Multiple sequence alignment - TraesCS6D01G004600

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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 TraesCS6D01G004600 chr6D 100.000 3925 0 0 1 3925 2168671 2172595 0.000000e+00 7249.0
1 TraesCS6D01G004600 chr6D 90.643 684 52 5 2485 3156 2188077 2188760 0.000000e+00 898.0
2 TraesCS6D01G004600 chr6D 98.008 502 9 1 30 531 4205037 4205537 0.000000e+00 870.0
3 TraesCS6D01G004600 chr6D 91.797 256 17 4 3155 3409 2188790 2189042 1.730000e-93 353.0
4 TraesCS6D01G004600 chr6D 90.514 253 21 2 3671 3922 2189034 2189284 8.130000e-87 331.0
5 TraesCS6D01G004600 chr6D 83.288 365 39 18 2588 2945 2241592 2241941 2.280000e-82 316.0
6 TraesCS6D01G004600 chr6D 91.150 226 20 0 1266 1491 2153672 2153897 1.370000e-79 307.0
7 TraesCS6D01G004600 chr6D 79.412 476 50 20 2505 2974 2277596 2277163 3.840000e-75 292.0
8 TraesCS6D01G004600 chr6D 83.557 298 39 6 2782 3079 2190653 2190940 1.800000e-68 270.0
9 TraesCS6D01G004600 chr6D 100.000 37 0 0 1 37 4204927 4204963 7.040000e-08 69.4
10 TraesCS6D01G004600 chr6B 91.554 2522 141 29 30 2512 4173108 4170620 0.000000e+00 3411.0
11 TraesCS6D01G004600 chr6B 87.900 1438 114 31 2516 3925 4170558 4169153 0.000000e+00 1637.0
12 TraesCS6D01G004600 chr6B 89.009 928 88 8 2234 3155 4154248 4153329 0.000000e+00 1136.0
13 TraesCS6D01G004600 chr6B 89.885 781 51 9 3155 3925 4153298 4152536 0.000000e+00 979.0
14 TraesCS6D01G004600 chr6B 85.050 602 51 21 1023 1604 4161996 4161414 9.460000e-161 577.0
15 TraesCS6D01G004600 chr6B 84.899 596 55 15 1027 1604 3872792 3873370 1.580000e-158 569.0
16 TraesCS6D01G004600 chr6B 85.231 562 41 13 2490 3040 3873861 3874391 1.240000e-149 540.0
17 TraesCS6D01G004600 chr6B 83.694 509 52 16 2248 2725 4161405 4160897 5.980000e-123 451.0
18 TraesCS6D01G004600 chr6B 90.074 272 26 1 1333 1604 4154526 4154256 6.240000e-93 351.0
19 TraesCS6D01G004600 chr6B 80.493 446 51 16 2505 2945 4141268 4140854 3.810000e-80 309.0
20 TraesCS6D01G004600 chr6B 88.372 258 14 5 3155 3405 3876008 3876256 2.970000e-76 296.0
21 TraesCS6D01G004600 chr6B 86.275 255 18 5 3671 3925 3876251 3876488 1.080000e-65 261.0
22 TraesCS6D01G004600 chr6B 87.234 188 19 3 674 857 680723309 680723123 3.970000e-50 209.0
23 TraesCS6D01G004600 chr6B 94.048 84 4 1 2996 3079 4160262 4160180 4.120000e-25 126.0
24 TraesCS6D01G004600 chr6A 91.111 540 37 4 1077 1608 684899 684363 0.000000e+00 721.0
25 TraesCS6D01G004600 chr6A 85.552 616 65 12 30 637 733339 732740 1.200000e-174 623.0
26 TraesCS6D01G004600 chr6A 78.670 797 81 35 2297 3068 731833 731101 7.740000e-122 448.0
27 TraesCS6D01G004600 chr6A 80.269 446 52 16 2505 2945 611691 612105 1.770000e-78 303.0
28 TraesCS6D01G004600 chr6A 89.333 225 24 0 1394 1618 662675 662451 2.310000e-72 283.0
29 TraesCS6D01G004600 chr6A 82.258 310 44 7 1302 1604 490540 490845 1.400000e-64 257.0
30 TraesCS6D01G004600 chr6A 100.000 31 0 0 1034 1064 684960 684930 1.520000e-04 58.4
31 TraesCS6D01G004600 chr5B 75.735 408 84 12 50 451 591561445 591561047 1.440000e-44 191.0
32 TraesCS6D01G004600 chr5B 100.000 30 0 0 1600 1629 299680376 299680405 5.480000e-04 56.5
33 TraesCS6D01G004600 chr5D 100.000 30 0 0 1600 1629 20094992 20095021 5.480000e-04 56.5
34 TraesCS6D01G004600 chr3B 100.000 30 0 0 1600 1629 554901110 554901139 5.480000e-04 56.5
35 TraesCS6D01G004600 chr2B 100.000 30 0 0 1600 1629 188855285 188855256 5.480000e-04 56.5
36 TraesCS6D01G004600 chr2B 100.000 30 0 0 1600 1629 291851583 291851612 5.480000e-04 56.5
37 TraesCS6D01G004600 chr2B 100.000 30 0 0 1600 1629 532869093 532869064 5.480000e-04 56.5
38 TraesCS6D01G004600 chr1B 100.000 30 0 0 1600 1629 208343151 208343122 5.480000e-04 56.5


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 TraesCS6D01G004600 chr6D 2168671 2172595 3924 False 7249.000000 7249 100.000000 1 3925 1 chr6D.!!$F2 3924
1 TraesCS6D01G004600 chr6D 4204927 4205537 610 False 469.700000 870 99.004000 1 531 2 chr6D.!!$F5 530
2 TraesCS6D01G004600 chr6D 2188077 2190940 2863 False 463.000000 898 89.127750 2485 3922 4 chr6D.!!$F4 1437
3 TraesCS6D01G004600 chr6B 4169153 4173108 3955 True 2524.000000 3411 89.727000 30 3925 2 chr6B.!!$R5 3895
4 TraesCS6D01G004600 chr6B 4152536 4154526 1990 True 822.000000 1136 89.656000 1333 3925 3 chr6B.!!$R3 2592
5 TraesCS6D01G004600 chr6B 3872792 3876488 3696 False 416.500000 569 86.194250 1027 3925 4 chr6B.!!$F1 2898
6 TraesCS6D01G004600 chr6B 4160180 4161996 1816 True 384.666667 577 87.597333 1023 3079 3 chr6B.!!$R4 2056
7 TraesCS6D01G004600 chr6A 731101 733339 2238 True 535.500000 623 82.111000 30 3068 2 chr6A.!!$R3 3038
8 TraesCS6D01G004600 chr6A 684363 684960 597 True 389.700000 721 95.555500 1034 1608 2 chr6A.!!$R2 574

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
954 1056 0.174162 GCACATGGAGTCATTTGGCC 59.826 55.0 0.00 0.0 33.08 5.36 F
959 1061 0.321564 TGGAGTCATTTGGCCTCACG 60.322 55.0 3.32 0.0 0.00 4.35 F
960 1062 0.321653 GGAGTCATTTGGCCTCACGT 60.322 55.0 3.32 0.0 0.00 4.49 F
1405 1553 0.547712 ACCCTGGTGCTACTGGTCAT 60.548 55.0 0.00 0.0 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1767 1928 0.340208 CCCTTCCTCTACTCCTGGGT 59.660 60.000 0.0 0.0 0.00 4.51 R
2025 2187 0.679960 CATCCCACCCGTTTCTTCCC 60.680 60.000 0.0 0.0 0.00 3.97 R
2567 3238 1.003718 AGCCCGGTACAAGCTGTTC 60.004 57.895 0.0 0.0 34.92 3.18 R
3341 5967 0.861837 CGTATCGAGGGCAAGCAATC 59.138 55.000 0.0 0.0 0.00 2.67 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
249 337 1.981256 TCAACAAAGAAGGTGGAGCC 58.019 50.000 0.00 0.00 37.58 4.70
516 604 2.481568 TCAAAGTCAGCTTGCTTGATCG 59.518 45.455 0.80 0.00 34.71 3.69
580 670 9.067986 ACATAGTTTTCTTTTTCTTTCGAGGAT 57.932 29.630 0.00 0.00 0.00 3.24
589 679 9.284968 TCTTTTTCTTTCGAGGATGATAACTTT 57.715 29.630 0.00 0.00 0.00 2.66
693 785 2.682155 TTGTTTTGACAAAGGGTGGC 57.318 45.000 0.10 0.00 34.82 5.01
711 803 5.069516 GGGTGGCATTTTATTGACTCATGAT 59.930 40.000 0.00 0.00 0.00 2.45
712 804 5.981315 GGTGGCATTTTATTGACTCATGATG 59.019 40.000 0.00 0.00 0.00 3.07
713 805 6.183360 GGTGGCATTTTATTGACTCATGATGA 60.183 38.462 0.00 0.00 0.00 2.92
714 806 7.431249 GTGGCATTTTATTGACTCATGATGAT 58.569 34.615 0.00 0.00 0.00 2.45
715 807 7.381408 GTGGCATTTTATTGACTCATGATGATG 59.619 37.037 0.00 0.00 0.00 3.07
716 808 6.365247 GGCATTTTATTGACTCATGATGATGC 59.635 38.462 0.00 0.00 35.52 3.91
719 811 9.129209 CATTTTATTGACTCATGATGATGCATC 57.871 33.333 20.14 20.14 40.88 3.91
751 852 2.203139 CACAAGCACACACCCGGA 60.203 61.111 0.73 0.00 0.00 5.14
761 862 0.179100 CACACCCGGACTCTGCATAG 60.179 60.000 0.73 0.00 0.00 2.23
763 864 0.537188 CACCCGGACTCTGCATAGTT 59.463 55.000 0.73 0.00 0.00 2.24
764 865 1.754803 CACCCGGACTCTGCATAGTTA 59.245 52.381 0.73 0.00 0.00 2.24
766 867 1.341531 CCCGGACTCTGCATAGTTAGG 59.658 57.143 0.73 11.89 0.00 2.69
767 868 2.307768 CCGGACTCTGCATAGTTAGGA 58.692 52.381 16.67 0.00 31.73 2.94
769 870 2.294791 CGGACTCTGCATAGTTAGGAGG 59.705 54.545 6.17 0.00 0.00 4.30
770 871 2.036604 GGACTCTGCATAGTTAGGAGGC 59.963 54.545 6.17 0.00 0.00 4.70
813 914 3.184783 CACATAAACACGCCGACAACTAA 59.815 43.478 0.00 0.00 0.00 2.24
814 915 3.808726 ACATAAACACGCCGACAACTAAA 59.191 39.130 0.00 0.00 0.00 1.85
816 917 2.742954 AACACGCCGACAACTAAAAC 57.257 45.000 0.00 0.00 0.00 2.43
846 947 6.787085 ATTAGATCAAAGTTATGCGTAGGC 57.213 37.500 0.00 0.00 40.52 3.93
848 949 2.373540 TCAAAGTTATGCGTAGGCGT 57.626 45.000 7.37 7.37 44.10 5.68
893 995 5.452636 GGTTGAGTCATTGAGAGGAGGATAC 60.453 48.000 0.00 0.00 0.00 2.24
917 1019 3.221964 AGTTTTCATTCATCGCTTGGC 57.778 42.857 0.00 0.00 0.00 4.52
921 1023 2.855660 TCATTCATCGCTTGGCATTG 57.144 45.000 0.00 0.00 0.00 2.82
938 1040 2.751837 GCTTGGGCCCAGTAGCAC 60.752 66.667 34.33 15.68 36.41 4.40
951 1053 3.376234 CCAGTAGCACATGGAGTCATTTG 59.624 47.826 0.00 0.00 39.02 2.32
952 1054 3.376234 CAGTAGCACATGGAGTCATTTGG 59.624 47.826 0.00 0.00 33.08 3.28
954 1056 0.174162 GCACATGGAGTCATTTGGCC 59.826 55.000 0.00 0.00 33.08 5.36
956 1058 1.747355 CACATGGAGTCATTTGGCCTC 59.253 52.381 3.32 0.00 29.84 4.70
957 1059 1.355381 ACATGGAGTCATTTGGCCTCA 59.645 47.619 3.32 0.00 0.00 3.86
958 1060 1.747355 CATGGAGTCATTTGGCCTCAC 59.253 52.381 3.32 0.00 0.00 3.51
959 1061 0.321564 TGGAGTCATTTGGCCTCACG 60.322 55.000 3.32 0.00 0.00 4.35
960 1062 0.321653 GGAGTCATTTGGCCTCACGT 60.322 55.000 3.32 0.00 0.00 4.49
1016 1121 4.276058 TCTGCATGTCTCAATCACTTGA 57.724 40.909 0.00 0.00 39.07 3.02
1023 1128 3.304041 TCAATCACTTGAGCGTGCA 57.696 47.368 0.00 0.00 36.46 4.57
1024 1129 1.150827 TCAATCACTTGAGCGTGCAG 58.849 50.000 0.00 0.00 36.46 4.41
1107 1245 3.056678 CCGCTGATCTCTCTATTGCATCT 60.057 47.826 0.00 0.00 0.00 2.90
1344 1492 2.347490 GCCGCCAACTTCTCCTCA 59.653 61.111 0.00 0.00 0.00 3.86
1404 1552 1.152118 ACCCTGGTGCTACTGGTCA 60.152 57.895 0.00 0.00 0.00 4.02
1405 1553 0.547712 ACCCTGGTGCTACTGGTCAT 60.548 55.000 0.00 0.00 0.00 3.06
1420 1568 2.676121 CATGCAAACTCGCCCCCA 60.676 61.111 0.00 0.00 0.00 4.96
1624 1772 3.085533 GAGCATCTCTAGCCGATCCTTA 58.914 50.000 0.00 0.00 0.00 2.69
1667 1827 3.767673 AGTGGAGTAAAATAGAGGACGCA 59.232 43.478 0.00 0.00 0.00 5.24
1671 1831 4.120589 GAGTAAAATAGAGGACGCAAGGG 58.879 47.826 0.00 0.00 46.39 3.95
1707 1868 3.685139 TTCTTCTTCTTCATCACCGCT 57.315 42.857 0.00 0.00 0.00 5.52
1762 1923 1.207593 CTAGCACGTTTGGCACTGC 59.792 57.895 0.00 0.00 32.60 4.40
1780 1941 1.045911 GCCAGGACCCAGGAGTAGAG 61.046 65.000 4.77 0.00 0.00 2.43
1787 1948 1.051556 CCCAGGAGTAGAGGAAGGGC 61.052 65.000 0.00 0.00 0.00 5.19
1828 1989 4.660938 GTGGCCACCCCTGTGACC 62.661 72.222 26.31 0.00 45.76 4.02
1832 1993 2.282462 CCACCCCTGTGACCTTGC 60.282 66.667 0.00 0.00 45.76 4.01
1833 1994 2.515398 CACCCCTGTGACCTTGCA 59.485 61.111 0.00 0.00 45.76 4.08
1867 2028 3.552384 GGTGTGGTGGACCGGACA 61.552 66.667 9.46 3.42 39.43 4.02
1887 2048 6.538263 GGACAGGATTTTCTATGCCTAATCT 58.462 40.000 0.00 0.00 0.00 2.40
1888 2049 7.001073 GGACAGGATTTTCTATGCCTAATCTT 58.999 38.462 0.00 0.00 0.00 2.40
1889 2050 7.503902 GGACAGGATTTTCTATGCCTAATCTTT 59.496 37.037 0.00 0.00 0.00 2.52
1890 2051 8.829373 ACAGGATTTTCTATGCCTAATCTTTT 57.171 30.769 0.00 0.00 0.00 2.27
1891 2052 8.907885 ACAGGATTTTCTATGCCTAATCTTTTC 58.092 33.333 0.00 0.00 0.00 2.29
1892 2053 9.129532 CAGGATTTTCTATGCCTAATCTTTTCT 57.870 33.333 0.00 0.00 0.00 2.52
1893 2054 9.706529 AGGATTTTCTATGCCTAATCTTTTCTT 57.293 29.630 0.00 0.00 0.00 2.52
1964 2125 2.053865 CCATTCTGGCCGTGGCAAT 61.054 57.895 13.76 1.06 44.11 3.56
1978 2139 3.067480 GCAATGGTCATGGGCGGTG 62.067 63.158 0.00 0.00 0.00 4.94
2014 2176 0.975556 TCCAGCAGCGGGAAGTATCA 60.976 55.000 12.49 0.00 0.00 2.15
2047 2209 1.137594 AAGAAACGGGTGGGATGGGA 61.138 55.000 0.00 0.00 0.00 4.37
2067 2229 2.124445 ATTTTACTCGGCCGGGCC 60.124 61.111 28.82 28.61 46.75 5.80
2092 2254 3.554731 GGATAAGTATATTTAGGCGCCGC 59.445 47.826 23.20 0.00 0.00 6.53
2152 2314 1.571919 CCGATTTAGGACTTCGGCTG 58.428 55.000 0.00 0.00 45.04 4.85
2157 2319 2.180159 TTAGGACTTCGGCTGGGTGC 62.180 60.000 0.00 0.00 41.94 5.01
2158 2320 4.329545 GGACTTCGGCTGGGTGCA 62.330 66.667 0.00 0.00 45.15 4.57
2295 2696 6.000891 TGTTGTAGCTTCATTGTTGTGATC 57.999 37.500 0.00 0.00 0.00 2.92
2299 2700 7.275888 TGTAGCTTCATTGTTGTGATCTTTT 57.724 32.000 0.00 0.00 0.00 2.27
2306 2707 5.927689 TCATTGTTGTGATCTTTTCATTGCC 59.072 36.000 0.00 0.00 36.54 4.52
2307 2708 5.534207 TTGTTGTGATCTTTTCATTGCCT 57.466 34.783 0.00 0.00 36.54 4.75
2436 2846 4.194720 CGCCTTCCTCGACTCCCG 62.195 72.222 0.00 0.00 40.25 5.14
2467 2877 4.330074 CGTTACAATCCCAGCAAAGTCTAG 59.670 45.833 0.00 0.00 0.00 2.43
2478 2888 3.254166 AGCAAAGTCTAGCAACAACCATG 59.746 43.478 0.67 0.00 0.00 3.66
2495 3160 5.410355 ACCATGTTTTCCCAAGATTGATG 57.590 39.130 0.00 0.00 0.00 3.07
2499 3164 6.377996 CCATGTTTTCCCAAGATTGATGACTA 59.622 38.462 0.00 0.00 0.00 2.59
2501 3166 9.123902 CATGTTTTCCCAAGATTGATGACTATA 57.876 33.333 0.00 0.00 0.00 1.31
2529 3200 2.533266 AATGCTATAGGGTGCTCACG 57.467 50.000 1.04 0.00 0.00 4.35
2774 3489 7.727578 TCCAATTCTATGTACTGAGTTGGTA 57.272 36.000 23.23 14.78 44.84 3.25
2842 3559 1.504446 GCGAGTTCAGAGCGTCTCT 59.496 57.895 3.88 3.88 42.11 3.10
2850 3567 2.280835 AGAGCGTCTCTGATTGCCA 58.719 52.632 8.32 0.00 39.62 4.92
2863 3580 2.690497 TGATTGCCAAGTTTGTTTCGGA 59.310 40.909 0.00 0.00 0.00 4.55
2911 3628 2.596851 ATCACACAGGAAGCCGCCT 61.597 57.895 0.00 0.00 39.37 5.52
2950 3667 3.077359 CCGATCAAGAAGGAAGCAAGTT 58.923 45.455 0.00 0.00 0.00 2.66
3024 4144 6.206438 TGGAATTGATGAATTGAGTTGAACGA 59.794 34.615 0.00 0.00 31.58 3.85
3341 5967 5.927954 AACCACAAATAAAATTGCTGCTG 57.072 34.783 0.00 0.00 33.52 4.41
3373 5999 3.878103 CCTCGATACGTAGGGATCCATAG 59.122 52.174 15.23 7.62 0.00 2.23
3411 6038 4.547532 CTCCTAAGTGTGGTATATGTCGC 58.452 47.826 0.00 0.00 0.00 5.19
3424 6051 7.011109 GTGGTATATGTCGCTGTACTTTGAAAT 59.989 37.037 0.00 0.00 0.00 2.17
3439 6066 6.430007 ACTTTGAAATTGAGCCCTAGATCAT 58.570 36.000 0.00 0.00 38.43 2.45
3465 6092 4.697352 ACAAATACTCTGACTCAATGGCAC 59.303 41.667 0.00 0.00 0.00 5.01
3472 6099 1.364626 GACTCAATGGCACGGCTCTG 61.365 60.000 0.00 0.00 0.00 3.35
3522 6149 2.035066 GTGCAAGCAACCTCATTTGAGT 59.965 45.455 6.81 0.00 40.48 3.41
3535 6162 6.045955 CCTCATTTGAGTAGTTTCTCCTAGC 58.954 44.000 6.81 0.00 40.48 3.42
3536 6163 5.651530 TCATTTGAGTAGTTTCTCCTAGCG 58.348 41.667 0.00 0.00 33.93 4.26
3587 6214 4.991153 TTGGGTGCAAATAAATCGCATA 57.009 36.364 0.00 0.00 38.07 3.14
3647 6274 7.883229 TGTGTGTGTACATGTAACTGAATAG 57.117 36.000 7.25 0.00 39.39 1.73
3744 6376 3.181500 GGGATACAAGCACGGTTTTCATC 60.181 47.826 0.00 0.00 39.74 2.92
3810 6443 4.180057 TGTTCAGTGCCAAAAACATGAAC 58.820 39.130 0.00 8.52 44.17 3.18
3819 6452 7.230510 AGTGCCAAAAACATGAACACTTCTATA 59.769 33.333 0.00 0.00 35.40 1.31
3889 6527 2.414785 GCAATTCCGCCGGGTCAAT 61.415 57.895 1.90 0.00 33.83 2.57
3890 6528 1.433064 CAATTCCGCCGGGTCAATG 59.567 57.895 1.90 0.00 33.83 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
516 604 6.331369 TCTCAATCAACAAAAATCACCTCC 57.669 37.500 0.00 0.00 0.00 4.30
674 766 1.902508 TGCCACCCTTTGTCAAAACAA 59.097 42.857 0.00 0.00 43.58 2.83
680 772 4.590647 TCAATAAAATGCCACCCTTTGTCA 59.409 37.500 0.00 0.00 0.00 3.58
693 785 9.129209 GATGCATCATCATGAGTCAATAAAATG 57.871 33.333 21.92 0.60 40.28 2.32
711 803 7.774625 TGTGTTTTATATCCTCTTGATGCATCA 59.225 33.333 25.42 25.42 34.76 3.07
712 804 8.158169 TGTGTTTTATATCCTCTTGATGCATC 57.842 34.615 20.14 20.14 34.76 3.91
713 805 8.523915 TTGTGTTTTATATCCTCTTGATGCAT 57.476 30.769 0.00 0.00 34.76 3.96
714 806 7.415541 GCTTGTGTTTTATATCCTCTTGATGCA 60.416 37.037 0.00 0.00 34.76 3.96
715 807 6.914757 GCTTGTGTTTTATATCCTCTTGATGC 59.085 38.462 0.00 0.00 34.76 3.91
716 808 7.912250 GTGCTTGTGTTTTATATCCTCTTGATG 59.088 37.037 0.00 0.00 34.76 3.07
719 811 7.023575 GTGTGCTTGTGTTTTATATCCTCTTG 58.976 38.462 0.00 0.00 0.00 3.02
751 852 2.432510 GTGCCTCCTAACTATGCAGAGT 59.567 50.000 8.51 8.51 31.69 3.24
769 870 1.207593 GTCGATGTTGGCTGTGTGC 59.792 57.895 0.00 0.00 41.94 4.57
770 871 0.792640 GAGTCGATGTTGGCTGTGTG 59.207 55.000 0.00 0.00 0.00 3.82
781 882 3.481951 GCGTGTTTATGTGTGAGTCGATG 60.482 47.826 0.00 0.00 0.00 3.84
785 886 1.126113 CGGCGTGTTTATGTGTGAGTC 59.874 52.381 0.00 0.00 0.00 3.36
816 917 8.982685 ACGCATAACTTTGATCTAATATGACTG 58.017 33.333 12.04 5.92 0.00 3.51
835 936 2.096220 TTTTCCACGCCTACGCATAA 57.904 45.000 0.00 0.00 45.53 1.90
870 972 4.751767 ATCCTCCTCTCAATGACTCAAC 57.248 45.455 0.00 0.00 0.00 3.18
893 995 5.276270 CCAAGCGATGAATGAAAACTATGG 58.724 41.667 0.00 0.00 0.00 2.74
917 1019 1.669999 GCTACTGGGCCCAAGCAATG 61.670 60.000 34.33 21.61 42.56 2.82
921 1023 2.751837 GTGCTACTGGGCCCAAGC 60.752 66.667 33.23 33.23 38.76 4.01
938 1040 1.747355 GTGAGGCCAAATGACTCCATG 59.253 52.381 5.01 0.00 32.36 3.66
983 1088 4.428209 AGACATGCAGAACTCGATTGTAG 58.572 43.478 0.00 0.00 0.00 2.74
1107 1245 1.416243 ACGTGTTGGGAAGTGGAGTA 58.584 50.000 0.00 0.00 0.00 2.59
1249 1394 4.459089 GTGGGAGACAGAGGCGGC 62.459 72.222 0.00 0.00 0.00 6.53
1374 1522 0.830444 ACCAGGGTGCGTAGAAGTCA 60.830 55.000 0.00 0.00 0.00 3.41
1404 1552 1.978617 CTTGGGGGCGAGTTTGCAT 60.979 57.895 0.00 0.00 36.28 3.96
1405 1553 2.058125 TACTTGGGGGCGAGTTTGCA 62.058 55.000 0.00 0.00 36.28 4.08
1449 1597 1.153349 GACATCGAGCCCCTTGTCC 60.153 63.158 3.68 0.00 33.91 4.02
1667 1827 2.940124 AAAAACCTCCGGCCCCTT 59.060 55.556 0.00 0.00 0.00 3.95
1695 1856 1.699656 CCGAAGCAGCGGTGATGAAG 61.700 60.000 20.69 7.14 46.07 3.02
1762 1923 0.397816 CCTCTACTCCTGGGTCCTGG 60.398 65.000 6.59 6.59 36.53 4.45
1763 1924 0.631753 TCCTCTACTCCTGGGTCCTG 59.368 60.000 0.00 0.00 0.00 3.86
1765 1926 1.689892 CCTTCCTCTACTCCTGGGTCC 60.690 61.905 0.00 0.00 0.00 4.46
1766 1927 1.689892 CCCTTCCTCTACTCCTGGGTC 60.690 61.905 0.00 0.00 0.00 4.46
1767 1928 0.340208 CCCTTCCTCTACTCCTGGGT 59.660 60.000 0.00 0.00 0.00 4.51
1768 1929 1.051556 GCCCTTCCTCTACTCCTGGG 61.052 65.000 0.00 0.00 36.41 4.45
1822 1983 3.840437 GCTGGTTGCAAGGTCACA 58.160 55.556 0.00 0.00 42.31 3.58
1832 1993 2.263540 GGCTGCCATTGCTGGTTG 59.736 61.111 15.17 0.00 45.10 3.77
1833 1994 3.376078 CGGCTGCCATTGCTGGTT 61.376 61.111 20.29 0.00 45.10 3.67
1858 2019 3.467803 CATAGAAAATCCTGTCCGGTCC 58.532 50.000 0.00 0.00 0.00 4.46
1867 2028 9.706529 AAGAAAAGATTAGGCATAGAAAATCCT 57.293 29.630 0.00 0.00 0.00 3.24
1887 2048 2.725008 CGCCCGCACCAAAGAAAA 59.275 55.556 0.00 0.00 0.00 2.29
1888 2049 3.291383 CCGCCCGCACCAAAGAAA 61.291 61.111 0.00 0.00 0.00 2.52
1919 2080 2.204090 ACCCTTCCACGACCCCAT 60.204 61.111 0.00 0.00 0.00 4.00
1964 2125 2.271821 CATCACCGCCCATGACCA 59.728 61.111 0.00 0.00 0.00 4.02
1978 2139 4.344865 ACCCCACACGCCACCATC 62.345 66.667 0.00 0.00 0.00 3.51
2025 2187 0.679960 CATCCCACCCGTTTCTTCCC 60.680 60.000 0.00 0.00 0.00 3.97
2047 2209 1.525442 CCCGGCCGAGTAAAATCCT 59.475 57.895 30.73 0.00 0.00 3.24
2067 2229 4.117685 GCGCCTAAATATACTTATCCCCG 58.882 47.826 0.00 0.00 0.00 5.73
2096 2258 6.415798 AAATTTATTCCGCCGAAATTTTGG 57.584 33.333 18.91 18.91 38.84 3.28
2126 2288 4.608951 CGAAGTCCTAAATCGGTTAGAGG 58.391 47.826 3.35 3.35 41.70 3.69
2152 2314 5.763698 AGTTTTACTCTTCTAAACTGCACCC 59.236 40.000 0.00 0.00 39.79 4.61
2197 2507 3.644738 TCACTACCCGATCCCCTAAAATC 59.355 47.826 0.00 0.00 0.00 2.17
2204 2514 1.122019 AGCATCACTACCCGATCCCC 61.122 60.000 0.00 0.00 0.00 4.81
2295 2696 1.470098 CGTCCCTGAGGCAATGAAAAG 59.530 52.381 0.00 0.00 0.00 2.27
2299 2700 2.268920 GCGTCCCTGAGGCAATGA 59.731 61.111 0.00 0.00 42.14 2.57
2306 2707 2.187946 GACCATGGCGTCCCTGAG 59.812 66.667 13.04 0.00 0.00 3.35
2307 2708 3.770040 CGACCATGGCGTCCCTGA 61.770 66.667 13.04 0.00 0.00 3.86
2342 2749 2.997315 CTGCACCTCAGGGACCGA 60.997 66.667 0.00 0.00 39.15 4.69
2343 2750 2.583441 TTCTGCACCTCAGGGACCG 61.583 63.158 0.00 0.00 43.06 4.79
2436 2846 1.135024 TGGGATTGTAACGTACCGAGC 60.135 52.381 0.00 0.00 0.00 5.03
2448 2858 2.040278 TGCTAGACTTTGCTGGGATTGT 59.960 45.455 0.00 0.00 0.00 2.71
2467 2877 2.611225 TGGGAAAACATGGTTGTTGC 57.389 45.000 0.00 0.00 45.30 4.17
2499 3164 8.331740 AGCACCCTATAGCATTTGTTGATATAT 58.668 33.333 0.00 0.00 38.24 0.86
2501 3166 6.546484 AGCACCCTATAGCATTTGTTGATAT 58.454 36.000 0.00 0.00 40.05 1.63
2567 3238 1.003718 AGCCCGGTACAAGCTGTTC 60.004 57.895 0.00 0.00 34.92 3.18
2795 3512 7.716560 TCTGCAAGACACACATAGCATTATTAT 59.283 33.333 0.00 0.00 38.67 1.28
2796 3513 7.047271 TCTGCAAGACACACATAGCATTATTA 58.953 34.615 0.00 0.00 38.67 0.98
2842 3559 2.690497 TCCGAAACAAACTTGGCAATCA 59.310 40.909 0.00 0.00 0.00 2.57
2863 3580 5.804944 TGTGATCAATGGGATTTTGTTGT 57.195 34.783 0.00 0.00 36.00 3.32
2911 3628 7.404671 TGATCGGATTATCAAATATCGGAGA 57.595 36.000 0.00 0.00 34.99 3.71
2950 3667 2.485302 CCATGGCATACAACAGGATCGA 60.485 50.000 0.00 0.00 0.00 3.59
3024 4144 9.550406 CATCCATATAAACAAGCATTTCCATTT 57.450 29.630 0.00 0.00 0.00 2.32
3130 5721 2.624838 CAGTGTGCAATTCCTTGAACCT 59.375 45.455 0.00 0.00 39.83 3.50
3341 5967 0.861837 CGTATCGAGGGCAAGCAATC 59.138 55.000 0.00 0.00 0.00 2.67
3373 5999 2.661718 AGGAGCTAGCTGTACTTCCTC 58.338 52.381 24.99 3.92 0.00 3.71
3411 6038 6.173339 TCTAGGGCTCAATTTCAAAGTACAG 58.827 40.000 0.00 0.00 0.00 2.74
3424 6051 1.839354 TGTGCATGATCTAGGGCTCAA 59.161 47.619 0.00 0.00 0.00 3.02
3439 6066 4.696877 CCATTGAGTCAGAGTATTTGTGCA 59.303 41.667 0.00 0.00 0.00 4.57
3465 6092 0.674581 TTGATTCTGCCACAGAGCCG 60.675 55.000 0.00 0.00 41.75 5.52
3472 6099 0.947244 CGCCCTATTGATTCTGCCAC 59.053 55.000 0.00 0.00 0.00 5.01
3504 6131 5.695851 AACTACTCAAATGAGGTTGCTTG 57.304 39.130 14.50 0.00 46.13 4.01
3522 6149 0.032416 AGGGCCGCTAGGAGAAACTA 60.032 55.000 0.00 0.00 41.02 2.24
3565 6192 3.883830 TGCGATTTATTTGCACCCAAT 57.116 38.095 0.00 0.00 39.94 3.16
3587 6214 6.093633 GGTATTTTACGCCAGAAGAGAATTGT 59.906 38.462 0.00 0.00 0.00 2.71
3647 6274 8.970691 ACAATAATGATTGACTTTGTTACTGC 57.029 30.769 9.95 0.00 44.59 4.40
3688 6320 6.335777 ACTTGTTACGTTGTAACTGTCTTCT 58.664 36.000 17.72 0.00 0.00 2.85
3692 6324 6.335176 TCAACTTGTTACGTTGTAACTGTC 57.665 37.500 17.72 0.00 41.76 3.51
3773 6406 3.328931 ACTGAACAGACAATCCATGGTCT 59.671 43.478 12.58 3.99 44.84 3.85
3810 6443 9.907576 GAAGACGAATGTTCAAATATAGAAGTG 57.092 33.333 0.00 0.00 0.00 3.16
3870 6503 2.837031 ATTGACCCGGCGGAATTGCT 62.837 55.000 30.79 4.09 34.52 3.91
3889 6527 4.220602 TCAAGCATTCTACAGAGCTACACA 59.779 41.667 0.00 0.00 36.07 3.72
3890 6528 4.748892 TCAAGCATTCTACAGAGCTACAC 58.251 43.478 0.00 0.00 36.07 2.90


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

AutoCloner maintained by Alex Coulton.