Multiple sequence alignment - TraesCS5B01G073700

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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 TraesCS5B01G073700 chr5B 100.000 4815 0 0 1 4815 87763691 87768505 0.000000e+00 8892.0
1 TraesCS5B01G073700 chr5B 91.833 2302 141 14 1 2294 87967547 87969809 0.000000e+00 3166.0
2 TraesCS5B01G073700 chr5B 90.802 2207 111 31 2597 4775 87970304 87972446 0.000000e+00 2867.0
3 TraesCS5B01G073700 chr5B 88.289 2092 211 8 991 3055 87650469 87652553 0.000000e+00 2475.0
4 TraesCS5B01G073700 chr5B 80.662 1722 260 48 2655 4342 87293945 87295627 0.000000e+00 1267.0
5 TraesCS5B01G073700 chr5B 88.034 819 89 4 1783 2600 87292933 87293743 0.000000e+00 961.0
6 TraesCS5B01G073700 chr5B 92.123 457 35 1 1104 1560 87291075 87291530 1.130000e-180 643.0
7 TraesCS5B01G073700 chr5B 81.048 744 120 12 3114 3855 87652583 87653307 1.500000e-159 573.0
8 TraesCS5B01G073700 chr5B 92.157 306 24 0 2293 2598 87969968 87970273 2.660000e-117 433.0
9 TraesCS5B01G073700 chr5B 79.705 542 44 33 1 517 87649367 87649867 9.990000e-87 331.0
10 TraesCS5B01G073700 chr5B 82.192 292 32 12 4203 4491 87653571 87653845 2.900000e-57 233.0
11 TraesCS5B01G073700 chr5B 91.515 165 13 1 1615 1779 87291531 87291694 4.850000e-55 226.0
12 TraesCS5B01G073700 chr5D 94.487 4571 164 31 1 4556 78051468 78055965 0.000000e+00 6964.0
13 TraesCS5B01G073700 chr5D 88.569 2082 208 12 990 3047 78010360 78012435 0.000000e+00 2499.0
14 TraesCS5B01G073700 chr5D 88.271 989 108 7 1615 2600 77737708 77738691 0.000000e+00 1177.0
15 TraesCS5B01G073700 chr5D 82.496 1314 176 33 2658 3951 77738895 77740174 0.000000e+00 1103.0
16 TraesCS5B01G073700 chr5D 91.685 457 37 1 1104 1560 77737252 77737707 2.450000e-177 632.0
17 TraesCS5B01G073700 chr5D 76.604 1013 184 37 3114 4105 78012474 78013454 4.300000e-140 508.0
18 TraesCS5B01G073700 chr5D 84.091 528 39 15 13 517 78008878 78009383 7.300000e-128 468.0
19 TraesCS5B01G073700 chr5A 93.865 4303 169 41 9 4294 74671141 74675365 0.000000e+00 6396.0
20 TraesCS5B01G073700 chr5A 86.292 2918 330 32 990 3873 74590201 74593082 0.000000e+00 3109.0
21 TraesCS5B01G073700 chr5A 87.563 989 112 6 1615 2600 74496621 74497601 0.000000e+00 1134.0
22 TraesCS5B01G073700 chr5A 82.490 1285 178 28 2655 3919 74497802 74499059 0.000000e+00 1083.0
23 TraesCS5B01G073700 chr5A 91.904 457 36 1 1104 1560 74496165 74496620 5.260000e-179 638.0
24 TraesCS5B01G073700 chr5A 85.687 524 48 11 1 517 74589103 74589606 1.190000e-145 527.0
25 TraesCS5B01G073700 chr5A 88.571 70 8 0 4203 4272 74593474 74593543 8.590000e-13 86.1
26 TraesCS5B01G073700 chr1D 88.029 543 59 6 766 1305 16107270 16106731 5.260000e-179 638.0


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 TraesCS5B01G073700 chr5B 87763691 87768505 4814 False 8892.000000 8892 100.000000 1 4815 1 chr5B.!!$F1 4814
1 TraesCS5B01G073700 chr5B 87967547 87972446 4899 False 2155.333333 3166 91.597333 1 4775 3 chr5B.!!$F4 4774
2 TraesCS5B01G073700 chr5B 87649367 87653845 4478 False 903.000000 2475 82.808500 1 4491 4 chr5B.!!$F3 4490
3 TraesCS5B01G073700 chr5B 87291075 87295627 4552 False 774.250000 1267 88.083500 1104 4342 4 chr5B.!!$F2 3238
4 TraesCS5B01G073700 chr5D 78051468 78055965 4497 False 6964.000000 6964 94.487000 1 4556 1 chr5D.!!$F1 4555
5 TraesCS5B01G073700 chr5D 78008878 78013454 4576 False 1158.333333 2499 83.088000 13 4105 3 chr5D.!!$F3 4092
6 TraesCS5B01G073700 chr5D 77737252 77740174 2922 False 970.666667 1177 87.484000 1104 3951 3 chr5D.!!$F2 2847
7 TraesCS5B01G073700 chr5A 74671141 74675365 4224 False 6396.000000 6396 93.865000 9 4294 1 chr5A.!!$F1 4285
8 TraesCS5B01G073700 chr5A 74589103 74593543 4440 False 1240.700000 3109 86.850000 1 4272 3 chr5A.!!$F3 4271
9 TraesCS5B01G073700 chr5A 74496165 74499059 2894 False 951.666667 1134 87.319000 1104 3919 3 chr5A.!!$F2 2815
10 TraesCS5B01G073700 chr1D 16106731 16107270 539 True 638.000000 638 88.029000 766 1305 1 chr1D.!!$R1 539

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
99 109 0.804989 GCACTGCACCACAAGATACC 59.195 55.000 0.00 0.0 0.00 2.73 F
387 439 0.829182 CCTTTTGCTCTGGGCTTGGT 60.829 55.000 0.00 0.0 42.39 3.67 F
982 1649 0.846427 TTCCCTTGACTCCCCAGCAT 60.846 55.000 0.00 0.0 0.00 3.79 F
1723 2422 1.818674 GGTTCATGGTTGGCGATTTCT 59.181 47.619 0.00 0.0 0.00 2.52 F
2942 5192 0.105039 GAAGGAGGCCATCACCTACG 59.895 60.000 5.01 0.0 46.37 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1165 1862 1.303888 ATGCACCAGGACTTGCCAG 60.304 57.895 0.0 0.0 40.02 4.85 R
2315 4410 0.374758 CACAACGCCGATCATCAAGG 59.625 55.000 0.0 0.0 0.00 3.61 R
2495 4590 4.093998 GTCTTGTTCATGGCTGTGATGTAG 59.906 45.833 0.0 0.0 0.00 2.74 R
2992 5243 0.036010 AAGTTGGTGATCCTGAGCGG 60.036 55.000 0.0 0.0 34.23 5.52 R
4795 7274 0.031616 AGGGGCTTCTCCTCCTACTG 60.032 60.000 0.0 0.0 35.19 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
29 30 4.741342 AGCTACAATGCAGAATTTCTTGC 58.259 39.130 11.53 11.53 34.99 4.01
99 109 0.804989 GCACTGCACCACAAGATACC 59.195 55.000 0.00 0.00 0.00 2.73
135 146 1.066787 GTACTCCAACACTCTCTGGGC 60.067 57.143 0.00 0.00 33.19 5.36
160 187 7.666623 CCTTTACTCCTTGGAATTGCTAAAAA 58.333 34.615 0.00 0.00 0.00 1.94
161 188 7.814587 CCTTTACTCCTTGGAATTGCTAAAAAG 59.185 37.037 0.00 0.00 0.00 2.27
162 189 5.728637 ACTCCTTGGAATTGCTAAAAAGG 57.271 39.130 7.29 7.29 36.36 3.11
169 204 7.498900 CCTTGGAATTGCTAAAAAGGAAAACTT 59.501 33.333 7.74 0.00 42.52 2.66
208 243 6.155910 TCAGTAGATTCCTTCTGCTCAGATTT 59.844 38.462 0.00 0.00 43.11 2.17
227 262 7.020010 CAGATTTCAAAAGTTCTCGATTGGAG 58.980 38.462 0.00 0.00 44.58 3.86
255 290 4.014406 TGTCATGCTTTCATCTGCATCTT 58.986 39.130 0.00 0.00 46.65 2.40
264 299 6.625300 GCTTTCATCTGCATCTTTCTGAACAT 60.625 38.462 0.00 0.00 0.00 2.71
270 305 7.984422 TCTGCATCTTTCTGAACATCTTTTA 57.016 32.000 0.00 0.00 0.00 1.52
314 364 4.758674 CCCAAGATATGATGGCACTACAAG 59.241 45.833 0.00 0.00 0.00 3.16
315 365 5.455183 CCCAAGATATGATGGCACTACAAGA 60.455 44.000 0.00 0.00 0.00 3.02
316 366 6.057533 CCAAGATATGATGGCACTACAAGAA 58.942 40.000 0.00 0.00 0.00 2.52
317 367 6.017605 CCAAGATATGATGGCACTACAAGAAC 60.018 42.308 0.00 0.00 0.00 3.01
318 368 6.239217 AGATATGATGGCACTACAAGAACA 57.761 37.500 0.00 0.00 0.00 3.18
319 369 6.653020 AGATATGATGGCACTACAAGAACAA 58.347 36.000 0.00 0.00 0.00 2.83
320 370 6.765036 AGATATGATGGCACTACAAGAACAAG 59.235 38.462 0.00 0.00 0.00 3.16
321 371 4.350368 TGATGGCACTACAAGAACAAGA 57.650 40.909 0.00 0.00 0.00 3.02
322 372 4.065088 TGATGGCACTACAAGAACAAGAC 58.935 43.478 0.00 0.00 0.00 3.01
323 373 2.846193 TGGCACTACAAGAACAAGACC 58.154 47.619 0.00 0.00 0.00 3.85
324 374 2.152016 GGCACTACAAGAACAAGACCC 58.848 52.381 0.00 0.00 0.00 4.46
325 375 2.486548 GGCACTACAAGAACAAGACCCA 60.487 50.000 0.00 0.00 0.00 4.51
326 376 2.548480 GCACTACAAGAACAAGACCCAC 59.452 50.000 0.00 0.00 0.00 4.61
327 377 3.804036 CACTACAAGAACAAGACCCACA 58.196 45.455 0.00 0.00 0.00 4.17
328 378 3.809832 CACTACAAGAACAAGACCCACAG 59.190 47.826 0.00 0.00 0.00 3.66
387 439 0.829182 CCTTTTGCTCTGGGCTTGGT 60.829 55.000 0.00 0.00 42.39 3.67
446 501 2.158534 TGGCTCTTGGCAAAGGTAAGAA 60.159 45.455 0.00 0.00 46.03 2.52
479 535 6.713450 GTCCTTCTACTCTCTACATCCTTAGG 59.287 46.154 0.00 0.00 0.00 2.69
488 550 5.903010 TCTCTACATCCTTAGGGCATAAACA 59.097 40.000 0.00 0.00 0.00 2.83
515 790 6.381481 TGCAGCTTAAGATCATGTTTATGG 57.619 37.500 6.67 0.00 34.97 2.74
659 948 8.554528 GTGAAGTTGGAACATACTGATGATATG 58.445 37.037 0.00 0.00 39.30 1.78
660 949 8.485392 TGAAGTTGGAACATACTGATGATATGA 58.515 33.333 0.00 0.00 39.30 2.15
661 950 9.330063 GAAGTTGGAACATACTGATGATATGAA 57.670 33.333 0.00 0.00 39.30 2.57
662 951 8.668510 AGTTGGAACATACTGATGATATGAAC 57.331 34.615 0.00 0.00 39.30 3.18
663 952 8.267183 AGTTGGAACATACTGATGATATGAACA 58.733 33.333 0.00 0.00 39.30 3.18
664 953 8.338259 GTTGGAACATACTGATGATATGAACAC 58.662 37.037 0.00 0.00 39.30 3.32
900 1567 1.758862 AGATGCATCGATGTGAGGTCA 59.241 47.619 25.47 14.40 0.00 4.02
910 1577 3.305676 CGATGTGAGGTCAGAACAGACTT 60.306 47.826 0.00 0.00 38.57 3.01
982 1649 0.846427 TTCCCTTGACTCCCCAGCAT 60.846 55.000 0.00 0.00 0.00 3.79
988 1655 3.445096 CCTTGACTCCCCAGCATTTTTAG 59.555 47.826 0.00 0.00 0.00 1.85
1165 1862 4.637977 TGGTTGGCAATTTCCAAGAAAAAC 59.362 37.500 10.01 0.00 45.90 2.43
1205 1902 4.547671 TCGATACCCTTTCTCTCCTTCAT 58.452 43.478 0.00 0.00 0.00 2.57
1437 2136 2.093783 CGAACTAAAAGCGGGCTACTTG 59.906 50.000 0.00 0.00 0.00 3.16
1560 2259 4.711846 GGTCCTAATGCCCAAGAAAAAGAT 59.288 41.667 0.00 0.00 0.00 2.40
1596 2295 2.328099 GCTGCTGGGTGAAAGACGG 61.328 63.158 0.00 0.00 0.00 4.79
1651 2350 2.666190 GAAGGTGCGAGCACTGCA 60.666 61.111 24.79 0.00 45.52 4.41
1723 2422 1.818674 GGTTCATGGTTGGCGATTTCT 59.181 47.619 0.00 0.00 0.00 2.52
2281 4215 9.308000 AGAATTGAAGGGTTTCATGTACATTTA 57.692 29.630 5.37 0.00 42.60 1.40
2315 4410 7.145985 TCTATTCCGTAATTACTCACTGATGC 58.854 38.462 13.56 0.00 0.00 3.91
2495 4590 6.603599 AGAAAGTTAGGCCTGTAATTCCATTC 59.396 38.462 17.99 7.47 0.00 2.67
2717 4967 4.320494 GGATTATGCTGCCAAATACCTTCG 60.320 45.833 0.00 0.00 0.00 3.79
2791 5041 5.470777 TGGTTAGACAATTTGAAGGTTACCG 59.529 40.000 2.79 0.00 0.00 4.02
2942 5192 0.105039 GAAGGAGGCCATCACCTACG 59.895 60.000 5.01 0.00 46.37 3.51
2992 5243 6.474427 CCTGCACATATGACATGAAAAATCAC 59.526 38.462 10.38 0.00 0.00 3.06
3103 5359 5.163120 ACCTGAGACAGCATGGAATCAATAT 60.163 40.000 0.00 0.00 43.62 1.28
3329 5585 5.010516 GCTAGAAGAGATATTCAGGTCAGCA 59.989 44.000 0.00 0.00 0.00 4.41
3449 5705 7.682787 AATCACAGACTGGAATACCTAGATT 57.317 36.000 7.51 0.32 37.04 2.40
3497 5753 1.370609 TTGAACCGTCTGCGACAAAA 58.629 45.000 8.91 0.00 41.33 2.44
3500 5756 0.935196 AACCGTCTGCGACAAAACTC 59.065 50.000 8.91 0.00 41.33 3.01
3577 5836 1.740380 GCAGCTAAGCATCTCGTGGAA 60.740 52.381 0.00 0.00 0.00 3.53
3589 5848 0.034198 TCGTGGAAAGGTCGCATGAA 59.966 50.000 0.00 0.00 0.00 2.57
3689 5954 1.843851 ACAGTTCCTGGACCAAGTTCA 59.156 47.619 0.00 0.00 35.51 3.18
3819 6084 6.212791 AGGTTTGTTCTGCTGGACTAACTATA 59.787 38.462 21.98 0.00 0.00 1.31
3952 6284 4.201851 CCGTGTGAATGTTCATCCTGATTC 60.202 45.833 0.00 0.00 39.73 2.52
3953 6285 4.493057 CGTGTGAATGTTCATCCTGATTCG 60.493 45.833 0.00 0.00 39.73 3.34
3954 6286 4.393062 GTGTGAATGTTCATCCTGATTCGT 59.607 41.667 0.00 0.00 39.73 3.85
3955 6287 4.631377 TGTGAATGTTCATCCTGATTCGTC 59.369 41.667 0.00 0.00 39.73 4.20
3956 6288 4.872691 GTGAATGTTCATCCTGATTCGTCT 59.127 41.667 0.00 0.00 39.73 4.18
3957 6289 4.872124 TGAATGTTCATCCTGATTCGTCTG 59.128 41.667 0.00 0.00 31.01 3.51
3958 6290 2.621338 TGTTCATCCTGATTCGTCTGC 58.379 47.619 0.00 0.00 0.00 4.26
3959 6291 1.936547 GTTCATCCTGATTCGTCTGCC 59.063 52.381 0.00 0.00 0.00 4.85
3960 6292 1.194218 TCATCCTGATTCGTCTGCCA 58.806 50.000 0.00 0.00 0.00 4.92
3961 6293 1.764723 TCATCCTGATTCGTCTGCCAT 59.235 47.619 0.00 0.00 0.00 4.40
3962 6294 1.871676 CATCCTGATTCGTCTGCCATG 59.128 52.381 0.00 0.00 0.00 3.66
3963 6295 0.904649 TCCTGATTCGTCTGCCATGT 59.095 50.000 0.00 0.00 0.00 3.21
3964 6296 1.278985 TCCTGATTCGTCTGCCATGTT 59.721 47.619 0.00 0.00 0.00 2.71
3965 6297 1.667724 CCTGATTCGTCTGCCATGTTC 59.332 52.381 0.00 0.00 0.00 3.18
3966 6298 2.349590 CTGATTCGTCTGCCATGTTCA 58.650 47.619 0.00 0.00 0.00 3.18
3967 6299 2.941064 CTGATTCGTCTGCCATGTTCAT 59.059 45.455 0.00 0.00 0.00 2.57
3968 6300 2.938451 TGATTCGTCTGCCATGTTCATC 59.062 45.455 0.00 0.00 0.00 2.92
3969 6301 1.737838 TTCGTCTGCCATGTTCATCC 58.262 50.000 0.00 0.00 0.00 3.51
3970 6302 0.904649 TCGTCTGCCATGTTCATCCT 59.095 50.000 0.00 0.00 0.00 3.24
3971 6303 1.012086 CGTCTGCCATGTTCATCCTG 58.988 55.000 0.00 0.00 0.00 3.86
3972 6304 1.405933 CGTCTGCCATGTTCATCCTGA 60.406 52.381 0.00 0.00 0.00 3.86
3973 6305 2.744166 CGTCTGCCATGTTCATCCTGAT 60.744 50.000 0.00 0.00 0.00 2.90
3974 6306 3.285484 GTCTGCCATGTTCATCCTGATT 58.715 45.455 0.00 0.00 0.00 2.57
4173 6558 2.455032 CTTGTCTCAGCTAATCGACGG 58.545 52.381 0.00 0.00 0.00 4.79
4201 6650 3.889196 TTGTTGATTTTAACTCGCGCT 57.111 38.095 5.56 0.00 0.00 5.92
4288 6743 3.356639 CTCGCGGCTGCTCTGGTTA 62.357 63.158 17.03 0.00 39.65 2.85
4289 6744 2.202932 CGCGGCTGCTCTGGTTAT 60.203 61.111 17.03 0.00 39.65 1.89
4290 6745 1.815421 CGCGGCTGCTCTGGTTATT 60.815 57.895 17.03 0.00 39.65 1.40
4307 6762 4.744631 GGTTATTCTGTTGTGGCTTTTGTG 59.255 41.667 0.00 0.00 0.00 3.33
4352 6808 2.512885 CAGTTGCAAATGTCTGCGATC 58.487 47.619 18.38 0.00 45.74 3.69
4501 6962 4.205065 TCATAAACATACCGGGTTTCGT 57.795 40.909 4.31 0.00 39.12 3.85
4522 6983 6.378582 TCGTAATTTCAGAAATTTGTCAGGC 58.621 36.000 23.24 7.42 41.16 4.85
4581 7042 7.230510 TCAAGTGCTAACATATTCTGTTTTGGT 59.769 33.333 0.00 0.00 45.98 3.67
4582 7043 7.524717 AGTGCTAACATATTCTGTTTTGGTT 57.475 32.000 0.00 0.00 45.98 3.67
4597 7058 5.246656 TGTTTTGGTTACTAAGATCGAGGGA 59.753 40.000 0.00 0.00 0.00 4.20
4605 7067 7.014038 GGTTACTAAGATCGAGGGAAATGTAGA 59.986 40.741 0.00 0.00 0.00 2.59
4607 7069 6.366340 ACTAAGATCGAGGGAAATGTAGAGA 58.634 40.000 0.00 0.00 0.00 3.10
4619 7081 6.268566 GGAAATGTAGAGATTGTTTGGATGC 58.731 40.000 0.00 0.00 0.00 3.91
4643 7105 2.618045 CCTGTTCTAGCCCGGTCAAATT 60.618 50.000 0.00 0.00 0.00 1.82
4645 7107 2.224670 TGTTCTAGCCCGGTCAAATTGT 60.225 45.455 0.00 0.00 0.00 2.71
4652 7114 1.468985 CCGGTCAAATTGTGGGCATA 58.531 50.000 0.00 0.00 0.00 3.14
4667 7129 2.102578 GGCATACCAAATTGGCTGACT 58.897 47.619 12.67 0.00 42.67 3.41
4674 7136 3.278574 CCAAATTGGCTGACTATTCCGA 58.721 45.455 0.00 0.00 0.00 4.55
4675 7137 3.313526 CCAAATTGGCTGACTATTCCGAG 59.686 47.826 0.00 0.00 0.00 4.63
4676 7138 2.246719 ATTGGCTGACTATTCCGAGC 57.753 50.000 0.00 0.00 0.00 5.03
4677 7139 0.901827 TTGGCTGACTATTCCGAGCA 59.098 50.000 0.00 0.00 32.83 4.26
4678 7140 0.175760 TGGCTGACTATTCCGAGCAC 59.824 55.000 0.00 0.00 32.83 4.40
4679 7141 0.175760 GGCTGACTATTCCGAGCACA 59.824 55.000 0.00 0.00 32.83 4.57
4681 7143 1.927895 CTGACTATTCCGAGCACACC 58.072 55.000 0.00 0.00 0.00 4.16
4682 7144 1.204704 CTGACTATTCCGAGCACACCA 59.795 52.381 0.00 0.00 0.00 4.17
4715 7192 1.913451 GCAAGTGAGCTGAGCTGCTG 61.913 60.000 13.71 4.45 44.17 4.41
4717 7194 1.478526 AAGTGAGCTGAGCTGCTGGA 61.479 55.000 13.71 0.00 44.17 3.86
4739 7216 4.687215 GAGCGCCTGAGCACACCA 62.687 66.667 2.29 0.00 39.83 4.17
4775 7254 5.829924 TCTATCCAAATTTTCATGCTCCCTC 59.170 40.000 0.00 0.00 0.00 4.30
4776 7255 4.051661 TCCAAATTTTCATGCTCCCTCT 57.948 40.909 0.00 0.00 0.00 3.69
4777 7256 4.019174 TCCAAATTTTCATGCTCCCTCTC 58.981 43.478 0.00 0.00 0.00 3.20
4778 7257 3.765511 CCAAATTTTCATGCTCCCTCTCA 59.234 43.478 0.00 0.00 0.00 3.27
4779 7258 4.142227 CCAAATTTTCATGCTCCCTCTCAG 60.142 45.833 0.00 0.00 0.00 3.35
4780 7259 4.581309 AATTTTCATGCTCCCTCTCAGA 57.419 40.909 0.00 0.00 0.00 3.27
4781 7260 4.581309 ATTTTCATGCTCCCTCTCAGAA 57.419 40.909 0.00 0.00 0.00 3.02
4782 7261 4.371624 TTTTCATGCTCCCTCTCAGAAA 57.628 40.909 0.00 0.00 0.00 2.52
4783 7262 4.371624 TTTCATGCTCCCTCTCAGAAAA 57.628 40.909 0.00 0.00 0.00 2.29
4784 7263 4.371624 TTCATGCTCCCTCTCAGAAAAA 57.628 40.909 0.00 0.00 0.00 1.94
4807 7286 4.949966 AAACTAGACCAGTAGGAGGAGA 57.050 45.455 0.00 0.00 36.04 3.71
4808 7287 4.949966 AACTAGACCAGTAGGAGGAGAA 57.050 45.455 0.00 0.00 36.04 2.87
4809 7288 4.513406 ACTAGACCAGTAGGAGGAGAAG 57.487 50.000 0.00 0.00 34.98 2.85
4810 7289 2.153034 AGACCAGTAGGAGGAGAAGC 57.847 55.000 0.00 0.00 38.69 3.86
4811 7290 1.116308 GACCAGTAGGAGGAGAAGCC 58.884 60.000 0.00 0.00 38.69 4.35
4812 7291 0.325765 ACCAGTAGGAGGAGAAGCCC 60.326 60.000 0.00 0.00 38.69 5.19
4813 7292 1.051556 CCAGTAGGAGGAGAAGCCCC 61.052 65.000 0.00 0.00 37.37 5.80
4814 7293 0.031616 CAGTAGGAGGAGAAGCCCCT 60.032 60.000 0.00 0.00 39.67 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 5.227238 AGAAATTCTGCATTGTAGCTTCG 57.773 39.130 0.00 0.00 34.99 3.79
17 18 5.535333 ACAAGGATGTTGCAAGAAATTCTG 58.465 37.500 0.00 0.00 35.91 3.02
99 109 5.950883 TGGAGTACAAGTTAGATTCTGTCG 58.049 41.667 0.00 0.00 0.00 4.35
135 146 6.834168 TTTAGCAATTCCAAGGAGTAAAGG 57.166 37.500 0.00 0.00 0.00 3.11
160 187 9.566432 CTGAAATATGCTAGGATAAGTTTTCCT 57.434 33.333 17.61 17.61 45.59 3.36
161 188 9.343539 ACTGAAATATGCTAGGATAAGTTTTCC 57.656 33.333 18.49 4.29 0.00 3.13
169 204 9.775539 AGGAATCTACTGAAATATGCTAGGATA 57.224 33.333 6.40 6.40 0.00 2.59
182 217 5.019470 TCTGAGCAGAAGGAATCTACTGAA 58.981 41.667 0.00 0.00 36.32 3.02
227 262 4.720090 CAGATGAAAGCATGACACTTGTC 58.280 43.478 0.00 2.19 44.97 3.18
228 263 3.057736 GCAGATGAAAGCATGACACTTGT 60.058 43.478 0.00 0.00 34.11 3.16
230 265 3.151554 TGCAGATGAAAGCATGACACTT 58.848 40.909 0.00 0.00 35.51 3.16
231 266 2.786777 TGCAGATGAAAGCATGACACT 58.213 42.857 0.00 0.00 35.51 3.55
289 324 3.498774 AGTGCCATCATATCTTGGGTC 57.501 47.619 3.27 0.00 33.40 4.46
293 328 6.539826 TGTTCTTGTAGTGCCATCATATCTTG 59.460 38.462 0.00 0.00 0.00 3.02
314 364 3.008049 ACTGATACCTGTGGGTCTTGTTC 59.992 47.826 0.00 0.00 45.98 3.18
315 365 2.979678 ACTGATACCTGTGGGTCTTGTT 59.020 45.455 0.00 0.00 45.98 2.83
316 366 2.567615 GACTGATACCTGTGGGTCTTGT 59.432 50.000 0.00 0.00 45.98 3.16
317 367 2.417379 CGACTGATACCTGTGGGTCTTG 60.417 54.545 0.00 0.00 45.98 3.02
318 368 1.825474 CGACTGATACCTGTGGGTCTT 59.175 52.381 0.00 0.00 45.98 3.01
319 369 1.005569 TCGACTGATACCTGTGGGTCT 59.994 52.381 0.00 0.00 45.98 3.85
320 370 1.471119 TCGACTGATACCTGTGGGTC 58.529 55.000 0.00 0.00 45.98 4.46
322 372 3.056536 CCATATCGACTGATACCTGTGGG 60.057 52.174 0.00 0.00 39.81 4.61
323 373 3.574396 ACCATATCGACTGATACCTGTGG 59.426 47.826 0.00 0.00 39.81 4.17
324 374 4.038042 ACACCATATCGACTGATACCTGTG 59.962 45.833 0.00 0.00 39.81 3.66
325 375 4.038042 CACACCATATCGACTGATACCTGT 59.962 45.833 0.00 0.00 39.81 4.00
326 376 4.038042 ACACACCATATCGACTGATACCTG 59.962 45.833 0.00 0.00 39.81 4.00
327 377 4.215908 ACACACCATATCGACTGATACCT 58.784 43.478 0.00 0.00 39.81 3.08
328 378 4.585955 ACACACCATATCGACTGATACC 57.414 45.455 0.00 0.00 39.81 2.73
336 386 4.871933 ATGCAGATACACACCATATCGA 57.128 40.909 0.00 0.00 34.74 3.59
337 387 7.922811 ACATATATGCAGATACACACCATATCG 59.077 37.037 12.79 0.00 34.74 2.92
387 439 0.627451 AGCCAGAATGCCAAGGATGA 59.373 50.000 0.00 0.00 31.97 2.92
457 512 5.475564 GCCCTAAGGATGTAGAGAGTAGAAG 59.524 48.000 0.00 0.00 33.47 2.85
488 550 3.552875 ACATGATCTTAAGCTGCAGCAT 58.447 40.909 38.24 30.19 45.16 3.79
515 790 0.391130 TTCAGTATCCTGCGTGCCAC 60.391 55.000 0.00 0.00 38.66 5.01
803 1092 7.781548 TCAGGACAAACAGAAAGTAAAGTAC 57.218 36.000 0.00 0.00 0.00 2.73
846 1136 7.682981 GCCAGATAAATCAAAGAAAGATGTCCC 60.683 40.741 0.00 0.00 0.00 4.46
900 1567 8.367911 TGTGTGTTATTATGAGAAGTCTGTTCT 58.632 33.333 0.00 0.00 0.00 3.01
982 1649 8.018520 CGGCGCCATGATAAATATAACTAAAAA 58.981 33.333 28.98 0.00 0.00 1.94
988 1655 3.936453 TCCGGCGCCATGATAAATATAAC 59.064 43.478 28.98 0.00 0.00 1.89
1165 1862 1.303888 ATGCACCAGGACTTGCCAG 60.304 57.895 0.00 0.00 40.02 4.85
1205 1902 5.397360 TCTGAGACTGGATAGCATTCCATA 58.603 41.667 7.97 0.00 44.66 2.74
1437 2136 1.471676 CCGATGTACCTGAAGACCAGC 60.472 57.143 0.00 0.00 41.57 4.85
1560 2259 2.407521 GCGATCGCTCAAGATGAGTA 57.592 50.000 31.94 0.00 45.94 2.59
1572 2271 4.819761 TCACCCAGCAGCGATCGC 62.820 66.667 32.15 32.15 42.33 4.58
1596 2295 1.747355 CTTGATCCACCATTCTGGCAC 59.253 52.381 0.00 0.00 42.67 5.01
1651 2350 5.105269 TGTGATGCCAATAGAAATGCACATT 60.105 36.000 0.00 0.00 36.41 2.71
1723 2422 2.635915 AGGGTCTTACCATTTCGTGACA 59.364 45.455 0.00 0.00 41.02 3.58
2281 4215 8.488308 AGTAATTACGGAATAGATACCAAGGT 57.512 34.615 9.91 0.00 0.00 3.50
2315 4410 0.374758 CACAACGCCGATCATCAAGG 59.625 55.000 0.00 0.00 0.00 3.61
2495 4590 4.093998 GTCTTGTTCATGGCTGTGATGTAG 59.906 45.833 0.00 0.00 0.00 2.74
2717 4967 5.413833 AGTGTGATGAATTGGTCTTCATGTC 59.586 40.000 4.17 0.00 44.00 3.06
2942 5192 4.832248 TGAATGTGTTCCATACTCACCTC 58.168 43.478 0.00 0.00 33.45 3.85
2963 5214 6.622833 TTTCATGTCATATGTGCAGGTATG 57.377 37.500 1.90 10.59 0.00 2.39
2992 5243 0.036010 AAGTTGGTGATCCTGAGCGG 60.036 55.000 0.00 0.00 34.23 5.52
3042 5297 9.723447 GCTGGCTATTAAAGAAAAGAAATCTAC 57.277 33.333 0.00 0.00 0.00 2.59
3103 5359 2.747989 CGGTACAGAGACACTAGCTCAA 59.252 50.000 0.00 0.00 34.85 3.02
3176 5432 7.041098 ACAGGATAATCACACTTGTTTTGAGAC 60.041 37.037 0.00 0.00 0.00 3.36
3329 5585 2.498481 CACATTGCCCTGTTGGATCAAT 59.502 45.455 0.00 0.00 37.06 2.57
3577 5836 1.098050 GCAGGATTTCATGCGACCTT 58.902 50.000 1.08 0.00 43.83 3.50
3589 5848 2.381941 GGGCCTCAGGAGCAGGATT 61.382 63.158 0.84 0.00 31.91 3.01
3689 5954 1.016130 CGCAGCTTGTTGTCTCGGAT 61.016 55.000 0.00 0.00 0.00 4.18
3819 6084 2.196595 TGCAACTAGGCTGGAACCTAT 58.803 47.619 4.33 0.00 41.49 2.57
3868 6133 1.004044 CCAGTTCAGCTCCCAGTTCAT 59.996 52.381 0.00 0.00 0.00 2.57
3952 6284 1.012086 CAGGATGAACATGGCAGACG 58.988 55.000 0.00 0.00 39.69 4.18
3953 6285 2.408271 TCAGGATGAACATGGCAGAC 57.592 50.000 0.00 0.00 45.97 3.51
3965 6297 1.293924 GTGGCAGACGAATCAGGATG 58.706 55.000 0.00 0.00 37.54 3.51
3966 6298 3.768633 GTGGCAGACGAATCAGGAT 57.231 52.632 0.00 0.00 0.00 3.24
4173 6558 7.955020 CGAGTTAAAATCAACAATTTTTCGC 57.045 32.000 1.51 0.00 43.51 4.70
4201 6650 5.067674 CCACTTGAAGAATCCACACAAGAAA 59.932 40.000 0.00 0.00 39.84 2.52
4288 6743 3.953612 TCTCACAAAAGCCACAACAGAAT 59.046 39.130 0.00 0.00 0.00 2.40
4289 6744 3.128589 GTCTCACAAAAGCCACAACAGAA 59.871 43.478 0.00 0.00 0.00 3.02
4290 6745 2.682856 GTCTCACAAAAGCCACAACAGA 59.317 45.455 0.00 0.00 0.00 3.41
4307 6762 3.986572 CGCTTCATATCATCACAGGTCTC 59.013 47.826 0.00 0.00 0.00 3.36
4352 6808 1.709147 GGCAGGCATCAGCGTAAGTG 61.709 60.000 0.00 0.00 43.41 3.16
4522 6983 2.730928 GACGTTGTGATTGGCCATTTTG 59.269 45.455 6.09 0.00 0.00 2.44
4581 7042 7.997223 TCTCTACATTTCCCTCGATCTTAGTAA 59.003 37.037 0.00 0.00 0.00 2.24
4582 7043 7.515586 TCTCTACATTTCCCTCGATCTTAGTA 58.484 38.462 0.00 0.00 0.00 1.82
4597 7058 6.626623 GCAGCATCCAAACAATCTCTACATTT 60.627 38.462 0.00 0.00 0.00 2.32
4605 7067 1.822990 CAGGCAGCATCCAAACAATCT 59.177 47.619 0.00 0.00 0.00 2.40
4607 7069 1.636148 ACAGGCAGCATCCAAACAAT 58.364 45.000 0.00 0.00 0.00 2.71
4643 7105 0.901124 GCCAATTTGGTATGCCCACA 59.099 50.000 16.62 0.00 45.19 4.17
4645 7107 1.193323 CAGCCAATTTGGTATGCCCA 58.807 50.000 16.62 0.00 43.27 5.36
4652 7114 3.016736 CGGAATAGTCAGCCAATTTGGT 58.983 45.455 16.62 1.39 40.46 3.67
4663 7125 1.262417 TGGTGTGCTCGGAATAGTCA 58.738 50.000 0.00 0.00 0.00 3.41
4739 7216 9.710900 GAAAATTTGGATAGACACCAATTCTTT 57.289 29.630 0.00 0.00 45.09 2.52
4748 7225 6.268566 GGAGCATGAAAATTTGGATAGACAC 58.731 40.000 0.00 0.00 0.00 3.67
4755 7232 4.019174 GAGAGGGAGCATGAAAATTTGGA 58.981 43.478 0.00 0.00 0.00 3.53
4761 7240 4.371624 TTTCTGAGAGGGAGCATGAAAA 57.628 40.909 0.00 0.00 0.00 2.29
4762 7241 4.371624 TTTTCTGAGAGGGAGCATGAAA 57.628 40.909 0.00 0.00 0.00 2.69
4784 7263 5.652324 TCTCCTCCTACTGGTCTAGTTTTT 58.348 41.667 0.00 0.00 40.89 1.94
4785 7264 5.272405 TCTCCTCCTACTGGTCTAGTTTT 57.728 43.478 0.00 0.00 40.89 2.43
4786 7265 4.949966 TCTCCTCCTACTGGTCTAGTTT 57.050 45.455 0.00 0.00 40.89 2.66
4787 7266 4.862371 CTTCTCCTCCTACTGGTCTAGTT 58.138 47.826 0.00 0.00 40.89 2.24
4788 7267 3.372241 GCTTCTCCTCCTACTGGTCTAGT 60.372 52.174 0.00 0.00 43.56 2.57
4789 7268 3.219281 GCTTCTCCTCCTACTGGTCTAG 58.781 54.545 0.00 0.00 34.23 2.43
4790 7269 2.091775 GGCTTCTCCTCCTACTGGTCTA 60.092 54.545 0.00 0.00 34.23 2.59
4791 7270 1.342574 GGCTTCTCCTCCTACTGGTCT 60.343 57.143 0.00 0.00 34.23 3.85
4792 7271 1.116308 GGCTTCTCCTCCTACTGGTC 58.884 60.000 0.00 0.00 34.23 4.02
4793 7272 0.325765 GGGCTTCTCCTCCTACTGGT 60.326 60.000 0.00 0.00 34.39 4.00
4794 7273 1.051556 GGGGCTTCTCCTCCTACTGG 61.052 65.000 0.00 0.00 34.39 4.00
4795 7274 0.031616 AGGGGCTTCTCCTCCTACTG 60.032 60.000 0.00 0.00 35.19 2.74
4796 7275 2.427016 AGGGGCTTCTCCTCCTACT 58.573 57.895 0.00 0.00 35.19 2.57


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

AutoCloner maintained by Alex Coulton.