Multiple sequence alignment - TraesCS3A01G284800

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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 TraesCS3A01G284800 chr3A 100.000 4687 0 0 1 4687 513892877 513888191 0.000000e+00 8656
1 TraesCS3A01G284800 chr3D 90.794 3541 186 60 806 4291 394059746 394056291 0.000000e+00 4604
2 TraesCS3A01G284800 chr3D 91.840 723 31 13 1 705 394060497 394059785 0.000000e+00 983
3 TraesCS3A01G284800 chr3B 93.917 2762 125 19 1951 4687 513667123 513664380 0.000000e+00 4130
4 TraesCS3A01G284800 chr3B 84.428 1477 111 57 443 1879 513668539 513667142 0.000000e+00 1343
5 TraesCS3A01G284800 chr3B 92.727 220 16 0 1 220 513669227 513669008 7.570000e-83 318
6 TraesCS3A01G284800 chr3B 92.793 111 7 1 265 374 513668893 513668783 4.850000e-35 159
7 TraesCS3A01G284800 chr7B 88.693 398 34 6 1296 1692 413035665 413035278 4.240000e-130 475
8 TraesCS3A01G284800 chr5B 88.442 398 33 8 1296 1692 324260289 324260674 7.100000e-128 468
9 TraesCS3A01G284800 chr2B 87.940 398 39 5 1296 1692 127449601 127449212 1.190000e-125 460


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 TraesCS3A01G284800 chr3A 513888191 513892877 4686 True 8656.0 8656 100.00000 1 4687 1 chr3A.!!$R1 4686
1 TraesCS3A01G284800 chr3D 394056291 394060497 4206 True 2793.5 4604 91.31700 1 4291 2 chr3D.!!$R1 4290
2 TraesCS3A01G284800 chr3B 513664380 513669227 4847 True 1487.5 4130 90.96625 1 4687 4 chr3B.!!$R1 4686

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
529 812 0.109827 CATTGACAATTCCACGCGCA 60.110 50.0 5.73 0.0 0.00 6.09 F
1381 1702 0.039888 GCCTCTATCTCGTCCGCTTC 60.040 60.0 0.00 0.0 0.00 3.86 F
2182 2591 0.184451 ATGGTCAGCTTGGCTATGGG 59.816 55.0 0.00 0.0 36.40 4.00 F
2573 2990 0.392998 AGGTTGCCTGCGGTAATGAG 60.393 55.0 2.04 0.0 29.57 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1650 1971 0.033208 TGGACCCTGGGCATCATTTC 60.033 55.0 14.08 0.04 0.00 2.17 R
2468 2885 0.179026 CCCCATCATCAGTCTGCTGG 60.179 60.0 3.93 4.25 42.78 4.85 R
3005 3422 0.918258 TAGCATCTGGGCACAATCCA 59.082 50.0 0.00 0.00 35.83 3.41 R
4020 4443 1.467920 ATTTGCCTGCTGCTACCTTC 58.532 50.0 0.00 0.00 42.00 3.46 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
174 175 4.408821 TTCCTTGCCGCATCCGCT 62.409 61.111 0.00 0.00 35.30 5.52
212 213 3.754850 TGGCTGTCAAATCTGTGAGAATG 59.245 43.478 0.00 0.00 0.00 2.67
246 333 2.224670 TGGCAAACTAGTACACCCCTTG 60.225 50.000 0.00 0.00 0.00 3.61
260 347 2.646121 CCTTGGCAGGGAGTTCAAC 58.354 57.895 10.68 0.00 36.36 3.18
263 353 2.310538 CTTGGCAGGGAGTTCAACTTT 58.689 47.619 0.00 0.00 0.00 2.66
323 414 3.071167 ACCTGTAAAGTGTCCTGAAGTCC 59.929 47.826 0.00 0.00 0.00 3.85
342 433 1.543208 CCTGTGAGTTGGCTGCTTGTA 60.543 52.381 0.00 0.00 0.00 2.41
359 450 1.431243 TGTACAAATTGGAGCCCCCTT 59.569 47.619 0.00 0.00 35.38 3.95
384 475 0.928505 AATGGATGGCATCACCTGGA 59.071 50.000 27.39 5.56 40.22 3.86
385 476 1.155323 ATGGATGGCATCACCTGGAT 58.845 50.000 27.39 7.50 40.22 3.41
481 764 7.598189 CTCTGATCATATATGCAGAGTTTGG 57.402 40.000 26.56 12.99 45.69 3.28
482 765 7.071069 TCTGATCATATATGCAGAGTTTGGT 57.929 36.000 15.23 0.00 32.85 3.67
497 780 2.050442 GGTTTGGTTGCCGCTTCG 60.050 61.111 0.00 0.00 0.00 3.79
529 812 0.109827 CATTGACAATTCCACGCGCA 60.110 50.000 5.73 0.00 0.00 6.09
570 854 3.181455 ACACTGCCACTTGTCTACATTGA 60.181 43.478 0.00 0.00 0.00 2.57
571 855 4.005650 CACTGCCACTTGTCTACATTGAT 58.994 43.478 0.00 0.00 0.00 2.57
572 856 4.005650 ACTGCCACTTGTCTACATTGATG 58.994 43.478 0.00 0.00 0.00 3.07
602 886 3.244078 TGAGTACACATGAACACCTGTCC 60.244 47.826 0.00 0.00 0.00 4.02
629 921 0.773644 ACTCCCAATCAGCACACCTT 59.226 50.000 0.00 0.00 0.00 3.50
695 995 0.796927 CAGCCATATCTGCATCTGCG 59.203 55.000 0.00 0.00 45.83 5.18
740 1040 1.689352 GACACGCCCAAACCGATACG 61.689 60.000 0.00 0.00 0.00 3.06
741 1041 1.738830 CACGCCCAAACCGATACGT 60.739 57.895 0.00 0.00 0.00 3.57
744 1044 1.134226 CGCCCAAACCGATACGTATC 58.866 55.000 23.03 23.03 0.00 2.24
779 1079 2.155924 GGAGAAAAAGCGAAGACGACAG 59.844 50.000 0.00 0.00 42.66 3.51
781 1081 0.232303 AAAAAGCGAAGACGACAGCG 59.768 50.000 0.00 0.00 42.66 5.18
819 1119 4.130281 GGTACGCTCGCACGCAAC 62.130 66.667 0.00 0.00 36.19 4.17
820 1120 3.103911 GTACGCTCGCACGCAACT 61.104 61.111 0.00 0.00 36.19 3.16
821 1121 2.803670 TACGCTCGCACGCAACTC 60.804 61.111 0.00 0.00 36.19 3.01
822 1122 3.263503 TACGCTCGCACGCAACTCT 62.264 57.895 0.00 0.00 36.19 3.24
823 1123 3.832171 CGCTCGCACGCAACTCTC 61.832 66.667 0.00 0.00 0.00 3.20
824 1124 2.734723 GCTCGCACGCAACTCTCA 60.735 61.111 0.00 0.00 0.00 3.27
825 1125 3.004734 GCTCGCACGCAACTCTCAC 62.005 63.158 0.00 0.00 0.00 3.51
829 1129 1.566563 GCACGCAACTCTCACACTG 59.433 57.895 0.00 0.00 0.00 3.66
884 1184 3.377798 GTCGACTCCTTTATCGTCTTCCT 59.622 47.826 8.70 0.00 39.38 3.36
891 1191 4.079672 TCCTTTATCGTCTTCCTCTCCTCT 60.080 45.833 0.00 0.00 0.00 3.69
892 1192 4.277423 CCTTTATCGTCTTCCTCTCCTCTC 59.723 50.000 0.00 0.00 0.00 3.20
893 1193 2.358322 ATCGTCTTCCTCTCCTCTCC 57.642 55.000 0.00 0.00 0.00 3.71
921 1221 0.313987 CTTCCTTTTCAACCGCCACC 59.686 55.000 0.00 0.00 0.00 4.61
934 1234 4.821589 CCACCTTCCTCTCGCGGC 62.822 72.222 6.13 0.00 0.00 6.53
935 1235 4.821589 CACCTTCCTCTCGCGGCC 62.822 72.222 6.13 0.00 0.00 6.13
953 1256 2.161609 GGCCAATTCTTCCACTTGTACG 59.838 50.000 0.00 0.00 0.00 3.67
954 1257 2.161609 GCCAATTCTTCCACTTGTACGG 59.838 50.000 0.00 0.00 0.00 4.02
956 1259 3.818773 CCAATTCTTCCACTTGTACGGTT 59.181 43.478 0.00 0.00 0.00 4.44
957 1260 4.320202 CCAATTCTTCCACTTGTACGGTTG 60.320 45.833 0.00 0.00 0.00 3.77
958 1261 3.547054 TTCTTCCACTTGTACGGTTGT 57.453 42.857 0.00 0.00 0.00 3.32
959 1262 4.669206 TTCTTCCACTTGTACGGTTGTA 57.331 40.909 0.00 0.00 0.00 2.41
980 1292 2.716017 CCTGCCGTCTCCTCCACTC 61.716 68.421 0.00 0.00 0.00 3.51
981 1293 2.680352 TGCCGTCTCCTCCACTCC 60.680 66.667 0.00 0.00 0.00 3.85
982 1294 2.680352 GCCGTCTCCTCCACTCCA 60.680 66.667 0.00 0.00 0.00 3.86
983 1295 3.007973 GCCGTCTCCTCCACTCCAC 62.008 68.421 0.00 0.00 0.00 4.02
984 1296 2.352032 CCGTCTCCTCCACTCCACC 61.352 68.421 0.00 0.00 0.00 4.61
985 1297 2.701780 CGTCTCCTCCACTCCACCG 61.702 68.421 0.00 0.00 0.00 4.94
986 1298 2.680352 TCTCCTCCACTCCACCGC 60.680 66.667 0.00 0.00 0.00 5.68
987 1299 2.681778 CTCCTCCACTCCACCGCT 60.682 66.667 0.00 0.00 0.00 5.52
988 1300 2.997315 TCCTCCACTCCACCGCTG 60.997 66.667 0.00 0.00 0.00 5.18
989 1301 4.767255 CCTCCACTCCACCGCTGC 62.767 72.222 0.00 0.00 0.00 5.25
990 1302 4.767255 CTCCACTCCACCGCTGCC 62.767 72.222 0.00 0.00 0.00 4.85
1063 1375 1.153549 CTCGCCCTCACCAGTAAGC 60.154 63.158 0.00 0.00 0.00 3.09
1065 1381 1.741770 CGCCCTCACCAGTAAGCAC 60.742 63.158 0.00 0.00 0.00 4.40
1068 1384 1.299976 CCTCACCAGTAAGCACCCC 59.700 63.158 0.00 0.00 0.00 4.95
1069 1385 1.299976 CTCACCAGTAAGCACCCCC 59.700 63.158 0.00 0.00 0.00 5.40
1070 1386 2.046314 CACCAGTAAGCACCCCCG 60.046 66.667 0.00 0.00 0.00 5.73
1071 1387 2.203877 ACCAGTAAGCACCCCCGA 60.204 61.111 0.00 0.00 0.00 5.14
1072 1388 2.267961 CCAGTAAGCACCCCCGAC 59.732 66.667 0.00 0.00 0.00 4.79
1073 1389 2.267961 CAGTAAGCACCCCCGACC 59.732 66.667 0.00 0.00 0.00 4.79
1074 1390 3.007323 AGTAAGCACCCCCGACCC 61.007 66.667 0.00 0.00 0.00 4.46
1075 1391 4.105553 GTAAGCACCCCCGACCCC 62.106 72.222 0.00 0.00 0.00 4.95
1095 1411 2.520741 CCCCACGTGGCCACTTTT 60.521 61.111 32.28 14.62 0.00 2.27
1107 1428 0.591170 CCACTTTTGTCACGCGGATT 59.409 50.000 12.47 0.00 0.00 3.01
1150 1471 2.447443 GGGATCTGAAGGGTGGTTTTC 58.553 52.381 0.00 0.00 0.00 2.29
1381 1702 0.039888 GCCTCTATCTCGTCCGCTTC 60.040 60.000 0.00 0.00 0.00 3.86
1438 1759 4.384846 AGCGAAACTAGACATTGTTGTACG 59.615 41.667 0.00 0.00 35.79 3.67
1535 1856 1.759445 AGTGGTAGATGCACTAGCCTG 59.241 52.381 17.18 0.00 45.62 4.85
1536 1857 1.757118 GTGGTAGATGCACTAGCCTGA 59.243 52.381 17.18 3.09 45.62 3.86
1537 1858 2.168521 GTGGTAGATGCACTAGCCTGAA 59.831 50.000 17.18 2.83 45.62 3.02
1538 1859 2.837591 TGGTAGATGCACTAGCCTGAAA 59.162 45.455 17.18 2.57 45.62 2.69
1539 1860 3.263170 TGGTAGATGCACTAGCCTGAAAA 59.737 43.478 17.18 2.05 45.62 2.29
1569 1890 4.019411 TGGAATTGATCTTACAGTGGCTCA 60.019 41.667 0.00 0.00 0.00 4.26
1577 1898 1.588674 TACAGTGGCTCAAAACGTGG 58.411 50.000 0.00 0.00 0.00 4.94
1586 1907 0.817634 TCAAAACGTGGGACTGCCTG 60.818 55.000 0.00 0.00 0.00 4.85
1593 1914 0.678048 GTGGGACTGCCTGATTCCAC 60.678 60.000 0.00 0.00 37.98 4.02
1641 1962 4.439305 TTTATTTGCTGGTGATGCAGTC 57.561 40.909 0.00 0.00 41.71 3.51
1644 1965 1.239296 TTGCTGGTGATGCAGTCTGC 61.239 55.000 18.32 18.32 45.29 4.26
1728 2063 2.355756 GGCTTTCATACGATGTGTGCAT 59.644 45.455 0.00 0.00 38.18 3.96
1754 2094 5.446143 TGTGCATTGAATTTTTCTACCGT 57.554 34.783 0.00 0.00 0.00 4.83
1761 2101 7.951565 GCATTGAATTTTTCTACCGTTGATTTG 59.048 33.333 0.00 0.00 0.00 2.32
1764 2104 7.484975 TGAATTTTTCTACCGTTGATTTGTGT 58.515 30.769 0.00 0.00 0.00 3.72
1782 2122 3.192466 GTGTAACTGTTCGTGTGGTCTT 58.808 45.455 0.00 0.00 0.00 3.01
1796 2136 3.631453 GTCTTGACCTGACCATGCA 57.369 52.632 0.00 0.00 0.00 3.96
1809 2178 4.847198 TGACCATGCATTACTGACTGAAT 58.153 39.130 0.00 0.00 0.00 2.57
1829 2198 7.055667 TGAATTGATACAGTGAGAGTATCCC 57.944 40.000 0.00 0.52 44.50 3.85
1843 2216 5.416947 AGAGTATCCCGTACACAAAACATC 58.583 41.667 0.00 0.00 35.67 3.06
1883 2256 6.072286 ACTCTTGGTGCATGAGAAATAAGTTG 60.072 38.462 13.31 0.00 37.70 3.16
1887 2269 6.446318 TGGTGCATGAGAAATAAGTTGTTTC 58.554 36.000 15.18 15.18 36.15 2.78
1898 2280 9.868277 AGAAATAAGTTGTTTCATTTGTTGTGA 57.132 25.926 22.35 0.00 37.89 3.58
1907 2307 8.450578 TGTTTCATTTGTTGTGAGTCTTATCT 57.549 30.769 0.00 0.00 0.00 1.98
1936 2336 8.617290 AATGATTTCTTAACTTCAACGGTAGT 57.383 30.769 0.00 0.00 0.00 2.73
1945 2345 2.243602 TCAACGGTAGTGAAACACCC 57.756 50.000 0.00 0.00 41.43 4.61
1948 2348 2.249844 ACGGTAGTGAAACACCCTTG 57.750 50.000 0.00 0.00 41.43 3.61
1950 2350 1.244816 GGTAGTGAAACACCCTTGCC 58.755 55.000 0.00 0.00 41.43 4.52
1954 2354 2.397597 AGTGAAACACCCTTGCCAAAT 58.602 42.857 0.00 0.00 41.43 2.32
1955 2355 3.571590 AGTGAAACACCCTTGCCAAATA 58.428 40.909 0.00 0.00 41.43 1.40
1956 2356 3.573967 AGTGAAACACCCTTGCCAAATAG 59.426 43.478 0.00 0.00 41.43 1.73
1957 2357 3.320826 GTGAAACACCCTTGCCAAATAGT 59.679 43.478 0.00 0.00 36.32 2.12
2088 2489 9.994432 CCTTTATACTGCTTGTCTTATTTTGAG 57.006 33.333 0.00 0.00 0.00 3.02
2125 2526 9.132923 TCGAAATCACTCTAGTAATATCCTTGT 57.867 33.333 0.00 0.00 0.00 3.16
2182 2591 0.184451 ATGGTCAGCTTGGCTATGGG 59.816 55.000 0.00 0.00 36.40 4.00
2276 2685 3.873361 TGAAGAACAGAACACTCTTGCAG 59.127 43.478 0.00 0.00 29.59 4.41
2315 2724 5.728637 ATAAAAGAAGCACCCCTTTTCAG 57.271 39.130 0.00 0.00 41.30 3.02
2348 2758 3.865011 TGCAGACTCTAAGCTTGAGAG 57.135 47.619 23.88 22.65 45.08 3.20
2370 2780 2.787473 TTCTGCTTGATTGATCCCGT 57.213 45.000 0.00 0.00 0.00 5.28
2396 2813 6.704493 TGTATGTTCTGTTACAGTTGTCTTCC 59.296 38.462 12.41 0.00 32.61 3.46
2459 2876 4.447342 GCCCTGTGGATGTGGGGG 62.447 72.222 0.00 0.00 41.19 5.40
2549 2966 2.489329 GGATTTCCATGGTCACACTGTG 59.511 50.000 12.58 6.19 35.64 3.66
2573 2990 0.392998 AGGTTGCCTGCGGTAATGAG 60.393 55.000 2.04 0.00 29.57 2.90
2582 2999 2.935849 CTGCGGTAATGAGCATGTTGTA 59.064 45.455 0.00 0.00 42.95 2.41
2642 3059 2.308866 CCTTGTCTGTTATTCCTGGGGT 59.691 50.000 0.00 0.00 0.00 4.95
2669 3086 0.844661 ACCATGGGCAGTTGGGTCTA 60.845 55.000 18.09 0.00 37.32 2.59
2693 3110 2.029290 TGACAAGGAAAGTAGGTCTCGC 60.029 50.000 0.00 0.00 0.00 5.03
2720 3137 5.122239 CGTGCTTATCTCAGAATTTGGTGAA 59.878 40.000 0.00 0.00 0.00 3.18
2792 3209 3.674997 TGTGCTCACCAATAAGAAGTCC 58.325 45.455 0.00 0.00 0.00 3.85
2875 3292 4.251246 TGGAACAACTGCCACCAC 57.749 55.556 0.00 0.00 31.92 4.16
2957 3374 3.070131 GGATTGTTCCACACGGCAGTG 62.070 57.143 15.82 15.82 42.31 3.66
2969 3386 2.574399 GCAGTGGTCTCCTCCGAC 59.426 66.667 0.00 0.00 0.00 4.79
3002 3419 1.835693 CTGGGGAATGGAGAGAGGC 59.164 63.158 0.00 0.00 0.00 4.70
3005 3422 0.990818 GGGGAATGGAGAGAGGCCTT 60.991 60.000 6.77 0.00 0.00 4.35
3068 3485 2.039084 GGATGCTCTGTACCCCATAAGG 59.961 54.545 0.00 0.00 0.00 2.69
3107 3524 2.309136 ATGGGTTCAAGTTTCTGGGG 57.691 50.000 0.00 0.00 0.00 4.96
3286 3703 5.494724 TGAGAACTTCCAAGAGATTCATGG 58.505 41.667 0.00 0.00 36.63 3.66
3323 3740 3.119291 GTCGACATCAAGAGCGAATGAT 58.881 45.455 11.55 0.00 36.74 2.45
3542 3959 4.950050 ACATCTTGGATTCGTCAGATACC 58.050 43.478 0.00 0.00 0.00 2.73
3573 3990 2.222819 GCTCGCTTGGAGATGTTTTACG 60.223 50.000 0.00 0.00 46.23 3.18
3623 4040 6.038050 ACAAGCTTCTCAAGAGAAAAGTTCAG 59.962 38.462 13.04 1.92 45.75 3.02
3817 4235 7.739498 TCACCTATTTTGTCAACTTTCTACC 57.261 36.000 0.00 0.00 0.00 3.18
3829 4247 2.294233 ACTTTCTACCGCAACGTAGACA 59.706 45.455 5.12 0.00 43.40 3.41
3917 4335 8.180706 TGTGCTATCGTATAATTGTAGGGTTA 57.819 34.615 2.63 0.00 0.00 2.85
3934 4353 8.316214 TGTAGGGTTAATCGTGTTATTTTCTCT 58.684 33.333 0.00 0.00 0.00 3.10
4220 4646 7.120579 AGCGATATGTTTTAAAAGGTGACATGA 59.879 33.333 11.13 0.00 33.42 3.07
4273 4699 2.189594 CCAAACAGCTGGTGATCTCA 57.810 50.000 19.93 0.00 0.00 3.27
4306 4732 1.610379 TGACTAGCAGGCAGAGGCA 60.610 57.895 0.00 0.00 43.71 4.75
4335 4761 3.126879 CGCGCCCATGAAAGAGCA 61.127 61.111 0.00 0.00 0.00 4.26
4343 4769 3.675228 GCCCATGAAAGAGCATGTTCAAG 60.675 47.826 12.41 2.59 43.16 3.02
4420 4854 0.895530 TCTGTCTAGCCTTTGTCGGG 59.104 55.000 0.00 0.00 0.00 5.14
4485 4920 9.956720 AAATATGAAAGAGAATTTATGCTTCCG 57.043 29.630 0.00 0.00 0.00 4.30
4523 4958 8.751242 ACTTCTTATCTTAGGTCTGAAACTACC 58.249 37.037 0.00 0.00 35.91 3.18
4545 4980 7.239763 ACCCTAAACATCCAAAAACAATAGG 57.760 36.000 0.00 0.00 0.00 2.57
4609 5044 5.410355 ACAATACGGGAAAGTAAGCACTA 57.590 39.130 0.00 0.00 33.48 2.74
4623 5058 0.667993 GCACTACCTTGCAGCAAACA 59.332 50.000 9.65 0.00 42.49 2.83
4656 5091 6.032956 TGTAGTCTCATTTTACATCACGGT 57.967 37.500 0.00 0.00 0.00 4.83
4679 5114 8.012241 CGGTCTTGTTTTGTTTTCAATGAAAAA 58.988 29.630 21.03 10.11 42.09 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
174 175 5.163457 TGACAGCCAGATAACATCGATTACA 60.163 40.000 0.00 0.00 0.00 2.41
212 213 3.878778 AGTTTGCCACCATCTATCTCAC 58.121 45.455 0.00 0.00 0.00 3.51
246 333 1.882623 CTGAAAGTTGAACTCCCTGCC 59.117 52.381 0.00 0.00 0.00 4.85
260 347 0.825010 AAGGCACAGCACCCTGAAAG 60.825 55.000 0.00 0.00 41.77 2.62
263 353 0.036732 CTAAAGGCACAGCACCCTGA 59.963 55.000 0.00 0.00 41.77 3.86
323 414 1.532868 GTACAAGCAGCCAACTCACAG 59.467 52.381 0.00 0.00 0.00 3.66
342 433 0.545071 CCAAGGGGGCTCCAATTTGT 60.545 55.000 5.99 0.00 38.24 2.83
359 450 0.324460 TGATGCCATCCATTGCACCA 60.324 50.000 1.49 0.00 40.88 4.17
384 475 5.603596 ACACTGCAAATCAACAATCAACAT 58.396 33.333 0.00 0.00 0.00 2.71
385 476 5.008619 ACACTGCAAATCAACAATCAACA 57.991 34.783 0.00 0.00 0.00 3.33
386 477 5.730269 CAACACTGCAAATCAACAATCAAC 58.270 37.500 0.00 0.00 0.00 3.18
387 478 5.970140 CAACACTGCAAATCAACAATCAA 57.030 34.783 0.00 0.00 0.00 2.57
481 764 2.050442 CCGAAGCGGCAACCAAAC 60.050 61.111 1.45 0.00 41.17 2.93
497 780 7.708752 TGGAATTGTCAATGTTTTTACTGAACC 59.291 33.333 0.00 0.00 0.00 3.62
554 838 5.240891 ACTGTCATCAATGTAGACAAGTGG 58.759 41.667 10.48 3.85 41.27 4.00
570 854 6.015434 TGTTCATGTGTACTCACTACTGTCAT 60.015 38.462 0.00 0.00 44.14 3.06
571 855 5.300792 TGTTCATGTGTACTCACTACTGTCA 59.699 40.000 0.00 0.00 44.14 3.58
572 856 5.629849 GTGTTCATGTGTACTCACTACTGTC 59.370 44.000 0.00 0.00 44.14 3.51
592 876 0.884704 GTGCGATGTGGACAGGTGTT 60.885 55.000 0.00 0.00 39.04 3.32
597 881 1.448540 GGGAGTGCGATGTGGACAG 60.449 63.158 0.00 0.00 42.22 3.51
602 886 1.012086 CTGATTGGGAGTGCGATGTG 58.988 55.000 0.00 0.00 0.00 3.21
629 921 7.902087 CCATTAAGTGGTTGGAATTTAGGAAA 58.098 34.615 0.00 0.00 43.44 3.13
654 954 2.414481 CTGCTACCATGATGATAAGCGC 59.586 50.000 0.00 0.00 32.67 5.92
745 1045 0.753262 TTTCTCCGGAGCTATCCTGC 59.247 55.000 27.39 0.00 44.22 4.85
804 1104 2.803670 GAGTTGCGTGCGAGCGTA 60.804 61.111 0.00 0.00 40.67 4.42
813 1113 0.747255 AGTCAGTGTGAGAGTTGCGT 59.253 50.000 0.00 0.00 0.00 5.24
818 1118 1.539065 CGGCAAAGTCAGTGTGAGAGT 60.539 52.381 0.00 0.00 0.00 3.24
819 1119 1.143305 CGGCAAAGTCAGTGTGAGAG 58.857 55.000 0.00 0.00 0.00 3.20
820 1120 0.464036 ACGGCAAAGTCAGTGTGAGA 59.536 50.000 0.00 0.00 0.00 3.27
821 1121 1.299541 AACGGCAAAGTCAGTGTGAG 58.700 50.000 0.00 0.00 0.00 3.51
822 1122 1.668751 GAAACGGCAAAGTCAGTGTGA 59.331 47.619 0.00 0.00 0.00 3.58
823 1123 1.594518 CGAAACGGCAAAGTCAGTGTG 60.595 52.381 0.00 0.00 0.00 3.82
824 1124 0.655733 CGAAACGGCAAAGTCAGTGT 59.344 50.000 0.00 0.00 0.00 3.55
825 1125 0.934496 TCGAAACGGCAAAGTCAGTG 59.066 50.000 0.00 0.00 0.00 3.66
829 1129 2.961522 TGAATCGAAACGGCAAAGTC 57.038 45.000 0.00 0.00 0.00 3.01
884 1184 1.077357 GCTCGTGGAGGAGAGGAGA 60.077 63.158 0.52 0.00 36.08 3.71
891 1191 1.002087 GAAAAGGAAGCTCGTGGAGGA 59.998 52.381 0.00 0.00 0.00 3.71
892 1192 1.270839 TGAAAAGGAAGCTCGTGGAGG 60.271 52.381 0.00 0.00 0.00 4.30
893 1193 2.169832 TGAAAAGGAAGCTCGTGGAG 57.830 50.000 0.00 0.00 0.00 3.86
921 1221 1.432270 GAATTGGCCGCGAGAGGAAG 61.432 60.000 8.23 0.00 0.00 3.46
934 1234 3.408634 ACCGTACAAGTGGAAGAATTGG 58.591 45.455 0.00 0.00 0.00 3.16
935 1235 4.274950 ACAACCGTACAAGTGGAAGAATTG 59.725 41.667 0.00 0.00 0.00 2.32
936 1236 4.457466 ACAACCGTACAAGTGGAAGAATT 58.543 39.130 0.00 0.00 0.00 2.17
953 1256 2.046604 GACGGCAGGGGTACAACC 60.047 66.667 0.00 0.00 37.60 3.77
954 1257 1.079336 GAGACGGCAGGGGTACAAC 60.079 63.158 0.00 0.00 0.00 3.32
956 1259 2.682494 GGAGACGGCAGGGGTACA 60.682 66.667 0.00 0.00 0.00 2.90
957 1260 2.363925 AGGAGACGGCAGGGGTAC 60.364 66.667 0.00 0.00 0.00 3.34
958 1261 2.043248 GAGGAGACGGCAGGGGTA 60.043 66.667 0.00 0.00 0.00 3.69
964 1276 2.680352 GGAGTGGAGGAGACGGCA 60.680 66.667 0.00 0.00 0.00 5.69
1050 1362 1.299976 GGGGTGCTTACTGGTGAGG 59.700 63.158 0.00 0.00 0.00 3.86
1082 1398 1.711060 CGTGACAAAAGTGGCCACGT 61.711 55.000 29.68 24.78 44.12 4.49
1084 1400 1.299089 GCGTGACAAAAGTGGCCAC 60.299 57.895 29.22 29.22 32.41 5.01
1095 1411 4.590487 GGAAGAATCCGCGTGACA 57.410 55.556 4.92 0.00 35.59 3.58
1139 1460 0.816421 CCACGAACGAAAACCACCCT 60.816 55.000 0.14 0.00 0.00 4.34
1140 1461 1.650363 CCACGAACGAAAACCACCC 59.350 57.895 0.14 0.00 0.00 4.61
1150 1471 1.225376 TTACCTGCAAGCCACGAACG 61.225 55.000 0.00 0.00 0.00 3.95
1381 1702 6.036300 CACGAAGAGGAGTACAGTAGTAGAAG 59.964 46.154 0.00 0.00 0.00 2.85
1438 1759 2.647683 TTTTCCCAACCCAAATTGCC 57.352 45.000 0.00 0.00 0.00 4.52
1535 1856 9.965824 TGTAAGATCAATTCCAGTTTTCTTTTC 57.034 29.630 0.00 0.00 0.00 2.29
1536 1857 9.971922 CTGTAAGATCAATTCCAGTTTTCTTTT 57.028 29.630 0.00 0.00 34.07 2.27
1537 1858 9.136323 ACTGTAAGATCAATTCCAGTTTTCTTT 57.864 29.630 0.00 0.00 37.43 2.52
1538 1859 8.571336 CACTGTAAGATCAATTCCAGTTTTCTT 58.429 33.333 0.00 0.00 37.43 2.52
1539 1860 7.175641 CCACTGTAAGATCAATTCCAGTTTTCT 59.824 37.037 0.00 0.00 37.43 2.52
1569 1890 0.110486 ATCAGGCAGTCCCACGTTTT 59.890 50.000 0.00 0.00 35.39 2.43
1577 1898 2.206576 AAAGTGGAATCAGGCAGTCC 57.793 50.000 0.00 0.00 39.98 3.85
1593 1914 5.240623 TGCCAGTTTAGTGACAACCATAAAG 59.759 40.000 0.00 0.00 0.00 1.85
1604 1925 6.040391 AGCAAATAAAACTGCCAGTTTAGTGA 59.960 34.615 22.25 9.41 46.78 3.41
1611 1932 2.965147 ACCAGCAAATAAAACTGCCAGT 59.035 40.909 0.00 0.00 39.47 4.00
1641 1962 2.028839 TGGGCATCATTTCAACTTGCAG 60.029 45.455 0.00 0.00 35.04 4.41
1644 1965 2.093869 CCCTGGGCATCATTTCAACTTG 60.094 50.000 0.00 0.00 0.00 3.16
1650 1971 0.033208 TGGACCCTGGGCATCATTTC 60.033 55.000 14.08 0.04 0.00 2.17
1750 2090 4.260456 CGAACAGTTACACAAATCAACGGT 60.260 41.667 0.00 0.00 33.02 4.83
1754 2094 5.447954 CCACACGAACAGTTACACAAATCAA 60.448 40.000 0.00 0.00 0.00 2.57
1761 2101 2.817901 AGACCACACGAACAGTTACAC 58.182 47.619 0.00 0.00 0.00 2.90
1764 2104 3.450578 GTCAAGACCACACGAACAGTTA 58.549 45.455 0.00 0.00 0.00 2.24
1782 2122 2.571202 TCAGTAATGCATGGTCAGGTCA 59.429 45.455 0.00 0.00 0.00 4.02
1796 2136 8.753133 TCTCACTGTATCAATTCAGTCAGTAAT 58.247 33.333 0.00 0.00 42.05 1.89
1809 2178 4.533815 ACGGGATACTCTCACTGTATCAA 58.466 43.478 13.56 0.00 44.67 2.57
1843 2216 4.284746 ACCAAGAGTCTAGAGAAACAAGGG 59.715 45.833 0.00 0.00 0.00 3.95
1858 2231 5.564550 ACTTATTTCTCATGCACCAAGAGT 58.435 37.500 0.00 0.00 32.04 3.24
1883 2256 8.345565 ACAGATAAGACTCACAACAAATGAAAC 58.654 33.333 0.00 0.00 0.00 2.78
1907 2307 8.842280 ACCGTTGAAGTTAAGAAATCATTTACA 58.158 29.630 0.00 0.00 0.00 2.41
1923 2323 3.200483 GGTGTTTCACTACCGTTGAAGT 58.800 45.455 0.06 0.00 34.40 3.01
1925 2325 2.171027 AGGGTGTTTCACTACCGTTGAA 59.829 45.455 0.06 0.00 37.85 2.69
1931 2331 1.244816 GGCAAGGGTGTTTCACTACC 58.755 55.000 0.06 0.00 34.40 3.18
1936 2336 3.571590 ACTATTTGGCAAGGGTGTTTCA 58.428 40.909 0.00 0.00 0.00 2.69
2088 2489 9.088512 ACTAGAGTGATTTCGATATGACAAAAC 57.911 33.333 8.02 0.00 0.00 2.43
2348 2758 2.223433 CGGGATCAATCAAGCAGAAAGC 60.223 50.000 0.00 0.00 46.19 3.51
2363 2773 5.172934 TGTAACAGAACATACAACGGGATC 58.827 41.667 0.00 0.00 0.00 3.36
2370 2780 7.225931 GGAAGACAACTGTAACAGAACATACAA 59.774 37.037 0.00 0.00 35.18 2.41
2396 2813 2.361610 ATGCCCCCAGCTTTCACG 60.362 61.111 0.00 0.00 44.23 4.35
2468 2885 0.179026 CCCCATCATCAGTCTGCTGG 60.179 60.000 3.93 4.25 42.78 4.85
2549 2966 3.274067 CCGCAGGCAACCTTAACC 58.726 61.111 0.00 0.00 46.14 2.85
2573 2990 1.129998 CTGACAGCAGCTACAACATGC 59.870 52.381 0.00 0.00 40.29 4.06
2582 2999 2.032223 CCAGCACTGACAGCAGCT 59.968 61.111 15.17 15.17 46.26 4.24
2588 3005 1.637338 ATGTCTCTCCAGCACTGACA 58.363 50.000 0.00 0.00 41.07 3.58
2642 3059 2.363680 CAACTGCCCATGGTTGTTGTTA 59.636 45.455 22.77 0.94 38.27 2.41
2669 3086 3.579151 GAGACCTACTTTCCTTGTCACCT 59.421 47.826 0.00 0.00 0.00 4.00
2693 3110 2.918712 ATTCTGAGATAAGCACGGGG 57.081 50.000 0.00 0.00 0.00 5.73
2702 3119 5.190528 AGAGCCTTCACCAAATTCTGAGATA 59.809 40.000 0.00 0.00 0.00 1.98
2720 3137 0.548682 ACACCTCCCATGAAGAGCCT 60.549 55.000 0.00 0.00 0.00 4.58
2792 3209 5.466058 CCGAGATTCAAGATCCTGATCAAAG 59.534 44.000 9.65 0.00 40.22 2.77
2969 3386 2.047844 CAGCACCACACCTCTCCG 60.048 66.667 0.00 0.00 0.00 4.63
3002 3419 1.108776 CATCTGGGCACAATCCAAGG 58.891 55.000 0.00 0.00 33.36 3.61
3005 3422 0.918258 TAGCATCTGGGCACAATCCA 59.082 50.000 0.00 0.00 35.83 3.41
3295 3712 2.792290 CTTGATGTCGACGCCTGCG 61.792 63.158 11.62 10.40 46.03 5.18
3573 3990 1.470098 CACACCAGAAAGCATGCTACC 59.530 52.381 23.00 15.55 0.00 3.18
3623 4040 1.838112 TGCATTCTTGGACCATCACC 58.162 50.000 0.00 0.00 0.00 4.02
3817 4235 5.387279 ACCAAATAATTTGTCTACGTTGCG 58.613 37.500 0.00 0.00 38.98 4.85
4020 4443 1.467920 ATTTGCCTGCTGCTACCTTC 58.532 50.000 0.00 0.00 42.00 3.46
4021 4444 2.806945 TATTTGCCTGCTGCTACCTT 57.193 45.000 0.00 0.00 42.00 3.50
4112 4538 5.497464 TTAGGTTCATGACACAAGGATCA 57.503 39.130 0.00 0.00 0.00 2.92
4220 4646 3.904339 TCCCAAGCTACTTCAAGAGAACT 59.096 43.478 0.00 0.00 0.00 3.01
4273 4699 4.040461 TGCTAGTCAGTTTCCAAAGCTACT 59.960 41.667 0.00 0.00 0.00 2.57
4420 4854 5.302059 TGAGACTGGTTGATATACAGTAGGC 59.698 44.000 0.00 0.00 44.79 3.93
4523 4958 9.771534 TTTTCCTATTGTTTTTGGATGTTTAGG 57.228 29.630 0.00 0.00 0.00 2.69
4581 5016 6.920569 CTTACTTTCCCGTATTGTAAGCAT 57.079 37.500 0.00 0.00 35.42 3.79
4584 5019 5.873164 AGTGCTTACTTTCCCGTATTGTAAG 59.127 40.000 0.00 0.00 41.46 2.34
4585 5020 5.797051 AGTGCTTACTTTCCCGTATTGTAA 58.203 37.500 0.00 0.00 0.00 2.41
4586 5021 5.410355 AGTGCTTACTTTCCCGTATTGTA 57.590 39.130 0.00 0.00 0.00 2.41
4587 5022 4.281898 AGTGCTTACTTTCCCGTATTGT 57.718 40.909 0.00 0.00 0.00 2.71
4588 5023 4.569564 GGTAGTGCTTACTTTCCCGTATTG 59.430 45.833 0.00 0.00 32.61 1.90
4589 5024 4.468868 AGGTAGTGCTTACTTTCCCGTATT 59.531 41.667 0.00 0.00 32.61 1.89
4590 5025 4.028825 AGGTAGTGCTTACTTTCCCGTAT 58.971 43.478 0.00 0.00 32.61 3.06
4591 5026 3.434309 AGGTAGTGCTTACTTTCCCGTA 58.566 45.455 0.00 0.00 32.61 4.02
4592 5027 2.254508 AGGTAGTGCTTACTTTCCCGT 58.745 47.619 0.00 0.00 32.61 5.28
4593 5028 3.000727 CAAGGTAGTGCTTACTTTCCCG 58.999 50.000 0.00 0.00 29.91 5.14
4609 5044 2.965147 AGGTAATTGTTTGCTGCAAGGT 59.035 40.909 15.39 3.32 0.00 3.50


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

AutoCloner maintained by Alex Coulton.