Multiple sequence alignment - TraesCS2A01G405500

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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 TraesCS2A01G405500 chr2A 100.000 2279 0 0 1 2279 661228680 661226402 0.000000e+00 4209.0
1 TraesCS2A01G405500 chr2A 90.433 1202 95 4 1 1182 661245344 661244143 0.000000e+00 1565.0
2 TraesCS2A01G405500 chr2A 91.561 1102 93 0 1178 2279 661242566 661241465 0.000000e+00 1520.0
3 TraesCS2A01G405500 chr2A 84.037 545 62 19 1 525 239252246 239251707 3.380000e-138 501.0
4 TraesCS2A01G405500 chr2A 82.953 569 63 18 3 552 331521672 331522225 1.220000e-132 483.0
5 TraesCS2A01G405500 chr2A 83.119 545 67 21 1 525 239049912 239049373 7.370000e-130 473.0
6 TraesCS2A01G405500 chr2A 91.837 49 4 0 1322 1370 364642651 364642699 4.060000e-08 69.4
7 TraesCS2A01G405500 chr4D 87.297 677 67 16 1612 2279 191600799 191601465 0.000000e+00 756.0
8 TraesCS2A01G405500 chr4D 86.726 678 69 19 1612 2279 191608550 191609216 0.000000e+00 734.0
9 TraesCS2A01G405500 chr4D 86.784 227 28 2 1049 1274 331533669 331533444 3.760000e-63 252.0
10 TraesCS2A01G405500 chr2D 87.595 661 63 17 1612 2263 395192141 395191491 0.000000e+00 749.0
11 TraesCS2A01G405500 chr2D 91.860 86 7 0 1405 1490 249848823 249848908 1.110000e-23 121.0
12 TraesCS2A01G405500 chr2D 91.860 86 7 0 1405 1490 285360135 285360050 1.110000e-23 121.0
13 TraesCS2A01G405500 chr2D 91.860 86 7 0 1405 1490 581276391 581276306 1.110000e-23 121.0
14 TraesCS2A01G405500 chr3D 87.021 678 69 17 1612 2279 581952486 581953154 0.000000e+00 747.0
15 TraesCS2A01G405500 chr3D 86.892 679 68 19 1612 2279 405796792 405796124 0.000000e+00 741.0
16 TraesCS2A01G405500 chr3D 86.982 676 67 19 1612 2278 474142207 474142870 0.000000e+00 741.0
17 TraesCS2A01G405500 chr3D 80.432 833 106 46 1475 2279 254210316 254211119 1.170000e-162 582.0
18 TraesCS2A01G405500 chr3A 85.815 712 87 13 1576 2279 325471696 325472401 0.000000e+00 743.0
19 TraesCS2A01G405500 chr3A 78.532 545 84 19 2 526 495424781 495425312 6.070000e-86 327.0
20 TraesCS2A01G405500 chr3A 88.333 120 14 0 1358 1477 258713426 258713307 6.560000e-31 145.0
21 TraesCS2A01G405500 chr3A 87.395 119 15 0 1355 1473 321872346 321872228 1.100000e-28 137.0
22 TraesCS2A01G405500 chr3A 85.000 120 18 0 1358 1477 258770815 258770696 3.070000e-24 122.0
23 TraesCS2A01G405500 chr7D 86.263 677 75 15 1612 2279 241479759 241480426 0.000000e+00 719.0
24 TraesCS2A01G405500 chr7D 85.890 326 27 6 8 318 369154757 369155078 1.690000e-86 329.0
25 TraesCS2A01G405500 chr7D 85.890 326 27 6 8 318 369162841 369163162 1.690000e-86 329.0
26 TraesCS2A01G405500 chr7D 87.981 208 23 1 1049 1254 274827238 274827031 6.290000e-61 244.0
27 TraesCS2A01G405500 chr7D 87.560 209 22 3 1049 1254 274848343 274848136 2.930000e-59 239.0
28 TraesCS2A01G405500 chr7D 87.019 208 25 1 1049 1254 274836531 274836324 1.360000e-57 233.0
29 TraesCS2A01G405500 chr7D 79.725 291 47 8 33 316 359241968 359242253 1.380000e-47 200.0
30 TraesCS2A01G405500 chr7D 91.860 86 7 0 1405 1490 492005256 492005171 1.110000e-23 121.0
31 TraesCS2A01G405500 chr5A 85.362 567 54 15 1 549 354563754 354563199 5.500000e-156 560.0
32 TraesCS2A01G405500 chr5A 84.422 199 25 4 1146 1341 312157708 312157513 8.310000e-45 191.0
33 TraesCS2A01G405500 chr5A 90.000 120 9 1 1053 1172 362570210 362570094 3.920000e-33 152.0
34 TraesCS2A01G405500 chr5A 88.462 52 6 0 1324 1375 481594531 481594480 1.890000e-06 63.9
35 TraesCS2A01G405500 chr5B 88.184 347 41 0 1144 1490 93680820 93681166 4.530000e-112 414.0
36 TraesCS2A01G405500 chr4A 80.748 535 71 23 1 526 248257088 248257599 2.750000e-104 388.0
37 TraesCS2A01G405500 chr4A 80.000 540 74 19 3 523 409750576 409751100 3.580000e-98 368.0
38 TraesCS2A01G405500 chr4A 79.630 540 75 19 3 523 409742746 409743269 2.780000e-94 355.0
39 TraesCS2A01G405500 chr4A 84.184 196 27 2 1137 1331 556966608 556966800 1.070000e-43 187.0
40 TraesCS2A01G405500 chr4A 87.402 127 12 2 1046 1172 512728182 512728304 2.360000e-30 143.0
41 TraesCS2A01G405500 chr7B 86.145 332 30 4 1 318 627345700 627346029 6.030000e-91 344.0
42 TraesCS2A01G405500 chr7B 86.061 330 28 6 3 316 276971779 276972106 2.800000e-89 339.0
43 TraesCS2A01G405500 chr7B 85.843 332 31 4 1 318 627388986 627389315 2.800000e-89 339.0
44 TraesCS2A01G405500 chr7B 84.416 154 11 5 583 724 254514390 254514238 3.050000e-29 139.0
45 TraesCS2A01G405500 chr7B 83.969 131 9 9 606 724 277879092 277879222 5.140000e-22 115.0
46 TraesCS2A01G405500 chr7B 80.233 172 17 13 567 724 277886162 277886330 1.850000e-21 113.0
47 TraesCS2A01G405500 chr7B 86.111 108 7 6 625 724 184319891 184319784 2.390000e-20 110.0
48 TraesCS2A01G405500 chr7B 83.206 131 10 9 606 724 277894308 277894438 2.390000e-20 110.0
49 TraesCS2A01G405500 chr6B 86.322 329 30 3 3 318 332448225 332448551 6.030000e-91 344.0
50 TraesCS2A01G405500 chr5D 85.583 326 45 2 1014 1337 380370554 380370229 7.800000e-90 340.0
51 TraesCS2A01G405500 chr1D 82.019 317 43 10 3 316 69536610 69536305 8.080000e-65 257.0
52 TraesCS2A01G405500 chr1D 88.750 160 17 1 1180 1338 356008200 356008041 6.420000e-46 195.0
53 TraesCS2A01G405500 chr1D 89.091 55 6 0 1475 1529 116568381 116568327 4.060000e-08 69.4
54 TraesCS2A01G405500 chr1A 81.884 276 38 4 522 785 177532704 177532979 2.950000e-54 222.0
55 TraesCS2A01G405500 chr2B 86.432 199 14 8 540 725 482584923 482584725 2.970000e-49 206.0
56 TraesCS2A01G405500 chr2B 81.452 124 18 3 1545 1666 206307987 206308107 1.860000e-16 97.1
57 TraesCS2A01G405500 chr4B 81.579 228 37 5 1049 1274 409816829 409817053 1.390000e-42 183.0
58 TraesCS2A01G405500 chr4B 90.385 52 4 1 674 724 487081351 487081402 1.460000e-07 67.6
59 TraesCS2A01G405500 chr1B 84.530 181 14 9 558 724 258501739 258501559 1.400000e-37 167.0
60 TraesCS2A01G405500 chr1B 86.747 83 3 7 650 724 496651641 496651723 4.030000e-13 86.1
61 TraesCS2A01G405500 chr1B 96.154 52 1 1 674 724 260777265 260777214 1.450000e-12 84.2
62 TraesCS2A01G405500 chr1B 96.154 52 1 1 674 724 496643520 496643571 1.450000e-12 84.2
63 TraesCS2A01G405500 chr1B 94.231 52 2 1 674 724 260785773 260785722 6.750000e-11 78.7
64 TraesCS2A01G405500 chr3B 80.612 196 30 7 125 316 286922575 286922384 6.560000e-31 145.0


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 TraesCS2A01G405500 chr2A 661226402 661228680 2278 True 4209.0 4209 100.000 1 2279 1 chr2A.!!$R3 2278
1 TraesCS2A01G405500 chr2A 661241465 661245344 3879 True 1542.5 1565 90.997 1 2279 2 chr2A.!!$R4 2278
2 TraesCS2A01G405500 chr2A 239251707 239252246 539 True 501.0 501 84.037 1 525 1 chr2A.!!$R2 524
3 TraesCS2A01G405500 chr2A 331521672 331522225 553 False 483.0 483 82.953 3 552 1 chr2A.!!$F1 549
4 TraesCS2A01G405500 chr2A 239049373 239049912 539 True 473.0 473 83.119 1 525 1 chr2A.!!$R1 524
5 TraesCS2A01G405500 chr4D 191600799 191601465 666 False 756.0 756 87.297 1612 2279 1 chr4D.!!$F1 667
6 TraesCS2A01G405500 chr4D 191608550 191609216 666 False 734.0 734 86.726 1612 2279 1 chr4D.!!$F2 667
7 TraesCS2A01G405500 chr2D 395191491 395192141 650 True 749.0 749 87.595 1612 2263 1 chr2D.!!$R2 651
8 TraesCS2A01G405500 chr3D 581952486 581953154 668 False 747.0 747 87.021 1612 2279 1 chr3D.!!$F3 667
9 TraesCS2A01G405500 chr3D 405796124 405796792 668 True 741.0 741 86.892 1612 2279 1 chr3D.!!$R1 667
10 TraesCS2A01G405500 chr3D 474142207 474142870 663 False 741.0 741 86.982 1612 2278 1 chr3D.!!$F2 666
11 TraesCS2A01G405500 chr3D 254210316 254211119 803 False 582.0 582 80.432 1475 2279 1 chr3D.!!$F1 804
12 TraesCS2A01G405500 chr3A 325471696 325472401 705 False 743.0 743 85.815 1576 2279 1 chr3A.!!$F1 703
13 TraesCS2A01G405500 chr3A 495424781 495425312 531 False 327.0 327 78.532 2 526 1 chr3A.!!$F2 524
14 TraesCS2A01G405500 chr7D 241479759 241480426 667 False 719.0 719 86.263 1612 2279 1 chr7D.!!$F1 667
15 TraesCS2A01G405500 chr5A 354563199 354563754 555 True 560.0 560 85.362 1 549 1 chr5A.!!$R2 548
16 TraesCS2A01G405500 chr4A 248257088 248257599 511 False 388.0 388 80.748 1 526 1 chr4A.!!$F1 525
17 TraesCS2A01G405500 chr4A 409750576 409751100 524 False 368.0 368 80.000 3 523 1 chr4A.!!$F3 520
18 TraesCS2A01G405500 chr4A 409742746 409743269 523 False 355.0 355 79.630 3 523 1 chr4A.!!$F2 520

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
610 647 0.03496 CTCTCGTCCTCCCACTCTCA 60.035 60.0 0.0 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1597 3221 1.079888 GTGCATTTTTCGGGGCAGG 60.08 57.895 0.0 0.0 36.86 4.85 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
87 92 8.946085 TCACATGGTGATTTCTCTTTATAACAC 58.054 33.333 0.00 0.00 37.67 3.32
438 464 9.331282 CTCTCTTTCTTTTCTCCAAAGTTCTAA 57.669 33.333 0.00 0.00 42.47 2.10
610 647 0.034960 CTCTCGTCCTCCCACTCTCA 60.035 60.000 0.00 0.00 0.00 3.27
623 660 0.192064 ACTCTCATCCCGATCCCCAT 59.808 55.000 0.00 0.00 0.00 4.00
711 748 2.364842 TCAGCCTCTCCCTCTGGC 60.365 66.667 0.00 0.00 46.42 4.85
717 754 3.092511 TCTCCCTCTGGCCATGGC 61.093 66.667 29.47 29.47 41.06 4.40
718 755 3.414193 CTCCCTCTGGCCATGGCA 61.414 66.667 36.56 21.67 44.11 4.92
721 758 2.124403 CCTCTGGCCATGGCACTC 60.124 66.667 36.56 20.78 44.11 3.51
736 773 4.069232 CTCGCACCCCTTCTCGCA 62.069 66.667 0.00 0.00 0.00 5.10
744 781 2.045926 CCTTCTCGCACCCTTGGG 60.046 66.667 3.77 3.77 37.01 4.12
748 785 4.351054 CTCGCACCCTTGGGCCTT 62.351 66.667 4.53 0.00 35.63 4.35
750 787 2.917227 CGCACCCTTGGGCCTTTT 60.917 61.111 4.53 0.00 0.00 2.27
755 792 0.114364 ACCCTTGGGCCTTTTCGATT 59.886 50.000 4.53 0.00 0.00 3.34
759 796 1.591504 TTGGGCCTTTTCGATTCGGC 61.592 55.000 4.53 10.01 41.75 5.54
796 833 3.356639 GATGACCGCTGCTGTCCGA 62.357 63.158 19.32 4.47 31.60 4.55
822 859 4.166888 TGCTCTGCCTCGCCATCC 62.167 66.667 0.00 0.00 0.00 3.51
824 861 4.598894 CTCTGCCTCGCCATCCCG 62.599 72.222 0.00 0.00 0.00 5.14
830 867 3.822192 CTCGCCATCCCGTCGTCA 61.822 66.667 0.00 0.00 0.00 4.35
835 872 2.202570 CATCCCGTCGTCACGTCC 60.203 66.667 0.00 0.00 45.17 4.79
860 897 2.110213 GCTGGTGACCACGACCAA 59.890 61.111 0.00 0.00 43.02 3.67
862 899 1.954146 CTGGTGACCACGACCAACG 60.954 63.158 0.00 0.00 43.02 4.10
865 902 3.851128 TGACCACGACCAACGCCA 61.851 61.111 0.00 0.00 46.94 5.69
900 937 1.146041 GCATCGCCATGGGTGACTA 59.854 57.895 15.13 0.00 45.43 2.59
901 938 0.463654 GCATCGCCATGGGTGACTAA 60.464 55.000 15.13 0.00 45.43 2.24
903 940 1.875514 CATCGCCATGGGTGACTAATG 59.124 52.381 15.13 0.09 45.43 1.90
904 941 1.199615 TCGCCATGGGTGACTAATGA 58.800 50.000 15.13 0.00 37.29 2.57
906 943 1.680338 GCCATGGGTGACTAATGACC 58.320 55.000 15.13 0.00 0.00 4.02
917 954 2.427453 GACTAATGACCGAGCTCCAAGA 59.573 50.000 8.47 0.00 0.00 3.02
924 961 1.006102 CGAGCTCCAAGACCGTTGT 60.006 57.895 8.47 0.00 0.00 3.32
928 965 2.058675 CTCCAAGACCGTTGTCCCT 58.941 57.895 0.00 0.00 42.81 4.20
942 979 0.179070 GTCCCTCCTCCGCTTTGATC 60.179 60.000 0.00 0.00 0.00 2.92
946 983 0.813210 CTCCTCCGCTTTGATCTGGC 60.813 60.000 0.00 0.00 0.00 4.85
951 988 0.465097 CCGCTTTGATCTGGCAGGAT 60.465 55.000 15.73 6.90 0.00 3.24
963 1000 3.402681 CAGGATCGGTGCCCCACT 61.403 66.667 0.00 0.00 34.40 4.00
990 1027 0.744771 CTTCCTTAGCGCCAAGTCCC 60.745 60.000 14.47 0.00 0.00 4.46
1012 1049 4.101448 GCGCCATGTCCCACCTCT 62.101 66.667 0.00 0.00 0.00 3.69
1028 1065 0.181587 CTCTGCCTCGACCTCCTCTA 59.818 60.000 0.00 0.00 0.00 2.43
1088 1125 4.748144 CCTGCACCTCCCCTTGCC 62.748 72.222 0.00 0.00 38.00 4.52
1095 1132 4.101448 CTCCCCTTGCCGGACCTG 62.101 72.222 5.05 0.00 33.16 4.00
1104 1141 3.036429 GCCGGACCTGCTCCATCTT 62.036 63.158 5.05 0.00 39.39 2.40
1117 1154 1.667154 CCATCTTCGCCTCCTCGTCA 61.667 60.000 0.00 0.00 0.00 4.35
1121 1158 0.867753 CTTCGCCTCCTCGTCAATCG 60.868 60.000 0.00 0.00 41.41 3.34
1122 1159 2.884087 TTCGCCTCCTCGTCAATCGC 62.884 60.000 0.00 0.00 39.67 4.58
1157 1194 1.897560 CCAAGTCCCTGTTTGTCCTC 58.102 55.000 0.00 0.00 0.00 3.71
1159 1196 2.637872 CCAAGTCCCTGTTTGTCCTCTA 59.362 50.000 0.00 0.00 0.00 2.43
1163 1200 2.897969 GTCCCTGTTTGTCCTCTACTCA 59.102 50.000 0.00 0.00 0.00 3.41
1167 1204 3.321497 CTGTTTGTCCTCTACTCACAGC 58.679 50.000 0.00 0.00 34.28 4.40
1174 1211 1.686052 CCTCTACTCACAGCTCCATCC 59.314 57.143 0.00 0.00 0.00 3.51
1175 1212 2.382882 CTCTACTCACAGCTCCATCCA 58.617 52.381 0.00 0.00 0.00 3.41
1190 2808 3.721706 CCAGGGCCGCCTCTCTTT 61.722 66.667 9.86 0.00 0.00 2.52
1229 2847 0.463620 GGCCCTTTTGTGTTGCTTCA 59.536 50.000 0.00 0.00 0.00 3.02
1253 2871 0.179034 GGATGCGCCAAGATCCTCTT 60.179 55.000 15.35 0.00 37.14 2.85
1254 2872 1.224965 GATGCGCCAAGATCCTCTTC 58.775 55.000 4.18 0.00 33.78 2.87
1265 2883 1.996191 GATCCTCTTCGACAAGTGCAC 59.004 52.381 9.40 9.40 0.00 4.57
1267 2885 0.318699 CCTCTTCGACAAGTGCACGA 60.319 55.000 12.01 1.00 0.00 4.35
1270 2888 1.605232 TCTTCGACAAGTGCACGACTA 59.395 47.619 12.01 0.00 35.82 2.59
1273 2891 1.268625 TCGACAAGTGCACGACTACAT 59.731 47.619 12.01 0.00 33.09 2.29
1274 2892 1.386748 CGACAAGTGCACGACTACATG 59.613 52.381 12.01 5.91 33.09 3.21
1275 2893 1.726791 GACAAGTGCACGACTACATGG 59.273 52.381 12.01 0.00 33.09 3.66
1279 2897 1.550524 AGTGCACGACTACATGGTGAT 59.449 47.619 12.01 0.00 39.28 3.06
1281 2899 1.275010 TGCACGACTACATGGTGATGT 59.725 47.619 0.00 0.00 45.24 3.06
1282 2900 1.660607 GCACGACTACATGGTGATGTG 59.339 52.381 0.00 1.46 43.03 3.21
1292 2910 2.448926 TGGTGATGTGTCAAGTACCG 57.551 50.000 0.00 0.00 35.80 4.02
1295 2913 2.094390 GGTGATGTGTCAAGTACCGCTA 60.094 50.000 0.00 0.00 35.80 4.26
1332 2950 2.514458 CCAAGAAGGCCAAGTACCAT 57.486 50.000 5.01 0.00 0.00 3.55
1337 2955 0.690762 AAGGCCAAGTACCATGACGT 59.309 50.000 5.01 0.00 0.00 4.34
1338 2956 0.690762 AGGCCAAGTACCATGACGTT 59.309 50.000 5.01 0.00 0.00 3.99
1340 2958 0.719465 GCCAAGTACCATGACGTTCG 59.281 55.000 0.00 0.00 0.00 3.95
1344 2962 0.172803 AGTACCATGACGTTCGGAGC 59.827 55.000 5.92 0.00 0.00 4.70
1349 2967 1.982395 ATGACGTTCGGAGCCCTCA 60.982 57.895 0.00 0.00 0.00 3.86
1355 2973 0.030908 GTTCGGAGCCCTCAGATACG 59.969 60.000 0.00 0.00 34.02 3.06
1370 2988 4.093998 TCAGATACGTCAAGTTCGACTACC 59.906 45.833 0.00 0.00 33.54 3.18
1371 2989 4.005650 AGATACGTCAAGTTCGACTACCA 58.994 43.478 0.00 0.00 33.54 3.25
1380 2998 2.120232 GTTCGACTACCATCGCATGAG 58.880 52.381 0.00 0.00 41.97 2.90
1383 3001 0.390860 GACTACCATCGCATGAGCCT 59.609 55.000 0.00 0.00 37.52 4.58
1396 3014 3.126000 GCATGAGCCTCTACTTTCACAAC 59.874 47.826 0.00 0.00 33.58 3.32
1399 3017 2.987821 GAGCCTCTACTTTCACAACGAC 59.012 50.000 0.00 0.00 0.00 4.34
1433 3051 1.609794 GTCGACCCTCCAAGACCCT 60.610 63.158 3.51 0.00 0.00 4.34
1465 3083 0.391597 TTCCTTGTCGTGACCCTGAC 59.608 55.000 0.00 0.00 35.67 3.51
1505 3123 1.865788 CTACCGACGACCCCGAACAA 61.866 60.000 0.00 0.00 39.50 2.83
1515 3133 3.120442 CGACCCCGAACAACTATGAAAAC 60.120 47.826 0.00 0.00 38.22 2.43
1541 3159 0.389391 CATTACCGCCATCGAGGACT 59.611 55.000 0.00 0.00 41.22 3.85
1573 3191 3.960755 ACTACTTCCATGATGATCCGTGA 59.039 43.478 0.00 0.00 0.00 4.35
1597 3221 3.640000 CCATCGCATCGAACCCGC 61.640 66.667 0.00 0.00 39.99 6.13
1599 3223 3.849951 ATCGCATCGAACCCGCCT 61.850 61.111 0.00 0.00 39.99 5.52
1698 3323 5.889853 AGATGCATGTTTGGATGTTGTATCT 59.110 36.000 2.46 0.00 35.71 1.98
1701 3326 4.380761 GCATGTTTGGATGTTGTATCTGCA 60.381 41.667 0.00 0.00 0.00 4.41
1704 3330 1.368641 TGGATGTTGTATCTGCACGC 58.631 50.000 0.00 0.00 0.00 5.34
1734 3362 1.527380 GTTCCCTCGTTTGGCACCA 60.527 57.895 0.00 0.00 0.00 4.17
1737 3365 2.046285 CCCTCGTTTGGCACCATCC 61.046 63.158 0.00 0.00 0.00 3.51
1774 3402 1.440476 GGTAACCGGGATCACTCCG 59.560 63.158 6.32 2.21 43.11 4.63
1929 3569 3.909430 ACAAATGCTTCAGAACATGCTG 58.091 40.909 0.00 0.00 37.24 4.41
2209 3858 6.425417 TGTGAAGTTTCGTCAATATGCAACTA 59.575 34.615 0.00 0.00 0.00 2.24
2212 3861 6.648725 AGTTTCGTCAATATGCAACTAGTC 57.351 37.500 0.00 0.00 0.00 2.59
2268 3917 0.397187 TTGCACTTTGCCATGCCATT 59.603 45.000 0.00 0.00 44.23 3.16
2272 3921 1.276989 CACTTTGCCATGCCATTCCTT 59.723 47.619 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
610 647 1.539869 CAGGGATGGGGATCGGGAT 60.540 63.158 0.00 0.00 0.00 3.85
634 671 2.043551 TGGCTTTGTGTGGTGGCA 60.044 55.556 0.00 0.00 0.00 4.92
640 677 3.547249 CTGGCGCTGGCTTTGTGTG 62.547 63.158 7.64 0.00 39.81 3.82
717 754 2.125912 CGAGAAGGGGTGCGAGTG 60.126 66.667 0.00 0.00 0.00 3.51
718 755 4.070552 GCGAGAAGGGGTGCGAGT 62.071 66.667 0.00 0.00 0.00 4.18
736 773 0.114364 AATCGAAAAGGCCCAAGGGT 59.886 50.000 7.05 0.00 37.65 4.34
744 781 2.277310 GCGCCGAATCGAAAAGGC 60.277 61.111 15.63 15.63 45.67 4.35
748 785 3.122323 GGTGGCGCCGAATCGAAA 61.122 61.111 23.90 0.00 0.00 3.46
773 810 4.521062 AGCAGCGGTCATCGGAGC 62.521 66.667 0.00 0.00 39.69 4.70
780 817 4.357947 GTCGGACAGCAGCGGTCA 62.358 66.667 24.65 4.91 37.00 4.02
848 885 3.851128 TGGCGTTGGTCGTGGTCA 61.851 61.111 0.00 0.00 42.13 4.02
884 921 1.768275 TCATTAGTCACCCATGGCGAT 59.232 47.619 6.09 0.00 34.75 4.58
894 931 1.476891 TGGAGCTCGGTCATTAGTCAC 59.523 52.381 7.83 0.00 0.00 3.67
900 937 0.250513 GGTCTTGGAGCTCGGTCATT 59.749 55.000 7.83 0.00 0.00 2.57
901 938 1.901085 GGTCTTGGAGCTCGGTCAT 59.099 57.895 7.83 0.00 0.00 3.06
903 940 2.156051 AACGGTCTTGGAGCTCGGTC 62.156 60.000 7.83 0.00 0.00 4.79
904 941 2.207924 AACGGTCTTGGAGCTCGGT 61.208 57.895 7.83 0.00 0.00 4.69
906 943 1.006102 ACAACGGTCTTGGAGCTCG 60.006 57.895 7.83 0.00 0.00 5.03
917 954 2.995574 CGGAGGAGGGACAACGGT 60.996 66.667 0.00 0.00 0.00 4.83
924 961 0.325671 AGATCAAAGCGGAGGAGGGA 60.326 55.000 0.00 0.00 0.00 4.20
928 965 1.221840 GCCAGATCAAAGCGGAGGA 59.778 57.895 0.00 0.00 0.00 3.71
961 998 1.482593 CGCTAAGGAAGGATGTCCAGT 59.517 52.381 1.30 0.00 40.48 4.00
963 1000 0.178068 GCGCTAAGGAAGGATGTCCA 59.822 55.000 0.00 0.00 40.48 4.02
968 1005 0.912486 ACTTGGCGCTAAGGAAGGAT 59.088 50.000 32.87 11.90 31.94 3.24
1012 1049 0.039180 TTGTAGAGGAGGTCGAGGCA 59.961 55.000 0.00 0.00 0.00 4.75
1028 1065 4.643387 GCGGTGGCCTGTCCTTGT 62.643 66.667 3.32 0.00 35.26 3.16
1048 1085 2.037136 CAGAGCAGGGAACTTGGCG 61.037 63.158 0.00 0.00 40.21 5.69
1095 1132 1.068921 GAGGAGGCGAAGATGGAGC 59.931 63.158 0.00 0.00 0.00 4.70
1104 1141 2.798689 CGATTGACGAGGAGGCGA 59.201 61.111 0.00 0.00 45.77 5.54
1146 1183 3.006323 AGCTGTGAGTAGAGGACAAACAG 59.994 47.826 0.00 0.00 42.46 3.16
1157 1194 1.411977 CCTGGATGGAGCTGTGAGTAG 59.588 57.143 0.00 0.00 38.35 2.57
1159 1196 1.270414 CCCTGGATGGAGCTGTGAGT 61.270 60.000 0.00 0.00 38.35 3.41
1163 1200 3.415087 GGCCCTGGATGGAGCTGT 61.415 66.667 0.00 0.00 38.35 4.40
1174 1211 2.437359 CAAAGAGAGGCGGCCCTG 60.437 66.667 17.02 0.00 43.12 4.45
1175 1212 2.529744 AACAAAGAGAGGCGGCCCT 61.530 57.895 17.02 12.67 46.74 5.19
1190 2808 1.147376 CGGGTCTTGGTGGTCAACA 59.853 57.895 0.00 0.00 0.00 3.33
1253 2871 0.664224 TGTAGTCGTGCACTTGTCGA 59.336 50.000 16.19 3.45 36.43 4.20
1254 2872 1.386748 CATGTAGTCGTGCACTTGTCG 59.613 52.381 16.19 0.55 36.43 4.35
1265 2883 3.230743 TGACACATCACCATGTAGTCG 57.769 47.619 0.00 0.00 41.69 4.18
1267 2885 4.623932 ACTTGACACATCACCATGTAGT 57.376 40.909 0.00 0.00 41.69 2.73
1270 2888 3.674997 GGTACTTGACACATCACCATGT 58.325 45.455 0.00 0.00 44.72 3.21
1273 2891 1.606994 GCGGTACTTGACACATCACCA 60.607 52.381 0.00 0.00 33.38 4.17
1274 2892 1.076332 GCGGTACTTGACACATCACC 58.924 55.000 0.00 0.00 33.38 4.02
1275 2893 2.080286 AGCGGTACTTGACACATCAC 57.920 50.000 0.00 0.00 33.38 3.06
1279 2897 0.604578 GGGTAGCGGTACTTGACACA 59.395 55.000 22.84 0.00 0.00 3.72
1281 2899 1.597797 CGGGGTAGCGGTACTTGACA 61.598 60.000 22.84 0.00 0.00 3.58
1282 2900 1.140375 CGGGGTAGCGGTACTTGAC 59.860 63.158 22.84 11.52 0.00 3.18
1292 2910 0.105039 CATTCCAGAGACGGGGTAGC 59.895 60.000 0.00 0.00 0.00 3.58
1295 2913 2.670148 GCCATTCCAGAGACGGGGT 61.670 63.158 0.00 0.00 0.00 4.95
1320 2938 1.084289 GAACGTCATGGTACTTGGCC 58.916 55.000 0.00 0.00 0.00 5.36
1323 2941 2.259618 CTCCGAACGTCATGGTACTTG 58.740 52.381 0.00 0.00 0.00 3.16
1332 2950 2.599281 TGAGGGCTCCGAACGTCA 60.599 61.111 0.00 0.00 0.00 4.35
1337 2955 0.395311 ACGTATCTGAGGGCTCCGAA 60.395 55.000 0.00 0.00 0.00 4.30
1338 2956 0.818445 GACGTATCTGAGGGCTCCGA 60.818 60.000 0.00 0.00 0.00 4.55
1340 2958 1.067821 CTTGACGTATCTGAGGGCTCC 59.932 57.143 0.00 0.00 0.00 4.70
1344 2962 2.422479 TCGAACTTGACGTATCTGAGGG 59.578 50.000 0.00 0.00 0.00 4.30
1349 2967 4.005650 TGGTAGTCGAACTTGACGTATCT 58.994 43.478 0.00 0.00 43.70 1.98
1355 2973 1.918609 GCGATGGTAGTCGAACTTGAC 59.081 52.381 0.00 0.00 44.06 3.18
1370 2988 2.522836 AAGTAGAGGCTCATGCGATG 57.477 50.000 18.26 0.00 40.82 3.84
1371 2989 2.432146 TGAAAGTAGAGGCTCATGCGAT 59.568 45.455 18.26 0.00 40.82 4.58
1380 2998 1.719780 CGTCGTTGTGAAAGTAGAGGC 59.280 52.381 0.00 0.00 0.00 4.70
1383 3001 2.544277 CCCACGTCGTTGTGAAAGTAGA 60.544 50.000 10.61 0.00 42.55 2.59
1417 3035 1.913762 ACAGGGTCTTGGAGGGTCG 60.914 63.158 0.00 0.00 0.00 4.79
1465 3083 3.192844 AGTTGTACACAGTCCGTAGATGG 59.807 47.826 0.00 0.00 0.00 3.51
1515 3133 2.547007 TCGATGGCGGTAATGGTACATG 60.547 50.000 0.00 0.00 40.28 3.21
1561 3179 2.765699 TGGAGATGTTCACGGATCATCA 59.234 45.455 18.77 5.13 39.71 3.07
1573 3191 2.205074 GTTCGATGCGATGGAGATGTT 58.795 47.619 0.00 0.00 35.23 2.71
1597 3221 1.079888 GTGCATTTTTCGGGGCAGG 60.080 57.895 0.00 0.00 36.86 4.85
1599 3223 2.647875 CGTGCATTTTTCGGGGCA 59.352 55.556 0.00 0.00 0.00 5.36
1704 3330 1.717645 CGAGGGAACAACTAACGTTCG 59.282 52.381 2.82 0.00 43.00 3.95
1734 3362 1.605451 TGTCCCACGTGTCGAGGAT 60.605 57.895 15.65 0.00 39.84 3.24
1737 3365 2.049433 GGTGTCCCACGTGTCGAG 60.049 66.667 15.65 0.00 34.83 4.04
1774 3402 1.722751 CGAAACATGCAAGAGTGACGC 60.723 52.381 0.00 0.00 0.00 5.19
1887 3525 2.176798 TCACCATGGTGGAAAGAAAGGT 59.823 45.455 38.12 0.54 45.43 3.50
1920 3560 9.571810 TTATGAAAATGTTACATCAGCATGTTC 57.428 29.630 0.00 0.00 40.66 3.18
2042 3685 4.813697 ACCAAACAACAATTCCGGAAAATG 59.186 37.500 23.08 23.77 0.00 2.32
2116 3760 1.268352 TGGTTAAACATGGCAAGACGC 59.732 47.619 0.00 0.00 41.28 5.19
2118 3762 4.519540 ATGTGGTTAAACATGGCAAGAC 57.480 40.909 0.00 0.00 39.32 3.01
2209 3858 1.759445 AGTGGAGCTCAATATGCGACT 59.241 47.619 17.19 0.00 35.28 4.18
2212 3861 5.679734 AATTAAGTGGAGCTCAATATGCG 57.320 39.130 17.19 0.00 35.28 4.73


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

AutoCloner maintained by Alex Coulton.