Multiple sequence alignment - TraesCS4A01G025600

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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 TraesCS4A01G025600 chr4A 100.000 4815 0 0 1 4815 17737515 17732701 0.000000e+00 8892
1 TraesCS4A01G025600 chr4A 98.807 1006 8 1 1 1002 17744516 17743511 0.000000e+00 1788
2 TraesCS4A01G025600 chr7A 97.953 2003 30 7 2686 4682 663801585 663803582 0.000000e+00 3461
3 TraesCS4A01G025600 chr7A 97.356 1475 21 2 993 2467 663799681 663801137 0.000000e+00 2492
4 TraesCS4A01G025600 chr7A 88.484 1372 107 29 2723 4063 18100244 18098893 0.000000e+00 1611
5 TraesCS4A01G025600 chr7A 93.587 421 25 1 996 1414 91013230 91012810 1.140000e-175 627
6 TraesCS4A01G025600 chr7A 93.587 421 25 1 996 1414 186400651 186400231 1.140000e-175 627
7 TraesCS4A01G025600 chr7A 93.349 421 26 1 996 1414 718439367 718438947 5.290000e-174 621
8 TraesCS4A01G025600 chr7A 91.981 424 32 1 993 1414 48000977 48001400 1.150000e-165 593
9 TraesCS4A01G025600 chr7A 96.471 255 9 0 2473 2727 18100574 18100320 5.760000e-114 422
10 TraesCS4A01G025600 chr3B 94.880 1836 65 20 2473 4289 802892289 802894114 0.000000e+00 2843
11 TraesCS4A01G025600 chr3B 99.001 1001 7 1 1 998 4995973 4994973 0.000000e+00 1790
12 TraesCS4A01G025600 chr3B 91.381 1021 45 15 3680 4676 800651390 800650389 0.000000e+00 1358
13 TraesCS4A01G025600 chr3B 87.367 1037 66 33 3668 4675 410875924 410876924 0.000000e+00 1129
14 TraesCS4A01G025600 chr3B 94.539 531 28 1 1940 2470 800652389 800651860 0.000000e+00 819
15 TraesCS4A01G025600 chr3B 94.607 445 23 1 1932 2376 410875467 410875910 0.000000e+00 688
16 TraesCS4A01G025600 chr3B 93.396 424 26 1 993 1414 115499443 115499866 1.140000e-175 627
17 TraesCS4A01G025600 chr3B 95.276 381 17 1 1938 2318 802890076 802890455 1.920000e-168 603
18 TraesCS4A01G025600 chr1A 94.880 1836 65 20 2473 4289 576245515 576247340 0.000000e+00 2843
19 TraesCS4A01G025600 chr1A 99.197 996 7 1 1 995 577169115 577168120 0.000000e+00 1794
20 TraesCS4A01G025600 chr1A 95.013 381 18 1 1938 2318 576243302 576243681 8.920000e-167 597
21 TraesCS4A01G025600 chr1A 89.008 373 13 10 4329 4675 576247347 576247717 2.060000e-118 436
22 TraesCS4A01G025600 chr2B 94.743 1826 67 20 2483 4289 69014066 69015881 0.000000e+00 2813
23 TraesCS4A01G025600 chr2B 98.902 1002 11 0 1 1002 138607356 138606355 0.000000e+00 1790
24 TraesCS4A01G025600 chr2B 89.276 373 12 10 4329 4675 69015888 69016258 4.420000e-120 442
25 TraesCS4A01G025600 chr3A 94.281 1836 76 20 2473 4289 28721975 28720150 0.000000e+00 2782
26 TraesCS4A01G025600 chr3A 92.874 421 28 1 996 1414 217962530 217962110 1.150000e-170 610
27 TraesCS4A01G025600 chr3A 95.276 381 17 1 1938 2318 28724188 28723809 1.920000e-168 603
28 TraesCS4A01G025600 chr3A 91.449 421 29 5 996 1414 11236672 11236257 5.410000e-159 571
29 TraesCS4A01G025600 chr3A 88.679 371 18 12 4329 4675 28720143 28719773 9.570000e-117 431
30 TraesCS4A01G025600 chr6B 93.730 1834 60 24 2473 4289 480825532 480827327 0.000000e+00 2699
31 TraesCS4A01G025600 chr6B 88.484 1372 107 28 2723 4063 674923010 674924361 0.000000e+00 1611
32 TraesCS4A01G025600 chr6B 91.620 537 42 2 1932 2465 714427298 714427834 0.000000e+00 739
33 TraesCS4A01G025600 chr6B 89.067 375 13 11 4329 4677 480827334 480827706 1.590000e-119 440
34 TraesCS4A01G025600 chr6B 96.471 255 9 0 2473 2727 674922679 674922933 5.760000e-114 422
35 TraesCS4A01G025600 chr5B 99.297 996 7 0 1 996 576231372 576230377 0.000000e+00 1801
36 TraesCS4A01G025600 chr5B 99.102 1002 9 0 1 1002 576238356 576237355 0.000000e+00 1801
37 TraesCS4A01G025600 chr5B 99.197 996 8 0 1 996 107860904 107859909 0.000000e+00 1796
38 TraesCS4A01G025600 chr5B 92.279 531 38 2 1938 2465 412260683 412260153 0.000000e+00 750
39 TraesCS4A01G025600 chr5B 95.294 255 12 0 2473 2727 528557650 528557904 5.800000e-109 405
40 TraesCS4A01G025600 chr1B 99.002 1002 10 0 1 1002 20905026 20906027 0.000000e+00 1796
41 TraesCS4A01G025600 chr7B 92.025 1304 63 16 3395 4676 706978334 706977050 0.000000e+00 1794
42 TraesCS4A01G025600 chr7B 94.747 533 28 0 1938 2470 706979195 706978663 0.000000e+00 830
43 TraesCS4A01G025600 chr5A 99.097 997 8 1 1 996 483602398 483603394 0.000000e+00 1790
44 TraesCS4A01G025600 chr5A 93.587 421 25 1 996 1414 565690425 565690005 1.140000e-175 627
45 TraesCS4A01G025600 chrUn 88.411 1372 108 28 2723 4063 315537921 315536570 0.000000e+00 1605
46 TraesCS4A01G025600 chrUn 96.471 255 9 0 2473 2727 315538252 315537998 5.760000e-114 422
47 TraesCS4A01G025600 chr2D 85.291 911 80 31 3789 4682 28993345 28992472 0.000000e+00 891
48 TraesCS4A01G025600 chr2D 85.347 894 88 29 3788 4675 28986031 28985175 0.000000e+00 885
49 TraesCS4A01G025600 chr2D 85.657 251 26 9 1576 1823 637803846 637803603 6.180000e-64 255
50 TraesCS4A01G025600 chr2A 86.769 325 32 7 1502 1823 761540428 761540744 7.670000e-93 351


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 TraesCS4A01G025600 chr4A 17732701 17737515 4814 True 8892.0 8892 100.000000 1 4815 1 chr4A.!!$R1 4814
1 TraesCS4A01G025600 chr4A 17743511 17744516 1005 True 1788.0 1788 98.807000 1 1002 1 chr4A.!!$R2 1001
2 TraesCS4A01G025600 chr7A 663799681 663803582 3901 False 2976.5 3461 97.654500 993 4682 2 chr7A.!!$F2 3689
3 TraesCS4A01G025600 chr7A 18098893 18100574 1681 True 1016.5 1611 92.477500 2473 4063 2 chr7A.!!$R4 1590
4 TraesCS4A01G025600 chr3B 4994973 4995973 1000 True 1790.0 1790 99.001000 1 998 1 chr3B.!!$R1 997
5 TraesCS4A01G025600 chr3B 802890076 802894114 4038 False 1723.0 2843 95.078000 1938 4289 2 chr3B.!!$F3 2351
6 TraesCS4A01G025600 chr3B 800650389 800652389 2000 True 1088.5 1358 92.960000 1940 4676 2 chr3B.!!$R2 2736
7 TraesCS4A01G025600 chr3B 410875467 410876924 1457 False 908.5 1129 90.987000 1932 4675 2 chr3B.!!$F2 2743
8 TraesCS4A01G025600 chr1A 577168120 577169115 995 True 1794.0 1794 99.197000 1 995 1 chr1A.!!$R1 994
9 TraesCS4A01G025600 chr1A 576243302 576247717 4415 False 1292.0 2843 92.967000 1938 4675 3 chr1A.!!$F1 2737
10 TraesCS4A01G025600 chr2B 138606355 138607356 1001 True 1790.0 1790 98.902000 1 1002 1 chr2B.!!$R1 1001
11 TraesCS4A01G025600 chr2B 69014066 69016258 2192 False 1627.5 2813 92.009500 2483 4675 2 chr2B.!!$F1 2192
12 TraesCS4A01G025600 chr3A 28719773 28724188 4415 True 1272.0 2782 92.745333 1938 4675 3 chr3A.!!$R3 2737
13 TraesCS4A01G025600 chr6B 480825532 480827706 2174 False 1569.5 2699 91.398500 2473 4677 2 chr6B.!!$F2 2204
14 TraesCS4A01G025600 chr6B 674922679 674924361 1682 False 1016.5 1611 92.477500 2473 4063 2 chr6B.!!$F3 1590
15 TraesCS4A01G025600 chr6B 714427298 714427834 536 False 739.0 739 91.620000 1932 2465 1 chr6B.!!$F1 533
16 TraesCS4A01G025600 chr5B 576230377 576231372 995 True 1801.0 1801 99.297000 1 996 1 chr5B.!!$R3 995
17 TraesCS4A01G025600 chr5B 576237355 576238356 1001 True 1801.0 1801 99.102000 1 1002 1 chr5B.!!$R4 1001
18 TraesCS4A01G025600 chr5B 107859909 107860904 995 True 1796.0 1796 99.197000 1 996 1 chr5B.!!$R1 995
19 TraesCS4A01G025600 chr5B 412260153 412260683 530 True 750.0 750 92.279000 1938 2465 1 chr5B.!!$R2 527
20 TraesCS4A01G025600 chr1B 20905026 20906027 1001 False 1796.0 1796 99.002000 1 1002 1 chr1B.!!$F1 1001
21 TraesCS4A01G025600 chr7B 706977050 706979195 2145 True 1312.0 1794 93.386000 1938 4676 2 chr7B.!!$R1 2738
22 TraesCS4A01G025600 chr5A 483602398 483603394 996 False 1790.0 1790 99.097000 1 996 1 chr5A.!!$F1 995
23 TraesCS4A01G025600 chrUn 315536570 315538252 1682 True 1013.5 1605 92.441000 2473 4063 2 chrUn.!!$R1 1590
24 TraesCS4A01G025600 chr2D 28992472 28993345 873 True 891.0 891 85.291000 3789 4682 1 chr2D.!!$R2 893
25 TraesCS4A01G025600 chr2D 28985175 28986031 856 True 885.0 885 85.347000 3788 4675 1 chr2D.!!$R1 887

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
70 71 4.219725 TCGGTCATGTCTACATTGTTCTCA 59.780 41.667 0.00 0.0 33.61 3.27 F
1120 1125 1.673033 CGCTTGACTGGGAAGGTACAG 60.673 57.143 0.00 0.0 40.48 2.74 F
1903 1908 0.401738 AAAGGCTGCCTCTTGTGCTA 59.598 50.000 23.61 0.0 30.89 3.49 F
3297 5299 1.726853 ACCTTGAAGATACGTGCTGC 58.273 50.000 0.00 0.0 0.00 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1294 1299 1.000731 TGCATTTGCCAAGCCACTTAC 59.999 47.619 0.00 0.0 41.18 2.34 R
2569 4478 3.258123 AGCCGGAAATAGTGCATTGTTTT 59.742 39.130 5.05 0.0 0.00 2.43 R
3474 5476 3.858135 TCCTTCCTACTTGAGTTGAGGT 58.142 45.455 1.08 0.0 0.00 3.85 R
4707 6786 0.170339 GGCCCTGAACGAAAAATCGG 59.830 55.000 0.00 0.0 37.45 4.18 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
70 71 4.219725 TCGGTCATGTCTACATTGTTCTCA 59.780 41.667 0.00 0.00 33.61 3.27
1120 1125 1.673033 CGCTTGACTGGGAAGGTACAG 60.673 57.143 0.00 0.00 40.48 2.74
1144 1149 5.673337 TGTTCTTGATGCAGTTTCAGTAC 57.327 39.130 0.00 0.00 0.00 2.73
1294 1299 6.520913 GCTTTAGATTTAGGATAGGTCCCTGG 60.521 46.154 0.00 0.00 46.34 4.45
1298 1303 6.085416 AGATTTAGGATAGGTCCCTGGTAAG 58.915 44.000 0.00 0.00 46.34 2.34
1353 1358 7.119262 GGGTAAGAAAAATCGAGTCTTGATGAA 59.881 37.037 3.17 0.00 33.70 2.57
1584 1589 2.357517 GCACACCGCACTAGCTGT 60.358 61.111 0.00 0.00 41.79 4.40
1685 1690 9.466497 AACTTGAGTTGTTATGTATGATGGATT 57.534 29.630 0.00 0.00 36.80 3.01
1701 1706 1.339151 GGATTTTGCGAGTGACTCCCT 60.339 52.381 7.07 0.00 0.00 4.20
1716 1721 2.224209 ACTCCCTCGTAAACTGTGTTGG 60.224 50.000 0.00 0.00 0.00 3.77
1903 1908 0.401738 AAAGGCTGCCTCTTGTGCTA 59.598 50.000 23.61 0.00 30.89 3.49
1958 1963 4.515191 GCACAGAAAAGTAGATGTTGACCA 59.485 41.667 0.00 0.00 0.00 4.02
2241 2248 6.405842 GGTGTCCTTTTGTCACTTGATTTTCT 60.406 38.462 0.00 0.00 33.30 2.52
2467 2477 9.099454 TGGTATTTGTTTGTAAATTGTTTGGAC 57.901 29.630 0.00 0.00 32.79 4.02
2471 2481 7.835634 TTGTTTGTAAATTGTTTGGACTTCC 57.164 32.000 0.00 0.00 0.00 3.46
2569 4478 4.707105 CCATGAGGTATGCTGATACACAA 58.293 43.478 0.00 0.00 36.85 3.33
2582 4491 6.148948 GCTGATACACAAAAACAATGCACTA 58.851 36.000 0.00 0.00 0.00 2.74
2831 4821 7.433719 CGATAGCGAAGATATTAGATCCAAAGG 59.566 40.741 0.00 0.00 40.19 3.11
2984 4975 8.669946 TCCATTTCCTTTTGTTTTGTAATTCC 57.330 30.769 0.00 0.00 0.00 3.01
3271 5268 8.849168 CCTTGCATGTCATATAATTTACTTGGA 58.151 33.333 0.00 0.00 0.00 3.53
3297 5299 1.726853 ACCTTGAAGATACGTGCTGC 58.273 50.000 0.00 0.00 0.00 5.25
3474 5476 5.752955 GTGCTGTTTTTGAGAAAATAAGGCA 59.247 36.000 0.00 0.00 37.12 4.75
3487 5489 4.373156 AATAAGGCACCTCAACTCAAGT 57.627 40.909 0.00 0.00 0.00 3.16
3976 6009 6.593770 TGTTTATGCTCACTATGTACTGTTGG 59.406 38.462 0.00 0.00 0.00 3.77
4122 6155 9.457110 CTACTAGTGATGTTCTAATTGCTACTG 57.543 37.037 5.39 0.00 0.00 2.74
4191 6230 7.493971 AGTGCTGTTCTAAATGCTACTTATCAG 59.506 37.037 0.00 0.00 0.00 2.90
4303 6344 8.166132 GAAACTGGAGCTTTTTCAATGGAACAT 61.166 37.037 0.00 0.00 34.58 2.71
4413 6454 2.957680 TGCTTTGATGGCTGTCTTTTGA 59.042 40.909 0.00 0.00 0.00 2.69
4679 6758 3.987220 CGAATTTCGGCCAAATTTTGTCT 59.013 39.130 19.99 4.51 43.56 3.41
4682 6761 4.599047 TTTCGGCCAAATTTTGTCTGAT 57.401 36.364 2.24 0.00 0.00 2.90
4686 6765 4.749099 TCGGCCAAATTTTGTCTGATTTTG 59.251 37.500 2.24 0.00 0.00 2.44
4687 6766 4.511082 CGGCCAAATTTTGTCTGATTTTGT 59.489 37.500 2.24 0.00 0.00 2.83
4688 6767 5.694006 CGGCCAAATTTTGTCTGATTTTGTA 59.306 36.000 2.24 0.00 0.00 2.41
4689 6768 6.368516 CGGCCAAATTTTGTCTGATTTTGTAT 59.631 34.615 2.24 0.00 0.00 2.29
4691 6770 8.567104 GGCCAAATTTTGTCTGATTTTGTATTT 58.433 29.630 0.00 0.00 0.00 1.40
4692 6771 9.949174 GCCAAATTTTGTCTGATTTTGTATTTT 57.051 25.926 8.26 0.00 0.00 1.82
4697 6776 9.965824 ATTTTGTCTGATTTTGTATTTTCGTCT 57.034 25.926 0.00 0.00 0.00 4.18
4698 6777 8.781067 TTTGTCTGATTTTGTATTTTCGTCTG 57.219 30.769 0.00 0.00 0.00 3.51
4699 6778 7.722795 TGTCTGATTTTGTATTTTCGTCTGA 57.277 32.000 0.00 0.00 0.00 3.27
4700 6779 8.148807 TGTCTGATTTTGTATTTTCGTCTGAA 57.851 30.769 0.00 0.00 0.00 3.02
4701 6780 8.616942 TGTCTGATTTTGTATTTTCGTCTGAAA 58.383 29.630 0.00 0.00 42.21 2.69
4702 6781 9.612620 GTCTGATTTTGTATTTTCGTCTGAAAT 57.387 29.630 0.00 0.00 43.32 2.17
4707 6786 9.862585 ATTTTGTATTTTCGTCTGAAATTTTGC 57.137 25.926 0.00 0.00 43.32 3.68
4708 6787 7.401484 TTGTATTTTCGTCTGAAATTTTGCC 57.599 32.000 0.00 0.00 43.32 4.52
4709 6788 5.627367 TGTATTTTCGTCTGAAATTTTGCCG 59.373 36.000 0.00 0.00 43.32 5.69
4710 6789 3.972950 TTTCGTCTGAAATTTTGCCGA 57.027 38.095 0.00 0.00 39.13 5.54
4711 6790 4.497473 TTTCGTCTGAAATTTTGCCGAT 57.503 36.364 0.00 0.00 39.13 4.18
4712 6791 4.497473 TTCGTCTGAAATTTTGCCGATT 57.503 36.364 0.00 0.00 0.00 3.34
4713 6792 4.497473 TCGTCTGAAATTTTGCCGATTT 57.503 36.364 0.00 0.00 0.00 2.17
4714 6793 4.865776 TCGTCTGAAATTTTGCCGATTTT 58.134 34.783 0.00 0.00 0.00 1.82
4715 6794 5.285651 TCGTCTGAAATTTTGCCGATTTTT 58.714 33.333 0.00 0.00 0.00 1.94
4716 6795 5.401079 TCGTCTGAAATTTTGCCGATTTTTC 59.599 36.000 0.00 0.00 0.00 2.29
4717 6796 5.598783 GTCTGAAATTTTGCCGATTTTTCG 58.401 37.500 0.00 0.00 0.00 3.46
4718 6797 5.174943 GTCTGAAATTTTGCCGATTTTTCGT 59.825 36.000 0.00 0.00 0.00 3.85
4719 6798 5.751028 TCTGAAATTTTGCCGATTTTTCGTT 59.249 32.000 0.00 0.00 0.00 3.85
4720 6799 5.968604 TGAAATTTTGCCGATTTTTCGTTC 58.031 33.333 0.00 0.00 0.00 3.95
4721 6800 5.520288 TGAAATTTTGCCGATTTTTCGTTCA 59.480 32.000 0.00 0.00 0.00 3.18
4722 6801 5.574815 AATTTTGCCGATTTTTCGTTCAG 57.425 34.783 0.00 0.00 0.00 3.02
4723 6802 2.697431 TTGCCGATTTTTCGTTCAGG 57.303 45.000 0.00 0.00 0.00 3.86
4724 6803 0.878416 TGCCGATTTTTCGTTCAGGG 59.122 50.000 0.00 0.00 0.00 4.45
4725 6804 0.456142 GCCGATTTTTCGTTCAGGGC 60.456 55.000 0.00 0.00 0.00 5.19
4726 6805 0.170339 CCGATTTTTCGTTCAGGGCC 59.830 55.000 0.00 0.00 0.00 5.80
4727 6806 0.179200 CGATTTTTCGTTCAGGGCCG 60.179 55.000 0.00 0.00 0.00 6.13
4728 6807 1.161843 GATTTTTCGTTCAGGGCCGA 58.838 50.000 0.00 0.00 0.00 5.54
4729 6808 1.538075 GATTTTTCGTTCAGGGCCGAA 59.462 47.619 0.00 1.88 40.94 4.30
4731 6810 3.097461 TTTCGTTCAGGGCCGAAAA 57.903 47.368 11.42 2.77 46.47 2.29
4732 6811 1.390565 TTTCGTTCAGGGCCGAAAAA 58.609 45.000 11.42 7.73 46.47 1.94
4751 6830 3.810310 AAAATGCCAAACCGAAAGTCA 57.190 38.095 0.00 0.00 0.00 3.41
4752 6831 3.810310 AAATGCCAAACCGAAAGTCAA 57.190 38.095 0.00 0.00 0.00 3.18
4753 6832 3.810310 AATGCCAAACCGAAAGTCAAA 57.190 38.095 0.00 0.00 0.00 2.69
4754 6833 3.810310 ATGCCAAACCGAAAGTCAAAA 57.190 38.095 0.00 0.00 0.00 2.44
4755 6834 2.882324 TGCCAAACCGAAAGTCAAAAC 58.118 42.857 0.00 0.00 0.00 2.43
4756 6835 1.849829 GCCAAACCGAAAGTCAAAACG 59.150 47.619 0.00 0.00 0.00 3.60
4757 6836 1.849829 CCAAACCGAAAGTCAAAACGC 59.150 47.619 0.00 0.00 0.00 4.84
4758 6837 2.520979 CAAACCGAAAGTCAAAACGCA 58.479 42.857 0.00 0.00 0.00 5.24
4759 6838 2.468532 AACCGAAAGTCAAAACGCAG 57.531 45.000 0.00 0.00 0.00 5.18
4760 6839 1.658994 ACCGAAAGTCAAAACGCAGA 58.341 45.000 0.00 0.00 0.00 4.26
4761 6840 2.218603 ACCGAAAGTCAAAACGCAGAT 58.781 42.857 0.00 0.00 0.00 2.90
4762 6841 2.223377 ACCGAAAGTCAAAACGCAGATC 59.777 45.455 0.00 0.00 0.00 2.75
4763 6842 2.412847 CCGAAAGTCAAAACGCAGATCC 60.413 50.000 0.00 0.00 0.00 3.36
4764 6843 2.223144 CGAAAGTCAAAACGCAGATCCA 59.777 45.455 0.00 0.00 0.00 3.41
4765 6844 3.120199 CGAAAGTCAAAACGCAGATCCAT 60.120 43.478 0.00 0.00 0.00 3.41
4766 6845 3.837213 AAGTCAAAACGCAGATCCATG 57.163 42.857 0.00 0.00 0.00 3.66
4767 6846 2.086869 AGTCAAAACGCAGATCCATGG 58.913 47.619 4.97 4.97 0.00 3.66
4768 6847 0.810648 TCAAAACGCAGATCCATGGC 59.189 50.000 6.96 0.00 0.00 4.40
4772 6851 3.344215 CGCAGATCCATGGCGCTC 61.344 66.667 6.96 3.72 44.49 5.03
4773 6852 2.976903 GCAGATCCATGGCGCTCC 60.977 66.667 6.96 0.00 0.00 4.70
4774 6853 2.827423 CAGATCCATGGCGCTCCT 59.173 61.111 6.96 0.00 0.00 3.69
4775 6854 1.301558 CAGATCCATGGCGCTCCTC 60.302 63.158 6.96 0.00 0.00 3.71
4776 6855 2.031768 GATCCATGGCGCTCCTCC 59.968 66.667 6.96 0.00 0.00 4.30
4777 6856 2.769621 ATCCATGGCGCTCCTCCA 60.770 61.111 6.96 0.00 38.09 3.86
4778 6857 2.121992 GATCCATGGCGCTCCTCCAT 62.122 60.000 6.96 0.00 44.70 3.41
4786 6865 4.115199 GCTCCTCCATGCCCCGTT 62.115 66.667 0.00 0.00 0.00 4.44
4787 6866 2.124570 CTCCTCCATGCCCCGTTG 60.125 66.667 0.00 0.00 0.00 4.10
4788 6867 4.424711 TCCTCCATGCCCCGTTGC 62.425 66.667 0.00 0.00 0.00 4.17
4789 6868 4.431131 CCTCCATGCCCCGTTGCT 62.431 66.667 0.00 0.00 0.00 3.91
4790 6869 3.136123 CTCCATGCCCCGTTGCTG 61.136 66.667 0.00 0.00 0.00 4.41
4791 6870 3.626996 CTCCATGCCCCGTTGCTGA 62.627 63.158 0.00 0.00 0.00 4.26
4792 6871 3.136123 CCATGCCCCGTTGCTGAG 61.136 66.667 0.00 0.00 0.00 3.35
4793 6872 3.818787 CATGCCCCGTTGCTGAGC 61.819 66.667 0.00 0.00 0.00 4.26
4800 6879 4.749310 CGTTGCTGAGCGCCTCCT 62.749 66.667 2.29 0.00 38.05 3.69
4801 6880 2.817396 GTTGCTGAGCGCCTCCTC 60.817 66.667 2.29 0.00 38.05 3.71
4802 6881 4.441695 TTGCTGAGCGCCTCCTCG 62.442 66.667 2.29 0.00 38.05 4.63
4804 6883 4.863925 GCTGAGCGCCTCCTCGAC 62.864 72.222 2.29 0.00 34.56 4.20
4805 6884 4.544689 CTGAGCGCCTCCTCGACG 62.545 72.222 2.29 0.00 34.56 5.12
4811 6890 4.443266 GCCTCCTCGACGCTTGCT 62.443 66.667 0.00 0.00 0.00 3.91
4812 6891 2.507992 CCTCCTCGACGCTTGCTG 60.508 66.667 0.00 0.00 0.00 4.41
4813 6892 2.507992 CTCCTCGACGCTTGCTGG 60.508 66.667 0.00 0.00 0.00 4.85
4814 6893 4.742201 TCCTCGACGCTTGCTGGC 62.742 66.667 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
734 739 2.549349 GCAAAGTGTCGGGGAAGAGTTA 60.549 50.000 0.00 0.00 0.00 2.24
1120 1125 5.368256 ACTGAAACTGCATCAAGAACATC 57.632 39.130 0.00 0.00 0.00 3.06
1144 1149 3.740832 TGAAGACTGAAACTGCATACACG 59.259 43.478 0.00 0.00 0.00 4.49
1294 1299 1.000731 TGCATTTGCCAAGCCACTTAC 59.999 47.619 0.00 0.00 41.18 2.34
1298 1303 2.607631 ATATGCATTTGCCAAGCCAC 57.392 45.000 3.54 0.00 41.18 5.01
1353 1358 8.574251 TTAATAATGCCACTACTGTGTTCAAT 57.426 30.769 0.00 0.00 42.34 2.57
1390 1395 4.469586 TCCTTGGTGACTACAAGATGCATA 59.530 41.667 0.00 0.00 46.27 3.14
1584 1589 1.198178 GCGCGGAAGGAAACATAACAA 59.802 47.619 8.83 0.00 0.00 2.83
1701 1706 3.804786 TCTCACCAACACAGTTTACGA 57.195 42.857 0.00 0.00 0.00 3.43
1812 1817 3.439129 GCCTACCGTGCAAATAAGAAGTT 59.561 43.478 0.00 0.00 0.00 2.66
1903 1908 8.153550 ACTCAAGTGTGAAGTCTGATAGAAATT 58.846 33.333 0.00 0.00 31.88 1.82
1958 1963 8.137745 ACCACTGACCATTGAAATTAATCATT 57.862 30.769 0.00 0.00 0.00 2.57
2148 2155 6.115448 ACTAGGGTGTCCTCATATTAATGC 57.885 41.667 0.00 0.00 43.66 3.56
2241 2248 5.186256 TCCTATTTGCAGTTCCATTACCA 57.814 39.130 0.00 0.00 0.00 3.25
2467 2477 9.003658 ACATTACTAGACAAACATTCTTGGAAG 57.996 33.333 0.00 0.00 0.00 3.46
2470 2480 9.398170 CAAACATTACTAGACAAACATTCTTGG 57.602 33.333 0.00 0.00 0.00 3.61
2471 2481 9.398170 CCAAACATTACTAGACAAACATTCTTG 57.602 33.333 0.00 0.00 0.00 3.02
2569 4478 3.258123 AGCCGGAAATAGTGCATTGTTTT 59.742 39.130 5.05 0.00 0.00 2.43
2984 4975 6.585702 TGCAAGTATCACCAATGAAATTTTCG 59.414 34.615 4.76 0.00 38.69 3.46
3065 5057 4.139786 ACACATTGTGAGCAAACTCTCAT 58.860 39.130 23.12 0.00 43.80 2.90
3297 5299 7.395190 TCTCTCTCTTTCTCTTGATCTTCTG 57.605 40.000 0.00 0.00 0.00 3.02
3474 5476 3.858135 TCCTTCCTACTTGAGTTGAGGT 58.142 45.455 1.08 0.00 0.00 3.85
3487 5489 7.743116 TGTACCAACATAAGAATCCTTCCTA 57.257 36.000 0.00 0.00 33.94 2.94
4122 6155 8.347035 CAACTAGAATAGCACTACTAAGAGACC 58.653 40.741 0.00 0.00 44.39 3.85
4191 6230 6.806739 GGTACCATTTCAAAGACAAATACAGC 59.193 38.462 7.15 0.00 0.00 4.40
4303 6344 3.399181 GCATGGACGGGGAGGTCA 61.399 66.667 0.00 0.00 38.70 4.02
4413 6454 5.234466 AGGAGTTCACATAGAAACAGCTT 57.766 39.130 0.00 0.00 38.13 3.74
4682 6761 8.331742 GGCAAAATTTCAGACGAAAATACAAAA 58.668 29.630 0.00 0.00 44.12 2.44
4686 6765 5.854338 TCGGCAAAATTTCAGACGAAAATAC 59.146 36.000 16.40 0.00 44.12 1.89
4687 6766 6.003234 TCGGCAAAATTTCAGACGAAAATA 57.997 33.333 16.40 0.00 44.12 1.40
4688 6767 4.865776 TCGGCAAAATTTCAGACGAAAAT 58.134 34.783 16.40 0.00 44.12 1.82
4689 6768 4.294416 TCGGCAAAATTTCAGACGAAAA 57.706 36.364 16.40 0.00 44.12 2.29
4691 6770 4.497473 AATCGGCAAAATTTCAGACGAA 57.503 36.364 20.83 8.72 32.39 3.85
4692 6771 4.497473 AAATCGGCAAAATTTCAGACGA 57.503 36.364 19.70 19.70 0.00 4.20
4693 6772 5.574815 AAAAATCGGCAAAATTTCAGACG 57.425 34.783 11.43 11.43 0.00 4.18
4694 6773 5.174943 ACGAAAAATCGGCAAAATTTCAGAC 59.825 36.000 3.12 0.00 37.45 3.51
4695 6774 5.285651 ACGAAAAATCGGCAAAATTTCAGA 58.714 33.333 3.12 0.00 37.45 3.27
4696 6775 5.574815 ACGAAAAATCGGCAAAATTTCAG 57.425 34.783 3.12 0.00 37.45 3.02
4697 6776 5.520288 TGAACGAAAAATCGGCAAAATTTCA 59.480 32.000 3.12 0.00 37.45 2.69
4698 6777 5.968604 TGAACGAAAAATCGGCAAAATTTC 58.031 33.333 3.12 0.00 37.45 2.17
4699 6778 5.050431 CCTGAACGAAAAATCGGCAAAATTT 60.050 36.000 3.12 0.00 37.45 1.82
4700 6779 4.447389 CCTGAACGAAAAATCGGCAAAATT 59.553 37.500 3.12 0.00 37.45 1.82
4701 6780 3.987220 CCTGAACGAAAAATCGGCAAAAT 59.013 39.130 3.12 0.00 37.45 1.82
4702 6781 3.376540 CCTGAACGAAAAATCGGCAAAA 58.623 40.909 3.12 0.00 37.45 2.44
4703 6782 2.287909 CCCTGAACGAAAAATCGGCAAA 60.288 45.455 3.12 0.00 37.45 3.68
4704 6783 1.268352 CCCTGAACGAAAAATCGGCAA 59.732 47.619 3.12 0.00 37.45 4.52
4705 6784 0.878416 CCCTGAACGAAAAATCGGCA 59.122 50.000 3.12 0.36 37.45 5.69
4706 6785 0.456142 GCCCTGAACGAAAAATCGGC 60.456 55.000 3.12 0.00 37.45 5.54
4707 6786 0.170339 GGCCCTGAACGAAAAATCGG 59.830 55.000 0.00 0.00 37.45 4.18
4708 6787 0.179200 CGGCCCTGAACGAAAAATCG 60.179 55.000 0.00 0.00 39.31 3.34
4709 6788 1.161843 TCGGCCCTGAACGAAAAATC 58.838 50.000 0.00 0.00 36.01 2.17
4710 6789 1.611519 TTCGGCCCTGAACGAAAAAT 58.388 45.000 0.00 0.00 44.93 1.82
4711 6790 3.097461 TTCGGCCCTGAACGAAAAA 57.903 47.368 0.00 0.00 44.93 1.94
4712 6791 4.881057 TTCGGCCCTGAACGAAAA 57.119 50.000 0.00 0.00 44.93 2.29
4714 6793 3.097461 TTTTTCGGCCCTGAACGAA 57.903 47.368 0.00 0.00 46.05 3.85
4715 6794 4.881057 TTTTTCGGCCCTGAACGA 57.119 50.000 0.00 0.00 37.33 3.85
4730 6809 4.130286 TGACTTTCGGTTTGGCATTTTT 57.870 36.364 0.00 0.00 0.00 1.94
4731 6810 3.810310 TGACTTTCGGTTTGGCATTTT 57.190 38.095 0.00 0.00 0.00 1.82
4732 6811 3.810310 TTGACTTTCGGTTTGGCATTT 57.190 38.095 0.00 0.00 0.00 2.32
4733 6812 3.810310 TTTGACTTTCGGTTTGGCATT 57.190 38.095 0.00 0.00 0.00 3.56
4734 6813 3.453424 GTTTTGACTTTCGGTTTGGCAT 58.547 40.909 0.00 0.00 0.00 4.40
4735 6814 2.732597 CGTTTTGACTTTCGGTTTGGCA 60.733 45.455 0.00 0.00 0.00 4.92
4736 6815 1.849829 CGTTTTGACTTTCGGTTTGGC 59.150 47.619 0.00 0.00 0.00 4.52
4737 6816 1.849829 GCGTTTTGACTTTCGGTTTGG 59.150 47.619 0.00 0.00 0.00 3.28
4738 6817 2.520979 TGCGTTTTGACTTTCGGTTTG 58.479 42.857 0.00 0.00 0.00 2.93
4739 6818 2.420722 TCTGCGTTTTGACTTTCGGTTT 59.579 40.909 0.00 0.00 0.00 3.27
4740 6819 2.011222 TCTGCGTTTTGACTTTCGGTT 58.989 42.857 0.00 0.00 0.00 4.44
4741 6820 1.658994 TCTGCGTTTTGACTTTCGGT 58.341 45.000 0.00 0.00 0.00 4.69
4742 6821 2.412847 GGATCTGCGTTTTGACTTTCGG 60.413 50.000 0.00 0.00 0.00 4.30
4743 6822 2.223144 TGGATCTGCGTTTTGACTTTCG 59.777 45.455 0.00 0.00 0.00 3.46
4744 6823 3.896648 TGGATCTGCGTTTTGACTTTC 57.103 42.857 0.00 0.00 0.00 2.62
4745 6824 3.057315 CCATGGATCTGCGTTTTGACTTT 60.057 43.478 5.56 0.00 0.00 2.66
4746 6825 2.489329 CCATGGATCTGCGTTTTGACTT 59.511 45.455 5.56 0.00 0.00 3.01
4747 6826 2.086869 CCATGGATCTGCGTTTTGACT 58.913 47.619 5.56 0.00 0.00 3.41
4748 6827 1.468054 GCCATGGATCTGCGTTTTGAC 60.468 52.381 18.40 0.00 0.00 3.18
4749 6828 0.810648 GCCATGGATCTGCGTTTTGA 59.189 50.000 18.40 0.00 0.00 2.69
4750 6829 0.523968 CGCCATGGATCTGCGTTTTG 60.524 55.000 18.40 0.00 43.12 2.44
4751 6830 1.802636 CGCCATGGATCTGCGTTTT 59.197 52.632 18.40 0.00 43.12 2.43
4752 6831 3.501396 CGCCATGGATCTGCGTTT 58.499 55.556 18.40 0.00 43.12 3.60
4756 6835 2.976903 GGAGCGCCATGGATCTGC 60.977 66.667 18.40 12.58 0.00 4.26
4757 6836 1.301558 GAGGAGCGCCATGGATCTG 60.302 63.158 18.40 2.34 36.29 2.90
4758 6837 2.515071 GGAGGAGCGCCATGGATCT 61.515 63.158 18.40 11.18 36.29 2.75
4759 6838 2.031768 GGAGGAGCGCCATGGATC 59.968 66.667 18.40 9.74 36.29 3.36
4760 6839 2.152058 ATGGAGGAGCGCCATGGAT 61.152 57.895 18.40 0.00 42.19 3.41
4761 6840 2.769621 ATGGAGGAGCGCCATGGA 60.770 61.111 18.40 0.00 42.19 3.41
4764 6843 4.575973 GGCATGGAGGAGCGCCAT 62.576 66.667 9.88 3.36 44.50 4.40
4769 6848 4.115199 AACGGGGCATGGAGGAGC 62.115 66.667 0.00 0.00 0.00 4.70
4770 6849 2.124570 CAACGGGGCATGGAGGAG 60.125 66.667 0.00 0.00 0.00 3.69
4771 6850 4.424711 GCAACGGGGCATGGAGGA 62.425 66.667 0.00 0.00 0.00 3.71
4772 6851 4.431131 AGCAACGGGGCATGGAGG 62.431 66.667 3.39 0.00 35.83 4.30
4773 6852 3.136123 CAGCAACGGGGCATGGAG 61.136 66.667 3.39 0.00 35.83 3.86
4774 6853 3.626996 CTCAGCAACGGGGCATGGA 62.627 63.158 3.39 0.00 35.83 3.41
4775 6854 3.136123 CTCAGCAACGGGGCATGG 61.136 66.667 3.39 0.00 35.83 3.66
4776 6855 3.818787 GCTCAGCAACGGGGCATG 61.819 66.667 0.00 0.00 35.83 4.06
4788 6867 4.544689 CGTCGAGGAGGCGCTCAG 62.545 72.222 7.64 0.00 42.71 3.35
4794 6873 4.443266 AGCAAGCGTCGAGGAGGC 62.443 66.667 9.75 8.49 42.77 4.70
4795 6874 2.507992 CAGCAAGCGTCGAGGAGG 60.508 66.667 9.75 0.00 0.00 4.30
4796 6875 2.507992 CCAGCAAGCGTCGAGGAG 60.508 66.667 9.75 0.00 0.00 3.69
4797 6876 4.742201 GCCAGCAAGCGTCGAGGA 62.742 66.667 9.75 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.