Multiple sequence alignment - TraesCS2D01G387400

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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 TraesCS2D01G387400 chr2D 100.000 4019 0 0 1 4019 492712631 492716649 0.000000e+00 7422.0
1 TraesCS2D01G387400 chr2D 90.385 52 4 1 3166 3217 24948573 24948623 2.590000e-07 67.6
2 TraesCS2D01G387400 chr2A 94.911 3498 130 21 495 3966 638033315 638036790 0.000000e+00 5430.0
3 TraesCS2D01G387400 chr2A 87.580 314 26 9 43 343 638032745 638033058 6.390000e-93 351.0
4 TraesCS2D01G387400 chr2B 93.808 1938 70 11 493 2407 579382272 579384182 0.000000e+00 2868.0
5 TraesCS2D01G387400 chr2B 97.113 762 16 3 2405 3166 579384410 579385165 0.000000e+00 1280.0
6 TraesCS2D01G387400 chr2B 91.799 378 14 7 3578 3944 579385795 579386166 9.960000e-141 510.0
7 TraesCS2D01G387400 chr2B 87.949 390 33 5 3203 3580 579385171 579385558 7.920000e-122 448.0
8 TraesCS2D01G387400 chr2B 88.393 112 7 4 43 154 579381183 579381288 3.260000e-26 130.0
9 TraesCS2D01G387400 chr2B 98.077 52 1 0 3968 4019 579386169 579386220 1.540000e-14 91.6
10 TraesCS2D01G387400 chr2B 92.063 63 5 0 3380 3442 579385280 579385342 5.530000e-14 89.8
11 TraesCS2D01G387400 chr5B 79.969 644 76 27 1438 2066 678573687 678573082 3.710000e-115 425.0
12 TraesCS2D01G387400 chr5B 87.719 57 5 2 3162 3217 353017449 353017394 9.320000e-07 65.8
13 TraesCS2D01G387400 chr1D 95.652 46 2 0 3159 3204 474881320 474881275 1.550000e-09 75.0
14 TraesCS2D01G387400 chr4D 100.000 39 0 0 3166 3204 79706059 79706021 5.570000e-09 73.1
15 TraesCS2D01G387400 chrUn 92.000 50 4 0 3155 3204 110464831 110464782 2.000000e-08 71.3
16 TraesCS2D01G387400 chr4B 92.000 50 4 0 3155 3204 660491587 660491538 2.000000e-08 71.3
17 TraesCS2D01G387400 chr1B 93.750 48 2 1 3166 3213 44932827 44932873 2.000000e-08 71.3
18 TraesCS2D01G387400 chr3B 90.385 52 5 0 3166 3217 501117561 501117612 7.210000e-08 69.4


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 TraesCS2D01G387400 chr2D 492712631 492716649 4018 False 7422.000000 7422 100.000000 1 4019 1 chr2D.!!$F2 4018
1 TraesCS2D01G387400 chr2A 638032745 638036790 4045 False 2890.500000 5430 91.245500 43 3966 2 chr2A.!!$F1 3923
2 TraesCS2D01G387400 chr2B 579381183 579386220 5037 False 773.914286 2868 92.743143 43 4019 7 chr2B.!!$F1 3976
3 TraesCS2D01G387400 chr5B 678573082 678573687 605 True 425.000000 425 79.969000 1438 2066 1 chr5B.!!$R2 628

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
476 1291 0.035881 CACAGGCTTCTGCTTCTGGA 59.964 55.0 0.00 0.0 42.06 3.86 F
606 1425 0.390492 CACTCAGTCCAGTGAGCACA 59.610 55.0 10.79 0.0 46.90 4.57 F
963 1788 0.969894 ACAGTGACCACAGTAGGAGC 59.030 55.0 0.00 0.0 28.90 4.70 F
1509 2348 1.270971 CGAAATTGAGCCGCCATTTG 58.729 50.0 0.00 0.0 0.00 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1966 2831 0.038892 CCACATGAAACCAGCTGCAC 60.039 55.000 8.66 0.0 0.00 4.57 R
2497 3603 1.371183 CCTCTGCCGAACTCCACAA 59.629 57.895 0.00 0.0 0.00 3.33 R
2762 3868 5.810587 GGCTCGATCTACAAAGATACAAACA 59.189 40.000 0.00 0.0 42.73 2.83 R
3468 4585 0.679505 TTTCTCCAGTGGTCCGACAG 59.320 55.000 9.54 0.0 0.00 3.51 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
17 18 3.794270 CGCGTGATTCCGTCCATT 58.206 55.556 0.00 0.00 0.00 3.16
18 19 2.086510 CGCGTGATTCCGTCCATTT 58.913 52.632 0.00 0.00 0.00 2.32
19 20 0.446222 CGCGTGATTCCGTCCATTTT 59.554 50.000 0.00 0.00 0.00 1.82
20 21 1.661617 CGCGTGATTCCGTCCATTTTA 59.338 47.619 0.00 0.00 0.00 1.52
21 22 2.286833 CGCGTGATTCCGTCCATTTTAT 59.713 45.455 0.00 0.00 0.00 1.40
22 23 3.491639 CGCGTGATTCCGTCCATTTTATA 59.508 43.478 0.00 0.00 0.00 0.98
23 24 4.025563 CGCGTGATTCCGTCCATTTTATAA 60.026 41.667 0.00 0.00 0.00 0.98
24 25 5.333798 CGCGTGATTCCGTCCATTTTATAAT 60.334 40.000 0.00 0.00 0.00 1.28
25 26 6.128769 CGCGTGATTCCGTCCATTTTATAATA 60.129 38.462 0.00 0.00 0.00 0.98
26 27 7.569774 CGCGTGATTCCGTCCATTTTATAATAA 60.570 37.037 0.00 0.00 0.00 1.40
27 28 8.071368 GCGTGATTCCGTCCATTTTATAATAAA 58.929 33.333 0.00 0.00 0.00 1.40
28 29 9.938670 CGTGATTCCGTCCATTTTATAATAAAA 57.061 29.630 0.00 0.00 0.00 1.52
54 55 8.945758 AAGCATATCGTATACTGTAAAGTACG 57.054 34.615 11.34 11.34 40.74 3.67
127 129 2.614057 ACGGCGTATAGTGTACTGGTAC 59.386 50.000 12.58 4.15 36.63 3.34
131 133 5.049474 CGGCGTATAGTGTACTGGTACAATA 60.049 44.000 18.69 18.69 46.33 1.90
154 156 9.878667 AATAGATCAGAGATTCAGAATATGCAG 57.121 33.333 0.00 0.00 0.00 4.41
194 751 2.572095 ATACGCTTACGGCTGCTGCA 62.572 55.000 17.89 0.88 46.04 4.41
195 752 2.572095 TACGCTTACGGCTGCTGCAT 62.572 55.000 17.89 7.33 46.04 3.96
196 753 2.406401 GCTTACGGCTGCTGCATG 59.594 61.111 17.89 11.30 41.91 4.06
226 789 1.004277 GTGTGTCTCTTCTGTCGCCG 61.004 60.000 0.00 0.00 0.00 6.46
243 806 1.153549 CGTCTGCCTAGGGACAAGC 60.154 63.158 11.72 0.00 33.19 4.01
251 814 2.419574 GCCTAGGGACAAGCGTGAATTA 60.420 50.000 11.72 0.00 0.00 1.40
294 862 5.413309 AGATTAGACCTGTGACTTCAAGG 57.587 43.478 0.00 6.13 0.00 3.61
303 871 1.452108 GACTTCAAGGGCCCATCGG 60.452 63.158 27.56 12.31 0.00 4.18
316 884 1.516386 CATCGGTCGGAGTTGGACG 60.516 63.158 0.00 0.00 35.24 4.79
343 912 7.244192 AGTTAAATAATGAGCTCACGAAAAGC 58.756 34.615 20.97 6.49 40.14 3.51
357 936 2.614057 CGAAAAGCTGTGACAGTTCCTT 59.386 45.455 14.82 6.31 33.43 3.36
363 942 4.327680 AGCTGTGACAGTTCCTTAATTCC 58.672 43.478 14.82 0.00 33.43 3.01
377 1088 1.601248 AATTCCTCTGCTTAGCCCCT 58.399 50.000 0.29 0.00 0.00 4.79
393 1104 1.447838 CCTCCCACGTCATCAACCG 60.448 63.158 0.00 0.00 0.00 4.44
398 1109 2.742372 ACGTCATCAACCGCTGGC 60.742 61.111 0.00 0.00 0.00 4.85
404 1115 2.016318 TCATCAACCGCTGGCAATTAG 58.984 47.619 0.00 0.00 0.00 1.73
405 1116 1.745087 CATCAACCGCTGGCAATTAGT 59.255 47.619 0.00 0.00 0.00 2.24
406 1117 2.772077 TCAACCGCTGGCAATTAGTA 57.228 45.000 0.00 0.00 0.00 1.82
409 1120 2.483014 ACCGCTGGCAATTAGTACAA 57.517 45.000 0.00 0.00 0.00 2.41
412 1123 3.875134 ACCGCTGGCAATTAGTACAATAC 59.125 43.478 0.00 0.00 0.00 1.89
413 1124 3.250040 CCGCTGGCAATTAGTACAATACC 59.750 47.826 0.00 0.41 0.00 2.73
414 1125 3.874543 CGCTGGCAATTAGTACAATACCA 59.125 43.478 0.00 4.57 0.00 3.25
415 1126 4.515191 CGCTGGCAATTAGTACAATACCAT 59.485 41.667 0.00 0.00 0.00 3.55
416 1127 5.699001 CGCTGGCAATTAGTACAATACCATA 59.301 40.000 0.00 0.00 0.00 2.74
418 1129 7.547722 CGCTGGCAATTAGTACAATACCATATA 59.452 37.037 0.00 0.00 0.00 0.86
419 1130 9.396022 GCTGGCAATTAGTACAATACCATATAT 57.604 33.333 0.00 0.00 0.00 0.86
421 1132 9.173021 TGGCAATTAGTACAATACCATATATGC 57.827 33.333 7.24 0.00 0.00 3.14
428 1139 7.551585 AGTACAATACCATATATGCTGAGAGC 58.448 38.462 7.24 0.00 42.82 4.09
431 1142 6.127225 ACAATACCATATATGCTGAGAGCGAT 60.127 38.462 7.24 0.00 46.26 4.58
433 1144 5.921962 ACCATATATGCTGAGAGCGATTA 57.078 39.130 7.24 0.00 46.26 1.75
434 1145 6.477053 ACCATATATGCTGAGAGCGATTAT 57.523 37.500 7.24 0.00 46.26 1.28
436 1147 5.925397 CCATATATGCTGAGAGCGATTATCC 59.075 44.000 7.24 0.00 46.26 2.59
439 1150 4.717233 ATGCTGAGAGCGATTATCCTAG 57.283 45.455 0.00 0.00 46.26 3.02
440 1151 3.756117 TGCTGAGAGCGATTATCCTAGA 58.244 45.455 0.00 0.00 46.26 2.43
441 1152 4.339748 TGCTGAGAGCGATTATCCTAGAT 58.660 43.478 0.00 0.00 46.26 1.98
442 1153 5.501156 TGCTGAGAGCGATTATCCTAGATA 58.499 41.667 0.00 0.00 46.26 1.98
443 1154 6.125719 TGCTGAGAGCGATTATCCTAGATAT 58.874 40.000 0.00 0.00 46.26 1.63
444 1155 7.283329 TGCTGAGAGCGATTATCCTAGATATA 58.717 38.462 0.00 0.00 46.26 0.86
446 1157 8.236586 GCTGAGAGCGATTATCCTAGATATATG 58.763 40.741 0.00 0.00 0.00 1.78
464 1279 1.552578 TGTATACGTGACCACAGGCT 58.447 50.000 0.00 0.00 35.62 4.58
465 1280 1.897133 TGTATACGTGACCACAGGCTT 59.103 47.619 0.00 0.00 35.62 4.35
466 1281 2.094390 TGTATACGTGACCACAGGCTTC 60.094 50.000 0.00 0.00 35.62 3.86
467 1282 1.267121 ATACGTGACCACAGGCTTCT 58.733 50.000 0.00 0.00 35.62 2.85
468 1283 0.317160 TACGTGACCACAGGCTTCTG 59.683 55.000 0.00 0.00 43.84 3.02
469 1284 2.320587 CGTGACCACAGGCTTCTGC 61.321 63.158 0.85 0.00 42.06 4.26
470 1285 1.072159 GTGACCACAGGCTTCTGCT 59.928 57.895 0.00 0.00 42.06 4.24
471 1286 0.536006 GTGACCACAGGCTTCTGCTT 60.536 55.000 0.00 0.00 42.06 3.91
472 1287 0.250467 TGACCACAGGCTTCTGCTTC 60.250 55.000 0.00 0.00 42.06 3.86
473 1288 0.036022 GACCACAGGCTTCTGCTTCT 59.964 55.000 0.00 0.00 42.06 2.85
474 1289 0.250640 ACCACAGGCTTCTGCTTCTG 60.251 55.000 0.00 0.00 42.06 3.02
475 1290 0.959372 CCACAGGCTTCTGCTTCTGG 60.959 60.000 0.00 0.00 42.06 3.86
476 1291 0.035881 CACAGGCTTCTGCTTCTGGA 59.964 55.000 0.00 0.00 42.06 3.86
477 1292 0.990374 ACAGGCTTCTGCTTCTGGAT 59.010 50.000 0.00 0.00 42.06 3.41
478 1293 1.353694 ACAGGCTTCTGCTTCTGGATT 59.646 47.619 0.00 0.00 42.06 3.01
479 1294 2.224967 ACAGGCTTCTGCTTCTGGATTT 60.225 45.455 0.00 0.00 42.06 2.17
480 1295 2.422832 CAGGCTTCTGCTTCTGGATTTC 59.577 50.000 0.00 0.00 39.59 2.17
481 1296 1.399791 GGCTTCTGCTTCTGGATTTCG 59.600 52.381 0.00 0.00 39.59 3.46
482 1297 1.202121 GCTTCTGCTTCTGGATTTCGC 60.202 52.381 0.00 0.00 36.03 4.70
483 1298 2.079158 CTTCTGCTTCTGGATTTCGCA 58.921 47.619 0.00 0.00 0.00 5.10
484 1299 2.183478 TCTGCTTCTGGATTTCGCAA 57.817 45.000 0.00 0.00 0.00 4.85
485 1300 2.503331 TCTGCTTCTGGATTTCGCAAA 58.497 42.857 0.00 0.00 0.00 3.68
486 1301 2.884012 TCTGCTTCTGGATTTCGCAAAA 59.116 40.909 0.00 0.00 0.00 2.44
487 1302 3.317711 TCTGCTTCTGGATTTCGCAAAAA 59.682 39.130 0.00 0.00 0.00 1.94
488 1303 4.022068 TCTGCTTCTGGATTTCGCAAAAAT 60.022 37.500 0.00 0.00 0.00 1.82
489 1304 5.182950 TCTGCTTCTGGATTTCGCAAAAATA 59.817 36.000 0.00 0.00 0.00 1.40
490 1305 5.777802 TGCTTCTGGATTTCGCAAAAATAA 58.222 33.333 0.00 0.00 0.00 1.40
491 1306 6.219473 TGCTTCTGGATTTCGCAAAAATAAA 58.781 32.000 0.00 0.00 0.00 1.40
492 1307 6.703607 TGCTTCTGGATTTCGCAAAAATAAAA 59.296 30.769 0.00 0.00 0.00 1.52
493 1308 7.225538 TGCTTCTGGATTTCGCAAAAATAAAAA 59.774 29.630 0.00 0.00 0.00 1.94
606 1425 0.390492 CACTCAGTCCAGTGAGCACA 59.610 55.000 10.79 0.00 46.90 4.57
741 1561 6.293516 CCACACGTCATCTTCTAGTCCTATAC 60.294 46.154 0.00 0.00 0.00 1.47
746 1566 6.655425 CGTCATCTTCTAGTCCTATACCATCA 59.345 42.308 0.00 0.00 0.00 3.07
757 1577 1.729267 ATACCATCACCCCATGGCCC 61.729 60.000 6.09 0.00 46.71 5.80
913 1738 2.045926 CACCGGGGAAAGAGCAGG 60.046 66.667 6.32 0.00 0.00 4.85
963 1788 0.969894 ACAGTGACCACAGTAGGAGC 59.030 55.000 0.00 0.00 28.90 4.70
1393 2230 1.994779 AGATTACCGGCGTACGTTTTG 59.005 47.619 17.90 5.94 42.24 2.44
1422 2259 5.163764 TGCTTATGCATTTTACCTGTTCTCG 60.164 40.000 3.54 0.00 45.31 4.04
1474 2313 4.192317 AGTCCAACAAGTGTTCTGTTCTC 58.808 43.478 0.00 0.00 35.83 2.87
1509 2348 1.270971 CGAAATTGAGCCGCCATTTG 58.729 50.000 0.00 0.00 0.00 2.32
1529 2371 2.092323 GGTGGGGCAGTAAATTCAGTC 58.908 52.381 0.00 0.00 0.00 3.51
1594 2436 9.307121 AGATAAGATATGTGAAGTATAATGCGC 57.693 33.333 0.00 0.00 0.00 6.09
1806 2655 6.405842 GCCTACTTTATTTGCCAAGCTTACAT 60.406 38.462 0.00 0.00 0.00 2.29
1834 2683 9.872721 AGTAACTTCTATGTAAAGACTAAAGGC 57.127 33.333 0.00 0.00 0.00 4.35
1835 2684 9.872721 GTAACTTCTATGTAAAGACTAAAGGCT 57.127 33.333 0.00 0.00 0.00 4.58
1866 2731 1.602920 CCTTTTGGTTTCTCGGCTTGC 60.603 52.381 0.00 0.00 34.07 4.01
1877 2742 1.587088 CGGCTTGCCGATTCATTGC 60.587 57.895 27.61 0.00 34.88 3.56
1905 2770 3.865224 CAAGCATTGTTTTCCTTGTGC 57.135 42.857 0.00 0.00 42.34 4.57
2100 2973 6.823182 AGGTGGCAAATCCTAAAAATAATTGC 59.177 34.615 0.00 0.00 40.56 3.56
2227 3101 2.515926 TCTTGCACCTATCTCATCGC 57.484 50.000 0.00 0.00 0.00 4.58
2322 3196 8.758633 ACTGTGTTACAAACATACTATCAGTC 57.241 34.615 5.94 0.00 44.35 3.51
2760 3866 5.010282 GTCCTGAATATCCACACCTTTTGT 58.990 41.667 0.00 0.00 39.97 2.83
2761 3867 5.476945 GTCCTGAATATCCACACCTTTTGTT 59.523 40.000 0.00 0.00 35.67 2.83
2762 3868 6.015434 GTCCTGAATATCCACACCTTTTGTTT 60.015 38.462 0.00 0.00 35.67 2.83
2763 3869 6.015519 TCCTGAATATCCACACCTTTTGTTTG 60.016 38.462 0.00 0.00 35.67 2.93
3361 4470 8.184304 AGTGTGGCCAAAACTGTAAATTTATA 57.816 30.769 19.11 0.00 0.00 0.98
3446 4563 6.155827 TGTAAAATTATTTGCAGTGTGCCTC 58.844 36.000 0.00 0.00 44.23 4.70
3468 4585 4.518970 TCACAGAAACCTTCATAGTTTGGC 59.481 41.667 0.00 0.00 37.55 4.52
3503 4620 3.939592 GGAGAAAATACCTGTGCCTGTAC 59.060 47.826 0.00 0.00 0.00 2.90
3523 4640 7.704047 CCTGTACTTTACCCGTCTTAACTAATC 59.296 40.741 0.00 0.00 0.00 1.75
3524 4641 8.121305 TGTACTTTACCCGTCTTAACTAATCA 57.879 34.615 0.00 0.00 0.00 2.57
3726 5082 1.547372 GAAGCCAGCATTGTCAACCAT 59.453 47.619 0.00 0.00 0.00 3.55
3733 5089 5.581605 CCAGCATTGTCAACCATATAACAC 58.418 41.667 0.00 0.00 0.00 3.32
3831 5187 5.768317 TGGCTTTAGTAAATCAACACAAGC 58.232 37.500 0.00 0.00 36.59 4.01
3850 5206 1.879796 GCCACCTTCAGGACACTTCAG 60.880 57.143 0.00 0.00 38.94 3.02
3851 5207 1.417890 CCACCTTCAGGACACTTCAGT 59.582 52.381 0.00 0.00 38.94 3.41
3852 5208 2.158755 CCACCTTCAGGACACTTCAGTT 60.159 50.000 0.00 0.00 38.94 3.16
3853 5209 3.134458 CACCTTCAGGACACTTCAGTTC 58.866 50.000 0.00 0.00 38.94 3.01
3854 5210 3.041946 ACCTTCAGGACACTTCAGTTCT 58.958 45.455 0.00 0.00 38.94 3.01
3857 5213 4.991687 CCTTCAGGACACTTCAGTTCTAAC 59.008 45.833 0.00 0.00 37.39 2.34
3858 5214 5.221541 CCTTCAGGACACTTCAGTTCTAACT 60.222 44.000 0.00 0.00 37.22 2.24
3859 5215 7.232794 CCTTCAGGACACTTCAGTTCTAACTG 61.233 46.154 15.25 15.25 46.85 3.16
3871 5227 3.064931 GTTCTAACTGAACGAACCCCAG 58.935 50.000 0.00 0.00 44.49 4.45
4003 5372 1.304052 TTTGCGGCAGTAATGGGCT 60.304 52.632 1.67 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.446222 AAAATGGACGGAATCACGCG 59.554 50.000 3.53 3.53 37.37 6.01
1 2 3.963383 ATAAAATGGACGGAATCACGC 57.037 42.857 0.00 0.00 37.37 5.34
2 3 9.938670 TTTTATTATAAAATGGACGGAATCACG 57.061 29.630 6.08 0.00 40.31 4.35
28 29 9.390795 CGTACTTTACAGTATACGATATGCTTT 57.609 33.333 6.42 0.00 37.22 3.51
29 30 8.019669 CCGTACTTTACAGTATACGATATGCTT 58.980 37.037 12.02 0.00 37.22 3.91
30 31 7.173907 ACCGTACTTTACAGTATACGATATGCT 59.826 37.037 12.02 0.00 37.22 3.79
31 32 7.301054 ACCGTACTTTACAGTATACGATATGC 58.699 38.462 12.02 0.00 37.22 3.14
32 33 8.715998 AGACCGTACTTTACAGTATACGATATG 58.284 37.037 12.02 0.00 37.22 1.78
33 34 8.715998 CAGACCGTACTTTACAGTATACGATAT 58.284 37.037 12.02 0.00 37.22 1.63
34 35 7.710907 ACAGACCGTACTTTACAGTATACGATA 59.289 37.037 12.02 0.00 37.22 2.92
35 36 6.540189 ACAGACCGTACTTTACAGTATACGAT 59.460 38.462 12.02 0.00 37.22 3.73
36 37 5.874810 ACAGACCGTACTTTACAGTATACGA 59.125 40.000 12.02 0.00 37.22 3.43
37 38 5.961843 CACAGACCGTACTTTACAGTATACG 59.038 44.000 5.56 5.56 37.83 3.06
38 39 7.065085 TCTCACAGACCGTACTTTACAGTATAC 59.935 40.741 0.00 0.00 37.83 1.47
39 40 7.105588 TCTCACAGACCGTACTTTACAGTATA 58.894 38.462 0.00 0.00 37.83 1.47
40 41 5.942236 TCTCACAGACCGTACTTTACAGTAT 59.058 40.000 0.00 0.00 37.83 2.12
41 42 5.308014 TCTCACAGACCGTACTTTACAGTA 58.692 41.667 0.00 0.00 34.06 2.74
44 45 4.139786 ACTCTCACAGACCGTACTTTACA 58.860 43.478 0.00 0.00 0.00 2.41
127 129 9.654663 TGCATATTCTGAATCTCTGATCTATTG 57.345 33.333 6.10 0.00 0.00 1.90
131 133 6.167685 GCTGCATATTCTGAATCTCTGATCT 58.832 40.000 6.10 0.00 0.00 2.75
154 156 0.873743 GCTACGGTGATCTGCTCTGC 60.874 60.000 0.00 0.00 0.00 4.26
181 738 1.875262 CAACATGCAGCAGCCGTAA 59.125 52.632 0.00 0.00 41.13 3.18
194 751 1.785041 GACACACACCGCAGCAACAT 61.785 55.000 0.00 0.00 0.00 2.71
195 752 2.437537 ACACACACCGCAGCAACA 60.438 55.556 0.00 0.00 0.00 3.33
196 753 2.105960 GAGACACACACCGCAGCAAC 62.106 60.000 0.00 0.00 0.00 4.17
204 763 1.772182 CGACAGAAGAGACACACACC 58.228 55.000 0.00 0.00 0.00 4.16
226 789 1.153549 CGCTTGTCCCTAGGCAGAC 60.154 63.158 2.05 7.26 0.00 3.51
243 806 8.708075 TGATTCTTTCGAGTTTTTAATTCACG 57.292 30.769 0.00 0.00 0.00 4.35
294 862 3.782443 AACTCCGACCGATGGGCC 61.782 66.667 0.00 0.00 36.48 5.80
303 871 0.883833 TAACTCCGTCCAACTCCGAC 59.116 55.000 0.00 0.00 0.00 4.79
316 884 6.903883 TTCGTGAGCTCATTATTTAACTCC 57.096 37.500 21.47 0.82 0.00 3.85
333 902 2.309528 ACTGTCACAGCTTTTCGTGA 57.690 45.000 4.13 0.69 39.77 4.35
343 912 5.641209 CAGAGGAATTAAGGAACTGTCACAG 59.359 44.000 2.22 2.22 40.86 3.66
357 936 2.706190 GAGGGGCTAAGCAGAGGAATTA 59.294 50.000 0.00 0.00 0.00 1.40
363 942 1.690633 TGGGAGGGGCTAAGCAGAG 60.691 63.158 0.00 0.00 0.00 3.35
377 1088 2.047655 GCGGTTGATGACGTGGGA 60.048 61.111 0.00 0.00 0.00 4.37
393 1104 7.687941 ATATGGTATTGTACTAATTGCCAGC 57.312 36.000 0.00 0.00 0.00 4.85
404 1115 6.473778 CGCTCTCAGCATATATGGTATTGTAC 59.526 42.308 16.69 5.31 42.58 2.90
405 1116 6.377146 TCGCTCTCAGCATATATGGTATTGTA 59.623 38.462 16.69 1.74 42.58 2.41
406 1117 5.185828 TCGCTCTCAGCATATATGGTATTGT 59.814 40.000 16.69 0.00 42.58 2.71
409 1120 6.477053 AATCGCTCTCAGCATATATGGTAT 57.523 37.500 16.69 3.04 42.58 2.73
412 1123 5.925397 GGATAATCGCTCTCAGCATATATGG 59.075 44.000 14.51 0.00 42.58 2.74
413 1124 6.747125 AGGATAATCGCTCTCAGCATATATG 58.253 40.000 8.45 8.45 42.58 1.78
414 1125 6.975196 AGGATAATCGCTCTCAGCATATAT 57.025 37.500 0.00 0.00 42.58 0.86
415 1126 7.283329 TCTAGGATAATCGCTCTCAGCATATA 58.717 38.462 0.00 0.00 42.58 0.86
416 1127 6.125719 TCTAGGATAATCGCTCTCAGCATAT 58.874 40.000 0.00 0.00 42.58 1.78
418 1129 4.339748 TCTAGGATAATCGCTCTCAGCAT 58.660 43.478 0.00 0.00 42.58 3.79
419 1130 3.756117 TCTAGGATAATCGCTCTCAGCA 58.244 45.455 0.00 0.00 42.58 4.41
420 1131 4.981806 ATCTAGGATAATCGCTCTCAGC 57.018 45.455 0.00 0.00 38.02 4.26
421 1132 9.283768 ACATATATCTAGGATAATCGCTCTCAG 57.716 37.037 0.00 0.00 0.00 3.35
433 1144 9.339850 GTGGTCACGTATACATATATCTAGGAT 57.660 37.037 3.32 0.00 0.00 3.24
434 1145 8.323567 TGTGGTCACGTATACATATATCTAGGA 58.676 37.037 3.32 0.00 0.00 2.94
436 1147 8.613482 CCTGTGGTCACGTATACATATATCTAG 58.387 40.741 3.32 0.00 0.00 2.43
439 1150 6.034591 GCCTGTGGTCACGTATACATATATC 58.965 44.000 3.32 0.00 0.00 1.63
440 1151 5.715279 AGCCTGTGGTCACGTATACATATAT 59.285 40.000 3.32 0.00 0.00 0.86
441 1152 5.074804 AGCCTGTGGTCACGTATACATATA 58.925 41.667 3.32 0.00 0.00 0.86
442 1153 3.895656 AGCCTGTGGTCACGTATACATAT 59.104 43.478 3.32 0.00 0.00 1.78
443 1154 3.293337 AGCCTGTGGTCACGTATACATA 58.707 45.455 3.32 0.00 0.00 2.29
444 1155 2.108168 AGCCTGTGGTCACGTATACAT 58.892 47.619 3.32 0.00 0.00 2.29
446 1157 2.165845 AGAAGCCTGTGGTCACGTATAC 59.834 50.000 0.00 0.00 0.00 1.47
464 1279 2.183478 TGCGAAATCCAGAAGCAGAA 57.817 45.000 0.00 0.00 33.57 3.02
465 1280 2.183478 TTGCGAAATCCAGAAGCAGA 57.817 45.000 0.00 0.00 39.11 4.26
466 1281 2.995466 TTTGCGAAATCCAGAAGCAG 57.005 45.000 0.00 0.00 39.11 4.24
467 1282 3.724508 TTTTTGCGAAATCCAGAAGCA 57.275 38.095 0.00 0.00 35.90 3.91
468 1283 6.704512 TTTATTTTTGCGAAATCCAGAAGC 57.295 33.333 0.00 0.00 0.00 3.86
490 1305 1.966354 CCCAGAAGCAGAAGCCTTTTT 59.034 47.619 0.00 0.00 43.56 1.94
491 1306 1.625511 CCCAGAAGCAGAAGCCTTTT 58.374 50.000 0.00 0.00 43.56 2.27
492 1307 0.897401 GCCCAGAAGCAGAAGCCTTT 60.897 55.000 0.00 0.00 43.56 3.11
493 1308 1.303970 GCCCAGAAGCAGAAGCCTT 60.304 57.895 0.00 0.00 43.56 4.35
494 1309 2.354343 GCCCAGAAGCAGAAGCCT 59.646 61.111 0.00 0.00 43.56 4.58
495 1310 2.753446 GGCCCAGAAGCAGAAGCC 60.753 66.667 0.00 0.00 43.56 4.35
496 1311 2.753446 GGGCCCAGAAGCAGAAGC 60.753 66.667 19.95 0.00 42.56 3.86
497 1312 1.676967 GTGGGCCCAGAAGCAGAAG 60.677 63.158 29.55 0.00 0.00 2.85
606 1425 2.095008 CGTGCTCACTAGTCACATGAGT 60.095 50.000 12.23 0.00 41.62 3.41
741 1561 4.900704 CGGGCCATGGGGTGATGG 62.901 72.222 15.13 0.00 45.20 3.51
746 1566 2.833151 TTAGAGACGGGCCATGGGGT 62.833 60.000 15.13 0.00 36.17 4.95
757 1577 3.079960 ACATGCGGTACATTAGAGACG 57.920 47.619 0.00 0.00 36.64 4.18
913 1738 1.244816 CCTTTTGACCTTTCCGTCCC 58.755 55.000 0.00 0.00 31.35 4.46
1422 2259 5.705813 TCAATTTCATTGCAATTGCGATC 57.294 34.783 27.09 2.06 42.99 3.69
1474 2313 3.114616 CGGCAGGCACGAGACTTG 61.115 66.667 0.00 0.00 0.00 3.16
1509 2348 2.092323 GACTGAATTTACTGCCCCACC 58.908 52.381 0.00 0.00 0.00 4.61
1529 2371 8.487970 CACTTAGTATACTCCATACAAAATGCG 58.512 37.037 9.12 0.00 41.84 4.73
1582 2424 0.868602 ACGTCGCGCGCATTATACTT 60.869 50.000 32.61 7.67 46.11 2.24
1594 2436 2.442188 GGAAAGGCTACACGTCGCG 61.442 63.158 0.00 0.00 0.00 5.87
1830 2679 4.399303 CCAAAAGGAACGATCATTAGCCTT 59.601 41.667 0.00 0.00 37.34 4.35
1831 2680 3.947834 CCAAAAGGAACGATCATTAGCCT 59.052 43.478 0.00 0.00 0.00 4.58
1832 2681 3.694566 ACCAAAAGGAACGATCATTAGCC 59.305 43.478 0.00 0.00 0.00 3.93
1833 2682 4.965119 ACCAAAAGGAACGATCATTAGC 57.035 40.909 0.00 0.00 0.00 3.09
1834 2683 7.145932 AGAAACCAAAAGGAACGATCATTAG 57.854 36.000 0.00 0.00 0.00 1.73
1835 2684 6.128391 CGAGAAACCAAAAGGAACGATCATTA 60.128 38.462 0.00 0.00 0.00 1.90
1836 2685 5.334879 CGAGAAACCAAAAGGAACGATCATT 60.335 40.000 0.00 0.00 0.00 2.57
1866 2731 2.355197 TGTACCACAGCAATGAATCGG 58.645 47.619 0.00 0.00 0.00 4.18
1877 2742 4.037923 AGGAAAACAATGCTTGTACCACAG 59.962 41.667 14.91 0.00 44.59 3.66
1966 2831 0.038892 CCACATGAAACCAGCTGCAC 60.039 55.000 8.66 0.00 0.00 4.57
2100 2973 2.862541 TGTGTCAATTTCCACCTGGAG 58.137 47.619 0.00 0.00 46.36 3.86
2270 3144 2.159282 TGCGTAGACTAGCTTAAGGCAC 60.159 50.000 4.29 0.00 44.79 5.01
2497 3603 1.371183 CCTCTGCCGAACTCCACAA 59.629 57.895 0.00 0.00 0.00 3.33
2760 3866 7.148474 GGCTCGATCTACAAAGATACAAACAAA 60.148 37.037 0.00 0.00 42.73 2.83
2761 3867 6.312918 GGCTCGATCTACAAAGATACAAACAA 59.687 38.462 0.00 0.00 42.73 2.83
2762 3868 5.810587 GGCTCGATCTACAAAGATACAAACA 59.189 40.000 0.00 0.00 42.73 2.83
2763 3869 5.810587 TGGCTCGATCTACAAAGATACAAAC 59.189 40.000 0.00 0.00 42.73 2.93
3203 4309 1.858458 CGTCACATTGTCACAACGAGT 59.142 47.619 0.00 0.00 32.17 4.18
3256 4365 2.948979 ACCACTGAAACAGCGAATGAAA 59.051 40.909 0.00 0.00 34.37 2.69
3446 4563 4.520492 AGCCAAACTATGAAGGTTTCTGTG 59.480 41.667 0.00 0.00 35.09 3.66
3468 4585 0.679505 TTTCTCCAGTGGTCCGACAG 59.320 55.000 9.54 0.00 0.00 3.51
3503 4620 8.543862 ACTTTGATTAGTTAAGACGGGTAAAG 57.456 34.615 0.00 0.00 0.00 1.85
3523 4640 6.010294 AGAGCATCACATCTTCAAACTTTG 57.990 37.500 0.00 0.00 37.82 2.77
3524 4641 6.645790 AAGAGCATCACATCTTCAAACTTT 57.354 33.333 0.00 0.00 37.82 2.66
3613 4969 1.869767 GTTCTGAGCTCATAATGCCCG 59.130 52.381 18.63 2.66 0.00 6.13
3710 5066 5.125257 TGTGTTATATGGTTGACAATGCTGG 59.875 40.000 0.00 0.00 0.00 4.85
3757 5113 0.829182 AACAGCCCAGCAAAGGAAGG 60.829 55.000 0.00 0.00 0.00 3.46
3831 5187 1.417890 ACTGAAGTGTCCTGAAGGTGG 59.582 52.381 0.00 0.00 36.34 4.61
3851 5207 2.549349 GCTGGGGTTCGTTCAGTTAGAA 60.549 50.000 0.00 0.00 0.00 2.10
3852 5208 1.001633 GCTGGGGTTCGTTCAGTTAGA 59.998 52.381 0.00 0.00 0.00 2.10
3853 5209 1.439679 GCTGGGGTTCGTTCAGTTAG 58.560 55.000 0.00 0.00 0.00 2.34
3854 5210 0.035739 GGCTGGGGTTCGTTCAGTTA 59.964 55.000 0.00 0.00 0.00 2.24
3857 5213 1.966451 GTGGCTGGGGTTCGTTCAG 60.966 63.158 0.00 0.00 0.00 3.02
3858 5214 2.112297 GTGGCTGGGGTTCGTTCA 59.888 61.111 0.00 0.00 0.00 3.18
3859 5215 0.893727 ATTGTGGCTGGGGTTCGTTC 60.894 55.000 0.00 0.00 0.00 3.95
3860 5216 0.469144 AATTGTGGCTGGGGTTCGTT 60.469 50.000 0.00 0.00 0.00 3.85
3861 5217 0.893727 GAATTGTGGCTGGGGTTCGT 60.894 55.000 0.00 0.00 0.00 3.85
3862 5218 0.893270 TGAATTGTGGCTGGGGTTCG 60.893 55.000 0.00 0.00 0.00 3.95
3871 5227 3.733443 AAGTTCTGGTTGAATTGTGGC 57.267 42.857 0.00 0.00 36.99 5.01


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

AutoCloner maintained by Alex Coulton.