Multiple sequence alignment - TraesCS4B01G109200

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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 TraesCS4B01G109200 chr4B 100.000 5175 0 0 1 5175 121589343 121594517 0.000000e+00 9557.0
1 TraesCS4B01G109200 chr4B 90.000 60 2 4 1806 1863 121591068 121591125 2.000000e-09 75.0
2 TraesCS4B01G109200 chr4B 90.000 60 2 4 1726 1783 121591148 121591205 2.000000e-09 75.0
3 TraesCS4B01G109200 chr4D 95.805 3480 82 24 927 4371 84779460 84776010 0.000000e+00 5559.0
4 TraesCS4B01G109200 chr4D 86.667 225 11 8 4388 4607 84776023 84775813 1.120000e-56 231.0
5 TraesCS4B01G109200 chr4D 88.889 63 5 2 1726 1786 84778577 84778515 5.560000e-10 76.8
6 TraesCS4B01G109200 chr4A 93.137 1530 62 16 2027 3526 497908107 497906591 0.000000e+00 2204.0
7 TraesCS4B01G109200 chr4A 91.770 887 50 14 920 1794 497909484 497908609 0.000000e+00 1212.0
8 TraesCS4B01G109200 chr4A 93.233 798 38 4 3589 4371 497906590 497905794 0.000000e+00 1160.0
9 TraesCS4B01G109200 chr4A 88.492 504 39 14 1460 1954 497908595 497908102 4.460000e-165 592.0
10 TraesCS4B01G109200 chr4A 83.088 544 36 25 4663 5175 319916284 319916802 1.320000e-120 444.0
11 TraesCS4B01G109200 chr4A 88.031 259 10 11 4388 4632 497905807 497905556 2.360000e-73 287.0
12 TraesCS4B01G109200 chr4A 84.768 151 10 7 4663 4807 319916088 319916231 6.990000e-29 139.0
13 TraesCS4B01G109200 chr4A 94.231 52 2 1 4566 4616 552085806 552085755 1.540000e-10 78.7
14 TraesCS4B01G109200 chr4A 85.484 62 8 1 1806 1866 497908678 497908617 4.330000e-06 63.9
15 TraesCS4B01G109200 chr3A 98.920 926 10 0 1 926 513454365 513455290 0.000000e+00 1655.0
16 TraesCS4B01G109200 chr3A 98.188 938 15 2 1 938 674528183 674529118 0.000000e+00 1637.0
17 TraesCS4B01G109200 chr5B 98.811 925 11 0 1 925 348155329 348156253 0.000000e+00 1648.0
18 TraesCS4B01G109200 chr5B 98.291 936 16 0 1 936 618685072 618684137 0.000000e+00 1640.0
19 TraesCS4B01G109200 chr5A 98.707 928 12 0 1 928 70638773 70637846 0.000000e+00 1648.0
20 TraesCS4B01G109200 chr5A 98.707 928 12 0 1 928 188747595 188746668 0.000000e+00 1648.0
21 TraesCS4B01G109200 chr5A 84.436 514 47 21 4682 5175 654105647 654106147 4.690000e-130 475.0
22 TraesCS4B01G109200 chr2B 98.811 925 11 0 1 925 536053439 536054363 0.000000e+00 1648.0
23 TraesCS4B01G109200 chr2A 98.811 925 11 0 1 925 379266811 379267735 0.000000e+00 1648.0
24 TraesCS4B01G109200 chr2A 98.706 927 12 0 1 927 736971079 736970153 0.000000e+00 1646.0
25 TraesCS4B01G109200 chr7B 83.775 641 82 14 3190 3829 403563933 403563314 5.770000e-164 588.0
26 TraesCS4B01G109200 chr7B 83.775 641 82 14 3190 3829 403729784 403729165 5.770000e-164 588.0
27 TraesCS4B01G109200 chr7B 83.775 641 83 14 3190 3829 407940587 407939967 5.770000e-164 588.0
28 TraesCS4B01G109200 chr7B 83.568 639 80 18 3190 3826 408111523 408110908 4.490000e-160 575.0
29 TraesCS4B01G109200 chr7B 76.017 467 88 13 1020 1479 403732347 403731898 2.430000e-53 220.0
30 TraesCS4B01G109200 chr7B 75.100 498 87 22 997 1479 403566526 403566051 1.140000e-46 198.0
31 TraesCS4B01G109200 chr7B 88.889 108 12 0 1372 1479 408113785 408113678 3.250000e-27 134.0
32 TraesCS4B01G109200 chr7B 93.671 79 5 0 1372 1450 383502749 383502827 9.100000e-23 119.0
33 TraesCS4B01G109200 chr3D 84.000 525 44 22 4675 5175 527891262 527890754 7.850000e-128 468.0
34 TraesCS4B01G109200 chr3D 84.848 297 10 15 4670 4938 513629247 513628958 3.070000e-67 267.0
35 TraesCS4B01G109200 chr3D 83.209 268 31 9 4117 4372 96589091 96589356 3.120000e-57 233.0
36 TraesCS4B01G109200 chr7D 93.671 79 5 0 1372 1450 388022243 388022321 9.100000e-23 119.0
37 TraesCS4B01G109200 chr7A 93.590 78 5 0 1373 1450 438168963 438169040 3.270000e-22 117.0
38 TraesCS4B01G109200 chr3B 94.231 52 2 1 4566 4616 92275483 92275432 1.540000e-10 78.7
39 TraesCS4B01G109200 chrUn 92.308 52 3 1 4566 4616 182457866 182457917 7.190000e-09 73.1
40 TraesCS4B01G109200 chrUn 92.308 52 3 1 4566 4616 231548632 231548581 7.190000e-09 73.1
41 TraesCS4B01G109200 chrUn 92.308 52 3 1 4566 4616 323806455 323806404 7.190000e-09 73.1
42 TraesCS4B01G109200 chrUn 92.308 52 3 1 4566 4616 350576998 350576947 7.190000e-09 73.1
43 TraesCS4B01G109200 chrUn 92.308 52 3 1 4566 4616 358548839 358548890 7.190000e-09 73.1


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 TraesCS4B01G109200 chr4B 121589343 121594517 5174 False 3235.666667 9557 93.333333 1 5175 3 chr4B.!!$F1 5174
1 TraesCS4B01G109200 chr4D 84775813 84779460 3647 True 1955.600000 5559 90.453667 927 4607 3 chr4D.!!$R1 3680
2 TraesCS4B01G109200 chr4A 497905556 497909484 3928 True 919.816667 2204 90.024500 920 4632 6 chr4A.!!$R2 3712
3 TraesCS4B01G109200 chr4A 319916088 319916802 714 False 291.500000 444 83.928000 4663 5175 2 chr4A.!!$F1 512
4 TraesCS4B01G109200 chr3A 513454365 513455290 925 False 1655.000000 1655 98.920000 1 926 1 chr3A.!!$F1 925
5 TraesCS4B01G109200 chr3A 674528183 674529118 935 False 1637.000000 1637 98.188000 1 938 1 chr3A.!!$F2 937
6 TraesCS4B01G109200 chr5B 348155329 348156253 924 False 1648.000000 1648 98.811000 1 925 1 chr5B.!!$F1 924
7 TraesCS4B01G109200 chr5B 618684137 618685072 935 True 1640.000000 1640 98.291000 1 936 1 chr5B.!!$R1 935
8 TraesCS4B01G109200 chr5A 70637846 70638773 927 True 1648.000000 1648 98.707000 1 928 1 chr5A.!!$R1 927
9 TraesCS4B01G109200 chr5A 188746668 188747595 927 True 1648.000000 1648 98.707000 1 928 1 chr5A.!!$R2 927
10 TraesCS4B01G109200 chr5A 654105647 654106147 500 False 475.000000 475 84.436000 4682 5175 1 chr5A.!!$F1 493
11 TraesCS4B01G109200 chr2B 536053439 536054363 924 False 1648.000000 1648 98.811000 1 925 1 chr2B.!!$F1 924
12 TraesCS4B01G109200 chr2A 379266811 379267735 924 False 1648.000000 1648 98.811000 1 925 1 chr2A.!!$F1 924
13 TraesCS4B01G109200 chr2A 736970153 736971079 926 True 1646.000000 1646 98.706000 1 927 1 chr2A.!!$R1 926
14 TraesCS4B01G109200 chr7B 407939967 407940587 620 True 588.000000 588 83.775000 3190 3829 1 chr7B.!!$R1 639
15 TraesCS4B01G109200 chr7B 403729165 403732347 3182 True 404.000000 588 79.896000 1020 3829 2 chr7B.!!$R3 2809
16 TraesCS4B01G109200 chr7B 403563314 403566526 3212 True 393.000000 588 79.437500 997 3829 2 chr7B.!!$R2 2832
17 TraesCS4B01G109200 chr7B 408110908 408113785 2877 True 354.500000 575 86.228500 1372 3826 2 chr7B.!!$R4 2454
18 TraesCS4B01G109200 chr3D 527890754 527891262 508 True 468.000000 468 84.000000 4675 5175 1 chr3D.!!$R2 500

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
982 983 0.178947 CTAGGGCTAGGGCTAGTGCT 60.179 60.000 0.0 0.0 39.59 4.40 F
983 984 0.178958 TAGGGCTAGGGCTAGTGCTC 60.179 60.000 0.0 0.0 40.76 4.26 F
1581 1604 0.326595 TGGGTTGCATGGATGTACGT 59.673 50.000 0.0 0.0 0.00 3.57 F
1582 1605 1.555533 TGGGTTGCATGGATGTACGTA 59.444 47.619 0.0 0.0 0.00 3.57 F
3400 4757 2.945668 CCCCGATCTGATGTCCTTTTTC 59.054 50.000 0.0 0.0 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2662 3683 3.385755 GGCACTCCCATAATTGAAGCAAT 59.614 43.478 0.0 0.0 35.39 3.56 R
2879 3919 6.899089 TGAAAGGATAAATCTATGCTCCACA 58.101 36.000 0.0 0.0 35.31 4.17 R
3438 4795 1.078143 GATCTCCACGCTGCCCTTT 60.078 57.895 0.0 0.0 0.00 3.11 R
3450 4807 1.592669 CACATGGGCGACGATCTCC 60.593 63.158 0.0 0.0 0.00 3.71 R
4403 5777 1.071385 CTGGAGGTGAGTTGCTGTTCT 59.929 52.381 0.0 0.0 0.00 3.01 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
144 145 1.826921 GGAGGAGCCGACCGATACA 60.827 63.158 0.00 0.00 34.73 2.29
976 977 1.151908 CGAGTCTAGGGCTAGGGCT 59.848 63.158 0.00 0.00 38.73 5.19
977 978 0.400975 CGAGTCTAGGGCTAGGGCTA 59.599 60.000 0.00 0.00 38.73 3.93
978 979 1.612199 CGAGTCTAGGGCTAGGGCTAG 60.612 61.905 0.00 0.00 38.73 3.42
979 980 1.426215 GAGTCTAGGGCTAGGGCTAGT 59.574 57.143 0.00 0.00 38.73 2.57
980 981 1.146152 AGTCTAGGGCTAGGGCTAGTG 59.854 57.143 0.00 0.00 38.73 2.74
981 982 0.178958 TCTAGGGCTAGGGCTAGTGC 60.179 60.000 0.00 0.00 38.73 4.40
982 983 0.178947 CTAGGGCTAGGGCTAGTGCT 60.179 60.000 0.00 0.00 39.59 4.40
983 984 0.178958 TAGGGCTAGGGCTAGTGCTC 60.179 60.000 0.00 0.00 40.76 4.26
984 985 2.512355 GGGCTAGGGCTAGTGCTCC 61.512 68.421 0.00 0.00 41.57 4.70
985 986 1.458588 GGCTAGGGCTAGTGCTCCT 60.459 63.158 0.00 0.00 41.57 3.69
986 987 1.051556 GGCTAGGGCTAGTGCTCCTT 61.052 60.000 0.00 0.00 41.57 3.36
1054 1058 1.081641 CACGCGTACGACCAGAAGT 60.082 57.895 21.65 3.54 43.93 3.01
1120 1124 3.575351 GACAACGTCGGCTCCAGCT 62.575 63.158 0.00 0.00 41.70 4.24
1135 1139 2.127042 GCTAGCTCGCGGAGATCG 60.127 66.667 7.70 0.00 42.76 3.69
1189 1193 1.290134 GGGGAAGAACACCCTCATCT 58.710 55.000 0.00 0.00 46.03 2.90
1270 1274 1.636769 CCTCCTCCAAGTAAGCCCCC 61.637 65.000 0.00 0.00 0.00 5.40
1304 1313 0.747255 GCCGGATCTTCTACTCTGCA 59.253 55.000 5.05 0.00 0.00 4.41
1344 1353 1.295792 TTCGTTTTCTCAAGCGTGCT 58.704 45.000 0.00 0.00 37.81 4.40
1450 1461 2.570302 AGGTCGCCAAGTACAAGGTAAT 59.430 45.455 0.00 0.00 0.00 1.89
1514 1532 1.317613 TGATTGCTGCCGACTTTGTT 58.682 45.000 0.00 0.00 0.00 2.83
1531 1550 5.861787 ACTTTGTTTGTTGAAGTGTGCTAAC 59.138 36.000 0.00 0.00 32.73 2.34
1580 1603 1.458398 TTGGGTTGCATGGATGTACG 58.542 50.000 0.00 0.00 0.00 3.67
1581 1604 0.326595 TGGGTTGCATGGATGTACGT 59.673 50.000 0.00 0.00 0.00 3.57
1582 1605 1.555533 TGGGTTGCATGGATGTACGTA 59.444 47.619 0.00 0.00 0.00 3.57
1637 1668 4.748892 TGCTACTACTTCATCTTGCTGTC 58.251 43.478 0.00 0.00 0.00 3.51
1744 1788 6.044871 CCTTATTATGGAAGGGGTCTGAGATT 59.955 42.308 0.00 0.00 39.96 2.40
2191 3197 6.090628 GTGTGAGTGTTTGAAGCAATTTTTGA 59.909 34.615 0.00 0.00 0.00 2.69
2226 3233 8.514594 TCACACATAGATTGTCCTTTGAATTTC 58.485 33.333 0.00 0.00 36.00 2.17
2227 3234 7.482743 CACACATAGATTGTCCTTTGAATTTCG 59.517 37.037 0.00 0.00 36.00 3.46
2228 3235 7.174946 ACACATAGATTGTCCTTTGAATTTCGT 59.825 33.333 0.00 0.00 36.00 3.85
2229 3236 7.482743 CACATAGATTGTCCTTTGAATTTCGTG 59.517 37.037 0.00 0.00 36.00 4.35
2231 3238 6.391227 AGATTGTCCTTTGAATTTCGTGTT 57.609 33.333 0.00 0.00 0.00 3.32
2232 3239 6.208644 AGATTGTCCTTTGAATTTCGTGTTG 58.791 36.000 0.00 0.00 0.00 3.33
2233 3240 3.701241 TGTCCTTTGAATTTCGTGTTGC 58.299 40.909 0.00 0.00 0.00 4.17
2662 3683 7.089770 TGTGCGAATTAACTAATTTGGCATA 57.910 32.000 17.44 14.31 42.12 3.14
2709 3730 5.657745 ACTTGGGTGCATGAATTTGATGATA 59.342 36.000 0.00 0.00 0.00 2.15
2837 3861 3.254903 GGGTAGTTGGTGTTCATTTGTCC 59.745 47.826 0.00 0.00 0.00 4.02
2879 3919 4.365723 AGTTTCTCGTGTTACATGTCGTT 58.634 39.130 0.00 0.00 0.00 3.85
2947 4269 9.830975 TGTGCAGTAGATATAAATACATTGTGT 57.169 29.630 0.00 0.00 0.00 3.72
3310 4666 3.722101 TCCCTCCCAAACTTCTTTCTTCT 59.278 43.478 0.00 0.00 0.00 2.85
3400 4757 2.945668 CCCCGATCTGATGTCCTTTTTC 59.054 50.000 0.00 0.00 0.00 2.29
3438 4795 5.420739 GCTTAACATCCCCACCAAGATTAAA 59.579 40.000 0.00 0.00 0.00 1.52
3450 4807 3.244976 CAAGATTAAAAAGGGCAGCGTG 58.755 45.455 0.00 0.00 0.00 5.34
3923 5297 6.869315 TTGTTGTTATTTGTTCCGATCTCA 57.131 33.333 0.00 0.00 0.00 3.27
3937 5311 5.487433 TCCGATCTCAATGTTACATGTGTT 58.513 37.500 9.11 0.00 0.00 3.32
3973 5347 7.823799 TGTGAACATCTTGCTCTATTTCATACA 59.176 33.333 0.00 0.00 0.00 2.29
4286 5660 3.649073 CTCGGACTGTTGTGTGTATTCA 58.351 45.455 0.00 0.00 0.00 2.57
4331 5705 4.469657 TGGTTGGTAATATTGCCCTGATC 58.530 43.478 18.66 6.98 31.21 2.92
4371 5745 5.278957 GCTCATGACCTGCTTTCCTTTTAAA 60.279 40.000 0.00 0.00 0.00 1.52
4373 5747 7.301868 TCATGACCTGCTTTCCTTTTAAATT 57.698 32.000 0.00 0.00 0.00 1.82
4374 5748 7.734942 TCATGACCTGCTTTCCTTTTAAATTT 58.265 30.769 0.00 0.00 0.00 1.82
4375 5749 8.210265 TCATGACCTGCTTTCCTTTTAAATTTT 58.790 29.630 0.00 0.00 0.00 1.82
4376 5750 8.839343 CATGACCTGCTTTCCTTTTAAATTTTT 58.161 29.630 0.00 0.00 0.00 1.94
4397 5771 5.514274 TTTTTGAGACGATGCTTTCCTTT 57.486 34.783 0.00 0.00 0.00 3.11
4398 5772 5.514274 TTTTGAGACGATGCTTTCCTTTT 57.486 34.783 0.00 0.00 0.00 2.27
4399 5773 6.627395 TTTTGAGACGATGCTTTCCTTTTA 57.373 33.333 0.00 0.00 0.00 1.52
4400 5774 6.627395 TTTGAGACGATGCTTTCCTTTTAA 57.373 33.333 0.00 0.00 0.00 1.52
4401 5775 5.607119 TGAGACGATGCTTTCCTTTTAAC 57.393 39.130 0.00 0.00 0.00 2.01
4402 5776 5.305585 TGAGACGATGCTTTCCTTTTAACT 58.694 37.500 0.00 0.00 0.00 2.24
4403 5777 6.460781 TGAGACGATGCTTTCCTTTTAACTA 58.539 36.000 0.00 0.00 0.00 2.24
4404 5778 6.590292 TGAGACGATGCTTTCCTTTTAACTAG 59.410 38.462 0.00 0.00 0.00 2.57
4500 5874 8.548880 AAGAAGTAAGAAGGTAGCCATATGTA 57.451 34.615 1.24 0.00 0.00 2.29
4501 5875 8.728596 AGAAGTAAGAAGGTAGCCATATGTAT 57.271 34.615 1.24 0.00 0.00 2.29
4503 5877 8.492415 AAGTAAGAAGGTAGCCATATGTATGA 57.508 34.615 1.24 0.00 35.75 2.15
4504 5878 7.897864 AGTAAGAAGGTAGCCATATGTATGAC 58.102 38.462 1.24 0.00 35.75 3.06
4508 5882 5.887214 AGGTAGCCATATGTATGACACAA 57.113 39.130 1.24 0.00 41.55 3.33
4574 5961 9.159254 TCAACTAGATGTATGAATATGAACCCT 57.841 33.333 0.00 0.00 0.00 4.34
4584 5971 1.140312 TATGAACCCTGGATCTGGGC 58.860 55.000 19.60 8.79 45.01 5.36
4622 6009 5.049886 GGAACTCCAACAAGTTTTACTACCG 60.050 44.000 0.00 0.00 39.55 4.02
4625 6012 5.069516 ACTCCAACAAGTTTTACTACCGAGA 59.930 40.000 0.00 0.00 0.00 4.04
4630 6017 6.165700 ACAAGTTTTACTACCGAGAAGGAA 57.834 37.500 0.00 0.00 45.00 3.36
4631 6018 6.766429 ACAAGTTTTACTACCGAGAAGGAAT 58.234 36.000 0.00 0.00 45.00 3.01
4632 6019 7.899973 ACAAGTTTTACTACCGAGAAGGAATA 58.100 34.615 0.00 0.00 45.00 1.75
4633 6020 8.033626 ACAAGTTTTACTACCGAGAAGGAATAG 58.966 37.037 0.00 0.00 45.00 1.73
4634 6021 7.715266 AGTTTTACTACCGAGAAGGAATAGT 57.285 36.000 0.00 0.00 45.00 2.12
4635 6022 7.545489 AGTTTTACTACCGAGAAGGAATAGTG 58.455 38.462 0.00 0.00 45.00 2.74
4636 6023 5.511234 TTACTACCGAGAAGGAATAGTGC 57.489 43.478 0.00 0.00 45.00 4.40
4637 6024 3.362706 ACTACCGAGAAGGAATAGTGCA 58.637 45.455 0.00 0.00 45.00 4.57
4638 6025 2.674796 ACCGAGAAGGAATAGTGCAC 57.325 50.000 9.40 9.40 45.00 4.57
4639 6026 1.135083 ACCGAGAAGGAATAGTGCACG 60.135 52.381 12.01 0.00 45.00 5.34
4640 6027 1.135083 CCGAGAAGGAATAGTGCACGT 60.135 52.381 12.01 0.96 45.00 4.49
4641 6028 1.920574 CGAGAAGGAATAGTGCACGTG 59.079 52.381 12.28 12.28 0.00 4.49
4642 6029 2.271800 GAGAAGGAATAGTGCACGTGG 58.728 52.381 18.88 0.00 0.00 4.94
4643 6030 1.623811 AGAAGGAATAGTGCACGTGGT 59.376 47.619 18.88 0.00 0.00 4.16
4644 6031 2.038557 AGAAGGAATAGTGCACGTGGTT 59.961 45.455 18.88 5.00 0.00 3.67
4645 6032 3.259876 AGAAGGAATAGTGCACGTGGTTA 59.740 43.478 18.88 0.00 0.00 2.85
4646 6033 3.247006 AGGAATAGTGCACGTGGTTAG 57.753 47.619 18.88 0.00 0.00 2.34
4647 6034 2.829720 AGGAATAGTGCACGTGGTTAGA 59.170 45.455 18.88 0.00 0.00 2.10
4648 6035 3.259876 AGGAATAGTGCACGTGGTTAGAA 59.740 43.478 18.88 0.00 0.00 2.10
4649 6036 3.998341 GGAATAGTGCACGTGGTTAGAAA 59.002 43.478 18.88 0.00 0.00 2.52
4650 6037 4.453136 GGAATAGTGCACGTGGTTAGAAAA 59.547 41.667 18.88 0.00 0.00 2.29
4651 6038 5.049267 GGAATAGTGCACGTGGTTAGAAAAA 60.049 40.000 18.88 0.00 0.00 1.94
4652 6039 6.349033 GGAATAGTGCACGTGGTTAGAAAAAT 60.349 38.462 18.88 0.00 0.00 1.82
4653 6040 7.148373 GGAATAGTGCACGTGGTTAGAAAAATA 60.148 37.037 18.88 0.00 0.00 1.40
4654 6041 7.859325 ATAGTGCACGTGGTTAGAAAAATAT 57.141 32.000 18.88 0.00 0.00 1.28
4655 6042 6.178239 AGTGCACGTGGTTAGAAAAATATC 57.822 37.500 18.88 0.00 0.00 1.63
4656 6043 5.703592 AGTGCACGTGGTTAGAAAAATATCA 59.296 36.000 18.88 0.00 0.00 2.15
4657 6044 6.205853 AGTGCACGTGGTTAGAAAAATATCAA 59.794 34.615 18.88 0.00 0.00 2.57
4658 6045 7.027161 GTGCACGTGGTTAGAAAAATATCAAT 58.973 34.615 18.88 0.00 0.00 2.57
4659 6046 7.008266 GTGCACGTGGTTAGAAAAATATCAATG 59.992 37.037 18.88 0.00 0.00 2.82
4660 6047 7.094592 TGCACGTGGTTAGAAAAATATCAATGA 60.095 33.333 18.88 0.00 0.00 2.57
4661 6048 7.429340 GCACGTGGTTAGAAAAATATCAATGAG 59.571 37.037 18.88 0.00 0.00 2.90
4662 6049 8.664798 CACGTGGTTAGAAAAATATCAATGAGA 58.335 33.333 7.95 0.00 0.00 3.27
4663 6050 9.226606 ACGTGGTTAGAAAAATATCAATGAGAA 57.773 29.630 0.00 0.00 0.00 2.87
4727 6114 7.622502 ACCGTATAAAAGGGTAATATGGACT 57.377 36.000 6.78 0.00 44.60 3.85
4731 6118 9.550406 CGTATAAAAGGGTAATATGGACTTTCA 57.450 33.333 0.00 0.00 31.56 2.69
4887 6494 3.196207 AACGTGACCAGCAGGCCAT 62.196 57.895 5.01 0.00 39.06 4.40
4893 6500 0.749454 GACCAGCAGGCCATGTTAGG 60.749 60.000 5.01 0.89 39.06 2.69
4935 6542 9.872721 AGGTACAAAAGCTCTCTTAGTTATAAC 57.127 33.333 7.57 7.57 31.02 1.89
4943 6550 9.593134 AAGCTCTCTTAGTTATAACAATCAGTG 57.407 33.333 17.65 9.43 0.00 3.66
4946 6553 9.877178 CTCTCTTAGTTATAACAATCAGTGGTT 57.123 33.333 17.65 0.00 0.00 3.67
4962 6569 7.883229 TCAGTGGTTTTCTTTCTTTTGTTTC 57.117 32.000 0.00 0.00 0.00 2.78
4966 6573 4.868171 GGTTTTCTTTCTTTTGTTTCGGCT 59.132 37.500 0.00 0.00 0.00 5.52
4977 6584 5.759506 TTTGTTTCGGCTGAGTTTTCATA 57.240 34.783 0.00 0.00 31.68 2.15
4982 6589 4.944962 TCGGCTGAGTTTTCATATGTTG 57.055 40.909 1.90 0.00 31.68 3.33
5119 6728 3.367607 TCGTGAACTTTTTCCAAATGCG 58.632 40.909 0.00 0.00 0.00 4.73
5124 6733 2.393764 ACTTTTTCCAAATGCGCGAAG 58.606 42.857 12.10 2.33 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 2.825836 GGCTTCAGCGATGGGTGG 60.826 66.667 7.08 0.00 41.92 4.61
407 408 3.129638 CCACTCTACTGTCAGGCTTAGAC 59.870 52.174 4.53 0.00 36.55 2.59
945 946 2.680352 ACTCGGTGGATCTGCGGT 60.680 61.111 0.00 0.00 0.00 5.68
976 977 4.492160 CCGCGCGAAGGAGCACTA 62.492 66.667 34.63 0.00 39.11 2.74
1054 1058 2.343758 GTCGAGGAGCTGGCACAA 59.656 61.111 0.00 0.00 38.70 3.33
1120 1124 3.661131 GCCGATCTCCGCGAGCTA 61.661 66.667 8.23 0.00 36.84 3.32
1276 1285 4.888325 AGATCCGGCAGGGGGAGG 62.888 72.222 2.05 0.00 36.91 4.30
1278 1287 1.956639 TAGAAGATCCGGCAGGGGGA 61.957 60.000 2.05 0.00 38.33 4.81
1304 1313 1.616865 TCCTCGACGACAAAACCAGAT 59.383 47.619 0.00 0.00 0.00 2.90
1344 1353 2.668212 CCAAAAGGACAGGCGCGA 60.668 61.111 12.10 0.00 0.00 5.87
1450 1461 3.094572 GGGCAGTGGTACAGTAGTTAGA 58.905 50.000 0.00 0.00 41.96 2.10
1514 1532 3.691049 GCAGTTAGCACACTTCAACAA 57.309 42.857 0.00 0.00 44.79 2.83
1535 1554 5.450818 TCCTTTCCATAACTAGCAACCAT 57.549 39.130 0.00 0.00 0.00 3.55
1580 1603 9.169468 CAATTTCGGCAGACACATAATTATTAC 57.831 33.333 0.00 0.00 0.00 1.89
1581 1604 7.860373 GCAATTTCGGCAGACACATAATTATTA 59.140 33.333 0.00 0.00 0.00 0.98
1582 1605 6.697019 GCAATTTCGGCAGACACATAATTATT 59.303 34.615 0.00 0.00 0.00 1.40
1668 1710 7.728847 AGAAACAAATTTTCCTGCCATAAAC 57.271 32.000 0.00 0.00 0.00 2.01
2662 3683 3.385755 GGCACTCCCATAATTGAAGCAAT 59.614 43.478 0.00 0.00 35.39 3.56
2709 3730 9.131791 ACAAACAATCCATTTTACTACTGAAGT 57.868 29.630 0.00 0.00 42.62 3.01
2837 3861 8.656849 AGAAACTACTGCATACAAATACTTTCG 58.343 33.333 0.00 0.00 0.00 3.46
2879 3919 6.899089 TGAAAGGATAAATCTATGCTCCACA 58.101 36.000 0.00 0.00 35.31 4.17
2947 4269 9.803507 TCAAATTATTATCTCCCGACTCTACTA 57.196 33.333 0.00 0.00 0.00 1.82
3310 4666 9.485206 GTGTTATCAGACAAGAGTTTTTACCTA 57.515 33.333 0.00 0.00 0.00 3.08
3400 4757 5.450965 GGATGTTAAGCACCTGAATGAATGG 60.451 44.000 0.00 0.00 0.00 3.16
3438 4795 1.078143 GATCTCCACGCTGCCCTTT 60.078 57.895 0.00 0.00 0.00 3.11
3450 4807 1.592669 CACATGGGCGACGATCTCC 60.593 63.158 0.00 0.00 0.00 3.71
3826 5183 8.570068 TTTCAAACAGGAAAACAGTAGTAACT 57.430 30.769 0.00 0.00 34.05 2.24
3923 5297 7.763528 ACACATTCAAACAACACATGTAACATT 59.236 29.630 0.00 0.00 42.99 2.71
3937 5311 5.042593 GCAAGATGTTCACACATTCAAACA 58.957 37.500 0.00 0.00 44.22 2.83
3973 5347 7.147479 ACCATTACTTGTCTAGGCATTCAGTAT 60.147 37.037 7.93 0.00 0.00 2.12
3980 5354 4.844349 ACACCATTACTTGTCTAGGCAT 57.156 40.909 0.00 0.00 0.00 4.40
4059 5433 2.510411 CAGCACCACCACCAGACA 59.490 61.111 0.00 0.00 0.00 3.41
4286 5660 3.637229 AGTAGCAGTACGATAGCATTGGT 59.363 43.478 0.00 0.00 42.67 3.67
4331 5705 1.200948 TGAGCATCTCACACACGAGAG 59.799 52.381 0.00 0.00 44.97 3.20
4375 5749 5.514274 AAAGGAAAGCATCGTCTCAAAAA 57.486 34.783 0.00 0.00 0.00 1.94
4376 5750 5.514274 AAAAGGAAAGCATCGTCTCAAAA 57.486 34.783 0.00 0.00 0.00 2.44
4377 5751 6.262273 AGTTAAAAGGAAAGCATCGTCTCAAA 59.738 34.615 0.00 0.00 0.00 2.69
4378 5752 5.763204 AGTTAAAAGGAAAGCATCGTCTCAA 59.237 36.000 0.00 0.00 0.00 3.02
4379 5753 5.305585 AGTTAAAAGGAAAGCATCGTCTCA 58.694 37.500 0.00 0.00 0.00 3.27
4380 5754 5.864628 AGTTAAAAGGAAAGCATCGTCTC 57.135 39.130 0.00 0.00 0.00 3.36
4381 5755 6.698380 TCTAGTTAAAAGGAAAGCATCGTCT 58.302 36.000 0.00 0.00 0.00 4.18
4382 5756 6.963049 TCTAGTTAAAAGGAAAGCATCGTC 57.037 37.500 0.00 0.00 0.00 4.20
4383 5757 6.708949 TGTTCTAGTTAAAAGGAAAGCATCGT 59.291 34.615 0.00 0.00 0.00 3.73
4384 5758 7.129109 TGTTCTAGTTAAAAGGAAAGCATCG 57.871 36.000 0.00 0.00 0.00 3.84
4385 5759 7.024171 GCTGTTCTAGTTAAAAGGAAAGCATC 58.976 38.462 5.12 0.00 0.00 3.91
4386 5760 6.490040 TGCTGTTCTAGTTAAAAGGAAAGCAT 59.510 34.615 7.78 0.00 32.66 3.79
4387 5761 5.825679 TGCTGTTCTAGTTAAAAGGAAAGCA 59.174 36.000 7.78 7.78 33.81 3.91
4388 5762 6.313744 TGCTGTTCTAGTTAAAAGGAAAGC 57.686 37.500 3.47 3.47 0.00 3.51
4389 5763 7.931275 AGTTGCTGTTCTAGTTAAAAGGAAAG 58.069 34.615 0.00 0.00 0.00 2.62
4390 5764 7.554835 TGAGTTGCTGTTCTAGTTAAAAGGAAA 59.445 33.333 0.00 0.00 0.00 3.13
4391 5765 7.012044 GTGAGTTGCTGTTCTAGTTAAAAGGAA 59.988 37.037 0.00 0.00 0.00 3.36
4392 5766 6.482308 GTGAGTTGCTGTTCTAGTTAAAAGGA 59.518 38.462 0.00 0.00 0.00 3.36
4393 5767 6.293462 GGTGAGTTGCTGTTCTAGTTAAAAGG 60.293 42.308 0.00 0.00 0.00 3.11
4394 5768 6.483640 AGGTGAGTTGCTGTTCTAGTTAAAAG 59.516 38.462 0.00 0.00 0.00 2.27
4395 5769 6.354130 AGGTGAGTTGCTGTTCTAGTTAAAA 58.646 36.000 0.00 0.00 0.00 1.52
4396 5770 5.925509 AGGTGAGTTGCTGTTCTAGTTAAA 58.074 37.500 0.00 0.00 0.00 1.52
4397 5771 5.510861 GGAGGTGAGTTGCTGTTCTAGTTAA 60.511 44.000 0.00 0.00 0.00 2.01
4398 5772 4.021368 GGAGGTGAGTTGCTGTTCTAGTTA 60.021 45.833 0.00 0.00 0.00 2.24
4399 5773 3.244249 GGAGGTGAGTTGCTGTTCTAGTT 60.244 47.826 0.00 0.00 0.00 2.24
4400 5774 2.300437 GGAGGTGAGTTGCTGTTCTAGT 59.700 50.000 0.00 0.00 0.00 2.57
4401 5775 2.300152 TGGAGGTGAGTTGCTGTTCTAG 59.700 50.000 0.00 0.00 0.00 2.43
4402 5776 2.300152 CTGGAGGTGAGTTGCTGTTCTA 59.700 50.000 0.00 0.00 0.00 2.10
4403 5777 1.071385 CTGGAGGTGAGTTGCTGTTCT 59.929 52.381 0.00 0.00 0.00 3.01
4404 5778 1.202698 ACTGGAGGTGAGTTGCTGTTC 60.203 52.381 0.00 0.00 0.00 3.18
4477 5851 8.585881 TCATACATATGGCTACCTTCTTACTTC 58.414 37.037 7.80 0.00 34.50 3.01
4500 5874 5.109210 CGTAGTGTATGGTGATTGTGTCAT 58.891 41.667 0.00 0.00 39.48 3.06
4501 5875 4.490743 CGTAGTGTATGGTGATTGTGTCA 58.509 43.478 0.00 0.00 0.00 3.58
4503 5877 3.259064 GCGTAGTGTATGGTGATTGTGT 58.741 45.455 0.00 0.00 0.00 3.72
4504 5878 2.281498 CGCGTAGTGTATGGTGATTGTG 59.719 50.000 0.00 0.00 0.00 3.33
4508 5882 2.885266 AGATCGCGTAGTGTATGGTGAT 59.115 45.455 5.77 0.00 40.08 3.06
4574 5961 1.383109 ATCACCTCGCCCAGATCCA 60.383 57.895 0.00 0.00 0.00 3.41
4584 5971 3.781307 TTCCCCGCCATCACCTCG 61.781 66.667 0.00 0.00 0.00 4.63
4622 6009 2.271800 CCACGTGCACTATTCCTTCTC 58.728 52.381 16.19 0.00 0.00 2.87
4625 6012 2.561478 AACCACGTGCACTATTCCTT 57.439 45.000 16.19 0.00 0.00 3.36
4628 6015 5.600908 TTTTCTAACCACGTGCACTATTC 57.399 39.130 16.19 0.00 0.00 1.75
4630 6017 7.551262 TGATATTTTTCTAACCACGTGCACTAT 59.449 33.333 16.19 0.00 0.00 2.12
4631 6018 6.874664 TGATATTTTTCTAACCACGTGCACTA 59.125 34.615 16.19 0.00 0.00 2.74
4632 6019 5.703592 TGATATTTTTCTAACCACGTGCACT 59.296 36.000 16.19 0.00 0.00 4.40
4633 6020 5.933790 TGATATTTTTCTAACCACGTGCAC 58.066 37.500 10.91 6.82 0.00 4.57
4634 6021 6.561737 TTGATATTTTTCTAACCACGTGCA 57.438 33.333 10.91 0.00 0.00 4.57
4635 6022 7.247728 TCATTGATATTTTTCTAACCACGTGC 58.752 34.615 10.91 0.00 0.00 5.34
4636 6023 8.664798 TCTCATTGATATTTTTCTAACCACGTG 58.335 33.333 9.08 9.08 0.00 4.49
4637 6024 8.786826 TCTCATTGATATTTTTCTAACCACGT 57.213 30.769 0.00 0.00 0.00 4.49
4653 6040 8.160106 GGGTCTCATTTACCTATTCTCATTGAT 58.840 37.037 0.00 0.00 37.18 2.57
4654 6041 7.509546 GGGTCTCATTTACCTATTCTCATTGA 58.490 38.462 0.00 0.00 37.18 2.57
4655 6042 6.425114 CGGGTCTCATTTACCTATTCTCATTG 59.575 42.308 0.00 0.00 37.18 2.82
4656 6043 6.525629 CGGGTCTCATTTACCTATTCTCATT 58.474 40.000 0.00 0.00 37.18 2.57
4657 6044 5.511545 GCGGGTCTCATTTACCTATTCTCAT 60.512 44.000 0.00 0.00 37.18 2.90
4658 6045 4.202223 GCGGGTCTCATTTACCTATTCTCA 60.202 45.833 0.00 0.00 37.18 3.27
4659 6046 4.039366 AGCGGGTCTCATTTACCTATTCTC 59.961 45.833 0.00 0.00 37.18 2.87
4660 6047 3.967987 AGCGGGTCTCATTTACCTATTCT 59.032 43.478 0.00 0.00 37.18 2.40
4661 6048 4.338379 AGCGGGTCTCATTTACCTATTC 57.662 45.455 0.00 0.00 37.18 1.75
4662 6049 4.704965 GAAGCGGGTCTCATTTACCTATT 58.295 43.478 0.00 0.00 37.18 1.73
4663 6050 3.243771 CGAAGCGGGTCTCATTTACCTAT 60.244 47.826 0.00 0.00 37.18 2.57
4664 6051 2.100252 CGAAGCGGGTCTCATTTACCTA 59.900 50.000 0.00 0.00 37.18 3.08
4665 6052 1.134788 CGAAGCGGGTCTCATTTACCT 60.135 52.381 0.00 0.00 37.18 3.08
4666 6053 1.287425 CGAAGCGGGTCTCATTTACC 58.713 55.000 0.00 0.00 36.19 2.85
4667 6054 1.287425 CCGAAGCGGGTCTCATTTAC 58.713 55.000 0.00 0.00 44.15 2.01
4668 6055 3.752796 CCGAAGCGGGTCTCATTTA 57.247 52.632 0.00 0.00 44.15 1.40
4669 6056 4.617875 CCGAAGCGGGTCTCATTT 57.382 55.556 0.00 0.00 44.15 2.32
4727 6114 8.969121 TCGTTATACATACGAAAGAGTTGAAA 57.031 30.769 0.00 0.00 44.20 2.69
4731 6118 6.904011 CGACTCGTTATACATACGAAAGAGTT 59.096 38.462 0.00 0.00 46.12 3.01
4858 6465 1.207570 TGGTCACGTTGGTGTACAGTT 59.792 47.619 0.00 0.00 44.68 3.16
4887 6494 8.375493 ACCTCTAAATATCACAAGTCCTAACA 57.625 34.615 0.00 0.00 0.00 2.41
4935 6542 7.832503 ACAAAAGAAAGAAAACCACTGATTG 57.167 32.000 0.00 0.00 0.00 2.67
4943 6550 4.868171 AGCCGAAACAAAAGAAAGAAAACC 59.132 37.500 0.00 0.00 0.00 3.27
4946 6553 5.105917 ACTCAGCCGAAACAAAAGAAAGAAA 60.106 36.000 0.00 0.00 0.00 2.52
4962 6569 4.685169 ACAACATATGAAAACTCAGCCG 57.315 40.909 10.38 0.00 0.00 5.52
4966 6573 7.925993 ACGAGAAAACAACATATGAAAACTCA 58.074 30.769 10.38 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.