Multiple sequence alignment - TraesCS3A01G003700

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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 TraesCS3A01G003700 chr3A 100.000 2543 0 0 1 2543 1902883 1905425 0.000000e+00 4697.0
1 TraesCS3A01G003700 chr3B 91.981 2120 100 37 1 2096 4335722 4333649 0.000000e+00 2909.0
2 TraesCS3A01G003700 chr3B 91.201 716 52 8 1025 1737 4407111 4406404 0.000000e+00 963.0
3 TraesCS3A01G003700 chr3B 89.454 531 38 13 454 973 4407633 4407110 0.000000e+00 654.0
4 TraesCS3A01G003700 chr3B 87.643 437 27 12 36 471 4408055 4407645 1.370000e-132 483.0
5 TraesCS3A01G003700 chr3B 90.535 243 10 2 2194 2436 4333644 4333415 2.460000e-80 309.0
6 TraesCS3A01G003700 chrUn 100.000 1053 0 0 489 1541 351354263 351353211 0.000000e+00 1945.0
7 TraesCS3A01G003700 chrUn 100.000 829 0 0 1715 2543 351355369 351354541 0.000000e+00 1531.0
8 TraesCS3A01G003700 chr3D 91.681 1178 55 23 1 1156 2163953 2162797 0.000000e+00 1592.0
9 TraesCS3A01G003700 chr3D 90.789 836 44 10 1152 1980 2152463 2151654 0.000000e+00 1086.0
10 TraesCS3A01G003700 chr3D 93.458 107 6 1 2009 2114 2151655 2151549 9.420000e-35 158.0
11 TraesCS3A01G003700 chr3D 84.127 63 10 0 1127 1189 1893109 1893171 7.600000e-06 62.1
12 TraesCS3A01G003700 chr5D 95.455 44 0 1 1657 1698 519697047 519697090 4.540000e-08 69.4
13 TraesCS3A01G003700 chr1D 85.185 54 6 2 1648 1700 468981837 468981889 1.000000e-03 54.7


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 TraesCS3A01G003700 chr3A 1902883 1905425 2542 False 4697 4697 100.000000 1 2543 1 chr3A.!!$F1 2542
1 TraesCS3A01G003700 chr3B 4333415 4335722 2307 True 1609 2909 91.258000 1 2436 2 chr3B.!!$R1 2435
2 TraesCS3A01G003700 chr3B 4406404 4408055 1651 True 700 963 89.432667 36 1737 3 chr3B.!!$R2 1701
3 TraesCS3A01G003700 chrUn 351353211 351355369 2158 True 1738 1945 100.000000 489 2543 2 chrUn.!!$R1 2054
4 TraesCS3A01G003700 chr3D 2162797 2163953 1156 True 1592 1592 91.681000 1 1156 1 chr3D.!!$R1 1155
5 TraesCS3A01G003700 chr3D 2151549 2152463 914 True 622 1086 92.123500 1152 2114 2 chr3D.!!$R2 962

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
119 122 2.63116 TGAACATGGTCAAACGGTCT 57.369 45.0 12.03 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1872 2517 0.802222 GCTATGTCTCGCTTCGTGCA 60.802 55.0 4.36 0.0 43.06 4.57 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
54 56 9.198065 CTCAAAATTGTGAAATTTTCGTCAAAC 57.802 29.630 17.15 6.63 39.55 2.93
119 122 2.631160 TGAACATGGTCAAACGGTCT 57.369 45.000 12.03 0.00 0.00 3.85
1572 2210 4.537135 AGAACATTTCTCGGCTTGTCTA 57.463 40.909 0.00 0.00 34.07 2.59
1814 2457 3.491652 GCGAGCGCTTTGAGGACC 61.492 66.667 13.26 0.00 38.26 4.46
1872 2517 3.067461 CAGGCGAGACTAGCTTCTGTATT 59.933 47.826 7.53 0.00 34.52 1.89
1892 2537 1.483424 GCACGAAGCGAGACATAGCC 61.483 60.000 0.00 0.00 0.00 3.93
1941 2586 1.202604 CGTTTGGTACCATATCGCCCT 60.203 52.381 17.17 0.00 0.00 5.19
1942 2587 2.036217 CGTTTGGTACCATATCGCCCTA 59.964 50.000 17.17 0.00 0.00 3.53
1946 2591 2.043939 TGGTACCATATCGCCCTAGGAT 59.956 50.000 11.60 0.00 0.00 3.24
1948 2593 1.573108 ACCATATCGCCCTAGGATGG 58.427 55.000 20.04 20.04 42.37 3.51
1966 2611 1.607801 GGGGCCCAGAAGCAAATCAC 61.608 60.000 26.86 0.00 0.00 3.06
2004 2649 1.510623 GTGCTCTGTTTGCATCGCG 60.511 57.895 0.00 0.00 42.69 5.87
2044 2689 3.254166 AGCAAGCTGTCGAACAATTTCAT 59.746 39.130 0.00 0.00 0.00 2.57
2114 2764 9.777297 AACACATTTTAATGTCTAGGCAAAAAT 57.223 25.926 12.04 12.04 46.10 1.82
2115 2765 9.777297 ACACATTTTAATGTCTAGGCAAAAATT 57.223 25.926 14.28 6.93 46.10 1.82
2144 2794 7.838079 TTTTCTTTCTTTTCCCAGATCATCA 57.162 32.000 0.00 0.00 0.00 3.07
2145 2795 8.426569 TTTTCTTTCTTTTCCCAGATCATCAT 57.573 30.769 0.00 0.00 0.00 2.45
2146 2796 7.636150 TTCTTTCTTTTCCCAGATCATCATC 57.364 36.000 0.00 0.00 0.00 2.92
2147 2797 6.724351 TCTTTCTTTTCCCAGATCATCATCA 58.276 36.000 0.00 0.00 0.00 3.07
2148 2798 6.600822 TCTTTCTTTTCCCAGATCATCATCAC 59.399 38.462 0.00 0.00 0.00 3.06
2149 2799 4.445453 TCTTTTCCCAGATCATCATCACG 58.555 43.478 0.00 0.00 0.00 4.35
2150 2800 4.162131 TCTTTTCCCAGATCATCATCACGA 59.838 41.667 0.00 0.00 0.00 4.35
2151 2801 4.486125 TTTCCCAGATCATCATCACGAA 57.514 40.909 0.00 0.00 0.00 3.85
2152 2802 4.486125 TTCCCAGATCATCATCACGAAA 57.514 40.909 0.00 0.00 0.00 3.46
2153 2803 4.694760 TCCCAGATCATCATCACGAAAT 57.305 40.909 0.00 0.00 0.00 2.17
2154 2804 4.383173 TCCCAGATCATCATCACGAAATG 58.617 43.478 0.00 0.00 0.00 2.32
2155 2805 4.101430 TCCCAGATCATCATCACGAAATGA 59.899 41.667 6.88 6.88 43.13 2.57
2156 2806 4.451435 CCCAGATCATCATCACGAAATGAG 59.549 45.833 9.62 4.00 41.91 2.90
2157 2807 4.083961 CCAGATCATCATCACGAAATGAGC 60.084 45.833 9.62 3.96 41.91 4.26
2158 2808 4.510340 CAGATCATCATCACGAAATGAGCA 59.490 41.667 11.32 1.23 41.91 4.26
2159 2809 5.007332 CAGATCATCATCACGAAATGAGCAA 59.993 40.000 11.32 0.67 41.91 3.91
2160 2810 4.870221 TCATCATCACGAAATGAGCAAG 57.130 40.909 9.62 2.30 41.91 4.01
2161 2811 4.256110 TCATCATCACGAAATGAGCAAGT 58.744 39.130 9.62 0.00 41.91 3.16
2162 2812 5.418676 TCATCATCACGAAATGAGCAAGTA 58.581 37.500 9.62 0.00 41.91 2.24
2163 2813 5.521372 TCATCATCACGAAATGAGCAAGTAG 59.479 40.000 9.62 0.00 41.91 2.57
2164 2814 4.183865 TCATCACGAAATGAGCAAGTAGG 58.816 43.478 0.00 0.00 41.91 3.18
2165 2815 3.678056 TCACGAAATGAGCAAGTAGGT 57.322 42.857 0.00 0.00 31.91 3.08
2166 2816 4.002906 TCACGAAATGAGCAAGTAGGTT 57.997 40.909 0.00 0.00 31.91 3.50
2167 2817 5.142061 TCACGAAATGAGCAAGTAGGTTA 57.858 39.130 0.00 0.00 31.91 2.85
2168 2818 5.543714 TCACGAAATGAGCAAGTAGGTTAA 58.456 37.500 0.00 0.00 31.91 2.01
2169 2819 5.992829 TCACGAAATGAGCAAGTAGGTTAAA 59.007 36.000 0.00 0.00 31.91 1.52
2170 2820 6.483974 TCACGAAATGAGCAAGTAGGTTAAAA 59.516 34.615 0.00 0.00 31.91 1.52
2171 2821 6.577427 CACGAAATGAGCAAGTAGGTTAAAAC 59.423 38.462 0.00 0.00 0.00 2.43
2172 2822 6.261381 ACGAAATGAGCAAGTAGGTTAAAACA 59.739 34.615 0.00 0.00 0.00 2.83
2173 2823 7.040686 ACGAAATGAGCAAGTAGGTTAAAACAT 60.041 33.333 0.00 0.00 0.00 2.71
2174 2824 8.447833 CGAAATGAGCAAGTAGGTTAAAACATA 58.552 33.333 0.00 0.00 0.00 2.29
2177 2827 7.141100 TGAGCAAGTAGGTTAAAACATAAGC 57.859 36.000 0.00 0.00 0.00 3.09
2178 2828 6.712998 TGAGCAAGTAGGTTAAAACATAAGCA 59.287 34.615 9.15 0.00 0.00 3.91
2179 2829 7.229707 TGAGCAAGTAGGTTAAAACATAAGCAA 59.770 33.333 9.15 0.00 0.00 3.91
2180 2830 8.122472 AGCAAGTAGGTTAAAACATAAGCAAT 57.878 30.769 9.15 0.00 0.00 3.56
2181 2831 8.585018 AGCAAGTAGGTTAAAACATAAGCAATT 58.415 29.630 9.15 0.00 0.00 2.32
2182 2832 9.203421 GCAAGTAGGTTAAAACATAAGCAATTT 57.797 29.630 0.00 0.00 0.00 1.82
2261 2911 8.911918 TGTATTTTACAGTTCATACCAAGTGT 57.088 30.769 0.00 0.00 41.76 3.55
2262 2912 9.999660 TGTATTTTACAGTTCATACCAAGTGTA 57.000 29.630 0.00 0.00 39.96 2.90
2307 2957 5.047306 ACAGTTTCGGTCTCAACATGATAGA 60.047 40.000 0.00 0.00 0.00 1.98
2321 2971 7.604164 TCAACATGATAGAGTTGTTCCTTTCTC 59.396 37.037 0.00 0.00 44.08 2.87
2369 3019 7.912056 TCTTCTTGACCAACTTATCAATCAG 57.088 36.000 0.00 0.00 34.43 2.90
2374 3024 6.801539 TGACCAACTTATCAATCAGTGTTC 57.198 37.500 0.00 0.00 0.00 3.18
2437 3087 6.861065 ACACTTCGTATCAACTTTGATTGT 57.139 33.333 9.68 4.68 45.13 2.71
2438 3088 6.888430 ACACTTCGTATCAACTTTGATTGTC 58.112 36.000 9.68 1.83 45.13 3.18
2439 3089 6.706270 ACACTTCGTATCAACTTTGATTGTCT 59.294 34.615 9.68 0.00 45.13 3.41
2440 3090 7.226720 ACACTTCGTATCAACTTTGATTGTCTT 59.773 33.333 9.68 0.00 45.13 3.01
2441 3091 7.742089 CACTTCGTATCAACTTTGATTGTCTTC 59.258 37.037 9.68 0.00 45.13 2.87
2442 3092 7.441157 ACTTCGTATCAACTTTGATTGTCTTCA 59.559 33.333 9.68 0.00 45.13 3.02
2443 3093 7.905604 TCGTATCAACTTTGATTGTCTTCAT 57.094 32.000 9.68 0.00 45.13 2.57
2444 3094 8.322906 TCGTATCAACTTTGATTGTCTTCATT 57.677 30.769 9.68 0.00 45.13 2.57
2445 3095 8.783093 TCGTATCAACTTTGATTGTCTTCATTT 58.217 29.630 9.68 0.00 45.13 2.32
2446 3096 8.843733 CGTATCAACTTTGATTGTCTTCATTTG 58.156 33.333 9.68 0.00 45.13 2.32
2447 3097 9.683069 GTATCAACTTTGATTGTCTTCATTTGT 57.317 29.630 9.68 0.00 45.13 2.83
2450 3100 9.515020 TCAACTTTGATTGTCTTCATTTGTTAC 57.485 29.630 0.00 0.00 31.01 2.50
2451 3101 9.299963 CAACTTTGATTGTCTTCATTTGTTACA 57.700 29.630 0.00 0.00 0.00 2.41
2457 3107 9.681692 TGATTGTCTTCATTTGTTACATTCTTG 57.318 29.630 0.00 0.00 0.00 3.02
2458 3108 9.897744 GATTGTCTTCATTTGTTACATTCTTGA 57.102 29.630 0.00 0.00 0.00 3.02
2461 3111 9.515020 TGTCTTCATTTGTTACATTCTTGAAAC 57.485 29.630 0.00 0.00 0.00 2.78
2462 3112 9.515020 GTCTTCATTTGTTACATTCTTGAAACA 57.485 29.630 0.00 0.00 0.00 2.83
2470 3120 8.346476 TGTTACATTCTTGAAACAAAATTCCG 57.654 30.769 0.00 0.00 0.00 4.30
2471 3121 8.191446 TGTTACATTCTTGAAACAAAATTCCGA 58.809 29.630 0.00 0.00 0.00 4.55
2472 3122 8.476925 GTTACATTCTTGAAACAAAATTCCGAC 58.523 33.333 0.00 0.00 0.00 4.79
2473 3123 6.805713 ACATTCTTGAAACAAAATTCCGACT 58.194 32.000 0.00 0.00 0.00 4.18
2474 3124 6.918022 ACATTCTTGAAACAAAATTCCGACTC 59.082 34.615 0.00 0.00 0.00 3.36
2475 3125 6.443934 TTCTTGAAACAAAATTCCGACTCA 57.556 33.333 0.00 0.00 0.00 3.41
2476 3126 6.633500 TCTTGAAACAAAATTCCGACTCAT 57.367 33.333 0.00 0.00 0.00 2.90
2477 3127 6.437928 TCTTGAAACAAAATTCCGACTCATG 58.562 36.000 0.00 0.00 0.00 3.07
2478 3128 5.119931 TGAAACAAAATTCCGACTCATGG 57.880 39.130 0.00 0.00 0.00 3.66
2479 3129 4.824537 TGAAACAAAATTCCGACTCATGGA 59.175 37.500 0.00 0.00 0.00 3.41
2485 3135 1.808411 TTCCGACTCATGGAAAGCAC 58.192 50.000 0.00 0.00 42.37 4.40
2486 3136 0.684535 TCCGACTCATGGAAAGCACA 59.315 50.000 0.00 0.00 30.98 4.57
2487 3137 1.071542 TCCGACTCATGGAAAGCACAA 59.928 47.619 0.00 0.00 30.98 3.33
2488 3138 1.197721 CCGACTCATGGAAAGCACAAC 59.802 52.381 0.00 0.00 0.00 3.32
2489 3139 1.136252 CGACTCATGGAAAGCACAACG 60.136 52.381 0.00 0.00 0.00 4.10
2490 3140 1.197721 GACTCATGGAAAGCACAACGG 59.802 52.381 0.00 0.00 0.00 4.44
2491 3141 0.523072 CTCATGGAAAGCACAACGGG 59.477 55.000 0.00 0.00 0.00 5.28
2492 3142 0.109532 TCATGGAAAGCACAACGGGA 59.890 50.000 0.00 0.00 0.00 5.14
2493 3143 0.523072 CATGGAAAGCACAACGGGAG 59.477 55.000 0.00 0.00 0.00 4.30
2495 3145 0.759959 TGGAAAGCACAACGGGAGTA 59.240 50.000 0.00 0.00 46.69 2.59
2496 3146 1.154197 GGAAAGCACAACGGGAGTAC 58.846 55.000 0.00 0.00 46.69 2.73
2497 3147 1.541670 GGAAAGCACAACGGGAGTACA 60.542 52.381 0.00 0.00 46.69 2.90
2498 3148 2.423577 GAAAGCACAACGGGAGTACAT 58.576 47.619 0.00 0.00 46.69 2.29
2499 3149 2.561478 AAGCACAACGGGAGTACATT 57.439 45.000 0.00 0.00 46.69 2.71
2500 3150 2.561478 AGCACAACGGGAGTACATTT 57.439 45.000 0.00 0.00 46.69 2.32
2501 3151 3.688694 AGCACAACGGGAGTACATTTA 57.311 42.857 0.00 0.00 46.69 1.40
2502 3152 4.216411 AGCACAACGGGAGTACATTTAT 57.784 40.909 0.00 0.00 46.69 1.40
2503 3153 4.585879 AGCACAACGGGAGTACATTTATT 58.414 39.130 0.00 0.00 46.69 1.40
2504 3154 5.007682 AGCACAACGGGAGTACATTTATTT 58.992 37.500 0.00 0.00 46.69 1.40
2505 3155 5.092781 GCACAACGGGAGTACATTTATTTG 58.907 41.667 0.00 0.00 46.69 2.32
2506 3156 5.335348 GCACAACGGGAGTACATTTATTTGT 60.335 40.000 0.00 0.00 46.69 2.83
2507 3157 6.674066 CACAACGGGAGTACATTTATTTGTT 58.326 36.000 0.00 0.00 46.69 2.83
2508 3158 6.580791 CACAACGGGAGTACATTTATTTGTTG 59.419 38.462 0.00 0.00 46.69 3.33
2509 3159 6.487331 ACAACGGGAGTACATTTATTTGTTGA 59.513 34.615 0.00 0.00 46.69 3.18
2510 3160 7.175990 ACAACGGGAGTACATTTATTTGTTGAT 59.824 33.333 0.00 0.00 46.69 2.57
2511 3161 7.696992 ACGGGAGTACATTTATTTGTTGATT 57.303 32.000 0.00 0.00 44.60 2.57
2512 3162 8.117813 ACGGGAGTACATTTATTTGTTGATTT 57.882 30.769 0.00 0.00 44.60 2.17
2513 3163 8.026607 ACGGGAGTACATTTATTTGTTGATTTG 58.973 33.333 0.00 0.00 44.60 2.32
2514 3164 7.009174 CGGGAGTACATTTATTTGTTGATTTGC 59.991 37.037 0.00 0.00 0.00 3.68
2515 3165 7.816995 GGGAGTACATTTATTTGTTGATTTGCA 59.183 33.333 0.00 0.00 0.00 4.08
2516 3166 9.202273 GGAGTACATTTATTTGTTGATTTGCAA 57.798 29.630 0.00 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 122 9.542462 AAAAATCTCTAATTCGATCGTTCCATA 57.458 29.630 15.94 2.34 0.00 2.74
159 163 3.462333 GATCGCTCGCTCGACAGCT 62.462 63.158 1.16 0.00 44.40 4.24
161 165 2.352915 GGATCGCTCGCTCGACAG 60.353 66.667 1.16 0.00 41.62 3.51
162 166 3.113386 CTGGATCGCTCGCTCGACA 62.113 63.158 1.16 0.00 41.62 4.35
244 250 0.955919 GGGTTGCTGTACTGGCACTC 60.956 60.000 12.26 9.23 39.55 3.51
245 251 1.073199 GGGTTGCTGTACTGGCACT 59.927 57.895 12.26 0.00 39.55 4.40
256 262 3.649277 CTACGAGCGCTGGGTTGCT 62.649 63.158 23.76 4.52 45.90 3.91
272 278 1.539065 GGCAGCTCTTAATCAGCGCTA 60.539 52.381 10.99 0.00 41.96 4.26
492 536 9.142014 TGCCCACAGCTATAAATATTAAACAAT 57.858 29.630 0.00 0.00 44.23 2.71
1554 2192 4.080863 AGGAATAGACAAGCCGAGAAATGT 60.081 41.667 0.00 0.00 0.00 2.71
1766 2407 9.698309 TCTGTTTTCTTTCACATTGTTTTTGTA 57.302 25.926 0.00 0.00 0.00 2.41
1774 2415 7.591057 TCGCTATTTCTGTTTTCTTTCACATTG 59.409 33.333 0.00 0.00 0.00 2.82
1872 2517 0.802222 GCTATGTCTCGCTTCGTGCA 60.802 55.000 4.36 0.00 43.06 4.57
1941 2586 2.078665 GCTTCTGGGCCCCATCCTA 61.079 63.158 22.27 0.00 30.82 2.94
1942 2587 3.424105 GCTTCTGGGCCCCATCCT 61.424 66.667 22.27 0.00 30.82 3.24
1946 2591 1.305213 GATTTGCTTCTGGGCCCCA 60.305 57.895 22.27 6.42 0.00 4.96
1948 2593 0.899717 TGTGATTTGCTTCTGGGCCC 60.900 55.000 17.59 17.59 0.00 5.80
2004 2649 3.951663 TGCTAGGAAAGAAAAGCCTACC 58.048 45.455 0.00 0.00 33.99 3.18
2118 2768 8.873144 TGATGATCTGGGAAAAGAAAGAAAAAT 58.127 29.630 0.00 0.00 0.00 1.82
2119 2769 8.248904 TGATGATCTGGGAAAAGAAAGAAAAA 57.751 30.769 0.00 0.00 0.00 1.94
2120 2770 7.838079 TGATGATCTGGGAAAAGAAAGAAAA 57.162 32.000 0.00 0.00 0.00 2.29
2121 2771 7.670979 TGATGATGATCTGGGAAAAGAAAGAAA 59.329 33.333 0.00 0.00 0.00 2.52
2122 2772 7.121759 GTGATGATGATCTGGGAAAAGAAAGAA 59.878 37.037 0.00 0.00 0.00 2.52
2123 2773 6.600822 GTGATGATGATCTGGGAAAAGAAAGA 59.399 38.462 0.00 0.00 0.00 2.52
2124 2774 6.457934 CGTGATGATGATCTGGGAAAAGAAAG 60.458 42.308 0.00 0.00 0.00 2.62
2125 2775 5.355071 CGTGATGATGATCTGGGAAAAGAAA 59.645 40.000 0.00 0.00 0.00 2.52
2126 2776 4.877823 CGTGATGATGATCTGGGAAAAGAA 59.122 41.667 0.00 0.00 0.00 2.52
2127 2777 4.162131 TCGTGATGATGATCTGGGAAAAGA 59.838 41.667 0.00 0.00 0.00 2.52
2128 2778 4.445453 TCGTGATGATGATCTGGGAAAAG 58.555 43.478 0.00 0.00 0.00 2.27
2129 2779 4.486125 TCGTGATGATGATCTGGGAAAA 57.514 40.909 0.00 0.00 0.00 2.29
2130 2780 4.486125 TTCGTGATGATGATCTGGGAAA 57.514 40.909 0.00 0.00 0.00 3.13
2131 2781 4.486125 TTTCGTGATGATGATCTGGGAA 57.514 40.909 0.00 0.00 0.00 3.97
2132 2782 4.101430 TCATTTCGTGATGATGATCTGGGA 59.899 41.667 0.00 0.00 31.35 4.37
2133 2783 4.383173 TCATTTCGTGATGATGATCTGGG 58.617 43.478 0.00 0.00 31.35 4.45
2134 2784 4.083961 GCTCATTTCGTGATGATGATCTGG 60.084 45.833 0.00 0.00 35.62 3.86
2135 2785 4.510340 TGCTCATTTCGTGATGATGATCTG 59.490 41.667 0.00 0.00 35.62 2.90
2136 2786 4.700700 TGCTCATTTCGTGATGATGATCT 58.299 39.130 0.00 0.00 35.62 2.75
2137 2787 5.007430 ACTTGCTCATTTCGTGATGATGATC 59.993 40.000 4.42 0.00 35.62 2.92
2138 2788 4.880120 ACTTGCTCATTTCGTGATGATGAT 59.120 37.500 4.42 0.00 35.62 2.45
2139 2789 4.256110 ACTTGCTCATTTCGTGATGATGA 58.744 39.130 4.42 0.00 35.62 2.92
2140 2790 4.611310 ACTTGCTCATTTCGTGATGATG 57.389 40.909 4.42 0.00 35.62 3.07
2141 2791 4.813161 CCTACTTGCTCATTTCGTGATGAT 59.187 41.667 4.42 0.00 35.62 2.45
2142 2792 4.183865 CCTACTTGCTCATTTCGTGATGA 58.816 43.478 4.03 4.03 35.97 2.92
2143 2793 3.935203 ACCTACTTGCTCATTTCGTGATG 59.065 43.478 0.00 0.00 35.97 3.07
2144 2794 4.207891 ACCTACTTGCTCATTTCGTGAT 57.792 40.909 0.00 0.00 35.97 3.06
2145 2795 3.678056 ACCTACTTGCTCATTTCGTGA 57.322 42.857 0.00 0.00 35.05 4.35
2146 2796 5.856126 TTAACCTACTTGCTCATTTCGTG 57.144 39.130 0.00 0.00 0.00 4.35
2147 2797 6.261381 TGTTTTAACCTACTTGCTCATTTCGT 59.739 34.615 0.00 0.00 0.00 3.85
2148 2798 6.664515 TGTTTTAACCTACTTGCTCATTTCG 58.335 36.000 0.00 0.00 0.00 3.46
2151 2801 8.244113 GCTTATGTTTTAACCTACTTGCTCATT 58.756 33.333 0.00 0.00 0.00 2.57
2152 2802 7.393234 TGCTTATGTTTTAACCTACTTGCTCAT 59.607 33.333 0.00 0.00 0.00 2.90
2153 2803 6.712998 TGCTTATGTTTTAACCTACTTGCTCA 59.287 34.615 0.00 0.00 0.00 4.26
2154 2804 7.141100 TGCTTATGTTTTAACCTACTTGCTC 57.859 36.000 0.00 0.00 0.00 4.26
2155 2805 7.519032 TTGCTTATGTTTTAACCTACTTGCT 57.481 32.000 0.00 0.00 0.00 3.91
2156 2806 8.757164 AATTGCTTATGTTTTAACCTACTTGC 57.243 30.769 0.00 0.00 0.00 4.01
2182 2832 5.941555 TCTTAGTTTTTCCCCTGCAAAAA 57.058 34.783 0.00 0.00 31.70 1.94
2183 2833 5.941555 TTCTTAGTTTTTCCCCTGCAAAA 57.058 34.783 0.00 0.00 0.00 2.44
2184 2834 5.941555 TTTCTTAGTTTTTCCCCTGCAAA 57.058 34.783 0.00 0.00 0.00 3.68
2185 2835 5.423931 ACTTTTCTTAGTTTTTCCCCTGCAA 59.576 36.000 0.00 0.00 0.00 4.08
2186 2836 4.959839 ACTTTTCTTAGTTTTTCCCCTGCA 59.040 37.500 0.00 0.00 0.00 4.41
2187 2837 5.531122 ACTTTTCTTAGTTTTTCCCCTGC 57.469 39.130 0.00 0.00 0.00 4.85
2188 2838 7.327975 ACAAACTTTTCTTAGTTTTTCCCCTG 58.672 34.615 0.00 0.00 43.85 4.45
2189 2839 7.490657 ACAAACTTTTCTTAGTTTTTCCCCT 57.509 32.000 0.00 0.00 43.85 4.79
2190 2840 7.820386 TCAACAAACTTTTCTTAGTTTTTCCCC 59.180 33.333 0.00 0.00 43.85 4.81
2191 2841 8.653338 GTCAACAAACTTTTCTTAGTTTTTCCC 58.347 33.333 0.00 0.00 43.85 3.97
2192 2842 9.198837 TGTCAACAAACTTTTCTTAGTTTTTCC 57.801 29.630 0.00 0.00 43.85 3.13
2258 2908 1.459450 AATCCCGGTTGCACATACAC 58.541 50.000 0.00 0.00 0.00 2.90
2260 2910 2.870411 GTCTAATCCCGGTTGCACATAC 59.130 50.000 0.00 0.00 0.00 2.39
2261 2911 2.482316 CGTCTAATCCCGGTTGCACATA 60.482 50.000 0.00 0.00 0.00 2.29
2262 2912 1.742411 CGTCTAATCCCGGTTGCACAT 60.742 52.381 0.00 0.00 0.00 3.21
2263 2913 0.390603 CGTCTAATCCCGGTTGCACA 60.391 55.000 0.00 0.00 0.00 4.57
2264 2914 0.108520 TCGTCTAATCCCGGTTGCAC 60.109 55.000 0.00 0.00 0.00 4.57
2265 2915 0.108520 GTCGTCTAATCCCGGTTGCA 60.109 55.000 0.00 0.00 0.00 4.08
2266 2916 0.108520 TGTCGTCTAATCCCGGTTGC 60.109 55.000 0.00 0.00 0.00 4.17
2267 2917 1.203994 ACTGTCGTCTAATCCCGGTTG 59.796 52.381 0.00 0.00 0.00 3.77
2268 2918 1.553706 ACTGTCGTCTAATCCCGGTT 58.446 50.000 0.00 0.00 0.00 4.44
2269 2919 1.553706 AACTGTCGTCTAATCCCGGT 58.446 50.000 0.00 0.00 0.00 5.28
2270 2920 2.537401 GAAACTGTCGTCTAATCCCGG 58.463 52.381 0.00 0.00 0.00 5.73
2271 2921 2.182825 CGAAACTGTCGTCTAATCCCG 58.817 52.381 0.00 0.00 45.09 5.14
2307 2957 8.624776 CAATTAAGAACAGAGAAAGGAACAACT 58.375 33.333 0.00 0.00 0.00 3.16
2369 3019 9.139174 CACCACCTAAATTTTATCATTGAACAC 57.861 33.333 0.00 0.00 0.00 3.32
2374 3024 7.416964 TCCCACCACCTAAATTTTATCATTG 57.583 36.000 0.00 0.00 0.00 2.82
2432 3082 9.897744 TCAAGAATGTAACAAATGAAGACAATC 57.102 29.630 0.00 0.00 0.00 2.67
2436 3086 9.515020 TGTTTCAAGAATGTAACAAATGAAGAC 57.485 29.630 0.00 0.00 41.85 3.01
2445 3095 8.191446 TCGGAATTTTGTTTCAAGAATGTAACA 58.809 29.630 0.00 0.00 42.71 2.41
2446 3096 8.476925 GTCGGAATTTTGTTTCAAGAATGTAAC 58.523 33.333 0.00 0.00 37.35 2.50
2447 3097 8.410141 AGTCGGAATTTTGTTTCAAGAATGTAA 58.590 29.630 0.00 0.00 0.00 2.41
2448 3098 7.936584 AGTCGGAATTTTGTTTCAAGAATGTA 58.063 30.769 0.00 0.00 0.00 2.29
2449 3099 6.805713 AGTCGGAATTTTGTTTCAAGAATGT 58.194 32.000 0.00 0.00 0.00 2.71
2450 3100 6.917477 TGAGTCGGAATTTTGTTTCAAGAATG 59.083 34.615 0.00 0.00 0.00 2.67
2451 3101 7.038154 TGAGTCGGAATTTTGTTTCAAGAAT 57.962 32.000 0.00 0.00 0.00 2.40
2452 3102 6.443934 TGAGTCGGAATTTTGTTTCAAGAA 57.556 33.333 0.00 0.00 0.00 2.52
2453 3103 6.437928 CATGAGTCGGAATTTTGTTTCAAGA 58.562 36.000 0.00 0.00 0.00 3.02
2454 3104 5.630680 CCATGAGTCGGAATTTTGTTTCAAG 59.369 40.000 0.00 0.00 0.00 3.02
2455 3105 5.300539 TCCATGAGTCGGAATTTTGTTTCAA 59.699 36.000 0.00 0.00 0.00 2.69
2456 3106 4.824537 TCCATGAGTCGGAATTTTGTTTCA 59.175 37.500 0.00 0.00 0.00 2.69
2457 3107 5.371115 TCCATGAGTCGGAATTTTGTTTC 57.629 39.130 0.00 0.00 0.00 2.78
2458 3108 5.782893 TTCCATGAGTCGGAATTTTGTTT 57.217 34.783 0.00 0.00 37.62 2.83
2459 3109 5.772521 CTTTCCATGAGTCGGAATTTTGTT 58.227 37.500 0.00 0.00 42.07 2.83
2460 3110 4.321230 GCTTTCCATGAGTCGGAATTTTGT 60.321 41.667 0.00 0.00 42.07 2.83
2461 3111 4.168760 GCTTTCCATGAGTCGGAATTTTG 58.831 43.478 0.00 0.00 42.07 2.44
2462 3112 3.826157 TGCTTTCCATGAGTCGGAATTTT 59.174 39.130 0.00 0.00 42.07 1.82
2463 3113 3.191371 GTGCTTTCCATGAGTCGGAATTT 59.809 43.478 0.00 0.00 42.07 1.82
2464 3114 2.749621 GTGCTTTCCATGAGTCGGAATT 59.250 45.455 0.00 0.00 42.07 2.17
2465 3115 2.290260 TGTGCTTTCCATGAGTCGGAAT 60.290 45.455 0.00 0.00 42.07 3.01
2466 3116 1.071542 TGTGCTTTCCATGAGTCGGAA 59.928 47.619 0.00 0.00 40.81 4.30
2467 3117 0.684535 TGTGCTTTCCATGAGTCGGA 59.315 50.000 0.00 0.00 0.00 4.55
2468 3118 1.197721 GTTGTGCTTTCCATGAGTCGG 59.802 52.381 0.00 0.00 0.00 4.79
2469 3119 1.136252 CGTTGTGCTTTCCATGAGTCG 60.136 52.381 0.00 0.00 0.00 4.18
2470 3120 1.197721 CCGTTGTGCTTTCCATGAGTC 59.802 52.381 0.00 0.00 0.00 3.36
2471 3121 1.238439 CCGTTGTGCTTTCCATGAGT 58.762 50.000 0.00 0.00 0.00 3.41
2472 3122 0.523072 CCCGTTGTGCTTTCCATGAG 59.477 55.000 0.00 0.00 0.00 2.90
2473 3123 0.109532 TCCCGTTGTGCTTTCCATGA 59.890 50.000 0.00 0.00 0.00 3.07
2474 3124 0.523072 CTCCCGTTGTGCTTTCCATG 59.477 55.000 0.00 0.00 0.00 3.66
2475 3125 0.110486 ACTCCCGTTGTGCTTTCCAT 59.890 50.000 0.00 0.00 0.00 3.41
2476 3126 0.759959 TACTCCCGTTGTGCTTTCCA 59.240 50.000 0.00 0.00 0.00 3.53
2477 3127 1.154197 GTACTCCCGTTGTGCTTTCC 58.846 55.000 0.00 0.00 0.00 3.13
2478 3128 1.873698 TGTACTCCCGTTGTGCTTTC 58.126 50.000 0.00 0.00 0.00 2.62
2479 3129 2.561478 ATGTACTCCCGTTGTGCTTT 57.439 45.000 0.00 0.00 0.00 3.51
2480 3130 2.561478 AATGTACTCCCGTTGTGCTT 57.439 45.000 0.00 0.00 0.00 3.91
2481 3131 2.561478 AAATGTACTCCCGTTGTGCT 57.439 45.000 0.00 0.00 0.00 4.40
2482 3132 4.957759 AATAAATGTACTCCCGTTGTGC 57.042 40.909 0.00 0.00 0.00 4.57
2483 3133 6.249035 ACAAATAAATGTACTCCCGTTGTG 57.751 37.500 0.00 0.00 0.00 3.33
2484 3134 6.487331 TCAACAAATAAATGTACTCCCGTTGT 59.513 34.615 0.00 0.00 33.52 3.32
2485 3135 6.904498 TCAACAAATAAATGTACTCCCGTTG 58.096 36.000 0.00 0.00 32.02 4.10
2486 3136 7.696992 ATCAACAAATAAATGTACTCCCGTT 57.303 32.000 0.00 0.00 32.02 4.44
2487 3137 7.696992 AATCAACAAATAAATGTACTCCCGT 57.303 32.000 0.00 0.00 32.02 5.28
2488 3138 7.009174 GCAAATCAACAAATAAATGTACTCCCG 59.991 37.037 0.00 0.00 32.02 5.14
2489 3139 7.816995 TGCAAATCAACAAATAAATGTACTCCC 59.183 33.333 0.00 0.00 32.02 4.30
2490 3140 8.755696 TGCAAATCAACAAATAAATGTACTCC 57.244 30.769 0.00 0.00 32.02 3.85


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

AutoCloner maintained by Alex Coulton.