Multiple sequence alignment - TraesCS3A01G493600

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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 TraesCS3A01G493600 chr3A 100.000 6137 0 0 1 6137 719943455 719937319 0.000000e+00 11334.0
1 TraesCS3A01G493600 chr3A 92.555 1370 79 12 3130 4495 720082375 720081025 0.000000e+00 1943.0
2 TraesCS3A01G493600 chr3A 89.769 1388 98 10 4489 5854 720080609 720079244 0.000000e+00 1736.0
3 TraesCS3A01G493600 chr3A 87.396 1317 140 23 3908 5204 719778537 719779847 0.000000e+00 1489.0
4 TraesCS3A01G493600 chr3A 84.951 1329 157 32 3856 5161 719837886 719839194 0.000000e+00 1306.0
5 TraesCS3A01G493600 chr3A 86.025 644 78 6 1277 1917 720083077 720082443 0.000000e+00 680.0
6 TraesCS3A01G493600 chr3A 76.754 998 172 37 856 1812 719932862 719933840 2.550000e-138 503.0
7 TraesCS3A01G493600 chr3A 75.894 979 182 36 895 1836 720228129 720229090 9.380000e-123 451.0
8 TraesCS3A01G493600 chr3A 77.094 764 153 15 1063 1815 719775925 719776677 7.350000e-114 422.0
9 TraesCS3A01G493600 chr3A 88.803 259 29 0 3366 3624 719995392 719995650 9.930000e-83 318.0
10 TraesCS3A01G493600 chr3A 80.493 446 62 12 846 1282 720084249 720083820 9.930000e-83 318.0
11 TraesCS3A01G493600 chr3A 84.161 322 21 14 363 655 720084585 720084265 1.010000e-72 285.0
12 TraesCS3A01G493600 chr3A 96.154 104 4 0 6034 6137 720232215 720232112 2.940000e-38 171.0
13 TraesCS3A01G493600 chr3A 83.243 185 26 2 5851 6030 720223444 720223260 1.370000e-36 165.0
14 TraesCS3A01G493600 chr3A 90.476 105 4 1 5856 5960 720079121 720079023 3.860000e-27 134.0
15 TraesCS3A01G493600 chr3A 91.579 95 7 1 6044 6137 720078887 720078793 4.990000e-26 130.0
16 TraesCS3A01G493600 chr3A 84.746 118 13 2 5918 6030 720232385 720232268 5.030000e-21 113.0
17 TraesCS3A01G493600 chr3A 96.154 52 1 1 356 407 719991073 719991123 3.940000e-12 84.2
18 TraesCS3A01G493600 chr3A 95.349 43 2 0 5918 5960 720078986 720078944 1.100000e-07 69.4
19 TraesCS3A01G493600 chr3D 94.826 2706 114 14 2563 5248 590223138 590220439 0.000000e+00 4198.0
20 TraesCS3A01G493600 chr3D 93.492 2182 92 23 438 2582 590225354 590223186 0.000000e+00 3197.0
21 TraesCS3A01G493600 chr3D 87.729 1312 141 17 3908 5204 590043011 590044317 0.000000e+00 1513.0
22 TraesCS3A01G493600 chr3D 84.106 1315 171 29 3856 5160 590149171 590150457 0.000000e+00 1236.0
23 TraesCS3A01G493600 chr3D 84.353 1291 164 28 3868 5138 590091835 590090563 0.000000e+00 1230.0
24 TraesCS3A01G493600 chr3D 84.489 851 108 13 1063 1904 590040479 590041314 0.000000e+00 819.0
25 TraesCS3A01G493600 chr3D 90.843 415 16 7 1 400 590225758 590225351 2.520000e-148 536.0
26 TraesCS3A01G493600 chr3D 76.181 1037 183 39 856 1848 590238323 590239339 7.150000e-134 488.0
27 TraesCS3A01G493600 chr3D 79.234 679 96 23 3092 3739 590148490 590149154 1.220000e-116 431.0
28 TraesCS3A01G493600 chr3D 78.730 677 102 21 3091 3739 590092526 590091864 1.230000e-111 414.0
29 TraesCS3A01G493600 chr3D 91.096 292 21 3 5851 6137 590205664 590205373 2.070000e-104 390.0
30 TraesCS3A01G493600 chr3D 92.118 203 14 2 5601 5802 590205998 590205797 1.010000e-72 285.0
31 TraesCS3A01G493600 chr3D 87.854 247 16 5 5281 5513 590220440 590220194 1.680000e-70 278.0
32 TraesCS3A01G493600 chr3D 93.333 105 7 0 6033 6137 590309756 590309652 8.240000e-34 156.0
33 TraesCS3A01G493600 chr3D 96.471 85 2 1 5508 5591 590219126 590219042 8.290000e-29 139.0
34 TraesCS3A01G493600 chr3D 87.143 70 5 3 783 850 448426155 448426088 6.600000e-10 76.8
35 TraesCS3A01G493600 chr3B 93.171 2343 123 20 3069 5401 789184108 789181793 0.000000e+00 3406.0
36 TraesCS3A01G493600 chr3B 83.560 1326 175 34 3856 5159 788985076 788986380 0.000000e+00 1201.0
37 TraesCS3A01G493600 chr3B 86.238 901 112 11 3856 4750 789057308 789058202 0.000000e+00 966.0
38 TraesCS3A01G493600 chr3B 82.900 924 142 11 1005 1917 789185048 789184130 0.000000e+00 817.0
39 TraesCS3A01G493600 chr3B 76.958 1098 191 39 861 1911 789175902 789176984 2.480000e-158 569.0
40 TraesCS3A01G493600 chr3B 91.443 409 30 4 5397 5800 789181756 789181348 1.930000e-154 556.0
41 TraesCS3A01G493600 chr3B 79.056 678 98 23 3090 3739 788936216 788936877 5.690000e-115 425.0
42 TraesCS3A01G493600 chr3B 78.909 678 99 25 3090 3739 788984398 788985059 2.650000e-113 420.0
43 TraesCS3A01G493600 chr3B 78.957 556 73 22 3090 3613 789056623 789057166 7.620000e-89 339.0
44 TraesCS3A01G493600 chr3B 90.816 196 13 2 5851 6046 789181213 789181023 2.190000e-64 257.0
45 TraesCS3A01G493600 chr3B 94.286 105 6 0 6033 6137 789230433 789230329 1.770000e-35 161.0
46 TraesCS3A01G493600 chr3B 96.610 59 2 0 6079 6137 789181026 789180968 1.410000e-16 99.0
47 TraesCS3A01G493600 chr3B 98.000 50 1 0 356 405 789217248 789217297 3.050000e-13 87.9
48 TraesCS3A01G493600 chr3B 81.081 111 14 4 5918 6022 789230593 789230484 1.420000e-11 82.4
49 TraesCS3A01G493600 chr1A 91.803 61 4 1 783 843 555306657 555306598 3.940000e-12 84.2
50 TraesCS3A01G493600 chr4D 85.714 70 6 3 783 850 480458181 480458248 3.070000e-08 71.3
51 TraesCS3A01G493600 chr2B 88.333 60 5 2 783 842 151488506 151488449 3.070000e-08 71.3
52 TraesCS3A01G493600 chr4A 93.023 43 3 0 781 823 484357930 484357972 5.140000e-06 63.9
53 TraesCS3A01G493600 chr7D 86.207 58 7 1 2241 2297 77396061 77396004 1.850000e-05 62.1
54 TraesCS3A01G493600 chr7D 100.000 31 0 0 794 824 631571976 631571946 2.390000e-04 58.4


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 TraesCS3A01G493600 chr3A 719937319 719943455 6136 True 11334.000 11334 100.000000 1 6137 1 chr3A.!!$R1 6136
1 TraesCS3A01G493600 chr3A 719837886 719839194 1308 False 1306.000 1306 84.951000 3856 5161 1 chr3A.!!$F1 1305
2 TraesCS3A01G493600 chr3A 719775925 719779847 3922 False 955.500 1489 82.245000 1063 5204 2 chr3A.!!$F6 4141
3 TraesCS3A01G493600 chr3A 720078793 720084585 5792 True 661.925 1943 88.800875 363 6137 8 chr3A.!!$R3 5774
4 TraesCS3A01G493600 chr3A 719932862 719933840 978 False 503.000 503 76.754000 856 1812 1 chr3A.!!$F2 956
5 TraesCS3A01G493600 chr3A 720228129 720229090 961 False 451.000 451 75.894000 895 1836 1 chr3A.!!$F5 941
6 TraesCS3A01G493600 chr3D 590219042 590225758 6716 True 1669.600 4198 92.697200 1 5591 5 chr3D.!!$R5 5590
7 TraesCS3A01G493600 chr3D 590040479 590044317 3838 False 1166.000 1513 86.109000 1063 5204 2 chr3D.!!$F2 4141
8 TraesCS3A01G493600 chr3D 590148490 590150457 1967 False 833.500 1236 81.670000 3092 5160 2 chr3D.!!$F3 2068
9 TraesCS3A01G493600 chr3D 590090563 590092526 1963 True 822.000 1230 81.541500 3091 5138 2 chr3D.!!$R3 2047
10 TraesCS3A01G493600 chr3D 590238323 590239339 1016 False 488.000 488 76.181000 856 1848 1 chr3D.!!$F1 992
11 TraesCS3A01G493600 chr3D 590205373 590205998 625 True 337.500 390 91.607000 5601 6137 2 chr3D.!!$R4 536
12 TraesCS3A01G493600 chr3B 789180968 789185048 4080 True 1027.000 3406 90.988000 1005 6137 5 chr3B.!!$R1 5132
13 TraesCS3A01G493600 chr3B 788984398 788986380 1982 False 810.500 1201 81.234500 3090 5159 2 chr3B.!!$F4 2069
14 TraesCS3A01G493600 chr3B 789056623 789058202 1579 False 652.500 966 82.597500 3090 4750 2 chr3B.!!$F5 1660
15 TraesCS3A01G493600 chr3B 789175902 789176984 1082 False 569.000 569 76.958000 861 1911 1 chr3B.!!$F2 1050
16 TraesCS3A01G493600 chr3B 788936216 788936877 661 False 425.000 425 79.056000 3090 3739 1 chr3B.!!$F1 649

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
709 775 0.308993 GCTGTCTTTGCAGGTGTGAC 59.691 55.0 0.00 0.00 37.0 3.67 F
1051 1139 0.034186 GCCTTGTCACCCATGGATGA 60.034 55.0 15.22 9.78 40.1 2.92 F
1225 1325 0.754957 CACCACCCTCTTTGCAACCA 60.755 55.0 0.00 0.00 0.0 3.67 F
2817 4128 0.397564 ACCATTTTTGGGCCAGCAAG 59.602 50.0 6.23 0.00 0.0 4.01 F
4079 5831 0.324552 TGGGATGTTGCATTCTGGGG 60.325 55.0 0.00 0.00 0.0 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2583 3813 0.250513 GGTCCGACCAGATTTCAGCT 59.749 55.0 13.05 0.0 38.42 4.24 R
2795 4093 0.686789 GCTGGCCCAAAAATGGTTCT 59.313 50.0 0.00 0.0 0.00 3.01 R
2857 4169 1.654317 GAGCATCTCCAACAGCAGAG 58.346 55.0 0.00 0.0 0.00 3.35 R
4626 6811 1.157870 CCAAAGCTGAACACGTCGGT 61.158 55.0 0.00 0.0 34.76 4.69 R
5975 9430 0.038435 TCGTTTTACACCGATGGCGA 60.038 50.0 0.00 0.0 40.82 5.54 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
30 31 4.106925 GCCCCCTGGAGCAGACTG 62.107 72.222 0.00 0.00 32.44 3.51
31 32 4.106925 CCCCCTGGAGCAGACTGC 62.107 72.222 20.12 20.12 45.46 4.40
137 138 2.176889 TCCTGTGGTAAGCTCTGTACC 58.823 52.381 6.19 6.19 41.32 3.34
145 146 3.939592 GGTAAGCTCTGTACCAAATCACC 59.060 47.826 8.02 0.00 40.73 4.02
191 193 5.702670 TCATGGTTTAAGACAGCTTCTCTTG 59.297 40.000 12.06 3.79 35.56 3.02
217 219 2.797792 GCAGAGCTCTGTGGTCGAATAG 60.798 54.545 37.25 14.12 46.86 1.73
231 233 1.553248 CGAATAGGCCCCGATCCATAA 59.447 52.381 0.00 0.00 0.00 1.90
233 235 3.741388 CGAATAGGCCCCGATCCATAATC 60.741 52.174 0.00 0.00 0.00 1.75
237 239 1.843851 GGCCCCGATCCATAATCCATA 59.156 52.381 0.00 0.00 0.00 2.74
256 258 5.831525 TCCATAAGCCTCAACGAACTATCTA 59.168 40.000 0.00 0.00 0.00 1.98
334 348 5.368989 CGGGGCTAGATTCTTTATTGAGTT 58.631 41.667 0.00 0.00 0.00 3.01
349 363 8.624367 TTTATTGAGTTGAGAATTTTCGGGTA 57.376 30.769 0.00 0.00 0.00 3.69
419 433 4.518211 GCTTAATCCCTGATGTCTGAATGG 59.482 45.833 0.00 0.00 0.00 3.16
424 438 2.477825 CCTGATGTCTGAATGGCTACG 58.522 52.381 0.00 0.00 0.00 3.51
455 469 8.078596 ACATCTGAACTTTGAAATTTAGAGCAC 58.921 33.333 0.00 0.00 0.00 4.40
505 524 3.255888 ACACTTCTCTGATGCTTACACGA 59.744 43.478 0.00 0.00 0.00 4.35
518 539 3.626977 CTTACACGACAATTTTGCAGCA 58.373 40.909 0.00 0.00 0.00 4.41
624 669 3.239449 TCTTCTAGCTCCACAGGTTTCA 58.761 45.455 0.00 0.00 0.00 2.69
656 722 6.313411 GTGAATTTTTGCCAGCAATAGCATTA 59.687 34.615 5.80 0.00 45.49 1.90
660 726 5.657826 TTTGCCAGCAATAGCATTAAGAA 57.342 34.783 5.80 0.00 45.49 2.52
671 737 7.486232 GCAATAGCATTAAGAAAGAGAAACCAC 59.514 37.037 0.00 0.00 41.58 4.16
709 775 0.308993 GCTGTCTTTGCAGGTGTGAC 59.691 55.000 0.00 0.00 37.00 3.67
726 792 3.826157 TGTGACAAGATGGACATTTTCCC 59.174 43.478 0.00 0.00 45.17 3.97
728 794 4.156739 GTGACAAGATGGACATTTTCCCTC 59.843 45.833 0.00 0.00 45.17 4.30
813 881 2.828661 AAAGAAGGAATACCCCTGGC 57.171 50.000 0.00 0.00 36.49 4.85
829 897 0.540454 TGGCCTCTGCATCTCTTGAG 59.460 55.000 3.32 0.00 40.13 3.02
831 899 0.540923 GCCTCTGCATCTCTTGAGGT 59.459 55.000 16.32 0.00 45.64 3.85
842 910 2.906389 TCTCTTGAGGTACACAGCCATT 59.094 45.455 0.00 0.00 0.00 3.16
901 972 1.015607 GTATGTCCCCGCGTTTTCGT 61.016 55.000 4.92 0.00 46.03 3.85
940 1021 8.364894 GTTTTTGGTTAGTTGATTATGTTCCCT 58.635 33.333 0.00 0.00 0.00 4.20
998 1084 7.289084 AGAGTCCTCAGTTTCTCTTAGAAGTTT 59.711 37.037 0.00 0.00 35.37 2.66
1000 1086 7.070074 AGTCCTCAGTTTCTCTTAGAAGTTTCA 59.930 37.037 0.00 0.00 35.37 2.69
1024 1112 2.807108 GCGATGAAGTTCCTACCATCCC 60.807 54.545 0.00 0.00 33.70 3.85
1051 1139 0.034186 GCCTTGTCACCCATGGATGA 60.034 55.000 15.22 9.78 40.10 2.92
1092 1180 2.286523 CCTCCTCCTCGTGCCACTT 61.287 63.158 0.00 0.00 0.00 3.16
1225 1325 0.754957 CACCACCCTCTTTGCAACCA 60.755 55.000 0.00 0.00 0.00 3.67
1330 2178 2.280524 CCACCGCGTTTCAGGACA 60.281 61.111 4.92 0.00 0.00 4.02
1334 2182 2.452813 CCGCGTTTCAGGACATCCG 61.453 63.158 4.92 0.00 42.08 4.18
2029 3063 5.823045 AGTGATACATACAGCCCTTAAAAGC 59.177 40.000 0.00 0.00 0.00 3.51
2144 3374 5.461526 GCAATCTCCACTTACAAGGAAAAC 58.538 41.667 0.00 0.00 32.57 2.43
2164 3394 7.753580 GGAAAACCGGTACTTGAATATTTTCAG 59.246 37.037 8.00 0.00 42.60 3.02
2170 3400 9.028185 CCGGTACTTGAATATTTTCAGTAGTAC 57.972 37.037 21.04 21.04 45.27 2.73
2243 3473 4.795962 GCATCTCCAACGTCAAACCAAAAT 60.796 41.667 0.00 0.00 0.00 1.82
2296 3526 6.670027 AGAAGAGAGAAGATTTAGGTAGCCAA 59.330 38.462 0.00 0.00 0.00 4.52
2298 3528 6.825610 AGAGAGAAGATTTAGGTAGCCAATG 58.174 40.000 0.00 0.00 0.00 2.82
2299 3529 6.385467 AGAGAGAAGATTTAGGTAGCCAATGT 59.615 38.462 0.00 0.00 0.00 2.71
2300 3530 6.963322 AGAGAAGATTTAGGTAGCCAATGTT 58.037 36.000 0.00 0.00 0.00 2.71
2301 3531 7.406104 AGAGAAGATTTAGGTAGCCAATGTTT 58.594 34.615 0.00 0.00 0.00 2.83
2334 3564 9.743057 CTGTTTTTACAACATATCCAAAACTGA 57.257 29.630 0.00 0.00 36.19 3.41
2349 3579 8.028652 TCCAAAACTGAATACCCAAATTTTCT 57.971 30.769 0.00 0.00 0.00 2.52
2351 3581 9.942850 CCAAAACTGAATACCCAAATTTTCTAT 57.057 29.630 0.00 0.00 0.00 1.98
2382 3612 1.754803 ACATAAAGATCAGACGCCGGA 59.245 47.619 5.05 0.00 0.00 5.14
2485 3715 4.175489 CGACGTCGGAGCGGTGAT 62.175 66.667 29.70 0.00 35.98 3.06
2501 3731 1.678970 GATGCTTTTCGGTGGGGCT 60.679 57.895 0.00 0.00 0.00 5.19
2516 3746 2.044551 GCTTGGGAGGAAGGCAGG 60.045 66.667 0.00 0.00 0.00 4.85
2525 3755 3.580319 GAAGGCAGGGGTGGTGGT 61.580 66.667 0.00 0.00 0.00 4.16
2582 3812 4.410400 CGGTGGGGAGCTTGGGAC 62.410 72.222 0.00 0.00 0.00 4.46
2583 3813 3.256960 GGTGGGGAGCTTGGGACA 61.257 66.667 0.00 0.00 0.00 4.02
2593 3891 1.353694 AGCTTGGGACAGCTGAAATCT 59.646 47.619 23.35 7.17 42.39 2.40
2674 3972 1.065031 CGAAAATTCACCAAGCGGCG 61.065 55.000 0.51 0.51 34.57 6.46
2699 3997 2.671276 TCGGCGCCATGCTTTTGA 60.671 55.556 28.98 10.03 45.43 2.69
2720 4018 9.589461 TTTTGAGTTTATTTGGTAGGATGGTAA 57.411 29.630 0.00 0.00 0.00 2.85
2731 4029 1.298382 AGGATGGTAAGGAGGACCCAT 59.702 52.381 0.00 0.00 40.34 4.00
2735 4033 5.098663 GGATGGTAAGGAGGACCCATATAA 58.901 45.833 0.00 0.00 37.81 0.98
2785 4083 4.513692 GCTACCAAAAACAATTTGTTCCCC 59.486 41.667 14.80 0.00 40.14 4.81
2788 4086 3.432326 CCAAAAACAATTTGTTCCCCGGA 60.432 43.478 14.80 0.00 40.14 5.14
2790 4088 2.375014 AACAATTTGTTCCCCGGACT 57.625 45.000 0.73 0.00 35.27 3.85
2791 4089 3.512219 AACAATTTGTTCCCCGGACTA 57.488 42.857 0.73 0.00 35.27 2.59
2792 4090 2.786777 ACAATTTGTTCCCCGGACTAC 58.213 47.619 0.73 0.00 0.00 2.73
2794 4092 1.364269 ATTTGTTCCCCGGACTACCA 58.636 50.000 0.73 0.00 35.59 3.25
2795 4093 1.138568 TTTGTTCCCCGGACTACCAA 58.861 50.000 0.73 0.00 35.59 3.67
2817 4128 0.397564 ACCATTTTTGGGCCAGCAAG 59.602 50.000 6.23 0.00 0.00 4.01
2918 4230 8.938883 TGAGCCTAGGAACAGATAGATAAAAAT 58.061 33.333 14.75 0.00 0.00 1.82
2984 4296 7.676004 AGGAAGTTCAAACAAAAAGAAAAGGA 58.324 30.769 5.01 0.00 0.00 3.36
3013 4332 4.710324 TGTTAGAACGGTTCAAAGGTCAT 58.290 39.130 21.86 2.31 0.00 3.06
3085 4418 6.588719 TGGTGTAGCTTATTTTTCATTGCT 57.411 33.333 0.00 0.00 34.92 3.91
3087 4420 6.867816 TGGTGTAGCTTATTTTTCATTGCTTG 59.132 34.615 0.00 0.00 32.72 4.01
3173 4524 1.865788 GCAAATCACGCAAGAGGGCA 61.866 55.000 0.00 0.00 43.62 5.36
3300 4663 3.893200 TCACCAGAACGTTCCTCTAAAGA 59.107 43.478 24.22 10.75 0.00 2.52
3841 5243 6.015434 ACGTGTATTGGATATGTGATGCTCTA 60.015 38.462 0.00 0.00 0.00 2.43
3865 5277 0.686789 TATCCTCACATGGATGGCCG 59.313 55.000 0.00 0.00 45.58 6.13
3893 5305 8.517062 AATCCTCTTTCTGTCATTTCCATAAG 57.483 34.615 0.00 0.00 0.00 1.73
3901 5648 8.408043 TTCTGTCATTTCCATAAGAATGTTGT 57.592 30.769 0.00 0.00 33.44 3.32
3905 5653 7.148423 TGTCATTTCCATAAGAATGTTGTCTCG 60.148 37.037 0.00 0.00 33.44 4.04
4075 5827 2.097825 GCTCTTGGGATGTTGCATTCT 58.902 47.619 0.00 0.00 0.00 2.40
4079 5831 0.324552 TGGGATGTTGCATTCTGGGG 60.325 55.000 0.00 0.00 0.00 4.96
4328 6080 2.991866 CTCTCGATTGCGCATCATACAT 59.008 45.455 12.75 0.00 37.46 2.29
4626 6811 7.523293 TCTGAAGGCATTTACTCAATCAAAA 57.477 32.000 0.00 0.00 0.00 2.44
4698 6883 5.629079 AAGGAATTCTCGTTTCCATCAAC 57.371 39.130 5.23 0.00 44.25 3.18
5233 7432 7.210174 ACATTATCTGCTGAAGACGCTTAATA 58.790 34.615 0.00 0.00 37.88 0.98
5276 7475 7.242914 AGTAATTATGTAAAGTGCTTACGGC 57.757 36.000 0.00 0.00 42.57 5.68
5278 7477 2.483014 ATGTAAAGTGCTTACGGCCA 57.517 45.000 2.24 0.00 42.57 5.36
5297 7496 1.214325 CGTCCTCATGCACCGTGTA 59.786 57.895 0.00 0.00 0.00 2.90
5316 7517 1.680338 AAAAACTCAGAGGCGCAACT 58.320 45.000 10.83 4.48 0.00 3.16
5331 7532 1.800805 CAACTCAAGCGTGTCCAGAT 58.199 50.000 0.00 0.00 0.00 2.90
5388 7589 6.334989 TCGTATAGATGTTTTGGTCGATGTT 58.665 36.000 0.00 0.00 0.00 2.71
5390 7591 5.818136 ATAGATGTTTTGGTCGATGTTGG 57.182 39.130 0.00 0.00 0.00 3.77
5415 7656 5.922053 ACTCAGTTGAGATGCTATATTGCA 58.078 37.500 14.17 14.17 44.74 4.08
5416 7657 5.757320 ACTCAGTTGAGATGCTATATTGCAC 59.243 40.000 14.10 8.45 44.21 4.57
5591 8914 5.819991 AGGTCATCATATTTGGTCTGTTGT 58.180 37.500 0.00 0.00 0.00 3.32
5788 9111 4.497291 TGGACCGTTAGCAGGATAAATT 57.503 40.909 0.00 0.00 0.00 1.82
5814 9137 6.865205 CCAAAAAGATCTCCTTCATGTTTGTC 59.135 38.462 0.00 0.00 31.65 3.18
5840 9163 9.376075 CTTATCATGACAACTCTACAGAAATGT 57.624 33.333 0.00 0.00 0.00 2.71
5849 9172 8.956426 ACAACTCTACAGAAATGTTTCTTTTCA 58.044 29.630 5.30 0.00 44.70 2.69
5964 9419 6.433847 TCCTTTGGATTTCAAGTCTACAGA 57.566 37.500 0.00 0.00 36.62 3.41
5965 9420 6.467677 TCCTTTGGATTTCAAGTCTACAGAG 58.532 40.000 0.00 0.00 36.62 3.35
5967 9422 7.038017 TCCTTTGGATTTCAAGTCTACAGAGAT 60.038 37.037 0.00 0.00 36.62 2.75
5969 9424 9.092876 CTTTGGATTTCAAGTCTACAGAGATAC 57.907 37.037 0.00 0.00 36.62 2.24
5970 9425 7.718334 TGGATTTCAAGTCTACAGAGATACA 57.282 36.000 0.00 0.00 33.14 2.29
5972 9427 6.981559 GGATTTCAAGTCTACAGAGATACACC 59.018 42.308 0.00 0.00 33.14 4.16
5973 9428 5.562506 TTCAAGTCTACAGAGATACACCG 57.437 43.478 0.00 0.00 33.14 4.94
5974 9429 3.945921 TCAAGTCTACAGAGATACACCGG 59.054 47.826 0.00 0.00 33.14 5.28
5975 9430 3.648507 AGTCTACAGAGATACACCGGT 57.351 47.619 0.00 0.00 33.14 5.28
5976 9431 3.543665 AGTCTACAGAGATACACCGGTC 58.456 50.000 2.59 0.00 33.14 4.79
5977 9432 2.287373 GTCTACAGAGATACACCGGTCG 59.713 54.545 2.59 2.80 33.14 4.79
5978 9433 1.002684 CTACAGAGATACACCGGTCGC 60.003 57.143 2.59 0.00 0.00 5.19
5979 9434 1.065928 CAGAGATACACCGGTCGCC 59.934 63.158 2.59 0.00 0.00 5.54
5980 9435 1.379443 AGAGATACACCGGTCGCCA 60.379 57.895 2.59 0.00 0.00 5.69
5981 9436 0.755698 AGAGATACACCGGTCGCCAT 60.756 55.000 2.59 0.00 0.00 4.40
5982 9437 0.318784 GAGATACACCGGTCGCCATC 60.319 60.000 2.59 5.09 0.00 3.51
5983 9438 1.660575 GATACACCGGTCGCCATCG 60.661 63.158 2.59 0.00 0.00 3.84
6052 9559 1.012486 GGACCGAACAACCGCTACAG 61.012 60.000 0.00 0.00 0.00 2.74
6059 9566 3.427098 CGAACAACCGCTACAGAGATACA 60.427 47.826 0.00 0.00 0.00 2.29
6067 9574 1.002684 CTACAGAGATACACCGGTCGC 60.003 57.143 2.59 0.00 0.00 5.19
6070 9577 0.755698 AGAGATACACCGGTCGCCAT 60.756 55.000 2.59 0.00 0.00 4.40
6075 9582 1.952102 TACACCGGTCGCCATCCTTC 61.952 60.000 2.59 0.00 0.00 3.46
6076 9583 3.000819 ACCGGTCGCCATCCTTCA 61.001 61.111 0.00 0.00 0.00 3.02
6077 9584 2.202932 CCGGTCGCCATCCTTCAG 60.203 66.667 0.00 0.00 0.00 3.02
6130 9674 2.028020 CCTAGTTCACTTGACCTGGTCC 60.028 54.545 23.42 6.63 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 2.543012 CTCGCAAATGTATCCTCTGCAG 59.457 50.000 7.63 7.63 33.19 4.41
29 30 2.554142 CTCGCAAATGTATCCTCTGCA 58.446 47.619 0.00 0.00 33.19 4.41
30 31 1.262683 GCTCGCAAATGTATCCTCTGC 59.737 52.381 0.00 0.00 0.00 4.26
31 32 1.524355 CGCTCGCAAATGTATCCTCTG 59.476 52.381 0.00 0.00 0.00 3.35
32 33 1.858091 CGCTCGCAAATGTATCCTCT 58.142 50.000 0.00 0.00 0.00 3.69
33 34 0.233332 GCGCTCGCAAATGTATCCTC 59.767 55.000 9.59 0.00 41.49 3.71
34 35 1.160329 GGCGCTCGCAAATGTATCCT 61.160 55.000 16.36 0.00 44.11 3.24
126 127 4.373156 AAGGTGATTTGGTACAGAGCTT 57.627 40.909 0.00 0.00 42.39 3.74
217 219 0.625849 ATGGATTATGGATCGGGGCC 59.374 55.000 0.00 0.00 35.49 5.80
231 233 3.914426 AGTTCGTTGAGGCTTATGGAT 57.086 42.857 0.00 0.00 0.00 3.41
233 235 4.950050 AGATAGTTCGTTGAGGCTTATGG 58.050 43.478 0.00 0.00 0.00 2.74
237 239 4.463186 ACTGTAGATAGTTCGTTGAGGCTT 59.537 41.667 0.00 0.00 0.00 4.35
256 258 3.788142 ACTGGATTATGGATTGGGACTGT 59.212 43.478 0.00 0.00 0.00 3.55
300 302 2.802719 TCTAGCCCCGCAAAAGAATTT 58.197 42.857 0.00 0.00 42.41 1.82
301 303 2.507407 TCTAGCCCCGCAAAAGAATT 57.493 45.000 0.00 0.00 0.00 2.17
302 304 2.736670 ATCTAGCCCCGCAAAAGAAT 57.263 45.000 0.00 0.00 0.00 2.40
303 305 2.026262 AGAATCTAGCCCCGCAAAAGAA 60.026 45.455 0.00 0.00 0.00 2.52
304 306 1.559682 AGAATCTAGCCCCGCAAAAGA 59.440 47.619 0.00 0.00 0.00 2.52
305 307 2.044123 AGAATCTAGCCCCGCAAAAG 57.956 50.000 0.00 0.00 0.00 2.27
334 348 4.717778 TGGATAGGTACCCGAAAATTCTCA 59.282 41.667 8.74 0.00 0.00 3.27
349 363 2.812011 GTCAAAACACGCTTGGATAGGT 59.188 45.455 0.00 0.00 0.00 3.08
419 433 5.805486 TCAAAGTTCAGATGTCATACGTAGC 59.195 40.000 0.08 0.00 0.00 3.58
455 469 7.600375 TGCTCGCCAATTAATAAGAGATCTAAG 59.400 37.037 0.00 0.00 0.00 2.18
505 524 9.090692 GTTCTAAATATCATGCTGCAAAATTGT 57.909 29.630 6.36 0.00 0.00 2.71
624 669 5.124645 TGCTGGCAAAAATTCACAGAATTT 58.875 33.333 10.92 10.92 0.00 1.82
656 722 3.790089 ATCCCGTGGTTTCTCTTTCTT 57.210 42.857 0.00 0.00 0.00 2.52
660 726 2.421529 GCCATATCCCGTGGTTTCTCTT 60.422 50.000 0.00 0.00 39.01 2.85
671 737 0.890542 CACATGGTGGCCATATCCCG 60.891 60.000 9.72 2.06 43.15 5.14
755 823 4.829968 ACTGAAGTCTGGATCATCAACAG 58.170 43.478 0.00 0.00 0.00 3.16
789 857 5.083821 CCAGGGGTATTCCTTCTTTTCAAA 58.916 41.667 0.00 0.00 34.31 2.69
790 858 4.672899 CCAGGGGTATTCCTTCTTTTCAA 58.327 43.478 0.00 0.00 34.31 2.69
791 859 3.563479 GCCAGGGGTATTCCTTCTTTTCA 60.563 47.826 0.00 0.00 34.31 2.69
792 860 3.024547 GCCAGGGGTATTCCTTCTTTTC 58.975 50.000 0.00 0.00 34.31 2.29
793 861 2.292257 GGCCAGGGGTATTCCTTCTTTT 60.292 50.000 0.00 0.00 34.31 2.27
796 864 0.046397 AGGCCAGGGGTATTCCTTCT 59.954 55.000 5.01 0.00 34.31 2.85
797 865 0.474614 GAGGCCAGGGGTATTCCTTC 59.525 60.000 5.01 0.00 34.31 3.46
798 866 0.046397 AGAGGCCAGGGGTATTCCTT 59.954 55.000 5.01 0.00 34.31 3.36
799 867 0.695803 CAGAGGCCAGGGGTATTCCT 60.696 60.000 5.01 0.00 37.71 3.36
800 868 1.839894 CAGAGGCCAGGGGTATTCC 59.160 63.158 5.01 0.00 0.00 3.01
801 869 1.149401 GCAGAGGCCAGGGGTATTC 59.851 63.158 5.01 0.00 0.00 1.75
810 878 0.540454 CTCAAGAGATGCAGAGGCCA 59.460 55.000 5.01 0.00 40.13 5.36
829 897 4.408182 AGTCTGATAATGGCTGTGTACC 57.592 45.455 0.00 0.00 0.00 3.34
831 899 7.182817 ACTTAAGTCTGATAATGGCTGTGTA 57.817 36.000 1.12 0.00 0.00 2.90
842 910 8.645814 TCCACAAGTTCTACTTAAGTCTGATA 57.354 34.615 12.39 0.00 36.03 2.15
901 972 8.514330 ACTAACCAAAAACAATGTAGAGAACA 57.486 30.769 0.00 0.00 43.86 3.18
989 1075 5.245531 ACTTCATCGCCATGAAACTTCTAA 58.754 37.500 8.14 0.00 46.35 2.10
998 1084 2.158957 GGTAGGAACTTCATCGCCATGA 60.159 50.000 0.00 0.00 41.75 3.07
1000 1086 1.837439 TGGTAGGAACTTCATCGCCAT 59.163 47.619 0.00 0.00 41.75 4.40
1024 1112 2.263741 GGTGACAAGGCAGGTGCAG 61.264 63.158 4.01 0.00 44.36 4.41
1051 1139 2.695585 GAGAGGGAGGATAACCATGGT 58.304 52.381 13.00 13.00 38.94 3.55
1092 1180 2.747460 GACCATTGAGCAGCGGCA 60.747 61.111 12.44 0.00 44.61 5.69
1225 1325 1.117150 GGAACATTGCCCATGATGCT 58.883 50.000 0.00 0.00 36.24 3.79
1914 2840 2.287308 TGTTTATGTGAAGCCGTTGTGC 60.287 45.455 0.00 0.00 0.00 4.57
2144 3374 9.028185 GTACTACTGAAAATATTCAAGTACCGG 57.972 37.037 15.90 0.00 44.66 5.28
2212 3442 3.190874 GACGTTGGAGATGCTCTAAAGG 58.809 50.000 10.12 6.53 35.58 3.11
2213 3443 3.849911 TGACGTTGGAGATGCTCTAAAG 58.150 45.455 0.00 0.00 36.77 1.85
2318 3548 8.429237 TTTGGGTATTCAGTTTTGGATATGTT 57.571 30.769 0.00 0.00 27.65 2.71
2475 3705 1.425428 CGAAAAGCATCACCGCTCC 59.575 57.895 0.00 0.00 42.89 4.70
2482 3712 1.976474 GCCCCACCGAAAAGCATCA 60.976 57.895 0.00 0.00 0.00 3.07
2485 3715 2.197324 AAGCCCCACCGAAAAGCA 59.803 55.556 0.00 0.00 0.00 3.91
2493 3723 3.264845 TTCCTCCCAAGCCCCACC 61.265 66.667 0.00 0.00 0.00 4.61
2501 3731 2.941025 CCCCTGCCTTCCTCCCAA 60.941 66.667 0.00 0.00 0.00 4.12
2582 3812 1.363744 GTCCGACCAGATTTCAGCTG 58.636 55.000 7.63 7.63 0.00 4.24
2583 3813 0.250513 GGTCCGACCAGATTTCAGCT 59.749 55.000 13.05 0.00 38.42 4.24
2627 3925 3.508840 CGCGAACCTGCAATCCCC 61.509 66.667 0.00 0.00 34.15 4.81
2628 3926 3.508840 CCGCGAACCTGCAATCCC 61.509 66.667 8.23 0.00 34.15 3.85
2630 3928 4.520846 CGCCGCGAACCTGCAATC 62.521 66.667 8.23 0.00 34.15 2.67
2652 3950 1.591248 CGCTTGGTGAATTTTCGTCG 58.409 50.000 0.00 0.00 0.00 5.12
2660 3958 2.282180 AACCGCCGCTTGGTGAAT 60.282 55.556 0.00 0.00 46.68 2.57
2699 3997 7.366551 CCTCCTTACCATCCTACCAAATAAACT 60.367 40.741 0.00 0.00 0.00 2.66
2757 4055 4.163268 ACAAATTGTTTTTGGTAGCCACCT 59.837 37.500 2.16 0.00 45.98 4.00
2760 4058 5.119694 GGAACAAATTGTTTTTGGTAGCCA 58.880 37.500 13.00 0.00 41.28 4.75
2785 4083 4.320935 CCAAAAATGGTTCTTGGTAGTCCG 60.321 45.833 0.00 0.00 35.80 4.79
2788 4086 3.323691 GCCCAAAAATGGTTCTTGGTAGT 59.676 43.478 0.00 0.00 38.35 2.73
2790 4088 2.635427 GGCCCAAAAATGGTTCTTGGTA 59.365 45.455 0.00 0.00 38.35 3.25
2791 4089 1.419762 GGCCCAAAAATGGTTCTTGGT 59.580 47.619 0.00 0.00 38.35 3.67
2792 4090 1.419387 TGGCCCAAAAATGGTTCTTGG 59.581 47.619 0.00 0.00 39.51 3.61
2794 4092 1.072173 GCTGGCCCAAAAATGGTTCTT 59.928 47.619 0.00 0.00 0.00 2.52
2795 4093 0.686789 GCTGGCCCAAAAATGGTTCT 59.313 50.000 0.00 0.00 0.00 3.01
2857 4169 1.654317 GAGCATCTCCAACAGCAGAG 58.346 55.000 0.00 0.00 0.00 3.35
2984 4296 4.067972 TGAACCGTTCTAACAGCTTTCT 57.932 40.909 12.43 0.00 0.00 2.52
3085 4418 8.586570 AAAAACGAATTCATTTAGTGATGCAA 57.413 26.923 6.22 0.00 36.54 4.08
3143 4491 2.908626 GCGTGATTTGCGTCCTAAAAAG 59.091 45.455 0.00 0.00 0.00 2.27
3173 4524 3.826157 CCACCACAACAATAATCCACAGT 59.174 43.478 0.00 0.00 0.00 3.55
3650 5034 6.881602 TGCACACATGAATGTATTGGTTAGTA 59.118 34.615 0.00 0.00 39.39 1.82
3747 5142 6.540438 TTTAGTCCACTGTCGAAATAGGAT 57.460 37.500 0.02 0.00 0.00 3.24
3841 5243 5.012458 CGGCCATCCATGTGAGGATATATAT 59.988 44.000 2.24 0.00 46.54 0.86
3865 5277 5.882557 TGGAAATGACAGAAAGAGGATTAGC 59.117 40.000 0.00 0.00 0.00 3.09
3893 5305 6.435428 ACAACAATAAACCGAGACAACATTC 58.565 36.000 0.00 0.00 0.00 2.67
3901 5648 7.148540 GCAAGTATGTACAACAATAAACCGAGA 60.149 37.037 0.00 0.00 0.00 4.04
3905 5653 7.027161 CCTGCAAGTATGTACAACAATAAACC 58.973 38.462 0.00 0.00 0.00 3.27
4075 5827 2.725227 ACCAATAGTTTTTCCTCCCCCA 59.275 45.455 0.00 0.00 0.00 4.96
4079 5831 6.884836 ACTCATACACCAATAGTTTTTCCTCC 59.115 38.462 0.00 0.00 0.00 4.30
4328 6080 2.165357 TGCTGGCCTTGAGATCTCTA 57.835 50.000 22.95 14.97 0.00 2.43
4385 6137 9.264719 CTGAAAATTTTTGCTAGACCAAAATCT 57.735 29.630 4.63 0.00 42.36 2.40
4626 6811 1.157870 CCAAAGCTGAACACGTCGGT 61.158 55.000 0.00 0.00 34.76 4.69
4698 6883 3.988517 AGAAGGTTAAGAAAGTCTTCGCG 59.011 43.478 0.00 0.00 37.89 5.87
5255 7454 4.944930 TGGCCGTAAGCACTTTACATAATT 59.055 37.500 0.00 0.00 46.50 1.40
5273 7472 4.758251 TGCATGAGGACGTGGCCG 62.758 66.667 0.00 0.00 40.83 6.13
5276 7475 2.815211 CGGTGCATGAGGACGTGG 60.815 66.667 0.00 0.00 36.89 4.94
5278 7477 1.529152 TACACGGTGCATGAGGACGT 61.529 55.000 8.30 0.00 36.89 4.34
5297 7496 1.604278 GAGTTGCGCCTCTGAGTTTTT 59.396 47.619 4.18 0.00 0.00 1.94
5316 7517 3.514777 GTCATCTGGACACGCTTGA 57.485 52.632 0.00 0.00 46.19 3.02
5331 7532 7.956420 ACACTTTATAAACGTCTCAATGTCA 57.044 32.000 0.00 0.00 0.00 3.58
5388 7589 7.436933 CAATATAGCATCTCAACTGAGTACCA 58.563 38.462 6.61 0.00 42.60 3.25
5390 7591 6.925718 TGCAATATAGCATCTCAACTGAGTAC 59.074 38.462 6.61 0.00 40.26 2.73
5456 7697 9.975218 AATTCTGAGGTATACCAAACAATAAGT 57.025 29.630 23.87 12.64 38.89 2.24
5475 7719 6.403964 GCTTGTCTTGATATGTGCAATTCTGA 60.404 38.462 0.00 0.00 0.00 3.27
5476 7720 5.742453 GCTTGTCTTGATATGTGCAATTCTG 59.258 40.000 0.00 0.00 0.00 3.02
5670 8993 4.119136 GTGGCAAGTTTGTACTTTGCATT 58.881 39.130 19.08 0.00 41.85 3.56
5674 8997 3.414549 ACGTGGCAAGTTTGTACTTTG 57.585 42.857 0.00 0.00 41.85 2.77
5677 9000 5.761165 AATTTACGTGGCAAGTTTGTACT 57.239 34.783 12.12 0.00 35.68 2.73
5733 9056 8.818622 TCAACTGTACTACTCATTGGTACTAT 57.181 34.615 0.00 0.00 37.35 2.12
5753 9076 4.553330 ACGGTCCATAAGTTCATCAACT 57.447 40.909 0.00 0.00 45.43 3.16
5788 9111 6.550854 ACAAACATGAAGGAGATCTTTTTGGA 59.449 34.615 0.00 0.00 35.50 3.53
5814 9137 9.376075 ACATTTCTGTAGAGTTGTCATGATAAG 57.624 33.333 4.98 0.00 32.49 1.73
5849 9172 6.295292 GCCTTCCATGTTTTCTTCCAAGTTAT 60.295 38.462 0.00 0.00 0.00 1.89
5894 9349 3.690460 ACTGAATCCTGCTGGGTAAAAG 58.310 45.455 10.07 4.06 36.25 2.27
5960 9415 1.664321 GGCGACCGGTGTATCTCTGT 61.664 60.000 14.63 0.00 0.00 3.41
5962 9417 0.755698 ATGGCGACCGGTGTATCTCT 60.756 55.000 14.63 0.00 0.00 3.10
5963 9418 0.318784 GATGGCGACCGGTGTATCTC 60.319 60.000 14.63 0.00 0.00 2.75
5964 9419 1.740285 GATGGCGACCGGTGTATCT 59.260 57.895 14.63 0.00 0.00 1.98
5965 9420 1.660575 CGATGGCGACCGGTGTATC 60.661 63.158 14.63 9.30 40.82 2.24
5967 9422 3.829044 CCGATGGCGACCGGTGTA 61.829 66.667 14.63 0.00 40.78 2.90
5972 9427 1.015085 TTTTACACCGATGGCGACCG 61.015 55.000 0.00 0.00 40.82 4.79
5973 9428 0.445043 GTTTTACACCGATGGCGACC 59.555 55.000 0.00 0.00 40.82 4.79
5974 9429 0.094046 CGTTTTACACCGATGGCGAC 59.906 55.000 0.00 0.00 40.82 5.19
5975 9430 0.038435 TCGTTTTACACCGATGGCGA 60.038 50.000 0.00 0.00 40.82 5.54
5976 9431 1.003851 ATCGTTTTACACCGATGGCG 58.996 50.000 0.00 0.00 41.86 5.69
5980 9435 1.735571 GCACCATCGTTTTACACCGAT 59.264 47.619 0.00 0.00 44.07 4.18
5981 9436 1.149987 GCACCATCGTTTTACACCGA 58.850 50.000 0.00 0.00 37.51 4.69
5982 9437 0.179235 CGCACCATCGTTTTACACCG 60.179 55.000 0.00 0.00 0.00 4.94
5983 9438 0.167251 CCGCACCATCGTTTTACACC 59.833 55.000 0.00 0.00 0.00 4.16
6052 9559 0.318784 GATGGCGACCGGTGTATCTC 60.319 60.000 14.63 0.00 0.00 2.75
6059 9566 3.000819 TGAAGGATGGCGACCGGT 61.001 61.111 6.92 6.92 0.00 5.28
6067 9574 7.592885 ATCATATTTTGGTTCTGAAGGATGG 57.407 36.000 0.00 0.00 0.00 3.51
6070 9577 6.772716 GCCTATCATATTTTGGTTCTGAAGGA 59.227 38.462 0.00 0.00 0.00 3.36
6075 9582 8.682936 AGTAAGCCTATCATATTTTGGTTCTG 57.317 34.615 0.00 0.00 0.00 3.02
6076 9583 9.125026 CAAGTAAGCCTATCATATTTTGGTTCT 57.875 33.333 0.00 0.00 0.00 3.01
6077 9584 8.352942 CCAAGTAAGCCTATCATATTTTGGTTC 58.647 37.037 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.