Multiple sequence alignment - TraesCS6B01G126100

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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 TraesCS6B01G126100 chr6B 100.000 5559 0 0 1 5559 121524175 121529733 0.000000e+00 10266
1 TraesCS6B01G126100 chr6B 88.946 389 26 7 4524 4899 121716808 121717192 1.090000e-126 464
2 TraesCS6B01G126100 chr6B 86.753 385 26 12 5057 5435 121732298 121732663 6.710000e-109 405
3 TraesCS6B01G126100 chr6B 88.657 335 31 4 5082 5409 123724490 123724156 8.670000e-108 401
4 TraesCS6B01G126100 chr6B 88.119 101 12 0 5459 5559 121733315 121733415 2.720000e-23 121
5 TraesCS6B01G126100 chr6B 90.588 85 7 1 4967 5050 121731814 121731898 1.640000e-20 111
6 TraesCS6B01G126100 chr6D 96.372 3225 90 9 692 3913 49861050 49857850 0.000000e+00 5282
7 TraesCS6B01G126100 chr6D 96.338 1147 42 0 3904 5050 49857387 49856241 0.000000e+00 1886
8 TraesCS6B01G126100 chr6D 94.687 527 10 2 5048 5559 49855733 49855210 0.000000e+00 802
9 TraesCS6B01G126100 chr6D 92.748 524 14 5 5057 5559 49849353 49848833 0.000000e+00 736
10 TraesCS6B01G126100 chr6D 89.141 396 28 9 5048 5435 49843455 49843067 3.900000e-131 479
11 TraesCS6B01G126100 chr6D 89.556 383 25 7 5052 5425 47810549 47810925 6.520000e-129 472
12 TraesCS6B01G126100 chr6D 88.773 383 41 2 4527 4909 49852106 49851726 8.430000e-128 468
13 TraesCS6B01G126100 chr6D 83.650 526 53 15 4527 5050 49844333 49843839 1.090000e-126 464
14 TraesCS6B01G126100 chr6A 92.977 1908 98 15 1725 3618 65069054 65070939 0.000000e+00 2748
15 TraesCS6B01G126100 chr6A 93.876 1437 68 6 3619 5052 65071518 65072937 0.000000e+00 2148
16 TraesCS6B01G126100 chr6A 94.063 1179 30 12 692 1870 65067673 65068811 0.000000e+00 1753
17 TraesCS6B01G126100 chr6A 91.429 525 22 10 5048 5559 65073323 65073837 0.000000e+00 699
18 TraesCS6B01G126100 chr6A 90.076 524 28 6 5057 5559 65133550 65134070 0.000000e+00 658
19 TraesCS6B01G126100 chr6A 89.610 385 28 6 5057 5435 65140393 65140771 3.900000e-131 479
20 TraesCS6B01G126100 chr6A 91.250 320 25 2 4588 4905 65132727 65133045 3.080000e-117 433
21 TraesCS6B01G126100 chr6A 89.375 320 27 4 4588 4905 65139571 65139885 4.040000e-106 396
22 TraesCS6B01G126100 chr6A 87.826 115 11 1 1488 1602 65068810 65068921 1.260000e-26 132
23 TraesCS6B01G126100 chr6A 89.286 84 9 0 4967 5050 65139921 65140004 7.620000e-19 106
24 TraesCS6B01G126100 chr1B 95.686 649 28 0 1 649 642813071 642813719 0.000000e+00 1044
25 TraesCS6B01G126100 chr1B 95.231 650 31 0 1 650 643025152 643025801 0.000000e+00 1029
26 TraesCS6B01G126100 chr3B 94.910 668 29 3 1 666 708392562 708391898 0.000000e+00 1040
27 TraesCS6B01G126100 chr3B 95.216 648 29 2 1 647 780864743 780864097 0.000000e+00 1024
28 TraesCS6B01G126100 chr7B 95.144 659 25 1 1 659 191893361 191892710 0.000000e+00 1033
29 TraesCS6B01G126100 chr7B 95.231 650 31 0 1 650 498599570 498598921 0.000000e+00 1029
30 TraesCS6B01G126100 chr7B 95.231 650 31 0 1 650 739379496 739380145 0.000000e+00 1029
31 TraesCS6B01G126100 chr2B 95.253 653 28 1 1 653 776456833 776456184 0.000000e+00 1031
32 TraesCS6B01G126100 chr2B 95.231 650 30 1 1 650 452910377 452911025 0.000000e+00 1027


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 TraesCS6B01G126100 chr6B 121524175 121529733 5558 False 10266.000000 10266 100.000000 1 5559 1 chr6B.!!$F1 5558
1 TraesCS6B01G126100 chr6B 121731814 121733415 1601 False 212.333333 405 88.486667 4967 5559 3 chr6B.!!$F3 592
2 TraesCS6B01G126100 chr6D 49848833 49861050 12217 True 1834.800000 5282 93.783600 692 5559 5 chr6D.!!$R2 4867
3 TraesCS6B01G126100 chr6D 49843067 49844333 1266 True 471.500000 479 86.395500 4527 5435 2 chr6D.!!$R1 908
4 TraesCS6B01G126100 chr6A 65067673 65073837 6164 False 1496.000000 2748 92.034200 692 5559 5 chr6A.!!$F1 4867
5 TraesCS6B01G126100 chr6A 65132727 65134070 1343 False 545.500000 658 90.663000 4588 5559 2 chr6A.!!$F2 971
6 TraesCS6B01G126100 chr6A 65139571 65140771 1200 False 327.000000 479 89.423667 4588 5435 3 chr6A.!!$F3 847
7 TraesCS6B01G126100 chr1B 642813071 642813719 648 False 1044.000000 1044 95.686000 1 649 1 chr1B.!!$F1 648
8 TraesCS6B01G126100 chr1B 643025152 643025801 649 False 1029.000000 1029 95.231000 1 650 1 chr1B.!!$F2 649
9 TraesCS6B01G126100 chr3B 708391898 708392562 664 True 1040.000000 1040 94.910000 1 666 1 chr3B.!!$R1 665
10 TraesCS6B01G126100 chr3B 780864097 780864743 646 True 1024.000000 1024 95.216000 1 647 1 chr3B.!!$R2 646
11 TraesCS6B01G126100 chr7B 191892710 191893361 651 True 1033.000000 1033 95.144000 1 659 1 chr7B.!!$R1 658
12 TraesCS6B01G126100 chr7B 498598921 498599570 649 True 1029.000000 1029 95.231000 1 650 1 chr7B.!!$R2 649
13 TraesCS6B01G126100 chr7B 739379496 739380145 649 False 1029.000000 1029 95.231000 1 650 1 chr7B.!!$F1 649
14 TraesCS6B01G126100 chr2B 776456184 776456833 649 True 1031.000000 1031 95.253000 1 653 1 chr2B.!!$R1 652
15 TraesCS6B01G126100 chr2B 452910377 452911025 648 False 1027.000000 1027 95.231000 1 650 1 chr2B.!!$F1 649

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
662 664 0.236449 GGAAAACCGTACGCACAAGG 59.764 55.0 10.49 0.0 0.00 3.61 F
2355 2752 0.108138 CCCTGTTTAGAGGAGGCGTG 60.108 60.0 0.00 0.0 34.69 5.34 F
2372 2771 0.452122 GTGATGTTTGTACGTGCGCC 60.452 55.0 4.18 0.0 0.00 6.53 F
3880 4863 0.846427 ATCCACCTGCCCTTGGAGAA 60.846 55.0 3.89 0.0 45.20 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2372 2771 0.036765 TAGCAACAGCCCTTGTACCG 60.037 55.000 0.00 0.0 39.73 4.02 R
4275 5730 1.918262 ACATGATCAGAAGGGGCAGAA 59.082 47.619 0.00 0.0 0.00 3.02 R
4414 5869 2.171237 CCCCAGTGATCTCTGCATGTTA 59.829 50.000 17.52 0.0 34.47 2.41 R
5042 6514 1.419387 GGCCTGATCTCTGCCTTATGT 59.581 52.381 11.85 0.0 42.01 2.29 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
82 83 1.144969 GCCGTTGAACGAATCAGACA 58.855 50.000 20.47 0.00 46.05 3.41
102 103 4.572571 GGCAACACCCCGGACACA 62.573 66.667 0.73 0.00 0.00 3.72
205 206 0.597637 CAGCACACGTTCCGTCTTCT 60.598 55.000 0.00 0.00 38.32 2.85
371 372 6.202954 CGTCCTTACTTGAACAGACTGATTTT 59.797 38.462 10.08 0.00 0.00 1.82
426 427 3.119459 TCGTCAGAAAAGGATCCGAAGAG 60.119 47.826 5.98 0.00 0.00 2.85
609 611 1.923395 TTGGAAGATCGGCCCCTGT 60.923 57.895 0.00 0.00 0.00 4.00
659 661 0.390124 AGAGGAAAACCGTACGCACA 59.610 50.000 10.49 0.00 0.00 4.57
660 662 1.202557 AGAGGAAAACCGTACGCACAA 60.203 47.619 10.49 0.00 0.00 3.33
661 663 1.193874 GAGGAAAACCGTACGCACAAG 59.806 52.381 10.49 0.00 0.00 3.16
662 664 0.236449 GGAAAACCGTACGCACAAGG 59.764 55.000 10.49 0.00 0.00 3.61
663 665 1.219646 GAAAACCGTACGCACAAGGA 58.780 50.000 10.49 0.00 0.00 3.36
664 666 1.598601 GAAAACCGTACGCACAAGGAA 59.401 47.619 10.49 0.00 0.00 3.36
665 667 1.886886 AAACCGTACGCACAAGGAAT 58.113 45.000 10.49 0.00 0.00 3.01
666 668 1.435577 AACCGTACGCACAAGGAATC 58.564 50.000 10.49 0.00 0.00 2.52
667 669 0.734942 ACCGTACGCACAAGGAATCG 60.735 55.000 10.49 0.00 0.00 3.34
668 670 0.734942 CCGTACGCACAAGGAATCGT 60.735 55.000 10.49 0.00 38.75 3.73
669 671 1.065358 CGTACGCACAAGGAATCGTT 58.935 50.000 0.52 0.00 36.50 3.85
670 672 1.458064 CGTACGCACAAGGAATCGTTT 59.542 47.619 0.52 0.00 36.50 3.60
671 673 2.096614 CGTACGCACAAGGAATCGTTTT 60.097 45.455 0.52 0.00 36.50 2.43
672 674 3.121611 CGTACGCACAAGGAATCGTTTTA 59.878 43.478 0.52 0.00 36.50 1.52
673 675 3.806316 ACGCACAAGGAATCGTTTTAG 57.194 42.857 0.00 0.00 0.00 1.85
674 676 3.395639 ACGCACAAGGAATCGTTTTAGA 58.604 40.909 0.00 0.00 0.00 2.10
675 677 3.810941 ACGCACAAGGAATCGTTTTAGAA 59.189 39.130 0.00 0.00 0.00 2.10
676 678 4.084013 ACGCACAAGGAATCGTTTTAGAAG 60.084 41.667 0.00 0.00 0.00 2.85
677 679 4.151689 CGCACAAGGAATCGTTTTAGAAGA 59.848 41.667 0.00 0.00 0.00 2.87
678 680 5.333798 CGCACAAGGAATCGTTTTAGAAGAA 60.334 40.000 0.00 0.00 0.00 2.52
679 681 6.435428 GCACAAGGAATCGTTTTAGAAGAAA 58.565 36.000 0.00 0.00 0.00 2.52
680 682 6.915843 GCACAAGGAATCGTTTTAGAAGAAAA 59.084 34.615 0.00 0.00 0.00 2.29
681 683 7.595130 GCACAAGGAATCGTTTTAGAAGAAAAT 59.405 33.333 0.00 0.00 0.00 1.82
682 684 9.118236 CACAAGGAATCGTTTTAGAAGAAAATC 57.882 33.333 0.00 0.00 0.00 2.17
683 685 9.067986 ACAAGGAATCGTTTTAGAAGAAAATCT 57.932 29.630 0.00 0.00 0.00 2.40
684 686 9.899226 CAAGGAATCGTTTTAGAAGAAAATCTT 57.101 29.630 0.00 0.00 39.87 2.40
776 778 4.377897 GGCGAATTTACTGGCTACTGTAT 58.622 43.478 0.00 0.00 32.14 2.29
777 779 4.211374 GGCGAATTTACTGGCTACTGTATG 59.789 45.833 0.00 0.00 32.14 2.39
778 780 4.809426 GCGAATTTACTGGCTACTGTATGT 59.191 41.667 0.00 0.00 32.14 2.29
798 801 0.677731 ACAGCGCATTACAGGCACAT 60.678 50.000 11.47 0.00 0.00 3.21
805 808 2.483013 GCATTACAGGCACATCCGTAGA 60.483 50.000 0.00 0.00 40.77 2.59
883 886 4.856801 GATGACATGCGGGCCCGT 62.857 66.667 42.53 25.81 42.09 5.28
978 981 3.083349 CTCCCCCATCGCCACTGA 61.083 66.667 0.00 0.00 0.00 3.41
1407 1410 4.651008 TCCGTGCGGTTCGTGGTC 62.651 66.667 10.60 0.00 36.47 4.02
1570 1573 1.570967 GCGTACGGGAACACCAAAC 59.429 57.895 18.39 0.00 40.22 2.93
1622 1625 3.764434 TCTCTGTAGGATGTGGAGTGTTC 59.236 47.826 0.00 0.00 0.00 3.18
1624 1627 4.096681 TCTGTAGGATGTGGAGTGTTCAT 58.903 43.478 0.00 0.00 0.00 2.57
1633 1636 6.769822 GGATGTGGAGTGTTCATATCTGAAAT 59.230 38.462 0.00 0.00 42.85 2.17
1670 1673 2.089201 ACGCAATTTAGTTAGGCACCC 58.911 47.619 0.00 0.00 0.00 4.61
1689 1692 1.216178 GTGCACATTGACATGGGGC 59.784 57.895 13.17 0.00 33.88 5.80
1803 2193 4.694509 GCATGCCATTATCGAAGAGATCTT 59.305 41.667 6.36 0.00 43.63 2.40
1804 2194 5.390673 GCATGCCATTATCGAAGAGATCTTG 60.391 44.000 6.36 0.00 43.63 3.02
1948 2339 9.450807 CTGTTTGGTTTGTATAGCATTATAAGC 57.549 33.333 0.00 0.00 0.00 3.09
2061 2454 6.239036 GGATTTTGTGCTATGAAATACTCCCC 60.239 42.308 0.00 0.00 0.00 4.81
2064 2457 3.780294 TGTGCTATGAAATACTCCCCACT 59.220 43.478 0.00 0.00 0.00 4.00
2238 2635 2.991540 GGGGTGCTTGTCCTTGGC 60.992 66.667 0.00 0.00 0.00 4.52
2325 2722 6.978659 TGATGAATCGAGTAGGTGTGTTATTC 59.021 38.462 0.00 0.00 0.00 1.75
2355 2752 0.108138 CCCTGTTTAGAGGAGGCGTG 60.108 60.000 0.00 0.00 34.69 5.34
2356 2753 0.895530 CCTGTTTAGAGGAGGCGTGA 59.104 55.000 0.00 0.00 34.69 4.35
2372 2771 0.452122 GTGATGTTTGTACGTGCGCC 60.452 55.000 4.18 0.00 0.00 6.53
2470 2869 7.010923 TGCTTGTGTTTTGTTTAATTGCTTAGG 59.989 33.333 0.00 0.00 0.00 2.69
2490 2889 5.121221 AGGTTAATGCCTTTGTTCTTTCG 57.879 39.130 0.00 0.00 34.71 3.46
2726 3126 3.607741 CTCACTGAGCTTCAATGTCCAT 58.392 45.455 0.00 0.00 0.00 3.41
2757 3157 5.411831 AGTTCTGTCTGATAACAGCATCA 57.588 39.130 0.00 0.00 45.12 3.07
2986 3387 2.364324 GGGATGTATTGTAGACTCGGCA 59.636 50.000 0.00 0.00 0.00 5.69
3127 3529 9.706691 TGTGGAACATTTTGTTGTAAGTAAAAA 57.293 25.926 0.00 0.00 45.67 1.94
3274 3676 1.693062 CTGACTCCCCTGATGGATCTG 59.307 57.143 0.00 0.00 35.39 2.90
3422 3824 2.093128 ACCGGTAAGTCCATTCACCATC 60.093 50.000 4.49 0.00 35.57 3.51
3506 3908 3.496884 GCCAAGGCATATGCAATGAAATG 59.503 43.478 28.07 14.50 44.36 2.32
3761 4744 5.836358 ACCCTTCTAGTCTGGAATCTACATC 59.164 44.000 0.00 0.00 0.00 3.06
3780 4763 6.645790 ACATCCAGCCTAAAATCATCATTC 57.354 37.500 0.00 0.00 0.00 2.67
3797 4780 5.738619 TCATTCGGTACACATAGCCATAT 57.261 39.130 0.00 0.00 0.00 1.78
3880 4863 0.846427 ATCCACCTGCCCTTGGAGAA 60.846 55.000 3.89 0.00 45.20 2.87
4036 5491 1.491668 TATCCTAAGCTCCCAACGCA 58.508 50.000 0.00 0.00 0.00 5.24
4251 5706 1.388547 TTGACCACAGAAACACCAGC 58.611 50.000 0.00 0.00 0.00 4.85
4275 5730 7.443575 AGCTGCGTCTTCATATTCTGATATTTT 59.556 33.333 0.00 0.00 32.72 1.82
4414 5869 3.119291 CGAATGCGTAGAGAGCTTCATT 58.881 45.455 0.00 0.00 35.28 2.57
4468 5923 2.942376 AGCACACAATTTTGTCTCGTCA 59.058 40.909 0.00 0.00 39.91 4.35
4545 6000 1.700186 GTTCCTGAAGGTCTGTTCCCT 59.300 52.381 0.00 0.00 36.34 4.20
4571 6026 7.946207 AGTTAGTGTATGATGATGAATCGACT 58.054 34.615 0.00 0.00 38.22 4.18
4640 6095 3.544615 GTCTTTTGACCAACACGGC 57.455 52.632 0.00 0.00 43.37 5.68
4703 6158 4.556942 TTAGCGTATGTAGTGCGTGTAT 57.443 40.909 0.00 0.00 38.27 2.29
4705 6160 2.356695 AGCGTATGTAGTGCGTGTATGA 59.643 45.455 0.00 0.00 38.27 2.15
4748 6203 5.339695 GGGTGTTTGAAGAGGGGTAATATCA 60.340 44.000 0.00 0.00 0.00 2.15
4751 6206 5.251932 TGTTTGAAGAGGGGTAATATCACCA 59.748 40.000 0.00 0.00 40.65 4.17
4752 6207 5.367945 TTGAAGAGGGGTAATATCACCAC 57.632 43.478 0.00 0.00 42.84 4.16
4753 6208 4.367166 TGAAGAGGGGTAATATCACCACA 58.633 43.478 0.00 0.00 45.15 4.17
4754 6209 4.975147 TGAAGAGGGGTAATATCACCACAT 59.025 41.667 0.00 0.00 45.15 3.21
4755 6210 5.071788 TGAAGAGGGGTAATATCACCACATC 59.928 44.000 0.00 0.00 45.15 3.06
4756 6211 4.566837 AGAGGGGTAATATCACCACATCA 58.433 43.478 0.00 0.00 45.15 3.07
4757 6212 5.165652 AGAGGGGTAATATCACCACATCAT 58.834 41.667 0.00 0.00 45.15 2.45
4758 6213 5.249393 AGAGGGGTAATATCACCACATCATC 59.751 44.000 0.00 0.00 45.15 2.92
4759 6214 4.913355 AGGGGTAATATCACCACATCATCA 59.087 41.667 0.00 0.00 45.15 3.07
4760 6215 5.372363 AGGGGTAATATCACCACATCATCAA 59.628 40.000 0.00 0.00 45.15 2.57
4777 6244 1.558294 TCAAGCATCCATGTGAGCTCT 59.442 47.619 16.19 0.00 36.07 4.09
4811 6278 6.115448 ACTCAAGCAACTCTTTGTAGGTAT 57.885 37.500 0.00 0.00 34.90 2.73
4918 6388 7.390996 CCTAGTTAAGCATCTTATCTACTCCGA 59.609 40.741 0.00 0.00 0.00 4.55
4935 6405 2.890442 CGAGAGGCAAGAAAAAGCTC 57.110 50.000 0.00 0.00 0.00 4.09
4969 6440 6.368791 TGCCAATGATTATGTAATAGCGAGAC 59.631 38.462 0.00 0.00 0.00 3.36
4974 6445 7.141100 TGATTATGTAATAGCGAGACGATGA 57.859 36.000 0.00 0.00 0.00 2.92
5042 6514 9.176460 TGAAAGACATAGATAATTGCATTGTCA 57.824 29.630 0.00 0.00 35.60 3.58
5481 14750 0.798771 GACGCGATGCTCTTCTTCGT 60.799 55.000 15.93 0.00 42.32 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
125 126 1.870055 GCGTCTTAGTCGTGGTGGGA 61.870 60.000 0.68 0.00 0.00 4.37
159 160 0.743345 GGTTCGTGGATGGCAGGTAC 60.743 60.000 0.00 0.00 0.00 3.34
205 206 1.333931 GGTCTGCATCGACGACATCTA 59.666 52.381 0.00 0.00 34.75 1.98
272 273 2.372690 CGACGACGTTTGCTCCAGG 61.373 63.158 0.13 0.00 34.56 4.45
347 348 7.226720 TGAAAATCAGTCTGTTCAAGTAAGGAC 59.773 37.037 0.00 0.00 0.00 3.85
371 372 1.911454 ATGGTTGGGGATGGATCTGA 58.089 50.000 0.00 0.00 0.00 3.27
426 427 4.440103 ACGATGACGACGCTGAATAAATAC 59.560 41.667 0.00 0.00 42.66 1.89
630 632 1.753073 GGTTTTCCTCTCGTATCCGGA 59.247 52.381 6.61 6.61 36.94 5.14
672 674 8.787852 CCTGCTACTTACAAAAGATTTTCTTCT 58.212 33.333 0.00 0.00 35.27 2.85
673 675 7.539022 GCCTGCTACTTACAAAAGATTTTCTTC 59.461 37.037 0.00 0.00 35.27 2.87
674 676 7.014230 TGCCTGCTACTTACAAAAGATTTTCTT 59.986 33.333 0.00 0.00 38.59 2.52
675 677 6.490040 TGCCTGCTACTTACAAAAGATTTTCT 59.510 34.615 0.00 0.00 36.50 2.52
676 678 6.677913 TGCCTGCTACTTACAAAAGATTTTC 58.322 36.000 0.00 0.00 36.50 2.29
677 679 6.294731 CCTGCCTGCTACTTACAAAAGATTTT 60.295 38.462 0.00 0.00 36.50 1.82
678 680 5.183904 CCTGCCTGCTACTTACAAAAGATTT 59.816 40.000 0.00 0.00 36.50 2.17
679 681 4.702131 CCTGCCTGCTACTTACAAAAGATT 59.298 41.667 0.00 0.00 36.50 2.40
680 682 4.265073 CCTGCCTGCTACTTACAAAAGAT 58.735 43.478 0.00 0.00 36.50 2.40
681 683 3.674997 CCTGCCTGCTACTTACAAAAGA 58.325 45.455 0.00 0.00 36.50 2.52
682 684 2.162408 GCCTGCCTGCTACTTACAAAAG 59.838 50.000 0.00 0.00 38.77 2.27
683 685 2.159382 GCCTGCCTGCTACTTACAAAA 58.841 47.619 0.00 0.00 0.00 2.44
684 686 1.821216 GCCTGCCTGCTACTTACAAA 58.179 50.000 0.00 0.00 0.00 2.83
685 687 0.391130 CGCCTGCCTGCTACTTACAA 60.391 55.000 0.00 0.00 0.00 2.41
686 688 1.218047 CGCCTGCCTGCTACTTACA 59.782 57.895 0.00 0.00 0.00 2.41
687 689 0.458669 TACGCCTGCCTGCTACTTAC 59.541 55.000 0.00 0.00 0.00 2.34
688 690 0.744874 CTACGCCTGCCTGCTACTTA 59.255 55.000 0.00 0.00 0.00 2.24
689 691 1.258445 ACTACGCCTGCCTGCTACTT 61.258 55.000 0.00 0.00 0.00 2.24
690 692 1.682684 ACTACGCCTGCCTGCTACT 60.683 57.895 0.00 0.00 0.00 2.57
776 778 0.036858 TGCCTGTAATGCGCTGTACA 60.037 50.000 18.53 18.53 0.00 2.90
777 779 0.373716 GTGCCTGTAATGCGCTGTAC 59.626 55.000 9.73 11.43 35.01 2.90
778 780 0.036858 TGTGCCTGTAATGCGCTGTA 60.037 50.000 9.73 0.00 38.83 2.74
784 787 1.867233 CTACGGATGTGCCTGTAATGC 59.133 52.381 0.00 0.00 0.00 3.56
867 870 4.856801 GACGGGCCCGCATGTCAT 62.857 66.667 43.58 23.47 44.19 3.06
888 891 1.813178 CAGTTACAGAGACTCCGCTGA 59.187 52.381 0.00 0.00 41.89 4.26
899 902 1.713597 CATGCGCTCACAGTTACAGA 58.286 50.000 9.73 0.00 0.00 3.41
978 981 4.704833 ATGGCTGTTCCGCTGCGT 62.705 61.111 21.59 0.00 42.12 5.24
1597 1600 4.780021 ACACTCCACATCCTACAGAGAATT 59.220 41.667 0.00 0.00 0.00 2.17
1670 1673 1.507630 CCCCATGTCAATGTGCACG 59.492 57.895 13.13 0.00 31.27 5.34
1803 2193 3.636679 AGCATGCTCCTACTCTAACTCA 58.363 45.455 16.30 0.00 0.00 3.41
1804 2194 4.664150 AAGCATGCTCCTACTCTAACTC 57.336 45.455 22.93 0.00 0.00 3.01
2061 2454 8.723942 AAGGTGTTAGAGATAAATTGCTAGTG 57.276 34.615 0.00 0.00 0.00 2.74
2238 2635 0.386352 CACAGCAGAAACATGTGGCG 60.386 55.000 0.00 1.46 40.47 5.69
2287 2684 6.533723 ACTCGATTCATCAAGCACGTTTTATA 59.466 34.615 0.00 0.00 0.00 0.98
2325 2722 5.012148 TCCTCTAAACAGGGTTCTCTTTGAG 59.988 44.000 0.00 0.00 33.81 3.02
2355 2752 1.225637 CGGCGCACGTACAAACATC 60.226 57.895 10.83 0.00 37.93 3.06
2356 2753 2.673114 CCGGCGCACGTACAAACAT 61.673 57.895 10.83 0.00 42.24 2.71
2372 2771 0.036765 TAGCAACAGCCCTTGTACCG 60.037 55.000 0.00 0.00 39.73 4.02
2437 2836 4.666928 AACAAAACACAAGCAGCAAAAG 57.333 36.364 0.00 0.00 0.00 2.27
2470 2869 5.746721 ACAACGAAAGAACAAAGGCATTAAC 59.253 36.000 0.00 0.00 0.00 2.01
2490 2889 5.467705 CCCTACTGTGAGTACAAGTACAAC 58.532 45.833 12.43 10.18 38.48 3.32
2568 2967 6.355747 ACTCATCCAAAGATCTCCAAGAATC 58.644 40.000 0.00 0.00 0.00 2.52
2569 2968 6.324601 ACTCATCCAAAGATCTCCAAGAAT 57.675 37.500 0.00 0.00 0.00 2.40
2570 2969 5.768980 ACTCATCCAAAGATCTCCAAGAA 57.231 39.130 0.00 0.00 0.00 2.52
2571 2970 5.365025 CCTACTCATCCAAAGATCTCCAAGA 59.635 44.000 0.00 0.00 0.00 3.02
2572 2971 5.130145 ACCTACTCATCCAAAGATCTCCAAG 59.870 44.000 0.00 0.00 0.00 3.61
2573 2972 5.032846 ACCTACTCATCCAAAGATCTCCAA 58.967 41.667 0.00 0.00 0.00 3.53
2574 2973 4.624913 ACCTACTCATCCAAAGATCTCCA 58.375 43.478 0.00 0.00 0.00 3.86
2726 3126 7.676004 TGTTATCAGACAGAACTATTGGACAA 58.324 34.615 0.00 0.00 0.00 3.18
2757 3157 7.944729 AGAAGTATCCTTAACAACATGCAAT 57.055 32.000 0.00 0.00 0.00 3.56
2986 3387 6.080969 TCTGGTCTAATCTCTAGAACTGGT 57.919 41.667 0.00 0.00 33.00 4.00
3127 3529 9.965824 CAAGTTTGTCTGGTGAAATAGTATTTT 57.034 29.630 9.47 0.00 0.00 1.82
3128 3530 9.131791 ACAAGTTTGTCTGGTGAAATAGTATTT 57.868 29.630 7.87 7.87 36.50 1.40
3129 3531 8.691661 ACAAGTTTGTCTGGTGAAATAGTATT 57.308 30.769 0.00 0.00 36.50 1.89
3274 3676 2.224018 TGTTCAAGGCACCATTCAAAGC 60.224 45.455 0.00 0.00 0.00 3.51
3422 3824 8.134895 ACCATGTAACCGAAGCAATAATTATTG 58.865 33.333 26.99 26.99 44.44 1.90
3506 3908 6.861572 GCTAAAAGAACACCCATTGTAACTTC 59.138 38.462 0.00 0.00 37.51 3.01
3605 4010 9.905713 AAGCATATATCCTTAGTTTCTTGACAA 57.094 29.630 0.00 0.00 0.00 3.18
3761 4744 3.885297 ACCGAATGATGATTTTAGGCTGG 59.115 43.478 0.00 0.00 0.00 4.85
3780 4763 4.864806 GTCATGATATGGCTATGTGTACCG 59.135 45.833 0.00 0.00 30.66 4.02
3846 4829 5.220931 GCAGGTGGATGTAAGAAGCAAATAG 60.221 44.000 0.00 0.00 0.00 1.73
3880 4863 6.596869 TTCTCCTTAATCCAATCCTCCAAT 57.403 37.500 0.00 0.00 0.00 3.16
4251 5706 9.591404 GAAAAATATCAGAATATGAAGACGCAG 57.409 33.333 0.00 0.00 42.53 5.18
4275 5730 1.918262 ACATGATCAGAAGGGGCAGAA 59.082 47.619 0.00 0.00 0.00 3.02
4414 5869 2.171237 CCCCAGTGATCTCTGCATGTTA 59.829 50.000 17.52 0.00 34.47 2.41
4468 5923 1.295423 GTAGTGGTCCACATGCGGT 59.705 57.895 24.02 4.62 36.74 5.68
4545 6000 9.067986 AGTCGATTCATCATCATACACTAACTA 57.932 33.333 0.00 0.00 0.00 2.24
4640 6095 8.289618 TCAAATTTTCACTAGAATCTTCAACCG 58.710 33.333 0.00 0.00 32.89 4.44
4690 6145 3.949113 TCCTACATCATACACGCACTACA 59.051 43.478 0.00 0.00 0.00 2.74
4699 6154 6.976934 TGTAGAAGCATCCTACATCATACA 57.023 37.500 8.25 0.00 40.87 2.29
4748 6203 2.812836 TGGATGCTTGATGATGTGGT 57.187 45.000 0.00 0.00 0.00 4.16
4751 6206 3.883489 CTCACATGGATGCTTGATGATGT 59.117 43.478 7.12 0.00 0.00 3.06
4752 6207 3.304726 GCTCACATGGATGCTTGATGATG 60.305 47.826 7.12 0.00 0.00 3.07
4753 6208 2.885266 GCTCACATGGATGCTTGATGAT 59.115 45.455 7.12 0.00 0.00 2.45
4754 6209 2.092592 AGCTCACATGGATGCTTGATGA 60.093 45.455 7.12 6.25 30.96 2.92
4755 6210 2.290916 GAGCTCACATGGATGCTTGATG 59.709 50.000 9.40 2.51 35.76 3.07
4756 6211 2.172930 AGAGCTCACATGGATGCTTGAT 59.827 45.455 17.77 0.00 35.76 2.57
4757 6212 1.558294 AGAGCTCACATGGATGCTTGA 59.442 47.619 17.77 0.00 35.76 3.02
4758 6213 2.039818 AGAGCTCACATGGATGCTTG 57.960 50.000 17.77 0.00 35.76 4.01
4759 6214 3.647113 AGATAGAGCTCACATGGATGCTT 59.353 43.478 17.77 0.00 35.76 3.91
4760 6215 3.241156 AGATAGAGCTCACATGGATGCT 58.759 45.455 17.77 8.04 38.59 3.79
4777 6244 7.233389 AGAGTTGCTTGAGTTTGAGTAGATA 57.767 36.000 0.00 0.00 0.00 1.98
4811 6278 5.360999 AGGAATAGACAGTTCGATCATCACA 59.639 40.000 0.00 0.00 0.00 3.58
4918 6388 4.892345 AGAAAAGAGCTTTTTCTTGCCTCT 59.108 37.500 21.10 10.48 43.84 3.69
4963 6433 4.602995 AGAAAAGACTATCATCGTCTCGC 58.397 43.478 0.00 0.00 40.65 5.03
4969 6440 8.417780 ACTTCATCAAGAAAAGACTATCATCG 57.582 34.615 0.00 0.00 35.40 3.84
4974 6445 6.166279 TGCGACTTCATCAAGAAAAGACTAT 58.834 36.000 0.00 0.00 35.40 2.12
5042 6514 1.419387 GGCCTGATCTCTGCCTTATGT 59.581 52.381 11.85 0.00 42.01 2.29
5299 14102 2.436824 GCCTTCTTCAGGGACGCC 60.437 66.667 0.00 0.00 44.16 5.68


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

AutoCloner maintained by Alex Coulton.