Multiple sequence alignment - TraesCS7D01G443800

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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 TraesCS7D01G443800 chr7D 100.000 2320 0 0 2054 4373 564531793 564529474 0.000000e+00 4285.0
1 TraesCS7D01G443800 chr7D 100.000 1566 0 0 1 1566 564533846 564532281 0.000000e+00 2892.0
2 TraesCS7D01G443800 chr7D 91.556 450 26 8 3934 4373 564340734 564340287 1.040000e-170 610.0
3 TraesCS7D01G443800 chr7D 93.316 389 25 1 3536 3924 564341203 564340816 1.360000e-159 573.0
4 TraesCS7D01G443800 chr7D 85.472 530 72 4 3205 3733 564313854 564313329 8.270000e-152 547.0
5 TraesCS7D01G443800 chr7B 89.484 1569 117 24 12 1553 614295172 614296719 0.000000e+00 1940.0
6 TraesCS7D01G443800 chr7B 88.335 1243 113 21 2696 3924 614297295 614298519 0.000000e+00 1463.0
7 TraesCS7D01G443800 chr7B 85.958 762 90 11 2855 3607 614299932 614300685 0.000000e+00 798.0
8 TraesCS7D01G443800 chr7B 90.441 544 44 8 2057 2597 614296751 614297289 0.000000e+00 710.0
9 TraesCS7D01G443800 chr7B 89.648 454 32 3 3934 4373 614298600 614299052 8.210000e-157 564.0
10 TraesCS7D01G443800 chr7A 88.042 1246 120 15 2694 3927 649802634 649803862 0.000000e+00 1448.0
11 TraesCS7D01G443800 chr7A 88.439 1185 68 27 2057 3213 649480887 649482030 0.000000e+00 1365.0
12 TraesCS7D01G443800 chr7A 82.368 1208 131 40 376 1535 649800790 649801963 0.000000e+00 976.0
13 TraesCS7D01G443800 chr7A 86.936 842 84 18 2867 3693 649805133 649805963 0.000000e+00 922.0
14 TraesCS7D01G443800 chr7A 82.973 787 105 21 6 780 649478583 649479352 0.000000e+00 684.0
15 TraesCS7D01G443800 chr7A 89.338 544 41 12 2057 2597 649802101 649802630 0.000000e+00 667.0
16 TraesCS7D01G443800 chr7A 89.404 453 23 14 3934 4367 649803941 649804387 8.270000e-152 547.0
17 TraesCS7D01G443800 chr7A 84.532 278 32 10 336 607 649426419 649426691 9.330000e-67 265.0
18 TraesCS7D01G443800 chr3D 90.356 477 37 5 2106 2582 318683023 318683490 6.210000e-173 617.0
19 TraesCS7D01G443800 chr3D 87.597 387 29 9 781 1157 318682147 318682524 8.690000e-117 431.0
20 TraesCS7D01G443800 chr3D 84.549 233 32 4 1336 1566 318682727 318682957 1.220000e-55 228.0
21 TraesCS7D01G443800 chr3A 89.813 481 33 7 2106 2582 725527645 725527177 1.740000e-168 603.0
22 TraesCS7D01G443800 chr3A 89.813 481 33 7 2106 2582 725611667 725611199 1.740000e-168 603.0
23 TraesCS7D01G443800 chr3A 89.605 481 34 7 2106 2582 725569335 725568867 8.100000e-167 597.0
24 TraesCS7D01G443800 chr3A 88.068 352 23 8 781 1122 725550374 725550032 2.450000e-107 399.0
25 TraesCS7D01G443800 chr3A 87.500 352 25 6 781 1122 725592906 725592564 5.300000e-104 388.0
26 TraesCS7D01G443800 chr3A 87.500 352 25 8 781 1122 725633899 725633557 5.300000e-104 388.0
27 TraesCS7D01G443800 chr3A 84.979 233 31 4 1336 1566 725527941 725527711 2.630000e-57 233.0
28 TraesCS7D01G443800 chr3A 84.979 233 31 4 1336 1566 725611963 725611733 2.630000e-57 233.0
29 TraesCS7D01G443800 chr3A 84.549 233 32 4 1336 1566 725569631 725569401 1.220000e-55 228.0
30 TraesCS7D01G443800 chr2A 90.796 402 28 5 2106 2507 532362122 532361730 3.000000e-146 529.0
31 TraesCS7D01G443800 chr2A 86.458 384 31 11 783 1155 532362995 532362622 6.810000e-108 401.0
32 TraesCS7D01G443800 chr2A 83.262 233 35 4 1336 1566 532362418 532362188 1.230000e-50 211.0
33 TraesCS7D01G443800 chr5A 87.284 464 50 7 6 468 614168416 614168871 5.010000e-144 521.0
34 TraesCS7D01G443800 chr5A 83.425 181 19 9 2057 2234 543168238 543168410 1.630000e-34 158.0
35 TraesCS7D01G443800 chr6A 86.207 464 56 6 6 468 304900628 304901084 3.040000e-136 496.0
36 TraesCS7D01G443800 chr6A 87.382 317 21 13 860 1157 207162388 207162072 3.240000e-91 346.0
37 TraesCS7D01G443800 chr6A 92.391 184 14 0 2399 2582 207161559 207161376 3.350000e-66 263.0
38 TraesCS7D01G443800 chr6A 83.691 233 34 4 1336 1566 207161866 207161636 2.650000e-52 217.0
39 TraesCS7D01G443800 chr6A 86.154 65 5 4 470 531 571020154 571020091 2.820000e-07 67.6
40 TraesCS7D01G443800 chr4B 86.207 464 56 6 6 468 359900087 359900543 3.040000e-136 496.0
41 TraesCS7D01G443800 chr1A 85.915 355 43 5 115 468 562697575 562697227 5.340000e-99 372.0
42 TraesCS7D01G443800 chr1A 92.537 67 5 0 1415 1481 295543749 295543683 3.600000e-16 97.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G443800 chr7D 564529474 564533846 4372 True 3588.500000 4285 100.000000 1 4373 2 chr7D.!!$R3 4372
1 TraesCS7D01G443800 chr7D 564340287 564341203 916 True 591.500000 610 92.436000 3536 4373 2 chr7D.!!$R2 837
2 TraesCS7D01G443800 chr7D 564313329 564313854 525 True 547.000000 547 85.472000 3205 3733 1 chr7D.!!$R1 528
3 TraesCS7D01G443800 chr7B 614295172 614300685 5513 False 1095.000000 1940 88.773200 12 4373 5 chr7B.!!$F1 4361
4 TraesCS7D01G443800 chr7A 649478583 649482030 3447 False 1024.500000 1365 85.706000 6 3213 2 chr7A.!!$F2 3207
5 TraesCS7D01G443800 chr7A 649800790 649805963 5173 False 912.000000 1448 87.217600 376 4367 5 chr7A.!!$F3 3991
6 TraesCS7D01G443800 chr3D 318682147 318683490 1343 False 425.333333 617 87.500667 781 2582 3 chr3D.!!$F1 1801
7 TraesCS7D01G443800 chr3A 725527177 725527941 764 True 418.000000 603 87.396000 1336 2582 2 chr3A.!!$R4 1246
8 TraesCS7D01G443800 chr3A 725611199 725611963 764 True 418.000000 603 87.396000 1336 2582 2 chr3A.!!$R6 1246
9 TraesCS7D01G443800 chr3A 725568867 725569631 764 True 412.500000 597 87.077000 1336 2582 2 chr3A.!!$R5 1246
10 TraesCS7D01G443800 chr2A 532361730 532362995 1265 True 380.333333 529 86.838667 783 2507 3 chr2A.!!$R1 1724
11 TraesCS7D01G443800 chr6A 207161376 207162388 1012 True 275.333333 346 87.821333 860 2582 3 chr6A.!!$R2 1722

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
178 179 0.041090 AATCCCCACACCCCAATCAC 59.959 55.0 0.00 0.0 0.00 3.06 F
283 286 0.304705 CATCCGATTAACAGCACCGC 59.695 55.0 0.00 0.0 0.00 5.68 F
437 442 0.631753 AGATCAGTCGGGGAGAGGAA 59.368 55.0 0.00 0.0 0.00 3.36 F
1487 1586 0.960364 ATGGCGGTCGCAGTTCATTT 60.960 50.0 17.21 0.0 44.11 2.32 F
2764 4234 0.535335 GGCACGGTTCTCCATGTAGA 59.465 55.0 0.00 0.0 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1231 1311 0.036577 CAAGTGCCTGTCAGAGAGGG 60.037 60.0 15.42 0.0 0.00 4.30 R
1286 1368 0.836606 TTGCTGTCAGACCCTCACAA 59.163 50.0 3.32 0.0 0.00 3.33 R
2080 3517 0.865769 CACAACCAGTTGACGGTAGC 59.134 55.0 17.06 0.0 42.93 3.58 R
2880 4350 0.312102 GTCCAGAAAGCTTGCACCAC 59.688 55.0 7.33 0.0 0.00 4.16 R
3762 5248 0.593128 CAAAGAGGGAACTGGCAACG 59.407 55.0 0.00 0.0 44.43 4.10 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
34 35 9.290988 CTGGAGACTAATGTATTCTCTAGCTTA 57.709 37.037 0.00 0.00 36.69 3.09
60 61 2.806434 CCAATGGGGTCACAAGATGAA 58.194 47.619 0.00 0.00 39.72 2.57
78 79 6.466812 AGATGAAAATTCAAACCAACCCATC 58.533 36.000 0.00 0.00 41.13 3.51
83 84 0.250989 TCAAACCAACCCATCCGTCC 60.251 55.000 0.00 0.00 0.00 4.79
89 90 1.546773 CCAACCCATCCGTCCTTCAAA 60.547 52.381 0.00 0.00 0.00 2.69
100 101 4.812626 TCCGTCCTTCAAACAAGTTAACTC 59.187 41.667 8.95 0.00 0.00 3.01
128 129 3.182590 AAGGACCTGAGCTGCGCAA 62.183 57.895 13.05 0.00 0.00 4.85
131 132 2.033141 ACCTGAGCTGCGCAATGT 59.967 55.556 13.05 5.04 0.00 2.71
143 144 3.009026 TGCGCAATGTGATACTGAATGT 58.991 40.909 8.16 0.00 0.00 2.71
144 145 4.187694 TGCGCAATGTGATACTGAATGTA 58.812 39.130 8.16 0.00 35.37 2.29
169 170 0.693049 AGTGTCTCCAATCCCCACAC 59.307 55.000 0.00 0.00 38.10 3.82
178 179 0.041090 AATCCCCACACCCCAATCAC 59.959 55.000 0.00 0.00 0.00 3.06
227 229 1.208358 CAGCAGCATCAACACGGTG 59.792 57.895 6.58 6.58 0.00 4.94
231 233 2.173382 GCATCAACACGGTGCGAC 59.827 61.111 8.30 0.00 0.00 5.19
243 245 4.171005 CACGGTGCGACTTAAGAGAAATA 58.829 43.478 10.09 0.00 0.00 1.40
247 249 4.031426 GGTGCGACTTAAGAGAAATACACG 59.969 45.833 10.09 0.00 0.00 4.49
255 257 6.324254 ACTTAAGAGAAATACACGGCTCCTAT 59.676 38.462 10.09 0.00 0.00 2.57
283 286 0.304705 CATCCGATTAACAGCACCGC 59.695 55.000 0.00 0.00 0.00 5.68
301 305 1.712018 GCATTACGAAACCCCGCTCC 61.712 60.000 0.00 0.00 0.00 4.70
344 348 1.940883 AACATTCTACCGAGCGCCGA 61.941 55.000 17.96 0.22 41.76 5.54
374 378 4.897076 TGTAAATCTACCGAATCTGGGCTA 59.103 41.667 0.00 0.00 0.00 3.93
392 397 2.549349 GCTAGTTCGGAAACCAGGACAA 60.549 50.000 0.00 0.00 35.92 3.18
404 409 0.866061 CAGGACAATCGCTACGACCG 60.866 60.000 0.00 0.00 39.18 4.79
427 432 1.264557 CGCAGGTACCTAGATCAGTCG 59.735 57.143 15.80 5.71 0.00 4.18
428 433 1.609555 GCAGGTACCTAGATCAGTCGG 59.390 57.143 15.80 0.00 0.00 4.79
431 436 1.144503 GGTACCTAGATCAGTCGGGGA 59.855 57.143 4.06 0.00 0.00 4.81
437 442 0.631753 AGATCAGTCGGGGAGAGGAA 59.368 55.000 0.00 0.00 0.00 3.36
559 569 1.002087 GAAAGCTCAAAGGGTCGGAGA 59.998 52.381 0.00 0.00 0.00 3.71
877 898 1.227853 GGTGGTTGCGAGGTGAGTT 60.228 57.895 0.00 0.00 0.00 3.01
880 901 1.227853 GGTTGCGAGGTGAGTTGGT 60.228 57.895 0.00 0.00 0.00 3.67
909 932 2.362503 TCTCCGTCGATGGTGCCT 60.363 61.111 22.88 0.00 0.00 4.75
927 950 4.030216 TGCCTAGTAGGATTCATGTGTGA 58.970 43.478 21.02 0.00 37.67 3.58
975 1005 4.104738 TCCTTTTCTTGGAGTGACAGGAAT 59.895 41.667 0.00 0.00 36.52 3.01
989 1027 1.628340 CAGGAATAGTGGTGGTGGTGA 59.372 52.381 0.00 0.00 0.00 4.02
990 1028 2.239654 CAGGAATAGTGGTGGTGGTGAT 59.760 50.000 0.00 0.00 0.00 3.06
1125 1169 1.686110 GGATGTCGTCCAGGTCCCT 60.686 63.158 6.19 0.00 46.96 4.20
1131 1175 2.450243 GTCCAGGTCCCTCCCTCA 59.550 66.667 0.00 0.00 36.75 3.86
1163 1240 2.035632 CCCTCCCTCTCTGACATGTAC 58.964 57.143 0.00 0.00 0.00 2.90
1164 1241 2.358721 CCCTCCCTCTCTGACATGTACT 60.359 54.545 0.00 0.00 0.00 2.73
1165 1242 3.370104 CCTCCCTCTCTGACATGTACTT 58.630 50.000 0.00 0.00 0.00 2.24
1211 1291 6.482973 TCGATGATGCAACAGCTAAAATGATA 59.517 34.615 10.59 0.00 0.00 2.15
1213 1293 7.806487 CGATGATGCAACAGCTAAAATGATATT 59.194 33.333 10.59 0.00 0.00 1.28
1214 1294 9.125906 GATGATGCAACAGCTAAAATGATATTC 57.874 33.333 4.82 0.00 0.00 1.75
1216 1296 8.132995 TGATGCAACAGCTAAAATGATATTCAG 58.867 33.333 0.00 0.00 0.00 3.02
1217 1297 7.628769 TGCAACAGCTAAAATGATATTCAGA 57.371 32.000 0.00 0.00 0.00 3.27
1221 1301 9.713740 CAACAGCTAAAATGATATTCAGAAGAC 57.286 33.333 0.00 0.00 0.00 3.01
1224 1304 9.107177 CAGCTAAAATGATATTCAGAAGACACT 57.893 33.333 0.00 0.00 0.00 3.55
1225 1305 9.678260 AGCTAAAATGATATTCAGAAGACACTT 57.322 29.630 0.00 0.00 0.00 3.16
1229 1309 8.738645 AAATGATATTCAGAAGACACTTACCC 57.261 34.615 0.00 0.00 0.00 3.69
1231 1311 7.113658 TGATATTCAGAAGACACTTACCCTC 57.886 40.000 0.00 0.00 0.00 4.30
1232 1312 4.828072 ATTCAGAAGACACTTACCCTCC 57.172 45.455 0.00 0.00 0.00 4.30
1233 1313 2.537143 TCAGAAGACACTTACCCTCCC 58.463 52.381 0.00 0.00 0.00 4.30
1235 1315 2.498078 CAGAAGACACTTACCCTCCCTC 59.502 54.545 0.00 0.00 0.00 4.30
1236 1316 2.384029 AGAAGACACTTACCCTCCCTCT 59.616 50.000 0.00 0.00 0.00 3.69
1237 1317 2.535836 AGACACTTACCCTCCCTCTC 57.464 55.000 0.00 0.00 0.00 3.20
1238 1318 2.004589 AGACACTTACCCTCCCTCTCT 58.995 52.381 0.00 0.00 0.00 3.10
1239 1319 2.104170 GACACTTACCCTCCCTCTCTG 58.896 57.143 0.00 0.00 0.00 3.35
1240 1320 1.717077 ACACTTACCCTCCCTCTCTGA 59.283 52.381 0.00 0.00 0.00 3.27
1241 1321 2.104170 CACTTACCCTCCCTCTCTGAC 58.896 57.143 0.00 0.00 0.00 3.51
1254 1334 3.558746 CCTCTCTGACAGGCACTTGATTT 60.559 47.826 1.81 0.00 34.60 2.17
1286 1368 7.549488 GCTGGTTTAGTTCATCAACTGTACTAT 59.451 37.037 0.00 0.00 43.17 2.12
1299 1384 4.673968 ACTGTACTATTGTGAGGGTCTGA 58.326 43.478 0.00 0.00 0.00 3.27
1302 1387 4.462834 TGTACTATTGTGAGGGTCTGACAG 59.537 45.833 10.38 0.00 28.29 3.51
1437 1535 5.730296 ACCAGAATGATTCCTATCCTACG 57.270 43.478 0.75 0.00 39.69 3.51
1487 1586 0.960364 ATGGCGGTCGCAGTTCATTT 60.960 50.000 17.21 0.00 44.11 2.32
1554 2991 2.752030 AGTAGCTGATCTGGGCACTTA 58.248 47.619 0.00 0.00 0.00 2.24
2080 3517 2.027003 TTTCCTGTAATTACCGGGCG 57.973 50.000 21.71 1.83 32.22 6.13
2102 3539 2.177580 CCGTCAACTGGTTGTGCGT 61.178 57.895 20.60 0.00 41.16 5.24
2112 3549 0.917939 GGTTGTGCGTTTTTCCAACG 59.082 50.000 2.76 2.76 45.56 4.10
2117 3554 2.159366 TGTGCGTTTTTCCAACGAATGT 60.159 40.909 11.15 0.00 45.64 2.71
2146 3583 3.489355 TGGCTCTGTGTTTCATCATGTT 58.511 40.909 0.00 0.00 0.00 2.71
2163 3603 9.076781 TCATCATGTTAATTCCAAGTCTGAAAA 57.923 29.630 0.00 0.00 0.00 2.29
2419 3868 6.506500 AAGCAGTATCTGAGGAAAATGTTG 57.493 37.500 0.66 0.00 32.44 3.33
2464 3914 8.183830 TGCTCATGTTAAACTGTTTCTTTTTG 57.816 30.769 9.38 3.44 0.00 2.44
2598 4048 5.140747 CGAAAGCCTAATATGAGCCTACT 57.859 43.478 0.00 0.00 0.00 2.57
2653 4104 3.637273 GGAGTTGGTCAGCCCGGT 61.637 66.667 0.00 0.00 35.15 5.28
2655 4106 1.675219 GAGTTGGTCAGCCCGGTTA 59.325 57.895 0.00 0.00 35.15 2.85
2656 4107 0.672711 GAGTTGGTCAGCCCGGTTAC 60.673 60.000 0.00 0.00 35.15 2.50
2657 4108 1.071814 GTTGGTCAGCCCGGTTACA 59.928 57.895 0.00 0.00 35.15 2.41
2688 4158 3.868661 CACACACACAGTACAAACTAGCA 59.131 43.478 0.00 0.00 33.48 3.49
2728 4198 7.851508 AGAATTAAATATCGAACATGACACGG 58.148 34.615 0.00 0.00 0.00 4.94
2764 4234 0.535335 GGCACGGTTCTCCATGTAGA 59.465 55.000 0.00 0.00 0.00 2.59
2786 4256 6.823497 AGATGCAAATCCCTGAAATTTATGG 58.177 36.000 0.00 0.00 0.00 2.74
2816 4286 1.200760 TGCCTACCTCTGTGCCATGT 61.201 55.000 0.00 0.00 0.00 3.21
2817 4287 0.830648 GCCTACCTCTGTGCCATGTA 59.169 55.000 0.00 0.00 0.00 2.29
2818 4288 1.417890 GCCTACCTCTGTGCCATGTAT 59.582 52.381 0.00 0.00 0.00 2.29
2819 4289 2.808202 GCCTACCTCTGTGCCATGTATG 60.808 54.545 0.00 0.00 0.00 2.39
2820 4290 2.700371 CCTACCTCTGTGCCATGTATGA 59.300 50.000 0.00 0.00 0.00 2.15
2821 4291 3.326006 CCTACCTCTGTGCCATGTATGAT 59.674 47.826 0.00 0.00 0.00 2.45
2822 4292 3.204306 ACCTCTGTGCCATGTATGATG 57.796 47.619 0.00 0.00 0.00 3.07
2823 4293 1.878088 CCTCTGTGCCATGTATGATGC 59.122 52.381 0.00 0.00 0.00 3.91
2863 4333 4.082026 TGTTAGAAAGGTAGTTCGGTAGGC 60.082 45.833 0.00 0.00 32.50 3.93
2880 4350 0.970427 GGCTGGTTGGGTAACATGGG 60.970 60.000 0.00 0.00 38.58 4.00
2935 4405 3.291611 GCTGGGCCAGAAACCATG 58.708 61.111 37.07 9.42 35.93 3.66
2936 4406 2.353610 GCTGGGCCAGAAACCATGG 61.354 63.158 37.07 11.19 41.04 3.66
3027 4505 7.108847 TGTCCACCAAAATTGAACAAAAGAAT 58.891 30.769 0.00 0.00 0.00 2.40
3086 4568 4.361451 AGTGCTTCAAGAAACTGTTGTG 57.639 40.909 0.00 0.00 0.00 3.33
3087 4569 3.129287 AGTGCTTCAAGAAACTGTTGTGG 59.871 43.478 0.00 0.00 0.00 4.17
3128 4610 6.708054 GGAAGGACTCCATATATGTGTGAAAG 59.292 42.308 11.73 2.48 44.67 2.62
3196 4678 7.333921 GCTAGCGAGTATCCACTATAGTTTCTA 59.666 40.741 1.56 0.00 34.21 2.10
3213 4695 7.369803 AGTTTCTAGTGCACATACATTTCAG 57.630 36.000 21.04 1.84 0.00 3.02
3306 4790 1.004044 ACTGTGATTTGCAGGGAGGAG 59.996 52.381 0.00 0.00 38.22 3.69
3369 4853 1.221781 AGGGTAGAGGCCAAGCTAGAT 59.778 52.381 5.01 0.00 0.00 1.98
3382 4866 4.702131 CCAAGCTAGATTAAACAGCACCTT 59.298 41.667 0.00 0.00 37.78 3.50
3396 4880 1.666189 GCACCTTAATCCGTCTCAAGC 59.334 52.381 0.00 0.00 0.00 4.01
3413 4897 5.703592 TCTCAAGCGTGTGTGGTTATATTTT 59.296 36.000 0.00 0.00 0.00 1.82
3421 4905 7.231607 CGTGTGTGGTTATATTTTGTAGTGAC 58.768 38.462 0.00 0.00 0.00 3.67
3423 4907 6.655848 TGTGTGGTTATATTTTGTAGTGACCC 59.344 38.462 0.00 0.00 0.00 4.46
3450 4934 1.390123 CTAGGCGTCATGTTGAACACG 59.610 52.381 0.00 0.83 0.00 4.49
3470 4954 3.199071 ACGAGGCCTTGTGTTTGGATATA 59.801 43.478 25.63 0.00 0.00 0.86
3473 4957 5.299279 CGAGGCCTTGTGTTTGGATATATTT 59.701 40.000 6.77 0.00 0.00 1.40
3524 5010 6.318900 CCTATCCAGAAATAAGAAACGCCTTT 59.681 38.462 0.00 0.00 0.00 3.11
3542 5028 4.010349 CCTTTACAGGAGGTGAATTGGTC 58.990 47.826 0.00 0.00 44.19 4.02
3558 5044 0.868406 GGTCGAAGTTGCTGTTCTGG 59.132 55.000 0.00 0.00 0.00 3.86
3592 5078 5.968848 TGTAATTTCGTCTGACTTGTTTTGC 59.031 36.000 6.21 0.00 0.00 3.68
3599 5085 0.102120 TGACTTGTTTTGCGCCTTGG 59.898 50.000 4.18 0.00 0.00 3.61
3607 5093 0.955905 TTTGCGCCTTGGGAGTTAAC 59.044 50.000 4.18 0.00 0.00 2.01
3820 5306 2.426522 CAACTCATTTTGCGAGAGGGA 58.573 47.619 0.00 0.00 34.47 4.20
3833 5319 0.613260 AGAGGGATGCACGTGCTTTA 59.387 50.000 37.59 21.19 42.66 1.85
3834 5320 1.210478 AGAGGGATGCACGTGCTTTAT 59.790 47.619 37.59 24.89 42.66 1.40
3844 5330 1.014352 CGTGCTTTATGGTACCTGCC 58.986 55.000 14.36 3.91 0.00 4.85
3849 5335 3.264706 TGCTTTATGGTACCTGCCTGTTA 59.735 43.478 14.36 0.00 0.00 2.41
3910 5396 6.761714 ACCTTTCGTGATGAATACTAACATCC 59.238 38.462 0.00 0.00 41.21 3.51
3927 5413 3.058016 ACATCCAAGTTTGAGATTGCGTG 60.058 43.478 0.00 0.00 0.00 5.34
3928 5414 2.571212 TCCAAGTTTGAGATTGCGTGT 58.429 42.857 0.00 0.00 0.00 4.49
3929 5415 3.734463 TCCAAGTTTGAGATTGCGTGTA 58.266 40.909 0.00 0.00 0.00 2.90
3930 5416 4.130857 TCCAAGTTTGAGATTGCGTGTAA 58.869 39.130 0.00 0.00 0.00 2.41
3931 5417 4.576873 TCCAAGTTTGAGATTGCGTGTAAA 59.423 37.500 0.00 0.00 0.00 2.01
3936 5494 6.791303 AGTTTGAGATTGCGTGTAAAAAGAA 58.209 32.000 0.00 0.00 0.00 2.52
3942 5500 9.906660 TGAGATTGCGTGTAAAAAGAAAAATAT 57.093 25.926 0.00 0.00 0.00 1.28
3999 5557 3.960002 CGCAAAACAAACTGTCGAAGTAG 59.040 43.478 0.00 0.00 38.56 2.57
4031 5589 2.317040 AGACGGGATATAGTGTGTGGG 58.683 52.381 0.00 0.00 0.00 4.61
4120 5678 3.498018 TGTGATCACCGTGTTTCAGAATG 59.502 43.478 22.85 0.00 37.54 2.67
4184 5742 4.202233 TGCATCAGATTTTCCTTGTTGCAA 60.202 37.500 0.00 0.00 34.91 4.08
4217 5775 0.865111 TCACACGAAGAATTGCCACG 59.135 50.000 0.00 0.00 0.00 4.94
4237 5795 5.579511 CCACGGATGAAATAAACGAGTAGTT 59.420 40.000 0.00 0.00 46.76 2.24
4351 5926 2.357881 TGCCAGTGAGCAGCTTCG 60.358 61.111 0.00 0.00 38.00 3.79
4362 5937 1.351430 GCAGCTTCGTACATGCGTGA 61.351 55.000 14.17 0.00 0.00 4.35
4367 5942 2.285256 GCTTCGTACATGCGTGATTCTG 60.285 50.000 14.17 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.256228 AGAATACATTAGTCTCCAGTCTTGTTA 57.744 33.333 0.00 0.00 0.00 2.41
1 2 8.140112 AGAATACATTAGTCTCCAGTCTTGTT 57.860 34.615 0.00 0.00 0.00 2.83
52 53 6.054295 TGGGTTGGTTTGAATTTTCATCTTG 58.946 36.000 0.00 0.00 37.00 3.02
60 61 2.969262 ACGGATGGGTTGGTTTGAATTT 59.031 40.909 0.00 0.00 0.00 1.82
78 79 4.573201 TGAGTTAACTTGTTTGAAGGACGG 59.427 41.667 10.02 0.00 0.00 4.79
83 84 7.432252 GGATGTGTTGAGTTAACTTGTTTGAAG 59.568 37.037 10.02 0.00 40.05 3.02
89 90 5.299279 CCTTGGATGTGTTGAGTTAACTTGT 59.701 40.000 10.02 0.00 40.05 3.16
100 101 2.430465 CTCAGGTCCTTGGATGTGTTG 58.570 52.381 0.00 0.00 0.00 3.33
128 129 9.890629 ACACTTACATTACATTCAGTATCACAT 57.109 29.630 0.00 0.00 31.53 3.21
131 132 9.803315 GAGACACTTACATTACATTCAGTATCA 57.197 33.333 0.00 0.00 31.53 2.15
143 144 4.785914 TGGGGATTGGAGACACTTACATTA 59.214 41.667 0.00 0.00 42.67 1.90
144 145 3.591527 TGGGGATTGGAGACACTTACATT 59.408 43.478 0.00 0.00 42.67 2.71
169 170 1.935931 AAGGGGAGGGTGATTGGGG 60.936 63.158 0.00 0.00 0.00 4.96
178 179 2.040606 TCGGGAAGAAGGGGAGGG 59.959 66.667 0.00 0.00 0.00 4.30
227 229 3.000022 GCCGTGTATTTCTCTTAAGTCGC 60.000 47.826 1.63 0.00 0.00 5.19
231 233 5.012328 AGGAGCCGTGTATTTCTCTTAAG 57.988 43.478 0.00 0.00 0.00 1.85
243 245 0.255890 AATTGCCATAGGAGCCGTGT 59.744 50.000 0.00 0.00 0.00 4.49
247 249 2.560105 GGATGAAATTGCCATAGGAGCC 59.440 50.000 0.00 0.00 0.00 4.70
255 257 4.439974 GCTGTTAATCGGATGAAATTGCCA 60.440 41.667 0.00 0.00 0.00 4.92
283 286 0.391927 TGGAGCGGGGTTTCGTAATG 60.392 55.000 0.00 0.00 0.00 1.90
326 330 1.940883 TTCGGCGCTCGGTAGAATGT 61.941 55.000 7.64 0.00 39.77 2.71
344 348 6.313905 CAGATTCGGTAGATTTACAACAGCTT 59.686 38.462 0.00 0.00 0.00 3.74
354 358 3.967987 ACTAGCCCAGATTCGGTAGATTT 59.032 43.478 0.00 0.00 34.80 2.17
374 378 2.779506 GATTGTCCTGGTTTCCGAACT 58.220 47.619 0.00 0.00 36.03 3.01
404 409 1.609555 CTGATCTAGGTACCTGCGGTC 59.390 57.143 25.33 19.62 37.09 4.79
425 430 0.903454 GGTGAGTTTCCTCTCCCCGA 60.903 60.000 0.00 0.00 42.89 5.14
426 431 1.192146 TGGTGAGTTTCCTCTCCCCG 61.192 60.000 8.00 0.00 46.39 5.73
427 432 1.065126 CATGGTGAGTTTCCTCTCCCC 60.065 57.143 8.00 0.00 46.39 4.81
428 433 1.065126 CCATGGTGAGTTTCCTCTCCC 60.065 57.143 2.57 1.57 46.39 4.30
431 436 1.004044 CAGCCATGGTGAGTTTCCTCT 59.996 52.381 14.67 0.00 38.61 3.69
437 442 2.360350 CCGCAGCCATGGTGAGTT 60.360 61.111 14.67 0.00 32.22 3.01
546 556 2.970639 TCGCTCTCCGACCCTTTG 59.029 61.111 0.00 0.00 41.89 2.77
575 585 0.801067 GCCGCGCCCTCGTATATAAG 60.801 60.000 0.00 0.00 38.14 1.73
667 679 0.333312 ACCATTTCACCGGCCCAATA 59.667 50.000 0.00 0.00 0.00 1.90
698 711 5.416083 CATTTAGACCTTCGGTGTCACATA 58.584 41.667 5.12 0.00 35.25 2.29
877 898 0.333312 GGAGAGACCAGAGGAGACCA 59.667 60.000 0.00 0.00 38.79 4.02
880 901 0.253610 GACGGAGAGACCAGAGGAGA 59.746 60.000 0.00 0.00 38.90 3.71
927 950 1.488390 ATGGCGGCTCAAATCCAATT 58.512 45.000 11.43 0.00 31.66 2.32
975 1005 2.625883 CCTCCTATCACCACCACCACTA 60.626 54.545 0.00 0.00 0.00 2.74
989 1027 1.707989 TCTCGCTCATCCTCCTCCTAT 59.292 52.381 0.00 0.00 0.00 2.57
990 1028 1.073125 CTCTCGCTCATCCTCCTCCTA 59.927 57.143 0.00 0.00 0.00 2.94
1125 1169 1.267121 GGCAAGTGTCTAGTGAGGGA 58.733 55.000 0.00 0.00 0.00 4.20
1131 1175 0.117340 AGGGAGGGCAAGTGTCTAGT 59.883 55.000 0.00 0.00 0.00 2.57
1163 1240 9.905171 TCGATCTTCTGAATATCATCTACAAAG 57.095 33.333 13.91 0.00 0.00 2.77
1165 1242 9.852091 CATCGATCTTCTGAATATCATCTACAA 57.148 33.333 13.91 0.00 0.00 2.41
1211 1291 3.519913 GGGAGGGTAAGTGTCTTCTGAAT 59.480 47.826 0.00 0.00 0.00 2.57
1213 1293 2.111972 AGGGAGGGTAAGTGTCTTCTGA 59.888 50.000 0.00 0.00 0.00 3.27
1214 1294 2.498078 GAGGGAGGGTAAGTGTCTTCTG 59.502 54.545 0.00 0.00 0.00 3.02
1216 1296 2.761767 GAGAGGGAGGGTAAGTGTCTTC 59.238 54.545 0.00 0.00 0.00 2.87
1217 1297 2.384029 AGAGAGGGAGGGTAAGTGTCTT 59.616 50.000 0.00 0.00 0.00 3.01
1221 1301 2.104170 GTCAGAGAGGGAGGGTAAGTG 58.896 57.143 0.00 0.00 0.00 3.16
1224 1304 1.007238 CCTGTCAGAGAGGGAGGGTAA 59.993 57.143 5.64 0.00 0.00 2.85
1225 1305 0.631753 CCTGTCAGAGAGGGAGGGTA 59.368 60.000 5.64 0.00 0.00 3.69
1226 1306 1.390125 CCTGTCAGAGAGGGAGGGT 59.610 63.158 5.64 0.00 0.00 4.34
1228 1308 1.305633 TGCCTGTCAGAGAGGGAGG 60.306 63.158 15.42 0.00 0.00 4.30
1229 1309 0.614415 AGTGCCTGTCAGAGAGGGAG 60.614 60.000 15.42 0.00 30.44 4.30
1231 1311 0.036577 CAAGTGCCTGTCAGAGAGGG 60.037 60.000 15.42 0.00 0.00 4.30
1232 1312 0.972134 TCAAGTGCCTGTCAGAGAGG 59.028 55.000 9.41 9.41 0.00 3.69
1233 1313 3.331478 AATCAAGTGCCTGTCAGAGAG 57.669 47.619 0.00 0.00 0.00 3.20
1235 1315 4.843220 AAAAATCAAGTGCCTGTCAGAG 57.157 40.909 0.00 0.00 0.00 3.35
1254 1334 6.775629 AGTTGATGAACTAAACCAGCCTAAAA 59.224 34.615 0.00 0.00 40.85 1.52
1286 1368 0.836606 TTGCTGTCAGACCCTCACAA 59.163 50.000 3.32 0.00 0.00 3.33
1299 1384 9.816354 AAATTAAGTACTGAAACAATTTGCTGT 57.184 25.926 0.00 0.00 0.00 4.40
1437 1535 1.801178 GAAGCAGTAACCACAGCAGAC 59.199 52.381 0.00 0.00 39.51 3.51
1487 1586 5.245075 GGTCATTTCTAATTGTGTTTGGGGA 59.755 40.000 0.00 0.00 0.00 4.81
2053 3490 5.163693 CCGGTAATTACAGGAAATTCCACAC 60.164 44.000 25.44 1.21 43.08 3.82
2054 3491 4.944930 CCGGTAATTACAGGAAATTCCACA 59.055 41.667 25.44 0.00 43.08 4.17
2055 3492 4.337274 CCCGGTAATTACAGGAAATTCCAC 59.663 45.833 29.62 1.37 43.08 4.02
2080 3517 0.865769 CACAACCAGTTGACGGTAGC 59.134 55.000 17.06 0.00 42.93 3.58
2086 3523 2.271821 AAAACGCACAACCAGTTGAC 57.728 45.000 17.06 7.69 42.93 3.18
2102 3539 5.766150 ATGTCTGACATTCGTTGGAAAAA 57.234 34.783 17.24 0.00 34.67 1.94
2112 3549 3.126514 CACAGAGCCAATGTCTGACATTC 59.873 47.826 28.18 19.61 44.91 2.67
2117 3554 2.936919 AACACAGAGCCAATGTCTGA 57.063 45.000 7.71 0.00 43.65 3.27
2146 3583 8.859090 ACATGTTGATTTTCAGACTTGGAATTA 58.141 29.630 0.00 0.00 0.00 1.40
2163 3603 4.942761 AAGCAGACCAAAACATGTTGAT 57.057 36.364 12.82 1.20 0.00 2.57
2419 3868 5.420409 AGCATACTTAGCAACCACTAACTC 58.580 41.667 0.00 0.00 0.00 3.01
2464 3914 2.584492 AAAGCAAGCAACCACTGAAC 57.416 45.000 0.00 0.00 0.00 3.18
2667 4118 4.131649 TGCTAGTTTGTACTGTGTGTGT 57.868 40.909 0.00 0.00 35.78 3.72
2676 4146 6.803154 AGGAAGTCATTTGCTAGTTTGTAC 57.197 37.500 0.00 0.00 35.47 2.90
2715 4185 0.790207 CCTGTTCCGTGTCATGTTCG 59.210 55.000 0.00 0.00 0.00 3.95
2728 4198 0.957888 GCCTGAGCAACTCCCTGTTC 60.958 60.000 0.00 0.00 36.63 3.18
2764 4234 5.163174 CCCCATAAATTTCAGGGATTTGCAT 60.163 40.000 23.02 0.00 44.30 3.96
2863 4333 1.544724 CACCCATGTTACCCAACCAG 58.455 55.000 0.00 0.00 33.41 4.00
2880 4350 0.312102 GTCCAGAAAGCTTGCACCAC 59.688 55.000 7.33 0.00 0.00 4.16
3027 4505 1.064003 AAGCCATGTCACCAGGTACA 58.936 50.000 0.00 0.00 0.00 2.90
3062 4544 5.967674 CACAACAGTTTCTTGAAGCACTTAG 59.032 40.000 0.51 0.00 0.00 2.18
3086 4568 6.491403 AGTCCTTCCATAATATGCATTTCACC 59.509 38.462 3.54 0.00 0.00 4.02
3087 4569 7.308830 GGAGTCCTTCCATAATATGCATTTCAC 60.309 40.741 3.54 0.00 46.01 3.18
3128 4610 9.383519 TCATCATTAGAATTCTAAAGTCCACAC 57.616 33.333 27.21 0.00 41.27 3.82
3196 4678 5.047872 TGCAATTCTGAAATGTATGTGCACT 60.048 36.000 19.41 6.22 31.79 4.40
3228 4710 3.853355 AGGCAATAATCCCAGTCAGAG 57.147 47.619 0.00 0.00 0.00 3.35
3369 4853 4.901868 AGACGGATTAAGGTGCTGTTTAA 58.098 39.130 0.00 0.00 0.00 1.52
3382 4866 1.271379 ACACACGCTTGAGACGGATTA 59.729 47.619 0.00 0.00 34.00 1.75
3396 4880 7.231607 GTCACTACAAAATATAACCACACACG 58.768 38.462 0.00 0.00 0.00 4.49
3413 4897 4.471548 GCCTAGATAAGAGGGTCACTACA 58.528 47.826 0.00 0.00 34.35 2.74
3421 4905 2.894126 ACATGACGCCTAGATAAGAGGG 59.106 50.000 0.00 0.00 34.35 4.30
3423 4907 5.188327 TCAACATGACGCCTAGATAAGAG 57.812 43.478 0.00 0.00 0.00 2.85
3429 4913 2.683968 GTGTTCAACATGACGCCTAGA 58.316 47.619 0.00 0.00 0.00 2.43
3450 4934 6.715347 AAATATATCCAAACACAAGGCCTC 57.285 37.500 5.23 0.00 0.00 4.70
3493 4979 9.169592 CGTTTCTTATTTCTGGATAGGGTTTTA 57.830 33.333 0.00 0.00 0.00 1.52
3500 4986 6.927294 AAGGCGTTTCTTATTTCTGGATAG 57.073 37.500 0.00 0.00 0.00 2.08
3501 4987 7.825270 TGTAAAGGCGTTTCTTATTTCTGGATA 59.175 33.333 7.81 0.00 0.00 2.59
3524 5010 2.531771 TCGACCAATTCACCTCCTGTA 58.468 47.619 0.00 0.00 0.00 2.74
3542 5028 2.095567 CCATTCCAGAACAGCAACTTCG 60.096 50.000 0.00 0.00 0.00 3.79
3558 5044 6.967199 GTCAGACGAAATTACAAATCCCATTC 59.033 38.462 0.00 0.00 0.00 2.67
3599 5085 7.201741 GAAGCCATTCAATAAGGAGTTAACTCC 60.202 40.741 37.42 37.42 46.83 3.85
3607 5093 6.360618 ACCTTAGAAGCCATTCAATAAGGAG 58.639 40.000 16.72 0.71 41.52 3.69
3762 5248 0.593128 CAAAGAGGGAACTGGCAACG 59.407 55.000 0.00 0.00 44.43 4.10
3820 5306 2.014128 GGTACCATAAAGCACGTGCAT 58.986 47.619 39.21 27.93 45.16 3.96
3833 5319 4.689612 CTGTATAACAGGCAGGTACCAT 57.310 45.455 15.94 0.00 42.35 3.55
3857 5343 1.134670 GTGCTTAGAGTACCAGGCAGG 60.135 57.143 0.00 0.00 45.67 4.85
3870 5356 5.288712 CACGAAAGGTGTATGTAGTGCTTAG 59.711 44.000 0.00 0.00 41.89 2.18
3910 5396 6.690957 TCTTTTTACACGCAATCTCAAACTTG 59.309 34.615 0.00 0.00 0.00 3.16
3928 5414 9.206870 CCAGCTCAAGCAATATTTTTCTTTTTA 57.793 29.630 4.59 0.00 45.16 1.52
3929 5415 7.933033 TCCAGCTCAAGCAATATTTTTCTTTTT 59.067 29.630 4.59 0.00 45.16 1.94
3930 5416 7.444299 TCCAGCTCAAGCAATATTTTTCTTTT 58.556 30.769 4.59 0.00 45.16 2.27
3931 5417 6.996509 TCCAGCTCAAGCAATATTTTTCTTT 58.003 32.000 4.59 0.00 45.16 2.52
3936 5494 6.070653 TCCAAATCCAGCTCAAGCAATATTTT 60.071 34.615 4.59 0.00 45.16 1.82
3942 5500 1.888512 GTCCAAATCCAGCTCAAGCAA 59.111 47.619 4.59 0.00 45.16 3.91
3999 5557 9.032420 CACTATATCCCGTCTAGTTTTCTTTTC 57.968 37.037 0.00 0.00 0.00 2.29
4031 5589 5.587844 AGATAATCAGACAGTTTGCCATGAC 59.412 40.000 0.00 0.00 0.00 3.06
4081 5639 2.027745 TCACACAGAAGGAGCTCAATCC 60.028 50.000 17.19 0.00 39.89 3.01
4184 5742 3.361977 GTGAACGTTGCCCGGCAT 61.362 61.111 14.30 0.00 38.76 4.40
4217 5775 8.252964 AGTCAAACTACTCGTTTATTTCATCC 57.747 34.615 0.00 0.00 43.75 3.51
4237 5795 4.080863 GGGAATTGAGAGGCTTCTAGTCAA 60.081 45.833 0.00 0.00 32.53 3.18
4349 5924 2.931512 TCAGAATCACGCATGTACGA 57.068 45.000 0.00 0.00 36.70 3.43
4350 5925 2.282555 CCTTCAGAATCACGCATGTACG 59.717 50.000 0.00 0.00 39.50 3.67
4351 5926 2.030946 GCCTTCAGAATCACGCATGTAC 59.969 50.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.