Multiple sequence alignment - TraesCS4A01G473200

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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 TraesCS4A01G473200 chr4A 100.000 3470 0 0 1 3470 733387562 733391031 0.000000e+00 6408
1 TraesCS4A01G473200 chr4A 93.327 989 58 4 1535 2518 733605278 733604293 0.000000e+00 1454
2 TraesCS4A01G473200 chr4A 90.632 459 27 10 1093 1535 733605956 733605498 2.310000e-166 595
3 TraesCS4A01G473200 chr4A 88.814 295 31 1 536 828 677898148 677898442 9.160000e-96 361
4 TraesCS4A01G473200 chr7D 95.731 937 34 3 2538 3470 636607931 636606997 0.000000e+00 1504
5 TraesCS4A01G473200 chr7D 95.218 941 38 4 2534 3470 515477242 515476305 0.000000e+00 1482
6 TraesCS4A01G473200 chr7D 91.274 997 57 12 1535 2518 6793887 6792908 0.000000e+00 1332
7 TraesCS4A01G473200 chr7D 92.553 376 17 7 1171 1535 6794489 6794114 2.370000e-146 529
8 TraesCS4A01G473200 chr3D 95.624 937 39 2 2535 3470 559262847 559263782 0.000000e+00 1502
9 TraesCS4A01G473200 chr2D 95.513 936 41 1 2535 3470 298848265 298847331 0.000000e+00 1495
10 TraesCS4A01G473200 chr6D 95.494 932 40 2 2540 3470 203758233 203757303 0.000000e+00 1487
11 TraesCS4A01G473200 chr4D 95.238 924 42 2 2547 3470 483118704 483117783 0.000000e+00 1461
12 TraesCS4A01G473200 chr1D 94.675 939 45 4 2536 3470 296614335 296613398 0.000000e+00 1452
13 TraesCS4A01G473200 chr4B 93.955 943 48 7 2536 3470 569760570 569761511 0.000000e+00 1417
14 TraesCS4A01G473200 chr4B 95.227 880 21 1 1 880 629858295 629857437 0.000000e+00 1373
15 TraesCS4A01G473200 chr4B 93.923 543 23 6 310 847 543747975 543748512 0.000000e+00 811
16 TraesCS4A01G473200 chr4B 97.403 308 8 0 1 308 543747255 543747562 3.070000e-145 525
17 TraesCS4A01G473200 chr4B 94.146 205 10 2 888 1092 154206550 154206348 9.350000e-81 311
18 TraesCS4A01G473200 chr7A 91.773 1021 55 16 1535 2543 7773628 7772625 0.000000e+00 1393
19 TraesCS4A01G473200 chr7A 93.603 938 53 5 2539 3470 81148008 81147072 0.000000e+00 1393
20 TraesCS4A01G473200 chr7A 90.746 389 12 11 1171 1535 7774222 7773834 6.690000e-137 497
21 TraesCS4A01G473200 chr5A 97.638 762 18 0 111 872 505495074 505494313 0.000000e+00 1308
22 TraesCS4A01G473200 chr5A 98.505 602 8 1 1 601 505495672 505495071 0.000000e+00 1061
23 TraesCS4A01G473200 chr6A 93.474 567 28 6 310 872 531548559 531547998 0.000000e+00 833
24 TraesCS4A01G473200 chr6A 96.463 311 10 1 1 311 531549278 531548969 2.390000e-141 512
25 TraesCS4A01G473200 chr1A 92.982 570 28 7 310 872 335105521 335104957 0.000000e+00 821
26 TraesCS4A01G473200 chr1A 96.785 311 10 0 1 311 335106241 335105931 1.430000e-143 520
27 TraesCS4A01G473200 chr3B 97.115 312 7 2 1 311 3784321 3784011 3.070000e-145 525
28 TraesCS4A01G473200 chr3B 97.115 312 7 2 1 311 4684199 4683889 3.070000e-145 525
29 TraesCS4A01G473200 chr3B 97.411 309 6 2 1 308 614904986 614905293 3.070000e-145 525
30 TraesCS4A01G473200 chr3B 90.608 362 28 3 536 892 4682097 4681737 3.130000e-130 475
31 TraesCS4A01G473200 chr3B 91.098 337 24 3 536 867 3781485 3781150 5.280000e-123 451
32 TraesCS4A01G473200 chr3B 97.248 218 4 2 310 527 614905708 614905923 5.470000e-98 368
33 TraesCS4A01G473200 chr3B 97.248 218 3 2 310 527 3783600 3783386 1.970000e-97 366
34 TraesCS4A01G473200 chr3B 97.248 218 3 2 310 527 4683477 4683263 1.970000e-97 366
35 TraesCS4A01G473200 chr3B 92.611 203 13 2 888 1090 782427194 782427394 1.220000e-74 291
36 TraesCS4A01G473200 chr3B 92.268 194 14 1 696 889 614907953 614908145 1.230000e-69 274
37 TraesCS4A01G473200 chr6B 95.122 205 8 2 888 1092 88873990 88873788 4.320000e-84 322
38 TraesCS4A01G473200 chr2A 83.654 208 32 2 888 1095 38760937 38760732 9.830000e-46 195


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 TraesCS4A01G473200 chr4A 733387562 733391031 3469 False 6408.000000 6408 100.000000 1 3470 1 chr4A.!!$F2 3469
1 TraesCS4A01G473200 chr4A 733604293 733605956 1663 True 1024.500000 1454 91.979500 1093 2518 2 chr4A.!!$R1 1425
2 TraesCS4A01G473200 chr7D 636606997 636607931 934 True 1504.000000 1504 95.731000 2538 3470 1 chr7D.!!$R2 932
3 TraesCS4A01G473200 chr7D 515476305 515477242 937 True 1482.000000 1482 95.218000 2534 3470 1 chr7D.!!$R1 936
4 TraesCS4A01G473200 chr7D 6792908 6794489 1581 True 930.500000 1332 91.913500 1171 2518 2 chr7D.!!$R3 1347
5 TraesCS4A01G473200 chr3D 559262847 559263782 935 False 1502.000000 1502 95.624000 2535 3470 1 chr3D.!!$F1 935
6 TraesCS4A01G473200 chr2D 298847331 298848265 934 True 1495.000000 1495 95.513000 2535 3470 1 chr2D.!!$R1 935
7 TraesCS4A01G473200 chr6D 203757303 203758233 930 True 1487.000000 1487 95.494000 2540 3470 1 chr6D.!!$R1 930
8 TraesCS4A01G473200 chr4D 483117783 483118704 921 True 1461.000000 1461 95.238000 2547 3470 1 chr4D.!!$R1 923
9 TraesCS4A01G473200 chr1D 296613398 296614335 937 True 1452.000000 1452 94.675000 2536 3470 1 chr1D.!!$R1 934
10 TraesCS4A01G473200 chr4B 569760570 569761511 941 False 1417.000000 1417 93.955000 2536 3470 1 chr4B.!!$F1 934
11 TraesCS4A01G473200 chr4B 629857437 629858295 858 True 1373.000000 1373 95.227000 1 880 1 chr4B.!!$R2 879
12 TraesCS4A01G473200 chr4B 543747255 543748512 1257 False 668.000000 811 95.663000 1 847 2 chr4B.!!$F2 846
13 TraesCS4A01G473200 chr7A 81147072 81148008 936 True 1393.000000 1393 93.603000 2539 3470 1 chr7A.!!$R1 931
14 TraesCS4A01G473200 chr7A 7772625 7774222 1597 True 945.000000 1393 91.259500 1171 2543 2 chr7A.!!$R2 1372
15 TraesCS4A01G473200 chr5A 505494313 505495672 1359 True 1184.500000 1308 98.071500 1 872 2 chr5A.!!$R1 871
16 TraesCS4A01G473200 chr6A 531547998 531549278 1280 True 672.500000 833 94.968500 1 872 2 chr6A.!!$R1 871
17 TraesCS4A01G473200 chr1A 335104957 335106241 1284 True 670.500000 821 94.883500 1 872 2 chr1A.!!$R1 871
18 TraesCS4A01G473200 chr3B 4681737 4684199 2462 True 455.333333 525 94.990333 1 892 3 chr3B.!!$R2 891
19 TraesCS4A01G473200 chr3B 3781150 3784321 3171 True 447.333333 525 95.153667 1 867 3 chr3B.!!$R1 866
20 TraesCS4A01G473200 chr3B 614904986 614908145 3159 False 389.000000 525 95.642333 1 889 3 chr3B.!!$F2 888

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
694 3983 1.672356 CAAGCTCGAACCACCCAGG 60.672 63.158 0.0 0.0 45.67 4.45 F
1085 4374 0.249489 CGGTCTTTATCCTGGCTCCG 60.249 60.000 0.0 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1563 5123 0.036388 GACCTCATCGGGAACAGCAA 60.036 55.0 0.0 0.0 36.97 3.91 R
3044 6631 0.179121 CGTTGTAGCACTCCGCCATA 60.179 55.0 0.0 0.0 44.04 2.74 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
308 311 6.739331 TTTTGTGGATTCCTACACCATTTT 57.261 33.333 3.95 0.00 36.80 1.82
574 3123 6.808008 ATGATATGTTTTTATGCGAGAGGG 57.192 37.500 0.00 0.00 0.00 4.30
694 3983 1.672356 CAAGCTCGAACCACCCAGG 60.672 63.158 0.00 0.00 45.67 4.45
903 4192 7.066307 AGGTAAAGATTTTGGCAATGAAACT 57.934 32.000 0.00 0.00 0.00 2.66
904 4193 7.508687 AGGTAAAGATTTTGGCAATGAAACTT 58.491 30.769 0.00 0.95 0.00 2.66
905 4194 7.442062 AGGTAAAGATTTTGGCAATGAAACTTG 59.558 33.333 0.00 0.00 0.00 3.16
906 4195 7.226523 GGTAAAGATTTTGGCAATGAAACTTGT 59.773 33.333 0.00 0.00 0.00 3.16
907 4196 6.849588 AAGATTTTGGCAATGAAACTTGTC 57.150 33.333 0.00 0.00 0.00 3.18
908 4197 5.916318 AGATTTTGGCAATGAAACTTGTCA 58.084 33.333 0.00 0.00 38.88 3.58
909 4198 6.527423 AGATTTTGGCAATGAAACTTGTCAT 58.473 32.000 0.00 0.00 40.20 3.06
910 4199 7.669427 AGATTTTGGCAATGAAACTTGTCATA 58.331 30.769 0.00 0.00 40.20 2.15
911 4200 7.816031 AGATTTTGGCAATGAAACTTGTCATAG 59.184 33.333 0.00 0.00 40.20 2.23
912 4201 6.403866 TTTGGCAATGAAACTTGTCATAGT 57.596 33.333 0.00 0.00 40.20 2.12
913 4202 6.403866 TTGGCAATGAAACTTGTCATAGTT 57.596 33.333 0.00 0.00 40.20 2.24
914 4203 7.517614 TTGGCAATGAAACTTGTCATAGTTA 57.482 32.000 0.00 0.00 40.20 2.24
915 4204 6.908825 TGGCAATGAAACTTGTCATAGTTAC 58.091 36.000 0.00 0.00 35.90 2.50
916 4205 6.488344 TGGCAATGAAACTTGTCATAGTTACA 59.512 34.615 0.00 0.00 35.90 2.41
917 4206 7.176515 TGGCAATGAAACTTGTCATAGTTACAT 59.823 33.333 0.00 0.00 35.90 2.29
918 4207 7.485913 GGCAATGAAACTTGTCATAGTTACATG 59.514 37.037 0.00 0.00 37.25 3.21
919 4208 8.023128 GCAATGAAACTTGTCATAGTTACATGT 58.977 33.333 2.69 2.69 37.25 3.21
920 4209 9.333497 CAATGAAACTTGTCATAGTTACATGTG 57.667 33.333 9.11 0.00 37.25 3.21
921 4210 8.621532 ATGAAACTTGTCATAGTTACATGTGT 57.378 30.769 9.11 0.00 37.37 3.72
922 4211 7.860613 TGAAACTTGTCATAGTTACATGTGTG 58.139 34.615 9.11 0.00 37.37 3.82
923 4212 7.713073 TGAAACTTGTCATAGTTACATGTGTGA 59.287 33.333 9.11 2.37 37.37 3.58
924 4213 8.621532 AAACTTGTCATAGTTACATGTGTGAT 57.378 30.769 9.11 0.00 37.37 3.06
925 4214 7.601073 ACTTGTCATAGTTACATGTGTGATG 57.399 36.000 9.11 7.02 34.87 3.07
926 4215 7.386059 ACTTGTCATAGTTACATGTGTGATGA 58.614 34.615 9.11 9.22 34.87 2.92
927 4216 8.043113 ACTTGTCATAGTTACATGTGTGATGAT 58.957 33.333 9.11 0.00 34.87 2.45
928 4217 9.533253 CTTGTCATAGTTACATGTGTGATGATA 57.467 33.333 9.11 7.72 0.00 2.15
963 4252 8.547967 AAGAAAGTATACGATTTTGCTTCTGA 57.452 30.769 0.00 0.00 0.00 3.27
964 4253 7.965045 AGAAAGTATACGATTTTGCTTCTGAC 58.035 34.615 0.00 0.00 0.00 3.51
965 4254 7.602644 AGAAAGTATACGATTTTGCTTCTGACA 59.397 33.333 0.00 0.00 0.00 3.58
966 4255 6.648725 AGTATACGATTTTGCTTCTGACAC 57.351 37.500 0.00 0.00 0.00 3.67
967 4256 6.163476 AGTATACGATTTTGCTTCTGACACA 58.837 36.000 0.00 0.00 0.00 3.72
968 4257 6.818644 AGTATACGATTTTGCTTCTGACACAT 59.181 34.615 0.00 0.00 0.00 3.21
969 4258 4.836125 ACGATTTTGCTTCTGACACATT 57.164 36.364 0.00 0.00 0.00 2.71
970 4259 5.940192 ACGATTTTGCTTCTGACACATTA 57.060 34.783 0.00 0.00 0.00 1.90
971 4260 6.500684 ACGATTTTGCTTCTGACACATTAT 57.499 33.333 0.00 0.00 0.00 1.28
972 4261 7.609760 ACGATTTTGCTTCTGACACATTATA 57.390 32.000 0.00 0.00 0.00 0.98
973 4262 8.213518 ACGATTTTGCTTCTGACACATTATAT 57.786 30.769 0.00 0.00 0.00 0.86
974 4263 8.124823 ACGATTTTGCTTCTGACACATTATATG 58.875 33.333 0.00 0.00 0.00 1.78
975 4264 8.124823 CGATTTTGCTTCTGACACATTATATGT 58.875 33.333 0.00 0.00 46.22 2.29
979 4268 7.425577 TGCTTCTGACACATTATATGTATGC 57.574 36.000 0.00 0.00 42.70 3.14
980 4269 7.219322 TGCTTCTGACACATTATATGTATGCT 58.781 34.615 0.00 0.00 42.70 3.79
981 4270 7.716560 TGCTTCTGACACATTATATGTATGCTT 59.283 33.333 0.00 0.00 42.70 3.91
982 4271 8.013947 GCTTCTGACACATTATATGTATGCTTG 58.986 37.037 0.00 0.00 42.70 4.01
983 4272 8.962884 TTCTGACACATTATATGTATGCTTGT 57.037 30.769 0.00 0.00 42.70 3.16
984 4273 8.369218 TCTGACACATTATATGTATGCTTGTG 57.631 34.615 0.00 0.00 42.70 3.33
985 4274 8.203485 TCTGACACATTATATGTATGCTTGTGA 58.797 33.333 7.11 0.00 42.70 3.58
986 4275 8.369218 TGACACATTATATGTATGCTTGTGAG 57.631 34.615 7.11 0.00 42.70 3.51
987 4276 7.442062 TGACACATTATATGTATGCTTGTGAGG 59.558 37.037 7.11 0.00 42.70 3.86
988 4277 7.282585 ACACATTATATGTATGCTTGTGAGGT 58.717 34.615 7.11 0.00 42.70 3.85
989 4278 7.775093 ACACATTATATGTATGCTTGTGAGGTT 59.225 33.333 7.11 0.00 42.70 3.50
990 4279 8.071967 CACATTATATGTATGCTTGTGAGGTTG 58.928 37.037 0.00 0.00 42.70 3.77
991 4280 7.229306 ACATTATATGTATGCTTGTGAGGTTGG 59.771 37.037 0.00 0.00 42.78 3.77
992 4281 2.949177 TGTATGCTTGTGAGGTTGGT 57.051 45.000 0.00 0.00 0.00 3.67
993 4282 3.222173 TGTATGCTTGTGAGGTTGGTT 57.778 42.857 0.00 0.00 0.00 3.67
994 4283 3.561143 TGTATGCTTGTGAGGTTGGTTT 58.439 40.909 0.00 0.00 0.00 3.27
995 4284 3.957497 TGTATGCTTGTGAGGTTGGTTTT 59.043 39.130 0.00 0.00 0.00 2.43
996 4285 4.404073 TGTATGCTTGTGAGGTTGGTTTTT 59.596 37.500 0.00 0.00 0.00 1.94
1033 4322 9.745880 ACCTATTAGTTCGTATACATGTTTCTG 57.254 33.333 2.30 0.00 0.00 3.02
1034 4323 9.961265 CCTATTAGTTCGTATACATGTTTCTGA 57.039 33.333 2.30 0.00 0.00 3.27
1060 4349 5.767816 AAAAATCATATACCTCGTTGCCC 57.232 39.130 0.00 0.00 0.00 5.36
1061 4350 3.418684 AATCATATACCTCGTTGCCCC 57.581 47.619 0.00 0.00 0.00 5.80
1062 4351 1.053424 TCATATACCTCGTTGCCCCC 58.947 55.000 0.00 0.00 0.00 5.40
1063 4352 1.056660 CATATACCTCGTTGCCCCCT 58.943 55.000 0.00 0.00 0.00 4.79
1064 4353 1.002087 CATATACCTCGTTGCCCCCTC 59.998 57.143 0.00 0.00 0.00 4.30
1065 4354 0.263765 TATACCTCGTTGCCCCCTCT 59.736 55.000 0.00 0.00 0.00 3.69
1066 4355 1.049289 ATACCTCGTTGCCCCCTCTC 61.049 60.000 0.00 0.00 0.00 3.20
1067 4356 4.148825 CCTCGTTGCCCCCTCTCG 62.149 72.222 0.00 0.00 0.00 4.04
1068 4357 4.148825 CTCGTTGCCCCCTCTCGG 62.149 72.222 0.00 0.00 0.00 4.63
1070 4359 4.452733 CGTTGCCCCCTCTCGGTC 62.453 72.222 0.00 0.00 0.00 4.79
1071 4360 3.003763 GTTGCCCCCTCTCGGTCT 61.004 66.667 0.00 0.00 0.00 3.85
1072 4361 2.203938 TTGCCCCCTCTCGGTCTT 60.204 61.111 0.00 0.00 0.00 3.01
1073 4362 1.846124 TTGCCCCCTCTCGGTCTTT 60.846 57.895 0.00 0.00 0.00 2.52
1074 4363 0.545787 TTGCCCCCTCTCGGTCTTTA 60.546 55.000 0.00 0.00 0.00 1.85
1075 4364 0.326238 TGCCCCCTCTCGGTCTTTAT 60.326 55.000 0.00 0.00 0.00 1.40
1076 4365 0.393448 GCCCCCTCTCGGTCTTTATC 59.607 60.000 0.00 0.00 0.00 1.75
1077 4366 1.049402 CCCCCTCTCGGTCTTTATCC 58.951 60.000 0.00 0.00 0.00 2.59
1078 4367 1.413227 CCCCCTCTCGGTCTTTATCCT 60.413 57.143 0.00 0.00 0.00 3.24
1079 4368 1.689273 CCCCTCTCGGTCTTTATCCTG 59.311 57.143 0.00 0.00 0.00 3.86
1080 4369 1.689273 CCCTCTCGGTCTTTATCCTGG 59.311 57.143 0.00 0.00 0.00 4.45
1081 4370 1.069358 CCTCTCGGTCTTTATCCTGGC 59.931 57.143 0.00 0.00 0.00 4.85
1082 4371 2.035632 CTCTCGGTCTTTATCCTGGCT 58.964 52.381 0.00 0.00 0.00 4.75
1083 4372 2.032620 TCTCGGTCTTTATCCTGGCTC 58.967 52.381 0.00 0.00 0.00 4.70
1084 4373 1.069358 CTCGGTCTTTATCCTGGCTCC 59.931 57.143 0.00 0.00 0.00 4.70
1085 4374 0.249489 CGGTCTTTATCCTGGCTCCG 60.249 60.000 0.00 0.00 0.00 4.63
1086 4375 0.533085 GGTCTTTATCCTGGCTCCGC 60.533 60.000 0.00 0.00 0.00 5.54
1189 4478 4.933064 CGTCTCGGCTCCGGCATC 62.933 72.222 8.59 0.00 40.87 3.91
1304 4593 2.331451 GACACGCAAACCACCTGC 59.669 61.111 0.00 0.00 36.41 4.85
1441 4753 2.124403 CTGGTGAGCATCCTGGCC 60.124 66.667 0.00 0.00 0.00 5.36
1507 4819 2.509336 CAGGCCGTCGTCATGGAC 60.509 66.667 0.00 0.00 36.86 4.02
1563 5123 3.884900 GCACGACGGTGGCTTATT 58.115 55.556 0.00 0.00 44.54 1.40
1590 5150 2.885644 CGATGAGGTCGTTGGGCG 60.886 66.667 0.00 0.00 45.19 6.13
1642 5202 1.686325 GGGAGCTACATTGGCGGAGA 61.686 60.000 0.00 0.00 34.52 3.71
1648 5208 3.580458 AGCTACATTGGCGGAGATAATCT 59.420 43.478 0.00 0.00 34.52 2.40
1655 5215 6.014242 ACATTGGCGGAGATAATCTAATCAGA 60.014 38.462 0.00 0.00 34.56 3.27
1667 5227 2.160615 TCTAATCAGATAGCTCGCTCGC 59.839 50.000 0.00 0.00 0.00 5.03
1722 5282 1.202417 AGTCTGACGAACACACTGTGG 60.202 52.381 13.77 3.85 37.94 4.17
1728 5288 1.412710 ACGAACACACTGTGGTCTGAT 59.587 47.619 22.11 7.48 46.83 2.90
1729 5289 1.794701 CGAACACACTGTGGTCTGATG 59.205 52.381 22.11 5.69 46.83 3.07
1730 5290 2.803133 CGAACACACTGTGGTCTGATGT 60.803 50.000 22.11 3.25 46.83 3.06
1737 5297 2.373169 ACTGTGGTCTGATGTTCATGGT 59.627 45.455 0.00 0.00 0.00 3.55
1831 5391 1.519455 GGCGGACAACCTCATCTCG 60.519 63.158 0.00 0.00 0.00 4.04
1850 5410 2.885861 CGCTCTACTTCACGGCCT 59.114 61.111 0.00 0.00 0.00 5.19
1901 5461 4.680237 CCAAGAGCGCCACGTCCA 62.680 66.667 2.29 0.00 0.00 4.02
2139 5706 0.879400 CGCTCATCCTCATGCAGGTC 60.879 60.000 0.00 0.00 43.95 3.85
2440 6007 2.896854 GCATCGGCTTCGGCATGA 60.897 61.111 0.00 0.00 43.96 3.07
2471 6038 2.584236 GAGGATGTCCGGCTTCTAGTA 58.416 52.381 0.00 0.00 42.08 1.82
2687 6274 5.935945 TCCTCTCTCTCTATTTCATCTCGT 58.064 41.667 0.00 0.00 0.00 4.18
2708 6295 0.910088 GGTCCCTACCTCAGTTGGCT 60.910 60.000 0.00 0.00 43.08 4.75
2724 6311 4.794439 CTGTCGCCGATCACCGCA 62.794 66.667 0.00 0.00 36.84 5.69
2746 6333 2.835431 CCGGCCGTCCTCATCTCT 60.835 66.667 26.12 0.00 0.00 3.10
2756 6343 1.270414 CCTCATCTCTGGTGGCCACT 61.270 60.000 33.91 11.78 0.00 4.00
2842 6429 2.594303 CGTGGCCTGCTTCAACCA 60.594 61.111 3.32 0.00 0.00 3.67
2846 6433 1.529244 GGCCTGCTTCAACCAGTGT 60.529 57.895 0.00 0.00 0.00 3.55
2930 6517 3.503363 GCTGCAGACATGGCGGAC 61.503 66.667 20.43 0.00 40.08 4.79
2980 6567 4.978083 TGCTACAACCGTTAACCAAAAA 57.022 36.364 0.00 0.00 0.00 1.94
3063 6650 0.179121 TATGGCGGAGTGCTACAACG 60.179 55.000 0.00 0.00 45.43 4.10
3130 6717 6.202954 CCCGAAACGATAGAGAAAGCATTAAT 59.797 38.462 0.00 0.00 41.38 1.40
3136 6723 7.500992 ACGATAGAGAAAGCATTAATCAAGGA 58.499 34.615 0.00 0.00 41.38 3.36
3178 6768 4.037446 TGCAACCGTTGATAGAAAAGCTTT 59.963 37.500 15.63 5.69 0.00 3.51
3285 6876 5.482908 AGAGAAAGCTTCAATCGTATGTGT 58.517 37.500 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 104 4.142556 TGTCGAATCTGCGTATACTTGTGA 60.143 41.667 0.56 0.00 0.00 3.58
641 3925 5.733121 GGTAGACCAAGGTTCGAACCCTG 62.733 56.522 37.53 34.07 42.21 4.45
654 3943 0.543410 TCTTGCCTCGGGTAGACCAA 60.543 55.000 0.21 0.00 40.22 3.67
724 4013 5.195379 GCGTCTGGTTAATATAAAGCAACG 58.805 41.667 13.55 13.55 40.32 4.10
838 4127 0.389817 CAATCGCTTCTGGTCGTCCA 60.390 55.000 0.39 0.39 42.05 4.02
892 4181 6.908825 TGTAACTATGACAAGTTTCATTGCC 58.091 36.000 7.88 0.00 40.20 4.52
893 4182 8.023128 ACATGTAACTATGACAAGTTTCATTGC 58.977 33.333 0.00 0.00 41.75 3.56
894 4183 9.333497 CACATGTAACTATGACAAGTTTCATTG 57.667 33.333 0.00 12.67 41.75 2.82
895 4184 9.066892 ACACATGTAACTATGACAAGTTTCATT 57.933 29.630 0.00 8.10 41.75 2.57
896 4185 8.506437 CACACATGTAACTATGACAAGTTTCAT 58.494 33.333 0.00 12.45 43.84 2.57
897 4186 7.713073 TCACACATGTAACTATGACAAGTTTCA 59.287 33.333 0.00 9.09 39.89 2.69
898 4187 8.083462 TCACACATGTAACTATGACAAGTTTC 57.917 34.615 0.00 4.99 40.20 2.78
899 4188 8.506437 CATCACACATGTAACTATGACAAGTTT 58.494 33.333 0.00 0.00 40.20 2.66
900 4189 7.877612 TCATCACACATGTAACTATGACAAGTT 59.122 33.333 0.00 7.75 42.31 2.66
901 4190 7.386059 TCATCACACATGTAACTATGACAAGT 58.614 34.615 0.00 0.00 0.00 3.16
902 4191 7.832503 TCATCACACATGTAACTATGACAAG 57.167 36.000 0.00 0.00 0.00 3.16
937 4226 9.647797 TCAGAAGCAAAATCGTATACTTTCTTA 57.352 29.630 0.56 0.00 0.00 2.10
938 4227 8.443937 GTCAGAAGCAAAATCGTATACTTTCTT 58.556 33.333 0.56 0.00 0.00 2.52
939 4228 7.602644 TGTCAGAAGCAAAATCGTATACTTTCT 59.397 33.333 0.56 0.00 0.00 2.52
940 4229 7.688578 GTGTCAGAAGCAAAATCGTATACTTTC 59.311 37.037 0.56 0.00 0.00 2.62
941 4230 7.172532 TGTGTCAGAAGCAAAATCGTATACTTT 59.827 33.333 0.56 0.00 0.00 2.66
942 4231 6.649141 TGTGTCAGAAGCAAAATCGTATACTT 59.351 34.615 0.56 0.00 0.00 2.24
943 4232 6.163476 TGTGTCAGAAGCAAAATCGTATACT 58.837 36.000 0.56 0.00 0.00 2.12
944 4233 6.403333 TGTGTCAGAAGCAAAATCGTATAC 57.597 37.500 0.00 0.00 0.00 1.47
945 4234 7.609760 AATGTGTCAGAAGCAAAATCGTATA 57.390 32.000 0.00 0.00 0.00 1.47
946 4235 6.500684 AATGTGTCAGAAGCAAAATCGTAT 57.499 33.333 0.00 0.00 0.00 3.06
947 4236 5.940192 AATGTGTCAGAAGCAAAATCGTA 57.060 34.783 0.00 0.00 0.00 3.43
948 4237 4.836125 AATGTGTCAGAAGCAAAATCGT 57.164 36.364 0.00 0.00 0.00 3.73
949 4238 8.124823 ACATATAATGTGTCAGAAGCAAAATCG 58.875 33.333 0.00 0.00 43.01 3.34
953 4242 8.344831 GCATACATATAATGTGTCAGAAGCAAA 58.655 33.333 2.83 0.00 44.60 3.68
954 4243 7.716560 AGCATACATATAATGTGTCAGAAGCAA 59.283 33.333 2.83 0.00 44.60 3.91
955 4244 7.219322 AGCATACATATAATGTGTCAGAAGCA 58.781 34.615 2.83 0.00 44.60 3.91
956 4245 7.664082 AGCATACATATAATGTGTCAGAAGC 57.336 36.000 2.83 0.00 44.60 3.86
957 4246 9.049523 ACAAGCATACATATAATGTGTCAGAAG 57.950 33.333 2.83 0.00 44.60 2.85
958 4247 8.829612 CACAAGCATACATATAATGTGTCAGAA 58.170 33.333 2.83 0.00 44.60 3.02
959 4248 8.203485 TCACAAGCATACATATAATGTGTCAGA 58.797 33.333 2.83 0.00 44.60 3.27
960 4249 8.369218 TCACAAGCATACATATAATGTGTCAG 57.631 34.615 2.83 0.00 44.60 3.51
961 4250 7.442062 CCTCACAAGCATACATATAATGTGTCA 59.558 37.037 2.83 0.00 44.60 3.58
962 4251 7.442364 ACCTCACAAGCATACATATAATGTGTC 59.558 37.037 2.83 0.00 44.60 3.67
963 4252 7.282585 ACCTCACAAGCATACATATAATGTGT 58.717 34.615 2.83 0.00 44.60 3.72
964 4253 7.734924 ACCTCACAAGCATACATATAATGTG 57.265 36.000 2.83 0.00 44.60 3.21
965 4254 7.229306 CCAACCTCACAAGCATACATATAATGT 59.771 37.037 0.00 0.00 46.92 2.71
966 4255 7.229306 ACCAACCTCACAAGCATACATATAATG 59.771 37.037 0.00 0.00 0.00 1.90
967 4256 7.290061 ACCAACCTCACAAGCATACATATAAT 58.710 34.615 0.00 0.00 0.00 1.28
968 4257 6.658849 ACCAACCTCACAAGCATACATATAA 58.341 36.000 0.00 0.00 0.00 0.98
969 4258 6.247229 ACCAACCTCACAAGCATACATATA 57.753 37.500 0.00 0.00 0.00 0.86
970 4259 5.116084 ACCAACCTCACAAGCATACATAT 57.884 39.130 0.00 0.00 0.00 1.78
971 4260 4.568072 ACCAACCTCACAAGCATACATA 57.432 40.909 0.00 0.00 0.00 2.29
972 4261 3.439857 ACCAACCTCACAAGCATACAT 57.560 42.857 0.00 0.00 0.00 2.29
973 4262 2.949177 ACCAACCTCACAAGCATACA 57.051 45.000 0.00 0.00 0.00 2.29
974 4263 4.584327 AAAACCAACCTCACAAGCATAC 57.416 40.909 0.00 0.00 0.00 2.39
1007 4296 9.745880 CAGAAACATGTATACGAACTAATAGGT 57.254 33.333 0.00 0.00 0.00 3.08
1008 4297 9.961265 TCAGAAACATGTATACGAACTAATAGG 57.039 33.333 0.00 0.00 0.00 2.57
1038 4327 4.583073 GGGGCAACGAGGTATATGATTTTT 59.417 41.667 0.00 0.00 37.60 1.94
1039 4328 4.142038 GGGGCAACGAGGTATATGATTTT 58.858 43.478 0.00 0.00 37.60 1.82
1040 4329 3.497942 GGGGGCAACGAGGTATATGATTT 60.498 47.826 0.00 0.00 37.60 2.17
1041 4330 2.039879 GGGGGCAACGAGGTATATGATT 59.960 50.000 0.00 0.00 37.60 2.57
1042 4331 1.628846 GGGGGCAACGAGGTATATGAT 59.371 52.381 0.00 0.00 37.60 2.45
1043 4332 1.053424 GGGGGCAACGAGGTATATGA 58.947 55.000 0.00 0.00 37.60 2.15
1044 4333 1.002087 GAGGGGGCAACGAGGTATATG 59.998 57.143 0.00 0.00 37.60 1.78
1045 4334 1.132817 AGAGGGGGCAACGAGGTATAT 60.133 52.381 0.00 0.00 37.60 0.86
1046 4335 0.263765 AGAGGGGGCAACGAGGTATA 59.736 55.000 0.00 0.00 37.60 1.47
1047 4336 1.003051 AGAGGGGGCAACGAGGTAT 59.997 57.895 0.00 0.00 37.60 2.73
1048 4337 1.684734 GAGAGGGGGCAACGAGGTA 60.685 63.158 0.00 0.00 37.60 3.08
1049 4338 3.003763 GAGAGGGGGCAACGAGGT 61.004 66.667 0.00 0.00 37.60 3.85
1050 4339 4.148825 CGAGAGGGGGCAACGAGG 62.149 72.222 0.00 0.00 37.60 4.63
1062 4351 2.035321 GAGCCAGGATAAAGACCGAGAG 59.965 54.545 0.00 0.00 0.00 3.20
1063 4352 2.032620 GAGCCAGGATAAAGACCGAGA 58.967 52.381 0.00 0.00 0.00 4.04
1064 4353 1.069358 GGAGCCAGGATAAAGACCGAG 59.931 57.143 0.00 0.00 0.00 4.63
1065 4354 1.120530 GGAGCCAGGATAAAGACCGA 58.879 55.000 0.00 0.00 0.00 4.69
1066 4355 0.249489 CGGAGCCAGGATAAAGACCG 60.249 60.000 0.00 0.00 0.00 4.79
1067 4356 3.688553 CGGAGCCAGGATAAAGACC 57.311 57.895 0.00 0.00 0.00 3.85
1081 4370 4.168291 GAAGAGGCAGGGGCGGAG 62.168 72.222 0.00 0.00 42.47 4.63
1084 4373 4.033776 TTGGAAGAGGCAGGGGCG 62.034 66.667 0.00 0.00 42.47 6.13
1085 4374 2.361737 GTTGGAAGAGGCAGGGGC 60.362 66.667 0.00 0.00 40.13 5.80
1086 4375 2.045926 CGTTGGAAGAGGCAGGGG 60.046 66.667 0.00 0.00 0.00 4.79
1087 4376 2.747855 GCGTTGGAAGAGGCAGGG 60.748 66.667 0.00 0.00 0.00 4.45
1088 4377 2.747855 GGCGTTGGAAGAGGCAGG 60.748 66.667 0.00 0.00 32.33 4.85
1089 4378 3.121030 CGGCGTTGGAAGAGGCAG 61.121 66.667 0.00 0.00 32.33 4.85
1174 4463 3.219928 GAGATGCCGGAGCCGAGA 61.220 66.667 5.05 0.00 42.83 4.04
1348 4660 1.139734 CACGGACGGATCACTCCTG 59.860 63.158 0.00 0.00 39.65 3.86
1507 4819 4.208686 GCGACGGGGAGCAGGTAG 62.209 72.222 0.00 0.00 0.00 3.18
1537 5097 1.009903 CACCGTCGTGCCGATTACAA 61.010 55.000 0.67 0.00 38.42 2.41
1563 5123 0.036388 GACCTCATCGGGAACAGCAA 60.036 55.000 0.00 0.00 36.97 3.91
1584 5144 0.980754 TTCCAGCTATCCTCGCCCAA 60.981 55.000 0.00 0.00 0.00 4.12
1590 5150 1.067213 GGCGATCTTCCAGCTATCCTC 60.067 57.143 0.00 0.00 0.00 3.71
1642 5202 6.724263 CGAGCGAGCTATCTGATTAGATTAT 58.276 40.000 5.18 0.00 40.79 1.28
1648 5208 2.620779 GCGAGCGAGCTATCTGATTA 57.379 50.000 0.00 0.00 0.00 1.75
1667 5227 7.322938 CGATCAAATGCATCAGTAATTTAGCAG 59.677 37.037 0.00 0.00 35.26 4.24
1714 5274 3.405831 CATGAACATCAGACCACAGTGT 58.594 45.455 0.00 0.00 0.00 3.55
1722 5282 0.729116 CGCCACCATGAACATCAGAC 59.271 55.000 0.00 0.00 0.00 3.51
1728 5288 2.672651 CTGCCGCCACCATGAACA 60.673 61.111 0.00 0.00 0.00 3.18
1729 5289 4.120331 GCTGCCGCCACCATGAAC 62.120 66.667 0.00 0.00 0.00 3.18
1831 5391 2.886124 GCCGTGAAGTAGAGCGCC 60.886 66.667 2.29 0.00 0.00 6.53
2124 5691 3.204526 GAAGAAGACCTGCATGAGGATG 58.795 50.000 15.51 0.00 46.33 3.51
2139 5706 1.966451 GCCCACCACCGTGAAGAAG 60.966 63.158 0.00 0.00 43.14 2.85
2471 6038 4.824537 GGAGAAGAAGAAAGAAAGCCACTT 59.175 41.667 0.00 0.00 0.00 3.16
2544 6123 1.609210 CCCGGCCCCAAATGTTTCT 60.609 57.895 0.00 0.00 0.00 2.52
2836 6423 1.342074 CTCTCCTGGACACTGGTTGA 58.658 55.000 0.00 0.00 37.05 3.18
2842 6429 2.289532 GGCAGCTCTCCTGGACACT 61.290 63.158 0.00 0.00 42.03 3.55
2846 6433 0.693430 ATGATGGCAGCTCTCCTGGA 60.693 55.000 3.69 0.00 42.03 3.86
3044 6631 0.179121 CGTTGTAGCACTCCGCCATA 60.179 55.000 0.00 0.00 44.04 2.74
3063 6650 4.201881 GGGTTGTAGCATTTTATGTCGACC 60.202 45.833 14.12 0.00 34.52 4.79
3285 6876 1.911293 GCGCAGGTCGAAGCATTTCA 61.911 55.000 0.30 0.00 41.67 2.69
3314 6905 1.737735 CACTGTGATTGCGGCTCGA 60.738 57.895 0.32 0.00 0.00 4.04


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

AutoCloner maintained by Alex Coulton.