Multiple sequence alignment - TraesCS7A01G330100

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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 TraesCS7A01G330100 chr7A 100.000 5371 0 0 1 5371 482329846 482324476 0.000000e+00 9919.0
1 TraesCS7A01G330100 chr7A 87.223 587 42 15 391 951 219168002 219167423 5.870000e-179 638.0
2 TraesCS7A01G330100 chr7A 90.886 395 29 6 1 392 638566865 638567255 1.710000e-144 523.0
3 TraesCS7A01G330100 chr7A 87.333 150 13 5 4392 4537 15493954 15493807 3.330000e-37 167.0
4 TraesCS7A01G330100 chr7A 97.727 88 0 2 5018 5103 299735 299648 3.350000e-32 150.0
5 TraesCS7A01G330100 chr7A 97.619 84 1 1 5021 5103 292409 292326 5.610000e-30 143.0
6 TraesCS7A01G330100 chr7D 95.143 3706 97 35 950 4635 417615569 417611927 0.000000e+00 5770.0
7 TraesCS7A01G330100 chr7D 92.523 428 23 4 4520 4938 417611977 417611550 5.950000e-169 604.0
8 TraesCS7A01G330100 chr7D 91.919 396 23 8 1 392 586687849 586687459 3.660000e-151 545.0
9 TraesCS7A01G330100 chr7D 83.729 590 41 19 388 951 4171066 4171626 1.730000e-139 507.0
10 TraesCS7A01G330100 chr7D 92.537 268 18 2 388 653 431153909 431154176 3.040000e-102 383.0
11 TraesCS7A01G330100 chr7D 91.935 248 18 2 391 637 586687405 586687159 3.980000e-91 346.0
12 TraesCS7A01G330100 chr7D 83.436 326 25 13 648 957 33694603 33694291 5.300000e-70 276.0
13 TraesCS7A01G330100 chr7D 90.411 219 8 9 5154 5371 417610138 417609932 5.300000e-70 276.0
14 TraesCS7A01G330100 chr7D 93.798 129 7 1 4989 5117 417611409 417611282 5.490000e-45 193.0
15 TraesCS7A01G330100 chr7B 94.723 3468 121 27 950 4388 433300384 433296950 0.000000e+00 5334.0
16 TraesCS7A01G330100 chr7B 89.224 232 11 5 5145 5371 433294916 433294694 1.470000e-70 278.0
17 TraesCS7A01G330100 chr7B 80.997 321 32 16 4784 5102 433296693 433296400 1.500000e-55 228.0
18 TraesCS7A01G330100 chr7B 91.453 117 9 1 3933 4049 598011537 598011422 5.570000e-35 159.0
19 TraesCS7A01G330100 chr7B 88.372 129 11 3 4394 4520 202891996 202891870 9.320000e-33 152.0
20 TraesCS7A01G330100 chr7B 85.938 128 18 0 4623 4750 433296915 433296788 2.610000e-28 137.0
21 TraesCS7A01G330100 chr6A 98.845 952 10 1 1 952 107170456 107169506 0.000000e+00 1696.0
22 TraesCS7A01G330100 chr6A 90.164 122 11 1 4392 4513 161396215 161396335 2.000000e-34 158.0
23 TraesCS7A01G330100 chr6A 87.313 134 12 4 4396 4527 1451256 1451126 1.210000e-31 148.0
24 TraesCS7A01G330100 chr5B 98.636 953 12 1 1 952 400664964 400664012 0.000000e+00 1687.0
25 TraesCS7A01G330100 chr5B 95.389 976 27 8 1 961 859860 860832 0.000000e+00 1537.0
26 TraesCS7A01G330100 chr5B 92.658 395 22 6 1 392 407242412 407242802 3.630000e-156 562.0
27 TraesCS7A01G330100 chrUn 86.341 593 54 8 388 960 49961331 49961916 5.910000e-174 621.0
28 TraesCS7A01G330100 chr5D 85.763 590 35 19 391 955 72364631 72364066 3.610000e-161 579.0
29 TraesCS7A01G330100 chr5D 90.886 395 29 6 1 392 536867048 536867438 1.710000e-144 523.0
30 TraesCS7A01G330100 chr2A 91.667 396 25 7 1 392 733098409 733098018 4.730000e-150 542.0
31 TraesCS7A01G330100 chr2A 98.750 80 1 0 5015 5094 51513468 51513547 5.610000e-30 143.0
32 TraesCS7A01G330100 chr3A 91.667 396 24 8 1 392 357059431 357059041 1.700000e-149 540.0
33 TraesCS7A01G330100 chr2B 84.825 514 40 15 464 952 547098350 547098850 2.910000e-132 483.0
34 TraesCS7A01G330100 chr2B 94.898 98 4 1 5015 5111 76882502 76882599 9.320000e-33 152.0
35 TraesCS7A01G330100 chr2B 83.562 73 7 3 3807 3874 787814083 787814155 4.490000e-06 63.9
36 TraesCS7A01G330100 chr2D 85.045 448 22 15 530 955 189689488 189689064 1.080000e-111 414.0
37 TraesCS7A01G330100 chr2D 95.604 91 2 2 5014 5103 49204385 49204474 1.560000e-30 145.0
38 TraesCS7A01G330100 chr4D 84.944 445 22 13 530 952 400894449 400894870 5.010000e-110 409.0
39 TraesCS7A01G330100 chr4D 84.598 448 25 14 530 956 472925166 472925590 6.480000e-109 405.0
40 TraesCS7A01G330100 chr4D 97.701 87 1 1 5020 5105 313932720 313932634 1.210000e-31 148.0
41 TraesCS7A01G330100 chr4B 81.387 274 24 10 709 963 66189215 66189480 1.180000e-46 198.0
42 TraesCS7A01G330100 chr3B 90.164 122 11 1 4392 4513 489697973 489698093 2.000000e-34 158.0
43 TraesCS7A01G330100 chr3B 90.678 118 10 1 4394 4511 422472299 422472183 7.200000e-34 156.0
44 TraesCS7A01G330100 chr5A 88.372 129 11 3 4394 4520 484650066 484649940 9.320000e-33 152.0
45 TraesCS7A01G330100 chr6B 94.624 93 2 3 5013 5103 41858416 41858507 2.020000e-29 141.0
46 TraesCS7A01G330100 chr6D 83.226 155 21 5 4387 4538 8836363 8836211 2.610000e-28 137.0


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 TraesCS7A01G330100 chr7A 482324476 482329846 5370 True 9919.00 9919 100.00000 1 5371 1 chr7A.!!$R5 5370
1 TraesCS7A01G330100 chr7A 219167423 219168002 579 True 638.00 638 87.22300 391 951 1 chr7A.!!$R4 560
2 TraesCS7A01G330100 chr7D 417609932 417615569 5637 True 1710.75 5770 92.96875 950 5371 4 chr7D.!!$R2 4421
3 TraesCS7A01G330100 chr7D 4171066 4171626 560 False 507.00 507 83.72900 388 951 1 chr7D.!!$F1 563
4 TraesCS7A01G330100 chr7D 586687159 586687849 690 True 445.50 545 91.92700 1 637 2 chr7D.!!$R3 636
5 TraesCS7A01G330100 chr7B 433294694 433300384 5690 True 1494.25 5334 87.72050 950 5371 4 chr7B.!!$R3 4421
6 TraesCS7A01G330100 chr6A 107169506 107170456 950 True 1696.00 1696 98.84500 1 952 1 chr6A.!!$R2 951
7 TraesCS7A01G330100 chr5B 400664012 400664964 952 True 1687.00 1687 98.63600 1 952 1 chr5B.!!$R1 951
8 TraesCS7A01G330100 chr5B 859860 860832 972 False 1537.00 1537 95.38900 1 961 1 chr5B.!!$F1 960
9 TraesCS7A01G330100 chrUn 49961331 49961916 585 False 621.00 621 86.34100 388 960 1 chrUn.!!$F1 572
10 TraesCS7A01G330100 chr5D 72364066 72364631 565 True 579.00 579 85.76300 391 955 1 chr5D.!!$R1 564
11 TraesCS7A01G330100 chr2B 547098350 547098850 500 False 483.00 483 84.82500 464 952 1 chr2B.!!$F2 488

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
997 1102 0.100861 GTCTAGTAGCGTGGACAGCC 59.899 60.000 0.00 0.00 34.64 4.85 F
998 1103 1.064296 CTAGTAGCGTGGACAGCCG 59.936 63.158 0.00 0.00 36.79 5.52 F
1219 1333 1.139853 CCTCCTAGCTAGGGTTTGCTG 59.860 57.143 34.43 17.32 43.79 4.41 F
3045 3171 0.456628 GCACACACATGGCATATGCA 59.543 50.000 28.07 15.05 44.36 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2195 2312 0.238289 ATGTCGGACAAAGCTTTGCG 59.762 50.000 33.72 28.66 41.79 4.85 R
2409 2527 3.744426 CCGGGTACACAAACTTAAGACTG 59.256 47.826 10.09 8.14 0.00 3.51 R
3117 3243 2.860009 CTGCCATGCAAGATCCTACAT 58.140 47.619 0.00 0.00 38.41 2.29 R
4856 5129 0.038618 TCCAACACGATCAGACGGTG 60.039 55.000 0.00 1.91 37.61 4.94 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
45 46 1.586154 CCGTTGCAACCCCTCATGTC 61.586 60.000 23.42 0.00 0.00 3.06
415 472 2.564947 TGTTTTTGTGTTGGAACTGGCT 59.435 40.909 0.00 0.00 0.00 4.75
974 1079 3.436700 AAAAAGAAGCGAAAGGGTGTG 57.563 42.857 0.00 0.00 0.00 3.82
994 1099 2.286872 GCTAGTCTAGTAGCGTGGACA 58.713 52.381 8.68 0.00 36.34 4.02
995 1100 2.288458 GCTAGTCTAGTAGCGTGGACAG 59.712 54.545 8.68 0.00 36.34 3.51
996 1101 1.096416 AGTCTAGTAGCGTGGACAGC 58.904 55.000 0.00 0.00 0.00 4.40
997 1102 0.100861 GTCTAGTAGCGTGGACAGCC 59.899 60.000 0.00 0.00 34.64 4.85
998 1103 1.064296 CTAGTAGCGTGGACAGCCG 59.936 63.158 0.00 0.00 36.79 5.52
1034 1139 3.414549 GAGTGTTCTCCTCGTCTCATC 57.585 52.381 0.00 0.00 34.87 2.92
1035 1140 3.013921 GAGTGTTCTCCTCGTCTCATCT 58.986 50.000 0.00 0.00 34.87 2.90
1036 1141 2.752354 AGTGTTCTCCTCGTCTCATCTG 59.248 50.000 0.00 0.00 0.00 2.90
1037 1142 2.750166 GTGTTCTCCTCGTCTCATCTGA 59.250 50.000 0.00 0.00 0.00 3.27
1089 1203 4.483243 TGCTCGCCGGGGAATTCC 62.483 66.667 22.77 16.74 0.00 3.01
1219 1333 1.139853 CCTCCTAGCTAGGGTTTGCTG 59.860 57.143 34.43 17.32 43.79 4.41
1339 1453 3.010584 ACCACCATAACATGCTCTCCTTT 59.989 43.478 0.00 0.00 0.00 3.11
1354 1468 2.945668 CTCCTTTCAATCCAATCCCGAC 59.054 50.000 0.00 0.00 0.00 4.79
1561 1675 1.652012 GCTGTTTTGCTACCACGCA 59.348 52.632 0.00 0.00 38.31 5.24
1584 1699 4.775780 AGGCACTGGTTGACTTATACTGTA 59.224 41.667 0.00 0.00 43.43 2.74
1591 1706 9.032624 ACTGGTTGACTTATACTGTACTAATGT 57.967 33.333 0.00 0.00 0.00 2.71
1726 1841 2.167487 GTGTTCTTTCCCCTGTTGCAAA 59.833 45.455 0.00 0.00 0.00 3.68
1842 1957 5.759059 AGGAAACCTGATGAATTCTATGCA 58.241 37.500 7.05 0.00 29.57 3.96
2135 2252 1.691434 GCAAATGAAGGTTGGTCCCAA 59.309 47.619 0.00 0.00 36.75 4.12
2139 2256 5.338300 GCAAATGAAGGTTGGTCCCAAATAT 60.338 40.000 0.00 0.00 37.70 1.28
2140 2257 6.710278 CAAATGAAGGTTGGTCCCAAATATT 58.290 36.000 0.00 0.00 37.70 1.28
2141 2258 6.950860 AATGAAGGTTGGTCCCAAATATTT 57.049 33.333 0.00 0.00 37.70 1.40
2143 2260 6.353404 TGAAGGTTGGTCCCAAATATTTTC 57.647 37.500 0.00 2.33 37.70 2.29
2144 2261 5.841237 TGAAGGTTGGTCCCAAATATTTTCA 59.159 36.000 0.00 4.59 37.70 2.69
2154 2271 8.992073 GGTCCCAAATATTTTCATTATTGATGC 58.008 33.333 0.00 0.00 35.64 3.91
2183 2300 2.392662 TGGCCAAATGTTGTTTCCTCA 58.607 42.857 0.61 0.00 0.00 3.86
2187 2304 4.051237 GCCAAATGTTGTTTCCTCACTTC 58.949 43.478 0.00 0.00 0.00 3.01
2195 2312 4.305989 TGTTTCCTCACTTCAAATGTGC 57.694 40.909 0.00 0.00 35.58 4.57
2244 2361 8.661352 AAAATCCTATTTTGTGGTTGAAGTTG 57.339 30.769 0.00 0.00 0.00 3.16
2245 2362 7.595819 AATCCTATTTTGTGGTTGAAGTTGA 57.404 32.000 0.00 0.00 0.00 3.18
2246 2363 7.781324 ATCCTATTTTGTGGTTGAAGTTGAT 57.219 32.000 0.00 0.00 0.00 2.57
2306 2423 9.807921 TTAATTACATGGAGATAATTCCTTCCC 57.192 33.333 0.00 0.00 38.12 3.97
2346 2464 6.495181 ACCATAGATACCTGTATCACTTGGAG 59.505 42.308 24.57 10.78 43.27 3.86
2358 2476 8.856153 TGTATCACTTGGAGTTTAATGCTTAA 57.144 30.769 0.00 0.00 0.00 1.85
2409 2527 8.239998 AGCTGATGAGTTTAAAGAACTAAATGC 58.760 33.333 0.00 0.00 0.00 3.56
2455 2573 1.536766 TGCTAGTGTGATTTGCTGCAC 59.463 47.619 0.00 0.00 35.63 4.57
2466 2584 7.011389 GTGTGATTTGCTGCACTACATAATAGA 59.989 37.037 0.00 0.00 36.05 1.98
2605 2723 4.072131 TGTTAATGTTCTCAAGCAGTCCC 58.928 43.478 0.00 0.00 0.00 4.46
2606 2724 4.202461 TGTTAATGTTCTCAAGCAGTCCCT 60.202 41.667 0.00 0.00 0.00 4.20
2758 2884 1.006813 AATGGGTATTGGGCAGTGGA 58.993 50.000 0.00 0.00 0.00 4.02
3037 3163 4.858692 GCTACTTTAATTGCACACACATGG 59.141 41.667 0.00 0.00 0.00 3.66
3045 3171 0.456628 GCACACACATGGCATATGCA 59.543 50.000 28.07 15.05 44.36 3.96
3063 3189 9.740239 GCATATGCATAGGATTTATATGTTTGG 57.260 33.333 21.91 0.00 41.59 3.28
3100 3226 9.970395 TCTACTTTAATTCAGTTTGTTCGAGTA 57.030 29.630 0.00 0.00 0.00 2.59
3517 3646 8.991783 ATTCATACATGATCTCACCAAGATTT 57.008 30.769 0.00 0.00 45.06 2.17
3520 3649 8.485392 TCATACATGATCTCACCAAGATTTGTA 58.515 33.333 0.00 11.14 45.06 2.41
3588 3717 4.213059 GCAGGCTCTAACATAGCAGAAATC 59.787 45.833 0.00 0.00 41.93 2.17
3815 3945 2.025887 CCTGAAGGTTGCCTCTTATGGT 60.026 50.000 0.00 0.00 30.89 3.55
4178 4309 2.842496 TGGGAGCTGACTTGATTCAGAT 59.158 45.455 4.29 0.00 44.91 2.90
4203 4334 2.496871 TGTAAATATCGGGTGTGGTCGT 59.503 45.455 0.00 0.00 0.00 4.34
4210 4341 3.118454 GGTGTGGTCGTCGCATGG 61.118 66.667 0.00 0.00 38.25 3.66
4237 4368 6.650807 ACGTTTTACTTGTCTGATGATGATGT 59.349 34.615 0.00 0.00 0.00 3.06
4251 4382 8.344446 TGATGATGATGTTCAAACAAGAAGAT 57.656 30.769 0.00 0.00 43.03 2.40
4257 4388 8.322906 TGATGTTCAAACAAGAAGATATCGTT 57.677 30.769 0.00 0.00 43.03 3.85
4335 4473 2.552315 CTGTATTCCGGCTTGTGTTTGT 59.448 45.455 0.00 0.00 0.00 2.83
4361 4499 1.338973 CGGGAATTGGGCAGAATGATG 59.661 52.381 0.00 0.00 39.69 3.07
4379 4517 6.663336 ATGATGATATCAATGGTATGGGGT 57.337 37.500 9.99 0.00 43.50 4.95
4402 4540 6.228258 GTTGAAACTGTTGTATACTCCCTCA 58.772 40.000 4.17 0.00 0.00 3.86
4403 4541 6.037786 TGAAACTGTTGTATACTCCCTCAG 57.962 41.667 4.17 7.79 0.00 3.35
4408 4546 3.245839 TGTTGTATACTCCCTCAGTCCCA 60.246 47.826 4.17 0.00 36.43 4.37
4419 4557 3.507622 CCCTCAGTCCCAAAATTCTTGTC 59.492 47.826 0.00 0.00 0.00 3.18
4423 4561 6.150140 CCTCAGTCCCAAAATTCTTGTCTTAG 59.850 42.308 0.00 0.00 0.00 2.18
4424 4562 6.837312 TCAGTCCCAAAATTCTTGTCTTAGA 58.163 36.000 0.00 0.00 0.00 2.10
4425 4563 7.461749 TCAGTCCCAAAATTCTTGTCTTAGAT 58.538 34.615 0.00 0.00 0.00 1.98
4426 4564 7.944554 TCAGTCCCAAAATTCTTGTCTTAGATT 59.055 33.333 0.00 0.00 0.00 2.40
4427 4565 8.579863 CAGTCCCAAAATTCTTGTCTTAGATTT 58.420 33.333 0.00 0.00 0.00 2.17
4428 4566 9.807921 AGTCCCAAAATTCTTGTCTTAGATTTA 57.192 29.630 0.00 0.00 0.00 1.40
4479 4617 8.879759 CGTTTTAGTGTTAGATACATCCACATT 58.120 33.333 0.00 0.00 39.39 2.71
4524 4663 9.004231 AGAATCTTAGGACAGGGTAATATTTGT 57.996 33.333 0.00 0.00 0.00 2.83
4552 4691 2.976882 AGTTGTAGGGGTGAAACTGCTA 59.023 45.455 0.00 0.00 36.74 3.49
4625 4835 3.888930 AGGGGTGAAACTGTTGTGTATTG 59.111 43.478 0.00 0.00 36.74 1.90
4806 5078 6.207417 CCGAATATTAGCAATTCCACATCCTT 59.793 38.462 0.00 0.00 30.98 3.36
4856 5129 5.452078 TGTGTTTGGATGTCAAATCCTTC 57.548 39.130 0.00 0.00 45.79 3.46
4905 5178 7.896895 GGTTAACCACTTTCACCCTCAGTGT 62.897 48.000 20.12 0.00 40.81 3.55
4924 5197 2.288763 TGTCATGCTCTTAACACGCTCA 60.289 45.455 0.00 0.00 0.00 4.26
4945 5218 6.983906 TCAGATAGAGATGTGGAATTGCTA 57.016 37.500 0.00 0.00 0.00 3.49
4948 5221 7.876582 TCAGATAGAGATGTGGAATTGCTAATG 59.123 37.037 0.00 0.00 0.00 1.90
4949 5222 6.654161 AGATAGAGATGTGGAATTGCTAATGC 59.346 38.462 0.00 0.00 40.20 3.56
4952 5225 6.359804 AGAGATGTGGAATTGCTAATGCTAA 58.640 36.000 0.00 0.00 40.48 3.09
4953 5226 6.485984 AGAGATGTGGAATTGCTAATGCTAAG 59.514 38.462 0.00 0.00 40.48 2.18
4954 5227 6.359804 AGATGTGGAATTGCTAATGCTAAGA 58.640 36.000 0.00 0.00 40.48 2.10
4955 5228 6.830324 AGATGTGGAATTGCTAATGCTAAGAA 59.170 34.615 0.00 0.00 40.48 2.52
4956 5229 6.441093 TGTGGAATTGCTAATGCTAAGAAG 57.559 37.500 0.00 0.00 40.48 2.85
4957 5230 5.945784 TGTGGAATTGCTAATGCTAAGAAGT 59.054 36.000 0.00 0.00 40.48 3.01
4960 5233 6.434028 TGGAATTGCTAATGCTAAGAAGTGTT 59.566 34.615 0.00 0.00 40.48 3.32
4961 5234 6.749118 GGAATTGCTAATGCTAAGAAGTGTTG 59.251 38.462 0.00 0.00 40.48 3.33
4962 5235 5.627499 TTGCTAATGCTAAGAAGTGTTGG 57.373 39.130 0.00 0.00 40.48 3.77
4963 5236 4.651778 TGCTAATGCTAAGAAGTGTTGGT 58.348 39.130 0.00 0.00 40.48 3.67
4964 5237 4.455533 TGCTAATGCTAAGAAGTGTTGGTG 59.544 41.667 0.00 0.00 40.48 4.17
4965 5238 4.142600 GCTAATGCTAAGAAGTGTTGGTGG 60.143 45.833 0.00 0.00 36.03 4.61
4966 5239 1.604604 TGCTAAGAAGTGTTGGTGGC 58.395 50.000 0.00 0.00 0.00 5.01
4967 5240 1.133945 TGCTAAGAAGTGTTGGTGGCA 60.134 47.619 0.00 0.00 0.00 4.92
4968 5241 1.953686 GCTAAGAAGTGTTGGTGGCAA 59.046 47.619 0.00 0.00 0.00 4.52
4969 5242 2.360801 GCTAAGAAGTGTTGGTGGCAAA 59.639 45.455 0.00 0.00 0.00 3.68
4970 5243 2.959507 AAGAAGTGTTGGTGGCAAAC 57.040 45.000 0.00 0.00 0.00 2.93
5094 5491 1.227383 GATTCCCCGCACCTCCAAT 59.773 57.895 0.00 0.00 0.00 3.16
5124 5521 6.575244 TTATCCCCTCTTATCTGCTTCAAA 57.425 37.500 0.00 0.00 0.00 2.69
5128 5525 5.133322 TCCCCTCTTATCTGCTTCAAATGAT 59.867 40.000 0.00 0.00 0.00 2.45
5131 5528 6.205076 CCCTCTTATCTGCTTCAAATGATCTG 59.795 42.308 0.00 0.00 0.00 2.90
5132 5529 6.205076 CCTCTTATCTGCTTCAAATGATCTGG 59.795 42.308 0.00 0.00 0.00 3.86
5135 5532 3.614092 TCTGCTTCAAATGATCTGGTCC 58.386 45.455 0.00 0.00 0.00 4.46
5137 5534 2.027385 GCTTCAAATGATCTGGTCCCC 58.973 52.381 0.00 0.00 0.00 4.81
5138 5535 2.292267 CTTCAAATGATCTGGTCCCCG 58.708 52.381 0.00 0.00 0.00 5.73
5140 5537 0.394216 CAAATGATCTGGTCCCCGCA 60.394 55.000 0.00 0.00 0.00 5.69
5144 5541 3.083997 ATCTGGTCCCCGCACCTC 61.084 66.667 0.00 0.00 37.34 3.85
5146 5543 4.087892 CTGGTCCCCGCACCTCAG 62.088 72.222 0.00 0.00 37.34 3.35
5168 7337 1.677052 TGGGCCGCGTAATTATTTTCC 59.323 47.619 4.92 0.00 0.00 3.13
5191 7360 4.207019 CGTGAAATTTCTTTGCCAAGACAC 59.793 41.667 18.64 4.27 38.86 3.67
5199 7368 2.949177 TTGCCAAGACACCAGTACAT 57.051 45.000 0.00 0.00 0.00 2.29
5211 7380 2.158682 ACCAGTACATCACAAACCTGCA 60.159 45.455 0.00 0.00 0.00 4.41
5282 7456 1.487452 GAGTGCGCTGACACGACAAA 61.487 55.000 3.44 0.00 45.45 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 2.035259 GCTTTTTGTAAACACGGTTGCG 60.035 45.455 0.00 0.00 0.00 4.85
205 207 2.111999 TAGCAGCGCTTGGTCAAGGT 62.112 55.000 7.50 2.26 40.44 3.50
974 1079 2.286872 TGTCCACGCTACTAGACTAGC 58.713 52.381 9.52 0.00 36.53 3.42
1024 1129 1.740585 ACGGACTTCAGATGAGACGAG 59.259 52.381 0.00 0.00 0.00 4.18
1027 1132 2.882324 GGAACGGACTTCAGATGAGAC 58.118 52.381 0.00 0.00 0.00 3.36
1074 1188 2.203070 CTGGAATTCCCCGGCGAG 60.203 66.667 21.90 7.42 34.29 5.03
1089 1203 1.603172 GGGCACGAGGATACGATTCTG 60.603 57.143 0.00 0.00 46.39 3.02
1133 1247 1.081092 TAGGGAAGGCCTGCTCTGT 59.919 57.895 25.18 0.00 0.00 3.41
1339 1453 0.464036 CGGAGTCGGGATTGGATTGA 59.536 55.000 0.00 0.00 0.00 2.57
1436 1550 0.390124 ACGAACTTGTACTTGGGCGA 59.610 50.000 0.00 0.00 0.00 5.54
1561 1675 3.583086 ACAGTATAAGTCAACCAGTGCCT 59.417 43.478 0.00 0.00 0.00 4.75
1580 1695 4.894784 ACCTGGTGTTGACATTAGTACAG 58.105 43.478 0.00 0.00 0.00 2.74
1584 1699 4.019321 AGCATACCTGGTGTTGACATTAGT 60.019 41.667 10.23 0.00 0.00 2.24
1591 1706 0.973632 ACGAGCATACCTGGTGTTGA 59.026 50.000 10.23 0.00 30.70 3.18
1842 1957 4.183916 TCAAGTCCCTTATCCTTTTCCCT 58.816 43.478 0.00 0.00 0.00 4.20
2139 2256 9.806203 CCATTACTCAAGCATCAATAATGAAAA 57.194 29.630 10.08 0.00 39.49 2.29
2140 2257 7.922278 GCCATTACTCAAGCATCAATAATGAAA 59.078 33.333 10.08 0.00 39.49 2.69
2141 2258 7.428020 GCCATTACTCAAGCATCAATAATGAA 58.572 34.615 10.08 0.00 39.49 2.57
2143 2260 6.154445 GGCCATTACTCAAGCATCAATAATG 58.846 40.000 0.00 0.00 38.50 1.90
2144 2261 5.834742 TGGCCATTACTCAAGCATCAATAAT 59.165 36.000 0.00 0.00 0.00 1.28
2154 2271 5.138125 ACAACATTTGGCCATTACTCAAG 57.862 39.130 6.09 0.00 34.12 3.02
2157 2274 4.929211 GGAAACAACATTTGGCCATTACTC 59.071 41.667 6.09 0.00 34.12 2.59
2183 2300 1.067516 AGCTTTGCGCACATTTGAAGT 59.932 42.857 11.12 0.00 42.61 3.01
2187 2304 1.593933 ACAAAGCTTTGCGCACATTTG 59.406 42.857 33.72 23.44 41.79 2.32
2195 2312 0.238289 ATGTCGGACAAAGCTTTGCG 59.762 50.000 33.72 28.66 41.79 4.85
2206 2323 9.503427 CAAAATAGGATTTTAAAGATGTCGGAC 57.497 33.333 0.00 0.00 0.00 4.79
2240 2357 9.784531 TCTCAAGAAATTAGTCTTCAATCAACT 57.215 29.630 0.00 0.00 35.63 3.16
2246 2363 9.559732 TGACAATCTCAAGAAATTAGTCTTCAA 57.440 29.630 0.00 0.00 35.63 2.69
2269 2386 8.958119 TCTCCATGTAATTAACCATAACTGAC 57.042 34.615 0.00 0.00 0.00 3.51
2377 2495 6.748333 TCTTTAAACTCATCAGCTTCCATG 57.252 37.500 0.00 0.00 0.00 3.66
2409 2527 3.744426 CCGGGTACACAAACTTAAGACTG 59.256 47.826 10.09 8.14 0.00 3.51
2515 2633 7.307514 CCATGAAATCACACAAGGAAAACATTG 60.308 37.037 0.00 0.00 0.00 2.82
2605 2723 6.845302 TGCTGAGTTGCATTATCTAAAACAG 58.155 36.000 0.00 0.00 38.12 3.16
2606 2724 6.816134 TGCTGAGTTGCATTATCTAAAACA 57.184 33.333 0.00 0.00 38.12 2.83
2758 2884 4.941713 TGGATGCCCCTAATAAAAAGTGT 58.058 39.130 0.00 0.00 35.38 3.55
3037 3163 9.740239 CCAAACATATAAATCCTATGCATATGC 57.260 33.333 21.09 21.09 42.50 3.14
3117 3243 2.860009 CTGCCATGCAAGATCCTACAT 58.140 47.619 0.00 0.00 38.41 2.29
3262 3389 8.097038 TCTGTCTTGCATCTCACTACTTTAATT 58.903 33.333 0.00 0.00 0.00 1.40
3588 3717 6.533819 TCAAAACGTTGGTACAGATGTTAG 57.466 37.500 0.00 0.00 42.39 2.34
3646 3775 2.147958 TGTTGGCAGGTTTCGTATCAC 58.852 47.619 0.00 0.00 0.00 3.06
3835 3965 8.985315 TTAACTTCATGCTTCATCCTTCATAT 57.015 30.769 0.00 0.00 0.00 1.78
4178 4309 2.420827 CCACACCCGATATTTACAGCCA 60.421 50.000 0.00 0.00 0.00 4.75
4203 4334 1.801771 CAAGTAAAACGTCCCATGCGA 59.198 47.619 0.00 0.00 0.00 5.10
4210 4341 5.637810 TCATCATCAGACAAGTAAAACGTCC 59.362 40.000 0.00 0.00 0.00 4.79
4237 4368 9.140286 CAGTAGAACGATATCTTCTTGTTTGAA 57.860 33.333 17.16 2.14 0.00 2.69
4251 4382 8.047413 TGTACAATGAGAACAGTAGAACGATA 57.953 34.615 0.00 0.00 0.00 2.92
4311 4448 2.968675 ACACAAGCCGGAATACAGTAC 58.031 47.619 5.05 0.00 0.00 2.73
4335 4473 2.994417 GCCCAATTCCCGGCAACA 60.994 61.111 0.00 0.00 45.01 3.33
4361 4499 6.777580 AGTTTCAACCCCATACCATTGATATC 59.222 38.462 0.00 0.00 31.45 1.63
4379 4517 6.042781 ACTGAGGGAGTATACAACAGTTTCAA 59.957 38.462 5.50 0.00 34.21 2.69
4402 4540 8.712228 AAATCTAAGACAAGAATTTTGGGACT 57.288 30.769 5.68 0.00 0.00 3.85
4429 4567 9.049523 ACGTGACTAGATACATTCGTATTTAGA 57.950 33.333 13.92 0.00 41.85 2.10
4430 4568 9.661187 AACGTGACTAGATACATTCGTATTTAG 57.339 33.333 0.00 8.04 43.54 1.85
4432 4570 8.922058 AAACGTGACTAGATACATTCGTATTT 57.078 30.769 0.00 0.00 38.48 1.40
4433 4571 8.922058 AAAACGTGACTAGATACATTCGTATT 57.078 30.769 0.00 0.00 38.48 1.89
4434 4572 9.661187 CTAAAACGTGACTAGATACATTCGTAT 57.339 33.333 0.00 0.00 41.16 3.06
4435 4573 8.668353 ACTAAAACGTGACTAGATACATTCGTA 58.332 33.333 0.00 0.00 0.00 3.43
4436 4574 7.484007 CACTAAAACGTGACTAGATACATTCGT 59.516 37.037 0.00 0.00 37.06 3.85
4437 4575 7.484007 ACACTAAAACGTGACTAGATACATTCG 59.516 37.037 0.00 0.00 38.27 3.34
4438 4576 8.684973 ACACTAAAACGTGACTAGATACATTC 57.315 34.615 0.00 0.00 38.27 2.67
4440 4578 9.784680 CTAACACTAAAACGTGACTAGATACAT 57.215 33.333 0.00 0.00 38.27 2.29
4441 4579 9.002600 TCTAACACTAAAACGTGACTAGATACA 57.997 33.333 0.00 0.00 38.27 2.29
4453 4591 7.821595 TGTGGATGTATCTAACACTAAAACG 57.178 36.000 0.00 0.00 42.09 3.60
4508 4646 8.747538 ACTATCCAAACAAATATTACCCTGTC 57.252 34.615 0.00 0.00 0.00 3.51
4510 4648 8.966868 ACAACTATCCAAACAAATATTACCCTG 58.033 33.333 0.00 0.00 0.00 4.45
4524 4663 5.073965 AGTTTCACCCCTACAACTATCCAAA 59.926 40.000 0.00 0.00 0.00 3.28
4625 4835 1.282157 AGTTCCAGCACTATCCAACCC 59.718 52.381 0.00 0.00 0.00 4.11
4806 5078 6.148315 CAGTTTCAAATCAGAGTCTGCATGTA 59.852 38.462 15.72 5.28 0.00 2.29
4856 5129 0.038618 TCCAACACGATCAGACGGTG 60.039 55.000 0.00 1.91 37.61 4.94
4905 5178 2.231235 TCTGAGCGTGTTAAGAGCATGA 59.769 45.455 0.00 0.00 0.00 3.07
4924 5197 6.654161 GCATTAGCAATTCCACATCTCTATCT 59.346 38.462 0.00 0.00 41.58 1.98
4939 5212 5.711976 ACCAACACTTCTTAGCATTAGCAAT 59.288 36.000 0.00 0.00 45.49 3.56
4940 5213 5.048782 CACCAACACTTCTTAGCATTAGCAA 60.049 40.000 0.00 0.00 45.49 3.91
4945 5218 2.558359 GCCACCAACACTTCTTAGCATT 59.442 45.455 0.00 0.00 0.00 3.56
4948 5221 1.604604 TGCCACCAACACTTCTTAGC 58.395 50.000 0.00 0.00 0.00 3.09
4949 5222 3.243401 GGTTTGCCACCAACACTTCTTAG 60.243 47.826 0.00 0.00 46.42 2.18
4952 5225 1.111277 GGTTTGCCACCAACACTTCT 58.889 50.000 0.00 0.00 46.42 2.85
4953 5226 3.659850 GGTTTGCCACCAACACTTC 57.340 52.632 0.00 0.00 46.42 3.01
4962 5235 7.996385 ACTGTTAATATTATCAGGTTTGCCAC 58.004 34.615 26.31 8.00 35.69 5.01
4963 5236 8.588290 AACTGTTAATATTATCAGGTTTGCCA 57.412 30.769 26.31 0.00 35.69 4.92
5006 5403 3.189606 ACACCCCCTTTATGTCAGATCA 58.810 45.455 0.00 0.00 0.00 2.92
5102 5499 6.329986 TCATTTGAAGCAGATAAGAGGGGATA 59.670 38.462 0.00 0.00 0.00 2.59
5106 5503 6.205076 CAGATCATTTGAAGCAGATAAGAGGG 59.795 42.308 0.00 0.00 0.00 4.30
5109 5506 6.656902 ACCAGATCATTTGAAGCAGATAAGA 58.343 36.000 0.00 0.00 0.00 2.10
5132 5529 4.767255 CAGCTGAGGTGCGGGGAC 62.767 72.222 8.42 0.00 38.13 4.46
5144 5541 0.884704 ATAATTACGCGGCCCAGCTG 60.885 55.000 12.47 6.78 38.08 4.24
5146 5543 0.666374 AAATAATTACGCGGCCCAGC 59.334 50.000 12.47 0.00 0.00 4.85
5147 5544 2.287368 GGAAAATAATTACGCGGCCCAG 60.287 50.000 12.47 0.00 0.00 4.45
5152 7321 3.929417 TCACGGAAAATAATTACGCGG 57.071 42.857 12.47 0.00 0.00 6.46
5168 7337 4.207019 GTGTCTTGGCAAAGAAATTTCACG 59.793 41.667 19.99 8.73 44.01 4.35
5191 7360 2.503331 TGCAGGTTTGTGATGTACTGG 58.497 47.619 0.00 0.00 0.00 4.00
5199 7368 2.159254 GCTTCACTTTGCAGGTTTGTGA 60.159 45.455 0.00 0.00 36.10 3.58
5211 7380 3.403936 AGCTTCACGGCTTCACTTT 57.596 47.368 0.00 0.00 39.86 2.66
5282 7456 3.314331 CTGGACGCCTGGACCACT 61.314 66.667 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.