Multiple sequence alignment - TraesCS4D01G339100

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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 TraesCS4D01G339100 chr4D 100.000 2929 0 0 1 2929 497125030 497127958 0.000000e+00 5409.0
1 TraesCS4D01G339100 chr5A 89.161 2491 127 73 1 2423 676885873 676888288 0.000000e+00 2972.0
2 TraesCS4D01G339100 chr5A 83.366 505 48 21 2442 2929 676888371 676888856 4.480000e-118 435.0
3 TraesCS4D01G339100 chr5A 85.306 245 23 7 2692 2929 676888983 676889221 1.050000e-59 241.0
4 TraesCS4D01G339100 chr4B 90.976 2050 79 59 415 2425 637621201 637623183 0.000000e+00 2663.0
5 TraesCS4D01G339100 chr4B 91.667 336 15 9 12 341 637602662 637602990 1.240000e-123 453.0
6 TraesCS4D01G339100 chr4B 81.746 126 19 4 1152 1275 601792349 601792472 5.160000e-18 102.0
7 TraesCS4D01G339100 chr4B 91.549 71 2 3 2442 2509 637623271 637623340 8.640000e-16 95.3
8 TraesCS4D01G339100 chr3A 77.824 239 37 13 1045 1275 60297525 60297755 1.830000e-27 134.0
9 TraesCS4D01G339100 chr3D 81.818 165 18 8 1117 1275 48070740 48070898 8.520000e-26 128.0
10 TraesCS4D01G339100 chr2D 90.625 96 7 2 1455 1549 466723987 466723893 3.060000e-25 126.0
11 TraesCS4D01G339100 chr6A 82.517 143 23 2 1131 1272 421463946 421464087 1.100000e-24 124.0
12 TraesCS4D01G339100 chr6A 81.343 134 23 2 1140 1272 421226195 421226327 1.110000e-19 108.0
13 TraesCS4D01G339100 chr6A 87.234 94 10 2 1455 1547 428426488 428426580 3.990000e-19 106.0
14 TraesCS4D01G339100 chr6D 82.836 134 21 2 1140 1272 296993425 296993293 5.130000e-23 119.0
15 TraesCS4D01G339100 chr6D 82.836 134 21 2 1140 1272 298207150 298207018 5.130000e-23 119.0
16 TraesCS4D01G339100 chr6D 80.597 134 24 2 1140 1272 297489773 297489641 5.160000e-18 102.0
17 TraesCS4D01G339100 chr6D 86.170 94 11 2 1455 1547 292737751 292737659 1.860000e-17 100.0
18 TraesCS4D01G339100 chr2A 88.542 96 9 2 1455 1549 607841870 607841776 6.630000e-22 115.0
19 TraesCS4D01G339100 chr2B 87.500 96 10 2 1455 1549 545366056 545365962 3.090000e-20 110.0
20 TraesCS4D01G339100 chr6B 86.022 93 13 0 1455 1547 457216778 457216686 1.860000e-17 100.0
21 TraesCS4D01G339100 chr5D 87.500 80 10 0 1454 1533 200501539 200501618 3.110000e-15 93.5


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 TraesCS4D01G339100 chr4D 497125030 497127958 2928 False 5409.00 5409 100.000000 1 2929 1 chr4D.!!$F1 2928
1 TraesCS4D01G339100 chr5A 676885873 676889221 3348 False 1216.00 2972 85.944333 1 2929 3 chr5A.!!$F1 2928
2 TraesCS4D01G339100 chr4B 637621201 637623340 2139 False 1379.15 2663 91.262500 415 2509 2 chr4B.!!$F3 2094

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
218 220 0.492737 CGCTTCAAAACAACGCGTTC 59.507 50.0 23.92 6.48 36.59 3.95 F
1285 1338 0.392998 CAACAGGTAAGCTGCCCGAT 60.393 55.0 0.00 0.00 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1336 1389 0.471971 ACAGCCACTCCCACTGTAGT 60.472 55.0 0.0 0.0 42.65 2.73 R
2516 2684 0.034337 GCCCGTGGTTTCAGTCACTA 59.966 55.0 0.0 0.0 0.00 2.74 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
42 43 6.605995 TGCTTAGCTAGACACATCTTACCTTA 59.394 38.462 5.60 0.00 36.29 2.69
57 58 9.113876 CATCTTACCTTACGCTTTTACTTTTTG 57.886 33.333 0.00 0.00 0.00 2.44
65 66 6.144078 ACGCTTTTACTTTTTGGTCTTCAT 57.856 33.333 0.00 0.00 0.00 2.57
190 192 6.476053 AGACTAGCGAAATAATTTCCTTCGTC 59.524 38.462 14.05 8.89 42.94 4.20
196 198 6.402226 GCGAAATAATTTCCTTCGTCAGAGTT 60.402 38.462 14.05 0.00 42.94 3.01
199 201 6.969828 ATAATTTCCTTCGTCAGAGTTCAC 57.030 37.500 0.00 0.00 0.00 3.18
217 219 2.561366 CGCTTCAAAACAACGCGTT 58.439 47.368 20.79 20.79 40.50 4.84
218 220 0.492737 CGCTTCAAAACAACGCGTTC 59.507 50.000 23.92 6.48 36.59 3.95
219 221 1.540407 GCTTCAAAACAACGCGTTCA 58.460 45.000 23.92 0.00 36.59 3.18
220 222 2.116366 GCTTCAAAACAACGCGTTCAT 58.884 42.857 23.92 10.78 36.59 2.57
221 223 2.151172 GCTTCAAAACAACGCGTTCATC 59.849 45.455 23.92 0.18 36.59 2.92
222 224 2.011932 TCAAAACAACGCGTTCATCG 57.988 45.000 23.92 13.69 36.59 3.84
231 233 4.409342 CGTTCATCGCAGCTAGCT 57.591 55.556 12.68 12.68 42.61 3.32
232 234 2.670635 CGTTCATCGCAGCTAGCTT 58.329 52.632 16.46 0.00 42.61 3.74
233 235 1.840181 CGTTCATCGCAGCTAGCTTA 58.160 50.000 16.46 3.86 42.61 3.09
234 236 1.518929 CGTTCATCGCAGCTAGCTTAC 59.481 52.381 16.46 9.59 42.61 2.34
235 237 2.540515 GTTCATCGCAGCTAGCTTACA 58.459 47.619 16.46 1.07 42.61 2.41
236 238 3.126831 GTTCATCGCAGCTAGCTTACAT 58.873 45.455 16.46 3.75 42.61 2.29
237 239 4.299155 GTTCATCGCAGCTAGCTTACATA 58.701 43.478 16.46 1.84 42.61 2.29
238 240 4.584327 TCATCGCAGCTAGCTTACATAA 57.416 40.909 16.46 0.00 42.61 1.90
239 241 4.550422 TCATCGCAGCTAGCTTACATAAG 58.450 43.478 16.46 2.70 42.61 1.73
240 242 4.038042 TCATCGCAGCTAGCTTACATAAGT 59.962 41.667 16.46 0.00 42.61 2.24
241 243 4.386867 TCGCAGCTAGCTTACATAAGTT 57.613 40.909 16.46 0.00 42.61 2.66
270 272 5.705609 TTCCTTTTTGAAGCGAGCTAATT 57.294 34.783 0.00 0.00 0.00 1.40
353 356 1.476488 GGTCCAATACATGTTGTGGGC 59.524 52.381 21.26 20.18 34.90 5.36
375 378 3.940723 GCTAGTCGGCGACTTGTAT 57.059 52.632 42.62 23.90 40.28 2.29
413 416 7.767745 GGTCAAATACCTGCTAGTAGTTTAC 57.232 40.000 7.10 0.00 45.75 2.01
471 475 6.811253 TTTGAAAATACAGTGGACGCTTAT 57.189 33.333 0.00 0.00 0.00 1.73
473 477 6.811253 TGAAAATACAGTGGACGCTTATTT 57.189 33.333 0.00 0.00 0.00 1.40
474 478 7.908827 TGAAAATACAGTGGACGCTTATTTA 57.091 32.000 0.00 0.58 0.00 1.40
475 479 7.745015 TGAAAATACAGTGGACGCTTATTTAC 58.255 34.615 0.00 0.00 0.00 2.01
476 480 7.388224 TGAAAATACAGTGGACGCTTATTTACA 59.612 33.333 0.00 0.00 0.00 2.41
477 481 6.903883 AATACAGTGGACGCTTATTTACAG 57.096 37.500 0.00 0.00 0.00 2.74
482 486 6.976925 ACAGTGGACGCTTATTTACAGTATAC 59.023 38.462 0.00 0.00 0.00 1.47
524 530 1.135315 CTCACGCAAAAGGGCATCG 59.865 57.895 0.00 0.00 0.00 3.84
539 545 1.546476 GCATCGGATCGATAACCCTCT 59.454 52.381 0.00 0.00 45.19 3.69
540 546 2.416162 GCATCGGATCGATAACCCTCTC 60.416 54.545 0.00 0.00 45.19 3.20
563 569 6.714278 TCGATCATATGTGGGATGATTGATT 58.286 36.000 10.26 0.00 44.18 2.57
708 730 6.465439 TTTGTCAGCGAGAAGAGGAATATA 57.535 37.500 0.00 0.00 0.00 0.86
948 1000 5.897824 TCCTAGTGGCTAACTAACTAGCAAT 59.102 40.000 5.10 0.00 45.17 3.56
1278 1331 1.376037 GCTCGGCAACAGGTAAGCT 60.376 57.895 0.00 0.00 0.00 3.74
1279 1332 1.639298 GCTCGGCAACAGGTAAGCTG 61.639 60.000 0.00 0.00 36.00 4.24
1280 1333 1.639298 CTCGGCAACAGGTAAGCTGC 61.639 60.000 0.00 0.00 34.70 5.25
1282 1335 3.278157 GCAACAGGTAAGCTGCCC 58.722 61.111 0.00 0.00 0.00 5.36
1283 1336 2.690778 GCAACAGGTAAGCTGCCCG 61.691 63.158 0.00 0.00 0.00 6.13
1284 1337 1.003839 CAACAGGTAAGCTGCCCGA 60.004 57.895 0.00 0.00 0.00 5.14
1285 1338 0.392998 CAACAGGTAAGCTGCCCGAT 60.393 55.000 0.00 0.00 0.00 4.18
1286 1339 1.134521 CAACAGGTAAGCTGCCCGATA 60.135 52.381 0.00 0.00 0.00 2.92
1288 1341 1.768870 ACAGGTAAGCTGCCCGATATT 59.231 47.619 0.00 0.00 0.00 1.28
1289 1342 2.224305 ACAGGTAAGCTGCCCGATATTC 60.224 50.000 0.00 0.00 0.00 1.75
1298 1351 3.871463 GCTGCCCGATATTCCATCTCATT 60.871 47.826 0.00 0.00 0.00 2.57
1300 1353 4.326826 TGCCCGATATTCCATCTCATTTC 58.673 43.478 0.00 0.00 0.00 2.17
1301 1354 3.691609 GCCCGATATTCCATCTCATTTCC 59.308 47.826 0.00 0.00 0.00 3.13
1302 1355 4.807303 GCCCGATATTCCATCTCATTTCCA 60.807 45.833 0.00 0.00 0.00 3.53
1303 1356 5.503927 CCCGATATTCCATCTCATTTCCAT 58.496 41.667 0.00 0.00 0.00 3.41
1305 1358 6.435277 CCCGATATTCCATCTCATTTCCATTT 59.565 38.462 0.00 0.00 0.00 2.32
1307 1360 7.362401 CCGATATTCCATCTCATTTCCATTTCC 60.362 40.741 0.00 0.00 0.00 3.13
1308 1361 7.175467 CGATATTCCATCTCATTTCCATTTCCA 59.825 37.037 0.00 0.00 0.00 3.53
1309 1362 8.967779 ATATTCCATCTCATTTCCATTTCCAT 57.032 30.769 0.00 0.00 0.00 3.41
1311 1364 6.474140 TCCATCTCATTTCCATTTCCATTG 57.526 37.500 0.00 0.00 0.00 2.82
1312 1365 6.196434 TCCATCTCATTTCCATTTCCATTGA 58.804 36.000 0.00 0.00 0.00 2.57
1313 1366 6.668718 TCCATCTCATTTCCATTTCCATTGAA 59.331 34.615 0.00 0.00 0.00 2.69
1314 1367 7.180587 TCCATCTCATTTCCATTTCCATTGAAA 59.819 33.333 0.00 0.00 44.22 2.69
1316 1369 9.391006 CATCTCATTTCCATTTCCATTGAAATT 57.609 29.630 2.10 0.00 46.57 1.82
1335 1388 5.961396 AATTCAGACGTGTACAGTCTACT 57.039 39.130 20.45 10.41 46.16 2.57
1336 1389 7.173735 TGAAATTCAGACGTGTACAGTCTACTA 59.826 37.037 20.45 12.73 46.16 1.82
1337 1390 5.852738 TTCAGACGTGTACAGTCTACTAC 57.147 43.478 20.45 0.00 46.16 2.73
1345 1398 5.063186 CGTGTACAGTCTACTACTACAGTGG 59.937 48.000 0.00 0.00 38.24 4.00
1346 1399 5.353678 GTGTACAGTCTACTACTACAGTGGG 59.646 48.000 0.00 0.00 38.24 4.61
1383 1436 1.922570 CCCACGTACTGTATGACTGC 58.077 55.000 13.69 0.00 0.00 4.40
1388 1441 4.424626 CACGTACTGTATGACTGCATCTT 58.575 43.478 13.69 0.00 35.94 2.40
1389 1442 4.500837 CACGTACTGTATGACTGCATCTTC 59.499 45.833 13.69 0.00 35.94 2.87
1390 1443 4.399618 ACGTACTGTATGACTGCATCTTCT 59.600 41.667 13.69 0.00 35.94 2.85
1391 1444 5.105716 ACGTACTGTATGACTGCATCTTCTT 60.106 40.000 13.69 0.00 35.94 2.52
1392 1445 5.230936 CGTACTGTATGACTGCATCTTCTTG 59.769 44.000 0.61 0.00 35.94 3.02
1393 1446 4.511527 ACTGTATGACTGCATCTTCTTGG 58.488 43.478 0.00 0.00 35.94 3.61
1394 1447 3.875727 CTGTATGACTGCATCTTCTTGGG 59.124 47.826 0.00 0.00 35.94 4.12
1683 1736 3.395630 TGCAGATGGAGCAGCAGA 58.604 55.556 0.00 0.00 37.02 4.26
1684 1737 1.078637 TGCAGATGGAGCAGCAGAC 60.079 57.895 0.00 0.00 37.02 3.51
1688 1744 1.451028 GATGGAGCAGCAGACCCAC 60.451 63.158 0.00 0.00 0.00 4.61
1974 2037 1.965990 GCAATGTGCATGTGTCCCA 59.034 52.632 0.00 0.00 44.26 4.37
2006 2069 6.559157 AGAAAGAAAGAAAGGAAGGAGAGGTA 59.441 38.462 0.00 0.00 0.00 3.08
2084 2149 1.000052 GCGGTGATAGCTAGGAAGGAC 60.000 57.143 0.00 0.00 0.00 3.85
2172 2244 1.294041 TTACCCATGACCATGAGCCA 58.706 50.000 11.28 0.00 41.20 4.75
2173 2245 1.521764 TACCCATGACCATGAGCCAT 58.478 50.000 11.28 0.00 41.20 4.40
2174 2246 0.106369 ACCCATGACCATGAGCCATG 60.106 55.000 11.28 12.16 41.20 3.66
2291 2384 2.154854 TTTGGTCTCGCTTCTCAGTG 57.845 50.000 0.00 0.00 0.00 3.66
2299 2392 3.256879 TCTCGCTTCTCAGTGAATCAAGT 59.743 43.478 0.00 0.00 39.12 3.16
2308 2401 7.672983 TCTCAGTGAATCAAGTACATTTTCC 57.327 36.000 0.00 0.00 0.00 3.13
2322 2415 5.362556 ACATTTTCCTCAGTTCATGAACG 57.637 39.130 28.18 22.80 45.50 3.95
2340 2433 1.078637 GAGCAGTGCAGCAGATCCA 60.079 57.895 19.20 0.00 36.85 3.41
2357 2450 3.290948 TCCATACCCACTTGGCAATAC 57.709 47.619 0.00 0.00 37.83 1.89
2397 2492 1.904287 TTCGCTGTACAAAATGGCCT 58.096 45.000 3.32 0.00 0.00 5.19
2398 2493 2.772077 TCGCTGTACAAAATGGCCTA 57.228 45.000 3.32 0.00 0.00 3.93
2405 2500 0.881118 ACAAAATGGCCTAGCACACG 59.119 50.000 3.32 0.00 0.00 4.49
2410 2505 1.119684 ATGGCCTAGCACACGTATCA 58.880 50.000 3.32 0.00 0.00 2.15
2437 2591 7.341512 TCACAATTGGTTATTATGATCCAAGCA 59.658 33.333 10.83 0.00 42.09 3.91
2438 2592 8.145767 CACAATTGGTTATTATGATCCAAGCAT 58.854 33.333 10.83 0.00 42.09 3.79
2440 2594 8.582437 CAATTGGTTATTATGATCCAAGCATCT 58.418 33.333 0.00 0.00 42.09 2.90
2444 2609 9.639563 TGGTTATTATGATCCAAGCATCTTTTA 57.360 29.630 0.00 0.00 0.00 1.52
2452 2617 6.664816 TGATCCAAGCATCTTTTATCCTTTGT 59.335 34.615 0.00 0.00 0.00 2.83
2470 2636 5.104109 CCTTTGTATAATGGGAGGACAGGAA 60.104 44.000 0.00 0.00 0.00 3.36
2534 2702 2.762535 ATAGTGACTGAAACCACGGG 57.237 50.000 0.00 0.00 38.26 5.28
2535 2703 0.034337 TAGTGACTGAAACCACGGGC 59.966 55.000 0.00 0.00 38.26 6.13
2536 2704 1.227853 GTGACTGAAACCACGGGCT 60.228 57.895 0.00 0.00 0.00 5.19
2537 2705 0.034337 GTGACTGAAACCACGGGCTA 59.966 55.000 0.00 0.00 0.00 3.93
2538 2706 0.981183 TGACTGAAACCACGGGCTAT 59.019 50.000 0.00 0.00 0.00 2.97
2539 2707 1.066430 TGACTGAAACCACGGGCTATC 60.066 52.381 0.00 0.00 0.00 2.08
2540 2708 1.207329 GACTGAAACCACGGGCTATCT 59.793 52.381 0.00 0.00 0.00 1.98
2541 2709 2.429610 GACTGAAACCACGGGCTATCTA 59.570 50.000 0.00 0.00 0.00 1.98
2546 2714 3.753294 AACCACGGGCTATCTAATCTG 57.247 47.619 0.00 0.00 0.00 2.90
2559 2727 9.547753 GGCTATCTAATCTGAGTAACAAAATCA 57.452 33.333 0.00 0.00 0.00 2.57
2594 2774 4.483476 ACAAACATCAACGAGGTTTAGC 57.517 40.909 6.46 0.00 43.15 3.09
2608 2789 2.437413 GTTTAGCAGGAGTTTGAGGGG 58.563 52.381 0.00 0.00 0.00 4.79
2628 2809 1.740025 GTGAGTTGGCTGACTTATGGC 59.260 52.381 0.00 0.00 0.00 4.40
2654 2835 5.732528 GCAACTGCAAGATGATGATTGTAGG 60.733 44.000 7.70 0.00 39.37 3.18
2657 2838 5.163120 ACTGCAAGATGATGATTGTAGGGAT 60.163 40.000 7.70 0.00 41.65 3.85
2658 2839 6.043590 ACTGCAAGATGATGATTGTAGGGATA 59.956 38.462 7.70 0.00 41.65 2.59
2659 2840 7.024345 TGCAAGATGATGATTGTAGGGATAT 57.976 36.000 0.00 0.00 0.00 1.63
2660 2841 7.108194 TGCAAGATGATGATTGTAGGGATATC 58.892 38.462 0.00 0.00 0.00 1.63
2661 2842 7.108194 GCAAGATGATGATTGTAGGGATATCA 58.892 38.462 4.83 0.00 33.25 2.15
2662 2843 7.065563 GCAAGATGATGATTGTAGGGATATCAC 59.934 40.741 4.83 0.00 31.66 3.06
2663 2844 7.192852 AGATGATGATTGTAGGGATATCACC 57.807 40.000 0.00 1.67 31.66 4.02
2664 2845 6.732390 AGATGATGATTGTAGGGATATCACCA 59.268 38.462 0.00 0.00 31.66 4.17
2665 2846 6.957853 TGATGATTGTAGGGATATCACCAT 57.042 37.500 0.00 0.00 31.66 3.55
2666 2847 6.714278 TGATGATTGTAGGGATATCACCATG 58.286 40.000 0.00 0.00 31.66 3.66
2667 2848 5.503634 TGATTGTAGGGATATCACCATGG 57.496 43.478 11.19 11.19 0.00 3.66
2669 2850 2.990195 TGTAGGGATATCACCATGGCT 58.010 47.619 13.04 0.01 0.00 4.75
2671 2852 0.403271 AGGGATATCACCATGGCTGC 59.597 55.000 13.04 0.00 0.00 5.25
2672 2853 0.403271 GGGATATCACCATGGCTGCT 59.597 55.000 13.04 3.85 0.00 4.24
2674 2855 1.072806 GGATATCACCATGGCTGCTGA 59.927 52.381 13.04 8.59 0.00 4.26
2676 2857 2.265589 TATCACCATGGCTGCTGATG 57.734 50.000 20.49 7.68 0.00 3.07
2694 2876 3.269381 TGATGGGGCTTAATTCTTCTGGT 59.731 43.478 0.00 0.00 0.00 4.00
2705 2887 7.550906 GCTTAATTCTTCTGGTCAGATTACAGT 59.449 37.037 1.16 0.00 37.29 3.55
2706 2888 9.092876 CTTAATTCTTCTGGTCAGATTACAGTC 57.907 37.037 1.16 0.00 37.29 3.51
2710 2892 5.540337 TCTTCTGGTCAGATTACAGTCAAGT 59.460 40.000 1.16 0.00 37.29 3.16
2711 2893 6.719829 TCTTCTGGTCAGATTACAGTCAAGTA 59.280 38.462 1.16 0.00 37.29 2.24
2712 2894 6.268825 TCTGGTCAGATTACAGTCAAGTAC 57.731 41.667 0.00 0.00 34.02 2.73
2716 2898 5.335426 GGTCAGATTACAGTCAAGTACACGA 60.335 44.000 0.00 0.00 0.00 4.35
2717 2899 5.568296 GTCAGATTACAGTCAAGTACACGAC 59.432 44.000 6.58 6.58 0.00 4.34
2718 2900 4.553815 CAGATTACAGTCAAGTACACGACG 59.446 45.833 8.52 0.00 37.23 5.12
2719 2901 4.453478 AGATTACAGTCAAGTACACGACGA 59.547 41.667 0.00 0.00 37.23 4.20
2722 2904 4.754372 ACAGTCAAGTACACGACGATAA 57.246 40.909 0.00 0.00 37.23 1.75
2766 3307 5.784578 ACAAGGTTAATTGGTGTCCTTTC 57.215 39.130 0.00 0.00 36.52 2.62
2770 3311 3.056821 GGTTAATTGGTGTCCTTTCAGGC 60.057 47.826 0.00 0.00 34.61 4.85
2771 3312 2.683211 AATTGGTGTCCTTTCAGGCT 57.317 45.000 0.00 0.00 34.61 4.58
2774 3315 0.690762 TGGTGTCCTTTCAGGCTACC 59.309 55.000 7.85 7.85 39.79 3.18
2796 3337 4.403734 CCTGGTTCCTAAAAGTGCCTTTA 58.596 43.478 1.31 0.00 31.99 1.85
2873 3414 7.727181 TGAAGAATAACCTACATAAGAGAGGC 58.273 38.462 0.00 0.00 33.28 4.70
2901 3448 3.388024 TGGTAGTGAGAAGTGCAGTTTCT 59.612 43.478 8.48 10.54 37.59 2.52
2920 3467 3.211865 TCTGTGACTACGCGGAAGATAT 58.788 45.455 12.47 0.00 38.71 1.63
2923 3470 3.501062 TGTGACTACGCGGAAGATATAGG 59.499 47.826 12.47 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 5.570234 TGAAGACCAAAAAGTAAAAGCGT 57.430 34.783 0.00 0.00 0.00 5.07
57 58 6.701400 AGTTTTGCAAACACATTATGAAGACC 59.299 34.615 12.39 0.00 0.00 3.85
65 66 8.671384 ACTACTCTAGTTTTGCAAACACATTA 57.329 30.769 12.39 0.00 34.86 1.90
183 185 0.039074 AGCGTGAACTCTGACGAAGG 60.039 55.000 0.00 0.00 37.81 3.46
190 192 3.673746 TGTTTTGAAGCGTGAACTCTG 57.326 42.857 0.00 0.00 0.00 3.35
196 198 0.587737 CGCGTTGTTTTGAAGCGTGA 60.588 50.000 0.00 0.00 44.96 4.35
221 223 7.624344 AAGAAAAACTTATGTAAGCTAGCTGCG 60.624 37.037 20.16 4.46 41.08 5.18
222 224 7.078011 AGAAAAACTTATGTAAGCTAGCTGC 57.922 36.000 20.16 14.92 43.29 5.25
223 225 9.899226 AAAAGAAAAACTTATGTAAGCTAGCTG 57.101 29.630 20.16 6.19 37.93 4.24
225 227 9.343103 GGAAAAGAAAAACTTATGTAAGCTAGC 57.657 33.333 6.62 6.62 37.93 3.42
236 238 8.652463 CGCTTCAAAAAGGAAAAGAAAAACTTA 58.348 29.630 0.00 0.00 33.81 2.24
237 239 7.386573 TCGCTTCAAAAAGGAAAAGAAAAACTT 59.613 29.630 0.00 0.00 35.21 2.66
238 240 6.871492 TCGCTTCAAAAAGGAAAAGAAAAACT 59.129 30.769 0.00 0.00 32.79 2.66
239 241 7.056002 TCGCTTCAAAAAGGAAAAGAAAAAC 57.944 32.000 0.00 0.00 32.79 2.43
240 242 6.183360 GCTCGCTTCAAAAAGGAAAAGAAAAA 60.183 34.615 0.00 0.00 32.79 1.94
241 243 5.290885 GCTCGCTTCAAAAAGGAAAAGAAAA 59.709 36.000 0.00 0.00 32.79 2.29
270 272 6.837048 TGGTTAGGTATAGTCTTGTGATGCTA 59.163 38.462 0.00 0.00 0.00 3.49
322 325 6.005198 ACATGTATTGGACCGGAACTAAAAA 58.995 36.000 9.46 0.00 0.00 1.94
323 326 5.562635 ACATGTATTGGACCGGAACTAAAA 58.437 37.500 9.46 0.00 0.00 1.52
324 327 5.168647 ACATGTATTGGACCGGAACTAAA 57.831 39.130 9.46 1.76 0.00 1.85
329 332 3.078097 CACAACATGTATTGGACCGGAA 58.922 45.455 9.46 0.00 33.63 4.30
343 346 3.334891 TAGCGGGGCCCACAACAT 61.335 61.111 26.86 5.19 0.00 2.71
388 391 7.179694 AGTAAACTACTAGCAGGTATTTGACCA 59.820 37.037 0.00 0.00 43.72 4.02
389 392 7.554211 AGTAAACTACTAGCAGGTATTTGACC 58.446 38.462 0.00 0.00 42.46 4.02
406 409 8.701908 TGGTCTTCTTCTCAAGTAGTAAACTA 57.298 34.615 0.00 0.00 37.50 2.24
407 410 7.598759 TGGTCTTCTTCTCAAGTAGTAAACT 57.401 36.000 0.00 0.00 41.49 2.66
408 411 6.366604 GCTGGTCTTCTTCTCAAGTAGTAAAC 59.633 42.308 0.00 0.00 0.00 2.01
409 412 6.041637 TGCTGGTCTTCTTCTCAAGTAGTAAA 59.958 38.462 0.00 0.00 0.00 2.01
411 414 5.077564 TGCTGGTCTTCTTCTCAAGTAGTA 58.922 41.667 0.00 0.00 0.00 1.82
412 415 3.898123 TGCTGGTCTTCTTCTCAAGTAGT 59.102 43.478 0.00 0.00 0.00 2.73
413 416 4.493547 CTGCTGGTCTTCTTCTCAAGTAG 58.506 47.826 0.00 0.00 0.00 2.57
445 449 4.759693 AGCGTCCACTGTATTTTCAAATGA 59.240 37.500 0.00 0.00 0.00 2.57
473 477 8.542953 CGTCGTGTCAAATACTAGTATACTGTA 58.457 37.037 15.74 14.64 0.00 2.74
474 478 7.065085 ACGTCGTGTCAAATACTAGTATACTGT 59.935 37.037 15.74 13.07 0.00 3.55
475 479 7.404985 ACGTCGTGTCAAATACTAGTATACTG 58.595 38.462 15.74 15.07 0.00 2.74
476 480 7.545362 ACGTCGTGTCAAATACTAGTATACT 57.455 36.000 15.74 10.87 0.00 2.12
477 481 7.524201 CGTACGTCGTGTCAAATACTAGTATAC 59.476 40.741 15.74 10.91 34.52 1.47
507 513 2.331893 CCGATGCCCTTTTGCGTGA 61.332 57.895 0.00 0.00 0.00 4.35
509 515 1.376609 GATCCGATGCCCTTTTGCGT 61.377 55.000 0.00 0.00 0.00 5.24
539 545 5.743636 TCAATCATCCCACATATGATCGA 57.256 39.130 10.38 1.36 41.99 3.59
540 546 6.997239 AATCAATCATCCCACATATGATCG 57.003 37.500 10.38 0.00 41.99 3.69
563 569 9.485206 GTTTATTGTATCCTAAATTCCGAGCTA 57.515 33.333 0.00 0.00 0.00 3.32
708 730 6.425114 CCACTTGCTAAGCTTATCGACATATT 59.575 38.462 6.64 0.00 0.00 1.28
872 913 2.353323 TCTATTGCTGAGCTTGCTGTG 58.647 47.619 5.83 0.00 0.00 3.66
873 914 2.775911 TCTATTGCTGAGCTTGCTGT 57.224 45.000 5.83 5.34 0.00 4.40
910 958 9.720769 TTAGCCACTAGGATTAATACTATTTGC 57.279 33.333 7.89 9.86 36.89 3.68
948 1000 5.338381 CCTTCAACTGGCCAATCTCTAACTA 60.338 44.000 7.01 0.00 0.00 2.24
1278 1331 4.326826 GAAATGAGATGGAATATCGGGCA 58.673 43.478 0.00 0.00 37.37 5.36
1279 1332 3.691609 GGAAATGAGATGGAATATCGGGC 59.308 47.826 0.00 0.00 37.37 6.13
1280 1333 4.910195 TGGAAATGAGATGGAATATCGGG 58.090 43.478 0.00 0.00 37.37 5.14
1282 1335 7.175467 TGGAAATGGAAATGAGATGGAATATCG 59.825 37.037 0.00 0.00 37.37 2.92
1283 1336 8.413309 TGGAAATGGAAATGAGATGGAATATC 57.587 34.615 0.00 0.00 34.49 1.63
1284 1337 8.967779 ATGGAAATGGAAATGAGATGGAATAT 57.032 30.769 0.00 0.00 0.00 1.28
1285 1338 8.644216 CAATGGAAATGGAAATGAGATGGAATA 58.356 33.333 0.00 0.00 0.00 1.75
1286 1339 7.346175 TCAATGGAAATGGAAATGAGATGGAAT 59.654 33.333 0.00 0.00 0.00 3.01
1288 1341 6.196434 TCAATGGAAATGGAAATGAGATGGA 58.804 36.000 0.00 0.00 0.00 3.41
1289 1342 6.474140 TCAATGGAAATGGAAATGAGATGG 57.526 37.500 0.00 0.00 0.00 3.51
1303 1356 5.766150 ACACGTCTGAATTTCAATGGAAA 57.234 34.783 0.00 0.00 46.36 3.13
1305 1358 5.301555 TGTACACGTCTGAATTTCAATGGA 58.698 37.500 0.01 0.00 0.00 3.41
1307 1360 6.146184 AGACTGTACACGTCTGAATTTCAATG 59.854 38.462 20.31 0.33 40.07 2.82
1308 1361 6.223852 AGACTGTACACGTCTGAATTTCAAT 58.776 36.000 20.31 1.23 40.07 2.57
1309 1362 5.597806 AGACTGTACACGTCTGAATTTCAA 58.402 37.500 20.31 0.00 40.07 2.69
1311 1364 6.380190 AGTAGACTGTACACGTCTGAATTTC 58.620 40.000 25.53 14.53 41.52 2.17
1312 1365 6.328641 AGTAGACTGTACACGTCTGAATTT 57.671 37.500 25.53 10.67 41.52 1.82
1313 1366 5.961396 AGTAGACTGTACACGTCTGAATT 57.039 39.130 25.53 10.53 41.52 2.17
1314 1367 6.171921 AGTAGTAGACTGTACACGTCTGAAT 58.828 40.000 25.53 17.57 41.52 2.57
1315 1368 5.545588 AGTAGTAGACTGTACACGTCTGAA 58.454 41.667 25.53 12.67 41.52 3.02
1316 1369 5.144692 AGTAGTAGACTGTACACGTCTGA 57.855 43.478 25.53 14.71 41.52 3.27
1335 1388 1.203137 ACAGCCACTCCCACTGTAGTA 60.203 52.381 0.00 0.00 42.65 1.82
1336 1389 0.471971 ACAGCCACTCCCACTGTAGT 60.472 55.000 0.00 0.00 42.65 2.73
1337 1390 1.557099 TACAGCCACTCCCACTGTAG 58.443 55.000 0.00 0.00 42.65 2.74
1345 1398 1.069358 GGCATCTACTACAGCCACTCC 59.931 57.143 0.00 0.00 46.26 3.85
1346 1399 2.517650 GGCATCTACTACAGCCACTC 57.482 55.000 0.00 0.00 46.26 3.51
1383 1436 2.440409 CACCCAAGACCCAAGAAGATG 58.560 52.381 0.00 0.00 0.00 2.90
1388 1441 2.429930 CGCACCCAAGACCCAAGA 59.570 61.111 0.00 0.00 0.00 3.02
1389 1442 3.365265 GCGCACCCAAGACCCAAG 61.365 66.667 0.30 0.00 0.00 3.61
1667 1720 1.818785 GGTCTGCTGCTCCATCTGC 60.819 63.158 0.00 0.00 0.00 4.26
1671 1724 2.673523 GTGGGTCTGCTGCTCCAT 59.326 61.111 0.00 0.00 0.00 3.41
1672 1725 3.640407 GGTGGGTCTGCTGCTCCA 61.640 66.667 0.00 0.93 0.00 3.86
1674 1727 2.046507 CTGGTGGGTCTGCTGCTC 60.047 66.667 0.00 0.00 0.00 4.26
1688 1744 2.184830 CATCATCACCTGCGGCTGG 61.185 63.158 22.53 22.53 0.00 4.85
1693 1749 0.586802 CTGCATCATCATCACCTGCG 59.413 55.000 0.00 0.00 35.63 5.18
1779 1835 3.191539 GCAGTAGCACTCCGCAGC 61.192 66.667 0.00 0.00 46.13 5.25
1784 1840 2.125512 CACGGGCAGTAGCACTCC 60.126 66.667 0.00 0.00 43.86 3.85
1974 2037 9.421399 TCCTTCCTTTCTTTCTTTCTTTACAAT 57.579 29.630 0.00 0.00 0.00 2.71
2006 2069 3.652057 ACCTGCAGGCAGTATTGTATT 57.348 42.857 33.06 5.36 42.15 1.89
2172 2244 3.308473 CCTGATCATGGGCTCATCATCAT 60.308 47.826 14.05 0.00 39.54 2.45
2173 2245 2.039879 CCTGATCATGGGCTCATCATCA 59.960 50.000 12.99 12.99 38.32 3.07
2174 2246 2.040012 ACCTGATCATGGGCTCATCATC 59.960 50.000 3.00 3.00 32.41 2.92
2207 2279 2.977914 TGACATGCTAACTGAAGAGGC 58.022 47.619 0.00 0.00 0.00 4.70
2258 2336 5.007626 GCGAGACCAAAATTACATGATGCTA 59.992 40.000 0.00 0.00 0.00 3.49
2291 2384 8.099364 TGAACTGAGGAAAATGTACTTGATTC 57.901 34.615 0.00 0.00 0.00 2.52
2299 2392 6.227522 TCGTTCATGAACTGAGGAAAATGTA 58.772 36.000 30.45 6.92 39.08 2.29
2308 2401 2.411069 CACTGCTCGTTCATGAACTGAG 59.589 50.000 32.80 32.80 40.93 3.35
2322 2415 0.464013 ATGGATCTGCTGCACTGCTC 60.464 55.000 0.00 0.00 0.00 4.26
2340 2433 5.301805 GCATAAAGTATTGCCAAGTGGGTAT 59.698 40.000 0.00 0.00 39.65 2.73
2357 2450 6.422223 CGAATTAGCTACAAGGTGCATAAAG 58.578 40.000 0.00 0.00 0.00 1.85
2397 2492 4.570369 CCAATTGTGATGATACGTGTGCTA 59.430 41.667 4.43 0.00 0.00 3.49
2398 2493 3.374988 CCAATTGTGATGATACGTGTGCT 59.625 43.478 4.43 0.00 0.00 4.40
2437 2591 9.813826 CCTCCCATTATACAAAGGATAAAAGAT 57.186 33.333 0.00 0.00 0.00 2.40
2438 2592 9.009675 TCCTCCCATTATACAAAGGATAAAAGA 57.990 33.333 0.00 0.00 0.00 2.52
2440 2594 8.561769 TGTCCTCCCATTATACAAAGGATAAAA 58.438 33.333 0.00 0.00 35.50 1.52
2444 2609 5.073691 CCTGTCCTCCCATTATACAAAGGAT 59.926 44.000 0.00 0.00 35.50 3.24
2452 2617 5.130477 GTCAAGTTCCTGTCCTCCCATTATA 59.870 44.000 0.00 0.00 0.00 0.98
2514 2682 2.093869 GCCCGTGGTTTCAGTCACTATA 60.094 50.000 0.00 0.00 0.00 1.31
2515 2683 1.338769 GCCCGTGGTTTCAGTCACTAT 60.339 52.381 0.00 0.00 0.00 2.12
2516 2684 0.034337 GCCCGTGGTTTCAGTCACTA 59.966 55.000 0.00 0.00 0.00 2.74
2517 2685 1.227853 GCCCGTGGTTTCAGTCACT 60.228 57.895 0.00 0.00 0.00 3.41
2518 2686 0.034337 TAGCCCGTGGTTTCAGTCAC 59.966 55.000 0.00 0.00 0.00 3.67
2529 2697 5.009710 TGTTACTCAGATTAGATAGCCCGTG 59.990 44.000 0.00 0.00 0.00 4.94
2530 2698 5.138276 TGTTACTCAGATTAGATAGCCCGT 58.862 41.667 0.00 0.00 0.00 5.28
2531 2699 5.707242 TGTTACTCAGATTAGATAGCCCG 57.293 43.478 0.00 0.00 0.00 6.13
2562 2730 7.064134 CCTCGTTGATGTTTGTATTAGCTACAA 59.936 37.037 0.00 0.00 46.22 2.41
2576 2744 3.074412 CCTGCTAAACCTCGTTGATGTT 58.926 45.455 0.00 0.00 0.00 2.71
2577 2745 2.301870 TCCTGCTAAACCTCGTTGATGT 59.698 45.455 0.00 0.00 0.00 3.06
2578 2746 2.932614 CTCCTGCTAAACCTCGTTGATG 59.067 50.000 0.00 0.00 0.00 3.07
2583 2763 2.367567 TCAAACTCCTGCTAAACCTCGT 59.632 45.455 0.00 0.00 0.00 4.18
2585 2765 3.339141 CCTCAAACTCCTGCTAAACCTC 58.661 50.000 0.00 0.00 0.00 3.85
2594 2774 1.059913 ACTCACCCCTCAAACTCCTG 58.940 55.000 0.00 0.00 0.00 3.86
2608 2789 1.740025 GCCATAAGTCAGCCAACTCAC 59.260 52.381 0.00 0.00 0.00 3.51
2628 2809 4.105486 CAATCATCATCTTGCAGTTGCTG 58.895 43.478 5.62 0.00 42.66 4.41
2643 2824 6.118170 CCATGGTGATATCCCTACAATCATC 58.882 44.000 2.57 0.00 32.60 2.92
2646 2827 4.018960 AGCCATGGTGATATCCCTACAATC 60.019 45.833 14.67 0.00 0.00 2.67
2661 2842 2.277737 CCCATCAGCAGCCATGGT 59.722 61.111 14.67 0.00 38.37 3.55
2662 2843 2.520982 CCCCATCAGCAGCCATGG 60.521 66.667 7.63 7.63 39.58 3.66
2663 2844 3.224324 GCCCCATCAGCAGCCATG 61.224 66.667 0.00 0.00 0.00 3.66
2664 2845 1.648302 TAAGCCCCATCAGCAGCCAT 61.648 55.000 0.00 0.00 0.00 4.40
2665 2846 1.862049 TTAAGCCCCATCAGCAGCCA 61.862 55.000 0.00 0.00 0.00 4.75
2666 2847 0.468771 ATTAAGCCCCATCAGCAGCC 60.469 55.000 0.00 0.00 0.00 4.85
2667 2848 1.339291 GAATTAAGCCCCATCAGCAGC 59.661 52.381 0.00 0.00 0.00 5.25
2669 2850 3.053395 AGAAGAATTAAGCCCCATCAGCA 60.053 43.478 0.00 0.00 0.00 4.41
2671 2852 3.887716 CCAGAAGAATTAAGCCCCATCAG 59.112 47.826 0.00 0.00 0.00 2.90
2672 2853 3.269381 ACCAGAAGAATTAAGCCCCATCA 59.731 43.478 0.00 0.00 0.00 3.07
2674 2855 3.269381 TGACCAGAAGAATTAAGCCCCAT 59.731 43.478 0.00 0.00 0.00 4.00
2676 2857 3.054361 TCTGACCAGAAGAATTAAGCCCC 60.054 47.826 0.00 0.00 33.91 5.80
2694 2876 5.616204 CGTCGTGTACTTGACTGTAATCTGA 60.616 44.000 13.64 0.00 32.93 3.27
2705 2887 4.633126 AGCTAGTTATCGTCGTGTACTTGA 59.367 41.667 0.00 0.00 0.00 3.02
2706 2888 4.906423 AGCTAGTTATCGTCGTGTACTTG 58.094 43.478 0.00 0.00 0.00 3.16
2710 2892 5.351458 TCACTAGCTAGTTATCGTCGTGTA 58.649 41.667 23.94 0.00 33.46 2.90
2711 2893 4.186926 TCACTAGCTAGTTATCGTCGTGT 58.813 43.478 23.94 0.00 33.46 4.49
2712 2894 4.790810 TCACTAGCTAGTTATCGTCGTG 57.209 45.455 23.94 10.31 33.46 4.35
2716 2898 5.278561 GCTTCCATCACTAGCTAGTTATCGT 60.279 44.000 23.94 5.64 33.46 3.73
2717 2899 5.157781 GCTTCCATCACTAGCTAGTTATCG 58.842 45.833 23.94 14.21 33.46 2.92
2718 2900 5.245075 AGGCTTCCATCACTAGCTAGTTATC 59.755 44.000 23.94 9.02 33.46 1.75
2719 2901 5.151454 AGGCTTCCATCACTAGCTAGTTAT 58.849 41.667 23.94 18.44 33.46 1.89
2722 2904 3.039252 AGGCTTCCATCACTAGCTAGT 57.961 47.619 20.95 20.95 36.90 2.57
2766 3307 1.580059 TTAGGAACCAGGGTAGCCTG 58.420 55.000 30.36 30.36 35.55 4.85
2770 3311 3.344515 GCACTTTTAGGAACCAGGGTAG 58.655 50.000 0.00 0.00 0.00 3.18
2771 3312 2.040679 GGCACTTTTAGGAACCAGGGTA 59.959 50.000 0.00 0.00 0.00 3.69
2774 3315 2.586648 AGGCACTTTTAGGAACCAGG 57.413 50.000 0.00 0.00 27.25 4.45
2849 3390 7.870445 CAGCCTCTCTTATGTAGGTTATTCTTC 59.130 40.741 0.00 0.00 32.67 2.87
2854 3395 5.716979 TCCAGCCTCTCTTATGTAGGTTAT 58.283 41.667 0.00 0.00 32.67 1.89
2855 3396 5.138758 TCCAGCCTCTCTTATGTAGGTTA 57.861 43.478 0.00 0.00 32.67 2.85
2857 3398 3.052490 ACTCCAGCCTCTCTTATGTAGGT 60.052 47.826 0.00 0.00 32.67 3.08
2858 3399 3.320541 CACTCCAGCCTCTCTTATGTAGG 59.679 52.174 0.00 0.00 0.00 3.18
2859 3400 3.320541 CCACTCCAGCCTCTCTTATGTAG 59.679 52.174 0.00 0.00 0.00 2.74
2860 3401 3.300388 CCACTCCAGCCTCTCTTATGTA 58.700 50.000 0.00 0.00 0.00 2.29
2861 3402 2.114616 CCACTCCAGCCTCTCTTATGT 58.885 52.381 0.00 0.00 0.00 2.29
2873 3414 2.353208 GCACTTCTCACTACCACTCCAG 60.353 54.545 0.00 0.00 0.00 3.86
2901 3448 3.501062 CCTATATCTTCCGCGTAGTCACA 59.499 47.826 4.92 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.