Multiple sequence alignment - TraesCS2D01G496200

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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 TraesCS2D01G496200 chr2D 100.000 3859 0 0 1 3859 592631596 592635454 0.000000e+00 7127.0
1 TraesCS2D01G496200 chr2D 90.792 467 24 11 4 463 533818969 533818515 1.190000e-169 606.0
2 TraesCS2D01G496200 chr2D 97.727 44 1 0 2882 2925 592634434 592634477 4.130000e-10 76.8
3 TraesCS2D01G496200 chr2D 97.727 44 1 0 2839 2882 592634477 592634520 4.130000e-10 76.8
4 TraesCS2D01G496200 chr2A 91.508 3309 176 63 1 3268 727188695 727191939 0.000000e+00 4457.0
5 TraesCS2D01G496200 chr2A 91.915 470 20 10 1 463 576662370 576661912 3.250000e-180 641.0
6 TraesCS2D01G496200 chr2A 90.977 266 21 3 3449 3712 727192036 727192300 4.740000e-94 355.0
7 TraesCS2D01G496200 chr2A 93.000 100 6 1 3299 3397 727191916 727192015 1.120000e-30 145.0
8 TraesCS2D01G496200 chr2A 97.727 44 1 0 2882 2925 727191508 727191551 4.130000e-10 76.8
9 TraesCS2D01G496200 chr2B 90.864 1423 96 18 1 1393 718600551 718601969 0.000000e+00 1877.0
10 TraesCS2D01G496200 chr2B 96.086 741 17 8 2530 3268 718603055 718603785 0.000000e+00 1197.0
11 TraesCS2D01G496200 chr2B 87.459 909 77 19 1376 2268 718638599 718639486 0.000000e+00 1013.0
12 TraesCS2D01G496200 chr2B 86.513 912 83 27 1648 2533 718602046 718602943 0.000000e+00 966.0
13 TraesCS2D01G496200 chr2B 91.667 468 3 3 3404 3859 718603922 718604365 1.970000e-172 616.0
14 TraesCS2D01G496200 chr2B 81.899 337 46 6 2886 3207 718650103 718650439 1.770000e-68 270.0
15 TraesCS2D01G496200 chr2B 89.268 205 4 2 3299 3489 718603762 718603962 1.390000e-59 241.0
16 TraesCS2D01G496200 chr2B 97.727 44 1 0 2839 2882 718603398 718603441 4.130000e-10 76.8
17 TraesCS2D01G496200 chr2B 91.111 45 0 1 3404 3448 718603963 718604003 1.500000e-04 58.4
18 TraesCS2D01G496200 chr1D 90.065 463 30 11 4 463 263327256 263326807 1.540000e-163 586.0
19 TraesCS2D01G496200 chrUn 89.149 470 31 12 1 463 25806943 25807399 5.600000e-158 568.0
20 TraesCS2D01G496200 chrUn 89.149 470 31 12 1 463 287200835 287201291 5.600000e-158 568.0
21 TraesCS2D01G496200 chrUn 89.126 469 31 12 1 462 213905932 213906387 2.010000e-157 566.0
22 TraesCS2D01G496200 chr1A 88.017 459 42 9 1 457 419804227 419804674 7.340000e-147 531.0
23 TraesCS2D01G496200 chr6B 88.164 414 31 11 1 410 441044101 441044500 9.700000e-131 477.0
24 TraesCS2D01G496200 chr3B 87.712 236 22 5 1 233 47159028 47158797 6.350000e-68 268.0
25 TraesCS2D01G496200 chr7D 88.525 61 7 0 1458 1518 387912899 387912839 1.490000e-09 75.0
26 TraesCS2D01G496200 chr7B 86.885 61 8 0 1458 1518 382607667 382607607 6.920000e-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 TraesCS2D01G496200 chr2D 592631596 592635454 3858 False 2426.866667 7127 98.484667 1 3859 3 chr2D.!!$F1 3858
1 TraesCS2D01G496200 chr2A 727188695 727192300 3605 False 1258.450000 4457 93.303000 1 3712 4 chr2A.!!$F1 3711
2 TraesCS2D01G496200 chr2B 718638599 718639486 887 False 1013.000000 1013 87.459000 1376 2268 1 chr2B.!!$F1 892
3 TraesCS2D01G496200 chr2B 718600551 718604365 3814 False 718.885714 1877 91.890857 1 3859 7 chr2B.!!$F3 3858

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
645 670 0.037590 CGAGGGGGTGATGGTGAAAA 59.962 55.0 0.0 0.0 0.00 2.29 F
1480 1561 0.399949 TCCCTGGTCAGTTGGTCACT 60.400 55.0 0.0 0.0 35.35 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1923 2011 1.079503 GTGTCGCTCTTGCCTAAAGG 58.920 55.0 0.0 0.0 36.46 3.11 R
3305 3534 0.630673 TGGGGATGGCATAGCAAACT 59.369 50.0 0.0 0.0 0.00 2.66 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
115 116 3.014856 GCGCCAGCGGATCTAAAC 58.985 61.111 14.63 0.00 40.19 2.01
116 117 1.813753 GCGCCAGCGGATCTAAACA 60.814 57.895 14.63 0.00 40.19 2.83
117 118 1.766143 GCGCCAGCGGATCTAAACAG 61.766 60.000 14.63 0.00 40.19 3.16
519 532 4.008933 GGTCGGGTGTCTGCTGCT 62.009 66.667 0.00 0.00 0.00 4.24
520 533 2.433318 GTCGGGTGTCTGCTGCTC 60.433 66.667 0.00 0.00 0.00 4.26
522 535 3.699894 CGGGTGTCTGCTGCTCCT 61.700 66.667 0.00 0.00 0.00 3.69
570 592 2.289072 GCTTTGCTTCCCCTCTTTTTCC 60.289 50.000 0.00 0.00 0.00 3.13
637 659 1.265454 GGTTCTGTCGAGGGGGTGAT 61.265 60.000 0.00 0.00 0.00 3.06
639 661 1.264749 TTCTGTCGAGGGGGTGATGG 61.265 60.000 0.00 0.00 0.00 3.51
645 670 0.037590 CGAGGGGGTGATGGTGAAAA 59.962 55.000 0.00 0.00 0.00 2.29
653 678 2.557452 GGTGATGGTGAAAAGACCCCAT 60.557 50.000 0.00 0.00 40.34 4.00
697 722 0.802607 GCTCGTGGACGGTTCAGATC 60.803 60.000 0.00 0.00 40.29 2.75
730 755 3.586543 TGGCCCATCACCAGTTCA 58.413 55.556 0.00 0.00 32.06 3.18
731 756 1.074775 TGGCCCATCACCAGTTCAC 59.925 57.895 0.00 0.00 32.06 3.18
732 757 1.678970 GGCCCATCACCAGTTCACC 60.679 63.158 0.00 0.00 0.00 4.02
733 758 1.074775 GCCCATCACCAGTTCACCA 59.925 57.895 0.00 0.00 0.00 4.17
741 766 2.357034 CAGTTCACCACCGTCCCG 60.357 66.667 0.00 0.00 0.00 5.14
743 768 2.663852 GTTCACCACCGTCCCGTG 60.664 66.667 0.00 0.00 0.00 4.94
776 819 2.435586 TCGTCTCGTCTCCCGTCC 60.436 66.667 0.00 0.00 37.94 4.79
885 942 1.473278 GCACTTCTCCTGCGTACTACT 59.527 52.381 0.00 0.00 0.00 2.57
887 944 2.008329 ACTTCTCCTGCGTACTACTCG 58.992 52.381 0.00 0.00 0.00 4.18
892 949 1.736126 TCCTGCGTACTACTCGTCTTG 59.264 52.381 0.00 0.00 0.00 3.02
893 950 1.467734 CCTGCGTACTACTCGTCTTGT 59.532 52.381 0.00 0.00 0.00 3.16
894 951 2.095364 CCTGCGTACTACTCGTCTTGTT 60.095 50.000 0.00 0.00 0.00 2.83
895 952 2.909244 CTGCGTACTACTCGTCTTGTTG 59.091 50.000 0.00 0.00 0.00 3.33
896 953 2.291465 TGCGTACTACTCGTCTTGTTGT 59.709 45.455 0.00 0.00 0.00 3.32
903 960 1.407979 ACTCGTCTTGTTGTCGTTCCT 59.592 47.619 0.00 0.00 0.00 3.36
920 977 1.449353 CTAGCCCTGCCATCTCACC 59.551 63.158 0.00 0.00 0.00 4.02
922 979 4.864334 GCCCTGCCATCTCACCCG 62.864 72.222 0.00 0.00 0.00 5.28
929 986 1.303309 GCCATCTCACCCGATTTCTG 58.697 55.000 0.00 0.00 0.00 3.02
934 991 1.202417 TCTCACCCGATTTCTGCGATC 60.202 52.381 0.00 0.00 0.00 3.69
965 1022 1.112950 CTAGTTCCTCTCGGTTCCCC 58.887 60.000 0.00 0.00 0.00 4.81
987 1044 0.740868 TCGATTTCTTGGGCGCAGAG 60.741 55.000 10.83 3.34 0.00 3.35
1077 1134 2.182030 GACTTCGAGCAGGACCCG 59.818 66.667 0.00 0.00 0.00 5.28
1169 1226 3.257393 GTTGCTCATCACATTCGTCTCT 58.743 45.455 0.00 0.00 0.00 3.10
1210 1269 1.013596 CGAACTGACTGTGTTTGCCA 58.986 50.000 0.00 0.00 0.00 4.92
1322 1381 1.068748 CATTCCTGTCAGCACTTGTGC 60.069 52.381 16.98 16.98 0.00 4.57
1365 1435 8.492673 TTCAAATGGTTACTCTGTGATATGTC 57.507 34.615 0.00 0.00 0.00 3.06
1412 1483 1.238439 ATGACGAACCAAAGTGGCTG 58.762 50.000 0.00 0.00 42.67 4.85
1414 1485 1.021968 GACGAACCAAAGTGGCTGTT 58.978 50.000 0.00 0.00 42.67 3.16
1415 1486 1.002792 GACGAACCAAAGTGGCTGTTC 60.003 52.381 0.00 0.00 42.67 3.18
1416 1487 1.308998 CGAACCAAAGTGGCTGTTCT 58.691 50.000 0.00 0.00 42.67 3.01
1417 1488 1.676006 CGAACCAAAGTGGCTGTTCTT 59.324 47.619 0.00 0.00 42.67 2.52
1418 1489 2.541588 CGAACCAAAGTGGCTGTTCTTG 60.542 50.000 0.00 0.00 42.67 3.02
1440 1521 6.865834 TGGTTCAAAATACCAGCCAATAAT 57.134 33.333 0.00 0.00 40.65 1.28
1467 1548 3.303351 AACTGGCTGATTAATCCCTGG 57.697 47.619 12.90 7.56 0.00 4.45
1473 1554 3.372025 GGCTGATTAATCCCTGGTCAGTT 60.372 47.826 12.90 0.00 38.75 3.16
1480 1561 0.399949 TCCCTGGTCAGTTGGTCACT 60.400 55.000 0.00 0.00 35.35 3.41
1481 1562 0.474184 CCCTGGTCAGTTGGTCACTT 59.526 55.000 0.00 0.00 30.92 3.16
1497 1581 5.041940 GGTCACTTAGTAGCCGATTAACTG 58.958 45.833 0.00 0.00 0.00 3.16
1515 1599 9.394477 GATTAACTGATTTATCGGCCAATTAAC 57.606 33.333 2.24 0.00 36.64 2.01
1518 1602 5.181690 TGATTTATCGGCCAATTAACTGC 57.818 39.130 2.24 0.00 0.00 4.40
1553 1638 1.958288 ATCCCCTATTGCTAGCCGAT 58.042 50.000 13.29 9.03 0.00 4.18
1561 1646 1.823899 TGCTAGCCGATCGAGCAGA 60.824 57.895 21.86 12.34 46.24 4.26
1565 1650 1.131504 CTAGCCGATCGAGCAGATACC 59.868 57.143 24.07 0.87 40.26 2.73
1578 1663 7.722363 TCGAGCAGATACCAGTTAATGATTTA 58.278 34.615 0.00 0.00 0.00 1.40
1610 1695 8.491152 CATTGGACTTCTTATATACTTCAAGCG 58.509 37.037 0.00 0.00 0.00 4.68
1611 1696 5.983720 TGGACTTCTTATATACTTCAAGCGC 59.016 40.000 0.00 0.00 0.00 5.92
1612 1697 5.983720 GGACTTCTTATATACTTCAAGCGCA 59.016 40.000 11.47 0.00 0.00 6.09
1674 1760 6.211515 GGCTGGATATTTGCTAAACTGATTG 58.788 40.000 0.00 0.00 0.00 2.67
1765 1853 4.547532 CGGATATTTTAGTGGAGAGACCG 58.452 47.826 0.00 0.00 42.61 4.79
1884 1972 9.689976 CACAGTTTTTATTTCATGTGGTGAATA 57.310 29.630 0.00 0.00 45.77 1.75
1899 1987 7.416817 TGTGGTGAATATATTTCTGCAATTCG 58.583 34.615 0.00 0.00 30.79 3.34
1912 2000 4.122776 CTGCAATTCGCTACCATAACTCT 58.877 43.478 0.00 0.00 43.06 3.24
1913 2001 4.119862 TGCAATTCGCTACCATAACTCTC 58.880 43.478 0.00 0.00 43.06 3.20
1917 2005 6.183360 GCAATTCGCTACCATAACTCTCTTTT 60.183 38.462 0.00 0.00 37.77 2.27
1942 2035 1.079503 CCTTTAGGCAAGAGCGACAC 58.920 55.000 0.00 0.00 43.41 3.67
2391 2501 3.988976 ACCACTAACTGCATGTCAGAT 57.011 42.857 19.64 12.57 45.72 2.90
2533 2646 7.334171 TGATGTTGTTGATGTCGAATCAAGTAT 59.666 33.333 17.60 11.90 38.54 2.12
2594 2821 2.428544 TGGTTTGCCACTGTTGTACT 57.571 45.000 0.00 0.00 40.46 2.73
2595 2822 2.020720 TGGTTTGCCACTGTTGTACTG 58.979 47.619 0.00 0.00 40.46 2.74
2596 2823 2.021457 GGTTTGCCACTGTTGTACTGT 58.979 47.619 0.00 0.00 34.09 3.55
2597 2824 3.207778 GGTTTGCCACTGTTGTACTGTA 58.792 45.455 0.00 0.00 34.09 2.74
2598 2825 3.250040 GGTTTGCCACTGTTGTACTGTAG 59.750 47.826 0.00 0.00 34.09 2.74
3042 3270 8.517878 TGAGAAATTTCTAGCTTTCAAAGATGG 58.482 33.333 20.51 0.00 37.73 3.51
3262 3491 7.533289 AGGACTTAGGATAGAGTTTGCTATC 57.467 40.000 0.00 0.00 43.80 2.08
3263 3492 7.302184 AGGACTTAGGATAGAGTTTGCTATCT 58.698 38.462 10.24 0.00 43.93 1.98
3264 3493 8.449625 AGGACTTAGGATAGAGTTTGCTATCTA 58.550 37.037 10.24 0.00 43.93 1.98
3265 3494 9.250246 GGACTTAGGATAGAGTTTGCTATCTAT 57.750 37.037 10.24 0.00 43.93 1.98
3311 3540 6.664428 AAGGATAGAGAGGATAGAGTTTGC 57.336 41.667 0.00 0.00 0.00 3.68
3312 3541 5.964288 AGGATAGAGAGGATAGAGTTTGCT 58.036 41.667 0.00 0.00 0.00 3.91
3313 3542 7.097623 AGGATAGAGAGGATAGAGTTTGCTA 57.902 40.000 0.00 0.00 0.00 3.49
3314 3543 7.708624 AGGATAGAGAGGATAGAGTTTGCTAT 58.291 38.462 0.00 0.00 33.91 2.97
3332 3561 4.512914 GCCATCCCCAGCCCTGTC 62.513 72.222 0.00 0.00 0.00 3.51
3431 3675 1.283905 CTTCCCCATCCGTTTAACCCT 59.716 52.381 0.00 0.00 0.00 4.34
3432 3676 2.267160 TCCCCATCCGTTTAACCCTA 57.733 50.000 0.00 0.00 0.00 3.53
3433 3677 2.560080 TCCCCATCCGTTTAACCCTAA 58.440 47.619 0.00 0.00 0.00 2.69
3434 3678 2.918266 TCCCCATCCGTTTAACCCTAAA 59.082 45.455 0.00 0.00 0.00 1.85
3467 3748 3.502875 GCCCCTCTTCCCCATCCC 61.503 72.222 0.00 0.00 0.00 3.85
3596 3877 3.985279 TCAACTTACATGTACAGACGCAC 59.015 43.478 4.68 0.00 0.00 5.34
3674 3957 5.182001 AGCTGTAAGAAATAGTTGCCACTTG 59.818 40.000 0.00 0.00 34.07 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 115 3.077556 CCCTGGCCGTAGCTCTGT 61.078 66.667 0.00 0.00 39.73 3.41
115 116 4.537433 GCCCTGGCCGTAGCTCTG 62.537 72.222 0.00 0.00 39.73 3.35
515 528 2.508887 GTCGCAGCAGAGGAGCAG 60.509 66.667 0.00 0.00 36.85 4.24
516 529 4.426112 CGTCGCAGCAGAGGAGCA 62.426 66.667 0.00 0.00 36.85 4.26
542 564 0.597377 GGGGAAGCAAAGCACAAACG 60.597 55.000 0.00 0.00 0.00 3.60
543 565 0.752658 AGGGGAAGCAAAGCACAAAC 59.247 50.000 0.00 0.00 0.00 2.93
544 566 1.039856 GAGGGGAAGCAAAGCACAAA 58.960 50.000 0.00 0.00 0.00 2.83
545 567 0.185901 AGAGGGGAAGCAAAGCACAA 59.814 50.000 0.00 0.00 0.00 3.33
570 592 2.103042 CGCCTCCGCAAGAAAGGAG 61.103 63.158 4.61 4.61 43.96 3.69
637 659 0.037590 CGGATGGGGTCTTTTCACCA 59.962 55.000 0.00 0.00 45.53 4.17
639 661 1.644786 CGCGGATGGGGTCTTTTCAC 61.645 60.000 0.00 0.00 0.00 3.18
697 722 1.221840 CCAGGATCCACAGGGTTCG 59.778 63.158 15.82 0.00 34.29 3.95
703 728 1.150081 GATGGGCCAGGATCCACAG 59.850 63.158 15.82 2.68 35.67 3.66
878 935 4.139183 ACGACAACAAGACGAGTAGTAC 57.861 45.455 0.00 0.00 38.73 2.73
883 940 1.407979 AGGAACGACAACAAGACGAGT 59.592 47.619 0.00 0.00 38.73 4.18
885 942 2.606308 GCTAGGAACGACAACAAGACGA 60.606 50.000 0.00 0.00 38.73 4.20
887 944 2.067013 GGCTAGGAACGACAACAAGAC 58.933 52.381 0.00 0.00 0.00 3.01
892 949 1.019805 GCAGGGCTAGGAACGACAAC 61.020 60.000 0.00 0.00 0.00 3.32
893 950 1.295423 GCAGGGCTAGGAACGACAA 59.705 57.895 0.00 0.00 0.00 3.18
894 951 2.656069 GGCAGGGCTAGGAACGACA 61.656 63.158 0.00 0.00 0.00 4.35
895 952 1.972660 ATGGCAGGGCTAGGAACGAC 61.973 60.000 0.00 0.00 0.00 4.34
896 953 1.686325 GATGGCAGGGCTAGGAACGA 61.686 60.000 0.00 0.00 0.00 3.85
903 960 2.072487 GGGTGAGATGGCAGGGCTA 61.072 63.158 0.00 0.00 0.00 3.93
920 977 2.355756 ACATTTGGATCGCAGAAATCGG 59.644 45.455 0.00 0.00 43.58 4.18
922 979 5.273944 GGTTACATTTGGATCGCAGAAATC 58.726 41.667 0.00 0.00 43.58 2.17
929 986 3.805207 ACTAGGGTTACATTTGGATCGC 58.195 45.455 0.00 0.00 0.00 4.58
934 991 5.429130 GAGAGGAACTAGGGTTACATTTGG 58.571 45.833 0.00 0.00 41.55 3.28
965 1022 0.740868 TGCGCCCAAGAAATCGAGAG 60.741 55.000 4.18 0.00 0.00 3.20
987 1044 1.967319 TTGCCATCTCGCCTTATTCC 58.033 50.000 0.00 0.00 0.00 3.01
1210 1269 4.133820 CACATCCGTCTAGAGATCAGAGT 58.866 47.826 0.00 0.00 0.00 3.24
1322 1381 7.964559 CCATTTGAAGTACATTACACATCACTG 59.035 37.037 0.00 0.00 0.00 3.66
1331 1398 9.216117 ACAGAGTAACCATTTGAAGTACATTAC 57.784 33.333 0.00 0.00 0.00 1.89
1365 1435 7.534085 TTACGACAGTAGCCTTAATCATTTG 57.466 36.000 0.00 0.00 33.87 2.32
1412 1483 4.038642 TGGCTGGTATTTTGAACCAAGAAC 59.961 41.667 0.00 0.00 46.14 3.01
1414 1485 3.838565 TGGCTGGTATTTTGAACCAAGA 58.161 40.909 0.00 0.00 46.14 3.02
1415 1486 4.599047 TTGGCTGGTATTTTGAACCAAG 57.401 40.909 0.00 0.00 46.14 3.61
1416 1487 6.672266 TTATTGGCTGGTATTTTGAACCAA 57.328 33.333 0.00 0.00 46.14 3.67
1417 1488 6.865834 ATTATTGGCTGGTATTTTGAACCA 57.134 33.333 0.00 0.00 44.75 3.67
1418 1489 7.327214 TGAATTATTGGCTGGTATTTTGAACC 58.673 34.615 0.00 0.00 37.53 3.62
1440 1521 5.885912 GGGATTAATCAGCCAGTTAACTGAA 59.114 40.000 32.50 18.78 45.49 3.02
1467 1548 3.586892 GGCTACTAAGTGACCAACTGAC 58.413 50.000 0.00 0.00 39.81 3.51
1473 1554 4.708421 AGTTAATCGGCTACTAAGTGACCA 59.292 41.667 0.00 0.00 0.00 4.02
1480 1561 7.811236 CCGATAAATCAGTTAATCGGCTACTAA 59.189 37.037 9.40 0.00 43.32 2.24
1481 1562 7.310664 CCGATAAATCAGTTAATCGGCTACTA 58.689 38.462 9.40 0.00 43.32 1.82
1497 1581 4.546570 GGCAGTTAATTGGCCGATAAATC 58.453 43.478 12.84 0.00 38.04 2.17
1515 1599 2.245159 TTCATAGGCGAATCAGGCAG 57.755 50.000 0.00 0.00 39.37 4.85
1553 1638 5.791336 ATCATTAACTGGTATCTGCTCGA 57.209 39.130 0.00 0.00 0.00 4.04
1565 1650 9.559958 GTCCAATGTTCAGTAAATCATTAACTG 57.440 33.333 0.00 0.00 0.00 3.16
1606 1691 1.308998 AACAGTACTTTGCTGCGCTT 58.691 45.000 9.73 0.00 37.47 4.68
1610 1695 9.065871 CAAATAAGATAAACAGTACTTTGCTGC 57.934 33.333 0.00 0.00 37.47 5.25
1639 1725 5.132502 CAAATATCCAGCCCACTACATCAA 58.867 41.667 0.00 0.00 0.00 2.57
1640 1726 4.717877 CAAATATCCAGCCCACTACATCA 58.282 43.478 0.00 0.00 0.00 3.07
1641 1727 3.503748 GCAAATATCCAGCCCACTACATC 59.496 47.826 0.00 0.00 0.00 3.06
1642 1728 3.139025 AGCAAATATCCAGCCCACTACAT 59.861 43.478 0.00 0.00 0.00 2.29
1643 1729 2.509548 AGCAAATATCCAGCCCACTACA 59.490 45.455 0.00 0.00 0.00 2.74
1765 1853 1.227380 CCTGCGGGCATACTGAGAC 60.227 63.158 0.00 0.00 0.00 3.36
1923 2011 1.079503 GTGTCGCTCTTGCCTAAAGG 58.920 55.000 0.00 0.00 36.46 3.11
1942 2035 2.419851 GGCTCTCAAGGAGGTGAATCAG 60.420 54.545 0.00 0.00 42.08 2.90
2364 2474 4.905429 ACATGCAGTTAGTGGTATGAACA 58.095 39.130 0.00 0.00 32.40 3.18
2366 2476 5.046663 TCTGACATGCAGTTAGTGGTATGAA 60.047 40.000 14.21 0.00 45.14 2.57
2391 2501 3.428532 ACTAACCCGAGCTTTCTCTACA 58.571 45.455 0.00 0.00 37.19 2.74
2594 2821 3.260632 TGCCTGCTCACAAATACTCTACA 59.739 43.478 0.00 0.00 0.00 2.74
2595 2822 3.619038 GTGCCTGCTCACAAATACTCTAC 59.381 47.826 0.00 0.00 36.97 2.59
2596 2823 3.515502 AGTGCCTGCTCACAAATACTCTA 59.484 43.478 6.99 0.00 39.35 2.43
2597 2824 2.304180 AGTGCCTGCTCACAAATACTCT 59.696 45.455 6.99 0.00 39.35 3.24
2598 2825 2.417933 CAGTGCCTGCTCACAAATACTC 59.582 50.000 6.99 0.00 39.35 2.59
3042 3270 1.600957 AGCACACGCAGATGCATAATC 59.399 47.619 0.00 0.00 43.45 1.75
3285 3514 7.990314 GCAAACTCTATCCTCTCTATCCTTTTT 59.010 37.037 0.00 0.00 0.00 1.94
3286 3515 7.346960 AGCAAACTCTATCCTCTCTATCCTTTT 59.653 37.037 0.00 0.00 0.00 2.27
3287 3516 6.843861 AGCAAACTCTATCCTCTCTATCCTTT 59.156 38.462 0.00 0.00 0.00 3.11
3288 3517 6.381250 AGCAAACTCTATCCTCTCTATCCTT 58.619 40.000 0.00 0.00 0.00 3.36
3289 3518 5.964288 AGCAAACTCTATCCTCTCTATCCT 58.036 41.667 0.00 0.00 0.00 3.24
3290 3519 7.630513 GCATAGCAAACTCTATCCTCTCTATCC 60.631 44.444 0.00 0.00 0.00 2.59
3291 3520 7.257722 GCATAGCAAACTCTATCCTCTCTATC 58.742 42.308 0.00 0.00 0.00 2.08
3292 3521 6.154363 GGCATAGCAAACTCTATCCTCTCTAT 59.846 42.308 0.00 0.00 0.00 1.98
3293 3522 5.478679 GGCATAGCAAACTCTATCCTCTCTA 59.521 44.000 0.00 0.00 0.00 2.43
3294 3523 4.283212 GGCATAGCAAACTCTATCCTCTCT 59.717 45.833 0.00 0.00 0.00 3.10
3295 3524 4.039730 TGGCATAGCAAACTCTATCCTCTC 59.960 45.833 0.00 0.00 0.00 3.20
3296 3525 3.969976 TGGCATAGCAAACTCTATCCTCT 59.030 43.478 0.00 0.00 0.00 3.69
3297 3526 4.342862 TGGCATAGCAAACTCTATCCTC 57.657 45.455 0.00 0.00 0.00 3.71
3298 3527 4.263243 GGATGGCATAGCAAACTCTATCCT 60.263 45.833 0.00 0.00 0.00 3.24
3299 3528 4.006319 GGATGGCATAGCAAACTCTATCC 58.994 47.826 0.00 0.00 0.00 2.59
3300 3529 4.006319 GGGATGGCATAGCAAACTCTATC 58.994 47.826 0.00 0.00 0.00 2.08
3301 3530 3.245052 GGGGATGGCATAGCAAACTCTAT 60.245 47.826 0.00 0.00 0.00 1.98
3302 3531 2.106511 GGGGATGGCATAGCAAACTCTA 59.893 50.000 0.00 0.00 0.00 2.43
3303 3532 1.133668 GGGGATGGCATAGCAAACTCT 60.134 52.381 0.00 0.00 0.00 3.24
3304 3533 1.322442 GGGGATGGCATAGCAAACTC 58.678 55.000 0.00 0.00 0.00 3.01
3305 3534 0.630673 TGGGGATGGCATAGCAAACT 59.369 50.000 0.00 0.00 0.00 2.66
3306 3535 1.035139 CTGGGGATGGCATAGCAAAC 58.965 55.000 0.00 0.00 0.00 2.93
3307 3536 0.756442 GCTGGGGATGGCATAGCAAA 60.756 55.000 13.67 0.00 34.64 3.68
3308 3537 1.152694 GCTGGGGATGGCATAGCAA 60.153 57.895 13.67 0.00 34.64 3.91
3309 3538 2.517414 GCTGGGGATGGCATAGCA 59.483 61.111 13.67 0.00 34.64 3.49
3310 3539 2.282745 GGCTGGGGATGGCATAGC 60.283 66.667 10.78 10.78 0.00 2.97
3311 3540 2.158810 AGGGCTGGGGATGGCATAG 61.159 63.158 0.00 0.00 0.00 2.23
3312 3541 2.038438 AGGGCTGGGGATGGCATA 60.038 61.111 0.00 0.00 0.00 3.14
3313 3542 3.829226 CAGGGCTGGGGATGGCAT 61.829 66.667 0.00 0.00 0.00 4.40
3431 3675 1.892474 GCAGGTTGATGCAAGGGTTTA 59.108 47.619 0.00 0.00 45.77 2.01
3432 3676 0.681175 GCAGGTTGATGCAAGGGTTT 59.319 50.000 0.00 0.00 45.77 3.27
3433 3677 2.354902 GCAGGTTGATGCAAGGGTT 58.645 52.632 0.00 0.00 45.77 4.11
3434 3678 4.102113 GCAGGTTGATGCAAGGGT 57.898 55.556 0.00 0.00 45.77 4.34
3674 3957 3.181458 TGGTCTGGACTCTTTTGGTGTAC 60.181 47.826 0.67 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.