Multiple sequence alignment - TraesCS2D01G416300

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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 TraesCS2D01G416300 chr2D 100.000 3781 0 0 1 3781 529682706 529686486 0.000000e+00 6983.0
1 TraesCS2D01G416300 chr2D 76.492 1106 201 44 1435 2513 537338598 537339671 7.140000e-152 547.0
2 TraesCS2D01G416300 chr2D 85.256 156 20 2 2917 3071 591580254 591580101 1.410000e-34 158.0
3 TraesCS2D01G416300 chr2B 93.967 2105 105 14 581 2670 629814302 629816399 0.000000e+00 3164.0
4 TraesCS2D01G416300 chr2B 91.738 581 37 7 1 580 629813614 629814184 0.000000e+00 797.0
5 TraesCS2D01G416300 chr2B 96.596 235 7 1 3548 3781 629816832 629817066 4.580000e-104 388.0
6 TraesCS2D01G416300 chr2B 86.567 268 13 5 3253 3517 629816405 629816652 1.340000e-69 274.0
7 TraesCS2D01G416300 chr2A 95.229 1551 57 10 1035 2569 674532510 674534059 0.000000e+00 2438.0
8 TraesCS2D01G416300 chr2A 92.527 910 51 9 2876 3779 674535855 674536753 0.000000e+00 1288.0
9 TraesCS2D01G416300 chr2A 91.050 581 33 8 1 580 674531340 674531902 0.000000e+00 767.0
10 TraesCS2D01G416300 chr2A 91.264 435 31 7 581 1012 674532020 674532450 1.510000e-163 586.0
11 TraesCS2D01G416300 chr2A 76.394 1148 210 46 1435 2554 679964625 679965739 2.550000e-156 562.0
12 TraesCS2D01G416300 chr2A 94.118 119 7 0 2552 2670 674535025 674535143 8.340000e-42 182.0
13 TraesCS2D01G416300 chr1D 96.774 31 1 0 2916 2946 234414950 234414920 7.000000e-03 52.8


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 TraesCS2D01G416300 chr2D 529682706 529686486 3780 False 6983.00 6983 100.0000 1 3781 1 chr2D.!!$F1 3780
1 TraesCS2D01G416300 chr2D 537338598 537339671 1073 False 547.00 547 76.4920 1435 2513 1 chr2D.!!$F2 1078
2 TraesCS2D01G416300 chr2B 629813614 629817066 3452 False 1155.75 3164 92.2170 1 3781 4 chr2B.!!$F1 3780
3 TraesCS2D01G416300 chr2A 674531340 674536753 5413 False 1052.20 2438 92.8376 1 3779 5 chr2A.!!$F2 3778
4 TraesCS2D01G416300 chr2A 679964625 679965739 1114 False 562.00 562 76.3940 1435 2554 1 chr2A.!!$F1 1119

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
269 271 0.108804 CACATACCAGGACGCGACTT 60.109 55.0 15.93 0.0 0.00 3.01 F
358 360 0.179119 GTAGCGCGGTTCACCAGTAT 60.179 55.0 19.09 0.0 35.14 2.12 F
1024 1155 0.253327 AAAGAGGGGCGACATCTTCC 59.747 55.0 8.29 0.0 37.04 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1551 1728 0.251354 GCTTGGTGCTCTCCATCTGA 59.749 55.000 0.00 0.0 37.33 3.27 R
2006 2187 1.005037 CGTGTAGCTGCTGTCCCAA 60.005 57.895 13.43 0.0 0.00 4.12 R
2906 4595 0.530744 CTCCGCCACTGTAGTGCTAA 59.469 55.000 6.50 0.0 44.34 3.09 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
26 27 1.771255 AGTCATCAGTATTCAGCCCCC 59.229 52.381 0.00 0.00 0.00 5.40
57 58 0.321298 ACGCCGCTCATTTACAGGTT 60.321 50.000 0.00 0.00 0.00 3.50
59 60 0.733150 GCCGCTCATTTACAGGTTCC 59.267 55.000 0.00 0.00 0.00 3.62
66 67 3.146066 TCATTTACAGGTTCCACACAGC 58.854 45.455 0.00 0.00 0.00 4.40
81 82 2.172505 ACACAGCGGATTATCAATGGGA 59.827 45.455 0.00 0.00 0.00 4.37
110 112 7.065085 CGCTATATTCATTTGGGATAGTTCCTG 59.935 40.741 0.00 0.00 42.20 3.86
125 127 7.040409 GGATAGTTCCTGAACATGTTTGTTCTT 60.040 37.037 13.36 0.00 45.95 2.52
200 202 1.464608 CGGTTGGTCACTATGCTGTTG 59.535 52.381 0.00 0.00 0.00 3.33
206 208 3.324846 TGGTCACTATGCTGTTGACTCTT 59.675 43.478 0.00 0.00 0.00 2.85
209 211 5.106908 GGTCACTATGCTGTTGACTCTTTTC 60.107 44.000 0.00 0.00 0.00 2.29
247 249 3.343941 TCACCCTATAACACTTGTGGC 57.656 47.619 5.72 0.00 0.00 5.01
248 250 2.026636 TCACCCTATAACACTTGTGGCC 60.027 50.000 0.00 0.00 0.00 5.36
263 265 1.449601 GGCCACACATACCAGGACG 60.450 63.158 0.00 0.00 0.00 4.79
269 271 0.108804 CACATACCAGGACGCGACTT 60.109 55.000 15.93 0.00 0.00 3.01
305 307 4.924305 TGGAGCATTCTTGGCAAATATC 57.076 40.909 0.00 0.00 0.00 1.63
320 322 6.700960 TGGCAAATATCAAGGAATTTAATGCG 59.299 34.615 0.00 0.00 0.00 4.73
358 360 0.179119 GTAGCGCGGTTCACCAGTAT 60.179 55.000 19.09 0.00 35.14 2.12
421 423 8.552865 ACAAAAATCATGTGATGTGATGTTTTG 58.447 29.630 17.89 17.89 40.04 2.44
429 431 6.724263 TGTGATGTGATGTTTTGTACTTGAC 58.276 36.000 0.00 0.00 0.00 3.18
448 450 3.244770 TGACCAATTTCTACAGGACACCC 60.245 47.826 0.00 0.00 0.00 4.61
450 452 4.172807 ACCAATTTCTACAGGACACCCTA 58.827 43.478 0.00 0.00 42.02 3.53
489 491 5.596836 TTTTTGGAACAGAGCACAAAGAT 57.403 34.783 0.00 0.00 42.39 2.40
490 492 4.836125 TTTGGAACAGAGCACAAAGATC 57.164 40.909 0.00 0.00 42.39 2.75
587 706 3.250762 TGAACAAGCTGGTTTCAAGATCG 59.749 43.478 8.18 0.00 0.00 3.69
624 743 3.694072 TGTGCATAGGCCATTGTAGTTTC 59.306 43.478 5.01 0.00 40.13 2.78
627 746 2.032680 TAGGCCATTGTAGTTTCGGC 57.967 50.000 5.01 0.00 42.21 5.54
632 751 1.375013 ATTGTAGTTTCGGCGCGGT 60.375 52.632 15.06 0.00 0.00 5.68
633 752 0.952010 ATTGTAGTTTCGGCGCGGTT 60.952 50.000 15.06 2.57 0.00 4.44
639 758 1.812093 TTTCGGCGCGGTTATCCTG 60.812 57.895 15.06 0.00 0.00 3.86
643 762 1.831389 CGGCGCGGTTATCCTGAATG 61.831 60.000 8.83 0.00 0.00 2.67
659 778 6.661777 TCCTGAATGACATGATGTAAATGGA 58.338 36.000 0.00 0.00 0.00 3.41
676 795 2.946785 TGGATATGGTCATGCATGCAA 58.053 42.857 26.68 8.17 0.00 4.08
686 805 3.991773 GTCATGCATGCAATTCAACAAGT 59.008 39.130 26.68 0.00 0.00 3.16
687 806 3.991121 TCATGCATGCAATTCAACAAGTG 59.009 39.130 26.68 14.13 0.00 3.16
741 863 6.520272 AGTTGAGACTGTCAGATATATTGGC 58.480 40.000 10.88 0.00 36.21 4.52
759 881 4.359434 TGGCCTGTGTAATTGACTTGTA 57.641 40.909 3.32 0.00 0.00 2.41
770 892 9.463443 GTGTAATTGACTTGTAAATTGAAGCTT 57.537 29.630 0.00 0.00 0.00 3.74
890 1012 9.865321 ATGTTAATCATGGATCAAAAGTTGAAG 57.135 29.630 0.00 0.00 38.08 3.02
922 1044 1.276415 GTTGTGTTGCATTGCACGTT 58.724 45.000 11.66 0.00 38.71 3.99
964 1095 5.187772 TCCTCTATACATTATGCAATCCGCT 59.812 40.000 0.00 0.00 43.06 5.52
973 1104 8.284945 ACATTATGCAATCCGCTTATTATGAT 57.715 30.769 0.00 0.00 43.06 2.45
976 1107 4.650734 TGCAATCCGCTTATTATGATCCA 58.349 39.130 0.00 0.00 43.06 3.41
980 1111 6.127925 GCAATCCGCTTATTATGATCCATGAA 60.128 38.462 0.00 0.00 37.77 2.57
985 1116 8.708378 TCCGCTTATTATGATCCATGAATAGAT 58.292 33.333 0.00 0.00 0.00 1.98
999 1130 9.699410 TCCATGAATAGATCTGTTATTTTTGGT 57.301 29.630 5.18 0.00 31.52 3.67
1000 1131 9.956720 CCATGAATAGATCTGTTATTTTTGGTC 57.043 33.333 5.18 0.00 0.00 4.02
1017 1148 2.433239 TGGTCTATAAAAGAGGGGCGAC 59.567 50.000 0.00 0.00 33.88 5.19
1024 1155 0.253327 AAAGAGGGGCGACATCTTCC 59.747 55.000 8.29 0.00 37.04 3.46
1074 1243 4.565022 CTTCTCAACTCCTGTTCTTCTCC 58.435 47.826 0.00 0.00 33.52 3.71
1126 1300 6.316890 TGTGTTTGTTAGTTTCCAGTAGTTCC 59.683 38.462 0.00 0.00 0.00 3.62
1338 1512 3.138798 CAGCAGCTGGCCATGGTC 61.139 66.667 17.12 10.20 46.50 4.02
1482 1659 3.005539 AGCATGGTGGACCTCGCT 61.006 61.111 0.00 6.70 38.69 4.93
1676 1853 3.506096 CGGCTGCTACGACGAGGA 61.506 66.667 0.00 0.00 37.71 3.71
1677 1854 2.882876 GGCTGCTACGACGAGGAA 59.117 61.111 0.00 0.00 0.00 3.36
1763 1940 4.068302 GTACCTGCTGTACGCGTC 57.932 61.111 18.63 8.55 40.44 5.19
2003 2184 0.966370 CCCTCGACGAGAAACCTCCT 60.966 60.000 26.11 0.00 0.00 3.69
2006 2187 0.894184 TCGACGAGAAACCTCCTGCT 60.894 55.000 0.00 0.00 0.00 4.24
2072 2253 0.677731 ACTACATCGTCGGAACCGGA 60.678 55.000 9.46 4.20 40.25 5.14
2603 3781 4.760204 GTGTACAGGTTTGGCTACAAGAAT 59.240 41.667 0.00 0.00 37.97 2.40
2631 3809 0.102300 TATCATCACCGTGCTGACCG 59.898 55.000 7.20 0.00 0.00 4.79
2643 3821 4.673298 TGACCGTCGTTGGCGCAT 62.673 61.111 10.83 0.00 38.14 4.73
2673 3851 1.285578 GCTCGAGGCAATCAAGTCTC 58.714 55.000 15.58 0.00 41.35 3.36
2674 3852 1.134848 GCTCGAGGCAATCAAGTCTCT 60.135 52.381 15.58 0.00 38.09 3.10
2675 3853 2.676463 GCTCGAGGCAATCAAGTCTCTT 60.676 50.000 15.58 0.00 38.09 2.85
2677 3855 4.358851 CTCGAGGCAATCAAGTCTCTTAG 58.641 47.826 3.91 0.00 38.09 2.18
2678 3856 3.131223 TCGAGGCAATCAAGTCTCTTAGG 59.869 47.826 0.00 0.00 38.09 2.69
2680 3858 4.692228 GAGGCAATCAAGTCTCTTAGGAG 58.308 47.826 0.00 0.00 37.28 3.69
2681 3859 4.100373 AGGCAATCAAGTCTCTTAGGAGT 58.900 43.478 1.31 0.00 40.29 3.85
2682 3860 5.273208 AGGCAATCAAGTCTCTTAGGAGTA 58.727 41.667 1.31 0.00 40.29 2.59
2684 3862 6.045955 GGCAATCAAGTCTCTTAGGAGTAAG 58.954 44.000 1.31 0.00 40.29 2.34
2685 3863 6.351456 GGCAATCAAGTCTCTTAGGAGTAAGT 60.351 42.308 1.31 0.00 40.29 2.24
2686 3864 7.147880 GGCAATCAAGTCTCTTAGGAGTAAGTA 60.148 40.741 1.31 0.00 40.29 2.24
2687 3865 8.251721 GCAATCAAGTCTCTTAGGAGTAAGTAA 58.748 37.037 1.31 0.00 40.29 2.24
2688 3866 9.796120 CAATCAAGTCTCTTAGGAGTAAGTAAG 57.204 37.037 1.31 0.00 40.29 2.34
2689 3867 9.536510 AATCAAGTCTCTTAGGAGTAAGTAAGT 57.463 33.333 1.31 0.00 40.29 2.24
2744 4040 4.818546 ACTTACTGGATGCATGATAGTTGC 59.181 41.667 2.46 0.00 40.55 4.17
2764 4060 5.189659 TGCTGGTAAAATTTACCACACAC 57.810 39.130 28.16 19.07 42.21 3.82
2767 4063 5.689961 GCTGGTAAAATTTACCACACACTTG 59.310 40.000 28.16 19.10 42.21 3.16
2768 4064 6.681865 GCTGGTAAAATTTACCACACACTTGT 60.682 38.462 28.16 0.00 42.21 3.16
2778 4074 3.234368 CACACTTGTGGCGTTGTTC 57.766 52.632 5.72 0.00 42.10 3.18
2821 4117 9.691362 TTGAGTAATTTTAATCAGAAGTTTGCC 57.309 29.630 1.39 0.00 38.72 4.52
2849 4145 2.795329 CACAAAATGTGGAGGCCTAGT 58.205 47.619 4.42 0.00 44.27 2.57
2874 4170 3.868757 TGAGATGAAAGGAGTACACGG 57.131 47.619 0.00 0.00 0.00 4.94
2879 4175 3.308438 TGAAAGGAGTACACGGCTTAC 57.692 47.619 0.00 0.00 0.00 2.34
2885 4574 2.420022 GGAGTACACGGCTTACTCGTAA 59.580 50.000 11.82 0.00 44.43 3.18
2906 4595 1.000955 GTGTTCGTCATGAGTGGGAGT 59.999 52.381 0.00 0.00 0.00 3.85
2918 4607 2.826725 GAGTGGGAGTTAGCACTACAGT 59.173 50.000 0.00 0.00 35.14 3.55
2921 4610 1.405661 GGGAGTTAGCACTACAGTGGC 60.406 57.143 11.18 4.02 45.72 5.01
2972 4661 5.239525 GCCAGTGTCAGACTAAAAGTGAAAT 59.760 40.000 1.31 0.00 31.73 2.17
3016 4705 6.913170 ACTCGCAACATAAATTGTCAATTCT 58.087 32.000 11.19 5.08 37.68 2.40
3088 4777 7.387673 ACAGTATGAGTTTGTGATTGAAATCGA 59.612 33.333 0.00 0.00 39.69 3.59
3097 4786 4.332543 TGTGATTGAAATCGACATAGGTGC 59.667 41.667 0.00 0.00 38.26 5.01
3098 4787 3.876914 TGATTGAAATCGACATAGGTGCC 59.123 43.478 0.00 0.00 38.26 5.01
3108 4797 4.764336 TAGGTGCCGTTCGTCGCG 62.764 66.667 0.00 0.00 38.35 5.87
3115 4804 2.297912 CCGTTCGTCGCGACTTGTT 61.298 57.895 33.94 0.00 34.89 2.83
3191 4886 2.202623 CGACACTAGCGTGGGAGC 60.203 66.667 0.00 0.00 45.50 4.70
3213 4908 3.522731 CGAGAGGGAGTCGCTGGG 61.523 72.222 15.38 0.00 0.00 4.45
3220 4915 3.075005 GAGTCGCTGGGTGGCCTA 61.075 66.667 3.32 0.00 0.00 3.93
3232 4927 2.887152 GGGTGGCCTATGATGATGAAAC 59.113 50.000 3.32 0.00 0.00 2.78
3237 4932 4.079844 TGGCCTATGATGATGAAACCTGAA 60.080 41.667 3.32 0.00 0.00 3.02
3247 4942 3.762407 TGAAACCTGAAACCGATCTGA 57.238 42.857 0.00 0.00 0.00 3.27
3390 5087 1.518367 GTGGAGGATTGGGGGTATGA 58.482 55.000 0.00 0.00 0.00 2.15
3438 5135 2.345991 GCGGTGGTGGTGAGCTTA 59.654 61.111 0.00 0.00 0.00 3.09
3451 5148 1.190643 GAGCTTACTGAGGTGGCTCT 58.809 55.000 12.87 0.00 42.87 4.09
3474 5171 2.884012 CCATTGAGCACTACCAACAACA 59.116 45.455 0.00 0.00 0.00 3.33
3475 5172 3.317711 CCATTGAGCACTACCAACAACAA 59.682 43.478 0.00 0.00 0.00 2.83
3476 5173 4.290155 CATTGAGCACTACCAACAACAAC 58.710 43.478 0.00 0.00 0.00 3.32
3723 5575 0.888285 ACAAAGCTGAGCCTGCAGTC 60.888 55.000 13.81 5.09 38.17 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.202492 CGGCGTTGAGGAGAGACG 60.202 66.667 0.00 0.00 39.61 4.18
57 58 3.205338 CATTGATAATCCGCTGTGTGGA 58.795 45.455 2.17 2.17 46.70 4.02
59 60 2.291465 CCCATTGATAATCCGCTGTGTG 59.709 50.000 0.00 0.00 0.00 3.82
66 67 2.069273 GCGACTCCCATTGATAATCCG 58.931 52.381 0.00 0.00 0.00 4.18
81 82 7.246171 ACTATCCCAAATGAATATAGCGACT 57.754 36.000 0.00 0.00 0.00 4.18
125 127 4.500887 CGAGGTCGCCCTAGAAATATCAAA 60.501 45.833 0.00 0.00 42.86 2.69
128 130 2.557490 ACGAGGTCGCCCTAGAAATATC 59.443 50.000 0.00 0.00 42.86 1.63
136 138 2.617276 CCATCTATACGAGGTCGCCCTA 60.617 54.545 0.00 0.00 42.86 3.53
230 232 2.290641 TGTGGCCACAAGTGTTATAGGG 60.291 50.000 36.10 0.00 38.56 3.53
231 233 2.747446 GTGTGGCCACAAGTGTTATAGG 59.253 50.000 39.23 0.00 43.77 2.57
247 249 1.809619 CGCGTCCTGGTATGTGTGG 60.810 63.158 0.00 0.00 0.00 4.17
248 250 1.076533 GTCGCGTCCTGGTATGTGTG 61.077 60.000 5.77 0.00 0.00 3.82
252 254 1.135083 AGAAAGTCGCGTCCTGGTATG 60.135 52.381 5.77 0.00 0.00 2.39
263 265 4.795278 CCAAATTGCTCATAAGAAAGTCGC 59.205 41.667 0.00 0.00 0.00 5.19
269 271 6.379133 AGAATGCTCCAAATTGCTCATAAGAA 59.621 34.615 0.00 0.00 0.00 2.52
305 307 4.922692 TGTTTCTGCGCATTAAATTCCTTG 59.077 37.500 12.24 0.00 0.00 3.61
320 322 0.371645 CCTCTCGCGATTGTTTCTGC 59.628 55.000 10.36 0.00 0.00 4.26
344 346 5.587443 AGGTTATAAAATACTGGTGAACCGC 59.413 40.000 0.00 0.00 40.03 5.68
383 385 9.460019 TCACATGATTTTTGTGGATACTAATGA 57.540 29.630 0.00 0.00 43.67 2.57
386 388 9.241919 ACATCACATGATTTTTGTGGATACTAA 57.758 29.630 0.00 0.00 43.67 2.24
387 389 8.676401 CACATCACATGATTTTTGTGGATACTA 58.324 33.333 0.00 0.00 43.67 1.82
388 390 7.394077 TCACATCACATGATTTTTGTGGATACT 59.606 33.333 0.00 0.00 43.67 2.12
389 391 7.537715 TCACATCACATGATTTTTGTGGATAC 58.462 34.615 0.00 0.00 43.67 2.24
402 404 7.228308 TCAAGTACAAAACATCACATCACATGA 59.772 33.333 0.00 0.00 0.00 3.07
408 410 6.312399 TGGTCAAGTACAAAACATCACATC 57.688 37.500 0.00 0.00 0.00 3.06
417 419 7.776030 TCCTGTAGAAATTGGTCAAGTACAAAA 59.224 33.333 0.00 0.00 0.00 2.44
421 423 6.147328 GTGTCCTGTAGAAATTGGTCAAGTAC 59.853 42.308 0.00 0.00 0.00 2.73
429 431 3.721087 AGGGTGTCCTGTAGAAATTGG 57.279 47.619 0.00 0.00 42.98 3.16
448 450 6.238320 CCAAAAATCTCCTCTGCTTTCGATAG 60.238 42.308 0.00 0.00 0.00 2.08
450 452 4.397417 CCAAAAATCTCCTCTGCTTTCGAT 59.603 41.667 0.00 0.00 0.00 3.59
519 521 0.250124 AGGTTCACGATTGGTTGCGA 60.250 50.000 0.00 0.00 0.00 5.10
587 706 6.370166 GCCTATGCACAGATTTCTAAGGATAC 59.630 42.308 0.00 0.00 37.47 2.24
624 743 1.594293 ATTCAGGATAACCGCGCCG 60.594 57.895 0.00 0.00 41.83 6.46
627 746 1.934589 TGTCATTCAGGATAACCGCG 58.065 50.000 0.00 0.00 41.83 6.46
632 751 9.070179 CCATTTACATCATGTCATTCAGGATAA 57.930 33.333 0.00 0.00 44.25 1.75
633 752 8.439172 TCCATTTACATCATGTCATTCAGGATA 58.561 33.333 0.00 0.00 44.25 2.59
639 758 9.017509 ACCATATCCATTTACATCATGTCATTC 57.982 33.333 0.00 0.00 0.00 2.67
643 762 7.984422 TGACCATATCCATTTACATCATGTC 57.016 36.000 0.00 0.00 0.00 3.06
659 778 5.163395 TGTTGAATTGCATGCATGACCATAT 60.163 36.000 30.64 7.12 0.00 1.78
700 819 6.757010 GTCTCAACTCTCACTTGTTACAGAAA 59.243 38.462 0.00 0.00 0.00 2.52
703 822 5.689514 CAGTCTCAACTCTCACTTGTTACAG 59.310 44.000 0.00 0.00 31.71 2.74
705 824 5.593010 ACAGTCTCAACTCTCACTTGTTAC 58.407 41.667 0.00 0.00 31.71 2.50
706 825 5.359860 TGACAGTCTCAACTCTCACTTGTTA 59.640 40.000 1.31 0.00 31.71 2.41
715 836 7.471260 GCCAATATATCTGACAGTCTCAACTCT 60.471 40.741 1.59 0.00 31.71 3.24
716 837 6.644592 GCCAATATATCTGACAGTCTCAACTC 59.355 42.308 1.59 0.00 31.71 3.01
741 863 9.398170 CTTCAATTTACAAGTCAATTACACAGG 57.602 33.333 0.00 0.00 0.00 4.00
759 881 4.571984 GGTGCTGAAAACAAGCTTCAATTT 59.428 37.500 0.00 0.00 41.42 1.82
770 892 1.490490 AGACAGGAGGTGCTGAAAACA 59.510 47.619 5.40 0.00 0.00 2.83
890 1012 0.765510 ACACAACCTGGAGGAACCTC 59.234 55.000 11.97 11.97 42.04 3.85
922 1044 5.190677 AGAGGAAACCTTTCGACTTTTTCA 58.809 37.500 9.13 0.00 38.06 2.69
973 1104 9.699410 ACCAAAAATAACAGATCTATTCATGGA 57.301 29.630 18.55 0.00 33.18 3.41
991 1122 5.359860 CGCCCCTCTTTTATAGACCAAAAAT 59.640 40.000 0.00 0.00 0.00 1.82
994 1125 3.520317 TCGCCCCTCTTTTATAGACCAAA 59.480 43.478 0.00 0.00 0.00 3.28
995 1126 3.109151 TCGCCCCTCTTTTATAGACCAA 58.891 45.455 0.00 0.00 0.00 3.67
997 1128 2.433239 TGTCGCCCCTCTTTTATAGACC 59.567 50.000 0.00 0.00 0.00 3.85
998 1129 3.814005 TGTCGCCCCTCTTTTATAGAC 57.186 47.619 0.00 0.00 0.00 2.59
999 1130 4.223953 AGATGTCGCCCCTCTTTTATAGA 58.776 43.478 0.00 0.00 0.00 1.98
1000 1131 4.608948 AGATGTCGCCCCTCTTTTATAG 57.391 45.455 0.00 0.00 0.00 1.31
1001 1132 4.202326 GGAAGATGTCGCCCCTCTTTTATA 60.202 45.833 0.00 0.00 29.64 0.98
1002 1133 3.433740 GGAAGATGTCGCCCCTCTTTTAT 60.434 47.826 0.00 0.00 29.64 1.40
1003 1134 2.093128 GGAAGATGTCGCCCCTCTTTTA 60.093 50.000 0.00 0.00 29.64 1.52
1004 1135 1.340114 GGAAGATGTCGCCCCTCTTTT 60.340 52.381 0.00 0.00 29.64 2.27
1024 1155 1.009829 GCAACAGTTATCCTCCAGCG 58.990 55.000 0.00 0.00 0.00 5.18
1028 1159 3.618690 AGACTGCAACAGTTATCCTCC 57.381 47.619 1.15 0.00 45.44 4.30
1074 1243 3.878778 CCTAACCACCAGAGAATGAAGG 58.121 50.000 0.00 0.00 0.00 3.46
1126 1300 1.741706 CTGCATGTCAGCAACCTAAGG 59.258 52.381 4.55 0.00 45.13 2.69
1323 1497 4.783621 TCGACCATGGCCAGCTGC 62.784 66.667 13.05 3.68 40.16 5.25
1331 1505 1.448540 GTGGTGCTCTCGACCATGG 60.449 63.158 11.19 11.19 45.27 3.66
1338 1512 2.890847 GATGGTCGGTGGTGCTCTCG 62.891 65.000 0.00 0.00 0.00 4.04
1389 1566 3.418068 GCTGCTTGCTCGAACGCT 61.418 61.111 0.00 0.00 38.95 5.07
1399 1576 3.793144 GAACTCCCGCGCTGCTTG 61.793 66.667 5.56 0.00 0.00 4.01
1541 1718 1.949847 CTCCATCTGAAGGACGGCGT 61.950 60.000 14.65 14.65 0.00 5.68
1551 1728 0.251354 GCTTGGTGCTCTCCATCTGA 59.749 55.000 0.00 0.00 37.33 3.27
1676 1853 4.016706 CGAGACCCCGCACCCTTT 62.017 66.667 0.00 0.00 0.00 3.11
2006 2187 1.005037 CGTGTAGCTGCTGTCCCAA 60.005 57.895 13.43 0.00 0.00 4.12
2072 2253 1.179814 ACTCGGACGAGAGCTTGGTT 61.180 55.000 26.41 0.23 44.53 3.67
2279 2475 1.019278 CCATGTTGACGAGGAACCCG 61.019 60.000 0.00 0.00 34.03 5.28
2603 3781 4.584743 AGCACGGTGATGATAGTCTTCATA 59.415 41.667 13.29 0.00 36.48 2.15
2631 3809 1.792057 CGACAAATGCGCCAACGAC 60.792 57.895 4.18 0.00 43.93 4.34
2643 3821 1.503818 GCCTCGAGCAAACCGACAAA 61.504 55.000 6.99 0.00 42.97 2.83
2715 3893 8.361139 ACTATCATGCATCCAGTAAGTACTTAC 58.639 37.037 30.33 30.33 44.22 2.34
2716 3894 8.478775 ACTATCATGCATCCAGTAAGTACTTA 57.521 34.615 11.38 11.38 33.46 2.24
2717 3895 7.366847 ACTATCATGCATCCAGTAAGTACTT 57.633 36.000 13.68 13.68 33.46 2.24
2720 3898 5.991606 GCAACTATCATGCATCCAGTAAGTA 59.008 40.000 0.00 0.00 43.29 2.24
2721 3899 4.818546 GCAACTATCATGCATCCAGTAAGT 59.181 41.667 0.00 0.00 43.29 2.24
2722 3900 5.049612 CAGCAACTATCATGCATCCAGTAAG 60.050 44.000 0.00 0.00 46.22 2.34
2723 3901 4.818005 CAGCAACTATCATGCATCCAGTAA 59.182 41.667 0.00 0.00 46.22 2.24
2728 4024 2.579873 ACCAGCAACTATCATGCATCC 58.420 47.619 0.00 0.00 46.22 3.51
2730 4026 6.720112 ATTTTACCAGCAACTATCATGCAT 57.280 33.333 0.00 0.00 46.22 3.96
2733 4029 8.465999 TGGTAAATTTTACCAGCAACTATCATG 58.534 33.333 28.99 0.00 42.21 3.07
2764 4060 6.523676 AATTTATTTGAACAACGCCACAAG 57.476 33.333 0.00 0.00 0.00 3.16
2767 4063 6.418226 TGTGTAATTTATTTGAACAACGCCAC 59.582 34.615 0.00 0.00 0.00 5.01
2768 4064 6.504398 TGTGTAATTTATTTGAACAACGCCA 58.496 32.000 0.00 0.00 0.00 5.69
2770 4066 9.856803 AATTTGTGTAATTTATTTGAACAACGC 57.143 25.926 0.00 0.00 32.48 4.84
2802 4098 7.042119 CCGTTTTGGCAAACTTCTGATTAAAAT 60.042 33.333 13.10 0.00 40.31 1.82
2820 4116 1.596727 CCACATTTTGTGCCGTTTTGG 59.403 47.619 2.09 0.00 46.51 3.28
2821 4117 2.539274 CTCCACATTTTGTGCCGTTTTG 59.461 45.455 2.09 0.00 46.51 2.44
2827 4123 1.187567 AGGCCTCCACATTTTGTGCC 61.188 55.000 0.00 0.90 46.51 5.01
2833 4129 6.558775 TCTCATAATACTAGGCCTCCACATTT 59.441 38.462 9.68 0.00 0.00 2.32
2840 4136 7.179338 TCCTTTCATCTCATAATACTAGGCCTC 59.821 40.741 9.68 0.00 0.00 4.70
2841 4137 7.019388 TCCTTTCATCTCATAATACTAGGCCT 58.981 38.462 11.78 11.78 0.00 5.19
2842 4138 7.038658 ACTCCTTTCATCTCATAATACTAGGCC 60.039 40.741 0.00 0.00 0.00 5.19
2843 4139 7.902087 ACTCCTTTCATCTCATAATACTAGGC 58.098 38.462 0.00 0.00 0.00 3.93
2849 4145 7.658261 CCGTGTACTCCTTTCATCTCATAATA 58.342 38.462 0.00 0.00 0.00 0.98
2872 4168 1.909532 CGAACACTTACGAGTAAGCCG 59.090 52.381 19.50 14.33 44.74 5.52
2874 4170 3.558505 TGACGAACACTTACGAGTAAGC 58.441 45.455 19.50 5.82 44.74 3.09
2879 4175 3.604198 CACTCATGACGAACACTTACGAG 59.396 47.826 0.00 0.00 0.00 4.18
2885 4574 1.273606 CTCCCACTCATGACGAACACT 59.726 52.381 0.00 0.00 0.00 3.55
2906 4595 0.530744 CTCCGCCACTGTAGTGCTAA 59.469 55.000 6.50 0.00 44.34 3.09
2921 4610 2.551270 GTTGCTTGTCACGCTCCG 59.449 61.111 2.72 0.00 0.00 4.63
2926 4615 1.654220 CCCTTGGTTGCTTGTCACG 59.346 57.895 0.00 0.00 0.00 4.35
3016 4705 0.988832 CCTGGTGCTTAGGGTTGGTA 59.011 55.000 0.00 0.00 0.00 3.25
3062 4751 7.387673 TCGATTTCAATCACAAACTCATACTGT 59.612 33.333 0.62 0.00 35.11 3.55
3063 4752 7.689812 GTCGATTTCAATCACAAACTCATACTG 59.310 37.037 0.00 0.00 35.11 2.74
3065 4754 7.518161 TGTCGATTTCAATCACAAACTCATAC 58.482 34.615 0.00 0.00 35.11 2.39
3066 4755 7.665561 TGTCGATTTCAATCACAAACTCATA 57.334 32.000 0.00 0.00 35.11 2.15
3067 4756 6.558771 TGTCGATTTCAATCACAAACTCAT 57.441 33.333 0.00 0.00 35.11 2.90
3068 4757 6.558771 ATGTCGATTTCAATCACAAACTCA 57.441 33.333 0.00 0.00 35.11 3.41
3074 4763 4.332543 GCACCTATGTCGATTTCAATCACA 59.667 41.667 0.00 4.42 35.11 3.58
3088 4777 1.153901 CGACGAACGGCACCTATGT 60.154 57.895 0.11 0.00 38.46 2.29
3097 4786 2.297912 AACAAGTCGCGACGAACGG 61.298 57.895 31.56 21.59 42.83 4.44
3098 4787 1.155087 CAACAAGTCGCGACGAACG 60.155 57.895 31.56 22.51 45.66 3.95
3108 4797 4.142881 GCGGTTCTTCTAATCCAACAAGTC 60.143 45.833 0.00 0.00 0.00 3.01
3115 4804 2.028839 TCGTTGCGGTTCTTCTAATCCA 60.029 45.455 0.00 0.00 0.00 3.41
3176 4865 3.760035 CCGCTCCCACGCTAGTGT 61.760 66.667 2.24 2.24 46.56 3.55
3197 4892 2.363147 ACCCAGCGACTCCCTCTC 60.363 66.667 0.00 0.00 0.00 3.20
3213 4908 3.567164 CAGGTTTCATCATCATAGGCCAC 59.433 47.826 5.01 0.00 0.00 5.01
3219 4914 5.739959 TCGGTTTCAGGTTTCATCATCATA 58.260 37.500 0.00 0.00 0.00 2.15
3220 4915 4.588899 TCGGTTTCAGGTTTCATCATCAT 58.411 39.130 0.00 0.00 0.00 2.45
3232 4927 3.129287 CCCAAATTCAGATCGGTTTCAGG 59.871 47.826 0.00 0.00 0.00 3.86
3237 4932 3.154827 ACACCCAAATTCAGATCGGTT 57.845 42.857 0.00 0.00 0.00 4.44
3247 4942 0.034477 CCTCCGGCTACACCCAAATT 60.034 55.000 0.00 0.00 33.26 1.82
3304 4999 4.717629 CAAGAGGCGGCGACACGA 62.718 66.667 18.30 0.00 35.47 4.35
3317 5012 1.221466 CGTGACGGAAGCAAGCAAGA 61.221 55.000 0.00 0.00 0.00 3.02
3345 5040 0.396417 CAGACCGGACCTCCTCTCAT 60.396 60.000 9.46 0.00 0.00 2.90
3390 5087 0.183492 AGGTGCCATATTCATGCGGT 59.817 50.000 0.00 0.00 0.00 5.68
3394 5091 2.810274 CCTCGAAGGTGCCATATTCATG 59.190 50.000 0.00 0.00 0.00 3.07
3395 5092 2.705658 TCCTCGAAGGTGCCATATTCAT 59.294 45.455 0.00 0.00 36.53 2.57
3428 5125 0.976641 CCACCTCAGTAAGCTCACCA 59.023 55.000 0.00 0.00 0.00 4.17
3451 5148 1.202867 TGTTGGTAGTGCTCAATGGCA 60.203 47.619 0.00 0.00 40.15 4.92
3474 5171 1.921982 TGGCACATAAGCACATGGTT 58.078 45.000 0.00 1.47 39.33 3.67
3475 5172 1.921982 TTGGCACATAAGCACATGGT 58.078 45.000 0.00 0.00 39.30 3.55
3476 5173 2.883574 CTTTGGCACATAAGCACATGG 58.116 47.619 0.00 0.00 39.30 3.66
3723 5575 4.841246 ACATATCTAAGGGTCTAAGGCCAG 59.159 45.833 5.01 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.