Multiple sequence alignment - TraesCS4B01G072400

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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 TraesCS4B01G072400 chr4B 100.000 3505 0 0 1 3505 67770418 67773922 0.000000e+00 6473.0
1 TraesCS4B01G072400 chr4B 94.737 38 1 1 744 781 167958845 167958809 1.360000e-04 58.4
2 TraesCS4B01G072400 chr4A 95.833 1536 52 10 1211 2736 552698867 552700400 0.000000e+00 2471.0
3 TraesCS4B01G072400 chr4A 90.455 1142 55 19 93 1215 552697644 552698750 0.000000e+00 1456.0
4 TraesCS4B01G072400 chr4A 86.667 225 29 1 2736 2959 552700456 552700680 7.510000e-62 248.0
5 TraesCS4B01G072400 chr4D 95.389 1323 47 11 1424 2735 46292313 46290994 0.000000e+00 2093.0
6 TraesCS4B01G072400 chr4D 88.105 1177 51 40 100 1239 46293901 46292777 0.000000e+00 1315.0
7 TraesCS4B01G072400 chr4D 86.802 788 66 13 2734 3505 46290938 46290173 0.000000e+00 845.0
8 TraesCS4B01G072400 chr4D 90.698 172 8 5 1267 1433 46292783 46292615 4.550000e-54 222.0
9 TraesCS4B01G072400 chr4D 93.204 103 5 2 1 101 306374281 306374179 2.180000e-32 150.0
10 TraesCS4B01G072400 chr6B 94.949 99 2 2 1 96 129298770 129298868 6.060000e-33 152.0
11 TraesCS4B01G072400 chr6B 82.716 81 12 2 1685 1764 710105908 710105829 1.750000e-08 71.3
12 TraesCS4B01G072400 chr6A 94.059 101 5 1 1 101 610658459 610658360 6.060000e-33 152.0
13 TraesCS4B01G072400 chr5B 94.949 99 2 3 1 96 711881641 711881543 6.060000e-33 152.0
14 TraesCS4B01G072400 chr1D 94.949 99 2 2 1 96 395968776 395968874 6.060000e-33 152.0
15 TraesCS4B01G072400 chr1A 93.333 105 3 3 1 101 58286601 58286497 6.060000e-33 152.0
16 TraesCS4B01G072400 chr5D 94.845 97 4 1 1 96 386060594 386060690 2.180000e-32 150.0
17 TraesCS4B01G072400 chr7D 92.453 106 4 4 1 103 26977874 26977770 7.840000e-32 148.0
18 TraesCS4B01G072400 chr7D 81.879 149 22 3 1003 1146 438368470 438368618 1.710000e-23 121.0
19 TraesCS4B01G072400 chr7D 77.184 206 45 2 1646 1850 296497294 296497498 6.150000e-23 119.0
20 TraesCS4B01G072400 chr7D 76.647 167 30 9 997 1157 382255424 382255587 2.240000e-12 84.2
21 TraesCS4B01G072400 chr7A 90.265 113 6 4 1 109 7831963 7832074 3.650000e-30 143.0
22 TraesCS4B01G072400 chr7A 83.212 137 20 1 1013 1146 489163067 489163203 4.750000e-24 122.0
23 TraesCS4B01G072400 chr7A 77.246 167 29 9 997 1157 430240153 430240316 4.820000e-14 89.8
24 TraesCS4B01G072400 chrUn 76.699 206 46 2 1646 1850 116282999 116283203 2.860000e-21 113.0
25 TraesCS4B01G072400 chr7B 76.699 206 46 2 1646 1850 339606246 339606450 2.860000e-21 113.0
26 TraesCS4B01G072400 chr7B 82.090 134 21 1 1022 1152 455272180 455272047 1.030000e-20 111.0
27 TraesCS4B01G072400 chr7B 77.246 167 29 9 997 1157 376430996 376431159 4.820000e-14 89.8
28 TraesCS4B01G072400 chr2D 78.667 150 22 7 1019 1163 54487972 54487828 1.340000e-14 91.6
29 TraesCS4B01G072400 chr2B 79.137 139 19 7 1019 1152 85177903 85177770 1.730000e-13 87.9
30 TraesCS4B01G072400 chr2A 77.124 153 25 8 1013 1160 54882383 54882530 2.900000e-11 80.5
31 TraesCS4B01G072400 chr2A 94.118 51 1 2 1019 1068 54955471 54955422 3.750000e-10 76.8
32 TraesCS4B01G072400 chr2A 75.904 166 29 9 1002 1157 708058391 708058555 1.350000e-09 75.0


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 TraesCS4B01G072400 chr4B 67770418 67773922 3504 False 6473.000000 6473 100.0000 1 3505 1 chr4B.!!$F1 3504
1 TraesCS4B01G072400 chr4A 552697644 552700680 3036 False 1391.666667 2471 90.9850 93 2959 3 chr4A.!!$F1 2866
2 TraesCS4B01G072400 chr4D 46290173 46293901 3728 True 1118.750000 2093 90.2485 100 3505 4 chr4D.!!$R2 3405

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
994 1023 0.179108 CCGGAATCGAAGGTCAGGAC 60.179 60.0 0.0 0.0 39.0 3.85 F
1284 1442 0.181587 TTTTGTGCTCGTTCCCTGGA 59.818 50.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2036 2520 0.254462 TCTTGAACACCCTGCACACA 59.746 50.0 0.0 0.0 0.0 3.72 R
3210 3770 0.036164 TCGCACCATACCTGTTGCTT 59.964 50.0 0.0 0.0 0.0 3.91 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
22 23 5.266733 TGTACGACTTTGTAAGGTCTTGT 57.733 39.130 5.52 0.63 0.00 3.16
23 24 5.045215 TGTACGACTTTGTAAGGTCTTGTG 58.955 41.667 5.52 0.00 0.00 3.33
24 25 4.133013 ACGACTTTGTAAGGTCTTGTGT 57.867 40.909 5.52 0.00 0.00 3.72
25 26 3.869246 ACGACTTTGTAAGGTCTTGTGTG 59.131 43.478 5.52 0.00 0.00 3.82
26 27 4.116961 CGACTTTGTAAGGTCTTGTGTGA 58.883 43.478 5.52 0.00 0.00 3.58
27 28 4.569162 CGACTTTGTAAGGTCTTGTGTGAA 59.431 41.667 5.52 0.00 0.00 3.18
28 29 5.236478 CGACTTTGTAAGGTCTTGTGTGAAT 59.764 40.000 5.52 0.00 0.00 2.57
29 30 6.422701 CGACTTTGTAAGGTCTTGTGTGAATA 59.577 38.462 5.52 0.00 0.00 1.75
30 31 7.042321 CGACTTTGTAAGGTCTTGTGTGAATAA 60.042 37.037 5.52 0.00 0.00 1.40
31 32 8.691661 ACTTTGTAAGGTCTTGTGTGAATAAT 57.308 30.769 0.00 0.00 0.00 1.28
32 33 9.131791 ACTTTGTAAGGTCTTGTGTGAATAATT 57.868 29.630 0.00 0.00 0.00 1.40
50 51 9.695526 TGAATAATTAATAAAGTGGATGCATGC 57.304 29.630 11.82 11.82 0.00 4.06
51 52 9.695526 GAATAATTAATAAAGTGGATGCATGCA 57.304 29.630 25.04 25.04 0.00 3.96
60 61 2.996444 GATGCATGCATCGTCCAGA 58.004 52.632 37.33 7.98 42.55 3.86
61 62 1.520494 GATGCATGCATCGTCCAGAT 58.480 50.000 37.33 14.34 42.55 2.90
69 70 1.445095 ATCGTCCAGATGCAGAGGC 59.555 57.895 0.00 0.00 38.36 4.70
70 71 2.037620 ATCGTCCAGATGCAGAGGCC 62.038 60.000 0.00 0.00 38.36 5.19
71 72 2.202987 GTCCAGATGCAGAGGCCG 60.203 66.667 0.00 0.00 40.13 6.13
72 73 3.473647 TCCAGATGCAGAGGCCGG 61.474 66.667 0.00 0.00 40.13 6.13
73 74 4.559063 CCAGATGCAGAGGCCGGG 62.559 72.222 2.18 0.00 40.13 5.73
74 75 4.559063 CAGATGCAGAGGCCGGGG 62.559 72.222 2.18 0.00 40.13 5.73
80 81 3.787001 CAGAGGCCGGGGGTCTTC 61.787 72.222 2.18 0.00 38.01 2.87
85 86 3.009714 GCCGGGGGTCTTCCTCTT 61.010 66.667 2.18 0.00 33.94 2.85
86 87 2.603652 GCCGGGGGTCTTCCTCTTT 61.604 63.158 2.18 0.00 33.94 2.52
87 88 2.075837 CCGGGGGTCTTCCTCTTTT 58.924 57.895 0.00 0.00 33.94 2.27
88 89 1.282382 CCGGGGGTCTTCCTCTTTTA 58.718 55.000 0.00 0.00 33.94 1.52
89 90 1.631898 CCGGGGGTCTTCCTCTTTTAA 59.368 52.381 0.00 0.00 33.94 1.52
90 91 2.040679 CCGGGGGTCTTCCTCTTTTAAA 59.959 50.000 0.00 0.00 33.94 1.52
91 92 3.499021 CCGGGGGTCTTCCTCTTTTAAAA 60.499 47.826 0.00 0.00 33.94 1.52
92 93 4.146564 CGGGGGTCTTCCTCTTTTAAAAA 58.853 43.478 1.66 0.00 33.94 1.94
117 118 6.842437 AAGCATATACTCATACTCGATGGT 57.158 37.500 0.00 0.00 36.08 3.55
181 182 4.057406 TCCACTTTGTTGCATCTTTTGG 57.943 40.909 0.00 0.00 0.00 3.28
316 321 5.180868 ACCACCAATCTAGACGTACGATATC 59.819 44.000 24.41 9.41 0.00 1.63
317 322 5.314409 CACCAATCTAGACGTACGATATCG 58.686 45.833 24.41 23.18 46.33 2.92
318 323 5.119743 CACCAATCTAGACGTACGATATCGA 59.880 44.000 30.75 12.15 43.02 3.59
319 324 5.873712 ACCAATCTAGACGTACGATATCGAT 59.126 40.000 30.75 16.96 43.02 3.59
320 325 6.035866 ACCAATCTAGACGTACGATATCGATC 59.964 42.308 30.75 19.90 43.02 3.69
331 336 2.419649 GATATCGATCGAGTACGTGCG 58.580 52.381 23.84 0.00 40.69 5.34
332 337 1.490621 TATCGATCGAGTACGTGCGA 58.509 50.000 23.84 11.36 44.09 5.10
334 339 1.490621 TCGATCGAGTACGTGCGATA 58.509 50.000 15.15 5.95 46.13 2.92
335 340 2.064014 TCGATCGAGTACGTGCGATAT 58.936 47.619 15.15 5.35 46.13 1.63
397 404 1.016130 AGAGTGCAAAGCCGATCACG 61.016 55.000 0.00 0.00 34.84 4.35
483 495 2.750948 ACAGTGTCGTAATTCGTTGCT 58.249 42.857 0.00 0.00 40.80 3.91
484 496 3.904571 ACAGTGTCGTAATTCGTTGCTA 58.095 40.909 0.00 0.00 40.80 3.49
485 497 3.918591 ACAGTGTCGTAATTCGTTGCTAG 59.081 43.478 0.00 0.00 40.80 3.42
486 498 3.918591 CAGTGTCGTAATTCGTTGCTAGT 59.081 43.478 0.00 0.00 40.80 2.57
487 499 5.090757 CAGTGTCGTAATTCGTTGCTAGTA 58.909 41.667 0.00 0.00 40.80 1.82
488 500 5.227391 CAGTGTCGTAATTCGTTGCTAGTAG 59.773 44.000 0.00 0.00 40.80 2.57
489 501 5.091431 GTGTCGTAATTCGTTGCTAGTAGT 58.909 41.667 0.00 0.00 40.80 2.73
501 513 7.524912 TCGTTGCTAGTAGTACTAAGAAACTG 58.475 38.462 17.72 13.12 29.00 3.16
519 531 3.846360 ACTGTAGTTATTCCTGTCACGC 58.154 45.455 0.00 0.00 0.00 5.34
555 573 3.236003 AACAGAGGGGTCGCCGTTC 62.236 63.158 0.00 0.00 0.00 3.95
618 636 1.894756 TTGGCCGGAAAACACGAGG 60.895 57.895 5.05 0.00 0.00 4.63
620 638 2.668550 GCCGGAAAACACGAGGCT 60.669 61.111 5.05 0.00 44.06 4.58
622 640 1.004918 CCGGAAAACACGAGGCTCT 60.005 57.895 13.50 0.00 0.00 4.09
631 649 0.240145 CACGAGGCTCTCACGTACAA 59.760 55.000 13.50 0.00 38.47 2.41
632 650 1.135373 CACGAGGCTCTCACGTACAAT 60.135 52.381 13.50 0.00 38.47 2.71
649 667 0.686441 AATGACCCATGCATGCAGCT 60.686 50.000 26.69 7.33 45.94 4.24
707 725 2.125269 CCTTTTCGCCGGATCCGT 60.125 61.111 31.22 0.00 37.81 4.69
708 726 1.142314 CCTTTTCGCCGGATCCGTA 59.858 57.895 31.22 14.63 37.81 4.02
855 874 1.827789 ACATGTGCGCCCTTGTTGT 60.828 52.632 4.18 0.00 0.00 3.32
872 893 7.417612 CCTTGTTGTTGATATATAAGCACACC 58.582 38.462 0.00 0.00 0.00 4.16
875 896 7.266400 TGTTGTTGATATATAAGCACACCGTA 58.734 34.615 0.00 0.00 0.00 4.02
951 979 2.814604 ACTGTGCTGTGCAGTCGA 59.185 55.556 0.00 0.00 42.90 4.20
955 983 3.911698 TGCTGTGCAGTCGACCGT 61.912 61.111 13.01 0.00 33.32 4.83
957 985 2.335011 CTGTGCAGTCGACCGTCA 59.665 61.111 13.01 4.87 0.00 4.35
992 1021 1.521681 GCCGGAATCGAAGGTCAGG 60.522 63.158 5.05 8.35 39.00 3.86
993 1022 1.956629 GCCGGAATCGAAGGTCAGGA 61.957 60.000 5.05 0.00 39.00 3.86
994 1023 0.179108 CCGGAATCGAAGGTCAGGAC 60.179 60.000 0.00 0.00 39.00 3.85
995 1024 0.818296 CGGAATCGAAGGTCAGGACT 59.182 55.000 0.00 0.00 39.00 3.85
996 1025 1.202313 CGGAATCGAAGGTCAGGACTC 60.202 57.143 0.00 0.00 39.00 3.36
997 1026 1.825474 GGAATCGAAGGTCAGGACTCA 59.175 52.381 0.00 0.00 0.00 3.41
998 1027 2.159170 GGAATCGAAGGTCAGGACTCAG 60.159 54.545 0.00 0.00 0.00 3.35
1097 1126 1.166989 GTCTCCGACTTCTCCTTCGT 58.833 55.000 0.00 0.00 33.23 3.85
1104 1133 0.826672 ACTTCTCCTTCGTCACCCGT 60.827 55.000 0.00 0.00 37.94 5.28
1163 1192 2.570302 GGGACCTTCCAAGTAAGTGCTA 59.430 50.000 0.00 0.00 38.64 3.49
1165 1194 3.261137 GGACCTTCCAAGTAAGTGCTAGT 59.739 47.826 0.00 0.00 36.28 2.57
1167 1196 4.895961 ACCTTCCAAGTAAGTGCTAGTTC 58.104 43.478 0.00 0.00 0.00 3.01
1173 1202 4.452455 CCAAGTAAGTGCTAGTTCCAGTTG 59.548 45.833 0.00 0.00 0.00 3.16
1208 1243 2.058798 CGTTGCACATTCACTCGTACT 58.941 47.619 0.00 0.00 0.00 2.73
1217 1375 6.755141 GCACATTCACTCGTACTATAAGGAAA 59.245 38.462 0.00 0.00 0.00 3.13
1242 1400 8.844441 AAAAACTGATTTGAATTTGTGCAATG 57.156 26.923 0.00 0.00 0.00 2.82
1252 1410 1.993542 TTGTGCAATGCGCCAATTAG 58.006 45.000 16.68 0.00 41.33 1.73
1253 1411 0.887247 TGTGCAATGCGCCAATTAGT 59.113 45.000 16.68 0.00 41.33 2.24
1257 1415 1.798813 GCAATGCGCCAATTAGTCACC 60.799 52.381 4.18 0.00 32.94 4.02
1280 1438 6.485648 ACCTATATATTTTTGTGCTCGTTCCC 59.514 38.462 0.00 0.00 0.00 3.97
1281 1439 6.710744 CCTATATATTTTTGTGCTCGTTCCCT 59.289 38.462 0.00 0.00 0.00 4.20
1283 1441 1.028905 TTTTTGTGCTCGTTCCCTGG 58.971 50.000 0.00 0.00 0.00 4.45
1284 1442 0.181587 TTTTGTGCTCGTTCCCTGGA 59.818 50.000 0.00 0.00 0.00 3.86
1288 1446 1.626321 TGTGCTCGTTCCCTGGATTTA 59.374 47.619 0.00 0.00 0.00 1.40
1377 1538 1.804748 GTTTACTTGTGGCTTCCCTCG 59.195 52.381 0.00 0.00 0.00 4.63
1513 1989 4.727475 AGCGTACTAAAACTTAGTCGTCC 58.273 43.478 2.42 0.00 0.00 4.79
1700 2178 4.467084 ACCGGCATCCGCACGAAT 62.467 61.111 0.00 0.00 46.86 3.34
1793 2271 2.420022 CGGCATGAAGAAAACCCTAGTG 59.580 50.000 0.00 0.00 0.00 2.74
1859 2337 1.262417 TGCACGAGTACAGGATCCAA 58.738 50.000 15.82 0.00 0.00 3.53
1968 2451 9.462174 TGTTGCAACAAATATTCTAAGTTTGAG 57.538 29.630 29.36 0.00 36.58 3.02
2007 2491 4.647424 TGGTTGTGTGAAATGTTCCTTC 57.353 40.909 0.00 0.00 0.00 3.46
2036 2520 3.154710 GTTTTCGAAGGAGGAATGGGTT 58.845 45.455 0.00 0.00 0.00 4.11
2060 2544 1.490490 TGCAGGGTGTTCAAGAAGAGT 59.510 47.619 0.00 0.00 0.00 3.24
2122 2606 2.819595 CTCCCCATGCAACGACGG 60.820 66.667 0.00 0.00 0.00 4.79
2123 2607 3.605749 CTCCCCATGCAACGACGGT 62.606 63.158 0.00 0.00 0.00 4.83
2522 3006 7.067129 ACCTTCTGATCAATTCATCAGTTCATG 59.933 37.037 17.62 7.20 46.91 3.07
2524 3008 6.655930 TCTGATCAATTCATCAGTTCATGGA 58.344 36.000 17.62 0.00 46.91 3.41
2660 3144 9.872757 TCAATTAAAAGTTTAACTAGACAAGCG 57.127 29.630 0.00 0.00 35.65 4.68
2661 3145 9.659830 CAATTAAAAGTTTAACTAGACAAGCGT 57.340 29.630 0.00 0.00 35.65 5.07
2755 3299 1.476488 GTTGGCCGGCTGATATTTTGT 59.524 47.619 28.56 0.00 0.00 2.83
2756 3300 1.102154 TGGCCGGCTGATATTTTGTG 58.898 50.000 28.56 0.00 0.00 3.33
2762 3306 4.202050 GCCGGCTGATATTTTGTGAAGATT 60.202 41.667 22.15 0.00 0.00 2.40
2763 3307 5.276270 CCGGCTGATATTTTGTGAAGATTG 58.724 41.667 0.00 0.00 0.00 2.67
2789 3333 1.135746 GTCGACAACCGTTCGATCTCT 60.136 52.381 11.55 0.00 38.19 3.10
2791 3335 2.030540 TCGACAACCGTTCGATCTCTTT 60.031 45.455 0.00 0.00 39.75 2.52
2869 3413 1.898094 AGCCATTGCAACGCAGACA 60.898 52.632 19.41 0.00 40.61 3.41
2888 3432 2.289631 ACAATGTTGCGGTCTCTCATCA 60.290 45.455 0.00 0.00 0.00 3.07
2896 3440 2.932622 GCGGTCTCTCATCACAACACAT 60.933 50.000 0.00 0.00 0.00 3.21
2913 3457 1.259609 CATGCAACATTGTGGTCCCT 58.740 50.000 0.00 0.00 0.00 4.20
2915 3459 0.888736 TGCAACATTGTGGTCCCTCG 60.889 55.000 0.00 0.00 0.00 4.63
2990 3546 0.806868 ACTTCATCACAGCATTGCCG 59.193 50.000 4.70 0.00 0.00 5.69
3003 3559 1.469703 CATTGCCGACATTGCAGAAGA 59.530 47.619 0.00 0.00 40.35 2.87
3010 3566 2.279741 GACATTGCAGAAGACGCCATA 58.720 47.619 0.00 0.00 0.00 2.74
3020 3576 1.519408 AGACGCCATACAACAACACC 58.481 50.000 0.00 0.00 0.00 4.16
3040 3596 0.457035 GACATTGTAGTCGCCCCGTA 59.543 55.000 0.00 0.00 0.00 4.02
3058 3614 2.411031 CGTACAACAACACCGAGATTGC 60.411 50.000 0.00 0.00 0.00 3.56
3061 3617 1.603802 CAACAACACCGAGATTGCAGT 59.396 47.619 0.00 0.00 0.00 4.40
3079 3635 3.792401 CAGTCATCGCCACCTTAACATA 58.208 45.455 0.00 0.00 0.00 2.29
3089 3645 4.097892 GCCACCTTAACATAACCCTCATTG 59.902 45.833 0.00 0.00 0.00 2.82
3090 3646 4.097892 CCACCTTAACATAACCCTCATTGC 59.902 45.833 0.00 0.00 0.00 3.56
3123 3679 3.846360 CCCTTTTTCGTCGATGACTACT 58.154 45.455 6.88 0.00 0.00 2.57
3124 3680 3.858238 CCCTTTTTCGTCGATGACTACTC 59.142 47.826 6.88 0.00 0.00 2.59
3125 3681 4.482386 CCTTTTTCGTCGATGACTACTCA 58.518 43.478 6.88 0.00 0.00 3.41
3160 3720 1.301716 GACCCTGACAAGCTCGCAA 60.302 57.895 0.00 0.00 0.00 4.85
3162 3722 2.328099 CCCTGACAAGCTCGCAACC 61.328 63.158 0.00 0.00 0.00 3.77
3172 3732 2.915659 TCGCAACCCTGGAGTCGT 60.916 61.111 0.00 0.00 0.00 4.34
3185 3745 1.934220 GAGTCGTCCACCATCGCAGA 61.934 60.000 0.00 0.00 45.75 4.26
3186 3746 1.141881 GTCGTCCACCATCGCAGAT 59.858 57.895 0.00 0.00 45.12 2.90
3187 3747 0.460284 GTCGTCCACCATCGCAGATT 60.460 55.000 0.00 0.00 45.12 2.40
3188 3748 0.179111 TCGTCCACCATCGCAGATTC 60.179 55.000 0.00 0.00 45.12 2.52
3189 3749 1.482621 CGTCCACCATCGCAGATTCG 61.483 60.000 0.00 0.00 45.12 3.34
3190 3750 1.521457 TCCACCATCGCAGATTCGC 60.521 57.895 0.00 0.00 45.12 4.70
3191 3751 1.815003 CCACCATCGCAGATTCGCA 60.815 57.895 0.00 0.00 45.12 5.10
3192 3752 1.640069 CACCATCGCAGATTCGCAG 59.360 57.895 0.00 0.00 45.12 5.18
3193 3753 1.086067 CACCATCGCAGATTCGCAGT 61.086 55.000 0.00 0.00 45.12 4.40
3194 3754 1.086067 ACCATCGCAGATTCGCAGTG 61.086 55.000 0.00 0.00 45.12 3.66
3210 3770 0.322277 AGTGCCGACGACCTCTCTAA 60.322 55.000 0.00 0.00 0.00 2.10
3212 3772 0.809385 TGCCGACGACCTCTCTAAAG 59.191 55.000 0.00 0.00 0.00 1.85
3215 3775 1.201647 CCGACGACCTCTCTAAAGCAA 59.798 52.381 0.00 0.00 0.00 3.91
3217 3777 2.351447 CGACGACCTCTCTAAAGCAACA 60.351 50.000 0.00 0.00 0.00 3.33
3237 3797 4.155733 TATGGTGCGACCCCAGCG 62.156 66.667 3.33 0.00 37.50 5.18
3250 3810 2.320587 CCAGCGAGCTCACAACACC 61.321 63.158 15.40 0.00 0.00 4.16
3251 3811 1.595109 CAGCGAGCTCACAACACCA 60.595 57.895 15.40 0.00 0.00 4.17
3267 3827 2.260154 CCAGTGCGCCACATCACAA 61.260 57.895 4.18 0.00 36.74 3.33
3286 3846 1.459450 ACAGTGGTGTTGTTGTGACC 58.541 50.000 0.00 0.00 30.30 4.02
3305 3865 2.669569 GCAAGCTTGGAGCACCGA 60.670 61.111 27.10 0.00 45.56 4.69
3326 3886 2.109799 CCTCCTATGCACCAGCGG 59.890 66.667 0.00 0.00 46.23 5.52
3335 3895 2.186532 TGCACCAGCGGTTATGTTAA 57.813 45.000 0.00 0.00 46.23 2.01
3342 3902 1.910671 AGCGGTTATGTTAAGACCCCA 59.089 47.619 0.00 0.00 0.00 4.96
3360 3920 1.075425 CAGTGAGCTCGTAGCACAGC 61.075 60.000 9.64 0.00 45.56 4.40
3376 3936 2.824041 GCCGTCGCCCACAATCAT 60.824 61.111 0.00 0.00 0.00 2.45
3414 3974 1.606601 AGCAGTCACCGACCTAGCA 60.607 57.895 6.59 0.00 32.18 3.49
3436 3996 0.469917 ATGGTCATCCCCTTGTAGCG 59.530 55.000 0.00 0.00 0.00 4.26
3461 4021 2.182842 CCCGGCTTGTAGCAGCATC 61.183 63.158 0.00 0.00 44.75 3.91
3462 4022 2.182842 CCGGCTTGTAGCAGCATCC 61.183 63.158 0.00 0.00 44.75 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.045215 CACAAGACCTTACAAAGTCGTACA 58.955 41.667 0.00 0.00 0.00 2.90
1 2 5.045872 ACACAAGACCTTACAAAGTCGTAC 58.954 41.667 0.00 0.00 0.00 3.67
2 3 5.045215 CACACAAGACCTTACAAAGTCGTA 58.955 41.667 0.00 0.00 0.00 3.43
4 5 4.116961 TCACACAAGACCTTACAAAGTCG 58.883 43.478 0.00 0.00 0.00 4.18
5 6 6.619801 ATTCACACAAGACCTTACAAAGTC 57.380 37.500 0.00 0.00 0.00 3.01
6 7 8.691661 ATTATTCACACAAGACCTTACAAAGT 57.308 30.769 0.00 0.00 0.00 2.66
24 25 9.695526 GCATGCATCCACTTTATTAATTATTCA 57.304 29.630 14.21 0.00 0.00 2.57
25 26 9.695526 TGCATGCATCCACTTTATTAATTATTC 57.304 29.630 18.46 0.00 0.00 1.75
27 28 9.865321 GATGCATGCATCCACTTTATTAATTAT 57.135 29.630 39.28 12.91 45.06 1.28
42 43 1.197036 CATCTGGACGATGCATGCATC 59.803 52.381 39.25 39.25 46.71 3.91
43 44 1.235724 CATCTGGACGATGCATGCAT 58.764 50.000 32.66 32.66 42.75 3.96
44 45 2.697819 CATCTGGACGATGCATGCA 58.302 52.632 25.04 25.04 42.75 3.96
51 52 1.445095 GCCTCTGCATCTGGACGAT 59.555 57.895 0.00 0.00 37.47 3.73
52 53 2.725312 GGCCTCTGCATCTGGACGA 61.725 63.158 0.00 0.00 40.13 4.20
53 54 2.202987 GGCCTCTGCATCTGGACG 60.203 66.667 0.00 0.00 40.13 4.79
54 55 2.202987 CGGCCTCTGCATCTGGAC 60.203 66.667 0.00 0.35 40.13 4.02
55 56 3.473647 CCGGCCTCTGCATCTGGA 61.474 66.667 0.00 0.00 40.13 3.86
56 57 4.559063 CCCGGCCTCTGCATCTGG 62.559 72.222 0.00 0.00 40.13 3.86
57 58 4.559063 CCCCGGCCTCTGCATCTG 62.559 72.222 0.00 0.00 40.13 2.90
63 64 3.787001 GAAGACCCCCGGCCTCTG 61.787 72.222 0.00 0.00 0.00 3.35
68 69 2.138453 AAAAGAGGAAGACCCCCGGC 62.138 60.000 0.00 0.00 36.73 6.13
69 70 1.282382 TAAAAGAGGAAGACCCCCGG 58.718 55.000 0.00 0.00 36.73 5.73
70 71 3.428413 TTTAAAAGAGGAAGACCCCCG 57.572 47.619 0.00 0.00 36.73 5.73
91 92 8.150945 ACCATCGAGTATGAGTATATGCTTTTT 58.849 33.333 0.00 0.00 37.86 1.94
92 93 7.671302 ACCATCGAGTATGAGTATATGCTTTT 58.329 34.615 0.00 0.00 37.86 2.27
93 94 7.233389 ACCATCGAGTATGAGTATATGCTTT 57.767 36.000 0.00 0.00 37.86 3.51
94 95 6.842437 ACCATCGAGTATGAGTATATGCTT 57.158 37.500 0.00 0.00 37.86 3.91
95 96 7.939784 TTACCATCGAGTATGAGTATATGCT 57.060 36.000 0.00 0.00 37.86 3.79
96 97 9.587772 AATTTACCATCGAGTATGAGTATATGC 57.412 33.333 0.00 0.00 37.86 3.14
106 107 8.677148 ACATGCTAAAATTTACCATCGAGTAT 57.323 30.769 0.00 0.00 0.00 2.12
117 118 8.250332 GGAGGAAATGTGACATGCTAAAATTTA 58.750 33.333 0.00 0.00 0.00 1.40
181 182 3.632189 GAGCCGATCCAATTAACAATGC 58.368 45.455 0.00 0.00 0.00 3.56
229 234 4.516321 TCGATCATGCAGGTTTGATTATGG 59.484 41.667 0.00 0.00 32.84 2.74
316 321 2.505608 ATATCGCACGTACTCGATCG 57.494 50.000 18.44 9.36 43.42 3.69
317 322 5.131890 GCTATATATCGCACGTACTCGATC 58.868 45.833 18.44 4.81 43.42 3.69
318 323 4.317909 CGCTATATATCGCACGTACTCGAT 60.318 45.833 18.76 18.76 45.87 3.59
319 324 3.000376 CGCTATATATCGCACGTACTCGA 60.000 47.826 9.63 8.74 40.62 4.04
320 325 3.270123 CGCTATATATCGCACGTACTCG 58.730 50.000 9.63 0.00 43.34 4.18
330 335 5.338297 GTGAATCGAGATGCGCTATATATCG 59.662 44.000 14.78 14.78 39.76 2.92
331 336 5.627367 GGTGAATCGAGATGCGCTATATATC 59.373 44.000 9.73 2.22 40.61 1.63
332 337 5.067805 TGGTGAATCGAGATGCGCTATATAT 59.932 40.000 9.73 0.00 40.61 0.86
333 338 4.398044 TGGTGAATCGAGATGCGCTATATA 59.602 41.667 9.73 0.00 40.61 0.86
334 339 3.193479 TGGTGAATCGAGATGCGCTATAT 59.807 43.478 9.73 0.00 40.61 0.86
335 340 2.556622 TGGTGAATCGAGATGCGCTATA 59.443 45.455 9.73 0.00 40.61 1.31
347 354 2.169832 AAGTGACTGGTGGTGAATCG 57.830 50.000 0.00 0.00 0.00 3.34
446 457 5.777802 ACACTGTACTTGAGTTGATGAGAG 58.222 41.667 0.00 0.00 0.00 3.20
501 513 2.190981 CGGCGTGACAGGAATAACTAC 58.809 52.381 0.00 0.00 0.00 2.73
528 540 1.078143 CCCCTCTGTTGCCAGCTAC 60.078 63.158 0.00 0.00 38.66 3.58
537 549 3.236003 GAACGGCGACCCCTCTGTT 62.236 63.158 16.62 0.00 34.75 3.16
565 583 4.577246 CCACCGGAGCTAGCTCGC 62.577 72.222 32.78 24.92 43.59 5.03
566 584 3.905678 CCCACCGGAGCTAGCTCG 61.906 72.222 32.78 26.84 43.59 5.03
567 585 2.760385 ACCCACCGGAGCTAGCTC 60.760 66.667 32.65 32.65 42.04 4.09
568 586 3.077556 CACCCACCGGAGCTAGCT 61.078 66.667 19.45 19.45 0.00 3.32
618 636 1.067142 TGGGTCATTGTACGTGAGAGC 60.067 52.381 0.00 0.00 0.00 4.09
620 638 2.676750 GCATGGGTCATTGTACGTGAGA 60.677 50.000 0.00 0.00 0.00 3.27
622 640 1.002544 TGCATGGGTCATTGTACGTGA 59.997 47.619 0.00 0.00 0.00 4.35
631 649 1.076265 AGCTGCATGCATGGGTCAT 60.076 52.632 27.34 1.29 45.94 3.06
632 650 1.751544 GAGCTGCATGCATGGGTCA 60.752 57.895 27.34 15.83 45.94 4.02
649 667 4.365505 TCGATTGCACGCGTGGGA 62.366 61.111 37.47 18.86 0.00 4.37
855 874 7.396339 AGGAGATACGGTGTGCTTATATATCAA 59.604 37.037 0.00 0.00 0.00 2.57
872 893 1.688735 TCCATGGCAGAAGGAGATACG 59.311 52.381 6.96 0.00 0.00 3.06
875 896 1.347050 CGATCCATGGCAGAAGGAGAT 59.653 52.381 6.96 0.00 34.40 2.75
951 979 3.753434 CGCTGGCTCTCTGACGGT 61.753 66.667 0.00 0.00 30.99 4.83
955 983 3.385384 CACCCGCTGGCTCTCTGA 61.385 66.667 0.00 0.00 33.59 3.27
992 1021 1.406860 GCCCTCCTCCATCCTGAGTC 61.407 65.000 0.00 0.00 0.00 3.36
993 1022 1.383803 GCCCTCCTCCATCCTGAGT 60.384 63.158 0.00 0.00 0.00 3.41
994 1023 2.146061 GGCCCTCCTCCATCCTGAG 61.146 68.421 0.00 0.00 0.00 3.35
995 1024 2.040464 GGCCCTCCTCCATCCTGA 60.040 66.667 0.00 0.00 0.00 3.86
996 1025 1.695597 AAGGCCCTCCTCCATCCTG 60.696 63.158 0.00 0.00 43.40 3.86
997 1026 1.385206 GAAGGCCCTCCTCCATCCT 60.385 63.158 0.00 0.00 43.40 3.24
998 1027 2.456443 GGAAGGCCCTCCTCCATCC 61.456 68.421 13.67 0.00 43.40 3.51
1163 1192 1.972872 CTGGAACTGCAACTGGAACT 58.027 50.000 0.00 0.00 0.00 3.01
1217 1375 7.432838 GCATTGCACAAATTCAAATCAGTTTTT 59.567 29.630 3.15 0.00 0.00 1.94
1221 1379 4.150980 CGCATTGCACAAATTCAAATCAGT 59.849 37.500 9.69 0.00 0.00 3.41
1252 1410 7.478520 ACGAGCACAAAAATATATAGGTGAC 57.521 36.000 0.00 3.21 0.00 3.67
1253 1411 7.225931 GGAACGAGCACAAAAATATATAGGTGA 59.774 37.037 0.00 0.00 0.00 4.02
1257 1415 7.307989 CCAGGGAACGAGCACAAAAATATATAG 60.308 40.741 0.00 0.00 0.00 1.31
1513 1989 3.713858 TGCCAACTTGACATTGACAAG 57.286 42.857 21.82 21.82 46.69 3.16
1573 2049 2.485266 TAGTGCACGTACATCCATCG 57.515 50.000 12.01 0.00 0.00 3.84
1859 2337 4.290942 TGGGTTTGTATGGGAACTTGTTT 58.709 39.130 0.00 0.00 0.00 2.83
1911 2389 1.609208 AGTTGCAGTTACTTGGCCTG 58.391 50.000 3.32 0.00 0.00 4.85
1941 2423 9.809096 TCAAACTTAGAATATTTGTTGCAACAA 57.191 25.926 35.10 35.10 46.35 2.83
1968 2451 9.326413 ACACAACCATATTAGTAACAATCTAGC 57.674 33.333 0.00 0.00 0.00 3.42
2007 2491 2.223377 CCTCCTTCGAAAACCAAAGACG 59.777 50.000 0.00 0.00 0.00 4.18
2036 2520 0.254462 TCTTGAACACCCTGCACACA 59.746 50.000 0.00 0.00 0.00 3.72
2060 2544 3.386078 GGTGCCTCATCTTCACTATCTGA 59.614 47.826 0.00 0.00 0.00 3.27
2462 2946 2.282391 TGCATTTCCAGCTGCGGT 60.282 55.556 8.66 0.00 41.32 5.68
2659 3143 2.858344 GACATAGATCAACCGAACCACG 59.142 50.000 0.00 0.00 42.18 4.94
2660 3144 4.113354 GAGACATAGATCAACCGAACCAC 58.887 47.826 0.00 0.00 0.00 4.16
2661 3145 4.023980 AGAGACATAGATCAACCGAACCA 58.976 43.478 0.00 0.00 0.00 3.67
2755 3299 1.069978 TGTCGACCTGCACAATCTTCA 59.930 47.619 14.12 0.00 0.00 3.02
2756 3300 1.795768 TGTCGACCTGCACAATCTTC 58.204 50.000 14.12 0.00 0.00 2.87
2762 3306 2.279851 CGGTTGTCGACCTGCACA 60.280 61.111 14.12 0.00 46.92 4.57
2763 3307 1.828331 GAACGGTTGTCGACCTGCAC 61.828 60.000 14.12 4.47 46.92 4.57
2791 3335 2.942804 TGTGATCCAGTTGCTCCAAAA 58.057 42.857 0.00 0.00 0.00 2.44
2810 3354 7.116233 CCATGTTGCAATGACAATGATATGATG 59.884 37.037 0.59 0.00 0.00 3.07
2869 3413 2.289631 TGTGATGAGAGACCGCAACATT 60.290 45.455 0.00 0.00 29.07 2.71
2888 3432 2.168106 ACCACAATGTTGCATGTGTTGT 59.832 40.909 15.14 8.82 44.21 3.32
2896 3440 0.888736 CGAGGGACCACAATGTTGCA 60.889 55.000 0.00 0.00 0.00 4.08
2913 3457 2.104530 TCGTCCGTGTTGCAACGA 59.895 55.556 23.79 14.59 46.49 3.85
2915 3459 2.244382 CGTCGTCCGTGTTGCAAC 59.756 61.111 22.83 22.83 0.00 4.17
2958 3502 2.049063 GAAGTCCGACAGCGCAGT 60.049 61.111 11.47 8.04 35.83 4.40
2959 3503 1.416813 GATGAAGTCCGACAGCGCAG 61.417 60.000 11.47 3.33 35.83 5.18
2960 3504 1.446099 GATGAAGTCCGACAGCGCA 60.446 57.895 11.47 0.00 35.83 6.09
2961 3505 1.446099 TGATGAAGTCCGACAGCGC 60.446 57.895 0.00 0.00 35.83 5.92
2965 3521 0.678950 TGCTGTGATGAAGTCCGACA 59.321 50.000 0.40 0.00 0.00 4.35
2990 3546 1.089920 ATGGCGTCTTCTGCAATGTC 58.910 50.000 0.00 0.00 0.00 3.06
3001 3557 1.519408 GGTGTTGTTGTATGGCGTCT 58.481 50.000 0.00 0.00 0.00 4.18
3003 3559 0.249953 TCGGTGTTGTTGTATGGCGT 60.250 50.000 0.00 0.00 0.00 5.68
3010 3566 3.537580 ACTACAATGTCGGTGTTGTTGT 58.462 40.909 0.00 7.08 38.70 3.32
3040 3596 1.603802 CTGCAATCTCGGTGTTGTTGT 59.396 47.619 0.00 0.00 0.00 3.32
3058 3614 2.093306 TGTTAAGGTGGCGATGACTG 57.907 50.000 0.00 0.00 0.00 3.51
3061 3617 3.537580 GGTTATGTTAAGGTGGCGATGA 58.462 45.455 0.00 0.00 0.00 2.92
3079 3635 2.354902 GCCAACTGCAATGAGGGTT 58.645 52.632 0.85 0.00 40.77 4.11
3112 3668 0.378610 CGCTGCTGAGTAGTCATCGA 59.621 55.000 0.00 0.00 30.18 3.59
3123 3679 0.673333 CACAACATACCCGCTGCTGA 60.673 55.000 0.00 0.00 0.00 4.26
3124 3680 0.673333 TCACAACATACCCGCTGCTG 60.673 55.000 0.00 0.00 0.00 4.41
3125 3681 0.673644 GTCACAACATACCCGCTGCT 60.674 55.000 0.00 0.00 0.00 4.24
3147 3707 1.597854 CAGGGTTGCGAGCTTGTCA 60.598 57.895 7.09 0.00 0.00 3.58
3149 3709 2.281761 CCAGGGTTGCGAGCTTGT 60.282 61.111 13.57 0.00 0.00 3.16
3172 3732 1.521457 GCGAATCTGCGATGGTGGA 60.521 57.895 0.00 0.00 0.00 4.02
3185 3745 2.809601 GTCGTCGGCACTGCGAAT 60.810 61.111 0.00 0.00 34.54 3.34
3189 3749 3.973267 GAGAGGTCGTCGGCACTGC 62.973 68.421 0.00 0.00 0.00 4.40
3190 3750 1.025113 TAGAGAGGTCGTCGGCACTG 61.025 60.000 0.00 0.00 0.00 3.66
3191 3751 0.322277 TTAGAGAGGTCGTCGGCACT 60.322 55.000 0.00 0.00 0.00 4.40
3192 3752 0.524862 TTTAGAGAGGTCGTCGGCAC 59.475 55.000 0.00 0.00 0.00 5.01
3193 3753 0.809385 CTTTAGAGAGGTCGTCGGCA 59.191 55.000 0.00 0.00 0.00 5.69
3194 3754 0.525882 GCTTTAGAGAGGTCGTCGGC 60.526 60.000 0.00 0.00 0.00 5.54
3210 3770 0.036164 TCGCACCATACCTGTTGCTT 59.964 50.000 0.00 0.00 0.00 3.91
3212 3772 1.644786 GGTCGCACCATACCTGTTGC 61.645 60.000 1.01 0.00 38.42 4.17
3215 3775 2.666098 GGGGTCGCACCATACCTGT 61.666 63.158 7.49 0.00 41.02 4.00
3217 3777 2.285069 TGGGGTCGCACCATACCT 60.285 61.111 7.49 0.00 41.02 3.08
3237 3797 1.835483 CGCACTGGTGTTGTGAGCTC 61.835 60.000 6.82 6.82 37.60 4.09
3242 3802 3.208383 TGGCGCACTGGTGTTGTG 61.208 61.111 10.83 0.00 38.36 3.33
3243 3803 3.209097 GTGGCGCACTGGTGTTGT 61.209 61.111 10.83 0.00 0.00 3.32
3250 3810 1.081906 GTTGTGATGTGGCGCACTG 60.082 57.895 10.83 0.00 36.05 3.66
3251 3811 1.509644 CTGTTGTGATGTGGCGCACT 61.510 55.000 10.83 0.00 36.05 4.40
3267 3827 1.004277 AGGTCACAACAACACCACTGT 59.996 47.619 0.00 0.00 31.99 3.55
3286 3846 2.960170 GGTGCTCCAAGCTTGCAG 59.040 61.111 21.43 17.42 42.97 4.41
3305 3865 0.471617 GCTGGTGCATAGGAGGTCAT 59.528 55.000 0.00 0.00 39.41 3.06
3326 3886 3.939592 GCTCACTGGGGTCTTAACATAAC 59.060 47.826 0.00 0.00 0.00 1.89
3335 3895 0.681564 CTACGAGCTCACTGGGGTCT 60.682 60.000 15.40 0.00 0.00 3.85
3342 3902 1.214062 GCTGTGCTACGAGCTCACT 59.786 57.895 15.40 0.00 42.97 3.41
3360 3920 0.179084 ACTATGATTGTGGGCGACGG 60.179 55.000 0.00 0.00 0.00 4.79
3371 3931 6.007703 GCTAGTAGAGGAGGTCACTATGATT 58.992 44.000 0.00 0.00 0.00 2.57
3372 3932 5.073827 TGCTAGTAGAGGAGGTCACTATGAT 59.926 44.000 0.00 0.00 0.00 2.45
3376 3936 3.433882 GCTGCTAGTAGAGGAGGTCACTA 60.434 52.174 12.54 0.00 43.67 2.74
3436 3996 1.218316 CTACAAGCCGGGGAGTGAC 59.782 63.158 2.18 0.00 0.00 3.67
3461 4021 1.236616 TGCACTTTCAGTCCATGCGG 61.237 55.000 0.00 0.00 39.18 5.69
3462 4022 0.110056 GTGCACTTTCAGTCCATGCG 60.110 55.000 10.32 0.00 39.18 4.73
3471 4031 0.028770 CGCTTTTCCGTGCACTTTCA 59.971 50.000 16.19 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.