Multiple sequence alignment - TraesCS5D01G392000

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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 TraesCS5D01G392000 chr5D 100.000 4148 0 0 1 4148 460397047 460392900 0.000000e+00 7661.0
1 TraesCS5D01G392000 chr5D 91.722 302 21 2 2846 3143 460225444 460225745 2.310000e-112 416.0
2 TraesCS5D01G392000 chr5D 93.103 145 9 1 4004 4148 215255214 215255357 1.170000e-50 211.0
3 TraesCS5D01G392000 chr5D 95.918 98 3 1 3923 4019 139441012 139440915 1.540000e-34 158.0
4 TraesCS5D01G392000 chr5D 89.474 114 12 0 2481 2594 66755390 66755503 1.200000e-30 145.0
5 TraesCS5D01G392000 chr5D 83.784 111 18 0 2484 2594 457777065 457777175 5.670000e-19 106.0
6 TraesCS5D01G392000 chr5B 95.611 3828 93 30 243 4024 565932149 565928351 0.000000e+00 6069.0
7 TraesCS5D01G392000 chr5B 86.982 338 30 5 2838 3171 565897386 565897713 6.550000e-98 368.0
8 TraesCS5D01G392000 chr5B 89.434 265 18 3 2916 3171 565880099 565880362 4.000000e-85 326.0
9 TraesCS5D01G392000 chr5B 87.654 243 21 6 1 239 565932624 565932387 1.470000e-69 274.0
10 TraesCS5D01G392000 chr5B 95.238 105 4 1 3916 4019 166379079 166379183 9.230000e-37 165.0
11 TraesCS5D01G392000 chr5B 90.090 111 11 0 2484 2594 64266318 64266208 1.200000e-30 145.0
12 TraesCS5D01G392000 chr5B 83.784 111 18 0 2484 2594 559992112 559992222 5.670000e-19 106.0
13 TraesCS5D01G392000 chr5B 100.000 35 0 0 226 260 565932244 565932210 9.630000e-07 65.8
14 TraesCS5D01G392000 chr5A 93.590 4072 149 57 1 4025 580468416 580464410 0.000000e+00 5971.0
15 TraesCS5D01G392000 chr5A 85.246 305 24 10 2846 3144 580449588 580449877 1.130000e-75 294.0
16 TraesCS5D01G392000 chr5A 90.090 111 11 0 2484 2594 57376725 57376615 1.200000e-30 145.0
17 TraesCS5D01G392000 chr5A 97.727 44 1 0 2484 2527 575658477 575658520 4.450000e-10 76.8
18 TraesCS5D01G392000 chr3D 96.154 130 5 0 4019 4148 105119475 105119346 3.250000e-51 213.0
19 TraesCS5D01G392000 chr3D 94.161 137 6 2 4014 4148 556141154 556141018 1.510000e-49 207.0
20 TraesCS5D01G392000 chr3D 91.509 106 8 1 3922 4026 609983905 609983800 1.200000e-30 145.0
21 TraesCS5D01G392000 chr3D 96.429 56 2 0 2792 2847 134083624 134083679 4.420000e-15 93.5
22 TraesCS5D01G392000 chr2D 95.385 130 6 0 4019 4148 155440006 155439877 1.510000e-49 207.0
23 TraesCS5D01G392000 chr2B 96.032 126 5 0 4023 4148 689781886 689781761 5.440000e-49 206.0
24 TraesCS5D01G392000 chr2B 95.312 128 6 0 4021 4148 338749465 338749592 1.950000e-48 204.0
25 TraesCS5D01G392000 chr6D 96.000 125 5 0 4024 4148 109240318 109240442 1.950000e-48 204.0
26 TraesCS5D01G392000 chr6D 92.593 108 7 1 3921 4027 94768128 94768021 2.000000e-33 154.0
27 TraesCS5D01G392000 chr2A 94.030 134 8 0 4015 4148 398426101 398425968 1.950000e-48 204.0
28 TraesCS5D01G392000 chr7A 88.235 170 16 1 3983 4148 158665131 158664962 2.530000e-47 200.0
29 TraesCS5D01G392000 chr7B 94.845 97 4 1 3923 4018 162120908 162120812 2.580000e-32 150.0
30 TraesCS5D01G392000 chr3A 93.269 104 4 3 3918 4018 470095675 470095778 2.580000e-32 150.0
31 TraesCS5D01G392000 chr3A 93.814 97 5 1 3923 4018 12778806 12778902 1.200000e-30 145.0
32 TraesCS5D01G392000 chr3A 96.429 56 2 0 2792 2847 147791563 147791618 4.420000e-15 93.5
33 TraesCS5D01G392000 chr3B 96.429 56 2 0 2792 2847 190470961 190471016 4.420000e-15 93.5


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 TraesCS5D01G392000 chr5D 460392900 460397047 4147 True 7661.000000 7661 100.000000 1 4148 1 chr5D.!!$R2 4147
1 TraesCS5D01G392000 chr5B 565928351 565932624 4273 True 2136.266667 6069 94.421667 1 4024 3 chr5B.!!$R2 4023
2 TraesCS5D01G392000 chr5A 580464410 580468416 4006 True 5971.000000 5971 93.590000 1 4025 1 chr5A.!!$R2 4024

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
725 975 0.617249 CCCCACAGCCTTCTCTCTCT 60.617 60.0 0.0 0.0 0.0 3.10 F
2214 2517 0.251341 GAACCTCCAGCCACCATTGT 60.251 55.0 0.0 0.0 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2618 2928 0.401356 TCTTGCAGGTTCTGATGCCA 59.599 50.0 0.0 0.0 41.85 4.92 R
4025 4346 2.240493 ATATTTGCGAACGGAGGGAG 57.760 50.0 0.0 0.0 0.00 4.30 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
64 65 6.644592 GCCATCACTTTAGTATCACTCTCATC 59.355 42.308 0.00 0.00 0.00 2.92
76 77 3.812609 TCACTCTCATCGATGCTCTAGAC 59.187 47.826 20.81 0.00 0.00 2.59
83 85 7.716612 TCTCATCGATGCTCTAGACAAATAAA 58.283 34.615 20.81 0.00 0.00 1.40
109 111 3.006323 ACAAGTTCAAGCACACAACCAAA 59.994 39.130 0.00 0.00 0.00 3.28
111 113 4.264460 AGTTCAAGCACACAACCAAAAA 57.736 36.364 0.00 0.00 0.00 1.94
157 159 6.435430 TTCACCCGATTTTCATAATCAGTG 57.565 37.500 0.00 0.00 34.48 3.66
161 163 4.261322 CCCGATTTTCATAATCAGTGCCTG 60.261 45.833 0.00 0.00 0.00 4.85
331 572 7.038659 TGGACCAAAAATAATCCTTAAATGCG 58.961 34.615 0.00 0.00 32.06 4.73
346 587 4.385244 AAATGCGTCGACTAAAACTCAC 57.615 40.909 14.70 0.00 0.00 3.51
386 627 3.261643 ACACTGTGACAATGGATAGCTGA 59.738 43.478 15.86 0.00 0.00 4.26
455 697 7.170998 GGTGACTAATTATATTTCGACCCACTG 59.829 40.741 0.00 0.00 0.00 3.66
526 773 5.612725 AACATTCACCCTGTTGACATTTT 57.387 34.783 0.00 0.00 35.57 1.82
560 808 0.693049 AAGTTGGTAGGCCTCCACAG 59.307 55.000 19.83 0.00 34.45 3.66
565 813 1.481056 GGTAGGCCTCCACAGTGTGT 61.481 60.000 21.48 4.85 0.00 3.72
715 965 1.626825 TGTTCTAGTAACCCCACAGCC 59.373 52.381 0.00 0.00 0.00 4.85
716 966 1.907255 GTTCTAGTAACCCCACAGCCT 59.093 52.381 0.00 0.00 0.00 4.58
724 974 0.907230 ACCCCACAGCCTTCTCTCTC 60.907 60.000 0.00 0.00 0.00 3.20
725 975 0.617249 CCCCACAGCCTTCTCTCTCT 60.617 60.000 0.00 0.00 0.00 3.10
726 976 0.823460 CCCACAGCCTTCTCTCTCTC 59.177 60.000 0.00 0.00 0.00 3.20
727 977 1.619432 CCCACAGCCTTCTCTCTCTCT 60.619 57.143 0.00 0.00 0.00 3.10
728 978 1.750778 CCACAGCCTTCTCTCTCTCTC 59.249 57.143 0.00 0.00 0.00 3.20
729 979 2.621407 CCACAGCCTTCTCTCTCTCTCT 60.621 54.545 0.00 0.00 0.00 3.10
835 1087 1.003696 CCCAGTTCTTGGTTCCTCTCC 59.996 57.143 0.00 0.00 46.25 3.71
868 1120 3.846588 ACCACCATCTCCTAATCACAAGT 59.153 43.478 0.00 0.00 0.00 3.16
1297 1564 8.911662 CATTTCGTTAGTTTTTAACTTGGATGG 58.088 33.333 0.00 0.00 42.81 3.51
1299 1566 8.674263 TTCGTTAGTTTTTAACTTGGATGGTA 57.326 30.769 0.00 0.00 42.81 3.25
1309 1576 9.945904 TTTTAACTTGGATGGTAGTTTTGTTTT 57.054 25.926 0.00 0.00 36.16 2.43
1344 1615 9.173939 CATAGCATCGAGTAATTTGATTTTTCC 57.826 33.333 0.00 0.00 0.00 3.13
1382 1653 6.676632 TGGAACCTGATTATCTCCTTTCCTTA 59.323 38.462 12.85 0.00 33.75 2.69
1400 1671 4.949856 TCCTTATCTTTCCATTCTGGTTGC 59.050 41.667 0.00 0.00 39.03 4.17
1505 1789 7.448777 GGAACCTGATTAATTATCTCCTTTCCC 59.551 40.741 0.00 0.00 34.17 3.97
1882 2169 3.551046 CGGTACATACATGTCAGAGAGGC 60.551 52.174 0.00 0.00 41.97 4.70
1883 2170 2.879002 ACATACATGTCAGAGAGGCG 57.121 50.000 0.00 0.00 35.87 5.52
1896 2183 3.311871 CAGAGAGGCGAAGAAAATGATGG 59.688 47.826 0.00 0.00 0.00 3.51
1946 2234 3.057033 CAGATTCCACTGCAAAAGGAAGG 60.057 47.826 16.35 7.72 43.99 3.46
1956 2254 4.702831 TGCAAAAGGAAGGGTTTCATTTC 58.297 39.130 1.14 0.00 44.03 2.17
1986 2285 6.308371 TGAAAACGGAGAAATGTTTAGTCC 57.692 37.500 0.00 0.00 37.31 3.85
2085 2387 6.861055 GCCGTTTCAATTATACACCATAATGG 59.139 38.462 0.00 0.00 45.02 3.16
2100 2402 4.816385 CCATAATGGTAGTGGTACTGCTTG 59.184 45.833 0.00 0.00 31.18 4.01
2107 2409 3.927555 TGGTACTGCTTGCTACCAC 57.072 52.632 8.94 0.00 37.98 4.16
2108 2410 0.323629 TGGTACTGCTTGCTACCACC 59.676 55.000 8.94 5.03 37.98 4.61
2109 2411 0.323629 GGTACTGCTTGCTACCACCA 59.676 55.000 6.28 0.00 33.72 4.17
2162 2465 4.722700 GGAGCTGGCTGCCGGAAA 62.723 66.667 31.08 3.70 44.23 3.13
2180 2483 4.374707 CGGAAAGAATATAGTAACGTGCGC 60.375 45.833 0.00 0.00 0.00 6.09
2214 2517 0.251341 GAACCTCCAGCCACCATTGT 60.251 55.000 0.00 0.00 0.00 2.71
2273 2576 6.011981 TGGGTTGGACTTGGAACTAGATTATT 60.012 38.462 0.00 0.00 0.00 1.40
2275 2578 7.067129 GGGTTGGACTTGGAACTAGATTATTTC 59.933 40.741 0.00 0.00 0.00 2.17
2323 2627 4.854291 TGTAAATTTGTGGCTAATTTCGCG 59.146 37.500 0.00 0.00 36.75 5.87
2530 2840 2.110967 CCTGCGCAAGGTGGATCTG 61.111 63.158 13.05 0.00 41.74 2.90
2618 2928 1.203994 CTGGTAAGATCCGTCACCGTT 59.796 52.381 0.00 0.00 33.55 4.44
2653 2963 4.025015 GCAAGAGCATGTTATCAACTGG 57.975 45.455 0.00 0.00 41.58 4.00
2673 2983 3.192422 TGGTGTTAATGATTTTGCCTCGG 59.808 43.478 0.00 0.00 0.00 4.63
2675 2985 3.088532 TGTTAATGATTTTGCCTCGGCT 58.911 40.909 9.65 0.00 42.51 5.52
2676 2986 3.119531 TGTTAATGATTTTGCCTCGGCTG 60.120 43.478 9.65 0.00 42.51 4.85
2677 2987 0.819582 AATGATTTTGCCTCGGCTGG 59.180 50.000 9.65 0.00 42.51 4.85
2708 3018 6.945435 TGGATGGAGCTTAGTTTGAATTAACA 59.055 34.615 0.00 0.00 0.00 2.41
2715 3025 5.342259 GCTTAGTTTGAATTAACAAGTGCCG 59.658 40.000 0.00 0.00 0.00 5.69
3172 3486 1.909986 GGGGCAGTAAGAGGAAGACTT 59.090 52.381 0.00 0.00 0.00 3.01
3906 4220 5.958955 AGAAATGAACTGCTTAAAGGATGC 58.041 37.500 0.00 0.00 0.00 3.91
3947 4267 4.985538 TCCCTCCAATCCATAATAAGTGC 58.014 43.478 0.00 0.00 0.00 4.40
4025 4346 2.273538 TCGGAGGGAGTAGCATCTAC 57.726 55.000 0.00 0.00 0.00 2.59
4026 4347 1.775459 TCGGAGGGAGTAGCATCTACT 59.225 52.381 6.24 6.24 0.00 2.57
4027 4348 2.156098 CGGAGGGAGTAGCATCTACTC 58.844 57.143 20.17 20.17 42.28 2.59
4033 4354 2.156098 GAGTAGCATCTACTCCCTCCG 58.844 57.143 18.47 0.00 38.33 4.63
4034 4355 1.495574 AGTAGCATCTACTCCCTCCGT 59.504 52.381 0.94 0.00 0.00 4.69
4035 4356 2.091775 AGTAGCATCTACTCCCTCCGTT 60.092 50.000 0.94 0.00 0.00 4.44
4036 4357 1.404843 AGCATCTACTCCCTCCGTTC 58.595 55.000 0.00 0.00 0.00 3.95
4037 4358 0.030908 GCATCTACTCCCTCCGTTCG 59.969 60.000 0.00 0.00 0.00 3.95
4038 4359 0.030908 CATCTACTCCCTCCGTTCGC 59.969 60.000 0.00 0.00 0.00 4.70
4039 4360 0.395311 ATCTACTCCCTCCGTTCGCA 60.395 55.000 0.00 0.00 0.00 5.10
4040 4361 0.609957 TCTACTCCCTCCGTTCGCAA 60.610 55.000 0.00 0.00 0.00 4.85
4041 4362 0.245539 CTACTCCCTCCGTTCGCAAA 59.754 55.000 0.00 0.00 0.00 3.68
4042 4363 0.899720 TACTCCCTCCGTTCGCAAAT 59.100 50.000 0.00 0.00 0.00 2.32
4043 4364 0.899720 ACTCCCTCCGTTCGCAAATA 59.100 50.000 0.00 0.00 0.00 1.40
4044 4365 1.485066 ACTCCCTCCGTTCGCAAATAT 59.515 47.619 0.00 0.00 0.00 1.28
4045 4366 2.696707 ACTCCCTCCGTTCGCAAATATA 59.303 45.455 0.00 0.00 0.00 0.86
4046 4367 3.133362 ACTCCCTCCGTTCGCAAATATAA 59.867 43.478 0.00 0.00 0.00 0.98
4047 4368 3.724374 TCCCTCCGTTCGCAAATATAAG 58.276 45.455 0.00 0.00 0.00 1.73
4048 4369 3.133362 TCCCTCCGTTCGCAAATATAAGT 59.867 43.478 0.00 0.00 0.00 2.24
4049 4370 3.493503 CCCTCCGTTCGCAAATATAAGTC 59.506 47.826 0.00 0.00 0.00 3.01
4050 4371 4.369182 CCTCCGTTCGCAAATATAAGTCT 58.631 43.478 0.00 0.00 0.00 3.24
4051 4372 4.809426 CCTCCGTTCGCAAATATAAGTCTT 59.191 41.667 0.00 0.00 0.00 3.01
4052 4373 5.293569 CCTCCGTTCGCAAATATAAGTCTTT 59.706 40.000 0.00 0.00 0.00 2.52
4053 4374 6.340537 TCCGTTCGCAAATATAAGTCTTTC 57.659 37.500 0.00 0.00 0.00 2.62
4054 4375 6.103997 TCCGTTCGCAAATATAAGTCTTTCT 58.896 36.000 0.00 0.00 0.00 2.52
4055 4376 7.259882 TCCGTTCGCAAATATAAGTCTTTCTA 58.740 34.615 0.00 0.00 0.00 2.10
4056 4377 7.434307 TCCGTTCGCAAATATAAGTCTTTCTAG 59.566 37.037 0.00 0.00 0.00 2.43
4057 4378 7.434307 CCGTTCGCAAATATAAGTCTTTCTAGA 59.566 37.037 0.00 0.00 0.00 2.43
4058 4379 8.969267 CGTTCGCAAATATAAGTCTTTCTAGAT 58.031 33.333 0.00 0.00 31.86 1.98
4071 4392 9.442047 AAGTCTTTCTAGATATTCCAACAAGTG 57.558 33.333 0.00 0.00 31.86 3.16
4072 4393 8.816894 AGTCTTTCTAGATATTCCAACAAGTGA 58.183 33.333 0.00 0.00 31.86 3.41
4073 4394 8.874816 GTCTTTCTAGATATTCCAACAAGTGAC 58.125 37.037 0.00 0.00 31.86 3.67
4074 4395 8.816894 TCTTTCTAGATATTCCAACAAGTGACT 58.183 33.333 0.00 0.00 0.00 3.41
4076 4397 9.871238 TTTCTAGATATTCCAACAAGTGACTAC 57.129 33.333 0.00 0.00 0.00 2.73
4077 4398 8.589701 TCTAGATATTCCAACAAGTGACTACA 57.410 34.615 0.00 0.00 0.00 2.74
4078 4399 9.201989 TCTAGATATTCCAACAAGTGACTACAT 57.798 33.333 0.00 0.00 0.00 2.29
4081 4402 7.921214 AGATATTCCAACAAGTGACTACATACG 59.079 37.037 0.00 0.00 0.00 3.06
4082 4403 4.182693 TCCAACAAGTGACTACATACGG 57.817 45.455 0.00 0.00 0.00 4.02
4083 4404 3.827876 TCCAACAAGTGACTACATACGGA 59.172 43.478 0.00 0.00 0.00 4.69
4084 4405 4.082408 TCCAACAAGTGACTACATACGGAG 60.082 45.833 0.00 0.00 0.00 4.63
4085 4406 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
4086 4407 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
4087 4408 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
4088 4409 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
4089 4410 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
4090 4411 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
4091 4412 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
4092 4413 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
4093 4414 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
4094 4415 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
4095 4416 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
4096 4417 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
4097 4418 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
4098 4419 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
4099 4420 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
4100 4421 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
4101 4422 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
4102 4423 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
4103 4424 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
4104 4425 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
4117 4438 8.723942 AGTGAATCTACACTCCAAAATATGTC 57.276 34.615 0.00 0.00 46.36 3.06
4118 4439 8.543774 AGTGAATCTACACTCCAAAATATGTCT 58.456 33.333 0.00 0.00 46.36 3.41
4119 4440 9.817809 GTGAATCTACACTCCAAAATATGTCTA 57.182 33.333 0.00 0.00 37.73 2.59
4120 4441 9.817809 TGAATCTACACTCCAAAATATGTCTAC 57.182 33.333 0.00 0.00 0.00 2.59
4121 4442 9.817809 GAATCTACACTCCAAAATATGTCTACA 57.182 33.333 0.00 0.00 0.00 2.74
4127 4448 9.547753 ACACTCCAAAATATGTCTACATACATC 57.452 33.333 4.98 0.00 41.15 3.06
4128 4449 8.993121 CACTCCAAAATATGTCTACATACATCC 58.007 37.037 4.98 0.00 41.15 3.51
4129 4450 7.872993 ACTCCAAAATATGTCTACATACATCCG 59.127 37.037 4.98 0.00 41.15 4.18
4130 4451 7.732025 TCCAAAATATGTCTACATACATCCGT 58.268 34.615 4.98 0.00 41.15 4.69
4131 4452 8.862085 TCCAAAATATGTCTACATACATCCGTA 58.138 33.333 4.98 0.00 41.15 4.02
4132 4453 9.653287 CCAAAATATGTCTACATACATCCGTAT 57.347 33.333 4.98 0.00 41.15 3.06
4143 4464 5.838529 CATACATCCGTATGTTGTAGTCCA 58.161 41.667 0.00 0.00 46.70 4.02
4144 4465 6.455647 CATACATCCGTATGTTGTAGTCCAT 58.544 40.000 0.00 0.00 46.70 3.41
4145 4466 5.353394 ACATCCGTATGTTGTAGTCCATT 57.647 39.130 0.00 0.00 44.07 3.16
4146 4467 5.741011 ACATCCGTATGTTGTAGTCCATTT 58.259 37.500 0.00 0.00 44.07 2.32
4147 4468 5.584649 ACATCCGTATGTTGTAGTCCATTTG 59.415 40.000 0.00 0.00 44.07 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 7.168219 AGTGATACTAAAGTGATGGCAAGAAA 58.832 34.615 0.00 0.00 0.00 2.52
64 65 8.352752 TGTGTATTTATTTGTCTAGAGCATCG 57.647 34.615 0.00 0.00 42.67 3.84
76 77 8.479280 GTGTGCTTGAACTTGTGTATTTATTTG 58.521 33.333 0.00 0.00 0.00 2.32
83 85 4.202010 GGTTGTGTGCTTGAACTTGTGTAT 60.202 41.667 0.00 0.00 0.00 2.29
221 224 9.394767 TGAGTTGTTGCAGTTATCACATATATT 57.605 29.630 0.00 0.00 0.00 1.28
331 572 2.067013 GGCCTGTGAGTTTTAGTCGAC 58.933 52.381 7.70 7.70 0.00 4.20
346 587 2.030805 GTGTTTAGCTCTTTGTGGCCTG 60.031 50.000 3.32 0.00 0.00 4.85
386 627 2.596631 CTGCAGGCTGCTGGTGTT 60.597 61.111 36.50 0.00 45.31 3.32
396 637 2.203181 GGGAGATGAGCTGCAGGC 60.203 66.667 17.12 7.98 36.54 4.85
526 773 3.780294 ACCAACTTGGATCCAGTGCTATA 59.220 43.478 15.53 0.00 40.96 1.31
565 813 0.382515 GTTGCCGTGTTGCCAGTTAA 59.617 50.000 0.00 0.00 0.00 2.01
645 893 2.507407 TGGAGGTTGGAGCCAATAAC 57.493 50.000 5.09 0.00 38.28 1.89
715 965 3.202151 AGGGTGGTAGAGAGAGAGAGAAG 59.798 52.174 0.00 0.00 0.00 2.85
716 966 3.194620 AGGGTGGTAGAGAGAGAGAGAA 58.805 50.000 0.00 0.00 0.00 2.87
724 974 1.342076 TGCTGGTAGGGTGGTAGAGAG 60.342 57.143 0.00 0.00 0.00 3.20
725 975 0.708209 TGCTGGTAGGGTGGTAGAGA 59.292 55.000 0.00 0.00 0.00 3.10
726 976 1.115467 CTGCTGGTAGGGTGGTAGAG 58.885 60.000 0.00 0.00 0.00 2.43
727 977 0.708209 TCTGCTGGTAGGGTGGTAGA 59.292 55.000 0.00 0.00 0.00 2.59
728 978 1.115467 CTCTGCTGGTAGGGTGGTAG 58.885 60.000 0.00 0.00 0.00 3.18
729 979 0.976073 GCTCTGCTGGTAGGGTGGTA 60.976 60.000 0.00 0.00 0.00 3.25
835 1087 0.035056 GATGGTGGTGGTGGAAGAGG 60.035 60.000 0.00 0.00 0.00 3.69
868 1120 3.023832 TCTCTCCGTGTATGCAAGATGA 58.976 45.455 0.00 0.00 0.00 2.92
1353 1624 6.581388 AAGGAGATAATCAGGTTCCATTCA 57.419 37.500 0.00 0.00 0.00 2.57
1400 1671 6.317140 TCTGCACTTATGGATCTTTTGCTAAG 59.683 38.462 0.00 0.00 0.00 2.18
1474 1758 6.128172 GGAGATAATTAATCAGGTTCCATGCG 60.128 42.308 0.00 0.00 37.03 4.73
1505 1789 6.974965 AGCTAAACAACCAGAATGAAAAGAG 58.025 36.000 0.00 0.00 39.69 2.85
1882 2169 5.030295 GTGTATGCACCATCATTTTCTTCG 58.970 41.667 1.96 0.00 39.61 3.79
1883 2170 6.199937 AGTGTATGCACCATCATTTTCTTC 57.800 37.500 10.59 0.00 46.35 2.87
1896 2183 4.202441 AGATGGATGGAAAGTGTATGCAC 58.798 43.478 5.71 5.71 45.57 4.57
1946 2234 5.402270 CGTTTTCATCACAGGAAATGAAACC 59.598 40.000 9.38 3.44 46.23 3.27
1956 2254 4.216257 ACATTTCTCCGTTTTCATCACAGG 59.784 41.667 0.00 0.00 0.00 4.00
1986 2285 4.221703 AGCCCCAATCATCTATCTTCTACG 59.778 45.833 0.00 0.00 0.00 3.51
2085 2387 2.232941 TGGTAGCAAGCAGTACCACTAC 59.767 50.000 8.59 0.00 43.10 2.73
2100 2402 2.163613 GTGGCAACTTTATGGTGGTAGC 59.836 50.000 0.00 0.00 33.01 3.58
2132 2435 2.612672 GCCAGCTCCGTTTAACTAATCC 59.387 50.000 0.00 0.00 0.00 3.01
2162 2465 3.614159 TCGCGCACGTTACTATATTCT 57.386 42.857 8.75 0.00 41.18 2.40
2180 2483 1.615883 AGGTTCCATCCATCTCGATCG 59.384 52.381 9.36 9.36 0.00 3.69
2273 2576 3.243035 CCACTTGCAAATCAGTTCGTGAA 60.243 43.478 11.49 0.00 39.19 3.18
2275 2578 2.033299 ACCACTTGCAAATCAGTTCGTG 59.967 45.455 0.00 2.33 0.00 4.35
2323 2627 1.082117 CCCTGGTCGACGCATAACAC 61.082 60.000 9.92 0.00 0.00 3.32
2530 2840 5.638234 GTCCTTGTAGGTGTTGTACATCTTC 59.362 44.000 0.00 0.00 35.73 2.87
2618 2928 0.401356 TCTTGCAGGTTCTGATGCCA 59.599 50.000 0.00 0.00 41.85 4.92
2642 2952 8.647226 GCAAAATCATTAACACCAGTTGATAAC 58.353 33.333 0.00 0.00 38.69 1.89
2652 2962 3.769536 CCGAGGCAAAATCATTAACACC 58.230 45.455 0.00 0.00 0.00 4.16
2653 2963 3.119495 AGCCGAGGCAAAATCATTAACAC 60.119 43.478 17.18 0.00 44.88 3.32
2673 2983 0.536006 GCTCCATCCATACCACCAGC 60.536 60.000 0.00 0.00 0.00 4.85
2675 2985 1.595311 AAGCTCCATCCATACCACCA 58.405 50.000 0.00 0.00 0.00 4.17
2676 2986 2.706190 ACTAAGCTCCATCCATACCACC 59.294 50.000 0.00 0.00 0.00 4.61
2677 2987 4.423625 AACTAAGCTCCATCCATACCAC 57.576 45.455 0.00 0.00 0.00 4.16
2708 3018 1.538047 AGTTGATGATTGCGGCACTT 58.462 45.000 0.05 0.00 0.00 3.16
3906 4220 8.328758 TGGAGGGAGTATTTTATAGGCATAATG 58.671 37.037 0.00 0.00 0.00 1.90
3947 4267 3.314080 TCAACCTTAGTTCAAAACTGCGG 59.686 43.478 2.65 0.00 42.84 5.69
3990 4311 4.384208 CCCTCCGATCCAAAATAAGTGTCT 60.384 45.833 0.00 0.00 0.00 3.41
4025 4346 2.240493 ATATTTGCGAACGGAGGGAG 57.760 50.000 0.00 0.00 0.00 4.30
4026 4347 3.133362 ACTTATATTTGCGAACGGAGGGA 59.867 43.478 0.00 0.00 0.00 4.20
4027 4348 3.463944 ACTTATATTTGCGAACGGAGGG 58.536 45.455 0.00 0.00 0.00 4.30
4028 4349 4.369182 AGACTTATATTTGCGAACGGAGG 58.631 43.478 0.00 0.00 0.00 4.30
4029 4350 5.968387 AAGACTTATATTTGCGAACGGAG 57.032 39.130 0.00 0.00 0.00 4.63
4030 4351 6.103997 AGAAAGACTTATATTTGCGAACGGA 58.896 36.000 0.00 0.00 0.00 4.69
4031 4352 6.345920 AGAAAGACTTATATTTGCGAACGG 57.654 37.500 0.00 0.00 0.00 4.44
4032 4353 8.336498 TCTAGAAAGACTTATATTTGCGAACG 57.664 34.615 0.00 0.00 0.00 3.95
4045 4366 9.442047 CACTTGTTGGAATATCTAGAAAGACTT 57.558 33.333 0.00 0.00 33.57 3.01
4046 4367 8.816894 TCACTTGTTGGAATATCTAGAAAGACT 58.183 33.333 0.00 0.00 33.57 3.24
4047 4368 8.874816 GTCACTTGTTGGAATATCTAGAAAGAC 58.125 37.037 0.00 0.00 33.57 3.01
4048 4369 8.816894 AGTCACTTGTTGGAATATCTAGAAAGA 58.183 33.333 0.00 0.00 35.80 2.52
4050 4371 9.871238 GTAGTCACTTGTTGGAATATCTAGAAA 57.129 33.333 0.00 0.00 0.00 2.52
4051 4372 9.031537 TGTAGTCACTTGTTGGAATATCTAGAA 57.968 33.333 0.00 0.00 0.00 2.10
4052 4373 8.589701 TGTAGTCACTTGTTGGAATATCTAGA 57.410 34.615 0.00 0.00 0.00 2.43
4055 4376 7.921214 CGTATGTAGTCACTTGTTGGAATATCT 59.079 37.037 0.00 0.00 0.00 1.98
4056 4377 7.169308 CCGTATGTAGTCACTTGTTGGAATATC 59.831 40.741 0.00 0.00 0.00 1.63
4057 4378 6.984474 CCGTATGTAGTCACTTGTTGGAATAT 59.016 38.462 0.00 0.00 0.00 1.28
4058 4379 6.153170 TCCGTATGTAGTCACTTGTTGGAATA 59.847 38.462 0.00 0.00 0.00 1.75
4059 4380 5.046878 TCCGTATGTAGTCACTTGTTGGAAT 60.047 40.000 0.00 0.00 0.00 3.01
4060 4381 4.281435 TCCGTATGTAGTCACTTGTTGGAA 59.719 41.667 0.00 0.00 0.00 3.53
4061 4382 3.827876 TCCGTATGTAGTCACTTGTTGGA 59.172 43.478 0.00 0.00 0.00 3.53
4062 4383 4.174009 CTCCGTATGTAGTCACTTGTTGG 58.826 47.826 0.00 0.00 0.00 3.77
4063 4384 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
4064 4385 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
4065 4386 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
4066 4387 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
4067 4388 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
4068 4389 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
4069 4390 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
4070 4391 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
4071 4392 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
4072 4393 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
4073 4394 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
4074 4395 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
4075 4396 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
4076 4397 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
4077 4398 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
4078 4399 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
4079 4400 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
4080 4401 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
4081 4402 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
4082 4403 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
4093 4414 8.723942 AGACATATTTTGGAGTGTAGATTCAC 57.276 34.615 0.00 0.00 38.46 3.18
4094 4415 9.817809 GTAGACATATTTTGGAGTGTAGATTCA 57.182 33.333 0.00 0.00 0.00 2.57
4095 4416 9.817809 TGTAGACATATTTTGGAGTGTAGATTC 57.182 33.333 0.00 0.00 0.00 2.52
4101 4422 9.547753 GATGTATGTAGACATATTTTGGAGTGT 57.452 33.333 5.69 0.00 40.18 3.55
4102 4423 8.993121 GGATGTATGTAGACATATTTTGGAGTG 58.007 37.037 5.69 0.00 40.18 3.51
4103 4424 7.872993 CGGATGTATGTAGACATATTTTGGAGT 59.127 37.037 5.69 0.00 40.18 3.85
4104 4425 7.872993 ACGGATGTATGTAGACATATTTTGGAG 59.127 37.037 5.69 0.00 40.18 3.86
4105 4426 7.732025 ACGGATGTATGTAGACATATTTTGGA 58.268 34.615 5.69 0.00 40.18 3.53
4106 4427 7.962964 ACGGATGTATGTAGACATATTTTGG 57.037 36.000 5.69 0.21 40.18 3.28
4121 4442 6.665992 ATGGACTACAACATACGGATGTAT 57.334 37.500 15.10 8.21 45.93 2.29
4122 4443 6.474140 AATGGACTACAACATACGGATGTA 57.526 37.500 15.10 0.00 45.93 2.29
4124 4445 6.048073 CAAATGGACTACAACATACGGATG 57.952 41.667 5.94 5.94 39.16 3.51


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

AutoCloner maintained by Alex Coulton.