Multiple sequence alignment - TraesCS6B01G398300

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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 TraesCS6B01G398300 chr6B 100.000 4761 0 0 1 4761 673755500 673760260 0.000000e+00 8793.0
1 TraesCS6B01G398300 chr6B 91.574 985 71 8 2080 3063 672506937 672505964 0.000000e+00 1349.0
2 TraesCS6B01G398300 chr6B 86.802 1038 121 15 2083 3116 672894349 672895374 0.000000e+00 1144.0
3 TraesCS6B01G398300 chr6B 87.551 988 114 4 2080 3064 673365667 673364686 0.000000e+00 1134.0
4 TraesCS6B01G398300 chr6B 86.609 1038 124 14 2087 3121 672944929 672945954 0.000000e+00 1133.0
5 TraesCS6B01G398300 chr6B 86.570 1035 123 15 2086 3116 673608774 673607752 0.000000e+00 1127.0
6 TraesCS6B01G398300 chr6B 94.368 657 23 6 4118 4761 672502959 672502304 0.000000e+00 996.0
7 TraesCS6B01G398300 chr6B 93.725 494 25 5 1 493 672510221 672509733 0.000000e+00 736.0
8 TraesCS6B01G398300 chr6B 78.755 1012 123 33 3261 4212 673614634 673613655 1.140000e-165 593.0
9 TraesCS6B01G398300 chr6B 86.693 511 61 6 3207 3712 673607799 673607291 1.160000e-155 560.0
10 TraesCS6B01G398300 chr6B 86.180 521 65 6 3207 3722 672895327 672895845 1.500000e-154 556.0
11 TraesCS6B01G398300 chr6B 87.939 456 48 7 3238 3688 672619477 672619024 9.070000e-147 531.0
12 TraesCS6B01G398300 chr6B 87.692 455 51 5 3238 3688 673698568 673699021 4.220000e-145 525.0
13 TraesCS6B01G398300 chr6B 92.351 353 18 5 1024 1376 672507958 672507615 1.190000e-135 494.0
14 TraesCS6B01G398300 chr6B 88.537 410 44 2 1563 1969 673609342 673608933 1.190000e-135 494.0
15 TraesCS6B01G398300 chr6B 87.961 407 49 0 1563 1969 672883840 672884246 9.270000e-132 481.0
16 TraesCS6B01G398300 chr6B 83.838 495 67 8 1560 2049 672944356 672944842 4.340000e-125 459.0
17 TraesCS6B01G398300 chr6B 95.668 277 12 0 1 277 672534457 672534181 3.380000e-121 446.0
18 TraesCS6B01G398300 chr6B 85.870 368 43 5 1009 1376 672883328 672883686 2.690000e-102 383.0
19 TraesCS6B01G398300 chr6B 86.769 325 25 11 631 941 672508490 672508170 3.530000e-91 346.0
20 TraesCS6B01G398300 chr6B 84.943 352 41 8 1025 1376 673366778 673366439 3.530000e-91 346.0
21 TraesCS6B01G398300 chr6B 84.419 353 34 13 1024 1376 673696420 673696751 1.280000e-85 327.0
22 TraesCS6B01G398300 chr6B 83.662 355 33 19 1024 1376 672628592 672628261 1.290000e-80 311.0
23 TraesCS6B01G398300 chr6B 84.348 230 17 9 740 966 672509455 672509242 1.740000e-49 207.0
24 TraesCS6B01G398300 chr6B 77.961 363 47 18 4161 4513 672633446 672633107 3.760000e-46 196.0
25 TraesCS6B01G398300 chr6B 77.692 390 39 31 4338 4689 672947059 672947438 1.350000e-45 195.0
26 TraesCS6B01G398300 chr6B 75.208 480 78 24 3893 4353 672618839 672618382 6.290000e-44 189.0
27 TraesCS6B01G398300 chr6B 79.730 296 30 19 4359 4631 672896413 672896701 2.260000e-43 187.0
28 TraesCS6B01G398300 chr6B 79.000 300 32 18 4365 4636 673606718 673606422 4.900000e-40 176.0
29 TraesCS6B01G398300 chr6B 90.400 125 7 4 620 741 672509681 672509559 4.930000e-35 159.0
30 TraesCS6B01G398300 chr6B 81.560 141 24 2 4143 4282 672896254 672896393 1.080000e-21 115.0
31 TraesCS6B01G398300 chr6B 81.560 141 24 2 4143 4282 672946922 672947061 1.080000e-21 115.0
32 TraesCS6B01G398300 chr6B 81.560 141 24 2 4143 4282 673606883 673606744 1.080000e-21 115.0
33 TraesCS6B01G398300 chr6B 82.075 106 17 2 4249 4354 673699564 673699667 6.560000e-14 89.8
34 TraesCS6B01G398300 chr6B 84.000 75 11 1 4563 4636 672633087 672633013 2.380000e-08 71.3
35 TraesCS6B01G398300 chr6D 97.368 1596 27 3 1456 3051 445799525 445797945 0.000000e+00 2700.0
36 TraesCS6B01G398300 chr6D 94.872 741 26 6 638 1376 445800424 445799694 0.000000e+00 1147.0
37 TraesCS6B01G398300 chr6D 86.622 1039 118 19 2089 3121 445893803 445894826 0.000000e+00 1129.0
38 TraesCS6B01G398300 chr6D 86.698 857 57 18 3842 4661 445797111 445796275 0.000000e+00 898.0
39 TraesCS6B01G398300 chr6D 96.896 451 14 0 3243 3693 445797783 445797333 0.000000e+00 756.0
40 TraesCS6B01G398300 chr6D 82.958 710 98 16 3261 3954 445854357 445855059 1.880000e-173 619.0
41 TraesCS6B01G398300 chr6D 86.353 447 58 1 1545 1991 445852779 445853222 7.160000e-133 484.0
42 TraesCS6B01G398300 chr6D 91.843 331 20 4 54 384 445800746 445800423 5.620000e-124 455.0
43 TraesCS6B01G398300 chr6D 83.434 495 69 8 1560 2049 445893229 445893715 9.400000e-122 448.0
44 TraesCS6B01G398300 chr6D 85.366 410 57 2 1563 1969 445820119 445819710 5.700000e-114 422.0
45 TraesCS6B01G398300 chr6D 84.986 353 32 13 1024 1376 445812944 445812613 5.900000e-89 339.0
46 TraesCS6B01G398300 chr6D 82.776 389 41 20 989 1376 445820885 445820522 1.650000e-84 324.0
47 TraesCS6B01G398300 chr6D 88.889 270 21 6 1024 1293 445852273 445852533 1.650000e-84 324.0
48 TraesCS6B01G398300 chr6D 78.772 391 53 15 4131 4513 445822667 445822299 7.970000e-58 235.0
49 TraesCS6B01G398300 chr6D 75.688 436 65 27 3893 4308 445810145 445809731 3.790000e-41 180.0
50 TraesCS6B01G398300 chr6D 83.246 191 26 4 4109 4293 445855209 445855399 2.280000e-38 171.0
51 TraesCS6B01G398300 chr6D 81.538 130 14 9 4567 4690 445822281 445822156 1.090000e-16 99.0
52 TraesCS6B01G398300 chr6D 81.053 95 14 3 4001 4092 445840762 445840855 6.610000e-09 73.1
53 TraesCS6B01G398300 chr6D 84.507 71 10 1 4567 4636 445846704 445846774 8.550000e-08 69.4
54 TraesCS6B01G398300 chr6A 93.556 1614 94 4 2080 3693 592477383 592475780 0.000000e+00 2396.0
55 TraesCS6B01G398300 chr6A 86.551 1041 119 19 2087 3121 592549691 592550716 0.000000e+00 1127.0
56 TraesCS6B01G398300 chr6A 91.205 614 34 10 769 1376 592478820 592478221 0.000000e+00 817.0
57 TraesCS6B01G398300 chr6A 85.925 611 60 10 1374 1983 592478163 592477578 3.130000e-176 628.0
58 TraesCS6B01G398300 chr6A 85.595 597 67 16 3261 3846 592538722 592539310 4.070000e-170 608.0
59 TraesCS6B01G398300 chr6A 86.577 447 57 1 1545 1991 592537121 592537564 1.540000e-134 490.0
60 TraesCS6B01G398300 chr6A 91.060 302 21 3 667 967 592480178 592479882 2.060000e-108 403.0
61 TraesCS6B01G398300 chr6A 92.748 262 18 1 1 261 592482213 592481952 1.250000e-100 377.0
62 TraesCS6B01G398300 chr6A 94.606 241 11 1 245 485 592481740 592481502 5.820000e-99 372.0
63 TraesCS6B01G398300 chr6A 88.148 270 23 5 1024 1293 592536600 592536860 3.580000e-81 313.0
64 TraesCS6B01G398300 chr6A 90.667 225 15 3 4250 4472 592475159 592474939 1.300000e-75 294.0
65 TraesCS6B01G398300 chr6A 79.015 467 71 20 3842 4293 592539332 592539786 1.300000e-75 294.0
66 TraesCS6B01G398300 chr6A 86.617 269 27 6 3842 4109 592475558 592475298 6.030000e-74 289.0
67 TraesCS6B01G398300 chr6A 75.040 621 92 30 4041 4636 592499056 592498474 3.710000e-56 230.0
68 TraesCS6B01G398300 chr6A 81.818 220 26 5 3893 4109 592492294 592492086 6.330000e-39 172.0
69 TraesCS6B01G398300 chr6A 90.299 134 6 3 549 675 592481371 592481238 8.190000e-38 169.0
70 TraesCS6B01G398300 chr6A 89.167 120 13 0 4542 4661 592474910 592474791 2.970000e-32 150.0
71 TraesCS6B01G398300 chr6A 82.812 128 4 6 4105 4215 592475279 592475153 1.090000e-16 99.0


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 TraesCS6B01G398300 chr6B 673755500 673760260 4760 False 8793.000000 8793 100.000000 1 4761 1 chr6B.!!$F1 4760
1 TraesCS6B01G398300 chr6B 673364686 673366778 2092 True 740.000000 1134 86.247000 1025 3064 2 chr6B.!!$R7 2039
2 TraesCS6B01G398300 chr6B 672502304 672510221 7917 True 612.428571 1349 90.505000 1 4761 7 chr6B.!!$R4 4760
3 TraesCS6B01G398300 chr6B 673613655 673614634 979 True 593.000000 593 78.755000 3261 4212 1 chr6B.!!$R3 951
4 TraesCS6B01G398300 chr6B 672894349 672896701 2352 False 500.500000 1144 83.568000 2083 4631 4 chr6B.!!$F3 2548
5 TraesCS6B01G398300 chr6B 673606422 673609342 2920 True 494.400000 1127 84.472000 1563 4636 5 chr6B.!!$R8 3073
6 TraesCS6B01G398300 chr6B 672944356 672947438 3082 False 475.500000 1133 82.424750 1560 4689 4 chr6B.!!$F4 3129
7 TraesCS6B01G398300 chr6B 672883328 672884246 918 False 432.000000 481 86.915500 1009 1969 2 chr6B.!!$F2 960
8 TraesCS6B01G398300 chr6B 672618382 672619477 1095 True 360.000000 531 81.573500 3238 4353 2 chr6B.!!$R5 1115
9 TraesCS6B01G398300 chr6B 673696420 673699667 3247 False 313.933333 525 84.728667 1024 4354 3 chr6B.!!$F5 3330
10 TraesCS6B01G398300 chr6D 445796275 445800746 4471 True 1191.200000 2700 93.535400 54 4661 5 chr6D.!!$R1 4607
11 TraesCS6B01G398300 chr6D 445893229 445894826 1597 False 788.500000 1129 85.028000 1560 3121 2 chr6D.!!$F4 1561
12 TraesCS6B01G398300 chr6D 445852273 445855399 3126 False 399.500000 619 85.361500 1024 4293 4 chr6D.!!$F3 3269
13 TraesCS6B01G398300 chr6D 445819710 445822667 2957 True 270.000000 422 82.113000 989 4690 4 chr6D.!!$R3 3701
14 TraesCS6B01G398300 chr6D 445809731 445812944 3213 True 259.500000 339 80.337000 1024 4308 2 chr6D.!!$R2 3284
15 TraesCS6B01G398300 chr6A 592549691 592550716 1025 False 1127.000000 1127 86.551000 2087 3121 1 chr6A.!!$F1 1034
16 TraesCS6B01G398300 chr6A 592474791 592482213 7422 True 544.909091 2396 89.878364 1 4661 11 chr6A.!!$R3 4660
17 TraesCS6B01G398300 chr6A 592536600 592539786 3186 False 426.250000 608 84.833750 1024 4293 4 chr6A.!!$F2 3269
18 TraesCS6B01G398300 chr6A 592498474 592499056 582 True 230.000000 230 75.040000 4041 4636 1 chr6A.!!$R2 595

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
432 662 0.036952 CCTGACCGATGAGTTGCACT 60.037 55.0 0.00 0.00 0.00 4.40 F
665 989 0.101579 AACAAAGAAAACGTGGCCCG 59.898 50.0 11.48 11.48 44.03 6.13 F
2247 6881 0.036010 GCCATCACCTACACAGCAGT 60.036 55.0 0.00 0.00 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2122 6736 7.807977 TGCAGAGAAAGAAGAAACATAGTTT 57.192 32.000 0.00 0.0 0.00 2.66 R
3077 7720 2.607750 AGTGGGTCTGGATGGCGT 60.608 61.111 0.00 0.0 0.00 5.68 R
3794 8614 0.032952 TGTGACTGCCCTCACGTTAC 59.967 55.000 6.42 0.0 43.14 2.50 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
34 35 4.572571 GCCACGTGGGGTTGACCA 62.573 66.667 34.58 0.00 42.91 4.02
59 60 1.813513 CAACAGTCCCGATGCTTTCT 58.186 50.000 0.00 0.00 0.00 2.52
124 125 7.999042 TCCCCTTTATGATCATTCATGGAATA 58.001 34.615 14.65 0.00 42.60 1.75
133 134 6.543465 TGATCATTCATGGAATACAGTTGGTC 59.457 38.462 0.00 0.00 30.44 4.02
290 520 5.492855 TTGCTTTCCCTAACAGCTACTAA 57.507 39.130 0.00 0.00 34.42 2.24
306 536 6.097839 CAGCTACTAACCTCCCACTACAATTA 59.902 42.308 0.00 0.00 0.00 1.40
334 564 4.199310 TGTGTCTTTTAGCAGCTTCAAGT 58.801 39.130 0.00 0.00 0.00 3.16
393 623 1.506025 ACAATTTGGCCCAAACCAGT 58.494 45.000 11.91 7.58 41.82 4.00
409 639 0.794981 CAGTCGAGTCGAGAAAGGCG 60.795 60.000 17.12 0.00 36.23 5.52
432 662 0.036952 CCTGACCGATGAGTTGCACT 60.037 55.000 0.00 0.00 0.00 4.40
517 774 7.504403 TGAGAGAAATGGGAACTCTATGATTC 58.496 38.462 0.00 0.00 40.44 2.52
518 775 7.126268 TGAGAGAAATGGGAACTCTATGATTCA 59.874 37.037 0.00 0.00 40.44 2.57
596 900 9.495572 AAATTATCTCTAGCTAAATACTGCCAC 57.504 33.333 0.00 0.00 0.00 5.01
597 901 4.939052 TCTCTAGCTAAATACTGCCACC 57.061 45.455 0.00 0.00 0.00 4.61
598 902 3.641906 TCTCTAGCTAAATACTGCCACCC 59.358 47.826 0.00 0.00 0.00 4.61
600 904 3.778075 TCTAGCTAAATACTGCCACCCAA 59.222 43.478 0.00 0.00 0.00 4.12
602 906 2.576191 AGCTAAATACTGCCACCCAAGA 59.424 45.455 0.00 0.00 0.00 3.02
603 907 3.203040 AGCTAAATACTGCCACCCAAGAT 59.797 43.478 0.00 0.00 0.00 2.40
604 908 4.412199 AGCTAAATACTGCCACCCAAGATA 59.588 41.667 0.00 0.00 0.00 1.98
606 910 4.862641 AAATACTGCCACCCAAGATACT 57.137 40.909 0.00 0.00 0.00 2.12
607 911 4.862641 AATACTGCCACCCAAGATACTT 57.137 40.909 0.00 0.00 0.00 2.24
608 912 5.968676 AATACTGCCACCCAAGATACTTA 57.031 39.130 0.00 0.00 0.00 2.24
609 913 3.629142 ACTGCCACCCAAGATACTTAC 57.371 47.619 0.00 0.00 0.00 2.34
610 914 2.238898 ACTGCCACCCAAGATACTTACC 59.761 50.000 0.00 0.00 0.00 2.85
611 915 2.238646 CTGCCACCCAAGATACTTACCA 59.761 50.000 0.00 0.00 0.00 3.25
612 916 2.645297 TGCCACCCAAGATACTTACCAA 59.355 45.455 0.00 0.00 0.00 3.67
613 917 3.074687 TGCCACCCAAGATACTTACCAAA 59.925 43.478 0.00 0.00 0.00 3.28
614 918 4.083565 GCCACCCAAGATACTTACCAAAA 58.916 43.478 0.00 0.00 0.00 2.44
615 919 4.157840 GCCACCCAAGATACTTACCAAAAG 59.842 45.833 0.00 0.00 0.00 2.27
616 920 5.566469 CCACCCAAGATACTTACCAAAAGA 58.434 41.667 0.00 0.00 0.00 2.52
617 921 6.007703 CCACCCAAGATACTTACCAAAAGAA 58.992 40.000 0.00 0.00 0.00 2.52
618 922 6.492087 CCACCCAAGATACTTACCAAAAGAAA 59.508 38.462 0.00 0.00 0.00 2.52
657 981 8.689251 AAAGAGCAGTAAAGAACAAAGAAAAC 57.311 30.769 0.00 0.00 0.00 2.43
658 982 6.487103 AGAGCAGTAAAGAACAAAGAAAACG 58.513 36.000 0.00 0.00 0.00 3.60
660 984 6.027749 AGCAGTAAAGAACAAAGAAAACGTG 58.972 36.000 0.00 0.00 0.00 4.49
665 989 0.101579 AACAAAGAAAACGTGGCCCG 59.898 50.000 11.48 11.48 44.03 6.13
710 2103 1.047801 AAAAATGTGTGCCCCTCACC 58.952 50.000 0.00 0.00 45.03 4.02
733 2127 7.226325 CACCATGTTTCCAAATGCTTTTCTTTA 59.774 33.333 0.00 0.00 0.00 1.85
776 3357 2.930682 GTTTATGTGACCGGAGAAGAGC 59.069 50.000 9.46 0.00 0.00 4.09
895 3482 4.142687 CCAGGCAAGTCGTTTTATAACCAG 60.143 45.833 0.00 0.00 0.00 4.00
896 3483 3.439129 AGGCAAGTCGTTTTATAACCAGC 59.561 43.478 0.00 0.00 0.00 4.85
922 4769 7.831691 AGCTTATCTTGCTGACTCTTCTATA 57.168 36.000 0.00 0.00 39.56 1.31
931 4778 5.777223 TGCTGACTCTTCTATATATGGCTGT 59.223 40.000 0.00 0.00 0.00 4.40
1059 5068 0.396695 CCCTGCGGAAGTACCTCCTA 60.397 60.000 8.87 0.00 36.31 2.94
1227 5239 0.679505 TCTTCTACTGCAACGCCACT 59.320 50.000 0.00 0.00 0.00 4.00
1489 5675 3.023832 CCCAACTCTGAAACCAACAACT 58.976 45.455 0.00 0.00 0.00 3.16
1497 5683 2.606155 AAACCAACAACTGCGCCGTG 62.606 55.000 4.86 2.61 0.00 4.94
2247 6881 0.036010 GCCATCACCTACACAGCAGT 60.036 55.000 0.00 0.00 0.00 4.40
3071 7714 6.971527 TGAATAAAAATGGCAATTCAGCAG 57.028 33.333 7.31 0.00 34.34 4.24
3105 7748 1.229209 GACCCACTGGACAGGAGGA 60.229 63.158 14.45 0.00 34.81 3.71
3109 7752 1.606601 CACTGGACAGGAGGACGGA 60.607 63.158 4.14 0.00 0.00 4.69
3110 7753 1.304547 ACTGGACAGGAGGACGGAG 60.305 63.158 4.14 0.00 0.00 4.63
3117 7760 1.203075 ACAGGAGGACGGAGAAGAAGT 60.203 52.381 0.00 0.00 0.00 3.01
3129 7772 6.522054 ACGGAGAAGAAGTAAACAGAAATGA 58.478 36.000 0.00 0.00 0.00 2.57
3138 7781 8.153550 AGAAGTAAACAGAAATGACATCTCAGT 58.846 33.333 0.00 0.00 0.00 3.41
3144 7787 4.270566 CAGAAATGACATCTCAGTAGCTGC 59.729 45.833 0.00 0.00 0.00 5.25
3146 7789 3.731652 ATGACATCTCAGTAGCTGCTC 57.268 47.619 4.91 0.00 0.00 4.26
3147 7790 1.753649 TGACATCTCAGTAGCTGCTCC 59.246 52.381 4.91 0.00 0.00 4.70
3150 7793 2.069465 ATCTCAGTAGCTGCTCCGCG 62.069 60.000 4.91 0.00 34.40 6.46
3159 7802 2.755876 TGCTCCGCGATCCAGACT 60.756 61.111 8.23 0.00 0.00 3.24
3160 7803 2.279120 GCTCCGCGATCCAGACTG 60.279 66.667 8.23 0.00 0.00 3.51
3176 7819 0.188587 ACTGACTGGACAGGAGGACA 59.811 55.000 4.14 0.00 41.59 4.02
3177 7820 0.894141 CTGACTGGACAGGAGGACAG 59.106 60.000 4.14 0.00 37.01 3.51
3203 7846 5.397142 AGAAGAAAACAGAAATGGCATCC 57.603 39.130 0.00 0.00 0.00 3.51
3641 8380 1.004918 GGGTGGAAGACGTCTGTGG 60.005 63.158 20.85 0.00 0.00 4.17
3649 8388 0.458669 AGACGTCTGTGGTTGTCGTT 59.541 50.000 19.30 0.00 36.49 3.85
3713 8452 3.126001 AGCTTTCGACATGGTCTGAAA 57.874 42.857 0.00 12.30 35.57 2.69
3727 8466 1.005340 CTGAAAGTCGCCATGAGAGC 58.995 55.000 0.00 0.00 0.00 4.09
3730 8469 0.392193 AAAGTCGCCATGAGAGCCAG 60.392 55.000 0.00 0.00 0.00 4.85
3740 8511 3.312285 GAGAGCCAGCAGAGCAGCA 62.312 63.158 0.00 0.00 36.85 4.41
3742 8513 2.672307 AGCCAGCAGAGCAGCAAC 60.672 61.111 0.00 0.00 36.85 4.17
3749 8569 1.086696 GCAGAGCAGCAACGGAAATA 58.913 50.000 0.00 0.00 0.00 1.40
3752 8572 3.688272 CAGAGCAGCAACGGAAATAATG 58.312 45.455 0.00 0.00 0.00 1.90
3761 8581 4.158384 CAACGGAAATAATGCAGTGTGAC 58.842 43.478 0.00 0.00 0.00 3.67
3794 8614 0.108424 GCTCTGTGGTGTAGCTCCAG 60.108 60.000 0.00 0.00 35.49 3.86
3811 8631 0.317160 CAGTAACGTGAGGGCAGTCA 59.683 55.000 0.00 0.00 0.00 3.41
3812 8632 0.317479 AGTAACGTGAGGGCAGTCAC 59.683 55.000 8.73 8.73 43.01 3.67
3813 8633 0.032952 GTAACGTGAGGGCAGTCACA 59.967 55.000 16.62 0.00 46.19 3.58
3816 8636 0.532862 ACGTGAGGGCAGTCACAAAG 60.533 55.000 16.62 5.82 46.19 2.77
3825 9114 2.293399 GGCAGTCACAAAGTAACCCAAG 59.707 50.000 0.00 0.00 0.00 3.61
3879 10787 2.759535 CTCTGTCCAATCTCTCTGCTCA 59.240 50.000 0.00 0.00 0.00 4.26
3898 10848 0.902531 AAGCTAGCTCGCCCTGTTTA 59.097 50.000 19.65 0.00 0.00 2.01
3899 10849 0.175989 AGCTAGCTCGCCCTGTTTAC 59.824 55.000 12.68 0.00 0.00 2.01
3990 10957 2.032071 GGCTTACTGGGCGTGTGT 59.968 61.111 0.00 0.00 0.00 3.72
3991 10958 2.325082 GGCTTACTGGGCGTGTGTG 61.325 63.158 0.00 0.00 0.00 3.82
3992 10959 1.597027 GCTTACTGGGCGTGTGTGT 60.597 57.895 0.00 0.00 0.00 3.72
3993 10960 1.841663 GCTTACTGGGCGTGTGTGTG 61.842 60.000 0.00 0.00 0.00 3.82
3994 10961 0.531974 CTTACTGGGCGTGTGTGTGT 60.532 55.000 0.00 0.00 0.00 3.72
4010 10977 2.073056 TGTGTGTGTGTGTGTGTCTTC 58.927 47.619 0.00 0.00 0.00 2.87
4141 11290 1.311859 ACATGCTGTGTCACTTGGTG 58.688 50.000 4.27 1.58 35.77 4.17
4245 11479 4.521062 GCCAGCGGCGTGATCTCT 62.521 66.667 9.37 0.00 39.62 3.10
4308 11542 1.659622 CGCATGCAGATGGAGGCAAA 61.660 55.000 19.57 0.00 43.29 3.68
4310 11544 1.179152 CATGCAGATGGAGGCAAACA 58.821 50.000 0.00 0.00 44.20 2.83
4313 11547 0.529378 GCAGATGGAGGCAAACAAGG 59.471 55.000 0.00 0.00 0.00 3.61
4319 11553 2.203337 AGGCAAACAAGGCGAGCA 60.203 55.556 0.00 0.00 39.37 4.26
4323 11557 1.795170 GCAAACAAGGCGAGCAAGGA 61.795 55.000 0.00 0.00 0.00 3.36
4725 12023 4.305769 CTCCTGAGTTCTGACTTCACAAG 58.694 47.826 0.00 0.00 35.88 3.16
4727 12025 4.893524 TCCTGAGTTCTGACTTCACAAGTA 59.106 41.667 0.00 0.00 43.03 2.24
4730 12028 5.592054 TGAGTTCTGACTTCACAAGTACAG 58.408 41.667 0.00 0.00 43.03 2.74
4731 12029 5.127194 TGAGTTCTGACTTCACAAGTACAGT 59.873 40.000 0.00 0.00 43.03 3.55
4733 12031 7.108841 AGTTCTGACTTCACAAGTACAGTAA 57.891 36.000 0.00 6.38 43.03 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 1.815408 GCATCGGGACTGTTGCCATAT 60.815 52.381 3.38 0.00 30.80 1.78
124 125 3.417069 TGAATCAATCCGACCAACTGT 57.583 42.857 0.00 0.00 0.00 3.55
133 134 6.851609 TGTGGAAACTAAATGAATCAATCCG 58.148 36.000 0.00 0.00 0.00 4.18
290 520 5.193728 ACATGGATTAATTGTAGTGGGAGGT 59.806 40.000 0.00 0.00 0.00 3.85
306 536 4.338879 AGCTGCTAAAAGACACATGGATT 58.661 39.130 0.00 0.00 0.00 3.01
375 605 1.605202 CGACTGGTTTGGGCCAAATTG 60.605 52.381 32.51 25.06 38.18 2.32
393 623 2.178521 GCGCCTTTCTCGACTCGA 59.821 61.111 0.00 0.29 0.00 4.04
409 639 3.665675 AACTCATCGGTCAGGCGGC 62.666 63.158 0.00 0.00 0.00 6.53
425 655 5.233988 ACAGTCTCTTTCATCTAGTGCAAC 58.766 41.667 0.00 0.00 0.00 4.17
432 662 5.163468 GGATGCAGACAGTCTCTTTCATCTA 60.163 44.000 20.16 0.00 36.99 1.98
577 881 3.388024 TGGGTGGCAGTATTTAGCTAGAG 59.612 47.826 0.00 0.00 0.00 2.43
596 900 8.856103 TCTTTTTCTTTTGGTAAGTATCTTGGG 58.144 33.333 0.00 0.00 0.00 4.12
612 916 9.880064 GCTCTTTTCGTAAGTATCTTTTTCTTT 57.120 29.630 0.00 0.00 39.48 2.52
613 917 9.052759 TGCTCTTTTCGTAAGTATCTTTTTCTT 57.947 29.630 0.00 0.00 39.48 2.52
614 918 8.603242 TGCTCTTTTCGTAAGTATCTTTTTCT 57.397 30.769 0.00 0.00 39.48 2.52
615 919 8.496751 ACTGCTCTTTTCGTAAGTATCTTTTTC 58.503 33.333 0.00 0.00 39.48 2.29
616 920 8.379457 ACTGCTCTTTTCGTAAGTATCTTTTT 57.621 30.769 0.00 0.00 39.48 1.94
617 921 7.964604 ACTGCTCTTTTCGTAAGTATCTTTT 57.035 32.000 0.00 0.00 39.48 2.27
618 922 9.485206 TTTACTGCTCTTTTCGTAAGTATCTTT 57.515 29.630 0.00 0.00 39.48 2.52
665 989 2.477863 GCATATGTGTGTTTTCTCGGCC 60.478 50.000 4.29 0.00 0.00 6.13
776 3357 3.739519 CGGAGAAGGGAAGTAGCAATCAG 60.740 52.174 0.00 0.00 0.00 2.90
785 3366 0.251253 AGTCGTCGGAGAAGGGAAGT 60.251 55.000 0.00 0.00 39.69 3.01
914 4761 7.038799 TGCAGAATGACAGCCATATATAGAAGA 60.039 37.037 0.00 0.00 39.69 2.87
917 4764 6.610075 TGCAGAATGACAGCCATATATAGA 57.390 37.500 0.00 0.00 39.69 1.98
918 4765 7.769507 AGAATGCAGAATGACAGCCATATATAG 59.230 37.037 0.00 0.00 39.69 1.31
919 4766 7.627311 AGAATGCAGAATGACAGCCATATATA 58.373 34.615 0.00 0.00 39.69 0.86
920 4767 6.482524 AGAATGCAGAATGACAGCCATATAT 58.517 36.000 0.00 0.00 39.69 0.86
922 4769 4.726583 AGAATGCAGAATGACAGCCATAT 58.273 39.130 0.00 0.00 39.69 1.78
2122 6736 7.807977 TGCAGAGAAAGAAGAAACATAGTTT 57.192 32.000 0.00 0.00 0.00 2.66
3077 7720 2.607750 AGTGGGTCTGGATGGCGT 60.608 61.111 0.00 0.00 0.00 5.68
3105 7748 6.424207 GTCATTTCTGTTTACTTCTTCTCCGT 59.576 38.462 0.00 0.00 0.00 4.69
3109 7752 9.213799 GAGATGTCATTTCTGTTTACTTCTTCT 57.786 33.333 0.00 0.00 0.00 2.85
3110 7753 8.993121 TGAGATGTCATTTCTGTTTACTTCTTC 58.007 33.333 5.08 0.00 0.00 2.87
3117 7760 7.547019 CAGCTACTGAGATGTCATTTCTGTTTA 59.453 37.037 17.37 4.27 34.24 2.01
3129 7772 0.743688 CGGAGCAGCTACTGAGATGT 59.256 55.000 2.25 0.00 41.37 3.06
3144 7787 1.064946 GTCAGTCTGGATCGCGGAG 59.935 63.158 6.13 0.00 0.00 4.63
3146 7789 1.226802 CAGTCAGTCTGGATCGCGG 60.227 63.158 6.13 0.00 40.23 6.46
3147 7790 4.391539 CAGTCAGTCTGGATCGCG 57.608 61.111 0.00 0.00 40.23 5.87
3159 7802 0.482887 TCTGTCCTCCTGTCCAGTCA 59.517 55.000 0.00 0.00 0.00 3.41
3160 7803 1.181786 CTCTGTCCTCCTGTCCAGTC 58.818 60.000 0.00 0.00 0.00 3.51
3171 7814 5.878406 TCTGTTTTCTTCTTCTCTGTCCT 57.122 39.130 0.00 0.00 0.00 3.85
3176 7819 5.829924 TGCCATTTCTGTTTTCTTCTTCTCT 59.170 36.000 0.00 0.00 0.00 3.10
3177 7820 6.076981 TGCCATTTCTGTTTTCTTCTTCTC 57.923 37.500 0.00 0.00 0.00 2.87
3641 8380 0.443869 ATGATGAGCGCAACGACAAC 59.556 50.000 11.47 1.21 0.00 3.32
3649 8388 2.436469 ACGGCAATGATGAGCGCA 60.436 55.556 11.47 0.00 0.00 6.09
3713 8452 2.898738 CTGGCTCTCATGGCGACT 59.101 61.111 0.00 0.00 35.06 4.18
3727 8466 3.429141 CCGTTGCTGCTCTGCTGG 61.429 66.667 0.00 0.00 0.00 4.85
3730 8469 1.086696 TATTTCCGTTGCTGCTCTGC 58.913 50.000 0.00 0.00 0.00 4.26
3740 8511 4.072131 AGTCACACTGCATTATTTCCGTT 58.928 39.130 0.00 0.00 0.00 4.44
3742 8513 3.684305 TGAGTCACACTGCATTATTTCCG 59.316 43.478 0.00 0.00 0.00 4.30
3749 8569 5.353400 CACTGATAATGAGTCACACTGCATT 59.647 40.000 0.00 0.00 33.66 3.56
3752 8572 3.063180 GCACTGATAATGAGTCACACTGC 59.937 47.826 0.00 0.00 0.00 4.40
3761 8581 2.538861 CACAGAGCGCACTGATAATGAG 59.461 50.000 36.18 11.88 40.63 2.90
3794 8614 0.032952 TGTGACTGCCCTCACGTTAC 59.967 55.000 6.42 0.00 43.14 2.50
3811 8631 3.562182 CCCTGAACTTGGGTTACTTTGT 58.438 45.455 0.00 0.00 39.82 2.83
3812 8632 2.296190 GCCCTGAACTTGGGTTACTTTG 59.704 50.000 0.00 0.00 46.22 2.77
3813 8633 2.594131 GCCCTGAACTTGGGTTACTTT 58.406 47.619 0.00 0.00 46.22 2.66
3816 8636 0.035739 TCGCCCTGAACTTGGGTTAC 59.964 55.000 0.00 0.00 46.22 2.50
3825 9114 3.733337 ACAGATATCAATCGCCCTGAAC 58.267 45.455 5.32 0.00 37.19 3.18
3879 10787 0.902531 TAAACAGGGCGAGCTAGCTT 59.097 50.000 20.42 7.09 37.29 3.74
3898 10848 8.824756 TTACATCAACTAGACTAGGAATCTGT 57.175 34.615 14.03 11.64 0.00 3.41
3899 10849 9.906660 GATTACATCAACTAGACTAGGAATCTG 57.093 37.037 14.03 7.02 29.88 2.90
3977 10940 1.227409 CACACACACACGCCCAGTA 60.227 57.895 0.00 0.00 0.00 2.74
3989 10956 1.438651 AGACACACACACACACACAC 58.561 50.000 0.00 0.00 0.00 3.82
3990 10957 2.073056 GAAGACACACACACACACACA 58.927 47.619 0.00 0.00 0.00 3.72
3991 10958 2.073056 TGAAGACACACACACACACAC 58.927 47.619 0.00 0.00 0.00 3.82
3992 10959 2.464157 TGAAGACACACACACACACA 57.536 45.000 0.00 0.00 0.00 3.72
3993 10960 2.287915 GGATGAAGACACACACACACAC 59.712 50.000 0.00 0.00 0.00 3.82
3994 10961 2.093235 TGGATGAAGACACACACACACA 60.093 45.455 0.00 0.00 0.00 3.72
4010 10977 4.154737 CCTACCACGCATATTCATTGGATG 59.845 45.833 0.00 0.00 0.00 3.51
4141 11290 4.437930 GGATTGCACAATACTTGAGACTGC 60.438 45.833 0.00 0.00 31.76 4.40
4192 11425 2.348660 CCCGCGTTCAAGGTATGTTTA 58.651 47.619 4.92 0.00 0.00 2.01
4245 11479 3.372730 GTGAATTGCCCCGCTGCA 61.373 61.111 0.00 0.00 40.07 4.41
4308 11542 2.357517 CGTCCTTGCTCGCCTTGT 60.358 61.111 0.00 0.00 0.00 3.16
4597 11877 2.802106 CTCCTTCTCTCCGGCGAC 59.198 66.667 9.30 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.