Multiple sequence alignment - TraesCS1A01G165500

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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 TraesCS1A01G165500 chr1A 100.000 7742 0 0 1 7742 298108884 298116625 0.000000e+00 14297.0
1 TraesCS1A01G165500 chr1A 77.863 3537 713 53 2913 6426 302025833 302022344 0.000000e+00 2130.0
2 TraesCS1A01G165500 chr1A 79.099 1598 308 21 2907 4494 58249953 58248372 0.000000e+00 1077.0
3 TraesCS1A01G165500 chr6A 96.294 7096 240 13 17 7094 501818154 501825244 0.000000e+00 11625.0
4 TraesCS1A01G165500 chr6A 77.696 3533 736 47 2907 6414 447683370 447679865 0.000000e+00 2111.0
5 TraesCS1A01G165500 chr6A 73.584 2949 697 65 3526 6426 201352630 201355544 0.000000e+00 1055.0
6 TraesCS1A01G165500 chr6A 96.471 595 20 1 7148 7742 501883317 501883910 0.000000e+00 981.0
7 TraesCS1A01G165500 chr6A 95.161 62 3 0 7089 7150 501883229 501883290 1.780000e-16 99.0
8 TraesCS1A01G165500 chr6A 84.946 93 14 0 1144 1236 501819408 501819500 2.300000e-15 95.3
9 TraesCS1A01G165500 chr1B 78.489 3547 694 55 2907 6426 442212130 442208626 0.000000e+00 2259.0
10 TraesCS1A01G165500 chr7B 78.479 3536 692 56 2907 6411 99493196 99496693 0.000000e+00 2250.0
11 TraesCS1A01G165500 chr7B 79.779 905 174 6 1957 2855 412296413 412295512 0.000000e+00 649.0
12 TraesCS1A01G165500 chr7B 82.424 165 24 4 7200 7361 362062892 362062730 1.050000e-28 139.0
13 TraesCS1A01G165500 chr3A 77.517 3536 726 58 2907 6411 55060186 55056689 0.000000e+00 2061.0
14 TraesCS1A01G165500 chr3A 74.794 2908 678 42 3537 6426 11117298 11114428 0.000000e+00 1258.0
15 TraesCS1A01G165500 chr3A 76.343 875 195 11 1955 2823 11119142 11118274 7.080000e-125 459.0
16 TraesCS1A01G165500 chrUn 77.360 3401 704 56 3052 6426 286328942 286325582 0.000000e+00 1954.0
17 TraesCS1A01G165500 chr2B 76.416 3532 751 66 2912 6409 140590123 140586640 0.000000e+00 1832.0
18 TraesCS1A01G165500 chr4A 74.855 2923 690 38 3528 6426 574829011 574826110 0.000000e+00 1284.0
19 TraesCS1A01G165500 chr7A 74.462 2929 689 49 3528 6426 120476277 120473378 0.000000e+00 1210.0
20 TraesCS1A01G165500 chr4D 78.742 1844 365 23 2907 4735 6947647 6945816 0.000000e+00 1208.0
21 TraesCS1A01G165500 chr5B 77.755 1960 409 25 2907 4854 640534935 640532991 0.000000e+00 1179.0
22 TraesCS1A01G165500 chr5B 77.027 2072 450 23 2907 4967 703938989 703936933 0.000000e+00 1166.0
23 TraesCS1A01G165500 chr7D 73.801 2939 705 51 3526 6426 179200593 179197682 0.000000e+00 1101.0
24 TraesCS1A01G165500 chr7D 84.242 165 19 5 7200 7361 289266989 289266829 3.740000e-33 154.0
25 TraesCS1A01G165500 chr2A 73.589 2942 704 57 3526 6426 35641793 35644702 0.000000e+00 1061.0
26 TraesCS1A01G165500 chr2A 86.066 610 72 10 88 684 121584119 121583510 1.820000e-180 643.0
27 TraesCS1A01G165500 chr2A 81.749 526 95 1 2907 3432 569297710 569297186 9.220000e-119 438.0
28 TraesCS1A01G165500 chr5A 89.796 833 68 6 1 818 342497546 342498376 0.000000e+00 1051.0
29 TraesCS1A01G165500 chr4B 78.544 1538 305 20 2907 4434 512671378 512669856 0.000000e+00 989.0


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 TraesCS1A01G165500 chr1A 298108884 298116625 7741 False 14297.0 14297 100.0000 1 7742 1 chr1A.!!$F1 7741
1 TraesCS1A01G165500 chr1A 302022344 302025833 3489 True 2130.0 2130 77.8630 2913 6426 1 chr1A.!!$R2 3513
2 TraesCS1A01G165500 chr1A 58248372 58249953 1581 True 1077.0 1077 79.0990 2907 4494 1 chr1A.!!$R1 1587
3 TraesCS1A01G165500 chr6A 501818154 501825244 7090 False 11625.0 11625 96.2940 17 7094 1 chr6A.!!$F2 7077
4 TraesCS1A01G165500 chr6A 447679865 447683370 3505 True 2111.0 2111 77.6960 2907 6414 1 chr6A.!!$R1 3507
5 TraesCS1A01G165500 chr6A 201352630 201355544 2914 False 1055.0 1055 73.5840 3526 6426 1 chr6A.!!$F1 2900
6 TraesCS1A01G165500 chr6A 501883229 501883910 681 False 540.0 981 95.8160 7089 7742 2 chr6A.!!$F4 653
7 TraesCS1A01G165500 chr1B 442208626 442212130 3504 True 2259.0 2259 78.4890 2907 6426 1 chr1B.!!$R1 3519
8 TraesCS1A01G165500 chr7B 99493196 99496693 3497 False 2250.0 2250 78.4790 2907 6411 1 chr7B.!!$F1 3504
9 TraesCS1A01G165500 chr7B 412295512 412296413 901 True 649.0 649 79.7790 1957 2855 1 chr7B.!!$R2 898
10 TraesCS1A01G165500 chr3A 55056689 55060186 3497 True 2061.0 2061 77.5170 2907 6411 1 chr3A.!!$R1 3504
11 TraesCS1A01G165500 chr3A 11114428 11119142 4714 True 858.5 1258 75.5685 1955 6426 2 chr3A.!!$R2 4471
12 TraesCS1A01G165500 chrUn 286325582 286328942 3360 True 1954.0 1954 77.3600 3052 6426 1 chrUn.!!$R1 3374
13 TraesCS1A01G165500 chr2B 140586640 140590123 3483 True 1832.0 1832 76.4160 2912 6409 1 chr2B.!!$R1 3497
14 TraesCS1A01G165500 chr4A 574826110 574829011 2901 True 1284.0 1284 74.8550 3528 6426 1 chr4A.!!$R1 2898
15 TraesCS1A01G165500 chr7A 120473378 120476277 2899 True 1210.0 1210 74.4620 3528 6426 1 chr7A.!!$R1 2898
16 TraesCS1A01G165500 chr4D 6945816 6947647 1831 True 1208.0 1208 78.7420 2907 4735 1 chr4D.!!$R1 1828
17 TraesCS1A01G165500 chr5B 640532991 640534935 1944 True 1179.0 1179 77.7550 2907 4854 1 chr5B.!!$R1 1947
18 TraesCS1A01G165500 chr5B 703936933 703938989 2056 True 1166.0 1166 77.0270 2907 4967 1 chr5B.!!$R2 2060
19 TraesCS1A01G165500 chr7D 179197682 179200593 2911 True 1101.0 1101 73.8010 3526 6426 1 chr7D.!!$R1 2900
20 TraesCS1A01G165500 chr2A 35641793 35644702 2909 False 1061.0 1061 73.5890 3526 6426 1 chr2A.!!$F1 2900
21 TraesCS1A01G165500 chr2A 121583510 121584119 609 True 643.0 643 86.0660 88 684 1 chr2A.!!$R1 596
22 TraesCS1A01G165500 chr2A 569297186 569297710 524 True 438.0 438 81.7490 2907 3432 1 chr2A.!!$R2 525
23 TraesCS1A01G165500 chr5A 342497546 342498376 830 False 1051.0 1051 89.7960 1 818 1 chr5A.!!$F1 817
24 TraesCS1A01G165500 chr4B 512669856 512671378 1522 True 989.0 989 78.5440 2907 4434 1 chr4B.!!$R1 1527

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
648 670 0.098552 TGTGTTGTGCTTGTTGCTCG 59.901 50.000 0.00 0.0 43.37 5.03 F
1246 1268 0.533978 TGGTCGTGGTTGTGGTGATG 60.534 55.000 0.00 0.0 0.00 3.07 F
2166 2190 0.253044 CCGGGAGCTCCTTCATTTCA 59.747 55.000 31.36 0.0 35.95 2.69 F
2831 2866 2.341257 CTGATTGTTCCTCAGGACGTG 58.659 52.381 0.00 0.0 37.15 4.49 F
3841 4180 1.202336 CCTTATACCGACACCGTGACC 60.202 57.143 5.28 0.0 0.00 4.02 F
5482 5902 1.396648 CGATGCGGCAATCACAAACTA 59.603 47.619 6.82 0.0 0.00 2.24 F
5696 6117 0.310543 TGCTGATTCACACAAACGGC 59.689 50.000 0.00 0.0 0.00 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1458 1480 0.530870 GACGGGGCACATAGCTCTTC 60.531 60.000 0.00 0.00 45.61 2.87 R
2882 2917 0.895530 CGGGAGACTGGCTACTTGAA 59.104 55.000 0.00 0.00 0.00 2.69 R
3314 3605 0.749454 CCCGATCAGAAGGCCTTTGG 60.749 60.000 21.54 14.99 0.00 3.28 R
4334 4692 1.063792 CATCCCATGTCCACCCAATCA 60.064 52.381 0.00 0.00 0.00 2.57 R
5621 6042 0.986992 CGGTACCTCGCTTTGTAACG 59.013 55.000 10.90 0.00 41.16 3.18 R
6471 6901 0.871722 CCGGACAAAAGCAATCGTCA 59.128 50.000 0.00 0.00 0.00 4.35 R
7631 8092 0.390472 CTGGCGAGGTCCTTTCTGTC 60.390 60.000 0.00 0.00 0.00 3.51 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
163 182 1.885887 GCTGTTGTGGCAGGATGTTTA 59.114 47.619 0.00 0.00 39.31 2.01
392 414 2.167075 GTGCTGCTTTCCAGGCAATTAT 59.833 45.455 0.00 0.00 42.03 1.28
469 491 1.067821 CCACCTATCGAGACCTTGCTC 59.932 57.143 0.00 0.00 0.00 4.26
490 512 3.644884 GCTCAGCGGTTATTCTAGCTA 57.355 47.619 0.00 0.00 37.94 3.32
537 559 0.322816 TTGCTTCTGGTGATGGCTCC 60.323 55.000 0.00 0.00 0.00 4.70
648 670 0.098552 TGTGTTGTGCTTGTTGCTCG 59.901 50.000 0.00 0.00 43.37 5.03
718 740 4.872124 GTGTGTGCTTATGATGAGATGTCA 59.128 41.667 0.00 0.00 37.02 3.58
719 741 5.006455 GTGTGTGCTTATGATGAGATGTCAG 59.994 44.000 0.00 0.00 35.66 3.51
791 813 7.253783 CGTTCATGCCGCTTATGAGTAATATAG 60.254 40.741 0.00 0.00 36.07 1.31
795 817 4.268884 GCCGCTTATGAGTAATATAGCTGC 59.731 45.833 0.00 0.00 33.12 5.25
821 843 7.244898 TGTTTATGTGTTCTGTGTTGTACAAC 58.755 34.615 28.13 28.13 39.20 3.32
851 873 5.028549 ACCCTTCTCAGTATGCTACATTG 57.971 43.478 0.00 0.00 34.76 2.82
936 958 3.390135 TCAGTCAGGTTTACTTGCTTCG 58.610 45.455 0.00 0.00 0.00 3.79
984 1006 2.734755 TTCAGCCAATGGTATGAGGG 57.265 50.000 0.00 0.00 0.00 4.30
1012 1034 1.207593 GTTGTCATGCCACGTGCTC 59.792 57.895 10.91 4.46 42.00 4.26
1013 1035 1.965930 TTGTCATGCCACGTGCTCC 60.966 57.895 10.91 0.80 42.00 4.70
1030 1052 2.484062 CCGATTGCTGCCCATGGAC 61.484 63.158 15.22 0.55 0.00 4.02
1122 1144 1.648504 GTGGTCGTGGTAATGTAGCC 58.351 55.000 0.00 0.00 0.00 3.93
1123 1145 1.066716 GTGGTCGTGGTAATGTAGCCA 60.067 52.381 0.00 0.00 0.00 4.75
1127 1149 1.484653 TCGTGGTAATGTAGCCATGCT 59.515 47.619 0.00 0.00 40.57 3.79
1135 1157 1.326951 TGTAGCCATGCTCGTGCCTA 61.327 55.000 7.05 0.00 40.44 3.93
1150 1172 2.045280 CCTAGCGATGTCCTCCCTG 58.955 63.158 0.00 0.00 0.00 4.45
1184 1206 3.555324 TGGTGGTGCTCGAGCCAA 61.555 61.111 33.23 16.25 41.18 4.52
1186 1208 2.328099 GGTGGTGCTCGAGCCAAAG 61.328 63.158 33.23 0.00 41.18 2.77
1246 1268 0.533978 TGGTCGTGGTTGTGGTGATG 60.534 55.000 0.00 0.00 0.00 3.07
1251 1273 2.565391 TCGTGGTTGTGGTGATGTAGAT 59.435 45.455 0.00 0.00 0.00 1.98
1358 1380 3.652013 TGGGCGTGGGCATGGTAA 61.652 61.111 0.00 0.00 42.47 2.85
1370 1392 2.324860 GCATGGTAACGTTTCTTTGCC 58.675 47.619 5.91 0.00 42.51 4.52
1410 1432 1.268079 GCTGTTCCTCTTCTTGCCAAC 59.732 52.381 0.00 0.00 0.00 3.77
1426 1448 2.221299 AACGTTCAGCCTGGGCCTA 61.221 57.895 4.53 0.00 43.17 3.93
1485 1507 3.637273 GTGCCCCGTCCACCTCTT 61.637 66.667 0.00 0.00 0.00 2.85
1579 1601 4.080919 ACCATGTATCTTGCTTGCTCACTA 60.081 41.667 0.00 0.00 0.00 2.74
1587 1609 4.934001 TCTTGCTTGCTCACTATTCTTCTG 59.066 41.667 0.00 0.00 0.00 3.02
1719 1741 4.260212 CGGTCTAAATACGAAGGTGCATTG 60.260 45.833 0.00 0.00 0.00 2.82
1739 1761 6.414987 GCATTGAGTTCTTAGTTGTGTTGTTC 59.585 38.462 0.00 0.00 0.00 3.18
1754 1776 1.948104 TGTTCTGTTCCTGTTCCACG 58.052 50.000 0.00 0.00 0.00 4.94
1903 1925 4.238514 CGTTCTACTGTCTGCTTAGCTTT 58.761 43.478 5.60 0.00 0.00 3.51
1951 1973 2.710377 TCCCTGATCACATGTTTTCCG 58.290 47.619 0.00 0.00 0.00 4.30
2084 2106 7.762615 TCTTGGACGAAACGTAAGATCATTTAT 59.237 33.333 0.00 0.00 41.37 1.40
2161 2185 0.556258 TATCTCCGGGAGCTCCTTCA 59.444 55.000 31.36 14.39 35.95 3.02
2166 2190 0.253044 CCGGGAGCTCCTTCATTTCA 59.747 55.000 31.36 0.00 35.95 2.69
2426 2450 4.651045 AGGATAAATGCCTTGAATCCCAAC 59.349 41.667 10.78 0.00 37.43 3.77
2496 2520 6.471146 AGAGACATGCTTGATGAGTTTAACT 58.529 36.000 6.60 0.00 35.80 2.24
2609 2633 4.442612 CCTTCAGATGGTGATAGTCCACAG 60.443 50.000 0.00 0.00 38.74 3.66
2671 2698 9.167311 GGTTGTTAATGACTTCACATTAGAGAT 57.833 33.333 0.00 0.00 41.59 2.75
2811 2840 4.157840 GGTTCCAAATAGATGTTCCACACC 59.842 45.833 0.00 0.00 0.00 4.16
2830 2865 2.751166 CTGATTGTTCCTCAGGACGT 57.249 50.000 0.00 0.00 37.15 4.34
2831 2866 2.341257 CTGATTGTTCCTCAGGACGTG 58.659 52.381 0.00 0.00 37.15 4.49
3086 3376 5.936956 CAGAAATCAGGATATGCTTAGGTCC 59.063 44.000 0.00 0.00 0.00 4.46
3314 3605 1.889573 GGACGCATTAGAGCCAGGC 60.890 63.158 1.84 1.84 0.00 4.85
3317 3608 1.451927 CGCATTAGAGCCAGGCCAA 60.452 57.895 8.22 0.00 0.00 4.52
3448 3757 8.467598 TGGTACTGTGTTCTATTAGTTCAGATC 58.532 37.037 0.00 0.00 0.00 2.75
3462 3771 5.766222 AGTTCAGATCAATTGCACTGTTTC 58.234 37.500 21.73 15.83 0.00 2.78
3592 3928 1.202348 CGCATATCCTCATCTGGCGTA 59.798 52.381 0.00 0.00 38.36 4.42
3833 4172 1.629353 TGGGTTTGCCTTATACCGACA 59.371 47.619 0.00 0.00 32.61 4.35
3841 4180 1.202336 CCTTATACCGACACCGTGACC 60.202 57.143 5.28 0.00 0.00 4.02
3900 4242 4.315803 ACAACAGACATGTAGTGCCTTAC 58.684 43.478 0.00 0.00 39.29 2.34
4334 4692 6.090358 CGGTCATTTACGTACTGTGATTTTCT 59.910 38.462 0.00 0.00 0.00 2.52
4801 5213 6.344500 AGAGATATGCTTCTTGACGAATTGT 58.656 36.000 0.00 0.00 0.00 2.71
5104 5524 2.714250 TGTGCTTTCCTTAGGGGAGAAA 59.286 45.455 0.00 0.00 46.01 2.52
5240 5660 6.377429 AGTGTGATATTAAGAGAGGTTCACGA 59.623 38.462 0.00 0.00 35.84 4.35
5482 5902 1.396648 CGATGCGGCAATCACAAACTA 59.603 47.619 6.82 0.00 0.00 2.24
5621 6042 3.697166 TCTTGGAGAAGGTAAATTGCCC 58.303 45.455 0.00 0.00 0.00 5.36
5696 6117 0.310543 TGCTGATTCACACAAACGGC 59.689 50.000 0.00 0.00 0.00 5.68
5827 6250 3.003482 GCTGAAGAGATCAACATCCATGC 59.997 47.826 0.00 0.00 37.67 4.06
6007 6430 9.616156 TTAAAATAGGTGTTCCGATTATGCTTA 57.384 29.630 0.00 0.00 37.92 3.09
6126 6549 2.228925 TCACATGTGGGTGATTGTGTG 58.771 47.619 25.16 0.00 42.56 3.82
6435 6865 3.037851 TCTGCTGGGATAGTCTGATGT 57.962 47.619 0.00 0.00 0.00 3.06
6590 7022 5.390567 GGTTCTGTTTATGCTTTCCTGTACG 60.391 44.000 0.00 0.00 0.00 3.67
6595 7027 5.049267 TGTTTATGCTTTCCTGTACGTTTCC 60.049 40.000 0.00 0.00 0.00 3.13
6624 7056 8.532819 TGTATTTAACAAGGGTGTTCTGTTTTT 58.467 29.630 0.00 0.00 45.00 1.94
6636 7068 2.238521 TCTGTTTTTGGTCCTGATGCC 58.761 47.619 0.00 0.00 0.00 4.40
6637 7069 1.962807 CTGTTTTTGGTCCTGATGCCA 59.037 47.619 0.00 0.00 0.00 4.92
6679 7111 0.252239 TAGCTGCTCTTGTCCCAGGA 60.252 55.000 4.91 0.00 0.00 3.86
6698 7130 6.072452 CCCAGGAAACAAGAAGTTGACTATTC 60.072 42.308 0.00 0.00 41.19 1.75
6827 7259 7.986889 TGTGCTCTTGTGATATGTGTTATATGT 59.013 33.333 0.00 0.00 0.00 2.29
6861 7293 6.772716 CCTGTAATCTAATTGTGGTAATGGCT 59.227 38.462 0.00 0.00 0.00 4.75
6889 7321 0.112995 TTTGCTGGCAGGGTTCTCAT 59.887 50.000 17.64 0.00 0.00 2.90
6995 7427 2.556622 CTGGTGTTCCCAAATAAGCGTT 59.443 45.455 0.00 0.00 44.65 4.84
7010 7442 0.367887 GCGTTACTTTAAGGCCGTCG 59.632 55.000 0.00 0.00 42.08 5.12
7028 7460 2.353889 GTCGATGCAGCAAACATGATCT 59.646 45.455 1.53 0.00 0.00 2.75
7084 7516 2.742372 CTGGAGGTTGCGTTCCCG 60.742 66.667 0.00 0.00 32.29 5.14
7146 7578 4.955811 TGTAATCAGTACTATGCCCCAG 57.044 45.455 0.00 0.00 33.46 4.45
7173 7634 5.030820 ACCTGCATAAGACTACTACCCTTT 58.969 41.667 0.00 0.00 0.00 3.11
7192 7653 8.588290 ACCCTTTGCTATTGTAATTGTAATCA 57.412 30.769 0.00 0.00 0.00 2.57
7220 7681 3.782992 TCTAGATGGATGATAGCAGGCA 58.217 45.455 0.00 0.00 0.00 4.75
7228 7689 5.491070 TGGATGATAGCAGGCAATGTATAC 58.509 41.667 0.00 0.00 0.00 1.47
7237 7698 5.618056 CAGGCAATGTATACCTGCATAAG 57.382 43.478 21.85 6.89 44.16 1.73
7276 7737 5.011090 TCTCTGATTTATGAACCTGTCCG 57.989 43.478 0.00 0.00 0.00 4.79
7448 7909 7.116662 GCTCTGCTTCTCTATGTTGATATGAAG 59.883 40.741 0.00 0.00 32.83 3.02
7454 7915 6.470278 TCTCTATGTTGATATGAAGGCATGG 58.530 40.000 0.00 0.00 35.94 3.66
7585 8046 2.447582 ATATCCTTGGCTCCCTCCAT 57.552 50.000 0.00 0.00 35.77 3.41
7595 8056 1.972207 GCTCCCTCCATAGAACCTGGT 60.972 57.143 0.00 0.00 35.19 4.00
7598 8059 0.181350 CCTCCATAGAACCTGGTGGC 59.819 60.000 0.00 0.00 39.74 5.01
7642 8103 2.070028 GAAGCTTCGGACAGAAAGGAC 58.930 52.381 11.40 0.00 38.57 3.85
7646 8107 0.601558 TTCGGACAGAAAGGACCTCG 59.398 55.000 0.00 0.00 35.61 4.63
7661 8122 1.422402 ACCTCGCCAGGAAAGGTAAAA 59.578 47.619 3.62 0.00 43.65 1.52
7662 8123 2.084546 CCTCGCCAGGAAAGGTAAAAG 58.915 52.381 0.00 0.00 43.65 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.027377 AGATTTCCTCTCACACCTGCAG 60.027 50.000 6.78 6.78 0.00 4.41
45 46 8.147704 ACAGGAAAACAAAATCAATTTACGGAT 58.852 29.630 0.00 0.00 0.00 4.18
75 76 3.228453 ACAGACAAAGACGAGGTAAGGA 58.772 45.455 0.00 0.00 0.00 3.36
112 131 2.200373 AATAAGCAGACCCCACACAC 57.800 50.000 0.00 0.00 0.00 3.82
163 182 4.997395 GTGGATGTATGAACAACTGACAGT 59.003 41.667 1.07 1.07 39.58 3.55
243 262 4.102210 AGAACGTCTCCATCATCCATCATT 59.898 41.667 0.00 0.00 0.00 2.57
246 265 3.742433 AGAACGTCTCCATCATCCATC 57.258 47.619 0.00 0.00 0.00 3.51
392 414 3.874543 CCCATACAAACGCTGCAAGTATA 59.125 43.478 0.00 0.00 35.30 1.47
490 512 3.548770 TGGTAGATCTAACCGACGATGT 58.451 45.455 15.26 0.00 40.08 3.06
665 687 6.230472 TCCGGATACATGATAATCAACCAAG 58.770 40.000 0.00 0.00 0.00 3.61
742 764 4.161754 GCCAGGTACATAGGTAAGAACAGT 59.838 45.833 0.00 0.00 0.00 3.55
791 813 3.003689 ACACAGAACACATAAACAGCAGC 59.996 43.478 0.00 0.00 0.00 5.25
795 817 7.010697 TGTACAACACAGAACACATAAACAG 57.989 36.000 0.00 0.00 31.89 3.16
864 886 3.308402 CCATTGCAGGAGAAGGGTAAAGA 60.308 47.826 0.00 0.00 0.00 2.52
970 992 2.026641 CAAGCACCCTCATACCATTGG 58.973 52.381 0.00 0.00 0.00 3.16
984 1006 2.288334 TGGCATGACAACAATCAAGCAC 60.288 45.455 0.00 0.00 43.47 4.40
1012 1034 2.124193 TCCATGGGCAGCAATCGG 60.124 61.111 13.02 0.00 0.00 4.18
1013 1035 2.827051 CGTCCATGGGCAGCAATCG 61.827 63.158 18.31 0.00 0.00 3.34
1046 1068 3.197790 CTCGGGCATGAGCAACGG 61.198 66.667 0.00 0.00 44.61 4.44
1055 1077 2.670148 GGTCCAGAACCTCGGGCAT 61.670 63.158 0.00 0.00 45.45 4.40
1109 1131 1.867233 CGAGCATGGCTACATTACCAC 59.133 52.381 0.00 0.00 39.88 4.16
1127 1149 1.725557 GAGGACATCGCTAGGCACGA 61.726 60.000 0.00 0.00 44.75 4.35
1178 1200 2.919494 CGCCCAACACCTTTGGCTC 61.919 63.158 0.00 0.00 41.80 4.70
1184 1206 2.203294 GACCACGCCCAACACCTT 60.203 61.111 0.00 0.00 0.00 3.50
1186 1208 4.922026 ACGACCACGCCCAACACC 62.922 66.667 0.00 0.00 43.96 4.16
1246 1268 1.700042 CCAGGGAGGGTGCCATCTAC 61.700 65.000 2.83 0.00 0.00 2.59
1358 1380 2.484264 GCACTATCTGGCAAAGAAACGT 59.516 45.455 0.00 0.00 38.79 3.99
1394 1416 2.218603 GAACGTTGGCAAGAAGAGGAA 58.781 47.619 5.00 0.00 0.00 3.36
1410 1432 2.125106 GTAGGCCCAGGCTGAACG 60.125 66.667 17.94 3.86 39.30 3.95
1426 1448 1.375140 CATGTCCACGAGCAGCAGT 60.375 57.895 0.00 0.00 0.00 4.40
1458 1480 0.530870 GACGGGGCACATAGCTCTTC 60.531 60.000 0.00 0.00 45.61 2.87
1462 1484 2.687200 TGGACGGGGCACATAGCT 60.687 61.111 0.00 0.00 44.79 3.32
1506 1528 1.148310 GTGAACATGACAGACGTGGG 58.852 55.000 0.00 0.00 39.59 4.61
1579 1601 6.096001 ACAAGCAAGACAGAAAACAGAAGAAT 59.904 34.615 0.00 0.00 0.00 2.40
1587 1609 2.099756 AGGCACAAGCAAGACAGAAAAC 59.900 45.455 0.00 0.00 44.61 2.43
1719 1741 6.663944 ACAGAACAACACAACTAAGAACTC 57.336 37.500 0.00 0.00 0.00 3.01
1754 1776 2.101582 ACATAAGATCTGGTCAGCCGAC 59.898 50.000 0.00 0.00 41.80 4.79
1903 1925 2.834549 ACCCCATGACAACAAACAAACA 59.165 40.909 0.00 0.00 0.00 2.83
1951 1973 3.873910 TCTGCATAGGAAGCTAACAACC 58.126 45.455 0.00 0.00 0.00 3.77
1984 2006 4.048470 GGAACTCAGGGGCCCCAC 62.048 72.222 42.48 23.38 38.92 4.61
2084 2106 6.351881 CCTGAGCACCTTTACAATAGAGGTTA 60.352 42.308 0.00 0.00 41.72 2.85
2092 2114 5.700402 ATAGACCTGAGCACCTTTACAAT 57.300 39.130 0.00 0.00 0.00 2.71
2161 2185 3.181511 CGCACGTGATGTACCATTGAAAT 60.182 43.478 22.23 0.00 0.00 2.17
2166 2190 1.999735 CTTCGCACGTGATGTACCATT 59.000 47.619 22.23 0.00 0.00 3.16
2333 2357 4.348020 AGGAGTATCACTACCTTTGGGA 57.652 45.455 0.00 0.00 36.25 4.37
2426 2450 1.407979 ACAGCTCCTACCGGTTTATCG 59.592 52.381 15.04 0.00 0.00 2.92
2609 2633 3.933332 CAGTGGCAGTAGGTAAGCTAAAC 59.067 47.826 0.00 0.00 0.00 2.01
2671 2698 4.415881 ACAATAATATCCCGTGCAGACA 57.584 40.909 0.00 0.00 0.00 3.41
2811 2840 2.341257 CACGTCCTGAGGAACAATCAG 58.659 52.381 0.96 0.00 43.15 2.90
2830 2865 5.650703 GGATCAACATGCATATCATCATCCA 59.349 40.000 0.00 0.00 31.79 3.41
2831 2866 5.886474 AGGATCAACATGCATATCATCATCC 59.114 40.000 0.00 6.20 31.79 3.51
2875 2910 2.935201 GACTGGCTACTTGAAGCATCTG 59.065 50.000 0.00 0.00 44.64 2.90
2882 2917 0.895530 CGGGAGACTGGCTACTTGAA 59.104 55.000 0.00 0.00 0.00 2.69
3086 3376 2.463553 CAATACCTTGCATGTGCTCG 57.536 50.000 6.55 0.00 42.66 5.03
3314 3605 0.749454 CCCGATCAGAAGGCCTTTGG 60.749 60.000 21.54 14.99 0.00 3.28
3317 3608 2.592308 GCCCGATCAGAAGGCCTT 59.408 61.111 20.65 20.65 41.00 4.35
3448 3757 6.042143 AGGTAAAACAGAAACAGTGCAATTG 58.958 36.000 0.00 0.00 0.00 2.32
3462 3771 2.294479 CGACACGCAAGGTAAAACAG 57.706 50.000 0.00 0.00 46.39 3.16
3592 3928 2.224305 CGACCTCACCTTTGTCTCCTTT 60.224 50.000 0.00 0.00 0.00 3.11
3833 4172 2.602267 TCCGACCATGGTCACGGT 60.602 61.111 37.42 7.90 44.77 4.83
3841 4180 5.548706 TTTTTATAAACCGTCCGACCATG 57.451 39.130 0.00 0.00 0.00 3.66
3900 4242 7.226325 TGGAACTTTTTAAGAATTGCCATGTTG 59.774 33.333 0.00 0.00 0.00 3.33
4200 4555 1.516386 ACCAGCACGATAGCGAACG 60.516 57.895 7.69 0.00 41.64 3.95
4334 4692 1.063792 CATCCCATGTCCACCCAATCA 60.064 52.381 0.00 0.00 0.00 2.57
5240 5660 7.192852 AGAGACCATCATCAATTTACAGAGT 57.807 36.000 0.00 0.00 0.00 3.24
5621 6042 0.986992 CGGTACCTCGCTTTGTAACG 59.013 55.000 10.90 0.00 41.16 3.18
5696 6117 3.119291 GACAACAGCAGTGATAGGATCG 58.881 50.000 0.00 0.00 0.00 3.69
5827 6250 3.452627 AGCAGTGGGGACTAAGTTCATAG 59.547 47.826 0.00 0.00 0.00 2.23
6007 6430 6.993902 CCATTTGCCTGGCATAAATTTCTAAT 59.006 34.615 24.03 12.59 38.76 1.73
6126 6549 1.771255 AGCTCAATCCTGGGGATGTAC 59.229 52.381 0.00 0.00 42.27 2.90
6435 6865 5.977171 AATTATAATGCACTGTACGCGAA 57.023 34.783 15.93 0.00 0.00 4.70
6471 6901 0.871722 CCGGACAAAAGCAATCGTCA 59.128 50.000 0.00 0.00 0.00 4.35
6570 7002 5.607119 AACGTACAGGAAAGCATAAACAG 57.393 39.130 0.00 0.00 0.00 3.16
6590 7022 6.040054 ACACCCTTGTTAAATACAGTGGAAAC 59.960 38.462 0.00 0.00 38.19 2.78
6595 7027 6.262273 ACAGAACACCCTTGTTAAATACAGTG 59.738 38.462 0.00 0.00 46.43 3.66
6624 7056 0.904649 CTACAGTGGCATCAGGACCA 59.095 55.000 0.00 0.00 0.00 4.02
6636 7068 3.193263 GCAGTGATCACCATCTACAGTG 58.807 50.000 22.21 11.36 35.73 3.66
6637 7069 2.169352 GGCAGTGATCACCATCTACAGT 59.831 50.000 22.21 0.00 0.00 3.55
6679 7111 6.315393 ACACACGAATAGTCAACTTCTTGTTT 59.685 34.615 0.00 0.00 36.63 2.83
6698 7130 1.995484 CAGCCTTGAGACATACACACG 59.005 52.381 0.00 0.00 0.00 4.49
6728 7160 4.099573 AGGACCATTATCAGTAGTTCCACG 59.900 45.833 0.00 0.00 0.00 4.94
6827 7259 7.309744 CCACAATTAGATTACAGGGAAAAGCAA 60.310 37.037 0.00 0.00 0.00 3.91
6833 7265 7.777910 CCATTACCACAATTAGATTACAGGGAA 59.222 37.037 0.00 0.00 0.00 3.97
6861 7293 2.036992 CCCTGCCAGCAAACAATAAACA 59.963 45.455 0.00 0.00 0.00 2.83
6889 7321 9.230122 CAGTCTTTAGAGATCTCAGCATAGATA 57.770 37.037 24.39 2.88 36.33 1.98
6995 7427 1.205179 TGCATCGACGGCCTTAAAGTA 59.795 47.619 0.00 0.00 0.00 2.24
7010 7442 3.777465 ACAGATCATGTTTGCTGCATC 57.223 42.857 1.84 0.47 39.96 3.91
7028 7460 6.693466 TGACCGTAGTGAATCTATTGAAACA 58.307 36.000 0.00 0.00 0.00 2.83
7132 7564 4.417437 CAGGTATACTGGGGCATAGTACT 58.583 47.826 0.00 0.00 43.70 2.73
7146 7578 6.947158 AGGGTAGTAGTCTTATGCAGGTATAC 59.053 42.308 0.00 0.00 0.00 1.47
7192 7653 7.998383 CCTGCTATCATCCATCTAGATAGTACT 59.002 40.741 4.54 0.00 41.91 2.73
7220 7681 8.804204 GGTAGTAGTCTTATGCAGGTATACATT 58.196 37.037 5.01 0.00 0.00 2.71
7228 7689 3.577919 AGGGGTAGTAGTCTTATGCAGG 58.422 50.000 0.00 0.00 0.00 4.85
7237 7698 4.139038 CAGAGAGCTAAGGGGTAGTAGTC 58.861 52.174 0.00 0.00 31.78 2.59
7276 7737 8.255394 ACATACGTAATACCAAACTAAACACC 57.745 34.615 0.00 0.00 0.00 4.16
7408 7869 1.135094 CAGAGCCCAGGTGTATCCAT 58.865 55.000 0.00 0.00 39.02 3.41
7418 7879 1.761784 ACATAGAGAAGCAGAGCCCAG 59.238 52.381 0.00 0.00 0.00 4.45
7448 7909 2.661594 GAAAGAAACACGTTCCATGCC 58.338 47.619 0.00 0.00 36.86 4.40
7454 7915 5.757790 GTTGAAAACGAAAGAAACACGTTC 58.242 37.500 0.00 0.00 46.74 3.95
7585 8046 1.003839 CTTGCGCCACCAGGTTCTA 60.004 57.895 4.18 0.00 37.19 2.10
7595 8056 2.669569 GGCACTTCTCTTGCGCCA 60.670 61.111 4.18 0.00 42.50 5.69
7598 8059 0.532573 TAGAGGGCACTTCTCTTGCG 59.467 55.000 0.00 0.00 41.37 4.85
7628 8089 1.874345 GCGAGGTCCTTTCTGTCCGA 61.874 60.000 0.00 0.00 0.00 4.55
7631 8092 0.390472 CTGGCGAGGTCCTTTCTGTC 60.390 60.000 0.00 0.00 0.00 3.51
7632 8093 1.674057 CTGGCGAGGTCCTTTCTGT 59.326 57.895 0.00 0.00 0.00 3.41
7642 8103 2.084546 CTTTTACCTTTCCTGGCGAGG 58.915 52.381 8.78 8.78 41.39 4.63
7646 8107 1.627864 TGCCTTTTACCTTTCCTGGC 58.372 50.000 0.00 0.00 39.33 4.85
7661 8122 1.683385 GCAGGTGAAAAGAACTTGCCT 59.317 47.619 0.00 0.00 42.88 4.75
7662 8123 1.600413 CGCAGGTGAAAAGAACTTGCC 60.600 52.381 5.27 0.00 45.07 4.52


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

AutoCloner maintained by Alex Coulton.