Multiple sequence alignment - TraesCS4B01G308100

Loading Multiple Alignment...

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 TraesCS4B01G308100 chr4B 100.000 3670 0 0 1 3670 598460204 598456535 0.000000e+00 6778.0
1 TraesCS4B01G308100 chr4B 100.000 1865 0 0 3961 5825 598456244 598454380 0.000000e+00 3445.0
2 TraesCS4B01G308100 chr4B 85.932 789 80 16 1339 2114 598913592 598912822 0.000000e+00 813.0
3 TraesCS4B01G308100 chr4B 85.533 788 82 12 1339 2114 599170184 599169417 0.000000e+00 795.0
4 TraesCS4B01G308100 chr4B 91.500 400 29 4 948 1345 599170607 599170211 3.970000e-151 545.0
5 TraesCS4B01G308100 chr4B 90.704 398 33 3 948 1345 598914012 598913619 1.440000e-145 527.0
6 TraesCS4B01G308100 chr4B 92.308 299 23 0 1047 1345 598603090 598602792 5.400000e-115 425.0
7 TraesCS4B01G308100 chr4B 93.562 233 15 0 1882 2114 598602353 598602121 1.200000e-91 348.0
8 TraesCS4B01G308100 chr4B 74.860 895 126 53 4504 5323 598911540 598910670 1.220000e-81 315.0
9 TraesCS4B01G308100 chr4B 88.618 123 8 6 604 725 598603570 598603453 1.690000e-30 145.0
10 TraesCS4B01G308100 chr4B 88.618 123 8 6 604 725 598914228 598914111 1.690000e-30 145.0
11 TraesCS4B01G308100 chr4B 88.618 123 8 6 604 725 599170865 599170748 1.690000e-30 145.0
12 TraesCS4B01G308100 chr4B 84.459 148 17 5 1423 1564 14653486 14653339 2.190000e-29 141.0
13 TraesCS4B01G308100 chr4B 95.652 69 3 0 3174 3242 598456996 598456928 1.720000e-20 111.0
14 TraesCS4B01G308100 chr4B 95.652 69 3 0 3209 3277 598457031 598456963 1.720000e-20 111.0
15 TraesCS4B01G308100 chr4B 84.545 110 13 3 948 1057 598603341 598603236 7.980000e-19 106.0
16 TraesCS4B01G308100 chr4B 80.392 102 17 3 3 102 598915164 598915064 2.250000e-09 75.0
17 TraesCS4B01G308100 chr4A 94.619 1338 51 12 3961 5291 681610126 681611449 0.000000e+00 2052.0
18 TraesCS4B01G308100 chr4A 86.910 1864 128 40 4035 5824 681658030 681659851 0.000000e+00 1984.0
19 TraesCS4B01G308100 chr4A 94.274 1013 49 6 2406 3415 681608365 681609371 0.000000e+00 1541.0
20 TraesCS4B01G308100 chr4A 91.862 983 52 10 1339 2306 681653538 681654507 0.000000e+00 1347.0
21 TraesCS4B01G308100 chr4A 89.422 1021 74 10 1339 2341 681593406 681594410 0.000000e+00 1256.0
22 TraesCS4B01G308100 chr4A 94.071 506 27 2 5315 5819 681611445 681611948 0.000000e+00 765.0
23 TraesCS4B01G308100 chr4A 89.152 507 29 8 2527 3024 681654668 681655157 4.990000e-170 608.0
24 TraesCS4B01G308100 chr4A 94.819 386 20 0 948 1333 681592976 681593361 2.320000e-168 603.0
25 TraesCS4B01G308100 chr4A 90.843 415 32 4 931 1345 681653103 681653511 8.530000e-153 551.0
26 TraesCS4B01G308100 chr4A 96.183 262 9 1 3408 3668 681609789 681610050 1.500000e-115 427.0
27 TraesCS4B01G308100 chr4A 87.209 344 23 9 3332 3670 681656231 681656558 7.130000e-99 372.0
28 TraesCS4B01G308100 chr4A 95.135 185 7 2 2325 2508 681654496 681654679 2.050000e-74 291.0
29 TraesCS4B01G308100 chr4A 83.333 222 19 9 3024 3228 681656009 681656229 7.710000e-44 189.0
30 TraesCS4B01G308100 chr4A 92.857 70 5 0 2340 2409 681608017 681608086 1.030000e-17 102.0
31 TraesCS4B01G308100 chr4A 94.030 67 4 0 3176 3242 681609167 681609233 1.030000e-17 102.0
32 TraesCS4B01G308100 chr4A 87.838 74 7 1 601 674 681652883 681652954 1.040000e-12 86.1
33 TraesCS4B01G308100 chr4D 87.616 1728 114 33 4014 5668 474599922 474598222 0.000000e+00 1914.0
34 TraesCS4B01G308100 chr4D 93.095 840 28 8 765 1580 474603398 474602565 0.000000e+00 1203.0
35 TraesCS4B01G308100 chr4D 93.848 699 27 7 1621 2306 474602562 474601867 0.000000e+00 1038.0
36 TraesCS4B01G308100 chr4D 96.870 575 17 1 1 575 474604078 474603505 0.000000e+00 961.0
37 TraesCS4B01G308100 chr4D 85.714 791 77 16 1339 2114 474700958 474700189 0.000000e+00 802.0
38 TraesCS4B01G308100 chr4D 92.994 471 24 5 2645 3107 474601368 474600899 0.000000e+00 678.0
39 TraesCS4B01G308100 chr4D 92.677 396 24 4 951 1345 474701376 474700985 3.050000e-157 566.0
40 TraesCS4B01G308100 chr4D 91.282 390 25 5 3288 3670 474600802 474600415 1.860000e-144 523.0
41 TraesCS4B01G308100 chr4D 75.556 990 144 46 4404 5323 474699044 474698083 1.180000e-106 398.0
42 TraesCS4B01G308100 chr4D 94.022 184 9 2 2325 2508 474601878 474601697 1.600000e-70 278.0
43 TraesCS4B01G308100 chr4D 89.080 174 16 2 5654 5825 474592790 474592618 4.570000e-51 213.0
44 TraesCS4B01G308100 chr4D 96.800 125 4 0 601 725 474603520 474603396 5.910000e-50 209.0
45 TraesCS4B01G308100 chr4D 87.805 123 9 6 604 725 474701641 474701524 7.870000e-29 139.0
46 TraesCS4B01G308100 chr4D 98.361 61 1 0 3217 3277 474600805 474600865 2.220000e-19 108.0
47 TraesCS4B01G308100 chr3A 75.723 622 83 41 983 1569 11677531 11676943 3.490000e-62 250.0
48 TraesCS4B01G308100 chr3A 75.402 622 85 41 983 1569 11704977 11704389 7.540000e-59 239.0
49 TraesCS4B01G308100 chr3A 81.765 170 26 2 1630 1794 11676860 11676691 2.830000e-28 137.0
50 TraesCS4B01G308100 chr3A 81.765 170 26 2 1630 1794 11704307 11704138 2.830000e-28 137.0
51 TraesCS4B01G308100 chr5D 90.769 65 3 2 5755 5819 542633371 542633310 3.740000e-12 84.2
52 TraesCS4B01G308100 chr5D 90.566 53 2 2 3165 3217 495311484 495311533 3.770000e-07 67.6
53 TraesCS4B01G308100 chr7D 88.889 63 5 2 3244 3306 428723336 428723276 6.260000e-10 76.8
54 TraesCS4B01G308100 chr7D 95.652 46 2 0 3162 3207 195654119 195654074 2.250000e-09 75.0
55 TraesCS4B01G308100 chr7A 90.741 54 4 1 3166 3218 55160742 55160689 2.910000e-08 71.3
56 TraesCS4B01G308100 chr7A 88.333 60 5 2 3163 3220 680540609 680540668 2.910000e-08 71.3
57 TraesCS4B01G308100 chr7A 87.500 48 5 1 3209 3255 680540621 680540668 3.000000e-03 54.7
58 TraesCS4B01G308100 chr5B 88.525 61 4 3 5749 5808 588581087 588581145 2.910000e-08 71.3
59 TraesCS4B01G308100 chr1D 79.646 113 11 6 3165 3275 63636317 63636215 2.910000e-08 71.3
60 TraesCS4B01G308100 chr5A 87.500 64 3 4 3239 3301 219252576 219252517 1.050000e-07 69.4
61 TraesCS4B01G308100 chr7B 87.931 58 5 2 3244 3301 446152440 446152385 3.770000e-07 67.6
62 TraesCS4B01G308100 chr6D 86.885 61 5 2 3244 3301 9669760 9669820 1.350000e-06 65.8
63 TraesCS4B01G308100 chr6D 86.885 61 5 2 3244 3301 298384576 298384636 1.350000e-06 65.8
64 TraesCS4B01G308100 chr2A 100.000 35 0 0 3209 3243 723569495 723569461 1.350000e-06 65.8


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 TraesCS4B01G308100 chr4B 598454380 598460204 5824 True 2611.2500 6778 97.826000 1 5825 4 chr4B.!!$R2 5824
1 TraesCS4B01G308100 chr4B 599169417 599170865 1448 True 495.0000 795 88.550333 604 2114 3 chr4B.!!$R5 1510
2 TraesCS4B01G308100 chr4B 598910670 598915164 4494 True 375.0000 813 84.101200 3 5323 5 chr4B.!!$R4 5320
3 TraesCS4B01G308100 chr4B 598602121 598603570 1449 True 256.0000 425 89.758250 604 2114 4 chr4B.!!$R3 1510
4 TraesCS4B01G308100 chr4A 681592976 681594410 1434 False 929.5000 1256 92.120500 948 2341 2 chr4A.!!$F1 1393
5 TraesCS4B01G308100 chr4A 681608017 681611948 3931 False 831.5000 2052 94.339000 2340 5819 6 chr4A.!!$F2 3479
6 TraesCS4B01G308100 chr4A 681652883 681659851 6968 False 678.5125 1984 89.035250 601 5824 8 chr4A.!!$F3 5223
7 TraesCS4B01G308100 chr4D 474598222 474604078 5856 True 850.5000 1914 93.315875 1 5668 8 chr4D.!!$R2 5667
8 TraesCS4B01G308100 chr4D 474698083 474701641 3558 True 476.2500 802 85.438000 604 5323 4 chr4D.!!$R3 4719


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
498 1081 0.034186 CCAGCTGACATGGCCCTAAA 60.034 55.000 17.39 0.0 0.00 1.85 F
573 1156 0.037975 CCACCTGCATGCACCTTTTC 60.038 55.000 18.46 0.0 0.00 2.29 F
574 1157 0.037975 CACCTGCATGCACCTTTTCC 60.038 55.000 18.46 0.0 0.00 3.13 F
578 1161 0.112995 TGCATGCACCTTTTCCCTCT 59.887 50.000 18.46 0.0 0.00 3.69 F
2276 3196 0.530744 GTGGACGTATGCCTCTCACA 59.469 55.000 0.00 0.0 0.00 3.58 F
2371 3292 0.901114 TGCGCTAGGTAAGGGTGTCA 60.901 55.000 9.73 0.0 40.25 3.58 F
2395 3316 1.067283 ACAATGGCTGACTCAGTCTCG 60.067 52.381 11.90 0.0 36.97 4.04 F
4009 6920 0.106419 TTGCCGGAGTTTCTTTGGGT 60.106 50.000 5.05 0.0 0.00 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1870 2761 0.605319 CCGGCAGCTTGTTTCCAGTA 60.605 55.000 0.00 0.0 0.00 2.74 R
2114 3018 2.159338 ACGATTCCAATTGAGCATGTGC 60.159 45.455 7.12 0.0 42.49 4.57 R
2371 3292 2.234908 GACTGAGTCAGCCATTGTAGGT 59.765 50.000 20.31 0.0 34.37 3.08 R
2395 3316 2.968675 ACAACAACTATCCTACGTGGC 58.031 47.619 0.00 0.0 35.26 5.01 R
3994 6902 0.179001 ACCCACCCAAAGAAACTCCG 60.179 55.000 0.00 0.0 0.00 4.63 R
4009 6920 2.265367 TGCTAAGAACCATCTGACCCA 58.735 47.619 0.00 0.0 35.59 4.51 R
4346 8259 5.125900 TGAAGAATGTGCCATGTCCTAATTG 59.874 40.000 0.00 0.0 0.00 2.32 R
5768 10703 0.179142 GGGTTTCTAGTCGCTCGTCC 60.179 60.000 0.00 0.0 0.00 4.79 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
36 37 5.014123 AGACTGGAATTAATCAAGGTCACCA 59.986 40.000 0.00 0.00 32.84 4.17
71 72 4.886579 ACAAGATGTTTCCTTTCCAATGC 58.113 39.130 0.00 0.00 0.00 3.56
200 201 9.507329 ACAGAGTTTGTGTAAATCTCATTGTAT 57.493 29.630 0.00 0.00 38.99 2.29
252 253 5.655488 AGACAATAAATCTCACTCTCGTGG 58.345 41.667 0.00 0.00 41.53 4.94
406 981 5.358725 ACAACACTTATTTTGGAACGAAGGT 59.641 36.000 0.00 0.00 0.00 3.50
467 1050 4.263462 ACATTTTGAGACAGAGGGCATGTA 60.263 41.667 0.00 0.00 0.00 2.29
498 1081 0.034186 CCAGCTGACATGGCCCTAAA 60.034 55.000 17.39 0.00 0.00 1.85
503 1086 2.738743 CTGACATGGCCCTAAATTGGT 58.261 47.619 0.00 0.00 0.00 3.67
509 1092 5.466819 ACATGGCCCTAAATTGGTCAATAT 58.533 37.500 0.00 0.00 41.63 1.28
558 1141 0.611200 GGTATTTTTGCCCCACCACC 59.389 55.000 0.00 0.00 0.00 4.61
559 1142 1.639722 GTATTTTTGCCCCACCACCT 58.360 50.000 0.00 0.00 0.00 4.00
560 1143 1.275010 GTATTTTTGCCCCACCACCTG 59.725 52.381 0.00 0.00 0.00 4.00
561 1144 1.767654 ATTTTTGCCCCACCACCTGC 61.768 55.000 0.00 0.00 0.00 4.85
562 1145 3.686098 TTTTGCCCCACCACCTGCA 62.686 57.895 0.00 0.00 0.00 4.41
563 1146 2.961559 TTTTGCCCCACCACCTGCAT 62.962 55.000 0.00 0.00 33.08 3.96
564 1147 4.682334 TGCCCCACCACCTGCATG 62.682 66.667 0.00 0.00 0.00 4.06
566 1149 4.682334 CCCCACCACCTGCATGCA 62.682 66.667 21.29 21.29 0.00 3.96
567 1150 3.376078 CCCACCACCTGCATGCAC 61.376 66.667 18.46 0.00 0.00 4.57
568 1151 3.376078 CCACCACCTGCATGCACC 61.376 66.667 18.46 0.00 0.00 5.01
569 1152 2.282674 CACCACCTGCATGCACCT 60.283 61.111 18.46 0.65 0.00 4.00
570 1153 1.904865 CACCACCTGCATGCACCTT 60.905 57.895 18.46 0.00 0.00 3.50
571 1154 1.152483 ACCACCTGCATGCACCTTT 60.152 52.632 18.46 0.00 0.00 3.11
572 1155 0.760189 ACCACCTGCATGCACCTTTT 60.760 50.000 18.46 0.00 0.00 2.27
573 1156 0.037975 CCACCTGCATGCACCTTTTC 60.038 55.000 18.46 0.00 0.00 2.29
574 1157 0.037975 CACCTGCATGCACCTTTTCC 60.038 55.000 18.46 0.00 0.00 3.13
575 1158 1.187567 ACCTGCATGCACCTTTTCCC 61.188 55.000 18.46 0.00 0.00 3.97
576 1159 0.901580 CCTGCATGCACCTTTTCCCT 60.902 55.000 18.46 0.00 0.00 4.20
577 1160 0.529378 CTGCATGCACCTTTTCCCTC 59.471 55.000 18.46 0.00 0.00 4.30
578 1161 0.112995 TGCATGCACCTTTTCCCTCT 59.887 50.000 18.46 0.00 0.00 3.69
579 1162 1.260544 GCATGCACCTTTTCCCTCTT 58.739 50.000 14.21 0.00 0.00 2.85
580 1163 1.620323 GCATGCACCTTTTCCCTCTTT 59.380 47.619 14.21 0.00 0.00 2.52
581 1164 2.037641 GCATGCACCTTTTCCCTCTTTT 59.962 45.455 14.21 0.00 0.00 2.27
582 1165 3.494924 GCATGCACCTTTTCCCTCTTTTT 60.495 43.478 14.21 0.00 0.00 1.94
722 1306 4.336713 GCCCATTTGTTTTAGGCTAGAGAG 59.663 45.833 0.00 0.00 40.57 3.20
723 1307 4.884164 CCCATTTGTTTTAGGCTAGAGAGG 59.116 45.833 0.00 0.00 0.00 3.69
724 1308 4.884164 CCATTTGTTTTAGGCTAGAGAGGG 59.116 45.833 0.00 0.00 0.00 4.30
725 1309 4.569719 TTTGTTTTAGGCTAGAGAGGGG 57.430 45.455 0.00 0.00 0.00 4.79
726 1310 1.838077 TGTTTTAGGCTAGAGAGGGGC 59.162 52.381 0.00 0.00 0.00 5.80
727 1311 1.141254 GTTTTAGGCTAGAGAGGGGCC 59.859 57.143 0.00 0.00 45.57 5.80
730 1314 3.994000 GGCTAGAGAGGGGCCATT 58.006 61.111 4.39 0.00 44.69 3.16
734 1318 2.036929 GCTAGAGAGGGGCCATTGAGA 61.037 57.143 4.39 0.00 0.00 3.27
752 1336 1.912043 AGAGGCCTAGTGTGAGCAAAT 59.088 47.619 4.42 0.00 0.00 2.32
787 1371 4.501571 GGGAGCTTTTTCTTTTGGAGGAAC 60.502 45.833 0.00 0.00 0.00 3.62
985 1574 3.669122 GTCACGTGTGCTTAACTACTCTG 59.331 47.826 16.51 0.00 0.00 3.35
1049 1797 1.371389 GTACGGATCGGTCGATGCC 60.371 63.158 16.79 12.99 39.36 4.40
1172 1920 1.251527 GGCTTCTCGTGTCTCCAGGA 61.252 60.000 0.00 0.00 34.51 3.86
1197 1945 1.809869 CGATTCCTCGGAGCTGACA 59.190 57.895 0.00 0.00 41.27 3.58
1290 2038 4.395583 GCTGTGCACGAAGGCAGC 62.396 66.667 13.13 10.67 45.96 5.25
1300 2048 4.335647 AAGGCAGCTGGTCCACGG 62.336 66.667 17.12 0.00 0.00 4.94
1599 2485 2.472695 TGACTCAAATCTCCCAACCG 57.527 50.000 0.00 0.00 0.00 4.44
1602 2488 2.742589 GACTCAAATCTCCCAACCGTTC 59.257 50.000 0.00 0.00 0.00 3.95
1609 2495 1.829222 TCTCCCAACCGTTCCTACATC 59.171 52.381 0.00 0.00 0.00 3.06
1696 2587 2.537401 GACAAGGGGACGATTCTTACG 58.463 52.381 0.00 0.00 0.00 3.18
1699 2590 1.400737 AGGGGACGATTCTTACGGAG 58.599 55.000 0.00 0.00 34.93 4.63
1744 2635 2.557676 CCAAGAGAGGGTGAGGTCACTA 60.558 54.545 9.90 0.00 45.73 2.74
2231 3145 6.094048 GTGTGCCATTGTTAGAACATGTCTAT 59.906 38.462 0.00 0.00 38.67 1.98
2269 3189 3.569250 AAAATGTTGTGGACGTATGCC 57.431 42.857 0.00 0.00 0.00 4.40
2276 3196 0.530744 GTGGACGTATGCCTCTCACA 59.469 55.000 0.00 0.00 0.00 3.58
2277 3197 1.067142 GTGGACGTATGCCTCTCACAA 60.067 52.381 0.00 0.00 0.00 3.33
2371 3292 0.901114 TGCGCTAGGTAAGGGTGTCA 60.901 55.000 9.73 0.00 40.25 3.58
2395 3316 1.067283 ACAATGGCTGACTCAGTCTCG 60.067 52.381 11.90 0.00 36.97 4.04
2453 3656 2.204151 CTTGAGGGGAGTGGGGGT 60.204 66.667 0.00 0.00 0.00 4.95
2499 3703 9.436957 TGAGATTCCACTAAAATTTCTCTGTAC 57.563 33.333 0.00 0.00 0.00 2.90
2500 3704 9.660180 GAGATTCCACTAAAATTTCTCTGTACT 57.340 33.333 0.00 0.00 0.00 2.73
2521 3725 9.445786 TGTACTTTTAGAAGAAGAAAAATTGCG 57.554 29.630 0.00 0.00 36.69 4.85
2522 3726 7.930513 ACTTTTAGAAGAAGAAAAATTGCGG 57.069 32.000 0.00 0.00 36.69 5.69
2523 3727 7.712797 ACTTTTAGAAGAAGAAAAATTGCGGA 58.287 30.769 0.00 0.00 36.69 5.54
2524 3728 8.360390 ACTTTTAGAAGAAGAAAAATTGCGGAT 58.640 29.630 0.00 0.00 36.69 4.18
2525 3729 8.519492 TTTTAGAAGAAGAAAAATTGCGGATG 57.481 30.769 0.00 0.00 0.00 3.51
2821 4300 5.128499 TGCCAAATTCGTATGGAATCCATTT 59.872 36.000 21.06 5.18 42.23 2.32
2832 4311 8.786898 CGTATGGAATCCATTTCTATGTCATTT 58.213 33.333 21.06 0.00 42.23 2.32
2918 4397 3.305629 GCACTTGCACTCTTTCTCTATCG 59.694 47.826 0.00 0.00 41.59 2.92
2935 4418 1.669604 TCGACCCTCTCTCTCAATCG 58.330 55.000 0.00 0.00 0.00 3.34
2953 4436 6.607689 TCAATCGTCCAAAATACATGTGTTC 58.392 36.000 9.11 0.00 0.00 3.18
2980 4464 1.179152 TGCACCATCAAAGGCATCTG 58.821 50.000 0.00 0.00 0.00 2.90
2999 4483 7.221452 GGCATCTGTAATGAAATTCATGTGTTC 59.779 37.037 9.47 0.31 37.15 3.18
3294 5653 5.955488 TCACTAGTGATCAGTTTACAGAGC 58.045 41.667 21.74 0.00 34.14 4.09
3296 5655 3.238108 AGTGATCAGTTTACAGAGCGG 57.762 47.619 0.00 0.00 0.00 5.52
3301 5660 2.522185 TCAGTTTACAGAGCGGGTACT 58.478 47.619 0.00 0.00 0.00 2.73
3432 6217 4.729227 AAACTAGTTTTTGTGTGTGGGG 57.271 40.909 15.22 0.00 0.00 4.96
3554 6341 3.904339 AGTTGTGTCCAGTGTCTAGGAAT 59.096 43.478 0.00 0.00 35.29 3.01
3994 6902 3.118261 TCTCTCTCTCTCTCTCTCTTGCC 60.118 52.174 0.00 0.00 0.00 4.52
4009 6920 0.106419 TTGCCGGAGTTTCTTTGGGT 60.106 50.000 5.05 0.00 0.00 4.51
4012 7012 0.893727 CCGGAGTTTCTTTGGGTGGG 60.894 60.000 0.00 0.00 0.00 4.61
4139 8043 2.820178 TGCTCCATGACCACTCTAGAA 58.180 47.619 0.00 0.00 0.00 2.10
4256 8166 4.984785 GCAACTCAAAATCTCCTTGAAACC 59.015 41.667 0.00 0.00 32.57 3.27
4346 8259 5.429130 AGTACTTTCTCCGATCCAAAATCC 58.571 41.667 0.00 0.00 0.00 3.01
4577 9388 1.064240 TCGGTCTAGAGGCATGTGGTA 60.064 52.381 0.00 0.00 0.00 3.25
4578 9389 1.338337 CGGTCTAGAGGCATGTGGTAG 59.662 57.143 0.00 0.00 0.00 3.18
4579 9390 2.667470 GGTCTAGAGGCATGTGGTAGA 58.333 52.381 0.00 0.00 0.00 2.59
4580 9391 3.235200 GGTCTAGAGGCATGTGGTAGAT 58.765 50.000 0.00 0.00 0.00 1.98
4691 9517 5.648092 GGAACTAAACATGACCAGCTACATT 59.352 40.000 0.00 0.00 0.00 2.71
4701 9528 3.347216 ACCAGCTACATTTGTTAGGCTG 58.653 45.455 17.81 17.81 40.72 4.85
4771 9609 3.921021 CGTCAACACAGAGGAGATTGTAC 59.079 47.826 0.00 0.00 0.00 2.90
4931 9811 0.958876 ATGCGGAGGTCGGGTTTTTC 60.959 55.000 0.00 0.00 39.69 2.29
5144 10057 4.518249 GTCCACTTGGCTAAGCTCTAATT 58.482 43.478 10.10 0.00 37.43 1.40
5168 10085 0.257328 TTGGATCATGGCGCCCTTAA 59.743 50.000 26.77 4.98 0.00 1.85
5202 10119 8.062231 CGATTACATACAAATCGTAAAGCTCT 57.938 34.615 9.43 0.00 46.59 4.09
5262 10180 1.067060 TCTCACGATAATGGGCGACAG 59.933 52.381 0.00 0.00 0.00 3.51
5295 10213 2.417651 CGAAGGGCATGGTAGTCGTTTA 60.418 50.000 0.00 0.00 0.00 2.01
5300 10223 6.869206 AGGGCATGGTAGTCGTTTATATAT 57.131 37.500 0.00 0.00 0.00 0.86
5303 10226 7.069578 AGGGCATGGTAGTCGTTTATATATAGG 59.930 40.741 0.00 0.00 0.00 2.57
5305 10228 7.919621 GGCATGGTAGTCGTTTATATATAGGTC 59.080 40.741 0.00 0.00 0.00 3.85
5307 10230 8.886719 CATGGTAGTCGTTTATATATAGGTCGA 58.113 37.037 9.99 9.99 0.00 4.20
5328 10251 4.442403 CGATGTCCATAGTCATCTGAAACG 59.558 45.833 0.00 0.00 36.68 3.60
5355 10278 3.009143 GTCACCCCAAATGTTAGGAGAGT 59.991 47.826 0.00 0.00 0.00 3.24
5361 10284 5.414765 CCCCAAATGTTAGGAGAGTAACAAC 59.585 44.000 0.87 0.00 44.15 3.32
5393 10316 2.835764 ACTTTGGATCAGGCAAATGCAT 59.164 40.909 7.80 0.00 44.36 3.96
5618 10552 7.749666 AGATCGGTACACTACCCTAAATACTA 58.250 38.462 0.00 0.00 46.27 1.82
5668 10602 6.116806 TGTTTGTTTGCGGGTATATATGACT 58.883 36.000 0.00 0.00 0.00 3.41
5714 10649 5.598416 ATCAACACACGATCCATTAGAGA 57.402 39.130 0.00 0.00 0.00 3.10
5720 10655 3.191581 ACACGATCCATTAGAGATAGCCG 59.808 47.826 0.00 0.00 0.00 5.52
5766 10701 5.786311 TCTTTCGAATCGTTTTTCCCTCTA 58.214 37.500 1.52 0.00 0.00 2.43
5768 10703 4.119442 TCGAATCGTTTTTCCCTCTAGG 57.881 45.455 1.52 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 7.004086 GGATATGGTGACCTTGATTAATTCCA 58.996 38.462 2.11 0.00 0.00 3.53
28 29 3.910627 GTCTATTGGGGATATGGTGACCT 59.089 47.826 2.11 0.00 0.00 3.85
36 37 7.074237 AGGAAACATCTTGTCTATTGGGGATAT 59.926 37.037 0.00 0.00 0.00 1.63
71 72 8.925161 AAGATAAGATTGAGAAGAAGAAGACG 57.075 34.615 0.00 0.00 0.00 4.18
433 1008 9.092876 CTCTGTCTCAAAATGTAAGTATCTTCC 57.907 37.037 0.00 0.00 0.00 3.46
498 1081 9.113838 GTATGTTTGACTCTCATATTGACCAAT 57.886 33.333 0.64 0.64 34.93 3.16
503 1086 6.337356 TGCGTATGTTTGACTCTCATATTGA 58.663 36.000 0.00 0.00 0.00 2.57
509 1092 4.186856 TGATGCGTATGTTTGACTCTCA 57.813 40.909 0.00 0.00 0.00 3.27
558 1141 0.529378 GAGGGAAAAGGTGCATGCAG 59.471 55.000 23.41 0.00 0.00 4.41
559 1142 0.112995 AGAGGGAAAAGGTGCATGCA 59.887 50.000 18.46 18.46 0.00 3.96
560 1143 1.260544 AAGAGGGAAAAGGTGCATGC 58.739 50.000 11.82 11.82 0.00 4.06
561 1144 4.341366 AAAAAGAGGGAAAAGGTGCATG 57.659 40.909 0.00 0.00 0.00 4.06
599 1182 0.664166 CACGGAAAAGGTGCATGCAC 60.664 55.000 37.29 37.29 45.49 4.57
726 1310 1.833630 TCACACTAGGCCTCTCAATGG 59.166 52.381 9.68 0.00 0.00 3.16
727 1311 2.741228 GCTCACACTAGGCCTCTCAATG 60.741 54.545 9.68 4.13 0.00 2.82
728 1312 1.484240 GCTCACACTAGGCCTCTCAAT 59.516 52.381 9.68 0.00 0.00 2.57
729 1313 0.898320 GCTCACACTAGGCCTCTCAA 59.102 55.000 9.68 0.00 0.00 3.02
730 1314 0.251787 TGCTCACACTAGGCCTCTCA 60.252 55.000 9.68 0.00 0.00 3.27
734 1318 4.510167 AATATTTGCTCACACTAGGCCT 57.490 40.909 11.78 11.78 0.00 5.19
742 1326 4.629634 CCGTCACTGTAATATTTGCTCACA 59.370 41.667 0.00 0.00 0.00 3.58
752 1336 4.546829 AAAAGCTCCCGTCACTGTAATA 57.453 40.909 0.00 0.00 0.00 0.98
985 1574 3.433274 TGCAACATCGAGACAGAAATGAC 59.567 43.478 0.00 0.00 0.00 3.06
1159 1907 1.679305 GGAGCTCCTGGAGACACGA 60.679 63.158 27.53 0.00 35.60 4.35
1464 2260 4.884257 ACGTGGTCTTGCGCGTGT 62.884 61.111 8.43 0.00 36.16 4.49
1580 2466 1.697432 ACGGTTGGGAGATTTGAGTCA 59.303 47.619 0.00 0.00 0.00 3.41
1581 2467 2.474410 ACGGTTGGGAGATTTGAGTC 57.526 50.000 0.00 0.00 0.00 3.36
1582 2468 2.552373 GGAACGGTTGGGAGATTTGAGT 60.552 50.000 0.00 0.00 0.00 3.41
1583 2469 2.084546 GGAACGGTTGGGAGATTTGAG 58.915 52.381 0.00 0.00 0.00 3.02
1584 2470 1.702957 AGGAACGGTTGGGAGATTTGA 59.297 47.619 0.00 0.00 0.00 2.69
1585 2471 2.200373 AGGAACGGTTGGGAGATTTG 57.800 50.000 0.00 0.00 0.00 2.32
1586 2472 2.640826 TGTAGGAACGGTTGGGAGATTT 59.359 45.455 0.00 0.00 0.00 2.17
1587 2473 2.262637 TGTAGGAACGGTTGGGAGATT 58.737 47.619 0.00 0.00 0.00 2.40
1588 2474 1.946984 TGTAGGAACGGTTGGGAGAT 58.053 50.000 0.00 0.00 0.00 2.75
1589 2475 1.829222 GATGTAGGAACGGTTGGGAGA 59.171 52.381 0.00 0.00 0.00 3.71
1602 2488 9.040259 TCCTGAAGGAATATTATGAGATGTAGG 57.960 37.037 0.00 0.00 42.18 3.18
1653 2542 6.306837 GTCCATCTGATCGATCGAAACTAATC 59.693 42.308 23.50 14.21 0.00 1.75
1658 2547 3.706698 TGTCCATCTGATCGATCGAAAC 58.293 45.455 23.50 18.68 0.00 2.78
1870 2761 0.605319 CCGGCAGCTTGTTTCCAGTA 60.605 55.000 0.00 0.00 0.00 2.74
1880 2771 2.790791 CCTCGATCTCCGGCAGCTT 61.791 63.158 0.00 0.00 39.14 3.74
2114 3018 2.159338 ACGATTCCAATTGAGCATGTGC 60.159 45.455 7.12 0.00 42.49 4.57
2246 3166 4.854839 GGCATACGTCCACAACATTTTTAC 59.145 41.667 0.00 0.00 0.00 2.01
2247 3167 4.762765 AGGCATACGTCCACAACATTTTTA 59.237 37.500 0.00 0.00 0.00 1.52
2248 3168 3.572255 AGGCATACGTCCACAACATTTTT 59.428 39.130 0.00 0.00 0.00 1.94
2310 3230 6.006759 AGAGAAGAAAATTCTCCGCAAAAG 57.993 37.500 12.72 0.00 44.46 2.27
2316 3237 9.405587 GTATATGAGAGAGAAGAAAATTCTCCG 57.594 37.037 12.72 0.00 44.46 4.63
2371 3292 2.234908 GACTGAGTCAGCCATTGTAGGT 59.765 50.000 20.31 0.00 34.37 3.08
2395 3316 2.968675 ACAACAACTATCCTACGTGGC 58.031 47.619 0.00 0.00 35.26 5.01
2453 3656 6.001449 CTCATATTTTGAGTGGGGTCCTAA 57.999 41.667 0.00 0.00 45.79 2.69
2496 3700 8.902735 CCGCAATTTTTCTTCTTCTAAAAGTAC 58.097 33.333 0.00 0.00 33.95 2.73
2497 3701 8.842280 TCCGCAATTTTTCTTCTTCTAAAAGTA 58.158 29.630 0.00 0.00 33.95 2.24
2498 3702 7.712797 TCCGCAATTTTTCTTCTTCTAAAAGT 58.287 30.769 0.00 0.00 33.95 2.66
2499 3703 8.642020 CATCCGCAATTTTTCTTCTTCTAAAAG 58.358 33.333 0.00 0.00 0.00 2.27
2500 3704 7.598493 CCATCCGCAATTTTTCTTCTTCTAAAA 59.402 33.333 0.00 0.00 0.00 1.52
2501 3705 7.090173 CCATCCGCAATTTTTCTTCTTCTAAA 58.910 34.615 0.00 0.00 0.00 1.85
2502 3706 6.208599 ACCATCCGCAATTTTTCTTCTTCTAA 59.791 34.615 0.00 0.00 0.00 2.10
2503 3707 5.710099 ACCATCCGCAATTTTTCTTCTTCTA 59.290 36.000 0.00 0.00 0.00 2.10
2504 3708 4.524328 ACCATCCGCAATTTTTCTTCTTCT 59.476 37.500 0.00 0.00 0.00 2.85
2505 3709 4.809673 ACCATCCGCAATTTTTCTTCTTC 58.190 39.130 0.00 0.00 0.00 2.87
2506 3710 4.871933 ACCATCCGCAATTTTTCTTCTT 57.128 36.364 0.00 0.00 0.00 2.52
2507 3711 5.010282 AGTACCATCCGCAATTTTTCTTCT 58.990 37.500 0.00 0.00 0.00 2.85
2508 3712 5.310720 AGTACCATCCGCAATTTTTCTTC 57.689 39.130 0.00 0.00 0.00 2.87
2509 3713 5.722021 AAGTACCATCCGCAATTTTTCTT 57.278 34.783 0.00 0.00 0.00 2.52
2510 3714 5.722021 AAAGTACCATCCGCAATTTTTCT 57.278 34.783 0.00 0.00 0.00 2.52
2511 3715 7.309920 TCTAAAAGTACCATCCGCAATTTTTC 58.690 34.615 0.00 0.00 0.00 2.29
2512 3716 7.222000 TCTAAAAGTACCATCCGCAATTTTT 57.778 32.000 0.00 0.00 0.00 1.94
2513 3717 6.827586 TCTAAAAGTACCATCCGCAATTTT 57.172 33.333 0.00 0.00 0.00 1.82
2514 3718 6.827586 TTCTAAAAGTACCATCCGCAATTT 57.172 33.333 0.00 0.00 0.00 1.82
2515 3719 7.554835 TGTATTCTAAAAGTACCATCCGCAATT 59.445 33.333 0.00 0.00 0.00 2.32
2516 3720 7.051623 TGTATTCTAAAAGTACCATCCGCAAT 58.948 34.615 0.00 0.00 0.00 3.56
2517 3721 6.408035 TGTATTCTAAAAGTACCATCCGCAA 58.592 36.000 0.00 0.00 0.00 4.85
2518 3722 5.979993 TGTATTCTAAAAGTACCATCCGCA 58.020 37.500 0.00 0.00 0.00 5.69
2519 3723 6.913873 TTGTATTCTAAAAGTACCATCCGC 57.086 37.500 0.00 0.00 0.00 5.54
2520 3724 7.855904 GCATTTGTATTCTAAAAGTACCATCCG 59.144 37.037 0.00 0.00 0.00 4.18
2521 3725 8.903820 AGCATTTGTATTCTAAAAGTACCATCC 58.096 33.333 0.00 0.00 0.00 3.51
2915 4394 2.226330 CGATTGAGAGAGAGGGTCGAT 58.774 52.381 0.00 0.00 0.00 3.59
2918 4397 1.679153 GGACGATTGAGAGAGAGGGTC 59.321 57.143 0.00 0.00 0.00 4.46
2935 4418 5.940470 AGGAGAGAACACATGTATTTTGGAC 59.060 40.000 0.00 0.00 0.00 4.02
2953 4436 3.474600 CCTTTGATGGTGCATAGGAGAG 58.525 50.000 0.00 0.00 38.73 3.20
2999 4483 8.504815 CATGCATTGAGAATTCCTACAGATTAG 58.495 37.037 0.00 0.00 0.00 1.73
3001 4485 6.832384 ACATGCATTGAGAATTCCTACAGATT 59.168 34.615 0.00 0.00 0.00 2.40
3002 4486 6.363065 ACATGCATTGAGAATTCCTACAGAT 58.637 36.000 0.00 0.00 0.00 2.90
3003 4487 5.748402 ACATGCATTGAGAATTCCTACAGA 58.252 37.500 0.00 0.00 0.00 3.41
3279 5638 2.674796 ACCCGCTCTGTAAACTGATC 57.325 50.000 0.00 0.00 0.00 2.92
3554 6341 9.524106 CAATCAACATAGTGTAATACTTCCGTA 57.476 33.333 0.00 0.00 40.89 4.02
3627 6415 8.621532 TGCACTCTACAAGAAACTATTTGATT 57.378 30.769 0.00 0.00 0.00 2.57
3994 6902 0.179001 ACCCACCCAAAGAAACTCCG 60.179 55.000 0.00 0.00 0.00 4.63
4009 6920 2.265367 TGCTAAGAACCATCTGACCCA 58.735 47.619 0.00 0.00 35.59 4.51
4012 7012 5.181748 AGTCATTGCTAAGAACCATCTGAC 58.818 41.667 0.00 0.00 35.59 3.51
4104 8007 7.067494 GGTCATGGAGCATAGTGAAAATAAAGT 59.933 37.037 0.00 0.00 0.00 2.66
4187 8092 9.884636 TTACTATCTTATACTTTGCATGTGTGT 57.115 29.630 0.00 0.00 0.00 3.72
4346 8259 5.125900 TGAAGAATGTGCCATGTCCTAATTG 59.874 40.000 0.00 0.00 0.00 2.32
4577 9388 8.476064 TCTGAAGAGATTGATGCTTACTATCT 57.524 34.615 0.00 0.00 33.97 1.98
4578 9389 7.329226 GCTCTGAAGAGATTGATGCTTACTATC 59.671 40.741 11.56 0.00 44.74 2.08
4579 9390 7.153985 GCTCTGAAGAGATTGATGCTTACTAT 58.846 38.462 11.56 0.00 44.74 2.12
4580 9391 6.097412 TGCTCTGAAGAGATTGATGCTTACTA 59.903 38.462 11.56 0.00 44.74 1.82
4691 9517 5.799827 AATTTAAAGCCACAGCCTAACAA 57.200 34.783 0.00 0.00 41.25 2.83
4701 9528 7.648908 ACGGTAAAGTTGTAAATTTAAAGCCAC 59.351 33.333 0.00 0.00 0.00 5.01
4771 9609 2.057316 CAGTGCAGAGTTGAGTCTTCG 58.943 52.381 0.00 0.00 0.00 3.79
4908 9787 2.511600 CCCGACCTCCGCATCAAC 60.512 66.667 0.00 0.00 36.84 3.18
5144 10057 2.308570 AGGGCGCCATGATCCAATAATA 59.691 45.455 30.85 0.00 0.00 0.98
5168 10085 6.690957 CGATTTGTATGTAATCGCATGGTTTT 59.309 34.615 5.23 0.00 45.10 2.43
5202 10119 4.423913 AGAGATCTTCTATGCATGGGCTA 58.576 43.478 10.16 0.00 36.05 3.93
5273 10191 1.883084 CGACTACCATGCCCTTCGC 60.883 63.158 0.00 0.00 38.31 4.70
5295 10213 9.290988 GATGACTATGGACATCGACCTATATAT 57.709 37.037 5.85 0.00 35.67 0.86
5300 10223 4.762251 CAGATGACTATGGACATCGACCTA 59.238 45.833 13.91 0.00 44.79 3.08
5303 10226 4.837896 TCAGATGACTATGGACATCGAC 57.162 45.455 13.91 0.00 44.79 4.20
5305 10228 4.442403 CGTTTCAGATGACTATGGACATCG 59.558 45.833 13.91 10.07 44.79 3.84
5307 10230 5.344743 ACGTTTCAGATGACTATGGACAT 57.655 39.130 0.00 0.00 0.00 3.06
5361 10284 6.873605 TGCCTGATCCAAAGTGATATATTACG 59.126 38.462 2.27 0.00 0.00 3.18
5431 10355 9.364989 GTTTGCATAGAAAATAATGGCAAAGTA 57.635 29.630 8.89 0.00 33.72 2.24
5643 10577 6.770785 AGTCATATATACCCGCAAACAAACAT 59.229 34.615 0.00 0.00 0.00 2.71
5668 10602 5.677319 TGTGGGTATTTTTCCAACAACAA 57.323 34.783 0.00 0.00 36.13 2.83
5714 10649 3.698289 TCTAATCGAGATTCCCGGCTAT 58.302 45.455 0.00 0.00 32.50 2.97
5720 10655 4.345547 AGGGTCTTTCTAATCGAGATTCCC 59.654 45.833 1.11 5.22 32.88 3.97
5766 10701 0.810016 GTTTCTAGTCGCTCGTCCCT 59.190 55.000 0.00 0.00 0.00 4.20
5768 10703 0.179142 GGGTTTCTAGTCGCTCGTCC 60.179 60.000 0.00 0.00 0.00 4.79



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

AutoCloner maintained by Alex Coulton.