.06 2.24
1667 4707 2.545526 CTGGCGTCATTGGCATAAGTAG 59.454 50.000 0.00 0.00 44.06 2.57
1668 4708 1.873591 GGCGTCATTGGCATAAGTAGG 59.126 52.381 0.00 0.00 0.00 3.18
1669 4709 1.264288 GCGTCATTGGCATAAGTAGGC 59.736 52.381 0.00 0.00 0.00 3.93
1670 4710 2.560504 CGTCATTGGCATAAGTAGGCA 58.439 47.619 0.00 0.00 40.01 4.75
1671 4711 2.287915 CGTCATTGGCATAAGTAGGCAC 59.712 50.000 0.00 0.00 41.56 5.01
1672 4712 3.545703 GTCATTGGCATAAGTAGGCACT 58.454 45.455 0.00 0.00 41.56 4.40
1685 4725 3.364441 GCACTGGCGTCATTGGCA 61.364 61.111 9.54 0.00 42.76 4.92
1998 5056 8.450964 ACAACGATAATCTGAAACAAGTTATGG 58.549 33.333 0.00 0.00 0.00 2.74
2036 5094 8.830577 ATGTCTACATCATCGACGTGTACACG 62.831 46.154 39.06 39.06 45.92 4.49
2063 5121 3.297736 TGCCAATATTGTGGATCATGCA 58.702 40.909 14.25 10.48 41.65 3.96
2089 5155 6.073548 GCAGGTATGTATCTACAAGCATTCAC 60.074 42.308 0.00 0.00 39.99 3.18
2093 5159 6.932356 ATGTATCTACAAGCATTCACAAGG 57.068 37.500 0.00 0.00 39.99 3.61
2150 5217 6.134535 AGATGGGGTTTGATTGTGTACTTA 57.865 37.500 0.00 0.00 0.00 2.24
2197 5265 6.979817 TCAATTTCATGTGCATTAATGTAGGC 59.020 34.615 16.61 3.07 0.00 3.93
2210 5278 1.644509 TGTAGGCAAAGGCTCAGAGA 58.355 50.000 0.00 0.00 39.70 3.10
2235 5303 2.606725 CCAAACAATTCAAGCGCAAACA 59.393 40.909 11.47 0.00 0.00 2.83
2436 5504 1.127397 GTTTGTAAACCGAGCGTAGGC 59.873 52.381 0.00 0.00 34.41 3.93
2457 5525 4.540824 GCAGCTAGGCTTTATGTATTTGC 58.459 43.478 0.00 0.00 36.40 3.68
2488 5556 9.911788 ATCTTTGTATCTATGATGACAACCTTT 57.088 29.630 0.00 0.00 31.78 3.11
2672 5873 7.948357 ACAAATCGAGTACTTGCCTATATACA 58.052 34.615 5.12 0.00 0.00 2.29
2711 5916 3.428534 GCAATTTTCACACCGGTTGATTC 59.571 43.478 2.97 0.00 0.00 2.52
2714 5920 3.980646 TTTCACACCGGTTGATTCTTG 57.019 42.857 2.97 0.00 0.00 3.02
2733 5942 1.687660 TGTGTTGTCGGCTTGGTAGTA 59.312 47.619 0.00 0.00 0.00 1.82
2771 5981 0.542467 TACGGGTGACAGGTGCCTTA 60.542 55.000 0.00 0.00 0.00 2.69
2785 5995 2.096013 GTGCCTTATCTTTGAACTCGGC 59.904 50.000 0.00 0.00 36.85 5.54
2828 6038 9.725019 TTGCCTATGAATATGAGTATTTGTAGG 57.275 33.333 11.48 11.48 38.75 3.18
2830 6040 9.155975 GCCTATGAATATGAGTATTTGTAGGTG 57.844 37.037 14.44 0.00 38.44 4.00
2842 7656 6.710744 AGTATTTGTAGGTGTCCACTTCTTTG 59.289 38.462 0.00 0.00 0.00 2.77
2847 7661 3.697166 AGGTGTCCACTTCTTTGTGTTT 58.303 40.909 0.00 0.00 36.30 2.83
2859 7673 0.108898 TTGTGTTTGTGTGCAGTGCC 60.109 50.000 13.72 4.57 0.00 5.01
2866 7680 2.127232 GTGTGCAGTGCCCAAACCT 61.127 57.895 13.72 0.00 0.00 3.50
2879 7693 2.364970 CCCAAACCTGCTCAACAAATCA 59.635 45.455 0.00 0.00 0.00 2.57
2882 7696 4.501915 CCAAACCTGCTCAACAAATCATGT 60.502 41.667 0.00 0.00 46.82 3.21
2896 7710 7.595819 ACAAATCATGTTAGAAAAACCTGGA 57.404 32.000 0.00 0.00 40.06 3.86
2923 7737 1.479323 TCTATACCCGTGCAACCAGAC 59.521 52.381 0.00 0.00 0.00 3.51
2934 7748 0.182537 CAACCAGACCCAACAGTCCA 59.817 55.000 0.00 0.00 37.49 4.02
2935 7749 0.474184 AACCAGACCCAACAGTCCAG 59.526 55.000 0.00 0.00 37.49 3.86
2942 7756 4.454948 CAACAGTCCAGTTGGCGA 57.545 55.556 0.00 0.00 43.89 5.54
2946 7760 1.374758 CAGTCCAGTTGGCGAGGTC 60.375 63.158 0.00 0.00 34.44 3.85
2947 7761 1.837051 AGTCCAGTTGGCGAGGTCA 60.837 57.895 0.00 0.00 34.44 4.02
2961 7775 4.082733 GGCGAGGTCAATAGCTTTTTCTTT 60.083 41.667 0.00 0.00 32.30 2.52
3005 7819 3.834489 ACCTATTGCCATCTCAGAGTG 57.166 47.619 0.00 0.00 0.00 3.51
3006 7820 2.437281 ACCTATTGCCATCTCAGAGTGG 59.563 50.000 12.42 12.42 38.55 4.00
3044 7858 4.964593 TCCAAACAGTAGTTCACTAACCC 58.035 43.478 0.00 0.00 36.84 4.11
3055 7869 5.741953 AGTTCACTAACCCCAAGTCATGGT 61.742 45.833 0.00 0.00 39.29 3.55
3061 7875 4.084265 CCAAGTCATGGTGCAGCA 57.916 55.556 22.56 22.56 44.85 4.41
3063 7877 0.892358 CCAAGTCATGGTGCAGCAGT 60.892 55.000 24.45 9.66 44.85 4.40
3078 7892 1.364626 GCAGTTGAGGCTGGATGTCG 61.365 60.000 0.00 0.00 37.00 4.35
3101 7915 4.353437 GCGGGGTCGTTGTCGTCT 62.353 66.667 0.00 0.00 38.89 4.18
3102 7916 2.337532 CGGGGTCGTTGTCGTCTT 59.662 61.111 0.00 0.00 38.33 3.01
3111 7925 1.787155 CGTTGTCGTCTTGAGTTGGAG 59.213 52.381 0.00 0.00 0.00 3.86
3113 7927 0.318699 TGTCGTCTTGAGTTGGAGCG 60.319 55.000 0.00 0.00 0.00 5.03
3120 7934 2.048127 GAGTTGGAGCGGCTCGTT 60.048 61.111 22.63 8.66 0.00 3.85
3153 7967 1.818785 GCTCAGCAGCATCAGGTCC 60.819 63.158 0.00 0.00 46.06 4.46
3165 7979 2.630889 TCAGGTCCTGTCTGAATCCT 57.369 50.000 18.65 0.00 38.20 3.24
3244 8058 8.652810 AAATAATGGCAATTCTTGAGTTATGC 57.347 30.769 0.00 0.00 0.00 3.14
3249 8063 3.375299 GCAATTCTTGAGTTATGCGGACT 59.625 43.478 0.00 0.00 0.00 3.85
3272 8086 9.688592 GACTGATCATGTTTTTCTCAGAAAAAT 57.311 29.630 24.71 11.20 37.39 1.82
3297 8111 3.360775 GCAGCGCGATCAAGTTATATC 57.639 47.619 12.10 0.00 0.00 1.63
3302 8116 3.181536 GCGCGATCAAGTTATATCTGCAG 60.182 47.826 12.10 7.63 0.00 4.41
3311 8125 6.092670 TCAAGTTATATCTGCAGTTCACTTGC 59.907 38.462 25.38 10.68 39.70 4.01
3339 8153 7.256286 AGATGCTTCATCAAAGAGTAATTTGC 58.744 34.615 9.19 0.00 42.72 3.68
3340 8154 6.579666 TGCTTCATCAAAGAGTAATTTGCT 57.420 33.333 0.00 0.00 39.51 3.91
3341 8155 6.384224 TGCTTCATCAAAGAGTAATTTGCTG 58.616 36.000 0.00 0.00 39.51 4.41
3342 8156 6.016024 TGCTTCATCAAAGAGTAATTTGCTGT 60.016 34.615 0.00 0.00 39.51 4.40
3343 8157 6.865205 GCTTCATCAAAGAGTAATTTGCTGTT 59.135 34.615 0.00 0.00 39.51 3.16
3344 8158 7.061557 GCTTCATCAAAGAGTAATTTGCTGTTC 59.938 37.037 0.00 0.00 39.51 3.18
3345 8159 7.509141 TCATCAAAGAGTAATTTGCTGTTCA 57.491 32.000 0.00 0.00 39.51 3.18
3346 8160 7.587629 TCATCAAAGAGTAATTTGCTGTTCAG 58.412 34.615 0.00 0.00 39.51 3.02
3347 8161 5.762045 TCAAAGAGTAATTTGCTGTTCAGC 58.238 37.500 16.65 16.65 39.51 4.26
3349 8163 5.368256 AAGAGTAATTTGCTGTTCAGCAG 57.632 39.130 23.29 0.00 46.21 4.24
3350 8164 4.392940 AGAGTAATTTGCTGTTCAGCAGT 58.607 39.130 23.29 15.40 46.21 4.40
3351 8165 4.453819 AGAGTAATTTGCTGTTCAGCAGTC 59.546 41.667 23.29 15.06 46.21 3.51
3353 8167 4.580167 AGTAATTTGCTGTTCAGCAGTCAA 59.420 37.500 23.29 16.96 46.21 3.18
3355 8169 0.664761 TTGCTGTTCAGCAGTCAAGC 59.335 50.000 23.29 0.00 46.21 4.01
3357 8171 1.224069 GCTGTTCAGCAGTCAAGCGA 61.224 55.000 18.26 0.00 46.64 4.93
3358 8172 1.436600 CTGTTCAGCAGTCAAGCGAT 58.563 50.000 0.00 0.00 40.27 4.58
3359 8173 1.128136 CTGTTCAGCAGTCAAGCGATG 59.872 52.381 0.00 0.00 40.27 3.84
3360 8174 0.179205 GTTCAGCAGTCAAGCGATGC 60.179 55.000 0.00 0.00 40.15 3.91
3361 8175 0.603439 TTCAGCAGTCAAGCGATGCA 60.603 50.000 0.00 0.00 42.45 3.96
3362 8176 0.392060 TCAGCAGTCAAGCGATGCAT 60.392 50.000 0.00 0.00 42.45 3.96
3364 8178 0.675837 AGCAGTCAAGCGATGCATGT 60.676 50.000 2.46 0.00 42.45 3.21
3366 8180 1.398041 GCAGTCAAGCGATGCATGTTA 59.602 47.619 2.46 0.00 39.75 2.41
3368 8182 3.488047 GCAGTCAAGCGATGCATGTTATT 60.488 43.478 2.46 0.00 39.75 1.40
3369 8183 4.665212 CAGTCAAGCGATGCATGTTATTT 58.335 39.130 2.46 0.00 0.00 1.40
3370 8184 4.731961 CAGTCAAGCGATGCATGTTATTTC 59.268 41.667 2.46 0.00 0.00 2.17
3372 8186 4.731961 GTCAAGCGATGCATGTTATTTCTG 59.268 41.667 2.46 0.00 0.00 3.02
3373 8187 4.635324 TCAAGCGATGCATGTTATTTCTGA 59.365 37.500 2.46 0.00 0.00 3.27
3374 8188 5.297527 TCAAGCGATGCATGTTATTTCTGAT 59.702 36.000 2.46 0.00 0.00 2.90
3375 8189 5.104562 AGCGATGCATGTTATTTCTGATG 57.895 39.130 2.46 0.00 0.00 3.07
3376 8190 4.818005 AGCGATGCATGTTATTTCTGATGA 59.182 37.500 2.46 0.00 0.00 2.92
3379 8193 6.639686 GCGATGCATGTTATTTCTGATGAATT 59.360 34.615 2.46 0.00 31.56 2.17
3381 8195 9.836076 CGATGCATGTTATTTCTGATGAATTAT 57.164 29.630 2.46 0.00 31.56 1.28
3410 8224 9.106070 ACGTATCATTTAAATCTTGTAGGTTCC 57.894 33.333 0.00 0.00 0.00 3.62
3411 8225 8.557029 CGTATCATTTAAATCTTGTAGGTTCCC 58.443 37.037 0.00 0.00 0.00 3.97
3412 8226 9.403583 GTATCATTTAAATCTTGTAGGTTCCCA 57.596 33.333 0.00 0.00 0.00 4.37
3414 8228 8.292444 TCATTTAAATCTTGTAGGTTCCCATG 57.708 34.615 0.00 0.00 0.00 3.66
3415 8229 8.112822 TCATTTAAATCTTGTAGGTTCCCATGA 58.887 33.333 0.00 0.00 0.00 3.07
3417 8231 7.880160 TTAAATCTTGTAGGTTCCCATGATG 57.120 36.000 0.00 0.00 0.00 3.07
3418 8232 3.281727 TCTTGTAGGTTCCCATGATGC 57.718 47.619 0.00 0.00 0.00 3.91
3419 8233 2.846206 TCTTGTAGGTTCCCATGATGCT 59.154 45.455 0.00 0.00 0.00 3.79
3420 8234 3.266772 TCTTGTAGGTTCCCATGATGCTT 59.733 43.478 0.00 0.00 0.00 3.91
3421 8235 3.737559 TGTAGGTTCCCATGATGCTTT 57.262 42.857 0.00 0.00 0.00 3.51
3422 8236 3.355378 TGTAGGTTCCCATGATGCTTTG 58.645 45.455 0.00 0.00 0.00 2.77
3423 8237 1.856629 AGGTTCCCATGATGCTTTGG 58.143 50.000 0.00 0.00 0.00 3.28
3431 8245 4.062677 CCATGATGCTTTGGGGTTATTG 57.937 45.455 0.00 0.00 0.00 1.90
3432 8246 3.451902 CCATGATGCTTTGGGGTTATTGT 59.548 43.478 0.00 0.00 0.00 2.71
3433 8247 4.435425 CATGATGCTTTGGGGTTATTGTG 58.565 43.478 0.00 0.00 0.00 3.33
3434 8248 3.772387 TGATGCTTTGGGGTTATTGTGA 58.228 40.909 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
340 450 8.297426 GCTGGTACTAATAAGCATAATTTTCCC 58.703 37.037 0.00 0.00 35.69 3.97
427 2163 4.929808 AGAACATAAGCACTTAACCAGTCG 59.070 41.667 0.00 0.00 30.92 4.18
504 2429 3.197766 TCAGTAACAGTTGCATAGGGGAG 59.802 47.826 4.03 0.00 0.00 4.30
650 2625 3.319198 GTTGTCCTCGCCCCTCCA 61.319 66.667 0.00 0.00 0.00 3.86
807 2896 4.368543 GTCGGACACGGGTGGACC 62.369 72.222 0.00 5.65 41.39 4.46
838 2973 0.600255 CAAGTCGAAGTCGGGCTTGT 60.600 55.000 20.38 0.00 42.08 3.16
1086 4072 0.329261 CCTTCTTCTGATGGCCACCA 59.671 55.000 8.16 1.97 38.19 4.17
1161 4147 1.304217 GACTGGGTCGGTCAGAGGA 60.304 63.158 7.39 0.00 39.36 3.71
1184 4170 2.189499 GCCCATTGCCTCGACATCC 61.189 63.158 0.00 0.00 0.00 3.51
1365 4395 9.444600 AGTTATCAATAAACAACGAGTATGGTT 57.555 29.630 0.00 0.00 37.59 3.67
1366 4396 9.444600 AAGTTATCAATAAACAACGAGTATGGT 57.555 29.630 0.00 0.00 0.00 3.55
1368 4398 9.210426 GCAAGTTATCAATAAACAACGAGTATG 57.790 33.333 0.00 0.00 0.00 2.39
1371 4401 7.197071 TGCAAGTTATCAATAAACAACGAGT 57.803 32.000 0.00 0.00 0.00 4.18
1374 4404 5.855925 TGCTGCAAGTTATCAATAAACAACG 59.144 36.000 0.00 0.00 35.30 4.10
1375 4405 7.168972 TGTTGCTGCAAGTTATCAATAAACAAC 59.831 33.333 16.53 0.00 35.30 3.32
1378 4418 7.636259 TTGTTGCTGCAAGTTATCAATAAAC 57.364 32.000 16.53 0.07 35.30 2.01
1583 4623 3.525537 GAGCGACTCAATTGATTCTCCA 58.474 45.455 19.86 0.00 0.00 3.86
1647 4687 2.560504 CTACTTATGCCAATGACGCCA 58.439 47.619 0.00 0.00 0.00 5.69
1648 4688 1.873591 CCTACTTATGCCAATGACGCC 59.126 52.381 0.00 0.00 0.00 5.68
1649 4689 1.264288 GCCTACTTATGCCAATGACGC 59.736 52.381 0.00 0.00 0.00 5.19
1650 4690 2.287915 GTGCCTACTTATGCCAATGACG 59.712 50.000 0.00 0.00 0.00 4.35
1651 4691 3.313526 CAGTGCCTACTTATGCCAATGAC 59.686 47.826 0.00 0.00 34.07 3.06
1652 4692 3.544684 CAGTGCCTACTTATGCCAATGA 58.455 45.455 0.00 0.00 34.07 2.57
1653 4693 2.620115 CCAGTGCCTACTTATGCCAATG 59.380 50.000 0.00 0.00 34.07 2.82
1654 4694 2.936202 CCAGTGCCTACTTATGCCAAT 58.064 47.619 0.00 0.00 34.07 3.16
1655 4695 1.681780 GCCAGTGCCTACTTATGCCAA 60.682 52.381 0.00 0.00 34.07 4.52
1656 4696 0.107214 GCCAGTGCCTACTTATGCCA 60.107 55.000 0.00 0.00 34.07 4.92
1657 4697 1.160329 CGCCAGTGCCTACTTATGCC 61.160 60.000 0.00 0.00 34.07 4.40
1658 4698 0.462047 ACGCCAGTGCCTACTTATGC 60.462 55.000 0.00 0.00 34.07 3.14
1659 4699 1.134818 TGACGCCAGTGCCTACTTATG 60.135 52.381 0.00 0.00 34.07 1.90
1660 4700 1.191535 TGACGCCAGTGCCTACTTAT 58.808 50.000 0.00 0.00 34.07 1.73
1661 4701 1.191535 ATGACGCCAGTGCCTACTTA 58.808 50.000 0.00 0.00 34.07 2.24
1662 4702 0.324943 AATGACGCCAGTGCCTACTT 59.675 50.000 0.00 0.00 34.07 2.24
1663 4703 0.391661 CAATGACGCCAGTGCCTACT 60.392 55.000 0.00 0.00 37.75 2.57
1664 4704 1.369091 CCAATGACGCCAGTGCCTAC 61.369 60.000 0.00 0.00 37.08 3.18
1665 4705 1.078497 CCAATGACGCCAGTGCCTA 60.078 57.895 0.00 0.00 37.08 3.93
1666 4706 2.360350 CCAATGACGCCAGTGCCT 60.360 61.111 0.00 0.00 37.08 4.75
1667 4707 4.120331 GCCAATGACGCCAGTGCC 62.120 66.667 0.00 0.00 37.08 5.01
1668 4708 1.375853 TATGCCAATGACGCCAGTGC 61.376 55.000 0.00 0.00 37.08 4.40
1669 4709 1.064505 CTTATGCCAATGACGCCAGTG 59.935 52.381 0.00 0.00 38.05 3.66
1670 4710 1.340017 ACTTATGCCAATGACGCCAGT 60.340 47.619 0.00 0.00 0.00 4.00
1671 4711 1.382522 ACTTATGCCAATGACGCCAG 58.617 50.000 0.00 0.00 0.00 4.85
1672 4712 2.560504 CTACTTATGCCAATGACGCCA 58.439 47.619 0.00 0.00 0.00 5.69
1685 4725 1.070758 CACATCGCTGGGGCTACTTAT 59.929 52.381 0.00 0.00 36.09 1.73
1947 5005 3.731652 TGATGCACCCAAGTTTTCAAG 57.268 42.857 0.00 0.00 0.00 3.02
1998 5056 7.312657 TGATGTAGACATTCTTCTTTGATGC 57.687 36.000 0.00 0.00 36.57 3.91
2063 5121 5.815233 ATGCTTGTAGATACATACCTGCT 57.185 39.130 0.00 0.00 35.89 4.24
2173 5240 6.757478 TGCCTACATTAATGCACATGAAATTG 59.243 34.615 15.48 0.00 0.00 2.32
2197 5265 2.775911 TGGACATCTCTGAGCCTTTG 57.224 50.000 0.00 0.00 0.00 2.77
2210 5278 2.035704 TGCGCTTGAATTGTTTGGACAT 59.964 40.909 9.73 0.00 35.29 3.06
2253 5321 4.788100 CGCAGTAACCATTCGAATTCAAAG 59.212 41.667 8.21 0.00 0.00 2.77
2314 5382 0.459899 TGCTCGACTTGTCACACACT 59.540 50.000 1.59 0.00 0.00 3.55
2425 5493 2.333225 CTAGCTGCCTACGCTCGG 59.667 66.667 0.00 0.00 38.86 4.63
2436 5504 4.273480 ACGCAAATACATAAAGCCTAGCTG 59.727 41.667 0.00 0.00 39.62 4.24
2457 5525 9.899226 TTGTCATCATAGATACAAAGATCTACG 57.101 33.333 0.00 0.00 40.41 3.51
2695 5900 2.616376 CACAAGAATCAACCGGTGTGAA 59.384 45.455 8.52 0.00 38.90 3.18
2711 5916 1.531149 CTACCAAGCCGACAACACAAG 59.469 52.381 0.00 0.00 0.00 3.16
2714 5920 2.443887 TACTACCAAGCCGACAACAC 57.556 50.000 0.00 0.00 0.00 3.32
2771 5981 3.260884 TCCTTAGTGCCGAGTTCAAAGAT 59.739 43.478 0.00 0.00 0.00 2.40
2785 5995 4.600062 AGGCAAATTTACCCTCCTTAGTG 58.400 43.478 3.67 0.00 0.00 2.74
2828 6038 4.165779 CACAAACACAAAGAAGTGGACAC 58.834 43.478 0.00 0.00 43.72 3.67
2830 6040 4.165779 CACACAAACACAAAGAAGTGGAC 58.834 43.478 0.00 0.00 43.72 4.02
2842 7656 1.226945 GGGCACTGCACACAAACAC 60.227 57.895 2.82 0.00 0.00 3.32
2847 7661 2.422231 GGTTTGGGCACTGCACACA 61.422 57.895 5.14 0.00 43.74 3.72
2859 7673 3.731652 TGATTTGTTGAGCAGGTTTGG 57.268 42.857 0.00 0.00 0.00 3.28
2879 7693 8.164070 AGAGTTATGTCCAGGTTTTTCTAACAT 58.836 33.333 0.00 0.00 0.00 2.71
2885 7699 7.498239 GGGTATAGAGTTATGTCCAGGTTTTTC 59.502 40.741 0.00 0.00 0.00 2.29
2891 7705 4.022242 CACGGGTATAGAGTTATGTCCAGG 60.022 50.000 0.00 0.00 0.00 4.45
2893 7707 3.319972 GCACGGGTATAGAGTTATGTCCA 59.680 47.826 0.00 0.00 0.00 4.02
2894 7708 3.319972 TGCACGGGTATAGAGTTATGTCC 59.680 47.826 0.00 0.00 0.00 4.02
2896 7710 4.442472 GGTTGCACGGGTATAGAGTTATGT 60.442 45.833 0.00 0.00 0.00 2.29
2934 7748 0.905357 AGCTATTGACCTCGCCAACT 59.095 50.000 0.00 0.00 0.00 3.16
2935 7749 1.739067 AAGCTATTGACCTCGCCAAC 58.261 50.000 0.00 0.00 0.00 3.77
2939 7753 4.686839 AAGAAAAAGCTATTGACCTCGC 57.313 40.909 0.00 0.00 0.00 5.03
2940 7754 6.241207 TCAAAGAAAAAGCTATTGACCTCG 57.759 37.500 0.00 0.00 0.00 4.63
2942 7756 7.346751 TGTTCAAAGAAAAAGCTATTGACCT 57.653 32.000 0.00 0.00 30.34 3.85
2946 7760 7.382218 ACGGATTGTTCAAAGAAAAAGCTATTG 59.618 33.333 0.00 0.00 0.00 1.90
2947 7761 7.433680 ACGGATTGTTCAAAGAAAAAGCTATT 58.566 30.769 0.00 0.00 0.00 1.73
3015 7829 6.119536 AGTGAACTACTGTTTGGATGTTTGA 58.880 36.000 0.00 0.00 38.49 2.69
3028 7842 4.039973 TGACTTGGGGTTAGTGAACTACTG 59.960 45.833 0.00 0.00 40.65 2.74
3029 7843 4.228824 TGACTTGGGGTTAGTGAACTACT 58.771 43.478 0.00 0.00 43.56 2.57
3030 7844 4.612264 TGACTTGGGGTTAGTGAACTAC 57.388 45.455 0.00 0.00 35.74 2.73
3031 7845 4.019681 CCATGACTTGGGGTTAGTGAACTA 60.020 45.833 0.00 0.00 42.33 2.24
3032 7846 3.244911 CCATGACTTGGGGTTAGTGAACT 60.245 47.826 0.00 0.00 42.33 3.01
3061 7875 1.078848 GCGACATCCAGCCTCAACT 60.079 57.895 0.00 0.00 0.00 3.16
3085 7899 2.019951 CAAGACGACAACGACCCCG 61.020 63.158 0.00 0.00 42.66 5.73
3090 7904 1.406180 TCCAACTCAAGACGACAACGA 59.594 47.619 0.00 0.00 42.66 3.85
3092 7906 1.527311 GCTCCAACTCAAGACGACAAC 59.473 52.381 0.00 0.00 0.00 3.32
3094 7908 0.318699 CGCTCCAACTCAAGACGACA 60.319 55.000 0.00 0.00 0.00 4.35
3098 7912 1.004440 AGCCGCTCCAACTCAAGAC 60.004 57.895 0.00 0.00 0.00 3.01
3101 7915 2.048222 CGAGCCGCTCCAACTCAA 60.048 61.111 14.85 0.00 0.00 3.02
3102 7916 2.765250 GAACGAGCCGCTCCAACTCA 62.765 60.000 14.85 0.00 0.00 3.41
3113 7927 1.424493 CCTGATGAAGCGAACGAGCC 61.424 60.000 0.00 0.00 38.01 4.70
3120 7934 0.972471 TGAGCTCCCTGATGAAGCGA 60.972 55.000 12.15 0.00 0.00 4.93
3148 7962 2.359781 CCCTAGGATTCAGACAGGACCT 60.360 54.545 11.48 0.00 0.00 3.85
3153 7967 4.956700 TCAGTAACCCTAGGATTCAGACAG 59.043 45.833 11.48 0.00 0.00 3.51
3165 7979 4.669700 TGTGCTAGTCTTCAGTAACCCTA 58.330 43.478 0.00 0.00 0.00 3.53
3241 8055 4.012374 AGAAAAACATGATCAGTCCGCAT 58.988 39.130 0.00 0.00 0.00 4.73
3244 8058 4.931601 TCTGAGAAAAACATGATCAGTCCG 59.068 41.667 0.00 0.00 38.76 4.79
3291 8105 3.871006 CCGCAAGTGAACTGCAGATATAA 59.129 43.478 23.35 0.00 0.00 0.98
3292 8106 3.132111 TCCGCAAGTGAACTGCAGATATA 59.868 43.478 23.35 0.00 0.00 0.86
3296 8110 0.601046 CTCCGCAAGTGAACTGCAGA 60.601 55.000 23.35 0.00 0.00 4.26
3297 8111 0.601046 TCTCCGCAAGTGAACTGCAG 60.601 55.000 13.48 13.48 0.00 4.41
3302 8116 1.129437 GAAGCATCTCCGCAAGTGAAC 59.871 52.381 0.00 0.00 0.00 3.18
3311 8125 3.529533 ACTCTTTGATGAAGCATCTCCG 58.470 45.455 8.66 0.00 41.06 4.63
3340 8154 1.150827 CATCGCTTGACTGCTGAACA 58.849 50.000 0.00 0.00 0.00 3.18
3341 8155 0.179205 GCATCGCTTGACTGCTGAAC 60.179 55.000 0.00 0.00 33.15 3.18
3342 8156 0.603439 TGCATCGCTTGACTGCTGAA 60.603 50.000 0.00 0.00 36.84 3.02
3343 8157 0.392060 ATGCATCGCTTGACTGCTGA 60.392 50.000 0.00 0.00 36.84 4.26
3344 8158 0.248094 CATGCATCGCTTGACTGCTG 60.248 55.000 0.00 0.00 36.06 4.41
3345 8159 0.675837 ACATGCATCGCTTGACTGCT 60.676 50.000 0.00 0.00 37.20 4.24
3346 8160 0.169672 AACATGCATCGCTTGACTGC 59.830 50.000 0.00 0.00 37.20 4.40
3347 8161 3.957671 ATAACATGCATCGCTTGACTG 57.042 42.857 0.00 0.00 37.20 3.51
3349 8163 4.731961 CAGAAATAACATGCATCGCTTGAC 59.268 41.667 0.00 0.00 37.20 3.18
3350 8164 4.635324 TCAGAAATAACATGCATCGCTTGA 59.365 37.500 0.00 0.00 37.20 3.02
3351 8165 4.912214 TCAGAAATAACATGCATCGCTTG 58.088 39.130 0.00 0.76 39.19 4.01
3353 8167 4.818005 TCATCAGAAATAACATGCATCGCT 59.182 37.500 0.00 0.00 0.00 4.93
3355 8169 9.836076 ATAATTCATCAGAAATAACATGCATCG 57.164 29.630 0.00 0.00 37.29 3.84
3384 8198 9.106070 GGAACCTACAAGATTTAAATGATACGT 57.894 33.333 5.17 0.00 0.00 3.57
3410 8224 3.451902 ACAATAACCCCAAAGCATCATGG 59.548 43.478 0.00 0.00 36.42 3.66
3411 8225 4.160065 TCACAATAACCCCAAAGCATCATG 59.840 41.667 0.00 0.00 0.00 3.07
3412 8226 4.352009 TCACAATAACCCCAAAGCATCAT 58.648 39.130 0.00 0.00 0.00 2.45
3413 8227 3.772387 TCACAATAACCCCAAAGCATCA 58.228 40.909 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.