Multiple sequence alignment - TraesCS2D01G161200

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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 TraesCS2D01G161200 chr2D 100.000 3231 0 0 1 3231 106149731 106146501 0.000000e+00 5967.0
1 TraesCS2D01G161200 chr2D 75.071 702 123 28 1 663 365373414 365372726 2.450000e-71 279.0
2 TraesCS2D01G161200 chr2D 96.364 55 2 0 2623 2677 106147057 106147003 1.230000e-14 91.6
3 TraesCS2D01G161200 chr2D 96.364 55 2 0 2675 2729 106147109 106147055 1.230000e-14 91.6
4 TraesCS2D01G161200 chr2A 89.210 1659 77 39 843 2450 102406205 102404598 0.000000e+00 1978.0
5 TraesCS2D01G161200 chr2A 94.840 562 22 2 2675 3230 102402795 102402235 0.000000e+00 870.0
6 TraesCS2D01G161200 chr2A 80.600 933 85 35 1 847 102407438 102406516 1.640000e-177 632.0
7 TraesCS2D01G161200 chr2A 91.327 196 11 5 2484 2677 102402932 102402741 2.470000e-66 263.0
8 TraesCS2D01G161200 chr2A 87.770 139 15 2 2497 2633 524590862 524591000 9.280000e-36 161.0
9 TraesCS2D01G161200 chr2A 98.000 50 0 1 937 986 102407693 102407645 5.740000e-13 86.1
10 TraesCS2D01G161200 chr2B 89.928 1529 71 30 932 2400 154840375 154838870 0.000000e+00 1893.0
11 TraesCS2D01G161200 chr5D 77.674 645 81 28 1 594 449947077 449947709 5.170000e-88 335.0
12 TraesCS2D01G161200 chr5D 79.512 410 57 18 210 594 40929315 40929722 1.910000e-67 267.0
13 TraesCS2D01G161200 chr5D 84.112 214 21 8 462 666 20758935 20758726 9.150000e-46 195.0
14 TraesCS2D01G161200 chr6D 78.238 579 84 27 1 547 84289173 84289741 1.860000e-87 333.0
15 TraesCS2D01G161200 chr6A 78.209 592 74 23 2 543 617062208 617061622 8.640000e-86 327.0
16 TraesCS2D01G161200 chr5B 76.824 699 89 41 2 664 710729700 710729039 3.110000e-85 326.0
17 TraesCS2D01G161200 chr5B 76.748 658 83 38 1 594 322558832 322558181 1.460000e-78 303.0
18 TraesCS2D01G161200 chr3B 77.245 646 88 35 1 593 433686359 433686998 1.120000e-84 324.0
19 TraesCS2D01G161200 chr3B 80.220 455 54 21 170 594 292025099 292024651 3.130000e-80 309.0
20 TraesCS2D01G161200 chr3D 75.589 721 110 35 2 666 580329066 580329776 2.440000e-76 296.0
21 TraesCS2D01G161200 chr5A 81.288 326 41 12 367 678 536216329 536216648 2.490000e-61 246.0
22 TraesCS2D01G161200 chr7A 75.686 547 72 31 2 494 903959 903420 1.950000e-52 217.0
23 TraesCS2D01G161200 chr7A 75.641 546 72 34 16 510 54554035 54554570 7.020000e-52 215.0
24 TraesCS2D01G161200 chr7B 74.603 567 83 35 2 531 619142531 619143073 3.290000e-45 193.0
25 TraesCS2D01G161200 chr7B 83.732 209 29 5 387 593 748889399 748889604 3.290000e-45 193.0
26 TraesCS2D01G161200 chr7B 86.131 137 18 1 2497 2632 164582263 164582399 2.600000e-31 147.0
27 TraesCS2D01G161200 chr7B 82.209 163 24 3 2475 2632 513694578 513694416 5.620000e-28 135.0
28 TraesCS2D01G161200 chr6B 81.048 248 31 7 429 664 560655484 560655727 1.980000e-42 183.0
29 TraesCS2D01G161200 chr4A 87.970 133 15 1 2500 2632 42114849 42114718 4.320000e-34 156.0
30 TraesCS2D01G161200 chr1B 86.765 136 17 1 2497 2632 623238451 623238317 2.010000e-32 150.0


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 TraesCS2D01G161200 chr2D 106146501 106149731 3230 True 2050.066667 5967 97.5760 1 3231 3 chr2D.!!$R2 3230
1 TraesCS2D01G161200 chr2D 365372726 365373414 688 True 279.000000 279 75.0710 1 663 1 chr2D.!!$R1 662
2 TraesCS2D01G161200 chr2A 102402235 102407693 5458 True 765.820000 1978 90.7954 1 3230 5 chr2A.!!$R1 3229
3 TraesCS2D01G161200 chr2B 154838870 154840375 1505 True 1893.000000 1893 89.9280 932 2400 1 chr2B.!!$R1 1468
4 TraesCS2D01G161200 chr5D 449947077 449947709 632 False 335.000000 335 77.6740 1 594 1 chr5D.!!$F2 593
5 TraesCS2D01G161200 chr6D 84289173 84289741 568 False 333.000000 333 78.2380 1 547 1 chr6D.!!$F1 546
6 TraesCS2D01G161200 chr6A 617061622 617062208 586 True 327.000000 327 78.2090 2 543 1 chr6A.!!$R1 541
7 TraesCS2D01G161200 chr5B 710729039 710729700 661 True 326.000000 326 76.8240 2 664 1 chr5B.!!$R2 662
8 TraesCS2D01G161200 chr5B 322558181 322558832 651 True 303.000000 303 76.7480 1 594 1 chr5B.!!$R1 593
9 TraesCS2D01G161200 chr3B 433686359 433686998 639 False 324.000000 324 77.2450 1 593 1 chr3B.!!$F1 592
10 TraesCS2D01G161200 chr3D 580329066 580329776 710 False 296.000000 296 75.5890 2 666 1 chr3D.!!$F1 664
11 TraesCS2D01G161200 chr7A 903420 903959 539 True 217.000000 217 75.6860 2 494 1 chr7A.!!$R1 492
12 TraesCS2D01G161200 chr7A 54554035 54554570 535 False 215.000000 215 75.6410 16 510 1 chr7A.!!$F1 494

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
866 1622 0.106519 GGTGGTCCCATCATTCCAGG 60.107 60.0 0.0 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2584 5058 0.39382 AGTCTAACCCGGAAAACGCA 59.606 50.0 0.73 0.0 42.52 5.24 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
379 740 5.655893 AAATGTTTGCCGATTCACAAAAG 57.344 34.783 4.04 0.00 37.50 2.27
381 742 3.443037 TGTTTGCCGATTCACAAAAGTG 58.557 40.909 4.04 0.00 37.50 3.16
386 751 5.250235 TGCCGATTCACAAAAGTGTTTAA 57.750 34.783 0.00 0.00 35.07 1.52
619 1044 4.248859 GTCATGACCATCGGAGATTATGG 58.751 47.826 15.31 0.00 46.76 2.74
641 1066 5.653330 TGGTTATTATTTTTCTCCCGTTCCC 59.347 40.000 0.00 0.00 0.00 3.97
707 1145 4.172041 TCTTAAGGTCATCTCCCAGGGATA 59.828 45.833 9.31 1.17 0.00 2.59
713 1151 2.965831 TCATCTCCCAGGGATAGAAACG 59.034 50.000 9.31 0.00 0.00 3.60
715 1153 2.385803 TCTCCCAGGGATAGAAACGAC 58.614 52.381 9.31 0.00 0.00 4.34
716 1154 2.108168 CTCCCAGGGATAGAAACGACA 58.892 52.381 9.31 0.00 0.00 4.35
718 1156 2.434336 TCCCAGGGATAGAAACGACATG 59.566 50.000 3.01 0.00 0.00 3.21
733 1171 2.596862 CGACATGCGTTCGTTCATAAGA 59.403 45.455 0.00 0.00 34.64 2.10
747 1185 2.820197 TCATAAGAGCGAGTGTCTGTGT 59.180 45.455 0.00 0.00 0.00 3.72
752 1190 2.095008 AGAGCGAGTGTCTGTGTGTATG 60.095 50.000 0.00 0.00 0.00 2.39
756 1194 3.638484 CGAGTGTCTGTGTGTATGTGAA 58.362 45.455 0.00 0.00 0.00 3.18
757 1195 4.048504 CGAGTGTCTGTGTGTATGTGAAA 58.951 43.478 0.00 0.00 0.00 2.69
764 1202 6.019398 TGTCTGTGTGTATGTGAAAGTTTACG 60.019 38.462 0.00 0.00 0.00 3.18
768 1206 6.962116 TGTGTGTATGTGAAAGTTTACGTTTG 59.038 34.615 0.00 0.00 0.00 2.93
815 1254 9.554724 TTCATAAAAATCGTTAGACTGCATTTC 57.445 29.630 0.00 0.00 0.00 2.17
824 1263 6.206634 TCGTTAGACTGCATTTCCTGAAAAAT 59.793 34.615 0.00 0.00 33.56 1.82
825 1264 7.389330 TCGTTAGACTGCATTTCCTGAAAAATA 59.611 33.333 0.00 0.00 33.56 1.40
826 1265 8.184192 CGTTAGACTGCATTTCCTGAAAAATAT 58.816 33.333 0.00 0.00 33.56 1.28
827 1266 9.508567 GTTAGACTGCATTTCCTGAAAAATATC 57.491 33.333 0.00 0.00 33.56 1.63
832 1272 7.820872 ACTGCATTTCCTGAAAAATATCCAAAG 59.179 33.333 0.00 0.00 33.56 2.77
844 1284 2.380064 ATCCAAAGCAAACACCCAGA 57.620 45.000 0.00 0.00 0.00 3.86
847 1287 2.430332 TCCAAAGCAAACACCCAGAAAG 59.570 45.455 0.00 0.00 0.00 2.62
848 1288 2.483538 CCAAAGCAAACACCCAGAAAGG 60.484 50.000 0.00 0.00 37.03 3.11
849 1289 2.159179 AAGCAAACACCCAGAAAGGT 57.841 45.000 0.00 0.00 42.40 3.50
856 1612 1.386772 ACCCAGAAAGGTGGTCCCA 60.387 57.895 0.00 0.00 39.24 4.37
863 1619 2.024941 AGAAAGGTGGTCCCATCATTCC 60.025 50.000 10.16 0.00 35.95 3.01
866 1622 0.106519 GGTGGTCCCATCATTCCAGG 60.107 60.000 0.00 0.00 0.00 4.45
894 1650 1.447643 CCCGATCAGGATGTCACCC 59.552 63.158 5.32 0.00 45.00 4.61
895 1651 1.337384 CCCGATCAGGATGTCACCCA 61.337 60.000 5.32 0.00 45.00 4.51
896 1652 0.179073 CCGATCAGGATGTCACCCAC 60.179 60.000 0.00 0.00 45.00 4.61
897 1653 0.179073 CGATCAGGATGTCACCCACC 60.179 60.000 0.00 0.00 37.40 4.61
898 1654 0.181350 GATCAGGATGTCACCCACCC 59.819 60.000 0.00 0.00 37.40 4.61
925 1681 2.125106 GCCACCGCTTGTCCCTAG 60.125 66.667 0.00 0.00 0.00 3.02
926 1682 2.955881 GCCACCGCTTGTCCCTAGT 61.956 63.158 0.00 0.00 0.00 2.57
927 1683 1.218316 CCACCGCTTGTCCCTAGTC 59.782 63.158 0.00 0.00 0.00 2.59
928 1684 1.218316 CACCGCTTGTCCCTAGTCC 59.782 63.158 0.00 0.00 0.00 3.85
929 1685 2.348888 ACCGCTTGTCCCTAGTCCG 61.349 63.158 0.00 0.00 0.00 4.79
930 1686 2.494918 CGCTTGTCCCTAGTCCGG 59.505 66.667 0.00 0.00 0.00 5.14
999 1755 3.414700 GTGCCGACCTCAGCAACG 61.415 66.667 0.00 0.00 41.48 4.10
1000 1756 3.611674 TGCCGACCTCAGCAACGA 61.612 61.111 0.00 0.00 35.69 3.85
1007 1763 2.401766 CCTCAGCAACGATGGGCAC 61.402 63.158 0.00 0.00 0.00 5.01
1301 2057 4.862823 GCCCCTCTACGAGCCCCT 62.863 72.222 0.00 0.00 0.00 4.79
1315 2071 3.006728 CCCTGGGGGTAAGCGTCA 61.007 66.667 4.27 0.00 38.25 4.35
1335 2091 0.519519 GACATCGATCGATCTCCGCT 59.480 55.000 27.20 3.21 38.37 5.52
1341 2097 0.105039 GATCGATCTCCGCTTTGGGT 59.895 55.000 18.29 0.00 38.76 4.51
1391 2147 7.250445 TCGAATTGATTGATTGATTCATCGT 57.750 32.000 0.00 0.00 33.34 3.73
1599 2360 0.940991 TGCGGCTGATCGATCGATTG 60.941 55.000 29.89 24.45 34.60 2.67
1600 2361 0.941463 GCGGCTGATCGATCGATTGT 60.941 55.000 29.89 10.93 34.60 2.71
1601 2362 1.056103 CGGCTGATCGATCGATTGTC 58.944 55.000 29.89 24.00 34.60 3.18
1602 2363 1.335415 CGGCTGATCGATCGATTGTCT 60.335 52.381 29.89 10.11 34.60 3.41
1733 2494 1.430632 GACCTCCGAATCGTGCGTA 59.569 57.895 0.82 0.00 0.00 4.42
1755 2539 6.377429 CGTATACAGCCCTCCAATTCTATCTA 59.623 42.308 3.32 0.00 0.00 1.98
1901 2685 2.439701 CTCTACGCGGACAGGGGA 60.440 66.667 12.47 0.00 37.07 4.81
2027 2838 1.066605 GAGTCGGTAAGCATCGCCTTA 59.933 52.381 0.00 0.00 0.00 2.69
2054 2865 7.759489 TTGTGCCTAACAAAATCTCTGTTAT 57.241 32.000 0.00 0.00 45.85 1.89
2337 3176 4.054780 TGCATTCCCGTGTATAGAGTTC 57.945 45.455 0.00 0.00 0.00 3.01
2346 3185 4.904724 CCGTGTATAGAGTTCGATTCGAAG 59.095 45.833 21.05 6.14 46.54 3.79
2363 3202 2.418334 CGAAGTACCTGTAGGCCCTTTC 60.418 54.545 0.00 0.00 39.32 2.62
2423 3263 6.531021 TCCTTTAAAAGATGTCCGACTTTCT 58.469 36.000 0.00 0.00 35.66 2.52
2426 3266 3.662247 AAAGATGTCCGACTTTCTCGT 57.338 42.857 0.00 0.00 41.18 4.18
2450 3292 3.605634 CGATGGACTAACATGACCCAAA 58.394 45.455 0.00 0.00 0.00 3.28
2451 3293 4.199310 CGATGGACTAACATGACCCAAAT 58.801 43.478 0.00 0.00 0.00 2.32
2455 3297 3.875134 GGACTAACATGACCCAAATACGG 59.125 47.826 0.00 0.00 0.00 4.02
2465 3307 1.768870 CCCAAATACGGGGTCTGATCT 59.231 52.381 0.00 0.00 43.21 2.75
2469 3311 5.247564 CCCAAATACGGGGTCTGATCTTATA 59.752 44.000 0.00 0.00 43.21 0.98
2470 3312 6.164176 CCAAATACGGGGTCTGATCTTATAC 58.836 44.000 0.00 0.00 0.00 1.47
2472 3314 3.219176 ACGGGGTCTGATCTTATACGA 57.781 47.619 0.00 0.00 0.00 3.43
2474 3316 2.488545 CGGGGTCTGATCTTATACGAGG 59.511 54.545 0.00 0.00 0.00 4.63
2476 3318 3.506844 GGGGTCTGATCTTATACGAGGTC 59.493 52.174 0.00 0.00 0.00 3.85
2477 3319 3.506844 GGGTCTGATCTTATACGAGGTCC 59.493 52.174 0.00 0.00 0.00 4.46
2478 3320 4.142790 GGTCTGATCTTATACGAGGTCCA 58.857 47.826 0.00 0.00 0.00 4.02
2479 3321 4.767928 GGTCTGATCTTATACGAGGTCCAT 59.232 45.833 0.00 0.00 0.00 3.41
2480 3322 5.336055 GGTCTGATCTTATACGAGGTCCATG 60.336 48.000 0.00 0.00 0.00 3.66
2481 3323 5.473846 GTCTGATCTTATACGAGGTCCATGA 59.526 44.000 0.00 0.00 0.00 3.07
2493 4967 1.017387 GTCCATGATGTTTCTCCCGC 58.983 55.000 0.00 0.00 0.00 6.13
2501 4975 2.981400 TGTTTCTCCCGCGATTTTTC 57.019 45.000 8.23 0.00 0.00 2.29
2504 4978 4.066490 TGTTTCTCCCGCGATTTTTCTAA 58.934 39.130 8.23 0.00 0.00 2.10
2505 4979 4.515944 TGTTTCTCCCGCGATTTTTCTAAA 59.484 37.500 8.23 0.00 0.00 1.85
2514 4988 8.347035 TCCCGCGATTTTTCTAAATTTTATAGG 58.653 33.333 8.23 0.00 34.16 2.57
2541 5015 2.993008 GGGGTCTGATCTGCAGCA 59.007 61.111 9.47 0.70 44.52 4.41
2542 5016 1.530771 GGGGTCTGATCTGCAGCAT 59.469 57.895 9.47 3.41 44.52 3.79
2574 5048 1.015109 CGCAAATCTGATCTGCAGCT 58.985 50.000 15.57 0.00 44.52 4.24
2584 5058 5.982356 TCTGATCTGCAGCTAACTGTAAAT 58.018 37.500 9.47 0.00 46.30 1.40
2586 5060 4.333649 TGATCTGCAGCTAACTGTAAATGC 59.666 41.667 9.47 0.00 46.30 3.56
2588 5062 2.416547 CTGCAGCTAACTGTAAATGCGT 59.583 45.455 0.00 0.00 46.30 5.24
2592 5066 4.320953 GCAGCTAACTGTAAATGCGTTTTC 59.679 41.667 9.61 5.08 46.30 2.29
2593 5067 4.851558 CAGCTAACTGTAAATGCGTTTTCC 59.148 41.667 9.61 1.70 39.22 3.13
2601 5075 2.188062 AATGCGTTTTCCGGGTTAGA 57.812 45.000 0.00 0.00 36.94 2.10
2611 5085 2.524306 TCCGGGTTAGACTTTTACGGA 58.476 47.619 0.00 0.00 45.52 4.69
2614 5088 3.306294 CCGGGTTAGACTTTTACGGAGTT 60.306 47.826 0.00 0.00 37.78 3.01
2628 5102 2.234908 ACGGAGTTTGCTAGAGATGCTT 59.765 45.455 0.00 0.00 37.78 3.91
2642 5116 5.831997 AGAGATGCTTTAAACCAAACACAC 58.168 37.500 0.00 0.00 0.00 3.82
2643 5117 4.944048 AGATGCTTTAAACCAAACACACC 58.056 39.130 0.00 0.00 0.00 4.16
2644 5118 3.528597 TGCTTTAAACCAAACACACCC 57.471 42.857 0.00 0.00 0.00 4.61
2645 5119 3.100671 TGCTTTAAACCAAACACACCCT 58.899 40.909 0.00 0.00 0.00 4.34
2646 5120 3.118956 TGCTTTAAACCAAACACACCCTG 60.119 43.478 0.00 0.00 0.00 4.45
2647 5121 3.131400 GCTTTAAACCAAACACACCCTGA 59.869 43.478 0.00 0.00 0.00 3.86
2648 5122 4.382147 GCTTTAAACCAAACACACCCTGAA 60.382 41.667 0.00 0.00 0.00 3.02
2649 5123 5.725362 CTTTAAACCAAACACACCCTGAAA 58.275 37.500 0.00 0.00 0.00 2.69
2650 5124 3.603158 AAACCAAACACACCCTGAAAC 57.397 42.857 0.00 0.00 0.00 2.78
2651 5125 2.525105 ACCAAACACACCCTGAAACT 57.475 45.000 0.00 0.00 0.00 2.66
2652 5126 2.815158 ACCAAACACACCCTGAAACTT 58.185 42.857 0.00 0.00 0.00 2.66
2653 5127 3.169908 ACCAAACACACCCTGAAACTTT 58.830 40.909 0.00 0.00 0.00 2.66
2654 5128 3.194755 ACCAAACACACCCTGAAACTTTC 59.805 43.478 0.00 0.00 0.00 2.62
2655 5129 3.194542 CCAAACACACCCTGAAACTTTCA 59.805 43.478 4.16 4.16 38.17 2.69
2668 5142 6.169557 TGAAACTTTCAGGTAAGCTACTCA 57.830 37.500 0.00 0.00 34.08 3.41
2669 5143 6.588204 TGAAACTTTCAGGTAAGCTACTCAA 58.412 36.000 0.00 0.00 34.08 3.02
2670 5144 6.706270 TGAAACTTTCAGGTAAGCTACTCAAG 59.294 38.462 0.00 0.00 34.08 3.02
2671 5145 6.420913 AACTTTCAGGTAAGCTACTCAAGA 57.579 37.500 0.00 0.00 0.00 3.02
2672 5146 6.420913 ACTTTCAGGTAAGCTACTCAAGAA 57.579 37.500 0.00 0.00 0.00 2.52
2673 5147 6.459923 ACTTTCAGGTAAGCTACTCAAGAAG 58.540 40.000 0.00 0.00 0.00 2.85
2674 5148 5.407407 TTCAGGTAAGCTACTCAAGAAGG 57.593 43.478 0.00 0.00 0.00 3.46
2675 5149 4.673968 TCAGGTAAGCTACTCAAGAAGGA 58.326 43.478 0.00 0.00 0.00 3.36
2676 5150 5.273208 TCAGGTAAGCTACTCAAGAAGGAT 58.727 41.667 0.00 0.00 0.00 3.24
2677 5151 5.127845 TCAGGTAAGCTACTCAAGAAGGATG 59.872 44.000 0.00 0.00 0.00 3.51
2678 5152 4.123506 GGTAAGCTACTCAAGAAGGATGC 58.876 47.826 0.00 0.00 0.00 3.91
2679 5153 4.141824 GGTAAGCTACTCAAGAAGGATGCT 60.142 45.833 0.00 0.00 32.75 3.79
2680 5154 3.817709 AGCTACTCAAGAAGGATGCTC 57.182 47.619 0.00 0.00 0.00 4.26
2681 5155 3.373830 AGCTACTCAAGAAGGATGCTCT 58.626 45.455 0.00 0.00 0.00 4.09
2682 5156 4.541705 AGCTACTCAAGAAGGATGCTCTA 58.458 43.478 0.00 0.00 0.00 2.43
2683 5157 4.959210 AGCTACTCAAGAAGGATGCTCTAA 59.041 41.667 0.00 0.00 0.00 2.10
2684 5158 5.423610 AGCTACTCAAGAAGGATGCTCTAAA 59.576 40.000 0.00 0.00 0.00 1.85
2685 5159 5.522097 GCTACTCAAGAAGGATGCTCTAAAC 59.478 44.000 0.00 0.00 0.00 2.01
2686 5160 5.753721 ACTCAAGAAGGATGCTCTAAACT 57.246 39.130 0.00 0.00 0.00 2.66
2687 5161 6.859112 ACTCAAGAAGGATGCTCTAAACTA 57.141 37.500 0.00 0.00 0.00 2.24
2688 5162 7.246171 ACTCAAGAAGGATGCTCTAAACTAA 57.754 36.000 0.00 0.00 0.00 2.24
2689 5163 7.680730 ACTCAAGAAGGATGCTCTAAACTAAA 58.319 34.615 0.00 0.00 0.00 1.85
2690 5164 7.604545 ACTCAAGAAGGATGCTCTAAACTAAAC 59.395 37.037 0.00 0.00 0.00 2.01
2691 5165 7.450074 TCAAGAAGGATGCTCTAAACTAAACA 58.550 34.615 0.00 0.00 0.00 2.83
2692 5166 7.387948 TCAAGAAGGATGCTCTAAACTAAACAC 59.612 37.037 0.00 0.00 0.00 3.32
2693 5167 6.769512 AGAAGGATGCTCTAAACTAAACACA 58.230 36.000 0.00 0.00 0.00 3.72
2757 5231 4.579340 TGTGGCGTGATTTGTTACCTTTTA 59.421 37.500 0.00 0.00 0.00 1.52
2799 5279 7.954788 TTGCAAATAATAGTTTTGTTCCACC 57.045 32.000 0.00 0.00 36.63 4.61
2884 5364 9.981114 AATTTTTCCTCTGAACGAAACATAATT 57.019 25.926 0.00 2.59 0.00 1.40
2947 5427 6.403866 AAGCACCATTGTTAAGTCATTCAA 57.596 33.333 0.00 0.00 0.00 2.69
2955 5435 9.426837 CCATTGTTAAGTCATTCAATTTGTCAT 57.573 29.630 0.00 0.00 0.00 3.06
2983 5463 6.131264 TCTGATTGCTTTCCATACATCCAAT 58.869 36.000 0.00 0.00 0.00 3.16
2984 5464 6.608405 TCTGATTGCTTTCCATACATCCAATT 59.392 34.615 0.00 0.00 0.00 2.32
2986 5466 7.622713 TGATTGCTTTCCATACATCCAATTTT 58.377 30.769 0.00 0.00 0.00 1.82
2987 5467 8.102047 TGATTGCTTTCCATACATCCAATTTTT 58.898 29.630 0.00 0.00 0.00 1.94
3182 5662 9.762381 ACTTCAAAGACCCCAAAATATATGTTA 57.238 29.630 0.00 0.00 0.00 2.41
3192 5672 8.923270 CCCCAAAATATATGTTATGTGTTCCTT 58.077 33.333 0.00 0.00 0.00 3.36
3224 5704 7.165485 TGGCTCTTGTACAAAGCTTTAATAGA 58.835 34.615 26.95 9.37 36.29 1.98
3230 5710 9.394477 CTTGTACAAAGCTTTAATAGAAACACC 57.606 33.333 12.25 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
250 571 9.276590 TGAATCAGCGAATACTTTATGAATGAT 57.723 29.630 0.00 0.00 0.00 2.45
318 654 7.497249 TGGAACAAATTTTGGAATTCACGAATT 59.503 29.630 13.42 4.71 38.60 2.17
572 989 3.189495 AGCATCACCGAGATACACTATCG 59.811 47.826 0.00 0.00 40.12 2.92
619 1044 6.558009 GTGGGAACGGGAGAAAAATAATAAC 58.442 40.000 0.00 0.00 0.00 1.89
625 1050 1.530323 CGTGGGAACGGGAGAAAAAT 58.470 50.000 0.00 0.00 0.00 1.82
639 1064 0.179166 CAAAATGATCCGTGCGTGGG 60.179 55.000 0.00 0.00 0.00 4.61
641 1066 0.168788 AGCAAAATGATCCGTGCGTG 59.831 50.000 0.00 0.00 41.90 5.34
680 1108 5.549619 CCCTGGGAGATGACCTTAAGATTAT 59.450 44.000 7.01 0.00 0.00 1.28
691 1119 3.243907 CGTTTCTATCCCTGGGAGATGAC 60.244 52.174 21.99 13.34 34.05 3.06
713 1151 3.542291 GCTCTTATGAACGAACGCATGTC 60.542 47.826 0.00 0.00 0.00 3.06
715 1153 2.595188 CGCTCTTATGAACGAACGCATG 60.595 50.000 0.00 0.00 34.07 4.06
716 1154 1.588404 CGCTCTTATGAACGAACGCAT 59.412 47.619 0.00 0.00 34.07 4.73
718 1156 1.253034 CTCGCTCTTATGAACGAACGC 59.747 52.381 5.74 0.00 39.78 4.84
721 1159 3.190744 AGACACTCGCTCTTATGAACGAA 59.809 43.478 5.74 0.00 39.78 3.85
722 1160 2.747989 AGACACTCGCTCTTATGAACGA 59.252 45.455 4.34 4.34 38.30 3.85
733 1171 1.613925 ACATACACACAGACACTCGCT 59.386 47.619 0.00 0.00 0.00 4.93
743 1181 6.665474 AACGTAAACTTTCACATACACACA 57.335 33.333 0.00 0.00 0.00 3.72
744 1182 6.962678 ACAAACGTAAACTTTCACATACACAC 59.037 34.615 0.00 0.00 0.00 3.82
747 1185 9.653067 CAATACAAACGTAAACTTTCACATACA 57.347 29.630 0.00 0.00 0.00 2.29
752 1190 7.958112 ACACAATACAAACGTAAACTTTCAC 57.042 32.000 0.00 0.00 0.00 3.18
791 1230 8.184192 AGGAAATGCAGTCTAACGATTTTTATG 58.816 33.333 0.00 0.00 0.00 1.90
792 1231 8.184192 CAGGAAATGCAGTCTAACGATTTTTAT 58.816 33.333 0.00 0.00 0.00 1.40
815 1254 6.147656 GGTGTTTGCTTTGGATATTTTTCAGG 59.852 38.462 0.00 0.00 0.00 3.86
824 1263 3.517296 TCTGGGTGTTTGCTTTGGATA 57.483 42.857 0.00 0.00 0.00 2.59
825 1264 2.380064 TCTGGGTGTTTGCTTTGGAT 57.620 45.000 0.00 0.00 0.00 3.41
826 1265 2.151502 TTCTGGGTGTTTGCTTTGGA 57.848 45.000 0.00 0.00 0.00 3.53
827 1266 2.483538 CCTTTCTGGGTGTTTGCTTTGG 60.484 50.000 0.00 0.00 0.00 3.28
844 1284 1.715931 TGGAATGATGGGACCACCTTT 59.284 47.619 0.00 0.00 41.11 3.11
847 1287 0.106519 CCTGGAATGATGGGACCACC 60.107 60.000 0.00 0.00 40.81 4.61
848 1288 0.625849 ACCTGGAATGATGGGACCAC 59.374 55.000 0.00 0.00 0.00 4.16
849 1289 1.284785 GAACCTGGAATGATGGGACCA 59.715 52.381 0.00 0.00 0.00 4.02
850 1290 1.410224 GGAACCTGGAATGATGGGACC 60.410 57.143 0.00 0.00 0.00 4.46
851 1291 1.284785 TGGAACCTGGAATGATGGGAC 59.715 52.381 0.00 0.00 0.00 4.46
856 1612 1.341383 GCCACTGGAACCTGGAATGAT 60.341 52.381 0.00 0.00 0.00 2.45
863 1619 2.876368 GATCGGGCCACTGGAACCTG 62.876 65.000 4.39 0.00 0.00 4.00
866 1622 1.450312 CTGATCGGGCCACTGGAAC 60.450 63.158 4.39 0.00 0.00 3.62
925 1681 4.266962 GTAGGGGGACTACCGGAC 57.733 66.667 9.46 0.00 45.15 4.79
1139 1895 1.446966 GAGCAGACCAGCGTTCTCC 60.447 63.158 0.00 0.00 40.15 3.71
1301 2057 0.907704 ATGTCTGACGCTTACCCCCA 60.908 55.000 2.98 0.00 0.00 4.96
1314 2070 2.239751 CGGAGATCGATCGATGTCTG 57.760 55.000 38.22 36.88 42.40 3.51
1315 2071 0.519519 GCGGAGATCGATCGATGTCT 59.480 55.000 38.22 29.68 42.40 3.41
1335 2091 3.891977 TCATCGAATTCCAAACACCCAAA 59.108 39.130 0.00 0.00 0.00 3.28
1341 2097 5.389778 CGTGATTTCATCGAATTCCAAACA 58.610 37.500 0.00 0.00 0.00 2.83
1558 2319 3.450115 CACCGTCGTCCTCCCTCC 61.450 72.222 0.00 0.00 0.00 4.30
1559 2320 3.450115 CCACCGTCGTCCTCCCTC 61.450 72.222 0.00 0.00 0.00 4.30
1599 2360 1.936547 CCTCCTGCGCAAGAAATAGAC 59.063 52.381 13.05 0.00 43.02 2.59
1600 2361 1.831106 TCCTCCTGCGCAAGAAATAGA 59.169 47.619 13.05 2.57 43.02 1.98
1601 2362 2.208431 CTCCTCCTGCGCAAGAAATAG 58.792 52.381 13.05 4.57 43.02 1.73
1602 2363 1.555075 ACTCCTCCTGCGCAAGAAATA 59.445 47.619 13.05 0.00 43.02 1.40
1733 2494 9.153479 GATATAGATAGAATTGGAGGGCTGTAT 57.847 37.037 0.00 0.00 0.00 2.29
1886 2670 3.064987 CTGTCCCCTGTCCGCGTAG 62.065 68.421 4.92 0.00 0.00 3.51
2027 2838 5.536161 ACAGAGATTTTGTTAGGCACAACAT 59.464 36.000 5.65 0.00 45.54 2.71
2053 2864 3.176728 TCTCTCGGCGAGAACAGAT 57.823 52.632 35.75 0.00 45.55 2.90
2054 2865 4.716003 TCTCTCGGCGAGAACAGA 57.284 55.556 35.75 27.29 45.55 3.41
2215 3035 2.261215 CCTTCAGGCTTTGCTGTCC 58.739 57.895 0.00 0.00 0.00 4.02
2337 3176 2.543238 GGCCTACAGGTACTTCGAATCG 60.543 54.545 0.00 0.00 34.60 3.34
2346 3185 2.168728 CAGAGAAAGGGCCTACAGGTAC 59.831 54.545 6.41 0.00 37.57 3.34
2426 3266 1.134521 GGTCATGTTAGTCCATCGGCA 60.135 52.381 0.00 0.00 0.00 5.69
2450 3292 4.914983 TCGTATAAGATCAGACCCCGTAT 58.085 43.478 0.00 0.00 0.00 3.06
2451 3293 4.321718 CTCGTATAAGATCAGACCCCGTA 58.678 47.826 0.00 0.00 0.00 4.02
2455 3297 3.506844 GGACCTCGTATAAGATCAGACCC 59.493 52.174 0.00 0.00 0.00 4.46
2456 3298 4.142790 TGGACCTCGTATAAGATCAGACC 58.857 47.826 0.00 0.00 0.00 3.85
2457 3299 5.473846 TCATGGACCTCGTATAAGATCAGAC 59.526 44.000 0.00 0.00 0.00 3.51
2458 3300 5.631119 TCATGGACCTCGTATAAGATCAGA 58.369 41.667 0.00 0.00 0.00 3.27
2459 3301 5.966742 TCATGGACCTCGTATAAGATCAG 57.033 43.478 0.00 0.00 0.00 2.90
2460 3302 5.775195 ACATCATGGACCTCGTATAAGATCA 59.225 40.000 0.00 0.00 0.00 2.92
2461 3303 6.274157 ACATCATGGACCTCGTATAAGATC 57.726 41.667 0.00 0.00 0.00 2.75
2462 3304 6.672266 AACATCATGGACCTCGTATAAGAT 57.328 37.500 0.00 0.00 0.00 2.40
2463 3305 6.323996 AGAAACATCATGGACCTCGTATAAGA 59.676 38.462 0.00 0.00 0.00 2.10
2465 3307 6.462487 GGAGAAACATCATGGACCTCGTATAA 60.462 42.308 0.00 0.00 0.00 0.98
2469 3311 2.093447 GGAGAAACATCATGGACCTCGT 60.093 50.000 0.00 0.00 0.00 4.18
2470 3312 2.555199 GGAGAAACATCATGGACCTCG 58.445 52.381 0.00 0.00 0.00 4.63
2472 3314 1.210478 CGGGAGAAACATCATGGACCT 59.790 52.381 0.00 0.00 0.00 3.85
2474 3316 1.017387 GCGGGAGAAACATCATGGAC 58.983 55.000 0.00 0.00 0.00 4.02
2476 3318 0.461870 TCGCGGGAGAAACATCATGG 60.462 55.000 6.13 0.00 0.00 3.66
2477 3319 1.586422 ATCGCGGGAGAAACATCATG 58.414 50.000 6.13 0.00 0.00 3.07
2478 3320 2.332063 AATCGCGGGAGAAACATCAT 57.668 45.000 6.13 0.00 0.00 2.45
2479 3321 2.107950 AAATCGCGGGAGAAACATCA 57.892 45.000 6.13 0.00 0.00 3.07
2480 3322 3.127030 AGAAAAATCGCGGGAGAAACATC 59.873 43.478 6.13 1.93 0.00 3.06
2481 3323 3.081804 AGAAAAATCGCGGGAGAAACAT 58.918 40.909 6.13 0.00 0.00 2.71
2504 4978 8.887393 AGACCCCGTATATGAACCTATAAAATT 58.113 33.333 0.00 0.00 0.00 1.82
2505 4979 8.319146 CAGACCCCGTATATGAACCTATAAAAT 58.681 37.037 0.00 0.00 0.00 1.82
2514 4988 4.810790 CAGATCAGACCCCGTATATGAAC 58.189 47.826 0.00 0.00 0.00 3.18
2541 5015 0.745128 TTTGCGGGGCGAATTCGTAT 60.745 50.000 27.24 0.00 42.22 3.06
2542 5016 0.745128 ATTTGCGGGGCGAATTCGTA 60.745 50.000 27.24 0.00 39.34 3.43
2574 5048 3.188873 CCCGGAAAACGCATTTACAGTTA 59.811 43.478 0.73 0.00 42.52 2.24
2584 5058 0.393820 AGTCTAACCCGGAAAACGCA 59.606 50.000 0.73 0.00 42.52 5.24
2586 5060 4.376311 CGTAAAAGTCTAACCCGGAAAACG 60.376 45.833 0.73 0.00 43.80 3.60
2588 5062 4.064388 CCGTAAAAGTCTAACCCGGAAAA 58.936 43.478 0.73 0.00 36.12 2.29
2592 5066 2.232208 ACTCCGTAAAAGTCTAACCCGG 59.768 50.000 0.00 0.00 35.41 5.73
2593 5067 3.582714 ACTCCGTAAAAGTCTAACCCG 57.417 47.619 0.00 0.00 0.00 5.28
2601 5075 5.464030 TCTCTAGCAAACTCCGTAAAAGT 57.536 39.130 0.00 0.00 0.00 2.66
2611 5085 6.003950 TGGTTTAAAGCATCTCTAGCAAACT 58.996 36.000 15.83 0.00 0.00 2.66
2614 5088 6.264292 TGTTTGGTTTAAAGCATCTCTAGCAA 59.736 34.615 19.95 6.82 36.16 3.91
2628 5102 4.773149 AGTTTCAGGGTGTGTTTGGTTTAA 59.227 37.500 0.00 0.00 0.00 1.52
2645 5119 6.169557 TGAGTAGCTTACCTGAAAGTTTCA 57.830 37.500 17.16 17.16 38.17 2.69
2646 5120 6.929606 TCTTGAGTAGCTTACCTGAAAGTTTC 59.070 38.462 8.75 8.75 0.00 2.78
2647 5121 6.827727 TCTTGAGTAGCTTACCTGAAAGTTT 58.172 36.000 0.00 0.00 0.00 2.66
2648 5122 6.420913 TCTTGAGTAGCTTACCTGAAAGTT 57.579 37.500 0.00 0.00 0.00 2.66
2649 5123 6.420913 TTCTTGAGTAGCTTACCTGAAAGT 57.579 37.500 0.00 0.00 0.00 2.66
2650 5124 5.872070 CCTTCTTGAGTAGCTTACCTGAAAG 59.128 44.000 0.00 0.00 0.00 2.62
2651 5125 5.542635 TCCTTCTTGAGTAGCTTACCTGAAA 59.457 40.000 0.00 0.00 0.00 2.69
2652 5126 5.084519 TCCTTCTTGAGTAGCTTACCTGAA 58.915 41.667 0.00 0.00 0.00 3.02
2653 5127 4.673968 TCCTTCTTGAGTAGCTTACCTGA 58.326 43.478 0.00 0.00 0.00 3.86
2654 5128 5.355596 CATCCTTCTTGAGTAGCTTACCTG 58.644 45.833 0.00 0.00 0.00 4.00
2655 5129 4.141824 GCATCCTTCTTGAGTAGCTTACCT 60.142 45.833 0.00 0.00 0.00 3.08
2656 5130 4.123506 GCATCCTTCTTGAGTAGCTTACC 58.876 47.826 0.00 0.00 0.00 2.85
2657 5131 5.017294 AGCATCCTTCTTGAGTAGCTTAC 57.983 43.478 0.00 0.00 0.00 2.34
2658 5132 4.959210 AGAGCATCCTTCTTGAGTAGCTTA 59.041 41.667 0.00 0.00 33.66 3.09
2659 5133 3.774216 AGAGCATCCTTCTTGAGTAGCTT 59.226 43.478 0.00 0.00 33.66 3.74
2660 5134 3.373830 AGAGCATCCTTCTTGAGTAGCT 58.626 45.455 0.00 0.00 33.66 3.32
2661 5135 3.817709 AGAGCATCCTTCTTGAGTAGC 57.182 47.619 0.00 0.00 33.66 3.58
2662 5136 6.872920 AGTTTAGAGCATCCTTCTTGAGTAG 58.127 40.000 0.00 0.00 33.66 2.57
2663 5137 6.859112 AGTTTAGAGCATCCTTCTTGAGTA 57.141 37.500 0.00 0.00 33.66 2.59
2664 5138 5.753721 AGTTTAGAGCATCCTTCTTGAGT 57.246 39.130 0.00 0.00 33.66 3.41
2665 5139 7.604164 TGTTTAGTTTAGAGCATCCTTCTTGAG 59.396 37.037 0.00 0.00 33.66 3.02
2666 5140 7.387948 GTGTTTAGTTTAGAGCATCCTTCTTGA 59.612 37.037 0.00 0.00 33.66 3.02
2667 5141 7.173218 TGTGTTTAGTTTAGAGCATCCTTCTTG 59.827 37.037 0.00 0.00 33.66 3.02
2668 5142 7.173390 GTGTGTTTAGTTTAGAGCATCCTTCTT 59.827 37.037 0.00 0.00 33.66 2.52
2669 5143 6.651225 GTGTGTTTAGTTTAGAGCATCCTTCT 59.349 38.462 0.00 0.00 33.66 2.85
2670 5144 6.128254 GGTGTGTTTAGTTTAGAGCATCCTTC 60.128 42.308 0.00 0.00 33.66 3.46
2671 5145 5.705905 GGTGTGTTTAGTTTAGAGCATCCTT 59.294 40.000 0.00 0.00 33.66 3.36
2672 5146 5.246307 GGTGTGTTTAGTTTAGAGCATCCT 58.754 41.667 0.00 0.00 33.66 3.24
2673 5147 4.395231 GGGTGTGTTTAGTTTAGAGCATCC 59.605 45.833 0.00 0.00 33.66 3.51
2674 5148 5.122396 CAGGGTGTGTTTAGTTTAGAGCATC 59.878 44.000 0.00 0.00 0.00 3.91
2675 5149 5.003804 CAGGGTGTGTTTAGTTTAGAGCAT 58.996 41.667 0.00 0.00 0.00 3.79
2676 5150 4.101898 TCAGGGTGTGTTTAGTTTAGAGCA 59.898 41.667 0.00 0.00 0.00 4.26
2677 5151 4.638304 TCAGGGTGTGTTTAGTTTAGAGC 58.362 43.478 0.00 0.00 0.00 4.09
2678 5152 6.766467 AGTTTCAGGGTGTGTTTAGTTTAGAG 59.234 38.462 0.00 0.00 0.00 2.43
2679 5153 6.655930 AGTTTCAGGGTGTGTTTAGTTTAGA 58.344 36.000 0.00 0.00 0.00 2.10
2680 5154 6.937436 AGTTTCAGGGTGTGTTTAGTTTAG 57.063 37.500 0.00 0.00 0.00 1.85
2681 5155 7.393796 TGAAAGTTTCAGGGTGTGTTTAGTTTA 59.606 33.333 14.35 0.00 34.08 2.01
2682 5156 6.209788 TGAAAGTTTCAGGGTGTGTTTAGTTT 59.790 34.615 14.35 0.00 34.08 2.66
2683 5157 5.712917 TGAAAGTTTCAGGGTGTGTTTAGTT 59.287 36.000 14.35 0.00 34.08 2.24
2684 5158 5.258051 TGAAAGTTTCAGGGTGTGTTTAGT 58.742 37.500 14.35 0.00 34.08 2.24
2685 5159 5.828299 TGAAAGTTTCAGGGTGTGTTTAG 57.172 39.130 14.35 0.00 34.08 1.85
2799 5279 5.816919 ACAAGAACGAAACACCACAATAAG 58.183 37.500 0.00 0.00 0.00 1.73
2947 5427 7.177216 TGGAAAGCAATCAGAGTTATGACAAAT 59.823 33.333 0.00 0.00 30.46 2.32
2955 5435 6.767902 GGATGTATGGAAAGCAATCAGAGTTA 59.232 38.462 0.00 0.00 0.00 2.24
2988 5468 9.651913 GGTCCAGATTTATGAGCATTTTTAAAA 57.348 29.630 0.00 0.00 0.00 1.52
2989 5469 8.811017 TGGTCCAGATTTATGAGCATTTTTAAA 58.189 29.630 0.00 0.00 32.10 1.52
2990 5470 8.250332 GTGGTCCAGATTTATGAGCATTTTTAA 58.750 33.333 0.00 0.00 38.59 1.52
2991 5471 7.395772 TGTGGTCCAGATTTATGAGCATTTTTA 59.604 33.333 0.00 0.00 38.59 1.52
2993 5473 5.716228 TGTGGTCCAGATTTATGAGCATTTT 59.284 36.000 0.00 0.00 38.59 1.82
2994 5474 5.263599 TGTGGTCCAGATTTATGAGCATTT 58.736 37.500 0.00 0.00 38.59 2.32
3145 5625 7.410174 TGGGGTCTTTGAAGTTATATGTCATT 58.590 34.615 0.00 0.00 0.00 2.57
3160 5640 9.748708 CACATAACATATATTTTGGGGTCTTTG 57.251 33.333 0.00 0.00 0.00 2.77
3182 5662 3.233507 AGCCAATGAACAAGGAACACAT 58.766 40.909 0.00 0.00 0.00 3.21
3192 5672 4.261572 GCTTTGTACAAGAGCCAATGAACA 60.262 41.667 21.99 1.06 0.00 3.18


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

AutoCloner maintained by Alex Coulton.