Multiple sequence alignment - TraesCS1B01G278900

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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 TraesCS1B01G278900 chr1B 100.000 2001 0 0 1 2001 487169549 487171549 0.000000e+00 3696.0
1 TraesCS1B01G278900 chr1B 100.000 135 0 0 2334 2468 487171882 487172016 1.470000e-62 250.0
2 TraesCS1B01G278900 chr1B 76.735 245 46 8 1219 1455 487021648 487021407 2.580000e-25 126.0
3 TraesCS1B01G278900 chr1D 94.122 1259 55 13 651 1896 363856685 363857937 0.000000e+00 1897.0
4 TraesCS1B01G278900 chr1D 90.732 205 12 3 717 916 363856179 363856381 1.460000e-67 267.0
5 TraesCS1B01G278900 chr1D 96.296 108 3 1 1895 2001 363859152 363859259 2.520000e-40 176.0
6 TraesCS1B01G278900 chr1D 78.367 245 42 8 1219 1455 363804113 363803872 5.500000e-32 148.0
7 TraesCS1B01G278900 chr1D 97.561 41 1 0 609 649 363856617 363856657 1.220000e-08 71.3
8 TraesCS1B01G278900 chr1A 90.926 1047 67 16 675 1716 463194588 463195611 0.000000e+00 1382.0
9 TraesCS1B01G278900 chr1A 91.162 611 48 3 3 611 98254191 98254797 0.000000e+00 824.0
10 TraesCS1B01G278900 chr1A 77.551 196 42 2 1261 1455 463041301 463041107 1.550000e-22 117.0
11 TraesCS1B01G278900 chr7D 92.508 614 38 3 1 611 222001860 222002468 0.000000e+00 872.0
12 TraesCS1B01G278900 chr3D 92.308 611 38 4 3 611 157052165 157051562 0.000000e+00 859.0
13 TraesCS1B01G278900 chr5A 91.843 613 41 4 2 611 120899956 120899350 0.000000e+00 846.0
14 TraesCS1B01G278900 chr6A 91.354 613 47 3 1 611 263876890 263876282 0.000000e+00 833.0
15 TraesCS1B01G278900 chr6A 81.935 155 24 4 1842 1993 531514337 531514490 7.160000e-26 128.0
16 TraesCS1B01G278900 chr5D 91.354 613 45 4 1 611 397828596 397827990 0.000000e+00 832.0
17 TraesCS1B01G278900 chr3A 91.419 606 44 4 3 606 35120037 35119438 0.000000e+00 824.0
18 TraesCS1B01G278900 chr3A 91.419 606 44 4 3 606 35130622 35130023 0.000000e+00 824.0
19 TraesCS1B01G278900 chrUn 90.701 613 50 3 1 611 55804160 55803553 0.000000e+00 809.0


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 TraesCS1B01G278900 chr1B 487169549 487172016 2467 False 1973.000 3696 100.00000 1 2468 2 chr1B.!!$F1 2467
1 TraesCS1B01G278900 chr1D 363856179 363859259 3080 False 602.825 1897 94.67775 609 2001 4 chr1D.!!$F1 1392
2 TraesCS1B01G278900 chr1A 463194588 463195611 1023 False 1382.000 1382 90.92600 675 1716 1 chr1A.!!$F2 1041
3 TraesCS1B01G278900 chr1A 98254191 98254797 606 False 824.000 824 91.16200 3 611 1 chr1A.!!$F1 608
4 TraesCS1B01G278900 chr7D 222001860 222002468 608 False 872.000 872 92.50800 1 611 1 chr7D.!!$F1 610
5 TraesCS1B01G278900 chr3D 157051562 157052165 603 True 859.000 859 92.30800 3 611 1 chr3D.!!$R1 608
6 TraesCS1B01G278900 chr5A 120899350 120899956 606 True 846.000 846 91.84300 2 611 1 chr5A.!!$R1 609
7 TraesCS1B01G278900 chr6A 263876282 263876890 608 True 833.000 833 91.35400 1 611 1 chr6A.!!$R1 610
8 TraesCS1B01G278900 chr5D 397827990 397828596 606 True 832.000 832 91.35400 1 611 1 chr5D.!!$R1 610
9 TraesCS1B01G278900 chr3A 35119438 35120037 599 True 824.000 824 91.41900 3 606 1 chr3A.!!$R1 603
10 TraesCS1B01G278900 chr3A 35130023 35130622 599 True 824.000 824 91.41900 3 606 1 chr3A.!!$R2 603
11 TraesCS1B01G278900 chrUn 55803553 55804160 607 True 809.000 809 90.70100 1 611 1 chrUn.!!$R1 610

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
481 487 2.384309 CGACGCACCGCCAATGTAA 61.384 57.895 0.0 0.0 0.0 2.41 F
1180 1223 0.679505 CCCTCCGTCTCAGTGACAAA 59.320 55.000 3.6 0.0 45.6 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1401 1444 0.107508 CAGCTCCCATGTCAACCGAT 60.108 55.0 0.0 0.0 0.0 4.18 R
2363 3631 0.529992 CGGTGGGAAAGCTACGGATC 60.530 60.0 0.0 0.0 0.0 3.36 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
74 75 3.692593 GCAAGGAATTCCGGTTTAAGCTA 59.307 43.478 18.82 0.00 42.08 3.32
213 214 3.131577 CGCACTTCACCCCAAGTAGTATA 59.868 47.826 0.00 0.00 34.70 1.47
225 226 5.078256 CCAAGTAGTATACCTCCGGATCTT 58.922 45.833 3.57 0.00 44.47 2.40
259 260 3.715628 AACAGTGCCAGTCAAAATCAC 57.284 42.857 0.00 0.00 0.00 3.06
311 313 5.531122 TGGGAGGTGAAATTATCTCTACG 57.469 43.478 0.00 0.00 0.00 3.51
415 417 6.322126 AGACCTCTGCTATTCCAGAATATCT 58.678 40.000 0.72 0.00 41.02 1.98
481 487 2.384309 CGACGCACCGCCAATGTAA 61.384 57.895 0.00 0.00 0.00 2.41
533 540 3.885901 TGGTCTATCGTTCATCTCCTCAG 59.114 47.826 0.00 0.00 0.00 3.35
607 614 3.048600 CCCCTCTGAAACCATATCCTCA 58.951 50.000 0.00 0.00 0.00 3.86
611 618 4.349048 CCTCTGAAACCATATCCTCATCCA 59.651 45.833 0.00 0.00 0.00 3.41
612 619 5.013913 CCTCTGAAACCATATCCTCATCCAT 59.986 44.000 0.00 0.00 0.00 3.41
616 623 3.988976 ACCATATCCTCATCCATTCCG 57.011 47.619 0.00 0.00 0.00 4.30
649 656 8.815565 TGAATTTAGCCTACCAAAATGTCATA 57.184 30.769 0.00 0.00 0.00 2.15
653 686 5.041191 AGCCTACCAAAATGTCATAGGAG 57.959 43.478 1.83 0.00 35.38 3.69
780 818 2.611974 TTCTTTTTGCGCCGAATCTC 57.388 45.000 4.18 0.00 0.00 2.75
941 979 8.616076 GGTACGTTTACAAGCTTCTATCTACTA 58.384 37.037 0.00 0.00 0.00 1.82
942 980 9.649024 GTACGTTTACAAGCTTCTATCTACTAG 57.351 37.037 0.00 0.00 0.00 2.57
943 981 8.278729 ACGTTTACAAGCTTCTATCTACTAGT 57.721 34.615 0.00 0.00 0.00 2.57
1039 1082 5.394115 GCAAACCAAGTGGAGAAAGAAAAGA 60.394 40.000 3.83 0.00 38.94 2.52
1043 1086 5.952347 ACCAAGTGGAGAAAGAAAAGAAAGT 59.048 36.000 3.83 0.00 38.94 2.66
1044 1087 6.437477 ACCAAGTGGAGAAAGAAAAGAAAGTT 59.563 34.615 3.83 0.00 38.94 2.66
1109 1152 4.303086 AGAAATGCTATCATGTGCTTGC 57.697 40.909 0.00 0.00 32.23 4.01
1180 1223 0.679505 CCCTCCGTCTCAGTGACAAA 59.320 55.000 3.60 0.00 45.60 2.83
1213 1256 8.944029 CAGGTTCTTCATCATGGATATTCATAC 58.056 37.037 0.00 0.00 0.00 2.39
1299 1342 1.576421 CTTTCTGTGCAAGGCGACC 59.424 57.895 0.00 0.00 0.00 4.79
1341 1384 5.759506 TGTTTAATTGCGTTCTCAAGGAA 57.240 34.783 0.00 0.00 0.00 3.36
1357 1400 4.643387 AACACAGGTGCGAGGGGC 62.643 66.667 0.00 0.00 43.96 5.80
1401 1444 4.754322 TGTGCTATCTCTGCGACAAATAA 58.246 39.130 0.00 0.00 0.00 1.40
1408 1451 3.616821 TCTCTGCGACAAATAATCGGTTG 59.383 43.478 0.00 0.00 39.99 3.77
1444 1487 6.994496 TGAAGATAGCCTCATGATTACAAAGG 59.006 38.462 0.00 0.00 36.63 3.11
1451 1494 5.393461 GCCTCATGATTACAAAGGGTCAAAG 60.393 44.000 0.00 0.00 35.16 2.77
1504 1551 6.688073 AATAAGTATCCTCCAATCCGATGT 57.312 37.500 0.00 0.00 0.00 3.06
1603 1650 1.065564 TGTGGATGGCATGTCAATCGA 60.066 47.619 3.01 0.00 0.00 3.59
1604 1651 2.224606 GTGGATGGCATGTCAATCGAT 58.775 47.619 3.01 0.00 0.00 3.59
1606 1653 3.067180 GTGGATGGCATGTCAATCGATTT 59.933 43.478 8.21 0.00 0.00 2.17
1607 1654 4.275689 GTGGATGGCATGTCAATCGATTTA 59.724 41.667 8.21 0.00 0.00 1.40
1608 1655 4.275689 TGGATGGCATGTCAATCGATTTAC 59.724 41.667 14.24 14.24 0.00 2.01
1611 1658 5.833406 TGGCATGTCAATCGATTTACATT 57.167 34.783 27.36 14.86 30.32 2.71
1613 1660 6.264832 TGGCATGTCAATCGATTTACATTTC 58.735 36.000 27.36 22.32 30.32 2.17
1614 1661 5.396362 GGCATGTCAATCGATTTACATTTCG 59.604 40.000 27.36 19.77 36.72 3.46
1616 1663 6.075936 GCATGTCAATCGATTTACATTTCGTG 60.076 38.462 27.36 20.51 36.74 4.35
1617 1664 5.863898 TGTCAATCGATTTACATTTCGTGG 58.136 37.500 18.75 0.00 36.74 4.94
1618 1665 5.639931 TGTCAATCGATTTACATTTCGTGGA 59.360 36.000 18.75 2.24 36.74 4.02
1667 1718 2.731976 CACTTGAGCTAGTTTCACGGAC 59.268 50.000 0.00 0.00 0.00 4.79
1718 1769 3.910767 GGTAGTCGACAACAGAACTAACG 59.089 47.826 19.50 0.00 0.00 3.18
1812 1863 1.822990 GTACATGAGGAGGACGGACAA 59.177 52.381 0.00 0.00 0.00 3.18
1824 1875 1.509463 CGGACAACTAGCCGCAGTA 59.491 57.895 0.00 0.00 41.17 2.74
2350 3618 2.674754 GATCCGGCCTTTCCACCA 59.325 61.111 0.00 0.00 34.01 4.17
2351 3619 1.749258 GATCCGGCCTTTCCACCAC 60.749 63.158 0.00 0.00 34.01 4.16
2352 3620 3.282374 ATCCGGCCTTTCCACCACC 62.282 63.158 0.00 0.00 34.01 4.61
2371 3639 4.647615 CCGCCGCCAGATCCGTAG 62.648 72.222 0.00 0.00 0.00 3.51
2373 3641 3.917760 GCCGCCAGATCCGTAGCT 61.918 66.667 0.00 0.00 0.00 3.32
2374 3642 2.815308 CCGCCAGATCCGTAGCTT 59.185 61.111 0.00 0.00 0.00 3.74
2375 3643 1.144057 CCGCCAGATCCGTAGCTTT 59.856 57.895 0.00 0.00 0.00 3.51
2376 3644 0.876342 CCGCCAGATCCGTAGCTTTC 60.876 60.000 0.00 0.00 0.00 2.62
2377 3645 0.876342 CGCCAGATCCGTAGCTTTCC 60.876 60.000 0.00 0.00 0.00 3.13
2378 3646 0.533085 GCCAGATCCGTAGCTTTCCC 60.533 60.000 0.00 0.00 0.00 3.97
2379 3647 0.830648 CCAGATCCGTAGCTTTCCCA 59.169 55.000 0.00 0.00 0.00 4.37
2380 3648 1.473434 CCAGATCCGTAGCTTTCCCAC 60.473 57.143 0.00 0.00 0.00 4.61
2381 3649 0.831307 AGATCCGTAGCTTTCCCACC 59.169 55.000 0.00 0.00 0.00 4.61
2382 3650 0.529992 GATCCGTAGCTTTCCCACCG 60.530 60.000 0.00 0.00 0.00 4.94
2383 3651 2.588856 ATCCGTAGCTTTCCCACCGC 62.589 60.000 0.00 0.00 0.00 5.68
2384 3652 2.818274 CGTAGCTTTCCCACCGCC 60.818 66.667 0.00 0.00 0.00 6.13
2385 3653 2.349755 GTAGCTTTCCCACCGCCA 59.650 61.111 0.00 0.00 0.00 5.69
2386 3654 2.038837 GTAGCTTTCCCACCGCCAC 61.039 63.158 0.00 0.00 0.00 5.01
2387 3655 2.521451 TAGCTTTCCCACCGCCACA 61.521 57.895 0.00 0.00 0.00 4.17
2388 3656 2.741486 TAGCTTTCCCACCGCCACAC 62.741 60.000 0.00 0.00 0.00 3.82
2389 3657 3.353836 CTTTCCCACCGCCACACG 61.354 66.667 0.00 0.00 43.15 4.49
2399 3667 3.195698 GCCACACGCCTCGGAATC 61.196 66.667 0.00 0.00 0.00 2.52
2400 3668 2.885644 CCACACGCCTCGGAATCG 60.886 66.667 0.00 0.00 37.82 3.34
2401 3669 3.554692 CACACGCCTCGGAATCGC 61.555 66.667 0.00 0.00 36.13 4.58
2402 3670 4.814294 ACACGCCTCGGAATCGCC 62.814 66.667 0.00 0.00 36.13 5.54
2403 3671 4.812476 CACGCCTCGGAATCGCCA 62.812 66.667 0.00 0.00 35.94 5.69
2404 3672 3.849951 ACGCCTCGGAATCGCCAT 61.850 61.111 0.00 0.00 35.94 4.40
2405 3673 2.338620 CGCCTCGGAATCGCCATA 59.661 61.111 0.00 0.00 35.94 2.74
2406 3674 1.079819 CGCCTCGGAATCGCCATAT 60.080 57.895 0.00 0.00 35.94 1.78
2407 3675 0.670546 CGCCTCGGAATCGCCATATT 60.671 55.000 0.00 0.00 35.94 1.28
2408 3676 1.523758 GCCTCGGAATCGCCATATTT 58.476 50.000 0.00 0.00 35.94 1.40
2409 3677 1.197721 GCCTCGGAATCGCCATATTTG 59.802 52.381 0.00 0.00 35.94 2.32
2410 3678 2.766313 CCTCGGAATCGCCATATTTGA 58.234 47.619 0.00 0.00 35.94 2.69
2411 3679 3.138304 CCTCGGAATCGCCATATTTGAA 58.862 45.455 0.00 0.00 35.94 2.69
2412 3680 3.187227 CCTCGGAATCGCCATATTTGAAG 59.813 47.826 0.00 0.00 35.94 3.02
2413 3681 2.548057 TCGGAATCGCCATATTTGAAGC 59.452 45.455 0.00 0.00 35.94 3.86
2414 3682 2.350772 CGGAATCGCCATATTTGAAGCC 60.351 50.000 0.00 0.00 35.94 4.35
2415 3683 2.622942 GGAATCGCCATATTTGAAGCCA 59.377 45.455 0.00 0.00 36.34 4.75
2416 3684 3.550842 GGAATCGCCATATTTGAAGCCAC 60.551 47.826 0.00 0.00 36.34 5.01
2417 3685 1.388547 TCGCCATATTTGAAGCCACC 58.611 50.000 0.00 0.00 0.00 4.61
2418 3686 1.102154 CGCCATATTTGAAGCCACCA 58.898 50.000 0.00 0.00 0.00 4.17
2419 3687 1.202290 CGCCATATTTGAAGCCACCAC 60.202 52.381 0.00 0.00 0.00 4.16
2420 3688 1.136891 GCCATATTTGAAGCCACCACC 59.863 52.381 0.00 0.00 0.00 4.61
2421 3689 1.405105 CCATATTTGAAGCCACCACCG 59.595 52.381 0.00 0.00 0.00 4.94
2422 3690 1.102978 ATATTTGAAGCCACCACCGC 58.897 50.000 0.00 0.00 0.00 5.68
2423 3691 0.963355 TATTTGAAGCCACCACCGCC 60.963 55.000 0.00 0.00 0.00 6.13
2424 3692 4.966787 TTGAAGCCACCACCGCCC 62.967 66.667 0.00 0.00 0.00 6.13
2426 3694 4.966787 GAAGCCACCACCGCCCAA 62.967 66.667 0.00 0.00 0.00 4.12
2427 3695 4.299796 AAGCCACCACCGCCCAAT 62.300 61.111 0.00 0.00 0.00 3.16
2428 3696 3.826265 AAGCCACCACCGCCCAATT 62.826 57.895 0.00 0.00 0.00 2.32
2429 3697 3.758931 GCCACCACCGCCCAATTC 61.759 66.667 0.00 0.00 0.00 2.17
2430 3698 3.439540 CCACCACCGCCCAATTCG 61.440 66.667 0.00 0.00 0.00 3.34
2431 3699 2.359354 CACCACCGCCCAATTCGA 60.359 61.111 0.00 0.00 0.00 3.71
2432 3700 1.969064 CACCACCGCCCAATTCGAA 60.969 57.895 0.00 0.00 0.00 3.71
2433 3701 1.228306 ACCACCGCCCAATTCGAAA 60.228 52.632 0.00 0.00 0.00 3.46
2434 3702 1.211709 CCACCGCCCAATTCGAAAC 59.788 57.895 0.00 0.00 0.00 2.78
2435 3703 1.241315 CCACCGCCCAATTCGAAACT 61.241 55.000 0.00 0.00 0.00 2.66
2436 3704 0.596082 CACCGCCCAATTCGAAACTT 59.404 50.000 0.00 0.00 0.00 2.66
2437 3705 0.879090 ACCGCCCAATTCGAAACTTC 59.121 50.000 0.00 0.00 0.00 3.01
2438 3706 1.165270 CCGCCCAATTCGAAACTTCT 58.835 50.000 0.00 0.00 0.00 2.85
2439 3707 1.130561 CCGCCCAATTCGAAACTTCTC 59.869 52.381 0.00 0.00 0.00 2.87
2440 3708 1.130561 CGCCCAATTCGAAACTTCTCC 59.869 52.381 0.00 0.00 0.00 3.71
2441 3709 1.130561 GCCCAATTCGAAACTTCTCCG 59.869 52.381 0.00 0.00 0.00 4.63
2442 3710 1.130561 CCCAATTCGAAACTTCTCCGC 59.869 52.381 0.00 0.00 0.00 5.54
2443 3711 1.130561 CCAATTCGAAACTTCTCCGCC 59.869 52.381 0.00 0.00 0.00 6.13
2444 3712 1.804151 CAATTCGAAACTTCTCCGCCA 59.196 47.619 0.00 0.00 0.00 5.69
2445 3713 1.439679 ATTCGAAACTTCTCCGCCAC 58.560 50.000 0.00 0.00 0.00 5.01
2446 3714 0.601841 TTCGAAACTTCTCCGCCACC 60.602 55.000 0.00 0.00 0.00 4.61
2447 3715 2.380410 CGAAACTTCTCCGCCACCG 61.380 63.158 0.00 0.00 0.00 4.94
2448 3716 1.301479 GAAACTTCTCCGCCACCGT 60.301 57.895 0.00 0.00 0.00 4.83
2449 3717 1.289800 GAAACTTCTCCGCCACCGTC 61.290 60.000 0.00 0.00 0.00 4.79
2450 3718 3.569049 AACTTCTCCGCCACCGTCG 62.569 63.158 0.00 0.00 0.00 5.12
2451 3719 4.052229 CTTCTCCGCCACCGTCGT 62.052 66.667 0.00 0.00 0.00 4.34
2452 3720 3.966026 CTTCTCCGCCACCGTCGTC 62.966 68.421 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.078305 TGGGGATGAAAGGTTACCCATTT 59.922 43.478 0.00 0.00 42.89 2.32
18 19 5.650283 AGAATTTGTGGGGATGAAAGGTTA 58.350 37.500 0.00 0.00 0.00 2.85
98 99 0.609131 CTTCCGATGGGCTTTGGTGT 60.609 55.000 0.00 0.00 0.00 4.16
129 130 6.170506 TGCTATGAAATTTCGTGTAAGGTCT 58.829 36.000 20.83 0.00 0.00 3.85
225 226 1.702957 CACTGTTTACCTCCAAGGGGA 59.297 52.381 0.00 0.00 40.58 4.81
267 269 6.165577 CCAATTTCTCAACACCATTTTAGGG 58.834 40.000 0.00 0.00 0.00 3.53
311 313 5.852282 TTTTATGGCTTTATTGGAGAGGC 57.148 39.130 0.00 0.00 36.59 4.70
354 356 7.654116 GCTAAAAGAAGATTCCTTAGCGATACT 59.346 37.037 15.61 0.00 38.36 2.12
415 417 9.947433 AAAAATTCCATGCTGAAATATGAAAGA 57.053 25.926 0.00 0.00 0.00 2.52
475 481 7.928873 TGGAAGAGGAAGGTTTATCTTACATT 58.071 34.615 0.00 0.00 37.63 2.71
481 487 4.439860 ACCTGGAAGAGGAAGGTTTATCT 58.560 43.478 0.00 0.00 46.33 1.98
510 516 3.885901 TGAGGAGATGAACGATAGACCAG 59.114 47.826 0.00 0.00 41.38 4.00
515 522 3.998099 TGCTGAGGAGATGAACGATAG 57.002 47.619 0.00 0.00 46.19 2.08
520 527 3.603532 TCAACATGCTGAGGAGATGAAC 58.396 45.455 0.00 0.00 0.00 3.18
533 540 0.097674 GACACCGATGCTCAACATGC 59.902 55.000 0.00 0.00 39.84 4.06
612 619 9.444600 GGTAGGCTAAATTCATATATTTCGGAA 57.555 33.333 0.00 0.00 0.00 4.30
649 656 8.003629 ACTACCTCCGTTCTAAAATATACTCCT 58.996 37.037 0.00 0.00 0.00 3.69
677 710 4.947388 TGTGGGCATCTTTTGGTAATCTAC 59.053 41.667 0.00 0.00 0.00 2.59
679 712 4.019174 CTGTGGGCATCTTTTGGTAATCT 58.981 43.478 0.00 0.00 0.00 2.40
941 979 4.931661 TTGGAAGTCAAAGACTCGTACT 57.068 40.909 0.00 0.00 42.59 2.73
1043 1086 3.181509 TGTTGCGCGAAGTTTCAAGTAAA 60.182 39.130 12.10 0.00 0.00 2.01
1044 1087 2.352034 TGTTGCGCGAAGTTTCAAGTAA 59.648 40.909 12.10 0.00 0.00 2.24
1060 1103 2.282180 ATCGGTGGGTGGTGTTGC 60.282 61.111 0.00 0.00 0.00 4.17
1109 1152 5.391950 CCGGGAACAATACAAGAATCAACAG 60.392 44.000 0.00 0.00 0.00 3.16
1152 1195 2.363147 GACGGAGGGAGGAGCACT 60.363 66.667 0.00 0.00 0.00 4.40
1180 1223 4.382040 CCATGATGAAGAACCTGTAGTCGT 60.382 45.833 0.00 0.00 0.00 4.34
1213 1256 6.141211 GCAATGAATTAACACGCATGTATGAG 59.859 38.462 5.47 0.00 38.45 2.90
1299 1342 1.730501 TCTTCTCCGCAATCAAGCAG 58.269 50.000 0.00 0.00 0.00 4.24
1357 1400 1.268032 GCATTCGCTATTGAACGGTGG 60.268 52.381 0.00 0.00 34.30 4.61
1363 1406 2.684374 AGCACATGCATTCGCTATTGAA 59.316 40.909 16.21 0.00 45.16 2.69
1401 1444 0.107508 CAGCTCCCATGTCAACCGAT 60.108 55.000 0.00 0.00 0.00 4.18
1408 1451 2.549778 GGCTATCTTCAGCTCCCATGTC 60.550 54.545 0.00 0.00 41.50 3.06
1444 1487 9.371136 GAAATTATTCATTCCCTTTCTTTGACC 57.629 33.333 0.00 0.00 35.54 4.02
1494 1541 3.270027 TGCAGGAAACTACATCGGATTG 58.730 45.455 0.00 0.00 40.21 2.67
1613 1660 1.154225 GCTGCCATTTCGTTCCACG 60.154 57.895 0.00 0.00 44.19 4.94
1614 1661 0.598065 AAGCTGCCATTTCGTTCCAC 59.402 50.000 0.00 0.00 0.00 4.02
1616 1663 1.541588 AGAAAGCTGCCATTTCGTTCC 59.458 47.619 8.23 0.00 40.75 3.62
1617 1664 2.997485 AGAAAGCTGCCATTTCGTTC 57.003 45.000 8.23 0.00 40.75 3.95
1618 1665 2.029918 GGAAGAAAGCTGCCATTTCGTT 60.030 45.455 8.23 4.62 39.94 3.85
1625 1676 0.767375 AGTGAGGAAGAAAGCTGCCA 59.233 50.000 0.00 0.00 43.05 4.92
1679 1730 5.821470 CGACTACCTATAACTCTGACAGGAA 59.179 44.000 1.81 0.00 0.00 3.36
1680 1731 5.129980 TCGACTACCTATAACTCTGACAGGA 59.870 44.000 1.81 0.00 0.00 3.86
1682 1733 5.816258 TGTCGACTACCTATAACTCTGACAG 59.184 44.000 17.92 0.00 0.00 3.51
1683 1734 5.737860 TGTCGACTACCTATAACTCTGACA 58.262 41.667 17.92 0.00 0.00 3.58
1684 1735 6.093219 TGTTGTCGACTACCTATAACTCTGAC 59.907 42.308 24.00 0.00 0.00 3.51
1685 1736 6.175471 TGTTGTCGACTACCTATAACTCTGA 58.825 40.000 24.00 1.62 0.00 3.27
1686 1737 6.315642 TCTGTTGTCGACTACCTATAACTCTG 59.684 42.308 24.00 9.80 0.00 3.35
1718 1769 3.008485 AGAGGACAGTCATCAAACTTCCC 59.992 47.826 17.27 0.00 31.91 3.97
1787 1838 2.228059 CGTCCTCCTCATGTACCGTAT 58.772 52.381 0.00 0.00 0.00 3.06
1824 1875 5.459536 TGCTCTAACAGAGATAATCGCAT 57.540 39.130 7.37 0.00 45.07 4.73
1836 1887 5.009110 TCACCTATTCGAGATGCTCTAACAG 59.991 44.000 0.00 0.00 0.00 3.16
1957 3225 6.803320 CACCAAGTGATGCAAAATACAACTAG 59.197 38.462 0.00 0.00 35.23 2.57
1961 3229 5.781210 TCACCAAGTGATGCAAAATACAA 57.219 34.783 0.00 0.00 37.67 2.41
2333 3601 1.749258 GTGGTGGAAAGGCCGGATC 60.749 63.158 5.05 0.00 40.66 3.36
2334 3602 2.355115 GTGGTGGAAAGGCCGGAT 59.645 61.111 5.05 0.00 40.66 4.18
2335 3603 3.961414 GGTGGTGGAAAGGCCGGA 61.961 66.667 5.05 0.00 40.66 5.14
2354 3622 4.647615 CTACGGATCTGGCGGCGG 62.648 72.222 12.43 12.43 0.00 6.13
2356 3624 2.925162 AAAGCTACGGATCTGGCGGC 62.925 60.000 6.47 0.00 0.00 6.53
2357 3625 0.876342 GAAAGCTACGGATCTGGCGG 60.876 60.000 6.47 0.00 0.00 6.13
2358 3626 0.876342 GGAAAGCTACGGATCTGGCG 60.876 60.000 6.47 0.00 0.00 5.69
2359 3627 0.533085 GGGAAAGCTACGGATCTGGC 60.533 60.000 6.47 0.22 0.00 4.85
2360 3628 0.830648 TGGGAAAGCTACGGATCTGG 59.169 55.000 6.47 0.00 0.00 3.86
2361 3629 1.473434 GGTGGGAAAGCTACGGATCTG 60.473 57.143 0.00 0.00 0.00 2.90
2362 3630 0.831307 GGTGGGAAAGCTACGGATCT 59.169 55.000 0.00 0.00 0.00 2.75
2363 3631 0.529992 CGGTGGGAAAGCTACGGATC 60.530 60.000 0.00 0.00 0.00 3.36
2364 3632 1.520666 CGGTGGGAAAGCTACGGAT 59.479 57.895 0.00 0.00 0.00 4.18
2365 3633 2.975536 CGGTGGGAAAGCTACGGA 59.024 61.111 0.00 0.00 0.00 4.69
2366 3634 2.818274 GCGGTGGGAAAGCTACGG 60.818 66.667 0.00 0.00 0.00 4.02
2367 3635 2.818274 GGCGGTGGGAAAGCTACG 60.818 66.667 0.00 0.00 0.00 3.51
2368 3636 2.038837 GTGGCGGTGGGAAAGCTAC 61.039 63.158 0.00 0.00 35.40 3.58
2369 3637 2.349755 GTGGCGGTGGGAAAGCTA 59.650 61.111 0.00 0.00 0.00 3.32
2370 3638 3.884774 TGTGGCGGTGGGAAAGCT 61.885 61.111 0.00 0.00 0.00 3.74
2371 3639 3.670377 GTGTGGCGGTGGGAAAGC 61.670 66.667 0.00 0.00 0.00 3.51
2372 3640 3.353836 CGTGTGGCGGTGGGAAAG 61.354 66.667 0.00 0.00 36.85 2.62
2382 3650 3.195698 GATTCCGAGGCGTGTGGC 61.196 66.667 0.00 0.00 42.51 5.01
2383 3651 2.885644 CGATTCCGAGGCGTGTGG 60.886 66.667 0.00 0.00 38.22 4.17
2384 3652 3.554692 GCGATTCCGAGGCGTGTG 61.555 66.667 0.00 0.00 38.22 3.82
2385 3653 4.814294 GGCGATTCCGAGGCGTGT 62.814 66.667 0.00 0.00 38.22 4.49
2386 3654 2.693250 TATGGCGATTCCGAGGCGTG 62.693 60.000 0.00 0.00 38.22 5.34
2387 3655 1.816863 ATATGGCGATTCCGAGGCGT 61.817 55.000 0.00 0.00 38.22 5.68
2388 3656 0.670546 AATATGGCGATTCCGAGGCG 60.671 55.000 0.00 0.00 38.22 5.52
2389 3657 1.197721 CAAATATGGCGATTCCGAGGC 59.802 52.381 0.00 0.00 38.22 4.70
2390 3658 2.766313 TCAAATATGGCGATTCCGAGG 58.234 47.619 0.00 0.00 38.22 4.63
2391 3659 3.364366 GCTTCAAATATGGCGATTCCGAG 60.364 47.826 0.00 0.00 38.22 4.63
2392 3660 2.548057 GCTTCAAATATGGCGATTCCGA 59.452 45.455 0.00 0.00 38.22 4.55
2393 3661 2.350772 GGCTTCAAATATGGCGATTCCG 60.351 50.000 0.00 0.00 37.80 4.30
2394 3662 2.622942 TGGCTTCAAATATGGCGATTCC 59.377 45.455 0.00 0.00 0.00 3.01
2395 3663 3.550842 GGTGGCTTCAAATATGGCGATTC 60.551 47.826 0.00 0.00 0.00 2.52
2396 3664 2.362077 GGTGGCTTCAAATATGGCGATT 59.638 45.455 0.00 0.00 0.00 3.34
2397 3665 1.956477 GGTGGCTTCAAATATGGCGAT 59.044 47.619 0.00 0.00 0.00 4.58
2398 3666 1.340502 TGGTGGCTTCAAATATGGCGA 60.341 47.619 0.00 0.00 0.00 5.54
2399 3667 1.102154 TGGTGGCTTCAAATATGGCG 58.898 50.000 0.00 0.00 0.00 5.69
2400 3668 1.136891 GGTGGTGGCTTCAAATATGGC 59.863 52.381 0.00 0.00 0.00 4.40
2401 3669 1.405105 CGGTGGTGGCTTCAAATATGG 59.595 52.381 0.00 0.00 0.00 2.74
2402 3670 1.202290 GCGGTGGTGGCTTCAAATATG 60.202 52.381 0.00 0.00 0.00 1.78
2403 3671 1.102978 GCGGTGGTGGCTTCAAATAT 58.897 50.000 0.00 0.00 0.00 1.28
2404 3672 0.963355 GGCGGTGGTGGCTTCAAATA 60.963 55.000 0.00 0.00 0.00 1.40
2405 3673 2.275380 GGCGGTGGTGGCTTCAAAT 61.275 57.895 0.00 0.00 0.00 2.32
2406 3674 2.909965 GGCGGTGGTGGCTTCAAA 60.910 61.111 0.00 0.00 0.00 2.69
2407 3675 4.966787 GGGCGGTGGTGGCTTCAA 62.967 66.667 0.00 0.00 34.31 2.69
2409 3677 4.966787 TTGGGCGGTGGTGGCTTC 62.967 66.667 0.00 0.00 34.31 3.86
2410 3678 3.826265 AATTGGGCGGTGGTGGCTT 62.826 57.895 0.00 0.00 34.31 4.35
2411 3679 4.299796 AATTGGGCGGTGGTGGCT 62.300 61.111 0.00 0.00 34.31 4.75
2412 3680 3.758931 GAATTGGGCGGTGGTGGC 61.759 66.667 0.00 0.00 0.00 5.01
2413 3681 3.439540 CGAATTGGGCGGTGGTGG 61.440 66.667 0.00 0.00 0.00 4.61
2414 3682 1.519751 TTTCGAATTGGGCGGTGGTG 61.520 55.000 0.00 0.00 0.00 4.17
2415 3683 1.228306 TTTCGAATTGGGCGGTGGT 60.228 52.632 0.00 0.00 0.00 4.16
2416 3684 1.211709 GTTTCGAATTGGGCGGTGG 59.788 57.895 0.00 0.00 0.00 4.61
2417 3685 0.596082 AAGTTTCGAATTGGGCGGTG 59.404 50.000 0.00 0.00 0.00 4.94
2418 3686 0.879090 GAAGTTTCGAATTGGGCGGT 59.121 50.000 0.00 0.00 0.00 5.68
2419 3687 1.130561 GAGAAGTTTCGAATTGGGCGG 59.869 52.381 0.00 0.00 0.00 6.13
2420 3688 1.130561 GGAGAAGTTTCGAATTGGGCG 59.869 52.381 0.00 0.00 0.00 6.13
2421 3689 1.130561 CGGAGAAGTTTCGAATTGGGC 59.869 52.381 0.00 0.00 0.00 5.36
2422 3690 1.130561 GCGGAGAAGTTTCGAATTGGG 59.869 52.381 0.00 0.00 0.00 4.12
2423 3691 1.130561 GGCGGAGAAGTTTCGAATTGG 59.869 52.381 0.00 0.00 0.00 3.16
2424 3692 1.804151 TGGCGGAGAAGTTTCGAATTG 59.196 47.619 0.00 0.00 0.00 2.32
2425 3693 1.804748 GTGGCGGAGAAGTTTCGAATT 59.195 47.619 0.00 0.00 0.00 2.17
2426 3694 1.439679 GTGGCGGAGAAGTTTCGAAT 58.560 50.000 0.00 0.00 0.00 3.34
2427 3695 0.601841 GGTGGCGGAGAAGTTTCGAA 60.602 55.000 0.00 0.00 0.00 3.71
2428 3696 1.005394 GGTGGCGGAGAAGTTTCGA 60.005 57.895 0.00 0.00 0.00 3.71
2429 3697 2.380410 CGGTGGCGGAGAAGTTTCG 61.380 63.158 0.00 0.00 0.00 3.46
2430 3698 1.289800 GACGGTGGCGGAGAAGTTTC 61.290 60.000 0.00 0.00 0.00 2.78
2431 3699 1.301479 GACGGTGGCGGAGAAGTTT 60.301 57.895 0.00 0.00 0.00 2.66
2432 3700 2.342648 GACGGTGGCGGAGAAGTT 59.657 61.111 0.00 0.00 0.00 2.66
2433 3701 4.052229 CGACGGTGGCGGAGAAGT 62.052 66.667 0.00 0.00 0.00 3.01
2434 3702 3.966026 GACGACGGTGGCGGAGAAG 62.966 68.421 0.00 0.00 0.00 2.85
2435 3703 4.047059 GACGACGGTGGCGGAGAA 62.047 66.667 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.