Multiple sequence alignment - TraesCS2B01G231100

Loading Multiple Alignment...

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 TraesCS2B01G231100 chr2B 100.000 4855 0 0 1 4855 227115532 227110678 0.000000e+00 8966.0
1 TraesCS2B01G231100 chr2A 97.489 3783 61 9 811 4587 179818341 179814587 0.000000e+00 6429.0
2 TraesCS2B01G231100 chr2A 93.923 724 26 8 1 708 179819051 179818330 0.000000e+00 1077.0
3 TraesCS2B01G231100 chr2A 89.806 206 13 3 4616 4815 179814616 179814413 1.730000e-64 257.0
4 TraesCS2B01G231100 chr2D 97.364 3793 72 14 798 4588 170404992 170408758 0.000000e+00 6425.0
5 TraesCS2B01G231100 chr2D 92.938 708 22 8 1 695 170404299 170404991 0.000000e+00 1005.0
6 TraesCS2B01G231100 chr2D 89.177 231 16 5 4616 4840 170408728 170408955 3.700000e-71 279.0
7 TraesCS2B01G231100 chr1B 97.561 123 1 2 691 813 225811865 225811985 4.920000e-50 209.0
8 TraesCS2B01G231100 chr4A 98.305 118 0 2 691 808 420020484 420020369 6.370000e-49 206.0
9 TraesCS2B01G231100 chr4A 97.458 118 1 2 691 808 137542364 137542479 2.960000e-47 200.0
10 TraesCS2B01G231100 chrUn 99.115 113 1 0 688 800 310882995 310883107 2.290000e-48 204.0
11 TraesCS2B01G231100 chr7B 98.276 116 1 1 691 806 690699481 690699595 8.240000e-48 202.0
12 TraesCS2B01G231100 chr4B 96.721 122 3 1 691 812 648316468 648316348 8.240000e-48 202.0
13 TraesCS2B01G231100 chr3B 95.935 123 2 3 691 813 14474671 14474552 3.830000e-46 196.0
14 TraesCS2B01G231100 chr5B 93.893 131 4 4 691 819 654755847 654755719 1.380000e-45 195.0
15 TraesCS2B01G231100 chr1A 92.701 137 7 3 691 825 357776700 357776565 1.380000e-45 195.0
16 TraesCS2B01G231100 chr3D 91.379 58 5 0 4628 4685 415533123 415533066 4.030000e-11 80.5


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 TraesCS2B01G231100 chr2B 227110678 227115532 4854 True 8966.000000 8966 100.000000 1 4855 1 chr2B.!!$R1 4854
1 TraesCS2B01G231100 chr2A 179814413 179819051 4638 True 2587.666667 6429 93.739333 1 4815 3 chr2A.!!$R1 4814
2 TraesCS2B01G231100 chr2D 170404299 170408955 4656 False 2569.666667 6425 93.159667 1 4840 3 chr2D.!!$F1 4839

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
723 740 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.0 37.28 3.67 F
802 819 0.395724 CCGGGCTGCCCTTTATTCTT 60.396 55.000 33.39 0.0 42.67 2.52 F
984 1001 0.594284 GCTCGTGACTGGCGTATACC 60.594 60.000 0.00 0.0 0.00 2.73 F
1053 1070 0.620700 AGGGTCCCCGAATTGCTACT 60.621 55.000 3.51 0.0 41.95 2.57 F
3068 3085 1.337703 GCAACTTGATGTGAGTGCCAA 59.662 47.619 0.00 0.0 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1971 1988 1.228657 GGCAACCAGTTCGTGTCTCC 61.229 60.000 0.00 0.00 0.00 3.71 R
2076 2093 1.271217 ACAAGATCAGAAGCTGCTGCA 60.271 47.619 17.79 6.57 42.74 4.41 R
2436 2453 2.158564 ACCATAGCCTTGCACTGCATAT 60.159 45.455 4.10 0.00 38.76 1.78 R
3072 3089 1.322442 GAGGTGGCTTCTTTGTGCTT 58.678 50.000 0.00 0.00 0.00 3.91 R
4281 4299 1.594293 CGCTTGGTGGTCGAACAGT 60.594 57.895 1.63 0.00 0.00 3.55 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
46 47 4.240096 CATTTGTCATGCTTGGAAGTTCC 58.760 43.478 15.50 15.50 36.96 3.62
82 83 4.602340 AGGTATATTAGTTGACTGGGCG 57.398 45.455 0.00 0.00 0.00 6.13
141 142 3.745332 TGTGTTCATAATTGAGCTGCG 57.255 42.857 0.00 0.00 34.45 5.18
187 188 7.967854 TGGAAAATACTCTGAATTGCAAATACG 59.032 33.333 1.71 0.00 0.00 3.06
199 200 3.270027 TGCAAATACGAGGATTGAGGTG 58.730 45.455 0.00 0.00 0.00 4.00
200 201 2.614057 GCAAATACGAGGATTGAGGTGG 59.386 50.000 0.00 0.00 0.00 4.61
201 202 3.873910 CAAATACGAGGATTGAGGTGGT 58.126 45.455 0.00 0.00 0.00 4.16
202 203 4.682320 GCAAATACGAGGATTGAGGTGGTA 60.682 45.833 0.00 0.00 0.00 3.25
247 251 6.194796 TCTGCTTAAATCGGGATTTTTCAG 57.805 37.500 11.51 14.20 40.99 3.02
320 324 5.880901 ACATTCTTGTCCATTAGTGAGGTT 58.119 37.500 0.00 0.00 0.00 3.50
363 377 6.407752 GGCTTAAGTCTGCCTTACCTTACATA 60.408 42.308 4.02 0.00 45.26 2.29
443 460 0.755686 CAATTCCCTCTCCCTCCTCG 59.244 60.000 0.00 0.00 0.00 4.63
446 463 1.812113 TTCCCTCTCCCTCCTCGGTT 61.812 60.000 0.00 0.00 0.00 4.44
504 521 0.981183 TACAGTGAAATCCAGCCGGT 59.019 50.000 1.90 0.00 0.00 5.28
634 651 7.708051 TGTGATTTCTCGGTTGATTTTGTTTA 58.292 30.769 0.00 0.00 0.00 2.01
695 712 7.177878 TCTTTCATCCTCTTTTTATTGCCTCT 58.822 34.615 0.00 0.00 0.00 3.69
697 714 8.877864 TTTCATCCTCTTTTTATTGCCTCTTA 57.122 30.769 0.00 0.00 0.00 2.10
699 716 7.402054 TCATCCTCTTTTTATTGCCTCTTACA 58.598 34.615 0.00 0.00 0.00 2.41
700 717 7.554118 TCATCCTCTTTTTATTGCCTCTTACAG 59.446 37.037 0.00 0.00 0.00 2.74
701 718 7.016153 TCCTCTTTTTATTGCCTCTTACAGA 57.984 36.000 0.00 0.00 0.00 3.41
702 719 7.458397 TCCTCTTTTTATTGCCTCTTACAGAA 58.542 34.615 0.00 0.00 0.00 3.02
703 720 7.942341 TCCTCTTTTTATTGCCTCTTACAGAAA 59.058 33.333 0.00 0.00 0.00 2.52
704 721 8.743714 CCTCTTTTTATTGCCTCTTACAGAAAT 58.256 33.333 0.00 0.00 0.00 2.17
705 722 9.565213 CTCTTTTTATTGCCTCTTACAGAAATG 57.435 33.333 0.00 0.00 0.00 2.32
706 723 9.077885 TCTTTTTATTGCCTCTTACAGAAATGT 57.922 29.630 0.00 0.00 0.00 2.71
709 726 8.506168 TTTATTGCCTCTTACAGAAATGTAGG 57.494 34.615 0.00 0.00 0.00 3.18
710 727 4.487714 TGCCTCTTACAGAAATGTAGGG 57.512 45.455 0.00 0.66 0.00 3.53
711 728 4.101114 TGCCTCTTACAGAAATGTAGGGA 58.899 43.478 0.00 0.00 0.00 4.20
712 729 4.534500 TGCCTCTTACAGAAATGTAGGGAA 59.466 41.667 0.00 0.00 0.00 3.97
713 730 5.013704 TGCCTCTTACAGAAATGTAGGGAAA 59.986 40.000 0.00 0.00 0.00 3.13
714 731 5.586643 GCCTCTTACAGAAATGTAGGGAAAG 59.413 44.000 0.00 0.00 0.00 2.62
715 732 6.116126 CCTCTTACAGAAATGTAGGGAAAGG 58.884 44.000 0.00 0.00 0.00 3.11
716 733 5.497474 TCTTACAGAAATGTAGGGAAAGGC 58.503 41.667 0.00 0.00 0.00 4.35
717 734 5.250774 TCTTACAGAAATGTAGGGAAAGGCT 59.749 40.000 0.00 0.00 0.00 4.58
718 735 3.690460 ACAGAAATGTAGGGAAAGGCTG 58.310 45.455 0.00 0.00 0.00 4.85
719 736 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
720 737 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
721 738 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
722 739 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
723 740 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
724 741 0.535797 GTAGGGAAAGGCTGCGTACT 59.464 55.000 0.00 0.00 34.81 2.73
725 742 1.753073 GTAGGGAAAGGCTGCGTACTA 59.247 52.381 0.00 0.00 34.81 1.82
726 743 1.497161 AGGGAAAGGCTGCGTACTAT 58.503 50.000 0.00 0.00 0.00 2.12
727 744 2.674420 AGGGAAAGGCTGCGTACTATA 58.326 47.619 0.00 0.00 0.00 1.31
728 745 2.628657 AGGGAAAGGCTGCGTACTATAG 59.371 50.000 0.00 0.00 0.00 1.31
729 746 2.626743 GGGAAAGGCTGCGTACTATAGA 59.373 50.000 6.78 0.00 0.00 1.98
730 747 3.552478 GGGAAAGGCTGCGTACTATAGAC 60.552 52.174 6.78 0.00 0.00 2.59
731 748 3.552478 GGAAAGGCTGCGTACTATAGACC 60.552 52.174 6.78 0.00 0.00 3.85
732 749 1.618487 AGGCTGCGTACTATAGACCC 58.382 55.000 6.78 0.00 0.00 4.46
733 750 1.133575 AGGCTGCGTACTATAGACCCA 60.134 52.381 6.78 0.00 0.00 4.51
734 751 1.684983 GGCTGCGTACTATAGACCCAA 59.315 52.381 6.78 0.00 0.00 4.12
735 752 2.101917 GGCTGCGTACTATAGACCCAAA 59.898 50.000 6.78 0.00 0.00 3.28
736 753 3.381949 GCTGCGTACTATAGACCCAAAG 58.618 50.000 6.78 0.00 0.00 2.77
737 754 3.181478 GCTGCGTACTATAGACCCAAAGT 60.181 47.826 6.78 0.00 0.00 2.66
738 755 4.360563 CTGCGTACTATAGACCCAAAGTG 58.639 47.826 6.78 0.00 0.00 3.16
739 756 3.131577 TGCGTACTATAGACCCAAAGTGG 59.868 47.826 6.78 0.00 37.25 4.00
740 757 3.131755 GCGTACTATAGACCCAAAGTGGT 59.868 47.826 6.78 0.00 42.79 4.16
745 762 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
746 763 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
747 764 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
748 765 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
749 766 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
750 767 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
751 768 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
752 769 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
753 770 3.714001 GTGGTCGGACCCTTCCCC 61.714 72.222 23.81 0.00 38.99 4.81
760 777 4.735599 GACCCTTCCCCGGACCCT 62.736 72.222 0.73 0.00 0.00 4.34
787 804 2.203070 GGAGCTACATGCACCGGG 60.203 66.667 6.32 0.00 42.21 5.73
788 805 2.897350 GAGCTACATGCACCGGGC 60.897 66.667 6.32 7.25 45.94 6.13
789 806 3.391665 GAGCTACATGCACCGGGCT 62.392 63.158 6.32 0.81 45.94 5.19
790 807 3.204827 GCTACATGCACCGGGCTG 61.205 66.667 6.32 9.21 45.15 4.85
791 808 3.204827 CTACATGCACCGGGCTGC 61.205 66.667 6.32 8.50 45.15 5.25
792 809 4.794648 TACATGCACCGGGCTGCC 62.795 66.667 11.05 11.05 45.15 4.85
797 814 4.733542 GCACCGGGCTGCCCTTTA 62.734 66.667 33.39 0.00 42.67 1.85
798 815 2.275418 CACCGGGCTGCCCTTTAT 59.725 61.111 33.39 14.39 42.67 1.40
799 816 1.379843 CACCGGGCTGCCCTTTATT 60.380 57.895 33.39 11.43 42.67 1.40
800 817 1.076995 ACCGGGCTGCCCTTTATTC 60.077 57.895 33.39 7.46 42.67 1.75
801 818 1.227383 CCGGGCTGCCCTTTATTCT 59.773 57.895 33.39 0.00 42.67 2.40
802 819 0.395724 CCGGGCTGCCCTTTATTCTT 60.396 55.000 33.39 0.00 42.67 2.52
803 820 1.474330 CGGGCTGCCCTTTATTCTTT 58.526 50.000 33.39 0.00 42.67 2.52
804 821 2.650322 CGGGCTGCCCTTTATTCTTTA 58.350 47.619 33.39 0.00 42.67 1.85
805 822 2.618709 CGGGCTGCCCTTTATTCTTTAG 59.381 50.000 33.39 11.06 42.67 1.85
806 823 3.632333 GGGCTGCCCTTTATTCTTTAGT 58.368 45.455 30.42 0.00 41.34 2.24
807 824 4.685030 CGGGCTGCCCTTTATTCTTTAGTA 60.685 45.833 33.39 0.00 42.67 1.82
815 832 9.609346 TGCCCTTTATTCTTTAGTAGTATTCAC 57.391 33.333 0.00 0.00 0.00 3.18
915 932 0.682852 AGTTGTGTTGCCTAGCGGTA 59.317 50.000 0.00 0.00 0.00 4.02
984 1001 0.594284 GCTCGTGACTGGCGTATACC 60.594 60.000 0.00 0.00 0.00 2.73
1053 1070 0.620700 AGGGTCCCCGAATTGCTACT 60.621 55.000 3.51 0.00 41.95 2.57
1494 1511 3.469008 ACACTCTGGACAACATCGAAA 57.531 42.857 0.00 0.00 0.00 3.46
1971 1988 1.473278 AGAGTAAAGAAGCCTCGTCCG 59.527 52.381 0.00 0.00 0.00 4.79
2076 2093 2.034879 CAATCACGGTCTTGGCGCT 61.035 57.895 7.64 0.00 0.00 5.92
2193 2210 4.737054 ACGGCAAGCAAAATCTTATCAAG 58.263 39.130 0.00 0.00 0.00 3.02
2196 2213 5.450965 CGGCAAGCAAAATCTTATCAAGGAT 60.451 40.000 0.00 0.00 0.00 3.24
2212 2229 3.159213 AGGATGATGCCACTTCAAACA 57.841 42.857 0.00 0.00 0.00 2.83
2353 2370 5.591877 GCAGTAAAATCTGATGAAGATGGGT 59.408 40.000 0.00 0.00 45.37 4.51
2361 2378 5.026121 TCTGATGAAGATGGGTACTTGACT 58.974 41.667 0.00 0.00 0.00 3.41
2436 2453 5.366477 TGATGTAGTATGCCTTGATTCAGGA 59.634 40.000 0.00 0.00 35.71 3.86
2664 2681 1.714794 CAGTAAGTTGGCCTGAGACG 58.285 55.000 3.32 0.00 0.00 4.18
3068 3085 1.337703 GCAACTTGATGTGAGTGCCAA 59.662 47.619 0.00 0.00 0.00 4.52
3072 3089 3.489355 ACTTGATGTGAGTGCCAATCAA 58.511 40.909 0.00 0.00 0.00 2.57
3091 3108 1.322442 AAGCACAAAGAAGCCACCTC 58.678 50.000 0.00 0.00 0.00 3.85
3233 3250 7.957002 ACAATCTGTGAGTATAGGATAACTGG 58.043 38.462 0.00 0.00 0.00 4.00
3585 3602 4.051922 CGAGCATACTTATGGGTCAAGTC 58.948 47.826 0.00 0.00 37.42 3.01
3629 3646 3.307059 CCCCCTGACATAGCTGCTATTAC 60.307 52.174 19.11 15.38 0.00 1.89
3709 3726 5.809464 TGCACAATCATGCTAACTTTATCG 58.191 37.500 0.00 0.00 46.28 2.92
3750 3767 6.521151 ACTTGTTCAATCAAGATGATTCCC 57.479 37.500 12.38 0.00 43.03 3.97
3881 3898 3.990318 AACCACTTTCTTGCTACAAGC 57.010 42.857 2.41 0.00 42.82 4.01
3974 3991 8.642935 TTTACCCAAGATGTATCATTTGTTCA 57.357 30.769 0.00 0.00 0.00 3.18
4006 4023 6.442952 TGTTTGGGAAAATGTCTGTTTATCG 58.557 36.000 0.00 0.00 0.00 2.92
4009 4026 3.486875 GGGAAAATGTCTGTTTATCGCCG 60.487 47.826 0.00 0.00 0.00 6.46
4029 4046 4.754322 CCGGCCAGCAAATATTTAGTTTT 58.246 39.130 2.24 0.00 0.00 2.43
4135 4153 7.696981 ACTAATGAGCTGGGAATAATGATGAT 58.303 34.615 0.00 0.00 0.00 2.45
4164 4182 2.095110 TCGGCTGTGCAGATCATTTTTG 60.095 45.455 3.02 0.00 0.00 2.44
4174 4192 9.932207 TGTGCAGATCATTTTTGAATAGATTTT 57.068 25.926 0.00 0.00 0.00 1.82
4268 4286 1.591863 GGCGCCTCAGACCGATTAC 60.592 63.158 22.15 0.00 0.00 1.89
4281 4299 5.117355 GACCGATTACATATCAAGGTCGA 57.883 43.478 0.00 0.00 37.52 4.20
4310 4328 1.164411 CACCAAGCGGCAATGACTTA 58.836 50.000 1.45 0.00 34.57 2.24
4379 4403 0.455464 CTGTGTTGATGGTGCATGCG 60.455 55.000 14.09 0.00 0.00 4.73
4491 4515 4.342092 ACTGGCTGTCCATATAATTTTGGC 59.658 41.667 0.00 0.00 42.51 4.52
4547 4572 3.059665 CGCAAATTTTCAGGCCTTGTTTC 60.060 43.478 0.00 0.00 0.00 2.78
4705 4736 5.018539 TGATTTTATCCGGAGATTCGTGT 57.981 39.130 11.34 0.00 33.67 4.49
4711 4742 1.679680 TCCGGAGATTCGTGTGGATAC 59.320 52.381 0.00 0.00 0.00 2.24
4713 4744 2.287668 CCGGAGATTCGTGTGGATACTC 60.288 54.545 0.00 0.00 37.61 2.59
4761 4792 2.564947 CAGATGTGCCCTAGATAGACCC 59.435 54.545 0.00 0.00 0.00 4.46
4775 4806 5.735766 AGATAGACCCTTTTTCTTTCCTCG 58.264 41.667 0.00 0.00 0.00 4.63
4815 4846 2.309136 AAAGTGACCTGGGATTTGGG 57.691 50.000 0.00 0.00 0.00 4.12
4840 4871 0.250597 GTGAGCCCCGTACCAAAAGT 60.251 55.000 0.00 0.00 0.00 2.66
4841 4872 0.475044 TGAGCCCCGTACCAAAAGTT 59.525 50.000 0.00 0.00 0.00 2.66
4842 4873 1.698532 TGAGCCCCGTACCAAAAGTTA 59.301 47.619 0.00 0.00 0.00 2.24
4843 4874 2.106166 TGAGCCCCGTACCAAAAGTTAA 59.894 45.455 0.00 0.00 0.00 2.01
4844 4875 3.148412 GAGCCCCGTACCAAAAGTTAAA 58.852 45.455 0.00 0.00 0.00 1.52
4845 4876 3.564264 AGCCCCGTACCAAAAGTTAAAA 58.436 40.909 0.00 0.00 0.00 1.52
4846 4877 4.154176 AGCCCCGTACCAAAAGTTAAAAT 58.846 39.130 0.00 0.00 0.00 1.82
4847 4878 4.589798 AGCCCCGTACCAAAAGTTAAAATT 59.410 37.500 0.00 0.00 0.00 1.82
4848 4879 4.925054 GCCCCGTACCAAAAGTTAAAATTC 59.075 41.667 0.00 0.00 0.00 2.17
4849 4880 5.155643 CCCCGTACCAAAAGTTAAAATTCG 58.844 41.667 0.00 0.00 0.00 3.34
4850 4881 4.618067 CCCGTACCAAAAGTTAAAATTCGC 59.382 41.667 0.00 0.00 0.00 4.70
4851 4882 5.213675 CCGTACCAAAAGTTAAAATTCGCA 58.786 37.500 0.00 0.00 0.00 5.10
4852 4883 5.859648 CCGTACCAAAAGTTAAAATTCGCAT 59.140 36.000 0.00 0.00 0.00 4.73
4853 4884 7.022384 CCGTACCAAAAGTTAAAATTCGCATA 58.978 34.615 0.00 0.00 0.00 3.14
4854 4885 7.217447 CCGTACCAAAAGTTAAAATTCGCATAG 59.783 37.037 0.00 0.00 0.00 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 9.678260 ACTAATATACCTACTTATACCGACTGG 57.322 37.037 0.00 0.00 42.84 4.00
100 101 1.144057 GGCCACCACTACGGATCAG 59.856 63.158 0.00 0.00 38.63 2.90
141 142 3.202097 CAAAACATTCAAACCCACCACC 58.798 45.455 0.00 0.00 0.00 4.61
187 188 2.436173 CCTTCCTACCACCTCAATCCTC 59.564 54.545 0.00 0.00 0.00 3.71
199 200 2.202707 ACCACCCATTACCTTCCTACC 58.797 52.381 0.00 0.00 0.00 3.18
200 201 4.014406 CAAACCACCCATTACCTTCCTAC 58.986 47.826 0.00 0.00 0.00 3.18
201 202 3.917629 TCAAACCACCCATTACCTTCCTA 59.082 43.478 0.00 0.00 0.00 2.94
202 203 2.719705 TCAAACCACCCATTACCTTCCT 59.280 45.455 0.00 0.00 0.00 3.36
363 377 1.065199 CAGTGGTGGGCACATGACTAT 60.065 52.381 0.00 0.00 0.00 2.12
443 460 0.967380 TCGGGTAGGACGGAAGAACC 60.967 60.000 0.00 0.00 0.00 3.62
446 463 4.651867 CTCGGGTAGGACGGAAGA 57.348 61.111 0.00 0.00 0.00 2.87
504 521 0.674581 AGTCAAGCTATGCTGCGCAA 60.675 50.000 13.05 0.00 43.62 4.85
634 651 5.448654 TGGCCAAGAAATTAGCATAGATGT 58.551 37.500 0.61 0.00 0.00 3.06
695 712 5.253330 CAGCCTTTCCCTACATTTCTGTAA 58.747 41.667 0.00 0.00 37.41 2.41
697 714 3.690460 CAGCCTTTCCCTACATTTCTGT 58.310 45.455 0.00 0.00 39.49 3.41
699 716 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
700 717 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
701 718 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
702 719 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
703 720 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
704 721 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
705 722 0.535797 AGTACGCAGCCTTTCCCTAC 59.464 55.000 0.00 0.00 0.00 3.18
706 723 2.148446 TAGTACGCAGCCTTTCCCTA 57.852 50.000 0.00 0.00 0.00 3.53
707 724 1.497161 ATAGTACGCAGCCTTTCCCT 58.503 50.000 0.00 0.00 0.00 4.20
708 725 2.626743 TCTATAGTACGCAGCCTTTCCC 59.373 50.000 0.00 0.00 0.00 3.97
709 726 3.552478 GGTCTATAGTACGCAGCCTTTCC 60.552 52.174 0.00 0.00 0.00 3.13
710 727 3.552478 GGGTCTATAGTACGCAGCCTTTC 60.552 52.174 0.00 0.00 0.00 2.62
711 728 2.364647 GGGTCTATAGTACGCAGCCTTT 59.635 50.000 0.00 0.00 0.00 3.11
712 729 1.962100 GGGTCTATAGTACGCAGCCTT 59.038 52.381 0.00 0.00 0.00 4.35
713 730 1.133575 TGGGTCTATAGTACGCAGCCT 60.134 52.381 13.98 0.00 35.18 4.58
714 731 1.325355 TGGGTCTATAGTACGCAGCC 58.675 55.000 13.98 8.23 35.18 4.85
715 732 3.181478 ACTTTGGGTCTATAGTACGCAGC 60.181 47.826 16.00 2.07 40.36 5.25
716 733 4.360563 CACTTTGGGTCTATAGTACGCAG 58.639 47.826 16.00 11.29 40.36 5.18
717 734 3.131577 CCACTTTGGGTCTATAGTACGCA 59.868 47.826 13.98 13.98 37.94 5.24
718 735 3.131755 ACCACTTTGGGTCTATAGTACGC 59.868 47.826 0.00 6.13 43.37 4.42
719 736 4.996788 ACCACTTTGGGTCTATAGTACG 57.003 45.455 0.00 0.00 43.37 3.67
729 746 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
730 747 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
731 748 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
732 749 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
733 750 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
734 751 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
735 752 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
736 753 3.714001 GGGGAAGGGTCCGACCAC 61.714 72.222 19.43 8.70 46.04 4.16
743 760 4.735599 AGGGTCCGGGGAAGGGTC 62.736 72.222 0.00 0.00 0.00 4.46
759 776 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
762 779 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
763 780 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
764 781 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
765 782 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
771 788 2.897350 GCCCGGTGCATGTAGCTC 60.897 66.667 11.25 0.00 45.94 4.09
772 789 3.402681 AGCCCGGTGCATGTAGCT 61.403 61.111 15.92 4.82 45.94 3.32
773 790 3.204827 CAGCCCGGTGCATGTAGC 61.205 66.667 15.92 2.56 44.83 3.58
774 791 3.204827 GCAGCCCGGTGCATGTAG 61.205 66.667 13.70 0.91 43.41 2.74
775 792 4.794648 GGCAGCCCGGTGCATGTA 62.795 66.667 19.47 0.00 45.93 2.29
785 802 3.632333 ACTAAAGAATAAAGGGCAGCCC 58.368 45.455 24.90 24.90 45.90 5.19
786 803 5.437946 ACTACTAAAGAATAAAGGGCAGCC 58.562 41.667 1.26 1.26 0.00 4.85
787 804 8.678593 AATACTACTAAAGAATAAAGGGCAGC 57.321 34.615 0.00 0.00 0.00 5.25
788 805 9.832445 TGAATACTACTAAAGAATAAAGGGCAG 57.168 33.333 0.00 0.00 0.00 4.85
789 806 9.609346 GTGAATACTACTAAAGAATAAAGGGCA 57.391 33.333 0.00 0.00 0.00 5.36
790 807 8.762426 CGTGAATACTACTAAAGAATAAAGGGC 58.238 37.037 0.00 0.00 0.00 5.19
915 932 3.160679 AGCTTCTTGTAATTGCACCCT 57.839 42.857 0.00 0.00 0.00 4.34
917 934 4.503741 TGAAGCTTCTTGTAATTGCACC 57.496 40.909 26.09 0.00 0.00 5.01
984 1001 6.149308 TGCTGGACATTTTGTTCTACATACAG 59.851 38.462 0.00 0.00 0.00 2.74
1053 1070 4.329545 GGAGGTGGCACAAGCGGA 62.330 66.667 20.82 0.00 44.16 5.54
1300 1317 2.290896 CCACTGCTTCCTACCCATGAAA 60.291 50.000 0.00 0.00 0.00 2.69
1494 1511 5.965033 ATGTCCTCCTAGTGATGATGTTT 57.035 39.130 0.00 0.00 0.00 2.83
1971 1988 1.228657 GGCAACCAGTTCGTGTCTCC 61.229 60.000 0.00 0.00 0.00 3.71
2076 2093 1.271217 ACAAGATCAGAAGCTGCTGCA 60.271 47.619 17.79 6.57 42.74 4.41
2193 2210 2.821969 ACTGTTTGAAGTGGCATCATCC 59.178 45.455 0.00 0.00 0.00 3.51
2196 2213 3.213206 AGACTGTTTGAAGTGGCATCA 57.787 42.857 0.00 0.00 0.00 3.07
2212 2229 7.256368 CCTTTTCCAACTTCTACCTTCTAGACT 60.256 40.741 0.00 0.00 0.00 3.24
2353 2370 7.001674 TCTGCCCAAAGAAAATTAGTCAAGTA 58.998 34.615 0.00 0.00 0.00 2.24
2361 2378 6.269769 ACTTGGAATCTGCCCAAAGAAAATTA 59.730 34.615 0.00 0.00 42.51 1.40
2436 2453 2.158564 ACCATAGCCTTGCACTGCATAT 60.159 45.455 4.10 0.00 38.76 1.78
3068 3085 2.036346 GGTGGCTTCTTTGTGCTTTGAT 59.964 45.455 0.00 0.00 0.00 2.57
3072 3089 1.322442 GAGGTGGCTTCTTTGTGCTT 58.678 50.000 0.00 0.00 0.00 3.91
3091 3108 3.667960 GCTTGCCTTAATATTCGCATCGG 60.668 47.826 5.82 2.68 0.00 4.18
3233 3250 3.009723 TGATCTTTTGGATTGTCCTCGC 58.990 45.455 0.00 0.00 37.46 5.03
3585 3602 4.209080 GGGCTGTTTTCAAGAAATTGTTCG 59.791 41.667 0.00 0.00 38.90 3.95
3629 3646 1.808411 ACGGTCACAATTAGCACCAG 58.192 50.000 0.00 0.00 0.00 4.00
3709 3726 1.415659 AGTACCATCAGCAGAGCCATC 59.584 52.381 0.00 0.00 0.00 3.51
3750 3767 0.461961 TGCGACAAACAAAAAGGGGG 59.538 50.000 0.00 0.00 0.00 5.40
3766 3783 4.722194 AGCACTGTTAAATACATGTTGCG 58.278 39.130 2.30 0.00 35.85 4.85
3881 3898 9.790389 AGAATAGTTCTCTTACTACGTTTCATG 57.210 33.333 0.00 0.00 34.07 3.07
3883 3900 8.790718 ACAGAATAGTTCTCTTACTACGTTTCA 58.209 33.333 0.00 0.00 38.11 2.69
3974 3991 4.030216 ACATTTTCCCAAACAGGTCACTT 58.970 39.130 0.00 0.00 34.66 3.16
4006 4023 1.681264 ACTAAATATTTGCTGGCCGGC 59.319 47.619 30.57 30.57 0.00 6.13
4009 4026 6.648725 TGAACAAAACTAAATATTTGCTGGCC 59.351 34.615 11.05 0.00 39.55 5.36
4135 4153 2.124736 GCACAGCCGATAAGCCCA 60.125 61.111 0.00 0.00 0.00 5.36
4174 4192 4.944048 GAAAAGTTCCAGCAGCCTTAAAA 58.056 39.130 0.00 0.00 0.00 1.52
4175 4193 4.584327 GAAAAGTTCCAGCAGCCTTAAA 57.416 40.909 0.00 0.00 0.00 1.52
4281 4299 1.594293 CGCTTGGTGGTCGAACAGT 60.594 57.895 1.63 0.00 0.00 3.55
4310 4328 5.192522 ACCCTTTTCATCATCATCTACTGGT 59.807 40.000 0.00 0.00 0.00 4.00
4379 4403 1.955080 ACTAGTACATCTACAGGCGCC 59.045 52.381 21.89 21.89 0.00 6.53
4502 4526 8.029522 TGCGATTGCCTTGTTTGTATTTATTTA 58.970 29.630 1.50 0.00 41.78 1.40
4522 4547 3.244181 ACAAGGCCTGAAAATTTGCGATT 60.244 39.130 5.69 0.00 0.00 3.34
4631 4656 9.273016 GGCACATCTAGATATGCTTTAGTAAAA 57.727 33.333 29.70 0.00 40.81 1.52
4632 4657 7.878127 GGGCACATCTAGATATGCTTTAGTAAA 59.122 37.037 29.70 0.00 40.81 2.01
4633 4658 7.386851 GGGCACATCTAGATATGCTTTAGTAA 58.613 38.462 29.70 0.00 40.81 2.24
4634 4659 6.070767 GGGGCACATCTAGATATGCTTTAGTA 60.071 42.308 29.70 0.00 40.81 1.82
4635 4660 5.280215 GGGGCACATCTAGATATGCTTTAGT 60.280 44.000 29.70 8.79 40.81 2.24
4636 4661 5.181748 GGGGCACATCTAGATATGCTTTAG 58.818 45.833 29.70 8.18 40.81 1.85
4637 4662 4.597075 TGGGGCACATCTAGATATGCTTTA 59.403 41.667 29.70 16.18 40.81 1.85
4638 4663 3.395607 TGGGGCACATCTAGATATGCTTT 59.604 43.478 29.70 0.00 40.81 3.51
4639 4664 2.981784 TGGGGCACATCTAGATATGCTT 59.018 45.455 29.70 0.00 40.81 3.91
4640 4665 2.624495 TGGGGCACATCTAGATATGCT 58.376 47.619 29.70 0.00 40.81 3.79
4641 4666 3.244700 ACTTGGGGCACATCTAGATATGC 60.245 47.826 24.83 24.83 40.32 3.14
4642 4667 4.630644 ACTTGGGGCACATCTAGATATG 57.369 45.455 6.64 6.64 0.00 1.78
4643 4668 6.715280 CAATACTTGGGGCACATCTAGATAT 58.285 40.000 4.54 0.00 0.00 1.63
4644 4669 5.513094 GCAATACTTGGGGCACATCTAGATA 60.513 44.000 4.54 0.00 0.00 1.98
4645 4670 4.747931 GCAATACTTGGGGCACATCTAGAT 60.748 45.833 0.00 0.00 0.00 1.98
4659 4684 7.495606 TCATAGGACTTACATGTGCAATACTTG 59.504 37.037 9.11 0.00 39.60 3.16
4673 4698 7.893658 TCTCCGGATAAAATCATAGGACTTAC 58.106 38.462 3.57 0.00 0.00 2.34
4682 4707 5.466728 CACACGAATCTCCGGATAAAATCAT 59.533 40.000 3.57 0.00 0.00 2.45
4761 4792 4.911514 TTCCAACCGAGGAAAGAAAAAG 57.088 40.909 0.00 0.00 44.38 2.27
4775 4806 4.664150 TTCCTGTTGTTCATTTCCAACC 57.336 40.909 0.00 0.00 40.12 3.77


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

AutoCloner maintained by Alex Coulton.