Multiple sequence alignment - TraesCS4D01G257300

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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 TraesCS4D01G257300 chr4D 100.000 2680 0 0 1 2680 426869280 426871959 0.000000e+00 4950.0
1 TraesCS4D01G257300 chr4D 84.357 1937 187 59 816 2674 57840490 57842388 0.000000e+00 1792.0
2 TraesCS4D01G257300 chr4D 87.315 1419 135 28 844 2242 424169693 424168300 0.000000e+00 1581.0
3 TraesCS4D01G257300 chr4D 86.573 1430 135 32 844 2242 423989957 423988554 0.000000e+00 1524.0
4 TraesCS4D01G257300 chr4D 86.573 1430 135 33 844 2242 424110679 424109276 0.000000e+00 1524.0
5 TraesCS4D01G257300 chr4D 89.683 756 62 7 1500 2242 424196577 424195825 0.000000e+00 950.0
6 TraesCS4D01G257300 chr4D 91.667 504 33 3 731 1234 427208867 427209361 0.000000e+00 689.0
7 TraesCS4D01G257300 chr4D 89.159 452 27 9 2249 2679 427261688 427262138 8.010000e-151 544.0
8 TraesCS4D01G257300 chr4D 100.000 229 0 0 3053 3281 426872332 426872560 1.090000e-114 424.0
9 TraesCS4D01G257300 chr4D 82.540 315 24 14 2295 2588 428547191 428546887 7.030000e-62 248.0
10 TraesCS4D01G257300 chr4D 79.692 389 41 22 2289 2648 427323869 427324248 2.530000e-61 246.0
11 TraesCS4D01G257300 chr4D 80.565 283 21 14 2267 2530 428557093 428556826 1.550000e-43 187.0
12 TraesCS4D01G257300 chr4B 93.896 1966 88 16 731 2677 522669173 522671125 0.000000e+00 2937.0
13 TraesCS4D01G257300 chr4B 93.815 1633 62 11 900 2493 527644914 527643282 0.000000e+00 2420.0
14 TraesCS4D01G257300 chr4B 87.966 1529 125 22 735 2243 527781437 527779948 0.000000e+00 1749.0
15 TraesCS4D01G257300 chr4B 89.060 1362 112 22 905 2242 86132163 86130815 0.000000e+00 1655.0
16 TraesCS4D01G257300 chr4B 93.469 735 46 1 1 735 399040025 399039293 0.000000e+00 1090.0
17 TraesCS4D01G257300 chr4B 89.604 404 27 6 2251 2642 527748230 527747830 1.760000e-137 499.0
18 TraesCS4D01G257300 chr4B 88.889 171 9 5 731 900 527646624 527646463 5.550000e-48 202.0
19 TraesCS4D01G257300 chr4B 79.141 326 31 22 2264 2563 522683418 522683732 1.200000e-44 191.0
20 TraesCS4D01G257300 chr4B 85.088 114 9 3 2489 2594 527620180 527620067 3.460000e-20 110.0
21 TraesCS4D01G257300 chr4B 93.846 65 4 0 2615 2679 527594482 527594418 7.490000e-17 99.0
22 TraesCS4D01G257300 chr4B 83.721 86 9 3 2561 2646 522678641 522678721 3.510000e-10 76.8
23 TraesCS4D01G257300 chr4A 91.316 1520 69 20 779 2292 38682997 38681535 0.000000e+00 2017.0
24 TraesCS4D01G257300 chr4A 77.967 1702 254 60 994 2646 38675637 38674008 0.000000e+00 953.0
25 TraesCS4D01G257300 chr4A 87.531 401 19 8 2309 2679 38681481 38681082 5.030000e-118 435.0
26 TraesCS4D01G257300 chr4A 83.526 346 31 16 2249 2570 37834934 37835277 1.910000e-77 300.0
27 TraesCS4D01G257300 chr4A 95.833 48 2 0 2245 2292 38681528 38681481 9.760000e-11 78.7
28 TraesCS4D01G257300 chr3D 92.484 918 52 8 869 1779 543683994 543683087 0.000000e+00 1297.0
29 TraesCS4D01G257300 chr3D 93.605 735 41 5 1 735 100469229 100469957 0.000000e+00 1092.0
30 TraesCS4D01G257300 chr3D 88.983 236 19 7 2395 2625 543683086 543682853 5.360000e-73 285.0
31 TraesCS4D01G257300 chr7D 94.701 736 36 3 1 735 133689078 133689811 0.000000e+00 1140.0
32 TraesCS4D01G257300 chr2D 94.286 735 39 1 1 735 36580499 36579768 0.000000e+00 1122.0
33 TraesCS4D01G257300 chr2D 93.886 736 38 6 1 735 362291673 362290944 0.000000e+00 1103.0
34 TraesCS4D01G257300 chr6B 94.150 735 41 2 1 735 4466015 4466747 0.000000e+00 1118.0
35 TraesCS4D01G257300 chr6B 93.878 735 43 2 1 735 4462981 4463713 0.000000e+00 1107.0
36 TraesCS4D01G257300 chr6D 93.733 734 40 6 1 733 270581545 270582273 0.000000e+00 1096.0
37 TraesCS4D01G257300 chr6D 95.814 215 9 0 3067 3281 362178523 362178309 6.740000e-92 348.0
38 TraesCS4D01G257300 chr2B 93.724 733 43 3 1 733 399837825 399837096 0.000000e+00 1096.0
39 TraesCS4D01G257300 chr5B 95.890 219 8 1 3064 3281 517190912 517191130 1.450000e-93 353.0
40 TraesCS4D01G257300 chr2A 96.279 215 8 0 3067 3281 752763170 752762956 1.450000e-93 353.0
41 TraesCS4D01G257300 chr7A 95.814 215 9 0 3067 3281 29818258 29818044 6.740000e-92 348.0
42 TraesCS4D01G257300 chr1B 95.434 219 9 1 3064 3281 401339408 401339626 6.740000e-92 348.0
43 TraesCS4D01G257300 chr1B 94.954 218 11 0 3064 3281 60049336 60049553 3.130000e-90 342.0
44 TraesCS4D01G257300 chr1B 94.884 215 11 0 3064 3278 59962900 59963114 1.460000e-88 337.0
45 TraesCS4D01G257300 chr6A 93.886 229 14 0 3053 3281 28961963 28962191 2.420000e-91 346.0
46 TraesCS4D01G257300 chr6A 94.954 218 11 0 3064 3281 28903925 28904142 3.130000e-90 342.0


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 TraesCS4D01G257300 chr4D 426869280 426872560 3280 False 2687.000000 4950 100.0000 1 3281 2 chr4D.!!$F5 3280
1 TraesCS4D01G257300 chr4D 57840490 57842388 1898 False 1792.000000 1792 84.3570 816 2674 1 chr4D.!!$F1 1858
2 TraesCS4D01G257300 chr4D 424168300 424169693 1393 True 1581.000000 1581 87.3150 844 2242 1 chr4D.!!$R3 1398
3 TraesCS4D01G257300 chr4D 423988554 423989957 1403 True 1524.000000 1524 86.5730 844 2242 1 chr4D.!!$R1 1398
4 TraesCS4D01G257300 chr4D 424109276 424110679 1403 True 1524.000000 1524 86.5730 844 2242 1 chr4D.!!$R2 1398
5 TraesCS4D01G257300 chr4D 424195825 424196577 752 True 950.000000 950 89.6830 1500 2242 1 chr4D.!!$R4 742
6 TraesCS4D01G257300 chr4B 522669173 522671125 1952 False 2937.000000 2937 93.8960 731 2677 1 chr4B.!!$F1 1946
7 TraesCS4D01G257300 chr4B 527779948 527781437 1489 True 1749.000000 1749 87.9660 735 2243 1 chr4B.!!$R6 1508
8 TraesCS4D01G257300 chr4B 86130815 86132163 1348 True 1655.000000 1655 89.0600 905 2242 1 chr4B.!!$R1 1337
9 TraesCS4D01G257300 chr4B 527643282 527646624 3342 True 1311.000000 2420 91.3520 731 2493 2 chr4B.!!$R7 1762
10 TraesCS4D01G257300 chr4B 399039293 399040025 732 True 1090.000000 1090 93.4690 1 735 1 chr4B.!!$R2 734
11 TraesCS4D01G257300 chr4A 38674008 38675637 1629 True 953.000000 953 77.9670 994 2646 1 chr4A.!!$R1 1652
12 TraesCS4D01G257300 chr4A 38681082 38682997 1915 True 843.566667 2017 91.5600 779 2679 3 chr4A.!!$R2 1900
13 TraesCS4D01G257300 chr3D 100469229 100469957 728 False 1092.000000 1092 93.6050 1 735 1 chr3D.!!$F1 734
14 TraesCS4D01G257300 chr3D 543682853 543683994 1141 True 791.000000 1297 90.7335 869 2625 2 chr3D.!!$R1 1756
15 TraesCS4D01G257300 chr7D 133689078 133689811 733 False 1140.000000 1140 94.7010 1 735 1 chr7D.!!$F1 734
16 TraesCS4D01G257300 chr2D 36579768 36580499 731 True 1122.000000 1122 94.2860 1 735 1 chr2D.!!$R1 734
17 TraesCS4D01G257300 chr2D 362290944 362291673 729 True 1103.000000 1103 93.8860 1 735 1 chr2D.!!$R2 734
18 TraesCS4D01G257300 chr6B 4462981 4466747 3766 False 1112.500000 1118 94.0140 1 735 2 chr6B.!!$F1 734
19 TraesCS4D01G257300 chr6D 270581545 270582273 728 False 1096.000000 1096 93.7330 1 733 1 chr6D.!!$F1 732
20 TraesCS4D01G257300 chr2B 399837096 399837825 729 True 1096.000000 1096 93.7240 1 733 1 chr2B.!!$R1 732

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
697 702 0.168128 GCTCAGCCGCGTATGTTTTT 59.832 50.0 4.92 0.00 0.00 1.94 F
729 734 0.179225 CGATTTTCGTGAACCCGCAG 60.179 55.0 0.00 0.00 34.72 5.18 F
1506 3129 0.247460 TCATGTGGAAGCTCCTCACG 59.753 55.0 8.49 2.75 42.10 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1506 3129 4.408821 TGCATCGTCCTGGCACCC 62.409 66.667 0.00 0.00 31.58 4.61 R
2150 6342 4.715751 TAGATTCTTCTGTGGCATGGCCT 61.716 47.826 17.72 4.76 40.42 5.19 R
3149 7745 0.458543 CTTCATCGACGACCCACCAG 60.459 60.000 0.00 0.00 0.00 4.00 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
68 69 4.231753 CGTGTTCTTCGTACGCCA 57.768 55.556 11.24 0.00 0.00 5.69
238 243 3.073101 GGGCCCGAGGACTACGTT 61.073 66.667 5.69 0.00 0.00 3.99
456 461 2.427245 CCGGCGAGGAGGATTGAGT 61.427 63.158 9.30 0.00 45.00 3.41
497 502 4.680237 CCAGTTGCCGCGACCTCA 62.680 66.667 8.23 0.00 0.00 3.86
528 533 2.196742 TCCGACCCCCTAGTACTAGA 57.803 55.000 28.07 5.87 35.21 2.43
627 632 6.086222 GTGATGAACTATGTTCGTGCAATTT 58.914 36.000 9.52 0.00 0.00 1.82
628 633 6.249260 GTGATGAACTATGTTCGTGCAATTTC 59.751 38.462 9.52 0.00 0.00 2.17
629 634 5.940192 TGAACTATGTTCGTGCAATTTCT 57.060 34.783 0.00 0.00 0.00 2.52
630 635 5.927030 TGAACTATGTTCGTGCAATTTCTC 58.073 37.500 0.00 0.00 0.00 2.87
631 636 5.700832 TGAACTATGTTCGTGCAATTTCTCT 59.299 36.000 0.00 0.00 0.00 3.10
632 637 5.786401 ACTATGTTCGTGCAATTTCTCTC 57.214 39.130 0.00 0.00 0.00 3.20
633 638 3.729526 ATGTTCGTGCAATTTCTCTCG 57.270 42.857 0.00 0.00 0.00 4.04
634 639 1.194547 TGTTCGTGCAATTTCTCTCGC 59.805 47.619 0.00 0.00 0.00 5.03
635 640 1.194547 GTTCGTGCAATTTCTCTCGCA 59.805 47.619 0.00 0.00 0.00 5.10
636 641 1.507562 TCGTGCAATTTCTCTCGCAA 58.492 45.000 0.00 0.00 35.87 4.85
637 642 1.870402 TCGTGCAATTTCTCTCGCAAA 59.130 42.857 0.00 0.00 35.87 3.68
638 643 2.289274 TCGTGCAATTTCTCTCGCAAAA 59.711 40.909 0.00 0.00 35.87 2.44
639 644 2.401720 CGTGCAATTTCTCTCGCAAAAC 59.598 45.455 0.00 0.00 35.87 2.43
640 645 3.371168 GTGCAATTTCTCTCGCAAAACA 58.629 40.909 0.00 0.00 35.87 2.83
641 646 3.796178 GTGCAATTTCTCTCGCAAAACAA 59.204 39.130 0.00 0.00 35.87 2.83
642 647 4.445385 GTGCAATTTCTCTCGCAAAACAAT 59.555 37.500 0.00 0.00 35.87 2.71
643 648 5.049167 TGCAATTTCTCTCGCAAAACAATT 58.951 33.333 0.00 0.00 0.00 2.32
644 649 5.523188 TGCAATTTCTCTCGCAAAACAATTT 59.477 32.000 0.00 0.00 0.00 1.82
645 650 6.036953 TGCAATTTCTCTCGCAAAACAATTTT 59.963 30.769 0.00 0.00 0.00 1.82
646 651 6.906678 GCAATTTCTCTCGCAAAACAATTTTT 59.093 30.769 0.00 0.00 35.15 1.94
678 683 9.760077 ATTATACAAGTTTAGATACGGGTTCTG 57.240 33.333 0.00 0.00 0.00 3.02
679 684 4.251268 ACAAGTTTAGATACGGGTTCTGC 58.749 43.478 0.00 0.00 0.00 4.26
680 685 4.020485 ACAAGTTTAGATACGGGTTCTGCT 60.020 41.667 0.00 0.00 0.00 4.24
681 686 4.388378 AGTTTAGATACGGGTTCTGCTC 57.612 45.455 0.00 0.00 0.00 4.26
682 687 3.767673 AGTTTAGATACGGGTTCTGCTCA 59.232 43.478 0.00 0.00 0.00 4.26
683 688 4.113354 GTTTAGATACGGGTTCTGCTCAG 58.887 47.826 0.00 0.00 0.00 3.35
684 689 0.461961 AGATACGGGTTCTGCTCAGC 59.538 55.000 0.00 0.00 0.00 4.26
685 690 0.530870 GATACGGGTTCTGCTCAGCC 60.531 60.000 0.00 0.00 0.00 4.85
690 695 2.126071 GTTCTGCTCAGCCGCGTA 60.126 61.111 4.92 0.00 0.00 4.42
691 696 1.519455 GTTCTGCTCAGCCGCGTAT 60.519 57.895 4.92 0.00 0.00 3.06
692 697 1.519234 TTCTGCTCAGCCGCGTATG 60.519 57.895 4.92 2.99 0.00 2.39
693 698 2.202797 CTGCTCAGCCGCGTATGT 60.203 61.111 4.92 0.00 0.00 2.29
694 699 1.811266 CTGCTCAGCCGCGTATGTT 60.811 57.895 4.92 0.00 0.00 2.71
695 700 1.361668 CTGCTCAGCCGCGTATGTTT 61.362 55.000 4.92 0.00 0.00 2.83
696 701 0.953471 TGCTCAGCCGCGTATGTTTT 60.953 50.000 4.92 0.00 0.00 2.43
697 702 0.168128 GCTCAGCCGCGTATGTTTTT 59.832 50.000 4.92 0.00 0.00 1.94
698 703 1.395608 GCTCAGCCGCGTATGTTTTTA 59.604 47.619 4.92 0.00 0.00 1.52
699 704 2.159626 GCTCAGCCGCGTATGTTTTTAA 60.160 45.455 4.92 0.00 0.00 1.52
700 705 3.486875 GCTCAGCCGCGTATGTTTTTAAT 60.487 43.478 4.92 0.00 0.00 1.40
701 706 4.267357 TCAGCCGCGTATGTTTTTAATC 57.733 40.909 4.92 0.00 0.00 1.75
702 707 3.064271 TCAGCCGCGTATGTTTTTAATCC 59.936 43.478 4.92 0.00 0.00 3.01
703 708 2.031191 AGCCGCGTATGTTTTTAATCCG 59.969 45.455 4.92 0.00 0.00 4.18
704 709 2.368685 CCGCGTATGTTTTTAATCCGC 58.631 47.619 4.92 0.00 36.57 5.54
705 710 2.223066 CCGCGTATGTTTTTAATCCGCA 60.223 45.455 4.92 0.00 39.61 5.69
706 711 3.418094 CGCGTATGTTTTTAATCCGCAA 58.582 40.909 0.00 0.00 39.61 4.85
707 712 3.846896 CGCGTATGTTTTTAATCCGCAAA 59.153 39.130 0.00 0.00 39.61 3.68
708 713 4.321217 CGCGTATGTTTTTAATCCGCAAAA 59.679 37.500 0.00 0.00 39.61 2.44
709 714 5.164177 CGCGTATGTTTTTAATCCGCAAAAA 60.164 36.000 0.00 0.00 39.61 1.94
717 722 8.183377 GTTTTTAATCCGCAAAAACGATTTTC 57.817 30.769 0.00 0.00 42.60 2.29
718 723 5.732849 TTAATCCGCAAAAACGATTTTCG 57.267 34.783 0.00 7.80 46.93 3.46
727 732 4.737601 CGATTTTCGTGAACCCGC 57.262 55.556 0.00 0.00 34.72 6.13
728 733 1.863491 CGATTTTCGTGAACCCGCA 59.137 52.632 0.00 0.00 34.72 5.69
729 734 0.179225 CGATTTTCGTGAACCCGCAG 60.179 55.000 0.00 0.00 34.72 5.18
814 819 2.095466 GTCGATCTGTGGATCCTCGATC 60.095 54.545 21.58 22.89 43.90 3.69
832 841 4.162690 GCCTAGGTCCAGGGCGTG 62.163 72.222 11.31 0.00 36.37 5.34
1506 3129 0.247460 TCATGTGGAAGCTCCTCACG 59.753 55.000 8.49 2.75 42.10 4.35
2150 6342 0.911769 AGGATCAAGTTCATCCCGCA 59.088 50.000 1.53 0.00 40.90 5.69
2359 6886 0.107410 CGCCCATTAGTGTTGGCCTA 60.107 55.000 3.32 0.00 40.87 3.93
2427 6992 6.607198 TGTGATGTAGTGTTGAGAGATCCATA 59.393 38.462 0.00 0.00 0.00 2.74
2548 7134 8.396272 AGTACAAATGTTCTAAGCAACAGAAT 57.604 30.769 0.00 0.00 39.63 2.40
2550 7136 9.463443 GTACAAATGTTCTAAGCAACAGAATTT 57.537 29.630 0.00 0.00 39.63 1.82
2591 7177 5.815581 TGATGGTTAAAATGTCCTGCTAGT 58.184 37.500 0.00 0.00 0.00 2.57
2679 7275 4.986034 TGTACTTCAGTGTATGTGTTTCCG 59.014 41.667 0.00 0.00 0.00 4.30
3075 7671 2.907917 CCTCCCGAGGGCGACTAG 60.908 72.222 2.58 0.00 44.87 2.57
3076 7672 2.907917 CTCCCGAGGGCGACTAGG 60.908 72.222 2.58 0.00 41.27 3.02
3079 7675 2.758737 CCGAGGGCGACTAGGGTT 60.759 66.667 0.00 0.00 38.23 4.11
3080 7676 2.356780 CCGAGGGCGACTAGGGTTT 61.357 63.158 0.00 0.00 38.23 3.27
3081 7677 1.141234 CGAGGGCGACTAGGGTTTC 59.859 63.158 0.00 0.00 40.82 2.78
3082 7678 1.521141 GAGGGCGACTAGGGTTTCC 59.479 63.158 0.00 0.00 0.00 3.13
3083 7679 1.969200 GAGGGCGACTAGGGTTTCCC 61.969 65.000 0.00 0.00 45.90 3.97
3106 7702 4.410400 CCGCCAACCCCTCACTCC 62.410 72.222 0.00 0.00 0.00 3.85
3107 7703 4.410400 CGCCAACCCCTCACTCCC 62.410 72.222 0.00 0.00 0.00 4.30
3108 7704 3.256960 GCCAACCCCTCACTCCCA 61.257 66.667 0.00 0.00 0.00 4.37
3109 7705 3.081554 CCAACCCCTCACTCCCAG 58.918 66.667 0.00 0.00 0.00 4.45
3110 7706 2.352805 CAACCCCTCACTCCCAGC 59.647 66.667 0.00 0.00 0.00 4.85
3111 7707 2.936032 AACCCCTCACTCCCAGCC 60.936 66.667 0.00 0.00 0.00 4.85
3114 7710 4.748798 CCCTCACTCCCAGCCCCT 62.749 72.222 0.00 0.00 0.00 4.79
3115 7711 3.086600 CCTCACTCCCAGCCCCTC 61.087 72.222 0.00 0.00 0.00 4.30
3116 7712 3.086600 CTCACTCCCAGCCCCTCC 61.087 72.222 0.00 0.00 0.00 4.30
3117 7713 3.615811 TCACTCCCAGCCCCTCCT 61.616 66.667 0.00 0.00 0.00 3.69
3118 7714 3.086600 CACTCCCAGCCCCTCCTC 61.087 72.222 0.00 0.00 0.00 3.71
3119 7715 4.787280 ACTCCCAGCCCCTCCTCG 62.787 72.222 0.00 0.00 0.00 4.63
3137 7733 3.866582 CCGCCACCTGAGGGGATC 61.867 72.222 0.00 0.00 43.81 3.36
3138 7734 4.227134 CGCCACCTGAGGGGATCG 62.227 72.222 0.00 0.84 43.81 3.69
3139 7735 2.764128 GCCACCTGAGGGGATCGA 60.764 66.667 0.00 0.00 38.76 3.59
3140 7736 3.095347 GCCACCTGAGGGGATCGAC 62.095 68.421 0.00 0.00 38.76 4.20
3141 7737 2.786495 CCACCTGAGGGGATCGACG 61.786 68.421 0.00 0.00 38.76 5.12
3142 7738 2.442272 ACCTGAGGGGATCGACGG 60.442 66.667 2.38 0.00 38.76 4.79
3143 7739 3.227276 CCTGAGGGGATCGACGGG 61.227 72.222 0.00 0.00 37.23 5.28
3144 7740 3.917760 CTGAGGGGATCGACGGGC 61.918 72.222 0.00 0.00 0.00 6.13
3145 7741 4.770362 TGAGGGGATCGACGGGCA 62.770 66.667 0.00 0.00 0.00 5.36
3146 7742 3.467226 GAGGGGATCGACGGGCAA 61.467 66.667 0.00 0.00 0.00 4.52
3147 7743 3.447025 GAGGGGATCGACGGGCAAG 62.447 68.421 0.00 0.00 0.00 4.01
3150 7746 4.162690 GGATCGACGGGCAAGCCT 62.163 66.667 11.40 0.00 36.10 4.58
3152 7748 4.473520 ATCGACGGGCAAGCCTGG 62.474 66.667 22.93 12.15 46.47 4.45
3160 7756 4.643387 GCAAGCCTGGTGGGTCGT 62.643 66.667 0.00 0.00 44.35 4.34
3161 7757 2.358737 CAAGCCTGGTGGGTCGTC 60.359 66.667 0.00 0.00 44.35 4.20
3162 7758 4.003788 AAGCCTGGTGGGTCGTCG 62.004 66.667 0.00 0.00 44.35 5.12
3163 7759 4.988716 AGCCTGGTGGGTCGTCGA 62.989 66.667 0.00 0.00 40.58 4.20
3164 7760 3.771160 GCCTGGTGGGTCGTCGAT 61.771 66.667 0.00 0.00 37.43 3.59
3165 7761 2.184322 CCTGGTGGGTCGTCGATG 59.816 66.667 0.00 0.00 0.00 3.84
3166 7762 2.348104 CCTGGTGGGTCGTCGATGA 61.348 63.158 2.39 2.39 0.00 2.92
3167 7763 1.589630 CTGGTGGGTCGTCGATGAA 59.410 57.895 9.35 0.00 0.00 2.57
3168 7764 0.458543 CTGGTGGGTCGTCGATGAAG 60.459 60.000 9.35 0.00 0.00 3.02
3169 7765 1.153628 GGTGGGTCGTCGATGAAGG 60.154 63.158 9.35 0.00 0.00 3.46
3170 7766 1.590147 GTGGGTCGTCGATGAAGGT 59.410 57.895 9.35 0.00 0.00 3.50
3171 7767 0.736325 GTGGGTCGTCGATGAAGGTG 60.736 60.000 9.35 0.00 0.00 4.00
3172 7768 1.153628 GGGTCGTCGATGAAGGTGG 60.154 63.158 9.35 0.00 0.00 4.61
3173 7769 1.810030 GGTCGTCGATGAAGGTGGC 60.810 63.158 9.35 0.00 0.00 5.01
3174 7770 2.158959 GTCGTCGATGAAGGTGGCG 61.159 63.158 9.35 0.00 0.00 5.69
3175 7771 2.885644 CGTCGATGAAGGTGGCGG 60.886 66.667 0.00 0.00 0.00 6.13
3176 7772 2.264794 GTCGATGAAGGTGGCGGT 59.735 61.111 0.00 0.00 0.00 5.68
3177 7773 2.100631 GTCGATGAAGGTGGCGGTG 61.101 63.158 0.00 0.00 0.00 4.94
3178 7774 2.264480 CGATGAAGGTGGCGGTGA 59.736 61.111 0.00 0.00 0.00 4.02
3179 7775 1.811266 CGATGAAGGTGGCGGTGAG 60.811 63.158 0.00 0.00 0.00 3.51
3180 7776 1.450312 GATGAAGGTGGCGGTGAGG 60.450 63.158 0.00 0.00 0.00 3.86
3181 7777 2.185310 GATGAAGGTGGCGGTGAGGT 62.185 60.000 0.00 0.00 0.00 3.85
3182 7778 2.358737 GAAGGTGGCGGTGAGGTG 60.359 66.667 0.00 0.00 0.00 4.00
3183 7779 4.643387 AAGGTGGCGGTGAGGTGC 62.643 66.667 0.00 0.00 0.00 5.01
3190 7786 3.716006 CGGTGAGGTGCTGCGTTG 61.716 66.667 0.00 0.00 0.00 4.10
3191 7787 4.030452 GGTGAGGTGCTGCGTTGC 62.030 66.667 0.00 0.00 0.00 4.17
3192 7788 2.974698 GTGAGGTGCTGCGTTGCT 60.975 61.111 0.00 0.00 0.00 3.91
3193 7789 2.203195 TGAGGTGCTGCGTTGCTT 60.203 55.556 0.00 0.00 0.00 3.91
3194 7790 2.253758 TGAGGTGCTGCGTTGCTTC 61.254 57.895 0.00 0.00 0.00 3.86
3195 7791 3.300667 GAGGTGCTGCGTTGCTTCG 62.301 63.158 0.00 0.00 0.00 3.79
3196 7792 3.649986 GGTGCTGCGTTGCTTCGT 61.650 61.111 0.00 0.00 0.00 3.85
3197 7793 2.425773 GTGCTGCGTTGCTTCGTG 60.426 61.111 0.00 0.00 0.00 4.35
3198 7794 4.312231 TGCTGCGTTGCTTCGTGC 62.312 61.111 0.00 11.24 43.25 5.34
3200 7796 4.389576 CTGCGTTGCTTCGTGCCC 62.390 66.667 3.52 0.00 42.00 5.36
3217 7813 3.702048 CCCGCGAAGGACCTGGAA 61.702 66.667 8.23 0.00 45.00 3.53
3218 7814 2.125512 CCGCGAAGGACCTGGAAG 60.126 66.667 8.23 0.00 45.00 3.46
3219 7815 2.815647 CGCGAAGGACCTGGAAGC 60.816 66.667 0.00 0.00 0.00 3.86
3220 7816 2.436824 GCGAAGGACCTGGAAGCC 60.437 66.667 0.00 0.00 0.00 4.35
3221 7817 2.125512 CGAAGGACCTGGAAGCCG 60.126 66.667 0.00 0.00 0.00 5.52
3222 7818 2.269241 GAAGGACCTGGAAGCCGG 59.731 66.667 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 1.850549 CGGAGGAGGAGGAGGATCT 59.149 63.158 0.00 0.00 33.73 2.75
497 502 3.823330 GTCGGATCTGACGGCGGT 61.823 66.667 18.66 0.00 0.00 5.68
652 657 9.760077 CAGAACCCGTATCTAAACTTGTATAAT 57.240 33.333 0.00 0.00 0.00 1.28
653 658 7.707893 GCAGAACCCGTATCTAAACTTGTATAA 59.292 37.037 0.00 0.00 0.00 0.98
654 659 7.069085 AGCAGAACCCGTATCTAAACTTGTATA 59.931 37.037 0.00 0.00 0.00 1.47
655 660 6.047231 GCAGAACCCGTATCTAAACTTGTAT 58.953 40.000 0.00 0.00 0.00 2.29
656 661 5.186409 AGCAGAACCCGTATCTAAACTTGTA 59.814 40.000 0.00 0.00 0.00 2.41
657 662 4.020485 AGCAGAACCCGTATCTAAACTTGT 60.020 41.667 0.00 0.00 0.00 3.16
658 663 4.504858 AGCAGAACCCGTATCTAAACTTG 58.495 43.478 0.00 0.00 0.00 3.16
659 664 4.222145 TGAGCAGAACCCGTATCTAAACTT 59.778 41.667 0.00 0.00 0.00 2.66
660 665 3.767673 TGAGCAGAACCCGTATCTAAACT 59.232 43.478 0.00 0.00 0.00 2.66
661 666 4.113354 CTGAGCAGAACCCGTATCTAAAC 58.887 47.826 0.00 0.00 0.00 2.01
662 667 3.430374 GCTGAGCAGAACCCGTATCTAAA 60.430 47.826 0.00 0.00 0.00 1.85
663 668 2.100916 GCTGAGCAGAACCCGTATCTAA 59.899 50.000 0.00 0.00 0.00 2.10
664 669 1.681793 GCTGAGCAGAACCCGTATCTA 59.318 52.381 0.00 0.00 0.00 1.98
665 670 0.461961 GCTGAGCAGAACCCGTATCT 59.538 55.000 0.00 0.00 0.00 1.98
666 671 0.530870 GGCTGAGCAGAACCCGTATC 60.531 60.000 6.82 0.00 0.00 2.24
667 672 1.522569 GGCTGAGCAGAACCCGTAT 59.477 57.895 6.82 0.00 0.00 3.06
668 673 2.978824 GGCTGAGCAGAACCCGTA 59.021 61.111 6.82 0.00 0.00 4.02
669 674 4.379243 CGGCTGAGCAGAACCCGT 62.379 66.667 6.82 0.00 34.56 5.28
672 677 2.907897 ATACGCGGCTGAGCAGAACC 62.908 60.000 12.47 0.00 36.85 3.62
673 678 1.519455 ATACGCGGCTGAGCAGAAC 60.519 57.895 12.47 0.00 36.85 3.01
674 679 1.519234 CATACGCGGCTGAGCAGAA 60.519 57.895 12.47 0.00 36.85 3.02
675 680 2.104928 CATACGCGGCTGAGCAGA 59.895 61.111 12.47 0.00 36.85 4.26
676 681 1.361668 AAACATACGCGGCTGAGCAG 61.362 55.000 12.47 2.67 36.85 4.24
677 682 0.953471 AAAACATACGCGGCTGAGCA 60.953 50.000 12.47 0.00 36.85 4.26
678 683 0.168128 AAAAACATACGCGGCTGAGC 59.832 50.000 12.47 0.00 0.00 4.26
679 684 3.733024 TTAAAAACATACGCGGCTGAG 57.267 42.857 12.47 0.00 0.00 3.35
680 685 3.064271 GGATTAAAAACATACGCGGCTGA 59.936 43.478 12.47 0.00 0.00 4.26
681 686 3.359654 GGATTAAAAACATACGCGGCTG 58.640 45.455 12.47 10.06 0.00 4.85
682 687 2.031191 CGGATTAAAAACATACGCGGCT 59.969 45.455 12.47 0.00 0.00 5.52
683 688 2.368685 CGGATTAAAAACATACGCGGC 58.631 47.619 12.47 0.00 0.00 6.53
684 689 2.368685 GCGGATTAAAAACATACGCGG 58.631 47.619 12.47 0.00 43.80 6.46
692 697 7.056338 CGAAAATCGTTTTTGCGGATTAAAAAC 59.944 33.333 8.86 13.25 46.60 2.43
693 698 7.058005 CGAAAATCGTTTTTGCGGATTAAAAA 58.942 30.769 8.86 0.00 35.20 1.94
694 699 6.573358 CGAAAATCGTTTTTGCGGATTAAAA 58.427 32.000 8.86 0.00 35.20 1.52
695 700 6.129923 CGAAAATCGTTTTTGCGGATTAAA 57.870 33.333 8.86 0.00 35.20 1.52
696 701 5.732849 CGAAAATCGTTTTTGCGGATTAA 57.267 34.783 8.86 0.00 35.20 1.40
710 715 0.179225 CTGCGGGTTCACGAAAATCG 60.179 55.000 0.00 0.00 46.93 3.34
711 716 1.136057 GTCTGCGGGTTCACGAAAATC 60.136 52.381 0.00 0.00 35.47 2.17
712 717 0.872388 GTCTGCGGGTTCACGAAAAT 59.128 50.000 0.00 0.00 35.47 1.82
713 718 1.492319 CGTCTGCGGGTTCACGAAAA 61.492 55.000 0.00 0.00 34.06 2.29
714 719 1.952133 CGTCTGCGGGTTCACGAAA 60.952 57.895 0.00 0.00 34.06 3.46
715 720 2.355363 CGTCTGCGGGTTCACGAA 60.355 61.111 0.00 0.00 34.06 3.85
832 841 6.989291 GTCGGATTCAAATTCGAGTCGAAATC 60.989 42.308 29.89 24.66 46.28 2.17
1506 3129 4.408821 TGCATCGTCCTGGCACCC 62.409 66.667 0.00 0.00 31.58 4.61
2150 6342 4.715751 TAGATTCTTCTGTGGCATGGCCT 61.716 47.826 17.72 4.76 40.42 5.19
2427 6992 5.506317 GCATCTGTAAAACAACAGCACTCTT 60.506 40.000 0.00 0.00 45.34 2.85
2548 7134 6.127281 CCATCAATTCATCCATCACTCCAAAA 60.127 38.462 0.00 0.00 0.00 2.44
2550 7136 4.891168 CCATCAATTCATCCATCACTCCAA 59.109 41.667 0.00 0.00 0.00 3.53
2591 7177 6.751514 ACGTATTCATAAAATCTGCACCAA 57.248 33.333 0.00 0.00 0.00 3.67
2637 7233 6.996509 AGTACATGAACAAATCCAATTGCTT 58.003 32.000 0.00 0.00 33.52 3.91
2648 7244 7.497579 ACACATACACTGAAGTACATGAACAAA 59.502 33.333 0.00 0.00 0.00 2.83
3059 7655 2.907917 CCTAGTCGCCCTCGGGAG 60.908 72.222 6.08 2.12 37.50 4.30
3062 7658 2.294132 GAAACCCTAGTCGCCCTCGG 62.294 65.000 0.00 0.00 36.13 4.63
3063 7659 1.141234 GAAACCCTAGTCGCCCTCG 59.859 63.158 0.00 0.00 0.00 4.63
3064 7660 1.521141 GGAAACCCTAGTCGCCCTC 59.479 63.158 0.00 0.00 0.00 4.30
3065 7661 3.723245 GGAAACCCTAGTCGCCCT 58.277 61.111 0.00 0.00 0.00 5.19
3089 7685 4.410400 GGAGTGAGGGGTTGGCGG 62.410 72.222 0.00 0.00 0.00 6.13
3090 7686 4.410400 GGGAGTGAGGGGTTGGCG 62.410 72.222 0.00 0.00 0.00 5.69
3091 7687 3.256960 TGGGAGTGAGGGGTTGGC 61.257 66.667 0.00 0.00 0.00 4.52
3092 7688 3.081554 CTGGGAGTGAGGGGTTGG 58.918 66.667 0.00 0.00 0.00 3.77
3093 7689 2.352805 GCTGGGAGTGAGGGGTTG 59.647 66.667 0.00 0.00 0.00 3.77
3094 7690 2.936032 GGCTGGGAGTGAGGGGTT 60.936 66.667 0.00 0.00 0.00 4.11
3097 7693 4.748798 AGGGGCTGGGAGTGAGGG 62.749 72.222 0.00 0.00 0.00 4.30
3098 7694 3.086600 GAGGGGCTGGGAGTGAGG 61.087 72.222 0.00 0.00 0.00 3.86
3099 7695 3.086600 GGAGGGGCTGGGAGTGAG 61.087 72.222 0.00 0.00 0.00 3.51
3100 7696 3.615811 AGGAGGGGCTGGGAGTGA 61.616 66.667 0.00 0.00 0.00 3.41
3101 7697 3.086600 GAGGAGGGGCTGGGAGTG 61.087 72.222 0.00 0.00 0.00 3.51
3102 7698 4.787280 CGAGGAGGGGCTGGGAGT 62.787 72.222 0.00 0.00 0.00 3.85
3120 7716 3.866582 GATCCCCTCAGGTGGCGG 61.867 72.222 0.00 0.00 36.75 6.13
3121 7717 4.227134 CGATCCCCTCAGGTGGCG 62.227 72.222 0.00 0.00 36.75 5.69
3122 7718 2.764128 TCGATCCCCTCAGGTGGC 60.764 66.667 0.00 0.00 36.75 5.01
3123 7719 2.786495 CGTCGATCCCCTCAGGTGG 61.786 68.421 0.00 0.00 36.75 4.61
3124 7720 2.786495 CCGTCGATCCCCTCAGGTG 61.786 68.421 0.00 0.00 36.75 4.00
3125 7721 2.442272 CCGTCGATCCCCTCAGGT 60.442 66.667 0.00 0.00 36.75 4.00
3126 7722 3.227276 CCCGTCGATCCCCTCAGG 61.227 72.222 0.00 0.00 0.00 3.86
3127 7723 3.917760 GCCCGTCGATCCCCTCAG 61.918 72.222 0.00 0.00 0.00 3.35
3128 7724 4.770362 TGCCCGTCGATCCCCTCA 62.770 66.667 0.00 0.00 0.00 3.86
3129 7725 3.447025 CTTGCCCGTCGATCCCCTC 62.447 68.421 0.00 0.00 0.00 4.30
3130 7726 3.470888 CTTGCCCGTCGATCCCCT 61.471 66.667 0.00 0.00 0.00 4.79
3133 7729 4.162690 AGGCTTGCCCGTCGATCC 62.163 66.667 8.17 0.00 39.21 3.36
3134 7730 2.892425 CAGGCTTGCCCGTCGATC 60.892 66.667 8.17 0.00 39.21 3.69
3135 7731 4.473520 CCAGGCTTGCCCGTCGAT 62.474 66.667 8.17 0.00 39.21 3.59
3143 7739 4.643387 ACGACCCACCAGGCTTGC 62.643 66.667 0.00 0.00 40.58 4.01
3144 7740 2.358737 GACGACCCACCAGGCTTG 60.359 66.667 0.00 0.00 40.58 4.01
3145 7741 4.003788 CGACGACCCACCAGGCTT 62.004 66.667 0.00 0.00 40.58 4.35
3146 7742 4.988716 TCGACGACCCACCAGGCT 62.989 66.667 0.00 0.00 40.58 4.58
3147 7743 3.771160 ATCGACGACCCACCAGGC 61.771 66.667 0.00 0.00 40.58 4.85
3148 7744 1.884075 TTCATCGACGACCCACCAGG 61.884 60.000 0.00 0.00 43.78 4.45
3149 7745 0.458543 CTTCATCGACGACCCACCAG 60.459 60.000 0.00 0.00 0.00 4.00
3150 7746 1.589630 CTTCATCGACGACCCACCA 59.410 57.895 0.00 0.00 0.00 4.17
3151 7747 1.153628 CCTTCATCGACGACCCACC 60.154 63.158 0.00 0.00 0.00 4.61
3152 7748 0.736325 CACCTTCATCGACGACCCAC 60.736 60.000 0.00 0.00 0.00 4.61
3153 7749 1.589630 CACCTTCATCGACGACCCA 59.410 57.895 0.00 0.00 0.00 4.51
3154 7750 1.153628 CCACCTTCATCGACGACCC 60.154 63.158 0.00 0.00 0.00 4.46
3155 7751 1.810030 GCCACCTTCATCGACGACC 60.810 63.158 0.00 0.00 0.00 4.79
3156 7752 2.158959 CGCCACCTTCATCGACGAC 61.159 63.158 0.00 0.00 0.00 4.34
3157 7753 2.180769 CGCCACCTTCATCGACGA 59.819 61.111 0.00 0.00 0.00 4.20
3158 7754 2.885644 CCGCCACCTTCATCGACG 60.886 66.667 0.00 0.00 0.00 5.12
3159 7755 2.100631 CACCGCCACCTTCATCGAC 61.101 63.158 0.00 0.00 0.00 4.20
3160 7756 2.225791 CTCACCGCCACCTTCATCGA 62.226 60.000 0.00 0.00 0.00 3.59
3161 7757 1.811266 CTCACCGCCACCTTCATCG 60.811 63.158 0.00 0.00 0.00 3.84
3162 7758 1.450312 CCTCACCGCCACCTTCATC 60.450 63.158 0.00 0.00 0.00 2.92
3163 7759 2.224159 ACCTCACCGCCACCTTCAT 61.224 57.895 0.00 0.00 0.00 2.57
3164 7760 2.847234 ACCTCACCGCCACCTTCA 60.847 61.111 0.00 0.00 0.00 3.02
3165 7761 2.358737 CACCTCACCGCCACCTTC 60.359 66.667 0.00 0.00 0.00 3.46
3166 7762 4.643387 GCACCTCACCGCCACCTT 62.643 66.667 0.00 0.00 0.00 3.50
3173 7769 3.716006 CAACGCAGCACCTCACCG 61.716 66.667 0.00 0.00 0.00 4.94
3174 7770 4.030452 GCAACGCAGCACCTCACC 62.030 66.667 0.00 0.00 0.00 4.02
3175 7771 2.449556 GAAGCAACGCAGCACCTCAC 62.450 60.000 2.40 0.00 36.85 3.51
3176 7772 2.203195 AAGCAACGCAGCACCTCA 60.203 55.556 2.40 0.00 36.85 3.86
3177 7773 2.558313 GAAGCAACGCAGCACCTC 59.442 61.111 2.40 0.00 36.85 3.85
3178 7774 3.349006 CGAAGCAACGCAGCACCT 61.349 61.111 2.40 0.00 36.85 4.00
3179 7775 3.649986 ACGAAGCAACGCAGCACC 61.650 61.111 2.40 0.00 36.85 5.01
3180 7776 2.425773 CACGAAGCAACGCAGCAC 60.426 61.111 2.40 0.00 36.85 4.40
3181 7777 4.312231 GCACGAAGCAACGCAGCA 62.312 61.111 12.64 0.00 44.79 4.41
3200 7796 3.665675 CTTCCAGGTCCTTCGCGGG 62.666 68.421 6.13 0.00 0.00 6.13
3201 7797 2.125512 CTTCCAGGTCCTTCGCGG 60.126 66.667 6.13 0.00 0.00 6.46
3202 7798 2.815647 GCTTCCAGGTCCTTCGCG 60.816 66.667 0.00 0.00 0.00 5.87
3203 7799 2.436824 GGCTTCCAGGTCCTTCGC 60.437 66.667 0.00 0.00 0.00 4.70
3204 7800 2.125512 CGGCTTCCAGGTCCTTCG 60.126 66.667 0.00 0.00 0.00 3.79
3205 7801 2.269241 CCGGCTTCCAGGTCCTTC 59.731 66.667 0.00 0.00 0.00 3.46
3206 7802 3.330720 CCCGGCTTCCAGGTCCTT 61.331 66.667 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.