Multiple sequence alignment - TraesCS7D01G353000

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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 TraesCS7D01G353000 chr7D 100.000 3557 0 0 1 3557 454682069 454678513 0.000000e+00 6569.0
1 TraesCS7D01G353000 chr7D 78.865 1410 247 40 1130 2503 197674598 197673204 0.000000e+00 905.0
2 TraesCS7D01G353000 chr7D 80.380 158 29 2 1439 1595 454378600 454378756 6.240000e-23 119.0
3 TraesCS7D01G353000 chr7A 93.258 1869 73 21 1036 2860 543431012 543432871 0.000000e+00 2704.0
4 TraesCS7D01G353000 chr7A 86.855 814 60 18 1 794 543428505 543429291 0.000000e+00 867.0
5 TraesCS7D01G353000 chr7A 78.464 1393 242 34 1130 2490 206919605 206918239 0.000000e+00 857.0
6 TraesCS7D01G353000 chr7A 89.080 174 11 6 841 1007 543429552 543429724 3.600000e-50 209.0
7 TraesCS7D01G353000 chr7A 80.597 201 37 2 1486 1685 110099677 110099478 1.710000e-33 154.0
8 TraesCS7D01G353000 chr7A 92.045 88 3 4 1058 1143 543429822 543429907 1.730000e-23 121.0
9 TraesCS7D01G353000 chr7A 79.618 157 32 0 1439 1595 543597488 543597332 2.900000e-21 113.0
10 TraesCS7D01G353000 chr7A 77.049 122 24 4 3330 3449 1511199 1511080 2.290000e-07 67.6
11 TraesCS7D01G353000 chr7B 91.847 1018 50 16 2543 3557 478890521 478889534 0.000000e+00 1389.0
12 TraesCS7D01G353000 chr7B 94.053 908 53 1 1067 1974 478909459 478908553 0.000000e+00 1376.0
13 TraesCS7D01G353000 chr7B 79.969 1303 224 30 1130 2421 162082175 162080899 0.000000e+00 926.0
14 TraesCS7D01G353000 chr7B 92.562 484 36 0 1970 2453 478904817 478904334 0.000000e+00 695.0
15 TraesCS7D01G353000 chr7B 80.906 927 101 36 1 888 479057224 479056335 0.000000e+00 662.0
16 TraesCS7D01G353000 chr3A 78.061 392 64 16 1916 2302 90294160 90294534 9.930000e-56 228.0
17 TraesCS7D01G353000 chr3A 85.315 143 19 2 1544 1685 699576158 699576299 2.860000e-31 147.0
18 TraesCS7D01G353000 chr3A 84.058 138 21 1 3308 3444 734667756 734667893 8.010000e-27 132.0
19 TraesCS7D01G353000 chr3A 73.319 461 77 25 362 794 746454697 746454255 1.040000e-25 128.0
20 TraesCS7D01G353000 chr3A 84.848 99 12 3 3185 3283 646809439 646809344 2.920000e-16 97.1
21 TraesCS7D01G353000 chr3A 85.915 71 10 0 3443 3513 672444795 672444865 3.810000e-10 76.8
22 TraesCS7D01G353000 chr3D 77.551 392 66 16 1916 2302 75947655 75948029 2.150000e-52 217.0
23 TraesCS7D01G353000 chr3B 77.238 391 69 14 1916 2302 122827125 122827499 1.000000e-50 211.0
24 TraesCS7D01G353000 chr1A 79.216 255 44 8 2136 2384 130150337 130150588 6.110000e-38 169.0
25 TraesCS7D01G353000 chr1A 80.625 160 22 8 197 348 550838719 550838561 8.070000e-22 115.0
26 TraesCS7D01G353000 chr5A 84.000 150 14 8 187 329 294260131 294260277 6.190000e-28 135.0
27 TraesCS7D01G353000 chr5A 83.784 148 15 7 187 325 635777071 635777218 8.010000e-27 132.0
28 TraesCS7D01G353000 chr5B 82.550 149 18 7 206 348 338490585 338490439 1.340000e-24 124.0
29 TraesCS7D01G353000 chr5B 81.169 154 19 8 187 330 638835421 638835268 8.070000e-22 115.0
30 TraesCS7D01G353000 chr6A 80.645 155 29 1 3292 3445 578912214 578912368 6.240000e-23 119.0
31 TraesCS7D01G353000 chr6A 79.290 169 21 14 187 345 26532928 26532764 4.860000e-19 106.0
32 TraesCS7D01G353000 chr2D 87.000 100 13 0 3192 3291 627846495 627846594 2.900000e-21 113.0
33 TraesCS7D01G353000 chr2B 88.636 88 10 0 3194 3281 770091608 770091695 1.350000e-19 108.0
34 TraesCS7D01G353000 chr2B 72.362 199 46 7 388 581 67419001 67418807 2.000000e-03 54.7
35 TraesCS7D01G353000 chrUn 78.824 170 27 8 187 348 95000258 95000090 4.860000e-19 106.0
36 TraesCS7D01G353000 chr2A 85.714 98 14 0 3194 3291 758291783 758291880 1.750000e-18 104.0
37 TraesCS7D01G353000 chr4A 84.375 96 15 0 3297 3392 691143427 691143522 1.050000e-15 95.3
38 TraesCS7D01G353000 chr4A 82.022 89 15 1 3297 3385 446468269 446468182 1.370000e-09 75.0
39 TraesCS7D01G353000 chr6B 90.196 51 4 1 3198 3248 681023196 681023147 8.240000e-07 65.8
40 TraesCS7D01G353000 chr1D 81.690 71 5 4 487 557 363860022 363860084 6.000000e-03 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 TraesCS7D01G353000 chr7D 454678513 454682069 3556 True 6569.00 6569 100.0000 1 3557 1 chr7D.!!$R2 3556
1 TraesCS7D01G353000 chr7D 197673204 197674598 1394 True 905.00 905 78.8650 1130 2503 1 chr7D.!!$R1 1373
2 TraesCS7D01G353000 chr7A 543428505 543432871 4366 False 975.25 2704 90.3095 1 2860 4 chr7A.!!$F1 2859
3 TraesCS7D01G353000 chr7A 206918239 206919605 1366 True 857.00 857 78.4640 1130 2490 1 chr7A.!!$R3 1360
4 TraesCS7D01G353000 chr7B 478889534 478890521 987 True 1389.00 1389 91.8470 2543 3557 1 chr7B.!!$R2 1014
5 TraesCS7D01G353000 chr7B 478904334 478909459 5125 True 1035.50 1376 93.3075 1067 2453 2 chr7B.!!$R4 1386
6 TraesCS7D01G353000 chr7B 162080899 162082175 1276 True 926.00 926 79.9690 1130 2421 1 chr7B.!!$R1 1291
7 TraesCS7D01G353000 chr7B 479056335 479057224 889 True 662.00 662 80.9060 1 888 1 chr7B.!!$R3 887

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
560 589 0.032117 AGTGATCCCCATCGAGACCA 60.032 55.0 0.0 0.0 0.00 4.02 F
570 599 0.034380 ATCGAGACCAACGAGGAGGA 60.034 55.0 5.7 0.0 42.81 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2538 7880 0.522180 CTTACGTCACGTGCTCTCCT 59.478 55.0 14.62 0.0 41.39 3.69 R
2567 7939 0.028505 CCCAATGCGCAGATCGAAAG 59.971 55.0 18.32 0.0 41.67 2.62 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
28 29 5.596268 TGCATCATGAGCAATACGATAAC 57.404 39.130 14.81 0.00 39.39 1.89
46 50 8.018677 ACGATAACTCATGTACTCAAACTTTG 57.981 34.615 0.00 0.00 0.00 2.77
54 58 6.998074 TCATGTACTCAAACTTTGTCCATCTT 59.002 34.615 1.44 0.00 0.00 2.40
61 65 3.498774 ACTTTGTCCATCTTGCTGAGT 57.501 42.857 0.00 0.00 0.00 3.41
137 141 8.367943 TGTTTCACTAACACGTACAAATATGT 57.632 30.769 0.00 0.00 41.73 2.29
138 142 8.828644 TGTTTCACTAACACGTACAAATATGTT 58.171 29.630 0.00 0.00 41.73 2.71
139 143 9.098746 GTTTCACTAACACGTACAAATATGTTG 57.901 33.333 0.00 0.00 37.55 3.33
229 244 8.776470 CCTTCAAAATTCAAACATGTATGCTTT 58.224 29.630 0.00 0.00 0.00 3.51
336 355 7.499232 AGCTACACAAAAAGACAAATGTAGAGT 59.501 33.333 12.21 0.00 41.21 3.24
378 400 1.464734 AGAGAAGAAGTCGGCGATCA 58.535 50.000 14.79 0.00 0.00 2.92
392 414 0.744414 CGATCAACATTGCTCCCGGT 60.744 55.000 0.00 0.00 0.00 5.28
413 435 3.023832 TGAGAGTGATGAAGTGGCGATA 58.976 45.455 0.00 0.00 0.00 2.92
485 514 6.716628 AGTTCTATTGAAAGCATGACCTCAAA 59.283 34.615 0.00 0.00 33.52 2.69
486 515 7.231317 AGTTCTATTGAAAGCATGACCTCAAAA 59.769 33.333 0.00 0.00 33.52 2.44
487 516 7.523293 TCTATTGAAAGCATGACCTCAAAAA 57.477 32.000 0.00 0.00 31.94 1.94
492 521 5.593909 TGAAAGCATGACCTCAAAAAGAAGA 59.406 36.000 0.00 0.00 0.00 2.87
498 527 6.016777 GCATGACCTCAAAAAGAAGAAGAAGA 60.017 38.462 0.00 0.00 0.00 2.87
512 541 6.272090 AGAAGAAGAAGAAGGTGAAGAAGGAT 59.728 38.462 0.00 0.00 0.00 3.24
521 550 0.537188 TGAAGAAGGATGACGAGGCC 59.463 55.000 0.00 0.00 0.00 5.19
522 551 0.528684 GAAGAAGGATGACGAGGCCG 60.529 60.000 0.00 0.00 42.50 6.13
523 552 1.961180 AAGAAGGATGACGAGGCCGG 61.961 60.000 0.00 0.00 40.78 6.13
524 553 4.162690 AAGGATGACGAGGCCGGC 62.163 66.667 21.18 21.18 46.00 6.13
557 586 1.403814 GACAGTGATCCCCATCGAGA 58.596 55.000 0.00 0.00 0.00 4.04
560 589 0.032117 AGTGATCCCCATCGAGACCA 60.032 55.000 0.00 0.00 0.00 4.02
567 596 1.320344 CCCATCGAGACCAACGAGGA 61.320 60.000 0.00 0.00 42.68 3.71
568 597 0.101399 CCATCGAGACCAACGAGGAG 59.899 60.000 0.00 0.00 42.68 3.69
569 598 0.101399 CATCGAGACCAACGAGGAGG 59.899 60.000 5.70 0.00 42.68 4.30
570 599 0.034380 ATCGAGACCAACGAGGAGGA 60.034 55.000 5.70 0.00 42.81 3.71
571 600 0.677098 TCGAGACCAACGAGGAGGAG 60.677 60.000 5.70 0.00 41.22 3.69
572 601 1.658686 CGAGACCAACGAGGAGGAGG 61.659 65.000 5.70 0.00 41.22 4.30
573 602 0.323542 GAGACCAACGAGGAGGAGGA 60.324 60.000 5.70 0.00 41.22 3.71
574 603 0.323908 AGACCAACGAGGAGGAGGAG 60.324 60.000 5.70 0.00 41.22 3.69
575 604 0.323542 GACCAACGAGGAGGAGGAGA 60.324 60.000 5.70 0.00 41.22 3.71
601 630 1.204467 GAGGAGCTCCACAACTCTGAG 59.796 57.143 33.90 2.45 38.89 3.35
607 636 0.191064 TCCACAACTCTGAGGACCCT 59.809 55.000 9.85 0.00 37.39 4.34
608 637 0.322975 CCACAACTCTGAGGACCCTG 59.677 60.000 9.85 1.21 35.42 4.45
612 641 1.974236 CAACTCTGAGGACCCTGACTT 59.026 52.381 9.85 0.00 0.00 3.01
625 684 4.678256 ACCCTGACTTAGACTCATTCTGA 58.322 43.478 0.00 0.00 35.55 3.27
652 711 2.408022 GTGAGCGATACGGCGTCT 59.592 61.111 19.21 6.76 38.18 4.18
672 731 5.508573 CGTCTGACGAGTAGTTTTATGTCTG 59.491 44.000 24.86 0.00 46.05 3.51
794 854 4.696899 TTATACATCACCTATCGGAGCG 57.303 45.455 0.00 0.00 0.00 5.03
801 861 0.465824 ACCTATCGGAGCGCTAGTGT 60.466 55.000 11.50 1.02 0.00 3.55
804 864 1.170919 TATCGGAGCGCTAGTGTCCC 61.171 60.000 11.50 4.93 0.00 4.46
806 866 2.786495 CGGAGCGCTAGTGTCCCAT 61.786 63.158 11.50 0.00 0.00 4.00
822 882 5.536161 GTGTCCCATTGCCTATTTACATCAT 59.464 40.000 0.00 0.00 0.00 2.45
823 883 6.040842 GTGTCCCATTGCCTATTTACATCATT 59.959 38.462 0.00 0.00 0.00 2.57
825 885 7.125507 TGTCCCATTGCCTATTTACATCATTTT 59.874 33.333 0.00 0.00 0.00 1.82
826 886 8.637986 GTCCCATTGCCTATTTACATCATTTTA 58.362 33.333 0.00 0.00 0.00 1.52
839 899 2.745968 TCATTTTATGGGGTTGGAGGC 58.254 47.619 0.00 0.00 0.00 4.70
848 1131 2.314549 TGGGGTTGGAGGCTTTTATGAT 59.685 45.455 0.00 0.00 0.00 2.45
849 1132 2.695147 GGGGTTGGAGGCTTTTATGATG 59.305 50.000 0.00 0.00 0.00 3.07
850 1133 3.365472 GGGTTGGAGGCTTTTATGATGT 58.635 45.455 0.00 0.00 0.00 3.06
851 1134 4.532834 GGGTTGGAGGCTTTTATGATGTA 58.467 43.478 0.00 0.00 0.00 2.29
852 1135 4.953579 GGGTTGGAGGCTTTTATGATGTAA 59.046 41.667 0.00 0.00 0.00 2.41
853 1136 5.420739 GGGTTGGAGGCTTTTATGATGTAAA 59.579 40.000 0.00 0.00 0.00 2.01
854 1137 6.098266 GGGTTGGAGGCTTTTATGATGTAAAT 59.902 38.462 0.00 0.00 0.00 1.40
855 1138 7.286775 GGGTTGGAGGCTTTTATGATGTAAATA 59.713 37.037 0.00 0.00 0.00 1.40
856 1139 8.691797 GGTTGGAGGCTTTTATGATGTAAATAA 58.308 33.333 0.00 0.00 0.00 1.40
859 1142 9.249053 TGGAGGCTTTTATGATGTAAATAAACA 57.751 29.630 0.00 0.00 31.02 2.83
890 1173 6.147328 GGTGATGTATAATTTACTCGAAGGCC 59.853 42.308 0.00 0.00 0.00 5.19
895 1178 8.514330 TGTATAATTTACTCGAAGGCCAATTT 57.486 30.769 5.01 0.00 0.00 1.82
899 1182 9.965824 ATAATTTACTCGAAGGCCAATTTAATG 57.034 29.630 5.01 0.00 0.00 1.90
902 1185 5.505173 ACTCGAAGGCCAATTTAATGATG 57.495 39.130 5.01 0.00 0.00 3.07
944 1233 3.279434 AGATGTTTTTAGATGGCCGACC 58.721 45.455 0.00 0.00 0.00 4.79
997 1286 1.817099 CGTTGGAGATGCCCTGAGC 60.817 63.158 0.00 0.00 44.14 4.26
1013 1302 2.783275 GCTCATGCTGTGCTCGTG 59.217 61.111 0.00 0.00 34.37 4.35
1014 1303 2.783275 CTCATGCTGTGCTCGTGC 59.217 61.111 1.71 1.71 40.20 5.34
1015 1304 2.743538 TCATGCTGTGCTCGTGCC 60.744 61.111 7.05 0.00 38.71 5.01
1016 1305 2.745100 CATGCTGTGCTCGTGCCT 60.745 61.111 7.05 0.00 38.71 4.75
1018 1307 2.330372 ATGCTGTGCTCGTGCCTTG 61.330 57.895 7.05 0.00 38.71 3.61
1020 1309 4.081030 CTGTGCTCGTGCCTTGCG 62.081 66.667 7.05 0.00 38.71 4.85
1024 1313 4.742201 GCTCGTGCCTTGCGGAGA 62.742 66.667 10.08 0.00 34.96 3.71
1025 1314 2.811317 CTCGTGCCTTGCGGAGAC 60.811 66.667 1.99 0.00 34.96 3.36
1044 2592 0.237761 CGTGGAGACTTCGTCGACTT 59.762 55.000 14.70 0.00 37.67 3.01
1064 2612 2.066592 TCCCTCCACTCTCGGATCTAT 58.933 52.381 0.00 0.00 33.56 1.98
1065 2613 3.257578 TCCCTCCACTCTCGGATCTATA 58.742 50.000 0.00 0.00 33.56 1.31
1087 2635 2.651361 CAGAGAACCACGCCGTCT 59.349 61.111 0.00 0.00 0.00 4.18
1623 3186 3.127533 GCTTCCTGCGCCAACGAT 61.128 61.111 4.18 0.00 43.93 3.73
1697 3260 1.514228 CACTCCCGTCGATCGTGTG 60.514 63.158 15.94 11.25 37.94 3.82
1928 3512 4.430765 CGACGACGGGAAGGGGTG 62.431 72.222 0.00 0.00 35.72 4.61
2098 7422 2.032634 GGTGAATGCGCGACCTTGA 61.033 57.895 12.10 0.00 0.00 3.02
2145 7487 1.076549 GCAAGGGGTGGTGATGGAA 59.923 57.895 0.00 0.00 0.00 3.53
2198 7540 2.281484 GGTGGGCTGCTTCGTGAA 60.281 61.111 0.00 0.00 0.00 3.18
2496 7838 2.413453 GACGTCGGAGAGTAACTTACGT 59.587 50.000 0.00 0.00 41.60 3.57
2531 7873 0.317854 CTGTGCTCTGACGTGAACGA 60.318 55.000 10.26 0.00 43.02 3.85
2532 7874 0.313987 TGTGCTCTGACGTGAACGAT 59.686 50.000 10.26 0.00 43.02 3.73
2533 7875 0.710567 GTGCTCTGACGTGAACGATG 59.289 55.000 10.26 0.00 43.02 3.84
2544 7886 0.171231 TGAACGATGCACGAGGAGAG 59.829 55.000 14.18 0.00 45.77 3.20
2545 7887 1.142778 GAACGATGCACGAGGAGAGC 61.143 60.000 14.18 0.00 45.77 4.09
2553 7925 2.202362 CGAGGAGAGCACGTGACG 60.202 66.667 22.23 2.24 0.00 4.35
2656 8028 4.923871 GTCACGATTGATGACACTTGTACT 59.076 41.667 9.50 0.00 44.87 2.73
2657 8029 6.090783 GTCACGATTGATGACACTTGTACTA 58.909 40.000 9.50 0.00 44.87 1.82
2658 8030 6.251589 GTCACGATTGATGACACTTGTACTAG 59.748 42.308 2.56 2.56 44.87 2.57
2871 8254 1.474498 GGACTTGTCCCGACAGTGTTT 60.474 52.381 8.54 0.00 42.94 2.83
2872 8255 1.865340 GACTTGTCCCGACAGTGTTTC 59.135 52.381 0.00 0.00 42.94 2.78
2873 8256 0.859232 CTTGTCCCGACAGTGTTTCG 59.141 55.000 0.00 0.00 42.94 3.46
2874 8257 1.155424 TTGTCCCGACAGTGTTTCGC 61.155 55.000 0.00 0.00 42.94 4.70
2896 8279 2.288395 GGACATGCTTGGAAAACACCAG 60.288 50.000 4.44 0.00 41.19 4.00
2914 8297 3.084039 CCAGTTGTCCATGCATGTAACT 58.916 45.455 24.58 24.28 0.00 2.24
2918 8301 5.984926 CAGTTGTCCATGCATGTAACTTTTT 59.015 36.000 25.84 12.20 0.00 1.94
2945 8330 0.260230 TGACCCCAAGACCAGCAAAA 59.740 50.000 0.00 0.00 0.00 2.44
2955 8340 4.150897 AGACCAGCAAAAGTTCACTGTA 57.849 40.909 0.00 0.00 0.00 2.74
2970 8355 5.241403 TCACTGTAAGGGATGACATTTGT 57.759 39.130 0.00 0.00 45.21 2.83
2971 8356 5.003160 TCACTGTAAGGGATGACATTTGTG 58.997 41.667 0.00 0.00 45.21 3.33
2972 8357 5.003160 CACTGTAAGGGATGACATTTGTGA 58.997 41.667 0.00 0.00 43.23 3.58
2973 8358 5.473162 CACTGTAAGGGATGACATTTGTGAA 59.527 40.000 0.00 0.00 43.23 3.18
2974 8359 5.473504 ACTGTAAGGGATGACATTTGTGAAC 59.526 40.000 0.00 0.00 39.30 3.18
2975 8360 4.454161 TGTAAGGGATGACATTTGTGAACG 59.546 41.667 0.00 0.00 0.00 3.95
2976 8361 3.417069 AGGGATGACATTTGTGAACGA 57.583 42.857 0.00 0.00 0.00 3.85
2977 8362 3.955471 AGGGATGACATTTGTGAACGAT 58.045 40.909 0.00 0.00 0.00 3.73
2978 8363 4.335416 AGGGATGACATTTGTGAACGATT 58.665 39.130 0.00 0.00 0.00 3.34
2979 8364 4.766891 AGGGATGACATTTGTGAACGATTT 59.233 37.500 0.00 0.00 0.00 2.17
2980 8365 5.243730 AGGGATGACATTTGTGAACGATTTT 59.756 36.000 0.00 0.00 0.00 1.82
2981 8366 5.345741 GGGATGACATTTGTGAACGATTTTG 59.654 40.000 0.00 0.00 0.00 2.44
2982 8367 6.148948 GGATGACATTTGTGAACGATTTTGA 58.851 36.000 0.00 0.00 0.00 2.69
2983 8368 6.808212 GGATGACATTTGTGAACGATTTTGAT 59.192 34.615 0.00 0.00 0.00 2.57
2984 8369 6.989796 TGACATTTGTGAACGATTTTGATG 57.010 33.333 0.00 0.00 0.00 3.07
2985 8370 6.502652 TGACATTTGTGAACGATTTTGATGT 58.497 32.000 0.00 0.00 0.00 3.06
2986 8371 7.643579 TGACATTTGTGAACGATTTTGATGTA 58.356 30.769 0.00 0.00 0.00 2.29
2998 8383 8.280909 ACGATTTTGATGTAATTTGTGTTCAC 57.719 30.769 0.00 0.00 0.00 3.18
3002 8387 6.378710 TTGATGTAATTTGTGTTCACCGAA 57.621 33.333 0.37 0.00 0.00 4.30
3010 8395 2.627791 TGTTCACCGAACATGGCAG 58.372 52.632 5.47 0.00 45.88 4.85
3047 8432 1.824230 TGGCAAGTTCACTGCAGTTTT 59.176 42.857 18.94 6.73 0.00 2.43
3054 8439 4.494484 AGTTCACTGCAGTTTTGTTTTCC 58.506 39.130 18.94 0.00 0.00 3.13
3055 8440 4.021544 AGTTCACTGCAGTTTTGTTTTCCA 60.022 37.500 18.94 0.00 0.00 3.53
3093 8478 6.362016 CGTGCTTGCAAACTTAAATTGTCATA 59.638 34.615 0.00 0.00 0.00 2.15
3094 8479 7.062138 CGTGCTTGCAAACTTAAATTGTCATAT 59.938 33.333 0.00 0.00 0.00 1.78
3107 8492 2.627945 TGTCATATTTGCCGTCCTCAC 58.372 47.619 0.00 0.00 0.00 3.51
3241 8626 8.696043 AATCAATTATGGCAGTATAAAGAGCA 57.304 30.769 0.00 0.00 0.00 4.26
3244 8629 7.938490 TCAATTATGGCAGTATAAAGAGCATCA 59.062 33.333 0.00 0.00 37.82 3.07
3264 8649 8.082242 AGCATCAGAGGTAACAAAAATTACAAC 58.918 33.333 0.00 0.00 36.87 3.32
3275 8660 7.118496 ACAAAAATTACAACCAGGTTCATGA 57.882 32.000 0.12 0.00 0.00 3.07
3291 8676 3.609853 TCATGAACCACCTAGCAATGAC 58.390 45.455 0.00 0.00 0.00 3.06
3296 8681 0.327924 CCACCTAGCAATGACCCACA 59.672 55.000 0.00 0.00 0.00 4.17
3305 8690 1.426251 AATGACCCACAGGACCAGCA 61.426 55.000 0.00 0.00 36.73 4.41
3309 8694 2.822637 CCCACAGGACCAGCACACT 61.823 63.158 0.00 0.00 33.47 3.55
3315 8700 1.153745 GGACCAGCACACTAGAGCG 60.154 63.158 0.00 0.00 36.39 5.03
3324 8709 2.803133 GCACACTAGAGCGGCAATCATA 60.803 50.000 1.45 0.00 0.00 2.15
3390 8775 1.864711 TCCAAACAAAGACGAGCGAAG 59.135 47.619 0.00 0.00 0.00 3.79
3411 8797 3.118956 AGACCTGATCCAAACAGACGATC 60.119 47.826 0.00 0.00 37.54 3.69
3427 8813 1.732732 CGATCGGAGACCAACACTGAC 60.733 57.143 7.38 0.00 42.51 3.51
3448 8834 2.311294 GATCCCGCAAGATCCAACG 58.689 57.895 2.21 0.00 37.31 4.10
3452 8838 1.439353 CCCGCAAGATCCAACGATGG 61.439 60.000 5.13 5.13 45.23 3.51
3464 8850 2.267426 CAACGATGGTAGACGCATCAA 58.733 47.619 0.00 0.00 0.00 2.57
3475 8861 1.449423 CGCATCAACGGGACATGGA 60.449 57.895 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 6.652481 AGATGGACAAAGTTTGAGTACATGAG 59.348 38.462 22.23 0.00 0.00 2.90
46 50 6.985188 TGTTAATTACTCAGCAAGATGGAC 57.015 37.500 0.00 0.00 0.00 4.02
124 128 7.021196 GCAGATTTGACAACATATTTGTACGT 58.979 34.615 0.00 0.00 34.06 3.57
126 130 8.915871 ATGCAGATTTGACAACATATTTGTAC 57.084 30.769 0.00 0.00 34.06 2.90
131 135 8.698210 ACCAATATGCAGATTTGACAACATATT 58.302 29.630 11.69 12.06 39.85 1.28
136 140 6.968904 CAGTACCAATATGCAGATTTGACAAC 59.031 38.462 11.69 6.93 0.00 3.32
137 141 6.883756 TCAGTACCAATATGCAGATTTGACAA 59.116 34.615 11.69 0.00 0.00 3.18
138 142 6.413892 TCAGTACCAATATGCAGATTTGACA 58.586 36.000 11.69 0.00 0.00 3.58
139 143 6.540189 ACTCAGTACCAATATGCAGATTTGAC 59.460 38.462 11.69 6.84 0.00 3.18
255 273 9.872721 TTTACACATGTAAATTATGTCTCCGTA 57.127 29.630 12.17 0.00 43.28 4.02
256 274 8.780846 TTTACACATGTAAATTATGTCTCCGT 57.219 30.769 12.17 0.00 43.28 4.69
291 309 7.839837 GTGTAGCTCTCATTTTAACGTATTTCG 59.160 37.037 0.00 0.00 46.00 3.46
351 370 3.616379 GCCGACTTCTTCTCTTCAATCAG 59.384 47.826 0.00 0.00 0.00 2.90
356 375 1.244816 TCGCCGACTTCTTCTCTTCA 58.755 50.000 0.00 0.00 0.00 3.02
378 400 0.036010 CTCTCACCGGGAGCAATGTT 60.036 55.000 6.32 0.00 43.70 2.71
392 414 1.256812 TCGCCACTTCATCACTCTCA 58.743 50.000 0.00 0.00 0.00 3.27
413 435 2.678934 TCCCACGCTAACCTCGCT 60.679 61.111 0.00 0.00 0.00 4.93
437 466 5.885230 TCAACTCGTTCTAAACCTATCGA 57.115 39.130 0.00 0.00 0.00 3.59
439 468 7.813627 AGAACTTCAACTCGTTCTAAACCTATC 59.186 37.037 3.09 0.00 45.72 2.08
485 514 6.770303 CCTTCTTCACCTTCTTCTTCTTCTTT 59.230 38.462 0.00 0.00 0.00 2.52
486 515 6.100424 TCCTTCTTCACCTTCTTCTTCTTCTT 59.900 38.462 0.00 0.00 0.00 2.52
487 516 5.604650 TCCTTCTTCACCTTCTTCTTCTTCT 59.395 40.000 0.00 0.00 0.00 2.85
492 521 5.555966 GTCATCCTTCTTCACCTTCTTCTT 58.444 41.667 0.00 0.00 0.00 2.52
498 527 2.234908 CCTCGTCATCCTTCTTCACCTT 59.765 50.000 0.00 0.00 0.00 3.50
527 556 4.135153 CACTGTCGAGGGGCCGAG 62.135 72.222 0.00 0.00 39.43 4.63
557 586 0.114560 TTCTCCTCCTCCTCGTTGGT 59.885 55.000 0.00 0.00 37.07 3.67
560 589 0.705253 TCCTTCTCCTCCTCCTCGTT 59.295 55.000 0.00 0.00 0.00 3.85
567 596 0.933700 CTCCTCCTCCTTCTCCTCCT 59.066 60.000 0.00 0.00 0.00 3.69
568 597 0.759060 GCTCCTCCTCCTTCTCCTCC 60.759 65.000 0.00 0.00 0.00 4.30
569 598 0.261696 AGCTCCTCCTCCTTCTCCTC 59.738 60.000 0.00 0.00 0.00 3.71
570 599 0.261696 GAGCTCCTCCTCCTTCTCCT 59.738 60.000 0.87 0.00 0.00 3.69
571 600 0.759060 GGAGCTCCTCCTCCTTCTCC 60.759 65.000 26.25 0.00 46.41 3.71
572 601 2.820845 GGAGCTCCTCCTCCTTCTC 58.179 63.158 26.25 0.00 46.41 2.87
593 622 2.407340 AAGTCAGGGTCCTCAGAGTT 57.593 50.000 0.00 0.00 0.00 3.01
601 630 4.027437 AGAATGAGTCTAAGTCAGGGTCC 58.973 47.826 0.00 0.00 33.56 4.46
644 703 1.233285 AACTACTCGTCAGACGCCGT 61.233 55.000 18.62 18.16 42.21 5.68
652 711 4.081862 CCCCAGACATAAAACTACTCGTCA 60.082 45.833 0.00 0.00 0.00 4.35
672 731 1.117150 TACTACTTCACCATCGCCCC 58.883 55.000 0.00 0.00 0.00 5.80
728 787 7.230849 TCAAACATACCAAGCTCATTTCAAT 57.769 32.000 0.00 0.00 0.00 2.57
738 797 7.989826 ACTAGATCATTTCAAACATACCAAGC 58.010 34.615 0.00 0.00 0.00 4.01
801 861 7.673641 AAAATGATGTAAATAGGCAATGGGA 57.326 32.000 0.00 0.00 0.00 4.37
804 864 9.426837 CCCATAAAATGATGTAAATAGGCAATG 57.573 33.333 0.00 0.00 0.00 2.82
806 866 7.566879 ACCCCATAAAATGATGTAAATAGGCAA 59.433 33.333 0.00 0.00 0.00 4.52
822 882 3.268034 AAAGCCTCCAACCCCATAAAA 57.732 42.857 0.00 0.00 0.00 1.52
823 883 3.268034 AAAAGCCTCCAACCCCATAAA 57.732 42.857 0.00 0.00 0.00 1.40
825 885 3.529734 TCATAAAAGCCTCCAACCCCATA 59.470 43.478 0.00 0.00 0.00 2.74
826 886 2.314549 TCATAAAAGCCTCCAACCCCAT 59.685 45.455 0.00 0.00 0.00 4.00
913 1201 8.017946 GCCATCTAAAAACATCTCCGATAAATC 58.982 37.037 0.00 0.00 0.00 2.17
916 1204 5.763204 GGCCATCTAAAAACATCTCCGATAA 59.237 40.000 0.00 0.00 0.00 1.75
921 1209 3.312697 GTCGGCCATCTAAAAACATCTCC 59.687 47.826 2.24 0.00 0.00 3.71
922 1210 3.312697 GGTCGGCCATCTAAAAACATCTC 59.687 47.826 0.00 0.00 34.09 2.75
997 1286 2.747822 GGCACGAGCACAGCATGAG 61.748 63.158 7.26 0.00 44.61 2.90
1015 1304 1.444553 GTCTCCACGTCTCCGCAAG 60.445 63.158 0.00 0.00 37.70 4.01
1016 1305 1.461091 AAGTCTCCACGTCTCCGCAA 61.461 55.000 0.00 0.00 37.70 4.85
1018 1307 1.153997 GAAGTCTCCACGTCTCCGC 60.154 63.158 0.00 0.00 37.70 5.54
1020 1309 2.255430 ACGAAGTCTCCACGTCTCC 58.745 57.895 0.00 0.00 29.74 3.71
1033 1322 0.109226 GTGGAGGGAAGTCGACGAAG 60.109 60.000 10.46 0.00 0.00 3.79
1044 2592 1.519498 TAGATCCGAGAGTGGAGGGA 58.481 55.000 0.00 0.00 42.45 4.20
1064 2612 1.112113 GGCGTGGTTCTCTGGAGATA 58.888 55.000 0.88 0.00 37.29 1.98
1065 2613 1.901085 GGCGTGGTTCTCTGGAGAT 59.099 57.895 0.88 0.00 37.29 2.75
1087 2635 5.243730 CCATTGAGCTAAGTTTTTGGGAAGA 59.756 40.000 0.00 0.00 0.00 2.87
1376 2939 2.509336 CGCGCTCCTTGTAGGTGG 60.509 66.667 5.56 0.00 36.53 4.61
1642 3205 2.123854 TAGTCCCGGCAGCTCGAT 60.124 61.111 0.00 0.00 0.00 3.59
1697 3260 2.027751 GCTCCGGCGAGGTGATAC 59.972 66.667 9.30 0.00 41.99 2.24
1928 3512 2.042831 GTGTCCAGCCACTCCATGC 61.043 63.158 0.00 0.00 32.50 4.06
1977 7301 2.806945 TTGAAAGGATGCTCCCGAAT 57.193 45.000 0.00 0.00 37.19 3.34
1995 7319 1.748122 CTCCTGCCGCTTGCTCATT 60.748 57.895 0.00 0.00 42.00 2.57
2198 7540 3.537206 GAGTTCCACCCGCAGTGCT 62.537 63.158 14.33 0.00 45.83 4.40
2531 7873 2.182791 CGTGCTCTCCTCGTGCAT 59.817 61.111 0.00 0.00 43.22 3.96
2532 7874 3.295273 ACGTGCTCTCCTCGTGCA 61.295 61.111 0.00 0.00 41.56 4.57
2538 7880 0.522180 CTTACGTCACGTGCTCTCCT 59.478 55.000 14.62 0.00 41.39 3.69
2553 7925 1.068055 TCGAAAGGAGACACGGCTTAC 60.068 52.381 0.00 0.00 0.00 2.34
2567 7939 0.028505 CCCAATGCGCAGATCGAAAG 59.971 55.000 18.32 0.00 41.67 2.62
2788 8160 6.723977 TCTTACCCCTGCAAGAAAACAATTAT 59.276 34.615 0.00 0.00 34.07 1.28
2871 8254 0.886938 TTTTCCAAGCATGTCCGCGA 60.887 50.000 8.23 0.00 36.85 5.87
2872 8255 0.729140 GTTTTCCAAGCATGTCCGCG 60.729 55.000 0.00 0.00 36.85 6.46
2873 8256 0.313672 TGTTTTCCAAGCATGTCCGC 59.686 50.000 0.00 0.00 0.00 5.54
2874 8257 1.335872 GGTGTTTTCCAAGCATGTCCG 60.336 52.381 0.00 0.00 0.00 4.79
2922 8305 1.342474 TGCTGGTCTTGGGGTCAAAAA 60.342 47.619 0.00 0.00 31.77 1.94
2935 8320 4.261197 CCTTACAGTGAACTTTTGCTGGTC 60.261 45.833 0.00 0.00 33.62 4.02
2945 8330 5.505181 AATGTCATCCCTTACAGTGAACT 57.495 39.130 0.00 0.00 0.00 3.01
2955 8340 3.750371 TCGTTCACAAATGTCATCCCTT 58.250 40.909 0.00 0.00 0.00 3.95
2966 8351 9.307121 ACAAATTACATCAAAATCGTTCACAAA 57.693 25.926 0.00 0.00 0.00 2.83
2967 8352 8.750416 CACAAATTACATCAAAATCGTTCACAA 58.250 29.630 0.00 0.00 0.00 3.33
2968 8353 7.918033 ACACAAATTACATCAAAATCGTTCACA 59.082 29.630 0.00 0.00 0.00 3.58
2969 8354 8.280909 ACACAAATTACATCAAAATCGTTCAC 57.719 30.769 0.00 0.00 0.00 3.18
2970 8355 8.864069 AACACAAATTACATCAAAATCGTTCA 57.136 26.923 0.00 0.00 0.00 3.18
2971 8356 8.963130 TGAACACAAATTACATCAAAATCGTTC 58.037 29.630 0.00 0.00 0.00 3.95
2972 8357 8.751335 GTGAACACAAATTACATCAAAATCGTT 58.249 29.630 0.00 0.00 0.00 3.85
2973 8358 7.381139 GGTGAACACAAATTACATCAAAATCGT 59.619 33.333 7.25 0.00 0.00 3.73
2974 8359 7.409238 CGGTGAACACAAATTACATCAAAATCG 60.409 37.037 7.25 0.00 0.00 3.34
2975 8360 7.593273 TCGGTGAACACAAATTACATCAAAATC 59.407 33.333 7.25 0.00 0.00 2.17
2976 8361 7.429633 TCGGTGAACACAAATTACATCAAAAT 58.570 30.769 7.25 0.00 0.00 1.82
2977 8362 6.796426 TCGGTGAACACAAATTACATCAAAA 58.204 32.000 7.25 0.00 0.00 2.44
2978 8363 6.378710 TCGGTGAACACAAATTACATCAAA 57.621 33.333 7.25 0.00 0.00 2.69
2979 8364 6.183360 TGTTCGGTGAACACAAATTACATCAA 60.183 34.615 8.21 0.00 45.88 2.57
2980 8365 5.297029 TGTTCGGTGAACACAAATTACATCA 59.703 36.000 8.21 0.00 45.88 3.07
2981 8366 5.753744 TGTTCGGTGAACACAAATTACATC 58.246 37.500 8.21 0.00 45.88 3.06
2982 8367 5.759506 TGTTCGGTGAACACAAATTACAT 57.240 34.783 8.21 0.00 45.88 2.29
2998 8383 1.238439 ACTGAAACTGCCATGTTCGG 58.762 50.000 0.00 0.00 0.00 4.30
3002 8387 1.806542 CGCTAACTGAAACTGCCATGT 59.193 47.619 0.00 0.00 0.00 3.21
3010 8395 1.202076 GCCATGCTCGCTAACTGAAAC 60.202 52.381 0.00 0.00 0.00 2.78
3054 8439 3.362831 GCAAGCACGACAATTTTCTGATG 59.637 43.478 0.00 0.00 0.00 3.07
3055 8440 3.004629 TGCAAGCACGACAATTTTCTGAT 59.995 39.130 0.00 0.00 0.00 2.90
3067 8452 4.677584 ACAATTTAAGTTTGCAAGCACGA 58.322 34.783 16.04 0.00 0.00 4.35
3109 8494 9.023967 CAATATTTTGATAGCAAGGTTAGTTGC 57.976 33.333 0.20 0.20 42.93 4.17
3157 8542 5.633601 TGATAATCATAATCAGCGGACGTTC 59.366 40.000 0.00 0.00 0.00 3.95
3188 8573 7.277098 TGAATAAATCGAAAGTTTCTCCCGTAG 59.723 37.037 13.56 0.00 0.00 3.51
3223 8608 6.295518 CCTCTGATGCTCTTTATACTGCCATA 60.296 42.308 0.00 0.00 0.00 2.74
3231 8616 9.733556 TTTTTGTTACCTCTGATGCTCTTTATA 57.266 29.630 0.00 0.00 0.00 0.98
3241 8626 8.472007 TGGTTGTAATTTTTGTTACCTCTGAT 57.528 30.769 0.00 0.00 34.43 2.90
3244 8629 6.837048 ACCTGGTTGTAATTTTTGTTACCTCT 59.163 34.615 0.00 0.00 34.43 3.69
3275 8660 1.072266 TGGGTCATTGCTAGGTGGTT 58.928 50.000 0.00 0.00 0.00 3.67
3291 8676 1.480212 TAGTGTGCTGGTCCTGTGGG 61.480 60.000 0.00 0.00 0.00 4.61
3296 8681 1.599606 CGCTCTAGTGTGCTGGTCCT 61.600 60.000 0.00 0.00 0.00 3.85
3305 8690 3.819564 TTATGATTGCCGCTCTAGTGT 57.180 42.857 0.00 0.00 0.00 3.55
3309 8694 3.934457 TCGATTATGATTGCCGCTCTA 57.066 42.857 0.00 0.00 0.00 2.43
3315 8700 5.931146 ACTCTCTTCATCGATTATGATTGCC 59.069 40.000 0.00 0.00 44.13 4.52
3324 8709 6.261158 TCAATCTACGACTCTCTTCATCGATT 59.739 38.462 0.00 0.00 39.16 3.34
3363 8748 4.909880 GCTCGTCTTTGTTTGGATGTTTAC 59.090 41.667 0.00 0.00 0.00 2.01
3390 8775 2.743636 TCGTCTGTTTGGATCAGGTC 57.256 50.000 0.00 0.00 34.15 3.85
3411 8797 1.372997 CGGTCAGTGTTGGTCTCCG 60.373 63.158 0.00 0.00 0.00 4.63
3448 8834 1.209128 CCGTTGATGCGTCTACCATC 58.791 55.000 13.76 0.00 39.56 3.51
3452 8838 0.108992 TGTCCCGTTGATGCGTCTAC 60.109 55.000 10.09 10.09 0.00 2.59
3464 8850 2.368439 CATGTTTGATCCATGTCCCGT 58.632 47.619 3.10 0.00 35.94 5.28
3475 8861 4.590222 GGAATAATGCCTCCCATGTTTGAT 59.410 41.667 0.00 0.00 33.49 2.57


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

AutoCloner maintained by Alex Coulton.