Multiple sequence alignment - TraesCS2D01G594300

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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 TraesCS2D01G594300 chr2D 100.000 6272 0 0 1 6272 648209555 648215826 0.000000e+00 11546.0
1 TraesCS2D01G594300 chr2B 93.664 5098 177 70 107 5182 782149066 782154039 0.000000e+00 7491.0
2 TraesCS2D01G594300 chr2B 89.670 455 25 11 5181 5625 782154077 782154519 1.530000e-155 560.0
3 TraesCS2D01G594300 chr2B 81.607 560 49 28 33 570 782148960 782149487 1.260000e-111 414.0
4 TraesCS2D01G594300 chr2B 91.724 290 16 6 698 985 129747984 129747701 4.560000e-106 396.0
5 TraesCS2D01G594300 chr2B 100.000 33 0 0 566 598 481164321 481164353 1.890000e-05 62.1
6 TraesCS2D01G594300 chr2B 97.059 34 1 0 565 598 335527271 335527238 2.440000e-04 58.4
7 TraesCS2D01G594300 chr2B 92.308 39 1 2 562 598 321324288 321324326 3.000000e-03 54.7
8 TraesCS2D01G594300 chrUn 92.475 5236 230 60 14 5182 31216867 31211729 0.000000e+00 7336.0
9 TraesCS2D01G594300 chrUn 89.662 474 23 9 5181 5640 31211690 31211229 1.170000e-161 580.0
10 TraesCS2D01G594300 chr3D 95.679 324 13 1 5949 6271 80940018 80939695 2.590000e-143 520.0
11 TraesCS2D01G594300 chr3D 92.281 285 18 2 5657 5938 80940430 80940147 9.790000e-108 401.0
12 TraesCS2D01G594300 chr5B 93.231 325 21 1 5949 6272 10428147 10427823 1.580000e-130 477.0
13 TraesCS2D01G594300 chr5B 91.379 290 18 5 698 985 619716737 619716453 2.120000e-104 390.0
14 TraesCS2D01G594300 chr5B 90.690 290 20 4 698 985 7766469 7766185 4.590000e-101 379.0
15 TraesCS2D01G594300 chr5B 90.690 290 20 4 698 985 47428425 47428709 4.590000e-101 379.0
16 TraesCS2D01G594300 chr5B 89.744 234 19 3 5709 5938 10428514 10428282 1.710000e-75 294.0
17 TraesCS2D01G594300 chr5B 90.323 155 13 2 2445 2597 593233150 593233304 1.070000e-47 202.0
18 TraesCS2D01G594300 chr1B 92.000 325 25 1 5949 6272 587136500 587136176 7.410000e-124 455.0
19 TraesCS2D01G594300 chr6B 90.462 325 30 1 5949 6272 62620444 62620768 1.620000e-115 427.0
20 TraesCS2D01G594300 chr6B 88.000 325 38 1 5949 6272 39292881 39292557 3.550000e-102 383.0
21 TraesCS2D01G594300 chr6B 94.286 35 2 0 564 598 478479059 478479093 3.000000e-03 54.7
22 TraesCS2D01G594300 chr2A 89.846 325 32 1 5949 6272 15804271 15803947 3.500000e-112 416.0
23 TraesCS2D01G594300 chr5D 89.969 319 31 1 5951 6268 546829549 546829867 1.630000e-110 411.0
24 TraesCS2D01G594300 chr5A 89.538 325 33 1 5949 6272 636607350 636607026 1.630000e-110 411.0
25 TraesCS2D01G594300 chr5A 91.034 290 19 4 698 985 455891879 455891595 9.860000e-103 385.0
26 TraesCS2D01G594300 chr4D 88.923 325 29 4 5949 6272 28401137 28400819 1.640000e-105 394.0
27 TraesCS2D01G594300 chr4D 88.162 321 36 2 5954 6272 15568930 15568610 1.280000e-101 381.0
28 TraesCS2D01G594300 chr7B 91.379 290 18 4 698 985 113520402 113520118 2.120000e-104 390.0
29 TraesCS2D01G594300 chr7B 94.444 36 1 1 564 598 203031450 203031485 3.000000e-03 54.7
30 TraesCS2D01G594300 chr3B 97.143 35 1 0 565 599 417370231 417370197 6.790000e-05 60.2
31 TraesCS2D01G594300 chr6A 97.059 34 1 0 565 598 428071120 428071087 2.440000e-04 58.4
32 TraesCS2D01G594300 chr1A 94.595 37 2 0 562 598 85844098 85844062 2.440000e-04 58.4
33 TraesCS2D01G594300 chr4B 94.444 36 2 0 563 598 310167927 310167892 8.780000e-04 56.5


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 TraesCS2D01G594300 chr2D 648209555 648215826 6271 False 11546.000000 11546 100.000000 1 6272 1 chr2D.!!$F1 6271
1 TraesCS2D01G594300 chr2B 782148960 782154519 5559 False 2821.666667 7491 88.313667 33 5625 3 chr2B.!!$F3 5592
2 TraesCS2D01G594300 chrUn 31211229 31216867 5638 True 3958.000000 7336 91.068500 14 5640 2 chrUn.!!$R1 5626
3 TraesCS2D01G594300 chr3D 80939695 80940430 735 True 460.500000 520 93.980000 5657 6271 2 chr3D.!!$R1 614
4 TraesCS2D01G594300 chr5B 10427823 10428514 691 True 385.500000 477 91.487500 5709 6272 2 chr5B.!!$R3 563

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
589 630 0.186873 GGTACTCCCTCCGTCCCATA 59.813 60.0 0.00 0.0 0.00 2.74 F
1098 1151 1.338136 ACAAGGACAGGCGGGATAGG 61.338 60.0 0.00 0.0 0.00 2.57 F
2421 2475 1.301677 GAAGCTTACAAGGCTGCGCT 61.302 55.0 9.73 0.0 40.19 5.92 F
3438 3495 0.467290 TGGAAGAGTTTGTGTGGGGC 60.467 55.0 0.00 0.0 0.00 5.80 F
3970 4036 0.544357 TCCTACCCACCCTCACACTG 60.544 60.0 0.00 0.0 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2374 2428 1.005340 GCTTCTGCTCACCAATCTCG 58.995 55.000 0.00 0.00 36.03 4.04 R
3078 3135 1.435515 CTCCCTAGCAGACTGTCGC 59.564 63.158 13.97 13.97 0.00 5.19 R
3811 3876 0.251742 TGGTTCTGCCTCCCCAATTG 60.252 55.000 0.00 0.00 38.35 2.32 R
4843 4936 0.322456 TTCCATTCAAGCAGGACCGG 60.322 55.000 0.00 0.00 0.00 5.28 R
5647 5805 0.322997 CGCCACCCCCTGTATCAAAA 60.323 55.000 0.00 0.00 0.00 2.44 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
221 257 1.684734 GGAAGCCCTACCTCGTCCA 60.685 63.158 0.00 0.00 32.29 4.02
465 506 2.076863 GCTTGTGACCTGCGATTAGTT 58.923 47.619 0.00 0.00 0.00 2.24
469 510 1.128692 GTGACCTGCGATTAGTTGTGC 59.871 52.381 0.00 0.00 0.00 4.57
540 581 2.964464 TCTCTCTGAGAGGAATCCATGC 59.036 50.000 29.09 0.00 42.54 4.06
544 585 1.767088 CTGAGAGGAATCCATGCCTGA 59.233 52.381 0.61 0.00 33.84 3.86
551 592 3.718434 AGGAATCCATGCCTGAGAATGTA 59.282 43.478 0.61 0.00 32.06 2.29
577 618 7.624360 TTGATGTGTGAATAATTGGTACTCC 57.376 36.000 0.00 0.00 0.00 3.85
578 619 6.119536 TGATGTGTGAATAATTGGTACTCCC 58.880 40.000 0.00 0.00 0.00 4.30
579 620 5.772393 TGTGTGAATAATTGGTACTCCCT 57.228 39.130 0.00 0.00 0.00 4.20
580 621 5.741011 TGTGTGAATAATTGGTACTCCCTC 58.259 41.667 0.00 0.00 0.00 4.30
581 622 5.123936 GTGTGAATAATTGGTACTCCCTCC 58.876 45.833 0.00 0.00 0.00 4.30
582 623 4.141801 TGTGAATAATTGGTACTCCCTCCG 60.142 45.833 0.00 0.00 0.00 4.63
583 624 4.035112 TGAATAATTGGTACTCCCTCCGT 58.965 43.478 0.00 0.00 0.00 4.69
584 625 4.100498 TGAATAATTGGTACTCCCTCCGTC 59.900 45.833 0.00 0.00 0.00 4.79
585 626 1.201424 AATTGGTACTCCCTCCGTCC 58.799 55.000 0.00 0.00 0.00 4.79
586 627 0.690077 ATTGGTACTCCCTCCGTCCC 60.690 60.000 0.00 0.00 0.00 4.46
587 628 2.096707 TTGGTACTCCCTCCGTCCCA 62.097 60.000 0.00 0.00 0.00 4.37
588 629 1.075450 GGTACTCCCTCCGTCCCAT 60.075 63.158 0.00 0.00 0.00 4.00
589 630 0.186873 GGTACTCCCTCCGTCCCATA 59.813 60.000 0.00 0.00 0.00 2.74
590 631 1.412074 GGTACTCCCTCCGTCCCATAA 60.412 57.143 0.00 0.00 0.00 1.90
591 632 2.606378 GTACTCCCTCCGTCCCATAAT 58.394 52.381 0.00 0.00 0.00 1.28
592 633 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
593 634 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
594 635 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
595 636 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
596 637 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
597 638 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
604 645 5.983720 CCGTCCCATAATGTAAGAGTAGTTG 59.016 44.000 0.00 0.00 0.00 3.16
659 701 2.235891 GGGTCAATCGGTCCAGTTTTT 58.764 47.619 0.00 0.00 0.00 1.94
707 751 5.073311 TGCAGGTTTGAGTCTAGTGATAC 57.927 43.478 0.00 0.00 0.00 2.24
770 814 7.105588 GGGCATTTATGTTTCCTCAAATTCTT 58.894 34.615 0.00 0.00 0.00 2.52
838 883 1.430632 GGGCAATGCGACACATCAG 59.569 57.895 0.00 0.00 38.34 2.90
840 885 1.430632 GCAATGCGACACATCAGGG 59.569 57.895 0.00 0.00 38.34 4.45
857 902 6.782494 ACATCAGGGAAAACTTAAAACATCCT 59.218 34.615 0.00 0.00 0.00 3.24
880 925 2.885894 TGCAATCAACTGAAGTGCATGA 59.114 40.909 14.22 0.00 41.31 3.07
1090 1143 1.973812 GGCAAGGACAAGGACAGGC 60.974 63.158 0.00 0.00 0.00 4.85
1098 1151 1.338136 ACAAGGACAGGCGGGATAGG 61.338 60.000 0.00 0.00 0.00 2.57
1230 1283 3.236047 GGATAGGGAGAGGGAAAGAGAC 58.764 54.545 0.00 0.00 0.00 3.36
1242 1295 3.103742 GGAAAGAGACAGGGACAGAGAT 58.896 50.000 0.00 0.00 0.00 2.75
1305 1358 4.430765 GGCCGTGACCGTGATCGT 62.431 66.667 0.00 0.00 35.01 3.73
1587 1640 6.152831 GGTATGCCCTTGAGTAATTGTTTCTT 59.847 38.462 0.00 0.00 0.00 2.52
1595 1648 9.118236 CCTTGAGTAATTGTTTCTTTTCGATTC 57.882 33.333 0.00 0.00 0.00 2.52
1596 1649 9.663904 CTTGAGTAATTGTTTCTTTTCGATTCA 57.336 29.630 0.00 0.00 0.00 2.57
1618 1671 4.816385 CACACTAGCCTTTTCTTCAGTCAA 59.184 41.667 0.00 0.00 0.00 3.18
1914 1968 1.888512 GTTGTCCAGCATGACACCATT 59.111 47.619 7.73 0.00 44.55 3.16
1993 2047 9.416794 GAAAATAGTGATGACGACTATGATGAT 57.583 33.333 0.00 0.00 36.85 2.45
2188 2242 6.214412 ACTTATCTGGAGTGAAGGTTCTTCAT 59.786 38.462 12.63 3.75 0.00 2.57
2331 2385 2.820197 CCCCTAACCTTTTCTGACTTGC 59.180 50.000 0.00 0.00 0.00 4.01
2333 2387 2.095718 CCTAACCTTTTCTGACTTGCGC 60.096 50.000 0.00 0.00 0.00 6.09
2421 2475 1.301677 GAAGCTTACAAGGCTGCGCT 61.302 55.000 9.73 0.00 40.19 5.92
2533 2588 2.916269 TGGTAGGTTCAATGATGACCCA 59.084 45.455 0.74 0.00 40.46 4.51
2572 2627 3.062763 GCTCTCACATTATGATGACCCG 58.937 50.000 4.20 0.00 36.48 5.28
2621 2677 6.552445 ACTGCTTCAATTGGTAGATACTCT 57.448 37.500 5.42 0.00 0.00 3.24
2622 2678 6.578023 ACTGCTTCAATTGGTAGATACTCTC 58.422 40.000 5.42 0.00 0.00 3.20
2623 2679 5.918608 TGCTTCAATTGGTAGATACTCTCC 58.081 41.667 5.42 0.00 0.00 3.71
3078 3135 4.788925 TGGGTCCAGGAATAATGGTAAG 57.211 45.455 0.00 0.00 39.01 2.34
3357 3414 2.356673 GCTGCTGCAAACAAGGGC 60.357 61.111 11.11 0.00 39.41 5.19
3438 3495 0.467290 TGGAAGAGTTTGTGTGGGGC 60.467 55.000 0.00 0.00 0.00 5.80
3462 3519 5.393461 CCTGCAATTGAATGAAGGTAACCTC 60.393 44.000 10.34 0.00 40.78 3.85
3476 3534 7.447238 TGAAGGTAACCTCCTTGAAGTATTTTG 59.553 37.037 2.58 0.00 46.38 2.44
3481 3539 6.824305 ACCTCCTTGAAGTATTTTGTGATG 57.176 37.500 0.00 0.00 0.00 3.07
3511 3569 4.775058 ACAACTGTACAGAGCTGACTAG 57.225 45.455 29.30 9.54 0.00 2.57
3718 3783 2.229062 TGTAGAGGAGCAAGAAGTCACG 59.771 50.000 0.00 0.00 0.00 4.35
3946 4012 4.504461 CGAGTGGTAAGTAATCATCTGCAC 59.496 45.833 0.00 0.00 0.00 4.57
3970 4036 0.544357 TCCTACCCACCCTCACACTG 60.544 60.000 0.00 0.00 0.00 3.66
4015 4083 1.065854 AGTACTGAGGTGCATCTTGGC 60.066 52.381 0.00 0.00 0.00 4.52
4044 4117 6.304356 AGTATGATGCAACATTGGTTATCG 57.696 37.500 15.16 0.00 34.87 2.92
4086 4159 6.374333 ACCACTTGATATACGCATTTTTGACT 59.626 34.615 0.00 0.00 0.00 3.41
4120 4193 6.686630 TCCATGTGTATTTGTTTAGCCTTTG 58.313 36.000 0.00 0.00 0.00 2.77
4121 4194 6.491745 TCCATGTGTATTTGTTTAGCCTTTGA 59.508 34.615 0.00 0.00 0.00 2.69
4290 4369 7.871973 CAGAAGAAGTACCAGGATGATATGAAG 59.128 40.741 0.00 0.00 39.69 3.02
4425 4504 6.536582 CAGGGTATGTTCATGACTTACTTCTG 59.463 42.308 0.00 10.84 38.37 3.02
4476 4558 6.763135 CCTGTTGATGCTACTATGCTTTCTTA 59.237 38.462 0.00 0.00 0.00 2.10
4477 4559 7.042187 CCTGTTGATGCTACTATGCTTTCTTAG 60.042 40.741 0.00 0.00 0.00 2.18
4478 4560 7.331026 TGTTGATGCTACTATGCTTTCTTAGT 58.669 34.615 0.00 0.00 37.12 2.24
4497 4579 9.840427 TTCTTAGTCTTGACAAAACTTTCTTTG 57.160 29.630 0.00 0.00 41.24 2.77
4506 4588 6.425417 TGACAAAACTTTCTTTGGTTTGGTTC 59.575 34.615 8.73 0.27 39.00 3.62
4590 4677 5.215252 TGCTGGCTGTTAATCTAGGATAC 57.785 43.478 0.00 0.00 0.00 2.24
4598 4685 7.121611 GGCTGTTAATCTAGGATACCTACTCTC 59.878 44.444 0.00 0.00 34.61 3.20
4599 4686 7.886446 GCTGTTAATCTAGGATACCTACTCTCT 59.114 40.741 0.00 0.00 34.61 3.10
4606 4693 8.564364 TCTAGGATACCTACTCTCTAGTGAAA 57.436 38.462 0.00 0.00 35.18 2.69
4669 4756 3.164268 TGGATGAGGTTTGGGTGATTTG 58.836 45.455 0.00 0.00 0.00 2.32
4692 4782 7.872061 TGGATTTAGAGATTATAAGGGCTCA 57.128 36.000 12.52 1.09 0.00 4.26
4720 4810 5.523188 GCCACACTGATGATTTTTGTTTTGA 59.477 36.000 0.00 0.00 0.00 2.69
4809 4900 9.989869 CTACATATCAATCATCTCATCAAATGC 57.010 33.333 0.00 0.00 0.00 3.56
4813 4904 5.442391 TCAATCATCTCATCAAATGCCTCA 58.558 37.500 0.00 0.00 0.00 3.86
4841 4934 9.961265 CTGAATATTGCATGTTATCTGAAATGT 57.039 29.630 0.00 0.00 0.00 2.71
4843 4936 8.583810 AATATTGCATGTTATCTGAAATGTGC 57.416 30.769 0.00 0.00 0.00 4.57
4844 4937 4.374843 TGCATGTTATCTGAAATGTGCC 57.625 40.909 0.00 0.00 0.00 5.01
4885 4978 3.127030 GTGGCTAACTAACCTGCAATGTC 59.873 47.826 0.00 0.00 0.00 3.06
4888 4981 4.010349 GCTAACTAACCTGCAATGTCCTT 58.990 43.478 0.00 0.00 0.00 3.36
4920 5017 4.526970 TGTCTTCCTGTTTCTTTCTTGCT 58.473 39.130 0.00 0.00 0.00 3.91
4997 5094 4.704833 GCCAGCGTGGAGAAGGCA 62.705 66.667 8.04 0.00 44.59 4.75
5051 5148 6.046593 CGACAAAAAGGTAGGCTGACATATA 58.953 40.000 0.00 0.00 0.00 0.86
5060 5157 5.221461 GGTAGGCTGACATATAATATCCCCG 60.221 48.000 0.00 0.00 0.00 5.73
5071 5168 1.343069 ATATCCCCGCTCCTGTTCTC 58.657 55.000 0.00 0.00 0.00 2.87
5078 5175 1.683629 CCGCTCCTGTTCTCTACTCCT 60.684 57.143 0.00 0.00 0.00 3.69
5081 5178 3.361786 GCTCCTGTTCTCTACTCCTTCT 58.638 50.000 0.00 0.00 0.00 2.85
5090 5187 6.270000 TGTTCTCTACTCCTTCTGATCCAAAA 59.730 38.462 0.00 0.00 0.00 2.44
5095 5192 7.275920 TCTACTCCTTCTGATCCAAAATAAGC 58.724 38.462 0.00 0.00 0.00 3.09
5105 5202 2.927477 TCCAAAATAAGCGTCAGTAGCG 59.073 45.455 0.00 0.00 40.04 4.26
5108 5205 4.323751 CAAAATAAGCGTCAGTAGCGTTC 58.676 43.478 0.00 0.00 40.04 3.95
5145 5247 7.039313 ACTAAAAACACTTCCTTTGGATCAC 57.961 36.000 0.00 0.00 0.00 3.06
5148 5250 2.508526 ACACTTCCTTTGGATCACAGC 58.491 47.619 0.00 0.00 0.00 4.40
5152 5254 0.391661 TCCTTTGGATCACAGCGAGC 60.392 55.000 0.00 0.00 0.00 5.03
5167 5269 2.652662 CGAGCCGCATTTACTGAATC 57.347 50.000 0.00 0.00 0.00 2.52
5171 5273 1.663695 CCGCATTTACTGAATCGGGT 58.336 50.000 0.00 0.00 36.07 5.28
5174 5276 4.562082 CCGCATTTACTGAATCGGGTATA 58.438 43.478 0.00 0.00 36.07 1.47
5281 5423 2.550855 CCTAAGAACTGAGGTTGCAGCA 60.551 50.000 2.05 0.00 39.51 4.41
5308 5450 3.423154 GAACAGGAACCAGCGGCG 61.423 66.667 0.51 0.51 0.00 6.46
5360 5502 2.979814 TTATGAGTCACCGACATGGG 57.020 50.000 0.00 0.00 44.64 4.00
5412 5554 2.362503 ACCCGTCCTCAGATGCGA 60.363 61.111 0.00 0.00 0.00 5.10
5419 5571 3.490933 CCGTCCTCAGATGCGATAAGAAA 60.491 47.826 0.00 0.00 0.00 2.52
5461 5613 4.098654 AACCGATTGTTTTGATGGTGACAA 59.901 37.500 0.00 0.00 37.76 3.18
5538 5694 0.798776 GCACGCTCTACAAGTTGCAT 59.201 50.000 1.81 0.00 36.60 3.96
5626 5784 6.683974 AGGATTTATTTTCCATGACAGACG 57.316 37.500 0.00 0.00 35.59 4.18
5627 5785 6.180472 AGGATTTATTTTCCATGACAGACGT 58.820 36.000 0.00 0.00 35.59 4.34
5634 5792 5.605564 TTTCCATGACAGACGTTACAATG 57.394 39.130 0.00 0.00 0.00 2.82
5640 5798 2.742053 GACAGACGTTACAATGGCATGT 59.258 45.455 0.00 4.26 37.32 3.21
5641 5799 3.930229 GACAGACGTTACAATGGCATGTA 59.070 43.478 0.00 3.22 34.75 2.29
5642 5800 4.513442 ACAGACGTTACAATGGCATGTAT 58.487 39.130 0.00 0.00 35.80 2.29
5643 5801 4.570772 ACAGACGTTACAATGGCATGTATC 59.429 41.667 0.00 4.73 35.80 2.24
5644 5802 4.570369 CAGACGTTACAATGGCATGTATCA 59.430 41.667 0.00 0.00 35.80 2.15
5645 5803 5.237127 CAGACGTTACAATGGCATGTATCAT 59.763 40.000 0.00 0.00 35.80 2.45
5646 5804 5.822519 AGACGTTACAATGGCATGTATCATT 59.177 36.000 0.00 0.11 35.80 2.57
5647 5805 6.318648 AGACGTTACAATGGCATGTATCATTT 59.681 34.615 0.00 0.00 35.80 2.32
5648 5806 6.862209 ACGTTACAATGGCATGTATCATTTT 58.138 32.000 0.00 0.00 35.80 1.82
5649 5807 7.319646 ACGTTACAATGGCATGTATCATTTTT 58.680 30.769 0.00 0.00 35.80 1.94
5665 5823 1.931635 TTTTTGATACAGGGGGTGGC 58.068 50.000 0.00 0.00 0.00 5.01
5666 5824 0.322997 TTTTGATACAGGGGGTGGCG 60.323 55.000 0.00 0.00 0.00 5.69
5688 5846 4.349871 GCACACGACACGCGGTTC 62.350 66.667 12.47 4.93 46.49 3.62
5759 5920 1.580845 GATTTCTGCACGGTGCTGCT 61.581 55.000 30.81 18.46 45.31 4.24
5904 6065 4.893601 TTTCCGTGCCACGTCGCA 62.894 61.111 16.99 2.90 40.58 5.10
5980 6266 2.809174 CATGACGACGGCGAGCAA 60.809 61.111 22.49 0.00 41.64 3.91
6098 6384 0.475632 TGGGATGGTGAGGGACAAGT 60.476 55.000 0.00 0.00 0.00 3.16
6143 6429 1.885163 CTTCCCCAACTACGACCGCT 61.885 60.000 0.00 0.00 0.00 5.52
6181 6467 2.496341 CTCTGGGCGATGCTCGAA 59.504 61.111 9.32 0.00 43.74 3.71
6235 6521 1.375326 GAAGGTGTTCCGCTCCCTT 59.625 57.895 0.00 0.00 39.96 3.95
6246 6532 4.082523 CTCCCTTCGCTTCCGCCA 62.083 66.667 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.680937 CAGAGCAGAGAGAGCTTTCTTTG 59.319 47.826 17.69 17.69 43.58 2.77
1 2 3.306919 CCAGAGCAGAGAGAGCTTTCTTT 60.307 47.826 8.38 0.00 43.58 2.52
2 3 2.234414 CCAGAGCAGAGAGAGCTTTCTT 59.766 50.000 8.38 0.00 43.58 2.52
3 4 1.826720 CCAGAGCAGAGAGAGCTTTCT 59.173 52.381 6.45 6.45 43.58 2.52
5 6 0.903942 CCCAGAGCAGAGAGAGCTTT 59.096 55.000 0.00 0.00 43.58 3.51
6 7 0.252193 ACCCAGAGCAGAGAGAGCTT 60.252 55.000 0.00 0.00 43.58 3.74
7 8 0.252193 AACCCAGAGCAGAGAGAGCT 60.252 55.000 0.00 0.00 46.82 4.09
8 9 1.136110 GTAACCCAGAGCAGAGAGAGC 59.864 57.143 0.00 0.00 0.00 4.09
10 11 1.464734 CGTAACCCAGAGCAGAGAGA 58.535 55.000 0.00 0.00 0.00 3.10
11 12 0.179124 GCGTAACCCAGAGCAGAGAG 60.179 60.000 0.00 0.00 0.00 3.20
12 13 1.605058 GGCGTAACCCAGAGCAGAGA 61.605 60.000 0.00 0.00 0.00 3.10
379 416 1.098712 TTAATGGGCCGCACGAATCC 61.099 55.000 0.00 0.00 0.00 3.01
391 428 3.053619 AGCAAGACCTAGGGTTTAATGGG 60.054 47.826 14.81 0.00 35.25 4.00
465 506 1.051008 ATCTCACAGTCAGGTGCACA 58.949 50.000 20.43 0.00 38.66 4.57
469 510 1.620323 TCCACATCTCACAGTCAGGTG 59.380 52.381 0.00 0.00 40.16 4.00
540 581 6.990341 TCACACATCAATTACATTCTCAGG 57.010 37.500 0.00 0.00 0.00 3.86
551 592 8.686334 GGAGTACCAATTATTCACACATCAATT 58.314 33.333 0.00 0.00 35.97 2.32
570 611 0.186873 TATGGGACGGAGGGAGTACC 59.813 60.000 0.00 0.00 42.94 3.34
571 612 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
572 613 2.090943 ACATTATGGGACGGAGGGAGTA 60.091 50.000 0.00 0.00 0.00 2.59
573 614 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
574 615 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
575 616 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
576 617 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
577 618 3.641906 ACTCTTACATTATGGGACGGAGG 59.358 47.826 0.00 0.00 0.00 4.30
578 619 4.939052 ACTCTTACATTATGGGACGGAG 57.061 45.455 0.00 0.25 0.00 4.63
579 620 5.452255 ACTACTCTTACATTATGGGACGGA 58.548 41.667 0.00 0.00 0.00 4.69
580 621 5.786264 ACTACTCTTACATTATGGGACGG 57.214 43.478 0.00 0.00 0.00 4.79
581 622 6.475727 CACAACTACTCTTACATTATGGGACG 59.524 42.308 0.00 0.00 0.00 4.79
582 623 7.328737 ACACAACTACTCTTACATTATGGGAC 58.671 38.462 0.00 0.00 0.00 4.46
583 624 7.490657 ACACAACTACTCTTACATTATGGGA 57.509 36.000 0.00 0.00 0.00 4.37
584 625 7.606456 ACAACACAACTACTCTTACATTATGGG 59.394 37.037 0.00 0.00 0.00 4.00
585 626 8.547967 ACAACACAACTACTCTTACATTATGG 57.452 34.615 0.00 0.00 0.00 2.74
586 627 8.656849 GGACAACACAACTACTCTTACATTATG 58.343 37.037 0.00 0.00 0.00 1.90
587 628 8.372459 TGGACAACACAACTACTCTTACATTAT 58.628 33.333 0.00 0.00 0.00 1.28
588 629 7.728148 TGGACAACACAACTACTCTTACATTA 58.272 34.615 0.00 0.00 0.00 1.90
589 630 6.588204 TGGACAACACAACTACTCTTACATT 58.412 36.000 0.00 0.00 0.00 2.71
590 631 6.169557 TGGACAACACAACTACTCTTACAT 57.830 37.500 0.00 0.00 0.00 2.29
591 632 5.601583 TGGACAACACAACTACTCTTACA 57.398 39.130 0.00 0.00 0.00 2.41
592 633 5.408604 CCATGGACAACACAACTACTCTTAC 59.591 44.000 5.56 0.00 0.00 2.34
593 634 5.512404 CCCATGGACAACACAACTACTCTTA 60.512 44.000 15.22 0.00 0.00 2.10
594 635 4.389374 CCATGGACAACACAACTACTCTT 58.611 43.478 5.56 0.00 0.00 2.85
595 636 3.244561 CCCATGGACAACACAACTACTCT 60.245 47.826 15.22 0.00 0.00 3.24
596 637 3.074412 CCCATGGACAACACAACTACTC 58.926 50.000 15.22 0.00 0.00 2.59
597 638 2.814097 GCCCATGGACAACACAACTACT 60.814 50.000 15.22 0.00 0.00 2.57
604 645 1.252904 ATGCAGCCCATGGACAACAC 61.253 55.000 15.22 0.00 31.48 3.32
673 717 5.183904 ACTCAAACCTGCAATGAAAGGTATC 59.816 40.000 8.23 0.00 46.29 2.24
677 721 3.571401 AGACTCAAACCTGCAATGAAAGG 59.429 43.478 1.44 1.44 39.65 3.11
678 722 4.843220 AGACTCAAACCTGCAATGAAAG 57.157 40.909 0.00 0.00 0.00 2.62
679 723 5.239306 CACTAGACTCAAACCTGCAATGAAA 59.761 40.000 0.00 0.00 0.00 2.69
680 724 4.756642 CACTAGACTCAAACCTGCAATGAA 59.243 41.667 0.00 0.00 0.00 2.57
707 751 3.181477 TGTCCTCCAAACAAATGCACTTG 60.181 43.478 6.30 6.30 0.00 3.16
795 839 5.648092 CACCCCTCTAATTAAACAGGTTCTG 59.352 44.000 4.75 0.00 37.52 3.02
838 883 6.052360 TGCAAAGGATGTTTTAAGTTTTCCC 58.948 36.000 0.00 0.00 0.00 3.97
840 885 8.825745 TGATTGCAAAGGATGTTTTAAGTTTTC 58.174 29.630 1.71 0.00 0.00 2.29
857 902 3.797451 TGCACTTCAGTTGATTGCAAA 57.203 38.095 1.71 0.00 39.20 3.68
880 925 4.269183 TCAAATTCGGTGGCATTGTATCT 58.731 39.130 0.00 0.00 0.00 1.98
1090 1143 2.511452 CCCTCCTGTGCCTATCCCG 61.511 68.421 0.00 0.00 0.00 5.14
1098 1151 1.621672 CCTTCTCCTCCCTCCTGTGC 61.622 65.000 0.00 0.00 0.00 4.57
1230 1283 3.096092 GCTATCCCTATCTCTGTCCCTG 58.904 54.545 0.00 0.00 0.00 4.45
1242 1295 1.139654 CTGTGCTTGCTGCTATCCCTA 59.860 52.381 0.00 0.00 43.37 3.53
1305 1358 1.279025 CCCTTTCCCGATCCTTCCCA 61.279 60.000 0.00 0.00 0.00 4.37
1587 1640 5.305585 AGAAAAGGCTAGTGTGAATCGAAA 58.694 37.500 0.00 0.00 0.00 3.46
1595 1648 4.380531 TGACTGAAGAAAAGGCTAGTGTG 58.619 43.478 0.00 0.00 0.00 3.82
1596 1649 4.689612 TGACTGAAGAAAAGGCTAGTGT 57.310 40.909 0.00 0.00 0.00 3.55
1618 1671 7.889469 AGAGATTTAACAGTGTGCAAATTCAT 58.111 30.769 14.18 6.92 0.00 2.57
1897 1951 4.989279 ATAAAATGGTGTCATGCTGGAC 57.011 40.909 1.93 1.93 38.29 4.02
1993 2047 2.375174 ACCTCCACCAAGTTTATCAGCA 59.625 45.455 0.00 0.00 0.00 4.41
2188 2242 4.326826 CTTCTATGACTTTGTCAAGCCCA 58.673 43.478 4.46 0.00 45.96 5.36
2296 2350 6.920695 AGGTTAGGGGGAACAAGTAATAAT 57.079 37.500 0.00 0.00 0.00 1.28
2312 2366 2.095718 GCGCAAGTCAGAAAAGGTTAGG 60.096 50.000 0.30 0.00 41.68 2.69
2315 2369 1.388547 TGCGCAAGTCAGAAAAGGTT 58.611 45.000 8.16 0.00 41.68 3.50
2374 2428 1.005340 GCTTCTGCTCACCAATCTCG 58.995 55.000 0.00 0.00 36.03 4.04
2421 2475 7.884877 ACTTGTCATCATATGTTCCTTTCTTCA 59.115 33.333 1.90 0.00 0.00 3.02
2500 2555 5.042463 TGAACCTACCAACATGTTCAAGA 57.958 39.130 8.48 0.00 42.81 3.02
2533 2588 6.150140 GTGAGAGCATAGGTTTCTTTGACATT 59.850 38.462 0.00 0.00 0.00 2.71
2572 2627 5.008415 CAGCATGTTTACCTCATCTTCCATC 59.992 44.000 0.00 0.00 0.00 3.51
3078 3135 1.435515 CTCCCTAGCAGACTGTCGC 59.564 63.158 13.97 13.97 0.00 5.19
3357 3414 1.309950 CAGCATCTGCATCTCCTTGG 58.690 55.000 4.79 0.00 45.16 3.61
3438 3495 4.463891 AGGTTACCTTCATTCAATTGCAGG 59.536 41.667 0.00 3.57 36.27 4.85
3462 3519 9.480053 ACAAATTCATCACAAAATACTTCAAGG 57.520 29.630 0.00 0.00 0.00 3.61
3476 3534 8.556194 TCTGTACAGTTGTTACAAATTCATCAC 58.444 33.333 21.99 0.00 0.00 3.06
3481 3539 7.042051 TCAGCTCTGTACAGTTGTTACAAATTC 60.042 37.037 21.99 2.07 0.00 2.17
3494 3552 5.124617 TGATTCACTAGTCAGCTCTGTACAG 59.875 44.000 17.17 17.17 0.00 2.74
3718 3783 1.750399 ATGCACAACCTCATCCGGC 60.750 57.895 0.00 0.00 0.00 6.13
3811 3876 0.251742 TGGTTCTGCCTCCCCAATTG 60.252 55.000 0.00 0.00 38.35 2.32
3946 4012 2.683933 AGGGTGGGTAGGACAGCG 60.684 66.667 0.00 0.00 37.22 5.18
3970 4036 9.936759 CTATAAGATTTCATAGAAAGGAGACCC 57.063 37.037 0.00 0.00 0.00 4.46
4015 4083 4.260743 CCAATGTTGCATCATACTACCACG 60.261 45.833 10.60 0.00 0.00 4.94
4086 4159 7.479352 ACAAATACACATGGAAAATGATGGA 57.521 32.000 0.00 0.00 0.00 3.41
4120 4193 4.180057 TGTTTTGTGGCACATGTTCTTTC 58.820 39.130 22.73 7.05 44.52 2.62
4121 4194 4.199432 TGTTTTGTGGCACATGTTCTTT 57.801 36.364 22.73 0.00 44.52 2.52
4290 4369 6.032717 GTCAGAAGATTTCATTTGCTTAGCC 58.967 40.000 0.29 0.00 0.00 3.93
4425 4504 4.882671 ACAAACATGGACTATGCGAATC 57.117 40.909 0.00 0.00 40.59 2.52
4476 4558 6.590234 ACCAAAGAAAGTTTTGTCAAGACT 57.410 33.333 2.96 2.96 36.54 3.24
4477 4559 7.360017 CCAAACCAAAGAAAGTTTTGTCAAGAC 60.360 37.037 0.00 0.00 36.54 3.01
4478 4560 6.648725 CCAAACCAAAGAAAGTTTTGTCAAGA 59.351 34.615 0.00 0.00 36.54 3.02
4497 4579 6.981722 AGTCATGATTTAAGTGAACCAAACC 58.018 36.000 0.00 0.00 0.00 3.27
4550 4637 7.806487 CAGCCAGCAACAATATATTCATTACTG 59.194 37.037 10.08 10.08 0.00 2.74
4551 4638 7.503566 ACAGCCAGCAACAATATATTCATTACT 59.496 33.333 0.00 0.00 0.00 2.24
4552 4639 7.651808 ACAGCCAGCAACAATATATTCATTAC 58.348 34.615 0.00 0.00 0.00 1.89
4553 4640 7.822161 ACAGCCAGCAACAATATATTCATTA 57.178 32.000 0.00 0.00 0.00 1.90
4555 4642 6.720112 AACAGCCAGCAACAATATATTCAT 57.280 33.333 0.00 0.00 0.00 2.57
4556 4643 7.637631 TTAACAGCCAGCAACAATATATTCA 57.362 32.000 0.00 0.00 0.00 2.57
4557 4644 8.571336 AGATTAACAGCCAGCAACAATATATTC 58.429 33.333 0.00 0.00 0.00 1.75
4606 4693 1.542547 CGTAGCACCCCAAAGTGAGTT 60.543 52.381 0.00 0.00 40.34 3.01
4653 4740 4.890158 AAATCCAAATCACCCAAACCTC 57.110 40.909 0.00 0.00 0.00 3.85
4669 4756 7.826744 CCTTGAGCCCTTATAATCTCTAAATCC 59.173 40.741 9.49 0.00 0.00 3.01
4692 4782 2.610438 AAATCATCAGTGTGGCCCTT 57.390 45.000 0.00 0.00 0.00 3.95
4720 4810 7.980662 CAGTTATTCACATCTCAATCAGAGTCT 59.019 37.037 0.00 0.00 44.98 3.24
4757 4847 4.514401 ACATTAGAGTCGTTTGGGAATCC 58.486 43.478 0.00 0.00 31.69 3.01
4762 4852 4.315803 AGTTGACATTAGAGTCGTTTGGG 58.684 43.478 0.00 0.00 41.41 4.12
4809 4900 8.451748 CAGATAACATGCAATATTCAGATGAGG 58.548 37.037 0.00 0.00 0.00 3.86
4841 4934 1.675310 CATTCAAGCAGGACCGGCA 60.675 57.895 19.24 0.00 0.00 5.69
4843 4936 0.322456 TTCCATTCAAGCAGGACCGG 60.322 55.000 0.00 0.00 0.00 5.28
4844 4937 1.089920 CTTCCATTCAAGCAGGACCG 58.910 55.000 0.00 0.00 0.00 4.79
4885 4978 5.859495 ACAGGAAGACAGAAAACTAGAAGG 58.141 41.667 0.00 0.00 0.00 3.46
4888 4981 7.125792 AGAAACAGGAAGACAGAAAACTAGA 57.874 36.000 0.00 0.00 0.00 2.43
4920 5017 4.136796 CAAGAACTTGATCAACCACCTCA 58.863 43.478 3.38 0.00 42.93 3.86
4997 5094 2.052690 CGTCAGACTCCCGGGATGT 61.053 63.158 27.07 23.51 0.00 3.06
5051 5148 1.694696 GAGAACAGGAGCGGGGATATT 59.305 52.381 0.00 0.00 0.00 1.28
5056 5153 0.684805 AGTAGAGAACAGGAGCGGGG 60.685 60.000 0.00 0.00 0.00 5.73
5060 5157 3.130340 CAGAAGGAGTAGAGAACAGGAGC 59.870 52.174 0.00 0.00 0.00 4.70
5071 5168 6.201806 CGCTTATTTTGGATCAGAAGGAGTAG 59.798 42.308 0.00 0.00 0.00 2.57
5078 5175 5.245531 ACTGACGCTTATTTTGGATCAGAA 58.754 37.500 5.41 0.00 36.45 3.02
5081 5178 4.570772 GCTACTGACGCTTATTTTGGATCA 59.429 41.667 0.00 0.00 0.00 2.92
5090 5187 1.131883 ACGAACGCTACTGACGCTTAT 59.868 47.619 0.00 0.00 0.00 1.73
5095 5192 1.401530 TTGAACGAACGCTACTGACG 58.598 50.000 0.00 0.00 0.00 4.35
5128 5225 2.508526 GCTGTGATCCAAAGGAAGTGT 58.491 47.619 0.00 0.00 34.34 3.55
5132 5229 1.945819 GCTCGCTGTGATCCAAAGGAA 60.946 52.381 0.00 0.00 34.34 3.36
5133 5230 0.391661 GCTCGCTGTGATCCAAAGGA 60.392 55.000 0.00 0.00 35.55 3.36
5135 5232 1.699656 CGGCTCGCTGTGATCCAAAG 61.700 60.000 11.24 0.00 32.09 2.77
5148 5250 1.071239 CGATTCAGTAAATGCGGCTCG 60.071 52.381 0.00 0.00 0.00 5.03
5152 5254 1.663695 ACCCGATTCAGTAAATGCGG 58.336 50.000 0.00 0.00 37.58 5.69
5153 5255 7.821595 TTATATACCCGATTCAGTAAATGCG 57.178 36.000 0.00 0.00 0.00 4.73
5167 5269 7.331934 CACCTGATGAAGAACATTATATACCCG 59.668 40.741 0.00 0.00 39.56 5.28
5171 5273 8.097038 GCTCCACCTGATGAAGAACATTATATA 58.903 37.037 0.00 0.00 39.56 0.86
5174 5276 5.128919 GCTCCACCTGATGAAGAACATTAT 58.871 41.667 0.00 0.00 39.56 1.28
5250 5392 4.505742 CCTCAGTTCTTAGGCTTCTTTGGT 60.506 45.833 0.00 0.00 0.00 3.67
5281 5423 1.694696 GGTTCCTGTTCACTCCACTCT 59.305 52.381 0.00 0.00 0.00 3.24
5308 5450 2.586258 TGCAGATTCGCTAGAGAACC 57.414 50.000 11.34 1.09 32.39 3.62
5310 5452 4.662468 AGATTGCAGATTCGCTAGAGAA 57.338 40.909 11.50 11.50 34.31 2.87
5412 5554 7.539034 AGGGTGCAAATTTACAGTTTCTTAT 57.461 32.000 0.00 0.00 0.00 1.73
5419 5571 4.022676 CGGTTTAGGGTGCAAATTTACAGT 60.023 41.667 0.00 0.00 0.00 3.55
5461 5613 3.132824 TCTCTGTGTGTGTGTGTCAAGAT 59.867 43.478 0.00 0.00 0.00 2.40
5610 5768 6.349280 CCATTGTAACGTCTGTCATGGAAAAT 60.349 38.462 7.60 0.00 0.00 1.82
5646 5804 1.888826 CGCCACCCCCTGTATCAAAAA 60.889 52.381 0.00 0.00 0.00 1.94
5647 5805 0.322997 CGCCACCCCCTGTATCAAAA 60.323 55.000 0.00 0.00 0.00 2.44
5648 5806 1.301623 CGCCACCCCCTGTATCAAA 59.698 57.895 0.00 0.00 0.00 2.69
5649 5807 2.675242 CCGCCACCCCCTGTATCAA 61.675 63.158 0.00 0.00 0.00 2.57
5650 5808 2.907482 ATCCGCCACCCCCTGTATCA 62.907 60.000 0.00 0.00 0.00 2.15
5651 5809 2.147387 ATCCGCCACCCCCTGTATC 61.147 63.158 0.00 0.00 0.00 2.24
5652 5810 2.039831 ATCCGCCACCCCCTGTAT 60.040 61.111 0.00 0.00 0.00 2.29
5653 5811 3.087253 CATCCGCCACCCCCTGTA 61.087 66.667 0.00 0.00 0.00 2.74
5664 5822 3.788766 GTGTCGTGTGCCATCCGC 61.789 66.667 0.00 0.00 38.31 5.54
5665 5823 3.478394 CGTGTCGTGTGCCATCCG 61.478 66.667 0.00 0.00 0.00 4.18
5666 5824 3.788766 GCGTGTCGTGTGCCATCC 61.789 66.667 0.00 0.00 0.00 3.51
5904 6065 4.314440 TCAGCCGCCGCAAGTCTT 62.314 61.111 0.00 0.00 37.52 3.01
5980 6266 2.046892 GACAGCGCCCACATCTGT 60.047 61.111 2.29 0.00 43.06 3.41
6098 6384 3.849951 GATCTCCTCGCCCCGCAA 61.850 66.667 0.00 0.00 0.00 4.85
6181 6467 2.983433 CGGAATCAGCGATTCTGCT 58.017 52.632 21.93 0.00 44.79 4.24


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

AutoCloner maintained by Alex Coulton.