Multiple sequence alignment - TraesCS4A01G025900

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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 TraesCS4A01G025900 chr4A 100.000 4851 0 0 1 4851 17801482 17806332 0.000000e+00 8959.0
1 TraesCS4A01G025900 chr4A 88.595 982 83 14 736 1693 17852020 17852996 0.000000e+00 1166.0
2 TraesCS4A01G025900 chr4A 84.589 876 103 27 520 1377 17847798 17846937 0.000000e+00 841.0
3 TraesCS4A01G025900 chr4A 83.462 780 74 29 2946 3717 17854706 17855438 0.000000e+00 675.0
4 TraesCS4A01G025900 chr4A 81.569 510 54 17 2094 2591 17853610 17854091 7.620000e-103 385.0
5 TraesCS4A01G025900 chr4A 78.356 596 76 23 245 816 17851399 17851965 2.160000e-88 337.0
6 TraesCS4A01G025900 chr4A 86.475 244 16 6 181 408 17760710 17760468 8.060000e-63 252.0
7 TraesCS4A01G025900 chr4A 90.217 184 11 2 1 180 17851107 17851287 2.920000e-57 233.0
8 TraesCS4A01G025900 chr4A 77.644 416 57 24 235 647 18681827 18682209 2.270000e-53 220.0
9 TraesCS4A01G025900 chr4A 76.923 416 60 25 235 648 18648014 18648395 2.290000e-48 204.0
10 TraesCS4A01G025900 chr4A 89.172 157 17 0 24 180 17760899 17760743 3.830000e-46 196.0
11 TraesCS4A01G025900 chr4A 89.474 133 12 2 3608 3740 18650712 18650842 3.000000e-37 167.0
12 TraesCS4A01G025900 chr4A 88.722 133 13 2 3608 3740 18684525 18684655 1.400000e-35 161.0
13 TraesCS4A01G025900 chr4A 83.832 167 27 0 1854 2020 240370522 240370688 5.030000e-35 159.0
14 TraesCS4A01G025900 chr4A 84.211 133 18 3 4474 4604 675522751 675522620 5.100000e-25 126.0
15 TraesCS4A01G025900 chr4A 98.305 59 0 1 4667 4724 17806095 17806153 8.590000e-18 102.0
16 TraesCS4A01G025900 chr4A 98.305 59 0 1 4614 4672 17806148 17806205 8.590000e-18 102.0
17 TraesCS4A01G025900 chr4A 84.545 110 7 9 4670 4778 17728823 17728923 3.090000e-17 100.0
18 TraesCS4A01G025900 chr5A 97.380 2023 45 6 2036 4054 3980869 3978851 0.000000e+00 3435.0
19 TraesCS4A01G025900 chr5A 89.880 919 63 16 2498 3408 4047596 4048492 0.000000e+00 1155.0
20 TraesCS4A01G025900 chr5A 87.991 866 68 19 736 1567 4044344 4045207 0.000000e+00 990.0
21 TraesCS4A01G025900 chr5A 82.005 1167 145 38 2585 3735 3799852 3800969 0.000000e+00 931.0
22 TraesCS4A01G025900 chr5A 81.507 1168 149 40 2585 3735 3727178 3728295 0.000000e+00 898.0
23 TraesCS4A01G025900 chr5A 84.056 853 111 21 520 1357 4035131 4034289 0.000000e+00 798.0
24 TraesCS4A01G025900 chr5A 82.353 510 50 17 2094 2591 4047018 4047499 1.630000e-109 407.0
25 TraesCS4A01G025900 chr5A 85.013 387 30 11 4056 4435 3978775 3978410 7.670000e-98 368.0
26 TraesCS4A01G025900 chr5A 78.151 595 79 25 245 816 4043723 4044289 1.010000e-86 331.0
27 TraesCS4A01G025900 chr5A 82.339 419 34 13 245 643 3983023 3982625 1.300000e-85 327.0
28 TraesCS4A01G025900 chr5A 87.681 276 33 1 1745 2020 3981640 3981366 2.180000e-83 320.0
29 TraesCS4A01G025900 chr5A 76.958 664 83 37 181 810 4007064 4007691 1.010000e-81 315.0
30 TraesCS4A01G025900 chr5A 86.940 268 24 8 3475 3740 4048684 4048942 1.710000e-74 291.0
31 TraesCS4A01G025900 chr5A 82.081 346 26 11 1427 1737 4046120 4046464 3.720000e-66 263.0
32 TraesCS4A01G025900 chr5A 91.667 180 12 1 1 180 4043435 4043611 3.750000e-61 246.0
33 TraesCS4A01G025900 chr5A 88.108 185 19 3 3556 3740 4611382 4611563 2.940000e-52 217.0
34 TraesCS4A01G025900 chr5A 83.857 223 32 4 1787 2008 485847150 485847369 4.920000e-50 209.0
35 TraesCS4A01G025900 chr5A 80.970 268 38 10 245 509 4608658 4608915 2.960000e-47 200.0
36 TraesCS4A01G025900 chr5B 92.967 1948 87 19 2021 3936 48419052 48420981 0.000000e+00 2793.0
37 TraesCS4A01G025900 chr5B 95.286 1506 41 9 186 1675 48416995 48418486 0.000000e+00 2361.0
38 TraesCS4A01G025900 chr5B 86.991 1253 105 34 2498 3740 6853986 6852782 0.000000e+00 1358.0
39 TraesCS4A01G025900 chr5B 92.531 897 56 9 740 1626 6836749 6835854 0.000000e+00 1275.0
40 TraesCS4A01G025900 chr5B 92.299 896 60 9 740 1626 24629638 24628743 0.000000e+00 1264.0
41 TraesCS4A01G025900 chr5B 89.289 1027 81 13 740 1737 6856098 6855072 0.000000e+00 1260.0
42 TraesCS4A01G025900 chr5B 89.331 956 73 12 740 1667 24675817 24674863 0.000000e+00 1173.0
43 TraesCS4A01G025900 chr5B 82.334 1234 117 61 245 1430 48322856 48321676 0.000000e+00 977.0
44 TraesCS4A01G025900 chr5B 82.778 900 105 35 2617 3497 24627538 24626670 0.000000e+00 758.0
45 TraesCS4A01G025900 chr5B 82.131 929 120 31 2585 3497 6834682 6833784 0.000000e+00 754.0
46 TraesCS4A01G025900 chr5B 84.812 744 94 14 2585 3318 6669210 6669944 0.000000e+00 730.0
47 TraesCS4A01G025900 chr5B 80.194 929 135 33 2585 3497 30922788 30921893 0.000000e+00 651.0
48 TraesCS4A01G025900 chr5B 84.751 682 43 27 1 643 6837481 6836822 1.150000e-175 627.0
49 TraesCS4A01G025900 chr5B 97.191 356 10 0 1665 2020 48418635 48418990 1.930000e-168 603.0
50 TraesCS4A01G025900 chr5B 79.263 868 86 34 1 793 6857014 6856166 2.000000e-143 520.0
51 TraesCS4A01G025900 chr5B 83.802 605 39 20 1 549 24640645 24640044 2.000000e-143 520.0
52 TraesCS4A01G025900 chr5B 77.864 899 102 41 1 819 24676753 24675872 7.350000e-128 468.0
53 TraesCS4A01G025900 chr5B 90.164 366 22 6 3934 4293 48421265 48421622 9.510000e-127 464.0
54 TraesCS4A01G025900 chr5B 89.655 319 16 5 4340 4643 48421618 48421934 1.640000e-104 390.0
55 TraesCS4A01G025900 chr5B 81.532 509 56 12 2094 2591 6854567 6854086 7.620000e-103 385.0
56 TraesCS4A01G025900 chr5B 97.531 162 3 1 19 180 48416767 48416927 4.780000e-70 276.0
57 TraesCS4A01G025900 chr5B 90.374 187 10 8 4667 4851 48421904 48422084 6.270000e-59 239.0
58 TraesCS4A01G025900 chr5B 83.691 233 33 5 1789 2020 462121562 462121334 1.060000e-51 215.0
59 TraesCS4A01G025900 chr5B 88.824 170 15 4 3571 3740 30921885 30921720 6.360000e-49 206.0
60 TraesCS4A01G025900 chr5B 87.647 170 19 2 1741 1909 6835681 6835513 3.830000e-46 196.0
61 TraesCS4A01G025900 chr5B 87.349 166 19 2 1745 1909 24628565 24628401 6.410000e-44 189.0
62 TraesCS4A01G025900 chr5B 87.261 157 20 0 24 180 48323148 48322992 3.860000e-41 180.0
63 TraesCS4A01G025900 chr5B 82.888 187 26 5 1825 2009 6674421 6674603 3.880000e-36 163.0
64 TraesCS4A01G025900 chr5D 83.585 1389 140 45 2374 3740 3928647 3927325 0.000000e+00 1221.0
65 TraesCS4A01G025900 chr5D 84.946 744 94 13 2585 3318 5100888 5100153 0.000000e+00 737.0
66 TraesCS4A01G025900 chr5D 81.579 266 33 13 245 509 3930148 3929898 6.360000e-49 206.0
67 TraesCS4A01G025900 chr5D 84.615 208 27 5 1787 1993 384873402 384873605 8.230000e-48 202.0
68 TraesCS4A01G025900 chr5D 89.313 131 9 1 4721 4851 4401513 4401388 5.030000e-35 159.0
69 TraesCS4A01G025900 chr5D 89.313 131 9 1 4721 4851 4470003 4469878 5.030000e-35 159.0
70 TraesCS4A01G025900 chr5D 89.313 131 9 1 4721 4851 4551023 4550898 5.030000e-35 159.0
71 TraesCS4A01G025900 chr5D 89.313 131 9 1 4721 4851 4615355 4615230 5.030000e-35 159.0
72 TraesCS4A01G025900 chr5D 89.313 131 9 1 4721 4851 4705431 4705306 5.030000e-35 159.0
73 TraesCS4A01G025900 chr5D 88.550 131 10 1 4721 4851 4779409 4779284 2.340000e-33 154.0
74 TraesCS4A01G025900 chr5D 100.000 32 0 0 4604 4635 4401576 4401545 5.240000e-05 60.2
75 TraesCS4A01G025900 chr5D 100.000 32 0 0 4604 4635 4470066 4470035 5.240000e-05 60.2
76 TraesCS4A01G025900 chr5D 100.000 32 0 0 4604 4635 4615418 4615387 5.240000e-05 60.2
77 TraesCS4A01G025900 chr5D 100.000 32 0 0 4604 4635 4705494 4705463 5.240000e-05 60.2
78 TraesCS4A01G025900 chr5D 100.000 32 0 0 4604 4635 4779472 4779441 5.240000e-05 60.2
79 TraesCS4A01G025900 chr3B 84.543 744 96 14 2585 3318 62670627 62671361 0.000000e+00 719.0
80 TraesCS4A01G025900 chr4D 87.179 156 20 0 1865 2020 206061703 206061548 1.390000e-40 178.0
81 TraesCS4A01G025900 chrUn 88.235 119 9 1 4733 4851 480354132 480354019 2.350000e-28 137.0
82 TraesCS4A01G025900 chr6B 86.066 122 16 1 4482 4602 370126515 370126394 3.940000e-26 130.0


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 TraesCS4A01G025900 chr4A 17801482 17806332 4850 False 3054.333333 8959 98.870000 1 4851 3 chr4A.!!$F3 4850
1 TraesCS4A01G025900 chr4A 17846937 17847798 861 True 841.000000 841 84.589000 520 1377 1 chr4A.!!$R1 857
2 TraesCS4A01G025900 chr4A 17851107 17855438 4331 False 559.200000 1166 84.439800 1 3717 5 chr4A.!!$F4 3716
3 TraesCS4A01G025900 chr5A 3978410 3983023 4613 True 1112.500000 3435 88.103250 245 4435 4 chr5A.!!$R2 4190
4 TraesCS4A01G025900 chr5A 3799852 3800969 1117 False 931.000000 931 82.005000 2585 3735 1 chr5A.!!$F2 1150
5 TraesCS4A01G025900 chr5A 3727178 3728295 1117 False 898.000000 898 81.507000 2585 3735 1 chr5A.!!$F1 1150
6 TraesCS4A01G025900 chr5A 4034289 4035131 842 True 798.000000 798 84.056000 520 1357 1 chr5A.!!$R1 837
7 TraesCS4A01G025900 chr5A 4043435 4048942 5507 False 526.142857 1155 85.580429 1 3740 7 chr5A.!!$F5 3739
8 TraesCS4A01G025900 chr5A 4007064 4007691 627 False 315.000000 315 76.958000 181 810 1 chr5A.!!$F3 629
9 TraesCS4A01G025900 chr5A 4608658 4611563 2905 False 208.500000 217 84.539000 245 3740 2 chr5A.!!$F6 3495
10 TraesCS4A01G025900 chr5B 48416767 48422084 5317 False 1018.000000 2793 93.309714 19 4851 7 chr5B.!!$F3 4832
11 TraesCS4A01G025900 chr5B 6852782 6857014 4232 True 880.750000 1358 84.268750 1 3740 4 chr5B.!!$R4 3739
12 TraesCS4A01G025900 chr5B 24674863 24676753 1890 True 820.500000 1173 83.597500 1 1667 2 chr5B.!!$R6 1666
13 TraesCS4A01G025900 chr5B 24626670 24629638 2968 True 737.000000 1264 87.475333 740 3497 3 chr5B.!!$R5 2757
14 TraesCS4A01G025900 chr5B 6669210 6669944 734 False 730.000000 730 84.812000 2585 3318 1 chr5B.!!$F1 733
15 TraesCS4A01G025900 chr5B 6833784 6837481 3697 True 713.000000 1275 86.765000 1 3497 4 chr5B.!!$R3 3496
16 TraesCS4A01G025900 chr5B 48321676 48323148 1472 True 578.500000 977 84.797500 24 1430 2 chr5B.!!$R8 1406
17 TraesCS4A01G025900 chr5B 24640044 24640645 601 True 520.000000 520 83.802000 1 549 1 chr5B.!!$R1 548
18 TraesCS4A01G025900 chr5B 30921720 30922788 1068 True 428.500000 651 84.509000 2585 3740 2 chr5B.!!$R7 1155
19 TraesCS4A01G025900 chr5D 5100153 5100888 735 True 737.000000 737 84.946000 2585 3318 1 chr5D.!!$R2 733
20 TraesCS4A01G025900 chr5D 3927325 3930148 2823 True 713.500000 1221 82.582000 245 3740 2 chr5D.!!$R3 3495
21 TraesCS4A01G025900 chr3B 62670627 62671361 734 False 719.000000 719 84.543000 2585 3318 1 chr3B.!!$F1 733

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
100 105 4.070552 ACACCGCCGAGCTCTTCC 62.071 66.667 12.85 0.0 0.00 3.46 F
734 955 4.447290 TGCGATTTGCTTACTAGGCATTA 58.553 39.130 0.00 0.0 46.63 1.90 F
1008 1502 0.663153 GGAATCCAAGCATGTACCGC 59.337 55.000 0.00 0.0 0.00 5.68 F
1821 4767 0.818938 TGGTCTAACCTAATGCGCGA 59.181 50.000 12.10 0.0 39.58 5.87 F
3605 8101 1.386533 AGCAAAGCATCCATCTTCCG 58.613 50.000 0.00 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1008 1502 0.605319 AGTGCACATTGTGGTACCGG 60.605 55.000 21.04 0.00 33.64 5.28 R
1821 4767 1.570979 CTCCCTTTCCCCAAAGCCTAT 59.429 52.381 0.00 0.00 38.19 2.57 R
1893 4839 2.229792 GGCTGTCAGACCAAATTGTCA 58.770 47.619 3.32 0.00 37.73 3.58 R
3679 8180 2.287915 CACACAACTCAAAGTTAGCGCT 59.712 45.455 17.26 17.26 36.03 5.92 R
4647 9538 0.315251 CAGTGCGTCTTCTCACCTCA 59.685 55.000 0.00 0.00 33.90 3.86 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
100 105 4.070552 ACACCGCCGAGCTCTTCC 62.071 66.667 12.85 0.00 0.00 3.46
180 185 6.352737 GGGTTTCATCCTCTCTTGGTATGTAA 60.353 42.308 0.00 0.00 0.00 2.41
181 186 6.539103 GGTTTCATCCTCTCTTGGTATGTAAC 59.461 42.308 0.00 0.00 32.01 2.50
200 267 6.843752 TGTAACCCTCTCTGTTTTGGATTTA 58.156 36.000 0.00 0.00 0.00 1.40
531 709 4.986034 GTGTGTGTGTGTGTGCTACTATTA 59.014 41.667 0.00 0.00 0.00 0.98
556 741 7.886338 AGCCTTTCCTAGTAACAAAATGAAAG 58.114 34.615 0.00 0.00 37.83 2.62
734 955 4.447290 TGCGATTTGCTTACTAGGCATTA 58.553 39.130 0.00 0.00 46.63 1.90
1008 1502 0.663153 GGAATCCAAGCATGTACCGC 59.337 55.000 0.00 0.00 0.00 5.68
1307 2796 5.701750 TCCATTTTGCTCAATTGTTTGGATG 59.298 36.000 5.13 4.79 33.44 3.51
1509 3042 1.672881 GCATATCTGTTGGGTGCTGAC 59.327 52.381 0.00 0.00 33.25 3.51
1821 4767 0.818938 TGGTCTAACCTAATGCGCGA 59.181 50.000 12.10 0.00 39.58 5.87
1893 4839 1.452108 GCAGTTAATCGGCCCAGCT 60.452 57.895 0.00 0.00 0.00 4.24
2046 5792 2.089980 GAGCAAATGTGATCAGTGCCT 58.910 47.619 13.96 5.25 40.04 4.75
2092 5853 2.645838 ATGTCTGAACAAGTGGCTGT 57.354 45.000 0.00 0.00 39.30 4.40
2148 5933 1.821216 ATAAACAAGTGGGACCGCAG 58.179 50.000 4.54 0.00 0.00 5.18
2366 6219 9.396022 AGTTGTTCTCGGTCATATTGAAATATT 57.604 29.630 0.00 0.00 29.35 1.28
3536 8000 4.976224 ATCGTTTTGGTTAATAGGTGGC 57.024 40.909 0.00 0.00 0.00 5.01
3539 8003 3.058085 CGTTTTGGTTAATAGGTGGCGTT 60.058 43.478 0.00 0.00 0.00 4.84
3605 8101 1.386533 AGCAAAGCATCCATCTTCCG 58.613 50.000 0.00 0.00 0.00 4.30
3630 8127 7.011669 CGTTTGTAGACTTGAAAGTTTTAGGGA 59.988 37.037 0.00 0.00 39.88 4.20
3679 8180 1.689813 TGCTTGTAGGTTTGTCGAGGA 59.310 47.619 0.00 0.00 0.00 3.71
3726 8230 6.875195 ACATTTTGCAAAGAATGTGGATTAGG 59.125 34.615 22.60 5.66 42.96 2.69
3986 8783 8.481314 TGTGAGATTCTCTGTTCTGCTATAATT 58.519 33.333 14.54 0.00 0.00 1.40
3992 8789 7.112452 TCTCTGTTCTGCTATAATTACTGCA 57.888 36.000 11.97 11.97 0.00 4.41
4103 8975 2.237143 TCTTAGCCTGATGGGTTGTGAG 59.763 50.000 0.00 0.00 42.12 3.51
4168 9040 7.483691 GGTTTGTGTAATCGAATAAATGTCACC 59.516 37.037 0.00 0.00 0.00 4.02
4172 9044 8.568794 TGTGTAATCGAATAAATGTCACCAAAA 58.431 29.630 0.00 0.00 0.00 2.44
4237 9114 7.259088 ACAGATGGAATACTTTACCAAGAGT 57.741 36.000 0.00 0.00 37.24 3.24
4260 9137 1.830279 CTCTTGCTGGAGGAAATGCA 58.170 50.000 0.00 0.00 0.00 3.96
4297 9174 2.971660 CCGAGGTGGTTTTGGTTTTT 57.028 45.000 0.00 0.00 0.00 1.94
4298 9175 2.816689 CCGAGGTGGTTTTGGTTTTTC 58.183 47.619 0.00 0.00 0.00 2.29
4299 9176 2.429250 CCGAGGTGGTTTTGGTTTTTCT 59.571 45.455 0.00 0.00 0.00 2.52
4300 9177 3.118920 CCGAGGTGGTTTTGGTTTTTCTT 60.119 43.478 0.00 0.00 0.00 2.52
4301 9178 4.500127 CGAGGTGGTTTTGGTTTTTCTTT 58.500 39.130 0.00 0.00 0.00 2.52
4302 9179 4.932799 CGAGGTGGTTTTGGTTTTTCTTTT 59.067 37.500 0.00 0.00 0.00 2.27
4303 9180 5.410132 CGAGGTGGTTTTGGTTTTTCTTTTT 59.590 36.000 0.00 0.00 0.00 1.94
4322 9199 5.506730 TTTTTGAGGGAAAAGGTGGTTTT 57.493 34.783 0.00 0.00 41.29 2.43
4323 9200 4.479786 TTTGAGGGAAAAGGTGGTTTTG 57.520 40.909 0.00 0.00 38.54 2.44
4324 9201 2.393646 TGAGGGAAAAGGTGGTTTTGG 58.606 47.619 0.00 0.00 38.54 3.28
4325 9202 2.292587 TGAGGGAAAAGGTGGTTTTGGT 60.293 45.455 0.00 0.00 38.54 3.67
4326 9203 2.769663 GAGGGAAAAGGTGGTTTTGGTT 59.230 45.455 0.00 0.00 38.54 3.67
4327 9204 2.503765 AGGGAAAAGGTGGTTTTGGTTG 59.496 45.455 0.00 0.00 38.54 3.77
4364 9241 2.216750 CTGGTTTGGGCCATTGAGCG 62.217 60.000 7.26 0.02 37.96 5.03
4365 9242 2.573340 GTTTGGGCCATTGAGCGG 59.427 61.111 7.26 0.00 0.00 5.52
4368 9245 2.424842 TTTGGGCCATTGAGCGGAGT 62.425 55.000 7.26 0.00 0.00 3.85
4431 9309 1.786937 CTCAGCCCATGTAGAGGTCT 58.213 55.000 0.00 0.00 0.00 3.85
4470 9359 1.206610 CATGGCTATATCGCAGCTCCT 59.793 52.381 1.26 0.00 39.09 3.69
4474 9363 4.278310 TGGCTATATCGCAGCTCCTATAA 58.722 43.478 1.26 0.00 39.09 0.98
4475 9364 4.098044 TGGCTATATCGCAGCTCCTATAAC 59.902 45.833 1.26 0.00 39.09 1.89
4476 9365 4.500035 GGCTATATCGCAGCTCCTATAACC 60.500 50.000 1.26 0.00 39.09 2.85
4543 9434 3.391382 CCCAGGTCACCCCTCGAC 61.391 72.222 0.00 0.00 43.86 4.20
4636 9527 1.065764 CCGGCGTTGAGATCGATCA 59.934 57.895 26.47 6.39 0.00 2.92
4637 9528 0.319040 CCGGCGTTGAGATCGATCAT 60.319 55.000 26.47 12.09 0.00 2.45
4638 9529 1.068541 CCGGCGTTGAGATCGATCATA 60.069 52.381 26.47 12.36 0.00 2.15
4639 9530 1.979469 CGGCGTTGAGATCGATCATAC 59.021 52.381 26.47 18.24 0.00 2.39
4640 9531 2.604614 CGGCGTTGAGATCGATCATACA 60.605 50.000 26.47 19.00 0.00 2.29
4641 9532 2.983136 GGCGTTGAGATCGATCATACAG 59.017 50.000 26.47 15.18 0.00 2.74
4642 9533 2.983136 GCGTTGAGATCGATCATACAGG 59.017 50.000 26.47 17.22 0.00 4.00
4643 9534 3.551046 GCGTTGAGATCGATCATACAGGT 60.551 47.826 26.47 4.43 0.00 4.00
4644 9535 3.977579 CGTTGAGATCGATCATACAGGTG 59.022 47.826 26.47 12.30 0.00 4.00
4645 9536 4.261197 CGTTGAGATCGATCATACAGGTGA 60.261 45.833 26.47 6.71 0.00 4.02
4646 9537 4.837896 TGAGATCGATCATACAGGTGAC 57.162 45.455 26.47 5.90 0.00 3.67
4647 9538 4.464947 TGAGATCGATCATACAGGTGACT 58.535 43.478 26.47 1.56 46.44 3.41
4662 9553 0.598562 TGACTGAGGTGAGAAGACGC 59.401 55.000 0.00 0.00 0.00 5.19
4663 9554 0.598562 GACTGAGGTGAGAAGACGCA 59.401 55.000 0.00 0.00 0.00 5.24
4664 9555 0.315568 ACTGAGGTGAGAAGACGCAC 59.684 55.000 0.00 0.00 44.00 5.34
4665 9556 0.600557 CTGAGGTGAGAAGACGCACT 59.399 55.000 0.00 0.00 44.14 4.40
4666 9557 0.315251 TGAGGTGAGAAGACGCACTG 59.685 55.000 0.00 0.00 44.14 3.66
4667 9558 1.005630 AGGTGAGAAGACGCACTGC 60.006 57.895 0.00 0.00 44.14 4.40
4668 9559 2.029844 GGTGAGAAGACGCACTGCC 61.030 63.158 0.00 0.00 44.14 4.85
4669 9560 2.049156 TGAGAAGACGCACTGCCG 60.049 61.111 0.00 0.00 0.00 5.69
4670 9561 3.482783 GAGAAGACGCACTGCCGC 61.483 66.667 0.00 0.00 0.00 6.53
4685 9576 4.847516 CGCCGGCGTTGAGATCGA 62.848 66.667 39.71 0.00 34.35 3.59
4686 9577 2.279517 GCCGGCGTTGAGATCGAT 60.280 61.111 12.58 0.00 0.00 3.59
4687 9578 2.303676 GCCGGCGTTGAGATCGATC 61.304 63.158 17.91 17.91 0.00 3.69
4688 9579 1.065764 CCGGCGTTGAGATCGATCA 59.934 57.895 26.47 6.39 0.00 2.92
4689 9580 0.319040 CCGGCGTTGAGATCGATCAT 60.319 55.000 26.47 12.09 0.00 2.45
4690 9581 1.068541 CCGGCGTTGAGATCGATCATA 60.069 52.381 26.47 12.36 0.00 2.15
4691 9582 1.979469 CGGCGTTGAGATCGATCATAC 59.021 52.381 26.47 18.24 0.00 2.39
4692 9583 2.604614 CGGCGTTGAGATCGATCATACA 60.605 50.000 26.47 19.00 0.00 2.29
4693 9584 2.983136 GGCGTTGAGATCGATCATACAG 59.017 50.000 26.47 15.18 0.00 2.74
4694 9585 2.983136 GCGTTGAGATCGATCATACAGG 59.017 50.000 26.47 17.22 0.00 4.00
4695 9586 3.551046 GCGTTGAGATCGATCATACAGGT 60.551 47.826 26.47 4.43 0.00 4.00
4696 9587 3.977579 CGTTGAGATCGATCATACAGGTG 59.022 47.826 26.47 12.30 0.00 4.00
4697 9588 4.261197 CGTTGAGATCGATCATACAGGTGA 60.261 45.833 26.47 6.71 0.00 4.02
4698 9589 4.837896 TGAGATCGATCATACAGGTGAC 57.162 45.455 26.47 5.90 0.00 3.67
4699 9590 4.464947 TGAGATCGATCATACAGGTGACT 58.535 43.478 26.47 1.56 46.44 3.41
4711 9602 2.685106 AGGTGACTGAGGTGAGAAGA 57.315 50.000 0.00 0.00 41.13 2.87
4712 9603 2.243810 AGGTGACTGAGGTGAGAAGAC 58.756 52.381 0.00 0.00 41.13 3.01
4751 9642 1.679153 GTCAAAGAAAACGAGGCCCAA 59.321 47.619 0.00 0.00 0.00 4.12
4758 9649 2.994643 AAACGAGGCCCAAACCCAGG 62.995 60.000 0.00 0.00 0.00 4.45
4800 9691 2.033492 GTGTTTTACGTACAAGCGCAGT 60.033 45.455 11.47 10.82 34.88 4.40
4801 9692 2.033577 TGTTTTACGTACAAGCGCAGTG 60.034 45.455 11.47 10.20 34.88 3.66
4830 9721 7.040823 TGCCAAAAGAAATTCACACAAGTTTTT 60.041 29.630 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
180 185 7.010160 TCAATTAAATCCAAAACAGAGAGGGT 58.990 34.615 0.00 0.00 0.00 4.34
181 186 7.466746 TCAATTAAATCCAAAACAGAGAGGG 57.533 36.000 0.00 0.00 0.00 4.30
182 187 8.193438 GGATCAATTAAATCCAAAACAGAGAGG 58.807 37.037 12.17 0.00 42.01 3.69
222 311 3.679502 TGTGTGATTCAAGCACGATACAG 59.320 43.478 0.48 0.00 39.07 2.74
509 681 3.744238 ATAGTAGCACACACACACACA 57.256 42.857 0.00 0.00 0.00 3.72
510 682 5.763444 CTAATAGTAGCACACACACACAC 57.237 43.478 0.00 0.00 0.00 3.82
531 709 7.523873 GCTTTCATTTTGTTACTAGGAAAGGCT 60.524 37.037 15.39 0.00 39.82 4.58
542 724 3.376540 TGTGCCGCTTTCATTTTGTTAC 58.623 40.909 0.00 0.00 0.00 2.50
546 728 2.156117 CACATGTGCCGCTTTCATTTTG 59.844 45.455 13.94 0.00 0.00 2.44
556 741 0.039617 TAAGCAAACACATGTGCCGC 60.040 50.000 25.68 22.98 41.88 6.53
614 808 7.915293 TGAACAGTGAACTGAAGAAAAGTTA 57.085 32.000 17.11 0.00 46.59 2.24
934 1428 7.569240 AGATTTAAGGAATTGTCTCTTCCGAT 58.431 34.615 0.00 0.00 45.63 4.18
1008 1502 0.605319 AGTGCACATTGTGGTACCGG 60.605 55.000 21.04 0.00 33.64 5.28
1307 2796 5.248870 ACAAACCGATATTTCTTCCATGC 57.751 39.130 0.00 0.00 0.00 4.06
1509 3042 5.112686 GCTGATAAGCCGATTAATCCCTAG 58.887 45.833 9.87 2.89 0.00 3.02
1577 4182 5.395682 TGGAAAAGAAATTCAGATGCAGG 57.604 39.130 0.00 0.00 0.00 4.85
1793 4739 2.661176 AGGTTAGACCATTCCCTCCA 57.339 50.000 0.00 0.00 41.95 3.86
1821 4767 1.570979 CTCCCTTTCCCCAAAGCCTAT 59.429 52.381 0.00 0.00 38.19 2.57
1893 4839 2.229792 GGCTGTCAGACCAAATTGTCA 58.770 47.619 3.32 0.00 37.73 3.58
2010 5141 4.944619 TTGCTCTGAGAACATATCGGAT 57.055 40.909 9.28 0.00 31.78 4.18
2148 5933 4.391830 TCATGAACCATTTTGTAGTCTCGC 59.608 41.667 0.00 0.00 0.00 5.03
2952 7247 4.566004 GTGAAGCTACCAACTATCACACA 58.434 43.478 6.13 0.00 37.65 3.72
3536 8000 6.223138 TCTACACAATTTACTTGCTGAACG 57.777 37.500 0.00 0.00 38.50 3.95
3539 8003 7.990917 TGTTTTCTACACAATTTACTTGCTGA 58.009 30.769 0.00 0.00 38.50 4.26
3605 8101 8.217131 TCCCTAAAACTTTCAAGTCTACAAAC 57.783 34.615 0.00 0.00 38.57 2.93
3637 8136 5.182001 GCACAAACATACATCTCTTGTTCCT 59.818 40.000 0.00 0.00 39.87 3.36
3679 8180 2.287915 CACACAACTCAAAGTTAGCGCT 59.712 45.455 17.26 17.26 36.03 5.92
3931 8442 6.018180 GGTTGCTACTTTGGCACTATATACAC 60.018 42.308 0.00 0.00 39.55 2.90
3986 8783 7.527796 AGGTCTATATAAACCTCTCTGCAGTA 58.472 38.462 14.67 2.31 42.28 2.74
4237 9114 3.548770 CATTTCCTCCAGCAAGAGCATA 58.451 45.455 0.00 0.00 45.49 3.14
4300 9177 5.249420 CAAAACCACCTTTTCCCTCAAAAA 58.751 37.500 0.00 0.00 33.40 1.94
4301 9178 4.323868 CCAAAACCACCTTTTCCCTCAAAA 60.324 41.667 0.00 0.00 28.85 2.44
4302 9179 3.198853 CCAAAACCACCTTTTCCCTCAAA 59.801 43.478 0.00 0.00 28.85 2.69
4303 9180 2.769095 CCAAAACCACCTTTTCCCTCAA 59.231 45.455 0.00 0.00 28.85 3.02
4304 9181 2.292587 ACCAAAACCACCTTTTCCCTCA 60.293 45.455 0.00 0.00 28.85 3.86
4305 9182 2.394632 ACCAAAACCACCTTTTCCCTC 58.605 47.619 0.00 0.00 28.85 4.30
4307 9184 2.420827 CCAACCAAAACCACCTTTTCCC 60.421 50.000 0.00 0.00 28.85 3.97
4308 9185 2.912771 CCAACCAAAACCACCTTTTCC 58.087 47.619 0.00 0.00 28.85 3.13
4309 9186 2.285083 GCCAACCAAAACCACCTTTTC 58.715 47.619 0.00 0.00 28.85 2.29
4310 9187 1.065053 GGCCAACCAAAACCACCTTTT 60.065 47.619 0.00 0.00 35.26 2.27
4311 9188 0.544223 GGCCAACCAAAACCACCTTT 59.456 50.000 0.00 0.00 35.26 3.11
4312 9189 1.681486 CGGCCAACCAAAACCACCTT 61.681 55.000 2.24 0.00 34.57 3.50
4313 9190 2.131067 CGGCCAACCAAAACCACCT 61.131 57.895 2.24 0.00 34.57 4.00
4314 9191 2.082629 CTCGGCCAACCAAAACCACC 62.083 60.000 2.24 0.00 34.57 4.61
4315 9192 1.362355 CTCGGCCAACCAAAACCAC 59.638 57.895 2.24 0.00 34.57 4.16
4316 9193 2.494530 GCTCGGCCAACCAAAACCA 61.495 57.895 2.24 0.00 34.57 3.67
4317 9194 2.338620 GCTCGGCCAACCAAAACC 59.661 61.111 2.24 0.00 34.57 3.27
4364 9241 0.320508 GACCGGGTGAAACTGACTCC 60.321 60.000 3.30 0.00 36.74 3.85
4365 9242 0.320508 GGACCGGGTGAAACTGACTC 60.321 60.000 3.30 0.00 36.74 3.36
4368 9245 1.401318 TTCGGACCGGGTGAAACTGA 61.401 55.000 15.25 0.00 36.74 3.41
4431 9309 3.827817 TGGTAGAGGAAGAGGAGTTGA 57.172 47.619 0.00 0.00 0.00 3.18
4474 9363 3.749632 CGGTTTTTGGAACCTTCTAGGGT 60.750 47.826 6.40 0.00 38.64 4.34
4475 9364 2.817844 CGGTTTTTGGAACCTTCTAGGG 59.182 50.000 6.40 0.00 40.58 3.53
4476 9365 2.817844 CCGGTTTTTGGAACCTTCTAGG 59.182 50.000 6.40 0.00 42.49 3.02
4537 9428 4.504916 CAGAGCTGGCGGTCGAGG 62.505 72.222 0.00 0.00 42.35 4.63
4543 9434 3.932580 TAACGCACAGAGCTGGCGG 62.933 63.158 25.51 14.43 46.65 6.13
4547 9438 1.665544 CGACGTAACGCACAGAGCTG 61.666 60.000 0.00 0.00 42.61 4.24
4581 9472 2.297701 GAATTCCCTATTTGCCGCTCA 58.702 47.619 0.00 0.00 0.00 4.26
4620 9511 2.983136 CTGTATGATCGATCTCAACGCC 59.017 50.000 25.02 7.66 0.00 5.68
4636 9527 3.458044 TCTCACCTCAGTCACCTGTAT 57.542 47.619 0.00 0.00 39.82 2.29
4637 9528 2.971901 TCTCACCTCAGTCACCTGTA 57.028 50.000 0.00 0.00 39.82 2.74
4638 9529 1.967066 CTTCTCACCTCAGTCACCTGT 59.033 52.381 0.00 0.00 39.82 4.00
4639 9530 2.029470 GTCTTCTCACCTCAGTCACCTG 60.029 54.545 0.00 0.00 40.25 4.00
4640 9531 2.243810 GTCTTCTCACCTCAGTCACCT 58.756 52.381 0.00 0.00 0.00 4.00
4641 9532 1.068194 CGTCTTCTCACCTCAGTCACC 60.068 57.143 0.00 0.00 0.00 4.02
4642 9533 1.667467 GCGTCTTCTCACCTCAGTCAC 60.667 57.143 0.00 0.00 0.00 3.67
4643 9534 0.598562 GCGTCTTCTCACCTCAGTCA 59.401 55.000 0.00 0.00 0.00 3.41
4644 9535 0.598562 TGCGTCTTCTCACCTCAGTC 59.401 55.000 0.00 0.00 0.00 3.51
4645 9536 0.315568 GTGCGTCTTCTCACCTCAGT 59.684 55.000 0.00 0.00 0.00 3.41
4646 9537 0.600557 AGTGCGTCTTCTCACCTCAG 59.399 55.000 0.00 0.00 33.90 3.35
4647 9538 0.315251 CAGTGCGTCTTCTCACCTCA 59.685 55.000 0.00 0.00 33.90 3.86
4648 9539 1.011451 GCAGTGCGTCTTCTCACCTC 61.011 60.000 0.00 0.00 33.90 3.85
4652 9543 2.049156 CGGCAGTGCGTCTTCTCA 60.049 61.111 9.45 0.00 0.00 3.27
4668 9559 4.847516 TCGATCTCAACGCCGGCG 62.848 66.667 44.88 44.88 46.03 6.46
4669 9560 2.279517 ATCGATCTCAACGCCGGC 60.280 61.111 19.07 19.07 0.00 6.13
4670 9561 0.319040 ATGATCGATCTCAACGCCGG 60.319 55.000 25.02 0.00 0.00 6.13
4671 9562 1.979469 GTATGATCGATCTCAACGCCG 59.021 52.381 25.02 0.00 0.00 6.46
4672 9563 2.983136 CTGTATGATCGATCTCAACGCC 59.017 50.000 25.02 7.66 0.00 5.68
4673 9564 2.983136 CCTGTATGATCGATCTCAACGC 59.017 50.000 25.02 10.48 0.00 4.84
4674 9565 3.977579 CACCTGTATGATCGATCTCAACG 59.022 47.826 25.02 15.06 0.00 4.10
4675 9566 4.979197 GTCACCTGTATGATCGATCTCAAC 59.021 45.833 25.02 18.98 0.00 3.18
4676 9567 4.889995 AGTCACCTGTATGATCGATCTCAA 59.110 41.667 25.02 6.67 0.00 3.02
4677 9568 4.276926 CAGTCACCTGTATGATCGATCTCA 59.723 45.833 25.02 18.67 33.80 3.27
4678 9569 4.517075 TCAGTCACCTGTATGATCGATCTC 59.483 45.833 25.02 15.56 39.82 2.75
4679 9570 4.464947 TCAGTCACCTGTATGATCGATCT 58.535 43.478 25.02 13.51 39.82 2.75
4680 9571 4.320861 CCTCAGTCACCTGTATGATCGATC 60.321 50.000 18.72 18.72 39.82 3.69
4681 9572 3.571828 CCTCAGTCACCTGTATGATCGAT 59.428 47.826 0.00 0.00 39.82 3.59
4682 9573 2.952310 CCTCAGTCACCTGTATGATCGA 59.048 50.000 0.00 0.00 39.82 3.59
4683 9574 2.690497 ACCTCAGTCACCTGTATGATCG 59.310 50.000 0.00 0.00 39.82 3.69
4684 9575 3.701542 TCACCTCAGTCACCTGTATGATC 59.298 47.826 0.00 0.00 39.82 2.92
4685 9576 3.703556 CTCACCTCAGTCACCTGTATGAT 59.296 47.826 0.00 0.00 39.82 2.45
4686 9577 3.092301 CTCACCTCAGTCACCTGTATGA 58.908 50.000 0.00 0.00 39.82 2.15
4687 9578 3.092301 TCTCACCTCAGTCACCTGTATG 58.908 50.000 0.00 0.00 39.82 2.39
4688 9579 3.458044 TCTCACCTCAGTCACCTGTAT 57.542 47.619 0.00 0.00 39.82 2.29
4689 9580 2.971901 TCTCACCTCAGTCACCTGTA 57.028 50.000 0.00 0.00 39.82 2.74
4690 9581 1.967066 CTTCTCACCTCAGTCACCTGT 59.033 52.381 0.00 0.00 39.82 4.00
4691 9582 2.029470 GTCTTCTCACCTCAGTCACCTG 60.029 54.545 0.00 0.00 40.25 4.00
4692 9583 2.243810 GTCTTCTCACCTCAGTCACCT 58.756 52.381 0.00 0.00 0.00 4.00
4693 9584 1.068194 CGTCTTCTCACCTCAGTCACC 60.068 57.143 0.00 0.00 0.00 4.02
4694 9585 1.667467 GCGTCTTCTCACCTCAGTCAC 60.667 57.143 0.00 0.00 0.00 3.67
4695 9586 0.598562 GCGTCTTCTCACCTCAGTCA 59.401 55.000 0.00 0.00 0.00 3.41
4696 9587 0.598562 TGCGTCTTCTCACCTCAGTC 59.401 55.000 0.00 0.00 0.00 3.51
4697 9588 0.315568 GTGCGTCTTCTCACCTCAGT 59.684 55.000 0.00 0.00 0.00 3.41
4698 9589 0.600557 AGTGCGTCTTCTCACCTCAG 59.399 55.000 0.00 0.00 33.90 3.35
4699 9590 0.315251 CAGTGCGTCTTCTCACCTCA 59.685 55.000 0.00 0.00 33.90 3.86
4700 9591 1.011451 GCAGTGCGTCTTCTCACCTC 61.011 60.000 0.00 0.00 33.90 3.85
4701 9592 1.005630 GCAGTGCGTCTTCTCACCT 60.006 57.895 0.00 0.00 33.90 4.00
4702 9593 2.029844 GGCAGTGCGTCTTCTCACC 61.030 63.158 9.45 0.00 33.90 4.02
4703 9594 2.375766 CGGCAGTGCGTCTTCTCAC 61.376 63.158 9.45 0.00 0.00 3.51
4704 9595 2.049156 CGGCAGTGCGTCTTCTCA 60.049 61.111 9.45 0.00 0.00 3.27
4705 9596 3.482783 GCGGCAGTGCGTCTTCTC 61.483 66.667 9.45 0.00 0.00 2.87
4742 9633 1.921869 ATACCTGGGTTTGGGCCTCG 61.922 60.000 4.53 0.00 0.00 4.63
4751 9642 1.342672 CCGCCCTACATACCTGGGTT 61.343 60.000 0.00 0.00 42.77 4.11
4800 9691 4.462508 TGTGAATTTCTTTTGGCACACA 57.537 36.364 0.00 0.00 39.29 3.72
4801 9692 4.777140 GTGTGAATTTCTTTTGGCACAC 57.223 40.909 0.00 0.00 45.90 3.82


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

AutoCloner maintained by Alex Coulton.