Multiple sequence alignment - TraesCS3A01G244400

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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 TraesCS3A01G244400 chr3A 100.000 2886 0 0 1 2886 457489249 457492134 0.000000e+00 5330.0
1 TraesCS3A01G244400 chr3D 95.971 1117 30 4 950 2066 346307740 346306639 0.000000e+00 1799.0
2 TraesCS3A01G244400 chr3D 92.880 309 20 2 364 672 346308417 346308111 5.670000e-122 448.0
3 TraesCS3A01G244400 chr3D 85.824 261 14 13 143 392 346308761 346308513 3.690000e-64 255.0
4 TraesCS3A01G244400 chr3D 89.933 149 9 2 1 149 346309243 346309101 1.370000e-43 187.0
5 TraesCS3A01G244400 chr3B 95.701 977 25 8 950 1925 445588212 445587252 0.000000e+00 1555.0
6 TraesCS3A01G244400 chr3B 89.888 534 31 6 429 956 445588752 445588236 0.000000e+00 665.0
7 TraesCS3A01G244400 chr3B 85.799 338 29 12 36 373 445592931 445592613 9.900000e-90 340.0
8 TraesCS3A01G244400 chr3B 97.778 45 1 0 2065 2109 55726885 55726929 8.570000e-11 78.7
9 TraesCS3A01G244400 chr3B 94.737 38 2 0 1 38 445593061 445593024 3.110000e-05 60.2
10 TraesCS3A01G244400 chr2A 98.297 822 14 0 2065 2886 502066458 502065637 0.000000e+00 1441.0
11 TraesCS3A01G244400 chr2A 92.157 51 3 1 2066 2116 719997127 719997078 1.430000e-08 71.3
12 TraesCS3A01G244400 chr6B 92.635 706 44 8 2185 2886 145348822 145348121 0.000000e+00 1009.0
13 TraesCS3A01G244400 chr6B 84.033 858 84 26 2064 2886 11008422 11009261 0.000000e+00 776.0
14 TraesCS3A01G244400 chr6B 91.429 175 10 4 2063 2233 145348976 145348803 4.810000e-58 235.0
15 TraesCS3A01G244400 chr6B 78.889 270 38 9 2065 2323 345803401 345803140 6.400000e-37 165.0
16 TraesCS3A01G244400 chr6B 85.600 125 12 4 2064 2183 701431476 701431353 3.020000e-25 126.0
17 TraesCS3A01G244400 chr5B 79.259 270 37 9 2065 2323 38916252 38915991 1.380000e-38 171.0
18 TraesCS3A01G244400 chr5B 77.885 208 28 13 2066 2263 162342879 162343078 2.350000e-21 113.0
19 TraesCS3A01G244400 chr5B 81.752 137 17 5 2065 2193 337179595 337179459 1.090000e-19 108.0
20 TraesCS3A01G244400 chr1B 79.911 224 30 13 2066 2287 91991137 91991347 1.790000e-32 150.0
21 TraesCS3A01G244400 chr1B 77.820 266 40 9 2065 2319 98384049 98384306 2.320000e-31 147.0
22 TraesCS3A01G244400 chr1B 77.820 266 40 9 2065 2319 98411345 98411602 2.320000e-31 147.0
23 TraesCS3A01G244400 chr1B 77.820 266 40 9 2065 2319 98431400 98431657 2.320000e-31 147.0
24 TraesCS3A01G244400 chr1B 81.022 137 18 5 2065 2193 435710887 435711023 5.090000e-18 102.0
25 TraesCS3A01G244400 chr1D 80.000 200 29 9 2066 2263 487582309 487582499 1.390000e-28 137.0
26 TraesCS3A01G244400 chr4B 78.916 166 25 8 2102 2263 538950669 538950828 1.410000e-18 104.0
27 TraesCS3A01G244400 chr7A 97.778 45 1 0 2065 2109 150089493 150089449 8.570000e-11 78.7
28 TraesCS3A01G244400 chr5A 94.231 52 2 1 2065 2116 29311487 29311437 8.570000e-11 78.7


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 TraesCS3A01G244400 chr3A 457489249 457492134 2885 False 5330.00 5330 100.00000 1 2886 1 chr3A.!!$F1 2885
1 TraesCS3A01G244400 chr3D 346306639 346309243 2604 True 672.25 1799 91.15200 1 2066 4 chr3D.!!$R1 2065
2 TraesCS3A01G244400 chr3B 445587252 445593061 5809 True 655.05 1555 91.53125 1 1925 4 chr3B.!!$R1 1924
3 TraesCS3A01G244400 chr2A 502065637 502066458 821 True 1441.00 1441 98.29700 2065 2886 1 chr2A.!!$R1 821
4 TraesCS3A01G244400 chr6B 11008422 11009261 839 False 776.00 776 84.03300 2064 2886 1 chr6B.!!$F1 822
5 TraesCS3A01G244400 chr6B 145348121 145348976 855 True 622.00 1009 92.03200 2063 2886 2 chr6B.!!$R3 823

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
347 798 0.033504 TCTCTGCTGGTGTTCCGTTC 59.966 55.0 0.0 0.0 36.3 3.95 F
348 799 0.034059 CTCTGCTGGTGTTCCGTTCT 59.966 55.0 0.0 0.0 36.3 3.01 F
1180 5697 0.320160 ACCCTTTAAGCCACGTCGTC 60.320 55.0 0.0 0.0 0.0 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1193 5710 0.179166 GCTCGACTCAGAGAGTGCAG 60.179 60.000 3.79 1.58 43.53 4.41 R
1196 5713 0.373370 CTCGCTCGACTCAGAGAGTG 59.627 60.000 3.79 8.51 43.53 3.51 R
2628 7195 1.349688 CTGGTGTACTTAACCTGGGCA 59.650 52.381 0.00 0.00 38.60 5.36 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 9.762381 TTGTAATTGGGAGGTATATTTTCTTGT 57.238 29.630 0.00 0.00 0.00 3.16
93 189 1.000843 CTGCCATCATCATGCCCAATG 59.999 52.381 0.00 0.00 37.66 2.82
108 204 3.756434 GCCCAATGCTTAACAACTACAGA 59.244 43.478 0.00 0.00 36.87 3.41
117 213 7.667557 TGCTTAACAACTACAGATACAGAACT 58.332 34.615 0.00 0.00 0.00 3.01
118 214 8.799367 TGCTTAACAACTACAGATACAGAACTA 58.201 33.333 0.00 0.00 0.00 2.24
119 215 9.291664 GCTTAACAACTACAGATACAGAACTAG 57.708 37.037 0.00 0.00 0.00 2.57
178 629 8.231692 TCTTGTGTGTCTAATTTGAATTTCCA 57.768 30.769 0.00 0.00 0.00 3.53
266 717 4.970860 AATCCTGGATCCTCACACATAG 57.029 45.455 14.23 0.00 0.00 2.23
267 718 2.042464 TCCTGGATCCTCACACATAGC 58.958 52.381 14.23 0.00 0.00 2.97
268 719 1.764723 CCTGGATCCTCACACATAGCA 59.235 52.381 14.23 0.00 0.00 3.49
269 720 2.224233 CCTGGATCCTCACACATAGCAG 60.224 54.545 14.23 0.00 0.00 4.24
270 721 1.764723 TGGATCCTCACACATAGCAGG 59.235 52.381 14.23 0.00 0.00 4.85
271 722 2.042464 GGATCCTCACACATAGCAGGA 58.958 52.381 3.84 0.00 39.42 3.86
272 723 2.036992 GGATCCTCACACATAGCAGGAG 59.963 54.545 3.84 0.00 38.47 3.69
273 724 2.238084 TCCTCACACATAGCAGGAGT 57.762 50.000 0.00 0.00 31.10 3.85
274 725 1.827344 TCCTCACACATAGCAGGAGTG 59.173 52.381 0.00 0.00 39.12 3.51
293 744 1.003580 TGCAGGACAGAAGGGTTCATC 59.996 52.381 0.00 0.00 0.00 2.92
326 777 2.596851 CCAGTCCCACTGTCCCCAG 61.597 68.421 3.07 0.00 44.50 4.45
347 798 0.033504 TCTCTGCTGGTGTTCCGTTC 59.966 55.000 0.00 0.00 36.30 3.95
348 799 0.034059 CTCTGCTGGTGTTCCGTTCT 59.966 55.000 0.00 0.00 36.30 3.01
361 812 1.148310 CCGTTCTGGTTGCTGTACAG 58.852 55.000 18.93 18.93 0.00 2.74
379 965 4.680171 ACAGTTATCTTTTGCCGCTTAC 57.320 40.909 0.00 0.00 0.00 2.34
394 980 4.143179 GCCGCTTACTGTAAACTTGTAGTG 60.143 45.833 1.46 0.00 0.00 2.74
404 990 8.545420 ACTGTAAACTTGTAGTGAACATAAACG 58.455 33.333 0.00 0.00 38.10 3.60
410 996 4.827692 TGTAGTGAACATAAACGAGCCAT 58.172 39.130 0.00 0.00 31.43 4.40
431 1017 6.198591 GCCATTATCGTGTAGACAACTAAGTC 59.801 42.308 0.00 0.00 38.81 3.01
455 4797 6.310711 TCGTTAATACATGTGTTGTTGCGATA 59.689 34.615 17.19 0.00 39.87 2.92
535 4877 6.827251 TCAGATAGTTCAGTTCGGTGTATACT 59.173 38.462 4.17 0.00 0.00 2.12
536 4878 7.338703 TCAGATAGTTCAGTTCGGTGTATACTT 59.661 37.037 4.17 0.00 0.00 2.24
581 4923 4.672587 TGTTCTTCACACAAGCTAGAGT 57.327 40.909 0.00 0.00 0.00 3.24
647 4989 4.916041 TCCACAGGTTTCATTCAGATCT 57.084 40.909 0.00 0.00 0.00 2.75
648 4990 4.582869 TCCACAGGTTTCATTCAGATCTG 58.417 43.478 17.07 17.07 0.00 2.90
649 4991 4.286808 TCCACAGGTTTCATTCAGATCTGA 59.713 41.667 21.67 21.67 37.91 3.27
650 4992 5.045359 TCCACAGGTTTCATTCAGATCTGAT 60.045 40.000 25.64 13.08 39.64 2.90
651 4993 5.066117 CCACAGGTTTCATTCAGATCTGATG 59.934 44.000 25.64 22.42 39.64 3.07
652 4994 4.639310 ACAGGTTTCATTCAGATCTGATGC 59.361 41.667 25.64 11.84 39.64 3.91
653 4995 3.875727 AGGTTTCATTCAGATCTGATGCG 59.124 43.478 25.64 16.34 39.64 4.73
654 4996 3.624861 GGTTTCATTCAGATCTGATGCGT 59.375 43.478 25.64 9.96 39.64 5.24
655 4997 4.095483 GGTTTCATTCAGATCTGATGCGTT 59.905 41.667 25.64 6.54 39.64 4.84
656 4998 5.261661 GTTTCATTCAGATCTGATGCGTTC 58.738 41.667 25.64 11.79 39.64 3.95
657 4999 3.461061 TCATTCAGATCTGATGCGTTCC 58.539 45.455 25.64 0.00 39.64 3.62
658 5000 3.118665 TCATTCAGATCTGATGCGTTCCA 60.119 43.478 25.64 9.01 39.64 3.53
659 5001 3.333029 TTCAGATCTGATGCGTTCCAA 57.667 42.857 25.64 5.06 39.64 3.53
660 5002 3.548745 TCAGATCTGATGCGTTCCAAT 57.451 42.857 21.67 0.00 34.14 3.16
661 5003 3.200483 TCAGATCTGATGCGTTCCAATG 58.800 45.455 21.67 0.00 34.14 2.82
662 5004 1.945394 AGATCTGATGCGTTCCAATGC 59.055 47.619 0.00 0.00 41.27 3.56
663 5005 1.945394 GATCTGATGCGTTCCAATGCT 59.055 47.619 0.00 0.00 41.45 3.79
664 5006 1.825090 TCTGATGCGTTCCAATGCTT 58.175 45.000 5.16 0.00 41.45 3.91
665 5007 2.161855 TCTGATGCGTTCCAATGCTTT 58.838 42.857 5.16 0.00 41.45 3.51
666 5008 2.557924 TCTGATGCGTTCCAATGCTTTT 59.442 40.909 5.16 0.00 41.45 2.27
667 5009 3.755905 TCTGATGCGTTCCAATGCTTTTA 59.244 39.130 5.16 0.00 41.45 1.52
668 5010 4.217334 TCTGATGCGTTCCAATGCTTTTAA 59.783 37.500 5.16 0.00 41.45 1.52
669 5011 4.233789 TGATGCGTTCCAATGCTTTTAAC 58.766 39.130 5.16 0.00 41.45 2.01
670 5012 3.019933 TGCGTTCCAATGCTTTTAACC 57.980 42.857 5.16 0.00 41.45 2.85
671 5013 2.288518 TGCGTTCCAATGCTTTTAACCC 60.289 45.455 5.16 0.00 41.45 4.11
672 5014 2.288518 GCGTTCCAATGCTTTTAACCCA 60.289 45.455 0.00 0.00 37.92 4.51
673 5015 3.616317 GCGTTCCAATGCTTTTAACCCAT 60.616 43.478 0.00 0.00 37.92 4.00
674 5016 4.173256 CGTTCCAATGCTTTTAACCCATC 58.827 43.478 0.00 0.00 0.00 3.51
675 5017 4.321601 CGTTCCAATGCTTTTAACCCATCA 60.322 41.667 0.00 0.00 0.00 3.07
676 5018 5.624281 CGTTCCAATGCTTTTAACCCATCAT 60.624 40.000 0.00 0.00 0.00 2.45
677 5019 6.172630 GTTCCAATGCTTTTAACCCATCATT 58.827 36.000 0.00 0.00 0.00 2.57
678 5020 5.976458 TCCAATGCTTTTAACCCATCATTC 58.024 37.500 0.00 0.00 0.00 2.67
679 5021 5.104982 TCCAATGCTTTTAACCCATCATTCC 60.105 40.000 0.00 0.00 0.00 3.01
680 5022 5.338219 CCAATGCTTTTAACCCATCATTCCA 60.338 40.000 0.00 0.00 0.00 3.53
681 5023 6.350906 CAATGCTTTTAACCCATCATTCCAT 58.649 36.000 0.00 0.00 0.00 3.41
682 5024 7.418827 CCAATGCTTTTAACCCATCATTCCATA 60.419 37.037 0.00 0.00 0.00 2.74
683 5025 7.673641 ATGCTTTTAACCCATCATTCCATAA 57.326 32.000 0.00 0.00 0.00 1.90
684 5026 7.487822 TGCTTTTAACCCATCATTCCATAAA 57.512 32.000 0.00 0.00 0.00 1.40
685 5027 7.555087 TGCTTTTAACCCATCATTCCATAAAG 58.445 34.615 0.00 0.00 0.00 1.85
686 5028 7.180051 TGCTTTTAACCCATCATTCCATAAAGT 59.820 33.333 0.00 0.00 0.00 2.66
687 5029 8.040727 GCTTTTAACCCATCATTCCATAAAGTT 58.959 33.333 0.00 0.00 0.00 2.66
703 5086 3.788227 AAGTTTGATGCACTCCCTGTA 57.212 42.857 0.00 0.00 0.00 2.74
780 5163 1.195448 CTGCTGCGTTAACTTCTGGTG 59.805 52.381 3.71 0.00 0.00 4.17
791 5174 1.202855 ACTTCTGGTGTCTGCTGCATT 60.203 47.619 1.31 0.00 0.00 3.56
794 5177 3.354948 TCTGGTGTCTGCTGCATTATT 57.645 42.857 1.31 0.00 0.00 1.40
799 5182 4.280425 TGGTGTCTGCTGCATTATTTTTCA 59.720 37.500 1.31 0.00 0.00 2.69
827 5210 5.391097 CGTGGTAGTGTAAAGTCTGAGAGAG 60.391 48.000 0.00 0.00 0.00 3.20
895 5378 9.685276 CATGGCTACCTTTTTATATGGATCATA 57.315 33.333 0.00 0.00 0.00 2.15
909 5392 5.635278 TGGATCATATGACCACATTGACT 57.365 39.130 17.79 0.00 37.87 3.41
922 5405 5.418840 ACCACATTGACTTTGACTTTGACTT 59.581 36.000 0.00 0.00 0.00 3.01
936 5420 3.924114 TTGACTTTGACTCCAAGGTGA 57.076 42.857 0.00 0.00 41.79 4.02
939 5423 5.152623 TGACTTTGACTCCAAGGTGATAG 57.847 43.478 0.00 0.00 41.79 2.08
940 5424 4.593206 TGACTTTGACTCCAAGGTGATAGT 59.407 41.667 0.00 0.00 41.79 2.12
944 5428 5.916661 TTGACTCCAAGGTGATAGTAGTC 57.083 43.478 0.00 0.00 34.00 2.59
945 5429 5.194473 TGACTCCAAGGTGATAGTAGTCT 57.806 43.478 0.00 0.00 34.41 3.24
946 5430 6.323210 TGACTCCAAGGTGATAGTAGTCTA 57.677 41.667 0.00 0.00 34.41 2.59
947 5431 6.912426 TGACTCCAAGGTGATAGTAGTCTAT 58.088 40.000 0.00 0.00 39.31 1.98
948 5432 8.042286 TGACTCCAAGGTGATAGTAGTCTATA 57.958 38.462 0.00 0.00 37.05 1.31
954 5471 9.930693 CCAAGGTGATAGTAGTCTATAAATTCC 57.069 37.037 0.00 0.00 37.05 3.01
980 5497 3.394674 TTTGACAGACGGCAGTTGATA 57.605 42.857 0.00 0.00 0.00 2.15
1180 5697 0.320160 ACCCTTTAAGCCACGTCGTC 60.320 55.000 0.00 0.00 0.00 4.20
1183 5700 1.604693 CCTTTAAGCCACGTCGTCTGT 60.605 52.381 0.00 0.00 0.00 3.41
1185 5702 2.228138 TTAAGCCACGTCGTCTGTTT 57.772 45.000 0.00 0.00 0.00 2.83
1186 5703 1.493772 TAAGCCACGTCGTCTGTTTG 58.506 50.000 0.00 0.00 0.00 2.93
1187 5704 0.461339 AAGCCACGTCGTCTGTTTGT 60.461 50.000 0.00 0.00 0.00 2.83
1188 5705 0.461339 AGCCACGTCGTCTGTTTGTT 60.461 50.000 0.00 0.00 0.00 2.83
1189 5706 0.375803 GCCACGTCGTCTGTTTGTTT 59.624 50.000 0.00 0.00 0.00 2.83
1190 5707 1.854434 GCCACGTCGTCTGTTTGTTTG 60.854 52.381 0.00 0.00 0.00 2.93
1191 5708 1.661617 CCACGTCGTCTGTTTGTTTGA 59.338 47.619 0.00 0.00 0.00 2.69
1192 5709 2.286833 CCACGTCGTCTGTTTGTTTGAT 59.713 45.455 0.00 0.00 0.00 2.57
1193 5710 3.531982 CACGTCGTCTGTTTGTTTGATC 58.468 45.455 0.00 0.00 0.00 2.92
1194 5711 3.245284 CACGTCGTCTGTTTGTTTGATCT 59.755 43.478 0.00 0.00 0.00 2.75
1195 5712 3.245284 ACGTCGTCTGTTTGTTTGATCTG 59.755 43.478 0.00 0.00 0.00 2.90
1196 5713 3.545633 GTCGTCTGTTTGTTTGATCTGC 58.454 45.455 0.00 0.00 0.00 4.26
1197 5714 3.002246 GTCGTCTGTTTGTTTGATCTGCA 59.998 43.478 0.00 0.00 0.00 4.41
1198 5715 3.002246 TCGTCTGTTTGTTTGATCTGCAC 59.998 43.478 0.00 0.00 0.00 4.57
1199 5716 3.002656 CGTCTGTTTGTTTGATCTGCACT 59.997 43.478 0.00 0.00 0.00 4.40
1224 5741 2.089349 GTCGAGCGAGCACCTGAAC 61.089 63.158 0.00 0.00 0.00 3.18
1225 5742 2.259818 CGAGCGAGCACCTGAACT 59.740 61.111 0.00 0.00 0.00 3.01
1226 5743 2.091112 CGAGCGAGCACCTGAACTG 61.091 63.158 0.00 0.00 0.00 3.16
1227 5744 1.290324 GAGCGAGCACCTGAACTGA 59.710 57.895 0.00 0.00 0.00 3.41
1228 5745 0.319900 GAGCGAGCACCTGAACTGAA 60.320 55.000 0.00 0.00 0.00 3.02
1241 5758 4.022849 CCTGAACTGAAAAGCGAAAATCCT 60.023 41.667 0.00 0.00 0.00 3.24
1244 5761 4.756084 ACTGAAAAGCGAAAATCCTCTG 57.244 40.909 0.00 0.00 0.00 3.35
1482 5999 2.182030 GAACCGCGTCCTCAGGAG 59.818 66.667 4.92 0.00 29.39 3.69
1549 6066 2.032528 TTCGGGGACAAGCTGCAG 59.967 61.111 10.11 10.11 0.00 4.41
1901 6418 2.158842 AGGTGATAGATGAACTGCTGGC 60.159 50.000 0.00 0.00 0.00 4.85
1917 6434 0.703488 TGGCTGGTGAATTGGGATCA 59.297 50.000 0.00 0.00 0.00 2.92
1936 6453 7.013655 TGGGATCAGTACCGTAGAGTAAAATAC 59.986 40.741 0.00 0.00 0.00 1.89
2109 6626 1.730612 GCGTTTCGTTTCCCCTCTTAG 59.269 52.381 0.00 0.00 0.00 2.18
2150 6667 0.384974 CTCGTCGCTCCTCTAATCGC 60.385 60.000 0.00 0.00 0.00 4.58
2410 6959 0.323633 CCCATGGTGATGTGCTGGAA 60.324 55.000 11.73 0.00 0.00 3.53
2628 7195 5.968676 TCAGTAATGCCCAGGTTAAGTAT 57.031 39.130 0.00 0.00 0.00 2.12
2629 7196 5.680619 TCAGTAATGCCCAGGTTAAGTATG 58.319 41.667 0.00 0.00 0.00 2.39
2630 7197 4.275936 CAGTAATGCCCAGGTTAAGTATGC 59.724 45.833 0.00 0.00 0.00 3.14
2631 7198 2.364972 ATGCCCAGGTTAAGTATGCC 57.635 50.000 0.00 0.00 0.00 4.40
2632 7199 0.257616 TGCCCAGGTTAAGTATGCCC 59.742 55.000 0.00 0.00 0.00 5.36
2633 7200 0.257616 GCCCAGGTTAAGTATGCCCA 59.742 55.000 0.00 0.00 0.00 5.36
2634 7201 1.750682 GCCCAGGTTAAGTATGCCCAG 60.751 57.143 0.00 0.00 0.00 4.45
2635 7202 1.133792 CCCAGGTTAAGTATGCCCAGG 60.134 57.143 0.00 0.00 0.00 4.45
2636 7203 1.564348 CCAGGTTAAGTATGCCCAGGT 59.436 52.381 0.00 0.00 0.00 4.00
2637 7204 2.025321 CCAGGTTAAGTATGCCCAGGTT 60.025 50.000 0.00 0.00 0.00 3.50
2638 7205 3.201266 CCAGGTTAAGTATGCCCAGGTTA 59.799 47.826 0.00 0.00 0.00 2.85
2639 7206 4.324719 CCAGGTTAAGTATGCCCAGGTTAA 60.325 45.833 0.00 0.00 0.00 2.01
2640 7207 4.881850 CAGGTTAAGTATGCCCAGGTTAAG 59.118 45.833 0.00 0.00 0.00 1.85
2641 7208 4.538891 AGGTTAAGTATGCCCAGGTTAAGT 59.461 41.667 0.00 0.00 0.00 2.24
2642 7209 5.727766 AGGTTAAGTATGCCCAGGTTAAGTA 59.272 40.000 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 189 9.291664 CTAGTTCTGTATCTGTAGTTGTTAAGC 57.708 37.037 0.00 0.00 0.00 3.09
118 214 9.561069 ACTGAACAATCTTTGTATTGAACTACT 57.439 29.630 3.73 0.00 44.59 2.57
167 610 7.053316 TGATGAGAAAAGCTGGAAATTCAAA 57.947 32.000 0.00 0.00 0.00 2.69
176 627 3.377485 CCTGTCATGATGAGAAAAGCTGG 59.623 47.826 0.00 0.00 0.00 4.85
178 629 4.260170 GACCTGTCATGATGAGAAAAGCT 58.740 43.478 0.00 0.00 0.00 3.74
266 717 0.673022 CTTCTGTCCTGCACTCCTGC 60.673 60.000 0.00 0.00 44.52 4.85
267 718 0.036577 CCTTCTGTCCTGCACTCCTG 60.037 60.000 0.00 0.00 0.00 3.86
268 719 1.197430 CCCTTCTGTCCTGCACTCCT 61.197 60.000 0.00 0.00 0.00 3.69
269 720 1.298014 CCCTTCTGTCCTGCACTCC 59.702 63.158 0.00 0.00 0.00 3.85
270 721 0.398318 AACCCTTCTGTCCTGCACTC 59.602 55.000 0.00 0.00 0.00 3.51
271 722 0.398318 GAACCCTTCTGTCCTGCACT 59.602 55.000 0.00 0.00 0.00 4.40
272 723 0.108585 TGAACCCTTCTGTCCTGCAC 59.891 55.000 0.00 0.00 0.00 4.57
273 724 1.003580 GATGAACCCTTCTGTCCTGCA 59.996 52.381 0.00 0.00 0.00 4.41
274 725 1.680249 GGATGAACCCTTCTGTCCTGC 60.680 57.143 0.00 0.00 34.48 4.85
293 744 0.251354 ACTGGCATAGCAGACACAGG 59.749 55.000 0.00 0.00 0.00 4.00
326 777 0.249911 ACGGAACACCAGCAGAGAAC 60.250 55.000 0.00 0.00 0.00 3.01
339 790 1.529865 GTACAGCAACCAGAACGGAAC 59.470 52.381 0.00 0.00 38.63 3.62
347 798 6.373779 CAAAAGATAACTGTACAGCAACCAG 58.626 40.000 22.90 0.00 0.00 4.00
348 799 5.278266 GCAAAAGATAACTGTACAGCAACCA 60.278 40.000 22.90 4.00 0.00 3.67
361 812 4.680171 ACAGTAAGCGGCAAAAGATAAC 57.320 40.909 1.45 0.00 0.00 1.89
379 965 8.757789 TCGTTTATGTTCACTACAAGTTTACAG 58.242 33.333 0.00 0.00 40.89 2.74
394 980 5.006358 ACACGATAATGGCTCGTTTATGTTC 59.994 40.000 0.00 0.00 46.49 3.18
404 990 4.683832 AGTTGTCTACACGATAATGGCTC 58.316 43.478 0.00 0.00 0.00 4.70
410 996 6.486253 ACGACTTAGTTGTCTACACGATAA 57.514 37.500 0.00 0.00 35.00 1.75
431 1017 4.703424 TCGCAACAACACATGTATTAACG 58.297 39.130 0.00 0.00 42.99 3.18
455 4797 5.774690 TGGGAACACTTCAAGATGCTTAAAT 59.225 36.000 0.00 0.00 33.40 1.40
502 4844 6.045318 CGAACTGAACTATCTGAACATCCAT 58.955 40.000 0.00 0.00 0.00 3.41
535 4877 5.049818 CCATTTTTGCTTCGCCAACATAAAA 60.050 36.000 0.00 0.00 0.00 1.52
536 4878 4.450419 CCATTTTTGCTTCGCCAACATAAA 59.550 37.500 0.00 0.00 0.00 1.40
563 4905 4.280929 TGCTTACTCTAGCTTGTGTGAAGA 59.719 41.667 12.20 0.00 41.76 2.87
581 4923 3.192844 CCAGACGTAGGAGACTTTGCTTA 59.807 47.826 0.23 0.00 43.67 3.09
647 4989 4.233789 GTTAAAAGCATTGGAACGCATCA 58.766 39.130 0.00 0.00 0.00 3.07
648 4990 3.612423 GGTTAAAAGCATTGGAACGCATC 59.388 43.478 0.00 0.00 0.00 3.91
649 4991 3.584834 GGTTAAAAGCATTGGAACGCAT 58.415 40.909 0.00 0.00 0.00 4.73
650 4992 2.288518 GGGTTAAAAGCATTGGAACGCA 60.289 45.455 10.16 0.00 32.68 5.24
651 4993 2.288518 TGGGTTAAAAGCATTGGAACGC 60.289 45.455 8.80 8.80 32.87 4.84
652 4994 3.651803 TGGGTTAAAAGCATTGGAACG 57.348 42.857 0.00 0.00 0.00 3.95
653 4995 5.146010 TGATGGGTTAAAAGCATTGGAAC 57.854 39.130 0.00 0.00 0.00 3.62
654 4996 6.371595 AATGATGGGTTAAAAGCATTGGAA 57.628 33.333 0.00 0.00 0.00 3.53
655 4997 5.104982 GGAATGATGGGTTAAAAGCATTGGA 60.105 40.000 0.00 0.00 0.00 3.53
656 4998 5.118286 GGAATGATGGGTTAAAAGCATTGG 58.882 41.667 0.00 0.00 0.00 3.16
657 4999 5.732633 TGGAATGATGGGTTAAAAGCATTG 58.267 37.500 0.00 0.00 0.00 2.82
658 5000 6.564557 ATGGAATGATGGGTTAAAAGCATT 57.435 33.333 0.00 0.00 0.00 3.56
659 5001 7.673641 TTATGGAATGATGGGTTAAAAGCAT 57.326 32.000 0.00 0.00 0.00 3.79
660 5002 7.180051 ACTTTATGGAATGATGGGTTAAAAGCA 59.820 33.333 0.00 0.00 0.00 3.91
661 5003 7.555965 ACTTTATGGAATGATGGGTTAAAAGC 58.444 34.615 0.00 0.00 0.00 3.51
662 5004 9.942850 AAACTTTATGGAATGATGGGTTAAAAG 57.057 29.630 0.00 0.00 0.00 2.27
663 5005 9.717942 CAAACTTTATGGAATGATGGGTTAAAA 57.282 29.630 0.00 0.00 0.00 1.52
664 5006 9.094578 TCAAACTTTATGGAATGATGGGTTAAA 57.905 29.630 0.00 0.00 0.00 1.52
665 5007 8.657387 TCAAACTTTATGGAATGATGGGTTAA 57.343 30.769 0.00 0.00 0.00 2.01
666 5008 8.694540 CATCAAACTTTATGGAATGATGGGTTA 58.305 33.333 5.82 0.00 40.09 2.85
667 5009 7.558604 CATCAAACTTTATGGAATGATGGGTT 58.441 34.615 5.82 0.00 40.09 4.11
668 5010 6.407299 GCATCAAACTTTATGGAATGATGGGT 60.407 38.462 13.53 0.00 42.60 4.51
669 5011 5.987347 GCATCAAACTTTATGGAATGATGGG 59.013 40.000 13.53 0.00 42.60 4.00
670 5012 6.477688 GTGCATCAAACTTTATGGAATGATGG 59.522 38.462 13.53 0.00 42.60 3.51
671 5013 7.262772 AGTGCATCAAACTTTATGGAATGATG 58.737 34.615 8.73 8.73 44.24 3.07
672 5014 7.414222 AGTGCATCAAACTTTATGGAATGAT 57.586 32.000 0.00 0.00 0.00 2.45
673 5015 6.127647 GGAGTGCATCAAACTTTATGGAATGA 60.128 38.462 0.00 0.00 0.00 2.57
674 5016 6.038356 GGAGTGCATCAAACTTTATGGAATG 58.962 40.000 0.00 0.00 0.00 2.67
675 5017 5.127682 GGGAGTGCATCAAACTTTATGGAAT 59.872 40.000 0.00 0.00 0.00 3.01
676 5018 4.462483 GGGAGTGCATCAAACTTTATGGAA 59.538 41.667 0.00 0.00 0.00 3.53
677 5019 4.016444 GGGAGTGCATCAAACTTTATGGA 58.984 43.478 0.00 0.00 0.00 3.41
678 5020 4.019174 AGGGAGTGCATCAAACTTTATGG 58.981 43.478 0.00 0.00 0.00 2.74
679 5021 4.460382 ACAGGGAGTGCATCAAACTTTATG 59.540 41.667 0.00 0.00 0.00 1.90
680 5022 4.666512 ACAGGGAGTGCATCAAACTTTAT 58.333 39.130 0.00 0.00 0.00 1.40
681 5023 4.098914 ACAGGGAGTGCATCAAACTTTA 57.901 40.909 0.00 0.00 0.00 1.85
682 5024 2.949447 ACAGGGAGTGCATCAAACTTT 58.051 42.857 0.00 0.00 0.00 2.66
683 5025 2.664402 ACAGGGAGTGCATCAAACTT 57.336 45.000 0.00 0.00 0.00 2.66
684 5026 4.307032 AATACAGGGAGTGCATCAAACT 57.693 40.909 0.00 0.00 0.00 2.66
685 5027 5.163652 GGTAAATACAGGGAGTGCATCAAAC 60.164 44.000 0.00 0.00 0.00 2.93
686 5028 4.947388 GGTAAATACAGGGAGTGCATCAAA 59.053 41.667 0.00 0.00 0.00 2.69
687 5029 4.523083 GGTAAATACAGGGAGTGCATCAA 58.477 43.478 0.00 0.00 0.00 2.57
703 5086 1.716503 AGGAAAGCCACAGGGGTAAAT 59.283 47.619 0.00 0.00 46.38 1.40
791 5174 4.382291 ACACTACCACGTGCTGAAAAATA 58.618 39.130 10.91 0.00 38.45 1.40
794 5177 2.319136 ACACTACCACGTGCTGAAAA 57.681 45.000 10.91 0.00 38.45 2.29
799 5182 2.626743 AGACTTTACACTACCACGTGCT 59.373 45.455 10.91 0.00 38.45 4.40
827 5210 7.086376 TCAGAATCTTAAACTGCAGCAATTTC 58.914 34.615 15.27 11.04 0.00 2.17
867 5250 8.224025 TGATCCATATAAAAAGGTAGCCATGAA 58.776 33.333 0.00 0.00 0.00 2.57
895 5378 5.593909 TCAAAGTCAAAGTCAATGTGGTCAT 59.406 36.000 0.00 0.00 35.59 3.06
909 5392 5.125417 CCTTGGAGTCAAAGTCAAAGTCAAA 59.875 40.000 6.52 0.00 28.51 2.69
922 5405 5.580998 AGACTACTATCACCTTGGAGTCAA 58.419 41.667 7.24 0.00 35.40 3.18
939 5423 8.560374 GTCAAATGCCTGGAATTTATAGACTAC 58.440 37.037 12.34 0.36 0.00 2.73
940 5424 8.271458 TGTCAAATGCCTGGAATTTATAGACTA 58.729 33.333 21.00 10.96 0.00 2.59
944 5428 7.420800 GTCTGTCAAATGCCTGGAATTTATAG 58.579 38.462 12.34 10.64 0.00 1.31
945 5429 6.038161 CGTCTGTCAAATGCCTGGAATTTATA 59.962 38.462 12.34 1.66 0.00 0.98
946 5430 5.163622 CGTCTGTCAAATGCCTGGAATTTAT 60.164 40.000 12.34 0.00 0.00 1.40
947 5431 4.155826 CGTCTGTCAAATGCCTGGAATTTA 59.844 41.667 12.34 0.00 0.00 1.40
948 5432 3.057315 CGTCTGTCAAATGCCTGGAATTT 60.057 43.478 6.83 6.83 0.00 1.82
954 5471 1.236616 TGCCGTCTGTCAAATGCCTG 61.237 55.000 0.00 0.00 0.00 4.85
1180 5697 4.514441 AGAGAGTGCAGATCAAACAAACAG 59.486 41.667 0.00 0.00 0.00 3.16
1183 5700 4.707105 TCAGAGAGTGCAGATCAAACAAA 58.293 39.130 0.00 0.00 0.00 2.83
1185 5702 3.323115 ACTCAGAGAGTGCAGATCAAACA 59.677 43.478 3.79 0.00 41.76 2.83
1186 5703 3.924144 ACTCAGAGAGTGCAGATCAAAC 58.076 45.455 3.79 0.00 41.76 2.93
1187 5704 3.366781 CGACTCAGAGAGTGCAGATCAAA 60.367 47.826 3.79 0.00 43.53 2.69
1188 5705 2.163211 CGACTCAGAGAGTGCAGATCAA 59.837 50.000 3.79 0.00 43.53 2.57
1189 5706 1.742268 CGACTCAGAGAGTGCAGATCA 59.258 52.381 3.79 0.00 43.53 2.92
1190 5707 2.013400 TCGACTCAGAGAGTGCAGATC 58.987 52.381 3.79 0.00 43.53 2.75
1191 5708 2.016318 CTCGACTCAGAGAGTGCAGAT 58.984 52.381 3.79 0.00 43.53 2.90
1192 5709 1.447945 CTCGACTCAGAGAGTGCAGA 58.552 55.000 3.79 1.24 43.53 4.26
1193 5710 0.179166 GCTCGACTCAGAGAGTGCAG 60.179 60.000 3.79 1.58 43.53 4.41
1194 5711 1.879480 GCTCGACTCAGAGAGTGCA 59.121 57.895 3.79 0.00 43.53 4.57
1195 5712 1.226267 CGCTCGACTCAGAGAGTGC 60.226 63.158 3.79 9.14 43.53 4.40
1196 5713 0.373370 CTCGCTCGACTCAGAGAGTG 59.627 60.000 3.79 8.51 43.53 3.51
1197 5714 1.366111 GCTCGCTCGACTCAGAGAGT 61.366 60.000 3.79 0.12 46.42 3.24
1198 5715 1.351707 GCTCGCTCGACTCAGAGAG 59.648 63.158 3.79 0.00 41.80 3.20
1199 5716 1.376037 TGCTCGCTCGACTCAGAGA 60.376 57.895 3.79 0.00 40.57 3.10
1224 5741 3.190118 AGCAGAGGATTTTCGCTTTTCAG 59.810 43.478 0.00 0.00 0.00 3.02
1225 5742 3.149196 AGCAGAGGATTTTCGCTTTTCA 58.851 40.909 0.00 0.00 0.00 2.69
1226 5743 3.189287 TGAGCAGAGGATTTTCGCTTTTC 59.811 43.478 0.00 0.00 31.86 2.29
1227 5744 3.149196 TGAGCAGAGGATTTTCGCTTTT 58.851 40.909 0.00 0.00 31.86 2.27
1228 5745 2.746362 CTGAGCAGAGGATTTTCGCTTT 59.254 45.455 0.00 0.00 31.86 3.51
1241 5758 3.114650 CTCCGCGATCTGAGCAGA 58.885 61.111 8.23 2.23 42.37 4.26
1400 5917 1.079127 CCACGATGACCAGGTCCAC 60.079 63.158 17.59 9.77 0.00 4.02
1901 6418 3.545703 GGTACTGATCCCAATTCACCAG 58.454 50.000 0.00 0.00 0.00 4.00
1936 6453 8.728088 AATAAGTCGCAAACTTCACATTTTAG 57.272 30.769 4.84 0.00 45.28 1.85
2017 6534 5.913137 ATGACAACTTGGTGAAACTTGAA 57.087 34.783 0.00 0.00 36.74 2.69
2029 6546 9.530129 GATTTTTAGACTACGAATGACAACTTG 57.470 33.333 0.00 0.00 0.00 3.16
2094 6611 1.547372 CGAACCTAAGAGGGGAAACGA 59.453 52.381 0.00 0.00 40.58 3.85
2150 6667 2.703798 CCTTTGGCCCATGTGCGAG 61.704 63.158 0.00 0.00 0.00 5.03
2628 7195 1.349688 CTGGTGTACTTAACCTGGGCA 59.650 52.381 0.00 0.00 38.60 5.36
2629 7196 1.949079 GCTGGTGTACTTAACCTGGGC 60.949 57.143 0.00 4.84 38.60 5.36
2630 7197 1.349688 TGCTGGTGTACTTAACCTGGG 59.650 52.381 0.00 0.00 38.60 4.45
2631 7198 2.301870 TCTGCTGGTGTACTTAACCTGG 59.698 50.000 9.02 0.00 38.60 4.45
2632 7199 3.678056 TCTGCTGGTGTACTTAACCTG 57.322 47.619 2.84 3.48 38.60 4.00
2633 7200 4.141574 TGTTTCTGCTGGTGTACTTAACCT 60.142 41.667 2.84 0.00 38.60 3.50
2634 7201 4.131596 TGTTTCTGCTGGTGTACTTAACC 58.868 43.478 0.00 0.00 38.26 2.85
2635 7202 5.744666 TTGTTTCTGCTGGTGTACTTAAC 57.255 39.130 0.00 0.00 0.00 2.01
2636 7203 6.761099 TTTTGTTTCTGCTGGTGTACTTAA 57.239 33.333 0.00 0.00 0.00 1.85
2637 7204 6.151312 TGTTTTTGTTTCTGCTGGTGTACTTA 59.849 34.615 0.00 0.00 0.00 2.24
2638 7205 5.047660 TGTTTTTGTTTCTGCTGGTGTACTT 60.048 36.000 0.00 0.00 0.00 2.24
2639 7206 4.461081 TGTTTTTGTTTCTGCTGGTGTACT 59.539 37.500 0.00 0.00 0.00 2.73
2640 7207 4.561213 GTGTTTTTGTTTCTGCTGGTGTAC 59.439 41.667 0.00 0.00 0.00 2.90
2641 7208 4.673061 CGTGTTTTTGTTTCTGCTGGTGTA 60.673 41.667 0.00 0.00 0.00 2.90
2642 7209 3.584834 GTGTTTTTGTTTCTGCTGGTGT 58.415 40.909 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.