Multiple sequence alignment - TraesCS3B01G128900

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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 TraesCS3B01G128900 chr3B 100.000 4408 0 0 1 4408 108237918 108242325 0.000000e+00 8141.0
1 TraesCS3B01G128900 chr3B 72.210 457 119 8 191 643 60766029 60765577 2.770000e-27 134.0
2 TraesCS3B01G128900 chr3B 82.609 92 11 5 853 941 73077735 73077824 4.730000e-10 76.8
3 TraesCS3B01G128900 chr3D 94.024 3196 123 23 898 4076 64855977 64859121 0.000000e+00 4782.0
4 TraesCS3B01G128900 chr3D 81.047 707 116 15 1 698 541402136 541401439 8.340000e-152 547.0
5 TraesCS3B01G128900 chr3D 93.803 355 11 2 4059 4408 64859286 64859634 1.400000e-144 523.0
6 TraesCS3B01G128900 chr3A 96.031 2444 79 6 970 3412 75590139 75592565 0.000000e+00 3960.0
7 TraesCS3B01G128900 chr3A 93.825 583 29 5 3630 4207 75592564 75593144 0.000000e+00 870.0
8 TraesCS3B01G128900 chr3A 82.147 773 96 22 1 765 75588967 75589705 3.740000e-175 625.0
9 TraesCS3B01G128900 chr3A 79.858 705 129 10 1 698 676903016 676902318 1.830000e-138 503.0
10 TraesCS3B01G128900 chr3A 80.610 557 68 20 1 550 75530123 75530646 1.150000e-105 394.0
11 TraesCS3B01G128900 chr3A 90.909 209 15 3 4204 4408 75593400 75593608 1.210000e-70 278.0
12 TraesCS3B01G128900 chr4D 79.345 702 136 9 2 698 64611129 64610432 6.630000e-133 484.0
13 TraesCS3B01G128900 chr7D 79.446 686 135 6 1 682 180076365 180077048 8.570000e-132 481.0
14 TraesCS3B01G128900 chr7D 78.582 705 130 13 1 698 264070686 264069996 3.130000e-121 446.0
15 TraesCS3B01G128900 chr2B 79.197 697 138 7 1 693 772369119 772368426 1.110000e-130 477.0
16 TraesCS3B01G128900 chr2B 78.766 697 141 7 1 693 772360038 772359345 1.120000e-125 460.0
17 TraesCS3B01G128900 chr2B 74.462 697 162 16 11 698 324720910 324721599 2.010000e-73 287.0
18 TraesCS3B01G128900 chr1D 76.600 500 113 4 196 694 7826882 7826386 5.620000e-69 272.0
19 TraesCS3B01G128900 chr1D 71.799 578 148 15 68 637 320170619 320170049 2.750000e-32 150.0


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 TraesCS3B01G128900 chr3B 108237918 108242325 4407 False 8141.00 8141 100.0000 1 4408 1 chr3B.!!$F2 4407
1 TraesCS3B01G128900 chr3D 64855977 64859634 3657 False 2652.50 4782 93.9135 898 4408 2 chr3D.!!$F1 3510
2 TraesCS3B01G128900 chr3D 541401439 541402136 697 True 547.00 547 81.0470 1 698 1 chr3D.!!$R1 697
3 TraesCS3B01G128900 chr3A 75588967 75593608 4641 False 1433.25 3960 90.7280 1 4408 4 chr3A.!!$F2 4407
4 TraesCS3B01G128900 chr3A 676902318 676903016 698 True 503.00 503 79.8580 1 698 1 chr3A.!!$R1 697
5 TraesCS3B01G128900 chr3A 75530123 75530646 523 False 394.00 394 80.6100 1 550 1 chr3A.!!$F1 549
6 TraesCS3B01G128900 chr4D 64610432 64611129 697 True 484.00 484 79.3450 2 698 1 chr4D.!!$R1 696
7 TraesCS3B01G128900 chr7D 180076365 180077048 683 False 481.00 481 79.4460 1 682 1 chr7D.!!$F1 681
8 TraesCS3B01G128900 chr7D 264069996 264070686 690 True 446.00 446 78.5820 1 698 1 chr7D.!!$R1 697
9 TraesCS3B01G128900 chr2B 772368426 772369119 693 True 477.00 477 79.1970 1 693 1 chr2B.!!$R2 692
10 TraesCS3B01G128900 chr2B 772359345 772360038 693 True 460.00 460 78.7660 1 693 1 chr2B.!!$R1 692
11 TraesCS3B01G128900 chr2B 324720910 324721599 689 False 287.00 287 74.4620 11 698 1 chr2B.!!$F1 687

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
968 1264 0.041833 TGGAGAAGCTCTAGGGCTGT 59.958 55.000 20.25 8.91 42.24 4.40 F
981 1277 1.377987 GGCTGTTTGACCCCGCATA 60.378 57.895 0.00 0.00 0.00 3.14 F
1010 1306 1.808411 TCTGTTTTGATGGAGACGCC 58.192 50.000 0.00 0.00 37.10 5.68 F
1336 1632 2.264794 GGTTCATCGGGACTGCGT 59.735 61.111 0.00 0.00 0.00 5.24 F
1933 2230 0.390860 ATATCTGTGTGCCGAGAGCC 59.609 55.000 0.00 0.00 42.71 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1928 2225 0.041386 ACCCTAAAGTCTCGGGCTCT 59.959 55.0 0.0 0.0 41.86 4.09 R
1930 2227 0.041386 AGACCCTAAAGTCTCGGGCT 59.959 55.0 0.0 0.0 43.76 5.19 R
1931 2228 0.903236 AAGACCCTAAAGTCTCGGGC 59.097 55.0 0.0 0.0 46.44 6.13 R
3298 3595 1.115467 ATTCAGCTCTACCCGACTGG 58.885 55.0 0.0 0.0 41.37 4.00 R
3610 3907 0.397675 TTGTTGCCCATTGACCACCA 60.398 50.0 0.0 0.0 0.00 4.17 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
206 212 0.545071 AAGTTCCAGGGGCCCAAATG 60.545 55.000 27.72 18.69 0.00 2.32
279 285 4.521639 AGATTATAGGTTACACCGCGATGA 59.478 41.667 7.92 0.00 44.90 2.92
280 286 4.859304 TTATAGGTTACACCGCGATGAT 57.141 40.909 7.92 0.00 44.90 2.45
297 303 4.637534 CGATGATGAACAAGTCTGGGAATT 59.362 41.667 0.00 0.00 0.00 2.17
361 368 3.066814 GGTAGACGCACCCGACCT 61.067 66.667 0.00 0.00 38.29 3.85
397 405 2.822399 GATGCGAAGGACCGGGAT 59.178 61.111 6.32 0.00 0.00 3.85
432 440 1.934220 CTGCCAGAACTACGAGCCGA 61.934 60.000 1.50 0.00 0.00 5.54
435 443 1.269998 GCCAGAACTACGAGCCGATAT 59.730 52.381 1.50 0.00 0.00 1.63
544 552 0.235665 CACAACCATCGTGTCAGCAC 59.764 55.000 0.00 0.00 41.97 4.40
555 563 1.154413 GTCAGCACGGCAATGTTCG 60.154 57.895 0.00 0.00 0.00 3.95
556 564 2.176546 CAGCACGGCAATGTTCGG 59.823 61.111 3.70 0.00 0.00 4.30
557 565 2.031919 AGCACGGCAATGTTCGGA 59.968 55.556 3.70 0.00 0.00 4.55
559 567 2.867472 CACGGCAATGTTCGGACC 59.133 61.111 0.00 0.00 0.00 4.46
560 568 1.963855 CACGGCAATGTTCGGACCA 60.964 57.895 0.00 0.00 0.00 4.02
561 569 1.671054 ACGGCAATGTTCGGACCAG 60.671 57.895 0.00 0.00 0.00 4.00
562 570 2.877691 GGCAATGTTCGGACCAGC 59.122 61.111 0.00 0.00 0.00 4.85
567 575 0.321653 AATGTTCGGACCAGCAGACC 60.322 55.000 0.00 0.00 0.00 3.85
569 577 1.296715 GTTCGGACCAGCAGACCAT 59.703 57.895 0.00 0.00 0.00 3.55
573 581 0.250038 CGGACCAGCAGACCATATGG 60.250 60.000 20.68 20.68 42.17 2.74
584 592 1.843376 CCATATGGTCCCGAGCCCT 60.843 63.158 14.09 0.00 0.00 5.19
666 676 1.956869 TCTCTGGCCCAGAAGAATCA 58.043 50.000 15.67 0.00 40.18 2.57
676 686 4.325119 CCCAGAAGAATCATGCCTGATAG 58.675 47.826 4.81 0.00 41.34 2.08
699 709 1.539929 GGCGATCTTGTGATGGAGGAG 60.540 57.143 0.00 0.00 32.19 3.69
702 712 2.167281 CGATCTTGTGATGGAGGAGTGT 59.833 50.000 0.00 0.00 32.19 3.55
705 715 2.300152 TCTTGTGATGGAGGAGTGTGTC 59.700 50.000 0.00 0.00 0.00 3.67
714 724 1.795286 GAGGAGTGTGTCGCTTTTCAG 59.205 52.381 0.00 0.00 0.00 3.02
730 740 5.934043 GCTTTTCAGCCCATGTTTTTATTCT 59.066 36.000 0.00 0.00 40.61 2.40
737 747 6.589907 CAGCCCATGTTTTTATTCTTTGTACC 59.410 38.462 0.00 0.00 0.00 3.34
740 750 6.584563 CCCATGTTTTTATTCTTTGTACCACG 59.415 38.462 0.00 0.00 0.00 4.94
751 761 4.634004 TCTTTGTACCACGGCTCATAATTG 59.366 41.667 0.00 0.00 0.00 2.32
754 764 4.580868 TGTACCACGGCTCATAATTGAAA 58.419 39.130 0.00 0.00 0.00 2.69
816 826 5.612725 GGGGGCATTTTGAAGATATTTCA 57.387 39.130 0.00 0.00 0.00 2.69
817 827 6.178607 GGGGGCATTTTGAAGATATTTCAT 57.821 37.500 0.00 0.00 0.00 2.57
818 828 6.594744 GGGGGCATTTTGAAGATATTTCATT 58.405 36.000 0.00 0.00 0.00 2.57
819 829 6.484308 GGGGGCATTTTGAAGATATTTCATTG 59.516 38.462 0.00 3.29 0.00 2.82
820 830 7.049754 GGGGCATTTTGAAGATATTTCATTGT 58.950 34.615 0.00 0.00 0.00 2.71
894 904 7.203910 TGCCGAGCTGAAAAGTTTAAATTTAA 58.796 30.769 6.54 6.54 0.00 1.52
895 905 7.707035 TGCCGAGCTGAAAAGTTTAAATTTAAA 59.293 29.630 17.45 17.45 0.00 1.52
944 954 3.373565 GCCTCCAAAACGCCCCTG 61.374 66.667 0.00 0.00 0.00 4.45
945 955 3.373565 CCTCCAAAACGCCCCTGC 61.374 66.667 0.00 0.00 0.00 4.85
961 971 1.098869 CTGCTCGTGGAGAAGCTCTA 58.901 55.000 0.00 0.00 33.10 2.43
968 1264 0.041833 TGGAGAAGCTCTAGGGCTGT 59.958 55.000 20.25 8.91 42.24 4.40
981 1277 1.377987 GGCTGTTTGACCCCGCATA 60.378 57.895 0.00 0.00 0.00 3.14
994 1290 2.878406 CCCCGCATAACCAAACTATCTG 59.122 50.000 0.00 0.00 0.00 2.90
1010 1306 1.808411 TCTGTTTTGATGGAGACGCC 58.192 50.000 0.00 0.00 37.10 5.68
1273 1569 4.724602 GCTGCGCCGACTCTGTGA 62.725 66.667 4.18 0.00 0.00 3.58
1336 1632 2.264794 GGTTCATCGGGACTGCGT 59.735 61.111 0.00 0.00 0.00 5.24
1486 1782 5.116180 TCTGTGCTTATTATTTGGTCGGAG 58.884 41.667 0.00 0.00 0.00 4.63
1490 1786 6.207810 TGTGCTTATTATTTGGTCGGAGTTTT 59.792 34.615 0.00 0.00 0.00 2.43
1499 1795 4.764679 TGGTCGGAGTTTTGATCATTTG 57.235 40.909 0.00 0.00 0.00 2.32
1520 1816 2.523015 GATCAATCCAACTTTGCTGCG 58.477 47.619 0.00 0.00 0.00 5.18
1550 1846 6.128090 GGGTGCTTTGGTAATAGTTTGTCTAC 60.128 42.308 0.00 0.00 0.00 2.59
1553 1849 7.120726 GTGCTTTGGTAATAGTTTGTCTACCAT 59.879 37.037 0.90 0.00 0.00 3.55
1554 1850 7.668052 TGCTTTGGTAATAGTTTGTCTACCATT 59.332 33.333 0.90 0.00 0.00 3.16
1555 1851 7.968405 GCTTTGGTAATAGTTTGTCTACCATTG 59.032 37.037 0.90 0.00 0.00 2.82
1556 1852 6.995511 TGGTAATAGTTTGTCTACCATTGC 57.004 37.500 0.00 0.00 0.00 3.56
1557 1853 6.477253 TGGTAATAGTTTGTCTACCATTGCA 58.523 36.000 0.00 0.00 0.00 4.08
1558 1854 7.116075 TGGTAATAGTTTGTCTACCATTGCAT 58.884 34.615 0.00 0.00 0.00 3.96
1559 1855 8.268605 TGGTAATAGTTTGTCTACCATTGCATA 58.731 33.333 0.00 0.00 0.00 3.14
1560 1856 9.284968 GGTAATAGTTTGTCTACCATTGCATAT 57.715 33.333 0.00 0.00 0.00 1.78
1567 1863 6.597262 TGTCTACCATTGCATATTTGTACG 57.403 37.500 0.00 0.00 0.00 3.67
1570 1866 6.256975 GTCTACCATTGCATATTTGTACGTCA 59.743 38.462 0.00 0.00 0.00 4.35
1576 1872 6.487689 TTGCATATTTGTACGTCATGTCAA 57.512 33.333 0.00 0.00 0.00 3.18
1733 2030 7.865889 CCAACTAATTGTTCTAAGGTTGAAACC 59.134 37.037 3.91 3.91 42.34 3.27
1764 2061 9.587772 TTAACTAGATCAGCACTTGATAAGTTC 57.412 33.333 15.15 0.00 46.51 3.01
1789 2086 6.832520 TTCCTAGATCTCTAGCAGCATAAG 57.167 41.667 0.00 0.00 43.47 1.73
1863 2160 6.147821 ACTTTCTCTGTCGATTGTTTGTATGG 59.852 38.462 0.00 0.00 0.00 2.74
1914 2211 7.545265 GCATGCAATATTTAGGTTTCTTCAACA 59.455 33.333 14.21 0.00 37.07 3.33
1928 2225 3.056179 TCTTCAACATATCTGTGTGCCGA 60.056 43.478 0.00 0.00 35.22 5.54
1929 2226 2.892374 TCAACATATCTGTGTGCCGAG 58.108 47.619 0.00 0.00 35.22 4.63
1930 2227 2.495669 TCAACATATCTGTGTGCCGAGA 59.504 45.455 0.00 0.00 35.22 4.04
1931 2228 2.862536 CAACATATCTGTGTGCCGAGAG 59.137 50.000 0.00 0.00 35.22 3.20
1932 2229 1.202463 ACATATCTGTGTGCCGAGAGC 60.202 52.381 0.00 0.00 36.62 4.09
1933 2230 0.390860 ATATCTGTGTGCCGAGAGCC 59.609 55.000 0.00 0.00 42.71 4.70
1934 2231 1.676678 TATCTGTGTGCCGAGAGCCC 61.677 60.000 0.00 0.00 42.71 5.19
2068 2365 9.077885 ACTTTTCAGCAATTGTATTTTCCTCTA 57.922 29.630 7.40 0.00 0.00 2.43
2119 2416 1.920574 CGGCAGTTATTGTCAGACTCG 59.079 52.381 1.31 0.00 0.00 4.18
2285 2582 5.869888 ACTGGTCTCAGACATTTTTATCGAC 59.130 40.000 7.24 0.00 43.49 4.20
2432 2729 8.017946 GGATATGCTAAGAATGGAAAAATCGAC 58.982 37.037 0.00 0.00 0.00 4.20
2460 2757 4.631131 TCGCTCCATATTCAACTGTATGG 58.369 43.478 5.29 5.29 45.64 2.74
2567 2864 5.420725 AAGATATGCAAGAGTGTGGTGTA 57.579 39.130 0.00 0.00 0.00 2.90
2679 2976 7.437748 TGTTGTGAATAATGGGTTTTGTAAGG 58.562 34.615 0.00 0.00 0.00 2.69
2873 3170 4.401925 AGATGAAAAGTGAAGGGGTTGAG 58.598 43.478 0.00 0.00 0.00 3.02
2924 3221 1.808531 TTGCCTGTTGTCATGCTGGC 61.809 55.000 14.68 14.68 45.88 4.85
2957 3254 1.418373 GCCGTTCCTTGTTTGAATGC 58.582 50.000 0.00 0.00 0.00 3.56
3002 3299 2.313317 CCCAAGCATGAGCATTATGGT 58.687 47.619 0.00 0.00 45.49 3.55
3239 3536 4.079253 ACGCAAAATCTGGTAACTGGAAT 58.921 39.130 0.00 0.00 35.97 3.01
3330 3627 1.637553 AGCTGAATGGGATTGTCCACT 59.362 47.619 0.00 0.00 39.97 4.00
3370 3667 7.890127 AGGTGAGAAACATCAGGAAAATCATAA 59.110 33.333 0.00 0.00 30.93 1.90
3435 3732 6.670695 TCATGGCTATGCTAGTCTTTATGA 57.329 37.500 4.95 0.00 34.21 2.15
3438 3735 8.473219 TCATGGCTATGCTAGTCTTTATGATAG 58.527 37.037 4.95 0.00 34.21 2.08
3442 3739 7.327214 GCTATGCTAGTCTTTATGATAGCCTT 58.673 38.462 0.00 0.00 39.90 4.35
3462 3759 5.187772 GCCTTGTAAATTTCTGAAAGGGGAT 59.812 40.000 8.95 0.00 35.71 3.85
3463 3760 6.628175 GCCTTGTAAATTTCTGAAAGGGGATC 60.628 42.308 8.95 0.00 35.71 3.36
3464 3761 6.665248 CCTTGTAAATTTCTGAAAGGGGATCT 59.335 38.462 8.95 0.00 32.30 2.75
3465 3762 7.179160 CCTTGTAAATTTCTGAAAGGGGATCTT 59.821 37.037 8.95 0.00 37.28 2.40
3466 3763 7.703058 TGTAAATTTCTGAAAGGGGATCTTC 57.297 36.000 8.95 0.00 33.94 2.87
3467 3764 7.237982 TGTAAATTTCTGAAAGGGGATCTTCA 58.762 34.615 8.95 0.00 33.94 3.02
3468 3765 7.895429 TGTAAATTTCTGAAAGGGGATCTTCAT 59.105 33.333 8.95 0.00 33.94 2.57
3512 3809 4.265073 ACTTGCAGGTAATCATGAGGAAC 58.735 43.478 0.00 0.00 0.00 3.62
3514 3811 4.508551 TGCAGGTAATCATGAGGAACAT 57.491 40.909 0.09 0.00 40.17 2.71
3610 3907 7.747155 GATTCATCACAGGAATCATCTCATT 57.253 36.000 9.56 0.00 46.26 2.57
3659 3956 6.063404 TCATATTTATGGCTGCATCAGTTGA 58.937 36.000 0.50 0.00 34.50 3.18
3661 3958 5.864418 ATTTATGGCTGCATCAGTTGAAT 57.136 34.783 0.50 0.00 33.43 2.57
3691 3988 7.518161 TCGTTATGTAATCAAAGCTGAACAAG 58.482 34.615 0.00 0.00 34.49 3.16
3712 4009 4.401925 AGAAGTCAGCTGGCTAATTTTGT 58.598 39.130 23.54 3.15 0.00 2.83
3769 4066 1.062488 AAGGGAAGACACAGGCAGGT 61.062 55.000 0.00 0.00 0.00 4.00
3851 4164 4.649267 TGAGATAATTGGTGTGGTTCCA 57.351 40.909 0.00 0.00 0.00 3.53
3853 4166 4.202514 TGAGATAATTGGTGTGGTTCCACA 60.203 41.667 19.12 19.12 43.62 4.17
3888 4201 3.068024 CCTCTGTCAGGCTGAAGATAGTC 59.932 52.174 20.62 5.38 34.56 2.59
3921 4234 4.202245 AGAAGCTGAACTTTATGCCGTA 57.798 40.909 0.00 0.00 39.29 4.02
3930 4243 4.906065 ACTTTATGCCGTATGAGTCGTA 57.094 40.909 0.00 0.00 0.00 3.43
3963 4276 2.289002 GTCTTTCAGTTGTGTGAGCTGG 59.711 50.000 0.00 0.00 0.00 4.85
4019 4332 2.469516 GGTATTTCACGGGGCAGCG 61.470 63.158 0.00 0.00 0.00 5.18
4076 4389 5.321102 TGTAACATATTCTGGCAACACCTT 58.679 37.500 0.00 0.00 46.17 3.50
4077 4390 4.789012 AACATATTCTGGCAACACCTTG 57.211 40.909 0.00 0.00 46.17 3.61
4120 4615 8.521176 GCTTATTCAGGATTATTTGATGAGCAT 58.479 33.333 0.00 0.00 0.00 3.79
4272 5026 5.446860 AGATGAATCATGTGGAAGCATCTT 58.553 37.500 0.00 0.00 42.75 2.40
4348 5107 5.420104 GGGTCAAATCAATGGAATGAAGAGT 59.580 40.000 0.00 0.00 32.06 3.24
4368 5127 9.127277 GAAGAGTTAGTATGAGAGGTGTCTATT 57.873 37.037 0.00 0.00 30.97 1.73
4402 5161 6.043590 TGCTGATCTCATTATCCAACTACCAT 59.956 38.462 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.035056 ATTTGGGCGCTTAGACTGCT 60.035 50.000 7.64 0.00 0.00 4.24
268 274 1.078709 CTTGTTCATCATCGCGGTGT 58.921 50.000 20.53 3.75 0.00 4.16
279 285 3.434309 CCCAATTCCCAGACTTGTTCAT 58.566 45.455 0.00 0.00 0.00 2.57
280 286 2.875296 CCCAATTCCCAGACTTGTTCA 58.125 47.619 0.00 0.00 0.00 3.18
373 380 2.682136 TCCTTCGCATCGGGACCA 60.682 61.111 0.00 0.00 0.00 4.02
397 405 1.065199 GGCAGTCCATCATCCAGTTGA 60.065 52.381 0.00 0.00 0.00 3.18
424 432 3.216800 TGTTAGTGGTATATCGGCTCGT 58.783 45.455 0.00 0.00 0.00 4.18
432 440 4.262079 GCTCGCCTTCTGTTAGTGGTATAT 60.262 45.833 0.00 0.00 0.00 0.86
435 443 1.203994 GCTCGCCTTCTGTTAGTGGTA 59.796 52.381 0.00 0.00 0.00 3.25
463 471 5.928976 TCATCCGGAACAAATATCTGTGAT 58.071 37.500 9.01 0.00 0.00 3.06
504 512 0.463654 CGGATTGCGAATGGGGAAGA 60.464 55.000 0.00 0.00 0.00 2.87
544 552 3.039202 GCTGGTCCGAACATTGCCG 62.039 63.158 0.00 0.00 0.00 5.69
555 563 3.713902 CCATATGGTCTGCTGGTCC 57.286 57.895 14.09 0.00 0.00 4.46
567 575 1.674057 GAGGGCTCGGGACCATATG 59.326 63.158 11.62 0.00 45.05 1.78
569 577 2.122989 GGAGGGCTCGGGACCATA 60.123 66.667 11.62 0.00 45.05 2.74
676 686 1.667724 CTCCATCACAAGATCGCCAAC 59.332 52.381 0.00 0.00 30.20 3.77
699 709 1.282875 GGGCTGAAAAGCGACACAC 59.717 57.895 0.00 0.00 35.24 3.82
702 712 0.537143 ACATGGGCTGAAAAGCGACA 60.537 50.000 0.00 0.00 35.24 4.35
705 715 2.153366 AAAACATGGGCTGAAAAGCG 57.847 45.000 0.00 0.00 35.24 4.68
714 724 6.367695 GTGGTACAAAGAATAAAAACATGGGC 59.632 38.462 0.00 0.00 44.16 5.36
730 740 4.580868 TCAATTATGAGCCGTGGTACAAA 58.419 39.130 0.00 0.00 44.16 2.83
737 747 7.471721 TGAAATACTTTCAATTATGAGCCGTG 58.528 34.615 0.00 0.00 45.94 4.94
794 804 5.612725 TGAAATATCTTCAAAATGCCCCC 57.387 39.130 0.00 0.00 0.00 5.40
795 805 7.049754 ACAATGAAATATCTTCAAAATGCCCC 58.950 34.615 0.00 0.00 31.55 5.80
796 806 9.598517 TTACAATGAAATATCTTCAAAATGCCC 57.401 29.630 0.00 0.00 31.55 5.36
861 871 4.518970 ACTTTTCAGCTCGGCAAAATTCTA 59.481 37.500 0.00 0.00 0.00 2.10
870 880 7.631915 TTAAATTTAAACTTTTCAGCTCGGC 57.368 32.000 8.20 0.00 0.00 5.54
912 922 0.034616 GAGGCCGAGATCCATGAAGG 59.965 60.000 0.00 0.00 39.47 3.46
922 932 2.358247 GCGTTTTGGAGGCCGAGA 60.358 61.111 0.00 0.00 33.08 4.04
944 954 0.383949 CCTAGAGCTTCTCCACGAGC 59.616 60.000 0.00 0.00 0.00 5.03
945 955 1.028905 CCCTAGAGCTTCTCCACGAG 58.971 60.000 0.00 0.00 0.00 4.18
968 1264 1.614413 GTTTGGTTATGCGGGGTCAAA 59.386 47.619 0.00 0.00 0.00 2.69
994 1290 0.169009 GCTGGCGTCTCCATCAAAAC 59.831 55.000 0.00 0.00 45.50 2.43
1099 1395 4.424566 GCGGTCAGGTTCGGCGTA 62.425 66.667 6.85 0.00 0.00 4.42
1511 1807 1.798735 CACCCAGATCGCAGCAAAG 59.201 57.895 0.00 0.00 0.00 2.77
1520 1816 4.781934 ACTATTACCAAAGCACCCAGATC 58.218 43.478 0.00 0.00 0.00 2.75
1550 1846 5.820131 ACATGACGTACAAATATGCAATGG 58.180 37.500 0.00 0.00 0.00 3.16
1553 1849 6.487689 TTGACATGACGTACAAATATGCAA 57.512 33.333 0.00 0.00 0.00 4.08
1554 1850 6.676237 ATTGACATGACGTACAAATATGCA 57.324 33.333 0.00 0.00 0.00 3.96
1555 1851 7.969387 AAATTGACATGACGTACAAATATGC 57.031 32.000 0.00 0.00 0.00 3.14
1556 1852 9.773328 AGAAAATTGACATGACGTACAAATATG 57.227 29.630 0.00 0.00 0.00 1.78
1557 1853 9.773328 CAGAAAATTGACATGACGTACAAATAT 57.227 29.630 0.00 0.00 0.00 1.28
1558 1854 7.748683 GCAGAAAATTGACATGACGTACAAATA 59.251 33.333 0.00 0.00 0.00 1.40
1559 1855 6.582295 GCAGAAAATTGACATGACGTACAAAT 59.418 34.615 0.00 0.00 0.00 2.32
1560 1856 5.912396 GCAGAAAATTGACATGACGTACAAA 59.088 36.000 0.00 0.00 0.00 2.83
1567 1863 5.687285 AGAAAACGCAGAAAATTGACATGAC 59.313 36.000 0.00 0.00 0.00 3.06
1570 1866 5.050837 GCAAGAAAACGCAGAAAATTGACAT 60.051 36.000 0.00 0.00 0.00 3.06
1576 1872 5.793026 TTTTGCAAGAAAACGCAGAAAAT 57.207 30.435 0.00 0.00 39.75 1.82
1764 2061 5.726980 ATGCTGCTAGAGATCTAGGAAAG 57.273 43.478 16.61 6.24 44.46 2.62
1789 2086 7.945033 TTGCATTCCTTTGAAACTTATCAAC 57.055 32.000 0.00 0.00 38.95 3.18
1863 2160 7.095899 GCATCAATTTCCAACTTTCAAGAAGAC 60.096 37.037 0.00 0.00 0.00 3.01
1914 2211 0.390860 GGCTCTCGGCACACAGATAT 59.609 55.000 0.00 0.00 44.01 1.63
1928 2225 0.041386 ACCCTAAAGTCTCGGGCTCT 59.959 55.000 0.00 0.00 41.86 4.09
1929 2226 0.460722 GACCCTAAAGTCTCGGGCTC 59.539 60.000 0.00 0.00 41.86 4.70
1930 2227 0.041386 AGACCCTAAAGTCTCGGGCT 59.959 55.000 0.00 0.00 43.76 5.19
1931 2228 0.903236 AAGACCCTAAAGTCTCGGGC 59.097 55.000 0.00 0.00 46.44 6.13
1932 2229 1.900486 ACAAGACCCTAAAGTCTCGGG 59.100 52.381 0.00 0.00 46.44 5.14
1933 2230 2.561419 TCACAAGACCCTAAAGTCTCGG 59.439 50.000 0.00 0.00 46.44 4.63
1934 2231 3.005472 TGTCACAAGACCCTAAAGTCTCG 59.995 47.826 0.00 0.00 46.44 4.04
1935 2232 4.602340 TGTCACAAGACCCTAAAGTCTC 57.398 45.455 0.00 0.00 46.44 3.36
2018 2315 4.899352 AGAAGCATACAAACTGGAGACT 57.101 40.909 0.00 0.00 0.00 3.24
2063 2360 5.600484 AGAGGTCAGTCATGGTTTATAGAGG 59.400 44.000 0.00 0.00 0.00 3.69
2065 2362 6.436027 AGAGAGGTCAGTCATGGTTTATAGA 58.564 40.000 0.00 0.00 0.00 1.98
2068 2365 6.440647 TGTTAGAGAGGTCAGTCATGGTTTAT 59.559 38.462 0.00 0.00 0.00 1.40
2079 2376 3.429547 CCGGTTGATGTTAGAGAGGTCAG 60.430 52.174 0.00 0.00 0.00 3.51
2119 2416 4.122143 AGCAATGCTTCTCTGTAGTCTC 57.878 45.455 0.00 0.00 33.89 3.36
2432 2729 3.562973 AGTTGAATATGGAGCGAGCAATG 59.437 43.478 0.00 0.00 0.00 2.82
2460 2757 4.446371 CAAGATACCACATCCTTCTCCAC 58.554 47.826 0.00 0.00 0.00 4.02
2567 2864 7.815383 TCAATAGGGTAATTTCATCAGGACAT 58.185 34.615 0.00 0.00 0.00 3.06
2679 2976 5.002464 AGAGCATTGCAAATGGACAATAC 57.998 39.130 11.91 0.00 34.80 1.89
2720 3017 2.033424 GGCAAGAGTCAAACTTCCACAC 59.967 50.000 0.00 0.00 0.00 3.82
2924 3221 2.678336 GGAACGGCCTTCATCAACTAAG 59.322 50.000 14.39 0.00 0.00 2.18
2957 3254 4.139786 CAATCCTGTATTCCTGGACCATG 58.860 47.826 0.00 0.00 43.20 3.66
3002 3299 5.985175 TTCCCATAAGATCCACCATACAA 57.015 39.130 0.00 0.00 0.00 2.41
3155 3452 5.337571 GGGATCCAACTCCAAAATTTTCCTC 60.338 44.000 15.23 0.00 37.01 3.71
3239 3536 1.403814 CCCTCACCTCTCGAGCATTA 58.596 55.000 7.81 0.00 0.00 1.90
3298 3595 1.115467 ATTCAGCTCTACCCGACTGG 58.885 55.000 0.00 0.00 41.37 4.00
3330 3627 3.181329 TCTCACCTCCAGCTCCAAAATA 58.819 45.455 0.00 0.00 0.00 1.40
3370 3667 3.519913 CCCACTAAGCTTTAGAAGGGTCT 59.480 47.826 3.20 0.00 37.95 3.85
3420 3717 7.072263 ACAAGGCTATCATAAAGACTAGCAT 57.928 36.000 0.00 0.00 36.20 3.79
3435 3732 6.381133 CCCCTTTCAGAAATTTACAAGGCTAT 59.619 38.462 0.00 0.00 31.10 2.97
3438 3735 4.526650 TCCCCTTTCAGAAATTTACAAGGC 59.473 41.667 0.00 0.00 31.10 4.35
3442 3739 7.237982 TGAAGATCCCCTTTCAGAAATTTACA 58.762 34.615 0.00 0.00 34.68 2.41
3546 3843 9.513906 TTATGGAACTTCATCAATTGTGAGTTA 57.486 29.630 5.13 0.00 37.14 2.24
3596 3893 3.524789 TGACCACCAATGAGATGATTCCT 59.475 43.478 0.00 0.00 0.00 3.36
3597 3894 3.889815 TGACCACCAATGAGATGATTCC 58.110 45.455 0.00 0.00 0.00 3.01
3610 3907 0.397675 TTGTTGCCCATTGACCACCA 60.398 50.000 0.00 0.00 0.00 4.17
3659 3956 9.507280 CAGCTTTGATTACATAACGAATTCATT 57.493 29.630 6.22 0.00 0.00 2.57
3661 3958 8.262715 TCAGCTTTGATTACATAACGAATTCA 57.737 30.769 6.22 0.00 0.00 2.57
3691 3988 4.773323 ACAAAATTAGCCAGCTGACTTC 57.227 40.909 17.39 1.00 0.00 3.01
3888 4201 1.001293 TCAGCTTCTACTGCACAGTGG 59.999 52.381 13.50 10.58 42.52 4.00
3921 4234 2.621998 CCCATTACCGACTACGACTCAT 59.378 50.000 0.00 0.00 42.66 2.90
3930 4243 2.904434 ACTGAAAGACCCATTACCGACT 59.096 45.455 0.00 0.00 37.43 4.18
3963 4276 7.027778 TCAAAGTTCTTAAGAAAGGTTCTGC 57.972 36.000 19.30 4.94 40.59 4.26
3990 4303 2.695359 GTGAAATACCCGTGCTTCTGA 58.305 47.619 0.00 0.00 0.00 3.27
4019 4332 3.997021 CTGTGGAATGTTGTCTGACTACC 59.003 47.826 17.43 5.11 0.00 3.18
4076 4389 7.123997 TGAATAAGCCCATGATTTTTAGAAGCA 59.876 33.333 0.00 0.00 0.00 3.91
4077 4390 7.491682 TGAATAAGCCCATGATTTTTAGAAGC 58.508 34.615 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.