Multiple sequence alignment - TraesCS4A01G007700

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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 TraesCS4A01G007700 chr4A 100.000 2366 0 0 1 2366 4821985 4824350 0.000000e+00 4370
1 TraesCS4A01G007700 chr4A 90.769 325 26 4 24 346 679973317 679973639 4.670000e-117 431
2 TraesCS4A01G007700 chr4A 81.250 128 22 2 364 490 655470330 655470204 4.160000e-18 102
3 TraesCS4A01G007700 chr4B 90.105 1334 86 16 636 1941 582751996 582750681 0.000000e+00 1690
4 TraesCS4A01G007700 chr4B 90.373 322 22 6 27 341 595270119 595270438 4.700000e-112 414
5 TraesCS4A01G007700 chr4B 81.653 496 74 13 883 1369 651147547 651148034 1.700000e-106 396
6 TraesCS4A01G007700 chr4B 84.553 123 17 2 361 482 5733992 5734113 1.150000e-23 121
7 TraesCS4A01G007700 chr4D 88.952 1231 94 21 636 1843 465757944 465756733 0.000000e+00 1482
8 TraesCS4A01G007700 chr4D 87.925 530 59 3 1840 2365 465753507 465752979 9.290000e-174 619
9 TraesCS4A01G007700 chr4D 95.518 357 14 1 1 357 465758513 465758159 9.490000e-159 569
10 TraesCS4A01G007700 chr4D 91.515 330 26 2 19 347 472923971 472924299 9.970000e-124 453
11 TraesCS4A01G007700 chr4D 80.990 505 71 12 883 1369 504561986 504562483 6.170000e-101 377
12 TraesCS4A01G007700 chr4D 80.792 505 72 12 883 1369 504511513 504512010 2.870000e-99 372
13 TraesCS4A01G007700 chrUn 87.240 337 41 2 1016 1351 394590667 394590332 1.330000e-102 383
14 TraesCS4A01G007700 chrUn 82.443 131 21 2 361 490 69322128 69322257 1.920000e-21 113
15 TraesCS4A01G007700 chr5A 87.059 340 42 2 1013 1351 689185787 689186125 1.330000e-102 383
16 TraesCS4A01G007700 chr5A 81.935 465 68 9 883 1335 689177284 689177744 1.720000e-101 379
17 TraesCS4A01G007700 chr5A 86.066 122 17 0 369 490 600932994 600932873 5.310000e-27 132
18 TraesCS4A01G007700 chr6D 89.231 130 14 0 361 490 268286558 268286429 1.880000e-36 163
19 TraesCS4A01G007700 chr2B 93.333 105 7 0 2261 2365 758374265 758374369 3.150000e-34 156
20 TraesCS4A01G007700 chr2B 84.962 133 19 1 357 488 799553216 799553348 1.480000e-27 134
21 TraesCS4A01G007700 chr2B 83.077 130 20 2 362 490 587480020 587480148 1.490000e-22 117
22 TraesCS4A01G007700 chr7D 87.692 130 16 0 361 490 631661186 631661315 4.070000e-33 152
23 TraesCS4A01G007700 chr3D 83.562 146 21 3 361 505 545281214 545281071 1.480000e-27 134


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 TraesCS4A01G007700 chr4A 4821985 4824350 2365 False 4370 4370 100.000000 1 2366 1 chr4A.!!$F1 2365
1 TraesCS4A01G007700 chr4B 582750681 582751996 1315 True 1690 1690 90.105000 636 1941 1 chr4B.!!$R1 1305
2 TraesCS4A01G007700 chr4D 465752979 465758513 5534 True 890 1482 90.798333 1 2365 3 chr4D.!!$R1 2364

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
983 1110 0.179032 TCCACACACCGCAGTCAAAT 60.179 50.0 0.0 0.0 0.0 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2179 5560 0.398522 TAGGAGGGGACGATGCACAT 60.399 55.0 0.0 0.0 0.0 3.21 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
154 155 5.769662 TGGTTAGCAACTCAAACTTGATGAT 59.230 36.000 0.00 0.00 36.46 2.45
301 302 9.755804 TTTCAAAAATTGTGTGTGCTATATTCA 57.244 25.926 0.00 0.00 0.00 2.57
305 306 9.502145 AAAAATTGTGTGTGCTATATTCATACG 57.498 29.630 0.00 0.00 0.00 3.06
366 367 2.734755 CCATCTGGTAGGGCAATGAA 57.265 50.000 0.00 0.00 0.00 2.57
367 368 3.017048 CCATCTGGTAGGGCAATGAAA 57.983 47.619 0.00 0.00 0.00 2.69
368 369 3.364549 CCATCTGGTAGGGCAATGAAAA 58.635 45.455 0.00 0.00 0.00 2.29
369 370 3.768757 CCATCTGGTAGGGCAATGAAAAA 59.231 43.478 0.00 0.00 0.00 1.94
406 407 5.427036 AAAAATAGCGTCGTCCTTGAAAA 57.573 34.783 0.00 0.00 0.00 2.29
407 408 5.622770 AAAATAGCGTCGTCCTTGAAAAT 57.377 34.783 0.00 0.00 0.00 1.82
408 409 6.730960 AAAATAGCGTCGTCCTTGAAAATA 57.269 33.333 0.00 0.00 0.00 1.40
409 410 6.920569 AAATAGCGTCGTCCTTGAAAATAT 57.079 33.333 0.00 0.00 0.00 1.28
410 411 5.907197 ATAGCGTCGTCCTTGAAAATATG 57.093 39.130 0.00 0.00 0.00 1.78
411 412 2.351726 AGCGTCGTCCTTGAAAATATGC 59.648 45.455 0.00 0.00 0.00 3.14
412 413 2.351726 GCGTCGTCCTTGAAAATATGCT 59.648 45.455 0.00 0.00 0.00 3.79
413 414 3.554324 GCGTCGTCCTTGAAAATATGCTA 59.446 43.478 0.00 0.00 0.00 3.49
414 415 4.211374 GCGTCGTCCTTGAAAATATGCTAT 59.789 41.667 0.00 0.00 0.00 2.97
415 416 5.277345 GCGTCGTCCTTGAAAATATGCTATT 60.277 40.000 0.00 0.00 0.00 1.73
416 417 6.073980 GCGTCGTCCTTGAAAATATGCTATTA 60.074 38.462 0.00 0.00 0.00 0.98
417 418 7.502339 CGTCGTCCTTGAAAATATGCTATTAG 58.498 38.462 0.00 0.00 0.00 1.73
418 419 7.291567 GTCGTCCTTGAAAATATGCTATTAGC 58.708 38.462 8.80 8.80 42.82 3.09
419 420 6.145534 TCGTCCTTGAAAATATGCTATTAGCG 59.854 38.462 10.94 0.00 46.26 4.26
420 421 6.073765 CGTCCTTGAAAATATGCTATTAGCGT 60.074 38.462 14.53 14.53 46.26 5.07
421 422 7.072030 GTCCTTGAAAATATGCTATTAGCGTG 58.928 38.462 18.61 1.55 46.26 5.34
422 423 5.853282 CCTTGAAAATATGCTATTAGCGTGC 59.147 40.000 18.61 5.49 46.26 5.34
423 424 6.293626 CCTTGAAAATATGCTATTAGCGTGCT 60.294 38.462 18.61 0.00 46.26 4.40
424 425 7.095229 CCTTGAAAATATGCTATTAGCGTGCTA 60.095 37.037 18.61 0.00 46.26 3.49
425 426 7.905604 TGAAAATATGCTATTAGCGTGCTAT 57.094 32.000 18.61 5.81 46.26 2.97
426 427 8.322906 TGAAAATATGCTATTAGCGTGCTATT 57.677 30.769 18.61 9.02 46.26 1.73
427 428 9.430623 TGAAAATATGCTATTAGCGTGCTATTA 57.569 29.630 18.61 3.20 46.26 0.98
428 429 9.907576 GAAAATATGCTATTAGCGTGCTATTAG 57.092 33.333 18.61 19.28 46.26 1.73
429 430 7.470289 AATATGCTATTAGCGTGCTATTAGC 57.530 36.000 30.40 30.40 46.26 3.09
430 431 3.890705 GCTATTAGCGTGCTATTAGCG 57.109 47.619 26.76 10.68 46.26 4.26
431 432 3.499048 GCTATTAGCGTGCTATTAGCGA 58.501 45.455 26.76 5.81 46.26 4.93
432 433 3.544285 GCTATTAGCGTGCTATTAGCGAG 59.456 47.826 26.76 11.17 46.26 5.03
433 434 3.917329 ATTAGCGTGCTATTAGCGAGA 57.083 42.857 10.94 0.00 46.26 4.04
434 435 2.971430 TAGCGTGCTATTAGCGAGAG 57.029 50.000 10.94 3.72 46.26 3.20
435 436 1.309950 AGCGTGCTATTAGCGAGAGA 58.690 50.000 10.94 0.00 46.26 3.10
436 437 1.883275 AGCGTGCTATTAGCGAGAGAT 59.117 47.619 10.94 0.00 46.26 2.75
437 438 2.294791 AGCGTGCTATTAGCGAGAGATT 59.705 45.455 10.94 0.00 46.26 2.40
438 439 3.053455 GCGTGCTATTAGCGAGAGATTT 58.947 45.455 10.94 0.00 46.26 2.17
439 440 3.491267 GCGTGCTATTAGCGAGAGATTTT 59.509 43.478 10.94 0.00 46.26 1.82
440 441 4.680110 GCGTGCTATTAGCGAGAGATTTTA 59.320 41.667 10.94 0.00 46.26 1.52
441 442 5.346281 GCGTGCTATTAGCGAGAGATTTTAT 59.654 40.000 10.94 0.00 46.26 1.40
442 443 6.527023 GCGTGCTATTAGCGAGAGATTTTATA 59.473 38.462 10.94 0.00 46.26 0.98
443 444 7.221067 GCGTGCTATTAGCGAGAGATTTTATAT 59.779 37.037 10.94 0.00 46.26 0.86
444 445 9.077674 CGTGCTATTAGCGAGAGATTTTATATT 57.922 33.333 10.94 0.00 46.26 1.28
482 483 7.197071 AGACAATTCTCTACACTCTATAGCG 57.803 40.000 0.00 0.00 0.00 4.26
483 484 5.764131 ACAATTCTCTACACTCTATAGCGC 58.236 41.667 0.00 0.00 0.00 5.92
484 485 4.671880 ATTCTCTACACTCTATAGCGCG 57.328 45.455 0.00 0.00 0.00 6.86
485 486 1.799403 TCTCTACACTCTATAGCGCGC 59.201 52.381 26.66 26.66 0.00 6.86
486 487 1.801771 CTCTACACTCTATAGCGCGCT 59.198 52.381 38.01 38.01 0.00 5.92
487 488 2.994578 CTCTACACTCTATAGCGCGCTA 59.005 50.000 39.72 39.72 0.00 4.26
488 489 3.597255 TCTACACTCTATAGCGCGCTAT 58.403 45.455 44.16 44.16 41.58 2.97
489 490 4.001652 TCTACACTCTATAGCGCGCTATT 58.998 43.478 46.76 33.37 39.65 1.73
490 491 3.644884 ACACTCTATAGCGCGCTATTT 57.355 42.857 46.76 32.85 39.65 1.40
491 492 3.978687 ACACTCTATAGCGCGCTATTTT 58.021 40.909 46.76 32.19 39.65 1.82
492 493 4.369182 ACACTCTATAGCGCGCTATTTTT 58.631 39.130 46.76 31.85 39.65 1.94
575 576 3.821033 GACTATTGCCTTGTGACCAAACT 59.179 43.478 0.00 0.00 0.00 2.66
578 579 0.257328 TGCCTTGTGACCAAACTGGA 59.743 50.000 0.00 0.00 40.96 3.86
599 600 8.299570 ACTGGAAAGCAAAGATAACAGTAATTG 58.700 33.333 0.00 0.00 36.30 2.32
650 735 7.361457 GCCTTCATGTTTTACCTTACATTACGT 60.361 37.037 0.00 0.00 32.88 3.57
697 815 9.935241 GATCAGGAGAAAATAACAGCTCATATA 57.065 33.333 0.00 0.00 0.00 0.86
712 830 8.050325 ACAGCTCATATATATCGACTTAGGACT 58.950 37.037 0.00 0.00 0.00 3.85
730 848 5.420409 AGGACTATCTTAAAACGGCTCAAG 58.580 41.667 0.00 0.00 0.00 3.02
748 867 4.261801 TCAAGACTAGCACCAATTTAGGC 58.738 43.478 0.00 0.00 0.00 3.93
912 1031 2.400158 CCGTCGGACGCTCTCTTCT 61.400 63.158 24.26 0.00 40.91 2.85
927 1046 2.808543 CTCTTCTGCCCATAAATACCGC 59.191 50.000 0.00 0.00 0.00 5.68
971 1090 0.671472 CAGCTCGAAGCATCCACACA 60.671 55.000 9.09 0.00 45.56 3.72
972 1091 0.671781 AGCTCGAAGCATCCACACAC 60.672 55.000 9.09 0.00 45.56 3.82
974 1093 1.354337 CTCGAAGCATCCACACACCG 61.354 60.000 0.00 0.00 0.00 4.94
983 1110 0.179032 TCCACACACCGCAGTCAAAT 60.179 50.000 0.00 0.00 0.00 2.32
984 1111 0.238289 CCACACACCGCAGTCAAATC 59.762 55.000 0.00 0.00 0.00 2.17
996 1123 4.975502 CGCAGTCAAATCTCTCTATCAGTC 59.024 45.833 0.00 0.00 0.00 3.51
997 1124 5.288804 GCAGTCAAATCTCTCTATCAGTCC 58.711 45.833 0.00 0.00 0.00 3.85
1005 1132 3.139957 TCTCTCTATCAGTCCAGATGGCT 59.860 47.826 0.00 0.00 34.44 4.75
1011 1138 1.202330 CAGTCCAGATGGCTTCCTCT 58.798 55.000 0.00 0.00 34.44 3.69
1223 1350 3.346426 CCTTGACCAAGAAGGGTGG 57.654 57.895 11.06 0.00 42.53 4.61
1241 1368 1.513622 GCTTCTGGGAGGTCTCGTC 59.486 63.158 0.00 0.00 0.00 4.20
1242 1369 1.950973 GCTTCTGGGAGGTCTCGTCC 61.951 65.000 0.52 0.52 37.65 4.79
1244 1371 0.898789 TTCTGGGAGGTCTCGTCCAC 60.899 60.000 10.02 1.92 39.85 4.02
1248 1375 1.477685 GGGAGGTCTCGTCCACCAAA 61.478 60.000 10.02 0.00 39.85 3.28
1260 1387 2.027625 CACCAAAGACCTCGTCGGC 61.028 63.158 0.00 0.00 37.67 5.54
1285 1412 0.443869 CAACTTCCGCTTCATGTCCG 59.556 55.000 0.00 0.00 0.00 4.79
1360 1487 1.003476 GAAACCTACGCCCCGGAAA 60.003 57.895 0.73 0.00 0.00 3.13
1383 1510 0.458025 GATCCTTCCGTCGGTGTGTC 60.458 60.000 11.88 1.27 0.00 3.67
1384 1511 1.183030 ATCCTTCCGTCGGTGTGTCA 61.183 55.000 11.88 0.00 0.00 3.58
1385 1512 1.663702 CCTTCCGTCGGTGTGTCAC 60.664 63.158 11.88 0.00 0.00 3.67
1398 1525 3.303495 GGTGTGTCACATTAGTCGATTCG 59.697 47.826 9.31 0.00 35.86 3.34
1426 1553 7.762588 TTTCCCTTGTTTCCGTTTCATTATA 57.237 32.000 0.00 0.00 0.00 0.98
1427 1554 7.948034 TTCCCTTGTTTCCGTTTCATTATAT 57.052 32.000 0.00 0.00 0.00 0.86
1518 1658 0.955428 GCGGATGTGTTTGCTCTCCA 60.955 55.000 0.00 0.00 0.00 3.86
1519 1659 1.742761 CGGATGTGTTTGCTCTCCAT 58.257 50.000 0.00 0.00 0.00 3.41
1520 1660 2.086869 CGGATGTGTTTGCTCTCCATT 58.913 47.619 0.00 0.00 0.00 3.16
1530 1675 1.307097 GCTCTCCATTCATCCACTGC 58.693 55.000 0.00 0.00 0.00 4.40
1628 1773 8.478877 TGTCACCTTTATTTTGGTTATGTTTGT 58.521 29.630 0.00 0.00 33.75 2.83
1652 1797 4.726416 TCTACTTACTTTGAGGTAACGCG 58.274 43.478 3.53 3.53 46.39 6.01
1663 1808 3.379057 TGAGGTAACGCGATACAAGATCA 59.621 43.478 25.04 19.00 46.39 2.92
1666 1811 5.172934 AGGTAACGCGATACAAGATCAAAA 58.827 37.500 25.04 0.00 46.39 2.44
1677 1822 7.709182 CGATACAAGATCAAAAGGTGGTATGTA 59.291 37.037 0.00 0.00 0.00 2.29
1695 1840 7.235606 TGGTATGTAAAGGATCTAAGAGGATGG 59.764 40.741 0.00 0.00 0.00 3.51
1696 1841 7.455008 GGTATGTAAAGGATCTAAGAGGATGGA 59.545 40.741 0.00 0.00 0.00 3.41
1708 1853 7.776107 TCTAAGAGGATGGAGATATATTTGCG 58.224 38.462 0.00 0.00 0.00 4.85
1721 1866 6.886459 AGATATATTTGCGTTGCCTATTCCAT 59.114 34.615 0.00 0.00 0.00 3.41
1722 1867 5.789643 ATATTTGCGTTGCCTATTCCATT 57.210 34.783 0.00 0.00 0.00 3.16
1725 1870 3.951775 TGCGTTGCCTATTCCATTTTT 57.048 38.095 0.00 0.00 0.00 1.94
1816 1963 4.022849 GGGAAAGTCAAGAACCATGTTCAG 60.023 45.833 9.42 2.25 0.00 3.02
1822 1969 5.888161 AGTCAAGAACCATGTTCAGTTTCTT 59.112 36.000 9.42 0.00 0.00 2.52
1903 5280 5.986004 AGTTGCGCTTTATCCACTTATAC 57.014 39.130 9.73 0.00 0.00 1.47
1930 5307 1.609208 AGCAGAGTCGCCAAATTTGT 58.391 45.000 16.73 0.00 0.00 2.83
1943 5320 6.024664 CGCCAAATTTGTAATCGTCATGTTA 58.975 36.000 16.73 0.00 0.00 2.41
1944 5321 6.021782 CGCCAAATTTGTAATCGTCATGTTAC 60.022 38.462 16.73 0.00 0.00 2.50
1954 5331 3.638484 TCGTCATGTTACATATGGAGCG 58.362 45.455 7.80 0.00 0.00 5.03
1985 5362 2.407090 CGATGTGCAAACTCAGAGTCA 58.593 47.619 2.72 0.00 0.00 3.41
1986 5363 2.802247 CGATGTGCAAACTCAGAGTCAA 59.198 45.455 2.72 0.00 0.00 3.18
1992 5369 6.463360 TGTGCAAACTCAGAGTCAACATATA 58.537 36.000 2.72 0.00 0.00 0.86
1994 5371 7.278646 TGTGCAAACTCAGAGTCAACATATATC 59.721 37.037 2.72 0.00 0.00 1.63
2003 5380 5.011533 AGAGTCAACATATATCAGCCTCCAC 59.988 44.000 0.00 0.00 0.00 4.02
2004 5381 4.655649 AGTCAACATATATCAGCCTCCACA 59.344 41.667 0.00 0.00 0.00 4.17
2012 5392 8.220559 ACATATATCAGCCTCCACATTTTTACT 58.779 33.333 0.00 0.00 0.00 2.24
2066 5446 6.697892 TCCAAAATCAAACGTTTTATCACACC 59.302 34.615 11.66 0.00 0.00 4.16
2080 5461 7.655236 TTTATCACACCATTTCAAAGCAATG 57.345 32.000 0.00 0.00 0.00 2.82
2089 5470 6.629128 CCATTTCAAAGCAATGGTGTACATA 58.371 36.000 0.00 0.00 44.04 2.29
2099 5480 9.988815 AAGCAATGGTGTACATAATTTTAACAA 57.011 25.926 0.00 0.00 39.40 2.83
2129 5510 7.969387 ATGAACAAAATCATTTAATCGACGG 57.031 32.000 0.00 0.00 36.67 4.79
2131 5512 4.339429 ACAAAATCATTTAATCGACGGCG 58.661 39.130 2.87 2.87 39.35 6.46
2132 5513 4.142773 ACAAAATCATTTAATCGACGGCGT 60.143 37.500 14.65 14.65 38.98 5.68
2136 5517 2.853594 TCATTTAATCGACGGCGTGTAC 59.146 45.455 21.19 1.14 38.98 2.90
2143 5524 0.365523 CGACGGCGTGTACAAATCAG 59.634 55.000 21.19 0.00 0.00 2.90
2149 5530 3.483574 CGGCGTGTACAAATCAGATGTTC 60.484 47.826 0.00 0.00 32.27 3.18
2151 5532 4.394795 GCGTGTACAAATCAGATGTTCAC 58.605 43.478 0.00 6.41 42.29 3.18
2159 5540 2.502213 TCAGATGTTCACGACGTGTT 57.498 45.000 26.01 10.86 34.79 3.32
2163 5544 0.306533 ATGTTCACGACGTGTTTGCC 59.693 50.000 26.01 11.73 34.79 4.52
2164 5545 1.367195 GTTCACGACGTGTTTGCCG 60.367 57.895 26.01 0.17 34.79 5.69
2176 5557 1.372499 TTTGCCGTCGTCTTCTCCG 60.372 57.895 0.00 0.00 0.00 4.63
2187 5568 1.929836 GTCTTCTCCGACATGTGCATC 59.070 52.381 1.15 0.00 34.11 3.91
2196 5577 1.524621 CATGTGCATCGTCCCCTCC 60.525 63.158 0.00 0.00 0.00 4.30
2198 5579 0.398522 ATGTGCATCGTCCCCTCCTA 60.399 55.000 0.00 0.00 0.00 2.94
2203 5584 1.067776 GCATCGTCCCCTCCTATAACG 60.068 57.143 0.00 0.00 34.80 3.18
2206 5587 0.957362 CGTCCCCTCCTATAACGTCC 59.043 60.000 0.00 0.00 0.00 4.79
2240 5621 2.104111 TGGTCACCATTCACGTCTTCTT 59.896 45.455 0.00 0.00 0.00 2.52
2268 5649 1.374343 CTCGCACCACTAGACGGCTA 61.374 60.000 0.00 0.00 0.00 3.93
2276 5657 4.097437 CACCACTAGACGGCTAAGATGTTA 59.903 45.833 0.00 0.00 0.00 2.41
2288 5669 1.853963 AGATGTTACCGCCAGAGAGT 58.146 50.000 0.00 0.00 0.00 3.24
2291 5672 2.450609 TGTTACCGCCAGAGAGTTTC 57.549 50.000 0.00 0.00 0.00 2.78
2304 5685 5.220873 CCAGAGAGTTTCGATTACGATCTGA 60.221 44.000 22.60 0.00 45.42 3.27
2305 5686 5.679355 CAGAGAGTTTCGATTACGATCTGAC 59.321 44.000 19.45 2.77 45.42 3.51
2311 5692 2.287103 TCGATTACGATCTGACGACTGG 59.713 50.000 0.00 0.00 43.81 4.00
2325 5706 2.086869 CGACTGGAAATCATTGCCACT 58.913 47.619 0.00 0.00 0.00 4.00
2347 5728 0.108774 GCACCAAGTAGGATAGGGGC 59.891 60.000 0.00 0.00 44.24 5.80
2360 5741 3.139211 GGATAGGGGCTTCTTCTTGGAAT 59.861 47.826 0.00 0.00 0.00 3.01
2365 5746 3.562176 GGGGCTTCTTCTTGGAATCTGAA 60.562 47.826 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 7.120138 TGGCATTGACATGATGATATATCACAC 59.880 37.037 17.60 14.39 40.03 3.82
280 281 8.673711 ACGTATGAATATAGCACACACAATTTT 58.326 29.630 0.00 0.00 0.00 1.82
285 286 8.880878 AAATACGTATGAATATAGCACACACA 57.119 30.769 9.24 0.00 0.00 3.72
286 287 9.193133 AGAAATACGTATGAATATAGCACACAC 57.807 33.333 9.24 0.00 0.00 3.82
301 302 8.893219 ATGTGACATTCATGAGAAATACGTAT 57.107 30.769 1.14 1.14 37.29 3.06
384 385 5.427036 TTTTCAAGGACGACGCTATTTTT 57.573 34.783 0.00 0.00 0.00 1.94
385 386 5.622770 ATTTTCAAGGACGACGCTATTTT 57.377 34.783 0.00 0.00 0.00 1.82
386 387 6.715464 CATATTTTCAAGGACGACGCTATTT 58.285 36.000 0.00 0.00 0.00 1.40
387 388 5.277345 GCATATTTTCAAGGACGACGCTATT 60.277 40.000 0.00 0.00 0.00 1.73
388 389 4.211374 GCATATTTTCAAGGACGACGCTAT 59.789 41.667 0.00 0.00 0.00 2.97
389 390 3.554324 GCATATTTTCAAGGACGACGCTA 59.446 43.478 0.00 0.00 0.00 4.26
390 391 2.351726 GCATATTTTCAAGGACGACGCT 59.648 45.455 0.00 0.00 0.00 5.07
391 392 2.351726 AGCATATTTTCAAGGACGACGC 59.648 45.455 0.00 0.00 0.00 5.19
392 393 5.907197 ATAGCATATTTTCAAGGACGACG 57.093 39.130 0.00 0.00 0.00 5.12
393 394 7.291567 GCTAATAGCATATTTTCAAGGACGAC 58.708 38.462 7.49 0.00 41.89 4.34
394 395 6.145534 CGCTAATAGCATATTTTCAAGGACGA 59.854 38.462 13.15 0.00 42.58 4.20
395 396 6.073765 ACGCTAATAGCATATTTTCAAGGACG 60.074 38.462 13.15 0.00 42.58 4.79
396 397 7.072030 CACGCTAATAGCATATTTTCAAGGAC 58.928 38.462 13.15 0.00 42.58 3.85
397 398 6.293407 GCACGCTAATAGCATATTTTCAAGGA 60.293 38.462 13.15 0.00 42.58 3.36
398 399 5.853282 GCACGCTAATAGCATATTTTCAAGG 59.147 40.000 13.15 0.00 42.58 3.61
399 400 6.662616 AGCACGCTAATAGCATATTTTCAAG 58.337 36.000 13.15 0.00 42.58 3.02
400 401 6.618287 AGCACGCTAATAGCATATTTTCAA 57.382 33.333 13.15 0.00 42.58 2.69
401 402 7.905604 ATAGCACGCTAATAGCATATTTTCA 57.094 32.000 13.15 0.00 42.58 2.69
402 403 9.907576 CTAATAGCACGCTAATAGCATATTTTC 57.092 33.333 13.15 0.00 42.58 2.29
410 411 3.499048 TCGCTAATAGCACGCTAATAGC 58.501 45.455 25.98 25.98 46.52 2.97
411 412 4.971008 TCTCGCTAATAGCACGCTAATAG 58.029 43.478 13.15 14.28 42.58 1.73
412 413 4.694037 TCTCTCGCTAATAGCACGCTAATA 59.306 41.667 13.15 0.00 42.58 0.98
413 414 3.502595 TCTCTCGCTAATAGCACGCTAAT 59.497 43.478 13.15 0.00 42.58 1.73
414 415 2.876550 TCTCTCGCTAATAGCACGCTAA 59.123 45.455 13.15 0.00 42.58 3.09
415 416 2.490991 TCTCTCGCTAATAGCACGCTA 58.509 47.619 13.15 0.39 42.58 4.26
416 417 1.309950 TCTCTCGCTAATAGCACGCT 58.690 50.000 13.15 0.00 42.58 5.07
417 418 2.339728 ATCTCTCGCTAATAGCACGC 57.660 50.000 13.15 0.00 42.58 5.34
418 419 6.936222 ATAAAATCTCTCGCTAATAGCACG 57.064 37.500 13.15 2.42 42.58 5.34
457 458 8.042952 GCGCTATAGAGTGTAGAGAATTGTCTC 61.043 44.444 8.63 0.00 41.74 3.36
458 459 6.293735 GCGCTATAGAGTGTAGAGAATTGTCT 60.294 42.308 10.33 10.33 35.48 3.41
459 460 5.854338 GCGCTATAGAGTGTAGAGAATTGTC 59.146 44.000 3.21 0.00 35.48 3.18
460 461 5.561145 CGCGCTATAGAGTGTAGAGAATTGT 60.561 44.000 5.56 0.00 35.48 2.71
461 462 4.848841 CGCGCTATAGAGTGTAGAGAATTG 59.151 45.833 5.56 0.00 35.48 2.32
462 463 4.614078 GCGCGCTATAGAGTGTAGAGAATT 60.614 45.833 26.67 0.00 35.48 2.17
463 464 3.120130 GCGCGCTATAGAGTGTAGAGAAT 60.120 47.826 26.67 0.00 35.48 2.40
464 465 2.223611 GCGCGCTATAGAGTGTAGAGAA 59.776 50.000 26.67 0.00 35.48 2.87
465 466 1.799403 GCGCGCTATAGAGTGTAGAGA 59.201 52.381 26.67 0.00 35.48 3.10
466 467 1.801771 AGCGCGCTATAGAGTGTAGAG 59.198 52.381 35.79 0.00 35.48 2.43
467 468 1.880271 AGCGCGCTATAGAGTGTAGA 58.120 50.000 35.79 0.00 35.48 2.59
468 469 4.343811 AATAGCGCGCTATAGAGTGTAG 57.656 45.455 43.81 0.00 38.20 2.74
469 470 4.761235 AAATAGCGCGCTATAGAGTGTA 57.239 40.909 43.81 23.77 38.20 2.90
470 471 3.644884 AAATAGCGCGCTATAGAGTGT 57.355 42.857 43.81 29.07 38.20 3.55
471 472 4.974103 AAAAATAGCGCGCTATAGAGTG 57.026 40.909 43.81 12.17 38.20 3.51
491 492 7.721842 TGACACTGTATTCTACCCATTGAAAAA 59.278 33.333 0.00 0.00 0.00 1.94
492 493 7.227873 TGACACTGTATTCTACCCATTGAAAA 58.772 34.615 0.00 0.00 0.00 2.29
493 494 6.774673 TGACACTGTATTCTACCCATTGAAA 58.225 36.000 0.00 0.00 0.00 2.69
494 495 6.367374 TGACACTGTATTCTACCCATTGAA 57.633 37.500 0.00 0.00 0.00 2.69
495 496 6.170506 GTTGACACTGTATTCTACCCATTGA 58.829 40.000 0.00 0.00 0.00 2.57
496 497 5.937540 TGTTGACACTGTATTCTACCCATTG 59.062 40.000 0.00 0.00 0.00 2.82
497 498 5.938125 GTGTTGACACTGTATTCTACCCATT 59.062 40.000 7.01 0.00 43.25 3.16
498 499 5.488341 GTGTTGACACTGTATTCTACCCAT 58.512 41.667 7.01 0.00 43.25 4.00
499 500 4.890088 GTGTTGACACTGTATTCTACCCA 58.110 43.478 7.01 0.00 43.25 4.51
549 550 3.008923 TGGTCACAAGGCAATAGTCATCA 59.991 43.478 0.00 0.00 0.00 3.07
561 562 2.223805 GCTTTCCAGTTTGGTCACAAGG 60.224 50.000 0.00 0.00 39.03 3.61
575 576 7.450014 TCCAATTACTGTTATCTTTGCTTTCCA 59.550 33.333 0.00 0.00 0.00 3.53
613 614 5.975693 AAACATGAAGGCGGATAAAGAAA 57.024 34.783 0.00 0.00 0.00 2.52
617 618 5.258051 AGGTAAAACATGAAGGCGGATAAA 58.742 37.500 0.00 0.00 0.00 1.40
623 624 5.560966 ATGTAAGGTAAAACATGAAGGCG 57.439 39.130 0.00 0.00 35.06 5.52
650 735 8.712228 TGATCTGAAGGCTGATATTACTCTTA 57.288 34.615 0.00 0.00 33.46 2.10
698 816 8.562892 CCGTTTTAAGATAGTCCTAAGTCGATA 58.437 37.037 0.00 0.00 0.00 2.92
699 817 7.424001 CCGTTTTAAGATAGTCCTAAGTCGAT 58.576 38.462 0.00 0.00 0.00 3.59
700 818 6.678900 GCCGTTTTAAGATAGTCCTAAGTCGA 60.679 42.308 0.00 0.00 0.00 4.20
701 819 5.458126 GCCGTTTTAAGATAGTCCTAAGTCG 59.542 44.000 0.00 0.00 0.00 4.18
702 820 6.571605 AGCCGTTTTAAGATAGTCCTAAGTC 58.428 40.000 0.00 0.00 0.00 3.01
712 830 6.040878 GCTAGTCTTGAGCCGTTTTAAGATA 58.959 40.000 0.00 0.00 33.60 1.98
730 848 2.298610 GGGCCTAAATTGGTGCTAGTC 58.701 52.381 0.84 0.00 0.00 2.59
748 867 0.532115 GCCTGCAATTAAGTGGTGGG 59.468 55.000 4.91 0.00 0.00 4.61
912 1031 3.739167 GCGCGGTATTTATGGGCA 58.261 55.556 8.83 0.00 40.80 5.36
927 1046 2.483106 GGATTCTGATGGATCATGTGCG 59.517 50.000 0.00 0.00 36.02 5.34
971 1090 3.701542 TGATAGAGAGATTTGACTGCGGT 59.298 43.478 0.00 0.00 0.00 5.68
972 1091 4.202101 ACTGATAGAGAGATTTGACTGCGG 60.202 45.833 0.00 0.00 0.00 5.69
974 1093 5.163468 TGGACTGATAGAGAGATTTGACTGC 60.163 44.000 0.00 0.00 0.00 4.40
983 1110 3.139957 AGCCATCTGGACTGATAGAGAGA 59.860 47.826 0.00 0.00 37.39 3.10
984 1111 3.499338 AGCCATCTGGACTGATAGAGAG 58.501 50.000 0.00 0.00 37.39 3.20
996 1123 0.539051 ACGAAGAGGAAGCCATCTGG 59.461 55.000 0.00 0.00 38.53 3.86
997 1124 1.472376 GGACGAAGAGGAAGCCATCTG 60.472 57.143 0.00 0.00 0.00 2.90
1005 1132 0.608640 GCCTTGAGGACGAAGAGGAA 59.391 55.000 0.06 0.00 37.39 3.36
1011 1138 1.293498 GAGCAGCCTTGAGGACGAA 59.707 57.895 0.06 0.00 37.39 3.85
1131 1258 0.029567 CTGGTCTGGCGTAGTCGATC 59.970 60.000 0.00 0.00 39.71 3.69
1223 1350 1.513622 GACGAGACCTCCCAGAAGC 59.486 63.158 0.00 0.00 0.00 3.86
1241 1368 1.374252 CCGACGAGGTCTTTGGTGG 60.374 63.158 0.00 0.00 34.51 4.61
1242 1369 2.027625 GCCGACGAGGTCTTTGGTG 61.028 63.158 0.00 0.00 43.70 4.17
1244 1371 2.434359 GGCCGACGAGGTCTTTGG 60.434 66.667 0.00 0.00 42.70 3.28
1248 1375 4.698625 AAGGGGCCGACGAGGTCT 62.699 66.667 0.00 0.00 46.10 3.85
1260 1387 0.250727 TGAAGCGGAAGTTGAAGGGG 60.251 55.000 0.00 0.00 0.00 4.79
1285 1412 0.389948 ACGTTCCTCATGCCGTTCTC 60.390 55.000 0.00 0.00 0.00 2.87
1342 1469 0.606130 TTTTCCGGGGCGTAGGTTTC 60.606 55.000 0.00 0.00 0.00 2.78
1360 1487 0.246635 CACCGACGGAAGGATCACTT 59.753 55.000 23.38 0.00 43.65 3.16
1383 1510 5.220416 GGGAAAACTCGAATCGACTAATGTG 60.220 44.000 0.00 0.00 0.00 3.21
1384 1511 4.868734 GGGAAAACTCGAATCGACTAATGT 59.131 41.667 0.00 0.00 0.00 2.71
1385 1512 5.109903 AGGGAAAACTCGAATCGACTAATG 58.890 41.667 0.00 0.00 0.00 1.90
1398 1525 4.142337 TGAAACGGAAACAAGGGAAAACTC 60.142 41.667 0.00 0.00 0.00 3.01
1426 1553 2.653726 TGAGGGCGAATACATGCAAAT 58.346 42.857 0.00 0.00 0.00 2.32
1427 1554 2.121291 TGAGGGCGAATACATGCAAA 57.879 45.000 0.00 0.00 0.00 3.68
1530 1675 2.868583 CGGAACAAGACAGATGCATAGG 59.131 50.000 0.00 0.00 0.00 2.57
1540 1685 3.061322 CGGATACAAACGGAACAAGACA 58.939 45.455 0.00 0.00 0.00 3.41
1603 1748 8.880878 ACAAACATAACCAAAATAAAGGTGAC 57.119 30.769 0.00 0.00 38.37 3.67
1628 1773 5.630680 CGCGTTACCTCAAAGTAAGTAGAAA 59.369 40.000 0.00 0.00 33.00 2.52
1652 1797 7.865706 ACATACCACCTTTTGATCTTGTATC 57.134 36.000 0.00 0.00 0.00 2.24
1663 1808 8.832735 TCTTAGATCCTTTACATACCACCTTTT 58.167 33.333 0.00 0.00 0.00 2.27
1666 1811 6.555360 CCTCTTAGATCCTTTACATACCACCT 59.445 42.308 0.00 0.00 0.00 4.00
1695 1840 6.371548 TGGAATAGGCAACGCAAATATATCTC 59.628 38.462 0.00 0.00 46.39 2.75
1696 1841 6.237901 TGGAATAGGCAACGCAAATATATCT 58.762 36.000 0.00 0.00 46.39 1.98
1743 1889 3.380320 AGTTAGTTTGTGACTGGTTTGCC 59.620 43.478 0.00 0.00 39.48 4.52
1920 5297 6.804295 TGTAACATGACGATTACAAATTTGGC 59.196 34.615 21.74 7.64 38.13 4.52
1930 5307 5.861787 CGCTCCATATGTAACATGACGATTA 59.138 40.000 0.00 0.00 0.00 1.75
1943 5320 2.111878 GCCAGCCGCTCCATATGT 59.888 61.111 1.24 0.00 0.00 2.29
1944 5321 2.670934 GGCCAGCCGCTCCATATG 60.671 66.667 0.00 0.00 37.74 1.78
1968 5345 2.984562 TGTTGACTCTGAGTTTGCACA 58.015 42.857 12.27 9.46 0.00 4.57
1985 5362 7.902920 AAAAATGTGGAGGCTGATATATGTT 57.097 32.000 0.00 0.00 0.00 2.71
1986 5363 8.220559 AGTAAAAATGTGGAGGCTGATATATGT 58.779 33.333 0.00 0.00 0.00 2.29
1992 5369 6.670695 AAAAGTAAAAATGTGGAGGCTGAT 57.329 33.333 0.00 0.00 0.00 2.90
1994 5371 6.515832 AGAAAAAGTAAAAATGTGGAGGCTG 58.484 36.000 0.00 0.00 0.00 4.85
2053 5433 5.689514 TGCTTTGAAATGGTGTGATAAAACG 59.310 36.000 0.00 0.00 0.00 3.60
2066 5446 8.706492 ATTATGTACACCATTGCTTTGAAATG 57.294 30.769 0.00 0.00 34.86 2.32
2103 5484 9.663904 CCGTCGATTAAATGATTTTGTTCATAT 57.336 29.630 0.00 0.00 35.29 1.78
2104 5485 7.642194 GCCGTCGATTAAATGATTTTGTTCATA 59.358 33.333 0.00 0.00 35.29 2.15
2115 5496 1.999048 ACACGCCGTCGATTAAATGA 58.001 45.000 0.00 0.00 39.41 2.57
2129 5510 4.394795 GTGAACATCTGATTTGTACACGC 58.605 43.478 0.00 0.00 0.00 5.34
2131 5512 5.609088 GTCGTGAACATCTGATTTGTACAC 58.391 41.667 0.00 0.00 0.00 2.90
2132 5513 4.384547 CGTCGTGAACATCTGATTTGTACA 59.615 41.667 0.00 0.00 0.00 2.90
2136 5517 3.184379 ACACGTCGTGAACATCTGATTTG 59.816 43.478 30.95 0.15 36.96 2.32
2143 5524 1.658968 GCAAACACGTCGTGAACATC 58.341 50.000 30.95 11.96 36.96 3.06
2159 5540 2.257371 CGGAGAAGACGACGGCAA 59.743 61.111 2.19 0.00 0.00 4.52
2167 5548 1.929836 GATGCACATGTCGGAGAAGAC 59.070 52.381 0.00 0.00 39.69 3.01
2176 5557 0.811616 GAGGGGACGATGCACATGTC 60.812 60.000 0.00 6.31 0.00 3.06
2179 5560 0.398522 TAGGAGGGGACGATGCACAT 60.399 55.000 0.00 0.00 0.00 3.21
2187 5568 0.957362 GGACGTTATAGGAGGGGACG 59.043 60.000 0.00 0.00 39.43 4.79
2196 5577 7.335422 ACCATACGTTCTATAGGGACGTTATAG 59.665 40.741 27.74 19.81 38.10 1.31
2198 5579 6.006449 ACCATACGTTCTATAGGGACGTTAT 58.994 40.000 27.74 19.42 38.10 1.89
2203 5584 4.022503 GGTGACCATACGTTCTATAGGGAC 60.023 50.000 0.00 0.00 0.00 4.46
2206 5587 5.723672 ATGGTGACCATACGTTCTATAGG 57.276 43.478 16.93 0.00 43.19 2.57
2240 5621 2.270352 AGTGGTGCGAGAATTTTGGA 57.730 45.000 0.00 0.00 0.00 3.53
2268 5649 2.180276 ACTCTCTGGCGGTAACATCTT 58.820 47.619 0.00 0.00 0.00 2.40
2276 5657 0.608640 AATCGAAACTCTCTGGCGGT 59.391 50.000 0.00 0.00 0.00 5.68
2291 5672 2.287103 TCCAGTCGTCAGATCGTAATCG 59.713 50.000 0.00 0.00 36.97 3.34
2304 5685 1.812571 GTGGCAATGATTTCCAGTCGT 59.187 47.619 0.00 0.00 0.00 4.34
2305 5686 2.086869 AGTGGCAATGATTTCCAGTCG 58.913 47.619 0.00 0.00 0.00 4.18
2325 5706 1.843851 CCCTATCCTACTTGGTGCCAA 59.156 52.381 3.43 3.43 37.07 4.52


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

AutoCloner maintained by Alex Coulton.