Multiple sequence alignment - TraesCS5A01G228200

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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 TraesCS5A01G228200 chr5A 100.000 5119 0 0 1 5119 444538767 444543885 0.000000e+00 9454
1 TraesCS5A01G228200 chr5A 83.173 208 22 10 4831 5035 444555232 444555035 1.460000e-40 178
2 TraesCS5A01G228200 chr5D 96.719 2438 68 5 1613 4048 347436843 347434416 0.000000e+00 4048
3 TraesCS5A01G228200 chr5D 93.921 1645 68 19 1 1627 347438507 347436877 0.000000e+00 2455
4 TraesCS5A01G228200 chr5D 91.011 712 43 7 4045 4750 347434387 347433691 0.000000e+00 941
5 TraesCS5A01G228200 chr5D 91.375 371 28 2 4753 5119 347433659 347433289 5.920000e-139 505
6 TraesCS5A01G228200 chr5D 82.574 373 58 7 4320 4688 453858894 453858525 6.390000e-84 322
7 TraesCS5A01G228200 chr5B 94.757 2556 110 12 518 3059 403715193 403717738 0.000000e+00 3956
8 TraesCS5A01G228200 chr5B 96.866 989 28 3 3061 4048 403717918 403718904 0.000000e+00 1652
9 TraesCS5A01G228200 chr5B 90.125 638 48 6 4045 4680 403718933 403719557 0.000000e+00 815
10 TraesCS5A01G228200 chr5B 92.055 365 21 5 1 361 403714039 403714399 1.640000e-139 507
11 TraesCS5A01G228200 chr5B 90.909 297 19 6 4680 4973 403721966 403722257 4.800000e-105 392
12 TraesCS5A01G228200 chr5B 97.222 108 3 0 5012 5119 403722735 403722842 3.150000e-42 183
13 TraesCS5A01G228200 chr5B 86.614 127 13 3 4315 4439 554582899 554582775 2.490000e-28 137
14 TraesCS5A01G228200 chr6B 82.210 371 50 8 4316 4674 460511198 460511564 6.440000e-79 305
15 TraesCS5A01G228200 chr6D 81.844 358 59 4 4339 4692 296673628 296673273 3.880000e-76 296


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 TraesCS5A01G228200 chr5A 444538767 444543885 5118 False 9454.000000 9454 100.000000 1 5119 1 chr5A.!!$F1 5118
1 TraesCS5A01G228200 chr5D 347433289 347438507 5218 True 1987.250000 4048 93.256500 1 5119 4 chr5D.!!$R2 5118
2 TraesCS5A01G228200 chr5B 403714039 403722842 8803 False 1250.833333 3956 93.655667 1 5119 6 chr5B.!!$F1 5118

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
540 1203 0.248784 GCATCAAGAAATGGAGCGGC 60.249 55.0 0.0 0.0 0.00 6.53 F
999 1678 0.319813 GGGTCCATGTTGCAAAGTGC 60.320 55.0 0.0 0.0 45.29 4.40 F
1537 2228 0.754957 TGGTTGAGGGTTGGCTGTTG 60.755 55.0 0.0 0.0 0.00 3.33 F
2682 3425 0.179234 TGTGTGAACAAGAGGGCGAA 59.821 50.0 0.0 0.0 0.00 4.70 F
2961 3704 0.467384 ATCTCATCCCTTGTGGCTCG 59.533 55.0 0.0 0.0 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2028 2770 1.174712 AGAAAGCCATGCACAACGCT 61.175 50.000 0.00 0.00 43.06 5.07 R
2682 3425 2.290323 GCCACAGAAACTACATGGTCCT 60.290 50.000 0.00 0.00 32.71 3.85 R
3373 4303 3.631250 AGGTTTGTCTTTTCCTGAAGCA 58.369 40.909 0.00 0.00 0.00 3.91 R
3604 4534 0.179097 GGTCAGATTCCGACTCTGCC 60.179 60.000 10.22 10.66 39.98 4.85 R
4566 5532 0.675633 GCAACTTGTGGATGCAAGGT 59.324 50.000 10.07 0.95 46.25 3.50 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 7.260558 GGATACTTTCTTAGGGTTAACATGC 57.739 40.000 8.10 0.00 0.00 4.06
91 95 2.897271 ATAGGCATCACCAACCACAA 57.103 45.000 0.00 0.00 43.14 3.33
109 113 4.498513 CCACAACCAGCATGCATATACAAG 60.499 45.833 21.98 4.23 31.97 3.16
110 114 4.336153 CACAACCAGCATGCATATACAAGA 59.664 41.667 21.98 0.00 31.97 3.02
111 115 5.009310 CACAACCAGCATGCATATACAAGAT 59.991 40.000 21.98 0.00 31.97 2.40
205 209 0.385390 CAACAGTTTGCCACTCCCAC 59.615 55.000 0.00 0.00 30.92 4.61
272 276 4.793216 GCTTACATCCAAATAACGCAACAG 59.207 41.667 0.00 0.00 0.00 3.16
291 295 2.233186 CAGAGTCTGATTGTCAGCAGGA 59.767 50.000 15.46 0.00 43.95 3.86
305 309 3.008330 CAGCAGGACAAGATCAGAAAGG 58.992 50.000 0.00 0.00 0.00 3.11
310 314 1.742268 GACAAGATCAGAAAGGCAGGC 59.258 52.381 0.00 0.00 0.00 4.85
379 383 9.911980 GATAATATCGTTGCACATAGATTGATG 57.088 33.333 0.00 0.00 0.00 3.07
380 384 7.734924 AATATCGTTGCACATAGATTGATGT 57.265 32.000 0.00 0.00 40.78 3.06
387 391 4.094739 TGCACATAGATTGATGTTTCACCG 59.905 41.667 0.00 0.00 37.99 4.94
393 397 3.949754 AGATTGATGTTTCACCGATGCAT 59.050 39.130 0.00 0.00 0.00 3.96
443 1078 5.099575 GGACGTGTTTCAAATTTCAACACT 58.900 37.500 26.04 18.49 45.40 3.55
540 1203 0.248784 GCATCAAGAAATGGAGCGGC 60.249 55.000 0.00 0.00 0.00 6.53
556 1219 2.607892 GGCGGCGCATCACCTTATC 61.608 63.158 34.36 8.04 0.00 1.75
812 1475 2.193248 GAGGCCATCGGAAAGGGG 59.807 66.667 5.01 0.00 0.00 4.79
854 1518 3.382803 CTCTGCTCGCTGGGGAAGG 62.383 68.421 0.00 0.00 0.00 3.46
861 1525 2.273776 GCTGGGGAAGGAAGCCTC 59.726 66.667 0.00 0.00 30.89 4.70
862 1526 2.606587 GCTGGGGAAGGAAGCCTCA 61.607 63.158 0.00 0.00 34.03 3.86
863 1527 1.301293 CTGGGGAAGGAAGCCTCAC 59.699 63.158 0.00 0.00 31.22 3.51
864 1528 2.269241 GGGGAAGGAAGCCTCACG 59.731 66.667 0.00 0.00 30.89 4.35
865 1529 2.269241 GGGAAGGAAGCCTCACGG 59.731 66.667 0.00 0.00 30.89 4.94
892 1564 1.335132 GCCTCGTGGGGATAAGGTGA 61.335 60.000 5.54 0.00 35.12 4.02
910 1582 5.629079 GGTGAGGACCTTTCTGTAAATTG 57.371 43.478 0.00 0.00 39.47 2.32
918 1590 8.803235 AGGACCTTTCTGTAAATTGGATAAAAC 58.197 33.333 0.00 0.00 0.00 2.43
968 1647 2.422479 GGAGACCCCTTCGTTTATTTGC 59.578 50.000 0.00 0.00 0.00 3.68
987 1666 1.335145 CCGTATAACTCGGGGTCCAT 58.665 55.000 0.00 0.00 43.68 3.41
988 1667 1.000506 CCGTATAACTCGGGGTCCATG 59.999 57.143 0.00 0.00 43.68 3.66
999 1678 0.319813 GGGTCCATGTTGCAAAGTGC 60.320 55.000 0.00 0.00 45.29 4.40
1008 1687 4.056097 GCAAAGTGCAATACGCCG 57.944 55.556 0.00 0.00 44.26 6.46
1181 1868 1.883732 CCTCGTCTCCTTCTGCGAA 59.116 57.895 0.00 0.00 32.84 4.70
1419 2107 4.007659 AGTAAATTTGGCTGACGTTAGGG 58.992 43.478 9.62 0.00 0.00 3.53
1429 2117 3.408634 CTGACGTTAGGGTTGGTTTCAT 58.591 45.455 0.00 0.00 0.00 2.57
1454 2142 4.040829 TCAGATCAACCTTCAGAGCTTGAA 59.959 41.667 9.84 9.84 43.40 2.69
1531 2222 2.755103 GCTATTTCTGGTTGAGGGTTGG 59.245 50.000 0.00 0.00 0.00 3.77
1537 2228 0.754957 TGGTTGAGGGTTGGCTGTTG 60.755 55.000 0.00 0.00 0.00 3.33
1611 2302 3.412386 AGTGGAGAACATGGTGCTTAAC 58.588 45.455 0.00 0.00 0.00 2.01
1656 2398 6.644592 CCCATTTTGTAACCTAATGTGTTGTG 59.355 38.462 0.00 0.00 0.00 3.33
1666 2408 7.435068 ACCTAATGTGTTGTGAGTATGTTTC 57.565 36.000 0.00 0.00 0.00 2.78
1667 2409 6.995686 ACCTAATGTGTTGTGAGTATGTTTCA 59.004 34.615 0.00 0.00 0.00 2.69
1723 2465 1.929806 ATGTGCATGTTCGCTGGCAG 61.930 55.000 10.94 10.94 36.86 4.85
1855 2597 8.665643 ATGAAAATGATTTGCTTTCTTGTGAA 57.334 26.923 0.00 0.00 31.67 3.18
1989 2731 2.504367 ACTAATGTGTGCCCTTGACAC 58.496 47.619 0.00 0.00 43.42 3.67
2028 2770 6.922957 GTGTTGCATTAACCTTTCTCAATTGA 59.077 34.615 8.12 8.12 38.55 2.57
2205 2947 2.849880 ATTATGCACACGCCATGAAC 57.150 45.000 0.00 0.00 37.32 3.18
2480 3223 6.951198 TCTTCTTCTAGTCAGAGTTCCAAGAT 59.049 38.462 0.00 0.00 30.73 2.40
2644 3387 3.568538 CACAATCTTGTTAGCAACTGCC 58.431 45.455 0.00 0.00 39.86 4.85
2682 3425 0.179234 TGTGTGAACAAGAGGGCGAA 59.821 50.000 0.00 0.00 0.00 4.70
2961 3704 0.467384 ATCTCATCCCTTGTGGCTCG 59.533 55.000 0.00 0.00 0.00 5.03
3049 3792 9.932207 TTTAGTGATTAAGTCATACCGAAAGAA 57.068 29.630 0.00 0.00 39.48 2.52
3078 3999 6.427150 AGCTATTAACCGAAATTTGCATACG 58.573 36.000 0.00 0.00 0.00 3.06
3187 4116 3.696051 GCCCATTTCAGCAATCAACTCTA 59.304 43.478 0.00 0.00 0.00 2.43
3188 4117 4.201990 GCCCATTTCAGCAATCAACTCTAG 60.202 45.833 0.00 0.00 0.00 2.43
3189 4118 5.188434 CCCATTTCAGCAATCAACTCTAGA 58.812 41.667 0.00 0.00 0.00 2.43
3190 4119 5.296283 CCCATTTCAGCAATCAACTCTAGAG 59.704 44.000 18.49 18.49 0.00 2.43
3191 4120 5.879223 CCATTTCAGCAATCAACTCTAGAGT 59.121 40.000 20.00 20.00 44.94 3.24
3192 4121 6.036953 CCATTTCAGCAATCAACTCTAGAGTC 59.963 42.308 25.34 11.90 41.58 3.36
3193 4122 5.728637 TTCAGCAATCAACTCTAGAGTCA 57.271 39.130 25.34 15.39 41.58 3.41
3194 4123 5.929058 TCAGCAATCAACTCTAGAGTCAT 57.071 39.130 25.34 16.89 41.58 3.06
3198 4127 8.481314 TCAGCAATCAACTCTAGAGTCATTTAT 58.519 33.333 25.34 13.29 41.58 1.40
3365 4295 7.365741 ACAAAGACATTTATTGCAGTTCTCTG 58.634 34.615 0.00 0.00 43.87 3.35
3373 4303 9.252962 CATTTATTGCAGTTCTCTGTTTTTCTT 57.747 29.630 0.00 0.00 43.05 2.52
3536 4466 9.097257 CAGTTTGGAAGCTTTCAATAAGAAAAA 57.903 29.630 20.84 0.46 45.11 1.94
3594 4524 6.317789 TCTTCTGCAGGTAATTTTGAACAG 57.682 37.500 15.13 0.00 0.00 3.16
3595 4525 5.827797 TCTTCTGCAGGTAATTTTGAACAGT 59.172 36.000 15.13 0.00 0.00 3.55
3604 4534 5.569059 GGTAATTTTGAACAGTGATGAAGCG 59.431 40.000 0.00 0.00 0.00 4.68
3730 4660 0.550914 AAACAGGACCTGTGAAGCCA 59.449 50.000 27.79 0.00 44.62 4.75
3736 4666 1.202818 GGACCTGTGAAGCCAAGAACT 60.203 52.381 0.00 0.00 0.00 3.01
3907 4837 5.047306 TCAAGTTCGTGAAGGTGATGACTAT 60.047 40.000 0.00 0.00 0.00 2.12
3933 4863 4.219288 GTGCTCCCTTGATTTTGATTGAGT 59.781 41.667 0.00 0.00 0.00 3.41
3935 4865 4.381292 GCTCCCTTGATTTTGATTGAGTGG 60.381 45.833 0.00 0.00 0.00 4.00
4188 5152 2.614057 GGCCAAAGTATGTTCTGGATCG 59.386 50.000 0.00 0.00 0.00 3.69
4217 5181 7.033530 ACTCTGTAGTGCTATCTGTACAATC 57.966 40.000 0.00 0.00 33.57 2.67
4226 5190 5.582269 TGCTATCTGTACAATCTTGCACTTC 59.418 40.000 0.00 0.00 0.00 3.01
4259 5223 1.334689 GGAAAACAGCAACTACGCCAC 60.335 52.381 0.00 0.00 0.00 5.01
4267 5231 0.433492 CAACTACGCCACGTCTTTCG 59.567 55.000 0.00 0.00 41.54 3.46
4334 5298 3.119495 CCCTTTATTTTGAGAACTGCCCG 60.119 47.826 0.00 0.00 0.00 6.13
4336 5300 4.022329 CCTTTATTTTGAGAACTGCCCGTT 60.022 41.667 0.00 0.00 38.91 4.44
4396 5360 4.090761 ACAGGCTCAATCAGAAACTCAA 57.909 40.909 0.00 0.00 0.00 3.02
4407 5371 8.102676 TCAATCAGAAACTCAAGGATTACATCA 58.897 33.333 0.00 0.00 0.00 3.07
4448 5414 5.407407 TCTAAGGAAAAGGAGTGTAGCAG 57.593 43.478 0.00 0.00 0.00 4.24
4453 5419 3.189495 GGAAAAGGAGTGTAGCAGAAAGC 59.811 47.826 0.00 0.00 46.19 3.51
4469 5435 2.747460 GCTGAGCGGCCACATTGA 60.747 61.111 2.24 0.00 0.00 2.57
4551 5517 2.417933 CTCTCTGAAAACTTGCCATCCG 59.582 50.000 0.00 0.00 0.00 4.18
4555 5521 0.454452 GAAAACTTGCCATCCGACGC 60.454 55.000 0.00 0.00 0.00 5.19
4558 5524 2.741985 CTTGCCATCCGACGCACA 60.742 61.111 0.00 0.00 33.97 4.57
4566 5532 0.175531 ATCCGACGCACATGTCATCA 59.824 50.000 0.00 0.00 38.84 3.07
4723 8098 0.179094 TGGTTGTGTCTGTCACCGAC 60.179 55.000 2.72 0.00 45.61 4.79
4724 8099 0.179094 GGTTGTGTCTGTCACCGACA 60.179 55.000 0.00 0.00 45.61 4.35
4725 8100 1.647346 GTTGTGTCTGTCACCGACAA 58.353 50.000 3.29 0.00 45.61 3.18
4751 8155 9.720769 AGTATTTCGAAGGTTCTAAAAAGATGA 57.279 29.630 0.00 0.00 0.00 2.92
4762 8166 6.834959 TCTAAAAAGATGAGCGATCATGAC 57.165 37.500 22.75 7.62 32.86 3.06
4818 8224 8.182881 CCATGATGAAAGAAGATGAAAAGACTC 58.817 37.037 0.00 0.00 0.00 3.36
4879 8285 1.202486 GCTTCATTGGCCCATGTGATG 60.202 52.381 15.99 10.03 0.00 3.07
4900 8306 2.134789 ACCCTGATTGAATGGCAGAC 57.865 50.000 0.00 0.00 0.00 3.51
4969 8380 7.120726 GGTAGGTGTTATGCAGTAATGAACTTT 59.879 37.037 0.00 0.00 35.76 2.66
4996 8407 6.838382 AGTATCAACTTTTGGGTCTAACTGT 58.162 36.000 0.00 0.00 29.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 1.901159 TGCCTATTTGCAGTTTGGCAT 59.099 42.857 17.68 0.00 44.35 4.40
59 60 1.336131 TGCCTATTTGCAGTTTGGCA 58.664 45.000 17.68 17.68 46.59 4.92
60 61 2.094078 TGATGCCTATTTGCAGTTTGGC 60.094 45.455 13.82 13.82 45.93 4.52
61 62 3.514645 GTGATGCCTATTTGCAGTTTGG 58.485 45.455 0.00 0.00 45.93 3.28
91 95 6.364568 TCTATCTTGTATATGCATGCTGGT 57.635 37.500 20.33 7.62 0.00 4.00
291 295 1.074405 TGCCTGCCTTTCTGATCTTGT 59.926 47.619 0.00 0.00 0.00 3.16
295 299 4.023365 GTGAATATGCCTGCCTTTCTGATC 60.023 45.833 0.00 0.00 0.00 2.92
305 309 2.042686 TGGACTGTGAATATGCCTGC 57.957 50.000 0.00 0.00 0.00 4.85
310 314 7.323420 TGAACTCTAGTTGGACTGTGAATATG 58.677 38.462 0.00 0.00 38.56 1.78
387 391 2.159198 AGAAAAATGTGGCCGATGCATC 60.159 45.455 17.10 17.10 40.13 3.91
393 397 4.439974 GCATCAATAGAAAAATGTGGCCGA 60.440 41.667 0.00 0.00 0.00 5.54
443 1078 7.275920 AGCTTCTTGAAAGAACAGAAGAACTA 58.724 34.615 11.48 0.00 39.95 2.24
540 1203 2.310233 CCGATAAGGTGATGCGCCG 61.310 63.158 4.18 0.00 39.30 6.46
728 1391 0.105760 GCAGATCCCTCCTCCTCTCA 60.106 60.000 0.00 0.00 0.00 3.27
812 1475 2.185608 GAGGAGTGAGAAGCGCCC 59.814 66.667 2.29 0.00 0.00 6.13
892 1564 8.803235 GTTTTATCCAATTTACAGAAAGGTCCT 58.197 33.333 0.00 0.00 0.00 3.85
910 1582 2.408368 GCTTTGCACTTGCGTTTTATCC 59.592 45.455 0.00 0.00 45.83 2.59
918 1590 2.676016 TTTCCGGCTTTGCACTTGCG 62.676 55.000 0.00 0.00 45.83 4.85
924 1596 0.589223 CTACGTTTTCCGGCTTTGCA 59.411 50.000 0.00 0.00 42.24 4.08
933 1605 1.403382 GGTCTCCCGTCTACGTTTTCC 60.403 57.143 0.00 0.00 37.74 3.13
955 1634 6.118195 CGAGTTATACGGCAAATAAACGAAG 58.882 40.000 0.00 0.00 0.00 3.79
999 1678 3.726782 GCAGTAAAAGAACCGGCGTATTG 60.727 47.826 6.01 0.00 0.00 1.90
1000 1679 2.417586 GCAGTAAAAGAACCGGCGTATT 59.582 45.455 6.01 0.00 0.00 1.89
1002 1681 1.431496 GCAGTAAAAGAACCGGCGTA 58.569 50.000 6.01 0.00 0.00 4.42
1008 1687 0.803117 GGCCTCGCAGTAAAAGAACC 59.197 55.000 0.00 0.00 0.00 3.62
1367 2054 4.378459 CGCACAAACCCTAATCTGAGAAAC 60.378 45.833 0.00 0.00 0.00 2.78
1419 2107 4.520492 AGGTTGATCTGACATGAAACCAAC 59.480 41.667 0.00 5.90 39.61 3.77
1429 2117 2.902486 AGCTCTGAAGGTTGATCTGACA 59.098 45.455 0.00 0.00 0.00 3.58
1473 2164 3.011818 CAATGCAGCAACCAGACTATCA 58.988 45.455 0.00 0.00 0.00 2.15
1531 2222 6.922957 TCATTCATCAGTTTAAAACCAACAGC 59.077 34.615 0.00 0.00 0.00 4.40
1537 2228 8.650714 GCTTTGATCATTCATCAGTTTAAAACC 58.349 33.333 0.00 0.00 42.76 3.27
1611 2302 7.803279 ATGGGATTCATGATGATATGATTCG 57.197 36.000 0.00 0.00 37.89 3.34
1656 2398 8.430801 ACAGATAAGATGCTTGAAACATACTC 57.569 34.615 0.00 0.00 0.00 2.59
1666 2408 9.539825 AAGTACATAGAACAGATAAGATGCTTG 57.460 33.333 0.00 0.00 0.00 4.01
1723 2465 6.853720 TGTAACTACATCTCAAGCTCTACAC 58.146 40.000 0.00 0.00 0.00 2.90
1855 2597 6.350110 GCCAAACCAATAGTCAATGTACATGT 60.350 38.462 9.63 2.69 0.00 3.21
2028 2770 1.174712 AGAAAGCCATGCACAACGCT 61.175 50.000 0.00 0.00 43.06 5.07
2102 2844 6.399639 ACAGGTACAATTCCAAACGAATTT 57.600 33.333 0.00 0.00 46.93 1.82
2122 2864 4.400884 AGAAGCAGTCTGGAGTATGTACAG 59.599 45.833 0.33 0.00 34.29 2.74
2205 2947 5.632347 CACCTAAGTAACAGTAGTTTCCACG 59.368 44.000 0.00 0.00 39.15 4.94
2292 3035 2.630889 ACTCCTGAATGAGGTCCTGA 57.369 50.000 0.00 0.00 43.37 3.86
2480 3223 3.268330 GTCTCAGCAGCATCTGATTGAA 58.732 45.455 8.14 0.00 41.73 2.69
2644 3387 7.369607 TCACACACAATTTTTCCACATGATAG 58.630 34.615 0.00 0.00 0.00 2.08
2682 3425 2.290323 GCCACAGAAACTACATGGTCCT 60.290 50.000 0.00 0.00 32.71 3.85
2799 3542 4.623932 TCTGTCATAGTCAACAAGCCTT 57.376 40.909 0.00 0.00 0.00 4.35
2961 3704 9.121658 TCGGAATGAGTGGATATATATGAGTAC 57.878 37.037 0.00 0.00 0.00 2.73
3049 3792 9.816354 ATGCAAATTTCGGTTAATAGCTAAAAT 57.184 25.926 0.00 0.00 0.00 1.82
3078 3999 6.699575 ATTTTCACATTATGGCTAGGTGTC 57.300 37.500 0.00 0.00 0.00 3.67
3270 4200 8.668510 AACAGTCACATAACATCCTATCATTC 57.331 34.615 0.00 0.00 0.00 2.67
3365 4295 6.099341 TGTCTTTTCCTGAAGCAAGAAAAAC 58.901 36.000 0.00 0.00 38.60 2.43
3373 4303 3.631250 AGGTTTGTCTTTTCCTGAAGCA 58.369 40.909 0.00 0.00 0.00 3.91
3594 4524 1.416813 CGACTCTGCCGCTTCATCAC 61.417 60.000 0.00 0.00 0.00 3.06
3595 4525 1.153765 CGACTCTGCCGCTTCATCA 60.154 57.895 0.00 0.00 0.00 3.07
3604 4534 0.179097 GGTCAGATTCCGACTCTGCC 60.179 60.000 10.22 10.66 39.98 4.85
3730 4660 5.367945 TCTGTTTTACCCTGTCAGTTCTT 57.632 39.130 0.00 0.00 0.00 2.52
3736 4666 3.135712 TCTTGCTCTGTTTTACCCTGTCA 59.864 43.478 0.00 0.00 0.00 3.58
3907 4837 3.507162 TCAAAATCAAGGGAGCACTCA 57.493 42.857 0.00 0.00 0.00 3.41
3933 4863 2.159393 GCATCAAAATTCGCAGCTACCA 60.159 45.455 0.00 0.00 0.00 3.25
3935 4865 2.104144 CGCATCAAAATTCGCAGCTAC 58.896 47.619 0.00 0.00 0.00 3.58
4085 5047 4.222810 TCAGTGCTTGACCTTCTGCTTATA 59.777 41.667 0.00 0.00 0.00 0.98
4086 5048 3.008375 TCAGTGCTTGACCTTCTGCTTAT 59.992 43.478 0.00 0.00 0.00 1.73
4091 5053 1.071385 ACCTCAGTGCTTGACCTTCTG 59.929 52.381 0.00 0.00 0.00 3.02
4093 5055 2.262423 AACCTCAGTGCTTGACCTTC 57.738 50.000 0.00 0.00 0.00 3.46
4188 5152 2.359531 AGATAGCACTACAGAGTTCGCC 59.640 50.000 0.00 0.00 31.73 5.54
4217 5181 2.138596 ATGCCGTTTTGAAGTGCAAG 57.861 45.000 0.00 0.00 37.87 4.01
4226 5190 3.545822 GCTGTTTTCCAAATGCCGTTTTG 60.546 43.478 0.00 0.00 36.55 2.44
4334 5298 5.227184 CGCTTGAACGAATAAAATGCCTAAC 59.773 40.000 0.00 0.00 34.06 2.34
4336 5300 4.201871 CCGCTTGAACGAATAAAATGCCTA 60.202 41.667 0.00 0.00 34.06 3.93
4427 5391 5.407407 TCTGCTACACTCCTTTTCCTTAG 57.593 43.478 0.00 0.00 0.00 2.18
4448 5414 1.589716 AATGTGGCCGCTCAGCTTTC 61.590 55.000 18.96 0.00 0.00 2.62
4453 5419 2.401766 GGTCAATGTGGCCGCTCAG 61.402 63.158 18.96 6.97 29.54 3.35
4459 5425 2.736670 ATAGGAAGGTCAATGTGGCC 57.263 50.000 0.00 0.00 44.07 5.36
4469 5435 6.724905 ACTTGTCTACACTTGTATAGGAAGGT 59.275 38.462 0.00 0.00 0.00 3.50
4551 5517 1.129251 CAAGGTGATGACATGTGCGTC 59.871 52.381 1.15 6.81 36.40 5.19
4555 5521 2.098607 GGATGCAAGGTGATGACATGTG 59.901 50.000 1.15 0.00 0.00 3.21
4558 5524 2.291089 TGTGGATGCAAGGTGATGACAT 60.291 45.455 0.00 0.00 0.00 3.06
4566 5532 0.675633 GCAACTTGTGGATGCAAGGT 59.324 50.000 10.07 0.95 46.25 3.50
4623 5589 6.367695 TGTGACTAACTATGGACAAATCGTTG 59.632 38.462 0.00 0.00 40.84 4.10
4725 8100 9.720769 TCATCTTTTTAGAACCTTCGAAATACT 57.279 29.630 0.00 0.00 33.04 2.12
4762 8166 1.854126 CAACTTTTTGCCAGTTCTGCG 59.146 47.619 0.00 0.00 31.83 5.18
4818 8224 2.104792 TGACCTGAAGGAACCTGAACAG 59.895 50.000 2.62 12.38 38.94 3.16
4879 8285 2.424956 GTCTGCCATTCAATCAGGGTTC 59.575 50.000 0.00 0.00 0.00 3.62
4942 8352 4.689071 TCATTACTGCATAACACCTACCG 58.311 43.478 0.00 0.00 0.00 4.02
4969 8380 7.876068 CAGTTAGACCCAAAAGTTGATACTACA 59.124 37.037 0.00 0.00 33.17 2.74


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

AutoCloner maintained by Alex Coulton.