Multiple sequence alignment - TraesCS2B01G173000

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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 TraesCS2B01G173000 chr2B 100.000 3116 0 0 1 3116 146962926 146966041 0.000000e+00 5755.0
1 TraesCS2B01G173000 chr2B 83.404 470 51 12 2519 2965 701119748 701119283 8.040000e-111 411.0
2 TraesCS2B01G173000 chr2B 75.273 732 140 31 1326 2047 146992844 146993544 8.390000e-81 311.0
3 TraesCS2B01G173000 chr2B 73.533 801 160 33 1324 2110 147285844 147285082 1.110000e-64 257.0
4 TraesCS2B01G173000 chr2D 90.622 2474 134 40 37 2472 95514914 95517327 0.000000e+00 3193.0
5 TraesCS2B01G173000 chr2D 85.370 622 53 18 2519 3116 641567286 641566679 7.390000e-171 610.0
6 TraesCS2B01G173000 chr2D 73.750 800 160 33 1324 2110 95654888 95654126 5.120000e-68 268.0
7 TraesCS2B01G173000 chr2D 79.241 395 68 10 1324 1711 95684402 95684789 2.380000e-66 263.0
8 TraesCS2B01G173000 chr2D 84.646 254 35 3 1321 1572 95667596 95667847 1.860000e-62 250.0
9 TraesCS2B01G173000 chr2A 89.728 2502 124 46 41 2517 94107024 94109417 0.000000e+00 3073.0
10 TraesCS2B01G173000 chr2A 78.030 396 71 14 1324 1711 94204753 94204366 5.200000e-58 235.0
11 TraesCS2B01G173000 chr2A 77.945 399 72 13 1321 1711 94275988 94276378 5.200000e-58 235.0
12 TraesCS2B01G173000 chr4A 86.473 621 54 17 2521 3116 704190558 704191173 0.000000e+00 654.0
13 TraesCS2B01G173000 chr4A 85.990 621 57 17 2521 3116 704217343 704217958 3.390000e-179 638.0
14 TraesCS2B01G173000 chr4A 80.456 614 96 15 2521 3116 698356461 698357068 6.130000e-122 448.0
15 TraesCS2B01G173000 chr4A 80.929 603 68 25 2519 3116 436440968 436440408 1.720000e-117 433.0
16 TraesCS2B01G173000 chr4A 76.662 647 85 32 2518 3116 655722730 655723358 6.530000e-77 298.0
17 TraesCS2B01G173000 chr4A 95.349 43 2 0 185 227 574913879 574913837 5.580000e-08 69.4
18 TraesCS2B01G173000 chrUn 85.971 613 61 16 2521 3116 95601876 95601272 1.580000e-177 632.0
19 TraesCS2B01G173000 chr3B 85.270 611 64 11 2521 3116 666190918 666190319 9.560000e-170 606.0
20 TraesCS2B01G173000 chr3B 84.142 618 68 19 2521 3114 545428424 545427813 3.490000e-159 571.0
21 TraesCS2B01G173000 chr3B 83.306 599 81 12 2521 3116 725857235 725857817 4.570000e-148 534.0
22 TraesCS2B01G173000 chr3B 83.092 621 68 25 2521 3116 545481155 545480547 5.920000e-147 531.0
23 TraesCS2B01G173000 chr6B 84.943 611 69 17 2521 3114 32649928 32650532 5.750000e-167 597.0
24 TraesCS2B01G173000 chr6B 84.630 540 44 27 2521 3034 287152736 287153262 4.640000e-138 501.0
25 TraesCS2B01G173000 chr7B 84.808 599 71 12 2521 3115 658452882 658452300 4.480000e-163 584.0
26 TraesCS2B01G173000 chr7B 88.136 59 6 1 1174 1232 640915040 640915097 5.580000e-08 69.4
27 TraesCS2B01G173000 chr3A 83.412 422 45 12 2521 2917 737348862 737349283 4.910000e-98 368.0
28 TraesCS2B01G173000 chr3A 73.783 801 165 33 1326 2114 628219906 628219139 1.100000e-69 274.0
29 TraesCS2B01G173000 chr7A 75.000 748 149 31 1326 2063 57864379 57865098 8.390000e-81 311.0
30 TraesCS2B01G173000 chr7A 73.573 806 165 37 1324 2117 574971719 574972488 6.630000e-67 265.0
31 TraesCS2B01G173000 chr7A 73.848 738 157 29 1326 2054 57802972 57803682 8.570000e-66 261.0
32 TraesCS2B01G173000 chr7A 89.831 59 5 1 1174 1232 669727976 669728033 1.200000e-09 75.0
33 TraesCS2B01G173000 chr7D 73.526 797 174 30 1326 2114 54319681 54320448 5.120000e-68 268.0
34 TraesCS2B01G173000 chr7D 73.559 798 172 30 1326 2114 54353773 54354540 5.120000e-68 268.0
35 TraesCS2B01G173000 chr7D 73.259 804 169 35 1325 2117 506882895 506883663 5.160000e-63 252.0
36 TraesCS2B01G173000 chr7D 72.591 799 178 32 1326 2114 54336592 54337359 1.120000e-54 224.0
37 TraesCS2B01G173000 chr7D 88.136 59 6 1 1174 1232 577594982 577595039 5.580000e-08 69.4
38 TraesCS2B01G173000 chr1B 72.255 674 149 30 1451 2114 584798547 584799192 1.150000e-39 174.0


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 TraesCS2B01G173000 chr2B 146962926 146966041 3115 False 5755 5755 100.000 1 3116 1 chr2B.!!$F1 3115
1 TraesCS2B01G173000 chr2B 146992844 146993544 700 False 311 311 75.273 1326 2047 1 chr2B.!!$F2 721
2 TraesCS2B01G173000 chr2B 147285082 147285844 762 True 257 257 73.533 1324 2110 1 chr2B.!!$R1 786
3 TraesCS2B01G173000 chr2D 95514914 95517327 2413 False 3193 3193 90.622 37 2472 1 chr2D.!!$F1 2435
4 TraesCS2B01G173000 chr2D 641566679 641567286 607 True 610 610 85.370 2519 3116 1 chr2D.!!$R2 597
5 TraesCS2B01G173000 chr2D 95654126 95654888 762 True 268 268 73.750 1324 2110 1 chr2D.!!$R1 786
6 TraesCS2B01G173000 chr2A 94107024 94109417 2393 False 3073 3073 89.728 41 2517 1 chr2A.!!$F1 2476
7 TraesCS2B01G173000 chr4A 704190558 704191173 615 False 654 654 86.473 2521 3116 1 chr4A.!!$F3 595
8 TraesCS2B01G173000 chr4A 704217343 704217958 615 False 638 638 85.990 2521 3116 1 chr4A.!!$F4 595
9 TraesCS2B01G173000 chr4A 698356461 698357068 607 False 448 448 80.456 2521 3116 1 chr4A.!!$F2 595
10 TraesCS2B01G173000 chr4A 436440408 436440968 560 True 433 433 80.929 2519 3116 1 chr4A.!!$R1 597
11 TraesCS2B01G173000 chr4A 655722730 655723358 628 False 298 298 76.662 2518 3116 1 chr4A.!!$F1 598
12 TraesCS2B01G173000 chrUn 95601272 95601876 604 True 632 632 85.971 2521 3116 1 chrUn.!!$R1 595
13 TraesCS2B01G173000 chr3B 666190319 666190918 599 True 606 606 85.270 2521 3116 1 chr3B.!!$R3 595
14 TraesCS2B01G173000 chr3B 545427813 545428424 611 True 571 571 84.142 2521 3114 1 chr3B.!!$R1 593
15 TraesCS2B01G173000 chr3B 725857235 725857817 582 False 534 534 83.306 2521 3116 1 chr3B.!!$F1 595
16 TraesCS2B01G173000 chr3B 545480547 545481155 608 True 531 531 83.092 2521 3116 1 chr3B.!!$R2 595
17 TraesCS2B01G173000 chr6B 32649928 32650532 604 False 597 597 84.943 2521 3114 1 chr6B.!!$F1 593
18 TraesCS2B01G173000 chr6B 287152736 287153262 526 False 501 501 84.630 2521 3034 1 chr6B.!!$F2 513
19 TraesCS2B01G173000 chr7B 658452300 658452882 582 True 584 584 84.808 2521 3115 1 chr7B.!!$R1 594
20 TraesCS2B01G173000 chr3A 628219139 628219906 767 True 274 274 73.783 1326 2114 1 chr3A.!!$R1 788
21 TraesCS2B01G173000 chr7A 57864379 57865098 719 False 311 311 75.000 1326 2063 1 chr7A.!!$F2 737
22 TraesCS2B01G173000 chr7A 574971719 574972488 769 False 265 265 73.573 1324 2117 1 chr7A.!!$F3 793
23 TraesCS2B01G173000 chr7A 57802972 57803682 710 False 261 261 73.848 1326 2054 1 chr7A.!!$F1 728
24 TraesCS2B01G173000 chr7D 54319681 54320448 767 False 268 268 73.526 1326 2114 1 chr7D.!!$F1 788
25 TraesCS2B01G173000 chr7D 54353773 54354540 767 False 268 268 73.559 1326 2114 1 chr7D.!!$F3 788
26 TraesCS2B01G173000 chr7D 506882895 506883663 768 False 252 252 73.259 1325 2117 1 chr7D.!!$F4 792
27 TraesCS2B01G173000 chr7D 54336592 54337359 767 False 224 224 72.591 1326 2114 1 chr7D.!!$F2 788

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
933 938 0.029567 ACGCTTGATCCGTCGATCTC 59.97 55.0 0.0 0.0 44.61 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2432 2507 0.39034 GGAGCTTGTCACGCATGAGA 60.39 55.0 2.5 0.0 34.75 3.27 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
22 23 5.209944 GCTTCGCTTACCATGCTTATATC 57.790 43.478 0.00 0.00 0.00 1.63
23 24 4.201628 GCTTCGCTTACCATGCTTATATCG 60.202 45.833 0.00 0.00 0.00 2.92
24 25 4.514781 TCGCTTACCATGCTTATATCGT 57.485 40.909 0.00 0.00 0.00 3.73
25 26 4.234574 TCGCTTACCATGCTTATATCGTG 58.765 43.478 0.00 0.00 0.00 4.35
26 27 3.367932 CGCTTACCATGCTTATATCGTGG 59.632 47.826 10.56 10.56 44.23 4.94
27 28 3.684788 GCTTACCATGCTTATATCGTGGG 59.315 47.826 14.62 0.00 43.24 4.61
28 29 2.185004 ACCATGCTTATATCGTGGGC 57.815 50.000 14.62 0.00 43.24 5.36
29 30 1.271379 ACCATGCTTATATCGTGGGCC 60.271 52.381 14.62 0.00 43.24 5.80
30 31 1.271325 CCATGCTTATATCGTGGGCCA 60.271 52.381 0.00 0.00 37.05 5.36
31 32 2.618816 CCATGCTTATATCGTGGGCCAT 60.619 50.000 10.70 0.00 37.05 4.40
32 33 3.370421 CCATGCTTATATCGTGGGCCATA 60.370 47.826 10.70 0.66 37.05 2.74
33 34 4.454678 CATGCTTATATCGTGGGCCATAT 58.545 43.478 10.70 9.66 0.00 1.78
34 35 3.872696 TGCTTATATCGTGGGCCATATG 58.127 45.455 10.70 2.82 0.00 1.78
35 36 3.517500 TGCTTATATCGTGGGCCATATGA 59.482 43.478 10.70 9.19 0.00 2.15
36 37 4.019771 TGCTTATATCGTGGGCCATATGAA 60.020 41.667 10.70 5.34 0.00 2.57
37 38 4.941263 GCTTATATCGTGGGCCATATGAAA 59.059 41.667 10.70 5.21 0.00 2.69
38 39 5.163754 GCTTATATCGTGGGCCATATGAAAC 60.164 44.000 10.70 0.00 0.00 2.78
39 40 2.727123 ATCGTGGGCCATATGAAACA 57.273 45.000 10.70 0.00 0.00 2.83
42 43 1.202290 CGTGGGCCATATGAAACAAGC 60.202 52.381 10.70 0.00 0.00 4.01
49 50 1.366111 ATATGAAACAAGCGCGCCGT 61.366 50.000 30.33 23.12 0.00 5.68
88 89 2.726821 ACATCATGACCGAGGCAAATT 58.273 42.857 0.00 0.00 0.00 1.82
103 104 1.123928 AAATTTTTGGGTCACCGCCA 58.876 45.000 0.00 0.00 40.75 5.69
113 114 0.884704 GTCACCGCCAGAGCAAAGAA 60.885 55.000 0.00 0.00 39.83 2.52
122 123 3.339141 CCAGAGCAAAGAAGTTAGGGTC 58.661 50.000 0.00 0.00 0.00 4.46
123 124 2.996621 CAGAGCAAAGAAGTTAGGGTCG 59.003 50.000 0.00 0.00 0.00 4.79
127 128 3.260884 AGCAAAGAAGTTAGGGTCGATCA 59.739 43.478 0.00 0.00 0.00 2.92
144 145 5.597235 CGATCATGTCGCGAGAATAATAG 57.403 43.478 10.24 0.27 44.33 1.73
159 160 8.380644 CGAGAATAATAGTTCATGTCGTGTTTT 58.619 33.333 0.00 0.00 0.00 2.43
197 198 8.923683 ACAAACTCTACGCTCTTCTTAATTAAC 58.076 33.333 0.00 0.00 0.00 2.01
205 206 5.977725 CGCTCTTCTTAATTAACGGATGAGA 59.022 40.000 21.95 9.66 34.21 3.27
206 207 6.074782 CGCTCTTCTTAATTAACGGATGAGAC 60.075 42.308 21.95 15.82 34.21 3.36
227 228 6.496524 GACAAATCTTTTGTCTCCGTTTTG 57.503 37.500 20.39 0.00 43.91 2.44
228 229 6.202516 ACAAATCTTTTGTCTCCGTTTTGA 57.797 33.333 0.00 0.00 0.00 2.69
229 230 6.626302 ACAAATCTTTTGTCTCCGTTTTGAA 58.374 32.000 0.00 0.00 0.00 2.69
233 234 7.755582 ATCTTTTGTCTCCGTTTTGAAAAAG 57.244 32.000 0.00 0.00 35.49 2.27
253 254 7.568199 AAAAGAAAAGAGTTCTGAATTCCGA 57.432 32.000 9.02 0.00 0.00 4.55
259 260 3.741344 AGAGTTCTGAATTCCGACAAACG 59.259 43.478 9.02 0.00 42.18 3.60
376 377 0.655733 AGTCACGCCTGTTTTGTTCG 59.344 50.000 0.00 0.00 0.00 3.95
379 380 0.316689 CACGCCTGTTTTGTTCGGTC 60.317 55.000 0.00 0.00 0.00 4.79
551 552 2.051345 CGTTCACAAGGCGCCAAC 60.051 61.111 31.54 21.97 0.00 3.77
568 569 0.680921 AACAGCCGGTCCCAATCATG 60.681 55.000 1.90 0.00 0.00 3.07
569 570 1.224315 CAGCCGGTCCCAATCATGA 59.776 57.895 1.90 0.00 0.00 3.07
570 571 0.179009 CAGCCGGTCCCAATCATGAT 60.179 55.000 1.18 1.18 0.00 2.45
571 572 0.179009 AGCCGGTCCCAATCATGATG 60.179 55.000 9.46 3.68 0.00 3.07
711 712 1.407979 GGAGGCATCTGCTTGGAATTG 59.592 52.381 0.00 0.00 41.70 2.32
890 891 4.322567 CTGCCTATAAATTGGCTCTCCTC 58.677 47.826 14.95 0.00 46.65 3.71
902 903 1.609320 GCTCTCCTCACCAAGAACACC 60.609 57.143 0.00 0.00 0.00 4.16
933 938 0.029567 ACGCTTGATCCGTCGATCTC 59.970 55.000 0.00 0.00 44.61 2.75
937 942 2.095466 GCTTGATCCGTCGATCTCTAGG 60.095 54.545 0.00 0.00 44.61 3.02
940 945 2.104281 TGATCCGTCGATCTCTAGGTGA 59.896 50.000 0.00 0.00 44.61 4.02
944 949 4.907809 TCCGTCGATCTCTAGGTGATAAT 58.092 43.478 0.00 0.00 0.00 1.28
945 950 6.046290 TCCGTCGATCTCTAGGTGATAATA 57.954 41.667 0.00 0.00 0.00 0.98
946 951 6.470278 TCCGTCGATCTCTAGGTGATAATAA 58.530 40.000 0.00 0.00 0.00 1.40
947 952 6.370994 TCCGTCGATCTCTAGGTGATAATAAC 59.629 42.308 0.00 0.00 0.00 1.89
948 953 6.242107 CGTCGATCTCTAGGTGATAATAACG 58.758 44.000 0.00 0.00 0.00 3.18
949 954 6.090493 CGTCGATCTCTAGGTGATAATAACGA 59.910 42.308 0.00 0.00 0.00 3.85
950 955 7.457868 GTCGATCTCTAGGTGATAATAACGAG 58.542 42.308 0.00 0.00 0.00 4.18
951 956 7.331440 GTCGATCTCTAGGTGATAATAACGAGA 59.669 40.741 0.00 0.00 0.00 4.04
952 957 8.041919 TCGATCTCTAGGTGATAATAACGAGAT 58.958 37.037 0.00 0.00 39.07 2.75
953 958 8.670135 CGATCTCTAGGTGATAATAACGAGATT 58.330 37.037 0.00 0.00 37.19 2.40
1119 1152 1.677217 GGGTACTACGAGGAGACGTGT 60.677 57.143 0.00 0.00 46.02 4.49
1240 1276 0.103390 CGTCCAGGTACACACACACA 59.897 55.000 0.00 0.00 0.00 3.72
1245 1281 3.118223 TCCAGGTACACACACACATTCAA 60.118 43.478 0.00 0.00 0.00 2.69
1252 1288 1.333115 CACACACATTCAAGCATGCG 58.667 50.000 13.01 0.00 0.00 4.73
1287 1323 2.830772 GCAAATACTCGCATTGCTCA 57.169 45.000 7.12 0.00 44.54 4.26
1288 1324 2.444351 GCAAATACTCGCATTGCTCAC 58.556 47.619 7.12 0.00 44.54 3.51
1308 1352 1.391485 CTGAGTTGCTGACACGTATGC 59.609 52.381 0.00 0.00 0.00 3.14
1842 1893 1.301401 CACCGACGGAAAGGAGCAA 60.301 57.895 23.38 0.00 0.00 3.91
1848 1899 0.038159 ACGGAAAGGAGCAAGACGAG 60.038 55.000 0.00 0.00 0.00 4.18
2123 2174 3.746492 GTCGTCAACTACTGAAAGCCATT 59.254 43.478 0.00 0.00 37.60 3.16
2133 2184 4.585879 ACTGAAAGCCATTAACGTATGGT 58.414 39.130 16.78 3.65 45.65 3.55
2160 2221 0.892814 TGCATGCGTCCATTGTTCCA 60.893 50.000 14.09 0.00 0.00 3.53
2161 2222 0.457035 GCATGCGTCCATTGTTCCAT 59.543 50.000 0.00 0.00 0.00 3.41
2162 2223 1.675483 GCATGCGTCCATTGTTCCATA 59.325 47.619 0.00 0.00 0.00 2.74
2163 2224 2.294233 GCATGCGTCCATTGTTCCATAT 59.706 45.455 0.00 0.00 0.00 1.78
2193 2254 2.863346 CGTTCCCGTCACCCTGTGA 61.863 63.158 0.00 0.00 40.50 3.58
2240 2301 0.164002 GGTTTCGTTCTTGCGAGCTC 59.836 55.000 2.73 2.73 42.10 4.09
2251 2312 4.872485 CGAGCTCGCCGTCTCGTC 62.872 72.222 25.07 0.00 44.95 4.20
2254 2315 4.104417 GCTCGCCGTCTCGTCTGT 62.104 66.667 0.00 0.00 0.00 3.41
2384 2456 2.681344 ACGGACAACAAAGAACACTTCC 59.319 45.455 0.00 0.00 0.00 3.46
2385 2457 2.286184 CGGACAACAAAGAACACTTCCG 60.286 50.000 0.00 0.00 0.00 4.30
2394 2466 0.596600 GAACACTTCCGTGCGTCTCA 60.597 55.000 0.00 0.00 45.10 3.27
2430 2505 0.105224 TCCAGTTGTCGCGAAAGGAA 59.895 50.000 12.06 0.00 0.00 3.36
2432 2507 1.535462 CCAGTTGTCGCGAAAGGAAAT 59.465 47.619 12.06 0.00 0.00 2.17
2444 2519 3.484229 CGAAAGGAAATCTCATGCGTGAC 60.484 47.826 3.97 0.00 0.00 3.67
2449 2524 2.105006 AATCTCATGCGTGACAAGCT 57.895 45.000 14.49 0.00 35.28 3.74
2540 2620 2.244117 GAGCATCTCCGGCTGTTGGA 62.244 60.000 0.00 0.00 42.78 3.53
2568 2650 0.022853 GACACGTAAAATCGCCGTCG 59.977 55.000 0.00 0.00 31.46 5.12
2732 2846 7.433708 TTTGGCATATATTAGACATGTTCGG 57.566 36.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.923871 ACGATATAAGCATGGTAAGCGAAG 59.076 41.667 16.08 2.19 37.01 3.79
2 3 4.684242 CACGATATAAGCATGGTAAGCGAA 59.316 41.667 16.08 0.00 37.01 4.70
3 4 4.234574 CACGATATAAGCATGGTAAGCGA 58.765 43.478 16.08 0.00 37.01 4.93
4 5 3.367932 CCACGATATAAGCATGGTAAGCG 59.632 47.826 0.00 4.39 37.01 4.68
6 7 3.684788 GCCCACGATATAAGCATGGTAAG 59.315 47.826 0.00 0.00 0.00 2.34
7 8 3.558321 GGCCCACGATATAAGCATGGTAA 60.558 47.826 0.00 0.00 0.00 2.85
8 9 2.027561 GGCCCACGATATAAGCATGGTA 60.028 50.000 0.00 0.00 0.00 3.25
9 10 1.271379 GGCCCACGATATAAGCATGGT 60.271 52.381 0.00 0.00 0.00 3.55
10 11 1.271325 TGGCCCACGATATAAGCATGG 60.271 52.381 0.00 0.00 0.00 3.66
11 12 2.183478 TGGCCCACGATATAAGCATG 57.817 50.000 0.00 0.00 0.00 4.06
12 13 4.164030 TCATATGGCCCACGATATAAGCAT 59.836 41.667 0.00 0.00 0.00 3.79
13 14 3.517500 TCATATGGCCCACGATATAAGCA 59.482 43.478 0.00 0.00 0.00 3.91
14 15 4.137116 TCATATGGCCCACGATATAAGC 57.863 45.455 0.00 0.00 0.00 3.09
15 16 5.937540 TGTTTCATATGGCCCACGATATAAG 59.062 40.000 0.00 0.00 0.00 1.73
16 17 5.870706 TGTTTCATATGGCCCACGATATAA 58.129 37.500 0.00 0.00 0.00 0.98
17 18 5.491323 TGTTTCATATGGCCCACGATATA 57.509 39.130 0.00 0.00 0.00 0.86
18 19 4.365514 TGTTTCATATGGCCCACGATAT 57.634 40.909 0.00 0.00 0.00 1.63
19 20 3.847671 TGTTTCATATGGCCCACGATA 57.152 42.857 0.00 0.00 0.00 2.92
20 21 2.727123 TGTTTCATATGGCCCACGAT 57.273 45.000 0.00 0.00 0.00 3.73
21 22 2.364632 CTTGTTTCATATGGCCCACGA 58.635 47.619 0.00 0.00 0.00 4.35
22 23 1.202290 GCTTGTTTCATATGGCCCACG 60.202 52.381 0.00 0.00 0.00 4.94
23 24 1.202290 CGCTTGTTTCATATGGCCCAC 60.202 52.381 0.00 0.00 0.00 4.61
24 25 1.102154 CGCTTGTTTCATATGGCCCA 58.898 50.000 0.00 0.00 0.00 5.36
25 26 0.249031 GCGCTTGTTTCATATGGCCC 60.249 55.000 0.00 0.00 0.00 5.80
26 27 0.592247 CGCGCTTGTTTCATATGGCC 60.592 55.000 5.56 0.00 0.00 5.36
27 28 1.202348 GCGCGCTTGTTTCATATGGC 61.202 55.000 26.67 0.00 0.00 4.40
28 29 0.592247 GGCGCGCTTGTTTCATATGG 60.592 55.000 32.29 0.00 0.00 2.74
29 30 0.925267 CGGCGCGCTTGTTTCATATG 60.925 55.000 32.29 0.00 0.00 1.78
30 31 1.351707 CGGCGCGCTTGTTTCATAT 59.648 52.632 32.29 0.00 0.00 1.78
31 32 1.962092 GACGGCGCGCTTGTTTCATA 61.962 55.000 32.29 0.00 0.00 2.15
32 33 3.308878 GACGGCGCGCTTGTTTCAT 62.309 57.895 32.29 0.00 0.00 2.57
33 34 4.007940 GACGGCGCGCTTGTTTCA 62.008 61.111 32.29 0.00 0.00 2.69
34 35 3.515286 TTGACGGCGCGCTTGTTTC 62.515 57.895 32.29 19.02 0.00 2.78
35 36 3.578272 TTGACGGCGCGCTTGTTT 61.578 55.556 32.29 10.67 0.00 2.83
36 37 4.307908 GTTGACGGCGCGCTTGTT 62.308 61.111 32.29 12.66 0.00 2.83
38 39 3.593551 ATTGTTGACGGCGCGCTTG 62.594 57.895 32.29 25.17 0.00 4.01
39 40 2.400896 AAATTGTTGACGGCGCGCTT 62.401 50.000 32.29 18.79 0.00 4.68
42 43 1.766176 CAAAATTGTTGACGGCGCG 59.234 52.632 6.90 0.00 0.00 6.86
49 50 8.549548 CATGATGTTGTTTAGCAAAATTGTTGA 58.450 29.630 0.00 0.00 35.26 3.18
88 89 1.228124 CTCTGGCGGTGACCCAAAA 60.228 57.895 0.00 0.00 31.48 2.44
103 104 2.897969 TCGACCCTAACTTCTTTGCTCT 59.102 45.455 0.00 0.00 0.00 4.09
108 109 5.420409 GACATGATCGACCCTAACTTCTTT 58.580 41.667 0.00 0.00 0.00 2.52
123 124 6.582672 TGAACTATTATTCTCGCGACATGATC 59.417 38.462 3.71 0.00 0.00 2.92
127 128 6.216569 ACATGAACTATTATTCTCGCGACAT 58.783 36.000 3.71 2.53 0.00 3.06
144 145 2.098443 ACCACCAAAACACGACATGAAC 59.902 45.455 0.00 0.00 0.00 3.18
159 160 4.571580 CGTAGAGTTTGTTACAAACCACCA 59.428 41.667 29.95 15.43 0.00 4.17
205 206 6.202516 TCAAAACGGAGACAAAAGATTTGT 57.797 33.333 8.11 8.11 34.97 2.83
206 207 7.518731 TTTCAAAACGGAGACAAAAGATTTG 57.481 32.000 1.47 1.47 0.00 2.32
226 227 7.915397 CGGAATTCAGAACTCTTTTCTTTTTCA 59.085 33.333 7.93 0.00 0.00 2.69
227 228 8.129211 TCGGAATTCAGAACTCTTTTCTTTTTC 58.871 33.333 5.77 0.00 0.00 2.29
228 229 7.915923 GTCGGAATTCAGAACTCTTTTCTTTTT 59.084 33.333 9.99 0.00 0.00 1.94
229 230 7.067008 TGTCGGAATTCAGAACTCTTTTCTTTT 59.933 33.333 9.99 0.00 0.00 2.27
233 234 5.924475 TGTCGGAATTCAGAACTCTTTTC 57.076 39.130 9.99 0.00 0.00 2.29
253 254 3.132289 TCTTCAGAACTCTGGTCGTTTGT 59.868 43.478 6.87 0.00 43.91 2.83
259 260 3.520569 GAGCATCTTCAGAACTCTGGTC 58.479 50.000 6.87 0.00 43.91 4.02
349 350 2.842462 AGGCGTGACTGACACCCA 60.842 61.111 15.54 0.00 45.73 4.51
551 552 0.179009 ATCATGATTGGGACCGGCTG 60.179 55.000 0.00 0.00 0.00 4.85
568 569 0.179089 AGCAGAGCGATGTGTCCATC 60.179 55.000 0.00 0.00 43.41 3.51
569 570 0.179089 GAGCAGAGCGATGTGTCCAT 60.179 55.000 0.00 0.00 0.00 3.41
570 571 1.216444 GAGCAGAGCGATGTGTCCA 59.784 57.895 0.00 0.00 0.00 4.02
571 572 1.875813 CGAGCAGAGCGATGTGTCC 60.876 63.158 0.00 0.00 0.00 4.02
857 858 6.326323 CCAATTTATAGGCAGGGGTAAACATT 59.674 38.462 0.00 0.00 0.00 2.71
890 891 3.070018 GTGAGATGAGGTGTTCTTGGTG 58.930 50.000 0.00 0.00 0.00 4.17
902 903 2.643933 TCAAGCGTGAGTGAGATGAG 57.356 50.000 0.00 0.00 0.00 2.90
933 938 8.731605 TGAGCTAATCTCGTTATTATCACCTAG 58.268 37.037 0.00 0.00 44.86 3.02
937 942 7.087639 AGCTGAGCTAATCTCGTTATTATCAC 58.912 38.462 4.49 0.00 44.86 3.06
940 945 7.757624 GCTAAGCTGAGCTAATCTCGTTATTAT 59.242 37.037 16.54 0.00 44.86 1.28
944 949 4.861210 GCTAAGCTGAGCTAATCTCGTTA 58.139 43.478 16.54 0.00 44.86 3.18
945 950 3.712187 GCTAAGCTGAGCTAATCTCGTT 58.288 45.455 16.54 0.00 44.86 3.85
946 951 3.363341 GCTAAGCTGAGCTAATCTCGT 57.637 47.619 16.54 0.00 44.86 4.18
981 1002 1.197812 TGGCTCTTGATCAGCAGCTA 58.802 50.000 21.19 15.62 38.77 3.32
985 1006 0.750546 GCCATGGCTCTTGATCAGCA 60.751 55.000 29.98 0.00 38.77 4.41
986 1007 2.031360 GCCATGGCTCTTGATCAGC 58.969 57.895 29.98 0.00 38.26 4.26
1081 1102 4.500116 GACCTCGAGCTCGGGCAC 62.500 72.222 33.98 22.76 38.81 5.01
1268 1304 2.096496 AGTGAGCAATGCGAGTATTTGC 59.904 45.455 0.00 0.00 0.00 3.68
1269 1305 3.371898 TCAGTGAGCAATGCGAGTATTTG 59.628 43.478 0.00 0.00 0.00 2.32
1270 1306 3.599343 TCAGTGAGCAATGCGAGTATTT 58.401 40.909 0.00 0.00 0.00 1.40
1271 1307 3.193263 CTCAGTGAGCAATGCGAGTATT 58.807 45.455 7.33 0.00 0.00 1.89
1287 1323 2.677199 CATACGTGTCAGCAACTCAGT 58.323 47.619 0.00 0.00 0.00 3.41
1288 1324 1.391485 GCATACGTGTCAGCAACTCAG 59.609 52.381 0.00 0.00 0.00 3.35
1575 1623 2.202797 TCTGAGGCATTCGAGCGC 60.203 61.111 0.00 0.00 34.64 5.92
1817 1865 1.566018 CTTTCCGTCGGTGCTGTTCC 61.566 60.000 11.88 0.00 0.00 3.62
1842 1893 3.432588 CTCACCGTCGGCTCGTCT 61.433 66.667 12.28 0.00 0.00 4.18
2076 2127 3.074369 TTCGCCCTGATCTCGGCA 61.074 61.111 19.55 7.65 46.04 5.69
2240 2301 0.732880 AATCAACAGACGAGACGGCG 60.733 55.000 4.80 4.80 41.28 6.46
2251 2312 4.911610 GTGGACAAATCAACGAATCAACAG 59.088 41.667 0.00 0.00 0.00 3.16
2306 2367 6.384258 TCGGAGAAAACAATCAAAACATCA 57.616 33.333 0.00 0.00 0.00 3.07
2422 2497 2.672874 TCACGCATGAGATTTCCTTTCG 59.327 45.455 2.50 0.00 0.00 3.46
2430 2505 2.005451 GAGCTTGTCACGCATGAGATT 58.995 47.619 2.50 0.00 34.75 2.40
2432 2507 0.390340 GGAGCTTGTCACGCATGAGA 60.390 55.000 2.50 0.00 34.75 3.27
2488 2568 8.220755 AGTATCTAGCACAAACTTTGAAACAA 57.779 30.769 8.55 0.00 0.00 2.83
2534 2614 2.856988 GTCCCCTGGGGTCCAACA 60.857 66.667 30.69 8.18 44.74 3.33
2540 2620 1.061324 TTTTACGTGTCCCCTGGGGT 61.061 55.000 30.69 14.26 44.74 4.95
2580 2662 1.438710 CAGACCGACTTTTTGCGCG 60.439 57.895 0.00 0.00 0.00 6.86
2590 2672 2.675772 ACTCGTCCCCAGACCGAC 60.676 66.667 0.00 0.00 40.12 4.79
2767 2888 3.775261 TCGCCCCTTAGTTGTAGTTTT 57.225 42.857 0.00 0.00 0.00 2.43
2835 3035 2.492090 CCGCGTCAAGGAGGAGAG 59.508 66.667 4.92 0.00 0.00 3.20
2965 3178 2.430244 CACTACGAACAGCGCCGT 60.430 61.111 13.65 13.65 46.04 5.68
3008 3222 3.003793 CGCGACTATCTCAAGATGGAGAA 59.996 47.826 0.00 0.00 46.28 2.87


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

AutoCloner maintained by Alex Coulton.