Multiple sequence alignment - TraesCS7A01G526500

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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 TraesCS7A01G526500 chr7A 100.000 2894 0 0 1 2894 708318097 708320990 0.000000e+00 5345.0
1 TraesCS7A01G526500 chr7A 81.864 1180 127 48 1000 2137 708326520 708327654 0.000000e+00 913.0
2 TraesCS7A01G526500 chr7A 85.878 262 17 12 708 961 708326197 708326446 7.950000e-66 261.0
3 TraesCS7A01G526500 chr7B 87.768 1635 126 37 554 2145 708445613 708447216 0.000000e+00 1844.0
4 TraesCS7A01G526500 chr7B 87.969 1546 103 36 623 2146 708511240 708512724 0.000000e+00 1748.0
5 TraesCS7A01G526500 chr7B 89.722 1333 98 16 833 2146 708529259 708530571 0.000000e+00 1666.0
6 TraesCS7A01G526500 chr7B 80.845 1514 126 85 708 2143 708552163 708553590 0.000000e+00 1038.0
7 TraesCS7A01G526500 chr7B 81.507 584 91 10 53 628 708510642 708511216 5.650000e-127 464.0
8 TraesCS7A01G526500 chr7B 86.025 322 30 12 2434 2750 708513337 708513648 5.980000e-87 331.0
9 TraesCS7A01G526500 chr7B 87.190 242 27 4 2159 2398 708512972 708513211 3.670000e-69 272.0
10 TraesCS7A01G526500 chr7B 92.424 132 4 1 711 842 708518208 708518333 1.770000e-42 183.0
11 TraesCS7A01G526500 chr7D 90.539 1279 67 18 880 2146 615765409 615766645 0.000000e+00 1642.0
12 TraesCS7A01G526500 chr7D 87.879 1452 100 28 726 2145 615559725 615558318 0.000000e+00 1637.0
13 TraesCS7A01G526500 chr7D 88.581 937 76 21 997 1923 615774913 615775828 0.000000e+00 1109.0
14 TraesCS7A01G526500 chr7D 80.400 500 72 22 2302 2787 615767057 615767544 9.860000e-95 357.0
15 TraesCS7A01G526500 chr7D 84.894 331 38 6 2141 2467 615766859 615767181 1.000000e-84 324.0
16 TraesCS7A01G526500 chr7D 86.425 221 17 7 708 925 615774599 615774809 2.240000e-56 230.0
17 TraesCS7A01G526500 chr7D 78.779 344 39 19 2544 2881 615554845 615554530 1.760000e-47 200.0
18 TraesCS7A01G526500 chr7D 85.946 185 13 6 705 888 615763811 615763983 4.920000e-43 185.0
19 TraesCS7A01G526500 chr7D 83.186 113 17 2 2645 2756 615554916 615554805 5.100000e-18 102.0
20 TraesCS7A01G526500 chr6D 85.312 320 47 0 1009 1328 142139101 142138782 5.980000e-87 331.0
21 TraesCS7A01G526500 chr5B 82.065 368 61 4 44 409 707875036 707874672 2.800000e-80 309.0
22 TraesCS7A01G526500 chr5D 97.368 38 1 0 372 409 565350412 565350449 6.690000e-07 65.8


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 TraesCS7A01G526500 chr7A 708318097 708320990 2893 False 5345.000000 5345 100.000000 1 2894 1 chr7A.!!$F1 2893
1 TraesCS7A01G526500 chr7A 708326197 708327654 1457 False 587.000000 913 83.871000 708 2137 2 chr7A.!!$F2 1429
2 TraesCS7A01G526500 chr7B 708445613 708447216 1603 False 1844.000000 1844 87.768000 554 2145 1 chr7B.!!$F1 1591
3 TraesCS7A01G526500 chr7B 708529259 708530571 1312 False 1666.000000 1666 89.722000 833 2146 1 chr7B.!!$F3 1313
4 TraesCS7A01G526500 chr7B 708552163 708553590 1427 False 1038.000000 1038 80.845000 708 2143 1 chr7B.!!$F4 1435
5 TraesCS7A01G526500 chr7B 708510642 708513648 3006 False 703.750000 1748 85.672750 53 2750 4 chr7B.!!$F5 2697
6 TraesCS7A01G526500 chr7D 615774599 615775828 1229 False 669.500000 1109 87.503000 708 1923 2 chr7D.!!$F2 1215
7 TraesCS7A01G526500 chr7D 615554530 615559725 5195 True 646.333333 1637 83.281333 726 2881 3 chr7D.!!$R1 2155
8 TraesCS7A01G526500 chr7D 615763811 615767544 3733 False 627.000000 1642 85.444750 705 2787 4 chr7D.!!$F1 2082

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
548 564 0.099082 GTCGAAGTACCAGAGCGAGG 59.901 60.0 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1971 3594 0.730834 CAGTTCAGACTCGGCTGTCG 60.731 60.0 0.0 0.0 41.47 4.35 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
17 18 4.792087 TCGCTCCTTTGTTGGGAC 57.208 55.556 0.00 0.00 0.00 4.46
18 19 2.142220 TCGCTCCTTTGTTGGGACT 58.858 52.632 0.00 0.00 0.00 3.85
19 20 1.344065 TCGCTCCTTTGTTGGGACTA 58.656 50.000 0.00 0.00 0.00 2.59
20 21 1.906574 TCGCTCCTTTGTTGGGACTAT 59.093 47.619 0.00 0.00 0.00 2.12
21 22 2.093658 TCGCTCCTTTGTTGGGACTATC 60.094 50.000 0.00 0.00 0.00 2.08
22 23 2.280628 GCTCCTTTGTTGGGACTATCG 58.719 52.381 0.00 0.00 0.00 2.92
23 24 2.354805 GCTCCTTTGTTGGGACTATCGT 60.355 50.000 0.00 0.00 0.00 3.73
24 25 3.262420 CTCCTTTGTTGGGACTATCGTG 58.738 50.000 0.00 0.00 0.00 4.35
25 26 1.737793 CCTTTGTTGGGACTATCGTGC 59.262 52.381 0.00 0.00 0.00 5.34
26 27 2.422597 CTTTGTTGGGACTATCGTGCA 58.577 47.619 0.00 0.00 32.44 4.57
27 28 2.779755 TTGTTGGGACTATCGTGCAT 57.220 45.000 0.00 0.00 32.44 3.96
28 29 2.022764 TGTTGGGACTATCGTGCATG 57.977 50.000 0.00 0.00 32.44 4.06
29 30 1.299541 GTTGGGACTATCGTGCATGG 58.700 55.000 5.98 0.00 32.44 3.66
30 31 1.134521 GTTGGGACTATCGTGCATGGA 60.135 52.381 5.98 0.00 32.44 3.41
31 32 0.464036 TGGGACTATCGTGCATGGAC 59.536 55.000 7.39 7.39 32.44 4.02
32 33 0.464036 GGGACTATCGTGCATGGACA 59.536 55.000 18.05 5.13 32.44 4.02
33 34 1.571919 GGACTATCGTGCATGGACAC 58.428 55.000 18.05 5.80 37.19 3.67
34 35 1.134818 GGACTATCGTGCATGGACACA 60.135 52.381 18.05 3.22 40.73 3.72
35 36 2.483714 GGACTATCGTGCATGGACACAT 60.484 50.000 18.05 10.63 40.73 3.21
45 46 1.830279 ATGGACACATGAGTTGCAGG 58.170 50.000 0.00 0.00 35.57 4.85
46 47 0.473755 TGGACACATGAGTTGCAGGT 59.526 50.000 0.00 0.00 43.29 4.00
47 48 1.160137 GGACACATGAGTTGCAGGTC 58.840 55.000 0.00 0.00 39.96 3.85
48 49 1.160137 GACACATGAGTTGCAGGTCC 58.840 55.000 0.00 0.00 39.96 4.46
49 50 0.767375 ACACATGAGTTGCAGGTCCT 59.233 50.000 0.00 0.00 39.96 3.85
50 51 1.162698 CACATGAGTTGCAGGTCCTG 58.837 55.000 15.15 15.15 39.96 3.86
62 63 2.665185 GTCCTGCGTTGCGTTCCT 60.665 61.111 0.00 0.00 0.00 3.36
69 70 2.943653 GTTGCGTTCCTTCGGTGG 59.056 61.111 0.00 0.00 0.00 4.61
70 71 2.975799 TTGCGTTCCTTCGGTGGC 60.976 61.111 0.00 0.00 0.00 5.01
99 100 2.305927 GTCCAGGTTGATCTTCAAGGGA 59.694 50.000 0.00 0.00 37.00 4.20
100 101 3.054065 GTCCAGGTTGATCTTCAAGGGAT 60.054 47.826 0.00 0.00 37.00 3.85
101 102 4.164221 GTCCAGGTTGATCTTCAAGGGATA 59.836 45.833 0.00 0.00 37.00 2.59
108 109 9.170890 AGGTTGATCTTCAAGGGATATATGTAA 57.829 33.333 0.00 0.00 37.00 2.41
136 137 1.026182 TGGTGCGTCCAAGATGATGC 61.026 55.000 0.00 0.00 44.12 3.91
150 151 0.684535 TGATGCCTTTCTCGTGACCA 59.315 50.000 0.00 0.00 0.00 4.02
156 157 2.350522 CCTTTCTCGTGACCATCCAAG 58.649 52.381 0.00 0.00 0.00 3.61
157 158 2.289694 CCTTTCTCGTGACCATCCAAGT 60.290 50.000 0.00 0.00 0.00 3.16
158 159 3.403038 CTTTCTCGTGACCATCCAAGTT 58.597 45.455 0.00 0.00 0.00 2.66
160 161 3.040147 TCTCGTGACCATCCAAGTTTC 57.960 47.619 0.00 0.00 0.00 2.78
161 162 1.726791 CTCGTGACCATCCAAGTTTCG 59.273 52.381 0.00 0.00 0.00 3.46
162 163 0.165944 CGTGACCATCCAAGTTTCGC 59.834 55.000 0.00 0.00 0.00 4.70
163 164 0.521735 GTGACCATCCAAGTTTCGCC 59.478 55.000 0.00 0.00 0.00 5.54
164 165 0.109532 TGACCATCCAAGTTTCGCCA 59.890 50.000 0.00 0.00 0.00 5.69
166 167 1.234615 ACCATCCAAGTTTCGCCACG 61.235 55.000 0.00 0.00 0.00 4.94
170 173 0.390124 TCCAAGTTTCGCCACGTACT 59.610 50.000 0.00 0.00 0.00 2.73
186 189 3.254166 ACGTACTCGCCAGTCTCTTTTAA 59.746 43.478 0.00 0.00 41.18 1.52
198 201 4.952335 AGTCTCTTTTAAGCATTCATGGGG 59.048 41.667 0.00 0.00 0.00 4.96
206 209 1.751349 GCATTCATGGGGTGGATGGC 61.751 60.000 0.00 0.00 43.06 4.40
208 211 1.936767 ATTCATGGGGTGGATGGCGT 61.937 55.000 0.00 0.00 0.00 5.68
209 212 2.829914 CATGGGGTGGATGGCGTG 60.830 66.667 0.00 0.00 0.00 5.34
210 213 3.338250 ATGGGGTGGATGGCGTGT 61.338 61.111 0.00 0.00 0.00 4.49
211 214 2.917897 ATGGGGTGGATGGCGTGTT 61.918 57.895 0.00 0.00 0.00 3.32
227 230 2.671351 CGTGTTGGCGAGTGAAGTCTAT 60.671 50.000 0.00 0.00 0.00 1.98
232 235 3.089284 TGGCGAGTGAAGTCTATCTTGA 58.911 45.455 0.00 0.00 36.40 3.02
244 247 7.600375 TGAAGTCTATCTTGATGTGTTGTCTTC 59.400 37.037 0.00 0.00 36.40 2.87
246 249 5.289675 GTCTATCTTGATGTGTTGTCTTCGG 59.710 44.000 0.00 0.00 0.00 4.30
252 255 2.027625 GTGTTGTCTTCGGAGGCGG 61.028 63.158 0.00 0.00 0.00 6.13
275 278 0.249489 GTGTTGGTCGAGACACTGCT 60.249 55.000 15.57 0.00 42.13 4.24
276 279 0.464036 TGTTGGTCGAGACACTGCTT 59.536 50.000 5.55 0.00 0.00 3.91
277 280 1.134521 TGTTGGTCGAGACACTGCTTT 60.135 47.619 5.55 0.00 0.00 3.51
278 281 1.940613 GTTGGTCGAGACACTGCTTTT 59.059 47.619 5.55 0.00 0.00 2.27
279 282 2.325583 TGGTCGAGACACTGCTTTTT 57.674 45.000 5.55 0.00 0.00 1.94
284 287 4.201920 GGTCGAGACACTGCTTTTTCTTTT 60.202 41.667 5.55 0.00 0.00 2.27
296 299 8.951243 ACTGCTTTTTCTTTTAGCTTAGGATAG 58.049 33.333 0.00 0.00 35.93 2.08
298 301 7.148069 TGCTTTTTCTTTTAGCTTAGGATAGGC 60.148 37.037 0.00 0.00 45.05 3.93
306 309 2.090153 AGCTTAGGATAGGCCCCTTGTA 60.090 50.000 4.18 0.00 45.98 2.41
313 316 0.257616 TAGGCCCCTTGTATTGTGGC 59.742 55.000 0.00 0.00 41.42 5.01
331 334 1.595093 GCTGTAATGGGTGTGGTGGC 61.595 60.000 0.00 0.00 0.00 5.01
340 343 0.537143 GGTGTGGTGGCTTGTCATCA 60.537 55.000 0.00 0.00 0.00 3.07
341 344 0.877071 GTGTGGTGGCTTGTCATCAG 59.123 55.000 0.00 0.00 0.00 2.90
345 348 1.271001 TGGTGGCTTGTCATCAGACTG 60.271 52.381 0.00 0.00 45.20 3.51
346 349 1.002430 GGTGGCTTGTCATCAGACTGA 59.998 52.381 7.80 7.80 45.20 3.41
369 372 1.702401 TGATGGGTGTTGGCTTGTCTA 59.298 47.619 0.00 0.00 0.00 2.59
371 374 0.250124 TGGGTGTTGGCTTGTCTACG 60.250 55.000 0.00 0.00 0.00 3.51
402 405 1.146041 TGTGGAGTGGAGTGTGCAC 59.854 57.895 10.75 10.75 39.13 4.57
416 419 3.717775 TGCACTGCACTTGTTGTTG 57.282 47.368 0.00 0.00 31.71 3.33
417 420 0.173029 TGCACTGCACTTGTTGTTGG 59.827 50.000 0.00 0.00 31.71 3.77
419 422 0.173029 CACTGCACTTGTTGTTGGCA 59.827 50.000 0.00 0.00 0.00 4.92
435 438 1.039856 GGCAACAAGGGCTTTCTTCA 58.960 50.000 0.00 0.00 0.00 3.02
437 440 2.825532 GGCAACAAGGGCTTTCTTCATA 59.174 45.455 0.00 0.00 0.00 2.15
473 476 8.721019 TCGTCTTTTATAAAAATATGGTCCGT 57.279 30.769 11.62 0.00 0.00 4.69
475 478 8.066000 CGTCTTTTATAAAAATATGGTCCGTCC 58.934 37.037 11.62 0.00 0.00 4.79
483 486 2.445085 TGGTCCGTCCAGGTGTGT 60.445 61.111 0.00 0.00 41.93 3.72
484 487 2.067605 TGGTCCGTCCAGGTGTGTT 61.068 57.895 0.00 0.00 41.93 3.32
485 488 1.597027 GGTCCGTCCAGGTGTGTTG 60.597 63.158 0.00 0.00 41.99 3.33
486 489 1.145377 GTCCGTCCAGGTGTGTTGT 59.855 57.895 0.00 0.00 41.99 3.32
487 490 0.463116 GTCCGTCCAGGTGTGTTGTT 60.463 55.000 0.00 0.00 41.99 2.83
488 491 1.121378 TCCGTCCAGGTGTGTTGTTA 58.879 50.000 0.00 0.00 41.99 2.41
489 492 1.485480 TCCGTCCAGGTGTGTTGTTAA 59.515 47.619 0.00 0.00 41.99 2.01
490 493 2.105134 TCCGTCCAGGTGTGTTGTTAAT 59.895 45.455 0.00 0.00 41.99 1.40
491 494 2.882137 CCGTCCAGGTGTGTTGTTAATT 59.118 45.455 0.00 0.00 34.51 1.40
492 495 3.316868 CCGTCCAGGTGTGTTGTTAATTT 59.683 43.478 0.00 0.00 34.51 1.82
493 496 4.202070 CCGTCCAGGTGTGTTGTTAATTTT 60.202 41.667 0.00 0.00 34.51 1.82
494 497 4.973663 CGTCCAGGTGTGTTGTTAATTTTC 59.026 41.667 0.00 0.00 0.00 2.29
495 498 5.220970 CGTCCAGGTGTGTTGTTAATTTTCT 60.221 40.000 0.00 0.00 0.00 2.52
496 499 6.569780 GTCCAGGTGTGTTGTTAATTTTCTT 58.430 36.000 0.00 0.00 0.00 2.52
548 564 0.099082 GTCGAAGTACCAGAGCGAGG 59.901 60.000 0.00 0.00 0.00 4.63
568 584 1.933853 GACGAACAAACACTCTGTGCT 59.066 47.619 0.00 0.00 36.98 4.40
581 597 0.385223 CTGTGCTGCGCTTTCACTTC 60.385 55.000 21.16 3.66 0.00 3.01
583 599 2.174349 GCTGCGCTTTCACTTCCG 59.826 61.111 9.73 0.00 0.00 4.30
589 605 0.512952 CGCTTTCACTTCCGGAACTG 59.487 55.000 14.35 15.03 0.00 3.16
590 606 1.872237 CGCTTTCACTTCCGGAACTGA 60.872 52.381 19.07 19.07 0.00 3.41
591 607 2.218603 GCTTTCACTTCCGGAACTGAA 58.781 47.619 26.11 26.11 0.00 3.02
592 608 2.616842 GCTTTCACTTCCGGAACTGAAA 59.383 45.455 32.18 32.18 34.41 2.69
594 610 1.860676 TCACTTCCGGAACTGAAACG 58.139 50.000 20.25 9.46 29.71 3.60
601 620 0.232303 CGGAACTGAAACGACAGCAC 59.768 55.000 0.00 0.00 41.06 4.40
620 639 1.135228 ACACTCGCAAACAAACCAACC 60.135 47.619 0.00 0.00 0.00 3.77
629 648 0.374410 ACAAACCAACCGAAACGACG 59.626 50.000 0.00 0.00 0.00 5.12
633 652 0.665369 ACCAACCGAAACGACGCTAG 60.665 55.000 0.00 0.00 0.00 3.42
681 734 2.942376 CAAAATATGCCACCGCTGTCTA 59.058 45.455 0.00 0.00 35.36 2.59
763 816 3.158648 CCGCGGGTGGGATAGGAA 61.159 66.667 20.10 0.00 0.00 3.36
764 817 2.516888 CCGCGGGTGGGATAGGAAT 61.517 63.158 20.10 0.00 0.00 3.01
765 818 1.189524 CCGCGGGTGGGATAGGAATA 61.190 60.000 20.10 0.00 0.00 1.75
766 819 0.246635 CGCGGGTGGGATAGGAATAG 59.753 60.000 0.00 0.00 0.00 1.73
767 820 0.613777 GCGGGTGGGATAGGAATAGG 59.386 60.000 0.00 0.00 0.00 2.57
775 828 1.817447 GGATAGGAATAGGACCGGACG 59.183 57.143 9.46 0.00 0.00 4.79
875 937 4.697756 CCACATCACCGGCCGTGT 62.698 66.667 26.12 19.00 43.51 4.49
912 2416 2.040884 TCCCATCTCCTTCCCCCG 60.041 66.667 0.00 0.00 0.00 5.73
913 2417 2.040884 CCCATCTCCTTCCCCCGA 60.041 66.667 0.00 0.00 0.00 5.14
914 2418 2.444256 CCCATCTCCTTCCCCCGAC 61.444 68.421 0.00 0.00 0.00 4.79
915 2419 1.689233 CCATCTCCTTCCCCCGACA 60.689 63.158 0.00 0.00 0.00 4.35
916 2420 1.271840 CCATCTCCTTCCCCCGACAA 61.272 60.000 0.00 0.00 0.00 3.18
917 2421 0.107654 CATCTCCTTCCCCCGACAAC 60.108 60.000 0.00 0.00 0.00 3.32
918 2422 1.272554 ATCTCCTTCCCCCGACAACC 61.273 60.000 0.00 0.00 0.00 3.77
921 2425 2.033602 CTTCCCCCGACAACCACC 59.966 66.667 0.00 0.00 0.00 4.61
971 2512 2.893637 AGAATCAATCGTCTTCCCGTG 58.106 47.619 0.00 0.00 0.00 4.94
972 2513 2.496070 AGAATCAATCGTCTTCCCGTGA 59.504 45.455 0.00 0.00 0.00 4.35
973 2514 3.133003 AGAATCAATCGTCTTCCCGTGAT 59.867 43.478 0.00 0.00 0.00 3.06
974 2515 2.579207 TCAATCGTCTTCCCGTGATC 57.421 50.000 0.00 0.00 0.00 2.92
975 2516 1.136305 TCAATCGTCTTCCCGTGATCC 59.864 52.381 0.00 0.00 0.00 3.36
976 2517 0.464452 AATCGTCTTCCCGTGATCCC 59.536 55.000 0.00 0.00 0.00 3.85
977 2518 0.686441 ATCGTCTTCCCGTGATCCCA 60.686 55.000 0.00 0.00 0.00 4.37
978 2519 0.686441 TCGTCTTCCCGTGATCCCAT 60.686 55.000 0.00 0.00 0.00 4.00
979 2520 0.178068 CGTCTTCCCGTGATCCCATT 59.822 55.000 0.00 0.00 0.00 3.16
980 2521 1.806623 CGTCTTCCCGTGATCCCATTC 60.807 57.143 0.00 0.00 0.00 2.67
981 2522 0.837272 TCTTCCCGTGATCCCATTCC 59.163 55.000 0.00 0.00 0.00 3.01
982 2523 0.532862 CTTCCCGTGATCCCATTCCG 60.533 60.000 0.00 0.00 0.00 4.30
983 2524 1.268992 TTCCCGTGATCCCATTCCGT 61.269 55.000 0.00 0.00 0.00 4.69
989 2530 1.037493 TGATCCCATTCCGTCGTAGG 58.963 55.000 0.00 0.00 0.00 3.18
1351 2917 3.164977 TTGGTGCTGACGGGGTCA 61.165 61.111 0.00 0.00 40.50 4.02
1368 2934 4.035843 ACCGAGGGTGATCTGGAC 57.964 61.111 0.00 0.00 32.98 4.02
1701 3303 4.065281 GCTACGGCGTCCACCACT 62.065 66.667 19.21 0.00 0.00 4.00
1971 3594 2.676839 TCGACTCGACCAATCACTCTAC 59.323 50.000 0.00 0.00 0.00 2.59
2146 6533 4.808364 TGTTTTCCTCCGAAAGCAAAAATG 59.192 37.500 0.41 0.00 43.58 2.32
2147 6534 3.658757 TTCCTCCGAAAGCAAAAATGG 57.341 42.857 0.00 0.00 0.00 3.16
2148 6535 1.892474 TCCTCCGAAAGCAAAAATGGG 59.108 47.619 0.00 0.00 0.00 4.00
2149 6536 1.672737 CCTCCGAAAGCAAAAATGGGC 60.673 52.381 0.00 0.00 0.00 5.36
2150 6537 1.000731 CTCCGAAAGCAAAAATGGGCA 59.999 47.619 0.00 0.00 0.00 5.36
2152 6539 1.539929 CCGAAAGCAAAAATGGGCACA 60.540 47.619 0.00 0.00 0.00 4.57
2153 6540 2.208431 CGAAAGCAAAAATGGGCACAA 58.792 42.857 0.00 0.00 0.00 3.33
2155 6542 1.596603 AAGCAAAAATGGGCACAAGC 58.403 45.000 0.00 0.00 41.10 4.01
2156 6543 0.760572 AGCAAAAATGGGCACAAGCT 59.239 45.000 0.00 0.00 41.70 3.74
2157 6544 0.869730 GCAAAAATGGGCACAAGCTG 59.130 50.000 0.00 0.00 41.70 4.24
2260 6893 7.324354 TCCCAAAAGTTAGTGAACTACAAAC 57.676 36.000 0.00 0.00 45.50 2.93
2306 6988 7.224362 TCGTGAAATTCAAAGATTGTTTGCAAT 59.776 29.630 0.00 0.00 46.99 3.56
2307 6989 7.851963 CGTGAAATTCAAAGATTGTTTGCAATT 59.148 29.630 0.00 6.27 44.61 2.32
2351 7068 6.917477 TGTTTAAGAAATGTTCATGCAGTGTC 59.083 34.615 0.00 0.00 0.00 3.67
2663 7519 9.256715 GTTTTAAACCATTTTCAAAAGTGTTCG 57.743 29.630 0.00 0.00 0.00 3.95
2671 7527 2.115595 TCAAAAGTGTTCGCGCATTTG 58.884 42.857 8.75 3.45 43.48 2.32
2676 7532 2.116366 AGTGTTCGCGCATTTGAAAAC 58.884 42.857 8.75 8.10 33.40 2.43
2722 7579 6.927933 AAATGCACGCATAGTTAAAAGAAC 57.072 33.333 4.68 0.00 35.31 3.01
2769 7626 6.809630 TCACATATTTCCGAAATGTGTTCA 57.190 33.333 25.33 16.10 46.68 3.18
2853 7712 8.611757 TGTTTCCTATCATTCACACAATATTCG 58.388 33.333 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.344065 TAGTCCCAACAAAGGAGCGA 58.656 50.000 0.00 0.00 32.84 4.93
2 3 2.280628 CGATAGTCCCAACAAAGGAGC 58.719 52.381 0.00 0.00 32.84 4.70
14 15 4.591591 CATGTGTCCATGCACGATAGTCC 61.592 52.174 0.00 0.00 44.08 3.85
15 16 2.541346 CATGTGTCCATGCACGATAGTC 59.459 50.000 0.00 0.00 44.08 2.59
16 17 2.554142 CATGTGTCCATGCACGATAGT 58.446 47.619 0.00 0.00 45.37 2.12
17 18 2.798847 CTCATGTGTCCATGCACGATAG 59.201 50.000 0.00 0.00 46.64 2.08
18 19 2.168313 ACTCATGTGTCCATGCACGATA 59.832 45.455 0.00 0.00 46.64 2.92
19 20 1.065926 ACTCATGTGTCCATGCACGAT 60.066 47.619 0.00 0.00 46.64 3.73
20 21 0.321346 ACTCATGTGTCCATGCACGA 59.679 50.000 0.00 0.00 46.64 4.35
21 22 1.135888 CAACTCATGTGTCCATGCACG 60.136 52.381 0.03 0.00 46.64 5.34
22 23 1.401931 GCAACTCATGTGTCCATGCAC 60.402 52.381 14.91 0.00 46.64 4.57
23 24 0.883153 GCAACTCATGTGTCCATGCA 59.117 50.000 14.91 0.00 46.64 3.96
24 25 0.883153 TGCAACTCATGTGTCCATGC 59.117 50.000 13.54 13.54 46.64 4.06
26 27 1.074405 ACCTGCAACTCATGTGTCCAT 59.926 47.619 0.03 0.00 0.00 3.41
27 28 0.473755 ACCTGCAACTCATGTGTCCA 59.526 50.000 0.03 1.57 0.00 4.02
28 29 1.160137 GACCTGCAACTCATGTGTCC 58.840 55.000 0.03 0.00 0.00 4.02
29 30 1.160137 GGACCTGCAACTCATGTGTC 58.840 55.000 0.03 0.00 0.00 3.67
30 31 0.767375 AGGACCTGCAACTCATGTGT 59.233 50.000 0.00 0.00 0.00 3.72
31 32 1.162698 CAGGACCTGCAACTCATGTG 58.837 55.000 8.99 0.00 0.00 3.21
32 33 3.639099 CAGGACCTGCAACTCATGT 57.361 52.632 8.99 0.00 0.00 3.21
42 43 2.954753 GAACGCAACGCAGGACCTG 61.955 63.158 17.83 17.83 34.12 4.00
43 44 2.665185 GAACGCAACGCAGGACCT 60.665 61.111 0.00 0.00 0.00 3.85
44 45 3.723348 GGAACGCAACGCAGGACC 61.723 66.667 0.00 0.00 0.00 4.46
45 46 2.171489 GAAGGAACGCAACGCAGGAC 62.171 60.000 0.00 0.00 0.00 3.85
46 47 1.959226 GAAGGAACGCAACGCAGGA 60.959 57.895 0.00 0.00 0.00 3.86
47 48 2.556287 GAAGGAACGCAACGCAGG 59.444 61.111 0.00 0.00 0.00 4.85
48 49 2.170985 CGAAGGAACGCAACGCAG 59.829 61.111 0.00 0.00 0.00 5.18
69 70 2.594592 AACCTGGACAGCAACGGC 60.595 61.111 0.00 0.00 41.61 5.68
70 71 0.606401 ATCAACCTGGACAGCAACGG 60.606 55.000 0.00 0.00 0.00 4.44
71 72 0.798776 GATCAACCTGGACAGCAACG 59.201 55.000 0.00 0.00 0.00 4.10
99 100 5.171476 GCACCAGCGATGACTTACATATAT 58.829 41.667 0.06 0.00 39.56 0.86
100 101 4.556233 GCACCAGCGATGACTTACATATA 58.444 43.478 0.06 0.00 39.56 0.86
101 102 3.393800 GCACCAGCGATGACTTACATAT 58.606 45.455 0.06 0.00 39.56 1.78
136 137 2.289694 ACTTGGATGGTCACGAGAAAGG 60.290 50.000 0.00 0.00 0.00 3.11
150 151 1.001633 AGTACGTGGCGAAACTTGGAT 59.998 47.619 0.00 0.00 0.00 3.41
156 157 2.723719 GGCGAGTACGTGGCGAAAC 61.724 63.158 0.00 0.00 41.98 2.78
157 158 2.431260 GGCGAGTACGTGGCGAAA 60.431 61.111 0.00 0.00 41.98 3.46
158 159 3.620300 CTGGCGAGTACGTGGCGAA 62.620 63.158 0.00 0.00 41.98 4.70
160 161 4.415332 ACTGGCGAGTACGTGGCG 62.415 66.667 0.00 0.00 41.98 5.69
161 162 2.506438 GACTGGCGAGTACGTGGC 60.506 66.667 0.00 6.94 41.98 5.01
162 163 1.136984 GAGACTGGCGAGTACGTGG 59.863 63.158 0.00 0.00 41.98 4.94
163 164 0.522180 AAGAGACTGGCGAGTACGTG 59.478 55.000 0.00 0.00 41.98 4.49
164 165 1.245732 AAAGAGACTGGCGAGTACGT 58.754 50.000 0.00 0.00 41.98 3.57
166 167 3.613299 GCTTAAAAGAGACTGGCGAGTAC 59.387 47.826 0.00 0.00 30.16 2.73
170 173 2.831685 TGCTTAAAAGAGACTGGCGA 57.168 45.000 0.00 0.00 0.00 5.54
186 189 0.105862 CCATCCACCCCATGAATGCT 60.106 55.000 0.00 0.00 0.00 3.79
198 201 4.101790 CGCCAACACGCCATCCAC 62.102 66.667 0.00 0.00 0.00 4.02
206 209 0.597637 AGACTTCACTCGCCAACACG 60.598 55.000 0.00 0.00 0.00 4.49
208 211 2.826128 AGATAGACTTCACTCGCCAACA 59.174 45.455 0.00 0.00 0.00 3.33
209 212 3.512033 AGATAGACTTCACTCGCCAAC 57.488 47.619 0.00 0.00 0.00 3.77
210 213 3.509967 TCAAGATAGACTTCACTCGCCAA 59.490 43.478 0.00 0.00 36.61 4.52
211 214 3.089284 TCAAGATAGACTTCACTCGCCA 58.911 45.455 0.00 0.00 36.61 5.69
227 230 3.554960 CCTCCGAAGACAACACATCAAGA 60.555 47.826 0.00 0.00 0.00 3.02
232 235 0.670546 CGCCTCCGAAGACAACACAT 60.671 55.000 0.00 0.00 36.29 3.21
246 249 4.643387 ACCAACACCTGCCGCCTC 62.643 66.667 0.00 0.00 0.00 4.70
252 255 1.069090 TGTCTCGACCAACACCTGC 59.931 57.895 0.00 0.00 0.00 4.85
275 278 6.605995 GGGCCTATCCTAAGCTAAAAGAAAAA 59.394 38.462 0.84 0.00 34.39 1.94
276 279 6.127101 GGGCCTATCCTAAGCTAAAAGAAAA 58.873 40.000 0.84 0.00 34.39 2.29
277 280 5.398695 GGGGCCTATCCTAAGCTAAAAGAAA 60.399 44.000 0.84 0.00 34.39 2.52
278 281 4.104261 GGGGCCTATCCTAAGCTAAAAGAA 59.896 45.833 0.84 0.00 34.39 2.52
279 282 3.651423 GGGGCCTATCCTAAGCTAAAAGA 59.349 47.826 0.84 0.00 34.39 2.52
284 287 2.090153 ACAAGGGGCCTATCCTAAGCTA 60.090 50.000 0.84 0.00 33.58 3.32
296 299 1.000359 AGCCACAATACAAGGGGCC 60.000 57.895 2.30 0.00 45.72 5.80
298 301 2.799126 TACAGCCACAATACAAGGGG 57.201 50.000 0.00 0.00 0.00 4.79
306 309 2.170166 CACACCCATTACAGCCACAAT 58.830 47.619 0.00 0.00 0.00 2.71
313 316 0.038166 AGCCACCACACCCATTACAG 59.962 55.000 0.00 0.00 0.00 2.74
340 343 2.290514 CCAACACCCATCATGTCAGTCT 60.291 50.000 0.00 0.00 0.00 3.24
341 344 2.086869 CCAACACCCATCATGTCAGTC 58.913 52.381 0.00 0.00 0.00 3.51
345 348 1.203052 CAAGCCAACACCCATCATGTC 59.797 52.381 0.00 0.00 0.00 3.06
346 349 1.259609 CAAGCCAACACCCATCATGT 58.740 50.000 0.00 0.00 0.00 3.21
348 351 1.076024 AGACAAGCCAACACCCATCAT 59.924 47.619 0.00 0.00 0.00 2.45
351 354 1.610624 CGTAGACAAGCCAACACCCAT 60.611 52.381 0.00 0.00 0.00 4.00
369 372 1.594293 CACACCGAGGCAAGTTCGT 60.594 57.895 0.00 0.00 36.37 3.85
371 374 0.951040 CTCCACACCGAGGCAAGTTC 60.951 60.000 0.00 0.00 0.00 3.01
402 405 3.737127 TTGCCAACAACAAGTGCAG 57.263 47.368 0.00 0.00 31.70 4.41
416 419 1.039856 TGAAGAAAGCCCTTGTTGCC 58.960 50.000 0.00 0.00 0.00 4.52
417 420 4.725790 ATATGAAGAAAGCCCTTGTTGC 57.274 40.909 0.00 0.00 0.00 4.17
419 422 9.700831 ATAAGTTATATGAAGAAAGCCCTTGTT 57.299 29.630 0.00 0.00 0.00 2.83
449 452 8.066000 GGACGGACCATATTTTTATAAAAGACG 58.934 37.037 10.40 10.69 38.79 4.18
468 471 0.463116 AACAACACACCTGGACGGAC 60.463 55.000 0.00 0.00 36.31 4.79
470 473 1.956297 TTAACAACACACCTGGACGG 58.044 50.000 0.00 0.00 39.35 4.79
471 474 4.561735 AAATTAACAACACACCTGGACG 57.438 40.909 0.00 0.00 0.00 4.79
473 476 6.783708 AAGAAAATTAACAACACACCTGGA 57.216 33.333 0.00 0.00 0.00 3.86
475 478 8.930760 TCAAAAAGAAAATTAACAACACACCTG 58.069 29.630 0.00 0.00 0.00 4.00
476 479 9.495572 TTCAAAAAGAAAATTAACAACACACCT 57.504 25.926 0.00 0.00 32.05 4.00
525 541 0.524862 GCTCTGGTACTTCGACCGAA 59.475 55.000 4.72 4.72 42.99 4.30
529 545 0.099082 CCTCGCTCTGGTACTTCGAC 59.901 60.000 0.00 0.00 0.00 4.20
539 555 0.784778 GTTTGTTCGTCCTCGCTCTG 59.215 55.000 0.00 0.00 36.96 3.35
540 556 0.387929 TGTTTGTTCGTCCTCGCTCT 59.612 50.000 0.00 0.00 36.96 4.09
548 564 1.933853 AGCACAGAGTGTTTGTTCGTC 59.066 47.619 0.00 0.00 35.75 4.20
568 584 1.227704 TTCCGGAAGTGAAAGCGCA 60.228 52.632 14.35 0.00 0.00 6.09
581 597 0.878523 TGCTGTCGTTTCAGTTCCGG 60.879 55.000 0.00 0.00 37.70 5.14
583 599 1.003866 GTGTGCTGTCGTTTCAGTTCC 60.004 52.381 0.00 0.00 37.70 3.62
589 605 1.201825 GCGAGTGTGCTGTCGTTTC 59.798 57.895 0.00 0.00 38.48 2.78
590 606 1.087202 TTGCGAGTGTGCTGTCGTTT 61.087 50.000 0.00 0.00 38.48 3.60
591 607 1.087202 TTTGCGAGTGTGCTGTCGTT 61.087 50.000 0.00 0.00 38.48 3.85
592 608 1.520564 TTTGCGAGTGTGCTGTCGT 60.521 52.632 0.00 0.00 38.48 4.34
594 610 0.376852 TTGTTTGCGAGTGTGCTGTC 59.623 50.000 0.00 0.00 35.36 3.51
601 620 1.555477 GGTTGGTTTGTTTGCGAGTG 58.445 50.000 0.00 0.00 0.00 3.51
620 639 0.387622 TGAACCCTAGCGTCGTTTCG 60.388 55.000 0.00 0.00 0.00 3.46
666 719 2.187946 GCTAGACAGCGGTGGCAT 59.812 61.111 24.58 10.38 43.41 4.40
690 743 4.101448 GCGTCTCACTGGCCCCAT 62.101 66.667 0.00 0.00 0.00 4.00
762 815 1.380785 TGCCTCGTCCGGTCCTATT 60.381 57.895 0.00 0.00 0.00 1.73
763 816 1.828660 CTGCCTCGTCCGGTCCTAT 60.829 63.158 0.00 0.00 0.00 2.57
764 817 2.439701 CTGCCTCGTCCGGTCCTA 60.440 66.667 0.00 0.00 0.00 2.94
767 820 3.827898 CTCCTGCCTCGTCCGGTC 61.828 72.222 0.00 0.00 0.00 4.79
775 828 1.157585 GAAACGAAACCTCCTGCCTC 58.842 55.000 0.00 0.00 0.00 4.70
874 936 1.283736 CGTGGTATTTGTAGCCGGAC 58.716 55.000 5.05 0.00 0.00 4.79
875 937 0.460635 GCGTGGTATTTGTAGCCGGA 60.461 55.000 5.05 0.00 0.00 5.14
912 2416 1.826487 GGTGGTGGTGGTGGTTGTC 60.826 63.158 0.00 0.00 0.00 3.18
913 2417 2.277404 GGTGGTGGTGGTGGTTGT 59.723 61.111 0.00 0.00 0.00 3.32
914 2418 2.124693 GTGGTGGTGGTGGTGGTTG 61.125 63.158 0.00 0.00 0.00 3.77
915 2419 2.277404 GTGGTGGTGGTGGTGGTT 59.723 61.111 0.00 0.00 0.00 3.67
916 2420 3.816090 GGTGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.00 0.00 4.16
917 2421 4.947147 CGGTGGTGGTGGTGGTGG 62.947 72.222 0.00 0.00 0.00 4.61
971 2512 0.319641 GCCTACGACGGAATGGGATC 60.320 60.000 0.00 0.00 0.00 3.36
972 2513 0.759436 AGCCTACGACGGAATGGGAT 60.759 55.000 0.00 0.00 0.00 3.85
973 2514 1.380785 AGCCTACGACGGAATGGGA 60.381 57.895 0.00 0.00 0.00 4.37
974 2515 1.067582 GAGCCTACGACGGAATGGG 59.932 63.158 0.00 0.00 0.00 4.00
975 2516 1.299165 CGAGCCTACGACGGAATGG 60.299 63.158 0.00 0.00 35.09 3.16
976 2517 0.659427 TACGAGCCTACGACGGAATG 59.341 55.000 0.00 0.00 37.03 2.67
977 2518 0.659957 GTACGAGCCTACGACGGAAT 59.340 55.000 0.00 0.00 37.03 3.01
978 2519 0.391661 AGTACGAGCCTACGACGGAA 60.392 55.000 0.00 0.00 37.03 4.30
979 2520 0.459899 TAGTACGAGCCTACGACGGA 59.540 55.000 0.00 0.00 37.03 4.69
980 2521 0.857935 CTAGTACGAGCCTACGACGG 59.142 60.000 0.00 0.00 37.03 4.79
981 2522 1.845266 TCTAGTACGAGCCTACGACG 58.155 55.000 0.00 0.00 37.03 5.12
982 2523 2.479656 CCATCTAGTACGAGCCTACGAC 59.520 54.545 0.00 0.00 37.03 4.34
983 2524 2.366590 TCCATCTAGTACGAGCCTACGA 59.633 50.000 0.00 0.00 37.03 3.43
989 2530 1.249407 CCCCTCCATCTAGTACGAGC 58.751 60.000 0.00 0.00 0.00 5.03
1351 2917 2.052690 CGTCCAGATCACCCTCGGT 61.053 63.158 0.00 0.00 35.62 4.69
1608 3198 1.307647 GTGGAACCCATGGGCATCT 59.692 57.895 31.73 12.96 39.32 2.90
1971 3594 0.730834 CAGTTCAGACTCGGCTGTCG 60.731 60.000 0.00 0.00 41.47 4.35
2008 3679 4.974645 TTGCCTAGTTCTTCTTTCTCCA 57.025 40.909 0.00 0.00 0.00 3.86
2163 6795 5.828299 TTTTGAAATTCACGTCCAGAACT 57.172 34.783 0.00 0.00 0.00 3.01
2247 6880 5.583061 TGAATTCGTGTGTTTGTAGTTCACT 59.417 36.000 0.04 0.00 33.82 3.41
2320 7037 5.103290 TGAACATTTCTTAAACAGCCGAC 57.897 39.130 0.00 0.00 0.00 4.79
2324 7041 5.922544 ACTGCATGAACATTTCTTAAACAGC 59.077 36.000 0.00 0.00 0.00 4.40
2326 7043 6.804677 ACACTGCATGAACATTTCTTAAACA 58.195 32.000 0.00 0.00 0.00 2.83
2651 7507 2.115595 CAAATGCGCGAACACTTTTGA 58.884 42.857 12.10 0.00 34.55 2.69
2652 7508 2.115595 TCAAATGCGCGAACACTTTTG 58.884 42.857 12.10 7.51 34.16 2.44
2702 7558 5.682943 AAGTTCTTTTAACTATGCGTGCA 57.317 34.783 0.00 0.00 0.00 4.57
2703 7559 6.986424 AAAAGTTCTTTTAACTATGCGTGC 57.014 33.333 8.52 0.00 0.00 5.34
2750 7607 7.389803 TGACATGAACACATTTCGGAAATAT 57.610 32.000 15.13 1.76 0.00 1.28
2827 7686 8.611757 CGAATATTGTGTGAATGATAGGAAACA 58.388 33.333 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.