Multiple sequence alignment - TraesCS2A01G256200

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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 TraesCS2A01G256200 chr2A 100.000 3373 0 0 1 3373 392857029 392853657 0.000000e+00 6229
1 TraesCS2A01G256200 chr2A 93.287 1013 37 6 2187 3197 28832729 28831746 0.000000e+00 1465
2 TraesCS2A01G256200 chr2A 95.890 219 7 2 2187 2405 762282711 762282927 1.490000e-93 353
3 TraesCS2A01G256200 chr2A 93.191 235 16 0 2963 3197 762282925 762283159 2.490000e-91 346
4 TraesCS2A01G256200 chr2D 89.599 2096 86 49 1 2024 325321412 325323447 0.000000e+00 2542
5 TraesCS2A01G256200 chr2B 91.700 1771 61 36 338 2080 394317153 394318865 0.000000e+00 2377
6 TraesCS2A01G256200 chr2B 81.659 458 52 18 2460 2904 203244238 203244676 5.350000e-93 351
7 TraesCS2A01G256200 chr2B 90.775 271 12 4 1 261 394316501 394316768 1.930000e-92 350
8 TraesCS2A01G256200 chr2B 81.619 457 52 14 2460 2904 690072861 690073297 1.930000e-92 350
9 TraesCS2A01G256200 chr2B 89.952 209 16 4 2191 2395 690072649 690072856 7.180000e-67 265
10 TraesCS2A01G256200 chr2B 86.190 210 26 3 2988 3197 203244984 203245190 1.220000e-54 224
11 TraesCS2A01G256200 chr2B 89.266 177 4 4 3200 3373 394319130 394319294 1.230000e-49 207
12 TraesCS2A01G256200 chr2B 83.516 91 3 2 2101 2191 394319059 394319137 1.300000e-09 75
13 TraesCS2A01G256200 chr4D 90.981 1009 55 17 2191 3197 34674841 34675815 0.000000e+00 1327
14 TraesCS2A01G256200 chr1D 85.067 750 78 10 2460 3197 442816419 442815692 0.000000e+00 734
15 TraesCS2A01G256200 chr3A 91.784 499 13 8 2188 2683 191884065 191884538 0.000000e+00 669
16 TraesCS2A01G256200 chr3A 92.063 189 15 0 3009 3197 191884536 191884724 2.000000e-67 267
17 TraesCS2A01G256200 chr1B 82.705 451 47 15 2460 2898 619483019 619483450 4.110000e-99 372
18 TraesCS2A01G256200 chr1B 80.556 432 61 4 2461 2886 624218306 624217892 9.090000e-81 311
19 TraesCS2A01G256200 chr1B 89.474 209 18 3 2191 2395 619482806 619483014 9.280000e-66 261
20 TraesCS2A01G256200 chr4A 82.276 457 50 15 2460 2904 676992609 676993046 1.910000e-97 366
21 TraesCS2A01G256200 chr4A 90.431 209 16 3 2191 2395 676992396 676992604 4.290000e-69 272
22 TraesCS2A01G256200 chr1A 95.890 219 8 1 2186 2404 307708240 307708457 1.490000e-93 353
23 TraesCS2A01G256200 chr1A 93.191 235 16 0 2963 3197 307708455 307708689 2.490000e-91 346
24 TraesCS2A01G256200 chr5B 89.151 212 19 3 2188 2395 163904638 163904849 9.280000e-66 261
25 TraesCS2A01G256200 chr5B 94.488 127 5 1 2460 2584 163904854 163904980 9.550000e-46 195
26 TraesCS2A01G256200 chr6A 81.579 304 50 5 2897 3197 208844386 208844686 2.600000e-61 246


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 TraesCS2A01G256200 chr2A 392853657 392857029 3372 True 6229.00 6229 100.00000 1 3373 1 chr2A.!!$R2 3372
1 TraesCS2A01G256200 chr2A 28831746 28832729 983 True 1465.00 1465 93.28700 2187 3197 1 chr2A.!!$R1 1010
2 TraesCS2A01G256200 chr2D 325321412 325323447 2035 False 2542.00 2542 89.59900 1 2024 1 chr2D.!!$F1 2023
3 TraesCS2A01G256200 chr2B 394316501 394319294 2793 False 752.25 2377 88.81425 1 3373 4 chr2B.!!$F2 3372
4 TraesCS2A01G256200 chr2B 690072649 690073297 648 False 307.50 350 85.78550 2191 2904 2 chr2B.!!$F3 713
5 TraesCS2A01G256200 chr2B 203244238 203245190 952 False 287.50 351 83.92450 2460 3197 2 chr2B.!!$F1 737
6 TraesCS2A01G256200 chr4D 34674841 34675815 974 False 1327.00 1327 90.98100 2191 3197 1 chr4D.!!$F1 1006
7 TraesCS2A01G256200 chr1D 442815692 442816419 727 True 734.00 734 85.06700 2460 3197 1 chr1D.!!$R1 737
8 TraesCS2A01G256200 chr3A 191884065 191884724 659 False 468.00 669 91.92350 2188 3197 2 chr3A.!!$F1 1009
9 TraesCS2A01G256200 chr1B 619482806 619483450 644 False 316.50 372 86.08950 2191 2898 2 chr1B.!!$F1 707
10 TraesCS2A01G256200 chr4A 676992396 676993046 650 False 319.00 366 86.35350 2191 2904 2 chr4A.!!$F1 713

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
602 940 0.527385 GCAGCTCGTCTCCATCTCAC 60.527 60.0 0.00 0.0 0.00 3.51 F
763 1102 0.988145 CTTCCCATCCACAGGGCCTA 60.988 60.0 5.28 0.0 46.36 3.93 F
1645 2013 1.169577 TCGTCTCCTCTCTTGTCAGC 58.830 55.0 0.00 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1659 2028 0.321122 GCCCTCCGAGCTTATGATGG 60.321 60.0 0.0 0.0 0.0 3.51 R
1660 2029 0.394192 TGCCCTCCGAGCTTATGATG 59.606 55.0 0.0 0.0 0.0 3.07 R
3254 4139 0.113190 TCCACACAGAGAGAGCTGGA 59.887 55.0 0.0 0.0 40.2 3.86 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 30 6.202379 CGTAGTAGATGTGTACTGCTAGCTAA 59.798 42.308 17.23 0.00 34.46 3.09
53 55 9.683069 AACTATGCACTCAAATTAAGACAAAAG 57.317 29.630 0.00 0.00 0.00 2.27
100 102 2.668550 GCACCCTGTGAACCGTCC 60.669 66.667 0.00 0.00 35.23 4.79
142 154 4.214758 CCCTGTTTTAAACCCTTACACTCG 59.785 45.833 5.32 0.00 0.00 4.18
162 174 1.070776 GTCGTCTTTTCCAAGTGCGTC 60.071 52.381 0.00 0.00 33.96 5.19
204 216 2.017049 GTCACCACATCATTAGCCCAC 58.983 52.381 0.00 0.00 0.00 4.61
355 692 6.510879 TGTACTGTATGAACCTGTGAGTAG 57.489 41.667 0.00 0.00 0.00 2.57
483 821 2.137425 CTGAGTCGTACGTGGCACCA 62.137 60.000 16.05 5.67 0.00 4.17
500 838 1.091771 CCATGTAGCTGGCAACTCCG 61.092 60.000 0.00 0.00 37.80 4.63
602 940 0.527385 GCAGCTCGTCTCCATCTCAC 60.527 60.000 0.00 0.00 0.00 3.51
624 962 3.406361 CTGCTGTGCCGACGTCAC 61.406 66.667 17.16 7.67 35.14 3.67
763 1102 0.988145 CTTCCCATCCACAGGGCCTA 60.988 60.000 5.28 0.00 46.36 3.93
843 1186 3.697542 TGTGTACACGGCAGACAGTATAT 59.302 43.478 20.61 0.00 0.00 0.86
844 1187 4.883006 TGTGTACACGGCAGACAGTATATA 59.117 41.667 20.61 0.00 0.00 0.86
845 1188 5.533528 TGTGTACACGGCAGACAGTATATAT 59.466 40.000 20.61 0.00 0.00 0.86
846 1189 6.711645 TGTGTACACGGCAGACAGTATATATA 59.288 38.462 20.61 0.00 0.00 0.86
884 1228 8.694394 GTGAGTTGATTAAAAAGCTTCAATCAC 58.306 33.333 21.50 18.18 37.18 3.06
896 1240 4.629200 AGCTTCAATCACTCGTTTCATCTC 59.371 41.667 0.00 0.00 0.00 2.75
928 1272 5.308927 CAGTAGCAAAGATTCTTCGTTTCG 58.691 41.667 0.00 0.00 0.00 3.46
946 1295 5.945824 CGTTTCGTTTCTTTTCTTTGCTTTG 59.054 36.000 0.00 0.00 0.00 2.77
947 1296 5.448926 TTCGTTTCTTTTCTTTGCTTTGC 57.551 34.783 0.00 0.00 0.00 3.68
948 1297 4.743493 TCGTTTCTTTTCTTTGCTTTGCT 58.257 34.783 0.00 0.00 0.00 3.91
949 1298 5.167845 TCGTTTCTTTTCTTTGCTTTGCTT 58.832 33.333 0.00 0.00 0.00 3.91
950 1299 5.062058 TCGTTTCTTTTCTTTGCTTTGCTTG 59.938 36.000 0.00 0.00 0.00 4.01
961 1310 1.481871 CTTTGCTTGCCATCCATCCT 58.518 50.000 0.00 0.00 0.00 3.24
989 1342 4.548513 CGGAGGGAGGGAGGGAGG 62.549 77.778 0.00 0.00 0.00 4.30
1012 1374 3.942115 GAGCTAGTTGATTCCAGTTTCCC 59.058 47.826 0.00 0.00 0.00 3.97
1015 1377 3.502123 AGTTGATTCCAGTTTCCCGAA 57.498 42.857 0.00 0.00 0.00 4.30
1016 1378 3.412386 AGTTGATTCCAGTTTCCCGAAG 58.588 45.455 0.00 0.00 0.00 3.79
1017 1379 1.821216 TGATTCCAGTTTCCCGAAGC 58.179 50.000 0.00 0.00 0.00 3.86
1018 1380 1.351017 TGATTCCAGTTTCCCGAAGCT 59.649 47.619 0.00 0.00 31.86 3.74
1633 2001 2.865670 GCACCTCATCATCATCGTCTCC 60.866 54.545 0.00 0.00 0.00 3.71
1635 2003 2.890311 ACCTCATCATCATCGTCTCCTC 59.110 50.000 0.00 0.00 0.00 3.71
1636 2004 3.156293 CCTCATCATCATCGTCTCCTCT 58.844 50.000 0.00 0.00 0.00 3.69
1637 2005 3.191162 CCTCATCATCATCGTCTCCTCTC 59.809 52.174 0.00 0.00 0.00 3.20
1638 2006 4.074259 CTCATCATCATCGTCTCCTCTCT 58.926 47.826 0.00 0.00 0.00 3.10
1639 2007 4.468713 TCATCATCATCGTCTCCTCTCTT 58.531 43.478 0.00 0.00 0.00 2.85
1640 2008 4.277921 TCATCATCATCGTCTCCTCTCTTG 59.722 45.833 0.00 0.00 0.00 3.02
1641 2009 3.625853 TCATCATCGTCTCCTCTCTTGT 58.374 45.455 0.00 0.00 0.00 3.16
1642 2010 3.629855 TCATCATCGTCTCCTCTCTTGTC 59.370 47.826 0.00 0.00 0.00 3.18
1643 2011 3.073274 TCATCGTCTCCTCTCTTGTCA 57.927 47.619 0.00 0.00 0.00 3.58
1644 2012 3.013219 TCATCGTCTCCTCTCTTGTCAG 58.987 50.000 0.00 0.00 0.00 3.51
1645 2013 1.169577 TCGTCTCCTCTCTTGTCAGC 58.830 55.000 0.00 0.00 0.00 4.26
1683 2052 0.466124 ATAAGCTCGGAGGGCACTTC 59.534 55.000 7.20 0.00 0.00 3.01
1767 2136 2.482494 AGGATAGGAGGTGTGGGAAAG 58.518 52.381 0.00 0.00 0.00 2.62
1779 2148 5.073144 AGGTGTGGGAAAGTATGAAGAAGAA 59.927 40.000 0.00 0.00 0.00 2.52
1780 2149 5.768164 GGTGTGGGAAAGTATGAAGAAGAAA 59.232 40.000 0.00 0.00 0.00 2.52
1832 2201 0.109086 CTCCTGCACTGTGGAGTACG 60.109 60.000 24.64 12.05 43.49 3.67
1833 2202 0.826256 TCCTGCACTGTGGAGTACGT 60.826 55.000 24.64 0.00 33.66 3.57
1834 2203 0.885879 CCTGCACTGTGGAGTACGTA 59.114 55.000 24.64 0.00 33.66 3.57
1835 2204 1.402456 CCTGCACTGTGGAGTACGTAC 60.402 57.143 24.64 18.10 33.66 3.67
1836 2205 1.540267 CTGCACTGTGGAGTACGTACT 59.460 52.381 27.71 27.71 39.71 2.73
2013 2396 0.322008 TGTTGGCGTATGCATGGTCA 60.322 50.000 10.16 6.09 45.35 4.02
2025 2408 3.966979 TGCATGGTCAGTTGGATTACAT 58.033 40.909 0.00 0.00 0.00 2.29
2026 2409 3.947196 TGCATGGTCAGTTGGATTACATC 59.053 43.478 0.00 0.00 0.00 3.06
2063 2457 5.271625 AGTATTTCTCACTGTATACACGCG 58.728 41.667 3.53 3.53 0.00 6.01
2074 2468 0.039074 ATACACGCGCTAGAGATGGC 60.039 55.000 5.73 0.00 0.00 4.40
2079 2486 1.519751 CGCGCTAGAGATGGCCTAGT 61.520 60.000 5.56 0.00 36.77 2.57
2087 2494 1.761198 GAGATGGCCTAGTTTACGGGT 59.239 52.381 3.32 0.00 0.00 5.28
2139 2706 4.570772 GCGAATTAACCTGCATCAAGTAGA 59.429 41.667 0.00 0.00 30.56 2.59
2140 2707 5.277058 GCGAATTAACCTGCATCAAGTAGAG 60.277 44.000 0.00 0.00 30.56 2.43
2141 2708 5.812642 CGAATTAACCTGCATCAAGTAGAGT 59.187 40.000 0.00 0.00 30.56 3.24
2142 2709 6.978659 CGAATTAACCTGCATCAAGTAGAGTA 59.021 38.462 0.00 0.00 30.56 2.59
2143 2710 7.168302 CGAATTAACCTGCATCAAGTAGAGTAG 59.832 40.741 0.00 0.00 30.56 2.57
2144 2711 6.852420 TTAACCTGCATCAAGTAGAGTAGT 57.148 37.500 0.00 0.00 30.56 2.73
2145 2712 7.949690 TTAACCTGCATCAAGTAGAGTAGTA 57.050 36.000 0.00 0.00 30.56 1.82
2146 2713 5.838531 ACCTGCATCAAGTAGAGTAGTAC 57.161 43.478 0.00 0.00 30.56 2.73
2147 2714 5.511363 ACCTGCATCAAGTAGAGTAGTACT 58.489 41.667 1.37 1.37 34.56 2.73
2148 2715 6.660800 ACCTGCATCAAGTAGAGTAGTACTA 58.339 40.000 1.88 0.00 32.69 1.82
2149 2716 6.768861 ACCTGCATCAAGTAGAGTAGTACTAG 59.231 42.308 1.87 0.00 32.69 2.57
2150 2717 6.768861 CCTGCATCAAGTAGAGTAGTACTAGT 59.231 42.308 10.09 10.09 32.69 2.57
2151 2718 7.932491 CCTGCATCAAGTAGAGTAGTACTAGTA 59.068 40.741 10.28 0.00 32.69 1.82
2167 2734 1.582680 GTAAATTGGCCGCGCGAAG 60.583 57.895 34.63 17.45 28.65 3.79
2193 2760 1.143183 GAGGAGCGCATTTACGGGA 59.857 57.895 11.47 0.00 0.00 5.14
2223 2791 1.074951 GTGGGCAAGGTTAGCTGGT 59.925 57.895 0.00 0.00 0.00 4.00
2325 2893 9.699703 GTAGCCAATTTTATGTTTGGTAAGAAA 57.300 29.630 3.85 0.00 43.54 2.52
2335 2903 6.877611 TGTTTGGTAAGAAAGATGGAAGAC 57.122 37.500 0.00 0.00 0.00 3.01
2794 3382 1.152881 GGAGGCGGAAATGCAGGAT 60.153 57.895 0.00 0.00 36.28 3.24
2815 3403 5.105473 GGATAGCAGGTCAGTACTTGTTGTA 60.105 44.000 0.00 0.00 35.24 2.41
2936 3571 2.124901 TCGCCGCCGATCCAAATT 60.125 55.556 0.00 0.00 38.82 1.82
3102 3985 9.170890 TGGAATATTCTCAGGTATCTGGTTATT 57.829 33.333 14.95 2.41 41.23 1.40
3154 4037 4.695606 AGTGGTATCCCCTCTAAAACTGA 58.304 43.478 0.00 0.00 35.27 3.41
3160 4045 6.783482 GGTATCCCCTCTAAAACTGACTATCT 59.217 42.308 0.00 0.00 0.00 1.98
3162 4047 5.838955 TCCCCTCTAAAACTGACTATCTCA 58.161 41.667 0.00 0.00 0.00 3.27
3167 4052 7.070571 CCCTCTAAAACTGACTATCTCAATCCT 59.929 40.741 0.00 0.00 0.00 3.24
3197 4082 0.596082 ATCCTTTGAACCAAACGCCG 59.404 50.000 0.00 0.00 0.00 6.46
3198 4083 0.464013 TCCTTTGAACCAAACGCCGA 60.464 50.000 0.00 0.00 0.00 5.54
3199 4084 0.317519 CCTTTGAACCAAACGCCGAC 60.318 55.000 0.00 0.00 0.00 4.79
3254 4139 0.179094 TTGTGAAGTGAAGGACGCGT 60.179 50.000 13.85 13.85 0.00 6.01
3265 4150 2.101380 GACGCGTCCAGCTCTCTC 59.899 66.667 28.61 0.00 45.59 3.20
3268 4153 2.695759 CGCGTCCAGCTCTCTCTGT 61.696 63.158 0.00 0.00 45.59 3.41
3269 4154 1.153862 GCGTCCAGCTCTCTCTGTG 60.154 63.158 0.00 0.00 44.04 3.66
3270 4155 1.872197 GCGTCCAGCTCTCTCTGTGT 61.872 60.000 0.00 0.00 44.04 3.72
3271 4156 0.109365 CGTCCAGCTCTCTCTGTGTG 60.109 60.000 0.00 0.00 32.32 3.82
3273 4158 0.113190 TCCAGCTCTCTCTGTGTGGA 59.887 55.000 0.00 0.00 32.32 4.02
3274 4159 0.246086 CCAGCTCTCTCTGTGTGGAC 59.754 60.000 0.00 0.00 32.32 4.02
3276 4161 1.214062 GCTCTCTCTGTGTGGACCG 59.786 63.158 0.00 0.00 0.00 4.79
3318 4203 1.735700 CGCTTAGATTGACAGGCACGA 60.736 52.381 0.00 0.00 0.00 4.35
3319 4204 1.929836 GCTTAGATTGACAGGCACGAG 59.070 52.381 0.00 0.00 0.00 4.18
3320 4205 2.417379 GCTTAGATTGACAGGCACGAGA 60.417 50.000 0.00 0.00 0.00 4.04
3321 4206 2.941453 TAGATTGACAGGCACGAGAC 57.059 50.000 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 14 4.401202 TGCATAGTTAGCTAGCAGTACACA 59.599 41.667 18.83 2.40 32.10 3.72
13 15 4.740695 GTGCATAGTTAGCTAGCAGTACAC 59.259 45.833 18.83 9.79 34.49 2.90
28 30 8.299570 CCTTTTGTCTTAATTTGAGTGCATAGT 58.700 33.333 0.00 0.00 0.00 2.12
53 55 1.153549 GTCGTCATGAGTGAGCCCC 60.154 63.158 0.00 0.00 34.36 5.80
100 102 1.208009 GGCACGCACACAACACATTG 61.208 55.000 0.00 0.00 41.98 2.82
142 154 0.935196 ACGCACTTGGAAAAGACGAC 59.065 50.000 10.82 0.00 0.00 4.34
162 174 8.554528 GTGACATCCTTATGTAATCATGAACAG 58.445 37.037 0.00 0.00 46.49 3.16
225 237 7.088905 ACAAGTAGTAGTACAATTTGAGTCGG 58.911 38.462 10.33 0.00 0.00 4.79
332 669 6.243148 TCTACTCACAGGTTCATACAGTACA 58.757 40.000 0.00 0.00 0.00 2.90
333 670 6.754702 TCTACTCACAGGTTCATACAGTAC 57.245 41.667 0.00 0.00 0.00 2.73
334 671 7.956328 ATTCTACTCACAGGTTCATACAGTA 57.044 36.000 0.00 0.00 0.00 2.74
335 672 6.859112 ATTCTACTCACAGGTTCATACAGT 57.141 37.500 0.00 0.00 0.00 3.55
336 673 8.001881 AGTATTCTACTCACAGGTTCATACAG 57.998 38.462 0.00 0.00 32.47 2.74
377 714 2.125391 GAGAGGACGCATGCTGCA 60.125 61.111 17.13 4.13 45.36 4.41
378 715 3.260483 CGAGAGGACGCATGCTGC 61.260 66.667 17.13 8.28 40.69 5.25
483 821 0.391661 CACGGAGTTGCCAGCTACAT 60.392 55.000 6.97 0.00 41.61 2.29
500 838 3.444818 TTTGTCCACCTGGGCCCAC 62.445 63.158 24.45 11.17 39.61 4.61
763 1102 1.479709 ATGAGAGCAAGGCTACGAGT 58.520 50.000 0.00 0.00 39.88 4.18
809 1152 4.099824 CCGTGTACACAAAACCAACTTTC 58.900 43.478 24.98 0.00 0.00 2.62
843 1186 6.599356 TCAACTCACACAAAGCCTACTATA 57.401 37.500 0.00 0.00 0.00 1.31
844 1187 5.483685 TCAACTCACACAAAGCCTACTAT 57.516 39.130 0.00 0.00 0.00 2.12
845 1188 4.948341 TCAACTCACACAAAGCCTACTA 57.052 40.909 0.00 0.00 0.00 1.82
846 1189 3.838244 TCAACTCACACAAAGCCTACT 57.162 42.857 0.00 0.00 0.00 2.57
884 1228 3.316588 TGGCTAGCTAGAGATGAAACGAG 59.683 47.826 25.15 0.00 0.00 4.18
928 1272 5.023920 GCAAGCAAAGCAAAGAAAAGAAAC 58.976 37.500 0.00 0.00 0.00 2.78
946 1295 1.477553 TGAAAGGATGGATGGCAAGC 58.522 50.000 0.00 0.00 0.00 4.01
947 1296 7.011763 CGTATATATGAAAGGATGGATGGCAAG 59.988 40.741 0.00 0.00 0.00 4.01
948 1297 6.823182 CGTATATATGAAAGGATGGATGGCAA 59.177 38.462 0.00 0.00 0.00 4.52
949 1298 6.348498 CGTATATATGAAAGGATGGATGGCA 58.652 40.000 0.00 0.00 0.00 4.92
950 1299 5.760253 CCGTATATATGAAAGGATGGATGGC 59.240 44.000 3.36 0.00 0.00 4.40
961 1310 5.269991 CTCCCTCCCTCCGTATATATGAAA 58.730 45.833 3.36 0.00 0.00 2.69
989 1342 3.942115 GGAAACTGGAATCAACTAGCTCC 59.058 47.826 0.00 0.00 0.00 4.70
1316 1684 0.807667 GAGCTCGCCACGTGATGATT 60.808 55.000 19.30 5.59 0.00 2.57
1392 1760 3.838795 CGTAGCCGTGCTGTTCGC 61.839 66.667 8.44 0.00 40.10 4.70
1393 1761 3.179265 CCGTAGCCGTGCTGTTCG 61.179 66.667 8.44 9.59 40.10 3.95
1394 1762 3.488090 GCCGTAGCCGTGCTGTTC 61.488 66.667 8.44 0.00 40.10 3.18
1633 2001 3.425577 CTAGCTGAGCTGACAAGAGAG 57.574 52.381 18.79 0.00 40.10 3.20
1645 2013 5.622007 GCTTATGATGGAGTAGCTAGCTGAG 60.622 48.000 27.68 4.21 0.00 3.35
1657 2026 1.274728 CCCTCCGAGCTTATGATGGAG 59.725 57.143 0.00 0.00 44.65 3.86
1658 2027 1.342074 CCCTCCGAGCTTATGATGGA 58.658 55.000 0.00 0.00 0.00 3.41
1659 2028 0.321122 GCCCTCCGAGCTTATGATGG 60.321 60.000 0.00 0.00 0.00 3.51
1660 2029 0.394192 TGCCCTCCGAGCTTATGATG 59.606 55.000 0.00 0.00 0.00 3.07
1661 2030 0.394565 GTGCCCTCCGAGCTTATGAT 59.605 55.000 0.00 0.00 0.00 2.45
1683 2052 2.684881 CGAATGATCCAACAGGAAAGGG 59.315 50.000 0.00 0.00 34.49 3.95
1686 2055 8.044309 TCTTATAACGAATGATCCAACAGGAAA 58.956 33.333 0.00 0.00 34.49 3.13
1687 2056 7.561251 TCTTATAACGAATGATCCAACAGGAA 58.439 34.615 0.00 0.00 34.49 3.36
1688 2057 7.119709 TCTTATAACGAATGATCCAACAGGA 57.880 36.000 0.00 0.00 35.50 3.86
1689 2058 7.571983 GCATCTTATAACGAATGATCCAACAGG 60.572 40.741 0.00 0.00 0.00 4.00
1690 2059 7.041848 TGCATCTTATAACGAATGATCCAACAG 60.042 37.037 0.00 0.00 0.00 3.16
1738 2107 6.272324 CCCACACCTCCTATCCTAATTCATAA 59.728 42.308 0.00 0.00 0.00 1.90
1821 2190 4.959596 ACATACAGTACGTACTCCACAG 57.040 45.455 25.10 15.73 33.46 3.66
1823 2192 4.574013 AGCTACATACAGTACGTACTCCAC 59.426 45.833 25.10 9.08 33.46 4.02
1832 2201 3.119291 CTGCAGCAGCTACATACAGTAC 58.881 50.000 10.14 0.00 42.74 2.73
1833 2202 2.101415 CCTGCAGCAGCTACATACAGTA 59.899 50.000 17.81 0.00 42.74 2.74
1834 2203 1.134580 CCTGCAGCAGCTACATACAGT 60.135 52.381 17.81 0.00 42.74 3.55
1835 2204 1.134580 ACCTGCAGCAGCTACATACAG 60.135 52.381 17.81 2.41 42.74 2.74
1836 2205 0.904649 ACCTGCAGCAGCTACATACA 59.095 50.000 17.81 0.00 42.74 2.29
2025 2408 2.661176 ATACTCCCAACTCCCAAGGA 57.339 50.000 0.00 0.00 0.00 3.36
2026 2409 3.267031 AGAAATACTCCCAACTCCCAAGG 59.733 47.826 0.00 0.00 0.00 3.61
2029 2412 3.263425 GTGAGAAATACTCCCAACTCCCA 59.737 47.826 0.00 0.00 44.34 4.37
2030 2413 3.519913 AGTGAGAAATACTCCCAACTCCC 59.480 47.826 0.00 0.00 44.34 4.30
2031 2414 4.020128 ACAGTGAGAAATACTCCCAACTCC 60.020 45.833 0.00 0.00 44.34 3.85
2032 2415 5.153950 ACAGTGAGAAATACTCCCAACTC 57.846 43.478 0.00 0.00 44.34 3.01
2033 2416 6.875972 ATACAGTGAGAAATACTCCCAACT 57.124 37.500 0.00 0.00 44.34 3.16
2063 2457 3.305471 CCGTAAACTAGGCCATCTCTAGC 60.305 52.174 5.01 0.00 38.13 3.42
2087 2494 3.367992 TTCTGTTTTGGAGCGTACGTA 57.632 42.857 17.90 0.00 0.00 3.57
2139 2706 4.498682 CGCGGCCAATTTACTAGTACTACT 60.499 45.833 2.24 0.00 0.00 2.57
2140 2707 3.732721 CGCGGCCAATTTACTAGTACTAC 59.267 47.826 2.24 0.00 0.00 2.73
2141 2708 3.796504 GCGCGGCCAATTTACTAGTACTA 60.797 47.826 8.83 1.89 0.00 1.82
2142 2709 2.817901 CGCGGCCAATTTACTAGTACT 58.182 47.619 2.24 0.00 0.00 2.73
2143 2710 1.259770 GCGCGGCCAATTTACTAGTAC 59.740 52.381 8.83 0.00 0.00 2.73
2144 2711 1.574134 GCGCGGCCAATTTACTAGTA 58.426 50.000 8.83 0.00 0.00 1.82
2145 2712 1.426041 CGCGCGGCCAATTTACTAGT 61.426 55.000 24.84 0.00 0.00 2.57
2146 2713 1.149361 TCGCGCGGCCAATTTACTAG 61.149 55.000 31.69 0.00 0.00 2.57
2147 2714 0.740164 TTCGCGCGGCCAATTTACTA 60.740 50.000 31.69 1.90 0.00 1.82
2148 2715 1.977594 CTTCGCGCGGCCAATTTACT 61.978 55.000 31.69 0.00 0.00 2.24
2149 2716 1.582680 CTTCGCGCGGCCAATTTAC 60.583 57.895 31.69 0.00 0.00 2.01
2150 2717 1.701545 CTCTTCGCGCGGCCAATTTA 61.702 55.000 31.69 4.34 0.00 1.40
2151 2718 3.039202 CTCTTCGCGCGGCCAATTT 62.039 57.895 31.69 0.00 0.00 1.82
2193 2760 3.284449 GCCCACGAACCAAACGCT 61.284 61.111 0.00 0.00 0.00 5.07
2242 2810 6.239317 CGAGAATAAGGATATCTCCAACCACA 60.239 42.308 2.05 0.00 44.79 4.17
2794 3382 4.321750 GCTACAACAAGTACTGACCTGCTA 60.322 45.833 0.00 0.00 0.00 3.49
2834 3422 4.789075 GCGCGTGAAGTAGGCCGA 62.789 66.667 8.43 0.00 36.86 5.54
3068 3951 9.566432 GATACCTGAGAATATTCCATCAAAAGT 57.434 33.333 11.92 9.72 0.00 2.66
3102 3985 4.937201 TTATGAGCGAAGATGGCTAAGA 57.063 40.909 0.00 0.00 41.72 2.10
3154 4037 3.310954 ACCACCCAGAGGATTGAGATAGT 60.311 47.826 0.00 0.00 36.73 2.12
3160 4045 2.777692 GGATAACCACCCAGAGGATTGA 59.222 50.000 0.00 0.00 36.73 2.57
3162 4047 3.151542 AGGATAACCACCCAGAGGATT 57.848 47.619 0.00 0.00 38.94 3.01
3167 4052 3.245122 GGTTCAAAGGATAACCACCCAGA 60.245 47.826 0.00 0.00 43.84 3.86
3197 4082 1.443872 CTGGCCACTCGTACACGTC 60.444 63.158 0.00 0.00 40.80 4.34
3198 4083 2.649034 CTGGCCACTCGTACACGT 59.351 61.111 0.00 0.00 40.80 4.49
3199 4084 2.126071 CCTGGCCACTCGTACACG 60.126 66.667 0.00 0.00 41.45 4.49
3200 4085 1.614241 ATCCCTGGCCACTCGTACAC 61.614 60.000 0.00 0.00 0.00 2.90
3201 4086 1.305802 ATCCCTGGCCACTCGTACA 60.306 57.895 0.00 0.00 0.00 2.90
3202 4087 1.144057 CATCCCTGGCCACTCGTAC 59.856 63.158 0.00 0.00 0.00 3.67
3203 4088 1.305802 ACATCCCTGGCCACTCGTA 60.306 57.895 0.00 0.00 0.00 3.43
3204 4089 2.607750 ACATCCCTGGCCACTCGT 60.608 61.111 0.00 0.00 0.00 4.18
3205 4090 2.187946 GACATCCCTGGCCACTCG 59.812 66.667 0.00 0.00 0.00 4.18
3224 4109 1.800586 CACTTCACAATGGTCACGGAG 59.199 52.381 0.00 0.00 0.00 4.63
3225 4110 1.414550 TCACTTCACAATGGTCACGGA 59.585 47.619 0.00 0.00 0.00 4.69
3226 4111 1.877637 TCACTTCACAATGGTCACGG 58.122 50.000 0.00 0.00 0.00 4.94
3227 4112 2.224079 CCTTCACTTCACAATGGTCACG 59.776 50.000 0.00 0.00 0.00 4.35
3254 4139 0.113190 TCCACACAGAGAGAGCTGGA 59.887 55.000 0.00 0.00 40.20 3.86
3263 4148 1.665916 CAGCACGGTCCACACAGAG 60.666 63.158 0.00 0.00 0.00 3.35
3265 4150 2.108976 ACAGCACGGTCCACACAG 59.891 61.111 0.00 0.00 0.00 3.66
3268 4153 4.168291 TGCACAGCACGGTCCACA 62.168 61.111 0.00 0.00 31.71 4.17
3318 4203 0.678395 CTGGTCAGTGCTGTCTGTCT 59.322 55.000 0.00 0.00 36.85 3.41
3319 4204 0.948141 GCTGGTCAGTGCTGTCTGTC 60.948 60.000 0.00 0.00 36.85 3.51
3320 4205 1.070445 GCTGGTCAGTGCTGTCTGT 59.930 57.895 0.00 0.00 36.85 3.41
3321 4206 0.949588 CTGCTGGTCAGTGCTGTCTG 60.950 60.000 0.00 0.00 38.02 3.51
3348 4233 2.037620 CTCTATGAGCTTGCCGGCCT 62.038 60.000 26.77 14.60 0.00 5.19


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

AutoCloner maintained by Alex Coulton.