Multiple sequence alignment - TraesCS2A01G382100

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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 TraesCS2A01G382100 chr2A 100.000 2273 0 0 1 2273 625563976 625566248 0.000000e+00 4198.0
1 TraesCS2A01G382100 chr2A 88.070 285 33 1 151 435 187819547 187819264 1.010000e-88 337.0
2 TraesCS2A01G382100 chr2D 92.857 1484 60 18 819 2272 483066962 483068429 0.000000e+00 2111.0
3 TraesCS2A01G382100 chr2D 89.796 49 5 0 1892 1940 174242459 174242411 1.880000e-06 63.9
4 TraesCS2A01G382100 chr7A 90.595 1478 66 27 846 2273 307378371 307376917 0.000000e+00 1892.0
5 TraesCS2A01G382100 chr2B 88.786 1516 66 29 819 2273 567577865 567579337 0.000000e+00 1762.0
6 TraesCS2A01G382100 chr2B 91.962 734 31 11 826 1543 567576418 567577139 0.000000e+00 1003.0
7 TraesCS2A01G382100 chr7B 91.179 1247 58 21 862 2059 264005186 264006429 0.000000e+00 1646.0
8 TraesCS2A01G382100 chr7B 93.701 127 7 1 2144 2270 264006440 264006565 2.980000e-44 189.0
9 TraesCS2A01G382100 chr7B 94.444 36 1 1 770 804 708092692 708092657 1.000000e-03 54.7
10 TraesCS2A01G382100 chr7D 91.050 838 40 16 839 1645 273855558 273854725 0.000000e+00 1099.0
11 TraesCS2A01G382100 chr7D 89.073 604 63 3 151 752 638594445 638595047 0.000000e+00 747.0
12 TraesCS2A01G382100 chr7D 88.350 618 23 12 1686 2273 273854717 273854119 0.000000e+00 697.0
13 TraesCS2A01G382100 chr5B 91.954 609 45 4 148 752 476076787 476077395 0.000000e+00 850.0
14 TraesCS2A01G382100 chr5B 85.470 117 17 0 1088 1204 697499833 697499717 3.070000e-24 122.0
15 TraesCS2A01G382100 chr6D 90.998 611 52 3 143 751 16088634 16089243 0.000000e+00 821.0
16 TraesCS2A01G382100 chr5D 88.167 600 69 2 154 752 370314348 370313750 0.000000e+00 713.0
17 TraesCS2A01G382100 chr1D 87.725 611 67 7 146 752 309535269 309534663 0.000000e+00 706.0
18 TraesCS2A01G382100 chr5A 87.049 610 77 2 144 752 469134535 469133927 0.000000e+00 688.0
19 TraesCS2A01G382100 chr3B 86.184 608 74 8 151 752 568938804 568938201 0.000000e+00 649.0
20 TraesCS2A01G382100 chr6A 84.186 430 59 4 323 752 522068360 522067940 2.100000e-110 409.0
21 TraesCS2A01G382100 chr6B 91.696 289 20 3 151 438 588311827 588312112 4.550000e-107 398.0
22 TraesCS2A01G382100 chr6B 100.000 28 0 0 745 772 556780518 556780545 4.000000e-03 52.8
23 TraesCS2A01G382100 chr4A 85.470 117 17 0 1088 1204 615164054 615163938 3.070000e-24 122.0
24 TraesCS2A01G382100 chr1A 100.000 30 0 0 775 804 22069823 22069852 3.150000e-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 TraesCS2A01G382100 chr2A 625563976 625566248 2272 False 4198.0 4198 100.000 1 2273 1 chr2A.!!$F1 2272
1 TraesCS2A01G382100 chr2D 483066962 483068429 1467 False 2111.0 2111 92.857 819 2272 1 chr2D.!!$F1 1453
2 TraesCS2A01G382100 chr7A 307376917 307378371 1454 True 1892.0 1892 90.595 846 2273 1 chr7A.!!$R1 1427
3 TraesCS2A01G382100 chr2B 567576418 567579337 2919 False 1382.5 1762 90.374 819 2273 2 chr2B.!!$F1 1454
4 TraesCS2A01G382100 chr7B 264005186 264006565 1379 False 917.5 1646 92.440 862 2270 2 chr7B.!!$F1 1408
5 TraesCS2A01G382100 chr7D 273854119 273855558 1439 True 898.0 1099 89.700 839 2273 2 chr7D.!!$R1 1434
6 TraesCS2A01G382100 chr7D 638594445 638595047 602 False 747.0 747 89.073 151 752 1 chr7D.!!$F1 601
7 TraesCS2A01G382100 chr5B 476076787 476077395 608 False 850.0 850 91.954 148 752 1 chr5B.!!$F1 604
8 TraesCS2A01G382100 chr6D 16088634 16089243 609 False 821.0 821 90.998 143 751 1 chr6D.!!$F1 608
9 TraesCS2A01G382100 chr5D 370313750 370314348 598 True 713.0 713 88.167 154 752 1 chr5D.!!$R1 598
10 TraesCS2A01G382100 chr1D 309534663 309535269 606 True 706.0 706 87.725 146 752 1 chr1D.!!$R1 606
11 TraesCS2A01G382100 chr5A 469133927 469134535 608 True 688.0 688 87.049 144 752 1 chr5A.!!$R1 608
12 TraesCS2A01G382100 chr3B 568938201 568938804 603 True 649.0 649 86.184 151 752 1 chr3B.!!$R1 601

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
104 105 0.179163 TGTGAGAGCTATGACACGCG 60.179 55.0 3.53 3.53 36.25 6.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2062 3639 1.156645 GCATGCGGCAGGAGAGTTAG 61.157 60.0 19.93 0.0 43.97 2.34 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
27 28 7.984422 ATGTATGACATGAGTTTGTTCTTGA 57.016 32.000 0.00 0.00 37.45 3.02
28 29 7.800155 TGTATGACATGAGTTTGTTCTTGAA 57.200 32.000 0.00 0.00 0.00 2.69
29 30 8.394971 TGTATGACATGAGTTTGTTCTTGAAT 57.605 30.769 0.00 0.00 0.00 2.57
30 31 8.506437 TGTATGACATGAGTTTGTTCTTGAATC 58.494 33.333 0.00 0.00 0.00 2.52
31 32 6.940831 TGACATGAGTTTGTTCTTGAATCA 57.059 33.333 0.00 0.00 0.00 2.57
32 33 6.728200 TGACATGAGTTTGTTCTTGAATCAC 58.272 36.000 0.00 0.00 0.00 3.06
33 34 6.318396 TGACATGAGTTTGTTCTTGAATCACA 59.682 34.615 0.00 0.00 0.00 3.58
34 35 7.013559 TGACATGAGTTTGTTCTTGAATCACAT 59.986 33.333 0.00 0.00 0.00 3.21
35 36 8.394971 ACATGAGTTTGTTCTTGAATCACATA 57.605 30.769 0.00 0.00 0.00 2.29
36 37 8.849168 ACATGAGTTTGTTCTTGAATCACATAA 58.151 29.630 0.00 0.00 0.00 1.90
37 38 9.850628 CATGAGTTTGTTCTTGAATCACATAAT 57.149 29.630 0.00 0.00 0.00 1.28
77 78 9.586732 TCCTTATATTATTGGGAAAGATTGTGG 57.413 33.333 0.00 0.00 0.00 4.17
78 79 9.367160 CCTTATATTATTGGGAAAGATTGTGGT 57.633 33.333 0.00 0.00 0.00 4.16
81 82 8.837099 ATATTATTGGGAAAGATTGTGGTTCA 57.163 30.769 0.00 0.00 0.00 3.18
82 83 7.738437 ATTATTGGGAAAGATTGTGGTTCAT 57.262 32.000 0.00 0.00 0.00 2.57
83 84 5.665916 ATTGGGAAAGATTGTGGTTCATC 57.334 39.130 0.00 0.00 0.00 2.92
84 85 3.081061 TGGGAAAGATTGTGGTTCATCG 58.919 45.455 0.00 0.00 0.00 3.84
85 86 3.081804 GGGAAAGATTGTGGTTCATCGT 58.918 45.455 0.00 0.00 0.00 3.73
86 87 3.119849 GGGAAAGATTGTGGTTCATCGTG 60.120 47.826 0.00 0.00 0.00 4.35
87 88 3.502211 GGAAAGATTGTGGTTCATCGTGT 59.498 43.478 0.00 0.00 0.00 4.49
88 89 4.466828 GAAAGATTGTGGTTCATCGTGTG 58.533 43.478 0.00 0.00 0.00 3.82
89 90 3.401033 AGATTGTGGTTCATCGTGTGA 57.599 42.857 0.00 0.00 34.25 3.58
90 91 3.329386 AGATTGTGGTTCATCGTGTGAG 58.671 45.455 0.00 0.00 38.29 3.51
91 92 2.900716 TTGTGGTTCATCGTGTGAGA 57.099 45.000 0.00 0.00 38.29 3.27
92 93 2.438868 TGTGGTTCATCGTGTGAGAG 57.561 50.000 0.00 0.00 38.29 3.20
93 94 1.071605 GTGGTTCATCGTGTGAGAGC 58.928 55.000 0.00 0.00 38.29 4.09
94 95 0.969149 TGGTTCATCGTGTGAGAGCT 59.031 50.000 0.00 0.00 38.29 4.09
95 96 2.094700 GTGGTTCATCGTGTGAGAGCTA 60.095 50.000 0.00 0.00 38.29 3.32
96 97 2.760650 TGGTTCATCGTGTGAGAGCTAT 59.239 45.455 0.00 0.00 38.29 2.97
97 98 3.119291 GGTTCATCGTGTGAGAGCTATG 58.881 50.000 0.00 0.00 38.29 2.23
98 99 3.181486 GGTTCATCGTGTGAGAGCTATGA 60.181 47.826 0.00 0.00 38.29 2.15
99 100 3.699779 TCATCGTGTGAGAGCTATGAC 57.300 47.619 0.00 0.00 31.80 3.06
100 101 3.016736 TCATCGTGTGAGAGCTATGACA 58.983 45.455 0.00 0.00 31.80 3.58
101 102 2.921634 TCGTGTGAGAGCTATGACAC 57.078 50.000 19.46 19.46 36.23 3.67
103 104 1.272781 GTGTGAGAGCTATGACACGC 58.727 55.000 15.16 11.47 36.25 5.34
104 105 0.179163 TGTGAGAGCTATGACACGCG 60.179 55.000 3.53 3.53 36.25 6.01
105 106 1.226688 TGAGAGCTATGACACGCGC 60.227 57.895 5.73 0.00 0.00 6.86
106 107 1.226688 GAGAGCTATGACACGCGCA 60.227 57.895 5.73 0.00 0.00 6.09
107 108 0.802222 GAGAGCTATGACACGCGCAA 60.802 55.000 5.73 0.00 0.00 4.85
108 109 0.389817 AGAGCTATGACACGCGCAAA 60.390 50.000 5.73 0.00 0.00 3.68
109 110 0.442310 GAGCTATGACACGCGCAAAA 59.558 50.000 5.73 0.00 0.00 2.44
110 111 0.871722 AGCTATGACACGCGCAAAAA 59.128 45.000 5.73 0.00 0.00 1.94
190 193 8.632679 CCAAGTTTATTCATACATAAGCCACAT 58.367 33.333 0.00 0.00 0.00 3.21
252 256 3.712907 TGGCGCCCCTGACCTAAC 61.713 66.667 26.77 0.00 0.00 2.34
365 370 7.386059 TGAAGTATCTCTGAAACAATAGTGCA 58.614 34.615 0.00 0.00 0.00 4.57
507 512 0.249741 CCAAAGTCGTCGGGTCTTGT 60.250 55.000 0.00 0.00 0.00 3.16
527 532 2.299326 AGTCCCCGTACAACTAGTGT 57.701 50.000 0.00 0.00 44.82 3.55
560 565 6.213397 CCCATATAGTTACCATGGTCATCTCA 59.787 42.308 23.76 9.94 38.02 3.27
568 573 5.241403 ACCATGGTCATCTCAACAAACTA 57.759 39.130 13.00 0.00 0.00 2.24
583 588 2.095978 AACTACGGCTGCGACACCTT 62.096 55.000 0.00 0.00 0.00 3.50
629 635 4.142403 ACATGGATTTTTGCGTATCCTGTG 60.142 41.667 0.00 0.00 40.80 3.66
630 636 3.680490 TGGATTTTTGCGTATCCTGTGA 58.320 40.909 0.00 0.00 40.80 3.58
685 691 1.557443 GCTGCAGCGTTTGTACTCGT 61.557 55.000 25.23 0.00 0.00 4.18
687 693 0.942410 TGCAGCGTTTGTACTCGTCC 60.942 55.000 0.00 0.00 0.00 4.79
688 694 1.941476 GCAGCGTTTGTACTCGTCCG 61.941 60.000 0.00 0.00 0.00 4.79
697 703 3.647649 TACTCGTCCGCGACCTCGA 62.648 63.158 8.23 10.98 42.81 4.04
700 706 2.202570 CGTCCGCGACCTCGATTT 60.203 61.111 8.23 0.00 43.02 2.17
701 707 1.804326 CGTCCGCGACCTCGATTTT 60.804 57.895 8.23 0.00 43.02 1.82
757 763 2.330231 AACATATGTGTTGCACGTGC 57.670 45.000 33.11 33.11 46.43 5.34
772 778 5.127371 GCACGTGCATACTTACTAGTTTC 57.873 43.478 34.52 0.00 41.59 2.78
773 779 4.863131 GCACGTGCATACTTACTAGTTTCT 59.137 41.667 34.52 0.00 41.59 2.52
774 780 5.004535 GCACGTGCATACTTACTAGTTTCTC 59.995 44.000 34.52 0.00 41.59 2.87
775 781 5.515626 CACGTGCATACTTACTAGTTTCTCC 59.484 44.000 0.82 0.00 35.78 3.71
776 782 5.184479 ACGTGCATACTTACTAGTTTCTCCA 59.816 40.000 0.00 0.00 35.78 3.86
777 783 6.127423 ACGTGCATACTTACTAGTTTCTCCAT 60.127 38.462 0.00 0.00 35.78 3.41
778 784 7.067859 ACGTGCATACTTACTAGTTTCTCCATA 59.932 37.037 0.00 0.00 35.78 2.74
779 785 7.919091 CGTGCATACTTACTAGTTTCTCCATAA 59.081 37.037 0.00 0.00 35.78 1.90
780 786 9.250624 GTGCATACTTACTAGTTTCTCCATAAG 57.749 37.037 0.00 0.00 35.78 1.73
781 787 7.926555 TGCATACTTACTAGTTTCTCCATAAGC 59.073 37.037 0.00 0.00 35.78 3.09
782 788 8.145122 GCATACTTACTAGTTTCTCCATAAGCT 58.855 37.037 0.00 0.00 35.78 3.74
783 789 9.469807 CATACTTACTAGTTTCTCCATAAGCTG 57.530 37.037 0.00 0.00 35.78 4.24
784 790 6.342111 ACTTACTAGTTTCTCCATAAGCTGC 58.658 40.000 0.00 0.00 0.00 5.25
785 791 6.155393 ACTTACTAGTTTCTCCATAAGCTGCT 59.845 38.462 0.00 0.00 0.00 4.24
786 792 7.342284 ACTTACTAGTTTCTCCATAAGCTGCTA 59.658 37.037 0.90 0.00 0.00 3.49
787 793 6.155475 ACTAGTTTCTCCATAAGCTGCTAG 57.845 41.667 0.90 0.00 0.00 3.42
788 794 5.894393 ACTAGTTTCTCCATAAGCTGCTAGA 59.106 40.000 0.90 0.00 0.00 2.43
789 795 5.683876 AGTTTCTCCATAAGCTGCTAGAA 57.316 39.130 0.90 5.08 0.00 2.10
790 796 5.669477 AGTTTCTCCATAAGCTGCTAGAAG 58.331 41.667 0.90 0.00 31.16 2.85
791 797 3.742433 TCTCCATAAGCTGCTAGAAGC 57.258 47.619 15.63 15.63 43.88 3.86
792 798 2.366916 TCTCCATAAGCTGCTAGAAGCC 59.633 50.000 19.77 1.43 44.68 4.35
793 799 2.103771 CTCCATAAGCTGCTAGAAGCCA 59.896 50.000 19.77 8.12 44.68 4.75
794 800 2.158900 TCCATAAGCTGCTAGAAGCCAC 60.159 50.000 19.77 0.00 44.68 5.01
795 801 2.420547 CCATAAGCTGCTAGAAGCCACA 60.421 50.000 19.77 5.01 44.68 4.17
796 802 3.273434 CATAAGCTGCTAGAAGCCACAA 58.727 45.455 19.77 2.73 44.68 3.33
797 803 2.276732 AAGCTGCTAGAAGCCACAAA 57.723 45.000 19.77 0.00 44.68 2.83
798 804 2.276732 AGCTGCTAGAAGCCACAAAA 57.723 45.000 19.77 0.00 44.68 2.44
799 805 2.157738 AGCTGCTAGAAGCCACAAAAG 58.842 47.619 19.77 0.00 44.68 2.27
800 806 2.154462 GCTGCTAGAAGCCACAAAAGA 58.846 47.619 12.21 0.00 41.51 2.52
801 807 2.554032 GCTGCTAGAAGCCACAAAAGAA 59.446 45.455 12.21 0.00 41.51 2.52
802 808 3.610349 GCTGCTAGAAGCCACAAAAGAAC 60.610 47.826 12.21 0.00 41.51 3.01
803 809 3.817647 CTGCTAGAAGCCACAAAAGAACT 59.182 43.478 0.00 0.00 41.51 3.01
804 810 4.207165 TGCTAGAAGCCACAAAAGAACTT 58.793 39.130 0.00 0.00 41.51 2.66
805 811 4.644685 TGCTAGAAGCCACAAAAGAACTTT 59.355 37.500 0.00 0.00 41.51 2.66
806 812 5.127031 TGCTAGAAGCCACAAAAGAACTTTT 59.873 36.000 6.70 6.70 41.51 2.27
807 813 6.042777 GCTAGAAGCCACAAAAGAACTTTTT 58.957 36.000 9.42 0.95 36.60 1.94
914 920 0.898326 CCCACAAAAGGCCCACTACC 60.898 60.000 0.00 0.00 0.00 3.18
920 926 3.857521 AAGGCCCACTACCCCGTCA 62.858 63.158 0.00 0.00 0.00 4.35
921 927 3.324108 GGCCCACTACCCCGTCAA 61.324 66.667 0.00 0.00 0.00 3.18
933 948 1.816224 CCCCGTCAATCCGACAAAAAT 59.184 47.619 0.00 0.00 45.70 1.82
989 1019 3.008375 TCCTCCAGTCCAGATCAAAACAG 59.992 47.826 0.00 0.00 0.00 3.16
1012 1042 4.794439 CGAGCATGGCGTCGTCCA 62.794 66.667 10.19 10.19 40.97 4.02
1312 1351 1.283793 CGTCTTTGTTGCCTGCTGG 59.716 57.895 5.03 5.03 0.00 4.85
1316 1355 1.741327 CTTTGTTGCCTGCTGGTGCT 61.741 55.000 11.69 0.00 40.48 4.40
1344 2839 8.817100 TCACATTTCGTTTTGCTAGTATCATAG 58.183 33.333 0.00 0.00 0.00 2.23
1347 2842 7.534085 TTTCGTTTTGCTAGTATCATAGGTG 57.466 36.000 0.00 0.00 0.00 4.00
1351 2846 6.583562 GTTTTGCTAGTATCATAGGTGGTCT 58.416 40.000 0.00 0.00 0.00 3.85
1398 2900 1.680207 GGGAGAAAGATCATGCCTTGC 59.320 52.381 0.00 0.41 0.00 4.01
1496 3023 8.028354 TGTTTGTTTGTGATGCCTATTTAGATG 58.972 33.333 0.00 0.00 0.00 2.90
1507 3037 5.011635 TGCCTATTTAGATGCATACTCGGAA 59.988 40.000 0.00 0.00 0.00 4.30
1571 3102 4.302455 CTCTGATATTGCTACTTCCACCG 58.698 47.826 0.00 0.00 0.00 4.94
1631 3167 3.327757 TGTTGCTCCTTGTACTGATCCTT 59.672 43.478 0.00 0.00 0.00 3.36
1766 3322 1.305297 TGAGTCGGCTGATGGGTCT 60.305 57.895 0.00 0.00 0.00 3.85
1772 3328 1.452833 GGCTGATGGGTCTCAAGGC 60.453 63.158 0.00 0.00 0.00 4.35
1957 3513 9.508721 AAATTCCTAGTCTTCTAATCCTTAGGT 57.491 33.333 0.00 0.00 34.00 3.08
1962 3518 9.602568 CCTAGTCTTCTAATCCTTAGGTTTTTC 57.397 37.037 0.00 0.00 34.00 2.29
1980 3540 7.890127 AGGTTTTTCTTCTCATACAATCCATGA 59.110 33.333 0.00 0.00 0.00 3.07
2062 3639 1.605457 GCAAAGCAGGTAAACAAGCCC 60.605 52.381 0.00 0.00 0.00 5.19
2090 3667 3.202001 GCCGCATGCTCCGCTAAA 61.202 61.111 17.13 0.00 36.87 1.85
2140 3717 2.957402 AACAAGTCATCAGCCCAGAA 57.043 45.000 0.00 0.00 0.00 3.02
2163 3740 7.449704 AGAAAAATTACTCAGTCTTGCTCCATT 59.550 33.333 0.00 0.00 0.00 3.16
2177 3754 0.036765 TCCATTTCTTGGCGCGTAGT 60.037 50.000 8.43 0.00 46.01 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 8.506437 GTGATTCAAGAACAAACTCATGTCATA 58.494 33.333 0.00 0.00 31.81 2.15
7 8 7.013559 TGTGATTCAAGAACAAACTCATGTCAT 59.986 33.333 0.00 0.00 31.81 3.06
8 9 6.318396 TGTGATTCAAGAACAAACTCATGTCA 59.682 34.615 0.00 0.00 31.81 3.58
9 10 6.728200 TGTGATTCAAGAACAAACTCATGTC 58.272 36.000 0.00 0.00 31.81 3.06
10 11 6.698008 TGTGATTCAAGAACAAACTCATGT 57.302 33.333 0.00 0.00 34.24 3.21
11 12 9.850628 ATTATGTGATTCAAGAACAAACTCATG 57.149 29.630 0.00 0.00 0.00 3.07
51 52 9.586732 CCACAATCTTTCCCAATAATATAAGGA 57.413 33.333 0.00 0.00 0.00 3.36
52 53 9.367160 ACCACAATCTTTCCCAATAATATAAGG 57.633 33.333 0.00 0.00 0.00 2.69
55 56 9.928618 TGAACCACAATCTTTCCCAATAATATA 57.071 29.630 0.00 0.00 0.00 0.86
56 57 8.837099 TGAACCACAATCTTTCCCAATAATAT 57.163 30.769 0.00 0.00 0.00 1.28
57 58 8.837099 ATGAACCACAATCTTTCCCAATAATA 57.163 30.769 0.00 0.00 0.00 0.98
58 59 7.416664 CGATGAACCACAATCTTTCCCAATAAT 60.417 37.037 0.00 0.00 0.00 1.28
59 60 6.127758 CGATGAACCACAATCTTTCCCAATAA 60.128 38.462 0.00 0.00 0.00 1.40
60 61 5.356751 CGATGAACCACAATCTTTCCCAATA 59.643 40.000 0.00 0.00 0.00 1.90
61 62 4.158394 CGATGAACCACAATCTTTCCCAAT 59.842 41.667 0.00 0.00 0.00 3.16
62 63 3.505680 CGATGAACCACAATCTTTCCCAA 59.494 43.478 0.00 0.00 0.00 4.12
63 64 3.081061 CGATGAACCACAATCTTTCCCA 58.919 45.455 0.00 0.00 0.00 4.37
64 65 3.081804 ACGATGAACCACAATCTTTCCC 58.918 45.455 0.00 0.00 0.00 3.97
65 66 3.502211 ACACGATGAACCACAATCTTTCC 59.498 43.478 0.00 0.00 0.00 3.13
66 67 4.213270 TCACACGATGAACCACAATCTTTC 59.787 41.667 0.00 0.00 33.02 2.62
67 68 4.133820 TCACACGATGAACCACAATCTTT 58.866 39.130 0.00 0.00 33.02 2.52
68 69 3.738982 TCACACGATGAACCACAATCTT 58.261 40.909 0.00 0.00 33.02 2.40
69 70 3.006859 TCTCACACGATGAACCACAATCT 59.993 43.478 0.00 0.00 36.69 2.40
70 71 3.325870 TCTCACACGATGAACCACAATC 58.674 45.455 0.00 0.00 36.69 2.67
71 72 3.329386 CTCTCACACGATGAACCACAAT 58.671 45.455 0.00 0.00 36.69 2.71
72 73 2.754472 CTCTCACACGATGAACCACAA 58.246 47.619 0.00 0.00 36.69 3.33
73 74 1.605457 GCTCTCACACGATGAACCACA 60.605 52.381 0.00 0.00 36.69 4.17
74 75 1.071605 GCTCTCACACGATGAACCAC 58.928 55.000 0.00 0.00 36.69 4.16
75 76 0.969149 AGCTCTCACACGATGAACCA 59.031 50.000 0.00 0.00 36.69 3.67
76 77 2.941453 TAGCTCTCACACGATGAACC 57.059 50.000 0.00 0.00 36.69 3.62
77 78 3.794028 GTCATAGCTCTCACACGATGAAC 59.206 47.826 0.00 0.00 36.69 3.18
78 79 3.443681 TGTCATAGCTCTCACACGATGAA 59.556 43.478 0.00 0.00 36.69 2.57
79 80 3.016736 TGTCATAGCTCTCACACGATGA 58.983 45.455 0.00 0.00 35.45 2.92
80 81 3.111838 GTGTCATAGCTCTCACACGATG 58.888 50.000 0.00 0.00 30.49 3.84
81 82 3.428746 GTGTCATAGCTCTCACACGAT 57.571 47.619 0.00 0.00 30.49 3.73
82 83 2.921634 GTGTCATAGCTCTCACACGA 57.078 50.000 0.00 0.00 30.49 4.35
84 85 1.272781 GCGTGTCATAGCTCTCACAC 58.727 55.000 10.55 10.55 36.57 3.82
85 86 0.179163 CGCGTGTCATAGCTCTCACA 60.179 55.000 0.00 0.00 0.00 3.58
86 87 1.475441 GCGCGTGTCATAGCTCTCAC 61.475 60.000 8.43 0.00 0.00 3.51
87 88 1.226688 GCGCGTGTCATAGCTCTCA 60.227 57.895 8.43 0.00 0.00 3.27
88 89 0.802222 TTGCGCGTGTCATAGCTCTC 60.802 55.000 8.43 0.00 0.00 3.20
89 90 0.389817 TTTGCGCGTGTCATAGCTCT 60.390 50.000 8.43 0.00 0.00 4.09
90 91 0.442310 TTTTGCGCGTGTCATAGCTC 59.558 50.000 8.43 0.00 0.00 4.09
91 92 0.871722 TTTTTGCGCGTGTCATAGCT 59.128 45.000 8.43 0.00 0.00 3.32
92 93 3.376347 TTTTTGCGCGTGTCATAGC 57.624 47.368 8.43 0.00 0.00 2.97
158 161 9.184523 CTTATGTATGAATAAACTTGGTTCCCA 57.815 33.333 0.00 0.00 0.00 4.37
190 193 7.720957 CCATGATCCTTGATGTATTCCACTTTA 59.279 37.037 0.00 0.00 0.00 1.85
206 210 1.311059 GGCCAACCCCATGATCCTT 59.689 57.895 0.00 0.00 0.00 3.36
207 211 1.517538 TTGGCCAACCCCATGATCCT 61.518 55.000 16.05 0.00 34.21 3.24
252 256 1.144969 TAGCCAAGTTTGCTCGTTCG 58.855 50.000 4.45 0.00 40.23 3.95
365 370 6.486657 CCACAATTCTAATCGTGGGTGATATT 59.513 38.462 5.09 0.00 44.26 1.28
507 512 3.347216 GACACTAGTTGTACGGGGACTA 58.653 50.000 0.00 0.00 39.17 2.59
527 532 4.989277 TGGTAACTATATGGGTAGCTCGA 58.011 43.478 13.60 0.00 37.61 4.04
560 565 0.531090 TGTCGCAGCCGTAGTTTGTT 60.531 50.000 0.00 0.00 35.54 2.83
568 573 4.681978 GGAAGGTGTCGCAGCCGT 62.682 66.667 5.60 0.00 35.54 5.68
583 588 0.391661 CGCTAGGCTTTCAGCAAGGA 60.392 55.000 8.38 0.00 44.75 3.36
599 605 2.676076 GCAAAAATCCATGTTGACGCT 58.324 42.857 0.00 0.00 0.00 5.07
629 635 2.171489 GACGACAAAAGGCGCCACTC 62.171 60.000 31.54 13.52 0.00 3.51
630 636 2.203153 ACGACAAAAGGCGCCACT 60.203 55.556 31.54 13.00 0.00 4.00
752 758 5.184479 TGGAGAAACTAGTAAGTATGCACGT 59.816 40.000 0.00 0.00 33.75 4.49
753 759 5.647589 TGGAGAAACTAGTAAGTATGCACG 58.352 41.667 0.00 0.00 33.75 5.34
754 760 9.250624 CTTATGGAGAAACTAGTAAGTATGCAC 57.749 37.037 0.00 0.00 33.75 4.57
755 761 7.926555 GCTTATGGAGAAACTAGTAAGTATGCA 59.073 37.037 0.00 0.00 33.75 3.96
756 762 8.145122 AGCTTATGGAGAAACTAGTAAGTATGC 58.855 37.037 0.00 0.00 33.75 3.14
757 763 9.469807 CAGCTTATGGAGAAACTAGTAAGTATG 57.530 37.037 0.00 0.00 33.75 2.39
758 764 8.145122 GCAGCTTATGGAGAAACTAGTAAGTAT 58.855 37.037 0.00 0.00 33.75 2.12
759 765 7.342284 AGCAGCTTATGGAGAAACTAGTAAGTA 59.658 37.037 0.00 0.00 33.75 2.24
760 766 6.155393 AGCAGCTTATGGAGAAACTAGTAAGT 59.845 38.462 0.00 0.00 37.65 2.24
761 767 6.578023 AGCAGCTTATGGAGAAACTAGTAAG 58.422 40.000 0.00 0.00 0.00 2.34
762 768 6.546428 AGCAGCTTATGGAGAAACTAGTAA 57.454 37.500 0.00 0.00 0.00 2.24
763 769 7.061054 TCTAGCAGCTTATGGAGAAACTAGTA 58.939 38.462 0.00 0.00 0.00 1.82
764 770 5.894393 TCTAGCAGCTTATGGAGAAACTAGT 59.106 40.000 0.00 0.00 0.00 2.57
765 771 6.398234 TCTAGCAGCTTATGGAGAAACTAG 57.602 41.667 0.00 0.00 0.00 2.57
766 772 6.684111 GCTTCTAGCAGCTTATGGAGAAACTA 60.684 42.308 7.16 0.00 41.89 2.24
767 773 5.669477 CTTCTAGCAGCTTATGGAGAAACT 58.331 41.667 0.00 0.00 0.00 2.66
768 774 4.272261 GCTTCTAGCAGCTTATGGAGAAAC 59.728 45.833 7.16 0.00 41.89 2.78
769 775 4.446371 GCTTCTAGCAGCTTATGGAGAAA 58.554 43.478 7.16 0.00 41.89 2.52
770 776 3.181461 GGCTTCTAGCAGCTTATGGAGAA 60.181 47.826 14.16 1.96 44.75 2.87
771 777 2.366916 GGCTTCTAGCAGCTTATGGAGA 59.633 50.000 14.16 0.00 44.75 3.71
772 778 2.103771 TGGCTTCTAGCAGCTTATGGAG 59.896 50.000 14.16 0.00 44.75 3.86
773 779 2.118679 TGGCTTCTAGCAGCTTATGGA 58.881 47.619 14.16 0.00 44.75 3.41
774 780 2.216898 GTGGCTTCTAGCAGCTTATGG 58.783 52.381 14.16 0.00 44.75 2.74
775 781 2.910199 TGTGGCTTCTAGCAGCTTATG 58.090 47.619 14.16 0.00 44.75 1.90
776 782 3.634397 TTGTGGCTTCTAGCAGCTTAT 57.366 42.857 14.16 0.00 44.75 1.73
777 783 3.417069 TTTGTGGCTTCTAGCAGCTTA 57.583 42.857 14.16 1.36 44.75 3.09
778 784 2.276732 TTTGTGGCTTCTAGCAGCTT 57.723 45.000 14.16 0.00 44.75 3.74
779 785 2.157738 CTTTTGTGGCTTCTAGCAGCT 58.842 47.619 14.16 0.00 44.75 4.24
780 786 2.154462 TCTTTTGTGGCTTCTAGCAGC 58.846 47.619 5.74 5.74 44.75 5.25
781 787 3.817647 AGTTCTTTTGTGGCTTCTAGCAG 59.182 43.478 0.67 0.00 44.75 4.24
782 788 3.820557 AGTTCTTTTGTGGCTTCTAGCA 58.179 40.909 0.67 0.00 44.75 3.49
783 789 4.837896 AAGTTCTTTTGTGGCTTCTAGC 57.162 40.909 0.00 0.00 41.46 3.42
806 812 4.543590 TTTGTGGCTTTGTCTCCAAAAA 57.456 36.364 0.00 0.00 39.95 1.94
807 813 4.221703 TCTTTTGTGGCTTTGTCTCCAAAA 59.778 37.500 0.00 0.00 39.95 2.44
808 814 3.766591 TCTTTTGTGGCTTTGTCTCCAAA 59.233 39.130 0.00 0.00 38.22 3.28
809 815 3.360867 TCTTTTGTGGCTTTGTCTCCAA 58.639 40.909 0.00 0.00 33.57 3.53
810 816 3.011566 TCTTTTGTGGCTTTGTCTCCA 57.988 42.857 0.00 0.00 0.00 3.86
811 817 3.381590 AGTTCTTTTGTGGCTTTGTCTCC 59.618 43.478 0.00 0.00 0.00 3.71
812 818 4.354587 CAGTTCTTTTGTGGCTTTGTCTC 58.645 43.478 0.00 0.00 0.00 3.36
813 819 3.131046 CCAGTTCTTTTGTGGCTTTGTCT 59.869 43.478 0.00 0.00 0.00 3.41
814 820 3.447742 CCAGTTCTTTTGTGGCTTTGTC 58.552 45.455 0.00 0.00 0.00 3.18
815 821 3.525268 CCAGTTCTTTTGTGGCTTTGT 57.475 42.857 0.00 0.00 0.00 2.83
824 830 3.222603 AGTGTTAGGGCCAGTTCTTTTG 58.777 45.455 6.18 0.00 0.00 2.44
825 831 3.595190 AGTGTTAGGGCCAGTTCTTTT 57.405 42.857 6.18 0.00 0.00 2.27
1312 1351 2.216263 GCAAAACGAAATGTGACAGCAC 59.784 45.455 0.00 0.00 45.35 4.40
1316 1355 6.425417 TGATACTAGCAAAACGAAATGTGACA 59.575 34.615 0.00 0.00 0.00 3.58
1344 2839 8.697292 AGACTAGTGATAAAATTCTAGACCACC 58.303 37.037 0.00 0.00 35.34 4.61
1398 2900 1.445754 CGAGCAGGAGCAGTCACAG 60.446 63.158 0.00 0.00 45.49 3.66
1496 3023 7.331934 ACAATCATGTATGTATTCCGAGTATGC 59.668 37.037 4.66 0.00 38.24 3.14
1507 3037 6.016024 GGGCATTGTGACAATCATGTATGTAT 60.016 38.462 8.03 0.00 40.74 2.29
1571 3102 2.172717 TCCCTAACCTGCTAATTCTGGC 59.827 50.000 0.00 0.00 0.00 4.85
1631 3167 5.282510 CAACGCCTTGTTTTGGTTATTACA 58.717 37.500 0.00 0.00 39.29 2.41
1649 3185 1.953559 TCATGGGATAAGAGCAACGC 58.046 50.000 0.00 0.00 0.00 4.84
1848 3404 6.642733 AGGATTTCCTCCAAAATAGAGTGA 57.357 37.500 0.00 0.00 44.77 3.41
1980 3540 5.623956 TGATAGTGTAACCCGATCCATTT 57.376 39.130 0.00 0.00 37.80 2.32
1994 3554 9.739276 TCTGTTCCATTATCTTTTTGATAGTGT 57.261 29.630 0.00 0.00 41.17 3.55
2062 3639 1.156645 GCATGCGGCAGGAGAGTTAG 61.157 60.000 19.93 0.00 43.97 2.34
2140 3717 7.449704 AGAAATGGAGCAAGACTGAGTAATTTT 59.550 33.333 0.00 0.00 0.00 1.82
2163 3740 1.144969 CAGAAACTACGCGCCAAGAA 58.855 50.000 5.73 0.00 0.00 2.52
2177 3754 6.983984 TCAAACAATGAAGATGATGCAGAAA 58.016 32.000 0.00 0.00 34.30 2.52


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

AutoCloner maintained by Alex Coulton.