Multiple sequence alignment - TraesCS2D01G062800

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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 TraesCS2D01G062800 chr2D 100.000 3934 0 0 1 3934 26561169 26557236 0.000000e+00 7265.0
1 TraesCS2D01G062800 chr2D 86.268 284 29 7 3068 3345 277675379 277675658 2.300000e-77 300.0
2 TraesCS2D01G062800 chr2A 91.974 1682 107 15 1730 3394 28808953 28807283 0.000000e+00 2333.0
3 TraesCS2D01G062800 chr2A 91.006 845 44 18 758 1600 28809864 28809050 0.000000e+00 1110.0
4 TraesCS2D01G062800 chr2A 88.909 541 48 4 1 530 761449861 761449322 0.000000e+00 656.0
5 TraesCS2D01G062800 chr2A 87.963 540 55 2 1 530 681691971 681692510 2.580000e-176 628.0
6 TraesCS2D01G062800 chr2A 84.074 540 65 7 1 530 757310299 757310827 5.870000e-138 501.0
7 TraesCS2D01G062800 chr2A 91.964 224 16 2 3709 3932 28806777 28806556 2.950000e-81 313.0
8 TraesCS2D01G062800 chr2A 91.403 221 17 2 3499 3718 28807286 28807067 6.390000e-78 302.0
9 TraesCS2D01G062800 chr2B 89.895 1613 108 19 2 1602 41866801 41865232 0.000000e+00 2025.0
10 TraesCS2D01G062800 chr2B 92.903 1240 57 20 1730 2944 41865144 41863911 0.000000e+00 1773.0
11 TraesCS2D01G062800 chr2B 93.487 998 58 6 1952 2944 41848013 41847018 0.000000e+00 1476.0
12 TraesCS2D01G062800 chr2B 89.495 733 58 15 2998 3718 41846896 41846171 0.000000e+00 909.0
13 TraesCS2D01G062800 chr2B 94.667 225 12 0 3710 3934 41845850 41845626 2.250000e-92 350.0
14 TraesCS2D01G062800 chr2B 89.000 100 7 1 475 570 41884939 41884840 1.920000e-23 121.0
15 TraesCS2D01G062800 chr2B 90.361 83 5 3 2998 3077 41863789 41863707 5.380000e-19 106.0
16 TraesCS2D01G062800 chr5D 81.627 996 145 28 1730 2717 3766293 3767258 0.000000e+00 791.0
17 TraesCS2D01G062800 chr5D 88.487 608 67 1 990 1597 44494148 44494752 0.000000e+00 732.0
18 TraesCS2D01G062800 chr5D 83.636 770 100 16 1962 2725 44495105 44495854 0.000000e+00 701.0
19 TraesCS2D01G062800 chr5D 86.140 570 76 2 1030 1596 3765227 3765796 2.600000e-171 612.0
20 TraesCS2D01G062800 chr5B 88.725 612 66 2 990 1601 44225734 44225126 0.000000e+00 745.0
21 TraesCS2D01G062800 chr5B 89.876 563 57 0 1039 1601 43925307 43925869 0.000000e+00 725.0
22 TraesCS2D01G062800 chr5B 83.075 774 107 18 1962 2729 44224764 44224009 0.000000e+00 682.0
23 TraesCS2D01G062800 chr5B 82.750 771 109 17 1962 2726 43926229 43926981 0.000000e+00 665.0
24 TraesCS2D01G062800 chr5A 87.974 607 70 1 991 1597 34908987 34909590 0.000000e+00 713.0
25 TraesCS2D01G062800 chr5A 82.558 774 111 18 1962 2729 34909955 34910710 0.000000e+00 660.0
26 TraesCS2D01G062800 chr5A 85.451 543 67 6 2 533 705852599 705852058 4.440000e-154 555.0
27 TraesCS2D01G062800 chr5A 98.113 53 1 0 478 530 705334357 705334305 4.190000e-15 93.5
28 TraesCS2D01G062800 chr7D 89.259 540 47 3 1 530 488607056 488607594 0.000000e+00 665.0
29 TraesCS2D01G062800 chr7D 82.199 573 81 15 1039 1592 60499827 60499257 1.280000e-129 473.0
30 TraesCS2D01G062800 chr7D 79.749 558 99 6 1952 2500 60470123 60469571 3.690000e-105 392.0
31 TraesCS2D01G062800 chr7D 86.364 286 29 7 3066 3345 607214419 607214700 1.780000e-78 303.0
32 TraesCS2D01G062800 chrUn 88.170 541 52 5 1 530 314599241 314598702 5.550000e-178 634.0
33 TraesCS2D01G062800 chrUn 85.625 160 21 2 3372 3529 206982220 206982379 2.430000e-37 167.0
34 TraesCS2D01G062800 chr4D 88.148 540 53 4 1 530 120067428 120066890 1.990000e-177 632.0
35 TraesCS2D01G062800 chr1B 88.491 530 50 3 1 519 11982779 11983308 7.170000e-177 630.0
36 TraesCS2D01G062800 chr1B 87.778 540 55 2 1 530 136073288 136073826 4.320000e-174 621.0
37 TraesCS2D01G062800 chr1B 86.282 277 30 6 3068 3341 592264864 592264593 1.070000e-75 294.0
38 TraesCS2D01G062800 chr1B 86.282 277 30 6 3068 3341 592305995 592305724 1.070000e-75 294.0
39 TraesCS2D01G062800 chr1A 87.823 542 53 5 1 530 347909593 347909053 1.200000e-174 623.0
40 TraesCS2D01G062800 chr7A 87.828 534 54 2 1 524 162763228 162762696 2.010000e-172 616.0
41 TraesCS2D01G062800 chr4B 87.902 529 51 5 2 519 647691399 647691925 9.350000e-171 610.0
42 TraesCS2D01G062800 chr6B 86.525 282 29 7 3069 3345 277627267 277627544 6.390000e-78 302.0
43 TraesCS2D01G062800 chr6B 96.429 56 2 0 475 530 211509407 211509462 4.190000e-15 93.5
44 TraesCS2D01G062800 chr4A 86.380 279 28 7 3072 3345 698370694 698370421 2.970000e-76 296.0
45 TraesCS2D01G062800 chr6D 85.614 285 31 7 3066 3345 339681764 339681485 1.380000e-74 291.0
46 TraesCS2D01G062800 chr6D 96.000 50 2 0 475 524 223950352 223950303 9.060000e-12 82.4
47 TraesCS2D01G062800 chr7B 94.643 56 3 0 475 530 614668040 614667985 1.950000e-13 87.9


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 TraesCS2D01G062800 chr2D 26557236 26561169 3933 True 7265.000000 7265 100.000000 1 3934 1 chr2D.!!$R1 3933
1 TraesCS2D01G062800 chr2A 28806556 28809864 3308 True 1014.500000 2333 91.586750 758 3932 4 chr2A.!!$R2 3174
2 TraesCS2D01G062800 chr2A 761449322 761449861 539 True 656.000000 656 88.909000 1 530 1 chr2A.!!$R1 529
3 TraesCS2D01G062800 chr2A 681691971 681692510 539 False 628.000000 628 87.963000 1 530 1 chr2A.!!$F1 529
4 TraesCS2D01G062800 chr2A 757310299 757310827 528 False 501.000000 501 84.074000 1 530 1 chr2A.!!$F2 529
5 TraesCS2D01G062800 chr2B 41863707 41866801 3094 True 1301.333333 2025 91.053000 2 3077 3 chr2B.!!$R3 3075
6 TraesCS2D01G062800 chr2B 41845626 41848013 2387 True 911.666667 1476 92.549667 1952 3934 3 chr2B.!!$R2 1982
7 TraesCS2D01G062800 chr5D 44494148 44495854 1706 False 716.500000 732 86.061500 990 2725 2 chr5D.!!$F2 1735
8 TraesCS2D01G062800 chr5D 3765227 3767258 2031 False 701.500000 791 83.883500 1030 2717 2 chr5D.!!$F1 1687
9 TraesCS2D01G062800 chr5B 44224009 44225734 1725 True 713.500000 745 85.900000 990 2729 2 chr5B.!!$R1 1739
10 TraesCS2D01G062800 chr5B 43925307 43926981 1674 False 695.000000 725 86.313000 1039 2726 2 chr5B.!!$F1 1687
11 TraesCS2D01G062800 chr5A 34908987 34910710 1723 False 686.500000 713 85.266000 991 2729 2 chr5A.!!$F1 1738
12 TraesCS2D01G062800 chr5A 705852058 705852599 541 True 555.000000 555 85.451000 2 533 1 chr5A.!!$R2 531
13 TraesCS2D01G062800 chr7D 488607056 488607594 538 False 665.000000 665 89.259000 1 530 1 chr7D.!!$F1 529
14 TraesCS2D01G062800 chr7D 60499257 60499827 570 True 473.000000 473 82.199000 1039 1592 1 chr7D.!!$R2 553
15 TraesCS2D01G062800 chr7D 60469571 60470123 552 True 392.000000 392 79.749000 1952 2500 1 chr7D.!!$R1 548
16 TraesCS2D01G062800 chrUn 314598702 314599241 539 True 634.000000 634 88.170000 1 530 1 chrUn.!!$R1 529
17 TraesCS2D01G062800 chr4D 120066890 120067428 538 True 632.000000 632 88.148000 1 530 1 chr4D.!!$R1 529
18 TraesCS2D01G062800 chr1B 11982779 11983308 529 False 630.000000 630 88.491000 1 519 1 chr1B.!!$F1 518
19 TraesCS2D01G062800 chr1B 136073288 136073826 538 False 621.000000 621 87.778000 1 530 1 chr1B.!!$F2 529
20 TraesCS2D01G062800 chr1A 347909053 347909593 540 True 623.000000 623 87.823000 1 530 1 chr1A.!!$R1 529
21 TraesCS2D01G062800 chr7A 162762696 162763228 532 True 616.000000 616 87.828000 1 524 1 chr7A.!!$R1 523
22 TraesCS2D01G062800 chr4B 647691399 647691925 526 False 610.000000 610 87.902000 2 519 1 chr4B.!!$F1 517

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
819 838 0.099082 CTCGTCTCCGGTCAGTTAGC 59.901 60.0 0.0 0.0 33.95 3.09 F
1637 1756 0.041312 CGTTTTTGACACGCTGGGAG 60.041 55.0 0.0 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2056 2547 0.107993 CGTCCTCCATGTGCATCAGT 60.108 55.0 0.0 0.0 0.00 3.41 R
3335 3955 0.377905 TCATGCATCCGTCATTTGCG 59.622 50.0 0.0 0.0 39.23 4.85 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
28 29 2.094906 CGGATGACACGTACAGAAGGAA 60.095 50.000 0.00 0.00 0.00 3.36
130 133 3.058914 CACAAGGTGACGGTGAAATTCTC 60.059 47.826 0.00 0.00 41.24 2.87
302 308 7.550906 GGAGCACAAAGTAGAGTAATGAGAAAT 59.449 37.037 0.00 0.00 0.00 2.17
341 348 3.627732 TGACTGTGAAGAAGACGAGAC 57.372 47.619 0.00 0.00 0.00 3.36
385 392 0.404812 ACGTGGAGTCTGGGAGTAGT 59.595 55.000 0.00 0.00 0.00 2.73
390 397 1.408544 GGAGTCTGGGAGTAGTAGCGT 60.409 57.143 0.00 0.00 0.00 5.07
400 407 2.099263 GAGTAGTAGCGTTGCTCATGGA 59.901 50.000 0.00 0.00 40.44 3.41
422 429 8.492673 TGGAGTATCTCAAATTCAATGTACAC 57.507 34.615 0.00 0.00 33.73 2.90
536 553 1.544246 GGATTTGGTTTTGGTCCTCGG 59.456 52.381 0.00 0.00 0.00 4.63
544 561 3.118371 GGTTTTGGTCCTCGGTAGATCAT 60.118 47.826 0.00 0.00 0.00 2.45
547 564 1.142262 TGGTCCTCGGTAGATCATCGA 59.858 52.381 0.00 0.11 0.00 3.59
561 578 6.425210 AGATCATCGATGGTCTTGGATTTA 57.575 37.500 31.13 6.43 45.59 1.40
572 589 7.880160 TGGTCTTGGATTTATTCTAACATGG 57.120 36.000 0.00 0.00 0.00 3.66
576 593 8.616076 GTCTTGGATTTATTCTAACATGGTGAG 58.384 37.037 0.00 0.00 0.00 3.51
577 594 8.328758 TCTTGGATTTATTCTAACATGGTGAGT 58.671 33.333 0.00 0.00 0.00 3.41
580 597 6.543831 GGATTTATTCTAACATGGTGAGTGCT 59.456 38.462 0.00 0.00 0.00 4.40
581 598 6.985188 TTTATTCTAACATGGTGAGTGCTC 57.015 37.500 0.00 0.00 0.00 4.26
582 599 2.654749 TCTAACATGGTGAGTGCTCG 57.345 50.000 0.00 0.00 0.00 5.03
583 600 1.204704 TCTAACATGGTGAGTGCTCGG 59.795 52.381 0.00 0.00 0.00 4.63
584 601 0.973632 TAACATGGTGAGTGCTCGGT 59.026 50.000 0.00 0.00 0.00 4.69
585 602 0.603707 AACATGGTGAGTGCTCGGTG 60.604 55.000 0.00 0.00 0.00 4.94
658 675 2.166821 CTGATTAGCCAGCTAGCCAG 57.833 55.000 12.13 5.01 0.00 4.85
682 699 0.665835 CCAGTACGTGCTGCCAAAAA 59.334 50.000 26.10 0.00 35.28 1.94
718 735 2.031120 CCAAAACCACACACATCACCT 58.969 47.619 0.00 0.00 0.00 4.00
751 768 1.680735 AGCCAAAATCACAACGCAAGA 59.319 42.857 0.00 0.00 43.62 3.02
774 793 7.497595 AGAAACCAAAACCCAAAGAGATTTAC 58.502 34.615 0.00 0.00 0.00 2.01
810 829 2.556534 ACGTAATTTCTCGTCTCCGG 57.443 50.000 0.00 0.00 35.30 5.14
811 830 1.815003 ACGTAATTTCTCGTCTCCGGT 59.185 47.619 0.00 0.00 35.30 5.28
812 831 2.159462 ACGTAATTTCTCGTCTCCGGTC 60.159 50.000 0.00 0.00 35.30 4.79
813 832 2.159476 CGTAATTTCTCGTCTCCGGTCA 60.159 50.000 0.00 0.00 33.95 4.02
814 833 2.656560 AATTTCTCGTCTCCGGTCAG 57.343 50.000 0.00 0.00 33.95 3.51
815 834 1.546961 ATTTCTCGTCTCCGGTCAGT 58.453 50.000 0.00 0.00 33.95 3.41
816 835 1.325355 TTTCTCGTCTCCGGTCAGTT 58.675 50.000 0.00 0.00 33.95 3.16
817 836 2.189594 TTCTCGTCTCCGGTCAGTTA 57.810 50.000 0.00 0.00 33.95 2.24
818 837 1.735386 TCTCGTCTCCGGTCAGTTAG 58.265 55.000 0.00 0.00 33.95 2.34
819 838 0.099082 CTCGTCTCCGGTCAGTTAGC 59.901 60.000 0.00 0.00 33.95 3.09
820 839 1.139095 CGTCTCCGGTCAGTTAGCC 59.861 63.158 0.00 0.00 0.00 3.93
825 844 2.125106 CGGTCAGTTAGCCAGCCC 60.125 66.667 0.00 0.00 0.00 5.19
841 860 1.362355 CCCAGTTTTGTTCCCACGC 59.638 57.895 0.00 0.00 0.00 5.34
896 915 2.930682 TCCTCGCTCGATCGTCTATATG 59.069 50.000 15.94 0.23 0.00 1.78
904 923 4.179298 TCGATCGTCTATATGTACCTCCG 58.821 47.826 15.94 0.00 0.00 4.63
976 995 2.224378 GCTATTCATCCAGTGGCAGCTA 60.224 50.000 3.51 0.00 0.00 3.32
981 1000 1.139654 CATCCAGTGGCAGCTAAGCTA 59.860 52.381 3.51 0.00 36.40 3.32
982 1001 0.826715 TCCAGTGGCAGCTAAGCTAG 59.173 55.000 3.51 0.00 36.40 3.42
984 1003 0.179062 CAGTGGCAGCTAAGCTAGGG 60.179 60.000 0.00 0.00 36.40 3.53
985 1004 1.524849 GTGGCAGCTAAGCTAGGGC 60.525 63.158 0.00 0.00 36.40 5.19
1006 1025 1.735920 GCTAGCAGATCGATGGCGG 60.736 63.158 10.63 6.49 38.28 6.13
1130 1149 4.197498 GTACCGCGCCGCCTTCTA 62.197 66.667 2.28 0.00 0.00 2.10
1413 1453 4.057428 GAGCTCGTCGGCCACACT 62.057 66.667 2.24 0.00 0.00 3.55
1601 1720 9.720769 AACCGAGATCAAGAAAGTAAGAAATTA 57.279 29.630 0.00 0.00 0.00 1.40
1602 1721 9.152595 ACCGAGATCAAGAAAGTAAGAAATTAC 57.847 33.333 0.00 0.00 0.00 1.89
1606 1725 9.674068 AGATCAAGAAAGTAAGAAATTACTCCC 57.326 33.333 0.00 0.00 36.79 4.30
1608 1727 9.674068 ATCAAGAAAGTAAGAAATTACTCCCTC 57.326 33.333 1.41 0.71 36.79 4.30
1609 1728 8.101419 TCAAGAAAGTAAGAAATTACTCCCTCC 58.899 37.037 1.41 0.00 36.79 4.30
1610 1729 6.641474 AGAAAGTAAGAAATTACTCCCTCCG 58.359 40.000 1.41 0.00 36.79 4.63
1613 1732 7.486407 AAGTAAGAAATTACTCCCTCCGTTA 57.514 36.000 1.41 0.00 36.79 3.18
1614 1733 7.486407 AGTAAGAAATTACTCCCTCCGTTAA 57.514 36.000 0.00 0.00 32.66 2.01
1615 1734 7.554211 AGTAAGAAATTACTCCCTCCGTTAAG 58.446 38.462 0.00 0.00 32.66 1.85
1619 1738 1.386533 TACTCCCTCCGTTAAGAGCG 58.613 55.000 0.00 0.00 32.17 5.03
1620 1739 0.611340 ACTCCCTCCGTTAAGAGCGT 60.611 55.000 0.00 0.00 32.17 5.07
1625 1744 2.095919 CCCTCCGTTAAGAGCGTTTTTG 60.096 50.000 0.00 0.00 32.17 2.44
1628 1747 3.196463 TCCGTTAAGAGCGTTTTTGACA 58.804 40.909 0.00 0.00 0.00 3.58
1629 1748 3.001533 TCCGTTAAGAGCGTTTTTGACAC 59.998 43.478 0.00 0.00 0.00 3.67
1630 1749 2.955799 CGTTAAGAGCGTTTTTGACACG 59.044 45.455 0.00 0.00 40.75 4.49
1635 1754 4.607024 CGTTTTTGACACGCTGGG 57.393 55.556 0.00 0.00 0.00 4.45
1636 1755 2.018544 CGTTTTTGACACGCTGGGA 58.981 52.632 0.00 0.00 0.00 4.37
1637 1756 0.041312 CGTTTTTGACACGCTGGGAG 60.041 55.000 0.00 0.00 0.00 4.30
1639 1758 2.215196 GTTTTTGACACGCTGGGAGTA 58.785 47.619 0.00 0.00 0.00 2.59
1644 1763 2.453521 TGACACGCTGGGAGTATAAGT 58.546 47.619 0.00 0.00 0.00 2.24
1651 1770 3.707793 GCTGGGAGTATAAGTCAGTTCG 58.292 50.000 0.00 0.00 0.00 3.95
1685 1976 4.045636 CATGCATGCATCCATCCATATG 57.954 45.455 30.07 12.94 28.07 1.78
1686 1977 1.822371 TGCATGCATCCATCCATATGC 59.178 47.619 18.46 0.00 46.92 3.14
1728 2147 7.033791 GTCAATCTCGACATTAGTTTACTCCA 58.966 38.462 0.00 0.00 35.88 3.86
1908 2327 6.322491 TCGCAAGGTATATATGTTCTCATCG 58.678 40.000 0.00 0.00 35.05 3.84
2056 2547 2.034124 TGTGATGATCTGATGAGCGGA 58.966 47.619 0.00 0.00 36.05 5.54
2080 2571 1.375908 GCACATGGAGGACGAGCAA 60.376 57.895 0.00 0.00 0.00 3.91
2083 2574 1.817099 CATGGAGGACGAGCAAGGC 60.817 63.158 0.00 0.00 0.00 4.35
2252 2745 2.080286 GCTGAGCGAGAGTAAAACCA 57.920 50.000 0.00 0.00 0.00 3.67
2407 2909 1.444250 GTACATGATTCCGGCGGGA 59.556 57.895 27.98 20.48 41.83 5.14
2517 3019 8.148351 GGATGTAAGCACATTAACTATACCTGA 58.852 37.037 0.00 0.00 45.58 3.86
2543 3069 2.806818 GTCATCGATCATGCATCAGCTT 59.193 45.455 0.00 0.00 42.74 3.74
2548 3078 3.072211 CGATCATGCATCAGCTTATGGT 58.928 45.455 9.85 0.00 42.74 3.55
2552 3082 3.143728 CATGCATCAGCTTATGGTAGCA 58.856 45.455 9.85 0.00 43.68 3.49
2564 3094 9.109393 CAGCTTATGGTAGCAAAGAAACTAATA 57.891 33.333 16.10 0.00 43.68 0.98
2581 3113 7.969536 AACTAATAGATGAATCAATGGACGG 57.030 36.000 0.00 0.00 0.00 4.79
2849 3389 2.092538 CAGATGGGAGCTGTTGAATCCT 60.093 50.000 0.00 0.00 33.40 3.24
2916 3456 0.988832 AACCATGGCCTTCCGTAAGA 59.011 50.000 13.04 0.00 43.02 2.10
2977 3517 5.832539 ATGAACCAGCCTAGCTATTGTAT 57.167 39.130 0.00 0.00 36.40 2.29
3024 3632 4.335400 TGTGACAACTGCATCAAGTCTA 57.665 40.909 9.23 0.00 0.00 2.59
3068 3679 3.005897 AGAATGCGGCGTTGTCTCTATAT 59.994 43.478 12.95 0.00 0.00 0.86
3143 3762 4.023291 AGAATTGCCCGGTTAATTGATGT 58.977 39.130 15.42 0.00 0.00 3.06
3150 3769 4.082136 GCCCGGTTAATTGATGTAAAACCA 60.082 41.667 0.00 0.00 39.66 3.67
3160 3779 5.715434 TGATGTAAAACCAGGCTAAAACC 57.285 39.130 0.00 0.00 0.00 3.27
3231 3851 3.880040 ATGGAACACGCCATGATCA 57.120 47.368 0.00 0.00 46.62 2.92
3245 3865 3.507786 CATGATCAACACATGCCAACAG 58.492 45.455 0.00 0.00 38.58 3.16
3261 3881 1.962822 CAGATGGCCATACGCGCAT 60.963 57.895 20.84 0.00 38.94 4.73
3272 3892 1.832411 TACGCGCATGCAAACGACAA 61.832 50.000 25.64 11.54 42.97 3.18
3274 3894 2.364311 GCGCATGCAAACGACAACC 61.364 57.895 19.57 0.00 42.15 3.77
3283 3903 1.018910 AAACGACAACCCCGACTTTG 58.981 50.000 0.00 0.00 0.00 2.77
3291 3911 0.531311 ACCCCGACTTTGACAACGAC 60.531 55.000 0.00 0.00 0.00 4.34
3296 3916 1.137513 GACTTTGACAACGACCCTCG 58.862 55.000 0.00 0.00 46.93 4.63
3301 3921 2.027625 GACAACGACCCTCGCAAGG 61.028 63.158 0.00 0.00 45.12 3.61
3305 3925 0.179040 AACGACCCTCGCAAGGAAAA 60.179 50.000 0.00 0.00 46.67 2.29
3310 3930 2.024414 ACCCTCGCAAGGAAAATATGC 58.976 47.619 0.00 0.00 46.67 3.14
3354 3974 0.377905 CGCAAATGACGGATGCATGA 59.622 50.000 2.46 0.00 40.04 3.07
3369 3989 1.796617 GCATGAAACAAGCAGCGGATC 60.797 52.381 0.00 0.00 0.00 3.36
3370 3990 0.729116 ATGAAACAAGCAGCGGATCG 59.271 50.000 0.00 0.00 0.00 3.69
3371 3991 0.320334 TGAAACAAGCAGCGGATCGA 60.320 50.000 0.00 0.00 0.00 3.59
3372 3992 1.009829 GAAACAAGCAGCGGATCGAT 58.990 50.000 0.00 0.00 0.00 3.59
3391 4011 7.095857 GGATCGATGACTCAAAGTATAAGCAAG 60.096 40.741 0.54 0.00 0.00 4.01
3398 4018 7.606073 TGACTCAAAGTATAAGCAAGCAATGTA 59.394 33.333 0.00 0.00 0.00 2.29
3450 4070 0.679640 CCAAATTGGTCCGGCTAGCA 60.680 55.000 18.24 0.00 31.35 3.49
3454 4074 0.839946 ATTGGTCCGGCTAGCAGATT 59.160 50.000 18.24 0.00 0.00 2.40
3506 4127 1.300311 CCGACACTACAACACGGCA 60.300 57.895 0.00 0.00 37.32 5.69
3546 4168 6.024049 GCTTCACATCAAAAAGTATCTTCCG 58.976 40.000 0.00 0.00 0.00 4.30
3569 4191 2.699954 CTACTTTCACCAAGGCGACAT 58.300 47.619 0.00 0.00 36.72 3.06
3597 4219 0.885196 TAAAATTGGTGCCTCGTGCC 59.115 50.000 0.00 0.00 40.16 5.01
3625 4248 2.286365 ATCTTGGAAAAAGCCACCGA 57.714 45.000 0.00 0.00 37.75 4.69
3635 4258 2.359975 GCCACCGACCCCTTTCAG 60.360 66.667 0.00 0.00 0.00 3.02
3681 4304 5.474876 GGAAATTCTCCAGCGGATTATGAAT 59.525 40.000 0.00 2.07 44.67 2.57
3695 4318 7.012421 GCGGATTATGAATAAGTTGTTCTTCCT 59.988 37.037 12.82 0.00 37.56 3.36
3790 4741 0.171679 GGGGTAAAATGGCCGAAACG 59.828 55.000 0.00 0.00 0.00 3.60
3792 4743 1.270274 GGGTAAAATGGCCGAAACGTT 59.730 47.619 0.00 0.00 0.00 3.99
3793 4744 2.487372 GGGTAAAATGGCCGAAACGTTA 59.513 45.455 0.00 0.00 0.00 3.18
3854 4805 0.106318 AGCCCATGCCAGAAGGATTC 60.106 55.000 0.00 0.00 41.90 2.52
3880 4831 6.007936 TGGTGATTTTGTTTTCCTATGTCG 57.992 37.500 0.00 0.00 0.00 4.35
3896 4847 2.839975 TGTCGATTTGGCTGTGTACAA 58.160 42.857 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 0.526662 ACTCCGCTTCCTTCTGTACG 59.473 55.000 0.00 0.00 0.00 3.67
130 133 7.374272 TCTTGACTATCTGTCTGAAACTTGAG 58.626 38.462 0.00 0.00 45.54 3.02
302 308 6.094325 ACAGTCAACACTCGTCCAAAATTAAA 59.906 34.615 0.00 0.00 0.00 1.52
312 319 3.079960 TCTTCACAGTCAACACTCGTC 57.920 47.619 0.00 0.00 0.00 4.20
313 320 3.130516 TCTTCTTCACAGTCAACACTCGT 59.869 43.478 0.00 0.00 0.00 4.18
341 348 0.670546 CACCTGCAACTGTAGTCCCG 60.671 60.000 0.00 0.00 0.00 5.14
385 392 2.959030 AGATACTCCATGAGCAACGCTA 59.041 45.455 0.00 0.00 39.88 4.26
390 397 6.417258 TGAATTTGAGATACTCCATGAGCAA 58.583 36.000 0.00 0.00 32.04 3.91
400 407 7.327975 TCCGTGTACATTGAATTTGAGATACT 58.672 34.615 0.00 0.00 0.00 2.12
422 429 0.744414 ATCCATGCGTTGAACCTCCG 60.744 55.000 0.00 0.00 0.00 4.63
536 553 4.855715 TCCAAGACCATCGATGATCTAC 57.144 45.455 22.72 10.19 0.00 2.59
544 561 7.561251 TGTTAGAATAAATCCAAGACCATCGA 58.439 34.615 0.00 0.00 0.00 3.59
547 564 8.061304 ACCATGTTAGAATAAATCCAAGACCAT 58.939 33.333 0.00 0.00 0.00 3.55
561 578 3.525537 CGAGCACTCACCATGTTAGAAT 58.474 45.455 0.00 0.00 0.00 2.40
572 589 0.531974 TTCCAACACCGAGCACTCAC 60.532 55.000 0.00 0.00 0.00 3.51
576 593 1.798813 CTAAGTTCCAACACCGAGCAC 59.201 52.381 0.00 0.00 0.00 4.40
577 594 1.876416 GCTAAGTTCCAACACCGAGCA 60.876 52.381 0.00 0.00 0.00 4.26
580 597 1.876416 GCAGCTAAGTTCCAACACCGA 60.876 52.381 0.00 0.00 0.00 4.69
581 598 0.517316 GCAGCTAAGTTCCAACACCG 59.483 55.000 0.00 0.00 0.00 4.94
582 599 0.517316 CGCAGCTAAGTTCCAACACC 59.483 55.000 0.00 0.00 0.00 4.16
583 600 1.461127 CTCGCAGCTAAGTTCCAACAC 59.539 52.381 0.00 0.00 0.00 3.32
584 601 1.608025 CCTCGCAGCTAAGTTCCAACA 60.608 52.381 0.00 0.00 0.00 3.33
585 602 1.079503 CCTCGCAGCTAAGTTCCAAC 58.920 55.000 0.00 0.00 0.00 3.77
624 641 1.359848 ATCAGCGTGATTGTTCCGAC 58.640 50.000 0.00 0.00 32.13 4.79
625 642 2.093306 AATCAGCGTGATTGTTCCGA 57.907 45.000 10.97 0.00 44.68 4.55
654 671 1.153628 CACGTACTGGGTAGCTGGC 60.154 63.158 0.00 0.00 0.00 4.85
655 672 1.153628 GCACGTACTGGGTAGCTGG 60.154 63.158 0.00 0.00 0.00 4.85
656 673 0.458543 CAGCACGTACTGGGTAGCTG 60.459 60.000 7.98 6.86 42.69 4.24
657 674 1.890894 CAGCACGTACTGGGTAGCT 59.109 57.895 7.98 0.00 33.85 3.32
658 675 1.810030 GCAGCACGTACTGGGTAGC 60.810 63.158 17.32 0.00 38.16 3.58
659 676 1.153628 GGCAGCACGTACTGGGTAG 60.154 63.158 17.32 0.00 38.16 3.18
660 677 1.473497 TTGGCAGCACGTACTGGGTA 61.473 55.000 17.32 0.00 38.16 3.69
661 678 2.332312 TTTGGCAGCACGTACTGGGT 62.332 55.000 17.32 0.00 38.16 4.51
682 699 4.202212 GGTTTTGGCTTGATTTGGTAGTGT 60.202 41.667 0.00 0.00 0.00 3.55
725 742 2.409378 CGTTGTGATTTTGGCTTGATGC 59.591 45.455 0.00 0.00 41.94 3.91
751 768 6.588204 GGTAAATCTCTTTGGGTTTTGGTTT 58.412 36.000 0.00 0.00 0.00 3.27
774 793 1.584483 GTCGCAATTGCATGCTCGG 60.584 57.895 28.77 11.61 44.21 4.63
808 827 2.125106 GGGCTGGCTAACTGACCG 60.125 66.667 0.00 0.00 36.38 4.79
809 828 1.078143 CTGGGCTGGCTAACTGACC 60.078 63.158 0.00 0.00 46.03 4.02
810 829 0.036875 AACTGGGCTGGCTAACTGAC 59.963 55.000 0.00 0.00 0.00 3.51
811 830 0.771127 AAACTGGGCTGGCTAACTGA 59.229 50.000 0.00 0.00 0.00 3.41
812 831 1.270550 CAAAACTGGGCTGGCTAACTG 59.729 52.381 0.00 0.00 0.00 3.16
813 832 1.133482 ACAAAACTGGGCTGGCTAACT 60.133 47.619 0.00 0.00 0.00 2.24
814 833 1.328279 ACAAAACTGGGCTGGCTAAC 58.672 50.000 0.00 0.00 0.00 2.34
815 834 1.960689 GAACAAAACTGGGCTGGCTAA 59.039 47.619 0.00 0.00 0.00 3.09
816 835 1.616159 GAACAAAACTGGGCTGGCTA 58.384 50.000 0.00 0.00 0.00 3.93
817 836 1.115326 GGAACAAAACTGGGCTGGCT 61.115 55.000 0.00 0.00 0.00 4.75
818 837 1.367471 GGAACAAAACTGGGCTGGC 59.633 57.895 0.00 0.00 0.00 4.85
819 838 0.758685 TGGGAACAAAACTGGGCTGG 60.759 55.000 0.00 0.00 37.44 4.85
820 839 0.389025 GTGGGAACAAAACTGGGCTG 59.611 55.000 0.00 0.00 46.06 4.85
825 844 1.657181 GCGCGTGGGAACAAAACTG 60.657 57.895 8.43 0.00 46.06 3.16
896 915 0.662085 GGAGACGATGACGGAGGTAC 59.338 60.000 0.00 0.00 44.46 3.34
904 923 2.969628 ATGTTGGAGGAGACGATGAC 57.030 50.000 0.00 0.00 0.00 3.06
960 979 0.107508 GCTTAGCTGCCACTGGATGA 60.108 55.000 0.00 0.00 0.00 2.92
961 980 0.107312 AGCTTAGCTGCCACTGGATG 60.107 55.000 5.70 0.00 37.57 3.51
985 1004 1.467204 CGCCATCGATCTGCTAGCTAG 60.467 57.143 16.84 16.84 38.10 3.42
986 1005 0.523519 CGCCATCGATCTGCTAGCTA 59.476 55.000 17.23 4.41 38.10 3.32
987 1006 1.288439 CGCCATCGATCTGCTAGCT 59.712 57.895 17.23 0.00 38.10 3.32
988 1007 1.735920 CCGCCATCGATCTGCTAGC 60.736 63.158 8.10 8.10 38.10 3.42
1575 1615 8.622948 AATTTCTTACTTTCTTGATCTCGGTT 57.377 30.769 0.00 0.00 0.00 4.44
1601 1720 0.611340 ACGCTCTTAACGGAGGGAGT 60.611 55.000 13.59 0.00 45.31 3.85
1602 1721 0.531200 AACGCTCTTAACGGAGGGAG 59.469 55.000 13.59 0.29 45.31 4.30
1604 1723 1.804601 AAAACGCTCTTAACGGAGGG 58.195 50.000 7.10 7.10 46.99 4.30
1606 1725 3.246699 TGTCAAAAACGCTCTTAACGGAG 59.753 43.478 0.00 0.00 36.50 4.63
1608 1727 3.285745 GTGTCAAAAACGCTCTTAACGG 58.714 45.455 0.00 0.00 35.42 4.44
1609 1728 2.955799 CGTGTCAAAAACGCTCTTAACG 59.044 45.455 0.00 0.00 36.18 3.18
1619 1738 1.021968 ACTCCCAGCGTGTCAAAAAC 58.978 50.000 0.00 0.00 0.00 2.43
1620 1739 2.623878 TACTCCCAGCGTGTCAAAAA 57.376 45.000 0.00 0.00 0.00 1.94
1625 1744 2.426024 TGACTTATACTCCCAGCGTGTC 59.574 50.000 0.00 0.00 0.00 3.67
1628 1747 2.736347 ACTGACTTATACTCCCAGCGT 58.264 47.619 0.00 0.00 0.00 5.07
1629 1748 3.707793 GAACTGACTTATACTCCCAGCG 58.292 50.000 0.00 0.00 0.00 5.18
1630 1749 3.491104 CCGAACTGACTTATACTCCCAGC 60.491 52.174 0.00 0.00 0.00 4.85
1631 1750 3.700038 ACCGAACTGACTTATACTCCCAG 59.300 47.826 0.00 0.00 0.00 4.45
1632 1751 3.705051 ACCGAACTGACTTATACTCCCA 58.295 45.455 0.00 0.00 0.00 4.37
1633 1752 4.159135 TGAACCGAACTGACTTATACTCCC 59.841 45.833 0.00 0.00 0.00 4.30
1634 1753 5.100943 GTGAACCGAACTGACTTATACTCC 58.899 45.833 0.00 0.00 0.00 3.85
1635 1754 5.100943 GGTGAACCGAACTGACTTATACTC 58.899 45.833 0.00 0.00 0.00 2.59
1636 1755 5.069501 GGTGAACCGAACTGACTTATACT 57.930 43.478 0.00 0.00 0.00 2.12
1651 1770 1.308069 ATGCATGCTCACGGTGAACC 61.308 55.000 20.33 6.87 0.00 3.62
1679 1970 4.931661 AGAGAAAAAGGCATGCATATGG 57.068 40.909 21.36 0.00 34.79 2.74
1683 1974 4.951715 TGACATAGAGAAAAAGGCATGCAT 59.048 37.500 21.36 10.32 0.00 3.96
1685 1976 4.970662 TGACATAGAGAAAAAGGCATGC 57.029 40.909 9.90 9.90 0.00 4.06
1686 1977 7.330900 AGATTGACATAGAGAAAAAGGCATG 57.669 36.000 0.00 0.00 0.00 4.06
1687 1978 6.259608 CGAGATTGACATAGAGAAAAAGGCAT 59.740 38.462 0.00 0.00 0.00 4.40
1728 2147 3.596214 GAACGTCACCTGTCCAATGTAT 58.404 45.455 0.00 0.00 0.00 2.29
2056 2547 0.107993 CGTCCTCCATGTGCATCAGT 60.108 55.000 0.00 0.00 0.00 3.41
2080 2571 1.375268 GTCGCTCAGCTTCTTGCCT 60.375 57.895 0.00 0.00 44.23 4.75
2083 2574 1.075425 CCTCGTCGCTCAGCTTCTTG 61.075 60.000 0.00 0.00 0.00 3.02
2245 2738 2.623878 TCAACGGTGAGCTGGTTTTA 57.376 45.000 0.00 0.00 0.00 1.52
2249 2742 0.615331 ATCATCAACGGTGAGCTGGT 59.385 50.000 9.97 0.00 37.14 4.00
2252 2745 1.406069 GGTGATCATCAACGGTGAGCT 60.406 52.381 9.97 0.00 37.14 4.09
2359 2861 1.525995 CACGTCCTTGTTGGCCACT 60.526 57.895 3.88 0.00 35.26 4.00
2407 2909 2.032528 CACACCAGCACCGACCAT 59.967 61.111 0.00 0.00 0.00 3.55
2517 3019 4.638304 TGATGCATGATCGATGACAGAAT 58.362 39.130 2.46 0.00 33.31 2.40
2564 3094 2.923121 CACCCGTCCATTGATTCATCT 58.077 47.619 0.00 0.00 0.00 2.90
2849 3389 2.313317 AGGTAACCGATCTCCGCATTA 58.687 47.619 0.00 0.00 36.84 1.90
2964 3504 5.637809 CATGCATGCAATACAATAGCTAGG 58.362 41.667 26.68 0.00 0.00 3.02
3143 3762 6.072008 GGTTTATCGGTTTTAGCCTGGTTTTA 60.072 38.462 0.00 0.00 0.00 1.52
3150 3769 3.724732 TGGGTTTATCGGTTTTAGCCT 57.275 42.857 0.00 0.00 0.00 4.58
3160 3779 2.717390 TCATGTGGGTTGGGTTTATCG 58.283 47.619 0.00 0.00 0.00 2.92
3209 3829 3.889227 ATGGCGTGTTCCATGTCG 58.111 55.556 0.00 0.00 44.72 4.35
3229 3849 1.887854 CCATCTGTTGGCATGTGTTGA 59.112 47.619 0.00 0.00 39.09 3.18
3230 3850 2.357327 CCATCTGTTGGCATGTGTTG 57.643 50.000 0.00 0.00 39.09 3.33
3245 3865 2.557805 CATGCGCGTATGGCCATC 59.442 61.111 26.94 13.12 38.94 3.51
3261 3881 2.181521 GTCGGGGTTGTCGTTTGCA 61.182 57.895 0.00 0.00 0.00 4.08
3272 3892 0.531311 GTCGTTGTCAAAGTCGGGGT 60.531 55.000 0.00 0.00 0.00 4.95
3274 3894 1.226030 GGGTCGTTGTCAAAGTCGGG 61.226 60.000 0.00 0.00 0.00 5.14
3283 3903 2.027625 CCTTGCGAGGGTCGTTGTC 61.028 63.158 12.81 0.00 42.81 3.18
3291 3911 2.023673 TGCATATTTTCCTTGCGAGGG 58.976 47.619 20.46 2.97 43.72 4.30
3296 3916 4.427312 CAAGTCCTGCATATTTTCCTTGC 58.573 43.478 0.00 0.00 36.91 4.01
3335 3955 0.377905 TCATGCATCCGTCATTTGCG 59.622 50.000 0.00 0.00 39.23 4.85
3354 3974 0.729116 CATCGATCCGCTGCTTGTTT 59.271 50.000 0.00 0.00 0.00 2.83
3369 3989 5.291858 TGCTTGCTTATACTTTGAGTCATCG 59.708 40.000 0.00 0.00 0.00 3.84
3370 3990 6.668541 TGCTTGCTTATACTTTGAGTCATC 57.331 37.500 0.00 0.00 0.00 2.92
3371 3991 7.121759 ACATTGCTTGCTTATACTTTGAGTCAT 59.878 33.333 0.00 0.00 0.00 3.06
3372 3992 6.430925 ACATTGCTTGCTTATACTTTGAGTCA 59.569 34.615 0.00 0.00 0.00 3.41
3391 4011 5.808540 TGTCGATGGTAAGTAACTACATTGC 59.191 40.000 0.00 0.00 0.00 3.56
3398 4018 6.602406 AGAGTACATGTCGATGGTAAGTAACT 59.398 38.462 0.00 0.00 33.39 2.24
3407 4027 4.578516 AGAGAGAAGAGTACATGTCGATGG 59.421 45.833 0.00 0.00 33.39 3.51
3470 4090 1.839424 GGGAACTCAATGACAAGGGG 58.161 55.000 0.00 0.00 0.00 4.79
3474 4094 2.104111 AGTGTCGGGAACTCAATGACAA 59.896 45.455 0.00 0.00 40.84 3.18
3481 4102 2.033372 TGTTGTAGTGTCGGGAACTCA 58.967 47.619 0.00 0.00 0.00 3.41
3506 4127 3.578456 GCACAGCTGCGGTACAAT 58.422 55.556 15.27 0.00 32.44 2.71
3533 4155 4.838904 AAGTAGCCCGGAAGATACTTTT 57.161 40.909 13.55 0.00 35.48 2.27
3546 4168 1.305930 CGCCTTGGTGAAAGTAGCCC 61.306 60.000 0.00 0.00 33.66 5.19
3569 4191 3.135530 AGGCACCAATTTTAGTTTTGGCA 59.864 39.130 1.72 0.00 45.13 4.92
3597 4219 4.751600 GGCTTTTTCCAAGATTTTCCACTG 59.248 41.667 0.00 0.00 0.00 3.66
3602 4224 3.740832 CGGTGGCTTTTTCCAAGATTTTC 59.259 43.478 0.00 0.00 37.96 2.29
3625 4248 0.560688 TTTGAAGGGCTGAAAGGGGT 59.439 50.000 0.00 0.00 0.00 4.95
3635 4258 1.673477 CTTTGGGGCTTTGAAGGGC 59.327 57.895 0.00 0.00 0.00 5.19
3676 4299 8.463930 TTGTCAAGGAAGAACAACTTATTCAT 57.536 30.769 0.00 0.00 39.13 2.57
3681 4304 5.650266 TGCTTTGTCAAGGAAGAACAACTTA 59.350 36.000 0.00 0.00 39.13 2.24
3695 4318 3.826524 TGTCCCTAACATGCTTTGTCAA 58.173 40.909 0.00 0.00 37.68 3.18
3723 4674 5.823312 ACACCCTAACCTAATTAAACCAGG 58.177 41.667 0.00 0.00 35.45 4.45
3770 4721 0.533491 GTTTCGGCCATTTTACCCCC 59.467 55.000 2.24 0.00 0.00 5.40
3845 4796 3.356529 AAATCACCAGCGAATCCTTCT 57.643 42.857 0.00 0.00 0.00 2.85
3854 4805 3.369546 AGGAAAACAAAATCACCAGCG 57.630 42.857 0.00 0.00 0.00 5.18
3880 4831 8.293867 TGTATAGTTTTTGTACACAGCCAAATC 58.706 33.333 0.00 0.00 31.20 2.17
3896 4847 7.254590 GCGATCAAATGCTCTCTGTATAGTTTT 60.255 37.037 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.