Multiple sequence alignment - TraesCS5D01G146800

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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 TraesCS5D01G146800 chr5D 100.000 2759 0 0 1 2759 233410009 233412767 0 5096
1 TraesCS5D01G146800 chr5B 89.341 2627 155 48 1 2544 271668703 271666119 0 3184
2 TraesCS5D01G146800 chr5A 89.740 2076 131 37 723 2752 321325976 321328015 0 2579
3 TraesCS5D01G146800 chr5A 90.946 740 49 10 1 727 321325217 321325951 0 979


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 TraesCS5D01G146800 chr5D 233410009 233412767 2758 False 5096 5096 100.000 1 2759 1 chr5D.!!$F1 2758
1 TraesCS5D01G146800 chr5B 271666119 271668703 2584 True 3184 3184 89.341 1 2544 1 chr5B.!!$R1 2543
2 TraesCS5D01G146800 chr5A 321325217 321328015 2798 False 1779 2579 90.343 1 2752 2 chr5A.!!$F1 2751

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
150 153 0.959372 TCTCTTCTCCGTCCGTCCAC 60.959 60.0 0.0 0.00 0.00 4.02 F
822 876 0.962356 AGTGGCAGGATCCTTTTGCG 60.962 55.0 13.0 0.87 38.69 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1214 1285 0.176910 TGCAACCACGTTCAGAGTGA 59.823 50.0 0.0 0.0 41.83 3.41 R
2318 2418 0.179116 CGTCAGCCAGTCCATCAGAG 60.179 60.0 0.0 0.0 0.00 3.35 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
53 54 2.108075 CTGCTCCTCTCCATCTCCTCTA 59.892 54.545 0.00 0.00 0.00 2.43
150 153 0.959372 TCTCTTCTCCGTCCGTCCAC 60.959 60.000 0.00 0.00 0.00 4.02
169 172 2.358737 CCTCGCCGAACCAAGCTT 60.359 61.111 0.00 0.00 0.00 3.74
221 226 2.464459 GCGACCAATCTTCGGCTGG 61.464 63.158 0.00 0.00 36.96 4.85
228 233 2.636830 CAATCTTCGGCTGGATCAAGT 58.363 47.619 0.00 0.00 0.00 3.16
251 256 2.007608 GAAACAGGTATCGTGCCCTTC 58.992 52.381 0.00 0.00 0.00 3.46
253 258 1.227263 CAGGTATCGTGCCCTTCCG 60.227 63.158 0.00 0.00 0.00 4.30
255 260 2.499685 GTATCGTGCCCTTCCGCT 59.500 61.111 0.00 0.00 0.00 5.52
316 321 2.391879 GCGGTCCAATCTATCGTGTAC 58.608 52.381 0.00 0.00 0.00 2.90
323 328 4.743151 TCCAATCTATCGTGTACGCAATTC 59.257 41.667 7.29 0.00 39.60 2.17
349 354 4.945246 TCTCCGATTGATAAGTTGCTACC 58.055 43.478 0.00 0.00 0.00 3.18
359 364 1.666872 GTTGCTACCAGGCGTTCGT 60.667 57.895 0.00 0.00 34.52 3.85
386 391 6.211384 AGGTAATTGCTAGGCTTTGATTTGTT 59.789 34.615 0.00 0.00 0.00 2.83
390 395 6.398234 TTGCTAGGCTTTGATTTGTTGTAA 57.602 33.333 0.00 0.00 0.00 2.41
393 398 5.629435 GCTAGGCTTTGATTTGTTGTAACAC 59.371 40.000 0.00 0.00 38.92 3.32
457 462 5.795441 GGATGCGTGTTTCTGAAATACTTTC 59.205 40.000 22.11 16.28 40.08 2.62
458 463 6.348540 GGATGCGTGTTTCTGAAATACTTTCT 60.349 38.462 22.11 8.80 40.32 2.52
459 464 7.148474 GGATGCGTGTTTCTGAAATACTTTCTA 60.148 37.037 22.11 8.74 40.32 2.10
464 469 8.840867 CGTGTTTCTGAAATACTTTCTATTTGC 58.159 33.333 22.11 0.96 40.32 3.68
502 508 4.411212 GGGGTACTGTGGTTATAAGGATGT 59.589 45.833 0.00 0.00 0.00 3.06
599 612 8.336498 CATAGTTGCAGATCAGCTTAATTTTG 57.664 34.615 11.68 0.00 37.44 2.44
669 688 8.437360 TGATGTAATGTTTTTATCTCGAGCAT 57.563 30.769 7.81 5.12 0.00 3.79
673 697 3.609853 TGTTTTTATCTCGAGCATGCCT 58.390 40.909 15.66 1.01 0.00 4.75
742 795 2.668550 TGCTGCTGCTGCTGTCAG 60.669 61.111 27.67 18.94 43.16 3.51
755 808 2.682856 TGCTGTCAGTTCTTTTGTGACC 59.317 45.455 0.93 0.00 39.96 4.02
757 810 3.194861 CTGTCAGTTCTTTTGTGACCGA 58.805 45.455 0.00 0.00 39.96 4.69
761 814 2.549754 CAGTTCTTTTGTGACCGAGCAT 59.450 45.455 0.00 0.00 0.00 3.79
783 836 6.455646 GCATCGTGTTTATTCTGAAATCGTCT 60.456 38.462 0.00 0.00 0.00 4.18
784 837 7.456253 CATCGTGTTTATTCTGAAATCGTCTT 58.544 34.615 0.00 0.00 0.00 3.01
785 838 7.416154 TCGTGTTTATTCTGAAATCGTCTTT 57.584 32.000 0.00 0.00 0.00 2.52
786 839 7.857569 TCGTGTTTATTCTGAAATCGTCTTTT 58.142 30.769 0.00 0.00 0.00 2.27
787 840 7.796660 TCGTGTTTATTCTGAAATCGTCTTTTG 59.203 33.333 0.00 0.00 0.00 2.44
789 842 8.682016 GTGTTTATTCTGAAATCGTCTTTTGTG 58.318 33.333 0.00 0.00 0.00 3.33
795 848 8.827177 TTCTGAAATCGTCTTTTGTGTATAGT 57.173 30.769 0.00 0.00 0.00 2.12
797 850 8.922676 TCTGAAATCGTCTTTTGTGTATAGTTC 58.077 33.333 0.00 0.00 0.00 3.01
798 851 8.025243 TGAAATCGTCTTTTGTGTATAGTTCC 57.975 34.615 0.00 0.00 0.00 3.62
802 856 4.390909 CGTCTTTTGTGTATAGTTCCACCC 59.609 45.833 0.00 0.00 0.00 4.61
822 876 0.962356 AGTGGCAGGATCCTTTTGCG 60.962 55.000 13.00 0.87 38.69 4.85
823 877 2.342650 TGGCAGGATCCTTTTGCGC 61.343 57.895 13.00 12.20 38.69 6.09
824 878 2.491621 GCAGGATCCTTTTGCGCC 59.508 61.111 13.00 0.00 0.00 6.53
825 879 3.068729 GCAGGATCCTTTTGCGCCC 62.069 63.158 13.00 0.00 0.00 6.13
827 881 3.147595 GGATCCTTTTGCGCCCCC 61.148 66.667 4.18 0.00 0.00 5.40
896 950 6.267014 TGAGTAGTTTATGGCAGTATCTACCC 59.733 42.308 14.45 7.64 0.00 3.69
899 953 5.930135 AGTTTATGGCAGTATCTACCCTTG 58.070 41.667 0.00 0.00 0.00 3.61
919 973 6.127451 CCCTTGTACTGACCTTTTCTTTGTTT 60.127 38.462 0.00 0.00 0.00 2.83
1015 1071 4.431131 ACATGGCGGGGGCTGAAG 62.431 66.667 0.00 0.00 0.00 3.02
1016 1072 4.431131 CATGGCGGGGGCTGAAGT 62.431 66.667 0.00 0.00 0.00 3.01
1017 1073 2.690881 ATGGCGGGGGCTGAAGTA 60.691 61.111 0.00 0.00 0.00 2.24
1019 1075 4.176752 GGCGGGGGCTGAAGTAGG 62.177 72.222 0.00 0.00 0.00 3.18
1164 1235 5.622346 ACAAGGAAGACATAGAATCCCTC 57.378 43.478 0.00 0.00 32.15 4.30
1202 1273 5.357257 TCTTGAGAATAACGAGGGTAATGC 58.643 41.667 0.00 0.00 0.00 3.56
1224 1295 1.736681 GCTGAGGCAATCACTCTGAAC 59.263 52.381 0.00 0.00 36.40 3.18
1252 1323 5.426689 TGCACTAGAAATGTCCATCTCTT 57.573 39.130 0.00 0.00 0.00 2.85
1259 1330 1.760192 ATGTCCATCTCTTGCAAGGC 58.240 50.000 25.73 2.49 0.00 4.35
1261 1332 1.339438 TGTCCATCTCTTGCAAGGCTC 60.339 52.381 25.73 10.25 0.00 4.70
1320 1391 2.826128 GGGAAACATCTTTGACCCCTTC 59.174 50.000 0.00 0.00 32.47 3.46
1347 1418 3.073735 CCAGAGGAGGCGCTCTGT 61.074 66.667 19.36 6.69 43.91 3.41
1371 1442 1.615107 CGCCGAAGAAGAACGTGGTC 61.615 60.000 0.00 0.00 0.00 4.02
1398 1469 2.285889 TAGAGACCCTCTCCCGCAGG 62.286 65.000 0.00 0.00 44.42 4.85
1569 1640 1.537135 GGCGAGGCTGTTCTGATAGAC 60.537 57.143 0.00 0.00 0.00 2.59
1605 1679 1.840635 AGCTACAAGACCCCTGAATCC 59.159 52.381 0.00 0.00 0.00 3.01
1765 1839 3.262915 AGACAATAAGAGCTGAGCCTGTT 59.737 43.478 0.00 0.00 0.00 3.16
1960 2044 1.134280 CCCAGTCTTACTGCCCTGATG 60.134 57.143 1.43 0.00 44.63 3.07
1983 2071 3.008835 TGATGTAGTAGTACCGGCACT 57.991 47.619 13.02 13.02 0.00 4.40
2067 2155 0.670162 TGCTTGCCTTGAACTGAAGC 59.330 50.000 0.00 0.00 39.59 3.86
2069 2157 1.335689 GCTTGCCTTGAACTGAAGCAG 60.336 52.381 0.00 0.00 39.09 4.24
2098 2186 4.261114 GCAGATTCATCCTTGCTTAGCTTC 60.261 45.833 5.60 0.00 0.00 3.86
2099 2187 4.025061 CAGATTCATCCTTGCTTAGCTTCG 60.025 45.833 5.60 0.00 0.00 3.79
2113 2202 2.771089 AGCTTCGATCTTTGCACTTGA 58.229 42.857 0.00 0.00 0.00 3.02
2114 2203 3.341823 AGCTTCGATCTTTGCACTTGAT 58.658 40.909 0.00 0.00 0.00 2.57
2115 2204 3.126514 AGCTTCGATCTTTGCACTTGATG 59.873 43.478 0.00 0.00 0.00 3.07
2116 2205 3.120060 GCTTCGATCTTTGCACTTGATGT 60.120 43.478 0.00 0.00 0.00 3.06
2117 2206 4.093408 GCTTCGATCTTTGCACTTGATGTA 59.907 41.667 0.00 0.00 0.00 2.29
2118 2207 5.220739 GCTTCGATCTTTGCACTTGATGTAT 60.221 40.000 0.00 0.00 0.00 2.29
2119 2208 6.676456 GCTTCGATCTTTGCACTTGATGTATT 60.676 38.462 0.00 0.00 0.00 1.89
2120 2209 7.465916 GCTTCGATCTTTGCACTTGATGTATTA 60.466 37.037 0.00 0.00 0.00 0.98
2125 2217 7.601073 TCTTTGCACTTGATGTATTACTCTG 57.399 36.000 0.00 0.00 0.00 3.35
2156 2248 1.027357 ATGATGCAGTGGCGAATTCC 58.973 50.000 0.00 0.00 45.35 3.01
2163 2255 1.811965 CAGTGGCGAATTCCAACATGA 59.188 47.619 0.00 0.00 37.96 3.07
2165 2257 1.812571 GTGGCGAATTCCAACATGACT 59.187 47.619 0.00 0.00 37.96 3.41
2166 2258 2.228822 GTGGCGAATTCCAACATGACTT 59.771 45.455 0.00 0.00 37.96 3.01
2167 2259 2.228582 TGGCGAATTCCAACATGACTTG 59.771 45.455 0.00 0.00 32.18 3.16
2168 2260 2.415893 GGCGAATTCCAACATGACTTGG 60.416 50.000 8.47 8.47 42.04 3.61
2169 2261 2.228822 GCGAATTCCAACATGACTTGGT 59.771 45.455 13.25 0.00 41.49 3.67
2268 2368 5.220662 CCTTATTAATTGTGCTGGTCTGTCG 60.221 44.000 0.00 0.00 0.00 4.35
2299 2399 2.991250 TGGCTGCTCTTCCTGTTAATC 58.009 47.619 0.00 0.00 0.00 1.75
2318 2418 2.231529 TCTTAGCCGTCAGATAGAGCC 58.768 52.381 0.00 0.00 0.00 4.70
2450 2550 4.600692 ACAGGGTTTATTTTTCACTGCC 57.399 40.909 0.00 0.00 36.22 4.85
2452 2552 4.039124 ACAGGGTTTATTTTTCACTGCCTG 59.961 41.667 0.00 0.00 36.22 4.85
2453 2553 3.006859 AGGGTTTATTTTTCACTGCCTGC 59.993 43.478 0.00 0.00 0.00 4.85
2503 2603 0.392863 TGGTGGCATCACGAATCCAG 60.393 55.000 0.00 0.00 44.50 3.86
2552 2659 1.686052 CACAGGTGGCTTGGCTTTAAA 59.314 47.619 0.00 0.00 0.00 1.52
2554 2661 1.273327 CAGGTGGCTTGGCTTTAAAGG 59.727 52.381 16.78 1.37 0.00 3.11
2555 2662 0.608130 GGTGGCTTGGCTTTAAAGGG 59.392 55.000 16.78 0.00 0.00 3.95
2557 2664 1.691976 GTGGCTTGGCTTTAAAGGGTT 59.308 47.619 16.78 0.00 0.00 4.11
2558 2665 2.894765 GTGGCTTGGCTTTAAAGGGTTA 59.105 45.455 16.78 0.00 0.00 2.85
2559 2666 3.513912 GTGGCTTGGCTTTAAAGGGTTAT 59.486 43.478 16.78 0.00 0.00 1.89
2560 2667 3.513515 TGGCTTGGCTTTAAAGGGTTATG 59.486 43.478 16.78 0.00 0.00 1.90
2561 2668 3.513912 GGCTTGGCTTTAAAGGGTTATGT 59.486 43.478 16.78 0.00 0.00 2.29
2562 2669 4.707934 GGCTTGGCTTTAAAGGGTTATGTA 59.292 41.667 16.78 0.00 0.00 2.29
2588 2698 4.808414 AATCAGAACATCAAGGACTCGA 57.192 40.909 0.00 0.00 0.00 4.04
2595 2705 1.827969 CATCAAGGACTCGAGGAAGGT 59.172 52.381 18.41 0.00 0.00 3.50
2599 2709 0.033894 AGGACTCGAGGAAGGTCTCC 60.034 60.000 18.41 12.38 45.81 3.71
2627 2737 3.073062 ACCCCCTAACAGCAAGCTATATG 59.927 47.826 0.00 0.00 0.00 1.78
2628 2738 3.560025 CCCCCTAACAGCAAGCTATATGG 60.560 52.174 0.00 0.00 0.00 2.74
2629 2739 3.327757 CCCCTAACAGCAAGCTATATGGA 59.672 47.826 0.00 0.00 0.00 3.41
2630 2740 4.564406 CCCCTAACAGCAAGCTATATGGAG 60.564 50.000 0.00 0.00 0.00 3.86
2631 2741 4.040952 CCCTAACAGCAAGCTATATGGAGT 59.959 45.833 0.00 0.00 0.00 3.85
2632 2742 5.246203 CCCTAACAGCAAGCTATATGGAGTA 59.754 44.000 0.00 0.00 0.00 2.59
2633 2743 6.070538 CCCTAACAGCAAGCTATATGGAGTAT 60.071 42.308 0.00 0.00 0.00 2.12
2635 2745 8.531982 CCTAACAGCAAGCTATATGGAGTATAA 58.468 37.037 0.00 0.00 0.00 0.98
2637 2747 8.839310 AACAGCAAGCTATATGGAGTATAAAG 57.161 34.615 0.00 0.00 0.00 1.85
2638 2748 6.876257 ACAGCAAGCTATATGGAGTATAAAGC 59.124 38.462 0.00 0.00 0.00 3.51
2639 2749 6.875726 CAGCAAGCTATATGGAGTATAAAGCA 59.124 38.462 0.00 0.00 30.14 3.91
2640 2750 7.551974 CAGCAAGCTATATGGAGTATAAAGCAT 59.448 37.037 0.00 0.00 30.14 3.79
2642 2752 8.821894 GCAAGCTATATGGAGTATAAAGCATAC 58.178 37.037 0.00 0.00 39.99 2.39
2644 2754 8.294954 AGCTATATGGAGTATAAAGCATACGT 57.705 34.615 0.00 0.00 43.75 3.57
2645 2755 9.404848 AGCTATATGGAGTATAAAGCATACGTA 57.595 33.333 0.00 0.00 43.75 3.57
2660 2770 8.943909 AAGCATACGTATAAGATAATAAGGCC 57.056 34.615 7.96 0.00 0.00 5.19
2661 2771 7.201145 AGCATACGTATAAGATAATAAGGCCG 58.799 38.462 7.96 0.00 0.00 6.13
2662 2772 6.074463 GCATACGTATAAGATAATAAGGCCGC 60.074 42.308 7.96 0.00 0.00 6.53
2680 2790 2.164663 CGCTTAGGATTCGTGCGCA 61.165 57.895 5.66 5.66 40.15 6.09
2713 2831 6.874664 AGAATCTAGACACATGATGATGATGC 59.125 38.462 0.00 0.00 33.36 3.91
2733 2851 3.181507 TGCGATGAACAATAAGAGCAAGC 60.182 43.478 0.00 0.00 0.00 4.01
2739 2857 6.381481 TGAACAATAAGAGCAAGCCATATG 57.619 37.500 0.00 0.00 0.00 1.78
2740 2858 5.887598 TGAACAATAAGAGCAAGCCATATGT 59.112 36.000 1.24 0.00 0.00 2.29
2742 2860 4.037208 ACAATAAGAGCAAGCCATATGTGC 59.963 41.667 8.37 8.37 38.59 4.57
2752 2870 5.389516 GCAAGCCATATGTGCGTATACTAAC 60.390 44.000 1.24 0.00 0.00 2.34
2753 2871 5.723672 AGCCATATGTGCGTATACTAACT 57.276 39.130 1.24 0.00 0.00 2.24
2754 2872 6.829229 AGCCATATGTGCGTATACTAACTA 57.171 37.500 1.24 0.00 0.00 2.24
2755 2873 6.853720 AGCCATATGTGCGTATACTAACTAG 58.146 40.000 1.24 0.00 0.00 2.57
2756 2874 5.515626 GCCATATGTGCGTATACTAACTAGC 59.484 44.000 1.24 0.00 0.00 3.42
2757 2875 6.034591 CCATATGTGCGTATACTAACTAGCC 58.965 44.000 1.24 0.00 0.00 3.93
2758 2876 3.996150 TGTGCGTATACTAACTAGCCC 57.004 47.619 0.56 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 3.675563 GCGCGGATCGAGGGAGAT 61.676 66.667 8.83 0.00 41.67 2.75
118 121 1.229209 AAGAGAGGGAGGGCGTCAA 60.229 57.895 9.66 0.00 0.00 3.18
119 122 1.682684 GAAGAGAGGGAGGGCGTCA 60.683 63.158 9.66 0.00 0.00 4.35
185 188 1.156736 GCCGATTAACATCCCCGATG 58.843 55.000 0.08 0.08 44.71 3.84
221 226 6.237861 GCACGATACCTGTTTCTAACTTGATC 60.238 42.308 0.00 0.00 0.00 2.92
228 233 2.835764 AGGGCACGATACCTGTTTCTAA 59.164 45.455 0.00 0.00 35.30 2.10
255 260 1.218047 CCGGAACCAGATCTGCGAA 59.782 57.895 17.76 0.00 0.00 4.70
316 321 3.190079 TCAATCGGAGAGAAGAATTGCG 58.810 45.455 0.00 0.00 43.63 4.85
323 328 5.355596 AGCAACTTATCAATCGGAGAGAAG 58.644 41.667 0.00 0.00 43.63 2.85
349 354 1.393539 CAATTACCTCACGAACGCCTG 59.606 52.381 0.00 0.00 0.00 4.85
359 364 4.568072 TCAAAGCCTAGCAATTACCTCA 57.432 40.909 0.00 0.00 0.00 3.86
386 391 1.300311 CGGTCGTGCAGGTGTTACA 60.300 57.895 6.26 0.00 0.00 2.41
414 419 5.702865 CATCCCTAATTTCGCAATACATGG 58.297 41.667 0.00 0.00 0.00 3.66
457 462 6.149474 CCCCAGATTAGTAATTCGGCAAATAG 59.851 42.308 0.00 0.00 0.00 1.73
458 463 6.001460 CCCCAGATTAGTAATTCGGCAAATA 58.999 40.000 0.00 0.00 0.00 1.40
459 464 4.827284 CCCCAGATTAGTAATTCGGCAAAT 59.173 41.667 0.00 0.00 0.00 2.32
464 469 5.070047 ACAGTACCCCAGATTAGTAATTCGG 59.930 44.000 0.00 1.18 0.00 4.30
527 533 8.448615 CGATGAAGATATATGGACTACACGTAA 58.551 37.037 0.00 0.00 0.00 3.18
664 683 2.758089 CGTGCTTCCAGGCATGCTC 61.758 63.158 18.92 7.89 44.34 4.26
669 688 1.148273 AAAGACGTGCTTCCAGGCA 59.852 52.632 0.00 0.00 40.15 4.75
673 697 0.874390 GATGCAAAGACGTGCTTCCA 59.126 50.000 0.00 0.00 45.17 3.53
742 795 2.411547 CGATGCTCGGTCACAAAAGAAC 60.412 50.000 0.00 0.00 36.00 3.01
755 808 4.840401 TTCAGAATAAACACGATGCTCG 57.160 40.909 0.00 4.36 46.93 5.03
757 810 5.351465 ACGATTTCAGAATAAACACGATGCT 59.649 36.000 0.00 0.00 0.00 3.79
761 814 7.416154 AAAGACGATTTCAGAATAAACACGA 57.584 32.000 0.00 0.00 0.00 4.35
763 816 8.682016 CACAAAAGACGATTTCAGAATAAACAC 58.318 33.333 0.00 0.00 0.00 3.32
779 832 4.390909 GGGTGGAACTATACACAAAAGACG 59.609 45.833 0.00 0.00 39.31 4.18
783 836 5.067273 CACTGGGTGGAACTATACACAAAA 58.933 41.667 0.00 0.00 39.31 2.44
784 837 4.647611 CACTGGGTGGAACTATACACAAA 58.352 43.478 0.00 0.00 39.31 2.83
785 838 4.280436 CACTGGGTGGAACTATACACAA 57.720 45.455 0.00 0.00 39.31 3.33
786 839 3.973206 CACTGGGTGGAACTATACACA 57.027 47.619 0.00 0.00 39.31 3.72
798 851 1.856539 AAGGATCCTGCCACTGGGTG 61.857 60.000 17.02 0.00 36.17 4.61
802 856 0.529378 GCAAAAGGATCCTGCCACTG 59.471 55.000 17.02 9.48 0.00 3.66
885 939 5.202004 AGGTCAGTACAAGGGTAGATACTG 58.798 45.833 0.00 4.27 43.85 2.74
896 950 7.535139 TGAAACAAAGAAAAGGTCAGTACAAG 58.465 34.615 0.00 0.00 0.00 3.16
899 953 6.095021 ACCTGAAACAAAGAAAAGGTCAGTAC 59.905 38.462 0.00 0.00 32.58 2.73
919 973 4.349636 TCCCACTTCAGTATCAAAACCTGA 59.650 41.667 0.00 0.00 38.81 3.86
1015 1071 2.851263 TCCAACACCACATGACCTAC 57.149 50.000 0.00 0.00 0.00 3.18
1016 1072 4.287326 TGTTATCCAACACCACATGACCTA 59.713 41.667 0.00 0.00 39.75 3.08
1017 1073 3.073798 TGTTATCCAACACCACATGACCT 59.926 43.478 0.00 0.00 39.75 3.85
1019 1075 3.119849 GCTGTTATCCAACACCACATGAC 60.120 47.826 0.00 0.00 39.75 3.06
1214 1285 0.176910 TGCAACCACGTTCAGAGTGA 59.823 50.000 0.00 0.00 41.83 3.41
1224 1295 2.159627 GGACATTTCTAGTGCAACCACG 59.840 50.000 0.00 0.00 46.62 4.94
1252 1323 1.074405 ACTTTCATCTGGAGCCTTGCA 59.926 47.619 0.00 0.00 0.00 4.08
1320 1391 2.363018 TCCTCTGGTCCTGGAGCG 60.363 66.667 19.98 14.61 32.15 5.03
1347 1418 1.959226 GTTCTTCTTCGGCGCACCA 60.959 57.895 10.83 0.00 34.57 4.17
1398 1469 7.536855 AGTCATCAGATTCAAAAATGAGCTTC 58.463 34.615 0.00 0.00 0.00 3.86
1569 1640 2.409870 GCTTTCAGGTGGGATGGCG 61.410 63.158 0.00 0.00 0.00 5.69
1617 1691 3.188786 GTGTCTGCGATGCCGGTC 61.189 66.667 1.90 0.00 36.06 4.79
1960 2044 4.037684 AGTGCCGGTACTACTACATCAATC 59.962 45.833 24.85 0.00 0.00 2.67
2067 2155 2.366533 AGGATGAATCTGCAACAGCTG 58.633 47.619 13.48 13.48 0.00 4.24
2069 2157 2.734492 GCAAGGATGAATCTGCAACAGC 60.734 50.000 0.00 0.00 0.00 4.40
2098 2186 7.223582 AGAGTAATACATCAAGTGCAAAGATCG 59.776 37.037 0.00 0.00 0.00 3.69
2099 2187 8.333908 CAGAGTAATACATCAAGTGCAAAGATC 58.666 37.037 0.00 0.00 0.00 2.75
2113 2202 4.021229 TCGGTGTCACCAGAGTAATACAT 58.979 43.478 21.91 0.00 38.47 2.29
2114 2203 3.423749 TCGGTGTCACCAGAGTAATACA 58.576 45.455 21.91 0.00 38.47 2.29
2115 2204 4.445452 TTCGGTGTCACCAGAGTAATAC 57.555 45.455 21.91 0.00 38.47 1.89
2116 2205 5.186215 TCATTTCGGTGTCACCAGAGTAATA 59.814 40.000 21.91 2.63 38.47 0.98
2117 2206 4.020573 TCATTTCGGTGTCACCAGAGTAAT 60.021 41.667 21.91 13.11 38.47 1.89
2118 2207 3.322541 TCATTTCGGTGTCACCAGAGTAA 59.677 43.478 21.91 11.65 38.47 2.24
2119 2208 2.894765 TCATTTCGGTGTCACCAGAGTA 59.105 45.455 21.91 11.40 38.47 2.59
2120 2209 1.691976 TCATTTCGGTGTCACCAGAGT 59.308 47.619 21.91 9.52 38.47 3.24
2125 2217 1.131126 CTGCATCATTTCGGTGTCACC 59.869 52.381 12.40 12.40 34.05 4.02
2156 2248 4.753233 TCAAACCAAACCAAGTCATGTTG 58.247 39.130 0.00 0.00 0.00 3.33
2163 2255 2.028130 TCGCATCAAACCAAACCAAGT 58.972 42.857 0.00 0.00 0.00 3.16
2165 2257 2.028130 AGTCGCATCAAACCAAACCAA 58.972 42.857 0.00 0.00 0.00 3.67
2166 2258 1.336440 CAGTCGCATCAAACCAAACCA 59.664 47.619 0.00 0.00 0.00 3.67
2167 2259 1.335872 CCAGTCGCATCAAACCAAACC 60.336 52.381 0.00 0.00 0.00 3.27
2168 2260 1.336755 ACCAGTCGCATCAAACCAAAC 59.663 47.619 0.00 0.00 0.00 2.93
2169 2261 1.336440 CACCAGTCGCATCAAACCAAA 59.664 47.619 0.00 0.00 0.00 3.28
2268 2368 0.237761 GAGCAGCCATCAATCATCGC 59.762 55.000 0.00 0.00 0.00 4.58
2299 2399 2.227865 GAGGCTCTATCTGACGGCTAAG 59.772 54.545 7.40 0.00 32.26 2.18
2318 2418 0.179116 CGTCAGCCAGTCCATCAGAG 60.179 60.000 0.00 0.00 0.00 3.35
2392 2492 3.117963 CCTCTGATCAATGAAAGCTCCCT 60.118 47.826 0.00 0.00 0.00 4.20
2450 2550 5.283717 GCAAATACAAGTCAAACATACGCAG 59.716 40.000 0.00 0.00 0.00 5.18
2452 2552 4.557301 GGCAAATACAAGTCAAACATACGC 59.443 41.667 0.00 0.00 0.00 4.42
2453 2553 4.786068 CGGCAAATACAAGTCAAACATACG 59.214 41.667 0.00 0.00 0.00 3.06
2503 2603 9.406828 GAAAGTAATTTTCAGGTTACAACATCC 57.593 33.333 0.00 0.00 43.79 3.51
2552 2659 9.614792 GATGTTCTGATTACTTTACATAACCCT 57.385 33.333 0.00 0.00 0.00 4.34
2558 2665 9.167311 GTCCTTGATGTTCTGATTACTTTACAT 57.833 33.333 0.00 0.00 0.00 2.29
2559 2666 8.375506 AGTCCTTGATGTTCTGATTACTTTACA 58.624 33.333 0.00 0.00 0.00 2.41
2560 2667 8.779354 AGTCCTTGATGTTCTGATTACTTTAC 57.221 34.615 0.00 0.00 0.00 2.01
2561 2668 7.759886 CGAGTCCTTGATGTTCTGATTACTTTA 59.240 37.037 0.00 0.00 0.00 1.85
2562 2669 6.591834 CGAGTCCTTGATGTTCTGATTACTTT 59.408 38.462 0.00 0.00 0.00 2.66
2574 2684 1.827969 CCTTCCTCGAGTCCTTGATGT 59.172 52.381 12.31 0.00 0.00 3.06
2575 2685 1.827969 ACCTTCCTCGAGTCCTTGATG 59.172 52.381 12.31 3.42 0.00 3.07
2582 2692 0.392729 TCGGAGACCTTCCTCGAGTC 60.393 60.000 12.31 2.43 44.41 3.36
2583 2693 0.393267 CTCGGAGACCTTCCTCGAGT 60.393 60.000 12.31 0.00 44.41 4.18
2588 2698 2.047443 GTCGCTCGGAGACCTTCCT 61.047 63.158 9.69 0.00 44.41 3.36
2595 2705 2.987596 TTAGGGGGTCGCTCGGAGA 61.988 63.158 9.69 0.00 0.00 3.71
2599 2709 2.494918 CTGTTAGGGGGTCGCTCG 59.505 66.667 0.00 0.00 0.00 5.03
2600 2710 2.180159 TTGCTGTTAGGGGGTCGCTC 62.180 60.000 0.00 0.00 0.00 5.03
2610 2720 9.929180 TTTATACTCCATATAGCTTGCTGTTAG 57.071 33.333 5.26 0.00 0.00 2.34
2635 2745 7.705325 CGGCCTTATTATCTTATACGTATGCTT 59.295 37.037 18.37 3.26 0.00 3.91
2637 2747 6.074463 GCGGCCTTATTATCTTATACGTATGC 60.074 42.308 18.37 7.81 0.00 3.14
2638 2748 6.141844 CGCGGCCTTATTATCTTATACGTATG 59.858 42.308 18.37 2.39 0.00 2.39
2639 2749 6.204359 CGCGGCCTTATTATCTTATACGTAT 58.796 40.000 13.54 13.54 0.00 3.06
2640 2750 5.572211 CGCGGCCTTATTATCTTATACGTA 58.428 41.667 0.00 0.00 0.00 3.57
2642 2752 3.242248 GCGCGGCCTTATTATCTTATACG 59.758 47.826 8.83 0.00 0.00 3.06
2644 2754 4.730949 AGCGCGGCCTTATTATCTTATA 57.269 40.909 8.83 0.00 0.00 0.98
2645 2755 3.611766 AGCGCGGCCTTATTATCTTAT 57.388 42.857 8.83 0.00 0.00 1.73
2646 2756 3.396260 AAGCGCGGCCTTATTATCTTA 57.604 42.857 8.83 0.00 0.00 2.10
2647 2757 2.256117 AAGCGCGGCCTTATTATCTT 57.744 45.000 8.83 0.00 0.00 2.40
2648 2758 2.353803 CCTAAGCGCGGCCTTATTATCT 60.354 50.000 8.83 0.00 0.00 1.98
2650 2760 1.621814 TCCTAAGCGCGGCCTTATTAT 59.378 47.619 8.83 0.00 0.00 1.28
2651 2761 1.042229 TCCTAAGCGCGGCCTTATTA 58.958 50.000 8.83 0.00 0.00 0.98
2652 2762 0.396811 ATCCTAAGCGCGGCCTTATT 59.603 50.000 8.83 0.00 0.00 1.40
2653 2763 0.396811 AATCCTAAGCGCGGCCTTAT 59.603 50.000 8.83 0.00 0.00 1.73
2654 2764 0.249741 GAATCCTAAGCGCGGCCTTA 60.250 55.000 8.83 7.14 0.00 2.69
2655 2765 1.523938 GAATCCTAAGCGCGGCCTT 60.524 57.895 8.83 6.19 0.00 4.35
2656 2766 2.109181 GAATCCTAAGCGCGGCCT 59.891 61.111 8.83 0.00 0.00 5.19
2657 2767 3.338676 CGAATCCTAAGCGCGGCC 61.339 66.667 8.83 0.00 0.00 6.13
2658 2768 2.585247 ACGAATCCTAAGCGCGGC 60.585 61.111 8.83 0.00 0.00 6.53
2659 2769 2.871427 GCACGAATCCTAAGCGCGG 61.871 63.158 8.83 0.00 0.00 6.46
2660 2770 2.621000 GCACGAATCCTAAGCGCG 59.379 61.111 0.00 0.00 0.00 6.86
2661 2771 2.621000 CGCACGAATCCTAAGCGC 59.379 61.111 0.00 0.00 41.95 5.92
2680 2790 6.233434 TCATGTGTCTAGATTCTTGCTTTGT 58.767 36.000 0.00 0.00 0.00 2.83
2713 2831 3.374988 TGGCTTGCTCTTATTGTTCATCG 59.625 43.478 0.00 0.00 0.00 3.84
2733 2851 6.034591 GGCTAGTTAGTATACGCACATATGG 58.965 44.000 7.80 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.