Multiple sequence alignment - TraesCS7A01G224000

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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 TraesCS7A01G224000 chr7A 100.000 4179 0 0 1 4179 193381473 193377295 0.000000e+00 7718.0
1 TraesCS7A01G224000 chr7A 90.330 1396 115 9 2796 4179 193503055 193501668 0.000000e+00 1812.0
2 TraesCS7A01G224000 chr7A 90.255 1375 104 15 2821 4179 193589420 193588060 0.000000e+00 1770.0
3 TraesCS7A01G224000 chr7A 100.000 632 0 0 4461 5092 193377013 193376382 0.000000e+00 1168.0
4 TraesCS7A01G224000 chr7A 87.921 1010 99 11 1805 2803 193590487 193589490 0.000000e+00 1168.0
5 TraesCS7A01G224000 chr7A 93.220 767 48 2 932 1696 193504925 193504161 0.000000e+00 1125.0
6 TraesCS7A01G224000 chr7A 91.713 724 56 3 940 1660 192987674 192986952 0.000000e+00 1002.0
7 TraesCS7A01G224000 chr7A 87.188 640 71 9 1067 1700 193591194 193590560 0.000000e+00 717.0
8 TraesCS7A01G224000 chr7A 81.707 574 65 21 2234 2803 193503642 193503105 4.680000e-120 442.0
9 TraesCS7A01G224000 chr7A 83.372 433 39 17 1805 2231 193504129 193503724 2.240000e-98 370.0
10 TraesCS7A01G224000 chr7A 86.316 285 39 0 2839 3123 192986114 192985830 1.380000e-80 311.0
11 TraesCS7A01G224000 chr7A 80.189 212 30 9 4775 4980 193586417 193586212 1.140000e-31 148.0
12 TraesCS7A01G224000 chr7A 95.122 41 1 1 948 987 193591285 193591245 4.260000e-06 63.9
13 TraesCS7A01G224000 chr7D 96.268 2358 77 7 1805 4155 185367887 185365534 0.000000e+00 3856.0
14 TraesCS7A01G224000 chr7D 89.274 1790 151 21 2405 4179 185375445 185373682 0.000000e+00 2204.0
15 TraesCS7A01G224000 chr7D 97.574 742 18 0 959 1700 185368702 185367961 0.000000e+00 1271.0
16 TraesCS7A01G224000 chr7D 88.751 969 84 12 3234 4179 185764040 185763074 0.000000e+00 1162.0
17 TraesCS7A01G224000 chr7D 86.207 957 72 21 1 933 185370093 185369173 0.000000e+00 981.0
18 TraesCS7A01G224000 chr7D 94.569 626 31 3 4468 5092 185365206 185364583 0.000000e+00 965.0
19 TraesCS7A01G224000 chr7D 90.162 742 58 7 932 1660 185222645 185221906 0.000000e+00 952.0
20 TraesCS7A01G224000 chr7D 87.445 677 71 13 1030 1697 185766135 185765464 0.000000e+00 767.0
21 TraesCS7A01G224000 chr7D 86.140 671 52 16 2586 3249 185764693 185764057 0.000000e+00 686.0
22 TraesCS7A01G224000 chr7D 90.728 453 38 4 1945 2395 185376805 185376355 7.290000e-168 601.0
23 TraesCS7A01G224000 chr7D 81.803 599 51 23 1805 2393 185765387 185764837 2.800000e-122 449.0
24 TraesCS7A01G224000 chr7D 80.460 609 95 17 4478 5077 185373621 185373028 1.300000e-120 444.0
25 TraesCS7A01G224000 chr7D 83.290 383 61 3 3501 3881 185220330 185219949 2.920000e-92 350.0
26 TraesCS7A01G224000 chr7D 82.991 341 58 0 3501 3841 185674908 185674568 4.950000e-80 309.0
27 TraesCS7A01G224000 chr7D 96.875 96 2 1 1805 1899 185376906 185376811 5.280000e-35 159.0
28 TraesCS7A01G224000 chr7D 86.047 86 8 2 1699 1780 583595231 583595316 7.020000e-14 89.8
29 TraesCS7A01G224000 chr7D 85.882 85 8 3 1699 1779 436113399 436113483 2.530000e-13 87.9
30 TraesCS7A01G224000 chr7D 95.122 41 1 1 948 987 185766193 185766153 4.260000e-06 63.9
31 TraesCS7A01G224000 chr7B 88.934 732 63 4 947 1660 327674419 327673688 0.000000e+00 887.0
32 TraesCS7A01G224000 chr7B 87.206 680 73 12 1030 1700 328493955 328493281 0.000000e+00 761.0
33 TraesCS7A01G224000 chr7B 90.584 531 47 1 1172 1699 328166166 328165636 0.000000e+00 701.0
34 TraesCS7A01G224000 chr7B 84.777 381 58 0 3501 3881 327672142 327671762 2.880000e-102 383.0
35 TraesCS7A01G224000 chr7B 83.478 345 52 3 2833 3174 327672892 327672550 2.960000e-82 316.0
36 TraesCS7A01G224000 chr7B 87.923 207 21 4 947 1152 328166358 328166155 1.830000e-59 241.0
37 TraesCS7A01G224000 chr7B 90.643 171 11 2 1805 1975 328493207 328493042 6.640000e-54 222.0
38 TraesCS7A01G224000 chr7B 94.000 100 5 1 1806 1904 328165567 328165468 3.180000e-32 150.0
39 TraesCS7A01G224000 chr7B 87.402 127 12 1 760 886 328179485 328179363 5.310000e-30 143.0
40 TraesCS7A01G224000 chr7B 94.203 69 4 0 949 1017 327674496 327674428 6.970000e-19 106.0
41 TraesCS7A01G224000 chr3B 89.412 85 6 1 1699 1780 783013694 783013610 2.510000e-18 104.0
42 TraesCS7A01G224000 chr3B 85.897 78 11 0 1699 1776 18746180 18746257 3.270000e-12 84.2
43 TraesCS7A01G224000 chr1D 86.047 86 7 3 1699 1779 478229641 478229726 2.530000e-13 87.9
44 TraesCS7A01G224000 chr1B 86.747 83 6 2 1699 1776 677299993 677300075 2.530000e-13 87.9
45 TraesCS7A01G224000 chr1B 85.714 84 6 4 1698 1776 92873764 92873846 3.270000e-12 84.2
46 TraesCS7A01G224000 chr5A 85.714 84 7 1 1698 1776 116590063 116590146 3.270000e-12 84.2
47 TraesCS7A01G224000 chr6A 85.366 82 6 1 1699 1780 116823352 116823277 4.230000e-11 80.5
48 TraesCS7A01G224000 chr5B 81.707 82 15 0 348 429 594344557 594344476 9.150000e-08 69.4
49 TraesCS7A01G224000 chr5B 80.952 84 16 0 303 386 25260655 25260572 3.290000e-07 67.6


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 TraesCS7A01G224000 chr7A 193376382 193381473 5091 True 4443.000 7718 100.000000 1 5092 2 chr7A.!!$R2 5091
1 TraesCS7A01G224000 chr7A 193501668 193504925 3257 True 937.250 1812 87.157250 932 4179 4 chr7A.!!$R3 3247
2 TraesCS7A01G224000 chr7A 193586212 193591285 5073 True 773.380 1770 88.135000 948 4980 5 chr7A.!!$R4 4032
3 TraesCS7A01G224000 chr7A 192985830 192987674 1844 True 656.500 1002 89.014500 940 3123 2 chr7A.!!$R1 2183
4 TraesCS7A01G224000 chr7D 185364583 185376906 12323 True 1310.125 3856 91.494375 1 5092 8 chr7D.!!$R3 5091
5 TraesCS7A01G224000 chr7D 185219949 185222645 2696 True 651.000 952 86.726000 932 3881 2 chr7D.!!$R2 2949
6 TraesCS7A01G224000 chr7D 185763074 185766193 3119 True 625.580 1162 87.852200 948 4179 5 chr7D.!!$R4 3231
7 TraesCS7A01G224000 chr7B 328493042 328493955 913 True 491.500 761 88.924500 1030 1975 2 chr7B.!!$R4 945
8 TraesCS7A01G224000 chr7B 327671762 327674496 2734 True 423.000 887 87.848000 947 3881 4 chr7B.!!$R2 2934
9 TraesCS7A01G224000 chr7B 328165468 328166358 890 True 364.000 701 90.835667 947 1904 3 chr7B.!!$R3 957

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
301 7139 0.173481 TCCTCGTCTCCGATTTGCAG 59.827 55.0 0.00 0.00 43.27 4.41 F
859 7697 0.248289 TACGCCTTGTAGAACCCAGC 59.752 55.0 0.00 0.00 0.00 4.85 F
937 7775 0.459237 CTCTCACCGACCATGTCTGC 60.459 60.0 0.00 0.00 0.00 4.26 F
2397 10178 0.828022 TGGTTCATGCTAGGGGTACG 59.172 55.0 0.00 0.00 0.00 3.67 F
2531 10313 0.750182 TAATACAAAGCGGGCCAGGC 60.750 55.0 4.39 1.26 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1540 8886 1.268352 CATAGTAGGGCTGCGTCTCTC 59.732 57.143 0.00 0.00 0.00 3.20 R
2409 10190 0.736053 GTTGGGTGTTTTGCGAGACA 59.264 50.000 0.00 0.00 0.00 3.41 R
2512 10294 0.750182 GCCTGGCCCGCTTTGTATTA 60.750 55.000 7.66 0.00 0.00 0.98 R
3819 11846 0.649475 CTTCGCTTTCTCCAGATGCG 59.351 55.000 14.52 14.52 43.48 4.73 R
4462 12537 0.728542 TGCATCAACTAGTGCGCATG 59.271 50.000 15.91 7.64 44.11 4.06 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
43 6857 2.285220 CGCGTCTCCAACATTGAATAGG 59.715 50.000 0.00 0.00 0.00 2.57
46 6860 3.063997 CGTCTCCAACATTGAATAGGCAC 59.936 47.826 0.00 0.00 0.00 5.01
53 6867 2.027192 ACATTGAATAGGCACGGACACT 60.027 45.455 0.00 0.00 0.00 3.55
98 6912 2.103042 GGCTAGTGTGCCGCTTCAG 61.103 63.158 0.00 0.00 43.74 3.02
103 6917 2.186826 GTGTGCCGCTTCAGTGGTT 61.187 57.895 8.22 0.00 46.99 3.67
145 6959 1.526887 CTCTGGGCCGGCTTCAATA 59.473 57.895 28.56 14.08 0.00 1.90
150 6964 0.251341 GGGCCGGCTTCAATATGGAT 60.251 55.000 28.56 0.00 0.00 3.41
151 6965 1.004277 GGGCCGGCTTCAATATGGATA 59.996 52.381 28.56 0.00 0.00 2.59
153 6967 1.740025 GCCGGCTTCAATATGGATAGC 59.260 52.381 22.15 5.98 0.00 2.97
165 6994 1.344953 TGGATAGCCAGAATGCGGGT 61.345 55.000 0.00 0.00 39.92 5.28
211 7049 2.325484 GAGAATGGTTTTGGGTGGGTT 58.675 47.619 0.00 0.00 0.00 4.11
213 7051 3.506398 AGAATGGTTTTGGGTGGGTTAG 58.494 45.455 0.00 0.00 0.00 2.34
214 7052 3.116900 AGAATGGTTTTGGGTGGGTTAGT 60.117 43.478 0.00 0.00 0.00 2.24
222 7060 1.605992 GGTGGGTTAGTGGGTAGCC 59.394 63.158 3.29 3.29 0.00 3.93
229 7067 0.909623 TTAGTGGGTAGCCAGAAGCC 59.090 55.000 15.48 1.67 45.47 4.35
255 7093 1.527380 GTGTTGTCCGGAAGCCCAA 60.527 57.895 5.23 2.80 0.00 4.12
261 7099 2.258286 CCGGAAGCCCAAAAAGCG 59.742 61.111 0.00 0.00 34.64 4.68
264 7102 2.574018 GGAAGCCCAAAAAGCGCCT 61.574 57.895 2.29 0.00 34.64 5.52
279 7117 2.692741 CCTTCCCCCTCCACCCTC 60.693 72.222 0.00 0.00 0.00 4.30
280 7118 2.456840 CTTCCCCCTCCACCCTCT 59.543 66.667 0.00 0.00 0.00 3.69
281 7119 1.690985 CTTCCCCCTCCACCCTCTC 60.691 68.421 0.00 0.00 0.00 3.20
282 7120 2.184631 TTCCCCCTCCACCCTCTCT 61.185 63.158 0.00 0.00 0.00 3.10
283 7121 2.041405 CCCCCTCCACCCTCTCTC 60.041 72.222 0.00 0.00 0.00 3.20
284 7122 2.041405 CCCCTCCACCCTCTCTCC 60.041 72.222 0.00 0.00 0.00 3.71
285 7123 2.641746 CCCCTCCACCCTCTCTCCT 61.642 68.421 0.00 0.00 0.00 3.69
286 7124 1.075600 CCCTCCACCCTCTCTCCTC 60.076 68.421 0.00 0.00 0.00 3.71
294 7132 1.523046 CCTCTCTCCTCGTCTCCGA 59.477 63.158 0.00 0.00 41.73 4.55
301 7139 0.173481 TCCTCGTCTCCGATTTGCAG 59.827 55.000 0.00 0.00 43.27 4.41
316 7154 0.250684 TGCAGGAGAAAATGCGTCCA 60.251 50.000 0.00 0.00 45.54 4.02
322 7160 1.129437 GAGAAAATGCGTCCAGACTGC 59.871 52.381 0.00 7.40 0.00 4.40
330 7168 1.982938 GTCCAGACTGCCCTACGGT 60.983 63.158 0.00 0.00 42.04 4.83
339 7177 3.138625 CCCTACGGTCCGATGCAT 58.861 61.111 20.51 0.00 0.00 3.96
340 7178 1.812686 GCCCTACGGTCCGATGCATA 61.813 60.000 20.51 0.00 0.00 3.14
343 7181 1.340248 CCTACGGTCCGATGCATAACT 59.660 52.381 20.51 0.00 0.00 2.24
344 7182 2.394708 CTACGGTCCGATGCATAACTG 58.605 52.381 20.51 6.41 0.00 3.16
354 7192 3.622612 CGATGCATAACTGTGTTGGATGA 59.377 43.478 0.00 0.00 0.00 2.92
374 7212 0.884259 CACAACACATCCAGACCGCA 60.884 55.000 0.00 0.00 0.00 5.69
377 7215 2.094757 AACACATCCAGACCGCACGA 62.095 55.000 0.00 0.00 0.00 4.35
381 7219 3.138930 ATCCAGACCGCACGATCCG 62.139 63.158 0.00 0.00 0.00 4.18
383 7221 2.278206 CAGACCGCACGATCCGAG 60.278 66.667 0.00 0.00 0.00 4.63
394 7232 1.591863 GATCCGAGCGGTTGTAGGC 60.592 63.158 8.96 0.00 36.47 3.93
403 7241 1.156736 CGGTTGTAGGCAGTTTGAGG 58.843 55.000 0.00 0.00 0.00 3.86
405 7243 2.152016 GGTTGTAGGCAGTTTGAGGAC 58.848 52.381 0.00 0.00 0.00 3.85
410 7248 2.281484 GCAGTTTGAGGACCGGCA 60.281 61.111 0.00 0.00 0.00 5.69
411 7249 1.675641 GCAGTTTGAGGACCGGCAT 60.676 57.895 0.00 0.00 0.00 4.40
504 7342 3.159472 TGCAAAAGAGGCATGTTCATCT 58.841 40.909 0.00 0.00 36.11 2.90
544 7382 6.884472 TTGAGGTGGGAACAGAAGATTATA 57.116 37.500 0.00 0.00 44.46 0.98
545 7383 7.451731 TTGAGGTGGGAACAGAAGATTATAT 57.548 36.000 0.00 0.00 44.46 0.86
639 7477 4.661993 TTGTCTCGTGCAATATTGTCAC 57.338 40.909 22.51 22.51 34.29 3.67
672 7510 0.529378 GTACGGCGGGGGAGTATATG 59.471 60.000 13.24 0.00 0.00 1.78
693 7531 3.068732 TGGCCATCTATTCTCTGAGAACG 59.931 47.826 21.47 15.29 37.00 3.95
708 7546 0.850856 GAACGTCACGTGTCCTTGAC 59.149 55.000 16.51 3.99 39.99 3.18
714 7552 1.067974 TCACGTGTCCTTGACAACGAT 59.932 47.619 16.51 7.06 44.49 3.73
722 7560 1.369625 CTTGACAACGATGGCCTACC 58.630 55.000 3.32 0.00 31.48 3.18
726 7564 1.479323 GACAACGATGGCCTACCTACA 59.521 52.381 3.32 0.00 36.63 2.74
727 7565 1.903860 ACAACGATGGCCTACCTACAA 59.096 47.619 3.32 0.00 36.63 2.41
729 7567 3.244630 ACAACGATGGCCTACCTACAAAA 60.245 43.478 3.32 0.00 36.63 2.44
730 7568 3.261981 ACGATGGCCTACCTACAAAAG 57.738 47.619 3.32 0.00 36.63 2.27
731 7569 2.835764 ACGATGGCCTACCTACAAAAGA 59.164 45.455 3.32 0.00 36.63 2.52
732 7570 3.262405 ACGATGGCCTACCTACAAAAGAA 59.738 43.478 3.32 0.00 36.63 2.52
733 7571 3.871594 CGATGGCCTACCTACAAAAGAAG 59.128 47.826 3.32 0.00 36.63 2.85
734 7572 4.623171 CGATGGCCTACCTACAAAAGAAGT 60.623 45.833 3.32 0.00 36.63 3.01
735 7573 4.015872 TGGCCTACCTACAAAAGAAGTG 57.984 45.455 3.32 0.00 36.63 3.16
736 7574 3.649023 TGGCCTACCTACAAAAGAAGTGA 59.351 43.478 3.32 0.00 36.63 3.41
737 7575 4.103469 TGGCCTACCTACAAAAGAAGTGAA 59.897 41.667 3.32 0.00 36.63 3.18
738 7576 4.695928 GGCCTACCTACAAAAGAAGTGAAG 59.304 45.833 0.00 0.00 0.00 3.02
739 7577 4.154375 GCCTACCTACAAAAGAAGTGAAGC 59.846 45.833 0.00 0.00 0.00 3.86
740 7578 5.305585 CCTACCTACAAAAGAAGTGAAGCA 58.694 41.667 0.00 0.00 0.00 3.91
741 7579 5.179555 CCTACCTACAAAAGAAGTGAAGCAC 59.820 44.000 0.00 0.00 34.10 4.40
742 7580 3.883489 ACCTACAAAAGAAGTGAAGCACC 59.117 43.478 0.00 0.00 34.49 5.01
743 7581 3.253432 CCTACAAAAGAAGTGAAGCACCC 59.747 47.826 0.00 0.00 34.49 4.61
744 7582 3.018423 ACAAAAGAAGTGAAGCACCCT 57.982 42.857 0.00 0.00 34.49 4.34
745 7583 2.952310 ACAAAAGAAGTGAAGCACCCTC 59.048 45.455 0.00 0.00 34.49 4.30
746 7584 3.217626 CAAAAGAAGTGAAGCACCCTCT 58.782 45.455 0.00 0.00 34.49 3.69
747 7585 2.849294 AAGAAGTGAAGCACCCTCTC 57.151 50.000 0.00 0.00 34.49 3.20
748 7586 1.722034 AGAAGTGAAGCACCCTCTCA 58.278 50.000 0.00 0.00 34.49 3.27
749 7587 2.050144 AGAAGTGAAGCACCCTCTCAA 58.950 47.619 0.00 0.00 34.49 3.02
750 7588 2.439507 AGAAGTGAAGCACCCTCTCAAA 59.560 45.455 0.00 0.00 34.49 2.69
751 7589 3.117888 AGAAGTGAAGCACCCTCTCAAAA 60.118 43.478 0.00 0.00 34.49 2.44
810 7648 7.831193 ACCTGTCAATCAAGTTAAATATGCTCT 59.169 33.333 0.00 0.00 0.00 4.09
859 7697 0.248289 TACGCCTTGTAGAACCCAGC 59.752 55.000 0.00 0.00 0.00 4.85
867 7705 1.895798 TGTAGAACCCAGCAGAGTGAG 59.104 52.381 0.00 0.00 0.00 3.51
892 7730 3.563808 AGTGTGTGTGTTTGTGCGATAAT 59.436 39.130 0.00 0.00 0.00 1.28
897 7735 6.592220 TGTGTGTGTTTGTGCGATAATACTAT 59.408 34.615 0.00 0.00 0.00 2.12
906 7744 3.760151 TGCGATAATACTATACACGGGCT 59.240 43.478 0.00 0.00 0.00 5.19
910 7748 6.623549 GCGATAATACTATACACGGGCTAACA 60.624 42.308 0.00 0.00 0.00 2.41
934 7772 1.153549 GGCTCTCACCGACCATGTC 60.154 63.158 0.00 0.00 0.00 3.06
937 7775 0.459237 CTCTCACCGACCATGTCTGC 60.459 60.000 0.00 0.00 0.00 4.26
1085 8389 4.594920 TGAATAGCTATGAAGGAAGGGAGG 59.405 45.833 7.09 0.00 0.00 4.30
1497 8843 1.181786 GCCGGGGAATGATTTCAACA 58.818 50.000 2.18 0.00 33.23 3.33
1523 8869 1.669115 CCGGTCACTGGAGCAACTG 60.669 63.158 0.00 0.00 41.62 3.16
1540 8886 2.279784 GGAAGATCTCGGCGGCAG 60.280 66.667 10.53 5.92 0.00 4.85
1669 9015 2.414481 GCTCTAAGGTATGCATGCATCG 59.586 50.000 35.35 17.37 37.82 3.84
1685 9034 2.601314 GCATCGTATTGTCTGCAACGTA 59.399 45.455 6.28 0.00 37.44 3.57
1698 9047 8.487313 TGTCTGCAACGTAATAATTATGTCTT 57.513 30.769 0.00 0.00 34.40 3.01
1699 9048 9.589111 TGTCTGCAACGTAATAATTATGTCTTA 57.411 29.630 0.00 0.00 34.40 2.10
1700 9049 9.845305 GTCTGCAACGTAATAATTATGTCTTAC 57.155 33.333 0.00 0.00 34.40 2.34
1701 9050 9.811995 TCTGCAACGTAATAATTATGTCTTACT 57.188 29.630 0.00 0.00 34.40 2.24
1703 9052 9.037737 TGCAACGTAATAATTATGTCTTACTCC 57.962 33.333 0.00 0.00 34.40 3.85
1704 9053 8.493547 GCAACGTAATAATTATGTCTTACTCCC 58.506 37.037 0.00 0.00 34.40 4.30
1705 9054 9.760077 CAACGTAATAATTATGTCTTACTCCCT 57.240 33.333 0.00 0.00 34.40 4.20
1706 9055 9.978044 AACGTAATAATTATGTCTTACTCCCTC 57.022 33.333 0.00 0.00 34.40 4.30
1707 9056 8.583296 ACGTAATAATTATGTCTTACTCCCTCC 58.417 37.037 0.00 0.00 29.63 4.30
1708 9057 7.754027 CGTAATAATTATGTCTTACTCCCTCCG 59.246 40.741 0.00 0.00 0.00 4.63
1709 9058 4.338379 AATTATGTCTTACTCCCTCCGC 57.662 45.455 0.00 0.00 0.00 5.54
1710 9059 2.750141 TATGTCTTACTCCCTCCGCT 57.250 50.000 0.00 0.00 0.00 5.52
1711 9060 1.867363 ATGTCTTACTCCCTCCGCTT 58.133 50.000 0.00 0.00 0.00 4.68
1712 9061 1.640917 TGTCTTACTCCCTCCGCTTT 58.359 50.000 0.00 0.00 0.00 3.51
1713 9062 2.811410 TGTCTTACTCCCTCCGCTTTA 58.189 47.619 0.00 0.00 0.00 1.85
1714 9063 3.167485 TGTCTTACTCCCTCCGCTTTAA 58.833 45.455 0.00 0.00 0.00 1.52
1715 9064 3.579586 TGTCTTACTCCCTCCGCTTTAAA 59.420 43.478 0.00 0.00 0.00 1.52
1716 9065 4.040706 TGTCTTACTCCCTCCGCTTTAAAA 59.959 41.667 0.00 0.00 0.00 1.52
1717 9066 5.183969 GTCTTACTCCCTCCGCTTTAAAAT 58.816 41.667 0.00 0.00 0.00 1.82
1718 9067 6.070653 TGTCTTACTCCCTCCGCTTTAAAATA 60.071 38.462 0.00 0.00 0.00 1.40
1719 9068 6.479331 GTCTTACTCCCTCCGCTTTAAAATAG 59.521 42.308 0.00 0.00 0.00 1.73
1720 9069 6.381994 TCTTACTCCCTCCGCTTTAAAATAGA 59.618 38.462 0.00 0.00 0.00 1.98
1721 9070 5.632034 ACTCCCTCCGCTTTAAAATAGAT 57.368 39.130 0.00 0.00 0.00 1.98
1722 9071 5.368989 ACTCCCTCCGCTTTAAAATAGATG 58.631 41.667 0.00 0.00 0.00 2.90
1723 9072 5.130477 ACTCCCTCCGCTTTAAAATAGATGA 59.870 40.000 0.00 0.00 0.00 2.92
1724 9073 6.183361 ACTCCCTCCGCTTTAAAATAGATGAT 60.183 38.462 0.00 0.00 0.00 2.45
1725 9074 6.601332 TCCCTCCGCTTTAAAATAGATGATT 58.399 36.000 0.00 0.00 0.00 2.57
1726 9075 7.060421 TCCCTCCGCTTTAAAATAGATGATTT 58.940 34.615 0.00 0.00 39.56 2.17
1727 9076 8.215050 TCCCTCCGCTTTAAAATAGATGATTTA 58.785 33.333 0.00 0.00 36.71 1.40
1728 9077 8.846211 CCCTCCGCTTTAAAATAGATGATTTAA 58.154 33.333 0.00 0.00 36.71 1.52
1729 9078 9.665264 CCTCCGCTTTAAAATAGATGATTTAAC 57.335 33.333 0.00 0.00 36.71 2.01
1907 9464 6.560361 AGGTGTAGTGGATCATAGATCTGAT 58.440 40.000 5.18 0.73 38.57 2.90
1982 9540 8.399425 ACTATTAAGATATAGAGAATGGTCGCG 58.601 37.037 0.00 0.00 33.31 5.87
2189 9798 8.697846 TTAATTTAGTCCATCGTACACTTCTG 57.302 34.615 0.00 0.00 0.00 3.02
2257 10031 2.094442 TCGTTCGATGCCAATACACTCA 60.094 45.455 0.00 0.00 0.00 3.41
2362 10143 4.862641 AGATGGGCTTTTTAGGCTAGAA 57.137 40.909 0.00 0.00 34.52 2.10
2397 10178 0.828022 TGGTTCATGCTAGGGGTACG 59.172 55.000 0.00 0.00 0.00 3.67
2528 10310 4.528920 AGTTTATAATACAAAGCGGGCCA 58.471 39.130 4.39 0.00 0.00 5.36
2531 10313 0.750182 TAATACAAAGCGGGCCAGGC 60.750 55.000 4.39 1.26 0.00 4.85
2716 10519 9.586150 GTTCTTGCATAGTAATAACAATGATCG 57.414 33.333 0.00 0.00 0.00 3.69
2767 10570 7.514721 TGAACCACTTTGATTTTCTACTAGGT 58.485 34.615 0.00 0.00 0.00 3.08
2772 10575 9.667107 CCACTTTGATTTTCTACTAGGTATCAA 57.333 33.333 0.00 0.00 32.07 2.57
2956 10830 5.121454 GCTGTTCCAACAACAATTCAAAACA 59.879 36.000 0.00 0.00 38.66 2.83
2986 10860 1.963338 GTTCCTTGCACTGCGCTCT 60.963 57.895 9.73 0.00 43.06 4.09
3308 11305 9.083080 CGTGTAAGACAGTGACATAAATTATCA 57.917 33.333 0.00 0.00 0.00 2.15
3643 11669 6.673106 TGATATCGAGCATGTTAGACTCTTC 58.327 40.000 0.00 0.00 0.00 2.87
3649 11675 4.355437 AGCATGTTAGACTCTTCGAATCG 58.645 43.478 0.00 0.00 0.00 3.34
3664 11690 2.159099 CGAATCGAACTGGGATCCTCAA 60.159 50.000 12.58 0.00 0.00 3.02
3819 11846 2.223144 TGTATGCTTCTGTCGTTGCAAC 59.777 45.455 19.89 19.89 38.96 4.17
3969 11998 1.530323 ACATTGTAAGGTTGACGCCC 58.470 50.000 0.00 0.00 0.00 6.13
4000 12057 8.965819 TGGTTAAATATCACATATGTGTTGCTT 58.034 29.630 30.03 21.50 45.76 3.91
4001 12058 9.236691 GGTTAAATATCACATATGTGTTGCTTG 57.763 33.333 30.03 8.14 45.76 4.01
4492 12582 2.094675 AGTTGATGCAGGCAACCATAC 58.905 47.619 23.71 7.14 45.05 2.39
4625 12716 5.646577 AGGTCTAGTGTAGCAACTACAAG 57.353 43.478 8.93 4.87 46.55 3.16
4653 12744 2.158608 AGTAGTGCTCCAAGCCAAAGTT 60.159 45.455 0.00 0.00 41.51 2.66
4654 12745 2.656947 AGTGCTCCAAGCCAAAGTTA 57.343 45.000 0.00 0.00 41.51 2.24
4745 12836 7.201848 GGATTTTCATGATGGAATTGTAGCTCA 60.202 37.037 0.00 0.00 0.00 4.26
4750 12841 2.806945 TGGAATTGTAGCTCAAGGGG 57.193 50.000 0.00 0.00 39.55 4.79
4755 12846 4.711846 GGAATTGTAGCTCAAGGGGAAAAT 59.288 41.667 0.00 0.00 39.55 1.82
4786 14164 0.603065 GAATGGTGGTTGCACTTCCC 59.397 55.000 0.00 0.00 0.00 3.97
4851 14229 0.035820 GGGTGGTGTATCAAAGGCGA 60.036 55.000 0.00 0.00 0.00 5.54
4882 14260 5.062934 GTGTAGCGCAACTATATTGTGTCAA 59.937 40.000 11.47 0.00 32.15 3.18
4904 14282 3.199946 AGAGGGAAGCCGTAATTCAATGA 59.800 43.478 0.00 0.00 0.00 2.57
4946 14325 4.693283 CGGTGCCTCATATTTGACTAGAA 58.307 43.478 0.00 0.00 0.00 2.10
4953 14332 6.699642 GCCTCATATTTGACTAGAAGTGAGAC 59.300 42.308 0.00 0.00 35.13 3.36
5087 14466 3.643792 ACACATAGGACATAAGAGAGGGC 59.356 47.826 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.448686 GTTACTGGACGAGACATGATGG 58.551 50.000 0.00 0.00 0.00 3.51
7 6821 1.208358 CGCGTTACTGGACGAGACA 59.792 57.895 0.00 0.00 45.47 3.41
11 6825 1.499056 GAGACGCGTTACTGGACGA 59.501 57.895 15.53 0.00 45.47 4.20
43 6857 3.883744 CTGTCCCCAGTGTCCGTGC 62.884 68.421 0.00 0.00 33.80 5.34
46 6860 2.923035 ACCTGTCCCCAGTGTCCG 60.923 66.667 0.00 0.00 36.95 4.79
84 6898 2.281070 CCACTGAAGCGGCACACT 60.281 61.111 1.45 0.00 0.00 3.55
103 6917 1.219124 GCGACCTCTCATTGGCTCA 59.781 57.895 0.00 0.00 0.00 4.26
110 6924 4.194720 GCCGACGCGACCTCTCAT 62.195 66.667 15.93 0.00 0.00 2.90
112 6926 4.539881 GAGCCGACGCGACCTCTC 62.540 72.222 15.93 10.99 41.18 3.20
133 6947 1.740025 GCTATCCATATTGAAGCCGGC 59.260 52.381 21.89 21.89 0.00 6.13
134 6948 2.359900 GGCTATCCATATTGAAGCCGG 58.640 52.381 0.00 0.00 42.98 6.13
138 6952 5.163784 CGCATTCTGGCTATCCATATTGAAG 60.164 44.000 0.00 0.00 42.51 3.02
145 6959 0.037303 CCCGCATTCTGGCTATCCAT 59.963 55.000 0.00 0.00 42.51 3.41
150 6964 1.048724 AGCTACCCGCATTCTGGCTA 61.049 55.000 0.00 0.00 42.61 3.93
151 6965 2.190578 GCTACCCGCATTCTGGCT 59.809 61.111 0.00 0.00 38.92 4.75
153 6967 0.811616 GTCAGCTACCCGCATTCTGG 60.812 60.000 0.00 0.00 42.61 3.86
155 6969 1.141881 CGTCAGCTACCCGCATTCT 59.858 57.895 0.00 0.00 42.61 2.40
176 7005 2.202987 CTCCCTCTCACATGCGCC 60.203 66.667 4.18 0.00 0.00 6.53
184 7022 2.041620 CCCAAAACCATTCTCCCTCTCA 59.958 50.000 0.00 0.00 0.00 3.27
211 7049 1.327690 CGGCTTCTGGCTACCCACTA 61.328 60.000 0.00 0.00 41.46 2.74
213 7051 2.125106 CGGCTTCTGGCTACCCAC 60.125 66.667 0.00 0.00 41.46 4.61
214 7052 3.399181 CCGGCTTCTGGCTACCCA 61.399 66.667 0.00 0.00 41.46 4.51
240 7078 1.036707 CTTTTTGGGCTTCCGGACAA 58.963 50.000 1.83 1.49 0.00 3.18
255 7093 2.035783 GAGGGGGAAGGCGCTTTT 59.964 61.111 6.11 1.22 0.00 2.27
264 7102 2.182858 GAGAGAGGGTGGAGGGGGAA 62.183 65.000 0.00 0.00 0.00 3.97
274 7112 1.610873 GGAGACGAGGAGAGAGGGT 59.389 63.158 0.00 0.00 0.00 4.34
275 7113 4.571243 GGAGACGAGGAGAGAGGG 57.429 66.667 0.00 0.00 0.00 4.30
294 7132 2.094545 GGACGCATTTTCTCCTGCAAAT 60.095 45.455 0.00 0.00 38.30 2.32
301 7139 1.734465 CAGTCTGGACGCATTTTCTCC 59.266 52.381 0.00 0.00 36.20 3.71
330 7168 2.027653 TCCAACACAGTTATGCATCGGA 60.028 45.455 0.19 0.00 0.00 4.55
332 7170 3.622612 TCATCCAACACAGTTATGCATCG 59.377 43.478 0.19 0.00 0.00 3.84
354 7192 0.884704 GCGGTCTGGATGTGTTGTGT 60.885 55.000 0.00 0.00 0.00 3.72
367 7205 4.194720 GCTCGGATCGTGCGGTCT 62.195 66.667 4.81 0.00 36.69 3.85
374 7212 1.432251 CTACAACCGCTCGGATCGT 59.568 57.895 15.95 10.58 38.96 3.73
377 7215 2.298158 CTGCCTACAACCGCTCGGAT 62.298 60.000 15.95 0.00 38.96 4.18
381 7219 0.517316 CAAACTGCCTACAACCGCTC 59.483 55.000 0.00 0.00 0.00 5.03
383 7221 0.517316 CTCAAACTGCCTACAACCGC 59.483 55.000 0.00 0.00 0.00 5.68
394 7232 0.523072 CAATGCCGGTCCTCAAACTG 59.477 55.000 1.90 0.00 0.00 3.16
410 7248 3.370840 TGCTGTTAGGGCATCTTCAAT 57.629 42.857 0.00 0.00 34.56 2.57
411 7249 2.877097 TGCTGTTAGGGCATCTTCAA 57.123 45.000 0.00 0.00 34.56 2.69
470 7308 7.535139 TGCCTCTTTTGCATACAACTTATAAC 58.465 34.615 0.00 0.00 34.87 1.89
504 7342 7.419057 CCCACCTCAATAGCTTCTTAGTTATGA 60.419 40.741 0.00 0.00 29.43 2.15
600 7438 2.158623 ACAAACATGCTCACTCCCAAGA 60.159 45.455 0.00 0.00 0.00 3.02
639 7477 1.463444 GCCGTACCAGCACTTAAGTTG 59.537 52.381 5.07 2.68 0.00 3.16
672 7510 3.068873 ACGTTCTCAGAGAATAGATGGCC 59.931 47.826 16.13 0.00 36.50 5.36
708 7546 2.684001 TTGTAGGTAGGCCATCGTTG 57.316 50.000 5.01 0.00 37.19 4.10
714 7552 3.649023 TCACTTCTTTTGTAGGTAGGCCA 59.351 43.478 5.01 0.00 37.19 5.36
722 7560 4.137543 AGGGTGCTTCACTTCTTTTGTAG 58.862 43.478 0.00 0.00 34.40 2.74
726 7564 3.117888 TGAGAGGGTGCTTCACTTCTTTT 60.118 43.478 0.00 0.00 34.40 2.27
727 7565 2.439507 TGAGAGGGTGCTTCACTTCTTT 59.560 45.455 0.00 0.00 34.40 2.52
729 7567 1.722034 TGAGAGGGTGCTTCACTTCT 58.278 50.000 0.00 1.54 34.40 2.85
730 7568 2.550830 TTGAGAGGGTGCTTCACTTC 57.449 50.000 0.00 0.00 34.40 3.01
731 7569 3.297134 TTTTGAGAGGGTGCTTCACTT 57.703 42.857 0.00 0.00 34.40 3.16
732 7570 3.297134 TTTTTGAGAGGGTGCTTCACT 57.703 42.857 0.00 0.00 34.40 3.41
763 7601 2.965831 TCACCTTGACTAAGAGTGTGCT 59.034 45.455 0.00 0.00 36.89 4.40
852 7690 0.683973 CTCACTCACTCTGCTGGGTT 59.316 55.000 0.00 0.00 0.00 4.11
859 7697 2.159184 ACACACACACTCACTCACTCTG 60.159 50.000 0.00 0.00 0.00 3.35
867 7705 1.790123 CGCACAAACACACACACTCAC 60.790 52.381 0.00 0.00 0.00 3.51
892 7730 3.312421 GTCGTGTTAGCCCGTGTATAGTA 59.688 47.826 0.00 0.00 0.00 1.82
897 7735 1.209898 CGTCGTGTTAGCCCGTGTA 59.790 57.895 0.00 0.00 0.00 2.90
906 7744 1.582968 GTGAGAGCCCGTCGTGTTA 59.417 57.895 0.00 0.00 0.00 2.41
1085 8389 2.757056 GGTAACCATGCGAACGCCC 61.757 63.158 16.27 4.86 41.09 6.13
1176 8487 3.207265 ACACAGTGCAGGATACAAACA 57.793 42.857 0.00 0.00 41.41 2.83
1274 8620 2.281484 GCCTTGTGAAGCACCGGA 60.281 61.111 9.46 0.00 32.73 5.14
1523 8869 2.279784 CTGCCGCCGAGATCTTCC 60.280 66.667 0.00 0.00 0.00 3.46
1540 8886 1.268352 CATAGTAGGGCTGCGTCTCTC 59.732 57.143 0.00 0.00 0.00 3.20
1685 9034 6.270231 AGCGGAGGGAGTAAGACATAATTATT 59.730 38.462 0.00 0.00 0.00 1.40
1698 9047 6.325545 TCATCTATTTTAAAGCGGAGGGAGTA 59.674 38.462 0.00 0.00 0.00 2.59
1699 9048 5.130477 TCATCTATTTTAAAGCGGAGGGAGT 59.870 40.000 0.00 0.00 0.00 3.85
1700 9049 5.611374 TCATCTATTTTAAAGCGGAGGGAG 58.389 41.667 0.00 0.00 0.00 4.30
1701 9050 5.623956 TCATCTATTTTAAAGCGGAGGGA 57.376 39.130 0.00 0.00 0.00 4.20
1702 9051 6.884280 AATCATCTATTTTAAAGCGGAGGG 57.116 37.500 0.00 0.00 0.00 4.30
1703 9052 9.665264 GTTAAATCATCTATTTTAAAGCGGAGG 57.335 33.333 0.00 0.00 38.71 4.30
1757 9106 9.638176 AGCTATTCCAAAATAGATGACTCAATT 57.362 29.630 8.91 0.00 44.87 2.32
1759 9108 9.770097 CTAGCTATTCCAAAATAGATGACTCAA 57.230 33.333 8.91 0.00 44.87 3.02
1760 9109 8.928448 ACTAGCTATTCCAAAATAGATGACTCA 58.072 33.333 8.91 0.00 44.87 3.41
1771 9120 9.515226 ACTTGAACATTACTAGCTATTCCAAAA 57.485 29.630 0.00 0.00 0.00 2.44
1772 9121 9.515226 AACTTGAACATTACTAGCTATTCCAAA 57.485 29.630 0.00 0.00 0.00 3.28
1773 9122 9.515226 AAACTTGAACATTACTAGCTATTCCAA 57.485 29.630 0.00 0.00 0.00 3.53
1774 9123 9.515226 AAAACTTGAACATTACTAGCTATTCCA 57.485 29.630 0.00 0.00 0.00 3.53
1965 9522 4.382040 CCAATCCGCGACCATTCTCTATAT 60.382 45.833 8.23 0.00 0.00 0.86
1982 9540 3.658709 TGGCGACAAAATTTTCCAATCC 58.341 40.909 0.00 0.30 37.44 3.01
2257 10031 7.834803 AGAACTACCGTAGCTTATTTTAGTGT 58.165 34.615 5.42 0.00 0.00 3.55
2409 10190 0.736053 GTTGGGTGTTTTGCGAGACA 59.264 50.000 0.00 0.00 0.00 3.41
2512 10294 0.750182 GCCTGGCCCGCTTTGTATTA 60.750 55.000 7.66 0.00 0.00 0.98
2663 10462 7.320399 TCGACTTATTCTCTGCATTTCAAGTA 58.680 34.615 0.00 0.00 0.00 2.24
2716 10519 2.766828 ACTGGCTAGTGACTTGTATCCC 59.233 50.000 0.13 0.00 35.34 3.85
2767 10570 6.512578 CGTTCACCCGCAATTAATCATTGATA 60.513 38.462 0.00 0.00 44.78 2.15
2772 10575 3.275143 TCGTTCACCCGCAATTAATCAT 58.725 40.909 0.00 0.00 0.00 2.45
2783 10587 3.060003 CGATAGTAGTACTCGTTCACCCG 60.060 52.174 5.96 0.00 0.00 5.28
2956 10830 3.378427 GTGCAAGGAACAACTCAAAGTCT 59.622 43.478 0.00 0.00 0.00 3.24
2986 10860 1.819288 CCTCCGTTGACAAGCTCTCTA 59.181 52.381 0.00 0.00 0.00 2.43
3308 11305 4.558226 TCACTTTGTATGCTCCTCATGT 57.442 40.909 0.00 0.00 36.63 3.21
3508 11534 2.093711 CACACGACCCTATCATCCAACA 60.094 50.000 0.00 0.00 0.00 3.33
3643 11669 1.409064 TGAGGATCCCAGTTCGATTCG 59.591 52.381 8.55 0.00 0.00 3.34
3649 11675 1.825474 TCGTCTTGAGGATCCCAGTTC 59.175 52.381 8.55 0.00 0.00 3.01
3664 11690 3.305676 CCACATCACTTTCTGAGTCGTCT 60.306 47.826 0.00 0.00 36.10 4.18
3819 11846 0.649475 CTTCGCTTTCTCCAGATGCG 59.351 55.000 14.52 14.52 43.48 4.73
3955 11984 2.277084 CATAGTGGGCGTCAACCTTAC 58.723 52.381 0.00 0.00 0.00 2.34
4000 12057 6.524101 ACTTTTGTCTTAGAAAAACAGGCA 57.476 33.333 0.00 0.00 0.00 4.75
4460 12535 1.933181 GCATCAACTAGTGCGCATGTA 59.067 47.619 15.91 7.90 0.00 2.29
4461 12536 0.729116 GCATCAACTAGTGCGCATGT 59.271 50.000 15.91 10.78 0.00 3.21
4462 12537 0.728542 TGCATCAACTAGTGCGCATG 59.271 50.000 15.91 7.64 44.11 4.06
4470 12560 1.825090 TGGTTGCCTGCATCAACTAG 58.175 50.000 22.87 0.00 42.40 2.57
4567 12657 3.640498 TGATGGCAACCACTCATGAAAAA 59.360 39.130 0.00 0.00 35.80 1.94
4601 12692 6.373774 TCTTGTAGTTGCTACACTAGACCTAC 59.626 42.308 8.33 0.00 45.13 3.18
4625 12716 3.127721 GGCTTGGAGCACTACTTTCATTC 59.872 47.826 2.04 0.00 44.75 2.67
4653 12744 3.646611 TTGTCGTCCATTTCACGAGTA 57.353 42.857 0.00 0.00 46.52 2.59
4654 12745 2.519377 TTGTCGTCCATTTCACGAGT 57.481 45.000 0.00 0.00 46.52 4.18
4745 12836 5.215845 TCTCTTTTTGGACATTTTCCCCTT 58.784 37.500 0.00 0.00 45.17 3.95
4750 12841 6.424812 CCACCATTCTCTTTTTGGACATTTTC 59.575 38.462 0.00 0.00 34.52 2.29
4755 12846 3.909732 ACCACCATTCTCTTTTTGGACA 58.090 40.909 0.00 0.00 34.52 4.02
4769 12860 0.105760 TTGGGAAGTGCAACCACCAT 60.106 50.000 7.87 0.00 43.09 3.55
4771 12862 1.739667 GTTGGGAAGTGCAACCACC 59.260 57.895 7.87 0.80 43.09 4.61
4851 14229 4.985538 ATAGTTGCGCTACACTTCTACT 57.014 40.909 23.41 3.22 31.59 2.57
4882 14260 3.199946 TCATTGAATTACGGCTTCCCTCT 59.800 43.478 0.00 0.00 0.00 3.69
4904 14282 0.178068 CCTACCCACGTAGCATGCTT 59.822 55.000 28.02 8.42 40.69 3.91
4946 14325 7.972469 AGAATCCGCTTCTTAAGTGTCTCACT 61.972 42.308 1.63 0.00 43.14 3.41
4953 14332 6.703607 ACATCATAGAATCCGCTTCTTAAGTG 59.296 38.462 1.63 0.00 41.60 3.16
4961 14340 6.352016 ACTCATACATCATAGAATCCGCTT 57.648 37.500 0.00 0.00 0.00 4.68
4962 14341 5.991933 ACTCATACATCATAGAATCCGCT 57.008 39.130 0.00 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.