Multiple sequence alignment - TraesCS7D01G535200

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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 TraesCS7D01G535200 chr7D 100.000 2459 0 0 1 2459 627304081 627306539 0.000000e+00 4542.0
1 TraesCS7D01G535200 chr7D 80.420 429 46 18 840 1263 627298130 627298525 2.390000e-75 292.0
2 TraesCS7D01G535200 chr7D 90.351 114 11 0 1246 1359 627298537 627298650 1.520000e-32 150.0
3 TraesCS7D01G535200 chr7B 94.095 779 38 2 581 1359 728012321 728013091 0.000000e+00 1177.0
4 TraesCS7D01G535200 chr7B 90.653 567 43 2 1891 2457 728014654 728015210 0.000000e+00 745.0
5 TraesCS7D01G535200 chr7B 91.283 413 31 3 179 586 728011722 728012134 2.140000e-155 558.0
6 TraesCS7D01G535200 chr7B 89.313 393 28 5 1387 1777 728013485 728013865 4.760000e-132 481.0
7 TraesCS7D01G535200 chr7B 81.149 435 46 17 841 1263 728005474 728005884 1.420000e-82 316.0
8 TraesCS7D01G535200 chr7B 84.528 265 34 6 589 851 728029600 728029859 3.140000e-64 255.0
9 TraesCS7D01G535200 chr7B 89.326 178 13 3 326 500 728004995 728005169 4.120000e-53 219.0
10 TraesCS7D01G535200 chr7B 90.058 171 12 3 1 167 728011567 728011736 1.480000e-52 217.0
11 TraesCS7D01G535200 chr7B 81.509 265 34 8 581 833 728053230 728053491 1.150000e-48 204.0
12 TraesCS7D01G535200 chr7B 92.982 114 8 0 1246 1359 728005896 728006009 1.510000e-37 167.0
13 TraesCS7D01G535200 chr7B 90.654 107 8 2 1787 1893 741866162 741866058 9.170000e-30 141.0
14 TraesCS7D01G535200 chr7B 90.566 106 8 2 1787 1891 13840905 13840801 3.300000e-29 139.0
15 TraesCS7D01G535200 chr7B 100.000 30 0 0 1057 1086 728212008 728212037 3.420000e-04 56.5
16 TraesCS7D01G535200 chr7A 94.066 573 32 2 1887 2459 722879870 722880440 0.000000e+00 869.0
17 TraesCS7D01G535200 chr7A 94.915 531 27 0 1887 2417 723076627 723077157 0.000000e+00 832.0
18 TraesCS7D01G535200 chr7A 93.298 567 28 4 1887 2453 722989804 722990360 0.000000e+00 828.0
19 TraesCS7D01G535200 chr7A 93.122 567 29 4 1887 2453 722900402 722900958 0.000000e+00 822.0
20 TraesCS7D01G535200 chr7A 93.781 402 20 4 1386 1783 722899233 722899633 1.260000e-167 599.0
21 TraesCS7D01G535200 chr7A 93.532 402 21 4 1386 1783 722988744 722989144 5.850000e-166 593.0
22 TraesCS7D01G535200 chr7A 91.127 417 18 8 1386 1783 723075445 723075861 4.620000e-152 547.0
23 TraesCS7D01G535200 chr7A 95.882 340 7 1 1027 1359 723030856 723031195 5.980000e-151 544.0
24 TraesCS7D01G535200 chr7A 95.294 340 9 1 1027 1359 722898502 722898841 1.290000e-147 532.0
25 TraesCS7D01G535200 chr7A 95.294 340 9 4 1027 1359 722936559 722936898 1.290000e-147 532.0
26 TraesCS7D01G535200 chr7A 95.266 338 9 1 1029 1359 723074737 723075074 1.670000e-146 529.0
27 TraesCS7D01G535200 chr7A 94.706 340 11 1 1027 1359 722988013 722988352 2.800000e-144 521.0
28 TraesCS7D01G535200 chr7A 90.909 396 24 5 2060 2453 723050027 723050412 2.800000e-144 521.0
29 TraesCS7D01G535200 chr7A 90.404 396 26 5 2060 2453 722959322 722959707 6.070000e-141 510.0
30 TraesCS7D01G535200 chr7A 89.103 312 33 1 584 895 723074341 723074651 1.070000e-103 387.0
31 TraesCS7D01G535200 chr7A 88.782 312 34 1 584 895 722987619 722987929 4.960000e-102 381.0
32 TraesCS7D01G535200 chr7A 88.462 312 35 1 584 895 723030462 723030772 2.310000e-100 375.0
33 TraesCS7D01G535200 chr7A 87.821 312 37 1 584 895 722936165 722936475 5.000000e-97 364.0
34 TraesCS7D01G535200 chr7A 80.653 429 54 16 840 1263 722792670 722793074 3.070000e-79 305.0
35 TraesCS7D01G535200 chr7A 94.000 200 11 1 1585 1783 722938566 722938765 3.970000e-78 302.0
36 TraesCS7D01G535200 chr7A 94.000 200 11 1 1585 1783 723031376 723031575 3.970000e-78 302.0
37 TraesCS7D01G535200 chr7A 80.420 429 55 18 840 1263 722877205 722877609 1.430000e-77 300.0
38 TraesCS7D01G535200 chr7A 95.135 185 9 0 1887 2071 722939534 722939718 2.390000e-75 292.0
39 TraesCS7D01G535200 chr7A 94.595 185 10 0 1887 2071 723032344 723032528 1.110000e-73 287.0
40 TraesCS7D01G535200 chr7A 89.474 114 12 0 1246 1359 722793086 722793199 7.090000e-31 145.0
41 TraesCS7D01G535200 chr5B 91.667 108 8 1 1784 1891 14215543 14215437 5.480000e-32 148.0
42 TraesCS7D01G535200 chr5B 94.915 59 3 0 2360 2418 326561546 326561488 2.600000e-15 93.5
43 TraesCS7D01G535200 chr4D 90.909 110 7 3 1784 1892 69819121 69819228 7.090000e-31 145.0
44 TraesCS7D01G535200 chr2D 90.654 107 8 2 1787 1893 572687814 572687918 9.170000e-30 141.0
45 TraesCS7D01G535200 chr2D 89.091 55 3 3 2311 2363 338329984 338329931 5.680000e-07 65.8
46 TraesCS7D01G535200 chr1A 90.090 111 7 2 1784 1891 571641478 571641369 9.170000e-30 141.0
47 TraesCS7D01G535200 chr6B 90.566 106 8 2 1787 1892 62380797 62380694 3.300000e-29 139.0
48 TraesCS7D01G535200 chr3D 89.286 112 9 2 1784 1892 566963965 566964076 1.190000e-28 137.0
49 TraesCS7D01G535200 chr2B 89.286 112 8 2 1784 1892 774696734 774696844 1.190000e-28 137.0
50 TraesCS7D01G535200 chr2A 100.000 32 0 0 2308 2339 751464952 751464983 2.640000e-05 60.2


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 TraesCS7D01G535200 chr7D 627304081 627306539 2458 False 4542.00 4542 100.000000 1 2459 1 chr7D.!!$F1 2458
1 TraesCS7D01G535200 chr7D 627298130 627298650 520 False 221.00 292 85.385500 840 1359 2 chr7D.!!$F2 519
2 TraesCS7D01G535200 chr7B 728011567 728015210 3643 False 635.60 1177 91.080400 1 2457 5 chr7B.!!$F5 2456
3 TraesCS7D01G535200 chr7B 728004995 728006009 1014 False 234.00 316 87.819000 326 1359 3 chr7B.!!$F4 1033
4 TraesCS7D01G535200 chr7A 722898502 722900958 2456 False 651.00 822 94.065667 1027 2453 3 chr7A.!!$F5 1426
5 TraesCS7D01G535200 chr7A 722877205 722880440 3235 False 584.50 869 87.243000 840 2459 2 chr7A.!!$F4 1619
6 TraesCS7D01G535200 chr7A 722987619 722990360 2741 False 580.75 828 92.579500 584 2453 4 chr7A.!!$F7 1869
7 TraesCS7D01G535200 chr7A 723074341 723077157 2816 False 573.75 832 92.602750 584 2417 4 chr7A.!!$F9 1833
8 TraesCS7D01G535200 chr7A 723030462 723032528 2066 False 377.00 544 93.234750 584 2071 4 chr7A.!!$F8 1487
9 TraesCS7D01G535200 chr7A 722936165 722939718 3553 False 372.50 532 93.062500 584 2071 4 chr7A.!!$F6 1487
10 TraesCS7D01G535200 chr7A 722792670 722793199 529 False 225.00 305 85.063500 840 1359 2 chr7A.!!$F3 519

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
402 407 0.321653 GCACCCTTGACGATCTTGGT 60.322 55.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1831 5439 1.009829 GTATTGCTTGAGCCTCGTGG 58.99 55.0 0.0 0.0 41.18 4.94 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
24 25 7.943413 ACATCAATATCACGAAATCTGAGAG 57.057 36.000 0.00 0.00 0.00 3.20
32 33 2.996621 ACGAAATCTGAGAGCCGAAAAG 59.003 45.455 7.68 0.00 0.00 2.27
33 34 2.222908 CGAAATCTGAGAGCCGAAAAGC 60.223 50.000 0.00 0.00 0.00 3.51
34 35 2.479566 AATCTGAGAGCCGAAAAGCA 57.520 45.000 0.00 0.00 34.23 3.91
39 40 1.160137 GAGAGCCGAAAAGCACACAT 58.840 50.000 0.00 0.00 34.23 3.21
49 50 4.142752 CGAAAAGCACACATGTCATGAGAT 60.143 41.667 19.77 0.00 0.00 2.75
52 53 1.674441 GCACACATGTCATGAGATGGG 59.326 52.381 28.45 28.45 40.88 4.00
77 80 4.118410 GGAGAGTGCTCAGTATTGATGTG 58.882 47.826 1.82 0.00 43.14 3.21
120 123 2.829120 GCCAAACTAGCCCATGGTTTTA 59.171 45.455 11.73 0.00 40.29 1.52
140 143 0.830023 GCAAAACCAGGGGTGGCTTA 60.830 55.000 0.00 0.00 35.34 3.09
142 145 1.824852 CAAAACCAGGGGTGGCTTATC 59.175 52.381 0.00 0.00 35.34 1.75
143 146 0.335019 AAACCAGGGGTGGCTTATCC 59.665 55.000 0.00 0.00 35.34 2.59
144 147 0.552615 AACCAGGGGTGGCTTATCCT 60.553 55.000 0.00 0.00 35.34 3.24
146 149 0.988145 CCAGGGGTGGCTTATCCTCA 60.988 60.000 0.00 0.00 35.26 3.86
147 150 0.918983 CAGGGGTGGCTTATCCTCAA 59.081 55.000 0.00 0.00 35.26 3.02
148 151 1.496429 CAGGGGTGGCTTATCCTCAAT 59.504 52.381 0.00 0.00 35.26 2.57
150 153 1.494721 GGGGTGGCTTATCCTCAATGA 59.505 52.381 0.00 0.00 35.26 2.57
151 154 2.487986 GGGGTGGCTTATCCTCAATGAG 60.488 54.545 2.68 2.68 35.26 2.90
153 156 3.117888 GGGTGGCTTATCCTCAATGAGAA 60.118 47.826 12.53 0.00 35.26 2.87
154 157 4.526970 GGTGGCTTATCCTCAATGAGAAA 58.473 43.478 12.53 0.00 35.26 2.52
155 158 4.336713 GGTGGCTTATCCTCAATGAGAAAC 59.663 45.833 12.53 0.00 35.26 2.78
156 159 5.189180 GTGGCTTATCCTCAATGAGAAACT 58.811 41.667 12.53 0.00 35.26 2.66
157 160 5.065731 GTGGCTTATCCTCAATGAGAAACTG 59.934 44.000 12.53 0.43 35.26 3.16
158 161 5.045651 TGGCTTATCCTCAATGAGAAACTGA 60.046 40.000 12.53 0.00 35.26 3.41
159 162 5.882557 GGCTTATCCTCAATGAGAAACTGAA 59.117 40.000 12.53 0.00 0.00 3.02
160 163 6.375455 GGCTTATCCTCAATGAGAAACTGAAA 59.625 38.462 12.53 0.00 0.00 2.69
161 164 7.067981 GGCTTATCCTCAATGAGAAACTGAAAT 59.932 37.037 12.53 0.00 0.00 2.17
162 165 8.465201 GCTTATCCTCAATGAGAAACTGAAATT 58.535 33.333 12.53 0.00 0.00 1.82
167 170 9.113838 TCCTCAATGAGAAACTGAAATTATAGC 57.886 33.333 12.53 0.00 0.00 2.97
168 171 8.348507 CCTCAATGAGAAACTGAAATTATAGCC 58.651 37.037 12.53 0.00 0.00 3.93
169 172 8.225603 TCAATGAGAAACTGAAATTATAGCCC 57.774 34.615 0.00 0.00 0.00 5.19
170 173 6.867662 ATGAGAAACTGAAATTATAGCCCG 57.132 37.500 0.00 0.00 0.00 6.13
171 174 5.123227 TGAGAAACTGAAATTATAGCCCGG 58.877 41.667 0.00 0.00 0.00 5.73
172 175 3.883489 AGAAACTGAAATTATAGCCCGGC 59.117 43.478 0.00 0.00 0.00 6.13
173 176 3.290948 AACTGAAATTATAGCCCGGCA 57.709 42.857 13.15 0.00 0.00 5.69
174 177 3.290948 ACTGAAATTATAGCCCGGCAA 57.709 42.857 13.15 0.00 0.00 4.52
175 178 3.626930 ACTGAAATTATAGCCCGGCAAA 58.373 40.909 13.15 3.16 0.00 3.68
176 179 4.020543 ACTGAAATTATAGCCCGGCAAAA 58.979 39.130 13.15 2.77 0.00 2.44
177 180 4.464597 ACTGAAATTATAGCCCGGCAAAAA 59.535 37.500 13.15 2.38 0.00 1.94
250 254 4.858935 TGTGCTACTTTTGCAGTCAAATC 58.141 39.130 0.00 0.00 41.37 2.17
256 260 8.359642 TGCTACTTTTGCAGTCAAATCTATTTT 58.640 29.630 0.00 0.00 41.37 1.82
289 293 9.713684 TTTTCATCCATTTAAGATGTTAGGGAT 57.286 29.630 6.69 6.69 41.56 3.85
298 302 9.720769 ATTTAAGATGTTAGGGATATACCAACG 57.279 33.333 6.78 0.00 41.20 4.10
304 308 5.068198 TGTTAGGGATATACCAACGTCAGAC 59.932 44.000 6.78 0.00 41.20 3.51
309 313 5.394883 GGGATATACCAACGTCAGACAAGAA 60.395 44.000 0.00 0.00 41.20 2.52
311 315 6.201044 GGATATACCAACGTCAGACAAGAATG 59.799 42.308 0.41 0.00 38.79 2.67
312 316 3.194005 ACCAACGTCAGACAAGAATGT 57.806 42.857 0.41 0.00 44.25 2.71
402 407 0.321653 GCACCCTTGACGATCTTGGT 60.322 55.000 0.00 0.00 0.00 3.67
506 514 7.681939 TCATTAATTATTAGGGCGTTGGATC 57.318 36.000 0.00 0.00 0.00 3.36
523 531 2.030946 GGATCGGCATCGTCTCAAAAAG 59.969 50.000 0.00 0.00 37.69 2.27
524 532 2.448926 TCGGCATCGTCTCAAAAAGA 57.551 45.000 0.00 0.00 37.69 2.52
531 539 2.476821 TCGTCTCAAAAAGAACCGGTC 58.523 47.619 8.04 0.95 35.21 4.79
546 554 1.670971 CGGTCGTCGATTGAACACGG 61.671 60.000 0.00 0.00 42.43 4.94
558 566 2.912771 TGAACACGGCTCTTTTCTTGA 58.087 42.857 0.00 0.00 0.00 3.02
559 567 2.612212 TGAACACGGCTCTTTTCTTGAC 59.388 45.455 0.00 0.00 0.00 3.18
586 594 4.070009 CACAACAAAGGGTACTAGGTTCC 58.930 47.826 0.00 0.00 0.00 3.62
587 595 3.717913 ACAACAAAGGGTACTAGGTTCCA 59.282 43.478 0.00 0.00 0.00 3.53
599 799 5.584551 ACTAGGTTCCATCCAGAACTTTT 57.415 39.130 4.58 0.00 44.56 2.27
613 813 2.489938 ACTTTTGGCCTGCGAATCTA 57.510 45.000 3.32 0.00 0.00 1.98
661 861 6.184789 GTGAAAGTGGACCCCATATTAGAAA 58.815 40.000 0.00 0.00 35.28 2.52
671 871 4.814771 CCCCATATTAGAAACCTTCACGAC 59.185 45.833 0.00 0.00 0.00 4.34
742 942 5.395435 GGGTTAGGAGAGTGCCTAGTTTTAG 60.395 48.000 0.00 0.00 41.34 1.85
842 1162 5.088739 GTCTCCATGTGAAATTACGCAAAG 58.911 41.667 0.00 0.00 34.01 2.77
847 1167 5.107530 CCATGTGAAATTACGCAAAGGTTTG 60.108 40.000 0.00 0.00 41.03 2.93
882 1202 4.016706 CTCCCCACCGGTGACACC 62.017 72.222 36.07 15.13 34.05 4.16
898 1218 6.483307 CGGTGACACCAGTATGAATGAATTAT 59.517 38.462 24.18 0.00 39.69 1.28
1042 1402 1.412343 TGCAGCTAGAGTGTGTTGTCA 59.588 47.619 0.00 0.00 0.00 3.58
1278 1675 1.143401 GCACCGGTAGAGCCTTACC 59.857 63.158 6.87 4.53 39.79 2.85
1372 3281 1.079750 GCTGGAACCTCTCGGTGAC 60.080 63.158 0.00 0.00 44.73 3.67
1425 3681 3.146066 TCCAGACTTGGTGTGCAAATAC 58.854 45.455 0.00 0.00 45.26 1.89
1500 3756 4.746729 TGCAATTAAGCTGGTTTGCTATG 58.253 39.130 21.30 2.62 43.24 2.23
1512 3768 4.454161 TGGTTTGCTATGTATGTGTGTCAC 59.546 41.667 0.00 0.00 34.56 3.67
1544 3800 8.668353 GTTTGATACTTTGATGCATCTAGAACA 58.332 33.333 26.32 19.15 0.00 3.18
1545 3801 8.969260 TTGATACTTTGATGCATCTAGAACAT 57.031 30.769 26.32 17.00 0.00 2.71
1600 4258 7.231317 AGTTTCTTGAGCTGATTTATTTGGTGA 59.769 33.333 0.00 0.00 0.00 4.02
1665 4342 5.424757 GTTAACTATACCATGTGTCCAGCA 58.575 41.667 0.00 0.00 0.00 4.41
1689 4366 6.907212 CACCAGCAATTTTATATCGTGACTTC 59.093 38.462 0.00 0.00 0.00 3.01
1783 4462 8.902806 TCAACAGTTCAAAAGAGAATAACATGT 58.097 29.630 0.00 0.00 0.00 3.21
1786 4465 8.784043 ACAGTTCAAAAGAGAATAACATGTACC 58.216 33.333 0.00 0.00 0.00 3.34
1788 4467 9.574516 AGTTCAAAAGAGAATAACATGTACCTT 57.425 29.630 0.00 0.00 0.00 3.50
1789 4468 9.612620 GTTCAAAAGAGAATAACATGTACCTTG 57.387 33.333 0.00 0.00 0.00 3.61
1790 4469 7.816640 TCAAAAGAGAATAACATGTACCTTGC 58.183 34.615 0.00 0.00 0.00 4.01
1794 4473 9.515226 AAAGAGAATAACATGTACCTTGCTTTA 57.485 29.630 0.00 0.00 0.00 1.85
1795 4474 9.686683 AAGAGAATAACATGTACCTTGCTTTAT 57.313 29.630 0.00 0.00 0.00 1.40
1800 4479 8.904099 ATAACATGTACCTTGCTTTATACTCC 57.096 34.615 0.00 0.00 0.00 3.85
1801 4480 6.308015 ACATGTACCTTGCTTTATACTCCA 57.692 37.500 0.00 0.00 0.00 3.86
1802 4481 6.717289 ACATGTACCTTGCTTTATACTCCAA 58.283 36.000 0.00 0.00 0.00 3.53
1804 4483 5.183228 TGTACCTTGCTTTATACTCCAAGC 58.817 41.667 0.73 0.73 44.87 4.01
1812 4491 6.238610 GCTTTATACTCCAAGCAGATCATG 57.761 41.667 0.00 0.00 44.18 3.07
1815 4494 7.095439 GCTTTATACTCCAAGCAGATCATGTAC 60.095 40.741 0.00 0.00 44.18 2.90
1817 4496 4.399004 ACTCCAAGCAGATCATGTACTC 57.601 45.455 0.00 0.00 0.00 2.59
1821 5429 4.956075 TCCAAGCAGATCATGTACTCACTA 59.044 41.667 0.00 0.00 0.00 2.74
1831 5439 9.058174 AGATCATGTACTCACTATATATACGCC 57.942 37.037 0.00 0.00 0.00 5.68
1832 5440 7.563888 TCATGTACTCACTATATATACGCCC 57.436 40.000 0.00 0.00 0.00 6.13
1833 5441 7.114095 TCATGTACTCACTATATATACGCCCA 58.886 38.462 0.00 0.00 0.00 5.36
1834 5442 6.748333 TGTACTCACTATATATACGCCCAC 57.252 41.667 0.00 0.00 0.00 4.61
1836 5444 4.582869 ACTCACTATATATACGCCCACGA 58.417 43.478 0.00 0.00 43.93 4.35
1837 5445 4.634883 ACTCACTATATATACGCCCACGAG 59.365 45.833 0.00 0.00 43.93 4.18
1847 5455 2.032528 CCCACGAGGCTCAAGCAA 59.967 61.111 15.95 0.00 44.36 3.91
1849 5457 0.107703 CCCACGAGGCTCAAGCAATA 60.108 55.000 15.95 0.00 44.36 1.90
1851 5459 1.675714 CCACGAGGCTCAAGCAATACA 60.676 52.381 15.95 0.00 44.36 2.29
1853 5461 2.076863 ACGAGGCTCAAGCAATACAAC 58.923 47.619 15.95 0.00 44.36 3.32
1854 5462 1.061131 CGAGGCTCAAGCAATACAACG 59.939 52.381 15.95 0.00 44.36 4.10
1855 5463 2.346803 GAGGCTCAAGCAATACAACGA 58.653 47.619 10.25 0.00 44.36 3.85
1857 5465 2.484264 AGGCTCAAGCAATACAACGAAC 59.516 45.455 4.13 0.00 44.36 3.95
1858 5466 2.484264 GGCTCAAGCAATACAACGAACT 59.516 45.455 4.13 0.00 44.36 3.01
1860 5468 4.332819 GGCTCAAGCAATACAACGAACTAT 59.667 41.667 4.13 0.00 44.36 2.12
1861 5469 5.163754 GGCTCAAGCAATACAACGAACTATT 60.164 40.000 4.13 0.00 44.36 1.73
1865 5473 6.597672 TCAAGCAATACAACGAACTATTCCAT 59.402 34.615 0.00 0.00 0.00 3.41
1866 5474 6.604735 AGCAATACAACGAACTATTCCATC 57.395 37.500 0.00 0.00 0.00 3.51
1868 5476 6.597672 AGCAATACAACGAACTATTCCATCAA 59.402 34.615 0.00 0.00 0.00 2.57
1869 5477 7.283127 AGCAATACAACGAACTATTCCATCAAT 59.717 33.333 0.00 0.00 0.00 2.57
1870 5478 7.587757 GCAATACAACGAACTATTCCATCAATC 59.412 37.037 0.00 0.00 0.00 2.67
1872 5480 4.881850 ACAACGAACTATTCCATCAATCCC 59.118 41.667 0.00 0.00 0.00 3.85
1873 5481 4.086706 ACGAACTATTCCATCAATCCCC 57.913 45.455 0.00 0.00 0.00 4.81
1874 5482 3.181443 ACGAACTATTCCATCAATCCCCC 60.181 47.826 0.00 0.00 0.00 5.40
1875 5483 3.073062 CGAACTATTCCATCAATCCCCCT 59.927 47.826 0.00 0.00 0.00 4.79
1876 5484 4.657013 GAACTATTCCATCAATCCCCCTC 58.343 47.826 0.00 0.00 0.00 4.30
1877 5485 3.959920 ACTATTCCATCAATCCCCCTCT 58.040 45.455 0.00 0.00 0.00 3.69
1878 5486 5.106631 ACTATTCCATCAATCCCCCTCTA 57.893 43.478 0.00 0.00 0.00 2.43
1879 5487 5.680327 ACTATTCCATCAATCCCCCTCTAT 58.320 41.667 0.00 0.00 0.00 1.98
1881 5489 2.921221 TCCATCAATCCCCCTCTATCC 58.079 52.381 0.00 0.00 0.00 2.59
1882 5490 2.460293 TCCATCAATCCCCCTCTATCCT 59.540 50.000 0.00 0.00 0.00 3.24
1883 5491 3.115803 TCCATCAATCCCCCTCTATCCTT 60.116 47.826 0.00 0.00 0.00 3.36
1884 5492 3.659686 CCATCAATCCCCCTCTATCCTTT 59.340 47.826 0.00 0.00 0.00 3.11
1885 5493 4.263683 CCATCAATCCCCCTCTATCCTTTC 60.264 50.000 0.00 0.00 0.00 2.62
1889 5859 5.607171 TCAATCCCCCTCTATCCTTTCTAAC 59.393 44.000 0.00 0.00 0.00 2.34
2021 5991 8.953990 CACACTTGCTACTTAAAATAAACACAC 58.046 33.333 0.00 0.00 0.00 3.82
2116 6086 4.534500 ACCTACCATTTCCACACACTCATA 59.466 41.667 0.00 0.00 0.00 2.15
2119 6089 4.724399 ACCATTTCCACACACTCATAACA 58.276 39.130 0.00 0.00 0.00 2.41
2239 6209 0.107410 AACGTCACAGGCCTTCACAA 60.107 50.000 0.00 0.00 0.00 3.33
2282 6252 6.481954 AGGTCGATCAACTGACAAATAAAC 57.518 37.500 0.00 0.00 36.83 2.01
2419 6389 9.993454 TGTCCAAATTTTCATGATGAAATACAA 57.007 25.926 20.04 6.92 44.75 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.079925 GTGCTTTTCGGCTCTCAGATT 58.920 47.619 0.00 0.00 0.00 2.40
22 23 0.593128 ACATGTGTGCTTTTCGGCTC 59.407 50.000 0.00 0.00 0.00 4.70
24 25 0.310543 TGACATGTGTGCTTTTCGGC 59.689 50.000 1.15 0.00 0.00 5.54
32 33 1.674441 CCCATCTCATGACATGTGTGC 59.326 52.381 14.98 0.00 0.00 4.57
33 34 2.995283 ACCCATCTCATGACATGTGTG 58.005 47.619 14.98 12.24 0.00 3.82
34 35 3.349927 CAACCCATCTCATGACATGTGT 58.650 45.455 14.98 2.10 0.00 3.72
39 40 2.502947 CTCTCCAACCCATCTCATGACA 59.497 50.000 0.00 0.00 0.00 3.58
49 50 0.764369 ACTGAGCACTCTCCAACCCA 60.764 55.000 0.00 0.00 38.58 4.51
52 53 4.193826 TCAATACTGAGCACTCTCCAAC 57.806 45.455 0.00 0.00 38.58 3.77
120 123 2.524148 GCCACCCCTGGTTTTGCT 60.524 61.111 0.00 0.00 40.17 3.91
142 145 8.348507 GGCTATAATTTCAGTTTCTCATTGAGG 58.651 37.037 13.59 0.00 0.00 3.86
143 146 8.348507 GGGCTATAATTTCAGTTTCTCATTGAG 58.651 37.037 7.38 7.38 0.00 3.02
144 147 7.012327 CGGGCTATAATTTCAGTTTCTCATTGA 59.988 37.037 0.00 0.00 0.00 2.57
146 149 6.263168 CCGGGCTATAATTTCAGTTTCTCATT 59.737 38.462 0.00 0.00 0.00 2.57
147 150 5.765182 CCGGGCTATAATTTCAGTTTCTCAT 59.235 40.000 0.00 0.00 0.00 2.90
148 151 5.123227 CCGGGCTATAATTTCAGTTTCTCA 58.877 41.667 0.00 0.00 0.00 3.27
150 153 3.883489 GCCGGGCTATAATTTCAGTTTCT 59.117 43.478 12.87 0.00 0.00 2.52
151 154 3.630312 TGCCGGGCTATAATTTCAGTTTC 59.370 43.478 21.46 0.00 0.00 2.78
153 156 3.290948 TGCCGGGCTATAATTTCAGTT 57.709 42.857 21.46 0.00 0.00 3.16
154 157 3.290948 TTGCCGGGCTATAATTTCAGT 57.709 42.857 21.46 0.00 0.00 3.41
155 158 4.647424 TTTTGCCGGGCTATAATTTCAG 57.353 40.909 21.46 0.00 0.00 3.02
199 202 9.028284 ACAATTCTTGTAATTTCACATGGAGAT 57.972 29.630 0.00 0.00 43.27 2.75
230 234 7.452880 AATAGATTTGACTGCAAAAGTAGCA 57.547 32.000 0.00 0.00 46.19 3.49
276 280 6.325545 TGACGTTGGTATATCCCTAACATCTT 59.674 38.462 0.00 0.00 34.77 2.40
278 282 6.015688 TCTGACGTTGGTATATCCCTAACATC 60.016 42.308 0.00 0.00 34.77 3.06
279 283 5.836898 TCTGACGTTGGTATATCCCTAACAT 59.163 40.000 0.00 0.00 34.77 2.71
289 293 6.032956 ACATTCTTGTCTGACGTTGGTATA 57.967 37.500 2.98 0.00 0.00 1.47
298 302 7.090808 TGACACATAGTACATTCTTGTCTGAC 58.909 38.462 0.00 0.00 37.28 3.51
304 308 6.348498 TCCCATGACACATAGTACATTCTTG 58.652 40.000 0.00 0.00 0.00 3.02
309 313 4.410228 AGCTTCCCATGACACATAGTACAT 59.590 41.667 0.00 0.00 0.00 2.29
311 315 4.408182 AGCTTCCCATGACACATAGTAC 57.592 45.455 0.00 0.00 0.00 2.73
312 316 4.141711 GGAAGCTTCCCATGACACATAGTA 60.142 45.833 31.91 0.00 41.62 1.82
491 499 1.227853 GCCGATCCAACGCCCTAAT 60.228 57.895 0.00 0.00 0.00 1.73
506 514 2.412847 GGTTCTTTTTGAGACGATGCCG 60.413 50.000 0.00 0.00 42.50 5.69
513 521 2.207590 ACGACCGGTTCTTTTTGAGAC 58.792 47.619 9.42 0.00 33.02 3.36
523 531 0.712222 GTTCAATCGACGACCGGTTC 59.288 55.000 9.42 1.38 40.05 3.62
524 532 0.032403 TGTTCAATCGACGACCGGTT 59.968 50.000 9.42 0.00 43.37 4.44
531 539 0.732880 AGAGCCGTGTTCAATCGACG 60.733 55.000 0.00 0.00 0.00 5.12
558 566 2.172717 AGTACCCTTTGTTGTGCTCTGT 59.827 45.455 0.00 0.00 0.00 3.41
559 567 2.851195 AGTACCCTTTGTTGTGCTCTG 58.149 47.619 0.00 0.00 0.00 3.35
586 594 1.067354 GCAGGCCAAAAGTTCTGGATG 60.067 52.381 5.01 0.00 35.85 3.51
587 595 1.260544 GCAGGCCAAAAGTTCTGGAT 58.739 50.000 5.01 0.00 35.85 3.41
599 799 0.175760 GTCTGTAGATTCGCAGGCCA 59.824 55.000 5.01 0.00 31.71 5.36
613 813 4.082523 CATCCGGCCACCGTCTGT 62.083 66.667 2.24 0.00 46.80 3.41
638 838 6.184789 GTTTCTAATATGGGGTCCACTTTCA 58.815 40.000 0.00 0.00 35.80 2.69
661 861 0.034896 AATCTTGCCGTCGTGAAGGT 59.965 50.000 3.81 0.00 32.29 3.50
671 871 3.486875 GGTCGGATTTTGTAATCTTGCCG 60.487 47.826 0.00 0.00 40.07 5.69
842 1162 5.008712 AGACTGTAAGCTTTGCTAACAAACC 59.991 40.000 3.20 0.00 38.07 3.27
847 1167 3.685272 GGGAGACTGTAAGCTTTGCTAAC 59.315 47.826 3.20 0.00 38.25 2.34
898 1218 9.415544 GTTTATCTAGTTCGGTCTTGTCTTTAA 57.584 33.333 0.00 0.00 0.00 1.52
911 1231 9.866936 GAGTACAGTATCTGTTTATCTAGTTCG 57.133 37.037 7.70 0.00 42.59 3.95
1042 1402 8.683615 TCTGTATTTGTGTATGTAGACGAAGAT 58.316 33.333 0.00 0.00 0.00 2.40
1143 1510 0.614979 ACGAGGTAGTGGACATGGCT 60.615 55.000 0.00 0.00 0.00 4.75
1207 1574 1.294659 CTCGTGCAGGGACTTGAAGC 61.295 60.000 6.56 0.00 34.60 3.86
1500 3756 5.874831 TCAAACACAAAGTGACACACATAC 58.125 37.500 8.59 0.00 36.74 2.39
1512 3768 7.811236 AGATGCATCAAAGTATCAAACACAAAG 59.189 33.333 27.81 0.00 33.67 2.77
1544 3800 9.584008 AATCACATGAAATAGCCTGAAGAATAT 57.416 29.630 0.00 0.00 0.00 1.28
1545 3801 8.985315 AATCACATGAAATAGCCTGAAGAATA 57.015 30.769 0.00 0.00 0.00 1.75
1600 4258 8.225603 AGATCGGCTAATGTGAAATAAAACAT 57.774 30.769 0.00 0.00 38.66 2.71
1641 4299 4.506654 GCTGGACACATGGTATAGTTAACG 59.493 45.833 0.00 0.00 0.00 3.18
1665 4342 6.597672 TGAAGTCACGATATAAAATTGCTGGT 59.402 34.615 0.00 0.00 0.00 4.00
1790 4469 8.147058 AGTACATGATCTGCTTGGAGTATAAAG 58.853 37.037 0.00 0.00 0.00 1.85
1794 4473 5.600069 TGAGTACATGATCTGCTTGGAGTAT 59.400 40.000 0.00 0.00 0.00 2.12
1795 4474 4.956075 TGAGTACATGATCTGCTTGGAGTA 59.044 41.667 0.00 0.00 0.00 2.59
1797 4476 4.118410 GTGAGTACATGATCTGCTTGGAG 58.882 47.826 0.00 0.00 0.00 3.86
1798 4477 3.771479 AGTGAGTACATGATCTGCTTGGA 59.229 43.478 0.00 0.00 0.00 3.53
1799 4478 4.134379 AGTGAGTACATGATCTGCTTGG 57.866 45.455 0.00 0.00 0.00 3.61
1804 4483 9.871299 GCGTATATATAGTGAGTACATGATCTG 57.129 37.037 0.00 0.00 0.00 2.90
1805 4484 9.058174 GGCGTATATATAGTGAGTACATGATCT 57.942 37.037 0.00 0.00 0.00 2.75
1806 4485 8.291032 GGGCGTATATATAGTGAGTACATGATC 58.709 40.741 0.00 0.00 0.00 2.92
1807 4486 7.778382 TGGGCGTATATATAGTGAGTACATGAT 59.222 37.037 0.00 0.00 0.00 2.45
1809 4488 7.194278 GTGGGCGTATATATAGTGAGTACATG 58.806 42.308 0.00 0.00 0.00 3.21
1810 4489 6.037940 CGTGGGCGTATATATAGTGAGTACAT 59.962 42.308 0.00 0.00 0.00 2.29
1812 4491 5.582269 TCGTGGGCGTATATATAGTGAGTAC 59.418 44.000 0.00 0.00 39.49 2.73
1815 4494 4.035324 CCTCGTGGGCGTATATATAGTGAG 59.965 50.000 0.00 0.00 39.49 3.51
1817 4496 4.288670 CCTCGTGGGCGTATATATAGTG 57.711 50.000 0.00 0.00 39.49 2.74
1831 5439 1.009829 GTATTGCTTGAGCCTCGTGG 58.990 55.000 0.00 0.00 41.18 4.94
1832 5440 1.725641 TGTATTGCTTGAGCCTCGTG 58.274 50.000 0.00 0.00 41.18 4.35
1833 5441 2.076863 GTTGTATTGCTTGAGCCTCGT 58.923 47.619 0.00 0.00 41.18 4.18
1834 5442 1.061131 CGTTGTATTGCTTGAGCCTCG 59.939 52.381 0.00 0.00 41.18 4.63
1836 5444 2.472695 TCGTTGTATTGCTTGAGCCT 57.527 45.000 0.00 0.00 41.18 4.58
1837 5445 2.484264 AGTTCGTTGTATTGCTTGAGCC 59.516 45.455 0.00 0.00 41.18 4.70
1839 5447 6.092122 TGGAATAGTTCGTTGTATTGCTTGAG 59.908 38.462 0.00 0.00 30.55 3.02
1841 5449 6.176975 TGGAATAGTTCGTTGTATTGCTTG 57.823 37.500 0.00 0.00 30.55 4.01
1842 5450 6.597672 TGATGGAATAGTTCGTTGTATTGCTT 59.402 34.615 0.00 0.00 30.55 3.91
1844 5452 6.358118 TGATGGAATAGTTCGTTGTATTGC 57.642 37.500 0.00 0.00 0.00 3.56
1845 5453 8.070171 GGATTGATGGAATAGTTCGTTGTATTG 58.930 37.037 0.00 0.00 0.00 1.90
1846 5454 7.228706 GGGATTGATGGAATAGTTCGTTGTATT 59.771 37.037 0.00 0.00 0.00 1.89
1847 5455 6.710744 GGGATTGATGGAATAGTTCGTTGTAT 59.289 38.462 0.00 0.00 0.00 2.29
1849 5457 4.881850 GGGATTGATGGAATAGTTCGTTGT 59.118 41.667 0.00 0.00 0.00 3.32
1851 5459 4.461198 GGGGATTGATGGAATAGTTCGTT 58.539 43.478 0.00 0.00 0.00 3.85
1853 5461 3.073062 AGGGGGATTGATGGAATAGTTCG 59.927 47.826 0.00 0.00 0.00 3.95
1854 5462 4.352298 AGAGGGGGATTGATGGAATAGTTC 59.648 45.833 0.00 0.00 0.00 3.01
1855 5463 4.319515 AGAGGGGGATTGATGGAATAGTT 58.680 43.478 0.00 0.00 0.00 2.24
1857 5465 5.131809 GGATAGAGGGGGATTGATGGAATAG 59.868 48.000 0.00 0.00 0.00 1.73
1858 5466 5.039645 GGATAGAGGGGGATTGATGGAATA 58.960 45.833 0.00 0.00 0.00 1.75
1860 5468 3.115803 AGGATAGAGGGGGATTGATGGAA 60.116 47.826 0.00 0.00 0.00 3.53
1861 5469 2.460293 AGGATAGAGGGGGATTGATGGA 59.540 50.000 0.00 0.00 0.00 3.41
1865 5473 4.302004 AGAAAGGATAGAGGGGGATTGA 57.698 45.455 0.00 0.00 0.00 2.57
1866 5474 5.369699 TGTTAGAAAGGATAGAGGGGGATTG 59.630 44.000 0.00 0.00 0.00 2.67
1868 5476 5.171541 TGTTAGAAAGGATAGAGGGGGAT 57.828 43.478 0.00 0.00 0.00 3.85
1869 5477 4.637288 TGTTAGAAAGGATAGAGGGGGA 57.363 45.455 0.00 0.00 0.00 4.81
1870 5478 5.913946 AATGTTAGAAAGGATAGAGGGGG 57.086 43.478 0.00 0.00 0.00 5.40
1872 5480 8.807948 TTCAAAATGTTAGAAAGGATAGAGGG 57.192 34.615 0.00 0.00 0.00 4.30
1873 5481 8.897752 CCTTCAAAATGTTAGAAAGGATAGAGG 58.102 37.037 0.00 0.00 0.00 3.69
1874 5482 9.672673 TCCTTCAAAATGTTAGAAAGGATAGAG 57.327 33.333 0.00 0.00 0.00 2.43
1878 5486 8.940397 TCTTCCTTCAAAATGTTAGAAAGGAT 57.060 30.769 2.74 0.00 0.00 3.24
1879 5487 8.630037 GTTCTTCCTTCAAAATGTTAGAAAGGA 58.370 33.333 0.00 0.00 0.00 3.36
1881 5489 8.633561 AGGTTCTTCCTTCAAAATGTTAGAAAG 58.366 33.333 0.00 0.00 45.67 2.62
1882 5490 8.533569 AGGTTCTTCCTTCAAAATGTTAGAAA 57.466 30.769 0.00 0.00 45.67 2.52
1883 5491 9.063615 GTAGGTTCTTCCTTCAAAATGTTAGAA 57.936 33.333 0.00 0.00 45.67 2.10
1884 5492 7.664318 GGTAGGTTCTTCCTTCAAAATGTTAGA 59.336 37.037 0.00 0.00 45.67 2.10
1885 5493 7.447238 TGGTAGGTTCTTCCTTCAAAATGTTAG 59.553 37.037 0.00 0.00 45.67 2.34
1889 5859 6.648879 TTGGTAGGTTCTTCCTTCAAAATG 57.351 37.500 0.00 0.00 45.67 2.32
1982 5952 9.672673 AAGTAGCAAGTGTGACATAATTCTAAT 57.327 29.630 0.00 0.00 0.00 1.73
2116 6086 5.073437 AGGACTCTATAGCTGGAGATGTT 57.927 43.478 16.38 0.00 34.29 2.71
2119 6089 6.069847 GGTACTAGGACTCTATAGCTGGAGAT 60.070 46.154 16.38 0.00 34.29 2.75
2239 6209 7.287005 TCGACCTAATTACATATCCAAGTGACT 59.713 37.037 0.00 0.00 0.00 3.41
2305 6275 7.546250 TTCAAAATTAAGGCCTCCATTTGTA 57.454 32.000 22.27 15.44 0.00 2.41
2306 6276 6.432403 TTCAAAATTAAGGCCTCCATTTGT 57.568 33.333 22.27 12.15 0.00 2.83


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

AutoCloner maintained by Alex Coulton.