Multiple sequence alignment - TraesCS1D01G354700

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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 TraesCS1D01G354700 chr1D 100.000 2591 0 0 1 2591 439725615 439728205 0.000000e+00 4785.0
1 TraesCS1D01G354700 chr1D 84.971 692 74 16 1085 1755 439733298 439733980 0.000000e+00 675.0
2 TraesCS1D01G354700 chr1D 80.975 636 78 28 1084 1678 439671308 439671941 5.050000e-127 464.0
3 TraesCS1D01G354700 chr1D 81.455 275 42 5 169 442 452466012 452466278 1.560000e-52 217.0
4 TraesCS1D01G354700 chr1D 89.286 112 6 5 844 953 439671085 439671192 4.500000e-28 135.0
5 TraesCS1D01G354700 chr1B 89.744 1131 61 24 624 1746 596999173 597000256 0.000000e+00 1395.0
6 TraesCS1D01G354700 chr1B 94.024 820 48 1 1772 2591 597001660 597002478 0.000000e+00 1242.0
7 TraesCS1D01G354700 chr1B 84.593 688 82 13 1085 1755 597068750 597069430 0.000000e+00 662.0
8 TraesCS1D01G354700 chr1B 80.987 689 83 29 1089 1731 596929263 596929949 1.070000e-138 503.0
9 TraesCS1D01G354700 chr1B 90.683 322 23 4 3 323 596946219 596946534 3.080000e-114 422.0
10 TraesCS1D01G354700 chr1B 90.370 270 21 4 320 588 596998907 596999172 1.480000e-92 350.0
11 TraesCS1D01G354700 chr1A 82.365 964 101 34 846 1755 538783876 538782928 0.000000e+00 774.0
12 TraesCS1D01G354700 chr2B 82.543 527 77 8 15 537 704717039 704716524 1.410000e-122 449.0
13 TraesCS1D01G354700 chr2B 82.851 484 71 11 15 493 510351450 510350974 8.570000e-115 424.0
14 TraesCS1D01G354700 chr5A 84.120 466 63 9 36 495 287149508 287149048 8.510000e-120 440.0
15 TraesCS1D01G354700 chr5A 87.952 83 6 3 570 651 315267699 315267778 7.630000e-16 95.3
16 TraesCS1D01G354700 chr6D 81.801 544 74 19 16 538 269235419 269234880 1.420000e-117 433.0
17 TraesCS1D01G354700 chr5B 81.149 435 66 13 45 469 545615202 545615630 4.130000e-88 335.0
18 TraesCS1D01G354700 chr2D 79.381 485 88 12 15 493 606397322 606396844 5.340000e-87 331.0
19 TraesCS1D01G354700 chr2D 83.553 152 22 3 2171 2321 354365741 354365890 3.480000e-29 139.0
20 TraesCS1D01G354700 chr3B 85.660 265 35 2 83 345 823433461 823433198 2.540000e-70 276.0
21 TraesCS1D01G354700 chr3B 79.532 171 35 0 2151 2321 454375812 454375642 3.500000e-24 122.0
22 TraesCS1D01G354700 chr3B 83.486 109 9 8 561 664 739228802 739228906 2.750000e-15 93.5
23 TraesCS1D01G354700 chr5D 77.157 394 81 9 16 402 48035963 48036354 1.210000e-53 220.0
24 TraesCS1D01G354700 chr4D 79.769 173 35 0 2151 2323 13838115 13838287 2.710000e-25 126.0
25 TraesCS1D01G354700 chr4D 79.769 173 35 0 2151 2323 13927590 13927762 2.710000e-25 126.0
26 TraesCS1D01G354700 chr4D 79.532 171 35 0 2151 2321 13743363 13743533 3.500000e-24 122.0
27 TraesCS1D01G354700 chr4D 86.364 110 15 0 2216 2325 256033679 256033788 1.260000e-23 121.0
28 TraesCS1D01G354700 chr4B 79.191 173 36 0 2151 2323 24537776 24537948 1.260000e-23 121.0
29 TraesCS1D01G354700 chr4B 86.916 107 12 2 2216 2321 334462229 334462124 4.530000e-23 119.0
30 TraesCS1D01G354700 chr7B 91.358 81 3 3 562 641 290078015 290078092 9.800000e-20 108.0
31 TraesCS1D01G354700 chr7B 86.585 82 7 3 570 650 262000003 261999925 1.280000e-13 87.9
32 TraesCS1D01G354700 chr7B 85.714 84 8 2 570 652 261999930 262000010 4.590000e-13 86.1
33 TraesCS1D01G354700 chr7A 93.151 73 1 3 570 641 353917946 353917877 1.270000e-18 104.0
34 TraesCS1D01G354700 chr7D 88.750 80 4 4 563 641 305134828 305134753 2.750000e-15 93.5
35 TraesCS1D01G354700 chr7D 83.146 89 11 3 564 651 274857996 274858081 7.690000e-11 78.7
36 TraesCS1D01G354700 chr2A 86.364 66 5 3 578 642 658911381 658911443 4.630000e-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 TraesCS1D01G354700 chr1D 439725615 439728205 2590 False 4785.000000 4785 100.000000 1 2591 1 chr1D.!!$F1 2590
1 TraesCS1D01G354700 chr1D 439733298 439733980 682 False 675.000000 675 84.971000 1085 1755 1 chr1D.!!$F2 670
2 TraesCS1D01G354700 chr1D 439671085 439671941 856 False 299.500000 464 85.130500 844 1678 2 chr1D.!!$F4 834
3 TraesCS1D01G354700 chr1B 596998907 597002478 3571 False 995.666667 1395 91.379333 320 2591 3 chr1B.!!$F4 2271
4 TraesCS1D01G354700 chr1B 597068750 597069430 680 False 662.000000 662 84.593000 1085 1755 1 chr1B.!!$F3 670
5 TraesCS1D01G354700 chr1B 596929263 596929949 686 False 503.000000 503 80.987000 1089 1731 1 chr1B.!!$F1 642
6 TraesCS1D01G354700 chr1A 538782928 538783876 948 True 774.000000 774 82.365000 846 1755 1 chr1A.!!$R1 909
7 TraesCS1D01G354700 chr2B 704716524 704717039 515 True 449.000000 449 82.543000 15 537 1 chr2B.!!$R2 522
8 TraesCS1D01G354700 chr6D 269234880 269235419 539 True 433.000000 433 81.801000 16 538 1 chr6D.!!$R1 522

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
85 87 0.244450 CGTGGTTAGTTCGGTGCCTA 59.756 55.0 0.0 0.0 0.0 3.93 F
352 371 0.325296 TCCAAGTATGAGGAGGCGGT 60.325 55.0 0.0 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1046 1079 2.202730 GAGAGAGGAGCACTGCGC 60.203 66.667 0.0 0.0 42.91 6.09 R
2199 3702 1.017701 GCCCTTCTGTACCGTTTCCG 61.018 60.000 0.0 0.0 0.00 4.30 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
83 85 1.005867 TCGTGGTTAGTTCGGTGCC 60.006 57.895 0.00 0.00 0.00 5.01
84 86 1.005394 CGTGGTTAGTTCGGTGCCT 60.005 57.895 0.00 0.00 0.00 4.75
85 87 0.244450 CGTGGTTAGTTCGGTGCCTA 59.756 55.000 0.00 0.00 0.00 3.93
91 93 3.555586 GGTTAGTTCGGTGCCTAGTTTCA 60.556 47.826 0.00 0.00 0.00 2.69
97 99 1.131126 CGGTGCCTAGTTTCAAGCATG 59.869 52.381 0.00 0.00 37.60 4.06
159 164 2.699954 AGGAGTGAGCCATTTTGTACG 58.300 47.619 0.00 0.00 0.00 3.67
163 168 3.998341 GAGTGAGCCATTTTGTACGGTTA 59.002 43.478 0.00 0.00 0.00 2.85
196 201 5.599359 TCGTCGCAATTTGAAACTCATTA 57.401 34.783 0.00 0.00 0.00 1.90
242 247 7.125507 AGGATGGATGCAAATTTTGGTATTGTA 59.874 33.333 10.96 0.00 0.00 2.41
245 250 8.316640 TGGATGCAAATTTTGGTATTGTAAAC 57.683 30.769 10.96 0.00 0.00 2.01
295 300 6.204688 TGAGAAAATTTGCTAGATGTTCGTGT 59.795 34.615 0.00 0.00 0.00 4.49
312 317 6.820152 TGTTCGTGTACTACTTGCTAGAGATA 59.180 38.462 1.04 0.00 0.00 1.98
317 336 7.011202 CGTGTACTACTTGCTAGAGATAAGACA 59.989 40.741 1.04 0.00 0.00 3.41
327 346 5.825679 GCTAGAGATAAGACAAGAGAGGACA 59.174 44.000 0.00 0.00 0.00 4.02
347 366 4.899502 ACACAAAGTCCAAGTATGAGGAG 58.100 43.478 0.00 0.00 33.85 3.69
352 371 0.325296 TCCAAGTATGAGGAGGCGGT 60.325 55.000 0.00 0.00 0.00 5.68
406 426 7.119846 GTCAATAGAGAAAGCAACAATGTAGGT 59.880 37.037 0.00 0.00 0.00 3.08
436 456 2.509052 TAGCGAACTCATTGATCGGG 57.491 50.000 10.68 0.00 40.60 5.14
449 469 1.686325 GATCGGGCTAGTGGGAGCAA 61.686 60.000 0.00 0.00 44.76 3.91
532 552 6.817184 AGCTTCTCTTAGCGAATAATTGGTA 58.183 36.000 0.00 0.00 45.82 3.25
543 563 8.732746 AGCGAATAATTGGTAAAGTAGATGTT 57.267 30.769 0.00 0.00 0.00 2.71
588 608 7.938140 ACTTTCTCCGATCCAAATTAATTGA 57.062 32.000 0.39 0.00 41.85 2.57
590 610 5.984233 TCTCCGATCCAAATTAATTGACG 57.016 39.130 0.39 4.11 41.85 4.35
591 611 4.272504 TCTCCGATCCAAATTAATTGACGC 59.727 41.667 0.39 0.00 41.85 5.19
592 612 3.942115 TCCGATCCAAATTAATTGACGCA 59.058 39.130 0.39 0.00 41.85 5.24
593 613 4.396478 TCCGATCCAAATTAATTGACGCAA 59.604 37.500 0.39 0.00 41.85 4.85
594 614 4.499040 CCGATCCAAATTAATTGACGCAAC 59.501 41.667 0.39 0.00 41.85 4.17
595 615 5.331902 CGATCCAAATTAATTGACGCAACT 58.668 37.500 0.39 0.00 41.85 3.16
596 616 5.799936 CGATCCAAATTAATTGACGCAACTT 59.200 36.000 0.39 0.00 41.85 2.66
597 617 6.307800 CGATCCAAATTAATTGACGCAACTTT 59.692 34.615 0.39 0.00 41.85 2.66
598 618 7.483375 CGATCCAAATTAATTGACGCAACTTTA 59.517 33.333 0.39 0.00 41.85 1.85
599 619 8.687824 ATCCAAATTAATTGACGCAACTTTAG 57.312 30.769 0.39 0.00 41.85 1.85
600 620 7.653647 TCCAAATTAATTGACGCAACTTTAGT 58.346 30.769 0.39 0.00 41.85 2.24
601 621 8.784994 TCCAAATTAATTGACGCAACTTTAGTA 58.215 29.630 0.39 0.00 41.85 1.82
602 622 8.846607 CCAAATTAATTGACGCAACTTTAGTAC 58.153 33.333 0.39 0.00 41.85 2.73
603 623 9.388346 CAAATTAATTGACGCAACTTTAGTACA 57.612 29.630 0.39 0.00 41.85 2.90
604 624 9.953697 AAATTAATTGACGCAACTTTAGTACAA 57.046 25.926 0.39 0.00 0.00 2.41
605 625 8.944212 ATTAATTGACGCAACTTTAGTACAAC 57.056 30.769 0.00 0.00 0.00 3.32
606 626 5.994887 ATTGACGCAACTTTAGTACAACA 57.005 34.783 0.00 0.00 0.00 3.33
607 627 5.798015 TTGACGCAACTTTAGTACAACAA 57.202 34.783 0.00 0.00 0.00 2.83
608 628 5.146482 TGACGCAACTTTAGTACAACAAC 57.854 39.130 0.00 0.00 0.00 3.32
609 629 4.871557 TGACGCAACTTTAGTACAACAACT 59.128 37.500 0.00 0.00 0.00 3.16
610 630 5.352016 TGACGCAACTTTAGTACAACAACTT 59.648 36.000 0.00 0.00 0.00 2.66
611 631 6.128227 TGACGCAACTTTAGTACAACAACTTT 60.128 34.615 0.00 0.00 0.00 2.66
612 632 6.025280 ACGCAACTTTAGTACAACAACTTTG 58.975 36.000 0.00 0.00 0.00 2.77
613 633 6.025280 CGCAACTTTAGTACAACAACTTTGT 58.975 36.000 0.00 0.00 44.72 2.83
614 634 7.148440 ACGCAACTTTAGTACAACAACTTTGTA 60.148 33.333 0.00 0.00 41.31 2.41
624 644 8.319225 GTACAACAACTTTGTACTAAAACTGC 57.681 34.615 16.51 0.00 46.69 4.40
625 645 6.025280 ACAACAACTTTGTACTAAAACTGCG 58.975 36.000 0.00 0.00 41.31 5.18
641 661 5.895636 AACTGCGTCAATTAATTGGATCA 57.104 34.783 24.40 17.76 38.30 2.92
666 686 5.047092 TGGGGAGTAGTTAAGTTTAAGTCGG 60.047 44.000 0.00 0.00 0.00 4.79
667 687 5.047021 GGGGAGTAGTTAAGTTTAAGTCGGT 60.047 44.000 0.00 0.00 0.00 4.69
670 690 5.233225 AGTAGTTAAGTTTAAGTCGGTGGC 58.767 41.667 0.00 0.00 0.00 5.01
674 694 0.475044 AGTTTAAGTCGGTGGCCCAA 59.525 50.000 0.00 0.00 0.00 4.12
687 707 4.940654 CGGTGGCCCAAAAATAAATGAAAT 59.059 37.500 0.00 0.00 0.00 2.17
714 735 9.567848 TTGACAAAACAATTACTCTTGAACTTC 57.432 29.630 0.00 0.00 0.00 3.01
717 738 9.353999 ACAAAACAATTACTCTTGAACTTCAAC 57.646 29.630 0.00 0.00 32.21 3.18
720 741 6.053005 ACAATTACTCTTGAACTTCAACGGA 58.947 36.000 0.00 0.00 32.21 4.69
733 754 5.475719 ACTTCAACGGATCGATTAGAAACA 58.524 37.500 0.00 0.00 0.00 2.83
737 758 6.623486 TCAACGGATCGATTAGAAACAACTA 58.377 36.000 0.00 0.00 0.00 2.24
738 759 7.262772 TCAACGGATCGATTAGAAACAACTAT 58.737 34.615 0.00 0.00 0.00 2.12
739 760 7.762615 TCAACGGATCGATTAGAAACAACTATT 59.237 33.333 0.00 0.00 0.00 1.73
740 761 8.388103 CAACGGATCGATTAGAAACAACTATTT 58.612 33.333 0.00 0.00 0.00 1.40
741 762 8.488651 ACGGATCGATTAGAAACAACTATTTT 57.511 30.769 0.00 0.00 0.00 1.82
796 817 6.927294 ACGGCTTCTAAATTTTAGGAGATG 57.073 37.500 23.23 16.97 0.00 2.90
817 838 6.437162 AGATGGATTAGAGGATGCTCTAAGAC 59.563 42.308 31.89 26.95 45.55 3.01
865 886 9.509956 ACAAGTAGTACTATAAATTTGCAACCA 57.490 29.630 5.75 0.00 0.00 3.67
905 926 5.334646 CGCAACGTATCATTCCTAGCTACTA 60.335 44.000 0.00 0.00 0.00 1.82
906 927 5.857517 GCAACGTATCATTCCTAGCTACTAC 59.142 44.000 0.00 0.00 0.00 2.73
907 928 6.294065 GCAACGTATCATTCCTAGCTACTACT 60.294 42.308 0.00 0.00 0.00 2.57
908 929 7.649973 CAACGTATCATTCCTAGCTACTACTT 58.350 38.462 0.00 0.00 0.00 2.24
948 970 1.641577 CTAGCTACGTTTGTCTGCCC 58.358 55.000 0.00 0.00 0.00 5.36
1046 1079 2.354604 GCCTTCTTCTGTTCTCCCTCTG 60.355 54.545 0.00 0.00 0.00 3.35
1068 1101 2.051518 AGTGCTCCTCTCTCTGCCG 61.052 63.158 0.00 0.00 0.00 5.69
1252 1345 2.149578 CCTTCATTCTGGCATCGATCC 58.850 52.381 0.00 0.59 0.00 3.36
1261 1354 4.717877 TCTGGCATCGATCCAAACATATT 58.282 39.130 14.75 0.00 32.41 1.28
1558 1656 1.344942 CTCCGTCGGCAACTTCTTCG 61.345 60.000 6.34 0.00 0.00 3.79
1594 1692 2.026822 CCCAACAACTGCTACTGATCCT 60.027 50.000 0.00 0.00 0.00 3.24
1629 1738 4.927425 TGTGCTCGTAGGACTTGAATAAAC 59.073 41.667 7.71 0.00 37.46 2.01
1665 1781 3.603532 TCAGCTGTTGGAGATGCTTTAG 58.396 45.455 14.67 0.00 38.04 1.85
1692 1814 3.446570 GGGGATGTGCTGTGCTGC 61.447 66.667 0.00 0.00 0.00 5.25
1710 1835 9.202273 CTGTGCTGCAAGGTTTATTTAAATTTA 57.798 29.630 2.77 0.00 0.00 1.40
1732 1857 2.297701 TCTCTTGTTGCAGTGGTTTCC 58.702 47.619 0.00 0.00 0.00 3.13
1766 2167 3.855689 ATTACCAACAACTGCATGCTC 57.144 42.857 20.33 0.00 0.00 4.26
1859 3362 7.283329 AGATGATCATTCAAGGTAGGTTTACC 58.717 38.462 10.14 0.00 40.66 2.85
1942 3445 5.534654 CCTGTTTGAATAAGAAACTGGGTCA 59.465 40.000 11.45 0.00 43.48 4.02
1965 3468 8.347771 GTCATGCTTTTATATTTGCTGAGATCA 58.652 33.333 0.00 0.00 0.00 2.92
1966 3469 8.905850 TCATGCTTTTATATTTGCTGAGATCAA 58.094 29.630 0.00 0.00 0.00 2.57
1969 3472 7.148035 TGCTTTTATATTTGCTGAGATCAAGCA 60.148 33.333 16.64 16.64 39.42 3.91
1996 3499 1.836802 TGCTTTTTGACCCAAAAGCCT 59.163 42.857 22.00 0.00 42.91 4.58
2011 3514 6.293571 CCCAAAAGCCTGCAAATCTTTTTAAG 60.294 38.462 14.02 8.59 37.78 1.85
2064 3567 2.159268 GCTCCCGAACTAGGTAAGTGAC 60.159 54.545 0.00 0.00 38.88 3.67
2068 3571 3.572584 CCGAACTAGGTAAGTGACACAC 58.427 50.000 8.59 0.00 38.88 3.82
2084 3587 2.890311 ACACACACTGAGAGAGGAAGAG 59.110 50.000 0.00 0.00 0.00 2.85
2127 3630 1.823169 ATTGCGTAGGTCCCACACGT 61.823 55.000 10.79 0.00 37.95 4.49
2147 3650 3.193691 CGTAAGTGACATTGGAGAGAGGT 59.806 47.826 0.00 0.00 0.00 3.85
2173 3676 6.894339 AAAAATATCCAGGAAACGTCTTGT 57.106 33.333 0.00 0.00 0.00 3.16
2223 3726 2.109425 ACGGTACAGAAGGGCATTTC 57.891 50.000 0.00 0.00 0.00 2.17
2263 3766 0.960364 GAGGGGCGAATTTGAGCACA 60.960 55.000 0.00 0.00 38.80 4.57
2272 3775 5.107875 GGCGAATTTGAGCACACTTTAAAAG 60.108 40.000 0.00 0.00 34.54 2.27
2286 3789 6.911250 ACTTTAAAAGTGGGGGTAAATCAG 57.089 37.500 0.00 0.00 41.01 2.90
2306 3809 4.458295 TCAGAGTAGTGGGTTCGAGTTAAG 59.542 45.833 0.00 0.00 0.00 1.85
2329 3832 4.485163 GGCTGAAATGTAAATGTCACACC 58.515 43.478 0.00 0.00 0.00 4.16
2367 3870 4.022849 AGGCAAAGCTCTTGAATTACACAC 60.023 41.667 11.34 0.00 0.00 3.82
2385 3888 3.636300 CACACTGGGTGGAGAAAAATTGA 59.364 43.478 1.04 0.00 44.04 2.57
2388 3891 3.758554 ACTGGGTGGAGAAAAATTGATCG 59.241 43.478 0.00 0.00 0.00 3.69
2392 3895 4.379499 GGGTGGAGAAAAATTGATCGTCAC 60.379 45.833 0.00 9.12 0.00 3.67
2395 3898 4.752604 TGGAGAAAAATTGATCGTCACGAA 59.247 37.500 2.76 0.00 39.99 3.85
2411 3914 2.747446 CACGAAATCAAGTACAAGGGGG 59.253 50.000 0.00 0.00 0.00 5.40
2421 3924 3.397527 AGTACAAGGGGGATCACATGAT 58.602 45.455 0.00 0.00 37.51 2.45
2469 3972 8.560355 TTTTGAAGTGCTATCATAACTTGCTA 57.440 30.769 0.00 0.00 34.37 3.49
2545 4048 5.813513 AAAAATTGATTCAGGTGCTCCTT 57.186 34.783 4.10 0.00 43.07 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.923942 ATGAGCTGATGGGCGCCG 62.924 66.667 22.54 7.20 37.29 6.46
12 13 2.976903 GATGAGCTGATGGGCGCC 60.977 66.667 21.18 21.18 37.29 6.53
13 14 3.344215 CGATGAGCTGATGGGCGC 61.344 66.667 0.00 0.00 37.29 6.53
20 21 2.184322 GGCGAACCGATGAGCTGA 59.816 61.111 0.00 0.00 0.00 4.26
65 66 1.005867 GGCACCGAACTAACCACGA 60.006 57.895 0.00 0.00 0.00 4.35
67 68 1.274447 ACTAGGCACCGAACTAACCAC 59.726 52.381 0.00 0.00 0.00 4.16
71 73 4.312443 CTTGAAACTAGGCACCGAACTAA 58.688 43.478 0.00 0.00 0.00 2.24
76 78 0.394938 TGCTTGAAACTAGGCACCGA 59.605 50.000 0.00 0.00 0.00 4.69
77 79 1.131126 CATGCTTGAAACTAGGCACCG 59.869 52.381 0.00 0.00 37.52 4.94
78 80 1.135286 GCATGCTTGAAACTAGGCACC 60.135 52.381 11.37 0.00 37.52 5.01
83 85 3.492313 GTTTCGGCATGCTTGAAACTAG 58.508 45.455 35.43 15.08 44.91 2.57
84 86 3.552604 GTTTCGGCATGCTTGAAACTA 57.447 42.857 35.43 19.17 44.91 2.24
85 87 2.422276 GTTTCGGCATGCTTGAAACT 57.578 45.000 35.43 0.00 44.91 2.66
91 93 1.656818 CGGGATGTTTCGGCATGCTT 61.657 55.000 18.92 0.00 37.36 3.91
97 99 1.727467 CCATTCGGGATGTTTCGGC 59.273 57.895 0.00 0.00 40.01 5.54
123 125 3.947834 CACTCCTTCCTTTTCACACTTGT 59.052 43.478 0.00 0.00 0.00 3.16
159 164 2.218075 GCGACGAATCCGAAGAATAACC 59.782 50.000 0.00 0.00 39.50 2.85
163 168 2.004583 TTGCGACGAATCCGAAGAAT 57.995 45.000 0.00 0.00 39.50 2.40
196 201 8.199449 CCATCCTACATACAATTTTGAGCAAAT 58.801 33.333 0.00 0.00 36.57 2.32
210 215 6.925165 CCAAAATTTGCATCCATCCTACATAC 59.075 38.462 0.00 0.00 0.00 2.39
274 279 7.435068 AGTACACGAACATCTAGCAAATTTT 57.565 32.000 0.00 0.00 0.00 1.82
295 300 9.332502 CTCTTGTCTTATCTCTAGCAAGTAGTA 57.667 37.037 0.00 0.00 35.96 1.82
312 317 4.698575 GACTTTGTGTCCTCTCTTGTCTT 58.301 43.478 0.00 0.00 39.69 3.01
327 346 3.307762 GCCTCCTCATACTTGGACTTTGT 60.308 47.826 0.00 0.00 0.00 2.83
347 366 1.264288 CACACTTCTTTCTTCACCGCC 59.736 52.381 0.00 0.00 0.00 6.13
352 371 3.282021 AGCTTGCACACTTCTTTCTTCA 58.718 40.909 0.00 0.00 0.00 3.02
406 426 7.264947 TCAATGAGTTCGCTATGTCTTCATTA 58.735 34.615 0.00 0.00 35.70 1.90
436 456 0.466124 CCCTAGTTGCTCCCACTAGC 59.534 60.000 2.12 0.00 43.08 3.42
449 469 8.990163 TCAAATAGAAAAACAACTTCCCTAGT 57.010 30.769 0.00 0.00 39.32 2.57
510 530 9.099454 ACTTTACCAATTATTCGCTAAGAGAAG 57.901 33.333 0.00 0.00 0.00 2.85
555 575 7.649533 TTGGATCGGAGAAAGTACTACATTA 57.350 36.000 0.00 0.00 43.58 1.90
561 581 8.893727 CAATTAATTTGGATCGGAGAAAGTACT 58.106 33.333 0.00 0.00 43.58 2.73
588 608 5.806366 AAGTTGTTGTACTAAAGTTGCGT 57.194 34.783 0.00 0.00 0.00 5.24
590 610 8.319225 GTACAAAGTTGTTGTACTAAAGTTGC 57.681 34.615 17.85 0.00 46.69 4.17
600 620 7.148440 ACGCAGTTTTAGTACAAAGTTGTTGTA 60.148 33.333 1.35 0.00 37.78 2.41
601 621 6.025280 CGCAGTTTTAGTACAAAGTTGTTGT 58.975 36.000 1.35 0.00 42.35 3.32
602 622 6.025280 ACGCAGTTTTAGTACAAAGTTGTTG 58.975 36.000 1.35 0.00 37.78 3.33
603 623 6.185852 ACGCAGTTTTAGTACAAAGTTGTT 57.814 33.333 1.35 0.00 37.78 2.83
604 624 5.806366 ACGCAGTTTTAGTACAAAGTTGT 57.194 34.783 1.75 1.75 37.78 3.32
621 641 5.217393 CCATGATCCAATTAATTGACGCAG 58.783 41.667 26.32 11.44 40.14 5.18
622 642 4.037803 CCCATGATCCAATTAATTGACGCA 59.962 41.667 26.32 19.64 40.14 5.24
623 643 4.549458 CCCATGATCCAATTAATTGACGC 58.451 43.478 26.32 15.52 40.14 5.19
624 644 4.826733 TCCCCATGATCCAATTAATTGACG 59.173 41.667 26.32 12.75 40.14 4.35
625 645 5.835280 ACTCCCCATGATCCAATTAATTGAC 59.165 40.000 26.32 17.35 40.14 3.18
641 661 6.351626 CCGACTTAAACTTAACTACTCCCCAT 60.352 42.308 0.00 0.00 0.00 4.00
666 686 7.807433 GTCAAATTTCATTTATTTTTGGGCCAC 59.193 33.333 5.23 0.00 0.00 5.01
667 687 7.503566 TGTCAAATTTCATTTATTTTTGGGCCA 59.496 29.630 0.00 0.00 0.00 5.36
687 707 9.921637 AAGTTCAAGAGTAATTGTTTTGTCAAA 57.078 25.926 0.00 0.00 0.00 2.69
708 729 6.090358 TGTTTCTAATCGATCCGTTGAAGTTC 59.910 38.462 0.00 0.00 0.00 3.01
711 732 6.090898 AGTTGTTTCTAATCGATCCGTTGAAG 59.909 38.462 0.00 0.00 0.00 3.02
714 735 5.779806 AGTTGTTTCTAATCGATCCGTTG 57.220 39.130 0.00 0.00 0.00 4.10
770 791 9.706691 CATCTCCTAAAATTTAGAAGCCGTATA 57.293 33.333 13.87 0.00 0.00 1.47
775 796 8.470657 AATCCATCTCCTAAAATTTAGAAGCC 57.529 34.615 13.87 0.00 0.00 4.35
786 807 6.087456 AGCATCCTCTAATCCATCTCCTAAA 58.913 40.000 0.00 0.00 0.00 1.85
817 838 0.039074 GACGACAGTGTGAGGTCCTG 60.039 60.000 0.00 0.00 0.00 3.86
865 886 3.123621 CGTTGCGAAGACAAGAAGCTATT 59.876 43.478 0.00 0.00 0.00 1.73
866 887 2.668457 CGTTGCGAAGACAAGAAGCTAT 59.332 45.455 0.00 0.00 0.00 2.97
905 926 4.851639 ATTGGCTAGGACAAGATCAAGT 57.148 40.909 0.00 0.00 32.43 3.16
906 927 4.754114 GCTATTGGCTAGGACAAGATCAAG 59.246 45.833 0.00 0.00 32.43 3.02
907 928 4.708177 GCTATTGGCTAGGACAAGATCAA 58.292 43.478 0.00 0.00 32.43 2.57
908 929 4.342862 GCTATTGGCTAGGACAAGATCA 57.657 45.455 0.00 0.00 32.43 2.92
948 970 4.664150 AGCTAGCTAGAAAAGGCTACTG 57.336 45.455 25.15 0.00 39.65 2.74
976 1002 1.271434 GGTGAGGTGGTCTTTTCCCTC 60.271 57.143 0.00 0.00 43.13 4.30
1046 1079 2.202730 GAGAGAGGAGCACTGCGC 60.203 66.667 0.00 0.00 42.91 6.09
1261 1354 4.202090 TGCTTGCATAAACACACACATCAA 60.202 37.500 0.00 0.00 0.00 2.57
1372 1470 3.490759 CATGTGCGCCGACTGGAC 61.491 66.667 4.18 0.00 37.49 4.02
1594 1692 3.950794 GAGCACATGACGGGCGGAA 62.951 63.158 0.00 0.00 0.00 4.30
1629 1738 6.254157 CCAACAGCTGATTAATCCAAATTTCG 59.746 38.462 23.35 0.00 0.00 3.46
1665 1781 2.880890 CAGCACATCCCCAGCTAATTAC 59.119 50.000 0.00 0.00 36.73 1.89
1710 1835 3.319122 GGAAACCACTGCAACAAGAGAAT 59.681 43.478 0.00 0.00 0.00 2.40
1766 2167 2.867975 ACGTTTTTCCTGTAGTGTTCCG 59.132 45.455 0.00 0.00 0.00 4.30
1842 3345 6.152154 CGGAAAATGGTAAACCTACCTTGAAT 59.848 38.462 0.02 0.00 46.97 2.57
1849 3352 5.963176 TTTCCGGAAAATGGTAAACCTAC 57.037 39.130 27.12 0.00 36.82 3.18
1859 3362 4.062293 GGGGAAAAGTTTTCCGGAAAATG 58.938 43.478 37.44 0.00 41.64 2.32
1865 3368 2.312390 TCTTGGGGAAAAGTTTTCCGG 58.688 47.619 31.56 22.90 36.63 5.14
1942 3445 7.866393 GCTTGATCTCAGCAAATATAAAAGCAT 59.134 33.333 11.40 0.00 36.16 3.79
1996 3499 6.264292 TCTGCACTACCTTAAAAAGATTTGCA 59.736 34.615 0.00 0.00 0.00 4.08
2064 3567 3.153130 TCTCTTCCTCTCTCAGTGTGTG 58.847 50.000 0.00 0.00 0.00 3.82
2068 3571 2.684881 GCTCTCTCTTCCTCTCTCAGTG 59.315 54.545 0.00 0.00 0.00 3.66
2109 3612 1.177895 TACGTGTGGGACCTACGCAA 61.178 55.000 20.06 5.99 42.81 4.85
2127 3630 4.160329 ACACCTCTCTCCAATGTCACTTA 58.840 43.478 0.00 0.00 0.00 2.24
2147 3650 7.446013 ACAAGACGTTTCCTGGATATTTTTACA 59.554 33.333 0.00 0.00 0.00 2.41
2173 3676 3.842007 TCAAAGGGTTTTGACCGTCTA 57.158 42.857 0.00 0.00 45.77 2.59
2185 3688 2.235891 GTTTCCGTCCAATCAAAGGGT 58.764 47.619 0.00 0.00 0.00 4.34
2199 3702 1.017701 GCCCTTCTGTACCGTTTCCG 61.018 60.000 0.00 0.00 0.00 4.30
2212 3715 4.336713 GGTGATCTTACAGAAATGCCCTTC 59.663 45.833 0.00 0.00 0.00 3.46
2223 3726 5.449314 CCTCTGTCGTTAGGTGATCTTACAG 60.449 48.000 0.00 0.00 35.54 2.74
2230 3733 1.486211 CCCCTCTGTCGTTAGGTGAT 58.514 55.000 0.00 0.00 0.00 3.06
2263 3766 6.616577 TCTGATTTACCCCCACTTTTAAAGT 58.383 36.000 4.30 4.30 44.06 2.66
2272 3775 3.118371 CCACTACTCTGATTTACCCCCAC 60.118 52.174 0.00 0.00 0.00 4.61
2274 3777 2.438392 CCCACTACTCTGATTTACCCCC 59.562 54.545 0.00 0.00 0.00 5.40
2286 3789 3.119209 CCCTTAACTCGAACCCACTACTC 60.119 52.174 0.00 0.00 0.00 2.59
2306 3809 4.485163 GTGTGACATTTACATTTCAGCCC 58.515 43.478 0.00 0.00 0.00 5.19
2329 3832 5.934043 AGCTTTGCCTTTGCCTAATAAAAAG 59.066 36.000 0.00 0.00 36.33 2.27
2337 3840 1.888512 CAAGAGCTTTGCCTTTGCCTA 59.111 47.619 0.00 0.00 36.33 3.93
2367 3870 3.758554 ACGATCAATTTTTCTCCACCCAG 59.241 43.478 0.00 0.00 0.00 4.45
2385 3888 4.625742 CCTTGTACTTGATTTCGTGACGAT 59.374 41.667 9.08 0.00 35.23 3.73
2388 3891 3.435671 CCCCTTGTACTTGATTTCGTGAC 59.564 47.826 0.00 0.00 0.00 3.67
2392 3895 3.343941 TCCCCCTTGTACTTGATTTCG 57.656 47.619 0.00 0.00 0.00 3.46
2395 3898 3.591527 TGTGATCCCCCTTGTACTTGATT 59.408 43.478 0.00 0.00 0.00 2.57
2421 3924 2.092699 TGTATGATGATTTGCCACCGGA 60.093 45.455 9.46 0.00 0.00 5.14
2427 3930 8.385111 CACTTCAAAATTGTATGATGATTTGCC 58.615 33.333 8.23 0.00 0.00 4.52
2457 3960 5.265191 ACCTCACTCTCTAGCAAGTTATGA 58.735 41.667 0.00 0.00 0.00 2.15
2469 3972 7.672239 AGAGAATGTAAAAGTACCTCACTCTCT 59.328 37.037 0.00 0.00 36.04 3.10


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

AutoCloner maintained by Alex Coulton.