Multiple sequence alignment - TraesCS7B01G287000

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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 TraesCS7B01G287000 chr7B 100.000 4224 0 0 1 4224 522532191 522527968 0.000000e+00 7801.0
1 TraesCS7B01G287000 chr7B 94.543 678 34 3 40 715 522544171 522543495 0.000000e+00 1044.0
2 TraesCS7B01G287000 chr7B 88.617 694 65 11 34 715 391515285 391515976 0.000000e+00 832.0
3 TraesCS7B01G287000 chr7D 95.817 2606 72 17 861 3448 494601138 494598552 0.000000e+00 4174.0
4 TraesCS7B01G287000 chr7D 93.861 619 22 5 3426 4042 494598543 494597939 0.000000e+00 918.0
5 TraesCS7B01G287000 chr7D 94.118 136 8 0 4089 4224 494597532 494597397 1.540000e-49 207.0
6 TraesCS7B01G287000 chr7D 73.574 333 59 25 3548 3872 590814052 590813741 2.690000e-17 100.0
7 TraesCS7B01G287000 chr7A 91.369 2943 138 56 783 3650 560254600 560251699 0.000000e+00 3921.0
8 TraesCS7B01G287000 chr7A 88.110 328 30 3 3897 4224 560251516 560251198 8.570000e-102 381.0
9 TraesCS7B01G287000 chr7A 84.036 332 26 6 3433 3742 560251914 560251588 1.150000e-75 294.0
10 TraesCS7B01G287000 chr7A 94.521 73 4 0 3784 3856 560251589 560251517 3.450000e-21 113.0
11 TraesCS7B01G287000 chr6B 91.605 679 48 8 40 715 577653655 577652983 0.000000e+00 929.0
12 TraesCS7B01G287000 chr6B 90.351 684 56 8 40 715 524623460 524624141 0.000000e+00 889.0
13 TraesCS7B01G287000 chr6B 88.792 687 62 14 40 715 275407251 275406569 0.000000e+00 828.0
14 TraesCS7B01G287000 chr5B 91.458 679 55 3 40 715 351033623 351034301 0.000000e+00 929.0
15 TraesCS7B01G287000 chr4B 89.343 685 62 9 40 715 317052703 317053385 0.000000e+00 850.0
16 TraesCS7B01G287000 chr3B 88.873 683 69 7 40 715 478456670 478455988 0.000000e+00 833.0
17 TraesCS7B01G287000 chr3B 88.712 691 61 16 40 715 381810686 381809998 0.000000e+00 828.0
18 TraesCS7B01G287000 chr6D 78.846 468 73 13 3663 4127 267239657 267240101 4.130000e-75 292.0
19 TraesCS7B01G287000 chr6D 81.145 297 45 5 3930 4224 59630978 59631265 1.180000e-55 228.0
20 TraesCS7B01G287000 chr6A 74.247 598 120 20 3566 4158 472356628 472356060 1.980000e-53 220.0
21 TraesCS7B01G287000 chr2B 87.255 102 12 1 3467 3567 521939151 521939050 9.600000e-22 115.0
22 TraesCS7B01G287000 chr1D 82.558 86 12 3 3527 3610 399262251 399262167 5.860000e-09 73.1


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 TraesCS7B01G287000 chr7B 522527968 522532191 4223 True 7801.000000 7801 100.000000 1 4224 1 chr7B.!!$R1 4223
1 TraesCS7B01G287000 chr7B 522543495 522544171 676 True 1044.000000 1044 94.543000 40 715 1 chr7B.!!$R2 675
2 TraesCS7B01G287000 chr7B 391515285 391515976 691 False 832.000000 832 88.617000 34 715 1 chr7B.!!$F1 681
3 TraesCS7B01G287000 chr7D 494597397 494601138 3741 True 1766.333333 4174 94.598667 861 4224 3 chr7D.!!$R2 3363
4 TraesCS7B01G287000 chr7A 560251198 560254600 3402 True 1177.250000 3921 89.509000 783 4224 4 chr7A.!!$R1 3441
5 TraesCS7B01G287000 chr6B 577652983 577653655 672 True 929.000000 929 91.605000 40 715 1 chr6B.!!$R2 675
6 TraesCS7B01G287000 chr6B 524623460 524624141 681 False 889.000000 889 90.351000 40 715 1 chr6B.!!$F1 675
7 TraesCS7B01G287000 chr6B 275406569 275407251 682 True 828.000000 828 88.792000 40 715 1 chr6B.!!$R1 675
8 TraesCS7B01G287000 chr5B 351033623 351034301 678 False 929.000000 929 91.458000 40 715 1 chr5B.!!$F1 675
9 TraesCS7B01G287000 chr4B 317052703 317053385 682 False 850.000000 850 89.343000 40 715 1 chr4B.!!$F1 675
10 TraesCS7B01G287000 chr3B 478455988 478456670 682 True 833.000000 833 88.873000 40 715 1 chr3B.!!$R2 675
11 TraesCS7B01G287000 chr3B 381809998 381810686 688 True 828.000000 828 88.712000 40 715 1 chr3B.!!$R1 675
12 TraesCS7B01G287000 chr6A 472356060 472356628 568 True 220.000000 220 74.247000 3566 4158 1 chr6A.!!$R1 592

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
893 921 0.037605 CAGCCCGTTTAACTCGGTCT 60.038 55.0 14.48 6.73 45.63 3.85 F
1783 1827 0.458716 GCGTGGAGCTACTTGGAGTC 60.459 60.0 0.00 0.00 44.04 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2698 2761 0.376852 TTGACAGACAAACGCTGCAC 59.623 50.0 0.0 0.0 36.86 4.57 R
3698 3838 0.539051 AAGATCTCGTTGAGGGCTGG 59.461 55.0 0.0 0.0 0.00 4.85 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
23 24 5.429681 TTCTGGGAAATCAATTACTCGGA 57.570 39.130 0.00 0.00 0.00 4.55
24 25 5.429681 TCTGGGAAATCAATTACTCGGAA 57.570 39.130 0.00 0.00 0.00 4.30
25 26 5.811190 TCTGGGAAATCAATTACTCGGAAA 58.189 37.500 0.00 0.00 0.00 3.13
26 27 6.242396 TCTGGGAAATCAATTACTCGGAAAA 58.758 36.000 0.00 0.00 0.00 2.29
27 28 6.150474 TCTGGGAAATCAATTACTCGGAAAAC 59.850 38.462 0.00 0.00 0.00 2.43
28 29 5.184287 TGGGAAATCAATTACTCGGAAAACC 59.816 40.000 0.00 0.00 0.00 3.27
29 30 5.329493 GGAAATCAATTACTCGGAAAACCG 58.671 41.667 0.00 0.00 0.00 4.44
30 31 4.957759 AATCAATTACTCGGAAAACCGG 57.042 40.909 0.00 0.00 0.00 5.28
31 32 3.405823 TCAATTACTCGGAAAACCGGT 57.594 42.857 0.00 0.00 0.00 5.28
32 33 3.328505 TCAATTACTCGGAAAACCGGTC 58.671 45.455 8.04 0.00 0.00 4.79
33 34 2.000429 ATTACTCGGAAAACCGGTCG 58.000 50.000 8.04 7.45 0.00 4.79
34 35 0.673437 TTACTCGGAAAACCGGTCGT 59.327 50.000 8.04 0.00 0.00 4.34
35 36 0.039256 TACTCGGAAAACCGGTCGTG 60.039 55.000 8.04 10.84 0.00 4.35
36 37 1.007038 CTCGGAAAACCGGTCGTGA 60.007 57.895 8.04 0.78 0.00 4.35
37 38 1.280206 CTCGGAAAACCGGTCGTGAC 61.280 60.000 8.04 0.00 0.00 3.67
38 39 1.592131 CGGAAAACCGGTCGTGACA 60.592 57.895 8.04 0.00 0.00 3.58
124 126 1.027255 TTCAGTCGCCTCTCTCTCCG 61.027 60.000 0.00 0.00 0.00 4.63
132 136 2.026905 GCCTCTCTCTCCGTGGATCTT 61.027 57.143 0.00 0.00 0.00 2.40
133 147 1.953686 CCTCTCTCTCCGTGGATCTTC 59.046 57.143 0.00 0.00 0.00 2.87
136 150 1.064803 CTCTCTCCGTGGATCTTCGTG 59.935 57.143 0.00 0.00 0.00 4.35
142 156 1.068474 CGTGGATCTTCGTGTTGGTC 58.932 55.000 0.00 0.00 0.00 4.02
279 300 6.838382 ACACTTATCCTGACTAAAGTTGGTT 58.162 36.000 0.00 0.09 29.93 3.67
358 380 1.301716 GCCGTTCTGCTGGTCTTGA 60.302 57.895 0.00 0.00 0.00 3.02
447 470 0.593128 GAAACAAGGACACTGCGCAT 59.407 50.000 12.24 0.00 0.00 4.73
633 657 2.802816 GAGCTTGTGTTGACGAAGATGT 59.197 45.455 0.00 0.00 0.00 3.06
635 659 2.287915 GCTTGTGTTGACGAAGATGTGT 59.712 45.455 0.00 0.00 0.00 3.72
715 741 3.876589 TTCCCAGAACGCCGACAGC 62.877 63.158 0.00 0.00 38.52 4.40
716 742 4.379243 CCCAGAACGCCGACAGCT 62.379 66.667 0.00 0.00 40.39 4.24
717 743 3.114616 CCAGAACGCCGACAGCTG 61.115 66.667 13.48 13.48 40.39 4.24
718 744 3.782244 CAGAACGCCGACAGCTGC 61.782 66.667 15.27 5.81 40.39 5.25
721 747 3.642778 GAACGCCGACAGCTGCCTA 62.643 63.158 15.27 0.00 40.39 3.93
722 748 3.234630 AACGCCGACAGCTGCCTAA 62.235 57.895 15.27 0.00 40.39 2.69
723 749 2.202932 CGCCGACAGCTGCCTAAT 60.203 61.111 15.27 0.00 40.39 1.73
724 750 1.815421 CGCCGACAGCTGCCTAATT 60.815 57.895 15.27 0.00 40.39 1.40
725 751 1.369091 CGCCGACAGCTGCCTAATTT 61.369 55.000 15.27 0.00 40.39 1.82
726 752 0.811281 GCCGACAGCTGCCTAATTTT 59.189 50.000 15.27 0.00 38.99 1.82
727 753 1.202348 GCCGACAGCTGCCTAATTTTT 59.798 47.619 15.27 0.00 38.99 1.94
761 787 9.646427 TTTTGTAATTTTGTATGATAGGGCAAC 57.354 29.630 0.00 0.00 0.00 4.17
762 788 7.022055 TGTAATTTTGTATGATAGGGCAACG 57.978 36.000 0.00 0.00 37.60 4.10
763 789 5.514274 AATTTTGTATGATAGGGCAACGG 57.486 39.130 0.00 0.00 37.60 4.44
764 790 3.916359 TTTGTATGATAGGGCAACGGA 57.084 42.857 0.00 0.00 37.60 4.69
765 791 3.916359 TTGTATGATAGGGCAACGGAA 57.084 42.857 0.00 0.00 37.60 4.30
766 792 3.916359 TGTATGATAGGGCAACGGAAA 57.084 42.857 0.00 0.00 37.60 3.13
767 793 3.804036 TGTATGATAGGGCAACGGAAAG 58.196 45.455 0.00 0.00 37.60 2.62
768 794 2.348411 ATGATAGGGCAACGGAAAGG 57.652 50.000 0.00 0.00 37.60 3.11
769 795 1.281419 TGATAGGGCAACGGAAAGGA 58.719 50.000 0.00 0.00 37.60 3.36
770 796 1.065709 TGATAGGGCAACGGAAAGGAC 60.066 52.381 0.00 0.00 37.60 3.85
771 797 1.209747 GATAGGGCAACGGAAAGGACT 59.790 52.381 0.00 0.00 37.60 3.85
772 798 0.323629 TAGGGCAACGGAAAGGACTG 59.676 55.000 0.00 0.00 37.60 3.51
773 799 1.228154 GGGCAACGGAAAGGACTGT 60.228 57.895 0.00 0.00 37.60 3.55
774 800 0.822121 GGGCAACGGAAAGGACTGTT 60.822 55.000 0.00 0.00 39.55 3.16
775 801 0.591659 GGCAACGGAAAGGACTGTTC 59.408 55.000 0.00 0.00 37.28 3.18
776 802 1.594331 GCAACGGAAAGGACTGTTCT 58.406 50.000 0.00 0.00 37.28 3.01
777 803 1.947456 GCAACGGAAAGGACTGTTCTT 59.053 47.619 0.00 0.00 37.28 2.52
778 804 3.135994 GCAACGGAAAGGACTGTTCTTA 58.864 45.455 0.87 0.00 37.28 2.10
779 805 3.751698 GCAACGGAAAGGACTGTTCTTAT 59.248 43.478 0.87 0.00 37.28 1.73
780 806 4.215613 GCAACGGAAAGGACTGTTCTTATT 59.784 41.667 0.87 0.00 37.28 1.40
781 807 5.617087 GCAACGGAAAGGACTGTTCTTATTC 60.617 44.000 0.87 0.00 37.28 1.75
793 819 7.346751 ACTGTTCTTATTCTTTTTGCCTCAA 57.653 32.000 0.00 0.00 0.00 3.02
817 843 4.286297 GCCCTAAAAAGGCCTCATTTTT 57.714 40.909 18.04 16.98 45.16 1.94
843 871 5.948842 TGAGAAGTAAAAAGGGCCTAGTTT 58.051 37.500 6.41 13.32 0.00 2.66
844 872 6.370453 TGAGAAGTAAAAAGGGCCTAGTTTT 58.630 36.000 17.55 17.55 0.00 2.43
845 873 6.837048 TGAGAAGTAAAAAGGGCCTAGTTTTT 59.163 34.615 18.39 17.34 38.89 1.94
893 921 0.037605 CAGCCCGTTTAACTCGGTCT 60.038 55.000 14.48 6.73 45.63 3.85
955 983 1.228306 CGCCCACCCACCTAACAAA 60.228 57.895 0.00 0.00 0.00 2.83
999 1027 2.042843 TTCCTCTCCTCCGCTCCC 60.043 66.667 0.00 0.00 0.00 4.30
1000 1028 3.680920 TTCCTCTCCTCCGCTCCCC 62.681 68.421 0.00 0.00 0.00 4.81
1001 1029 4.150454 CCTCTCCTCCGCTCCCCT 62.150 72.222 0.00 0.00 0.00 4.79
1031 1059 1.367471 CACCAACGCAGAGGAGTGA 59.633 57.895 0.00 0.00 0.00 3.41
1410 1441 0.541863 ATCCCCGTGGTGTTCTGATC 59.458 55.000 0.00 0.00 0.00 2.92
1423 1454 3.996363 TGTTCTGATCGATTTCCTGTGTG 59.004 43.478 0.00 0.00 0.00 3.82
1424 1455 3.961480 TCTGATCGATTTCCTGTGTGT 57.039 42.857 0.00 0.00 0.00 3.72
1425 1456 3.588955 TCTGATCGATTTCCTGTGTGTG 58.411 45.455 0.00 0.00 0.00 3.82
1426 1457 3.006859 TCTGATCGATTTCCTGTGTGTGT 59.993 43.478 0.00 0.00 0.00 3.72
1427 1458 3.066380 TGATCGATTTCCTGTGTGTGTG 58.934 45.455 0.00 0.00 0.00 3.82
1428 1459 2.613026 TCGATTTCCTGTGTGTGTGT 57.387 45.000 0.00 0.00 0.00 3.72
1552 1595 3.733960 GTTGCGCCCTTCGTTCCC 61.734 66.667 4.18 0.00 41.07 3.97
1703 1747 2.951642 CAGGCCCGATGAATTTGTATGT 59.048 45.455 0.00 0.00 0.00 2.29
1768 1812 5.588240 TGATTGTGTATAGTTAGAGGCGTG 58.412 41.667 0.00 0.00 0.00 5.34
1782 1826 1.592223 GCGTGGAGCTACTTGGAGT 59.408 57.895 0.00 0.00 44.04 3.85
1783 1827 0.458716 GCGTGGAGCTACTTGGAGTC 60.459 60.000 0.00 0.00 44.04 3.36
1784 1828 1.178276 CGTGGAGCTACTTGGAGTCT 58.822 55.000 0.00 0.00 0.00 3.24
1785 1829 1.546476 CGTGGAGCTACTTGGAGTCTT 59.454 52.381 0.00 0.00 0.00 3.01
1786 1830 2.672478 CGTGGAGCTACTTGGAGTCTTG 60.672 54.545 0.00 0.00 0.00 3.02
1787 1831 1.902508 TGGAGCTACTTGGAGTCTTGG 59.097 52.381 0.00 0.00 0.00 3.61
1788 1832 2.180276 GGAGCTACTTGGAGTCTTGGA 58.820 52.381 0.00 0.00 0.00 3.53
1789 1833 2.167487 GGAGCTACTTGGAGTCTTGGAG 59.833 54.545 0.00 0.00 0.00 3.86
1910 1954 9.667607 ATCCTCCTCTCTAAGAAATAATTCAGA 57.332 33.333 0.00 0.00 38.06 3.27
1962 2008 3.123804 CGTGAGCTGTGTTGTTTAGTCT 58.876 45.455 0.00 0.00 0.00 3.24
2096 2142 5.237815 TCATTTCAGTGTCACGCTATTCTT 58.762 37.500 0.00 0.00 0.00 2.52
2105 2151 3.182572 GTCACGCTATTCTTATTCAGGCG 59.817 47.826 0.00 0.00 45.31 5.52
2119 2165 8.385111 TCTTATTCAGGCGAAACTTTATTTACG 58.615 33.333 0.00 0.00 34.01 3.18
2693 2756 9.476202 GACCAGTTGATTAATTAAAGCAGTTTT 57.524 29.630 1.21 0.00 34.38 2.43
2727 2790 4.290155 GTTTGTCTGTCAAAATGCACGAT 58.710 39.130 1.77 0.00 45.84 3.73
2789 2856 6.485830 TGTGTTATAAGCTTAGCTCCTCAT 57.514 37.500 7.36 1.71 38.25 2.90
2822 2890 5.507077 TGCTGAAGCGTTTAAAGTACTTTG 58.493 37.500 27.40 13.76 45.83 2.77
2866 2934 4.175489 CTCGTGCATGCTGCTGCC 62.175 66.667 20.33 10.21 45.31 4.85
2950 3018 7.172703 GCCTATGAAACTGTTACACTACTGTTT 59.827 37.037 10.25 10.25 46.24 2.83
3275 3344 5.270083 TGACTAAAATGTTTGAACGCACAG 58.730 37.500 0.00 0.00 0.00 3.66
3276 3345 4.606961 ACTAAAATGTTTGAACGCACAGG 58.393 39.130 0.00 0.00 0.00 4.00
3556 3671 3.738982 ACATCAAACTCGTCAATCCACA 58.261 40.909 0.00 0.00 0.00 4.17
3697 3837 0.261109 TGTTGCCCATGCCATATCCA 59.739 50.000 0.00 0.00 36.33 3.41
3698 3838 0.675633 GTTGCCCATGCCATATCCAC 59.324 55.000 0.00 0.00 36.33 4.02
3699 3839 0.469705 TTGCCCATGCCATATCCACC 60.470 55.000 0.00 0.00 36.33 4.61
3721 3864 4.253685 CAGCCCTCAACGAGATCTTTTTA 58.746 43.478 0.00 0.00 0.00 1.52
3967 4111 3.067106 CGGTCCTCGCATAATAGCAAAT 58.933 45.455 0.00 0.00 0.00 2.32
3990 4134 3.732212 GGGCTTGCAAAATCTCAAAAGT 58.268 40.909 0.00 0.00 0.00 2.66
3992 4136 3.426525 GGCTTGCAAAATCTCAAAAGTCG 59.573 43.478 0.00 0.00 0.00 4.18
4015 4159 6.017440 TCGTTTTCAAATCTTTCCTGGTAGTG 60.017 38.462 0.00 0.00 0.00 2.74
4053 4198 8.378172 TGGAAGTAGAGTTCTTTTAACATGTG 57.622 34.615 0.00 0.00 0.00 3.21
4054 4199 7.444183 TGGAAGTAGAGTTCTTTTAACATGTGG 59.556 37.037 0.00 0.00 0.00 4.17
4055 4200 7.094762 GGAAGTAGAGTTCTTTTAACATGTGGG 60.095 40.741 0.00 0.00 0.00 4.61
4056 4201 6.238648 AGTAGAGTTCTTTTAACATGTGGGG 58.761 40.000 0.00 0.00 0.00 4.96
4057 4202 4.407365 AGAGTTCTTTTAACATGTGGGGG 58.593 43.478 0.00 0.00 0.00 5.40
4107 4611 5.306114 AGTAGCCCACTTTGGTTATATCC 57.694 43.478 0.00 0.00 35.17 2.59
4108 4612 4.724798 AGTAGCCCACTTTGGTTATATCCA 59.275 41.667 0.00 0.00 35.17 3.41
4145 4649 1.415288 CCATGTTGTACGTACGGCCG 61.415 60.000 26.86 26.86 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.811190 TCCGAGTAATTGATTTCCCAGAAA 58.189 37.500 0.00 0.00 0.00 2.52
2 3 5.429681 TTCCGAGTAATTGATTTCCCAGA 57.570 39.130 0.00 0.00 0.00 3.86
3 4 6.322491 GTTTTCCGAGTAATTGATTTCCCAG 58.678 40.000 0.00 0.00 0.00 4.45
4 5 5.184287 GGTTTTCCGAGTAATTGATTTCCCA 59.816 40.000 0.00 0.00 0.00 4.37
5 6 5.647589 GGTTTTCCGAGTAATTGATTTCCC 58.352 41.667 0.00 0.00 0.00 3.97
21 22 0.584876 CTTGTCACGACCGGTTTTCC 59.415 55.000 9.42 0.00 0.00 3.13
22 23 1.292992 ACTTGTCACGACCGGTTTTC 58.707 50.000 9.42 0.00 0.00 2.29
23 24 2.204237 GTACTTGTCACGACCGGTTTT 58.796 47.619 9.42 0.00 0.00 2.43
24 25 1.136695 TGTACTTGTCACGACCGGTTT 59.863 47.619 9.42 0.00 0.00 3.27
25 26 0.746063 TGTACTTGTCACGACCGGTT 59.254 50.000 9.42 0.00 0.00 4.44
26 27 0.746063 TTGTACTTGTCACGACCGGT 59.254 50.000 6.92 6.92 0.00 5.28
27 28 1.790623 CTTTGTACTTGTCACGACCGG 59.209 52.381 0.00 0.00 0.00 5.28
28 29 1.790623 CCTTTGTACTTGTCACGACCG 59.209 52.381 0.00 0.00 0.00 4.79
29 30 2.140717 CCCTTTGTACTTGTCACGACC 58.859 52.381 0.00 0.00 0.00 4.79
30 31 2.140717 CCCCTTTGTACTTGTCACGAC 58.859 52.381 0.00 0.00 0.00 4.34
31 32 2.040939 TCCCCTTTGTACTTGTCACGA 58.959 47.619 0.00 0.00 0.00 4.35
32 33 2.536761 TCCCCTTTGTACTTGTCACG 57.463 50.000 0.00 0.00 0.00 4.35
33 34 3.547746 TGTTCCCCTTTGTACTTGTCAC 58.452 45.455 0.00 0.00 0.00 3.67
34 35 3.935818 TGTTCCCCTTTGTACTTGTCA 57.064 42.857 0.00 0.00 0.00 3.58
35 36 3.317149 GGTTGTTCCCCTTTGTACTTGTC 59.683 47.826 0.00 0.00 0.00 3.18
36 37 3.053170 AGGTTGTTCCCCTTTGTACTTGT 60.053 43.478 0.00 0.00 36.75 3.16
37 38 3.562182 AGGTTGTTCCCCTTTGTACTTG 58.438 45.455 0.00 0.00 36.75 3.16
38 39 3.746432 CGAGGTTGTTCCCCTTTGTACTT 60.746 47.826 0.00 0.00 36.75 2.24
124 126 2.028930 AGAGACCAACACGAAGATCCAC 60.029 50.000 0.00 0.00 0.00 4.02
132 136 3.075148 CAGAGTAGAGAGACCAACACGA 58.925 50.000 0.00 0.00 0.00 4.35
133 147 2.814919 ACAGAGTAGAGAGACCAACACG 59.185 50.000 0.00 0.00 0.00 4.49
136 150 3.057174 CACCACAGAGTAGAGAGACCAAC 60.057 52.174 0.00 0.00 0.00 3.77
142 156 1.846007 AGCCACCACAGAGTAGAGAG 58.154 55.000 0.00 0.00 0.00 3.20
633 657 2.280552 GGAGTGGCCCAGTACGACA 61.281 63.158 0.00 0.00 0.00 4.35
635 659 1.229082 AAGGAGTGGCCCAGTACGA 60.229 57.895 0.00 0.00 37.37 3.43
735 761 9.646427 GTTGCCCTATCATACAAAATTACAAAA 57.354 29.630 0.00 0.00 0.00 2.44
736 762 7.971168 CGTTGCCCTATCATACAAAATTACAAA 59.029 33.333 0.00 0.00 0.00 2.83
737 763 7.415765 CCGTTGCCCTATCATACAAAATTACAA 60.416 37.037 0.00 0.00 0.00 2.41
738 764 6.038825 CCGTTGCCCTATCATACAAAATTACA 59.961 38.462 0.00 0.00 0.00 2.41
739 765 6.261381 TCCGTTGCCCTATCATACAAAATTAC 59.739 38.462 0.00 0.00 0.00 1.89
740 766 6.358178 TCCGTTGCCCTATCATACAAAATTA 58.642 36.000 0.00 0.00 0.00 1.40
741 767 5.197451 TCCGTTGCCCTATCATACAAAATT 58.803 37.500 0.00 0.00 0.00 1.82
742 768 4.787551 TCCGTTGCCCTATCATACAAAAT 58.212 39.130 0.00 0.00 0.00 1.82
743 769 4.223556 TCCGTTGCCCTATCATACAAAA 57.776 40.909 0.00 0.00 0.00 2.44
744 770 3.916359 TCCGTTGCCCTATCATACAAA 57.084 42.857 0.00 0.00 0.00 2.83
745 771 3.916359 TTCCGTTGCCCTATCATACAA 57.084 42.857 0.00 0.00 0.00 2.41
746 772 3.433031 CCTTTCCGTTGCCCTATCATACA 60.433 47.826 0.00 0.00 0.00 2.29
747 773 3.139077 CCTTTCCGTTGCCCTATCATAC 58.861 50.000 0.00 0.00 0.00 2.39
748 774 3.042682 TCCTTTCCGTTGCCCTATCATA 58.957 45.455 0.00 0.00 0.00 2.15
749 775 1.843851 TCCTTTCCGTTGCCCTATCAT 59.156 47.619 0.00 0.00 0.00 2.45
750 776 1.065709 GTCCTTTCCGTTGCCCTATCA 60.066 52.381 0.00 0.00 0.00 2.15
751 777 1.209747 AGTCCTTTCCGTTGCCCTATC 59.790 52.381 0.00 0.00 0.00 2.08
752 778 1.065418 CAGTCCTTTCCGTTGCCCTAT 60.065 52.381 0.00 0.00 0.00 2.57
753 779 0.323629 CAGTCCTTTCCGTTGCCCTA 59.676 55.000 0.00 0.00 0.00 3.53
754 780 1.073199 CAGTCCTTTCCGTTGCCCT 59.927 57.895 0.00 0.00 0.00 5.19
755 781 0.822121 AACAGTCCTTTCCGTTGCCC 60.822 55.000 0.00 0.00 0.00 5.36
756 782 0.591659 GAACAGTCCTTTCCGTTGCC 59.408 55.000 0.00 0.00 0.00 4.52
757 783 1.594331 AGAACAGTCCTTTCCGTTGC 58.406 50.000 0.00 0.00 0.00 4.17
758 784 5.701290 AGAATAAGAACAGTCCTTTCCGTTG 59.299 40.000 0.00 0.00 0.00 4.10
759 785 5.866207 AGAATAAGAACAGTCCTTTCCGTT 58.134 37.500 0.00 0.00 0.00 4.44
760 786 5.485209 AGAATAAGAACAGTCCTTTCCGT 57.515 39.130 0.00 0.00 0.00 4.69
761 787 6.803154 AAAGAATAAGAACAGTCCTTTCCG 57.197 37.500 0.00 0.00 0.00 4.30
762 788 7.382488 GCAAAAAGAATAAGAACAGTCCTTTCC 59.618 37.037 0.00 0.00 0.00 3.13
763 789 7.382488 GGCAAAAAGAATAAGAACAGTCCTTTC 59.618 37.037 0.00 0.00 0.00 2.62
764 790 7.069950 AGGCAAAAAGAATAAGAACAGTCCTTT 59.930 33.333 0.00 0.00 0.00 3.11
765 791 6.551227 AGGCAAAAAGAATAAGAACAGTCCTT 59.449 34.615 0.00 0.00 0.00 3.36
766 792 6.071320 AGGCAAAAAGAATAAGAACAGTCCT 58.929 36.000 0.00 0.00 0.00 3.85
767 793 6.016276 TGAGGCAAAAAGAATAAGAACAGTCC 60.016 38.462 0.00 0.00 0.00 3.85
768 794 6.970484 TGAGGCAAAAAGAATAAGAACAGTC 58.030 36.000 0.00 0.00 0.00 3.51
769 795 6.959639 TGAGGCAAAAAGAATAAGAACAGT 57.040 33.333 0.00 0.00 0.00 3.55
770 796 7.380602 CACTTGAGGCAAAAAGAATAAGAACAG 59.619 37.037 0.00 0.00 0.00 3.16
771 797 7.202526 CACTTGAGGCAAAAAGAATAAGAACA 58.797 34.615 0.00 0.00 0.00 3.18
772 798 6.144563 GCACTTGAGGCAAAAAGAATAAGAAC 59.855 38.462 0.00 0.00 0.00 3.01
773 799 6.215845 GCACTTGAGGCAAAAAGAATAAGAA 58.784 36.000 0.00 0.00 0.00 2.52
774 800 5.278957 GGCACTTGAGGCAAAAAGAATAAGA 60.279 40.000 0.00 0.00 0.00 2.10
775 801 4.925646 GGCACTTGAGGCAAAAAGAATAAG 59.074 41.667 1.51 0.00 0.00 1.73
776 802 4.262420 GGGCACTTGAGGCAAAAAGAATAA 60.262 41.667 1.51 0.00 35.46 1.40
777 803 3.258123 GGGCACTTGAGGCAAAAAGAATA 59.742 43.478 1.51 0.00 35.46 1.75
778 804 2.037641 GGGCACTTGAGGCAAAAAGAAT 59.962 45.455 1.51 0.00 35.46 2.40
779 805 1.412343 GGGCACTTGAGGCAAAAAGAA 59.588 47.619 1.51 0.00 35.46 2.52
780 806 1.039856 GGGCACTTGAGGCAAAAAGA 58.960 50.000 1.51 0.00 35.46 2.52
781 807 1.043022 AGGGCACTTGAGGCAAAAAG 58.957 50.000 0.00 0.00 35.46 2.27
817 843 6.370453 ACTAGGCCCTTTTTACTTCTCAAAA 58.630 36.000 0.00 0.00 0.00 2.44
844 872 4.972201 ACGCGTTTTACTTGTCTCAAAAA 58.028 34.783 5.58 0.00 0.00 1.94
845 873 4.603231 ACGCGTTTTACTTGTCTCAAAA 57.397 36.364 5.58 0.00 0.00 2.44
846 874 4.805192 AGTACGCGTTTTACTTGTCTCAAA 59.195 37.500 20.78 0.00 0.00 2.69
847 875 4.207635 CAGTACGCGTTTTACTTGTCTCAA 59.792 41.667 20.78 0.00 0.00 3.02
848 876 3.732219 CAGTACGCGTTTTACTTGTCTCA 59.268 43.478 20.78 0.00 0.00 3.27
850 878 2.473984 GCAGTACGCGTTTTACTTGTCT 59.526 45.455 20.78 0.00 0.00 3.41
851 879 2.819296 GCAGTACGCGTTTTACTTGTC 58.181 47.619 20.78 2.91 0.00 3.18
893 921 5.263872 TGGGCTTTAATTGGGTCTTTCTA 57.736 39.130 0.00 0.00 0.00 2.10
934 962 1.301954 GTTAGGTGGGTGGGCGATT 59.698 57.895 0.00 0.00 0.00 3.34
935 963 1.493854 TTGTTAGGTGGGTGGGCGAT 61.494 55.000 0.00 0.00 0.00 4.58
955 983 2.510906 CCGATCGGGAAGCCCAAT 59.489 61.111 26.95 0.00 45.83 3.16
979 1007 2.042435 AGCGGAGGAGAGGAAGGG 60.042 66.667 0.00 0.00 0.00 3.95
981 1009 2.131067 GGGAGCGGAGGAGAGGAAG 61.131 68.421 0.00 0.00 0.00 3.46
982 1010 2.042843 GGGAGCGGAGGAGAGGAA 60.043 66.667 0.00 0.00 0.00 3.36
983 1011 4.144727 GGGGAGCGGAGGAGAGGA 62.145 72.222 0.00 0.00 0.00 3.71
984 1012 4.150454 AGGGGAGCGGAGGAGAGG 62.150 72.222 0.00 0.00 0.00 3.69
985 1013 2.520741 GAGGGGAGCGGAGGAGAG 60.521 72.222 0.00 0.00 0.00 3.20
986 1014 2.243774 ATTGAGGGGAGCGGAGGAGA 62.244 60.000 0.00 0.00 0.00 3.71
999 1027 2.017049 GTTGGTGGATTCGGATTGAGG 58.983 52.381 0.00 0.00 0.00 3.86
1000 1028 1.665679 CGTTGGTGGATTCGGATTGAG 59.334 52.381 0.00 0.00 0.00 3.02
1001 1029 1.732941 CGTTGGTGGATTCGGATTGA 58.267 50.000 0.00 0.00 0.00 2.57
1031 1059 3.768878 TCTTCTCCGGAGTTTCTCTCTT 58.231 45.455 30.17 0.00 42.40 2.85
1410 1441 1.939934 ACACACACACACAGGAAATCG 59.060 47.619 0.00 0.00 0.00 3.34
1423 1454 0.529773 TTCTCCTGCGACACACACAC 60.530 55.000 0.00 0.00 0.00 3.82
1424 1455 0.529773 GTTCTCCTGCGACACACACA 60.530 55.000 0.00 0.00 0.00 3.72
1425 1456 1.222115 GGTTCTCCTGCGACACACAC 61.222 60.000 0.00 0.00 0.00 3.82
1426 1457 1.069090 GGTTCTCCTGCGACACACA 59.931 57.895 0.00 0.00 0.00 3.72
1427 1458 1.367840 AGGTTCTCCTGCGACACAC 59.632 57.895 0.00 0.00 43.33 3.82
1428 1459 3.870955 AGGTTCTCCTGCGACACA 58.129 55.556 0.00 0.00 43.33 3.72
1552 1595 4.988598 ACAGAGGCACCAACGGCG 62.989 66.667 4.80 4.80 36.37 6.46
1555 1598 0.029300 CACAAACAGAGGCACCAACG 59.971 55.000 0.00 0.00 0.00 4.10
1557 1600 0.257328 TCCACAAACAGAGGCACCAA 59.743 50.000 0.00 0.00 0.00 3.67
1660 1703 5.841810 TGAGTGATCAAAAACATTCCCAAC 58.158 37.500 0.00 0.00 0.00 3.77
1662 1705 4.523943 CCTGAGTGATCAAAAACATTCCCA 59.476 41.667 0.00 0.00 0.00 4.37
1754 1798 2.074729 AGCTCCACGCCTCTAACTAT 57.925 50.000 0.00 0.00 40.39 2.12
1768 1812 2.167487 CTCCAAGACTCCAAGTAGCTCC 59.833 54.545 0.00 0.00 0.00 4.70
1962 2008 5.768662 ACTACTCACTACAGCAGTTAGTTGA 59.231 40.000 4.21 0.00 38.33 3.18
2004 2050 5.123820 TGCAGTGAAGGTTAGCATTGAATAC 59.876 40.000 0.00 0.00 0.00 1.89
2007 2053 3.485394 TGCAGTGAAGGTTAGCATTGAA 58.515 40.909 0.00 0.00 0.00 2.69
2011 2057 2.226437 CGTTTGCAGTGAAGGTTAGCAT 59.774 45.455 0.00 0.00 34.87 3.79
2096 2142 7.830940 TCGTAAATAAAGTTTCGCCTGAATA 57.169 32.000 0.00 0.00 33.20 1.75
2119 2165 7.602265 GCCTCTATTCTCAAGGATAAACTGATC 59.398 40.741 0.00 0.00 31.44 2.92
2686 2749 0.848305 CGCTGCACAAAGAAAACTGC 59.152 50.000 0.00 0.00 0.00 4.40
2693 2756 1.063912 CAGACAAACGCTGCACAAAGA 59.936 47.619 0.00 0.00 0.00 2.52
2698 2761 0.376852 TTGACAGACAAACGCTGCAC 59.623 50.000 0.00 0.00 36.86 4.57
2727 2790 9.016438 ACAAAAGGTTTAGTCAAAAAGTAGTCA 57.984 29.630 0.00 0.00 0.00 3.41
2866 2934 9.903682 ATAAATATCATGAAATTTGCCTCTTCG 57.096 29.630 0.00 0.00 0.00 3.79
2908 2976 4.507879 GCATTGCATGGTCAAGGC 57.492 55.556 3.15 6.89 44.58 4.35
3058 3127 6.766467 TCTGGAAAAGTGAAAGTAAGTCCTTC 59.234 38.462 0.00 0.00 0.00 3.46
3138 3207 1.707427 AGAAACACATGGAAGGAGGCT 59.293 47.619 0.00 0.00 0.00 4.58
3171 3240 5.713025 AGCACAAAATAGTTGCCATACAAG 58.287 37.500 0.00 0.00 39.50 3.16
3295 3364 2.132996 CCAGCAAGGCCACCAAACA 61.133 57.895 5.01 0.00 0.00 2.83
3401 3475 5.067805 GGGGAGAACAATTTGTAATGCCTAG 59.932 44.000 17.95 0.00 30.60 3.02
3546 3661 9.853555 TGTAATAATTTGATGTTGTGGATTGAC 57.146 29.630 0.00 0.00 0.00 3.18
3589 3704 9.761504 TGACAAATTTGTGTTGATTATGATGTT 57.238 25.926 27.85 0.00 42.43 2.71
3697 3837 0.616111 AGATCTCGTTGAGGGCTGGT 60.616 55.000 0.00 0.00 0.00 4.00
3698 3838 0.539051 AAGATCTCGTTGAGGGCTGG 59.461 55.000 0.00 0.00 0.00 4.85
3699 3839 2.393271 AAAGATCTCGTTGAGGGCTG 57.607 50.000 0.00 0.00 0.00 4.85
3721 3864 4.002906 TCCTGTAAGCACAACGATCTTT 57.997 40.909 0.00 0.00 33.22 2.52
3791 3935 1.082117 CCGGTGCGGTCATGTAGAAC 61.082 60.000 0.00 0.00 42.73 3.01
3890 4034 6.593770 TGGTACATCATCACAACTTACATGAC 59.406 38.462 0.00 0.00 0.00 3.06
3967 4111 1.614996 TTGAGATTTTGCAAGCCCGA 58.385 45.000 0.00 0.00 0.00 5.14
3990 4134 6.017440 CACTACCAGGAAAGATTTGAAAACGA 60.017 38.462 0.00 0.00 0.00 3.85
3992 4136 6.447162 CCACTACCAGGAAAGATTTGAAAAC 58.553 40.000 0.00 0.00 0.00 2.43
4015 4159 9.478768 GAACTCTACTTCCATAATACTTAAGCC 57.521 37.037 1.29 0.00 0.00 4.35
4097 4601 3.137544 ACCTTGCGGATTGGATATAACCA 59.862 43.478 0.00 0.00 38.24 3.67
4107 4611 1.376609 GGCCACTACCTTGCGGATTG 61.377 60.000 0.00 0.00 0.00 2.67
4108 4612 1.077716 GGCCACTACCTTGCGGATT 60.078 57.895 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.