Multiple sequence alignment - TraesCS3A01G394600

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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 TraesCS3A01G394600 chr3A 100.000 5152 0 0 1 5152 642153342 642158493 0 9515
1 TraesCS3A01G394600 chr3D 92.069 5119 227 82 84 5152 503851569 503856558 0 7038
2 TraesCS3A01G394600 chr3B 91.101 5169 261 102 1 5116 665252251 665257273 0 6813


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 TraesCS3A01G394600 chr3A 642153342 642158493 5151 False 9515 9515 100.000 1 5152 1 chr3A.!!$F1 5151
1 TraesCS3A01G394600 chr3D 503851569 503856558 4989 False 7038 7038 92.069 84 5152 1 chr3D.!!$F1 5068
2 TraesCS3A01G394600 chr3B 665252251 665257273 5022 False 6813 6813 91.101 1 5116 1 chr3B.!!$F1 5115

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
892 906 0.310854 GTCCAGGCCTGTTGTTTTCG 59.689 55.0 30.63 13.19 0.00 3.46 F
1507 1526 0.308684 CACTGTGTTCGCTGCATGTT 59.691 50.0 0.00 0.00 0.00 2.71 F
2721 2741 0.458669 CCATGATTTCCAGCTGGTGC 59.541 55.0 31.58 18.78 40.05 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2886 2906 0.721718 CGCTGTTCATCGGTTCTTCC 59.278 55.0 0.0 0.0 0.00 3.46 R
3362 3383 0.032678 CAGCTAGGCGTGGATTCGAT 59.967 55.0 0.0 0.0 0.00 3.59 R
4271 4318 0.938192 ACCCAAACCCAAAGGAAGGA 59.062 50.0 0.0 0.0 36.73 3.36 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
57 58 2.193248 CCTCCCGAGGCATTTCCC 59.807 66.667 0.00 0.00 42.44 3.97
58 59 2.203070 CTCCCGAGGCATTTCCCG 60.203 66.667 0.00 0.00 34.51 5.14
136 146 0.458716 CGTTCCTCGCCTCTCCTTTC 60.459 60.000 0.00 0.00 0.00 2.62
166 176 1.272769 CGGTCCGGGAGATTAGGATTC 59.727 57.143 2.34 0.00 36.34 2.52
180 190 7.278875 AGATTAGGATTCAGAGTAAGCTTTGG 58.721 38.462 3.20 0.00 0.00 3.28
181 191 4.917906 AGGATTCAGAGTAAGCTTTGGT 57.082 40.909 3.20 0.00 0.00 3.67
223 233 3.745803 GCTCTGGGCTGCTTGTGC 61.746 66.667 0.00 0.00 38.06 4.57
226 236 3.730761 CTGGGCTGCTTGTGCGTC 61.731 66.667 0.00 0.00 43.34 5.19
234 244 2.386660 GCTTGTGCGTCCTCTCTGC 61.387 63.158 0.00 0.00 0.00 4.26
263 273 2.289320 TGTGCTTCTCTGCTCCTCTTTC 60.289 50.000 0.00 0.00 0.00 2.62
268 278 2.455557 TCTCTGCTCCTCTTTCTCTGG 58.544 52.381 0.00 0.00 0.00 3.86
380 391 2.431782 CCCGATGGATTTCTGGCATTTT 59.568 45.455 0.00 0.00 0.00 1.82
381 392 3.491447 CCCGATGGATTTCTGGCATTTTC 60.491 47.826 0.00 0.00 0.00 2.29
382 393 3.130869 CCGATGGATTTCTGGCATTTTCA 59.869 43.478 0.00 0.00 0.00 2.69
384 395 4.980434 CGATGGATTTCTGGCATTTTCATC 59.020 41.667 0.00 0.00 0.00 2.92
385 396 4.741321 TGGATTTCTGGCATTTTCATCC 57.259 40.909 0.00 0.00 0.00 3.51
386 397 3.130869 TGGATTTCTGGCATTTTCATCCG 59.869 43.478 0.00 0.00 32.78 4.18
387 398 3.381272 GGATTTCTGGCATTTTCATCCGA 59.619 43.478 0.00 0.00 0.00 4.55
389 400 2.042686 TCTGGCATTTTCATCCGAGG 57.957 50.000 0.00 0.00 0.00 4.63
391 402 2.026356 TCTGGCATTTTCATCCGAGGAA 60.026 45.455 0.00 0.00 0.00 3.36
392 403 2.091541 TGGCATTTTCATCCGAGGAAC 58.908 47.619 0.00 0.00 0.00 3.62
499 510 4.301072 AGCTGCTTTAAATCCCACACTA 57.699 40.909 0.00 0.00 0.00 2.74
518 529 0.605589 ACTTGTCAGGCCGAGAGAAG 59.394 55.000 25.92 25.92 40.88 2.85
550 561 3.378427 GCTGCCGACCTCATCTTAATTTT 59.622 43.478 0.00 0.00 0.00 1.82
551 562 4.496507 GCTGCCGACCTCATCTTAATTTTC 60.497 45.833 0.00 0.00 0.00 2.29
555 566 6.208599 TGCCGACCTCATCTTAATTTTCTTTT 59.791 34.615 0.00 0.00 0.00 2.27
557 568 7.574967 GCCGACCTCATCTTAATTTTCTTTTGA 60.575 37.037 0.00 0.00 0.00 2.69
558 569 7.965107 CCGACCTCATCTTAATTTTCTTTTGAG 59.035 37.037 0.00 0.00 0.00 3.02
559 570 8.507249 CGACCTCATCTTAATTTTCTTTTGAGT 58.493 33.333 0.00 0.00 0.00 3.41
571 585 6.613153 TTTCTTTTGAGTTTTTCTTGGGGA 57.387 33.333 0.00 0.00 0.00 4.81
724 738 1.267532 CGCGCGTCTCAAATTTAGCAT 60.268 47.619 24.19 0.00 0.00 3.79
725 739 2.104144 GCGCGTCTCAAATTTAGCATG 58.896 47.619 8.43 0.00 0.00 4.06
727 741 2.351418 CGCGTCTCAAATTTAGCATGGA 59.649 45.455 0.00 0.00 0.00 3.41
787 801 1.942657 CCTGGAGAACACTGTGTTGTG 59.057 52.381 29.06 13.92 41.28 3.33
892 906 0.310854 GTCCAGGCCTGTTGTTTTCG 59.689 55.000 30.63 13.19 0.00 3.46
968 982 5.867903 TTTTCCCTTCTGAATCTTGCAAA 57.132 34.783 0.00 0.00 0.00 3.68
969 983 6.423776 TTTTCCCTTCTGAATCTTGCAAAT 57.576 33.333 0.00 0.00 0.00 2.32
970 984 6.423776 TTTCCCTTCTGAATCTTGCAAATT 57.576 33.333 0.00 3.64 0.00 1.82
981 995 6.436847 TGAATCTTGCAAATTAGATGGTGGAA 59.563 34.615 0.00 0.00 0.00 3.53
984 998 5.183713 TCTTGCAAATTAGATGGTGGAACTG 59.816 40.000 0.00 0.00 36.74 3.16
1026 1040 2.066999 AATGGAGGTCGAGGAGGGC 61.067 63.158 0.00 0.00 0.00 5.19
1111 1125 9.890629 AGTGATAATATCTGTTGTTCAAGCTAA 57.109 29.630 1.66 0.00 0.00 3.09
1131 1147 5.689068 GCTAATTGGTCTGCAGATTATTTGC 59.311 40.000 21.47 23.15 41.86 3.68
1210 1226 9.944663 TTTGCTTTGTAAACTTACATCTTAGTG 57.055 29.630 3.25 0.00 42.66 2.74
1211 1227 8.896320 TGCTTTGTAAACTTACATCTTAGTGA 57.104 30.769 3.25 0.00 42.66 3.41
1212 1228 8.770828 TGCTTTGTAAACTTACATCTTAGTGAC 58.229 33.333 3.25 0.00 42.66 3.67
1213 1229 8.989980 GCTTTGTAAACTTACATCTTAGTGACT 58.010 33.333 3.25 0.00 42.66 3.41
1215 1231 9.826574 TTTGTAAACTTACATCTTAGTGACTGT 57.173 29.630 3.25 0.00 42.66 3.55
1216 1232 9.826574 TTGTAAACTTACATCTTAGTGACTGTT 57.173 29.630 3.25 0.00 42.66 3.16
1237 1253 5.106712 TGTTTTAGCAGCACTCTTAATTCCG 60.107 40.000 0.00 0.00 0.00 4.30
1243 1259 5.648092 AGCAGCACTCTTAATTCCGTTTTAT 59.352 36.000 0.00 0.00 0.00 1.40
1253 1269 9.947433 TCTTAATTCCGTTTTATTTCTACAGGA 57.053 29.630 0.00 0.00 0.00 3.86
1291 1309 6.737254 TTTGTACTGTATAGGAAGCAAAGC 57.263 37.500 0.00 0.00 0.00 3.51
1294 1312 7.119709 TGTACTGTATAGGAAGCAAAGCATA 57.880 36.000 0.00 0.00 0.00 3.14
1325 1343 7.741554 ATAACTGGAACCTTGTATCTTCTCT 57.258 36.000 0.00 0.00 0.00 3.10
1349 1368 1.846007 TGGGTGGATTTGTGTATGGC 58.154 50.000 0.00 0.00 0.00 4.40
1372 1391 5.105997 GCTGCCTAATCTGAAGAAATTGTGT 60.106 40.000 0.00 0.00 0.00 3.72
1376 1395 7.867403 TGCCTAATCTGAAGAAATTGTGTTTTC 59.133 33.333 0.00 0.00 36.13 2.29
1387 1406 7.491682 AGAAATTGTGTTTTCTGCAGTTACAT 58.508 30.769 14.67 1.59 42.78 2.29
1507 1526 0.308684 CACTGTGTTCGCTGCATGTT 59.691 50.000 0.00 0.00 0.00 2.71
1543 1562 4.037923 TCCAAAGGTCTTCTTCAACATTGC 59.962 41.667 0.00 0.00 33.94 3.56
1556 1575 1.153920 CATTGCGCAGATTGCAGCA 60.154 52.632 11.31 13.55 45.36 4.41
1561 1580 2.799371 GCAGATTGCAGCAGGCTC 59.201 61.111 0.00 0.00 44.26 4.70
1592 1611 1.571773 ATGTTGTACCCCTCCCTGCC 61.572 60.000 0.00 0.00 0.00 4.85
1602 1621 3.368190 CTCCCTGCCGAGCACTCTG 62.368 68.421 0.00 0.00 33.79 3.35
1605 1624 2.729479 CCTGCCGAGCACTCTGGAT 61.729 63.158 11.18 0.00 33.79 3.41
1606 1625 1.395045 CCTGCCGAGCACTCTGGATA 61.395 60.000 11.18 1.45 33.79 2.59
1607 1626 0.678395 CTGCCGAGCACTCTGGATAT 59.322 55.000 11.18 0.00 33.79 1.63
1687 1706 9.820229 TTGTGTCTTTAGAATAATTAAACTGCG 57.180 29.630 0.00 0.00 0.00 5.18
1709 1728 8.575565 TGCGAAACTCTTACACTGATAATATC 57.424 34.615 0.00 0.00 0.00 1.63
1843 1862 7.147983 TGGCCATAAGGTATGTTGTGTAAAATC 60.148 37.037 0.00 0.00 37.19 2.17
1919 1939 4.502950 CCCACATTATGCACCAGTTGTTTT 60.503 41.667 0.00 0.00 0.00 2.43
1949 1969 6.460664 AAACCATTTAGTAAATTTGCGTGC 57.539 33.333 5.34 0.00 0.00 5.34
2087 2107 5.182570 TGATCAATTTGCTCCAGAGAAACAG 59.817 40.000 0.00 0.00 0.00 3.16
2391 2411 2.119029 GTATGGCCCCTGCGGAAAC 61.119 63.158 0.00 0.00 38.85 2.78
2523 2543 2.289565 GAAAACATGTCGATCCCTCCC 58.710 52.381 0.00 0.00 0.00 4.30
2721 2741 0.458669 CCATGATTTCCAGCTGGTGC 59.541 55.000 31.58 18.78 40.05 5.01
2793 2813 5.951747 TGTAAATTGGAGGCTTGCTTTATCT 59.048 36.000 0.00 0.00 0.00 1.98
2805 2825 1.808133 GCTTTATCTGACTCCCAGGCG 60.808 57.143 0.00 0.00 43.12 5.52
2823 2843 2.421739 ACGGGCTGTGTGTCTGTC 59.578 61.111 0.00 0.00 34.17 3.51
2886 2906 1.205893 CCCCTGGAGAACGAGAGAAAG 59.794 57.143 0.00 0.00 0.00 2.62
2896 2916 2.236766 ACGAGAGAAAGGAAGAACCGA 58.763 47.619 0.00 0.00 44.74 4.69
2897 2917 2.826725 ACGAGAGAAAGGAAGAACCGAT 59.173 45.455 0.00 0.00 44.74 4.18
2898 2918 3.182967 CGAGAGAAAGGAAGAACCGATG 58.817 50.000 0.00 0.00 44.74 3.84
3096 3116 1.678970 AAATGGGTTCGCTGAGGCC 60.679 57.895 0.00 0.00 34.44 5.19
3171 3191 1.070601 GTTGGTGCCATGGCTCTTTTT 59.929 47.619 35.53 0.00 42.51 1.94
3200 3220 8.454106 CCTTGCAGTCAATAATAATAGGTATGC 58.546 37.037 0.00 0.00 0.00 3.14
3241 3261 2.995466 GTGCTTGTCATTTGCAGCTA 57.005 45.000 0.00 0.00 37.39 3.32
3242 3262 2.860062 GTGCTTGTCATTTGCAGCTAG 58.140 47.619 0.00 0.00 37.39 3.42
3243 3263 2.227388 GTGCTTGTCATTTGCAGCTAGT 59.773 45.455 0.00 0.00 37.39 2.57
3244 3264 2.886523 TGCTTGTCATTTGCAGCTAGTT 59.113 40.909 0.00 0.00 32.55 2.24
3261 3281 6.146347 CAGCTAGTTAGTTGACCTTGAACTTC 59.854 42.308 0.00 0.00 36.76 3.01
3272 3292 5.532406 TGACCTTGAACTTCTGAATTTCCAG 59.468 40.000 15.23 13.55 35.55 3.86
3284 3304 7.106439 TCTGAATTTCCAGTTTTTGCTTACA 57.894 32.000 0.00 0.00 35.71 2.41
3287 3307 7.969314 TGAATTTCCAGTTTTTGCTTACAAAC 58.031 30.769 0.00 0.00 45.29 2.93
3335 3356 1.517242 GACTTCTGTTGTCTGCTGGG 58.483 55.000 0.00 0.00 0.00 4.45
3362 3383 3.506067 TCGAACTACTTGAGCAGATGACA 59.494 43.478 0.00 0.00 0.00 3.58
3558 3579 0.977395 GCTGTACAACCTCTCCACCT 59.023 55.000 0.00 0.00 0.00 4.00
3629 3650 2.034376 ACGCTCCTGACGGACTCT 59.966 61.111 0.00 0.00 34.92 3.24
4155 4197 1.036707 CCTCTACCAGTGCTAGCCTC 58.963 60.000 13.29 5.56 0.00 4.70
4156 4198 1.410932 CCTCTACCAGTGCTAGCCTCT 60.411 57.143 13.29 7.99 0.00 3.69
4224 4271 6.692486 TCTGTACATCTCCTCTTTCTTGTTC 58.308 40.000 0.00 0.00 0.00 3.18
4272 4319 3.793144 CGCCGTGGCTGCTTCTTC 61.793 66.667 9.55 0.00 39.32 2.87
4425 4474 1.599542 GCCTTGTTACGAGATGATGCC 59.400 52.381 0.31 0.00 0.00 4.40
4427 4476 3.126831 CCTTGTTACGAGATGATGCCTC 58.873 50.000 0.31 0.00 0.00 4.70
4431 4480 3.701542 TGTTACGAGATGATGCCTCTCTT 59.298 43.478 0.00 0.00 37.57 2.85
4432 4481 4.202060 TGTTACGAGATGATGCCTCTCTTC 60.202 45.833 0.00 0.00 37.57 2.87
4433 4482 1.686052 ACGAGATGATGCCTCTCTTCC 59.314 52.381 0.00 0.00 37.57 3.46
4434 4483 1.000731 CGAGATGATGCCTCTCTTCCC 59.999 57.143 0.00 0.00 37.57 3.97
4435 4484 2.328319 GAGATGATGCCTCTCTTCCCT 58.672 52.381 0.00 0.00 36.91 4.20
4436 4485 2.705127 GAGATGATGCCTCTCTTCCCTT 59.295 50.000 0.00 0.00 36.91 3.95
4475 4524 4.729595 ACCGTTTGTTCTCTTTTGTCAAC 58.270 39.130 0.00 0.00 0.00 3.18
4549 4608 1.153745 CGTTCTTCAGGGAGGCTCG 60.154 63.158 8.69 0.00 0.00 5.03
4585 4644 5.817816 AGGAGATTTATTTACTTGCTCACGG 59.182 40.000 0.00 0.00 0.00 4.94
4613 4672 1.001764 TGCTTGCTCATCCAGGTGG 60.002 57.895 0.00 0.00 0.00 4.61
4658 4717 1.463831 CTGATTATCATCGGCTGCTGC 59.536 52.381 7.10 7.10 38.76 5.25
4674 4733 2.435059 GCCTCTGCGTGGAAGGAC 60.435 66.667 0.00 0.00 0.00 3.85
4675 4734 2.125912 CCTCTGCGTGGAAGGACG 60.126 66.667 0.00 0.00 42.42 4.79
4739 4809 4.499188 CCAACATGAATGGATGCATGAGAC 60.499 45.833 13.65 0.00 43.43 3.36
4740 4810 4.166246 ACATGAATGGATGCATGAGACT 57.834 40.909 13.65 0.00 43.43 3.24
4742 4812 3.639672 TGAATGGATGCATGAGACTGT 57.360 42.857 2.46 0.00 0.00 3.55
4743 4813 3.275999 TGAATGGATGCATGAGACTGTG 58.724 45.455 2.46 0.00 0.00 3.66
4745 4815 2.685850 TGGATGCATGAGACTGTGAG 57.314 50.000 2.46 0.00 0.00 3.51
4746 4816 2.181975 TGGATGCATGAGACTGTGAGA 58.818 47.619 2.46 0.00 0.00 3.27
4747 4817 2.167900 TGGATGCATGAGACTGTGAGAG 59.832 50.000 2.46 0.00 0.00 3.20
4748 4818 2.483363 GGATGCATGAGACTGTGAGAGG 60.483 54.545 2.46 0.00 0.00 3.69
4749 4819 0.900421 TGCATGAGACTGTGAGAGGG 59.100 55.000 0.00 0.00 0.00 4.30
4759 4829 2.106684 ACTGTGAGAGGGAAAAAGGACC 59.893 50.000 0.00 0.00 0.00 4.46
4797 4867 2.266055 GACAGCACGGAGGAAGGG 59.734 66.667 0.00 0.00 0.00 3.95
4798 4868 3.959991 GACAGCACGGAGGAAGGGC 62.960 68.421 0.00 0.00 0.00 5.19
4833 4903 2.022129 CACGTGCTGTCCCGTTCTC 61.022 63.158 0.82 0.00 34.59 2.87
4849 4919 2.513666 TCCGCACGGGATGATTGC 60.514 61.111 9.58 0.00 40.94 3.56
4858 4943 4.619140 GATGATTGCGCGGCAGGC 62.619 66.667 8.83 3.27 40.61 4.85
4871 4956 2.875711 CAGGCGCGCGAATTTTGG 60.876 61.111 37.18 10.84 0.00 3.28
4882 4967 2.719798 CGAATTTTGGCATCATCCGTC 58.280 47.619 0.00 0.00 0.00 4.79
4884 4969 1.024271 ATTTTGGCATCATCCGTCGG 58.976 50.000 4.39 4.39 0.00 4.79
4887 4972 2.189521 GGCATCATCCGTCGGGTT 59.810 61.111 12.29 0.00 33.83 4.11
4891 4977 1.006832 CATCATCCGTCGGGTTTCAC 58.993 55.000 12.29 0.00 33.83 3.18
4892 4978 0.107848 ATCATCCGTCGGGTTTCACC 60.108 55.000 12.29 0.00 37.60 4.02
4897 4983 1.666872 CGTCGGGTTTCACCTCACC 60.667 63.158 0.00 0.00 38.64 4.02
4909 4995 4.803426 CTCACCTGGTCGAGCGGC 62.803 72.222 18.04 0.00 0.00 6.53
5001 5095 0.450184 CGGTTATTTGTGGCGGGAAG 59.550 55.000 0.00 0.00 0.00 3.46
5037 5131 3.036959 GAGGGAGGGAGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
5038 5132 3.039526 AGGGAGGGAGGGAGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
5039 5133 4.179599 GGGAGGGAGGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
5040 5134 4.179599 GGAGGGAGGGAGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
5041 5135 3.036959 GAGGGAGGGAGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
5042 5136 3.039526 AGGGAGGGAGGGAGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
5043 5137 4.179599 GGGAGGGAGGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
5044 5138 4.179599 GGAGGGAGGGAGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
5045 5139 4.179599 GAGGGAGGGAGGGAGGGG 62.180 77.778 0.00 0.00 0.00 4.79
5139 5238 2.418628 TGAAAAGCGAATCCGATTCCAC 59.581 45.455 14.28 7.83 44.23 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 3.141488 GAAGAGAGCGAGGCGGGA 61.141 66.667 0.00 0.00 0.00 5.14
57 58 4.186433 AGCGAAGAGAGCGAGGCG 62.186 66.667 0.00 0.00 40.04 5.52
58 59 2.278531 GAGCGAAGAGAGCGAGGC 60.279 66.667 0.00 0.00 40.04 4.70
60 61 1.011242 CTCGAGCGAAGAGAGCGAG 60.011 63.158 0.00 0.00 41.77 5.03
61 62 1.448013 TCTCGAGCGAAGAGAGCGA 60.448 57.895 7.81 0.00 39.57 4.93
65 66 1.375652 ACCGTCTCGAGCGAAGAGA 60.376 57.895 24.28 5.02 41.91 3.10
166 176 1.826385 CCCCACCAAAGCTTACTCTG 58.174 55.000 0.00 0.00 0.00 3.35
180 190 4.796495 GGTCACATCCCGCCCCAC 62.796 72.222 0.00 0.00 0.00 4.61
207 217 3.429141 CGCACAAGCAGCCCAGAG 61.429 66.667 0.00 0.00 42.27 3.35
212 222 3.426568 GAGGACGCACAAGCAGCC 61.427 66.667 0.00 0.00 42.27 4.85
218 228 2.049156 CGCAGAGAGGACGCACAA 60.049 61.111 0.00 0.00 0.00 3.33
240 250 0.735632 GAGGAGCAGAGAAGCACACG 60.736 60.000 0.00 0.00 36.85 4.49
309 320 2.589442 TGGAACCGCACGAACACC 60.589 61.111 0.00 0.00 0.00 4.16
322 333 2.745281 GCGTAAAACTAGCATGGTGGAA 59.255 45.455 15.72 0.00 0.00 3.53
380 391 2.423898 GGGCTCGTTCCTCGGATGA 61.424 63.158 0.00 0.00 40.32 2.92
381 392 2.107141 GGGCTCGTTCCTCGGATG 59.893 66.667 0.00 0.00 40.32 3.51
382 393 3.528370 CGGGCTCGTTCCTCGGAT 61.528 66.667 0.00 0.00 40.32 4.18
384 395 3.077519 ATTCGGGCTCGTTCCTCGG 62.078 63.158 5.57 0.00 40.32 4.63
385 396 1.878522 CATTCGGGCTCGTTCCTCG 60.879 63.158 5.57 0.00 41.41 4.63
386 397 1.521681 CCATTCGGGCTCGTTCCTC 60.522 63.158 5.57 0.00 37.69 3.71
387 398 2.584608 CCATTCGGGCTCGTTCCT 59.415 61.111 5.57 0.00 37.69 3.36
479 490 4.010349 AGTAGTGTGGGATTTAAAGCAGC 58.990 43.478 5.72 0.00 0.00 5.25
499 510 0.605589 CTTCTCTCGGCCTGACAAGT 59.394 55.000 0.00 0.00 0.00 3.16
550 561 5.359860 GTCTCCCCAAGAAAAACTCAAAAGA 59.640 40.000 0.00 0.00 35.21 2.52
551 562 5.592054 GTCTCCCCAAGAAAAACTCAAAAG 58.408 41.667 0.00 0.00 35.21 2.27
555 566 2.846193 CGTCTCCCCAAGAAAAACTCA 58.154 47.619 0.00 0.00 35.21 3.41
557 568 1.605753 GCGTCTCCCCAAGAAAAACT 58.394 50.000 0.00 0.00 35.21 2.66
558 569 0.237498 CGCGTCTCCCCAAGAAAAAC 59.763 55.000 0.00 0.00 35.21 2.43
559 570 0.887387 CCGCGTCTCCCCAAGAAAAA 60.887 55.000 4.92 0.00 35.21 1.94
637 651 2.037208 AAATCCAAGGGCCACGGG 59.963 61.111 6.18 3.71 0.00 5.28
638 652 3.005540 GCAAATCCAAGGGCCACGG 62.006 63.158 6.18 5.44 0.00 4.94
639 653 1.978617 AGCAAATCCAAGGGCCACG 60.979 57.895 6.18 0.00 0.00 4.94
640 654 1.593265 CAGCAAATCCAAGGGCCAC 59.407 57.895 6.18 0.00 0.00 5.01
641 655 1.610086 CCAGCAAATCCAAGGGCCA 60.610 57.895 6.18 0.00 0.00 5.36
642 656 2.361567 CCCAGCAAATCCAAGGGCC 61.362 63.158 0.00 0.00 31.81 5.80
643 657 2.361567 CCCCAGCAAATCCAAGGGC 61.362 63.158 0.00 0.00 38.22 5.19
724 738 1.959226 GCGAGCACGACCTTTTCCA 60.959 57.895 8.01 0.00 42.66 3.53
725 739 1.228657 AAGCGAGCACGACCTTTTCC 61.229 55.000 8.01 0.00 42.66 3.13
727 741 1.507141 CCAAGCGAGCACGACCTTTT 61.507 55.000 8.01 0.00 42.66 2.27
813 827 3.120108 ACGAAAAGAGGGGATGGGAATA 58.880 45.455 0.00 0.00 0.00 1.75
819 833 2.236395 ACCAGTACGAAAAGAGGGGATG 59.764 50.000 0.00 0.00 0.00 3.51
892 906 1.153958 GCAAGCATTTCAGACCGGC 60.154 57.895 0.00 0.00 0.00 6.13
968 982 4.023980 TCTCGTCAGTTCCACCATCTAAT 58.976 43.478 0.00 0.00 0.00 1.73
969 983 3.427573 TCTCGTCAGTTCCACCATCTAA 58.572 45.455 0.00 0.00 0.00 2.10
970 984 3.081710 TCTCGTCAGTTCCACCATCTA 57.918 47.619 0.00 0.00 0.00 1.98
981 995 3.181482 CCATGCTTGACTATCTCGTCAGT 60.181 47.826 0.22 0.00 44.02 3.41
984 998 3.376540 GTCCATGCTTGACTATCTCGTC 58.623 50.000 0.22 0.00 34.52 4.20
1026 1040 2.502295 GCATCAATAGCCAAGAGAGGG 58.498 52.381 0.00 0.00 0.00 4.30
1210 1226 5.924475 TTAAGAGTGCTGCTAAAACAGTC 57.076 39.130 0.00 0.00 39.96 3.51
1211 1227 6.072452 GGAATTAAGAGTGCTGCTAAAACAGT 60.072 38.462 0.00 0.00 39.96 3.55
1212 1228 6.317857 GGAATTAAGAGTGCTGCTAAAACAG 58.682 40.000 0.00 0.00 40.80 3.16
1213 1229 5.106712 CGGAATTAAGAGTGCTGCTAAAACA 60.107 40.000 0.00 0.00 0.00 2.83
1214 1230 5.106673 ACGGAATTAAGAGTGCTGCTAAAAC 60.107 40.000 0.00 0.00 0.00 2.43
1215 1231 5.001232 ACGGAATTAAGAGTGCTGCTAAAA 58.999 37.500 0.00 0.00 0.00 1.52
1216 1232 4.575885 ACGGAATTAAGAGTGCTGCTAAA 58.424 39.130 0.00 0.00 0.00 1.85
1243 1259 7.639378 AGCTTTAAATACCCATCCTGTAGAAA 58.361 34.615 0.00 0.00 0.00 2.52
1253 1269 9.695155 ATACAGTACAAAGCTTTAAATACCCAT 57.305 29.630 12.25 5.99 0.00 4.00
1263 1279 6.472887 TGCTTCCTATACAGTACAAAGCTTT 58.527 36.000 5.69 5.69 38.68 3.51
1281 1299 9.455847 CAGTTATTTCTAATATGCTTTGCTTCC 57.544 33.333 0.00 0.00 0.00 3.46
1282 1300 9.455847 CCAGTTATTTCTAATATGCTTTGCTTC 57.544 33.333 0.00 0.00 0.00 3.86
1303 1321 6.441088 AAGAGAAGATACAAGGTTCCAGTT 57.559 37.500 0.00 0.00 0.00 3.16
1334 1353 1.005805 AGGCAGCCATACACAAATCCA 59.994 47.619 15.80 0.00 0.00 3.41
1349 1368 6.506500 ACACAATTTCTTCAGATTAGGCAG 57.493 37.500 0.00 0.00 0.00 4.85
1372 1391 3.485394 TCCAGCATGTAACTGCAGAAAA 58.515 40.909 23.35 3.13 44.77 2.29
1376 1395 2.751259 ACATTCCAGCATGTAACTGCAG 59.249 45.455 13.48 13.48 44.77 4.41
1387 1406 0.323087 ATGCTCTGCACATTCCAGCA 60.323 50.000 0.00 0.00 43.04 4.41
1498 1517 7.726442 GGATTTATCCAGAGCAACATGCAGC 62.726 48.000 5.01 1.94 45.67 5.25
1556 1575 4.532521 ACAACATCTTACCAAGTAGAGCCT 59.467 41.667 0.00 0.00 0.00 4.58
1561 1580 5.189145 AGGGGTACAACATCTTACCAAGTAG 59.811 44.000 0.00 0.00 39.77 2.57
1592 1611 9.862371 AACTAATTATAATATCCAGAGTGCTCG 57.138 33.333 0.00 0.00 34.09 5.03
1683 1702 6.893958 ATTATCAGTGTAAGAGTTTCGCAG 57.106 37.500 0.00 0.00 0.00 5.18
1709 1728 1.308069 CGGTGATGGCCTGAAAGTGG 61.308 60.000 3.32 0.00 0.00 4.00
2087 2107 4.742438 TCGCTGGAACTGTTCATTTTAC 57.258 40.909 21.01 4.35 0.00 2.01
2391 2411 1.134995 TGTCTACTGAATGCTCGGCTG 60.135 52.381 0.00 0.00 0.00 4.85
2523 2543 1.186200 TGGGACATCTGAGTTCCTCG 58.814 55.000 7.15 0.00 38.07 4.63
2721 2741 4.437930 GGAACTGGAAAATCATTCTGCTCG 60.438 45.833 0.00 0.00 0.00 5.03
2805 2825 1.664965 GACAGACACACAGCCCGTC 60.665 63.158 0.00 0.00 0.00 4.79
2823 2843 5.839262 TGTTGCTAGTGTCAAAACTATCG 57.161 39.130 0.00 0.00 32.32 2.92
2886 2906 0.721718 CGCTGTTCATCGGTTCTTCC 59.278 55.000 0.00 0.00 0.00 3.46
2896 2916 1.089920 GTGCCTGATTCGCTGTTCAT 58.910 50.000 0.00 0.00 0.00 2.57
2897 2917 0.250252 TGTGCCTGATTCGCTGTTCA 60.250 50.000 0.00 0.00 0.00 3.18
2898 2918 1.089920 ATGTGCCTGATTCGCTGTTC 58.910 50.000 0.00 0.00 0.00 3.18
3096 3116 8.532819 ACAGAATACCTTAAGAACTGAACTAGG 58.467 37.037 3.36 0.00 0.00 3.02
3200 3220 7.818930 AGCACCATTTAACTGAAAAATACATGG 59.181 33.333 0.00 0.00 34.51 3.66
3241 3261 6.235231 TCAGAAGTTCAAGGTCAACTAACT 57.765 37.500 5.50 0.00 32.71 2.24
3242 3262 6.920569 TTCAGAAGTTCAAGGTCAACTAAC 57.079 37.500 5.50 0.00 32.71 2.34
3243 3263 8.519799 AAATTCAGAAGTTCAAGGTCAACTAA 57.480 30.769 5.50 0.00 32.71 2.24
3244 3264 7.228706 GGAAATTCAGAAGTTCAAGGTCAACTA 59.771 37.037 21.65 0.00 37.22 2.24
3261 3281 7.769272 TTGTAAGCAAAAACTGGAAATTCAG 57.231 32.000 0.00 0.00 40.40 3.02
3272 3292 5.538118 AGCATAGGGTTTGTAAGCAAAAAC 58.462 37.500 0.00 0.00 45.01 2.43
3284 3304 7.775053 TCTGAAATAAACAAGCATAGGGTTT 57.225 32.000 0.00 0.00 38.25 3.27
3287 3307 7.601856 TGTTTCTGAAATAAACAAGCATAGGG 58.398 34.615 6.06 0.00 42.28 3.53
3335 3356 5.487153 TCTGCTCAAGTAGTTCGACTATC 57.513 43.478 0.00 0.00 32.65 2.08
3362 3383 0.032678 CAGCTAGGCGTGGATTCGAT 59.967 55.000 0.00 0.00 0.00 3.59
3437 3458 2.825836 GCCTGGGTGGAAGCGATG 60.826 66.667 0.00 0.00 38.35 3.84
3440 3461 4.335647 ACAGCCTGGGTGGAAGCG 62.336 66.667 27.75 4.03 38.35 4.68
3558 3579 3.479203 CGGGATGCTGGCCTGGTA 61.479 66.667 12.06 0.45 0.00 3.25
4155 4197 0.967380 CCCAAAACCCTGCCTGCTAG 60.967 60.000 0.00 0.00 0.00 3.42
4156 4198 1.076549 CCCAAAACCCTGCCTGCTA 59.923 57.895 0.00 0.00 0.00 3.49
4268 4315 2.425683 CCCAAACCCAAAGGAAGGAAGA 60.426 50.000 0.00 0.00 36.73 2.87
4269 4316 1.970640 CCCAAACCCAAAGGAAGGAAG 59.029 52.381 0.00 0.00 36.73 3.46
4270 4317 1.292546 ACCCAAACCCAAAGGAAGGAA 59.707 47.619 0.00 0.00 36.73 3.36
4271 4318 0.938192 ACCCAAACCCAAAGGAAGGA 59.062 50.000 0.00 0.00 36.73 3.36
4272 4319 1.801242 AACCCAAACCCAAAGGAAGG 58.199 50.000 0.00 0.00 36.73 3.46
4425 4474 4.040952 TGACTGAAAAGGAAGGGAAGAGAG 59.959 45.833 0.00 0.00 0.00 3.20
4427 4476 4.357918 TGACTGAAAAGGAAGGGAAGAG 57.642 45.455 0.00 0.00 0.00 2.85
4431 4480 2.174639 TGCTTGACTGAAAAGGAAGGGA 59.825 45.455 0.00 0.00 0.00 4.20
4432 4481 2.586425 TGCTTGACTGAAAAGGAAGGG 58.414 47.619 0.00 0.00 0.00 3.95
4433 4482 3.243535 GGTTGCTTGACTGAAAAGGAAGG 60.244 47.826 2.50 0.00 35.91 3.46
4434 4483 3.548818 CGGTTGCTTGACTGAAAAGGAAG 60.549 47.826 2.50 0.00 35.91 3.46
4435 4484 2.357637 CGGTTGCTTGACTGAAAAGGAA 59.642 45.455 0.00 0.00 33.25 3.36
4436 4485 1.946768 CGGTTGCTTGACTGAAAAGGA 59.053 47.619 0.00 0.00 0.00 3.36
4475 4524 2.179517 GAGCAGAGGACCGTCGTG 59.820 66.667 0.00 0.00 0.00 4.35
4482 4531 1.274728 ACATGTCAGTGAGCAGAGGAC 59.725 52.381 0.00 0.00 0.00 3.85
4613 4672 1.045407 GGACAAAAAGGAACCCACCC 58.955 55.000 0.00 0.00 0.00 4.61
4658 4717 2.125912 CGTCCTTCCACGCAGAGG 60.126 66.667 0.00 0.00 40.53 3.69
4668 4727 2.185608 GAGGCCTCTGCGTCCTTC 59.814 66.667 26.25 0.00 44.61 3.46
4718 4788 4.338400 CAGTCTCATGCATCCATTCATGTT 59.662 41.667 0.00 0.00 40.54 2.71
4739 4809 2.784347 GGTCCTTTTTCCCTCTCACAG 58.216 52.381 0.00 0.00 0.00 3.66
4740 4810 1.071699 CGGTCCTTTTTCCCTCTCACA 59.928 52.381 0.00 0.00 0.00 3.58
4742 4812 0.690762 CCGGTCCTTTTTCCCTCTCA 59.309 55.000 0.00 0.00 0.00 3.27
4743 4813 0.677098 GCCGGTCCTTTTTCCCTCTC 60.677 60.000 1.90 0.00 0.00 3.20
4745 4815 1.677966 GGCCGGTCCTTTTTCCCTC 60.678 63.158 1.90 0.00 0.00 4.30
4746 4816 2.439245 GGCCGGTCCTTTTTCCCT 59.561 61.111 1.90 0.00 0.00 4.20
4747 4817 2.116556 TGGCCGGTCCTTTTTCCC 59.883 61.111 2.12 0.00 35.26 3.97
4748 4818 2.273179 GGTGGCCGGTCCTTTTTCC 61.273 63.158 2.12 0.00 35.26 3.13
4749 4819 1.529713 TGGTGGCCGGTCCTTTTTC 60.530 57.895 2.12 0.00 35.26 2.29
4779 4849 2.125912 CCTTCCTCCGTGCTGTCG 60.126 66.667 0.00 0.00 0.00 4.35
4797 4867 2.411547 CGTGAGTGAAAATGAACCTCGC 60.412 50.000 0.00 0.00 0.00 5.03
4798 4868 2.800544 ACGTGAGTGAAAATGAACCTCG 59.199 45.455 0.00 0.00 46.97 4.63
4858 4943 0.866906 ATGATGCCAAAATTCGCGCG 60.867 50.000 26.76 26.76 0.00 6.86
4859 4944 0.848305 GATGATGCCAAAATTCGCGC 59.152 50.000 0.00 0.00 0.00 6.86
4861 4946 1.202290 ACGGATGATGCCAAAATTCGC 60.202 47.619 0.00 0.00 0.00 4.70
4862 4947 2.719798 GACGGATGATGCCAAAATTCG 58.280 47.619 0.00 0.00 0.00 3.34
4863 4948 2.541588 CCGACGGATGATGCCAAAATTC 60.542 50.000 8.64 0.00 0.00 2.17
4866 4951 1.029408 CCCGACGGATGATGCCAAAA 61.029 55.000 17.49 0.00 0.00 2.44
4871 4956 0.742990 TGAAACCCGACGGATGATGC 60.743 55.000 17.49 0.00 0.00 3.91
4887 4972 1.816863 GCTCGACCAGGTGAGGTGAA 61.817 60.000 16.43 0.00 43.38 3.18
4891 4977 4.135153 CCGCTCGACCAGGTGAGG 62.135 72.222 16.43 3.17 32.78 3.86
4892 4978 4.803426 GCCGCTCGACCAGGTGAG 62.803 72.222 0.00 5.74 35.30 3.51
4909 4995 3.947841 CGCTCCGCTCCTCGAGAG 61.948 72.222 15.71 10.58 46.29 3.20
4954 5040 6.176896 GCTCCTAATTAAATCAGATCCCCTC 58.823 44.000 0.00 0.00 0.00 4.30
4959 5045 5.257262 GGGGGCTCCTAATTAAATCAGATC 58.743 45.833 0.52 0.00 0.00 2.75
4960 5046 4.263506 CGGGGGCTCCTAATTAAATCAGAT 60.264 45.833 0.52 0.00 0.00 2.90
4961 5047 3.072476 CGGGGGCTCCTAATTAAATCAGA 59.928 47.826 0.52 0.00 0.00 3.27
4962 5048 3.412386 CGGGGGCTCCTAATTAAATCAG 58.588 50.000 0.52 0.00 0.00 2.90
4963 5049 2.107552 CCGGGGGCTCCTAATTAAATCA 59.892 50.000 0.52 0.00 0.00 2.57
5025 5119 3.039526 CTCCCTCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
5026 5120 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
5125 5224 2.244651 GGGCGTGGAATCGGATTCG 61.245 63.158 21.03 13.52 40.17 3.34


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

AutoCloner maintained by Alex Coulton.