Multiple sequence alignment - TraesCS5D01G324700

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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 TraesCS5D01G324700 chr5D 100.000 5757 0 0 1 5757 416411136 416416892 0.000000e+00 10632.0
1 TraesCS5D01G324700 chr5D 86.254 1033 103 27 2096 3109 529216487 529217499 0.000000e+00 1085.0
2 TraesCS5D01G324700 chr5D 84.654 997 80 35 3732 4673 529218344 529219322 0.000000e+00 926.0
3 TraesCS5D01G324700 chr5D 78.740 508 58 25 1281 1782 529215463 529215926 1.570000e-75 294.0
4 TraesCS5D01G324700 chr5D 79.389 131 17 3 2327 2447 533283991 533283861 3.700000e-12 84.2
5 TraesCS5D01G324700 chr5B 91.276 4562 198 62 1053 5516 503213238 503217697 0.000000e+00 6035.0
6 TraesCS5D01G324700 chr5B 96.366 908 26 4 1 907 503211850 503212751 0.000000e+00 1487.0
7 TraesCS5D01G324700 chr5B 86.447 1033 100 28 2096 3109 667673445 667674456 0.000000e+00 1096.0
8 TraesCS5D01G324700 chr5B 84.453 997 83 31 3732 4673 667675376 667676355 0.000000e+00 917.0
9 TraesCS5D01G324700 chr5B 87.025 316 23 10 3435 3736 667674894 667675205 1.990000e-89 340.0
10 TraesCS5D01G324700 chr5B 85.028 354 27 14 5430 5757 503217657 503218010 2.570000e-88 337.0
11 TraesCS5D01G324700 chr5B 78.486 502 56 31 1281 1774 667672234 667672691 1.220000e-71 281.0
12 TraesCS5D01G324700 chr5B 94.444 90 4 1 957 1046 503212751 503212839 2.800000e-28 137.0
13 TraesCS5D01G324700 chr5B 93.878 49 3 0 2399 2447 673353079 673353031 2.220000e-09 75.0
14 TraesCS5D01G324700 chr5B 93.878 49 3 0 2399 2447 673422910 673422862 2.220000e-09 75.0
15 TraesCS5D01G324700 chr5B 93.878 49 3 0 2399 2447 673452454 673452406 2.220000e-09 75.0
16 TraesCS5D01G324700 chr5A 95.725 1310 33 6 3442 4730 529085722 529087029 0.000000e+00 2087.0
17 TraesCS5D01G324700 chr5A 88.003 1542 103 31 526 2043 529083469 529084952 0.000000e+00 1748.0
18 TraesCS5D01G324700 chr5A 96.234 770 28 1 2266 3034 529084956 529085725 0.000000e+00 1260.0
19 TraesCS5D01G324700 chr5A 81.281 1592 182 51 1751 3302 657379132 657380647 0.000000e+00 1182.0
20 TraesCS5D01G324700 chr5A 83.333 1140 100 45 3461 4552 657380658 657381755 0.000000e+00 970.0
21 TraesCS5D01G324700 chr5A 85.816 564 44 12 4807 5349 529087252 529087800 3.010000e-157 566.0
22 TraesCS5D01G324700 chr5A 92.105 342 27 0 65 406 529083125 529083466 3.120000e-132 483.0
23 TraesCS5D01G324700 chr5A 81.818 319 34 15 1271 1582 657378639 657378940 4.460000e-61 246.0
24 TraesCS5D01G324700 chr5A 81.786 280 20 14 5479 5729 529087968 529088245 7.560000e-49 206.0
25 TraesCS5D01G324700 chr5A 86.861 137 16 1 4934 5068 657382435 657382571 9.990000e-33 152.0
26 TraesCS5D01G324700 chr2B 81.046 459 66 10 2 457 140790966 140790526 4.270000e-91 346.0
27 TraesCS5D01G324700 chr2A 79.464 448 72 11 2 446 88004613 88004183 3.370000e-77 300.0
28 TraesCS5D01G324700 chr4A 77.591 357 63 7 111 457 473947765 473947416 3.520000e-47 200.0
29 TraesCS5D01G324700 chr4D 79.866 149 24 5 660 806 134122678 134122822 2.840000e-18 104.0
30 TraesCS5D01G324700 chr1D 94.118 51 2 1 3527 3577 37516654 37516703 6.190000e-10 76.8
31 TraesCS5D01G324700 chr1D 93.878 49 3 0 3529 3577 37528644 37528692 2.220000e-09 75.0
32 TraesCS5D01G324700 chr1A 94.118 51 2 1 3527 3577 36765343 36765392 6.190000e-10 76.8


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 TraesCS5D01G324700 chr5D 416411136 416416892 5756 False 10632.000000 10632 100.000000 1 5757 1 chr5D.!!$F1 5756
1 TraesCS5D01G324700 chr5D 529215463 529219322 3859 False 768.333333 1085 83.216000 1281 4673 3 chr5D.!!$F2 3392
2 TraesCS5D01G324700 chr5B 503211850 503218010 6160 False 1999.000000 6035 91.778500 1 5757 4 chr5B.!!$F1 5756
3 TraesCS5D01G324700 chr5B 667672234 667676355 4121 False 658.500000 1096 84.102750 1281 4673 4 chr5B.!!$F2 3392
4 TraesCS5D01G324700 chr5A 529083125 529088245 5120 False 1058.333333 2087 89.944833 65 5729 6 chr5A.!!$F1 5664
5 TraesCS5D01G324700 chr5A 657378639 657382571 3932 False 637.500000 1182 83.323250 1271 5068 4 chr5A.!!$F2 3797

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
951 961 0.515127 CGTGCCTGCGATGTTGTTTA 59.485 50.0 0.00 0.00 0.00 2.01 F
1559 1986 0.107459 GAGCCGGCTCAGATTTTCCT 60.107 55.0 44.10 14.21 42.31 3.36 F
1968 2885 0.812811 CTGACAGTGTGTGCAGCTGT 60.813 55.0 16.64 11.39 44.97 4.40 F
3377 4437 0.481567 AGCCCCATTGCTCTGCATAT 59.518 50.0 0.00 0.00 36.75 1.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1952 2869 1.133025 GAAAACAGCTGCACACACTGT 59.867 47.619 15.27 2.04 46.27 3.55 R
3359 4419 0.601558 CATATGCAGAGCAATGGGGC 59.398 55.000 0.00 0.00 43.62 5.80 R
3759 5076 4.642429 AGACGTATTTTGCCAAAGAGAGT 58.358 39.130 0.00 0.00 0.00 3.24 R
5251 7135 0.103390 TCTCAACGGCGTTTCTCACA 59.897 50.000 24.49 0.90 0.00 3.58 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
47 48 8.974060 ATATTGGTACGAAATTCCTATGTTGT 57.026 30.769 0.00 0.00 0.00 3.32
130 131 7.908601 CACTAAACTAGTTGTGTCCAAAGTTTC 59.091 37.037 9.34 0.00 39.29 2.78
423 424 4.319766 GGACTTCAACATGTTGCAGTAGTG 60.320 45.833 33.88 15.81 44.67 2.74
465 466 3.231734 CGGTGATTTCAGCACAGGA 57.768 52.632 10.09 0.00 44.00 3.86
520 521 7.472334 TTTTAGTCTAGTTGGGAGAATACGT 57.528 36.000 0.00 0.00 0.00 3.57
567 568 4.263905 TGAAACATGGGAACTAGCCAGAAT 60.264 41.667 0.00 0.00 0.00 2.40
916 926 2.287009 GCCCGCTCACTTATAAACATGC 60.287 50.000 0.00 0.00 0.00 4.06
920 930 4.997395 CCGCTCACTTATAAACATGCCTAT 59.003 41.667 0.00 0.00 0.00 2.57
947 957 4.465512 GCCGTGCCTGCGATGTTG 62.466 66.667 0.00 0.00 0.00 3.33
948 958 3.049674 CCGTGCCTGCGATGTTGT 61.050 61.111 0.00 0.00 0.00 3.32
949 959 2.616330 CCGTGCCTGCGATGTTGTT 61.616 57.895 0.00 0.00 0.00 2.83
950 960 1.282570 CGTGCCTGCGATGTTGTTT 59.717 52.632 0.00 0.00 0.00 2.83
951 961 0.515127 CGTGCCTGCGATGTTGTTTA 59.485 50.000 0.00 0.00 0.00 2.01
952 962 1.464023 CGTGCCTGCGATGTTGTTTAG 60.464 52.381 0.00 0.00 0.00 1.85
984 994 2.361865 GTGCCGGCCCAATTGGTA 60.362 61.111 26.77 0.00 36.04 3.25
993 1003 2.252714 GCCCAATTGGTAAGGTTTGGA 58.747 47.619 22.91 0.00 40.89 3.53
1030 1040 2.402572 CGCTCGACTGCTCCTCTGA 61.403 63.158 0.00 0.00 0.00 3.27
1040 1050 1.755008 CTCCTCTGACGACCCCTCC 60.755 68.421 0.00 0.00 0.00 4.30
1210 1612 3.086600 CCCAGCTCTCCCCTGTCC 61.087 72.222 0.00 0.00 0.00 4.02
1393 1797 3.005261 CCCTCATCGTCTACCTCATCTTG 59.995 52.174 0.00 0.00 0.00 3.02
1409 1813 0.517316 CTTGAAGCACCTGCCGTAAC 59.483 55.000 0.00 0.00 43.38 2.50
1431 1854 1.678970 CCTGCCTTTACCCACCTGC 60.679 63.158 0.00 0.00 0.00 4.85
1447 1871 0.108804 CTGCTTTGCTTGCCCATCTG 60.109 55.000 0.00 0.00 0.00 2.90
1448 1872 1.447314 GCTTTGCTTGCCCATCTGC 60.447 57.895 0.00 0.00 0.00 4.26
1449 1873 1.885163 GCTTTGCTTGCCCATCTGCT 61.885 55.000 0.00 0.00 0.00 4.24
1462 1886 4.749166 GCCCATCTGCTCATCCTCTTTTAT 60.749 45.833 0.00 0.00 0.00 1.40
1528 1955 1.005975 GCGTTCGTGATCCAGAATTCG 60.006 52.381 0.00 5.10 0.00 3.34
1559 1986 0.107459 GAGCCGGCTCAGATTTTCCT 60.107 55.000 44.10 14.21 42.31 3.36
1582 2009 4.822896 TGTTTGTAGATAAACTTTGGGCGT 59.177 37.500 3.94 0.00 40.36 5.68
1583 2010 5.299782 TGTTTGTAGATAAACTTTGGGCGTT 59.700 36.000 3.94 0.00 40.36 4.84
1586 2013 4.453136 TGTAGATAAACTTTGGGCGTTGTC 59.547 41.667 0.00 0.00 0.00 3.18
1691 2126 2.380084 TAGCACGCCTTTGGAACTAG 57.620 50.000 0.00 0.00 0.00 2.57
1726 2170 5.338953 GGATTCAGGCCATGAGATATGATCA 60.339 44.000 5.01 0.00 39.68 2.92
1727 2171 4.820894 TCAGGCCATGAGATATGATCAG 57.179 45.455 5.01 0.00 32.77 2.90
1729 2173 4.596212 TCAGGCCATGAGATATGATCAGTT 59.404 41.667 5.01 0.00 32.77 3.16
1730 2174 4.695928 CAGGCCATGAGATATGATCAGTTG 59.304 45.833 5.01 0.00 0.00 3.16
1731 2175 4.596212 AGGCCATGAGATATGATCAGTTGA 59.404 41.667 5.01 0.00 0.00 3.18
1732 2176 5.251005 AGGCCATGAGATATGATCAGTTGAT 59.749 40.000 5.01 0.00 37.51 2.57
1862 2592 5.869579 ACATAGATCAAAGGTGACAGTGTT 58.130 37.500 0.00 0.00 36.31 3.32
1868 2598 7.624549 AGATCAAAGGTGACAGTGTTATATGT 58.375 34.615 0.00 0.00 36.31 2.29
1875 2605 9.959721 AAGGTGACAGTGTTATATGTCTATTTT 57.040 29.630 0.00 0.00 44.90 1.82
1911 2828 5.411361 CGGTTCATGTTATTTCTCCAAGACA 59.589 40.000 0.00 0.00 0.00 3.41
1917 2834 5.324409 TGTTATTTCTCCAAGACAAGGCAT 58.676 37.500 0.00 0.00 0.00 4.40
1952 2869 3.516586 TCCAAAGTATGTCTGGTCCTGA 58.483 45.455 0.00 0.00 0.00 3.86
1968 2885 0.812811 CTGACAGTGTGTGCAGCTGT 60.813 55.000 16.64 11.39 44.97 4.40
1973 2890 1.402968 CAGTGTGTGCAGCTGTTTTCT 59.597 47.619 16.64 4.21 0.00 2.52
2007 2925 5.753921 CACTTAGCACTGTTTATACCCTAGC 59.246 44.000 0.00 0.00 0.00 3.42
2044 2962 3.441572 GTGCATCTGTGGCTAGTTTTGAT 59.558 43.478 0.00 0.00 0.00 2.57
2059 2977 2.634982 TTGATCGATTGCTGCAAACC 57.365 45.000 20.06 12.87 0.00 3.27
2203 3134 9.391006 GTAGTGGTTATTTTAGAATCCATCACA 57.609 33.333 0.00 0.00 0.00 3.58
2383 3325 6.262601 TGTTTTACTAAACTTGCTGCAACTC 58.737 36.000 11.69 0.00 43.25 3.01
2481 3424 3.491276 GCAGTTGCAGCAATTATATGGCA 60.491 43.478 11.96 0.00 41.59 4.92
2485 3428 4.325028 TGCAGCAATTATATGGCAAAGG 57.675 40.909 0.00 0.00 0.00 3.11
2919 3867 5.005971 CCAAAATATTTGCCAAGCTTCATCG 59.994 40.000 0.39 0.00 0.00 3.84
3090 4039 4.393680 TGCTCGTTTTTCAACAGTAACACT 59.606 37.500 0.00 0.00 32.54 3.55
3154 4103 5.646793 ACACTTACACTTCATAGAGTCGCTA 59.353 40.000 0.00 0.00 0.00 4.26
3234 4293 2.670148 GGACGGGGGCACTCATTCT 61.670 63.158 0.00 0.00 0.00 2.40
3235 4294 1.450312 GACGGGGGCACTCATTCTG 60.450 63.158 0.00 0.00 0.00 3.02
3236 4295 2.124570 CGGGGGCACTCATTCTGG 60.125 66.667 0.00 0.00 0.00 3.86
3237 4296 2.440980 GGGGGCACTCATTCTGGC 60.441 66.667 0.00 0.00 0.00 4.85
3280 4339 4.954875 AGAATCCAATTCTCGCCTTCTAG 58.045 43.478 0.00 0.00 46.17 2.43
3363 4423 2.851588 GAGGGATCCTCCAGCCCC 60.852 72.222 12.58 0.00 44.36 5.80
3377 4437 0.481567 AGCCCCATTGCTCTGCATAT 59.518 50.000 0.00 0.00 36.75 1.78
3433 4553 1.197721 CCACTCGATTGCTCGCTTTTT 59.802 47.619 0.00 0.00 44.65 1.94
3606 4726 5.764131 GAATATTCGAGATCCTCTTGTCGT 58.236 41.667 0.00 0.00 34.07 4.34
3759 5076 5.607939 TCTGTTCTGTTTTGACTGGTCTA 57.392 39.130 2.38 0.00 0.00 2.59
4224 5564 0.741915 GACACTTTTGCCGGTTTCCA 59.258 50.000 1.90 0.00 0.00 3.53
4326 5666 2.043939 TGTCAGGGCTACTAGGAAAGGA 59.956 50.000 0.00 0.00 0.00 3.36
4489 5841 2.352960 GCTCGGTGGATCTGAAATTGTC 59.647 50.000 0.00 0.00 0.00 3.18
4563 5944 5.447818 GCATGGTAGATGCTTGTTAGTGTTC 60.448 44.000 0.00 0.00 41.52 3.18
4638 6021 8.997621 TCAGACTTAGTTGAATTATGTACACC 57.002 34.615 0.00 0.00 0.00 4.16
4740 6193 5.129485 ACCTTGGGAGAACTATATGACTGTG 59.871 44.000 0.00 0.00 0.00 3.66
4794 6253 5.863935 GTGAACATTCCTTTTGCAGTTATCC 59.136 40.000 0.00 0.00 0.00 2.59
4901 6522 6.713450 GTGTAAAATACTCCAGGGAAGAACAA 59.287 38.462 0.00 0.00 0.00 2.83
4902 6523 6.940298 TGTAAAATACTCCAGGGAAGAACAAG 59.060 38.462 0.00 0.00 0.00 3.16
4974 6818 5.004922 TGTAAAGCACCCAAAAGAAGTTG 57.995 39.130 0.00 0.00 0.00 3.16
5029 6882 6.372659 ACAATACAACAAATACCAGAGAGCAG 59.627 38.462 0.00 0.00 0.00 4.24
5031 6884 4.573900 ACAACAAATACCAGAGAGCAGAG 58.426 43.478 0.00 0.00 0.00 3.35
5039 6892 1.317613 CAGAGAGCAGAGCGACCTAT 58.682 55.000 0.00 0.00 0.00 2.57
5095 6948 3.865745 CAGATGACTAAGTTAAGCCCACG 59.134 47.826 0.00 0.00 0.00 4.94
5098 6951 2.028748 TGACTAAGTTAAGCCCACGGTC 60.029 50.000 0.00 0.00 0.00 4.79
5100 6953 2.570302 ACTAAGTTAAGCCCACGGTCAT 59.430 45.455 0.00 0.00 0.00 3.06
5103 6956 3.706600 AGTTAAGCCCACGGTCATAAA 57.293 42.857 0.00 0.00 0.00 1.40
5136 6990 2.109425 ACCCCTACGACTTGATTTGC 57.891 50.000 0.00 0.00 0.00 3.68
5147 7001 5.766174 ACGACTTGATTTGCTAAAAAGGGTA 59.234 36.000 10.05 0.00 0.00 3.69
5161 7015 6.825944 AAAAAGGGTAGAAGAGAATTGCTC 57.174 37.500 0.00 0.00 44.29 4.26
5180 7045 3.311596 GCTCGGTTAATATGCGGAAAACT 59.688 43.478 0.00 0.00 0.00 2.66
5211 7076 2.260869 CCACAAGACAAGGCACCCG 61.261 63.158 0.00 0.00 0.00 5.28
5212 7077 1.227823 CACAAGACAAGGCACCCGA 60.228 57.895 0.00 0.00 0.00 5.14
5251 7135 3.918253 ATCCACGCACACCGCCAAT 62.918 57.895 0.00 0.00 41.76 3.16
5253 7137 3.659092 CACGCACACCGCCAATGT 61.659 61.111 0.00 0.00 41.76 2.71
5289 7173 6.066054 TGAGATTGTCTACGATCTGTCATC 57.934 41.667 16.00 4.21 44.86 2.92
5330 7283 2.095978 AACTCCGACTTCACCGTGGG 62.096 60.000 0.00 0.00 34.47 4.61
5360 7313 2.910482 CACGATCCTCAAAACAAATGCG 59.090 45.455 0.00 0.00 0.00 4.73
5362 7315 2.161410 CGATCCTCAAAACAAATGCGGA 59.839 45.455 0.00 0.00 36.22 5.54
5376 7329 1.757682 TGCGGAACAAGAAACCTGTT 58.242 45.000 0.00 0.00 0.00 3.16
5456 7409 2.897969 ACAAGCCTCGTAGGAGAAAGAA 59.102 45.455 13.99 0.00 43.27 2.52
5490 7451 3.199071 ACCAATATCGGTAACAAGCCTCA 59.801 43.478 0.00 0.00 37.57 3.86
5502 7463 4.479786 ACAAGCCTCATAGGAGAAAGAC 57.520 45.455 5.84 0.00 44.26 3.01
5512 7473 0.389426 GGAGAAAGACGCGCACCTTA 60.389 55.000 5.73 0.00 0.00 2.69
5527 7542 1.989586 ACCTTACACCAACATAGCCCA 59.010 47.619 0.00 0.00 0.00 5.36
5611 7637 3.161450 ATATGCCGCGACCCCACT 61.161 61.111 8.23 0.00 0.00 4.00
5617 7643 2.657237 CGCGACCCCACTCTTCTT 59.343 61.111 0.00 0.00 0.00 2.52
5618 7644 1.738099 CGCGACCCCACTCTTCTTG 60.738 63.158 0.00 0.00 0.00 3.02
5619 7645 2.035442 GCGACCCCACTCTTCTTGC 61.035 63.158 0.00 0.00 0.00 4.01
5712 7755 1.619827 ACCAATGATGTGCAAGTTGGG 59.380 47.619 16.33 0.00 42.73 4.12
5717 7760 2.382882 TGATGTGCAAGTTGGGTCAAA 58.617 42.857 4.75 0.00 0.00 2.69
5719 7762 2.663826 TGTGCAAGTTGGGTCAAAAC 57.336 45.000 4.75 0.00 0.00 2.43
5729 7772 4.770010 AGTTGGGTCAAAACTTTCAAGACA 59.230 37.500 0.00 0.00 34.16 3.41
5746 7789 2.597510 AGCGCCCAGGGAAACAAC 60.598 61.111 10.89 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 8.385491 AGGATCCAAGATATGTAAATGCATACA 58.615 33.333 15.82 1.36 39.91 2.29
46 47 8.798859 AGGATCCAAGATATGTAAATGCATAC 57.201 34.615 15.82 0.00 34.59 2.39
48 49 8.051535 CCTAGGATCCAAGATATGTAAATGCAT 58.948 37.037 15.82 0.00 0.00 3.96
103 104 6.412214 ACTTTGGACACAACTAGTTTAGTGT 58.588 36.000 24.17 24.17 46.85 3.55
130 131 8.554528 ACATCAGTGAAATAAGCAGAATATTCG 58.445 33.333 9.78 6.40 0.00 3.34
465 466 7.069578 ACTCCAAGACGGATACTTATAACACAT 59.930 37.037 0.00 0.00 45.19 3.21
494 495 6.476053 CGTATTCTCCCAACTAGACTAAAAGC 59.524 42.308 0.00 0.00 0.00 3.51
520 521 8.971073 TCAGAGTCATTAGTGTTCTCATCATAA 58.029 33.333 12.46 0.00 33.45 1.90
567 568 6.716934 TTTTTGTAATGTGTTGGGCTCTTA 57.283 33.333 0.00 0.00 0.00 2.10
685 691 4.184629 AGCCACGCTCTAAATTACAGAAG 58.815 43.478 0.00 0.00 30.62 2.85
722 731 7.336161 TGAAAACGTTCCATCCTTTAAAAGA 57.664 32.000 0.00 0.00 32.28 2.52
739 748 3.045601 AGTGACTCCCTCATGAAAACG 57.954 47.619 0.00 0.00 0.00 3.60
941 951 1.963747 GCACACGCCTAAACAACATC 58.036 50.000 0.00 0.00 0.00 3.06
984 994 2.034558 CGAAACAGCACATCCAAACCTT 59.965 45.455 0.00 0.00 0.00 3.50
993 1003 1.026718 GGGCTAGCGAAACAGCACAT 61.027 55.000 9.00 0.00 41.02 3.21
1051 1452 3.461773 GGCGGCAGAGGAGCAGTA 61.462 66.667 3.07 0.00 35.83 2.74
1073 1474 2.442272 CCGGACGGGAGAGTGGAT 60.442 66.667 0.00 0.00 38.47 3.41
1184 1586 4.742649 AGAGCTGGGGTCGAGCGA 62.743 66.667 8.77 0.00 41.61 4.93
1195 1597 4.154347 GCGGACAGGGGAGAGCTG 62.154 72.222 0.00 0.00 0.00 4.24
1284 1686 1.958205 GCTCCATTCTCCATCGCCG 60.958 63.158 0.00 0.00 0.00 6.46
1393 1797 2.038837 GGGTTACGGCAGGTGCTTC 61.039 63.158 1.26 0.00 41.70 3.86
1431 1854 0.172803 GAGCAGATGGGCAAGCAAAG 59.827 55.000 0.00 0.00 35.83 2.77
1447 1871 4.513318 CGGGAGAAATAAAAGAGGATGAGC 59.487 45.833 0.00 0.00 0.00 4.26
1448 1872 5.059833 CCGGGAGAAATAAAAGAGGATGAG 58.940 45.833 0.00 0.00 0.00 2.90
1449 1873 4.473559 ACCGGGAGAAATAAAAGAGGATGA 59.526 41.667 6.32 0.00 0.00 2.92
1462 1886 3.094572 CTCAACTACCTACCGGGAGAAA 58.905 50.000 17.91 0.67 44.86 2.52
1528 1955 1.964933 AGCCGGCTCTAAACCTATCTC 59.035 52.381 27.08 0.00 0.00 2.75
1559 1986 4.822896 ACGCCCAAAGTTTATCTACAAACA 59.177 37.500 1.99 0.00 40.22 2.83
1576 2003 1.891919 GCTGTCAAGACAACGCCCA 60.892 57.895 4.29 0.00 41.33 5.36
1582 2009 4.756642 AGATTTCGATTGCTGTCAAGACAA 59.243 37.500 4.29 0.00 41.33 3.18
1583 2010 4.318332 AGATTTCGATTGCTGTCAAGACA 58.682 39.130 2.56 2.56 39.32 3.41
1586 2013 5.455392 ACAAAGATTTCGATTGCTGTCAAG 58.545 37.500 0.00 0.00 35.37 3.02
1674 2102 1.235724 AACTAGTTCCAAAGGCGTGC 58.764 50.000 1.12 0.00 0.00 5.34
1691 2126 3.942748 TGGCCTGAATCCAACGTAATAAC 59.057 43.478 3.32 0.00 0.00 1.89
1726 2170 2.169144 TGAGATGCGATGGTGATCAACT 59.831 45.455 12.94 0.00 0.00 3.16
1727 2171 2.554142 TGAGATGCGATGGTGATCAAC 58.446 47.619 2.98 2.98 0.00 3.18
1729 2173 2.366266 TGATGAGATGCGATGGTGATCA 59.634 45.455 0.00 0.00 0.00 2.92
1730 2174 3.036075 TGATGAGATGCGATGGTGATC 57.964 47.619 0.00 0.00 0.00 2.92
1731 2175 3.244457 ACATGATGAGATGCGATGGTGAT 60.244 43.478 0.00 0.00 0.00 3.06
1732 2176 2.103601 ACATGATGAGATGCGATGGTGA 59.896 45.455 0.00 0.00 0.00 4.02
1733 2177 2.223377 CACATGATGAGATGCGATGGTG 59.777 50.000 0.00 0.00 0.00 4.17
1734 2178 2.158856 ACACATGATGAGATGCGATGGT 60.159 45.455 0.00 0.00 0.00 3.55
1735 2179 2.490991 ACACATGATGAGATGCGATGG 58.509 47.619 0.00 0.00 0.00 3.51
1736 2180 3.123116 GCTACACATGATGAGATGCGATG 59.877 47.826 0.00 0.00 0.00 3.84
1737 2181 3.006644 AGCTACACATGATGAGATGCGAT 59.993 43.478 0.00 0.00 0.00 4.58
1868 2598 8.624367 TGAACCGGAAACTATTTCAAAATAGA 57.376 30.769 22.94 1.06 46.87 1.98
1875 2605 7.931578 ATAACATGAACCGGAAACTATTTCA 57.068 32.000 9.46 6.10 41.43 2.69
1911 2828 5.332743 TGGATAACTCTGGAAAAATGCCTT 58.667 37.500 0.00 0.00 0.00 4.35
1917 2834 8.934023 ACATACTTTGGATAACTCTGGAAAAA 57.066 30.769 0.00 0.00 0.00 1.94
1952 2869 1.133025 GAAAACAGCTGCACACACTGT 59.867 47.619 15.27 2.04 46.27 3.55
1968 2885 5.176223 GTGCTAAGTGCTACGTAACAGAAAA 59.824 40.000 0.00 0.00 43.37 2.29
1973 2890 3.005050 ACAGTGCTAAGTGCTACGTAACA 59.995 43.478 0.00 0.00 43.37 2.41
2007 2925 4.750598 CAGATGCACTATGATGAAGGTCAG 59.249 45.833 0.00 0.00 0.00 3.51
2044 2962 1.732941 ATACGGTTTGCAGCAATCGA 58.267 45.000 27.46 16.41 0.00 3.59
2059 2977 8.999431 ACCAGTTGATATGGCTAATAAAATACG 58.001 33.333 0.00 0.00 41.87 3.06
2137 3067 1.322442 GAACCAACTCTTGCAAGCCT 58.678 50.000 21.99 5.73 0.00 4.58
2383 3325 5.103000 CGAACTTGGAATCACTACAGTAGG 58.897 45.833 12.42 1.58 0.00 3.18
2481 3424 8.891720 TGTTAAATTACTTACAACACGACCTTT 58.108 29.630 0.00 0.00 0.00 3.11
2485 3428 9.488124 TGTTTGTTAAATTACTTACAACACGAC 57.512 29.630 0.00 0.00 0.00 4.34
2870 3818 8.907885 GGCTGTTCAGAATAGAAAAAGGAATAT 58.092 33.333 10.97 0.00 0.00 1.28
2871 3819 7.888021 TGGCTGTTCAGAATAGAAAAAGGAATA 59.112 33.333 10.97 0.00 0.00 1.75
2919 3867 6.085555 TCGTTGAGTATATGATTCTCACCC 57.914 41.667 0.00 0.00 36.59 4.61
2940 3888 7.970061 TCTTTCTGGATAAATTCAAAAGCATCG 59.030 33.333 0.00 0.00 0.00 3.84
3090 4039 4.767409 AGTAGTCTGCATGTGAACTCTGTA 59.233 41.667 0.00 0.00 0.00 2.74
3154 4103 1.065418 GGACTTGATTGACCCCGACAT 60.065 52.381 0.00 0.00 0.00 3.06
3230 4289 2.431954 CCAGAATGAGTGGCCAGAAT 57.568 50.000 5.11 0.00 39.69 2.40
3237 4296 1.746615 CGGTGGCCAGAATGAGTGG 60.747 63.158 5.11 0.00 39.69 4.00
3238 4297 1.003355 ACGGTGGCCAGAATGAGTG 60.003 57.895 5.11 0.00 39.69 3.51
3239 4298 1.003355 CACGGTGGCCAGAATGAGT 60.003 57.895 5.11 0.00 39.69 3.41
3359 4419 0.601558 CATATGCAGAGCAATGGGGC 59.398 55.000 0.00 0.00 43.62 5.80
3759 5076 4.642429 AGACGTATTTTGCCAAAGAGAGT 58.358 39.130 0.00 0.00 0.00 3.24
4326 5666 6.819397 TCGATTACCTCTTCGATGTGATAT 57.181 37.500 2.25 0.00 39.29 1.63
4489 5841 3.443681 ACACAAGGCCTTTCAAATATCCG 59.556 43.478 17.61 2.59 0.00 4.18
4740 6193 8.564574 TGACCAACTAGTTGTTTTCATCAATAC 58.435 33.333 29.05 4.86 38.85 1.89
4794 6253 9.559958 CCTCTTGTTTATGTATTTTACTTGCAG 57.440 33.333 0.00 0.00 0.00 4.41
4850 6469 8.947055 TCTTAGGACCGGTTAAATTAACATAC 57.053 34.615 9.42 3.74 40.39 2.39
4865 6485 6.127535 TGGAGTATTTTACACTCTTAGGACCG 60.128 42.308 2.81 0.00 41.78 4.79
4866 6486 7.179076 TGGAGTATTTTACACTCTTAGGACC 57.821 40.000 2.81 0.00 41.78 4.46
4867 6487 7.266400 CCTGGAGTATTTTACACTCTTAGGAC 58.734 42.308 15.20 0.00 42.95 3.85
4901 6522 9.726438 GGTAGTTCCTTTGATGTAATATATGCT 57.274 33.333 0.00 0.00 0.00 3.79
4902 6523 9.726438 AGGTAGTTCCTTTGATGTAATATATGC 57.274 33.333 0.00 0.00 45.67 3.14
4945 6789 4.647424 TTTGGGTGCTTTACAGAAGTTG 57.353 40.909 0.00 0.00 0.00 3.16
4974 6818 4.624452 GCAACTTCTTCTGAAATGCATTCC 59.376 41.667 13.38 0.00 41.15 3.01
5029 6882 6.757010 TGTTTCTCAGAATTTATAGGTCGCTC 59.243 38.462 0.00 0.00 0.00 5.03
5031 6884 6.312918 TGTGTTTCTCAGAATTTATAGGTCGC 59.687 38.462 0.00 0.00 0.00 5.19
5039 6892 7.195646 CAGCAACTTGTGTTTCTCAGAATTTA 58.804 34.615 0.00 0.00 33.52 1.40
5103 6956 5.009310 GTCGTAGGGGTTGACTTCAATTTTT 59.991 40.000 0.00 0.00 38.24 1.94
5106 6959 3.326880 AGTCGTAGGGGTTGACTTCAATT 59.673 43.478 0.00 0.00 39.87 2.32
5117 6970 1.628846 AGCAAATCAAGTCGTAGGGGT 59.371 47.619 0.00 0.00 0.00 4.95
5124 6977 5.121221 ACCCTTTTTAGCAAATCAAGTCG 57.879 39.130 0.00 0.00 0.00 4.18
5136 6990 7.201565 CGAGCAATTCTCTTCTACCCTTTTTAG 60.202 40.741 0.00 0.00 39.70 1.85
5147 7001 6.203723 GCATATTAACCGAGCAATTCTCTTCT 59.796 38.462 0.00 0.00 39.70 2.85
5161 7015 7.853524 TGTAATAGTTTTCCGCATATTAACCG 58.146 34.615 0.00 0.00 0.00 4.44
5180 7045 5.554437 TGTCTTGTGGGAGTGTTGTAATA 57.446 39.130 0.00 0.00 0.00 0.98
5211 7076 1.789523 TGTGGGTAGCCAGGTAGATC 58.210 55.000 15.48 0.78 0.00 2.75
5212 7077 2.119495 CTTGTGGGTAGCCAGGTAGAT 58.881 52.381 15.48 0.00 0.00 1.98
5251 7135 0.103390 TCTCAACGGCGTTTCTCACA 59.897 50.000 24.49 0.90 0.00 3.58
5253 7137 1.798223 CAATCTCAACGGCGTTTCTCA 59.202 47.619 24.49 7.73 0.00 3.27
5289 7173 2.158449 GCTTGTTGGAGAAGTGATGACG 59.842 50.000 0.00 0.00 0.00 4.35
5330 7283 0.605319 TGAGGATCGTGGTTGGTTGC 60.605 55.000 0.00 0.00 38.61 4.17
5341 7294 2.161410 TCCGCATTTGTTTTGAGGATCG 59.839 45.455 0.00 0.00 38.02 3.69
5344 7297 2.690497 TGTTCCGCATTTGTTTTGAGGA 59.310 40.909 0.00 0.00 40.68 3.71
5360 7313 1.754226 TGCCAACAGGTTTCTTGTTCC 59.246 47.619 0.00 0.00 0.00 3.62
5362 7315 4.561326 GCATATGCCAACAGGTTTCTTGTT 60.561 41.667 17.26 0.00 34.31 2.83
5490 7451 0.179108 GGTGCGCGTCTTTCTCCTAT 60.179 55.000 8.43 0.00 0.00 2.57
5502 7463 1.573829 ATGTTGGTGTAAGGTGCGCG 61.574 55.000 0.00 0.00 0.00 6.86
5512 7473 0.777446 AGGTTGGGCTATGTTGGTGT 59.223 50.000 0.00 0.00 0.00 4.16
5556 7571 1.961793 TGGTTTTGTCTCGGACTTGG 58.038 50.000 5.77 0.00 33.15 3.61
5557 7572 3.691498 GTTTGGTTTTGTCTCGGACTTG 58.309 45.455 5.77 0.00 33.15 3.16
5558 7573 2.353579 CGTTTGGTTTTGTCTCGGACTT 59.646 45.455 5.77 0.00 33.15 3.01
5559 7574 1.937899 CGTTTGGTTTTGTCTCGGACT 59.062 47.619 5.77 0.00 33.15 3.85
5560 7575 1.003223 CCGTTTGGTTTTGTCTCGGAC 60.003 52.381 0.00 0.00 38.96 4.79
5561 7576 1.301423 CCGTTTGGTTTTGTCTCGGA 58.699 50.000 0.00 0.00 38.96 4.55
5587 7613 1.130613 GTCGCGGCATATCATTCGC 59.869 57.895 5.47 0.00 44.04 4.70
5611 7637 1.065926 ACGATGATGGCAGCAAGAAGA 60.066 47.619 10.46 0.00 0.00 2.87
5617 7643 2.409055 GGCAACGATGATGGCAGCA 61.409 57.895 8.33 8.33 42.45 4.41
5618 7644 2.409055 TGGCAACGATGATGGCAGC 61.409 57.895 0.00 0.00 46.85 5.25
5619 7645 3.908189 TGGCAACGATGATGGCAG 58.092 55.556 0.00 0.00 46.85 4.85
5712 7755 2.783832 GCGCTGTCTTGAAAGTTTTGAC 59.216 45.455 0.00 9.13 0.00 3.18
5717 7760 0.465460 TGGGCGCTGTCTTGAAAGTT 60.465 50.000 7.64 0.00 0.00 2.66
5719 7762 1.580845 CCTGGGCGCTGTCTTGAAAG 61.581 60.000 7.64 0.00 0.00 2.62
5729 7772 2.597510 GTTGTTTCCCTGGGCGCT 60.598 61.111 8.22 0.00 0.00 5.92


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

AutoCloner maintained by Alex Coulton.