Multiple sequence alignment - TraesCS2D01G138600

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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 TraesCS2D01G138600 chr2D 100.000 2267 0 0 1 2267 81459414 81457148 0.000000e+00 4187.0
1 TraesCS2D01G138600 chr2D 96.474 794 24 4 1285 2076 573964978 573965769 0.000000e+00 1308.0
2 TraesCS2D01G138600 chr2D 88.299 923 66 14 1 919 620878572 620879456 0.000000e+00 1068.0
3 TraesCS2D01G138600 chr2D 93.785 354 22 0 920 1273 81387443 81387090 1.190000e-147 532.0
4 TraesCS2D01G138600 chr2D 92.655 354 26 0 920 1273 81807685 81807332 5.590000e-141 510.0
5 TraesCS2D01G138600 chr4D 96.977 794 21 3 1285 2076 435224281 435223489 0.000000e+00 1330.0
6 TraesCS2D01G138600 chr4D 96.725 794 24 2 1285 2076 51989564 51990357 0.000000e+00 1321.0
7 TraesCS2D01G138600 chrUn 96.851 794 23 2 1285 2076 103386772 103385979 0.000000e+00 1327.0
8 TraesCS2D01G138600 chrUn 89.581 931 81 11 1 919 45318001 45317075 0.000000e+00 1168.0
9 TraesCS2D01G138600 chrUn 89.389 933 79 12 1 919 45360753 45359827 0.000000e+00 1157.0
10 TraesCS2D01G138600 chrUn 98.000 50 1 0 2076 2125 41387205 41387156 1.120000e-13 87.9
11 TraesCS2D01G138600 chrUn 98.000 50 1 0 2076 2125 103887081 103887130 1.120000e-13 87.9
12 TraesCS2D01G138600 chrUn 98.000 50 1 0 2076 2125 280215590 280215541 1.120000e-13 87.9
13 TraesCS2D01G138600 chr5D 95.956 816 28 5 1264 2076 479097583 479096770 0.000000e+00 1319.0
14 TraesCS2D01G138600 chr3D 95.936 812 31 2 1267 2076 611557090 611556279 0.000000e+00 1315.0
15 TraesCS2D01G138600 chr3D 97.297 37 0 1 1258 1293 595031622 595031658 6.760000e-06 62.1
16 TraesCS2D01G138600 chr7D 96.599 794 24 3 1285 2076 525708510 525707718 0.000000e+00 1314.0
17 TraesCS2D01G138600 chr3A 96.599 794 24 3 1285 2076 740310685 740311477 0.000000e+00 1314.0
18 TraesCS2D01G138600 chr3A 90.554 921 81 6 1 918 36679896 36678979 0.000000e+00 1214.0
19 TraesCS2D01G138600 chr3A 95.556 45 2 0 1258 1302 741413777 741413821 3.120000e-09 73.1
20 TraesCS2D01G138600 chr3A 95.556 45 2 0 1258 1302 741482983 741483027 3.120000e-09 73.1
21 TraesCS2D01G138600 chr1D 96.348 794 26 3 1285 2076 447461600 447462392 0.000000e+00 1303.0
22 TraesCS2D01G138600 chr2A 90.183 927 78 12 1 922 41180156 41179238 0.000000e+00 1195.0
23 TraesCS2D01G138600 chr2A 88.629 941 67 11 1 920 678715734 678716655 0.000000e+00 1109.0
24 TraesCS2D01G138600 chr2A 97.414 348 9 0 920 1267 82050559 82050212 5.390000e-166 593.0
25 TraesCS2D01G138600 chr2A 94.253 348 20 0 920 1267 82029617 82029270 1.190000e-147 532.0
26 TraesCS2D01G138600 chr2A 92.667 150 10 1 2119 2267 82046039 82045890 4.900000e-52 215.0
27 TraesCS2D01G138600 chr2A 89.933 149 10 3 2124 2267 82028593 82028445 1.070000e-43 187.0
28 TraesCS2D01G138600 chr1A 89.570 930 82 11 1 919 589550637 589551562 0.000000e+00 1166.0
29 TraesCS2D01G138600 chr4B 88.853 933 87 15 1 919 5247161 5246232 0.000000e+00 1131.0
30 TraesCS2D01G138600 chr3B 88.769 926 92 10 1 919 821592549 821591629 0.000000e+00 1123.0
31 TraesCS2D01G138600 chr3B 87.847 864 73 19 77 919 763627728 763628580 0.000000e+00 985.0
32 TraesCS2D01G138600 chr3B 100.000 34 0 0 1263 1296 237351061 237351094 1.880000e-06 63.9
33 TraesCS2D01G138600 chr2B 97.701 348 8 0 920 1267 133583136 133582789 1.160000e-167 599.0
34 TraesCS2D01G138600 chr2B 94.350 354 20 0 920 1273 133528992 133528639 5.510000e-151 544.0
35 TraesCS2D01G138600 chr2B 100.000 50 0 0 2076 2125 453709061 453709012 2.400000e-15 93.5
36 TraesCS2D01G138600 chr2B 100.000 33 0 0 1261 1293 399838450 399838418 6.760000e-06 62.1
37 TraesCS2D01G138600 chr6D 90.476 126 11 1 1297 1421 412381199 412381324 5.010000e-37 165.0
38 TraesCS2D01G138600 chr6D 98.000 50 1 0 2076 2125 8995612 8995563 1.120000e-13 87.9
39 TraesCS2D01G138600 chr6D 98.000 50 1 0 2076 2125 22948453 22948502 1.120000e-13 87.9
40 TraesCS2D01G138600 chr6D 97.222 36 1 0 1258 1293 160461752 160461787 6.760000e-06 62.1
41 TraesCS2D01G138600 chr7B 100.000 50 0 0 2076 2125 629050580 629050531 2.400000e-15 93.5
42 TraesCS2D01G138600 chr5B 100.000 50 0 0 2076 2125 382230774 382230823 2.400000e-15 93.5
43 TraesCS2D01G138600 chr5A 100.000 50 0 0 2076 2125 562814376 562814327 2.400000e-15 93.5


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 TraesCS2D01G138600 chr2D 81457148 81459414 2266 True 4187.0 4187 100.000 1 2267 1 chr2D.!!$R2 2266
1 TraesCS2D01G138600 chr2D 573964978 573965769 791 False 1308.0 1308 96.474 1285 2076 1 chr2D.!!$F1 791
2 TraesCS2D01G138600 chr2D 620878572 620879456 884 False 1068.0 1068 88.299 1 919 1 chr2D.!!$F2 918
3 TraesCS2D01G138600 chr4D 435223489 435224281 792 True 1330.0 1330 96.977 1285 2076 1 chr4D.!!$R1 791
4 TraesCS2D01G138600 chr4D 51989564 51990357 793 False 1321.0 1321 96.725 1285 2076 1 chr4D.!!$F1 791
5 TraesCS2D01G138600 chrUn 103385979 103386772 793 True 1327.0 1327 96.851 1285 2076 1 chrUn.!!$R4 791
6 TraesCS2D01G138600 chrUn 45317075 45318001 926 True 1168.0 1168 89.581 1 919 1 chrUn.!!$R2 918
7 TraesCS2D01G138600 chrUn 45359827 45360753 926 True 1157.0 1157 89.389 1 919 1 chrUn.!!$R3 918
8 TraesCS2D01G138600 chr5D 479096770 479097583 813 True 1319.0 1319 95.956 1264 2076 1 chr5D.!!$R1 812
9 TraesCS2D01G138600 chr3D 611556279 611557090 811 True 1315.0 1315 95.936 1267 2076 1 chr3D.!!$R1 809
10 TraesCS2D01G138600 chr7D 525707718 525708510 792 True 1314.0 1314 96.599 1285 2076 1 chr7D.!!$R1 791
11 TraesCS2D01G138600 chr3A 740310685 740311477 792 False 1314.0 1314 96.599 1285 2076 1 chr3A.!!$F1 791
12 TraesCS2D01G138600 chr3A 36678979 36679896 917 True 1214.0 1214 90.554 1 918 1 chr3A.!!$R1 917
13 TraesCS2D01G138600 chr1D 447461600 447462392 792 False 1303.0 1303 96.348 1285 2076 1 chr1D.!!$F1 791
14 TraesCS2D01G138600 chr2A 41179238 41180156 918 True 1195.0 1195 90.183 1 922 1 chr2A.!!$R1 921
15 TraesCS2D01G138600 chr2A 678715734 678716655 921 False 1109.0 1109 88.629 1 920 1 chr2A.!!$F1 919
16 TraesCS2D01G138600 chr2A 82028445 82029617 1172 True 359.5 532 92.093 920 2267 2 chr2A.!!$R4 1347
17 TraesCS2D01G138600 chr1A 589550637 589551562 925 False 1166.0 1166 89.570 1 919 1 chr1A.!!$F1 918
18 TraesCS2D01G138600 chr4B 5246232 5247161 929 True 1131.0 1131 88.853 1 919 1 chr4B.!!$R1 918
19 TraesCS2D01G138600 chr3B 821591629 821592549 920 True 1123.0 1123 88.769 1 919 1 chr3B.!!$R1 918
20 TraesCS2D01G138600 chr3B 763627728 763628580 852 False 985.0 985 87.847 77 919 1 chr3B.!!$F2 842

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
653 706 1.078708 ACCGTCGGCATAGGTTTGG 60.079 57.895 12.28 0.0 33.96 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2109 2371 0.30776 GCCAGAACTTGTTGGACACG 59.692 55.0 0.0 0.0 36.55 4.49 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
95 98 1.755380 AGCAACGTCCCCTCTGTATAC 59.245 52.381 0.00 0.00 0.00 1.47
99 102 1.287146 ACGTCCCCTCTGTATACACCT 59.713 52.381 0.08 0.00 0.00 4.00
298 303 6.119144 AGAACATGACGGCACATTATTAAC 57.881 37.500 0.00 0.00 0.00 2.01
593 646 1.467342 CATATCTACACCGCGGATCGA 59.533 52.381 35.90 20.52 41.67 3.59
601 654 1.300156 CCGCGGATCGATGATGTGT 60.300 57.895 24.07 0.00 41.67 3.72
653 706 1.078708 ACCGTCGGCATAGGTTTGG 60.079 57.895 12.28 0.00 33.96 3.28
674 727 2.048597 CGTTAGCCGCTGGTCACA 60.049 61.111 2.16 0.00 0.00 3.58
685 738 3.717294 GGTCACAGGCGGGGTCAT 61.717 66.667 0.00 0.00 0.00 3.06
697 750 4.489771 GGTCATCGGGCCCCACTG 62.490 72.222 18.66 11.53 0.00 3.66
700 753 3.087253 CATCGGGCCCCACTGGTA 61.087 66.667 18.66 0.00 36.04 3.25
701 754 2.039831 ATCGGGCCCCACTGGTAT 60.040 61.111 18.66 0.00 36.04 2.73
702 755 2.452064 ATCGGGCCCCACTGGTATG 61.452 63.158 18.66 0.00 36.04 2.39
703 756 4.875713 CGGGCCCCACTGGTATGC 62.876 72.222 18.66 0.00 36.04 3.14
704 757 4.522975 GGGCCCCACTGGTATGCC 62.523 72.222 12.23 10.66 41.42 4.40
705 758 4.875713 GGCCCCACTGGTATGCCG 62.876 72.222 0.00 0.00 37.67 5.69
706 759 3.792736 GCCCCACTGGTATGCCGA 61.793 66.667 0.00 0.00 37.67 5.54
707 760 2.189521 CCCCACTGGTATGCCGAC 59.810 66.667 0.00 0.00 37.67 4.79
708 761 2.202878 CCCACTGGTATGCCGACG 60.203 66.667 0.00 0.00 37.67 5.12
709 762 2.202878 CCACTGGTATGCCGACGG 60.203 66.667 10.29 10.29 37.67 4.79
970 1041 9.075712 CATGGACATGGTTTCAGTTAACACTGT 62.076 40.741 8.61 0.00 41.75 3.55
1046 1117 3.652869 AGGTCCAATCAACTGAAGGAGAA 59.347 43.478 4.91 0.00 34.43 2.87
1053 1124 8.960591 TCCAATCAACTGAAGGAGAAAATAATC 58.039 33.333 1.34 0.00 31.48 1.75
1069 1140 2.817538 AATCGGGTTATTTTCGTGCG 57.182 45.000 0.00 0.00 0.00 5.34
1116 1187 3.568443 TGTAGACACACTCCAACACCTA 58.432 45.455 0.00 0.00 0.00 3.08
1119 1190 2.143925 GACACACTCCAACACCTAAGC 58.856 52.381 0.00 0.00 0.00 3.09
1141 1212 7.558161 AGCGTAGATCATCATTTTCATGAAA 57.442 32.000 16.91 16.91 42.93 2.69
1165 1236 5.551760 AATTGACTCCACATTAAGAAGCG 57.448 39.130 0.00 0.00 0.00 4.68
1201 1272 3.482156 TCAATAGCTCCAGCCTTCATC 57.518 47.619 0.00 0.00 43.38 2.92
1208 1279 0.904649 TCCAGCCTTCATCATGTCGT 59.095 50.000 0.00 0.00 0.00 4.34
1228 1299 0.174845 CCTTCGGTTCCGCATACTGA 59.825 55.000 6.35 0.00 0.00 3.41
1254 1325 0.537371 AAGGCTTTTGGGTGTCTCCG 60.537 55.000 0.00 0.00 37.00 4.63
1261 1332 1.488390 TTGGGTGTCTCCGGGTATAC 58.512 55.000 0.00 0.00 37.00 1.47
1262 1333 0.335705 TGGGTGTCTCCGGGTATACA 59.664 55.000 0.00 0.00 37.00 2.29
1293 1364 0.618458 TCTAGCAGACCCCGCAAAAT 59.382 50.000 0.00 0.00 0.00 1.82
1318 1389 2.326550 CAGTTCGCGCAAAACCGT 59.673 55.556 16.51 0.00 0.00 4.83
1492 1581 8.599624 ATCTGAAATTTGTCATAGGGTTTCAT 57.400 30.769 0.00 0.00 35.71 2.57
1930 2024 4.104383 ACTTTTCTCTCCTCAATGGCAA 57.896 40.909 0.00 0.00 35.26 4.52
1976 2237 3.749609 AGCATTTGCCATTTTTCTTGCTC 59.250 39.130 0.00 0.00 43.38 4.26
2076 2338 3.371380 GGCATCAATCTTCTCCCTCAAGT 60.371 47.826 0.00 0.00 0.00 3.16
2077 2339 4.268359 GCATCAATCTTCTCCCTCAAGTT 58.732 43.478 0.00 0.00 0.00 2.66
2078 2340 4.704057 GCATCAATCTTCTCCCTCAAGTTT 59.296 41.667 0.00 0.00 0.00 2.66
2079 2341 5.392811 GCATCAATCTTCTCCCTCAAGTTTG 60.393 44.000 0.00 0.00 34.14 2.93
2080 2342 5.567037 TCAATCTTCTCCCTCAAGTTTGA 57.433 39.130 0.00 0.00 37.29 2.69
2081 2343 5.940617 TCAATCTTCTCCCTCAAGTTTGAA 58.059 37.500 4.27 0.00 36.95 2.69
2082 2344 6.364701 TCAATCTTCTCCCTCAAGTTTGAAA 58.635 36.000 4.27 0.00 36.95 2.69
2083 2345 6.488006 TCAATCTTCTCCCTCAAGTTTGAAAG 59.512 38.462 4.27 0.00 36.95 2.62
2084 2346 4.718961 TCTTCTCCCTCAAGTTTGAAAGG 58.281 43.478 0.00 0.96 36.64 3.11
2085 2347 3.508845 TCTCCCTCAAGTTTGAAAGGG 57.491 47.619 11.21 11.21 41.61 3.95
2086 2348 2.108250 TCTCCCTCAAGTTTGAAAGGGG 59.892 50.000 15.39 12.82 40.97 4.79
2087 2349 0.969149 CCCTCAAGTTTGAAAGGGGC 59.031 55.000 10.06 0.00 38.42 5.80
2088 2350 1.481242 CCCTCAAGTTTGAAAGGGGCT 60.481 52.381 10.06 0.00 38.42 5.19
2089 2351 2.319844 CCTCAAGTTTGAAAGGGGCTT 58.680 47.619 0.00 0.00 36.64 4.35
2090 2352 2.036346 CCTCAAGTTTGAAAGGGGCTTG 59.964 50.000 0.00 0.00 36.64 4.01
2091 2353 2.958355 CTCAAGTTTGAAAGGGGCTTGA 59.042 45.455 7.99 7.99 41.89 3.02
2092 2354 3.575687 CTCAAGTTTGAAAGGGGCTTGAT 59.424 43.478 8.52 0.00 42.76 2.57
2093 2355 3.573967 TCAAGTTTGAAAGGGGCTTGATC 59.426 43.478 5.04 0.00 40.07 2.92
2094 2356 3.243359 AGTTTGAAAGGGGCTTGATCA 57.757 42.857 0.00 0.00 0.00 2.92
2095 2357 3.575805 AGTTTGAAAGGGGCTTGATCAA 58.424 40.909 8.12 8.12 0.00 2.57
2096 2358 4.162651 AGTTTGAAAGGGGCTTGATCAAT 58.837 39.130 8.96 0.00 30.81 2.57
2097 2359 4.020839 AGTTTGAAAGGGGCTTGATCAATG 60.021 41.667 8.96 4.68 30.81 2.82
2098 2360 3.173953 TGAAAGGGGCTTGATCAATGT 57.826 42.857 8.96 0.00 0.00 2.71
2099 2361 3.091545 TGAAAGGGGCTTGATCAATGTC 58.908 45.455 8.96 4.87 0.00 3.06
2100 2362 2.905415 AAGGGGCTTGATCAATGTCA 57.095 45.000 8.96 0.00 0.00 3.58
2101 2363 2.905415 AGGGGCTTGATCAATGTCAA 57.095 45.000 8.96 0.00 36.70 3.18
2102 2364 2.450476 AGGGGCTTGATCAATGTCAAC 58.550 47.619 8.96 2.70 34.58 3.18
2103 2365 1.478105 GGGGCTTGATCAATGTCAACC 59.522 52.381 8.96 5.32 34.58 3.77
2104 2366 1.133025 GGGCTTGATCAATGTCAACCG 59.867 52.381 8.96 0.00 34.58 4.44
2105 2367 1.468054 GGCTTGATCAATGTCAACCGC 60.468 52.381 8.96 6.07 34.58 5.68
2106 2368 1.791555 GCTTGATCAATGTCAACCGCG 60.792 52.381 8.96 0.00 34.58 6.46
2107 2369 1.464608 CTTGATCAATGTCAACCGCGT 59.535 47.619 8.96 0.00 34.58 6.01
2108 2370 1.518325 TGATCAATGTCAACCGCGTT 58.482 45.000 4.92 0.00 0.00 4.84
2109 2371 1.463056 TGATCAATGTCAACCGCGTTC 59.537 47.619 4.92 0.00 0.00 3.95
2110 2372 0.442310 ATCAATGTCAACCGCGTTCG 59.558 50.000 4.92 0.00 0.00 3.95
2111 2373 0.876777 TCAATGTCAACCGCGTTCGT 60.877 50.000 4.92 0.00 0.00 3.85
2112 2374 0.721155 CAATGTCAACCGCGTTCGTG 60.721 55.000 4.92 0.00 0.00 4.35
2113 2375 1.155424 AATGTCAACCGCGTTCGTGT 61.155 50.000 4.92 0.00 0.00 4.49
2114 2376 1.554042 ATGTCAACCGCGTTCGTGTC 61.554 55.000 4.92 0.00 0.00 3.67
2115 2377 2.659244 TCAACCGCGTTCGTGTCC 60.659 61.111 4.92 0.00 0.00 4.02
2116 2378 2.962786 CAACCGCGTTCGTGTCCA 60.963 61.111 4.92 0.00 0.00 4.02
2117 2379 2.202905 AACCGCGTTCGTGTCCAA 60.203 55.556 4.92 0.00 0.00 3.53
2118 2380 2.527867 AACCGCGTTCGTGTCCAAC 61.528 57.895 4.92 0.00 0.00 3.77
2119 2381 2.962786 CCGCGTTCGTGTCCAACA 60.963 61.111 4.92 0.00 0.00 3.33
2120 2382 2.526993 CCGCGTTCGTGTCCAACAA 61.527 57.895 4.92 0.00 0.00 2.83
2121 2383 1.083657 CGCGTTCGTGTCCAACAAG 60.084 57.895 0.00 0.00 0.00 3.16
2122 2384 1.758319 CGCGTTCGTGTCCAACAAGT 61.758 55.000 0.00 0.00 0.00 3.16
2141 2403 7.396540 ACAAGTTCTGGCATTAAAGAATAGG 57.603 36.000 0.00 0.00 35.03 2.57
2217 2481 7.857885 GGAACAAAAGACAACTTTCAGTCATAG 59.142 37.037 0.00 0.00 44.32 2.23
2239 2503 6.910536 AGTTCTCATAAAATGAACCTAGCG 57.089 37.500 0.00 0.00 40.42 4.26
2247 2511 5.438761 AAAATGAACCTAGCGGCAATATC 57.561 39.130 1.45 0.00 0.00 1.63
2252 2518 2.480845 ACCTAGCGGCAATATCGTTTC 58.519 47.619 1.45 0.00 0.00 2.78
2263 2529 5.350365 GGCAATATCGTTTCTACAGAACACA 59.650 40.000 0.00 0.00 33.13 3.72
2265 2531 6.736853 GCAATATCGTTTCTACAGAACACAAC 59.263 38.462 0.00 0.00 33.13 3.32
2266 2532 7.570507 GCAATATCGTTTCTACAGAACACAACA 60.571 37.037 0.00 0.00 33.13 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 98 1.503542 GAAACAGCCGCATCAGGTG 59.496 57.895 0.00 0.00 0.00 4.00
215 219 5.057149 ACTGCTATGACGACAGAAGTTTTT 58.943 37.500 0.00 0.00 35.38 1.94
582 635 1.300156 CACATCATCGATCCGCGGT 60.300 57.895 27.15 12.96 41.33 5.68
601 654 0.038251 GTCGGCATATCTCCGCATGA 60.038 55.000 0.00 0.00 46.05 3.07
684 737 2.039831 ATACCAGTGGGGCCCGAT 60.040 61.111 19.83 5.66 42.05 4.18
685 738 3.087253 CATACCAGTGGGGCCCGA 61.087 66.667 19.83 9.88 42.05 5.14
703 756 2.890474 GCATACACCAGCCGTCGG 60.890 66.667 6.99 6.99 0.00 4.79
704 757 2.890474 GGCATACACCAGCCGTCG 60.890 66.667 0.00 0.00 41.70 5.12
709 762 2.890474 CCGTCGGCATACACCAGC 60.890 66.667 0.00 0.00 0.00 4.85
1053 1124 1.060986 GTACCGCACGAAAATAACCCG 59.939 52.381 0.00 0.00 0.00 5.28
1065 1136 1.287425 GCTCAACTATGGTACCGCAC 58.713 55.000 7.57 0.00 0.00 5.34
1116 1187 7.558161 TTCATGAAAATGATGATCTACGCTT 57.442 32.000 5.45 0.00 29.96 4.68
1141 1212 6.381801 CGCTTCTTAATGTGGAGTCAATTTT 58.618 36.000 0.00 0.00 0.00 1.82
1165 1236 3.795623 ATTGAATTCACCAGCATGAGC 57.204 42.857 7.89 0.00 39.69 4.26
1208 1279 2.229699 TCAGTATGCGGAACCGAAGGA 61.230 52.381 17.63 0.98 46.20 3.36
1228 1299 2.212110 CCCAAAAGCCTTGCTGCCT 61.212 57.895 0.00 0.00 39.62 4.75
1240 1311 1.364269 ATACCCGGAGACACCCAAAA 58.636 50.000 0.73 0.00 34.64 2.44
1254 1325 5.855740 AGAGTTGCTCTTAGTGTATACCC 57.144 43.478 0.00 0.00 37.60 3.69
1261 1332 4.420168 GTCTGCTAGAGTTGCTCTTAGTG 58.580 47.826 3.87 0.00 41.50 2.74
1262 1333 3.445805 GGTCTGCTAGAGTTGCTCTTAGT 59.554 47.826 3.87 0.00 41.50 2.24
1318 1389 3.350612 CTCGTCGGCCCGCAAAAA 61.351 61.111 0.00 0.00 0.00 1.94
1331 1402 1.743321 GCATCTGAGCTAGCCCTCGT 61.743 60.000 12.13 0.00 34.56 4.18
1343 1414 0.038166 GTTTGGGGGTCTGCATCTGA 59.962 55.000 0.00 0.00 0.00 3.27
1450 1539 7.524294 TTTCAGATTTGCAGTTTTTCTGTTC 57.476 32.000 10.96 0.00 45.23 3.18
1930 2024 1.835927 GAAGAGGGGCTGTGCAGAGT 61.836 60.000 13.05 0.00 0.00 3.24
1976 2237 2.997485 CCGAAAGAAGGCAAAAGAGG 57.003 50.000 0.00 0.00 0.00 3.69
2076 2338 3.903090 ACATTGATCAAGCCCCTTTCAAA 59.097 39.130 14.54 0.00 28.43 2.69
2077 2339 3.509442 ACATTGATCAAGCCCCTTTCAA 58.491 40.909 14.54 0.00 28.93 2.69
2078 2340 3.091545 GACATTGATCAAGCCCCTTTCA 58.908 45.455 14.54 0.00 0.00 2.69
2079 2341 3.091545 TGACATTGATCAAGCCCCTTTC 58.908 45.455 14.54 0.10 0.00 2.62
2080 2342 3.173953 TGACATTGATCAAGCCCCTTT 57.826 42.857 14.54 0.00 0.00 3.11
2081 2343 2.827921 GTTGACATTGATCAAGCCCCTT 59.172 45.455 14.54 0.00 39.25 3.95
2082 2344 2.450476 GTTGACATTGATCAAGCCCCT 58.550 47.619 14.54 0.00 39.25 4.79
2083 2345 1.478105 GGTTGACATTGATCAAGCCCC 59.522 52.381 14.54 4.27 46.61 5.80
2084 2346 2.947448 GGTTGACATTGATCAAGCCC 57.053 50.000 14.54 5.65 46.61 5.19
2087 2349 1.464608 ACGCGGTTGACATTGATCAAG 59.535 47.619 14.54 8.57 39.25 3.02
2088 2350 1.518325 ACGCGGTTGACATTGATCAA 58.482 45.000 11.26 11.26 36.23 2.57
2089 2351 1.463056 GAACGCGGTTGACATTGATCA 59.537 47.619 12.47 0.00 0.00 2.92
2090 2352 1.526986 CGAACGCGGTTGACATTGATC 60.527 52.381 12.47 0.00 0.00 2.92
2091 2353 0.442310 CGAACGCGGTTGACATTGAT 59.558 50.000 12.47 0.00 0.00 2.57
2092 2354 0.876777 ACGAACGCGGTTGACATTGA 60.877 50.000 20.55 0.00 43.17 2.57
2093 2355 0.721155 CACGAACGCGGTTGACATTG 60.721 55.000 20.55 1.17 43.17 2.82
2094 2356 1.155424 ACACGAACGCGGTTGACATT 61.155 50.000 20.55 0.00 43.17 2.71
2095 2357 1.554042 GACACGAACGCGGTTGACAT 61.554 55.000 20.55 2.03 43.17 3.06
2096 2358 2.202770 ACACGAACGCGGTTGACA 60.203 55.556 20.55 0.00 43.17 3.58
2097 2359 2.542896 GACACGAACGCGGTTGAC 59.457 61.111 20.55 0.00 43.17 3.18
2098 2360 2.659244 GGACACGAACGCGGTTGA 60.659 61.111 20.55 0.00 43.17 3.18
2099 2361 2.526993 TTGGACACGAACGCGGTTG 61.527 57.895 10.59 10.59 43.17 3.77
2100 2362 2.202905 TTGGACACGAACGCGGTT 60.203 55.556 12.47 1.69 43.17 4.44
2101 2363 2.963320 GTTGGACACGAACGCGGT 60.963 61.111 12.47 1.91 43.17 5.68
2102 2364 2.424576 CTTGTTGGACACGAACGCGG 62.425 60.000 12.47 0.00 43.17 6.46
2103 2365 1.083657 CTTGTTGGACACGAACGCG 60.084 57.895 3.53 3.53 44.79 6.01
2104 2366 0.375803 AACTTGTTGGACACGAACGC 59.624 50.000 0.00 0.00 0.00 4.84
2105 2367 1.931172 AGAACTTGTTGGACACGAACG 59.069 47.619 0.00 0.00 0.00 3.95
2106 2368 2.031683 CCAGAACTTGTTGGACACGAAC 59.968 50.000 0.00 0.00 36.55 3.95
2107 2369 2.285083 CCAGAACTTGTTGGACACGAA 58.715 47.619 0.00 0.00 36.55 3.85
2108 2370 1.948104 CCAGAACTTGTTGGACACGA 58.052 50.000 0.00 0.00 36.55 4.35
2109 2371 0.307760 GCCAGAACTTGTTGGACACG 59.692 55.000 0.00 0.00 36.55 4.49
2110 2372 1.388547 TGCCAGAACTTGTTGGACAC 58.611 50.000 0.00 0.00 36.55 3.67
2111 2373 2.363306 ATGCCAGAACTTGTTGGACA 57.637 45.000 0.00 0.00 36.55 4.02
2112 2374 4.846779 TTAATGCCAGAACTTGTTGGAC 57.153 40.909 0.00 0.00 36.55 4.02
2113 2375 5.136828 TCTTTAATGCCAGAACTTGTTGGA 58.863 37.500 0.00 0.00 36.55 3.53
2114 2376 5.452078 TCTTTAATGCCAGAACTTGTTGG 57.548 39.130 0.00 0.00 37.53 3.77
2115 2377 7.756722 CCTATTCTTTAATGCCAGAACTTGTTG 59.243 37.037 0.00 0.00 31.80 3.33
2116 2378 7.451566 ACCTATTCTTTAATGCCAGAACTTGTT 59.548 33.333 0.00 0.00 31.80 2.83
2117 2379 6.948309 ACCTATTCTTTAATGCCAGAACTTGT 59.052 34.615 0.00 0.00 31.80 3.16
2118 2380 7.396540 ACCTATTCTTTAATGCCAGAACTTG 57.603 36.000 0.00 0.00 31.80 3.16
2119 2381 9.528489 TTTACCTATTCTTTAATGCCAGAACTT 57.472 29.630 0.00 0.00 31.80 2.66
2120 2382 9.528489 TTTTACCTATTCTTTAATGCCAGAACT 57.472 29.630 0.00 0.00 31.80 3.01
2150 2412 9.732130 GGATTAGCATCCTAATATCAAGAACTT 57.268 33.333 0.00 0.00 45.41 2.66
2173 2435 3.918294 TCCGGGAAAATACGAAAGGAT 57.082 42.857 0.00 0.00 34.80 3.24
2174 2436 3.244491 TGTTCCGGGAAAATACGAAAGGA 60.244 43.478 11.82 0.00 0.00 3.36
2175 2437 3.075884 TGTTCCGGGAAAATACGAAAGG 58.924 45.455 11.82 0.00 0.00 3.11
2176 2438 4.752661 TTGTTCCGGGAAAATACGAAAG 57.247 40.909 11.82 0.00 0.00 2.62
2177 2439 5.298777 TCTTTTGTTCCGGGAAAATACGAAA 59.701 36.000 11.82 10.82 0.00 3.46
2178 2440 4.820716 TCTTTTGTTCCGGGAAAATACGAA 59.179 37.500 11.82 3.08 0.00 3.85
2180 2442 4.023878 TGTCTTTTGTTCCGGGAAAATACG 60.024 41.667 11.82 0.00 0.00 3.06
2181 2443 5.441709 TGTCTTTTGTTCCGGGAAAATAC 57.558 39.130 11.82 6.20 0.00 1.89
2217 2481 5.504173 GCCGCTAGGTTCATTTTATGAGAAC 60.504 44.000 0.00 0.00 40.58 3.01
2239 2503 5.350365 TGTGTTCTGTAGAAACGATATTGCC 59.650 40.000 0.00 0.00 35.58 4.52


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

AutoCloner maintained by Alex Coulton.