Multiple sequence alignment - TraesCS3D01G325400

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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 TraesCS3D01G325400 chr3D 100.000 3740 0 0 1 3740 438267230 438263491 0.000000e+00 6907.0
1 TraesCS3D01G325400 chr3D 80.303 264 31 16 3242 3491 373806322 373806578 2.970000e-41 180.0
2 TraesCS3D01G325400 chr3A 91.818 2982 136 55 279 3201 576606502 576603570 0.000000e+00 4056.0
3 TraesCS3D01G325400 chr3A 91.593 226 16 3 1 224 576607350 576607126 3.630000e-80 309.0
4 TraesCS3D01G325400 chr3B 92.000 1925 97 28 1205 3094 573620826 573618924 0.000000e+00 2649.0
5 TraesCS3D01G325400 chr3B 96.955 821 22 2 379 1199 573621821 573621004 0.000000e+00 1375.0
6 TraesCS3D01G325400 chr3B 93.639 393 24 1 1 393 573641032 573640641 1.500000e-163 586.0
7 TraesCS3D01G325400 chr3B 91.667 60 0 1 3671 3730 466635005 466635059 1.110000e-10 78.7
8 TraesCS3D01G325400 chr5D 96.693 514 15 1 3227 3740 331210715 331211226 0.000000e+00 854.0
9 TraesCS3D01G325400 chr5D 95.833 456 17 1 3287 3740 381781846 381782301 0.000000e+00 736.0
10 TraesCS3D01G325400 chr7D 96.825 504 12 2 3240 3740 83375315 83375817 0.000000e+00 839.0
11 TraesCS3D01G325400 chr7D 96.721 366 11 1 3244 3609 492136149 492136513 3.190000e-170 608.0
12 TraesCS3D01G325400 chr5A 93.775 498 27 2 3243 3740 377929511 377929018 0.000000e+00 745.0
13 TraesCS3D01G325400 chr5A 92.105 494 37 2 3247 3740 11690180 11690671 0.000000e+00 695.0
14 TraesCS3D01G325400 chr1A 95.205 438 16 2 3303 3740 93392151 93391719 0.000000e+00 688.0
15 TraesCS3D01G325400 chr1A 79.513 986 143 45 1618 2573 500960864 500961820 0.000000e+00 647.0
16 TraesCS3D01G325400 chr1A 88.636 176 18 2 1025 1199 500960453 500960627 2.930000e-51 213.0
17 TraesCS3D01G325400 chr5B 93.860 456 23 3 3278 3733 480245018 480245468 0.000000e+00 682.0
18 TraesCS3D01G325400 chr6B 91.207 489 43 0 3245 3733 514103613 514104101 0.000000e+00 665.0
19 TraesCS3D01G325400 chr1D 79.065 984 157 35 1618 2579 405402366 405403322 6.820000e-177 630.0
20 TraesCS3D01G325400 chr1D 78.772 391 57 24 2139 2508 348671852 348671467 4.830000e-59 239.0
21 TraesCS3D01G325400 chr1D 86.932 176 21 2 1025 1199 405401950 405402124 2.950000e-46 196.0
22 TraesCS3D01G325400 chr1B 78.803 986 154 41 1618 2579 545461751 545462705 2.470000e-171 612.0
23 TraesCS3D01G325400 chr1B 79.540 391 54 23 2139 2508 470307332 470306947 4.790000e-64 255.0
24 TraesCS3D01G325400 chr1B 88.701 177 16 4 1025 1199 545461313 545461487 2.930000e-51 213.0


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 TraesCS3D01G325400 chr3D 438263491 438267230 3739 True 6907.0 6907 100.0000 1 3740 1 chr3D.!!$R1 3739
1 TraesCS3D01G325400 chr3A 576603570 576607350 3780 True 2182.5 4056 91.7055 1 3201 2 chr3A.!!$R1 3200
2 TraesCS3D01G325400 chr3B 573618924 573621821 2897 True 2012.0 2649 94.4775 379 3094 2 chr3B.!!$R2 2715
3 TraesCS3D01G325400 chr5D 331210715 331211226 511 False 854.0 854 96.6930 3227 3740 1 chr5D.!!$F1 513
4 TraesCS3D01G325400 chr7D 83375315 83375817 502 False 839.0 839 96.8250 3240 3740 1 chr7D.!!$F1 500
5 TraesCS3D01G325400 chr1A 500960453 500961820 1367 False 430.0 647 84.0745 1025 2573 2 chr1A.!!$F1 1548
6 TraesCS3D01G325400 chr1D 405401950 405403322 1372 False 413.0 630 82.9985 1025 2579 2 chr1D.!!$F1 1554
7 TraesCS3D01G325400 chr1B 545461313 545462705 1392 False 412.5 612 83.7520 1025 2579 2 chr1B.!!$F1 1554

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
217 220 0.875059 CCGGCAAACTCTCCAGAAAC 59.125 55.0 0.0 0.0 0.00 2.78 F
336 910 0.957395 CAACCACTAGCTGGCCACTG 60.957 60.0 0.0 0.0 45.32 3.66 F
1485 2245 0.033796 ACTCCAATACGGGGACTCGA 60.034 55.0 0.0 0.0 37.51 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1475 2235 0.317479 ACAAAAGAGTCGAGTCCCCG 59.683 55.0 16.67 5.91 0.00 5.73 R
1710 2522 1.431488 CCATCACGAAGGTCATGGCG 61.431 60.0 0.00 0.00 29.71 5.69 R
3224 4158 0.106708 AGCTGCTTCGTTCAGTTCCA 59.893 50.0 0.00 0.00 34.21 3.53 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
45 46 6.084326 ACATGTGTTACCCAATTTTCTGAC 57.916 37.500 0.00 0.00 0.00 3.51
47 48 3.566322 TGTGTTACCCAATTTTCTGACCG 59.434 43.478 0.00 0.00 0.00 4.79
51 52 3.223674 ACCCAATTTTCTGACCGTTCT 57.776 42.857 0.00 0.00 0.00 3.01
54 55 3.758554 CCCAATTTTCTGACCGTTCTGAT 59.241 43.478 0.00 0.00 30.46 2.90
198 200 2.670414 CGTCTGAAATGAGTCTGCCTTC 59.330 50.000 0.00 0.00 0.00 3.46
217 220 0.875059 CCGGCAAACTCTCCAGAAAC 59.125 55.000 0.00 0.00 0.00 2.78
224 227 2.599408 ACTCTCCAGAAACCTACCGA 57.401 50.000 0.00 0.00 0.00 4.69
226 229 3.442076 ACTCTCCAGAAACCTACCGAAT 58.558 45.455 0.00 0.00 0.00 3.34
227 230 3.195825 ACTCTCCAGAAACCTACCGAATG 59.804 47.826 0.00 0.00 0.00 2.67
228 231 3.170717 TCTCCAGAAACCTACCGAATGT 58.829 45.455 0.00 0.00 0.00 2.71
229 232 3.194968 TCTCCAGAAACCTACCGAATGTC 59.805 47.826 0.00 0.00 0.00 3.06
230 233 2.901192 TCCAGAAACCTACCGAATGTCA 59.099 45.455 0.00 0.00 0.00 3.58
231 234 3.517901 TCCAGAAACCTACCGAATGTCAT 59.482 43.478 0.00 0.00 0.00 3.06
255 321 7.913674 TTTTTGGTGAAAGCTTACAAAACAT 57.086 28.000 20.94 0.00 39.76 2.71
256 322 9.606631 ATTTTTGGTGAAAGCTTACAAAACATA 57.393 25.926 20.94 12.93 39.76 2.29
336 910 0.957395 CAACCACTAGCTGGCCACTG 60.957 60.000 0.00 0.00 45.32 3.66
354 928 3.068590 CACTGGCAATTGTTTCTGGAACT 59.931 43.478 7.40 0.00 39.08 3.01
355 929 3.068590 ACTGGCAATTGTTTCTGGAACTG 59.931 43.478 7.40 0.00 39.08 3.16
357 931 2.224018 GGCAATTGTTTCTGGAACTGCA 60.224 45.455 7.40 0.00 38.18 4.41
464 1040 4.925646 GTGATGATTTCTTTGCCTTCCAAC 59.074 41.667 0.00 0.00 31.97 3.77
656 1232 6.238842 CCAGATTAACATGGCAGAAGGTAATG 60.239 42.308 11.01 0.00 0.00 1.90
657 1233 6.543465 CAGATTAACATGGCAGAAGGTAATGA 59.457 38.462 11.01 0.00 0.00 2.57
697 1273 2.019249 ACAGATGATCCCAACAATGCG 58.981 47.619 0.00 0.00 0.00 4.73
875 1451 2.079925 CAACTCAAGGTCTAGCTTGGC 58.920 52.381 18.83 0.00 0.00 4.52
962 1538 5.965091 ACTTATCCTCTAGTTAACCAAGGCT 59.035 40.000 0.88 1.51 0.00 4.58
987 1563 2.012673 CAGCCAGCAAGAAGTACCATC 58.987 52.381 0.00 0.00 0.00 3.51
1199 1779 4.765856 TGCCCTAATTCTCGAGAGGTATAC 59.234 45.833 15.94 4.97 0.00 1.47
1200 1780 4.142643 GCCCTAATTCTCGAGAGGTATACG 60.143 50.000 15.94 3.42 0.00 3.06
1203 1783 6.822676 CCCTAATTCTCGAGAGGTATACGTAT 59.177 42.308 15.94 13.54 0.00 3.06
1451 2211 5.337009 CCCAGCCTAAGTACTTTAAGAACGA 60.337 44.000 14.49 0.00 0.00 3.85
1452 2212 6.338937 CCAGCCTAAGTACTTTAAGAACGAT 58.661 40.000 14.49 0.00 0.00 3.73
1458 2218 8.808529 CCTAAGTACTTTAAGAACGATGACATG 58.191 37.037 14.49 0.00 0.00 3.21
1485 2245 0.033796 ACTCCAATACGGGGACTCGA 60.034 55.000 0.00 0.00 37.51 4.04
1525 2285 0.893727 AGGTGTCCGCCAAATGTTCC 60.894 55.000 0.00 0.00 0.00 3.62
1531 2292 3.637229 TGTCCGCCAAATGTTCCTTTTTA 59.363 39.130 0.00 0.00 0.00 1.52
1710 2522 1.396653 CCATGAGCAACATCCTTCCC 58.603 55.000 0.00 0.00 37.07 3.97
1776 2639 0.935898 GATGCATGCGTCTCTTCTGG 59.064 55.000 28.82 0.00 0.00 3.86
1793 2659 7.733955 TCTCTTCTGGGAATCTGAGATGAATAT 59.266 37.037 0.00 0.00 0.00 1.28
1838 2704 7.433425 GGAGCTAGCAAAACATTATTTGACATC 59.567 37.037 18.83 0.00 41.73 3.06
1963 2830 2.741759 TGCTGATGACGCTCTACAAA 57.258 45.000 0.00 0.00 0.00 2.83
2236 3115 1.075525 CCCCTCCGTCTGGACCATA 60.076 63.158 0.00 0.00 40.17 2.74
2289 3168 1.729472 CGCCGTCAGTACACTTCTCTG 60.729 57.143 0.00 0.00 0.00 3.35
2330 3227 4.033009 TGTCTCCTCAGCCAAATCTCATA 58.967 43.478 0.00 0.00 0.00 2.15
2367 3271 1.965930 GTTGCAGGGCATCGTGACA 60.966 57.895 0.00 0.00 38.76 3.58
2903 3830 5.872617 TGATTTCCACAACCAACGACTATAG 59.127 40.000 0.00 0.00 0.00 1.31
2931 3863 5.410439 TCCAGTACGCCTTGTATTTTTCTTC 59.590 40.000 0.00 0.00 35.02 2.87
2934 3866 7.015877 CAGTACGCCTTGTATTTTTCTTCTTC 58.984 38.462 0.00 0.00 35.02 2.87
2936 3868 6.635030 ACGCCTTGTATTTTTCTTCTTCTT 57.365 33.333 0.00 0.00 0.00 2.52
2937 3869 7.039313 ACGCCTTGTATTTTTCTTCTTCTTT 57.961 32.000 0.00 0.00 0.00 2.52
2938 3870 7.489160 ACGCCTTGTATTTTTCTTCTTCTTTT 58.511 30.769 0.00 0.00 0.00 2.27
2939 3871 7.979537 ACGCCTTGTATTTTTCTTCTTCTTTTT 59.020 29.630 0.00 0.00 0.00 1.94
2967 3899 2.029020 GGGGGAGAAAGAAATGTTGTGC 60.029 50.000 0.00 0.00 0.00 4.57
3097 4031 8.554528 AGTTCAATTCTGTGATAAATATCAGCG 58.445 33.333 3.40 0.00 42.84 5.18
3132 4066 5.429762 ACATCTAGGGTTCCTCAAATCATGA 59.570 40.000 0.00 0.00 34.61 3.07
3133 4067 6.069440 ACATCTAGGGTTCCTCAAATCATGAA 60.069 38.462 0.00 0.00 37.67 2.57
3135 4069 6.973642 TCTAGGGTTCCTCAAATCATGAAAT 58.026 36.000 0.00 0.00 37.67 2.17
3167 4101 5.912955 GTCGGGTAATTGACAAACTTGAAAG 59.087 40.000 0.00 0.00 35.20 2.62
3168 4102 5.009210 TCGGGTAATTGACAAACTTGAAAGG 59.991 40.000 0.00 0.00 0.00 3.11
3174 4108 7.628769 AATTGACAAACTTGAAAGGCAAAAT 57.371 28.000 0.00 0.00 35.74 1.82
3177 4111 5.104982 TGACAAACTTGAAAGGCAAAATCCT 60.105 36.000 0.00 0.00 35.74 3.24
3201 4135 3.248495 TGGTGAAATTCGCGTGGTATA 57.752 42.857 5.77 0.00 0.00 1.47
3202 4136 3.191669 TGGTGAAATTCGCGTGGTATAG 58.808 45.455 5.77 0.00 0.00 1.31
3203 4137 2.033151 GGTGAAATTCGCGTGGTATAGC 60.033 50.000 5.77 0.00 0.00 2.97
3204 4138 2.033151 GTGAAATTCGCGTGGTATAGCC 60.033 50.000 5.77 0.00 37.90 3.93
3205 4139 1.529865 GAAATTCGCGTGGTATAGCCC 59.470 52.381 5.77 0.00 36.04 5.19
3206 4140 0.599204 AATTCGCGTGGTATAGCCCG 60.599 55.000 5.77 2.25 36.04 6.13
3207 4141 1.457823 ATTCGCGTGGTATAGCCCGA 61.458 55.000 11.03 7.95 34.33 5.14
3208 4142 1.665264 TTCGCGTGGTATAGCCCGAA 61.665 55.000 11.03 12.93 36.55 4.30
3209 4143 1.227031 CGCGTGGTATAGCCCGAAA 60.227 57.895 11.03 0.00 34.33 3.46
3210 4144 1.213094 CGCGTGGTATAGCCCGAAAG 61.213 60.000 11.03 0.00 34.33 2.62
3211 4145 0.103572 GCGTGGTATAGCCCGAAAGA 59.896 55.000 11.03 0.00 34.33 2.52
3212 4146 1.472026 GCGTGGTATAGCCCGAAAGAA 60.472 52.381 11.03 0.00 34.33 2.52
3213 4147 2.805657 GCGTGGTATAGCCCGAAAGAAT 60.806 50.000 11.03 0.00 34.33 2.40
3214 4148 3.463944 CGTGGTATAGCCCGAAAGAATT 58.536 45.455 0.13 0.00 34.33 2.17
3215 4149 3.247648 CGTGGTATAGCCCGAAAGAATTG 59.752 47.826 0.13 0.00 34.33 2.32
3216 4150 4.448210 GTGGTATAGCCCGAAAGAATTGA 58.552 43.478 0.00 0.00 36.04 2.57
3217 4151 4.879545 GTGGTATAGCCCGAAAGAATTGAA 59.120 41.667 0.00 0.00 36.04 2.69
3218 4152 5.007724 GTGGTATAGCCCGAAAGAATTGAAG 59.992 44.000 0.00 0.00 36.04 3.02
3219 4153 4.515567 GGTATAGCCCGAAAGAATTGAAGG 59.484 45.833 0.00 0.00 0.00 3.46
3220 4154 2.586648 AGCCCGAAAGAATTGAAGGT 57.413 45.000 0.00 0.00 0.00 3.50
3221 4155 2.876581 AGCCCGAAAGAATTGAAGGTT 58.123 42.857 0.00 0.00 0.00 3.50
3222 4156 3.230976 AGCCCGAAAGAATTGAAGGTTT 58.769 40.909 0.00 0.00 0.00 3.27
3223 4157 3.641436 AGCCCGAAAGAATTGAAGGTTTT 59.359 39.130 0.00 0.00 0.00 2.43
3224 4158 4.100963 AGCCCGAAAGAATTGAAGGTTTTT 59.899 37.500 0.00 0.00 0.00 1.94
3225 4159 4.211164 GCCCGAAAGAATTGAAGGTTTTTG 59.789 41.667 0.00 0.00 0.00 2.44
3226 4160 4.749598 CCCGAAAGAATTGAAGGTTTTTGG 59.250 41.667 0.00 0.00 33.81 3.28
3227 4161 5.452636 CCCGAAAGAATTGAAGGTTTTTGGA 60.453 40.000 3.66 0.00 35.29 3.53
3228 4162 6.045955 CCGAAAGAATTGAAGGTTTTTGGAA 58.954 36.000 0.00 0.00 35.29 3.53
3229 4163 6.019075 CCGAAAGAATTGAAGGTTTTTGGAAC 60.019 38.462 0.00 0.00 35.29 3.62
3230 4164 6.756542 CGAAAGAATTGAAGGTTTTTGGAACT 59.243 34.615 0.00 0.00 0.00 3.01
3231 4165 7.254084 CGAAAGAATTGAAGGTTTTTGGAACTG 60.254 37.037 0.00 0.00 0.00 3.16
3232 4166 6.790232 AGAATTGAAGGTTTTTGGAACTGA 57.210 33.333 0.00 0.00 0.00 3.41
3233 4167 7.181569 AGAATTGAAGGTTTTTGGAACTGAA 57.818 32.000 0.00 0.00 0.00 3.02
3234 4168 7.041721 AGAATTGAAGGTTTTTGGAACTGAAC 58.958 34.615 0.00 0.00 0.00 3.18
3235 4169 4.364415 TGAAGGTTTTTGGAACTGAACG 57.636 40.909 0.00 0.00 0.00 3.95
3236 4170 4.011023 TGAAGGTTTTTGGAACTGAACGA 58.989 39.130 0.00 0.00 0.00 3.85
3237 4171 4.459685 TGAAGGTTTTTGGAACTGAACGAA 59.540 37.500 0.00 0.00 0.00 3.85
3238 4172 4.632538 AGGTTTTTGGAACTGAACGAAG 57.367 40.909 0.00 0.00 0.00 3.79
3239 4173 3.113322 GGTTTTTGGAACTGAACGAAGC 58.887 45.455 0.00 0.00 0.00 3.86
3240 4174 3.428316 GGTTTTTGGAACTGAACGAAGCA 60.428 43.478 0.00 0.00 0.00 3.91
3241 4175 3.691049 TTTTGGAACTGAACGAAGCAG 57.309 42.857 0.00 0.00 39.26 4.24
3242 4176 0.944386 TTGGAACTGAACGAAGCAGC 59.056 50.000 0.00 0.00 36.86 5.25
3243 4177 0.106708 TGGAACTGAACGAAGCAGCT 59.893 50.000 0.00 0.00 36.86 4.24
3244 4178 0.793250 GGAACTGAACGAAGCAGCTC 59.207 55.000 0.00 0.00 36.86 4.09
3545 4482 2.923035 CTGTGGGTCGTGAGGGGT 60.923 66.667 0.00 0.00 0.00 4.95
3595 4532 1.152525 TAGGAGGCTGGATCCGTCC 60.153 63.158 7.39 10.57 45.31 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 8.644374 AAATTGGGTAACACATGTAGTAACAT 57.356 30.769 0.00 0.00 43.21 2.71
32 33 3.146066 TCAGAACGGTCAGAAAATTGGG 58.854 45.455 1.87 0.00 0.00 4.12
34 35 7.698836 AAAAATCAGAACGGTCAGAAAATTG 57.301 32.000 1.87 0.00 0.00 2.32
69 70 7.446769 ACAATATTGTTTTCAACCCTAAACCC 58.553 34.615 15.47 0.00 42.94 4.11
172 174 3.506810 CAGACTCATTTCAGACGACCTC 58.493 50.000 0.00 0.00 0.00 3.85
198 200 0.875059 GTTTCTGGAGAGTTTGCCGG 59.125 55.000 0.00 0.00 0.00 6.13
204 207 2.885616 TCGGTAGGTTTCTGGAGAGTT 58.114 47.619 0.00 0.00 0.00 3.01
217 220 4.457603 TCACCAAAAATGACATTCGGTAGG 59.542 41.667 13.60 9.00 0.00 3.18
224 227 7.271511 TGTAAGCTTTCACCAAAAATGACATT 58.728 30.769 3.20 0.00 0.00 2.71
226 229 6.214191 TGTAAGCTTTCACCAAAAATGACA 57.786 33.333 3.20 0.00 0.00 3.58
227 230 7.532682 TTTGTAAGCTTTCACCAAAAATGAC 57.467 32.000 3.20 0.00 0.00 3.06
228 231 7.604164 TGTTTTGTAAGCTTTCACCAAAAATGA 59.396 29.630 18.95 9.78 36.93 2.57
229 232 7.746929 TGTTTTGTAAGCTTTCACCAAAAATG 58.253 30.769 18.95 0.00 36.93 2.32
230 233 7.913674 TGTTTTGTAAGCTTTCACCAAAAAT 57.086 28.000 18.95 0.00 36.93 1.82
231 234 7.913674 ATGTTTTGTAAGCTTTCACCAAAAA 57.086 28.000 18.95 9.95 36.93 1.94
256 322 9.880157 AGCTAATTTGATGCTTGAATTTATGTT 57.120 25.926 0.00 0.00 32.61 2.71
304 878 2.733956 AGTGGTTGCCAAACAGAAAGA 58.266 42.857 0.00 0.00 38.10 2.52
336 910 2.224018 TGCAGTTCCAGAAACAATTGCC 60.224 45.455 5.05 0.00 40.56 4.52
338 912 3.553508 CCCTGCAGTTCCAGAAACAATTG 60.554 47.826 13.81 3.24 40.56 2.32
354 928 1.907807 GTTGATTGCCACCCCTGCA 60.908 57.895 0.00 0.00 36.84 4.41
355 929 2.649129 GGTTGATTGCCACCCCTGC 61.649 63.158 0.00 0.00 0.00 4.85
357 931 0.542702 CTTGGTTGATTGCCACCCCT 60.543 55.000 0.00 0.00 35.46 4.79
398 974 2.418368 ACAGTGTTCTGCAACCTTGA 57.582 45.000 0.00 0.00 44.77 3.02
464 1040 2.552315 AGTGGGAAGCAAATGTTACGTG 59.448 45.455 0.00 0.00 0.00 4.49
656 1232 1.470890 CAGTCGAAGGAGGACACTCTC 59.529 57.143 0.00 0.00 43.46 3.20
657 1233 1.074084 TCAGTCGAAGGAGGACACTCT 59.926 52.381 0.00 0.00 43.46 3.24
697 1273 0.321653 ACCGAGTGGCTTCATTGGAC 60.322 55.000 0.00 0.00 39.70 4.02
789 1365 1.549037 GGGGCATTCCGGGCATTATTA 60.549 52.381 0.00 0.00 36.01 0.98
875 1451 2.354604 GGAACTCAAGGAGCAAGAGAGG 60.355 54.545 0.00 0.00 32.04 3.69
945 1521 4.518970 TGCAAAAGCCTTGGTTAACTAGAG 59.481 41.667 5.42 1.50 0.00 2.43
1199 1779 3.242511 TGGATCGTTCGTGTCTACATACG 60.243 47.826 8.25 8.25 41.38 3.06
1200 1780 4.282950 TGGATCGTTCGTGTCTACATAC 57.717 45.455 0.00 0.00 0.00 2.39
1203 1783 2.159296 CCATGGATCGTTCGTGTCTACA 60.159 50.000 5.56 0.00 0.00 2.74
1475 2235 0.317479 ACAAAAGAGTCGAGTCCCCG 59.683 55.000 16.67 5.91 0.00 5.73
1586 2353 6.509656 ACATGCATAAGGTTCATTAGCATTG 58.490 36.000 0.00 0.00 39.00 2.82
1589 2356 5.418524 ACAACATGCATAAGGTTCATTAGCA 59.581 36.000 0.00 0.00 34.78 3.49
1710 2522 1.431488 CCATCACGAAGGTCATGGCG 61.431 60.000 0.00 0.00 29.71 5.69
1776 2639 7.062839 GTCACGCTAATATTCATCTCAGATTCC 59.937 40.741 0.00 0.00 0.00 3.01
1859 2725 5.087323 GTCCACCTTCTCCATCCTATGATA 58.913 45.833 0.00 0.00 0.00 2.15
2330 3227 6.981722 TGCAACATCAGTCATACGATATACT 58.018 36.000 0.00 0.00 0.00 2.12
2367 3271 2.876992 CGTAGTACGCTATGCTCGAT 57.123 50.000 10.19 0.00 33.65 3.59
2630 3534 2.982130 CTCCGGTCACCTTGGAGG 59.018 66.667 9.47 0.00 44.49 4.30
2903 3830 4.382345 AATACAAGGCGTACTGGAGTAC 57.618 45.455 6.85 6.85 45.47 2.73
2938 3870 6.014012 ACATTTCTTTCTCCCCCGATAAAAA 58.986 36.000 0.00 0.00 0.00 1.94
2939 3871 5.576128 ACATTTCTTTCTCCCCCGATAAAA 58.424 37.500 0.00 0.00 0.00 1.52
2940 3872 5.187621 ACATTTCTTTCTCCCCCGATAAA 57.812 39.130 0.00 0.00 0.00 1.40
2967 3899 3.042733 TACATGCCCCTTGCCGGAG 62.043 63.158 5.05 0.00 40.16 4.63
2979 3912 1.917273 ACACGTACATCGGTACATGC 58.083 50.000 1.48 0.00 45.10 4.06
2983 3916 1.987770 CACCAACACGTACATCGGTAC 59.012 52.381 0.00 0.00 45.18 3.34
2984 3917 1.612950 ACACCAACACGTACATCGGTA 59.387 47.619 0.00 0.00 44.69 4.02
2985 3918 0.390124 ACACCAACACGTACATCGGT 59.610 50.000 0.00 0.00 44.69 4.69
2986 3919 2.350899 TACACCAACACGTACATCGG 57.649 50.000 0.00 0.00 44.69 4.18
2987 3920 3.567530 TCTTACACCAACACGTACATCG 58.432 45.455 0.00 0.00 46.00 3.84
2988 3921 4.801891 TCTCTTACACCAACACGTACATC 58.198 43.478 0.00 0.00 0.00 3.06
3000 3933 8.807581 CAAAAACACTCAAAATTCTCTTACACC 58.192 33.333 0.00 0.00 0.00 4.16
3097 4031 2.039879 ACCCTAGATGTTGTCACAACCC 59.960 50.000 18.17 9.82 36.16 4.11
3132 4066 5.751990 GTCAATTACCCGACGTGAGATATTT 59.248 40.000 0.00 0.00 0.00 1.40
3133 4067 5.163488 TGTCAATTACCCGACGTGAGATATT 60.163 40.000 0.00 0.00 34.78 1.28
3135 4069 3.695556 TGTCAATTACCCGACGTGAGATA 59.304 43.478 0.00 0.00 34.78 1.98
3167 4101 6.035975 CGAATTTCACCATAAAGGATTTTGCC 59.964 38.462 0.00 0.00 40.09 4.52
3168 4102 6.455513 GCGAATTTCACCATAAAGGATTTTGC 60.456 38.462 0.00 0.00 40.09 3.68
3174 4108 3.126171 CACGCGAATTTCACCATAAAGGA 59.874 43.478 15.93 0.00 41.22 3.36
3177 4111 2.814919 ACCACGCGAATTTCACCATAAA 59.185 40.909 15.93 0.00 0.00 1.40
3178 4112 2.428491 ACCACGCGAATTTCACCATAA 58.572 42.857 15.93 0.00 0.00 1.90
3180 4114 2.102070 TACCACGCGAATTTCACCAT 57.898 45.000 15.93 0.00 0.00 3.55
3185 4119 1.529865 GGGCTATACCACGCGAATTTC 59.470 52.381 15.93 0.00 42.05 2.17
3201 4135 2.586648 ACCTTCAATTCTTTCGGGCT 57.413 45.000 0.00 0.00 0.00 5.19
3202 4136 3.660501 AAACCTTCAATTCTTTCGGGC 57.339 42.857 0.00 0.00 0.00 6.13
3203 4137 4.749598 CCAAAAACCTTCAATTCTTTCGGG 59.250 41.667 0.00 0.00 0.00 5.14
3204 4138 5.596845 TCCAAAAACCTTCAATTCTTTCGG 58.403 37.500 0.00 0.00 0.00 4.30
3205 4139 6.756542 AGTTCCAAAAACCTTCAATTCTTTCG 59.243 34.615 0.00 0.00 0.00 3.46
3206 4140 7.763985 TCAGTTCCAAAAACCTTCAATTCTTTC 59.236 33.333 0.00 0.00 0.00 2.62
3207 4141 7.619965 TCAGTTCCAAAAACCTTCAATTCTTT 58.380 30.769 0.00 0.00 0.00 2.52
3208 4142 7.181569 TCAGTTCCAAAAACCTTCAATTCTT 57.818 32.000 0.00 0.00 0.00 2.52
3209 4143 6.790232 TCAGTTCCAAAAACCTTCAATTCT 57.210 33.333 0.00 0.00 0.00 2.40
3210 4144 6.019881 CGTTCAGTTCCAAAAACCTTCAATTC 60.020 38.462 0.00 0.00 0.00 2.17
3211 4145 5.810074 CGTTCAGTTCCAAAAACCTTCAATT 59.190 36.000 0.00 0.00 0.00 2.32
3212 4146 5.126384 TCGTTCAGTTCCAAAAACCTTCAAT 59.874 36.000 0.00 0.00 0.00 2.57
3213 4147 4.459685 TCGTTCAGTTCCAAAAACCTTCAA 59.540 37.500 0.00 0.00 0.00 2.69
3214 4148 4.011023 TCGTTCAGTTCCAAAAACCTTCA 58.989 39.130 0.00 0.00 0.00 3.02
3215 4149 4.625972 TCGTTCAGTTCCAAAAACCTTC 57.374 40.909 0.00 0.00 0.00 3.46
3216 4150 4.676986 GCTTCGTTCAGTTCCAAAAACCTT 60.677 41.667 0.00 0.00 0.00 3.50
3217 4151 3.181490 GCTTCGTTCAGTTCCAAAAACCT 60.181 43.478 0.00 0.00 0.00 3.50
3218 4152 3.113322 GCTTCGTTCAGTTCCAAAAACC 58.887 45.455 0.00 0.00 0.00 3.27
3219 4153 3.765026 TGCTTCGTTCAGTTCCAAAAAC 58.235 40.909 0.00 0.00 0.00 2.43
3220 4154 3.733684 GCTGCTTCGTTCAGTTCCAAAAA 60.734 43.478 0.00 0.00 34.21 1.94
3221 4155 2.223479 GCTGCTTCGTTCAGTTCCAAAA 60.223 45.455 0.00 0.00 34.21 2.44
3222 4156 1.333619 GCTGCTTCGTTCAGTTCCAAA 59.666 47.619 0.00 0.00 34.21 3.28
3223 4157 0.944386 GCTGCTTCGTTCAGTTCCAA 59.056 50.000 0.00 0.00 34.21 3.53
3224 4158 0.106708 AGCTGCTTCGTTCAGTTCCA 59.893 50.000 0.00 0.00 34.21 3.53
3225 4159 0.793250 GAGCTGCTTCGTTCAGTTCC 59.207 55.000 2.53 0.00 36.28 3.62
3226 4160 0.436531 CGAGCTGCTTCGTTCAGTTC 59.563 55.000 2.53 7.61 38.09 3.01
3227 4161 1.560860 GCGAGCTGCTTCGTTCAGTT 61.561 55.000 17.94 0.00 42.38 3.16
3228 4162 2.024319 GCGAGCTGCTTCGTTCAGT 61.024 57.895 17.94 0.00 42.38 3.41
3229 4163 2.774774 GCGAGCTGCTTCGTTCAG 59.225 61.111 17.94 0.00 42.38 3.02
3307 4244 2.607750 GAGCTGGGGTGGAGGTGA 60.608 66.667 0.00 0.00 0.00 4.02
3663 4600 2.599757 ATCCAGGAGCTGCAGCACA 61.600 57.895 38.24 18.08 45.16 4.57


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

AutoCloner maintained by Alex Coulton.