Multiple sequence alignment - TraesCS7B01G059800

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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 TraesCS7B01G059800 chr7B 100.000 4583 0 0 1 4583 62653751 62658333 0.000000e+00 8464.0
1 TraesCS7B01G059800 chr7B 97.811 731 16 0 1 731 43302093 43301363 0.000000e+00 1262.0
2 TraesCS7B01G059800 chr7B 93.570 731 44 3 3 731 673969958 673969229 0.000000e+00 1086.0
3 TraesCS7B01G059800 chr7D 96.726 3787 107 14 811 4583 104522440 104526223 0.000000e+00 6290.0
4 TraesCS7B01G059800 chr7D 96.970 33 1 0 731 763 104505241 104505273 6.410000e-04 56.5
5 TraesCS7B01G059800 chr7A 95.572 3591 113 21 840 4415 108750383 108753942 0.000000e+00 5709.0
6 TraesCS7B01G059800 chr7A 91.837 147 12 0 4411 4557 108759824 108759970 6.010000e-49 206.0
7 TraesCS7B01G059800 chr2A 92.497 733 43 7 1 731 673965699 673966421 0.000000e+00 1038.0
8 TraesCS7B01G059800 chr2A 89.333 150 16 0 3934 4083 741097592 741097443 6.050000e-44 189.0
9 TraesCS7B01G059800 chr2A 88.742 151 17 0 3933 4083 741227915 741227765 7.830000e-43 185.0
10 TraesCS7B01G059800 chr1B 91.700 747 54 6 1 744 142860383 142861124 0.000000e+00 1029.0
11 TraesCS7B01G059800 chr6B 93.078 549 30 8 200 744 234654391 234653847 0.000000e+00 797.0
12 TraesCS7B01G059800 chr6B 93.043 115 8 0 3934 4048 41202884 41202770 7.890000e-38 169.0
13 TraesCS7B01G059800 chr2D 88.667 150 17 0 3934 4083 609306083 609305934 2.820000e-42 183.0
14 TraesCS7B01G059800 chr6D 87.179 156 14 4 3934 4085 25031353 25031200 6.100000e-39 172.0
15 TraesCS7B01G059800 chrUn 92.373 118 9 0 3934 4051 71540203 71540086 7.890000e-38 169.0
16 TraesCS7B01G059800 chrUn 93.043 115 8 0 3934 4048 345345919 345346033 7.890000e-38 169.0


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 TraesCS7B01G059800 chr7B 62653751 62658333 4582 False 8464 8464 100.000 1 4583 1 chr7B.!!$F1 4582
1 TraesCS7B01G059800 chr7B 43301363 43302093 730 True 1262 1262 97.811 1 731 1 chr7B.!!$R1 730
2 TraesCS7B01G059800 chr7B 673969229 673969958 729 True 1086 1086 93.570 3 731 1 chr7B.!!$R2 728
3 TraesCS7B01G059800 chr7D 104522440 104526223 3783 False 6290 6290 96.726 811 4583 1 chr7D.!!$F2 3772
4 TraesCS7B01G059800 chr7A 108750383 108753942 3559 False 5709 5709 95.572 840 4415 1 chr7A.!!$F1 3575
5 TraesCS7B01G059800 chr2A 673965699 673966421 722 False 1038 1038 92.497 1 731 1 chr2A.!!$F1 730
6 TraesCS7B01G059800 chr1B 142860383 142861124 741 False 1029 1029 91.700 1 744 1 chr1B.!!$F1 743
7 TraesCS7B01G059800 chr6B 234653847 234654391 544 True 797 797 93.078 200 744 1 chr6B.!!$R2 544

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
763 775 0.253610 CGGTTGGTTATACTGCCCCA 59.746 55.000 0.0 0.0 0.00 4.96 F
767 779 0.985760 TGGTTATACTGCCCCAACGT 59.014 50.000 0.0 0.0 0.00 3.99 F
768 780 1.065998 TGGTTATACTGCCCCAACGTC 60.066 52.381 0.0 0.0 0.00 4.34 F
885 897 1.166531 ACAAGCAACCAACGGCTCTC 61.167 55.000 0.0 0.0 40.01 3.20 F
1686 1705 1.278985 TCGATGATCTTTGGGTGCTGT 59.721 47.619 0.0 0.0 0.00 4.40 F
2539 2558 0.887387 GGTGGCAGCGTGGAAAGTAA 60.887 55.000 0.0 0.0 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1620 1639 0.865111 TCATCTTGTCAAACACCGCG 59.135 50.000 0.00 0.0 0.00 6.46 R
2199 2218 1.078426 GCCACAGTATCCCGCTTGT 60.078 57.895 0.00 0.0 0.00 3.16 R
2446 2465 2.089201 CAGAACTGATTGCATCTGCCA 58.911 47.619 0.08 0.0 41.18 4.92 R
2539 2558 2.429933 ATACAGGCATGGATCTCCCT 57.570 50.000 2.31 0.0 35.38 4.20 R
3102 3121 1.272490 TCCTGCAGACTAGAAACCACG 59.728 52.381 17.39 0.0 0.00 4.94 R
3871 3893 0.991920 CCTGGAAAGGCTAACTCCCA 59.008 55.000 7.52 0.0 0.00 4.37 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
83 84 4.181578 GCTTCTTTGATTCGTAGCTACCA 58.818 43.478 18.16 7.35 0.00 3.25
601 612 8.018677 TGCATCTAGCTAAATTATTAAGACGC 57.981 34.615 0.00 0.00 45.94 5.19
732 744 4.024302 CACGCGTCTATCATGGTCTAGTAA 60.024 45.833 9.86 0.00 0.00 2.24
733 745 4.024218 ACGCGTCTATCATGGTCTAGTAAC 60.024 45.833 5.58 0.00 0.00 2.50
734 746 4.213694 CGCGTCTATCATGGTCTAGTAACT 59.786 45.833 0.00 0.00 0.00 2.24
735 747 5.277876 CGCGTCTATCATGGTCTAGTAACTT 60.278 44.000 0.00 0.00 0.00 2.66
736 748 6.505272 GCGTCTATCATGGTCTAGTAACTTT 58.495 40.000 0.00 0.00 0.00 2.66
737 749 7.519488 CGCGTCTATCATGGTCTAGTAACTTTA 60.519 40.741 0.00 0.00 0.00 1.85
738 750 8.298140 GCGTCTATCATGGTCTAGTAACTTTAT 58.702 37.037 0.00 0.00 0.00 1.40
747 759 9.804977 ATGGTCTAGTAACTTTATATAGTCGGT 57.195 33.333 0.00 0.00 0.00 4.69
748 760 9.632638 TGGTCTAGTAACTTTATATAGTCGGTT 57.367 33.333 0.00 0.00 0.00 4.44
749 761 9.890352 GGTCTAGTAACTTTATATAGTCGGTTG 57.110 37.037 0.00 0.00 0.00 3.77
750 762 9.890352 GTCTAGTAACTTTATATAGTCGGTTGG 57.110 37.037 0.00 0.00 0.00 3.77
751 763 9.632638 TCTAGTAACTTTATATAGTCGGTTGGT 57.367 33.333 0.00 0.00 0.00 3.67
759 771 9.136952 CTTTATATAGTCGGTTGGTTATACTGC 57.863 37.037 0.00 0.00 0.00 4.40
760 772 2.685850 AGTCGGTTGGTTATACTGCC 57.314 50.000 0.00 0.00 0.00 4.85
761 773 1.208776 AGTCGGTTGGTTATACTGCCC 59.791 52.381 0.00 0.00 0.00 5.36
762 774 0.542805 TCGGTTGGTTATACTGCCCC 59.457 55.000 0.00 0.00 0.00 5.80
763 775 0.253610 CGGTTGGTTATACTGCCCCA 59.746 55.000 0.00 0.00 0.00 4.96
764 776 1.340211 CGGTTGGTTATACTGCCCCAA 60.340 52.381 0.00 0.00 34.69 4.12
766 778 1.741145 GTTGGTTATACTGCCCCAACG 59.259 52.381 4.81 0.00 45.09 4.10
767 779 0.985760 TGGTTATACTGCCCCAACGT 59.014 50.000 0.00 0.00 0.00 3.99
768 780 1.065998 TGGTTATACTGCCCCAACGTC 60.066 52.381 0.00 0.00 0.00 4.34
769 781 1.208776 GGTTATACTGCCCCAACGTCT 59.791 52.381 0.00 0.00 0.00 4.18
770 782 2.355412 GGTTATACTGCCCCAACGTCTT 60.355 50.000 0.00 0.00 0.00 3.01
771 783 3.340928 GTTATACTGCCCCAACGTCTTT 58.659 45.455 0.00 0.00 0.00 2.52
772 784 2.579410 ATACTGCCCCAACGTCTTTT 57.421 45.000 0.00 0.00 0.00 2.27
773 785 3.706600 ATACTGCCCCAACGTCTTTTA 57.293 42.857 0.00 0.00 0.00 1.52
774 786 2.579410 ACTGCCCCAACGTCTTTTAT 57.421 45.000 0.00 0.00 0.00 1.40
775 787 2.871453 ACTGCCCCAACGTCTTTTATT 58.129 42.857 0.00 0.00 0.00 1.40
776 788 3.227614 ACTGCCCCAACGTCTTTTATTT 58.772 40.909 0.00 0.00 0.00 1.40
777 789 4.400120 ACTGCCCCAACGTCTTTTATTTA 58.600 39.130 0.00 0.00 0.00 1.40
778 790 4.457949 ACTGCCCCAACGTCTTTTATTTAG 59.542 41.667 0.00 0.00 0.00 1.85
779 791 3.759618 TGCCCCAACGTCTTTTATTTAGG 59.240 43.478 0.00 0.00 0.00 2.69
780 792 4.011698 GCCCCAACGTCTTTTATTTAGGA 58.988 43.478 0.00 0.00 0.00 2.94
781 793 4.460034 GCCCCAACGTCTTTTATTTAGGAA 59.540 41.667 0.00 0.00 0.00 3.36
782 794 5.620654 GCCCCAACGTCTTTTATTTAGGAAC 60.621 44.000 0.00 0.00 0.00 3.62
783 795 5.391203 CCCCAACGTCTTTTATTTAGGAACG 60.391 44.000 0.00 0.00 0.00 3.95
784 796 5.391203 CCCAACGTCTTTTATTTAGGAACGG 60.391 44.000 0.00 0.00 0.00 4.44
785 797 5.409214 CCAACGTCTTTTATTTAGGAACGGA 59.591 40.000 0.00 0.00 0.00 4.69
786 798 6.401796 CCAACGTCTTTTATTTAGGAACGGAG 60.402 42.308 0.00 0.00 0.00 4.63
787 799 6.029346 ACGTCTTTTATTTAGGAACGGAGA 57.971 37.500 0.00 0.00 0.00 3.71
788 800 5.866092 ACGTCTTTTATTTAGGAACGGAGAC 59.134 40.000 0.00 0.00 0.00 3.36
789 801 5.865552 CGTCTTTTATTTAGGAACGGAGACA 59.134 40.000 0.00 0.00 32.65 3.41
790 802 6.034683 CGTCTTTTATTTAGGAACGGAGACAG 59.965 42.308 0.00 0.00 32.65 3.51
791 803 6.872547 GTCTTTTATTTAGGAACGGAGACAGT 59.127 38.462 0.00 0.00 33.17 3.55
792 804 8.031277 GTCTTTTATTTAGGAACGGAGACAGTA 58.969 37.037 0.00 0.00 33.17 2.74
793 805 8.755977 TCTTTTATTTAGGAACGGAGACAGTAT 58.244 33.333 0.00 0.00 0.00 2.12
794 806 9.379791 CTTTTATTTAGGAACGGAGACAGTATT 57.620 33.333 0.00 0.00 0.00 1.89
797 809 9.807649 TTATTTAGGAACGGAGACAGTATTAAC 57.192 33.333 0.00 0.00 0.00 2.01
798 810 4.732672 AGGAACGGAGACAGTATTAACC 57.267 45.455 0.00 0.00 0.00 2.85
799 811 4.091549 AGGAACGGAGACAGTATTAACCA 58.908 43.478 0.00 0.00 0.00 3.67
800 812 4.715297 AGGAACGGAGACAGTATTAACCAT 59.285 41.667 0.00 0.00 0.00 3.55
801 813 4.809426 GGAACGGAGACAGTATTAACCATG 59.191 45.833 0.00 0.00 0.00 3.66
802 814 3.793559 ACGGAGACAGTATTAACCATGC 58.206 45.455 0.00 0.00 0.00 4.06
803 815 3.451178 ACGGAGACAGTATTAACCATGCT 59.549 43.478 0.00 0.00 0.00 3.79
804 816 4.051922 CGGAGACAGTATTAACCATGCTC 58.948 47.826 0.00 0.00 0.00 4.26
805 817 4.202161 CGGAGACAGTATTAACCATGCTCT 60.202 45.833 0.00 0.00 0.00 4.09
806 818 5.009710 CGGAGACAGTATTAACCATGCTCTA 59.990 44.000 0.00 0.00 0.00 2.43
807 819 6.461092 CGGAGACAGTATTAACCATGCTCTAA 60.461 42.308 0.00 0.00 0.00 2.10
808 820 6.926272 GGAGACAGTATTAACCATGCTCTAAG 59.074 42.308 0.00 0.00 0.00 2.18
809 821 7.418025 GGAGACAGTATTAACCATGCTCTAAGT 60.418 40.741 0.00 0.00 0.00 2.24
818 830 9.905713 ATTAACCATGCTCTAAGTGAAGAATTA 57.094 29.630 0.00 0.00 0.00 1.40
822 834 7.831193 ACCATGCTCTAAGTGAAGAATTATTGT 59.169 33.333 0.00 0.00 0.00 2.71
824 836 8.886719 CATGCTCTAAGTGAAGAATTATTGTGA 58.113 33.333 0.00 0.00 0.00 3.58
826 838 9.102757 TGCTCTAAGTGAAGAATTATTGTGATC 57.897 33.333 0.00 0.00 0.00 2.92
827 839 9.323985 GCTCTAAGTGAAGAATTATTGTGATCT 57.676 33.333 0.00 0.00 0.00 2.75
837 849 8.458573 AGAATTATTGTGATCTAGTCGAGAGT 57.541 34.615 0.00 0.00 37.70 3.24
871 883 2.334946 TGGCGCAATCTCCACAAGC 61.335 57.895 10.83 0.00 0.00 4.01
885 897 1.166531 ACAAGCAACCAACGGCTCTC 61.167 55.000 0.00 0.00 40.01 3.20
886 898 1.600916 AAGCAACCAACGGCTCTCC 60.601 57.895 0.00 0.00 40.01 3.71
913 931 4.891037 GCCCTCCCTGCAGCATCC 62.891 72.222 8.66 0.00 0.00 3.51
993 1012 2.364317 CCGCTCCTTCTCCCTCCA 60.364 66.667 0.00 0.00 0.00 3.86
998 1017 1.899438 GCTCCTTCTCCCTCCACTTCT 60.899 57.143 0.00 0.00 0.00 2.85
1103 1122 4.016706 CCGCCTCCAAGAACCGGT 62.017 66.667 0.00 0.00 34.56 5.28
1327 1346 3.806591 GAGGTGTTCGACGGAATGA 57.193 52.632 0.00 0.00 34.05 2.57
1392 1411 1.616921 CACCAGGGGCATCTTCCAT 59.383 57.895 0.00 0.00 0.00 3.41
1500 1519 2.654079 CGCTGAGGACCAGAGGCTT 61.654 63.158 0.00 0.00 45.78 4.35
1506 1525 1.920835 GGACCAGAGGCTTGGGAGT 60.921 63.158 16.56 0.00 42.76 3.85
1605 1624 5.647658 GGTGATGTATGTCAAATGTGGAGAA 59.352 40.000 0.00 0.00 0.00 2.87
1614 1633 1.779061 AATGTGGAGAACTGGGGCGT 61.779 55.000 0.00 0.00 0.00 5.68
1686 1705 1.278985 TCGATGATCTTTGGGTGCTGT 59.721 47.619 0.00 0.00 0.00 4.40
1687 1706 1.667724 CGATGATCTTTGGGTGCTGTC 59.332 52.381 0.00 0.00 0.00 3.51
1696 1715 3.414700 GGTGCTGTCGGTCTTGCG 61.415 66.667 0.00 0.00 0.00 4.85
1791 1810 3.193263 CACACTGATTTCGAGCTATGCT 58.807 45.455 0.00 0.00 43.88 3.79
2070 2089 7.415206 GCGATTAAGATTGGGACTGTAAACAAT 60.415 37.037 4.43 4.43 36.35 2.71
2073 2092 6.976934 AAGATTGGGACTGTAAACAATGTT 57.023 33.333 8.27 0.00 34.01 2.71
2079 2098 5.654650 TGGGACTGTAAACAATGTTTTGTCT 59.345 36.000 16.99 0.00 45.30 3.41
2223 2242 1.302949 GGGATACTGTGGCAAGGCA 59.697 57.895 0.00 0.00 0.00 4.75
2319 2338 1.420430 ACATACGGAATGGGGACGAT 58.580 50.000 0.00 0.00 40.16 3.73
2539 2558 0.887387 GGTGGCAGCGTGGAAAGTAA 60.887 55.000 0.00 0.00 0.00 2.24
3102 3121 5.163152 ACCCAATGATCCTAGAATCCAAGTC 60.163 44.000 0.00 0.00 0.00 3.01
3366 3385 4.696479 AGAAGAGAAGGAAGAAGTTGCA 57.304 40.909 0.00 0.00 0.00 4.08
3414 3433 9.822185 GCAATTATTGTTGGGATTTCTAATTCT 57.178 29.630 6.81 0.00 0.00 2.40
3493 3512 4.232221 CACCTTCGCTAAGTTAGTTTCGA 58.768 43.478 11.51 8.99 0.00 3.71
3570 3589 6.182627 TGAGAATGGTAATTGCTCTTGTGAT 58.817 36.000 0.00 0.00 0.00 3.06
3581 3600 5.823209 TGCTCTTGTGATGATTATTGGTG 57.177 39.130 0.00 0.00 0.00 4.17
3590 3609 6.942005 TGTGATGATTATTGGTGAACTCAACT 59.058 34.615 0.00 0.00 33.92 3.16
3652 3671 8.317679 GGCTAGACTGAAATGTTCCAGATATAT 58.682 37.037 0.00 0.00 34.65 0.86
3671 3690 8.820831 AGATATATGAATACAGCCAGCTAACTT 58.179 33.333 0.00 0.00 0.00 2.66
3749 3768 8.828688 TGCATTGTATTTGAATTTCATTGACA 57.171 26.923 0.00 2.37 0.00 3.58
3771 3790 6.186957 ACACTGAATATGGCCTCAACATTAA 58.813 36.000 3.32 0.00 0.00 1.40
3869 3891 4.566004 TGTATAGTTGACACTTGGCACTC 58.434 43.478 0.00 0.00 34.06 3.51
3870 3892 4.283467 TGTATAGTTGACACTTGGCACTCT 59.717 41.667 0.00 0.00 34.06 3.24
3871 3893 2.717639 AGTTGACACTTGGCACTCTT 57.282 45.000 0.00 0.00 29.05 2.85
3874 3896 0.179020 TGACACTTGGCACTCTTGGG 60.179 55.000 0.00 0.00 0.00 4.12
3875 3897 0.108585 GACACTTGGCACTCTTGGGA 59.891 55.000 0.00 0.00 0.00 4.37
3998 4020 9.004717 TGAATTCATTGTAAACGAATTGGTAGA 57.995 29.630 3.38 0.00 38.98 2.59
4201 4223 7.459795 TTTGAATGTATAAGGTGTGCATCAA 57.540 32.000 0.00 0.00 0.00 2.57
4247 4274 8.653338 TGCTCAATATTTTCTCACTTAACGTAC 58.347 33.333 0.00 0.00 0.00 3.67
4257 4284 7.918536 TCTCACTTAACGTACAAGAGACTAT 57.081 36.000 14.78 0.00 0.00 2.12
4429 4457 4.348656 TCACTTAGTTATCTGCTTACGCG 58.651 43.478 3.53 3.53 39.65 6.01
4440 4468 1.086067 GCTTACGCGTTTAGGGGGAC 61.086 60.000 20.78 0.00 37.07 4.46
4508 4536 8.976986 TCAGAATCATGTGAATCTACATATCG 57.023 34.615 0.55 0.00 39.17 2.92
4521 4549 8.709386 AATCTACATATCGCATGAGTAAATCC 57.291 34.615 0.00 0.00 0.00 3.01
4525 4553 7.369803 ACATATCGCATGAGTAAATCCAATC 57.630 36.000 0.00 0.00 0.00 2.67
4526 4554 6.936335 ACATATCGCATGAGTAAATCCAATCA 59.064 34.615 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
358 367 3.577649 AGTCATTCCACACGACTGTAG 57.422 47.619 0.00 0.00 38.55 2.74
601 612 9.632807 TTTTTAAAATGAGTCCAACGAATATGG 57.367 29.630 0.55 0.00 39.41 2.74
733 745 9.136952 GCAGTATAACCAACCGACTATATAAAG 57.863 37.037 0.00 0.00 0.00 1.85
734 746 8.090214 GGCAGTATAACCAACCGACTATATAAA 58.910 37.037 0.00 0.00 0.00 1.40
735 747 7.309990 GGGCAGTATAACCAACCGACTATATAA 60.310 40.741 0.00 0.00 0.00 0.98
736 748 6.153340 GGGCAGTATAACCAACCGACTATATA 59.847 42.308 0.00 0.00 0.00 0.86
737 749 5.046807 GGGCAGTATAACCAACCGACTATAT 60.047 44.000 0.00 0.00 0.00 0.86
738 750 4.281688 GGGCAGTATAACCAACCGACTATA 59.718 45.833 0.00 0.00 0.00 1.31
739 751 3.070590 GGGCAGTATAACCAACCGACTAT 59.929 47.826 0.00 0.00 0.00 2.12
740 752 2.431782 GGGCAGTATAACCAACCGACTA 59.568 50.000 0.00 0.00 0.00 2.59
741 753 1.208776 GGGCAGTATAACCAACCGACT 59.791 52.381 0.00 0.00 0.00 4.18
742 754 1.660167 GGGCAGTATAACCAACCGAC 58.340 55.000 0.00 0.00 0.00 4.79
743 755 0.542805 GGGGCAGTATAACCAACCGA 59.457 55.000 0.00 0.00 0.00 4.69
744 756 0.253610 TGGGGCAGTATAACCAACCG 59.746 55.000 0.00 0.00 0.00 4.44
745 757 2.517998 TTGGGGCAGTATAACCAACC 57.482 50.000 0.00 0.00 38.02 3.77
747 759 1.351683 ACGTTGGGGCAGTATAACCAA 59.648 47.619 0.00 0.00 40.44 3.67
748 760 0.985760 ACGTTGGGGCAGTATAACCA 59.014 50.000 0.00 0.00 0.00 3.67
749 761 1.208776 AGACGTTGGGGCAGTATAACC 59.791 52.381 0.00 0.00 0.00 2.85
750 762 2.685850 AGACGTTGGGGCAGTATAAC 57.314 50.000 0.00 0.00 0.00 1.89
751 763 3.706600 AAAGACGTTGGGGCAGTATAA 57.293 42.857 0.00 0.00 0.00 0.98
752 764 3.706600 AAAAGACGTTGGGGCAGTATA 57.293 42.857 0.00 0.00 0.00 1.47
753 765 2.579410 AAAAGACGTTGGGGCAGTAT 57.421 45.000 0.00 0.00 0.00 2.12
754 766 3.706600 ATAAAAGACGTTGGGGCAGTA 57.293 42.857 0.00 0.00 0.00 2.74
755 767 2.579410 ATAAAAGACGTTGGGGCAGT 57.421 45.000 0.00 0.00 0.00 4.40
756 768 3.934457 AAATAAAAGACGTTGGGGCAG 57.066 42.857 0.00 0.00 0.00 4.85
757 769 3.759618 CCTAAATAAAAGACGTTGGGGCA 59.240 43.478 0.00 0.00 0.00 5.36
758 770 4.011698 TCCTAAATAAAAGACGTTGGGGC 58.988 43.478 0.00 0.00 0.00 5.80
759 771 5.391203 CGTTCCTAAATAAAAGACGTTGGGG 60.391 44.000 0.00 0.00 0.00 4.96
760 772 5.391203 CCGTTCCTAAATAAAAGACGTTGGG 60.391 44.000 0.00 0.00 0.00 4.12
761 773 5.409214 TCCGTTCCTAAATAAAAGACGTTGG 59.591 40.000 0.00 0.00 0.00 3.77
762 774 6.366877 TCTCCGTTCCTAAATAAAAGACGTTG 59.633 38.462 0.00 0.00 0.00 4.10
763 775 6.367149 GTCTCCGTTCCTAAATAAAAGACGTT 59.633 38.462 0.00 0.00 0.00 3.99
764 776 5.866092 GTCTCCGTTCCTAAATAAAAGACGT 59.134 40.000 0.00 0.00 0.00 4.34
765 777 5.865552 TGTCTCCGTTCCTAAATAAAAGACG 59.134 40.000 0.00 0.00 34.72 4.18
766 778 6.872547 ACTGTCTCCGTTCCTAAATAAAAGAC 59.127 38.462 0.00 0.00 33.07 3.01
767 779 7.001099 ACTGTCTCCGTTCCTAAATAAAAGA 57.999 36.000 0.00 0.00 0.00 2.52
768 780 8.943909 ATACTGTCTCCGTTCCTAAATAAAAG 57.056 34.615 0.00 0.00 0.00 2.27
771 783 9.807649 GTTAATACTGTCTCCGTTCCTAAATAA 57.192 33.333 0.00 0.00 0.00 1.40
772 784 8.416329 GGTTAATACTGTCTCCGTTCCTAAATA 58.584 37.037 0.00 0.00 0.00 1.40
773 785 7.093201 TGGTTAATACTGTCTCCGTTCCTAAAT 60.093 37.037 0.00 0.00 0.00 1.40
774 786 6.211184 TGGTTAATACTGTCTCCGTTCCTAAA 59.789 38.462 0.00 0.00 0.00 1.85
775 787 5.716228 TGGTTAATACTGTCTCCGTTCCTAA 59.284 40.000 0.00 0.00 0.00 2.69
776 788 5.263599 TGGTTAATACTGTCTCCGTTCCTA 58.736 41.667 0.00 0.00 0.00 2.94
777 789 4.091549 TGGTTAATACTGTCTCCGTTCCT 58.908 43.478 0.00 0.00 0.00 3.36
778 790 4.460948 TGGTTAATACTGTCTCCGTTCC 57.539 45.455 0.00 0.00 0.00 3.62
779 791 4.270325 GCATGGTTAATACTGTCTCCGTTC 59.730 45.833 0.00 0.00 0.00 3.95
780 792 4.081087 AGCATGGTTAATACTGTCTCCGTT 60.081 41.667 0.00 0.00 0.00 4.44
781 793 3.451178 AGCATGGTTAATACTGTCTCCGT 59.549 43.478 0.00 0.00 0.00 4.69
782 794 4.051922 GAGCATGGTTAATACTGTCTCCG 58.948 47.826 0.00 0.00 0.00 4.63
783 795 5.283457 AGAGCATGGTTAATACTGTCTCC 57.717 43.478 0.00 0.00 0.00 3.71
784 796 7.436673 CACTTAGAGCATGGTTAATACTGTCTC 59.563 40.741 0.00 0.00 0.00 3.36
785 797 7.124298 TCACTTAGAGCATGGTTAATACTGTCT 59.876 37.037 0.00 0.00 0.00 3.41
786 798 7.265673 TCACTTAGAGCATGGTTAATACTGTC 58.734 38.462 0.00 0.00 0.00 3.51
787 799 7.182817 TCACTTAGAGCATGGTTAATACTGT 57.817 36.000 0.00 0.00 0.00 3.55
788 800 7.981789 TCTTCACTTAGAGCATGGTTAATACTG 59.018 37.037 0.00 0.00 0.00 2.74
789 801 8.079211 TCTTCACTTAGAGCATGGTTAATACT 57.921 34.615 0.00 0.00 0.00 2.12
790 802 8.718102 TTCTTCACTTAGAGCATGGTTAATAC 57.282 34.615 0.00 0.00 0.00 1.89
791 803 9.905713 AATTCTTCACTTAGAGCATGGTTAATA 57.094 29.630 0.00 0.00 0.00 0.98
792 804 8.814038 AATTCTTCACTTAGAGCATGGTTAAT 57.186 30.769 0.00 0.00 0.00 1.40
793 805 9.905713 ATAATTCTTCACTTAGAGCATGGTTAA 57.094 29.630 0.00 0.00 0.00 2.01
794 806 9.905713 AATAATTCTTCACTTAGAGCATGGTTA 57.094 29.630 0.00 0.00 0.00 2.85
795 807 8.680903 CAATAATTCTTCACTTAGAGCATGGTT 58.319 33.333 0.00 0.00 0.00 3.67
796 808 7.831193 ACAATAATTCTTCACTTAGAGCATGGT 59.169 33.333 0.00 0.00 0.00 3.55
797 809 8.127327 CACAATAATTCTTCACTTAGAGCATGG 58.873 37.037 0.00 0.00 0.00 3.66
798 810 8.886719 TCACAATAATTCTTCACTTAGAGCATG 58.113 33.333 0.00 0.00 0.00 4.06
799 811 9.624373 ATCACAATAATTCTTCACTTAGAGCAT 57.376 29.630 0.00 0.00 0.00 3.79
800 812 9.102757 GATCACAATAATTCTTCACTTAGAGCA 57.897 33.333 0.00 0.00 0.00 4.26
801 813 9.323985 AGATCACAATAATTCTTCACTTAGAGC 57.676 33.333 0.00 0.00 0.00 4.09
806 818 9.307121 CGACTAGATCACAATAATTCTTCACTT 57.693 33.333 0.00 0.00 0.00 3.16
807 819 8.687242 TCGACTAGATCACAATAATTCTTCACT 58.313 33.333 0.00 0.00 0.00 3.41
808 820 8.858003 TCGACTAGATCACAATAATTCTTCAC 57.142 34.615 0.00 0.00 0.00 3.18
809 821 8.903820 TCTCGACTAGATCACAATAATTCTTCA 58.096 33.333 0.00 0.00 0.00 3.02
818 830 6.116806 ACACTACTCTCGACTAGATCACAAT 58.883 40.000 0.00 0.00 32.41 2.71
822 834 5.581479 GTCAACACTACTCTCGACTAGATCA 59.419 44.000 0.00 0.00 32.41 2.92
824 836 5.736813 AGTCAACACTACTCTCGACTAGAT 58.263 41.667 0.00 0.00 32.18 1.98
826 838 4.330620 GGAGTCAACACTACTCTCGACTAG 59.669 50.000 0.00 0.00 42.48 2.57
827 839 4.252073 GGAGTCAACACTACTCTCGACTA 58.748 47.826 0.00 0.00 42.48 2.59
829 841 2.812591 TGGAGTCAACACTACTCTCGAC 59.187 50.000 0.00 0.00 42.48 4.20
837 849 0.032952 GCCACGTGGAGTCAACACTA 59.967 55.000 38.30 0.00 36.71 2.74
993 1012 1.519719 GGCGAGCTCCATGAGAAGT 59.480 57.895 8.47 0.00 0.00 3.01
998 1017 3.157252 GGAGGGCGAGCTCCATGA 61.157 66.667 8.47 0.00 39.45 3.07
1149 1168 3.362797 ACGCTTCTCGCCTCGTCA 61.363 61.111 0.00 0.00 43.23 4.35
1327 1346 3.325753 GAGCAGGTCCCTGTGGCT 61.326 66.667 14.56 5.83 45.24 4.75
1440 1459 1.546029 CGAGTGATCAGGAACCTGTCA 59.454 52.381 18.60 17.19 43.96 3.58
1485 1504 1.920325 CCCAAGCCTCTGGTCCTCA 60.920 63.158 0.00 0.00 34.33 3.86
1506 1525 2.674033 GCCATGGAGTGCAGCACA 60.674 61.111 27.35 7.52 36.74 4.57
1620 1639 0.865111 TCATCTTGTCAAACACCGCG 59.135 50.000 0.00 0.00 0.00 6.46
1659 1678 3.200825 ACCCAAAGATCATCGAGTTCCAT 59.799 43.478 0.00 0.00 0.00 3.41
1686 1705 2.599281 TCCCACTCGCAAGACCGA 60.599 61.111 0.00 0.00 45.01 4.69
1687 1706 2.125912 CTCCCACTCGCAAGACCG 60.126 66.667 0.00 0.00 45.01 4.79
1696 1715 4.821589 CCGCGCTTCCTCCCACTC 62.822 72.222 5.56 0.00 0.00 3.51
1774 1793 4.022416 AGACCTAGCATAGCTCGAAATCAG 60.022 45.833 0.00 0.00 40.44 2.90
1791 1810 3.041211 CACATCAAGATCCCCAGACCTA 58.959 50.000 0.00 0.00 0.00 3.08
2070 2089 3.287222 CAAGGAGTTCCCAGACAAAACA 58.713 45.455 0.00 0.00 37.41 2.83
2073 2092 1.850345 ACCAAGGAGTTCCCAGACAAA 59.150 47.619 0.00 0.00 37.41 2.83
2079 2098 1.217916 TGTCAACCAAGGAGTTCCCA 58.782 50.000 0.00 0.00 37.41 4.37
2199 2218 1.078426 GCCACAGTATCCCGCTTGT 60.078 57.895 0.00 0.00 0.00 3.16
2223 2242 4.160439 TCCATCTTGCAGAAGAGTTCGTAT 59.840 41.667 0.00 0.00 41.62 3.06
2319 2338 6.014242 TCTGGAATAGTTCAAAAGCTCTCTCA 60.014 38.462 0.00 0.00 0.00 3.27
2446 2465 2.089201 CAGAACTGATTGCATCTGCCA 58.911 47.619 0.08 0.00 41.18 4.92
2539 2558 2.429933 ATACAGGCATGGATCTCCCT 57.570 50.000 2.31 0.00 35.38 4.20
2613 2632 7.201884 CCAGCAAGATCACCAGATTTTGAATAT 60.202 37.037 11.49 0.00 44.75 1.28
3000 3019 6.261826 GCATTCTTGCTGAGGTTAGTAATGAT 59.738 38.462 0.00 0.00 45.77 2.45
3102 3121 1.272490 TCCTGCAGACTAGAAACCACG 59.728 52.381 17.39 0.00 0.00 4.94
3366 3385 6.189859 TGCTAATTTCTCACAATGGATTCCT 58.810 36.000 3.95 0.00 0.00 3.36
3407 3426 5.728471 TGCTTCTGAAGTGAGGAGAATTAG 58.272 41.667 17.97 0.00 0.00 1.73
3414 3433 2.166459 CCGTATGCTTCTGAAGTGAGGA 59.834 50.000 17.97 0.00 0.00 3.71
3493 3512 3.961408 AGTATCTGACGCCCATACTTCTT 59.039 43.478 0.00 0.00 30.57 2.52
3570 3589 5.630121 ACCAGTTGAGTTCACCAATAATCA 58.370 37.500 0.00 0.00 0.00 2.57
3581 3600 5.578727 CAGCTGACTTATACCAGTTGAGTTC 59.421 44.000 8.42 0.00 41.96 3.01
3590 3609 1.578897 TGCCCAGCTGACTTATACCA 58.421 50.000 17.39 0.00 0.00 3.25
3652 3671 6.649155 TCATAAAGTTAGCTGGCTGTATTCA 58.351 36.000 5.25 0.00 0.00 2.57
3771 3790 6.229936 TGCAACGACCTCTTACCTTTATAT 57.770 37.500 0.00 0.00 0.00 0.86
3812 3832 3.496884 TGTGTCAGAACAAGCCGAATAAC 59.503 43.478 0.00 0.00 37.08 1.89
3815 3835 2.146342 CTGTGTCAGAACAAGCCGAAT 58.854 47.619 0.00 0.00 37.08 3.34
3869 3891 2.619074 CCTGGAAAGGCTAACTCCCAAG 60.619 54.545 7.52 0.97 0.00 3.61
3870 3892 1.354368 CCTGGAAAGGCTAACTCCCAA 59.646 52.381 7.52 0.00 0.00 4.12
3871 3893 0.991920 CCTGGAAAGGCTAACTCCCA 59.008 55.000 7.52 0.00 0.00 4.37
3874 3896 4.849518 AGAATTCCTGGAAAGGCTAACTC 58.150 43.478 14.03 1.08 0.00 3.01
3875 3897 4.936685 AGAATTCCTGGAAAGGCTAACT 57.063 40.909 14.03 2.97 0.00 2.24
4086 4108 4.634883 GGAGATCATCGATGAATCCCATTG 59.365 45.833 33.05 9.63 40.69 2.82
4192 4214 8.929260 ATGAGAGGATTATTAATTGATGCACA 57.071 30.769 0.00 0.00 0.00 4.57
4201 4223 9.857656 TTGAGCAGAAATGAGAGGATTATTAAT 57.142 29.630 0.00 0.00 0.00 1.40
4220 4246 7.743104 ACGTTAAGTGAGAAAATATTGAGCAG 58.257 34.615 0.00 0.00 0.00 4.24
4221 4247 7.667043 ACGTTAAGTGAGAAAATATTGAGCA 57.333 32.000 0.00 0.00 0.00 4.26
4222 4248 8.653338 TGTACGTTAAGTGAGAAAATATTGAGC 58.347 33.333 0.00 0.00 0.00 4.26
4385 4413 3.485346 TTCAGGTCCGTTGGCACCC 62.485 63.158 0.00 0.00 32.45 4.61
4429 4457 1.913419 TGACATCCTGTCCCCCTAAAC 59.087 52.381 4.91 0.00 46.40 2.01
4440 4468 3.347077 AGCTTCCTTTCTGACATCCTG 57.653 47.619 0.00 0.00 0.00 3.86
4502 4530 7.368480 TGATTGGATTTACTCATGCGATATG 57.632 36.000 0.00 0.00 0.00 1.78
4503 4531 7.879677 TCTTGATTGGATTTACTCATGCGATAT 59.120 33.333 0.00 0.00 0.00 1.63
4552 4580 3.370840 ACCACTTATGCATGTGATGGT 57.629 42.857 16.55 16.59 36.38 3.55


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

AutoCloner maintained by Alex Coulton.