Multiple sequence alignment - TraesCS2A01G324900

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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 TraesCS2A01G324900 chr2A 100.000 5267 0 0 1 5267 554824827 554819561 0.000000e+00 9727.0
1 TraesCS2A01G324900 chr2B 94.309 4797 187 33 1 4737 510399239 510404009 0.000000e+00 7267.0
2 TraesCS2A01G324900 chr2B 92.277 505 25 6 4770 5267 510404010 510404507 0.000000e+00 704.0
3 TraesCS2A01G324900 chr2D 92.780 4654 236 54 1 4597 431514379 431518989 0.000000e+00 6641.0
4 TraesCS2A01G324900 chr2D 83.333 114 6 7 5165 5267 431531218 431531329 5.620000e-15 93.5
5 TraesCS2A01G324900 chr2D 76.355 203 27 7 4664 4860 431527061 431527248 7.270000e-14 89.8


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 TraesCS2A01G324900 chr2A 554819561 554824827 5266 True 9727.0 9727 100.000 1 5267 1 chr2A.!!$R1 5266
1 TraesCS2A01G324900 chr2B 510399239 510404507 5268 False 3985.5 7267 93.293 1 5267 2 chr2B.!!$F1 5266
2 TraesCS2A01G324900 chr2D 431514379 431518989 4610 False 6641.0 6641 92.780 1 4597 1 chr2D.!!$F1 4596

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
278 279 0.251165 AACAGTACCTTTGCCGCCAT 60.251 50.000 0.00 0.00 0.00 4.40 F
420 421 0.511221 CGCAGGACTTTACGGTGTTG 59.489 55.000 0.00 0.00 0.00 3.33 F
2148 2182 0.248784 GGAAATGCCATCGCTCTTGC 60.249 55.000 0.00 0.00 36.34 4.01 F
3783 3850 1.006878 ACTGTAGGTCCTGGTCTACCC 59.993 57.143 19.29 4.93 36.34 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1508 1520 1.892209 ACCGACATCAAGTCCAAACC 58.108 50.000 0.00 0.0 44.66 3.27 R
2375 2410 1.231641 CTCCCCGAGAGACCCTCAT 59.768 63.158 0.00 0.0 46.50 2.90 R
4114 4181 0.955428 TCGGTCAGGCACTTGCATTC 60.955 55.000 3.15 0.0 44.36 2.67 R
4738 4845 0.040204 CATGGCCCCTTCCTTCAGTT 59.960 55.000 0.00 0.0 0.00 3.16 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
138 139 3.820467 TCACCAATGTGACCTCATCAAAC 59.180 43.478 0.00 0.00 46.40 2.93
171 172 4.949856 ACCTCAAGCATACCCTTAAACATG 59.050 41.667 0.00 0.00 0.00 3.21
234 235 4.434725 GCTATCATCGCATTCCATGTAACG 60.435 45.833 0.00 0.00 0.00 3.18
249 250 2.064014 GTAACGACACCCTTTTCCTCG 58.936 52.381 0.00 0.00 0.00 4.63
278 279 0.251165 AACAGTACCTTTGCCGCCAT 60.251 50.000 0.00 0.00 0.00 4.40
297 298 1.048160 TGATATCCCCACAGCTCGCA 61.048 55.000 0.00 0.00 0.00 5.10
420 421 0.511221 CGCAGGACTTTACGGTGTTG 59.489 55.000 0.00 0.00 0.00 3.33
426 427 2.095415 GGACTTTACGGTGTTGGCAATC 60.095 50.000 1.92 0.00 0.00 2.67
543 544 3.131396 GGCACGGATAAGGATGTTGTAG 58.869 50.000 0.00 0.00 0.00 2.74
646 647 4.208686 GGAGCGTGGTAGCCTCGG 62.209 72.222 10.86 0.00 40.31 4.63
851 859 2.200170 CTTAAGCGCACCAGGCCAAC 62.200 60.000 11.47 0.00 40.31 3.77
878 886 3.762779 CTTGCCTTTCTTTGCTTATCCG 58.237 45.455 0.00 0.00 0.00 4.18
941 949 2.362760 TGGCCCCACATGTCATGC 60.363 61.111 12.91 0.00 0.00 4.06
975 983 0.823356 AGATCCGCCTCTCTGCTCTC 60.823 60.000 0.00 0.00 0.00 3.20
1022 1030 1.065782 GGCTTCTTCCTCTCCAACTCC 60.066 57.143 0.00 0.00 0.00 3.85
1023 1031 1.625818 GCTTCTTCCTCTCCAACTCCA 59.374 52.381 0.00 0.00 0.00 3.86
1062 1070 3.138798 GTCCTCCTAGCGTCCGCA 61.139 66.667 14.70 0.00 44.88 5.69
1430 1438 2.046314 CCGGGTAGGTGGTTGCTG 60.046 66.667 0.00 0.00 34.51 4.41
1471 1483 1.777272 GGTTATCCCCTGAGAAGCCAT 59.223 52.381 0.00 0.00 34.87 4.40
1508 1520 0.443869 CGGATTCCTGCGTTGTTCTG 59.556 55.000 0.30 0.00 0.00 3.02
1683 1705 6.091718 TGGAAGGTTAAGTTATGCCAAAAC 57.908 37.500 6.74 0.00 0.00 2.43
1809 1833 4.819630 ACTTCACAACACCGTATGTCAATT 59.180 37.500 0.00 0.00 42.31 2.32
1810 1834 5.992829 ACTTCACAACACCGTATGTCAATTA 59.007 36.000 0.00 0.00 42.31 1.40
1811 1835 6.653320 ACTTCACAACACCGTATGTCAATTAT 59.347 34.615 0.00 0.00 42.31 1.28
1812 1836 7.820386 ACTTCACAACACCGTATGTCAATTATA 59.180 33.333 0.00 0.00 42.31 0.98
1909 1934 6.985188 TGGATCAATTTGTCTGTAGCTAAC 57.015 37.500 0.00 0.00 0.00 2.34
1987 2013 9.584008 AACATTGCATATTAGAGGAATTCTGAT 57.416 29.630 5.23 0.00 36.61 2.90
2056 2089 8.487028 TCAGGGTATCCTTCTTTTCTCTTTATC 58.513 37.037 0.00 0.00 42.67 1.75
2148 2182 0.248784 GGAAATGCCATCGCTCTTGC 60.249 55.000 0.00 0.00 36.34 4.01
2155 2189 2.162208 TGCCATCGCTCTTGCTTAAAAG 59.838 45.455 0.00 0.00 36.97 2.27
2166 2200 6.575162 TCTTGCTTAAAAGATTGTCTTCCC 57.425 37.500 0.00 0.00 35.27 3.97
2312 2346 4.728772 TGTTTGGATGATGGGGATACATC 58.271 43.478 0.00 0.00 45.79 3.06
2317 2351 3.584406 GGATGATGGGGATACATCTCACA 59.416 47.826 0.00 0.00 45.78 3.58
2456 2491 8.828751 AGTCAAATAATGTAGTTACCCAACCTA 58.171 33.333 0.00 0.00 35.05 3.08
2472 2507 7.007723 ACCCAACCTATATGTTTTTCTTGTGA 58.992 34.615 0.00 0.00 0.00 3.58
2481 2516 5.554822 TGTTTTTCTTGTGACACACCTAC 57.445 39.130 8.05 2.15 32.73 3.18
2509 2544 5.916883 CAGGCTAAACATGAAGTGAAAACAG 59.083 40.000 0.00 0.00 0.00 3.16
2595 2630 6.272792 TGGGTCAAACTTAATAGGAAGTGGTA 59.727 38.462 0.00 0.00 39.62 3.25
2616 2651 2.356673 GCTTTGGCCAGCAACAGC 60.357 61.111 11.92 9.22 39.83 4.40
2646 2681 7.402054 TGGTCATACTTGATAACCAAATGACT 58.598 34.615 15.94 0.00 44.55 3.41
2838 2873 8.573035 CAAAATGTTAGTTTGTGGTACAGGTAT 58.427 33.333 0.00 0.00 41.80 2.73
3235 3270 1.317613 GGTTTGACATGTCTGGCACA 58.682 50.000 25.55 2.87 41.21 4.57
3262 3297 8.764287 CATATTGCTGACAATCGTTATCTTACA 58.236 33.333 0.00 0.00 43.08 2.41
3531 3566 4.923893 TGCTATCTGTTGCACATATTTGC 58.076 39.130 6.91 6.91 43.31 3.68
3533 3568 4.037208 GCTATCTGTTGCACATATTTGCCT 59.963 41.667 11.22 0.00 42.25 4.75
3542 3577 3.127895 GCACATATTTGCCTAACCGTTCA 59.872 43.478 2.23 0.00 36.42 3.18
3681 3716 8.624776 TCGATGATGATATATGTAGTAGCCAAG 58.375 37.037 0.00 0.00 0.00 3.61
3711 3746 7.675170 GCAAGAAAAACTAAAATCCACGCAAAA 60.675 33.333 0.00 0.00 0.00 2.44
3721 3756 3.617540 TCCACGCAAAATATAATGCCG 57.382 42.857 6.98 5.47 39.39 5.69
3783 3850 1.006878 ACTGTAGGTCCTGGTCTACCC 59.993 57.143 19.29 4.93 36.34 3.69
3982 4049 1.474077 GTGATACTGCAAAGCTTGGGG 59.526 52.381 0.00 0.00 0.00 4.96
4114 4181 1.423721 CGGCGTCATCACCACAGATG 61.424 60.000 0.00 0.00 45.28 2.90
4131 4198 1.133790 GATGAATGCAAGTGCCTGACC 59.866 52.381 0.00 0.00 41.18 4.02
4143 4210 0.744771 GCCTGACCGAAGATCCAACC 60.745 60.000 0.00 0.00 0.00 3.77
4158 4225 2.948720 AACCTGCGACCCTGAGAGC 61.949 63.158 0.00 0.00 0.00 4.09
4179 4246 5.815581 AGCCAGTGGTTCAAAGTTATATCA 58.184 37.500 11.74 0.00 0.00 2.15
4200 4267 2.599677 AGTAGTAGAGGCATACCAGGC 58.400 52.381 0.00 0.00 39.06 4.85
4203 4270 0.969894 GTAGAGGCATACCAGGCGAT 59.030 55.000 0.00 0.00 39.06 4.58
4204 4271 1.344763 GTAGAGGCATACCAGGCGATT 59.655 52.381 0.00 0.00 39.06 3.34
4217 4284 0.391661 GGCGATTCCTCTGTTCTGCA 60.392 55.000 0.00 0.00 0.00 4.41
4247 4314 2.538141 TTGGACCCTGGCCTCCAAG 61.538 63.158 17.90 0.39 40.89 3.61
4248 4315 3.732849 GGACCCTGGCCTCCAAGG 61.733 72.222 3.32 1.16 40.77 3.61
4342 4409 1.621107 TTCGACGACCGTAATCTTGC 58.379 50.000 0.00 0.00 39.75 4.01
4374 4441 2.967459 TACACGCAAAATGTCTGCAG 57.033 45.000 7.63 7.63 39.91 4.41
4375 4442 1.024271 ACACGCAAAATGTCTGCAGT 58.976 45.000 14.67 0.00 39.91 4.40
4377 4444 2.046313 CACGCAAAATGTCTGCAGTTC 58.954 47.619 14.67 9.03 39.91 3.01
4378 4445 1.675483 ACGCAAAATGTCTGCAGTTCA 59.325 42.857 14.67 14.44 39.91 3.18
4379 4446 2.046313 CGCAAAATGTCTGCAGTTCAC 58.954 47.619 14.67 5.26 39.91 3.18
4380 4447 2.287188 CGCAAAATGTCTGCAGTTCACT 60.287 45.455 14.67 1.65 39.91 3.41
4419 4488 3.630312 TGTGTCACCCTTTAAGCACTTTC 59.370 43.478 0.00 0.00 0.00 2.62
4511 4595 2.084546 CTAGTGCTTGTTGGCTTACCC 58.915 52.381 0.00 0.00 33.59 3.69
4512 4596 0.539669 AGTGCTTGTTGGCTTACCCC 60.540 55.000 0.00 0.00 33.59 4.95
4553 4637 0.466189 CACTTGTTGGCCACTGAGGT 60.466 55.000 3.88 0.00 40.61 3.85
4563 4647 1.063867 GCCACTGAGGTAGTCTAGGGA 60.064 57.143 0.00 0.00 37.60 4.20
4625 4728 3.369892 GGAGGAGATAGAGCTTGCACAAA 60.370 47.826 0.00 0.00 0.00 2.83
4640 4743 9.143631 AGCTTGCACAAATTTTCTTGTTATATC 57.856 29.630 0.00 0.00 37.43 1.63
4643 4746 7.327214 TGCACAAATTTTCTTGTTATATCCCC 58.673 34.615 0.00 0.00 37.43 4.81
4645 4748 7.580495 GCACAAATTTTCTTGTTATATCCCCCA 60.580 37.037 0.00 0.00 37.43 4.96
4649 4752 9.958180 AAATTTTCTTGTTATATCCCCCAAAAG 57.042 29.630 0.00 0.00 0.00 2.27
4657 4764 6.071051 TGTTATATCCCCCAAAAGAAAACTGC 60.071 38.462 0.00 0.00 0.00 4.40
4673 4780 6.717084 AGAAAACTGCTTACCTTTATTCAGCT 59.283 34.615 0.00 0.00 0.00 4.24
4712 4819 4.937201 AACTCAAACCAAACTGAATCCC 57.063 40.909 0.00 0.00 0.00 3.85
4726 4833 3.078837 TGAATCCCAAAGAACCTAACGC 58.921 45.455 0.00 0.00 0.00 4.84
4730 4837 4.133013 TCCCAAAGAACCTAACGCTATC 57.867 45.455 0.00 0.00 0.00 2.08
4732 4839 3.871594 CCCAAAGAACCTAACGCTATCTG 59.128 47.826 0.00 0.00 0.00 2.90
4737 4844 5.000012 AGAACCTAACGCTATCTGTTCTG 58.000 43.478 0.00 0.00 40.47 3.02
4738 4845 4.705507 AGAACCTAACGCTATCTGTTCTGA 59.294 41.667 0.00 0.00 40.47 3.27
4739 4846 5.185249 AGAACCTAACGCTATCTGTTCTGAA 59.815 40.000 0.00 0.00 40.47 3.02
4740 4847 4.745649 ACCTAACGCTATCTGTTCTGAAC 58.254 43.478 13.49 13.49 0.00 3.18
4741 4848 4.463186 ACCTAACGCTATCTGTTCTGAACT 59.537 41.667 20.18 4.26 0.00 3.01
4742 4849 4.800993 CCTAACGCTATCTGTTCTGAACTG 59.199 45.833 20.18 19.07 0.00 3.16
4743 4850 4.521130 AACGCTATCTGTTCTGAACTGA 57.479 40.909 25.57 25.57 42.37 3.41
4744 4851 4.521130 ACGCTATCTGTTCTGAACTGAA 57.479 40.909 26.62 17.30 41.66 3.02
4745 4852 4.489810 ACGCTATCTGTTCTGAACTGAAG 58.510 43.478 26.62 23.40 41.66 3.02
4746 4853 3.862267 CGCTATCTGTTCTGAACTGAAGG 59.138 47.826 26.62 22.16 41.66 3.46
4747 4854 4.380973 CGCTATCTGTTCTGAACTGAAGGA 60.381 45.833 26.62 16.82 41.66 3.36
4748 4855 5.482908 GCTATCTGTTCTGAACTGAAGGAA 58.517 41.667 26.62 15.11 41.66 3.36
4749 4856 5.580297 GCTATCTGTTCTGAACTGAAGGAAG 59.420 44.000 26.62 21.46 41.66 3.46
4750 4857 4.342862 TCTGTTCTGAACTGAAGGAAGG 57.657 45.455 22.61 4.17 36.58 3.46
4751 4858 3.071602 TCTGTTCTGAACTGAAGGAAGGG 59.928 47.826 22.61 2.97 36.58 3.95
4752 4859 2.106511 TGTTCTGAACTGAAGGAAGGGG 59.893 50.000 20.18 0.00 0.00 4.79
4753 4860 0.693049 TCTGAACTGAAGGAAGGGGC 59.307 55.000 0.00 0.00 0.00 5.80
4754 4861 0.322906 CTGAACTGAAGGAAGGGGCC 60.323 60.000 0.00 0.00 0.00 5.80
4755 4862 1.065410 TGAACTGAAGGAAGGGGCCA 61.065 55.000 4.39 0.00 0.00 5.36
4756 4863 0.332972 GAACTGAAGGAAGGGGCCAT 59.667 55.000 4.39 0.00 0.00 4.40
4757 4864 0.040204 AACTGAAGGAAGGGGCCATG 59.960 55.000 4.39 0.00 0.00 3.66
4758 4865 0.846427 ACTGAAGGAAGGGGCCATGA 60.846 55.000 4.39 0.00 0.00 3.07
4759 4866 0.106819 CTGAAGGAAGGGGCCATGAG 60.107 60.000 4.39 0.00 0.00 2.90
4760 4867 1.228510 GAAGGAAGGGGCCATGAGG 59.771 63.158 4.39 0.00 38.23 3.86
4761 4868 1.230281 AAGGAAGGGGCCATGAGGA 60.230 57.895 4.39 0.00 36.89 3.71
4762 4869 0.628668 AAGGAAGGGGCCATGAGGAT 60.629 55.000 4.39 0.00 36.89 3.24
4763 4870 1.064824 AGGAAGGGGCCATGAGGATC 61.065 60.000 4.39 0.00 36.89 3.36
4783 4890 0.323178 ACCCATTTCTCTGCCTGCAG 60.323 55.000 12.91 12.91 44.86 4.41
4788 4895 3.889134 TTCTCTGCCTGCAGCCGTG 62.889 63.158 14.22 2.10 43.31 4.94
4791 4898 2.187685 CTGCCTGCAGCCGTGATA 59.812 61.111 8.66 0.00 42.71 2.15
4865 4972 2.386661 TTGAAGGACGAGATTGCCTC 57.613 50.000 0.00 0.00 38.55 4.70
4875 4982 1.865970 GAGATTGCCTCGCATGAAGAG 59.134 52.381 0.00 4.14 38.76 2.85
4881 4988 1.005340 CCTCGCATGAAGAGCAGAAC 58.995 55.000 11.70 0.00 34.56 3.01
4893 5000 8.886719 CATGAAGAGCAGAACTTAACATTGATA 58.113 33.333 0.00 0.00 0.00 2.15
4941 5051 5.306419 TGAAAGATCTAGGATGCTAGCACAT 59.694 40.000 22.07 14.03 0.00 3.21
4944 5054 5.024785 AGATCTAGGATGCTAGCACATGAT 58.975 41.667 22.07 17.88 0.00 2.45
4964 5074 6.007936 TGATTTGGATTACGGTTGAAACAG 57.992 37.500 0.00 0.00 0.00 3.16
4991 5105 5.609382 TTCACGCTGTTAATTATACGACG 57.391 39.130 0.00 0.00 0.00 5.12
4994 5108 5.799435 TCACGCTGTTAATTATACGACGAAA 59.201 36.000 0.00 0.00 0.00 3.46
4996 5110 6.403214 CACGCTGTTAATTATACGACGAAAAC 59.597 38.462 0.00 0.00 0.00 2.43
5049 5163 7.463961 AGCAAATCTCTTGTGATGAGAAAAT 57.536 32.000 0.00 0.00 42.84 1.82
5077 5191 5.178797 TCTTCATTCGATGGAAAAGAGTCC 58.821 41.667 0.00 0.00 35.40 3.85
5081 5195 3.777465 TCGATGGAAAAGAGTCCTACG 57.223 47.619 0.00 0.00 38.62 3.51
5092 5206 4.993029 AGAGTCCTACGAAAAGATCCAG 57.007 45.455 0.00 0.00 0.00 3.86
5146 5260 0.037590 GGACCTGGCCATGTGTGTTA 59.962 55.000 19.24 0.00 0.00 2.41
5156 5270 3.091545 CCATGTGTGTTAAGCATTCCCT 58.908 45.455 0.00 0.00 0.00 4.20
5220 5334 2.158667 TGAACAGGAAGGAAACCCACTC 60.159 50.000 0.00 0.00 0.00 3.51
5255 5369 2.492881 TCAATTACCACGTCTCGCCTTA 59.507 45.455 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
138 139 3.972227 CTTGAGGTTCAGGCACCG 58.028 61.111 0.00 0.00 42.33 4.94
171 172 1.826096 GACTGGAAGGAGGTAGTGGAC 59.174 57.143 0.00 0.00 39.30 4.02
234 235 1.797025 CAGTCGAGGAAAAGGGTGTC 58.203 55.000 0.00 0.00 0.00 3.67
249 250 2.150397 AGGTACTGTTCAACGCAGTC 57.850 50.000 0.95 0.00 44.96 3.51
278 279 1.048160 TGCGAGCTGTGGGGATATCA 61.048 55.000 4.83 0.00 0.00 2.15
420 421 2.870372 GACCAGCACACGATTGCC 59.130 61.111 9.00 0.00 44.14 4.52
635 636 2.365105 CCTTCCCCGAGGCTACCA 60.365 66.667 0.00 0.00 0.00 3.25
646 647 0.906066 GAGTCCTTCCACTCCTTCCC 59.094 60.000 0.00 0.00 37.43 3.97
851 859 2.919494 AAAGAAAGGCAAGCGGCGG 61.919 57.895 9.78 0.00 46.16 6.13
855 863 2.704725 TAAGCAAAGAAAGGCAAGCG 57.295 45.000 0.00 0.00 0.00 4.68
878 886 1.503542 CACGGATTGGTTGCTGCTC 59.496 57.895 0.00 0.00 0.00 4.26
941 949 3.214328 CGGATCTGGAGTTTAAATGGGG 58.786 50.000 0.00 0.00 0.00 4.96
975 983 0.546747 TTACTGGGACTGGGACTGGG 60.547 60.000 0.00 0.00 0.00 4.45
1022 1030 4.154347 GGAGGCCGAGGAGCAGTG 62.154 72.222 0.00 0.00 0.00 3.66
1023 1031 4.390556 AGGAGGCCGAGGAGCAGT 62.391 66.667 0.00 0.00 0.00 4.40
1430 1438 3.242316 CCTCGGTTATTTAAAGCGCTGAC 60.242 47.826 12.58 1.26 40.50 3.51
1471 1483 6.756074 GGAATCCGAATAAACAAATGCAATCA 59.244 34.615 0.00 0.00 0.00 2.57
1508 1520 1.892209 ACCGACATCAAGTCCAAACC 58.108 50.000 0.00 0.00 44.66 3.27
1651 1669 5.523438 AACTTAACCTTCCAATTCGCAAA 57.477 34.783 0.00 0.00 0.00 3.68
1683 1705 6.017400 AGGTTGCATTAAAGACATGTTCAG 57.983 37.500 0.00 0.00 0.00 3.02
1738 1762 8.834465 ACTCTAGCAGCAACAAATATATTCAAG 58.166 33.333 0.00 0.00 0.00 3.02
1883 1908 4.885907 AGCTACAGACAAATTGATCCATGG 59.114 41.667 4.97 4.97 0.00 3.66
1888 1913 6.457528 GCTGGTTAGCTACAGACAAATTGATC 60.458 42.308 13.98 0.00 46.57 2.92
1909 1934 4.510038 AAACAGTGCTAATTTCAGCTGG 57.490 40.909 15.13 0.00 42.30 4.85
1987 2013 6.433716 TGTGAGTTCTGATGAATTATTTGCCA 59.566 34.615 0.00 0.00 34.40 4.92
2056 2089 2.118313 TGCATCAGATGGTGTCCTTG 57.882 50.000 12.54 0.00 0.00 3.61
2155 2189 4.398044 TGGCGAATAAAAGGGAAGACAATC 59.602 41.667 0.00 0.00 0.00 2.67
2166 2200 5.622770 ACCTAAACAGTGGCGAATAAAAG 57.377 39.130 0.00 0.00 0.00 2.27
2199 2233 7.442364 CCATCAATTTGGTGACTAGTAGGTATG 59.558 40.741 11.28 0.00 27.35 2.39
2312 2346 5.586243 ACCTAATCCATTCGTTTGATGTGAG 59.414 40.000 0.00 0.00 0.00 3.51
2317 2351 4.576463 GCTCACCTAATCCATTCGTTTGAT 59.424 41.667 0.00 0.00 0.00 2.57
2375 2410 1.231641 CTCCCCGAGAGACCCTCAT 59.768 63.158 0.00 0.00 46.50 2.90
2430 2465 7.696017 AGGTTGGGTAACTACATTATTTGACT 58.304 34.615 0.00 0.00 36.99 3.41
2431 2466 7.933215 AGGTTGGGTAACTACATTATTTGAC 57.067 36.000 0.00 0.00 36.99 3.18
2438 2473 9.984590 AAAACATATAGGTTGGGTAACTACATT 57.015 29.630 3.11 0.00 36.99 2.71
2441 2476 9.676861 AGAAAAACATATAGGTTGGGTAACTAC 57.323 33.333 3.11 0.00 36.99 2.73
2456 2491 6.959639 AGGTGTGTCACAAGAAAAACATAT 57.040 33.333 7.38 0.00 35.86 1.78
2472 2507 2.913603 TAGCCTGGTAGTAGGTGTGT 57.086 50.000 0.00 0.00 40.11 3.72
2481 2516 4.832248 TCACTTCATGTTTAGCCTGGTAG 58.168 43.478 0.00 0.00 0.00 3.18
2595 2630 0.828762 TGTTGCTGGCCAAAGCTGAT 60.829 50.000 17.08 0.00 43.90 2.90
2646 2681 2.388735 CTACAGCACCATCCTGGAGTA 58.611 52.381 1.52 0.00 40.96 2.59
2706 2741 2.472695 TCAACCATTCTTCAGGGTCG 57.527 50.000 0.00 0.00 32.67 4.79
2838 2873 0.771127 AGGGCCTTTGCTCAGTAACA 59.229 50.000 0.00 0.00 41.98 2.41
3235 3270 7.792374 AAGATAACGATTGTCAGCAATATGT 57.208 32.000 0.00 0.00 44.61 2.29
3262 3297 3.937706 CAGCTGCTACACTTAAGAAGCAT 59.062 43.478 22.71 12.60 46.58 3.79
3542 3577 4.559153 GCTTATGTGTTGGTTCAGCAAAT 58.441 39.130 0.00 0.00 0.00 2.32
3681 3716 7.410407 GCGTGGATTTTAGTTTTTCTTGCATAC 60.410 37.037 0.00 0.00 0.00 2.39
3783 3850 3.058016 CCTTGTATGGTTTGTGACTGCTG 60.058 47.826 0.00 0.00 0.00 4.41
4114 4181 0.955428 TCGGTCAGGCACTTGCATTC 60.955 55.000 3.15 0.00 44.36 2.67
4131 4198 1.084370 GGTCGCAGGTTGGATCTTCG 61.084 60.000 0.00 0.00 0.00 3.79
4143 4210 3.368190 CTGGCTCTCAGGGTCGCAG 62.368 68.421 0.00 0.00 39.76 5.18
4158 4225 7.687941 ACTTGATATAACTTTGAACCACTGG 57.312 36.000 0.00 0.00 0.00 4.00
4179 4246 2.966516 GCCTGGTATGCCTCTACTACTT 59.033 50.000 0.16 0.00 35.27 2.24
4247 4314 1.278238 CTACCGCGATGAACTTGACC 58.722 55.000 8.23 0.00 0.00 4.02
4248 4315 0.645868 GCTACCGCGATGAACTTGAC 59.354 55.000 8.23 0.00 0.00 3.18
4342 4409 1.278238 GCGTGTAACTTCCCAGATCG 58.722 55.000 0.00 0.00 31.75 3.69
4378 4445 8.244802 GTGACACATTATACACACTAGAGAAGT 58.755 37.037 0.00 0.00 39.81 3.01
4379 4446 7.702772 GGTGACACATTATACACACTAGAGAAG 59.297 40.741 8.08 0.00 35.33 2.85
4380 4447 7.363530 GGGTGACACATTATACACACTAGAGAA 60.364 40.741 8.08 0.00 34.38 2.87
4511 4595 4.096382 GGCATACATACTCAACCAAACAGG 59.904 45.833 0.00 0.00 45.67 4.00
4512 4596 4.699735 TGGCATACATACTCAACCAAACAG 59.300 41.667 0.00 0.00 0.00 3.16
4548 4632 5.134509 TCAGATCAATCCCTAGACTACCTCA 59.865 44.000 0.00 0.00 0.00 3.86
4553 4637 5.671463 ACCTCAGATCAATCCCTAGACTA 57.329 43.478 0.00 0.00 0.00 2.59
4563 4647 3.376234 CACGATTGCAACCTCAGATCAAT 59.624 43.478 0.00 0.00 0.00 2.57
4625 4728 8.909423 TCTTTTGGGGGATATAACAAGAAAAT 57.091 30.769 0.00 0.00 0.00 1.82
4640 4743 3.244078 GGTAAGCAGTTTTCTTTTGGGGG 60.244 47.826 0.00 0.00 0.00 5.40
4643 4746 8.887036 AATAAAGGTAAGCAGTTTTCTTTTGG 57.113 30.769 0.00 0.00 0.00 3.28
4645 4748 9.750125 CTGAATAAAGGTAAGCAGTTTTCTTTT 57.250 29.630 0.00 0.00 0.00 2.27
4649 4752 6.914259 AGCTGAATAAAGGTAAGCAGTTTTC 58.086 36.000 0.00 0.00 36.32 2.29
4657 4764 8.044060 TGTCATTCAAGCTGAATAAAGGTAAG 57.956 34.615 9.96 0.00 44.60 2.34
4673 4780 6.522625 TGAGTTTGTTTCCTTGTCATTCAA 57.477 33.333 0.00 0.00 34.61 2.69
4688 4795 5.395214 GGGATTCAGTTTGGTTTGAGTTTGT 60.395 40.000 0.00 0.00 0.00 2.83
4712 4819 5.869888 AGAACAGATAGCGTTAGGTTCTTTG 59.130 40.000 13.96 0.00 41.36 2.77
4726 4833 6.105333 CCTTCCTTCAGTTCAGAACAGATAG 58.895 44.000 15.85 11.73 0.00 2.08
4730 4837 3.406764 CCCTTCCTTCAGTTCAGAACAG 58.593 50.000 15.85 7.72 0.00 3.16
4732 4839 2.784347 CCCCTTCCTTCAGTTCAGAAC 58.216 52.381 5.00 5.00 0.00 3.01
4737 4844 0.332972 ATGGCCCCTTCCTTCAGTTC 59.667 55.000 0.00 0.00 0.00 3.01
4738 4845 0.040204 CATGGCCCCTTCCTTCAGTT 59.960 55.000 0.00 0.00 0.00 3.16
4739 4846 0.846427 TCATGGCCCCTTCCTTCAGT 60.846 55.000 0.00 0.00 0.00 3.41
4740 4847 0.106819 CTCATGGCCCCTTCCTTCAG 60.107 60.000 0.00 0.00 0.00 3.02
4741 4848 1.574526 CCTCATGGCCCCTTCCTTCA 61.575 60.000 0.00 0.00 0.00 3.02
4742 4849 1.228510 CCTCATGGCCCCTTCCTTC 59.771 63.158 0.00 0.00 0.00 3.46
4743 4850 0.628668 ATCCTCATGGCCCCTTCCTT 60.629 55.000 0.00 0.00 0.00 3.36
4744 4851 1.006631 ATCCTCATGGCCCCTTCCT 59.993 57.895 0.00 0.00 0.00 3.36
4745 4852 1.355718 TGATCCTCATGGCCCCTTCC 61.356 60.000 0.00 0.00 0.00 3.46
4746 4853 0.179006 GTGATCCTCATGGCCCCTTC 60.179 60.000 0.00 0.00 0.00 3.46
4747 4854 1.649271 GGTGATCCTCATGGCCCCTT 61.649 60.000 0.00 0.00 0.00 3.95
4748 4855 2.081161 GGTGATCCTCATGGCCCCT 61.081 63.158 0.00 0.00 0.00 4.79
4749 4856 2.517919 GGTGATCCTCATGGCCCC 59.482 66.667 0.00 0.00 0.00 5.80
4750 4857 1.723128 ATGGGTGATCCTCATGGCCC 61.723 60.000 0.00 0.00 36.20 5.80
4751 4858 0.186873 AATGGGTGATCCTCATGGCC 59.813 55.000 0.00 0.00 36.20 5.36
4752 4859 1.959282 GAAATGGGTGATCCTCATGGC 59.041 52.381 0.00 0.00 36.20 4.40
4753 4860 3.137913 AGAGAAATGGGTGATCCTCATGG 59.862 47.826 0.00 0.00 36.20 3.66
4754 4861 4.135306 CAGAGAAATGGGTGATCCTCATG 58.865 47.826 0.00 0.00 36.20 3.07
4755 4862 3.434739 GCAGAGAAATGGGTGATCCTCAT 60.435 47.826 0.00 0.00 36.20 2.90
4756 4863 2.092753 GCAGAGAAATGGGTGATCCTCA 60.093 50.000 0.00 0.00 36.20 3.86
4757 4864 2.570135 GCAGAGAAATGGGTGATCCTC 58.430 52.381 0.00 0.00 36.20 3.71
4758 4865 1.213926 GGCAGAGAAATGGGTGATCCT 59.786 52.381 0.00 0.00 36.20 3.24
4759 4866 1.213926 AGGCAGAGAAATGGGTGATCC 59.786 52.381 0.00 0.00 0.00 3.36
4760 4867 2.295885 CAGGCAGAGAAATGGGTGATC 58.704 52.381 0.00 0.00 0.00 2.92
4761 4868 1.684248 GCAGGCAGAGAAATGGGTGAT 60.684 52.381 0.00 0.00 0.00 3.06
4762 4869 0.322816 GCAGGCAGAGAAATGGGTGA 60.323 55.000 0.00 0.00 0.00 4.02
4763 4870 0.609957 TGCAGGCAGAGAAATGGGTG 60.610 55.000 0.00 0.00 0.00 4.61
4764 4871 0.323178 CTGCAGGCAGAGAAATGGGT 60.323 55.000 16.02 0.00 46.30 4.51
4765 4872 1.664321 GCTGCAGGCAGAGAAATGGG 61.664 60.000 24.46 0.00 46.30 4.00
4766 4873 1.664321 GGCTGCAGGCAGAGAAATGG 61.664 60.000 33.31 0.00 46.30 3.16
4767 4874 1.807886 GGCTGCAGGCAGAGAAATG 59.192 57.895 33.31 0.00 46.30 2.32
4768 4875 1.748122 CGGCTGCAGGCAGAGAAAT 60.748 57.895 35.84 0.00 46.30 2.17
4769 4876 2.359107 CGGCTGCAGGCAGAGAAA 60.359 61.111 35.84 0.00 46.30 2.52
4770 4877 3.630013 ACGGCTGCAGGCAGAGAA 61.630 61.111 35.84 0.00 46.30 2.87
4771 4878 4.383861 CACGGCTGCAGGCAGAGA 62.384 66.667 35.84 0.00 46.30 3.10
4772 4879 2.302199 TATCACGGCTGCAGGCAGAG 62.302 60.000 35.84 25.67 46.30 3.35
4783 4890 2.362397 TCAGTTCTGAGGATATCACGGC 59.638 50.000 4.83 0.00 33.22 5.68
4827 4934 6.039270 CCTTCAATTTATGATTGGACGGCTAA 59.961 38.462 0.00 0.00 38.03 3.09
4865 4972 3.433274 TGTTAAGTTCTGCTCTTCATGCG 59.567 43.478 0.00 0.00 0.00 4.73
4872 4979 8.607459 CGAATTATCAATGTTAAGTTCTGCTCT 58.393 33.333 0.00 0.00 0.00 4.09
4875 4982 8.391106 ACTCGAATTATCAATGTTAAGTTCTGC 58.609 33.333 0.00 0.00 0.00 4.26
4893 5000 2.672961 TCGCCTCATGAACTCGAATT 57.327 45.000 10.07 0.00 0.00 2.17
4941 5051 5.765677 TCTGTTTCAACCGTAATCCAAATCA 59.234 36.000 0.00 0.00 0.00 2.57
4944 5054 6.452494 TTTCTGTTTCAACCGTAATCCAAA 57.548 33.333 0.00 0.00 0.00 3.28
4964 5074 8.930982 GTCGTATAATTAACAGCGTGAATTTTC 58.069 33.333 8.62 0.00 30.20 2.29
5015 5129 7.161404 TCACAAGAGATTTGCTACTTACATGT 58.839 34.615 2.69 2.69 0.00 3.21
5023 5137 6.974932 TTCTCATCACAAGAGATTTGCTAC 57.025 37.500 0.00 0.00 41.42 3.58
5024 5138 7.984422 TTTTCTCATCACAAGAGATTTGCTA 57.016 32.000 0.00 0.00 41.42 3.49
5025 5139 6.889301 TTTTCTCATCACAAGAGATTTGCT 57.111 33.333 0.00 0.00 41.42 3.91
5026 5140 7.597743 ACAATTTTCTCATCACAAGAGATTTGC 59.402 33.333 0.00 0.00 41.42 3.68
5049 5163 7.013274 ACTCTTTTCCATCGAATGAAGAAACAA 59.987 33.333 0.00 0.00 33.01 2.83
5059 5173 4.401519 TCGTAGGACTCTTTTCCATCGAAT 59.598 41.667 0.00 0.00 38.84 3.34
5077 5191 3.181474 GGAGGTCCTGGATCTTTTCGTAG 60.181 52.174 11.53 0.00 0.00 3.51
5081 5195 3.457749 AGATGGAGGTCCTGGATCTTTTC 59.542 47.826 11.53 8.52 36.82 2.29
5146 5260 4.770010 TGGACGAAATTAAAGGGAATGCTT 59.230 37.500 0.00 0.00 0.00 3.91
5220 5334 3.376546 GGTAATTGAGCAAGCAGAGGAAG 59.623 47.826 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.