Multiple sequence alignment - TraesCS2A01G439400

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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 TraesCS2A01G439400 chr2A 100.000 3900 0 0 1 3900 690737159 690741058 0.000000e+00 7203.0
1 TraesCS2A01G439400 chr2A 87.097 465 60 0 2233 2697 689710082 689709618 9.600000e-146 527.0
2 TraesCS2A01G439400 chr2A 96.552 58 2 0 3773 3830 690740873 690740930 3.210000e-16 97.1
3 TraesCS2A01G439400 chr2A 96.552 58 2 0 3715 3772 690740931 690740988 3.210000e-16 97.1
4 TraesCS2A01G439400 chr2D 89.480 3137 167 70 246 3269 547249462 547252548 0.000000e+00 3814.0
5 TraesCS2A01G439400 chr2D 93.515 1064 56 7 2212 3269 555133696 555134752 0.000000e+00 1570.0
6 TraesCS2A01G439400 chr2D 86.486 481 64 1 2218 2697 546872603 546873083 9.600000e-146 527.0
7 TraesCS2A01G439400 chr2D 86.214 486 67 0 2212 2697 546932410 546932895 9.600000e-146 527.0
8 TraesCS2A01G439400 chr2D 88.125 160 16 3 2108 2265 29675311 29675153 1.850000e-43 187.0
9 TraesCS2A01G439400 chr2D 93.750 64 4 0 3837 3900 555135238 555135301 3.210000e-16 97.1
10 TraesCS2A01G439400 chr2B 89.451 2114 125 50 1616 3670 653746614 653748688 0.000000e+00 2579.0
11 TraesCS2A01G439400 chr2B 90.762 1050 69 20 590 1619 653745551 653746592 0.000000e+00 1376.0
12 TraesCS2A01G439400 chr2B 87.868 544 39 17 2 532 653745001 653745530 7.160000e-172 614.0
13 TraesCS2A01G439400 chr2B 87.421 477 60 0 2221 2697 653611135 653611611 2.050000e-152 549.0
14 TraesCS2A01G439400 chr2B 86.008 486 68 0 2212 2697 653619729 653620214 4.470000e-144 521.0
15 TraesCS2A01G439400 chr6B 88.762 703 68 7 918 1616 464408069 464408764 0.000000e+00 850.0
16 TraesCS2A01G439400 chr6B 85.366 82 9 3 1232 1313 532151725 532151647 8.980000e-12 82.4
17 TraesCS2A01G439400 chr7B 88.666 697 46 6 925 1616 616911545 616912213 0.000000e+00 819.0
18 TraesCS2A01G439400 chr3B 87.483 719 56 7 902 1616 280583873 280584561 0.000000e+00 798.0
19 TraesCS2A01G439400 chr3B 85.971 278 28 7 1937 2213 369097385 369097118 1.770000e-73 287.0
20 TraesCS2A01G439400 chr3B 89.375 160 14 3 2108 2265 717559892 717559734 8.550000e-47 198.0
21 TraesCS2A01G439400 chr3B 89.381 113 6 1 1118 1230 369101085 369100979 1.890000e-28 137.0
22 TraesCS2A01G439400 chr4B 87.246 690 55 10 928 1612 548863916 548863255 0.000000e+00 756.0
23 TraesCS2A01G439400 chr3D 84.861 502 76 0 2204 2705 33298448 33297947 1.250000e-139 507.0
24 TraesCS2A01G439400 chr3D 88.125 160 16 3 2108 2265 440213374 440213216 1.850000e-43 187.0
25 TraesCS2A01G439400 chr5A 85.612 278 30 6 1937 2213 262335446 262335714 2.290000e-72 283.0
26 TraesCS2A01G439400 chr1D 89.375 160 14 3 2108 2265 359549101 359548943 8.550000e-47 198.0
27 TraesCS2A01G439400 chr5D 88.750 160 15 3 2108 2265 12362691 12362849 3.980000e-45 193.0
28 TraesCS2A01G439400 chr6D 85.185 81 9 3 1232 1312 348029477 348029554 3.230000e-11 80.5
29 TraesCS2A01G439400 chr6A 85.185 81 9 3 1232 1312 495465163 495465086 3.230000e-11 80.5


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 TraesCS2A01G439400 chr2A 690737159 690741058 3899 False 2465.733333 7203 97.701333 1 3900 3 chr2A.!!$F1 3899
1 TraesCS2A01G439400 chr2D 547249462 547252548 3086 False 3814.000000 3814 89.480000 246 3269 1 chr2D.!!$F3 3023
2 TraesCS2A01G439400 chr2D 555133696 555135301 1605 False 833.550000 1570 93.632500 2212 3900 2 chr2D.!!$F4 1688
3 TraesCS2A01G439400 chr2B 653745001 653748688 3687 False 1523.000000 2579 89.360333 2 3670 3 chr2B.!!$F3 3668
4 TraesCS2A01G439400 chr6B 464408069 464408764 695 False 850.000000 850 88.762000 918 1616 1 chr6B.!!$F1 698
5 TraesCS2A01G439400 chr7B 616911545 616912213 668 False 819.000000 819 88.666000 925 1616 1 chr7B.!!$F1 691
6 TraesCS2A01G439400 chr3B 280583873 280584561 688 False 798.000000 798 87.483000 902 1616 1 chr3B.!!$F1 714
7 TraesCS2A01G439400 chr3B 369097118 369101085 3967 True 212.000000 287 87.676000 1118 2213 2 chr3B.!!$R2 1095
8 TraesCS2A01G439400 chr4B 548863255 548863916 661 True 756.000000 756 87.246000 928 1612 1 chr4B.!!$R1 684
9 TraesCS2A01G439400 chr3D 33297947 33298448 501 True 507.000000 507 84.861000 2204 2705 1 chr3D.!!$R1 501


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
568 584 0.101040 CGTAATTCGTGTCCCGCCTA 59.899 55.000 0.0 0.0 36.19 3.93 F
635 651 0.742281 CCTCTCGTTGGATGCCAGTG 60.742 60.000 0.0 0.0 33.81 3.66 F
955 984 1.416049 CGTCAGCATCAAACGACGG 59.584 57.895 0.0 0.0 45.60 4.79 F
1497 2285 1.681327 ATGGGAGACGTACACCGCT 60.681 57.895 0.0 0.0 41.42 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1727 3769 0.178068 ATGCTACATCCGTCACCCAC 59.822 55.0 0.00 0.0 0.00 4.61 R
1858 3902 0.459585 CATCCCCACGAACGAACGAT 60.460 55.0 11.97 0.0 37.03 3.73 R
2753 5817 0.107312 ACAGATGAGCATGGACTGGC 60.107 55.0 0.00 0.0 33.57 4.85 R
3430 6537 0.393267 CGGGGTTTAAAGGATGCGGA 60.393 55.0 0.00 0.0 0.00 5.54 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
101 107 1.134580 CATCTGCCGGAACACATCTCT 60.135 52.381 5.05 0.00 0.00 3.10
122 128 5.901552 TCTCATTTCGCTTTGTTTCCTTTT 58.098 33.333 0.00 0.00 0.00 2.27
144 150 1.202290 GCCAGATATTTGCCAACCGTG 60.202 52.381 0.00 0.00 0.00 4.94
146 152 2.951642 CCAGATATTTGCCAACCGTGAT 59.048 45.455 0.00 0.00 0.00 3.06
154 160 6.767524 ATTTGCCAACCGTGATAAAGATAA 57.232 33.333 0.00 0.00 0.00 1.75
156 162 5.554822 TGCCAACCGTGATAAAGATAAAC 57.445 39.130 0.00 0.00 0.00 2.01
157 163 4.093703 TGCCAACCGTGATAAAGATAAACG 59.906 41.667 0.00 0.00 0.00 3.60
190 196 1.109323 GCCAAGTGTGAAAGGGTGCT 61.109 55.000 0.00 0.00 0.00 4.40
205 211 5.717119 AGGGTGCTAAACAGAATATTCCT 57.283 39.130 11.92 0.00 0.00 3.36
208 214 5.760743 GGGTGCTAAACAGAATATTCCTCTC 59.239 44.000 11.92 0.00 0.00 3.20
215 221 6.642707 AACAGAATATTCCTCTCCTACGAG 57.357 41.667 11.92 0.00 37.48 4.18
243 255 3.334583 TCAGAACCTGATTGTACAGCC 57.665 47.619 0.00 0.00 35.39 4.85
259 271 1.599240 GCCAGGCTTCGATGATCCC 60.599 63.158 3.29 0.00 0.00 3.85
320 332 3.829886 AAATCGTCGTTCATTGTGCAT 57.170 38.095 0.00 0.00 0.00 3.96
367 380 4.021102 ACCACTAACCAAACTCCATGAG 57.979 45.455 0.00 0.00 35.52 2.90
379 392 4.308526 CATGAGTGGAGGCACACC 57.691 61.111 8.46 0.00 42.28 4.16
492 508 4.740741 AATGCCCGCAAAATAAACAAAC 57.259 36.364 0.00 0.00 0.00 2.93
495 511 4.192317 TGCCCGCAAAATAAACAAACTTT 58.808 34.783 0.00 0.00 0.00 2.66
542 558 1.933853 CGAGTGCTTACATGGCTAACC 59.066 52.381 0.00 0.00 0.00 2.85
568 584 0.101040 CGTAATTCGTGTCCCGCCTA 59.899 55.000 0.00 0.00 36.19 3.93
569 585 1.849097 GTAATTCGTGTCCCGCCTAG 58.151 55.000 0.00 0.00 36.19 3.02
581 597 2.125147 GCCTAGGCATCACACGCA 60.125 61.111 29.33 0.00 41.49 5.24
582 598 2.464459 GCCTAGGCATCACACGCAC 61.464 63.158 29.33 0.00 41.49 5.34
583 599 2.167219 CCTAGGCATCACACGCACG 61.167 63.158 0.00 0.00 0.00 5.34
584 600 2.802667 CTAGGCATCACACGCACGC 61.803 63.158 0.00 0.00 0.00 5.34
602 618 3.423154 CAGTCCGGTCGCAAAGCC 61.423 66.667 0.00 0.00 0.00 4.35
619 635 3.470567 CGCGAACACGTGAGCCTC 61.471 66.667 25.01 11.57 39.45 4.70
635 651 0.742281 CCTCTCGTTGGATGCCAGTG 60.742 60.000 0.00 0.00 33.81 3.66
648 664 2.357517 CAGTGGTCACAGGCCGTC 60.358 66.667 0.00 0.00 0.00 4.79
735 752 3.006967 TCGACTTGGAGGAGAAGAAAAGG 59.993 47.826 0.00 0.00 0.00 3.11
738 755 1.747444 TGGAGGAGAAGAAAAGGCCT 58.253 50.000 0.00 0.00 0.00 5.19
747 764 3.139211 AGAAGAAAAGGCCTCCTCAGTTT 59.861 43.478 5.23 0.44 30.89 2.66
841 859 2.419198 CATCGCTCCTCCTTCCCG 59.581 66.667 0.00 0.00 0.00 5.14
856 874 4.222145 TCCTTCCCGATATAAAATCCCTCG 59.778 45.833 0.00 0.00 0.00 4.63
860 878 2.027561 CCGATATAAAATCCCTCGGCCA 60.028 50.000 2.24 0.00 41.95 5.36
881 899 1.534729 AAGACCCTTCCATTCGCAAC 58.465 50.000 0.00 0.00 0.00 4.17
916 938 4.966787 CACCCCAACCACCCACCG 62.967 72.222 0.00 0.00 0.00 4.94
955 984 1.416049 CGTCAGCATCAAACGACGG 59.584 57.895 0.00 0.00 45.60 4.79
1178 1239 4.883354 GGATGAGGCGGCCAAGGG 62.883 72.222 23.09 0.00 0.00 3.95
1392 1475 2.353607 CCAGATCGGAGCGCGTAC 60.354 66.667 8.43 1.52 36.56 3.67
1426 1509 4.267690 GGCGCTGTTATTTTATTTCCTTGC 59.732 41.667 7.64 0.00 0.00 4.01
1497 2285 1.681327 ATGGGAGACGTACACCGCT 60.681 57.895 0.00 0.00 41.42 5.52
1692 3733 2.486636 TTCGCCGAAGACAGCACGAT 62.487 55.000 0.00 0.00 0.00 3.73
1727 3769 2.244436 CTTTGCGTGTCATGGCCTCG 62.244 60.000 3.32 7.47 0.00 4.63
1774 3817 4.209452 TGTCACGCTTTTGATTCTGTTC 57.791 40.909 0.00 0.00 0.00 3.18
1833 3876 2.791501 TTAGAACGCGGACCCAAGCC 62.792 60.000 12.47 0.00 0.00 4.35
1839 3882 2.511600 CGGACCCAAGCCGTCATC 60.512 66.667 0.00 0.00 43.66 2.92
1841 3884 2.124695 GACCCAAGCCGTCATCCC 60.125 66.667 0.00 0.00 0.00 3.85
1988 5049 4.757149 AGACTGTCAGCAAACATTAGGAAC 59.243 41.667 10.88 0.00 0.00 3.62
1991 5052 3.820467 TGTCAGCAAACATTAGGAACTGG 59.180 43.478 0.00 0.00 41.52 4.00
2009 5070 4.881920 ACTGGAAACACAAATAACATGGC 58.118 39.130 0.00 0.00 35.60 4.40
2031 5093 4.045104 CGACCTTGACATGCTACTACATC 58.955 47.826 0.00 0.00 0.00 3.06
2035 5097 3.710326 TGACATGCTACTACATCGGAC 57.290 47.619 0.00 0.00 0.00 4.79
2044 5106 9.203421 CATGCTACTACATCGGACATTTTATTA 57.797 33.333 0.00 0.00 0.00 0.98
2068 5130 4.774124 TGATTAAAGCACCAGAGAGGATG 58.226 43.478 0.00 0.00 41.22 3.51
2132 5194 7.116662 TCTGTTTATCATGATTTTTGCACAAGC 59.883 33.333 14.65 2.22 42.57 4.01
2151 5213 5.129980 ACAAGCTGTATCATCTTGATCTCCA 59.870 40.000 16.53 0.00 39.15 3.86
2169 5231 7.604164 TGATCTCCACTCTGTATTTTGAAGTTC 59.396 37.037 0.00 0.00 0.00 3.01
2251 5313 2.743928 CTGGAGACTGTTGCCGCC 60.744 66.667 0.00 0.00 0.00 6.13
2485 5547 1.741401 CATCTCGCCCAAGTTCGCA 60.741 57.895 0.00 0.00 0.00 5.10
2737 5799 3.128242 CCACAAGATCAGCAAGTCAATCC 59.872 47.826 0.00 0.00 0.00 3.01
2753 5817 0.929244 ATCCTGACCCCATTTCCTGG 59.071 55.000 0.00 0.00 45.51 4.45
2805 5871 4.005650 TGGTTCTGAACTTCTGATGATGC 58.994 43.478 19.05 0.12 0.00 3.91
2820 5888 2.730382 TGATGCATGCTGATTTGGTCT 58.270 42.857 20.33 0.00 0.00 3.85
2928 5996 3.114809 CGTGTTCTGCTGAATTTTGCAA 58.885 40.909 9.40 0.00 38.81 4.08
2937 6008 3.846335 GCTGAATTTTGCAACGCTACTAC 59.154 43.478 0.00 0.00 0.00 2.73
2938 6009 4.378459 GCTGAATTTTGCAACGCTACTACT 60.378 41.667 0.00 0.00 0.00 2.57
2939 6010 5.029650 TGAATTTTGCAACGCTACTACTG 57.970 39.130 0.00 0.00 0.00 2.74
3041 6116 5.600908 TTGTTGCTCGTTTGGTAACTATC 57.399 39.130 0.00 0.00 32.13 2.08
3189 6264 9.628500 ATTGATCTACCTCGCTATGTACATATA 57.372 33.333 15.81 4.09 0.00 0.86
3222 6298 8.877864 TGAATATTCTTCCTTTTCCTTGCTAA 57.122 30.769 16.24 0.00 0.00 3.09
3228 6304 6.068010 TCTTCCTTTTCCTTGCTAATGTTGA 58.932 36.000 0.00 0.00 0.00 3.18
3250 6326 8.457261 GTTGAATTTTCTGATCTGCAGTAGATT 58.543 33.333 14.67 7.77 46.12 2.40
3306 6396 1.594331 GCTTCTGACGGTTGGACTTT 58.406 50.000 0.00 0.00 0.00 2.66
3308 6398 2.357952 GCTTCTGACGGTTGGACTTTTT 59.642 45.455 0.00 0.00 0.00 1.94
3334 6424 2.573009 TGACAGAATTCTGAGCATCCCA 59.427 45.455 36.15 19.36 46.59 4.37
3355 6450 3.702048 CTTCCCGGGGCGAACTGA 61.702 66.667 23.50 0.00 0.00 3.41
3356 6451 3.006728 TTCCCGGGGCGAACTGAT 61.007 61.111 23.50 0.00 0.00 2.90
3357 6452 2.925162 CTTCCCGGGGCGAACTGATC 62.925 65.000 23.50 0.00 0.00 2.92
3362 6457 0.878416 CGGGGCGAACTGATCAAAAA 59.122 50.000 0.00 0.00 0.00 1.94
3365 6460 1.886542 GGGCGAACTGATCAAAAACCT 59.113 47.619 0.00 0.00 0.00 3.50
3369 6469 4.499019 GGCGAACTGATCAAAAACCTTTCA 60.499 41.667 0.00 0.00 0.00 2.69
3382 6482 3.652057 ACCTTTCACCCGATCATTGAT 57.348 42.857 0.00 0.00 0.00 2.57
3384 6484 3.054434 ACCTTTCACCCGATCATTGATCA 60.054 43.478 22.95 0.00 38.84 2.92
3391 6491 3.129109 CCCGATCATTGATCAGTCACAG 58.871 50.000 22.95 7.69 38.84 3.66
3399 6506 5.349543 TCATTGATCAGTCACAGAATCAACG 59.650 40.000 0.00 0.00 33.11 4.10
3400 6507 2.995939 TGATCAGTCACAGAATCAACGC 59.004 45.455 0.00 0.00 0.00 4.84
3421 6528 3.769300 GCAACCCTTCAAACCATCCTATT 59.231 43.478 0.00 0.00 0.00 1.73
3422 6529 4.142160 GCAACCCTTCAAACCATCCTATTC 60.142 45.833 0.00 0.00 0.00 1.75
3423 6530 3.886123 ACCCTTCAAACCATCCTATTCG 58.114 45.455 0.00 0.00 0.00 3.34
3424 6531 3.214328 CCCTTCAAACCATCCTATTCGG 58.786 50.000 0.00 0.00 0.00 4.30
3426 6533 2.341846 TCAAACCATCCTATTCGGGC 57.658 50.000 0.00 0.00 0.00 6.13
3427 6534 1.843851 TCAAACCATCCTATTCGGGCT 59.156 47.619 0.00 0.00 0.00 5.19
3428 6535 1.949525 CAAACCATCCTATTCGGGCTG 59.050 52.381 0.00 0.00 0.00 4.85
3430 6537 1.213296 ACCATCCTATTCGGGCTGTT 58.787 50.000 0.00 0.00 0.00 3.16
3431 6538 1.141053 ACCATCCTATTCGGGCTGTTC 59.859 52.381 0.00 0.00 0.00 3.18
3439 6546 4.473520 CGGGCTGTTCCGCATCCT 62.474 66.667 0.00 0.00 43.71 3.24
3466 6575 2.768253 CCGCATATCTATGAGGGCAA 57.232 50.000 11.02 0.00 46.05 4.52
3467 6576 3.272574 CCGCATATCTATGAGGGCAAT 57.727 47.619 11.02 0.00 46.05 3.56
3485 6594 4.320275 GGCAATTATTAGAAGGCCTAACGC 60.320 45.833 5.16 1.90 39.93 4.84
3498 6607 1.470805 CCTAACGCGTCCATCATGTCA 60.471 52.381 14.44 0.00 0.00 3.58
3501 6610 0.458543 ACGCGTCCATCATGTCAGAC 60.459 55.000 5.58 0.00 0.00 3.51
3524 6633 3.416880 ATAACCTGGCCCACCCCG 61.417 66.667 0.00 0.00 33.59 5.73
3535 6644 4.609018 CACCCCGAGCCATAGCCG 62.609 72.222 0.00 0.00 41.25 5.52
3555 6664 0.322008 CTTGCCACTCCACTTCCTCC 60.322 60.000 0.00 0.00 0.00 4.30
3670 6789 4.140900 TCCCAGGAGGAAACAAATTTACCA 60.141 41.667 0.00 0.00 43.78 3.25
3671 6790 4.591072 CCCAGGAGGAAACAAATTTACCAA 59.409 41.667 0.00 0.00 38.24 3.67
3672 6791 5.071115 CCCAGGAGGAAACAAATTTACCAAA 59.929 40.000 0.00 0.00 38.24 3.28
3673 6792 6.239858 CCCAGGAGGAAACAAATTTACCAAAT 60.240 38.462 0.00 0.00 38.24 2.32
3674 6793 7.223584 CCAGGAGGAAACAAATTTACCAAATT 58.776 34.615 0.00 0.00 38.90 1.82
3675 6794 7.719193 CCAGGAGGAAACAAATTTACCAAATTT 59.281 33.333 4.23 4.23 43.41 1.82
3676 6795 9.771534 CAGGAGGAAACAAATTTACCAAATTTA 57.228 29.630 8.78 0.00 46.34 1.40
3677 6796 9.772973 AGGAGGAAACAAATTTACCAAATTTAC 57.227 29.630 8.78 3.32 46.34 2.01
3681 6800 7.095144 GGAAACAAATTTACCAAATTTACCCCG 60.095 37.037 8.78 1.31 46.34 5.73
3684 6803 2.197283 TTACCAAATTTACCCCGCGT 57.803 45.000 4.92 0.00 0.00 6.01
3686 6805 0.883153 ACCAAATTTACCCCGCGTTC 59.117 50.000 4.92 0.00 0.00 3.95
3706 6825 2.173356 TCCGCCATTCAATCCTTCTGAT 59.827 45.455 0.00 0.00 34.22 2.90
3727 6846 2.500910 TGGGAATCCATTGTTTCCATGC 59.499 45.455 0.09 2.59 40.65 4.06
3728 6847 2.500910 GGGAATCCATTGTTTCCATGCA 59.499 45.455 0.09 0.00 40.65 3.96
3729 6848 3.055240 GGGAATCCATTGTTTCCATGCAA 60.055 43.478 0.09 0.00 40.65 4.08
3730 6849 4.186159 GGAATCCATTGTTTCCATGCAAG 58.814 43.478 0.00 0.00 39.29 4.01
3731 6850 4.322953 GGAATCCATTGTTTCCATGCAAGT 60.323 41.667 0.00 0.00 39.29 3.16
3732 6851 3.663995 TCCATTGTTTCCATGCAAGTG 57.336 42.857 0.00 0.00 0.00 3.16
3733 6852 2.299582 TCCATTGTTTCCATGCAAGTGG 59.700 45.455 0.00 0.00 40.76 4.00
3734 6853 2.613474 CCATTGTTTCCATGCAAGTGGG 60.613 50.000 6.50 0.00 39.80 4.61
3735 6854 0.392336 TTGTTTCCATGCAAGTGGGC 59.608 50.000 6.50 0.00 39.80 5.36
3736 6855 1.080569 GTTTCCATGCAAGTGGGCG 60.081 57.895 6.50 0.00 39.80 6.13
3737 6856 2.929903 TTTCCATGCAAGTGGGCGC 61.930 57.895 6.50 0.00 39.80 6.53
3738 6857 3.866379 TTCCATGCAAGTGGGCGCT 62.866 57.895 7.64 0.00 39.80 5.92
3739 6858 4.124351 CCATGCAAGTGGGCGCTG 62.124 66.667 7.64 0.00 35.55 5.18
3740 6859 4.124351 CATGCAAGTGGGCGCTGG 62.124 66.667 7.64 0.00 36.28 4.85
3781 6900 1.034292 GGAGGCTCCACATTGCTTCC 61.034 60.000 28.55 0.00 45.59 3.46
3782 6901 0.322816 GAGGCTCCACATTGCTTCCA 60.323 55.000 2.15 0.00 30.50 3.53
3794 6913 2.879907 CTTCCATGCAAGTGGGCG 59.120 61.111 6.50 0.00 39.80 6.13
3796 6915 3.866379 TTCCATGCAAGTGGGCGCT 62.866 57.895 7.64 0.00 39.80 5.92
3797 6916 4.124351 CCATGCAAGTGGGCGCTG 62.124 66.667 7.64 0.00 35.55 5.18
3798 6917 4.124351 CATGCAAGTGGGCGCTGG 62.124 66.667 7.64 0.00 36.28 4.85
3835 6954 2.665603 GCGGAGGCTCCAGAACTT 59.334 61.111 31.69 0.00 35.91 2.66
3850 6980 0.884704 AACTTGTGGCAGTACAGGCG 60.885 55.000 7.32 0.00 36.77 5.52
3891 7021 1.583495 GCTGGTCGCAAAACCCCTAC 61.583 60.000 0.00 0.00 38.65 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.992715 GGCAACCGCTATTAATAGATCCATAT 59.007 38.462 23.84 2.59 38.60 1.78
3 4 4.575885 GGCAACCGCTATTAATAGATCCA 58.424 43.478 23.84 0.00 38.60 3.41
57 59 5.814040 GCCCATCCATCCATCCCAATATTTA 60.814 44.000 0.00 0.00 0.00 1.40
65 67 0.324091 GATGCCCATCCATCCATCCC 60.324 60.000 0.00 0.00 36.46 3.85
93 99 4.675190 ACAAAGCGAAATGAGAGATGTG 57.325 40.909 0.00 0.00 0.00 3.21
101 107 4.737765 CGAAAAGGAAACAAAGCGAAATGA 59.262 37.500 0.00 0.00 0.00 2.57
122 128 1.388547 GGTTGGCAAATATCTGGCGA 58.611 50.000 0.00 0.00 44.56 5.54
144 150 3.308866 ACGTGCAGCCGTTTATCTTTATC 59.691 43.478 3.38 0.00 37.96 1.75
146 152 2.690786 ACGTGCAGCCGTTTATCTTTA 58.309 42.857 3.38 0.00 37.96 1.85
174 180 3.626930 TGTTTAGCACCCTTTCACACTT 58.373 40.909 0.00 0.00 0.00 3.16
190 196 7.997223 TCTCGTAGGAGAGGAATATTCTGTTTA 59.003 37.037 14.95 0.00 44.28 2.01
208 214 4.701171 AGGTTCTGAAGTAGTTCTCGTAGG 59.299 45.833 11.52 0.00 33.38 3.18
215 221 7.152645 TGTACAATCAGGTTCTGAAGTAGTTC 58.847 38.462 3.15 3.15 44.04 3.01
243 255 2.216898 GAAAGGGATCATCGAAGCCTG 58.783 52.381 0.00 0.00 0.00 4.85
317 329 8.768957 ATATAATATGTGAGACAGTGTCATGC 57.231 34.615 24.73 13.73 34.60 4.06
367 380 2.665185 GTGACGGTGTGCCTCCAC 60.665 66.667 0.00 0.00 42.40 4.02
379 392 5.675970 AGTGAACGTATTCAATTTGTGACG 58.324 37.500 14.40 14.40 46.40 4.35
474 490 4.804608 AAAGTTTGTTTATTTTGCGGGC 57.195 36.364 0.00 0.00 0.00 6.13
511 527 6.293190 CCATGTAAGCACTCGTTTTAACTTCA 60.293 38.462 0.00 0.00 0.00 3.02
583 599 3.423154 CTTTGCGACCGGACTGGC 61.423 66.667 9.46 6.11 43.94 4.85
584 600 3.423154 GCTTTGCGACCGGACTGG 61.423 66.667 9.46 0.00 46.41 4.00
585 601 3.423154 GGCTTTGCGACCGGACTG 61.423 66.667 9.46 0.00 0.00 3.51
602 618 3.470567 GAGGCTCACGTGTTCGCG 61.471 66.667 16.51 0.00 41.18 5.87
605 621 0.318784 AACGAGAGGCTCACGTGTTC 60.319 55.000 34.19 13.95 42.48 3.18
619 635 1.003355 ACCACTGGCATCCAACGAG 60.003 57.895 0.00 0.00 30.80 4.18
635 651 3.311110 TGGAGACGGCCTGTGACC 61.311 66.667 0.00 6.96 0.00 4.02
675 692 1.135774 GGTCGTTGCGATTTTCTTCCC 60.136 52.381 0.00 0.00 38.42 3.97
735 752 0.915364 ATCCCAGAAACTGAGGAGGC 59.085 55.000 0.00 0.00 35.48 4.70
738 755 1.584724 GGGATCCCAGAAACTGAGGA 58.415 55.000 26.95 0.00 36.08 3.71
747 764 4.172232 CCTCCCGGGGATCCCAGA 62.172 72.222 32.07 22.42 45.83 3.86
829 847 5.338463 GGGATTTTATATCGGGAAGGAGGAG 60.338 48.000 0.00 0.00 0.00 3.69
841 859 5.768164 TCTTTTGGCCGAGGGATTTTATATC 59.232 40.000 0.00 0.00 0.00 1.63
856 874 1.550524 GAATGGAAGGGTCTTTTGGCC 59.449 52.381 0.00 0.00 45.31 5.36
860 878 2.286365 TGCGAATGGAAGGGTCTTTT 57.714 45.000 0.00 0.00 0.00 2.27
905 927 4.514585 TTGCTGCGGTGGGTGGTT 62.515 61.111 0.00 0.00 0.00 3.67
916 938 2.356673 GCTTGCCCTTGTTGCTGC 60.357 61.111 0.00 0.00 0.00 5.25
987 1021 4.598894 CTCATCTGGGCGCCGAGG 62.599 72.222 34.26 22.15 0.00 4.63
1441 1524 5.358922 ACAAAACCAACCAATCAATCACAG 58.641 37.500 0.00 0.00 0.00 3.66
1497 2285 1.062148 GTCAGATCGATCGACGTGTCA 59.938 52.381 22.06 3.03 43.13 3.58
1706 3748 1.210155 GGCCATGACACGCAAAGAC 59.790 57.895 0.00 0.00 0.00 3.01
1727 3769 0.178068 ATGCTACATCCGTCACCCAC 59.822 55.000 0.00 0.00 0.00 4.61
1739 3781 0.613260 GTGACAGGGACCATGCTACA 59.387 55.000 5.94 1.65 0.00 2.74
1852 3896 2.159393 CCCACGAACGAACGATTAGGTA 60.159 50.000 11.97 0.00 37.03 3.08
1853 3897 1.403249 CCCACGAACGAACGATTAGGT 60.403 52.381 11.97 0.00 37.03 3.08
1855 3899 1.135315 TCCCCACGAACGAACGATTAG 60.135 52.381 11.97 0.00 37.03 1.73
1856 3900 0.887247 TCCCCACGAACGAACGATTA 59.113 50.000 11.97 0.00 37.03 1.75
1858 3902 0.459585 CATCCCCACGAACGAACGAT 60.460 55.000 11.97 0.00 37.03 3.73
1859 3903 1.080366 CATCCCCACGAACGAACGA 60.080 57.895 11.97 0.00 37.03 3.85
1860 3904 2.098233 CCATCCCCACGAACGAACG 61.098 63.158 0.14 0.00 39.31 3.95
1861 3905 1.743995 CCCATCCCCACGAACGAAC 60.744 63.158 0.14 0.00 0.00 3.95
1862 3906 2.218454 ACCCATCCCCACGAACGAA 61.218 57.895 0.14 0.00 0.00 3.85
1946 5007 8.101654 ACAGTCTATAATCTGTCGATACTTCC 57.898 38.462 0.00 0.00 40.28 3.46
1988 5049 3.919804 CGCCATGTTATTTGTGTTTCCAG 59.080 43.478 0.00 0.00 0.00 3.86
1991 5052 3.917985 GGTCGCCATGTTATTTGTGTTTC 59.082 43.478 0.00 0.00 0.00 2.78
2009 5070 3.503827 TGTAGTAGCATGTCAAGGTCG 57.496 47.619 0.00 0.00 0.00 4.79
2044 5106 5.441718 TCCTCTCTGGTGCTTTAATCAAT 57.558 39.130 0.00 0.00 37.07 2.57
2068 5130 3.663025 AGTACATGGCAAAACAAATGGC 58.337 40.909 0.00 0.00 43.15 4.40
2132 5194 6.040729 ACAGAGTGGAGATCAAGATGATACAG 59.959 42.308 0.00 0.00 37.20 2.74
2151 5213 8.853077 TCATGATGAACTTCAAAATACAGAGT 57.147 30.769 0.00 0.00 0.00 3.24
2169 5231 3.139850 GGGTCAGCTTCAGATCATGATG 58.860 50.000 14.30 0.68 37.89 3.07
2452 5514 2.099263 CGAGATGAGGTAGCCGAAGAAA 59.901 50.000 0.00 0.00 0.00 2.52
2753 5817 0.107312 ACAGATGAGCATGGACTGGC 60.107 55.000 0.00 0.00 33.57 4.85
2805 5871 2.743664 TCGACAAGACCAAATCAGCATG 59.256 45.455 0.00 0.00 37.54 4.06
2820 5888 1.840630 CTGCACGGCACAATCGACAA 61.841 55.000 0.00 0.00 33.79 3.18
2928 5996 2.941720 GTGGTAGTAGCAGTAGTAGCGT 59.058 50.000 1.37 0.00 35.94 5.07
2937 6008 2.472695 TTGCTTGGTGGTAGTAGCAG 57.527 50.000 1.37 0.00 43.71 4.24
2938 6009 2.940994 TTTGCTTGGTGGTAGTAGCA 57.059 45.000 0.00 0.00 41.51 3.49
2939 6010 3.343617 TCATTTGCTTGGTGGTAGTAGC 58.656 45.455 0.00 0.00 0.00 3.58
3041 6116 5.287274 CACACTGCTTATTTCTCAGTACTCG 59.713 44.000 0.00 0.00 38.85 4.18
3189 6264 9.201989 GGAAAAGGAAGAATATTCAAATAGGGT 57.798 33.333 17.56 0.00 0.00 4.34
3222 6298 6.585695 ACTGCAGATCAGAAAATTCAACAT 57.414 33.333 23.35 0.00 45.72 2.71
3228 6304 8.270744 ACCTAATCTACTGCAGATCAGAAAATT 58.729 33.333 23.35 12.47 43.56 1.82
3250 6326 1.134340 ACGTCAAGCCACAAACACCTA 60.134 47.619 0.00 0.00 0.00 3.08
3309 6399 5.047802 GGGATGCTCAGAATTCTGTCAAAAA 60.048 40.000 29.80 12.62 44.12 1.94
3310 6400 4.460382 GGGATGCTCAGAATTCTGTCAAAA 59.540 41.667 29.80 13.27 44.12 2.44
3311 6401 4.012374 GGGATGCTCAGAATTCTGTCAAA 58.988 43.478 29.80 16.98 44.12 2.69
3312 6402 3.009363 TGGGATGCTCAGAATTCTGTCAA 59.991 43.478 29.80 18.49 44.12 3.18
3313 6403 2.573009 TGGGATGCTCAGAATTCTGTCA 59.427 45.455 29.80 26.71 44.12 3.58
3314 6404 2.941720 GTGGGATGCTCAGAATTCTGTC 59.058 50.000 29.80 22.99 44.12 3.51
3315 6405 2.679059 CGTGGGATGCTCAGAATTCTGT 60.679 50.000 29.80 14.62 44.12 3.41
3316 6406 1.938577 CGTGGGATGCTCAGAATTCTG 59.061 52.381 26.56 26.56 45.08 3.02
3317 6407 1.745141 GCGTGGGATGCTCAGAATTCT 60.745 52.381 0.88 0.88 0.00 2.40
3318 6408 0.659957 GCGTGGGATGCTCAGAATTC 59.340 55.000 0.00 0.00 0.00 2.17
3319 6409 0.749454 GGCGTGGGATGCTCAGAATT 60.749 55.000 0.00 0.00 0.00 2.17
3320 6410 1.153086 GGCGTGGGATGCTCAGAAT 60.153 57.895 0.00 0.00 0.00 2.40
3321 6411 1.841302 AAGGCGTGGGATGCTCAGAA 61.841 55.000 0.00 0.00 0.00 3.02
3322 6412 2.244117 GAAGGCGTGGGATGCTCAGA 62.244 60.000 0.00 0.00 0.00 3.27
3323 6413 1.817099 GAAGGCGTGGGATGCTCAG 60.817 63.158 0.00 0.00 0.00 3.35
3324 6414 2.268920 GAAGGCGTGGGATGCTCA 59.731 61.111 0.00 0.00 0.00 4.26
3353 6448 3.556999 TCGGGTGAAAGGTTTTTGATCA 58.443 40.909 0.00 0.00 0.00 2.92
3355 6450 4.148838 TGATCGGGTGAAAGGTTTTTGAT 58.851 39.130 0.00 0.00 0.00 2.57
3356 6451 3.556999 TGATCGGGTGAAAGGTTTTTGA 58.443 40.909 0.00 0.00 0.00 2.69
3357 6452 4.519540 ATGATCGGGTGAAAGGTTTTTG 57.480 40.909 0.00 0.00 0.00 2.44
3362 6457 3.054434 TGATCAATGATCGGGTGAAAGGT 60.054 43.478 17.31 0.00 41.51 3.50
3365 6460 4.191544 GACTGATCAATGATCGGGTGAAA 58.808 43.478 29.26 6.95 46.40 2.69
3369 6469 2.501316 TGTGACTGATCAATGATCGGGT 59.499 45.455 29.26 22.98 46.40 5.28
3382 6482 2.524569 TGCGTTGATTCTGTGACTGA 57.475 45.000 0.00 0.00 0.00 3.41
3384 6484 1.873591 GGTTGCGTTGATTCTGTGACT 59.126 47.619 0.00 0.00 0.00 3.41
3391 6491 3.049912 GTTTGAAGGGTTGCGTTGATTC 58.950 45.455 0.00 0.00 0.00 2.52
3399 6506 1.632589 AGGATGGTTTGAAGGGTTGC 58.367 50.000 0.00 0.00 0.00 4.17
3400 6507 4.096382 CGAATAGGATGGTTTGAAGGGTTG 59.904 45.833 0.00 0.00 0.00 3.77
3426 6533 2.163613 GGGTTTAAAGGATGCGGAACAG 59.836 50.000 0.00 0.00 0.00 3.16
3427 6534 2.164338 GGGTTTAAAGGATGCGGAACA 58.836 47.619 0.00 0.00 0.00 3.18
3428 6535 1.475280 GGGGTTTAAAGGATGCGGAAC 59.525 52.381 0.00 0.00 0.00 3.62
3430 6537 0.393267 CGGGGTTTAAAGGATGCGGA 60.393 55.000 0.00 0.00 0.00 5.54
3431 6538 2.000215 GCGGGGTTTAAAGGATGCGG 62.000 60.000 0.00 0.00 0.00 5.69
3433 6540 1.111277 ATGCGGGGTTTAAAGGATGC 58.889 50.000 0.00 0.00 0.00 3.91
3434 6541 4.398319 AGATATGCGGGGTTTAAAGGATG 58.602 43.478 0.00 0.00 0.00 3.51
3435 6542 4.724279 AGATATGCGGGGTTTAAAGGAT 57.276 40.909 0.00 0.00 0.00 3.24
3436 6543 5.308497 TCATAGATATGCGGGGTTTAAAGGA 59.692 40.000 0.00 0.00 33.76 3.36
3437 6544 5.556915 TCATAGATATGCGGGGTTTAAAGG 58.443 41.667 0.00 0.00 33.76 3.11
3438 6545 5.643777 CCTCATAGATATGCGGGGTTTAAAG 59.356 44.000 1.58 0.00 35.46 1.85
3439 6546 5.556915 CCTCATAGATATGCGGGGTTTAAA 58.443 41.667 1.58 0.00 35.46 1.52
3466 6575 4.304939 GACGCGTTAGGCCTTCTAATAAT 58.695 43.478 15.53 0.00 39.82 1.28
3467 6576 3.491447 GGACGCGTTAGGCCTTCTAATAA 60.491 47.826 15.53 0.00 39.82 1.40
3485 6594 0.536724 TGGGTCTGACATGATGGACG 59.463 55.000 10.38 0.00 0.00 4.79
3498 6607 1.609783 GCCAGGTTATGCTGGGTCT 59.390 57.895 0.00 0.00 40.87 3.85
3501 6610 2.123726 GGGCCAGGTTATGCTGGG 60.124 66.667 4.39 0.00 40.87 4.45
3524 6633 3.282920 GGCAAGCGGCTATGGCTC 61.283 66.667 22.08 10.59 40.53 4.70
3526 6635 3.892581 GTGGCAAGCGGCTATGGC 61.893 66.667 22.37 22.37 44.01 4.40
3529 6638 2.190578 GGAGTGGCAAGCGGCTAT 59.809 61.111 1.35 0.00 44.01 2.97
3535 6644 0.957888 GAGGAAGTGGAGTGGCAAGC 60.958 60.000 0.00 0.00 0.00 4.01
3568 6677 4.323333 CCGGAGATGAGCTATGATTGGATT 60.323 45.833 0.00 0.00 0.00 3.01
3684 6803 2.026356 TCAGAAGGATTGAATGGCGGAA 60.026 45.455 0.00 0.00 0.00 4.30
3686 6805 2.042686 TCAGAAGGATTGAATGGCGG 57.957 50.000 0.00 0.00 0.00 6.13
3718 6837 1.080569 CGCCCACTTGCATGGAAAC 60.081 57.895 7.97 0.00 43.02 2.78
3719 6838 2.929903 GCGCCCACTTGCATGGAAA 61.930 57.895 7.97 0.00 43.02 3.13
3720 6839 3.372730 GCGCCCACTTGCATGGAA 61.373 61.111 7.97 0.00 43.02 3.53
3721 6840 4.349503 AGCGCCCACTTGCATGGA 62.350 61.111 7.97 0.00 43.02 3.41
3722 6841 4.124351 CAGCGCCCACTTGCATGG 62.124 66.667 2.29 1.66 39.71 3.66
3723 6842 4.124351 CCAGCGCCCACTTGCATG 62.124 66.667 2.29 0.00 0.00 4.06
3741 6860 3.741476 GTTGGCCGCCTTGAGCTG 61.741 66.667 11.61 0.00 40.39 4.24
3754 6873 3.636231 TGGAGCCTCCACGGTTGG 61.636 66.667 10.05 0.00 42.67 3.77
3761 6880 0.322816 GAAGCAATGTGGAGCCTCCA 60.323 55.000 10.05 10.05 45.98 3.86
3762 6881 1.034292 GGAAGCAATGTGGAGCCTCC 61.034 60.000 2.98 2.98 34.52 4.30
3763 6882 0.322816 TGGAAGCAATGTGGAGCCTC 60.323 55.000 0.00 0.00 0.00 4.70
3764 6883 0.333993 ATGGAAGCAATGTGGAGCCT 59.666 50.000 0.00 0.00 0.00 4.58
3765 6884 0.458669 CATGGAAGCAATGTGGAGCC 59.541 55.000 0.00 0.00 0.00 4.70
3766 6885 0.179119 GCATGGAAGCAATGTGGAGC 60.179 55.000 0.00 0.00 0.00 4.70
3767 6886 1.179152 TGCATGGAAGCAATGTGGAG 58.821 50.000 0.00 0.00 42.46 3.86
3768 6887 3.360296 TGCATGGAAGCAATGTGGA 57.640 47.368 0.00 0.00 42.46 4.02
3775 6894 2.277591 GCCCACTTGCATGGAAGCA 61.278 57.895 25.09 0.00 43.02 3.91
3781 6900 4.124351 CCAGCGCCCACTTGCATG 62.124 66.667 2.29 0.00 0.00 4.06
3799 6918 3.741476 GTTGGCCGCCTTGAGCTG 61.741 66.667 11.61 0.00 40.39 4.24
3835 6954 3.589654 GAGCGCCTGTACTGCCACA 62.590 63.158 2.29 0.00 0.00 4.17



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

AutoCloner maintained by Alex Coulton.