Multiple sequence alignment - TraesCS4A01G079600

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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 TraesCS4A01G079600 chr4A 100.000 3959 0 0 1 3959 81762630 81766588 0.000000e+00 7312
1 TraesCS4A01G079600 chr4D 93.589 3697 135 47 276 3917 381901513 381897864 0.000000e+00 5421
2 TraesCS4A01G079600 chr4D 90.062 161 10 2 3800 3959 381897919 381897764 1.870000e-48 204
3 TraesCS4A01G079600 chr4D 85.906 149 16 4 56 199 381902540 381902392 1.910000e-33 154
4 TraesCS4A01G079600 chr4B 94.296 3436 118 30 560 3959 469249442 469246049 0.000000e+00 5188


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 TraesCS4A01G079600 chr4A 81762630 81766588 3958 False 7312.000000 7312 100.000000 1 3959 1 chr4A.!!$F1 3958
1 TraesCS4A01G079600 chr4D 381897764 381902540 4776 True 1926.333333 5421 89.852333 56 3959 3 chr4D.!!$R1 3903
2 TraesCS4A01G079600 chr4B 469246049 469249442 3393 True 5188.000000 5188 94.296000 560 3959 1 chr4B.!!$R1 3399

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
26 27 0.033109 TCCTCGCATCCTCTTCCTGA 60.033 55.0 0.00 0.0 0.00 3.86 F
259 285 0.039074 CGGAAGGCGGTAGAGCATAG 60.039 60.0 0.00 0.0 39.27 2.23 F
464 1291 0.107703 TTGGCATCGGAGCAAGTAGG 60.108 55.0 0.00 0.0 35.83 3.18 F
551 1378 0.684805 TTTGTCACCGGTTTTGGGCT 60.685 50.0 2.97 0.0 0.00 5.19 F
1734 2592 0.747283 CTGGACAGCCTGATTCTGCC 60.747 60.0 0.00 0.0 35.28 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1734 2592 0.873312 CACGTCCTGGCGATGAGATG 60.873 60.000 15.53 1.22 35.59 2.90 R
2244 3102 6.505048 TCACCTTCCTCATTGACATCATAT 57.495 37.500 0.00 0.00 0.00 1.78 R
2346 3204 1.217779 GACCACCTCTGCTCTGAGC 59.782 63.158 22.38 22.38 42.82 4.26 R
2754 3612 4.324563 CCATCTTCATCCCCACAGTTAAGT 60.325 45.833 0.00 0.00 0.00 2.24 R
3259 4123 0.038435 CCAAATTCCACACATGCGCA 60.038 50.000 14.96 14.96 0.00 6.09 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
18 19 2.510664 GTCTCCTTCCTCGCATCCT 58.489 57.895 0.00 0.00 0.00 3.24
19 20 0.387565 GTCTCCTTCCTCGCATCCTC 59.612 60.000 0.00 0.00 0.00 3.71
20 21 0.260230 TCTCCTTCCTCGCATCCTCT 59.740 55.000 0.00 0.00 0.00 3.69
21 22 1.118838 CTCCTTCCTCGCATCCTCTT 58.881 55.000 0.00 0.00 0.00 2.85
22 23 1.068434 CTCCTTCCTCGCATCCTCTTC 59.932 57.143 0.00 0.00 0.00 2.87
23 24 0.105778 CCTTCCTCGCATCCTCTTCC 59.894 60.000 0.00 0.00 0.00 3.46
24 25 1.118838 CTTCCTCGCATCCTCTTCCT 58.881 55.000 0.00 0.00 0.00 3.36
25 26 0.826715 TTCCTCGCATCCTCTTCCTG 59.173 55.000 0.00 0.00 0.00 3.86
26 27 0.033109 TCCTCGCATCCTCTTCCTGA 60.033 55.000 0.00 0.00 0.00 3.86
27 28 1.047002 CCTCGCATCCTCTTCCTGAT 58.953 55.000 0.00 0.00 0.00 2.90
28 29 1.415659 CCTCGCATCCTCTTCCTGATT 59.584 52.381 0.00 0.00 0.00 2.57
29 30 2.547642 CCTCGCATCCTCTTCCTGATTC 60.548 54.545 0.00 0.00 0.00 2.52
30 31 2.102084 CTCGCATCCTCTTCCTGATTCA 59.898 50.000 0.00 0.00 0.00 2.57
31 32 2.501316 TCGCATCCTCTTCCTGATTCAA 59.499 45.455 0.00 0.00 0.00 2.69
32 33 2.611292 CGCATCCTCTTCCTGATTCAAC 59.389 50.000 0.00 0.00 0.00 3.18
33 34 3.614092 GCATCCTCTTCCTGATTCAACA 58.386 45.455 0.00 0.00 0.00 3.33
34 35 4.205587 GCATCCTCTTCCTGATTCAACAT 58.794 43.478 0.00 0.00 0.00 2.71
35 36 4.275443 GCATCCTCTTCCTGATTCAACATC 59.725 45.833 0.00 0.00 0.00 3.06
36 37 4.494091 TCCTCTTCCTGATTCAACATCC 57.506 45.455 0.00 0.00 0.00 3.51
37 38 3.118629 TCCTCTTCCTGATTCAACATCCG 60.119 47.826 0.00 0.00 0.00 4.18
38 39 2.611292 CTCTTCCTGATTCAACATCCGC 59.389 50.000 0.00 0.00 0.00 5.54
39 40 1.672881 CTTCCTGATTCAACATCCGCC 59.327 52.381 0.00 0.00 0.00 6.13
40 41 0.107214 TCCTGATTCAACATCCGCCC 60.107 55.000 0.00 0.00 0.00 6.13
41 42 0.394216 CCTGATTCAACATCCGCCCA 60.394 55.000 0.00 0.00 0.00 5.36
42 43 1.683943 CTGATTCAACATCCGCCCAT 58.316 50.000 0.00 0.00 0.00 4.00
43 44 1.605710 CTGATTCAACATCCGCCCATC 59.394 52.381 0.00 0.00 0.00 3.51
44 45 1.064832 TGATTCAACATCCGCCCATCA 60.065 47.619 0.00 0.00 0.00 3.07
45 46 2.023673 GATTCAACATCCGCCCATCAA 58.976 47.619 0.00 0.00 0.00 2.57
46 47 1.916506 TTCAACATCCGCCCATCAAA 58.083 45.000 0.00 0.00 0.00 2.69
47 48 2.142356 TCAACATCCGCCCATCAAAT 57.858 45.000 0.00 0.00 0.00 2.32
48 49 2.023673 TCAACATCCGCCCATCAAATC 58.976 47.619 0.00 0.00 0.00 2.17
49 50 1.067516 CAACATCCGCCCATCAAATCC 59.932 52.381 0.00 0.00 0.00 3.01
50 51 0.258484 ACATCCGCCCATCAAATCCA 59.742 50.000 0.00 0.00 0.00 3.41
51 52 1.133388 ACATCCGCCCATCAAATCCAT 60.133 47.619 0.00 0.00 0.00 3.41
52 53 1.271379 CATCCGCCCATCAAATCCATG 59.729 52.381 0.00 0.00 0.00 3.66
53 54 0.258484 TCCGCCCATCAAATCCATGT 59.742 50.000 0.00 0.00 0.00 3.21
54 55 0.670162 CCGCCCATCAAATCCATGTC 59.330 55.000 0.00 0.00 0.00 3.06
69 70 2.421107 CCATGTCAGATGGAGGTTCTGG 60.421 54.545 0.00 0.00 41.64 3.86
81 82 1.153147 GTTCTGGGGCGGAGGAATC 60.153 63.158 0.00 0.00 0.00 2.52
89 90 4.918201 CGGAGGAATCAGGCGGGC 62.918 72.222 0.00 0.00 0.00 6.13
156 157 4.664677 GTGTCGGGCTGCAGACGT 62.665 66.667 20.43 0.00 40.05 4.34
180 186 0.828343 ATAGGCGGGTCTAGCTCACC 60.828 60.000 6.25 6.25 34.52 4.02
183 189 1.755008 GCGGGTCTAGCTCACCTCT 60.755 63.158 13.25 0.00 33.96 3.69
185 191 0.394488 CGGGTCTAGCTCACCTCTGA 60.394 60.000 13.25 0.00 33.96 3.27
199 205 4.180946 CTGAGGACGGAGGTCGCG 62.181 72.222 0.00 0.00 44.39 5.87
256 282 4.143333 GCGGAAGGCGGTAGAGCA 62.143 66.667 0.00 0.00 39.27 4.26
257 283 2.815308 CGGAAGGCGGTAGAGCAT 59.185 61.111 0.00 0.00 39.27 3.79
258 284 2.038690 CGGAAGGCGGTAGAGCATA 58.961 57.895 0.00 0.00 39.27 3.14
259 285 0.039074 CGGAAGGCGGTAGAGCATAG 60.039 60.000 0.00 0.00 39.27 2.23
260 286 0.318762 GGAAGGCGGTAGAGCATAGG 59.681 60.000 0.00 0.00 39.27 2.57
271 297 4.301027 GCATAGGAGACCGGCGGG 62.301 72.222 31.78 12.53 40.11 6.13
299 1110 1.831389 CGGTGTCGTGCAAAGTCCAG 61.831 60.000 0.00 0.00 0.00 3.86
304 1115 3.286751 GTGCAAAGTCCAGCGGCA 61.287 61.111 1.45 0.00 0.00 5.69
305 1116 2.518112 TGCAAAGTCCAGCGGCAA 60.518 55.556 1.45 0.00 0.00 4.52
340 1151 1.142748 GCTCACCAGAGACGATGGG 59.857 63.158 0.00 0.00 44.98 4.00
347 1158 0.809241 CAGAGACGATGGGCTGAAGC 60.809 60.000 0.00 0.00 41.14 3.86
349 1160 2.892425 GACGATGGGCTGAAGCGG 60.892 66.667 0.00 0.00 43.26 5.52
363 1174 3.270027 TGAAGCGGAGGTACAATTCATG 58.730 45.455 0.00 0.00 37.06 3.07
375 1186 4.297299 ACAATTCATGGCTATTGCTTCG 57.703 40.909 12.84 0.00 39.59 3.79
380 1191 0.461870 ATGGCTATTGCTTCGCGTGA 60.462 50.000 5.77 0.00 39.59 4.35
381 1192 1.348594 GGCTATTGCTTCGCGTGAC 59.651 57.895 5.77 0.00 39.59 3.67
384 1196 1.786928 GCTATTGCTTCGCGTGACAAC 60.787 52.381 5.77 0.00 36.03 3.32
386 1198 1.790755 ATTGCTTCGCGTGACAACTA 58.209 45.000 5.77 0.00 0.00 2.24
390 1202 1.387084 GCTTCGCGTGACAACTAAGAG 59.613 52.381 5.77 0.00 0.00 2.85
393 1205 2.148768 TCGCGTGACAACTAAGAGAGA 58.851 47.619 5.77 0.00 0.00 3.10
395 1207 2.848887 CGCGTGACAACTAAGAGAGATG 59.151 50.000 0.00 0.00 34.20 2.90
397 1209 3.775202 CGTGACAACTAAGAGAGATGGG 58.225 50.000 0.00 0.00 32.30 4.00
398 1210 3.193691 CGTGACAACTAAGAGAGATGGGT 59.806 47.826 0.00 0.00 32.30 4.51
399 1211 4.675671 CGTGACAACTAAGAGAGATGGGTC 60.676 50.000 0.00 0.00 32.30 4.46
413 1225 3.947834 AGATGGGTCGTGAAATGGATTTC 59.052 43.478 5.32 5.32 44.83 2.17
416 1228 3.505680 TGGGTCGTGAAATGGATTTCTTG 59.494 43.478 12.22 5.96 44.85 3.02
419 1231 5.508994 GGGTCGTGAAATGGATTTCTTGTTT 60.509 40.000 12.22 0.00 44.85 2.83
420 1232 6.294286 GGGTCGTGAAATGGATTTCTTGTTTA 60.294 38.462 12.22 0.00 44.85 2.01
421 1233 7.312899 GGTCGTGAAATGGATTTCTTGTTTAT 58.687 34.615 12.22 0.00 44.85 1.40
423 1235 8.638565 GTCGTGAAATGGATTTCTTGTTTATTG 58.361 33.333 12.22 0.00 44.85 1.90
424 1236 7.328249 TCGTGAAATGGATTTCTTGTTTATTGC 59.672 33.333 12.22 0.00 44.85 3.56
426 1238 8.992073 GTGAAATGGATTTCTTGTTTATTGCTT 58.008 29.630 12.22 0.00 44.85 3.91
464 1291 0.107703 TTGGCATCGGAGCAAGTAGG 60.108 55.000 0.00 0.00 35.83 3.18
470 1297 2.922740 TCGGAGCAAGTAGGTGTTTT 57.077 45.000 0.00 0.00 0.00 2.43
472 1299 2.103432 TCGGAGCAAGTAGGTGTTTTGA 59.897 45.455 0.00 0.00 0.00 2.69
476 1303 3.221771 AGCAAGTAGGTGTTTTGATGCA 58.778 40.909 0.00 0.00 35.11 3.96
487 1314 6.037391 AGGTGTTTTGATGCACTGAAATTTTG 59.963 34.615 0.00 0.00 36.03 2.44
488 1315 6.183360 GGTGTTTTGATGCACTGAAATTTTGT 60.183 34.615 0.00 0.00 36.03 2.83
489 1316 7.242783 GTGTTTTGATGCACTGAAATTTTGTT 58.757 30.769 0.00 0.00 33.22 2.83
493 1320 4.809958 TGATGCACTGAAATTTTGTTGTGG 59.190 37.500 0.00 0.00 0.00 4.17
495 1322 2.935201 GCACTGAAATTTTGTTGTGGCA 59.065 40.909 12.33 0.00 0.00 4.92
496 1323 3.242381 GCACTGAAATTTTGTTGTGGCAC 60.242 43.478 11.55 11.55 0.00 5.01
497 1324 3.309410 CACTGAAATTTTGTTGTGGCACC 59.691 43.478 16.26 0.43 0.00 5.01
498 1325 2.539274 CTGAAATTTTGTTGTGGCACCG 59.461 45.455 16.26 0.00 0.00 4.94
499 1326 1.260297 GAAATTTTGTTGTGGCACCGC 59.740 47.619 16.26 8.36 0.00 5.68
542 1369 3.011949 CAAAAGTGGATTTGTCACCGG 57.988 47.619 0.00 0.00 35.93 5.28
549 1376 1.000394 GGATTTGTCACCGGTTTTGGG 60.000 52.381 2.97 0.00 0.00 4.12
551 1378 0.684805 TTTGTCACCGGTTTTGGGCT 60.685 50.000 2.97 0.00 0.00 5.19
554 1381 0.958876 GTCACCGGTTTTGGGCTAGG 60.959 60.000 2.97 0.00 0.00 3.02
595 1438 1.202818 GGTTATGAGATGGGACCCAGC 60.203 57.143 21.76 21.76 40.67 4.85
646 1489 1.146263 GAACTACCGGCCCCATCAG 59.854 63.158 0.00 0.00 0.00 2.90
666 1509 2.158204 AGGTAGGCTTCCATACCGGTAT 60.158 50.000 21.72 21.72 45.12 2.73
752 1609 2.507992 CGAACAGCCGAGCAGAGG 60.508 66.667 0.00 0.00 0.00 3.69
792 1650 1.338020 CTCAAACAAACCCACCAGAGC 59.662 52.381 0.00 0.00 0.00 4.09
828 1686 3.400590 GTTCACGCGTCCCACGAC 61.401 66.667 9.86 0.00 46.05 4.34
859 1717 2.946762 GGTGGCACAAGCTCGAAC 59.053 61.111 20.82 0.00 44.16 3.95
946 1804 2.063541 AACAGCAGGCGCAGTGAAAC 62.064 55.000 10.83 0.00 38.00 2.78
947 1805 2.980233 AGCAGGCGCAGTGAAACC 60.980 61.111 10.83 0.00 42.27 3.27
1071 1929 2.612251 CTCCCCTCCTCCTCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
1072 1930 2.018086 CTCCCCTCCTCCTCCTCCT 61.018 68.421 0.00 0.00 0.00 3.69
1073 1931 2.015726 TCCCCTCCTCCTCCTCCTC 61.016 68.421 0.00 0.00 0.00 3.71
1074 1932 2.612251 CCCTCCTCCTCCTCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
1075 1933 2.018086 CCCTCCTCCTCCTCCTCCT 61.018 68.421 0.00 0.00 0.00 3.69
1076 1934 1.541672 CCTCCTCCTCCTCCTCCTC 59.458 68.421 0.00 0.00 0.00 3.71
1618 2476 1.298190 GACACCGTCGAGCGTATCC 60.298 63.158 0.00 0.00 39.32 2.59
1734 2592 0.747283 CTGGACAGCCTGATTCTGCC 60.747 60.000 0.00 0.00 35.28 4.85
1752 2610 1.439228 CATCTCATCGCCAGGACGT 59.561 57.895 0.00 0.00 0.00 4.34
2244 3102 6.599244 GGACATTTGAGTTTGATCCAGACATA 59.401 38.462 0.00 0.00 0.00 2.29
2278 3136 1.988846 AGGAAGGTGAGCCTAGCTTTT 59.011 47.619 0.00 0.00 46.33 2.27
2279 3137 2.376855 AGGAAGGTGAGCCTAGCTTTTT 59.623 45.455 0.00 0.00 46.33 1.94
2346 3204 2.032528 TTGCAGCAAGTCCGGGAG 59.967 61.111 2.83 0.00 0.00 4.30
2619 3477 5.290885 TGACGATGATACTGATTTTGGTTCG 59.709 40.000 0.00 0.00 0.00 3.95
2981 3839 5.336102 AGATTTGTGATTCACCCCTGATTT 58.664 37.500 14.05 0.00 32.73 2.17
3155 4017 4.092091 CCGCTGTTGATTACTGTCTTCTTC 59.908 45.833 0.00 0.00 0.00 2.87
3174 4036 5.192927 TCTTCCAAGACAGTTGAACATTGT 58.807 37.500 0.00 0.00 0.00 2.71
3317 4185 7.843490 AGCACGACAATTGTGTTATTACTAT 57.157 32.000 17.58 0.00 38.41 2.12
3431 4299 2.742774 AGTCGTTCATTTTTGCCTTGC 58.257 42.857 0.00 0.00 0.00 4.01
3478 4346 6.003950 TGCAATAGCTAAAGAAACTGAACCT 58.996 36.000 0.00 0.00 42.74 3.50
3479 4347 6.072508 TGCAATAGCTAAAGAAACTGAACCTG 60.073 38.462 0.00 0.00 42.74 4.00
3480 4348 6.149474 GCAATAGCTAAAGAAACTGAACCTGA 59.851 38.462 0.00 0.00 37.91 3.86
3481 4349 7.148171 GCAATAGCTAAAGAAACTGAACCTGAT 60.148 37.037 0.00 0.00 37.91 2.90
3482 4350 9.383519 CAATAGCTAAAGAAACTGAACCTGATA 57.616 33.333 0.00 0.00 0.00 2.15
3566 4434 8.793592 AGTTCCTCTTGTGTGGTTTAATTTATC 58.206 33.333 0.00 0.00 0.00 1.75
3606 4474 2.306805 TGTGAGATGGATGTTGCTTCCT 59.693 45.455 3.33 0.00 34.17 3.36
3612 4480 0.109597 GGATGTTGCTTCCTTGTGCG 60.110 55.000 0.00 0.00 0.00 5.34
3648 4516 4.134563 GACTGGTTGGTGTTTACTGTGAT 58.865 43.478 0.00 0.00 0.00 3.06
3664 4532 6.678568 ACTGTGATAAGGGATATTCCTCAG 57.321 41.667 1.95 8.49 36.57 3.35
3673 4541 4.916424 AGGGATATTCCTCAGCTTATGGTT 59.084 41.667 0.00 0.00 36.57 3.67
3809 4690 6.564557 AAATTCTTGGAACATTATGGGCAT 57.435 33.333 0.00 0.00 39.30 4.40
3818 4699 7.068702 TGGAACATTATGGGCATCTAAAATCT 58.931 34.615 0.00 0.00 0.00 2.40
3930 4875 5.705905 ACAGTGCTAGAAATTGTAGGGAAAC 59.294 40.000 0.00 0.00 0.00 2.78
3947 4892 9.974980 GTAGGGAAACTTTTGATTTACATTCAA 57.025 29.630 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.387565 GAGGATGCGAGGAAGGAGAC 59.612 60.000 0.00 0.00 0.00 3.36
1 2 0.260230 AGAGGATGCGAGGAAGGAGA 59.740 55.000 0.00 0.00 0.00 3.71
2 3 1.068434 GAAGAGGATGCGAGGAAGGAG 59.932 57.143 0.00 0.00 0.00 3.69
3 4 1.115467 GAAGAGGATGCGAGGAAGGA 58.885 55.000 0.00 0.00 0.00 3.36
4 5 0.105778 GGAAGAGGATGCGAGGAAGG 59.894 60.000 0.00 0.00 0.00 3.46
5 6 1.118838 AGGAAGAGGATGCGAGGAAG 58.881 55.000 0.00 0.00 0.00 3.46
6 7 0.826715 CAGGAAGAGGATGCGAGGAA 59.173 55.000 0.00 0.00 0.00 3.36
7 8 0.033109 TCAGGAAGAGGATGCGAGGA 60.033 55.000 0.00 0.00 0.00 3.71
8 9 1.047002 ATCAGGAAGAGGATGCGAGG 58.953 55.000 0.00 0.00 0.00 4.63
9 10 2.102084 TGAATCAGGAAGAGGATGCGAG 59.898 50.000 0.00 0.00 0.00 5.03
10 11 2.110578 TGAATCAGGAAGAGGATGCGA 58.889 47.619 0.00 0.00 0.00 5.10
11 12 2.609427 TGAATCAGGAAGAGGATGCG 57.391 50.000 0.00 0.00 0.00 4.73
12 13 3.614092 TGTTGAATCAGGAAGAGGATGC 58.386 45.455 0.00 0.00 0.00 3.91
13 14 4.820716 GGATGTTGAATCAGGAAGAGGATG 59.179 45.833 0.00 0.00 0.00 3.51
14 15 4.444022 CGGATGTTGAATCAGGAAGAGGAT 60.444 45.833 0.00 0.00 0.00 3.24
15 16 3.118629 CGGATGTTGAATCAGGAAGAGGA 60.119 47.826 0.00 0.00 0.00 3.71
16 17 3.201290 CGGATGTTGAATCAGGAAGAGG 58.799 50.000 0.00 0.00 0.00 3.69
17 18 2.611292 GCGGATGTTGAATCAGGAAGAG 59.389 50.000 0.00 0.00 0.00 2.85
18 19 2.632377 GCGGATGTTGAATCAGGAAGA 58.368 47.619 0.00 0.00 0.00 2.87
19 20 1.672881 GGCGGATGTTGAATCAGGAAG 59.327 52.381 0.00 0.00 0.00 3.46
20 21 1.681780 GGGCGGATGTTGAATCAGGAA 60.682 52.381 0.00 0.00 0.00 3.36
21 22 0.107214 GGGCGGATGTTGAATCAGGA 60.107 55.000 0.00 0.00 0.00 3.86
22 23 0.394216 TGGGCGGATGTTGAATCAGG 60.394 55.000 0.00 0.00 0.00 3.86
23 24 1.605710 GATGGGCGGATGTTGAATCAG 59.394 52.381 0.00 0.00 0.00 2.90
24 25 1.064832 TGATGGGCGGATGTTGAATCA 60.065 47.619 0.00 0.00 0.00 2.57
25 26 1.679139 TGATGGGCGGATGTTGAATC 58.321 50.000 0.00 0.00 0.00 2.52
26 27 2.142356 TTGATGGGCGGATGTTGAAT 57.858 45.000 0.00 0.00 0.00 2.57
27 28 1.916506 TTTGATGGGCGGATGTTGAA 58.083 45.000 0.00 0.00 0.00 2.69
28 29 2.023673 GATTTGATGGGCGGATGTTGA 58.976 47.619 0.00 0.00 0.00 3.18
29 30 1.067516 GGATTTGATGGGCGGATGTTG 59.932 52.381 0.00 0.00 0.00 3.33
30 31 1.341877 TGGATTTGATGGGCGGATGTT 60.342 47.619 0.00 0.00 0.00 2.71
31 32 0.258484 TGGATTTGATGGGCGGATGT 59.742 50.000 0.00 0.00 0.00 3.06
32 33 1.271379 CATGGATTTGATGGGCGGATG 59.729 52.381 0.00 0.00 0.00 3.51
33 34 1.133388 ACATGGATTTGATGGGCGGAT 60.133 47.619 0.00 0.00 0.00 4.18
34 35 0.258484 ACATGGATTTGATGGGCGGA 59.742 50.000 0.00 0.00 0.00 5.54
35 36 0.670162 GACATGGATTTGATGGGCGG 59.330 55.000 0.00 0.00 0.00 6.13
36 37 1.335810 CTGACATGGATTTGATGGGCG 59.664 52.381 0.00 0.00 0.00 6.13
37 38 2.658285 TCTGACATGGATTTGATGGGC 58.342 47.619 0.00 0.00 0.00 5.36
38 39 3.572682 CCATCTGACATGGATTTGATGGG 59.427 47.826 18.97 8.04 44.08 4.00
39 40 4.519350 CTCCATCTGACATGGATTTGATGG 59.481 45.833 19.91 19.91 46.12 3.51
40 41 4.519350 CCTCCATCTGACATGGATTTGATG 59.481 45.833 3.77 3.89 46.12 3.07
41 42 4.167502 ACCTCCATCTGACATGGATTTGAT 59.832 41.667 3.77 0.00 46.12 2.57
42 43 3.524789 ACCTCCATCTGACATGGATTTGA 59.475 43.478 3.77 0.00 46.12 2.69
43 44 3.894759 ACCTCCATCTGACATGGATTTG 58.105 45.455 3.77 0.00 46.12 2.32
44 45 4.229123 AGAACCTCCATCTGACATGGATTT 59.771 41.667 3.77 1.39 46.12 2.17
45 46 3.784763 AGAACCTCCATCTGACATGGATT 59.215 43.478 3.77 0.00 46.12 3.01
46 47 3.136077 CAGAACCTCCATCTGACATGGAT 59.864 47.826 3.77 0.00 46.12 3.41
47 48 2.502947 CAGAACCTCCATCTGACATGGA 59.497 50.000 3.33 3.33 45.74 3.41
48 49 2.421107 CCAGAACCTCCATCTGACATGG 60.421 54.545 5.16 0.00 45.74 3.66
49 50 2.421107 CCCAGAACCTCCATCTGACATG 60.421 54.545 5.16 0.00 45.74 3.21
50 51 1.842562 CCCAGAACCTCCATCTGACAT 59.157 52.381 5.16 0.00 45.74 3.06
51 52 1.279496 CCCAGAACCTCCATCTGACA 58.721 55.000 5.16 0.00 45.74 3.58
52 53 0.543749 CCCCAGAACCTCCATCTGAC 59.456 60.000 5.16 0.00 45.74 3.51
53 54 1.274703 GCCCCAGAACCTCCATCTGA 61.275 60.000 5.16 0.00 45.74 3.27
54 55 1.225704 GCCCCAGAACCTCCATCTG 59.774 63.158 0.00 0.00 43.15 2.90
69 70 4.918201 CGCCTGATTCCTCCGCCC 62.918 72.222 0.00 0.00 0.00 6.13
145 146 3.680620 TATGCCCACGTCTGCAGCC 62.681 63.158 9.47 0.00 41.46 4.85
147 148 1.522355 CCTATGCCCACGTCTGCAG 60.522 63.158 7.63 7.63 41.46 4.41
148 149 2.584064 CCTATGCCCACGTCTGCA 59.416 61.111 10.62 10.62 42.52 4.41
149 150 2.897350 GCCTATGCCCACGTCTGC 60.897 66.667 0.00 0.00 0.00 4.26
151 152 3.849951 CCGCCTATGCCCACGTCT 61.850 66.667 0.00 0.00 0.00 4.18
152 153 4.910585 CCCGCCTATGCCCACGTC 62.911 72.222 0.00 0.00 0.00 4.34
154 155 4.910585 GACCCGCCTATGCCCACG 62.911 72.222 0.00 0.00 0.00 4.94
156 157 1.837051 CTAGACCCGCCTATGCCCA 60.837 63.158 0.00 0.00 0.00 5.36
159 160 1.290639 GAGCTAGACCCGCCTATGC 59.709 63.158 0.00 0.00 0.00 3.14
160 161 0.315568 GTGAGCTAGACCCGCCTATG 59.684 60.000 0.00 0.00 0.00 2.23
161 162 0.828343 GGTGAGCTAGACCCGCCTAT 60.828 60.000 3.34 0.00 0.00 2.57
162 163 1.455217 GGTGAGCTAGACCCGCCTA 60.455 63.158 3.34 0.00 0.00 3.93
180 186 2.766400 GCGACCTCCGTCCTCAGAG 61.766 68.421 0.00 0.00 41.15 3.35
209 215 1.513158 CTGCCTTCGGTCGTGAGAT 59.487 57.895 0.00 0.00 45.19 2.75
210 216 2.636412 CCTGCCTTCGGTCGTGAGA 61.636 63.158 0.00 0.00 38.16 3.27
211 217 2.125912 CCTGCCTTCGGTCGTGAG 60.126 66.667 0.00 0.00 0.00 3.51
243 269 1.133450 TCTCCTATGCTCTACCGCCTT 60.133 52.381 0.00 0.00 0.00 4.35
279 305 2.604174 GGACTTTGCACGACACCGG 61.604 63.158 0.00 0.00 40.78 5.28
280 306 1.831389 CTGGACTTTGCACGACACCG 61.831 60.000 0.00 0.00 42.50 4.94
304 1115 1.961277 CTCTTTGCCGCCTGTCGTT 60.961 57.895 0.00 0.00 36.19 3.85
305 1116 2.357517 CTCTTTGCCGCCTGTCGT 60.358 61.111 0.00 0.00 36.19 4.34
340 1151 1.666189 GAATTGTACCTCCGCTTCAGC 59.334 52.381 0.00 0.00 37.78 4.26
347 1158 2.332063 AGCCATGAATTGTACCTCCG 57.668 50.000 0.00 0.00 0.00 4.63
349 1160 4.823989 AGCAATAGCCATGAATTGTACCTC 59.176 41.667 13.46 0.00 43.56 3.85
375 1186 3.182967 CCATCTCTCTTAGTTGTCACGC 58.817 50.000 0.00 0.00 0.00 5.34
380 1191 3.193691 CACGACCCATCTCTCTTAGTTGT 59.806 47.826 0.00 0.00 0.00 3.32
381 1192 3.444034 TCACGACCCATCTCTCTTAGTTG 59.556 47.826 0.00 0.00 0.00 3.16
384 1196 4.720649 TTTCACGACCCATCTCTCTTAG 57.279 45.455 0.00 0.00 0.00 2.18
386 1198 3.369892 CCATTTCACGACCCATCTCTCTT 60.370 47.826 0.00 0.00 0.00 2.85
390 1202 2.691409 TCCATTTCACGACCCATCTC 57.309 50.000 0.00 0.00 0.00 2.75
393 1205 3.968265 AGAAATCCATTTCACGACCCAT 58.032 40.909 13.30 0.00 46.50 4.00
395 1207 3.506067 ACAAGAAATCCATTTCACGACCC 59.494 43.478 13.30 0.00 46.50 4.46
397 1209 8.638565 CAATAAACAAGAAATCCATTTCACGAC 58.361 33.333 13.30 0.00 46.50 4.34
398 1210 7.328249 GCAATAAACAAGAAATCCATTTCACGA 59.672 33.333 13.30 0.00 46.50 4.35
399 1211 7.329226 AGCAATAAACAAGAAATCCATTTCACG 59.671 33.333 13.30 6.90 46.50 4.35
428 1240 9.173021 CCGATGCCAAATTCACCTATAATATAA 57.827 33.333 0.00 0.00 0.00 0.98
430 1242 7.402054 TCCGATGCCAAATTCACCTATAATAT 58.598 34.615 0.00 0.00 0.00 1.28
431 1243 6.774673 TCCGATGCCAAATTCACCTATAATA 58.225 36.000 0.00 0.00 0.00 0.98
433 1245 5.042463 TCCGATGCCAAATTCACCTATAA 57.958 39.130 0.00 0.00 0.00 0.98
435 1247 3.480470 CTCCGATGCCAAATTCACCTAT 58.520 45.455 0.00 0.00 0.00 2.57
436 1248 2.917933 CTCCGATGCCAAATTCACCTA 58.082 47.619 0.00 0.00 0.00 3.08
438 1250 0.101219 GCTCCGATGCCAAATTCACC 59.899 55.000 0.00 0.00 0.00 4.02
439 1251 0.810648 TGCTCCGATGCCAAATTCAC 59.189 50.000 0.00 0.00 0.00 3.18
441 1253 1.474077 ACTTGCTCCGATGCCAAATTC 59.526 47.619 0.00 0.00 0.00 2.17
442 1254 1.549203 ACTTGCTCCGATGCCAAATT 58.451 45.000 0.00 0.00 0.00 1.82
443 1255 2.292267 CTACTTGCTCCGATGCCAAAT 58.708 47.619 0.00 0.00 0.00 2.32
445 1257 0.107703 CCTACTTGCTCCGATGCCAA 60.108 55.000 0.00 0.00 0.00 4.52
447 1259 0.811616 CACCTACTTGCTCCGATGCC 60.812 60.000 0.00 0.00 0.00 4.40
464 1291 6.774084 ACAAAATTTCAGTGCATCAAAACAC 58.226 32.000 0.00 0.00 37.05 3.32
470 1297 4.809958 CCACAACAAAATTTCAGTGCATCA 59.190 37.500 0.00 0.00 0.00 3.07
472 1299 3.560896 GCCACAACAAAATTTCAGTGCAT 59.439 39.130 0.00 0.00 0.00 3.96
476 1303 3.530535 GGTGCCACAACAAAATTTCAGT 58.469 40.909 0.00 0.00 0.00 3.41
500 1327 2.383245 ATAGATGCCCCGTTGCCGAG 62.383 60.000 0.00 0.00 35.63 4.63
501 1328 2.439960 ATAGATGCCCCGTTGCCGA 61.440 57.895 0.00 0.00 35.63 5.54
502 1329 2.111043 ATAGATGCCCCGTTGCCG 59.889 61.111 0.00 0.00 0.00 5.69
503 1330 3.749981 CATAGATGCCCCGTTGCC 58.250 61.111 0.00 0.00 0.00 4.52
514 1341 5.716228 TGACAAATCCACTTTTGGCATAGAT 59.284 36.000 1.46 0.00 46.91 1.98
521 1348 2.288152 CCGGTGACAAATCCACTTTTGG 60.288 50.000 0.00 0.00 45.56 3.28
536 1363 1.377229 CCTAGCCCAAAACCGGTGA 59.623 57.895 8.52 0.00 0.00 4.02
549 1376 1.684450 GTCAGTCTCTAAGGCCCTAGC 59.316 57.143 3.22 0.00 38.76 3.42
551 1378 2.042569 TGTGTCAGTCTCTAAGGCCCTA 59.957 50.000 0.00 0.00 0.00 3.53
554 1381 2.419297 CCATGTGTCAGTCTCTAAGGCC 60.419 54.545 0.00 0.00 0.00 5.19
595 1438 2.427232 TTTTGTACGGTCTCTGGTCG 57.573 50.000 0.00 0.00 0.00 4.79
646 1489 1.708341 TACCGGTATGGAAGCCTACC 58.292 55.000 11.16 0.00 42.00 3.18
666 1509 2.298610 CATACCTCTGCGTCTCTGGTA 58.701 52.381 0.00 0.00 37.62 3.25
752 1609 4.202010 TGAGTTACTTTTTCTTGGCACTGC 60.202 41.667 0.00 0.00 0.00 4.40
757 1614 7.412563 GGTTTGTTTGAGTTACTTTTTCTTGGC 60.413 37.037 0.00 0.00 0.00 4.52
792 1650 1.805869 CTGAGCCTCTTTGTCAGTGG 58.194 55.000 0.00 0.00 38.97 4.00
801 1659 1.373497 CGCGTGAACTGAGCCTCTT 60.373 57.895 0.00 0.00 0.00 2.85
885 1743 5.508153 CCTCTAGTCTCCGGTTGTTATGATG 60.508 48.000 0.00 0.00 0.00 3.07
886 1744 4.585162 CCTCTAGTCTCCGGTTGTTATGAT 59.415 45.833 0.00 0.00 0.00 2.45
887 1745 3.952323 CCTCTAGTCTCCGGTTGTTATGA 59.048 47.826 0.00 0.00 0.00 2.15
946 1804 0.741221 CGCTTTCCTCTTCCTTCCGG 60.741 60.000 0.00 0.00 0.00 5.14
947 1805 0.246635 TCGCTTTCCTCTTCCTTCCG 59.753 55.000 0.00 0.00 0.00 4.30
953 1811 2.017782 GGGGAATTCGCTTTCCTCTTC 58.982 52.381 20.49 0.00 42.15 2.87
954 1812 1.341089 GGGGGAATTCGCTTTCCTCTT 60.341 52.381 20.49 0.00 44.43 2.85
1071 1929 2.436173 GTGGGATTTGAGGTAGGAGGAG 59.564 54.545 0.00 0.00 0.00 3.69
1072 1930 2.478292 GTGGGATTTGAGGTAGGAGGA 58.522 52.381 0.00 0.00 0.00 3.71
1073 1931 1.490910 GGTGGGATTTGAGGTAGGAGG 59.509 57.143 0.00 0.00 0.00 4.30
1074 1932 2.092914 GTGGTGGGATTTGAGGTAGGAG 60.093 54.545 0.00 0.00 0.00 3.69
1075 1933 1.913419 GTGGTGGGATTTGAGGTAGGA 59.087 52.381 0.00 0.00 0.00 2.94
1076 1934 1.064685 GGTGGTGGGATTTGAGGTAGG 60.065 57.143 0.00 0.00 0.00 3.18
1362 2220 4.316823 ACGGAGAGGGAGGTGGCA 62.317 66.667 0.00 0.00 0.00 4.92
1373 2231 4.742649 AGGAGGCGAGCACGGAGA 62.743 66.667 5.52 0.00 40.15 3.71
1413 2271 1.445582 GTAGGCGGTGTCCTCGTTG 60.446 63.158 0.00 0.00 37.66 4.10
1734 2592 0.873312 CACGTCCTGGCGATGAGATG 60.873 60.000 15.53 1.22 35.59 2.90
2244 3102 6.505048 TCACCTTCCTCATTGACATCATAT 57.495 37.500 0.00 0.00 0.00 1.78
2278 3136 6.159575 TCAACATCTACATCCCCCTTAATCAA 59.840 38.462 0.00 0.00 0.00 2.57
2279 3137 5.669904 TCAACATCTACATCCCCCTTAATCA 59.330 40.000 0.00 0.00 0.00 2.57
2346 3204 1.217779 GACCACCTCTGCTCTGAGC 59.782 63.158 22.38 22.38 42.82 4.26
2754 3612 4.324563 CCATCTTCATCCCCACAGTTAAGT 60.325 45.833 0.00 0.00 0.00 2.24
2981 3839 6.187727 ACAGAATTTACAAGACCTTCCTGA 57.812 37.500 0.00 0.00 0.00 3.86
3105 3967 9.706691 CACTATAGACAAGTTAAGAAGGTTGAA 57.293 33.333 6.78 0.00 0.00 2.69
3155 4017 5.745294 CAGAAACAATGTTCAACTGTCTTGG 59.255 40.000 0.00 0.00 0.00 3.61
3256 4120 0.458889 AATTCCACACATGCGCATGC 60.459 50.000 42.18 7.91 42.39 4.06
3257 4121 1.656594 CAAATTCCACACATGCGCATG 59.343 47.619 41.02 41.02 44.15 4.06
3258 4122 1.404449 CCAAATTCCACACATGCGCAT 60.404 47.619 19.28 19.28 0.00 4.73
3259 4123 0.038435 CCAAATTCCACACATGCGCA 60.038 50.000 14.96 14.96 0.00 6.09
3260 4124 1.353609 GCCAAATTCCACACATGCGC 61.354 55.000 0.00 0.00 0.00 6.09
3261 4125 1.072116 CGCCAAATTCCACACATGCG 61.072 55.000 0.00 0.00 34.52 4.73
3262 4126 1.353609 GCGCCAAATTCCACACATGC 61.354 55.000 0.00 0.00 0.00 4.06
3297 4161 8.175069 ACTTGCATAGTAATAACACAATTGTCG 58.825 33.333 8.48 7.26 32.22 4.35
3338 4206 3.485394 TGGATGCAACTAAGAAGCAACA 58.515 40.909 0.00 0.00 42.15 3.33
3392 4260 7.966246 ACGACTAAGTATAGTAGGATCACTG 57.034 40.000 0.00 0.00 42.47 3.66
3448 4316 8.175069 TCAGTTTCTTTAGCTATTGCATTAACG 58.825 33.333 1.12 0.00 42.74 3.18
3481 4349 8.833493 GCATAAGCAACAGCATATCATATCATA 58.167 33.333 0.00 0.00 41.58 2.15
3482 4350 7.704271 GCATAAGCAACAGCATATCATATCAT 58.296 34.615 0.00 0.00 41.58 2.45
3566 4434 4.688879 TCACACATAAAAGCTGAGGTTACG 59.311 41.667 0.00 0.00 0.00 3.18
3582 4450 3.361281 AGCAACATCCATCTCACACAT 57.639 42.857 0.00 0.00 0.00 3.21
3606 4474 3.435327 GTCAACCATAGATCAACGCACAA 59.565 43.478 0.00 0.00 0.00 3.33
3612 4480 4.396166 CCAACCAGTCAACCATAGATCAAC 59.604 45.833 0.00 0.00 0.00 3.18
3648 4516 6.091555 ACCATAAGCTGAGGAATATCCCTTA 58.908 40.000 6.37 0.00 37.19 2.69
3688 4556 2.742774 ACCGATTTTGTTTCTGCAAGC 58.257 42.857 0.00 0.00 0.00 4.01
3771 4639 8.918202 TCCAAGAATTTTGTGAATACTGTAGT 57.082 30.769 0.00 0.00 0.00 2.73
3773 4641 9.126151 TGTTCCAAGAATTTTGTGAATACTGTA 57.874 29.630 0.00 0.00 0.00 2.74
3786 4667 6.384886 AGATGCCCATAATGTTCCAAGAATTT 59.615 34.615 0.00 0.00 0.00 1.82
3809 4690 9.685276 TTTCCTGAGCATGATAAAGATTTTAGA 57.315 29.630 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.