Multiple sequence alignment - TraesCS6A01G253100

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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 TraesCS6A01G253100 chr6A 100.000 3598 0 0 1 3598 468259415 468255818 0.000000e+00 6645.0
1 TraesCS6A01G253100 chr6A 100.000 50 0 0 1344 1393 468258033 468257984 3.820000e-15 93.5
2 TraesCS6A01G253100 chr6A 100.000 50 0 0 1383 1432 468258072 468258023 3.820000e-15 93.5
3 TraesCS6A01G253100 chr6B 93.090 1317 62 10 1382 2693 493319028 493317736 0.000000e+00 1901.0
4 TraesCS6A01G253100 chr6B 92.091 1277 72 10 118 1374 493320264 493318997 0.000000e+00 1772.0
5 TraesCS6A01G253100 chr6B 100.000 29 0 0 265 293 88571755 88571727 2.000000e-03 54.7
6 TraesCS6A01G253100 chr6D 92.249 1316 50 21 1382 2693 328964909 328963642 0.000000e+00 1818.0
7 TraesCS6A01G253100 chr6D 89.298 1140 59 14 271 1376 328965986 328964876 0.000000e+00 1371.0
8 TraesCS6A01G253100 chr6D 78.444 617 89 27 3009 3595 322430163 322429561 2.640000e-96 363.0
9 TraesCS6A01G253100 chr6D 87.786 131 16 0 1 131 328966384 328966254 1.730000e-33 154.0
10 TraesCS6A01G253100 chr6D 92.857 42 2 1 265 306 345388068 345388028 3.880000e-05 60.2
11 TraesCS6A01G253100 chr7B 90.181 937 54 10 2694 3598 442353066 442352136 0.000000e+00 1186.0
12 TraesCS6A01G253100 chr7B 81.129 567 68 28 2960 3510 6216083 6216626 5.560000e-113 418.0
13 TraesCS6A01G253100 chr7B 93.023 43 2 1 265 307 387838745 387838704 1.080000e-05 62.1
14 TraesCS6A01G253100 chr1B 85.463 853 51 22 2694 3496 313484785 313485614 0.000000e+00 821.0
15 TraesCS6A01G253100 chr2A 81.508 557 81 19 2960 3502 678958713 678958165 4.260000e-119 438.0
16 TraesCS6A01G253100 chr3D 79.843 635 88 22 2995 3596 46631644 46631017 9.230000e-116 427.0
17 TraesCS6A01G253100 chr3D 88.987 227 20 4 2694 2918 309694858 309695081 3.540000e-70 276.0
18 TraesCS6A01G253100 chr3A 79.018 672 101 29 2960 3598 19886134 19886798 1.190000e-114 424.0
19 TraesCS6A01G253100 chr2D 79.875 641 77 34 2995 3588 552531961 552532596 4.300000e-114 422.0
20 TraesCS6A01G253100 chr3B 79.695 591 94 21 2960 3537 794882361 794881784 1.560000e-108 403.0
21 TraesCS6A01G253100 chr3B 82.857 70 7 4 266 333 63016155 63016221 1.400000e-04 58.4
22 TraesCS6A01G253100 chr3B 100.000 28 0 0 3571 3598 761043516 761043543 6.000000e-03 52.8
23 TraesCS6A01G253100 chr7A 83.296 449 59 14 3160 3597 2418703 2418260 2.010000e-107 399.0
24 TraesCS6A01G253100 chr7A 82.597 385 37 12 3242 3597 2418729 2418346 2.700000e-81 313.0
25 TraesCS6A01G253100 chr7A 81.743 241 33 7 3366 3598 716249543 716249780 1.320000e-44 191.0
26 TraesCS6A01G253100 chr5D 83.221 447 61 14 3067 3502 237841485 237841042 7.240000e-107 398.0
27 TraesCS6A01G253100 chr4D 79.439 535 71 29 3020 3533 417930270 417930786 3.440000e-90 342.0
28 TraesCS6A01G253100 chr2B 76.936 607 108 17 2996 3588 652821167 652820579 2.080000e-82 316.0
29 TraesCS6A01G253100 chrUn 82.857 70 8 4 266 333 429073256 429073189 3.880000e-05 60.2


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 TraesCS6A01G253100 chr6A 468255818 468259415 3597 True 2277.333333 6645 100.000000 1 3598 3 chr6A.!!$R1 3597
1 TraesCS6A01G253100 chr6B 493317736 493320264 2528 True 1836.500000 1901 92.590500 118 2693 2 chr6B.!!$R2 2575
2 TraesCS6A01G253100 chr6D 328963642 328966384 2742 True 1114.333333 1818 89.777667 1 2693 3 chr6D.!!$R3 2692
3 TraesCS6A01G253100 chr6D 322429561 322430163 602 True 363.000000 363 78.444000 3009 3595 1 chr6D.!!$R1 586
4 TraesCS6A01G253100 chr7B 442352136 442353066 930 True 1186.000000 1186 90.181000 2694 3598 1 chr7B.!!$R2 904
5 TraesCS6A01G253100 chr7B 6216083 6216626 543 False 418.000000 418 81.129000 2960 3510 1 chr7B.!!$F1 550
6 TraesCS6A01G253100 chr1B 313484785 313485614 829 False 821.000000 821 85.463000 2694 3496 1 chr1B.!!$F1 802
7 TraesCS6A01G253100 chr2A 678958165 678958713 548 True 438.000000 438 81.508000 2960 3502 1 chr2A.!!$R1 542
8 TraesCS6A01G253100 chr3D 46631017 46631644 627 True 427.000000 427 79.843000 2995 3596 1 chr3D.!!$R1 601
9 TraesCS6A01G253100 chr3A 19886134 19886798 664 False 424.000000 424 79.018000 2960 3598 1 chr3A.!!$F1 638
10 TraesCS6A01G253100 chr2D 552531961 552532596 635 False 422.000000 422 79.875000 2995 3588 1 chr2D.!!$F1 593
11 TraesCS6A01G253100 chr3B 794881784 794882361 577 True 403.000000 403 79.695000 2960 3537 1 chr3B.!!$R1 577
12 TraesCS6A01G253100 chr4D 417930270 417930786 516 False 342.000000 342 79.439000 3020 3533 1 chr4D.!!$F1 513
13 TraesCS6A01G253100 chr2B 652820579 652821167 588 True 316.000000 316 76.936000 2996 3588 1 chr2B.!!$R1 592

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
563 754 0.038744 AAGTGGGATGACAAGGCCAG 59.961 55.0 5.01 0.0 0.00 4.85 F
574 765 0.107312 CAAGGCCAGAGGGATGAGTG 60.107 60.0 5.01 0.0 35.59 3.51 F
1701 1938 0.036732 GCAGGTTGGTGAGGTCATCA 59.963 55.0 0.00 0.0 34.72 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1384 1611 0.108615 AAGGAAGTGACTGCCGATCG 60.109 55.0 8.51 8.51 33.44 3.69 R
2245 2483 0.250513 AAGACGAAGGAGACCATGGC 59.749 55.0 13.04 4.70 0.00 4.40 R
3030 3296 0.249238 AAAAGCCGAAAACGCATGCA 60.249 45.0 19.57 0.00 0.00 3.96 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
57 58 4.323417 TCGGTTTGATGCTGACTGTTAAT 58.677 39.130 0.00 0.00 0.00 1.40
58 59 4.154015 TCGGTTTGATGCTGACTGTTAATG 59.846 41.667 0.00 0.00 0.00 1.90
63 64 7.148086 GGTTTGATGCTGACTGTTAATGGATTA 60.148 37.037 0.00 0.00 0.00 1.75
210 379 4.488126 ACATTGTTCACGAATTGGTGAG 57.512 40.909 20.49 12.67 46.68 3.51
237 406 8.924511 AGTTCTCAGGTTTGAAGATTATTCAA 57.075 30.769 2.41 2.41 36.71 2.69
265 434 5.578005 TGAAAATTGTACGTGGTTTCCAA 57.422 34.783 0.00 0.00 34.18 3.53
274 443 4.729227 ACGTGGTTTCCAAAAAGTTCAT 57.271 36.364 0.00 0.00 34.18 2.57
335 504 9.124807 GTCTGTGGATTTTAGAAAATAAAACGG 57.875 33.333 0.28 5.28 38.64 4.44
368 537 8.958119 AAAAAGGAACAGAAAATAGGAAAACC 57.042 30.769 0.00 0.00 0.00 3.27
369 538 6.665992 AAGGAACAGAAAATAGGAAAACCC 57.334 37.500 0.00 0.00 0.00 4.11
390 562 6.127101 ACCCTGTTAGAAGCTTTACAAAACT 58.873 36.000 0.00 0.00 0.00 2.66
468 640 1.799157 AAGGCAACCTACATGGGCCA 61.799 55.000 9.61 9.61 43.14 5.36
524 715 2.032799 TGTAAAAACGCCTGCAAGTGAG 59.967 45.455 2.16 0.00 0.00 3.51
556 747 3.509575 GCCAAATACAAAGTGGGATGACA 59.490 43.478 0.00 0.00 32.71 3.58
557 748 4.021544 GCCAAATACAAAGTGGGATGACAA 60.022 41.667 0.00 0.00 32.71 3.18
558 749 5.713025 CCAAATACAAAGTGGGATGACAAG 58.287 41.667 0.00 0.00 0.00 3.16
559 750 5.336690 CCAAATACAAAGTGGGATGACAAGG 60.337 44.000 0.00 0.00 0.00 3.61
560 751 1.620822 ACAAAGTGGGATGACAAGGC 58.379 50.000 0.00 0.00 0.00 4.35
561 752 0.890683 CAAAGTGGGATGACAAGGCC 59.109 55.000 0.00 0.00 0.00 5.19
562 753 0.482446 AAAGTGGGATGACAAGGCCA 59.518 50.000 5.01 0.00 0.00 5.36
563 754 0.038744 AAGTGGGATGACAAGGCCAG 59.961 55.000 5.01 0.00 0.00 4.85
564 755 0.842030 AGTGGGATGACAAGGCCAGA 60.842 55.000 5.01 0.00 0.00 3.86
565 756 0.393537 GTGGGATGACAAGGCCAGAG 60.394 60.000 5.01 0.00 0.00 3.35
566 757 1.225704 GGGATGACAAGGCCAGAGG 59.774 63.158 5.01 0.00 0.00 3.69
567 758 1.225704 GGATGACAAGGCCAGAGGG 59.774 63.158 5.01 0.00 37.18 4.30
568 759 1.274703 GGATGACAAGGCCAGAGGGA 61.275 60.000 5.01 0.00 35.59 4.20
569 760 0.842635 GATGACAAGGCCAGAGGGAT 59.157 55.000 5.01 0.00 35.59 3.85
570 761 0.549950 ATGACAAGGCCAGAGGGATG 59.450 55.000 5.01 0.00 35.59 3.51
571 762 0.547471 TGACAAGGCCAGAGGGATGA 60.547 55.000 5.01 0.00 35.59 2.92
572 763 0.179936 GACAAGGCCAGAGGGATGAG 59.820 60.000 5.01 0.00 35.59 2.90
573 764 0.548682 ACAAGGCCAGAGGGATGAGT 60.549 55.000 5.01 0.00 35.59 3.41
574 765 0.107312 CAAGGCCAGAGGGATGAGTG 60.107 60.000 5.01 0.00 35.59 3.51
575 766 0.548682 AAGGCCAGAGGGATGAGTGT 60.549 55.000 5.01 0.00 35.59 3.55
576 767 0.980231 AGGCCAGAGGGATGAGTGTC 60.980 60.000 5.01 0.00 35.59 3.67
791 1018 4.141680 CGCACTTGTTTAACAACGATCTC 58.858 43.478 6.41 0.00 33.96 2.75
795 1022 6.590357 CACTTGTTTAACAACGATCTCGAAT 58.410 36.000 6.41 0.00 43.39 3.34
866 1093 9.346725 CTTCAAACCTCTTTAAAAGATGCATAC 57.653 33.333 0.00 0.00 36.82 2.39
897 1124 3.433274 CGCAGTCAGCTGAAATTACAAGA 59.567 43.478 20.19 0.00 45.28 3.02
898 1125 4.435253 CGCAGTCAGCTGAAATTACAAGAG 60.435 45.833 20.19 1.51 45.28 2.85
899 1126 4.142730 GCAGTCAGCTGAAATTACAAGAGG 60.143 45.833 20.19 0.00 45.28 3.69
936 1163 2.049063 CCAGCTAGCGGGCGATAC 60.049 66.667 21.28 0.00 37.29 2.24
962 1189 4.394920 TCGATGAAAACTGCTGGGTAAATC 59.605 41.667 0.00 0.00 0.00 2.17
1136 1363 4.838152 GAGGCATGCCGAGGCGAA 62.838 66.667 30.50 0.00 45.51 4.70
1173 1400 1.800315 CGCGATCTTCGTGTTCGGT 60.800 57.895 0.00 0.00 44.47 4.69
1209 1436 1.002792 GTCGGCAACAACAACTTCCTC 60.003 52.381 0.00 0.00 0.00 3.71
1270 1497 2.513259 GGTGTGGACTTCCCGACCA 61.513 63.158 7.61 0.00 39.01 4.02
1316 1543 1.598130 GCTTCAACACGGCAGACCT 60.598 57.895 0.00 0.00 0.00 3.85
1340 1567 0.373716 GGTACTACGTGCATTGCAGC 59.626 55.000 12.53 6.38 40.08 5.25
1342 1569 1.324736 GTACTACGTGCATTGCAGCTC 59.675 52.381 12.53 0.00 40.08 4.09
1367 1594 0.976641 TCGGCAGTCACTTCCTTCAT 59.023 50.000 0.00 0.00 0.00 2.57
1370 1597 2.079925 GGCAGTCACTTCCTTCATCAC 58.920 52.381 0.00 0.00 0.00 3.06
1371 1598 1.728971 GCAGTCACTTCCTTCATCACG 59.271 52.381 0.00 0.00 0.00 4.35
1372 1599 2.610479 GCAGTCACTTCCTTCATCACGA 60.610 50.000 0.00 0.00 0.00 4.35
1373 1600 3.249091 CAGTCACTTCCTTCATCACGAG 58.751 50.000 0.00 0.00 0.00 4.18
1374 1601 2.894126 AGTCACTTCCTTCATCACGAGT 59.106 45.455 0.00 0.00 0.00 4.18
1375 1602 3.322254 AGTCACTTCCTTCATCACGAGTT 59.678 43.478 0.00 0.00 0.00 3.01
1376 1603 3.430218 GTCACTTCCTTCATCACGAGTTG 59.570 47.826 0.00 0.00 0.00 3.16
1377 1604 3.069586 TCACTTCCTTCATCACGAGTTGT 59.930 43.478 0.00 0.00 0.00 3.32
1378 1605 3.430218 CACTTCCTTCATCACGAGTTGTC 59.570 47.826 0.00 0.00 0.00 3.18
1394 1621 3.587095 TCGAGTTCGATCGGCAGT 58.413 55.556 16.41 5.23 44.22 4.40
1395 1622 1.428219 TCGAGTTCGATCGGCAGTC 59.572 57.895 16.41 13.18 44.22 3.51
1396 1623 1.136774 CGAGTTCGATCGGCAGTCA 59.863 57.895 16.41 0.00 43.02 3.41
1397 1624 1.134530 CGAGTTCGATCGGCAGTCAC 61.135 60.000 16.41 3.13 43.02 3.67
1398 1625 0.171455 GAGTTCGATCGGCAGTCACT 59.829 55.000 16.41 7.84 0.00 3.41
1399 1626 0.603569 AGTTCGATCGGCAGTCACTT 59.396 50.000 16.41 0.00 0.00 3.16
1400 1627 0.992802 GTTCGATCGGCAGTCACTTC 59.007 55.000 16.41 0.00 0.00 3.01
1401 1628 0.108804 TTCGATCGGCAGTCACTTCC 60.109 55.000 16.41 0.00 0.00 3.46
1402 1629 0.965866 TCGATCGGCAGTCACTTCCT 60.966 55.000 16.41 0.00 0.00 3.36
1403 1630 0.108615 CGATCGGCAGTCACTTCCTT 60.109 55.000 7.38 0.00 0.00 3.36
1404 1631 1.646189 GATCGGCAGTCACTTCCTTC 58.354 55.000 0.00 0.00 0.00 3.46
1405 1632 0.976641 ATCGGCAGTCACTTCCTTCA 59.023 50.000 0.00 0.00 0.00 3.02
1406 1633 0.976641 TCGGCAGTCACTTCCTTCAT 59.023 50.000 0.00 0.00 0.00 2.57
1407 1634 1.066858 TCGGCAGTCACTTCCTTCATC 60.067 52.381 0.00 0.00 0.00 2.92
1408 1635 1.338105 CGGCAGTCACTTCCTTCATCA 60.338 52.381 0.00 0.00 0.00 3.07
1409 1636 2.079925 GGCAGTCACTTCCTTCATCAC 58.920 52.381 0.00 0.00 0.00 3.06
1410 1637 1.728971 GCAGTCACTTCCTTCATCACG 59.271 52.381 0.00 0.00 0.00 4.35
1411 1638 2.610479 GCAGTCACTTCCTTCATCACGA 60.610 50.000 0.00 0.00 0.00 4.35
1412 1639 3.249091 CAGTCACTTCCTTCATCACGAG 58.751 50.000 0.00 0.00 0.00 4.18
1413 1640 2.894126 AGTCACTTCCTTCATCACGAGT 59.106 45.455 0.00 0.00 0.00 4.18
1414 1641 3.322254 AGTCACTTCCTTCATCACGAGTT 59.678 43.478 0.00 0.00 0.00 3.01
1415 1642 3.430218 GTCACTTCCTTCATCACGAGTTG 59.570 47.826 0.00 0.00 0.00 3.16
1416 1643 3.069586 TCACTTCCTTCATCACGAGTTGT 59.930 43.478 0.00 0.00 0.00 3.32
1471 1698 3.247886 CCATTCGATGATGAACAGCTCAG 59.752 47.826 0.00 0.00 37.52 3.35
1472 1699 1.931906 TCGATGATGAACAGCTCAGC 58.068 50.000 0.00 0.00 41.07 4.26
1522 1749 1.369321 CCTCTCCCTGAATAGGCGC 59.631 63.158 0.00 0.00 43.16 6.53
1609 1836 2.412323 CGGCCGCTCAGTGGTACTA 61.412 63.158 14.67 0.00 35.34 1.82
1611 1838 1.141234 GCCGCTCAGTGGTACTACC 59.859 63.158 6.03 0.00 39.22 3.18
1612 1839 1.432251 CCGCTCAGTGGTACTACCG 59.568 63.158 5.65 2.43 42.58 4.02
1624 1851 1.856597 GTACTACCGCATTGTTAGCCG 59.143 52.381 0.00 0.00 0.00 5.52
1635 1866 5.557514 CGCATTGTTAGCCGTTACGAATTAT 60.558 40.000 6.24 0.00 0.00 1.28
1649 1880 8.995906 CGTTACGAATTATCTTTCATTTCAACC 58.004 33.333 0.00 0.00 0.00 3.77
1650 1881 9.834628 GTTACGAATTATCTTTCATTTCAACCA 57.165 29.630 0.00 0.00 0.00 3.67
1662 1899 9.459640 CTTTCATTTCAACCATATGACATGATC 57.540 33.333 3.65 0.00 42.76 2.92
1663 1900 8.756486 TTCATTTCAACCATATGACATGATCT 57.244 30.769 3.65 0.00 42.76 2.75
1664 1901 8.161699 TCATTTCAACCATATGACATGATCTG 57.838 34.615 3.65 6.38 40.03 2.90
1665 1902 7.994334 TCATTTCAACCATATGACATGATCTGA 59.006 33.333 3.65 8.23 40.03 3.27
1666 1903 8.626526 CATTTCAACCATATGACATGATCTGAA 58.373 33.333 3.65 0.00 38.97 3.02
1667 1904 7.797038 TTCAACCATATGACATGATCTGAAG 57.203 36.000 3.65 0.00 0.00 3.02
1668 1905 6.892485 TCAACCATATGACATGATCTGAAGT 58.108 36.000 3.65 0.00 0.00 3.01
1669 1906 6.988580 TCAACCATATGACATGATCTGAAGTC 59.011 38.462 3.65 0.00 0.00 3.01
1701 1938 0.036732 GCAGGTTGGTGAGGTCATCA 59.963 55.000 0.00 0.00 34.72 3.07
1763 2000 1.451567 CATGCACCAGAGCTCAGGG 60.452 63.158 27.01 23.15 34.99 4.45
1811 2048 3.626670 CCAAGTCCATCTTCTTCATCAGC 59.373 47.826 0.00 0.00 33.63 4.26
1875 2112 1.291877 CGACAGGAAGTTCTTGGCCG 61.292 60.000 18.18 15.93 25.51 6.13
1918 2155 4.275443 GGACTATCTGAAGGTACCACTACG 59.725 50.000 15.94 0.00 0.00 3.51
1919 2156 4.853007 ACTATCTGAAGGTACCACTACGT 58.147 43.478 15.94 0.00 0.00 3.57
1920 2157 5.994250 ACTATCTGAAGGTACCACTACGTA 58.006 41.667 15.94 0.00 0.00 3.57
1921 2158 6.054295 ACTATCTGAAGGTACCACTACGTAG 58.946 44.000 20.97 20.97 0.00 3.51
1942 2179 7.120285 ACGTAGTAGTACTCAGCAAATCAGTTA 59.880 37.037 5.96 0.00 41.94 2.24
2000 2237 2.687935 ACGAACCACAAGAACTGCAAAT 59.312 40.909 0.00 0.00 0.00 2.32
2009 2247 3.996150 AGAACTGCAAATTGACCTGTG 57.004 42.857 0.00 0.00 0.00 3.66
2010 2248 3.554934 AGAACTGCAAATTGACCTGTGA 58.445 40.909 0.00 0.00 0.00 3.58
2014 2252 5.280654 ACTGCAAATTGACCTGTGAAATT 57.719 34.783 0.00 0.00 0.00 1.82
2277 2515 1.671054 CGTCTTCGCCAACCCACAT 60.671 57.895 0.00 0.00 0.00 3.21
2345 2583 1.134220 TGCAAATACCCCGTGGATCTC 60.134 52.381 0.00 0.00 34.81 2.75
2564 2802 0.097325 GCAACCACACGTTCGTCAAA 59.903 50.000 0.00 0.00 29.93 2.69
2568 2806 1.274476 CACACGTTCGTCAAACCCG 59.726 57.895 0.00 0.00 34.11 5.28
2605 2843 2.320587 CCAAGCTGTGACCGTGCTC 61.321 63.158 0.00 0.00 35.85 4.26
2647 2885 9.988815 AGCGATATGTATTTTGTCTTCTCTATT 57.011 29.630 0.00 0.00 0.00 1.73
2796 3035 0.944386 GTCTCGCGGGTATACGGTAA 59.056 55.000 5.57 0.00 0.00 2.85
2843 3082 2.187946 GGGCTGATGTGCTAGCGT 59.812 61.111 10.77 0.00 40.78 5.07
2858 3097 2.654877 CGTTGTACGTGGGCCTCT 59.345 61.111 4.53 0.00 36.74 3.69
2873 3112 1.399714 CCTCTAGTGTGCGGGATACA 58.600 55.000 0.00 0.00 39.74 2.29
2888 3127 3.517602 GGATACACAAGCACGTCATGTA 58.482 45.455 0.00 0.00 0.00 2.29
2965 3227 4.787293 TCTTTCGGATCGCGCGCA 62.787 61.111 32.61 18.69 0.00 6.09
2981 3243 1.086067 CGCACTCTGCCATTCGTCAT 61.086 55.000 0.00 0.00 41.12 3.06
3478 3952 3.793144 CTTCCGCAAGAGGCACGC 61.793 66.667 0.00 0.00 45.17 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.001974 TGATCCAAGTGAACCGAGTGG 59.998 52.381 0.00 0.00 42.84 4.00
11 12 1.284785 TGGGGATGATCCAAGTGAACC 59.715 52.381 14.36 3.80 38.64 3.62
16 17 1.566231 GAAGGTGGGGATGATCCAAGT 59.434 52.381 14.36 0.00 38.64 3.16
58 59 6.530019 AAGTCAATGGTTGATGGTTAATCC 57.470 37.500 0.00 0.00 42.47 3.01
63 64 5.598005 TCTCAAAAGTCAATGGTTGATGGTT 59.402 36.000 0.00 0.00 42.47 3.67
210 379 9.003658 TGAATAATCTTCAAACCTGAGAACTTC 57.996 33.333 0.00 0.00 31.69 3.01
237 406 7.436970 GGAAACCACGTACAATTTTCAAATTCT 59.563 33.333 0.00 0.00 36.52 2.40
253 422 4.158764 TCATGAACTTTTTGGAAACCACGT 59.841 37.500 0.00 0.00 30.78 4.49
311 480 9.685828 TTCCGTTTTATTTTCTAAAATCCACAG 57.314 29.630 4.02 0.00 39.24 3.66
358 527 5.780958 AGCTTCTAACAGGGTTTTCCTAT 57.219 39.130 0.00 0.00 46.12 2.57
367 536 6.262273 TCAGTTTTGTAAAGCTTCTAACAGGG 59.738 38.462 0.00 0.00 0.00 4.45
368 537 7.012421 AGTCAGTTTTGTAAAGCTTCTAACAGG 59.988 37.037 0.00 0.00 0.00 4.00
369 538 7.920738 AGTCAGTTTTGTAAAGCTTCTAACAG 58.079 34.615 0.00 0.00 0.00 3.16
370 539 7.859325 AGTCAGTTTTGTAAAGCTTCTAACA 57.141 32.000 0.00 2.04 0.00 2.41
450 622 2.215451 CTGGCCCATGTAGGTTGCCT 62.215 60.000 0.00 0.00 43.14 4.75
468 640 0.106015 GGGCACATAGGAAATGGGCT 60.106 55.000 11.64 0.00 46.94 5.19
556 747 0.548682 ACACTCATCCCTCTGGCCTT 60.549 55.000 3.32 0.00 0.00 4.35
557 748 0.980231 GACACTCATCCCTCTGGCCT 60.980 60.000 3.32 0.00 0.00 5.19
558 749 1.524482 GACACTCATCCCTCTGGCC 59.476 63.158 0.00 0.00 0.00 5.36
559 750 0.980231 AGGACACTCATCCCTCTGGC 60.980 60.000 0.00 0.00 39.91 4.85
560 751 0.829333 CAGGACACTCATCCCTCTGG 59.171 60.000 0.00 0.00 39.91 3.86
561 752 1.206610 CACAGGACACTCATCCCTCTG 59.793 57.143 0.00 0.00 39.91 3.35
562 753 1.566211 CACAGGACACTCATCCCTCT 58.434 55.000 0.00 0.00 39.91 3.69
563 754 0.539051 CCACAGGACACTCATCCCTC 59.461 60.000 0.00 0.00 39.91 4.30
564 755 0.178891 ACCACAGGACACTCATCCCT 60.179 55.000 0.00 0.00 39.91 4.20
565 756 1.482593 CTACCACAGGACACTCATCCC 59.517 57.143 0.00 0.00 39.91 3.85
566 757 2.180276 ACTACCACAGGACACTCATCC 58.820 52.381 0.00 0.00 39.28 3.51
567 758 4.270834 TCTACTACCACAGGACACTCATC 58.729 47.826 0.00 0.00 0.00 2.92
568 759 4.317530 TCTACTACCACAGGACACTCAT 57.682 45.455 0.00 0.00 0.00 2.90
569 760 3.801307 TCTACTACCACAGGACACTCA 57.199 47.619 0.00 0.00 0.00 3.41
570 761 3.181485 GCATCTACTACCACAGGACACTC 60.181 52.174 0.00 0.00 0.00 3.51
571 762 2.761208 GCATCTACTACCACAGGACACT 59.239 50.000 0.00 0.00 0.00 3.55
572 763 2.761208 AGCATCTACTACCACAGGACAC 59.239 50.000 0.00 0.00 0.00 3.67
573 764 3.024547 GAGCATCTACTACCACAGGACA 58.975 50.000 0.00 0.00 0.00 4.02
574 765 3.719173 GAGCATCTACTACCACAGGAC 57.281 52.381 0.00 0.00 0.00 3.85
771 998 5.570262 TCGAGATCGTTGTTAAACAAGTG 57.430 39.130 1.70 0.00 39.00 3.16
866 1093 1.735920 GCTGACTGCGTGTCCTCAG 60.736 63.158 7.12 0.00 44.75 3.35
897 1124 2.781174 TGTTTTGGAGGGTTGTCTACCT 59.219 45.455 3.39 0.00 46.86 3.08
898 1125 2.882761 GTGTTTTGGAGGGTTGTCTACC 59.117 50.000 0.00 0.00 46.99 3.18
899 1126 2.882761 GGTGTTTTGGAGGGTTGTCTAC 59.117 50.000 0.00 0.00 0.00 2.59
936 1163 1.466167 CCCAGCAGTTTTCATCGAGTG 59.534 52.381 0.00 0.00 0.00 3.51
1067 1294 1.743995 ACGTATGAGGCGGTTTGGC 60.744 57.895 0.00 0.00 45.27 4.52
1095 1322 4.694233 AGCACGAGCAGGCACAGG 62.694 66.667 7.77 0.00 45.49 4.00
1173 1400 2.592574 ACGTCGACGGTGGAGTCA 60.593 61.111 37.89 0.00 44.95 3.41
1232 1459 2.221299 TACTGCGGGAAGTTGGCCT 61.221 57.895 3.32 0.00 0.00 5.19
1316 1543 2.737359 GCAATGCACGTAGTACCTAGCA 60.737 50.000 0.00 10.26 41.61 3.49
1340 1567 0.453793 AGTGACTGCCGATCGAAGAG 59.546 55.000 18.66 11.28 43.63 2.85
1342 1569 1.272781 GAAGTGACTGCCGATCGAAG 58.727 55.000 18.66 15.86 0.00 3.79
1367 1594 0.939419 TCGAACTCGACAACTCGTGA 59.061 50.000 0.00 0.00 44.22 4.35
1378 1605 1.134530 GTGACTGCCGATCGAACTCG 61.135 60.000 18.66 1.41 41.45 4.18
1379 1606 0.171455 AGTGACTGCCGATCGAACTC 59.829 55.000 18.66 5.93 0.00 3.01
1380 1607 0.603569 AAGTGACTGCCGATCGAACT 59.396 50.000 18.66 7.15 0.00 3.01
1381 1608 0.992802 GAAGTGACTGCCGATCGAAC 59.007 55.000 18.66 9.01 0.00 3.95
1382 1609 0.108804 GGAAGTGACTGCCGATCGAA 60.109 55.000 18.66 3.24 0.00 3.71
1383 1610 0.965866 AGGAAGTGACTGCCGATCGA 60.966 55.000 18.66 0.00 33.44 3.59
1384 1611 0.108615 AAGGAAGTGACTGCCGATCG 60.109 55.000 8.51 8.51 33.44 3.69
1385 1612 1.066858 TGAAGGAAGTGACTGCCGATC 60.067 52.381 3.41 7.69 33.44 3.69
1386 1613 0.976641 TGAAGGAAGTGACTGCCGAT 59.023 50.000 3.41 0.00 33.44 4.18
1387 1614 0.976641 ATGAAGGAAGTGACTGCCGA 59.023 50.000 3.41 0.00 33.44 5.54
1388 1615 1.338105 TGATGAAGGAAGTGACTGCCG 60.338 52.381 3.41 0.00 33.44 5.69
1389 1616 2.079925 GTGATGAAGGAAGTGACTGCC 58.920 52.381 0.00 0.00 0.00 4.85
1390 1617 1.728971 CGTGATGAAGGAAGTGACTGC 59.271 52.381 0.00 0.00 0.00 4.40
1391 1618 3.249091 CTCGTGATGAAGGAAGTGACTG 58.751 50.000 0.00 0.00 0.00 3.51
1392 1619 2.894126 ACTCGTGATGAAGGAAGTGACT 59.106 45.455 0.00 0.00 0.00 3.41
1393 1620 3.305398 ACTCGTGATGAAGGAAGTGAC 57.695 47.619 0.00 0.00 0.00 3.67
1394 1621 3.069586 ACAACTCGTGATGAAGGAAGTGA 59.930 43.478 1.52 0.00 0.00 3.41
1395 1622 3.393800 ACAACTCGTGATGAAGGAAGTG 58.606 45.455 1.52 0.00 0.00 3.16
1396 1623 3.654414 GACAACTCGTGATGAAGGAAGT 58.346 45.455 1.52 0.00 0.00 3.01
1397 1624 2.663602 CGACAACTCGTGATGAAGGAAG 59.336 50.000 1.52 0.00 35.00 3.46
1398 1625 2.295070 TCGACAACTCGTGATGAAGGAA 59.705 45.455 1.52 0.00 41.02 3.36
1399 1626 1.883926 TCGACAACTCGTGATGAAGGA 59.116 47.619 1.52 0.00 41.02 3.36
1400 1627 2.254459 CTCGACAACTCGTGATGAAGG 58.746 52.381 1.52 0.00 41.02 3.46
1401 1628 2.935042 ACTCGACAACTCGTGATGAAG 58.065 47.619 1.52 0.00 41.02 3.02
1402 1629 3.305964 GAACTCGACAACTCGTGATGAA 58.694 45.455 1.52 0.00 41.02 2.57
1403 1630 2.664698 CGAACTCGACAACTCGTGATGA 60.665 50.000 1.52 0.00 43.02 2.92
1404 1631 1.644295 CGAACTCGACAACTCGTGATG 59.356 52.381 0.00 0.00 43.02 3.07
1405 1632 1.534163 TCGAACTCGACAACTCGTGAT 59.466 47.619 0.00 0.00 44.22 3.06
1406 1633 0.939419 TCGAACTCGACAACTCGTGA 59.061 50.000 0.00 0.00 44.22 4.35
1407 1634 3.449789 TCGAACTCGACAACTCGTG 57.550 52.632 0.00 0.00 44.22 4.35
1471 1698 3.342477 AGGGGGAAGCCAAGGAGC 61.342 66.667 0.00 0.00 0.00 4.70
1472 1699 1.919600 CTCAGGGGGAAGCCAAGGAG 61.920 65.000 0.00 0.00 0.00 3.69
1522 1749 2.662006 ACATCTGTGATCTGACGGTG 57.338 50.000 0.00 0.00 0.00 4.94
1609 1836 1.081094 GTAACGGCTAACAATGCGGT 58.919 50.000 0.00 0.00 43.94 5.68
1611 1838 0.993532 TCGTAACGGCTAACAATGCG 59.006 50.000 0.00 0.00 0.00 4.73
1612 1839 3.668596 ATTCGTAACGGCTAACAATGC 57.331 42.857 0.00 0.00 0.00 3.56
1624 1851 9.834628 TGGTTGAAATGAAAGATAATTCGTAAC 57.165 29.630 0.00 0.00 31.80 2.50
1635 1866 8.578448 TCATGTCATATGGTTGAAATGAAAGA 57.422 30.769 2.13 0.00 43.92 2.52
1649 1880 7.709613 TGTTCAGACTTCAGATCATGTCATATG 59.290 37.037 0.00 0.00 32.41 1.78
1650 1881 7.789026 TGTTCAGACTTCAGATCATGTCATAT 58.211 34.615 0.00 0.00 32.41 1.78
1662 1899 5.163784 CCTGCACATAATGTTCAGACTTCAG 60.164 44.000 0.00 0.00 42.83 3.02
1663 1900 4.696877 CCTGCACATAATGTTCAGACTTCA 59.303 41.667 0.00 0.00 42.83 3.02
1664 1901 4.697352 ACCTGCACATAATGTTCAGACTTC 59.303 41.667 0.00 0.00 42.83 3.01
1665 1902 4.655963 ACCTGCACATAATGTTCAGACTT 58.344 39.130 0.00 0.00 42.83 3.01
1666 1903 4.292186 ACCTGCACATAATGTTCAGACT 57.708 40.909 0.00 0.00 42.83 3.24
1667 1904 4.379813 CCAACCTGCACATAATGTTCAGAC 60.380 45.833 0.00 0.00 42.83 3.51
1668 1905 3.758023 CCAACCTGCACATAATGTTCAGA 59.242 43.478 0.00 0.00 42.83 3.27
1669 1906 3.507233 ACCAACCTGCACATAATGTTCAG 59.493 43.478 0.00 0.00 40.50 3.02
1763 2000 2.182030 CTGGCCGTTCTCCTCGAC 59.818 66.667 0.00 0.00 0.00 4.20
1827 2064 3.670091 CGGGAGAAAGAGTACTCGAACAC 60.670 52.174 17.07 9.88 34.40 3.32
1918 2155 7.432838 GCTAACTGATTTGCTGAGTACTACTAC 59.567 40.741 0.00 0.00 34.22 2.73
1919 2156 7.339721 AGCTAACTGATTTGCTGAGTACTACTA 59.660 37.037 0.00 0.00 43.93 1.82
1920 2157 6.153680 AGCTAACTGATTTGCTGAGTACTACT 59.846 38.462 0.00 0.00 43.93 2.57
1921 2158 6.334202 AGCTAACTGATTTGCTGAGTACTAC 58.666 40.000 0.00 0.00 43.93 2.73
1942 2179 2.103094 TGAACACAACTGCAGACTAGCT 59.897 45.455 23.35 0.00 34.99 3.32
2000 2237 1.266718 GCGCAGAATTTCACAGGTCAA 59.733 47.619 0.30 0.00 0.00 3.18
2245 2483 0.250513 AAGACGAAGGAGACCATGGC 59.749 55.000 13.04 4.70 0.00 4.40
2277 2515 1.660560 GCTTACTCCAGTCGGGCGTA 61.661 60.000 0.00 0.00 35.77 4.42
2333 2571 2.101582 CAGTTAGAAGAGATCCACGGGG 59.898 54.545 0.00 0.00 0.00 5.73
2345 2583 3.670627 GCCGGCAAAATCACAGTTAGAAG 60.671 47.826 24.80 0.00 0.00 2.85
2537 2775 4.025401 GTGTGGTTGCCGGCGAAG 62.025 66.667 20.60 0.00 0.00 3.79
2564 2802 2.135581 TTGGAGGACGTTGACGGGT 61.136 57.895 8.52 0.00 44.95 5.28
2568 2806 1.499049 GTCAGTTGGAGGACGTTGAC 58.501 55.000 0.00 0.00 0.00 3.18
2605 2843 1.071764 TCGCTATAAATTTCGCGCACG 60.072 47.619 18.73 7.80 44.72 5.34
2796 3035 9.912634 GGCACATATGTATTTGCATTTACTATT 57.087 29.630 8.32 0.00 40.24 1.73
2843 3082 0.892755 CACTAGAGGCCCACGTACAA 59.107 55.000 0.00 0.00 0.00 2.41
2858 3097 1.404986 GCTTGTGTATCCCGCACACTA 60.405 52.381 7.10 0.00 45.20 2.74
2873 3112 1.148310 GCAGTACATGACGTGCTTGT 58.852 50.000 0.00 2.29 38.70 3.16
2888 3127 1.891150 CTTTCAAATCAGCCCAGCAGT 59.109 47.619 0.00 0.00 0.00 4.40
2940 3179 0.802222 CGATCCGAAAGAAGCGCTCA 60.802 55.000 12.06 0.00 0.00 4.26
2965 3227 1.002430 ACACATGACGAATGGCAGAGT 59.998 47.619 0.00 0.00 40.94 3.24
3030 3296 0.249238 AAAAGCCGAAAACGCATGCA 60.249 45.000 19.57 0.00 0.00 3.96
3075 3345 6.464222 AGACCAGTAGAAAATCGAAATGTCA 58.536 36.000 0.00 0.00 0.00 3.58
3299 3647 1.815003 CATGGCCGTGATTCTCGCA 60.815 57.895 21.08 0.00 0.00 5.10
3357 3831 2.210116 GAAGCAAAACCGTGTCTCTCA 58.790 47.619 0.00 0.00 0.00 3.27
3478 3952 1.858458 TGACTCTCGCGAAAACACAAG 59.142 47.619 11.33 0.00 0.00 3.16
3484 3958 1.019278 GGCCATGACTCTCGCGAAAA 61.019 55.000 11.33 0.00 0.00 2.29
3505 3979 4.364415 TTTTTCCCATTTTCGATAGGCG 57.636 40.909 0.00 0.00 42.69 5.52


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

AutoCloner maintained by Alex Coulton.