Multiple sequence alignment - TraesCS6B01G091000

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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 TraesCS6B01G091000 chr6B 100.000 5207 0 0 1 5207 66787624 66782418 0.000000e+00 9616.0
1 TraesCS6B01G091000 chr6B 94.214 5168 213 27 57 5207 66756951 66751853 0.000000e+00 7808.0
2 TraesCS6B01G091000 chr6B 87.010 2194 217 48 1203 3365 66862627 66860471 0.000000e+00 2410.0
3 TraesCS6B01G091000 chr6B 86.764 2191 227 48 1208 3365 66945094 66942934 0.000000e+00 2381.0
4 TraesCS6B01G091000 chr6B 86.202 2196 229 44 1203 3365 66920498 66918344 0.000000e+00 2309.0
5 TraesCS6B01G091000 chr6B 92.211 796 52 9 3385 4177 66860500 66859712 0.000000e+00 1118.0
6 TraesCS6B01G091000 chr6B 92.075 795 56 6 3385 4177 66942963 66942174 0.000000e+00 1112.0
7 TraesCS6B01G091000 chr6B 91.834 796 56 8 3385 4177 66918373 66917584 0.000000e+00 1101.0
8 TraesCS6B01G091000 chr6B 83.802 1031 86 25 22 996 66863762 66862757 0.000000e+00 904.0
9 TraesCS6B01G091000 chr6B 83.333 1038 88 26 22 996 66921643 66920628 0.000000e+00 880.0
10 TraesCS6B01G091000 chr6B 89.510 286 22 5 4 286 66761567 66761287 6.410000e-94 355.0
11 TraesCS6B01G091000 chr6B 89.862 217 14 4 7 221 66905796 66905586 6.640000e-69 272.0
12 TraesCS6B01G091000 chr6B 89.401 217 15 4 7 221 66928384 66928174 3.090000e-67 267.0
13 TraesCS6B01G091000 chr6B 85.263 190 15 5 125 306 66867487 66867303 3.200000e-42 183.0
14 TraesCS6B01G091000 chr6B 94.167 120 5 2 4 121 66792173 66792054 1.150000e-41 182.0
15 TraesCS6B01G091000 chr6B 97.059 34 1 0 1047 1080 625364909 625364942 2.030000e-04 58.4
16 TraesCS6B01G091000 chr6A 88.058 2194 214 31 1203 3365 35990576 35988400 0.000000e+00 2556.0
17 TraesCS6B01G091000 chr6A 88.053 2193 216 29 1203 3365 36055969 36053793 0.000000e+00 2556.0
18 TraesCS6B01G091000 chr6A 91.862 811 58 7 3369 4177 36053836 36053032 0.000000e+00 1125.0
19 TraesCS6B01G091000 chr6A 91.369 811 61 8 3369 4177 35988443 35987640 0.000000e+00 1101.0
20 TraesCS6B01G091000 chr6A 82.540 945 83 39 60 986 36056985 36056105 0.000000e+00 756.0
21 TraesCS6B01G091000 chr6A 82.729 828 76 32 165 986 35991478 35990712 0.000000e+00 675.0
22 TraesCS6B01G091000 chrUn 87.836 2195 217 30 1203 3365 100490259 100492435 0.000000e+00 2529.0
23 TraesCS6B01G091000 chrUn 86.600 1791 207 24 1203 2973 100637665 100639442 0.000000e+00 1947.0
24 TraesCS6B01G091000 chrUn 87.087 1603 147 27 1815 3365 100620877 100622471 0.000000e+00 1759.0
25 TraesCS6B01G091000 chrUn 91.864 1057 79 7 3369 4422 100492390 100493442 0.000000e+00 1469.0
26 TraesCS6B01G091000 chrUn 92.232 811 55 7 3369 4177 100622428 100623232 0.000000e+00 1142.0
27 TraesCS6B01G091000 chrUn 93.203 765 49 3 4445 5207 100493435 100494198 0.000000e+00 1122.0
28 TraesCS6B01G091000 chrUn 92.588 769 47 9 3369 4134 344892063 344892824 0.000000e+00 1096.0
29 TraesCS6B01G091000 chrUn 86.550 855 85 14 2533 3365 344891260 344892106 0.000000e+00 915.0
30 TraesCS6B01G091000 chrUn 83.069 1010 86 40 1 986 323635564 323636512 0.000000e+00 839.0
31 TraesCS6B01G091000 chrUn 83.069 1010 86 40 1 986 323667421 323668369 0.000000e+00 839.0
32 TraesCS6B01G091000 chrUn 83.069 1010 86 40 1 986 329023632 329024580 0.000000e+00 839.0
33 TraesCS6B01G091000 chrUn 83.069 1010 86 40 1 986 329102995 329103943 0.000000e+00 839.0
34 TraesCS6B01G091000 chrUn 83.069 1010 86 40 1 986 361925646 361926594 0.000000e+00 839.0
35 TraesCS6B01G091000 chrUn 82.562 1015 88 39 1 986 100489169 100490123 0.000000e+00 811.0
36 TraesCS6B01G091000 chrUn 89.086 394 30 6 2982 3365 100660346 100660736 1.310000e-130 477.0
37 TraesCS6B01G091000 chrUn 90.113 354 28 4 1 353 100627681 100628028 2.210000e-123 453.0
38 TraesCS6B01G091000 chrUn 91.727 278 18 2 1 278 100468624 100468896 1.060000e-101 381.0
39 TraesCS6B01G091000 chrUn 91.411 163 13 1 1 163 100596579 100596740 6.790000e-54 222.0
40 TraesCS6B01G091000 chrUn 85.950 121 3 6 109 229 100488664 100488770 3.290000e-22 117.0
41 TraesCS6B01G091000 chr7A 88.039 1622 175 13 1290 2898 255897066 255895451 0.000000e+00 1903.0
42 TraesCS6B01G091000 chr5A 87.452 526 64 2 4663 5186 548462611 548462086 5.770000e-169 604.0
43 TraesCS6B01G091000 chr5A 87.048 525 67 1 4663 5186 548481556 548481032 4.490000e-165 592.0
44 TraesCS6B01G091000 chr5A 86.857 525 68 1 4663 5186 548433860 548433336 2.090000e-163 586.0
45 TraesCS6B01G091000 chr5A 82.171 129 16 5 1048 1170 295089951 295089824 2.560000e-18 104.0
46 TraesCS6B01G091000 chr4B 86.364 550 70 5 4659 5205 359718016 359717469 3.470000e-166 595.0
47 TraesCS6B01G091000 chr4B 88.525 61 6 1 1073 1132 172791525 172791585 7.230000e-09 73.1
48 TraesCS6B01G091000 chr3A 85.742 512 69 4 4664 5174 532910809 532910301 5.930000e-149 538.0
49 TraesCS6B01G091000 chr3A 84.517 549 77 6 4663 5205 387280784 387280238 2.130000e-148 536.0
50 TraesCS6B01G091000 chr3D 84.095 547 80 4 4661 5205 417746409 417746950 5.980000e-144 521.0
51 TraesCS6B01G091000 chr3D 79.630 162 25 4 1051 1208 143237602 143237759 5.510000e-20 110.0
52 TraesCS6B01G091000 chr3D 97.561 41 1 0 1082 1122 600494980 600494940 2.600000e-08 71.3
53 TraesCS6B01G091000 chr6D 83.168 202 21 6 1018 1207 368370450 368370650 6.930000e-39 172.0
54 TraesCS6B01G091000 chr6D 100.000 33 0 0 1082 1114 429612250 429612218 1.570000e-05 62.1
55 TraesCS6B01G091000 chr4A 84.106 151 22 2 4475 4624 712846013 712845864 1.510000e-30 145.0
56 TraesCS6B01G091000 chr4A 81.818 88 10 4 1051 1132 121480218 121480305 9.360000e-08 69.4
57 TraesCS6B01G091000 chr5D 81.679 131 16 6 1047 1170 220707752 220707623 9.220000e-18 102.0
58 TraesCS6B01G091000 chr7B 92.424 66 3 2 1144 1207 362034008 362034073 5.550000e-15 93.5
59 TraesCS6B01G091000 chr1B 79.286 140 21 6 1040 1172 464138008 464137870 2.000000e-14 91.6
60 TraesCS6B01G091000 chr4D 85.227 88 7 5 1051 1132 399957250 399957337 9.290000e-13 86.1
61 TraesCS6B01G091000 chr4D 97.297 37 1 0 1045 1081 93712197 93712233 4.350000e-06 63.9
62 TraesCS6B01G091000 chr2A 90.196 51 4 1 1083 1132 196518390 196518440 1.210000e-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 TraesCS6B01G091000 chr6B 66782418 66787624 5206 True 9616.00 9616 100.000000 1 5207 1 chr6B.!!$R3 5206
1 TraesCS6B01G091000 chr6B 66751853 66756951 5098 True 7808.00 7808 94.214000 57 5207 1 chr6B.!!$R1 5150
2 TraesCS6B01G091000 chr6B 66942174 66945094 2920 True 1746.50 2381 89.419500 1208 4177 2 chr6B.!!$R9 2969
3 TraesCS6B01G091000 chr6B 66917584 66921643 4059 True 1430.00 2309 87.123000 22 4177 3 chr6B.!!$R8 4155
4 TraesCS6B01G091000 chr6B 66859712 66867487 7775 True 1153.75 2410 87.071500 22 4177 4 chr6B.!!$R7 4155
5 TraesCS6B01G091000 chr6A 36053032 36056985 3953 True 1479.00 2556 87.485000 60 4177 3 chr6A.!!$R2 4117
6 TraesCS6B01G091000 chr6A 35987640 35991478 3838 True 1444.00 2556 87.385333 165 4177 3 chr6A.!!$R1 4012
7 TraesCS6B01G091000 chrUn 100637665 100639442 1777 False 1947.00 1947 86.600000 1203 2973 1 chrUn.!!$F4 1770
8 TraesCS6B01G091000 chrUn 100620877 100623232 2355 False 1450.50 1759 89.659500 1815 4177 2 chrUn.!!$F12 2362
9 TraesCS6B01G091000 chrUn 100488664 100494198 5534 False 1209.60 2529 88.283000 1 5207 5 chrUn.!!$F11 5206
10 TraesCS6B01G091000 chrUn 344891260 344892824 1564 False 1005.50 1096 89.569000 2533 4134 2 chrUn.!!$F13 1601
11 TraesCS6B01G091000 chrUn 323635564 323636512 948 False 839.00 839 83.069000 1 986 1 chrUn.!!$F6 985
12 TraesCS6B01G091000 chrUn 323667421 323668369 948 False 839.00 839 83.069000 1 986 1 chrUn.!!$F7 985
13 TraesCS6B01G091000 chrUn 329023632 329024580 948 False 839.00 839 83.069000 1 986 1 chrUn.!!$F8 985
14 TraesCS6B01G091000 chrUn 329102995 329103943 948 False 839.00 839 83.069000 1 986 1 chrUn.!!$F9 985
15 TraesCS6B01G091000 chrUn 361925646 361926594 948 False 839.00 839 83.069000 1 986 1 chrUn.!!$F10 985
16 TraesCS6B01G091000 chr7A 255895451 255897066 1615 True 1903.00 1903 88.039000 1290 2898 1 chr7A.!!$R1 1608
17 TraesCS6B01G091000 chr5A 548462086 548462611 525 True 604.00 604 87.452000 4663 5186 1 chr5A.!!$R3 523
18 TraesCS6B01G091000 chr5A 548481032 548481556 524 True 592.00 592 87.048000 4663 5186 1 chr5A.!!$R4 523
19 TraesCS6B01G091000 chr5A 548433336 548433860 524 True 586.00 586 86.857000 4663 5186 1 chr5A.!!$R2 523
20 TraesCS6B01G091000 chr4B 359717469 359718016 547 True 595.00 595 86.364000 4659 5205 1 chr4B.!!$R1 546
21 TraesCS6B01G091000 chr3A 532910301 532910809 508 True 538.00 538 85.742000 4664 5174 1 chr3A.!!$R2 510
22 TraesCS6B01G091000 chr3A 387280238 387280784 546 True 536.00 536 84.517000 4663 5205 1 chr3A.!!$R1 542
23 TraesCS6B01G091000 chr3D 417746409 417746950 541 False 521.00 521 84.095000 4661 5205 1 chr3D.!!$F2 544

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
50 3755 0.464036 TTGTCGTGAGCTTGACAGGT 59.536 50.000 14.43 0.0 45.08 4.00 F
191 3937 0.941542 TACGTGTGTGGCTCTTTTGC 59.058 50.000 0.00 0.0 0.00 3.68 F
1144 4945 0.040425 GCAACTTCATGCGTCGGTTT 60.040 50.000 0.00 0.0 36.45 3.27 F
1854 5702 1.227674 CATGCGCCTAAGACCCCTC 60.228 63.158 4.18 0.0 0.00 4.30 F
2644 6535 1.470098 AGGCGATCAAAATGTGAGCAC 59.530 47.619 0.00 0.0 43.14 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1094 4895 0.652592 CTAAAGTTGCCATCCTCGCG 59.347 55.0 0.00 0.00 0.00 5.87 R
1674 5518 1.021202 TGCACTCAAGTTTCCCAACG 58.979 50.0 0.00 0.00 38.03 4.10 R
2287 6164 0.106669 GGTAGGTGGGCAAATCTCCC 60.107 60.0 0.00 0.00 44.17 4.30 R
3337 7249 1.075601 AGATGCCCACTCCAAGGAAA 58.924 50.0 0.00 0.00 0.00 3.13 R
4427 8343 0.098728 GTCACACGCACTTGTGCTTT 59.901 50.0 21.17 7.41 45.58 3.51 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
50 3755 0.464036 TTGTCGTGAGCTTGACAGGT 59.536 50.000 14.43 0.00 45.08 4.00
130 3868 1.273606 AGGTGTCAGATGGAGACGTTG 59.726 52.381 0.00 0.00 40.58 4.10
143 3881 2.029073 CGTTGACGTGGCAGGACT 59.971 61.111 14.98 0.00 34.11 3.85
156 3894 5.452776 CGTGGCAGGACTTACAAATATAGGA 60.453 44.000 0.00 0.00 0.00 2.94
157 3895 6.354130 GTGGCAGGACTTACAAATATAGGAA 58.646 40.000 0.00 0.00 0.00 3.36
158 3896 6.260271 GTGGCAGGACTTACAAATATAGGAAC 59.740 42.308 0.00 0.00 0.00 3.62
188 3934 2.614829 ACTTACGTGTGTGGCTCTTT 57.385 45.000 0.00 0.00 0.00 2.52
189 3935 2.914059 ACTTACGTGTGTGGCTCTTTT 58.086 42.857 0.00 0.00 0.00 2.27
190 3936 2.612212 ACTTACGTGTGTGGCTCTTTTG 59.388 45.455 0.00 0.00 0.00 2.44
191 3937 0.941542 TACGTGTGTGGCTCTTTTGC 59.058 50.000 0.00 0.00 0.00 3.68
205 3958 2.290122 TTTTGCCAGTTGTGGGTGCG 62.290 55.000 0.00 0.00 45.17 5.34
357 4110 1.737816 GCATGGTGCATTAGCCCTG 59.262 57.895 0.00 0.00 44.26 4.45
505 4269 2.521126 CATGCATTGCTCATATCCCCA 58.479 47.619 10.49 0.00 0.00 4.96
574 4338 6.931281 CGTACTCTTGTTCATCCCATATCATT 59.069 38.462 0.00 0.00 0.00 2.57
644 4430 4.083324 ACACGTCACATTAATCAAGCAAGG 60.083 41.667 0.00 0.00 0.00 3.61
948 4749 7.676683 TTGCTAATTATACTTCCTCTGTCCT 57.323 36.000 0.00 0.00 0.00 3.85
975 4776 3.366440 ACTGGCGTATAAATCGAGTCC 57.634 47.619 0.00 0.00 0.00 3.85
1080 4881 5.148568 GCACATGGCAAATTGAACATTTTC 58.851 37.500 0.00 0.00 43.97 2.29
1081 4882 5.277876 GCACATGGCAAATTGAACATTTTCA 60.278 36.000 0.00 0.00 43.97 2.69
1090 4891 9.766277 GCAAATTGAACATTTTCACAAGTTTAA 57.234 25.926 0.00 0.00 41.64 1.52
1104 4905 2.550978 AGTTTAATGACGCGAGGATGG 58.449 47.619 15.93 0.00 0.00 3.51
1114 4915 0.378610 GCGAGGATGGCAACTTTAGC 59.621 55.000 0.00 0.00 40.68 3.09
1144 4945 0.040425 GCAACTTCATGCGTCGGTTT 60.040 50.000 0.00 0.00 36.45 3.27
1181 4982 2.248280 TGCCGTGTGTGTCAACTAAT 57.752 45.000 0.00 0.00 0.00 1.73
1199 5000 1.477553 ATTTGCCATCCTTGCGTCAT 58.522 45.000 0.00 0.00 0.00 3.06
1200 5001 1.255882 TTTGCCATCCTTGCGTCATT 58.744 45.000 0.00 0.00 0.00 2.57
1206 5043 3.316308 GCCATCCTTGCGTCATTAGAATT 59.684 43.478 0.00 0.00 0.00 2.17
1218 5055 7.484641 TGCGTCATTAGAATTAGCACAATTTTC 59.515 33.333 0.00 0.00 0.00 2.29
1219 5056 7.304849 GCGTCATTAGAATTAGCACAATTTTCG 60.305 37.037 0.00 0.00 0.00 3.46
1233 5075 7.023575 GCACAATTTTCGATCTCTATGTTTGT 58.976 34.615 0.00 0.00 0.00 2.83
1406 5249 8.518430 TTGCTCTATGTGCAATAATAGGAAAA 57.482 30.769 10.73 3.27 44.24 2.29
1533 5377 9.336171 TCCACGATGAAATTGATAACATAATGA 57.664 29.630 0.00 0.00 0.00 2.57
1580 5424 3.926527 GTGATGATCTACTTGACGCAACA 59.073 43.478 0.00 0.00 0.00 3.33
1595 5439 3.071479 CGCAACACTTTCCTTAAGGCTA 58.929 45.455 17.32 4.34 38.23 3.93
1674 5518 6.898041 TGTTGAGTTAGATAAACACACATGC 58.102 36.000 0.00 0.00 38.23 4.06
1766 5613 7.104290 AGTCTTAGAGTGGCCAAGTTTAATAC 58.896 38.462 7.24 7.00 0.00 1.89
1854 5702 1.227674 CATGCGCCTAAGACCCCTC 60.228 63.158 4.18 0.00 0.00 4.30
2016 5867 4.473444 ACAAGGCAAAGGAATTCTCAAGA 58.527 39.130 5.23 0.00 0.00 3.02
2094 5945 2.877154 AGTCACTGGACCATCCCTAT 57.123 50.000 0.00 0.00 45.48 2.57
2143 5994 3.378512 AGGCATCATCTGAGTTACCTCA 58.621 45.455 0.00 0.00 45.44 3.86
2287 6164 7.066781 ACACCCCTTCCATTATTAGTTATTGG 58.933 38.462 0.00 0.00 34.11 3.16
2291 6168 6.948309 CCCTTCCATTATTAGTTATTGGGGAG 59.052 42.308 0.00 0.00 33.77 4.30
2388 6272 3.989167 CACAATTAATGGTGTGGTGCTTG 59.011 43.478 14.00 0.00 41.19 4.01
2461 6346 2.159462 GCTCAAGAAATACCAGCTGCAC 60.159 50.000 8.66 0.00 0.00 4.57
2508 6393 2.894126 GTGGTCCATGACTATCCTCGAT 59.106 50.000 0.00 0.00 32.47 3.59
2583 6468 5.525378 GGTCTACATTGTGGATGACATCTTC 59.475 44.000 14.95 8.91 39.15 2.87
2644 6535 1.470098 AGGCGATCAAAATGTGAGCAC 59.530 47.619 0.00 0.00 43.14 4.40
2662 6554 6.318648 GTGAGCACTGATGTTCCCATAATAAA 59.681 38.462 0.00 0.00 35.29 1.40
2674 6566 7.068839 TGTTCCCATAATAAACAACAACACTGT 59.931 33.333 0.00 0.00 37.39 3.55
2909 6807 6.870769 AGCATTGCATATTGAAAGCTACTTT 58.129 32.000 11.91 0.00 36.29 2.66
2980 6878 7.094634 GGGTTAGTTGAGACCATATGCATAATG 60.095 40.741 11.13 9.41 37.68 1.90
3070 6977 4.763279 TGAGTCACTACCGAGTTACATGAA 59.237 41.667 0.00 0.00 33.01 2.57
3177 7084 7.487484 TCATCTCAAGAAAGCAGTATGTCTAG 58.513 38.462 0.00 0.00 39.31 2.43
3333 7245 5.288827 CTGGAAGAGTTGCATTCATGCCC 62.289 52.174 9.30 2.19 45.82 5.36
3365 7277 2.229784 GGAGTGGGCATCTTTGTTTGAG 59.770 50.000 0.00 0.00 0.00 3.02
3380 7292 8.358895 TCTTTGTTTGAGTAATTGCATTCATGA 58.641 29.630 0.00 0.00 0.00 3.07
3382 7294 9.491675 TTTGTTTGAGTAATTGCATTCATGAAT 57.508 25.926 15.36 15.36 0.00 2.57
3502 7414 2.359981 ATGGCATCATCACTTCAGGG 57.640 50.000 0.00 0.00 0.00 4.45
3556 7468 3.392285 TGCTAGGGCATGATGTAACAGAT 59.608 43.478 0.00 0.00 44.28 2.90
3566 7478 5.940192 TGATGTAACAGATGACAACAACC 57.060 39.130 0.00 0.00 0.00 3.77
3583 7495 3.396611 ACAACCACCACATACTTAGGGTT 59.603 43.478 0.00 0.00 37.62 4.11
3656 7568 6.072508 TGCAAAGGTCAGAATACATCAAGAAC 60.073 38.462 0.00 0.00 0.00 3.01
3894 7808 2.032636 CACATGTTGCATATGATCGCGT 60.033 45.455 15.86 0.00 0.00 6.01
3904 7818 0.815213 ATGATCGCGTGTGAATGGGG 60.815 55.000 5.77 0.00 0.00 4.96
3954 7868 2.508300 ACAAAGTCCACACTACCACCTT 59.492 45.455 0.00 0.00 30.14 3.50
4177 8092 2.613595 TCATGCACCATTAGCGAATGTC 59.386 45.455 16.91 7.51 40.87 3.06
4196 8111 4.342359 TGTCTTCCTACTTCCTAGTGGTC 58.658 47.826 0.00 0.00 35.78 4.02
4230 8145 7.573968 ATTTACTTGTCAAAAGACTTGAGCT 57.426 32.000 0.00 0.00 0.00 4.09
4294 8209 7.649306 GCATGTGAAGTTATGGAATCAAATACC 59.351 37.037 0.00 0.00 0.00 2.73
4322 8238 9.264719 CTATCTATATGAAACTGTCAATGCACA 57.735 33.333 0.00 0.00 40.50 4.57
4327 8243 6.822667 ATGAAACTGTCAATGCACAGATTA 57.177 33.333 15.92 5.62 45.92 1.75
4416 8332 2.057316 CACAGCGAACTTCTCACAGAG 58.943 52.381 0.00 0.00 0.00 3.35
4422 8338 3.701241 CGAACTTCTCACAGAGCCTATC 58.299 50.000 0.00 0.00 0.00 2.08
4450 8366 1.881252 ACAAGTGCGTGTGACCGTC 60.881 57.895 0.00 0.00 0.00 4.79
4641 8558 6.294176 CCGATTCTTTGGTTCAATCTTGTTCT 60.294 38.462 0.00 0.00 0.00 3.01
4732 8650 8.223769 GTCATTTACAAGCATATGAGGAATACG 58.776 37.037 6.97 0.00 0.00 3.06
4756 8674 5.321927 GTCTGGAGGGGTAAAATCTCAAAA 58.678 41.667 0.00 0.00 0.00 2.44
4807 8725 8.746922 TGTTTTGCTAAAGATTTTGCTATCTG 57.253 30.769 11.85 0.00 39.18 2.90
4820 8738 6.762702 TTTGCTATCTGATTTGCTTCATGA 57.237 33.333 13.63 0.00 0.00 3.07
4852 8770 6.432783 TGATCATACGAAACTGTCCCAAAATT 59.567 34.615 0.00 0.00 0.00 1.82
5174 9097 0.107800 GAAACCCTAAGGCGGTCTCC 60.108 60.000 0.00 0.00 36.11 3.71
5179 9103 0.760945 CCTAAGGCGGTCTCCTCCAT 60.761 60.000 0.00 0.00 34.82 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.016360 ACGTATGCCACATATAACCTACGTAA 60.016 38.462 0.00 0.00 41.23 3.18
50 3755 3.482436 ACCAGTTTTTCATCGGTTGCTA 58.518 40.909 0.00 0.00 0.00 3.49
62 3767 2.293399 GTCTGCCGATTGACCAGTTTTT 59.707 45.455 0.00 0.00 0.00 1.94
130 3868 1.873698 TTTGTAAGTCCTGCCACGTC 58.126 50.000 0.00 0.00 0.00 4.34
188 3934 3.215568 CGCACCCACAACTGGCAA 61.216 61.111 0.00 0.00 36.00 4.52
191 3937 3.286751 CACCGCACCCACAACTGG 61.287 66.667 0.00 0.00 37.29 4.00
192 3938 3.964875 GCACCGCACCCACAACTG 61.965 66.667 0.00 0.00 0.00 3.16
193 3939 4.497984 TGCACCGCACCCACAACT 62.498 61.111 0.00 0.00 31.71 3.16
194 3940 3.964875 CTGCACCGCACCCACAAC 61.965 66.667 0.00 0.00 33.79 3.32
205 3958 1.966451 CACGGTTTCTCCCTGCACC 60.966 63.158 0.00 0.00 0.00 5.01
349 4102 2.642154 TGTTTTTCGTCCAGGGCTAA 57.358 45.000 0.00 0.00 0.00 3.09
357 4110 6.344702 CGCTAATCAAGTTTTGTTTTTCGTCC 60.345 38.462 0.00 0.00 0.00 4.79
436 4192 2.255252 GTTGAGCAATGCCGCGTT 59.745 55.556 4.92 0.00 36.85 4.84
505 4269 3.718434 TCTGCTATGTCTTGGGATGGATT 59.282 43.478 0.00 0.00 0.00 3.01
543 4307 3.858238 GGATGAACAAGAGTACGTAGCAC 59.142 47.826 0.00 0.00 0.00 4.40
544 4308 3.119245 GGGATGAACAAGAGTACGTAGCA 60.119 47.826 0.00 0.00 0.00 3.49
545 4309 3.119245 TGGGATGAACAAGAGTACGTAGC 60.119 47.826 0.00 0.00 0.00 3.58
546 4310 4.713824 TGGGATGAACAAGAGTACGTAG 57.286 45.455 0.00 0.00 0.00 3.51
547 4311 6.548251 TGATATGGGATGAACAAGAGTACGTA 59.452 38.462 0.00 0.00 0.00 3.57
548 4312 5.362717 TGATATGGGATGAACAAGAGTACGT 59.637 40.000 0.00 0.00 0.00 3.57
574 4338 1.075542 CGGCTGATTTTGTAGCGTGA 58.924 50.000 0.00 0.00 40.78 4.35
840 4626 9.567776 TGGTCCTATAAATATGTTTGTACCATG 57.432 33.333 0.00 0.00 0.00 3.66
942 4742 8.428186 TTTATACGCCAGTTATTTAAGGACAG 57.572 34.615 0.00 0.00 0.00 3.51
948 4749 8.876275 ACTCGATTTATACGCCAGTTATTTAA 57.124 30.769 0.00 0.00 0.00 1.52
1031 4832 2.002586 CCTGACATTCAGCGTTACCAG 58.997 52.381 0.00 0.00 42.98 4.00
1041 4842 1.616374 TGTGCTCGTACCTGACATTCA 59.384 47.619 0.00 0.00 0.00 2.57
1070 4871 7.043722 GCGTCATTAAACTTGTGAAAATGTTCA 60.044 33.333 0.00 0.00 41.57 3.18
1080 4881 2.734606 TCCTCGCGTCATTAAACTTGTG 59.265 45.455 5.77 0.00 0.00 3.33
1081 4882 3.034721 TCCTCGCGTCATTAAACTTGT 57.965 42.857 5.77 0.00 0.00 3.16
1090 4891 1.815421 GTTGCCATCCTCGCGTCAT 60.815 57.895 5.77 0.00 0.00 3.06
1094 4895 0.652592 CTAAAGTTGCCATCCTCGCG 59.347 55.000 0.00 0.00 0.00 5.87
1151 4952 3.378742 ACACACACGGCAATTTTCTGTTA 59.621 39.130 0.00 0.00 0.00 2.41
1154 4955 2.223456 TGACACACACGGCAATTTTCTG 60.223 45.455 0.00 0.00 0.00 3.02
1181 4982 1.255882 AATGACGCAAGGATGGCAAA 58.744 45.000 0.00 0.00 46.39 3.68
1199 5000 9.383519 AGAGATCGAAAATTGTGCTAATTCTAA 57.616 29.630 0.00 0.00 0.00 2.10
1200 5001 8.948631 AGAGATCGAAAATTGTGCTAATTCTA 57.051 30.769 0.00 0.00 0.00 2.10
1206 5043 8.390354 CAAACATAGAGATCGAAAATTGTGCTA 58.610 33.333 0.00 0.00 0.00 3.49
1346 5188 9.640963 TTAGCAAGAATACAAAGTCTAGAGAAC 57.359 33.333 0.00 0.00 27.85 3.01
1406 5249 4.201950 GCAATGCTTGAACATTCGATAGGT 60.202 41.667 0.00 0.00 38.19 3.08
1533 5377 3.238108 GATGAGATCCACACACGAGTT 57.762 47.619 0.00 0.00 0.00 3.01
1580 5424 6.875972 TCTCTCATTAGCCTTAAGGAAAGT 57.124 37.500 26.21 8.38 37.39 2.66
1595 5439 9.723601 GAAATAGAATATCCAGCTTCTCTCATT 57.276 33.333 0.00 0.00 33.83 2.57
1674 5518 1.021202 TGCACTCAAGTTTCCCAACG 58.979 50.000 0.00 0.00 38.03 4.10
1777 5625 2.672961 TCTATGCTCCACAAAGGACG 57.327 50.000 0.00 0.00 43.07 4.79
1978 5829 3.056179 GCCTTGTAGAGTGAAGCTTCTCT 60.056 47.826 26.66 26.66 42.62 3.10
2016 5867 8.675705 ACTTAATTGCAAATTTAAGGTGCTTT 57.324 26.923 25.44 9.77 38.93 3.51
2094 5945 4.263435 TGTATTGCATCAAGCTCACATGA 58.737 39.130 0.00 0.00 45.94 3.07
2287 6164 0.106669 GGTAGGTGGGCAAATCTCCC 60.107 60.000 0.00 0.00 44.17 4.30
2291 6168 3.883489 GTCAATAGGTAGGTGGGCAAATC 59.117 47.826 0.00 0.00 0.00 2.17
2461 6346 1.812571 CCATTTCAGAACTTGGTCCCG 59.187 52.381 3.86 0.00 0.00 5.14
2508 6393 6.663953 CCCGATATCTAGAGAAGGATAAACCA 59.336 42.308 12.24 0.00 42.04 3.67
2623 6514 2.677836 GTGCTCACATTTTGATCGCCTA 59.322 45.455 0.00 0.00 32.17 3.93
2662 6554 7.051623 TCATTCCTAAAGTACAGTGTTGTTGT 58.948 34.615 0.00 0.00 38.76 3.32
2794 6688 7.833786 TCGTAACCTAATGTTTATGTCAGACT 58.166 34.615 1.31 0.00 38.42 3.24
2877 6774 9.467258 GCTTTCAATATGCAATGCTTTATCTTA 57.533 29.630 6.82 0.00 0.00 2.10
2878 6775 8.202137 AGCTTTCAATATGCAATGCTTTATCTT 58.798 29.630 6.82 0.00 30.90 2.40
3070 6977 7.613801 TGGTGTAAATAGCCTTGTAACATGATT 59.386 33.333 0.00 0.00 0.00 2.57
3087 6994 7.927629 GGCAATATCATTTGTGATGGTGTAAAT 59.072 33.333 1.37 0.00 0.00 1.40
3335 7247 2.158325 AGATGCCCACTCCAAGGAAAAA 60.158 45.455 0.00 0.00 0.00 1.94
3336 7248 1.428912 AGATGCCCACTCCAAGGAAAA 59.571 47.619 0.00 0.00 0.00 2.29
3337 7249 1.075601 AGATGCCCACTCCAAGGAAA 58.924 50.000 0.00 0.00 0.00 3.13
3502 7414 5.906073 AGATGCATAAATAAAAGTGGTGCC 58.094 37.500 0.00 0.00 0.00 5.01
3548 7460 3.880490 TGGTGGTTGTTGTCATCTGTTAC 59.120 43.478 0.00 0.00 0.00 2.50
3556 7468 3.569194 AGTATGTGGTGGTTGTTGTCA 57.431 42.857 0.00 0.00 0.00 3.58
3566 7478 5.602978 AGGAGATAACCCTAAGTATGTGGTG 59.397 44.000 0.00 0.00 30.92 4.17
3583 7495 1.583556 TCTTTGCAGGGCAGGAGATA 58.416 50.000 0.00 0.00 40.61 1.98
3882 7796 2.158254 CCCATTCACACGCGATCATATG 59.842 50.000 15.93 10.50 0.00 1.78
3904 7818 3.584733 AGCATTCCCTGTTTAGATCCC 57.415 47.619 0.00 0.00 0.00 3.85
3954 7868 3.371097 GAGACGCCCCGATGAAGCA 62.371 63.158 0.00 0.00 0.00 3.91
4143 8058 3.445805 TGGTGCATGATACTAGTTCACGA 59.554 43.478 0.00 0.00 0.00 4.35
4177 8092 8.707796 TTATATGACCACTAGGAAGTAGGAAG 57.292 38.462 0.00 0.00 38.69 3.46
4222 8137 1.602888 CCTTGCAGGCAGCTCAAGT 60.603 57.895 16.05 0.00 45.94 3.16
4257 8172 4.952262 ACTTCACATGCATCACATACAC 57.048 40.909 0.00 0.00 36.64 2.90
4294 8209 9.264719 TGCATTGACAGTTTCATATAGATAGTG 57.735 33.333 0.00 0.00 35.50 2.74
4322 8238 9.536510 GGTGGATTAGGATCTAACTAGTAATCT 57.463 37.037 0.00 0.00 28.59 2.40
4327 8243 7.169287 AGAGGTGGATTAGGATCTAACTAGT 57.831 40.000 0.00 0.00 40.48 2.57
4346 8262 6.072008 CGATGATGAGACAATGAGATAGAGGT 60.072 42.308 0.00 0.00 0.00 3.85
4422 8338 2.295052 CGCACTTGTGCTTTTGCCG 61.295 57.895 21.17 2.73 46.87 5.69
4427 8343 0.098728 GTCACACGCACTTGTGCTTT 59.901 50.000 21.17 7.41 45.58 3.51
4641 8558 3.754965 AGTATTTCCTGCAAGCAGAACA 58.245 40.909 22.76 6.57 46.30 3.18
4732 8650 2.844348 TGAGATTTTACCCCTCCAGACC 59.156 50.000 0.00 0.00 0.00 3.85
4796 8714 7.160547 TCATGAAGCAAATCAGATAGCAAAA 57.839 32.000 9.70 0.00 31.76 2.44
4820 8738 4.997395 ACAGTTTCGTATGATCACTGCTTT 59.003 37.500 18.45 3.86 38.48 3.51
4826 8744 3.857052 TGGGACAGTTTCGTATGATCAC 58.143 45.455 0.00 0.00 0.00 3.06
4852 8770 5.076873 GGGAATGCCATAACCTTGCTAATA 58.923 41.667 0.00 0.00 35.15 0.98
5174 9097 5.444416 TCGAAAGCGTTTCCACATATGGAG 61.444 45.833 7.80 0.00 46.51 3.86
5179 9103 3.185594 CAGTTCGAAAGCGTTTCCACATA 59.814 43.478 0.00 0.00 38.98 2.29


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

AutoCloner maintained by Alex Coulton.