Multiple sequence alignment - TraesCS6B01G072200

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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 TraesCS6B01G072200 chr6B 100.000 2979 0 0 1 2979 48544163 48547141 0.000000e+00 5502.0
1 TraesCS6B01G072200 chrUn 89.579 1948 152 23 1 1925 112251962 112253881 0.000000e+00 2425.0
2 TraesCS6B01G072200 chrUn 88.032 986 64 19 1924 2896 112253941 112254885 0.000000e+00 1118.0
3 TraesCS6B01G072200 chr6A 92.142 1578 93 11 362 1925 27764673 27766233 0.000000e+00 2198.0
4 TraesCS6B01G072200 chr6A 86.754 921 61 27 1924 2824 27766293 27767172 0.000000e+00 968.0
5 TraesCS6B01G072200 chr6A 94.977 219 8 1 1 216 27764336 27764554 1.020000e-89 340.0
6 TraesCS6B01G072200 chr6A 87.135 171 11 6 2811 2979 27767188 27767349 1.820000e-42 183.0
7 TraesCS6B01G072200 chr6A 85.057 87 8 5 226 311 27764598 27764680 1.900000e-12 84.2
8 TraesCS6B01G072200 chr4A 85.507 1449 125 40 523 1925 603636118 603634709 0.000000e+00 1434.0
9 TraesCS6B01G072200 chr4D 85.898 1397 135 31 569 1925 1205309 1206683 0.000000e+00 1432.0
10 TraesCS6B01G072200 chr4D 89.630 135 7 2 1924 2058 1206734 1206861 6.610000e-37 165.0
11 TraesCS6B01G072200 chr4D 77.707 157 21 8 48 190 1204970 1205126 1.900000e-12 84.2
12 TraesCS6B01G072200 chr4D 100.000 31 0 0 2337 2367 1221966 1221996 1.150000e-04 58.4
13 TraesCS6B01G072200 chr4B 88.774 775 60 12 593 1360 806434 805680 0.000000e+00 924.0
14 TraesCS6B01G072200 chr4B 81.275 502 67 10 1403 1888 805677 805187 6.030000e-102 381.0
15 TraesCS6B01G072200 chr4B 81.757 444 63 10 1481 1923 672108 671682 3.650000e-94 355.0
16 TraesCS6B01G072200 chr4B 85.494 324 39 6 1924 2240 671633 671311 6.150000e-87 331.0
17 TraesCS6B01G072200 chr4B 83.846 130 17 4 55 183 806953 806827 1.450000e-23 121.0
18 TraesCS6B01G072200 chr4B 87.500 80 7 2 1923 2000 805002 804924 4.090000e-14 89.8
19 TraesCS6B01G072200 chr4B 92.982 57 4 0 2843 2899 804377 804321 1.900000e-12 84.2
20 TraesCS6B01G072200 chr7D 82.456 342 39 13 593 922 412486014 412486346 2.260000e-71 279.0
21 TraesCS6B01G072200 chr7D 85.065 154 15 6 55 207 412485671 412485817 1.850000e-32 150.0


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 TraesCS6B01G072200 chr6B 48544163 48547141 2978 False 5502.00 5502 100.000000 1 2979 1 chr6B.!!$F1 2978
1 TraesCS6B01G072200 chrUn 112251962 112254885 2923 False 1771.50 2425 88.805500 1 2896 2 chrUn.!!$F1 2895
2 TraesCS6B01G072200 chr6A 27764336 27767349 3013 False 754.64 2198 89.213000 1 2979 5 chr6A.!!$F1 2978
3 TraesCS6B01G072200 chr4A 603634709 603636118 1409 True 1434.00 1434 85.507000 523 1925 1 chr4A.!!$R1 1402
4 TraesCS6B01G072200 chr4D 1204970 1206861 1891 False 560.40 1432 84.411667 48 2058 3 chr4D.!!$F2 2010
5 TraesCS6B01G072200 chr4B 671311 672108 797 True 343.00 355 83.625500 1481 2240 2 chr4B.!!$R1 759
6 TraesCS6B01G072200 chr4B 804321 806953 2632 True 320.00 924 86.875400 55 2899 5 chr4B.!!$R2 2844
7 TraesCS6B01G072200 chr7D 412485671 412486346 675 False 214.50 279 83.760500 55 922 2 chr7D.!!$F1 867

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
487 668 1.805943 CATCAGCGGTTTGACACATCA 59.194 47.619 0.0 0.0 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2262 2784 0.034896 TCCTGTCTTCCCAGTTTCGC 59.965 55.0 0.0 0.0 0.0 4.7 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
139 150 6.622549 AGGTTATGACTACTCAAGAAGAACG 58.377 40.000 0.00 0.00 0.00 3.95
219 248 4.333926 GGCACCTAGCTTCATTTCTAAGTG 59.666 45.833 0.00 0.00 44.79 3.16
220 249 5.178797 GCACCTAGCTTCATTTCTAAGTGA 58.821 41.667 0.00 0.00 41.15 3.41
224 253 9.553064 CACCTAGCTTCATTTCTAAGTGATATT 57.447 33.333 0.00 0.00 31.97 1.28
344 500 4.161565 AGAACGGGCACTCTTGATATACAA 59.838 41.667 0.00 0.00 36.97 2.41
347 503 4.876107 ACGGGCACTCTTGATATACAAAAG 59.124 41.667 0.00 0.00 38.08 2.27
350 506 6.093495 CGGGCACTCTTGATATACAAAAGAAA 59.907 38.462 0.00 0.00 38.08 2.52
351 507 7.361713 CGGGCACTCTTGATATACAAAAGAAAA 60.362 37.037 0.00 0.00 38.08 2.29
445 626 6.985059 CAGTTAGAAGGGTATACTTAGGTTGC 59.015 42.308 2.25 0.00 0.00 4.17
486 667 2.076100 TCATCAGCGGTTTGACACATC 58.924 47.619 0.00 0.00 0.00 3.06
487 668 1.805943 CATCAGCGGTTTGACACATCA 59.194 47.619 0.00 0.00 0.00 3.07
500 681 7.271223 GGTTTGACACATCAGATTAAATGAACG 59.729 37.037 0.00 0.00 35.83 3.95
501 682 7.433708 TTGACACATCAGATTAAATGAACGT 57.566 32.000 0.00 0.00 35.83 3.99
502 683 8.541133 TTGACACATCAGATTAAATGAACGTA 57.459 30.769 0.00 0.00 35.83 3.57
503 684 8.185003 TGACACATCAGATTAAATGAACGTAG 57.815 34.615 0.00 0.00 0.00 3.51
504 685 8.032451 TGACACATCAGATTAAATGAACGTAGA 58.968 33.333 0.00 0.00 0.00 2.59
505 686 8.412608 ACACATCAGATTAAATGAACGTAGAG 57.587 34.615 0.00 0.00 0.00 2.43
544 725 2.835605 AACATTACGTGGTGAGCGG 58.164 52.632 0.00 0.00 0.00 5.52
550 731 2.486636 TACGTGGTGAGCGGCTTGAG 62.487 60.000 2.97 0.00 0.00 3.02
576 758 6.997655 TGGGCTTGAGAATGAGTACATATAG 58.002 40.000 0.00 0.00 35.50 1.31
625 813 3.269381 TCATTCTACCAGCTTTCCCCAAT 59.731 43.478 0.00 0.00 0.00 3.16
642 830 3.321682 CCCAATCTCAACCTTTTGCTCAA 59.678 43.478 0.00 0.00 32.17 3.02
685 876 6.957920 TGATTCCTGAAGTTGACATTTTGA 57.042 33.333 0.00 0.00 0.00 2.69
1043 1278 4.447138 AGGAACAAGAATACACCACCAA 57.553 40.909 0.00 0.00 0.00 3.67
1179 1414 0.471591 AAGGGGCTGCACATTTTGGA 60.472 50.000 3.46 0.00 0.00 3.53
1203 1438 2.507407 TCCATAAGGTCTTTGGTGCC 57.493 50.000 9.83 0.00 35.89 5.01
1297 1532 1.821332 GCACAGGCCAGGCTACATC 60.821 63.158 12.43 0.00 0.00 3.06
1305 1540 1.542108 GCCAGGCTACATCATCCTGTC 60.542 57.143 3.29 0.00 44.41 3.51
1379 1614 2.420642 CATTAGTGCTGCACTCACACT 58.579 47.619 35.98 16.11 41.21 3.55
1411 1646 9.033481 CAACAACAATTCTATTGCTTTCTGAAA 57.967 29.630 2.44 2.44 0.00 2.69
1469 1714 9.507329 AGTAATAACTCAAAACTGATGTCATGT 57.493 29.630 0.00 0.00 0.00 3.21
1470 1715 9.546909 GTAATAACTCAAAACTGATGTCATGTG 57.453 33.333 0.00 0.00 0.00 3.21
1513 1774 1.242076 GCAAGCACAGTTGGAGTCAT 58.758 50.000 0.00 0.00 0.00 3.06
1521 1782 3.191371 CACAGTTGGAGTCATTAAAGGCC 59.809 47.826 0.00 0.00 0.00 5.19
1587 1857 5.104735 CCCTGAAGAAGACAGTATTAAGGCT 60.105 44.000 0.00 0.00 34.04 4.58
1588 1858 5.814705 CCTGAAGAAGACAGTATTAAGGCTG 59.185 44.000 7.32 7.32 38.58 4.85
1601 1871 2.134789 AAGGCTGAGGTTATGGCTTG 57.865 50.000 0.00 0.00 43.35 4.01
1617 1887 1.228862 TTGCCAGAAAGGGGAAGCC 60.229 57.895 0.00 0.00 38.09 4.35
1700 1973 2.530460 AATGGCCTTATGACCTGCAA 57.470 45.000 3.32 0.00 0.00 4.08
1750 2026 7.880713 ACAACATTTCACATGTATACACACCTA 59.119 33.333 7.96 0.00 37.54 3.08
1776 2058 3.297134 ACAGCCCCGTTTAATGATGAT 57.703 42.857 0.00 0.00 0.00 2.45
1854 2136 2.580322 TGGGAATTATTGGCACTGAGGA 59.420 45.455 0.00 0.00 0.00 3.71
1889 2271 3.947196 TGCCTTTGCATATGTCAACTAGG 59.053 43.478 17.49 17.49 44.23 3.02
1890 2272 3.947834 GCCTTTGCATATGTCAACTAGGT 59.052 43.478 20.11 0.00 37.47 3.08
1990 2503 4.827284 AGGGTGTAGAAGACATGGTTTTTG 59.173 41.667 0.00 0.00 41.14 2.44
2026 2539 6.127810 GAAGTATGCTGAAATGCTTCATCA 57.872 37.500 13.05 0.00 44.23 3.07
2089 2611 9.532494 TTTTCTCTCCTTTGATCATTAATCCAA 57.468 29.630 0.00 0.00 33.01 3.53
2119 2641 4.098914 AGCCAGACATTTGGTTTAGTGA 57.901 40.909 0.00 0.00 40.49 3.41
2146 2668 4.750098 CCAGAAAGAAGTTTCGTGCTTAGA 59.250 41.667 0.00 0.00 45.90 2.10
2153 2675 6.402222 AGAAGTTTCGTGCTTAGAGAATCAT 58.598 36.000 0.00 0.00 37.82 2.45
2208 2730 5.466728 CCAAACGATAGGGATGACATAACAG 59.533 44.000 0.00 0.00 43.77 3.16
2209 2731 5.871396 AACGATAGGGATGACATAACAGT 57.129 39.130 0.00 0.00 43.77 3.55
2214 2736 2.578021 AGGGATGACATAACAGTGCCTT 59.422 45.455 0.00 0.00 0.00 4.35
2219 2741 6.058183 GGATGACATAACAGTGCCTTATCTT 58.942 40.000 0.00 0.00 0.00 2.40
2250 2772 4.326504 AAAAGAAGCAACATCAACTGGG 57.673 40.909 0.00 0.00 0.00 4.45
2262 2784 1.962807 TCAACTGGGCTGGAAAACATG 59.037 47.619 0.00 0.00 0.00 3.21
2274 2796 2.035321 GGAAAACATGCGAAACTGGGAA 59.965 45.455 0.00 0.00 0.00 3.97
2320 2842 5.824624 ACATAACAATGATGGTGGAGCTAAG 59.175 40.000 0.00 0.00 0.00 2.18
2385 2907 7.409697 CAATACGTGGAATGGAAGTTAAGATG 58.590 38.462 0.00 0.00 0.00 2.90
2392 2914 5.529060 GGAATGGAAGTTAAGATGCGATTCT 59.471 40.000 0.00 0.00 0.00 2.40
2398 2920 6.414408 AAGTTAAGATGCGATTCTGTTGAG 57.586 37.500 0.00 0.00 0.00 3.02
2420 2944 9.871238 TTGAGCTCAACTAAATTACTAGTTAGG 57.129 33.333 25.16 1.63 39.57 2.69
2421 2945 8.475639 TGAGCTCAACTAAATTACTAGTTAGGG 58.524 37.037 15.67 0.00 39.57 3.53
2446 2970 2.594592 ACAGACGCCAAACTGCCC 60.595 61.111 0.00 0.00 37.61 5.36
2487 3011 1.337728 CGGCTCATAGGTGTGTGACAA 60.338 52.381 0.00 0.00 0.00 3.18
2503 3027 4.699735 TGTGACAAAGTCAGAAAGCAGAAA 59.300 37.500 0.00 0.00 43.57 2.52
2505 3029 6.092748 GTGACAAAGTCAGAAAGCAGAAAAA 58.907 36.000 0.00 0.00 43.57 1.94
2529 3053 8.414629 AAAAGCCTAGGATTATGATGGAATTC 57.585 34.615 13.77 0.00 0.00 2.17
2550 3074 9.182214 GAATTCATTAGGATATGTGGTATGCAT 57.818 33.333 3.79 3.79 33.88 3.96
2551 3075 9.537852 AATTCATTAGGATATGTGGTATGCATT 57.462 29.630 3.54 0.00 33.88 3.56
2616 3175 1.508632 CATTCCGTCGAACAGGTTGT 58.491 50.000 0.00 0.00 0.00 3.32
2717 3287 1.813753 GCAGGCGAGGCATTTCGTA 60.814 57.895 0.00 0.00 42.38 3.43
2723 3293 1.003866 GCGAGGCATTTCGTATCCAAC 60.004 52.381 6.41 0.00 42.38 3.77
2821 3456 1.056660 CGTGGGAGTATGGGCCTATT 58.943 55.000 7.02 0.00 0.00 1.73
2822 3457 1.002087 CGTGGGAGTATGGGCCTATTC 59.998 57.143 7.02 1.33 0.00 1.75
2824 3459 2.039084 GTGGGAGTATGGGCCTATTCTG 59.961 54.545 13.08 0.00 0.00 3.02
2826 3461 2.039084 GGGAGTATGGGCCTATTCTGTG 59.961 54.545 13.08 0.00 0.00 3.66
2827 3462 2.551071 GGAGTATGGGCCTATTCTGTGC 60.551 54.545 13.08 0.00 0.00 4.57
2828 3463 1.421646 AGTATGGGCCTATTCTGTGCC 59.578 52.381 7.02 0.00 44.59 5.01
2831 3466 1.819753 TGGGCCTATTCTGTGCCTAT 58.180 50.000 4.53 0.00 44.71 2.57
2900 3563 4.082733 GGGCTTCCAAGTACATTTCAACTC 60.083 45.833 0.00 0.00 0.00 3.01
2910 3573 3.406764 ACATTTCAACTCAGCTCTGACC 58.593 45.455 0.00 0.00 35.46 4.02
2911 3574 2.550830 TTTCAACTCAGCTCTGACCC 57.449 50.000 0.00 0.00 35.46 4.46
2912 3575 1.423584 TTCAACTCAGCTCTGACCCA 58.576 50.000 0.00 0.00 35.46 4.51
2913 3576 1.649321 TCAACTCAGCTCTGACCCAT 58.351 50.000 0.00 0.00 35.46 4.00
2914 3577 1.277273 TCAACTCAGCTCTGACCCATG 59.723 52.381 0.00 0.00 35.46 3.66
2915 3578 1.277273 CAACTCAGCTCTGACCCATGA 59.723 52.381 0.00 0.00 35.46 3.07
2922 3586 0.179026 CTCTGACCCATGATGCCTGG 60.179 60.000 0.00 0.00 0.00 4.45
2927 3591 1.490490 GACCCATGATGCCTGGTCTTA 59.510 52.381 10.81 0.00 43.16 2.10
2928 3592 1.922447 ACCCATGATGCCTGGTCTTAA 59.078 47.619 0.00 0.00 31.44 1.85
2960 3624 4.270153 TCCCAGTGTCCCCTGCCT 62.270 66.667 0.00 0.00 0.00 4.75
2963 3627 2.528818 CCAGTGTCCCCTGCCTTGA 61.529 63.158 0.00 0.00 0.00 3.02
2975 3639 0.401738 TGCCTTGACCCTGAGAAAGG 59.598 55.000 0.00 0.00 46.94 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
208 237 7.546358 TGGCAAACCAATATCACTTAGAAATG 58.454 34.615 0.00 0.00 45.37 2.32
224 253 1.890573 GCTATTGGTCCTGGCAAACCA 60.891 52.381 15.41 15.41 46.51 3.67
305 461 7.597369 GTGCCCGTTCTTCTTGTTTATTTATTT 59.403 33.333 0.00 0.00 0.00 1.40
311 467 3.751518 AGTGCCCGTTCTTCTTGTTTAT 58.248 40.909 0.00 0.00 0.00 1.40
315 471 0.759346 AGAGTGCCCGTTCTTCTTGT 59.241 50.000 0.00 0.00 0.00 3.16
316 472 1.532868 CAAGAGTGCCCGTTCTTCTTG 59.467 52.381 0.00 0.00 31.53 3.02
321 477 3.704566 TGTATATCAAGAGTGCCCGTTCT 59.295 43.478 0.00 0.00 0.00 3.01
322 478 4.054780 TGTATATCAAGAGTGCCCGTTC 57.945 45.455 0.00 0.00 0.00 3.95
325 481 5.116180 TCTTTTGTATATCAAGAGTGCCCG 58.884 41.667 0.00 0.00 38.75 6.13
327 483 9.860898 ATTTTTCTTTTGTATATCAAGAGTGCC 57.139 29.630 0.00 0.00 38.75 5.01
374 555 8.035394 TCTGCCTGAGACTTTAATAGTTGTAAG 58.965 37.037 0.00 0.00 37.17 2.34
420 601 6.985059 GCAACCTAAGTATACCCTTCTAACTG 59.015 42.308 0.00 0.00 0.00 3.16
445 626 6.769608 TGATGCGCATAATACTCTGTTAAG 57.230 37.500 25.40 0.00 0.00 1.85
486 667 7.096966 GCGACTACTCTACGTTCATTTAATCTG 60.097 40.741 0.00 0.00 0.00 2.90
487 668 6.911511 GCGACTACTCTACGTTCATTTAATCT 59.088 38.462 0.00 0.00 0.00 2.40
500 681 7.018826 GTGAGATGATTATGCGACTACTCTAC 58.981 42.308 0.00 0.00 0.00 2.59
501 682 6.710744 TGTGAGATGATTATGCGACTACTCTA 59.289 38.462 0.00 0.00 0.00 2.43
502 683 5.532779 TGTGAGATGATTATGCGACTACTCT 59.467 40.000 0.00 0.00 0.00 3.24
503 684 5.763088 TGTGAGATGATTATGCGACTACTC 58.237 41.667 0.00 0.00 0.00 2.59
504 685 5.774498 TGTGAGATGATTATGCGACTACT 57.226 39.130 0.00 0.00 0.00 2.57
505 686 5.748630 TGTTGTGAGATGATTATGCGACTAC 59.251 40.000 0.00 0.00 0.00 2.73
543 724 0.254178 TCTCAAGCCCATCTCAAGCC 59.746 55.000 0.00 0.00 0.00 4.35
544 725 2.119801 TTCTCAAGCCCATCTCAAGC 57.880 50.000 0.00 0.00 0.00 4.01
550 731 4.142609 TGTACTCATTCTCAAGCCCATC 57.857 45.455 0.00 0.00 0.00 3.51
576 758 6.200854 CCAAAGAAAATAACTGCTGTTCAACC 59.799 38.462 12.67 0.78 37.59 3.77
625 813 3.648339 GCATTGAGCAAAAGGTTGAGA 57.352 42.857 0.00 0.00 44.79 3.27
642 830 9.333724 GGAATCAATCAATGAATTAAAAGGCAT 57.666 29.630 0.00 0.00 42.54 4.40
685 876 2.225467 GAGTACTATCCTTACGGGCGT 58.775 52.381 0.00 0.00 34.39 5.68
705 896 9.971922 AACTTCTCCTTTCTTTTTAACATGATG 57.028 29.630 0.00 0.00 0.00 3.07
707 898 9.184523 TCAACTTCTCCTTTCTTTTTAACATGA 57.815 29.630 0.00 0.00 0.00 3.07
726 942 6.861065 TGAGTTTATGAGGTGTTCAACTTC 57.139 37.500 0.00 0.00 39.77 3.01
795 1018 3.639672 AAGGAGGTAACAATAACCCGG 57.360 47.619 0.00 0.00 37.77 5.73
847 1072 5.368989 CAGGTTCCCAGTTCTATACCAATC 58.631 45.833 0.00 0.00 0.00 2.67
1043 1278 1.959985 CTCCTGCTACCTGATCGATGT 59.040 52.381 0.54 0.00 0.00 3.06
1179 1414 2.582636 ACCAAAGACCTTATGGATGGCT 59.417 45.455 0.81 0.00 37.66 4.75
1203 1438 2.419324 GAGGAGCTTTGAGACATTGCTG 59.581 50.000 0.00 0.00 33.83 4.41
1297 1532 2.205074 GACGCAACCATAGACAGGATG 58.795 52.381 0.00 0.00 46.00 3.51
1367 1602 2.229675 TGAAGTCAGTGTGAGTGCAG 57.770 50.000 0.00 0.00 30.52 4.41
1379 1614 7.275888 AGCAATAGAATTGTTGTTGAAGTCA 57.724 32.000 1.94 0.00 0.00 3.41
1411 1646 6.369615 GCAATTAGCAGTTCACCAAATGAAAT 59.630 34.615 0.00 0.00 46.34 2.17
1469 1714 4.890158 TTCACAGCCTAAGAGAACATCA 57.110 40.909 0.00 0.00 0.00 3.07
1470 1715 5.523188 CAGATTCACAGCCTAAGAGAACATC 59.477 44.000 0.00 0.00 0.00 3.06
1513 1774 1.228737 GTGGTGCCTGGGCCTTTAA 60.229 57.895 4.53 0.00 41.09 1.52
1539 1809 5.682862 GCTTGATGCGGAATAAGTATTTGTG 59.317 40.000 5.65 0.00 0.00 3.33
1540 1810 5.221048 GGCTTGATGCGGAATAAGTATTTGT 60.221 40.000 5.65 0.00 44.05 2.83
1541 1811 5.215160 GGCTTGATGCGGAATAAGTATTTG 58.785 41.667 5.65 0.00 44.05 2.32
1542 1812 4.278419 GGGCTTGATGCGGAATAAGTATTT 59.722 41.667 5.65 0.00 44.05 1.40
1543 1813 3.821033 GGGCTTGATGCGGAATAAGTATT 59.179 43.478 5.65 0.00 44.05 1.89
1544 1814 3.073062 AGGGCTTGATGCGGAATAAGTAT 59.927 43.478 5.65 0.00 44.05 2.12
1587 1857 0.991146 TCTGGCAAGCCATAACCTCA 59.009 50.000 15.09 0.00 46.15 3.86
1588 1858 2.128771 TTCTGGCAAGCCATAACCTC 57.871 50.000 15.09 0.00 46.15 3.85
1601 1871 1.680314 CTGGCTTCCCCTTTCTGGC 60.680 63.158 0.00 0.00 0.00 4.85
1677 1947 2.949963 GCAGGTCATAAGGCCATTTCCA 60.950 50.000 5.01 0.00 0.00 3.53
1685 1955 2.378038 TGGAATTGCAGGTCATAAGGC 58.622 47.619 0.00 0.00 0.00 4.35
1700 1973 4.515028 TCCTGAGAAGATTGCATGGAAT 57.485 40.909 12.76 12.76 0.00 3.01
1750 2026 5.362105 TCATTAAACGGGGCTGTATAGTT 57.638 39.130 0.00 0.00 0.00 2.24
1776 2058 1.945580 TGGTGCTACTGTGGATACCA 58.054 50.000 13.81 13.81 35.97 3.25
1854 2136 1.002087 CAAAGGCAACCGACTAGAGGT 59.998 52.381 8.48 8.48 45.29 3.85
1990 2503 3.871594 AGCATACTTCAACGATGGTTAGC 59.128 43.478 0.00 0.00 33.72 3.09
2000 2513 5.702865 TGAAGCATTTCAGCATACTTCAAC 58.297 37.500 0.00 0.00 40.21 3.18
2119 2641 3.181490 GCACGAAACTTCTTTCTGGGTTT 60.181 43.478 0.00 0.00 34.62 3.27
2124 2646 5.692204 TCTCTAAGCACGAAACTTCTTTCTG 59.308 40.000 0.00 0.00 34.62 3.02
2153 2675 7.799447 GCACACGACAAACTACAATGTTAATTA 59.201 33.333 0.00 0.00 0.00 1.40
2208 2730 3.194005 TCGATCCCAAAGATAAGGCAC 57.806 47.619 0.00 0.00 34.42 5.01
2209 2731 3.924114 TTCGATCCCAAAGATAAGGCA 57.076 42.857 0.00 0.00 34.42 4.75
2214 2736 5.943416 TGCTTCTTTTTCGATCCCAAAGATA 59.057 36.000 8.64 2.44 36.62 1.98
2219 2741 3.634448 TGTTGCTTCTTTTTCGATCCCAA 59.366 39.130 0.00 0.00 0.00 4.12
2250 2772 2.053627 CAGTTTCGCATGTTTTCCAGC 58.946 47.619 0.00 0.00 0.00 4.85
2262 2784 0.034896 TCCTGTCTTCCCAGTTTCGC 59.965 55.000 0.00 0.00 0.00 4.70
2274 2796 2.057137 TGCTTTGCTGTTTCCTGTCT 57.943 45.000 0.00 0.00 0.00 3.41
2320 2842 3.313526 TGAACTTGACAGAAGAAGCTTGC 59.686 43.478 2.10 0.00 0.00 4.01
2398 2920 8.255905 TGACCCTAACTAGTAATTTAGTTGAGC 58.744 37.037 11.27 0.00 42.31 4.26
2410 2934 5.651139 GTCTGTGTCATGACCCTAACTAGTA 59.349 44.000 22.85 0.00 0.00 1.82
2420 2944 0.602638 TTGGCGTCTGTGTCATGACC 60.603 55.000 22.85 14.28 0.00 4.02
2421 2945 1.069906 GTTTGGCGTCTGTGTCATGAC 60.070 52.381 19.27 19.27 0.00 3.06
2463 2987 1.146930 CACACCTATGAGCCGCCAT 59.853 57.895 0.00 0.00 0.00 4.40
2470 2994 4.631131 TGACTTTGTCACACACCTATGAG 58.369 43.478 0.00 0.00 37.67 2.90
2503 3027 8.788238 AATTCCATCATAATCCTAGGCTTTTT 57.212 30.769 2.96 0.00 0.00 1.94
2505 3029 7.529555 TGAATTCCATCATAATCCTAGGCTTT 58.470 34.615 2.96 2.86 0.00 3.51
2509 3033 9.624373 CCTAATGAATTCCATCATAATCCTAGG 57.376 37.037 0.82 0.82 39.08 3.02
2529 3053 6.319658 GGGAATGCATACCACATATCCTAATG 59.680 42.308 13.84 0.00 31.22 1.90
2537 3061 6.884295 GCTAATTAGGGAATGCATACCACATA 59.116 38.462 19.21 4.10 0.00 2.29
2550 3074 3.383185 CCGCCATTTTGCTAATTAGGGAA 59.617 43.478 14.28 0.40 0.00 3.97
2551 3075 2.955660 CCGCCATTTTGCTAATTAGGGA 59.044 45.455 14.28 0.00 0.00 4.20
2616 3175 1.344065 AGTACCATCCACCACGAACA 58.656 50.000 0.00 0.00 0.00 3.18
2717 3287 3.396570 GTCCCCGACCCGTTGGAT 61.397 66.667 2.40 0.00 36.15 3.41
2723 3293 2.758327 TCAGATGTCCCCGACCCG 60.758 66.667 0.00 0.00 0.00 5.28
2724 3294 2.435693 CCTCAGATGTCCCCGACCC 61.436 68.421 0.00 0.00 0.00 4.46
2731 3305 1.439644 GTCCGAGCCTCAGATGTCC 59.560 63.158 0.00 0.00 0.00 4.02
2900 3563 0.818445 GGCATCATGGGTCAGAGCTG 60.818 60.000 0.00 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.