Multiple sequence alignment - TraesCS5B01G405100

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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 TraesCS5B01G405100 chr5B 100.000 2796 0 0 1 2796 580741195 580738400 0.000000e+00 5164.0
1 TraesCS5B01G405100 chr5D 92.986 1996 89 25 15 1980 473487674 473485700 0.000000e+00 2863.0
2 TraesCS5B01G405100 chr5D 92.173 626 33 7 2037 2660 473485696 473485085 0.000000e+00 870.0
3 TraesCS5B01G405100 chr5D 93.443 122 8 0 2675 2796 473485037 473484916 6.150000e-42 182.0
4 TraesCS5B01G405100 chr5A 89.387 1828 97 42 263 2029 593242695 593240904 0.000000e+00 2211.0
5 TraesCS5B01G405100 chr5A 88.889 531 39 8 2131 2660 593240709 593240198 1.090000e-178 636.0
6 TraesCS5B01G405100 chr5A 91.912 272 11 5 1 268 593243141 593242877 1.220000e-98 370.0
7 TraesCS5B01G405100 chr5A 94.059 101 3 1 2033 2133 593240934 593240837 1.730000e-32 150.0
8 TraesCS5B01G405100 chr5A 75.472 212 38 13 2188 2394 520586703 520586905 1.070000e-14 91.6
9 TraesCS5B01G405100 chr6D 81.000 200 27 9 2195 2389 144066037 144066230 6.240000e-32 148.0
10 TraesCS5B01G405100 chr6B 77.717 184 31 10 2190 2369 686863931 686864108 1.370000e-18 104.0
11 TraesCS5B01G405100 chr1A 81.600 125 15 7 2223 2346 38740541 38740424 2.290000e-16 97.1


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 TraesCS5B01G405100 chr5B 580738400 580741195 2795 True 5164.00 5164 100.000000 1 2796 1 chr5B.!!$R1 2795
1 TraesCS5B01G405100 chr5D 473484916 473487674 2758 True 1305.00 2863 92.867333 15 2796 3 chr5D.!!$R1 2781
2 TraesCS5B01G405100 chr5A 593240198 593243141 2943 True 841.75 2211 91.061750 1 2660 4 chr5A.!!$R1 2659

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
222 228 0.246086 AAGAGCAAGTCCAGAGCGAG 59.754 55.0 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2204 2624 0.177141 GTATAGCACCGAGGGCAACA 59.823 55.0 0.98 0.0 39.74 3.33 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
28 29 0.393673 TCACGCTCCTCTCTCTCAGG 60.394 60.000 0.00 0.00 0.00 3.86
129 135 5.758296 ACACTCGGGCATGTAATTTATGTAG 59.242 40.000 0.00 0.00 0.00 2.74
130 136 5.179368 CACTCGGGCATGTAATTTATGTAGG 59.821 44.000 0.00 0.00 0.00 3.18
131 137 4.647611 TCGGGCATGTAATTTATGTAGGG 58.352 43.478 0.00 0.00 0.00 3.53
135 141 5.009610 GGGCATGTAATTTATGTAGGGTGTG 59.990 44.000 0.00 0.00 0.00 3.82
212 218 2.986306 GCATGCCGCAAGAGCAAGT 61.986 57.895 6.36 0.00 44.46 3.16
222 228 0.246086 AAGAGCAAGTCCAGAGCGAG 59.754 55.000 0.00 0.00 0.00 5.03
223 229 1.809209 GAGCAAGTCCAGAGCGAGC 60.809 63.158 0.00 0.00 0.00 5.03
280 473 2.818432 CAGTCCTAGTGTACTCCGTTGT 59.182 50.000 0.00 0.00 0.00 3.32
284 477 3.006110 TCCTAGTGTACTCCGTTGTTTGG 59.994 47.826 0.00 0.00 0.00 3.28
285 478 1.589803 AGTGTACTCCGTTGTTTGGC 58.410 50.000 0.00 0.00 0.00 4.52
286 479 1.134340 AGTGTACTCCGTTGTTTGGCA 60.134 47.619 0.00 0.00 0.00 4.92
287 480 1.877443 GTGTACTCCGTTGTTTGGCAT 59.123 47.619 0.00 0.00 0.00 4.40
407 608 5.480073 TCCTTCTCTCTTTCTTCTTCAGAGG 59.520 44.000 0.00 0.00 35.65 3.69
408 609 5.480073 CCTTCTCTCTTTCTTCTTCAGAGGA 59.520 44.000 0.00 0.00 35.65 3.71
409 610 6.350445 CCTTCTCTCTTTCTTCTTCAGAGGAG 60.350 46.154 0.00 0.00 36.80 3.69
410 611 5.886609 TCTCTCTTTCTTCTTCAGAGGAGA 58.113 41.667 0.00 0.00 38.66 3.71
411 612 6.199937 CTCTCTTTCTTCTTCAGAGGAGAG 57.800 45.833 14.12 14.12 44.59 3.20
412 613 5.640147 TCTCTTTCTTCTTCAGAGGAGAGT 58.360 41.667 6.43 0.00 38.75 3.24
413 614 5.476599 TCTCTTTCTTCTTCAGAGGAGAGTG 59.523 44.000 6.43 4.90 38.75 3.51
414 615 5.389520 TCTTTCTTCTTCAGAGGAGAGTGA 58.610 41.667 6.43 0.00 38.75 3.41
415 616 5.476599 TCTTTCTTCTTCAGAGGAGAGTGAG 59.523 44.000 6.43 0.00 38.75 3.51
416 617 4.649267 TCTTCTTCAGAGGAGAGTGAGA 57.351 45.455 0.00 0.00 32.34 3.27
417 618 4.588899 TCTTCTTCAGAGGAGAGTGAGAG 58.411 47.826 0.00 0.00 32.34 3.20
418 619 4.288366 TCTTCTTCAGAGGAGAGTGAGAGA 59.712 45.833 0.00 0.00 32.34 3.10
429 630 2.774234 AGAGTGAGAGAGAGGAGAGAGG 59.226 54.545 0.00 0.00 0.00 3.69
453 654 2.844839 GGGAGAGGGACGGATGGG 60.845 72.222 0.00 0.00 0.00 4.00
473 674 2.738521 CGACGGTCTGCTGGTTGG 60.739 66.667 6.57 0.00 0.00 3.77
549 750 3.186409 CGATAGCGAGAAGAGAAGAGGAG 59.814 52.174 0.00 0.00 40.82 3.69
563 764 4.459089 GGAGCAGGGCCGAGTGAC 62.459 72.222 0.00 0.00 0.00 3.67
583 784 1.895798 CTGGTAGTTGGAGCTCAGTGA 59.104 52.381 17.19 0.00 0.00 3.41
617 818 6.241645 TCTTGAGTCACTTCTCTGACATCTA 58.758 40.000 0.00 0.00 42.74 1.98
618 819 6.374053 TCTTGAGTCACTTCTCTGACATCTAG 59.626 42.308 0.00 4.05 42.74 2.43
663 869 5.222007 TGAGCTCATTTCCCTCTCTTCTTTT 60.222 40.000 13.74 0.00 0.00 2.27
671 877 3.844804 TCCCTCTCTTCTTTTCCCTTACC 59.155 47.826 0.00 0.00 0.00 2.85
727 933 6.165577 TCAATCATTTTTAGGCCTTTTCAGC 58.834 36.000 12.58 0.00 0.00 4.26
746 953 2.700371 AGCCTTCTTTTTCCTTTGGGTG 59.300 45.455 0.00 0.00 0.00 4.61
784 991 1.548269 ACAGTTACTCCAGCAGAGAGC 59.452 52.381 10.46 0.00 46.50 4.09
834 1042 3.926671 TCCCCTCCTTTATTTCCTTTCCA 59.073 43.478 0.00 0.00 0.00 3.53
862 1070 1.693627 ATCTAGTGCCCGATTCTCGT 58.306 50.000 0.00 0.00 38.40 4.18
890 1098 1.266718 TCGAAAGCTCCAATTGTGTGC 59.733 47.619 4.43 8.48 0.00 4.57
901 1129 3.247442 CAATTGTGTGCCTGCATTGTAG 58.753 45.455 0.00 0.00 0.00 2.74
903 1131 2.849294 TGTGTGCCTGCATTGTAGTA 57.151 45.000 0.00 0.00 0.00 1.82
904 1132 2.422597 TGTGTGCCTGCATTGTAGTAC 58.577 47.619 0.00 0.00 0.00 2.73
905 1133 1.393539 GTGTGCCTGCATTGTAGTACG 59.606 52.381 0.00 0.00 0.00 3.67
906 1134 1.273886 TGTGCCTGCATTGTAGTACGA 59.726 47.619 0.00 0.00 0.00 3.43
907 1135 1.927174 GTGCCTGCATTGTAGTACGAG 59.073 52.381 0.00 0.00 0.00 4.18
908 1136 1.822371 TGCCTGCATTGTAGTACGAGA 59.178 47.619 0.98 0.00 0.00 4.04
909 1137 2.159240 TGCCTGCATTGTAGTACGAGAG 60.159 50.000 0.98 0.00 0.00 3.20
910 1138 2.099263 GCCTGCATTGTAGTACGAGAGA 59.901 50.000 0.98 0.00 0.00 3.10
911 1139 3.243569 GCCTGCATTGTAGTACGAGAGAT 60.244 47.826 0.98 0.00 0.00 2.75
912 1140 4.541779 CCTGCATTGTAGTACGAGAGATC 58.458 47.826 0.98 0.00 0.00 2.75
913 1141 4.036852 CCTGCATTGTAGTACGAGAGATCA 59.963 45.833 0.00 0.00 0.00 2.92
914 1142 5.175090 TGCATTGTAGTACGAGAGATCAG 57.825 43.478 0.00 0.00 0.00 2.90
915 1143 3.978217 GCATTGTAGTACGAGAGATCAGC 59.022 47.826 0.00 0.00 0.00 4.26
916 1144 4.261405 GCATTGTAGTACGAGAGATCAGCT 60.261 45.833 0.00 0.00 0.00 4.24
917 1145 5.448438 CATTGTAGTACGAGAGATCAGCTC 58.552 45.833 0.00 0.22 44.29 4.09
934 1162 1.325943 GCTCGTATGCTCACTTTCTGC 59.674 52.381 0.00 0.00 0.00 4.26
940 1168 1.233019 TGCTCACTTTCTGCTCAAGC 58.767 50.000 0.00 0.00 42.50 4.01
954 1182 5.537674 TCTGCTCAAGCTCATATCTGTATGA 59.462 40.000 3.32 0.00 43.20 2.15
957 1185 6.164876 GCTCAAGCTCATATCTGTATGACAT 58.835 40.000 0.00 0.00 41.28 3.06
977 1205 7.312899 TGACATGATACAGTGTAGTGTAGTTG 58.687 38.462 9.25 2.69 36.36 3.16
982 1210 7.903145 TGATACAGTGTAGTGTAGTTGGAAAT 58.097 34.615 9.25 0.00 36.36 2.17
1028 1256 3.118531 ACCTATTTCTCCATGCAGGTCT 58.881 45.455 0.00 0.00 39.02 3.85
1031 1259 0.329261 TTTCTCCATGCAGGTCTGGG 59.671 55.000 4.27 0.00 39.02 4.45
1037 1265 0.107312 CATGCAGGTCTGGGGAAGAG 60.107 60.000 0.00 0.00 34.84 2.85
1058 1289 5.041191 AGGAAGAAACAGAGCAAGAAAGA 57.959 39.130 0.00 0.00 0.00 2.52
1104 1335 0.167470 CCTTCATGCACTGCGACAAG 59.833 55.000 0.00 0.00 0.00 3.16
1167 1398 6.155221 CCTTCAGGCAGCAGGTATATAAGATA 59.845 42.308 0.00 0.00 0.00 1.98
1190 1435 9.226345 GATAAGAATTCATAAGTTTTTGCCTCG 57.774 33.333 8.44 0.00 0.00 4.63
1199 1444 0.605319 TTTTTGCCTCGCCGTCTCAT 60.605 50.000 0.00 0.00 0.00 2.90
1317 1565 1.611474 ATCAAGAGCCAGCAGAGCGA 61.611 55.000 0.00 0.00 34.64 4.93
1408 1659 1.139947 GTCCTCCTACGAGCAGCAC 59.860 63.158 0.00 0.00 34.49 4.40
1882 2171 6.210784 TGTTTGTTGAGCTGTAGTAGGAGTAT 59.789 38.462 0.00 0.00 0.00 2.12
1995 2285 0.178861 ACAGGTGGAGAGGGGTGAAT 60.179 55.000 0.00 0.00 0.00 2.57
1996 2286 0.254178 CAGGTGGAGAGGGGTGAATG 59.746 60.000 0.00 0.00 0.00 2.67
1997 2287 0.178861 AGGTGGAGAGGGGTGAATGT 60.179 55.000 0.00 0.00 0.00 2.71
1998 2288 1.080498 AGGTGGAGAGGGGTGAATGTA 59.920 52.381 0.00 0.00 0.00 2.29
1999 2289 1.486726 GGTGGAGAGGGGTGAATGTAG 59.513 57.143 0.00 0.00 0.00 2.74
2000 2290 1.486726 GTGGAGAGGGGTGAATGTAGG 59.513 57.143 0.00 0.00 0.00 3.18
2001 2291 1.132500 GGAGAGGGGTGAATGTAGGG 58.868 60.000 0.00 0.00 0.00 3.53
2002 2292 1.132500 GAGAGGGGTGAATGTAGGGG 58.868 60.000 0.00 0.00 0.00 4.79
2003 2293 0.988678 AGAGGGGTGAATGTAGGGGC 60.989 60.000 0.00 0.00 0.00 5.80
2004 2294 0.988678 GAGGGGTGAATGTAGGGGCT 60.989 60.000 0.00 0.00 0.00 5.19
2005 2295 0.552615 AGGGGTGAATGTAGGGGCTT 60.553 55.000 0.00 0.00 0.00 4.35
2006 2296 0.335019 GGGGTGAATGTAGGGGCTTT 59.665 55.000 0.00 0.00 0.00 3.51
2007 2297 1.273041 GGGGTGAATGTAGGGGCTTTT 60.273 52.381 0.00 0.00 0.00 2.27
2008 2298 2.100197 GGGTGAATGTAGGGGCTTTTC 58.900 52.381 0.00 0.00 0.00 2.29
2009 2299 2.556559 GGGTGAATGTAGGGGCTTTTCA 60.557 50.000 0.00 0.00 0.00 2.69
2010 2300 2.755103 GGTGAATGTAGGGGCTTTTCAG 59.245 50.000 0.00 0.00 0.00 3.02
2011 2301 3.561313 GGTGAATGTAGGGGCTTTTCAGA 60.561 47.826 0.00 0.00 0.00 3.27
2012 2302 4.273318 GTGAATGTAGGGGCTTTTCAGAT 58.727 43.478 0.00 0.00 0.00 2.90
2013 2303 4.706962 GTGAATGTAGGGGCTTTTCAGATT 59.293 41.667 0.00 0.00 0.00 2.40
2014 2304 5.885912 GTGAATGTAGGGGCTTTTCAGATTA 59.114 40.000 0.00 0.00 0.00 1.75
2015 2305 6.377146 GTGAATGTAGGGGCTTTTCAGATTAA 59.623 38.462 0.00 0.00 0.00 1.40
2016 2306 6.603201 TGAATGTAGGGGCTTTTCAGATTAAG 59.397 38.462 0.00 0.00 0.00 1.85
2017 2307 4.270008 TGTAGGGGCTTTTCAGATTAAGC 58.730 43.478 8.60 8.60 44.62 3.09
2018 2308 3.746792 AGGGGCTTTTCAGATTAAGCT 57.253 42.857 14.28 0.00 44.70 3.74
2019 2309 4.862641 AGGGGCTTTTCAGATTAAGCTA 57.137 40.909 14.28 0.00 44.70 3.32
2020 2310 5.193099 AGGGGCTTTTCAGATTAAGCTAA 57.807 39.130 14.28 0.00 44.70 3.09
2021 2311 5.196695 AGGGGCTTTTCAGATTAAGCTAAG 58.803 41.667 14.28 0.00 44.70 2.18
2022 2312 4.202060 GGGGCTTTTCAGATTAAGCTAAGC 60.202 45.833 15.26 15.26 44.70 3.09
2023 2313 4.642437 GGGCTTTTCAGATTAAGCTAAGCT 59.358 41.667 20.31 0.00 44.70 3.74
2057 2347 3.693578 GGCTTTTCAGATGAAGCTAAGCT 59.306 43.478 21.07 0.00 45.72 3.74
2155 2575 2.421529 GGGGCAGTCTTTCGGTATGAAT 60.422 50.000 0.00 0.00 36.22 2.57
2188 2608 7.993183 TCACAAGAACTAAGAACAGAATTTCCT 59.007 33.333 0.00 0.00 0.00 3.36
2204 2624 8.844244 CAGAATTTCCTATCGAATGAGGATTTT 58.156 33.333 13.18 10.32 41.54 1.82
2205 2625 8.844244 AGAATTTCCTATCGAATGAGGATTTTG 58.156 33.333 13.18 0.00 41.54 2.44
2206 2626 8.525290 AATTTCCTATCGAATGAGGATTTTGT 57.475 30.769 13.18 0.00 41.54 2.83
2207 2627 7.938140 TTTCCTATCGAATGAGGATTTTGTT 57.062 32.000 13.18 0.00 41.54 2.83
2208 2628 6.925610 TCCTATCGAATGAGGATTTTGTTG 57.074 37.500 9.41 0.00 36.92 3.33
2209 2629 5.296780 TCCTATCGAATGAGGATTTTGTTGC 59.703 40.000 9.41 0.00 36.92 4.17
2210 2630 3.848272 TCGAATGAGGATTTTGTTGCC 57.152 42.857 0.00 0.00 0.00 4.52
2314 2734 8.593945 ATCAAACATGGGTTTCATTATACACT 57.406 30.769 0.00 0.00 45.18 3.55
2362 2782 3.132289 TGCCAGAGGTAATCTCGGTAAAG 59.868 47.826 0.00 0.00 46.82 1.85
2413 2833 1.971357 AGACCAAGACCACTCATTCGT 59.029 47.619 0.00 0.00 0.00 3.85
2452 2874 0.110486 ACAGTCGGCACCCAGATTTT 59.890 50.000 0.00 0.00 0.00 1.82
2457 2879 4.821805 CAGTCGGCACCCAGATTTTATATT 59.178 41.667 0.00 0.00 0.00 1.28
2564 2987 4.760204 TCATTTCTCGTTTCCCTTTTCCTC 59.240 41.667 0.00 0.00 0.00 3.71
2565 2988 2.853235 TCTCGTTTCCCTTTTCCTCC 57.147 50.000 0.00 0.00 0.00 4.30
2566 2989 2.335933 TCTCGTTTCCCTTTTCCTCCT 58.664 47.619 0.00 0.00 0.00 3.69
2660 3083 7.445402 ACATCTTAGTTGTGCATGTAACTCTTT 59.555 33.333 14.61 0.00 38.11 2.52
2662 3085 6.765989 TCTTAGTTGTGCATGTAACTCTTTGT 59.234 34.615 14.61 0.00 38.11 2.83
2665 3088 2.293122 TGTGCATGTAACTCTTTGTGGC 59.707 45.455 0.00 0.00 0.00 5.01
2668 3091 2.513753 CATGTAACTCTTTGTGGCCCA 58.486 47.619 0.00 0.00 0.00 5.36
2669 3092 2.969821 TGTAACTCTTTGTGGCCCAT 57.030 45.000 0.00 0.00 0.00 4.00
2670 3093 4.269183 CATGTAACTCTTTGTGGCCCATA 58.731 43.478 0.00 0.00 0.00 2.74
2672 3095 4.331968 TGTAACTCTTTGTGGCCCATAAG 58.668 43.478 0.00 0.37 0.00 1.73
2710 3166 2.733218 CCGTCATGTGTCGCGTGT 60.733 61.111 5.77 0.00 35.64 4.49
2712 3168 1.154854 CGTCATGTGTCGCGTGTTG 60.155 57.895 5.77 0.00 35.64 3.33
2725 3181 1.202582 GCGTGTTGGCTTCTCTCTCTA 59.797 52.381 0.00 0.00 0.00 2.43
2773 3229 4.963276 TGCGTTTTCAGGATTTAGATGG 57.037 40.909 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 0.707024 TTGCTCCCTGAGAGAGAGGA 59.293 55.000 0.00 0.00 46.50 3.71
28 29 4.301628 CAAAAGATTGGACTTGTTGCTCC 58.698 43.478 0.00 0.00 32.69 4.70
212 218 1.817520 CTCTCTCGCTCGCTCTGGA 60.818 63.158 0.00 0.00 0.00 3.86
222 228 5.057149 AGTATCTTTCTCTCTCTCTCTCGC 58.943 45.833 0.00 0.00 0.00 5.03
223 229 5.696724 GGAGTATCTTTCTCTCTCTCTCTCG 59.303 48.000 0.00 0.00 33.73 4.04
285 478 2.441348 TGCAGGGAGGCATGCATG 60.441 61.111 22.70 22.70 46.97 4.06
407 608 3.181461 CCTCTCTCCTCTCTCTCACTCTC 60.181 56.522 0.00 0.00 0.00 3.20
408 609 2.774234 CCTCTCTCCTCTCTCTCACTCT 59.226 54.545 0.00 0.00 0.00 3.24
409 610 2.158755 CCCTCTCTCCTCTCTCTCACTC 60.159 59.091 0.00 0.00 0.00 3.51
410 611 1.846439 CCCTCTCTCCTCTCTCTCACT 59.154 57.143 0.00 0.00 0.00 3.41
411 612 1.843851 TCCCTCTCTCCTCTCTCTCAC 59.156 57.143 0.00 0.00 0.00 3.51
412 613 2.126882 CTCCCTCTCTCCTCTCTCTCA 58.873 57.143 0.00 0.00 0.00 3.27
413 614 2.370189 CTCTCCCTCTCTCCTCTCTCTC 59.630 59.091 0.00 0.00 0.00 3.20
414 615 2.022035 TCTCTCCCTCTCTCCTCTCTCT 60.022 54.545 0.00 0.00 0.00 3.10
415 616 2.370189 CTCTCTCCCTCTCTCCTCTCTC 59.630 59.091 0.00 0.00 0.00 3.20
416 617 2.412591 CTCTCTCCCTCTCTCCTCTCT 58.587 57.143 0.00 0.00 0.00 3.10
417 618 1.421646 CCTCTCTCCCTCTCTCCTCTC 59.578 61.905 0.00 0.00 0.00 3.20
418 619 1.522900 CCTCTCTCCCTCTCTCCTCT 58.477 60.000 0.00 0.00 0.00 3.69
429 630 1.152839 CGTCCCTCTCCCTCTCTCC 60.153 68.421 0.00 0.00 0.00 3.71
453 654 3.222354 AACCAGCAGACCGTCGTCC 62.222 63.158 0.00 0.00 40.12 4.79
473 674 4.765339 ACAGGCTTTCCCTTTTATACACAC 59.235 41.667 0.00 0.00 43.06 3.82
549 750 4.767255 CCAGTCACTCGGCCCTGC 62.767 72.222 0.00 0.00 0.00 4.85
563 764 1.895798 TCACTGAGCTCCAACTACCAG 59.104 52.381 12.15 1.99 0.00 4.00
583 784 4.744795 AGTGACTCAAGAACTGAAGTGT 57.255 40.909 0.00 0.00 32.17 3.55
617 818 7.930865 GCTCATTTCTCACCTATCAATTACTCT 59.069 37.037 0.00 0.00 0.00 3.24
618 819 7.930865 AGCTCATTTCTCACCTATCAATTACTC 59.069 37.037 0.00 0.00 0.00 2.59
671 877 1.871676 CAGATTGATGAGCACCGGATG 59.128 52.381 9.46 3.68 0.00 3.51
727 933 3.038280 ACCACCCAAAGGAAAAAGAAGG 58.962 45.455 0.00 0.00 36.73 3.46
746 953 4.319177 ACTGTATTCTGAAGCAAGTCACC 58.681 43.478 0.00 0.00 0.00 4.02
784 991 2.074576 CAGTGTGCATGACAGGAGAAG 58.925 52.381 0.00 0.00 34.28 2.85
834 1042 1.501582 GGGCACTAGATTCAGAGGGT 58.498 55.000 0.00 0.00 0.00 4.34
862 1070 0.762418 TGGAGCTTTCGAAGTGGGAA 59.238 50.000 0.00 0.00 0.00 3.97
890 1098 4.036852 TGATCTCTCGTACTACAATGCAGG 59.963 45.833 0.00 0.00 0.00 4.85
905 1133 2.551887 TGAGCATACGAGCTGATCTCTC 59.448 50.000 6.51 0.00 46.75 3.20
906 1134 2.293122 GTGAGCATACGAGCTGATCTCT 59.707 50.000 6.51 0.00 46.75 3.10
907 1135 2.293122 AGTGAGCATACGAGCTGATCTC 59.707 50.000 6.51 2.19 46.75 2.75
908 1136 2.305928 AGTGAGCATACGAGCTGATCT 58.694 47.619 6.51 0.86 46.75 2.75
909 1137 2.791383 AGTGAGCATACGAGCTGATC 57.209 50.000 6.51 1.45 46.75 2.92
910 1138 3.131933 AGAAAGTGAGCATACGAGCTGAT 59.868 43.478 6.51 0.00 46.75 2.90
911 1139 2.493675 AGAAAGTGAGCATACGAGCTGA 59.506 45.455 6.51 0.00 46.75 4.26
912 1140 2.602211 CAGAAAGTGAGCATACGAGCTG 59.398 50.000 6.51 0.00 46.75 4.24
914 1142 1.325943 GCAGAAAGTGAGCATACGAGC 59.674 52.381 0.00 0.00 0.00 5.03
915 1143 2.857152 GAGCAGAAAGTGAGCATACGAG 59.143 50.000 0.00 0.00 0.00 4.18
916 1144 2.231235 TGAGCAGAAAGTGAGCATACGA 59.769 45.455 0.00 0.00 0.00 3.43
917 1145 2.610433 TGAGCAGAAAGTGAGCATACG 58.390 47.619 0.00 0.00 0.00 3.06
918 1146 3.181512 GCTTGAGCAGAAAGTGAGCATAC 60.182 47.826 0.00 0.00 41.59 2.39
919 1147 3.005554 GCTTGAGCAGAAAGTGAGCATA 58.994 45.455 0.00 0.00 41.59 3.14
920 1148 1.811359 GCTTGAGCAGAAAGTGAGCAT 59.189 47.619 0.00 0.00 41.59 3.79
921 1149 1.202734 AGCTTGAGCAGAAAGTGAGCA 60.203 47.619 5.70 0.00 45.16 4.26
922 1150 1.464219 GAGCTTGAGCAGAAAGTGAGC 59.536 52.381 5.70 0.00 45.16 4.26
934 1162 7.376615 TCATGTCATACAGATATGAGCTTGAG 58.623 38.462 0.00 0.00 46.11 3.02
954 1182 6.436218 TCCAACTACACTACACTGTATCATGT 59.564 38.462 0.00 6.29 0.00 3.21
957 1185 6.904463 TTCCAACTACACTACACTGTATCA 57.096 37.500 0.00 0.00 0.00 2.15
977 1205 2.293170 GCCTCTGCTCCAAGTATTTCC 58.707 52.381 0.00 0.00 33.53 3.13
1028 1256 2.639839 CTCTGTTTCTTCCTCTTCCCCA 59.360 50.000 0.00 0.00 0.00 4.96
1031 1259 3.409026 TGCTCTGTTTCTTCCTCTTCC 57.591 47.619 0.00 0.00 0.00 3.46
1037 1265 5.059833 TCTCTTTCTTGCTCTGTTTCTTCC 58.940 41.667 0.00 0.00 0.00 3.46
1104 1335 1.077429 GGCCATCTTGAGGGTGTCC 60.077 63.158 0.00 0.00 0.00 4.02
1137 1368 1.551908 CCTGCTGCCTGAAGGTCTCT 61.552 60.000 0.00 0.00 36.69 3.10
1167 1398 5.863935 GCGAGGCAAAAACTTATGAATTCTT 59.136 36.000 7.05 2.84 0.00 2.52
1176 1407 0.869730 GACGGCGAGGCAAAAACTTA 59.130 50.000 16.62 0.00 0.00 2.24
1180 1411 0.605319 ATGAGACGGCGAGGCAAAAA 60.605 50.000 16.62 0.00 0.00 1.94
1199 1444 2.224843 ACAAATCATGAGGCCACAGTCA 60.225 45.455 9.30 1.39 0.00 3.41
1882 2171 3.485394 TGGAAGCACAGAAACATAGCAA 58.515 40.909 0.00 0.00 0.00 3.91
1939 2229 7.047891 CCTACATAATCCTCAGCAACAAGTTA 58.952 38.462 0.00 0.00 0.00 2.24
1947 2237 2.634940 GGCTCCTACATAATCCTCAGCA 59.365 50.000 0.00 0.00 0.00 4.41
1949 2239 3.900601 AGTGGCTCCTACATAATCCTCAG 59.099 47.826 0.00 0.00 0.00 3.35
1955 2245 4.227300 TGTGGAAAGTGGCTCCTACATAAT 59.773 41.667 0.00 0.00 33.77 1.28
1957 2247 3.178046 TGTGGAAAGTGGCTCCTACATA 58.822 45.455 0.00 0.00 33.77 2.29
1995 2285 4.270008 GCTTAATCTGAAAAGCCCCTACA 58.730 43.478 14.02 0.00 41.80 2.74
1996 2286 4.902443 GCTTAATCTGAAAAGCCCCTAC 57.098 45.455 14.02 0.00 41.80 3.18
2015 2305 5.519808 AGCCCCTTAAAATTAAGCTTAGCT 58.480 37.500 0.00 0.00 42.56 3.32
2016 2306 5.854010 AGCCCCTTAAAATTAAGCTTAGC 57.146 39.130 6.24 0.00 38.99 3.09
2017 2307 8.311109 TGAAAAGCCCCTTAAAATTAAGCTTAG 58.689 33.333 6.24 0.00 38.99 2.18
2018 2308 8.196378 TGAAAAGCCCCTTAAAATTAAGCTTA 57.804 30.769 0.86 0.86 38.99 3.09
2019 2309 7.016170 TCTGAAAAGCCCCTTAAAATTAAGCTT 59.984 33.333 3.48 3.48 38.99 3.74
2020 2310 6.496911 TCTGAAAAGCCCCTTAAAATTAAGCT 59.503 34.615 7.29 0.98 38.99 3.74
2021 2311 6.697395 TCTGAAAAGCCCCTTAAAATTAAGC 58.303 36.000 7.29 0.00 38.99 3.09
2022 2312 8.531146 TCATCTGAAAAGCCCCTTAAAATTAAG 58.469 33.333 6.04 6.04 39.80 1.85
2023 2313 8.429237 TCATCTGAAAAGCCCCTTAAAATTAA 57.571 30.769 0.00 0.00 0.00 1.40
2024 2314 8.429237 TTCATCTGAAAAGCCCCTTAAAATTA 57.571 30.769 0.00 0.00 0.00 1.40
2025 2315 6.933514 TCATCTGAAAAGCCCCTTAAAATT 57.066 33.333 0.00 0.00 0.00 1.82
2026 2316 6.575056 GCTTCATCTGAAAAGCCCCTTAAAAT 60.575 38.462 14.01 0.00 41.60 1.82
2027 2317 5.279456 GCTTCATCTGAAAAGCCCCTTAAAA 60.279 40.000 14.01 0.00 41.60 1.52
2028 2318 4.220602 GCTTCATCTGAAAAGCCCCTTAAA 59.779 41.667 14.01 0.00 41.60 1.52
2029 2319 3.763897 GCTTCATCTGAAAAGCCCCTTAA 59.236 43.478 14.01 0.00 41.60 1.85
2030 2320 3.356290 GCTTCATCTGAAAAGCCCCTTA 58.644 45.455 14.01 0.00 41.60 2.69
2031 2321 2.174360 GCTTCATCTGAAAAGCCCCTT 58.826 47.619 14.01 0.00 41.60 3.95
2057 2347 3.826524 TGCACTGAGACCCAACAATTAA 58.173 40.909 0.00 0.00 0.00 1.40
2058 2348 3.500448 TGCACTGAGACCCAACAATTA 57.500 42.857 0.00 0.00 0.00 1.40
2059 2349 2.363306 TGCACTGAGACCCAACAATT 57.637 45.000 0.00 0.00 0.00 2.32
2062 2352 0.546122 ACTTGCACTGAGACCCAACA 59.454 50.000 0.00 0.00 0.00 3.33
2068 2358 6.487689 AAATTAAGCTACTTGCACTGAGAC 57.512 37.500 0.00 0.00 45.94 3.36
2155 2575 9.173021 TCTGTTCTTAGTTCTTGTGAATTTGAA 57.827 29.630 0.00 0.00 34.40 2.69
2188 2608 4.338118 GGGCAACAAAATCCTCATTCGATA 59.662 41.667 0.00 0.00 39.74 2.92
2204 2624 0.177141 GTATAGCACCGAGGGCAACA 59.823 55.000 0.98 0.00 39.74 3.33
2205 2625 0.532196 GGTATAGCACCGAGGGCAAC 60.532 60.000 0.00 0.00 37.63 4.17
2206 2626 1.827394 GGTATAGCACCGAGGGCAA 59.173 57.895 0.00 0.00 37.63 4.52
2207 2627 3.546009 GGTATAGCACCGAGGGCA 58.454 61.111 0.00 0.00 37.63 5.36
2296 2716 7.450014 TGAACACAAGTGTATAATGAAACCCAT 59.550 33.333 6.24 0.00 44.13 4.00
2314 2734 4.768130 TTTTCCACGAAACTGAACACAA 57.232 36.364 0.00 0.00 30.83 3.33
2384 2804 7.496346 TGAGTGGTCTTGGTCTTTTCTATAT 57.504 36.000 0.00 0.00 0.00 0.86
2399 2819 1.244816 TCGTCACGAATGAGTGGTCT 58.755 50.000 0.00 0.00 42.10 3.85
2406 2826 5.381477 CATGTTCAATTTCGTCACGAATGA 58.619 37.500 14.61 12.74 45.28 2.57
2413 2833 4.390264 TGTACCCATGTTCAATTTCGTCA 58.610 39.130 0.00 0.00 0.00 4.35
2516 2939 2.609747 GAGCTCCACACCCCTATATGA 58.390 52.381 0.87 0.00 0.00 2.15
2517 2940 1.625818 GGAGCTCCACACCCCTATATG 59.374 57.143 28.43 0.00 35.64 1.78
2519 2942 0.639943 TGGAGCTCCACACCCCTATA 59.360 55.000 32.00 4.48 42.01 1.31
2520 2943 1.396185 TGGAGCTCCACACCCCTAT 59.604 57.895 32.00 0.00 42.01 2.57
2521 2944 2.866378 TGGAGCTCCACACCCCTA 59.134 61.111 32.00 6.16 42.01 3.53
2529 2952 3.273434 CGAGAAATGAATTGGAGCTCCA 58.727 45.455 32.00 32.00 45.94 3.86
2541 2964 4.725490 AGGAAAAGGGAAACGAGAAATGA 58.275 39.130 0.00 0.00 0.00 2.57
2665 3088 2.297033 GTGCATTACATGGGCTTATGGG 59.703 50.000 0.00 0.00 32.32 4.00
2668 3091 3.225104 CAGGTGCATTACATGGGCTTAT 58.775 45.455 0.00 0.00 37.43 1.73
2669 3092 2.653726 CAGGTGCATTACATGGGCTTA 58.346 47.619 0.00 0.00 37.43 3.09
2670 3093 1.477553 CAGGTGCATTACATGGGCTT 58.522 50.000 0.00 0.00 37.43 4.35
2672 3095 1.438814 GCAGGTGCATTACATGGGC 59.561 57.895 0.00 0.00 41.23 5.36
2710 3166 7.246171 ACTACAATTTAGAGAGAGAAGCCAA 57.754 36.000 2.84 0.00 0.00 4.52
2712 3168 9.089601 GTAAACTACAATTTAGAGAGAGAAGCC 57.910 37.037 2.84 0.00 0.00 4.35
2752 3208 3.694072 CCCATCTAAATCCTGAAAACGCA 59.306 43.478 0.00 0.00 0.00 5.24


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

AutoCloner maintained by Alex Coulton.