Multiple sequence alignment - TraesCS4D01G251900

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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 TraesCS4D01G251900 chr4D 100.000 1903 0 0 1 1903 420502897 420504799 0.000000e+00 3515.0
1 TraesCS4D01G251900 chr4D 100.000 498 0 0 2368 2865 420505264 420505761 0.000000e+00 920.0
2 TraesCS4D01G251900 chr4B 90.371 997 28 19 408 1359 517759598 517758625 0.000000e+00 1247.0
3 TraesCS4D01G251900 chr4B 95.249 442 19 2 1463 1903 517758480 517758040 0.000000e+00 699.0
4 TraesCS4D01G251900 chr4B 91.006 467 38 2 2403 2865 517757491 517757025 6.740000e-176 627.0
5 TraesCS4D01G251900 chr4B 90.215 419 31 9 1 418 517760281 517759872 3.250000e-149 538.0
6 TraesCS4D01G251900 chr4A 90.788 673 35 11 717 1380 43697074 43697728 0.000000e+00 874.0
7 TraesCS4D01G251900 chr4A 89.400 500 27 5 2368 2865 43698280 43698755 8.780000e-170 606.0
8 TraesCS4D01G251900 chr4A 84.753 446 50 12 1462 1902 43697740 43698172 5.670000e-117 431.0
9 TraesCS4D01G251900 chr4A 100.000 56 0 0 1379 1434 715367534 715367589 1.400000e-18 104.0
10 TraesCS4D01G251900 chr5A 98.333 60 1 0 1379 1438 29712694 29712635 3.900000e-19 106.0
11 TraesCS4D01G251900 chr3B 100.000 57 0 0 1379 1435 63469065 63469121 3.900000e-19 106.0
12 TraesCS4D01G251900 chr3B 98.333 60 1 0 1379 1438 738378116 738378057 3.900000e-19 106.0
13 TraesCS4D01G251900 chr2B 98.333 60 1 0 1379 1438 56775364 56775423 3.900000e-19 106.0
14 TraesCS4D01G251900 chr2B 96.721 61 2 0 1379 1439 180426676 180426616 5.050000e-18 102.0
15 TraesCS4D01G251900 chr2B 96.721 61 1 1 1379 1439 66708820 66708761 1.820000e-17 100.0
16 TraesCS4D01G251900 chr7A 96.825 63 0 2 1379 1440 645026114 645026175 1.400000e-18 104.0
17 TraesCS4D01G251900 chr5B 90.541 74 5 2 1379 1452 559999802 559999731 2.350000e-16 97.1


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 TraesCS4D01G251900 chr4D 420502897 420505761 2864 False 2217.50 3515 100.000000 1 2865 2 chr4D.!!$F1 2864
1 TraesCS4D01G251900 chr4B 517757025 517760281 3256 True 777.75 1247 91.710250 1 2865 4 chr4B.!!$R1 2864
2 TraesCS4D01G251900 chr4A 43697074 43698755 1681 False 637.00 874 88.313667 717 2865 3 chr4A.!!$F2 2148

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
983 1303 0.038251 CACTGAACACTAGCGAGGCA 60.038 55.0 0.0 0.0 0.0 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2430 3216 0.836606 TGACAGAACAAGAGGCCACA 59.163 50.0 5.01 0.0 0.0 4.17 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
20 21 3.660501 GAACCTCCAAAAACCACCATC 57.339 47.619 0.00 0.00 0.00 3.51
85 86 5.868454 TCTGATTCAAGAACTGATCCACAA 58.132 37.500 0.00 0.00 32.78 3.33
144 145 1.133025 GCATTGTAGCCCACACATCAC 59.867 52.381 0.00 0.00 36.69 3.06
146 147 2.183478 TTGTAGCCCACACATCACAG 57.817 50.000 0.00 0.00 36.69 3.66
167 169 2.483714 GGATATGAGCAGACGAGCCAAA 60.484 50.000 0.00 0.00 34.23 3.28
176 178 4.278419 AGCAGACGAGCCAAATTAAAAGTT 59.722 37.500 0.00 0.00 34.23 2.66
211 213 3.578282 CCCCAATTTTGCAAGACCTAACT 59.422 43.478 0.00 0.00 0.00 2.24
231 233 7.924947 CCTAACTCTAACCCTAATTTAGAACCG 59.075 40.741 4.96 0.00 35.59 4.44
233 235 5.723405 ACTCTAACCCTAATTTAGAACCGGT 59.277 40.000 0.00 0.00 35.59 5.28
235 237 7.112452 TCTAACCCTAATTTAGAACCGGTAC 57.888 40.000 8.00 0.00 33.52 3.34
237 239 8.058847 TCTAACCCTAATTTAGAACCGGTACTA 58.941 37.037 8.00 0.00 33.52 1.82
262 264 3.991121 GAGTGTGGACTTACAAAGAGCTC 59.009 47.826 5.27 5.27 30.16 4.09
309 311 1.153329 TCGTCCGAGCTCTCCTCTC 60.153 63.158 12.85 0.00 38.49 3.20
341 343 3.813596 GGCATTCTCAACGCCGAT 58.186 55.556 0.00 0.00 35.79 4.18
345 347 0.302890 CATTCTCAACGCCGATGAGC 59.697 55.000 18.28 0.00 43.19 4.26
351 353 0.179215 CAACGCCGATGAGCAAGAAC 60.179 55.000 0.00 0.00 0.00 3.01
353 355 2.802667 CGCCGATGAGCAAGAACGG 61.803 63.158 0.00 0.00 45.26 4.44
363 365 4.250305 AAGAACGGTGGCGGCAGT 62.250 61.111 13.91 4.64 0.00 4.40
385 387 1.576421 GGCAGCGTGGTCAGAAAAG 59.424 57.895 0.00 0.00 0.00 2.27
399 401 5.422012 GGTCAGAAAAGAAGGAGAGAGAGAT 59.578 44.000 0.00 0.00 0.00 2.75
400 402 6.070824 GGTCAGAAAAGAAGGAGAGAGAGATT 60.071 42.308 0.00 0.00 0.00 2.40
404 406 6.725834 AGAAAAGAAGGAGAGAGAGATTGAGT 59.274 38.462 0.00 0.00 0.00 3.41
405 407 6.933514 AAAGAAGGAGAGAGAGATTGAGTT 57.066 37.500 0.00 0.00 0.00 3.01
406 408 5.920193 AGAAGGAGAGAGAGATTGAGTTG 57.080 43.478 0.00 0.00 0.00 3.16
440 722 4.200283 GCGAGTGGGGAGAGAGCG 62.200 72.222 0.00 0.00 0.00 5.03
469 751 0.685785 TGCCTTTTTGACCAGCACCA 60.686 50.000 0.00 0.00 0.00 4.17
474 756 2.363306 TTTTGACCAGCACCAGACAT 57.637 45.000 0.00 0.00 0.00 3.06
484 766 3.826282 CCAGACATGGTCCCACCT 58.174 61.111 0.00 0.00 42.17 4.00
530 812 4.002982 TCAATGCTGACACATCACCTAAC 58.997 43.478 0.00 0.00 0.00 2.34
574 856 4.584874 TCAGGCTTAAAACATCCGAATCA 58.415 39.130 0.00 0.00 0.00 2.57
575 857 4.635765 TCAGGCTTAAAACATCCGAATCAG 59.364 41.667 0.00 0.00 0.00 2.90
576 858 3.378427 AGGCTTAAAACATCCGAATCAGC 59.622 43.478 0.00 0.00 0.00 4.26
583 865 2.359900 ACATCCGAATCAGCCACTTTC 58.640 47.619 0.00 0.00 0.00 2.62
596 878 2.876079 GCCACTTTCCTGACTTGGTAGG 60.876 54.545 0.00 0.00 35.34 3.18
606 888 4.642885 CCTGACTTGGTAGGTTTTTGTCAA 59.357 41.667 0.00 0.00 33.47 3.18
658 952 4.104261 AGTGGTAGTTTTCAGCTAGGGTTT 59.896 41.667 0.00 0.00 0.00 3.27
675 969 5.960704 AGGGTTTAATGGAAAGTGGTAGTT 58.039 37.500 0.00 0.00 0.00 2.24
756 1054 1.975363 GCCGCTGCAAGACTCACATC 61.975 60.000 0.00 0.00 34.07 3.06
757 1055 0.390866 CCGCTGCAAGACTCACATCT 60.391 55.000 0.00 0.00 34.07 2.90
760 1058 2.416566 CGCTGCAAGACTCACATCTACT 60.417 50.000 0.00 0.00 34.07 2.57
761 1059 3.186119 GCTGCAAGACTCACATCTACTC 58.814 50.000 0.00 0.00 34.07 2.59
762 1060 3.779759 CTGCAAGACTCACATCTACTCC 58.220 50.000 0.00 0.00 34.07 3.85
763 1061 3.435275 TGCAAGACTCACATCTACTCCT 58.565 45.455 0.00 0.00 0.00 3.69
764 1062 4.600062 TGCAAGACTCACATCTACTCCTA 58.400 43.478 0.00 0.00 0.00 2.94
765 1063 4.399618 TGCAAGACTCACATCTACTCCTAC 59.600 45.833 0.00 0.00 0.00 3.18
766 1064 4.642885 GCAAGACTCACATCTACTCCTACT 59.357 45.833 0.00 0.00 0.00 2.57
866 1164 2.689813 CCACCCTTCCCCAATCCC 59.310 66.667 0.00 0.00 0.00 3.85
983 1303 0.038251 CACTGAACACTAGCGAGGCA 60.038 55.000 0.00 0.00 0.00 4.75
984 1304 0.244994 ACTGAACACTAGCGAGGCAG 59.755 55.000 0.00 3.19 0.00 4.85
985 1305 1.079819 TGAACACTAGCGAGGCAGC 60.080 57.895 0.00 0.00 37.41 5.25
986 1306 1.811679 GAACACTAGCGAGGCAGCC 60.812 63.158 1.84 1.84 38.01 4.85
987 1307 2.507110 GAACACTAGCGAGGCAGCCA 62.507 60.000 15.80 0.00 38.01 4.75
988 1308 2.202851 CACTAGCGAGGCAGCCAG 60.203 66.667 15.80 8.51 38.01 4.85
989 1309 3.465403 ACTAGCGAGGCAGCCAGG 61.465 66.667 15.80 5.72 38.01 4.45
990 1310 4.906792 CTAGCGAGGCAGCCAGGC 62.907 72.222 15.80 16.41 44.61 4.85
1169 1489 0.400594 ACCCCAGGTAGAGTGCAAAC 59.599 55.000 0.00 0.00 32.11 2.93
1188 1514 2.947852 ACTCTTCACACATAGTCACGC 58.052 47.619 0.00 0.00 0.00 5.34
1241 1576 0.233590 CCGTTGAAATTCGTGTGCGA 59.766 50.000 0.00 0.00 46.36 5.10
1356 1691 2.119801 ATGGTTGGTTCAGCTAGCTG 57.880 50.000 34.48 34.48 44.86 4.24
1380 1715 5.673568 GCTTGCTCTACGCTATCTCATCTAG 60.674 48.000 0.00 0.00 40.11 2.43
1402 1769 9.350951 TCTAGTTCTAGATACATCCATTTTCGA 57.649 33.333 5.56 0.00 0.00 3.71
1415 1782 6.737254 TCCATTTTCGAGACAAGTAATTCC 57.263 37.500 0.00 0.00 0.00 3.01
1430 1797 2.083628 ATTCCGAACGGAGGGAGTAT 57.916 50.000 15.34 3.38 46.06 2.12
1431 1798 2.734755 TTCCGAACGGAGGGAGTATA 57.265 50.000 15.34 0.00 46.06 1.47
1434 1801 2.107031 TCCGAACGGAGGGAGTATATGA 59.893 50.000 12.04 0.00 39.76 2.15
1435 1802 2.488545 CCGAACGGAGGGAGTATATGAG 59.511 54.545 7.53 0.00 37.50 2.90
1436 1803 3.409570 CGAACGGAGGGAGTATATGAGA 58.590 50.000 0.00 0.00 0.00 3.27
1437 1804 3.819337 CGAACGGAGGGAGTATATGAGAA 59.181 47.826 0.00 0.00 0.00 2.87
1438 1805 4.459685 CGAACGGAGGGAGTATATGAGAAT 59.540 45.833 0.00 0.00 0.00 2.40
1440 1807 4.345854 ACGGAGGGAGTATATGAGAATCC 58.654 47.826 0.00 0.00 0.00 3.01
1441 1808 4.044825 ACGGAGGGAGTATATGAGAATCCT 59.955 45.833 0.00 0.00 0.00 3.24
1443 1810 5.482175 CGGAGGGAGTATATGAGAATCCTTT 59.518 44.000 0.00 0.00 0.00 3.11
1447 1814 8.574309 AGGGAGTATATGAGAATCCTTTTCTT 57.426 34.615 0.00 0.00 0.00 2.52
1448 1815 9.008584 AGGGAGTATATGAGAATCCTTTTCTTT 57.991 33.333 0.00 0.00 0.00 2.52
1456 1823 6.742109 TGAGAATCCTTTTCTTTTTGCTCAG 58.258 36.000 0.00 0.00 0.00 3.35
1457 1824 6.322201 TGAGAATCCTTTTCTTTTTGCTCAGT 59.678 34.615 0.00 0.00 0.00 3.41
1458 1825 7.502226 TGAGAATCCTTTTCTTTTTGCTCAGTA 59.498 33.333 0.00 0.00 0.00 2.74
1460 1827 8.302438 AGAATCCTTTTCTTTTTGCTCAGTATG 58.698 33.333 0.00 0.00 37.54 2.39
1473 1849 9.453572 TTTTGCTCAGTATGTTTATTCATCTCT 57.546 29.630 0.00 0.00 37.40 3.10
1475 1851 7.212976 TGCTCAGTATGTTTATTCATCTCTCC 58.787 38.462 0.00 0.00 37.40 3.71
1478 1854 9.258826 CTCAGTATGTTTATTCATCTCTCCTTG 57.741 37.037 0.00 0.00 37.40 3.61
1489 1865 3.063510 TCTCTCCTTGATTTGCACTGG 57.936 47.619 0.00 0.00 0.00 4.00
1492 1868 4.015084 CTCTCCTTGATTTGCACTGGATT 58.985 43.478 0.00 0.00 31.54 3.01
1493 1869 4.410099 TCTCCTTGATTTGCACTGGATTT 58.590 39.130 0.00 0.00 31.54 2.17
1525 1901 0.896226 AGAACCAGAGGAAGTACGCC 59.104 55.000 0.04 0.04 0.00 5.68
1616 1992 3.956199 AGAAAAGTATGTGATGCCATGGG 59.044 43.478 15.13 0.00 0.00 4.00
1646 2022 3.145228 GCTCTAGCTGCCGTTCTTT 57.855 52.632 0.00 0.00 38.21 2.52
1712 2088 2.641197 GCCTCTCTTGGGCGAAAAA 58.359 52.632 0.00 0.00 40.19 1.94
1865 2241 4.044571 TCAGGAAAAGAGTTGGGGAATGAT 59.955 41.667 0.00 0.00 0.00 2.45
2400 2776 7.244192 GCAAATACACAATCTAGTTCAGAACC 58.756 38.462 9.85 0.00 36.67 3.62
2420 3206 3.005367 ACCGCAGATGGTTTAAAAAGGTG 59.995 43.478 0.00 0.00 39.99 4.00
2430 3216 7.142995 TGGTTTAAAAAGGTGAATGGGAATT 57.857 32.000 0.00 0.00 0.00 2.17
2467 3253 3.699538 TGTCAGTAGTACTCCATGCGAAT 59.300 43.478 0.00 0.00 0.00 3.34
2471 3257 6.755141 GTCAGTAGTACTCCATGCGAATTTTA 59.245 38.462 0.00 0.00 0.00 1.52
2500 3286 1.867233 CCGTCAGTTCTTGAACCACAG 59.133 52.381 9.58 4.77 37.61 3.66
2502 3288 1.261619 GTCAGTTCTTGAACCACAGCG 59.738 52.381 9.58 0.00 37.61 5.18
2504 3290 1.166531 AGTTCTTGAACCACAGCGGC 61.167 55.000 9.58 0.00 39.03 6.53
2524 3310 4.560108 CGGCCTGTTACTGTTAGTGTAAGT 60.560 45.833 0.00 0.00 31.54 2.24
2535 3325 7.376615 ACTGTTAGTGTAAGTCTTACCATCAC 58.623 38.462 18.11 10.60 35.25 3.06
2576 3367 2.526120 GGTGGCGCACTTCGATAGC 61.526 63.158 10.83 0.00 41.67 2.97
2582 3373 1.267087 GCGCACTTCGATAGCTCAAAC 60.267 52.381 0.30 0.00 41.67 2.93
2610 3401 6.371548 CCATTTGAATACCGACGGATATGAAT 59.628 38.462 23.38 10.14 0.00 2.57
2613 3404 5.709966 TGAATACCGACGGATATGAATCTG 58.290 41.667 23.38 0.00 43.19 2.90
2664 3455 4.141846 ACAAGAGATGAGCATACAACCGAT 60.142 41.667 0.00 0.00 0.00 4.18
2678 3469 4.028131 ACAACCGATATTCTCCCTGTACA 58.972 43.478 0.00 0.00 0.00 2.90
2679 3470 4.099573 ACAACCGATATTCTCCCTGTACAG 59.900 45.833 16.34 16.34 0.00 2.74
2715 3506 6.558009 CACATGAATAAAACCATCACAGAGG 58.442 40.000 0.00 0.00 0.00 3.69
2718 3509 2.107950 TAAAACCATCACAGAGGGCG 57.892 50.000 0.00 0.00 36.94 6.13
2773 3564 4.944048 TCGATCGATCTTTTCATTAGCCA 58.056 39.130 22.43 0.00 0.00 4.75
2856 3647 8.488651 AAACCCTAATACATCTAACGTGAAAG 57.511 34.615 0.00 0.00 0.00 2.62
2857 3648 7.179076 ACCCTAATACATCTAACGTGAAAGT 57.821 36.000 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 103 1.134250 TGCAGCAAACACCTGACACTA 60.134 47.619 0.00 0.00 32.03 2.74
134 135 3.136763 GCTCATATCCTGTGATGTGTGG 58.863 50.000 0.00 0.00 40.08 4.17
144 145 1.336702 GGCTCGTCTGCTCATATCCTG 60.337 57.143 0.00 0.00 0.00 3.86
146 147 0.676184 TGGCTCGTCTGCTCATATCC 59.324 55.000 0.00 0.00 0.00 2.59
187 189 2.906568 AGGTCTTGCAAAATTGGGGAT 58.093 42.857 0.00 0.00 0.00 3.85
188 190 2.397044 AGGTCTTGCAAAATTGGGGA 57.603 45.000 0.00 0.00 0.00 4.81
189 191 3.578282 AGTTAGGTCTTGCAAAATTGGGG 59.422 43.478 0.00 0.00 0.00 4.96
195 197 5.067954 GGGTTAGAGTTAGGTCTTGCAAAA 58.932 41.667 0.00 0.00 0.00 2.44
211 213 6.897413 AGTACCGGTTCTAAATTAGGGTTAGA 59.103 38.462 15.04 0.00 36.12 2.10
231 233 4.708421 TGTAAGTCCACACTCCATAGTACC 59.292 45.833 0.00 0.00 33.48 3.34
233 235 6.722590 TCTTTGTAAGTCCACACTCCATAGTA 59.277 38.462 0.00 0.00 33.48 1.82
235 237 6.037786 TCTTTGTAAGTCCACACTCCATAG 57.962 41.667 0.00 0.00 29.93 2.23
237 239 4.804261 GCTCTTTGTAAGTCCACACTCCAT 60.804 45.833 0.00 0.00 29.93 3.41
277 279 1.135112 CGGACGACAACATCTCCATGA 60.135 52.381 0.00 0.00 33.72 3.07
293 295 2.184167 CGGAGAGGAGAGCTCGGAC 61.184 68.421 8.37 2.51 35.47 4.79
294 296 2.190843 CGGAGAGGAGAGCTCGGA 59.809 66.667 8.37 0.00 35.47 4.55
325 327 0.302890 CTCATCGGCGTTGAGAATGC 59.697 55.000 33.38 0.00 42.63 3.56
341 343 2.664851 CGCCACCGTTCTTGCTCA 60.665 61.111 0.00 0.00 0.00 4.26
345 347 3.726517 CTGCCGCCACCGTTCTTG 61.727 66.667 0.00 0.00 0.00 3.02
361 363 4.436998 GACCACGCTGCCGCTACT 62.437 66.667 0.00 0.00 38.22 2.57
363 365 4.435436 CTGACCACGCTGCCGCTA 62.435 66.667 0.00 0.00 38.22 4.26
370 372 1.416401 TCCTTCTTTTCTGACCACGCT 59.584 47.619 0.00 0.00 0.00 5.07
373 375 4.282195 TCTCTCTCCTTCTTTTCTGACCAC 59.718 45.833 0.00 0.00 0.00 4.16
374 376 4.483950 TCTCTCTCCTTCTTTTCTGACCA 58.516 43.478 0.00 0.00 0.00 4.02
379 381 6.725834 ACTCAATCTCTCTCTCCTTCTTTTCT 59.274 38.462 0.00 0.00 0.00 2.52
380 382 6.935167 ACTCAATCTCTCTCTCCTTCTTTTC 58.065 40.000 0.00 0.00 0.00 2.29
381 383 6.933514 ACTCAATCTCTCTCTCCTTCTTTT 57.066 37.500 0.00 0.00 0.00 2.27
382 384 6.496565 TCAACTCAATCTCTCTCTCCTTCTTT 59.503 38.462 0.00 0.00 0.00 2.52
385 387 5.679638 GCTCAACTCAATCTCTCTCTCCTTC 60.680 48.000 0.00 0.00 0.00 3.46
399 401 3.225940 TCACTCTCTCTGCTCAACTCAA 58.774 45.455 0.00 0.00 0.00 3.02
400 402 2.819019 CTCACTCTCTCTGCTCAACTCA 59.181 50.000 0.00 0.00 0.00 3.41
404 406 1.271934 GCACTCACTCTCTCTGCTCAA 59.728 52.381 0.00 0.00 0.00 3.02
405 407 0.887247 GCACTCACTCTCTCTGCTCA 59.113 55.000 0.00 0.00 0.00 4.26
406 408 0.179166 CGCACTCACTCTCTCTGCTC 60.179 60.000 0.00 0.00 0.00 4.26
440 722 0.040067 CAAAAAGGCACGACCAGCTC 60.040 55.000 0.00 0.00 43.14 4.09
469 751 0.983378 GGCTAGGTGGGACCATGTCT 60.983 60.000 0.00 0.00 41.95 3.41
574 856 0.846693 ACCAAGTCAGGAAAGTGGCT 59.153 50.000 0.00 0.00 32.23 4.75
575 857 2.427506 CTACCAAGTCAGGAAAGTGGC 58.572 52.381 0.00 0.00 32.27 5.01
576 858 2.372172 ACCTACCAAGTCAGGAAAGTGG 59.628 50.000 0.00 0.00 35.76 4.00
583 865 4.204012 TGACAAAAACCTACCAAGTCAGG 58.796 43.478 0.00 0.00 37.97 3.86
631 914 4.811557 CCTAGCTGAAAACTACCACTATGC 59.188 45.833 0.00 0.00 0.00 3.14
632 915 5.104900 ACCCTAGCTGAAAACTACCACTATG 60.105 44.000 0.00 0.00 0.00 2.23
756 1054 6.975772 CGGATCTTTTTCTTCAGTAGGAGTAG 59.024 42.308 0.00 0.00 0.00 2.57
757 1055 6.662234 TCGGATCTTTTTCTTCAGTAGGAGTA 59.338 38.462 0.00 0.00 0.00 2.59
760 1058 5.995565 TCGGATCTTTTTCTTCAGTAGGA 57.004 39.130 0.00 0.00 0.00 2.94
761 1059 5.582665 CCTTCGGATCTTTTTCTTCAGTAGG 59.417 44.000 0.00 0.00 0.00 3.18
762 1060 5.582665 CCCTTCGGATCTTTTTCTTCAGTAG 59.417 44.000 0.00 0.00 0.00 2.57
763 1061 5.488341 CCCTTCGGATCTTTTTCTTCAGTA 58.512 41.667 0.00 0.00 0.00 2.74
764 1062 4.327680 CCCTTCGGATCTTTTTCTTCAGT 58.672 43.478 0.00 0.00 0.00 3.41
765 1063 3.127721 GCCCTTCGGATCTTTTTCTTCAG 59.872 47.826 0.00 0.00 0.00 3.02
766 1064 3.081804 GCCCTTCGGATCTTTTTCTTCA 58.918 45.455 0.00 0.00 0.00 3.02
983 1303 3.534704 ATGGTGCTTTGGCCTGGCT 62.535 57.895 19.68 0.00 37.74 4.75
984 1304 2.999063 ATGGTGCTTTGGCCTGGC 60.999 61.111 11.05 11.05 37.74 4.85
985 1305 2.975536 CATGGTGCTTTGGCCTGG 59.024 61.111 3.32 0.00 37.74 4.45
986 1306 2.263540 GCATGGTGCTTTGGCCTG 59.736 61.111 3.32 0.00 40.96 4.85
1169 1489 2.946564 TGCGTGACTATGTGTGAAGAG 58.053 47.619 0.00 0.00 0.00 2.85
1216 1542 1.778591 CACGAATTTCAACGGTGTTGC 59.221 47.619 0.00 0.00 0.00 4.17
1380 1715 7.921214 TGTCTCGAAAATGGATGTATCTAGAAC 59.079 37.037 0.00 0.00 0.00 3.01
1397 1764 4.383649 CGTTCGGAATTACTTGTCTCGAAA 59.616 41.667 0.00 0.00 37.00 3.46
1398 1765 3.916172 CGTTCGGAATTACTTGTCTCGAA 59.084 43.478 0.00 0.00 33.66 3.71
1399 1766 3.495193 CGTTCGGAATTACTTGTCTCGA 58.505 45.455 0.00 0.00 0.00 4.04
1400 1767 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
1402 1769 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
1415 1782 3.409570 TCTCATATACTCCCTCCGTTCG 58.590 50.000 0.00 0.00 0.00 3.95
1430 1797 8.408043 TGAGCAAAAAGAAAAGGATTCTCATA 57.592 30.769 0.00 0.00 0.00 2.15
1431 1798 7.015001 ACTGAGCAAAAAGAAAAGGATTCTCAT 59.985 33.333 0.00 0.00 0.00 2.90
1434 1801 6.721704 ACTGAGCAAAAAGAAAAGGATTCT 57.278 33.333 0.00 0.00 0.00 2.40
1435 1802 8.084684 ACATACTGAGCAAAAAGAAAAGGATTC 58.915 33.333 0.00 0.00 0.00 2.52
1436 1803 7.955918 ACATACTGAGCAAAAAGAAAAGGATT 58.044 30.769 0.00 0.00 0.00 3.01
1437 1804 7.530426 ACATACTGAGCAAAAAGAAAAGGAT 57.470 32.000 0.00 0.00 0.00 3.24
1438 1805 6.959639 ACATACTGAGCAAAAAGAAAAGGA 57.040 33.333 0.00 0.00 0.00 3.36
1447 1814 9.453572 AGAGATGAATAAACATACTGAGCAAAA 57.546 29.630 0.00 0.00 0.00 2.44
1448 1815 9.102757 GAGAGATGAATAAACATACTGAGCAAA 57.897 33.333 0.00 0.00 0.00 3.68
1450 1817 7.070447 AGGAGAGATGAATAAACATACTGAGCA 59.930 37.037 0.00 0.00 0.00 4.26
1451 1818 7.441017 AGGAGAGATGAATAAACATACTGAGC 58.559 38.462 0.00 0.00 0.00 4.26
1453 1820 8.981659 TCAAGGAGAGATGAATAAACATACTGA 58.018 33.333 0.00 0.00 0.00 3.41
1454 1821 9.775854 ATCAAGGAGAGATGAATAAACATACTG 57.224 33.333 0.00 0.00 0.00 2.74
1458 1825 8.411683 GCAAATCAAGGAGAGATGAATAAACAT 58.588 33.333 0.00 0.00 0.00 2.71
1460 1827 7.699812 GTGCAAATCAAGGAGAGATGAATAAAC 59.300 37.037 0.00 0.00 0.00 2.01
1467 1843 3.377485 CCAGTGCAAATCAAGGAGAGATG 59.623 47.826 0.00 0.00 0.00 2.90
1470 1846 3.063510 TCCAGTGCAAATCAAGGAGAG 57.936 47.619 0.00 0.00 30.44 3.20
1472 1848 4.796038 AAATCCAGTGCAAATCAAGGAG 57.204 40.909 0.00 0.00 35.45 3.69
1473 1849 6.664816 AGAATAAATCCAGTGCAAATCAAGGA 59.335 34.615 0.00 0.00 36.13 3.36
1475 1851 7.541162 TCAGAATAAATCCAGTGCAAATCAAG 58.459 34.615 0.00 0.00 0.00 3.02
1478 1854 6.474751 GCTTCAGAATAAATCCAGTGCAAATC 59.525 38.462 0.00 0.00 0.00 2.17
1489 1865 4.876107 TGGTTCTCCGCTTCAGAATAAATC 59.124 41.667 0.00 0.00 32.50 2.17
1492 1868 3.513912 TCTGGTTCTCCGCTTCAGAATAA 59.486 43.478 0.00 0.00 32.50 1.40
1493 1869 3.096852 TCTGGTTCTCCGCTTCAGAATA 58.903 45.455 0.00 0.00 32.50 1.75
1636 2012 2.341846 ACAAGAGGAAAAGAACGGCA 57.658 45.000 0.00 0.00 0.00 5.69
1646 2022 5.246203 AGCTATCACACAAGTACAAGAGGAA 59.754 40.000 0.00 0.00 0.00 3.36
1712 2088 2.353011 CGTTCCTGAAAGCAATGCCATT 60.353 45.455 0.00 0.00 0.00 3.16
1713 2089 1.203052 CGTTCCTGAAAGCAATGCCAT 59.797 47.619 0.00 0.00 0.00 4.40
1716 2092 1.806542 TCTCGTTCCTGAAAGCAATGC 59.193 47.619 0.00 0.00 0.00 3.56
1724 2100 2.379972 GATCTCCCTCTCGTTCCTGAA 58.620 52.381 0.00 0.00 0.00 3.02
1865 2241 3.244281 ATGCTGCAGCGTGGTCTGA 62.244 57.895 31.99 13.21 45.83 3.27
2400 2776 4.497473 TCACCTTTTTAAACCATCTGCG 57.503 40.909 0.00 0.00 0.00 5.18
2420 3206 2.149973 AGAGGCCACAATTCCCATTC 57.850 50.000 5.01 0.00 0.00 2.67
2430 3216 0.836606 TGACAGAACAAGAGGCCACA 59.163 50.000 5.01 0.00 0.00 4.17
2467 3253 8.679100 TCAAGAACTGACGGAGAAAATTTAAAA 58.321 29.630 0.00 0.00 0.00 1.52
2471 3257 6.459710 GGTTCAAGAACTGACGGAGAAAATTT 60.460 38.462 12.22 0.00 40.94 1.82
2500 3286 1.076332 CACTAACAGTAACAGGCCGC 58.924 55.000 0.00 0.00 0.00 6.53
2502 3288 4.891260 ACTTACACTAACAGTAACAGGCC 58.109 43.478 0.00 0.00 0.00 5.19
2504 3290 7.811713 GGTAAGACTTACACTAACAGTAACAGG 59.188 40.741 23.42 0.00 37.88 4.00
2524 3310 5.251932 TCCTTATGGTTTGGTGATGGTAAGA 59.748 40.000 0.00 0.00 34.23 2.10
2535 3325 6.266786 ACCAGTTACTTTTCCTTATGGTTTGG 59.733 38.462 0.00 0.00 36.41 3.28
2576 3367 6.258160 GTCGGTATTCAAATGGATGTTTGAG 58.742 40.000 2.80 0.00 45.67 3.02
2582 3373 3.462982 TCCGTCGGTATTCAAATGGATG 58.537 45.455 11.88 0.00 0.00 3.51
2624 3415 2.524569 TGTGTTGAGCAATCTGACGA 57.475 45.000 0.00 0.00 0.00 4.20
2626 3417 4.060900 TCTCTTGTGTTGAGCAATCTGAC 58.939 43.478 0.00 0.00 0.00 3.51
2664 3455 7.824289 CAGTTTGATTTCTGTACAGGGAGAATA 59.176 37.037 22.48 0.00 0.00 1.75
2678 3469 8.981647 GTTTTATTCATGTGCAGTTTGATTTCT 58.018 29.630 0.00 0.00 0.00 2.52
2679 3470 8.223100 GGTTTTATTCATGTGCAGTTTGATTTC 58.777 33.333 0.00 0.00 0.00 2.17
2715 3506 1.168714 ACTTCCTTTTCAGATGCGCC 58.831 50.000 4.18 0.00 0.00 6.53
2718 3509 5.633830 TGATCAACTTCCTTTTCAGATGC 57.366 39.130 0.00 0.00 0.00 3.91
2801 3592 6.582636 TCTTGAAGTTGAGTTTCTAGCTTCA 58.417 36.000 0.00 0.00 40.01 3.02


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

AutoCloner maintained by Alex Coulton.