Multiple sequence alignment - TraesCS1B01G389100

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 TraesCS1B01G389100 chr1B 100.000 1411 0 0 1667 3077 622701237 622702647 0.000000e+00 2606.0
1 TraesCS1B01G389100 chr1B 100.000 1268 0 0 1 1268 622699571 622700838 0.000000e+00 2342.0
2 TraesCS1B01G389100 chr1B 83.924 423 46 9 1672 2094 588498156 588497756 4.810000e-103 385.0
3 TraesCS1B01G389100 chr1B 89.965 289 19 4 989 1268 588498486 588498199 6.270000e-97 364.0
4 TraesCS1B01G389100 chr1B 94.231 52 3 0 2506 2557 622701869 622701920 2.540000e-11 80.5
5 TraesCS1B01G389100 chr1B 94.231 52 3 0 2299 2350 622702076 622702127 2.540000e-11 80.5
6 TraesCS1B01G389100 chr1D 92.606 1420 71 12 1669 3077 452621104 452622500 0.000000e+00 2010.0
7 TraesCS1B01G389100 chr1D 93.534 464 22 3 812 1268 452620604 452621066 0.000000e+00 684.0
8 TraesCS1B01G389100 chr1D 85.203 615 69 14 9 611 452619815 452620419 2.030000e-171 612.0
9 TraesCS1B01G389100 chr1D 85.849 424 46 7 1669 2092 435274188 435273779 3.640000e-119 438.0
10 TraesCS1B01G389100 chr1D 89.394 264 19 3 1014 1268 435274487 435274224 1.060000e-84 324.0
11 TraesCS1B01G389100 chr1D 87.006 177 19 2 652 828 452620417 452620589 2.420000e-46 196.0
12 TraesCS1B01G389100 chr2D 91.657 887 63 5 1667 2543 25919444 25918559 0.000000e+00 1218.0
13 TraesCS1B01G389100 chr2D 90.826 218 19 1 1051 1268 25919694 25919478 1.080000e-74 291.0
14 TraesCS1B01G389100 chr7A 90.449 890 62 8 1667 2546 10419635 10418759 0.000000e+00 1151.0
15 TraesCS1B01G389100 chr7A 83.036 224 18 1 1045 1268 10419870 10419667 5.240000e-43 185.0
16 TraesCS1B01G389100 chr7A 97.674 43 1 0 2299 2341 10418799 10418757 1.180000e-09 75.0
17 TraesCS1B01G389100 chr6A 89.563 709 61 7 1667 2364 407124131 407124837 0.000000e+00 887.0
18 TraesCS1B01G389100 chr6A 97.753 89 2 0 1179 1267 407124008 407124096 1.480000e-33 154.0
19 TraesCS1B01G389100 chr1A 89.592 711 41 14 1716 2414 547385210 547385899 0.000000e+00 872.0
20 TraesCS1B01G389100 chr1A 89.074 421 30 5 861 1268 547384729 547385146 2.740000e-140 508.0
21 TraesCS1B01G389100 chr1A 87.879 429 38 8 1672 2094 532776056 532775636 2.760000e-135 492.0
22 TraesCS1B01G389100 chr1A 85.641 390 46 3 1705 2094 532761913 532761534 4.780000e-108 401.0
23 TraesCS1B01G389100 chr1A 84.455 431 42 12 1 430 547383865 547384271 4.780000e-108 401.0
24 TraesCS1B01G389100 chr1A 90.152 264 17 3 1014 1268 532776362 532776099 4.920000e-88 335.0
25 TraesCS1B01G389100 chr1A 93.443 183 12 0 2364 2546 547385894 547386076 3.910000e-69 272.0
26 TraesCS1B01G389100 chr1A 93.827 81 1 2 2798 2875 547386076 547386155 5.390000e-23 119.0
27 TraesCS1B01G389100 chr1A 97.674 43 1 0 2299 2341 547386036 547386078 1.180000e-09 75.0
28 TraesCS1B01G389100 chr2A 89.571 163 13 4 2387 2546 767489301 767489140 1.450000e-48 204.0


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 TraesCS1B01G389100 chr1B 622699571 622702647 3076 False 1277.250000 2606 97.115500 1 3077 4 chr1B.!!$F1 3076
1 TraesCS1B01G389100 chr1B 588497756 588498486 730 True 374.500000 385 86.944500 989 2094 2 chr1B.!!$R1 1105
2 TraesCS1B01G389100 chr1D 452619815 452622500 2685 False 875.500000 2010 89.587250 9 3077 4 chr1D.!!$F1 3068
3 TraesCS1B01G389100 chr1D 435273779 435274487 708 True 381.000000 438 87.621500 1014 2092 2 chr1D.!!$R1 1078
4 TraesCS1B01G389100 chr2D 25918559 25919694 1135 True 754.500000 1218 91.241500 1051 2543 2 chr2D.!!$R1 1492
5 TraesCS1B01G389100 chr7A 10418757 10419870 1113 True 470.333333 1151 90.386333 1045 2546 3 chr7A.!!$R1 1501
6 TraesCS1B01G389100 chr6A 407124008 407124837 829 False 520.500000 887 93.658000 1179 2364 2 chr6A.!!$F1 1185
7 TraesCS1B01G389100 chr1A 532775636 532776362 726 True 413.500000 492 89.015500 1014 2094 2 chr1A.!!$R2 1080
8 TraesCS1B01G389100 chr1A 547383865 547386155 2290 False 374.500000 872 91.344167 1 2875 6 chr1A.!!$F1 2874

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
647 761 0.242825 CTTCATTGCTGCCACCAGTG 59.757 55.0 0.0 0.0 41.26 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2161 2495 0.106819 GCTGCAATCTCATGTCCCCT 60.107 55.0 0.0 0.0 0.0 4.79 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
21 22 1.400494 CCGGGCTTTCTATTTGAACCG 59.600 52.381 0.00 0.00 39.82 4.44
27 28 4.335594 GGCTTTCTATTTGAACCGCTATGT 59.664 41.667 0.00 0.00 33.88 2.29
37 38 3.615056 TGAACCGCTATGTTATGTTCGTG 59.385 43.478 0.00 0.00 38.46 4.35
38 39 2.546778 ACCGCTATGTTATGTTCGTGG 58.453 47.619 0.00 0.00 0.00 4.94
57 58 4.033358 CGTGGTGCTATTGATCTGTTTCTC 59.967 45.833 0.00 0.00 0.00 2.87
100 102 8.915871 TTTATGCAATCTGATTTAGCAAGTTC 57.084 30.769 16.28 0.00 38.85 3.01
113 115 9.479278 GATTTAGCAAGTTCGAAGTTCTTAATC 57.521 33.333 22.85 22.85 0.00 1.75
114 116 5.864628 AGCAAGTTCGAAGTTCTTAATCC 57.135 39.130 15.30 0.00 0.00 3.01
143 146 2.091775 AGTATCTGAGGTAGTCGCCCTT 60.092 50.000 0.00 0.00 30.60 3.95
145 148 1.030488 TCTGAGGTAGTCGCCCTTCG 61.030 60.000 0.00 0.00 40.15 3.79
162 165 2.483288 GTGCGTGGTATTTGGCCG 59.517 61.111 0.00 0.00 0.00 6.13
207 210 6.257630 GCATGTTTGTCCACTTGTTTAACAAT 59.742 34.615 11.12 0.00 37.48 2.71
216 219 6.204688 TCCACTTGTTTAACAATCAGCTGTAG 59.795 38.462 14.67 7.41 37.48 2.74
217 220 6.017109 CCACTTGTTTAACAATCAGCTGTAGT 60.017 38.462 14.67 8.07 37.48 2.73
218 221 7.172532 CCACTTGTTTAACAATCAGCTGTAGTA 59.827 37.037 14.67 0.00 37.48 1.82
220 223 9.284968 ACTTGTTTAACAATCAGCTGTAGTAAT 57.715 29.630 14.67 0.00 37.48 1.89
225 228 5.683876 ACAATCAGCTGTAGTAATGAGGT 57.316 39.130 14.67 0.00 0.00 3.85
229 232 7.928706 ACAATCAGCTGTAGTAATGAGGTATTC 59.071 37.037 14.67 0.00 0.00 1.75
322 325 2.014128 GAGAGAGACGAAGACTGAGGG 58.986 57.143 0.00 0.00 29.49 4.30
357 366 0.537188 GCTACCTCCACAGCAGCTTA 59.463 55.000 0.00 0.00 37.73 3.09
366 375 3.076621 CCACAGCAGCTTATGTTCAGAA 58.923 45.455 0.00 0.00 0.00 3.02
367 376 3.693085 CCACAGCAGCTTATGTTCAGAAT 59.307 43.478 0.00 0.00 0.00 2.40
368 377 4.157289 CCACAGCAGCTTATGTTCAGAATT 59.843 41.667 0.00 0.00 0.00 2.17
369 378 5.330295 CACAGCAGCTTATGTTCAGAATTC 58.670 41.667 0.00 0.00 0.00 2.17
370 379 5.005740 ACAGCAGCTTATGTTCAGAATTCA 58.994 37.500 8.44 0.00 0.00 2.57
371 380 5.123502 ACAGCAGCTTATGTTCAGAATTCAG 59.876 40.000 8.44 0.00 0.00 3.02
372 381 5.353400 CAGCAGCTTATGTTCAGAATTCAGA 59.647 40.000 8.44 1.71 0.00 3.27
388 397 7.966753 CAGAATTCAGATGATGTTTGTTACCAG 59.033 37.037 8.44 0.00 0.00 4.00
390 399 8.408043 AATTCAGATGATGTTTGTTACCAGAA 57.592 30.769 0.00 0.00 0.00 3.02
395 404 8.517878 CAGATGATGTTTGTTACCAGAATCTTT 58.482 33.333 0.00 0.00 0.00 2.52
401 410 8.974060 TGTTTGTTACCAGAATCTTTAACTCT 57.026 30.769 10.96 0.00 0.00 3.24
409 418 5.586643 CCAGAATCTTTAACTCTAAGGCACC 59.413 44.000 0.00 0.00 0.00 5.01
412 421 8.041323 CAGAATCTTTAACTCTAAGGCACCTTA 58.959 37.037 8.80 8.80 37.47 2.69
425 434 2.364002 GGCACCTTATGTGGTTGTGTTT 59.636 45.455 0.00 0.00 45.55 2.83
426 435 3.380142 GCACCTTATGTGGTTGTGTTTG 58.620 45.455 0.00 0.00 45.55 2.93
427 436 3.067461 GCACCTTATGTGGTTGTGTTTGA 59.933 43.478 0.00 0.00 45.55 2.69
428 437 4.440802 GCACCTTATGTGGTTGTGTTTGAA 60.441 41.667 0.00 0.00 45.55 2.69
429 438 5.040635 CACCTTATGTGGTTGTGTTTGAAC 58.959 41.667 0.00 0.00 41.52 3.18
430 439 4.953579 ACCTTATGTGGTTGTGTTTGAACT 59.046 37.500 0.00 0.00 36.89 3.01
431 440 5.420739 ACCTTATGTGGTTGTGTTTGAACTT 59.579 36.000 0.00 0.00 36.89 2.66
432 441 5.977129 CCTTATGTGGTTGTGTTTGAACTTC 59.023 40.000 0.00 0.00 0.00 3.01
433 442 3.859411 TGTGGTTGTGTTTGAACTTCC 57.141 42.857 0.00 0.00 0.00 3.46
464 482 1.050204 AGCACCGTGTACCCTGTTTA 58.950 50.000 0.00 0.00 0.00 2.01
466 484 2.039348 AGCACCGTGTACCCTGTTTATT 59.961 45.455 0.00 0.00 0.00 1.40
467 485 2.160813 GCACCGTGTACCCTGTTTATTG 59.839 50.000 0.00 0.00 0.00 1.90
468 486 2.160813 CACCGTGTACCCTGTTTATTGC 59.839 50.000 0.00 0.00 0.00 3.56
469 487 2.224572 ACCGTGTACCCTGTTTATTGCA 60.225 45.455 0.00 0.00 0.00 4.08
499 613 6.814506 GGATCTTTATCCCTGTTCATGATG 57.185 41.667 0.00 0.00 45.37 3.07
518 632 1.395826 GGTCGTATCTGCCTCCTGCT 61.396 60.000 0.00 0.00 42.00 4.24
565 679 2.026641 AGCAGCACATGTTGAAGTTGT 58.973 42.857 0.00 0.00 0.00 3.32
611 725 2.319472 GTTTTTCATGTTCCTGCGAGC 58.681 47.619 0.00 0.00 0.00 5.03
612 726 1.896220 TTTTCATGTTCCTGCGAGCT 58.104 45.000 0.00 0.00 0.00 4.09
616 730 3.984193 ATGTTCCTGCGAGCTGGCC 62.984 63.158 18.69 0.00 35.38 5.36
617 731 4.400961 GTTCCTGCGAGCTGGCCT 62.401 66.667 18.69 0.00 35.38 5.19
618 732 4.087892 TTCCTGCGAGCTGGCCTC 62.088 66.667 18.69 0.00 37.22 4.70
620 734 4.527583 CCTGCGAGCTGGCCTCTC 62.528 72.222 18.69 9.92 38.49 3.20
621 735 3.459965 CTGCGAGCTGGCCTCTCT 61.460 66.667 18.69 7.65 38.49 3.10
622 736 3.719883 CTGCGAGCTGGCCTCTCTG 62.720 68.421 18.69 14.36 38.49 3.35
632 746 3.396767 CCTCTCTGCCAGGCTTCA 58.603 61.111 14.15 0.00 0.00 3.02
633 747 1.913722 CCTCTCTGCCAGGCTTCAT 59.086 57.895 14.15 0.00 0.00 2.57
634 748 0.255318 CCTCTCTGCCAGGCTTCATT 59.745 55.000 14.15 0.00 0.00 2.57
635 749 1.380524 CTCTCTGCCAGGCTTCATTG 58.619 55.000 14.15 0.00 0.00 2.82
636 750 0.679002 TCTCTGCCAGGCTTCATTGC 60.679 55.000 14.15 0.00 0.00 3.56
637 751 0.680280 CTCTGCCAGGCTTCATTGCT 60.680 55.000 14.15 0.00 0.00 3.91
638 752 0.963856 TCTGCCAGGCTTCATTGCTG 60.964 55.000 14.15 0.00 0.00 4.41
639 753 2.183555 GCCAGGCTTCATTGCTGC 59.816 61.111 3.29 0.00 0.00 5.25
640 754 2.890371 CCAGGCTTCATTGCTGCC 59.110 61.111 10.47 10.47 46.42 4.85
643 757 2.575461 GGCTTCATTGCTGCCACC 59.425 61.111 12.70 0.00 45.46 4.61
644 758 2.277591 GGCTTCATTGCTGCCACCA 61.278 57.895 12.70 0.00 45.46 4.17
645 759 1.214589 GCTTCATTGCTGCCACCAG 59.785 57.895 0.00 0.00 42.13 4.00
646 760 1.530013 GCTTCATTGCTGCCACCAGT 61.530 55.000 0.00 0.00 41.26 4.00
647 761 0.242825 CTTCATTGCTGCCACCAGTG 59.757 55.000 0.00 0.00 41.26 3.66
656 770 4.087892 CCACCAGTGGCGGAGGAG 62.088 72.222 11.06 0.00 44.73 3.69
657 771 4.087892 CACCAGTGGCGGAGGAGG 62.088 72.222 9.78 0.00 0.00 4.30
677 791 4.018409 GGGGGAAGCATGAACCAC 57.982 61.111 0.00 0.00 0.00 4.16
682 796 1.305930 GGAAGCATGAACCACCGTCC 61.306 60.000 0.00 0.00 0.00 4.79
685 799 3.124921 CATGAACCACCGTCCGCC 61.125 66.667 0.00 0.00 0.00 6.13
710 824 1.679032 GCCGCCACATCTCCTTTTACT 60.679 52.381 0.00 0.00 0.00 2.24
722 836 7.181125 ACATCTCCTTTTACTGGAACTACAGAT 59.819 37.037 0.00 0.00 40.97 2.90
724 838 5.488341 TCCTTTTACTGGAACTACAGATGC 58.512 41.667 0.00 0.00 40.97 3.91
726 840 5.352569 CCTTTTACTGGAACTACAGATGCAG 59.647 44.000 6.49 6.49 40.97 4.41
730 844 3.118956 ACTGGAACTACAGATGCAGTAGC 60.119 47.826 11.10 0.00 44.84 3.58
731 845 5.597133 ACTGGAACTACAGATGCAGTAGCA 61.597 45.833 11.10 0.00 44.84 3.49
732 846 7.578928 ACTGGAACTACAGATGCAGTAGCAC 62.579 48.000 11.10 6.02 44.84 4.40
753 867 5.226396 CACCTGATATCTCACCTCGATTTC 58.774 45.833 3.98 0.00 0.00 2.17
757 871 6.462207 CCTGATATCTCACCTCGATTTCACTT 60.462 42.308 3.98 0.00 29.77 3.16
765 879 4.692625 CACCTCGATTTCACTTGAGATGTT 59.307 41.667 0.00 0.00 0.00 2.71
790 904 4.328983 GCAGCAAATTGGATGAATCTGTTG 59.671 41.667 1.22 0.00 0.00 3.33
975 1209 2.374525 CCATCCCCACACATCCCGA 61.375 63.158 0.00 0.00 0.00 5.14
996 1230 4.515404 CGGGAGGAAAAGCTACCG 57.485 61.111 0.00 0.00 35.01 4.02
1004 1238 0.107165 GAAAAGCTACCGGGGATGCT 60.107 55.000 6.32 6.67 37.37 3.79
1009 1243 1.749033 CTACCGGGGATGCTTCTCC 59.251 63.158 6.32 8.50 39.39 3.71
1747 2050 1.664965 GACGGCTGCTTCTTCGTGT 60.665 57.895 5.65 0.00 35.91 4.49
1748 2051 1.222115 GACGGCTGCTTCTTCGTGTT 61.222 55.000 5.65 0.00 35.91 3.32
1749 2052 1.222115 ACGGCTGCTTCTTCGTGTTC 61.222 55.000 0.00 0.00 34.40 3.18
1750 2053 1.493311 GGCTGCTTCTTCGTGTTCG 59.507 57.895 0.00 0.00 38.55 3.95
1751 2054 1.222115 GGCTGCTTCTTCGTGTTCGT 61.222 55.000 0.00 0.00 38.33 3.85
1752 2055 0.111089 GCTGCTTCTTCGTGTTCGTG 60.111 55.000 0.00 0.00 38.33 4.35
1947 2263 6.414079 CGCTTGCTGACAACTAATAGTAATG 58.586 40.000 0.00 0.00 0.00 1.90
1948 2264 6.195165 GCTTGCTGACAACTAATAGTAATGC 58.805 40.000 0.00 0.00 0.00 3.56
1949 2265 6.037610 GCTTGCTGACAACTAATAGTAATGCT 59.962 38.462 0.00 0.00 0.00 3.79
1950 2266 7.224753 GCTTGCTGACAACTAATAGTAATGCTA 59.775 37.037 0.00 0.00 0.00 3.49
1951 2267 8.420374 TTGCTGACAACTAATAGTAATGCTAC 57.580 34.615 0.00 0.00 31.59 3.58
1957 2273 8.594881 ACAACTAATAGTAATGCTACATCTGC 57.405 34.615 0.00 0.00 31.59 4.26
1960 2276 7.957002 ACTAATAGTAATGCTACATCTGCTGT 58.043 34.615 0.00 0.00 42.13 4.40
2071 2388 4.081185 TCAGCGCGGAGGCAATCA 62.081 61.111 8.83 0.00 39.92 2.57
2113 2447 5.174037 AGAACCATTTGGAATAGGACGAA 57.826 39.130 3.01 0.00 38.94 3.85
2127 2461 8.713271 GGAATAGGACGAATTTTATCTCATGAC 58.287 37.037 0.00 0.00 0.00 3.06
2135 2469 7.904977 ACGAATTTTATCTCATGACGAAACATG 59.095 33.333 12.79 12.79 46.01 3.21
2153 2487 0.806102 TGTCGCCTTCGCATAAGCTC 60.806 55.000 0.00 0.00 39.10 4.09
2161 2495 2.867855 CGCATAAGCTCCGGGCCTA 61.868 63.158 0.84 0.00 43.05 3.93
2194 2528 5.954335 AGATTGCAGCTTTGTTGGTAATAC 58.046 37.500 0.00 0.00 0.00 1.89
2205 2539 3.187637 TGTTGGTAATACTTCGTTGCAGC 59.812 43.478 0.00 0.00 0.00 5.25
2297 2633 0.877071 GGTGTTCATGCTGACTGTGG 59.123 55.000 0.00 0.00 0.00 4.17
2322 2658 7.228706 GGTAGGAACTGAAGAATTTCAACAGAA 59.771 37.037 21.10 0.00 42.48 3.02
2350 2686 4.769688 TGAACCACTAGGCATATTCAGTG 58.230 43.478 0.00 0.00 39.06 3.66
2369 2708 1.552337 TGGATCACTTCAGTCTGCTCC 59.448 52.381 0.00 0.00 0.00 4.70
2370 2709 1.552337 GGATCACTTCAGTCTGCTCCA 59.448 52.381 0.00 0.00 0.00 3.86
2376 2715 5.204292 TCACTTCAGTCTGCTCCATACTAT 58.796 41.667 0.00 0.00 0.00 2.12
2381 2720 6.398234 TCAGTCTGCTCCATACTATTTCTC 57.602 41.667 0.00 0.00 0.00 2.87
2444 2828 7.880713 GTGAAGAGAGGAAGAAAGGAAATAACT 59.119 37.037 0.00 0.00 0.00 2.24
2546 2931 6.426937 TCAACAGAATAACTTGAACCACTAGC 59.573 38.462 0.00 0.00 0.00 3.42
2604 2989 9.107177 TGCTTGTATCATGTTTGTTTGAATTTT 57.893 25.926 0.00 0.00 0.00 1.82
2615 3000 9.170734 TGTTTGTTTGAATTTTCATTGGATTGA 57.829 25.926 0.00 0.00 37.00 2.57
2630 3015 9.334947 TCATTGGATTGATTCTTCATTAGAGAC 57.665 33.333 0.00 0.00 33.51 3.36
2646 3031 3.665190 AGAGACCGACTCCAACAATTTC 58.335 45.455 6.09 0.00 45.96 2.17
2648 3033 3.403038 AGACCGACTCCAACAATTTCAG 58.597 45.455 0.00 0.00 0.00 3.02
2660 3045 5.509501 CCAACAATTTCAGCTCTTAGCCAAA 60.510 40.000 0.00 0.00 43.77 3.28
2685 3070 1.068741 GAACTGGACGTGGTTCTCACT 59.931 52.381 14.45 0.00 43.94 3.41
2702 3087 4.952335 TCTCACTCTCATATTGTGCTCTGA 59.048 41.667 0.00 0.00 0.00 3.27
2735 3120 4.140924 AGGAAAGTGGGAGAAGGAACAATT 60.141 41.667 0.00 0.00 0.00 2.32
2738 3123 4.453480 AGTGGGAGAAGGAACAATTGAA 57.547 40.909 13.59 0.00 0.00 2.69
2764 3149 2.372172 AGAAGTAAGGCGGGGGATAATG 59.628 50.000 0.00 0.00 0.00 1.90
2897 3285 0.676782 ACAGTAAGCATCAACCCCGC 60.677 55.000 0.00 0.00 0.00 6.13
3024 3412 6.356556 TCACATACATACCATTTCAAGGAGG 58.643 40.000 0.00 0.00 0.00 4.30
3051 3439 4.526970 ACAATAGAATTGATGACCGCCTT 58.473 39.130 6.64 0.00 0.00 4.35
3065 3453 0.741221 CGCCTTTAGGACTGACTGGC 60.741 60.000 0.00 0.00 37.39 4.85
3072 3460 0.617413 AGGACTGACTGGCAATGAGG 59.383 55.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.092323 AGCGGTTCAAATAGAAAGCCC 58.908 47.619 0.00 0.00 40.74 5.19
6 7 8.612619 ACATAACATAGCGGTTCAAATAGAAAG 58.387 33.333 0.00 0.00 38.13 2.62
21 22 2.936498 AGCACCACGAACATAACATAGC 59.064 45.455 0.00 0.00 0.00 2.97
27 28 5.523552 CAGATCAATAGCACCACGAACATAA 59.476 40.000 0.00 0.00 0.00 1.90
37 38 5.181748 ACAGAGAAACAGATCAATAGCACC 58.818 41.667 0.00 0.00 0.00 5.01
38 39 6.734104 AACAGAGAAACAGATCAATAGCAC 57.266 37.500 0.00 0.00 0.00 4.40
72 73 9.880157 ACTTGCTAAATCAGATTGCATAAAATT 57.120 25.926 8.56 0.00 33.50 1.82
82 84 7.389053 AGAACTTCGAACTTGCTAAATCAGATT 59.611 33.333 0.00 0.00 0.00 2.40
100 102 7.611213 ACTGGTAAATGGATTAAGAACTTCG 57.389 36.000 0.00 0.00 0.00 3.79
113 115 6.515200 CGACTACCTCAGATACTGGTAAATGG 60.515 46.154 0.00 0.00 36.11 3.16
114 116 6.439599 CGACTACCTCAGATACTGGTAAATG 58.560 44.000 0.00 0.00 36.11 2.32
143 146 2.036006 GGCCAAATACCACGCACGA 61.036 57.895 0.00 0.00 0.00 4.35
145 148 1.020333 TACGGCCAAATACCACGCAC 61.020 55.000 2.24 0.00 0.00 5.34
151 154 4.193865 ACAATGTAGTACGGCCAAATACC 58.806 43.478 2.24 0.00 0.00 2.73
207 210 7.561722 AGAAGAATACCTCATTACTACAGCTGA 59.438 37.037 23.35 2.95 0.00 4.26
242 245 8.495148 CAACACCAGAAAAATAGGTTTTAATGC 58.505 33.333 0.00 0.00 39.60 3.56
322 325 5.241285 GGAGGTAGCACTATAGTACCAACTC 59.759 48.000 20.53 14.62 39.02 3.01
357 366 8.118976 ACAAACATCATCTGAATTCTGAACAT 57.881 30.769 17.62 10.31 0.00 2.71
388 397 8.831550 CATAAGGTGCCTTAGAGTTAAAGATTC 58.168 37.037 14.99 0.00 41.18 2.52
390 399 7.770897 CACATAAGGTGCCTTAGAGTTAAAGAT 59.229 37.037 14.99 0.00 41.18 2.40
395 404 4.781087 ACCACATAAGGTGCCTTAGAGTTA 59.219 41.667 14.99 0.00 46.50 2.24
397 406 3.182152 ACCACATAAGGTGCCTTAGAGT 58.818 45.455 14.99 12.78 46.50 3.24
401 410 3.181438 ACACAACCACATAAGGTGCCTTA 60.181 43.478 12.51 12.51 46.50 2.69
409 418 5.977129 GGAAGTTCAAACACAACCACATAAG 59.023 40.000 5.01 0.00 0.00 1.73
412 421 4.023291 AGGAAGTTCAAACACAACCACAT 58.977 39.130 5.01 0.00 0.00 3.21
425 434 5.470098 GTGCTAAAGATGTTCAGGAAGTTCA 59.530 40.000 5.01 0.00 0.00 3.18
426 435 5.106515 GGTGCTAAAGATGTTCAGGAAGTTC 60.107 44.000 0.00 0.00 0.00 3.01
427 436 4.762251 GGTGCTAAAGATGTTCAGGAAGTT 59.238 41.667 0.00 0.00 0.00 2.66
428 437 4.327680 GGTGCTAAAGATGTTCAGGAAGT 58.672 43.478 0.00 0.00 0.00 3.01
429 438 3.372206 CGGTGCTAAAGATGTTCAGGAAG 59.628 47.826 0.00 0.00 0.00 3.46
430 439 3.244422 ACGGTGCTAAAGATGTTCAGGAA 60.244 43.478 0.00 0.00 0.00 3.36
431 440 2.301870 ACGGTGCTAAAGATGTTCAGGA 59.698 45.455 0.00 0.00 0.00 3.86
432 441 2.416547 CACGGTGCTAAAGATGTTCAGG 59.583 50.000 0.00 0.00 0.00 3.86
433 442 3.067106 ACACGGTGCTAAAGATGTTCAG 58.933 45.455 8.30 0.00 0.00 3.02
499 613 1.068250 GCAGGAGGCAGATACGACC 59.932 63.158 0.00 0.00 43.97 4.79
518 632 8.071967 GCAATTCGATTCAATCATTCACAGATA 58.928 33.333 0.00 0.00 0.00 1.98
565 679 6.259387 CAGAGCATAGCATCTCAACAACATTA 59.741 38.462 0.00 0.00 0.00 1.90
616 730 1.380524 CAATGAAGCCTGGCAGAGAG 58.619 55.000 22.65 0.00 0.00 3.20
617 731 0.679002 GCAATGAAGCCTGGCAGAGA 60.679 55.000 22.65 1.51 0.00 3.10
618 732 0.680280 AGCAATGAAGCCTGGCAGAG 60.680 55.000 22.65 7.37 34.23 3.35
619 733 0.963856 CAGCAATGAAGCCTGGCAGA 60.964 55.000 22.65 3.93 34.23 4.26
620 734 1.511305 CAGCAATGAAGCCTGGCAG 59.489 57.895 22.65 7.75 34.23 4.85
621 735 2.642254 GCAGCAATGAAGCCTGGCA 61.642 57.895 22.65 0.00 34.23 4.92
622 736 2.183555 GCAGCAATGAAGCCTGGC 59.816 61.111 11.65 11.65 34.23 4.85
623 737 2.890371 GGCAGCAATGAAGCCTGG 59.110 61.111 8.77 0.00 44.92 4.45
627 741 1.214589 CTGGTGGCAGCAATGAAGC 59.785 57.895 20.97 0.00 0.00 3.86
628 742 0.242825 CACTGGTGGCAGCAATGAAG 59.757 55.000 22.23 11.52 0.00 3.02
629 743 1.180456 CCACTGGTGGCAGCAATGAA 61.180 55.000 27.40 1.42 44.73 2.57
630 744 1.604308 CCACTGGTGGCAGCAATGA 60.604 57.895 27.40 1.82 44.73 2.57
631 745 2.967397 CCACTGGTGGCAGCAATG 59.033 61.111 20.11 20.11 44.73 2.82
640 754 4.087892 CCTCCTCCGCCACTGGTG 62.088 72.222 1.13 1.13 0.00 4.17
664 778 1.635663 CGGACGGTGGTTCATGCTTC 61.636 60.000 0.00 0.00 0.00 3.86
665 779 1.671054 CGGACGGTGGTTCATGCTT 60.671 57.895 0.00 0.00 0.00 3.91
700 814 5.582665 GCATCTGTAGTTCCAGTAAAAGGAG 59.417 44.000 0.00 0.00 36.33 3.69
710 824 2.831526 TGCTACTGCATCTGTAGTTCCA 59.168 45.455 6.25 2.29 45.31 3.53
724 838 3.894427 AGGTGAGATATCAGGTGCTACTG 59.106 47.826 5.32 2.32 39.84 2.74
726 840 3.057876 CGAGGTGAGATATCAGGTGCTAC 60.058 52.174 5.32 0.00 0.00 3.58
730 844 4.862902 AATCGAGGTGAGATATCAGGTG 57.137 45.455 5.32 0.00 0.00 4.00
731 845 4.895889 TGAAATCGAGGTGAGATATCAGGT 59.104 41.667 5.32 0.00 0.00 4.00
732 846 5.010516 AGTGAAATCGAGGTGAGATATCAGG 59.989 44.000 5.32 0.00 0.00 3.86
742 856 4.248859 ACATCTCAAGTGAAATCGAGGTG 58.751 43.478 0.00 0.00 41.44 4.00
753 867 1.241165 TGCTGCCAACATCTCAAGTG 58.759 50.000 0.00 0.00 0.00 3.16
757 871 2.028839 CCAATTTGCTGCCAACATCTCA 60.029 45.455 0.00 0.00 0.00 3.27
765 879 3.101437 AGATTCATCCAATTTGCTGCCA 58.899 40.909 0.00 0.00 0.00 4.92
790 904 2.987821 GACTCTGTCGAACAGTTTAGCC 59.012 50.000 12.62 0.00 46.03 3.93
892 1113 0.745486 TCAAGCCATCTGCCGATGTG 60.745 55.000 15.83 8.67 44.45 3.21
975 1209 2.288025 TAGCTTTTCCTCCCGGCGT 61.288 57.895 6.01 0.00 0.00 5.68
996 1230 1.148048 GCTCAGGAGAAGCATCCCC 59.852 63.158 0.00 0.00 40.53 4.81
1004 1238 4.135153 GCGCGAGGCTCAGGAGAA 62.135 66.667 12.10 0.00 39.11 2.87
1747 2050 4.704833 GGCTCCAGGCTGCACGAA 62.705 66.667 9.56 0.00 41.46 3.85
1957 2273 1.202568 CGAACTTGACGCTGCACAG 59.797 57.895 0.00 0.00 0.00 3.66
2061 2378 2.508526 ACTTGTCACTTGATTGCCTCC 58.491 47.619 0.00 0.00 0.00 4.30
2113 2447 7.401860 CGACATGTTTCGTCATGAGATAAAAT 58.598 34.615 18.65 0.00 45.41 1.82
2127 2461 1.225745 GCGAAGGCGACATGTTTCG 60.226 57.895 20.70 20.70 43.70 3.46
2135 2469 1.491505 GGAGCTTATGCGAAGGCGAC 61.492 60.000 0.00 0.00 45.42 5.19
2153 2487 3.560251 CATGTCCCCTAGGCCCGG 61.560 72.222 2.05 0.00 0.00 5.73
2161 2495 0.106819 GCTGCAATCTCATGTCCCCT 60.107 55.000 0.00 0.00 0.00 4.79
2194 2528 0.886490 ACAGGAAGGCTGCAACGAAG 60.886 55.000 0.50 0.00 0.00 3.79
2272 2606 0.184692 TCAGCATGAACACCCAACCA 59.815 50.000 0.00 0.00 45.97 3.67
2297 2633 7.730364 TCTGTTGAAATTCTTCAGTTCCTAC 57.270 36.000 13.81 0.00 42.48 3.18
2322 2658 8.995027 TGAATATGCCTAGTGGTTCAAATTAT 57.005 30.769 0.00 0.00 35.27 1.28
2350 2686 2.307934 GGAGCAGACTGAAGTGATCC 57.692 55.000 6.65 0.00 41.76 3.36
2369 2708 3.784883 GCAGCAGCGAGAAATAGTATG 57.215 47.619 0.00 0.00 0.00 2.39
2444 2828 3.462483 TTTGTGAACTAAGCAGACCGA 57.538 42.857 0.00 0.00 0.00 4.69
2546 2931 4.452455 GGTTCACTGAAGTACTGAACATGG 59.548 45.833 20.23 7.83 40.18 3.66
2604 2989 9.334947 GTCTCTAATGAAGAATCAATCCAATGA 57.665 33.333 0.00 0.00 39.49 2.57
2607 2992 6.763135 CGGTCTCTAATGAAGAATCAATCCAA 59.237 38.462 0.00 0.00 39.49 3.53
2608 2993 6.098266 TCGGTCTCTAATGAAGAATCAATCCA 59.902 38.462 0.00 0.00 39.49 3.41
2615 3000 4.956700 TGGAGTCGGTCTCTAATGAAGAAT 59.043 41.667 2.44 0.00 42.40 2.40
2630 3015 2.154462 AGCTGAAATTGTTGGAGTCGG 58.846 47.619 0.00 0.00 0.00 4.79
2646 3031 3.325293 TCTCAGTTTGGCTAAGAGCTG 57.675 47.619 0.00 5.27 41.99 4.24
2648 3033 3.434984 CAGTTCTCAGTTTGGCTAAGAGC 59.565 47.826 0.00 0.00 41.46 4.09
2660 3045 1.068741 GAACCACGTCCAGTTCTCAGT 59.931 52.381 12.96 0.00 39.42 3.41
2685 3070 5.204292 ACCTACTCAGAGCACAATATGAGA 58.796 41.667 7.97 0.00 41.35 3.27
2702 3087 3.323775 TCCCACTTTCCTGAAACCTACT 58.676 45.455 0.00 0.00 0.00 2.57
2735 3120 1.336517 CCGCCTTACTTCTCACGTTCA 60.337 52.381 0.00 0.00 0.00 3.18
2738 3123 1.590147 CCCGCCTTACTTCTCACGT 59.410 57.895 0.00 0.00 0.00 4.49
2764 3149 0.320421 TGTCTTTGCTACTCCCGCAC 60.320 55.000 0.00 0.00 37.07 5.34
3014 3402 9.762933 CAATTCTATTGTTTTTCCTCCTTGAAA 57.237 29.630 0.00 0.00 32.60 2.69
3024 3412 6.253512 GGCGGTCATCAATTCTATTGTTTTTC 59.746 38.462 0.00 0.00 0.00 2.29
3051 3439 2.237143 CCTCATTGCCAGTCAGTCCTAA 59.763 50.000 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.