Multiple sequence alignment - TraesCS4A01G221200

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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 TraesCS4A01G221200 chr4A 100.000 4960 0 0 1 4960 526639028 526643987 0.000000e+00 9160
1 TraesCS4A01G221200 chr4D 95.457 3610 119 19 828 4408 71295420 71291827 0.000000e+00 5716
2 TraesCS4A01G221200 chr4D 88.673 565 51 11 4401 4958 71092542 71091984 0.000000e+00 676
3 TraesCS4A01G221200 chr4D 96.032 126 5 0 643 768 71299685 71299560 6.510000e-49 206
4 TraesCS4A01G221200 chr4B 93.725 3315 140 30 1054 4326 105001693 105004981 0.000000e+00 4907
5 TraesCS4A01G221200 chr4B 83.971 418 32 17 643 1059 105001276 105001659 7.840000e-98 368
6 TraesCS4A01G221200 chr6A 94.841 659 24 3 1 649 457405920 457406578 0.000000e+00 1020
7 TraesCS4A01G221200 chr7D 93.231 650 34 3 1 641 87678480 87677832 0.000000e+00 948
8 TraesCS4A01G221200 chr7D 92.545 617 36 7 1 608 619072989 619072374 0.000000e+00 876
9 TraesCS4A01G221200 chr2D 93.231 650 34 3 1 641 364830600 364831248 0.000000e+00 948
10 TraesCS4A01G221200 chr5D 92.769 650 36 4 1 641 535592296 535592943 0.000000e+00 929
11 TraesCS4A01G221200 chr5D 87.755 98 12 0 2545 2642 190498070 190498167 1.130000e-21 115
12 TraesCS4A01G221200 chr3D 92.462 650 39 3 1 641 538480430 538479782 0.000000e+00 920
13 TraesCS4A01G221200 chr1D 92.000 650 34 4 1 641 77746416 77745776 0.000000e+00 896
14 TraesCS4A01G221200 chr6B 89.771 655 47 4 1 645 454767010 454766366 0.000000e+00 821
15 TraesCS4A01G221200 chr2B 86.335 644 75 7 7 640 759483974 759484614 0.000000e+00 689
16 TraesCS4A01G221200 chr3A 97.917 192 4 0 1 192 50983763 50983954 2.860000e-87 333
17 TraesCS4A01G221200 chr5B 87.755 98 12 0 2545 2642 214129290 214129387 1.130000e-21 115
18 TraesCS4A01G221200 chr5A 89.888 89 9 0 2554 2642 229499211 229499123 1.130000e-21 115


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 TraesCS4A01G221200 chr4A 526639028 526643987 4959 False 9160.0 9160 100.000 1 4960 1 chr4A.!!$F1 4959
1 TraesCS4A01G221200 chr4D 71291827 71295420 3593 True 5716.0 5716 95.457 828 4408 1 chr4D.!!$R2 3580
2 TraesCS4A01G221200 chr4D 71091984 71092542 558 True 676.0 676 88.673 4401 4958 1 chr4D.!!$R1 557
3 TraesCS4A01G221200 chr4B 105001276 105004981 3705 False 2637.5 4907 88.848 643 4326 2 chr4B.!!$F1 3683
4 TraesCS4A01G221200 chr6A 457405920 457406578 658 False 1020.0 1020 94.841 1 649 1 chr6A.!!$F1 648
5 TraesCS4A01G221200 chr7D 87677832 87678480 648 True 948.0 948 93.231 1 641 1 chr7D.!!$R1 640
6 TraesCS4A01G221200 chr7D 619072374 619072989 615 True 876.0 876 92.545 1 608 1 chr7D.!!$R2 607
7 TraesCS4A01G221200 chr2D 364830600 364831248 648 False 948.0 948 93.231 1 641 1 chr2D.!!$F1 640
8 TraesCS4A01G221200 chr5D 535592296 535592943 647 False 929.0 929 92.769 1 641 1 chr5D.!!$F2 640
9 TraesCS4A01G221200 chr3D 538479782 538480430 648 True 920.0 920 92.462 1 641 1 chr3D.!!$R1 640
10 TraesCS4A01G221200 chr1D 77745776 77746416 640 True 896.0 896 92.000 1 641 1 chr1D.!!$R1 640
11 TraesCS4A01G221200 chr6B 454766366 454767010 644 True 821.0 821 89.771 1 645 1 chr6B.!!$R1 644
12 TraesCS4A01G221200 chr2B 759483974 759484614 640 False 689.0 689 86.335 7 640 1 chr2B.!!$F1 633

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
823 835 0.394352 ACCCTTGTGATGGCGAATCC 60.394 55.0 0.00 0.00 34.00 3.01 F
1523 1587 0.396139 ATCATGAAACGGCAGCCCAT 60.396 50.0 5.63 0.00 0.00 4.00 F
1525 1589 1.033746 CATGAAACGGCAGCCCATCT 61.034 55.0 5.63 0.00 0.00 2.90 F
3161 3243 0.105039 CGGATTCCAGGTACCTGCTC 59.895 60.0 32.98 25.86 42.35 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2128 2204 0.318762 GTCAGGTCCTTGCTCGACTT 59.681 55.0 0.00 0.0 0.00 3.01 R
3124 3206 0.108615 CGGTGATCTTCTTCGCCTGT 60.109 55.0 0.00 0.0 42.90 4.00 R
3199 3285 0.914551 CATCCGACGTCAACATCGAC 59.085 55.0 17.16 0.0 40.86 4.20 R
4061 4163 0.454600 ACCGATCTTGTGCGTCGTAT 59.545 50.0 0.00 0.0 33.77 3.06 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
374 384 0.745845 CGGGGAGCAGAGGTGATTTG 60.746 60.000 0.00 0.00 0.00 2.32
398 408 2.703416 TGCGATCTGATTTGAGTGCTT 58.297 42.857 0.00 0.00 0.00 3.91
423 433 1.080498 TGTTGGTAGGGGATGAGGAGT 59.920 52.381 0.00 0.00 0.00 3.85
641 653 4.088648 GTCTGCCGATTGTAAACATTTCG 58.911 43.478 8.28 8.28 34.03 3.46
646 658 4.201485 GCCGATTGTAAACATTTCGCTTTG 60.201 41.667 9.30 0.79 33.37 2.77
649 661 6.077197 CGATTGTAAACATTTCGCTTTGAGA 58.923 36.000 3.90 0.00 0.00 3.27
658 670 4.927978 TTTCGCTTTGAGAAATGGGAAA 57.072 36.364 10.49 10.49 38.43 3.13
666 678 5.818136 TTGAGAAATGGGAAATGTCGATC 57.182 39.130 0.00 0.00 0.00 3.69
671 683 3.751479 ATGGGAAATGTCGATCGATGA 57.249 42.857 22.50 11.64 0.00 2.92
680 692 6.791887 AATGTCGATCGATGATTAGCAATT 57.208 33.333 22.50 7.43 0.00 2.32
687 699 4.939271 TCGATGATTAGCAATTACGACCA 58.061 39.130 0.00 0.00 0.00 4.02
693 705 5.926542 TGATTAGCAATTACGACCAGATAGC 59.073 40.000 0.00 0.00 0.00 2.97
701 713 6.910536 ATTACGACCAGATAGCTCTTTTTG 57.089 37.500 0.00 0.00 0.00 2.44
751 763 9.209048 TCTATAAAGTCAGGCTCATACCTTTTA 57.791 33.333 0.00 0.00 38.26 1.52
756 768 9.528489 AAAGTCAGGCTCATACCTTTTATTTAA 57.472 29.630 0.00 0.00 38.26 1.52
758 770 9.528489 AGTCAGGCTCATACCTTTTATTTAAAA 57.472 29.630 0.00 0.00 38.26 1.52
816 828 7.226441 TCAAATAGATGATACCCTTGTGATGG 58.774 38.462 0.00 0.00 0.00 3.51
817 829 3.498774 AGATGATACCCTTGTGATGGC 57.501 47.619 0.00 0.00 0.00 4.40
818 830 2.146342 GATGATACCCTTGTGATGGCG 58.854 52.381 0.00 0.00 0.00 5.69
819 831 1.199615 TGATACCCTTGTGATGGCGA 58.800 50.000 0.00 0.00 0.00 5.54
821 833 2.172505 TGATACCCTTGTGATGGCGAAT 59.827 45.455 0.00 0.00 0.00 3.34
822 834 2.325583 TACCCTTGTGATGGCGAATC 57.674 50.000 0.00 0.00 35.67 2.52
823 835 0.394352 ACCCTTGTGATGGCGAATCC 60.394 55.000 0.00 0.00 34.00 3.01
824 836 1.439353 CCCTTGTGATGGCGAATCCG 61.439 60.000 0.00 0.00 37.80 4.18
825 837 0.744414 CCTTGTGATGGCGAATCCGT 60.744 55.000 0.00 0.00 37.80 4.69
826 838 1.472552 CCTTGTGATGGCGAATCCGTA 60.473 52.381 0.00 0.00 37.80 4.02
827 839 2.276201 CTTGTGATGGCGAATCCGTAA 58.724 47.619 0.00 0.00 37.80 3.18
828 840 2.388310 TGTGATGGCGAATCCGTAAA 57.612 45.000 0.00 0.00 37.80 2.01
829 841 2.701107 TGTGATGGCGAATCCGTAAAA 58.299 42.857 0.00 0.00 37.80 1.52
830 842 3.075148 TGTGATGGCGAATCCGTAAAAA 58.925 40.909 0.00 0.00 37.80 1.94
831 843 3.692101 TGTGATGGCGAATCCGTAAAAAT 59.308 39.130 0.00 0.00 37.80 1.82
832 844 4.876679 TGTGATGGCGAATCCGTAAAAATA 59.123 37.500 0.00 0.00 37.80 1.40
833 845 5.354513 TGTGATGGCGAATCCGTAAAAATAA 59.645 36.000 0.00 0.00 37.80 1.40
834 846 5.679792 GTGATGGCGAATCCGTAAAAATAAC 59.320 40.000 0.00 0.00 37.80 1.89
860 872 6.749923 ACTATTTTGACTCTTCTCCAATGC 57.250 37.500 0.00 0.00 0.00 3.56
1001 1014 1.383803 GGGTCTCTCTCCCAGGCAT 60.384 63.158 0.00 0.00 44.05 4.40
1523 1587 0.396139 ATCATGAAACGGCAGCCCAT 60.396 50.000 5.63 0.00 0.00 4.00
1525 1589 1.033746 CATGAAACGGCAGCCCATCT 61.034 55.000 5.63 0.00 0.00 2.90
1642 1706 3.121030 CTCTGCAAGGTTCGCCCG 61.121 66.667 0.00 0.00 38.74 6.13
1716 1780 2.776913 GGACGAAGGCGGAGGAGAG 61.777 68.421 0.00 0.00 43.17 3.20
1734 1798 5.013599 AGGAGAGAATAGAAACTGCAACCTT 59.986 40.000 0.00 0.00 0.00 3.50
1758 1822 1.085501 ACGGCAAAGTGTTCGTCGTT 61.086 50.000 0.00 0.00 0.00 3.85
1843 1907 2.429930 CCCCGCTGGTGAAACAGA 59.570 61.111 0.00 0.00 40.97 3.41
2172 2248 1.521681 GTACATGCGGCAGGAGGTC 60.522 63.158 22.55 4.71 33.97 3.85
2214 2290 1.427020 GAGCATCAAGTTCAGCGCC 59.573 57.895 2.29 0.00 33.17 6.53
2326 2402 1.590259 GATCTCTCGACCGGCAAGC 60.590 63.158 0.00 0.00 0.00 4.01
2554 2630 1.901948 TCCAAGCAGTCGTCGAGGT 60.902 57.895 4.85 0.00 0.00 3.85
2627 2703 4.030452 GTGCCTGCAGGTGTTCGC 62.030 66.667 32.81 18.96 37.57 4.70
2810 2886 1.330521 CGACGGCCAGGTTCATTAATG 59.669 52.381 9.29 9.29 0.00 1.90
2913 2994 5.571357 ACGTGTGTTGTTCAAACTTCAATTC 59.429 36.000 0.00 0.00 32.40 2.17
2982 3063 6.814146 GGTTCTACAAGACAAGAGGTAATCTG 59.186 42.308 0.00 0.00 38.67 2.90
2993 3074 7.551585 ACAAGAGGTAATCTGAATGTCAGTAG 58.448 38.462 5.23 0.00 44.58 2.57
3006 3088 2.230266 TGTCAGTAGCACGCAATCTGTA 59.770 45.455 0.00 0.00 0.00 2.74
3007 3089 2.854777 GTCAGTAGCACGCAATCTGTAG 59.145 50.000 0.00 0.00 0.00 2.74
3015 3097 5.661458 AGCACGCAATCTGTAGTACTAAAT 58.339 37.500 3.61 0.00 0.00 1.40
3017 3099 6.594159 AGCACGCAATCTGTAGTACTAAATTT 59.406 34.615 3.61 0.00 0.00 1.82
3019 3101 8.548721 GCACGCAATCTGTAGTACTAAATTTAT 58.451 33.333 3.61 0.00 0.00 1.40
3124 3206 2.760634 TATCCAAGAAGCGCAAGTCA 57.239 45.000 11.47 0.00 41.68 3.41
3161 3243 0.105039 CGGATTCCAGGTACCTGCTC 59.895 60.000 32.98 25.86 42.35 4.26
3173 3259 2.557920 ACCTGCTCCTTGTTCTTGAG 57.442 50.000 0.00 0.00 0.00 3.02
3199 3285 0.525761 AACAATGGCAAACGGATCGG 59.474 50.000 0.00 0.00 0.00 4.18
3210 3296 0.179145 ACGGATCGGTCGATGTTGAC 60.179 55.000 10.77 0.00 38.17 3.18
3224 3317 1.862201 TGTTGACGTCGGATGTTGTTC 59.138 47.619 11.62 0.00 0.00 3.18
3937 4035 1.272092 CCAGAACTTTGGGATGCCAGA 60.272 52.381 5.91 0.02 34.46 3.86
3977 4075 7.068348 CAGAAGTGATGGATCTTGATTTGGAAT 59.932 37.037 0.00 0.00 0.00 3.01
4014 4116 1.734465 GAGTGGGTCTTGATCTTTGCG 59.266 52.381 0.00 0.00 0.00 4.85
4032 4134 1.153208 GGCAGGACAGGAGCATGAG 60.153 63.158 0.00 0.00 0.00 2.90
4061 4163 3.805422 AGCTTTACAAACGATCGAACACA 59.195 39.130 24.34 0.42 0.00 3.72
4073 4175 0.779408 CGAACACATACGACGCACAA 59.221 50.000 0.00 0.00 0.00 3.33
4074 4176 1.201661 CGAACACATACGACGCACAAG 60.202 52.381 0.00 0.00 0.00 3.16
4101 4210 4.860907 GGTCGACGAACATATGTACTTGTT 59.139 41.667 9.21 8.50 38.71 2.83
4102 4211 5.346822 GGTCGACGAACATATGTACTTGTTT 59.653 40.000 9.21 0.00 36.25 2.83
4103 4212 6.231365 GTCGACGAACATATGTACTTGTTTG 58.769 40.000 9.21 16.21 41.18 2.93
4104 4213 6.088483 GTCGACGAACATATGTACTTGTTTGA 59.912 38.462 21.05 4.63 38.84 2.69
4113 4222 5.920193 ATGTACTTGTTTGATTGATGGGG 57.080 39.130 0.00 0.00 0.00 4.96
4157 4266 1.673337 GTGTTTGGGTAGGGCGGAC 60.673 63.158 0.00 0.00 0.00 4.79
4275 4386 5.473066 AATGTAAACACGGTACAGTACCT 57.527 39.130 24.67 10.35 46.81 3.08
4313 4424 9.860898 AAACAGGAGAAATATCTTAATGCAAAC 57.139 29.630 0.00 0.00 35.54 2.93
4351 4462 5.025453 ACTTTTTGGATGGTCATAATGCCT 58.975 37.500 0.00 0.00 0.00 4.75
4363 4474 5.447818 GGTCATAATGCCTTCTTGAACTTCG 60.448 44.000 0.00 0.00 0.00 3.79
4374 4485 0.035439 TGAACTTCGGATTGAGGCCC 60.035 55.000 0.00 0.00 0.00 5.80
4429 4540 1.535462 CAATTGGAGTTCGACCGCTTT 59.465 47.619 0.00 0.00 0.00 3.51
4469 4581 4.335594 GCCTACACATAACTTTGGCCTTAG 59.664 45.833 3.32 3.42 33.45 2.18
4471 4583 6.357367 CCTACACATAACTTTGGCCTTAGAT 58.643 40.000 3.32 0.00 0.00 1.98
4485 4597 6.658849 TGGCCTTAGATGAGTTTGCTATTTA 58.341 36.000 3.32 0.00 0.00 1.40
4486 4598 7.290061 TGGCCTTAGATGAGTTTGCTATTTAT 58.710 34.615 3.32 0.00 0.00 1.40
4488 4600 7.663493 GGCCTTAGATGAGTTTGCTATTTATCT 59.337 37.037 0.00 0.00 0.00 1.98
4489 4601 9.712305 GCCTTAGATGAGTTTGCTATTTATCTA 57.288 33.333 0.00 0.00 0.00 1.98
4496 4608 8.542497 TGAGTTTGCTATTTATCTACGTGTTT 57.458 30.769 0.00 0.00 0.00 2.83
4509 4621 3.408288 ACGTGTTTTTGTATGCGTGTT 57.592 38.095 0.00 0.00 0.00 3.32
4510 4622 4.533225 ACGTGTTTTTGTATGCGTGTTA 57.467 36.364 0.00 0.00 0.00 2.41
4511 4623 4.906423 ACGTGTTTTTGTATGCGTGTTAA 58.094 34.783 0.00 0.00 0.00 2.01
4512 4624 5.512473 ACGTGTTTTTGTATGCGTGTTAAT 58.488 33.333 0.00 0.00 0.00 1.40
4513 4625 5.972382 ACGTGTTTTTGTATGCGTGTTAATT 59.028 32.000 0.00 0.00 0.00 1.40
4515 4627 7.009357 ACGTGTTTTTGTATGCGTGTTAATTTT 59.991 29.630 0.00 0.00 0.00 1.82
4516 4628 7.314481 CGTGTTTTTGTATGCGTGTTAATTTTG 59.686 33.333 0.00 0.00 0.00 2.44
4517 4629 7.109532 GTGTTTTTGTATGCGTGTTAATTTTGC 59.890 33.333 0.00 0.00 0.00 3.68
4518 4630 7.010552 TGTTTTTGTATGCGTGTTAATTTTGCT 59.989 29.630 0.00 0.00 0.00 3.91
4544 4658 4.963237 GCATTCTAGTTATGCAGAGTCG 57.037 45.455 20.32 0.00 45.93 4.18
4553 4667 1.758440 ATGCAGAGTCGGGTGTGTGT 61.758 55.000 0.00 0.00 0.00 3.72
4595 4709 3.498481 CCCACCTGAACTTTGGATTGAGA 60.498 47.826 0.00 0.00 31.39 3.27
4645 4759 4.853924 AGTTGACTCAAAATTTCGCCAT 57.146 36.364 0.00 0.00 0.00 4.40
4646 4760 5.200368 AGTTGACTCAAAATTTCGCCATT 57.800 34.783 0.00 0.00 0.00 3.16
4660 4774 3.334691 TCGCCATTAAAAGGTGACTCAG 58.665 45.455 8.92 0.00 42.68 3.35
4674 4788 8.423906 AAGGTGACTCAGAAAGAATTAGAGTA 57.576 34.615 0.00 0.00 42.68 2.59
4679 4793 9.025041 TGACTCAGAAAGAATTAGAGTATGTCA 57.975 33.333 0.00 0.00 39.47 3.58
4727 4842 2.009051 TGCCATGAGTTCAAGCATACG 58.991 47.619 0.00 0.00 35.27 3.06
4728 4843 1.331756 GCCATGAGTTCAAGCATACGG 59.668 52.381 0.00 0.00 31.79 4.02
4743 4858 1.528129 TACGGTGTCAAATGCATGCA 58.472 45.000 25.04 25.04 0.00 3.96
4749 4864 4.244066 GGTGTCAAATGCATGCATGTTTA 58.756 39.130 32.79 15.51 36.68 2.01
4756 4871 7.321746 GTCAAATGCATGCATGTTTACAAAAAG 59.678 33.333 32.79 12.68 36.68 2.27
4774 4889 2.226962 AGTTGTACTCCCTCCGCTAA 57.773 50.000 0.00 0.00 0.00 3.09
4788 4903 5.476614 CCTCCGCTAAAGTTGTACTAAAGT 58.523 41.667 0.00 0.00 0.00 2.66
4791 4906 4.992951 CCGCTAAAGTTGTACTAAAGTGGT 59.007 41.667 10.50 0.00 36.64 4.16
4792 4907 5.119743 CCGCTAAAGTTGTACTAAAGTGGTC 59.880 44.000 10.50 0.00 36.64 4.02
4809 4924 8.606040 AAAGTGGTCACAATTAATTTGGATTG 57.394 30.769 0.00 7.11 39.80 2.67
4810 4925 6.165577 AGTGGTCACAATTAATTTGGATTGC 58.834 36.000 0.00 0.00 39.80 3.56
4813 4928 6.014755 TGGTCACAATTAATTTGGATTGCAGA 60.015 34.615 0.00 5.37 39.80 4.26
4863 4978 9.767228 TTAACTAAGGGCTTTTACCAAAATTTC 57.233 29.630 0.00 0.00 0.00 2.17
4884 4999 6.435292 TTCTACTTCTAGTTGAGGGCTTTT 57.565 37.500 0.00 0.00 32.05 2.27
4885 5000 6.435292 TCTACTTCTAGTTGAGGGCTTTTT 57.565 37.500 0.00 0.00 0.00 1.94
4902 5017 5.447144 GGCTTTTTCAAAATGTTGTGTGGTC 60.447 40.000 0.00 0.00 36.07 4.02
4903 5018 5.121454 GCTTTTTCAAAATGTTGTGTGGTCA 59.879 36.000 0.00 0.00 36.07 4.02
4904 5019 6.473397 TTTTTCAAAATGTTGTGTGGTCAC 57.527 33.333 0.00 0.00 44.08 3.67
4939 5054 4.979943 TGAAGCTTGTGTTGTCAAATGA 57.020 36.364 2.10 0.00 0.00 2.57
4942 5057 5.978919 TGAAGCTTGTGTTGTCAAATGAATC 59.021 36.000 2.10 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
213 221 1.477685 TTGTCCTCCCCCTTGACGAC 61.478 60.000 0.00 0.00 0.00 4.34
219 227 0.423544 ATCTCCTTGTCCTCCCCCTT 59.576 55.000 0.00 0.00 0.00 3.95
322 331 3.760738 TGCATCTAGATCTGGTCGAGAT 58.239 45.455 5.18 7.62 46.34 2.75
374 384 3.545624 GCACTCAAATCAGATCGCATGAC 60.546 47.826 0.00 0.00 0.00 3.06
398 408 0.327924 CATCCCCTACCAACAGCACA 59.672 55.000 0.00 0.00 0.00 4.57
423 433 1.062428 CATCCCCTACCTCTACCACCA 60.062 57.143 0.00 0.00 0.00 4.17
641 653 4.082787 TCGACATTTCCCATTTCTCAAAGC 60.083 41.667 0.00 0.00 0.00 3.51
646 658 4.119862 TCGATCGACATTTCCCATTTCTC 58.880 43.478 15.15 0.00 0.00 2.87
649 661 4.450976 TCATCGATCGACATTTCCCATTT 58.549 39.130 22.06 0.00 0.00 2.32
655 667 5.829233 TGCTAATCATCGATCGACATTTC 57.171 39.130 22.06 15.33 0.00 2.17
657 669 6.791887 AATTGCTAATCATCGATCGACATT 57.208 33.333 22.06 21.77 0.00 2.71
658 670 6.033937 CGTAATTGCTAATCATCGATCGACAT 59.966 38.462 22.06 12.71 0.00 3.06
666 678 4.982295 TCTGGTCGTAATTGCTAATCATCG 59.018 41.667 0.00 0.00 0.00 3.84
671 683 6.015010 AGAGCTATCTGGTCGTAATTGCTAAT 60.015 38.462 0.00 0.00 46.86 1.73
680 692 4.464951 TCCAAAAAGAGCTATCTGGTCGTA 59.535 41.667 0.00 0.00 46.86 3.43
687 699 5.187186 TCGTTACCTCCAAAAAGAGCTATCT 59.813 40.000 0.00 0.00 37.39 1.98
788 800 9.872684 ATCACAAGGGTATCATCTATTTGATTT 57.127 29.630 0.00 0.00 37.51 2.17
789 801 9.293404 CATCACAAGGGTATCATCTATTTGATT 57.707 33.333 0.00 0.00 37.51 2.57
792 804 6.072286 GCCATCACAAGGGTATCATCTATTTG 60.072 42.308 0.00 0.00 0.00 2.32
793 805 6.006449 GCCATCACAAGGGTATCATCTATTT 58.994 40.000 0.00 0.00 0.00 1.40
795 807 4.323028 CGCCATCACAAGGGTATCATCTAT 60.323 45.833 0.00 0.00 0.00 1.98
799 811 1.768275 TCGCCATCACAAGGGTATCAT 59.232 47.619 0.00 0.00 0.00 2.45
808 820 2.388310 TTACGGATTCGCCATCACAA 57.612 45.000 0.00 0.00 40.63 3.33
810 822 3.750639 TTTTTACGGATTCGCCATCAC 57.249 42.857 0.00 0.00 40.63 3.06
833 845 9.442047 CATTGGAGAAGAGTCAAAATAGTTAGT 57.558 33.333 0.00 0.00 0.00 2.24
834 846 8.394121 GCATTGGAGAAGAGTCAAAATAGTTAG 58.606 37.037 0.00 0.00 0.00 2.34
843 855 3.055891 TGATCGCATTGGAGAAGAGTCAA 60.056 43.478 0.00 0.00 0.00 3.18
898 910 0.254178 CCTGCTCCAGTAAGGCATGT 59.746 55.000 0.00 0.00 37.29 3.21
1167 1219 1.678300 GTCGTCGGAGGGGAAGACT 60.678 63.158 0.00 0.00 40.70 3.24
1497 1561 0.462047 GCCGTTTCATGATCTCGGGT 60.462 55.000 24.45 0.00 41.24 5.28
1523 1587 2.774687 GGCAACGTTTAAGGAAGGAGA 58.225 47.619 0.00 0.00 0.00 3.71
1642 1706 3.695606 TCGGAGAGCCCTGTGCAC 61.696 66.667 10.75 10.75 44.83 4.57
1707 1771 3.131223 TGCAGTTTCTATTCTCTCCTCCG 59.869 47.826 0.00 0.00 0.00 4.63
1716 1780 6.317857 GTCATCAAGGTTGCAGTTTCTATTC 58.682 40.000 0.00 0.00 0.00 1.75
1734 1798 0.865111 CGAACACTTTGCCGTCATCA 59.135 50.000 0.00 0.00 0.00 3.07
1758 1822 2.745037 GTGGACTGGGTGCCGTTA 59.255 61.111 0.00 0.00 0.00 3.18
2128 2204 0.318762 GTCAGGTCCTTGCTCGACTT 59.681 55.000 0.00 0.00 0.00 3.01
2190 2266 3.186001 CGCTGAACTTGATGCTCCATATC 59.814 47.826 0.00 0.00 0.00 1.63
2258 2334 2.280797 GCACGACCTGCCAGACAA 60.281 61.111 0.00 0.00 40.42 3.18
2290 2366 1.528542 CCGGCGTCAGGATAGAGGA 60.529 63.158 6.01 0.00 0.00 3.71
2326 2402 3.689002 GAGCCAGCGGGGGAAGAAG 62.689 68.421 4.64 0.00 37.04 2.85
2390 2466 0.605589 CAGGACCTTTCTCGACAGCT 59.394 55.000 0.00 0.00 0.00 4.24
2391 2467 1.016653 GCAGGACCTTTCTCGACAGC 61.017 60.000 0.00 0.00 0.00 4.40
2392 2468 0.734253 CGCAGGACCTTTCTCGACAG 60.734 60.000 0.00 0.00 0.00 3.51
2400 2476 3.901797 CTTCCCGCGCAGGACCTTT 62.902 63.158 13.08 0.00 45.00 3.11
2489 2565 4.373116 GGCCCTCGAAGACGCACA 62.373 66.667 0.00 0.00 39.58 4.57
2554 2630 1.374125 CCATGGACGACGACAGCAA 60.374 57.895 5.56 0.00 0.00 3.91
2713 2789 4.803426 CTCCGCCACGCTCCAGAC 62.803 72.222 0.00 0.00 0.00 3.51
2733 2809 0.732880 CGCTCCAATCGACGACTTGT 60.733 55.000 0.00 0.00 0.00 3.16
2810 2886 9.680315 ATTAGTTGATACTACTACAAGAATCGC 57.320 33.333 0.00 0.00 36.61 4.58
2913 2994 1.212616 CGATCGCAGCCTAGGAAAAG 58.787 55.000 14.75 0.25 0.00 2.27
2982 3063 2.932614 AGATTGCGTGCTACTGACATTC 59.067 45.455 0.00 0.00 0.00 2.67
2993 3074 5.968387 ATTTAGTACTACAGATTGCGTGC 57.032 39.130 0.91 0.00 0.00 5.34
3030 3112 7.501225 ACACATCAGAATGCTCATTGATCATAA 59.499 33.333 3.57 0.00 36.26 1.90
3124 3206 0.108615 CGGTGATCTTCTTCGCCTGT 60.109 55.000 0.00 0.00 42.90 4.00
3161 3243 3.378112 TGTTTGTCAGCTCAAGAACAAGG 59.622 43.478 0.00 0.00 0.00 3.61
3173 3259 1.522258 CGTTTGCCATTGTTTGTCAGC 59.478 47.619 0.00 0.00 0.00 4.26
3199 3285 0.914551 CATCCGACGTCAACATCGAC 59.085 55.000 17.16 0.00 40.86 4.20
3210 3296 1.129809 GCGTGAACAACATCCGACG 59.870 57.895 0.00 0.00 0.00 5.12
3216 3302 1.838913 GCAAACTGCGTGAACAACAT 58.161 45.000 0.00 0.00 31.71 2.71
3217 3303 3.320884 GCAAACTGCGTGAACAACA 57.679 47.368 0.00 0.00 31.71 3.33
3351 3446 1.980052 CTGGTAAAGGTGAGGCGGA 59.020 57.895 0.00 0.00 0.00 5.54
3567 3662 2.499685 GGCCTTGACGCCGATACT 59.500 61.111 0.00 0.00 39.64 2.12
3937 4035 0.627986 CTTCTGCCCTTTGATCCCCT 59.372 55.000 0.00 0.00 0.00 4.79
3977 4075 1.298953 CTCCCTCCCTTGGAATCCAA 58.701 55.000 14.73 14.73 41.69 3.53
3985 4083 0.842467 AAGACCCACTCCCTCCCTTG 60.842 60.000 0.00 0.00 0.00 3.61
4014 4116 1.153208 CTCATGCTCCTGTCCTGCC 60.153 63.158 0.00 0.00 0.00 4.85
4032 4134 1.002900 TCGTTTGTAAAGCTGCTGCAC 60.003 47.619 18.42 7.90 42.74 4.57
4061 4163 0.454600 ACCGATCTTGTGCGTCGTAT 59.545 50.000 0.00 0.00 33.77 3.06
4073 4175 2.617308 ACATATGTTCGTCGACCGATCT 59.383 45.455 10.58 0.00 46.75 2.75
4074 4176 2.996155 ACATATGTTCGTCGACCGATC 58.004 47.619 10.58 10.12 46.75 3.69
4095 4204 2.819608 CGACCCCATCAATCAAACAAGT 59.180 45.455 0.00 0.00 0.00 3.16
4101 4210 1.077068 GGCCGACCCCATCAATCAA 60.077 57.895 0.00 0.00 0.00 2.57
4102 4211 2.595095 GGCCGACCCCATCAATCA 59.405 61.111 0.00 0.00 0.00 2.57
4157 4266 4.351874 TCCTCCCTACACTTGAAACTTG 57.648 45.455 0.00 0.00 0.00 3.16
4340 4451 5.447818 CCGAAGTTCAAGAAGGCATTATGAC 60.448 44.000 3.32 0.00 0.00 3.06
4351 4462 3.074412 GCCTCAATCCGAAGTTCAAGAA 58.926 45.455 3.32 0.00 0.00 2.52
4363 4474 3.440522 GCGATAAATTAGGGCCTCAATCC 59.559 47.826 10.74 0.00 0.00 3.01
4448 4560 7.047891 TCATCTAAGGCCAAAGTTATGTGTAG 58.952 38.462 5.01 0.00 0.00 2.74
4453 4565 7.253422 CAAACTCATCTAAGGCCAAAGTTATG 58.747 38.462 5.01 2.74 0.00 1.90
4469 4581 8.354011 ACACGTAGATAAATAGCAAACTCATC 57.646 34.615 0.00 0.00 0.00 2.92
4471 4583 8.542497 AAACACGTAGATAAATAGCAAACTCA 57.458 30.769 0.00 0.00 0.00 3.41
4485 4597 4.449743 ACACGCATACAAAAACACGTAGAT 59.550 37.500 0.00 0.00 31.70 1.98
4486 4598 3.803231 ACACGCATACAAAAACACGTAGA 59.197 39.130 0.00 0.00 31.70 2.59
4488 4600 4.533225 AACACGCATACAAAAACACGTA 57.467 36.364 0.00 0.00 31.70 3.57
4489 4601 3.408288 AACACGCATACAAAAACACGT 57.592 38.095 0.00 0.00 0.00 4.49
4490 4602 6.427300 AATTAACACGCATACAAAAACACG 57.573 33.333 0.00 0.00 0.00 4.49
4496 4608 7.810282 ACATAGCAAAATTAACACGCATACAAA 59.190 29.630 0.00 0.00 0.00 2.83
4501 4613 4.562394 GCACATAGCAAAATTAACACGCAT 59.438 37.500 0.00 0.00 44.79 4.73
4527 4641 2.688446 CACCCGACTCTGCATAACTAGA 59.312 50.000 0.00 0.00 0.00 2.43
4531 4645 1.337823 ACACACCCGACTCTGCATAAC 60.338 52.381 0.00 0.00 0.00 1.89
4559 4673 3.654321 TCAGGTGGGCATTATGATCATCT 59.346 43.478 12.53 0.00 0.00 2.90
4576 4690 3.138283 TGGTCTCAATCCAAAGTTCAGGT 59.862 43.478 0.00 0.00 31.50 4.00
4646 4760 9.712305 CTCTAATTCTTTCTGAGTCACCTTTTA 57.288 33.333 0.00 0.00 0.00 1.52
4704 4819 1.089112 TGCTTGAACTCATGGCATCG 58.911 50.000 0.00 0.00 32.83 3.84
4727 4842 2.373540 ACATGCATGCATTTGACACC 57.626 45.000 30.32 0.00 33.90 4.16
4728 4843 4.685165 TGTAAACATGCATGCATTTGACAC 59.315 37.500 30.32 21.91 33.90 3.67
4756 4871 2.233186 ACTTTAGCGGAGGGAGTACAAC 59.767 50.000 0.00 0.00 0.00 3.32
4774 4889 7.875327 AATTGTGACCACTTTAGTACAACTT 57.125 32.000 0.00 0.00 31.75 2.66
4788 4903 6.014755 TCTGCAATCCAAATTAATTGTGACCA 60.015 34.615 0.39 0.82 37.32 4.02
4791 4906 7.177216 ACTCTCTGCAATCCAAATTAATTGTGA 59.823 33.333 0.39 2.11 37.32 3.58
4792 4907 7.318141 ACTCTCTGCAATCCAAATTAATTGTG 58.682 34.615 0.39 2.93 37.32 3.33
4809 4924 7.076842 TGTGCAAAAAGATATTACTCTCTGC 57.923 36.000 0.00 0.00 0.00 4.26
4840 4955 7.612065 AGAAATTTTGGTAAAAGCCCTTAGT 57.388 32.000 0.00 0.00 33.22 2.24
4860 4975 6.435292 AAAGCCCTCAACTAGAAGTAGAAA 57.565 37.500 0.00 0.00 0.00 2.52
4863 4978 6.231211 TGAAAAAGCCCTCAACTAGAAGTAG 58.769 40.000 0.00 0.00 0.00 2.57
4875 4990 4.875536 ACACAACATTTTGAAAAAGCCCTC 59.124 37.500 0.00 0.00 36.48 4.30
4902 5017 3.501062 AGCTTCAACTGACATCATGTGTG 59.499 43.478 0.00 3.05 42.36 3.82
4903 5018 3.748083 AGCTTCAACTGACATCATGTGT 58.252 40.909 0.00 0.00 45.83 3.72
4904 5019 4.023450 ACAAGCTTCAACTGACATCATGTG 60.023 41.667 0.00 0.00 0.00 3.21
4912 5027 3.126858 TGACAACACAAGCTTCAACTGAC 59.873 43.478 0.00 0.00 0.00 3.51
4916 5031 5.101628 TCATTTGACAACACAAGCTTCAAC 58.898 37.500 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.