Multiple sequence alignment - TraesCS2B01G546700

Loading Multiple Alignment...

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 TraesCS2B01G546700 chr2B 100.000 2843 0 0 1 2843 743725671 743728513 0.000000e+00 5251.0
1 TraesCS2B01G546700 chr2D 92.648 1197 44 15 1144 2332 609431819 609432979 0.000000e+00 1683.0
2 TraesCS2B01G546700 chr2D 89.067 997 46 20 335 1297 609430952 609431919 0.000000e+00 1179.0
3 TraesCS2B01G546700 chr2D 85.938 512 42 10 2333 2842 609433166 609433649 1.170000e-143 520.0
4 TraesCS2B01G546700 chr2A 92.067 1021 48 13 1140 2156 741378833 741379824 0.000000e+00 1406.0
5 TraesCS2B01G546700 chr2A 90.333 900 41 10 1334 2230 742130631 742131487 0.000000e+00 1138.0
6 TraesCS2B01G546700 chr2A 85.011 914 58 40 437 1297 741377995 741378882 0.000000e+00 856.0
7 TraesCS2B01G546700 chr2A 83.764 542 29 26 2307 2842 742131803 742132291 2.580000e-125 459.0
8 TraesCS2B01G546700 chr2A 87.895 190 12 3 2587 2776 741416077 741416255 2.220000e-51 213.0
9 TraesCS2B01G546700 chr2A 97.087 103 3 0 2154 2256 742131695 742131797 1.050000e-39 174.0
10 TraesCS2B01G546700 chr2A 94.059 101 6 0 8 108 741377156 741377256 1.360000e-33 154.0
11 TraesCS2B01G546700 chrUn 75.141 177 28 14 1591 1756 279543423 279543594 5.080000e-08 69.4
12 TraesCS2B01G546700 chrUn 97.436 39 1 0 1591 1629 154542732 154542770 1.830000e-07 67.6
13 TraesCS2B01G546700 chrUn 100.000 36 0 0 1594 1629 189561775 189561740 1.830000e-07 67.6
14 TraesCS2B01G546700 chrUn 97.436 39 1 0 1591 1629 201369286 201369324 1.830000e-07 67.6
15 TraesCS2B01G546700 chrUn 97.436 39 1 0 1591 1629 363337004 363337042 1.830000e-07 67.6
16 TraesCS2B01G546700 chr4B 100.000 34 0 0 1596 1629 654707102 654707069 2.360000e-06 63.9


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 TraesCS2B01G546700 chr2B 743725671 743728513 2842 False 5251.000000 5251 100.000000 1 2843 1 chr2B.!!$F1 2842
1 TraesCS2B01G546700 chr2D 609430952 609433649 2697 False 1127.333333 1683 89.217667 335 2842 3 chr2D.!!$F1 2507
2 TraesCS2B01G546700 chr2A 741377156 741379824 2668 False 805.333333 1406 90.379000 8 2156 3 chr2A.!!$F2 2148
3 TraesCS2B01G546700 chr2A 742130631 742132291 1660 False 590.333333 1138 90.394667 1334 2842 3 chr2A.!!$F3 1508

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
494 951 0.249868 CGAGGAAGACCAACACAGCA 60.25 55.0 0.0 0.0 38.94 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2380 3493 1.621107 CGCATGTGCTGAAAATCCAC 58.379 50.0 3.25 0.0 39.32 4.02 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
22 23 4.393834 TCTCTACTGTATCAGCTGGCTAG 58.606 47.826 15.13 9.91 34.37 3.42
27 28 2.034878 TGTATCAGCTGGCTAGAGGTG 58.965 52.381 15.13 2.50 41.86 4.00
74 75 2.051345 CCAAACGCAACGCTGGAC 60.051 61.111 3.32 0.00 35.88 4.02
91 92 4.003648 CTGGACGGAAGCAGTTTTCTTAT 58.996 43.478 0.00 0.00 0.00 1.73
108 109 5.164620 TCTTATTGTGAAGCAGACATGGA 57.835 39.130 0.00 0.00 0.00 3.41
110 111 1.511850 TTGTGAAGCAGACATGGACG 58.488 50.000 0.00 0.00 0.00 4.79
141 348 1.231641 GCCCAGCTCTCCCTCTCTA 59.768 63.158 0.00 0.00 0.00 2.43
163 374 8.023021 TCTACATGTAAGCAAGGTATCTCAAT 57.977 34.615 7.06 0.00 0.00 2.57
172 383 4.041444 GCAAGGTATCTCAATGGAGGATCT 59.959 45.833 0.00 0.00 41.69 2.75
181 392 8.857374 ATCTCAATGGAGGATCTGATATGTAT 57.143 34.615 0.00 0.00 41.69 2.29
182 393 8.075761 TCTCAATGGAGGATCTGATATGTATG 57.924 38.462 0.00 0.00 41.69 2.39
184 395 8.899887 TCAATGGAGGATCTGATATGTATGTA 57.100 34.615 0.00 0.00 33.73 2.29
185 396 8.753133 TCAATGGAGGATCTGATATGTATGTAC 58.247 37.037 0.00 0.00 33.73 2.90
186 397 7.667575 ATGGAGGATCTGATATGTATGTACC 57.332 40.000 0.00 0.00 33.73 3.34
187 398 6.805150 TGGAGGATCTGATATGTATGTACCT 58.195 40.000 0.00 0.00 33.73 3.08
188 399 6.665248 TGGAGGATCTGATATGTATGTACCTG 59.335 42.308 0.00 0.00 33.73 4.00
189 400 6.892456 GGAGGATCTGATATGTATGTACCTGA 59.108 42.308 0.00 0.00 33.73 3.86
191 402 8.128322 AGGATCTGATATGTATGTACCTGAAC 57.872 38.462 0.00 0.00 0.00 3.18
216 427 3.827505 GCCCATGGCTCCTCAATTA 57.172 52.632 6.09 0.00 46.69 1.40
245 456 7.665690 TGCAATTAATAAAGCCAGAAACTTCA 58.334 30.769 0.00 0.00 0.00 3.02
246 457 7.814107 TGCAATTAATAAAGCCAGAAACTTCAG 59.186 33.333 0.00 0.00 0.00 3.02
247 458 7.201470 GCAATTAATAAAGCCAGAAACTTCAGC 60.201 37.037 0.00 0.00 0.00 4.26
248 459 7.709149 ATTAATAAAGCCAGAAACTTCAGCT 57.291 32.000 2.20 2.20 39.70 4.24
256 471 3.152341 CAGAAACTTCAGCTTCACCCAT 58.848 45.455 0.00 0.00 0.00 4.00
279 494 0.473694 TTCCTCTCCTGCACCCTTCA 60.474 55.000 0.00 0.00 0.00 3.02
288 503 1.614903 CTGCACCCTTCATGCTGAAAA 59.385 47.619 0.00 0.00 42.73 2.29
292 746 2.028839 CACCCTTCATGCTGAAAATGCA 60.029 45.455 0.00 0.00 44.95 3.96
299 753 3.321396 TCATGCTGAAAATGCAGGTTGAA 59.679 39.130 0.00 0.00 44.04 2.69
310 764 9.585099 GAAAATGCAGGTTGAAATGAACATATA 57.415 29.630 0.00 0.00 0.00 0.86
312 766 7.886629 ATGCAGGTTGAAATGAACATATACT 57.113 32.000 0.00 0.00 0.00 2.12
324 778 9.618890 AAATGAACATATACTACATGAACTGCT 57.381 29.630 0.00 0.00 0.00 4.24
326 780 7.781056 TGAACATATACTACATGAACTGCTCA 58.219 34.615 0.00 0.00 38.81 4.26
327 781 8.424133 TGAACATATACTACATGAACTGCTCAT 58.576 33.333 0.00 0.00 46.25 2.90
343 797 5.273674 TGCTCATGCATATATAGCTCCTC 57.726 43.478 17.92 0.00 45.31 3.71
348 802 7.930325 GCTCATGCATATATAGCTCCTCAATTA 59.070 37.037 0.00 0.00 39.41 1.40
362 816 4.646945 TCCTCAATTACACTGCCACAAAAA 59.353 37.500 0.00 0.00 0.00 1.94
363 817 5.304101 TCCTCAATTACACTGCCACAAAAAT 59.696 36.000 0.00 0.00 0.00 1.82
364 818 5.634859 CCTCAATTACACTGCCACAAAAATC 59.365 40.000 0.00 0.00 0.00 2.17
365 819 6.154203 TCAATTACACTGCCACAAAAATCA 57.846 33.333 0.00 0.00 0.00 2.57
366 820 6.215121 TCAATTACACTGCCACAAAAATCAG 58.785 36.000 0.00 0.00 0.00 2.90
367 821 4.582701 TTACACTGCCACAAAAATCAGG 57.417 40.909 0.00 0.00 0.00 3.86
369 823 2.624838 ACACTGCCACAAAAATCAGGAG 59.375 45.455 0.00 0.00 0.00 3.69
375 829 3.613432 GCCACAAAAATCAGGAGCTTCAG 60.613 47.826 0.00 0.00 0.00 3.02
378 832 5.452356 CCACAAAAATCAGGAGCTTCAGTTT 60.452 40.000 0.00 0.00 0.00 2.66
493 950 1.569479 GCGAGGAAGACCAACACAGC 61.569 60.000 0.00 0.00 38.94 4.40
494 951 0.249868 CGAGGAAGACCAACACAGCA 60.250 55.000 0.00 0.00 38.94 4.41
497 954 0.947244 GGAAGACCAACACAGCACAG 59.053 55.000 0.00 0.00 35.97 3.66
514 971 1.476891 ACAGACAGAACACACGACACT 59.523 47.619 0.00 0.00 0.00 3.55
531 988 4.514441 CGACACTGGTACCTATCGATTACT 59.486 45.833 14.36 0.00 0.00 2.24
561 1018 3.511934 CACACATATCTAGCCCTAGTCCC 59.488 52.174 2.53 0.00 34.84 4.46
751 1208 3.561213 CAGCTGCACTGGCGATCG 61.561 66.667 11.69 11.69 45.35 3.69
840 1349 2.342650 ACCGCACACCAATGGCATC 61.343 57.895 0.00 0.00 0.00 3.91
841 1350 2.100797 CGCACACCAATGGCATCG 59.899 61.111 0.00 0.00 0.00 3.84
940 1449 2.377628 GACCGGAGACACAGGCACAA 62.378 60.000 9.46 0.00 37.36 3.33
941 1450 1.227823 CCGGAGACACAGGCACAAA 60.228 57.895 0.00 0.00 0.00 2.83
942 1451 1.507141 CCGGAGACACAGGCACAAAC 61.507 60.000 0.00 0.00 0.00 2.93
943 1452 0.813610 CGGAGACACAGGCACAAACA 60.814 55.000 0.00 0.00 0.00 2.83
944 1453 0.663153 GGAGACACAGGCACAAACAC 59.337 55.000 0.00 0.00 0.00 3.32
945 1454 1.378531 GAGACACAGGCACAAACACA 58.621 50.000 0.00 0.00 0.00 3.72
962 1471 1.599518 CAGCAGCACCCCACGTAAA 60.600 57.895 0.00 0.00 0.00 2.01
963 1472 1.302511 AGCAGCACCCCACGTAAAG 60.303 57.895 0.00 0.00 0.00 1.85
984 1493 1.818785 GACTCGGTCGATCGGAGGT 60.819 63.158 19.53 14.41 44.40 3.85
985 1494 0.531532 GACTCGGTCGATCGGAGGTA 60.532 60.000 19.53 0.00 44.40 3.08
986 1495 0.813210 ACTCGGTCGATCGGAGGTAC 60.813 60.000 19.53 5.24 44.40 3.34
987 1496 1.829349 CTCGGTCGATCGGAGGTACG 61.829 65.000 19.53 10.82 39.04 3.67
1015 1531 0.955428 TGCAATGGAGTCCACGAAGC 60.955 55.000 15.86 15.98 35.80 3.86
1112 1631 3.349006 CAGCAGCACACCGTCCAC 61.349 66.667 0.00 0.00 0.00 4.02
1148 1667 3.860605 CGGCATCACCATCCCCGA 61.861 66.667 0.00 0.00 41.34 5.14
1149 1668 2.203209 GGCATCACCATCCCCGAC 60.203 66.667 0.00 0.00 38.86 4.79
1180 1702 1.961277 GTTGGCACTGTCACTCCGG 60.961 63.158 0.00 0.00 0.00 5.14
1422 2052 1.997669 GAGTTGTCACTCCCGTCATC 58.002 55.000 0.00 0.00 43.50 2.92
1423 2053 1.272490 GAGTTGTCACTCCCGTCATCA 59.728 52.381 0.00 0.00 43.50 3.07
1424 2054 1.273606 AGTTGTCACTCCCGTCATCAG 59.726 52.381 0.00 0.00 0.00 2.90
1425 2055 1.000955 GTTGTCACTCCCGTCATCAGT 59.999 52.381 0.00 0.00 0.00 3.41
1426 2056 0.888619 TGTCACTCCCGTCATCAGTC 59.111 55.000 0.00 0.00 0.00 3.51
1427 2057 0.173708 GTCACTCCCGTCATCAGTCC 59.826 60.000 0.00 0.00 0.00 3.85
1428 2058 0.970937 TCACTCCCGTCATCAGTCCC 60.971 60.000 0.00 0.00 0.00 4.46
1429 2059 2.052690 ACTCCCGTCATCAGTCCCG 61.053 63.158 0.00 0.00 0.00 5.14
1430 2060 2.036731 TCCCGTCATCAGTCCCGT 59.963 61.111 0.00 0.00 0.00 5.28
1431 2061 2.005960 CTCCCGTCATCAGTCCCGTC 62.006 65.000 0.00 0.00 0.00 4.79
1856 2489 2.408022 CTGATCCGTCCGTCCGTC 59.592 66.667 0.00 0.00 0.00 4.79
1910 2543 6.966435 AGTTTGAAATCAAGGTTGTTGTTG 57.034 33.333 0.00 0.00 37.15 3.33
1913 2546 2.908688 AATCAAGGTTGTTGTTGGGC 57.091 45.000 0.00 0.00 0.00 5.36
2061 2697 6.567687 TGGAAGGTGTAATTGTATTGTGTG 57.432 37.500 0.00 0.00 0.00 3.82
2070 2706 2.647683 TGTATTGTGTGCCAACCTCA 57.352 45.000 0.00 0.00 35.44 3.86
2109 2745 5.817816 GGTGATGTAATTCCATTCTCGTCTT 59.182 40.000 0.00 0.00 0.00 3.01
2263 3188 2.122768 CTCTAGCCTCCAACCTCCATT 58.877 52.381 0.00 0.00 0.00 3.16
2421 3534 5.389516 GCGCTCTTTGGTATTAATATCCACG 60.390 44.000 0.00 13.38 0.00 4.94
2422 3535 5.120208 CGCTCTTTGGTATTAATATCCACGG 59.880 44.000 13.23 10.27 0.00 4.94
2423 3536 6.228258 GCTCTTTGGTATTAATATCCACGGA 58.772 40.000 13.23 12.65 0.00 4.69
2424 3537 6.879458 GCTCTTTGGTATTAATATCCACGGAT 59.121 38.462 13.23 3.62 38.54 4.18
2425 3538 7.390718 GCTCTTTGGTATTAATATCCACGGATT 59.609 37.037 3.41 0.00 36.17 3.01
2426 3539 9.284968 CTCTTTGGTATTAATATCCACGGATTT 57.715 33.333 3.41 1.96 36.17 2.17
2427 3540 9.062524 TCTTTGGTATTAATATCCACGGATTTG 57.937 33.333 3.41 3.92 36.17 2.32
2428 3541 6.811253 TGGTATTAATATCCACGGATTTGC 57.189 37.500 3.41 0.00 36.17 3.68
2429 3542 6.539173 TGGTATTAATATCCACGGATTTGCT 58.461 36.000 3.41 0.00 36.17 3.91
2430 3543 7.681679 TGGTATTAATATCCACGGATTTGCTA 58.318 34.615 3.41 0.00 36.17 3.49
2431 3544 8.325787 TGGTATTAATATCCACGGATTTGCTAT 58.674 33.333 3.41 0.00 36.17 2.97
2432 3545 9.826574 GGTATTAATATCCACGGATTTGCTATA 57.173 33.333 3.41 0.00 36.17 1.31
2473 3586 6.260936 CCACGGATTTGCTATTAACAGAAGAT 59.739 38.462 0.00 0.00 0.00 2.40
2477 3590 7.420800 GGATTTGCTATTAACAGAAGATGTGG 58.579 38.462 0.00 0.00 43.00 4.17
2580 3707 9.984190 CCCTATAAAACCATCTACTAAGACTTC 57.016 37.037 0.00 0.00 33.57 3.01
2622 3749 7.975750 AGATATACAAAAGAAAAGGAACTCGC 58.024 34.615 0.00 0.00 38.49 5.03
2654 3781 7.285401 AGTGAGATGCGGTCCATAAATTAATTT 59.715 33.333 17.18 17.18 33.29 1.82
2682 3809 2.220133 CACGACGGTAACAGGTTTTCAG 59.780 50.000 0.00 0.00 0.00 3.02
2691 3818 1.065709 ACAGGTTTTCAGGTGTCACGT 60.066 47.619 0.00 0.00 0.00 4.49
2692 3819 2.168936 ACAGGTTTTCAGGTGTCACGTA 59.831 45.455 0.00 0.00 0.00 3.57
2693 3820 2.542595 CAGGTTTTCAGGTGTCACGTAC 59.457 50.000 0.00 0.00 0.00 3.67
2728 3855 8.798859 AAAGGTAGCACCATATTCATATCATC 57.201 34.615 7.86 0.00 41.95 2.92
2729 3856 7.500629 AGGTAGCACCATATTCATATCATCA 57.499 36.000 7.86 0.00 41.95 3.07
2730 3857 8.098963 AGGTAGCACCATATTCATATCATCAT 57.901 34.615 7.86 0.00 41.95 2.45
2750 3877 7.615757 TCATCATATGTACAGATCGAACCCTAT 59.384 37.037 0.00 0.00 0.00 2.57
2755 3882 3.460857 ACAGATCGAACCCTATCAAGC 57.539 47.619 0.00 0.00 0.00 4.01
2757 3884 3.126831 CAGATCGAACCCTATCAAGCAC 58.873 50.000 0.00 0.00 0.00 4.40
2842 3971 1.297664 CACATCAAGAGCTAGCAGCC 58.702 55.000 18.83 5.57 43.77 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.304911 AGCCAGCTGATACAGTAGAGA 57.695 47.619 17.39 0.00 33.43 3.10
1 2 4.393834 TCTAGCCAGCTGATACAGTAGAG 58.606 47.826 17.39 0.00 33.43 2.43
3 4 3.505680 CCTCTAGCCAGCTGATACAGTAG 59.494 52.174 17.39 6.47 33.43 2.57
4 5 3.117474 ACCTCTAGCCAGCTGATACAGTA 60.117 47.826 17.39 0.00 33.43 2.74
5 6 2.315176 CCTCTAGCCAGCTGATACAGT 58.685 52.381 17.39 0.00 33.43 3.55
6 7 2.035704 CACCTCTAGCCAGCTGATACAG 59.964 54.545 17.39 6.76 34.12 2.74
22 23 3.964031 AGTACTCCAATCATCTCCACCTC 59.036 47.826 0.00 0.00 0.00 3.85
27 28 2.224402 GGCCAGTACTCCAATCATCTCC 60.224 54.545 0.00 0.00 0.00 3.71
74 75 5.356882 TCACAATAAGAAAACTGCTTCCG 57.643 39.130 0.00 0.00 0.00 4.30
79 80 5.626955 GTCTGCTTCACAATAAGAAAACTGC 59.373 40.000 0.00 0.00 0.00 4.40
83 84 6.489700 TCCATGTCTGCTTCACAATAAGAAAA 59.510 34.615 0.00 0.00 0.00 2.29
91 92 1.511850 CGTCCATGTCTGCTTCACAA 58.488 50.000 0.00 0.00 0.00 3.33
124 331 0.260230 TGTAGAGAGGGAGAGCTGGG 59.740 60.000 0.00 0.00 0.00 4.45
130 337 4.251103 TGCTTACATGTAGAGAGGGAGA 57.749 45.455 5.56 0.00 0.00 3.71
133 340 3.452627 ACCTTGCTTACATGTAGAGAGGG 59.547 47.826 20.97 16.71 0.00 4.30
134 341 4.744795 ACCTTGCTTACATGTAGAGAGG 57.255 45.455 17.85 17.85 0.00 3.69
141 348 5.824624 CCATTGAGATACCTTGCTTACATGT 59.175 40.000 2.69 2.69 0.00 3.21
163 374 6.665248 CAGGTACATACATATCAGATCCTCCA 59.335 42.308 0.00 0.00 0.00 3.86
172 383 8.197439 CAGTTCAGTTCAGGTACATACATATCA 58.803 37.037 0.00 0.00 0.00 2.15
181 392 1.071699 GGGCAGTTCAGTTCAGGTACA 59.928 52.381 0.00 0.00 0.00 2.90
182 393 1.071699 TGGGCAGTTCAGTTCAGGTAC 59.928 52.381 0.00 0.00 0.00 3.34
184 395 0.773644 ATGGGCAGTTCAGTTCAGGT 59.226 50.000 0.00 0.00 0.00 4.00
185 396 1.171308 CATGGGCAGTTCAGTTCAGG 58.829 55.000 0.00 0.00 0.00 3.86
186 397 1.171308 CCATGGGCAGTTCAGTTCAG 58.829 55.000 2.85 0.00 0.00 3.02
187 398 3.344703 CCATGGGCAGTTCAGTTCA 57.655 52.632 2.85 0.00 0.00 3.18
216 427 6.588719 TTCTGGCTTTATTAATTGCAGTGT 57.411 33.333 0.00 0.00 0.00 3.55
232 443 2.225467 GTGAAGCTGAAGTTTCTGGCT 58.775 47.619 8.16 6.95 38.09 4.75
245 456 0.779997 AGGAAACCATGGGTGAAGCT 59.220 50.000 18.09 0.00 35.34 3.74
246 457 1.177401 GAGGAAACCATGGGTGAAGC 58.823 55.000 18.09 0.00 35.34 3.86
247 458 2.619074 GGAGAGGAAACCATGGGTGAAG 60.619 54.545 18.09 0.00 35.34 3.02
248 459 1.354368 GGAGAGGAAACCATGGGTGAA 59.646 52.381 18.09 0.00 35.34 3.18
256 471 1.761174 GGTGCAGGAGAGGAAACCA 59.239 57.895 0.00 0.00 0.00 3.67
279 494 4.339872 TTTCAACCTGCATTTTCAGCAT 57.660 36.364 0.00 0.00 41.82 3.79
288 503 7.886629 AGTATATGTTCATTTCAACCTGCAT 57.113 32.000 0.00 0.00 0.00 3.96
299 753 9.265901 GAGCAGTTCATGTAGTATATGTTCATT 57.734 33.333 6.76 0.00 0.00 2.57
324 778 8.761689 TGTAATTGAGGAGCTATATATGCATGA 58.238 33.333 10.16 0.00 0.00 3.07
326 780 8.766476 AGTGTAATTGAGGAGCTATATATGCAT 58.234 33.333 3.79 3.79 0.00 3.96
327 781 8.037166 CAGTGTAATTGAGGAGCTATATATGCA 58.963 37.037 0.00 0.00 0.00 3.96
328 782 7.010923 GCAGTGTAATTGAGGAGCTATATATGC 59.989 40.741 0.00 0.00 0.00 3.14
329 783 7.493971 GGCAGTGTAATTGAGGAGCTATATATG 59.506 40.741 0.00 0.00 0.00 1.78
330 784 7.180946 TGGCAGTGTAATTGAGGAGCTATATAT 59.819 37.037 0.00 0.00 0.00 0.86
331 785 6.496911 TGGCAGTGTAATTGAGGAGCTATATA 59.503 38.462 0.00 0.00 0.00 0.86
332 786 5.307976 TGGCAGTGTAATTGAGGAGCTATAT 59.692 40.000 0.00 0.00 0.00 0.86
333 787 4.653801 TGGCAGTGTAATTGAGGAGCTATA 59.346 41.667 0.00 0.00 0.00 1.31
343 797 5.406175 CCTGATTTTTGTGGCAGTGTAATTG 59.594 40.000 0.00 0.00 0.00 2.32
348 802 2.624838 CTCCTGATTTTTGTGGCAGTGT 59.375 45.455 0.00 0.00 0.00 3.55
362 816 2.290577 GGGTGAAACTGAAGCTCCTGAT 60.291 50.000 0.00 0.00 36.74 2.90
363 817 1.072331 GGGTGAAACTGAAGCTCCTGA 59.928 52.381 0.00 0.00 36.74 3.86
364 818 1.202806 TGGGTGAAACTGAAGCTCCTG 60.203 52.381 0.00 0.00 36.74 3.86
365 819 1.140312 TGGGTGAAACTGAAGCTCCT 58.860 50.000 0.00 0.00 36.74 3.69
366 820 2.087646 GATGGGTGAAACTGAAGCTCC 58.912 52.381 0.00 0.00 36.74 4.70
367 821 1.734465 CGATGGGTGAAACTGAAGCTC 59.266 52.381 0.00 0.00 36.74 4.09
369 823 1.523758 ACGATGGGTGAAACTGAAGC 58.476 50.000 0.00 0.00 36.74 3.86
375 829 1.399727 CGCAGAAACGATGGGTGAAAC 60.400 52.381 0.00 0.00 34.06 2.78
378 832 2.032634 GCGCAGAAACGATGGGTGA 61.033 57.895 0.30 0.00 34.06 4.02
445 902 5.066593 GGGTTCAGTTTCAGAATTCAGACT 58.933 41.667 8.44 3.02 0.00 3.24
447 904 5.047566 TGGGTTCAGTTTCAGAATTCAGA 57.952 39.130 8.44 1.71 0.00 3.27
448 905 4.320788 GCTGGGTTCAGTTTCAGAATTCAG 60.321 45.833 8.44 0.00 42.78 3.02
449 906 3.569701 GCTGGGTTCAGTTTCAGAATTCA 59.430 43.478 8.44 0.00 42.78 2.57
450 907 3.365364 CGCTGGGTTCAGTTTCAGAATTC 60.365 47.826 0.00 0.00 42.78 2.17
451 908 2.554032 CGCTGGGTTCAGTTTCAGAATT 59.446 45.455 0.00 0.00 42.78 2.17
452 909 2.154462 CGCTGGGTTCAGTTTCAGAAT 58.846 47.619 0.00 0.00 42.78 2.40
453 910 1.593196 CGCTGGGTTCAGTTTCAGAA 58.407 50.000 0.00 0.00 42.78 3.02
485 942 2.009051 TGTTCTGTCTGTGCTGTGTTG 58.991 47.619 0.00 0.00 0.00 3.33
493 950 1.588404 GTGTCGTGTGTTCTGTCTGTG 59.412 52.381 0.00 0.00 0.00 3.66
494 951 1.476891 AGTGTCGTGTGTTCTGTCTGT 59.523 47.619 0.00 0.00 0.00 3.41
497 954 1.209128 CCAGTGTCGTGTGTTCTGTC 58.791 55.000 0.00 0.00 0.00 3.51
514 971 5.466728 GTGTACGAGTAATCGATAGGTACCA 59.533 44.000 20.67 0.00 36.85 3.25
531 988 3.317149 GGCTAGATATGTGTGGTGTACGA 59.683 47.826 0.00 0.00 0.00 3.43
561 1018 2.353610 GCTTCCATGGTTGGGCCTG 61.354 63.158 12.58 0.00 43.81 4.85
909 1418 0.313672 CTCCGGTCTAGAGCATGCTC 59.686 60.000 35.57 35.57 43.03 4.26
940 1449 2.519302 GTGGGGTGCTGCTGTGTT 60.519 61.111 0.00 0.00 0.00 3.32
941 1450 4.935495 CGTGGGGTGCTGCTGTGT 62.935 66.667 0.00 0.00 0.00 3.72
942 1451 3.529341 TACGTGGGGTGCTGCTGTG 62.529 63.158 0.00 0.00 0.00 3.66
943 1452 2.332312 TTTACGTGGGGTGCTGCTGT 62.332 55.000 0.00 0.00 0.00 4.40
944 1453 1.577328 CTTTACGTGGGGTGCTGCTG 61.577 60.000 0.00 0.00 0.00 4.41
945 1454 1.302511 CTTTACGTGGGGTGCTGCT 60.303 57.895 0.00 0.00 0.00 4.24
962 1471 3.574445 CGATCGACCGAGTCCGCT 61.574 66.667 10.26 0.00 0.00 5.52
963 1472 4.609247 CCGATCGACCGAGTCCGC 62.609 72.222 18.66 0.00 0.00 5.54
984 1493 0.461870 CCATTGCAGGCAGCTACGTA 60.462 55.000 2.86 0.00 45.94 3.57
985 1494 1.746615 CCATTGCAGGCAGCTACGT 60.747 57.895 2.86 0.00 45.94 3.57
986 1495 1.434622 CTCCATTGCAGGCAGCTACG 61.435 60.000 2.86 0.00 45.94 3.51
987 1496 0.393537 ACTCCATTGCAGGCAGCTAC 60.394 55.000 2.86 0.00 45.94 3.58
1096 1612 4.626081 GGTGGACGGTGTGCTGCT 62.626 66.667 0.00 0.00 0.00 4.24
1135 1654 2.782222 CGACGTCGGGGATGGTGAT 61.782 63.158 29.70 0.00 35.37 3.06
1147 1666 4.988486 AACGACACCGCCGACGTC 62.988 66.667 5.18 5.18 39.95 4.34
1257 1791 4.657824 CCGACAACACCGCCGACT 62.658 66.667 0.00 0.00 0.00 4.18
1344 1974 2.333417 GCCGACGACAGGAGAGACA 61.333 63.158 0.00 0.00 0.00 3.41
1429 2059 4.796231 AGCCACGACGCCGATGAC 62.796 66.667 0.00 0.00 39.50 3.06
1430 2060 4.492160 GAGCCACGACGCCGATGA 62.492 66.667 0.00 0.00 39.50 2.92
1856 2489 3.783478 TATGCGCGTCGGATGTGGG 62.783 63.158 4.79 0.98 38.55 4.61
1986 2619 8.147642 AGATGAATATCAAACGGAAAGATGAC 57.852 34.615 0.00 0.00 35.70 3.06
2061 2697 6.405842 CCAGGATAAATAGTTTTGAGGTTGGC 60.406 42.308 0.00 0.00 0.00 4.52
2109 2745 2.942804 TGTTGTTCAAGGGAGCATTGA 58.057 42.857 0.00 0.00 34.05 2.57
2149 2785 6.001460 TGGGTAGAAATCGTCACTTTTTGAT 58.999 36.000 0.00 0.00 36.32 2.57
2380 3493 1.621107 CGCATGTGCTGAAAATCCAC 58.379 50.000 3.25 0.00 39.32 4.02
2402 3515 7.807907 GCAAATCCGTGGATATTAATACCAAAG 59.192 37.037 14.52 12.25 35.40 2.77
2436 3549 4.677584 CAAATCCGTGGAGTTGTCAAAAA 58.322 39.130 18.33 0.00 42.84 1.94
2437 3550 4.300189 CAAATCCGTGGAGTTGTCAAAA 57.700 40.909 18.33 0.00 42.84 2.44
2438 3551 3.980646 CAAATCCGTGGAGTTGTCAAA 57.019 42.857 18.33 0.00 42.84 2.69
2444 3557 5.250200 TGTTAATAGCAAATCCGTGGAGTT 58.750 37.500 0.00 0.00 32.32 3.01
2445 3558 4.839121 TGTTAATAGCAAATCCGTGGAGT 58.161 39.130 0.00 0.00 0.00 3.85
2446 3559 5.116180 TCTGTTAATAGCAAATCCGTGGAG 58.884 41.667 0.00 0.00 0.00 3.86
2447 3560 5.092554 TCTGTTAATAGCAAATCCGTGGA 57.907 39.130 0.00 0.00 0.00 4.02
2448 3561 5.584649 TCTTCTGTTAATAGCAAATCCGTGG 59.415 40.000 0.00 0.00 0.00 4.94
2449 3562 6.662414 TCTTCTGTTAATAGCAAATCCGTG 57.338 37.500 0.00 0.00 0.00 4.94
2450 3563 6.823689 ACATCTTCTGTTAATAGCAAATCCGT 59.176 34.615 0.00 0.00 32.90 4.69
2451 3564 7.128331 CACATCTTCTGTTAATAGCAAATCCG 58.872 38.462 0.00 0.00 35.29 4.18
2473 3586 4.456911 TGTTGTAACCGTTTTTGTACCACA 59.543 37.500 0.00 0.00 0.00 4.17
2477 3590 7.218014 GGTTTACTGTTGTAACCGTTTTTGTAC 59.782 37.037 0.00 0.00 38.26 2.90
2526 3653 8.785329 AAATACCACCGCATATTTTTCATTTT 57.215 26.923 0.00 0.00 28.68 1.82
2601 3728 6.385649 TTGCGAGTTCCTTTTCTTTTGTAT 57.614 33.333 0.00 0.00 0.00 2.29
2606 3733 7.606456 TCACTATATTGCGAGTTCCTTTTCTTT 59.394 33.333 0.00 0.00 0.00 2.52
2622 3749 4.257267 TGGACCGCATCTCACTATATTG 57.743 45.455 0.00 0.00 0.00 1.90
2654 3781 1.081242 GTTACCGTCGTGCCGAAGA 60.081 57.895 10.92 0.00 37.53 2.87
2682 3809 1.538512 TGTGAGCTAGTACGTGACACC 59.461 52.381 0.00 0.00 0.00 4.16
2691 3818 4.322499 GGTGCTACCTTTTGTGAGCTAGTA 60.322 45.833 0.00 0.00 34.73 1.82
2692 3819 3.557264 GGTGCTACCTTTTGTGAGCTAGT 60.557 47.826 0.00 0.00 34.73 2.57
2693 3820 3.003480 GGTGCTACCTTTTGTGAGCTAG 58.997 50.000 0.00 0.00 34.73 3.42
2728 3855 7.158099 TGATAGGGTTCGATCTGTACATATG 57.842 40.000 0.00 0.00 0.00 1.78
2729 3856 7.577807 GCTTGATAGGGTTCGATCTGTACATAT 60.578 40.741 0.00 0.00 0.00 1.78
2730 3857 6.294564 GCTTGATAGGGTTCGATCTGTACATA 60.295 42.308 0.00 0.00 0.00 2.29
2750 3877 1.300620 CGGGAGTTCGTGTGCTTGA 60.301 57.895 0.00 0.00 0.00 3.02
2755 3882 4.003788 AGCCCGGGAGTTCGTGTG 62.004 66.667 29.31 0.00 0.00 3.82
2757 3884 3.649277 CTCAGCCCGGGAGTTCGTG 62.649 68.421 29.31 10.84 0.00 4.35


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

AutoCloner maintained by Alex Coulton.