Multiple sequence alignment - TraesCS2A01G440700

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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 TraesCS2A01G440700 chr2A 100.000 3228 0 0 1 3228 691175530 691172303 0.000000e+00 5962.0
1 TraesCS2A01G440700 chr2A 86.325 819 82 17 1593 2398 691143527 691142726 0.000000e+00 865.0
2 TraesCS2A01G440700 chr2A 87.810 525 44 12 1664 2177 691121745 691121230 5.960000e-167 597.0
3 TraesCS2A01G440700 chr2A 83.673 245 31 9 1206 1444 691143767 691143526 4.190000e-54 222.0
4 TraesCS2A01G440700 chr2A 81.746 252 38 7 1173 1418 691122142 691121893 1.520000e-48 204.0
5 TraesCS2A01G440700 chr2A 88.608 158 16 2 1437 1593 549290431 549290275 1.180000e-44 191.0
6 TraesCS2A01G440700 chr2A 89.394 66 7 0 605 670 23482664 23482729 2.060000e-12 84.2
7 TraesCS2A01G440700 chr2D 85.374 2810 227 83 26 2761 547770420 547773119 0.000000e+00 2743.0
8 TraesCS2A01G440700 chr2D 80.511 626 91 27 73 677 44472618 44472003 4.910000e-123 451.0
9 TraesCS2A01G440700 chr2D 79.556 675 84 27 52 677 611216098 611216767 1.780000e-117 433.0
10 TraesCS2A01G440700 chr2D 86.667 285 33 2 2007 2287 547777706 547777989 8.700000e-81 311.0
11 TraesCS2A01G440700 chr2D 82.659 346 49 5 1983 2322 547954426 547954766 2.440000e-76 296.0
12 TraesCS2A01G440700 chr2D 82.081 346 50 11 338 677 537711891 537711552 5.270000e-73 285.0
13 TraesCS2A01G440700 chr2B 87.073 820 76 18 1593 2398 654529157 654529960 0.000000e+00 900.0
14 TraesCS2A01G440700 chr2B 88.411 768 53 18 1611 2345 654374444 654375208 0.000000e+00 893.0
15 TraesCS2A01G440700 chr2B 88.951 715 35 17 730 1428 654373759 654374445 0.000000e+00 843.0
16 TraesCS2A01G440700 chr2B 90.404 396 19 4 2383 2760 654375209 654375603 1.340000e-138 503.0
17 TraesCS2A01G440700 chr2B 85.645 411 53 2 1994 2398 654718316 654718726 8.280000e-116 427.0
18 TraesCS2A01G440700 chr2B 85.401 411 54 2 1994 2398 654646239 654646649 3.850000e-114 422.0
19 TraesCS2A01G440700 chr2B 85.158 411 55 2 1994 2398 654696299 654696709 1.790000e-112 416.0
20 TraesCS2A01G440700 chr2B 84.672 411 57 2 1994 2398 654677516 654677926 3.880000e-109 405.0
21 TraesCS2A01G440700 chr2B 85.564 381 49 2 1994 2368 654667429 654667809 8.390000e-106 394.0
22 TraesCS2A01G440700 chr2B 93.487 261 16 1 2968 3228 654375603 654375862 1.400000e-103 387.0
23 TraesCS2A01G440700 chr2B 82.801 407 51 11 1593 1990 654644037 654644433 2.380000e-91 346.0
24 TraesCS2A01G440700 chr2B 82.801 407 51 12 1593 1990 654665322 654665718 2.380000e-91 346.0
25 TraesCS2A01G440700 chr2B 82.801 407 51 11 1593 1990 654675319 654675715 2.380000e-91 346.0
26 TraesCS2A01G440700 chr2B 82.801 407 51 11 1593 1990 654694105 654694501 2.380000e-91 346.0
27 TraesCS2A01G440700 chr2B 81.572 407 56 14 1593 1990 654716090 654716486 5.200000e-83 318.0
28 TraesCS2A01G440700 chr2B 82.671 277 35 12 1176 1444 654528887 654529158 1.940000e-57 233.0
29 TraesCS2A01G440700 chr2B 82.014 278 41 9 1173 1444 654693832 654694106 9.010000e-56 228.0
30 TraesCS2A01G440700 chr2B 82.014 278 41 9 1173 1444 654715817 654716091 9.010000e-56 228.0
31 TraesCS2A01G440700 chr3D 81.606 685 88 18 26 676 611379195 611379875 1.700000e-147 532.0
32 TraesCS2A01G440700 chr3D 78.550 676 98 21 43 676 35357992 35357322 5.020000e-108 401.0
33 TraesCS2A01G440700 chr3D 98.333 120 2 0 2762 2881 24168152 24168033 9.070000e-51 211.0
34 TraesCS2A01G440700 chr3D 87.898 157 17 2 1443 1598 322435444 322435289 1.980000e-42 183.0
35 TraesCS2A01G440700 chr3D 76.821 302 45 16 363 657 275129561 275129278 2.600000e-31 147.0
36 TraesCS2A01G440700 chr7D 81.465 669 89 20 43 681 119561618 119560955 1.720000e-142 516.0
37 TraesCS2A01G440700 chr7D 81.865 579 80 14 35 593 65760907 65761480 6.310000e-127 464.0
38 TraesCS2A01G440700 chr7D 81.944 576 76 15 40 593 25329141 25329710 2.270000e-126 462.0
39 TraesCS2A01G440700 chr7D 89.542 153 15 1 1443 1594 34756866 34757018 3.290000e-45 193.0
40 TraesCS2A01G440700 chr6D 81.268 678 85 23 29 677 59176357 59177021 7.990000e-141 510.0
41 TraesCS2A01G440700 chr6D 88.535 157 17 1 1443 1598 410398279 410398435 4.250000e-44 189.0
42 TraesCS2A01G440700 chr1D 81.664 589 77 17 29 591 473336972 473336389 8.160000e-126 460.0
43 TraesCS2A01G440700 chr7A 79.825 684 93 27 19 670 8903976 8904646 1.060000e-124 457.0
44 TraesCS2A01G440700 chr7A 77.355 605 105 27 2 590 134518906 134518318 2.400000e-86 329.0
45 TraesCS2A01G440700 chr7A 97.826 92 2 0 2879 2970 537836976 537836885 3.330000e-35 159.0
46 TraesCS2A01G440700 chr1B 78.190 674 91 35 29 682 676186315 676186952 2.350000e-101 379.0
47 TraesCS2A01G440700 chr5D 84.680 359 31 10 340 679 493832186 493832539 1.430000e-88 337.0
48 TraesCS2A01G440700 chr5D 99.167 120 0 1 2762 2881 503214559 503214441 7.010000e-52 215.0
49 TraesCS2A01G440700 chr5D 98.333 120 1 1 2762 2881 560881153 560881035 3.260000e-50 209.0
50 TraesCS2A01G440700 chr5D 97.849 93 2 0 2878 2970 6248830 6248738 9.270000e-36 161.0
51 TraesCS2A01G440700 chr4A 98.361 122 2 0 2760 2881 448772137 448772258 7.010000e-52 215.0
52 TraesCS2A01G440700 chr3B 99.167 120 0 1 2762 2881 201523351 201523233 7.010000e-52 215.0
53 TraesCS2A01G440700 chr3B 86.905 168 18 4 1433 1598 396272041 396271876 5.500000e-43 185.0
54 TraesCS2A01G440700 chrUn 98.333 120 2 0 2762 2881 93415660 93415779 9.070000e-51 211.0
55 TraesCS2A01G440700 chrUn 98.333 120 1 1 2762 2881 93413292 93413410 3.260000e-50 209.0
56 TraesCS2A01G440700 chrUn 98.333 120 1 1 2762 2881 425406491 425406609 3.260000e-50 209.0
57 TraesCS2A01G440700 chrUn 97.826 92 2 0 2879 2970 379173574 379173483 3.330000e-35 159.0
58 TraesCS2A01G440700 chrUn 97.826 92 2 0 2879 2970 433229814 433229723 3.330000e-35 159.0
59 TraesCS2A01G440700 chr7B 97.500 120 3 0 2762 2881 559141663 559141544 4.220000e-49 206.0
60 TraesCS2A01G440700 chr7B 88.387 155 17 1 1442 1595 505937467 505937313 5.500000e-43 185.0
61 TraesCS2A01G440700 chr7B 98.876 89 1 0 2879 2967 622426376 622426464 3.330000e-35 159.0
62 TraesCS2A01G440700 chr1A 89.308 159 15 2 1441 1597 155857861 155857703 7.060000e-47 198.0
63 TraesCS2A01G440700 chr1A 98.876 89 1 0 2879 2967 554486472 554486560 3.330000e-35 159.0
64 TraesCS2A01G440700 chr4B 90.000 150 14 1 1446 1594 146469365 146469216 3.290000e-45 193.0
65 TraesCS2A01G440700 chr4D 88.961 154 15 2 1443 1594 74079504 74079351 4.250000e-44 189.0
66 TraesCS2A01G440700 chr4D 98.876 89 1 0 2879 2967 270704001 270704089 3.330000e-35 159.0
67 TraesCS2A01G440700 chr4D 98.876 89 1 0 2879 2967 270704514 270704602 3.330000e-35 159.0
68 TraesCS2A01G440700 chr4D 98.876 89 1 0 2879 2967 270705033 270705121 3.330000e-35 159.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G440700 chr2A 691172303 691175530 3227 True 5962.000000 5962 100.000000 1 3228 1 chr2A.!!$R2 3227
1 TraesCS2A01G440700 chr2A 691142726 691143767 1041 True 543.500000 865 84.999000 1206 2398 2 chr2A.!!$R4 1192
2 TraesCS2A01G440700 chr2A 691121230 691122142 912 True 400.500000 597 84.778000 1173 2177 2 chr2A.!!$R3 1004
3 TraesCS2A01G440700 chr2D 547770420 547773119 2699 False 2743.000000 2743 85.374000 26 2761 1 chr2D.!!$F1 2735
4 TraesCS2A01G440700 chr2D 44472003 44472618 615 True 451.000000 451 80.511000 73 677 1 chr2D.!!$R1 604
5 TraesCS2A01G440700 chr2D 611216098 611216767 669 False 433.000000 433 79.556000 52 677 1 chr2D.!!$F4 625
6 TraesCS2A01G440700 chr2B 654373759 654375862 2103 False 656.500000 893 90.313250 730 3228 4 chr2B.!!$F1 2498
7 TraesCS2A01G440700 chr2B 654528887 654529960 1073 False 566.500000 900 84.872000 1176 2398 2 chr2B.!!$F2 1222
8 TraesCS2A01G440700 chr2B 654644037 654646649 2612 False 384.000000 422 84.101000 1593 2398 2 chr2B.!!$F3 805
9 TraesCS2A01G440700 chr2B 654675319 654677926 2607 False 375.500000 405 83.736500 1593 2398 2 chr2B.!!$F5 805
10 TraesCS2A01G440700 chr2B 654665322 654667809 2487 False 370.000000 394 84.182500 1593 2368 2 chr2B.!!$F4 775
11 TraesCS2A01G440700 chr2B 654693832 654696709 2877 False 330.000000 416 83.324333 1173 2398 3 chr2B.!!$F6 1225
12 TraesCS2A01G440700 chr2B 654715817 654718726 2909 False 324.333333 427 83.077000 1173 2398 3 chr2B.!!$F7 1225
13 TraesCS2A01G440700 chr3D 611379195 611379875 680 False 532.000000 532 81.606000 26 676 1 chr3D.!!$F1 650
14 TraesCS2A01G440700 chr3D 35357322 35357992 670 True 401.000000 401 78.550000 43 676 1 chr3D.!!$R2 633
15 TraesCS2A01G440700 chr7D 119560955 119561618 663 True 516.000000 516 81.465000 43 681 1 chr7D.!!$R1 638
16 TraesCS2A01G440700 chr7D 65760907 65761480 573 False 464.000000 464 81.865000 35 593 1 chr7D.!!$F3 558
17 TraesCS2A01G440700 chr7D 25329141 25329710 569 False 462.000000 462 81.944000 40 593 1 chr7D.!!$F1 553
18 TraesCS2A01G440700 chr6D 59176357 59177021 664 False 510.000000 510 81.268000 29 677 1 chr6D.!!$F1 648
19 TraesCS2A01G440700 chr1D 473336389 473336972 583 True 460.000000 460 81.664000 29 591 1 chr1D.!!$R1 562
20 TraesCS2A01G440700 chr7A 8903976 8904646 670 False 457.000000 457 79.825000 19 670 1 chr7A.!!$F1 651
21 TraesCS2A01G440700 chr7A 134518318 134518906 588 True 329.000000 329 77.355000 2 590 1 chr7A.!!$R1 588
22 TraesCS2A01G440700 chr1B 676186315 676186952 637 False 379.000000 379 78.190000 29 682 1 chr1B.!!$F1 653
23 TraesCS2A01G440700 chrUn 93413292 93415779 2487 False 210.000000 211 98.333000 2762 2881 2 chrUn.!!$F2 119

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
970 1108 0.245813 GTCCCACCACCGTAAGACTC 59.754 60.0 0.0 0.0 43.02 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2903 7582 0.109597 CGTGGCTCTTTCCATTGTGC 60.11 55.0 0.0 0.0 38.57 4.57 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
122 135 3.187637 CGAGAAGCACGGTTTTATTTCCA 59.812 43.478 0.00 0.00 0.00 3.53
236 264 1.359848 GATTTTGCTTCCGCGAGAGA 58.640 50.000 8.23 0.00 39.65 3.10
253 281 4.813161 CGAGAGATATGGTTGTGCTTTCAT 59.187 41.667 0.00 0.00 0.00 2.57
370 453 1.126846 GTTGTGATTTCGTGAGAGGCG 59.873 52.381 0.00 0.00 43.69 5.52
607 716 2.664185 CGAGGCGCATATGCAGCT 60.664 61.111 29.75 20.98 42.21 4.24
623 732 1.174712 AGCTCGCCACTTGTTGCAAT 61.175 50.000 0.59 0.00 0.00 3.56
643 753 2.907892 TCTGAGAAGGTGGGAGTGATT 58.092 47.619 0.00 0.00 0.00 2.57
684 794 4.804139 TCGATTAGTGATTTCGGAGAAAGC 59.196 41.667 4.08 4.08 45.90 3.51
708 818 6.041296 GCTTCATGGGAATCAAAATATGACCT 59.959 38.462 0.00 0.00 41.93 3.85
709 819 7.231317 GCTTCATGGGAATCAAAATATGACCTA 59.769 37.037 0.00 0.00 41.93 3.08
727 863 3.458487 ACCTAACCTGGCCCAGTAATAAG 59.542 47.826 10.47 0.00 0.00 1.73
736 872 3.181500 GGCCCAGTAATAAGCGACAAAAG 60.181 47.826 0.00 0.00 0.00 2.27
864 1001 1.032794 GCCCATCGATTTTTCCCCTC 58.967 55.000 0.00 0.00 0.00 4.30
970 1108 0.245813 GTCCCACCACCGTAAGACTC 59.754 60.000 0.00 0.00 43.02 3.36
1017 1167 4.779733 ATGCGGGGAGTCGGAGGT 62.780 66.667 0.00 0.00 33.32 3.85
1110 1260 2.344203 CGACGCCTCTGTTCCCTCT 61.344 63.158 0.00 0.00 0.00 3.69
1140 1290 2.202987 GCGCATCAGGTGGAGGAG 60.203 66.667 0.30 0.00 0.00 3.69
1257 1414 2.065993 TCGTTTCTTGCTCCTTCGAG 57.934 50.000 0.00 0.00 39.33 4.04
1299 1457 3.437049 GTCCATCAGCTGTTCTGTTAACC 59.563 47.826 14.67 0.00 43.32 2.85
1333 1491 7.411912 CCATGAACTACTCAATTGTGTTCTACG 60.412 40.741 17.51 12.38 37.67 3.51
1412 1654 8.528044 TGTTGGATATTGGGGTTAATTAAGAC 57.472 34.615 0.00 0.00 0.00 3.01
1452 1694 6.102897 AGTTCATAATTCATACTCCCTCCG 57.897 41.667 0.00 0.00 0.00 4.63
1465 1707 5.687166 ACTCCCTCCGTTCACAAATATAA 57.313 39.130 0.00 0.00 0.00 0.98
1489 1731 8.783833 AAGATGTTTTGGATATCTCGATATGG 57.216 34.615 2.05 0.00 35.41 2.74
1490 1732 7.334090 AGATGTTTTGGATATCTCGATATGGG 58.666 38.462 2.05 0.00 31.25 4.00
1491 1733 6.433847 TGTTTTGGATATCTCGATATGGGT 57.566 37.500 2.05 0.00 34.36 4.51
1492 1734 6.837312 TGTTTTGGATATCTCGATATGGGTT 58.163 36.000 2.05 0.00 34.36 4.11
1493 1735 7.969004 TGTTTTGGATATCTCGATATGGGTTA 58.031 34.615 2.05 0.00 34.36 2.85
1494 1736 7.876068 TGTTTTGGATATCTCGATATGGGTTAC 59.124 37.037 2.05 0.00 34.36 2.50
1513 1755 6.828785 GGGTTACATATGGACTGAAATGAGTT 59.171 38.462 7.80 0.00 0.00 3.01
1522 1764 6.491394 TGGACTGAAATGAGTTAACAAAACG 58.509 36.000 8.61 0.00 0.00 3.60
1529 1772 7.704472 TGAAATGAGTTAACAAAACGCTGAAAT 59.296 29.630 8.61 0.00 0.00 2.17
1530 1773 6.991485 ATGAGTTAACAAAACGCTGAAATG 57.009 33.333 8.61 0.00 0.00 2.32
1565 1808 8.197988 ACATCCGATTCACAAATAAGTTAGAC 57.802 34.615 0.00 0.00 0.00 2.59
1603 1996 2.758979 ACGGAGGTAGTATCTTGTGGTG 59.241 50.000 0.00 0.00 0.00 4.17
1615 2008 1.871039 CTTGTGGTGGGTTAGTTCACG 59.129 52.381 0.00 0.00 34.93 4.35
1620 2013 1.084289 GTGGGTTAGTTCACGCATCC 58.916 55.000 0.00 0.00 41.24 3.51
1623 2016 0.727398 GGTTAGTTCACGCATCCTGC 59.273 55.000 0.00 0.00 40.69 4.85
1642 2035 2.026356 TGCCCAGCTTAACAGATTGCTA 60.026 45.455 0.00 0.00 34.10 3.49
1647 2040 5.183904 CCCAGCTTAACAGATTGCTAAGTTT 59.816 40.000 0.00 0.00 30.82 2.66
1658 2051 8.097038 ACAGATTGCTAAGTTTCTGATGTTCTA 58.903 33.333 8.21 0.00 38.25 2.10
1659 2052 8.386606 CAGATTGCTAAGTTTCTGATGTTCTAC 58.613 37.037 0.00 0.00 38.25 2.59
1911 2348 0.037303 CCCTGATGCTGAAGGTGTGT 59.963 55.000 0.00 0.00 0.00 3.72
1952 2389 1.405872 ACTGTGGACGTAACCTGTGA 58.594 50.000 0.00 0.00 0.00 3.58
1961 2399 6.815142 GTGGACGTAACCTGTGATTATTTACT 59.185 38.462 0.00 0.00 0.00 2.24
1962 2400 7.975616 GTGGACGTAACCTGTGATTATTTACTA 59.024 37.037 0.00 0.00 0.00 1.82
1963 2401 8.192774 TGGACGTAACCTGTGATTATTTACTAG 58.807 37.037 0.00 0.00 0.00 2.57
2251 4527 1.404986 GCTGTGGTGGCGTAGATGTTA 60.405 52.381 0.00 0.00 0.00 2.41
2286 4562 4.404715 CCAAATCAGGATTCATGCCTTTCT 59.595 41.667 0.00 0.00 32.12 2.52
2355 4637 4.335315 TGAACTGAACGAACTGAAATGCTT 59.665 37.500 0.00 0.00 0.00 3.91
2409 4691 2.117941 GAAGTGTTGTGGCAGTCCGC 62.118 60.000 0.00 0.00 43.16 5.54
2420 4702 0.669625 GCAGTCCGCCGGATAATACC 60.670 60.000 10.04 0.00 32.73 2.73
2612 4904 8.693120 TGGTCTAGTTTATATCTACTCCACTG 57.307 38.462 0.00 0.00 0.00 3.66
2688 4995 2.680339 GCACCTAGTCCTTCAGAAATGC 59.320 50.000 0.00 0.00 0.00 3.56
2710 5021 6.934056 TGCATATTTTTCTAGTGCAACCAAT 58.066 32.000 0.00 0.00 42.22 3.16
2892 7571 8.635765 TTGGAATATTATGAGCTAATCCAACC 57.364 34.615 0.00 0.00 31.31 3.77
2893 7572 7.754624 TGGAATATTATGAGCTAATCCAACCA 58.245 34.615 0.00 0.00 32.26 3.67
2894 7573 8.224025 TGGAATATTATGAGCTAATCCAACCAA 58.776 33.333 0.00 0.00 32.26 3.67
2895 7574 9.247861 GGAATATTATGAGCTAATCCAACCAAT 57.752 33.333 0.00 0.00 32.26 3.16
2899 7578 7.572523 TTATGAGCTAATCCAACCAATCTTG 57.427 36.000 0.00 0.00 0.00 3.02
2900 7579 3.696051 TGAGCTAATCCAACCAATCTTGC 59.304 43.478 0.00 0.00 0.00 4.01
2901 7580 3.950395 GAGCTAATCCAACCAATCTTGCT 59.050 43.478 0.00 0.00 0.00 3.91
2902 7581 4.347607 AGCTAATCCAACCAATCTTGCTT 58.652 39.130 0.00 0.00 0.00 3.91
2903 7582 4.159135 AGCTAATCCAACCAATCTTGCTTG 59.841 41.667 0.00 0.00 0.00 4.01
2904 7583 3.323751 AATCCAACCAATCTTGCTTGC 57.676 42.857 0.00 0.00 0.00 4.01
2905 7584 1.702182 TCCAACCAATCTTGCTTGCA 58.298 45.000 0.00 0.00 0.00 4.08
2906 7585 1.340889 TCCAACCAATCTTGCTTGCAC 59.659 47.619 0.00 0.00 0.00 4.57
2907 7586 1.068895 CCAACCAATCTTGCTTGCACA 59.931 47.619 0.00 0.00 0.00 4.57
2908 7587 2.483363 CCAACCAATCTTGCTTGCACAA 60.483 45.455 0.00 0.00 0.00 3.33
2909 7588 3.395639 CAACCAATCTTGCTTGCACAAT 58.604 40.909 0.00 0.00 0.00 2.71
2910 7589 3.034721 ACCAATCTTGCTTGCACAATG 57.965 42.857 0.00 0.00 0.00 2.82
2911 7590 2.289195 ACCAATCTTGCTTGCACAATGG 60.289 45.455 11.71 11.71 34.69 3.16
2912 7591 2.028839 CCAATCTTGCTTGCACAATGGA 60.029 45.455 9.06 0.00 31.61 3.41
2913 7592 3.555377 CCAATCTTGCTTGCACAATGGAA 60.555 43.478 9.06 0.00 31.61 3.53
2914 7593 4.059511 CAATCTTGCTTGCACAATGGAAA 58.940 39.130 0.00 0.00 0.00 3.13
2915 7594 3.374220 TCTTGCTTGCACAATGGAAAG 57.626 42.857 0.00 0.00 0.00 2.62
2916 7595 2.957680 TCTTGCTTGCACAATGGAAAGA 59.042 40.909 0.00 0.00 0.00 2.52
2917 7596 3.005050 TCTTGCTTGCACAATGGAAAGAG 59.995 43.478 0.00 0.00 0.00 2.85
2918 7597 1.000060 TGCTTGCACAATGGAAAGAGC 60.000 47.619 0.00 0.00 0.00 4.09
2919 7598 1.670967 GCTTGCACAATGGAAAGAGCC 60.671 52.381 0.00 0.00 0.00 4.70
2920 7599 1.614903 CTTGCACAATGGAAAGAGCCA 59.385 47.619 0.00 0.00 43.23 4.75
2921 7600 0.961019 TGCACAATGGAAAGAGCCAC 59.039 50.000 0.00 0.00 41.56 5.01
2922 7601 0.109597 GCACAATGGAAAGAGCCACG 60.110 55.000 0.00 0.00 41.56 4.94
2923 7602 0.523072 CACAATGGAAAGAGCCACGG 59.477 55.000 0.00 0.00 41.56 4.94
2924 7603 0.609131 ACAATGGAAAGAGCCACGGG 60.609 55.000 0.00 0.00 41.56 5.28
2934 7613 4.760757 GCCACGGGCTTATCTCTC 57.239 61.111 7.58 0.00 46.69 3.20
2935 7614 1.069935 GCCACGGGCTTATCTCTCC 59.930 63.158 7.58 0.00 46.69 3.71
2936 7615 1.686325 GCCACGGGCTTATCTCTCCA 61.686 60.000 7.58 0.00 46.69 3.86
2937 7616 0.390860 CCACGGGCTTATCTCTCCAG 59.609 60.000 0.00 0.00 0.00 3.86
2938 7617 0.249657 CACGGGCTTATCTCTCCAGC 60.250 60.000 0.00 0.00 0.00 4.85
2939 7618 1.006805 CGGGCTTATCTCTCCAGCG 60.007 63.158 0.00 0.00 34.09 5.18
2940 7619 1.456196 CGGGCTTATCTCTCCAGCGA 61.456 60.000 0.00 0.00 34.09 4.93
2941 7620 0.753262 GGGCTTATCTCTCCAGCGAA 59.247 55.000 0.00 0.00 34.09 4.70
2942 7621 1.346068 GGGCTTATCTCTCCAGCGAAT 59.654 52.381 0.00 0.00 34.09 3.34
2943 7622 2.224402 GGGCTTATCTCTCCAGCGAATT 60.224 50.000 0.00 0.00 34.09 2.17
2944 7623 3.006967 GGGCTTATCTCTCCAGCGAATTA 59.993 47.826 0.00 0.00 34.09 1.40
2945 7624 4.503296 GGGCTTATCTCTCCAGCGAATTAA 60.503 45.833 0.00 0.00 34.09 1.40
2946 7625 5.057149 GGCTTATCTCTCCAGCGAATTAAA 58.943 41.667 0.00 0.00 34.09 1.52
2947 7626 5.703130 GGCTTATCTCTCCAGCGAATTAAAT 59.297 40.000 0.00 0.00 34.09 1.40
2948 7627 6.205658 GGCTTATCTCTCCAGCGAATTAAATT 59.794 38.462 0.00 0.00 34.09 1.82
2949 7628 7.387948 GGCTTATCTCTCCAGCGAATTAAATTA 59.612 37.037 0.00 0.00 34.09 1.40
2950 7629 8.224437 GCTTATCTCTCCAGCGAATTAAATTAC 58.776 37.037 0.00 0.00 0.00 1.89
2951 7630 8.603242 TTATCTCTCCAGCGAATTAAATTACC 57.397 34.615 0.00 0.00 0.00 2.85
2952 7631 6.235231 TCTCTCCAGCGAATTAAATTACCT 57.765 37.500 0.00 0.00 0.00 3.08
2953 7632 7.356089 TCTCTCCAGCGAATTAAATTACCTA 57.644 36.000 0.00 0.00 0.00 3.08
2954 7633 7.788026 TCTCTCCAGCGAATTAAATTACCTAA 58.212 34.615 0.00 0.00 0.00 2.69
2955 7634 8.262227 TCTCTCCAGCGAATTAAATTACCTAAA 58.738 33.333 0.00 0.00 0.00 1.85
2956 7635 8.433421 TCTCCAGCGAATTAAATTACCTAAAG 57.567 34.615 0.00 0.00 0.00 1.85
2957 7636 7.497909 TCTCCAGCGAATTAAATTACCTAAAGG 59.502 37.037 0.00 0.00 42.17 3.11
2989 7668 3.751518 TGTAAGAAACAAGAAGGCCCTC 58.248 45.455 0.00 0.00 34.29 4.30
3000 7679 2.708325 AGAAGGCCCTCCATATGAACTC 59.292 50.000 3.65 0.00 33.74 3.01
3012 7691 4.323028 CCATATGAACTCAGTGGTGTCAGT 60.323 45.833 3.65 0.00 33.47 3.41
3041 7720 7.857389 TCTTTCGCATAACATATGAAATCAAGC 59.143 33.333 10.38 3.32 0.00 4.01
3044 7723 5.561499 CGCATAACATATGAAATCAAGCGTC 59.439 40.000 10.38 0.00 36.06 5.19
3046 7725 6.912051 GCATAACATATGAAATCAAGCGTCAA 59.088 34.615 10.38 0.00 0.00 3.18
3047 7726 7.592533 GCATAACATATGAAATCAAGCGTCAAT 59.407 33.333 10.38 0.00 0.00 2.57
3048 7727 9.454585 CATAACATATGAAATCAAGCGTCAATT 57.545 29.630 10.38 0.00 0.00 2.32
3101 7780 5.298276 GTCTTGTCCAGGTTGACATTTGTAA 59.702 40.000 0.00 0.00 44.27 2.41
3121 7800 7.581213 TGTAAAAGGCTGAGAGAAAATCAAA 57.419 32.000 0.00 0.00 0.00 2.69
3175 7854 1.300971 CCTCACGGTGAATGCAGTGG 61.301 60.000 12.54 4.21 35.72 4.00
3203 7882 1.652619 GTTCGAAACACGGTAGCTAGC 59.347 52.381 13.03 13.03 42.82 3.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 129 0.110486 AACTGTGCCCTCGTGGAAAT 59.890 50.000 4.76 0.00 35.39 2.17
117 130 0.817634 CAACTGTGCCCTCGTGGAAA 60.818 55.000 4.76 0.00 35.39 3.13
200 225 2.563471 ATCGTACCTCTCGTGAAAGC 57.437 50.000 0.00 0.00 0.00 3.51
236 264 4.885907 CCTCTCATGAAAGCACAACCATAT 59.114 41.667 0.00 0.00 0.00 1.78
307 367 1.451028 GCGCCTCTTGCAGAAGGAT 60.451 57.895 18.03 0.00 41.33 3.24
331 391 1.156736 CCGTGCCTCTCGTGAAAATT 58.843 50.000 0.00 0.00 0.00 1.82
390 473 1.228459 AGCACGGGGTTTTTCTCCC 60.228 57.895 0.00 0.00 43.90 4.30
391 474 1.241990 GGAGCACGGGGTTTTTCTCC 61.242 60.000 0.00 0.00 34.13 3.71
607 716 0.592637 CAGATTGCAACAAGTGGCGA 59.407 50.000 0.00 0.00 0.00 5.54
623 732 2.630889 ATCACTCCCACCTTCTCAGA 57.369 50.000 0.00 0.00 0.00 3.27
643 753 8.746530 ACTAATCGAGGAGTACTCATTACAAAA 58.253 33.333 23.91 2.81 46.98 2.44
684 794 7.592885 AGGTCATATTTTGATTCCCATGAAG 57.407 36.000 0.00 0.00 36.54 3.02
708 818 2.158871 CGCTTATTACTGGGCCAGGTTA 60.159 50.000 35.34 20.74 35.51 2.85
709 819 1.408266 CGCTTATTACTGGGCCAGGTT 60.408 52.381 35.34 21.68 35.51 3.50
727 863 1.327764 CCGCTAATCTCCTTTTGTCGC 59.672 52.381 0.00 0.00 0.00 5.19
736 872 0.815615 CTTGTGGGCCGCTAATCTCC 60.816 60.000 19.39 0.00 0.00 3.71
783 919 1.423845 CATGCGGCTGGTAAACGAC 59.576 57.895 0.00 0.00 0.00 4.34
845 982 1.032794 GAGGGGAAAAATCGATGGGC 58.967 55.000 0.00 0.00 0.00 5.36
956 1094 1.836802 GAGAGGAGTCTTACGGTGGT 58.163 55.000 0.00 0.00 30.97 4.16
1017 1167 1.368950 GCTGACAGTGAGCAGTGGA 59.631 57.895 7.20 0.00 36.40 4.02
1098 1248 0.252927 AGGGGGAAGAGGGAACAGAG 60.253 60.000 0.00 0.00 0.00 3.35
1257 1414 0.387239 GCATGGCTCGGACAACAAAC 60.387 55.000 0.00 0.00 0.00 2.93
1299 1457 5.885230 TTGAGTAGTTCATGGCAATTCAG 57.115 39.130 0.00 0.00 35.27 3.02
1333 1491 0.322816 TGGGCAGCAAGATCCTTCAC 60.323 55.000 0.00 0.00 0.00 3.18
1412 1654 9.751542 ATTATGAACTTAAGTTAGATGAGACCG 57.248 33.333 20.58 0.00 38.56 4.79
1465 1707 7.038017 ACCCATATCGAGATATCCAAAACATCT 60.038 37.037 0.00 0.00 31.98 2.90
1480 1722 6.152831 TCAGTCCATATGTAACCCATATCGAG 59.847 42.308 1.24 0.00 43.46 4.04
1481 1723 6.014012 TCAGTCCATATGTAACCCATATCGA 58.986 40.000 1.24 0.00 43.46 3.59
1482 1724 6.280855 TCAGTCCATATGTAACCCATATCG 57.719 41.667 1.24 0.00 43.46 2.92
1483 1725 8.950210 CATTTCAGTCCATATGTAACCCATATC 58.050 37.037 1.24 0.00 43.46 1.63
1484 1726 8.668653 TCATTTCAGTCCATATGTAACCCATAT 58.331 33.333 1.24 0.00 45.67 1.78
1485 1727 8.040002 TCATTTCAGTCCATATGTAACCCATA 57.960 34.615 1.24 0.00 40.27 2.74
1486 1728 6.910191 TCATTTCAGTCCATATGTAACCCAT 58.090 36.000 1.24 0.00 37.58 4.00
1487 1729 6.069673 ACTCATTTCAGTCCATATGTAACCCA 60.070 38.462 1.24 0.00 0.00 4.51
1488 1730 6.357367 ACTCATTTCAGTCCATATGTAACCC 58.643 40.000 1.24 0.00 0.00 4.11
1489 1731 7.865706 AACTCATTTCAGTCCATATGTAACC 57.134 36.000 1.24 0.00 0.00 2.85
1491 1733 9.952030 TGTTAACTCATTTCAGTCCATATGTAA 57.048 29.630 7.22 0.00 0.00 2.41
1492 1734 9.952030 TTGTTAACTCATTTCAGTCCATATGTA 57.048 29.630 7.22 0.00 0.00 2.29
1493 1735 8.862325 TTGTTAACTCATTTCAGTCCATATGT 57.138 30.769 7.22 0.00 0.00 2.29
1506 1748 6.978080 ACATTTCAGCGTTTTGTTAACTCATT 59.022 30.769 7.22 0.00 0.00 2.57
1513 1755 5.493133 AGACACATTTCAGCGTTTTGTTA 57.507 34.783 0.00 0.00 0.00 2.41
1520 1762 6.868864 GGATGTATATAGACACATTTCAGCGT 59.131 38.462 1.52 0.00 35.55 5.07
1521 1763 6.033937 CGGATGTATATAGACACATTTCAGCG 59.966 42.308 1.52 0.00 35.55 5.18
1522 1764 7.090808 TCGGATGTATATAGACACATTTCAGC 58.909 38.462 1.52 0.00 35.55 4.26
1529 1772 7.519032 TGTGAATCGGATGTATATAGACACA 57.481 36.000 1.52 0.00 30.52 3.72
1530 1773 8.812147 TTTGTGAATCGGATGTATATAGACAC 57.188 34.615 1.52 0.00 30.52 3.67
1564 1807 5.509163 CCTCCGTTCACGAATATAAGATGGT 60.509 44.000 0.00 0.00 43.02 3.55
1565 1808 4.923871 CCTCCGTTCACGAATATAAGATGG 59.076 45.833 0.00 0.00 43.02 3.51
1603 1996 1.369625 CAGGATGCGTGAACTAACCC 58.630 55.000 0.00 0.00 0.00 4.11
1620 2013 1.133790 GCAATCTGTTAAGCTGGGCAG 59.866 52.381 0.00 0.00 0.00 4.85
1623 2016 4.265073 ACTTAGCAATCTGTTAAGCTGGG 58.735 43.478 9.39 0.00 42.52 4.45
1642 2035 6.773638 ACATGAGGTAGAACATCAGAAACTT 58.226 36.000 0.00 0.00 42.47 2.66
1647 2040 6.114187 ACAAACATGAGGTAGAACATCAGA 57.886 37.500 0.00 0.00 42.47 3.27
1658 2051 4.081752 TGAAGCAAACAACAAACATGAGGT 60.082 37.500 0.00 0.00 0.00 3.85
1659 2052 4.431809 TGAAGCAAACAACAAACATGAGG 58.568 39.130 0.00 0.00 0.00 3.86
1744 2145 4.324402 GCGCACCACTTTAAATTGATGAAG 59.676 41.667 0.30 0.00 0.00 3.02
1806 2243 9.654663 TTGATGATGAATGCACAAATGAATTAA 57.345 25.926 0.00 0.00 33.82 1.40
1911 2348 7.179516 ACAGTAAACAAAAAGGAAGGGAAGAAA 59.820 33.333 0.00 0.00 0.00 2.52
1961 2399 3.621268 GCATCCAGCAACGAATTGTACTA 59.379 43.478 0.00 0.00 44.79 1.82
1962 2400 2.420022 GCATCCAGCAACGAATTGTACT 59.580 45.455 0.00 0.00 44.79 2.73
1963 2401 2.785679 GCATCCAGCAACGAATTGTAC 58.214 47.619 0.00 0.00 44.79 2.90
2251 4527 9.204337 TGAATCCTGATTTGGATAATCAAACAT 57.796 29.630 0.00 0.00 45.35 2.71
2274 4550 0.604578 GCTGGCAAGAAAGGCATGAA 59.395 50.000 0.00 0.00 43.56 2.57
2355 4637 3.269381 AGAAATGGACCCTGGAAGCATAA 59.731 43.478 0.00 0.00 0.00 1.90
2409 4691 2.542595 GCACGTCTTTGGTATTATCCGG 59.457 50.000 0.00 0.00 0.00 5.14
2410 4692 3.191669 TGCACGTCTTTGGTATTATCCG 58.808 45.455 0.00 0.00 0.00 4.18
2420 4702 6.198687 TCTTTAGAAAACATGCACGTCTTTG 58.801 36.000 0.00 0.00 0.00 2.77
2646 4938 4.710865 TGCATTGCATAGGGAAGAATTTCA 59.289 37.500 7.38 0.00 32.00 2.69
2688 4995 8.863049 GTTGATTGGTTGCACTAGAAAAATATG 58.137 33.333 0.00 0.00 0.00 1.78
2710 5021 8.918202 ACCAGTAGAATTGAAATGTAAGTTGA 57.082 30.769 0.00 0.00 0.00 3.18
2881 7560 4.725790 AAGCAAGATTGGTTGGATTAGC 57.274 40.909 9.07 0.00 46.03 3.09
2890 7569 2.289195 CCATTGTGCAAGCAAGATTGGT 60.289 45.455 0.00 0.00 41.27 3.67
2891 7570 2.028839 TCCATTGTGCAAGCAAGATTGG 60.029 45.455 0.00 2.55 0.00 3.16
2892 7571 3.306917 TCCATTGTGCAAGCAAGATTG 57.693 42.857 0.00 0.00 0.00 2.67
2893 7572 4.039488 TCTTTCCATTGTGCAAGCAAGATT 59.961 37.500 0.00 0.00 0.00 2.40
2894 7573 3.575256 TCTTTCCATTGTGCAAGCAAGAT 59.425 39.130 0.00 0.00 0.00 2.40
2895 7574 2.957680 TCTTTCCATTGTGCAAGCAAGA 59.042 40.909 0.00 0.00 0.00 3.02
2896 7575 3.314553 CTCTTTCCATTGTGCAAGCAAG 58.685 45.455 0.00 0.00 0.00 4.01
2897 7576 2.546373 GCTCTTTCCATTGTGCAAGCAA 60.546 45.455 0.00 0.00 0.00 3.91
2898 7577 1.000060 GCTCTTTCCATTGTGCAAGCA 60.000 47.619 0.00 0.00 0.00 3.91
2899 7578 1.670967 GGCTCTTTCCATTGTGCAAGC 60.671 52.381 0.00 0.00 0.00 4.01
2900 7579 1.614903 TGGCTCTTTCCATTGTGCAAG 59.385 47.619 0.00 0.00 0.00 4.01
2901 7580 1.340889 GTGGCTCTTTCCATTGTGCAA 59.659 47.619 0.00 0.00 38.57 4.08
2902 7581 0.961019 GTGGCTCTTTCCATTGTGCA 59.039 50.000 0.00 0.00 38.57 4.57
2903 7582 0.109597 CGTGGCTCTTTCCATTGTGC 60.110 55.000 0.00 0.00 38.57 4.57
2904 7583 0.523072 CCGTGGCTCTTTCCATTGTG 59.477 55.000 0.00 0.00 38.57 3.33
2905 7584 0.609131 CCCGTGGCTCTTTCCATTGT 60.609 55.000 0.00 0.00 38.57 2.71
2906 7585 1.937546 GCCCGTGGCTCTTTCCATTG 61.938 60.000 7.58 0.00 46.69 2.82
2907 7586 1.678970 GCCCGTGGCTCTTTCCATT 60.679 57.895 7.58 0.00 46.69 3.16
2908 7587 2.044946 GCCCGTGGCTCTTTCCAT 60.045 61.111 7.58 0.00 46.69 3.41
2918 7597 0.390860 CTGGAGAGATAAGCCCGTGG 59.609 60.000 0.00 0.00 0.00 4.94
2919 7598 0.249657 GCTGGAGAGATAAGCCCGTG 60.250 60.000 0.00 0.00 0.00 4.94
2920 7599 1.739338 CGCTGGAGAGATAAGCCCGT 61.739 60.000 0.00 0.00 33.24 5.28
2921 7600 1.006805 CGCTGGAGAGATAAGCCCG 60.007 63.158 0.00 0.00 33.24 6.13
2922 7601 0.753262 TTCGCTGGAGAGATAAGCCC 59.247 55.000 0.00 0.00 33.24 5.19
2923 7602 2.829741 ATTCGCTGGAGAGATAAGCC 57.170 50.000 0.00 0.00 33.24 4.35
2924 7603 6.793492 ATTTAATTCGCTGGAGAGATAAGC 57.207 37.500 0.00 0.00 0.00 3.09
2925 7604 8.713271 GGTAATTTAATTCGCTGGAGAGATAAG 58.287 37.037 0.00 0.00 0.00 1.73
2926 7605 8.429641 AGGTAATTTAATTCGCTGGAGAGATAA 58.570 33.333 0.00 0.00 0.00 1.75
2927 7606 7.963532 AGGTAATTTAATTCGCTGGAGAGATA 58.036 34.615 0.00 0.00 0.00 1.98
2928 7607 6.831976 AGGTAATTTAATTCGCTGGAGAGAT 58.168 36.000 0.00 0.00 0.00 2.75
2929 7608 6.235231 AGGTAATTTAATTCGCTGGAGAGA 57.765 37.500 0.00 0.00 0.00 3.10
2930 7609 8.433421 TTTAGGTAATTTAATTCGCTGGAGAG 57.567 34.615 0.00 0.00 0.00 3.20
2931 7610 7.497909 CCTTTAGGTAATTTAATTCGCTGGAGA 59.502 37.037 0.00 0.00 0.00 3.71
2932 7611 7.639945 CCTTTAGGTAATTTAATTCGCTGGAG 58.360 38.462 0.00 0.00 0.00 3.86
2933 7612 7.562454 CCTTTAGGTAATTTAATTCGCTGGA 57.438 36.000 0.00 0.00 0.00 3.86
2948 7627 9.298373 TCTTACAAGAACGCACACCTTTAGGTA 62.298 40.741 0.14 0.00 38.08 3.08
2949 7628 8.579838 TCTTACAAGAACGCACACCTTTAGGT 62.580 42.308 0.00 0.00 39.75 3.08
2950 7629 2.218603 ACAAGAACGCACACCTTTAGG 58.781 47.619 0.00 0.00 42.17 2.69
2951 7630 4.748102 TCTTACAAGAACGCACACCTTTAG 59.252 41.667 0.00 0.00 30.73 1.85
2952 7631 4.695396 TCTTACAAGAACGCACACCTTTA 58.305 39.130 0.00 0.00 30.73 1.85
2953 7632 3.537580 TCTTACAAGAACGCACACCTTT 58.462 40.909 0.00 0.00 30.73 3.11
2954 7633 3.188159 TCTTACAAGAACGCACACCTT 57.812 42.857 0.00 0.00 30.73 3.50
2955 7634 2.902705 TCTTACAAGAACGCACACCT 57.097 45.000 0.00 0.00 30.73 4.00
2956 7635 3.064271 TGTTTCTTACAAGAACGCACACC 59.936 43.478 3.91 0.00 44.18 4.16
2957 7636 4.267357 TGTTTCTTACAAGAACGCACAC 57.733 40.909 3.91 1.14 44.18 3.82
2958 7637 4.948608 TTGTTTCTTACAAGAACGCACA 57.051 36.364 3.91 4.19 44.18 4.57
2989 7668 4.186926 CTGACACCACTGAGTTCATATGG 58.813 47.826 2.13 9.76 37.77 2.74
3000 7679 2.797156 CGAAAGAGAACTGACACCACTG 59.203 50.000 0.00 0.00 0.00 3.66
3012 7691 9.108284 TGATTTCATATGTTATGCGAAAGAGAA 57.892 29.630 1.90 0.00 0.00 2.87
3066 7745 2.203153 ACAAGACCGCGGCACTTT 60.203 55.556 28.58 17.13 0.00 2.66
3072 7751 3.530910 AACCTGGACAAGACCGCGG 62.531 63.158 26.86 26.86 0.00 6.46
3088 7767 6.017109 TCTCTCAGCCTTTTACAAATGTCAAC 60.017 38.462 0.00 0.00 0.00 3.18
3101 7780 4.021632 GCCTTTGATTTTCTCTCAGCCTTT 60.022 41.667 0.00 0.00 0.00 3.11
3134 7813 8.082852 TGAGGATTAAACTGATTCTAGCGTATC 58.917 37.037 0.00 0.00 0.00 2.24
3203 7882 4.142425 GGTGCCCCATTTTATGCAAATTTG 60.142 41.667 14.03 14.03 32.24 2.32


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

AutoCloner maintained by Alex Coulton.