Multiple sequence alignment - TraesCS2A01G368800

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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 TraesCS2A01G368800 chr2A 100.000 2828 0 0 1 2828 612080906 612078079 0.000000e+00 5223.0
1 TraesCS2A01G368800 chr2A 84.542 1682 192 31 959 2622 611999586 611997955 0.000000e+00 1604.0
2 TraesCS2A01G368800 chr2A 88.122 623 55 8 1 622 769639117 769639721 0.000000e+00 723.0
3 TraesCS2A01G368800 chr2A 87.755 147 14 2 2619 2764 611997778 611997635 4.850000e-38 169.0
4 TraesCS2A01G368800 chr2D 91.879 1884 110 18 908 2772 470240480 470238621 0.000000e+00 2591.0
5 TraesCS2A01G368800 chr2D 82.785 517 56 14 1 501 531178840 531179339 5.600000e-117 431.0
6 TraesCS2A01G368800 chr2D 97.368 38 1 0 870 907 470240543 470240506 6.540000e-07 65.8
7 TraesCS2A01G368800 chr2B 90.232 1894 121 19 833 2690 549249472 549247607 0.000000e+00 2414.0
8 TraesCS2A01G368800 chr4B 89.383 810 66 10 1 804 562578885 562578090 0.000000e+00 1002.0
9 TraesCS2A01G368800 chr4B 83.560 663 76 15 1 632 424745565 424744905 8.730000e-165 590.0
10 TraesCS2A01G368800 chr4B 91.071 56 5 0 756 811 59861032 59860977 3.020000e-10 76.8
11 TraesCS2A01G368800 chr4B 93.878 49 3 0 756 804 672272953 672273001 1.090000e-09 75.0
12 TraesCS2A01G368800 chr7B 89.557 632 61 4 1 631 87824717 87824090 0.000000e+00 797.0
13 TraesCS2A01G368800 chr3B 89.082 632 63 5 1 631 815472612 815471986 0.000000e+00 780.0
14 TraesCS2A01G368800 chr3B 71.521 1545 331 69 1076 2575 749485018 749486498 5.880000e-82 315.0
15 TraesCS2A01G368800 chr3B 91.176 102 9 0 505 606 614247858 614247757 3.800000e-29 139.0
16 TraesCS2A01G368800 chr3B 93.878 49 3 0 756 804 372249794 372249842 1.090000e-09 75.0
17 TraesCS2A01G368800 chr6B 89.068 622 53 11 3 622 655305872 655306480 0.000000e+00 758.0
18 TraesCS2A01G368800 chr3D 86.905 504 61 4 1 501 462451863 462451362 6.840000e-156 560.0
19 TraesCS2A01G368800 chr3D 90.083 121 8 4 644 762 592004618 592004736 1.360000e-33 154.0
20 TraesCS2A01G368800 chr3A 82.919 644 77 10 1 613 605237487 605236846 1.480000e-152 549.0
21 TraesCS2A01G368800 chr3A 85.429 501 70 2 1 500 721840941 721840443 4.180000e-143 518.0
22 TraesCS2A01G368800 chr3A 88.722 133 12 2 633 762 721840339 721840207 2.920000e-35 159.0
23 TraesCS2A01G368800 chr3A 87.786 131 9 5 505 632 54445071 54444945 2.270000e-31 147.0
24 TraesCS2A01G368800 chr1B 72.764 1476 304 67 1057 2503 604201219 604199813 2.620000e-110 409.0
25 TraesCS2A01G368800 chr1B 72.696 1476 305 69 1057 2500 603744924 603746333 1.220000e-108 403.0
26 TraesCS2A01G368800 chr1B 75.109 458 86 24 1323 1772 604204305 604203868 3.720000e-44 189.0
27 TraesCS2A01G368800 chr1B 95.833 48 2 0 757 804 137131462 137131415 8.400000e-11 78.7
28 TraesCS2A01G368800 chr1D 72.941 1190 247 52 1330 2500 444136051 444137184 7.500000e-91 344.0
29 TraesCS2A01G368800 chr1D 72.582 1189 253 49 1330 2500 443961242 443962375 3.510000e-84 322.0
30 TraesCS2A01G368800 chr1A 91.228 57 5 0 756 812 548973845 548973789 8.400000e-11 78.7
31 TraesCS2A01G368800 chr1A 93.878 49 3 0 756 804 232075705 232075657 1.090000e-09 75.0
32 TraesCS2A01G368800 chr1A 93.878 49 3 0 756 804 360985507 360985459 1.090000e-09 75.0
33 TraesCS2A01G368800 chr7A 93.878 49 3 0 756 804 694555225 694555177 1.090000e-09 75.0


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 TraesCS2A01G368800 chr2A 612078079 612080906 2827 True 5223.0 5223 100.0000 1 2828 1 chr2A.!!$R1 2827
1 TraesCS2A01G368800 chr2A 611997635 611999586 1951 True 886.5 1604 86.1485 959 2764 2 chr2A.!!$R2 1805
2 TraesCS2A01G368800 chr2A 769639117 769639721 604 False 723.0 723 88.1220 1 622 1 chr2A.!!$F1 621
3 TraesCS2A01G368800 chr2D 470238621 470240543 1922 True 1328.4 2591 94.6235 870 2772 2 chr2D.!!$R1 1902
4 TraesCS2A01G368800 chr2B 549247607 549249472 1865 True 2414.0 2414 90.2320 833 2690 1 chr2B.!!$R1 1857
5 TraesCS2A01G368800 chr4B 562578090 562578885 795 True 1002.0 1002 89.3830 1 804 1 chr4B.!!$R3 803
6 TraesCS2A01G368800 chr4B 424744905 424745565 660 True 590.0 590 83.5600 1 632 1 chr4B.!!$R2 631
7 TraesCS2A01G368800 chr7B 87824090 87824717 627 True 797.0 797 89.5570 1 631 1 chr7B.!!$R1 630
8 TraesCS2A01G368800 chr3B 815471986 815472612 626 True 780.0 780 89.0820 1 631 1 chr3B.!!$R2 630
9 TraesCS2A01G368800 chr3B 749485018 749486498 1480 False 315.0 315 71.5210 1076 2575 1 chr3B.!!$F2 1499
10 TraesCS2A01G368800 chr6B 655305872 655306480 608 False 758.0 758 89.0680 3 622 1 chr6B.!!$F1 619
11 TraesCS2A01G368800 chr3D 462451362 462451863 501 True 560.0 560 86.9050 1 501 1 chr3D.!!$R1 500
12 TraesCS2A01G368800 chr3A 605236846 605237487 641 True 549.0 549 82.9190 1 613 1 chr3A.!!$R2 612
13 TraesCS2A01G368800 chr3A 721840207 721840941 734 True 338.5 518 87.0755 1 762 2 chr3A.!!$R3 761
14 TraesCS2A01G368800 chr1B 603744924 603746333 1409 False 403.0 403 72.6960 1057 2500 1 chr1B.!!$F1 1443
15 TraesCS2A01G368800 chr1B 604199813 604204305 4492 True 299.0 409 73.9365 1057 2503 2 chr1B.!!$R2 1446
16 TraesCS2A01G368800 chr1D 444136051 444137184 1133 False 344.0 344 72.9410 1330 2500 1 chr1D.!!$F2 1170
17 TraesCS2A01G368800 chr1D 443961242 443962375 1133 False 322.0 322 72.5820 1330 2500 1 chr1D.!!$F1 1170

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
158 160 0.247185 TGATGCAGCTGATGTCGTCA 59.753 50.0 20.43 13.59 32.26 4.35 F
509 600 0.530870 TGTCACGCAACATTGACGGA 60.531 50.0 11.29 5.21 44.35 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1001 1135 0.251386 CCTCCCGCTCCTAGCTATCA 60.251 60.0 0.00 0.00 39.60 2.15 R
2506 4580 0.319040 CGGTCCACTGTGACTGTGAG 60.319 60.0 21.86 12.79 36.96 3.51 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
43 44 1.978580 GGGGATAGTGACATGGGTAGG 59.021 57.143 0.00 0.00 0.00 3.18
47 49 2.082140 TAGTGACATGGGTAGGCGAT 57.918 50.000 0.00 0.00 0.00 4.58
125 127 5.147162 CAAGTGAAAATAAGCTGGACGTTC 58.853 41.667 0.00 0.00 0.00 3.95
158 160 0.247185 TGATGCAGCTGATGTCGTCA 59.753 50.000 20.43 13.59 32.26 4.35
181 183 0.937304 TCGACGCCGTACCATAGTAC 59.063 55.000 0.00 0.00 44.62 2.73
509 600 0.530870 TGTCACGCAACATTGACGGA 60.531 50.000 11.29 5.21 44.35 4.69
622 714 5.052481 GTCGGTTTTGTAGTAGTGGTTTCT 58.948 41.667 0.00 0.00 0.00 2.52
632 724 9.802039 TTGTAGTAGTGGTTTCTATGGAAAATT 57.198 29.630 5.74 0.00 42.22 1.82
633 725 9.226606 TGTAGTAGTGGTTTCTATGGAAAATTG 57.773 33.333 5.74 0.00 42.22 2.32
634 726 7.703058 AGTAGTGGTTTCTATGGAAAATTGG 57.297 36.000 5.74 0.00 42.22 3.16
636 728 5.650283 AGTGGTTTCTATGGAAAATTGGGA 58.350 37.500 5.74 0.00 42.22 4.37
646 744 2.700371 GGAAAATTGGGATAAGGCAGGG 59.300 50.000 0.00 0.00 0.00 4.45
658 756 1.197812 AGGCAGGGAAATCAATTGGC 58.802 50.000 5.42 0.00 34.87 4.52
666 764 2.515912 GAAATCAATTGGCGTCGGTTC 58.484 47.619 5.42 0.00 0.00 3.62
738 838 2.363975 AATAGCTCGGGTGCGGGAA 61.364 57.895 0.00 0.00 38.13 3.97
744 844 4.090588 CGGGTGCGGGAAGGCTTA 62.091 66.667 0.00 0.00 0.00 3.09
767 867 3.166657 CGAAACTAACGACGTAAGAGGG 58.833 50.000 0.00 0.00 43.62 4.30
768 868 3.505836 GAAACTAACGACGTAAGAGGGG 58.494 50.000 0.00 0.00 43.62 4.79
769 869 2.496899 ACTAACGACGTAAGAGGGGA 57.503 50.000 0.00 0.00 43.62 4.81
770 870 2.363683 ACTAACGACGTAAGAGGGGAG 58.636 52.381 0.00 0.00 43.62 4.30
857 957 1.874019 CCACGCACTCGAATCTCCG 60.874 63.158 0.00 0.00 39.41 4.63
859 959 2.956964 CGCACTCGAATCTCCGCC 60.957 66.667 0.00 0.00 38.10 6.13
862 962 1.227089 CACTCGAATCTCCGCCCAG 60.227 63.158 0.00 0.00 0.00 4.45
900 1000 6.150641 CGGATACTATTTCTACTCCGATTCCA 59.849 42.308 2.78 0.00 46.47 3.53
918 1043 1.671979 CAGGTCGTACCGTATCCAGA 58.328 55.000 0.00 0.00 44.90 3.86
935 1060 2.989840 CCAGACAGATTTCAGTGTCGAC 59.010 50.000 9.11 9.11 46.43 4.20
938 1063 1.269569 ACAGATTTCAGTGTCGACGCA 60.270 47.619 29.21 10.50 0.00 5.24
957 1091 2.479049 GCAGACGGTCTATTTAGTCGCA 60.479 50.000 10.87 0.00 38.53 5.10
1000 1134 0.677288 CGGTGGAGGTAGTTCACACA 59.323 55.000 0.00 0.00 33.91 3.72
1001 1135 1.275291 CGGTGGAGGTAGTTCACACAT 59.725 52.381 0.00 0.00 33.91 3.21
1002 1136 2.699954 GGTGGAGGTAGTTCACACATG 58.300 52.381 0.00 0.00 33.91 3.21
1005 1139 4.161565 GGTGGAGGTAGTTCACACATGATA 59.838 45.833 0.00 0.00 33.85 2.15
1029 1163 1.749033 GAGCGGGAGGGATCGATTT 59.251 57.895 0.00 0.00 0.00 2.17
1210 3241 2.679287 ACCCCGTCCTCGACTTCC 60.679 66.667 0.00 0.00 39.71 3.46
1293 3324 0.183971 TCACCGGTTTCCACCACAAT 59.816 50.000 2.97 0.00 44.53 2.71
1478 3533 0.179000 ATCAACCGGCTCATCTCCAC 59.821 55.000 0.00 0.00 0.00 4.02
1702 3760 4.735132 CCATGTCGACGCCCGTGT 62.735 66.667 11.62 0.00 39.75 4.49
1703 3761 3.179265 CATGTCGACGCCCGTGTC 61.179 66.667 11.62 0.00 39.75 3.67
1787 3845 0.459899 CCTGCTACACCGCTGACATA 59.540 55.000 0.00 0.00 0.00 2.29
1788 3846 1.560923 CTGCTACACCGCTGACATAC 58.439 55.000 0.00 0.00 0.00 2.39
1789 3847 0.179148 TGCTACACCGCTGACATACG 60.179 55.000 0.00 0.00 0.00 3.06
1790 3848 0.099968 GCTACACCGCTGACATACGA 59.900 55.000 0.00 0.00 0.00 3.43
1845 3915 4.517703 CGGAGCTCGTCGTCGACC 62.518 72.222 19.29 5.94 41.35 4.79
1846 3916 4.517703 GGAGCTCGTCGTCGACCG 62.518 72.222 19.29 14.03 41.35 4.79
1932 4002 2.176140 ACGAGAGTGAGCTTCGAGG 58.824 57.895 11.49 0.00 46.97 4.63
1976 4046 2.410322 AATGCAACCTCGCCCTGTGA 62.410 55.000 0.00 0.00 0.00 3.58
2223 4294 1.985116 GCCTCCTCCTTGAGACGGT 60.985 63.158 0.00 0.00 34.11 4.83
2252 4323 1.517832 GAGACCCTCCATGTCCACG 59.482 63.158 0.00 0.00 33.09 4.94
2365 4439 5.163561 GGAGTTTGTGATGACTGGTTTTGAA 60.164 40.000 0.00 0.00 0.00 2.69
2396 4470 1.019805 GCAGGTTTACCTCGTCAGGC 61.020 60.000 0.00 0.00 46.65 4.85
2508 4582 3.786586 GACGCAGCAGCAGCACTC 61.787 66.667 10.77 0.00 45.49 3.51
2509 4583 4.614112 ACGCAGCAGCAGCACTCA 62.614 61.111 10.77 0.00 45.49 3.41
2510 4584 4.086178 CGCAGCAGCAGCACTCAC 62.086 66.667 10.77 0.00 45.49 3.51
2511 4585 2.976350 GCAGCAGCAGCACTCACA 60.976 61.111 4.63 0.00 45.49 3.58
2512 4586 2.967473 GCAGCAGCAGCACTCACAG 61.967 63.158 4.63 0.00 45.49 3.66
2551 4625 3.323979 AGGAGAAGGACAAGACGCTTAAA 59.676 43.478 0.00 0.00 0.00 1.52
2577 4651 5.433051 AGATCATGAATGGGGTTCCTTCTTA 59.567 40.000 0.00 0.00 35.91 2.10
2608 4682 4.939439 GCTTCTCCGGTTATAGTTTTTGGA 59.061 41.667 0.00 0.00 0.00 3.53
2648 4905 6.627395 TTTTCATCCATAACGTGAAAGTGT 57.373 33.333 0.00 0.00 41.31 3.55
2658 4915 2.223479 ACGTGAAAGTGTGCATTTGTCC 60.223 45.455 0.00 0.00 0.00 4.02
2674 4931 5.715434 TTTGTCCAGTTAATTTGTAGGCC 57.285 39.130 0.00 0.00 0.00 5.19
2733 4994 7.308589 GGTGCTGTTGTACTCAAATTCTAATGT 60.309 37.037 0.00 0.00 35.20 2.71
2764 5025 1.009389 GGAAGACACCGTCGAGCTTG 61.009 60.000 0.00 0.00 37.67 4.01
2766 5027 3.470567 GACACCGTCGAGCTTGCG 61.471 66.667 9.89 9.89 0.00 4.85
2772 5033 1.351430 CCGTCGAGCTTGCGAAATGA 61.351 55.000 16.31 0.00 42.55 2.57
2773 5034 0.438445 CGTCGAGCTTGCGAAATGAA 59.562 50.000 11.03 0.00 42.55 2.57
2774 5035 1.136363 CGTCGAGCTTGCGAAATGAAA 60.136 47.619 11.03 0.00 42.55 2.69
2775 5036 2.661709 CGTCGAGCTTGCGAAATGAAAA 60.662 45.455 11.03 0.00 42.55 2.29
2776 5037 3.296628 GTCGAGCTTGCGAAATGAAAAA 58.703 40.909 0.00 0.00 42.55 1.94
2777 5038 3.117994 GTCGAGCTTGCGAAATGAAAAAC 59.882 43.478 0.00 0.00 42.55 2.43
2778 5039 3.003275 TCGAGCTTGCGAAATGAAAAACT 59.997 39.130 0.00 0.00 37.35 2.66
2779 5040 4.212425 TCGAGCTTGCGAAATGAAAAACTA 59.788 37.500 0.00 0.00 37.35 2.24
2780 5041 4.551126 CGAGCTTGCGAAATGAAAAACTAG 59.449 41.667 0.00 0.00 0.00 2.57
2781 5042 4.229876 AGCTTGCGAAATGAAAAACTAGC 58.770 39.130 0.00 0.00 0.00 3.42
2782 5043 3.058129 GCTTGCGAAATGAAAAACTAGCG 59.942 43.478 0.00 0.00 0.00 4.26
2783 5044 3.196007 TGCGAAATGAAAAACTAGCGG 57.804 42.857 0.00 0.00 0.00 5.52
2784 5045 2.550606 TGCGAAATGAAAAACTAGCGGT 59.449 40.909 0.00 0.00 0.00 5.68
2785 5046 3.747010 TGCGAAATGAAAAACTAGCGGTA 59.253 39.130 0.00 0.00 0.00 4.02
2786 5047 4.086574 GCGAAATGAAAAACTAGCGGTAC 58.913 43.478 0.00 0.00 0.00 3.34
2787 5048 4.644954 CGAAATGAAAAACTAGCGGTACC 58.355 43.478 0.16 0.16 0.00 3.34
2788 5049 4.644954 GAAATGAAAAACTAGCGGTACCG 58.355 43.478 30.06 30.06 43.09 4.02
2789 5050 2.083167 TGAAAAACTAGCGGTACCGG 57.917 50.000 33.98 20.56 40.19 5.28
2790 5051 0.723414 GAAAAACTAGCGGTACCGGC 59.277 55.000 33.98 25.09 40.19 6.13
2791 5052 0.322648 AAAAACTAGCGGTACCGGCT 59.677 50.000 33.98 29.73 40.19 5.52
2792 5053 0.322648 AAAACTAGCGGTACCGGCTT 59.677 50.000 33.98 13.49 40.19 4.35
2793 5054 0.108472 AAACTAGCGGTACCGGCTTC 60.108 55.000 33.98 18.16 40.19 3.86
2794 5055 0.969409 AACTAGCGGTACCGGCTTCT 60.969 55.000 33.98 23.87 40.19 2.85
2795 5056 0.107017 ACTAGCGGTACCGGCTTCTA 60.107 55.000 33.98 23.71 40.19 2.10
2796 5057 0.310232 CTAGCGGTACCGGCTTCTAC 59.690 60.000 33.98 16.32 40.19 2.59
2797 5058 1.103398 TAGCGGTACCGGCTTCTACC 61.103 60.000 33.98 15.58 40.19 3.18
2813 5074 2.417516 CCGAGTAGGTGGATGCCG 59.582 66.667 0.00 0.00 34.51 5.69
2814 5075 2.423898 CCGAGTAGGTGGATGCCGT 61.424 63.158 0.00 0.00 34.51 5.68
2815 5076 1.515954 CGAGTAGGTGGATGCCGTT 59.484 57.895 0.00 0.00 0.00 4.44
2816 5077 0.806102 CGAGTAGGTGGATGCCGTTG 60.806 60.000 0.00 0.00 0.00 4.10
2817 5078 0.462047 GAGTAGGTGGATGCCGTTGG 60.462 60.000 0.00 0.00 0.00 3.77
2818 5079 0.907704 AGTAGGTGGATGCCGTTGGA 60.908 55.000 0.00 0.00 0.00 3.53
2819 5080 0.180406 GTAGGTGGATGCCGTTGGAT 59.820 55.000 0.00 0.00 0.00 3.41
2820 5081 0.180171 TAGGTGGATGCCGTTGGATG 59.820 55.000 0.00 0.00 0.00 3.51
2821 5082 1.378514 GGTGGATGCCGTTGGATGT 60.379 57.895 0.00 0.00 0.00 3.06
2822 5083 0.965363 GGTGGATGCCGTTGGATGTT 60.965 55.000 0.00 0.00 0.00 2.71
2823 5084 0.887933 GTGGATGCCGTTGGATGTTT 59.112 50.000 0.00 0.00 0.00 2.83
2824 5085 2.088423 GTGGATGCCGTTGGATGTTTA 58.912 47.619 0.00 0.00 0.00 2.01
2825 5086 2.687935 GTGGATGCCGTTGGATGTTTAT 59.312 45.455 0.00 0.00 0.00 1.40
2826 5087 2.687425 TGGATGCCGTTGGATGTTTATG 59.313 45.455 0.00 0.00 0.00 1.90
2827 5088 2.948979 GGATGCCGTTGGATGTTTATGA 59.051 45.455 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 2.817423 CTCGCCCTTTGCAGATCGC 61.817 63.158 3.07 3.07 41.33 4.58
47 49 1.308069 GCAATCTCGCCCTTTGCAGA 61.308 55.000 2.25 0.00 43.95 4.26
78 80 1.524355 GTACGTGCTGCTGATGCTATG 59.476 52.381 0.00 0.00 40.48 2.23
125 127 3.464907 CTGCATCAACCTCTACCTGATG 58.535 50.000 6.87 6.87 46.04 3.07
158 160 1.102809 TATGGTACGGCGTCGATGGT 61.103 55.000 20.03 0.00 40.11 3.55
181 183 1.135083 ACTCACGATACGGCAAGAAGG 60.135 52.381 0.00 0.00 0.00 3.46
335 337 1.604378 CACGCCCCATTCTTCTCCT 59.396 57.895 0.00 0.00 0.00 3.69
413 415 3.103742 GGAGAGAGTTCATGTCTTCCCT 58.896 50.000 0.00 0.00 30.04 4.20
474 476 0.323629 GACACCCAAGGATTCACCGA 59.676 55.000 0.00 0.00 44.74 4.69
572 663 0.036875 GATTCCCCTGCCTTATCCCG 59.963 60.000 0.00 0.00 0.00 5.14
622 714 5.147032 CCTGCCTTATCCCAATTTTCCATA 58.853 41.667 0.00 0.00 0.00 2.74
632 724 2.213310 TGATTTCCCTGCCTTATCCCA 58.787 47.619 0.00 0.00 0.00 4.37
633 725 3.312736 TTGATTTCCCTGCCTTATCCC 57.687 47.619 0.00 0.00 0.00 3.85
634 726 4.039609 CCAATTGATTTCCCTGCCTTATCC 59.960 45.833 7.12 0.00 0.00 2.59
636 728 3.389002 GCCAATTGATTTCCCTGCCTTAT 59.611 43.478 7.12 0.00 0.00 1.73
646 744 2.161609 AGAACCGACGCCAATTGATTTC 59.838 45.455 7.12 0.00 0.00 2.17
658 756 1.271656 ACCACTCCTAAAGAACCGACG 59.728 52.381 0.00 0.00 0.00 5.12
666 764 4.301072 TCCATGGAAACCACTCCTAAAG 57.699 45.455 13.46 0.00 35.80 1.85
738 838 2.982470 CGTCGTTAGTTTCGTTAAGCCT 59.018 45.455 0.00 0.00 0.00 4.58
744 844 4.222114 CCTCTTACGTCGTTAGTTTCGTT 58.778 43.478 1.78 0.00 37.66 3.85
763 863 1.273666 TGTAAGGTTCCCTCTCCCCTC 60.274 57.143 0.00 0.00 30.89 4.30
767 867 3.174779 AGAACTGTAAGGTTCCCTCTCC 58.825 50.000 4.09 0.00 44.56 3.71
768 868 4.893829 AAGAACTGTAAGGTTCCCTCTC 57.106 45.455 4.09 0.00 44.56 3.20
769 869 5.648330 AAAAGAACTGTAAGGTTCCCTCT 57.352 39.130 4.09 0.00 44.56 3.69
770 870 5.938710 CCTAAAAGAACTGTAAGGTTCCCTC 59.061 44.000 4.09 0.00 44.56 4.30
806 906 9.610104 TCTACAGTTACCTCTATCTCTATCTCT 57.390 37.037 0.00 0.00 0.00 3.10
837 937 0.108804 GGAGATTCGAGTGCGTGGAA 60.109 55.000 0.00 0.00 38.98 3.53
843 943 2.586357 GGGCGGAGATTCGAGTGC 60.586 66.667 0.00 0.00 0.00 4.40
857 957 2.282745 AAACAGCTCTGCCTGGGC 60.283 61.111 4.43 4.43 37.16 5.36
859 959 2.037136 CCGAAACAGCTCTGCCTGG 61.037 63.158 0.00 0.00 37.16 4.45
862 962 1.134670 AGTATCCGAAACAGCTCTGCC 60.135 52.381 0.00 0.00 0.00 4.85
918 1043 1.269569 TGCGTCGACACTGAAATCTGT 60.270 47.619 17.16 0.00 0.00 3.41
935 1060 2.373269 CGACTAAATAGACCGTCTGCG 58.627 52.381 11.52 0.56 37.95 5.18
938 1063 2.223525 GCTGCGACTAAATAGACCGTCT 60.224 50.000 6.25 6.25 0.00 4.18
1000 1134 1.618345 CCTCCCGCTCCTAGCTATCAT 60.618 57.143 0.00 0.00 39.60 2.45
1001 1135 0.251386 CCTCCCGCTCCTAGCTATCA 60.251 60.000 0.00 0.00 39.60 2.15
1002 1136 0.968393 CCCTCCCGCTCCTAGCTATC 60.968 65.000 0.00 0.00 39.60 2.08
1005 1139 2.723464 GATCCCTCCCGCTCCTAGCT 62.723 65.000 0.00 0.00 39.60 3.32
1193 3224 2.679287 GGAAGTCGAGGACGGGGT 60.679 66.667 0.00 0.00 37.67 4.95
1210 3241 2.025727 GAGTATGTCCCCGACGCG 59.974 66.667 3.53 3.53 34.95 6.01
1242 3273 3.670898 ATGGAGGAGGAGCCATCTT 57.329 52.632 0.00 0.00 40.83 2.40
1478 3533 3.282157 CCCAAGCATCGATGGCCG 61.282 66.667 26.00 12.12 35.28 6.13
1787 3845 2.680352 ACGGTGATCTGCCCTCGT 60.680 61.111 0.00 0.00 0.00 4.18
1788 3846 2.202797 CACGGTGATCTGCCCTCG 60.203 66.667 0.74 0.00 0.00 4.63
1789 3847 2.187946 CCACGGTGATCTGCCCTC 59.812 66.667 10.28 0.00 0.00 4.30
1790 3848 2.284625 TCCACGGTGATCTGCCCT 60.285 61.111 10.28 0.00 0.00 5.19
1845 3915 2.202690 TATGAACCCGACGCAGCG 60.203 61.111 14.82 14.82 0.00 5.18
1846 3916 1.883084 CCTATGAACCCGACGCAGC 60.883 63.158 0.00 0.00 0.00 5.25
2038 4108 1.586154 GGATGCACCCACAAACGAGG 61.586 60.000 0.00 0.00 0.00 4.63
2132 4203 1.757699 GAGGTTAGGTAGCAGGGACAG 59.242 57.143 0.00 0.00 0.00 3.51
2136 4207 2.125178 CGGAGGTTAGGTAGCAGGG 58.875 63.158 0.00 0.00 0.00 4.45
2223 4294 2.683933 GGGTCTCGAGGGAAGGCA 60.684 66.667 13.56 0.00 0.00 4.75
2365 4439 3.547787 AACCTGCCTCTCCGTCCCT 62.548 63.158 0.00 0.00 0.00 4.20
2396 4470 1.162698 CTGCACACTCCCATGACAAG 58.837 55.000 0.00 0.00 0.00 3.16
2469 4543 0.911525 CATCTCCCAGTCCCAGTGGT 60.912 60.000 8.74 0.00 36.97 4.16
2470 4544 1.630126 CCATCTCCCAGTCCCAGTGG 61.630 65.000 0.63 0.63 38.45 4.00
2506 4580 0.319040 CGGTCCACTGTGACTGTGAG 60.319 60.000 21.86 12.79 36.96 3.51
2507 4581 0.753848 TCGGTCCACTGTGACTGTGA 60.754 55.000 21.86 7.28 41.46 3.58
2508 4582 0.597637 GTCGGTCCACTGTGACTGTG 60.598 60.000 14.67 14.67 41.46 3.66
2509 4583 1.740285 GTCGGTCCACTGTGACTGT 59.260 57.895 9.86 0.00 41.46 3.55
2510 4584 1.371758 CGTCGGTCCACTGTGACTG 60.372 63.158 9.86 10.50 41.98 3.51
2511 4585 1.516365 CTCGTCGGTCCACTGTGACT 61.516 60.000 9.86 0.00 35.54 3.41
2512 4586 1.081376 CTCGTCGGTCCACTGTGAC 60.081 63.158 9.86 5.67 34.42 3.67
2551 4625 2.854967 AGGAACCCCATTCATGATCTGT 59.145 45.455 0.00 0.00 39.30 3.41
2577 4651 1.755393 AACCGGAGAAGCGGTTGAGT 61.755 55.000 9.46 0.00 45.46 3.41
2626 4881 5.561919 GCACACTTTCACGTTATGGATGAAA 60.562 40.000 0.00 0.00 39.42 2.69
2628 4883 3.435327 GCACACTTTCACGTTATGGATGA 59.565 43.478 0.00 0.00 0.00 2.92
2648 4905 6.686630 CCTACAAATTAACTGGACAAATGCA 58.313 36.000 0.00 0.00 0.00 3.96
2658 4915 2.943033 CCGGAGGCCTACAAATTAACTG 59.057 50.000 17.35 0.00 46.14 3.16
2696 4957 7.333423 TGAGTACAACAGCACCTTATAAATCAC 59.667 37.037 0.00 0.00 0.00 3.06
2733 4994 1.059584 TGTCTTCCACCCTCCAAGCA 61.060 55.000 0.00 0.00 0.00 3.91
2764 5025 3.197434 ACCGCTAGTTTTTCATTTCGC 57.803 42.857 0.00 0.00 0.00 4.70
2766 5027 4.436451 CCGGTACCGCTAGTTTTTCATTTC 60.436 45.833 29.15 0.00 38.24 2.17
2772 5033 0.322648 AGCCGGTACCGCTAGTTTTT 59.677 50.000 29.15 3.91 38.24 1.94
2773 5034 0.322648 AAGCCGGTACCGCTAGTTTT 59.677 50.000 29.15 12.16 38.24 2.43
2774 5035 0.108472 GAAGCCGGTACCGCTAGTTT 60.108 55.000 29.15 18.60 38.24 2.66
2775 5036 0.969409 AGAAGCCGGTACCGCTAGTT 60.969 55.000 29.15 17.21 38.24 2.24
2776 5037 0.107017 TAGAAGCCGGTACCGCTAGT 60.107 55.000 29.15 19.27 38.24 2.57
2777 5038 0.310232 GTAGAAGCCGGTACCGCTAG 59.690 60.000 29.15 16.39 38.24 3.42
2778 5039 1.103398 GGTAGAAGCCGGTACCGCTA 61.103 60.000 29.15 20.23 38.24 4.26
2779 5040 2.421399 GGTAGAAGCCGGTACCGCT 61.421 63.158 29.15 24.38 38.24 5.52
2780 5041 2.105729 GGTAGAAGCCGGTACCGC 59.894 66.667 29.15 22.58 38.24 5.68
2787 5048 0.381089 CACCTACTCGGTAGAAGCCG 59.619 60.000 11.31 0.00 46.94 5.52
2788 5049 0.745468 CCACCTACTCGGTAGAAGCC 59.255 60.000 11.31 0.00 46.94 4.35
2789 5050 1.760192 TCCACCTACTCGGTAGAAGC 58.240 55.000 11.31 0.00 46.94 3.86
2790 5051 2.034812 GCATCCACCTACTCGGTAGAAG 59.965 54.545 11.31 4.91 46.94 2.85
2791 5052 2.029623 GCATCCACCTACTCGGTAGAA 58.970 52.381 11.31 0.00 46.94 2.10
2792 5053 1.688772 GCATCCACCTACTCGGTAGA 58.311 55.000 11.31 0.00 46.94 2.59
2793 5054 0.674534 GGCATCCACCTACTCGGTAG 59.325 60.000 4.60 4.60 46.94 3.18
2794 5055 1.105167 CGGCATCCACCTACTCGGTA 61.105 60.000 0.00 0.00 46.94 4.02
2796 5057 1.956629 AACGGCATCCACCTACTCGG 61.957 60.000 0.00 0.00 39.35 4.63
2797 5058 0.806102 CAACGGCATCCACCTACTCG 60.806 60.000 0.00 0.00 0.00 4.18
2798 5059 0.462047 CCAACGGCATCCACCTACTC 60.462 60.000 0.00 0.00 0.00 2.59
2799 5060 0.907704 TCCAACGGCATCCACCTACT 60.908 55.000 0.00 0.00 0.00 2.57
2800 5061 0.180406 ATCCAACGGCATCCACCTAC 59.820 55.000 0.00 0.00 0.00 3.18
2801 5062 0.180171 CATCCAACGGCATCCACCTA 59.820 55.000 0.00 0.00 0.00 3.08
2802 5063 1.077501 CATCCAACGGCATCCACCT 60.078 57.895 0.00 0.00 0.00 4.00
2803 5064 0.965363 AACATCCAACGGCATCCACC 60.965 55.000 0.00 0.00 0.00 4.61
2804 5065 0.887933 AAACATCCAACGGCATCCAC 59.112 50.000 0.00 0.00 0.00 4.02
2805 5066 2.498644 TAAACATCCAACGGCATCCA 57.501 45.000 0.00 0.00 0.00 3.41
2806 5067 2.948979 TCATAAACATCCAACGGCATCC 59.051 45.455 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.