Multiple sequence alignment - TraesCS4D01G238700

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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 TraesCS4D01G238700 chr4D 100.000 3443 0 0 1 3443 400826100 400829542 0.000000e+00 6359.0
1 TraesCS4D01G238700 chr4D 94.032 1441 80 5 1011 2445 400928393 400926953 0.000000e+00 2180.0
2 TraesCS4D01G238700 chr4D 93.293 1148 74 1 1239 2383 417422532 417421385 0.000000e+00 1690.0
3 TraesCS4D01G238700 chr4D 92.492 666 44 5 1 663 480852276 480851614 0.000000e+00 948.0
4 TraesCS4D01G238700 chr4D 90.654 107 10 0 1011 1117 417422669 417422563 3.580000e-30 143.0
5 TraesCS4D01G238700 chr4D 94.444 36 1 1 2542 2577 417419663 417419629 2.000000e-03 54.7
6 TraesCS4D01G238700 chr4B 97.323 1905 35 5 838 2728 495147892 495149794 0.000000e+00 3221.0
7 TraesCS4D01G238700 chr4B 93.824 1441 83 4 1011 2445 495356620 495355180 0.000000e+00 2163.0
8 TraesCS4D01G238700 chr4B 91.570 344 23 4 2722 3062 495150577 495150917 1.450000e-128 470.0
9 TraesCS4D01G238700 chr4B 91.471 340 20 3 3107 3443 495150920 495151253 3.130000e-125 459.0
10 TraesCS4D01G238700 chr4B 97.561 41 0 1 2536 2576 495355061 495355022 6.170000e-08 69.4
11 TraesCS4D01G238700 chr4A 96.246 1971 52 13 785 2735 58569879 58571847 0.000000e+00 3210.0
12 TraesCS4D01G238700 chr4A 91.861 1585 98 22 1011 2576 58810212 58808640 0.000000e+00 2183.0
13 TraesCS4D01G238700 chr4A 89.959 727 52 8 2721 3443 58572565 58573274 0.000000e+00 918.0
14 TraesCS4D01G238700 chr3D 96.061 660 20 5 1 657 64671973 64672629 0.000000e+00 1070.0
15 TraesCS4D01G238700 chr3D 93.769 658 36 5 1 655 591823116 591823771 0.000000e+00 983.0
16 TraesCS4D01G238700 chr3D 93.192 661 41 4 1 657 30399851 30399191 0.000000e+00 968.0
17 TraesCS4D01G238700 chr3D 83.505 97 13 3 2736 2832 509310547 509310454 1.700000e-13 87.9
18 TraesCS4D01G238700 chr1D 95.320 641 27 3 20 657 366708167 366708807 0.000000e+00 1014.0
19 TraesCS4D01G238700 chr1D 77.982 218 37 8 2821 3035 414741388 414741597 3.610000e-25 126.0
20 TraesCS4D01G238700 chr2D 94.118 663 33 5 1 658 9516593 9515932 0.000000e+00 1003.0
21 TraesCS4D01G238700 chr2D 93.816 663 36 5 1 658 9507812 9507150 0.000000e+00 992.0
22 TraesCS4D01G238700 chr2D 83.092 207 33 2 2825 3031 372329669 372329873 1.630000e-43 187.0
23 TraesCS4D01G238700 chr6A 93.383 665 37 7 1 660 540830637 540829975 0.000000e+00 977.0
24 TraesCS4D01G238700 chr6A 81.043 211 36 2 3220 3427 572856025 572856234 7.640000e-37 165.0
25 TraesCS4D01G238700 chr6A 82.836 134 13 8 2698 2822 499461687 499461555 1.010000e-20 111.0
26 TraesCS4D01G238700 chr7D 93.030 660 40 6 1 657 39581732 39581076 0.000000e+00 959.0
27 TraesCS4D01G238700 chr7D 83.898 118 13 5 2961 3077 235513551 235513439 1.310000e-19 108.0
28 TraesCS4D01G238700 chr3A 81.043 211 37 1 3220 3427 40388194 40387984 7.640000e-37 165.0
29 TraesCS4D01G238700 chr3A 85.075 134 14 4 2691 2818 562912765 562912898 7.750000e-27 132.0
30 TraesCS4D01G238700 chr2B 82.199 191 31 3 2821 3009 56626753 56626942 9.890000e-36 161.0
31 TraesCS4D01G238700 chr2B 88.235 85 8 2 2735 2818 16263012 16263095 2.190000e-17 100.0
32 TraesCS4D01G238700 chr2B 87.356 87 9 2 2733 2818 644521715 644521630 7.860000e-17 99.0
33 TraesCS4D01G238700 chr2B 88.889 81 6 3 2737 2815 765556323 765556402 2.830000e-16 97.1
34 TraesCS4D01G238700 chr1A 78.367 245 43 9 2815 3055 511489759 511489997 2.140000e-32 150.0
35 TraesCS4D01G238700 chr5A 81.818 176 28 3 2907 3082 48353331 48353502 9.960000e-31 145.0
36 TraesCS4D01G238700 chr5A 87.654 81 7 3 2732 2810 680221315 680221394 1.320000e-14 91.6
37 TraesCS4D01G238700 chr5D 93.220 59 4 0 2835 2893 253237920 253237862 1.700000e-13 87.9


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 TraesCS4D01G238700 chr4D 400826100 400829542 3442 False 6359.000000 6359 100.000000 1 3443 1 chr4D.!!$F1 3442
1 TraesCS4D01G238700 chr4D 400926953 400928393 1440 True 2180.000000 2180 94.032000 1011 2445 1 chr4D.!!$R1 1434
2 TraesCS4D01G238700 chr4D 480851614 480852276 662 True 948.000000 948 92.492000 1 663 1 chr4D.!!$R2 662
3 TraesCS4D01G238700 chr4D 417419629 417422669 3040 True 629.233333 1690 92.797000 1011 2577 3 chr4D.!!$R3 1566
4 TraesCS4D01G238700 chr4B 495147892 495151253 3361 False 1383.333333 3221 93.454667 838 3443 3 chr4B.!!$F1 2605
5 TraesCS4D01G238700 chr4B 495355022 495356620 1598 True 1116.200000 2163 95.692500 1011 2576 2 chr4B.!!$R1 1565
6 TraesCS4D01G238700 chr4A 58808640 58810212 1572 True 2183.000000 2183 91.861000 1011 2576 1 chr4A.!!$R1 1565
7 TraesCS4D01G238700 chr4A 58569879 58573274 3395 False 2064.000000 3210 93.102500 785 3443 2 chr4A.!!$F1 2658
8 TraesCS4D01G238700 chr3D 64671973 64672629 656 False 1070.000000 1070 96.061000 1 657 1 chr3D.!!$F1 656
9 TraesCS4D01G238700 chr3D 591823116 591823771 655 False 983.000000 983 93.769000 1 655 1 chr3D.!!$F2 654
10 TraesCS4D01G238700 chr3D 30399191 30399851 660 True 968.000000 968 93.192000 1 657 1 chr3D.!!$R1 656
11 TraesCS4D01G238700 chr1D 366708167 366708807 640 False 1014.000000 1014 95.320000 20 657 1 chr1D.!!$F1 637
12 TraesCS4D01G238700 chr2D 9515932 9516593 661 True 1003.000000 1003 94.118000 1 658 1 chr2D.!!$R2 657
13 TraesCS4D01G238700 chr2D 9507150 9507812 662 True 992.000000 992 93.816000 1 658 1 chr2D.!!$R1 657
14 TraesCS4D01G238700 chr6A 540829975 540830637 662 True 977.000000 977 93.383000 1 660 1 chr6A.!!$R2 659
15 TraesCS4D01G238700 chr7D 39581076 39581732 656 True 959.000000 959 93.030000 1 657 1 chr7D.!!$R1 656

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
719 730 0.106419 TACCAATGGGAATTCCGCCC 60.106 55.0 18.30 6.07 46.22 6.13 F
778 789 0.665369 ACTCGTTAGCCGTTCCGTTG 60.665 55.0 0.00 0.00 37.94 4.10 F
2244 2277 1.108727 ACGTGTACTGGTCCAACGGA 61.109 55.0 16.18 0.00 0.00 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2244 2277 1.380650 GGGGCTCTCGGTCTCTCTT 60.381 63.158 0.0 0.0 0.00 2.85 R
2247 2280 2.043450 CTGGGGCTCTCGGTCTCT 60.043 66.667 0.0 0.0 0.00 3.10 R
3173 5858 0.248289 GTAGGTTTCCGCTGTAGCCA 59.752 55.000 0.0 0.0 37.91 4.75 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
310 312 1.347707 AGGTCATTTTCAGAGCCACGA 59.652 47.619 0.00 0.00 34.17 4.35
311 313 2.026822 AGGTCATTTTCAGAGCCACGAT 60.027 45.455 0.00 0.00 34.17 3.73
553 561 9.386010 TGTGTGAGCTACTTTTTACTTTTCTTA 57.614 29.630 0.00 0.00 0.00 2.10
579 587 5.478332 GGAGATTTTGAGACCTTGTTGGAAT 59.522 40.000 0.00 0.00 39.71 3.01
636 644 3.473647 CTGATGCAGAGGCCGGGA 61.474 66.667 2.18 0.00 40.13 5.14
699 710 8.680001 ACTACAACATATATCACGTTAGACACA 58.320 33.333 0.00 0.00 0.00 3.72
700 711 9.678941 CTACAACATATATCACGTTAGACACAT 57.321 33.333 0.00 0.00 0.00 3.21
702 713 9.459640 ACAACATATATCACGTTAGACACATAC 57.540 33.333 0.00 0.00 0.00 2.39
703 714 8.912658 CAACATATATCACGTTAGACACATACC 58.087 37.037 0.00 0.00 0.00 2.73
704 715 8.173542 ACATATATCACGTTAGACACATACCA 57.826 34.615 0.00 0.00 0.00 3.25
705 716 8.635328 ACATATATCACGTTAGACACATACCAA 58.365 33.333 0.00 0.00 0.00 3.67
706 717 9.639601 CATATATCACGTTAGACACATACCAAT 57.360 33.333 0.00 0.00 0.00 3.16
707 718 7.946655 ATATCACGTTAGACACATACCAATG 57.053 36.000 0.00 0.00 39.17 2.82
708 719 4.500127 TCACGTTAGACACATACCAATGG 58.500 43.478 0.00 0.00 37.43 3.16
709 720 3.621268 CACGTTAGACACATACCAATGGG 59.379 47.826 3.55 0.00 42.66 4.00
710 721 3.516300 ACGTTAGACACATACCAATGGGA 59.484 43.478 3.55 0.00 38.98 4.37
711 722 4.020039 ACGTTAGACACATACCAATGGGAA 60.020 41.667 3.55 0.00 38.98 3.97
712 723 5.123227 CGTTAGACACATACCAATGGGAAT 58.877 41.667 3.55 0.00 38.98 3.01
713 724 5.588648 CGTTAGACACATACCAATGGGAATT 59.411 40.000 3.55 0.00 38.98 2.17
714 725 6.238374 CGTTAGACACATACCAATGGGAATTC 60.238 42.308 3.55 0.00 38.98 2.17
715 726 4.536765 AGACACATACCAATGGGAATTCC 58.463 43.478 16.74 16.74 38.98 3.01
716 727 3.287222 ACACATACCAATGGGAATTCCG 58.713 45.455 18.30 6.59 38.98 4.30
717 728 2.034558 CACATACCAATGGGAATTCCGC 59.965 50.000 18.30 11.61 38.98 5.54
718 729 1.613437 CATACCAATGGGAATTCCGCC 59.387 52.381 18.30 6.11 38.76 6.13
719 730 0.106419 TACCAATGGGAATTCCGCCC 60.106 55.000 18.30 6.07 46.22 6.13
720 731 2.133641 CCAATGGGAATTCCGCCCC 61.134 63.158 18.30 5.68 45.40 5.80
721 732 1.076044 CAATGGGAATTCCGCCCCT 60.076 57.895 18.30 0.00 45.40 4.79
722 733 1.109323 CAATGGGAATTCCGCCCCTC 61.109 60.000 18.30 3.89 45.40 4.30
723 734 1.289244 AATGGGAATTCCGCCCCTCT 61.289 55.000 18.30 0.00 45.40 3.69
724 735 1.999634 ATGGGAATTCCGCCCCTCTG 62.000 60.000 18.30 0.00 45.40 3.35
725 736 2.193248 GGAATTCCGCCCCTCTGG 59.807 66.667 9.17 0.00 37.09 3.86
726 737 2.375345 GGAATTCCGCCCCTCTGGA 61.375 63.158 9.17 0.00 35.39 3.86
729 740 2.998097 TTCCGCCCCTCTGGAATG 59.002 61.111 0.00 0.00 39.29 2.67
730 741 3.344137 TTCCGCCCCTCTGGAATGC 62.344 63.158 0.00 0.00 39.29 3.56
731 742 3.801997 CCGCCCCTCTGGAATGCT 61.802 66.667 0.00 0.00 35.39 3.79
732 743 2.273449 CGCCCCTCTGGAATGCTT 59.727 61.111 0.00 0.00 35.39 3.91
733 744 1.379044 CGCCCCTCTGGAATGCTTT 60.379 57.895 0.00 0.00 35.39 3.51
734 745 0.967380 CGCCCCTCTGGAATGCTTTT 60.967 55.000 0.00 0.00 35.39 2.27
735 746 1.681780 CGCCCCTCTGGAATGCTTTTA 60.682 52.381 0.00 0.00 35.39 1.52
736 747 2.670939 GCCCCTCTGGAATGCTTTTAT 58.329 47.619 0.00 0.00 35.39 1.40
737 748 2.625314 GCCCCTCTGGAATGCTTTTATC 59.375 50.000 0.00 0.00 35.39 1.75
738 749 3.225940 CCCCTCTGGAATGCTTTTATCC 58.774 50.000 0.00 0.00 35.39 2.59
739 750 3.117360 CCCCTCTGGAATGCTTTTATCCT 60.117 47.826 0.00 0.00 35.39 3.24
740 751 3.887716 CCCTCTGGAATGCTTTTATCCTG 59.112 47.826 0.00 0.00 34.24 3.86
741 752 4.530875 CCTCTGGAATGCTTTTATCCTGT 58.469 43.478 0.00 0.00 34.74 4.00
742 753 4.337555 CCTCTGGAATGCTTTTATCCTGTG 59.662 45.833 0.00 0.00 34.74 3.66
743 754 4.922206 TCTGGAATGCTTTTATCCTGTGT 58.078 39.130 0.00 0.00 34.74 3.72
744 755 4.943705 TCTGGAATGCTTTTATCCTGTGTC 59.056 41.667 0.00 0.00 34.74 3.67
745 756 4.661222 TGGAATGCTTTTATCCTGTGTCA 58.339 39.130 0.00 0.00 34.24 3.58
746 757 4.701651 TGGAATGCTTTTATCCTGTGTCAG 59.298 41.667 0.00 0.00 34.24 3.51
747 758 4.702131 GGAATGCTTTTATCCTGTGTCAGT 59.298 41.667 0.00 0.00 0.00 3.41
748 759 5.183904 GGAATGCTTTTATCCTGTGTCAGTT 59.816 40.000 0.00 0.00 0.00 3.16
749 760 6.294731 GGAATGCTTTTATCCTGTGTCAGTTT 60.295 38.462 0.00 0.00 0.00 2.66
750 761 5.689383 TGCTTTTATCCTGTGTCAGTTTC 57.311 39.130 0.00 0.00 0.00 2.78
751 762 5.129634 TGCTTTTATCCTGTGTCAGTTTCA 58.870 37.500 0.00 0.00 0.00 2.69
752 763 5.592282 TGCTTTTATCCTGTGTCAGTTTCAA 59.408 36.000 0.00 0.00 0.00 2.69
753 764 5.915196 GCTTTTATCCTGTGTCAGTTTCAAC 59.085 40.000 0.00 0.00 0.00 3.18
754 765 5.666969 TTTATCCTGTGTCAGTTTCAACG 57.333 39.130 0.00 0.00 0.00 4.10
755 766 1.295792 TCCTGTGTCAGTTTCAACGC 58.704 50.000 0.00 0.00 0.00 4.84
756 767 1.134521 TCCTGTGTCAGTTTCAACGCT 60.135 47.619 0.00 0.00 0.00 5.07
757 768 2.101750 TCCTGTGTCAGTTTCAACGCTA 59.898 45.455 0.00 0.00 0.00 4.26
758 769 3.067106 CCTGTGTCAGTTTCAACGCTAT 58.933 45.455 0.00 0.00 0.00 2.97
759 770 4.021807 TCCTGTGTCAGTTTCAACGCTATA 60.022 41.667 0.00 0.00 0.00 1.31
760 771 4.091509 CCTGTGTCAGTTTCAACGCTATAC 59.908 45.833 0.00 0.00 0.00 1.47
761 772 4.878439 TGTGTCAGTTTCAACGCTATACT 58.122 39.130 0.00 0.00 0.00 2.12
762 773 4.921515 TGTGTCAGTTTCAACGCTATACTC 59.078 41.667 0.00 0.00 0.00 2.59
763 774 4.030306 GTGTCAGTTTCAACGCTATACTCG 59.970 45.833 0.00 0.00 0.00 4.18
764 775 4.164294 GTCAGTTTCAACGCTATACTCGT 58.836 43.478 0.00 0.00 42.54 4.18
766 777 5.796935 GTCAGTTTCAACGCTATACTCGTTA 59.203 40.000 7.46 0.00 46.81 3.18
767 778 6.021626 GTCAGTTTCAACGCTATACTCGTTAG 60.022 42.308 7.46 4.30 46.81 2.34
768 779 4.797349 AGTTTCAACGCTATACTCGTTAGC 59.203 41.667 7.46 0.00 46.81 3.09
769 780 3.344904 TCAACGCTATACTCGTTAGCC 57.655 47.619 7.46 0.00 46.81 3.93
770 781 2.041966 CAACGCTATACTCGTTAGCCG 58.958 52.381 7.46 0.00 46.81 5.52
771 782 1.303309 ACGCTATACTCGTTAGCCGT 58.697 50.000 0.00 0.00 39.09 5.68
772 783 1.672881 ACGCTATACTCGTTAGCCGTT 59.327 47.619 0.00 0.00 39.09 4.44
773 784 2.286654 ACGCTATACTCGTTAGCCGTTC 60.287 50.000 0.00 0.00 39.09 3.95
774 785 2.659387 GCTATACTCGTTAGCCGTTCC 58.341 52.381 0.00 0.00 36.82 3.62
775 786 2.913613 CTATACTCGTTAGCCGTTCCG 58.086 52.381 0.00 0.00 37.94 4.30
776 787 1.098050 ATACTCGTTAGCCGTTCCGT 58.902 50.000 0.00 0.00 37.94 4.69
777 788 0.881118 TACTCGTTAGCCGTTCCGTT 59.119 50.000 0.00 0.00 37.94 4.44
778 789 0.665369 ACTCGTTAGCCGTTCCGTTG 60.665 55.000 0.00 0.00 37.94 4.10
779 790 1.952266 CTCGTTAGCCGTTCCGTTGC 61.952 60.000 0.00 0.00 37.94 4.17
780 791 2.472934 GTTAGCCGTTCCGTTGCG 59.527 61.111 0.00 0.00 0.00 4.85
781 792 3.416382 TTAGCCGTTCCGTTGCGC 61.416 61.111 0.00 0.00 0.00 6.09
782 793 3.869473 TTAGCCGTTCCGTTGCGCT 62.869 57.895 9.73 0.00 0.00 5.92
790 801 1.771073 TTCCGTTGCGCTCACTTGTG 61.771 55.000 9.73 0.00 0.00 3.33
792 803 2.050985 GTTGCGCTCACTTGTGGC 60.051 61.111 9.73 3.09 0.00 5.01
833 847 1.644786 GCGTATGCGGTCCTGCTTTT 61.645 55.000 5.09 0.00 38.78 2.27
1314 1344 2.122729 CCCTCCACCTCCCTCACA 59.877 66.667 0.00 0.00 0.00 3.58
1317 1347 1.229336 CTCCACCTCCCTCACAGGT 60.229 63.158 0.00 0.00 45.89 4.00
1473 1503 3.671411 ACCGTCGAGTCGCAGCTT 61.671 61.111 7.92 0.00 0.00 3.74
1502 1532 1.608590 CGGCAAGTCCAACTTCAACAT 59.391 47.619 0.00 0.00 36.03 2.71
2244 2277 1.108727 ACGTGTACTGGTCCAACGGA 61.109 55.000 16.18 0.00 0.00 4.69
2247 2280 1.342174 GTGTACTGGTCCAACGGAAGA 59.658 52.381 0.00 0.00 31.38 2.87
2686 4343 5.705905 GCCTCAGTCAACTAATGGTTAAGTT 59.294 40.000 0.00 0.00 36.23 2.66
2693 4350 7.041576 AGTCAACTAATGGTTAAGTTTCGGTTC 60.042 37.037 0.00 0.00 36.23 3.62
2730 4388 7.752239 CACAAGATTTACATTGAGATTCACACC 59.248 37.037 0.00 0.00 0.00 4.16
2735 4393 9.643693 GATTTACATTGAGATTCACACCATTTT 57.356 29.630 0.00 0.00 0.00 1.82
2828 5512 1.005450 AGCCACACCCGTAATGGAAAT 59.995 47.619 0.00 0.00 42.00 2.17
2846 5531 8.786826 ATGGAAATACTAAAAATCTGACGTCA 57.213 30.769 18.88 18.88 0.00 4.35
2964 5649 4.783764 AAAATGAACTGGGACGGATTTC 57.216 40.909 0.00 0.00 38.67 2.17
3010 5695 5.817816 GTCATCCTCGGAGAACACAATTTAT 59.182 40.000 6.58 0.00 34.09 1.40
3020 5705 9.357652 CGGAGAACACAATTTATCATGAAAAAT 57.642 29.630 0.00 0.00 0.00 1.82
3156 5841 4.487714 TCTAATCGCTGAATCAAACCCT 57.512 40.909 0.00 0.00 0.00 4.34
3157 5842 5.607939 TCTAATCGCTGAATCAAACCCTA 57.392 39.130 0.00 0.00 0.00 3.53
3180 5865 0.252513 TAGCTCCCAAGGTGGCTACA 60.253 55.000 1.52 0.00 35.79 2.74
3233 5918 3.234730 CCTAGGGCCGGCCTACAG 61.235 72.222 42.70 32.75 36.10 2.74
3279 5964 4.103469 ACAATAATGGGCCCGTATTGACTA 59.897 41.667 39.41 22.92 33.67 2.59
3361 6049 8.822652 AAATGATGATCTTTGGACTTCAAAAC 57.177 30.769 0.00 0.00 43.88 2.43
3364 6052 6.547141 TGATGATCTTTGGACTTCAAAACTGT 59.453 34.615 0.00 0.00 43.88 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
177 179 1.378119 TCTCGCTAACTCGGGCTCA 60.378 57.895 0.00 0.00 0.00 4.26
310 312 2.739292 CGACCACGAACGGATCAATAT 58.261 47.619 0.00 0.00 42.66 1.28
311 313 1.799917 GCGACCACGAACGGATCAATA 60.800 52.381 0.00 0.00 42.66 1.90
352 354 2.920524 TCCAGTAACCAAACGCTTCAA 58.079 42.857 0.00 0.00 0.00 2.69
553 561 4.768968 CCAACAAGGTCTCAAAATCTCCAT 59.231 41.667 0.00 0.00 0.00 3.41
560 568 8.477419 AAATAGATTCCAACAAGGTCTCAAAA 57.523 30.769 0.00 0.00 39.02 2.44
673 684 8.680001 TGTGTCTAACGTGATATATGTTGTAGT 58.320 33.333 0.00 0.00 38.88 2.73
674 685 9.678941 ATGTGTCTAACGTGATATATGTTGTAG 57.321 33.333 0.00 0.00 38.88 2.74
676 687 9.459640 GTATGTGTCTAACGTGATATATGTTGT 57.540 33.333 0.00 0.00 38.88 3.32
677 688 8.912658 GGTATGTGTCTAACGTGATATATGTTG 58.087 37.037 0.00 0.00 38.88 3.33
678 689 8.635328 TGGTATGTGTCTAACGTGATATATGTT 58.365 33.333 0.00 0.00 41.31 2.71
679 690 8.173542 TGGTATGTGTCTAACGTGATATATGT 57.826 34.615 0.00 0.00 0.00 2.29
680 691 9.639601 ATTGGTATGTGTCTAACGTGATATATG 57.360 33.333 0.00 0.00 0.00 1.78
681 692 9.639601 CATTGGTATGTGTCTAACGTGATATAT 57.360 33.333 0.00 0.00 0.00 0.86
682 693 8.085909 CCATTGGTATGTGTCTAACGTGATATA 58.914 37.037 0.00 0.00 0.00 0.86
683 694 6.929049 CCATTGGTATGTGTCTAACGTGATAT 59.071 38.462 0.00 0.00 0.00 1.63
684 695 6.277605 CCATTGGTATGTGTCTAACGTGATA 58.722 40.000 0.00 0.00 0.00 2.15
685 696 5.116180 CCATTGGTATGTGTCTAACGTGAT 58.884 41.667 0.00 0.00 0.00 3.06
686 697 4.500127 CCATTGGTATGTGTCTAACGTGA 58.500 43.478 0.00 0.00 0.00 4.35
687 698 3.621268 CCCATTGGTATGTGTCTAACGTG 59.379 47.826 1.20 0.00 0.00 4.49
688 699 3.516300 TCCCATTGGTATGTGTCTAACGT 59.484 43.478 1.20 0.00 0.00 3.99
689 700 4.131649 TCCCATTGGTATGTGTCTAACG 57.868 45.455 1.20 0.00 0.00 3.18
690 701 6.039382 GGAATTCCCATTGGTATGTGTCTAAC 59.961 42.308 14.03 0.00 34.14 2.34
691 702 6.126409 GGAATTCCCATTGGTATGTGTCTAA 58.874 40.000 14.03 0.00 34.14 2.10
692 703 5.686387 CGGAATTCCCATTGGTATGTGTCTA 60.686 44.000 19.01 0.00 34.14 2.59
693 704 4.536765 GGAATTCCCATTGGTATGTGTCT 58.463 43.478 14.03 0.00 34.14 3.41
694 705 3.315191 CGGAATTCCCATTGGTATGTGTC 59.685 47.826 19.01 0.00 34.14 3.67
695 706 3.287222 CGGAATTCCCATTGGTATGTGT 58.713 45.455 19.01 0.00 34.14 3.72
696 707 2.034558 GCGGAATTCCCATTGGTATGTG 59.965 50.000 19.01 1.25 34.14 3.21
697 708 2.306847 GCGGAATTCCCATTGGTATGT 58.693 47.619 19.01 0.00 34.14 2.29
698 709 1.613437 GGCGGAATTCCCATTGGTATG 59.387 52.381 19.01 2.50 34.14 2.39
699 710 1.480498 GGGCGGAATTCCCATTGGTAT 60.480 52.381 19.01 0.00 43.37 2.73
700 711 0.106419 GGGCGGAATTCCCATTGGTA 60.106 55.000 19.01 0.00 43.37 3.25
701 712 1.381191 GGGCGGAATTCCCATTGGT 60.381 57.895 19.01 0.00 43.37 3.67
702 713 2.133641 GGGGCGGAATTCCCATTGG 61.134 63.158 19.01 5.45 45.73 3.16
703 714 1.076044 AGGGGCGGAATTCCCATTG 60.076 57.895 19.01 5.84 45.73 2.82
704 715 1.230212 GAGGGGCGGAATTCCCATT 59.770 57.895 19.01 0.26 45.73 3.16
705 716 1.697754 AGAGGGGCGGAATTCCCAT 60.698 57.895 19.01 2.93 45.73 4.00
706 717 2.286121 AGAGGGGCGGAATTCCCA 60.286 61.111 19.01 0.00 45.73 4.37
707 718 2.193248 CAGAGGGGCGGAATTCCC 59.807 66.667 19.01 11.21 43.46 3.97
708 719 1.921869 TTCCAGAGGGGCGGAATTCC 61.922 60.000 15.01 15.01 36.36 3.01
709 720 1.607612 TTCCAGAGGGGCGGAATTC 59.392 57.895 0.00 0.00 36.36 2.17
710 721 3.835134 TTCCAGAGGGGCGGAATT 58.165 55.556 0.00 0.00 36.36 2.17
711 722 4.089839 ATTCCAGAGGGGCGGAAT 57.910 55.556 0.00 0.00 44.89 3.01
712 723 2.998097 CATTCCAGAGGGGCGGAA 59.002 61.111 0.00 0.00 45.12 4.30
713 724 3.797353 GCATTCCAGAGGGGCGGA 61.797 66.667 0.00 0.00 36.21 5.54
714 725 2.843912 AAAGCATTCCAGAGGGGCGG 62.844 60.000 0.00 0.00 36.21 6.13
715 726 0.967380 AAAAGCATTCCAGAGGGGCG 60.967 55.000 0.00 0.00 36.21 6.13
716 727 2.143876 TAAAAGCATTCCAGAGGGGC 57.856 50.000 0.00 0.00 36.21 5.80
717 728 3.117360 AGGATAAAAGCATTCCAGAGGGG 60.117 47.826 0.00 0.00 38.37 4.79
718 729 3.887716 CAGGATAAAAGCATTCCAGAGGG 59.112 47.826 0.00 0.00 31.65 4.30
719 730 4.337555 CACAGGATAAAAGCATTCCAGAGG 59.662 45.833 0.00 0.00 31.65 3.69
720 731 4.946157 ACACAGGATAAAAGCATTCCAGAG 59.054 41.667 0.00 0.00 31.65 3.35
721 732 4.922206 ACACAGGATAAAAGCATTCCAGA 58.078 39.130 0.00 0.00 31.65 3.86
722 733 4.701651 TGACACAGGATAAAAGCATTCCAG 59.298 41.667 0.00 0.00 31.65 3.86
723 734 4.661222 TGACACAGGATAAAAGCATTCCA 58.339 39.130 0.00 0.00 31.65 3.53
724 735 4.702131 ACTGACACAGGATAAAAGCATTCC 59.298 41.667 0.00 0.00 35.51 3.01
725 736 5.886960 ACTGACACAGGATAAAAGCATTC 57.113 39.130 0.00 0.00 35.51 2.67
726 737 6.265196 TGAAACTGACACAGGATAAAAGCATT 59.735 34.615 0.00 0.00 35.51 3.56
727 738 5.769662 TGAAACTGACACAGGATAAAAGCAT 59.230 36.000 0.00 0.00 35.51 3.79
728 739 5.129634 TGAAACTGACACAGGATAAAAGCA 58.870 37.500 0.00 0.00 35.51 3.91
729 740 5.689383 TGAAACTGACACAGGATAAAAGC 57.311 39.130 0.00 0.00 35.51 3.51
730 741 6.136071 CGTTGAAACTGACACAGGATAAAAG 58.864 40.000 0.00 0.00 35.51 2.27
731 742 5.504994 GCGTTGAAACTGACACAGGATAAAA 60.505 40.000 0.00 0.00 35.51 1.52
732 743 4.024387 GCGTTGAAACTGACACAGGATAAA 60.024 41.667 0.00 0.00 35.51 1.40
733 744 3.496884 GCGTTGAAACTGACACAGGATAA 59.503 43.478 0.00 0.00 35.51 1.75
734 745 3.064207 GCGTTGAAACTGACACAGGATA 58.936 45.455 0.00 0.00 35.51 2.59
735 746 1.873591 GCGTTGAAACTGACACAGGAT 59.126 47.619 0.00 0.00 35.51 3.24
736 747 1.134521 AGCGTTGAAACTGACACAGGA 60.135 47.619 0.00 0.00 35.51 3.86
737 748 1.299541 AGCGTTGAAACTGACACAGG 58.700 50.000 0.00 0.00 35.51 4.00
738 749 4.923871 AGTATAGCGTTGAAACTGACACAG 59.076 41.667 0.00 0.00 37.52 3.66
739 750 4.878439 AGTATAGCGTTGAAACTGACACA 58.122 39.130 0.00 0.00 0.00 3.72
740 751 4.030306 CGAGTATAGCGTTGAAACTGACAC 59.970 45.833 0.00 0.00 0.00 3.67
741 752 4.163552 CGAGTATAGCGTTGAAACTGACA 58.836 43.478 0.00 0.00 0.00 3.58
742 753 4.164294 ACGAGTATAGCGTTGAAACTGAC 58.836 43.478 0.00 0.00 39.18 3.51
743 754 4.430137 ACGAGTATAGCGTTGAAACTGA 57.570 40.909 0.00 0.00 39.18 3.41
770 781 1.082756 CAAGTGAGCGCAACGGAAC 60.083 57.895 11.47 0.00 0.00 3.62
771 782 1.522806 ACAAGTGAGCGCAACGGAA 60.523 52.632 11.47 0.00 0.00 4.30
772 783 2.108157 ACAAGTGAGCGCAACGGA 59.892 55.556 11.47 0.00 0.00 4.69
773 784 2.249309 CACAAGTGAGCGCAACGG 59.751 61.111 11.47 8.19 0.00 4.44
774 785 2.249309 CCACAAGTGAGCGCAACG 59.751 61.111 11.47 0.00 0.00 4.10
775 786 2.050985 GCCACAAGTGAGCGCAAC 60.051 61.111 11.47 7.80 0.00 4.17
776 787 1.823470 AAGCCACAAGTGAGCGCAA 60.823 52.632 11.47 0.00 33.82 4.85
777 788 2.203195 AAGCCACAAGTGAGCGCA 60.203 55.556 11.47 0.00 33.82 6.09
778 789 2.253452 CAAGCCACAAGTGAGCGC 59.747 61.111 0.00 0.00 33.82 5.92
779 790 2.949106 CCAAGCCACAAGTGAGCG 59.051 61.111 0.94 0.00 33.82 5.03
780 791 2.647297 GCCAAGCCACAAGTGAGC 59.353 61.111 0.94 3.87 0.00 4.26
792 803 1.153168 CTATCGTGGGTGGGCCAAG 60.153 63.158 8.40 0.00 36.17 3.61
928 958 1.537135 GGATCTGCTTACACTCTCGCC 60.537 57.143 0.00 0.00 0.00 5.54
1473 1503 2.357034 GACTTGCCGCCGAGAACA 60.357 61.111 0.00 0.00 0.00 3.18
1502 1532 0.033504 GGAGGTGAAGTCGTTGAGCA 59.966 55.000 0.00 0.00 0.00 4.26
2244 2277 1.380650 GGGGCTCTCGGTCTCTCTT 60.381 63.158 0.00 0.00 0.00 2.85
2247 2280 2.043450 CTGGGGCTCTCGGTCTCT 60.043 66.667 0.00 0.00 0.00 3.10
2686 4343 7.591421 TCTTGTGGATATAGTATGAACCGAA 57.409 36.000 0.00 0.00 0.00 4.30
2748 5432 6.646653 GTCAAGTGACATGTCATGTAGAAAGA 59.353 38.462 30.10 16.24 45.03 2.52
2846 5531 6.208204 GTCAGATTTGCCATGCCTAAATATCT 59.792 38.462 0.00 0.00 0.00 1.98
2954 5639 1.090052 CGAGCAAGGGAAATCCGTCC 61.090 60.000 0.00 0.00 41.52 4.79
2964 5649 0.804989 CTTTAGTTGGCGAGCAAGGG 59.195 55.000 0.00 0.00 0.00 3.95
3010 5695 5.536260 TGGCAAATCGAACATTTTTCATGA 58.464 33.333 0.00 0.00 0.00 3.07
3020 5705 4.855715 TTTTACCATGGCAAATCGAACA 57.144 36.364 13.04 0.00 0.00 3.18
3053 5738 6.380079 AAGGACTCCACTTACAAATCTGAT 57.620 37.500 0.00 0.00 0.00 2.90
3105 5790 3.441572 CGGATGGCTCAAAAGATCAACTT 59.558 43.478 0.00 0.00 40.98 2.66
3106 5791 3.012518 CGGATGGCTCAAAAGATCAACT 58.987 45.455 0.00 0.00 0.00 3.16
3109 5794 2.237143 AGTCGGATGGCTCAAAAGATCA 59.763 45.455 0.00 0.00 0.00 2.92
3156 5841 1.327690 CCACCTTGGGAGCTACGCTA 61.328 60.000 0.00 0.00 39.88 4.26
3157 5842 2.660064 CCACCTTGGGAGCTACGCT 61.660 63.158 0.00 0.00 43.88 5.07
3173 5858 0.248289 GTAGGTTTCCGCTGTAGCCA 59.752 55.000 0.00 0.00 37.91 4.75
3260 5945 4.774660 TTTAGTCAATACGGGCCCATTA 57.225 40.909 24.92 13.02 0.00 1.90
3279 5964 9.088987 TGGAATAGAAAATAGTTTGAGCCTTTT 57.911 29.630 0.00 0.00 0.00 2.27
3361 6049 8.515414 TGATCGATAAATAGGATGTAGTGACAG 58.485 37.037 0.00 0.00 39.50 3.51
3364 6052 9.078990 ACTTGATCGATAAATAGGATGTAGTGA 57.921 33.333 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.