Multiple sequence alignment - TraesCS2D01G038400

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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 TraesCS2D01G038400 chr2D 100.000 2768 0 0 1 2768 14129052 14126285 0.000000e+00 5112.0
1 TraesCS2D01G038400 chr2A 90.652 1872 103 26 909 2766 16497402 16495589 0.000000e+00 2422.0
2 TraesCS2D01G038400 chr2A 91.636 538 23 8 1 535 16497957 16497439 0.000000e+00 725.0
3 TraesCS2D01G038400 chr2B 88.801 1768 140 26 1013 2768 25844290 25842569 0.000000e+00 2115.0
4 TraesCS2D01G038400 chr2B 90.443 994 73 9 1522 2504 25787936 25786954 0.000000e+00 1290.0
5 TraesCS2D01G038400 chr2B 91.667 516 34 5 1013 1524 25794384 25793874 0.000000e+00 706.0
6 TraesCS2D01G038400 chr2B 97.091 275 8 0 2492 2766 25779408 25779134 5.400000e-127 464.0
7 TraesCS2D01G038400 chr2B 88.506 261 21 6 1 256 25848072 25847816 9.630000e-80 307.0
8 TraesCS2D01G038400 chr4B 81.806 1484 207 33 1063 2515 665975901 665974450 0.000000e+00 1186.0
9 TraesCS2D01G038400 chr4B 79.098 665 101 20 2095 2737 665972931 665972283 9.160000e-115 424.0
10 TraesCS2D01G038400 chr4B 88.889 45 4 1 674 718 497163722 497163765 1.000000e-03 54.7
11 TraesCS2D01G038400 chrUn 81.507 1460 220 28 1086 2526 108250682 108252110 0.000000e+00 1155.0
12 TraesCS2D01G038400 chrUn 79.834 1448 199 57 1075 2468 108254975 108256383 0.000000e+00 970.0
13 TraesCS2D01G038400 chrUn 77.066 1718 306 53 1044 2705 108305207 108303522 0.000000e+00 909.0
14 TraesCS2D01G038400 chr7D 81.464 1284 195 31 1128 2390 45838790 45837529 0.000000e+00 1013.0
15 TraesCS2D01G038400 chr1A 77.075 1675 303 56 1118 2748 552216701 552218338 0.000000e+00 891.0
16 TraesCS2D01G038400 chr1D 76.084 1706 315 60 1110 2752 461142994 461144669 0.000000e+00 804.0
17 TraesCS2D01G038400 chr6A 77.273 1276 241 28 1040 2295 617803741 617804987 0.000000e+00 704.0
18 TraesCS2D01G038400 chr1B 75.315 1588 285 67 1157 2698 633351955 633353481 0.000000e+00 662.0
19 TraesCS2D01G038400 chr6B 75.915 1312 215 61 1042 2316 707307739 707306492 1.850000e-161 579.0
20 TraesCS2D01G038400 chr5D 77.778 162 30 4 2175 2333 441233829 441233987 8.160000e-16 95.3


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 TraesCS2D01G038400 chr2D 14126285 14129052 2767 True 5112.0 5112 100.0000 1 2768 1 chr2D.!!$R1 2767
1 TraesCS2D01G038400 chr2A 16495589 16497957 2368 True 1573.5 2422 91.1440 1 2766 2 chr2A.!!$R1 2765
2 TraesCS2D01G038400 chr2B 25786954 25787936 982 True 1290.0 1290 90.4430 1522 2504 1 chr2B.!!$R2 982
3 TraesCS2D01G038400 chr2B 25842569 25848072 5503 True 1211.0 2115 88.6535 1 2768 2 chr2B.!!$R4 2767
4 TraesCS2D01G038400 chr2B 25793874 25794384 510 True 706.0 706 91.6670 1013 1524 1 chr2B.!!$R3 511
5 TraesCS2D01G038400 chr4B 665972283 665975901 3618 True 805.0 1186 80.4520 1063 2737 2 chr4B.!!$R1 1674
6 TraesCS2D01G038400 chrUn 108250682 108256383 5701 False 1062.5 1155 80.6705 1075 2526 2 chrUn.!!$F1 1451
7 TraesCS2D01G038400 chrUn 108303522 108305207 1685 True 909.0 909 77.0660 1044 2705 1 chrUn.!!$R1 1661
8 TraesCS2D01G038400 chr7D 45837529 45838790 1261 True 1013.0 1013 81.4640 1128 2390 1 chr7D.!!$R1 1262
9 TraesCS2D01G038400 chr1A 552216701 552218338 1637 False 891.0 891 77.0750 1118 2748 1 chr1A.!!$F1 1630
10 TraesCS2D01G038400 chr1D 461142994 461144669 1675 False 804.0 804 76.0840 1110 2752 1 chr1D.!!$F1 1642
11 TraesCS2D01G038400 chr6A 617803741 617804987 1246 False 704.0 704 77.2730 1040 2295 1 chr6A.!!$F1 1255
12 TraesCS2D01G038400 chr1B 633351955 633353481 1526 False 662.0 662 75.3150 1157 2698 1 chr1B.!!$F1 1541
13 TraesCS2D01G038400 chr6B 707306492 707307739 1247 True 579.0 579 75.9150 1042 2316 1 chr6B.!!$R1 1274

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
900 1797 0.110678 ACTCACTGTCTCGGAGGTGA 59.889 55.0 12.82 12.82 37.21 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1935 4765 0.036671 GTCCTTAGTGTCCCCAACGG 60.037 60.0 0.0 0.0 0.0 4.44 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
128 131 2.364002 TGCAAATGGATGAGGATGCATG 59.636 45.455 2.46 0.00 39.57 4.06
129 132 2.626266 GCAAATGGATGAGGATGCATGA 59.374 45.455 2.46 0.00 39.57 3.07
130 133 3.069016 GCAAATGGATGAGGATGCATGAA 59.931 43.478 2.46 0.00 39.57 2.57
145 148 8.202137 AGGATGCATGAATTTATTTCCTTCTTG 58.798 33.333 2.46 0.00 33.04 3.02
268 761 9.331282 GGAATGCAGAAATATCTTTAGTACACT 57.669 33.333 0.00 0.00 32.03 3.55
283 776 3.646637 AGTACACTGAGGTTGCTAAGGTT 59.353 43.478 0.00 0.00 0.00 3.50
309 802 6.797454 ACATTTAAAACGTGCTAACAAAGGA 58.203 32.000 0.00 0.00 0.00 3.36
401 920 2.803956 AGTTTGAATAACGTGTCGGGTG 59.196 45.455 0.00 0.00 0.00 4.61
543 1121 1.270094 CCGTCAACCAGTGAGCACTTA 60.270 52.381 0.00 0.00 40.20 2.24
556 1134 7.094205 CCAGTGAGCACTTATAAGGAACAAAAT 60.094 37.037 16.73 0.00 40.20 1.82
558 1136 8.947115 AGTGAGCACTTATAAGGAACAAAATAC 58.053 33.333 16.73 4.47 38.83 1.89
562 1142 8.947115 AGCACTTATAAGGAACAAAATACAGAC 58.053 33.333 16.73 0.00 0.00 3.51
571 1151 8.608844 AGGAACAAAATACAGACTCACTTAAG 57.391 34.615 0.00 0.00 0.00 1.85
580 1160 9.868277 AATACAGACTCACTTAAGAAAGATCAG 57.132 33.333 10.09 6.09 36.50 2.90
582 1162 7.731054 ACAGACTCACTTAAGAAAGATCAGTT 58.269 34.615 10.09 0.00 36.50 3.16
583 1163 7.655328 ACAGACTCACTTAAGAAAGATCAGTTG 59.345 37.037 10.09 0.00 36.50 3.16
588 1168 8.908786 TCACTTAAGAAAGATCAGTTGACATT 57.091 30.769 10.09 0.00 36.50 2.71
619 1516 5.996669 TTCATCATGTAGCAGTGCTAATG 57.003 39.130 26.04 25.74 43.07 1.90
628 1525 6.409704 TGTAGCAGTGCTAATGAAGAAGAAT 58.590 36.000 26.04 0.00 43.07 2.40
651 1548 9.153721 GAATTGCTTTATAGATCCTCATCTGAG 57.846 37.037 0.00 0.00 39.90 3.35
665 1562 7.126061 TCCTCATCTGAGTTATGGTTCTAAGA 58.874 38.462 6.46 0.00 40.48 2.10
689 1586 1.016627 TGTGCAAGTGTGAACTGAGC 58.983 50.000 0.00 0.00 33.90 4.26
713 1610 2.699846 AGCTCAGATGATCAGGTTCCTC 59.300 50.000 0.09 0.00 0.00 3.71
716 1613 2.428530 TCAGATGATCAGGTTCCTCGTG 59.571 50.000 0.09 0.00 0.00 4.35
717 1614 2.428530 CAGATGATCAGGTTCCTCGTGA 59.571 50.000 0.09 0.00 43.54 4.35
727 1624 2.178912 TTCCTCGTGATGGAACCAAC 57.821 50.000 0.00 0.00 38.53 3.77
734 1631 0.558220 TGATGGAACCAACCCACCAA 59.442 50.000 0.00 0.00 36.36 3.67
736 1633 0.831711 ATGGAACCAACCCACCAAGC 60.832 55.000 0.00 0.00 36.36 4.01
738 1635 1.179174 GGAACCAACCCACCAAGCTC 61.179 60.000 0.00 0.00 0.00 4.09
739 1636 0.178990 GAACCAACCCACCAAGCTCT 60.179 55.000 0.00 0.00 0.00 4.09
763 1660 4.988029 AGTCCTAGACTTGACACTACTGT 58.012 43.478 0.00 0.00 40.28 3.55
816 1713 7.770801 TTCTGATGATATTCGTTTAGTGGTG 57.229 36.000 0.00 0.00 0.00 4.17
819 1716 6.280643 TGATGATATTCGTTTAGTGGTGGAG 58.719 40.000 0.00 0.00 0.00 3.86
822 1719 2.825861 TTCGTTTAGTGGTGGAGGAC 57.174 50.000 0.00 0.00 0.00 3.85
825 1722 1.269936 CGTTTAGTGGTGGAGGACGTT 60.270 52.381 0.00 0.00 0.00 3.99
828 1725 0.178955 TAGTGGTGGAGGACGTTCCA 60.179 55.000 4.82 4.82 44.84 3.53
832 1729 4.611119 TGGAGGACGTTCCAGTCA 57.389 55.556 4.82 0.00 42.24 3.41
837 1734 2.496470 GGAGGACGTTCCAGTCAACTAT 59.504 50.000 1.23 0.00 42.62 2.12
839 1736 2.233922 AGGACGTTCCAGTCAACTATGG 59.766 50.000 6.78 0.00 42.62 2.74
840 1737 2.232941 GGACGTTCCAGTCAACTATGGA 59.767 50.000 0.00 0.00 43.87 3.41
852 1749 7.869937 CCAGTCAACTATGGAATGTCTATAGTG 59.130 40.741 13.13 8.85 46.20 2.74
853 1750 8.633561 CAGTCAACTATGGAATGTCTATAGTGA 58.366 37.037 13.13 10.44 46.20 3.41
854 1751 8.855110 AGTCAACTATGGAATGTCTATAGTGAG 58.145 37.037 13.13 10.01 46.20 3.51
855 1752 8.634444 GTCAACTATGGAATGTCTATAGTGAGT 58.366 37.037 13.13 0.00 46.20 3.41
856 1753 9.201989 TCAACTATGGAATGTCTATAGTGAGTT 57.798 33.333 13.13 0.06 46.20 3.01
857 1754 9.469807 CAACTATGGAATGTCTATAGTGAGTTC 57.530 37.037 13.13 1.42 46.20 3.01
859 1756 4.933330 TGGAATGTCTATAGTGAGTTCGC 58.067 43.478 0.00 0.00 0.00 4.70
864 1761 5.339008 TGTCTATAGTGAGTTCGCCAATT 57.661 39.130 0.00 0.00 0.00 2.32
866 1763 6.170506 TGTCTATAGTGAGTTCGCCAATTTT 58.829 36.000 0.00 0.00 0.00 1.82
869 1766 8.114905 GTCTATAGTGAGTTCGCCAATTTTAAC 58.885 37.037 0.00 0.00 0.00 2.01
870 1767 4.141855 AGTGAGTTCGCCAATTTTAACG 57.858 40.909 0.00 0.00 0.00 3.18
872 1769 4.751098 AGTGAGTTCGCCAATTTTAACGTA 59.249 37.500 0.00 0.00 0.00 3.57
885 1782 3.300852 TTAACGTATTGTGCCGACTCA 57.699 42.857 0.00 0.00 0.00 3.41
886 1783 1.425412 AACGTATTGTGCCGACTCAC 58.575 50.000 0.00 0.00 37.48 3.51
888 1785 0.992072 CGTATTGTGCCGACTCACTG 59.008 55.000 0.00 0.00 37.81 3.66
893 1790 1.442857 GTGCCGACTCACTGTCTCG 60.443 63.158 0.00 0.00 43.25 4.04
896 1793 1.797441 CCGACTCACTGTCTCGGAG 59.203 63.158 11.00 0.00 45.77 4.63
900 1797 0.110678 ACTCACTGTCTCGGAGGTGA 59.889 55.000 12.82 12.82 37.21 4.02
901 1798 1.248486 CTCACTGTCTCGGAGGTGAA 58.752 55.000 13.93 2.77 38.08 3.18
902 1799 1.201181 CTCACTGTCTCGGAGGTGAAG 59.799 57.143 13.93 6.41 38.08 3.02
907 1804 1.228894 TCTCGGAGGTGAAGGTGCT 60.229 57.895 4.96 0.00 0.00 4.40
953 3709 1.924524 CTACTTGGACCATTGCGTACG 59.075 52.381 11.84 11.84 0.00 3.67
1360 4151 2.597805 AGGTCGACGTCAGCACCT 60.598 61.111 20.14 20.14 34.18 4.00
1698 4523 1.153881 GCCGACGTGTCTAGGGTTC 60.154 63.158 0.00 0.00 0.00 3.62
1699 4524 1.136147 CCGACGTGTCTAGGGTTCG 59.864 63.158 0.00 0.00 0.00 3.95
1784 4611 3.461061 GGTGAGTACGGCCTAAATTACC 58.539 50.000 0.00 0.09 0.00 2.85
1862 4692 4.034048 GTGTGATTAGGATAAACACAGCCG 59.966 45.833 11.45 0.00 41.09 5.52
1935 4765 0.108520 TACGGGCAGGTCGATTTCAC 60.109 55.000 0.00 0.00 0.00 3.18
1954 4784 0.036671 CCGTTGGGGACACTAAGGAC 60.037 60.000 0.00 0.00 42.67 3.85
2146 5019 3.259064 GGATGCGTGTACTTGTACATGT 58.741 45.455 24.90 17.45 38.76 3.21
2161 5034 4.410555 TGTACATGTCATGCATAACCCCTA 59.589 41.667 12.91 0.00 35.74 3.53
2347 9564 2.551032 CACTGAAATCTGCAGCTGTTCA 59.449 45.455 16.64 15.06 36.86 3.18
2356 9573 1.009078 GCAGCTGTTCATCGTATGCA 58.991 50.000 16.64 0.00 32.58 3.96
2517 9777 3.341823 AGGTGCTTTCAGACTATTGCTG 58.658 45.455 0.00 0.00 34.71 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
257 750 5.869888 CCTTAGCAACCTCAGTGTACTAAAG 59.130 44.000 0.00 0.00 0.00 1.85
268 761 3.788227 ATGTCAACCTTAGCAACCTCA 57.212 42.857 0.00 0.00 0.00 3.86
283 776 6.693545 CCTTTGTTAGCACGTTTTAAATGTCA 59.306 34.615 0.00 0.00 0.00 3.58
309 802 1.481772 CAAATCATGGTTTCCGGCCAT 59.518 47.619 2.24 6.28 46.77 4.40
489 1066 3.571401 GGCATATTTCACCATCCAAGGAG 59.429 47.826 0.00 0.00 0.00 3.69
490 1067 3.053019 TGGCATATTTCACCATCCAAGGA 60.053 43.478 0.00 0.00 0.00 3.36
495 1072 5.072741 ACTATGTGGCATATTTCACCATCC 58.927 41.667 0.94 0.00 35.53 3.51
556 1134 8.410673 ACTGATCTTTCTTAAGTGAGTCTGTA 57.589 34.615 1.63 0.00 32.98 2.74
558 1136 7.869937 TCAACTGATCTTTCTTAAGTGAGTCTG 59.130 37.037 1.63 8.27 32.98 3.51
562 1142 7.953158 TGTCAACTGATCTTTCTTAAGTGAG 57.047 36.000 1.63 2.25 32.98 3.51
577 1157 9.460019 TGATGAAATGGTATAAATGTCAACTGA 57.540 29.630 0.00 0.00 0.00 3.41
583 1163 9.831737 GCTACATGATGAAATGGTATAAATGTC 57.168 33.333 0.00 0.00 31.46 3.06
588 1168 7.041167 GCACTGCTACATGATGAAATGGTATAA 60.041 37.037 0.00 0.00 31.46 0.98
590 1170 5.240183 GCACTGCTACATGATGAAATGGTAT 59.760 40.000 0.00 0.00 31.46 2.73
597 1177 5.673514 TCATTAGCACTGCTACATGATGAA 58.326 37.500 20.52 6.49 41.12 2.57
619 1516 9.553064 TGAGGATCTATAAAGCAATTCTTCTTC 57.447 33.333 0.00 0.00 31.79 2.87
628 1525 7.609097 ACTCAGATGAGGATCTATAAAGCAA 57.391 36.000 14.09 0.00 46.13 3.91
642 1539 7.384660 GCATCTTAGAACCATAACTCAGATGAG 59.615 40.741 17.02 8.30 42.53 2.90
651 1548 5.514279 GCACATGCATCTTAGAACCATAAC 58.486 41.667 0.00 0.00 41.59 1.89
689 1586 3.551863 GGAACCTGATCATCTGAGCTACG 60.552 52.174 0.00 0.00 0.00 3.51
694 1591 2.692557 ACGAGGAACCTGATCATCTGAG 59.307 50.000 0.00 0.00 0.00 3.35
696 1593 2.428530 TCACGAGGAACCTGATCATCTG 59.571 50.000 0.00 0.00 0.00 2.90
700 1597 1.482182 CCATCACGAGGAACCTGATCA 59.518 52.381 0.00 0.00 0.00 2.92
702 1599 1.866015 TCCATCACGAGGAACCTGAT 58.134 50.000 0.00 0.00 30.71 2.90
713 1610 1.241315 GGTGGGTTGGTTCCATCACG 61.241 60.000 11.29 0.00 35.54 4.35
716 1613 1.256812 CTTGGTGGGTTGGTTCCATC 58.743 55.000 0.00 0.00 36.58 3.51
717 1614 0.831711 GCTTGGTGGGTTGGTTCCAT 60.832 55.000 0.00 0.00 36.58 3.41
719 1616 1.152546 AGCTTGGTGGGTTGGTTCC 60.153 57.895 0.00 0.00 0.00 3.62
726 1623 0.984995 GGACTTAGAGCTTGGTGGGT 59.015 55.000 0.00 0.00 0.00 4.51
727 1624 1.280457 AGGACTTAGAGCTTGGTGGG 58.720 55.000 0.00 0.00 0.00 4.61
738 1635 7.175293 AACAGTAGTGTCAAGTCTAGGACTTAG 59.825 40.741 11.80 7.68 42.63 2.18
739 1636 7.002879 AACAGTAGTGTCAAGTCTAGGACTTA 58.997 38.462 11.80 0.00 42.63 2.24
789 1686 9.226606 ACCACTAAACGAATATCATCAGAAAAA 57.773 29.630 0.00 0.00 0.00 1.94
790 1687 8.664798 CACCACTAAACGAATATCATCAGAAAA 58.335 33.333 0.00 0.00 0.00 2.29
794 1691 6.280643 TCCACCACTAAACGAATATCATCAG 58.719 40.000 0.00 0.00 0.00 2.90
795 1692 6.228616 TCCACCACTAAACGAATATCATCA 57.771 37.500 0.00 0.00 0.00 3.07
802 1699 2.353406 CGTCCTCCACCACTAAACGAAT 60.353 50.000 0.00 0.00 0.00 3.34
803 1700 1.000060 CGTCCTCCACCACTAAACGAA 60.000 52.381 0.00 0.00 0.00 3.85
805 1702 0.316204 ACGTCCTCCACCACTAAACG 59.684 55.000 0.00 0.00 35.00 3.60
806 1703 2.410939 GAACGTCCTCCACCACTAAAC 58.589 52.381 0.00 0.00 0.00 2.01
816 1713 0.680061 AGTTGACTGGAACGTCCTCC 59.320 55.000 0.00 0.00 37.46 4.30
819 1716 2.232941 TCCATAGTTGACTGGAACGTCC 59.767 50.000 0.00 0.00 38.59 4.79
825 1722 7.785028 ACTATAGACATTCCATAGTTGACTGGA 59.215 37.037 6.78 0.00 39.78 3.86
828 1725 8.768501 TCACTATAGACATTCCATAGTTGACT 57.231 34.615 6.78 0.00 34.11 3.41
829 1726 8.634444 ACTCACTATAGACATTCCATAGTTGAC 58.366 37.037 6.78 0.00 34.11 3.18
832 1729 8.353684 CGAACTCACTATAGACATTCCATAGTT 58.646 37.037 6.78 2.74 34.11 2.24
837 1734 4.202121 GGCGAACTCACTATAGACATTCCA 60.202 45.833 6.78 0.00 0.00 3.53
839 1736 4.933330 TGGCGAACTCACTATAGACATTC 58.067 43.478 6.78 4.11 0.00 2.67
840 1737 5.339008 TTGGCGAACTCACTATAGACATT 57.661 39.130 6.78 0.00 0.00 2.71
842 1739 5.339008 AATTGGCGAACTCACTATAGACA 57.661 39.130 6.78 0.00 0.00 3.41
843 1740 6.663944 AAAATTGGCGAACTCACTATAGAC 57.336 37.500 6.78 0.00 0.00 2.59
847 1744 5.410439 ACGTTAAAATTGGCGAACTCACTAT 59.590 36.000 0.00 0.00 0.00 2.12
848 1745 4.751098 ACGTTAAAATTGGCGAACTCACTA 59.249 37.500 0.00 0.00 0.00 2.74
849 1746 3.562557 ACGTTAAAATTGGCGAACTCACT 59.437 39.130 0.00 0.00 0.00 3.41
851 1748 5.866335 ATACGTTAAAATTGGCGAACTCA 57.134 34.783 0.00 0.00 0.00 3.41
852 1749 6.032042 CACAATACGTTAAAATTGGCGAACTC 59.968 38.462 12.18 0.00 37.40 3.01
853 1750 5.854338 CACAATACGTTAAAATTGGCGAACT 59.146 36.000 12.18 0.00 37.40 3.01
854 1751 5.442260 GCACAATACGTTAAAATTGGCGAAC 60.442 40.000 12.18 0.00 37.40 3.95
855 1752 4.617645 GCACAATACGTTAAAATTGGCGAA 59.382 37.500 12.18 0.00 37.40 4.70
856 1753 4.159857 GCACAATACGTTAAAATTGGCGA 58.840 39.130 12.18 0.00 37.40 5.54
857 1754 3.302170 GGCACAATACGTTAAAATTGGCG 59.698 43.478 12.18 5.34 37.40 5.69
859 1756 4.555747 GTCGGCACAATACGTTAAAATTGG 59.444 41.667 12.18 4.18 37.40 3.16
864 1761 3.429543 GTGAGTCGGCACAATACGTTAAA 59.570 43.478 0.00 0.00 38.63 1.52
866 1763 2.229543 AGTGAGTCGGCACAATACGTTA 59.770 45.455 0.00 0.00 41.19 3.18
869 1766 0.992072 CAGTGAGTCGGCACAATACG 59.008 55.000 0.00 0.00 41.19 3.06
870 1767 1.993370 GACAGTGAGTCGGCACAATAC 59.007 52.381 0.00 0.00 41.19 1.89
872 1769 3.217242 GACAGTGAGTCGGCACAAT 57.783 52.632 0.00 0.00 41.19 2.71
885 1782 0.178958 ACCTTCACCTCCGAGACAGT 60.179 55.000 0.00 0.00 0.00 3.55
886 1783 0.244994 CACCTTCACCTCCGAGACAG 59.755 60.000 0.00 0.00 0.00 3.51
888 1785 1.079750 GCACCTTCACCTCCGAGAC 60.080 63.158 0.00 0.00 0.00 3.36
893 1790 2.360475 GCCAGCACCTTCACCTCC 60.360 66.667 0.00 0.00 0.00 4.30
896 1793 2.360475 GGAGCCAGCACCTTCACC 60.360 66.667 0.00 0.00 0.00 4.02
900 1797 2.142292 ATTTCGGGAGCCAGCACCTT 62.142 55.000 6.07 0.00 0.00 3.50
901 1798 1.271840 TATTTCGGGAGCCAGCACCT 61.272 55.000 6.07 0.00 0.00 4.00
902 1799 0.393808 TTATTTCGGGAGCCAGCACC 60.394 55.000 0.00 0.00 0.00 5.01
907 1804 5.068460 CCATGTAAATTTATTTCGGGAGCCA 59.932 40.000 0.31 0.00 0.00 4.75
953 3709 1.200948 GACTTCATGCTTTCAGCCCAC 59.799 52.381 0.00 0.00 41.51 4.61
1121 3903 4.329545 CGAGGGTGGTGGTGGTGG 62.330 72.222 0.00 0.00 0.00 4.61
1149 3931 2.355310 GGATATGGTTGTGGTTCCGTCA 60.355 50.000 0.00 0.00 0.00 4.35
1935 4765 0.036671 GTCCTTAGTGTCCCCAACGG 60.037 60.000 0.00 0.00 0.00 4.44
1954 4784 2.095110 CAGATGCATAGAGAGCTCTCCG 60.095 54.545 34.87 25.31 43.88 4.63
2146 5019 2.176581 TGCCAATAGGGGTTATGCATGA 59.823 45.455 10.16 0.00 37.04 3.07
2161 5034 2.195567 AGCAGCGTTGTGTGCCAAT 61.196 52.632 0.00 0.00 40.81 3.16
2245 5118 4.049186 GCCATAATATACGGATAGGCACG 58.951 47.826 10.09 0.00 40.50 5.34
2347 9564 8.213518 ACTTTACATTCATTTCTGCATACGAT 57.786 30.769 0.00 0.00 0.00 3.73
2356 9573 6.877611 ACCGACAACTTTACATTCATTTCT 57.122 33.333 0.00 0.00 0.00 2.52
2505 9765 3.943381 TCCAGATTTGCAGCAATAGTCTG 59.057 43.478 24.89 24.89 32.63 3.51
2727 9998 6.355747 TGTTAGAATCACATATGCATGTCCA 58.644 36.000 10.16 0.00 43.73 4.02


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

AutoCloner maintained by Alex Coulton.