Multiple sequence alignment - TraesCS7A01G524300

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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 TraesCS7A01G524300 chr7A 100.000 5461 0 0 1 5461 706833626 706839086 0.000000e+00 10085
1 TraesCS7A01G524300 chr7D 93.088 5527 258 60 1 5461 614504965 614510433 0.000000e+00 7976
2 TraesCS7A01G524300 chr7B 90.764 2826 193 47 692 3491 706811923 706814706 0.000000e+00 3711
3 TraesCS7A01G524300 chr7B 87.559 1921 142 27 3607 5461 706814677 706816566 0.000000e+00 2134
4 TraesCS7A01G524300 chr7B 91.766 1421 95 14 50 1460 706649467 706650875 0.000000e+00 1956
5 TraesCS7A01G524300 chr7B 89.031 547 37 12 1523 2053 706661229 706661768 0.000000e+00 656
6 TraesCS7A01G524300 chr7B 84.588 558 61 14 1 548 706810446 706810988 1.040000e-146 531
7 TraesCS7A01G524300 chr7B 89.820 167 8 1 5295 5461 706821456 706821613 7.170000e-49 206
8 TraesCS7A01G524300 chr2D 79.418 1375 238 19 2169 3508 639165926 639164562 0.000000e+00 929
9 TraesCS7A01G524300 chr2D 82.203 118 21 0 1179 1296 638902038 638901921 9.680000e-18 102
10 TraesCS7A01G524300 chr2B 79.428 1259 229 21 2167 3415 798380082 798378844 0.000000e+00 863
11 TraesCS7A01G524300 chr2A 77.009 1344 249 39 2195 3495 764669835 764668509 0.000000e+00 715
12 TraesCS7A01G524300 chr2A 78.692 413 60 16 1538 1946 764674653 764674265 3.270000e-62 250
13 TraesCS7A01G524300 chrUn 79.167 456 64 22 1533 1974 303377750 303378188 2.490000e-73 287
14 TraesCS7A01G524300 chrUn 89.820 167 8 1 5295 5461 260047132 260047289 7.170000e-49 206
15 TraesCS7A01G524300 chrUn 89.820 167 8 1 5295 5461 260052116 260052273 7.170000e-49 206


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 TraesCS7A01G524300 chr7A 706833626 706839086 5460 False 10085.000000 10085 100.000 1 5461 1 chr7A.!!$F1 5460
1 TraesCS7A01G524300 chr7D 614504965 614510433 5468 False 7976.000000 7976 93.088 1 5461 1 chr7D.!!$F1 5460
2 TraesCS7A01G524300 chr7B 706810446 706816566 6120 False 2125.333333 3711 87.637 1 5461 3 chr7B.!!$F4 5460
3 TraesCS7A01G524300 chr7B 706649467 706650875 1408 False 1956.000000 1956 91.766 50 1460 1 chr7B.!!$F1 1410
4 TraesCS7A01G524300 chr7B 706661229 706661768 539 False 656.000000 656 89.031 1523 2053 1 chr7B.!!$F2 530
5 TraesCS7A01G524300 chr2D 639164562 639165926 1364 True 929.000000 929 79.418 2169 3508 1 chr2D.!!$R2 1339
6 TraesCS7A01G524300 chr2B 798378844 798380082 1238 True 863.000000 863 79.428 2167 3415 1 chr2B.!!$R1 1248
7 TraesCS7A01G524300 chr2A 764668509 764669835 1326 True 715.000000 715 77.009 2195 3495 1 chr2A.!!$R1 1300

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
992 1823 0.106335 CTTCAGATGGAGATGGCGCT 59.894 55.000 7.64 0.00 0.00 5.92 F
1026 1860 0.031857 CTCTAGATGCCGTGCTCCTG 59.968 60.000 0.00 0.00 0.00 3.86 F
1152 1992 0.598562 GACAGAGTCTTCTCGGTGCA 59.401 55.000 5.84 0.00 45.93 4.57 F
1245 2085 1.144716 CGCTAGCTTCATGGCCAGA 59.855 57.895 13.05 6.16 0.00 3.86 F
1862 2718 1.154282 CAGCATGCTCGCACAACTG 60.154 57.895 19.68 0.00 0.00 3.16 F
1872 2728 1.518056 CGCACAACTGAAGGCACCAT 61.518 55.000 0.00 0.00 0.00 3.55 F
3517 4449 1.130054 TTCAGCCAGCTCACCTTCCT 61.130 55.000 0.00 0.00 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1841 2697 1.003959 TTGTGCGAGCATGCTGGTA 60.004 52.632 28.27 21.59 35.36 3.25 R
2028 2890 1.376683 TGCCTGACACGCCATAACC 60.377 57.895 0.00 0.00 0.00 2.85 R
2534 3405 2.472695 ATTCGCTTGCTAACAGACCA 57.527 45.000 0.00 0.00 0.00 4.02 R
2570 3441 3.281727 TTCTGTATGTGCCTCCAATCC 57.718 47.619 0.00 0.00 0.00 3.01 R
3416 4346 0.322008 AGTGGTGAGCAAGCTAAGGC 60.322 55.000 0.00 0.00 39.06 4.35 R
3732 4691 0.894141 TGAGAGGAGACTGAAGCAGC 59.106 55.000 0.00 0.00 44.43 5.25 R
4764 5777 0.323360 GGCCTGTCCCTTGTTGCATA 60.323 55.000 0.00 0.00 0.00 3.14 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
38 39 5.365403 TTGTACAGGAATAAAGCCAAACG 57.635 39.130 0.00 0.00 0.00 3.60
51 52 1.595794 GCCAAACGTATGTATCCGGTG 59.404 52.381 0.00 0.00 0.00 4.94
59 60 2.865343 ATGTATCCGGTGAGTCGTTC 57.135 50.000 0.00 0.00 0.00 3.95
211 212 1.739067 GCAAGAAACTCATAGGCCGT 58.261 50.000 0.00 0.00 0.00 5.68
220 221 0.671796 TCATAGGCCGTACATGGTCG 59.328 55.000 0.00 0.93 39.14 4.79
325 326 0.947180 TTAGCTTCAACACGGCGACC 60.947 55.000 16.62 0.00 0.00 4.79
382 383 3.181467 CCATCGATCTCTCTTTCCTTGCT 60.181 47.826 0.00 0.00 0.00 3.91
463 464 2.229784 GTGTTGCCTGAAATGGAAGAGG 59.770 50.000 0.00 0.00 0.00 3.69
466 467 1.710244 TGCCTGAAATGGAAGAGGGAA 59.290 47.619 0.00 0.00 0.00 3.97
565 578 2.501316 TGATGGTCGACTCATGGTCATT 59.499 45.455 19.88 0.38 44.70 2.57
739 1565 0.543410 TCCGGTCTTCTAAGCACCCA 60.543 55.000 0.00 0.00 0.00 4.51
772 1599 1.687123 CCTTCCCCGTGTATGTAGAGG 59.313 57.143 0.00 0.00 0.00 3.69
979 1810 2.613026 TTCGTGGTTCTTGCTTCAGA 57.387 45.000 0.00 0.00 0.00 3.27
989 1820 1.948145 CTTGCTTCAGATGGAGATGGC 59.052 52.381 0.00 0.00 0.00 4.40
990 1821 0.179065 TGCTTCAGATGGAGATGGCG 60.179 55.000 0.00 0.00 0.00 5.69
991 1822 1.505477 GCTTCAGATGGAGATGGCGC 61.505 60.000 0.00 0.00 0.00 6.53
992 1823 0.106335 CTTCAGATGGAGATGGCGCT 59.894 55.000 7.64 0.00 0.00 5.92
993 1824 0.179065 TTCAGATGGAGATGGCGCTG 60.179 55.000 7.64 0.00 0.00 5.18
994 1825 1.597302 CAGATGGAGATGGCGCTGG 60.597 63.158 7.64 0.00 0.00 4.85
1026 1860 0.031857 CTCTAGATGCCGTGCTCCTG 59.968 60.000 0.00 0.00 0.00 3.86
1033 1867 4.147449 CCGTGCTCCTGATGGCGA 62.147 66.667 0.00 0.00 0.00 5.54
1076 1916 1.673337 AAGCAGCGATGCAAGCTCA 60.673 52.632 29.24 0.00 44.06 4.26
1119 1959 2.609920 GTCCTCCTCCTCCGGGAT 59.390 66.667 0.00 0.00 41.36 3.85
1122 1962 1.234529 CCTCCTCCTCCGGGATCTT 59.765 63.158 0.00 0.00 41.36 2.40
1152 1992 0.598562 GACAGAGTCTTCTCGGTGCA 59.401 55.000 5.84 0.00 45.93 4.57
1171 2011 2.874849 CAGAGGAGCTTCGTCTTCTTC 58.125 52.381 0.00 0.00 39.34 2.87
1245 2085 1.144716 CGCTAGCTTCATGGCCAGA 59.855 57.895 13.05 6.16 0.00 3.86
1480 2320 2.358737 ACCGCCGCTTCTCCAAAG 60.359 61.111 0.00 0.00 0.00 2.77
1481 2321 3.804193 CCGCCGCTTCTCCAAAGC 61.804 66.667 0.00 0.00 39.77 3.51
1482 2322 2.743928 CGCCGCTTCTCCAAAGCT 60.744 61.111 8.03 0.00 40.94 3.74
1495 2335 3.749284 AAAGCTTTGGCCCGGGTGT 62.749 57.895 24.63 0.00 39.73 4.16
1506 2346 2.358247 CGGGTGTCGGGTTCCTTG 60.358 66.667 0.00 0.00 34.75 3.61
1513 2353 1.460689 TCGGGTTCCTTGGGTGTCT 60.461 57.895 0.00 0.00 0.00 3.41
1640 2486 6.849085 AATTGGATGTGCAGGTACAATAAA 57.151 33.333 8.68 0.00 33.69 1.40
1663 2509 6.516739 ACTATCTTCAACTCGAATGTCTCA 57.483 37.500 0.00 0.00 31.69 3.27
1810 2666 3.035576 GCCGGGCTTTCGTAAGTGC 62.036 63.158 12.87 0.00 39.48 4.40
1862 2718 1.154282 CAGCATGCTCGCACAACTG 60.154 57.895 19.68 0.00 0.00 3.16
1872 2728 1.518056 CGCACAACTGAAGGCACCAT 61.518 55.000 0.00 0.00 0.00 3.55
2028 2890 6.128902 GCATAGACATATTTTACGAGGTTCCG 60.129 42.308 0.00 0.00 0.00 4.30
2109 2973 5.277106 GGTGTTTACCCGCAAAAGAAAATTG 60.277 40.000 0.00 0.00 41.36 2.32
2130 2994 1.571460 GCACTTGCTCAGGTGAACG 59.429 57.895 15.03 0.00 40.38 3.95
2131 2995 1.571460 CACTTGCTCAGGTGAACGC 59.429 57.895 6.30 0.00 40.38 4.84
2293 3164 2.966309 GCGCTTTTCCTCGTGGTGG 61.966 63.158 0.00 0.00 34.23 4.61
2510 3381 9.396022 GAGATTATCAGGAAATGTGAAGGTTTA 57.604 33.333 0.00 0.00 0.00 2.01
2570 3441 3.363378 GCGAATTAAGCATCGTCATGGAG 60.363 47.826 9.07 0.00 41.01 3.86
3039 3958 3.627123 CGCATACATTCCAGAAACCATCA 59.373 43.478 0.00 0.00 0.00 3.07
3396 4326 2.125512 GCCCGCGTGAGATCTGTT 60.126 61.111 4.92 0.00 0.00 3.16
3405 4335 2.609916 CGTGAGATCTGTTCGCTCTCTA 59.390 50.000 0.00 0.00 37.04 2.43
3416 4346 2.865079 TCGCTCTCTAGGGTATCTTGG 58.135 52.381 0.00 0.00 37.01 3.61
3469 4401 2.002586 CTTGTACGGCTGACCAATCTG 58.997 52.381 0.00 0.00 34.57 2.90
3517 4449 1.130054 TTCAGCCAGCTCACCTTCCT 61.130 55.000 0.00 0.00 0.00 3.36
3534 4466 3.006112 TCCTGAGCGAGTCTATTCTGT 57.994 47.619 0.00 0.00 0.00 3.41
3949 4911 3.232213 TGCAATTAGGAGTCTGTCGAC 57.768 47.619 9.11 9.11 40.54 4.20
3955 4917 0.956410 AGGAGTCTGTCGACGAGTGG 60.956 60.000 18.14 4.73 44.93 4.00
3980 4942 2.754552 CGAAATCCTGGAAAGAATGCCA 59.245 45.455 0.00 0.00 0.00 4.92
4187 5149 6.462487 GGAGATCGGATACCATTGAAACTGTA 60.462 42.308 8.27 0.00 0.00 2.74
4235 5197 3.555956 CGGATGTATGTGTAAGACTTGGC 59.444 47.826 0.00 0.00 0.00 4.52
4278 5240 1.269206 ACGTAAAAGTTGCCGAGTCGA 60.269 47.619 15.64 0.00 0.00 4.20
4322 5284 1.765314 CACCCCAACTCTCCTAGGATG 59.235 57.143 13.12 10.98 0.00 3.51
4328 5290 4.283212 CCCAACTCTCCTAGGATGAGAATC 59.717 50.000 29.75 0.00 38.34 2.52
4369 5331 3.120468 TGATGGTGAGGAGGATGAGAA 57.880 47.619 0.00 0.00 0.00 2.87
4698 5684 6.581171 ATTCAATGAACCAAAAGAGACCTC 57.419 37.500 0.00 0.00 0.00 3.85
4777 5790 3.306641 GGCAAACAATATGCAACAAGGGA 60.307 43.478 0.00 0.00 45.60 4.20
4779 5792 4.798924 GCAAACAATATGCAACAAGGGACA 60.799 41.667 0.00 0.00 43.29 4.02
4780 5793 4.789012 AACAATATGCAACAAGGGACAG 57.211 40.909 0.00 0.00 0.00 3.51
4783 5796 0.323360 TATGCAACAAGGGACAGGCC 60.323 55.000 0.00 0.00 0.00 5.19
4791 5804 0.779997 AAGGGACAGGCCTCAACAAT 59.220 50.000 0.00 0.00 36.66 2.71
4794 5807 0.251341 GGACAGGCCTCAACAATGGT 60.251 55.000 0.00 0.00 0.00 3.55
4814 5827 2.282110 CCACCAATGACCGCACCA 60.282 61.111 0.00 0.00 0.00 4.17
4845 5858 2.887568 CGGCATCGAGGAGCACAC 60.888 66.667 0.00 0.00 39.00 3.82
4851 5864 0.615331 ATCGAGGAGCACACCAATGT 59.385 50.000 0.00 0.00 40.80 2.71
4862 5875 2.036098 CCAATGTGGGCCAGAGCA 59.964 61.111 6.40 0.89 42.56 4.26
4864 5877 0.974010 CCAATGTGGGCCAGAGCATT 60.974 55.000 6.40 11.02 42.56 3.56
4883 5896 4.269183 CATTATCAAAGGCAGTACCACCA 58.731 43.478 4.69 0.00 43.14 4.17
4884 5897 2.200373 ATCAAAGGCAGTACCACCAC 57.800 50.000 4.69 0.00 43.14 4.16
4972 6012 4.410400 CCCACCAAGGTCGAGGCC 62.410 72.222 0.00 0.00 34.66 5.19
5187 6227 5.248640 TCTTTCTTGTCATGAAGTCCATCC 58.751 41.667 0.00 0.00 31.94 3.51
5189 6229 2.831526 TCTTGTCATGAAGTCCATCCGA 59.168 45.455 0.00 0.00 31.94 4.55
5245 6285 7.816640 TGTGCTGGAATCTAACTTATTCAAAC 58.183 34.615 0.00 0.00 35.46 2.93
5285 6331 4.023291 GCTTATTTTCATCCCTGACCCAA 58.977 43.478 0.00 0.00 0.00 4.12
5288 6334 0.776810 TTTCATCCCTGACCCAAGCA 59.223 50.000 0.00 0.00 0.00 3.91
5319 6365 2.688507 CGCATCATCCCGCTTATTAGT 58.311 47.619 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 3.549625 GGAACGACTCACCGGATACATAC 60.550 52.174 9.46 0.00 0.00 2.39
51 52 1.273886 AGAGCTCAAAGGGAACGACTC 59.726 52.381 17.77 0.00 0.00 3.36
59 60 2.399916 CTCAAGGAGAGCTCAAAGGG 57.600 55.000 17.77 2.33 37.59 3.95
220 221 2.027377 AGCTACCATGCTAGATCATGCC 60.027 50.000 0.00 0.00 42.10 4.40
382 383 2.182827 CAGGAGGAGTGATCTGTGGAA 58.817 52.381 0.00 0.00 0.00 3.53
433 434 2.032965 TCAGGCAACACTAACCCCTA 57.967 50.000 0.00 0.00 41.41 3.53
463 464 1.694525 CCCCCTTCCCTCTCCTTCC 60.695 68.421 0.00 0.00 0.00 3.46
466 467 3.626596 TGCCCCCTTCCCTCTCCT 61.627 66.667 0.00 0.00 0.00 3.69
588 1008 6.440647 TCTGAACAACAGTATAGGACAGGATT 59.559 38.462 0.00 0.00 45.86 3.01
589 1009 5.958380 TCTGAACAACAGTATAGGACAGGAT 59.042 40.000 0.00 0.00 45.86 3.24
590 1010 5.330233 TCTGAACAACAGTATAGGACAGGA 58.670 41.667 0.00 0.00 45.86 3.86
739 1565 2.209758 GGGGAAGGAGAGGAAGGATTT 58.790 52.381 0.00 0.00 0.00 2.17
772 1599 0.988678 ACTCAACAGGCCCCTATCCC 60.989 60.000 0.00 0.00 0.00 3.85
979 1810 4.923942 CGCCAGCGCCATCTCCAT 62.924 66.667 2.29 0.00 0.00 3.41
991 1822 4.172512 AGCCTCCATCTGCGCCAG 62.173 66.667 4.18 2.24 0.00 4.85
992 1823 4.166888 GAGCCTCCATCTGCGCCA 62.167 66.667 4.18 0.00 0.00 5.69
993 1824 2.433231 CTAGAGCCTCCATCTGCGCC 62.433 65.000 4.18 0.00 0.00 6.53
994 1825 1.006337 CTAGAGCCTCCATCTGCGC 60.006 63.158 0.00 0.00 0.00 6.09
1007 1838 0.031857 CAGGAGCACGGCATCTAGAG 59.968 60.000 0.00 0.00 0.00 2.43
1019 1853 0.469892 TATCCTCGCCATCAGGAGCA 60.470 55.000 0.00 0.00 43.56 4.26
1026 1860 2.433318 GCCGCTATCCTCGCCATC 60.433 66.667 0.00 0.00 0.00 3.51
1033 1867 4.541648 AGGGTCGGCCGCTATCCT 62.542 66.667 23.51 17.56 33.97 3.24
1044 1878 1.649664 CTGCTTGAAGATCAGGGTCG 58.350 55.000 0.00 0.00 0.00 4.79
1076 1916 3.681594 CGGACCCAGCATAACAGTAACAT 60.682 47.826 0.00 0.00 0.00 2.71
1119 1959 3.165875 ACTCTGTCCGGAAGAATCAAGA 58.834 45.455 5.23 0.01 0.00 3.02
1122 1962 2.808919 AGACTCTGTCCGGAAGAATCA 58.191 47.619 19.86 9.03 32.18 2.57
1152 1992 1.470890 CGAAGAAGACGAAGCTCCTCT 59.529 52.381 0.00 0.00 0.00 3.69
1245 2085 3.071602 CCCGAACTATCTTCATCCACCAT 59.928 47.826 0.00 0.00 0.00 3.55
1492 2332 1.599797 CACCCAAGGAACCCGACAC 60.600 63.158 0.00 0.00 0.00 3.67
1495 2335 1.460689 AGACACCCAAGGAACCCGA 60.461 57.895 0.00 0.00 0.00 5.14
1640 2486 6.516739 TGAGACATTCGAGTTGAAGATAGT 57.483 37.500 4.63 0.00 40.65 2.12
1658 2504 2.224314 CGGGCAGAAAAAGACTTGAGAC 59.776 50.000 0.00 0.00 0.00 3.36
1663 2509 1.179174 GGCCGGGCAGAAAAAGACTT 61.179 55.000 25.33 0.00 0.00 3.01
1810 2666 4.082300 CCCTCATATCTGGATTCTGAGACG 60.082 50.000 17.06 8.51 34.21 4.18
1841 2697 1.003959 TTGTGCGAGCATGCTGGTA 60.004 52.632 28.27 21.59 35.36 3.25
2003 2859 6.128902 CGGAACCTCGTAAAATATGTCTATGC 60.129 42.308 0.00 0.00 0.00 3.14
2009 2865 4.476628 ACCGGAACCTCGTAAAATATGT 57.523 40.909 9.46 0.00 0.00 2.29
2019 2881 1.881252 CGCCATAACCGGAACCTCG 60.881 63.158 9.46 0.00 0.00 4.63
2028 2890 1.376683 TGCCTGACACGCCATAACC 60.377 57.895 0.00 0.00 0.00 2.85
2091 2954 4.278669 TGCTACAATTTTCTTTTGCGGGTA 59.721 37.500 0.00 0.00 0.00 3.69
2130 2994 6.698766 GGCAGCATATATATTAATTTGCCTGC 59.301 38.462 17.29 15.49 43.84 4.85
2131 2995 7.703621 GTGGCAGCATATATATTAATTTGCCTG 59.296 37.037 21.30 12.26 46.51 4.85
2190 3054 9.503427 GCATAATTTTGTATGTTAGGTCAGAAC 57.497 33.333 0.00 0.00 34.51 3.01
2293 3164 3.621268 TGTTATTATTCTGCTGCCGTGAC 59.379 43.478 0.00 0.00 0.00 3.67
2298 3169 6.093495 TGTGTAGTTGTTATTATTCTGCTGCC 59.907 38.462 0.00 0.00 0.00 4.85
2510 3381 7.445402 CCAGCTATACTTACAATTGCTAATGGT 59.555 37.037 5.05 2.60 34.38 3.55
2534 3405 2.472695 ATTCGCTTGCTAACAGACCA 57.527 45.000 0.00 0.00 0.00 4.02
2570 3441 3.281727 TTCTGTATGTGCCTCCAATCC 57.718 47.619 0.00 0.00 0.00 3.01
3396 4326 2.865079 CCAAGATACCCTAGAGAGCGA 58.135 52.381 0.00 0.00 0.00 4.93
3405 4335 2.173569 CAAGCTAAGGCCAAGATACCCT 59.826 50.000 5.01 0.00 39.73 4.34
3416 4346 0.322008 AGTGGTGAGCAAGCTAAGGC 60.322 55.000 0.00 0.00 39.06 4.35
3469 4401 0.908198 AGGTGAGGTGAAGATCCTGC 59.092 55.000 0.00 0.00 35.20 4.85
3517 4449 3.610911 TGAGACAGAATAGACTCGCTCA 58.389 45.455 0.00 0.00 33.87 4.26
3534 4466 1.833630 CATGTGGGCTACTCCTTGAGA 59.166 52.381 1.79 0.00 33.32 3.27
3732 4691 0.894141 TGAGAGGAGACTGAAGCAGC 59.106 55.000 0.00 0.00 44.43 5.25
3949 4911 2.361119 TCCAGGATTTCGATACCACTCG 59.639 50.000 0.00 0.00 39.99 4.18
3955 4917 5.278022 GGCATTCTTTCCAGGATTTCGATAC 60.278 44.000 0.00 0.00 0.00 2.24
4187 5149 2.549778 GCTTCTCAAGTGACTCAAGCCT 60.550 50.000 7.08 0.00 31.88 4.58
4278 5240 0.036952 CTGACGACAGCCTCCAATGT 60.037 55.000 1.13 0.00 37.33 2.71
4322 5284 8.767478 AAATCACATCCACAAATTTGATTCTC 57.233 30.769 24.64 0.00 35.85 2.87
4328 5290 8.018520 CCATCAAAAATCACATCCACAAATTTG 58.981 33.333 16.67 16.67 0.00 2.32
4369 5331 1.863662 ATTCTCGTGAGTCGCGGTGT 61.864 55.000 24.68 7.22 37.97 4.16
4698 5684 3.302365 AAAATGATGAACGCCCTGTTG 57.698 42.857 0.00 0.00 42.09 3.33
4764 5777 0.323360 GGCCTGTCCCTTGTTGCATA 60.323 55.000 0.00 0.00 0.00 3.14
4777 5790 0.540365 CCACCATTGTTGAGGCCTGT 60.540 55.000 12.00 0.00 0.00 4.00
4779 5792 1.607467 GCCACCATTGTTGAGGCCT 60.607 57.895 3.86 3.86 37.68 5.19
4780 5793 2.973082 GCCACCATTGTTGAGGCC 59.027 61.111 0.00 0.00 37.68 5.19
4829 5842 2.512515 GGTGTGCTCCTCGATGCC 60.513 66.667 0.00 0.00 0.00 4.40
4833 5846 2.057830 ACATTGGTGTGCTCCTCGA 58.942 52.632 0.00 0.00 37.14 4.04
4845 5858 0.974010 AATGCTCTGGCCCACATTGG 60.974 55.000 0.00 0.00 37.74 3.16
4851 5864 2.658285 CTTTGATAATGCTCTGGCCCA 58.342 47.619 0.00 0.00 37.74 5.36
4852 5865 1.959282 CCTTTGATAATGCTCTGGCCC 59.041 52.381 0.00 0.00 37.74 5.80
4856 5869 4.274459 GGTACTGCCTTTGATAATGCTCTG 59.726 45.833 0.00 0.00 0.00 3.35
4857 5870 4.080356 TGGTACTGCCTTTGATAATGCTCT 60.080 41.667 0.00 0.00 38.35 4.09
4862 5875 4.270008 GTGGTGGTACTGCCTTTGATAAT 58.730 43.478 7.54 0.00 38.35 1.28
4864 5877 2.026636 GGTGGTGGTACTGCCTTTGATA 60.027 50.000 7.54 0.00 38.35 2.15
4883 5896 2.757077 GGTACTGCTGCCCTTGGT 59.243 61.111 0.00 0.00 0.00 3.67
4884 5897 2.436646 CGGTACTGCTGCCCTTGG 60.437 66.667 0.00 0.00 0.00 3.61
5041 6081 5.000591 TGGTGCACGAAGAAGAAATAATCA 58.999 37.500 11.45 0.00 0.00 2.57
5080 6120 6.127730 AGCAAGGCTGTAAATGGTACATTAAC 60.128 38.462 0.00 0.00 40.12 2.01
5187 6227 6.297582 TCTAGAGGGAAGAAAGTAGGTATCG 58.702 44.000 0.00 0.00 0.00 2.92
5189 6229 8.123780 AGTTTCTAGAGGGAAGAAAGTAGGTAT 58.876 37.037 4.51 0.00 42.21 2.73
5245 6285 1.002868 CACCTGGCCCAGTTCTGAG 60.003 63.158 10.47 0.00 0.00 3.35
5285 6331 3.574074 ATGCGCTCAACCCCTTGCT 62.574 57.895 9.73 0.00 0.00 3.91
5288 6334 0.749454 GATGATGCGCTCAACCCCTT 60.749 55.000 9.73 0.00 37.44 3.95
5352 6398 2.456119 CCGCTTGGTGCATCGTCTC 61.456 63.158 0.00 0.00 43.06 3.36
5394 6440 2.107953 GACTGCTCCTCGGATGCC 59.892 66.667 5.39 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.