Multiple sequence alignment - TraesCS2A01G436700

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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 TraesCS2A01G436700 chr2A 100.000 4274 0 0 1 4274 688623665 688619392 0.000000e+00 7893.0
1 TraesCS2A01G436700 chr2A 100.000 31 0 0 2716 2746 688620526 688620496 1.660000e-04 58.4
2 TraesCS2A01G436700 chr2A 100.000 31 0 0 3140 3170 688620950 688620920 1.660000e-04 58.4
3 TraesCS2A01G436700 chr2B 89.550 1933 121 38 2 1880 651358728 651360633 0.000000e+00 2375.0
4 TraesCS2A01G436700 chr2B 90.555 847 55 17 1971 2802 651360755 651361591 0.000000e+00 1098.0
5 TraesCS2A01G436700 chr2B 93.020 702 31 12 2928 3614 651361788 651362486 0.000000e+00 1009.0
6 TraesCS2A01G436700 chr2B 88.226 637 42 12 3662 4269 651362574 651363206 0.000000e+00 730.0
7 TraesCS2A01G436700 chr2B 97.436 39 1 0 3137 3175 651361499 651361537 2.760000e-07 67.6
8 TraesCS2A01G436700 chr2D 93.290 1550 81 12 1971 3502 544883275 544884819 0.000000e+00 2265.0
9 TraesCS2A01G436700 chr2D 91.945 807 50 11 2 803 544880522 544881318 0.000000e+00 1116.0
10 TraesCS2A01G436700 chr2D 95.865 653 25 2 3620 4272 544885000 544885650 0.000000e+00 1055.0
11 TraesCS2A01G436700 chr2D 93.893 524 22 5 926 1442 544882005 544882525 0.000000e+00 782.0
12 TraesCS2A01G436700 chr2D 88.827 179 19 1 1507 1685 544882686 544882863 7.200000e-53 219.0
13 TraesCS2A01G436700 chr2D 94.872 39 2 0 3137 3175 544884025 544884063 1.280000e-05 62.1
14 TraesCS2A01G436700 chrUn 92.857 42 3 0 3621 3662 216303000 216303041 1.280000e-05 62.1
15 TraesCS2A01G436700 chr5A 86.207 58 6 2 3605 3662 585092658 585092713 1.280000e-05 62.1
16 TraesCS2A01G436700 chr4D 92.857 42 3 0 3621 3662 131330633 131330674 1.280000e-05 62.1
17 TraesCS2A01G436700 chr7A 92.500 40 3 0 3620 3659 121396066 121396105 1.660000e-04 58.4


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 TraesCS2A01G436700 chr2A 688619392 688623665 4273 True 2669.933333 7893 100.000000 1 4274 3 chr2A.!!$R1 4273
1 TraesCS2A01G436700 chr2B 651358728 651363206 4478 False 1055.920000 2375 91.757400 2 4269 5 chr2B.!!$F1 4267
2 TraesCS2A01G436700 chr2D 544880522 544885650 5128 False 916.516667 2265 93.115333 2 4272 6 chr2D.!!$F1 4270

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
136 137 0.033894 GCCCTGGGGTAATTTCCGAA 60.034 55.0 16.03 0.00 37.65 4.30 F
1445 2045 0.730834 CGTGAACTGGAGTCTCAGCG 60.731 60.0 1.47 1.93 38.26 5.18 F
1661 2366 0.173708 CCTTCCCTCTGTGACTACGC 59.826 60.0 0.00 0.00 0.00 4.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1642 2347 0.173708 GCGTAGTCACAGAGGGAAGG 59.826 60.0 0.0 0.0 0.00 3.46 R
2314 3192 0.512952 GCTACAGTTGCCACGTTCAG 59.487 55.0 0.0 0.0 0.00 3.02 R
3509 4503 0.179113 CCGGGTGGCAAATTACATGC 60.179 55.0 0.0 0.0 43.08 4.06 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
75 76 1.026718 CGATGGGGAGTCACCAAAGC 61.027 60.000 20.41 10.13 42.17 3.51
108 109 4.008453 CCTCCCTATGGCATGGGT 57.992 61.111 25.85 0.00 43.74 4.51
132 133 1.685180 GGAGTGCCCTGGGGTAATTTC 60.685 57.143 16.03 0.00 37.65 2.17
134 135 1.035385 GTGCCCTGGGGTAATTTCCG 61.035 60.000 16.03 0.00 37.65 4.30
135 136 1.208844 TGCCCTGGGGTAATTTCCGA 61.209 55.000 16.03 0.00 37.65 4.55
136 137 0.033894 GCCCTGGGGTAATTTCCGAA 60.034 55.000 16.03 0.00 37.65 4.30
138 139 1.683938 CCCTGGGGTAATTTCCGAACC 60.684 57.143 4.27 0.00 0.00 3.62
147 148 3.842732 AATTTCCGAACCCTTTTAGCG 57.157 42.857 0.00 0.00 0.00 4.26
150 151 0.906775 TCCGAACCCTTTTAGCGGAT 59.093 50.000 0.00 0.00 45.18 4.18
152 153 1.669265 CCGAACCCTTTTAGCGGATTC 59.331 52.381 0.00 0.00 44.43 2.52
165 166 1.726853 CGGATTCGAGAAGCACCTTT 58.273 50.000 3.47 0.00 39.00 3.11
183 184 8.360390 AGCACCTTTTCTTTTGGTATTCTTAAG 58.640 33.333 0.00 0.00 32.13 1.85
184 185 8.141909 GCACCTTTTCTTTTGGTATTCTTAAGT 58.858 33.333 1.63 0.00 32.13 2.24
211 212 1.490490 TCCTAATTTGCGCAGGAGGAT 59.510 47.619 21.01 6.92 33.48 3.24
286 287 9.631452 GAAAAGATTATGGGAGCATATTTTAGC 57.369 33.333 0.00 0.00 0.00 3.09
373 374 3.065371 CGATGGTTCTGGCTATTGGTTTC 59.935 47.826 0.00 0.00 0.00 2.78
442 443 3.259374 TCCCTGATTGTCAAGACAGTCTC 59.741 47.826 21.23 12.38 45.00 3.36
529 530 1.448985 TTTCGAGCCTTTGGAATCCG 58.551 50.000 0.00 0.00 0.00 4.18
539 540 1.541310 TTGGAATCCGGACTCAGCGT 61.541 55.000 15.87 0.00 0.00 5.07
540 541 1.519455 GGAATCCGGACTCAGCGTG 60.519 63.158 15.87 0.00 0.00 5.34
541 542 1.215647 GAATCCGGACTCAGCGTGT 59.784 57.895 6.12 0.00 0.00 4.49
673 678 4.042271 TGGGAGTTTTTCCTTGATACCC 57.958 45.455 0.00 0.00 45.98 3.69
687 692 3.334691 TGATACCCGCAGAAACTGAAAG 58.665 45.455 2.81 0.00 42.29 2.62
699 704 5.300286 CAGAAACTGAAAGGTTTCCAGTGAT 59.700 40.000 14.00 0.00 45.56 3.06
715 720 4.404640 CAGTGATATTCATGGGCTCCAAT 58.595 43.478 0.00 0.00 36.95 3.16
717 722 3.760684 GTGATATTCATGGGCTCCAATCC 59.239 47.826 0.00 0.00 36.95 3.01
718 723 3.398629 TGATATTCATGGGCTCCAATCCA 59.601 43.478 0.00 0.00 36.95 3.41
719 724 2.852714 ATTCATGGGCTCCAATCCAA 57.147 45.000 0.00 0.00 36.95 3.53
720 725 2.619697 TTCATGGGCTCCAATCCAAA 57.380 45.000 0.00 0.00 36.95 3.28
721 726 2.852714 TCATGGGCTCCAATCCAAAT 57.147 45.000 0.00 0.00 36.95 2.32
745 750 2.019156 GCCGAAATTCCCCTTCTGAGG 61.019 57.143 0.00 0.00 43.15 3.86
818 846 6.452242 TGTTCTCTAGTCATTTGCGAACTTA 58.548 36.000 0.00 0.00 32.71 2.24
840 868 7.775561 ACTTATGAGGTTCTGTATGAAATTCCC 59.224 37.037 0.00 0.00 36.30 3.97
861 1447 3.331150 CGTTTATGTAACACCCTGAGCA 58.669 45.455 0.00 0.00 36.50 4.26
904 1491 2.970639 GCGGGGAAAAGGAAAGCC 59.029 61.111 0.00 0.00 0.00 4.35
962 1562 2.364448 GCTCGTTCCCCTCTCCCT 60.364 66.667 0.00 0.00 0.00 4.20
964 1564 1.308326 CTCGTTCCCCTCTCCCTCT 59.692 63.158 0.00 0.00 0.00 3.69
1160 1760 3.839432 CTTCGGGGAGGTCGAGGC 61.839 72.222 0.00 0.00 37.93 4.70
1445 2045 0.730834 CGTGAACTGGAGTCTCAGCG 60.731 60.000 1.47 1.93 38.26 5.18
1504 2209 2.095768 TGAGCAGCGTCTGTAATTTTGC 60.096 45.455 8.32 0.00 33.43 3.68
1505 2210 2.154462 AGCAGCGTCTGTAATTTTGCT 58.846 42.857 8.32 0.00 35.75 3.91
1530 2235 3.588336 CAGGAGCTTCTTGCAGCC 58.412 61.111 0.00 0.00 45.94 4.85
1590 2295 4.565166 CGAGTTCAGCATTACGGTTATGAA 59.435 41.667 11.03 1.21 0.00 2.57
1635 2340 6.683286 CGATCTTGTAAGTATATGATCGTCCG 59.317 42.308 17.62 2.54 44.36 4.79
1642 2347 5.312120 AGTATATGATCGTCCGGATTGTC 57.688 43.478 7.81 6.71 34.82 3.18
1658 2363 2.992847 TGTCCTTCCCTCTGTGACTA 57.007 50.000 0.00 0.00 0.00 2.59
1659 2364 2.526432 TGTCCTTCCCTCTGTGACTAC 58.474 52.381 0.00 0.00 0.00 2.73
1661 2366 0.173708 CCTTCCCTCTGTGACTACGC 59.826 60.000 0.00 0.00 0.00 4.42
1667 2372 0.244994 CTCTGTGACTACGCTTGCCT 59.755 55.000 0.00 0.00 0.00 4.75
1686 2391 7.707774 TTGCCTTTTTGCAATTAGTTAGTTC 57.292 32.000 0.00 0.00 45.77 3.01
1687 2392 7.049799 TGCCTTTTTGCAATTAGTTAGTTCT 57.950 32.000 0.00 0.00 38.56 3.01
1690 2395 9.290483 GCCTTTTTGCAATTAGTTAGTTCTATC 57.710 33.333 0.00 0.00 0.00 2.08
1715 2420 9.444600 TCTATCTATTGGTTACCTTGTTTTGTC 57.555 33.333 2.07 0.00 0.00 3.18
1718 2423 9.802039 ATCTATTGGTTACCTTGTTTTGTCTAA 57.198 29.630 2.07 0.00 0.00 2.10
1724 2429 9.411189 TGGTTACCTTGTTTTGTCTAATAAGTT 57.589 29.630 2.07 0.00 0.00 2.66
1764 2569 7.903145 TGGTACAATAAGTTCATGTACTGTCT 58.097 34.615 21.24 0.00 45.43 3.41
1766 2571 9.865321 GGTACAATAAGTTCATGTACTGTCTAA 57.135 33.333 21.24 0.00 45.43 2.10
1769 2574 8.812972 ACAATAAGTTCATGTACTGTCTAAGGA 58.187 33.333 5.68 0.00 0.00 3.36
1770 2575 9.823647 CAATAAGTTCATGTACTGTCTAAGGAT 57.176 33.333 5.68 0.00 0.00 3.24
1806 2611 9.586435 CTTTCTTCAGTACAAAATGAAAAAGGT 57.414 29.630 0.00 0.00 35.14 3.50
1807 2612 9.936759 TTTCTTCAGTACAAAATGAAAAAGGTT 57.063 25.926 0.00 0.00 35.14 3.50
1809 2614 8.194769 TCTTCAGTACAAAATGAAAAAGGTTCC 58.805 33.333 0.00 0.00 35.14 3.62
1814 2619 6.800072 ACAAAATGAAAAAGGTTCCCACTA 57.200 33.333 0.00 0.00 0.00 2.74
1818 2628 8.611757 CAAAATGAAAAAGGTTCCCACTAAAAG 58.388 33.333 0.00 0.00 0.00 2.27
1842 2652 2.144730 TGTCAATTGCATTTTGCCTGC 58.855 42.857 0.00 0.00 44.23 4.85
1843 2653 1.465777 GTCAATTGCATTTTGCCTGCC 59.534 47.619 0.00 0.00 44.23 4.85
1844 2654 1.071857 TCAATTGCATTTTGCCTGCCA 59.928 42.857 0.00 0.00 44.23 4.92
1851 2661 3.072944 GCATTTTGCCTGCCATTGTTAA 58.927 40.909 0.00 0.00 37.42 2.01
1855 2665 1.544724 TGCCTGCCATTGTTAACTCC 58.455 50.000 7.22 0.00 0.00 3.85
1880 2690 2.547640 ATCAGTGCTCGCCTGCCATT 62.548 55.000 3.48 0.00 0.00 3.16
1881 2691 2.034687 AGTGCTCGCCTGCCATTT 59.965 55.556 0.00 0.00 0.00 2.32
1882 2692 1.604593 AGTGCTCGCCTGCCATTTT 60.605 52.632 0.00 0.00 0.00 1.82
1883 2693 1.444895 GTGCTCGCCTGCCATTTTG 60.445 57.895 0.00 0.00 0.00 2.44
1884 2694 2.182537 GCTCGCCTGCCATTTTGG 59.817 61.111 0.00 0.00 41.55 3.28
1901 2711 8.652810 CCATTTTGGCAAATTCTTATCCTTAG 57.347 34.615 14.29 0.00 29.41 2.18
1902 2712 7.225341 CCATTTTGGCAAATTCTTATCCTTAGC 59.775 37.037 14.29 0.00 29.41 3.09
1903 2713 5.852282 TTGGCAAATTCTTATCCTTAGCC 57.148 39.130 0.00 0.00 39.95 3.93
1916 2780 8.107095 TCTTATCCTTAGCCTTGTGTACAAAAT 58.893 33.333 0.00 0.00 35.15 1.82
1918 2782 4.764823 TCCTTAGCCTTGTGTACAAAATGG 59.235 41.667 0.00 4.63 35.15 3.16
1935 2799 8.750515 ACAAAATGGAAATTGGACAAAAGAAT 57.249 26.923 0.00 0.00 0.00 2.40
1938 2802 9.506018 AAAATGGAAATTGGACAAAAGAATAGG 57.494 29.630 0.00 0.00 0.00 2.57
1940 2804 6.318913 TGGAAATTGGACAAAAGAATAGGGA 58.681 36.000 0.00 0.00 0.00 4.20
1943 2807 7.765819 GGAAATTGGACAAAAGAATAGGGATTG 59.234 37.037 0.00 0.00 0.00 2.67
1944 2808 7.797121 AATTGGACAAAAGAATAGGGATTGT 57.203 32.000 0.00 0.00 36.96 2.71
1946 2810 7.610580 TTGGACAAAAGAATAGGGATTGTTT 57.389 32.000 0.00 0.00 39.53 2.83
1948 2812 8.893563 TGGACAAAAGAATAGGGATTGTTTAT 57.106 30.769 0.00 0.00 37.50 1.40
1949 2813 8.748412 TGGACAAAAGAATAGGGATTGTTTATG 58.252 33.333 0.00 0.00 37.50 1.90
1950 2814 8.749354 GGACAAAAGAATAGGGATTGTTTATGT 58.251 33.333 0.00 0.00 37.50 2.29
1968 2832 9.616156 TGTTTATGTAACAAGAACTACTTTCCA 57.384 29.630 0.00 0.00 43.58 3.53
1986 2850 5.621197 TTCCATAGTTTCACCGTGAAATG 57.379 39.130 25.50 19.74 46.55 2.32
2006 2870 9.013229 TGAAATGATATGCAGTCAACTTAACTT 57.987 29.630 8.45 0.00 0.00 2.66
2015 2880 6.479001 TGCAGTCAACTTAACTTCTTCTGTAC 59.521 38.462 0.00 0.00 0.00 2.90
2017 2882 7.011109 GCAGTCAACTTAACTTCTTCTGTACAA 59.989 37.037 0.00 0.00 0.00 2.41
2019 2884 9.444600 AGTCAACTTAACTTCTTCTGTACAAAA 57.555 29.630 0.00 0.00 0.00 2.44
2057 2929 6.935167 ACCATGAACAATTTTCCATAGTTCC 58.065 36.000 0.00 0.00 38.17 3.62
2094 2972 7.628580 GCCACTCCTTACCTTTAATCATCAAAC 60.629 40.741 0.00 0.00 0.00 2.93
2177 3055 4.520492 AGGAATGTTGATTCGAAGCAGTTT 59.480 37.500 16.49 11.09 39.22 2.66
2255 3133 4.504864 CCTGGTGTGAAGAATTGTACTGGA 60.505 45.833 0.00 0.00 0.00 3.86
2288 3166 5.357032 GGATCAATTGACGGTAAGTTTCCAT 59.643 40.000 11.07 0.00 0.00 3.41
2320 3198 3.119637 ACTGTTTTGGTTTCCACTGAACG 60.120 43.478 0.00 0.00 30.78 3.95
2359 3238 3.878160 TTTCCTGTTGTTGGTTTGGTC 57.122 42.857 0.00 0.00 0.00 4.02
2364 3243 0.812549 GTTGTTGGTTTGGTCACGGT 59.187 50.000 0.00 0.00 0.00 4.83
2414 3293 9.776158 CTTATCTATCACTAACAGTATTAGCGG 57.224 37.037 0.00 0.00 0.00 5.52
2423 3302 4.267349 ACAGTATTAGCGGTTGACAACT 57.733 40.909 17.52 1.21 0.00 3.16
2424 3303 3.994392 ACAGTATTAGCGGTTGACAACTG 59.006 43.478 20.78 20.78 40.80 3.16
2428 3307 3.394674 TTAGCGGTTGACAACTGATGA 57.605 42.857 27.66 17.29 40.26 2.92
2609 3488 0.813610 CGTGCTCCAAGTGTGGTCAA 60.814 55.000 0.00 0.00 46.11 3.18
2628 3507 4.333926 GTCAATGGAACTGATGAAGGTAGC 59.666 45.833 0.00 0.00 0.00 3.58
2656 3535 4.464008 AGATCCACAATGCATACGGAAAT 58.536 39.130 13.80 5.11 0.00 2.17
2772 3658 8.622948 AGTCAGTATTTTGTTCCTCCTTTAAG 57.377 34.615 0.00 0.00 0.00 1.85
2777 3663 9.528489 AGTATTTTGTTCCTCCTTTAAGCATAA 57.472 29.630 0.00 0.00 0.00 1.90
2869 3755 4.945543 TGTCGTACTCCAGCTCTAAACATA 59.054 41.667 0.00 0.00 0.00 2.29
2870 3756 5.163683 TGTCGTACTCCAGCTCTAAACATAC 60.164 44.000 0.00 0.00 0.00 2.39
2877 3763 6.069963 ACTCCAGCTCTAAACATACCATTTCT 60.070 38.462 0.00 0.00 0.00 2.52
2915 3801 4.839796 CCGCCAAGGTACATAAATTAACG 58.160 43.478 0.00 0.00 34.51 3.18
3102 4093 5.119588 AGTCATTAAAAGAAATTCGCGACGA 59.880 36.000 9.15 0.00 0.00 4.20
3138 4129 3.214328 ACGAAAGGTCTGCTGTCAATTT 58.786 40.909 0.00 0.00 0.00 1.82
3139 4130 3.003689 ACGAAAGGTCTGCTGTCAATTTG 59.996 43.478 0.00 0.00 0.00 2.32
3189 4180 2.778299 TGATGTGGCTGGTTTACTCAC 58.222 47.619 0.00 0.00 0.00 3.51
3338 4330 3.548818 GCTACACCATTGGCGAATTCATC 60.549 47.826 6.22 0.00 0.00 2.92
3402 4396 3.046374 AGGACAACCACTCCAACTAAGT 58.954 45.455 0.00 0.00 38.94 2.24
3421 4415 6.814146 ACTAAGTAAAGTCAGCTGAAGCATAC 59.186 38.462 20.19 17.78 45.16 2.39
3441 4435 7.775093 AGCATACTTGAGCAAACCAATAGATAA 59.225 33.333 0.00 0.00 0.00 1.75
3622 4702 9.061610 CATATTGTTAATTCTTGTCGTGGTTTC 57.938 33.333 0.00 0.00 0.00 2.78
3652 4732 4.787551 ACCACGGCAAGAATTATGGAATA 58.212 39.130 0.00 0.00 0.00 1.75
3659 4739 5.942826 GGCAAGAATTATGGAATAGAGGGAG 59.057 44.000 0.00 0.00 0.00 4.30
3721 4801 5.288804 TCATTTGAACTTTAGTGCTTTGGC 58.711 37.500 0.00 0.00 39.26 4.52
3727 4807 3.007635 ACTTTAGTGCTTTGGCGTATCC 58.992 45.455 0.00 0.00 42.25 2.59
3731 4811 1.077787 TGCTTTGGCGTATCCCTGG 60.078 57.895 0.00 0.00 42.25 4.45
4030 5136 3.367932 ACATGAATGTTTACAGCGTCTCG 59.632 43.478 0.00 0.00 37.90 4.04
4111 5217 6.820152 CACATGTCAGGTCTCAGAATTAATGA 59.180 38.462 0.00 0.00 0.00 2.57
4116 5222 6.481644 GTCAGGTCTCAGAATTAATGATGTCC 59.518 42.308 0.00 0.00 0.00 4.02
4137 5243 1.578423 GCTGCAGCTGGTTCTTCAC 59.422 57.895 31.33 0.00 38.21 3.18
4190 5298 3.548770 TGTTTCATCTCTGATGGATGCC 58.451 45.455 7.58 0.00 40.02 4.40
4246 5354 1.079197 ATGCGATGTTGTCTCGGCA 60.079 52.632 0.00 0.00 36.65 5.69
4263 5371 0.315251 GCACACTTGCTCCCCTTTTC 59.685 55.000 0.00 0.00 46.17 2.29
4270 5378 0.251742 TGCTCCCCTTTTCACCATGG 60.252 55.000 11.19 11.19 0.00 3.66
4271 5379 1.607801 GCTCCCCTTTTCACCATGGC 61.608 60.000 13.04 0.00 0.00 4.40
4272 5380 0.251742 CTCCCCTTTTCACCATGGCA 60.252 55.000 13.04 0.00 0.00 4.92
4273 5381 0.251742 TCCCCTTTTCACCATGGCAG 60.252 55.000 13.04 4.85 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.824904 ATCTCGGTTGAAGAAATTGATGG 57.175 39.130 0.00 0.00 0.00 3.51
132 133 1.669265 GAATCCGCTAAAAGGGTTCGG 59.331 52.381 0.00 0.00 38.88 4.30
134 135 2.608090 CTCGAATCCGCTAAAAGGGTTC 59.392 50.000 0.00 0.00 43.58 3.62
135 136 2.235402 TCTCGAATCCGCTAAAAGGGTT 59.765 45.455 0.00 0.00 34.21 4.11
136 137 1.829222 TCTCGAATCCGCTAAAAGGGT 59.171 47.619 0.00 0.00 35.37 4.34
138 139 2.285488 GCTTCTCGAATCCGCTAAAAGG 59.715 50.000 0.00 0.00 35.37 3.11
147 148 3.339141 AGAAAAGGTGCTTCTCGAATCC 58.661 45.455 0.00 0.00 0.00 3.01
150 151 4.202010 CCAAAAGAAAAGGTGCTTCTCGAA 60.202 41.667 0.00 0.00 31.85 3.71
152 153 3.066760 ACCAAAAGAAAAGGTGCTTCTCG 59.933 43.478 0.00 0.00 31.85 4.04
183 184 4.403453 CTGCGCAAATTAGGACAACTTAC 58.597 43.478 13.05 0.00 0.00 2.34
184 185 3.438781 CCTGCGCAAATTAGGACAACTTA 59.561 43.478 13.05 0.00 33.33 2.24
211 212 1.017177 GTAAACGGATGCACGCCTGA 61.017 55.000 5.94 0.00 37.37 3.86
286 287 1.519455 GCATTCCTCCGAGTCCACG 60.519 63.158 0.00 0.00 0.00 4.94
373 374 5.662211 CAACATTGCAGGAAAGAAAAAGG 57.338 39.130 0.00 0.00 0.00 3.11
521 522 1.982395 ACGCTGAGTCCGGATTCCA 60.982 57.895 22.80 12.81 0.00 3.53
529 530 1.813786 ACTCTAAGACACGCTGAGTCC 59.186 52.381 0.00 0.00 36.68 3.85
539 540 7.179966 TCTGGGATAGTTGTAACTCTAAGACA 58.820 38.462 0.00 0.00 40.37 3.41
540 541 7.642082 TCTGGGATAGTTGTAACTCTAAGAC 57.358 40.000 0.00 0.00 40.37 3.01
541 542 8.840200 AATCTGGGATAGTTGTAACTCTAAGA 57.160 34.615 0.00 0.52 40.37 2.10
580 585 4.960938 ACAGTGAGAGCAATGAACAGTTA 58.039 39.130 0.00 0.00 42.40 2.24
687 692 3.319122 GCCCATGAATATCACTGGAAACC 59.681 47.826 0.00 0.00 31.23 3.27
699 704 3.969466 TTGGATTGGAGCCCATGAATA 57.031 42.857 0.00 0.00 31.53 1.75
715 720 3.551846 GGGAATTTCGGCTCTATTTGGA 58.448 45.455 0.00 0.00 0.00 3.53
717 722 3.555966 AGGGGAATTTCGGCTCTATTTG 58.444 45.455 0.00 0.00 0.00 2.32
718 723 3.953542 AGGGGAATTTCGGCTCTATTT 57.046 42.857 0.00 0.00 0.00 1.40
719 724 3.459969 AGAAGGGGAATTTCGGCTCTATT 59.540 43.478 0.00 0.00 0.00 1.73
720 725 3.049344 AGAAGGGGAATTTCGGCTCTAT 58.951 45.455 0.00 0.00 0.00 1.98
721 726 2.170607 CAGAAGGGGAATTTCGGCTCTA 59.829 50.000 0.00 0.00 0.00 2.43
745 750 2.307049 CACGGAACTTCGACAAAATGC 58.693 47.619 0.00 0.00 0.00 3.56
803 808 4.946784 ACCTCATAAGTTCGCAAATGAC 57.053 40.909 0.00 0.00 0.00 3.06
804 809 5.122239 CAGAACCTCATAAGTTCGCAAATGA 59.878 40.000 0.00 0.00 46.58 2.57
818 846 5.126067 CGGGAATTTCATACAGAACCTCAT 58.874 41.667 0.00 0.00 35.56 2.90
840 868 3.331150 TGCTCAGGGTGTTACATAAACG 58.669 45.455 0.00 0.00 41.30 3.60
861 1447 1.737201 CCCAGTTTCGGCCGTTTTT 59.263 52.632 27.15 7.12 0.00 1.94
950 1543 0.551879 CGAGTAGAGGGAGAGGGGAA 59.448 60.000 0.00 0.00 0.00 3.97
952 1545 0.774908 ATCGAGTAGAGGGAGAGGGG 59.225 60.000 0.00 0.00 0.00 4.79
956 1549 1.345089 CGGAGATCGAGTAGAGGGAGA 59.655 57.143 0.00 0.00 42.43 3.71
962 1562 1.167155 GCAGCCGGAGATCGAGTAGA 61.167 60.000 5.05 0.00 42.43 2.59
964 1564 2.194212 GGCAGCCGGAGATCGAGTA 61.194 63.158 5.05 0.00 42.43 2.59
1381 1981 2.495084 GAACTCCTGGACCAAGTGAAC 58.505 52.381 0.00 0.00 0.00 3.18
1445 2045 2.639327 AAGCAAGCCGCCAATGGAC 61.639 57.895 2.05 0.00 44.04 4.02
1530 2235 2.126071 CACGGCCTACTGTCCACG 60.126 66.667 0.00 0.00 31.05 4.94
1590 2295 9.877178 AAGATCGAACTTACTTCATACAGAAAT 57.123 29.630 6.09 0.00 35.40 2.17
1629 2334 1.610554 GGGAAGGACAATCCGGACGA 61.611 60.000 6.12 0.00 42.75 4.20
1631 2336 0.178301 GAGGGAAGGACAATCCGGAC 59.822 60.000 6.12 0.00 42.75 4.79
1635 2340 1.909302 TCACAGAGGGAAGGACAATCC 59.091 52.381 0.00 0.00 36.58 3.01
1642 2347 0.173708 GCGTAGTCACAGAGGGAAGG 59.826 60.000 0.00 0.00 0.00 3.46
1690 2395 9.449719 AGACAAAACAAGGTAACCAATAGATAG 57.550 33.333 0.00 0.00 37.17 2.08
1692 2397 9.802039 TTAGACAAAACAAGGTAACCAATAGAT 57.198 29.630 0.00 0.00 37.17 1.98
1693 2398 9.802039 ATTAGACAAAACAAGGTAACCAATAGA 57.198 29.630 0.00 0.00 37.17 1.98
1697 2402 9.411189 ACTTATTAGACAAAACAAGGTAACCAA 57.589 29.630 0.00 0.00 37.17 3.67
1698 2403 8.983702 ACTTATTAGACAAAACAAGGTAACCA 57.016 30.769 0.00 0.00 37.17 3.67
1738 2443 8.372459 AGACAGTACATGAACTTATTGTACCAA 58.628 33.333 0.00 0.00 44.25 3.67
1739 2444 7.903145 AGACAGTACATGAACTTATTGTACCA 58.097 34.615 0.00 0.00 44.25 3.25
1743 2448 8.812972 TCCTTAGACAGTACATGAACTTATTGT 58.187 33.333 0.00 0.00 0.00 2.71
1744 2449 9.823647 ATCCTTAGACAGTACATGAACTTATTG 57.176 33.333 0.00 0.00 0.00 1.90
1806 2611 6.928492 GCAATTGACATTTCTTTTAGTGGGAA 59.072 34.615 10.34 0.00 0.00 3.97
1807 2612 6.041409 TGCAATTGACATTTCTTTTAGTGGGA 59.959 34.615 10.34 0.00 0.00 4.37
1809 2614 7.894376 ATGCAATTGACATTTCTTTTAGTGG 57.106 32.000 10.34 0.00 0.00 4.00
1814 2619 7.917720 GCAAAATGCAATTGACATTTCTTTT 57.082 28.000 26.49 16.60 44.76 2.27
1842 2652 4.188462 TGATGCTACGGAGTTAACAATGG 58.812 43.478 8.61 0.00 37.78 3.16
1843 2653 4.870426 ACTGATGCTACGGAGTTAACAATG 59.130 41.667 8.61 0.00 37.78 2.82
1844 2654 4.870426 CACTGATGCTACGGAGTTAACAAT 59.130 41.667 8.61 0.00 37.78 2.71
1880 2690 5.957774 AGGCTAAGGATAAGAATTTGCCAAA 59.042 36.000 11.18 0.00 44.13 3.28
1881 2691 5.518865 AGGCTAAGGATAAGAATTTGCCAA 58.481 37.500 11.18 0.00 44.13 4.52
1882 2692 5.129368 AGGCTAAGGATAAGAATTTGCCA 57.871 39.130 11.18 0.00 44.13 4.92
1883 2693 5.360999 ACAAGGCTAAGGATAAGAATTTGCC 59.639 40.000 0.00 0.00 42.69 4.52
1884 2694 6.127619 ACACAAGGCTAAGGATAAGAATTTGC 60.128 38.462 0.00 0.00 0.00 3.68
1885 2695 7.396540 ACACAAGGCTAAGGATAAGAATTTG 57.603 36.000 0.00 0.00 0.00 2.32
1886 2696 8.107095 TGTACACAAGGCTAAGGATAAGAATTT 58.893 33.333 0.00 0.00 0.00 1.82
1887 2697 7.630082 TGTACACAAGGCTAAGGATAAGAATT 58.370 34.615 0.00 0.00 0.00 2.17
1889 2699 6.614694 TGTACACAAGGCTAAGGATAAGAA 57.385 37.500 0.00 0.00 0.00 2.52
1890 2700 6.614694 TTGTACACAAGGCTAAGGATAAGA 57.385 37.500 0.00 0.00 0.00 2.10
1893 2703 6.601613 CCATTTTGTACACAAGGCTAAGGATA 59.398 38.462 0.00 0.00 37.15 2.59
1894 2704 5.418840 CCATTTTGTACACAAGGCTAAGGAT 59.581 40.000 0.00 0.00 37.15 3.24
1896 2706 4.764823 TCCATTTTGTACACAAGGCTAAGG 59.235 41.667 0.00 0.00 37.15 2.69
1897 2707 5.957842 TCCATTTTGTACACAAGGCTAAG 57.042 39.130 0.00 0.00 37.15 2.18
1899 2709 6.909550 ATTTCCATTTTGTACACAAGGCTA 57.090 33.333 0.00 0.00 37.15 3.93
1900 2710 5.806654 ATTTCCATTTTGTACACAAGGCT 57.193 34.783 0.00 0.00 37.15 4.58
1901 2711 5.179182 CCAATTTCCATTTTGTACACAAGGC 59.821 40.000 0.00 0.00 37.15 4.35
1902 2712 6.423604 GTCCAATTTCCATTTTGTACACAAGG 59.576 38.462 0.00 0.00 37.15 3.61
1903 2713 6.983307 TGTCCAATTTCCATTTTGTACACAAG 59.017 34.615 0.00 0.00 37.15 3.16
1916 2780 6.318913 TCCCTATTCTTTTGTCCAATTTCCA 58.681 36.000 0.00 0.00 0.00 3.53
1918 2782 8.314021 ACAATCCCTATTCTTTTGTCCAATTTC 58.686 33.333 0.00 0.00 0.00 2.17
1948 2812 9.841295 AAACTATGGAAAGTAGTTCTTGTTACA 57.159 29.630 0.00 0.00 40.49 2.41
1951 2815 8.837389 GTGAAACTATGGAAAGTAGTTCTTGTT 58.163 33.333 0.00 0.00 40.49 2.83
1952 2816 7.444487 GGTGAAACTATGGAAAGTAGTTCTTGT 59.556 37.037 0.00 0.00 40.49 3.16
1953 2817 7.360101 CGGTGAAACTATGGAAAGTAGTTCTTG 60.360 40.741 0.00 0.00 40.49 3.02
1954 2818 6.649557 CGGTGAAACTATGGAAAGTAGTTCTT 59.350 38.462 0.00 0.00 40.49 2.52
1955 2819 6.164176 CGGTGAAACTATGGAAAGTAGTTCT 58.836 40.000 0.00 0.00 40.49 3.01
1956 2820 5.930569 ACGGTGAAACTATGGAAAGTAGTTC 59.069 40.000 0.00 0.00 40.49 3.01
1957 2821 5.699458 CACGGTGAAACTATGGAAAGTAGTT 59.301 40.000 0.74 0.00 42.53 2.24
1958 2822 5.011329 TCACGGTGAAACTATGGAAAGTAGT 59.989 40.000 8.68 0.00 36.74 2.73
1959 2823 5.475719 TCACGGTGAAACTATGGAAAGTAG 58.524 41.667 8.68 0.00 36.74 2.57
1960 2824 5.471556 TCACGGTGAAACTATGGAAAGTA 57.528 39.130 8.68 0.00 36.74 2.24
1961 2825 4.345859 TCACGGTGAAACTATGGAAAGT 57.654 40.909 8.68 0.00 36.74 2.66
1962 2826 5.682943 TTTCACGGTGAAACTATGGAAAG 57.317 39.130 27.49 0.00 41.02 2.62
1986 2850 8.386606 CAGAAGAAGTTAAGTTGACTGCATATC 58.613 37.037 8.41 3.97 0.00 1.63
2006 2870 7.942341 ACATAAACCATCCTTTTGTACAGAAGA 59.058 33.333 23.85 12.43 0.00 2.87
2057 2929 3.922171 AAGGAGTGGCAAAGGAGATAG 57.078 47.619 0.00 0.00 0.00 2.08
2094 2972 1.093159 GAGCAGCCTTCACATCAAGG 58.907 55.000 0.00 0.00 45.35 3.61
2177 3055 4.141528 ACAAAAGATGGCAATTCACCCAAA 60.142 37.500 0.00 0.00 34.25 3.28
2255 3133 3.255642 CCGTCAATTGATCCACCAGTTTT 59.744 43.478 12.12 0.00 0.00 2.43
2314 3192 0.512952 GCTACAGTTGCCACGTTCAG 59.487 55.000 0.00 0.00 0.00 3.02
2320 3198 5.048013 AGGAAATTTAAGCTACAGTTGCCAC 60.048 40.000 3.10 0.00 0.00 5.01
2323 3201 6.013842 ACAGGAAATTTAAGCTACAGTTGC 57.986 37.500 0.00 0.00 0.00 4.17
2359 3238 6.657836 AAAGAAATCCGTAATTAGACCGTG 57.342 37.500 0.00 0.00 0.00 4.94
2388 3267 9.776158 CCGCTAATACTGTTAGTGATAGATAAG 57.224 37.037 7.49 0.00 35.20 1.73
2398 3277 5.395682 TGTCAACCGCTAATACTGTTAGT 57.604 39.130 0.00 0.00 0.00 2.24
2413 3292 8.398665 GGTTAATTCTATCATCAGTTGTCAACC 58.601 37.037 12.17 0.00 0.00 3.77
2414 3293 9.167311 AGGTTAATTCTATCATCAGTTGTCAAC 57.833 33.333 7.68 7.68 0.00 3.18
2423 3302 7.994911 AGCACAATCAGGTTAATTCTATCATCA 59.005 33.333 0.00 0.00 0.00 3.07
2424 3303 8.388484 AGCACAATCAGGTTAATTCTATCATC 57.612 34.615 0.00 0.00 0.00 2.92
2428 3307 9.113838 CTGTAAGCACAATCAGGTTAATTCTAT 57.886 33.333 0.00 0.00 33.22 1.98
2609 3488 4.445448 GGATGCTACCTTCATCAGTTCCAT 60.445 45.833 5.50 0.00 41.46 3.41
2628 3507 4.319984 CGTATGCATTGTGGATCTTGGATG 60.320 45.833 3.54 0.00 29.08 3.51
2772 3658 9.580916 CGTATTACTGTATGTTCAATGTTATGC 57.419 33.333 0.00 0.00 0.00 3.14
2805 3691 9.509855 CACTTACAGAGATTACTAGCTAACTTG 57.490 37.037 0.00 0.00 0.00 3.16
2869 3755 7.065803 CGGTTGAATTACTGTATGAGAAATGGT 59.934 37.037 0.00 0.00 0.00 3.55
2870 3756 7.409697 CGGTTGAATTACTGTATGAGAAATGG 58.590 38.462 0.00 0.00 0.00 3.16
2877 3763 4.209307 TGGCGGTTGAATTACTGTATGA 57.791 40.909 0.00 0.00 0.00 2.15
2915 3801 8.567948 TCCTGTGAATAAAAATGAAGTTCAGTC 58.432 33.333 11.91 0.00 30.27 3.51
3102 4093 5.434408 ACCTTTCGTAAAGTGAAGGAAACT 58.566 37.500 7.89 0.00 38.63 2.66
3138 4129 5.823861 ATGGTGTGGTATATAGTGATGCA 57.176 39.130 0.00 0.00 0.00 3.96
3139 4130 6.818644 CCTTATGGTGTGGTATATAGTGATGC 59.181 42.308 0.00 0.00 0.00 3.91
3338 4330 1.100510 CCAGCCTGTGATTGGTGATG 58.899 55.000 0.00 0.00 0.00 3.07
3402 4396 5.793817 TCAAGTATGCTTCAGCTGACTTTA 58.206 37.500 18.03 4.74 41.38 1.85
3421 4415 7.912250 GTGACATTATCTATTGGTTTGCTCAAG 59.088 37.037 0.00 0.00 0.00 3.02
3509 4503 0.179113 CCGGGTGGCAAATTACATGC 60.179 55.000 0.00 0.00 43.08 4.06
3571 4565 9.031537 TGAGAATAAAGGTGATCACTGTAGTTA 57.968 33.333 24.50 14.97 0.00 2.24
3622 4702 3.701532 TTCTTGCCGTGGTTTTAGTTG 57.298 42.857 0.00 0.00 0.00 3.16
3634 4714 4.697352 CCCTCTATTCCATAATTCTTGCCG 59.303 45.833 0.00 0.00 0.00 5.69
3636 4716 6.538263 ACTCCCTCTATTCCATAATTCTTGC 58.462 40.000 0.00 0.00 0.00 4.01
3652 4732 5.396213 GCAGTGAAAGAATCATACTCCCTCT 60.396 44.000 0.00 0.00 40.97 3.69
3659 4739 4.265073 ACCCAGCAGTGAAAGAATCATAC 58.735 43.478 0.00 0.00 40.97 2.39
3721 4801 0.108329 ACTGAAACGCCAGGGATACG 60.108 55.000 0.00 0.00 38.44 3.06
3727 4807 2.731217 CAAAAGAACTGAAACGCCAGG 58.269 47.619 0.00 0.00 38.44 4.45
3731 4811 2.119457 CCAGCAAAAGAACTGAAACGC 58.881 47.619 0.00 0.00 35.90 4.84
4030 5136 8.587952 AATTTTTGTTCATACTTGTTGCTACC 57.412 30.769 0.00 0.00 0.00 3.18
4137 5243 0.391661 CGAGACCATGAACCACTGGG 60.392 60.000 0.00 0.00 36.82 4.45
4246 5354 1.692411 GTGAAAAGGGGAGCAAGTGT 58.308 50.000 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.