Multiple sequence alignment - TraesCS6B01G078500

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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 TraesCS6B01G078500 chr6B 100.000 5796 0 0 1 5796 54890585 54896380 0.000000e+00 10704.0
1 TraesCS6B01G078500 chr6B 93.197 735 39 7 940 1670 54764971 54764244 0.000000e+00 1070.0
2 TraesCS6B01G078500 chr6B 88.225 569 43 6 4246 4808 54732799 54732249 0.000000e+00 658.0
3 TraesCS6B01G078500 chr6B 85.792 549 56 11 382 918 54765581 54765043 3.920000e-156 562.0
4 TraesCS6B01G078500 chr6B 86.618 411 31 9 4404 4808 54779995 54779603 3.210000e-117 433.0
5 TraesCS6B01G078500 chr6B 76.584 726 135 26 3977 4687 134769362 134770067 3.300000e-97 366.0
6 TraesCS6B01G078500 chr6B 79.282 362 65 8 3373 3732 134487376 134487023 1.610000e-60 244.0
7 TraesCS6B01G078500 chr6B 96.875 32 1 0 245 276 54869967 54869998 3.000000e-03 54.7
8 TraesCS6B01G078500 chrUn 90.603 3416 221 46 1425 4801 103533432 103536786 0.000000e+00 4438.0
9 TraesCS6B01G078500 chrUn 90.828 2137 127 22 2695 4823 103504578 103502503 0.000000e+00 2796.0
10 TraesCS6B01G078500 chrUn 91.296 540 39 5 383 918 103532387 103532922 0.000000e+00 730.0
11 TraesCS6B01G078500 chrUn 91.667 408 28 5 940 1344 103532997 103533401 1.410000e-155 560.0
12 TraesCS6B01G078500 chrUn 95.087 346 16 1 1 346 103531667 103532011 1.420000e-150 544.0
13 TraesCS6B01G078500 chrUn 89.008 373 33 3 545 916 103509165 103508800 6.850000e-124 455.0
14 TraesCS6B01G078500 chrUn 86.093 151 15 3 369 514 103509314 103509165 2.160000e-34 158.0
15 TraesCS6B01G078500 chrUn 100.000 29 0 0 367 395 103532343 103532371 3.000000e-03 54.7
16 TraesCS6B01G078500 chr6A 92.699 2753 147 18 2063 4801 29076015 29073303 0.000000e+00 3921.0
17 TraesCS6B01G078500 chr6A 90.664 964 44 15 1 918 29078264 29077301 0.000000e+00 1240.0
18 TraesCS6B01G078500 chr6A 88.000 525 45 10 917 1428 29077044 29076525 6.420000e-169 604.0
19 TraesCS6B01G078500 chr6A 82.527 641 83 19 1427 2055 29076607 29075984 2.380000e-148 536.0
20 TraesCS6B01G078500 chr6A 80.109 367 62 9 3369 3732 77160017 77160375 4.450000e-66 263.0
21 TraesCS6B01G078500 chr6A 79.006 362 66 8 3373 3732 77009395 77009042 7.510000e-59 239.0
22 TraesCS6B01G078500 chr1D 92.806 987 47 11 4828 5796 463054447 463053467 0.000000e+00 1408.0
23 TraesCS6B01G078500 chr7A 92.690 985 49 13 4828 5795 271726167 271725189 0.000000e+00 1399.0
24 TraesCS6B01G078500 chr7A 93.750 160 9 1 5637 5796 271725824 271725666 7.510000e-59 239.0
25 TraesCS6B01G078500 chr4D 93.319 958 43 12 4857 5796 365401221 365400267 0.000000e+00 1395.0
26 TraesCS6B01G078500 chr4D 81.536 1641 209 64 2620 4236 111039456 111041026 0.000000e+00 1266.0
27 TraesCS6B01G078500 chr5D 92.300 987 51 11 4828 5796 494633042 494632063 0.000000e+00 1378.0
28 TraesCS6B01G078500 chr5D 82.176 432 56 12 1874 2301 386761168 386760754 9.240000e-93 351.0
29 TraesCS6B01G078500 chr3B 91.397 988 63 14 4822 5796 685256327 685255349 0.000000e+00 1334.0
30 TraesCS6B01G078500 chr3B 91.048 983 69 13 4826 5796 367123921 367122946 0.000000e+00 1310.0
31 TraesCS6B01G078500 chr3B 80.888 518 60 20 1877 2361 565727085 565726574 7.090000e-99 372.0
32 TraesCS6B01G078500 chr3B 82.492 297 48 3 2062 2355 417730691 417730396 2.070000e-64 257.0
33 TraesCS6B01G078500 chr3B 93.082 159 10 1 5638 5796 367123581 367123424 1.260000e-56 231.0
34 TraesCS6B01G078500 chr6D 91.129 992 58 19 4828 5796 472639461 472638477 0.000000e+00 1317.0
35 TraesCS6B01G078500 chr6D 79.834 362 63 8 3373 3732 60390164 60389811 7.450000e-64 255.0
36 TraesCS6B01G078500 chr6D 81.538 260 48 0 3977 4236 60495989 60496248 1.260000e-51 215.0
37 TraesCS6B01G078500 chr2B 90.881 987 69 14 4823 5796 663835464 663836442 0.000000e+00 1304.0
38 TraesCS6B01G078500 chr3D 89.757 986 53 19 4828 5796 589506519 589507473 0.000000e+00 1218.0
39 TraesCS6B01G078500 chr4B 80.442 1130 157 40 2620 3732 171183350 171182268 0.000000e+00 804.0
40 TraesCS6B01G078500 chr4B 88.361 421 47 2 3817 4236 171182270 171181851 6.700000e-139 505.0
41 TraesCS6B01G078500 chr4A 79.699 1128 169 38 2620 3732 466109966 466108884 0.000000e+00 760.0
42 TraesCS6B01G078500 chr4A 88.599 421 46 2 3817 4236 466108886 466108467 1.440000e-140 510.0
43 TraesCS6B01G078500 chr5A 82.353 493 68 16 1874 2361 488441092 488440614 1.500000e-110 411.0
44 TraesCS6B01G078500 chr1A 79.158 499 61 24 1874 2361 481926860 481927326 7.300000e-79 305.0
45 TraesCS6B01G078500 chr2D 79.433 423 67 9 1874 2277 277681075 277681496 1.230000e-71 281.0
46 TraesCS6B01G078500 chr2D 75.720 486 72 22 1874 2357 528085165 528085606 9.850000e-48 202.0
47 TraesCS6B01G078500 chr2A 77.622 429 66 19 1874 2277 293935646 293935223 3.490000e-57 233.0
48 TraesCS6B01G078500 chr3A 79.448 326 59 4 2040 2358 12328814 12329138 2.100000e-54 224.0
49 TraesCS6B01G078500 chr7D 85.417 96 11 3 2233 2326 34000184 34000278 4.780000e-16 97.1


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 TraesCS6B01G078500 chr6B 54890585 54896380 5795 False 10704.00 10704 100.0000 1 5796 1 chr6B.!!$F2 5795
1 TraesCS6B01G078500 chr6B 54764244 54765581 1337 True 816.00 1070 89.4945 382 1670 2 chr6B.!!$R4 1288
2 TraesCS6B01G078500 chr6B 54732249 54732799 550 True 658.00 658 88.2250 4246 4808 1 chr6B.!!$R1 562
3 TraesCS6B01G078500 chr6B 134769362 134770067 705 False 366.00 366 76.5840 3977 4687 1 chr6B.!!$F3 710
4 TraesCS6B01G078500 chrUn 103502503 103504578 2075 True 2796.00 2796 90.8280 2695 4823 1 chrUn.!!$R1 2128
5 TraesCS6B01G078500 chrUn 103531667 103536786 5119 False 1265.34 4438 93.7306 1 4801 5 chrUn.!!$F1 4800
6 TraesCS6B01G078500 chrUn 103508800 103509314 514 True 306.50 455 87.5505 369 916 2 chrUn.!!$R2 547
7 TraesCS6B01G078500 chr6A 29073303 29078264 4961 True 1575.25 3921 88.4725 1 4801 4 chr6A.!!$R2 4800
8 TraesCS6B01G078500 chr1D 463053467 463054447 980 True 1408.00 1408 92.8060 4828 5796 1 chr1D.!!$R1 968
9 TraesCS6B01G078500 chr7A 271725189 271726167 978 True 819.00 1399 93.2200 4828 5796 2 chr7A.!!$R1 968
10 TraesCS6B01G078500 chr4D 365400267 365401221 954 True 1395.00 1395 93.3190 4857 5796 1 chr4D.!!$R1 939
11 TraesCS6B01G078500 chr4D 111039456 111041026 1570 False 1266.00 1266 81.5360 2620 4236 1 chr4D.!!$F1 1616
12 TraesCS6B01G078500 chr5D 494632063 494633042 979 True 1378.00 1378 92.3000 4828 5796 1 chr5D.!!$R2 968
13 TraesCS6B01G078500 chr3B 685255349 685256327 978 True 1334.00 1334 91.3970 4822 5796 1 chr3B.!!$R3 974
14 TraesCS6B01G078500 chr3B 367122946 367123921 975 True 770.50 1310 92.0650 4826 5796 2 chr3B.!!$R4 970
15 TraesCS6B01G078500 chr3B 565726574 565727085 511 True 372.00 372 80.8880 1877 2361 1 chr3B.!!$R2 484
16 TraesCS6B01G078500 chr6D 472638477 472639461 984 True 1317.00 1317 91.1290 4828 5796 1 chr6D.!!$R2 968
17 TraesCS6B01G078500 chr2B 663835464 663836442 978 False 1304.00 1304 90.8810 4823 5796 1 chr2B.!!$F1 973
18 TraesCS6B01G078500 chr3D 589506519 589507473 954 False 1218.00 1218 89.7570 4828 5796 1 chr3D.!!$F1 968
19 TraesCS6B01G078500 chr4B 171181851 171183350 1499 True 654.50 804 84.4015 2620 4236 2 chr4B.!!$R1 1616
20 TraesCS6B01G078500 chr4A 466108467 466109966 1499 True 635.00 760 84.1490 2620 4236 2 chr4A.!!$R1 1616

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
933 1321 0.235926 GCGCACAGTTCTTTGAGGTC 59.764 55.0 0.30 0.0 0.00 3.85 F
1807 2500 0.034337 TGTCCTAGAAAAAGCGGCGT 59.966 50.0 9.37 0.0 0.00 5.68 F
1822 2515 0.037975 GGCGTGGGTTCTCTAACGAA 60.038 55.0 0.00 0.0 38.27 3.85 F
2987 3816 0.041238 TCAGACGGGATCCAGAGGTT 59.959 55.0 19.55 0.0 0.00 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2824 3653 0.462225 CTCAGCATCACCAGCCTGAG 60.462 60.0 0.00 2.56 33.95 3.35 R
2970 3799 0.041238 TGAACCTCTGGATCCCGTCT 59.959 55.0 9.90 0.00 0.00 4.18 R
3619 4485 0.683973 ACCTGTCTCTGACCAGCAAG 59.316 55.0 0.00 0.00 0.00 4.01 R
4855 5756 0.321034 GGTTGGGACTTCACCGGTAC 60.321 60.0 6.87 0.00 0.00 3.34 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
170 171 1.079503 GTCCTCAGCCACGAAATGTC 58.920 55.000 0.00 0.00 0.00 3.06
175 176 1.375523 AGCCACGAAATGTCCGGAC 60.376 57.895 28.17 28.17 0.00 4.79
199 200 1.838073 GATCCAACACCGGTGAGGGT 61.838 60.000 40.21 33.52 46.96 4.34
202 203 1.597027 CAACACCGGTGAGGGTCAC 60.597 63.158 40.21 0.00 46.23 3.67
211 212 2.204461 TGAGGGTCACGAAGGCGAA 61.204 57.895 0.00 0.00 41.64 4.70
231 232 0.251474 AGCCTTCCTTTGCATGCTGA 60.251 50.000 20.33 7.44 0.00 4.26
437 805 5.812652 TCATGAAAACTTTAGCGAACGTTT 58.187 33.333 0.46 8.10 0.00 3.60
564 941 0.454957 CGGCGCAAAGTCATTGGAAG 60.455 55.000 10.83 0.00 39.54 3.46
613 990 2.128035 GTTCCGACGCATAGAATCTGG 58.872 52.381 0.00 0.00 0.00 3.86
616 995 1.399572 CGACGCATAGAATCTGGTCG 58.600 55.000 11.34 11.34 40.77 4.79
874 1262 2.365105 CCGCTCCAGGGACCCTAA 60.365 66.667 14.38 3.42 29.64 2.69
887 1275 2.509786 CCTAAGCGCCGGCGTTAA 60.510 61.111 45.02 29.81 46.35 2.01
929 1317 2.176926 TGCGCGCACAGTTCTTTGA 61.177 52.632 33.09 1.47 0.00 2.69
930 1318 1.439365 GCGCGCACAGTTCTTTGAG 60.439 57.895 29.10 0.00 0.00 3.02
932 1320 1.498865 CGCGCACAGTTCTTTGAGGT 61.499 55.000 8.75 0.00 0.00 3.85
933 1321 0.235926 GCGCACAGTTCTTTGAGGTC 59.764 55.000 0.30 0.00 0.00 3.85
934 1322 1.581934 CGCACAGTTCTTTGAGGTCA 58.418 50.000 0.00 0.00 0.00 4.02
936 1479 2.549754 CGCACAGTTCTTTGAGGTCATT 59.450 45.455 0.00 0.00 0.00 2.57
938 1481 3.304928 GCACAGTTCTTTGAGGTCATTGG 60.305 47.826 0.00 0.00 0.00 3.16
945 1594 7.004086 AGTTCTTTGAGGTCATTGGAAATGTA 58.996 34.615 0.26 0.00 0.00 2.29
1003 1652 7.035004 GTGACATAATGTAATGGTTTGCATGT 58.965 34.615 0.00 0.00 38.07 3.21
1029 1678 2.191109 GTGGTGGTGGACAACGGT 59.809 61.111 0.00 0.00 40.67 4.83
1151 1801 3.431766 GGCGGGTATGTCTGTTATGTCTT 60.432 47.826 0.00 0.00 0.00 3.01
1479 2165 9.968870 TTTTATATTTTCTAACACGTTTTGCCT 57.031 25.926 0.00 0.00 0.00 4.75
1735 2428 1.918293 TCCATGTGGCGGAGACCTT 60.918 57.895 0.00 0.00 34.44 3.50
1744 2437 2.040544 CGGAGACCTTGCCGCAATT 61.041 57.895 6.19 0.00 41.17 2.32
1765 2458 1.611851 CCTCTCTGCCACAGGGACT 60.612 63.158 0.00 0.00 35.88 3.85
1800 2493 5.415701 CCTTTGCTATGCTGTCCTAGAAAAA 59.584 40.000 0.00 0.00 0.00 1.94
1801 2494 6.404074 CCTTTGCTATGCTGTCCTAGAAAAAG 60.404 42.308 0.00 0.00 0.00 2.27
1802 2495 3.941483 TGCTATGCTGTCCTAGAAAAAGC 59.059 43.478 0.00 0.00 0.00 3.51
1804 2497 1.808411 TGCTGTCCTAGAAAAAGCGG 58.192 50.000 0.00 0.00 36.66 5.52
1805 2498 0.448197 GCTGTCCTAGAAAAAGCGGC 59.552 55.000 0.00 0.00 0.00 6.53
1806 2499 0.721718 CTGTCCTAGAAAAAGCGGCG 59.278 55.000 0.51 0.51 0.00 6.46
1807 2500 0.034337 TGTCCTAGAAAAAGCGGCGT 59.966 50.000 9.37 0.00 0.00 5.68
1812 2505 0.535553 TAGAAAAAGCGGCGTGGGTT 60.536 50.000 9.37 0.00 0.00 4.11
1813 2506 1.371267 GAAAAAGCGGCGTGGGTTC 60.371 57.895 9.37 4.30 0.00 3.62
1822 2515 0.037975 GGCGTGGGTTCTCTAACGAA 60.038 55.000 0.00 0.00 38.27 3.85
1827 2520 4.676196 GCGTGGGTTCTCTAACGAATTAGA 60.676 45.833 0.00 0.00 43.75 2.10
1909 2614 2.278206 CGTGAGGCATCGGACGAG 60.278 66.667 5.41 0.00 33.64 4.18
1917 2622 0.382158 GCATCGGACGAGACAGATCA 59.618 55.000 0.00 0.00 0.00 2.92
1918 2623 1.000827 GCATCGGACGAGACAGATCAT 60.001 52.381 0.00 0.00 0.00 2.45
1925 2630 4.438880 CGGACGAGACAGATCATGTAAACT 60.439 45.833 0.00 0.00 44.17 2.66
1982 2687 1.275291 CGCTTCTTCTTCCCTGGTACA 59.725 52.381 0.00 0.00 0.00 2.90
1993 2698 0.107703 CCTGGTACACACGCATGGAT 60.108 55.000 0.00 0.00 0.00 3.41
1997 2702 2.288666 GGTACACACGCATGGATGAAT 58.711 47.619 0.00 0.00 0.00 2.57
1999 2704 3.128589 GGTACACACGCATGGATGAATTT 59.871 43.478 0.00 0.00 0.00 1.82
2053 2758 2.823147 GCTTGCTCTGGCGATGCT 60.823 61.111 0.00 0.00 42.25 3.79
2054 2759 2.821688 GCTTGCTCTGGCGATGCTC 61.822 63.158 0.00 0.00 42.25 4.26
2055 2760 1.153409 CTTGCTCTGGCGATGCTCT 60.153 57.895 0.00 0.00 42.25 4.09
2056 2761 1.429927 CTTGCTCTGGCGATGCTCTG 61.430 60.000 0.00 0.00 42.25 3.35
2057 2762 3.270839 GCTCTGGCGATGCTCTGC 61.271 66.667 0.00 0.00 0.00 4.26
2064 2769 4.862092 CGATGCTCTGCCGACGCT 62.862 66.667 0.00 0.00 35.36 5.07
2065 2770 2.959071 GATGCTCTGCCGACGCTC 60.959 66.667 0.00 0.00 35.36 5.03
2066 2771 4.521062 ATGCTCTGCCGACGCTCC 62.521 66.667 0.00 0.00 35.36 4.70
2094 2866 2.186384 GTGCTCCAGCGATGCTCT 59.814 61.111 0.00 0.00 45.83 4.09
2181 2953 1.575922 GGCGTTGACCGGTTTTACC 59.424 57.895 9.42 3.41 36.94 2.85
2336 3112 2.159310 TGTGAAGGTTTGACCGCTTTTG 60.159 45.455 0.00 0.00 44.90 2.44
2519 3296 6.041409 ACATGTACATATCCTCAGTTCCTCAG 59.959 42.308 8.32 0.00 0.00 3.35
2534 3311 2.093973 TCCTCAGTGCTAGTAGCTTTGC 60.094 50.000 22.34 10.30 42.97 3.68
2761 3546 2.182842 GCGCACCACTCCATCATCC 61.183 63.158 0.30 0.00 0.00 3.51
2762 3547 1.524621 CGCACCACTCCATCATCCC 60.525 63.158 0.00 0.00 0.00 3.85
2763 3548 1.609239 GCACCACTCCATCATCCCA 59.391 57.895 0.00 0.00 0.00 4.37
2764 3549 0.465097 GCACCACTCCATCATCCCAG 60.465 60.000 0.00 0.00 0.00 4.45
2780 3581 1.276421 CCCAGTTCTTCATGGACGTCT 59.724 52.381 16.46 0.00 39.02 4.18
2793 3594 3.057019 TGGACGTCTTGATTTCGAAGTG 58.943 45.455 16.46 0.00 0.00 3.16
2804 3605 4.333649 TGATTTCGAAGTGGATCTTGATGC 59.666 41.667 0.00 0.00 36.40 3.91
2886 3715 2.510238 GCCATCTTCGAGCACGCT 60.510 61.111 0.00 0.00 39.58 5.07
2970 3799 1.262417 TCAACTACATGGCCGTCTCA 58.738 50.000 0.00 0.00 0.00 3.27
2987 3816 0.041238 TCAGACGGGATCCAGAGGTT 59.959 55.000 19.55 0.00 0.00 3.50
2994 3823 0.548031 GGATCCAGAGGTTCATGCCA 59.452 55.000 6.95 0.00 0.00 4.92
3337 4169 4.062991 GTTCCAGGAAGACACAAACGTAT 58.937 43.478 0.54 0.00 0.00 3.06
3341 4173 3.432252 CAGGAAGACACAAACGTATCCAC 59.568 47.826 0.00 0.00 30.76 4.02
3480 4346 2.496070 TCATCTACCTCAACTCCAACCG 59.504 50.000 0.00 0.00 0.00 4.44
3481 4347 1.263356 TCTACCTCAACTCCAACCGG 58.737 55.000 0.00 0.00 0.00 5.28
3482 4348 0.391263 CTACCTCAACTCCAACCGGC 60.391 60.000 0.00 0.00 0.00 6.13
3513 4379 2.125350 CTTCCACGAGCTCTGGGC 60.125 66.667 23.63 0.00 42.19 5.36
3798 4667 4.776435 TGGATATGCTCATCCTTGTTGA 57.224 40.909 15.43 0.00 44.26 3.18
4186 5056 1.952102 GCGACCCCGTCTTCACCATA 61.952 60.000 0.00 0.00 38.24 2.74
4207 5077 2.747686 GTGAGCAACCCCTCCGAA 59.252 61.111 0.00 0.00 0.00 4.30
4323 5212 0.249868 TTGTGACGGTGCAGGAAGAG 60.250 55.000 0.00 0.00 0.00 2.85
4324 5213 1.367840 GTGACGGTGCAGGAAGAGT 59.632 57.895 0.00 0.00 0.00 3.24
4411 5300 2.815211 ACCTACACGCTGCGCATG 60.815 61.111 23.51 16.34 0.00 4.06
4576 5465 0.030908 GCTTCGAGTTCCCGATCGAT 59.969 55.000 18.66 0.00 46.35 3.59
4582 5471 4.602259 TTCCCGATCGATGGGCGC 62.602 66.667 20.20 0.00 46.92 6.53
4699 5588 4.571236 TCCGGTTGGGATTCTGGA 57.429 55.556 0.00 0.00 40.94 3.86
4817 5718 6.481644 GTGATACAGAAGTCCATGGATCTTTC 59.518 42.308 19.62 20.18 37.60 2.62
4823 5724 2.697751 AGTCCATGGATCTTTCCTCTCG 59.302 50.000 19.62 0.00 43.07 4.04
4824 5725 2.042464 TCCATGGATCTTTCCTCTCGG 58.958 52.381 11.44 0.00 43.07 4.63
4825 5726 1.542108 CCATGGATCTTTCCTCTCGGC 60.542 57.143 5.56 0.00 43.07 5.54
4826 5727 1.415659 CATGGATCTTTCCTCTCGGCT 59.584 52.381 0.00 0.00 43.07 5.52
4827 5728 2.454336 TGGATCTTTCCTCTCGGCTA 57.546 50.000 0.00 0.00 43.07 3.93
4828 5729 2.747177 TGGATCTTTCCTCTCGGCTAA 58.253 47.619 0.00 0.00 43.07 3.09
4829 5730 2.695666 TGGATCTTTCCTCTCGGCTAAG 59.304 50.000 0.00 0.00 43.07 2.18
4830 5731 2.696187 GGATCTTTCCTCTCGGCTAAGT 59.304 50.000 0.00 0.00 39.14 2.24
4831 5732 3.133183 GGATCTTTCCTCTCGGCTAAGTT 59.867 47.826 0.00 0.00 39.14 2.66
4832 5733 4.383226 GGATCTTTCCTCTCGGCTAAGTTT 60.383 45.833 0.00 0.00 39.14 2.66
4853 5754 2.725203 TTTTACCGGTGCTGCGAGCT 62.725 55.000 19.93 0.00 42.97 4.09
4854 5755 1.879737 TTTACCGGTGCTGCGAGCTA 61.880 55.000 19.93 0.00 42.97 3.32
4855 5756 2.279502 TTACCGGTGCTGCGAGCTAG 62.280 60.000 19.93 0.00 42.97 3.42
4948 5849 7.182817 AGTGTTGTATTTGGCTAGTATCTCA 57.817 36.000 0.00 0.00 0.00 3.27
5001 5910 5.500234 ACTGAGTGCATCTTTTATGCCTAA 58.500 37.500 7.46 0.00 43.94 2.69
5026 5937 1.097232 CATGCATGTTGTCGGACCAT 58.903 50.000 18.91 0.00 0.00 3.55
5036 5947 1.005512 TCGGACCATTCCACACACG 60.006 57.895 0.00 0.00 43.00 4.49
5160 6071 7.898309 CCGACAACGTGATCTTTAAAATAAGAG 59.102 37.037 0.00 0.00 36.39 2.85
5386 6312 5.499139 TCAATTCAAAGACAGTGTTCACC 57.501 39.130 0.00 0.00 0.00 4.02
5631 6560 8.559536 GTTCACTCAATTGAGATGTGAAACTTA 58.440 33.333 36.15 15.36 44.74 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
170 171 0.810031 GTGTTGGATCCATCGTCCGG 60.810 60.000 17.06 0.00 38.64 5.14
175 176 1.089481 CACCGGTGTTGGATCCATCG 61.089 60.000 26.95 16.20 0.00 3.84
211 212 0.606604 CAGCATGCAAAGGAAGGCTT 59.393 50.000 21.98 0.00 0.00 4.35
361 660 8.537016 TGAAATAATTCTTCGGAAGTTCTCCTA 58.463 33.333 16.78 3.30 38.01 2.94
437 805 6.374333 GCACCAAAGGATTTTCACAGTATAGA 59.626 38.462 0.00 0.00 35.03 1.98
544 921 0.886938 TTCCAATGACTTTGCGCCGA 60.887 50.000 4.18 0.00 33.73 5.54
616 995 1.153025 GAGCCGGTGGAATTACCCC 60.153 63.158 1.90 0.00 37.44 4.95
858 1246 3.095347 GCTTAGGGTCCCTGGAGCG 62.095 68.421 24.34 9.78 42.90 5.03
918 1306 4.437682 TCCAATGACCTCAAAGAACTGT 57.562 40.909 0.00 0.00 0.00 3.55
920 1308 5.835280 ACATTTCCAATGACCTCAAAGAACT 59.165 36.000 3.47 0.00 0.00 3.01
921 1309 6.089249 ACATTTCCAATGACCTCAAAGAAC 57.911 37.500 3.47 0.00 0.00 3.01
922 1310 7.004086 ACTACATTTCCAATGACCTCAAAGAA 58.996 34.615 3.47 0.00 0.00 2.52
923 1311 6.542821 ACTACATTTCCAATGACCTCAAAGA 58.457 36.000 3.47 0.00 0.00 2.52
924 1312 6.824305 ACTACATTTCCAATGACCTCAAAG 57.176 37.500 3.47 0.00 0.00 2.77
925 1313 7.458397 AGTACTACATTTCCAATGACCTCAAA 58.542 34.615 0.00 0.00 0.00 2.69
926 1314 7.016153 AGTACTACATTTCCAATGACCTCAA 57.984 36.000 0.00 0.00 0.00 3.02
929 1317 5.726793 AGGAGTACTACATTTCCAATGACCT 59.273 40.000 8.10 0.00 32.02 3.85
930 1318 5.990668 AGGAGTACTACATTTCCAATGACC 58.009 41.667 8.10 0.00 32.02 4.02
976 1625 6.986250 TGCAAACCATTACATTATGTCACAA 58.014 32.000 0.00 0.00 0.00 3.33
1003 1652 1.134037 GTCCACCACCACCTGTTGTAA 60.134 52.381 0.00 0.00 0.00 2.41
1029 1678 1.673993 CACCGCCACCTGCACAATA 60.674 57.895 0.00 0.00 41.33 1.90
1329 1984 6.183360 CGAAAAAGTTCAAAAATGTTCGTGGT 60.183 34.615 0.00 0.00 33.72 4.16
1462 2148 4.336993 ACAATCAGGCAAAACGTGTTAGAA 59.663 37.500 0.00 0.00 35.61 2.10
1593 2282 8.117813 AGAAGAAGGTCACAACTTTTAAAACA 57.882 30.769 0.00 0.00 0.00 2.83
1594 2283 8.860128 CAAGAAGAAGGTCACAACTTTTAAAAC 58.140 33.333 0.00 0.00 0.00 2.43
1598 2287 7.931578 TTCAAGAAGAAGGTCACAACTTTTA 57.068 32.000 0.00 0.00 0.00 1.52
1603 2292 6.196079 AGTTTTCAAGAAGAAGGTCACAAC 57.804 37.500 0.00 0.00 37.57 3.32
1610 2299 9.971922 AATATTCACAAGTTTTCAAGAAGAAGG 57.028 29.630 0.00 0.00 37.57 3.46
1735 2428 0.674581 CAGAGAGGACAATTGCGGCA 60.675 55.000 5.05 0.00 0.00 5.69
1741 2434 1.004044 CCTGTGGCAGAGAGGACAATT 59.996 52.381 14.03 0.00 37.28 2.32
1742 2435 0.617413 CCTGTGGCAGAGAGGACAAT 59.383 55.000 14.03 0.00 37.28 2.71
1744 2437 1.915266 CCCTGTGGCAGAGAGGACA 60.915 63.158 14.03 0.00 37.28 4.02
1765 2458 2.282180 GCAAAGGCGTCCTCCCAA 60.282 61.111 0.00 0.00 30.89 4.12
1800 2493 2.280552 TTAGAGAACCCACGCCGCT 61.281 57.895 0.00 0.00 0.00 5.52
1801 2494 2.098831 GTTAGAGAACCCACGCCGC 61.099 63.158 0.00 0.00 0.00 6.53
1802 2495 1.804326 CGTTAGAGAACCCACGCCG 60.804 63.158 0.00 0.00 31.28 6.46
1804 2497 2.005971 ATTCGTTAGAGAACCCACGC 57.994 50.000 0.00 0.00 32.39 5.34
1805 2498 4.990257 TCTAATTCGTTAGAGAACCCACG 58.010 43.478 0.00 0.00 32.39 4.94
1855 2548 6.700960 TCGTTTTACGAGATTTTAACAGGTGA 59.299 34.615 0.00 0.00 46.73 4.02
1894 2599 1.657751 CTGTCTCGTCCGATGCCTCA 61.658 60.000 0.00 0.00 0.00 3.86
1909 2614 9.764363 TTATGGTATGAGTTTACATGATCTGTC 57.236 33.333 0.00 0.00 39.39 3.51
1982 2687 3.507233 AGTTCAAATTCATCCATGCGTGT 59.493 39.130 4.96 0.00 0.00 4.49
1993 2698 0.958382 CCGGCCGGAGTTCAAATTCA 60.958 55.000 41.82 0.00 37.50 2.57
2039 2744 2.186125 CAGAGCATCGCCAGAGCA 59.814 61.111 0.00 0.00 42.67 4.26
2040 2745 3.270839 GCAGAGCATCGCCAGAGC 61.271 66.667 0.00 0.00 42.67 4.09
2047 2752 4.862092 AGCGTCGGCAGAGCATCG 62.862 66.667 9.92 1.53 43.41 3.84
2048 2753 2.959071 GAGCGTCGGCAGAGCATC 60.959 66.667 9.92 3.16 43.41 3.91
2049 2754 4.521062 GGAGCGTCGGCAGAGCAT 62.521 66.667 9.92 0.00 43.41 3.79
2073 2778 3.190849 CATCGCTGGAGCACGTGG 61.191 66.667 18.88 0.44 42.21 4.94
2074 2779 3.857854 GCATCGCTGGAGCACGTG 61.858 66.667 12.28 12.28 42.21 4.49
2075 2780 3.997064 GAGCATCGCTGGAGCACGT 62.997 63.158 0.00 0.00 39.88 4.49
2259 3032 7.574021 AGATCCTGTAAAATAGCATATCCCA 57.426 36.000 0.00 0.00 0.00 4.37
2310 3086 4.079253 AGCGGTCAAACCTTCACATTTAT 58.921 39.130 0.00 0.00 35.66 1.40
2414 3191 8.907222 ACCTGCAAAATTTCAGATACAAAATT 57.093 26.923 8.15 0.00 36.81 1.82
2430 3207 2.969821 ACATCCCAGTACCTGCAAAA 57.030 45.000 0.00 0.00 0.00 2.44
2519 3296 0.729690 GCCTGCAAAGCTACTAGCAC 59.270 55.000 10.73 0.00 45.56 4.40
2534 3311 6.048509 AGAAACAAGGTGTAAAATTTGCCTG 58.951 36.000 0.00 0.00 0.00 4.85
2566 3343 5.942872 AGCAAGGTGTTCATTTTTATCTCG 58.057 37.500 0.00 0.00 0.00 4.04
2579 3356 3.769300 GGGATTCCATTAAGCAAGGTGTT 59.231 43.478 4.80 0.00 0.00 3.32
2761 3546 2.738846 CAAGACGTCCATGAAGAACTGG 59.261 50.000 13.01 0.00 0.00 4.00
2762 3547 3.653344 TCAAGACGTCCATGAAGAACTG 58.347 45.455 13.01 0.00 0.00 3.16
2763 3548 4.543590 ATCAAGACGTCCATGAAGAACT 57.456 40.909 21.22 6.10 0.00 3.01
2764 3549 5.613358 AAATCAAGACGTCCATGAAGAAC 57.387 39.130 21.22 0.00 0.00 3.01
2780 3581 5.163723 GCATCAAGATCCACTTCGAAATCAA 60.164 40.000 9.57 0.00 36.61 2.57
2824 3653 0.462225 CTCAGCATCACCAGCCTGAG 60.462 60.000 0.00 2.56 33.95 3.35
2970 3799 0.041238 TGAACCTCTGGATCCCGTCT 59.959 55.000 9.90 0.00 0.00 4.18
3337 4169 1.984424 TGATGACATGAACCAGGTGGA 59.016 47.619 2.10 0.00 38.94 4.02
3480 4346 4.814041 AGCCTCCCCTCTCTGGCC 62.814 72.222 0.00 0.00 45.94 5.36
3481 4347 2.690510 AAGCCTCCCCTCTCTGGC 60.691 66.667 0.00 0.00 45.21 4.85
3482 4348 2.069430 GGAAGCCTCCCCTCTCTGG 61.069 68.421 0.00 0.00 35.42 3.86
3619 4485 0.683973 ACCTGTCTCTGACCAGCAAG 59.316 55.000 0.00 0.00 0.00 4.01
3719 4585 1.341531 CCTATGTACCTTGCTCTCCGG 59.658 57.143 0.00 0.00 0.00 5.14
3798 4667 1.679944 CCTGAATCCATGGCAAGTCGT 60.680 52.381 6.96 0.00 0.00 4.34
4207 5077 1.016130 CATGCGCGAAGAACCAGTCT 61.016 55.000 12.10 0.00 38.69 3.24
4323 5212 4.072088 CGTTCTCGCCGTTGCCAC 62.072 66.667 0.00 0.00 0.00 5.01
4643 5532 2.545113 CGTAATCGTACATGACCCCCAG 60.545 54.545 0.00 0.00 0.00 4.45
4848 5749 1.063764 GACTTCACCGGTACTAGCTCG 59.936 57.143 6.87 0.00 0.00 5.03
4853 5754 1.895131 GTTGGGACTTCACCGGTACTA 59.105 52.381 6.87 0.00 0.00 1.82
4854 5755 0.683412 GTTGGGACTTCACCGGTACT 59.317 55.000 6.87 0.00 0.00 2.73
4855 5756 0.321034 GGTTGGGACTTCACCGGTAC 60.321 60.000 6.87 0.00 0.00 3.34
4947 5848 7.283807 TCTGACATTGATTTGACCTAATGGATG 59.716 37.037 0.00 0.00 35.42 3.51
4948 5849 7.284034 GTCTGACATTGATTTGACCTAATGGAT 59.716 37.037 2.24 0.00 35.42 3.41
5020 5931 0.250553 TTCCGTGTGTGGAATGGTCC 60.251 55.000 0.00 0.00 43.01 4.46
5026 5937 0.394488 TGCCTTTTCCGTGTGTGGAA 60.394 50.000 0.00 0.00 46.12 3.53
5139 6050 9.394477 GTTTGCTCTTATTTTAAAGATCACGTT 57.606 29.630 0.00 0.00 32.82 3.99
5160 6071 7.167468 ACTCGTTCAAAATGTATTCAAGTTTGC 59.833 33.333 6.86 0.00 35.00 3.68
5178 6089 7.753659 TGTTGTAAGAATTTTGAACTCGTTCA 58.246 30.769 8.32 8.32 46.72 3.18


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

AutoCloner maintained by Alex Coulton.