Multiple sequence alignment - TraesCS3A01G301900

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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 TraesCS3A01G301900 chr3A 100.000 2630 0 0 1 2630 535221126 535223755 0.000000e+00 4857
1 TraesCS3A01G301900 chr3D 89.381 1243 56 34 803 2022 414910410 414909221 0.000000e+00 1495
2 TraesCS3A01G301900 chr3D 87.642 615 62 11 1 611 414911446 414910842 0.000000e+00 702
3 TraesCS3A01G301900 chr3D 87.108 574 28 11 2040 2578 414909164 414908602 2.240000e-170 608
4 TraesCS3A01G301900 chr3D 78.716 545 101 13 1 540 497653770 497654304 1.500000e-92 350
5 TraesCS3A01G301900 chr3B 88.484 1181 71 25 869 2024 540733135 540731995 0.000000e+00 1367
6 TraesCS3A01G301900 chr3B 88.548 489 34 10 2146 2630 540731865 540731395 8.170000e-160 573
7 TraesCS3A01G301900 chr3B 86.611 478 53 10 139 611 540738735 540738264 3.880000e-143 518
8 TraesCS3A01G301900 chr3B 92.982 114 5 1 2009 2119 540731978 540731865 2.090000e-36 163
9 TraesCS3A01G301900 chr3B 93.478 92 6 0 786 877 540738111 540738020 1.270000e-28 137
10 TraesCS3A01G301900 chr5D 83.670 545 83 5 1 544 135093600 135093061 2.340000e-140 508
11 TraesCS3A01G301900 chr4D 80.455 527 94 7 1 527 202362864 202363381 6.820000e-106 394
12 TraesCS3A01G301900 chr4D 79.444 540 99 10 9 544 312938631 312938100 3.200000e-99 372
13 TraesCS3A01G301900 chr4D 78.793 547 105 9 1 544 312918562 312918024 8.950000e-95 357
14 TraesCS3A01G301900 chr4D 78.611 547 104 9 1 544 312941649 312941113 1.500000e-92 350
15 TraesCS3A01G301900 chr6D 81.859 441 76 2 36 476 462490118 462489682 4.140000e-98 368


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 TraesCS3A01G301900 chr3A 535221126 535223755 2629 False 4857.0 4857 100.000000 1 2630 1 chr3A.!!$F1 2629
1 TraesCS3A01G301900 chr3D 414908602 414911446 2844 True 935.0 1495 88.043667 1 2578 3 chr3D.!!$R1 2577
2 TraesCS3A01G301900 chr3D 497653770 497654304 534 False 350.0 350 78.716000 1 540 1 chr3D.!!$F1 539
3 TraesCS3A01G301900 chr3B 540731395 540733135 1740 True 701.0 1367 90.004667 869 2630 3 chr3B.!!$R1 1761
4 TraesCS3A01G301900 chr3B 540738020 540738735 715 True 327.5 518 90.044500 139 877 2 chr3B.!!$R2 738
5 TraesCS3A01G301900 chr5D 135093061 135093600 539 True 508.0 508 83.670000 1 544 1 chr5D.!!$R1 543
6 TraesCS3A01G301900 chr4D 202362864 202363381 517 False 394.0 394 80.455000 1 527 1 chr4D.!!$F1 526
7 TraesCS3A01G301900 chr4D 312938100 312941649 3549 True 361.0 372 79.027500 1 544 2 chr4D.!!$R2 543
8 TraesCS3A01G301900 chr4D 312918024 312918562 538 True 357.0 357 78.793000 1 544 1 chr4D.!!$R1 543

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
681 3705 0.10741 TACGGCCATGTCCATTCCAC 60.107 55.0 2.24 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1859 5191 0.098728 GATTTGCCGCGTGTGCTATT 59.901 50.0 4.92 0.0 39.65 1.73 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
25 27 8.877808 AAACTAGCAAGAGAAAAATCAAAAGG 57.122 30.769 0.00 0.00 0.00 3.11
30 32 5.106830 GCAAGAGAAAAATCAAAAGGCCATG 60.107 40.000 5.01 0.27 0.00 3.66
82 86 1.489649 CTCCTGCAGAATGTCCTCCAT 59.510 52.381 17.39 0.00 39.31 3.41
120 124 7.981789 GTCAATGACTTCCATGTTATCAGAGTA 59.018 37.037 6.07 0.00 35.24 2.59
176 181 6.716934 TCAACAATAAACCAAACCTAAGCA 57.283 33.333 0.00 0.00 0.00 3.91
182 187 9.523168 ACAATAAACCAAACCTAAGCACTAATA 57.477 29.630 0.00 0.00 0.00 0.98
187 192 7.017319 ACCAAACCTAAGCACTAATACTTCT 57.983 36.000 0.00 0.00 0.00 2.85
231 236 4.232221 CACTCAATCTTTCAATTTGCGCT 58.768 39.130 9.73 0.00 0.00 5.92
239 244 4.922692 TCTTTCAATTTGCGCTAACAATGG 59.077 37.500 9.73 0.00 0.00 3.16
297 3315 1.555075 GCCCCTTAGCGGATCATGATA 59.445 52.381 8.54 0.00 33.16 2.15
323 3341 3.893326 AAAAGGCATCCACATTTAGCC 57.107 42.857 0.00 0.00 45.54 3.93
428 3449 0.904649 AGCACGGATCCTCATGAACA 59.095 50.000 10.75 0.00 0.00 3.18
438 3459 4.280436 TCCTCATGAACATTTGGTACGT 57.720 40.909 0.00 0.00 0.00 3.57
502 3523 8.902540 TCCATCATAAATACCACACAGTTATC 57.097 34.615 0.00 0.00 0.00 1.75
515 3536 1.000827 CAGTTATCGCGATCAGCTCCT 60.001 52.381 27.45 10.24 45.59 3.69
532 3553 1.672030 CTGTGCATTCTGGACGCCA 60.672 57.895 0.00 0.00 41.94 5.69
541 3562 4.083802 GCATTCTGGACGCCAAATATAGAC 60.084 45.833 0.35 0.00 30.80 2.59
552 3573 4.323104 GCCAAATATAGACAGAGGCCTAGG 60.323 50.000 4.42 3.67 34.71 3.02
570 3591 4.218852 CCTAGGGCAAATGTTTTTCGGTTA 59.781 41.667 0.00 0.00 0.00 2.85
571 3592 4.882842 AGGGCAAATGTTTTTCGGTTAT 57.117 36.364 0.00 0.00 0.00 1.89
572 3593 4.565022 AGGGCAAATGTTTTTCGGTTATG 58.435 39.130 0.00 0.00 0.00 1.90
573 3594 3.124466 GGGCAAATGTTTTTCGGTTATGC 59.876 43.478 0.00 0.00 0.00 3.14
574 3595 3.993736 GGCAAATGTTTTTCGGTTATGCT 59.006 39.130 0.00 0.00 0.00 3.79
575 3596 4.091365 GGCAAATGTTTTTCGGTTATGCTC 59.909 41.667 0.00 0.00 0.00 4.26
576 3597 4.923281 GCAAATGTTTTTCGGTTATGCTCT 59.077 37.500 0.00 0.00 0.00 4.09
577 3598 5.060940 GCAAATGTTTTTCGGTTATGCTCTC 59.939 40.000 0.00 0.00 0.00 3.20
580 3601 6.575162 ATGTTTTTCGGTTATGCTCTCTTT 57.425 33.333 0.00 0.00 0.00 2.52
581 3602 6.385649 TGTTTTTCGGTTATGCTCTCTTTT 57.614 33.333 0.00 0.00 0.00 2.27
582 3603 6.801575 TGTTTTTCGGTTATGCTCTCTTTTT 58.198 32.000 0.00 0.00 0.00 1.94
611 3635 0.465460 AAGGCTTCCGTTGCTTCACA 60.465 50.000 0.00 0.00 0.00 3.58
612 3636 0.465460 AGGCTTCCGTTGCTTCACAA 60.465 50.000 0.00 0.00 35.33 3.33
613 3637 0.383949 GGCTTCCGTTGCTTCACAAA 59.616 50.000 0.00 0.00 40.82 2.83
614 3638 1.477105 GCTTCCGTTGCTTCACAAAC 58.523 50.000 0.00 0.00 40.82 2.93
615 3639 1.202245 GCTTCCGTTGCTTCACAAACA 60.202 47.619 0.00 0.00 40.82 2.83
616 3640 2.543653 GCTTCCGTTGCTTCACAAACAT 60.544 45.455 0.00 0.00 40.82 2.71
617 3641 3.300009 CTTCCGTTGCTTCACAAACATC 58.700 45.455 0.00 0.00 40.82 3.06
618 3642 1.262950 TCCGTTGCTTCACAAACATCG 59.737 47.619 0.00 0.00 40.82 3.84
619 3643 1.044725 CGTTGCTTCACAAACATCGC 58.955 50.000 0.00 0.00 40.82 4.58
620 3644 1.596709 CGTTGCTTCACAAACATCGCA 60.597 47.619 0.00 0.00 40.82 5.10
622 3646 1.308047 TGCTTCACAAACATCGCAGT 58.692 45.000 0.00 0.00 0.00 4.40
624 3648 1.264020 GCTTCACAAACATCGCAGTCA 59.736 47.619 0.00 0.00 0.00 3.41
625 3649 2.286950 GCTTCACAAACATCGCAGTCAA 60.287 45.455 0.00 0.00 0.00 3.18
626 3650 3.791789 GCTTCACAAACATCGCAGTCAAA 60.792 43.478 0.00 0.00 0.00 2.69
628 3652 2.680339 TCACAAACATCGCAGTCAAACA 59.320 40.909 0.00 0.00 0.00 2.83
629 3653 3.314913 TCACAAACATCGCAGTCAAACAT 59.685 39.130 0.00 0.00 0.00 2.71
630 3654 3.665409 CACAAACATCGCAGTCAAACATC 59.335 43.478 0.00 0.00 0.00 3.06
631 3655 2.880822 AACATCGCAGTCAAACATCG 57.119 45.000 0.00 0.00 0.00 3.84
632 3656 0.443869 ACATCGCAGTCAAACATCGC 59.556 50.000 0.00 0.00 0.00 4.58
633 3657 0.443478 CATCGCAGTCAAACATCGCA 59.557 50.000 0.00 0.00 0.00 5.10
634 3658 0.723414 ATCGCAGTCAAACATCGCAG 59.277 50.000 0.00 0.00 0.00 5.18
637 3661 1.926511 GCAGTCAAACATCGCAGGGG 61.927 60.000 0.00 0.00 0.00 4.79
638 3662 1.002134 AGTCAAACATCGCAGGGGG 60.002 57.895 0.00 0.00 0.00 5.40
639 3663 1.303317 GTCAAACATCGCAGGGGGT 60.303 57.895 0.00 0.00 0.00 4.95
640 3664 1.303236 TCAAACATCGCAGGGGGTG 60.303 57.895 0.00 0.00 0.00 4.61
642 3666 1.303317 AAACATCGCAGGGGGTGTC 60.303 57.895 2.56 0.00 0.00 3.67
643 3667 2.063015 AAACATCGCAGGGGGTGTCA 62.063 55.000 2.56 0.00 0.00 3.58
644 3668 1.852157 AACATCGCAGGGGGTGTCAT 61.852 55.000 2.56 0.00 0.00 3.06
645 3669 0.980754 ACATCGCAGGGGGTGTCATA 60.981 55.000 0.00 0.00 0.00 2.15
646 3670 0.397941 CATCGCAGGGGGTGTCATAT 59.602 55.000 0.00 0.00 0.00 1.78
647 3671 0.687354 ATCGCAGGGGGTGTCATATC 59.313 55.000 0.00 0.00 0.00 1.63
648 3672 1.071471 CGCAGGGGGTGTCATATCC 59.929 63.158 0.00 0.00 0.00 2.59
649 3673 1.071471 GCAGGGGGTGTCATATCCG 59.929 63.158 0.00 0.00 0.00 4.18
650 3674 1.754745 CAGGGGGTGTCATATCCGG 59.245 63.158 0.00 0.00 0.00 5.14
651 3675 2.147387 AGGGGGTGTCATATCCGGC 61.147 63.158 0.00 0.00 0.00 6.13
652 3676 2.448582 GGGGGTGTCATATCCGGCA 61.449 63.158 0.00 0.00 0.00 5.69
653 3677 1.071471 GGGGTGTCATATCCGGCAG 59.929 63.158 0.00 0.00 0.00 4.85
654 3678 1.598130 GGGTGTCATATCCGGCAGC 60.598 63.158 0.00 0.00 0.00 5.25
655 3679 1.447643 GGTGTCATATCCGGCAGCT 59.552 57.895 0.00 0.00 0.00 4.24
656 3680 0.679505 GGTGTCATATCCGGCAGCTA 59.320 55.000 0.00 0.00 0.00 3.32
657 3681 1.605712 GGTGTCATATCCGGCAGCTAC 60.606 57.143 0.00 0.00 0.00 3.58
658 3682 0.313987 TGTCATATCCGGCAGCTACG 59.686 55.000 0.00 3.21 0.00 3.51
681 3705 0.107410 TACGGCCATGTCCATTCCAC 60.107 55.000 2.24 0.00 0.00 4.02
699 3723 0.261991 ACCGGCTCCTCTTCATCCTA 59.738 55.000 0.00 0.00 0.00 2.94
700 3724 1.133009 ACCGGCTCCTCTTCATCCTAT 60.133 52.381 0.00 0.00 0.00 2.57
701 3725 1.274728 CCGGCTCCTCTTCATCCTATG 59.725 57.143 0.00 0.00 0.00 2.23
703 3727 2.630098 CGGCTCCTCTTCATCCTATGAA 59.370 50.000 2.60 2.60 46.30 2.57
720 3771 6.492087 TCCTATGAAAAAGAAAACGGTGGAAT 59.508 34.615 0.00 0.00 0.00 3.01
755 3806 2.510238 GCCTAGCAGTCACCGCAG 60.510 66.667 0.00 0.00 0.00 5.18
762 3813 1.373497 CAGTCACCGCAGAGTCCAC 60.373 63.158 0.00 0.00 0.00 4.02
764 3815 1.115930 AGTCACCGCAGAGTCCACTT 61.116 55.000 0.00 0.00 0.00 3.16
886 4161 2.162608 TGTGCCATATGTTTGTTACCGC 59.837 45.455 1.24 0.00 0.00 5.68
892 4169 0.515564 ATGTTTGTTACCGCGTGCTC 59.484 50.000 4.92 0.00 0.00 4.26
976 4259 1.761780 TTCCACCCCTTCCTCCTCCT 61.762 60.000 0.00 0.00 0.00 3.69
978 4261 1.081092 CACCCCTTCCTCCTCCTCA 59.919 63.158 0.00 0.00 0.00 3.86
980 4263 2.069430 CCCCTTCCTCCTCCTCAGC 61.069 68.421 0.00 0.00 0.00 4.26
986 4270 2.063378 CCTCCTCCTCAGCCTCCAC 61.063 68.421 0.00 0.00 0.00 4.02
989 4273 2.363018 CTCCTCAGCCTCCACCGA 60.363 66.667 0.00 0.00 0.00 4.69
1024 4311 2.770048 CGCCCAATCTCCCCCTCT 60.770 66.667 0.00 0.00 0.00 3.69
1031 4318 0.029577 AATCTCCCCCTCTTCCTCCC 60.030 60.000 0.00 0.00 0.00 4.30
1034 4321 4.416601 CCCCCTCTTCCTCCCCGT 62.417 72.222 0.00 0.00 0.00 5.28
1036 4323 3.083997 CCCTCTTCCTCCCCGTGG 61.084 72.222 0.00 0.00 0.00 4.94
1097 4384 3.170585 GAAGTTCGTCGTCGGCGG 61.171 66.667 20.32 0.51 38.89 6.13
1197 4484 2.689034 CACCCCACTCCTCCTCCC 60.689 72.222 0.00 0.00 0.00 4.30
1200 4495 1.234529 CCCCACTCCTCCTCCCTAG 59.765 68.421 0.00 0.00 0.00 3.02
1237 4536 2.671351 CGATCGATCTACCATTTCCCGG 60.671 54.545 22.43 0.00 0.00 5.73
1362 4664 3.406361 AAGTGCGACGCGAGCAAG 61.406 61.111 28.37 10.31 46.97 4.01
1373 4675 2.347490 GAGCAAGCCCCTCGTCAA 59.653 61.111 0.00 0.00 0.00 3.18
1374 4676 1.302511 GAGCAAGCCCCTCGTCAAA 60.303 57.895 0.00 0.00 0.00 2.69
1488 4790 2.981909 ACCGTGCTCGTCGAGGAA 60.982 61.111 23.09 0.00 30.58 3.36
1491 4793 1.081376 CGTGCTCGTCGAGGAAAGT 60.081 57.895 23.09 0.00 30.58 2.66
1630 4932 1.750780 TTTGCGGTGTGGCTGTGAA 60.751 52.632 0.00 0.00 0.00 3.18
1631 4933 1.106351 TTTGCGGTGTGGCTGTGAAT 61.106 50.000 0.00 0.00 0.00 2.57
1634 4936 1.575922 CGGTGTGGCTGTGAATGTG 59.424 57.895 0.00 0.00 0.00 3.21
1635 4937 0.884259 CGGTGTGGCTGTGAATGTGA 60.884 55.000 0.00 0.00 0.00 3.58
1636 4938 0.593128 GGTGTGGCTGTGAATGTGAC 59.407 55.000 0.00 0.00 0.00 3.67
1637 4939 0.593128 GTGTGGCTGTGAATGTGACC 59.407 55.000 0.00 0.00 0.00 4.02
1805 5109 3.057174 TGTTCCGGCATTTTGGTAATGAC 60.057 43.478 0.00 0.00 32.38 3.06
1824 5156 3.930838 CGCACACGCAACTGTAGA 58.069 55.556 0.00 0.00 38.40 2.59
1825 5157 2.221676 CGCACACGCAACTGTAGAA 58.778 52.632 0.00 0.00 38.40 2.10
1826 5158 0.579630 CGCACACGCAACTGTAGAAA 59.420 50.000 0.00 0.00 38.40 2.52
1827 5159 1.004398 CGCACACGCAACTGTAGAAAA 60.004 47.619 0.00 0.00 38.40 2.29
1828 5160 2.537931 CGCACACGCAACTGTAGAAAAA 60.538 45.455 0.00 0.00 38.40 1.94
1845 5177 2.015736 AAAACAAAACGGCACATGCA 57.984 40.000 6.15 0.00 44.36 3.96
1859 5191 2.033675 CACATGCAGTGCTGAGACAAAA 59.966 45.455 17.60 0.00 42.15 2.44
1868 5200 4.488126 TGCTGAGACAAAAATAGCACAC 57.512 40.909 0.00 0.00 39.26 3.82
1871 5203 2.096466 TGAGACAAAAATAGCACACGCG 60.096 45.455 3.53 3.53 45.49 6.01
1879 5211 1.024046 ATAGCACACGCGGCAAATCA 61.024 50.000 12.47 0.00 45.49 2.57
1890 5223 3.578688 GCGGCAAATCATGAAAAGAAGT 58.421 40.909 0.00 0.00 0.00 3.01
1945 5278 4.519906 AAAGAAGTTCCCTCAGGTTTGA 57.480 40.909 0.00 0.00 0.00 2.69
1979 5318 4.082733 GGAAATGTGTCTTAAAGGGACTGC 60.083 45.833 0.00 0.00 40.86 4.40
2089 5501 0.671781 AGAGACACGAGGCACAATGC 60.672 55.000 0.00 0.00 44.08 3.56
2100 5512 1.980951 GCACAATGCGAGCGAATCCA 61.981 55.000 0.00 0.00 31.71 3.41
2101 5513 0.659427 CACAATGCGAGCGAATCCAT 59.341 50.000 0.00 0.00 0.00 3.41
2121 5533 6.353323 TCCATCTGCGGTTGATTTTAGATTA 58.647 36.000 5.11 0.00 0.00 1.75
2177 5617 1.597854 CCAAGTGCGGCAGTCTTGA 60.598 57.895 25.97 0.00 40.35 3.02
2219 5659 4.093408 GCTCTGTTTGCTCGTCATTTCATA 59.907 41.667 0.00 0.00 0.00 2.15
2224 5664 5.647658 TGTTTGCTCGTCATTTCATATCCTT 59.352 36.000 0.00 0.00 0.00 3.36
2239 5679 6.288294 TCATATCCTTATTCTTCGTGTTGGG 58.712 40.000 0.00 0.00 0.00 4.12
2240 5680 2.706890 TCCTTATTCTTCGTGTTGGGC 58.293 47.619 0.00 0.00 0.00 5.36
2241 5681 2.304761 TCCTTATTCTTCGTGTTGGGCT 59.695 45.455 0.00 0.00 0.00 5.19
2242 5682 2.420022 CCTTATTCTTCGTGTTGGGCTG 59.580 50.000 0.00 0.00 0.00 4.85
2243 5683 1.448985 TATTCTTCGTGTTGGGCTGC 58.551 50.000 0.00 0.00 0.00 5.25
2244 5684 0.250901 ATTCTTCGTGTTGGGCTGCT 60.251 50.000 0.00 0.00 0.00 4.24
2245 5685 1.165907 TTCTTCGTGTTGGGCTGCTG 61.166 55.000 0.00 0.00 0.00 4.41
2246 5686 2.594303 TTCGTGTTGGGCTGCTGG 60.594 61.111 0.00 0.00 0.00 4.85
2247 5687 3.414136 TTCGTGTTGGGCTGCTGGT 62.414 57.895 0.00 0.00 0.00 4.00
2298 5740 1.201769 CGTTTATGTGCGTGTTCTCCG 60.202 52.381 0.00 0.00 0.00 4.63
2324 5766 2.076863 CGTCACCCTCAAAACCTCATC 58.923 52.381 0.00 0.00 0.00 2.92
2332 5775 6.660949 CACCCTCAAAACCTCATCTCTTAAAT 59.339 38.462 0.00 0.00 0.00 1.40
2333 5776 7.177392 CACCCTCAAAACCTCATCTCTTAAATT 59.823 37.037 0.00 0.00 0.00 1.82
2378 5821 3.459598 TCCCAGGAGGAAGGAAACATATG 59.540 47.826 0.00 0.00 43.78 1.78
2573 6016 3.463533 TTTGCCATTCGTGACATTACG 57.536 42.857 0.00 0.00 44.98 3.18
2593 6036 2.010582 TTTTGCAACCGAGTGCCCAC 62.011 55.000 0.00 0.00 44.26 4.61
2621 6064 3.454082 TGGGTGCACCTTTGAAATTCTTT 59.546 39.130 33.91 0.00 41.11 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 9 6.225318 TCATGGCCTTTTGATTTTTCTCTTG 58.775 36.000 3.32 0.00 0.00 3.02
21 23 3.700538 TGATTGCTAGTTCATGGCCTTT 58.299 40.909 3.32 0.00 33.66 3.11
25 27 4.906065 TTGATGATTGCTAGTTCATGGC 57.094 40.909 8.94 0.00 32.84 4.40
30 32 7.324616 GTGACAGTTTTTGATGATTGCTAGTTC 59.675 37.037 0.00 0.00 0.00 3.01
82 86 6.320926 TGGAAGTCATTGACACAATGAAGAAA 59.679 34.615 22.74 9.86 38.27 2.52
120 124 3.877508 GGGCTGCAATAGTCTCGTTATTT 59.122 43.478 0.50 0.00 0.00 1.40
152 156 6.981559 GTGCTTAGGTTTGGTTTATTGTTGAA 59.018 34.615 0.00 0.00 0.00 2.69
231 236 8.093927 GGGATGACAAAGAAAATTCCATTGTTA 58.906 33.333 13.07 10.68 37.65 2.41
239 244 5.711976 TCCTCAGGGATGACAAAGAAAATTC 59.288 40.000 0.00 0.00 36.57 2.17
307 3325 3.287222 TGTTAGGCTAAATGTGGATGCC 58.713 45.455 8.86 0.00 43.52 4.40
323 3341 5.896073 AGACCTCCTATGGGATTTGTTAG 57.104 43.478 0.00 0.00 41.36 2.34
420 3441 5.147330 AGAGACGTACCAAATGTTCATGA 57.853 39.130 0.00 0.00 0.00 3.07
438 3459 4.420206 TCATGAGGGAAAGTCTCAAGAGA 58.580 43.478 0.00 0.00 43.43 3.10
502 3523 3.260483 GCACAGGAGCTGATCGCG 61.260 66.667 0.00 0.00 45.59 5.87
515 3536 0.821301 TTTGGCGTCCAGAATGCACA 60.821 50.000 0.00 0.00 42.04 4.57
532 3553 3.841255 GCCCTAGGCCTCTGTCTATATTT 59.159 47.826 9.68 0.00 44.06 1.40
552 3573 3.993736 AGCATAACCGAAAAACATTTGCC 59.006 39.130 0.00 0.00 0.00 4.52
555 3576 6.575162 AGAGAGCATAACCGAAAAACATTT 57.425 33.333 0.00 0.00 0.00 2.32
558 3579 6.385649 AAAAGAGAGCATAACCGAAAAACA 57.614 33.333 0.00 0.00 0.00 2.83
591 3615 0.668535 GTGAAGCAACGGAAGCCTTT 59.331 50.000 0.00 0.00 0.00 3.11
595 3619 1.202245 TGTTTGTGAAGCAACGGAAGC 60.202 47.619 0.00 0.00 36.72 3.86
611 3635 2.665519 GCGATGTTTGACTGCGATGTTT 60.666 45.455 0.00 0.00 0.00 2.83
612 3636 1.135972 GCGATGTTTGACTGCGATGTT 60.136 47.619 0.00 0.00 0.00 2.71
613 3637 0.443869 GCGATGTTTGACTGCGATGT 59.556 50.000 0.00 0.00 0.00 3.06
614 3638 0.443478 TGCGATGTTTGACTGCGATG 59.557 50.000 0.00 0.00 0.00 3.84
615 3639 0.723414 CTGCGATGTTTGACTGCGAT 59.277 50.000 0.00 0.00 0.00 4.58
616 3640 1.291184 CCTGCGATGTTTGACTGCGA 61.291 55.000 0.00 0.00 0.00 5.10
617 3641 1.133253 CCTGCGATGTTTGACTGCG 59.867 57.895 0.00 0.00 0.00 5.18
618 3642 1.503542 CCCTGCGATGTTTGACTGC 59.496 57.895 0.00 0.00 0.00 4.40
619 3643 1.308069 CCCCCTGCGATGTTTGACTG 61.308 60.000 0.00 0.00 0.00 3.51
620 3644 1.002134 CCCCCTGCGATGTTTGACT 60.002 57.895 0.00 0.00 0.00 3.41
622 3646 1.303236 CACCCCCTGCGATGTTTGA 60.303 57.895 0.00 0.00 0.00 2.69
624 3648 1.303317 GACACCCCCTGCGATGTTT 60.303 57.895 0.00 0.00 0.00 2.83
625 3649 1.852157 ATGACACCCCCTGCGATGTT 61.852 55.000 0.00 0.00 0.00 2.71
626 3650 0.980754 TATGACACCCCCTGCGATGT 60.981 55.000 0.00 0.00 0.00 3.06
628 3652 0.687354 GATATGACACCCCCTGCGAT 59.313 55.000 0.00 0.00 0.00 4.58
629 3653 1.407656 GGATATGACACCCCCTGCGA 61.408 60.000 0.00 0.00 0.00 5.10
630 3654 1.071471 GGATATGACACCCCCTGCG 59.929 63.158 0.00 0.00 0.00 5.18
631 3655 1.071471 CGGATATGACACCCCCTGC 59.929 63.158 0.00 0.00 0.00 4.85
632 3656 1.754745 CCGGATATGACACCCCCTG 59.245 63.158 0.00 0.00 0.00 4.45
633 3657 2.147387 GCCGGATATGACACCCCCT 61.147 63.158 5.05 0.00 0.00 4.79
634 3658 2.397413 CTGCCGGATATGACACCCCC 62.397 65.000 5.05 0.00 0.00 5.40
637 3661 0.679505 TAGCTGCCGGATATGACACC 59.320 55.000 5.05 0.00 0.00 4.16
638 3662 1.784525 GTAGCTGCCGGATATGACAC 58.215 55.000 5.05 0.00 0.00 3.67
639 3663 0.313987 CGTAGCTGCCGGATATGACA 59.686 55.000 5.05 0.00 0.00 3.58
640 3664 3.108521 CGTAGCTGCCGGATATGAC 57.891 57.895 5.05 0.00 0.00 3.06
649 3673 4.587189 CCGTAGGCCGTAGCTGCC 62.587 72.222 5.41 5.41 46.14 4.85
681 3705 1.274728 CATAGGATGAAGAGGAGCCGG 59.725 57.143 0.00 0.00 0.00 6.13
699 3723 7.857734 AAAATTCCACCGTTTTCTTTTTCAT 57.142 28.000 0.00 0.00 0.00 2.57
700 3724 7.674471 AAAAATTCCACCGTTTTCTTTTTCA 57.326 28.000 0.00 0.00 0.00 2.69
701 3725 8.875803 AGTAAAAATTCCACCGTTTTCTTTTTC 58.124 29.630 0.00 0.00 0.00 2.29
703 3727 9.872721 TTAGTAAAAATTCCACCGTTTTCTTTT 57.127 25.926 0.00 0.00 0.00 2.27
706 3730 9.524106 CTTTTAGTAAAAATTCCACCGTTTTCT 57.476 29.630 9.28 0.00 34.18 2.52
708 3732 7.225145 GCCTTTTAGTAAAAATTCCACCGTTTT 59.775 33.333 9.28 0.00 34.18 2.43
720 3771 1.894466 GGCGGGGCCTTTTAGTAAAAA 59.106 47.619 0.84 0.00 46.69 1.94
755 3806 0.108281 GCCTCCGGTAAAGTGGACTC 60.108 60.000 0.00 0.00 0.00 3.36
762 3813 2.202892 GGAGCGCCTCCGGTAAAG 60.203 66.667 2.29 0.00 46.40 1.85
892 4169 1.226018 GGAATTCGAACAAGCGGCG 60.226 57.895 0.51 0.51 0.00 6.46
976 4259 1.758514 GGAGATCGGTGGAGGCTGA 60.759 63.158 0.00 0.00 0.00 4.26
978 4261 0.909610 TTTGGAGATCGGTGGAGGCT 60.910 55.000 0.00 0.00 0.00 4.58
980 4263 2.489938 TTTTTGGAGATCGGTGGAGG 57.510 50.000 0.00 0.00 0.00 4.30
1024 4311 4.011517 GAACGCCACGGGGAGGAA 62.012 66.667 8.67 0.00 38.47 3.36
1036 4323 4.856607 CGCGAGGAGGAGGAACGC 62.857 72.222 0.00 0.00 44.64 4.84
1097 4384 2.982744 GCGGCCCAGTTCTTCTTGC 61.983 63.158 0.00 0.00 0.00 4.01
1197 4484 2.486982 TCGAGAAGACGGTGGAAACTAG 59.513 50.000 0.00 0.00 0.00 2.57
1200 4495 2.260481 GATCGAGAAGACGGTGGAAAC 58.740 52.381 0.00 0.00 0.00 2.78
1333 4635 4.130281 GCACTTGTCGTACGCCGC 62.130 66.667 11.24 3.89 36.19 6.53
1623 4925 0.235665 CACACGGTCACATTCACAGC 59.764 55.000 0.00 0.00 0.00 4.40
1624 4926 1.794701 CTCACACGGTCACATTCACAG 59.205 52.381 0.00 0.00 0.00 3.66
1637 4939 2.125912 CTTCCCTCCGCTCACACG 60.126 66.667 0.00 0.00 0.00 4.49
1675 4978 3.151710 CGGACGGCCCATACTGGA 61.152 66.667 0.00 0.00 40.96 3.86
1676 4979 4.235762 CCGGACGGCCCATACTGG 62.236 72.222 0.00 0.00 37.25 4.00
1677 4980 4.235762 CCCGGACGGCCCATACTG 62.236 72.222 0.00 0.00 34.14 2.74
1719 5022 7.857456 TCTTAATCAGCAAGTACCTTCCATAA 58.143 34.615 0.00 0.00 0.00 1.90
1734 5037 3.477899 AAGCACGCTTTCTTAATCAGC 57.522 42.857 0.00 0.00 31.29 4.26
1740 5043 3.211045 ACTTCCAAAGCACGCTTTCTTA 58.789 40.909 13.93 0.58 43.56 2.10
1825 5157 2.350522 TGCATGTGCCGTTTTGTTTTT 58.649 38.095 2.07 0.00 41.18 1.94
1826 5158 1.932511 CTGCATGTGCCGTTTTGTTTT 59.067 42.857 2.07 0.00 41.18 2.43
1827 5159 1.134848 ACTGCATGTGCCGTTTTGTTT 60.135 42.857 2.07 0.00 41.18 2.83
1828 5160 0.459489 ACTGCATGTGCCGTTTTGTT 59.541 45.000 2.07 0.00 41.18 2.83
1829 5161 0.248990 CACTGCATGTGCCGTTTTGT 60.249 50.000 2.07 0.00 40.06 2.83
1830 5162 2.508743 CACTGCATGTGCCGTTTTG 58.491 52.632 2.07 0.00 40.06 2.44
1839 5171 1.971481 TTTGTCTCAGCACTGCATGT 58.029 45.000 3.30 0.00 0.00 3.21
1840 5172 3.358707 TTTTTGTCTCAGCACTGCATG 57.641 42.857 3.30 0.00 0.00 4.06
1841 5173 4.380233 GCTATTTTTGTCTCAGCACTGCAT 60.380 41.667 3.30 0.00 32.46 3.96
1842 5174 3.058016 GCTATTTTTGTCTCAGCACTGCA 60.058 43.478 3.30 0.00 32.46 4.41
1843 5175 3.058016 TGCTATTTTTGTCTCAGCACTGC 60.058 43.478 0.00 0.00 37.32 4.40
1844 5176 4.754372 TGCTATTTTTGTCTCAGCACTG 57.246 40.909 0.00 0.00 37.32 3.66
1859 5191 0.098728 GATTTGCCGCGTGTGCTATT 59.901 50.000 4.92 0.00 39.65 1.73
1868 5200 2.261037 TCTTTTCATGATTTGCCGCG 57.739 45.000 0.00 0.00 0.00 6.46
1871 5203 8.816640 TTTTCTACTTCTTTTCATGATTTGCC 57.183 30.769 0.00 0.00 0.00 4.52
1918 5251 4.166144 ACCTGAGGGAACTTCTTTTCTCAA 59.834 41.667 2.38 0.00 44.43 3.02
1919 5252 3.716872 ACCTGAGGGAACTTCTTTTCTCA 59.283 43.478 2.38 0.00 44.43 3.27
1945 5278 3.074412 GACACATTTCCATCGGTTGTCT 58.926 45.455 0.00 0.00 0.00 3.41
1948 5281 5.621197 TTAAGACACATTTCCATCGGTTG 57.379 39.130 0.00 0.00 0.00 3.77
1952 5285 4.941263 TCCCTTTAAGACACATTTCCATCG 59.059 41.667 0.00 0.00 0.00 3.84
1999 5338 5.550290 TGATTGTCAAGAGTTATGAGCACA 58.450 37.500 0.00 0.00 0.00 4.57
2089 5501 2.305853 CCGCAGATGGATTCGCTCG 61.306 63.158 0.00 0.00 0.00 5.03
2128 5541 6.148150 CGTGTCACTAAAATAAACCTTGCCTA 59.852 38.462 0.65 0.00 0.00 3.93
2177 5617 1.537990 GCACGGCATTTGGAAAAGTGT 60.538 47.619 0.00 0.00 0.00 3.55
2219 5659 3.054361 AGCCCAACACGAAGAATAAGGAT 60.054 43.478 0.00 0.00 0.00 3.24
2224 5664 1.003118 AGCAGCCCAACACGAAGAATA 59.997 47.619 0.00 0.00 0.00 1.75
2239 5679 3.181450 ACCTTCCATAGATAACCAGCAGC 60.181 47.826 0.00 0.00 0.00 5.25
2240 5680 4.696479 ACCTTCCATAGATAACCAGCAG 57.304 45.455 0.00 0.00 0.00 4.24
2241 5681 6.763715 AATACCTTCCATAGATAACCAGCA 57.236 37.500 0.00 0.00 0.00 4.41
2242 5682 9.740710 AATTAATACCTTCCATAGATAACCAGC 57.259 33.333 0.00 0.00 0.00 4.85
2298 5740 1.069227 GTTTTGAGGGTGACGATGCAC 60.069 52.381 0.00 0.00 38.05 4.57
2337 5780 9.535170 TCCTGGGACACATAAATGTTTTTAATA 57.465 29.630 0.00 0.00 39.39 0.98
2351 5794 0.119155 TCCTTCCTCCTGGGACACAT 59.881 55.000 0.00 0.00 45.03 3.21
2402 5845 6.911484 CGAAAGCAATAGACGTTCAATTTT 57.089 33.333 0.00 0.00 0.00 1.82
2424 5867 1.788308 CAAACTTTTGCTCCATGTGCG 59.212 47.619 0.00 0.00 0.00 5.34
2451 5894 5.841810 TCTGTGCTTGTAAAATTTCTTGGG 58.158 37.500 0.00 0.00 0.00 4.12
2497 5940 5.488919 ACCAATTCCTTTCTGGACTCATCTA 59.511 40.000 0.00 0.00 46.14 1.98
2573 6016 1.299850 GGGCACTCGGTTGCAAAAC 60.300 57.895 0.00 0.00 44.94 2.43
2593 6036 1.202806 TCAAAGGTGCACCCAAGAGAG 60.203 52.381 32.29 14.93 36.42 3.20
2598 6041 3.037549 AGAATTTCAAAGGTGCACCCAA 58.962 40.909 32.29 16.72 36.42 4.12


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

AutoCloner maintained by Alex Coulton.