Multiple sequence alignment - TraesCS1D01G275800

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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 TraesCS1D01G275800 chr1D 100.000 3391 0 0 1 3391 371752023 371748633 0.000000e+00 6263.0
1 TraesCS1D01G275800 chr1A 89.219 2727 181 58 715 3391 471489896 471487233 0.000000e+00 3302.0
2 TraesCS1D01G275800 chr1A 91.145 655 32 9 56 694 471490595 471489951 0.000000e+00 865.0
3 TraesCS1D01G275800 chr1B 90.066 1822 99 34 1 1775 496563536 496561750 0.000000e+00 2287.0
4 TraesCS1D01G275800 chr1B 92.024 1354 64 24 1765 3111 496561459 496560143 0.000000e+00 1862.0
5 TraesCS1D01G275800 chr1B 81.720 279 24 5 3117 3389 496512700 496512443 1.230000e-49 207.0
6 TraesCS1D01G275800 chrUn 80.556 108 19 2 48 155 123881573 123881468 7.800000e-12 82.4
7 TraesCS1D01G275800 chrUn 80.556 108 19 2 48 155 131896596 131896701 7.800000e-12 82.4
8 TraesCS1D01G275800 chr3B 80.556 108 19 2 48 155 515214561 515214666 7.800000e-12 82.4
9 TraesCS1D01G275800 chr3B 80.734 109 17 4 48 155 515474813 515474918 7.800000e-12 82.4
10 TraesCS1D01G275800 chr3B 80.734 109 17 4 48 155 515999789 515999894 7.800000e-12 82.4
11 TraesCS1D01G275800 chr3B 80.734 109 17 4 48 155 516472794 516472899 7.800000e-12 82.4
12 TraesCS1D01G275800 chr3B 80.734 109 17 4 48 155 518914413 518914308 7.800000e-12 82.4
13 TraesCS1D01G275800 chr7B 74.595 185 28 13 3207 3389 522811286 522811119 2.820000e-06 63.9


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 TraesCS1D01G275800 chr1D 371748633 371752023 3390 True 6263.0 6263 100.000 1 3391 1 chr1D.!!$R1 3390
1 TraesCS1D01G275800 chr1A 471487233 471490595 3362 True 2083.5 3302 90.182 56 3391 2 chr1A.!!$R1 3335
2 TraesCS1D01G275800 chr1B 496560143 496563536 3393 True 2074.5 2287 91.045 1 3111 2 chr1B.!!$R2 3110

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
342 359 0.179018 ACACAGACAGAGGTTTGCCC 60.179 55.0 0.0 0.0 32.6 5.36 F
1549 1651 0.038618 GTTTTTGGCCCTTAGCACCG 60.039 55.0 0.0 0.0 46.5 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1580 1682 0.178990 GCCAGTTCTGTCCCCACTTT 60.179 55.0 0.0 0.0 0.0 2.66 R
3127 3546 0.234884 GAAGAACGGCGTGACAAAGG 59.765 55.0 15.7 0.0 0.0 3.11 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
40 41 2.607631 TACATAACCTAACGGGCAGC 57.392 50.000 0.00 0.00 39.10 5.25
48 49 1.338769 CCTAACGGGCAGCAGTTAGTT 60.339 52.381 25.61 13.73 44.87 2.24
78 79 5.220931 CCTGCATCAAACCAAGCTAGTATTC 60.221 44.000 0.00 0.00 0.00 1.75
100 101 8.954834 ATTCTCCATAAGATGTATCTCTCTGT 57.045 34.615 0.00 0.00 35.76 3.41
102 103 9.868160 TTCTCCATAAGATGTATCTCTCTGTAA 57.132 33.333 0.00 0.00 35.76 2.41
105 106 7.026562 CCATAAGATGTATCTCTCTGTAAGCG 58.973 42.308 0.00 0.00 35.76 4.68
108 109 4.517453 AGATGTATCTCTCTGTAAGCGTCC 59.483 45.833 0.00 0.00 29.30 4.79
204 205 4.947388 TGTATCTAATTTTGGTCCCTGTGC 59.053 41.667 0.00 0.00 0.00 4.57
218 219 2.164219 CCCTGTGCATGTAACAATCACC 59.836 50.000 0.00 0.00 0.00 4.02
227 244 6.183360 TGCATGTAACAATCACCGTTATGTAC 60.183 38.462 0.00 0.00 31.85 2.90
321 338 1.748329 TAGGCTTCTGATCGCGGCAT 61.748 55.000 6.13 0.00 0.00 4.40
324 341 1.930100 CTTCTGATCGCGGCATGAC 59.070 57.895 6.13 0.00 0.00 3.06
325 342 0.807275 CTTCTGATCGCGGCATGACA 60.807 55.000 6.13 0.00 0.00 3.58
342 359 0.179018 ACACAGACAGAGGTTTGCCC 60.179 55.000 0.00 0.00 32.60 5.36
386 403 4.329545 GTTGGCTCCTCGGTGGCA 62.330 66.667 9.80 9.80 41.24 4.92
393 410 4.838152 CCTCGGTGGCATGACCCG 62.838 72.222 19.15 19.15 43.03 5.28
405 422 3.083997 GACCCGGCACCAGAGGAT 61.084 66.667 0.00 0.00 0.00 3.24
439 456 3.438360 CCGCTAATTGTCATTTTCTGGC 58.562 45.455 0.00 0.00 0.00 4.85
599 616 1.267732 CGAACGGAGCTGATTCATTGC 60.268 52.381 0.00 0.00 0.00 3.56
600 617 2.012673 GAACGGAGCTGATTCATTGCT 58.987 47.619 0.00 0.37 40.02 3.91
605 624 5.555017 ACGGAGCTGATTCATTGCTATATT 58.445 37.500 0.00 0.00 37.16 1.28
647 668 6.354130 TGCCTCTACCTGGTGATTAAATAAC 58.646 40.000 10.23 0.00 0.00 1.89
710 743 1.067821 TGTTTTGCGTGATTTGACCCC 59.932 47.619 0.00 0.00 0.00 4.95
735 790 2.580815 CCTGATGTGCGGCTCTGA 59.419 61.111 0.00 0.00 0.00 3.27
736 791 1.812922 CCTGATGTGCGGCTCTGAC 60.813 63.158 0.00 0.00 0.00 3.51
737 792 1.217511 CTGATGTGCGGCTCTGACT 59.782 57.895 0.00 0.00 0.00 3.41
738 793 1.079612 TGATGTGCGGCTCTGACTG 60.080 57.895 0.00 0.00 0.00 3.51
766 828 1.334869 CCGCTTTGAGTTTGTCTGCTT 59.665 47.619 0.00 0.00 0.00 3.91
779 841 0.606130 TCTGCTTGATGCGCCTTTGA 60.606 50.000 4.18 0.00 46.63 2.69
805 867 1.950758 TTTTTAGTGGAACCGGCGC 59.049 52.632 0.00 0.00 37.80 6.53
944 1021 4.916249 CGTGAACTAAACTACTCCAGTGAC 59.084 45.833 0.00 0.00 37.63 3.67
1195 1273 2.234414 CCCCTATTAATAAGGCGCCGTA 59.766 50.000 24.35 24.35 32.34 4.02
1367 1453 2.125512 CCACCCTCTTCGCTTCCG 60.126 66.667 0.00 0.00 0.00 4.30
1370 1456 2.207924 ACCCTCTTCGCTTCCGTGT 61.208 57.895 0.00 0.00 35.54 4.49
1541 1643 1.340697 GGTCGATAGGTTTTTGGCCCT 60.341 52.381 0.00 0.00 34.74 5.19
1548 1650 0.320374 GGTTTTTGGCCCTTAGCACC 59.680 55.000 0.00 0.00 46.50 5.01
1549 1651 0.038618 GTTTTTGGCCCTTAGCACCG 60.039 55.000 0.00 0.00 46.50 4.94
1569 1671 4.022242 ACCGTACTACTGTCCATATCATGC 60.022 45.833 0.00 0.00 0.00 4.06
1580 1682 3.969312 TCCATATCATGCTGAACTCTGGA 59.031 43.478 0.00 0.00 0.00 3.86
1581 1683 4.409901 TCCATATCATGCTGAACTCTGGAA 59.590 41.667 0.00 0.00 0.00 3.53
1623 1725 4.846779 TTGTACAAGAAATCCACTTGCC 57.153 40.909 3.59 0.00 45.66 4.52
1651 1753 7.560262 AGTTATTAGGGGCTTCTAATTTGAACC 59.440 37.037 15.00 5.70 39.71 3.62
1657 1759 4.460034 GGGCTTCTAATTTGAACCGGTTTA 59.540 41.667 23.22 15.63 0.00 2.01
1661 1763 7.274904 GGCTTCTAATTTGAACCGGTTTAAATC 59.725 37.037 36.08 26.01 37.65 2.17
1688 1790 3.096092 AGTGATTTGGTGTTGGTGTTGT 58.904 40.909 0.00 0.00 0.00 3.32
1809 2217 5.953183 TGCATGATTACAACCTAAAAGCTG 58.047 37.500 0.00 0.00 0.00 4.24
1885 2295 7.593825 ACAAAGTTGTGATACTTAATTCTGCC 58.406 34.615 0.00 0.00 40.49 4.85
1934 2347 6.203530 TCTGTGTTTTCTTCAGTATCAGCAAG 59.796 38.462 0.00 0.00 0.00 4.01
1975 2388 4.082125 CCAGGAGTGTCCTTTGCTAAATT 58.918 43.478 0.00 0.00 46.91 1.82
1980 2393 2.817844 GTGTCCTTTGCTAAATTCGGGT 59.182 45.455 0.00 0.00 0.00 5.28
2192 2605 0.321919 TCGAGGCAGCTGAAAATGCT 60.322 50.000 20.43 0.00 42.19 3.79
2415 2828 0.750911 TCACATGTGCTTGTGTGGCA 60.751 50.000 21.38 0.00 45.73 4.92
2431 2844 3.123050 GTGGCACAATTGTTGAAGTTCC 58.877 45.455 13.86 2.68 44.16 3.62
2436 2849 3.742369 CACAATTGTTGAAGTTCCATGGC 59.258 43.478 8.77 0.00 0.00 4.40
2450 2863 0.801872 CATGGCGGATTCGTTGTTCA 59.198 50.000 0.00 0.00 38.89 3.18
2503 2916 1.203440 AGGTGGGTGTATCTTCCTGGT 60.203 52.381 0.00 0.00 0.00 4.00
2504 2917 1.065418 GGTGGGTGTATCTTCCTGGTG 60.065 57.143 0.00 0.00 0.00 4.17
2593 3006 4.341806 TGTCAATCCAAACTGCATCTGTTT 59.658 37.500 0.00 0.00 36.28 2.83
2630 3043 4.082408 TCGAACTACCATACACTGTTGGAG 60.082 45.833 13.97 10.30 36.79 3.86
2653 3066 7.227910 GGAGGTCTTGAAAACATGTTGTACTTA 59.772 37.037 12.82 0.00 0.00 2.24
2668 3081 5.160607 TGTACTTATGGGTCACTTCCTTG 57.839 43.478 0.00 0.00 0.00 3.61
2686 3099 5.070001 TCCTTGAGGAATTATATTTGGCCG 58.930 41.667 0.00 0.00 42.18 6.13
2691 3104 3.074538 AGGAATTATATTTGGCCGCTCCT 59.925 43.478 0.00 0.00 35.26 3.69
2703 3116 1.737838 CCGCTCCTCTGTTTGCATTA 58.262 50.000 0.00 0.00 0.00 1.90
2889 3305 6.604735 AATGGAAAATGATACGAGTAGCAC 57.395 37.500 3.17 0.00 34.01 4.40
3095 3514 3.519913 AGGTTCCTTCCAGTAATCCAGTC 59.480 47.826 0.00 0.00 0.00 3.51
3123 3542 8.975439 ACATAATTTATACTTTCGAGGCTAACG 58.025 33.333 0.00 0.00 0.00 3.18
3124 3543 8.975439 CATAATTTATACTTTCGAGGCTAACGT 58.025 33.333 0.00 0.00 0.00 3.99
3127 3546 2.061740 ACTTTCGAGGCTAACGTGTC 57.938 50.000 0.00 0.00 0.00 3.67
3144 3563 0.878961 GTCCTTTGTCACGCCGTTCT 60.879 55.000 0.00 0.00 0.00 3.01
3147 3566 0.111266 CTTTGTCACGCCGTTCTTCG 60.111 55.000 0.00 0.00 39.52 3.79
3192 3611 4.700213 TCTCTAGCAGGTTATTTTGTTGGC 59.300 41.667 0.00 0.00 0.00 4.52
3197 3616 4.126437 GCAGGTTATTTTGTTGGCTGTTT 58.874 39.130 0.00 0.00 0.00 2.83
3199 3618 4.444056 CAGGTTATTTTGTTGGCTGTTTCG 59.556 41.667 0.00 0.00 0.00 3.46
3214 3633 5.854866 GGCTGTTTCGTTTTGGTTTATCTAC 59.145 40.000 0.00 0.00 0.00 2.59
3218 3637 4.914312 TCGTTTTGGTTTATCTACGCTG 57.086 40.909 0.00 0.00 0.00 5.18
3224 3643 2.235155 TGGTTTATCTACGCTGGCTTGA 59.765 45.455 0.00 0.00 0.00 3.02
3225 3644 3.267483 GGTTTATCTACGCTGGCTTGAA 58.733 45.455 0.00 0.00 0.00 2.69
3231 3650 7.618502 TTATCTACGCTGGCTTGAATTTTAA 57.381 32.000 0.00 0.00 0.00 1.52
3233 3652 7.801716 ATCTACGCTGGCTTGAATTTTAATA 57.198 32.000 0.00 0.00 0.00 0.98
3281 3702 4.161565 TCGTATATCAAGTTGGGCTTCTGT 59.838 41.667 2.34 0.00 34.69 3.41
3282 3703 4.876107 CGTATATCAAGTTGGGCTTCTGTT 59.124 41.667 2.34 0.00 34.69 3.16
3283 3704 5.220662 CGTATATCAAGTTGGGCTTCTGTTG 60.221 44.000 2.34 0.00 34.69 3.33
3284 3705 1.691196 TCAAGTTGGGCTTCTGTTGG 58.309 50.000 2.34 0.00 34.69 3.77
3285 3706 0.675633 CAAGTTGGGCTTCTGTTGGG 59.324 55.000 0.00 0.00 34.69 4.12
3286 3707 0.469892 AAGTTGGGCTTCTGTTGGGG 60.470 55.000 0.00 0.00 30.06 4.96
3287 3708 1.152830 GTTGGGCTTCTGTTGGGGA 59.847 57.895 0.00 0.00 0.00 4.81
3288 3709 1.152830 TTGGGCTTCTGTTGGGGAC 59.847 57.895 0.00 0.00 0.00 4.46
3289 3710 2.359975 GGGCTTCTGTTGGGGACG 60.360 66.667 0.00 0.00 0.00 4.79
3290 3711 2.747686 GGCTTCTGTTGGGGACGA 59.252 61.111 0.00 0.00 0.00 4.20
3291 3712 1.299976 GGCTTCTGTTGGGGACGAT 59.700 57.895 0.00 0.00 0.00 3.73
3292 3713 0.539986 GGCTTCTGTTGGGGACGATA 59.460 55.000 0.00 0.00 0.00 2.92
3293 3714 1.141053 GGCTTCTGTTGGGGACGATAT 59.859 52.381 0.00 0.00 0.00 1.63
3294 3715 2.421529 GGCTTCTGTTGGGGACGATATT 60.422 50.000 0.00 0.00 0.00 1.28
3295 3716 3.279434 GCTTCTGTTGGGGACGATATTT 58.721 45.455 0.00 0.00 0.00 1.40
3296 3717 3.065371 GCTTCTGTTGGGGACGATATTTG 59.935 47.826 0.00 0.00 0.00 2.32
3297 3718 3.992943 TCTGTTGGGGACGATATTTGT 57.007 42.857 0.00 0.00 0.00 2.83
3298 3719 4.295141 TCTGTTGGGGACGATATTTGTT 57.705 40.909 0.00 0.00 0.00 2.83
3299 3720 4.258543 TCTGTTGGGGACGATATTTGTTC 58.741 43.478 0.00 0.00 0.00 3.18
3300 3721 4.019681 TCTGTTGGGGACGATATTTGTTCT 60.020 41.667 0.00 0.00 0.00 3.01
3301 3722 4.006989 TGTTGGGGACGATATTTGTTCTG 58.993 43.478 0.00 0.00 0.00 3.02
3317 3738 4.219115 TGTTCTGAGAGAAGAGTGGAGTT 58.781 43.478 0.00 0.00 34.42 3.01
3338 3759 2.198827 TTAGGTGCATGGTTGTGGAG 57.801 50.000 0.00 0.00 0.00 3.86
3343 3764 0.036732 TGCATGGTTGTGGAGTCCTC 59.963 55.000 11.33 7.59 0.00 3.71
3344 3765 1.021390 GCATGGTTGTGGAGTCCTCG 61.021 60.000 11.33 0.00 0.00 4.63
3347 3768 1.668151 GGTTGTGGAGTCCTCGCAC 60.668 63.158 11.33 7.68 33.97 5.34
3358 3780 3.479269 CTCGCACGTTTCGGCCTC 61.479 66.667 0.00 0.00 0.00 4.70
3364 3786 1.445582 ACGTTTCGGCCTCGATGTC 60.446 57.895 0.00 0.00 45.51 3.06
3388 3810 3.248602 GTCGATGTTGATTATGTGAGCCC 59.751 47.826 0.00 0.00 0.00 5.19
3389 3811 3.134623 TCGATGTTGATTATGTGAGCCCT 59.865 43.478 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 2.747989 GGTAAAGAACTAACTGCTGCCC 59.252 50.000 0.00 0.00 0.00 5.36
40 41 6.801539 TTGATGCAGGTAAAGAACTAACTG 57.198 37.500 0.00 0.00 39.26 3.16
48 49 3.255642 GCTTGGTTTGATGCAGGTAAAGA 59.744 43.478 0.00 0.00 0.00 2.52
78 79 8.243426 GCTTACAGAGAGATACATCTTATGGAG 58.757 40.741 0.00 0.00 37.25 3.86
99 100 3.004839 TCATATCAGCTGAGGACGCTTAC 59.995 47.826 22.96 0.00 35.07 2.34
100 101 3.222603 TCATATCAGCTGAGGACGCTTA 58.777 45.455 22.96 7.97 35.07 3.09
101 102 2.034878 TCATATCAGCTGAGGACGCTT 58.965 47.619 22.96 5.74 35.07 4.68
102 103 1.697284 TCATATCAGCTGAGGACGCT 58.303 50.000 22.96 6.52 38.49 5.07
105 106 4.626042 ACGAAATCATATCAGCTGAGGAC 58.374 43.478 22.96 7.10 0.00 3.85
108 109 4.625028 TGGACGAAATCATATCAGCTGAG 58.375 43.478 22.96 8.88 0.00 3.35
227 244 1.608966 CGCAGCGGCTGATACATACG 61.609 60.000 32.72 19.85 38.10 3.06
321 338 1.475034 GGCAAACCTCTGTCTGTGTCA 60.475 52.381 0.00 0.00 0.00 3.58
324 341 0.179020 TGGGCAAACCTCTGTCTGTG 60.179 55.000 0.00 0.00 41.11 3.66
325 342 0.179018 GTGGGCAAACCTCTGTCTGT 60.179 55.000 0.00 0.00 41.11 3.41
342 359 1.476074 ATCAACTGCGCAAAAACGTG 58.524 45.000 13.05 0.00 34.88 4.49
386 403 3.402681 CCTCTGGTGCCGGGTCAT 61.403 66.667 2.18 0.00 0.00 3.06
405 422 1.480789 TTAGCGGGAGTATCACAGCA 58.519 50.000 0.00 0.00 39.81 4.41
599 616 7.254590 GCAGGCAGTTTACAACTCAGAATATAG 60.255 40.741 0.00 0.00 40.46 1.31
600 617 6.538742 GCAGGCAGTTTACAACTCAGAATATA 59.461 38.462 0.00 0.00 40.46 0.86
605 624 2.494059 GCAGGCAGTTTACAACTCAGA 58.506 47.619 0.00 0.00 40.46 3.27
647 668 5.041287 CACCATGAGCAAAGCAGATTTATG 58.959 41.667 0.00 0.00 0.00 1.90
710 743 1.224075 CCGCACATCAGGCTTGATAG 58.776 55.000 11.43 8.37 42.12 2.08
735 790 1.738099 CAAAGCGGACTAGCGCAGT 60.738 57.895 11.47 11.48 43.00 4.40
736 791 1.416813 CTCAAAGCGGACTAGCGCAG 61.417 60.000 11.47 7.81 43.00 5.18
737 792 1.446099 CTCAAAGCGGACTAGCGCA 60.446 57.895 11.47 0.00 43.00 6.09
738 793 1.014564 AACTCAAAGCGGACTAGCGC 61.015 55.000 0.00 0.00 43.00 5.92
766 828 1.065199 AGGAGAATCAAAGGCGCATCA 60.065 47.619 10.83 0.00 36.25 3.07
944 1021 3.984633 GCTTCTTATTTCGAGAGGGATCG 59.015 47.826 0.00 0.00 44.07 3.69
1175 1253 2.467566 ACGGCGCCTTATTAATAGGG 57.532 50.000 26.68 17.27 33.19 3.53
1176 1254 2.919229 CGTACGGCGCCTTATTAATAGG 59.081 50.000 26.68 7.01 35.80 2.57
1340 1426 3.458163 GAGGGTGGCGGATCGACA 61.458 66.667 0.00 0.00 45.13 4.35
1367 1453 2.595188 CGTGCGATCGATCAATCAACAC 60.595 50.000 24.40 18.14 32.80 3.32
1370 1456 0.576798 GCGTGCGATCGATCAATCAA 59.423 50.000 24.40 2.62 0.00 2.57
1408 1494 2.912025 CAAACAACGGGGCAGCCT 60.912 61.111 12.43 0.00 0.00 4.58
1541 1643 2.794103 TGGACAGTAGTACGGTGCTAA 58.206 47.619 21.70 4.27 35.84 3.09
1548 1650 5.048713 TCAGCATGATATGGACAGTAGTACG 60.049 44.000 0.00 0.00 42.56 3.67
1549 1651 6.332735 TCAGCATGATATGGACAGTAGTAC 57.667 41.667 0.00 0.00 42.56 2.73
1569 1671 1.699634 TCCCCACTTTCCAGAGTTCAG 59.300 52.381 0.00 0.00 0.00 3.02
1580 1682 0.178990 GCCAGTTCTGTCCCCACTTT 60.179 55.000 0.00 0.00 0.00 2.66
1581 1683 1.062488 AGCCAGTTCTGTCCCCACTT 61.062 55.000 0.00 0.00 0.00 3.16
1623 1725 8.519799 TCAAATTAGAAGCCCCTAATAACTTG 57.480 34.615 8.18 9.13 38.12 3.16
1651 1753 2.690786 TCACTGTCCCGATTTAAACCG 58.309 47.619 0.00 0.00 0.00 4.44
1657 1759 2.819608 CACCAAATCACTGTCCCGATTT 59.180 45.455 0.00 0.00 41.39 2.17
1661 1763 1.266718 CAACACCAAATCACTGTCCCG 59.733 52.381 0.00 0.00 0.00 5.14
1688 1790 5.047306 CAGAGTATGTGGTTGTCTGGTAGAA 60.047 44.000 0.00 0.00 32.59 2.10
1809 2217 2.819608 TCACCAAAATTCCTAGCTGCAC 59.180 45.455 1.02 0.00 0.00 4.57
1881 2291 5.751990 AGGTCGAAATAAAGTATAACGGCAG 59.248 40.000 0.00 0.00 0.00 4.85
1910 2323 5.929697 TGCTGATACTGAAGAAAACACAG 57.070 39.130 0.00 0.00 37.62 3.66
1934 2347 0.801251 GAGCAGTGGCAGTTGACATC 59.199 55.000 0.00 0.00 44.61 3.06
1994 2407 2.125552 CTGATCGCCGGAGCAACA 60.126 61.111 5.05 1.88 38.26 3.33
2126 2539 1.173444 ACTCGTGCTCTTCACCGTCT 61.173 55.000 0.00 0.00 42.69 4.18
2267 2680 1.758514 GGAGCCCTCCGACTGATCA 60.759 63.158 0.00 0.00 40.36 2.92
2330 2743 2.128535 TCCGCCTTGGGGTATGAAATA 58.871 47.619 3.09 0.00 38.76 1.40
2415 2828 3.552684 CGCCATGGAACTTCAACAATTGT 60.553 43.478 18.40 4.92 0.00 2.71
2431 2844 0.801872 TGAACAACGAATCCGCCATG 59.198 50.000 0.00 0.00 39.95 3.66
2436 2849 1.399727 GGCAACTGAACAACGAATCCG 60.400 52.381 0.00 0.00 42.50 4.18
2503 2916 3.260632 TCATCAAAAGACCGGACTGATCA 59.739 43.478 9.46 0.00 0.00 2.92
2504 2917 3.861840 TCATCAAAAGACCGGACTGATC 58.138 45.455 9.46 0.00 0.00 2.92
2593 3006 4.570772 GGTAGTTCGAATTGCTGCAATCTA 59.429 41.667 26.40 19.10 32.43 1.98
2630 3043 7.807907 CCATAAGTACAACATGTTTTCAAGACC 59.192 37.037 8.77 0.00 0.00 3.85
2653 3066 2.044793 TCCTCAAGGAAGTGACCCAT 57.955 50.000 0.00 0.00 42.18 4.00
2668 3081 3.440522 GGAGCGGCCAAATATAATTCCTC 59.559 47.826 2.24 0.00 36.34 3.71
2675 3088 2.047061 ACAGAGGAGCGGCCAAATATA 58.953 47.619 2.24 0.00 40.02 0.86
2676 3089 0.839946 ACAGAGGAGCGGCCAAATAT 59.160 50.000 2.24 0.00 40.02 1.28
2686 3099 4.708726 AACATAATGCAAACAGAGGAGC 57.291 40.909 0.00 0.00 0.00 4.70
2691 3104 7.721402 AGTAACCAAAACATAATGCAAACAGA 58.279 30.769 0.00 0.00 0.00 3.41
2703 3116 7.015098 TGACATCCATTCAAGTAACCAAAACAT 59.985 33.333 0.00 0.00 0.00 2.71
2777 3193 2.545113 CGCGCTAGGACCAAGCTATTTA 60.545 50.000 5.56 0.00 37.85 1.40
2778 3194 1.806623 CGCGCTAGGACCAAGCTATTT 60.807 52.381 5.56 0.00 37.85 1.40
2889 3305 3.503748 CCAGAGGAAAGGCTAACAAACAG 59.496 47.826 0.00 0.00 0.00 3.16
3095 3514 7.730364 AGCCTCGAAAGTATAAATTATGTGG 57.270 36.000 0.00 0.00 0.00 4.17
3111 3530 0.963962 AAGGACACGTTAGCCTCGAA 59.036 50.000 1.47 0.00 0.00 3.71
3112 3531 0.963962 AAAGGACACGTTAGCCTCGA 59.036 50.000 1.47 0.00 0.00 4.04
3113 3532 1.068474 CAAAGGACACGTTAGCCTCG 58.932 55.000 1.47 0.00 0.00 4.63
3123 3542 1.433837 AACGGCGTGACAAAGGACAC 61.434 55.000 15.70 0.00 36.53 3.67
3124 3543 1.153329 AACGGCGTGACAAAGGACA 60.153 52.632 15.70 0.00 0.00 4.02
3127 3546 0.234884 GAAGAACGGCGTGACAAAGG 59.765 55.000 15.70 0.00 0.00 3.11
3144 3563 3.981071 AGAGTTGATCCCATGAACGAA 57.019 42.857 0.00 0.00 31.39 3.85
3192 3611 5.562623 GCGTAGATAAACCAAAACGAAACAG 59.437 40.000 0.00 0.00 32.35 3.16
3197 3616 3.680937 CCAGCGTAGATAAACCAAAACGA 59.319 43.478 0.00 0.00 32.35 3.85
3199 3618 3.439129 AGCCAGCGTAGATAAACCAAAAC 59.561 43.478 0.00 0.00 0.00 2.43
3214 3633 7.524294 AACATTATTAAAATTCAAGCCAGCG 57.476 32.000 0.00 0.00 0.00 5.18
3218 3637 9.739786 CGTCAAAACATTATTAAAATTCAAGCC 57.260 29.630 0.00 0.00 0.00 4.35
3231 3650 9.912634 ATGAAAAGAACATCGTCAAAACATTAT 57.087 25.926 0.00 0.00 0.00 1.28
3233 3652 8.647143 AATGAAAAGAACATCGTCAAAACATT 57.353 26.923 0.00 0.00 0.00 2.71
3270 3691 1.152830 GTCCCCAACAGAAGCCCAA 59.847 57.895 0.00 0.00 0.00 4.12
3281 3702 4.224147 TCTCAGAACAAATATCGTCCCCAA 59.776 41.667 0.00 0.00 0.00 4.12
3282 3703 3.772572 TCTCAGAACAAATATCGTCCCCA 59.227 43.478 0.00 0.00 0.00 4.96
3283 3704 4.099573 TCTCTCAGAACAAATATCGTCCCC 59.900 45.833 0.00 0.00 0.00 4.81
3284 3705 5.263968 TCTCTCAGAACAAATATCGTCCC 57.736 43.478 0.00 0.00 0.00 4.46
3285 3706 6.565234 TCTTCTCTCAGAACAAATATCGTCC 58.435 40.000 0.00 0.00 29.89 4.79
3286 3707 7.219917 CACTCTTCTCTCAGAACAAATATCGTC 59.780 40.741 0.00 0.00 29.89 4.20
3287 3708 7.032580 CACTCTTCTCTCAGAACAAATATCGT 58.967 38.462 0.00 0.00 29.89 3.73
3288 3709 6.475076 CCACTCTTCTCTCAGAACAAATATCG 59.525 42.308 0.00 0.00 29.89 2.92
3289 3710 7.551585 TCCACTCTTCTCTCAGAACAAATATC 58.448 38.462 0.00 0.00 29.89 1.63
3290 3711 7.180051 ACTCCACTCTTCTCTCAGAACAAATAT 59.820 37.037 0.00 0.00 29.89 1.28
3291 3712 6.495181 ACTCCACTCTTCTCTCAGAACAAATA 59.505 38.462 0.00 0.00 29.89 1.40
3292 3713 5.306678 ACTCCACTCTTCTCTCAGAACAAAT 59.693 40.000 0.00 0.00 29.89 2.32
3293 3714 4.651503 ACTCCACTCTTCTCTCAGAACAAA 59.348 41.667 0.00 0.00 29.89 2.83
3294 3715 4.219115 ACTCCACTCTTCTCTCAGAACAA 58.781 43.478 0.00 0.00 29.89 2.83
3295 3716 3.838565 ACTCCACTCTTCTCTCAGAACA 58.161 45.455 0.00 0.00 29.89 3.18
3296 3717 4.864704 AACTCCACTCTTCTCTCAGAAC 57.135 45.455 0.00 0.00 29.89 3.01
3297 3718 7.340743 CCTAATAACTCCACTCTTCTCTCAGAA 59.659 40.741 0.00 0.00 32.50 3.02
3298 3719 6.831353 CCTAATAACTCCACTCTTCTCTCAGA 59.169 42.308 0.00 0.00 0.00 3.27
3299 3720 6.605594 ACCTAATAACTCCACTCTTCTCTCAG 59.394 42.308 0.00 0.00 0.00 3.35
3300 3721 6.378564 CACCTAATAACTCCACTCTTCTCTCA 59.621 42.308 0.00 0.00 0.00 3.27
3301 3722 6.681865 GCACCTAATAACTCCACTCTTCTCTC 60.682 46.154 0.00 0.00 0.00 3.20
3317 3738 3.265737 ACTCCACAACCATGCACCTAATA 59.734 43.478 0.00 0.00 0.00 0.98
3338 3759 3.774702 GCCGAAACGTGCGAGGAC 61.775 66.667 12.05 0.00 0.00 3.85
3358 3780 5.460091 ACATAATCAACATCGACTGACATCG 59.540 40.000 0.00 0.00 43.63 3.84
3364 3786 4.025396 GGCTCACATAATCAACATCGACTG 60.025 45.833 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.