Multiple sequence alignment - TraesCS1B01G111000

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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 TraesCS1B01G111000 chr1B 100.000 3256 0 0 1 3256 127026844 127023589 0.000000e+00 6013
1 TraesCS1B01G111000 chr4D 93.253 2505 137 12 1 2483 459190867 459193361 0.000000e+00 3661
2 TraesCS1B01G111000 chr4D 82.172 976 152 13 1189 2160 145379889 145378932 0.000000e+00 819
3 TraesCS1B01G111000 chr4D 79.472 1213 197 33 937 2119 348041285 348040095 0.000000e+00 813
4 TraesCS1B01G111000 chr4D 92.282 298 18 3 2187 2480 101391974 101392270 5.020000e-113 418
5 TraesCS1B01G111000 chr2D 92.763 2501 117 22 1 2481 631750041 631747585 0.000000e+00 3557
6 TraesCS1B01G111000 chr2D 92.308 2184 148 10 1 2174 469108412 469106239 0.000000e+00 3085
7 TraesCS1B01G111000 chr2D 88.043 1313 104 19 890 2174 330864576 330863289 0.000000e+00 1506
8 TraesCS1B01G111000 chr2D 86.269 772 76 13 2484 3254 561401886 561402628 0.000000e+00 811
9 TraesCS1B01G111000 chr2D 85.917 774 88 11 2484 3256 342654332 342655085 0.000000e+00 806
10 TraesCS1B01G111000 chr2D 85.788 774 89 10 2484 3256 488167064 488166311 0.000000e+00 800
11 TraesCS1B01G111000 chr2D 91.536 319 21 4 2166 2482 469106165 469105851 4.990000e-118 435
12 TraesCS1B01G111000 chr1A 92.156 2180 154 12 1 2174 461967264 461965096 0.000000e+00 3062
13 TraesCS1B01G111000 chr1A 92.667 1541 96 12 1 1535 35564479 35562950 0.000000e+00 2204
14 TraesCS1B01G111000 chr1A 80.127 1419 239 28 1086 2485 80283703 80282309 0.000000e+00 1018
15 TraesCS1B01G111000 chr1A 90.373 644 48 7 1531 2174 35559048 35558419 0.000000e+00 833
16 TraesCS1B01G111000 chr1A 91.463 328 19 5 2166 2486 385892639 385892314 2.980000e-120 442
17 TraesCS1B01G111000 chr1A 91.185 329 21 5 2159 2486 461965054 461964733 1.070000e-119 440
18 TraesCS1B01G111000 chr1A 90.184 326 25 4 2159 2483 35558377 35558058 5.020000e-113 418
19 TraesCS1B01G111000 chr3B 91.743 2180 157 17 1 2170 597426312 597428478 0.000000e+00 3007
20 TraesCS1B01G111000 chr3B 92.920 1695 83 16 812 2483 8505203 8506883 0.000000e+00 2431
21 TraesCS1B01G111000 chr3B 86.070 201 21 5 890 1087 597427123 597427319 3.290000e-50 209
22 TraesCS1B01G111000 chr3B 95.312 128 6 0 960 1087 8505193 8505320 1.530000e-48 204
23 TraesCS1B01G111000 chr7B 91.621 2184 156 19 1 2175 551485194 551483029 0.000000e+00 2994
24 TraesCS1B01G111000 chr2B 92.432 1546 80 20 969 2485 677292341 677293878 0.000000e+00 2172
25 TraesCS1B01G111000 chr2B 94.807 982 47 4 1 979 677291529 677292509 0.000000e+00 1528
26 TraesCS1B01G111000 chr3D 94.745 1313 48 4 1189 2483 6991411 6992720 0.000000e+00 2023
27 TraesCS1B01G111000 chr3D 92.366 655 32 3 1848 2485 5544737 5545390 0.000000e+00 917
28 TraesCS1B01G111000 chr3D 86.211 776 78 13 2480 3253 462375070 462374322 0.000000e+00 813
29 TraesCS1B01G111000 chr7A 93.521 1281 65 13 969 2236 48781641 48782916 0.000000e+00 1890
30 TraesCS1B01G111000 chr7A 95.510 980 42 2 1 978 48780829 48781808 0.000000e+00 1565
31 TraesCS1B01G111000 chrUn 91.879 1293 87 8 890 2174 96553413 96554695 0.000000e+00 1790
32 TraesCS1B01G111000 chrUn 92.236 322 19 4 2166 2485 96554769 96555086 4.950000e-123 451
33 TraesCS1B01G111000 chr7D 89.148 986 73 7 1517 2484 422343534 422344503 0.000000e+00 1197
34 TraesCS1B01G111000 chr7D 87.855 774 73 10 2484 3256 469140344 469141097 0.000000e+00 889
35 TraesCS1B01G111000 chr7D 86.658 772 76 12 2484 3254 54861135 54860390 0.000000e+00 830
36 TraesCS1B01G111000 chr7D 86.658 772 76 12 2484 3254 452809811 452810556 0.000000e+00 830
37 TraesCS1B01G111000 chr7D 86.305 774 84 12 2484 3256 368587906 368588658 0.000000e+00 822
38 TraesCS1B01G111000 chr7D 86.340 776 79 16 2484 3256 277245815 277245064 0.000000e+00 821
39 TraesCS1B01G111000 chr7D 92.236 322 19 3 2166 2485 69948616 69948933 4.950000e-123 451
40 TraesCS1B01G111000 chr5D 80.948 1202 198 20 969 2157 538687093 538688276 0.000000e+00 922
41 TraesCS1B01G111000 chr5D 86.805 773 74 13 2484 3254 330341757 330341011 0.000000e+00 837
42 TraesCS1B01G111000 chr5D 86.788 772 75 12 2484 3254 412700713 412701458 0.000000e+00 835
43 TraesCS1B01G111000 chr5D 85.548 775 81 17 2484 3256 217197947 217198692 0.000000e+00 782
44 TraesCS1B01G111000 chr5D 77.717 1288 219 37 890 2141 420019256 420020511 0.000000e+00 726
45 TraesCS1B01G111000 chr5D 84.326 772 80 18 2484 3254 301958574 301959305 0.000000e+00 717
46 TraesCS1B01G111000 chr1D 86.693 774 82 10 2484 3256 339170363 339169610 0.000000e+00 839
47 TraesCS1B01G111000 chr1D 86.528 772 77 12 2484 3254 154363968 154363223 0.000000e+00 824
48 TraesCS1B01G111000 chr6D 86.136 779 86 12 2480 3256 358893668 358894426 0.000000e+00 821
49 TraesCS1B01G111000 chr3A 85.714 770 89 11 2484 3252 518834453 518835202 0.000000e+00 793
50 TraesCS1B01G111000 chr6B 84.685 777 94 15 2483 3256 449334319 449335073 0.000000e+00 752
51 TraesCS1B01G111000 chr6B 89.908 327 25 5 2166 2488 658405706 658405384 6.500000e-112 414
52 TraesCS1B01G111000 chr4A 91.049 324 22 4 2166 2483 445298243 445297921 6.450000e-117 431


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 TraesCS1B01G111000 chr1B 127023589 127026844 3255 True 6013.000000 6013 100.000000 1 3256 1 chr1B.!!$R1 3255
1 TraesCS1B01G111000 chr4D 459190867 459193361 2494 False 3661.000000 3661 93.253000 1 2483 1 chr4D.!!$F2 2482
2 TraesCS1B01G111000 chr4D 145378932 145379889 957 True 819.000000 819 82.172000 1189 2160 1 chr4D.!!$R1 971
3 TraesCS1B01G111000 chr4D 348040095 348041285 1190 True 813.000000 813 79.472000 937 2119 1 chr4D.!!$R2 1182
4 TraesCS1B01G111000 chr2D 631747585 631750041 2456 True 3557.000000 3557 92.763000 1 2481 1 chr2D.!!$R3 2480
5 TraesCS1B01G111000 chr2D 469105851 469108412 2561 True 1760.000000 3085 91.922000 1 2482 2 chr2D.!!$R4 2481
6 TraesCS1B01G111000 chr2D 330863289 330864576 1287 True 1506.000000 1506 88.043000 890 2174 1 chr2D.!!$R1 1284
7 TraesCS1B01G111000 chr2D 561401886 561402628 742 False 811.000000 811 86.269000 2484 3254 1 chr2D.!!$F2 770
8 TraesCS1B01G111000 chr2D 342654332 342655085 753 False 806.000000 806 85.917000 2484 3256 1 chr2D.!!$F1 772
9 TraesCS1B01G111000 chr2D 488166311 488167064 753 True 800.000000 800 85.788000 2484 3256 1 chr2D.!!$R2 772
10 TraesCS1B01G111000 chr1A 461964733 461967264 2531 True 1751.000000 3062 91.670500 1 2486 2 chr1A.!!$R4 2485
11 TraesCS1B01G111000 chr1A 35558058 35564479 6421 True 1151.666667 2204 91.074667 1 2483 3 chr1A.!!$R3 2482
12 TraesCS1B01G111000 chr1A 80282309 80283703 1394 True 1018.000000 1018 80.127000 1086 2485 1 chr1A.!!$R1 1399
13 TraesCS1B01G111000 chr3B 597426312 597428478 2166 False 1608.000000 3007 88.906500 1 2170 2 chr3B.!!$F2 2169
14 TraesCS1B01G111000 chr3B 8505193 8506883 1690 False 1317.500000 2431 94.116000 812 2483 2 chr3B.!!$F1 1671
15 TraesCS1B01G111000 chr7B 551483029 551485194 2165 True 2994.000000 2994 91.621000 1 2175 1 chr7B.!!$R1 2174
16 TraesCS1B01G111000 chr2B 677291529 677293878 2349 False 1850.000000 2172 93.619500 1 2485 2 chr2B.!!$F1 2484
17 TraesCS1B01G111000 chr3D 6991411 6992720 1309 False 2023.000000 2023 94.745000 1189 2483 1 chr3D.!!$F2 1294
18 TraesCS1B01G111000 chr3D 5544737 5545390 653 False 917.000000 917 92.366000 1848 2485 1 chr3D.!!$F1 637
19 TraesCS1B01G111000 chr3D 462374322 462375070 748 True 813.000000 813 86.211000 2480 3253 1 chr3D.!!$R1 773
20 TraesCS1B01G111000 chr7A 48780829 48782916 2087 False 1727.500000 1890 94.515500 1 2236 2 chr7A.!!$F1 2235
21 TraesCS1B01G111000 chrUn 96553413 96555086 1673 False 1120.500000 1790 92.057500 890 2485 2 chrUn.!!$F1 1595
22 TraesCS1B01G111000 chr7D 422343534 422344503 969 False 1197.000000 1197 89.148000 1517 2484 1 chr7D.!!$F3 967
23 TraesCS1B01G111000 chr7D 469140344 469141097 753 False 889.000000 889 87.855000 2484 3256 1 chr7D.!!$F5 772
24 TraesCS1B01G111000 chr7D 54860390 54861135 745 True 830.000000 830 86.658000 2484 3254 1 chr7D.!!$R1 770
25 TraesCS1B01G111000 chr7D 452809811 452810556 745 False 830.000000 830 86.658000 2484 3254 1 chr7D.!!$F4 770
26 TraesCS1B01G111000 chr7D 368587906 368588658 752 False 822.000000 822 86.305000 2484 3256 1 chr7D.!!$F2 772
27 TraesCS1B01G111000 chr7D 277245064 277245815 751 True 821.000000 821 86.340000 2484 3256 1 chr7D.!!$R2 772
28 TraesCS1B01G111000 chr5D 538687093 538688276 1183 False 922.000000 922 80.948000 969 2157 1 chr5D.!!$F5 1188
29 TraesCS1B01G111000 chr5D 330341011 330341757 746 True 837.000000 837 86.805000 2484 3254 1 chr5D.!!$R1 770
30 TraesCS1B01G111000 chr5D 412700713 412701458 745 False 835.000000 835 86.788000 2484 3254 1 chr5D.!!$F3 770
31 TraesCS1B01G111000 chr5D 217197947 217198692 745 False 782.000000 782 85.548000 2484 3256 1 chr5D.!!$F1 772
32 TraesCS1B01G111000 chr5D 420019256 420020511 1255 False 726.000000 726 77.717000 890 2141 1 chr5D.!!$F4 1251
33 TraesCS1B01G111000 chr5D 301958574 301959305 731 False 717.000000 717 84.326000 2484 3254 1 chr5D.!!$F2 770
34 TraesCS1B01G111000 chr1D 339169610 339170363 753 True 839.000000 839 86.693000 2484 3256 1 chr1D.!!$R2 772
35 TraesCS1B01G111000 chr1D 154363223 154363968 745 True 824.000000 824 86.528000 2484 3254 1 chr1D.!!$R1 770
36 TraesCS1B01G111000 chr6D 358893668 358894426 758 False 821.000000 821 86.136000 2480 3256 1 chr6D.!!$F1 776
37 TraesCS1B01G111000 chr3A 518834453 518835202 749 False 793.000000 793 85.714000 2484 3252 1 chr3A.!!$F1 768
38 TraesCS1B01G111000 chr6B 449334319 449335073 754 False 752.000000 752 84.685000 2483 3256 1 chr6B.!!$F1 773


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
353 357 0.679960 ATGCCGGTTAAGGAGCCAAC 60.680 55.0 1.90 0.00 0.00 3.77 F
1623 5675 0.761187 ACTATCATGCCATGGCGACT 59.239 50.0 30.87 15.88 45.51 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1972 6025 0.893727 GCCGTCTTGGGGTTGTCAAT 60.894 55.0 0.00 0.00 38.63 2.57 R
3059 7254 0.107897 TTAGCGCAATGGTCCACGAT 60.108 50.0 11.47 0.69 0.00 3.73 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
27 28 5.971763 AGGATTGTATTGGAGCTATCGATC 58.028 41.667 0.00 0.00 0.00 3.69
70 71 1.915141 ACCAAAGATGTGGAGCCTTG 58.085 50.000 0.00 0.00 41.65 3.61
153 154 3.376859 CCGCTTCACATATGTTTTGGCTA 59.623 43.478 5.37 0.00 0.00 3.93
245 246 1.616865 CCACCTGGTAAGAAGTCGACA 59.383 52.381 19.50 0.00 0.00 4.35
344 348 3.770933 ACTACCTAGTTGATGCCGGTTAA 59.229 43.478 1.90 0.00 31.13 2.01
353 357 0.679960 ATGCCGGTTAAGGAGCCAAC 60.680 55.000 1.90 0.00 0.00 3.77
375 379 1.762370 CAGGGTTCTTGCCACCTTTTT 59.238 47.619 0.00 0.00 34.36 1.94
376 380 2.039418 AGGGTTCTTGCCACCTTTTTC 58.961 47.619 0.00 0.00 34.36 2.29
490 494 1.272704 GGTGGAGAGGGCTTTTGGATT 60.273 52.381 0.00 0.00 0.00 3.01
491 495 2.095461 GTGGAGAGGGCTTTTGGATTC 58.905 52.381 0.00 0.00 0.00 2.52
494 498 2.291865 GGAGAGGGCTTTTGGATTCCTT 60.292 50.000 3.95 0.00 0.00 3.36
542 546 5.538053 TGATGCCAAACCATTCTTCACTTTA 59.462 36.000 0.00 0.00 0.00 1.85
543 547 6.211184 TGATGCCAAACCATTCTTCACTTTAT 59.789 34.615 0.00 0.00 0.00 1.40
664 668 3.005367 ACCCAACCAATTCGAACATCAAC 59.995 43.478 0.00 0.00 0.00 3.18
665 669 3.255642 CCCAACCAATTCGAACATCAACT 59.744 43.478 0.00 0.00 0.00 3.16
767 773 7.338957 TCATGTATGCAAATTTATGAGTGACCA 59.661 33.333 0.00 0.00 0.00 4.02
994 1079 2.777114 TGGCTGGGCAGATTGTATCTTA 59.223 45.455 0.00 0.00 37.58 2.10
1043 1131 6.978343 ATGATTTCATCCATTTTGTTGCAG 57.022 33.333 0.00 0.00 28.78 4.41
1075 1164 4.207165 GGCTGGGCAGATTGTATCTTTAA 58.793 43.478 0.00 0.00 37.58 1.52
1076 1165 4.829492 GGCTGGGCAGATTGTATCTTTAAT 59.171 41.667 0.00 0.00 37.58 1.40
1077 1166 6.003950 GGCTGGGCAGATTGTATCTTTAATA 58.996 40.000 0.00 0.00 37.58 0.98
1078 1167 6.660949 GGCTGGGCAGATTGTATCTTTAATAT 59.339 38.462 0.00 0.00 37.58 1.28
1079 1168 7.362401 GGCTGGGCAGATTGTATCTTTAATATG 60.362 40.741 0.00 0.00 37.58 1.78
1080 1169 7.175641 GCTGGGCAGATTGTATCTTTAATATGT 59.824 37.037 0.00 0.00 37.58 2.29
1081 1170 8.995027 TGGGCAGATTGTATCTTTAATATGTT 57.005 30.769 0.00 0.00 37.58 2.71
1082 1171 9.066892 TGGGCAGATTGTATCTTTAATATGTTC 57.933 33.333 0.00 0.00 37.58 3.18
1360 1493 6.931281 TCACTTCTGATCAAGTTAGAAACCAG 59.069 38.462 0.00 0.00 34.17 4.00
1492 1632 5.175859 GCAAGTCACTGTATGGTAAGCTTA 58.824 41.667 0.86 0.86 0.00 3.09
1623 5675 0.761187 ACTATCATGCCATGGCGACT 59.239 50.000 30.87 15.88 45.51 4.18
1660 5713 1.322442 GGCTAAGGGGATGAATGCAC 58.678 55.000 0.00 0.00 0.00 4.57
1705 5758 6.228995 TCTATTGACATTGATGATGAGGAGC 58.771 40.000 0.00 0.00 39.15 4.70
1878 5931 3.864789 ACTCTTGTGAAATCTGGTGGT 57.135 42.857 0.00 0.00 0.00 4.16
1880 5933 2.816087 CTCTTGTGAAATCTGGTGGTGG 59.184 50.000 0.00 0.00 0.00 4.61
1931 5984 6.497259 TGGGATGTAGTCTCTAGTTTGAAAGT 59.503 38.462 0.00 0.00 0.00 2.66
1972 6025 5.823861 TGCCCACTATTATGCTCATCTTA 57.176 39.130 0.00 0.00 0.00 2.10
2016 6073 3.077359 AGCCTTCATGAAACTTTCCGAG 58.923 45.455 9.88 0.00 0.00 4.63
2144 6214 4.021981 GCCATTGGGTTGCTTTAGGATATC 60.022 45.833 4.53 0.00 36.17 1.63
2147 6217 5.708736 TTGGGTTGCTTTAGGATATCTGA 57.291 39.130 2.05 0.00 0.00 3.27
2556 6749 2.743752 CGGCGTTGGTGATGAGCTG 61.744 63.158 0.00 0.00 0.00 4.24
2608 6802 2.348998 CTGCGGTCCAAGAAGGCT 59.651 61.111 0.00 0.00 37.29 4.58
2609 6803 1.302832 CTGCGGTCCAAGAAGGCTT 60.303 57.895 0.00 0.00 37.29 4.35
2673 6867 4.041740 CGATTTTCTCGTAGATGTGGGA 57.958 45.455 0.00 0.00 42.56 4.37
2682 6876 5.833667 TCTCGTAGATGTGGGAGATTATGTT 59.166 40.000 0.00 0.00 33.89 2.71
2693 6887 5.665360 TGGGAGATTATGTTGATGGTGTCTA 59.335 40.000 0.00 0.00 0.00 2.59
2702 6896 3.391665 ATGGTGTCTAGCTGCGCCC 62.392 63.158 4.18 0.00 34.57 6.13
2704 6898 4.129737 GTGTCTAGCTGCGCCCGA 62.130 66.667 4.18 0.00 0.00 5.14
2813 7007 0.988832 ACCATAAAGGCCGTTGAGGA 59.011 50.000 23.71 2.88 43.14 3.71
2817 7011 0.988832 TAAAGGCCGTTGAGGATGGT 59.011 50.000 14.75 0.00 45.00 3.55
2830 7024 1.451927 GATGGTGGGCATCGCAGAA 60.452 57.895 0.00 0.00 43.58 3.02
2836 7030 3.512516 GGCATCGCAGAACCTGGC 61.513 66.667 0.00 0.00 43.58 4.85
2842 7036 1.973281 CGCAGAACCTGGCCATGTT 60.973 57.895 24.40 24.40 31.21 2.71
2862 7056 1.153628 GCTGGAGGCGTACGTCAAT 60.154 57.895 23.51 1.02 32.18 2.57
2910 7104 3.319122 GTGAACTTGTTGAGGAAGCCAAT 59.681 43.478 0.00 0.00 0.00 3.16
2913 7107 2.887152 ACTTGTTGAGGAAGCCAATGAC 59.113 45.455 0.00 0.00 0.00 3.06
2917 7111 0.976641 TGAGGAAGCCAATGACGAGT 59.023 50.000 0.00 0.00 0.00 4.18
2934 7128 3.120792 CGAGTTCGTCAAACAAGGAGAA 58.879 45.455 0.00 0.00 40.56 2.87
2983 7178 4.680237 CGGCCTCAAGCACGACCA 62.680 66.667 0.00 0.00 46.50 4.02
3041 7236 1.133976 GTGGACCATCTGGCATAGCTT 60.134 52.381 0.00 0.00 39.32 3.74
3042 7237 1.141657 TGGACCATCTGGCATAGCTTC 59.858 52.381 0.00 0.00 39.32 3.86
3043 7238 1.419387 GGACCATCTGGCATAGCTTCT 59.581 52.381 0.00 0.00 39.32 2.85
3044 7239 2.634940 GGACCATCTGGCATAGCTTCTA 59.365 50.000 0.00 0.00 39.32 2.10
3046 7241 2.636893 ACCATCTGGCATAGCTTCTAGG 59.363 50.000 0.00 0.00 39.32 3.02
3047 7242 2.027377 CCATCTGGCATAGCTTCTAGGG 60.027 54.545 0.00 0.00 0.00 3.53
3048 7243 2.478872 TCTGGCATAGCTTCTAGGGT 57.521 50.000 0.00 0.00 0.00 4.34
3049 7244 2.042464 TCTGGCATAGCTTCTAGGGTG 58.958 52.381 0.00 0.00 0.00 4.61
3050 7245 1.765314 CTGGCATAGCTTCTAGGGTGT 59.235 52.381 0.00 0.00 0.00 4.16
3051 7246 1.486310 TGGCATAGCTTCTAGGGTGTG 59.514 52.381 0.00 0.00 0.00 3.82
3052 7247 1.762957 GGCATAGCTTCTAGGGTGTGA 59.237 52.381 0.00 0.00 0.00 3.58
3053 7248 2.483889 GGCATAGCTTCTAGGGTGTGAC 60.484 54.545 0.00 0.00 0.00 3.67
3054 7249 2.483889 GCATAGCTTCTAGGGTGTGACC 60.484 54.545 0.00 0.00 37.60 4.02
3055 7250 2.615986 TAGCTTCTAGGGTGTGACCA 57.384 50.000 0.00 0.00 41.02 4.02
3056 7251 1.958288 AGCTTCTAGGGTGTGACCAT 58.042 50.000 0.00 0.00 41.02 3.55
3057 7252 1.834263 AGCTTCTAGGGTGTGACCATC 59.166 52.381 0.00 0.00 41.02 3.51
3058 7253 1.134371 GCTTCTAGGGTGTGACCATCC 60.134 57.143 0.00 0.00 42.74 3.51
3059 7254 2.187958 CTTCTAGGGTGTGACCATCCA 58.812 52.381 0.00 0.00 45.07 3.41
3060 7255 2.568546 TCTAGGGTGTGACCATCCAT 57.431 50.000 0.00 0.00 45.07 3.41
3061 7256 2.398588 TCTAGGGTGTGACCATCCATC 58.601 52.381 0.00 0.00 45.07 3.51
3062 7257 1.069204 CTAGGGTGTGACCATCCATCG 59.931 57.143 0.00 0.00 45.07 3.84
3063 7258 0.909610 AGGGTGTGACCATCCATCGT 60.910 55.000 0.00 0.00 45.07 3.73
3064 7259 0.744414 GGGTGTGACCATCCATCGTG 60.744 60.000 0.00 0.00 41.92 4.35
3065 7260 0.744414 GGTGTGACCATCCATCGTGG 60.744 60.000 0.00 0.00 42.55 4.94
3077 7272 0.809636 CATCGTGGACCATTGCGCTA 60.810 55.000 9.73 0.00 0.00 4.26
3104 7299 3.437198 CCTCCATGGGTCTAGCTTCTAGA 60.437 52.174 13.02 0.00 0.00 2.43
3105 7300 3.826157 CTCCATGGGTCTAGCTTCTAGAG 59.174 52.174 13.02 0.00 0.00 2.43
3148 7343 5.073144 AGTGATCACTCTTTCCCTTGGTTAA 59.927 40.000 22.89 0.00 36.92 2.01
3188 7383 4.816385 GGATTTCATAGATTGAACTGGCGA 59.184 41.667 0.00 0.00 43.99 5.54
3216 7411 5.819901 GCCTTTATATGAGAAGTGCAGACTT 59.180 40.000 0.00 0.00 45.59 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 0.093535 CTTGCTCGCACATGTGTACG 59.906 55.000 26.01 21.03 36.22 3.67
70 71 1.162698 GGCCTTCCTACCACGAAAAC 58.837 55.000 0.00 0.00 0.00 2.43
153 154 0.475632 TGTGTGGACCCTTCCCATCT 60.476 55.000 0.00 0.00 42.01 2.90
168 169 4.557605 AACGGTCGCGTCGTGTGT 62.558 61.111 24.60 11.31 40.96 3.72
241 242 9.645059 ACATATGGACAATTTCTATCTATGTCG 57.355 33.333 7.80 0.00 40.92 4.35
315 319 5.041940 GGCATCAACTAGGTAGTACTTTCG 58.958 45.833 0.00 0.00 34.99 3.46
344 348 2.452491 AACCCTGGGTTGGCTCCT 60.452 61.111 29.76 3.99 45.07 3.69
353 357 2.283173 GGTGGCAAGAACCCTGGG 60.283 66.667 12.28 12.28 0.00 4.45
375 379 0.981183 AAATGGTACCTCACGCCAGA 59.019 50.000 14.36 0.00 35.56 3.86
376 380 1.086696 CAAATGGTACCTCACGCCAG 58.913 55.000 14.36 0.00 35.56 4.85
490 494 6.399639 AAATTTTGAAACGCCTCTTAAGGA 57.600 33.333 1.85 0.00 46.67 3.36
491 495 8.079809 TCTAAAATTTTGAAACGCCTCTTAAGG 58.920 33.333 13.76 0.00 46.44 2.69
494 498 8.788806 TCATCTAAAATTTTGAAACGCCTCTTA 58.211 29.630 13.76 0.00 0.00 2.10
542 546 1.275291 ACAATGTCGACTTGGACCGAT 59.725 47.619 22.82 4.34 37.14 4.18
543 547 0.677288 ACAATGTCGACTTGGACCGA 59.323 50.000 22.82 2.31 36.07 4.69
664 668 5.066505 GGCCCTATGTCACTTAATTGTTGAG 59.933 44.000 0.00 0.00 0.00 3.02
665 669 4.947388 GGCCCTATGTCACTTAATTGTTGA 59.053 41.667 0.00 0.00 0.00 3.18
802 808 5.435686 TGTCCAGCCATCAAGTAAATACT 57.564 39.130 0.00 0.00 38.39 2.12
810 816 3.581755 CACAATTTGTCCAGCCATCAAG 58.418 45.455 0.00 0.00 0.00 3.02
951 1036 6.251801 GCCATCAAAATGTTGCAATAAAATGC 59.748 34.615 0.59 0.00 46.58 3.56
1037 1125 1.730064 CAGCCATCAAAATGCTGCAAC 59.270 47.619 6.36 0.00 33.44 4.17
1043 1131 0.461339 CTGCCCAGCCATCAAAATGC 60.461 55.000 0.00 0.00 0.00 3.56
1360 1493 3.625649 ATCTTCCTCCACTTCTTGAGC 57.374 47.619 0.00 0.00 0.00 4.26
1413 1552 3.237746 TCTTCATCCCATAGAGCTCCAG 58.762 50.000 10.93 0.00 0.00 3.86
1472 1611 6.947464 ACAATAAGCTTACCATACAGTGACT 58.053 36.000 8.70 0.00 0.00 3.41
1623 5675 3.436243 AGCCCCGATTGTTCCAAAAATA 58.564 40.909 0.00 0.00 0.00 1.40
1660 5713 3.550437 AAGGAGATCATTTCCAGACCG 57.450 47.619 0.00 0.00 37.18 4.79
1705 5758 2.026915 TCTCACCATTCACCTCACCATG 60.027 50.000 0.00 0.00 0.00 3.66
1878 5931 5.022787 TCATCGGGTATATCATCATCACCA 58.977 41.667 0.00 0.00 0.00 4.17
1880 5933 5.127845 AGGTCATCGGGTATATCATCATCAC 59.872 44.000 0.00 0.00 0.00 3.06
1931 5984 3.696051 GGCAAGGTGCTCTTCATCAAATA 59.304 43.478 0.00 0.00 44.28 1.40
1972 6025 0.893727 GCCGTCTTGGGGTTGTCAAT 60.894 55.000 0.00 0.00 38.63 2.57
2016 6073 5.010012 ACTCATCCAAACAGATTTGTTGGTC 59.990 40.000 1.85 0.00 46.54 4.02
2035 6092 7.726033 AGTTCTTCTTCACATACCTACTCAT 57.274 36.000 0.00 0.00 0.00 2.90
2144 6214 6.680810 ACAACCATACATGTTCACATTTCAG 58.319 36.000 2.30 0.00 33.61 3.02
2147 6217 8.028354 CACATACAACCATACATGTTCACATTT 58.972 33.333 2.30 0.00 33.61 2.32
2286 6479 3.485947 TCGGCAGCATTTCATTTGTAC 57.514 42.857 0.00 0.00 0.00 2.90
2341 6534 4.464069 CCAGTGTTTGGTTTGGAAGAAA 57.536 40.909 0.00 0.00 42.41 2.52
2394 6587 3.143728 GTTCCGTTCCTGTGTTTGGTAT 58.856 45.455 0.00 0.00 0.00 2.73
2549 6742 3.345508 TCAGAAGCATGTTCAGCTCAT 57.654 42.857 9.64 0.00 42.53 2.90
2550 6743 2.810274 GTTCAGAAGCATGTTCAGCTCA 59.190 45.455 9.64 0.00 42.53 4.26
2556 6749 4.153986 CGACATTGTTCAGAAGCATGTTC 58.846 43.478 8.10 0.00 0.00 3.18
2608 6802 0.395311 AGGAGGACGATAGGACGCAA 60.395 55.000 0.00 0.00 43.77 4.85
2609 6803 0.818445 GAGGAGGACGATAGGACGCA 60.818 60.000 0.00 0.00 43.77 5.24
2658 6852 5.386060 ACATAATCTCCCACATCTACGAGA 58.614 41.667 0.00 0.00 35.91 4.04
2673 6867 6.286758 CAGCTAGACACCATCAACATAATCT 58.713 40.000 0.00 0.00 0.00 2.40
2702 6896 4.415501 GCTTGTCACGCAGCGTCG 62.416 66.667 19.98 13.99 38.32 5.12
2800 6994 1.002134 CACCATCCTCAACGGCCTT 60.002 57.895 0.00 0.00 0.00 4.35
2813 7007 1.750399 GTTCTGCGATGCCCACCAT 60.750 57.895 0.00 0.00 36.70 3.55
2817 7011 2.046023 CAGGTTCTGCGATGCCCA 60.046 61.111 0.00 0.00 0.00 5.36
2836 7030 2.535485 TACGCCTCCAGCCAACATGG 62.535 60.000 0.00 0.00 41.55 3.66
2842 7036 3.755628 GACGTACGCCTCCAGCCA 61.756 66.667 16.72 0.00 38.78 4.75
2862 7056 0.737367 CAAGAAGCTCGCGGATGACA 60.737 55.000 6.13 0.00 0.00 3.58
2913 7107 2.739292 TCTCCTTGTTTGACGAACTCG 58.261 47.619 7.10 0.00 46.33 4.18
2917 7111 4.766375 ACTTCTTCTCCTTGTTTGACGAA 58.234 39.130 0.00 0.00 0.00 3.85
2934 7128 1.270358 GCCTCTTGGACGACAACTTCT 60.270 52.381 0.00 0.00 34.76 2.85
2983 7178 1.179814 AGCACCGAGGAACGTCTCTT 61.180 55.000 0.00 0.00 40.78 2.85
3041 7236 2.398588 GATGGATGGTCACACCCTAGA 58.601 52.381 0.00 0.00 37.50 2.43
3042 7237 1.069204 CGATGGATGGTCACACCCTAG 59.931 57.143 0.00 0.00 37.50 3.02
3043 7238 1.119684 CGATGGATGGTCACACCCTA 58.880 55.000 0.00 0.00 37.50 3.53
3044 7239 0.909610 ACGATGGATGGTCACACCCT 60.910 55.000 0.00 0.00 37.50 4.34
3046 7241 0.744414 CCACGATGGATGGTCACACC 60.744 60.000 0.00 0.00 40.96 4.16
3047 7242 0.249120 TCCACGATGGATGGTCACAC 59.751 55.000 3.02 0.00 42.67 3.82
3048 7243 2.677508 TCCACGATGGATGGTCACA 58.322 52.632 3.02 0.00 42.67 3.58
3056 7251 1.449423 CGCAATGGTCCACGATGGA 60.449 57.895 0.00 3.02 45.98 3.41
3057 7252 3.101209 CGCAATGGTCCACGATGG 58.899 61.111 0.00 0.00 39.43 3.51
3058 7253 0.809636 TAGCGCAATGGTCCACGATG 60.810 55.000 11.47 1.21 0.00 3.84
3059 7254 0.107897 TTAGCGCAATGGTCCACGAT 60.108 50.000 11.47 0.69 0.00 3.73
3060 7255 0.107897 ATTAGCGCAATGGTCCACGA 60.108 50.000 11.47 0.00 0.00 4.35
3061 7256 0.304705 GATTAGCGCAATGGTCCACG 59.695 55.000 11.47 0.00 0.00 4.94
3062 7257 0.304705 CGATTAGCGCAATGGTCCAC 59.695 55.000 11.47 0.00 0.00 4.02
3063 7258 2.689083 CGATTAGCGCAATGGTCCA 58.311 52.632 11.47 0.00 0.00 4.02
3077 7272 1.051812 CTAGACCCATGGAGGCGATT 58.948 55.000 15.22 0.00 35.39 3.34
3148 7343 0.251474 TCCTACACACCTACGCACCT 60.251 55.000 0.00 0.00 0.00 4.00
3188 7383 4.410228 TGCACTTCTCATATAAAGGCTCCT 59.590 41.667 0.00 0.00 0.00 3.69



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

AutoCloner maintained by Alex Coulton.