Multiple sequence alignment - TraesCS3A01G378300

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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 TraesCS3A01G378300 chr3A 100.000 3849 0 0 1 3849 627862341 627866189 0.000000e+00 7108
1 TraesCS3A01G378300 chr3B 91.290 3766 182 68 1 3699 647678180 647681866 0.000000e+00 5003
2 TraesCS3A01G378300 chr3D 90.286 3953 188 79 1 3836 484820441 484824314 0.000000e+00 4992
3 TraesCS3A01G378300 chr1D 77.756 1016 168 34 1873 2849 367430174 367429178 4.310000e-159 571
4 TraesCS3A01G378300 chr1D 84.167 120 15 4 1476 1591 367430499 367430380 3.140000e-21 113
5 TraesCS3A01G378300 chr1B 77.308 1018 167 39 1873 2849 491983661 491982667 3.380000e-150 542
6 TraesCS3A01G378300 chr1B 87.069 116 12 3 1476 1588 491983963 491983848 1.120000e-25 128
7 TraesCS3A01G378300 chr1A 78.709 573 99 17 1854 2413 466928381 466927819 1.020000e-95 361
8 TraesCS3A01G378300 chr1A 82.029 345 32 12 2535 2849 466927706 466927362 2.280000e-67 267
9 TraesCS3A01G378300 chr1A 85.841 113 15 1 1476 1587 466928725 466928613 6.760000e-23 119
10 TraesCS3A01G378300 chr7D 86.667 135 17 1 2525 2659 412885774 412885641 8.620000e-32 148
11 TraesCS3A01G378300 chr7B 86.667 135 17 1 2525 2659 427302955 427302822 8.620000e-32 148
12 TraesCS3A01G378300 chr7A 87.302 126 16 0 2534 2659 474296329 474296204 1.110000e-30 145
13 TraesCS3A01G378300 chr2D 85.714 126 18 0 2534 2659 644095596 644095721 2.410000e-27 134


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 TraesCS3A01G378300 chr3A 627862341 627866189 3848 False 7108 7108 100.0000 1 3849 1 chr3A.!!$F1 3848
1 TraesCS3A01G378300 chr3B 647678180 647681866 3686 False 5003 5003 91.2900 1 3699 1 chr3B.!!$F1 3698
2 TraesCS3A01G378300 chr3D 484820441 484824314 3873 False 4992 4992 90.2860 1 3836 1 chr3D.!!$F1 3835
3 TraesCS3A01G378300 chr1D 367429178 367430499 1321 True 342 571 80.9615 1476 2849 2 chr1D.!!$R1 1373
4 TraesCS3A01G378300 chr1B 491982667 491983963 1296 True 335 542 82.1885 1476 2849 2 chr1B.!!$R1 1373
5 TraesCS3A01G378300 chr1A 466927362 466928725 1363 True 249 361 82.1930 1476 2849 3 chr1A.!!$R1 1373

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
825 874 0.036858 GTTCTCACAGGGACAGCTCC 60.037 60.000 0.0 0.0 35.50 4.70 F
829 878 0.409876 TCACAGGGACAGCTCCTAGT 59.590 55.000 0.0 0.0 36.68 2.57 F
1974 2223 1.003580 TCTGCCAACACCTCAAGATCC 59.996 52.381 0.0 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2716 3060 0.534412 ACTGCAGGATCACCTTCTCG 59.466 55.000 19.93 0.00 45.36 4.04 R
2725 3069 1.272147 ACCTTCCCAAACTGCAGGATC 60.272 52.381 19.93 0.00 0.00 3.36 R
3615 4015 0.179181 CGTGCATGCCACTGATTGAC 60.179 55.000 16.68 1.82 42.42 3.18 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
20 21 0.387565 CTGGTTTCCGTGGGTTTTGG 59.612 55.000 0.00 0.00 0.00 3.28
45 57 2.583593 TGTTTTTGCGCGGGTTGC 60.584 55.556 8.83 0.00 41.47 4.17
58 70 1.885850 GGTTGCGTTCCGTGAGTGT 60.886 57.895 0.00 0.00 0.00 3.55
124 136 3.672361 GATCGGTAGATCGTACGCC 57.328 57.895 11.24 4.48 43.17 5.68
134 154 0.820891 ATCGTACGCCCCGTAGATGT 60.821 55.000 11.24 0.00 43.06 3.06
144 164 1.076533 CCGTAGATGTGCGCGTTCTT 61.077 55.000 8.43 0.00 0.00 2.52
281 301 8.426881 TTTTCAAAACTGGGCTTGTTTATTAC 57.573 30.769 8.32 0.00 36.72 1.89
287 309 8.507524 AAACTGGGCTTGTTTATTACTATCTC 57.492 34.615 6.61 0.00 36.07 2.75
290 312 6.827727 TGGGCTTGTTTATTACTATCTCTCC 58.172 40.000 0.00 0.00 0.00 3.71
306 328 6.832520 ATCTCTCCACAGTATAGTATGCTG 57.167 41.667 22.35 22.35 46.66 4.41
340 362 9.178427 CGTACATCCTAGTATTAAACTTGCTAC 57.822 37.037 0.00 0.00 39.80 3.58
363 399 9.258826 CTACTAGATTAGTACTAGCGTGAAGAA 57.741 37.037 2.23 0.00 40.40 2.52
404 440 0.746063 TTTGGTTCTGCAAGGCACAG 59.254 50.000 0.00 0.00 33.79 3.66
461 497 2.165437 GCGGCAACTAATTGGGATTTGA 59.835 45.455 0.00 0.00 36.23 2.69
509 558 0.978907 TTCCACGGGAAGTTACCTCC 59.021 55.000 1.73 0.00 36.71 4.30
516 565 1.003233 GGGAAGTTACCTCCCACACAG 59.997 57.143 13.86 0.00 43.06 3.66
644 693 8.689061 AGTGACGTCTGGTTTATATGTATGTAA 58.311 33.333 17.92 0.00 0.00 2.41
681 730 0.109179 GCGCCATGAGCAATTTGTGA 60.109 50.000 0.00 0.00 44.04 3.58
690 739 1.615392 AGCAATTTGTGAGTTCAGGGC 59.385 47.619 0.00 0.00 0.00 5.19
704 753 3.814504 TCAGGGCTTCCTCTTTGATTT 57.185 42.857 0.00 0.00 39.29 2.17
736 785 4.730657 CCTACCTAGTTGTTACACAGTCG 58.269 47.826 0.00 0.00 0.00 4.18
773 822 4.943705 TCAATCAAATCCCTCAGTGTTAGC 59.056 41.667 0.00 0.00 0.00 3.09
798 847 0.961019 TGCCTTGTTTGCTCATGGAC 59.039 50.000 11.08 0.00 35.49 4.02
825 874 0.036858 GTTCTCACAGGGACAGCTCC 60.037 60.000 0.00 0.00 35.50 4.70
829 878 0.409876 TCACAGGGACAGCTCCTAGT 59.590 55.000 0.00 0.00 36.68 2.57
900 949 3.922240 TGCGGTAATCTACTTGTTCGTTC 59.078 43.478 0.00 0.00 0.00 3.95
905 962 6.033619 CGGTAATCTACTTGTTCGTTCTTCTG 59.966 42.308 0.00 0.00 0.00 3.02
945 1002 7.428282 AAAAGTTTGTTGGTAACCTTGTTTG 57.572 32.000 0.00 0.00 0.00 2.93
993 1050 2.818432 CCTTATCATCTGGCATTGGCTC 59.182 50.000 11.84 0.00 40.87 4.70
1056 1113 1.347320 GTTTCGGTAGCTTGTCGAGG 58.653 55.000 0.00 0.00 34.33 4.63
1146 1203 3.526931 TCATTGGATGACTTCCTCGAC 57.473 47.619 8.71 0.00 45.68 4.20
1446 1504 3.547054 AAAACCGTGAGTAGTGGACAA 57.453 42.857 0.00 0.00 0.00 3.18
1481 1539 5.912955 GCTTCATACGCTACAACTTTTGTTT 59.087 36.000 0.00 0.00 42.22 2.83
1603 1661 3.515562 TGTTATGCTTCCCCCATTTGTT 58.484 40.909 0.00 0.00 0.00 2.83
1625 1683 3.937079 TCTAGCAATGCTCATCAGTTGTG 59.063 43.478 12.53 0.00 40.44 3.33
1692 1761 3.068560 CCGAGGATGAAAACGTAACCAA 58.931 45.455 0.00 0.00 0.00 3.67
1693 1762 3.499157 CCGAGGATGAAAACGTAACCAAA 59.501 43.478 0.00 0.00 0.00 3.28
1735 1804 7.319646 TGTTTGAGTGCTTAAATTGACTGTTT 58.680 30.769 0.00 0.00 0.00 2.83
1749 1818 3.003275 TGACTGTTTTGCCTCGTTTCATC 59.997 43.478 0.00 0.00 0.00 2.92
1798 1868 8.519526 GTGACATGGGAAATGTTTTTCTGTATA 58.480 33.333 0.00 0.00 40.91 1.47
1799 1869 8.739039 TGACATGGGAAATGTTTTTCTGTATAG 58.261 33.333 0.00 0.00 40.91 1.31
1845 1915 7.451731 TCTCCTCCCACTTAATCAAATATGT 57.548 36.000 0.00 0.00 0.00 2.29
1887 2136 1.265905 GTTGTTACTGCGGAAACTGGG 59.734 52.381 0.00 0.00 0.00 4.45
1897 2146 1.610886 CGGAAACTGGGAAGTTCCTCC 60.611 57.143 21.25 17.46 36.57 4.30
1974 2223 1.003580 TCTGCCAACACCTCAAGATCC 59.996 52.381 0.00 0.00 0.00 3.36
2008 2257 6.759497 ACATTGGAAAGCTGAGGTAATTAC 57.241 37.500 7.09 7.09 0.00 1.89
2056 2346 1.962807 TGACATTCTGCTTGTTTGGGG 59.037 47.619 0.00 0.00 0.00 4.96
2407 2697 1.416813 GCAGCATCACGTCCTTCTCG 61.417 60.000 0.00 0.00 0.00 4.04
2725 3069 2.663196 GTGGACCCCGAGAAGGTG 59.337 66.667 0.00 0.00 37.88 4.00
2749 3093 1.896660 GCAGTTTGGGAAGGTCGCA 60.897 57.895 0.00 0.00 37.56 5.10
2862 3206 6.511416 CCTGTGAATAATTTGTGACACCAAA 58.489 36.000 2.45 4.59 38.58 3.28
2974 3325 0.810823 TCGCCGTCGTGTTTTTCCTT 60.811 50.000 0.00 0.00 36.96 3.36
3053 3404 0.685458 ATGTGATTCTTGGCCTGCCC 60.685 55.000 3.32 0.00 34.56 5.36
3054 3405 2.054453 GTGATTCTTGGCCTGCCCC 61.054 63.158 3.32 0.00 34.56 5.80
3055 3406 2.830370 GATTCTTGGCCTGCCCCG 60.830 66.667 3.32 0.00 34.56 5.73
3070 3429 2.642254 CCCGCCCTCTCGTACAACA 61.642 63.158 0.00 0.00 0.00 3.33
3080 3439 2.874751 GTACAACATGCACCCGGC 59.125 61.111 0.00 0.00 45.13 6.13
3098 3457 4.415150 CCACGCAGGCATCACCCT 62.415 66.667 0.00 0.00 40.58 4.34
3103 3462 2.273449 CAGGCATCACCCTCACCC 59.727 66.667 0.00 0.00 40.58 4.61
3111 3470 0.044702 TCACCCTCACCCATCCATCT 59.955 55.000 0.00 0.00 0.00 2.90
3117 3476 2.176364 CCTCACCCATCCATCTTCCATT 59.824 50.000 0.00 0.00 0.00 3.16
3159 3518 4.019919 GCAGTGCCACACAATAATACAG 57.980 45.455 2.85 0.00 36.74 2.74
3160 3519 3.440173 GCAGTGCCACACAATAATACAGT 59.560 43.478 2.85 0.00 36.74 3.55
3161 3520 4.634004 GCAGTGCCACACAATAATACAGTA 59.366 41.667 2.85 0.00 36.74 2.74
3182 3541 8.293157 ACAGTAAGAAGAAAGTTACGTAGTACC 58.707 37.037 0.00 0.00 45.76 3.34
3183 3542 8.292448 CAGTAAGAAGAAAGTTACGTAGTACCA 58.708 37.037 0.00 0.00 45.76 3.25
3184 3543 9.018582 AGTAAGAAGAAAGTTACGTAGTACCAT 57.981 33.333 0.00 0.00 45.76 3.55
3185 3544 9.631452 GTAAGAAGAAAGTTACGTAGTACCATT 57.369 33.333 0.00 0.00 45.76 3.16
3186 3545 8.754230 AAGAAGAAAGTTACGTAGTACCATTC 57.246 34.615 0.00 1.13 45.76 2.67
3187 3546 7.889469 AGAAGAAAGTTACGTAGTACCATTCA 58.111 34.615 12.42 0.00 45.76 2.57
3188 3547 8.027771 AGAAGAAAGTTACGTAGTACCATTCAG 58.972 37.037 12.42 0.00 45.76 3.02
3189 3548 6.628185 AGAAAGTTACGTAGTACCATTCAGG 58.372 40.000 12.42 0.00 45.76 3.86
3203 3562 0.961019 TTCAGGCATTGACCAACTGC 59.039 50.000 0.00 7.92 34.94 4.40
3216 3575 2.127232 AACTGCCCTGTGCGCTTTT 61.127 52.632 9.73 0.00 45.60 2.27
3229 3588 4.023279 TGTGCGCTTTTGTACATGATTTCT 60.023 37.500 9.73 0.00 0.00 2.52
3231 3590 4.023279 TGCGCTTTTGTACATGATTTCTGT 60.023 37.500 9.73 0.00 0.00 3.41
3237 3596 8.690840 GCTTTTGTACATGATTTCTGTAACAAC 58.309 33.333 0.00 0.00 31.27 3.32
3372 3734 1.810197 CGTGCCGCTTTTATTAGTGC 58.190 50.000 0.00 0.00 0.00 4.40
3373 3735 1.396996 CGTGCCGCTTTTATTAGTGCT 59.603 47.619 0.00 0.00 0.00 4.40
3374 3736 2.159572 CGTGCCGCTTTTATTAGTGCTT 60.160 45.455 0.00 0.00 0.00 3.91
3375 3737 3.171277 GTGCCGCTTTTATTAGTGCTTG 58.829 45.455 0.00 0.00 0.00 4.01
3395 3757 1.219124 CCATGGTCAGTCACGGAGG 59.781 63.158 2.57 0.00 0.00 4.30
3396 3758 1.257750 CCATGGTCAGTCACGGAGGA 61.258 60.000 2.57 0.00 0.00 3.71
3432 3824 0.249031 GGGTTAATCATTGCCTGCGC 60.249 55.000 0.00 0.00 0.00 6.09
3476 3876 2.097466 GTCACACAGGACAAAACAGTGG 59.903 50.000 0.00 0.00 37.73 4.00
3528 3928 3.740128 ATCGTCTCACATGGGGCGC 62.740 63.158 0.00 0.00 0.00 6.53
3567 3967 0.685097 TTTCCCGTCTCCTTGAGTGG 59.315 55.000 0.00 0.00 0.00 4.00
3600 4000 3.304123 CGTGCCAACGTCTTTTAATTGGA 60.304 43.478 7.33 0.00 43.66 3.53
3615 4015 4.434713 AATTGGATTCGGGTTTCTTTCG 57.565 40.909 0.00 0.00 0.00 3.46
3641 4041 4.429522 TGGCATGCACGCAGGGAT 62.430 61.111 21.36 0.00 0.00 3.85
3662 4062 2.757508 CGAGCTGAGGAGGCAGGA 60.758 66.667 0.00 0.00 36.41 3.86
3663 4063 2.132996 CGAGCTGAGGAGGCAGGAT 61.133 63.158 0.00 0.00 36.41 3.24
3664 4064 1.446791 GAGCTGAGGAGGCAGGATG 59.553 63.158 0.00 0.00 36.41 3.51
3665 4065 1.002662 AGCTGAGGAGGCAGGATGA 59.997 57.895 0.00 0.00 39.69 2.92
3740 4148 1.190323 GTGTGTCGCTGTTTCTTCGAG 59.810 52.381 0.00 0.00 32.54 4.04
3752 4160 2.720758 CTTCGAGCTGGAACGCACG 61.721 63.158 7.12 0.00 41.02 5.34
3805 4213 2.125753 CTTTCTGGCTCGCTCGCT 60.126 61.111 0.00 0.00 0.00 4.93
3806 4214 2.125912 TTTCTGGCTCGCTCGCTC 60.126 61.111 0.00 0.00 0.00 5.03
3807 4215 2.555565 CTTTCTGGCTCGCTCGCTCT 62.556 60.000 0.00 0.00 0.00 4.09
3808 4216 2.825726 TTTCTGGCTCGCTCGCTCTG 62.826 60.000 0.00 0.00 0.00 3.35
3809 4217 4.127040 CTGGCTCGCTCGCTCTGT 62.127 66.667 0.00 0.00 0.00 3.41
3810 4218 4.121669 TGGCTCGCTCGCTCTGTC 62.122 66.667 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.300620 GCGCAAAAACAGAACCCCC 60.301 57.895 0.30 0.00 0.00 5.40
124 136 2.508439 AACGCGCACATCTACGGG 60.508 61.111 5.73 0.00 46.35 5.28
281 301 7.609918 ACAGCATACTATACTGTGGAGAGATAG 59.390 40.741 1.63 0.00 42.83 2.08
287 309 6.004574 TCCTACAGCATACTATACTGTGGAG 58.995 44.000 12.32 4.19 43.31 3.86
290 312 7.119407 ACGTATCCTACAGCATACTATACTGTG 59.881 40.741 11.00 3.36 44.12 3.66
299 321 5.638783 GGATGTACGTATCCTACAGCATAC 58.361 45.833 9.69 0.00 42.73 2.39
340 362 9.784680 TTTTTCTTCACGCTAGTACTAATCTAG 57.215 33.333 3.76 0.00 38.22 2.43
363 399 5.485209 ACCATAGACCTCTCTTCGTTTTT 57.515 39.130 0.00 0.00 0.00 1.94
378 414 3.420893 CCTTGCAGAACCAAACCATAGA 58.579 45.455 0.00 0.00 0.00 1.98
430 466 5.406649 CAATTAGTTGCCGCCAATTTCTAA 58.593 37.500 0.00 0.00 32.75 2.10
461 497 2.423577 GGAACGTAGCACCAAGAACAT 58.576 47.619 0.00 0.00 0.00 2.71
505 554 2.294233 CACATGTTTTCTGTGTGGGAGG 59.706 50.000 0.00 0.00 39.54 4.30
509 558 2.354510 ACGTCACATGTTTTCTGTGTGG 59.645 45.455 0.00 0.65 43.53 4.17
516 565 0.951558 AGGGCACGTCACATGTTTTC 59.048 50.000 0.00 0.00 0.00 2.29
644 693 3.552068 GGCGCAAGAATACACTTTTTGGT 60.552 43.478 10.83 0.00 43.02 3.67
656 705 2.570365 TTGCTCATGGCGCAAGAAT 58.430 47.368 10.83 0.00 41.97 2.40
681 730 2.057922 TCAAAGAGGAAGCCCTGAACT 58.942 47.619 0.00 0.00 44.53 3.01
690 739 6.540551 GGCCTAACTAGAAATCAAAGAGGAAG 59.459 42.308 0.00 0.00 0.00 3.46
773 822 1.614903 TGAGCAAACAAGGCAGGATTG 59.385 47.619 0.00 0.00 0.00 2.67
825 874 2.277969 CATGACTGAAGCAGCCACTAG 58.722 52.381 0.00 0.00 34.37 2.57
829 878 1.073548 TGCATGACTGAAGCAGCCA 59.926 52.632 0.00 0.00 34.37 4.75
900 949 0.735632 GCTGCTCCAGTCGACAGAAG 60.736 60.000 19.50 11.52 33.43 2.85
905 962 1.996191 CTTTTAGCTGCTCCAGTCGAC 59.004 52.381 4.91 7.70 33.43 4.20
945 1002 3.798337 CGATATTGCCTGCAATTGGAAAC 59.202 43.478 21.18 3.18 43.32 2.78
977 1034 1.820906 GCGAGCCAATGCCAGATGA 60.821 57.895 0.00 0.00 38.69 2.92
978 1035 1.381928 AAGCGAGCCAATGCCAGATG 61.382 55.000 0.00 0.00 38.69 2.90
993 1050 2.213575 GCTACGAAACGACATCTAAGCG 59.786 50.000 0.00 0.00 0.00 4.68
1056 1113 1.014044 TCGTCACATCAAAGCTCCGC 61.014 55.000 0.00 0.00 0.00 5.54
1074 1131 2.565841 AGACCATAAAGGCTTGCGATC 58.434 47.619 0.00 0.00 43.14 3.69
1146 1203 3.539604 CTCTTGAATTACAGGAGCTGGG 58.460 50.000 0.00 0.00 43.65 4.45
1380 1437 2.103263 AGCAAAGGATGTCGGTATCTCC 59.897 50.000 0.00 0.00 0.00 3.71
1437 1495 3.118038 AGCACAAGGAAAGTTGTCCACTA 60.118 43.478 6.80 0.00 38.65 2.74
1446 1504 2.484264 GCGTATGAAGCACAAGGAAAGT 59.516 45.455 0.00 0.00 34.19 2.66
1481 1539 2.129555 GAGGGCCAGGCTGTCAAGAA 62.130 60.000 12.43 0.00 0.00 2.52
1603 1661 3.937079 CACAACTGATGAGCATTGCTAGA 59.063 43.478 11.96 1.42 39.88 2.43
1749 1818 8.794553 TCACAAGTTAGAACTAGAGAGGTTTAG 58.205 37.037 0.00 0.00 38.57 1.85
1798 1868 7.288560 AGATAATTCAGGCATTTGATCACTCT 58.711 34.615 0.00 0.00 0.00 3.24
1799 1869 7.308469 GGAGATAATTCAGGCATTTGATCACTC 60.308 40.741 0.00 0.00 0.00 3.51
1845 1915 7.818930 ACAACTGCTCAAAAGAAAAAGATTCAA 59.181 29.630 0.00 0.00 0.00 2.69
1887 2136 5.044558 CGTTTAGCAGATAGGAGGAACTTC 58.955 45.833 0.00 0.00 41.55 3.01
1897 2146 1.859080 GCGGTTCCGTTTAGCAGATAG 59.141 52.381 12.81 0.00 0.00 2.08
1974 2223 4.520492 AGCTTTCCAATGTAGGTTCTGTTG 59.480 41.667 0.00 0.00 0.00 3.33
2485 2775 4.899239 CCACCGCCGCTGATCTCC 62.899 72.222 0.00 0.00 0.00 3.71
2617 2931 3.771160 ACGGAGGCGATGGTCACC 61.771 66.667 0.00 0.00 0.00 4.02
2632 2946 1.795286 GTGAGCTGGAAGTTCTTCACG 59.205 52.381 13.44 5.70 45.30 4.35
2716 3060 0.534412 ACTGCAGGATCACCTTCTCG 59.466 55.000 19.93 0.00 45.36 4.04
2725 3069 1.272147 ACCTTCCCAAACTGCAGGATC 60.272 52.381 19.93 0.00 0.00 3.36
2862 3206 0.868406 CTTCGCTTTCGCTTTGGTCT 59.132 50.000 0.00 0.00 35.26 3.85
2974 3325 3.287312 GCAGCAAGCACAATTACAAGA 57.713 42.857 0.00 0.00 44.79 3.02
3000 3351 6.756542 TGTATGATACGTCCAGTTCTTCAATG 59.243 38.462 0.00 0.00 0.00 2.82
3053 3404 0.806102 CATGTTGTACGAGAGGGCGG 60.806 60.000 0.00 0.00 35.12 6.13
3054 3405 1.421410 GCATGTTGTACGAGAGGGCG 61.421 60.000 0.00 0.00 37.29 6.13
3055 3406 0.391130 TGCATGTTGTACGAGAGGGC 60.391 55.000 0.00 0.00 0.00 5.19
3058 3409 1.359848 GGGTGCATGTTGTACGAGAG 58.640 55.000 0.00 0.00 33.61 3.20
3059 3410 0.389296 CGGGTGCATGTTGTACGAGA 60.389 55.000 0.00 0.00 33.61 4.04
3060 3411 1.358725 CCGGGTGCATGTTGTACGAG 61.359 60.000 0.00 0.00 33.61 4.18
3061 3412 1.374885 CCGGGTGCATGTTGTACGA 60.375 57.895 0.00 0.00 33.61 3.43
3062 3413 3.034370 GCCGGGTGCATGTTGTACG 62.034 63.158 2.18 0.00 40.77 3.67
3063 3414 2.696759 GGCCGGGTGCATGTTGTAC 61.697 63.158 2.18 0.00 43.89 2.90
3094 3453 1.216990 GAAGATGGATGGGTGAGGGT 58.783 55.000 0.00 0.00 0.00 4.34
3095 3454 0.475906 GGAAGATGGATGGGTGAGGG 59.524 60.000 0.00 0.00 0.00 4.30
3096 3455 1.216064 TGGAAGATGGATGGGTGAGG 58.784 55.000 0.00 0.00 0.00 3.86
3097 3456 3.220110 CAATGGAAGATGGATGGGTGAG 58.780 50.000 0.00 0.00 0.00 3.51
3098 3457 2.582172 ACAATGGAAGATGGATGGGTGA 59.418 45.455 0.00 0.00 0.00 4.02
3103 3462 4.368315 CATTGCACAATGGAAGATGGATG 58.632 43.478 14.29 0.00 43.25 3.51
3117 3476 1.545136 CAGGGCATGTTACATTGCACA 59.455 47.619 18.67 0.00 44.80 4.57
3157 3516 8.292448 TGGTACTACGTAACTTTCTTCTTACTG 58.708 37.037 0.00 0.00 0.00 2.74
3158 3517 8.396272 TGGTACTACGTAACTTTCTTCTTACT 57.604 34.615 0.00 0.00 0.00 2.24
3159 3518 9.631452 AATGGTACTACGTAACTTTCTTCTTAC 57.369 33.333 0.00 0.00 0.00 2.34
3160 3519 9.846248 GAATGGTACTACGTAACTTTCTTCTTA 57.154 33.333 0.00 0.00 37.11 2.10
3161 3520 8.362639 TGAATGGTACTACGTAACTTTCTTCTT 58.637 33.333 14.65 0.00 39.23 2.52
3178 3537 2.722094 TGGTCAATGCCTGAATGGTAC 58.278 47.619 0.00 0.00 35.22 3.34
3179 3538 3.088532 GTTGGTCAATGCCTGAATGGTA 58.911 45.455 0.00 0.00 35.22 3.25
3180 3539 1.895131 GTTGGTCAATGCCTGAATGGT 59.105 47.619 0.00 0.00 35.22 3.55
3181 3540 2.094390 CAGTTGGTCAATGCCTGAATGG 60.094 50.000 0.00 0.00 35.22 3.16
3182 3541 2.673043 GCAGTTGGTCAATGCCTGAATG 60.673 50.000 4.62 0.00 35.22 2.67
3183 3542 1.547372 GCAGTTGGTCAATGCCTGAAT 59.453 47.619 4.62 0.00 35.22 2.57
3184 3543 0.961019 GCAGTTGGTCAATGCCTGAA 59.039 50.000 4.62 0.00 35.22 3.02
3185 3544 2.644887 GCAGTTGGTCAATGCCTGA 58.355 52.632 4.62 0.00 33.81 3.86
3189 3548 1.181098 ACAGGGCAGTTGGTCAATGC 61.181 55.000 8.52 8.52 39.25 3.56
3203 3562 0.881118 ATGTACAAAAGCGCACAGGG 59.119 50.000 11.47 0.00 0.00 4.45
3216 3575 5.467063 TGCGTTGTTACAGAAATCATGTACA 59.533 36.000 0.00 0.00 33.01 2.90
3229 3588 4.416620 CTTTTGTTTCCTGCGTTGTTACA 58.583 39.130 0.00 0.00 0.00 2.41
3231 3590 3.129638 AGCTTTTGTTTCCTGCGTTGTTA 59.870 39.130 0.00 0.00 0.00 2.41
3237 3596 0.940991 GCCAGCTTTTGTTTCCTGCG 60.941 55.000 0.00 0.00 0.00 5.18
3278 3638 4.520846 CAATTCGGGCGACGCAGC 62.521 66.667 23.09 4.70 43.86 5.25
3372 3734 1.300971 CGTGACTGACCATGGCCAAG 61.301 60.000 10.96 4.76 0.00 3.61
3373 3735 1.302431 CGTGACTGACCATGGCCAA 60.302 57.895 10.96 0.00 0.00 4.52
3374 3736 2.347114 CGTGACTGACCATGGCCA 59.653 61.111 13.04 8.56 0.00 5.36
3375 3737 2.436646 CCGTGACTGACCATGGCC 60.437 66.667 13.04 0.00 36.52 5.36
3395 3757 1.156645 CCGCACTTGCATAGCTCCTC 61.157 60.000 1.48 0.00 42.21 3.71
3396 3758 1.153289 CCGCACTTGCATAGCTCCT 60.153 57.895 1.48 0.00 42.21 3.69
3432 3824 2.582498 GAAGGGGCGTCGACATCG 60.582 66.667 17.16 2.55 41.45 3.84
3536 3936 3.385384 GGGAAAAGGCAGGCAGGC 61.385 66.667 0.00 0.00 44.61 4.85
3537 3937 3.064324 CGGGAAAAGGCAGGCAGG 61.064 66.667 0.00 0.00 0.00 4.85
3587 3987 6.920817 AGAAACCCGAATCCAATTAAAAGAC 58.079 36.000 0.00 0.00 0.00 3.01
3600 4000 4.069304 TGATTGACGAAAGAAACCCGAAT 58.931 39.130 0.00 0.00 0.00 3.34
3615 4015 0.179181 CGTGCATGCCACTGATTGAC 60.179 55.000 16.68 1.82 42.42 3.18
3641 4041 3.456365 GCCTCCTCAGCTCGCTCA 61.456 66.667 0.00 0.00 0.00 4.26
3646 4046 1.047596 TCATCCTGCCTCCTCAGCTC 61.048 60.000 0.00 0.00 32.87 4.09
3647 4047 0.619832 TTCATCCTGCCTCCTCAGCT 60.620 55.000 0.00 0.00 32.87 4.24
3649 4049 4.387598 CTTTATTCATCCTGCCTCCTCAG 58.612 47.826 0.00 0.00 0.00 3.35
3662 4062 7.068716 CCTTTCGATCTTTTCCCCTTTATTCAT 59.931 37.037 0.00 0.00 0.00 2.57
3663 4063 6.377146 CCTTTCGATCTTTTCCCCTTTATTCA 59.623 38.462 0.00 0.00 0.00 2.57
3664 4064 6.183360 CCCTTTCGATCTTTTCCCCTTTATTC 60.183 42.308 0.00 0.00 0.00 1.75
3665 4065 5.656859 CCCTTTCGATCTTTTCCCCTTTATT 59.343 40.000 0.00 0.00 0.00 1.40
3740 4148 4.077188 GTCTGCGTGCGTTCCAGC 62.077 66.667 0.00 0.00 37.71 4.85
3801 4209 3.506096 CTACGGGCGACAGAGCGA 61.506 66.667 0.00 0.00 38.18 4.93
3805 4213 2.675423 AGCACTACGGGCGACAGA 60.675 61.111 0.00 0.00 36.08 3.41
3806 4214 2.202623 GAGCACTACGGGCGACAG 60.203 66.667 0.00 0.00 36.08 3.51
3807 4215 3.755628 GGAGCACTACGGGCGACA 61.756 66.667 0.00 0.00 36.08 4.35
3808 4216 3.755628 TGGAGCACTACGGGCGAC 61.756 66.667 0.00 0.00 36.08 5.19
3809 4217 3.755628 GTGGAGCACTACGGGCGA 61.756 66.667 0.00 0.00 36.08 5.54


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

AutoCloner maintained by Alex Coulton.