Multiple sequence alignment - TraesCS4D01G072200

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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 TraesCS4D01G072200 chr4D 100.000 4399 0 0 1 4399 47337763 47333365 0.000000e+00 8124
1 TraesCS4D01G072200 chr4D 85.049 2040 219 47 963 2929 54446539 54448565 0.000000e+00 1999
2 TraesCS4D01G072200 chr4D 83.294 1287 134 43 3086 4351 54476014 54477240 0.000000e+00 1110
3 TraesCS4D01G072200 chr4D 85.510 980 99 13 815 1776 54474744 54475698 0.000000e+00 983
4 TraesCS4D01G072200 chr4D 86.218 907 87 18 883 1776 54604229 54605110 0.000000e+00 948
5 TraesCS4D01G072200 chr4D 82.908 1018 108 31 3076 4071 54605465 54606438 0.000000e+00 856
6 TraesCS4D01G072200 chr4D 85.782 422 45 8 289 703 54603734 54604147 2.430000e-117 433
7 TraesCS4D01G072200 chr4D 82.194 556 44 21 164 697 54474190 54474712 1.130000e-115 427
8 TraesCS4D01G072200 chr4D 84.982 273 21 9 4061 4330 54608381 54608636 4.360000e-65 259
9 TraesCS4D01G072200 chr4B 85.439 2026 218 42 955 2935 80556952 80558945 0.000000e+00 2036
10 TraesCS4D01G072200 chr4B 85.439 2026 218 42 955 2935 80585622 80587615 0.000000e+00 2036
11 TraesCS4D01G072200 chr4B 92.946 1290 50 7 2056 3340 68960801 68959548 0.000000e+00 1840
12 TraesCS4D01G072200 chr4B 89.510 1306 98 20 3064 4351 68730194 68728910 0.000000e+00 1616
13 TraesCS4D01G072200 chr4B 90.525 971 63 13 3436 4399 68959248 68958300 0.000000e+00 1256
14 TraesCS4D01G072200 chr4B 83.948 1302 135 46 3075 4351 80594768 80596020 0.000000e+00 1179
15 TraesCS4D01G072200 chr4B 92.470 757 48 5 809 1562 68961919 68961169 0.000000e+00 1074
16 TraesCS4D01G072200 chr4B 95.041 363 18 0 1590 1952 68961170 68960808 4.940000e-159 571
17 TraesCS4D01G072200 chr4B 89.783 460 18 2 289 745 68962355 68961922 2.970000e-156 562
18 TraesCS4D01G072200 chr4B 85.632 348 37 8 812 1146 80593372 80593719 1.950000e-93 353
19 TraesCS4D01G072200 chr4B 91.810 232 13 5 1 232 68730858 68730633 7.100000e-83 318
20 TraesCS4D01G072200 chr4B 79.474 380 62 12 3138 3514 80559198 80559564 5.650000e-64 255
21 TraesCS4D01G072200 chr4B 79.474 380 62 12 3138 3514 80587868 80588234 5.650000e-64 255
22 TraesCS4D01G072200 chr4B 86.607 224 11 5 217 421 68730601 68730378 3.420000e-56 230
23 TraesCS4D01G072200 chr4B 82.836 268 22 8 211 457 80592739 80593003 7.410000e-53 219
24 TraesCS4D01G072200 chr4B 88.701 177 14 5 1 176 68980723 68980552 1.240000e-50 211
25 TraesCS4D01G072200 chr4B 91.729 133 11 0 1629 1761 68730350 68730218 7.510000e-43 185
26 TraesCS4D01G072200 chr4B 95.455 66 2 1 167 232 68962538 68962474 2.160000e-18 104
27 TraesCS4D01G072200 chr4A 90.819 1307 90 18 3061 4351 551133528 551134820 0.000000e+00 1722
28 TraesCS4D01G072200 chr4A 91.988 986 53 14 809 1784 551132225 551133194 0.000000e+00 1360
29 TraesCS4D01G072200 chr4A 87.822 1166 122 13 960 2112 542555949 542554791 0.000000e+00 1349
30 TraesCS4D01G072200 chr4A 84.725 982 106 22 815 1776 542533688 542532731 0.000000e+00 942
31 TraesCS4D01G072200 chr4A 81.566 1188 121 45 3075 4237 542532428 542531314 0.000000e+00 891
32 TraesCS4D01G072200 chr4A 82.143 840 90 26 2142 2935 542554798 542553973 0.000000e+00 665
33 TraesCS4D01G072200 chr4A 86.301 584 27 18 1 537 551131450 551132027 1.760000e-163 586
34 TraesCS4D01G072200 chr4A 80.357 672 85 25 63 703 542534363 542533708 2.400000e-127 466
35 TraesCS4D01G072200 chr4A 94.222 225 13 0 569 793 551132027 551132251 1.170000e-90 344
36 TraesCS4D01G072200 chr4A 89.691 194 15 5 4208 4399 551134859 551135049 4.400000e-60 243


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 TraesCS4D01G072200 chr4D 47333365 47337763 4398 True 8124.000000 8124 100.000000 1 4399 1 chr4D.!!$R1 4398
1 TraesCS4D01G072200 chr4D 54446539 54448565 2026 False 1999.000000 1999 85.049000 963 2929 1 chr4D.!!$F1 1966
2 TraesCS4D01G072200 chr4D 54474190 54477240 3050 False 840.000000 1110 83.666000 164 4351 3 chr4D.!!$F2 4187
3 TraesCS4D01G072200 chr4D 54603734 54608636 4902 False 624.000000 948 84.972500 289 4330 4 chr4D.!!$F3 4041
4 TraesCS4D01G072200 chr4B 80556952 80559564 2612 False 1145.500000 2036 82.456500 955 3514 2 chr4B.!!$F1 2559
5 TraesCS4D01G072200 chr4B 80585622 80588234 2612 False 1145.500000 2036 82.456500 955 3514 2 chr4B.!!$F2 2559
6 TraesCS4D01G072200 chr4B 68958300 68962538 4238 True 901.166667 1840 92.703333 167 4399 6 chr4B.!!$R3 4232
7 TraesCS4D01G072200 chr4B 68728910 68730858 1948 True 587.250000 1616 89.914000 1 4351 4 chr4B.!!$R2 4350
8 TraesCS4D01G072200 chr4B 80592739 80596020 3281 False 583.666667 1179 84.138667 211 4351 3 chr4B.!!$F3 4140
9 TraesCS4D01G072200 chr4A 542553973 542555949 1976 True 1007.000000 1349 84.982500 960 2935 2 chr4A.!!$R2 1975
10 TraesCS4D01G072200 chr4A 551131450 551135049 3599 False 851.000000 1722 90.604200 1 4399 5 chr4A.!!$F1 4398
11 TraesCS4D01G072200 chr4A 542531314 542534363 3049 True 766.333333 942 82.216000 63 4237 3 chr4A.!!$R1 4174

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
419 532 0.882042 CAGCGTTGTGAGCCTTGAGT 60.882 55.0 0.0 0.0 34.64 3.41 F
1137 1451 0.101219 GCCTTGGTCATTGAATCGGC 59.899 55.0 0.0 0.0 0.00 5.54 F
2292 2785 0.583438 CTCGCACACTTTCCACACAG 59.417 55.0 0.0 0.0 0.00 3.66 F
2440 2937 0.820871 AGGGAGATCTGTGCGTCTTC 59.179 55.0 0.0 0.0 0.00 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1566 1940 0.250467 TGAGCTTCCACTCTGGCAAC 60.250 55.000 0.00 0.0 37.47 4.17 R
2743 3284 2.135139 CTTCTGCAGTTGCGTTAGACA 58.865 47.619 14.67 0.0 45.83 3.41 R
3382 4002 1.464997 GAAACTAGCAAAGCTCACGGG 59.535 52.381 0.00 0.0 40.44 5.28 R
3642 4497 4.072131 GTGGCTTCCTCATACAAACTTCA 58.928 43.478 0.00 0.0 0.00 3.02 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
38 39 3.810310 TTGTCCGTTCAAATTTGGCTT 57.190 38.095 17.90 0.00 0.00 4.35
55 56 9.955208 AATTTGGCTTCAAAATTGATTCTTTTC 57.045 25.926 0.00 0.00 42.77 2.29
198 200 2.743636 TTTGCCAACGTTTTGACCAA 57.256 40.000 0.00 0.00 34.24 3.67
217 223 1.208165 AAACCTCCCCGCTTCTCCAT 61.208 55.000 0.00 0.00 0.00 3.41
265 344 1.348064 CCATCATCCTAGGGCCGTAA 58.652 55.000 9.46 0.00 0.00 3.18
267 346 2.105821 CCATCATCCTAGGGCCGTAAAA 59.894 50.000 9.46 0.00 0.00 1.52
278 357 2.222027 GGCCGTAAAATCCCATCAGAG 58.778 52.381 0.00 0.00 0.00 3.35
399 512 2.682856 TCTTCAAGTTCCAGCAACACAC 59.317 45.455 0.00 0.00 37.48 3.82
413 526 2.591715 ACACCAGCGTTGTGAGCC 60.592 61.111 9.75 0.00 37.18 4.70
414 527 2.281070 CACCAGCGTTGTGAGCCT 60.281 61.111 0.00 0.00 35.74 4.58
415 528 1.893808 CACCAGCGTTGTGAGCCTT 60.894 57.895 0.00 0.00 35.74 4.35
416 529 1.893808 ACCAGCGTTGTGAGCCTTG 60.894 57.895 0.00 0.00 34.64 3.61
417 530 1.597854 CCAGCGTTGTGAGCCTTGA 60.598 57.895 0.00 0.00 34.64 3.02
418 531 1.572085 CCAGCGTTGTGAGCCTTGAG 61.572 60.000 0.00 0.00 34.64 3.02
419 532 0.882042 CAGCGTTGTGAGCCTTGAGT 60.882 55.000 0.00 0.00 34.64 3.41
420 533 0.882042 AGCGTTGTGAGCCTTGAGTG 60.882 55.000 0.00 0.00 34.64 3.51
421 534 1.571460 CGTTGTGAGCCTTGAGTGC 59.429 57.895 0.00 0.00 0.00 4.40
422 535 0.882042 CGTTGTGAGCCTTGAGTGCT 60.882 55.000 0.00 0.00 43.03 4.40
427 540 3.913107 AGCCTTGAGTGCTCCCTT 58.087 55.556 0.00 0.00 32.41 3.95
428 541 1.682257 AGCCTTGAGTGCTCCCTTC 59.318 57.895 0.00 0.00 32.41 3.46
429 542 1.377856 GCCTTGAGTGCTCCCTTCC 60.378 63.158 0.00 0.00 0.00 3.46
430 543 1.078848 CCTTGAGTGCTCCCTTCCG 60.079 63.158 0.00 0.00 0.00 4.30
431 544 1.078848 CTTGAGTGCTCCCTTCCGG 60.079 63.158 0.00 0.00 0.00 5.14
432 545 3.254024 TTGAGTGCTCCCTTCCGGC 62.254 63.158 0.00 0.00 0.00 6.13
433 546 4.475135 GAGTGCTCCCTTCCGGCC 62.475 72.222 0.00 0.00 0.00 6.13
435 548 4.785453 GTGCTCCCTTCCGGCCTG 62.785 72.222 0.00 0.00 0.00 4.85
439 552 3.764160 CTCCCTTCCGGCCTGCATC 62.764 68.421 0.00 0.00 0.00 3.91
484 630 1.472878 GCTGCCTAGCCTTTGGTTTAC 59.527 52.381 0.00 0.00 44.33 2.01
494 640 3.162666 CCTTTGGTTTACCTCTTTCCCC 58.837 50.000 0.00 0.00 36.82 4.81
541 752 2.031120 CAGTCCTTTTGTTGGGCTCAA 58.969 47.619 0.00 0.00 37.44 3.02
556 767 1.065564 GCTCAACAAGATCTGCTCCCT 60.066 52.381 0.00 0.00 0.00 4.20
697 967 1.171308 TTTGCTTGATCTCTGGCTGC 58.829 50.000 0.00 0.00 0.00 5.25
737 1007 5.634859 CCCTGTAATTTTGCTTGATGTTGAC 59.365 40.000 0.00 0.00 0.00 3.18
751 1021 1.764134 TGTTGACGGTACAAACTCCCT 59.236 47.619 0.00 0.00 0.00 4.20
752 1022 2.171027 TGTTGACGGTACAAACTCCCTT 59.829 45.455 0.00 0.00 0.00 3.95
766 1036 3.671716 ACTCCCTTTACTTAGGCGTTTG 58.328 45.455 0.00 0.00 33.73 2.93
767 1037 3.072038 ACTCCCTTTACTTAGGCGTTTGT 59.928 43.478 0.00 0.00 33.73 2.83
768 1038 4.284234 ACTCCCTTTACTTAGGCGTTTGTA 59.716 41.667 0.00 0.00 33.73 2.41
769 1039 4.568956 TCCCTTTACTTAGGCGTTTGTAC 58.431 43.478 0.00 0.00 33.73 2.90
770 1040 4.040217 TCCCTTTACTTAGGCGTTTGTACA 59.960 41.667 0.00 0.00 33.73 2.90
771 1041 4.756135 CCCTTTACTTAGGCGTTTGTACAA 59.244 41.667 3.59 3.59 33.73 2.41
772 1042 5.239087 CCCTTTACTTAGGCGTTTGTACAAA 59.761 40.000 17.01 17.01 33.73 2.83
773 1043 6.138088 CCTTTACTTAGGCGTTTGTACAAAC 58.862 40.000 32.43 32.43 45.25 2.93
774 1044 6.017687 CCTTTACTTAGGCGTTTGTACAAACT 60.018 38.462 35.97 25.34 46.21 2.66
775 1045 6.529463 TTACTTAGGCGTTTGTACAAACTC 57.471 37.500 35.97 31.24 46.21 3.01
778 1048 1.601166 GGCGTTTGTACAAACTCCCT 58.399 50.000 35.11 0.00 45.55 4.20
779 1049 1.265905 GGCGTTTGTACAAACTCCCTG 59.734 52.381 35.11 25.20 45.55 4.45
780 1050 1.944709 GCGTTTGTACAAACTCCCTGT 59.055 47.619 35.97 0.00 46.21 4.00
781 1051 3.132925 GCGTTTGTACAAACTCCCTGTA 58.867 45.455 35.97 8.12 46.21 2.74
782 1052 3.059393 GCGTTTGTACAAACTCCCTGTAC 60.059 47.826 35.97 17.22 46.21 2.90
783 1053 4.374399 CGTTTGTACAAACTCCCTGTACT 58.626 43.478 35.97 0.00 46.14 2.73
784 1054 4.446719 CGTTTGTACAAACTCCCTGTACTC 59.553 45.833 35.97 15.43 46.14 2.59
785 1055 5.608449 GTTTGTACAAACTCCCTGTACTCT 58.392 41.667 33.99 0.00 46.14 3.24
786 1056 4.866508 TGTACAAACTCCCTGTACTCTG 57.133 45.455 12.78 0.00 46.14 3.35
787 1057 4.220724 TGTACAAACTCCCTGTACTCTGT 58.779 43.478 12.78 0.00 46.14 3.41
788 1058 4.652421 TGTACAAACTCCCTGTACTCTGTT 59.348 41.667 12.78 0.00 46.14 3.16
789 1059 4.772886 ACAAACTCCCTGTACTCTGTTT 57.227 40.909 0.00 0.00 0.00 2.83
790 1060 4.704965 ACAAACTCCCTGTACTCTGTTTC 58.295 43.478 0.00 0.00 0.00 2.78
791 1061 4.409247 ACAAACTCCCTGTACTCTGTTTCT 59.591 41.667 0.00 0.00 0.00 2.52
792 1062 5.104485 ACAAACTCCCTGTACTCTGTTTCTT 60.104 40.000 0.00 0.00 0.00 2.52
793 1063 5.632034 AACTCCCTGTACTCTGTTTCTTT 57.368 39.130 0.00 0.00 0.00 2.52
794 1064 5.632034 ACTCCCTGTACTCTGTTTCTTTT 57.368 39.130 0.00 0.00 0.00 2.27
795 1065 6.002653 ACTCCCTGTACTCTGTTTCTTTTT 57.997 37.500 0.00 0.00 0.00 1.94
796 1066 6.056236 ACTCCCTGTACTCTGTTTCTTTTTC 58.944 40.000 0.00 0.00 0.00 2.29
797 1067 6.126739 ACTCCCTGTACTCTGTTTCTTTTTCT 60.127 38.462 0.00 0.00 0.00 2.52
798 1068 6.659824 TCCCTGTACTCTGTTTCTTTTTCTT 58.340 36.000 0.00 0.00 0.00 2.52
799 1069 7.116736 TCCCTGTACTCTGTTTCTTTTTCTTT 58.883 34.615 0.00 0.00 0.00 2.52
800 1070 7.614192 TCCCTGTACTCTGTTTCTTTTTCTTTT 59.386 33.333 0.00 0.00 0.00 2.27
801 1071 8.251026 CCCTGTACTCTGTTTCTTTTTCTTTTT 58.749 33.333 0.00 0.00 0.00 1.94
841 1116 5.641209 CCCTGTACTCTGTTTCTTGATTCTG 59.359 44.000 0.00 0.00 0.00 3.02
906 1196 5.597813 AAGAAACTTGATGAGTAGTTGCG 57.402 39.130 0.00 0.00 37.72 4.85
1026 1332 1.580845 ATTCCTGCGAGTGCTGCAAC 61.581 55.000 2.77 0.53 42.70 4.17
1107 1413 4.039730 CACTCTAGGCATAGCATGGTAAGT 59.960 45.833 8.98 3.15 0.00 2.24
1115 1424 4.769688 CATAGCATGGTAAGTTCAGTGGA 58.230 43.478 8.98 0.00 0.00 4.02
1124 1433 1.915141 AGTTCAGTGGATTGCCTTGG 58.085 50.000 0.00 0.00 34.31 3.61
1137 1451 0.101219 GCCTTGGTCATTGAATCGGC 59.899 55.000 0.00 0.00 0.00 5.54
1146 1460 4.439974 GGTCATTGAATCGGCAGCAATAAA 60.440 41.667 0.00 0.00 31.54 1.40
1161 1509 6.789877 GCAGCAATAAAACATGTTTTAAACCG 59.210 34.615 35.21 25.91 44.92 4.44
1272 1626 2.127708 ACTAGAAGCCCCCAATGGTAG 58.872 52.381 0.00 0.00 0.00 3.18
1287 1641 5.410132 CCAATGGTAGTGTTTACGATGTTGA 59.590 40.000 0.00 0.00 0.00 3.18
1292 1646 7.356540 TGGTAGTGTTTACGATGTTGAAATTG 58.643 34.615 0.00 0.00 0.00 2.32
1566 1940 1.485838 GCACGAGCACGATCAGATGG 61.486 60.000 11.40 0.00 42.66 3.51
1593 1967 2.530151 TGGAAGCTCAGGCCACCT 60.530 61.111 5.01 0.00 39.73 4.00
1680 2055 7.582435 ACAACTGACTTGTAACTATTGATCG 57.418 36.000 0.00 0.00 41.63 3.69
1690 2134 6.674066 TGTAACTATTGATCGCATCATACGA 58.326 36.000 0.00 0.00 44.75 3.43
1776 2230 6.711194 CCTTATGAGCATGAGTCATCTGAATT 59.289 38.462 12.82 0.00 0.00 2.17
1996 2451 8.081633 CCATGAAAAAGAAGTTAACTGTATGCA 58.918 33.333 9.34 2.94 0.00 3.96
1997 2452 9.462174 CATGAAAAAGAAGTTAACTGTATGCAA 57.538 29.630 9.34 0.00 0.00 4.08
1998 2453 9.683069 ATGAAAAAGAAGTTAACTGTATGCAAG 57.317 29.630 9.34 0.00 0.00 4.01
2085 2540 3.750130 ACAGTGAAAGATGCACACTCATC 59.250 43.478 4.06 3.60 41.93 2.92
2086 2541 3.749609 CAGTGAAAGATGCACACTCATCA 59.250 43.478 4.06 5.77 43.94 3.07
2164 2656 4.081406 TGCTTTACAGTGGAAATCATGCT 58.919 39.130 0.00 0.00 0.00 3.79
2242 2735 2.227388 AGTTTCAGATTCTGCGCCTTTG 59.773 45.455 4.18 0.00 0.00 2.77
2292 2785 0.583438 CTCGCACACTTTCCACACAG 59.417 55.000 0.00 0.00 0.00 3.66
2440 2937 0.820871 AGGGAGATCTGTGCGTCTTC 59.179 55.000 0.00 0.00 0.00 2.87
2520 3017 3.028094 AGCAAGCATTGATCATCCCTT 57.972 42.857 0.00 0.00 44.15 3.95
2894 3440 6.624352 TTCTTCTGATTTTGAGTTGACAGG 57.376 37.500 0.00 0.00 0.00 4.00
3014 3603 3.648545 CTCCAACTTAGATTAGGGGGAGG 59.351 52.174 0.00 0.00 36.62 4.30
3027 3616 1.680860 GGGGGAGGTATGTTTCAACCG 60.681 57.143 0.00 0.00 40.88 4.44
3051 3640 6.173339 GGTCATCCACTGTATCAAGAGAAAA 58.827 40.000 0.00 0.00 0.00 2.29
3082 3693 4.651503 CCTACCACTCCTCTACATGATTGT 59.348 45.833 0.00 0.00 39.98 2.71
3175 3792 1.542915 GTACTCTGCCACGTACCTTCA 59.457 52.381 0.00 0.00 31.98 3.02
3212 3829 2.529744 GGTGCTTCAGGTGGAGGGT 61.530 63.158 0.00 0.00 0.00 4.34
3382 4002 7.251321 AGAAGATGGTGGTCTATATCATTCC 57.749 40.000 0.00 0.00 0.00 3.01
3467 4291 4.021280 TGGCATTTTGTATGTTGCTGATGT 60.021 37.500 0.00 0.00 35.46 3.06
3539 4374 6.712547 CCACTTTCTGGAATGAGTAAGAAACT 59.287 38.462 0.00 0.00 43.95 2.66
3540 4375 7.308229 CCACTTTCTGGAATGAGTAAGAAACTG 60.308 40.741 0.00 0.00 43.95 3.16
3549 4386 9.994432 GGAATGAGTAAGAAACTGATATTTGTG 57.006 33.333 0.00 0.00 39.07 3.33
3615 4465 1.545582 TCAGTGGCAGCCTTATTTTGC 59.454 47.619 14.15 0.00 37.11 3.68
3642 4497 7.308435 GCATGAAGTTTAAACTAGTTGCTGAT 58.692 34.615 26.21 10.87 38.57 2.90
3896 4753 4.578105 GGATGGATGGATCTTGTCTTCAAC 59.422 45.833 0.00 0.00 0.00 3.18
3911 4768 5.049680 TGTCTTCAACGTGGCTTCTATTTTC 60.050 40.000 0.00 0.00 0.00 2.29
3961 4823 4.219070 CACCATTGAAATTGGCTCTGAGAA 59.781 41.667 9.28 0.00 0.00 2.87
4132 6951 8.518430 AAAACAATTAGGCTGTTTGGATTTTT 57.482 26.923 13.57 9.29 44.25 1.94
4145 6964 7.484975 TGTTTGGATTTTTGTCACGTAGAAAT 58.515 30.769 0.00 0.00 0.00 2.17
4154 6973 9.796120 TTTTTGTCACGTAGAAATCTTTCAAAT 57.204 25.926 5.53 0.00 39.61 2.32
4230 7053 6.923928 CCATTGAGTGGTTTGAACATTTTT 57.076 33.333 0.00 0.00 43.44 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 5.671742 ATTTTGAAGCCAAATTTGAACGG 57.328 34.783 19.86 3.80 41.43 4.44
198 200 1.208165 ATGGAGAAGCGGGGAGGTTT 61.208 55.000 0.00 0.00 41.18 3.27
217 223 1.754803 CATAGACTTGTAGGCCCGTCA 59.245 52.381 0.00 0.00 0.00 4.35
265 344 1.562942 TCTGCTGCTCTGATGGGATTT 59.437 47.619 0.00 0.00 0.00 2.17
267 346 0.759959 CTCTGCTGCTCTGATGGGAT 59.240 55.000 0.00 0.00 0.00 3.85
278 357 1.093159 CCCTGATTTGTCTCTGCTGC 58.907 55.000 0.00 0.00 0.00 5.25
330 441 1.756538 GAGGAGGGAGAGAAGAAGCAG 59.243 57.143 0.00 0.00 0.00 4.24
399 512 1.572085 CTCAAGGCTCACAACGCTGG 61.572 60.000 0.00 0.00 0.00 4.85
413 526 4.606071 CGGAAGGGAGCACTCAAG 57.394 61.111 0.00 0.00 0.00 3.02
434 547 0.671472 CAAGGACTCACTGCGATGCA 60.671 55.000 0.00 0.00 36.92 3.96
435 548 1.364626 CCAAGGACTCACTGCGATGC 61.365 60.000 0.00 0.00 0.00 3.91
436 549 1.364626 GCCAAGGACTCACTGCGATG 61.365 60.000 0.00 0.00 0.00 3.84
439 552 0.886490 AAAGCCAAGGACTCACTGCG 60.886 55.000 0.00 0.00 0.00 5.18
484 630 0.251297 TGCACATGTGGGGAAAGAGG 60.251 55.000 26.55 0.00 0.00 3.69
556 767 6.119536 TCTGAAAGTTTCCTTTGTCTAAGCA 58.880 36.000 13.01 0.00 40.98 3.91
737 1007 5.173664 CCTAAGTAAAGGGAGTTTGTACCG 58.826 45.833 0.00 0.00 32.55 4.02
767 1037 5.601313 AGAAACAGAGTACAGGGAGTTTGTA 59.399 40.000 0.00 0.00 30.23 2.41
768 1038 4.409247 AGAAACAGAGTACAGGGAGTTTGT 59.591 41.667 0.00 0.00 30.23 2.83
769 1039 4.962155 AGAAACAGAGTACAGGGAGTTTG 58.038 43.478 0.00 0.00 30.23 2.93
770 1040 5.632034 AAGAAACAGAGTACAGGGAGTTT 57.368 39.130 0.00 0.00 32.48 2.66
771 1041 5.632034 AAAGAAACAGAGTACAGGGAGTT 57.368 39.130 0.00 0.00 0.00 3.01
772 1042 5.632034 AAAAGAAACAGAGTACAGGGAGT 57.368 39.130 0.00 0.00 0.00 3.85
773 1043 6.292150 AGAAAAAGAAACAGAGTACAGGGAG 58.708 40.000 0.00 0.00 0.00 4.30
774 1044 6.248569 AGAAAAAGAAACAGAGTACAGGGA 57.751 37.500 0.00 0.00 0.00 4.20
775 1045 6.944234 AAGAAAAAGAAACAGAGTACAGGG 57.056 37.500 0.00 0.00 0.00 4.45
841 1116 8.880750 GGACAAGTTCTTGTGGTATATTAAGAC 58.119 37.037 20.61 3.95 34.90 3.01
859 1148 2.086869 CCGAATCATGCAGGACAAGTT 58.913 47.619 1.71 0.00 0.00 2.66
861 1150 1.019673 CCCGAATCATGCAGGACAAG 58.980 55.000 1.71 0.00 0.00 3.16
932 1225 4.072131 ACTGGCAGCGAAAGAAAATCTTA 58.928 39.130 15.89 0.00 35.27 2.10
977 1282 0.750850 GCCGCCTACTTATGTCCTGA 59.249 55.000 0.00 0.00 0.00 3.86
1026 1332 4.275196 CCATGCAAATGAGTCCAGTATCTG 59.725 45.833 0.00 0.00 0.00 2.90
1107 1413 1.144708 TGACCAAGGCAATCCACTGAA 59.855 47.619 0.00 0.00 33.74 3.02
1115 1424 2.428171 CCGATTCAATGACCAAGGCAAT 59.572 45.455 0.00 0.00 0.00 3.56
1124 1433 2.857592 ATTGCTGCCGATTCAATGAC 57.142 45.000 0.00 0.00 0.00 3.06
1137 1451 8.066668 TCGGTTTAAAACATGTTTTATTGCTG 57.933 30.769 33.29 28.16 42.48 4.41
1146 1460 9.933723 ACTACTAGTATCGGTTTAAAACATGTT 57.066 29.630 4.92 4.92 0.00 2.71
1272 1626 5.912396 TCAGCAATTTCAACATCGTAAACAC 59.088 36.000 0.00 0.00 0.00 3.32
1287 1641 2.778299 TGTTCCTACGCTCAGCAATTT 58.222 42.857 0.00 0.00 0.00 1.82
1292 1646 1.871039 TGTTTTGTTCCTACGCTCAGC 59.129 47.619 0.00 0.00 0.00 4.26
1566 1940 0.250467 TGAGCTTCCACTCTGGCAAC 60.250 55.000 0.00 0.00 37.47 4.17
1593 1967 6.142817 GCATCTTTCTTTGCTCGTTTTCTAA 58.857 36.000 0.00 0.00 35.95 2.10
1690 2134 4.897140 TGGTAACTGCAGTAAAACGGTAT 58.103 39.130 22.01 3.16 37.61 2.73
1695 2141 3.887110 AGGGTTGGTAACTGCAGTAAAAC 59.113 43.478 22.01 19.67 37.61 2.43
1776 2230 0.751643 TGGGAGCGTCTGATCATCGA 60.752 55.000 19.66 2.96 30.14 3.59
1955 2409 6.435430 TTTTCATGGGAGTTCATACGATTG 57.565 37.500 0.00 0.00 0.00 2.67
1967 2421 7.277174 ACAGTTAACTTCTTTTTCATGGGAG 57.723 36.000 5.07 0.00 0.00 4.30
2137 2629 2.605837 TTCCACTGTAAAGCACGACA 57.394 45.000 0.00 0.00 0.00 4.35
2164 2656 7.016661 TGCAATAAAAGTGAAATCCCCCTAAAA 59.983 33.333 0.00 0.00 0.00 1.52
2242 2735 3.947834 CCTTGGGAATTACCTGATCACAC 59.052 47.826 8.55 0.00 38.98 3.82
2292 2785 6.091441 CAGCTGTAGTTTGATAGTCTGGTTTC 59.909 42.308 5.25 0.00 0.00 2.78
2440 2937 2.549064 TACGATTCATCATGGGCTGG 57.451 50.000 0.00 0.00 0.00 4.85
2520 3017 4.098044 TGCTTGTCAAACCATTTTTACCGA 59.902 37.500 0.00 0.00 0.00 4.69
2743 3284 2.135139 CTTCTGCAGTTGCGTTAGACA 58.865 47.619 14.67 0.00 45.83 3.41
2755 3296 6.742109 TCTCCAAAATTTTCTTCTTCTGCAG 58.258 36.000 7.63 7.63 0.00 4.41
2894 3440 9.833182 GGACTGATTTCTCTCAAAAGAAAATAC 57.167 33.333 3.45 0.81 45.62 1.89
2971 3518 5.655532 GGAGAAACTACTAGTACCACATCCA 59.344 44.000 0.00 0.00 0.00 3.41
3014 3603 3.126343 GTGGATGACCGGTTGAAACATAC 59.874 47.826 9.42 8.66 39.42 2.39
3027 3616 5.344743 TTCTCTTGATACAGTGGATGACC 57.655 43.478 0.00 0.00 0.00 4.02
3051 3640 2.644798 AGAGGAGTGGTAGGTTGCAAAT 59.355 45.455 0.00 0.00 0.00 2.32
3175 3792 1.539124 AAACTCCCGCTCCCCTTCT 60.539 57.895 0.00 0.00 0.00 2.85
3366 3986 3.576982 TCACGGGGAATGATATAGACCAC 59.423 47.826 0.00 0.00 0.00 4.16
3382 4002 1.464997 GAAACTAGCAAAGCTCACGGG 59.535 52.381 0.00 0.00 40.44 5.28
3615 4465 4.851558 GCAACTAGTTTAAACTTCATGCCG 59.148 41.667 25.07 9.54 40.37 5.69
3642 4497 4.072131 GTGGCTTCCTCATACAAACTTCA 58.928 43.478 0.00 0.00 0.00 3.02
3764 4621 9.618890 ATTTACCGTAGTGAGTAGAGTACATTA 57.381 33.333 0.00 0.00 0.00 1.90
3896 4753 5.768317 TGGAAAAAGAAAATAGAAGCCACG 58.232 37.500 0.00 0.00 0.00 4.94
3911 4768 5.467035 TGTCTAGGCCAAAATGGAAAAAG 57.533 39.130 5.01 0.00 40.96 2.27
3961 4823 6.939730 TGTTTCATAATCGTATATGGCATGGT 59.060 34.615 10.98 1.07 34.66 3.55


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

AutoCloner maintained by Alex Coulton.