Multiple sequence alignment - TraesCS6D01G223900

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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 TraesCS6D01G223900 chr6D 100.000 4491 0 0 1 4491 315960728 315956238 0.000000e+00 8294
1 TraesCS6D01G223900 chr6D 93.881 621 22 1 1 605 315966191 315965571 0.000000e+00 922
2 TraesCS6D01G223900 chr6B 93.587 2152 71 18 601 2728 508939066 508941174 0.000000e+00 3147
3 TraesCS6D01G223900 chr6B 93.917 1085 31 12 2725 3790 508941254 508942322 0.000000e+00 1605
4 TraesCS6D01G223900 chr6B 93.646 362 20 2 4055 4415 508942505 508942864 5.110000e-149 538
5 TraesCS6D01G223900 chr6B 95.425 153 5 1 3906 4056 508942324 508942476 4.490000e-60 243
6 TraesCS6D01G223900 chr6B 97.059 68 2 0 4424 4491 508944441 508944508 1.020000e-21 115
7 TraesCS6D01G223900 chr6A 92.941 1615 63 20 2204 3790 453826208 453824617 0.000000e+00 2303
8 TraesCS6D01G223900 chr6A 96.530 1268 29 4 606 1859 453828171 453826905 0.000000e+00 2084
9 TraesCS6D01G223900 chr6A 88.728 621 29 15 3906 4491 453824615 453824001 0.000000e+00 721
10 TraesCS6D01G223900 chr6A 90.609 394 23 8 1823 2211 453826901 453826517 1.110000e-140 510
11 TraesCS6D01G223900 chr3A 93.720 621 23 1 1 605 748203927 748203307 0.000000e+00 917
12 TraesCS6D01G223900 chr3A 93.076 621 27 1 1 605 748198446 748197826 0.000000e+00 894
13 TraesCS6D01G223900 chr3A 92.110 621 33 8 1 605 14064578 14063958 0.000000e+00 861
14 TraesCS6D01G223900 chr2D 93.559 621 24 1 1 605 644353058 644352438 0.000000e+00 911
15 TraesCS6D01G223900 chr2D 91.787 621 35 1 1 605 432017715 432017095 0.000000e+00 850
16 TraesCS6D01G223900 chr2D 91.391 151 12 1 1618 1767 497925691 497925541 5.890000e-49 206
17 TraesCS6D01G223900 chr1B 93.076 621 27 1 1 605 6158300 6157680 0.000000e+00 894
18 TraesCS6D01G223900 chrUn 92.754 621 29 8 1 605 30845167 30844547 0.000000e+00 883
19 TraesCS6D01G223900 chrUn 93.211 383 10 1 2 368 30201614 30201996 2.360000e-152 549
20 TraesCS6D01G223900 chr1D 92.754 621 29 1 1 605 202399894 202400514 0.000000e+00 883
21 TraesCS6D01G223900 chr1D 91.948 621 34 1 1 605 394705996 394706616 0.000000e+00 856
22 TraesCS6D01G223900 chr7D 92.135 623 33 3 1 607 113817847 113818469 0.000000e+00 865
23 TraesCS6D01G223900 chr7D 94.118 493 13 1 129 605 136305033 136304541 0.000000e+00 736
24 TraesCS6D01G223900 chr4D 92.122 622 33 1 1 606 30465371 30465992 0.000000e+00 863
25 TraesCS6D01G223900 chr4A 93.783 563 19 1 59 605 5019406 5019968 0.000000e+00 832
26 TraesCS6D01G223900 chr4A 90.177 621 31 6 1 605 573311853 573312459 0.000000e+00 782
27 TraesCS6D01G223900 chr1A 93.204 515 29 4 95 608 572717883 572718392 0.000000e+00 752
28 TraesCS6D01G223900 chr2A 92.053 151 11 1 1618 1767 642227519 642227369 1.270000e-50 211
29 TraesCS6D01G223900 chr2B 91.667 132 11 0 3321 3452 583788152 583788021 2.760000e-42 183


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 TraesCS6D01G223900 chr6D 315956238 315960728 4490 True 8294.0 8294 100.0000 1 4491 1 chr6D.!!$R1 4490
1 TraesCS6D01G223900 chr6D 315965571 315966191 620 True 922.0 922 93.8810 1 605 1 chr6D.!!$R2 604
2 TraesCS6D01G223900 chr6B 508939066 508944508 5442 False 1129.6 3147 94.7268 601 4491 5 chr6B.!!$F1 3890
3 TraesCS6D01G223900 chr6A 453824001 453828171 4170 True 1404.5 2303 92.2020 606 4491 4 chr6A.!!$R1 3885
4 TraesCS6D01G223900 chr3A 748203307 748203927 620 True 917.0 917 93.7200 1 605 1 chr3A.!!$R3 604
5 TraesCS6D01G223900 chr3A 748197826 748198446 620 True 894.0 894 93.0760 1 605 1 chr3A.!!$R2 604
6 TraesCS6D01G223900 chr3A 14063958 14064578 620 True 861.0 861 92.1100 1 605 1 chr3A.!!$R1 604
7 TraesCS6D01G223900 chr2D 644352438 644353058 620 True 911.0 911 93.5590 1 605 1 chr2D.!!$R3 604
8 TraesCS6D01G223900 chr2D 432017095 432017715 620 True 850.0 850 91.7870 1 605 1 chr2D.!!$R1 604
9 TraesCS6D01G223900 chr1B 6157680 6158300 620 True 894.0 894 93.0760 1 605 1 chr1B.!!$R1 604
10 TraesCS6D01G223900 chrUn 30844547 30845167 620 True 883.0 883 92.7540 1 605 1 chrUn.!!$R1 604
11 TraesCS6D01G223900 chr1D 202399894 202400514 620 False 883.0 883 92.7540 1 605 1 chr1D.!!$F1 604
12 TraesCS6D01G223900 chr1D 394705996 394706616 620 False 856.0 856 91.9480 1 605 1 chr1D.!!$F2 604
13 TraesCS6D01G223900 chr7D 113817847 113818469 622 False 865.0 865 92.1350 1 607 1 chr7D.!!$F1 606
14 TraesCS6D01G223900 chr4D 30465371 30465992 621 False 863.0 863 92.1220 1 606 1 chr4D.!!$F1 605
15 TraesCS6D01G223900 chr4A 5019406 5019968 562 False 832.0 832 93.7830 59 605 1 chr4A.!!$F1 546
16 TraesCS6D01G223900 chr4A 573311853 573312459 606 False 782.0 782 90.1770 1 605 1 chr4A.!!$F2 604
17 TraesCS6D01G223900 chr1A 572717883 572718392 509 False 752.0 752 93.2040 95 608 1 chr1A.!!$F1 513

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
424 441 2.497293 CCCGCTGCACCGTATGTA 59.503 61.111 0.0 0.0 0.00 2.29 F
1185 1219 2.105006 TGCTCTCTTCTGACCATTGC 57.895 50.000 0.0 0.0 0.00 3.56 F
1309 1343 0.392336 GGCTGAGGAGGTATGCTCTG 59.608 60.000 0.0 0.0 43.87 3.35 F
1848 1928 1.439543 ACTCCTCAAGACCTTTGCCT 58.560 50.000 0.0 0.0 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1289 1323 0.264359 AGAGCATACCTCCTCAGCCT 59.736 55.000 0.00 0.0 41.74 4.58 R
2306 2714 1.080093 GCACACGATCGAGACCCAA 60.080 57.895 24.34 0.0 0.00 4.12 R
2500 2908 2.564721 GCCACTGCCTTTCCACACC 61.565 63.158 0.00 0.0 0.00 4.16 R
3833 4367 0.459934 AAAACGAACACGTCCGGACA 60.460 50.000 32.80 0.0 39.39 4.02 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
44 45 2.995258 GGACGCGTTAATTACTGAACCA 59.005 45.455 15.53 0.00 0.00 3.67
424 441 2.497293 CCCGCTGCACCGTATGTA 59.503 61.111 0.00 0.00 0.00 2.29
499 516 4.802248 GCCCTAGATGTGATCTGTTCATCC 60.802 50.000 13.03 0.00 40.51 3.51
590 607 9.590451 TTCGGATTAAATCTCGTAGTAATTTGT 57.410 29.630 0.00 0.00 0.00 2.83
1080 1114 4.281657 TCAGTGTGCCAGATCACTACTAT 58.718 43.478 0.00 0.00 42.05 2.12
1185 1219 2.105006 TGCTCTCTTCTGACCATTGC 57.895 50.000 0.00 0.00 0.00 3.56
1289 1323 4.819630 GGTCGGTTTCATGCCTAATATTGA 59.180 41.667 0.00 0.00 0.00 2.57
1309 1343 0.392336 GGCTGAGGAGGTATGCTCTG 59.608 60.000 0.00 0.00 43.87 3.35
1436 1470 1.958288 AGAGTTGGCTATGAGGGTGT 58.042 50.000 0.00 0.00 0.00 4.16
1766 1804 2.044492 AGAACAGTCTCCATCCCAGGTA 59.956 50.000 0.00 0.00 0.00 3.08
1815 1853 9.831682 AGAACCCTAACCTATTTCCATTTTTAA 57.168 29.630 0.00 0.00 0.00 1.52
1848 1928 1.439543 ACTCCTCAAGACCTTTGCCT 58.560 50.000 0.00 0.00 0.00 4.75
1867 1947 2.571212 CTGTCTCTGCTAGGATCGAGT 58.429 52.381 0.00 0.00 0.00 4.18
1868 1948 3.495276 CCTGTCTCTGCTAGGATCGAGTA 60.495 52.174 0.00 0.00 33.33 2.59
1869 1949 3.734463 TGTCTCTGCTAGGATCGAGTAG 58.266 50.000 5.35 5.35 0.00 2.57
1870 1950 3.388350 TGTCTCTGCTAGGATCGAGTAGA 59.612 47.826 11.74 11.74 34.87 2.59
1871 1951 4.141688 TGTCTCTGCTAGGATCGAGTAGAA 60.142 45.833 12.84 4.78 35.57 2.10
1872 1952 4.212636 GTCTCTGCTAGGATCGAGTAGAAC 59.787 50.000 12.84 10.62 35.57 3.01
1936 2016 7.163441 TGTGGTAGTGGTAGGTTAATCTTTTC 58.837 38.462 0.00 0.00 0.00 2.29
1967 2047 4.249661 GCTAGCAGCTTCAGAAGTAACTT 58.750 43.478 10.63 0.00 38.45 2.66
1982 2062 9.057089 CAGAAGTAACTTGGTTGTAGAGAAATT 57.943 33.333 0.00 0.00 0.00 1.82
2178 2263 7.063191 GCACAAATGTAATATGCATGAAACACA 59.937 33.333 10.16 6.67 36.30 3.72
2185 2270 6.432607 AATATGCATGAAACACACTCTCAG 57.567 37.500 10.16 0.00 0.00 3.35
2197 2282 8.621532 AAACACACTCTCAGCATAGAATAAAA 57.378 30.769 0.00 0.00 0.00 1.52
2198 2283 7.840342 ACACACTCTCAGCATAGAATAAAAG 57.160 36.000 0.00 0.00 0.00 2.27
2228 2627 6.084326 TCTCTTAATTTGTGGTTTTGAGGC 57.916 37.500 0.00 0.00 0.00 4.70
2352 2760 8.204836 TCTTCAGATAAATACAGAAGGCCTAAC 58.795 37.037 5.16 3.23 37.04 2.34
2379 2787 9.883142 AGAGTTCTGTTCTATTATCTGGAAAAG 57.117 33.333 0.00 0.00 32.31 2.27
2422 2830 9.483489 TCTATATCCTCCGGTGCTAATTTATTA 57.517 33.333 0.00 0.00 0.00 0.98
2461 2869 3.257624 ACGGGTGAACTAAGGAGTACTTG 59.742 47.826 0.00 0.00 40.37 3.16
2500 2908 3.053831 TCTAAAAGAACAGAAGGGGCG 57.946 47.619 0.00 0.00 0.00 6.13
2520 2928 1.827789 TGTGGAAAGGCAGTGGCAC 60.828 57.895 20.04 10.29 43.71 5.01
2732 3226 8.092521 ACACAAGACAAAATGAGATACTTCAG 57.907 34.615 0.00 0.00 0.00 3.02
2917 3412 8.347004 TGATTGCATAGTTGTTATCCTTTGAA 57.653 30.769 0.00 0.00 0.00 2.69
2926 3421 7.280356 AGTTGTTATCCTTTGAACACTGTAGT 58.720 34.615 0.00 0.00 35.35 2.73
2984 3485 5.657302 AGGGCAAATAGGATATAGTAGACGG 59.343 44.000 0.00 0.00 0.00 4.79
3163 3664 6.743575 AACTGTGTACTGGCTAATGATTTC 57.256 37.500 0.00 0.00 0.00 2.17
3219 3720 3.008049 TCCTTTAGAAGTGGTTCTGGAGC 59.992 47.826 0.00 0.00 43.29 4.70
3246 3761 0.743345 CTACCTAAAGCGGGGCACAC 60.743 60.000 0.00 0.00 0.00 3.82
3312 3828 9.416794 CATACTGTAATAAACATTTTGTTGCCA 57.583 29.630 0.00 0.00 40.14 4.92
3499 4015 0.747283 CCTGCTTCTGATCACCTGCC 60.747 60.000 0.00 0.00 0.00 4.85
3579 4100 1.004200 ACCGACCCACGTTTGATCC 60.004 57.895 0.00 0.00 40.78 3.36
3697 4222 1.992667 CACGTACCAGTACTGCATGTG 59.007 52.381 22.94 22.94 34.04 3.21
3698 4223 0.999406 CGTACCAGTACTGCATGTGC 59.001 55.000 17.86 12.19 42.50 4.57
3743 4276 6.184580 CCGTAGGCAATAGAGATAGTAGTG 57.815 45.833 0.00 0.00 46.14 2.74
3744 4277 5.392165 CCGTAGGCAATAGAGATAGTAGTGC 60.392 48.000 0.00 0.00 46.14 4.40
3745 4278 5.181433 CGTAGGCAATAGAGATAGTAGTGCA 59.819 44.000 5.10 0.00 42.01 4.57
3790 4324 3.375642 CATGTGATGGACTAGCTACACG 58.624 50.000 5.70 0.00 0.00 4.49
3791 4325 2.718563 TGTGATGGACTAGCTACACGA 58.281 47.619 0.00 0.00 0.00 4.35
3792 4326 2.683362 TGTGATGGACTAGCTACACGAG 59.317 50.000 0.00 0.00 0.00 4.18
3801 4335 3.814577 GCTACACGAGCCTCTTCAA 57.185 52.632 0.00 0.00 46.41 2.69
3802 4336 1.351153 GCTACACGAGCCTCTTCAAC 58.649 55.000 0.00 0.00 46.41 3.18
3803 4337 1.997669 CTACACGAGCCTCTTCAACC 58.002 55.000 0.00 0.00 0.00 3.77
3804 4338 1.272490 CTACACGAGCCTCTTCAACCA 59.728 52.381 0.00 0.00 0.00 3.67
3805 4339 0.249911 ACACGAGCCTCTTCAACCAC 60.250 55.000 0.00 0.00 0.00 4.16
3806 4340 1.006102 ACGAGCCTCTTCAACCACG 60.006 57.895 0.00 0.00 0.00 4.94
3807 4341 1.006102 CGAGCCTCTTCAACCACGT 60.006 57.895 0.00 0.00 0.00 4.49
3808 4342 0.242825 CGAGCCTCTTCAACCACGTA 59.757 55.000 0.00 0.00 0.00 3.57
3809 4343 1.336517 CGAGCCTCTTCAACCACGTAA 60.337 52.381 0.00 0.00 0.00 3.18
3810 4344 2.067013 GAGCCTCTTCAACCACGTAAC 58.933 52.381 0.00 0.00 0.00 2.50
3811 4345 0.788391 GCCTCTTCAACCACGTAACG 59.212 55.000 0.00 0.00 0.00 3.18
3812 4346 1.870993 GCCTCTTCAACCACGTAACGT 60.871 52.381 0.00 0.00 42.36 3.99
3813 4347 2.056577 CCTCTTCAACCACGTAACGTC 58.943 52.381 0.00 0.00 38.32 4.34
3814 4348 2.056577 CTCTTCAACCACGTAACGTCC 58.943 52.381 0.00 0.00 38.32 4.79
3815 4349 1.408340 TCTTCAACCACGTAACGTCCA 59.592 47.619 0.00 0.00 38.32 4.02
3816 4350 1.523934 CTTCAACCACGTAACGTCCAC 59.476 52.381 0.00 0.00 38.32 4.02
3817 4351 0.594540 TCAACCACGTAACGTCCACG 60.595 55.000 17.96 17.96 44.80 4.94
3818 4352 1.300080 AACCACGTAACGTCCACGG 60.300 57.895 21.90 13.01 43.59 4.94
3819 4353 1.733402 AACCACGTAACGTCCACGGA 61.733 55.000 21.90 0.00 43.59 4.69
3820 4354 1.730547 CCACGTAACGTCCACGGAC 60.731 63.158 21.90 6.12 43.59 4.79
3821 4355 1.008652 CACGTAACGTCCACGGACA 60.009 57.895 21.90 0.00 44.77 4.02
3822 4356 1.008538 ACGTAACGTCCACGGACAC 60.009 57.895 21.90 6.13 44.77 3.67
3823 4357 2.076628 CGTAACGTCCACGGACACG 61.077 63.158 16.23 13.72 44.77 4.49
3824 4358 2.050168 TAACGTCCACGGACACGC 60.050 61.111 16.23 0.00 44.77 5.34
3825 4359 3.556543 TAACGTCCACGGACACGCC 62.557 63.158 16.23 0.00 44.77 5.68
3836 4370 4.626081 ACACGCCTGGCCAGTGTC 62.626 66.667 30.63 17.76 44.75 3.67
3841 4375 4.394712 CCTGGCCAGTGTCCGGAC 62.395 72.222 30.63 28.17 31.56 4.79
3842 4376 4.742201 CTGGCCAGTGTCCGGACG 62.742 72.222 28.70 15.86 32.30 4.79
3845 4379 4.295119 GCCAGTGTCCGGACGTGT 62.295 66.667 28.70 13.44 0.00 4.49
3846 4380 2.420043 CCAGTGTCCGGACGTGTT 59.580 61.111 28.70 11.72 0.00 3.32
3847 4381 1.663702 CCAGTGTCCGGACGTGTTC 60.664 63.158 28.70 15.83 0.00 3.18
3848 4382 2.014554 CAGTGTCCGGACGTGTTCG 61.015 63.158 28.70 10.56 43.34 3.95
3897 4431 7.576861 TTTTTCCTAATTTTCTTCGTCCAGT 57.423 32.000 0.00 0.00 0.00 4.00
3898 4432 6.796705 TTTCCTAATTTTCTTCGTCCAGTC 57.203 37.500 0.00 0.00 0.00 3.51
3899 4433 5.477607 TCCTAATTTTCTTCGTCCAGTCA 57.522 39.130 0.00 0.00 0.00 3.41
3900 4434 5.235516 TCCTAATTTTCTTCGTCCAGTCAC 58.764 41.667 0.00 0.00 0.00 3.67
3901 4435 5.011738 TCCTAATTTTCTTCGTCCAGTCACT 59.988 40.000 0.00 0.00 0.00 3.41
3902 4436 5.701290 CCTAATTTTCTTCGTCCAGTCACTT 59.299 40.000 0.00 0.00 0.00 3.16
3903 4437 5.424121 AATTTTCTTCGTCCAGTCACTTG 57.576 39.130 0.00 0.00 0.00 3.16
3904 4438 1.865865 TTCTTCGTCCAGTCACTTGC 58.134 50.000 0.00 0.00 0.00 4.01
4108 4674 2.250939 GCAACGTGCCACAGCTGTA 61.251 57.895 21.20 0.18 37.42 2.74
4327 4893 2.496871 TCGCCGGTTAAAGGAGTATCAA 59.503 45.455 1.90 0.00 36.25 2.57
4330 4896 3.118519 GCCGGTTAAAGGAGTATCAAGGA 60.119 47.826 1.90 0.00 36.25 3.36
4341 4907 4.402793 GGAGTATCAAGGAGTGTGAGCTTA 59.597 45.833 0.00 0.00 36.25 3.09
4356 4922 4.393371 GTGAGCTTAGGGTGTGAGAAAATC 59.607 45.833 0.00 0.00 0.00 2.17
4361 4927 6.069963 AGCTTAGGGTGTGAGAAAATCAGTAT 60.070 38.462 0.00 0.00 39.07 2.12
4362 4928 7.125811 AGCTTAGGGTGTGAGAAAATCAGTATA 59.874 37.037 0.00 0.00 39.07 1.47
4363 4929 7.439655 GCTTAGGGTGTGAGAAAATCAGTATAG 59.560 40.741 0.00 0.00 39.07 1.31
4364 4930 6.240549 AGGGTGTGAGAAAATCAGTATAGG 57.759 41.667 0.00 0.00 39.07 2.57
4415 4982 7.937394 ACTACCAGTTTAGCACTAAAATGTCTT 59.063 33.333 22.03 12.55 44.70 3.01
4416 4983 7.582667 ACCAGTTTAGCACTAAAATGTCTTT 57.417 32.000 22.03 7.31 44.70 2.52
4417 4984 8.007405 ACCAGTTTAGCACTAAAATGTCTTTT 57.993 30.769 22.03 5.51 44.70 2.27
4418 4985 7.920682 ACCAGTTTAGCACTAAAATGTCTTTTG 59.079 33.333 22.03 12.32 44.70 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 6.402550 CGTCACGATCCAAAAGAATCAGAAAT 60.403 38.462 0.00 0.00 0.00 2.17
330 347 2.506438 CGGGGAAGAAGTCGTCGC 60.506 66.667 3.27 3.27 36.78 5.19
424 441 6.920758 CGATCTCGAACAAGAAGGATAGAATT 59.079 38.462 0.00 0.00 43.02 2.17
748 766 5.467705 GTGGGTACAGTACTTACTTCAGTG 58.532 45.833 10.62 0.00 33.46 3.66
914 932 6.806668 TGTCAATCTCTCTCTCTCTCTCTA 57.193 41.667 0.00 0.00 0.00 2.43
1080 1114 1.982958 GAAAGAGGAACAGGGGTGGTA 59.017 52.381 0.00 0.00 0.00 3.25
1289 1323 0.264359 AGAGCATACCTCCTCAGCCT 59.736 55.000 0.00 0.00 41.74 4.58
1368 1402 7.832685 TGATCAGGAAGAGACATCAAATCAAAT 59.167 33.333 0.00 0.00 0.00 2.32
1413 1447 1.293924 CCTCATAGCCAACTCTTGCG 58.706 55.000 0.00 0.00 0.00 4.85
1436 1470 5.435686 AGAATAACCATTACAGGCAGTGA 57.564 39.130 0.00 0.00 0.00 3.41
1766 1804 9.444600 TTCTTAATTGCTTATAGAACCGAAGTT 57.555 29.630 0.00 0.00 39.54 2.66
1815 1853 5.954752 TCTTGAGGAGTTCATAGATGACAGT 59.045 40.000 0.00 0.00 36.36 3.55
1820 1858 5.867903 AGGTCTTGAGGAGTTCATAGATG 57.132 43.478 0.00 0.00 35.27 2.90
1848 1928 2.719531 ACTCGATCCTAGCAGAGACA 57.280 50.000 8.35 0.00 34.98 3.41
1867 1947 6.598457 ACAATCTGTACGAGCTTCTAGTTCTA 59.402 38.462 0.00 0.00 0.00 2.10
1868 1948 5.416326 ACAATCTGTACGAGCTTCTAGTTCT 59.584 40.000 0.00 0.00 0.00 3.01
1869 1949 5.642686 ACAATCTGTACGAGCTTCTAGTTC 58.357 41.667 0.00 0.00 0.00 3.01
1870 1950 5.646577 ACAATCTGTACGAGCTTCTAGTT 57.353 39.130 0.00 0.00 0.00 2.24
1871 1951 5.646577 AACAATCTGTACGAGCTTCTAGT 57.353 39.130 0.00 0.00 0.00 2.57
1872 1952 6.093404 TCAAACAATCTGTACGAGCTTCTAG 58.907 40.000 0.00 0.00 0.00 2.43
1936 2016 4.852962 GCTGCTAGCTCTCAAGGG 57.147 61.111 17.23 0.00 38.45 3.95
1967 2047 8.677300 GCAAATAGATCAATTTCTCTACAACCA 58.323 33.333 0.00 0.00 0.00 3.67
2011 2091 3.587797 AGCCACAATTGATTGAAGCAG 57.412 42.857 13.59 0.00 40.14 4.24
2021 2101 4.763793 CCCTGGATCTATTAGCCACAATTG 59.236 45.833 3.24 3.24 39.26 2.32
2052 2133 7.839907 TGTTGCAGGCTAATTAATCTCAAATT 58.160 30.769 0.00 0.00 0.00 1.82
2178 2263 8.317679 ACACTTCTTTTATTCTATGCTGAGAGT 58.682 33.333 0.00 0.00 0.00 3.24
2197 2282 7.881775 AACCACAAATTAAGAGAACACTTCT 57.118 32.000 0.00 0.00 44.21 2.85
2198 2283 8.807581 CAAAACCACAAATTAAGAGAACACTTC 58.192 33.333 0.00 0.00 0.00 3.01
2245 2648 7.360861 CGTTAAGCTTGTGTATCCAATGAAAGA 60.361 37.037 9.86 0.00 0.00 2.52
2306 2714 1.080093 GCACACGATCGAGACCCAA 60.080 57.895 24.34 0.00 0.00 4.12
2379 2787 9.579932 AGGATATAGATGGTTTGGAAGATTTTC 57.420 33.333 0.00 0.00 0.00 2.29
2422 2830 3.773119 ACCCGTTGTACCAGTCTGATAAT 59.227 43.478 0.00 0.00 0.00 1.28
2437 2845 2.833631 ACTCCTTAGTTCACCCGTTG 57.166 50.000 0.00 0.00 29.00 4.10
2461 2869 9.274065 CTTTTAGAAACTTTACTGTGTGACAAC 57.726 33.333 0.00 0.00 0.00 3.32
2500 2908 2.564721 GCCACTGCCTTTCCACACC 61.565 63.158 0.00 0.00 0.00 4.16
2520 2928 6.015519 CCCTTCTACAATCTCCTCTGTCATAG 60.016 46.154 0.00 0.00 0.00 2.23
2711 3122 9.950496 ATACACTGAAGTATCTCATTTTGTCTT 57.050 29.630 0.00 0.00 28.82 3.01
2877 3372 5.794687 TGCAATCAGTATAAAACGTGGAG 57.205 39.130 0.00 0.00 0.00 3.86
3163 3664 4.652421 TCTATTCTTCAGCAGAGCAGAG 57.348 45.455 0.00 0.00 31.12 3.35
3219 3720 3.317430 CCCCGCTTTAGGTAGTACTACTG 59.683 52.174 27.71 15.68 36.36 2.74
3246 3761 8.375506 ACTATGATGTTTACACTATGGGGTATG 58.624 37.037 0.00 0.00 0.00 2.39
3310 3826 2.792947 GCTCCTGCATGGCCATTGG 61.793 63.158 17.92 18.24 39.41 3.16
3312 3828 0.466922 GTAGCTCCTGCATGGCCATT 60.467 55.000 17.92 0.71 42.74 3.16
3511 4027 1.021390 AGCACTTGCATGGCTACGAC 61.021 55.000 11.96 0.00 45.16 4.34
3544 4064 1.034292 GGTGGATGCCCTTTGCTCTC 61.034 60.000 0.00 0.00 42.00 3.20
3545 4065 1.000396 GGTGGATGCCCTTTGCTCT 60.000 57.895 0.00 0.00 42.00 4.09
3579 4100 5.869344 TCAAAATATAAGGAGCCGATCGATG 59.131 40.000 18.66 1.12 0.00 3.84
3741 4274 6.415280 CAGATACTCGTACATAGAAAGTGCAC 59.585 42.308 9.40 9.40 0.00 4.57
3742 4275 6.095021 ACAGATACTCGTACATAGAAAGTGCA 59.905 38.462 0.00 0.00 0.00 4.57
3743 4276 6.415280 CACAGATACTCGTACATAGAAAGTGC 59.585 42.308 0.00 0.00 0.00 4.40
3744 4277 6.415280 GCACAGATACTCGTACATAGAAAGTG 59.585 42.308 0.00 0.00 0.00 3.16
3745 4278 6.095021 TGCACAGATACTCGTACATAGAAAGT 59.905 38.462 0.00 0.00 0.00 2.66
3790 4324 2.067013 GTTACGTGGTTGAAGAGGCTC 58.933 52.381 6.34 6.34 0.00 4.70
3791 4325 1.604693 CGTTACGTGGTTGAAGAGGCT 60.605 52.381 0.00 0.00 0.00 4.58
3792 4326 0.788391 CGTTACGTGGTTGAAGAGGC 59.212 55.000 0.00 0.00 0.00 4.70
3793 4327 2.056577 GACGTTACGTGGTTGAAGAGG 58.943 52.381 17.19 0.00 41.37 3.69
3794 4328 2.056577 GGACGTTACGTGGTTGAAGAG 58.943 52.381 17.19 0.00 41.37 2.85
3795 4329 1.408340 TGGACGTTACGTGGTTGAAGA 59.592 47.619 17.19 0.00 41.37 2.87
3796 4330 1.523934 GTGGACGTTACGTGGTTGAAG 59.476 52.381 17.19 0.00 41.37 3.02
3797 4331 1.569708 GTGGACGTTACGTGGTTGAA 58.430 50.000 17.19 0.00 41.37 2.69
3798 4332 0.594540 CGTGGACGTTACGTGGTTGA 60.595 55.000 17.19 0.00 41.37 3.18
3799 4333 1.550659 CCGTGGACGTTACGTGGTTG 61.551 60.000 17.19 2.41 41.37 3.77
3800 4334 1.300080 CCGTGGACGTTACGTGGTT 60.300 57.895 17.19 0.00 41.37 3.67
3801 4335 2.192861 TCCGTGGACGTTACGTGGT 61.193 57.895 17.19 0.00 41.37 4.16
3802 4336 1.730547 GTCCGTGGACGTTACGTGG 60.731 63.158 17.19 10.54 41.37 4.94
3803 4337 3.832981 GTCCGTGGACGTTACGTG 58.167 61.111 17.19 0.00 41.37 4.49
3818 4352 4.626081 ACACTGGCCAGGCGTGTC 62.626 66.667 35.42 0.00 37.30 3.67
3819 4353 4.626081 GACACTGGCCAGGCGTGT 62.626 66.667 35.42 29.74 43.89 4.49
3824 4358 4.394712 GTCCGGACACTGGCCAGG 62.395 72.222 35.42 25.43 0.00 4.45
3825 4359 4.742201 CGTCCGGACACTGGCCAG 62.742 72.222 32.80 31.60 0.00 4.85
3828 4362 3.802418 AACACGTCCGGACACTGGC 62.802 63.158 32.80 6.40 0.00 4.85
3829 4363 1.663702 GAACACGTCCGGACACTGG 60.664 63.158 32.80 19.29 0.00 4.00
3830 4364 2.014554 CGAACACGTCCGGACACTG 61.015 63.158 32.80 26.92 0.00 3.66
3831 4365 2.008268 AACGAACACGTCCGGACACT 62.008 55.000 32.80 15.43 39.39 3.55
3832 4366 1.147557 AAACGAACACGTCCGGACAC 61.148 55.000 32.80 16.71 39.39 3.67
3833 4367 0.459934 AAAACGAACACGTCCGGACA 60.460 50.000 32.80 0.00 39.39 4.02
3834 4368 0.652071 AAAAACGAACACGTCCGGAC 59.348 50.000 25.28 25.28 39.39 4.79
3835 4369 3.062585 AAAAACGAACACGTCCGGA 57.937 47.368 0.00 0.00 39.39 5.14
3873 4407 7.283580 TGACTGGACGAAGAAAATTAGGAAAAA 59.716 33.333 0.00 0.00 0.00 1.94
3874 4408 6.768861 TGACTGGACGAAGAAAATTAGGAAAA 59.231 34.615 0.00 0.00 0.00 2.29
3875 4409 6.204108 GTGACTGGACGAAGAAAATTAGGAAA 59.796 38.462 0.00 0.00 0.00 3.13
3876 4410 5.699458 GTGACTGGACGAAGAAAATTAGGAA 59.301 40.000 0.00 0.00 0.00 3.36
3877 4411 5.011738 AGTGACTGGACGAAGAAAATTAGGA 59.988 40.000 0.00 0.00 0.00 2.94
3878 4412 5.238583 AGTGACTGGACGAAGAAAATTAGG 58.761 41.667 0.00 0.00 0.00 2.69
3879 4413 6.593978 CAAGTGACTGGACGAAGAAAATTAG 58.406 40.000 0.00 0.00 0.00 1.73
3880 4414 5.049680 GCAAGTGACTGGACGAAGAAAATTA 60.050 40.000 0.00 0.00 0.00 1.40
3881 4415 4.261197 GCAAGTGACTGGACGAAGAAAATT 60.261 41.667 0.00 0.00 0.00 1.82
3882 4416 3.251004 GCAAGTGACTGGACGAAGAAAAT 59.749 43.478 0.00 0.00 0.00 1.82
3883 4417 2.612212 GCAAGTGACTGGACGAAGAAAA 59.388 45.455 0.00 0.00 0.00 2.29
3884 4418 2.210116 GCAAGTGACTGGACGAAGAAA 58.790 47.619 0.00 0.00 0.00 2.52
3885 4419 1.138069 TGCAAGTGACTGGACGAAGAA 59.862 47.619 0.00 0.00 0.00 2.52
3886 4420 0.750249 TGCAAGTGACTGGACGAAGA 59.250 50.000 0.00 0.00 0.00 2.87
3887 4421 1.261619 GTTGCAAGTGACTGGACGAAG 59.738 52.381 0.00 0.00 0.00 3.79
3888 4422 1.295792 GTTGCAAGTGACTGGACGAA 58.704 50.000 0.00 0.00 0.00 3.85
3889 4423 0.874175 CGTTGCAAGTGACTGGACGA 60.874 55.000 0.00 0.00 0.00 4.20
3890 4424 1.564622 CGTTGCAAGTGACTGGACG 59.435 57.895 0.00 0.00 0.00 4.79
3891 4425 1.279840 GCGTTGCAAGTGACTGGAC 59.720 57.895 0.00 0.00 0.00 4.02
3892 4426 2.243957 CGCGTTGCAAGTGACTGGA 61.244 57.895 0.00 0.00 0.00 3.86
3893 4427 2.249309 CGCGTTGCAAGTGACTGG 59.751 61.111 0.00 0.00 0.00 4.00
3894 4428 1.368019 CACGCGTTGCAAGTGACTG 60.368 57.895 10.22 0.00 38.06 3.51
3895 4429 2.534019 CCACGCGTTGCAAGTGACT 61.534 57.895 10.22 0.00 38.06 3.41
3896 4430 1.492319 TACCACGCGTTGCAAGTGAC 61.492 55.000 10.22 0.00 38.06 3.67
3897 4431 1.218875 CTACCACGCGTTGCAAGTGA 61.219 55.000 10.22 0.07 38.06 3.41
3898 4432 1.204062 CTACCACGCGTTGCAAGTG 59.796 57.895 10.22 4.71 35.79 3.16
3899 4433 2.604174 GCTACCACGCGTTGCAAGT 61.604 57.895 10.22 4.86 42.09 3.16
3900 4434 2.173382 GCTACCACGCGTTGCAAG 59.827 61.111 10.22 9.05 42.09 4.01
3903 4437 4.445545 GCTGCTACCACGCGTTGC 62.446 66.667 10.22 12.67 42.73 4.17
3904 4438 3.015293 CTGCTGCTACCACGCGTTG 62.015 63.158 10.22 9.54 0.00 4.10
3932 4466 1.541670 GGCACCGGTTTGAGTAGTTGA 60.542 52.381 2.97 0.00 0.00 3.18
4108 4674 3.698463 CGTGTTCGTTTCGGCGCT 61.698 61.111 7.64 0.00 0.00 5.92
4135 4701 2.094442 CCGGAATTAATGGCGGTTTTGT 60.094 45.455 0.00 0.00 0.00 2.83
4308 4874 3.118519 TCCTTGATACTCCTTTAACCGGC 60.119 47.826 0.00 0.00 0.00 6.13
4327 4893 1.270907 CACCCTAAGCTCACACTCCT 58.729 55.000 0.00 0.00 0.00 3.69
4330 4896 1.620819 CTCACACCCTAAGCTCACACT 59.379 52.381 0.00 0.00 0.00 3.55
4341 4907 5.131142 CCCTATACTGATTTTCTCACACCCT 59.869 44.000 0.00 0.00 0.00 4.34
4356 4922 0.759346 GGGACTGGTGCCCTATACTG 59.241 60.000 0.00 0.00 42.56 2.74
4404 4971 8.925161 TGGAACAGTTTCAAAAGACATTTTAG 57.075 30.769 0.00 0.00 36.47 1.85
4415 4982 4.462508 TGCATGTTGGAACAGTTTCAAA 57.537 36.364 8.71 0.72 43.04 2.69
4416 4983 4.341806 AGATGCATGTTGGAACAGTTTCAA 59.658 37.500 2.46 2.51 43.04 2.69
4417 4984 3.890756 AGATGCATGTTGGAACAGTTTCA 59.109 39.130 2.46 0.00 43.04 2.69
4418 4985 4.510038 AGATGCATGTTGGAACAGTTTC 57.490 40.909 2.46 0.00 43.04 2.78
4422 4989 5.758924 CATGATAGATGCATGTTGGAACAG 58.241 41.667 2.46 0.00 43.04 3.16


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

AutoCloner maintained by Alex Coulton.