Multiple sequence alignment - TraesCS5B01G144400

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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 TraesCS5B01G144400 chr5B 100.000 2777 0 0 1 2777 271668683 271665907 0 5129
1 TraesCS5B01G144400 chr5A 89.422 2836 164 57 1 2776 321325237 321327996 0 3450
2 TraesCS5B01G144400 chr5D 89.336 2607 153 48 1 2565 233410029 233412552 0 3158


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 TraesCS5B01G144400 chr5B 271665907 271668683 2776 True 5129 5129 100.000 1 2777 1 chr5B.!!$R1 2776
1 TraesCS5B01G144400 chr5A 321325237 321327996 2759 False 3450 3450 89.422 1 2776 1 chr5A.!!$F1 2775
2 TraesCS5B01G144400 chr5D 233410029 233412552 2523 False 3158 3158 89.336 1 2565 1 chr5D.!!$F1 2564

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
487 509 0.867746 GACAATTGCTGTGCGACTCA 59.132 50.0 5.05 0.0 38.84 3.41 F
1026 1062 0.179018 GGGCTGAATCCGCATTACCT 60.179 55.0 0.00 0.0 0.00 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1614 1650 0.17668 GCAGAGGCTTCGATTCAGGA 59.823 55.0 0.00 0.0 36.96 3.86 R
2574 2628 0.17902 CCAGACCACCTGTGCTGAAA 60.179 55.0 6.51 0.0 41.33 2.69 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
79 84 2.284921 CCCTGCTCTCCTCCACCA 60.285 66.667 0.00 0.00 0.00 4.17
80 85 2.365586 CCCTGCTCTCCTCCACCAG 61.366 68.421 0.00 0.00 0.00 4.00
118 124 1.002274 GCCCTCCCTCTCTTCTCCA 59.998 63.158 0.00 0.00 0.00 3.86
156 162 3.060615 CCAAGCTGGGAGTGCTGC 61.061 66.667 0.00 0.00 41.03 5.25
157 163 3.429141 CAAGCTGGGAGTGCTGCG 61.429 66.667 0.00 0.00 41.03 5.18
234 240 1.153025 GGTATCGTGCCCTTTCCCC 60.153 63.158 0.00 0.00 0.00 4.81
265 271 1.810755 GGTTCCGGTGTTCCTCATTTC 59.189 52.381 0.00 0.00 0.00 2.17
277 283 1.003839 TCATTTCGCCTGTTCCGCT 60.004 52.632 0.00 0.00 0.00 5.52
325 331 4.060038 TCTCTCCGATTGATAAGTTGCC 57.940 45.455 0.00 0.00 0.00 4.52
350 356 1.347221 CGTTCGCGAGGTAATTGCC 59.653 57.895 9.59 4.07 44.71 4.52
426 448 7.432838 GCGTGTTTCTGAAATACTTTTGGTTTA 59.567 33.333 22.11 0.00 31.22 2.01
427 449 8.953990 CGTGTTTCTGAAATACTTTTGGTTTAG 58.046 33.333 22.11 4.79 31.22 1.85
433 455 8.234546 TCTGAAATACTTTTGGTTTAGCGAATC 58.765 33.333 0.00 0.00 0.00 2.52
434 456 7.877003 TGAAATACTTTTGGTTTAGCGAATCA 58.123 30.769 0.00 0.00 0.00 2.57
447 469 2.771943 AGCGAATCAACTAATCTGGGGA 59.228 45.455 0.00 0.00 0.00 4.81
456 478 2.572104 ACTAATCTGGGGAACTGTGGTC 59.428 50.000 0.00 0.00 0.00 4.02
469 491 1.138859 CTGTGGTCATAAGGATGCCGA 59.861 52.381 0.00 0.00 34.04 5.54
483 505 2.965147 GCCGACAATTGCTGTGCGA 61.965 57.895 5.05 0.00 38.84 5.10
487 509 0.867746 GACAATTGCTGTGCGACTCA 59.132 50.000 5.05 0.00 38.84 3.41
519 541 9.217278 ACGTAGGTGTAGTACATATATCTTCAG 57.783 37.037 6.21 0.00 0.00 3.02
520 542 9.217278 CGTAGGTGTAGTACATATATCTTCAGT 57.783 37.037 6.21 0.00 0.00 3.41
668 699 2.413371 GGAAGCTCGTCTTTGCATCAAC 60.413 50.000 0.00 0.00 34.56 3.18
686 717 4.430007 TCAACAGGATGACGTAATGTAGC 58.570 43.478 0.00 0.00 39.69 3.58
707 738 4.217118 AGCAATCTGAATTCTGAAAGCGTT 59.783 37.500 23.65 11.87 34.96 4.84
717 748 3.275143 TCTGAAAGCGTTCTGTTCCAAA 58.725 40.909 13.57 0.00 35.01 3.28
850 884 6.128007 ACTCCTTTTTGTTGTGTAGTTCTGTG 60.128 38.462 0.00 0.00 0.00 3.66
953 989 4.282496 ACTGAAGTGGGAGAGTGGTATAG 58.718 47.826 0.00 0.00 0.00 1.31
1021 1057 4.569180 CGGGGGCTGAATCCGCAT 62.569 66.667 0.00 0.00 40.48 4.73
1026 1062 0.179018 GGGCTGAATCCGCATTACCT 60.179 55.000 0.00 0.00 0.00 3.08
1045 1081 0.461870 TGCCGTAGATCATGTGGTGC 60.462 55.000 0.00 0.00 0.00 5.01
1053 1089 4.719026 AGATCATGTGGTGCTGGATAAT 57.281 40.909 0.00 0.00 0.00 1.28
1059 1095 2.135933 GTGGTGCTGGATAATAGCGAC 58.864 52.381 0.00 0.00 44.01 5.19
1086 1122 2.894126 AGTCTCAGAAGTCGTGGAATGT 59.106 45.455 0.00 0.00 0.00 2.71
1111 1147 2.632512 TCCACAGTTGTAGATGTGCTGA 59.367 45.455 0.00 0.00 44.35 4.26
1355 1391 1.390125 CTCCAGGACCAGAGGAGGT 59.610 63.158 16.10 0.00 44.10 3.85
1503 1539 2.301583 GGAAGATCTGTATCTCCAGGGC 59.698 54.545 0.00 0.00 41.81 5.19
1590 1626 2.485124 GGCTGTTCTGATAGATGCTGCT 60.485 50.000 0.00 0.00 30.95 4.24
1597 1633 4.359996 TCTGATAGATGCTGCTATCCCAT 58.640 43.478 17.82 0.00 43.87 4.00
1614 1650 3.840666 TCCCATCTGAAAGCTACAAGACT 59.159 43.478 0.00 0.00 0.00 3.24
1623 1659 3.791973 AGCTACAAGACTCCTGAATCG 57.208 47.619 0.00 0.00 0.00 3.34
1674 1710 3.531207 CCGGATGCTCCTCTGCGA 61.531 66.667 0.00 0.00 33.30 5.10
1734 1770 3.796667 GAAGCTCGACTTCGGTTCT 57.203 52.632 10.56 0.00 45.16 3.01
1737 1773 0.039074 AGCTCGACTTCGGTTCTGTG 60.039 55.000 0.00 0.00 40.29 3.66
1740 1776 1.267261 CTCGACTTCGGTTCTGTGAGT 59.733 52.381 0.00 0.00 40.29 3.41
1808 1849 1.586154 GGGAACATGGTCTTGGTGCG 61.586 60.000 11.29 0.00 0.00 5.34
1809 1850 0.889186 GGAACATGGTCTTGGTGCGT 60.889 55.000 11.29 0.00 0.00 5.24
1810 1851 0.951558 GAACATGGTCTTGGTGCGTT 59.048 50.000 2.64 0.00 0.00 4.84
1811 1852 1.336755 GAACATGGTCTTGGTGCGTTT 59.663 47.619 2.64 0.00 0.00 3.60
1812 1853 0.951558 ACATGGTCTTGGTGCGTTTC 59.048 50.000 0.00 0.00 0.00 2.78
1813 1854 1.238439 CATGGTCTTGGTGCGTTTCT 58.762 50.000 0.00 0.00 0.00 2.52
1814 1855 1.197721 CATGGTCTTGGTGCGTTTCTC 59.802 52.381 0.00 0.00 0.00 2.87
1815 1856 0.468226 TGGTCTTGGTGCGTTTCTCT 59.532 50.000 0.00 0.00 0.00 3.10
1816 1857 1.134220 TGGTCTTGGTGCGTTTCTCTT 60.134 47.619 0.00 0.00 0.00 2.85
1889 1930 2.159184 TGTACAGAGCTAGCAGTGATGC 60.159 50.000 18.83 9.32 0.00 3.91
2001 2046 8.923270 TGATTGATCATTGATGTAGTAGTACCA 58.077 33.333 3.32 0.00 0.00 3.25
2086 2131 1.952296 CTCTGTGCTTGCCTTGAACTT 59.048 47.619 0.00 0.00 0.00 2.66
2109 2154 4.298103 AGGAACTGTTGCAGATTCATCT 57.702 40.909 14.52 0.00 37.18 2.90
2116 2161 4.552355 TGTTGCAGATTCATCTTTGCTTG 58.448 39.130 3.49 0.00 34.22 4.01
2122 2167 4.863131 CAGATTCATCTTTGCTTGGCTTTC 59.137 41.667 0.00 0.00 34.22 2.62
2134 2182 0.752054 TGGCTTTCCTTTGCACTTGG 59.248 50.000 0.00 0.00 0.00 3.61
2135 2183 1.039856 GGCTTTCCTTTGCACTTGGA 58.960 50.000 0.00 0.00 0.00 3.53
2136 2184 1.620323 GGCTTTCCTTTGCACTTGGAT 59.380 47.619 2.82 0.00 0.00 3.41
2137 2185 2.611224 GGCTTTCCTTTGCACTTGGATG 60.611 50.000 2.82 1.79 0.00 3.51
2138 2186 2.036346 GCTTTCCTTTGCACTTGGATGT 59.964 45.455 2.82 0.00 0.00 3.06
2139 2187 3.255642 GCTTTCCTTTGCACTTGGATGTA 59.744 43.478 2.82 0.00 0.00 2.29
2140 2188 4.261994 GCTTTCCTTTGCACTTGGATGTAA 60.262 41.667 2.82 0.00 0.00 2.41
2141 2189 5.567423 GCTTTCCTTTGCACTTGGATGTAAT 60.567 40.000 2.82 0.00 0.00 1.89
2142 2190 6.350110 GCTTTCCTTTGCACTTGGATGTAATA 60.350 38.462 2.82 0.00 0.00 0.98
2143 2191 6.509418 TTCCTTTGCACTTGGATGTAATAC 57.491 37.500 2.82 0.00 0.00 1.89
2144 2192 5.815581 TCCTTTGCACTTGGATGTAATACT 58.184 37.500 0.00 0.00 0.00 2.12
2149 2197 6.299805 TGCACTTGGATGTAATACTCTCTT 57.700 37.500 0.00 0.00 0.00 2.85
2165 2213 3.390135 TCTCTTGTGACACCGAAATGAC 58.610 45.455 2.45 0.00 0.00 3.06
2185 2233 0.452784 GCAGTGGCGAATTCGAACAC 60.453 55.000 31.54 31.54 43.79 3.32
2248 2301 5.005107 GCGTACTAGTAGTGTTAATTGTGCC 59.995 44.000 13.29 0.00 0.00 5.01
2276 2329 9.007901 AGCTGTAATTCATCTGCCTTATTAATC 57.992 33.333 0.00 0.00 0.00 1.75
2291 2344 3.610040 TTAATCGTGCTGGTCTGTCAT 57.390 42.857 0.00 0.00 0.00 3.06
2370 2423 4.827481 GCTGACGGCCTCGATTTA 57.173 55.556 0.00 0.00 40.11 1.40
2379 2432 0.108585 GCCTCGATTTATCCCTGGCA 59.891 55.000 2.01 0.00 38.79 4.92
2382 2435 3.490348 CCTCGATTTATCCCTGGCATTT 58.510 45.455 0.00 0.00 0.00 2.32
2383 2436 3.254166 CCTCGATTTATCCCTGGCATTTG 59.746 47.826 0.00 0.00 0.00 2.32
2474 2527 6.969993 ACAGGGTTTATTTTTCACTGCTTA 57.030 33.333 0.00 0.00 36.22 3.09
2475 2528 7.539034 ACAGGGTTTATTTTTCACTGCTTAT 57.461 32.000 0.00 0.00 36.22 1.73
2478 2531 7.872483 CAGGGTTTATTTTTCACTGCTTATGTT 59.128 33.333 0.00 0.00 0.00 2.71
2525 2579 2.098293 GTGGCATCACGAATCCACC 58.902 57.895 8.91 0.00 42.25 4.61
2528 2582 1.488393 TGGCATCACGAATCCACCATA 59.512 47.619 0.00 0.00 0.00 2.74
2538 2592 6.098552 TCACGAATCCACCATATTGTAACCTA 59.901 38.462 0.00 0.00 0.00 3.08
2565 2619 1.035139 CTTTCAGCACAGGTGGCTTT 58.965 50.000 1.10 0.00 40.23 3.51
2566 2620 1.410153 CTTTCAGCACAGGTGGCTTTT 59.590 47.619 1.10 0.00 40.23 2.27
2567 2621 1.484038 TTCAGCACAGGTGGCTTTTT 58.516 45.000 1.10 0.00 40.23 1.94
2586 2640 4.799564 TTTTTGAACTTTCAGCACAGGT 57.200 36.364 0.00 0.00 38.61 4.00
2587 2641 3.781079 TTTGAACTTTCAGCACAGGTG 57.219 42.857 0.00 0.00 38.61 4.00
2588 2642 1.679139 TGAACTTTCAGCACAGGTGG 58.321 50.000 1.10 0.00 32.50 4.61
2589 2643 1.064758 TGAACTTTCAGCACAGGTGGT 60.065 47.619 0.00 0.00 42.74 4.16
2590 2644 1.604278 GAACTTTCAGCACAGGTGGTC 59.396 52.381 0.38 0.00 39.58 4.02
2604 2658 1.168714 GTGGTCTGGCTTGGCTTTAG 58.831 55.000 0.00 0.00 0.00 1.85
2605 2659 1.064003 TGGTCTGGCTTGGCTTTAGA 58.936 50.000 0.00 0.00 0.00 2.10
2607 2661 1.680249 GGTCTGGCTTGGCTTTAGAGG 60.680 57.143 0.00 0.00 0.00 3.69
2608 2662 1.279271 GTCTGGCTTGGCTTTAGAGGA 59.721 52.381 0.00 0.00 0.00 3.71
2610 2664 2.578021 TCTGGCTTGGCTTTAGAGGATT 59.422 45.455 0.00 0.00 0.00 3.01
2611 2665 3.780294 TCTGGCTTGGCTTTAGAGGATTA 59.220 43.478 0.00 0.00 0.00 1.75
2612 2666 4.413520 TCTGGCTTGGCTTTAGAGGATTAT 59.586 41.667 0.00 0.00 0.00 1.28
2613 2667 4.464008 TGGCTTGGCTTTAGAGGATTATG 58.536 43.478 0.00 0.00 0.00 1.90
2614 2668 4.079787 TGGCTTGGCTTTAGAGGATTATGT 60.080 41.667 0.00 0.00 0.00 2.29
2635 2692 9.534565 TTATGTAGAGTAATCAGAACATCAAGC 57.465 33.333 8.48 0.00 0.00 4.01
2636 2693 6.935167 TGTAGAGTAATCAGAACATCAAGCA 58.065 36.000 0.00 0.00 0.00 3.91
2641 2698 3.599730 ATCAGAACATCAAGCACTCGA 57.400 42.857 0.00 0.00 0.00 4.04
2648 2705 1.066573 CATCAAGCACTCGAGGAAGGT 60.067 52.381 18.41 8.96 0.00 3.50
2652 2709 0.968393 AGCACTCGAGGAAGGTCTCC 60.968 60.000 18.41 0.00 45.81 3.71
2681 2738 4.530946 ACCCCGTAACAGCAAGCTATATAT 59.469 41.667 0.00 0.00 0.00 0.86
2682 2739 5.718130 ACCCCGTAACAGCAAGCTATATATA 59.282 40.000 0.00 0.00 0.00 0.86
2723 2780 1.079474 TGCTTAGGATTCGTGCGCA 60.079 52.632 5.66 5.66 0.00 6.09
2725 2782 1.084370 GCTTAGGATTCGTGCGCACT 61.084 55.000 35.27 19.61 0.00 4.40
2739 2796 3.370978 GTGCGCACTAAGCAAGAATCTAA 59.629 43.478 32.55 0.00 46.97 2.10
2776 2841 5.300969 TGTGATGAACAATAAGAGCAAGC 57.699 39.130 0.00 0.00 35.24 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 2.200989 CTCTGGTGGAGGAGAGCAG 58.799 63.158 0.00 0.00 39.76 4.24
65 66 4.449638 CTCTGGTGGAGGAGAGCA 57.550 61.111 0.00 0.00 38.35 4.26
67 68 4.449638 TGCTCTGGTGGAGGAGAG 57.550 61.111 0.00 0.00 42.08 3.20
70 71 3.385384 CGCTGCTCTGGTGGAGGA 61.385 66.667 0.00 0.00 42.08 3.71
118 124 2.194212 CGACGAGGGATGGACGGAT 61.194 63.158 0.00 0.00 0.00 4.18
198 204 6.918569 ACGATACCTGTTTCTATCTTGATTCG 59.081 38.462 0.00 0.00 0.00 3.34
234 240 1.227089 CCGGAACCAGATCTGCGAG 60.227 63.158 17.76 6.56 0.00 5.03
265 271 4.680237 TGGACAGCGGAACAGGCG 62.680 66.667 0.00 0.00 35.00 5.52
277 283 4.664150 TGCATACACGATAGATTGGACA 57.336 40.909 0.00 0.00 41.38 4.02
325 331 1.985447 TACCTCGCGAACGCCTAGTG 61.985 60.000 11.33 0.00 39.84 2.74
350 356 1.666888 GCACGGTCAAATCAAAGCCTG 60.667 52.381 0.00 0.00 0.00 4.85
390 412 4.746535 TCAGAAACACGCATCCCTAATA 57.253 40.909 0.00 0.00 0.00 0.98
426 448 2.771943 TCCCCAGATTAGTTGATTCGCT 59.228 45.455 0.00 0.00 0.00 4.93
427 449 3.194005 TCCCCAGATTAGTTGATTCGC 57.806 47.619 0.00 0.00 0.00 4.70
433 455 3.244911 ACCACAGTTCCCCAGATTAGTTG 60.245 47.826 0.00 0.00 0.00 3.16
434 456 2.986728 ACCACAGTTCCCCAGATTAGTT 59.013 45.455 0.00 0.00 0.00 2.24
447 469 2.680805 CGGCATCCTTATGACCACAGTT 60.681 50.000 0.00 0.00 37.93 3.16
456 478 2.620115 AGCAATTGTCGGCATCCTTATG 59.380 45.455 7.40 0.00 36.09 1.90
469 491 0.588252 GTGAGTCGCACAGCAATTGT 59.412 50.000 7.40 0.00 46.91 2.71
497 519 9.509956 GAGACTGAAGATATATGTACTACACCT 57.490 37.037 0.00 0.00 0.00 4.00
498 520 8.444715 CGAGACTGAAGATATATGTACTACACC 58.555 40.741 0.00 0.00 0.00 4.16
499 521 9.205719 TCGAGACTGAAGATATATGTACTACAC 57.794 37.037 0.00 0.00 0.00 2.90
506 528 8.402798 ACAGAATCGAGACTGAAGATATATGT 57.597 34.615 22.42 0.00 37.54 2.29
519 541 8.855279 GCTTCATATACATTACAGAATCGAGAC 58.145 37.037 0.00 0.00 0.00 3.36
520 542 8.576442 TGCTTCATATACATTACAGAATCGAGA 58.424 33.333 0.00 0.00 0.00 4.04
521 543 8.748380 TGCTTCATATACATTACAGAATCGAG 57.252 34.615 0.00 0.00 0.00 4.04
572 594 9.258629 TCATCCTTCCAAAAACAATCATCTAAT 57.741 29.630 0.00 0.00 0.00 1.73
583 605 9.271828 ACAAAATTACATCATCCTTCCAAAAAC 57.728 29.630 0.00 0.00 0.00 2.43
589 611 8.964476 TCTAGACAAAATTACATCATCCTTCC 57.036 34.615 0.00 0.00 0.00 3.46
642 668 3.934391 AAAGACGAGCTTCCGGGCG 62.934 63.158 0.00 0.50 35.24 6.13
653 684 2.542020 TCCTGTTGATGCAAAGACGA 57.458 45.000 0.00 0.00 0.00 4.20
668 699 5.176406 CAGATTGCTACATTACGTCATCCTG 59.824 44.000 0.00 0.00 0.00 3.86
684 715 3.755378 ACGCTTTCAGAATTCAGATTGCT 59.245 39.130 8.44 1.41 0.00 3.91
686 717 5.793952 CAGAACGCTTTCAGAATTCAGATTG 59.206 40.000 8.44 2.67 33.72 2.67
707 738 5.181811 CAGCAGAACATACATTTGGAACAGA 59.818 40.000 0.00 0.00 42.39 3.41
717 748 2.014857 CAGCAGCAGCAGAACATACAT 58.985 47.619 3.17 0.00 45.49 2.29
759 790 5.304101 ACAATTTCAGAATAAACAGGGTGCA 59.696 36.000 0.00 0.00 0.00 4.57
872 906 6.437162 ACGGTAGATACTACCAAAAACTACCA 59.563 38.462 22.32 0.00 44.64 3.25
873 907 6.867550 ACGGTAGATACTACCAAAAACTACC 58.132 40.000 22.32 0.00 42.49 3.18
881 915 7.445402 GGTCAGTATAACGGTAGATACTACCAA 59.555 40.741 22.32 11.11 36.87 3.67
1021 1057 2.102420 CCACATGATCTACGGCAGGTAA 59.898 50.000 0.00 0.00 0.00 2.85
1026 1062 0.461870 GCACCACATGATCTACGGCA 60.462 55.000 0.00 0.00 0.00 5.69
1029 1065 1.136891 TCCAGCACCACATGATCTACG 59.863 52.381 0.00 0.00 0.00 3.51
1032 1068 4.719026 ATTATCCAGCACCACATGATCT 57.281 40.909 0.00 0.00 0.00 2.75
1045 1081 4.938080 ACTTCAGTGTCGCTATTATCCAG 58.062 43.478 0.00 0.00 0.00 3.86
1086 1122 4.002982 GCACATCTACAACTGTGGAATCA 58.997 43.478 0.00 0.00 42.37 2.57
1104 1140 0.469494 TGGCACTCTTCTTCAGCACA 59.531 50.000 0.00 0.00 0.00 4.57
1111 1147 6.015940 CCAAATTCTTTACTGGCACTCTTCTT 60.016 38.462 0.00 0.00 0.00 2.52
1299 1335 2.065899 TTCCCCTTGGTGTTTGACAG 57.934 50.000 0.00 0.00 0.00 3.51
1557 1593 1.229951 AACAGCCTCCCCATCTCCA 60.230 57.895 0.00 0.00 0.00 3.86
1566 1602 2.368221 AGCATCTATCAGAACAGCCTCC 59.632 50.000 0.00 0.00 0.00 4.30
1590 1626 5.663106 AGTCTTGTAGCTTTCAGATGGGATA 59.337 40.000 0.00 0.00 0.00 2.59
1597 1633 4.152647 TCAGGAGTCTTGTAGCTTTCAGA 58.847 43.478 1.77 0.00 0.00 3.27
1614 1650 0.176680 GCAGAGGCTTCGATTCAGGA 59.823 55.000 0.00 0.00 36.96 3.86
1740 1776 1.691976 TCAGCGAAAAGAGTCTTGGGA 59.308 47.619 6.06 0.00 0.00 4.37
1808 1849 4.187694 CTCTGTAGGATGCCAAGAGAAAC 58.812 47.826 3.23 0.00 0.00 2.78
1809 1850 4.478206 CTCTGTAGGATGCCAAGAGAAA 57.522 45.455 3.23 0.00 0.00 2.52
1842 1883 5.546621 TCAGAGTTAGCAAAGTTACCACT 57.453 39.130 0.00 0.00 33.11 4.00
1889 1930 2.777832 AAGGCTGCTTCCTACTCAAG 57.222 50.000 0.00 0.00 34.82 3.02
1942 1987 8.595362 AAGACTGGGCTTAGCTAAAATTAAAT 57.405 30.769 7.74 0.00 0.00 1.40
2086 2131 5.809001 AGATGAATCTGCAACAGTTCCTTA 58.191 37.500 0.00 0.00 35.42 2.69
2109 2154 1.209019 TGCAAAGGAAAGCCAAGCAAA 59.791 42.857 0.00 0.00 35.49 3.68
2116 2161 1.039856 TCCAAGTGCAAAGGAAAGCC 58.960 50.000 0.00 0.00 0.00 4.35
2122 2167 5.882557 AGAGTATTACATCCAAGTGCAAAGG 59.117 40.000 0.00 0.00 0.00 3.11
2134 2182 5.744345 CGGTGTCACAAGAGAGTATTACATC 59.256 44.000 5.12 0.00 0.00 3.06
2135 2183 5.417894 TCGGTGTCACAAGAGAGTATTACAT 59.582 40.000 5.12 0.00 0.00 2.29
2136 2184 4.763279 TCGGTGTCACAAGAGAGTATTACA 59.237 41.667 5.12 0.00 0.00 2.41
2137 2185 5.306532 TCGGTGTCACAAGAGAGTATTAC 57.693 43.478 5.12 0.00 0.00 1.89
2138 2186 5.970317 TTCGGTGTCACAAGAGAGTATTA 57.030 39.130 5.12 0.00 0.00 0.98
2139 2187 4.866508 TTCGGTGTCACAAGAGAGTATT 57.133 40.909 5.12 0.00 0.00 1.89
2140 2188 4.866508 TTTCGGTGTCACAAGAGAGTAT 57.133 40.909 5.12 0.00 0.00 2.12
2141 2189 4.279922 TCATTTCGGTGTCACAAGAGAGTA 59.720 41.667 5.12 0.00 0.00 2.59
2142 2190 3.069586 TCATTTCGGTGTCACAAGAGAGT 59.930 43.478 5.12 0.00 0.00 3.24
2143 2191 3.430218 GTCATTTCGGTGTCACAAGAGAG 59.570 47.826 5.12 0.00 0.00 3.20
2144 2192 3.390135 GTCATTTCGGTGTCACAAGAGA 58.610 45.455 5.12 0.00 0.00 3.10
2149 2197 0.530870 TGCGTCATTTCGGTGTCACA 60.531 50.000 5.12 0.00 0.00 3.58
2185 2233 1.154225 GTCGCATCAAACCAAGCCG 60.154 57.895 0.00 0.00 0.00 5.52
2231 2284 3.000727 GCTCGGCACAATTAACACTACT 58.999 45.455 0.00 0.00 0.00 2.57
2232 2285 3.000727 AGCTCGGCACAATTAACACTAC 58.999 45.455 0.00 0.00 0.00 2.73
2233 2286 3.000041 CAGCTCGGCACAATTAACACTA 59.000 45.455 0.00 0.00 0.00 2.74
2248 2301 2.831333 AGGCAGATGAATTACAGCTCG 58.169 47.619 0.00 0.00 43.79 5.03
2276 2329 1.004595 CATCATGACAGACCAGCACG 58.995 55.000 0.00 0.00 0.00 5.34
2291 2344 3.211865 GAAGAGCAGCCATCAATCATCA 58.788 45.455 0.00 0.00 0.00 3.07
2370 2423 3.979501 AAGGATACAAATGCCAGGGAT 57.020 42.857 0.00 0.00 41.41 3.85
2379 2432 4.930696 AGGGGACGAAAAAGGATACAAAT 58.069 39.130 0.00 0.00 41.41 2.32
2382 2435 4.076394 CAAAGGGGACGAAAAAGGATACA 58.924 43.478 0.00 0.00 41.41 2.29
2383 2436 4.077108 ACAAAGGGGACGAAAAAGGATAC 58.923 43.478 0.00 0.00 0.00 2.24
2474 2527 6.200097 GTCGGCAAATAAAGTCAAACAAACAT 59.800 34.615 0.00 0.00 0.00 2.71
2475 2528 5.517054 GTCGGCAAATAAAGTCAAACAAACA 59.483 36.000 0.00 0.00 0.00 2.83
2478 2531 5.250235 TGTCGGCAAATAAAGTCAAACAA 57.750 34.783 0.00 0.00 0.00 2.83
2538 2592 5.600696 CCACCTGTGCTGAAAGTAATTTTT 58.399 37.500 0.00 0.00 35.30 1.94
2565 2619 4.493547 CACCTGTGCTGAAAGTTCAAAAA 58.506 39.130 0.00 0.00 36.64 1.94
2566 2620 3.119173 CCACCTGTGCTGAAAGTTCAAAA 60.119 43.478 0.00 0.00 36.64 2.44
2567 2621 2.426738 CCACCTGTGCTGAAAGTTCAAA 59.573 45.455 0.00 0.00 36.64 2.69
2568 2622 2.023673 CCACCTGTGCTGAAAGTTCAA 58.976 47.619 0.00 0.00 36.64 2.69
2569 2623 1.064758 ACCACCTGTGCTGAAAGTTCA 60.065 47.619 0.00 0.00 35.30 3.18
2570 2624 1.604278 GACCACCTGTGCTGAAAGTTC 59.396 52.381 0.00 0.00 35.30 3.01
2571 2625 1.212935 AGACCACCTGTGCTGAAAGTT 59.787 47.619 0.00 0.00 35.30 2.66
2572 2626 0.839946 AGACCACCTGTGCTGAAAGT 59.160 50.000 0.00 0.00 35.30 2.66
2573 2627 1.233019 CAGACCACCTGTGCTGAAAG 58.767 55.000 0.00 0.00 38.10 2.62
2574 2628 0.179020 CCAGACCACCTGTGCTGAAA 60.179 55.000 6.51 0.00 41.33 2.69
2575 2629 1.451504 CCAGACCACCTGTGCTGAA 59.548 57.895 6.51 0.00 41.33 3.02
2576 2630 3.150949 CCAGACCACCTGTGCTGA 58.849 61.111 6.51 0.00 41.33 4.26
2577 2631 2.670934 GCCAGACCACCTGTGCTG 60.671 66.667 0.00 0.00 41.33 4.41
2578 2632 2.455565 AAGCCAGACCACCTGTGCT 61.456 57.895 0.00 0.00 45.18 4.40
2579 2633 2.113986 AAGCCAGACCACCTGTGC 59.886 61.111 0.00 0.00 41.33 4.57
2580 2634 1.601759 CCAAGCCAGACCACCTGTG 60.602 63.158 0.00 0.00 41.33 3.66
2581 2635 2.839098 CCAAGCCAGACCACCTGT 59.161 61.111 0.00 0.00 41.33 4.00
2582 2636 2.674380 GCCAAGCCAGACCACCTG 60.674 66.667 0.00 0.00 42.55 4.00
2583 2637 2.011617 AAAGCCAAGCCAGACCACCT 62.012 55.000 0.00 0.00 0.00 4.00
2584 2638 0.251165 TAAAGCCAAGCCAGACCACC 60.251 55.000 0.00 0.00 0.00 4.61
2585 2639 1.168714 CTAAAGCCAAGCCAGACCAC 58.831 55.000 0.00 0.00 0.00 4.16
2586 2640 1.003580 CTCTAAAGCCAAGCCAGACCA 59.996 52.381 0.00 0.00 0.00 4.02
2587 2641 1.680249 CCTCTAAAGCCAAGCCAGACC 60.680 57.143 0.00 0.00 0.00 3.85
2588 2642 1.279271 TCCTCTAAAGCCAAGCCAGAC 59.721 52.381 0.00 0.00 0.00 3.51
2589 2643 1.656587 TCCTCTAAAGCCAAGCCAGA 58.343 50.000 0.00 0.00 0.00 3.86
2590 2644 2.725221 ATCCTCTAAAGCCAAGCCAG 57.275 50.000 0.00 0.00 0.00 4.85
2610 2664 8.695456 TGCTTGATGTTCTGATTACTCTACATA 58.305 33.333 0.00 0.00 0.00 2.29
2611 2665 7.493971 GTGCTTGATGTTCTGATTACTCTACAT 59.506 37.037 0.00 0.00 0.00 2.29
2612 2666 6.813649 GTGCTTGATGTTCTGATTACTCTACA 59.186 38.462 0.00 0.00 0.00 2.74
2613 2667 7.038659 AGTGCTTGATGTTCTGATTACTCTAC 58.961 38.462 0.00 0.00 0.00 2.59
2614 2668 7.175347 AGTGCTTGATGTTCTGATTACTCTA 57.825 36.000 0.00 0.00 0.00 2.43
2627 2684 1.066573 CCTTCCTCGAGTGCTTGATGT 60.067 52.381 12.31 0.00 0.00 3.06
2628 2685 1.066573 ACCTTCCTCGAGTGCTTGATG 60.067 52.381 12.31 3.42 0.00 3.07
2635 2692 0.677098 TCGGAGACCTTCCTCGAGTG 60.677 60.000 12.31 3.02 44.41 3.51
2636 2693 0.393267 CTCGGAGACCTTCCTCGAGT 60.393 60.000 12.31 0.00 44.41 4.18
2641 2698 2.047443 GTCGCTCGGAGACCTTCCT 61.047 63.158 9.69 0.00 44.41 3.36
2648 2705 3.626996 TTACGGGGTCGCTCGGAGA 62.627 63.158 9.69 0.00 40.63 3.71
2652 2709 2.202570 CTGTTACGGGGTCGCTCG 60.203 66.667 0.00 0.00 40.63 5.03
2653 2710 2.508663 GCTGTTACGGGGTCGCTC 60.509 66.667 0.00 0.00 40.63 5.03
2681 2738 7.041721 CACGGCCTCATCTTATATTATGCTTA 58.958 38.462 0.00 0.00 0.00 3.09
2682 2739 5.877012 CACGGCCTCATCTTATATTATGCTT 59.123 40.000 0.00 0.00 0.00 3.91
2694 2751 0.687757 TCCTAAGCACGGCCTCATCT 60.688 55.000 0.00 0.00 0.00 2.90
2702 2759 1.752501 CGCACGAATCCTAAGCACGG 61.753 60.000 0.00 0.00 0.00 4.94
2723 2780 8.671921 CATCATGTGTTTAGATTCTTGCTTAGT 58.328 33.333 0.00 0.00 0.00 2.24
2725 2782 8.791327 TCATCATGTGTTTAGATTCTTGCTTA 57.209 30.769 0.00 0.00 0.00 3.09


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

AutoCloner maintained by Alex Coulton.