Multiple sequence alignment - TraesCS1B01G395600

Loading Multiple Alignment...

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 TraesCS1B01G395600 chr1B 100.000 4727 0 0 1 4727 627159514 627154788 0.000000e+00 8730.0
1 TraesCS1B01G395600 chr1B 85.464 743 87 7 3016 3755 627924564 627925288 0.000000e+00 754.0
2 TraesCS1B01G395600 chr1B 89.526 506 41 7 2387 2886 627923957 627924456 8.630000e-177 630.0
3 TraesCS1B01G395600 chr1B 83.671 692 76 15 3098 3772 627783225 627783896 6.720000e-173 617.0
4 TraesCS1B01G395600 chr1B 87.759 531 52 9 2387 2911 627782560 627783083 4.040000e-170 608.0
5 TraesCS1B01G395600 chr1B 82.621 702 77 24 2195 2870 627886504 627887186 3.170000e-161 579.0
6 TraesCS1B01G395600 chr1B 85.345 580 56 13 1352 1916 627922876 627923441 1.480000e-159 573.0
7 TraesCS1B01G395600 chr1B 79.110 584 105 13 3199 3772 322475666 322476242 2.060000e-103 387.0
8 TraesCS1B01G395600 chr1B 78.415 593 102 17 3189 3772 327229781 327230356 3.480000e-96 363.0
9 TraesCS1B01G395600 chr1B 77.344 640 75 35 1128 1716 627885028 627885648 9.870000e-82 315.0
10 TraesCS1B01G395600 chr1B 80.576 417 42 8 1724 2117 627885894 627886294 7.740000e-73 285.0
11 TraesCS1B01G395600 chr1B 88.406 207 17 5 3824 4024 627785294 627785499 4.730000e-60 243.0
12 TraesCS1B01G395600 chr1B 84.937 239 24 8 3779 4010 627888100 627888333 1.020000e-56 231.0
13 TraesCS1B01G395600 chr1B 92.857 56 4 0 2922 2977 627924453 627924508 1.090000e-11 82.4
14 TraesCS1B01G395600 chr1A 94.436 1995 59 16 2108 4073 550137003 550135032 0.000000e+00 3022.0
15 TraesCS1B01G395600 chr1A 92.038 1369 60 16 757 2116 550138354 550137026 0.000000e+00 1879.0
16 TraesCS1B01G395600 chr1A 83.541 1683 192 51 2387 4024 550217981 550219623 0.000000e+00 1495.0
17 TraesCS1B01G395600 chr1A 82.982 1140 104 33 2387 3494 550299315 550300396 0.000000e+00 948.0
18 TraesCS1B01G395600 chr1A 82.793 709 78 24 2195 2879 550209993 550210681 1.130000e-165 593.0
19 TraesCS1B01G395600 chr1A 89.646 396 34 5 1724 2117 550298585 550298975 9.140000e-137 497.0
20 TraesCS1B01G395600 chr1A 83.243 370 27 14 23 386 550139055 550138715 1.650000e-79 307.0
21 TraesCS1B01G395600 chr1A 89.700 233 22 1 1487 1719 550216957 550217187 3.580000e-76 296.0
22 TraesCS1B01G395600 chr1A 79.665 418 65 10 3530 3936 550301633 550302041 2.780000e-72 283.0
23 TraesCS1B01G395600 chr1A 84.192 291 35 4 1434 1716 550203602 550203889 6.030000e-69 272.0
24 TraesCS1B01G395600 chr1A 84.141 227 36 0 1891 2117 550209382 550209608 2.210000e-53 220.0
25 TraesCS1B01G395600 chr1A 86.154 195 16 3 1724 1916 550217264 550217449 2.880000e-47 200.0
26 TraesCS1B01G395600 chr1A 81.991 211 30 7 2105 2312 550298995 550299200 6.290000e-39 172.0
27 TraesCS1B01G395600 chr1A 89.908 109 4 5 467 572 550138688 550138584 2.970000e-27 134.0
28 TraesCS1B01G395600 chr1D 92.722 2116 106 23 17 2117 457549887 457547805 0.000000e+00 3011.0
29 TraesCS1B01G395600 chr1D 94.322 1990 52 20 2108 4073 457547783 457545831 0.000000e+00 2992.0
30 TraesCS1B01G395600 chr1D 82.379 1589 176 47 2387 3936 457845181 457846704 0.000000e+00 1288.0
31 TraesCS1B01G395600 chr1D 90.661 439 34 7 2387 2821 457583466 457583901 1.140000e-160 577.0
32 TraesCS1B01G395600 chr1D 82.394 710 80 25 2195 2879 457820592 457821281 1.140000e-160 577.0
33 TraesCS1B01G395600 chr1D 80.429 792 97 22 3267 4010 457584233 457585014 6.910000e-153 551.0
34 TraesCS1B01G395600 chr1D 80.389 668 92 26 3014 3661 457821365 457822013 5.540000e-129 472.0
35 TraesCS1B01G395600 chr1D 87.798 377 34 7 1352 1719 457582377 457582750 9.400000e-117 431.0
36 TraesCS1B01G395600 chr1D 79.412 578 93 21 3192 3758 223164468 223165030 7.420000e-103 385.0
37 TraesCS1B01G395600 chr1D 78.141 581 106 16 3187 3759 208413068 208412501 2.710000e-92 350.0
38 TraesCS1B01G395600 chr1D 81.235 421 43 11 1724 2117 457812513 457812924 1.650000e-79 307.0
39 TraesCS1B01G395600 chr1D 91.429 210 18 0 1908 2117 457844632 457844841 5.990000e-74 289.0
40 TraesCS1B01G395600 chr1D 84.746 295 33 7 1434 1719 457812138 457812429 7.740000e-73 285.0
41 TraesCS1B01G395600 chr1D 84.775 289 33 6 1434 1714 457811626 457811911 3.600000e-71 279.0
42 TraesCS1B01G395600 chr1D 81.250 368 48 18 3663 4013 457822189 457822552 1.300000e-70 278.0
43 TraesCS1B01G395600 chr1D 89.286 168 16 2 2171 2338 226468031 226468196 4.790000e-50 209.0
44 TraesCS1B01G395600 chr1D 84.834 211 24 7 2105 2312 457844861 457845066 6.200000e-49 206.0
45 TraesCS1B01G395600 chr4D 96.651 657 21 1 4072 4727 417672232 417672888 0.000000e+00 1090.0
46 TraesCS1B01G395600 chr5D 95.672 647 26 1 4081 4727 332214103 332213459 0.000000e+00 1038.0
47 TraesCS1B01G395600 chr2A 94.444 648 35 1 4080 4727 565291122 565290476 0.000000e+00 996.0
48 TraesCS1B01G395600 chr2D 92.178 652 48 1 4075 4726 574117639 574116991 0.000000e+00 918.0
49 TraesCS1B01G395600 chr7B 92.025 652 49 2 4076 4727 59329462 59328814 0.000000e+00 913.0
50 TraesCS1B01G395600 chr7B 91.616 656 49 3 4075 4727 482027348 482028000 0.000000e+00 902.0
51 TraesCS1B01G395600 chr3B 91.577 653 49 3 4075 4727 31653200 31652554 0.000000e+00 896.0
52 TraesCS1B01G395600 chr3B 87.562 201 20 5 2144 2341 705148316 705148514 1.320000e-55 228.0
53 TraesCS1B01G395600 chr3A 91.258 652 51 4 4076 4726 437665600 437664954 0.000000e+00 883.0
54 TraesCS1B01G395600 chr3A 84.082 245 29 6 2106 2341 668225601 668225844 1.320000e-55 228.0
55 TraesCS1B01G395600 chr3A 83.806 247 28 8 2106 2341 668583412 668583657 1.710000e-54 224.0
56 TraesCS1B01G395600 chr7A 91.231 650 53 2 4079 4727 49054782 49054136 0.000000e+00 881.0


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 TraesCS1B01G395600 chr1B 627154788 627159514 4726 True 8730.000000 8730 100.000000 1 4727 1 chr1B.!!$R1 4726
1 TraesCS1B01G395600 chr1B 627922876 627925288 2412 False 509.850000 754 88.298000 1352 3755 4 chr1B.!!$F5 2403
2 TraesCS1B01G395600 chr1B 627782560 627785499 2939 False 489.333333 617 86.612000 2387 4024 3 chr1B.!!$F3 1637
3 TraesCS1B01G395600 chr1B 322475666 322476242 576 False 387.000000 387 79.110000 3199 3772 1 chr1B.!!$F1 573
4 TraesCS1B01G395600 chr1B 327229781 327230356 575 False 363.000000 363 78.415000 3189 3772 1 chr1B.!!$F2 583
5 TraesCS1B01G395600 chr1B 627885028 627888333 3305 False 352.500000 579 81.369500 1128 4010 4 chr1B.!!$F4 2882
6 TraesCS1B01G395600 chr1A 550135032 550139055 4023 True 1335.500000 3022 89.906250 23 4073 4 chr1A.!!$R1 4050
7 TraesCS1B01G395600 chr1A 550216957 550219623 2666 False 663.666667 1495 86.465000 1487 4024 3 chr1A.!!$F3 2537
8 TraesCS1B01G395600 chr1A 550298585 550302041 3456 False 475.000000 948 83.571000 1724 3936 4 chr1A.!!$F4 2212
9 TraesCS1B01G395600 chr1A 550209382 550210681 1299 False 406.500000 593 83.467000 1891 2879 2 chr1A.!!$F2 988
10 TraesCS1B01G395600 chr1D 457545831 457549887 4056 True 3001.500000 3011 93.522000 17 4073 2 chr1D.!!$R2 4056
11 TraesCS1B01G395600 chr1D 457844632 457846704 2072 False 594.333333 1288 86.214000 1908 3936 3 chr1D.!!$F6 2028
12 TraesCS1B01G395600 chr1D 457582377 457585014 2637 False 519.666667 577 86.296000 1352 4010 3 chr1D.!!$F3 2658
13 TraesCS1B01G395600 chr1D 457820592 457822552 1960 False 442.333333 577 81.344333 2195 4013 3 chr1D.!!$F5 1818
14 TraesCS1B01G395600 chr1D 223164468 223165030 562 False 385.000000 385 79.412000 3192 3758 1 chr1D.!!$F1 566
15 TraesCS1B01G395600 chr1D 208412501 208413068 567 True 350.000000 350 78.141000 3187 3759 1 chr1D.!!$R1 572
16 TraesCS1B01G395600 chr1D 457811626 457812924 1298 False 290.333333 307 83.585333 1434 2117 3 chr1D.!!$F4 683
17 TraesCS1B01G395600 chr4D 417672232 417672888 656 False 1090.000000 1090 96.651000 4072 4727 1 chr4D.!!$F1 655
18 TraesCS1B01G395600 chr5D 332213459 332214103 644 True 1038.000000 1038 95.672000 4081 4727 1 chr5D.!!$R1 646
19 TraesCS1B01G395600 chr2A 565290476 565291122 646 True 996.000000 996 94.444000 4080 4727 1 chr2A.!!$R1 647
20 TraesCS1B01G395600 chr2D 574116991 574117639 648 True 918.000000 918 92.178000 4075 4726 1 chr2D.!!$R1 651
21 TraesCS1B01G395600 chr7B 59328814 59329462 648 True 913.000000 913 92.025000 4076 4727 1 chr7B.!!$R1 651
22 TraesCS1B01G395600 chr7B 482027348 482028000 652 False 902.000000 902 91.616000 4075 4727 1 chr7B.!!$F1 652
23 TraesCS1B01G395600 chr3B 31652554 31653200 646 True 896.000000 896 91.577000 4075 4727 1 chr3B.!!$R1 652
24 TraesCS1B01G395600 chr3A 437664954 437665600 646 True 883.000000 883 91.258000 4076 4726 1 chr3A.!!$R1 650
25 TraesCS1B01G395600 chr7A 49054136 49054782 646 True 881.000000 881 91.231000 4079 4727 1 chr7A.!!$R1 648

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
791 885 0.317160 TTGGTGATCGTCTTCGTGCT 59.683 50.0 0.00 0.00 38.33 4.40 F
794 888 0.635731 GTGATCGTCTTCGTGCTTCG 59.364 55.0 0.00 0.00 41.41 3.79 F
2031 3070 0.661187 CACGGTGCATGCAGTGTTTC 60.661 55.0 23.41 8.01 0.00 2.78 F
2086 3125 0.999406 CGTGGATGCAAAGGTAGACG 59.001 55.0 0.00 0.00 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2122 3161 0.260816 TCGACTATGTACCCCCAGCT 59.739 55.000 0.0 0.0 0.00 4.24 R
2123 3162 0.388294 GTCGACTATGTACCCCCAGC 59.612 60.000 8.7 0.0 0.00 4.85 R
3398 5038 1.420138 TGAAACACCTTCCTGGACTCC 59.580 52.381 0.0 0.0 39.71 3.85 R
3772 6813 2.270352 TCAACACCACCATCAACTCC 57.730 50.000 0.0 0.0 0.00 3.85 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
69 70 3.715273 CAGGACGCTGCATGCTAG 58.285 61.111 20.33 15.13 40.11 3.42
112 114 3.087065 GGCTACCTTTGCCTGGGA 58.913 61.111 0.00 0.00 46.38 4.37
159 161 1.461091 ATATGCGTGGGATCGGACGT 61.461 55.000 14.43 0.00 37.89 4.34
160 162 1.669049 TATGCGTGGGATCGGACGTT 61.669 55.000 14.43 7.22 37.89 3.99
179 181 2.819550 CCGGGCGTGGCTTATACT 59.180 61.111 0.00 0.00 0.00 2.12
180 182 1.594293 CCGGGCGTGGCTTATACTG 60.594 63.158 0.00 0.00 0.00 2.74
181 183 1.143183 CGGGCGTGGCTTATACTGT 59.857 57.895 0.00 0.00 0.00 3.55
182 184 0.386476 CGGGCGTGGCTTATACTGTA 59.614 55.000 0.00 0.00 0.00 2.74
183 185 1.861971 GGGCGTGGCTTATACTGTAC 58.138 55.000 0.00 0.00 0.00 2.90
185 187 2.419021 GGGCGTGGCTTATACTGTACAA 60.419 50.000 0.00 0.00 0.00 2.41
278 284 1.143969 GGTTCACGCGGAATCCTACG 61.144 60.000 12.47 9.55 37.93 3.51
364 372 4.607293 TCAGGATTAAGGACGATGGATG 57.393 45.455 0.00 0.00 0.00 3.51
445 453 1.151668 AGATTTCGTCTGTGCACTGC 58.848 50.000 19.41 12.39 35.31 4.40
541 553 4.076394 CCCGAGTTGGTTAGAATCCAAAA 58.924 43.478 0.00 0.00 44.91 2.44
664 679 2.745884 CAATCCGCGCCCAAGTCA 60.746 61.111 0.00 0.00 0.00 3.41
706 721 1.202521 CCCACTTTTGCTTTCGCCTTT 60.203 47.619 0.00 0.00 34.43 3.11
724 739 3.304190 CCTTTTACGTTGAAGGGTTTCGG 60.304 47.826 17.42 0.00 38.98 4.30
776 870 8.648693 AGTAAGTACTGTATTGACTTTCTTGGT 58.351 33.333 0.00 0.00 35.17 3.67
777 871 7.730364 AAGTACTGTATTGACTTTCTTGGTG 57.270 36.000 0.00 0.00 29.02 4.17
778 872 7.062749 AGTACTGTATTGACTTTCTTGGTGA 57.937 36.000 0.00 0.00 0.00 4.02
779 873 7.680730 AGTACTGTATTGACTTTCTTGGTGAT 58.319 34.615 0.00 0.00 0.00 3.06
780 874 7.819900 AGTACTGTATTGACTTTCTTGGTGATC 59.180 37.037 0.00 0.00 0.00 2.92
781 875 5.639506 ACTGTATTGACTTTCTTGGTGATCG 59.360 40.000 0.00 0.00 0.00 3.69
782 876 5.547465 TGTATTGACTTTCTTGGTGATCGT 58.453 37.500 0.00 0.00 0.00 3.73
783 877 5.637810 TGTATTGACTTTCTTGGTGATCGTC 59.362 40.000 0.00 0.00 0.00 4.20
784 878 4.336889 TTGACTTTCTTGGTGATCGTCT 57.663 40.909 0.00 0.00 0.00 4.18
785 879 4.336889 TGACTTTCTTGGTGATCGTCTT 57.663 40.909 0.00 0.00 0.00 3.01
786 880 4.307432 TGACTTTCTTGGTGATCGTCTTC 58.693 43.478 0.00 0.00 0.00 2.87
787 881 3.318017 ACTTTCTTGGTGATCGTCTTCG 58.682 45.455 0.00 0.00 38.55 3.79
788 882 3.243771 ACTTTCTTGGTGATCGTCTTCGT 60.244 43.478 0.00 0.00 38.33 3.85
789 883 2.347697 TCTTGGTGATCGTCTTCGTG 57.652 50.000 0.00 0.00 38.33 4.35
790 884 0.716108 CTTGGTGATCGTCTTCGTGC 59.284 55.000 0.00 0.00 38.33 5.34
791 885 0.317160 TTGGTGATCGTCTTCGTGCT 59.683 50.000 0.00 0.00 38.33 4.40
792 886 0.317160 TGGTGATCGTCTTCGTGCTT 59.683 50.000 0.00 0.00 38.33 3.91
793 887 0.992802 GGTGATCGTCTTCGTGCTTC 59.007 55.000 0.00 0.00 38.33 3.86
794 888 0.635731 GTGATCGTCTTCGTGCTTCG 59.364 55.000 0.00 0.00 41.41 3.79
856 956 0.669619 TCTGCATTGCGGCAATATGG 59.330 50.000 26.24 15.99 44.40 2.74
891 991 5.420725 TGCCTTAGTAACTGTGTGATCAT 57.579 39.130 0.00 0.00 0.00 2.45
897 997 7.712639 CCTTAGTAACTGTGTGATCATGCTATT 59.287 37.037 0.00 0.00 0.00 1.73
910 1010 4.357018 CATGCTATTGCTATGAGGCATG 57.643 45.455 20.49 20.49 46.49 4.06
979 1082 4.679662 GATGATCAATTTCACTTGCAGGG 58.320 43.478 0.00 0.00 0.00 4.45
987 1090 1.001641 CACTTGCAGGGGAAGAGGG 60.002 63.158 0.00 0.00 0.00 4.30
991 1094 2.041265 GCAGGGGAAGAGGGAGGA 59.959 66.667 0.00 0.00 0.00 3.71
1014 1117 1.686325 GAGCTATGGGCAACTCCGGA 61.686 60.000 2.93 2.93 44.79 5.14
1038 1141 4.171103 GGTATGTTCGCCCGCCCT 62.171 66.667 0.00 0.00 0.00 5.19
1039 1142 2.124860 GTATGTTCGCCCGCCCTT 60.125 61.111 0.00 0.00 0.00 3.95
1040 1143 1.747745 GTATGTTCGCCCGCCCTTT 60.748 57.895 0.00 0.00 0.00 3.11
1041 1144 1.747367 TATGTTCGCCCGCCCTTTG 60.747 57.895 0.00 0.00 0.00 2.77
1042 1145 2.472414 TATGTTCGCCCGCCCTTTGT 62.472 55.000 0.00 0.00 0.00 2.83
1043 1146 4.038080 GTTCGCCCGCCCTTTGTG 62.038 66.667 0.00 0.00 0.00 3.33
1058 1161 4.397417 CCCTTTGTGATTGAACCTCAGATC 59.603 45.833 0.00 0.00 0.00 2.75
1084 1187 7.793902 GTTTCTGCTATAAACGAAAAGTCAGA 58.206 34.615 0.00 0.00 0.00 3.27
1086 1189 6.688578 TCTGCTATAAACGAAAAGTCAGACT 58.311 36.000 0.00 0.00 0.00 3.24
1139 1245 1.135915 CACGGTGAGATCTCTCCCTTG 59.864 57.143 29.43 23.71 42.20 3.61
1170 1281 3.201266 AGGTAGAAGTGAGATCTCTCCGT 59.799 47.826 22.95 11.85 42.20 4.69
1195 1306 2.456073 AACTCGGATAGCACCCTAGT 57.544 50.000 0.00 0.00 0.00 2.57
1199 1310 1.147191 TCGGATAGCACCCTAGTGGAT 59.853 52.381 4.45 0.00 44.69 3.41
1203 1314 2.868964 TAGCACCCTAGTGGATTCCT 57.131 50.000 3.95 0.00 44.69 3.36
1270 1398 1.215423 ACCTGAACTCCTGCCACTTTT 59.785 47.619 0.00 0.00 0.00 2.27
1416 1610 6.721318 ACTATTCTGCACCCTTCTATTTTCA 58.279 36.000 0.00 0.00 0.00 2.69
1443 1637 7.601886 CCATGGTGAATATTGCAACTTGTTTAA 59.398 33.333 0.00 0.00 0.00 1.52
1748 2708 9.630098 GTCATGTTTCAGTCATGTTGAAATATT 57.370 29.630 22.19 13.15 43.90 1.28
1791 2751 2.034053 TGAAAACAGCCGGACAATGAAC 59.966 45.455 5.05 0.00 0.00 3.18
1807 2769 3.657398 TGAACCTTGAGGATGCATCAT 57.343 42.857 27.25 21.75 38.94 2.45
1916 2903 4.036734 GTGACTCCAAAGCACAATCAAGAA 59.963 41.667 0.00 0.00 32.89 2.52
2031 3070 0.661187 CACGGTGCATGCAGTGTTTC 60.661 55.000 23.41 8.01 0.00 2.78
2086 3125 0.999406 CGTGGATGCAAAGGTAGACG 59.001 55.000 0.00 0.00 0.00 4.18
2117 3156 5.825151 TGTGTTTGTTCAAGTACATCCATCA 59.175 36.000 0.00 0.00 0.00 3.07
2119 3158 7.023575 GTGTTTGTTCAAGTACATCCATCATC 58.976 38.462 0.00 0.00 0.00 2.92
2122 3161 8.946085 GTTTGTTCAAGTACATCCATCATCTTA 58.054 33.333 0.00 0.00 0.00 2.10
2123 3162 8.722480 TTGTTCAAGTACATCCATCATCTTAG 57.278 34.615 0.00 0.00 0.00 2.18
2125 3164 6.737720 TCAAGTACATCCATCATCTTAGCT 57.262 37.500 0.00 0.00 0.00 3.32
2126 3165 6.519382 TCAAGTACATCCATCATCTTAGCTG 58.481 40.000 0.00 0.00 0.00 4.24
2345 3752 7.117523 CCTTCTAGAGTACATATGCATGCTTTC 59.882 40.741 20.33 5.95 35.39 2.62
2431 3869 6.869388 GCGGGAAAAGGTTGATTATTTGTTAA 59.131 34.615 0.00 0.00 0.00 2.01
2574 4014 6.093771 AGCTACTGAAATCATCTGCTTTTCTG 59.906 38.462 0.00 0.00 35.61 3.02
3115 4670 4.708177 ACTGTAGTCATGTTTTGCTCAGT 58.292 39.130 0.00 0.00 0.00 3.41
3334 4966 2.534019 GCATGTATCCGCGTGGTGG 61.534 63.158 16.01 0.00 36.30 4.61
3398 5038 3.320541 AGTCCTCGGATGAGCTCTTTATG 59.679 47.826 16.19 3.11 41.13 1.90
3460 5100 6.795590 TGGACCAAAAGAATGGGAAATACTA 58.204 36.000 0.00 0.00 45.18 1.82
3462 5102 6.183360 GGACCAAAAGAATGGGAAATACTACG 60.183 42.308 0.00 0.00 45.18 3.51
3463 5103 6.478129 ACCAAAAGAATGGGAAATACTACGA 58.522 36.000 0.00 0.00 45.18 3.43
3502 6351 5.143376 GTTGTCCTTAGCAACTACCAGTA 57.857 43.478 0.00 0.00 41.94 2.74
3528 6391 6.632834 CAGTGTGTGAATTACTGTTTGTAAGC 59.367 38.462 0.00 0.00 43.46 3.09
3538 6401 3.137728 ACTGTTTGTAAGCTGTAACCCCT 59.862 43.478 0.00 0.00 0.00 4.79
3589 6589 1.001641 ATGGCAGGTCTCTTGGTGC 60.002 57.895 0.00 0.00 35.07 5.01
3682 6721 8.076781 GCTATCTTATAGAATCGAACTGTGTCA 58.923 37.037 0.00 0.00 0.00 3.58
3772 6813 7.445121 TGTAGAGTTAATATGCCTTCATCCTG 58.555 38.462 0.00 0.00 34.22 3.86
3773 6814 5.874093 AGAGTTAATATGCCTTCATCCTGG 58.126 41.667 0.00 0.00 34.22 4.45
3774 6815 5.608437 AGAGTTAATATGCCTTCATCCTGGA 59.392 40.000 0.00 0.00 34.22 3.86
3775 6816 5.874093 AGTTAATATGCCTTCATCCTGGAG 58.126 41.667 1.52 0.00 34.22 3.86
3776 6817 5.370880 AGTTAATATGCCTTCATCCTGGAGT 59.629 40.000 1.52 0.00 34.22 3.85
3983 8438 3.117776 TGGTTCCATGATCCCATCTTCAG 60.118 47.826 0.00 0.00 0.00 3.02
3986 8441 1.779092 CCATGATCCCATCTTCAGGGT 59.221 52.381 0.00 0.00 46.82 4.34
4063 8518 7.915508 TCATATAAACTGTAAGGCGTTGATTG 58.084 34.615 0.97 0.00 39.30 2.67
4065 8520 4.911514 AAACTGTAAGGCGTTGATTGTT 57.088 36.364 0.97 0.00 39.30 2.83
4066 8521 4.911514 AACTGTAAGGCGTTGATTGTTT 57.088 36.364 0.97 0.00 39.30 2.83
4073 8528 4.489679 AGGCGTTGATTGTTTTCTTCTC 57.510 40.909 0.00 0.00 0.00 2.87
4148 8604 2.303022 CCTGATACAACCACACTCACCT 59.697 50.000 0.00 0.00 0.00 4.00
4196 8654 1.704641 TGGATACATAGGCGCTGAGT 58.295 50.000 7.64 3.86 46.17 3.41
4330 8791 3.325425 TCAAGAAGGATACAACACCGGAA 59.675 43.478 9.46 0.00 41.41 4.30
4356 8817 0.178068 CACCGTCCGATCCAAGGATT 59.822 55.000 2.62 0.00 40.30 3.01
4404 8865 0.869880 CAATGATAGCCGCGACGACA 60.870 55.000 8.23 0.00 0.00 4.35
4662 9124 1.534476 TACCCCAACCGCAGAGACA 60.534 57.895 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 8.357402 ACGATCCTTTTTACAGCTGTAATTTTT 58.643 29.630 33.72 19.18 39.89 1.94
11 12 7.882179 ACGATCCTTTTTACAGCTGTAATTTT 58.118 30.769 33.72 18.30 39.89 1.82
12 13 7.174253 TGACGATCCTTTTTACAGCTGTAATTT 59.826 33.333 33.72 17.71 39.89 1.82
13 14 6.653320 TGACGATCCTTTTTACAGCTGTAATT 59.347 34.615 33.72 17.41 39.89 1.40
14 15 6.170506 TGACGATCCTTTTTACAGCTGTAAT 58.829 36.000 33.72 21.00 39.89 1.89
15 16 5.543714 TGACGATCCTTTTTACAGCTGTAA 58.456 37.500 30.81 30.81 38.60 2.41
63 64 4.338400 TGAGCTCGTAACATGTACTAGCAT 59.662 41.667 22.04 13.47 38.30 3.79
64 65 3.692593 TGAGCTCGTAACATGTACTAGCA 59.307 43.478 22.04 9.39 38.30 3.49
65 66 4.036352 GTGAGCTCGTAACATGTACTAGC 58.964 47.826 9.64 16.86 36.76 3.42
66 67 4.033702 TCGTGAGCTCGTAACATGTACTAG 59.966 45.833 9.64 1.14 0.00 2.57
67 68 3.934579 TCGTGAGCTCGTAACATGTACTA 59.065 43.478 9.64 0.00 0.00 1.82
68 69 2.745821 TCGTGAGCTCGTAACATGTACT 59.254 45.455 9.64 0.00 0.00 2.73
69 70 3.127081 TCGTGAGCTCGTAACATGTAC 57.873 47.619 9.64 0.00 0.00 2.90
82 83 1.448013 GTAGCCCACCTTCGTGAGC 60.448 63.158 0.00 0.00 43.66 4.26
107 108 0.034059 ACGCTTCTGTGTCTTCCCAG 59.966 55.000 0.00 0.00 29.93 4.45
112 114 1.583054 GTGGAACGCTTCTGTGTCTT 58.417 50.000 0.00 0.00 35.64 3.01
145 147 3.186047 GCAACGTCCGATCCCACG 61.186 66.667 9.07 9.07 41.90 4.94
166 168 4.390909 ACTTTTGTACAGTATAAGCCACGC 59.609 41.667 0.00 0.00 0.00 5.34
228 230 6.497259 TCTCCCTTATTGCGAGACCTATTAAT 59.503 38.462 0.00 0.00 0.00 1.40
230 232 5.391256 TCTCCCTTATTGCGAGACCTATTA 58.609 41.667 0.00 0.00 0.00 0.98
231 233 4.223953 TCTCCCTTATTGCGAGACCTATT 58.776 43.478 0.00 0.00 0.00 1.73
364 372 4.695217 TTGCAACCTAACGGATGATTTC 57.305 40.909 0.00 0.00 35.22 2.17
379 387 5.234757 TGCTGATTTGTGAAAAGATTGCAAC 59.765 36.000 0.00 0.00 0.00 4.17
445 453 2.536761 TAAAACCACTCTGGACACGG 57.463 50.000 0.00 0.00 40.96 4.94
517 525 3.112263 TGGATTCTAACCAACTCGGGAT 58.888 45.455 0.00 0.00 40.22 3.85
518 526 2.542550 TGGATTCTAACCAACTCGGGA 58.457 47.619 0.00 0.00 40.22 5.14
541 553 2.427453 CCTGTGCTCCGTATTCTACAGT 59.573 50.000 0.00 0.00 35.09 3.55
706 721 1.202675 AGCCGAAACCCTTCAACGTAA 60.203 47.619 0.00 0.00 0.00 3.18
724 739 0.032540 CACTGCCAAACCCTGAAAGC 59.967 55.000 0.00 0.00 0.00 3.51
775 869 0.635731 CGAAGCACGAAGACGATCAC 59.364 55.000 0.00 0.00 45.77 3.06
776 870 3.015799 CGAAGCACGAAGACGATCA 57.984 52.632 0.00 0.00 45.77 2.92
786 880 1.201921 CCCGATTTCTTTCGAAGCACG 60.202 52.381 0.00 0.69 41.62 5.34
787 881 1.804748 ACCCGATTTCTTTCGAAGCAC 59.195 47.619 0.00 0.00 41.62 4.40
788 882 2.178912 ACCCGATTTCTTTCGAAGCA 57.821 45.000 0.00 0.00 41.62 3.91
789 883 3.554259 AAACCCGATTTCTTTCGAAGC 57.446 42.857 0.00 0.00 41.62 3.86
790 884 5.857822 ACTAAACCCGATTTCTTTCGAAG 57.142 39.130 0.00 0.00 41.62 3.79
791 885 6.622833 AAACTAAACCCGATTTCTTTCGAA 57.377 33.333 0.00 0.00 41.62 3.71
792 886 7.910441 ATAAACTAAACCCGATTTCTTTCGA 57.090 32.000 0.00 0.00 41.62 3.71
793 887 8.959734 AAATAAACTAAACCCGATTTCTTTCG 57.040 30.769 0.00 0.00 38.83 3.46
812 906 8.934023 AGGTACAAGATGAACCTGAAAATAAA 57.066 30.769 0.00 0.00 42.08 1.40
979 1082 2.042843 TCCGCTCCTCCCTCTTCC 60.043 66.667 0.00 0.00 0.00 3.46
987 1090 3.055580 CCCATAGCTCCGCTCCTC 58.944 66.667 0.00 0.00 40.44 3.71
991 1094 2.190578 GTTGCCCATAGCTCCGCT 59.809 61.111 0.00 0.00 44.23 5.52
1014 1117 0.676782 GGGCGAACATACCTGTGCTT 60.677 55.000 0.00 0.00 35.22 3.91
1038 1141 4.641396 ACGATCTGAGGTTCAATCACAAA 58.359 39.130 0.00 0.00 0.00 2.83
1039 1142 4.271696 ACGATCTGAGGTTCAATCACAA 57.728 40.909 0.00 0.00 0.00 3.33
1040 1143 3.961480 ACGATCTGAGGTTCAATCACA 57.039 42.857 0.00 0.00 0.00 3.58
1041 1144 4.932200 AGAAACGATCTGAGGTTCAATCAC 59.068 41.667 0.00 0.00 36.88 3.06
1042 1145 5.152623 AGAAACGATCTGAGGTTCAATCA 57.847 39.130 0.00 0.00 36.88 2.57
1084 1187 9.533831 AGGGATTAATTGTTGTGAATTTCTAGT 57.466 29.630 0.00 0.00 0.00 2.57
1112 1218 5.244178 GGGAGAGATCTCACCGTGTATTTAT 59.756 44.000 26.74 2.88 44.60 1.40
1116 1222 2.588620 GGGAGAGATCTCACCGTGTAT 58.411 52.381 26.74 4.97 44.60 2.29
1139 1245 8.288689 AGATCTCACTTCTACCTAAGAAAGTC 57.711 38.462 0.00 0.00 43.66 3.01
1170 1281 3.709653 AGGGTGCTATCCGAGTTTATTCA 59.290 43.478 0.00 0.00 0.00 2.57
1203 1314 1.320344 CGTTCGAGTCCTCCCCATGA 61.320 60.000 0.00 0.00 0.00 3.07
1215 1326 3.695022 CTACCCACCGGCGTTCGAG 62.695 68.421 6.01 0.00 42.43 4.04
1289 1417 5.241403 TGAAGAGGCCACTTTTCTCATAA 57.759 39.130 17.05 0.00 38.34 1.90
1338 1467 7.346751 TCTTGCATACAGATACAGTACATGA 57.653 36.000 0.00 0.00 0.00 3.07
1416 1610 4.527816 ACAAGTTGCAATATTCACCATGGT 59.472 37.500 13.00 13.00 0.00 3.55
1648 2365 3.241963 CGTTATGATGCGTACCACTTGTG 60.242 47.826 0.00 0.00 0.00 3.33
1748 2708 3.149981 TGGGTTTGCGTGATTGTGATTA 58.850 40.909 0.00 0.00 0.00 1.75
1791 2751 2.927028 TCACATGATGCATCCTCAAGG 58.073 47.619 23.67 9.40 0.00 3.61
1807 2769 9.905713 AATGAGTATAAGCCTAATTTCTTCACA 57.094 29.630 0.00 0.00 0.00 3.58
1916 2903 2.693069 CGATTTGGAGACACTTGAGCT 58.307 47.619 0.00 0.00 42.67 4.09
2031 3070 6.841119 TCGAATGGTTGAATATTGACAACTG 58.159 36.000 15.67 5.73 43.68 3.16
2086 3125 3.434637 ACTTGAACAAACACATTCACGC 58.565 40.909 0.00 0.00 34.61 5.34
2117 3156 4.161102 GACTATGTACCCCCAGCTAAGAT 58.839 47.826 0.00 0.00 0.00 2.40
2119 3158 2.296471 CGACTATGTACCCCCAGCTAAG 59.704 54.545 0.00 0.00 0.00 2.18
2122 3161 0.260816 TCGACTATGTACCCCCAGCT 59.739 55.000 0.00 0.00 0.00 4.24
2123 3162 0.388294 GTCGACTATGTACCCCCAGC 59.612 60.000 8.70 0.00 0.00 4.85
2125 3164 1.771565 CAGTCGACTATGTACCCCCA 58.228 55.000 19.57 0.00 0.00 4.96
2126 3165 0.388294 GCAGTCGACTATGTACCCCC 59.612 60.000 19.57 0.00 0.00 5.40
2324 3723 7.014615 TCTCAGAAAGCATGCATATGTACTCTA 59.985 37.037 21.98 0.00 36.65 2.43
2574 4014 5.473504 ACCAAAGACACAACTATCATCAACC 59.526 40.000 0.00 0.00 0.00 3.77
3300 4932 2.658285 CATGCCCATGTACCTGTTGAT 58.342 47.619 0.13 0.00 34.23 2.57
3334 4966 3.696782 CAATCAGTGCTGCTCTTGC 57.303 52.632 0.74 0.00 40.20 4.01
3398 5038 1.420138 TGAAACACCTTCCTGGACTCC 59.580 52.381 0.00 0.00 39.71 3.85
3460 5100 5.878669 ACAACTTAACCTGAAGTTCTTTCGT 59.121 36.000 4.17 0.00 44.52 3.85
3462 5102 6.542735 AGGACAACTTAACCTGAAGTTCTTTC 59.457 38.462 4.17 0.00 44.52 2.62
3463 5103 6.424032 AGGACAACTTAACCTGAAGTTCTTT 58.576 36.000 4.17 0.00 44.52 2.52
3522 6385 5.765576 TTATCAAGGGGTTACAGCTTACA 57.234 39.130 0.00 0.00 0.00 2.41
3523 6386 7.771826 TGTAATTATCAAGGGGTTACAGCTTAC 59.228 37.037 0.00 0.00 32.21 2.34
3524 6387 7.863722 TGTAATTATCAAGGGGTTACAGCTTA 58.136 34.615 0.00 0.00 32.21 3.09
3525 6388 6.727394 TGTAATTATCAAGGGGTTACAGCTT 58.273 36.000 0.00 0.00 32.21 3.74
3526 6389 6.321821 TGTAATTATCAAGGGGTTACAGCT 57.678 37.500 0.00 0.00 32.21 4.24
3527 6390 6.619801 CTGTAATTATCAAGGGGTTACAGC 57.380 41.667 9.71 0.00 42.71 4.40
3589 6589 2.489971 TGACCAGCCTTGACTAAAACG 58.510 47.619 0.00 0.00 0.00 3.60
3682 6721 7.222872 CCAAAGATAGTAAGATCAGCCTTGAT 58.777 38.462 0.00 0.00 46.61 2.57
3721 6760 4.422214 GCCACGAGGTAAGCATCTAGCA 62.422 54.545 0.00 0.00 41.24 3.49
3772 6813 2.270352 TCAACACCACCATCAACTCC 57.730 50.000 0.00 0.00 0.00 3.85
3773 6814 4.037923 ACAAATCAACACCACCATCAACTC 59.962 41.667 0.00 0.00 0.00 3.01
3774 6815 3.960102 ACAAATCAACACCACCATCAACT 59.040 39.130 0.00 0.00 0.00 3.16
3775 6816 4.320608 ACAAATCAACACCACCATCAAC 57.679 40.909 0.00 0.00 0.00 3.18
3776 6817 5.350504 AAACAAATCAACACCACCATCAA 57.649 34.783 0.00 0.00 0.00 2.57
4063 8518 5.913514 GCCTTTTTCGGTAAGAGAAGAAAAC 59.086 40.000 2.25 0.00 40.76 2.43
4065 8520 5.374071 AGCCTTTTTCGGTAAGAGAAGAAA 58.626 37.500 0.00 0.00 0.00 2.52
4066 8521 4.969484 AGCCTTTTTCGGTAAGAGAAGAA 58.031 39.130 0.00 0.00 0.00 2.52
4148 8604 1.804748 TGTGTGTGTGCGTTTGTGTTA 59.195 42.857 0.00 0.00 0.00 2.41
4196 8654 0.035317 CTAGGGAGTGTGTTGCTGCA 59.965 55.000 0.00 0.00 0.00 4.41
4253 8711 1.627550 GGCTTCACTTCTTCGCGGTC 61.628 60.000 6.13 0.00 0.00 4.79
4303 8764 4.072131 GTGTTGTATCCTTCTTGAAGGCA 58.928 43.478 21.16 12.59 39.80 4.75
4321 8782 4.178169 TGGTGGCGTTCCGGTGTT 62.178 61.111 0.00 0.00 34.14 3.32
4335 8796 2.656069 CCTTGGATCGGACGGTGGT 61.656 63.158 0.00 0.00 0.00 4.16
4342 8803 4.101119 GGAAACTCTAATCCTTGGATCGGA 59.899 45.833 2.27 4.01 32.75 4.55
4356 8817 1.628846 GTTGCTCCAGGGGAAACTCTA 59.371 52.381 2.25 0.00 41.55 2.43
4404 8865 1.208293 GATCGCTCCCTTCTTGAAGGT 59.792 52.381 23.12 7.87 38.28 3.50
4662 9124 4.176752 GGCCGATCCTTTCCGCCT 62.177 66.667 0.00 0.00 43.18 5.52


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

AutoCloner maintained by Alex Coulton.