Multiple sequence alignment - TraesCS1D01G120000

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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 TraesCS1D01G120000 chr1D 100.000 3678 0 0 1 3678 117401966 117398289 0.000000e+00 6793
1 TraesCS1D01G120000 chr1A 94.357 2215 67 27 1125 3297 129005027 129002829 0.000000e+00 3345
2 TraesCS1D01G120000 chr1A 96.429 196 5 2 3483 3678 129002593 129002400 4.580000e-84 322
3 TraesCS1D01G120000 chr1A 93.333 150 9 1 3294 3442 129002742 129002593 1.720000e-53 220
4 TraesCS1D01G120000 chr1B 95.302 2001 54 20 792 2766 179631517 179629531 0.000000e+00 3138
5 TraesCS1D01G120000 chr1B 93.784 740 46 0 6 745 179632257 179631518 0.000000e+00 1112
6 TraesCS1D01G120000 chr1B 88.084 663 29 21 3056 3678 179629372 179628720 0.000000e+00 741
7 TraesCS1D01G120000 chr1B 95.031 161 4 3 2863 3023 179629530 179629374 2.190000e-62 250
8 TraesCS1D01G120000 chr3A 82.105 855 124 17 1672 2504 93042429 93041582 0.000000e+00 704
9 TraesCS1D01G120000 chr3A 81.132 848 139 17 1672 2501 93337803 93338647 0.000000e+00 660
10 TraesCS1D01G120000 chr3A 79.742 854 145 24 1672 2502 93264201 93265049 8.790000e-166 593
11 TraesCS1D01G120000 chr3D 81.871 855 126 19 1672 2504 79420927 79420080 0.000000e+00 693
12 TraesCS1D01G120000 chr3D 81.360 853 133 21 1672 2502 79504707 79505555 0.000000e+00 671
13 TraesCS1D01G120000 chr3D 80.706 850 141 15 1672 2502 79428523 79429368 1.110000e-179 640
14 TraesCS1D01G120000 chr3B 81.170 855 132 20 1672 2504 125523911 125523064 0.000000e+00 660
15 TraesCS1D01G120000 chr3B 81.522 552 98 4 1 550 610475574 610475025 5.600000e-123 451
16 TraesCS1D01G120000 chr4D 83.363 553 87 5 1 550 292031205 292031755 1.180000e-139 507
17 TraesCS1D01G120000 chr4D 83.063 555 82 12 1 548 128556204 128556753 9.180000e-136 494
18 TraesCS1D01G120000 chr4B 83.363 553 81 10 1 550 388218133 388217589 5.480000e-138 501
19 TraesCS1D01G120000 chr4B 81.949 554 93 7 1 550 262884051 262884601 2.590000e-126 462
20 TraesCS1D01G120000 chr7A 82.577 551 85 8 1 548 282385387 282385929 3.320000e-130 475
21 TraesCS1D01G120000 chr5D 82.162 555 91 8 1 551 477977058 477976508 1.550000e-128 470
22 TraesCS1D01G120000 chr5A 81.982 555 93 7 1 551 387586644 387587195 7.190000e-127 464


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 TraesCS1D01G120000 chr1D 117398289 117401966 3677 True 6793.000000 6793 100.000000 1 3678 1 chr1D.!!$R1 3677
1 TraesCS1D01G120000 chr1A 129002400 129005027 2627 True 1295.666667 3345 94.706333 1125 3678 3 chr1A.!!$R1 2553
2 TraesCS1D01G120000 chr1B 179628720 179632257 3537 True 1310.250000 3138 93.050250 6 3678 4 chr1B.!!$R1 3672
3 TraesCS1D01G120000 chr3A 93041582 93042429 847 True 704.000000 704 82.105000 1672 2504 1 chr3A.!!$R1 832
4 TraesCS1D01G120000 chr3A 93337803 93338647 844 False 660.000000 660 81.132000 1672 2501 1 chr3A.!!$F2 829
5 TraesCS1D01G120000 chr3A 93264201 93265049 848 False 593.000000 593 79.742000 1672 2502 1 chr3A.!!$F1 830
6 TraesCS1D01G120000 chr3D 79420080 79420927 847 True 693.000000 693 81.871000 1672 2504 1 chr3D.!!$R1 832
7 TraesCS1D01G120000 chr3D 79504707 79505555 848 False 671.000000 671 81.360000 1672 2502 1 chr3D.!!$F2 830
8 TraesCS1D01G120000 chr3D 79428523 79429368 845 False 640.000000 640 80.706000 1672 2502 1 chr3D.!!$F1 830
9 TraesCS1D01G120000 chr3B 125523064 125523911 847 True 660.000000 660 81.170000 1672 2504 1 chr3B.!!$R1 832
10 TraesCS1D01G120000 chr3B 610475025 610475574 549 True 451.000000 451 81.522000 1 550 1 chr3B.!!$R2 549
11 TraesCS1D01G120000 chr4D 292031205 292031755 550 False 507.000000 507 83.363000 1 550 1 chr4D.!!$F2 549
12 TraesCS1D01G120000 chr4D 128556204 128556753 549 False 494.000000 494 83.063000 1 548 1 chr4D.!!$F1 547
13 TraesCS1D01G120000 chr4B 388217589 388218133 544 True 501.000000 501 83.363000 1 550 1 chr4B.!!$R1 549
14 TraesCS1D01G120000 chr4B 262884051 262884601 550 False 462.000000 462 81.949000 1 550 1 chr4B.!!$F1 549
15 TraesCS1D01G120000 chr7A 282385387 282385929 542 False 475.000000 475 82.577000 1 548 1 chr7A.!!$F1 547
16 TraesCS1D01G120000 chr5D 477976508 477977058 550 True 470.000000 470 82.162000 1 551 1 chr5D.!!$R1 550
17 TraesCS1D01G120000 chr5A 387586644 387587195 551 False 464.000000 464 81.982000 1 551 1 chr5A.!!$F1 550

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
941 956 0.045008 TCCCTGCCTACCCCAACATA 59.955 55.0 0.0 0.0 0.0 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2726 2798 0.828022 CCGTTGCCCACTACCATCTA 59.172 55.0 0.0 0.0 0.0 1.98 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
79 81 7.391148 TGTTTTATTCCTCTCCTTTGCATAC 57.609 36.000 0.00 0.00 0.00 2.39
380 392 4.093472 TGTGCCAAGTAAAGCCTTTAGA 57.907 40.909 0.00 0.00 0.00 2.10
412 425 7.801104 TGGGTGATAGTTGCTTTGATTCTATA 58.199 34.615 0.00 0.00 0.00 1.31
477 490 6.619801 AATCACAGAAGCTACGAAAGTTTT 57.380 33.333 0.00 0.00 46.40 2.43
532 546 5.649782 TCCTACGTCGTCCTAATTTTTCT 57.350 39.130 0.00 0.00 0.00 2.52
554 568 7.439157 TCTGAATTGTTGGAGTTACAATCTG 57.561 36.000 0.00 0.00 43.44 2.90
573 587 9.082313 ACAATCTGGAATTTTCTGTATCAAACT 57.918 29.630 0.00 0.00 0.00 2.66
598 612 5.362717 TGGTCATCCATTCTACTCACGTATT 59.637 40.000 0.00 0.00 39.03 1.89
625 639 0.928229 GCTAAGTATTGACACCCGCG 59.072 55.000 0.00 0.00 0.00 6.46
626 640 1.567504 CTAAGTATTGACACCCGCGG 58.432 55.000 21.04 21.04 0.00 6.46
636 650 0.179092 ACACCCGCGGTATTCTTAGC 60.179 55.000 26.12 0.00 32.11 3.09
655 669 8.547967 TCTTAGCGAAGAAAATACAATTGAGT 57.452 30.769 13.59 0.00 38.80 3.41
657 671 9.612620 CTTAGCGAAGAAAATACAATTGAGTTT 57.387 29.630 13.59 9.44 34.25 2.66
724 738 4.161942 TCATTTTTGGCCAGAATACCATGG 59.838 41.667 11.19 11.19 39.73 3.66
734 748 6.449698 GCCAGAATACCATGGATGTTATTTG 58.550 40.000 21.47 11.71 39.02 2.32
736 750 7.417797 GCCAGAATACCATGGATGTTATTTGTT 60.418 37.037 21.47 0.00 39.02 2.83
738 752 7.857389 CAGAATACCATGGATGTTATTTGTTCG 59.143 37.037 21.47 1.12 27.45 3.95
745 759 7.065803 CCATGGATGTTATTTGTTCGTAGAACT 59.934 37.037 5.56 0.00 45.90 3.01
746 760 7.972832 TGGATGTTATTTGTTCGTAGAACTT 57.027 32.000 13.17 2.77 45.90 2.66
747 761 8.025243 TGGATGTTATTTGTTCGTAGAACTTC 57.975 34.615 13.17 0.00 45.90 3.01
748 762 7.658167 TGGATGTTATTTGTTCGTAGAACTTCA 59.342 33.333 13.17 5.20 45.90 3.02
749 763 8.665685 GGATGTTATTTGTTCGTAGAACTTCAT 58.334 33.333 13.17 8.63 45.90 2.57
752 766 8.641155 TGTTATTTGTTCGTAGAACTTCATACG 58.359 33.333 13.17 11.49 45.90 3.06
753 767 5.505165 TTTGTTCGTAGAACTTCATACGC 57.495 39.130 13.17 4.87 45.90 4.42
754 768 4.163458 TGTTCGTAGAACTTCATACGCA 57.837 40.909 13.17 3.89 45.90 5.24
755 769 3.916172 TGTTCGTAGAACTTCATACGCAC 59.084 43.478 13.17 12.28 45.90 5.34
756 770 2.777494 TCGTAGAACTTCATACGCACG 58.223 47.619 12.32 0.00 43.36 5.34
757 771 1.252015 CGTAGAACTTCATACGCACGC 59.748 52.381 7.43 0.00 38.42 5.34
758 772 2.256174 GTAGAACTTCATACGCACGCA 58.744 47.619 0.00 0.00 0.00 5.24
759 773 2.010145 AGAACTTCATACGCACGCAT 57.990 45.000 0.00 0.00 0.00 4.73
760 774 3.159353 AGAACTTCATACGCACGCATA 57.841 42.857 0.00 0.00 0.00 3.14
761 775 2.858344 AGAACTTCATACGCACGCATAC 59.142 45.455 0.00 0.00 0.00 2.39
762 776 1.567504 ACTTCATACGCACGCATACC 58.432 50.000 0.00 0.00 0.00 2.73
763 777 1.134936 ACTTCATACGCACGCATACCA 60.135 47.619 0.00 0.00 0.00 3.25
764 778 1.522676 CTTCATACGCACGCATACCAG 59.477 52.381 0.00 0.00 0.00 4.00
765 779 0.874175 TCATACGCACGCATACCAGC 60.874 55.000 0.00 0.00 0.00 4.85
766 780 1.594293 ATACGCACGCATACCAGCC 60.594 57.895 0.00 0.00 0.00 4.85
767 781 2.304901 ATACGCACGCATACCAGCCA 62.305 55.000 0.00 0.00 0.00 4.75
768 782 3.864686 CGCACGCATACCAGCCAC 61.865 66.667 0.00 0.00 0.00 5.01
769 783 3.508840 GCACGCATACCAGCCACC 61.509 66.667 0.00 0.00 0.00 4.61
770 784 2.824041 CACGCATACCAGCCACCC 60.824 66.667 0.00 0.00 0.00 4.61
771 785 3.326578 ACGCATACCAGCCACCCA 61.327 61.111 0.00 0.00 0.00 4.51
772 786 2.045438 CGCATACCAGCCACCCAA 60.045 61.111 0.00 0.00 0.00 4.12
773 787 1.677300 CGCATACCAGCCACCCAAA 60.677 57.895 0.00 0.00 0.00 3.28
774 788 1.247419 CGCATACCAGCCACCCAAAA 61.247 55.000 0.00 0.00 0.00 2.44
775 789 0.972883 GCATACCAGCCACCCAAAAA 59.027 50.000 0.00 0.00 0.00 1.94
850 865 6.038271 CCACTTTACTATTCATAAGGGTGCAC 59.962 42.308 8.80 8.80 0.00 4.57
872 887 5.851177 CACGTGGAACAATGTTCACTAAATC 59.149 40.000 25.14 8.56 44.16 2.17
920 935 9.757859 AAATAAAAATAAAATTCACGCTGCATG 57.242 25.926 0.00 0.00 0.00 4.06
921 936 4.845621 AAATAAAATTCACGCTGCATGC 57.154 36.364 11.82 11.82 38.57 4.06
922 937 3.788333 ATAAAATTCACGCTGCATGCT 57.212 38.095 20.33 0.00 40.11 3.79
923 938 1.986698 AAAATTCACGCTGCATGCTC 58.013 45.000 20.33 9.76 40.11 4.26
926 941 2.547640 ATTCACGCTGCATGCTCCCT 62.548 55.000 20.33 0.00 40.11 4.20
927 942 3.506096 CACGCTGCATGCTCCCTG 61.506 66.667 20.33 6.83 40.11 4.45
930 945 4.816984 GCTGCATGCTCCCTGCCT 62.817 66.667 20.33 0.00 42.00 4.75
931 946 2.913501 CTGCATGCTCCCTGCCTA 59.086 61.111 20.33 0.00 42.00 3.93
932 947 1.525535 CTGCATGCTCCCTGCCTAC 60.526 63.158 20.33 0.00 42.00 3.18
933 948 2.203266 GCATGCTCCCTGCCTACC 60.203 66.667 11.37 0.00 42.00 3.18
934 949 2.512896 CATGCTCCCTGCCTACCC 59.487 66.667 0.00 0.00 42.00 3.69
936 951 3.658346 ATGCTCCCTGCCTACCCCA 62.658 63.158 0.00 0.00 42.00 4.96
937 952 3.015145 GCTCCCTGCCTACCCCAA 61.015 66.667 0.00 0.00 35.15 4.12
938 953 2.998949 CTCCCTGCCTACCCCAAC 59.001 66.667 0.00 0.00 0.00 3.77
939 954 1.923395 CTCCCTGCCTACCCCAACA 60.923 63.158 0.00 0.00 0.00 3.33
940 955 1.230149 TCCCTGCCTACCCCAACAT 60.230 57.895 0.00 0.00 0.00 2.71
941 956 0.045008 TCCCTGCCTACCCCAACATA 59.955 55.000 0.00 0.00 0.00 2.29
942 957 0.182775 CCCTGCCTACCCCAACATAC 59.817 60.000 0.00 0.00 0.00 2.39
943 958 0.916086 CCTGCCTACCCCAACATACA 59.084 55.000 0.00 0.00 0.00 2.29
944 959 1.134098 CCTGCCTACCCCAACATACAG 60.134 57.143 0.00 0.00 0.00 2.74
958 978 3.428532 ACATACAGTCTACCGAACACCT 58.571 45.455 0.00 0.00 0.00 4.00
1040 1060 7.327761 CACTTCAATTCAATTCACTCCATCAAC 59.672 37.037 0.00 0.00 0.00 3.18
1055 1075 1.598685 CAACCACACGTACCCACCC 60.599 63.158 0.00 0.00 0.00 4.61
1056 1076 2.821518 AACCACACGTACCCACCCC 61.822 63.158 0.00 0.00 0.00 4.95
1250 1270 2.754658 CTCGACCGCTACCCCACT 60.755 66.667 0.00 0.00 0.00 4.00
1259 1279 1.626356 GCTACCCCACTCAGATGGCA 61.626 60.000 0.00 0.00 38.55 4.92
1373 1395 2.056223 GGAGTACTACCCGCTGGCA 61.056 63.158 0.00 0.00 33.59 4.92
1427 1449 4.357947 GTGGACTGCAGCGACGGA 62.358 66.667 15.27 0.00 0.00 4.69
1502 1524 4.849329 GAGTACCCGCTCGCCGTG 62.849 72.222 0.00 0.00 34.38 4.94
1621 1643 3.529341 ATTGCGCTGTGTCGGTGGA 62.529 57.895 9.73 0.00 0.00 4.02
1725 1755 2.112297 GGTTCCGGTTCAGCCACA 59.888 61.111 0.00 0.00 36.97 4.17
2045 2084 1.663702 CGTTTGCTTCGACGAGGGT 60.664 57.895 9.18 0.00 41.53 4.34
2644 2716 1.299541 ACCGAGCAAGAATAATGGCG 58.700 50.000 0.00 0.00 0.00 5.69
2651 2723 4.202441 AGCAAGAATAATGGCGAACAGAT 58.798 39.130 0.00 0.00 0.00 2.90
2652 2724 5.368145 AGCAAGAATAATGGCGAACAGATA 58.632 37.500 0.00 0.00 0.00 1.98
2653 2725 5.237344 AGCAAGAATAATGGCGAACAGATAC 59.763 40.000 0.00 0.00 0.00 2.24
2654 2726 5.237344 GCAAGAATAATGGCGAACAGATACT 59.763 40.000 0.00 0.00 0.00 2.12
2655 2727 6.653183 CAAGAATAATGGCGAACAGATACTG 58.347 40.000 0.00 0.00 37.52 2.74
2657 2729 7.050970 AGAATAATGGCGAACAGATACTGTA 57.949 36.000 4.84 0.00 44.62 2.74
2696 2768 1.641577 AGTGGAAGAAGAATACGCGC 58.358 50.000 5.73 0.00 0.00 6.86
2726 2798 2.448453 GGACAGGTAGACACAGCTAGT 58.552 52.381 0.00 0.00 0.00 2.57
2727 2799 3.618351 GGACAGGTAGACACAGCTAGTA 58.382 50.000 0.00 0.00 0.00 1.82
2728 2800 3.628487 GGACAGGTAGACACAGCTAGTAG 59.372 52.174 0.00 0.00 0.00 2.57
2805 2881 3.797256 GCGTTGCAGGAAGTGTATACTAG 59.203 47.826 4.17 0.00 35.69 2.57
2806 2882 4.677250 GCGTTGCAGGAAGTGTATACTAGT 60.677 45.833 0.00 0.00 35.69 2.57
2807 2883 5.449588 GCGTTGCAGGAAGTGTATACTAGTA 60.450 44.000 4.77 4.77 35.69 1.82
2833 2909 9.809096 ACATCCTTTTCTTCTTCTTTCTTTTTC 57.191 29.630 0.00 0.00 0.00 2.29
2841 2917 9.467796 TTCTTCTTCTTTCTTTTTCTTCCTTCT 57.532 29.630 0.00 0.00 0.00 2.85
2899 2975 2.862780 TGGTGGGAAGCTACCAACT 58.137 52.632 21.89 0.00 46.01 3.16
2928 3004 3.119919 CCCTCGACTTGTGTACTGTACTC 60.120 52.174 17.98 14.84 0.00 2.59
2932 3008 4.818005 TCGACTTGTGTACTGTACTCTTCA 59.182 41.667 17.98 9.62 0.00 3.02
2937 3013 9.472361 GACTTGTGTACTGTACTCTTCATTTTA 57.528 33.333 17.98 0.00 0.00 1.52
3052 3129 7.701539 TGGTATAATGTGAAAAACAGCTCAT 57.298 32.000 0.00 0.00 43.64 2.90
3054 3131 7.148086 TGGTATAATGTGAAAAACAGCTCATCC 60.148 37.037 0.00 0.00 43.64 3.51
3075 3152 1.668751 TGGTGTCGTCTTTTTCACAGC 59.331 47.619 0.00 0.00 37.69 4.40
3183 3267 5.091910 TCACGATACTTACATGCGAGTAG 57.908 43.478 12.58 5.03 32.37 2.57
3396 3576 2.952978 ACAGAGGTGGTCATCGTCTATC 59.047 50.000 0.00 0.00 0.00 2.08
3409 3596 7.279313 GGTCATCGTCTATCTATACTCTTCCTC 59.721 44.444 0.00 0.00 0.00 3.71
3423 3610 2.176889 CTTCCTCCTACCGTTCCAAGA 58.823 52.381 0.00 0.00 0.00 3.02
3439 3626 3.316868 TCCAAGACCGACAAAATTGGAAC 59.683 43.478 2.59 0.00 44.79 3.62
3478 3665 1.525077 GCAACCGGTGACTTGACCA 60.525 57.895 8.52 0.00 35.50 4.02
3527 3714 6.382919 AAGTAGGTAGAAATGCCAAAGGTA 57.617 37.500 0.00 0.00 0.00 3.08
3654 3841 1.065997 AGTTGTAGGGGTTGGTGCCT 61.066 55.000 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 49 7.454260 AGGAGAGGAATAAAACATTGACAAC 57.546 36.000 0.00 0.00 0.00 3.32
124 126 5.593095 AGTCTAACATACTTCCTATGCACGA 59.407 40.000 0.00 0.00 36.41 4.35
126 128 7.701809 GAAGTCTAACATACTTCCTATGCAC 57.298 40.000 4.94 0.00 44.60 4.57
380 392 3.778265 AGCAACTATCACCCAAACCATT 58.222 40.909 0.00 0.00 0.00 3.16
532 546 6.303054 TCCAGATTGTAACTCCAACAATTCA 58.697 36.000 3.23 0.00 45.24 2.57
554 568 7.657336 TGACCAAGTTTGATACAGAAAATTCC 58.343 34.615 0.00 0.00 0.00 3.01
598 612 6.036300 CGGGTGTCAATACTTAGCGAAAATTA 59.964 38.462 0.00 0.00 0.00 1.40
686 700 9.112725 GGCCAAAAATGATAAAATTGAAGCTAT 57.887 29.630 0.00 0.00 0.00 2.97
710 724 6.040842 ACAAATAACATCCATGGTATTCTGGC 59.959 38.462 12.58 0.00 46.79 4.85
734 748 3.002344 CGTGCGTATGAAGTTCTACGAAC 60.002 47.826 25.59 24.18 43.40 3.95
736 750 2.777494 CGTGCGTATGAAGTTCTACGA 58.223 47.619 25.59 14.80 42.45 3.43
738 752 2.256174 TGCGTGCGTATGAAGTTCTAC 58.744 47.619 4.17 3.86 0.00 2.59
745 759 1.566404 CTGGTATGCGTGCGTATGAA 58.434 50.000 5.48 0.00 0.00 2.57
746 760 0.874175 GCTGGTATGCGTGCGTATGA 60.874 55.000 5.48 0.00 0.00 2.15
747 761 1.564622 GCTGGTATGCGTGCGTATG 59.435 57.895 5.48 0.00 0.00 2.39
748 762 1.594293 GGCTGGTATGCGTGCGTAT 60.594 57.895 0.00 0.50 0.00 3.06
749 763 2.202824 GGCTGGTATGCGTGCGTA 60.203 61.111 0.00 0.00 0.00 4.42
750 764 4.386951 TGGCTGGTATGCGTGCGT 62.387 61.111 0.00 0.00 0.00 5.24
751 765 3.864686 GTGGCTGGTATGCGTGCG 61.865 66.667 0.00 0.00 0.00 5.34
752 766 3.508840 GGTGGCTGGTATGCGTGC 61.509 66.667 0.00 0.00 0.00 5.34
753 767 2.824041 GGGTGGCTGGTATGCGTG 60.824 66.667 0.00 0.00 0.00 5.34
754 768 2.419011 TTTGGGTGGCTGGTATGCGT 62.419 55.000 0.00 0.00 0.00 5.24
755 769 1.247419 TTTTGGGTGGCTGGTATGCG 61.247 55.000 0.00 0.00 0.00 4.73
756 770 0.972883 TTTTTGGGTGGCTGGTATGC 59.027 50.000 0.00 0.00 0.00 3.14
826 841 6.238103 CGTGCACCCTTATGAATAGTAAAGTG 60.238 42.308 12.15 0.00 0.00 3.16
850 865 5.079406 CGATTTAGTGAACATTGTTCCACG 58.921 41.667 23.22 14.56 34.93 4.94
872 887 3.513662 TGTCCGAATTGTATGTACACCG 58.486 45.455 0.00 0.00 35.64 4.94
920 935 3.015145 TTGGGGTAGGCAGGGAGC 61.015 66.667 0.00 0.00 44.65 4.70
921 936 1.281925 ATGTTGGGGTAGGCAGGGAG 61.282 60.000 0.00 0.00 0.00 4.30
922 937 0.045008 TATGTTGGGGTAGGCAGGGA 59.955 55.000 0.00 0.00 0.00 4.20
923 938 0.182775 GTATGTTGGGGTAGGCAGGG 59.817 60.000 0.00 0.00 0.00 4.45
926 941 1.557832 GACTGTATGTTGGGGTAGGCA 59.442 52.381 0.00 0.00 0.00 4.75
927 942 1.838077 AGACTGTATGTTGGGGTAGGC 59.162 52.381 0.00 0.00 0.00 3.93
928 943 3.387050 GGTAGACTGTATGTTGGGGTAGG 59.613 52.174 0.00 0.00 0.00 3.18
929 944 3.067742 CGGTAGACTGTATGTTGGGGTAG 59.932 52.174 0.00 0.00 0.00 3.18
930 945 3.025978 CGGTAGACTGTATGTTGGGGTA 58.974 50.000 0.00 0.00 0.00 3.69
931 946 1.829222 CGGTAGACTGTATGTTGGGGT 59.171 52.381 0.00 0.00 0.00 4.95
932 947 2.104967 TCGGTAGACTGTATGTTGGGG 58.895 52.381 0.00 0.00 0.00 4.96
933 948 3.056393 TGTTCGGTAGACTGTATGTTGGG 60.056 47.826 0.00 0.00 0.00 4.12
934 949 3.924686 GTGTTCGGTAGACTGTATGTTGG 59.075 47.826 0.00 0.00 0.00 3.77
936 951 3.830755 AGGTGTTCGGTAGACTGTATGTT 59.169 43.478 0.00 0.00 0.00 2.71
937 952 3.428532 AGGTGTTCGGTAGACTGTATGT 58.571 45.455 0.00 0.00 0.00 2.29
938 953 4.880120 TCTAGGTGTTCGGTAGACTGTATG 59.120 45.833 0.00 0.00 0.00 2.39
939 954 4.880696 GTCTAGGTGTTCGGTAGACTGTAT 59.119 45.833 0.00 0.00 39.65 2.29
940 955 4.256920 GTCTAGGTGTTCGGTAGACTGTA 58.743 47.826 0.00 0.00 39.65 2.74
941 956 3.080319 GTCTAGGTGTTCGGTAGACTGT 58.920 50.000 0.00 0.00 39.65 3.55
942 957 3.079578 TGTCTAGGTGTTCGGTAGACTG 58.920 50.000 9.49 0.00 42.14 3.51
943 958 3.080319 GTGTCTAGGTGTTCGGTAGACT 58.920 50.000 9.49 0.00 42.14 3.24
944 959 2.163211 GGTGTCTAGGTGTTCGGTAGAC 59.837 54.545 0.00 0.00 42.03 2.59
958 978 4.894705 TGCGTGGGTTTATATAGGTGTCTA 59.105 41.667 0.00 0.00 0.00 2.59
1040 1060 4.024545 GGGGGTGGGTACGTGTGG 62.025 72.222 0.00 0.00 0.00 4.17
1055 1075 1.656441 GTGAGCTGTTGTTGCTGGG 59.344 57.895 0.00 0.00 41.30 4.45
1056 1076 1.656441 GGTGAGCTGTTGTTGCTGG 59.344 57.895 0.00 0.00 41.30 4.85
1259 1279 1.153939 GTGCAGCGACTCGATGAGT 60.154 57.895 20.45 0.00 46.56 3.41
1427 1449 0.606401 CCTCAATGAACCACACGCCT 60.606 55.000 0.00 0.00 0.00 5.52
1502 1524 1.446966 GAGCAGCTCGTCCTTGTCC 60.447 63.158 6.67 0.00 0.00 4.02
1621 1643 3.378427 GCTCGCAGTAAAATCCAAATCCT 59.622 43.478 0.00 0.00 0.00 3.24
1892 1931 3.511934 AGATGTCTATGGCGAGGTATTCC 59.488 47.826 0.00 0.00 0.00 3.01
2045 2084 3.636231 CAGAGGTGCACGGGGGAA 61.636 66.667 11.45 0.00 0.00 3.97
2270 2318 3.392595 CTGGTACGGGTCGACGCTC 62.393 68.421 27.29 17.54 37.37 5.03
2644 2716 9.344309 GTTTCTTCACTACTACAGTATCTGTTC 57.656 37.037 7.70 0.00 42.59 3.18
2652 2724 9.837525 CTTTATACGTTTCTTCACTACTACAGT 57.162 33.333 0.00 0.00 38.32 3.55
2653 2725 9.837525 ACTTTATACGTTTCTTCACTACTACAG 57.162 33.333 0.00 0.00 0.00 2.74
2654 2726 9.616634 CACTTTATACGTTTCTTCACTACTACA 57.383 33.333 0.00 0.00 0.00 2.74
2655 2727 9.070149 CCACTTTATACGTTTCTTCACTACTAC 57.930 37.037 0.00 0.00 0.00 2.73
2656 2728 9.013229 TCCACTTTATACGTTTCTTCACTACTA 57.987 33.333 0.00 0.00 0.00 1.82
2657 2729 7.889469 TCCACTTTATACGTTTCTTCACTACT 58.111 34.615 0.00 0.00 0.00 2.57
2696 2768 2.900546 GTCTACCTGTCCCCCATATCTG 59.099 54.545 0.00 0.00 0.00 2.90
2726 2798 0.828022 CCGTTGCCCACTACCATCTA 59.172 55.000 0.00 0.00 0.00 1.98
2727 2799 1.602237 CCGTTGCCCACTACCATCT 59.398 57.895 0.00 0.00 0.00 2.90
2728 2800 2.112815 GCCGTTGCCCACTACCATC 61.113 63.158 0.00 0.00 0.00 3.51
2807 2883 9.809096 GAAAAAGAAAGAAGAAGAAAAGGATGT 57.191 29.630 0.00 0.00 0.00 3.06
2857 2933 2.420547 CCCAGCTTCGATCCTTCAATCA 60.421 50.000 0.00 0.00 0.00 2.57
2937 3013 5.127491 TGCGGGTTTATATTCGAAAGGAAT 58.873 37.500 0.00 0.00 46.86 3.01
2940 3016 4.844267 CTTGCGGGTTTATATTCGAAAGG 58.156 43.478 0.00 0.00 35.34 3.11
3042 3119 1.609061 CGACACCAGGATGAGCTGTTT 60.609 52.381 0.00 0.00 39.69 2.83
3052 3129 2.093394 TGTGAAAAAGACGACACCAGGA 60.093 45.455 0.00 0.00 33.08 3.86
3054 3131 2.286418 GCTGTGAAAAAGACGACACCAG 60.286 50.000 0.00 0.00 33.08 4.00
3100 3177 5.116882 GTCAAGTTTATACCCGCAGATCTT 58.883 41.667 0.00 0.00 0.00 2.40
3315 3494 1.471119 CAGCTGGATTGCAAGGACAT 58.529 50.000 5.57 0.00 34.99 3.06
3396 3576 4.761227 GGAACGGTAGGAGGAAGAGTATAG 59.239 50.000 0.00 0.00 0.00 1.31
3409 3596 0.108945 GTCGGTCTTGGAACGGTAGG 60.109 60.000 5.16 0.00 43.55 3.18
3423 3610 3.181480 CCTGTTGTTCCAATTTTGTCGGT 60.181 43.478 0.00 0.00 0.00 4.69
3478 3665 0.255890 CCACCGGATGGGAACTGAAT 59.744 55.000 9.46 0.00 45.95 2.57
3527 3714 4.330074 CGATTTGTTCGGTAAAGATGAGCT 59.670 41.667 0.00 0.00 44.28 4.09
3654 3841 6.975196 TGATTTTTCCTTCTCATCACCAAA 57.025 33.333 0.00 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.