Multiple sequence alignment - TraesCS2A01G053500

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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 TraesCS2A01G053500 chr2A 100.000 4477 0 0 1 4477 21535385 21530909 0.000000e+00 8268.0
1 TraesCS2A01G053500 chr2A 95.556 45 0 2 4409 4452 218142720 218142677 2.230000e-08 71.3
2 TraesCS2A01G053500 chr2B 92.734 3179 199 16 1 3152 34066240 34063067 0.000000e+00 4562.0
3 TraesCS2A01G053500 chr2B 93.113 726 43 4 3170 3893 34063079 34062359 0.000000e+00 1057.0
4 TraesCS2A01G053500 chr2B 88.945 597 58 5 3168 3764 34043233 34042645 0.000000e+00 730.0
5 TraesCS2A01G053500 chr2B 85.639 571 59 10 3796 4354 34042651 34042092 3.000000e-161 579.0
6 TraesCS2A01G053500 chr2B 84.615 520 60 10 2104 2618 33976906 33976402 2.400000e-137 499.0
7 TraesCS2A01G053500 chr2B 84.615 520 60 10 2104 2618 33986159 33985655 2.400000e-137 499.0
8 TraesCS2A01G053500 chr2B 84.423 520 61 10 2104 2618 33967653 33967149 1.120000e-135 494.0
9 TraesCS2A01G053500 chr2B 84.423 520 61 10 2104 2618 33995412 33994908 1.120000e-135 494.0
10 TraesCS2A01G053500 chr2B 84.423 520 61 10 2104 2618 34014021 34013517 1.120000e-135 494.0
11 TraesCS2A01G053500 chr2B 86.779 416 44 5 3170 3581 33966323 33965915 1.900000e-123 453.0
12 TraesCS2A01G053500 chr2B 84.672 274 35 2 2614 2887 33976002 33975736 2.650000e-67 267.0
13 TraesCS2A01G053500 chr2B 84.672 274 35 2 2614 2887 34013118 34012852 2.650000e-67 267.0
14 TraesCS2A01G053500 chr2B 85.603 257 31 1 2614 2870 34003865 34003615 9.550000e-67 265.0
15 TraesCS2A01G053500 chr2B 84.307 274 36 2 2614 2887 33985255 33984989 1.240000e-65 261.0
16 TraesCS2A01G053500 chr2B 88.701 177 17 3 2976 3152 33966484 33966311 3.510000e-51 213.0
17 TraesCS2A01G053500 chr2B 88.701 177 17 3 2976 3152 33975737 33975564 3.510000e-51 213.0
18 TraesCS2A01G053500 chr2B 88.701 177 17 3 2976 3152 33994243 33994070 3.510000e-51 213.0
19 TraesCS2A01G053500 chr2B 88.701 177 17 3 2976 3152 34003600 34003427 3.510000e-51 213.0
20 TraesCS2A01G053500 chr2B 88.701 177 17 3 2976 3152 34012853 34012680 3.510000e-51 213.0
21 TraesCS2A01G053500 chr6D 93.177 2477 122 10 704 3152 109897627 109895170 0.000000e+00 3594.0
22 TraesCS2A01G053500 chr6D 89.571 815 59 11 3668 4473 109894651 109893854 0.000000e+00 1011.0
23 TraesCS2A01G053500 chr6D 95.635 504 18 3 3170 3673 109895182 109894683 0.000000e+00 806.0
24 TraesCS2A01G053500 chr6D 86.313 716 66 13 1 705 109898356 109897662 0.000000e+00 750.0
25 TraesCS2A01G053500 chrUn 84.808 520 59 10 2104 2618 359919340 359918836 5.170000e-139 505.0
26 TraesCS2A01G053500 chrUn 84.672 274 35 2 2614 2887 371490515 371490781 2.650000e-67 267.0
27 TraesCS2A01G053500 chrUn 84.672 274 35 2 2614 2887 431613858 431613592 2.650000e-67 267.0
28 TraesCS2A01G053500 chrUn 84.838 277 24 9 2347 2618 431614521 431614258 3.430000e-66 263.0
29 TraesCS2A01G053500 chrUn 84.307 274 36 2 2614 2887 322599149 322598883 1.240000e-65 261.0
30 TraesCS2A01G053500 chrUn 88.701 177 17 3 2976 3152 371490780 371490953 3.510000e-51 213.0
31 TraesCS2A01G053500 chrUn 88.701 177 17 3 2976 3152 431613593 431613420 3.510000e-51 213.0
32 TraesCS2A01G053500 chr4D 88.496 113 12 1 1931 2043 440257139 440257028 7.810000e-28 135.0
33 TraesCS2A01G053500 chr4A 88.182 110 11 2 1931 2040 242675583 242675690 3.630000e-26 130.0
34 TraesCS2A01G053500 chr4B 92.771 83 6 0 1958 2040 340785901 340785983 2.190000e-23 121.0
35 TraesCS2A01G053500 chr3B 86.486 111 13 2 1933 2043 379944177 379944069 2.190000e-23 121.0
36 TraesCS2A01G053500 chr3B 89.535 86 9 0 1958 2043 347916354 347916269 4.730000e-20 110.0
37 TraesCS2A01G053500 chr3B 84.545 110 15 2 1931 2040 151853196 151853303 1.700000e-19 108.0
38 TraesCS2A01G053500 chr3B 85.507 69 8 2 4411 4477 602297702 602297770 2.230000e-08 71.3
39 TraesCS2A01G053500 chr5B 90.361 83 8 0 1958 2040 344200354 344200436 4.730000e-20 110.0
40 TraesCS2A01G053500 chr1A 87.500 64 6 2 4410 4471 241997707 241997770 6.210000e-09 73.1
41 TraesCS2A01G053500 chr2D 85.507 69 8 2 4411 4477 571882465 571882397 2.230000e-08 71.3
42 TraesCS2A01G053500 chr7D 95.349 43 2 0 4410 4452 320290904 320290946 8.040000e-08 69.4
43 TraesCS2A01G053500 chr1D 95.349 43 2 0 4410 4452 194462617 194462659 8.040000e-08 69.4
44 TraesCS2A01G053500 chr3A 91.837 49 3 1 4405 4452 598544616 598544664 2.890000e-07 67.6
45 TraesCS2A01G053500 chr6B 84.058 69 9 2 4411 4477 713162544 713162612 1.040000e-06 65.8


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 TraesCS2A01G053500 chr2A 21530909 21535385 4476 True 8268.000000 8268 100.000000 1 4477 1 chr2A.!!$R1 4476
1 TraesCS2A01G053500 chr2B 34062359 34066240 3881 True 2809.500000 4562 92.923500 1 3893 2 chr2B.!!$R8 3892
2 TraesCS2A01G053500 chr2B 34042092 34043233 1141 True 654.500000 730 87.292000 3168 4354 2 chr2B.!!$R7 1186
3 TraesCS2A01G053500 chr2B 33965915 33967653 1738 True 386.666667 494 86.634333 2104 3581 3 chr2B.!!$R1 1477
4 TraesCS2A01G053500 chr2B 33984989 33986159 1170 True 380.000000 499 84.461000 2104 2887 2 chr2B.!!$R3 783
5 TraesCS2A01G053500 chr2B 33994070 33995412 1342 True 353.500000 494 86.562000 2104 3152 2 chr2B.!!$R4 1048
6 TraesCS2A01G053500 chr2B 33975564 33976906 1342 True 326.333333 499 85.996000 2104 3152 3 chr2B.!!$R2 1048
7 TraesCS2A01G053500 chr2B 34012680 34014021 1341 True 324.666667 494 85.932000 2104 3152 3 chr2B.!!$R6 1048
8 TraesCS2A01G053500 chr6D 109893854 109898356 4502 True 1540.250000 3594 91.174000 1 4473 4 chr6D.!!$R1 4472
9 TraesCS2A01G053500 chrUn 359918836 359919340 504 True 505.000000 505 84.808000 2104 2618 1 chrUn.!!$R2 514
10 TraesCS2A01G053500 chrUn 431613420 431614521 1101 True 247.666667 267 86.070333 2347 3152 3 chrUn.!!$R3 805

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
347 363 0.037790 GCTCTGCTTCTGTTCGAGGT 60.038 55.0 0.00 0.00 0.00 3.85 F
1248 1322 0.108615 ACTCCTGCAGTCCGAATTCG 60.109 55.0 20.92 20.92 39.44 3.34 F
1442 1532 0.950836 TGAATTCTGTGGTTGCGTGG 59.049 50.0 7.05 0.00 0.00 4.94 F
2584 2680 0.829333 ATGGCTCTGCATCGACTTCT 59.171 50.0 0.00 0.00 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1839 1929 1.132500 ACCCTGGTTGATAGCTAGGC 58.868 55.000 0.00 0.00 0.00 3.93 R
2487 2583 0.395686 ATCTACGCCATCTGCAGCAT 59.604 50.000 9.47 0.43 41.33 3.79 R
3161 3662 1.138661 TCACATATCAGCATCCACGCA 59.861 47.619 0.00 0.00 0.00 5.24 R
4407 4962 0.328258 GCCAAGCTTCCCCTTCAGTA 59.672 55.000 0.00 0.00 0.00 2.74 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
29 30 1.250328 TTCTCGTGAGGTTTAGCCGA 58.750 50.000 0.00 0.00 43.70 5.54
33 34 0.529992 CGTGAGGTTTAGCCGATCCC 60.530 60.000 0.00 0.00 43.70 3.85
235 245 2.126618 TCGATTCGCGCGTGTTCT 60.127 55.556 30.98 10.79 40.61 3.01
236 246 0.860203 CTCGATTCGCGCGTGTTCTA 60.860 55.000 30.98 15.10 40.61 2.10
239 249 1.140407 GATTCGCGCGTGTTCTAGCT 61.140 55.000 30.98 4.67 0.00 3.32
240 250 1.413767 ATTCGCGCGTGTTCTAGCTG 61.414 55.000 30.98 0.00 0.00 4.24
262 272 2.901192 TCGTGAATCTGGTAGGGTTTGA 59.099 45.455 0.00 0.00 0.00 2.69
270 280 3.968649 TCTGGTAGGGTTTGACTTGTACA 59.031 43.478 0.00 0.00 0.00 2.90
272 282 3.712733 TGGTAGGGTTTGACTTGTACAGT 59.287 43.478 0.00 0.00 39.07 3.55
288 299 3.672767 ACAGTACGGTTGTTTAGAGGG 57.327 47.619 0.00 0.00 0.00 4.30
346 362 0.037882 TGCTCTGCTTCTGTTCGAGG 60.038 55.000 0.00 0.00 0.00 4.63
347 363 0.037790 GCTCTGCTTCTGTTCGAGGT 60.038 55.000 0.00 0.00 0.00 3.85
348 364 1.707632 CTCTGCTTCTGTTCGAGGTG 58.292 55.000 0.00 0.00 0.00 4.00
392 411 0.315251 CTGAATGGCTCGCTCGGATA 59.685 55.000 0.00 0.00 0.00 2.59
410 429 3.945285 GGATATTTCTTGGGCGTTCTTGA 59.055 43.478 0.00 0.00 0.00 3.02
430 449 2.717639 ACCTGCTGTTTGTTCTCTGT 57.282 45.000 0.00 0.00 0.00 3.41
455 474 2.552315 TCTGATTTCGTTGGTCTTTGCC 59.448 45.455 0.00 0.00 0.00 4.52
483 505 7.651808 AGGATCATAACTGTGTTTGTTTCTTG 58.348 34.615 0.00 0.00 0.00 3.02
500 522 3.247442 TCTTGTCCGCGTAAATGTACTG 58.753 45.455 4.92 0.00 0.00 2.74
501 523 2.728690 TGTCCGCGTAAATGTACTGT 57.271 45.000 4.92 0.00 0.00 3.55
502 524 2.598589 TGTCCGCGTAAATGTACTGTC 58.401 47.619 4.92 0.00 0.00 3.51
617 642 5.874810 TGCTGTAGGTTTATTCTAGCAACAG 59.125 40.000 0.00 0.00 0.00 3.16
618 643 5.294552 GCTGTAGGTTTATTCTAGCAACAGG 59.705 44.000 0.00 0.00 0.00 4.00
649 674 2.234908 GGGTGTAGATTGCTCTGTCACT 59.765 50.000 10.48 0.00 37.58 3.41
702 728 6.560253 TCTTTCTGCTACCAAGTTGAATTC 57.440 37.500 3.87 0.00 0.00 2.17
721 783 5.549742 ATTCTATTTCTCTGAGCCCTGAG 57.450 43.478 0.00 0.00 39.04 3.35
801 863 7.310664 ACTGATAATGTTCAATTTGCTCACTG 58.689 34.615 0.00 0.00 0.00 3.66
841 913 8.659925 ATTGTTCACACTTTTGCAATCATTTA 57.340 26.923 0.00 0.00 0.00 1.40
868 940 6.429692 TCTGAAGGAAATGTGAGCGAATTAAA 59.570 34.615 0.00 0.00 0.00 1.52
880 953 5.294306 TGAGCGAATTAAATTCCTACAGCAG 59.706 40.000 0.00 0.00 35.89 4.24
884 957 6.650372 CGAATTAAATTCCTACAGCAGTAGC 58.350 40.000 10.63 0.00 45.15 3.58
886 959 7.041780 CGAATTAAATTCCTACAGCAGTAGCAT 60.042 37.037 10.63 2.62 45.15 3.79
894 967 3.071874 ACAGCAGTAGCATTTTAGGCA 57.928 42.857 0.00 0.00 45.49 4.75
896 969 3.191371 ACAGCAGTAGCATTTTAGGCAAC 59.809 43.478 0.00 0.00 45.49 4.17
902 975 6.128007 GCAGTAGCATTTTAGGCAACTTTAGA 60.128 38.462 0.00 0.00 43.54 2.10
912 985 4.558538 GGCAACTTTAGACATGGCATAG 57.441 45.455 0.00 0.00 38.16 2.23
919 992 2.495155 AGACATGGCATAGTGTTGCA 57.505 45.000 0.00 0.00 44.59 4.08
920 993 2.362736 AGACATGGCATAGTGTTGCAG 58.637 47.619 0.00 0.00 44.59 4.41
939 1012 2.426024 CAGCATTGCCTGTTTGCTAGAT 59.574 45.455 4.70 0.00 44.54 1.98
941 1014 3.629398 AGCATTGCCTGTTTGCTAGATAC 59.371 43.478 4.70 0.00 44.51 2.24
942 1015 3.629398 GCATTGCCTGTTTGCTAGATACT 59.371 43.478 0.00 0.00 33.61 2.12
943 1016 4.816385 GCATTGCCTGTTTGCTAGATACTA 59.184 41.667 0.00 0.00 33.61 1.82
948 1021 4.212214 GCCTGTTTGCTAGATACTACATGC 59.788 45.833 0.00 0.00 0.00 4.06
1065 1138 3.055891 TCAGTGATTCTTGGAGCGATGAA 60.056 43.478 0.00 0.00 0.00 2.57
1122 1195 1.079543 CTCCCTGCCAGAGAACGTG 60.080 63.158 0.00 0.00 32.86 4.49
1141 1214 1.187567 GCTTGTGGGCATGGACCTTT 61.188 55.000 0.00 0.00 0.00 3.11
1157 1230 4.323792 GGACCTTTCTCTCATTCATCCACA 60.324 45.833 0.00 0.00 0.00 4.17
1167 1240 2.630889 TTCATCCACAGGACTCCTCT 57.369 50.000 0.00 0.00 32.98 3.69
1241 1315 3.198872 GCTGTAAATACTCCTGCAGTCC 58.801 50.000 13.81 0.00 36.43 3.85
1248 1322 0.108615 ACTCCTGCAGTCCGAATTCG 60.109 55.000 20.92 20.92 39.44 3.34
1351 1441 6.483307 TGGATAAACTGCACATAGCTGATAAC 59.517 38.462 0.00 0.00 44.15 1.89
1403 1493 4.566545 TGTCCAAACTTGTTAGCATGTG 57.433 40.909 0.00 0.00 33.92 3.21
1409 1499 3.369546 ACTTGTTAGCATGTGGTTTGC 57.630 42.857 0.00 0.00 40.45 3.68
1438 1528 3.451141 TTTGGTGAATTCTGTGGTTGC 57.549 42.857 7.05 0.00 0.00 4.17
1442 1532 0.950836 TGAATTCTGTGGTTGCGTGG 59.049 50.000 7.05 0.00 0.00 4.94
1469 1559 8.401955 ACTAGGTATTATTTCCCCTTTCTGAA 57.598 34.615 0.00 0.00 0.00 3.02
1479 1569 2.167075 CCCCTTTCTGAAATCCATGTGC 59.833 50.000 2.88 0.00 0.00 4.57
1820 1910 2.999185 AGCCCATTTTTCTCCCTGAA 57.001 45.000 0.00 0.00 0.00 3.02
1834 1924 5.123227 TCTCCCTGAACAAAAGTTACACAG 58.877 41.667 0.00 0.00 0.00 3.66
1875 1965 2.042162 AGGGTTGATGACTGATGCCTTT 59.958 45.455 0.00 0.00 0.00 3.11
1877 1967 3.084039 GGTTGATGACTGATGCCTTTGA 58.916 45.455 0.00 0.00 0.00 2.69
1879 1969 4.201990 GGTTGATGACTGATGCCTTTGATC 60.202 45.833 0.00 0.00 0.00 2.92
1938 2028 2.238521 TGCAGGGGAGCAAAAAGTTAG 58.761 47.619 0.00 0.00 42.46 2.34
2124 2214 1.212935 ACCACCTGCTCTCTGTTTGTT 59.787 47.619 0.00 0.00 0.00 2.83
2147 2237 9.914834 TGTTCTTATGCTAGGGTAAATTATGTT 57.085 29.630 0.00 0.00 0.00 2.71
2184 2274 6.463995 AAACTCTTTGCTGGTTTGTCATTA 57.536 33.333 0.00 0.00 32.84 1.90
2193 2283 7.238486 TGCTGGTTTGTCATTATAAATTGGT 57.762 32.000 0.00 0.00 0.00 3.67
2231 2321 7.443575 CAGGATCCTCTTATTGTAAATCACCTG 59.556 40.741 12.69 0.00 33.24 4.00
2285 2375 6.582677 TGGATTCATTCAAAAACCATACGT 57.417 33.333 0.00 0.00 0.00 3.57
2330 2422 4.794248 TCAACTTCGTGTCATTCACTTG 57.206 40.909 0.00 0.00 44.16 3.16
2342 2434 7.042992 CGTGTCATTCACTTGTTACTAGTTTGA 60.043 37.037 0.00 0.00 44.16 2.69
2380 2473 6.146184 CCGATGGTATGTCATTCATGTTAGTC 59.854 42.308 6.20 0.00 37.91 2.59
2434 2527 8.621532 TTTACATATGCCAGATTGTATCTTCC 57.378 34.615 1.58 0.00 37.58 3.46
2527 2623 6.385033 AGATTTTGTGAATGCTCTTGCTAAC 58.615 36.000 0.00 0.00 40.48 2.34
2584 2680 0.829333 ATGGCTCTGCATCGACTTCT 59.171 50.000 0.00 0.00 0.00 2.85
2644 3145 4.037803 TCTGATGCATTACTGAGAGAGCTC 59.962 45.833 5.27 5.27 41.67 4.09
2701 3202 2.618709 GGACTGCAACCATAACATAGCC 59.381 50.000 4.93 0.00 0.00 3.93
2850 3351 2.683968 GTGTAGCCACACGAAGAATCA 58.316 47.619 0.00 0.00 45.27 2.57
2871 3372 6.877611 TCATTTGGAAACCTAGAACAGTTC 57.122 37.500 5.00 5.00 0.00 3.01
2924 3425 2.868583 GACCCACATGATGAATGAGTCG 59.131 50.000 0.00 0.00 38.72 4.18
2999 3500 1.158007 TTTTTCTCCTGGGAGGGCTT 58.842 50.000 15.66 0.00 42.20 4.35
3152 3653 9.102757 CTGTACAATAGTTTGCTGATAAGTGAT 57.897 33.333 0.00 0.00 36.22 3.06
3153 3654 9.448438 TGTACAATAGTTTGCTGATAAGTGATT 57.552 29.630 0.00 0.00 36.22 2.57
3197 3698 8.510243 TGATATGTGAAGTTAATGCATCTGTT 57.490 30.769 0.00 0.00 0.00 3.16
3299 3801 3.724508 AGAGATCAACATTCGAGCGAT 57.275 42.857 0.00 0.00 0.00 4.58
3488 3993 4.472833 GGATCATTCTAGTCCCCTGCATAT 59.527 45.833 0.00 0.00 0.00 1.78
3489 3994 5.663106 GGATCATTCTAGTCCCCTGCATATA 59.337 44.000 0.00 0.00 0.00 0.86
3593 4098 0.906775 TGGTATTCGGACCTTGACCC 59.093 55.000 4.13 0.00 40.46 4.46
3594 4099 1.201424 GGTATTCGGACCTTGACCCT 58.799 55.000 0.00 0.00 36.47 4.34
3617 4122 5.432645 TGTCACCTGAACAAACTGTTGATA 58.567 37.500 0.00 0.00 41.28 2.15
3663 4168 1.730501 TCCGAAGCAGCATGAGAAAG 58.269 50.000 0.00 0.00 39.69 2.62
3803 4345 6.112734 TGTTCAGTACAATGAGTTCAGTTGT 58.887 36.000 0.00 11.70 39.26 3.32
3811 4353 3.358111 TGAGTTCAGTTGTGGTTTCCA 57.642 42.857 0.00 0.00 0.00 3.53
3832 4376 0.622665 CTCTCACCAGCCCCTCATTT 59.377 55.000 0.00 0.00 0.00 2.32
3879 4424 7.049140 GTGCAATGTAATTTCACCTTTTAGC 57.951 36.000 0.00 0.00 43.27 3.09
3922 4467 4.843220 ACTTTGCAATCTTCTGTTCTGG 57.157 40.909 0.00 0.00 0.00 3.86
3929 4474 4.320788 GCAATCTTCTGTTCTGGTGAAAGG 60.321 45.833 0.00 0.00 33.52 3.11
3932 4477 5.623956 TCTTCTGTTCTGGTGAAAGGTAA 57.376 39.130 0.00 0.00 33.52 2.85
3933 4478 6.187727 TCTTCTGTTCTGGTGAAAGGTAAT 57.812 37.500 0.00 0.00 33.52 1.89
3935 4480 7.741785 TCTTCTGTTCTGGTGAAAGGTAATTA 58.258 34.615 0.00 0.00 33.52 1.40
3936 4481 7.878127 TCTTCTGTTCTGGTGAAAGGTAATTAG 59.122 37.037 0.00 0.00 33.52 1.73
3937 4482 7.074653 TCTGTTCTGGTGAAAGGTAATTAGT 57.925 36.000 0.00 0.00 33.52 2.24
3938 4483 7.159372 TCTGTTCTGGTGAAAGGTAATTAGTC 58.841 38.462 0.00 0.00 33.52 2.59
3939 4484 5.929992 TGTTCTGGTGAAAGGTAATTAGTCG 59.070 40.000 0.00 0.00 33.52 4.18
3974 4519 8.934023 AATGAGAACTGAAGGTTGGTAATTAA 57.066 30.769 0.00 0.00 38.41 1.40
3998 4543 2.523015 GTTTCAGCAGGAATCATTGCG 58.477 47.619 3.87 0.82 44.80 4.85
4007 4552 3.624777 AGGAATCATTGCGTCCTGAATT 58.375 40.909 7.05 0.00 40.37 2.17
4032 4577 3.393472 CTCTATGGAGCCAGCAACC 57.607 57.895 0.00 0.00 32.43 3.77
4064 4609 2.675317 GCGATGTGACTGCTTTACTCCT 60.675 50.000 0.00 0.00 0.00 3.69
4067 4612 1.347707 TGTGACTGCTTTACTCCTGGG 59.652 52.381 0.00 0.00 0.00 4.45
4068 4613 1.623811 GTGACTGCTTTACTCCTGGGA 59.376 52.381 0.00 0.00 0.00 4.37
4092 4637 4.082523 GCTGTCGTGCTGGCCCTA 62.083 66.667 0.00 0.00 0.00 3.53
4143 4688 0.323302 TGATGCTGGCACGGTAAAGA 59.677 50.000 0.00 0.00 36.83 2.52
4383 4938 4.263905 TGAATTCTGGCCTTGAACCTATGT 60.264 41.667 3.32 0.00 0.00 2.29
4387 4942 4.479158 TCTGGCCTTGAACCTATGTTTTT 58.521 39.130 3.32 0.00 33.97 1.94
4419 4974 4.733077 TTTGGACAATACTGAAGGGGAA 57.267 40.909 0.00 0.00 0.00 3.97
4420 4975 4.301072 TTGGACAATACTGAAGGGGAAG 57.699 45.455 0.00 0.00 0.00 3.46
4451 5006 1.334960 CGGTAAAGCTGTTGCCTTGTG 60.335 52.381 11.70 0.00 40.80 3.33
4457 5012 1.681264 AGCTGTTGCCTTGTGGTTTAC 59.319 47.619 0.00 0.00 40.80 2.01
4462 5017 2.264005 TGCCTTGTGGTTTACGTCAT 57.736 45.000 0.00 0.00 35.27 3.06
4468 5023 2.933573 TGTGGTTTACGTCATGGGTTT 58.066 42.857 0.00 0.00 0.00 3.27
4473 5028 4.585162 TGGTTTACGTCATGGGTTTGAATT 59.415 37.500 0.00 0.00 0.00 2.17
4474 5029 5.158494 GGTTTACGTCATGGGTTTGAATTC 58.842 41.667 0.00 0.00 0.00 2.17
4475 5030 5.048294 GGTTTACGTCATGGGTTTGAATTCT 60.048 40.000 7.05 0.00 0.00 2.40
4476 5031 5.621197 TTACGTCATGGGTTTGAATTCTG 57.379 39.130 7.05 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 1.448497 GATTACGAATCCCGCCCCA 59.552 57.895 0.00 0.00 43.32 4.96
124 132 2.387445 CGGCGCCGAATCAAGAACA 61.387 57.895 44.86 0.00 42.83 3.18
235 245 2.688446 CCTACCAGATTCACGACAGCTA 59.312 50.000 0.00 0.00 0.00 3.32
236 246 1.478510 CCTACCAGATTCACGACAGCT 59.521 52.381 0.00 0.00 0.00 4.24
239 249 1.933021 ACCCTACCAGATTCACGACA 58.067 50.000 0.00 0.00 0.00 4.35
240 250 3.000727 CAAACCCTACCAGATTCACGAC 58.999 50.000 0.00 0.00 0.00 4.34
262 272 6.147864 TCTAAACAACCGTACTGTACAAGT 57.852 37.500 17.35 11.00 43.40 3.16
270 280 2.893424 TCCCCTCTAAACAACCGTACT 58.107 47.619 0.00 0.00 0.00 2.73
272 282 4.914177 AAATCCCCTCTAAACAACCGTA 57.086 40.909 0.00 0.00 0.00 4.02
346 362 1.399727 CCAGGCAAAAATCGACGACAC 60.400 52.381 0.00 0.00 0.00 3.67
347 363 0.871722 CCAGGCAAAAATCGACGACA 59.128 50.000 0.00 0.00 0.00 4.35
348 364 0.168128 CCCAGGCAAAAATCGACGAC 59.832 55.000 0.00 0.00 0.00 4.34
351 367 1.611491 TGAACCCAGGCAAAAATCGAC 59.389 47.619 0.00 0.00 0.00 4.20
392 411 2.296190 GGTTCAAGAACGCCCAAGAAAT 59.704 45.455 6.84 0.00 42.02 2.17
410 429 3.004752 ACAGAGAACAAACAGCAGGTT 57.995 42.857 0.00 0.00 42.98 3.50
430 449 5.106712 GCAAAGACCAACGAAATCAGACATA 60.107 40.000 0.00 0.00 0.00 2.29
455 474 5.862924 ACAAACACAGTTATGATCCTTCG 57.137 39.130 0.00 0.00 0.00 3.79
472 494 3.322230 TTACGCGGACAAGAAACAAAC 57.678 42.857 12.47 0.00 0.00 2.93
483 505 1.580704 CGACAGTACATTTACGCGGAC 59.419 52.381 12.47 0.00 32.93 4.79
500 522 6.033513 GGCATGCACTTTATTTTCTTTACGAC 59.966 38.462 21.36 0.00 0.00 4.34
501 523 6.072175 AGGCATGCACTTTATTTTCTTTACGA 60.072 34.615 21.36 0.00 0.00 3.43
502 524 6.033831 CAGGCATGCACTTTATTTTCTTTACG 59.966 38.462 21.36 0.00 0.00 3.18
617 642 0.604578 TCTACACCCGTACTGCAACC 59.395 55.000 0.00 0.00 0.00 3.77
618 643 2.667473 ATCTACACCCGTACTGCAAC 57.333 50.000 0.00 0.00 0.00 4.17
649 674 4.042062 AGACAGTGGATCCTGACATGAAAA 59.958 41.667 14.23 0.00 36.30 2.29
721 783 7.148590 GCACCATCATAACAAAGGTTTCATTTC 60.149 37.037 0.00 0.00 38.45 2.17
801 863 1.726853 ACAATACAGCGCTTCCAGTC 58.273 50.000 7.50 0.00 0.00 3.51
841 913 3.942829 TCGCTCACATTTCCTTCAGATT 58.057 40.909 0.00 0.00 0.00 2.40
880 953 7.141100 TGTCTAAAGTTGCCTAAAATGCTAC 57.859 36.000 0.00 0.00 35.19 3.58
884 957 5.807011 GCCATGTCTAAAGTTGCCTAAAATG 59.193 40.000 0.00 0.00 0.00 2.32
886 959 4.830046 TGCCATGTCTAAAGTTGCCTAAAA 59.170 37.500 0.00 0.00 0.00 1.52
894 967 5.106157 GCAACACTATGCCATGTCTAAAGTT 60.106 40.000 0.00 0.00 40.49 2.66
896 969 4.395854 TGCAACACTATGCCATGTCTAAAG 59.604 41.667 0.00 0.00 45.83 1.85
902 975 0.813184 GCTGCAACACTATGCCATGT 59.187 50.000 0.00 0.00 45.83 3.21
920 993 3.629398 AGTATCTAGCAAACAGGCAATGC 59.371 43.478 0.00 0.00 40.34 3.56
927 1000 5.043903 ACGCATGTAGTATCTAGCAAACAG 58.956 41.667 0.00 0.00 0.00 3.16
939 1012 8.712285 AGCTATAAAAAGAAACGCATGTAGTA 57.288 30.769 0.00 0.00 0.00 1.82
941 1014 7.011482 AGGAGCTATAAAAAGAAACGCATGTAG 59.989 37.037 0.00 0.00 0.00 2.74
942 1015 6.821665 AGGAGCTATAAAAAGAAACGCATGTA 59.178 34.615 0.00 0.00 0.00 2.29
943 1016 5.648092 AGGAGCTATAAAAAGAAACGCATGT 59.352 36.000 0.00 0.00 0.00 3.21
1033 1106 7.101652 TCCAAGAATCACTGATACTGTAGTC 57.898 40.000 0.00 0.00 0.00 2.59
1065 1138 1.537202 GCCAAGAATCGCACAAGTTCT 59.463 47.619 0.00 0.00 33.86 3.01
1122 1195 1.187567 AAAGGTCCATGCCCACAAGC 61.188 55.000 0.00 0.00 0.00 4.01
1141 1214 3.703556 GAGTCCTGTGGATGAATGAGAGA 59.296 47.826 0.00 0.00 32.73 3.10
1167 1240 8.955952 TGTGCATCACTAGGTACTAACCAGGA 62.956 46.154 0.00 0.00 42.17 3.86
1210 1283 5.815740 AGGAGTATTTACAGCACCATTTACG 59.184 40.000 0.00 0.00 0.00 3.18
1241 1315 4.584029 AGTGAATAACAGCACGAATTCG 57.416 40.909 25.64 25.64 46.33 3.34
1248 1322 7.596749 AGTACAACATAGTGAATAACAGCAC 57.403 36.000 0.00 0.00 35.30 4.40
1351 1441 4.440880 AGTTGCTGCTTTATGCTAGAGAG 58.559 43.478 0.00 0.00 43.37 3.20
1403 1493 7.614124 ATTCACCAAATCAAATATGCAAACC 57.386 32.000 0.00 0.00 0.00 3.27
1409 1499 8.036575 ACCACAGAATTCACCAAATCAAATATG 58.963 33.333 8.44 0.00 0.00 1.78
1438 1528 4.262765 GGGGAAATAATACCTAGTCCCACG 60.263 50.000 11.69 0.00 37.88 4.94
1442 1532 7.072076 TCAGAAAGGGGAAATAATACCTAGTCC 59.928 40.741 0.00 0.00 31.88 3.85
1469 1559 6.015688 CAGATTATAAGGCAAGCACATGGATT 60.016 38.462 0.00 0.00 0.00 3.01
1479 1569 8.388484 AGAATTAGCACAGATTATAAGGCAAG 57.612 34.615 0.00 0.00 0.00 4.01
1597 1687 6.367422 CCTTTCTAATATCTGACTCGCCATTC 59.633 42.308 0.00 0.00 0.00 2.67
1834 1924 3.397482 CTGGTTGATAGCTAGGCACATC 58.603 50.000 0.00 0.00 0.00 3.06
1839 1929 1.132500 ACCCTGGTTGATAGCTAGGC 58.868 55.000 0.00 0.00 0.00 3.93
1875 1965 4.047627 TGTACTCCTGTCAGGAAGATCA 57.952 45.455 22.08 15.00 45.28 2.92
1877 1967 4.421131 ACTTGTACTCCTGTCAGGAAGAT 58.579 43.478 22.08 12.97 45.28 2.40
1879 1969 3.829601 AGACTTGTACTCCTGTCAGGAAG 59.170 47.826 22.08 17.49 45.28 3.46
1916 2006 1.260544 ACTTTTTGCTCCCCTGCATC 58.739 50.000 0.00 0.00 42.96 3.91
1938 2028 7.809331 CAGAGATAGCAGTTCATCTTCAGTATC 59.191 40.741 0.00 0.00 31.63 2.24
2124 2214 9.555727 GACAACATAATTTACCCTAGCATAAGA 57.444 33.333 0.00 0.00 0.00 2.10
2147 2237 5.470098 GCAAAGAGTTTAGACAATCCAGACA 59.530 40.000 0.00 0.00 0.00 3.41
2184 2274 7.889178 TCCTGGGGAACTATTTACCAATTTAT 58.111 34.615 0.00 0.00 37.47 1.40
2193 2283 5.171541 AGAGGATCCTGGGGAACTATTTA 57.828 43.478 22.02 0.00 34.34 1.40
2231 2321 8.292448 TCTGCAAGACTGATTCTTCAAATAAAC 58.708 33.333 0.00 0.00 43.23 2.01
2330 2422 8.618677 GGGTTTATATTGCCTCAAACTAGTAAC 58.381 37.037 0.00 0.00 32.69 2.50
2371 2464 7.323420 TCAAGATTACAGGTCAGACTAACATG 58.677 38.462 0.00 0.00 34.73 3.21
2380 2473 6.590068 AGGATTCATCAAGATTACAGGTCAG 58.410 40.000 0.00 0.00 0.00 3.51
2434 2527 2.098770 GGAAGAGCTATTTTGCTGGCTG 59.901 50.000 0.00 0.00 44.17 4.85
2487 2583 0.395686 ATCTACGCCATCTGCAGCAT 59.604 50.000 9.47 0.43 41.33 3.79
2527 2623 8.356657 AGATCTTTCATTTCTATGTAGTCCTCG 58.643 37.037 0.00 0.00 33.34 4.63
2584 2680 5.849510 TCAGACCGTCTACTTGAAAATTCA 58.150 37.500 0.00 0.00 34.92 2.57
2644 3145 7.012327 TCTCTAGTTGTGTTTTGGTCATTCAAG 59.988 37.037 0.00 0.00 0.00 3.02
2701 3202 3.736252 CGCAATCAGATTTAGTAGGTCCG 59.264 47.826 0.00 0.00 0.00 4.79
2850 3351 7.839680 ATTGAACTGTTCTAGGTTTCCAAAT 57.160 32.000 20.18 5.97 0.00 2.32
2871 3372 5.634859 GTGGGACTTCATAGTTGCAAAATTG 59.365 40.000 0.00 0.00 33.84 2.32
2924 3425 4.202151 ACTGGCTTTGTTGAAAGTTCCATC 60.202 41.667 0.00 0.00 40.77 3.51
3157 3658 3.443329 ACATATCAGCATCCACGCAAAAA 59.557 39.130 0.00 0.00 0.00 1.94
3158 3659 3.016031 ACATATCAGCATCCACGCAAAA 58.984 40.909 0.00 0.00 0.00 2.44
3159 3660 2.355444 CACATATCAGCATCCACGCAAA 59.645 45.455 0.00 0.00 0.00 3.68
3160 3661 1.941975 CACATATCAGCATCCACGCAA 59.058 47.619 0.00 0.00 0.00 4.85
3161 3662 1.138661 TCACATATCAGCATCCACGCA 59.861 47.619 0.00 0.00 0.00 5.24
3162 3663 1.869774 TCACATATCAGCATCCACGC 58.130 50.000 0.00 0.00 0.00 5.34
3163 3664 3.461061 ACTTCACATATCAGCATCCACG 58.539 45.455 0.00 0.00 0.00 4.94
3164 3665 6.925610 TTAACTTCACATATCAGCATCCAC 57.074 37.500 0.00 0.00 0.00 4.02
3165 3666 6.016860 GCATTAACTTCACATATCAGCATCCA 60.017 38.462 0.00 0.00 0.00 3.41
3166 3667 6.016860 TGCATTAACTTCACATATCAGCATCC 60.017 38.462 0.00 0.00 0.00 3.51
3167 3668 6.962686 TGCATTAACTTCACATATCAGCATC 58.037 36.000 0.00 0.00 0.00 3.91
3168 3669 6.947644 TGCATTAACTTCACATATCAGCAT 57.052 33.333 0.00 0.00 0.00 3.79
3169 3670 6.769341 AGATGCATTAACTTCACATATCAGCA 59.231 34.615 0.00 0.00 0.00 4.41
3170 3671 7.076362 CAGATGCATTAACTTCACATATCAGC 58.924 38.462 0.00 0.00 0.00 4.26
3171 3672 8.151141 ACAGATGCATTAACTTCACATATCAG 57.849 34.615 0.00 0.00 0.00 2.90
3172 3673 8.510243 AACAGATGCATTAACTTCACATATCA 57.490 30.769 0.00 0.00 0.00 2.15
3173 3674 8.834465 AGAACAGATGCATTAACTTCACATATC 58.166 33.333 0.00 0.00 0.00 1.63
3174 3675 8.743085 AGAACAGATGCATTAACTTCACATAT 57.257 30.769 0.00 0.00 0.00 1.78
3175 3676 8.565896 AAGAACAGATGCATTAACTTCACATA 57.434 30.769 0.00 0.00 0.00 2.29
3176 3677 7.458409 AAGAACAGATGCATTAACTTCACAT 57.542 32.000 0.00 0.00 0.00 3.21
3177 3678 6.882610 AAGAACAGATGCATTAACTTCACA 57.117 33.333 0.00 0.00 0.00 3.58
3197 3698 3.547746 GTTGTGAACCAACCCTGTAAGA 58.452 45.455 0.00 0.00 46.39 2.10
3299 3801 1.833630 GGATGGTGATCCAGACACTGA 59.166 52.381 0.00 0.00 46.93 3.41
3488 3993 6.821160 TCCTGTACAAAATCGATGAAATGCTA 59.179 34.615 0.00 0.00 0.00 3.49
3489 3994 5.647658 TCCTGTACAAAATCGATGAAATGCT 59.352 36.000 0.00 0.00 0.00 3.79
3500 4005 5.765182 CCTATGTCCCATCCTGTACAAAATC 59.235 44.000 0.00 0.00 0.00 2.17
3593 4098 3.689161 TCAACAGTTTGTTCAGGTGACAG 59.311 43.478 0.00 0.00 38.77 3.51
3594 4099 3.680490 TCAACAGTTTGTTCAGGTGACA 58.320 40.909 0.00 0.00 38.77 3.58
3617 4122 1.480137 CCTCGTTCTGCCAGAAGATCT 59.520 52.381 7.55 0.00 34.42 2.75
3692 4234 5.334414 GGTTCAACAGAATCATCAGTGTCAC 60.334 44.000 0.00 0.00 0.00 3.67
3748 4290 6.763355 AGAATCGATAACAGAACTGGCATAT 58.237 36.000 0.00 2.64 34.19 1.78
3749 4291 6.161855 AGAATCGATAACAGAACTGGCATA 57.838 37.500 0.00 0.00 34.19 3.14
3787 4329 4.097892 GGAAACCACAACTGAACTCATTGT 59.902 41.667 0.00 0.00 37.02 2.71
3811 4353 0.548682 ATGAGGGGCTGGTGAGAGTT 60.549 55.000 0.00 0.00 0.00 3.01
3832 4376 9.624697 GCACAGAATTTTACAATAGAATTCACA 57.375 29.630 8.44 0.00 40.50 3.58
3905 4450 3.490439 TCACCAGAACAGAAGATTGCA 57.510 42.857 0.00 0.00 0.00 4.08
3922 4467 6.588756 TGACATGTCGACTAATTACCTTTCAC 59.411 38.462 20.54 0.00 0.00 3.18
3929 4474 7.915923 TCTCATTCTGACATGTCGACTAATTAC 59.084 37.037 20.54 4.35 0.00 1.89
3932 4477 6.456795 TCTCATTCTGACATGTCGACTAAT 57.543 37.500 20.54 13.45 0.00 1.73
3933 4478 5.897377 TCTCATTCTGACATGTCGACTAA 57.103 39.130 20.54 11.89 0.00 2.24
3935 4480 4.219507 AGTTCTCATTCTGACATGTCGACT 59.780 41.667 20.54 11.86 0.00 4.18
3936 4481 4.325741 CAGTTCTCATTCTGACATGTCGAC 59.674 45.833 20.54 9.11 34.02 4.20
3937 4482 4.218417 TCAGTTCTCATTCTGACATGTCGA 59.782 41.667 20.54 16.82 36.04 4.20
3938 4483 4.488879 TCAGTTCTCATTCTGACATGTCG 58.511 43.478 20.54 14.91 36.04 4.35
3939 4484 5.350914 CCTTCAGTTCTCATTCTGACATGTC 59.649 44.000 19.27 19.27 39.87 3.06
3965 4510 4.638421 CCTGCTGAAACCGATTAATTACCA 59.362 41.667 0.00 0.00 0.00 3.25
3974 4519 2.787473 TGATTCCTGCTGAAACCGAT 57.213 45.000 0.00 0.00 36.33 4.18
3998 4543 6.349300 TCCATAGAGCTAACAAATTCAGGAC 58.651 40.000 0.00 0.00 0.00 3.85
4032 4577 4.406069 CAGTCACATCGCAAATTTACCAG 58.594 43.478 0.00 0.00 0.00 4.00
4064 4609 1.995066 ACGACAGCATCCCATCCCA 60.995 57.895 0.00 0.00 0.00 4.37
4067 4612 1.153289 AGCACGACAGCATCCCATC 60.153 57.895 0.00 0.00 36.85 3.51
4068 4613 1.450848 CAGCACGACAGCATCCCAT 60.451 57.895 0.00 0.00 36.85 4.00
4092 4637 4.415150 CCCACCACCAGCGCATCT 62.415 66.667 11.47 0.00 0.00 2.90
4115 4660 2.916052 GCCAGCATCATCGGCATGG 61.916 63.158 0.00 0.00 45.52 3.66
4143 4688 5.976458 TGCAGGAAACAAAACAGAGATTTT 58.024 33.333 0.00 0.00 31.87 1.82
4188 4733 4.893524 ACCTTTTAGTCTTTTTGGAGGTGG 59.106 41.667 0.00 0.00 35.11 4.61
4261 4812 2.832498 GACCTGCCTATGGAGCCC 59.168 66.667 0.00 0.00 0.00 5.19
4396 4951 4.599041 TCCCCTTCAGTATTGTCCAAATG 58.401 43.478 0.00 0.00 0.00 2.32
4406 4961 1.064389 GCCAAGCTTCCCCTTCAGTAT 60.064 52.381 0.00 0.00 0.00 2.12
4407 4962 0.328258 GCCAAGCTTCCCCTTCAGTA 59.672 55.000 0.00 0.00 0.00 2.74
4451 5006 4.776795 ATTCAAACCCATGACGTAAACC 57.223 40.909 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.