Multiple sequence alignment - TraesCS6B01G175300

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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 TraesCS6B01G175300 chr6B 100.000 2921 0 0 1 2921 191199297 191202217 0.000000e+00 5395.0
1 TraesCS6B01G175300 chr6A 93.164 2092 101 27 1 2077 126915372 126917436 0.000000e+00 3033.0
2 TraesCS6B01G175300 chr6A 87.375 301 33 3 2626 2921 127009281 127009581 1.000000e-89 340.0
3 TraesCS6B01G175300 chr6D 94.329 1393 47 11 785 2157 104783036 104784416 0.000000e+00 2106.0
4 TraesCS6B01G175300 chr6D 93.476 797 38 8 1 789 104768285 104769075 0.000000e+00 1171.0
5 TraesCS6B01G175300 chr6D 89.128 791 68 9 2145 2921 104833321 104834107 0.000000e+00 968.0
6 TraesCS6B01G175300 chr6D 75.479 261 46 13 2639 2889 311249996 311249744 8.560000e-21 111.0
7 TraesCS6B01G175300 chr6D 79.433 141 20 7 2639 2775 427698000 427697865 1.110000e-14 91.6
8 TraesCS6B01G175300 chr5B 75.096 261 47 11 2639 2883 418551985 418551727 3.980000e-19 106.0
9 TraesCS6B01G175300 chr5D 88.235 68 2 4 2636 2698 270227466 270227532 3.120000e-10 76.8
10 TraesCS6B01G175300 chr2A 76.429 140 22 9 2624 2754 771301687 771301824 6.760000e-07 65.8
11 TraesCS6B01G175300 chr2B 86.792 53 3 2 2639 2687 691013893 691013841 4.070000e-04 56.5


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 TraesCS6B01G175300 chr6B 191199297 191202217 2920 False 5395 5395 100.000 1 2921 1 chr6B.!!$F1 2920
1 TraesCS6B01G175300 chr6A 126915372 126917436 2064 False 3033 3033 93.164 1 2077 1 chr6A.!!$F1 2076
2 TraesCS6B01G175300 chr6D 104783036 104784416 1380 False 2106 2106 94.329 785 2157 1 chr6D.!!$F2 1372
3 TraesCS6B01G175300 chr6D 104768285 104769075 790 False 1171 1171 93.476 1 789 1 chr6D.!!$F1 788
4 TraesCS6B01G175300 chr6D 104833321 104834107 786 False 968 968 89.128 2145 2921 1 chr6D.!!$F3 776

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
632 636 0.107456 CCATGACATCTTCCCCTCCG 59.893 60.0 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2396 2453 2.276201 TCGCTGGATGACCAAATTACG 58.724 47.619 0.0 0.0 46.32 3.18 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
19 20 1.870941 TTCGGGAGCTCCTAGGACCA 61.871 60.000 31.36 10.35 35.95 4.02
61 62 1.377994 CAAGACCCCTGCTCAAGCT 59.622 57.895 3.32 0.00 42.66 3.74
158 159 1.203174 CCACCTTGGGATTTGAAGGGT 60.203 52.381 0.00 0.00 42.79 4.34
169 170 1.981256 TTGAAGGGTTGAAGGCTGTC 58.019 50.000 0.00 0.00 0.00 3.51
248 249 0.953471 TTCGGTGATGGAACTTGGCG 60.953 55.000 0.00 0.00 0.00 5.69
298 299 2.328473 TCTGCTTTGTTCGATCGTGAG 58.672 47.619 15.94 8.07 0.00 3.51
378 379 5.222151 TGGCTTAGATCCTAGAGCTAGCTTA 60.222 44.000 20.42 11.88 32.08 3.09
471 472 7.664552 ATTGGAAATCATGATTACATGGTGT 57.335 32.000 21.00 3.05 45.73 4.16
490 491 3.437395 GTGTGGTGGTACGAATATTTGCA 59.563 43.478 2.34 0.00 0.00 4.08
507 508 1.066787 TGCATCCACGGTTTGATACGA 60.067 47.619 0.00 0.00 0.00 3.43
528 529 7.997107 ACGAAAGTATATGAATGCGAAACTA 57.003 32.000 0.00 0.00 46.88 2.24
533 534 7.390918 AGTATATGAATGCGAAACTACGTTC 57.609 36.000 0.00 0.00 35.59 3.95
543 544 3.673809 CGAAACTACGTTCTTTGGAGAGG 59.326 47.826 0.00 0.00 32.44 3.69
566 567 5.354234 GGCAACTAAGCTATTTGTGCTTCTA 59.646 40.000 4.18 0.00 46.39 2.10
627 631 3.922171 AACTCTCCATGACATCTTCCC 57.078 47.619 0.00 0.00 0.00 3.97
631 635 1.419387 CTCCATGACATCTTCCCCTCC 59.581 57.143 0.00 0.00 0.00 4.30
632 636 0.107456 CCATGACATCTTCCCCTCCG 59.893 60.000 0.00 0.00 0.00 4.63
647 654 2.484594 CCCTCCGTTTTTGCCACAAATT 60.485 45.455 0.00 0.00 0.00 1.82
648 655 2.799978 CCTCCGTTTTTGCCACAAATTC 59.200 45.455 0.00 0.00 0.00 2.17
692 700 7.036220 ACATCTCTAAATTCCGCCGATATAAG 58.964 38.462 0.00 0.00 0.00 1.73
717 725 0.461548 TGATGACCGACTCCATCTGC 59.538 55.000 0.00 0.00 39.75 4.26
741 752 0.524180 GCGACTTAAGCATTGCCAGC 60.524 55.000 4.70 0.00 34.19 4.85
743 754 1.176527 GACTTAAGCATTGCCAGCCA 58.823 50.000 4.70 0.00 0.00 4.75
744 755 1.753073 GACTTAAGCATTGCCAGCCAT 59.247 47.619 4.70 0.00 0.00 4.40
746 757 2.689983 ACTTAAGCATTGCCAGCCATAC 59.310 45.455 4.70 0.00 0.00 2.39
748 759 2.734755 AAGCATTGCCAGCCATACTA 57.265 45.000 4.70 0.00 0.00 1.82
750 761 3.234234 AGCATTGCCAGCCATACTATT 57.766 42.857 4.70 0.00 0.00 1.73
753 764 4.406649 AGCATTGCCAGCCATACTATTTTT 59.593 37.500 4.70 0.00 0.00 1.94
754 765 4.746611 GCATTGCCAGCCATACTATTTTTC 59.253 41.667 0.00 0.00 0.00 2.29
755 766 5.452356 GCATTGCCAGCCATACTATTTTTCT 60.452 40.000 0.00 0.00 0.00 2.52
756 767 6.576185 CATTGCCAGCCATACTATTTTTCTT 58.424 36.000 0.00 0.00 0.00 2.52
757 768 6.603940 TTGCCAGCCATACTATTTTTCTTT 57.396 33.333 0.00 0.00 0.00 2.52
809 826 0.815213 GCCGATGATGCAGCTGGTTA 60.815 55.000 17.12 0.00 0.00 2.85
818 835 5.252547 TGATGCAGCTGGTTATTAAGTTGA 58.747 37.500 17.12 0.00 0.00 3.18
837 881 1.154016 CAGACGTGCCCACTACTCG 60.154 63.158 0.00 0.00 0.00 4.18
838 882 1.303074 AGACGTGCCCACTACTCGA 60.303 57.895 0.00 0.00 0.00 4.04
839 883 0.680280 AGACGTGCCCACTACTCGAT 60.680 55.000 0.00 0.00 0.00 3.59
840 884 0.248539 GACGTGCCCACTACTCGATC 60.249 60.000 0.00 0.00 0.00 3.69
841 885 0.680280 ACGTGCCCACTACTCGATCT 60.680 55.000 0.00 0.00 0.00 2.75
842 886 0.248661 CGTGCCCACTACTCGATCTG 60.249 60.000 0.00 0.00 0.00 2.90
843 887 0.528684 GTGCCCACTACTCGATCTGC 60.529 60.000 0.00 0.00 0.00 4.26
844 888 1.068250 GCCCACTACTCGATCTGCC 59.932 63.158 0.00 0.00 0.00 4.85
845 889 1.395826 GCCCACTACTCGATCTGCCT 61.396 60.000 0.00 0.00 0.00 4.75
846 890 0.387202 CCCACTACTCGATCTGCCTG 59.613 60.000 0.00 0.00 0.00 4.85
847 891 1.107114 CCACTACTCGATCTGCCTGT 58.893 55.000 0.00 0.00 0.00 4.00
848 892 1.066303 CCACTACTCGATCTGCCTGTC 59.934 57.143 0.00 0.00 0.00 3.51
849 893 1.745653 CACTACTCGATCTGCCTGTCA 59.254 52.381 0.00 0.00 0.00 3.58
850 894 1.746220 ACTACTCGATCTGCCTGTCAC 59.254 52.381 0.00 0.00 0.00 3.67
851 895 1.066303 CTACTCGATCTGCCTGTCACC 59.934 57.143 0.00 0.00 0.00 4.02
852 896 1.226802 CTCGATCTGCCTGTCACCG 60.227 63.158 0.00 0.00 0.00 4.94
853 897 1.938657 CTCGATCTGCCTGTCACCGT 61.939 60.000 0.00 0.00 0.00 4.83
854 898 1.517257 CGATCTGCCTGTCACCGTC 60.517 63.158 0.00 0.00 0.00 4.79
855 899 1.517257 GATCTGCCTGTCACCGTCG 60.517 63.158 0.00 0.00 0.00 5.12
856 900 3.649277 ATCTGCCTGTCACCGTCGC 62.649 63.158 0.00 0.00 0.00 5.19
859 903 4.681978 GCCTGTCACCGTCGCCTT 62.682 66.667 0.00 0.00 0.00 4.35
860 904 2.967397 CCTGTCACCGTCGCCTTA 59.033 61.111 0.00 0.00 0.00 2.69
861 905 1.515954 CCTGTCACCGTCGCCTTAT 59.484 57.895 0.00 0.00 0.00 1.73
862 906 0.108329 CCTGTCACCGTCGCCTTATT 60.108 55.000 0.00 0.00 0.00 1.40
863 907 1.135527 CCTGTCACCGTCGCCTTATTA 59.864 52.381 0.00 0.00 0.00 0.98
864 908 2.417651 CCTGTCACCGTCGCCTTATTAA 60.418 50.000 0.00 0.00 0.00 1.40
928 975 6.183360 GCTTTTGCAATGGAGTAGATCTCATT 60.183 38.462 0.00 0.00 46.58 2.57
992 1040 2.125673 CGTCGGCGGGTCTGATTT 60.126 61.111 7.21 0.00 31.70 2.17
1018 1066 3.742433 AGATGAACGATCTGATGACCC 57.258 47.619 0.00 0.00 40.19 4.46
1144 1192 1.447838 GCGGCCAAGAACGAGATGA 60.448 57.895 2.24 0.00 0.00 2.92
1904 1952 0.814457 GCCAGTGTTGGTGTGTTTCA 59.186 50.000 0.00 0.00 46.80 2.69
2013 2070 1.558233 ATTTCGGTCTCCTCGGTTCT 58.442 50.000 0.00 0.00 0.00 3.01
2031 2088 5.566826 CGGTTCTTTCACTATCTGGTCTTCA 60.567 44.000 0.00 0.00 0.00 3.02
2052 2109 4.511454 TCAGTCTCTTTTGAATGGTGTTCG 59.489 41.667 0.00 0.00 33.48 3.95
2053 2110 4.273480 CAGTCTCTTTTGAATGGTGTTCGT 59.727 41.667 0.00 0.00 0.00 3.85
2101 2158 8.421784 TCCATCCTACAACTTAGATTCATGTAC 58.578 37.037 0.00 0.00 0.00 2.90
2119 2176 9.625747 TTCATGTACATTCCATTACATATGTGT 57.374 29.630 18.81 7.51 36.90 3.72
2120 2177 9.271828 TCATGTACATTCCATTACATATGTGTC 57.728 33.333 18.81 1.29 36.90 3.67
2121 2178 9.276590 CATGTACATTCCATTACATATGTGTCT 57.723 33.333 18.81 0.00 36.90 3.41
2122 2179 8.661352 TGTACATTCCATTACATATGTGTCTG 57.339 34.615 18.81 11.85 39.77 3.51
2123 2180 6.624352 ACATTCCATTACATATGTGTCTGC 57.376 37.500 18.81 0.00 39.77 4.26
2124 2181 6.121590 ACATTCCATTACATATGTGTCTGCA 58.878 36.000 18.81 0.00 39.77 4.41
2125 2182 6.602803 ACATTCCATTACATATGTGTCTGCAA 59.397 34.615 18.81 3.79 39.77 4.08
2126 2183 6.682423 TTCCATTACATATGTGTCTGCAAG 57.318 37.500 18.81 0.00 39.77 4.01
2127 2184 4.576053 TCCATTACATATGTGTCTGCAAGC 59.424 41.667 18.81 0.00 39.77 4.01
2128 2185 4.336153 CCATTACATATGTGTCTGCAAGCA 59.664 41.667 18.81 0.00 39.77 3.91
2129 2186 4.944962 TTACATATGTGTCTGCAAGCAC 57.055 40.909 18.81 11.94 40.04 4.40
2134 2191 2.276472 TGTGTCTGCAAGCACAAAAC 57.724 45.000 17.33 0.00 44.04 2.43
2135 2192 1.818060 TGTGTCTGCAAGCACAAAACT 59.182 42.857 17.33 0.00 44.04 2.66
2136 2193 2.230992 TGTGTCTGCAAGCACAAAACTT 59.769 40.909 17.33 0.00 44.04 2.66
2137 2194 3.441922 TGTGTCTGCAAGCACAAAACTTA 59.558 39.130 17.33 0.00 44.04 2.24
2138 2195 4.037690 GTGTCTGCAAGCACAAAACTTAG 58.962 43.478 13.45 0.00 39.61 2.18
2139 2196 3.944650 TGTCTGCAAGCACAAAACTTAGA 59.055 39.130 0.00 0.00 0.00 2.10
2140 2197 4.580167 TGTCTGCAAGCACAAAACTTAGAT 59.420 37.500 0.00 0.00 0.00 1.98
2141 2198 5.067674 TGTCTGCAAGCACAAAACTTAGATT 59.932 36.000 0.00 0.00 0.00 2.40
2142 2199 5.626955 GTCTGCAAGCACAAAACTTAGATTC 59.373 40.000 0.00 0.00 0.00 2.52
2143 2200 5.299028 TCTGCAAGCACAAAACTTAGATTCA 59.701 36.000 0.00 0.00 0.00 2.57
2239 2296 7.164171 GCAAGCATAATTTAGACAACATGTACG 59.836 37.037 0.00 0.00 0.00 3.67
2316 2373 4.525874 TGTGTTCAATCATATTGGTGCCAA 59.474 37.500 6.08 6.08 40.47 4.52
2326 2383 7.473735 TCATATTGGTGCCAAAAACATCTAA 57.526 32.000 7.81 0.00 39.55 2.10
2363 2420 8.297470 AGGATTGTGCTAATTGTGTCATAAAT 57.703 30.769 0.00 0.00 0.00 1.40
2369 2426 8.839343 TGTGCTAATTGTGTCATAAATATCCAG 58.161 33.333 0.00 0.00 0.00 3.86
2379 2436 9.113838 GTGTCATAAATATCCAGAGAATTGTGT 57.886 33.333 0.00 0.00 0.00 3.72
2389 2446 5.241506 TCCAGAGAATTGTGTCAATTTGGTC 59.758 40.000 16.82 11.33 0.00 4.02
2396 2453 9.167311 AGAATTGTGTCAATTTGGTCTATCTAC 57.833 33.333 8.72 0.00 0.00 2.59
2414 2471 4.439057 TCTACGTAATTTGGTCATCCAGC 58.561 43.478 0.00 0.00 45.22 4.85
2415 2472 2.006888 ACGTAATTTGGTCATCCAGCG 58.993 47.619 0.00 0.00 45.22 5.18
2422 2479 1.489481 TGGTCATCCAGCGAAGATCT 58.511 50.000 0.00 0.00 39.03 2.75
2453 2510 4.459390 TGACGAATGATTTTAGTCCGGA 57.541 40.909 0.00 0.00 0.00 5.14
2459 2516 7.144000 ACGAATGATTTTAGTCCGGACTATAC 58.856 38.462 38.07 27.85 42.83 1.47
2469 2526 2.486951 CGGACTATACGGGTTCAGTG 57.513 55.000 0.00 0.00 0.00 3.66
2484 2541 4.583073 GGTTCAGTGTCAGTTTTTATGGGT 59.417 41.667 0.00 0.00 0.00 4.51
2485 2542 5.068591 GGTTCAGTGTCAGTTTTTATGGGTT 59.931 40.000 0.00 0.00 0.00 4.11
2486 2543 6.206498 GTTCAGTGTCAGTTTTTATGGGTTC 58.794 40.000 0.00 0.00 0.00 3.62
2487 2544 5.441500 TCAGTGTCAGTTTTTATGGGTTCA 58.558 37.500 0.00 0.00 0.00 3.18
2501 2558 2.143925 GGGTTCAGTCTTTGGTCTTCG 58.856 52.381 0.00 0.00 0.00 3.79
2515 2572 3.823873 TGGTCTTCGGTTTTTATGCACAT 59.176 39.130 0.00 0.00 0.00 3.21
2521 2578 5.378292 TCGGTTTTTATGCACATGCTTAA 57.622 34.783 5.31 6.75 42.66 1.85
2532 2589 6.324561 TGCACATGCTTAATTGTGAGTTTA 57.675 33.333 14.21 0.00 44.74 2.01
2539 2596 9.016623 CATGCTTAATTGTGAGTTTATGACATG 57.983 33.333 0.00 0.00 0.00 3.21
2545 2602 5.611796 TGTGAGTTTATGACATGAGTTGC 57.388 39.130 0.00 0.00 0.00 4.17
2549 2606 5.063817 TGAGTTTATGACATGAGTTGCGATG 59.936 40.000 0.00 0.00 0.00 3.84
2554 2611 4.654091 TGACATGAGTTGCGATGATCTA 57.346 40.909 0.00 0.00 0.00 1.98
2664 2721 8.839310 AGAGGATACAAATATAATGAGCACAC 57.161 34.615 0.00 0.00 41.41 3.82
2668 2725 5.835113 ACAAATATAATGAGCACACACCC 57.165 39.130 0.00 0.00 0.00 4.61
2669 2726 5.260424 ACAAATATAATGAGCACACACCCA 58.740 37.500 0.00 0.00 0.00 4.51
2670 2727 5.357878 ACAAATATAATGAGCACACACCCAG 59.642 40.000 0.00 0.00 0.00 4.45
2674 2731 2.359230 GAGCACACACCCAGCCTC 60.359 66.667 0.00 0.00 0.00 4.70
2694 2751 2.500098 TCTAGGTAGGATGCACACAACC 59.500 50.000 0.00 0.00 39.00 3.77
2703 2760 1.661197 GCACACAACCAATGCACGG 60.661 57.895 2.38 2.38 39.23 4.94
2704 2761 1.007502 CACACAACCAATGCACGGG 60.008 57.895 8.78 6.45 0.00 5.28
2723 2786 0.891904 GCACACACCCAAATACCCGT 60.892 55.000 0.00 0.00 0.00 5.28
2724 2787 1.611519 CACACACCCAAATACCCGTT 58.388 50.000 0.00 0.00 0.00 4.44
2725 2788 1.268352 CACACACCCAAATACCCGTTG 59.732 52.381 0.00 0.00 0.00 4.10
2759 2823 4.319177 AGCCATAAAGACCGAAGATATGC 58.681 43.478 0.00 0.00 0.00 3.14
2764 2828 6.934645 CCATAAAGACCGAAGATATGCCTAAA 59.065 38.462 0.00 0.00 0.00 1.85
2769 2833 2.036733 CCGAAGATATGCCTAAACGGGA 59.963 50.000 0.00 0.00 37.60 5.14
2801 2871 3.244345 GCGAAACGATCAAATCCGTGATA 59.756 43.478 0.00 0.00 38.38 2.15
2810 2880 6.508563 CGATCAAATCCGTGATAGACAAACTG 60.509 42.308 0.00 0.00 38.38 3.16
2816 2886 3.246226 CCGTGATAGACAAACTGCTATGC 59.754 47.826 0.00 0.00 0.00 3.14
2817 2887 3.865164 CGTGATAGACAAACTGCTATGCA 59.135 43.478 0.00 0.00 36.92 3.96
2818 2888 4.329801 CGTGATAGACAAACTGCTATGCAA 59.670 41.667 0.00 0.00 38.41 4.08
2819 2889 5.007039 CGTGATAGACAAACTGCTATGCAAT 59.993 40.000 0.00 0.00 38.41 3.56
2820 2890 6.200854 CGTGATAGACAAACTGCTATGCAATA 59.799 38.462 0.00 0.00 38.41 1.90
2821 2891 7.095481 CGTGATAGACAAACTGCTATGCAATAT 60.095 37.037 0.00 0.00 38.41 1.28
2823 2893 8.777413 TGATAGACAAACTGCTATGCAATATTC 58.223 33.333 0.00 0.00 38.41 1.75
2824 2894 8.681486 ATAGACAAACTGCTATGCAATATTCA 57.319 30.769 0.00 0.00 38.41 2.57
2835 2906 7.149973 GCTATGCAATATTCACACCAATCATT 58.850 34.615 0.00 0.00 0.00 2.57
2866 2937 6.150140 ACATCACAAGGACAATTAGCTTCTTC 59.850 38.462 0.00 0.00 0.00 2.87
2869 2940 6.017109 TCACAAGGACAATTAGCTTCTTCAAC 60.017 38.462 0.00 0.00 0.00 3.18
2871 2942 6.321181 ACAAGGACAATTAGCTTCTTCAACAA 59.679 34.615 0.00 0.00 0.00 2.83
2872 2943 6.566197 AGGACAATTAGCTTCTTCAACAAG 57.434 37.500 0.00 0.00 0.00 3.16
2884 2955 5.560966 TCTTCAACAAGAACACCTTCAAC 57.439 39.130 0.00 0.00 35.57 3.18
2890 2961 3.621715 ACAAGAACACCTTCAACGAAGTC 59.378 43.478 3.25 0.00 37.92 3.01
2891 2962 2.835027 AGAACACCTTCAACGAAGTCC 58.165 47.619 3.25 0.00 45.00 3.85
2892 2963 2.169769 AGAACACCTTCAACGAAGTCCA 59.830 45.455 3.25 0.00 45.00 4.02
2907 2978 1.153765 TCCAGACGCTCAAGCATCG 60.154 57.895 2.50 0.00 38.42 3.84
2913 2984 1.140589 CGCTCAAGCATCGTCCTCT 59.859 57.895 2.50 0.00 42.21 3.69
2914 2985 1.144565 CGCTCAAGCATCGTCCTCTG 61.145 60.000 2.50 0.00 42.21 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 3.194968 ACGAGACACCGATGATTTTACCT 59.805 43.478 0.00 0.00 0.00 3.08
61 62 2.203983 TCCCTCCAAGCCTGCTCA 60.204 61.111 0.00 0.00 0.00 4.26
169 170 0.319297 GCAACTTTGAAGCCAGGCAG 60.319 55.000 15.80 3.92 0.00 4.85
248 249 2.437413 GACACCTTTGAGATTGGGGAC 58.563 52.381 0.00 0.00 0.00 4.46
378 379 4.399303 CCCTTGACAAAACAAGAGAAGTGT 59.601 41.667 9.55 0.00 46.85 3.55
471 472 3.880490 GGATGCAAATATTCGTACCACCA 59.120 43.478 0.00 0.00 0.00 4.17
490 491 3.934068 ACTTTCGTATCAAACCGTGGAT 58.066 40.909 0.00 0.00 0.00 3.41
507 508 7.766219 ACGTAGTTTCGCATTCATATACTTT 57.234 32.000 0.00 0.00 37.78 2.66
526 527 2.737252 GTTGCCTCTCCAAAGAACGTAG 59.263 50.000 0.00 0.00 0.00 3.51
528 529 1.141053 AGTTGCCTCTCCAAAGAACGT 59.859 47.619 0.00 0.00 0.00 3.99
533 534 3.064900 AGCTTAGTTGCCTCTCCAAAG 57.935 47.619 0.00 0.00 0.00 2.77
627 631 2.524569 ATTTGTGGCAAAAACGGAGG 57.475 45.000 4.67 0.00 0.00 4.30
631 635 5.040635 ACTACAGAATTTGTGGCAAAAACG 58.959 37.500 4.67 0.00 41.61 3.60
632 636 5.234116 CCACTACAGAATTTGTGGCAAAAAC 59.766 40.000 4.67 0.00 41.61 2.43
717 725 1.063174 GCAATGCTTAAGTCGCCTCTG 59.937 52.381 4.02 0.00 0.00 3.35
753 764 8.871629 AGAGAGATAGTACACTTCAGAAAAGA 57.128 34.615 0.00 0.00 0.00 2.52
754 765 8.735315 TGAGAGAGATAGTACACTTCAGAAAAG 58.265 37.037 0.00 0.00 0.00 2.27
755 766 8.637196 TGAGAGAGATAGTACACTTCAGAAAA 57.363 34.615 0.00 0.00 0.00 2.29
756 767 8.637196 TTGAGAGAGATAGTACACTTCAGAAA 57.363 34.615 0.00 0.00 0.00 2.52
757 768 8.637196 TTTGAGAGAGATAGTACACTTCAGAA 57.363 34.615 0.00 0.00 0.00 3.02
809 826 2.224426 TGGGCACGTCTGTCAACTTAAT 60.224 45.455 0.00 0.00 0.00 1.40
818 835 1.863662 CGAGTAGTGGGCACGTCTGT 61.864 60.000 0.00 0.00 36.20 3.41
837 881 1.517257 CGACGGTGACAGGCAGATC 60.517 63.158 0.00 0.00 0.00 2.75
838 882 2.573869 CGACGGTGACAGGCAGAT 59.426 61.111 0.00 0.00 0.00 2.90
839 883 4.357947 GCGACGGTGACAGGCAGA 62.358 66.667 0.00 0.00 0.00 4.26
842 886 2.573609 ATAAGGCGACGGTGACAGGC 62.574 60.000 0.00 0.00 0.00 4.85
843 887 0.108329 AATAAGGCGACGGTGACAGG 60.108 55.000 0.00 0.00 0.00 4.00
844 888 2.572191 TAATAAGGCGACGGTGACAG 57.428 50.000 0.00 0.00 0.00 3.51
845 889 3.530265 ATTAATAAGGCGACGGTGACA 57.470 42.857 0.00 0.00 0.00 3.58
846 890 6.535274 AATTATTAATAAGGCGACGGTGAC 57.465 37.500 13.15 0.00 0.00 3.67
847 891 8.659925 TTTAATTATTAATAAGGCGACGGTGA 57.340 30.769 13.15 0.00 0.00 4.02
848 892 9.377383 CTTTTAATTATTAATAAGGCGACGGTG 57.623 33.333 13.15 0.00 0.00 4.94
849 893 9.328845 TCTTTTAATTATTAATAAGGCGACGGT 57.671 29.630 13.15 0.00 0.00 4.83
928 975 3.563808 GTGTTGTCAAATGCCACTACTCA 59.436 43.478 0.00 0.00 0.00 3.41
963 1011 2.174319 GCCGACGAAGGAGATTGGC 61.174 63.158 0.00 0.00 0.00 4.52
992 1040 4.342092 TCATCAGATCGTTCATCTTGGCTA 59.658 41.667 0.00 0.00 40.20 3.93
1095 1143 1.580845 CCAAGAACGCCTGGAGCTTG 61.581 60.000 0.00 4.37 40.39 4.01
1101 1149 2.032528 TCTGCCAAGAACGCCTGG 59.967 61.111 0.00 0.00 0.00 4.45
1904 1952 3.259123 GGCTCATCACAACCCAAGAAAAT 59.741 43.478 0.00 0.00 0.00 1.82
2013 2070 6.013379 AGAGACTGAAGACCAGATAGTGAAA 58.987 40.000 0.00 0.00 45.78 2.69
2031 2088 4.451900 ACGAACACCATTCAAAAGAGACT 58.548 39.130 0.00 0.00 0.00 3.24
2052 2109 6.403964 GGAAATTAGTATGTTTGGTCGGGAAC 60.404 42.308 0.00 0.00 0.00 3.62
2053 2110 5.648960 GGAAATTAGTATGTTTGGTCGGGAA 59.351 40.000 0.00 0.00 0.00 3.97
2101 2158 6.622833 TGCAGACACATATGTAATGGAATG 57.377 37.500 8.32 2.56 39.95 2.67
2108 2165 4.322567 TGTGCTTGCAGACACATATGTAA 58.677 39.130 17.12 0.00 41.67 2.41
2119 2176 5.299028 TGAATCTAAGTTTTGTGCTTGCAGA 59.701 36.000 0.00 0.00 0.00 4.26
2120 2177 5.522456 TGAATCTAAGTTTTGTGCTTGCAG 58.478 37.500 0.00 0.00 0.00 4.41
2121 2178 5.512753 TGAATCTAAGTTTTGTGCTTGCA 57.487 34.783 0.00 0.00 0.00 4.08
2122 2179 5.922544 ACATGAATCTAAGTTTTGTGCTTGC 59.077 36.000 0.00 0.00 0.00 4.01
2123 2180 8.075574 TGTACATGAATCTAAGTTTTGTGCTTG 58.924 33.333 0.00 0.00 0.00 4.01
2124 2181 8.165239 TGTACATGAATCTAAGTTTTGTGCTT 57.835 30.769 0.00 0.00 0.00 3.91
2125 2182 7.744087 TGTACATGAATCTAAGTTTTGTGCT 57.256 32.000 0.00 0.00 0.00 4.40
2126 2183 8.970691 AATGTACATGAATCTAAGTTTTGTGC 57.029 30.769 9.63 0.00 0.00 4.57
2239 2296 9.840427 AATTTTAGTTGCATACATCTGTTACAC 57.160 29.630 0.00 0.00 0.00 2.90
2284 2341 9.996554 CCAATATGATTGAACACACCTACTATA 57.003 33.333 0.70 0.00 0.00 1.31
2296 2353 6.426328 TGTTTTTGGCACCAATATGATTGAAC 59.574 34.615 2.31 0.80 35.70 3.18
2305 2362 7.450014 TCTCTTTAGATGTTTTTGGCACCAATA 59.550 33.333 2.31 0.00 35.70 1.90
2307 2364 5.596361 TCTCTTTAGATGTTTTTGGCACCAA 59.404 36.000 0.00 0.00 0.00 3.67
2316 2373 7.967908 TCCTCAGTCTTCTCTTTAGATGTTTT 58.032 34.615 0.00 0.00 0.00 2.43
2326 2383 3.582208 AGCACAATCCTCAGTCTTCTCTT 59.418 43.478 0.00 0.00 0.00 2.85
2363 2420 6.947733 ACCAAATTGACACAATTCTCTGGATA 59.052 34.615 22.21 0.00 0.00 2.59
2369 2426 8.273780 AGATAGACCAAATTGACACAATTCTC 57.726 34.615 9.60 6.03 0.00 2.87
2379 2436 9.104965 CCAAATTACGTAGATAGACCAAATTGA 57.895 33.333 0.00 0.00 0.00 2.57
2389 2446 6.366332 GCTGGATGACCAAATTACGTAGATAG 59.634 42.308 0.00 0.00 46.32 2.08
2396 2453 2.276201 TCGCTGGATGACCAAATTACG 58.724 47.619 0.00 0.00 46.32 3.18
2414 2471 4.447724 TCGTCAAAAACTGGAAGATCTTCG 59.552 41.667 25.40 16.71 40.37 3.79
2415 2472 5.924475 TCGTCAAAAACTGGAAGATCTTC 57.076 39.130 24.68 24.68 37.43 2.87
2422 2479 8.410141 ACTAAAATCATTCGTCAAAAACTGGAA 58.590 29.630 0.00 0.00 0.00 3.53
2453 2510 3.428532 ACTGACACTGAACCCGTATAGT 58.571 45.455 0.00 0.00 0.00 2.12
2459 2516 4.320202 CCATAAAAACTGACACTGAACCCG 60.320 45.833 0.00 0.00 0.00 5.28
2469 2526 6.635030 AAGACTGAACCCATAAAAACTGAC 57.365 37.500 0.00 0.00 0.00 3.51
2484 2541 3.553828 AACCGAAGACCAAAGACTGAA 57.446 42.857 0.00 0.00 0.00 3.02
2485 2542 3.553828 AAACCGAAGACCAAAGACTGA 57.446 42.857 0.00 0.00 0.00 3.41
2486 2543 4.632538 AAAAACCGAAGACCAAAGACTG 57.367 40.909 0.00 0.00 0.00 3.51
2487 2544 5.278315 GCATAAAAACCGAAGACCAAAGACT 60.278 40.000 0.00 0.00 0.00 3.24
2501 2558 7.117523 TCACAATTAAGCATGTGCATAAAAACC 59.882 33.333 7.83 0.00 45.08 3.27
2515 2572 8.334263 TCATGTCATAAACTCACAATTAAGCA 57.666 30.769 0.00 0.00 0.00 3.91
2521 2578 6.615088 GCAACTCATGTCATAAACTCACAAT 58.385 36.000 0.00 0.00 0.00 2.71
2532 2589 4.069300 AGATCATCGCAACTCATGTCAT 57.931 40.909 0.00 0.00 0.00 3.06
2539 2596 5.743398 GCTCATCTATAGATCATCGCAACTC 59.257 44.000 12.50 0.00 31.21 3.01
2545 2602 5.972973 GCTTGAGCTCATCTATAGATCATCG 59.027 44.000 19.04 2.08 39.00 3.84
2638 2695 9.277783 GTGTGCTCATTATATTTGTATCCTCTT 57.722 33.333 0.00 0.00 0.00 2.85
2664 2721 0.261991 TCCTACCTAGAGGCTGGGTG 59.738 60.000 12.09 3.40 44.93 4.61
2668 2725 1.342819 GTGCATCCTACCTAGAGGCTG 59.657 57.143 0.00 0.00 41.45 4.85
2669 2726 1.062886 TGTGCATCCTACCTAGAGGCT 60.063 52.381 0.00 0.00 41.45 4.58
2670 2727 1.069358 GTGTGCATCCTACCTAGAGGC 59.931 57.143 0.00 0.00 41.27 4.70
2674 2731 2.236146 TGGTTGTGTGCATCCTACCTAG 59.764 50.000 16.05 0.00 35.89 3.02
2703 2760 1.591504 CGGGTATTTGGGTGTGTGCC 61.592 60.000 0.00 0.00 0.00 5.01
2704 2761 0.891904 ACGGGTATTTGGGTGTGTGC 60.892 55.000 0.00 0.00 0.00 4.57
2710 2773 0.178958 TTGCCAACGGGTATTTGGGT 60.179 50.000 4.15 0.00 43.39 4.51
2725 2788 4.805719 GTCTTTATGGCTTTGCTATTTGCC 59.194 41.667 0.00 0.00 45.10 4.52
2737 2800 4.319177 GCATATCTTCGGTCTTTATGGCT 58.681 43.478 0.00 0.00 0.00 4.75
2739 2802 4.899502 AGGCATATCTTCGGTCTTTATGG 58.100 43.478 0.00 0.00 0.00 2.74
2774 2838 3.181520 CGGATTTGATCGTTTCGCTTTCT 60.182 43.478 0.00 0.00 0.00 2.52
2781 2851 5.518847 TGTCTATCACGGATTTGATCGTTTC 59.481 40.000 0.00 0.00 37.42 2.78
2785 2855 5.520288 AGTTTGTCTATCACGGATTTGATCG 59.480 40.000 0.00 0.00 37.42 3.69
2787 2857 5.065218 GCAGTTTGTCTATCACGGATTTGAT 59.935 40.000 0.00 0.00 39.61 2.57
2801 2871 6.375174 TGTGAATATTGCATAGCAGTTTGTCT 59.625 34.615 0.00 0.00 40.61 3.41
2810 2880 6.075762 TGATTGGTGTGAATATTGCATAGC 57.924 37.500 0.00 0.41 0.00 2.97
2835 2906 6.127925 GCTAATTGTCCTTGTGATGTCATGAA 60.128 38.462 0.00 0.00 0.00 2.57
2866 2937 4.142687 ACTTCGTTGAAGGTGTTCTTGTTG 60.143 41.667 10.95 0.00 43.25 3.33
2869 2940 3.002348 GGACTTCGTTGAAGGTGTTCTTG 59.998 47.826 10.95 0.00 43.25 3.02
2871 2942 2.169769 TGGACTTCGTTGAAGGTGTTCT 59.830 45.455 10.95 0.00 43.25 3.01
2872 2943 2.544267 CTGGACTTCGTTGAAGGTGTTC 59.456 50.000 10.95 0.03 43.25 3.18
2884 2955 1.347817 GCTTGAGCGTCTGGACTTCG 61.348 60.000 0.00 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.