Multiple sequence alignment - TraesCS2B01G478400

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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 TraesCS2B01G478400 chr2B 100.000 4091 0 0 1 4091 675513404 675517494 0.000000e+00 7555.0
1 TraesCS2B01G478400 chr2D 93.040 2543 116 30 1561 4091 564384727 564387220 0.000000e+00 3659.0
2 TraesCS2B01G478400 chr2D 95.195 1311 43 9 68 1372 564382939 564384235 0.000000e+00 2054.0
3 TraesCS2B01G478400 chr2A 92.510 2390 136 25 1716 4091 705069221 705071581 0.000000e+00 3382.0
4 TraesCS2B01G478400 chr2A 93.333 1395 59 19 1 1382 705067348 705068721 0.000000e+00 2030.0
5 TraesCS2B01G478400 chr2A 90.071 141 9 2 1398 1534 705068706 705068845 1.170000e-40 178.0
6 TraesCS2B01G478400 chr2A 93.750 48 1 2 1675 1721 683140152 683140198 2.040000e-08 71.3
7 TraesCS2B01G478400 chr2A 86.667 60 5 3 1675 1732 769218647 769218705 3.410000e-06 63.9
8 TraesCS2B01G478400 chr4B 79.459 185 28 8 1112 1291 519824622 519824443 5.550000e-24 122.0
9 TraesCS2B01G478400 chr4B 91.837 49 2 2 1675 1723 626739013 626738967 2.640000e-07 67.6
10 TraesCS2B01G478400 chr4D 80.556 144 24 4 1150 1291 423429820 423429679 1.550000e-19 108.0
11 TraesCS2B01G478400 chr4D 95.745 47 0 2 1675 1720 502713783 502713828 1.580000e-09 75.0
12 TraesCS2B01G478400 chr4A 78.333 180 29 8 1114 1288 40860220 40860394 1.550000e-19 108.0
13 TraesCS2B01G478400 chr4A 92.000 50 1 2 1675 1724 615436845 615436891 2.640000e-07 67.6
14 TraesCS2B01G478400 chr3B 77.209 215 24 16 1124 1315 823028985 823029197 7.230000e-18 102.0
15 TraesCS2B01G478400 chr3B 95.745 47 0 2 1675 1721 203376667 203376711 1.580000e-09 75.0
16 TraesCS2B01G478400 chr5B 79.310 145 24 6 1150 1291 580366672 580366531 3.370000e-16 97.1
17 TraesCS2B01G478400 chr3A 75.814 215 27 17 1124 1315 749469722 749469934 7.290000e-13 86.1
18 TraesCS2B01G478400 chr3D 75.701 214 27 17 1124 1314 613779925 613780136 2.620000e-12 84.2
19 TraesCS2B01G478400 chr1A 92.000 50 0 3 1675 1724 42681081 42681036 2.640000e-07 67.6
20 TraesCS2B01G478400 chr5A 89.091 55 3 3 1675 1729 48918127 48918178 9.490000e-07 65.8
21 TraesCS2B01G478400 chr1B 85.714 63 4 5 1675 1734 164832124 164832184 1.230000e-05 62.1


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 TraesCS2B01G478400 chr2B 675513404 675517494 4090 False 7555.000000 7555 100.000000 1 4091 1 chr2B.!!$F1 4090
1 TraesCS2B01G478400 chr2D 564382939 564387220 4281 False 2856.500000 3659 94.117500 68 4091 2 chr2D.!!$F1 4023
2 TraesCS2B01G478400 chr2A 705067348 705071581 4233 False 1863.333333 3382 91.971333 1 4091 3 chr2A.!!$F3 4090

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
929 944 0.036952 TAGGCAGCACAAGTCAGAGC 60.037 55.0 0.0 0.0 0.0 4.09 F
2036 2515 0.665835 CCGAGCAGCTAACGAGAGAT 59.334 55.0 5.1 0.0 0.0 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2677 3165 0.380024 CACGTGGATTGTTGTGCACA 59.620 50.0 17.42 17.42 40.04 4.57 R
4000 4504 0.395586 TCAGCCACAAAAGCCACACT 60.396 50.0 0.00 0.00 0.00 3.55 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
23 24 0.916086 TCTCTCCTCTTCTCTCGGCT 59.084 55.000 0.00 0.00 0.00 5.52
26 27 1.000270 TCCTCTTCTCTCGGCTGCT 60.000 57.895 0.00 0.00 0.00 4.24
53 55 4.212143 ACGTATCATGGATGGATGGATG 57.788 45.455 0.00 0.00 0.00 3.51
54 56 3.054875 ACGTATCATGGATGGATGGATGG 60.055 47.826 0.00 0.00 0.00 3.51
55 57 3.198417 CGTATCATGGATGGATGGATGGA 59.802 47.826 0.00 0.00 0.00 3.41
56 58 4.141551 CGTATCATGGATGGATGGATGGAT 60.142 45.833 0.00 0.00 0.00 3.41
111 113 2.629051 GGCTTAAACATCAGCCGTACT 58.371 47.619 0.00 0.00 46.19 2.73
115 117 2.113860 AAACATCAGCCGTACTGCAT 57.886 45.000 12.05 0.00 46.76 3.96
308 315 3.044959 GCTTTCTGATCTGTAAAGCGC 57.955 47.619 21.52 0.00 43.81 5.92
309 316 2.223135 GCTTTCTGATCTGTAAAGCGCC 60.223 50.000 21.52 0.00 43.81 6.53
310 317 2.760634 TTCTGATCTGTAAAGCGCCA 57.239 45.000 2.29 0.00 0.00 5.69
311 318 2.010145 TCTGATCTGTAAAGCGCCAC 57.990 50.000 2.29 0.00 0.00 5.01
312 319 1.550524 TCTGATCTGTAAAGCGCCACT 59.449 47.619 2.29 0.00 0.00 4.00
326 333 1.808234 GCCACTACGCGCTATCGTTG 61.808 60.000 5.73 0.00 43.15 4.10
329 336 2.278989 TACGCGCTATCGTTGGCC 60.279 61.111 5.73 0.00 43.15 5.36
392 403 5.639757 TGGTCATTTTATGTGATTTCTGCG 58.360 37.500 0.00 0.00 0.00 5.18
413 424 0.735471 GGGCTTTTCTTCTCCATCGC 59.265 55.000 0.00 0.00 0.00 4.58
592 604 1.765230 AAACGATAGGAGTCCTCGCT 58.235 50.000 17.09 2.58 43.77 4.93
666 678 3.364964 GCAAGTACCTGAAAACCATCACG 60.365 47.826 0.00 0.00 0.00 4.35
675 687 2.798148 AAACCATCACGACCGGAGCC 62.798 60.000 9.46 0.00 0.00 4.70
698 710 4.020128 TTTTTGCCTTTTCGCGCC 57.980 50.000 0.00 0.00 0.00 6.53
778 790 1.339631 GCCTATATAATGGCCGCCACA 60.340 52.381 16.16 6.07 43.11 4.17
807 819 2.734723 CTACGCACACGCAGCAGT 60.735 61.111 0.00 0.00 45.53 4.40
924 939 2.166270 GCAGTAGGCAGCACAAGTC 58.834 57.895 0.00 0.00 43.97 3.01
925 940 0.603707 GCAGTAGGCAGCACAAGTCA 60.604 55.000 0.00 0.00 43.97 3.41
926 941 1.436600 CAGTAGGCAGCACAAGTCAG 58.563 55.000 0.00 0.00 0.00 3.51
927 942 1.001293 CAGTAGGCAGCACAAGTCAGA 59.999 52.381 0.00 0.00 0.00 3.27
928 943 1.274728 AGTAGGCAGCACAAGTCAGAG 59.725 52.381 0.00 0.00 0.00 3.35
929 944 0.036952 TAGGCAGCACAAGTCAGAGC 60.037 55.000 0.00 0.00 0.00 4.09
1218 1233 2.529744 GGAGGACCACAGCCAGGTT 61.530 63.158 0.00 0.00 40.09 3.50
1224 1239 1.344953 ACCACAGCCAGGTTGAGACA 61.345 55.000 10.86 0.00 35.33 3.41
1356 1371 6.354829 CCCTTCCTTCTACCCCATTTATTTCT 60.355 42.308 0.00 0.00 0.00 2.52
1357 1372 7.126061 CCTTCCTTCTACCCCATTTATTTCTT 58.874 38.462 0.00 0.00 0.00 2.52
1359 1374 7.278724 TCCTTCTACCCCATTTATTTCTTCA 57.721 36.000 0.00 0.00 0.00 3.02
1360 1375 7.346471 TCCTTCTACCCCATTTATTTCTTCAG 58.654 38.462 0.00 0.00 0.00 3.02
1361 1376 6.039829 CCTTCTACCCCATTTATTTCTTCAGC 59.960 42.308 0.00 0.00 0.00 4.26
1362 1377 6.327386 TCTACCCCATTTATTTCTTCAGCT 57.673 37.500 0.00 0.00 0.00 4.24
1363 1378 7.446106 TCTACCCCATTTATTTCTTCAGCTA 57.554 36.000 0.00 0.00 0.00 3.32
1364 1379 8.045720 TCTACCCCATTTATTTCTTCAGCTAT 57.954 34.615 0.00 0.00 0.00 2.97
1365 1380 6.966534 ACCCCATTTATTTCTTCAGCTATG 57.033 37.500 0.00 0.00 0.00 2.23
1366 1381 6.435164 ACCCCATTTATTTCTTCAGCTATGT 58.565 36.000 0.00 0.00 0.00 2.29
1367 1382 6.897413 ACCCCATTTATTTCTTCAGCTATGTT 59.103 34.615 0.00 0.00 0.00 2.71
1368 1383 7.400052 ACCCCATTTATTTCTTCAGCTATGTTT 59.600 33.333 0.00 0.00 0.00 2.83
1369 1384 8.260114 CCCCATTTATTTCTTCAGCTATGTTTT 58.740 33.333 0.00 0.00 0.00 2.43
1370 1385 9.090692 CCCATTTATTTCTTCAGCTATGTTTTG 57.909 33.333 0.00 0.00 0.00 2.44
1371 1386 9.643693 CCATTTATTTCTTCAGCTATGTTTTGT 57.356 29.630 0.00 0.00 0.00 2.83
1374 1389 9.677567 TTTATTTCTTCAGCTATGTTTTGTCAC 57.322 29.630 0.00 0.00 0.00 3.67
1375 1390 6.942532 TTTCTTCAGCTATGTTTTGTCACT 57.057 33.333 0.00 0.00 0.00 3.41
1376 1391 5.929697 TCTTCAGCTATGTTTTGTCACTG 57.070 39.130 0.00 0.00 0.00 3.66
1377 1392 5.368145 TCTTCAGCTATGTTTTGTCACTGT 58.632 37.500 0.00 0.00 0.00 3.55
1378 1393 6.521162 TCTTCAGCTATGTTTTGTCACTGTA 58.479 36.000 0.00 0.00 0.00 2.74
1379 1394 6.423905 TCTTCAGCTATGTTTTGTCACTGTAC 59.576 38.462 0.00 0.00 0.00 2.90
1380 1395 5.853936 TCAGCTATGTTTTGTCACTGTACT 58.146 37.500 0.00 0.00 0.00 2.73
1381 1396 6.288294 TCAGCTATGTTTTGTCACTGTACTT 58.712 36.000 0.00 0.00 0.00 2.24
1382 1397 6.765989 TCAGCTATGTTTTGTCACTGTACTTT 59.234 34.615 0.00 0.00 0.00 2.66
1383 1398 7.282224 TCAGCTATGTTTTGTCACTGTACTTTT 59.718 33.333 0.00 0.00 0.00 2.27
1384 1399 7.915397 CAGCTATGTTTTGTCACTGTACTTTTT 59.085 33.333 0.00 0.00 0.00 1.94
1418 1434 5.424757 AGTTTTGTCACTGTACTTGTGCTA 58.575 37.500 12.56 4.16 35.58 3.49
1452 1571 7.011016 GCTTACAAATTGGTAGCAGTTGTTTTT 59.989 33.333 23.00 8.69 34.43 1.94
1584 2063 4.846137 GCAACATAGTTCAACTGCGTTTAG 59.154 41.667 0.00 0.00 0.00 1.85
1621 2100 5.809001 TCCTTTGATGACTGCTACAGATTT 58.191 37.500 0.78 0.00 35.18 2.17
1666 2145 5.434408 TCTGATTCATCTCCCTGACAATTG 58.566 41.667 3.24 3.24 0.00 2.32
1672 2151 5.248640 TCATCTCCCTGACAATTGTTCTTC 58.751 41.667 13.36 0.00 0.00 2.87
1676 2155 4.906618 TCCCTGACAATTGTTCTTCCTAC 58.093 43.478 13.36 0.00 0.00 3.18
1678 2157 5.783360 TCCCTGACAATTGTTCTTCCTACTA 59.217 40.000 13.36 0.00 0.00 1.82
1680 2159 6.940298 CCCTGACAATTGTTCTTCCTACTAAA 59.060 38.462 13.36 0.00 0.00 1.85
1681 2160 7.119846 CCCTGACAATTGTTCTTCCTACTAAAG 59.880 40.741 13.36 0.00 0.00 1.85
1682 2161 7.661847 CCTGACAATTGTTCTTCCTACTAAAGT 59.338 37.037 13.36 0.00 0.00 2.66
1683 2162 8.974060 TGACAATTGTTCTTCCTACTAAAGTT 57.026 30.769 13.36 0.00 0.00 2.66
1688 2167 8.834749 ATTGTTCTTCCTACTAAAGTTGAGTC 57.165 34.615 0.00 0.00 0.00 3.36
1689 2168 7.356089 TGTTCTTCCTACTAAAGTTGAGTCA 57.644 36.000 0.00 0.00 0.00 3.41
1691 2170 8.088981 TGTTCTTCCTACTAAAGTTGAGTCATC 58.911 37.037 0.00 0.00 0.00 2.92
1693 2172 9.529823 TTCTTCCTACTAAAGTTGAGTCATCTA 57.470 33.333 4.14 0.00 0.00 1.98
1694 2173 9.702253 TCTTCCTACTAAAGTTGAGTCATCTAT 57.298 33.333 4.14 0.00 0.00 1.98
1701 2180 9.793259 ACTAAAGTTGAGTCATCTATTTTGGAA 57.207 29.630 4.14 0.00 28.91 3.53
1703 2182 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
1704 2183 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
1705 2184 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
1706 2185 5.800296 TGAGTCATCTATTTTGGAACGGAA 58.200 37.500 0.00 0.00 0.00 4.30
1707 2186 5.874810 TGAGTCATCTATTTTGGAACGGAAG 59.125 40.000 0.00 0.00 0.00 3.46
1708 2187 5.186198 AGTCATCTATTTTGGAACGGAAGG 58.814 41.667 0.00 0.00 0.00 3.46
1709 2188 5.045869 AGTCATCTATTTTGGAACGGAAGGA 60.046 40.000 0.00 0.00 0.00 3.36
1710 2189 5.294552 GTCATCTATTTTGGAACGGAAGGAG 59.705 44.000 0.00 0.00 0.00 3.69
1711 2190 4.903045 TCTATTTTGGAACGGAAGGAGT 57.097 40.909 0.00 0.00 0.00 3.85
1712 2191 6.155565 TCATCTATTTTGGAACGGAAGGAGTA 59.844 38.462 0.00 0.00 0.00 2.59
1713 2192 6.363167 TCTATTTTGGAACGGAAGGAGTAA 57.637 37.500 0.00 0.00 0.00 2.24
1714 2193 6.168389 TCTATTTTGGAACGGAAGGAGTAAC 58.832 40.000 0.00 0.00 0.00 2.50
1823 2302 5.181748 GGAGCAGTATCTGAGAATGTTGTT 58.818 41.667 1.60 0.00 32.44 2.83
1835 2314 4.798574 AGAATGTTGTTCGAAATGCCTTC 58.201 39.130 0.00 1.30 0.00 3.46
1992 2471 2.030862 GGGCGGTTGTCGGTTGTA 59.969 61.111 0.00 0.00 39.69 2.41
2036 2515 0.665835 CCGAGCAGCTAACGAGAGAT 59.334 55.000 5.10 0.00 0.00 2.75
2106 2585 5.882000 CACCCTGATGATTCACAGATTGTTA 59.118 40.000 14.14 0.00 36.38 2.41
2202 2682 9.349713 CCTTGTATATTTATGAAGCTTGGGTAA 57.650 33.333 2.10 0.00 0.00 2.85
2205 2685 9.688091 TGTATATTTATGAAGCTTGGGTAAACA 57.312 29.630 2.10 0.00 0.00 2.83
2349 2837 0.685097 GGTGGTCACTAGGTGCAGAA 59.315 55.000 0.00 0.00 32.98 3.02
2377 2865 8.995220 TGTATCACTATGTTCAGGTGTTTTTAC 58.005 33.333 0.00 0.00 33.30 2.01
2453 2941 6.486657 TCTTCTTTGGAACATTCGTCTGATTT 59.513 34.615 0.00 0.00 39.30 2.17
2626 3114 8.169268 CGTCCACAAGATAGTTTTGTTATCTTC 58.831 37.037 4.90 0.00 42.85 2.87
2632 3120 8.390354 CAAGATAGTTTTGTTATCTTCGCATCA 58.610 33.333 4.90 0.00 42.85 3.07
2677 3165 0.889186 ACCAGCAAGCCGTCGAAATT 60.889 50.000 0.00 0.00 0.00 1.82
2826 3315 7.222417 TGTGTTGATGTGTAAAATTCTGCTTTG 59.778 33.333 0.00 0.00 0.00 2.77
2834 3323 7.010367 TGTGTAAAATTCTGCTTTGCTTCTTTG 59.990 33.333 0.00 0.00 0.00 2.77
2856 3345 1.490490 CAGGGTATTGCAAGGAGGCTA 59.510 52.381 4.94 0.00 34.04 3.93
2934 3423 5.813513 TTACGAAACTAGAGAAAGGGGTT 57.186 39.130 0.00 0.00 0.00 4.11
2937 3426 2.764439 AACTAGAGAAAGGGGTTCGC 57.236 50.000 0.00 0.00 41.52 4.70
3381 3874 0.244721 CTCGTGAGATGTGGTCTGCA 59.755 55.000 0.00 0.00 40.84 4.41
3388 3881 3.245016 TGAGATGTGGTCTGCAGGAATTT 60.245 43.478 15.13 0.00 37.29 1.82
3408 3901 7.981225 GGAATTTGTGGTTTATCTAATGTGCAT 59.019 33.333 0.00 0.00 0.00 3.96
3474 3968 5.393068 TCTGAGATGGGCCTTGATAAAAT 57.607 39.130 4.53 0.00 0.00 1.82
3550 4044 6.703165 GCTTCAATTGAGTGAAATGTCCTTTT 59.297 34.615 8.41 0.00 37.08 2.27
3591 4087 5.522456 TCTATATGCGGTGGTACTTAAACG 58.478 41.667 0.00 0.00 0.00 3.60
3669 4171 1.358787 TGGATGTGGAATTCTGGCCTT 59.641 47.619 3.32 0.00 0.00 4.35
3711 4213 4.228210 TCAGGGATGCTATTCAGGAAAAGT 59.772 41.667 0.00 0.00 0.00 2.66
3771 4273 5.359576 TGTGAATCTTGGTGGTATATTTGGC 59.640 40.000 0.00 0.00 0.00 4.52
3820 4322 1.681793 GATGGTAGCTCTCAACCGCTA 59.318 52.381 0.00 0.00 38.70 4.26
3828 4330 2.678190 GCTCTCAACCGCTATGTTTCCT 60.678 50.000 0.00 0.00 0.00 3.36
3832 4334 0.611714 AACCGCTATGTTTCCTCCGT 59.388 50.000 0.00 0.00 0.00 4.69
3862 4366 2.540383 TCTATGGTTGTCTCTGGCACT 58.460 47.619 0.00 0.00 0.00 4.40
3954 4458 4.084849 GCAATGACATCTCGACGATAAAGG 60.085 45.833 0.00 0.00 0.00 3.11
3957 4461 1.269102 ACATCTCGACGATAAAGGCGG 60.269 52.381 0.00 0.00 44.03 6.13
3962 4466 0.643820 CGACGATAAAGGCGGTGTTC 59.356 55.000 0.00 0.00 39.34 3.18
3982 4486 2.771943 TCGTCTGGAATAAAGGCTCCAT 59.228 45.455 0.00 0.00 40.92 3.41
3983 4487 3.964688 TCGTCTGGAATAAAGGCTCCATA 59.035 43.478 0.00 0.00 40.92 2.74
3984 4488 4.407621 TCGTCTGGAATAAAGGCTCCATAA 59.592 41.667 0.00 0.00 40.92 1.90
3991 4495 5.047731 GGAATAAAGGCTCCATAATTCTGCC 60.048 44.000 0.00 0.00 43.52 4.85
4000 4504 4.044308 TCCATAATTCTGCCCCAGTTCTA 58.956 43.478 0.00 0.00 32.61 2.10
4054 4558 3.004315 CGCAAAGGATGTGGTGTTTTAGT 59.996 43.478 0.00 0.00 35.84 2.24
4075 4580 0.859232 CCGCGGTTAATGATTCTCCG 59.141 55.000 19.50 13.80 43.37 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.021968 GCCGAGAGAAGAGGAGAGAC 58.978 60.000 0.00 0.00 0.00 3.36
23 24 1.611491 TCCATGATACGTATCGCAGCA 59.389 47.619 26.12 12.66 35.48 4.41
26 27 2.823154 TCCATCCATGATACGTATCGCA 59.177 45.455 26.12 13.99 35.48 5.10
111 113 2.187685 CTAGTGGAGGCGCATGCA 59.812 61.111 13.54 13.54 45.35 3.96
115 117 0.752009 CCTAGTCTAGTGGAGGCGCA 60.752 60.000 10.83 0.00 33.72 6.09
224 231 0.456824 GCGCTGACAGATGAGTCGAA 60.457 55.000 6.65 0.00 41.41 3.71
308 315 1.206745 CCAACGATAGCGCGTAGTGG 61.207 60.000 8.43 2.38 44.86 4.00
309 316 1.808234 GCCAACGATAGCGCGTAGTG 61.808 60.000 8.43 0.00 44.86 2.74
310 317 1.588139 GCCAACGATAGCGCGTAGT 60.588 57.895 8.43 0.00 44.86 2.73
311 318 2.300787 GGCCAACGATAGCGCGTAG 61.301 63.158 8.43 0.00 44.86 3.51
312 319 1.446516 TAGGCCAACGATAGCGCGTA 61.447 55.000 8.43 0.00 44.86 4.42
316 323 0.308684 TACGTAGGCCAACGATAGCG 59.691 55.000 15.81 0.00 45.68 4.26
392 403 2.284190 CGATGGAGAAGAAAAGCCCTC 58.716 52.381 0.00 0.00 0.00 4.30
517 529 3.309682 GCATGCAGTGTAAAGCGAGATTA 59.690 43.478 14.21 0.00 0.00 1.75
592 604 0.898320 CTTTCTCGCTTCCCTCTCCA 59.102 55.000 0.00 0.00 0.00 3.86
698 710 3.733337 CCGGAGACCTATCATGGAAAAG 58.267 50.000 0.00 0.00 0.00 2.27
863 875 0.907230 AGGCCAGGTCTCACTCCTTC 60.907 60.000 5.01 0.00 32.37 3.46
910 925 0.036952 GCTCTGACTTGTGCTGCCTA 60.037 55.000 0.00 0.00 0.00 3.93
911 926 1.302351 GCTCTGACTTGTGCTGCCT 60.302 57.895 0.00 0.00 0.00 4.75
912 927 1.297456 GAGCTCTGACTTGTGCTGCC 61.297 60.000 6.43 0.00 36.99 4.85
913 928 0.602106 TGAGCTCTGACTTGTGCTGC 60.602 55.000 16.19 0.00 36.99 5.25
914 929 1.799403 CTTGAGCTCTGACTTGTGCTG 59.201 52.381 16.19 0.00 36.99 4.41
915 930 1.877258 GCTTGAGCTCTGACTTGTGCT 60.877 52.381 16.19 0.00 39.15 4.40
916 931 0.516439 GCTTGAGCTCTGACTTGTGC 59.484 55.000 16.19 4.01 38.21 4.57
919 934 2.223611 CAGTTGCTTGAGCTCTGACTTG 59.776 50.000 16.19 1.43 41.87 3.16
921 936 1.877258 GCAGTTGCTTGAGCTCTGACT 60.877 52.381 16.19 8.49 41.87 3.41
922 937 0.516439 GCAGTTGCTTGAGCTCTGAC 59.484 55.000 16.19 4.40 41.87 3.51
924 939 1.226686 ACGCAGTTGCTTGAGCTCTG 61.227 55.000 16.19 17.50 37.78 3.35
925 940 1.070445 ACGCAGTTGCTTGAGCTCT 59.930 52.632 16.19 0.62 37.78 4.09
926 941 3.647824 ACGCAGTTGCTTGAGCTC 58.352 55.556 6.82 6.82 37.78 4.09
1155 1170 4.436998 AAGGAGAAGTCGCCCGCG 62.437 66.667 0.00 0.00 36.39 6.46
1161 1176 1.514443 GACGGCGAAGGAGAAGTCG 60.514 63.158 16.62 0.00 40.24 4.18
1356 1371 6.288294 AGTACAGTGACAAAACATAGCTGAA 58.712 36.000 0.00 0.00 0.00 3.02
1357 1372 5.853936 AGTACAGTGACAAAACATAGCTGA 58.146 37.500 0.00 0.00 0.00 4.26
1359 1374 7.568199 AAAAGTACAGTGACAAAACATAGCT 57.432 32.000 0.00 0.00 0.00 3.32
1384 1399 3.743396 AGTGACAAAACTTTGCGCAAAAA 59.257 34.783 32.96 15.36 41.79 1.94
1385 1400 3.122613 CAGTGACAAAACTTTGCGCAAAA 59.877 39.130 32.96 18.50 41.79 2.44
1386 1401 2.665537 CAGTGACAAAACTTTGCGCAAA 59.334 40.909 31.75 31.75 41.79 3.68
1387 1402 2.257894 CAGTGACAAAACTTTGCGCAA 58.742 42.857 21.02 21.02 41.79 4.85
1388 1403 1.201181 ACAGTGACAAAACTTTGCGCA 59.799 42.857 5.66 5.66 41.79 6.09
1389 1404 1.908065 ACAGTGACAAAACTTTGCGC 58.092 45.000 0.00 0.00 41.79 6.09
1390 1405 4.273005 AGTACAGTGACAAAACTTTGCG 57.727 40.909 0.00 0.00 41.79 4.85
1391 1406 5.286082 CACAAGTACAGTGACAAAACTTTGC 59.714 40.000 11.73 0.00 41.79 3.68
1392 1407 5.286082 GCACAAGTACAGTGACAAAACTTTG 59.714 40.000 19.01 0.60 39.30 2.77
1393 1408 5.183140 AGCACAAGTACAGTGACAAAACTTT 59.817 36.000 19.01 0.00 39.30 2.66
1394 1409 4.700213 AGCACAAGTACAGTGACAAAACTT 59.300 37.500 19.01 0.00 39.30 2.66
1395 1410 4.261801 AGCACAAGTACAGTGACAAAACT 58.738 39.130 19.01 5.73 39.30 2.66
1396 1411 4.616181 AGCACAAGTACAGTGACAAAAC 57.384 40.909 19.01 3.88 39.30 2.43
1418 1434 5.007724 GCTACCAATTTGTAAGCTAGCGAAT 59.992 40.000 9.55 2.38 0.00 3.34
1452 1571 5.329035 GCTTATGCAATTCTGAGGGAAAA 57.671 39.130 0.00 0.00 37.00 2.29
1453 1572 4.989279 GCTTATGCAATTCTGAGGGAAA 57.011 40.909 0.00 0.00 37.00 3.13
1557 1832 3.665323 CGCAGTTGAACTATGTTGCAGAC 60.665 47.826 0.00 0.00 0.00 3.51
1584 2063 5.473504 TCATCAAAGGAAGTAAAGGAACAGC 59.526 40.000 0.00 0.00 0.00 4.40
1666 2145 8.308207 AGATGACTCAACTTTAGTAGGAAGAAC 58.692 37.037 0.00 0.00 0.00 3.01
1678 2157 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
1680 2159 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
1681 2160 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
1682 2161 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
1683 2162 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
1688 2167 5.186198 ACTCCTTCCGTTCCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
1689 2168 5.437191 ACTCCTTCCGTTCCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
1691 2170 5.935789 TGTTACTCCTTCCGTTCCAAAATAG 59.064 40.000 0.00 0.00 0.00 1.73
1693 2172 4.721132 TGTTACTCCTTCCGTTCCAAAAT 58.279 39.130 0.00 0.00 0.00 1.82
1694 2173 4.153673 TGTTACTCCTTCCGTTCCAAAA 57.846 40.909 0.00 0.00 0.00 2.44
1695 2174 3.842007 TGTTACTCCTTCCGTTCCAAA 57.158 42.857 0.00 0.00 0.00 3.28
1696 2175 3.842007 TTGTTACTCCTTCCGTTCCAA 57.158 42.857 0.00 0.00 0.00 3.53
1697 2176 5.012354 AGTTATTGTTACTCCTTCCGTTCCA 59.988 40.000 0.00 0.00 0.00 3.53
1698 2177 5.485620 AGTTATTGTTACTCCTTCCGTTCC 58.514 41.667 0.00 0.00 0.00 3.62
1699 2178 6.755607 CCTAGTTATTGTTACTCCTTCCGTTC 59.244 42.308 0.00 0.00 0.00 3.95
1700 2179 6.438425 TCCTAGTTATTGTTACTCCTTCCGTT 59.562 38.462 0.00 0.00 0.00 4.44
1701 2180 5.954150 TCCTAGTTATTGTTACTCCTTCCGT 59.046 40.000 0.00 0.00 0.00 4.69
1702 2181 6.461110 TCCTAGTTATTGTTACTCCTTCCG 57.539 41.667 0.00 0.00 0.00 4.30
1703 2182 9.682465 AAAATCCTAGTTATTGTTACTCCTTCC 57.318 33.333 0.00 0.00 0.00 3.46
1707 2186 9.327628 GGAGAAAATCCTAGTTATTGTTACTCC 57.672 37.037 0.00 0.00 45.64 3.85
1754 2233 9.685828 GTAATAACAGCAGTTTCCATTACAAAA 57.314 29.630 15.67 0.00 37.02 2.44
1823 2302 2.233676 TGTAGCAGAGAAGGCATTTCGA 59.766 45.455 0.00 0.00 40.86 3.71
1967 2446 1.814169 GACAACCGCCCGAGAATCC 60.814 63.158 0.00 0.00 0.00 3.01
2036 2515 1.291184 CCTCGATGCTTGCGTTGTGA 61.291 55.000 5.89 0.00 0.00 3.58
2106 2585 3.057315 CGCCAGACACCATTTTTCAGAAT 60.057 43.478 0.00 0.00 0.00 2.40
2241 2729 9.014297 ACTAAAAATAGAAGGTTGGTCATCTTG 57.986 33.333 0.00 0.00 0.00 3.02
2325 2813 1.878102 GCACCTAGTGACCACCAGTTG 60.878 57.143 0.00 0.00 35.23 3.16
2329 2817 0.471022 TCTGCACCTAGTGACCACCA 60.471 55.000 0.00 0.00 35.23 4.17
2349 2837 8.635765 AAAACACCTGAACATAGTGATACAAT 57.364 30.769 10.56 0.00 35.47 2.71
2435 2923 3.411446 AGCAAATCAGACGAATGTTCCA 58.589 40.909 0.00 0.00 0.00 3.53
2453 2941 6.098409 CCTATAGACCTTGAAACCTAAGAGCA 59.902 42.308 0.00 0.00 0.00 4.26
2626 3114 3.268330 CTCCCATAATCCATCTGATGCG 58.732 50.000 12.17 6.03 32.68 4.73
2632 3120 2.711174 AGGTGCTCCCATAATCCATCT 58.289 47.619 0.00 0.00 34.66 2.90
2677 3165 0.380024 CACGTGGATTGTTGTGCACA 59.620 50.000 17.42 17.42 40.04 4.57
2804 3293 6.514947 AGCAAAGCAGAATTTTACACATCAA 58.485 32.000 0.00 0.00 0.00 2.57
2807 3296 6.752168 AGAAGCAAAGCAGAATTTTACACAT 58.248 32.000 0.00 0.00 0.00 3.21
2811 3300 6.564686 GCCAAAGAAGCAAAGCAGAATTTTAC 60.565 38.462 0.00 0.00 0.00 2.01
2815 3304 3.181463 TGCCAAAGAAGCAAAGCAGAATT 60.181 39.130 0.00 0.00 37.28 2.17
2826 3315 1.134995 GCAATACCCTGCCAAAGAAGC 60.135 52.381 0.00 0.00 36.25 3.86
2834 3323 0.753111 CCTCCTTGCAATACCCTGCC 60.753 60.000 0.00 0.00 41.90 4.85
2856 3345 6.775939 GCTTCTTTCAAAGCTGCTTTTATT 57.224 33.333 24.04 1.35 46.51 1.40
2934 3423 1.412343 TCATCATGGAAGAATCGGCGA 59.588 47.619 13.87 13.87 0.00 5.54
2937 3426 4.212847 GTGATGTCATCATGGAAGAATCGG 59.787 45.833 18.32 0.00 42.04 4.18
3381 3874 7.178274 TGCACATTAGATAAACCACAAATTCCT 59.822 33.333 0.00 0.00 0.00 3.36
3388 3881 6.413892 TCTCATGCACATTAGATAAACCACA 58.586 36.000 0.00 0.00 0.00 4.17
3408 3901 1.606480 CGAGCCAAGCTTCAACTCTCA 60.606 52.381 14.64 0.00 39.88 3.27
3474 3968 1.949525 GGAGTGACAAGAGCTGCAAAA 59.050 47.619 1.02 0.00 0.00 2.44
3576 4072 2.753296 TCAACCGTTTAAGTACCACCG 58.247 47.619 0.00 0.00 0.00 4.94
3591 4087 3.081061 TGTCACCAAGTGCATATCAACC 58.919 45.455 0.00 0.00 32.98 3.77
3687 4189 4.860802 TTTCCTGAATAGCATCCCTGAA 57.139 40.909 0.00 0.00 0.00 3.02
3711 4213 4.040339 TCTCTGTTTGCCATGTCAGTTCTA 59.960 41.667 0.00 0.00 0.00 2.10
3771 4273 1.539065 GGTGGATCCATAGTCGTGCAG 60.539 57.143 19.62 0.00 35.97 4.41
3820 4322 1.004394 GAGGGGAAACGGAGGAAACAT 59.996 52.381 0.00 0.00 0.00 2.71
3828 4330 2.047061 CCATAGATGAGGGGAAACGGA 58.953 52.381 0.00 0.00 0.00 4.69
3832 4334 4.111577 AGACAACCATAGATGAGGGGAAA 58.888 43.478 0.00 0.00 31.20 3.13
3862 4366 2.314071 TTGGTTCCCCTCGTCTTCTA 57.686 50.000 0.00 0.00 0.00 2.10
3954 4458 1.717194 TTATTCCAGACGAACACCGC 58.283 50.000 0.00 0.00 43.32 5.68
3957 4461 3.335579 AGCCTTTATTCCAGACGAACAC 58.664 45.455 0.00 0.00 31.79 3.32
3962 4466 2.691409 TGGAGCCTTTATTCCAGACG 57.309 50.000 0.00 0.00 38.53 4.18
3982 4486 3.844211 ACACTAGAACTGGGGCAGAATTA 59.156 43.478 0.00 0.00 35.18 1.40
3983 4487 2.644798 ACACTAGAACTGGGGCAGAATT 59.355 45.455 0.00 0.00 35.18 2.17
3984 4488 2.026822 CACACTAGAACTGGGGCAGAAT 60.027 50.000 0.00 0.00 35.18 2.40
3991 4495 2.554032 CAAAAGCCACACTAGAACTGGG 59.446 50.000 0.00 0.00 0.00 4.45
4000 4504 0.395586 TCAGCCACAAAAGCCACACT 60.396 50.000 0.00 0.00 0.00 3.55
4054 4558 1.202604 GGAGAATCATTAACCGCGGGA 60.203 52.381 31.76 17.21 36.25 5.14


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

AutoCloner maintained by Alex Coulton.