Multiple sequence alignment - TraesCS6D01G120300

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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 TraesCS6D01G120300 chr6D 100.000 2396 0 0 1 2396 85108568 85106173 0.000000e+00 4425.0
1 TraesCS6D01G120300 chr6D 88.519 601 32 7 826 1416 456414515 456415088 0.000000e+00 693.0
2 TraesCS6D01G120300 chr6D 89.437 426 27 6 272 681 84775868 84776291 2.730000e-144 521.0
3 TraesCS6D01G120300 chr6D 84.364 275 31 2 8 270 84775512 84775786 2.360000e-65 259.0
4 TraesCS6D01G120300 chr6A 90.732 669 55 5 1703 2365 101989648 101990315 0.000000e+00 885.0
5 TraesCS6D01G120300 chr6A 84.160 827 51 20 7 786 101988377 101989170 0.000000e+00 728.0
6 TraesCS6D01G120300 chr6A 89.865 148 12 3 1559 1703 101989384 101989531 1.130000e-43 187.0
7 TraesCS6D01G120300 chr3B 90.789 608 39 4 826 1416 23917028 23916421 0.000000e+00 797.0
8 TraesCS6D01G120300 chr5D 91.638 574 31 4 858 1416 445401375 445400804 0.000000e+00 778.0
9 TraesCS6D01G120300 chr5D 86.029 544 60 3 888 1416 387709200 387708658 9.610000e-159 569.0
10 TraesCS6D01G120300 chr5B 89.769 606 39 8 826 1416 543241954 543241357 0.000000e+00 754.0
11 TraesCS6D01G120300 chr5B 88.218 331 37 2 1010 1339 466198724 466198395 6.210000e-106 394.0
12 TraesCS6D01G120300 chr2B 87.086 573 54 4 859 1411 59066939 59066367 4.350000e-177 630.0
13 TraesCS6D01G120300 chr5A 89.610 308 31 1 1109 1416 490597166 490596860 8.030000e-105 390.0
14 TraesCS6D01G120300 chr5A 81.720 279 37 6 829 1093 490632920 490632642 1.110000e-53 220.0
15 TraesCS6D01G120300 chr6B 83.333 438 37 15 8 432 161450817 161451231 2.910000e-99 372.0
16 TraesCS6D01G120300 chr6B 82.877 438 39 16 8 432 161439705 161440119 6.300000e-96 361.0
17 TraesCS6D01G120300 chr6B 82.838 437 40 17 8 432 161450199 161450612 2.260000e-95 359.0
18 TraesCS6D01G120300 chr6B 81.402 328 28 13 8 323 161440323 161440629 1.110000e-58 237.0
19 TraesCS6D01G120300 chr6B 82.528 269 23 9 525 786 161451322 161451573 5.190000e-52 215.0
20 TraesCS6D01G120300 chr6B 97.619 42 1 0 439 480 161451298 161451257 3.300000e-09 73.1


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 TraesCS6D01G120300 chr6D 85106173 85108568 2395 True 4425.000000 4425 100.000000 1 2396 1 chr6D.!!$R1 2395
1 TraesCS6D01G120300 chr6D 456414515 456415088 573 False 693.000000 693 88.519000 826 1416 1 chr6D.!!$F1 590
2 TraesCS6D01G120300 chr6D 84775512 84776291 779 False 390.000000 521 86.900500 8 681 2 chr6D.!!$F2 673
3 TraesCS6D01G120300 chr6A 101988377 101990315 1938 False 600.000000 885 88.252333 7 2365 3 chr6A.!!$F1 2358
4 TraesCS6D01G120300 chr3B 23916421 23917028 607 True 797.000000 797 90.789000 826 1416 1 chr3B.!!$R1 590
5 TraesCS6D01G120300 chr5D 445400804 445401375 571 True 778.000000 778 91.638000 858 1416 1 chr5D.!!$R2 558
6 TraesCS6D01G120300 chr5D 387708658 387709200 542 True 569.000000 569 86.029000 888 1416 1 chr5D.!!$R1 528
7 TraesCS6D01G120300 chr5B 543241357 543241954 597 True 754.000000 754 89.769000 826 1416 1 chr5B.!!$R2 590
8 TraesCS6D01G120300 chr2B 59066367 59066939 572 True 630.000000 630 87.086000 859 1411 1 chr2B.!!$R1 552
9 TraesCS6D01G120300 chr6B 161450199 161451573 1374 False 315.333333 372 82.899667 8 786 3 chr6B.!!$F2 778
10 TraesCS6D01G120300 chr6B 161439705 161440629 924 False 299.000000 361 82.139500 8 432 2 chr6B.!!$F1 424

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
558 1328 0.039437 CTGAAAAGGCTGCAGCAGTG 60.039 55.0 37.63 16.88 44.36 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1520 2589 0.478942 TTTCCATCCCCAACCGTTGA 59.521 50.0 13.04 0.0 0.0 3.18 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
99 713 0.855349 CCGCATTGCTATCGTCAGAC 59.145 55.000 7.12 0.00 0.00 3.51
100 714 0.855349 CGCATTGCTATCGTCAGACC 59.145 55.000 7.12 0.00 0.00 3.85
101 715 1.536922 CGCATTGCTATCGTCAGACCT 60.537 52.381 7.12 0.00 0.00 3.85
118 732 5.061853 CAGACCTGATTTTGATCGGATGAT 58.938 41.667 0.00 0.00 37.60 2.45
170 784 1.152756 GGGACTTGCAACACCACCT 60.153 57.895 15.94 0.00 0.00 4.00
171 785 1.455383 GGGACTTGCAACACCACCTG 61.455 60.000 15.94 0.00 0.00 4.00
300 1005 4.996788 ATCATGAGAAATTCCTGCCAAC 57.003 40.909 0.09 0.00 0.00 3.77
428 1134 2.711922 GGCGTCACGAGGATCCACT 61.712 63.158 15.82 0.00 0.00 4.00
473 1228 1.654220 CTGCCACTTTCACCAACCG 59.346 57.895 0.00 0.00 0.00 4.44
483 1238 2.131067 CACCAACCGGGCCAAAAGT 61.131 57.895 6.32 0.00 42.05 2.66
485 1240 0.538746 ACCAACCGGGCCAAAAGTAG 60.539 55.000 6.32 0.00 42.05 2.57
486 1241 0.250989 CCAACCGGGCCAAAAGTAGA 60.251 55.000 6.32 0.00 0.00 2.59
487 1242 1.165270 CAACCGGGCCAAAAGTAGAG 58.835 55.000 6.32 0.00 0.00 2.43
558 1328 0.039437 CTGAAAAGGCTGCAGCAGTG 60.039 55.000 37.63 16.88 44.36 3.66
603 1374 3.363178 CTGTTTTGTCTTCAAAGGCGAC 58.637 45.455 0.00 0.00 43.17 5.19
639 1413 1.204312 GTGCAACGAACGAGGAAGC 59.796 57.895 0.14 0.00 0.00 3.86
640 1414 1.227409 TGCAACGAACGAGGAAGCA 60.227 52.632 0.14 0.00 0.00 3.91
643 1417 1.725931 GCAACGAACGAGGAAGCATTG 60.726 52.381 0.14 0.00 0.00 2.82
672 1446 2.099405 CTGTCCACCACAACAAACCTT 58.901 47.619 0.00 0.00 33.31 3.50
681 1455 3.130693 CCACAACAAACCTTTCCCGTAAA 59.869 43.478 0.00 0.00 0.00 2.01
682 1456 4.381718 CCACAACAAACCTTTCCCGTAAAA 60.382 41.667 0.00 0.00 0.00 1.52
683 1457 4.801516 CACAACAAACCTTTCCCGTAAAAG 59.198 41.667 0.94 0.94 36.26 2.27
684 1458 4.705991 ACAACAAACCTTTCCCGTAAAAGA 59.294 37.500 8.01 0.00 38.30 2.52
685 1459 4.906065 ACAAACCTTTCCCGTAAAAGAC 57.094 40.909 8.01 0.00 38.30 3.01
686 1460 4.271661 ACAAACCTTTCCCGTAAAAGACA 58.728 39.130 8.01 0.00 38.30 3.41
687 1461 4.891168 ACAAACCTTTCCCGTAAAAGACAT 59.109 37.500 8.01 0.00 38.30 3.06
688 1462 5.009310 ACAAACCTTTCCCGTAAAAGACATC 59.991 40.000 8.01 0.00 38.30 3.06
689 1463 3.332034 ACCTTTCCCGTAAAAGACATCG 58.668 45.455 8.01 0.00 38.30 3.84
690 1464 2.095372 CCTTTCCCGTAAAAGACATCGC 59.905 50.000 8.01 0.00 38.30 4.58
691 1465 1.729284 TTCCCGTAAAAGACATCGCC 58.271 50.000 0.00 0.00 0.00 5.54
692 1466 0.609151 TCCCGTAAAAGACATCGCCA 59.391 50.000 0.00 0.00 0.00 5.69
693 1467 1.208535 TCCCGTAAAAGACATCGCCAT 59.791 47.619 0.00 0.00 0.00 4.40
794 1628 0.684535 TGTCTGGAAAGACATCGCCA 59.315 50.000 4.48 0.00 43.09 5.69
809 1643 4.632251 ACATCGCCATGTGTATTTCGTTAA 59.368 37.500 0.00 0.00 42.05 2.01
815 1649 6.019398 CGCCATGTGTATTTCGTTAAGACATA 60.019 38.462 4.39 2.91 39.88 2.29
816 1650 7.464844 CGCCATGTGTATTTCGTTAAGACATAA 60.465 37.037 4.39 0.00 39.88 1.90
821 1655 7.385478 TGTGTATTTCGTTAAGACATAACTGCA 59.615 33.333 4.39 0.00 39.88 4.41
881 1715 0.108329 GTCGCTGATTCCCTTCCGAA 60.108 55.000 0.00 0.00 0.00 4.30
977 1822 2.889617 CGGATGACGGTACAGCCA 59.110 61.111 12.54 0.00 45.28 4.75
1001 1850 0.908910 TGGCATGGTCCGAAGTGTAT 59.091 50.000 0.00 0.00 0.00 2.29
1236 2095 0.815734 CGTTCCTTCTAGAGCGGGAA 59.184 55.000 15.39 15.39 36.90 3.97
1416 2465 3.418684 ACTCAGTTTTACCCTCGCAAT 57.581 42.857 0.00 0.00 0.00 3.56
1417 2466 3.751518 ACTCAGTTTTACCCTCGCAATT 58.248 40.909 0.00 0.00 0.00 2.32
1418 2467 4.142038 ACTCAGTTTTACCCTCGCAATTT 58.858 39.130 0.00 0.00 0.00 1.82
1419 2468 4.583073 ACTCAGTTTTACCCTCGCAATTTT 59.417 37.500 0.00 0.00 0.00 1.82
1420 2469 5.068591 ACTCAGTTTTACCCTCGCAATTTTT 59.931 36.000 0.00 0.00 0.00 1.94
1469 2538 2.033372 TGTGAGACCAACGGTAGTCAA 58.967 47.619 0.95 0.00 35.25 3.18
1473 2542 5.046878 TGTGAGACCAACGGTAGTCAAATAT 60.047 40.000 0.95 0.00 35.25 1.28
1491 2560 7.611770 TCAAATATCCTTGACTATATCACCCG 58.388 38.462 0.00 0.00 36.92 5.28
1498 2567 5.299279 CCTTGACTATATCACCCGCAAAAAT 59.701 40.000 0.00 0.00 36.92 1.82
1499 2568 6.485313 CCTTGACTATATCACCCGCAAAAATA 59.515 38.462 0.00 0.00 36.92 1.40
1500 2569 7.012894 CCTTGACTATATCACCCGCAAAAATAA 59.987 37.037 0.00 0.00 36.92 1.40
1501 2570 8.458573 TTGACTATATCACCCGCAAAAATAAT 57.541 30.769 0.00 0.00 36.92 1.28
1502 2571 9.562408 TTGACTATATCACCCGCAAAAATAATA 57.438 29.630 0.00 0.00 36.92 0.98
1503 2572 9.562408 TGACTATATCACCCGCAAAAATAATAA 57.438 29.630 0.00 0.00 29.99 1.40
1508 2577 6.079424 TCACCCGCAAAAATAATAATAGCC 57.921 37.500 0.00 0.00 0.00 3.93
1509 2578 5.830991 TCACCCGCAAAAATAATAATAGCCT 59.169 36.000 0.00 0.00 0.00 4.58
1510 2579 6.322712 TCACCCGCAAAAATAATAATAGCCTT 59.677 34.615 0.00 0.00 0.00 4.35
1511 2580 6.420604 CACCCGCAAAAATAATAATAGCCTTG 59.579 38.462 0.00 0.00 0.00 3.61
1512 2581 5.925969 CCCGCAAAAATAATAATAGCCTTGG 59.074 40.000 0.00 0.00 0.00 3.61
1513 2582 5.405269 CCGCAAAAATAATAATAGCCTTGGC 59.595 40.000 2.97 2.97 0.00 4.52
1514 2583 6.215845 CGCAAAAATAATAATAGCCTTGGCT 58.784 36.000 18.74 18.74 0.00 4.75
1515 2584 7.367285 CGCAAAAATAATAATAGCCTTGGCTA 58.633 34.615 21.79 21.79 0.00 3.93
1516 2585 8.028938 CGCAAAAATAATAATAGCCTTGGCTAT 58.971 33.333 24.02 24.02 34.82 2.97
1525 2594 9.547753 AATAATAGCCTTGGCTATATATCAACG 57.452 33.333 28.10 0.00 33.23 4.10
1526 2595 4.207891 AGCCTTGGCTATATATCAACGG 57.792 45.455 13.08 0.00 0.00 4.44
1527 2596 3.583086 AGCCTTGGCTATATATCAACGGT 59.417 43.478 13.08 0.00 0.00 4.83
1528 2597 4.041691 AGCCTTGGCTATATATCAACGGTT 59.958 41.667 13.08 0.00 0.00 4.44
1529 2598 4.154195 GCCTTGGCTATATATCAACGGTTG 59.846 45.833 14.62 14.62 0.00 3.77
1530 2599 4.695455 CCTTGGCTATATATCAACGGTTGG 59.305 45.833 19.91 4.11 0.00 3.77
1531 2600 4.280436 TGGCTATATATCAACGGTTGGG 57.720 45.455 19.91 0.00 0.00 4.12
1532 2601 3.008594 TGGCTATATATCAACGGTTGGGG 59.991 47.826 19.91 0.00 0.00 4.96
1533 2602 3.262405 GGCTATATATCAACGGTTGGGGA 59.738 47.826 19.91 6.85 0.00 4.81
1534 2603 4.080526 GGCTATATATCAACGGTTGGGGAT 60.081 45.833 19.91 12.88 0.00 3.85
1535 2604 4.876107 GCTATATATCAACGGTTGGGGATG 59.124 45.833 19.91 6.87 0.00 3.51
1536 2605 2.656947 ATATCAACGGTTGGGGATGG 57.343 50.000 19.91 0.00 0.00 3.51
1541 2610 1.899142 CAACGGTTGGGGATGGAAAAT 59.101 47.619 13.03 0.00 0.00 1.82
1543 2612 3.680777 ACGGTTGGGGATGGAAAATAT 57.319 42.857 0.00 0.00 0.00 1.28
1544 2613 3.989056 ACGGTTGGGGATGGAAAATATT 58.011 40.909 0.00 0.00 0.00 1.28
1545 2614 4.358214 ACGGTTGGGGATGGAAAATATTT 58.642 39.130 0.00 0.00 0.00 1.40
1642 2714 4.102524 TGTCTTTGAGATTGGTGGTACAGT 59.897 41.667 0.00 0.00 41.80 3.55
1650 2722 8.958119 TGAGATTGGTGGTACAGTATAAATTC 57.042 34.615 0.00 0.00 41.80 2.17
1654 2726 6.877668 TGGTGGTACAGTATAAATTCTCCA 57.122 37.500 0.00 0.00 41.80 3.86
1724 2913 0.679002 AGCCACCGACTTACGCTCTA 60.679 55.000 0.00 0.00 41.07 2.43
1731 2920 3.119919 ACCGACTTACGCTCTAACTCAAG 60.120 47.826 0.00 0.00 41.07 3.02
1753 2943 5.546526 AGCTTTTGTTGTTTTGACTTCCAA 58.453 33.333 0.00 0.00 0.00 3.53
1762 2952 7.920151 TGTTGTTTTGACTTCCAATGTATTCAG 59.080 33.333 0.00 0.00 34.23 3.02
1777 2967 8.720562 CAATGTATTCAGTGTTGTTCTCATGTA 58.279 33.333 0.00 0.00 35.32 2.29
1782 2972 5.161358 TCAGTGTTGTTCTCATGTATCGTC 58.839 41.667 0.00 0.00 0.00 4.20
1810 3000 6.678568 TTGATCTGAGAGAAGTTTCCTCTT 57.321 37.500 0.00 0.00 40.78 2.85
1826 3016 5.068215 TCCTCTTCTCTCCGATCCTTTAT 57.932 43.478 0.00 0.00 0.00 1.40
1880 3073 0.895530 CTCCTTCGCCAGTAGGTTGA 59.104 55.000 0.00 0.00 36.44 3.18
1882 3075 0.736325 CCTTCGCCAGTAGGTTGACG 60.736 60.000 0.00 0.00 37.19 4.35
1889 3082 1.078710 AGTAGGTTGACGCCCTCCT 59.921 57.895 0.00 0.00 33.35 3.69
1893 3086 2.593956 GGTTGACGCCCTCCTCCTT 61.594 63.158 0.00 0.00 0.00 3.36
1894 3087 1.376037 GTTGACGCCCTCCTCCTTG 60.376 63.158 0.00 0.00 0.00 3.61
1897 3090 3.003763 ACGCCCTCCTCCTTGTCC 61.004 66.667 0.00 0.00 0.00 4.02
1900 3093 3.003173 CCCTCCTCCTTGTCCGCA 61.003 66.667 0.00 0.00 0.00 5.69
1937 3130 2.776526 TGGATGCCCCGGCCTATT 60.777 61.111 0.00 0.00 41.09 1.73
1957 3150 7.278875 CCTATTGATGGAGCTCTAGTTTTTCT 58.721 38.462 14.64 0.00 0.00 2.52
1976 3169 2.548057 TCTCGCTTTGTGGCTTTTAGTG 59.452 45.455 0.00 0.00 0.00 2.74
1977 3170 1.001815 TCGCTTTGTGGCTTTTAGTGC 60.002 47.619 0.00 0.00 0.00 4.40
1985 3178 1.150827 GGCTTTTAGTGCGGTTACGT 58.849 50.000 0.00 0.00 43.45 3.57
1986 3179 2.288702 TGGCTTTTAGTGCGGTTACGTA 60.289 45.455 0.00 0.00 43.45 3.57
1997 3190 0.794605 GGTTACGTAGTGGCGACGAC 60.795 60.000 12.47 0.00 45.73 4.34
2008 3201 2.126463 CGACGACGCTGATGTGGT 60.126 61.111 0.00 0.00 33.21 4.16
2084 3277 5.179045 CAATGGCTCATTGGTGTAGATTC 57.821 43.478 15.98 0.00 45.03 2.52
2117 3310 6.395629 TCTCTACACCAAAAATTCGGACTAG 58.604 40.000 0.00 0.00 0.00 2.57
2149 3342 6.405278 AATTCTCCTTTTTCATTCAACGGT 57.595 33.333 0.00 0.00 0.00 4.83
2171 3364 2.039084 ACAAACCCAAAACCTTGCACAA 59.961 40.909 0.00 0.00 0.00 3.33
2176 3369 2.955660 CCCAAAACCTTGCACAACTCTA 59.044 45.455 0.00 0.00 0.00 2.43
2201 3394 3.708451 AGGCCTAGGTTAACCAAATTGG 58.292 45.455 26.26 18.74 45.02 3.16
2220 3413 9.165035 CAAATTGGAGTTTGGCATGTAAATTAT 57.835 29.630 0.00 0.00 35.86 1.28
2258 3451 9.862585 GCCAATTGTTAGTGTTTTCAAATAAAG 57.137 29.630 4.43 0.00 0.00 1.85
2273 3466 5.637810 TCAAATAAAGTTGCTCTACTCACCG 59.362 40.000 0.00 0.00 0.00 4.94
2291 3485 4.456566 TCACCGGTACAAAAATAAAGGAGC 59.543 41.667 6.87 0.00 0.00 4.70
2298 3492 5.722021 ACAAAAATAAAGGAGCGTCCATT 57.278 34.783 6.78 3.94 39.61 3.16
2299 3493 5.709966 ACAAAAATAAAGGAGCGTCCATTC 58.290 37.500 6.78 0.00 39.61 2.67
2332 3526 7.228314 TCCTTGAAATATCTGTATACCTCGG 57.772 40.000 0.00 0.00 0.00 4.63
2362 3556 9.603921 ATTTTGAAGCCTTTGGATTAATATGTG 57.396 29.630 0.00 0.00 28.48 3.21
2363 3557 6.147864 TGAAGCCTTTGGATTAATATGTGC 57.852 37.500 0.00 0.00 28.48 4.57
2364 3558 5.893255 TGAAGCCTTTGGATTAATATGTGCT 59.107 36.000 0.00 0.00 28.48 4.40
2365 3559 6.039717 TGAAGCCTTTGGATTAATATGTGCTC 59.960 38.462 0.00 0.00 28.48 4.26
2366 3560 4.829492 AGCCTTTGGATTAATATGTGCTCC 59.171 41.667 0.00 0.00 0.00 4.70
2367 3561 4.584325 GCCTTTGGATTAATATGTGCTCCA 59.416 41.667 0.00 0.00 34.27 3.86
2368 3562 5.244626 GCCTTTGGATTAATATGTGCTCCAT 59.755 40.000 0.00 0.00 35.99 3.41
2369 3563 6.571150 GCCTTTGGATTAATATGTGCTCCATC 60.571 42.308 0.00 0.00 35.99 3.51
2370 3564 6.718454 CCTTTGGATTAATATGTGCTCCATCT 59.282 38.462 0.00 0.00 35.99 2.90
2371 3565 7.309012 CCTTTGGATTAATATGTGCTCCATCTG 60.309 40.741 0.00 0.00 35.99 2.90
2372 3566 6.191657 TGGATTAATATGTGCTCCATCTGT 57.808 37.500 0.00 0.00 34.86 3.41
2373 3567 7.315066 TGGATTAATATGTGCTCCATCTGTA 57.685 36.000 0.00 0.00 34.86 2.74
2374 3568 7.161404 TGGATTAATATGTGCTCCATCTGTAC 58.839 38.462 0.00 0.00 34.86 2.90
2375 3569 6.595716 GGATTAATATGTGCTCCATCTGTACC 59.404 42.308 0.00 0.00 34.86 3.34
2376 3570 6.493189 TTAATATGTGCTCCATCTGTACCA 57.507 37.500 0.00 0.00 34.86 3.25
2377 3571 5.573380 AATATGTGCTCCATCTGTACCAT 57.427 39.130 0.00 0.00 34.86 3.55
2378 3572 6.686484 AATATGTGCTCCATCTGTACCATA 57.314 37.500 0.00 0.00 34.86 2.74
2379 3573 6.686484 ATATGTGCTCCATCTGTACCATAA 57.314 37.500 0.00 0.00 34.86 1.90
2380 3574 5.573380 ATGTGCTCCATCTGTACCATAAT 57.427 39.130 0.00 0.00 0.00 1.28
2381 3575 6.686484 ATGTGCTCCATCTGTACCATAATA 57.314 37.500 0.00 0.00 0.00 0.98
2382 3576 6.686484 TGTGCTCCATCTGTACCATAATAT 57.314 37.500 0.00 0.00 0.00 1.28
2383 3577 7.790782 TGTGCTCCATCTGTACCATAATATA 57.209 36.000 0.00 0.00 0.00 0.86
2384 3578 8.379428 TGTGCTCCATCTGTACCATAATATAT 57.621 34.615 0.00 0.00 0.00 0.86
2385 3579 8.260114 TGTGCTCCATCTGTACCATAATATATG 58.740 37.037 0.00 0.00 0.00 1.78
2386 3580 8.478066 GTGCTCCATCTGTACCATAATATATGA 58.522 37.037 0.00 0.00 0.00 2.15
2387 3581 9.217336 TGCTCCATCTGTACCATAATATATGAT 57.783 33.333 0.00 0.00 0.00 2.45
2388 3582 9.486497 GCTCCATCTGTACCATAATATATGATG 57.514 37.037 3.26 3.26 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 1.079819 GCGAGCCAGCTGTCAGTAA 60.080 57.895 13.81 0.00 0.00 2.24
76 689 1.835483 GACGATAGCAATGCGGCTGG 61.835 60.000 0.00 0.00 45.44 4.85
84 697 4.679373 AATCAGGTCTGACGATAGCAAT 57.321 40.909 2.46 0.00 43.11 3.56
99 713 3.566742 TGCATCATCCGATCAAAATCAGG 59.433 43.478 0.00 0.00 31.76 3.86
100 714 4.035909 TGTGCATCATCCGATCAAAATCAG 59.964 41.667 0.00 0.00 31.76 2.90
101 715 3.946558 TGTGCATCATCCGATCAAAATCA 59.053 39.130 0.00 0.00 31.76 2.57
189 803 2.393271 CTGCAGGTTGTAGCTTAGCT 57.607 50.000 12.67 12.67 43.41 3.32
270 895 7.805071 GCAGGAATTTCTCATGATTATTAACGG 59.195 37.037 0.00 0.00 38.11 4.44
473 1228 1.450025 CGGAACTCTACTTTTGGCCC 58.550 55.000 0.00 0.00 0.00 5.80
483 1238 2.415608 CGGAGGCAGCGGAACTCTA 61.416 63.158 8.40 0.00 0.00 2.43
485 1240 2.781595 TTTCGGAGGCAGCGGAACTC 62.782 60.000 0.00 0.00 0.00 3.01
486 1241 2.788191 CTTTCGGAGGCAGCGGAACT 62.788 60.000 0.00 0.00 0.00 3.01
487 1242 2.358247 TTTCGGAGGCAGCGGAAC 60.358 61.111 0.00 0.00 0.00 3.62
577 1347 2.842208 TTGAAGACAAAACAGGTGCG 57.158 45.000 0.00 0.00 32.73 5.34
603 1374 0.178973 ACGGAGAAAAGGTTTGGGGG 60.179 55.000 0.00 0.00 0.00 5.40
634 1408 0.545646 AGAGAGAGGCCAATGCTTCC 59.454 55.000 5.01 0.00 44.22 3.46
635 1409 1.065564 ACAGAGAGAGGCCAATGCTTC 60.066 52.381 5.01 0.00 43.53 3.86
639 1413 0.907486 TGGACAGAGAGAGGCCAATG 59.093 55.000 5.01 0.00 0.00 2.82
640 1414 0.908198 GTGGACAGAGAGAGGCCAAT 59.092 55.000 5.01 0.00 0.00 3.16
643 1417 1.610673 TGGTGGACAGAGAGAGGCC 60.611 63.158 0.00 0.00 0.00 5.19
672 1446 1.002201 TGGCGATGTCTTTTACGGGAA 59.998 47.619 0.00 0.00 0.00 3.97
681 1455 2.365617 CCTGGTACTATGGCGATGTCTT 59.634 50.000 0.00 0.00 0.00 3.01
682 1456 1.964223 CCTGGTACTATGGCGATGTCT 59.036 52.381 0.00 0.00 0.00 3.41
683 1457 1.000955 CCCTGGTACTATGGCGATGTC 59.999 57.143 0.00 0.00 0.00 3.06
684 1458 1.048601 CCCTGGTACTATGGCGATGT 58.951 55.000 0.00 0.00 0.00 3.06
685 1459 1.338107 TCCCTGGTACTATGGCGATG 58.662 55.000 0.00 0.00 0.00 3.84
686 1460 2.097110 TTCCCTGGTACTATGGCGAT 57.903 50.000 0.00 0.00 0.00 4.58
687 1461 2.097110 ATTCCCTGGTACTATGGCGA 57.903 50.000 0.00 0.00 0.00 5.54
688 1462 2.930826 AATTCCCTGGTACTATGGCG 57.069 50.000 0.00 0.00 0.00 5.69
689 1463 3.883489 GTGAAATTCCCTGGTACTATGGC 59.117 47.826 0.00 0.00 0.00 4.40
690 1464 4.127171 CGTGAAATTCCCTGGTACTATGG 58.873 47.826 0.00 0.00 0.00 2.74
691 1465 3.560068 GCGTGAAATTCCCTGGTACTATG 59.440 47.826 0.00 0.00 0.00 2.23
692 1466 3.199071 TGCGTGAAATTCCCTGGTACTAT 59.801 43.478 0.00 0.00 0.00 2.12
693 1467 2.568062 TGCGTGAAATTCCCTGGTACTA 59.432 45.455 0.00 0.00 0.00 1.82
736 1516 4.329392 GTGGCACCCTTTTAACTAGCTAA 58.671 43.478 6.29 0.00 0.00 3.09
752 1537 0.040425 GAACACAATCACGGTGGCAC 60.040 55.000 9.70 9.70 40.54 5.01
794 1628 8.388103 GCAGTTATGTCTTAACGAAATACACAT 58.612 33.333 0.00 0.00 44.15 3.21
809 1643 7.332926 CAGTACTCAGAAAATGCAGTTATGTCT 59.667 37.037 0.00 0.00 0.00 3.41
815 1649 5.822519 TGTTCAGTACTCAGAAAATGCAGTT 59.177 36.000 0.00 0.00 0.00 3.16
816 1650 5.368145 TGTTCAGTACTCAGAAAATGCAGT 58.632 37.500 0.00 0.00 0.00 4.40
881 1715 2.241880 CGCGGTCGGACAACAGTTT 61.242 57.895 10.76 0.00 0.00 2.66
934 1779 1.356124 AAGAGCCATCCACTGACAGT 58.644 50.000 1.07 1.07 0.00 3.55
977 1822 2.809861 CTTCGGACCATGCCAGCACT 62.810 60.000 0.00 0.00 0.00 4.40
982 1827 0.908910 ATACACTTCGGACCATGCCA 59.091 50.000 0.00 0.00 0.00 4.92
1001 1850 3.386078 TGCAGCAAAAATAACTTCACCCA 59.614 39.130 0.00 0.00 0.00 4.51
1271 2130 9.935241 CATAATTAGCTAGACAATGTGATACCT 57.065 33.333 0.00 0.00 0.00 3.08
1383 2432 7.201794 GGGTAAAACTGAGTTTATTCCATAGCC 60.202 40.741 11.43 13.07 34.43 3.93
1425 2474 8.967918 ACATATGAGCGAATTACTAGGCTTATA 58.032 33.333 10.38 0.00 38.03 0.98
1427 2476 7.039993 TCACATATGAGCGAATTACTAGGCTTA 60.040 37.037 10.38 0.00 35.54 3.09
1429 2478 5.243954 TCACATATGAGCGAATTACTAGGCT 59.756 40.000 10.38 0.00 38.70 4.58
1447 2496 3.423749 TGACTACCGTTGGTCTCACATA 58.576 45.455 0.00 0.00 37.09 2.29
1456 2505 5.424757 TCAAGGATATTTGACTACCGTTGG 58.575 41.667 0.00 0.00 32.39 3.77
1469 2538 5.483937 TGCGGGTGATATAGTCAAGGATATT 59.516 40.000 0.00 0.00 38.90 1.28
1473 2542 2.673258 TGCGGGTGATATAGTCAAGGA 58.327 47.619 0.00 0.00 38.90 3.36
1506 2575 3.939066 ACCGTTGATATATAGCCAAGGC 58.061 45.455 2.02 2.02 42.33 4.35
1507 2576 4.695455 CCAACCGTTGATATATAGCCAAGG 59.305 45.833 13.04 3.07 0.00 3.61
1508 2577 4.695455 CCCAACCGTTGATATATAGCCAAG 59.305 45.833 13.04 0.00 0.00 3.61
1509 2578 4.505918 CCCCAACCGTTGATATATAGCCAA 60.506 45.833 13.04 0.00 0.00 4.52
1510 2579 3.008594 CCCCAACCGTTGATATATAGCCA 59.991 47.826 13.04 0.00 0.00 4.75
1511 2580 3.262405 TCCCCAACCGTTGATATATAGCC 59.738 47.826 13.04 0.00 0.00 3.93
1512 2581 4.546829 TCCCCAACCGTTGATATATAGC 57.453 45.455 13.04 0.00 0.00 2.97
1513 2582 5.188948 TCCATCCCCAACCGTTGATATATAG 59.811 44.000 13.04 0.00 0.00 1.31
1514 2583 5.095097 TCCATCCCCAACCGTTGATATATA 58.905 41.667 13.04 0.00 0.00 0.86
1515 2584 3.913799 TCCATCCCCAACCGTTGATATAT 59.086 43.478 13.04 0.00 0.00 0.86
1516 2585 3.319220 TCCATCCCCAACCGTTGATATA 58.681 45.455 13.04 0.00 0.00 0.86
1517 2586 2.131854 TCCATCCCCAACCGTTGATAT 58.868 47.619 13.04 0.61 0.00 1.63
1518 2587 1.585895 TCCATCCCCAACCGTTGATA 58.414 50.000 13.04 0.00 0.00 2.15
1519 2588 0.701731 TTCCATCCCCAACCGTTGAT 59.298 50.000 13.04 0.00 0.00 2.57
1520 2589 0.478942 TTTCCATCCCCAACCGTTGA 59.521 50.000 13.04 0.00 0.00 3.18
1521 2590 1.333177 TTTTCCATCCCCAACCGTTG 58.667 50.000 4.12 4.12 0.00 4.10
1522 2591 2.319025 ATTTTCCATCCCCAACCGTT 57.681 45.000 0.00 0.00 0.00 4.44
1523 2592 3.680777 ATATTTTCCATCCCCAACCGT 57.319 42.857 0.00 0.00 0.00 4.83
1524 2593 6.472686 TTAAATATTTTCCATCCCCAACCG 57.527 37.500 5.91 0.00 0.00 4.44
1525 2594 7.625469 TGTTTAAATATTTTCCATCCCCAACC 58.375 34.615 5.91 0.00 0.00 3.77
1526 2595 9.508642 TTTGTTTAAATATTTTCCATCCCCAAC 57.491 29.630 5.91 0.00 0.00 3.77
1528 2597 9.508642 GTTTTGTTTAAATATTTTCCATCCCCA 57.491 29.630 5.91 0.00 0.00 4.96
1529 2598 9.733556 AGTTTTGTTTAAATATTTTCCATCCCC 57.266 29.630 5.91 0.00 0.00 4.81
1616 2688 6.774673 TGTACCACCAATCTCAAAGACAATA 58.225 36.000 0.00 0.00 0.00 1.90
1650 2722 8.224389 TGATCAATGGTTGTTGTATAATGGAG 57.776 34.615 0.00 0.00 0.00 3.86
1714 2903 5.177696 ACAAAAGCTTGAGTTAGAGCGTAAG 59.822 40.000 0.00 0.00 43.53 2.34
1724 2913 6.223120 AGTCAAAACAACAAAAGCTTGAGTT 58.777 32.000 0.00 5.27 36.55 3.01
1731 2920 5.854431 TTGGAAGTCAAAACAACAAAAGC 57.146 34.783 0.00 0.00 31.46 3.51
1753 2943 9.102757 GATACATGAGAACAACACTGAATACAT 57.897 33.333 0.00 0.00 0.00 2.29
1762 2952 3.241678 GCGACGATACATGAGAACAACAC 60.242 47.826 0.00 0.00 0.00 3.32
1782 2972 3.077229 ACTTCTCTCAGATCAATCGCG 57.923 47.619 0.00 0.00 0.00 5.87
1810 3000 8.713708 AAATCTTCTATAAAGGATCGGAGAGA 57.286 34.615 0.00 0.00 43.63 3.10
1880 3073 3.003763 GGACAAGGAGGAGGGCGT 61.004 66.667 0.00 0.00 0.00 5.68
1882 3075 4.475135 GCGGACAAGGAGGAGGGC 62.475 72.222 0.00 0.00 0.00 5.19
1889 3082 2.244117 GATGAGCCTGCGGACAAGGA 62.244 60.000 0.00 0.00 0.00 3.36
1897 3090 2.413437 CTAGACCCGATGAGCCTGCG 62.413 65.000 0.00 0.00 0.00 5.18
1900 3093 1.152440 CCCTAGACCCGATGAGCCT 60.152 63.158 0.00 0.00 0.00 4.58
1929 3122 0.683973 AGAGCTCCATCAATAGGCCG 59.316 55.000 10.93 0.00 0.00 6.13
1937 3130 4.748892 CGAGAAAAACTAGAGCTCCATCA 58.251 43.478 10.93 0.00 0.00 3.07
1957 3150 1.001815 GCACTAAAAGCCACAAAGCGA 60.002 47.619 0.00 0.00 38.01 4.93
1976 3169 2.154569 GTCGCCACTACGTAACCGC 61.155 63.158 0.00 0.00 37.70 5.68
1977 3170 1.864750 CGTCGCCACTACGTAACCG 60.865 63.158 0.00 0.00 40.83 4.44
1997 3190 2.995466 AAATGTTCACCACATCAGCG 57.005 45.000 0.00 0.00 46.23 5.18
2102 3295 3.506067 AGCCCAACTAGTCCGAATTTTTG 59.494 43.478 0.00 0.00 0.00 2.44
2103 3296 3.763057 AGCCCAACTAGTCCGAATTTTT 58.237 40.909 0.00 0.00 0.00 1.94
2111 3304 4.164413 AGGAGAATTAAGCCCAACTAGTCC 59.836 45.833 0.00 0.00 0.00 3.85
2117 3310 6.096673 TGAAAAAGGAGAATTAAGCCCAAC 57.903 37.500 0.00 0.00 0.00 3.77
2149 3342 2.832129 TGTGCAAGGTTTTGGGTTTGTA 59.168 40.909 0.00 0.00 34.79 2.41
2171 3364 4.224594 GGTTAACCTAGGCCTTGTTAGAGT 59.775 45.833 12.58 0.00 0.00 3.24
2176 3369 3.887916 TTGGTTAACCTAGGCCTTGTT 57.112 42.857 24.78 17.80 36.82 2.83
2220 3413 7.179338 ACACTAACAATTGGCCCAATGTTAATA 59.821 33.333 21.30 10.26 34.04 0.98
2228 3421 4.162320 TGAAAACACTAACAATTGGCCCAA 59.838 37.500 10.83 0.00 0.00 4.12
2258 3451 1.542915 TGTACCGGTGAGTAGAGCAAC 59.457 52.381 19.93 3.26 0.00 4.17
2273 3466 4.456566 TGGACGCTCCTTTATTTTTGTACC 59.543 41.667 5.77 0.00 37.46 3.34
2291 3485 5.001232 TCAAGGAACCTAAAAGAATGGACG 58.999 41.667 0.00 0.00 0.00 4.79
2320 3514 6.421202 GCTTCAAAATAGACCGAGGTATACAG 59.579 42.308 5.01 0.00 0.00 2.74
2325 3519 3.773119 AGGCTTCAAAATAGACCGAGGTA 59.227 43.478 0.00 0.00 0.00 3.08
2328 3522 4.142600 CCAAAGGCTTCAAAATAGACCGAG 60.143 45.833 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.