Multiple sequence alignment - TraesCS3A01G162500

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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 TraesCS3A01G162500 chr3A 100.000 2550 0 0 1 2550 164804014 164801465 0.000000e+00 4710
1 TraesCS3A01G162500 chr2D 94.299 1947 94 12 615 2550 16065485 16067425 0.000000e+00 2964
2 TraesCS3A01G162500 chr2D 92.928 1923 100 11 660 2550 636788883 636786965 0.000000e+00 2765
3 TraesCS3A01G162500 chr2D 92.562 363 26 1 608 970 498471651 498471290 1.050000e-143 520
4 TraesCS3A01G162500 chr2D 91.268 355 27 1 616 970 547242743 547242393 4.930000e-132 481
5 TraesCS3A01G162500 chr2D 92.174 115 7 2 1 113 546926766 546926880 7.300000e-36 161
6 TraesCS3A01G162500 chr4D 93.422 1961 97 15 616 2550 459886443 459884489 0.000000e+00 2878
7 TraesCS3A01G162500 chr4D 95.556 1620 59 8 941 2550 43272394 43270778 0.000000e+00 2580
8 TraesCS3A01G162500 chr4D 85.686 503 70 1 113 615 302941088 302940588 1.740000e-146 529
9 TraesCS3A01G162500 chr4D 85.887 496 67 2 113 606 161249658 161250152 2.250000e-145 525
10 TraesCS3A01G162500 chr7D 93.388 1966 89 15 616 2550 94497477 94495522 0.000000e+00 2872
11 TraesCS3A01G162500 chr7D 92.982 114 5 2 2 112 413128157 413128270 2.030000e-36 163
12 TraesCS3A01G162500 chr3B 92.835 1968 104 14 615 2550 599079412 599077450 0.000000e+00 2819
13 TraesCS3A01G162500 chr4A 92.413 1964 117 13 616 2550 724524709 724522749 0.000000e+00 2772
14 TraesCS3A01G162500 chr4A 87.352 506 60 3 113 615 383041353 383040849 6.120000e-161 577
15 TraesCS3A01G162500 chr4A 87.726 497 58 2 113 609 410878556 410879049 6.120000e-161 577
16 TraesCS3A01G162500 chr4A 87.575 499 56 5 113 609 410945802 410946296 7.910000e-160 573
17 TraesCS3A01G162500 chr4A 85.968 506 64 3 113 615 188778172 188777671 3.730000e-148 534
18 TraesCS3A01G162500 chr1B 91.896 1962 127 13 613 2550 641549870 641547917 0.000000e+00 2713
19 TraesCS3A01G162500 chr5D 93.275 1710 93 11 608 2297 357075975 357074268 0.000000e+00 2501
20 TraesCS3A01G162500 chr5D 93.860 114 5 1 1 112 350356363 350356250 1.210000e-38 171
21 TraesCS3A01G162500 chr5D 93.043 115 5 2 1 112 370435241 370435355 5.640000e-37 165
22 TraesCS3A01G162500 chr5A 86.733 505 64 2 113 615 210828311 210827808 2.220000e-155 558
23 TraesCS3A01G162500 chr5B 87.221 493 51 9 616 1098 18695162 18694672 3.710000e-153 551
24 TraesCS3A01G162500 chr2A 87.216 485 58 2 113 595 235261621 235261139 1.330000e-152 549
25 TraesCS3A01G162500 chr2A 90.191 367 33 2 605 970 233255250 233255614 2.300000e-130 475
26 TraesCS3A01G162500 chr2A 90.000 360 34 2 612 970 611725139 611724781 4.970000e-127 464
27 TraesCS3A01G162500 chr2A 89.344 366 36 3 607 970 6302720 6302356 8.320000e-125 457
28 TraesCS3A01G162500 chr2A 93.860 114 5 1 1 112 182326085 182325972 1.210000e-38 171
29 TraesCS3A01G162500 chr6A 85.714 497 70 1 113 609 390571363 390571858 8.080000e-145 523
30 TraesCS3A01G162500 chr1D 91.597 357 28 1 616 970 17040736 17040380 2.280000e-135 492
31 TraesCS3A01G162500 chr1D 92.308 117 7 2 1 115 286823692 286823576 5.640000e-37 165
32 TraesCS3A01G162500 chr3D 93.043 115 5 2 1 112 525444220 525444106 5.640000e-37 165
33 TraesCS3A01G162500 chr3D 91.597 119 6 3 1 115 511716781 511716899 7.300000e-36 161
34 TraesCS3A01G162500 chr1A 89.844 128 6 5 1 124 452420325 452420449 9.440000e-35 158


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 TraesCS3A01G162500 chr3A 164801465 164804014 2549 True 4710 4710 100.000 1 2550 1 chr3A.!!$R1 2549
1 TraesCS3A01G162500 chr2D 16065485 16067425 1940 False 2964 2964 94.299 615 2550 1 chr2D.!!$F1 1935
2 TraesCS3A01G162500 chr2D 636786965 636788883 1918 True 2765 2765 92.928 660 2550 1 chr2D.!!$R3 1890
3 TraesCS3A01G162500 chr4D 459884489 459886443 1954 True 2878 2878 93.422 616 2550 1 chr4D.!!$R3 1934
4 TraesCS3A01G162500 chr4D 43270778 43272394 1616 True 2580 2580 95.556 941 2550 1 chr4D.!!$R1 1609
5 TraesCS3A01G162500 chr4D 302940588 302941088 500 True 529 529 85.686 113 615 1 chr4D.!!$R2 502
6 TraesCS3A01G162500 chr7D 94495522 94497477 1955 True 2872 2872 93.388 616 2550 1 chr7D.!!$R1 1934
7 TraesCS3A01G162500 chr3B 599077450 599079412 1962 True 2819 2819 92.835 615 2550 1 chr3B.!!$R1 1935
8 TraesCS3A01G162500 chr4A 724522749 724524709 1960 True 2772 2772 92.413 616 2550 1 chr4A.!!$R3 1934
9 TraesCS3A01G162500 chr4A 383040849 383041353 504 True 577 577 87.352 113 615 1 chr4A.!!$R2 502
10 TraesCS3A01G162500 chr4A 188777671 188778172 501 True 534 534 85.968 113 615 1 chr4A.!!$R1 502
11 TraesCS3A01G162500 chr1B 641547917 641549870 1953 True 2713 2713 91.896 613 2550 1 chr1B.!!$R1 1937
12 TraesCS3A01G162500 chr5D 357074268 357075975 1707 True 2501 2501 93.275 608 2297 1 chr5D.!!$R2 1689
13 TraesCS3A01G162500 chr5A 210827808 210828311 503 True 558 558 86.733 113 615 1 chr5A.!!$R1 502

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
45 46 0.178958 ACACACTCTCCCCTCTCGTT 60.179 55.0 0.0 0.0 0.0 3.85 F
703 707 0.323629 CAGTTTTGCCCCTAGTCCGA 59.676 55.0 0.0 0.0 0.0 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1022 1061 0.036952 CTCTGCATTCCACGAGGTGT 60.037 55.0 0.0 0.0 35.89 4.16 R
1767 1822 0.173481 CTGCACTTGGCTCTACGCTA 59.827 55.0 0.0 0.0 45.15 4.26 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
25 26 2.101700 GGTCTACGAGGGTACGTGG 58.898 63.158 0.00 0.00 46.02 4.94
27 28 3.159298 TCTACGAGGGTACGTGGAC 57.841 57.895 0.00 0.00 45.53 4.02
28 29 0.324614 TCTACGAGGGTACGTGGACA 59.675 55.000 0.00 0.00 45.53 4.02
29 30 0.449388 CTACGAGGGTACGTGGACAC 59.551 60.000 0.00 0.00 44.98 3.67
30 31 0.250684 TACGAGGGTACGTGGACACA 60.251 55.000 0.00 0.00 46.02 3.72
31 32 1.080974 CGAGGGTACGTGGACACAC 60.081 63.158 0.00 0.00 44.23 3.82
32 33 1.521450 CGAGGGTACGTGGACACACT 61.521 60.000 0.00 0.00 45.50 3.55
33 34 0.243095 GAGGGTACGTGGACACACTC 59.757 60.000 2.84 2.84 45.50 3.51
34 35 0.178970 AGGGTACGTGGACACACTCT 60.179 55.000 0.00 0.00 45.50 3.24
35 36 0.243095 GGGTACGTGGACACACTCTC 59.757 60.000 0.00 0.00 45.50 3.20
36 37 0.243095 GGTACGTGGACACACTCTCC 59.757 60.000 0.00 0.00 45.50 3.71
37 38 0.243095 GTACGTGGACACACTCTCCC 59.757 60.000 0.00 0.00 45.50 4.30
38 39 0.896940 TACGTGGACACACTCTCCCC 60.897 60.000 0.00 0.00 45.50 4.81
39 40 1.908793 CGTGGACACACTCTCCCCT 60.909 63.158 3.12 0.00 45.50 4.79
40 41 1.878656 CGTGGACACACTCTCCCCTC 61.879 65.000 3.12 0.00 45.50 4.30
41 42 0.543174 GTGGACACACTCTCCCCTCT 60.543 60.000 0.00 0.00 44.29 3.69
42 43 0.251832 TGGACACACTCTCCCCTCTC 60.252 60.000 0.00 0.00 0.00 3.20
43 44 1.316706 GGACACACTCTCCCCTCTCG 61.317 65.000 0.00 0.00 0.00 4.04
44 45 0.609681 GACACACTCTCCCCTCTCGT 60.610 60.000 0.00 0.00 0.00 4.18
45 46 0.178958 ACACACTCTCCCCTCTCGTT 60.179 55.000 0.00 0.00 0.00 3.85
46 47 0.969894 CACACTCTCCCCTCTCGTTT 59.030 55.000 0.00 0.00 0.00 3.60
47 48 1.067495 CACACTCTCCCCTCTCGTTTC 60.067 57.143 0.00 0.00 0.00 2.78
48 49 1.203075 ACACTCTCCCCTCTCGTTTCT 60.203 52.381 0.00 0.00 0.00 2.52
49 50 2.041350 ACACTCTCCCCTCTCGTTTCTA 59.959 50.000 0.00 0.00 0.00 2.10
50 51 3.292460 CACTCTCCCCTCTCGTTTCTAT 58.708 50.000 0.00 0.00 0.00 1.98
51 52 3.067461 CACTCTCCCCTCTCGTTTCTATG 59.933 52.174 0.00 0.00 0.00 2.23
52 53 2.032620 TCTCCCCTCTCGTTTCTATGC 58.967 52.381 0.00 0.00 0.00 3.14
53 54 1.757118 CTCCCCTCTCGTTTCTATGCA 59.243 52.381 0.00 0.00 0.00 3.96
54 55 2.366916 CTCCCCTCTCGTTTCTATGCAT 59.633 50.000 3.79 3.79 0.00 3.96
55 56 2.365617 TCCCCTCTCGTTTCTATGCATC 59.634 50.000 0.19 0.00 0.00 3.91
56 57 2.103094 CCCCTCTCGTTTCTATGCATCA 59.897 50.000 0.19 0.00 0.00 3.07
57 58 3.126831 CCCTCTCGTTTCTATGCATCAC 58.873 50.000 0.19 0.00 0.00 3.06
58 59 3.126831 CCTCTCGTTTCTATGCATCACC 58.873 50.000 0.19 0.00 0.00 4.02
59 60 3.181471 CCTCTCGTTTCTATGCATCACCT 60.181 47.826 0.19 0.00 0.00 4.00
60 61 4.038042 CCTCTCGTTTCTATGCATCACCTA 59.962 45.833 0.19 0.00 0.00 3.08
61 62 5.188327 TCTCGTTTCTATGCATCACCTAG 57.812 43.478 0.19 0.00 0.00 3.02
62 63 4.887655 TCTCGTTTCTATGCATCACCTAGA 59.112 41.667 0.19 0.00 0.00 2.43
63 64 5.536538 TCTCGTTTCTATGCATCACCTAGAT 59.463 40.000 0.19 0.00 37.48 1.98
75 76 4.743057 TCACCTAGATGGATCTTGTGTG 57.257 45.455 14.05 12.24 38.51 3.82
76 77 4.096681 TCACCTAGATGGATCTTGTGTGT 58.903 43.478 14.05 0.00 38.51 3.72
77 78 4.081476 TCACCTAGATGGATCTTGTGTGTG 60.081 45.833 14.05 8.27 38.51 3.82
78 79 3.840666 ACCTAGATGGATCTTGTGTGTGT 59.159 43.478 0.00 0.00 38.32 3.72
79 80 5.023452 ACCTAGATGGATCTTGTGTGTGTA 58.977 41.667 0.00 0.00 38.32 2.90
80 81 5.663106 ACCTAGATGGATCTTGTGTGTGTAT 59.337 40.000 0.00 0.00 38.32 2.29
81 82 5.987953 CCTAGATGGATCTTGTGTGTGTATG 59.012 44.000 0.00 0.00 38.32 2.39
82 83 4.194640 AGATGGATCTTGTGTGTGTATGC 58.805 43.478 0.00 0.00 31.97 3.14
83 84 3.415457 TGGATCTTGTGTGTGTATGCA 57.585 42.857 0.00 0.00 0.00 3.96
84 85 3.749226 TGGATCTTGTGTGTGTATGCAA 58.251 40.909 0.00 0.00 0.00 4.08
85 86 4.140536 TGGATCTTGTGTGTGTATGCAAA 58.859 39.130 0.00 0.00 0.00 3.68
86 87 4.766373 TGGATCTTGTGTGTGTATGCAAAT 59.234 37.500 0.00 0.00 0.00 2.32
87 88 5.243507 TGGATCTTGTGTGTGTATGCAAATT 59.756 36.000 0.00 0.00 0.00 1.82
88 89 6.158598 GGATCTTGTGTGTGTATGCAAATTT 58.841 36.000 0.00 0.00 0.00 1.82
89 90 6.646240 GGATCTTGTGTGTGTATGCAAATTTT 59.354 34.615 0.00 0.00 0.00 1.82
90 91 7.171337 GGATCTTGTGTGTGTATGCAAATTTTT 59.829 33.333 0.00 0.00 0.00 1.94
91 92 7.231705 TCTTGTGTGTGTATGCAAATTTTTG 57.768 32.000 0.00 0.00 41.03 2.44
92 93 7.038048 TCTTGTGTGTGTATGCAAATTTTTGA 58.962 30.769 7.21 0.00 40.55 2.69
93 94 7.547019 TCTTGTGTGTGTATGCAAATTTTTGAA 59.453 29.630 7.21 0.00 40.55 2.69
94 95 7.601073 TGTGTGTGTATGCAAATTTTTGAAA 57.399 28.000 7.21 0.00 40.55 2.69
95 96 8.206325 TGTGTGTGTATGCAAATTTTTGAAAT 57.794 26.923 7.21 2.85 40.55 2.17
96 97 9.317936 TGTGTGTGTATGCAAATTTTTGAAATA 57.682 25.926 7.21 2.01 40.55 1.40
97 98 9.579610 GTGTGTGTATGCAAATTTTTGAAATAC 57.420 29.630 7.21 12.43 40.55 1.89
98 99 9.539825 TGTGTGTATGCAAATTTTTGAAATACT 57.460 25.926 19.25 0.00 40.55 2.12
102 103 9.900710 TGTATGCAAATTTTTGAAATACTACGT 57.099 25.926 19.25 0.00 40.55 3.57
106 107 8.756864 TGCAAATTTTTGAAATACTACGTTTCC 58.243 29.630 7.21 0.00 40.55 3.13
107 108 8.218441 GCAAATTTTTGAAATACTACGTTTCCC 58.782 33.333 7.21 0.00 40.55 3.97
108 109 9.250624 CAAATTTTTGAAATACTACGTTTCCCA 57.749 29.630 0.00 0.00 40.55 4.37
109 110 9.819267 AAATTTTTGAAATACTACGTTTCCCAA 57.181 25.926 0.00 0.00 35.28 4.12
110 111 8.806177 ATTTTTGAAATACTACGTTTCCCAAC 57.194 30.769 0.00 0.00 35.28 3.77
111 112 6.939132 TTTGAAATACTACGTTTCCCAACA 57.061 33.333 0.00 0.00 35.28 3.33
121 122 4.011698 ACGTTTCCCAACACATATAACCC 58.988 43.478 0.00 0.00 32.54 4.11
140 141 5.041191 ACCCCTAGATCAATGACATTCAC 57.959 43.478 0.00 0.00 0.00 3.18
185 186 5.690464 ACAGATTCTCAGGCTTAGTGAAT 57.310 39.130 2.81 2.81 33.39 2.57
200 201 4.826274 AGTGAATAACAGAGCAAGGCTA 57.174 40.909 0.00 0.00 39.88 3.93
208 209 2.887152 ACAGAGCAAGGCTAAAAACAGG 59.113 45.455 0.00 0.00 39.88 4.00
209 210 2.229784 CAGAGCAAGGCTAAAAACAGGG 59.770 50.000 0.00 0.00 39.88 4.45
218 219 4.016444 GGCTAAAAACAGGGTCATGATGA 58.984 43.478 0.00 0.00 0.00 2.92
264 265 4.299586 TGCTACAGGAACATTTCATGGA 57.700 40.909 5.64 0.00 45.11 3.41
276 277 5.240121 ACATTTCATGGAATCAAAAGGCAC 58.760 37.500 0.00 0.00 33.60 5.01
310 311 5.574891 ACATGTCAAGCACTACAAAACAA 57.425 34.783 0.00 0.00 0.00 2.83
318 319 6.989759 TCAAGCACTACAAAACAAGATCACTA 59.010 34.615 0.00 0.00 0.00 2.74
344 345 5.105675 GCTACTGCTAGAAACCACTAGAACT 60.106 44.000 0.00 0.00 41.42 3.01
368 369 3.863424 GCTCAAAACATCATGGCAAGATG 59.137 43.478 26.19 26.19 46.38 2.90
417 421 7.014230 ACAGTGAAATAAACTAAACATGGCAGT 59.986 33.333 0.00 0.00 0.00 4.40
477 481 7.315142 CAACTCAACACAAAGCATATAATGGT 58.685 34.615 0.00 0.00 43.93 3.55
480 484 9.189156 ACTCAACACAAAGCATATAATGGTATT 57.811 29.630 0.00 0.00 40.65 1.89
557 561 4.623932 TGGTCATAGGATGCATAGAACC 57.376 45.455 0.00 2.79 0.00 3.62
580 584 5.652014 CCCTAGCTATTCACATGGAAAAACA 59.348 40.000 0.00 0.00 39.39 2.83
627 631 8.821686 ACAGAAATGTTATGGGTTAATCATCA 57.178 30.769 0.00 0.00 0.00 3.07
640 644 3.814005 AATCATCATTTTGCCCTCAGC 57.186 42.857 0.00 0.00 44.14 4.26
658 662 1.742880 CGGTGTCCATGTGCTCAGG 60.743 63.158 0.00 0.00 0.00 3.86
703 707 0.323629 CAGTTTTGCCCCTAGTCCGA 59.676 55.000 0.00 0.00 0.00 4.55
788 792 4.351054 GTGGGACCAGGTGGCAGG 62.351 72.222 0.00 0.00 39.32 4.85
810 814 4.941873 GGGACGACCAATTTTATTCAGACT 59.058 41.667 6.20 0.00 39.85 3.24
819 823 5.689383 ATTTTATTCAGACTGTTGCACGT 57.311 34.783 1.59 0.00 0.00 4.49
837 841 2.197324 GTGGCTTGTGGGACCCAA 59.803 61.111 16.98 0.00 34.18 4.12
852 871 0.609957 CCCAACAGAGAGCCATTGCA 60.610 55.000 0.00 0.00 41.13 4.08
877 900 3.639561 TGTGCTATATAAGAGGGCGACAA 59.360 43.478 0.00 0.00 0.00 3.18
881 904 1.766494 TATAAGAGGGCGACAACGGA 58.234 50.000 0.00 0.00 40.15 4.69
937 976 1.029408 GGCGAGAGAGAGAGAGCACA 61.029 60.000 0.00 0.00 0.00 4.57
939 978 1.737838 CGAGAGAGAGAGAGCACAGT 58.262 55.000 0.00 0.00 0.00 3.55
1020 1059 0.832135 TGTCTTCCTCAAGCTCCCGT 60.832 55.000 0.00 0.00 0.00 5.28
1022 1061 0.541998 TCTTCCTCAAGCTCCCGTGA 60.542 55.000 0.00 0.00 0.00 4.35
1030 1069 3.681835 GCTCCCGTGACACCTCGT 61.682 66.667 0.00 0.00 0.00 4.18
1033 1072 3.299977 CCCGTGACACCTCGTGGA 61.300 66.667 11.17 0.00 37.94 4.02
1106 1145 3.508840 CGGGCGTTGATTGGAGGC 61.509 66.667 0.00 0.00 0.00 4.70
1210 1249 2.466846 TCATGGTCGGGATCTTTGAGA 58.533 47.619 0.00 0.00 0.00 3.27
1264 1303 3.960102 TGACATGCTTCTTTCTTTGGGTT 59.040 39.130 0.00 0.00 0.00 4.11
1281 1320 0.807496 GTTGATGCTCTGGCCAAGAC 59.193 55.000 7.01 0.00 37.74 3.01
1282 1321 0.694771 TTGATGCTCTGGCCAAGACT 59.305 50.000 7.01 0.00 37.74 3.24
1340 1381 3.422303 GCATGCTGCCACGAACGA 61.422 61.111 11.37 0.00 37.42 3.85
1398 1439 3.112075 CGAAGCACGCACGGACAT 61.112 61.111 0.00 0.00 34.51 3.06
1481 1522 3.824443 ACTACCAGTACCCATTTGCAAAC 59.176 43.478 15.41 0.66 0.00 2.93
1767 1822 1.941377 TGCTCTTGGGCCAAATTCAT 58.059 45.000 21.28 0.00 0.00 2.57
1914 1971 7.721402 TGCTGAAACTTTTTATGGAAGCTAAA 58.279 30.769 0.00 0.00 0.00 1.85
2055 2114 1.999648 TGGAAAATGTGCCTCAGCTT 58.000 45.000 0.00 0.00 40.80 3.74
2056 2115 3.153369 TGGAAAATGTGCCTCAGCTTA 57.847 42.857 0.00 0.00 40.80 3.09
2187 2252 1.352622 TGTGGCTGGGGACTTGAACT 61.353 55.000 0.00 0.00 0.00 3.01
2439 2506 6.348786 CCACATGATTTTGGTTAGAGTGACAG 60.349 42.308 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.226603 CCCTCGTAGACCGAAAGCG 60.227 63.158 0.00 0.00 46.75 4.68
1 2 1.098050 TACCCTCGTAGACCGAAAGC 58.902 55.000 0.00 0.00 46.75 3.51
2 3 1.063174 CGTACCCTCGTAGACCGAAAG 59.937 57.143 0.00 0.00 46.75 2.62
6 7 1.709147 CCACGTACCCTCGTAGACCG 61.709 65.000 0.00 0.00 42.27 4.79
7 8 0.392998 TCCACGTACCCTCGTAGACC 60.393 60.000 0.00 0.00 42.27 3.85
8 9 0.729690 GTCCACGTACCCTCGTAGAC 59.270 60.000 0.00 2.79 42.50 2.59
9 10 0.324614 TGTCCACGTACCCTCGTAGA 59.675 55.000 0.00 0.00 42.27 2.59
10 11 0.449388 GTGTCCACGTACCCTCGTAG 59.551 60.000 0.00 0.00 42.27 3.51
11 12 0.250684 TGTGTCCACGTACCCTCGTA 60.251 55.000 0.00 0.00 42.27 3.43
12 13 1.529010 TGTGTCCACGTACCCTCGT 60.529 57.895 0.00 0.00 45.10 4.18
13 14 1.080974 GTGTGTCCACGTACCCTCG 60.081 63.158 0.00 0.00 0.00 4.63
14 15 0.243095 GAGTGTGTCCACGTACCCTC 59.757 60.000 0.00 0.00 46.56 4.30
15 16 0.178970 AGAGTGTGTCCACGTACCCT 60.179 55.000 0.00 0.00 46.56 4.34
16 17 0.243095 GAGAGTGTGTCCACGTACCC 59.757 60.000 0.00 0.00 46.56 3.69
17 18 0.243095 GGAGAGTGTGTCCACGTACC 59.757 60.000 0.00 0.00 46.56 3.34
18 19 0.243095 GGGAGAGTGTGTCCACGTAC 59.757 60.000 0.00 0.00 46.56 3.67
19 20 0.896940 GGGGAGAGTGTGTCCACGTA 60.897 60.000 0.00 0.00 46.56 3.57
20 21 2.207924 GGGGAGAGTGTGTCCACGT 61.208 63.158 0.00 0.00 46.56 4.49
21 22 1.878656 GAGGGGAGAGTGTGTCCACG 61.879 65.000 0.00 0.00 46.56 4.94
22 23 0.543174 AGAGGGGAGAGTGTGTCCAC 60.543 60.000 0.00 0.00 42.17 4.02
23 24 0.251832 GAGAGGGGAGAGTGTGTCCA 60.252 60.000 0.00 0.00 35.57 4.02
24 25 1.316706 CGAGAGGGGAGAGTGTGTCC 61.317 65.000 0.00 0.00 0.00 4.02
25 26 0.609681 ACGAGAGGGGAGAGTGTGTC 60.610 60.000 0.00 0.00 0.00 3.67
26 27 0.178958 AACGAGAGGGGAGAGTGTGT 60.179 55.000 0.00 0.00 0.00 3.72
27 28 0.969894 AAACGAGAGGGGAGAGTGTG 59.030 55.000 0.00 0.00 0.00 3.82
28 29 1.203075 AGAAACGAGAGGGGAGAGTGT 60.203 52.381 0.00 0.00 0.00 3.55
29 30 1.551452 AGAAACGAGAGGGGAGAGTG 58.449 55.000 0.00 0.00 0.00 3.51
30 31 3.292460 CATAGAAACGAGAGGGGAGAGT 58.708 50.000 0.00 0.00 0.00 3.24
31 32 2.035321 GCATAGAAACGAGAGGGGAGAG 59.965 54.545 0.00 0.00 0.00 3.20
32 33 2.032620 GCATAGAAACGAGAGGGGAGA 58.967 52.381 0.00 0.00 0.00 3.71
33 34 1.757118 TGCATAGAAACGAGAGGGGAG 59.243 52.381 0.00 0.00 0.00 4.30
34 35 1.860641 TGCATAGAAACGAGAGGGGA 58.139 50.000 0.00 0.00 0.00 4.81
35 36 2.103094 TGATGCATAGAAACGAGAGGGG 59.897 50.000 0.00 0.00 0.00 4.79
36 37 3.126831 GTGATGCATAGAAACGAGAGGG 58.873 50.000 0.00 0.00 0.00 4.30
37 38 3.126831 GGTGATGCATAGAAACGAGAGG 58.873 50.000 0.00 0.00 0.00 3.69
38 39 4.052159 AGGTGATGCATAGAAACGAGAG 57.948 45.455 0.00 0.00 0.00 3.20
39 40 4.887655 TCTAGGTGATGCATAGAAACGAGA 59.112 41.667 0.00 0.00 37.52 4.04
40 41 5.188327 TCTAGGTGATGCATAGAAACGAG 57.812 43.478 0.00 0.00 37.52 4.18
41 42 5.532557 CATCTAGGTGATGCATAGAAACGA 58.467 41.667 0.00 0.00 44.96 3.85
42 43 5.835911 CATCTAGGTGATGCATAGAAACG 57.164 43.478 0.00 0.00 44.96 3.60
53 54 4.718774 ACACACAAGATCCATCTAGGTGAT 59.281 41.667 20.14 0.00 41.24 3.06
54 55 4.081476 CACACACAAGATCCATCTAGGTGA 60.081 45.833 20.14 0.00 41.24 4.02
55 56 4.186926 CACACACAAGATCCATCTAGGTG 58.813 47.826 14.98 14.98 42.86 4.00
56 57 3.840666 ACACACACAAGATCCATCTAGGT 59.159 43.478 0.00 0.00 35.76 3.08
57 58 4.478206 ACACACACAAGATCCATCTAGG 57.522 45.455 0.00 0.00 35.76 3.02
58 59 5.464722 GCATACACACACAAGATCCATCTAG 59.535 44.000 0.00 0.00 35.76 2.43
59 60 5.104982 TGCATACACACACAAGATCCATCTA 60.105 40.000 0.00 0.00 35.76 1.98
60 61 4.194640 GCATACACACACAAGATCCATCT 58.805 43.478 0.00 0.00 39.22 2.90
61 62 3.940852 TGCATACACACACAAGATCCATC 59.059 43.478 0.00 0.00 0.00 3.51
62 63 3.954200 TGCATACACACACAAGATCCAT 58.046 40.909 0.00 0.00 0.00 3.41
63 64 3.415457 TGCATACACACACAAGATCCA 57.585 42.857 0.00 0.00 0.00 3.41
64 65 4.764679 TTTGCATACACACACAAGATCC 57.235 40.909 0.00 0.00 0.00 3.36
65 66 7.642071 AAAATTTGCATACACACACAAGATC 57.358 32.000 0.00 0.00 0.00 2.75
66 67 7.710044 TCAAAAATTTGCATACACACACAAGAT 59.290 29.630 0.98 0.00 38.05 2.40
67 68 7.038048 TCAAAAATTTGCATACACACACAAGA 58.962 30.769 0.98 0.00 38.05 3.02
68 69 7.231705 TCAAAAATTTGCATACACACACAAG 57.768 32.000 0.98 0.00 38.05 3.16
69 70 7.601073 TTCAAAAATTTGCATACACACACAA 57.399 28.000 0.98 0.00 38.05 3.33
70 71 7.601073 TTTCAAAAATTTGCATACACACACA 57.399 28.000 0.98 0.00 38.05 3.72
71 72 9.579610 GTATTTCAAAAATTTGCATACACACAC 57.420 29.630 15.78 0.63 38.05 3.82
72 73 9.539825 AGTATTTCAAAAATTTGCATACACACA 57.460 25.926 19.41 0.00 36.97 3.72
76 77 9.900710 ACGTAGTATTTCAAAAATTTGCATACA 57.099 25.926 19.41 10.21 41.94 2.29
80 81 8.756864 GGAAACGTAGTATTTCAAAAATTTGCA 58.243 29.630 0.98 0.00 45.00 4.08
81 82 8.218441 GGGAAACGTAGTATTTCAAAAATTTGC 58.782 33.333 0.98 0.00 45.00 3.68
82 83 9.250624 TGGGAAACGTAGTATTTCAAAAATTTG 57.749 29.630 0.00 0.00 45.00 2.32
83 84 9.819267 TTGGGAAACGTAGTATTTCAAAAATTT 57.181 25.926 0.00 0.00 45.00 1.82
84 85 9.251792 GTTGGGAAACGTAGTATTTCAAAAATT 57.748 29.630 0.00 0.00 45.00 1.82
85 86 8.414778 TGTTGGGAAACGTAGTATTTCAAAAAT 58.585 29.630 0.00 0.00 45.00 1.82
86 87 7.701501 GTGTTGGGAAACGTAGTATTTCAAAAA 59.298 33.333 0.00 0.00 45.00 1.94
87 88 7.148120 TGTGTTGGGAAACGTAGTATTTCAAAA 60.148 33.333 0.00 0.00 45.00 2.44
88 89 6.318144 TGTGTTGGGAAACGTAGTATTTCAAA 59.682 34.615 0.00 0.00 45.00 2.69
89 90 5.821470 TGTGTTGGGAAACGTAGTATTTCAA 59.179 36.000 0.00 0.00 45.00 2.69
90 91 5.366460 TGTGTTGGGAAACGTAGTATTTCA 58.634 37.500 0.00 0.00 45.00 2.69
91 92 5.927954 TGTGTTGGGAAACGTAGTATTTC 57.072 39.130 0.00 0.00 45.00 2.17
92 93 9.669887 TTATATGTGTTGGGAAACGTAGTATTT 57.330 29.630 0.00 0.00 45.00 1.40
93 94 9.101655 GTTATATGTGTTGGGAAACGTAGTATT 57.898 33.333 0.00 0.00 45.00 1.89
94 95 7.712205 GGTTATATGTGTTGGGAAACGTAGTAT 59.288 37.037 0.00 0.00 45.00 2.12
95 96 7.041107 GGTTATATGTGTTGGGAAACGTAGTA 58.959 38.462 0.00 0.00 45.00 1.82
97 98 5.295045 GGGTTATATGTGTTGGGAAACGTAG 59.705 44.000 0.00 0.00 0.00 3.51
98 99 5.184711 GGGTTATATGTGTTGGGAAACGTA 58.815 41.667 0.00 0.00 0.00 3.57
99 100 4.011698 GGGTTATATGTGTTGGGAAACGT 58.988 43.478 0.00 0.00 0.00 3.99
100 101 3.379057 GGGGTTATATGTGTTGGGAAACG 59.621 47.826 0.00 0.00 0.00 3.60
101 102 4.606210 AGGGGTTATATGTGTTGGGAAAC 58.394 43.478 0.00 0.00 0.00 2.78
102 103 4.957606 AGGGGTTATATGTGTTGGGAAA 57.042 40.909 0.00 0.00 0.00 3.13
103 104 5.290335 TCTAGGGGTTATATGTGTTGGGAA 58.710 41.667 0.00 0.00 0.00 3.97
104 105 4.898268 TCTAGGGGTTATATGTGTTGGGA 58.102 43.478 0.00 0.00 0.00 4.37
105 106 5.309543 TGATCTAGGGGTTATATGTGTTGGG 59.690 44.000 0.00 0.00 0.00 4.12
106 107 6.433847 TGATCTAGGGGTTATATGTGTTGG 57.566 41.667 0.00 0.00 0.00 3.77
107 108 8.156820 TCATTGATCTAGGGGTTATATGTGTTG 58.843 37.037 0.00 0.00 0.00 3.33
108 109 8.157476 GTCATTGATCTAGGGGTTATATGTGTT 58.843 37.037 0.00 0.00 0.00 3.32
109 110 7.292356 TGTCATTGATCTAGGGGTTATATGTGT 59.708 37.037 0.00 0.00 0.00 3.72
110 111 7.679783 TGTCATTGATCTAGGGGTTATATGTG 58.320 38.462 0.00 0.00 0.00 3.21
111 112 7.872061 TGTCATTGATCTAGGGGTTATATGT 57.128 36.000 0.00 0.00 0.00 2.29
121 122 6.259608 GTCTTGGTGAATGTCATTGATCTAGG 59.740 42.308 1.88 0.00 0.00 3.02
140 141 6.204688 TGTTATGACTTGCTTACTTGTCTTGG 59.795 38.462 0.00 0.00 0.00 3.61
185 186 4.518970 CCTGTTTTTAGCCTTGCTCTGTTA 59.481 41.667 0.00 0.00 40.44 2.41
200 201 7.781324 AAGTATTCATCATGACCCTGTTTTT 57.219 32.000 0.00 0.00 0.00 1.94
208 209 7.119699 TGTTGTCTCAAAGTATTCATCATGACC 59.880 37.037 0.00 0.00 0.00 4.02
209 210 8.032952 TGTTGTCTCAAAGTATTCATCATGAC 57.967 34.615 0.00 0.00 0.00 3.06
264 265 1.686052 TGCTTTCCGTGCCTTTTGATT 59.314 42.857 0.00 0.00 0.00 2.57
276 277 3.728864 GCTTGACATGTACATGCTTTCCG 60.729 47.826 31.19 17.41 42.39 4.30
344 345 3.321396 TCTTGCCATGATGTTTTGAGCAA 59.679 39.130 0.00 4.85 37.24 3.91
368 369 4.391830 TCTGTGAATCTGTTATCGTTTGCC 59.608 41.667 0.00 0.00 0.00 4.52
406 410 5.068987 ACTTGTCATTGTTACTGCCATGTTT 59.931 36.000 0.00 0.00 0.00 2.83
417 421 6.488344 TCAAACATGCCTACTTGTCATTGTTA 59.512 34.615 0.00 0.00 33.33 2.41
423 427 4.318332 CTCTCAAACATGCCTACTTGTCA 58.682 43.478 0.00 0.00 33.33 3.58
442 446 1.672881 GTGTTGAGTTGCACAAGCTCT 59.327 47.619 11.54 0.00 42.74 4.09
491 495 7.660112 TGCATAAACATGTCTTCTTGATGTTT 58.340 30.769 0.00 12.49 46.74 2.83
508 512 2.945008 TGCCATGAGTAGCTGCATAAAC 59.055 45.455 4.12 0.00 0.00 2.01
512 516 1.211212 TCTTGCCATGAGTAGCTGCAT 59.789 47.619 4.12 0.00 0.00 3.96
557 561 6.599244 TCTGTTTTTCCATGTGAATAGCTAGG 59.401 38.462 0.00 0.00 31.67 3.02
580 584 8.812972 TCTGTCACCATGTTATTAGTAAGTTCT 58.187 33.333 0.00 0.00 0.00 3.01
597 601 4.380843 ACCCATAACATTTCTGTCACCA 57.619 40.909 0.00 0.00 33.36 4.17
599 603 8.050778 TGATTAACCCATAACATTTCTGTCAC 57.949 34.615 0.00 0.00 33.36 3.67
610 614 6.705825 GGGCAAAATGATGATTAACCCATAAC 59.294 38.462 5.32 0.00 32.15 1.89
627 631 1.228552 ACACCGCTGAGGGCAAAAT 60.229 52.632 1.66 0.00 46.96 1.82
640 644 1.742880 CCTGAGCACATGGACACCG 60.743 63.158 0.00 0.00 0.00 4.94
658 662 1.098050 ATTCGCATCTGAGGGCAAAC 58.902 50.000 5.18 0.00 0.00 2.93
703 707 2.338984 GGAACGAGTCGGTGCACT 59.661 61.111 17.92 0.00 34.42 4.40
788 792 5.411669 ACAGTCTGAATAAAATTGGTCGTCC 59.588 40.000 6.91 0.00 0.00 4.79
810 814 2.043405 ACAAGCCACACGTGCAACA 61.043 52.632 17.22 0.00 35.74 3.33
819 823 2.694920 TTGGGTCCCACAAGCCACA 61.695 57.895 11.24 0.00 46.05 4.17
837 841 0.322277 CACCTGCAATGGCTCTCTGT 60.322 55.000 0.00 0.00 41.91 3.41
852 871 2.563179 CGCCCTCTTATATAGCACACCT 59.437 50.000 0.00 0.00 0.00 4.00
868 887 4.003788 CACCTCCGTTGTCGCCCT 62.004 66.667 0.00 0.00 35.54 5.19
877 900 4.082523 CGCCATGGTCACCTCCGT 62.083 66.667 14.67 0.00 0.00 4.69
881 904 1.892819 CTCTGTCGCCATGGTCACCT 61.893 60.000 14.67 0.00 0.00 4.00
907 930 3.723235 CTCTCGCCATGGTCACCGG 62.723 68.421 14.67 0.00 0.00 5.28
917 940 1.029408 GTGCTCTCTCTCTCTCGCCA 61.029 60.000 0.00 0.00 0.00 5.69
937 976 0.838122 ACAGCTAGCTTCCCACCACT 60.838 55.000 16.46 0.00 0.00 4.00
939 978 1.679311 CACAGCTAGCTTCCCACCA 59.321 57.895 16.46 0.00 0.00 4.17
1020 1059 0.320683 CTGCATTCCACGAGGTGTCA 60.321 55.000 0.00 0.00 35.89 3.58
1022 1061 0.036952 CTCTGCATTCCACGAGGTGT 60.037 55.000 0.00 0.00 35.89 4.16
1030 1069 4.802051 GCCCGGCTCTGCATTCCA 62.802 66.667 0.71 0.00 0.00 3.53
1100 1139 0.108585 GGTGTGTGAGAAAGCCTCCA 59.891 55.000 0.00 0.00 41.25 3.86
1106 1145 2.135933 GTTCCTCGGTGTGTGAGAAAG 58.864 52.381 0.00 0.00 35.43 2.62
1210 1249 6.496565 TGAACACCAAATAGATCAACCCATTT 59.503 34.615 0.00 0.00 0.00 2.32
1264 1303 0.251354 GAGTCTTGGCCAGAGCATCA 59.749 55.000 5.11 0.00 42.56 3.07
1281 1320 5.642491 TCTTCTTGCAGTTCATTCATCAGAG 59.358 40.000 0.00 0.00 0.00 3.35
1282 1321 5.554070 TCTTCTTGCAGTTCATTCATCAGA 58.446 37.500 0.00 0.00 0.00 3.27
1357 1398 0.826715 CCATCTCTTCTTCCGGAGCA 59.173 55.000 3.34 0.00 0.00 4.26
1393 1434 3.798548 GCTCAACAGCTAGCTCTATGTCC 60.799 52.174 16.15 6.15 43.09 4.02
1466 1507 4.272261 CCAAAAGTGTTTGCAAATGGGTAC 59.728 41.667 16.21 9.70 42.44 3.34
1481 1522 5.410067 CATACCTACAAATGCCCAAAAGTG 58.590 41.667 0.00 0.00 0.00 3.16
1691 1742 7.874016 AGCTGCATTTCATTGATCAAAAGTTTA 59.126 29.630 13.09 0.00 0.00 2.01
1767 1822 0.173481 CTGCACTTGGCTCTACGCTA 59.827 55.000 0.00 0.00 45.15 4.26
1903 1960 9.075678 CTCTGGAATAATTCATTTAGCTTCCAT 57.924 33.333 0.00 0.00 39.73 3.41
1914 1971 6.855763 TTGTTTGGCTCTGGAATAATTCAT 57.144 33.333 0.00 0.00 0.00 2.57
2069 2128 5.540337 TGTTCATTTATTTTGGCACCAGGTA 59.460 36.000 0.00 0.00 0.00 3.08
2140 2203 2.906691 TTGTGCATTTTCCACCCTTG 57.093 45.000 0.00 0.00 32.30 3.61
2314 2381 1.601903 GCAAACATTCACGGTCTCACA 59.398 47.619 0.00 0.00 0.00 3.58
2439 2506 2.093606 GCCACTCTAACCCTAGACCAAC 60.094 54.545 0.00 0.00 30.68 3.77
2445 2512 2.093447 CCAAGTGCCACTCTAACCCTAG 60.093 54.545 0.00 0.00 0.00 3.02
2530 2605 2.491675 AAATCGAAGGGGGTGAGAAC 57.508 50.000 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.