Multiple sequence alignment - TraesCS7D01G424400

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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 TraesCS7D01G424400 chr7D 100.000 6063 0 0 1 6063 544988809 544994871 0.000000e+00 11197.0
1 TraesCS7D01G424400 chr7D 97.877 424 8 1 42 464 29778252 29778675 0.000000e+00 732.0
2 TraesCS7D01G424400 chr7D 96.096 333 11 1 485 817 29778770 29779100 5.350000e-150 542.0
3 TraesCS7D01G424400 chr7D 100.000 51 0 0 1 51 634235259 634235309 1.800000e-15 95.3
4 TraesCS7D01G424400 chr7D 91.489 47 3 1 1872 1917 519146438 519146484 5.070000e-06 63.9
5 TraesCS7D01G424400 chr7B 94.333 5117 183 36 822 5913 588374942 588379976 0.000000e+00 7744.0
6 TraesCS7D01G424400 chr7B 93.548 124 8 0 5925 6048 588379956 588380079 1.040000e-42 185.0
7 TraesCS7D01G424400 chr7A 94.178 1563 57 15 2881 4430 626879018 626880559 0.000000e+00 2351.0
8 TraesCS7D01G424400 chr7A 93.931 1071 37 7 813 1879 626877046 626878092 0.000000e+00 1592.0
9 TraesCS7D01G424400 chr7A 93.111 929 53 8 4462 5381 626880672 626881598 0.000000e+00 1351.0
10 TraesCS7D01G424400 chr7A 91.167 917 45 16 1946 2850 626878124 626879016 0.000000e+00 1212.0
11 TraesCS7D01G424400 chr7A 93.463 566 28 6 5355 5916 626881620 626882180 0.000000e+00 832.0
12 TraesCS7D01G424400 chr7A 93.206 471 25 4 29 496 282557630 282557164 0.000000e+00 686.0
13 TraesCS7D01G424400 chr7A 92.086 139 11 0 5925 6063 626882157 626882295 4.790000e-46 196.0
14 TraesCS7D01G424400 chr5A 89.109 808 42 9 44 815 218884703 218885500 0.000000e+00 963.0
15 TraesCS7D01G424400 chr5D 87.028 794 80 14 42 818 291521198 291520411 0.000000e+00 874.0
16 TraesCS7D01G424400 chr5D 97.130 453 12 1 42 494 374629306 374628855 0.000000e+00 763.0
17 TraesCS7D01G424400 chr5D 95.029 342 13 3 485 825 374627137 374626799 8.940000e-148 534.0
18 TraesCS7D01G424400 chr1D 95.604 455 13 2 42 496 66767011 66766564 0.000000e+00 723.0
19 TraesCS7D01G424400 chr1D 93.682 459 22 5 42 494 470209297 470208840 0.000000e+00 680.0
20 TraesCS7D01G424400 chr1D 90.909 44 2 2 1874 1917 103407865 103407906 2.360000e-04 58.4
21 TraesCS7D01G424400 chr2D 96.690 423 13 1 74 496 642827075 642826654 0.000000e+00 702.0
22 TraesCS7D01G424400 chr2D 94.298 456 14 5 42 491 155508205 155508654 0.000000e+00 688.0
23 TraesCS7D01G424400 chr2D 95.821 335 14 0 485 819 572790883 572791217 5.350000e-150 542.0
24 TraesCS7D01G424400 chr2D 88.462 52 4 1 1882 1933 326408221 326408172 1.820000e-05 62.1
25 TraesCS7D01G424400 chrUn 97.605 334 8 0 485 818 93261865 93262198 1.900000e-159 573.0
26 TraesCS7D01G424400 chrUn 97.329 337 9 0 485 821 252510850 252510514 1.900000e-159 573.0
27 TraesCS7D01G424400 chrUn 94.000 50 2 1 1872 1921 95760815 95760767 2.340000e-09 75.0
28 TraesCS7D01G424400 chr3D 96.439 337 12 0 485 821 602048214 602047878 1.910000e-154 556.0
29 TraesCS7D01G424400 chr3D 92.857 42 2 1 1874 1915 369550224 369550264 6.560000e-05 60.2
30 TraesCS7D01G424400 chr6D 96.697 333 11 0 485 817 108455410 108455742 6.870000e-154 555.0
31 TraesCS7D01G424400 chr6D 96.154 52 1 1 1 52 354544136 354544186 3.890000e-12 84.2
32 TraesCS7D01G424400 chr6D 96.078 51 1 1 1 50 10674549 10674599 1.400000e-11 82.4
33 TraesCS7D01G424400 chr6D 92.683 41 2 1 1874 1914 79868240 79868279 2.360000e-04 58.4
34 TraesCS7D01G424400 chr4D 96.078 51 1 1 1 50 81327026 81327076 1.400000e-11 82.4
35 TraesCS7D01G424400 chr6B 95.455 44 2 0 1874 1917 157912684 157912641 3.030000e-08 71.3
36 TraesCS7D01G424400 chr2B 91.489 47 4 0 1871 1917 777832390 777832436 1.410000e-06 65.8
37 TraesCS7D01G424400 chr1A 93.023 43 2 1 1874 1916 363640040 363639999 1.820000e-05 62.1
38 TraesCS7D01G424400 chr6A 92.683 41 2 1 1874 1914 96597955 96597994 2.360000e-04 58.4


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 TraesCS7D01G424400 chr7D 544988809 544994871 6062 False 11197.000000 11197 100.000000 1 6063 1 chr7D.!!$F2 6062
1 TraesCS7D01G424400 chr7D 29778252 29779100 848 False 637.000000 732 96.986500 42 817 2 chr7D.!!$F4 775
2 TraesCS7D01G424400 chr7B 588374942 588380079 5137 False 3964.500000 7744 93.940500 822 6048 2 chr7B.!!$F1 5226
3 TraesCS7D01G424400 chr7A 626877046 626882295 5249 False 1255.666667 2351 92.989333 813 6063 6 chr7A.!!$F1 5250
4 TraesCS7D01G424400 chr5A 218884703 218885500 797 False 963.000000 963 89.109000 44 815 1 chr5A.!!$F1 771
5 TraesCS7D01G424400 chr5D 291520411 291521198 787 True 874.000000 874 87.028000 42 818 1 chr5D.!!$R1 776
6 TraesCS7D01G424400 chr5D 374626799 374629306 2507 True 648.500000 763 96.079500 42 825 2 chr5D.!!$R2 783

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
561 2337 1.074775 GTCCATGGGGTGCAGTTCA 59.925 57.895 13.02 0.0 34.93 3.18 F
1435 3218 0.774908 TCGTCTGGAAACCCCCAAAT 59.225 50.000 0.00 0.0 35.47 2.32 F
2063 3868 0.455410 TCTGCAGCTGCGTTGTTTTT 59.545 45.000 32.11 0.0 45.83 1.94 F
2871 4687 4.701651 TGACAGCTCATGATTAAAACCCTG 59.298 41.667 0.00 0.0 0.00 4.45 F
3803 5622 1.512926 ACTTGCCTTGTCTGTAAGCG 58.487 50.000 0.00 0.0 0.00 4.68 F
4581 6507 0.036294 GGCTGTGTACTTGAGGGGTC 60.036 60.000 0.00 0.0 0.00 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1780 3566 0.108804 ACGTACACTCCATGCCTTCG 60.109 55.000 0.00 0.0 0.00 3.79 R
2714 4527 2.093973 CGCAGAAGAACCACTGGATAGT 60.094 50.000 0.71 0.0 37.75 2.12 R
3004 4820 2.760374 GGTGGAAGCATAAGATCTCCG 58.240 52.381 0.00 0.0 0.00 4.63 R
4455 6379 0.034896 CCTGGCTACAACTTCACGGT 59.965 55.000 0.00 0.0 0.00 4.83 R
5002 6935 0.105964 TCCAACAGACGAACCCTGTG 59.894 55.000 0.00 0.0 43.42 3.66 R
5769 7761 0.376152 CGTGTACGCCTACGATCAGT 59.624 55.000 0.00 0.0 43.93 3.41 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
17 18 3.451894 GCCCATCGCCTGGTTTGG 61.452 66.667 0.00 0.14 44.30 3.28
242 268 6.144854 ACACAAATGAAAGACACATCATTCG 58.855 36.000 1.88 0.00 43.54 3.34
408 452 2.749621 GGAGGCACATCGAAAGACATTT 59.250 45.455 0.00 0.00 46.97 2.32
480 524 3.065787 ATGGCTCCCATGGTGCTCC 62.066 63.158 21.32 12.81 43.39 4.70
526 2302 1.352083 GCTATAGGATGGGGTGAGCA 58.648 55.000 1.04 0.00 0.00 4.26
561 2337 1.074775 GTCCATGGGGTGCAGTTCA 59.925 57.895 13.02 0.00 34.93 3.18
880 2659 1.745890 CTCCACCTCACCACGAACA 59.254 57.895 0.00 0.00 0.00 3.18
1119 2899 3.952628 CTCCAAGGTTCGTCCCGCC 62.953 68.421 0.00 0.00 36.75 6.13
1120 2900 4.016706 CCAAGGTTCGTCCCGCCT 62.017 66.667 0.00 0.00 36.75 5.52
1121 2901 2.434359 CAAGGTTCGTCCCGCCTC 60.434 66.667 0.00 0.00 36.75 4.70
1122 2902 3.703127 AAGGTTCGTCCCGCCTCC 61.703 66.667 0.00 0.00 36.75 4.30
1197 2977 2.017559 GCTAACTCCGTCCATCCGCT 62.018 60.000 0.00 0.00 0.00 5.52
1269 3049 2.415010 CTCCACATCTCCCGCTCG 59.585 66.667 0.00 0.00 0.00 5.03
1371 3154 4.436998 CTTCGCGCCCTCCGAACT 62.437 66.667 0.00 0.00 39.50 3.01
1385 3168 1.543429 CCGAACTTCTCCTGGCACTTT 60.543 52.381 0.00 0.00 0.00 2.66
1435 3218 0.774908 TCGTCTGGAAACCCCCAAAT 59.225 50.000 0.00 0.00 35.47 2.32
1618 3401 3.807538 CTGCTGATGTGGTGCGGC 61.808 66.667 0.00 0.00 36.93 6.53
1767 3553 9.201989 TGTTCTGATATCCTAGTATGTTTGTCT 57.798 33.333 0.00 0.00 0.00 3.41
1772 3558 4.737855 TCCTAGTATGTTTGTCTGGCTC 57.262 45.455 0.00 0.00 0.00 4.70
1780 3566 2.610374 TGTTTGTCTGGCTCGTGTTTAC 59.390 45.455 0.00 0.00 0.00 2.01
1907 3693 2.163818 TCTATAAAGCGGGGCGAATG 57.836 50.000 0.00 0.00 0.00 2.67
1943 3734 3.319122 GGGAACTGGATTGGTATTGATGC 59.681 47.826 0.00 0.00 0.00 3.91
2063 3868 0.455410 TCTGCAGCTGCGTTGTTTTT 59.545 45.000 32.11 0.00 45.83 1.94
2088 3893 4.742438 GTGCGATTCACTGGAACTTAAA 57.258 40.909 0.00 0.00 42.38 1.52
2119 3927 5.023533 AGTTGTTCAGACTGCTCTTGTTA 57.976 39.130 0.00 0.00 0.00 2.41
2134 3943 6.034577 TGCTCTTGTTATCTTCGTTATTGTCG 59.965 38.462 0.00 0.00 0.00 4.35
2364 4175 6.113411 CGAAGATAAAGGTTTACATCCTGGT 58.887 40.000 0.00 0.00 35.27 4.00
2488 4301 9.355215 CTAACTAGGTGTCTTGTACATAACTTG 57.645 37.037 0.00 0.00 41.10 3.16
2709 4522 8.846943 TGTCAGTAATGTTGTTCTGATTATGT 57.153 30.769 0.00 0.00 38.80 2.29
2710 4523 9.936759 TGTCAGTAATGTTGTTCTGATTATGTA 57.063 29.630 0.00 0.00 38.80 2.29
2870 4686 4.922206 TGACAGCTCATGATTAAAACCCT 58.078 39.130 0.00 0.00 0.00 4.34
2871 4687 4.701651 TGACAGCTCATGATTAAAACCCTG 59.298 41.667 0.00 0.00 0.00 4.45
2877 4693 5.643379 TCATGATTAAAACCCTGTGAAGC 57.357 39.130 0.00 0.00 0.00 3.86
2957 4773 9.665719 TGTAGACAGCTCATGATTGTAATTTTA 57.334 29.630 11.66 1.11 0.00 1.52
3037 4853 4.337145 TGCTTCCACCGGTTATTGTTTAT 58.663 39.130 2.97 0.00 0.00 1.40
3246 5065 6.994496 TGAGAGACACCATTAATGATCATTCC 59.006 38.462 23.95 5.36 32.50 3.01
3297 5116 2.629617 CCCTCCAGCAGTTCAAACAAAT 59.370 45.455 0.00 0.00 0.00 2.32
3534 5353 1.915078 ATGGTCCTTTCTCTGGCGGG 61.915 60.000 0.00 0.00 0.00 6.13
3586 5405 6.070424 TCCTCGACCTCAAATAAACCAAGTAT 60.070 38.462 0.00 0.00 0.00 2.12
3744 5563 3.259374 TGGTCTCTTCTGTAGCCTCTTTG 59.741 47.826 0.00 0.00 0.00 2.77
3803 5622 1.512926 ACTTGCCTTGTCTGTAAGCG 58.487 50.000 0.00 0.00 0.00 4.68
3970 5791 8.806146 GGTAAAAGGTTGCATATCATTATGGAT 58.194 33.333 0.00 0.00 36.24 3.41
3984 5805 7.002250 TCATTATGGATCTCTTAGCTTCTGG 57.998 40.000 0.00 0.00 0.00 3.86
4140 5961 7.519008 CGGTATCTAGAATTGACCTTTTCATGC 60.519 40.741 0.00 0.00 32.84 4.06
4170 5996 4.337836 GGAATGATCCAGAAGAAAGGCTTC 59.662 45.833 0.00 0.00 45.79 3.86
4230 6056 4.261952 CCAATTGAATGTGGTGTTGTGCTA 60.262 41.667 7.12 0.00 0.00 3.49
4239 6065 1.801178 GGTGTTGTGCTACTTCTGCTC 59.199 52.381 0.00 0.00 0.00 4.26
4296 6122 3.007940 TGCCAAGTTGTGCTACAGTAGAT 59.992 43.478 12.15 0.00 0.00 1.98
4300 6126 6.316390 GCCAAGTTGTGCTACAGTAGATTAAT 59.684 38.462 12.15 0.00 0.00 1.40
4333 6159 6.500684 AACACGAATATATCATGGAATGGC 57.499 37.500 0.00 0.00 46.73 4.40
4334 6160 4.943705 ACACGAATATATCATGGAATGGCC 59.056 41.667 0.00 0.00 46.73 5.36
4362 6188 8.773033 AAACTCCTAATCATGCATAGGAAAAT 57.227 30.769 20.29 10.87 45.31 1.82
4382 6208 7.064728 GGAAAATAAGAGTGCTTACTACACCTG 59.935 40.741 0.00 0.00 39.29 4.00
4383 6209 3.320673 AAGAGTGCTTACTACACCTGC 57.679 47.619 0.00 0.00 38.87 4.85
4451 6375 8.046294 TGTATTGCGCTCCTTAAAGAAAATTA 57.954 30.769 9.73 0.00 0.00 1.40
4452 6376 8.682710 TGTATTGCGCTCCTTAAAGAAAATTAT 58.317 29.630 9.73 0.00 0.00 1.28
4453 6377 7.992180 ATTGCGCTCCTTAAAGAAAATTATG 57.008 32.000 9.73 0.00 0.00 1.90
4454 6378 6.509418 TGCGCTCCTTAAAGAAAATTATGT 57.491 33.333 9.73 0.00 0.00 2.29
4455 6379 7.618502 TGCGCTCCTTAAAGAAAATTATGTA 57.381 32.000 9.73 0.00 0.00 2.29
4456 6380 7.469260 TGCGCTCCTTAAAGAAAATTATGTAC 58.531 34.615 9.73 0.00 0.00 2.90
4457 6381 6.910972 GCGCTCCTTAAAGAAAATTATGTACC 59.089 38.462 0.00 0.00 0.00 3.34
4458 6382 7.123830 CGCTCCTTAAAGAAAATTATGTACCG 58.876 38.462 0.00 0.00 0.00 4.02
4459 6383 7.201582 CGCTCCTTAAAGAAAATTATGTACCGT 60.202 37.037 0.00 0.00 0.00 4.83
4460 6384 7.908601 GCTCCTTAAAGAAAATTATGTACCGTG 59.091 37.037 0.00 0.00 0.00 4.94
4461 6385 9.158233 CTCCTTAAAGAAAATTATGTACCGTGA 57.842 33.333 0.00 0.00 0.00 4.35
4462 6386 9.504708 TCCTTAAAGAAAATTATGTACCGTGAA 57.495 29.630 0.00 0.00 0.00 3.18
4463 6387 9.769093 CCTTAAAGAAAATTATGTACCGTGAAG 57.231 33.333 0.00 0.00 0.00 3.02
4477 6401 2.218603 CGTGAAGTTGTAGCCAGGTTT 58.781 47.619 0.00 0.00 0.00 3.27
4478 6402 2.032030 CGTGAAGTTGTAGCCAGGTTTG 60.032 50.000 0.00 0.00 0.00 2.93
4479 6403 3.211045 GTGAAGTTGTAGCCAGGTTTGA 58.789 45.455 0.00 0.00 0.00 2.69
4482 6406 4.202461 TGAAGTTGTAGCCAGGTTTGAGAT 60.202 41.667 0.00 0.00 0.00 2.75
4500 6426 2.573462 AGATGCACAATGGGTCTACTGT 59.427 45.455 0.00 0.00 0.00 3.55
4515 6441 4.333926 GTCTACTGTTTGCATGATCCCTTC 59.666 45.833 0.00 0.00 0.00 3.46
4522 6448 3.003394 TGCATGATCCCTTCGTTTGAT 57.997 42.857 0.00 0.00 0.00 2.57
4529 6455 3.980646 TCCCTTCGTTTGATGTGTTTG 57.019 42.857 0.00 0.00 0.00 2.93
4530 6456 2.034053 TCCCTTCGTTTGATGTGTTTGC 59.966 45.455 0.00 0.00 0.00 3.68
4533 6459 4.320861 CCCTTCGTTTGATGTGTTTGCATA 60.321 41.667 0.00 0.00 0.00 3.14
4577 6503 2.555199 GCTATGGCTGTGTACTTGAGG 58.445 52.381 0.00 0.00 35.22 3.86
4581 6507 0.036294 GGCTGTGTACTTGAGGGGTC 60.036 60.000 0.00 0.00 0.00 4.46
4586 6512 3.576982 CTGTGTACTTGAGGGGTCTTGTA 59.423 47.826 0.00 0.00 0.00 2.41
4593 6519 4.165372 ACTTGAGGGGTCTTGTAGTTTGAA 59.835 41.667 0.00 0.00 0.00 2.69
4618 6548 5.688807 CATTCTGACACTTAATGGATCCCT 58.311 41.667 9.90 0.00 0.00 4.20
4620 6550 3.118261 TCTGACACTTAATGGATCCCTGC 60.118 47.826 9.90 0.00 0.00 4.85
4621 6551 2.575735 TGACACTTAATGGATCCCTGCA 59.424 45.455 9.90 0.00 0.00 4.41
4627 6557 5.471456 CACTTAATGGATCCCTGCATAACTC 59.529 44.000 9.90 0.00 31.37 3.01
4629 6559 4.363991 AATGGATCCCTGCATAACTCTC 57.636 45.455 9.90 0.00 31.37 3.20
4630 6560 3.051940 TGGATCCCTGCATAACTCTCT 57.948 47.619 9.90 0.00 0.00 3.10
4641 6571 5.683681 TGCATAACTCTCTATGGCAATGAA 58.316 37.500 0.00 0.00 31.10 2.57
4745 6675 9.825109 GCTCTTTTCTAATAATAGACCTGAAGT 57.175 33.333 0.00 0.00 37.88 3.01
4890 6820 0.954452 AAGAACTGGAGCGCCAAAAG 59.046 50.000 11.38 1.10 45.41 2.27
4917 6847 9.088512 CAAACATCATGTACTACCTCTAACTTC 57.911 37.037 0.00 0.00 0.00 3.01
4961 6894 5.696822 CATGATCTGAGTTTGACCTGTTTG 58.303 41.667 0.00 0.00 0.00 2.93
5002 6935 2.924290 GGTCATCAACTTACTCGCTGAC 59.076 50.000 0.00 0.00 0.00 3.51
5196 7132 2.957402 TGGCTCAGTCTTCCATTTGT 57.043 45.000 0.00 0.00 0.00 2.83
5200 7136 4.072131 GGCTCAGTCTTCCATTTGTACAA 58.928 43.478 3.59 3.59 0.00 2.41
5206 7142 4.631813 AGTCTTCCATTTGTACAATCGAGC 59.368 41.667 9.56 1.17 0.00 5.03
5303 7239 4.268359 TGCAATATGGTCATGCTTGTGTA 58.732 39.130 0.00 0.00 40.66 2.90
5312 7248 2.223144 TCATGCTTGTGTACTTGCGTTC 59.777 45.455 0.00 0.00 0.00 3.95
5317 7253 3.844943 GCTTGTGTACTTGCGTTCTGTTC 60.845 47.826 0.00 0.00 0.00 3.18
5381 7367 8.380742 TGATCTATCCTTCTGTTTACCTCTTT 57.619 34.615 0.00 0.00 0.00 2.52
5497 7487 7.168219 TGAACTTGCTCCTCAAATGTACTATT 58.832 34.615 0.00 0.00 33.65 1.73
5660 7650 8.040727 TGCATTGTCTTCTAGTTTAGCTTATCA 58.959 33.333 0.00 0.00 0.00 2.15
5820 7812 7.029563 CCAAAAGCTAGTGTGTCAATAATTCC 58.970 38.462 0.00 0.00 0.00 3.01
5844 7836 6.555360 CCTAATCCTCCTATCCAACTAACACT 59.445 42.308 0.00 0.00 0.00 3.55
5891 7883 4.157289 GTCTGAACCCTCTACGTGTTATCA 59.843 45.833 0.00 0.00 0.00 2.15
5938 7930 8.918202 TTTTGTTTGAGTAATCCATCTGTAGT 57.082 30.769 0.00 0.00 0.00 2.73
5972 7964 8.410673 TCTGGAGGTCACATATAATAGTTCTC 57.589 38.462 0.00 0.00 0.00 2.87
5976 7968 8.037758 GGAGGTCACATATAATAGTTCTCCATG 58.962 40.741 0.00 0.00 37.56 3.66
5991 7983 6.545298 AGTTCTCCATGGATTGAATTTAGAGC 59.455 38.462 16.63 7.69 0.00 4.09
5994 7986 6.489022 TCTCCATGGATTGAATTTAGAGCATG 59.511 38.462 16.63 0.00 0.00 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
242 268 1.064357 GAAGATGAGGACGAGGACGAC 59.936 57.143 0.00 0.00 42.66 4.34
743 2519 1.373246 TTTAGCACGCGCGTAACCT 60.373 52.632 37.24 30.15 45.49 3.50
748 2524 3.411351 CCAGTTTAGCACGCGCGT 61.411 61.111 32.73 32.73 45.49 6.01
755 2531 3.504134 TCGCAAATTTAGCCAGTTTAGCA 59.496 39.130 0.00 0.00 0.00 3.49
956 2736 2.196229 TGGGTTGGTTCCGGTTGG 59.804 61.111 0.00 0.00 0.00 3.77
957 2737 2.548295 CGTGGGTTGGTTCCGGTTG 61.548 63.158 0.00 0.00 0.00 3.77
958 2738 2.203238 CGTGGGTTGGTTCCGGTT 60.203 61.111 0.00 0.00 0.00 4.44
959 2739 4.941309 GCGTGGGTTGGTTCCGGT 62.941 66.667 0.00 0.00 0.00 5.28
962 2742 4.629523 TCGGCGTGGGTTGGTTCC 62.630 66.667 6.85 0.00 0.00 3.62
963 2743 3.351416 GTCGGCGTGGGTTGGTTC 61.351 66.667 6.85 0.00 0.00 3.62
1366 3149 1.884235 AAAGTGCCAGGAGAAGTTCG 58.116 50.000 0.00 0.00 0.00 3.95
1371 3154 4.410228 AGCAGATATAAAGTGCCAGGAGAA 59.590 41.667 0.00 0.00 37.98 2.87
1435 3218 3.109547 CTAACCTGCGCGCACGAA 61.110 61.111 33.09 17.98 43.93 3.85
1570 3353 9.387123 GAATCTAGTTGAAAGTTGAAACATGAC 57.613 33.333 0.00 0.00 0.00 3.06
1767 3553 0.947180 GCCTTCGTAAACACGAGCCA 60.947 55.000 0.00 0.00 43.33 4.75
1772 3558 1.393539 CTCCATGCCTTCGTAAACACG 59.606 52.381 0.00 0.00 0.00 4.49
1780 3566 0.108804 ACGTACACTCCATGCCTTCG 60.109 55.000 0.00 0.00 0.00 3.79
1907 3693 0.591659 GTTCCCTTCACGAAACAGGC 59.408 55.000 0.00 0.00 0.00 4.85
1911 3697 2.249844 TCCAGTTCCCTTCACGAAAC 57.750 50.000 0.00 0.00 0.00 2.78
1943 3734 6.461698 GCTTTGTTCGTACAACAAATAGATCG 59.538 38.462 23.94 16.89 45.56 3.69
2088 3893 4.130118 CAGTCTGAACAACTAGGCAAACT 58.870 43.478 0.00 0.00 0.00 2.66
2119 3927 3.446161 TGGAGGTCGACAATAACGAAGAT 59.554 43.478 18.91 0.00 41.31 2.40
2134 3943 2.375146 ACAAAACTTGGTGTGGAGGTC 58.625 47.619 0.00 0.00 34.12 3.85
2364 4175 8.717821 GTGCACTAATACATAGACAAGTGAAAA 58.282 33.333 10.32 0.00 37.18 2.29
2435 4248 9.561069 AACAAACTGACACAGAGATAACTATTT 57.439 29.630 5.76 0.00 35.18 1.40
2488 4301 8.514594 TGATACTTTCAAACAAAGTCATCCATC 58.485 33.333 3.04 2.52 40.58 3.51
2714 4527 2.093973 CGCAGAAGAACCACTGGATAGT 60.094 50.000 0.71 0.00 37.75 2.12
2715 4528 2.093973 ACGCAGAAGAACCACTGGATAG 60.094 50.000 0.71 0.00 35.05 2.08
2870 4686 5.880332 GGAAATATAGGACAGTTGCTTCACA 59.120 40.000 0.00 0.00 0.00 3.58
2871 4687 5.880332 TGGAAATATAGGACAGTTGCTTCAC 59.120 40.000 0.00 0.00 0.00 3.18
2877 4693 6.884295 TGGAAAGTGGAAATATAGGACAGTTG 59.116 38.462 0.00 0.00 0.00 3.16
3004 4820 2.760374 GGTGGAAGCATAAGATCTCCG 58.240 52.381 0.00 0.00 0.00 4.63
3141 4960 4.455533 GTCTGAGTATTTTCCATGTGCACA 59.544 41.667 24.08 24.08 0.00 4.57
3246 5065 5.876460 CCCTTGCATCTTTAAAATGGAAAGG 59.124 40.000 12.91 12.91 34.61 3.11
3297 5116 6.707608 CAGAATAAGGCACATGAGTATAAGCA 59.292 38.462 0.00 0.00 0.00 3.91
3370 5189 3.496309 CTGCAGGTGGGAGTTGCCA 62.496 63.158 5.57 0.00 38.95 4.92
3534 5353 7.767500 AAGCTGAACTTGATGGTCTCTCACC 62.768 48.000 0.00 0.00 40.85 4.02
3683 5502 5.010617 TCAAGTATATAATCGGCAGCTCACA 59.989 40.000 0.00 0.00 0.00 3.58
3744 5563 7.040961 TGGTACATAAAACAGAAGGCACTAAAC 60.041 37.037 0.00 0.00 38.49 2.01
3829 5650 3.575630 CTGAGTAAGCTGCAAACTACGA 58.424 45.455 1.02 0.00 0.00 3.43
3970 5791 3.192844 CCGTTACACCAGAAGCTAAGAGA 59.807 47.826 0.00 0.00 0.00 3.10
3984 5805 4.751600 ACCTAACTAAGCAAACCGTTACAC 59.248 41.667 0.00 0.00 0.00 2.90
4107 5928 5.715753 GGTCAATTCTAGATACCGGACCTAT 59.284 44.000 9.46 0.00 40.23 2.57
4114 5935 7.519008 GCATGAAAAGGTCAATTCTAGATACCG 60.519 40.741 0.00 0.00 40.50 4.02
4118 5939 8.897752 GTTAGCATGAAAAGGTCAATTCTAGAT 58.102 33.333 0.00 0.00 40.50 1.98
4193 6019 3.164268 TCAATTGGACCCATTGGACTTG 58.836 45.455 16.21 0.00 34.81 3.16
4230 6056 5.602628 AGTTTTCTTTACTCGAGCAGAAGT 58.397 37.500 13.61 4.33 0.00 3.01
4239 6065 7.072030 CAGACCAATCAAGTTTTCTTTACTCG 58.928 38.462 0.00 0.00 38.17 4.18
4315 6141 7.836183 AGTTTAGGGCCATTCCATGATATATTC 59.164 37.037 6.18 0.00 36.21 1.75
4333 6159 6.013379 TCCTATGCATGATTAGGAGTTTAGGG 60.013 42.308 10.16 0.00 39.22 3.53
4334 6160 7.009179 TCCTATGCATGATTAGGAGTTTAGG 57.991 40.000 10.16 3.08 39.22 2.69
4362 6188 4.087182 AGCAGGTGTAGTAAGCACTCTTA 58.913 43.478 0.00 0.00 36.14 2.10
4416 6244 3.669122 GGAGCGCAATACATAGTAACGAG 59.331 47.826 11.47 0.00 0.00 4.18
4418 6246 3.639538 AGGAGCGCAATACATAGTAACG 58.360 45.455 11.47 0.00 0.00 3.18
4419 6247 7.437267 TCTTTAAGGAGCGCAATACATAGTAAC 59.563 37.037 11.47 0.00 0.00 2.50
4451 6375 2.300723 TGGCTACAACTTCACGGTACAT 59.699 45.455 0.00 0.00 0.00 2.29
4452 6376 1.687660 TGGCTACAACTTCACGGTACA 59.312 47.619 0.00 0.00 0.00 2.90
4453 6377 2.334838 CTGGCTACAACTTCACGGTAC 58.665 52.381 0.00 0.00 0.00 3.34
4454 6378 1.274167 CCTGGCTACAACTTCACGGTA 59.726 52.381 0.00 0.00 0.00 4.02
4455 6379 0.034896 CCTGGCTACAACTTCACGGT 59.965 55.000 0.00 0.00 0.00 4.83
4456 6380 0.034896 ACCTGGCTACAACTTCACGG 59.965 55.000 0.00 0.00 0.00 4.94
4457 6381 1.878953 AACCTGGCTACAACTTCACG 58.121 50.000 0.00 0.00 0.00 4.35
4458 6382 3.211045 TCAAACCTGGCTACAACTTCAC 58.789 45.455 0.00 0.00 0.00 3.18
4459 6383 3.135712 TCTCAAACCTGGCTACAACTTCA 59.864 43.478 0.00 0.00 0.00 3.02
4460 6384 3.740115 TCTCAAACCTGGCTACAACTTC 58.260 45.455 0.00 0.00 0.00 3.01
4461 6385 3.857157 TCTCAAACCTGGCTACAACTT 57.143 42.857 0.00 0.00 0.00 2.66
4462 6386 3.679389 CATCTCAAACCTGGCTACAACT 58.321 45.455 0.00 0.00 0.00 3.16
4463 6387 2.162408 GCATCTCAAACCTGGCTACAAC 59.838 50.000 0.00 0.00 0.00 3.32
4464 6388 2.224744 TGCATCTCAAACCTGGCTACAA 60.225 45.455 0.00 0.00 0.00 2.41
4465 6389 1.350684 TGCATCTCAAACCTGGCTACA 59.649 47.619 0.00 0.00 0.00 2.74
4477 6401 2.840038 AGTAGACCCATTGTGCATCTCA 59.160 45.455 0.00 0.00 0.00 3.27
4478 6402 3.201290 CAGTAGACCCATTGTGCATCTC 58.799 50.000 0.00 0.00 0.00 2.75
4479 6403 2.573462 ACAGTAGACCCATTGTGCATCT 59.427 45.455 0.00 0.00 0.00 2.90
4482 6406 2.884012 CAAACAGTAGACCCATTGTGCA 59.116 45.455 0.00 0.00 0.00 4.57
4500 6426 3.153130 TCAAACGAAGGGATCATGCAAA 58.847 40.909 0.00 0.00 0.00 3.68
4529 6455 9.384682 CAACCTTTCAATTGAATTGTTTTATGC 57.615 29.630 21.10 0.00 41.02 3.14
4533 6459 7.553760 AGCTCAACCTTTCAATTGAATTGTTTT 59.446 29.630 21.10 8.12 41.02 2.43
4537 6463 7.277098 CCATAGCTCAACCTTTCAATTGAATTG 59.723 37.037 21.10 20.42 41.57 2.32
4567 6493 3.853207 ACTACAAGACCCCTCAAGTACA 58.147 45.455 0.00 0.00 0.00 2.90
4568 6494 4.886496 AACTACAAGACCCCTCAAGTAC 57.114 45.455 0.00 0.00 0.00 2.73
4574 6500 3.075148 GCTTCAAACTACAAGACCCCTC 58.925 50.000 0.00 0.00 0.00 4.30
4577 6503 4.762251 AGAATGCTTCAAACTACAAGACCC 59.238 41.667 0.00 0.00 0.00 4.46
4581 6507 6.017605 AGTGTCAGAATGCTTCAAACTACAAG 60.018 38.462 0.00 0.00 34.76 3.16
4586 6512 6.942532 TTAAGTGTCAGAATGCTTCAAACT 57.057 33.333 0.00 0.00 34.76 2.66
4593 6519 5.128919 GGATCCATTAAGTGTCAGAATGCT 58.871 41.667 6.95 0.00 34.76 3.79
4618 6548 5.294734 TCATTGCCATAGAGAGTTATGCA 57.705 39.130 0.00 0.00 31.15 3.96
4620 6550 7.446319 TGGAATTCATTGCCATAGAGAGTTATG 59.554 37.037 7.93 0.00 0.00 1.90
4621 6551 7.446625 GTGGAATTCATTGCCATAGAGAGTTAT 59.553 37.037 7.93 0.00 33.66 1.89
4627 6557 6.543465 TGTAAGTGGAATTCATTGCCATAGAG 59.457 38.462 7.93 0.00 33.66 2.43
4629 6559 6.095300 TGTGTAAGTGGAATTCATTGCCATAG 59.905 38.462 7.93 0.00 33.66 2.23
4630 6560 5.948758 TGTGTAAGTGGAATTCATTGCCATA 59.051 36.000 7.93 0.00 33.66 2.74
4641 6571 3.156293 TGCTGCAATGTGTAAGTGGAAT 58.844 40.909 0.00 0.00 0.00 3.01
4745 6675 0.746063 CAGCCTGGTTGTTGAAGCAA 59.254 50.000 1.90 0.00 39.06 3.91
4890 6820 7.042335 AGTTAGAGGTAGTACATGATGTTTGC 58.958 38.462 2.29 0.00 0.00 3.68
5002 6935 0.105964 TCCAACAGACGAACCCTGTG 59.894 55.000 0.00 0.00 43.42 3.66
5141 7077 2.232239 CAACAGTGCACTTACATCGC 57.768 50.000 18.94 0.00 0.00 4.58
5196 7132 3.028130 TGGTATCACCTGCTCGATTGTA 58.972 45.455 0.00 0.00 39.58 2.41
5200 7136 1.781786 ACTGGTATCACCTGCTCGAT 58.218 50.000 2.47 0.00 40.43 3.59
5290 7226 2.232239 CGCAAGTACACAAGCATGAC 57.768 50.000 0.00 0.00 0.00 3.06
5312 7248 5.479716 AGAAAAGTGTTGTAACGGAACAG 57.520 39.130 0.00 0.00 34.02 3.16
5317 7253 7.430211 GGAAAAACTAGAAAAGTGTTGTAACGG 59.570 37.037 0.00 0.00 35.70 4.44
5381 7367 5.533528 GGGGAACAGCAGAGTTAAAACTTAA 59.466 40.000 0.00 0.00 39.88 1.85
5383 7369 3.889538 GGGGAACAGCAGAGTTAAAACTT 59.110 43.478 0.00 0.00 39.88 2.66
5384 7370 3.487372 GGGGAACAGCAGAGTTAAAACT 58.513 45.455 0.00 0.00 43.16 2.66
5385 7371 2.557056 GGGGGAACAGCAGAGTTAAAAC 59.443 50.000 0.00 0.00 0.00 2.43
5438 7425 3.768757 CCAGGCAAAAGTTTATGGGATCA 59.231 43.478 0.00 0.00 0.00 2.92
5497 7487 3.436704 GCAATGAATCGGACAAGACAGAA 59.563 43.478 0.00 0.00 0.00 3.02
5660 7650 7.669089 TTTTGGGAAGACAACCTAAAAGAAT 57.331 32.000 0.00 0.00 40.84 2.40
5673 7664 6.128145 GCAGATAAGACTTCTTTTGGGAAGAC 60.128 42.308 10.60 5.19 43.70 3.01
5769 7761 0.376152 CGTGTACGCCTACGATCAGT 59.624 55.000 0.00 0.00 43.93 3.41
5820 7812 7.604657 AGTGTTAGTTGGATAGGAGGATTAG 57.395 40.000 0.00 0.00 0.00 1.73
5913 7905 8.918202 ACTACAGATGGATTACTCAAACAAAA 57.082 30.769 0.00 0.00 0.00 2.44
5920 7912 9.642343 ACAAGTATACTACAGATGGATTACTCA 57.358 33.333 5.65 0.00 0.00 3.41
5925 7917 8.424918 CCAGAACAAGTATACTACAGATGGATT 58.575 37.037 16.00 0.74 0.00 3.01
5926 7918 7.785028 TCCAGAACAAGTATACTACAGATGGAT 59.215 37.037 18.21 4.30 0.00 3.41
5927 7919 7.123383 TCCAGAACAAGTATACTACAGATGGA 58.877 38.462 18.21 18.21 0.00 3.41
5928 7920 7.348080 TCCAGAACAAGTATACTACAGATGG 57.652 40.000 5.65 11.94 0.00 3.51
5929 7921 7.068839 ACCTCCAGAACAAGTATACTACAGATG 59.931 40.741 5.65 2.85 0.00 2.90
5930 7922 7.126733 ACCTCCAGAACAAGTATACTACAGAT 58.873 38.462 5.65 0.00 0.00 2.90
5931 7923 6.491383 ACCTCCAGAACAAGTATACTACAGA 58.509 40.000 5.65 0.00 0.00 3.41
5932 7924 6.377429 TGACCTCCAGAACAAGTATACTACAG 59.623 42.308 5.65 2.24 0.00 2.74
5933 7925 6.152323 GTGACCTCCAGAACAAGTATACTACA 59.848 42.308 5.65 0.00 0.00 2.74
5934 7926 6.152323 TGTGACCTCCAGAACAAGTATACTAC 59.848 42.308 5.65 0.00 0.00 2.73
5935 7927 6.250711 TGTGACCTCCAGAACAAGTATACTA 58.749 40.000 5.65 0.00 0.00 1.82
5936 7928 5.084519 TGTGACCTCCAGAACAAGTATACT 58.915 41.667 0.00 0.00 0.00 2.12
5937 7929 5.401531 TGTGACCTCCAGAACAAGTATAC 57.598 43.478 0.00 0.00 0.00 1.47
5938 7930 7.914427 ATATGTGACCTCCAGAACAAGTATA 57.086 36.000 0.00 0.00 0.00 1.47
5939 7931 6.814954 ATATGTGACCTCCAGAACAAGTAT 57.185 37.500 0.00 0.00 0.00 2.12
5940 7932 7.727578 TTATATGTGACCTCCAGAACAAGTA 57.272 36.000 0.00 0.00 0.00 2.24
5941 7933 6.620877 TTATATGTGACCTCCAGAACAAGT 57.379 37.500 0.00 0.00 0.00 3.16
5942 7934 8.424918 ACTATTATATGTGACCTCCAGAACAAG 58.575 37.037 0.00 0.00 0.00 3.16
5943 7935 8.319057 ACTATTATATGTGACCTCCAGAACAA 57.681 34.615 0.00 0.00 0.00 2.83
5944 7936 7.914427 ACTATTATATGTGACCTCCAGAACA 57.086 36.000 0.00 0.00 0.00 3.18
5972 7964 5.537295 TCCATGCTCTAAATTCAATCCATGG 59.463 40.000 4.97 4.97 46.02 3.66
5976 7968 5.771666 TCCATCCATGCTCTAAATTCAATCC 59.228 40.000 0.00 0.00 0.00 3.01
5985 7977 4.019411 TGACTTGTTCCATCCATGCTCTAA 60.019 41.667 0.00 0.00 0.00 2.10
5991 7983 4.178540 GCAATTGACTTGTTCCATCCATG 58.821 43.478 10.34 0.00 37.18 3.66
5994 7986 2.827921 AGGCAATTGACTTGTTCCATCC 59.172 45.455 8.40 0.00 37.18 3.51


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

AutoCloner maintained by Alex Coulton.