Multiple sequence alignment - TraesCS6D01G159200

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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 TraesCS6D01G159200 chr6D 100.000 3632 0 0 1 3632 136387972 136391603 0.000000e+00 6708.0
1 TraesCS6D01G159200 chr6D 90.998 1433 77 19 1225 2633 121346188 121344784 0.000000e+00 1884.0
2 TraesCS6D01G159200 chr6D 82.714 538 75 7 1706 2237 379338983 379338458 2.550000e-126 462.0
3 TraesCS6D01G159200 chr6D 88.214 280 26 5 1250 1526 379339371 379339096 9.720000e-86 327.0
4 TraesCS6D01G159200 chr6D 86.667 240 17 4 998 1222 121346469 121346230 6.020000e-63 252.0
5 TraesCS6D01G159200 chr6B 90.350 1430 94 19 1233 2633 213467014 213468428 0.000000e+00 1836.0
6 TraesCS6D01G159200 chr6B 87.975 632 51 17 2539 3166 234658900 234659510 0.000000e+00 723.0
7 TraesCS6D01G159200 chr6B 81.533 574 88 7 1670 2237 567611756 567612317 1.190000e-124 457.0
8 TraesCS6D01G159200 chr6B 92.437 238 17 1 3396 3632 234662510 234662747 4.490000e-89 339.0
9 TraesCS6D01G159200 chr6B 87.050 278 30 4 1247 1521 567611409 567611683 3.520000e-80 309.0
10 TraesCS6D01G159200 chr6B 91.892 74 6 0 1295 1368 695474266 695474339 1.780000e-18 104.0
11 TraesCS6D01G159200 chr6B 94.828 58 2 1 852 908 490339166 490339223 5.000000e-14 89.8
12 TraesCS6D01G159200 chr6A 88.889 1449 88 26 1247 2633 162310604 162309167 0.000000e+00 1716.0
13 TraesCS6D01G159200 chr6A 87.604 960 90 8 1641 2590 177697006 177697946 0.000000e+00 1086.0
14 TraesCS6D01G159200 chr6A 84.796 1105 99 31 1 1038 177688560 177689662 0.000000e+00 1046.0
15 TraesCS6D01G159200 chr6A 87.279 283 29 4 1247 1526 521648652 521648930 2.100000e-82 316.0
16 TraesCS6D01G159200 chr6A 92.045 176 14 0 2423 2598 521649715 521649890 7.790000e-62 248.0
17 TraesCS6D01G159200 chr6A 85.200 250 22 6 3388 3625 177805329 177805575 3.620000e-60 243.0
18 TraesCS6D01G159200 chr6A 89.444 180 17 2 3162 3339 428279636 428279815 3.650000e-55 226.0
19 TraesCS6D01G159200 chr6A 87.831 189 18 5 3154 3338 7988443 7988630 2.200000e-52 217.0
20 TraesCS6D01G159200 chr6A 79.808 208 29 7 2962 3166 177768474 177768671 4.890000e-29 139.0
21 TraesCS6D01G159200 chr7D 85.000 780 103 12 1 771 32601475 32600701 0.000000e+00 780.0
22 TraesCS6D01G159200 chr7D 76.536 179 34 7 2419 2596 170729870 170729699 1.390000e-14 91.6
23 TraesCS6D01G159200 chr2D 83.825 779 114 9 1 771 350641889 350641115 0.000000e+00 730.0
24 TraesCS6D01G159200 chr2D 83.511 752 114 8 6 750 484319013 484319761 0.000000e+00 693.0
25 TraesCS6D01G159200 chr2B 82.411 813 123 13 1 802 535016020 535016823 0.000000e+00 691.0
26 TraesCS6D01G159200 chr2B 82.959 757 125 3 1 753 390967440 390968196 0.000000e+00 680.0
27 TraesCS6D01G159200 chr2B 91.379 58 4 1 852 908 10675286 10675229 1.080000e-10 78.7
28 TraesCS6D01G159200 chr2B 91.379 58 4 1 852 908 390968335 390968392 1.080000e-10 78.7
29 TraesCS6D01G159200 chr7B 80.526 950 138 25 1 908 364196342 364195398 0.000000e+00 686.0
30 TraesCS6D01G159200 chr5A 82.798 779 118 12 1 771 609827261 609826491 0.000000e+00 682.0
31 TraesCS6D01G159200 chr4A 82.648 778 121 11 1 771 17242188 17242958 0.000000e+00 676.0
32 TraesCS6D01G159200 chr4A 89.385 179 19 0 3160 3338 124610413 124610235 3.650000e-55 226.0
33 TraesCS6D01G159200 chr4A 88.398 181 19 2 3160 3338 47138086 47137906 2.200000e-52 217.0
34 TraesCS6D01G159200 chr7A 89.326 178 19 0 3161 3338 134435059 134434882 1.310000e-54 224.0
35 TraesCS6D01G159200 chr7A 88.827 179 17 2 3160 3338 701621301 701621126 2.200000e-52 217.0
36 TraesCS6D01G159200 chr1A 88.525 183 20 1 3157 3338 309178222 309178404 1.700000e-53 220.0
37 TraesCS6D01G159200 chr1A 89.205 176 19 0 3163 3338 330765864 330766039 1.700000e-53 220.0
38 TraesCS6D01G159200 chr1B 88.043 184 20 2 3157 3338 242247014 242246831 2.200000e-52 217.0
39 TraesCS6D01G159200 chr1B 91.379 58 4 1 852 908 674634628 674634685 1.080000e-10 78.7
40 TraesCS6D01G159200 chr3B 93.103 58 3 1 852 908 272803026 272802969 2.320000e-12 84.2
41 TraesCS6D01G159200 chr3D 97.222 36 1 0 1333 1368 136564786 136564751 1.090000e-05 62.1


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 TraesCS6D01G159200 chr6D 136387972 136391603 3631 False 6708.00 6708 100.0000 1 3632 1 chr6D.!!$F1 3631
1 TraesCS6D01G159200 chr6D 121344784 121346469 1685 True 1068.00 1884 88.8325 998 2633 2 chr6D.!!$R1 1635
2 TraesCS6D01G159200 chr6D 379338458 379339371 913 True 394.50 462 85.4640 1250 2237 2 chr6D.!!$R2 987
3 TraesCS6D01G159200 chr6B 213467014 213468428 1414 False 1836.00 1836 90.3500 1233 2633 1 chr6B.!!$F1 1400
4 TraesCS6D01G159200 chr6B 234658900 234662747 3847 False 531.00 723 90.2060 2539 3632 2 chr6B.!!$F4 1093
5 TraesCS6D01G159200 chr6B 567611409 567612317 908 False 383.00 457 84.2915 1247 2237 2 chr6B.!!$F5 990
6 TraesCS6D01G159200 chr6A 162309167 162310604 1437 True 1716.00 1716 88.8890 1247 2633 1 chr6A.!!$R1 1386
7 TraesCS6D01G159200 chr6A 177697006 177697946 940 False 1086.00 1086 87.6040 1641 2590 1 chr6A.!!$F3 949
8 TraesCS6D01G159200 chr6A 177688560 177689662 1102 False 1046.00 1046 84.7960 1 1038 1 chr6A.!!$F2 1037
9 TraesCS6D01G159200 chr6A 521648652 521649890 1238 False 282.00 316 89.6620 1247 2598 2 chr6A.!!$F7 1351
10 TraesCS6D01G159200 chr7D 32600701 32601475 774 True 780.00 780 85.0000 1 771 1 chr7D.!!$R1 770
11 TraesCS6D01G159200 chr2D 350641115 350641889 774 True 730.00 730 83.8250 1 771 1 chr2D.!!$R1 770
12 TraesCS6D01G159200 chr2D 484319013 484319761 748 False 693.00 693 83.5110 6 750 1 chr2D.!!$F1 744
13 TraesCS6D01G159200 chr2B 535016020 535016823 803 False 691.00 691 82.4110 1 802 1 chr2B.!!$F1 801
14 TraesCS6D01G159200 chr2B 390967440 390968392 952 False 379.35 680 87.1690 1 908 2 chr2B.!!$F2 907
15 TraesCS6D01G159200 chr7B 364195398 364196342 944 True 686.00 686 80.5260 1 908 1 chr7B.!!$R1 907
16 TraesCS6D01G159200 chr5A 609826491 609827261 770 True 682.00 682 82.7980 1 771 1 chr5A.!!$R1 770
17 TraesCS6D01G159200 chr4A 17242188 17242958 770 False 676.00 676 82.6480 1 771 1 chr4A.!!$F1 770

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
753 762 0.527565 CCTACTTGCCATGTTGCACC 59.472 55.0 0.0 0.0 41.88 5.01 F
1315 1453 0.033504 CTACACCAACCTGACGTGCT 59.966 55.0 0.0 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1573 1738 0.034574 ACATGCTATTCCCGTGCCAA 60.035 50.0 0.0 0.0 0.0 4.52 R
3039 3292 0.181587 TTGTTTTCGAGTGCCTCCCA 59.818 50.0 0.0 0.0 0.0 4.37 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
168 170 5.678483 GCACGATGTTTGAGCAAGTATAATG 59.322 40.000 0.00 0.00 0.00 1.90
204 206 6.325919 TCAACTCATACCCATTCAACAAAC 57.674 37.500 0.00 0.00 0.00 2.93
217 219 7.918033 CCCATTCAACAAACGCAATATATGTAA 59.082 33.333 0.00 0.00 0.00 2.41
352 356 5.103940 ACAAAATAGCCAGACATATCCCTGT 60.104 40.000 0.00 0.00 0.00 4.00
576 583 3.379688 GCCCCAGAATTTTTAGCTCTGAG 59.620 47.826 0.00 0.00 39.15 3.35
635 642 4.397103 ACAACATGCATCTTTGTCGATGAT 59.603 37.500 14.80 0.00 42.63 2.45
639 646 5.761726 ACATGCATCTTTGTCGATGATGTAT 59.238 36.000 14.44 12.97 42.15 2.29
646 653 7.643528 TCTTTGTCGATGATGTATAAGATGC 57.356 36.000 0.00 0.00 0.00 3.91
674 681 7.858879 TCGACTGATGAATGCATATGAAAAATG 59.141 33.333 6.97 0.00 34.11 2.32
718 726 9.912634 ATTAGAAACAACAATAAACCATGACAG 57.087 29.630 0.00 0.00 0.00 3.51
753 762 0.527565 CCTACTTGCCATGTTGCACC 59.472 55.000 0.00 0.00 41.88 5.01
779 801 3.514309 AGGTTGTTGTCTATTCGCTACCT 59.486 43.478 0.00 0.00 32.21 3.08
797 819 5.182380 GCTACCTAACAAAGTTGCCAACATA 59.818 40.000 10.69 0.00 0.00 2.29
819 855 5.695851 ATGAACGCAGAACTTTTGATCTT 57.304 34.783 0.00 0.00 28.49 2.40
829 865 7.862372 GCAGAACTTTTGATCTTGTGTTGAATA 59.138 33.333 0.00 0.00 28.49 1.75
944 1016 9.122779 AGATATATAGAATAGCTGTCCGTTACC 57.877 37.037 0.00 0.00 0.00 2.85
949 1021 3.729862 ATAGCTGTCCGTTACCTAAGC 57.270 47.619 0.00 0.00 0.00 3.09
953 1025 2.000447 CTGTCCGTTACCTAAGCAAGC 59.000 52.381 0.00 0.00 0.00 4.01
982 1063 2.528564 AGCTGGCTCCTGATCTCTATC 58.471 52.381 0.00 0.00 0.00 2.08
983 1064 1.202114 GCTGGCTCCTGATCTCTATCG 59.798 57.143 0.00 0.00 34.60 2.92
994 1075 2.265589 TCTCTATCGCGTACATCCCA 57.734 50.000 5.77 0.00 0.00 4.37
995 1076 1.878088 TCTCTATCGCGTACATCCCAC 59.122 52.381 5.77 0.00 0.00 4.61
996 1077 1.607148 CTCTATCGCGTACATCCCACA 59.393 52.381 5.77 0.00 0.00 4.17
1048 1129 2.506472 GGAAGATCTCCGTGGCCC 59.494 66.667 0.00 0.00 33.37 5.80
1066 1147 2.125552 TTGCCACGCTGATCCTCG 60.126 61.111 2.66 2.66 0.00 4.63
1074 1155 1.227205 GCTGATCCTCGTCCTGCTG 60.227 63.158 0.00 0.00 0.00 4.41
1125 1209 0.317479 ACTTCACCGACAGCTACCAC 59.683 55.000 0.00 0.00 0.00 4.16
1134 1218 2.286831 CGACAGCTACCACTACATACGG 60.287 54.545 0.00 0.00 0.00 4.02
1158 1254 0.526524 CCTCCTCTGCATCGTCGTTC 60.527 60.000 0.00 0.00 0.00 3.95
1174 1270 4.974438 TCCCGGCAACCACCTCCT 62.974 66.667 0.00 0.00 0.00 3.69
1237 1372 2.264124 TCGAAGACCAACTCCTCGG 58.736 57.895 0.00 0.00 31.99 4.63
1244 1379 2.583441 CCAACTCCTCGGCCACTGA 61.583 63.158 2.24 0.00 0.00 3.41
1315 1453 0.033504 CTACACCAACCTGACGTGCT 59.966 55.000 0.00 0.00 0.00 4.40
1374 1515 3.917760 CCGGGCCTCGACCTCATC 61.918 72.222 14.30 0.00 42.43 2.92
1375 1516 3.147595 CGGGCCTCGACCTCATCA 61.148 66.667 0.84 0.00 42.43 3.07
1376 1517 2.502492 CGGGCCTCGACCTCATCAT 61.502 63.158 0.84 0.00 42.43 2.45
1400 1541 4.373116 GCGGTGGAAGCCTCACGA 62.373 66.667 0.00 0.00 36.09 4.35
1470 1611 1.244019 GCAAGTCCATGGCCTTCGTT 61.244 55.000 4.71 0.00 0.00 3.85
1534 1688 1.079819 CTGTCCCAGGTGCGTACAG 60.080 63.158 5.86 0.00 32.39 2.74
1535 1689 1.816863 CTGTCCCAGGTGCGTACAGT 61.817 60.000 5.86 0.00 34.28 3.55
1541 1697 1.079127 AGGTGCGTACAGTGCATCC 60.079 57.895 5.86 3.72 44.58 3.51
1548 1712 2.083774 CGTACAGTGCATCCCATGTTT 58.916 47.619 0.00 0.00 0.00 2.83
1549 1713 2.159531 CGTACAGTGCATCCCATGTTTG 60.160 50.000 0.00 0.00 0.00 2.93
1572 1737 1.652563 GTTGGACAACCCGTTGCTC 59.347 57.895 7.48 4.93 44.03 4.26
1573 1738 0.818040 GTTGGACAACCCGTTGCTCT 60.818 55.000 7.48 0.00 44.03 4.09
1612 1799 2.752939 CGCGACTCATGCATGGCAA 61.753 57.895 25.97 6.62 43.62 4.52
1613 1800 1.226491 GCGACTCATGCATGGCAAC 60.226 57.895 25.97 13.76 43.62 4.17
1614 1801 1.430632 CGACTCATGCATGGCAACC 59.569 57.895 25.97 10.36 43.62 3.77
1790 1979 4.116328 TCGCTCTTCTGGTCGCCG 62.116 66.667 0.00 0.00 0.00 6.46
2148 2350 1.533469 CGAGAACGGGGAGTGGAACT 61.533 60.000 0.00 0.00 43.16 3.01
2272 2479 2.203252 ATGCAGCCCCATACGCAG 60.203 61.111 0.00 0.00 37.88 5.18
2283 2490 2.136878 ATACGCAGGCCCCTCTCTG 61.137 63.158 0.00 0.00 0.00 3.35
2298 2507 3.805307 CTGTCTCTCGACGCGGCT 61.805 66.667 11.76 0.00 43.21 5.52
2314 2523 2.750712 GCGGCTACTGGAAAATTGGTTA 59.249 45.455 0.00 0.00 0.00 2.85
2397 2633 2.043450 CTCAGGGAGACGGAGGCT 60.043 66.667 0.00 0.00 0.00 4.58
2609 2855 3.646976 CATGCTGGCGGCTCATCG 61.647 66.667 20.66 5.43 42.39 3.84
2708 2957 6.073711 GCAGTGAACAACTAAAGTACTCCTTC 60.074 42.308 0.00 0.00 36.83 3.46
2711 2960 4.532314 ACAACTAAAGTACTCCTTCGGG 57.468 45.455 0.00 0.00 31.27 5.14
2737 2987 0.683973 CTGCAAGGTCACCTCTCAGT 59.316 55.000 14.32 0.00 32.23 3.41
2741 2991 0.540830 AAGGTCACCTCTCAGTCGCT 60.541 55.000 0.00 0.00 30.89 4.93
2743 2993 1.445238 GTCACCTCTCAGTCGCTGC 60.445 63.158 2.45 0.00 0.00 5.25
2744 2994 1.604879 TCACCTCTCAGTCGCTGCT 60.605 57.895 0.00 0.00 0.00 4.24
2745 2995 1.445754 CACCTCTCAGTCGCTGCTG 60.446 63.158 0.00 0.00 37.81 4.41
2746 2996 2.508887 CCTCTCAGTCGCTGCTGC 60.509 66.667 5.34 5.34 36.49 5.25
2770 3020 3.295273 TCGTGCTGTGCGACCTCT 61.295 61.111 0.00 0.00 33.09 3.69
2772 3022 2.653702 GTGCTGTGCGACCTCTCT 59.346 61.111 0.00 0.00 0.00 3.10
2775 3025 0.966179 TGCTGTGCGACCTCTCTTTA 59.034 50.000 0.00 0.00 0.00 1.85
2777 3027 2.028112 TGCTGTGCGACCTCTCTTTAAT 60.028 45.455 0.00 0.00 0.00 1.40
2778 3028 3.003480 GCTGTGCGACCTCTCTTTAATT 58.997 45.455 0.00 0.00 0.00 1.40
2779 3029 3.062774 GCTGTGCGACCTCTCTTTAATTC 59.937 47.826 0.00 0.00 0.00 2.17
2780 3030 4.499183 CTGTGCGACCTCTCTTTAATTCT 58.501 43.478 0.00 0.00 0.00 2.40
2781 3031 4.894784 TGTGCGACCTCTCTTTAATTCTT 58.105 39.130 0.00 0.00 0.00 2.52
2811 3061 4.851014 TCGCATGCATTTTCGACTTTTTAG 59.149 37.500 19.57 0.00 0.00 1.85
2814 3064 6.686679 CGCATGCATTTTCGACTTTTTAGATA 59.313 34.615 19.57 0.00 0.00 1.98
2858 3110 8.752254 GTTTTCTCCGATTTTTCTTAGGTTTTG 58.248 33.333 0.00 0.00 0.00 2.44
2860 3112 6.066032 TCTCCGATTTTTCTTAGGTTTTGGT 58.934 36.000 0.00 0.00 0.00 3.67
2965 3218 7.016361 TCTTTTCTTTTTCCTTTCGTGAGAG 57.984 36.000 0.00 0.00 43.69 3.20
2967 3220 3.139077 TCTTTTTCCTTTCGTGAGAGGC 58.861 45.455 1.64 0.00 43.69 4.70
2979 3232 1.184970 TGAGAGGCACGGTCATGACA 61.185 55.000 26.47 0.00 0.00 3.58
2993 3246 3.123621 GTCATGACACTCGAAGCGAAAAT 59.876 43.478 21.07 0.00 34.74 1.82
2996 3249 5.407084 TCATGACACTCGAAGCGAAAATAAA 59.593 36.000 0.00 0.00 34.74 1.40
2998 3251 5.437263 TGACACTCGAAGCGAAAATAAAAC 58.563 37.500 0.00 0.00 34.74 2.43
2999 3252 5.006844 TGACACTCGAAGCGAAAATAAAACA 59.993 36.000 0.00 0.00 34.74 2.83
3000 3253 5.202640 ACACTCGAAGCGAAAATAAAACAC 58.797 37.500 0.00 0.00 34.74 3.32
3001 3254 5.201910 CACTCGAAGCGAAAATAAAACACA 58.798 37.500 0.00 0.00 34.74 3.72
3002 3255 5.851177 CACTCGAAGCGAAAATAAAACACAT 59.149 36.000 0.00 0.00 34.74 3.21
3024 3277 0.762418 TTTTCCTTCGGTGAGAGGCA 59.238 50.000 0.00 0.00 0.00 4.75
3039 3292 5.012239 TGAGAGGCATGAATTAGCTTTTGT 58.988 37.500 0.00 0.00 0.00 2.83
3143 3396 2.278332 AGCCCAGGAAACAAAGACTC 57.722 50.000 0.00 0.00 0.00 3.36
3149 3402 3.751175 CCAGGAAACAAAGACTCGCATTA 59.249 43.478 0.00 0.00 0.00 1.90
3207 3531 9.794685 ATATCTAGATGTGCAATACTTATGACG 57.205 33.333 15.79 0.00 0.00 4.35
3218 3542 6.642950 GCAATACTTATGACGCATCTAAGTCT 59.357 38.462 7.57 0.00 38.16 3.24
3219 3543 7.148885 GCAATACTTATGACGCATCTAAGTCTC 60.149 40.741 7.57 0.00 38.16 3.36
3221 3545 6.398234 ACTTATGACGCATCTAAGTCTCAT 57.602 37.500 0.00 0.00 38.16 2.90
3237 3561 9.761504 CTAAGTCTCATGTCATTGATCTTACAT 57.238 33.333 0.00 0.00 32.91 2.29
3281 3605 9.567776 TTTTCTTTTTCCCTTTTTGTTTTCTCT 57.432 25.926 0.00 0.00 0.00 3.10
3296 3620 9.985730 TTTGTTTTCTCTTTATGCTTGATTCAT 57.014 25.926 0.00 0.00 0.00 2.57
3298 3622 9.630098 TGTTTTCTCTTTATGCTTGATTCATTC 57.370 29.630 0.00 0.00 0.00 2.67
3380 3840 4.851558 GTCATTATTTGTGTTGCGACTTCC 59.148 41.667 5.50 0.00 0.00 3.46
3383 3843 0.375454 TTTGTGTTGCGACTTCCACG 59.625 50.000 5.50 0.00 0.00 4.94
3394 3854 4.150980 TGCGACTTCCACGTATTTTAGTTG 59.849 41.667 0.00 0.00 0.00 3.16
3402 3862 7.591006 TCCACGTATTTTAGTTGAAGATCAC 57.409 36.000 0.00 0.00 0.00 3.06
3410 3870 0.953960 GTTGAAGATCACGCCCCGTT 60.954 55.000 0.00 0.00 38.32 4.44
3411 3871 0.953471 TTGAAGATCACGCCCCGTTG 60.953 55.000 0.00 0.00 38.32 4.10
3412 3872 1.079405 GAAGATCACGCCCCGTTGA 60.079 57.895 0.00 0.00 38.32 3.18
3414 3874 0.828022 AAGATCACGCCCCGTTGATA 59.172 50.000 0.00 0.00 38.32 2.15
3465 6496 2.947652 TCTATTCCCTTGTACGACTCCG 59.052 50.000 0.00 0.00 42.50 4.63
3493 6524 2.779951 TAGCCATTGCGCGAGTGTGT 62.780 55.000 12.10 0.00 44.33 3.72
3533 6564 8.791675 TGTTTGTCTATGCTTACATCAAATTCA 58.208 29.630 0.00 0.00 37.74 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 76 4.615949 AGCGCATCAAGTAGATCTTAGTG 58.384 43.478 11.47 0.00 33.72 2.74
137 139 0.505231 TCAAACATCGTGCGAACGAC 59.495 50.000 23.36 0.00 45.30 4.34
140 142 0.234625 TGCTCAAACATCGTGCGAAC 59.765 50.000 0.00 0.00 0.00 3.95
168 170 6.325596 GGTATGAGTTGAGGAAGCAATTTTC 58.674 40.000 0.00 0.00 0.00 2.29
204 206 9.619727 GTATTCGTGCTAATTACATATATTGCG 57.380 33.333 0.00 0.00 0.00 4.85
407 414 7.095607 GCATAGACGGGTAGTAAATTCAGAATG 60.096 40.741 0.00 0.00 37.54 2.67
576 583 5.940470 GGACCCTATTCATACATCACAATCC 59.060 44.000 0.00 0.00 0.00 3.01
718 726 5.562890 GCAAGTAGGTCTTTTGTCCATTGTC 60.563 44.000 0.00 0.00 33.63 3.18
753 762 3.935203 AGCGAATAGACAACAACCTCATG 59.065 43.478 0.00 0.00 0.00 3.07
772 794 2.147958 TGGCAACTTTGTTAGGTAGCG 58.852 47.619 0.00 0.00 37.61 4.26
779 801 6.146216 CGTTCATATGTTGGCAACTTTGTTA 58.854 36.000 28.71 9.94 37.61 2.41
797 819 5.009010 ACAAGATCAAAAGTTCTGCGTTCAT 59.991 36.000 0.00 0.00 0.00 2.57
929 998 3.028850 TGCTTAGGTAACGGACAGCTAT 58.971 45.455 0.00 0.00 46.39 2.97
930 999 2.449464 TGCTTAGGTAACGGACAGCTA 58.551 47.619 0.00 0.00 46.39 3.32
933 1005 2.000447 GCTTGCTTAGGTAACGGACAG 59.000 52.381 0.00 0.00 46.39 3.51
938 1010 0.645868 GCTCGCTTGCTTAGGTAACG 59.354 55.000 0.00 0.00 46.39 3.18
944 1016 1.471964 CTACTCGCTCGCTTGCTTAG 58.528 55.000 0.00 0.00 0.00 2.18
966 1038 0.170116 CGCGATAGAGATCAGGAGCC 59.830 60.000 0.00 0.00 38.63 4.70
982 1063 0.742990 ATGGTTGTGGGATGTACGCG 60.743 55.000 3.53 3.53 0.00 6.01
983 1064 0.732571 CATGGTTGTGGGATGTACGC 59.267 55.000 0.00 0.00 0.00 4.42
994 1075 0.105760 TTGTGGGGCTTCATGGTTGT 60.106 50.000 0.00 0.00 0.00 3.32
995 1076 0.604578 CTTGTGGGGCTTCATGGTTG 59.395 55.000 0.00 0.00 0.00 3.77
996 1077 0.482446 TCTTGTGGGGCTTCATGGTT 59.518 50.000 0.00 0.00 0.00 3.67
1047 1128 1.817099 GAGGATCAGCGTGGCAAGG 60.817 63.158 1.91 0.00 33.17 3.61
1048 1129 2.169789 CGAGGATCAGCGTGGCAAG 61.170 63.158 0.00 0.00 33.17 4.01
1058 1139 2.725312 GCCAGCAGGACGAGGATCA 61.725 63.158 0.00 0.00 36.89 2.92
1101 1182 1.871080 AGCTGTCGGTGAAGTTGAAG 58.129 50.000 0.00 0.00 0.00 3.02
1111 1192 1.848652 ATGTAGTGGTAGCTGTCGGT 58.151 50.000 0.00 0.00 0.00 4.69
1125 1209 2.729862 GAGGCGCGCCGTATGTAG 60.730 66.667 41.70 0.00 41.95 2.74
1158 1254 4.410400 GAGGAGGTGGTTGCCGGG 62.410 72.222 2.18 0.00 0.00 5.73
1164 1260 1.609794 GGGAGACGAGGAGGTGGTT 60.610 63.158 0.00 0.00 0.00 3.67
1188 1284 4.397832 GGTAAGGTTGCCGCCGGA 62.398 66.667 7.68 0.00 0.00 5.14
1222 1318 1.841556 TGGCCGAGGAGTTGGTCTT 60.842 57.895 0.00 0.00 32.15 3.01
1223 1319 2.203788 TGGCCGAGGAGTTGGTCT 60.204 61.111 0.00 0.00 32.15 3.85
1396 1537 4.436998 GGGGAGGTCGCAGTCGTG 62.437 72.222 0.00 0.00 36.96 4.35
1534 1688 1.402720 CCGAACAAACATGGGATGCAC 60.403 52.381 0.00 0.00 0.00 4.57
1535 1689 0.887247 CCGAACAAACATGGGATGCA 59.113 50.000 0.00 0.00 0.00 3.96
1541 1697 1.678627 TGTCCAACCGAACAAACATGG 59.321 47.619 0.00 0.00 0.00 3.66
1570 1735 0.107703 TGCTATTCCCGTGCCAAGAG 60.108 55.000 0.00 0.00 0.00 2.85
1572 1737 0.664761 CATGCTATTCCCGTGCCAAG 59.335 55.000 0.00 0.00 0.00 3.61
1573 1738 0.034574 ACATGCTATTCCCGTGCCAA 60.035 50.000 0.00 0.00 0.00 4.52
1612 1799 1.916181 CTAGAAGTGGATGGTTGGGGT 59.084 52.381 0.00 0.00 0.00 4.95
1613 1800 1.408822 GCTAGAAGTGGATGGTTGGGG 60.409 57.143 0.00 0.00 0.00 4.96
1614 1801 1.561542 AGCTAGAAGTGGATGGTTGGG 59.438 52.381 0.00 0.00 0.00 4.12
1617 1804 1.912043 AGCAGCTAGAAGTGGATGGTT 59.088 47.619 0.00 0.00 0.00 3.67
1619 1806 2.547642 GCTAGCAGCTAGAAGTGGATGG 60.548 54.545 30.45 3.79 38.45 3.51
2238 2440 1.742761 CATGCATGGTTTCCGTCTCT 58.257 50.000 19.40 0.00 0.00 3.10
2272 2479 2.124693 CGAGAGACAGAGAGGGGCC 61.125 68.421 0.00 0.00 0.00 5.80
2298 2507 5.521544 GCGTTTGTAACCAATTTTCCAGTA 58.478 37.500 0.00 0.00 0.00 2.74
2314 2523 1.006571 ATCACGTCTCCGCGTTTGT 60.007 52.632 4.92 0.00 43.83 2.83
2665 2914 3.181504 ACTGCGTCGTTTATTTTATGGGC 60.182 43.478 0.00 0.00 0.00 5.36
2711 2960 1.376553 GTGACCTTGCAGGGAGCTC 60.377 63.158 23.57 9.49 45.94 4.09
2720 2969 0.389166 CGACTGAGAGGTGACCTTGC 60.389 60.000 5.21 1.19 31.76 4.01
2760 3010 5.864628 AAAGAATTAAAGAGAGGTCGCAC 57.135 39.130 0.00 0.00 0.00 5.34
2790 3040 6.875926 ATCTAAAAAGTCGAAAATGCATGC 57.124 33.333 11.82 11.82 0.00 4.06
2832 3084 8.752254 CAAAACCTAAGAAAAATCGGAGAAAAC 58.248 33.333 0.00 0.00 43.58 2.43
2833 3085 7.923878 CCAAAACCTAAGAAAAATCGGAGAAAA 59.076 33.333 0.00 0.00 43.58 2.29
2837 3089 6.327279 ACCAAAACCTAAGAAAAATCGGAG 57.673 37.500 0.00 0.00 0.00 4.63
2965 3218 2.094659 CGAGTGTCATGACCGTGCC 61.095 63.158 22.85 7.00 0.00 5.01
2967 3220 1.340658 CTTCGAGTGTCATGACCGTG 58.659 55.000 22.85 10.28 0.00 4.94
2979 3232 5.412526 TGTGTTTTATTTTCGCTTCGAGT 57.587 34.783 0.00 0.00 37.14 4.18
3024 3277 3.448660 GCCTCCCACAAAAGCTAATTCAT 59.551 43.478 0.00 0.00 0.00 2.57
3039 3292 0.181587 TTGTTTTCGAGTGCCTCCCA 59.818 50.000 0.00 0.00 0.00 4.37
3064 3317 3.365520 GTGGCGAAAAAGAAAACGTGTTT 59.634 39.130 0.00 0.00 0.00 2.83
3065 3318 2.918600 GTGGCGAAAAAGAAAACGTGTT 59.081 40.909 0.00 0.00 0.00 3.32
3066 3319 2.095161 TGTGGCGAAAAAGAAAACGTGT 60.095 40.909 0.00 0.00 0.00 4.49
3069 3322 4.770351 AATTGTGGCGAAAAAGAAAACG 57.230 36.364 0.00 0.00 0.00 3.60
3082 3335 8.141835 ACTTTTGTTTCAAGATAAATTGTGGC 57.858 30.769 0.00 0.00 0.00 5.01
3117 3370 6.099701 AGTCTTTGTTTCCTGGGCTTATTTTT 59.900 34.615 0.00 0.00 0.00 1.94
3128 3381 3.904136 AATGCGAGTCTTTGTTTCCTG 57.096 42.857 0.00 0.00 0.00 3.86
3177 3501 9.814899 ATAAGTATTGCACATCTAGATATGCTC 57.185 33.333 30.50 19.49 41.52 4.26
3182 3506 7.755373 GCGTCATAAGTATTGCACATCTAGATA 59.245 37.037 4.54 0.00 0.00 1.98
3190 3514 4.441792 AGATGCGTCATAAGTATTGCACA 58.558 39.130 8.99 0.00 34.86 4.57
3191 3515 6.201044 ACTTAGATGCGTCATAAGTATTGCAC 59.799 38.462 20.16 0.00 37.84 4.57
3195 3519 7.941919 TGAGACTTAGATGCGTCATAAGTATT 58.058 34.615 20.95 15.61 39.28 1.89
3199 3523 6.212235 ACATGAGACTTAGATGCGTCATAAG 58.788 40.000 8.99 14.15 32.68 1.73
3200 3524 6.149129 ACATGAGACTTAGATGCGTCATAA 57.851 37.500 8.99 3.57 32.68 1.90
3204 3528 4.033990 TGACATGAGACTTAGATGCGTC 57.966 45.455 0.00 0.00 0.00 5.19
3207 3531 6.930164 AGATCAATGACATGAGACTTAGATGC 59.070 38.462 0.00 0.00 31.76 3.91
3264 3588 7.360113 AGCATAAAGAGAAAACAAAAAGGGA 57.640 32.000 0.00 0.00 0.00 4.20
3269 3593 9.814899 TGAATCAAGCATAAAGAGAAAACAAAA 57.185 25.926 0.00 0.00 0.00 2.44
3270 3594 9.985730 ATGAATCAAGCATAAAGAGAAAACAAA 57.014 25.926 0.00 0.00 0.00 2.83
3271 3595 9.985730 AATGAATCAAGCATAAAGAGAAAACAA 57.014 25.926 0.00 0.00 0.00 2.83
3272 3596 9.630098 GAATGAATCAAGCATAAAGAGAAAACA 57.370 29.630 0.00 0.00 0.00 2.83
3273 3597 9.630098 TGAATGAATCAAGCATAAAGAGAAAAC 57.370 29.630 0.00 0.00 34.30 2.43
3296 3620 8.830580 GCTCTAGTTATTGCACATCTAAATGAA 58.169 33.333 0.00 0.00 36.67 2.57
3298 3622 8.146479 TGCTCTAGTTATTGCACATCTAAATG 57.854 34.615 0.00 0.00 38.93 2.32
3353 3813 7.320443 AGTCGCAACACAAATAATGACATAT 57.680 32.000 0.00 0.00 0.00 1.78
3361 3821 3.303461 CGTGGAAGTCGCAACACAAATAA 60.303 43.478 0.00 0.00 33.62 1.40
3374 3834 7.647907 TCTTCAACTAAAATACGTGGAAGTC 57.352 36.000 0.00 0.00 40.47 3.01
3380 3840 5.952064 GCGTGATCTTCAACTAAAATACGTG 59.048 40.000 0.00 0.00 0.00 4.49
3383 3843 5.220796 GGGGCGTGATCTTCAACTAAAATAC 60.221 44.000 0.00 0.00 0.00 1.89
3394 3854 0.462047 ATCAACGGGGCGTGATCTTC 60.462 55.000 0.00 0.00 39.99 2.87
3402 3862 1.301716 CCATCCTATCAACGGGGCG 60.302 63.158 0.00 0.00 0.00 6.13
3410 3870 3.927476 TGTGATCAGGTCCATCCTATCA 58.073 45.455 0.00 0.00 46.24 2.15
3411 3871 4.529769 TCATGTGATCAGGTCCATCCTATC 59.470 45.833 0.00 0.00 46.24 2.08
3412 3872 4.285517 GTCATGTGATCAGGTCCATCCTAT 59.714 45.833 0.00 0.00 46.24 2.57
3465 6496 1.926510 GCGCAATGGCTATTGAAAACC 59.073 47.619 25.24 7.08 45.21 3.27
3493 6524 7.148423 GCATAGACAAACACTTGTATCATCACA 60.148 37.037 0.00 0.00 45.98 3.58
3533 6564 8.185505 ACCGTACATCGTGCATTATTTTAAAAT 58.814 29.630 17.18 17.18 37.94 1.82
3537 6568 6.665474 AACCGTACATCGTGCATTATTTTA 57.335 33.333 0.00 0.00 37.94 1.52
3542 6573 6.665474 AAATAAACCGTACATCGTGCATTA 57.335 33.333 0.00 0.00 37.94 1.90
3548 6579 8.254178 TCAATACAAAATAAACCGTACATCGT 57.746 30.769 0.00 0.00 37.94 3.73


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

AutoCloner maintained by Alex Coulton.