Multiple sequence alignment - TraesCS3B01G226100

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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 TraesCS3B01G226100 chr3B 100.000 2114 0 0 1 2114 312893037 312895150 0.000000e+00 3904.0
1 TraesCS3B01G226100 chr3B 94.804 1405 58 11 105 1506 201506396 201507788 0.000000e+00 2176.0
2 TraesCS3B01G226100 chr3B 90.826 109 10 0 2 110 468243127 468243235 1.690000e-31 147.0
3 TraesCS3B01G226100 chr2A 94.377 1405 67 9 105 1506 335826096 335827491 0.000000e+00 2146.0
4 TraesCS3B01G226100 chr2A 94.494 563 29 2 105 666 276441256 276440695 0.000000e+00 867.0
5 TraesCS3B01G226100 chr1D 94.113 1410 66 12 105 1506 394178727 394180127 0.000000e+00 2128.0
6 TraesCS3B01G226100 chr1D 93.808 1405 70 10 105 1506 254489518 254490908 0.000000e+00 2097.0
7 TraesCS3B01G226100 chr1D 95.726 819 29 4 690 1506 483922562 483921748 0.000000e+00 1314.0
8 TraesCS3B01G226100 chr1D 89.908 109 11 0 2 110 106043680 106043572 7.860000e-30 141.0
9 TraesCS3B01G226100 chrUn 93.688 1410 69 12 105 1506 317473373 317471976 0.000000e+00 2093.0
10 TraesCS3B01G226100 chrUn 94.470 1085 41 11 105 1181 404958051 404959124 0.000000e+00 1653.0
11 TraesCS3B01G226100 chrUn 93.525 695 29 7 105 797 53261820 53261140 0.000000e+00 1020.0
12 TraesCS3B01G226100 chr2D 93.737 1405 65 11 105 1506 334225742 334227126 0.000000e+00 2085.0
13 TraesCS3B01G226100 chr6D 93.599 1406 70 12 105 1506 431399847 431401236 0.000000e+00 2080.0
14 TraesCS3B01G226100 chr6D 89.437 568 58 2 1526 2093 100720094 100720659 0.000000e+00 715.0
15 TraesCS3B01G226100 chr6D 89.043 575 60 3 1520 2093 218532675 218532103 0.000000e+00 710.0
16 TraesCS3B01G226100 chr5D 93.305 1404 73 11 105 1506 6207997 6206613 0.000000e+00 2052.0
17 TraesCS3B01G226100 chr5D 94.381 1050 45 10 463 1506 554200515 554201556 0.000000e+00 1600.0
18 TraesCS3B01G226100 chr1A 93.333 675 29 7 105 776 256026350 256025689 0.000000e+00 983.0
19 TraesCS3B01G226100 chr5A 95.390 564 25 1 105 667 684325405 684325968 0.000000e+00 896.0
20 TraesCS3B01G226100 chr4A 93.805 565 25 5 105 666 677309936 677309379 0.000000e+00 841.0
21 TraesCS3B01G226100 chr3D 90.317 568 54 1 1526 2093 61024803 61025369 0.000000e+00 743.0
22 TraesCS3B01G226100 chr3D 88.416 587 66 2 1526 2111 385687888 385687303 0.000000e+00 706.0
23 TraesCS3B01G226100 chr3D 89.583 48 1 1 687 734 268499083 268499126 8.150000e-05 58.4
24 TraesCS3B01G226100 chr7D 89.982 569 54 3 1526 2093 276684138 276683572 0.000000e+00 732.0
25 TraesCS3B01G226100 chr7D 89.085 568 61 1 1526 2093 356786764 356787330 0.000000e+00 704.0
26 TraesCS3B01G226100 chr7D 88.376 585 65 3 1529 2111 377723029 377722446 0.000000e+00 701.0
27 TraesCS3B01G226100 chr7D 89.189 111 12 0 2 112 391221715 391221825 2.830000e-29 139.0
28 TraesCS3B01G226100 chr4D 89.123 570 59 2 1526 2093 344803356 344803924 0.000000e+00 706.0
29 TraesCS3B01G226100 chr4D 92.661 109 8 0 2 110 123844575 123844683 7.810000e-35 158.0
30 TraesCS3B01G226100 chr7B 88.075 587 66 2 1526 2111 385927359 385926776 0.000000e+00 693.0
31 TraesCS3B01G226100 chr7B 90.826 109 10 0 2 110 662470240 662470132 1.690000e-31 147.0
32 TraesCS3B01G226100 chr5B 90.826 109 10 0 2 110 104314244 104314352 1.690000e-31 147.0
33 TraesCS3B01G226100 chr5B 90.826 109 10 0 2 110 196342400 196342292 1.690000e-31 147.0
34 TraesCS3B01G226100 chr7A 90.654 107 10 0 4 110 625451295 625451401 2.190000e-30 143.0
35 TraesCS3B01G226100 chr1B 90.654 107 10 0 4 110 607494558 607494664 2.190000e-30 143.0


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 TraesCS3B01G226100 chr3B 312893037 312895150 2113 False 3904 3904 100.000 1 2114 1 chr3B.!!$F2 2113
1 TraesCS3B01G226100 chr3B 201506396 201507788 1392 False 2176 2176 94.804 105 1506 1 chr3B.!!$F1 1401
2 TraesCS3B01G226100 chr2A 335826096 335827491 1395 False 2146 2146 94.377 105 1506 1 chr2A.!!$F1 1401
3 TraesCS3B01G226100 chr2A 276440695 276441256 561 True 867 867 94.494 105 666 1 chr2A.!!$R1 561
4 TraesCS3B01G226100 chr1D 394178727 394180127 1400 False 2128 2128 94.113 105 1506 1 chr1D.!!$F2 1401
5 TraesCS3B01G226100 chr1D 254489518 254490908 1390 False 2097 2097 93.808 105 1506 1 chr1D.!!$F1 1401
6 TraesCS3B01G226100 chr1D 483921748 483922562 814 True 1314 1314 95.726 690 1506 1 chr1D.!!$R2 816
7 TraesCS3B01G226100 chrUn 317471976 317473373 1397 True 2093 2093 93.688 105 1506 1 chrUn.!!$R2 1401
8 TraesCS3B01G226100 chrUn 404958051 404959124 1073 False 1653 1653 94.470 105 1181 1 chrUn.!!$F1 1076
9 TraesCS3B01G226100 chrUn 53261140 53261820 680 True 1020 1020 93.525 105 797 1 chrUn.!!$R1 692
10 TraesCS3B01G226100 chr2D 334225742 334227126 1384 False 2085 2085 93.737 105 1506 1 chr2D.!!$F1 1401
11 TraesCS3B01G226100 chr6D 431399847 431401236 1389 False 2080 2080 93.599 105 1506 1 chr6D.!!$F2 1401
12 TraesCS3B01G226100 chr6D 100720094 100720659 565 False 715 715 89.437 1526 2093 1 chr6D.!!$F1 567
13 TraesCS3B01G226100 chr6D 218532103 218532675 572 True 710 710 89.043 1520 2093 1 chr6D.!!$R1 573
14 TraesCS3B01G226100 chr5D 6206613 6207997 1384 True 2052 2052 93.305 105 1506 1 chr5D.!!$R1 1401
15 TraesCS3B01G226100 chr5D 554200515 554201556 1041 False 1600 1600 94.381 463 1506 1 chr5D.!!$F1 1043
16 TraesCS3B01G226100 chr1A 256025689 256026350 661 True 983 983 93.333 105 776 1 chr1A.!!$R1 671
17 TraesCS3B01G226100 chr5A 684325405 684325968 563 False 896 896 95.390 105 667 1 chr5A.!!$F1 562
18 TraesCS3B01G226100 chr4A 677309379 677309936 557 True 841 841 93.805 105 666 1 chr4A.!!$R1 561
19 TraesCS3B01G226100 chr3D 61024803 61025369 566 False 743 743 90.317 1526 2093 1 chr3D.!!$F1 567
20 TraesCS3B01G226100 chr3D 385687303 385687888 585 True 706 706 88.416 1526 2111 1 chr3D.!!$R1 585
21 TraesCS3B01G226100 chr7D 276683572 276684138 566 True 732 732 89.982 1526 2093 1 chr7D.!!$R1 567
22 TraesCS3B01G226100 chr7D 356786764 356787330 566 False 704 704 89.085 1526 2093 1 chr7D.!!$F1 567
23 TraesCS3B01G226100 chr7D 377722446 377723029 583 True 701 701 88.376 1529 2111 1 chr7D.!!$R2 582
24 TraesCS3B01G226100 chr4D 344803356 344803924 568 False 706 706 89.123 1526 2093 1 chr4D.!!$F2 567
25 TraesCS3B01G226100 chr7B 385926776 385927359 583 True 693 693 88.075 1526 2111 1 chr7B.!!$R1 585

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
31 32 0.036765 TAGGCATCACCGTTGTCCAC 60.037 55.0 0.0 0.0 46.52 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1984 2016 0.108041 AACCTTGGCCGTACGTATGG 60.108 55.0 26.57 26.57 35.42 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
17 18 2.448383 ACGTCCCCTTCCTAGGCA 59.552 61.111 2.96 0.00 40.50 4.75
18 19 1.003051 ACGTCCCCTTCCTAGGCAT 59.997 57.895 2.96 0.00 40.50 4.40
19 20 1.049289 ACGTCCCCTTCCTAGGCATC 61.049 60.000 2.96 0.00 40.50 3.91
20 21 1.048724 CGTCCCCTTCCTAGGCATCA 61.049 60.000 2.96 0.00 40.50 3.07
21 22 0.470341 GTCCCCTTCCTAGGCATCAC 59.530 60.000 2.96 0.00 40.50 3.06
22 23 0.694444 TCCCCTTCCTAGGCATCACC 60.694 60.000 2.96 0.00 40.50 4.02
23 24 1.447643 CCCTTCCTAGGCATCACCG 59.552 63.158 2.96 0.00 46.52 4.94
24 25 1.338136 CCCTTCCTAGGCATCACCGT 61.338 60.000 2.96 0.00 46.52 4.83
25 26 0.541863 CCTTCCTAGGCATCACCGTT 59.458 55.000 2.96 0.00 46.52 4.44
26 27 1.656652 CTTCCTAGGCATCACCGTTG 58.343 55.000 2.96 0.00 46.52 4.10
27 28 0.981183 TTCCTAGGCATCACCGTTGT 59.019 50.000 2.96 0.00 46.52 3.32
28 29 0.535335 TCCTAGGCATCACCGTTGTC 59.465 55.000 2.96 0.00 46.52 3.18
29 30 0.462047 CCTAGGCATCACCGTTGTCC 60.462 60.000 0.00 0.00 46.52 4.02
30 31 0.249120 CTAGGCATCACCGTTGTCCA 59.751 55.000 0.00 0.00 46.52 4.02
31 32 0.036765 TAGGCATCACCGTTGTCCAC 60.037 55.000 0.00 0.00 46.52 4.02
32 33 2.332654 GGCATCACCGTTGTCCACC 61.333 63.158 0.00 0.00 0.00 4.61
33 34 1.599518 GCATCACCGTTGTCCACCA 60.600 57.895 0.00 0.00 0.00 4.17
34 35 1.852067 GCATCACCGTTGTCCACCAC 61.852 60.000 0.00 0.00 0.00 4.16
35 36 1.072505 ATCACCGTTGTCCACCACC 59.927 57.895 0.00 0.00 0.00 4.61
36 37 1.415672 ATCACCGTTGTCCACCACCT 61.416 55.000 0.00 0.00 0.00 4.00
37 38 1.153046 CACCGTTGTCCACCACCTT 60.153 57.895 0.00 0.00 0.00 3.50
38 39 1.153046 ACCGTTGTCCACCACCTTG 60.153 57.895 0.00 0.00 0.00 3.61
39 40 1.896660 CCGTTGTCCACCACCTTGG 60.897 63.158 0.00 0.00 45.02 3.61
48 49 2.046892 CCACCTTGGTGCTCTCGG 60.047 66.667 13.93 0.00 31.35 4.63
49 50 2.743928 CACCTTGGTGCTCTCGGC 60.744 66.667 6.88 0.00 42.22 5.54
50 51 4.379243 ACCTTGGTGCTCTCGGCG 62.379 66.667 0.00 0.00 45.43 6.46
66 67 4.777781 CGCAGCATGGTCAATGTG 57.222 55.556 0.00 0.00 38.65 3.21
67 68 1.138036 CGCAGCATGGTCAATGTGG 59.862 57.895 0.00 0.00 38.65 4.17
68 69 1.588824 CGCAGCATGGTCAATGTGGT 61.589 55.000 0.00 0.00 38.65 4.16
69 70 0.171903 GCAGCATGGTCAATGTGGTC 59.828 55.000 0.00 0.00 38.65 4.02
70 71 1.536940 CAGCATGGTCAATGTGGTCA 58.463 50.000 0.00 0.00 38.65 4.02
71 72 2.097036 CAGCATGGTCAATGTGGTCAT 58.903 47.619 0.00 0.00 38.65 3.06
72 73 2.097036 AGCATGGTCAATGTGGTCATG 58.903 47.619 0.00 0.00 38.65 3.07
73 74 1.135527 GCATGGTCAATGTGGTCATGG 59.864 52.381 0.00 0.00 38.65 3.66
74 75 2.725637 CATGGTCAATGTGGTCATGGA 58.274 47.619 0.00 0.00 34.19 3.41
75 76 2.967745 TGGTCAATGTGGTCATGGAA 57.032 45.000 0.00 0.00 35.98 3.53
76 77 2.513753 TGGTCAATGTGGTCATGGAAC 58.486 47.619 0.00 0.00 40.96 3.62
77 78 1.468520 GGTCAATGTGGTCATGGAACG 59.531 52.381 0.00 0.00 35.98 3.95
78 79 2.422597 GTCAATGTGGTCATGGAACGA 58.577 47.619 0.00 0.00 35.98 3.85
79 80 2.159627 GTCAATGTGGTCATGGAACGAC 59.840 50.000 0.00 0.00 35.98 4.34
80 81 2.038426 TCAATGTGGTCATGGAACGACT 59.962 45.455 0.00 0.00 31.73 4.18
81 82 2.813754 CAATGTGGTCATGGAACGACTT 59.186 45.455 0.00 0.00 34.19 3.01
82 83 2.163818 TGTGGTCATGGAACGACTTC 57.836 50.000 0.00 0.00 33.73 3.01
83 84 1.270625 TGTGGTCATGGAACGACTTCC 60.271 52.381 0.00 0.00 45.89 3.46
90 91 3.826637 GGAACGACTTCCATCGGAA 57.173 52.632 0.08 0.00 46.56 4.30
102 103 5.943349 TTCCATCGGAAGTTTACTATCCA 57.057 39.130 0.00 1.83 36.71 3.41
103 104 6.494666 TTCCATCGGAAGTTTACTATCCAT 57.505 37.500 0.00 3.33 36.71 3.41
107 108 5.531122 TCGGAAGTTTACTATCCATGGAG 57.469 43.478 21.33 10.10 32.58 3.86
184 185 5.223449 TCTACTTTGGTTGGAGTTCGAAT 57.777 39.130 0.00 0.00 0.00 3.34
185 186 5.617252 TCTACTTTGGTTGGAGTTCGAATT 58.383 37.500 0.00 0.00 0.00 2.17
226 232 8.918116 AGTAAATTCAAGGAAGAGCTTTCTTTT 58.082 29.630 0.99 0.00 36.30 2.27
261 273 1.648467 GGCAGGTCGTGGAATGCTTC 61.648 60.000 0.00 0.00 38.71 3.86
345 357 4.373527 TCGATCGTTCACTCCAAAAAGAA 58.626 39.130 15.94 0.00 0.00 2.52
454 472 8.574196 TCCTTGAAAATCGAACTTCATTTTTC 57.426 30.769 11.91 10.90 37.01 2.29
479 497 7.233632 CCATTCAATGGGGTTAGATGATCTAA 58.766 38.462 8.78 10.70 46.86 2.10
607 626 9.944663 CACTTCTGTATCTTACTCTATCTTGTC 57.055 37.037 0.00 0.00 0.00 3.18
671 690 7.956420 TCCATAACTTAGGTAAATGTATGCG 57.044 36.000 0.00 0.00 0.00 4.73
672 691 6.932400 TCCATAACTTAGGTAAATGTATGCGG 59.068 38.462 0.00 0.00 0.00 5.69
674 693 7.117812 CCATAACTTAGGTAAATGTATGCGGAG 59.882 40.741 0.00 0.00 0.00 4.63
675 694 5.609533 ACTTAGGTAAATGTATGCGGAGT 57.390 39.130 0.00 0.00 0.00 3.85
677 696 7.116075 ACTTAGGTAAATGTATGCGGAGTAA 57.884 36.000 0.00 0.00 0.00 2.24
678 697 7.558604 ACTTAGGTAAATGTATGCGGAGTAAA 58.441 34.615 0.00 0.00 0.00 2.01
679 698 7.493645 ACTTAGGTAAATGTATGCGGAGTAAAC 59.506 37.037 0.00 0.00 0.00 2.01
680 699 5.985911 AGGTAAATGTATGCGGAGTAAACT 58.014 37.500 0.00 0.00 0.00 2.66
681 700 6.047231 AGGTAAATGTATGCGGAGTAAACTC 58.953 40.000 1.30 1.30 42.14 3.01
682 701 6.047231 GGTAAATGTATGCGGAGTAAACTCT 58.953 40.000 9.84 0.00 42.48 3.24
683 702 6.537660 GGTAAATGTATGCGGAGTAAACTCTT 59.462 38.462 9.84 0.00 42.48 2.85
684 703 7.065443 GGTAAATGTATGCGGAGTAAACTCTTT 59.935 37.037 9.84 3.31 42.48 2.52
685 704 6.663944 AATGTATGCGGAGTAAACTCTTTC 57.336 37.500 9.84 1.17 42.48 2.62
688 707 6.869695 TGTATGCGGAGTAAACTCTTTCATA 58.130 36.000 9.84 10.95 42.48 2.15
763 789 9.636789 AACTAGTTATTTTGGTTTTCTACTGGT 57.363 29.630 6.26 0.00 0.00 4.00
783 809 5.642165 TGGTTGCTTTAACTATAACCCCAA 58.358 37.500 0.00 0.00 39.95 4.12
790 816 8.208903 TGCTTTAACTATAACCCCAACTCTATC 58.791 37.037 0.00 0.00 0.00 2.08
797 823 8.239478 ACTATAACCCCAACTCTATCTATTGGA 58.761 37.037 3.80 0.00 44.84 3.53
1016 1043 8.764287 ACAAATCGAAATGATTGAAGTTTTTCC 58.236 29.630 7.70 0.00 46.65 3.13
1066 1093 8.197592 TCCTATTACTTTAGCGGGATTATTCA 57.802 34.615 0.00 0.00 0.00 2.57
1072 1099 7.062749 ACTTTAGCGGGATTATTCATGACTA 57.937 36.000 0.00 0.00 0.00 2.59
1122 1149 6.169094 TCAGTTGGATCTTTGATTGAGTCTC 58.831 40.000 0.00 0.00 0.00 3.36
1288 1318 2.345760 GGAGACCCGCGTTCTACCA 61.346 63.158 4.92 0.00 0.00 3.25
1383 1413 7.331193 ACGTATAGTCTCCACAAATTCAAGTTC 59.669 37.037 0.00 0.00 0.00 3.01
1399 1429 8.762481 ATTCAAGTTCTACCCACTTTACTTTT 57.238 30.769 0.00 0.00 31.83 2.27
1416 1446 8.867112 TTTACTTTTATTGATCTCGTCGCTAT 57.133 30.769 0.00 0.00 0.00 2.97
1454 1484 9.453830 AAGAAAGAAGTAATAGGTAGGGATGAT 57.546 33.333 0.00 0.00 0.00 2.45
1468 1498 5.574970 AGGGATGATAGGATTTGAACCTC 57.425 43.478 0.00 0.00 38.76 3.85
1470 1500 6.393897 AGGGATGATAGGATTTGAACCTCTA 58.606 40.000 0.00 0.00 38.76 2.43
1495 1525 3.870633 TTTGTACCCAAAACAAACGCT 57.129 38.095 0.00 0.00 40.83 5.07
1506 1536 3.396260 AACAAACGCTCTACCAAGCTA 57.604 42.857 0.00 0.00 40.23 3.32
1507 1537 3.611766 ACAAACGCTCTACCAAGCTAT 57.388 42.857 0.00 0.00 40.23 2.97
1508 1538 3.262420 ACAAACGCTCTACCAAGCTATG 58.738 45.455 0.00 0.00 40.23 2.23
1509 1539 3.056107 ACAAACGCTCTACCAAGCTATGA 60.056 43.478 0.00 0.00 40.23 2.15
1510 1540 4.122776 CAAACGCTCTACCAAGCTATGAT 58.877 43.478 0.00 0.00 40.23 2.45
1511 1541 3.377346 ACGCTCTACCAAGCTATGATG 57.623 47.619 0.00 0.00 40.23 3.07
1512 1542 2.036475 ACGCTCTACCAAGCTATGATGG 59.964 50.000 0.37 0.37 40.23 3.51
1513 1543 2.297315 CGCTCTACCAAGCTATGATGGA 59.703 50.000 9.19 0.00 40.23 3.41
1514 1544 3.243873 CGCTCTACCAAGCTATGATGGAA 60.244 47.826 9.19 0.00 40.23 3.53
1515 1545 4.562347 CGCTCTACCAAGCTATGATGGAAT 60.562 45.833 9.19 0.00 40.23 3.01
1516 1546 5.336770 CGCTCTACCAAGCTATGATGGAATA 60.337 44.000 9.19 0.00 40.23 1.75
1517 1547 6.105333 GCTCTACCAAGCTATGATGGAATAG 58.895 44.000 9.19 2.00 39.12 1.73
1518 1548 6.611613 TCTACCAAGCTATGATGGAATAGG 57.388 41.667 9.19 0.00 39.12 2.57
1519 1549 4.647564 ACCAAGCTATGATGGAATAGGG 57.352 45.455 9.19 0.00 39.12 3.53
1520 1550 4.242811 ACCAAGCTATGATGGAATAGGGA 58.757 43.478 9.19 0.00 39.12 4.20
1521 1551 4.665009 ACCAAGCTATGATGGAATAGGGAA 59.335 41.667 9.19 0.00 39.12 3.97
1522 1552 5.134339 ACCAAGCTATGATGGAATAGGGAAA 59.866 40.000 9.19 0.00 39.12 3.13
1523 1553 5.709164 CCAAGCTATGATGGAATAGGGAAAG 59.291 44.000 0.00 0.00 39.12 2.62
1524 1554 6.466326 CCAAGCTATGATGGAATAGGGAAAGA 60.466 42.308 0.00 0.00 39.12 2.52
1588 1620 0.722676 TCCCCCTTGACTACTGGGAT 59.277 55.000 0.00 0.00 43.47 3.85
1612 1644 1.404717 CCAGCTACATCTTCGCACACT 60.405 52.381 0.00 0.00 0.00 3.55
1641 1673 2.540157 GCGTCCATATTACGGGCAAAAC 60.540 50.000 8.90 0.00 40.64 2.43
1656 1688 4.218312 GGCAAAACATATGATTCTCCCCT 58.782 43.478 10.38 0.00 0.00 4.79
1660 1692 6.041296 GCAAAACATATGATTCTCCCCTTGAT 59.959 38.462 10.38 0.00 0.00 2.57
1683 1715 3.336997 AGCTGGGACCCACTAGCTATATA 59.663 47.826 21.25 0.00 44.10 0.86
1715 1747 1.574263 GAAGTGCCTCCTTACCTCCT 58.426 55.000 0.00 0.00 0.00 3.69
1773 1805 2.616842 GGTTGTTTGTCTGGTCGTGAAT 59.383 45.455 0.00 0.00 0.00 2.57
1846 1878 2.202892 GCCGAGTAAGGAAGGGCG 60.203 66.667 0.00 0.00 33.58 6.13
1847 1879 3.015312 GCCGAGTAAGGAAGGGCGT 62.015 63.158 0.00 0.00 33.58 5.68
1870 1902 1.337387 GTCGTAGTAGAGGCATGGACC 59.663 57.143 0.00 0.00 0.00 4.46
1871 1903 0.674534 CGTAGTAGAGGCATGGACCC 59.325 60.000 0.00 0.00 0.00 4.46
1873 1905 2.330216 GTAGTAGAGGCATGGACCCAT 58.670 52.381 0.00 0.00 37.08 4.00
1880 1912 1.168407 GGCATGGACCCATCATGTCG 61.168 60.000 0.00 0.00 42.72 4.35
1936 1968 2.171003 GCCAGGGTGCAAGAAAGTAAT 58.829 47.619 0.00 0.00 0.00 1.89
1966 1998 2.279918 CGTACATACGGGCAGGGC 60.280 66.667 3.47 0.00 45.30 5.19
1984 2016 1.139095 CCTCGAACACCTACTCGCC 59.861 63.158 0.00 0.00 35.04 5.54
1999 2031 2.187424 GCCCATACGTACGGCCAA 59.813 61.111 21.06 2.14 36.63 4.52
2002 2034 1.518774 CCATACGTACGGCCAAGGT 59.481 57.895 21.06 4.49 0.00 3.50
2022 2054 3.609853 GTTCATGTACATGGAGAGGCAA 58.390 45.455 30.56 15.82 39.24 4.52
2031 2063 1.153667 GGAGAGGCAACAGAGAGCG 60.154 63.158 0.00 0.00 41.41 5.03
2053 2085 2.180769 CGGCGTCCTGTTCATCGA 59.819 61.111 0.00 0.00 0.00 3.59
2098 2130 3.181530 CGGAGAAATTGTGTCGTCATGTC 60.182 47.826 0.00 0.00 0.00 3.06
2108 2140 0.107703 TCGTCATGTCCATTGGGAGC 60.108 55.000 2.09 0.00 46.12 4.70
2109 2141 0.392863 CGTCATGTCCATTGGGAGCA 60.393 55.000 2.09 0.63 46.12 4.26
2112 2144 2.762327 GTCATGTCCATTGGGAGCAAAT 59.238 45.455 2.09 0.00 46.12 2.32
2113 2145 2.761767 TCATGTCCATTGGGAGCAAATG 59.238 45.455 2.09 0.00 46.12 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.003051 ATGCCTAGGAAGGGGACGT 59.997 57.895 14.75 0.00 43.87 4.34
1 2 1.048724 TGATGCCTAGGAAGGGGACG 61.049 60.000 14.75 0.00 43.87 4.79
2 3 0.470341 GTGATGCCTAGGAAGGGGAC 59.530 60.000 14.75 0.00 43.87 4.46
3 4 0.694444 GGTGATGCCTAGGAAGGGGA 60.694 60.000 14.75 0.00 43.87 4.81
4 5 1.839894 GGTGATGCCTAGGAAGGGG 59.160 63.158 14.75 0.00 43.87 4.79
5 6 1.338136 ACGGTGATGCCTAGGAAGGG 61.338 60.000 14.75 0.00 43.87 3.95
6 7 0.541863 AACGGTGATGCCTAGGAAGG 59.458 55.000 14.75 0.00 46.76 3.46
7 8 1.066143 ACAACGGTGATGCCTAGGAAG 60.066 52.381 14.75 0.00 34.25 3.46
8 9 0.981183 ACAACGGTGATGCCTAGGAA 59.019 50.000 14.75 0.50 34.25 3.36
9 10 0.535335 GACAACGGTGATGCCTAGGA 59.465 55.000 14.75 0.00 34.25 2.94
10 11 0.462047 GGACAACGGTGATGCCTAGG 60.462 60.000 7.88 3.67 34.25 3.02
11 12 0.249120 TGGACAACGGTGATGCCTAG 59.751 55.000 7.88 0.00 34.25 3.02
12 13 0.036765 GTGGACAACGGTGATGCCTA 60.037 55.000 7.88 0.00 34.25 3.93
13 14 1.302511 GTGGACAACGGTGATGCCT 60.303 57.895 7.88 0.00 34.25 4.75
14 15 2.332654 GGTGGACAACGGTGATGCC 61.333 63.158 7.88 6.10 0.00 4.40
15 16 1.599518 TGGTGGACAACGGTGATGC 60.600 57.895 7.88 0.00 0.00 3.91
16 17 1.234615 GGTGGTGGACAACGGTGATG 61.235 60.000 7.88 0.00 0.00 3.07
17 18 1.072505 GGTGGTGGACAACGGTGAT 59.927 57.895 7.88 0.00 0.00 3.06
18 19 1.628238 AAGGTGGTGGACAACGGTGA 61.628 55.000 7.88 0.00 43.31 4.02
19 20 1.153046 AAGGTGGTGGACAACGGTG 60.153 57.895 0.00 0.00 43.31 4.94
20 21 1.153046 CAAGGTGGTGGACAACGGT 60.153 57.895 0.00 0.00 43.31 4.83
21 22 1.896660 CCAAGGTGGTGGACAACGG 60.897 63.158 0.00 0.00 43.31 4.44
22 23 3.744559 CCAAGGTGGTGGACAACG 58.255 61.111 0.00 0.00 43.31 4.10
31 32 2.046892 CCGAGAGCACCAAGGTGG 60.047 66.667 20.02 3.49 45.49 4.61
33 34 4.379243 CGCCGAGAGCACCAAGGT 62.379 66.667 0.00 0.00 44.04 3.50
42 43 4.827087 ACCATGCTGCGCCGAGAG 62.827 66.667 4.18 0.00 0.00 3.20
43 44 4.819761 GACCATGCTGCGCCGAGA 62.820 66.667 4.18 0.00 0.00 4.04
45 46 3.974835 ATTGACCATGCTGCGCCGA 62.975 57.895 4.18 0.00 0.00 5.54
46 47 3.511595 ATTGACCATGCTGCGCCG 61.512 61.111 4.18 0.00 0.00 6.46
47 48 2.103538 CATTGACCATGCTGCGCC 59.896 61.111 4.18 0.00 0.00 6.53
48 49 1.515519 CACATTGACCATGCTGCGC 60.516 57.895 0.00 0.00 36.14 6.09
49 50 1.138036 CCACATTGACCATGCTGCG 59.862 57.895 0.00 0.00 36.14 5.18
50 51 0.171903 GACCACATTGACCATGCTGC 59.828 55.000 0.00 0.00 36.14 5.25
51 52 1.536940 TGACCACATTGACCATGCTG 58.463 50.000 0.00 0.00 36.14 4.41
52 53 2.097036 CATGACCACATTGACCATGCT 58.903 47.619 0.00 0.00 36.14 3.79
53 54 1.135527 CCATGACCACATTGACCATGC 59.864 52.381 0.00 0.00 36.14 4.06
54 55 2.725637 TCCATGACCACATTGACCATG 58.274 47.619 0.00 0.00 39.07 3.66
55 56 3.091545 GTTCCATGACCACATTGACCAT 58.908 45.455 0.00 0.00 34.15 3.55
56 57 2.513753 GTTCCATGACCACATTGACCA 58.486 47.619 0.00 0.00 34.15 4.02
57 58 1.468520 CGTTCCATGACCACATTGACC 59.531 52.381 0.00 0.00 34.15 4.02
58 59 2.159627 GTCGTTCCATGACCACATTGAC 59.840 50.000 0.00 0.00 34.15 3.18
59 60 2.038426 AGTCGTTCCATGACCACATTGA 59.962 45.455 0.00 0.00 34.73 2.57
60 61 2.426522 AGTCGTTCCATGACCACATTG 58.573 47.619 0.00 0.00 34.73 2.82
61 62 2.859165 AGTCGTTCCATGACCACATT 57.141 45.000 0.00 0.00 34.73 2.71
62 63 2.699954 GAAGTCGTTCCATGACCACAT 58.300 47.619 0.00 0.00 34.73 3.21
63 64 2.163818 GAAGTCGTTCCATGACCACA 57.836 50.000 0.00 0.00 34.73 4.17
80 81 5.943349 TGGATAGTAAACTTCCGATGGAA 57.057 39.130 0.00 0.00 39.66 3.53
81 82 5.221641 CCATGGATAGTAAACTTCCGATGGA 60.222 44.000 5.56 0.00 38.79 3.41
82 83 4.997395 CCATGGATAGTAAACTTCCGATGG 59.003 45.833 5.56 16.56 34.69 3.51
83 84 5.853936 TCCATGGATAGTAAACTTCCGATG 58.146 41.667 11.44 3.58 31.90 3.84
84 85 5.839063 TCTCCATGGATAGTAAACTTCCGAT 59.161 40.000 16.63 0.00 31.90 4.18
85 86 5.205821 TCTCCATGGATAGTAAACTTCCGA 58.794 41.667 16.63 0.75 31.90 4.55
86 87 5.302059 TCTCTCCATGGATAGTAAACTTCCG 59.698 44.000 22.67 4.96 31.90 4.30
87 88 6.098409 TGTCTCTCCATGGATAGTAAACTTCC 59.902 42.308 22.67 6.50 0.00 3.46
88 89 7.068839 TCTGTCTCTCCATGGATAGTAAACTTC 59.931 40.741 22.67 9.36 0.00 3.01
89 90 6.897966 TCTGTCTCTCCATGGATAGTAAACTT 59.102 38.462 22.67 0.00 0.00 2.66
90 91 6.436027 TCTGTCTCTCCATGGATAGTAAACT 58.564 40.000 22.67 0.00 0.00 2.66
91 92 6.716934 TCTGTCTCTCCATGGATAGTAAAC 57.283 41.667 22.67 15.67 0.00 2.01
92 93 7.126061 TCTTCTGTCTCTCCATGGATAGTAAA 58.874 38.462 22.67 13.31 0.00 2.01
93 94 6.673583 TCTTCTGTCTCTCCATGGATAGTAA 58.326 40.000 22.67 13.28 0.00 2.24
94 95 6.267492 TCTTCTGTCTCTCCATGGATAGTA 57.733 41.667 22.67 14.03 0.00 1.82
95 96 5.136068 TCTTCTGTCTCTCCATGGATAGT 57.864 43.478 22.67 0.00 0.00 2.12
96 97 7.174413 TCTATCTTCTGTCTCTCCATGGATAG 58.826 42.308 16.63 17.92 34.50 2.08
97 98 7.096402 TCTATCTTCTGTCTCTCCATGGATA 57.904 40.000 16.63 7.37 0.00 2.59
98 99 5.963092 TCTATCTTCTGTCTCTCCATGGAT 58.037 41.667 16.63 0.00 0.00 3.41
99 100 5.394562 TCTATCTTCTGTCTCTCCATGGA 57.605 43.478 15.27 15.27 0.00 3.41
100 101 6.669125 ATTCTATCTTCTGTCTCTCCATGG 57.331 41.667 4.97 4.97 0.00 3.66
101 102 8.634335 TCTATTCTATCTTCTGTCTCTCCATG 57.366 38.462 0.00 0.00 0.00 3.66
102 103 9.077885 GTTCTATTCTATCTTCTGTCTCTCCAT 57.922 37.037 0.00 0.00 0.00 3.41
103 104 8.278639 AGTTCTATTCTATCTTCTGTCTCTCCA 58.721 37.037 0.00 0.00 0.00 3.86
261 273 7.308450 TCCATATGGAATAAGAGGAGAACAG 57.692 40.000 22.52 0.00 42.18 3.16
345 357 9.768215 TGGATAATTTCTTTTTCAATAGGACCT 57.232 29.630 0.00 0.00 0.00 3.85
454 472 7.233632 TTAGATCATCTAACCCCATTGAATGG 58.766 38.462 17.22 17.22 40.67 3.16
505 523 8.971321 CAAGAGATTTGTTGTGGAATTTGTTAG 58.029 33.333 0.00 0.00 0.00 2.34
507 525 7.555087 TCAAGAGATTTGTTGTGGAATTTGTT 58.445 30.769 0.00 0.00 0.00 2.83
544 562 9.043548 TGGATTCATCAGATGATACATGAGTAT 57.956 33.333 14.11 1.28 43.49 2.12
545 563 8.309656 GTGGATTCATCAGATGATACATGAGTA 58.690 37.037 14.11 0.00 39.39 2.59
667 686 7.653713 CACTATATGAAAGAGTTTACTCCGCAT 59.346 37.037 6.28 9.63 43.88 4.73
669 688 6.979238 ACACTATATGAAAGAGTTTACTCCGC 59.021 38.462 6.28 0.00 43.88 5.54
670 689 9.666626 CTACACTATATGAAAGAGTTTACTCCG 57.333 37.037 6.28 0.00 43.88 4.63
763 789 6.786122 AGAGTTGGGGTTATAGTTAAAGCAA 58.214 36.000 0.00 0.00 0.00 3.91
790 816 8.511604 AAGGTGTATCTTGTTCAATCCAATAG 57.488 34.615 0.00 0.00 0.00 1.73
850 876 6.652062 CCAGGAATCCCAAAGAAAGATTTTTG 59.348 38.462 0.00 0.00 34.79 2.44
1016 1043 3.545703 AGGCCTAAGACGATTCCAAATG 58.454 45.455 1.29 0.00 0.00 2.32
1066 1093 5.236478 GCCTGTATTGCAAATACGTAGTCAT 59.764 40.000 1.71 0.00 43.93 3.06
1072 1099 2.095213 CACGCCTGTATTGCAAATACGT 59.905 45.455 1.71 5.37 0.00 3.57
1129 1159 2.314852 TCTGGTCTGGAGGAGGTCAATA 59.685 50.000 0.00 0.00 0.00 1.90
1206 1236 8.985315 ATTCCATCTATCTTATGTTGAAGCAA 57.015 30.769 0.00 0.00 0.00 3.91
1213 1243 7.015682 AGACCGTGATTCCATCTATCTTATGTT 59.984 37.037 0.00 0.00 0.00 2.71
1288 1318 4.127171 TGAAAGCGCTCTTAGTTCAGTTT 58.873 39.130 12.06 0.00 31.02 2.66
1347 1377 4.748600 TGGAGACTATACGTACGTGAGATG 59.251 45.833 30.25 16.79 0.00 2.90
1383 1413 8.818057 CGAGATCAATAAAAGTAAAGTGGGTAG 58.182 37.037 0.00 0.00 0.00 3.18
1399 1429 3.255888 AGGCAATAGCGACGAGATCAATA 59.744 43.478 0.00 0.00 43.41 1.90
1454 1484 8.934023 ACAAAATGTTAGAGGTTCAAATCCTA 57.066 30.769 0.00 0.00 35.20 2.94
1495 1525 5.485353 CCCTATTCCATCATAGCTTGGTAGA 59.515 44.000 0.00 0.00 34.48 2.59
1506 1536 4.105377 CCCTGTCTTTCCCTATTCCATCAT 59.895 45.833 0.00 0.00 0.00 2.45
1507 1537 3.459598 CCCTGTCTTTCCCTATTCCATCA 59.540 47.826 0.00 0.00 0.00 3.07
1508 1538 3.716872 TCCCTGTCTTTCCCTATTCCATC 59.283 47.826 0.00 0.00 0.00 3.51
1509 1539 3.459969 GTCCCTGTCTTTCCCTATTCCAT 59.540 47.826 0.00 0.00 0.00 3.41
1510 1540 2.844348 GTCCCTGTCTTTCCCTATTCCA 59.156 50.000 0.00 0.00 0.00 3.53
1511 1541 2.172930 GGTCCCTGTCTTTCCCTATTCC 59.827 54.545 0.00 0.00 0.00 3.01
1512 1542 2.172930 GGGTCCCTGTCTTTCCCTATTC 59.827 54.545 0.00 0.00 35.63 1.75
1513 1543 2.206223 GGGTCCCTGTCTTTCCCTATT 58.794 52.381 0.00 0.00 35.63 1.73
1514 1544 1.082194 TGGGTCCCTGTCTTTCCCTAT 59.918 52.381 10.00 0.00 38.95 2.57
1515 1545 0.494551 TGGGTCCCTGTCTTTCCCTA 59.505 55.000 10.00 0.00 38.95 3.53
1516 1546 1.134438 GTGGGTCCCTGTCTTTCCCT 61.134 60.000 10.00 0.00 38.95 4.20
1517 1547 1.379146 GTGGGTCCCTGTCTTTCCC 59.621 63.158 10.00 0.00 38.68 3.97
1518 1548 1.379146 GGTGGGTCCCTGTCTTTCC 59.621 63.158 10.00 0.00 0.00 3.13
1519 1549 1.003718 CGGTGGGTCCCTGTCTTTC 60.004 63.158 10.00 0.00 0.00 2.62
1520 1550 2.526046 CCGGTGGGTCCCTGTCTTT 61.526 63.158 10.00 0.00 0.00 2.52
1521 1551 2.928396 CCGGTGGGTCCCTGTCTT 60.928 66.667 10.00 0.00 0.00 3.01
1522 1552 3.923645 TCCGGTGGGTCCCTGTCT 61.924 66.667 10.00 0.00 33.83 3.41
1523 1553 3.703127 GTCCGGTGGGTCCCTGTC 61.703 72.222 10.00 0.00 33.83 3.51
1575 1607 2.187958 CTGGTGGATCCCAGTAGTCAA 58.812 52.381 9.90 0.00 45.81 3.18
1588 1620 0.175760 GCGAAGATGTAGCTGGTGGA 59.824 55.000 0.00 0.00 0.00 4.02
1612 1644 3.005050 CCGTAATATGGACGCACTTCCTA 59.995 47.826 5.16 0.00 38.99 2.94
1641 1673 6.114089 CAGCTATCAAGGGGAGAATCATATG 58.886 44.000 0.00 0.00 36.25 1.78
1656 1688 2.398588 CTAGTGGGTCCCAGCTATCAA 58.601 52.381 12.21 0.00 32.34 2.57
1660 1692 0.931468 TAGCTAGTGGGTCCCAGCTA 59.069 55.000 21.13 21.13 34.94 3.32
1683 1715 1.868997 CACTTCCTTGCGTGCGAAT 59.131 52.632 0.00 0.00 0.00 3.34
1715 1747 1.768684 GAGTGGGTCCCAGCTGTCAA 61.769 60.000 12.21 0.00 32.34 3.18
1773 1805 3.333804 TCGACCAGTATGTACGTACACA 58.666 45.455 29.54 17.26 39.30 3.72
1846 1878 2.479730 CCATGCCTCTACTACGACACAC 60.480 54.545 0.00 0.00 0.00 3.82
1847 1879 1.749063 CCATGCCTCTACTACGACACA 59.251 52.381 0.00 0.00 0.00 3.72
1870 1902 2.528743 GGACTGCGCGACATGATGG 61.529 63.158 12.10 0.00 0.00 3.51
1871 1903 2.528743 GGGACTGCGCGACATGATG 61.529 63.158 12.10 0.00 0.00 3.07
1880 1912 0.454620 CGATATAGACGGGACTGCGC 60.455 60.000 0.00 0.00 0.00 6.09
1966 1998 1.139095 GGCGAGTAGGTGTTCGAGG 59.861 63.158 0.00 0.00 39.06 4.63
1984 2016 0.108041 AACCTTGGCCGTACGTATGG 60.108 55.000 26.57 26.57 35.42 2.74
1999 2031 2.171448 GCCTCTCCATGTACATGAACCT 59.829 50.000 32.72 0.00 41.20 3.50
2002 2034 3.008923 TGTTGCCTCTCCATGTACATGAA 59.991 43.478 32.72 16.08 41.20 2.57
2022 2054 4.057428 GCCGTCACCGCTCTCTGT 62.057 66.667 0.00 0.00 0.00 3.41
2031 2063 2.737376 GAACAGGACGCCGTCACC 60.737 66.667 20.08 2.81 33.68 4.02
2084 2116 2.150390 CCAATGGACATGACGACACAA 58.850 47.619 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.