Multiple sequence alignment - TraesCS3B01G351800

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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 TraesCS3B01G351800 chr3B 100.000 3184 0 0 1 3184 561589530 561592713 0.000000e+00 5880.0
1 TraesCS3B01G351800 chr3B 90.894 615 31 10 2590 3184 561840316 561840925 0.000000e+00 802.0
2 TraesCS3B01G351800 chr3B 93.617 188 12 0 2071 2258 561695142 561695329 6.720000e-72 281.0
3 TraesCS3B01G351800 chr3B 90.210 143 14 0 3040 3182 561039106 561038964 1.510000e-43 187.0
4 TraesCS3B01G351800 chr3B 89.404 151 13 1 3035 3182 561044761 561044611 1.510000e-43 187.0
5 TraesCS3B01G351800 chr3B 100.000 33 0 0 1 33 561571616 561571648 9.540000e-06 62.1
6 TraesCS3B01G351800 chr3A 93.505 2371 113 22 33 2373 556357195 556354836 0.000000e+00 3487.0
7 TraesCS3B01G351800 chr3A 85.016 634 46 19 2590 3182 556341132 556340507 1.630000e-167 599.0
8 TraesCS3B01G351800 chr3A 86.458 576 38 17 2629 3181 556354400 556353842 2.110000e-166 595.0
9 TraesCS3B01G351800 chr3A 78.523 447 46 31 2770 3182 556261163 556260733 6.820000e-62 248.0
10 TraesCS3B01G351800 chr3A 86.709 158 18 1 3028 3182 556678410 556678567 4.220000e-39 172.0
11 TraesCS3B01G351800 chr3A 82.114 123 12 3 2469 2584 556341326 556341207 2.610000e-16 97.1
12 TraesCS3B01G351800 chr3D 93.480 1365 61 11 904 2258 429632631 429633977 0.000000e+00 2002.0
13 TraesCS3B01G351800 chr3D 91.388 569 31 11 2630 3182 429636845 429637411 0.000000e+00 763.0
14 TraesCS3B01G351800 chr3D 79.455 550 49 40 2670 3182 429647108 429647630 6.580000e-87 331.0
15 TraesCS3B01G351800 chr3D 87.919 149 15 1 3033 3181 428994403 428994258 4.220000e-39 172.0
16 TraesCS3B01G351800 chr7B 87.281 857 101 6 53 904 580663278 580662425 0.000000e+00 972.0
17 TraesCS3B01G351800 chr1B 86.521 868 105 8 43 904 328644177 328645038 0.000000e+00 944.0
18 TraesCS3B01G351800 chr1B 100.000 32 0 0 1 32 60554261 60554230 3.430000e-05 60.2
19 TraesCS3B01G351800 chr2D 86.490 866 104 10 43 902 551154003 551154861 0.000000e+00 939.0
20 TraesCS3B01G351800 chr2D 85.948 854 108 9 34 881 493073673 493074520 0.000000e+00 902.0
21 TraesCS3B01G351800 chr5A 85.436 872 121 4 33 900 84148416 84147547 0.000000e+00 902.0
22 TraesCS3B01G351800 chr1D 85.402 870 121 4 33 899 484432362 484433228 0.000000e+00 898.0
23 TraesCS3B01G351800 chr7D 85.240 874 119 7 33 901 621300935 621300067 0.000000e+00 891.0
24 TraesCS3B01G351800 chr1A 85.240 874 115 9 33 902 342866311 342865448 0.000000e+00 887.0


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 TraesCS3B01G351800 chr3B 561589530 561592713 3183 False 5880.00 5880 100.0000 1 3184 1 chr3B.!!$F2 3183
1 TraesCS3B01G351800 chr3B 561840316 561840925 609 False 802.00 802 90.8940 2590 3184 1 chr3B.!!$F4 594
2 TraesCS3B01G351800 chr3A 556353842 556357195 3353 True 2041.00 3487 89.9815 33 3181 2 chr3A.!!$R3 3148
3 TraesCS3B01G351800 chr3A 556340507 556341326 819 True 348.05 599 83.5650 2469 3182 2 chr3A.!!$R2 713
4 TraesCS3B01G351800 chr3D 429632631 429637411 4780 False 1382.50 2002 92.4340 904 3182 2 chr3D.!!$F2 2278
5 TraesCS3B01G351800 chr3D 429647108 429647630 522 False 331.00 331 79.4550 2670 3182 1 chr3D.!!$F1 512
6 TraesCS3B01G351800 chr7B 580662425 580663278 853 True 972.00 972 87.2810 53 904 1 chr7B.!!$R1 851
7 TraesCS3B01G351800 chr1B 328644177 328645038 861 False 944.00 944 86.5210 43 904 1 chr1B.!!$F1 861
8 TraesCS3B01G351800 chr2D 551154003 551154861 858 False 939.00 939 86.4900 43 902 1 chr2D.!!$F2 859
9 TraesCS3B01G351800 chr2D 493073673 493074520 847 False 902.00 902 85.9480 34 881 1 chr2D.!!$F1 847
10 TraesCS3B01G351800 chr5A 84147547 84148416 869 True 902.00 902 85.4360 33 900 1 chr5A.!!$R1 867
11 TraesCS3B01G351800 chr1D 484432362 484433228 866 False 898.00 898 85.4020 33 899 1 chr1D.!!$F1 866
12 TraesCS3B01G351800 chr7D 621300067 621300935 868 True 891.00 891 85.2400 33 901 1 chr7D.!!$R1 868
13 TraesCS3B01G351800 chr1A 342865448 342866311 863 True 887.00 887 85.2400 33 902 1 chr1A.!!$R1 869

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
474 478 0.179029 GGTGGTACTTGGCGGCATAT 60.179 55.0 14.32 6.61 0.00 1.78 F
857 866 0.541296 AAAGAAGGCTGCATGCACCT 60.541 50.0 26.48 26.48 45.15 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1635 1652 0.253044 GGAGCCATGTAGCCACTGAA 59.747 55.0 0.00 0.0 0.0 3.02 R
2726 5426 0.173255 GTGATTTTGACCGGGCATGG 59.827 55.0 13.08 0.0 0.0 3.66 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
29 30 8.824756 ACAGAAAGAGGACTATACACATCTAA 57.175 34.615 0.00 0.00 0.00 2.10
30 31 8.688151 ACAGAAAGAGGACTATACACATCTAAC 58.312 37.037 0.00 0.00 0.00 2.34
31 32 8.687242 CAGAAAGAGGACTATACACATCTAACA 58.313 37.037 0.00 0.00 0.00 2.41
40 41 5.939764 ATACACATCTAACAGGCTTGAGA 57.060 39.130 1.40 0.00 0.00 3.27
41 42 4.833478 ACACATCTAACAGGCTTGAGAT 57.167 40.909 1.40 0.00 0.00 2.75
109 110 0.252197 GGGAGACATAGTTGCCGGTT 59.748 55.000 1.90 0.00 0.00 4.44
149 150 4.704833 ATGGCGGCGTTCTGTGCT 62.705 61.111 9.37 0.00 0.00 4.40
446 450 5.126869 CAGATCTTCCAGAGACTTCAAGCTA 59.873 44.000 0.00 0.00 37.17 3.32
473 477 1.222387 GGTGGTACTTGGCGGCATA 59.778 57.895 14.32 0.00 0.00 3.14
474 478 0.179029 GGTGGTACTTGGCGGCATAT 60.179 55.000 14.32 6.61 0.00 1.78
599 604 4.002316 GGCAAGGATAATGCAGATCTCTC 58.998 47.826 10.35 0.00 45.60 3.20
662 669 6.270156 TCTTAACCGTATGTGTGATGTACA 57.730 37.500 0.00 0.00 36.82 2.90
765 772 4.128925 GTGAGAGCACTCCACATTATCA 57.871 45.455 8.77 0.00 41.84 2.15
769 777 4.511527 AGAGCACTCCACATTATCAAGTG 58.488 43.478 0.00 0.00 40.19 3.16
832 841 8.641498 ATTTCTTGTCAGACCTTGTTGAATAT 57.359 30.769 0.00 0.00 0.00 1.28
855 864 3.515330 AATAAAGAAGGCTGCATGCAC 57.485 42.857 18.46 13.69 45.15 4.57
857 866 0.541296 AAAGAAGGCTGCATGCACCT 60.541 50.000 26.48 26.48 45.15 4.00
1027 1041 2.493278 CAGGGCAACTTACCAAATGGAG 59.507 50.000 6.42 0.00 38.94 3.86
1040 1054 3.508762 CAAATGGAGAAGATGTTGCTGC 58.491 45.455 0.00 0.00 0.00 5.25
1179 1193 7.270779 ACGGGGAAGAAATGTTACTAATCTAC 58.729 38.462 0.00 0.00 0.00 2.59
1405 1420 0.976641 TCTCCACAAGCATTCTCGGT 59.023 50.000 0.00 0.00 0.00 4.69
1444 1459 3.181466 GGACCTGAAACCAAGCAACATTT 60.181 43.478 0.00 0.00 0.00 2.32
1447 1462 4.190772 CCTGAAACCAAGCAACATTTTGT 58.809 39.130 0.00 0.00 34.90 2.83
1449 1464 5.814705 CCTGAAACCAAGCAACATTTTGTTA 59.185 36.000 0.00 0.00 38.77 2.41
1553 1568 5.979288 AGAGTCGTTGGAACATAGTAAGT 57.021 39.130 0.00 0.00 39.30 2.24
1583 1598 9.952030 TCTATTGGTATTTGACATGTAAAGTGA 57.048 29.630 0.00 0.00 0.00 3.41
1588 1603 9.295825 TGGTATTTGACATGTAAAGTGAAAGAT 57.704 29.630 0.00 0.00 0.00 2.40
1590 1605 9.478019 GTATTTGACATGTAAAGTGAAAGATCG 57.522 33.333 0.00 0.00 0.00 3.69
1591 1606 5.530519 TGACATGTAAAGTGAAAGATCGC 57.469 39.130 0.00 0.00 36.28 4.58
1593 1608 6.394809 TGACATGTAAAGTGAAAGATCGCTA 58.605 36.000 0.00 0.00 45.53 4.26
1594 1609 7.041721 TGACATGTAAAGTGAAAGATCGCTAT 58.958 34.615 0.00 0.00 45.53 2.97
1595 1610 8.194769 TGACATGTAAAGTGAAAGATCGCTATA 58.805 33.333 0.00 0.00 45.53 1.31
1596 1611 8.354011 ACATGTAAAGTGAAAGATCGCTATAC 57.646 34.615 0.00 0.00 45.53 1.47
1597 1612 7.979537 ACATGTAAAGTGAAAGATCGCTATACA 59.020 33.333 0.00 0.00 45.53 2.29
1598 1613 7.987268 TGTAAAGTGAAAGATCGCTATACAG 57.013 36.000 0.00 0.00 45.53 2.74
1599 1614 7.768240 TGTAAAGTGAAAGATCGCTATACAGA 58.232 34.615 0.00 0.00 45.53 3.41
1652 1669 2.584835 TTTTCAGTGGCTACATGGCT 57.415 45.000 2.02 0.00 42.34 4.75
1655 1672 0.618680 TCAGTGGCTACATGGCTCCT 60.619 55.000 2.02 0.00 42.34 3.69
1713 1730 4.159135 CCGATGTATTTAGCTACGGGGTAT 59.841 45.833 8.43 0.00 36.08 2.73
1730 1747 4.446889 GGGGTATTGCTTCTGGAGATCATT 60.447 45.833 0.00 0.00 0.00 2.57
1801 1818 2.109834 TCCTTGGTCATGTGGGTCAAAT 59.890 45.455 0.00 0.00 0.00 2.32
1818 1835 5.759763 GGTCAAATTTCCAACAAGCTCAAAT 59.240 36.000 0.00 0.00 0.00 2.32
1827 1844 6.680810 TCCAACAAGCTCAAATTGTTCTATG 58.319 36.000 1.29 0.00 45.33 2.23
1833 1850 8.025445 ACAAGCTCAAATTGTTCTATGATTGTC 58.975 33.333 0.00 0.00 37.61 3.18
1846 1863 9.309516 GTTCTATGATTGTCGTACCTGATTTTA 57.690 33.333 0.00 0.00 0.00 1.52
1847 1864 9.878667 TTCTATGATTGTCGTACCTGATTTTAA 57.121 29.630 0.00 0.00 0.00 1.52
1964 1981 4.202441 GTGCATGTCCTGAGAATATGGTT 58.798 43.478 0.00 0.00 0.00 3.67
1989 2006 4.166011 GCATTCACGTCGGCCTGC 62.166 66.667 0.00 0.00 0.00 4.85
2060 2077 9.274065 GTCATTTCCATGATTACTAACGAAAAC 57.726 33.333 0.00 0.00 41.64 2.43
2188 2205 2.628657 GCCTGGATGGTAGGTAGTACTG 59.371 54.545 5.39 0.00 37.64 2.74
2254 2278 4.020307 TGTTCAGGCAACAGAGTATCATGA 60.020 41.667 0.00 0.00 40.29 3.07
2258 2282 7.071069 TCAGGCAACAGAGTATCATGATATT 57.929 36.000 18.18 14.22 37.82 1.28
2344 3775 4.098894 AGTAAGACGGTATTTTCAGGGGA 58.901 43.478 0.00 0.00 0.00 4.81
2346 3777 4.376225 AAGACGGTATTTTCAGGGGAAA 57.624 40.909 0.00 0.00 41.13 3.13
2351 3782 3.190535 CGGTATTTTCAGGGGAAACTGTG 59.809 47.826 0.00 0.00 42.48 3.66
2357 3788 0.890683 CAGGGGAAACTGTGATTGGC 59.109 55.000 0.00 0.00 33.81 4.52
2373 3804 9.537192 CTGTGATTGGCATATTTTGACATATTT 57.463 29.630 0.00 0.00 44.92 1.40
2374 3805 9.887629 TGTGATTGGCATATTTTGACATATTTT 57.112 25.926 0.00 0.00 44.92 1.82
2378 4215 8.945481 TTGGCATATTTTGACATATTTTCAGG 57.055 30.769 0.00 0.00 44.92 3.86
2380 4217 6.930722 GGCATATTTTGACATATTTTCAGGGG 59.069 38.462 0.00 0.00 31.51 4.79
2388 4225 2.806945 TATTTTCAGGGGGAGCTGTG 57.193 50.000 0.00 0.00 0.00 3.66
2394 4231 1.927527 AGGGGGAGCTGTGATTGCT 60.928 57.895 0.00 0.00 44.24 3.91
2395 4232 0.621571 AGGGGGAGCTGTGATTGCTA 60.622 55.000 0.00 0.00 41.30 3.49
2398 4235 2.551071 GGGGGAGCTGTGATTGCTATAC 60.551 54.545 0.00 0.00 41.30 1.47
2401 4238 2.805099 GGAGCTGTGATTGCTATACTGC 59.195 50.000 0.00 0.00 41.30 4.40
2402 4239 2.474359 GAGCTGTGATTGCTATACTGCG 59.526 50.000 0.00 0.00 41.99 5.18
2404 4241 2.609459 GCTGTGATTGCTATACTGCGTT 59.391 45.455 0.00 0.00 35.36 4.84
2405 4242 3.302740 GCTGTGATTGCTATACTGCGTTC 60.303 47.826 0.00 0.00 35.36 3.95
2406 4243 2.857748 TGTGATTGCTATACTGCGTTCG 59.142 45.455 0.00 0.00 35.36 3.95
2407 4244 2.858344 GTGATTGCTATACTGCGTTCGT 59.142 45.455 0.00 0.00 35.36 3.85
2408 4245 2.857748 TGATTGCTATACTGCGTTCGTG 59.142 45.455 0.00 0.00 35.36 4.35
2409 4246 0.996462 TTGCTATACTGCGTTCGTGC 59.004 50.000 0.00 0.00 35.36 5.34
2410 4247 0.804544 TGCTATACTGCGTTCGTGCC 60.805 55.000 0.00 0.00 35.36 5.01
2412 4249 0.921347 CTATACTGCGTTCGTGCCAC 59.079 55.000 0.00 0.00 0.00 5.01
2426 4563 0.881159 TGCCACCTTTTCCGTACACG 60.881 55.000 0.00 0.00 39.44 4.49
2446 4583 1.346365 GCTGCGTTCTCGTGTGATTA 58.654 50.000 0.00 0.00 39.49 1.75
2447 4584 1.059264 GCTGCGTTCTCGTGTGATTAC 59.941 52.381 0.00 0.00 39.49 1.89
2449 4586 2.324860 TGCGTTCTCGTGTGATTACAG 58.675 47.619 0.00 0.00 37.52 2.74
2481 5090 9.832445 TTCTTTTTCTATCACTGAACTACACTT 57.168 29.630 0.00 0.00 0.00 3.16
2504 5113 2.603412 CCGCACAGATCGAGAGTGATAC 60.603 54.545 16.05 1.43 35.33 2.24
2505 5114 2.289274 CGCACAGATCGAGAGTGATACT 59.711 50.000 16.05 0.00 35.33 2.12
2506 5115 3.626977 GCACAGATCGAGAGTGATACTG 58.373 50.000 16.05 0.00 35.33 2.74
2532 5141 2.228822 ACAATCGCATTTCACACCTTCC 59.771 45.455 0.00 0.00 0.00 3.46
2542 5151 6.587608 GCATTTCACACCTTCCTTTTCTTATG 59.412 38.462 0.00 0.00 0.00 1.90
2543 5152 7.661040 CATTTCACACCTTCCTTTTCTTATGT 58.339 34.615 0.00 0.00 0.00 2.29
2547 5163 8.934023 TCACACCTTCCTTTTCTTATGTAAAT 57.066 30.769 0.00 0.00 0.00 1.40
2576 5192 0.721718 GATCTGTGTACAGGTTGCGC 59.278 55.000 11.76 0.00 43.91 6.09
2579 5195 1.568612 CTGTGTACAGGTTGCGCAGG 61.569 60.000 11.31 4.45 40.20 4.85
2621 5311 5.017490 CCTACTGTCCTCTCTCCTTTGTTA 58.983 45.833 0.00 0.00 0.00 2.41
2624 5314 2.561419 TGTCCTCTCTCCTTTGTTACGG 59.439 50.000 0.00 0.00 0.00 4.02
2639 5329 2.288961 TACGGTCGATTCCTTCTTGC 57.711 50.000 0.00 0.00 0.00 4.01
2753 5454 1.442017 GTCAAAATCACACGGCGGC 60.442 57.895 13.24 0.00 0.00 6.53
2835 5540 3.551846 CCGGCCTGTAAATGTTAGGAAT 58.448 45.455 0.00 0.00 33.33 3.01
2868 5577 1.662629 CCGTTCTCAGCATAAGCAGTG 59.337 52.381 0.00 0.00 45.49 3.66
2899 5608 3.379445 GGACGCCGTCTCCAAGGA 61.379 66.667 17.76 0.00 32.47 3.36
3142 5898 3.554692 GCCGACGCCAAGATCACG 61.555 66.667 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.916360 TTAGATGTGTATAGTCCTCTTTCTGTA 57.084 33.333 0.00 0.00 0.00 2.74
4 5 8.688151 GTTAGATGTGTATAGTCCTCTTTCTGT 58.312 37.037 0.00 0.00 0.00 3.41
5 6 8.687242 TGTTAGATGTGTATAGTCCTCTTTCTG 58.313 37.037 0.00 0.00 0.00 3.02
6 7 8.824756 TGTTAGATGTGTATAGTCCTCTTTCT 57.175 34.615 0.00 0.00 0.00 2.52
7 8 8.138712 CCTGTTAGATGTGTATAGTCCTCTTTC 58.861 40.741 0.00 0.00 0.00 2.62
8 9 7.418025 GCCTGTTAGATGTGTATAGTCCTCTTT 60.418 40.741 0.00 0.00 0.00 2.52
9 10 6.041069 GCCTGTTAGATGTGTATAGTCCTCTT 59.959 42.308 0.00 0.00 0.00 2.85
10 11 5.536916 GCCTGTTAGATGTGTATAGTCCTCT 59.463 44.000 0.00 0.00 0.00 3.69
11 12 5.536916 AGCCTGTTAGATGTGTATAGTCCTC 59.463 44.000 0.00 0.00 0.00 3.71
12 13 5.459505 AGCCTGTTAGATGTGTATAGTCCT 58.540 41.667 0.00 0.00 0.00 3.85
13 14 5.793030 AGCCTGTTAGATGTGTATAGTCC 57.207 43.478 0.00 0.00 0.00 3.85
14 15 6.806751 TCAAGCCTGTTAGATGTGTATAGTC 58.193 40.000 0.00 0.00 0.00 2.59
15 16 6.607600 TCTCAAGCCTGTTAGATGTGTATAGT 59.392 38.462 0.00 0.00 0.00 2.12
16 17 7.043961 TCTCAAGCCTGTTAGATGTGTATAG 57.956 40.000 0.00 0.00 0.00 1.31
17 18 7.603180 ATCTCAAGCCTGTTAGATGTGTATA 57.397 36.000 0.00 0.00 0.00 1.47
18 19 5.939764 TCTCAAGCCTGTTAGATGTGTAT 57.060 39.130 0.00 0.00 0.00 2.29
19 20 5.939764 ATCTCAAGCCTGTTAGATGTGTA 57.060 39.130 0.00 0.00 0.00 2.90
20 21 4.833478 ATCTCAAGCCTGTTAGATGTGT 57.167 40.909 0.00 0.00 0.00 3.72
21 22 4.334759 CCAATCTCAAGCCTGTTAGATGTG 59.665 45.833 0.00 0.00 0.00 3.21
22 23 4.521146 CCAATCTCAAGCCTGTTAGATGT 58.479 43.478 0.00 0.00 0.00 3.06
23 24 3.881688 CCCAATCTCAAGCCTGTTAGATG 59.118 47.826 0.00 0.00 0.00 2.90
24 25 3.525199 ACCCAATCTCAAGCCTGTTAGAT 59.475 43.478 0.00 0.00 0.00 1.98
25 26 2.912956 ACCCAATCTCAAGCCTGTTAGA 59.087 45.455 0.00 0.00 0.00 2.10
26 27 3.012518 CACCCAATCTCAAGCCTGTTAG 58.987 50.000 0.00 0.00 0.00 2.34
27 28 2.375174 ACACCCAATCTCAAGCCTGTTA 59.625 45.455 0.00 0.00 0.00 2.41
28 29 1.145738 ACACCCAATCTCAAGCCTGTT 59.854 47.619 0.00 0.00 0.00 3.16
29 30 0.773644 ACACCCAATCTCAAGCCTGT 59.226 50.000 0.00 0.00 0.00 4.00
30 31 1.815003 GAACACCCAATCTCAAGCCTG 59.185 52.381 0.00 0.00 0.00 4.85
31 32 1.611673 CGAACACCCAATCTCAAGCCT 60.612 52.381 0.00 0.00 0.00 4.58
40 41 0.178068 CCGAGATCCGAACACCCAAT 59.822 55.000 5.32 0.00 41.76 3.16
41 42 1.594833 CCGAGATCCGAACACCCAA 59.405 57.895 5.32 0.00 41.76 4.12
109 110 4.211986 GCCATCGGCTCGGTTTTA 57.788 55.556 0.00 0.00 46.69 1.52
411 415 1.534175 GGAAGATCTGTCGTGCGTAGG 60.534 57.143 0.00 0.00 0.00 3.18
446 450 0.036388 CAAGTACCACCAGCCGACAT 60.036 55.000 0.00 0.00 0.00 3.06
473 477 1.596934 CGGTACACCTCAGCACCAT 59.403 57.895 0.00 0.00 0.00 3.55
474 478 2.579657 CCGGTACACCTCAGCACCA 61.580 63.158 0.00 0.00 0.00 4.17
599 604 0.179089 CGCTGACCCATCTTCAGGAG 60.179 60.000 1.76 0.00 40.84 3.69
626 631 2.024414 GGTTAAGAAGGCGCCATCATT 58.976 47.619 31.30 22.91 0.00 2.57
662 669 4.546829 TCCGGTGTAGCAAATCTAAAGT 57.453 40.909 0.00 0.00 0.00 2.66
765 772 2.116238 ACCACTCACACCTACACACTT 58.884 47.619 0.00 0.00 0.00 3.16
769 777 0.602905 GCCACCACTCACACCTACAC 60.603 60.000 0.00 0.00 0.00 2.90
832 841 5.410067 GTGCATGCAGCCTTCTTTATTAAA 58.590 37.500 23.41 0.00 44.83 1.52
855 864 0.604780 CCCGCCTCTGCATCAATAGG 60.605 60.000 0.00 0.00 37.32 2.57
857 866 1.451504 CCCCGCCTCTGCATCAATA 59.548 57.895 0.00 0.00 37.32 1.90
972 986 6.203530 TGTCAGATTTTCAACAGTCAGACATC 59.796 38.462 2.66 0.00 33.87 3.06
1027 1041 4.502962 AGTCTCTTAGCAGCAACATCTTC 58.497 43.478 0.00 0.00 0.00 2.87
1040 1054 3.928992 TGAATTCGCTGCAAGTCTCTTAG 59.071 43.478 0.00 0.00 35.30 2.18
1179 1193 5.235305 AGCTTTTGTTTGGCATATACTCG 57.765 39.130 0.00 0.00 0.00 4.18
1405 1420 5.250543 TCAGGTCCCTGTGAATAATTCTCAA 59.749 40.000 12.88 0.00 43.96 3.02
1444 1459 6.620877 AGGGTTCATATCAGTGTCTAACAA 57.379 37.500 0.00 0.00 0.00 2.83
1447 1462 8.783660 ATCTTAGGGTTCATATCAGTGTCTAA 57.216 34.615 0.00 0.00 0.00 2.10
1449 1464 7.072562 AGATCTTAGGGTTCATATCAGTGTCT 58.927 38.462 0.00 0.00 0.00 3.41
1570 1585 5.786401 AGCGATCTTTCACTTTACATGTC 57.214 39.130 0.00 0.00 0.00 3.06
1583 1598 7.047891 TGTCCATTTTCTGTATAGCGATCTTT 58.952 34.615 0.00 0.00 0.00 2.52
1588 1603 4.982295 CGATGTCCATTTTCTGTATAGCGA 59.018 41.667 0.00 0.00 0.00 4.93
1590 1605 6.844696 TTCGATGTCCATTTTCTGTATAGC 57.155 37.500 0.00 0.00 0.00 2.97
1593 1608 9.396022 AGTAAATTCGATGTCCATTTTCTGTAT 57.604 29.630 0.00 0.00 0.00 2.29
1594 1609 8.786826 AGTAAATTCGATGTCCATTTTCTGTA 57.213 30.769 0.00 0.00 0.00 2.74
1595 1610 7.687941 AGTAAATTCGATGTCCATTTTCTGT 57.312 32.000 0.00 0.00 0.00 3.41
1596 1611 9.098355 TCTAGTAAATTCGATGTCCATTTTCTG 57.902 33.333 8.20 1.84 0.00 3.02
1597 1612 9.838339 ATCTAGTAAATTCGATGTCCATTTTCT 57.162 29.630 0.00 1.76 0.00 2.52
1635 1652 0.253044 GGAGCCATGTAGCCACTGAA 59.747 55.000 0.00 0.00 0.00 3.02
1636 1653 0.618680 AGGAGCCATGTAGCCACTGA 60.619 55.000 0.00 0.00 0.00 3.41
1713 1730 4.471025 TCCACTAATGATCTCCAGAAGCAA 59.529 41.667 0.00 0.00 0.00 3.91
1730 1747 2.235155 TGCGGCATTTCTTAGTCCACTA 59.765 45.455 0.00 0.00 0.00 2.74
1790 1807 3.431486 GCTTGTTGGAAATTTGACCCACA 60.431 43.478 0.00 0.00 31.54 4.17
1801 1818 5.976458 AGAACAATTTGAGCTTGTTGGAAA 58.024 33.333 5.48 0.00 44.56 3.13
1818 1835 6.275494 TCAGGTACGACAATCATAGAACAA 57.725 37.500 0.00 0.00 0.00 2.83
1852 1869 9.561069 AAGTTCAGTTGTAGACATCAAATTACT 57.439 29.630 0.00 0.00 0.00 2.24
1867 1884 1.473258 TGCCTGCAAAGTTCAGTTGT 58.527 45.000 0.00 0.00 0.00 3.32
1964 1981 1.533129 CCGACGTGAATGCATCGTAGA 60.533 52.381 17.15 0.00 45.75 2.59
1989 2006 0.445436 GCATTCTCCTGAACGCACAG 59.555 55.000 2.97 2.97 40.62 3.66
2188 2205 9.982651 TGTAACACTCTTTATCTAATGGATAGC 57.017 33.333 0.00 0.00 38.07 2.97
2254 2278 8.806146 ACTTCAAAAGTGCTGTCCAATTAATAT 58.194 29.630 0.00 0.00 41.01 1.28
2344 3775 6.757237 TGTCAAAATATGCCAATCACAGTTT 58.243 32.000 0.00 0.00 0.00 2.66
2346 3777 5.981088 TGTCAAAATATGCCAATCACAGT 57.019 34.783 0.00 0.00 0.00 3.55
2357 3788 8.248904 TCCCCCTGAAAATATGTCAAAATATG 57.751 34.615 0.00 0.00 0.00 1.78
2373 3804 0.329261 CAATCACAGCTCCCCCTGAA 59.671 55.000 0.00 0.00 36.67 3.02
2374 3805 1.993653 CAATCACAGCTCCCCCTGA 59.006 57.895 0.00 0.00 36.67 3.86
2375 3806 1.751927 GCAATCACAGCTCCCCCTG 60.752 63.158 0.00 0.00 38.78 4.45
2378 4215 2.370189 AGTATAGCAATCACAGCTCCCC 59.630 50.000 0.00 0.00 42.32 4.81
2380 4217 2.805099 GCAGTATAGCAATCACAGCTCC 59.195 50.000 0.00 0.00 42.32 4.70
2388 4225 2.347661 GCACGAACGCAGTATAGCAATC 60.348 50.000 0.00 0.00 45.00 2.67
2394 4231 0.458889 GGTGGCACGAACGCAGTATA 60.459 55.000 12.17 0.00 45.00 1.47
2395 4232 1.740296 GGTGGCACGAACGCAGTAT 60.740 57.895 12.17 0.00 45.00 2.12
2398 4235 2.058829 AAAAGGTGGCACGAACGCAG 62.059 55.000 12.17 0.00 0.00 5.18
2401 4238 1.281656 GGAAAAGGTGGCACGAACG 59.718 57.895 12.17 0.00 0.00 3.95
2402 4239 1.281656 CGGAAAAGGTGGCACGAAC 59.718 57.895 12.17 0.00 0.00 3.95
2404 4241 0.600782 GTACGGAAAAGGTGGCACGA 60.601 55.000 12.17 0.00 0.00 4.35
2405 4242 0.881159 TGTACGGAAAAGGTGGCACG 60.881 55.000 12.17 0.15 0.00 5.34
2406 4243 0.589708 GTGTACGGAAAAGGTGGCAC 59.410 55.000 9.70 9.70 0.00 5.01
2407 4244 0.881159 CGTGTACGGAAAAGGTGGCA 60.881 55.000 0.00 0.00 35.37 4.92
2408 4245 1.864176 CGTGTACGGAAAAGGTGGC 59.136 57.895 0.00 0.00 35.37 5.01
2426 4563 1.291877 AATCACACGAGAACGCAGCC 61.292 55.000 0.00 0.00 43.96 4.85
2446 4583 9.396022 TCAGTGATAGAAAAAGAAGAAAACTGT 57.604 29.630 0.00 0.00 33.58 3.55
2467 4604 2.729882 GTGCGGTAAGTGTAGTTCAGTG 59.270 50.000 0.00 0.00 0.00 3.66
2481 5090 0.733150 CACTCTCGATCTGTGCGGTA 59.267 55.000 0.00 0.00 0.00 4.02
2504 5113 3.236816 GTGAAATGCGATTGTTGTCCAG 58.763 45.455 0.00 0.00 0.00 3.86
2505 5114 2.620585 TGTGAAATGCGATTGTTGTCCA 59.379 40.909 0.00 0.00 0.00 4.02
2506 5115 2.979813 GTGTGAAATGCGATTGTTGTCC 59.020 45.455 0.00 0.00 0.00 4.02
2547 5163 6.427441 ACCTGTACACAGATCAGAGAGATTA 58.573 40.000 10.96 0.00 46.59 1.75
2579 5195 0.527385 GATCAGAGAGACAGGCACGC 60.527 60.000 0.00 0.00 0.00 5.34
2584 5200 3.882888 GACAGTAGGATCAGAGAGACAGG 59.117 52.174 0.00 0.00 0.00 4.00
2586 5202 3.525609 AGGACAGTAGGATCAGAGAGACA 59.474 47.826 0.00 0.00 0.00 3.41
2587 5203 4.134563 GAGGACAGTAGGATCAGAGAGAC 58.865 52.174 0.00 0.00 0.00 3.36
2588 5204 4.044308 AGAGGACAGTAGGATCAGAGAGA 58.956 47.826 0.00 0.00 0.00 3.10
2621 5311 0.608640 AGCAAGAAGGAATCGACCGT 59.391 50.000 0.00 0.00 34.73 4.83
2624 5314 2.933260 GGAGAAGCAAGAAGGAATCGAC 59.067 50.000 0.00 0.00 0.00 4.20
2639 5329 1.287730 GCGCAGTGACAGTGGAGAAG 61.288 60.000 12.19 0.00 0.00 2.85
2698 5388 1.670811 CACTCACGTTGCTCACCTTTT 59.329 47.619 0.00 0.00 0.00 2.27
2702 5392 1.860676 TTACACTCACGTTGCTCACC 58.139 50.000 0.00 0.00 0.00 4.02
2726 5426 0.173255 GTGATTTTGACCGGGCATGG 59.827 55.000 13.08 0.00 0.00 3.66
2727 5427 0.887247 TGTGATTTTGACCGGGCATG 59.113 50.000 13.08 0.00 0.00 4.06
2753 5454 7.277981 ACTGCTTTGTACTGTAATATTCTTCGG 59.722 37.037 0.00 0.00 0.00 4.30
2835 5540 2.829120 TGAGAACGGTATGGACATGTCA 59.171 45.455 26.47 13.45 0.00 3.58
2868 5577 3.790177 GTCCAATGTACGGGCGAC 58.210 61.111 0.00 0.00 0.00 5.19
2899 5608 1.224592 GTGGAGATTCCGGCCATGT 59.775 57.895 2.24 0.00 40.17 3.21
3135 5891 4.479993 GCAGCTGCCCCGTGATCT 62.480 66.667 28.76 0.00 34.31 2.75


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

AutoCloner maintained by Alex Coulton.