Multiple sequence alignment - TraesCS6A01G215000

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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 TraesCS6A01G215000 chr6A 100.000 5262 0 0 1 5262 394638477 394643738 0.000000e+00 9718
1 TraesCS6A01G215000 chr3A 96.184 3538 97 10 1748 5259 224965927 224969452 0.000000e+00 5751
2 TraesCS6A01G215000 chr3A 95.970 2109 72 6 1 2107 224963376 224965473 0.000000e+00 3411
3 TraesCS6A01G215000 chr3A 73.502 317 82 2 593 908 594621315 594621630 9.260000e-23 119
4 TraesCS6A01G215000 chr4A 97.423 2134 45 5 3129 5262 574768420 574766297 0.000000e+00 3627
5 TraesCS6A01G215000 chr4A 92.830 2385 96 24 800 3169 574770668 574768344 0.000000e+00 3387
6 TraesCS6A01G215000 chr4A 94.319 1461 74 6 3804 5262 602465413 602463960 0.000000e+00 2230
7 TraesCS6A01G215000 chr4A 84.202 1842 163 58 1364 3169 218047035 218048784 0.000000e+00 1672
8 TraesCS6A01G215000 chr4A 90.551 1016 76 7 1 1016 620474882 620475877 0.000000e+00 1327
9 TraesCS6A01G215000 chr4A 97.644 764 18 0 1 764 574771429 574770666 0.000000e+00 1312
10 TraesCS6A01G215000 chr4A 94.910 609 25 4 3144 3751 602467223 602466620 0.000000e+00 948
11 TraesCS6A01G215000 chr4A 94.069 607 30 4 3146 3751 218048723 218049324 0.000000e+00 917
12 TraesCS6A01G215000 chr4A 83.607 793 114 7 1 778 175850155 175850946 0.000000e+00 730
13 TraesCS6A01G215000 chr4A 78.895 706 72 28 1633 2317 602468832 602468183 1.760000e-109 407
14 TraesCS6A01G215000 chr4A 91.275 149 4 3 2603 2751 602468016 602467877 1.500000e-45 195
15 TraesCS6A01G215000 chr4A 83.190 232 15 13 1364 1594 602469042 602468834 1.930000e-44 191
16 TraesCS6A01G215000 chr2B 94.327 1463 72 8 3804 5262 435353580 435352125 0.000000e+00 2231
17 TraesCS6A01G215000 chr2B 92.599 608 39 3 3144 3751 622033302 622032701 0.000000e+00 869
18 TraesCS6A01G215000 chr2B 91.688 397 30 2 2773 3169 622033627 622033234 9.960000e-152 547
19 TraesCS6A01G215000 chr2B 84.544 537 65 11 2224 2760 622034413 622033895 2.810000e-142 516
20 TraesCS6A01G215000 chr2B 76.316 532 80 26 1615 2145 622042411 622041925 5.260000e-60 243
21 TraesCS6A01G215000 chr6B 94.190 1463 75 7 3804 5262 617028307 617029763 0.000000e+00 2222
22 TraesCS6A01G215000 chr6B 93.575 1463 83 8 3804 5262 399208777 399207322 0.000000e+00 2170
23 TraesCS6A01G215000 chr6B 84.330 1589 129 47 1639 3169 399212050 399210524 0.000000e+00 1445
24 TraesCS6A01G215000 chr6B 89.189 925 66 11 2248 3169 617026106 617026999 0.000000e+00 1123
25 TraesCS6A01G215000 chr6B 94.599 611 28 3 3141 3751 617026933 617027538 0.000000e+00 941
26 TraesCS6A01G215000 chr6B 94.089 609 30 4 3144 3751 399210587 399209984 0.000000e+00 920
27 TraesCS6A01G215000 chr6B 81.426 603 65 22 1368 1955 617025330 617025900 2.890000e-122 449
28 TraesCS6A01G215000 chr5A 94.190 1463 75 7 3804 5262 692978945 692980401 0.000000e+00 2222
29 TraesCS6A01G215000 chr1B 93.438 1463 86 7 3804 5262 651732278 651730822 0.000000e+00 2161
30 TraesCS6A01G215000 chr1B 85.780 1308 86 25 1918 3169 17133123 17134386 0.000000e+00 1293
31 TraesCS6A01G215000 chr1B 93.596 609 35 4 3144 3751 60952592 60951987 0.000000e+00 905
32 TraesCS6A01G215000 chr1B 92.308 481 26 4 2689 3169 60952993 60952524 0.000000e+00 673
33 TraesCS6A01G215000 chr1B 80.504 754 83 39 1901 2634 60953707 60952998 2.170000e-143 520
34 TraesCS6A01G215000 chr1B 80.901 644 66 23 1364 1991 17132631 17133233 6.210000e-124 455
35 TraesCS6A01G215000 chr1B 74.613 323 75 6 676 994 392718375 392718056 9.190000e-28 135
36 TraesCS6A01G215000 chr1B 83.206 131 13 7 1046 1176 424436215 424436336 1.550000e-20 111
37 TraesCS6A01G215000 chr5B 93.106 1465 88 9 3804 5262 576501171 576502628 0.000000e+00 2134
38 TraesCS6A01G215000 chr5B 88.757 925 70 10 2248 3169 576498970 576499863 0.000000e+00 1101
39 TraesCS6A01G215000 chr5B 93.781 611 33 3 3141 3751 576499797 576500402 0.000000e+00 913
40 TraesCS6A01G215000 chr5B 83.234 674 77 20 1918 2565 155251732 155251069 2.110000e-163 586
41 TraesCS6A01G215000 chr2D 92.409 685 49 2 1 685 119841318 119841999 0.000000e+00 974
42 TraesCS6A01G215000 chr2D 87.903 496 45 8 2076 2565 66187679 66187193 2.130000e-158 569
43 TraesCS6A01G215000 chr2D 79.167 336 62 8 1240 1569 536296062 536296395 5.300000e-55 226
44 TraesCS6A01G215000 chr7A 85.402 870 122 4 1 869 93256477 93255612 0.000000e+00 898
45 TraesCS6A01G215000 chr7D 85.080 878 115 7 1 869 91689766 91688896 0.000000e+00 881
46 TraesCS6A01G215000 chr7D 93.440 564 37 0 1 564 98997654 98997091 0.000000e+00 837
47 TraesCS6A01G215000 chr7D 85.264 794 72 18 1790 2565 637026917 637026151 0.000000e+00 776
48 TraesCS6A01G215000 chr4B 84.798 842 120 6 1 840 377950720 377949885 0.000000e+00 839
49 TraesCS6A01G215000 chr7B 83.594 896 111 14 2 866 43245547 43246437 0.000000e+00 808
50 TraesCS6A01G215000 chr3D 83.540 808 89 18 1790 2565 500872134 500872929 0.000000e+00 715
51 TraesCS6A01G215000 chr3D 81.306 781 104 26 1816 2565 9583893 9583124 3.510000e-166 595
52 TraesCS6A01G215000 chr4D 82.472 793 90 19 1810 2565 484991627 484990847 0.000000e+00 649
53 TraesCS6A01G215000 chr1A 77.485 342 65 11 1236 1569 419806395 419806058 1.500000e-45 195
54 TraesCS6A01G215000 chr6D 70.686 846 223 25 143 978 414629581 414630411 1.170000e-36 165
55 TraesCS6A01G215000 chr6D 76.036 338 68 9 1239 1569 67717135 67716804 4.220000e-36 163
56 TraesCS6A01G215000 chr5D 75.224 335 67 8 1240 1569 511767585 511767262 1.530000e-30 145
57 TraesCS6A01G215000 chr3B 72.034 354 97 2 556 908 111988691 111989043 2.590000e-18 104


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 TraesCS6A01G215000 chr6A 394638477 394643738 5261 False 9718.000000 9718 100.000000 1 5262 1 chr6A.!!$F1 5261
1 TraesCS6A01G215000 chr3A 224963376 224969452 6076 False 4581.000000 5751 96.077000 1 5259 2 chr3A.!!$F2 5258
2 TraesCS6A01G215000 chr4A 574766297 574771429 5132 True 2775.333333 3627 95.965667 1 5262 3 chr4A.!!$R1 5261
3 TraesCS6A01G215000 chr4A 620474882 620475877 995 False 1327.000000 1327 90.551000 1 1016 1 chr4A.!!$F2 1015
4 TraesCS6A01G215000 chr4A 218047035 218049324 2289 False 1294.500000 1672 89.135500 1364 3751 2 chr4A.!!$F3 2387
5 TraesCS6A01G215000 chr4A 602463960 602469042 5082 True 794.200000 2230 88.517800 1364 5262 5 chr4A.!!$R2 3898
6 TraesCS6A01G215000 chr4A 175850155 175850946 791 False 730.000000 730 83.607000 1 778 1 chr4A.!!$F1 777
7 TraesCS6A01G215000 chr2B 435352125 435353580 1455 True 2231.000000 2231 94.327000 3804 5262 1 chr2B.!!$R1 1458
8 TraesCS6A01G215000 chr2B 622032701 622034413 1712 True 644.000000 869 89.610333 2224 3751 3 chr2B.!!$R3 1527
9 TraesCS6A01G215000 chr6B 399207322 399212050 4728 True 1511.666667 2170 90.664667 1639 5262 3 chr6B.!!$R1 3623
10 TraesCS6A01G215000 chr6B 617025330 617029763 4433 False 1183.750000 2222 89.851000 1368 5262 4 chr6B.!!$F1 3894
11 TraesCS6A01G215000 chr5A 692978945 692980401 1456 False 2222.000000 2222 94.190000 3804 5262 1 chr5A.!!$F1 1458
12 TraesCS6A01G215000 chr1B 651730822 651732278 1456 True 2161.000000 2161 93.438000 3804 5262 1 chr1B.!!$R2 1458
13 TraesCS6A01G215000 chr1B 17132631 17134386 1755 False 874.000000 1293 83.340500 1364 3169 2 chr1B.!!$F2 1805
14 TraesCS6A01G215000 chr1B 60951987 60953707 1720 True 699.333333 905 88.802667 1901 3751 3 chr1B.!!$R3 1850
15 TraesCS6A01G215000 chr5B 576498970 576502628 3658 False 1382.666667 2134 91.881333 2248 5262 3 chr5B.!!$F1 3014
16 TraesCS6A01G215000 chr5B 155251069 155251732 663 True 586.000000 586 83.234000 1918 2565 1 chr5B.!!$R1 647
17 TraesCS6A01G215000 chr2D 119841318 119841999 681 False 974.000000 974 92.409000 1 685 1 chr2D.!!$F1 684
18 TraesCS6A01G215000 chr7A 93255612 93256477 865 True 898.000000 898 85.402000 1 869 1 chr7A.!!$R1 868
19 TraesCS6A01G215000 chr7D 91688896 91689766 870 True 881.000000 881 85.080000 1 869 1 chr7D.!!$R1 868
20 TraesCS6A01G215000 chr7D 98997091 98997654 563 True 837.000000 837 93.440000 1 564 1 chr7D.!!$R2 563
21 TraesCS6A01G215000 chr7D 637026151 637026917 766 True 776.000000 776 85.264000 1790 2565 1 chr7D.!!$R3 775
22 TraesCS6A01G215000 chr4B 377949885 377950720 835 True 839.000000 839 84.798000 1 840 1 chr4B.!!$R1 839
23 TraesCS6A01G215000 chr7B 43245547 43246437 890 False 808.000000 808 83.594000 2 866 1 chr7B.!!$F1 864
24 TraesCS6A01G215000 chr3D 500872134 500872929 795 False 715.000000 715 83.540000 1790 2565 1 chr3D.!!$F1 775
25 TraesCS6A01G215000 chr3D 9583124 9583893 769 True 595.000000 595 81.306000 1816 2565 1 chr3D.!!$R1 749
26 TraesCS6A01G215000 chr4D 484990847 484991627 780 True 649.000000 649 82.472000 1810 2565 1 chr4D.!!$R1 755

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
912 981 1.352352 CCCCTGTGGTCTTGTCAGAAT 59.648 52.381 0.0 0.0 0.00 2.40 F
1777 1865 1.067142 TCGAACTAATTCAGCCGCACT 60.067 47.619 0.0 0.0 34.14 4.40 F
2121 3123 0.251354 CTAGCAGCACACTCCACCAT 59.749 55.000 0.0 0.0 0.00 3.55 F
2217 3263 3.435169 GGTTGAAGAGGTGGAAAGGAAGT 60.435 47.826 0.0 0.0 0.00 3.01 F
4028 7112 1.209747 GGTTCTCGCCCCTACATTTCT 59.790 52.381 0.0 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2103 3103 0.250234 GATGGTGGAGTGTGCTGCTA 59.750 55.000 0.00 0.0 33.91 3.49 R
3024 4436 1.250476 GCACGAAACTATGCAAAGCG 58.750 50.000 0.00 0.0 41.65 4.68 R
3441 4930 3.448686 CCATCGGTGATGACACTACTTC 58.551 50.000 8.32 0.0 42.09 3.01 R
4034 7118 4.471025 TGAGAGATCCTTACCAAAGCATGA 59.529 41.667 0.00 0.0 0.00 3.07 R
5183 8274 4.164221 ACCTGTTGAACTTCTTCTTGGAGA 59.836 41.667 0.00 0.0 0.00 3.71 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
37 38 2.685999 GGAGGCCATGGCTTTCCT 59.314 61.111 34.57 25.90 38.98 3.36
105 106 2.038557 GAGTCCTCAAGGTGCCAAGTAA 59.961 50.000 0.00 0.00 36.34 2.24
792 861 5.044919 TCAGTCCATTCAGACCATAACCAAT 60.045 40.000 0.00 0.00 37.49 3.16
819 888 4.398598 GGGCGCGCACGAATTTGT 62.399 61.111 34.42 0.00 43.93 2.83
912 981 1.352352 CCCCTGTGGTCTTGTCAGAAT 59.648 52.381 0.00 0.00 0.00 2.40
914 983 2.341257 CCTGTGGTCTTGTCAGAATCG 58.659 52.381 0.00 0.00 0.00 3.34
970 1039 2.496817 GAGAGTGCTCGGCGGAAT 59.503 61.111 7.21 0.00 34.09 3.01
1080 1149 2.664851 CCGCACGAGAGGCAAACA 60.665 61.111 0.00 0.00 0.00 2.83
1463 1535 9.614792 GAATAACTGTTCATACTTAGGGTTGAT 57.385 33.333 0.00 0.00 0.00 2.57
1679 1767 1.337167 GCTGCTGGCGAAAATTTTCCT 60.337 47.619 22.15 0.00 33.68 3.36
1688 1776 3.798548 GCGAAAATTTTCCTGCTCCACAA 60.799 43.478 22.15 0.00 33.68 3.33
1777 1865 1.067142 TCGAACTAATTCAGCCGCACT 60.067 47.619 0.00 0.00 34.14 4.40
1788 1876 4.673298 CCGCACTGCACCGTACCA 62.673 66.667 1.11 0.00 0.00 3.25
1867 1994 4.176752 GAACCCTAGCCGCCCCTG 62.177 72.222 0.00 0.00 0.00 4.45
1872 1999 4.554036 CTAGCCGCCCCTGCCTTC 62.554 72.222 0.00 0.00 0.00 3.46
1880 2007 3.474570 CCCTGCCTTCCCCTCGAG 61.475 72.222 5.13 5.13 0.00 4.04
1881 2008 4.168291 CCTGCCTTCCCCTCGAGC 62.168 72.222 6.99 0.00 0.00 5.03
2089 3089 3.710722 CCTGTGCTTCCCCGCTCT 61.711 66.667 0.00 0.00 0.00 4.09
2103 3103 2.726351 GCTCTAGCTCGCCCAACCT 61.726 63.158 0.00 0.00 38.21 3.50
2121 3123 0.251354 CTAGCAGCACACTCCACCAT 59.749 55.000 0.00 0.00 0.00 3.55
2200 3246 4.979335 TGTTATGTCATGGTGAAGGTTGA 58.021 39.130 0.00 0.00 0.00 3.18
2217 3263 3.435169 GGTTGAAGAGGTGGAAAGGAAGT 60.435 47.826 0.00 0.00 0.00 3.01
2467 3574 5.127194 ACTCATGATATTACGTGACCACACT 59.873 40.000 0.00 0.00 43.99 3.55
2708 3815 6.315393 GCTAAAAATGTGTAGGCTACAGCTTA 59.685 38.462 26.87 16.80 39.77 3.09
2890 4302 3.790089 AGCAAGGCAAGTAAACTAGGT 57.210 42.857 0.00 0.00 0.00 3.08
2905 4317 4.910458 ACTAGGTAACAACCAAGCTGAT 57.090 40.909 0.00 0.00 41.41 2.90
2924 4336 4.922206 TGATTAGCACAGTTCCAATTCCT 58.078 39.130 0.00 0.00 0.00 3.36
2976 4388 4.372656 GAGCAAGAAACTCGCAGGTATAT 58.627 43.478 0.00 0.00 0.00 0.86
3024 4436 4.083003 TGGTTTTCTATGGACGTGAATTGC 60.083 41.667 0.00 0.00 0.00 3.56
3120 4602 6.902771 ATAGTTCGCTCCTGATATGTACTT 57.097 37.500 0.00 0.00 0.00 2.24
3152 4639 6.822073 AAACAAAATAAAACAGTTCGCTCC 57.178 33.333 0.00 0.00 0.00 4.70
3153 4640 5.767816 ACAAAATAAAACAGTTCGCTCCT 57.232 34.783 0.00 0.00 0.00 3.69
3154 4641 5.519722 ACAAAATAAAACAGTTCGCTCCTG 58.480 37.500 0.00 0.00 36.01 3.86
3155 4642 5.298276 ACAAAATAAAACAGTTCGCTCCTGA 59.702 36.000 0.00 0.00 34.04 3.86
3156 4643 6.016276 ACAAAATAAAACAGTTCGCTCCTGAT 60.016 34.615 0.00 0.00 34.04 2.90
3157 4644 7.174253 ACAAAATAAAACAGTTCGCTCCTGATA 59.826 33.333 0.00 0.00 34.04 2.15
3158 4645 7.865706 AAATAAAACAGTTCGCTCCTGATAT 57.134 32.000 0.00 0.00 34.04 1.63
3159 4646 6.851222 ATAAAACAGTTCGCTCCTGATATG 57.149 37.500 0.00 0.00 34.04 1.78
3160 4647 3.895232 AACAGTTCGCTCCTGATATGT 57.105 42.857 0.00 0.00 34.04 2.29
3161 4648 5.339008 AAACAGTTCGCTCCTGATATGTA 57.661 39.130 0.00 0.00 34.04 2.29
3162 4649 4.308899 ACAGTTCGCTCCTGATATGTAC 57.691 45.455 0.00 0.00 34.04 2.90
3163 4650 3.954904 ACAGTTCGCTCCTGATATGTACT 59.045 43.478 0.00 0.00 34.04 2.73
3164 4651 4.036971 ACAGTTCGCTCCTGATATGTACTC 59.963 45.833 0.00 0.00 34.04 2.59
3165 4652 4.277174 CAGTTCGCTCCTGATATGTACTCT 59.723 45.833 0.00 0.00 31.38 3.24
3166 4653 4.277174 AGTTCGCTCCTGATATGTACTCTG 59.723 45.833 0.00 0.00 0.00 3.35
3167 4654 3.821748 TCGCTCCTGATATGTACTCTGT 58.178 45.455 0.00 0.00 0.00 3.41
3168 4655 4.969484 TCGCTCCTGATATGTACTCTGTA 58.031 43.478 0.00 0.00 0.00 2.74
3169 4656 4.998033 TCGCTCCTGATATGTACTCTGTAG 59.002 45.833 0.00 0.00 0.00 2.74
3170 4657 4.757657 CGCTCCTGATATGTACTCTGTAGT 59.242 45.833 0.00 0.00 39.91 2.73
3171 4658 5.932883 CGCTCCTGATATGTACTCTGTAGTA 59.067 44.000 0.00 0.00 37.15 1.82
3172 4659 6.427242 CGCTCCTGATATGTACTCTGTAGTAA 59.573 42.308 0.00 0.00 39.90 2.24
3173 4660 7.041303 CGCTCCTGATATGTACTCTGTAGTAAA 60.041 40.741 0.00 0.00 39.90 2.01
3174 4661 8.630917 GCTCCTGATATGTACTCTGTAGTAAAA 58.369 37.037 0.00 0.00 39.90 1.52
3441 4930 2.434761 GAACTCAAATCGAATGCAGCG 58.565 47.619 5.48 5.48 0.00 5.18
3492 4981 3.568538 CTTCTGCCATAACACAACAAGC 58.431 45.455 0.00 0.00 0.00 4.01
3573 5062 8.861086 TGATATTGTAGTGGAGAAGGAAGATAC 58.139 37.037 0.00 0.00 0.00 2.24
3633 5122 7.094205 GGGCTATTTGTATGCTATATGTGCTTT 60.094 37.037 4.57 0.00 0.00 3.51
3879 6963 2.558359 GCTGCATACCCTTTTGAACTGT 59.442 45.455 0.00 0.00 0.00 3.55
4028 7112 1.209747 GGTTCTCGCCCCTACATTTCT 59.790 52.381 0.00 0.00 0.00 2.52
4034 7118 2.238646 TCGCCCCTACATTTCTCATGTT 59.761 45.455 0.00 0.00 33.76 2.71
4203 7289 2.507484 CCACAATGGCAAGAAGACTGA 58.493 47.619 0.00 0.00 0.00 3.41
4537 7623 6.107901 AGAGAGAGTGTTGTATGCTCTTTT 57.892 37.500 0.00 0.00 39.43 2.27
4592 7679 4.894784 TCTTACTTGCTTTCGAAGTGGAT 58.105 39.130 0.00 0.00 35.30 3.41
5044 8135 9.897744 ACATGTGTACATCTTTCTTTAAATGTG 57.102 29.630 0.00 0.00 33.61 3.21
5183 8274 4.220382 TCAAAATGTTGGCCTTGATTCGAT 59.780 37.500 3.32 0.00 35.29 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 2.203480 GCAAGAGCACCCCCAACA 60.203 61.111 0.00 0.00 41.58 3.33
105 106 9.167311 GGTACATTTAGAAGATCTTGACACATT 57.833 33.333 14.00 0.00 0.00 2.71
327 342 1.271163 GGATCACACGGTTTGGAAGGA 60.271 52.381 0.00 0.00 0.00 3.36
766 835 4.080863 GGTTATGGTCTGAATGGACTGAGT 60.081 45.833 0.00 0.00 36.55 3.41
770 839 4.927267 TTGGTTATGGTCTGAATGGACT 57.073 40.909 0.00 0.00 36.55 3.85
970 1039 7.090808 GGTATACTTCATCACATCGCTCATTA 58.909 38.462 2.25 0.00 0.00 1.90
1039 1108 1.401199 GGGAAGAGAACGAGTCGTAGG 59.599 57.143 20.23 0.00 39.99 3.18
1080 1149 2.529632 GGGCAATGGTTTCTCTTCCTT 58.470 47.619 0.00 0.00 0.00 3.36
1329 1399 1.750780 GGCCTAGCTGCTGGGAAAC 60.751 63.158 32.97 18.70 33.74 2.78
1407 1478 2.791383 TGACTGCATTTTGAAACCGG 57.209 45.000 0.00 0.00 0.00 5.28
1463 1535 9.905713 ATAGATATACCAAGAGTTTTGCAAGAA 57.094 29.630 0.00 0.00 0.00 2.52
1679 1767 3.737559 AATACCCTCATTTGTGGAGCA 57.262 42.857 0.28 0.00 0.00 4.26
1688 1776 5.640147 TCTGGTGACAAAAATACCCTCATT 58.360 37.500 0.00 0.00 42.06 2.57
1777 1865 4.367023 GAGCGGTGGTACGGTGCA 62.367 66.667 0.00 0.00 45.44 4.57
1783 1871 4.139234 GGACGGGAGCGGTGGTAC 62.139 72.222 0.00 0.00 0.00 3.34
1846 1963 3.766691 GGCGGCTAGGGTTCGTGA 61.767 66.667 0.00 0.00 0.00 4.35
1884 2011 4.708968 CTAGATCGGCCGCGGCTC 62.709 72.222 45.23 35.05 41.60 4.70
2030 2206 3.414700 GTCAAGGTCACGCCGCTG 61.415 66.667 0.00 0.00 43.70 5.18
2031 2207 4.681978 GGTCAAGGTCACGCCGCT 62.682 66.667 0.00 0.00 43.70 5.52
2032 2208 4.681978 AGGTCAAGGTCACGCCGC 62.682 66.667 0.00 0.00 43.70 6.53
2033 2209 2.432628 GAGGTCAAGGTCACGCCG 60.433 66.667 0.00 0.00 43.70 6.46
2034 2210 1.079750 GAGAGGTCAAGGTCACGCC 60.080 63.158 0.00 0.00 37.58 5.68
2089 3089 1.676678 CTGCTAGGTTGGGCGAGCTA 61.677 60.000 0.00 0.00 35.89 3.32
2103 3103 0.250234 GATGGTGGAGTGTGCTGCTA 59.750 55.000 0.00 0.00 33.91 3.49
2121 3123 4.964897 AGAGAGAGAGAGAGAGAGATGTGA 59.035 45.833 0.00 0.00 0.00 3.58
2200 3246 5.155905 TCTTCTACTTCCTTTCCACCTCTT 58.844 41.667 0.00 0.00 0.00 2.85
2217 3263 0.609957 TCGAACGGCACCCTCTTCTA 60.610 55.000 0.00 0.00 0.00 2.10
2467 3574 0.898320 GGACTGGCAGAACTAGAGCA 59.102 55.000 23.66 0.00 0.00 4.26
2548 3655 7.872163 TTTGCAGAAATTAAGTGTAGCAATG 57.128 32.000 9.06 0.00 40.00 2.82
2708 3815 3.181462 ACATCAGTCACACTGTCACACAT 60.181 43.478 3.64 0.00 46.03 3.21
2905 4317 4.098914 ACAGGAATTGGAACTGTGCTAA 57.901 40.909 0.00 0.00 43.29 3.09
2976 4388 4.457603 ACAGCACACTCAACAAACAAGTTA 59.542 37.500 0.00 0.00 0.00 2.24
3024 4436 1.250476 GCACGAAACTATGCAAAGCG 58.750 50.000 0.00 0.00 41.65 4.68
3093 4505 6.902771 ACATATCAGGAGCGAACTATTAGT 57.097 37.500 0.00 0.00 0.00 2.24
3132 4619 5.757886 TCAGGAGCGAACTGTTTTATTTTG 58.242 37.500 0.00 0.00 37.25 2.44
3133 4620 6.575162 ATCAGGAGCGAACTGTTTTATTTT 57.425 33.333 0.00 0.00 37.25 1.82
3134 4621 7.336931 ACATATCAGGAGCGAACTGTTTTATTT 59.663 33.333 0.00 0.00 37.25 1.40
3135 4622 6.823689 ACATATCAGGAGCGAACTGTTTTATT 59.176 34.615 0.00 0.00 37.25 1.40
3136 4623 6.349300 ACATATCAGGAGCGAACTGTTTTAT 58.651 36.000 0.00 1.23 37.25 1.40
3137 4624 5.730550 ACATATCAGGAGCGAACTGTTTTA 58.269 37.500 0.00 0.00 37.25 1.52
3138 4625 4.579869 ACATATCAGGAGCGAACTGTTTT 58.420 39.130 0.00 0.00 37.25 2.43
3139 4626 4.207891 ACATATCAGGAGCGAACTGTTT 57.792 40.909 0.00 0.00 37.25 2.83
3140 4627 3.895232 ACATATCAGGAGCGAACTGTT 57.105 42.857 0.00 0.00 37.25 3.16
3141 4628 3.954904 AGTACATATCAGGAGCGAACTGT 59.045 43.478 0.00 0.00 37.25 3.55
3142 4629 4.277174 AGAGTACATATCAGGAGCGAACTG 59.723 45.833 0.00 0.00 37.30 3.16
3143 4630 4.277174 CAGAGTACATATCAGGAGCGAACT 59.723 45.833 0.00 0.00 0.00 3.01
3144 4631 4.036971 ACAGAGTACATATCAGGAGCGAAC 59.963 45.833 0.00 0.00 0.00 3.95
3145 4632 4.207955 ACAGAGTACATATCAGGAGCGAA 58.792 43.478 0.00 0.00 0.00 4.70
3146 4633 3.821748 ACAGAGTACATATCAGGAGCGA 58.178 45.455 0.00 0.00 0.00 4.93
3147 4634 4.757657 ACTACAGAGTACATATCAGGAGCG 59.242 45.833 0.00 0.00 32.65 5.03
3148 4635 7.747155 TTACTACAGAGTACATATCAGGAGC 57.253 40.000 0.00 0.00 37.91 4.70
3192 4679 9.838339 CCTAGAATACAATTACAAATCAGGAGT 57.162 33.333 0.00 0.00 0.00 3.85
3441 4930 3.448686 CCATCGGTGATGACACTACTTC 58.551 50.000 8.32 0.00 42.09 3.01
3573 5062 7.646130 TCAAAAACAAAAGTAGAATTAGCACCG 59.354 33.333 0.00 0.00 0.00 4.94
3633 5122 9.162764 GTATTTCCAGAATTAGTCAAAGCACTA 57.837 33.333 0.00 0.00 0.00 2.74
3879 6963 6.095440 GCTCCTAAAGATTGCAATCCAAGTTA 59.905 38.462 31.05 22.08 36.76 2.24
4028 7112 4.661222 TCCTTACCAAAGCATGAACATGA 58.339 39.130 17.40 0.00 41.20 3.07
4034 7118 4.471025 TGAGAGATCCTTACCAAAGCATGA 59.529 41.667 0.00 0.00 0.00 3.07
4203 7289 5.495640 CCTTCTTAACTGGCTCAGAGAAAT 58.504 41.667 0.00 0.00 35.18 2.17
4315 7401 5.541868 ACCCATCTCTATCAAATCTGTCGAT 59.458 40.000 0.00 0.00 0.00 3.59
5044 8135 5.220931 CCATAGCTTTTTACATGTCAGCCTC 60.221 44.000 0.00 0.00 0.00 4.70
5183 8274 4.164221 ACCTGTTGAACTTCTTCTTGGAGA 59.836 41.667 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.