Multiple sequence alignment - TraesCS7A01G466000

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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 TraesCS7A01G466000 chr7A 100.000 2807 0 0 1 2807 662966047 662968853 0.000000e+00 5184
1 TraesCS7A01G466000 chr7A 95.333 150 7 0 2658 2807 694023375 694023226 3.610000e-59 239
2 TraesCS7A01G466000 chr7D 95.197 2644 91 19 6 2635 573191839 573194460 0.000000e+00 4146
3 TraesCS7A01G466000 chr7B 93.619 2680 122 28 1 2659 631404210 631406861 0.000000e+00 3956
4 TraesCS7A01G466000 chr6D 88.124 421 47 3 1047 1464 94602363 94602783 5.400000e-137 497
5 TraesCS7A01G466000 chr6D 86.234 385 53 0 1054 1438 452722161 452721777 4.320000e-113 418
6 TraesCS7A01G466000 chr6B 89.027 401 44 0 1047 1447 178273232 178272832 5.400000e-137 497
7 TraesCS7A01G466000 chr6B 87.532 385 48 0 1054 1438 687525398 687525014 1.980000e-121 446
8 TraesCS7A01G466000 chr6A 87.471 431 51 3 1047 1474 114459016 114458586 6.980000e-136 494
9 TraesCS7A01G466000 chr6A 87.273 385 49 0 1054 1438 598619721 598619337 9.230000e-120 440
10 TraesCS7A01G466000 chr6A 95.333 150 7 0 2658 2807 135366294 135366443 3.610000e-59 239
11 TraesCS7A01G466000 chr2A 86.889 389 49 2 1051 1438 626589669 626589282 4.290000e-118 435
12 TraesCS7A01G466000 chr2A 95.333 150 7 0 2658 2807 490609782 490609931 3.610000e-59 239
13 TraesCS7A01G466000 chrUn 93.927 247 15 0 2413 2659 294908612 294908366 9.490000e-100 374
14 TraesCS7A01G466000 chr1A 96.667 150 5 0 2658 2807 8282737 8282588 1.670000e-62 250
15 TraesCS7A01G466000 chr3A 96.000 150 6 0 2658 2807 603307483 603307632 7.770000e-61 244
16 TraesCS7A01G466000 chr5A 95.333 150 7 0 2658 2807 528023561 528023710 3.610000e-59 239
17 TraesCS7A01G466000 chr5A 95.333 150 7 0 2658 2807 536150294 536150145 3.610000e-59 239
18 TraesCS7A01G466000 chr4A 95.333 150 7 0 2658 2807 619192296 619192147 3.610000e-59 239
19 TraesCS7A01G466000 chr4A 95.333 150 7 0 2658 2807 644689872 644690021 3.610000e-59 239


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 TraesCS7A01G466000 chr7A 662966047 662968853 2806 False 5184 5184 100.000 1 2807 1 chr7A.!!$F1 2806
1 TraesCS7A01G466000 chr7D 573191839 573194460 2621 False 4146 4146 95.197 6 2635 1 chr7D.!!$F1 2629
2 TraesCS7A01G466000 chr7B 631404210 631406861 2651 False 3956 3956 93.619 1 2659 1 chr7B.!!$F1 2658

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
480 492 0.321919 TGCTTGCCAGGTGAGATGTC 60.322 55.0 0.0 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1919 1957 1.137086 ACTCATCCTTCCATCGTTCCG 59.863 52.381 0.0 0.0 0.0 4.3 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
59 64 3.776781 CCGGGTGGGTGCATACGA 61.777 66.667 0.00 0.00 0.00 3.43
60 65 2.266372 CGGGTGGGTGCATACGAA 59.734 61.111 0.00 0.00 0.00 3.85
61 66 2.104253 CGGGTGGGTGCATACGAAC 61.104 63.158 0.00 0.00 0.00 3.95
62 67 2.104253 GGGTGGGTGCATACGAACG 61.104 63.158 0.00 0.00 0.00 3.95
299 310 3.303928 GCCGCGGCTATCTACCCT 61.304 66.667 41.71 0.00 38.26 4.34
358 369 2.018086 CCCTCTCCTCCTCCTCCCT 61.018 68.421 0.00 0.00 0.00 4.20
361 372 0.933700 CTCTCCTCCTCCTCCCTTCT 59.066 60.000 0.00 0.00 0.00 2.85
480 492 0.321919 TGCTTGCCAGGTGAGATGTC 60.322 55.000 0.00 0.00 0.00 3.06
554 566 2.031012 CTGGTTGTGCGGCTGAGA 59.969 61.111 0.00 0.00 0.00 3.27
560 572 2.110757 TTGTGCGGCTGAGATGACCA 62.111 55.000 0.00 0.00 0.00 4.02
666 683 2.809861 CTTGGATGCCACGCTCTGGT 62.810 60.000 0.00 0.00 42.99 4.00
667 684 2.512515 GGATGCCACGCTCTGGTC 60.513 66.667 0.00 0.00 42.99 4.02
668 685 2.512515 GATGCCACGCTCTGGTCC 60.513 66.667 0.00 0.00 42.99 4.46
669 686 4.457496 ATGCCACGCTCTGGTCCG 62.457 66.667 0.00 0.00 42.99 4.79
778 795 3.626680 TTCGTGCGCCCTCGAGAAG 62.627 63.158 15.71 5.99 38.10 2.85
780 797 4.443266 GTGCGCCCTCGAGAAGCT 62.443 66.667 15.71 0.00 38.10 3.74
824 841 1.331756 CGCCGATGCTTAGCTTGATTT 59.668 47.619 5.60 0.00 34.43 2.17
829 846 4.337763 CGATGCTTAGCTTGATTTGTCAC 58.662 43.478 5.60 0.00 0.00 3.67
836 853 2.158623 AGCTTGATTTGTCACCTCACCA 60.159 45.455 0.00 0.00 0.00 4.17
837 854 2.821969 GCTTGATTTGTCACCTCACCAT 59.178 45.455 0.00 0.00 0.00 3.55
862 891 1.817357 CTGAGCTGAAGAACCATGCA 58.183 50.000 0.00 0.00 0.00 3.96
906 935 2.033141 GGCTGGCTGCTGAGTGAA 59.967 61.111 16.14 0.00 42.39 3.18
940 969 1.295423 GGTTTCAGGCAGCTCCGTA 59.705 57.895 0.00 0.00 40.77 4.02
950 987 2.100252 GGCAGCTCCGTATGTACTAACA 59.900 50.000 0.00 0.00 40.69 2.41
1171 1208 1.241990 CCACGTCCTCGAGTTCCTCA 61.242 60.000 12.31 0.00 40.62 3.86
1173 1210 0.961358 ACGTCCTCGAGTTCCTCAGG 60.961 60.000 12.31 0.00 40.62 3.86
1197 1234 1.300620 CGACCAGTTCGGCAAGACA 60.301 57.895 0.00 0.00 44.60 3.41
1530 1567 2.996168 CTACCCATGTAGCAGCGCCC 62.996 65.000 2.29 0.00 38.20 6.13
1714 1751 1.974875 CACAGCAATGGCCAGAGCA 60.975 57.895 27.81 0.00 42.56 4.26
1811 1848 0.242825 TCCGTGTTCAACTAGCGAGG 59.757 55.000 0.00 0.00 0.00 4.63
1820 1857 1.542187 AACTAGCGAGGTTTCCGGCT 61.542 55.000 0.00 10.86 40.24 5.52
1919 1957 4.489810 AGCCGTAATCTTGATCGATCATC 58.510 43.478 27.75 13.04 36.56 2.92
1983 2023 8.891671 AACGTACTATTGTTCTTCTTACCAAA 57.108 30.769 0.00 0.00 0.00 3.28
2081 2121 1.008875 TTCTAGCAGCGTTCGTGCAG 61.009 55.000 16.66 12.90 43.82 4.41
2176 2216 1.326852 GAATGTGCACTGCTGATCGAG 59.673 52.381 19.41 0.00 0.00 4.04
2188 2228 2.830104 CTGATCGAGTGATTCATGGCA 58.170 47.619 0.00 0.00 34.09 4.92
2189 2229 3.200483 CTGATCGAGTGATTCATGGCAA 58.800 45.455 0.00 0.00 34.09 4.52
2263 2303 5.410067 TGTGCTGCTAGGATTTTAATTTGC 58.590 37.500 0.00 0.00 0.00 3.68
2281 2321 5.490139 TTTGCTCTTATGACTAGCATTGC 57.510 39.130 0.00 0.00 45.09 3.56
2305 2345 6.401796 GCCATGACATTTTCTGCAGAATTTTC 60.402 38.462 28.89 20.99 33.54 2.29
2306 2346 6.183360 CCATGACATTTTCTGCAGAATTTTCG 60.183 38.462 28.89 17.42 33.54 3.46
2307 2347 5.830912 TGACATTTTCTGCAGAATTTTCGT 58.169 33.333 28.89 20.14 33.54 3.85
2308 2348 5.686841 TGACATTTTCTGCAGAATTTTCGTG 59.313 36.000 28.89 20.60 33.54 4.35
2309 2349 5.591099 ACATTTTCTGCAGAATTTTCGTGT 58.409 33.333 28.89 21.14 33.54 4.49
2310 2350 5.459762 ACATTTTCTGCAGAATTTTCGTGTG 59.540 36.000 28.89 18.57 33.54 3.82
2311 2351 3.624326 TTCTGCAGAATTTTCGTGTGG 57.376 42.857 25.16 0.00 0.00 4.17
2312 2352 1.266718 TCTGCAGAATTTTCGTGTGGC 59.733 47.619 15.67 0.00 0.00 5.01
2313 2353 1.001487 CTGCAGAATTTTCGTGTGGCA 60.001 47.619 8.42 0.00 0.00 4.92
2314 2354 1.406898 TGCAGAATTTTCGTGTGGCAA 59.593 42.857 0.00 0.00 0.00 4.52
2315 2355 2.159184 TGCAGAATTTTCGTGTGGCAAA 60.159 40.909 0.00 0.00 0.00 3.68
2316 2356 3.059166 GCAGAATTTTCGTGTGGCAAAT 58.941 40.909 0.00 0.00 0.00 2.32
2317 2357 3.120923 GCAGAATTTTCGTGTGGCAAATG 60.121 43.478 0.00 0.00 0.00 2.32
2318 2358 4.050553 CAGAATTTTCGTGTGGCAAATGT 58.949 39.130 0.00 0.00 0.00 2.71
2319 2359 4.507388 CAGAATTTTCGTGTGGCAAATGTT 59.493 37.500 0.00 0.00 0.00 2.71
2320 2360 5.006552 CAGAATTTTCGTGTGGCAAATGTTT 59.993 36.000 0.00 0.00 0.00 2.83
2321 2361 5.234116 AGAATTTTCGTGTGGCAAATGTTTC 59.766 36.000 0.00 0.00 0.00 2.78
2322 2362 3.510388 TTTCGTGTGGCAAATGTTTCA 57.490 38.095 0.00 0.00 0.00 2.69
2323 2363 3.724508 TTCGTGTGGCAAATGTTTCAT 57.275 38.095 0.00 0.00 0.00 2.57
2324 2364 3.010624 TCGTGTGGCAAATGTTTCATG 57.989 42.857 0.00 0.00 0.00 3.07
2325 2365 1.456544 CGTGTGGCAAATGTTTCATGC 59.543 47.619 0.00 0.00 39.33 4.06
2326 2366 2.481854 GTGTGGCAAATGTTTCATGCA 58.518 42.857 0.00 0.00 41.80 3.96
2348 2388 8.058667 TGCATCATCTGTATGTTTCATCTTTT 57.941 30.769 0.00 0.00 34.50 2.27
2469 2515 7.735599 CCAATTGGTTTGCACGTTGGTGATA 62.736 44.000 16.90 0.00 46.09 2.15
2529 2575 7.440198 TGAATTTGCATAGAAAATCCACACAA 58.560 30.769 0.00 0.00 0.00 3.33
2579 2625 3.785887 TCATTACAAGTGGGGCCTAAGAT 59.214 43.478 0.84 0.00 0.00 2.40
2654 2700 3.324846 TGGATACACCTATCAGGATGCAC 59.675 47.826 0.00 0.00 46.17 4.57
2659 2705 3.133003 ACACCTATCAGGATGCACTGTAC 59.867 47.826 4.42 0.00 37.67 2.90
2660 2706 3.386078 CACCTATCAGGATGCACTGTACT 59.614 47.826 4.42 0.00 37.67 2.73
2661 2707 3.639094 ACCTATCAGGATGCACTGTACTC 59.361 47.826 4.42 0.00 37.67 2.59
2662 2708 3.006323 CCTATCAGGATGCACTGTACTCC 59.994 52.174 4.42 0.00 37.67 3.85
2663 2709 1.937191 TCAGGATGCACTGTACTCCA 58.063 50.000 4.66 0.00 39.48 3.86
2664 2710 2.470990 TCAGGATGCACTGTACTCCAT 58.529 47.619 4.66 0.00 39.48 3.41
2665 2711 2.432146 TCAGGATGCACTGTACTCCATC 59.568 50.000 4.66 1.31 39.48 3.51
2666 2712 2.246719 GGATGCACTGTACTCCATCC 57.753 55.000 14.36 14.36 44.71 3.51
2667 2713 1.765314 GGATGCACTGTACTCCATCCT 59.235 52.381 18.75 0.00 46.43 3.24
2668 2714 2.171448 GGATGCACTGTACTCCATCCTT 59.829 50.000 18.75 0.00 46.43 3.36
2669 2715 3.462021 GATGCACTGTACTCCATCCTTC 58.538 50.000 0.00 0.00 0.00 3.46
2670 2716 1.555075 TGCACTGTACTCCATCCTTCC 59.445 52.381 0.00 0.00 0.00 3.46
2671 2717 1.555075 GCACTGTACTCCATCCTTCCA 59.445 52.381 0.00 0.00 0.00 3.53
2672 2718 2.171448 GCACTGTACTCCATCCTTCCAT 59.829 50.000 0.00 0.00 0.00 3.41
2673 2719 3.742640 GCACTGTACTCCATCCTTCCATC 60.743 52.174 0.00 0.00 0.00 3.51
2674 2720 3.708631 CACTGTACTCCATCCTTCCATCT 59.291 47.826 0.00 0.00 0.00 2.90
2675 2721 4.895889 CACTGTACTCCATCCTTCCATCTA 59.104 45.833 0.00 0.00 0.00 1.98
2676 2722 5.541868 CACTGTACTCCATCCTTCCATCTAT 59.458 44.000 0.00 0.00 0.00 1.98
2677 2723 6.721668 CACTGTACTCCATCCTTCCATCTATA 59.278 42.308 0.00 0.00 0.00 1.31
2678 2724 7.398618 CACTGTACTCCATCCTTCCATCTATAT 59.601 40.741 0.00 0.00 0.00 0.86
2679 2725 8.624670 ACTGTACTCCATCCTTCCATCTATATA 58.375 37.037 0.00 0.00 0.00 0.86
2680 2726 9.130661 CTGTACTCCATCCTTCCATCTATATAG 57.869 40.741 3.10 3.10 0.00 1.31
2681 2727 8.061920 TGTACTCCATCCTTCCATCTATATAGG 58.938 40.741 9.89 0.00 0.00 2.57
2682 2728 6.448202 ACTCCATCCTTCCATCTATATAGGG 58.552 44.000 9.89 4.49 0.00 3.53
2683 2729 5.219739 TCCATCCTTCCATCTATATAGGGC 58.780 45.833 9.89 0.00 0.00 5.19
2684 2730 4.349342 CCATCCTTCCATCTATATAGGGCC 59.651 50.000 9.89 0.00 0.00 5.80
2685 2731 4.994411 TCCTTCCATCTATATAGGGCCT 57.006 45.455 12.58 12.58 0.00 5.19
2686 2732 6.385443 CATCCTTCCATCTATATAGGGCCTA 58.615 44.000 17.16 17.16 0.00 3.93
2687 2733 6.432190 TCCTTCCATCTATATAGGGCCTAA 57.568 41.667 18.91 7.61 0.00 2.69
2688 2734 7.009960 TCCTTCCATCTATATAGGGCCTAAT 57.990 40.000 18.91 14.19 0.00 1.73
2689 2735 6.846505 TCCTTCCATCTATATAGGGCCTAATG 59.153 42.308 18.91 15.42 0.00 1.90
2690 2736 6.465035 CCTTCCATCTATATAGGGCCTAATGC 60.465 46.154 18.91 0.00 40.16 3.56
2691 2737 4.588951 TCCATCTATATAGGGCCTAATGCG 59.411 45.833 18.91 10.04 42.61 4.73
2692 2738 4.345257 CCATCTATATAGGGCCTAATGCGT 59.655 45.833 18.91 2.76 42.61 5.24
2693 2739 5.163301 CCATCTATATAGGGCCTAATGCGTT 60.163 44.000 18.91 1.94 42.61 4.84
2694 2740 6.349300 CATCTATATAGGGCCTAATGCGTTT 58.651 40.000 18.91 1.12 42.61 3.60
2695 2741 6.368779 TCTATATAGGGCCTAATGCGTTTT 57.631 37.500 18.91 0.30 42.61 2.43
2696 2742 6.775708 TCTATATAGGGCCTAATGCGTTTTT 58.224 36.000 18.91 0.00 42.61 1.94
2697 2743 5.959618 ATATAGGGCCTAATGCGTTTTTC 57.040 39.130 18.91 0.00 42.61 2.29
2698 2744 1.917872 AGGGCCTAATGCGTTTTTCA 58.082 45.000 2.82 0.00 42.61 2.69
2699 2745 2.243810 AGGGCCTAATGCGTTTTTCAA 58.756 42.857 2.82 0.00 42.61 2.69
2700 2746 2.231235 AGGGCCTAATGCGTTTTTCAAG 59.769 45.455 2.82 0.00 42.61 3.02
2701 2747 2.230266 GGGCCTAATGCGTTTTTCAAGA 59.770 45.455 0.84 0.00 42.61 3.02
2702 2748 3.242518 GGCCTAATGCGTTTTTCAAGAC 58.757 45.455 0.00 0.00 42.61 3.01
2703 2749 2.908626 GCCTAATGCGTTTTTCAAGACG 59.091 45.455 0.00 0.00 41.89 4.18
2704 2750 3.488489 CCTAATGCGTTTTTCAAGACGG 58.512 45.455 0.00 0.00 39.52 4.79
2705 2751 3.058501 CCTAATGCGTTTTTCAAGACGGT 60.059 43.478 0.00 0.00 39.52 4.83
2706 2752 2.399396 ATGCGTTTTTCAAGACGGTG 57.601 45.000 4.95 0.00 39.52 4.94
2707 2753 1.088306 TGCGTTTTTCAAGACGGTGT 58.912 45.000 4.95 0.00 39.52 4.16
2708 2754 1.469308 TGCGTTTTTCAAGACGGTGTT 59.531 42.857 4.95 0.00 39.52 3.32
2709 2755 2.095161 TGCGTTTTTCAAGACGGTGTTT 60.095 40.909 4.95 0.00 39.52 2.83
2710 2756 2.277834 GCGTTTTTCAAGACGGTGTTTG 59.722 45.455 4.95 0.00 39.52 2.93
2711 2757 3.749404 CGTTTTTCAAGACGGTGTTTGA 58.251 40.909 0.00 0.00 35.74 2.69
2712 2758 3.540738 CGTTTTTCAAGACGGTGTTTGAC 59.459 43.478 4.65 0.00 35.74 3.18
2713 2759 4.670735 CGTTTTTCAAGACGGTGTTTGACT 60.671 41.667 4.65 0.00 35.74 3.41
2714 2760 5.446206 CGTTTTTCAAGACGGTGTTTGACTA 60.446 40.000 4.65 0.00 35.74 2.59
2715 2761 6.492254 GTTTTTCAAGACGGTGTTTGACTAT 58.508 36.000 4.65 0.00 33.36 2.12
2716 2762 6.687081 TTTTCAAGACGGTGTTTGACTATT 57.313 33.333 4.65 0.00 33.36 1.73
2717 2763 5.666969 TTCAAGACGGTGTTTGACTATTG 57.333 39.130 4.65 0.00 33.36 1.90
2718 2764 4.951254 TCAAGACGGTGTTTGACTATTGA 58.049 39.130 0.00 0.00 0.00 2.57
2719 2765 4.748102 TCAAGACGGTGTTTGACTATTGAC 59.252 41.667 0.00 0.00 0.00 3.18
2720 2766 4.330944 AGACGGTGTTTGACTATTGACA 57.669 40.909 0.00 0.00 0.00 3.58
2721 2767 4.699637 AGACGGTGTTTGACTATTGACAA 58.300 39.130 0.00 0.00 0.00 3.18
2722 2768 4.750098 AGACGGTGTTTGACTATTGACAAG 59.250 41.667 0.00 0.00 0.00 3.16
2723 2769 4.699637 ACGGTGTTTGACTATTGACAAGA 58.300 39.130 0.00 0.00 0.00 3.02
2724 2770 5.305585 ACGGTGTTTGACTATTGACAAGAT 58.694 37.500 0.00 0.00 0.00 2.40
2725 2771 5.763204 ACGGTGTTTGACTATTGACAAGATT 59.237 36.000 0.00 0.00 0.00 2.40
2726 2772 6.932400 ACGGTGTTTGACTATTGACAAGATTA 59.068 34.615 0.00 0.00 0.00 1.75
2727 2773 7.442969 ACGGTGTTTGACTATTGACAAGATTAA 59.557 33.333 0.00 0.00 0.00 1.40
2728 2774 8.450964 CGGTGTTTGACTATTGACAAGATTAAT 58.549 33.333 0.00 0.00 0.00 1.40
2742 2788 9.481340 TGACAAGATTAATAGTACATGAGATGC 57.519 33.333 0.00 0.00 0.00 3.91
2743 2789 9.481340 GACAAGATTAATAGTACATGAGATGCA 57.519 33.333 0.00 0.00 0.00 3.96
2752 2798 9.783081 AATAGTACATGAGATGCATAATGTGAA 57.217 29.630 22.90 13.29 34.82 3.18
2753 2799 9.783081 ATAGTACATGAGATGCATAATGTGAAA 57.217 29.630 22.90 13.06 34.82 2.69
2754 2800 8.510243 AGTACATGAGATGCATAATGTGAAAA 57.490 30.769 22.90 8.28 34.82 2.29
2755 2801 9.128404 AGTACATGAGATGCATAATGTGAAAAT 57.872 29.630 22.90 8.02 34.82 1.82
2756 2802 9.740239 GTACATGAGATGCATAATGTGAAAATT 57.260 29.630 22.90 5.92 34.82 1.82
2785 2831 8.956533 TCATTGAAATATCCTTTCACATACGA 57.043 30.769 0.12 0.00 38.05 3.43
2786 2832 9.389755 TCATTGAAATATCCTTTCACATACGAA 57.610 29.630 0.12 0.00 38.05 3.85
2793 2839 5.524511 TCCTTTCACATACGAATTTGACG 57.475 39.130 0.00 0.00 0.00 4.35
2794 2840 5.231702 TCCTTTCACATACGAATTTGACGA 58.768 37.500 0.00 0.00 34.70 4.20
2795 2841 5.119588 TCCTTTCACATACGAATTTGACGAC 59.880 40.000 0.00 0.00 34.70 4.34
2796 2842 5.107259 CCTTTCACATACGAATTTGACGACA 60.107 40.000 0.00 0.00 34.70 4.35
2797 2843 6.402118 CCTTTCACATACGAATTTGACGACAT 60.402 38.462 0.00 0.00 34.70 3.06
2798 2844 5.448926 TCACATACGAATTTGACGACATG 57.551 39.130 0.00 0.00 35.12 3.21
2799 2845 4.021822 CACATACGAATTTGACGACATGC 58.978 43.478 0.00 0.00 33.69 4.06
2800 2846 3.932710 ACATACGAATTTGACGACATGCT 59.067 39.130 0.00 0.00 33.69 3.79
2801 2847 4.391830 ACATACGAATTTGACGACATGCTT 59.608 37.500 0.00 0.00 33.69 3.91
2802 2848 3.896648 ACGAATTTGACGACATGCTTT 57.103 38.095 0.00 0.00 34.70 3.51
2803 2849 3.554524 ACGAATTTGACGACATGCTTTG 58.445 40.909 0.00 0.00 34.70 2.77
2804 2850 3.003275 ACGAATTTGACGACATGCTTTGT 59.997 39.130 0.00 0.00 42.79 2.83
2805 2851 3.358700 CGAATTTGACGACATGCTTTGTG 59.641 43.478 0.00 0.00 39.18 3.33
2806 2852 3.988379 ATTTGACGACATGCTTTGTGT 57.012 38.095 0.00 0.00 39.18 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.533731 CGCCCGTGTTTGTATTTCTGT 59.466 47.619 0.00 0.00 0.00 3.41
59 64 5.355071 TGTTCCTGATGTATCTACGTACGTT 59.645 40.000 27.92 11.51 0.00 3.99
60 65 4.877823 TGTTCCTGATGTATCTACGTACGT 59.122 41.667 25.98 25.98 0.00 3.57
61 66 5.007430 AGTGTTCCTGATGTATCTACGTACG 59.993 44.000 15.01 15.01 0.00 3.67
62 67 6.183360 ACAGTGTTCCTGATGTATCTACGTAC 60.183 42.308 0.00 0.00 44.49 3.67
154 159 2.741092 GGCGGGTGAGTGAGTGAA 59.259 61.111 0.00 0.00 0.00 3.18
299 310 2.600790 CGGGGGTGTGTGTATATAGGA 58.399 52.381 0.00 0.00 0.00 2.94
358 369 0.605319 GCGATTGGGTGTGGTGAGAA 60.605 55.000 0.00 0.00 0.00 2.87
361 372 2.033448 GGCGATTGGGTGTGGTGA 59.967 61.111 0.00 0.00 0.00 4.02
403 415 2.486203 CGGGTAGAAGGAGAGATCGATG 59.514 54.545 0.54 0.00 0.00 3.84
480 492 3.193691 ACAGTACGAGGAAGATCAACCAG 59.806 47.826 10.11 6.57 0.00 4.00
485 497 3.878103 GAGCTACAGTACGAGGAAGATCA 59.122 47.826 0.00 0.00 0.00 2.92
554 566 4.760047 GCGCTGGACCGTGGTCAT 62.760 66.667 20.02 0.00 46.20 3.06
584 596 2.017049 AGCCAAGAAACTGACACACAC 58.983 47.619 0.00 0.00 0.00 3.82
585 597 2.016318 CAGCCAAGAAACTGACACACA 58.984 47.619 0.00 0.00 35.90 3.72
778 795 3.799420 GTCTGTAGCTGTACATGCTAAGC 59.201 47.826 21.10 10.50 43.50 3.09
780 797 4.950475 AGAGTCTGTAGCTGTACATGCTAA 59.050 41.667 21.10 13.77 43.50 3.09
836 853 3.453717 TGGTTCTTCAGCTCAGCTCATAT 59.546 43.478 0.00 0.00 36.40 1.78
837 854 2.833943 TGGTTCTTCAGCTCAGCTCATA 59.166 45.455 0.00 0.00 36.40 2.15
862 891 2.801342 GCTAGCTGCTTATCAGTTCGCT 60.801 50.000 7.79 0.00 44.66 4.93
906 935 6.427853 GCCTGAAACCAAAAGCATCTTAATTT 59.572 34.615 0.00 0.00 0.00 1.82
940 969 1.143183 CGGCCGCCTGTTAGTACAT 59.857 57.895 14.67 0.00 32.86 2.29
1077 1114 3.509137 GAACGTGTGCCAGTCCCGA 62.509 63.158 0.00 0.00 0.00 5.14
1512 1549 2.504032 GGCGCTGCTACATGGGTA 59.496 61.111 7.64 0.00 0.00 3.69
1728 1765 1.228033 CATCGCCATGGCCATCTCA 60.228 57.895 30.79 8.29 37.98 3.27
1811 1848 1.434696 CATGGATGCAGCCGGAAAC 59.565 57.895 17.68 0.00 0.00 2.78
1919 1957 1.137086 ACTCATCCTTCCATCGTTCCG 59.863 52.381 0.00 0.00 0.00 4.30
1983 2023 3.525800 AGCCAAAAGGGTGAATAGTGT 57.474 42.857 0.00 0.00 39.65 3.55
2081 2121 3.253230 GCATACACAAATCAACCAAGCC 58.747 45.455 0.00 0.00 0.00 4.35
2176 2216 3.527533 AATGCATGTTGCCATGAATCAC 58.472 40.909 0.00 0.00 45.10 3.06
2188 2228 5.921004 ACGCAACAAATTAAATGCATGTT 57.079 30.435 0.00 0.00 38.69 2.71
2189 2229 5.695816 AGAACGCAACAAATTAAATGCATGT 59.304 32.000 0.00 0.00 38.69 3.21
2263 2303 5.178996 GTCATGGCAATGCTAGTCATAAGAG 59.821 44.000 4.82 0.00 34.33 2.85
2281 2321 6.183360 CGAAAATTCTGCAGAAAATGTCATGG 60.183 38.462 31.55 12.30 37.61 3.66
2305 2345 1.456544 GCATGAAACATTTGCCACACG 59.543 47.619 0.00 0.00 0.00 4.49
2306 2346 2.481854 TGCATGAAACATTTGCCACAC 58.518 42.857 0.00 0.00 35.51 3.82
2307 2347 2.904697 TGCATGAAACATTTGCCACA 57.095 40.000 0.00 0.00 35.51 4.17
2308 2348 3.327626 TGATGCATGAAACATTTGCCAC 58.672 40.909 2.46 0.00 35.51 5.01
2309 2349 3.679824 TGATGCATGAAACATTTGCCA 57.320 38.095 2.46 0.00 35.51 4.92
2310 2350 4.270084 CAGATGATGCATGAAACATTTGCC 59.730 41.667 2.46 0.00 35.51 4.52
2311 2351 4.868171 ACAGATGATGCATGAAACATTTGC 59.132 37.500 12.81 0.00 36.91 3.68
2312 2352 7.704899 ACATACAGATGATGCATGAAACATTTG 59.295 33.333 2.46 11.65 36.34 2.32
2313 2353 7.778083 ACATACAGATGATGCATGAAACATTT 58.222 30.769 2.46 0.00 36.34 2.32
2314 2354 7.342769 ACATACAGATGATGCATGAAACATT 57.657 32.000 2.46 0.00 36.34 2.71
2315 2355 6.954487 ACATACAGATGATGCATGAAACAT 57.046 33.333 2.46 0.04 36.34 2.71
2316 2356 6.762702 AACATACAGATGATGCATGAAACA 57.237 33.333 2.46 0.00 36.34 2.83
2317 2357 7.252708 TGAAACATACAGATGATGCATGAAAC 58.747 34.615 2.46 0.00 36.34 2.78
2318 2358 7.393841 TGAAACATACAGATGATGCATGAAA 57.606 32.000 2.46 0.00 36.34 2.69
2319 2359 7.501225 AGATGAAACATACAGATGATGCATGAA 59.499 33.333 2.46 0.00 36.34 2.57
2320 2360 6.996282 AGATGAAACATACAGATGATGCATGA 59.004 34.615 2.46 0.00 36.34 3.07
2321 2361 7.203255 AGATGAAACATACAGATGATGCATG 57.797 36.000 2.46 0.00 38.46 4.06
2322 2362 7.818997 AAGATGAAACATACAGATGATGCAT 57.181 32.000 0.00 0.00 36.48 3.96
2323 2363 7.634671 AAAGATGAAACATACAGATGATGCA 57.365 32.000 0.00 0.00 36.48 3.96
2324 2364 8.922058 AAAAAGATGAAACATACAGATGATGC 57.078 30.769 0.00 0.00 36.48 3.91
2348 2388 6.938507 AGCATATGAGAAATCAAGGCAAAAA 58.061 32.000 6.97 0.00 0.00 1.94
2408 2453 9.457436 CCAACATCATATCATATGAATCAAGGA 57.543 33.333 11.48 3.80 0.00 3.36
2409 2455 9.239551 ACCAACATCATATCATATGAATCAAGG 57.760 33.333 11.48 11.70 0.00 3.61
2506 2552 7.444299 AGTTGTGTGGATTTTCTATGCAAATT 58.556 30.769 0.00 0.00 0.00 1.82
2529 2575 4.460263 TGTGCAAAGACTTCAATGGTAGT 58.540 39.130 0.00 0.00 0.00 2.73
2579 2625 4.412796 AGAGAAGATGCATCGGAAATGA 57.587 40.909 20.67 0.00 0.00 2.57
2640 2686 3.006323 GGAGTACAGTGCATCCTGATAGG 59.994 52.174 11.03 0.00 36.30 2.57
2654 2700 7.969690 ATATAGATGGAAGGATGGAGTACAG 57.030 40.000 0.00 0.00 0.00 2.74
2659 2705 5.306678 GCCCTATATAGATGGAAGGATGGAG 59.693 48.000 11.53 0.00 0.00 3.86
2660 2706 5.219739 GCCCTATATAGATGGAAGGATGGA 58.780 45.833 11.53 0.00 0.00 3.41
2661 2707 4.349342 GGCCCTATATAGATGGAAGGATGG 59.651 50.000 11.53 1.18 0.00 3.51
2662 2708 5.222870 AGGCCCTATATAGATGGAAGGATG 58.777 45.833 11.53 0.00 0.00 3.51
2663 2709 5.511546 AGGCCCTATATAGATGGAAGGAT 57.488 43.478 11.53 0.00 0.00 3.24
2664 2710 4.994411 AGGCCCTATATAGATGGAAGGA 57.006 45.455 11.53 0.00 0.00 3.36
2665 2711 6.465035 GCATTAGGCCCTATATAGATGGAAGG 60.465 46.154 11.53 3.94 36.11 3.46
2666 2712 6.529220 GCATTAGGCCCTATATAGATGGAAG 58.471 44.000 11.53 0.00 36.11 3.46
2667 2713 5.070446 CGCATTAGGCCCTATATAGATGGAA 59.930 44.000 11.53 0.00 40.31 3.53
2668 2714 4.588951 CGCATTAGGCCCTATATAGATGGA 59.411 45.833 11.53 0.00 40.31 3.41
2669 2715 4.345257 ACGCATTAGGCCCTATATAGATGG 59.655 45.833 11.53 6.04 40.31 3.51
2670 2716 5.537300 ACGCATTAGGCCCTATATAGATG 57.463 43.478 11.53 6.87 40.31 2.90
2671 2717 6.561519 AAACGCATTAGGCCCTATATAGAT 57.438 37.500 11.53 0.00 40.31 1.98
2672 2718 6.368779 AAAACGCATTAGGCCCTATATAGA 57.631 37.500 11.53 0.00 40.31 1.98
2673 2719 6.653320 TGAAAAACGCATTAGGCCCTATATAG 59.347 38.462 0.00 2.46 40.31 1.31
2674 2720 6.535540 TGAAAAACGCATTAGGCCCTATATA 58.464 36.000 0.00 0.00 40.31 0.86
2675 2721 5.381757 TGAAAAACGCATTAGGCCCTATAT 58.618 37.500 0.00 0.00 40.31 0.86
2676 2722 4.783055 TGAAAAACGCATTAGGCCCTATA 58.217 39.130 0.00 0.00 40.31 1.31
2677 2723 3.626930 TGAAAAACGCATTAGGCCCTAT 58.373 40.909 0.00 0.00 40.31 2.57
2678 2724 3.074675 TGAAAAACGCATTAGGCCCTA 57.925 42.857 0.00 0.00 40.31 3.53
2679 2725 1.917872 TGAAAAACGCATTAGGCCCT 58.082 45.000 0.00 0.00 40.31 5.19
2680 2726 2.230266 TCTTGAAAAACGCATTAGGCCC 59.770 45.455 0.00 0.00 40.31 5.80
2681 2727 3.242518 GTCTTGAAAAACGCATTAGGCC 58.757 45.455 0.00 0.00 40.31 5.19
2682 2728 2.908626 CGTCTTGAAAAACGCATTAGGC 59.091 45.455 0.00 0.00 39.90 3.93
2683 2729 3.058501 ACCGTCTTGAAAAACGCATTAGG 60.059 43.478 0.00 0.00 37.56 2.69
2684 2730 3.906008 CACCGTCTTGAAAAACGCATTAG 59.094 43.478 0.00 0.00 37.56 1.73
2685 2731 3.312973 ACACCGTCTTGAAAAACGCATTA 59.687 39.130 0.00 0.00 37.56 1.90
2686 2732 2.098443 ACACCGTCTTGAAAAACGCATT 59.902 40.909 0.00 0.00 37.56 3.56
2687 2733 1.673920 ACACCGTCTTGAAAAACGCAT 59.326 42.857 0.00 0.00 37.56 4.73
2688 2734 1.088306 ACACCGTCTTGAAAAACGCA 58.912 45.000 0.00 0.00 37.56 5.24
2689 2735 2.182904 AACACCGTCTTGAAAAACGC 57.817 45.000 0.00 0.00 37.56 4.84
2690 2736 3.540738 GTCAAACACCGTCTTGAAAAACG 59.459 43.478 0.00 0.00 38.58 3.60
2691 2737 4.729595 AGTCAAACACCGTCTTGAAAAAC 58.270 39.130 0.00 0.00 33.52 2.43
2692 2738 6.687081 ATAGTCAAACACCGTCTTGAAAAA 57.313 33.333 0.00 0.00 33.52 1.94
2693 2739 6.316640 TCAATAGTCAAACACCGTCTTGAAAA 59.683 34.615 0.00 0.00 33.52 2.29
2694 2740 5.818336 TCAATAGTCAAACACCGTCTTGAAA 59.182 36.000 0.00 0.00 33.52 2.69
2695 2741 5.235616 GTCAATAGTCAAACACCGTCTTGAA 59.764 40.000 0.00 0.00 33.52 2.69
2696 2742 4.748102 GTCAATAGTCAAACACCGTCTTGA 59.252 41.667 0.00 0.00 0.00 3.02
2697 2743 4.509970 TGTCAATAGTCAAACACCGTCTTG 59.490 41.667 0.00 0.00 0.00 3.02
2698 2744 4.699637 TGTCAATAGTCAAACACCGTCTT 58.300 39.130 0.00 0.00 0.00 3.01
2699 2745 4.330944 TGTCAATAGTCAAACACCGTCT 57.669 40.909 0.00 0.00 0.00 4.18
2700 2746 4.748102 TCTTGTCAATAGTCAAACACCGTC 59.252 41.667 0.00 0.00 0.00 4.79
2701 2747 4.699637 TCTTGTCAATAGTCAAACACCGT 58.300 39.130 0.00 0.00 0.00 4.83
2702 2748 5.862924 ATCTTGTCAATAGTCAAACACCG 57.137 39.130 0.00 0.00 0.00 4.94
2716 2762 9.481340 GCATCTCATGTACTATTAATCTTGTCA 57.519 33.333 0.00 0.00 0.00 3.58
2717 2763 9.481340 TGCATCTCATGTACTATTAATCTTGTC 57.519 33.333 0.00 0.00 0.00 3.18
2726 2772 9.783081 TTCACATTATGCATCTCATGTACTATT 57.217 29.630 15.24 0.00 36.63 1.73
2727 2773 9.783081 TTTCACATTATGCATCTCATGTACTAT 57.217 29.630 15.24 0.00 36.63 2.12
2728 2774 9.612066 TTTTCACATTATGCATCTCATGTACTA 57.388 29.630 15.24 5.57 36.63 1.82
2729 2775 8.510243 TTTTCACATTATGCATCTCATGTACT 57.490 30.769 15.24 0.00 36.63 2.73
2730 2776 9.740239 AATTTTCACATTATGCATCTCATGTAC 57.260 29.630 15.24 0.00 36.63 2.90
2759 2805 9.559732 TCGTATGTGAAAGGATATTTCAATGAT 57.440 29.630 4.71 1.76 39.76 2.45
2760 2806 8.956533 TCGTATGTGAAAGGATATTTCAATGA 57.043 30.769 4.71 0.00 39.76 2.57
2767 2813 8.335356 CGTCAAATTCGTATGTGAAAGGATATT 58.665 33.333 0.00 0.00 29.80 1.28
2768 2814 7.709182 TCGTCAAATTCGTATGTGAAAGGATAT 59.291 33.333 0.00 0.00 29.80 1.63
2769 2815 7.009815 GTCGTCAAATTCGTATGTGAAAGGATA 59.990 37.037 0.00 0.00 29.80 2.59
2770 2816 5.872617 TCGTCAAATTCGTATGTGAAAGGAT 59.127 36.000 0.00 0.00 29.80 3.24
2771 2817 5.119588 GTCGTCAAATTCGTATGTGAAAGGA 59.880 40.000 0.00 0.00 29.80 3.36
2772 2818 5.107259 TGTCGTCAAATTCGTATGTGAAAGG 60.107 40.000 0.00 0.00 29.80 3.11
2773 2819 5.911421 TGTCGTCAAATTCGTATGTGAAAG 58.089 37.500 0.00 0.00 29.80 2.62
2774 2820 5.908916 TGTCGTCAAATTCGTATGTGAAA 57.091 34.783 0.00 0.00 29.80 2.69
2775 2821 5.670094 GCATGTCGTCAAATTCGTATGTGAA 60.670 40.000 0.00 0.00 29.80 3.18
2776 2822 4.201676 GCATGTCGTCAAATTCGTATGTGA 60.202 41.667 0.00 0.00 0.00 3.58
2777 2823 4.021822 GCATGTCGTCAAATTCGTATGTG 58.978 43.478 0.00 0.00 0.00 3.21
2778 2824 3.932710 AGCATGTCGTCAAATTCGTATGT 59.067 39.130 0.00 0.00 0.00 2.29
2779 2825 4.520743 AGCATGTCGTCAAATTCGTATG 57.479 40.909 0.00 0.00 0.00 2.39
2780 2826 5.106712 ACAAAGCATGTCGTCAAATTCGTAT 60.107 36.000 0.00 0.00 37.96 3.06
2781 2827 4.212425 ACAAAGCATGTCGTCAAATTCGTA 59.788 37.500 0.00 0.00 37.96 3.43
2782 2828 3.003275 ACAAAGCATGTCGTCAAATTCGT 59.997 39.130 0.00 0.00 37.96 3.85
2783 2829 3.358700 CACAAAGCATGTCGTCAAATTCG 59.641 43.478 0.00 0.00 41.46 3.34
2784 2830 4.290155 ACACAAAGCATGTCGTCAAATTC 58.710 39.130 0.00 0.00 41.46 2.17
2785 2831 4.305989 ACACAAAGCATGTCGTCAAATT 57.694 36.364 0.00 0.00 41.46 1.82
2786 2832 3.988379 ACACAAAGCATGTCGTCAAAT 57.012 38.095 0.00 0.00 41.46 2.32


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

AutoCloner maintained by Alex Coulton.