Multiple sequence alignment - TraesCS1D01G160100

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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 TraesCS1D01G160100 chr1D 100.000 4135 0 0 1 4135 226466621 226470755 0.000000e+00 7637
1 TraesCS1D01G160100 chr1D 98.731 788 8 2 1 787 452233881 452234667 0.000000e+00 1399
2 TraesCS1D01G160100 chr1D 98.604 788 10 1 1 787 495116659 495115872 0.000000e+00 1393
3 TraesCS1D01G160100 chr1D 82.637 933 107 31 2291 3178 223164120 223165042 0.000000e+00 774
4 TraesCS1D01G160100 chr1D 88.527 584 59 7 2615 3196 226827660 226828237 0.000000e+00 701
5 TraesCS1D01G160100 chr1D 87.914 604 55 12 2598 3196 226945235 226945825 0.000000e+00 695
6 TraesCS1D01G160100 chr1D 86.542 587 53 8 2612 3196 227375832 227376394 1.260000e-174 623
7 TraesCS1D01G160100 chr1D 88.517 418 45 3 2693 3108 227649889 227650305 1.720000e-138 503
8 TraesCS1D01G160100 chr1D 86.395 441 51 3 1795 2234 208415552 208415120 1.350000e-129 473
9 TraesCS1D01G160100 chr1D 81.913 575 60 18 1214 1773 457844741 457845286 2.930000e-121 446
10 TraesCS1D01G160100 chr1D 84.777 381 38 9 1214 1588 457547905 457547539 8.450000e-97 364
11 TraesCS1D01G160100 chr1D 83.333 228 26 7 968 1184 457582554 457582780 2.520000e-47 200
12 TraesCS1D01G160100 chr1A 97.538 2762 50 10 1306 4067 293736332 293739075 0.000000e+00 4708
13 TraesCS1D01G160100 chr1A 82.740 927 105 33 2292 3178 290126249 290127160 0.000000e+00 774
14 TraesCS1D01G160100 chr1A 80.174 575 71 22 1214 1773 550298875 550299421 1.390000e-104 390
15 TraesCS1D01G160100 chr1A 83.770 382 44 10 1214 1588 550137125 550136755 3.060000e-91 346
16 TraesCS1D01G160100 chr1A 96.575 146 5 0 938 1083 293731235 293731380 4.130000e-60 243
17 TraesCS1D01G160100 chr1A 84.052 232 27 6 968 1189 550298310 550298541 9.000000e-52 215
18 TraesCS1D01G160100 chr1A 84.264 197 23 4 968 1156 550137619 550137423 7.060000e-43 185
19 TraesCS1D01G160100 chr1A 94.059 101 5 1 788 888 293731140 293731239 7.160000e-33 152
20 TraesCS1D01G160100 chr1A 100.000 68 0 0 4068 4135 293739182 293739249 4.340000e-25 126
21 TraesCS1D01G160100 chr3A 85.721 2220 194 56 1242 3388 668225506 668227675 0.000000e+00 2230
22 TraesCS1D01G160100 chr3A 89.277 858 68 14 1629 2465 668583678 668584532 0.000000e+00 1053
23 TraesCS1D01G160100 chr3A 82.262 902 96 24 2548 3403 668584571 668585454 0.000000e+00 721
24 TraesCS1D01G160100 chr3A 88.325 394 26 7 1213 1594 668583287 668583672 4.870000e-124 455
25 TraesCS1D01G160100 chr3A 85.676 377 40 7 823 1189 668582605 668582977 6.480000e-103 385
26 TraesCS1D01G160100 chr3B 86.182 1831 159 42 1629 3388 705148535 705150342 0.000000e+00 1893
27 TraesCS1D01G160100 chr3B 87.032 401 28 8 1210 1594 705148137 705148529 8.210000e-117 431
28 TraesCS1D01G160100 chr3B 85.619 299 30 2 904 1189 705147578 705147876 6.720000e-78 302
29 TraesCS1D01G160100 chr3D 85.986 1841 170 43 1629 3403 532870057 532871875 0.000000e+00 1890
30 TraesCS1D01G160100 chr3D 85.604 389 34 8 823 1189 532868961 532869349 5.010000e-104 388
31 TraesCS1D01G160100 chr3D 84.655 391 32 17 1213 1594 532869680 532870051 8.450000e-97 364
32 TraesCS1D01G160100 chr2D 98.859 789 8 1 1 788 346285673 346286461 0.000000e+00 1406
33 TraesCS1D01G160100 chr2D 98.858 788 8 1 1 787 36685729 36686516 0.000000e+00 1404
34 TraesCS1D01G160100 chr7D 98.858 788 7 2 1 787 23679905 23680691 0.000000e+00 1404
35 TraesCS1D01G160100 chr7D 98.858 788 7 2 1 787 264048572 264047786 0.000000e+00 1404
36 TraesCS1D01G160100 chr7D 98.489 794 8 2 1 790 496101089 496100296 0.000000e+00 1397
37 TraesCS1D01G160100 chr7D 98.357 791 12 1 1 790 580057017 580057807 0.000000e+00 1387
38 TraesCS1D01G160100 chr7D 85.116 860 56 30 1451 2294 90409255 90410058 0.000000e+00 813
39 TraesCS1D01G160100 chr7D 83.371 896 93 35 2463 3341 90410250 90411106 0.000000e+00 778
40 TraesCS1D01G160100 chr7D 85.175 371 39 7 823 1184 90408466 90408829 2.350000e-97 366
41 TraesCS1D01G160100 chr5D 98.604 788 9 2 1 787 432795752 432796538 0.000000e+00 1393
42 TraesCS1D01G160100 chr7B 85.954 954 70 24 1451 2391 41285182 41286084 0.000000e+00 961
43 TraesCS1D01G160100 chr7B 81.267 726 84 28 2463 3185 41286233 41286909 1.310000e-149 540
44 TraesCS1D01G160100 chr7B 91.509 106 7 1 1214 1319 41285083 41285186 1.200000e-30 145
45 TraesCS1D01G160100 chr1B 82.988 917 104 31 2291 3166 322475323 322476228 0.000000e+00 782
46 TraesCS1D01G160100 chr1B 86.401 603 51 12 2598 3196 327229793 327230368 7.540000e-177 630
47 TraesCS1D01G160100 chr1B 86.168 441 55 2 1795 2234 327343238 327343673 4.840000e-129 472
48 TraesCS1D01G160100 chr1B 81.282 577 64 28 1215 1773 627923513 627924063 1.060000e-115 427
49 TraesCS1D01G160100 chr1B 88.889 171 17 2 1411 1579 627157344 627157174 4.190000e-50 209
50 TraesCS1D01G160100 chr1B 83.333 162 27 0 964 1125 665246263 665246102 2.570000e-32 150


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 TraesCS1D01G160100 chr1D 226466621 226470755 4134 False 7637.000000 7637 100.000000 1 4135 1 chr1D.!!$F2 4134
1 TraesCS1D01G160100 chr1D 452233881 452234667 786 False 1399.000000 1399 98.731000 1 787 1 chr1D.!!$F7 786
2 TraesCS1D01G160100 chr1D 495115872 495116659 787 True 1393.000000 1393 98.604000 1 787 1 chr1D.!!$R3 786
3 TraesCS1D01G160100 chr1D 223164120 223165042 922 False 774.000000 774 82.637000 2291 3178 1 chr1D.!!$F1 887
4 TraesCS1D01G160100 chr1D 226827660 226828237 577 False 701.000000 701 88.527000 2615 3196 1 chr1D.!!$F3 581
5 TraesCS1D01G160100 chr1D 226945235 226945825 590 False 695.000000 695 87.914000 2598 3196 1 chr1D.!!$F4 598
6 TraesCS1D01G160100 chr1D 227375832 227376394 562 False 623.000000 623 86.542000 2612 3196 1 chr1D.!!$F5 584
7 TraesCS1D01G160100 chr1D 457844741 457845286 545 False 446.000000 446 81.913000 1214 1773 1 chr1D.!!$F9 559
8 TraesCS1D01G160100 chr1A 293736332 293739249 2917 False 2417.000000 4708 98.769000 1306 4135 2 chr1A.!!$F3 2829
9 TraesCS1D01G160100 chr1A 290126249 290127160 911 False 774.000000 774 82.740000 2292 3178 1 chr1A.!!$F1 886
10 TraesCS1D01G160100 chr1A 550298310 550299421 1111 False 302.500000 390 82.113000 968 1773 2 chr1A.!!$F4 805
11 TraesCS1D01G160100 chr1A 550136755 550137619 864 True 265.500000 346 84.017000 968 1588 2 chr1A.!!$R1 620
12 TraesCS1D01G160100 chr3A 668225506 668227675 2169 False 2230.000000 2230 85.721000 1242 3388 1 chr3A.!!$F1 2146
13 TraesCS1D01G160100 chr3A 668582605 668585454 2849 False 653.500000 1053 86.385000 823 3403 4 chr3A.!!$F2 2580
14 TraesCS1D01G160100 chr3B 705147578 705150342 2764 False 875.333333 1893 86.277667 904 3388 3 chr3B.!!$F1 2484
15 TraesCS1D01G160100 chr3D 532868961 532871875 2914 False 880.666667 1890 85.415000 823 3403 3 chr3D.!!$F1 2580
16 TraesCS1D01G160100 chr2D 346285673 346286461 788 False 1406.000000 1406 98.859000 1 788 1 chr2D.!!$F2 787
17 TraesCS1D01G160100 chr2D 36685729 36686516 787 False 1404.000000 1404 98.858000 1 787 1 chr2D.!!$F1 786
18 TraesCS1D01G160100 chr7D 23679905 23680691 786 False 1404.000000 1404 98.858000 1 787 1 chr7D.!!$F1 786
19 TraesCS1D01G160100 chr7D 264047786 264048572 786 True 1404.000000 1404 98.858000 1 787 1 chr7D.!!$R1 786
20 TraesCS1D01G160100 chr7D 496100296 496101089 793 True 1397.000000 1397 98.489000 1 790 1 chr7D.!!$R2 789
21 TraesCS1D01G160100 chr7D 580057017 580057807 790 False 1387.000000 1387 98.357000 1 790 1 chr7D.!!$F2 789
22 TraesCS1D01G160100 chr7D 90408466 90411106 2640 False 652.333333 813 84.554000 823 3341 3 chr7D.!!$F3 2518
23 TraesCS1D01G160100 chr5D 432795752 432796538 786 False 1393.000000 1393 98.604000 1 787 1 chr5D.!!$F1 786
24 TraesCS1D01G160100 chr7B 41285083 41286909 1826 False 548.666667 961 86.243333 1214 3185 3 chr7B.!!$F1 1971
25 TraesCS1D01G160100 chr1B 322475323 322476228 905 False 782.000000 782 82.988000 2291 3166 1 chr1B.!!$F1 875
26 TraesCS1D01G160100 chr1B 327229793 327230368 575 False 630.000000 630 86.401000 2598 3196 1 chr1B.!!$F2 598
27 TraesCS1D01G160100 chr1B 627923513 627924063 550 False 427.000000 427 81.282000 1215 1773 1 chr1B.!!$F4 558

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
817 823 2.352127 GCCCAATTCAACTTCAGACTGC 60.352 50.0 0.0 0.0 0.0 4.40 F
1121 1145 0.859232 GGTACGCATCATAACCGCAG 59.141 55.0 0.0 0.0 0.0 5.18 F
1201 1245 1.171308 CTGCCTGGTTTGTCTGATGG 58.829 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2673 3457 2.638480 TGGGAGGTGACACTTCAAAG 57.362 50.000 18.31 0.0 31.90 2.77 R
2974 3766 1.273606 ACACCAAGAGACCTGTGATCG 59.726 52.381 0.00 0.0 33.08 3.69 R
3371 4207 1.600023 CGTTTAACCTCTTGTGGGCA 58.400 50.000 0.00 0.0 0.00 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
343 345 2.437343 GCCGTTTCTCGCTCGAGTG 61.437 63.158 19.99 19.99 42.49 3.51
790 796 5.777732 TGTAGTTGCCCATTCCTAACAAATT 59.222 36.000 0.00 0.00 0.00 1.82
791 797 5.823861 AGTTGCCCATTCCTAACAAATTT 57.176 34.783 0.00 0.00 0.00 1.82
792 798 5.550290 AGTTGCCCATTCCTAACAAATTTG 58.450 37.500 16.67 16.67 0.00 2.32
793 799 5.071653 AGTTGCCCATTCCTAACAAATTTGT 59.928 36.000 18.13 18.13 44.72 2.83
794 800 5.146010 TGCCCATTCCTAACAAATTTGTC 57.854 39.130 23.47 8.12 41.31 3.18
795 801 4.837860 TGCCCATTCCTAACAAATTTGTCT 59.162 37.500 23.47 15.50 41.31 3.41
796 802 5.170748 GCCCATTCCTAACAAATTTGTCTG 58.829 41.667 23.47 17.61 41.31 3.51
797 803 5.170748 CCCATTCCTAACAAATTTGTCTGC 58.829 41.667 23.47 0.00 41.31 4.26
798 804 5.170748 CCATTCCTAACAAATTTGTCTGCC 58.829 41.667 23.47 0.00 41.31 4.85
799 805 4.864704 TTCCTAACAAATTTGTCTGCCC 57.135 40.909 23.47 0.00 41.31 5.36
800 806 3.838565 TCCTAACAAATTTGTCTGCCCA 58.161 40.909 23.47 4.23 41.31 5.36
801 807 4.219115 TCCTAACAAATTTGTCTGCCCAA 58.781 39.130 23.47 4.30 41.31 4.12
802 808 4.837860 TCCTAACAAATTTGTCTGCCCAAT 59.162 37.500 23.47 8.51 41.31 3.16
803 809 5.306678 TCCTAACAAATTTGTCTGCCCAATT 59.693 36.000 23.47 7.82 41.31 2.32
804 810 5.639082 CCTAACAAATTTGTCTGCCCAATTC 59.361 40.000 23.47 0.00 41.31 2.17
805 811 4.686191 ACAAATTTGTCTGCCCAATTCA 57.314 36.364 18.13 0.00 36.50 2.57
806 812 5.033589 ACAAATTTGTCTGCCCAATTCAA 57.966 34.783 18.13 0.00 36.50 2.69
807 813 4.815846 ACAAATTTGTCTGCCCAATTCAAC 59.184 37.500 18.13 0.00 36.50 3.18
808 814 4.961438 AATTTGTCTGCCCAATTCAACT 57.039 36.364 0.00 0.00 0.00 3.16
809 815 4.961438 ATTTGTCTGCCCAATTCAACTT 57.039 36.364 0.00 0.00 0.00 2.66
810 816 4.320608 TTTGTCTGCCCAATTCAACTTC 57.679 40.909 0.00 0.00 0.00 3.01
811 817 2.942804 TGTCTGCCCAATTCAACTTCA 58.057 42.857 0.00 0.00 0.00 3.02
812 818 2.886523 TGTCTGCCCAATTCAACTTCAG 59.113 45.455 0.00 0.00 0.00 3.02
813 819 3.149196 GTCTGCCCAATTCAACTTCAGA 58.851 45.455 0.00 0.00 0.00 3.27
814 820 3.057946 GTCTGCCCAATTCAACTTCAGAC 60.058 47.826 0.00 0.00 41.07 3.51
815 821 3.152341 CTGCCCAATTCAACTTCAGACT 58.848 45.455 0.00 0.00 0.00 3.24
816 822 2.886523 TGCCCAATTCAACTTCAGACTG 59.113 45.455 0.00 0.00 0.00 3.51
817 823 2.352127 GCCCAATTCAACTTCAGACTGC 60.352 50.000 0.00 0.00 0.00 4.40
818 824 3.152341 CCCAATTCAACTTCAGACTGCT 58.848 45.455 0.00 0.00 0.00 4.24
819 825 4.326826 CCCAATTCAACTTCAGACTGCTA 58.673 43.478 0.00 0.00 0.00 3.49
820 826 4.154918 CCCAATTCAACTTCAGACTGCTAC 59.845 45.833 0.00 0.00 0.00 3.58
821 827 4.999950 CCAATTCAACTTCAGACTGCTACT 59.000 41.667 0.00 0.00 0.00 2.57
826 832 7.520451 TTCAACTTCAGACTGCTACTTACTA 57.480 36.000 0.00 0.00 0.00 1.82
848 854 7.431249 ACTACAATATATTAGTGGTGTCACCG 58.569 38.462 17.27 0.88 42.58 4.94
917 936 4.373156 AGACAACTATTCTGCACCCTTT 57.627 40.909 0.00 0.00 0.00 3.11
918 937 4.729868 AGACAACTATTCTGCACCCTTTT 58.270 39.130 0.00 0.00 0.00 2.27
920 939 5.940470 AGACAACTATTCTGCACCCTTTTAG 59.060 40.000 0.00 0.00 0.00 1.85
939 958 6.588719 TTTAGTTTCCCAAGGATGAACATG 57.411 37.500 0.00 0.00 28.08 3.21
947 966 5.185635 TCCCAAGGATGAACATGATTTTGAC 59.814 40.000 0.00 0.00 0.00 3.18
1013 1032 4.082125 GAGAGACCCATGTTCCACATTTT 58.918 43.478 0.00 0.00 36.53 1.82
1062 1081 3.367087 GCTACTTGAGACGAAAGCTACCA 60.367 47.826 0.00 0.00 0.00 3.25
1121 1145 0.859232 GGTACGCATCATAACCGCAG 59.141 55.000 0.00 0.00 0.00 5.18
1134 1171 5.644206 TCATAACCGCAGTAGCAAATTAACA 59.356 36.000 0.00 0.00 42.27 2.41
1185 1229 6.657836 TTTTCTAGCGGATAAAGTAACTGC 57.342 37.500 0.00 0.00 36.33 4.40
1189 1233 1.940613 GCGGATAAAGTAACTGCCTGG 59.059 52.381 0.00 0.00 0.00 4.45
1191 1235 3.606687 CGGATAAAGTAACTGCCTGGTT 58.393 45.455 0.00 0.00 0.00 3.67
1192 1236 4.007659 CGGATAAAGTAACTGCCTGGTTT 58.992 43.478 0.00 0.00 0.00 3.27
1193 1237 4.142687 CGGATAAAGTAACTGCCTGGTTTG 60.143 45.833 0.00 0.00 0.00 2.93
1195 1239 5.106277 GGATAAAGTAACTGCCTGGTTTGTC 60.106 44.000 0.00 0.00 0.00 3.18
1196 1240 3.577805 AAGTAACTGCCTGGTTTGTCT 57.422 42.857 0.00 0.00 0.00 3.41
1197 1241 2.851195 AGTAACTGCCTGGTTTGTCTG 58.149 47.619 0.00 0.00 0.00 3.51
1200 1244 1.901591 ACTGCCTGGTTTGTCTGATG 58.098 50.000 0.00 0.00 0.00 3.07
1201 1245 1.171308 CTGCCTGGTTTGTCTGATGG 58.829 55.000 0.00 0.00 0.00 3.51
1203 1247 1.271543 TGCCTGGTTTGTCTGATGGAG 60.272 52.381 0.00 0.00 0.00 3.86
1204 1248 1.271597 GCCTGGTTTGTCTGATGGAGT 60.272 52.381 0.00 0.00 0.00 3.85
1206 1250 3.559171 GCCTGGTTTGTCTGATGGAGTAA 60.559 47.826 0.00 0.00 0.00 2.24
1207 1251 4.848357 CCTGGTTTGTCTGATGGAGTAAT 58.152 43.478 0.00 0.00 0.00 1.89
1211 1621 7.066284 CCTGGTTTGTCTGATGGAGTAATTTAG 59.934 40.741 0.00 0.00 0.00 1.85
1216 1626 7.482169 TGTCTGATGGAGTAATTTAGAGTGT 57.518 36.000 0.00 0.00 0.00 3.55
1260 1670 9.087871 TCAATATTCAACCATTCAAAAGGAGAA 57.912 29.630 0.00 0.00 0.00 2.87
1402 1838 7.095439 GCATCACAAGTTTGAGCTATAGATACC 60.095 40.741 3.21 0.00 0.00 2.73
1403 1839 7.418337 TCACAAGTTTGAGCTATAGATACCA 57.582 36.000 3.21 0.00 0.00 3.25
1404 1840 7.847096 TCACAAGTTTGAGCTATAGATACCAA 58.153 34.615 3.21 0.00 0.00 3.67
1405 1841 8.486210 TCACAAGTTTGAGCTATAGATACCAAT 58.514 33.333 3.21 0.00 0.00 3.16
1406 1842 9.764363 CACAAGTTTGAGCTATAGATACCAATA 57.236 33.333 3.21 0.00 0.00 1.90
1494 1940 4.795278 GTCGCTTGATATTTTCTTTGCTGG 59.205 41.667 0.00 0.00 0.00 4.85
1576 2044 3.079960 ACGTTCCAGAGTACATATGCG 57.920 47.619 1.58 0.00 0.00 4.73
1773 2258 7.724305 TCTAACTTTTACCTAAACACAGCTG 57.276 36.000 13.48 13.48 0.00 4.24
1864 2363 6.222038 TCAAGAATACCTACTCGAAGCAAT 57.778 37.500 0.00 0.00 0.00 3.56
1896 2395 3.280295 TCCTCTTCAGGAGCTACTTACG 58.720 50.000 0.00 0.00 44.75 3.18
1928 2427 4.327982 TCCTAGTTGATGATAGCTGTGC 57.672 45.455 0.00 0.00 0.00 4.57
2271 2782 8.470002 GTTCCAACTGGATATTTTAGCTTGATT 58.530 33.333 0.00 0.00 44.98 2.57
2446 2987 9.284968 CATACGTTTAGGAGGAAAAATATCCAT 57.715 33.333 0.00 0.00 42.27 3.41
2524 3259 8.090214 CACACCATCAATTATTTTCTCAGGTTT 58.910 33.333 0.00 0.00 0.00 3.27
2673 3457 5.358725 ACATTTTCCCGTGTACCCAATTATC 59.641 40.000 0.00 0.00 0.00 1.75
2935 3720 2.568956 TGATTCAAGCAGCTAGTGTCCT 59.431 45.455 0.00 0.00 0.00 3.85
2944 3732 3.851098 CAGCTAGTGTCCTTAACCTCAC 58.149 50.000 0.00 0.00 0.00 3.51
3371 4207 1.215117 CCGCGGGCATTCAAACATT 59.785 52.632 20.10 0.00 0.00 2.71
3487 4324 3.391665 CTGCCATCGAGTGACCCCC 62.392 68.421 0.00 0.00 0.00 5.40
3541 4378 3.635331 CTGCATTTCAGGTTGAGTTGTG 58.365 45.455 0.00 0.00 39.15 3.33
3660 4497 6.003950 AGGTTACGGTGACTGTAGTACTTAA 58.996 40.000 0.00 0.00 0.00 1.85
3778 4615 7.756722 ACTTGGATTCGCAATTAGAAATTTCTG 59.243 33.333 27.37 14.42 38.19 3.02
3844 4681 7.546667 GCAACATTGGACATTTAATCTGATTGT 59.453 33.333 13.01 2.84 0.00 2.71
3871 4708 4.935808 CCTATACACCTGCGTTTTCTTCTT 59.064 41.667 0.00 0.00 0.00 2.52
3872 4709 5.063564 CCTATACACCTGCGTTTTCTTCTTC 59.936 44.000 0.00 0.00 0.00 2.87
3873 4710 2.919228 ACACCTGCGTTTTCTTCTTCT 58.081 42.857 0.00 0.00 0.00 2.85
3874 4711 3.279434 ACACCTGCGTTTTCTTCTTCTT 58.721 40.909 0.00 0.00 0.00 2.52
3885 4722 7.634522 CGTTTTCTTCTTCTTGAGAAATCTGT 58.365 34.615 0.00 0.00 43.56 3.41
4030 4867 6.622896 GCAAAGTTCATGCCTAGTTCGTTAAT 60.623 38.462 0.00 0.00 37.85 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
343 345 2.047844 TCGCAACTCAGCCTCTGC 60.048 61.111 0.00 0.00 37.95 4.26
790 796 3.295093 TGAAGTTGAATTGGGCAGACAA 58.705 40.909 0.00 0.00 34.41 3.18
791 797 2.886523 CTGAAGTTGAATTGGGCAGACA 59.113 45.455 0.00 0.00 0.00 3.41
792 798 3.057946 GTCTGAAGTTGAATTGGGCAGAC 60.058 47.826 0.00 0.00 42.38 3.51
793 799 3.149196 GTCTGAAGTTGAATTGGGCAGA 58.851 45.455 0.00 0.00 0.00 4.26
794 800 3.057736 CAGTCTGAAGTTGAATTGGGCAG 60.058 47.826 0.00 0.00 0.00 4.85
795 801 2.886523 CAGTCTGAAGTTGAATTGGGCA 59.113 45.455 0.00 0.00 0.00 5.36
796 802 2.352127 GCAGTCTGAAGTTGAATTGGGC 60.352 50.000 3.32 0.00 0.00 5.36
797 803 3.152341 AGCAGTCTGAAGTTGAATTGGG 58.848 45.455 3.32 0.00 0.00 4.12
798 804 4.999950 AGTAGCAGTCTGAAGTTGAATTGG 59.000 41.667 3.32 0.00 0.00 3.16
799 805 6.551385 AAGTAGCAGTCTGAAGTTGAATTG 57.449 37.500 3.32 0.00 0.00 2.32
800 806 7.445945 AGTAAGTAGCAGTCTGAAGTTGAATT 58.554 34.615 3.32 0.00 0.00 2.17
801 807 6.998802 AGTAAGTAGCAGTCTGAAGTTGAAT 58.001 36.000 3.32 0.00 0.00 2.57
802 808 6.406692 AGTAAGTAGCAGTCTGAAGTTGAA 57.593 37.500 3.32 0.00 0.00 2.69
803 809 6.489022 TGTAGTAAGTAGCAGTCTGAAGTTGA 59.511 38.462 3.32 0.00 0.00 3.18
804 810 6.678878 TGTAGTAAGTAGCAGTCTGAAGTTG 58.321 40.000 3.32 0.00 0.00 3.16
805 811 6.896021 TGTAGTAAGTAGCAGTCTGAAGTT 57.104 37.500 3.32 2.75 0.00 2.66
806 812 6.896021 TTGTAGTAAGTAGCAGTCTGAAGT 57.104 37.500 3.32 0.00 0.00 3.01
826 832 5.054477 GCGGTGACACCACTAATATATTGT 58.946 41.667 24.18 2.01 42.77 2.71
842 848 2.806244 ACAGTGATTTGTAAGCGGTGAC 59.194 45.455 0.00 0.00 0.00 3.67
843 849 3.120321 ACAGTGATTTGTAAGCGGTGA 57.880 42.857 0.00 0.00 0.00 4.02
844 850 4.727734 GCATACAGTGATTTGTAAGCGGTG 60.728 45.833 0.00 0.00 38.14 4.94
845 851 3.374058 GCATACAGTGATTTGTAAGCGGT 59.626 43.478 0.00 0.00 38.14 5.68
846 852 3.373748 TGCATACAGTGATTTGTAAGCGG 59.626 43.478 0.00 0.00 45.99 5.52
847 853 4.598406 TGCATACAGTGATTTGTAAGCG 57.402 40.909 0.00 0.00 45.99 4.68
848 854 6.182039 TCTTGCATACAGTGATTTGTAAGC 57.818 37.500 0.00 6.47 44.32 3.09
850 856 9.624697 GAAAATCTTGCATACAGTGATTTGTAA 57.375 29.630 0.00 0.00 39.03 2.41
851 857 8.791675 TGAAAATCTTGCATACAGTGATTTGTA 58.208 29.630 0.00 0.00 39.03 2.41
917 936 5.886609 TCATGTTCATCCTTGGGAAACTAA 58.113 37.500 0.00 0.00 34.34 2.24
918 937 5.512942 TCATGTTCATCCTTGGGAAACTA 57.487 39.130 0.00 0.00 34.34 2.24
920 939 5.665916 AATCATGTTCATCCTTGGGAAAC 57.334 39.130 0.00 0.00 34.34 2.78
939 958 4.550422 GAAGGAGGCAACAAGTCAAAATC 58.450 43.478 0.00 0.00 41.41 2.17
1013 1032 6.778821 TGAGAAGTCATGAACCTTCCATTTA 58.221 36.000 17.90 0.46 0.00 1.40
1062 1081 0.179045 AAAGCAGCAGAGAACACCGT 60.179 50.000 0.00 0.00 0.00 4.83
1170 1214 3.261981 ACCAGGCAGTTACTTTATCCG 57.738 47.619 0.00 0.00 0.00 4.18
1185 1229 2.867109 ACTCCATCAGACAAACCAGG 57.133 50.000 0.00 0.00 0.00 4.45
1189 1233 8.660373 CACTCTAAATTACTCCATCAGACAAAC 58.340 37.037 0.00 0.00 0.00 2.93
1191 1235 7.907389 ACACTCTAAATTACTCCATCAGACAA 58.093 34.615 0.00 0.00 0.00 3.18
1192 1236 7.482169 ACACTCTAAATTACTCCATCAGACA 57.518 36.000 0.00 0.00 0.00 3.41
1193 1237 9.469807 CATACACTCTAAATTACTCCATCAGAC 57.530 37.037 0.00 0.00 0.00 3.51
1195 1239 7.928167 TGCATACACTCTAAATTACTCCATCAG 59.072 37.037 0.00 0.00 0.00 2.90
1196 1240 7.791029 TGCATACACTCTAAATTACTCCATCA 58.209 34.615 0.00 0.00 0.00 3.07
1197 1241 7.928706 ACTGCATACACTCTAAATTACTCCATC 59.071 37.037 0.00 0.00 0.00 3.51
1200 1244 7.042335 ACACTGCATACACTCTAAATTACTCC 58.958 38.462 0.00 0.00 0.00 3.85
1201 1245 8.480643 AACACTGCATACACTCTAAATTACTC 57.519 34.615 0.00 0.00 0.00 2.59
1203 1247 8.717821 TCAAACACTGCATACACTCTAAATTAC 58.282 33.333 0.00 0.00 0.00 1.89
1204 1248 8.840833 TCAAACACTGCATACACTCTAAATTA 57.159 30.769 0.00 0.00 0.00 1.40
1206 1250 6.936900 ACTCAAACACTGCATACACTCTAAAT 59.063 34.615 0.00 0.00 0.00 1.40
1207 1251 6.288294 ACTCAAACACTGCATACACTCTAAA 58.712 36.000 0.00 0.00 0.00 1.85
1211 1621 4.273480 ACAACTCAAACACTGCATACACTC 59.727 41.667 0.00 0.00 0.00 3.51
1216 1626 7.686438 ATATTGACAACTCAAACACTGCATA 57.314 32.000 0.00 0.00 39.90 3.14
1260 1670 4.471386 AGTCTACCTTTGCATCCACAGTAT 59.529 41.667 0.00 0.00 0.00 2.12
1263 1673 3.265791 GAGTCTACCTTTGCATCCACAG 58.734 50.000 0.00 0.00 0.00 3.66
1470 1915 4.795278 CAGCAAAGAAAATATCAAGCGACC 59.205 41.667 0.00 0.00 0.00 4.79
1494 1940 2.428888 AGGTCGACGGACAAACTTAC 57.571 50.000 9.92 0.00 45.28 2.34
1773 2258 8.983307 TTAGAAGATTAGAGAACGAAGAAACC 57.017 34.615 0.00 0.00 0.00 3.27
1864 2363 5.698741 TCCTGAAGAGGAATCAAGCAATA 57.301 39.130 0.00 0.00 46.19 1.90
1895 2394 3.849911 TCAACTAGGAAAGCAGATGACG 58.150 45.455 0.00 0.00 0.00 4.35
1896 2395 5.423015 TCATCAACTAGGAAAGCAGATGAC 58.577 41.667 0.00 0.00 40.80 3.06
1928 2427 9.410556 CAATTTTTAGTATCTCCACACCAAAAG 57.589 33.333 0.00 0.00 0.00 2.27
2271 2782 7.408756 AAATATCTTGGTTGCATGCTTAGAA 57.591 32.000 20.33 1.02 0.00 2.10
2379 2904 5.228635 CGCCAACATACAGTTTAGTACTACG 59.771 44.000 0.91 0.00 38.74 3.51
2393 2922 6.034470 CCATGAAATTTTACACGCCAACATAC 59.966 38.462 0.00 0.00 0.00 2.39
2673 3457 2.638480 TGGGAGGTGACACTTCAAAG 57.362 50.000 18.31 0.00 31.90 2.77
2913 3698 3.199508 AGGACACTAGCTGCTTGAATCAT 59.800 43.478 17.66 8.93 0.00 2.45
2935 3720 6.693466 TCAACTGTAATCATCGTGAGGTTAA 58.307 36.000 0.00 0.00 0.00 2.01
2944 3732 9.694520 CAAAAGTAAGATCAACTGTAATCATCG 57.305 33.333 0.00 0.00 0.00 3.84
2974 3766 1.273606 ACACCAAGAGACCTGTGATCG 59.726 52.381 0.00 0.00 33.08 3.69
3371 4207 1.600023 CGTTTAACCTCTTGTGGGCA 58.400 50.000 0.00 0.00 0.00 5.36
3419 4256 9.990360 TCAGTTGATGAGTAGTAATGTAACAAA 57.010 29.630 0.00 0.00 32.77 2.83
3487 4324 2.101249 ACACCTGTGCAAAAGAACCATG 59.899 45.455 0.00 0.00 0.00 3.66
3541 4378 6.372659 TCATGCAAAACTCAGATTAGAAGTCC 59.627 38.462 0.00 0.00 0.00 3.85
3632 4469 0.893447 ACAGTCACCGTAACCTAGCC 59.107 55.000 0.00 0.00 0.00 3.93
3660 4497 4.981806 AAGTTGCACGTATATTGGCAAT 57.018 36.364 18.01 18.01 46.52 3.56
3737 4574 6.590234 AATCCAAGTTTCGGAAATTAGCTT 57.410 33.333 6.43 2.65 35.77 3.74
3844 4681 0.611200 AACGCAGGTGTATAGGCACA 59.389 50.000 0.00 0.00 40.89 4.57
3871 4708 5.488919 ACTGGGGATAACAGATTTCTCAAGA 59.511 40.000 0.00 0.00 39.24 3.02
3872 4709 5.749462 ACTGGGGATAACAGATTTCTCAAG 58.251 41.667 0.00 0.00 39.24 3.02
3873 4710 5.779241 ACTGGGGATAACAGATTTCTCAA 57.221 39.130 0.00 0.00 39.24 3.02
3874 4711 5.250543 TGAACTGGGGATAACAGATTTCTCA 59.749 40.000 0.00 0.00 39.24 3.27
3998 4835 7.232118 ACTAGGCATGAACTTTGCTAATTTT 57.768 32.000 0.00 0.00 40.03 1.82


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

AutoCloner maintained by Alex Coulton.