Multiple sequence alignment - TraesCS1D01G198700

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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 TraesCS1D01G198700 chr1D 100.000 6691 0 0 1 6691 280232192 280225502 0.000000e+00 12357.0
1 TraesCS1D01G198700 chr1D 82.642 530 79 9 34 552 421879330 421879857 2.200000e-124 457.0
2 TraesCS1D01G198700 chr1D 82.519 532 80 10 34 554 421873874 421874403 7.910000e-124 455.0
3 TraesCS1D01G198700 chr1D 82.973 370 54 7 193 554 401202612 401202980 6.470000e-85 326.0
4 TraesCS1D01G198700 chr1A 95.808 5224 161 17 1 5200 352180827 352175638 0.000000e+00 8381.0
5 TraesCS1D01G198700 chr1A 91.827 1505 56 21 5200 6691 352174723 352173273 0.000000e+00 2036.0
6 TraesCS1D01G198700 chr1B 96.182 2776 68 9 1952 4722 380895358 380892616 0.000000e+00 4505.0
7 TraesCS1D01G198700 chr1B 94.363 1987 62 15 4717 6691 380889301 380887353 0.000000e+00 3003.0
8 TraesCS1D01G198700 chr1B 97.579 1363 23 6 610 1971 380896722 380895369 0.000000e+00 2326.0
9 TraesCS1D01G198700 chr1B 82.283 508 76 10 52 547 659526462 659525957 1.720000e-115 427.0
10 TraesCS1D01G198700 chr1B 97.727 44 1 0 5745 5788 508392346 508392303 7.200000e-10 76.8
11 TraesCS1D01G198700 chr5B 91.993 1124 56 14 1081 2184 633788824 633789933 0.000000e+00 1546.0
12 TraesCS1D01G198700 chr3B 94.304 790 30 4 1204 1981 41668958 41668172 0.000000e+00 1195.0
13 TraesCS1D01G198700 chr3B 95.402 261 12 0 1721 1981 8755870 8755610 3.730000e-112 416.0
14 TraesCS1D01G198700 chr3B 94.007 267 13 1 1461 1724 8765249 8764983 1.050000e-107 401.0
15 TraesCS1D01G198700 chr6B 81.887 530 83 8 34 552 164863730 164863203 1.030000e-117 435.0
16 TraesCS1D01G198700 chr6B 83.505 97 13 2 1484 1580 158637004 158637097 3.320000e-13 87.9
17 TraesCS1D01G198700 chr6A 81.733 531 82 12 34 552 105639687 105639160 4.790000e-116 429.0
18 TraesCS1D01G198700 chr6A 81.461 534 82 12 34 552 572025010 572024479 8.020000e-114 422.0
19 TraesCS1D01G198700 chr6A 86.765 136 16 2 34 168 34067344 34067210 4.180000e-32 150.0
20 TraesCS1D01G198700 chr3D 81.664 529 80 10 34 554 58039349 58039868 2.230000e-114 424.0
21 TraesCS1D01G198700 chr3D 79.156 379 56 12 35 403 461022327 461021962 2.410000e-59 241.0
22 TraesCS1D01G198700 chr2B 80.603 531 90 9 34 553 510559124 510559652 1.350000e-106 398.0
23 TraesCS1D01G198700 chr2B 90.741 54 4 1 5787 5840 693312880 693312828 3.350000e-08 71.3
24 TraesCS1D01G198700 chr6D 80.488 533 89 9 34 554 87532089 87531560 1.750000e-105 394.0
25 TraesCS1D01G198700 chr3A 80.597 536 83 15 34 554 719954872 719955401 1.750000e-105 394.0
26 TraesCS1D01G198700 chr5D 83.594 256 36 3 34 285 480489080 480488827 1.120000e-57 235.0
27 TraesCS1D01G198700 chr5D 83.962 106 13 4 5742 5845 465001227 465001330 1.540000e-16 99.0
28 TraesCS1D01G198700 chr5D 84.848 99 5 5 5756 5845 114626536 114626439 2.570000e-14 91.6
29 TraesCS1D01G198700 chr7D 88.372 86 6 3 5754 5839 485833271 485833352 4.270000e-17 100.0
30 TraesCS1D01G198700 chr7D 88.750 80 5 2 5745 5824 485833346 485833271 1.990000e-15 95.3
31 TraesCS1D01G198700 chr7B 85.294 102 10 2 5742 5838 346677607 346677708 4.270000e-17 100.0
32 TraesCS1D01G198700 chr2A 83.036 112 7 7 5742 5845 6501869 6501762 2.570000e-14 91.6
33 TraesCS1D01G198700 chr4A 81.609 87 7 7 5742 5821 581333712 581333628 5.600000e-06 63.9


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 TraesCS1D01G198700 chr1D 280225502 280232192 6690 True 12357.0 12357 100.000000 1 6691 1 chr1D.!!$R1 6690
1 TraesCS1D01G198700 chr1D 421879330 421879857 527 False 457.0 457 82.642000 34 552 1 chr1D.!!$F3 518
2 TraesCS1D01G198700 chr1D 421873874 421874403 529 False 455.0 455 82.519000 34 554 1 chr1D.!!$F2 520
3 TraesCS1D01G198700 chr1A 352173273 352180827 7554 True 5208.5 8381 93.817500 1 6691 2 chr1A.!!$R1 6690
4 TraesCS1D01G198700 chr1B 380887353 380896722 9369 True 3278.0 4505 96.041333 610 6691 3 chr1B.!!$R3 6081
5 TraesCS1D01G198700 chr1B 659525957 659526462 505 True 427.0 427 82.283000 52 547 1 chr1B.!!$R2 495
6 TraesCS1D01G198700 chr5B 633788824 633789933 1109 False 1546.0 1546 91.993000 1081 2184 1 chr5B.!!$F1 1103
7 TraesCS1D01G198700 chr3B 41668172 41668958 786 True 1195.0 1195 94.304000 1204 1981 1 chr3B.!!$R3 777
8 TraesCS1D01G198700 chr6B 164863203 164863730 527 True 435.0 435 81.887000 34 552 1 chr6B.!!$R1 518
9 TraesCS1D01G198700 chr6A 105639160 105639687 527 True 429.0 429 81.733000 34 552 1 chr6A.!!$R2 518
10 TraesCS1D01G198700 chr6A 572024479 572025010 531 True 422.0 422 81.461000 34 552 1 chr6A.!!$R3 518
11 TraesCS1D01G198700 chr3D 58039349 58039868 519 False 424.0 424 81.664000 34 554 1 chr3D.!!$F1 520
12 TraesCS1D01G198700 chr2B 510559124 510559652 528 False 398.0 398 80.603000 34 553 1 chr2B.!!$F1 519
13 TraesCS1D01G198700 chr6D 87531560 87532089 529 True 394.0 394 80.488000 34 554 1 chr6D.!!$R1 520
14 TraesCS1D01G198700 chr3A 719954872 719955401 529 False 394.0 394 80.597000 34 554 1 chr3A.!!$F1 520

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
23 24 0.606604 GAAGGAGTTGGCCAGTACGA 59.393 55.000 5.11 0.0 0.00 3.43 F
32 33 1.214589 GCCAGTACGACCGACACAT 59.785 57.895 0.00 0.0 0.00 3.21 F
737 754 1.677052 GAGGAGAGGGACGTATGTGTC 59.323 57.143 0.00 0.0 38.17 3.67 F
2542 2626 3.883489 GCAGGTGAACTTGTCTAACCTTT 59.117 43.478 0.00 0.0 39.24 3.11 F
2827 2911 1.004628 TGCATCTTACCACATGGCACT 59.995 47.619 0.00 0.0 39.32 4.40 F
4638 4736 2.568696 TAGCTTCTGTCGCTGTGATC 57.431 50.000 0.00 0.0 38.38 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1999 2075 1.073763 TGCACCCTGTGAAAGCAGTAT 59.926 47.619 0.00 0.00 35.23 2.12 R
2327 2410 7.699566 TGTTAACAAATACCACTGTTCTGTTC 58.300 34.615 5.64 0.00 37.05 3.18 R
2568 2652 0.246635 GACGCCCAAGAAGCTAGTGA 59.753 55.000 0.00 0.00 0.00 3.41 R
4470 4568 0.389687 TATTTGCAGGCGCCAAAAGC 60.390 50.000 31.54 25.47 37.32 3.51 R
4963 8379 2.608268 TCGCATTGCAACATGGAAATG 58.392 42.857 0.00 0.00 29.75 2.32 R
6522 10881 0.037326 ACCACATGAGCACGGTGTAG 60.037 55.000 10.24 0.00 0.00 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
23 24 0.606604 GAAGGAGTTGGCCAGTACGA 59.393 55.000 5.11 0.00 0.00 3.43
32 33 1.214589 GCCAGTACGACCGACACAT 59.785 57.895 0.00 0.00 0.00 3.21
172 173 2.198304 ATCCCGTCCTTTGAGGTGCC 62.198 60.000 0.00 0.00 36.53 5.01
188 189 2.725008 CCGCCTAGGAGAAGAGCG 59.275 66.667 14.75 6.64 45.00 5.03
286 292 2.190313 GCATCGACTCCATGGCCA 59.810 61.111 8.56 8.56 0.00 5.36
392 407 4.089408 TGTTTATCCCCTATTTACCCGC 57.911 45.455 0.00 0.00 0.00 6.13
436 451 7.226720 ACTCTGTGTTCATAGATGTTTCGTTTT 59.773 33.333 0.17 0.00 0.00 2.43
469 484 2.886523 TGTGCTCACATGCTTAGCTTTT 59.113 40.909 5.60 0.00 36.21 2.27
539 555 9.214953 GTGATTAGATTAATCGAAAAAGTGCTG 57.785 33.333 13.94 0.00 45.82 4.41
572 588 7.165812 CGAACAATTGTCTAGAAAAGGTTTGTG 59.834 37.037 12.39 5.66 0.00 3.33
578 594 5.355910 TGTCTAGAAAAGGTTTGTGTGTTCC 59.644 40.000 0.00 0.00 0.00 3.62
579 595 5.355910 GTCTAGAAAAGGTTTGTGTGTTCCA 59.644 40.000 0.00 0.00 0.00 3.53
581 597 5.675684 AGAAAAGGTTTGTGTGTTCCATT 57.324 34.783 0.00 0.00 0.00 3.16
582 598 5.418676 AGAAAAGGTTTGTGTGTTCCATTG 58.581 37.500 0.00 0.00 0.00 2.82
583 599 5.186797 AGAAAAGGTTTGTGTGTTCCATTGA 59.813 36.000 0.00 0.00 0.00 2.57
584 600 5.413309 AAAGGTTTGTGTGTTCCATTGAA 57.587 34.783 0.00 0.00 0.00 2.69
585 601 5.612725 AAGGTTTGTGTGTTCCATTGAAT 57.387 34.783 0.00 0.00 31.98 2.57
586 602 6.723298 AAGGTTTGTGTGTTCCATTGAATA 57.277 33.333 0.00 0.00 31.98 1.75
587 603 6.723298 AGGTTTGTGTGTTCCATTGAATAA 57.277 33.333 0.00 0.00 31.98 1.40
588 604 7.118496 AGGTTTGTGTGTTCCATTGAATAAA 57.882 32.000 0.00 0.00 31.98 1.40
589 605 7.209475 AGGTTTGTGTGTTCCATTGAATAAAG 58.791 34.615 0.00 0.00 31.98 1.85
590 606 7.069331 AGGTTTGTGTGTTCCATTGAATAAAGA 59.931 33.333 0.00 0.00 31.98 2.52
591 607 7.382218 GGTTTGTGTGTTCCATTGAATAAAGAG 59.618 37.037 0.00 0.00 31.98 2.85
592 608 6.573664 TGTGTGTTCCATTGAATAAAGAGG 57.426 37.500 0.00 0.00 31.98 3.69
593 609 6.068010 TGTGTGTTCCATTGAATAAAGAGGT 58.932 36.000 0.00 0.00 31.98 3.85
594 610 6.016360 TGTGTGTTCCATTGAATAAAGAGGTG 60.016 38.462 0.00 0.00 31.98 4.00
595 611 6.206634 GTGTGTTCCATTGAATAAAGAGGTGA 59.793 38.462 0.00 0.00 31.98 4.02
596 612 6.947733 TGTGTTCCATTGAATAAAGAGGTGAT 59.052 34.615 0.00 0.00 31.98 3.06
597 613 7.121168 TGTGTTCCATTGAATAAAGAGGTGATC 59.879 37.037 0.00 0.00 31.98 2.92
598 614 6.603201 TGTTCCATTGAATAAAGAGGTGATCC 59.397 38.462 0.00 0.00 31.98 3.36
599 615 6.830838 GTTCCATTGAATAAAGAGGTGATCCT 59.169 38.462 0.00 0.00 38.70 3.24
600 616 7.690454 TCCATTGAATAAAGAGGTGATCCTA 57.310 36.000 0.00 0.00 45.24 2.94
601 617 8.101309 TCCATTGAATAAAGAGGTGATCCTAA 57.899 34.615 0.00 0.00 45.24 2.69
602 618 8.556589 TCCATTGAATAAAGAGGTGATCCTAAA 58.443 33.333 0.00 0.00 45.24 1.85
603 619 9.189156 CCATTGAATAAAGAGGTGATCCTAAAA 57.811 33.333 0.00 0.00 45.24 1.52
676 692 9.502145 TTTAAAATCGTGACAAATAGCATGATC 57.498 29.630 0.00 0.00 39.22 2.92
736 753 1.685491 GGAGGAGAGGGACGTATGTGT 60.685 57.143 0.00 0.00 0.00 3.72
737 754 1.677052 GAGGAGAGGGACGTATGTGTC 59.323 57.143 0.00 0.00 38.17 3.67
1297 1323 7.667043 TTGACTCGCACATTTATTAAGTCTT 57.333 32.000 0.00 0.00 34.27 3.01
1464 1497 7.532571 ACAACTTTGAAAACCTGTACTACAAC 58.467 34.615 0.00 0.00 0.00 3.32
1947 1993 4.198028 TCTCATGGACATCTTCTGTGTG 57.802 45.455 0.00 0.00 38.54 3.82
1999 2075 9.889128 TCATCAGACTCATTTGTTACAATATGA 57.111 29.630 16.09 16.09 0.00 2.15
2169 2252 4.260985 ACACATATTTCCATCGTGCTGAA 58.739 39.130 0.00 0.00 0.00 3.02
2493 2577 6.590292 ACTCTTATGTCGGTAACATTTCTGTG 59.410 38.462 0.00 0.00 46.73 3.66
2511 2595 6.550938 TCTGTGTTCAGTGATATGGAGAAT 57.449 37.500 0.00 0.00 41.91 2.40
2542 2626 3.883489 GCAGGTGAACTTGTCTAACCTTT 59.117 43.478 0.00 0.00 39.24 3.11
2568 2652 8.479689 TGTCATATTTTCTCATGAAATGCCAAT 58.520 29.630 0.00 0.00 46.21 3.16
2574 2658 6.688637 TTCTCATGAAATGCCAATCACTAG 57.311 37.500 0.00 0.00 46.21 2.57
2655 2739 4.733972 AGAAGAAAAGCAGAAACGCTAC 57.266 40.909 0.00 0.00 42.89 3.58
2663 2747 5.725110 AAGCAGAAACGCTACTATGAATG 57.275 39.130 0.00 0.00 42.89 2.67
2673 2757 5.760253 ACGCTACTATGAATGAGAAAATGGG 59.240 40.000 0.00 0.00 0.00 4.00
2700 2784 4.580167 CAGACTCCAAAGGTCACAAAATGA 59.420 41.667 0.00 0.00 36.29 2.57
2827 2911 1.004628 TGCATCTTACCACATGGCACT 59.995 47.619 0.00 0.00 39.32 4.40
2835 2919 3.259314 ACATGGCACTCCCCAGCA 61.259 61.111 0.00 0.00 38.50 4.41
3066 3150 5.125739 ACATAGTAAGGGAACTCTCTGAACG 59.874 44.000 0.00 0.00 42.68 3.95
3107 3191 5.409520 TGAATCATCATAAGCTAACCGCATC 59.590 40.000 0.00 0.00 42.61 3.91
3446 3531 7.706607 GTGGTTATTTTCATCCTATTTTCCTGC 59.293 37.037 0.00 0.00 0.00 4.85
3634 3722 7.177216 CCACATGGGTACATAAGCAATATTGAT 59.823 37.037 19.73 10.37 34.99 2.57
3903 3992 5.135383 AGGTTGCTGTGTATGATTATGCAT 58.865 37.500 3.79 3.79 31.49 3.96
3930 4020 8.592105 TTTTCTTTCAATCCAATGACATTGTC 57.408 30.769 23.27 9.93 38.59 3.18
3966 4056 3.778629 TGGGAGGGTACTATGAAAGAACC 59.221 47.826 0.00 0.00 0.00 3.62
4257 4355 4.978099 AGAAAGAGATTGGTGAGCAAAGA 58.022 39.130 0.00 0.00 0.00 2.52
4343 4441 3.464907 CTCAATCTCGGAATGCTGATGT 58.535 45.455 0.00 0.00 0.00 3.06
4353 4451 4.142403 CGGAATGCTGATGTGGTTTGTATT 60.142 41.667 0.00 0.00 0.00 1.89
4470 4568 8.748412 TGGTAGAACCATTCAATATTGGAAAAG 58.252 33.333 15.36 2.94 44.79 2.27
4548 4646 3.196463 TGCACATTCTGTTTGCCTTTTG 58.804 40.909 0.00 0.00 35.26 2.44
4638 4736 2.568696 TAGCTTCTGTCGCTGTGATC 57.431 50.000 0.00 0.00 38.38 2.92
4759 8175 7.657336 TGAATATGTACGCTATTCATCAGTGA 58.343 34.615 19.19 0.00 39.48 3.41
4799 8215 7.182760 TGGAAGTCTTCTTAGAGTGAATAGGA 58.817 38.462 12.31 0.00 34.26 2.94
4807 8223 7.246171 TCTTAGAGTGAATAGGAACAAAGCT 57.754 36.000 0.00 0.00 0.00 3.74
4828 8244 5.655532 AGCTTTAAGTCATGAATGATTGGCT 59.344 36.000 0.00 1.12 39.30 4.75
4873 8289 4.165779 GTGGGAATCAAGTTATTGTTGCG 58.834 43.478 0.00 0.00 37.68 4.85
4963 8379 1.379044 CCTTGGGACTGGTGGATGC 60.379 63.158 0.00 0.00 0.00 3.91
5146 8563 4.710865 TCTGCAAAAATAGGATCATTGGCA 59.289 37.500 0.00 0.00 0.00 4.92
5333 9670 3.834489 TGAAAATTCAAAAGGGCTGCA 57.166 38.095 0.50 0.00 33.55 4.41
5735 10072 6.040955 TGTTCTATACTGACCTGATCACCATC 59.959 42.308 0.00 0.00 32.37 3.51
5788 10129 4.497507 CGCTCAAACGGATGTATCTAGACA 60.498 45.833 0.00 0.00 0.00 3.41
5827 10176 2.167693 TCAGCGACAACTAATTCCGGAT 59.832 45.455 4.15 0.00 0.00 4.18
5914 10263 6.072948 CCAGTTTGGTAATTTGACATACGTGA 60.073 38.462 0.00 0.00 31.35 4.35
5915 10264 7.015289 CAGTTTGGTAATTTGACATACGTGAG 58.985 38.462 0.00 0.00 0.00 3.51
5973 10322 5.697633 GGACTTTTTGTGTACGTAGATTCCA 59.302 40.000 0.00 0.00 0.00 3.53
6143 10492 1.614413 GATCTAGTAAGCGACCCCTGG 59.386 57.143 0.00 0.00 0.00 4.45
6154 10503 2.422479 GCGACCCCTGGAAAAGATAAAC 59.578 50.000 0.00 0.00 0.00 2.01
6163 10512 6.598064 CCCTGGAAAAGATAAACGATTGTAGT 59.402 38.462 0.00 0.00 0.00 2.73
6164 10513 7.767198 CCCTGGAAAAGATAAACGATTGTAGTA 59.233 37.037 0.00 0.00 0.00 1.82
6221 10570 4.265073 GTTTCCATTCCTCATGTACTGCT 58.735 43.478 0.00 0.00 0.00 4.24
6264 10620 7.756558 CCAAAGATGGTTTTCTTAGCTTAGAG 58.243 38.462 2.24 0.00 42.18 2.43
6265 10621 7.148171 CCAAAGATGGTTTTCTTAGCTTAGAGG 60.148 40.741 2.24 0.00 42.18 3.69
6351 10710 6.405176 GCCTGGATTTCTCATTTCTTTTCGAT 60.405 38.462 0.00 0.00 0.00 3.59
6352 10711 6.971184 CCTGGATTTCTCATTTCTTTTCGATG 59.029 38.462 0.00 0.00 0.00 3.84
6356 10715 7.148171 GGATTTCTCATTTCTTTTCGATGGAGT 60.148 37.037 0.00 0.00 0.00 3.85
6404 10763 1.121407 GGTTTTTGCTGGGAAGGCCT 61.121 55.000 0.00 0.00 0.00 5.19
6405 10764 0.758734 GTTTTTGCTGGGAAGGCCTT 59.241 50.000 20.65 20.65 0.00 4.35
6406 10765 0.758123 TTTTTGCTGGGAAGGCCTTG 59.242 50.000 26.25 9.76 0.00 3.61
6433 10792 4.945246 ACTTTGATGTCGTCACAGTTACT 58.055 39.130 7.86 0.00 43.53 2.24
6434 10793 6.080648 ACTTTGATGTCGTCACAGTTACTA 57.919 37.500 7.86 0.00 43.53 1.82
6435 10794 6.509656 ACTTTGATGTCGTCACAGTTACTAA 58.490 36.000 7.86 0.00 43.53 2.24
6436 10795 7.152645 ACTTTGATGTCGTCACAGTTACTAAT 58.847 34.615 7.86 0.00 43.53 1.73
6437 10796 7.328737 ACTTTGATGTCGTCACAGTTACTAATC 59.671 37.037 7.86 0.00 43.53 1.75
6438 10797 6.262193 TGATGTCGTCACAGTTACTAATCA 57.738 37.500 0.00 0.00 35.41 2.57
6439 10798 6.863275 TGATGTCGTCACAGTTACTAATCAT 58.137 36.000 0.00 0.00 35.41 2.45
6520 10879 1.372582 AACCGTGTGATATGCTGCTG 58.627 50.000 0.00 0.00 0.00 4.41
6521 10880 1.091771 ACCGTGTGATATGCTGCTGC 61.092 55.000 8.89 8.89 40.20 5.25
6522 10881 1.645455 CGTGTGATATGCTGCTGCC 59.355 57.895 13.47 0.00 38.71 4.85
6523 10882 0.812811 CGTGTGATATGCTGCTGCCT 60.813 55.000 13.47 5.83 38.71 4.75
6532 10891 3.121030 CTGCTGCCTACACCGTGC 61.121 66.667 0.00 0.00 0.00 5.34
6539 10898 1.361668 GCCTACACCGTGCTCATGTG 61.362 60.000 0.00 4.01 36.11 3.21
6552 10913 2.481952 GCTCATGTGGTGACAAGAAGTC 59.518 50.000 0.00 0.00 46.06 3.01
6560 10921 3.814577 GACAAGAAGTCTGCGGCTA 57.185 52.632 0.00 0.00 44.09 3.93
6596 10957 2.472414 AAATAGCACGGCGGAACCCA 62.472 55.000 13.24 0.00 33.26 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 0.606604 TCGTACTGGCCAACTCCTTC 59.393 55.000 7.01 0.00 0.00 3.46
23 24 1.183549 GGGAGTGAGTATGTGTCGGT 58.816 55.000 0.00 0.00 0.00 4.69
32 33 1.605058 GCGCAAGGAGGGAGTGAGTA 61.605 60.000 0.30 0.00 38.28 2.59
61 62 1.112113 GAGAGGAACGGTAGATGGCA 58.888 55.000 0.00 0.00 0.00 4.92
172 173 2.725008 CCGCTCTTCTCCTAGGCG 59.275 66.667 2.96 0.00 44.48 5.52
222 228 1.530891 GGAGATGGGGACGGATCGA 60.531 63.158 0.00 0.00 0.00 3.59
547 563 7.973944 ACACAAACCTTTTCTAGACAATTGTTC 59.026 33.333 13.36 6.25 0.00 3.18
605 621 8.975295 CCTGAATTCCTCTTTGGATATTCTTTT 58.025 33.333 2.27 0.00 45.68 2.27
606 622 8.118600 ACCTGAATTCCTCTTTGGATATTCTTT 58.881 33.333 2.27 0.00 45.68 2.52
607 623 7.646884 ACCTGAATTCCTCTTTGGATATTCTT 58.353 34.615 2.27 0.00 45.68 2.52
608 624 7.218314 ACCTGAATTCCTCTTTGGATATTCT 57.782 36.000 2.27 1.41 45.68 2.40
691 707 5.249780 TCTCTCCGAATCTAGCCTCTATT 57.750 43.478 0.00 0.00 0.00 1.73
695 711 2.159382 CCTCTCTCCGAATCTAGCCTC 58.841 57.143 0.00 0.00 0.00 4.70
736 753 3.630312 GGCACCGCTCCTTTATATTTTGA 59.370 43.478 0.00 0.00 0.00 2.69
737 754 3.380004 TGGCACCGCTCCTTTATATTTTG 59.620 43.478 0.00 0.00 0.00 2.44
1297 1323 3.757947 TTCTGGGATCACTCCTCTACA 57.242 47.619 0.00 0.00 41.74 2.74
1464 1497 7.095607 GGAAGTATATTCACCGCATTCTTGTAG 60.096 40.741 0.00 0.00 0.00 2.74
1947 1993 7.880195 AGGCATAATGTATCACTATTCCTGTTC 59.120 37.037 0.00 0.00 0.00 3.18
1999 2075 1.073763 TGCACCCTGTGAAAGCAGTAT 59.926 47.619 0.00 0.00 35.23 2.12
2327 2410 7.699566 TGTTAACAAATACCACTGTTCTGTTC 58.300 34.615 5.64 0.00 37.05 3.18
2493 2577 5.609423 AGCTGATTCTCCATATCACTGAAC 58.391 41.667 0.00 0.00 0.00 3.18
2511 2595 1.301716 GTTCACCTGCCGAAGCTGA 60.302 57.895 0.00 0.00 40.18 4.26
2542 2626 7.407393 TGGCATTTCATGAGAAAATATGACA 57.593 32.000 0.00 0.57 46.06 3.58
2568 2652 0.246635 GACGCCCAAGAAGCTAGTGA 59.753 55.000 0.00 0.00 0.00 3.41
2574 2658 1.172812 AGGTTTGACGCCCAAGAAGC 61.173 55.000 0.00 0.00 35.94 3.86
2655 2739 7.227512 GTCTGGTACCCATTTTCTCATTCATAG 59.772 40.741 10.07 0.00 30.82 2.23
2663 2747 3.263425 TGGAGTCTGGTACCCATTTTCTC 59.737 47.826 10.07 8.45 30.82 2.87
2673 2757 2.367567 TGTGACCTTTGGAGTCTGGTAC 59.632 50.000 0.00 0.00 35.21 3.34
2700 2784 5.347342 CAAGTAAGCAACATCTCTCTCGAT 58.653 41.667 0.00 0.00 0.00 3.59
2827 2911 5.858876 ACATAAATATATGGTGCTGGGGA 57.141 39.130 1.38 0.00 42.71 4.81
2930 3014 2.602257 TGACCCTGCGATGACATAAG 57.398 50.000 0.00 0.00 0.00 1.73
2940 3024 3.009723 AGAACAACATTATGACCCTGCG 58.990 45.455 0.00 0.00 0.00 5.18
3066 3150 8.514594 TGATGATTCACAAGAAAATGGTAGTTC 58.485 33.333 0.00 0.00 37.29 3.01
3107 3191 2.868442 GCAAATGGGGTTTTTGGTACCG 60.868 50.000 7.57 0.00 36.49 4.02
3112 3196 4.469586 ACCTATAGCAAATGGGGTTTTTGG 59.530 41.667 6.45 0.00 35.18 3.28
3446 3531 4.993584 CACATCAATTAGGCTAGCTACTGG 59.006 45.833 15.72 0.69 0.00 4.00
3930 4020 2.440409 CCTCCCACTTCCTTTGTCATG 58.560 52.381 0.00 0.00 0.00 3.07
3943 4033 4.383880 GGTTCTTTCATAGTACCCTCCCAC 60.384 50.000 0.00 0.00 38.13 4.61
3966 4056 6.515043 AACAAAATCAATCTCTTTGTTGCG 57.485 33.333 10.43 0.00 46.29 4.85
4257 4355 4.594920 CCTACACCATGGAAGGATATCACT 59.405 45.833 21.47 0.00 0.00 3.41
4343 4441 9.829507 AAATGAAACATGAAAGAATACAAACCA 57.170 25.926 0.00 0.00 0.00 3.67
4390 4488 6.509418 AACACTTCACAAAAACTAGAGCAA 57.491 33.333 0.00 0.00 0.00 3.91
4470 4568 0.389687 TATTTGCAGGCGCCAAAAGC 60.390 50.000 31.54 25.47 37.32 3.51
4638 4736 3.921021 CAGTAGTTCTCAGTACAAAGGCG 59.079 47.826 0.00 0.00 31.82 5.52
4799 8215 9.199982 CAATCATTCATGACTTAAAGCTTTGTT 57.800 29.630 22.02 5.36 40.03 2.83
4807 8223 6.071221 AGCAAGCCAATCATTCATGACTTAAA 60.071 34.615 0.00 0.00 40.03 1.52
4828 8244 4.874966 CCCATCAAACAAAAACAAGAGCAA 59.125 37.500 0.00 0.00 0.00 3.91
4963 8379 2.608268 TCGCATTGCAACATGGAAATG 58.392 42.857 0.00 0.00 29.75 2.32
5319 9656 0.978151 ATGCATGCAGCCCTTTTGAA 59.022 45.000 26.69 0.00 44.83 2.69
5333 9670 2.381911 GATGAGGAACCCACAATGCAT 58.618 47.619 0.00 0.00 0.00 3.96
5735 10072 2.825264 GGATGGAGGGAGAAGCGG 59.175 66.667 0.00 0.00 0.00 5.52
5797 10146 1.537202 AGTTGTCGCTGAAAAGGATGC 59.463 47.619 0.00 0.00 0.00 3.91
5803 10152 3.187637 CCGGAATTAGTTGTCGCTGAAAA 59.812 43.478 0.00 0.00 0.00 2.29
5827 10176 5.133941 TGCAACAAACAAATACTACCTCCA 58.866 37.500 0.00 0.00 0.00 3.86
5914 10263 2.445682 TTGCACCAACCCAAACTACT 57.554 45.000 0.00 0.00 0.00 2.57
5915 10264 2.429250 ACTTTGCACCAACCCAAACTAC 59.571 45.455 0.00 0.00 0.00 2.73
5916 10265 2.428890 CACTTTGCACCAACCCAAACTA 59.571 45.455 0.00 0.00 0.00 2.24
5973 10322 7.786178 TCGACTAGCATAAACATAAAGCAAT 57.214 32.000 0.00 0.00 0.00 3.56
6264 10620 8.392612 CAAATGCAATCCATCAAATTAACTTCC 58.607 33.333 0.00 0.00 31.43 3.46
6265 10621 7.906527 GCAAATGCAATCCATCAAATTAACTTC 59.093 33.333 0.00 0.00 41.59 3.01
6301 10660 3.683365 AAATTGAAGGAGCCGCAAATT 57.317 38.095 0.00 0.00 0.00 1.82
6302 10661 3.006752 TGAAAATTGAAGGAGCCGCAAAT 59.993 39.130 0.00 0.00 0.00 2.32
6303 10662 2.363680 TGAAAATTGAAGGAGCCGCAAA 59.636 40.909 0.00 0.00 0.00 3.68
6351 10710 5.010112 GCACTATAGCAGTTCATCTACTCCA 59.990 44.000 0.00 0.00 34.26 3.86
6352 10711 5.010112 TGCACTATAGCAGTTCATCTACTCC 59.990 44.000 0.00 0.00 40.11 3.85
6356 10715 6.878317 ACTTTGCACTATAGCAGTTCATCTA 58.122 36.000 0.00 0.00 46.54 1.98
6378 10737 0.829990 CCCAGCAAAAACCCACAACT 59.170 50.000 0.00 0.00 0.00 3.16
6404 10763 6.424176 TGTGACGACATCAAAGTTTAACAA 57.576 33.333 0.00 0.00 39.72 2.83
6405 10764 6.043327 CTGTGACGACATCAAAGTTTAACA 57.957 37.500 0.00 0.00 37.83 2.41
6432 10791 2.074576 CGCAGCCTCATCCATGATTAG 58.925 52.381 0.00 0.00 36.02 1.73
6433 10792 1.693606 TCGCAGCCTCATCCATGATTA 59.306 47.619 0.00 0.00 36.02 1.75
6434 10793 0.471191 TCGCAGCCTCATCCATGATT 59.529 50.000 0.00 0.00 36.02 2.57
6435 10794 0.250209 GTCGCAGCCTCATCCATGAT 60.250 55.000 0.00 0.00 36.02 2.45
6436 10795 1.144716 GTCGCAGCCTCATCCATGA 59.855 57.895 0.00 0.00 35.16 3.07
6437 10796 2.242572 CGTCGCAGCCTCATCCATG 61.243 63.158 0.00 0.00 0.00 3.66
6438 10797 2.107750 CGTCGCAGCCTCATCCAT 59.892 61.111 0.00 0.00 0.00 3.41
6439 10798 4.147449 CCGTCGCAGCCTCATCCA 62.147 66.667 0.00 0.00 0.00 3.41
6520 10879 1.079127 ACATGAGCACGGTGTAGGC 60.079 57.895 10.24 0.00 0.00 3.93
6521 10880 0.740868 CCACATGAGCACGGTGTAGG 60.741 60.000 10.24 1.57 0.00 3.18
6522 10881 0.037326 ACCACATGAGCACGGTGTAG 60.037 55.000 10.24 0.00 0.00 2.74
6523 10882 0.320334 CACCACATGAGCACGGTGTA 60.320 55.000 10.24 0.00 43.23 2.90
6552 10913 2.871182 TAGACTGACAATAGCCGCAG 57.129 50.000 0.00 0.00 34.65 5.18
6553 10914 3.492656 GGATTAGACTGACAATAGCCGCA 60.493 47.826 0.00 0.00 0.00 5.69
6560 10921 7.653713 CGTGCTATTTAGGATTAGACTGACAAT 59.346 37.037 0.00 0.00 0.00 2.71
6619 10980 4.967437 GCAGTAGCTCTTCACAAAAGATG 58.033 43.478 0.00 0.00 37.91 2.90


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

AutoCloner maintained by Alex Coulton.