Multiple sequence alignment - TraesCS7D01G247900

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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 TraesCS7D01G247900 chr7D 100.000 3344 0 0 1 3344 218174892 218178235 0.000000e+00 6176.0
1 TraesCS7D01G247900 chr7D 77.953 127 25 3 3220 3344 78111675 78111800 3.580000e-10 76.8
2 TraesCS7D01G247900 chr7B 94.276 2673 95 18 706 3344 181634630 181631982 0.000000e+00 4036.0
3 TraesCS7D01G247900 chr7B 85.185 81 11 1 2945 3024 408565081 408565001 7.690000e-12 82.4
4 TraesCS7D01G247900 chr7A 95.082 2318 85 15 749 3048 230876343 230878649 0.000000e+00 3622.0
5 TraesCS7D01G247900 chr7A 92.654 667 38 8 4 667 80995770 80996428 0.000000e+00 950.0
6 TraesCS7D01G247900 chr7A 86.248 669 45 15 1 667 630620180 630620803 0.000000e+00 682.0
7 TraesCS7D01G247900 chr7A 80.902 665 84 24 13 667 65361666 65361035 5.020000e-133 484.0
8 TraesCS7D01G247900 chr7A 89.091 55 4 2 3220 3273 81527751 81527804 2.150000e-07 67.6
9 TraesCS7D01G247900 chr4D 89.851 670 57 8 1 666 282027548 282026886 0.000000e+00 850.0
10 TraesCS7D01G247900 chr5A 90.409 636 32 10 4 617 117365526 117366154 0.000000e+00 809.0
11 TraesCS7D01G247900 chr5A 88.490 669 64 9 4 667 112110566 112111226 0.000000e+00 797.0
12 TraesCS7D01G247900 chr5A 79.394 495 73 18 177 667 575205429 575204960 4.160000e-84 322.0
13 TraesCS7D01G247900 chr6A 82.589 672 71 27 6 667 332196363 332196998 4.880000e-153 551.0
14 TraesCS7D01G247900 chr6A 82.370 675 75 25 1 667 332232245 332232883 6.310000e-152 547.0
15 TraesCS7D01G247900 chr6A 74.074 351 78 12 2945 3288 32880035 32880379 7.530000e-27 132.0
16 TraesCS7D01G247900 chr6A 82.609 92 9 7 2951 3037 521471415 521471504 1.290000e-09 75.0
17 TraesCS7D01G247900 chr2B 81.967 671 89 18 4 667 284955881 284956526 1.060000e-149 540.0
18 TraesCS7D01G247900 chr1D 79.392 296 53 8 3053 3344 363060097 363059806 5.660000e-48 202.0
19 TraesCS7D01G247900 chr5D 76.821 302 62 8 3047 3344 508580655 508580952 2.670000e-36 163.0
20 TraesCS7D01G247900 chr2A 74.731 372 66 17 2945 3293 762724297 762724663 1.250000e-29 141.0
21 TraesCS7D01G247900 chr6D 87.356 87 5 5 2951 3032 379527692 379527607 9.880000e-16 95.3
22 TraesCS7D01G247900 chr2D 86.905 84 7 4 2945 3024 43513342 43513425 1.280000e-14 91.6
23 TraesCS7D01G247900 chr6B 81.915 94 9 7 2950 3037 481051263 481051354 4.630000e-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 TraesCS7D01G247900 chr7D 218174892 218178235 3343 False 6176 6176 100.000 1 3344 1 chr7D.!!$F2 3343
1 TraesCS7D01G247900 chr7B 181631982 181634630 2648 True 4036 4036 94.276 706 3344 1 chr7B.!!$R1 2638
2 TraesCS7D01G247900 chr7A 230876343 230878649 2306 False 3622 3622 95.082 749 3048 1 chr7A.!!$F3 2299
3 TraesCS7D01G247900 chr7A 80995770 80996428 658 False 950 950 92.654 4 667 1 chr7A.!!$F1 663
4 TraesCS7D01G247900 chr7A 630620180 630620803 623 False 682 682 86.248 1 667 1 chr7A.!!$F4 666
5 TraesCS7D01G247900 chr7A 65361035 65361666 631 True 484 484 80.902 13 667 1 chr7A.!!$R1 654
6 TraesCS7D01G247900 chr4D 282026886 282027548 662 True 850 850 89.851 1 666 1 chr4D.!!$R1 665
7 TraesCS7D01G247900 chr5A 117365526 117366154 628 False 809 809 90.409 4 617 1 chr5A.!!$F2 613
8 TraesCS7D01G247900 chr5A 112110566 112111226 660 False 797 797 88.490 4 667 1 chr5A.!!$F1 663
9 TraesCS7D01G247900 chr6A 332196363 332196998 635 False 551 551 82.589 6 667 1 chr6A.!!$F2 661
10 TraesCS7D01G247900 chr6A 332232245 332232883 638 False 547 547 82.370 1 667 1 chr6A.!!$F3 666
11 TraesCS7D01G247900 chr2B 284955881 284956526 645 False 540 540 81.967 4 667 1 chr2B.!!$F1 663

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
689 906 0.17897 TAGGAGCTCCCATACCGTCC 60.179 60.0 29.54 0.51 37.41 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2662 2896 0.811915 AGTAGCAGTAGCAGTGACGG 59.188 55.0 0.0 0.0 45.49 4.79 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
488 687 3.388024 AGTTACAGAACAGCAGAACCTGA 59.612 43.478 0.00 0.00 38.10 3.86
546 745 1.219124 GCCTGCGATCCTGAGTTCA 59.781 57.895 0.00 0.00 0.00 3.18
670 887 2.888998 GCCAGAACGCGAAACGGTT 61.889 57.895 15.93 0.00 46.28 4.44
671 888 1.559149 GCCAGAACGCGAAACGGTTA 61.559 55.000 15.93 0.00 46.28 2.85
672 889 0.437295 CCAGAACGCGAAACGGTTAG 59.563 55.000 15.93 0.00 46.28 2.34
673 890 0.437295 CAGAACGCGAAACGGTTAGG 59.563 55.000 15.93 0.00 46.28 2.69
674 891 0.314935 AGAACGCGAAACGGTTAGGA 59.685 50.000 15.93 0.00 46.28 2.94
675 892 0.712222 GAACGCGAAACGGTTAGGAG 59.288 55.000 15.93 0.00 46.28 3.69
676 893 1.287041 AACGCGAAACGGTTAGGAGC 61.287 55.000 15.93 0.00 40.34 4.70
677 894 1.445582 CGCGAAACGGTTAGGAGCT 60.446 57.895 0.00 0.00 38.44 4.09
678 895 1.411493 CGCGAAACGGTTAGGAGCTC 61.411 60.000 4.71 4.71 38.44 4.09
679 896 1.082679 GCGAAACGGTTAGGAGCTCC 61.083 60.000 26.22 26.22 0.00 4.70
680 897 0.459759 CGAAACGGTTAGGAGCTCCC 60.460 60.000 29.54 14.04 36.42 4.30
681 898 0.611714 GAAACGGTTAGGAGCTCCCA 59.388 55.000 29.54 14.08 37.41 4.37
682 899 1.209747 GAAACGGTTAGGAGCTCCCAT 59.790 52.381 29.54 14.62 37.41 4.00
683 900 2.170012 AACGGTTAGGAGCTCCCATA 57.830 50.000 29.54 13.48 37.41 2.74
684 901 1.411041 ACGGTTAGGAGCTCCCATAC 58.589 55.000 29.54 22.27 37.41 2.39
685 902 0.680061 CGGTTAGGAGCTCCCATACC 59.320 60.000 29.54 28.04 37.32 2.73
686 903 0.680061 GGTTAGGAGCTCCCATACCG 59.320 60.000 29.54 0.00 37.41 4.02
687 904 1.411041 GTTAGGAGCTCCCATACCGT 58.589 55.000 29.54 11.45 37.41 4.83
688 905 1.340568 GTTAGGAGCTCCCATACCGTC 59.659 57.143 29.54 7.70 37.41 4.79
689 906 0.178970 TAGGAGCTCCCATACCGTCC 60.179 60.000 29.54 0.51 37.41 4.79
690 907 1.760875 GGAGCTCCCATACCGTCCA 60.761 63.158 23.19 0.00 34.14 4.02
691 908 1.122019 GGAGCTCCCATACCGTCCAT 61.122 60.000 23.19 0.00 34.14 3.41
692 909 0.318762 GAGCTCCCATACCGTCCATC 59.681 60.000 0.87 0.00 0.00 3.51
693 910 1.006102 GCTCCCATACCGTCCATCG 60.006 63.158 0.00 0.00 39.52 3.84
694 911 1.006102 CTCCCATACCGTCCATCGC 60.006 63.158 0.00 0.00 38.35 4.58
695 912 2.030562 CCCATACCGTCCATCGCC 59.969 66.667 0.00 0.00 38.35 5.54
696 913 2.030562 CCATACCGTCCATCGCCC 59.969 66.667 0.00 0.00 38.35 6.13
697 914 2.507854 CCATACCGTCCATCGCCCT 61.508 63.158 0.00 0.00 38.35 5.19
698 915 1.445942 CATACCGTCCATCGCCCTT 59.554 57.895 0.00 0.00 38.35 3.95
699 916 0.880278 CATACCGTCCATCGCCCTTG 60.880 60.000 0.00 0.00 38.35 3.61
700 917 1.046472 ATACCGTCCATCGCCCTTGA 61.046 55.000 0.00 0.00 38.35 3.02
701 918 1.672854 TACCGTCCATCGCCCTTGAG 61.673 60.000 0.00 0.00 38.35 3.02
702 919 2.579201 CGTCCATCGCCCTTGAGT 59.421 61.111 0.00 0.00 0.00 3.41
703 920 1.079127 CGTCCATCGCCCTTGAGTT 60.079 57.895 0.00 0.00 0.00 3.01
704 921 1.361668 CGTCCATCGCCCTTGAGTTG 61.362 60.000 0.00 0.00 0.00 3.16
710 927 1.597854 CGCCCTTGAGTTGCTGACA 60.598 57.895 0.00 0.00 0.00 3.58
713 930 1.517242 CCCTTGAGTTGCTGACAGAC 58.483 55.000 6.65 0.00 0.00 3.51
720 937 4.702831 TGAGTTGCTGACAGACACAAATA 58.297 39.130 6.65 0.00 0.00 1.40
721 938 5.122519 TGAGTTGCTGACAGACACAAATAA 58.877 37.500 6.65 0.00 0.00 1.40
722 939 5.588246 TGAGTTGCTGACAGACACAAATAAA 59.412 36.000 6.65 0.00 0.00 1.40
723 940 6.262944 TGAGTTGCTGACAGACACAAATAAAT 59.737 34.615 6.65 0.00 0.00 1.40
809 1026 8.312564 GTCTGGTAAATTCTAGACCAACTAGTT 58.687 37.037 1.12 1.12 46.15 2.24
878 1095 2.332654 CCGTTCCCTTTCTTGCGGG 61.333 63.158 0.00 0.00 42.05 6.13
958 1175 3.155167 GAGGAAGCGGTCGGGGAT 61.155 66.667 0.00 0.00 0.00 3.85
1173 1390 1.130054 TCCAGAAGGAGCAGCAGGTT 61.130 55.000 0.00 0.00 39.61 3.50
1195 1412 6.379988 GGTTGATTTCCCCTTGCTAATTCTTA 59.620 38.462 0.00 0.00 0.00 2.10
1229 1446 6.994496 GTGATTGTCTTCTATTGGATGGATCA 59.006 38.462 0.00 0.00 0.00 2.92
1236 1453 3.906218 TCTATTGGATGGATCAGTCTGGG 59.094 47.826 0.00 0.00 0.00 4.45
1240 1457 1.544982 GGATGGATCAGTCTGGGCATG 60.545 57.143 0.00 0.00 0.00 4.06
1250 1467 0.674581 TCTGGGCATGTCGCTTTCTG 60.675 55.000 0.00 0.00 41.91 3.02
1253 1470 2.409870 GGCATGTCGCTTTCTGGGG 61.410 63.158 0.00 0.00 41.91 4.96
1292 1509 2.681976 GCAGTTGCCCACATCTCTACAT 60.682 50.000 0.00 0.00 34.31 2.29
1342 1563 4.503007 GTCGAAATGATGCGTGTATACTGT 59.497 41.667 4.17 0.00 0.00 3.55
1344 1565 4.740205 CGAAATGATGCGTGTATACTGTCT 59.260 41.667 4.17 0.00 0.00 3.41
1355 1576 5.864474 CGTGTATACTGTCTTCAAGAGCTTT 59.136 40.000 4.17 0.00 0.00 3.51
1356 1577 6.034044 CGTGTATACTGTCTTCAAGAGCTTTC 59.966 42.308 4.17 0.00 0.00 2.62
1357 1578 6.034044 GTGTATACTGTCTTCAAGAGCTTTCG 59.966 42.308 4.17 0.00 0.00 3.46
1358 1579 3.460857 ACTGTCTTCAAGAGCTTTCGT 57.539 42.857 0.00 0.00 0.00 3.85
1361 1582 5.357257 ACTGTCTTCAAGAGCTTTCGTTTA 58.643 37.500 0.00 0.00 0.00 2.01
1365 1586 6.982141 TGTCTTCAAGAGCTTTCGTTTAACTA 59.018 34.615 0.00 0.00 0.00 2.24
1366 1587 7.169308 TGTCTTCAAGAGCTTTCGTTTAACTAG 59.831 37.037 0.00 0.00 0.00 2.57
1367 1588 5.840940 TCAAGAGCTTTCGTTTAACTAGC 57.159 39.130 0.00 5.87 0.00 3.42
1390 1611 1.666209 AACTGTGCGTTGGCTTGCTT 61.666 50.000 0.00 0.00 40.82 3.91
1449 1671 7.138736 ACCGACTATTTGTCAACTTCATTTTG 58.861 34.615 0.00 0.00 45.60 2.44
1544 1766 1.838112 TGAGCTATTGTTGCTTGGGG 58.162 50.000 0.00 0.00 41.30 4.96
2007 2236 8.572828 TTACTTCAAATTGTTGCAGTGTTATG 57.427 30.769 2.61 0.00 40.76 1.90
2079 2308 8.786898 TGATTTTTCTTTCCACTCTGTTGATAG 58.213 33.333 0.00 0.00 0.00 2.08
2081 2310 9.793259 ATTTTTCTTTCCACTCTGTTGATAGTA 57.207 29.630 0.00 0.00 0.00 1.82
2128 2360 0.675837 CTGCTTTAGCTGCTGCCTCA 60.676 55.000 13.43 4.53 42.66 3.86
2216 2448 4.709397 CACTTTCACTAGATCCCTGAGACT 59.291 45.833 0.00 0.00 0.00 3.24
2238 2470 5.645497 ACTCAGACAACAAGCTATTCCATTC 59.355 40.000 0.00 0.00 0.00 2.67
2244 2476 3.019564 ACAAGCTATTCCATTCACTGGC 58.980 45.455 0.00 0.00 45.52 4.85
2365 2597 4.843728 GTTCATCTGGGAACATCCTGTAA 58.156 43.478 0.00 0.00 45.07 2.41
2496 2728 1.166531 AAGCCAGGTCTTGTTGTCGC 61.167 55.000 0.00 0.00 0.00 5.19
2523 2757 9.194271 GAGTCTCTTCGTTTTGAGTAATTTAGT 57.806 33.333 0.00 0.00 0.00 2.24
2662 2896 2.476185 GCTACAATCCGTGCATTGTGAC 60.476 50.000 12.56 2.46 44.92 3.67
2663 2897 0.881118 ACAATCCGTGCATTGTGACC 59.119 50.000 2.68 0.00 43.88 4.02
2664 2898 0.179192 CAATCCGTGCATTGTGACCG 60.179 55.000 0.00 0.00 0.00 4.79
2665 2899 0.605319 AATCCGTGCATTGTGACCGT 60.605 50.000 0.00 0.00 0.00 4.83
2666 2900 1.019278 ATCCGTGCATTGTGACCGTC 61.019 55.000 0.00 0.00 0.00 4.79
2667 2901 1.958715 CCGTGCATTGTGACCGTCA 60.959 57.895 0.00 0.00 0.00 4.35
2682 2922 1.468224 CCGTCACTGCTACTGCTACTG 60.468 57.143 0.00 0.00 40.48 2.74
2814 3054 8.571461 TCTGTATTTTCTTTTGATGCATCTCT 57.429 30.769 26.32 0.00 0.00 3.10
2977 3217 3.067180 CCGCCTCATCAAAATATGCAAGT 59.933 43.478 0.00 0.00 0.00 3.16
3048 3298 1.607148 CATCATCATGTGCGCCTTCAT 59.393 47.619 4.18 4.34 0.00 2.57
3125 3389 1.002315 CCCAAGCCAACAAATCCAAGG 59.998 52.381 0.00 0.00 0.00 3.61
3147 3411 1.129251 CTTGTGCACTATTGTCCAGCG 59.871 52.381 19.41 0.00 0.00 5.18
3189 3453 2.079925 GAACCTCATGACTGAAGCCAC 58.920 52.381 0.00 0.00 0.00 5.01
3228 3492 1.784358 TGTATAGGGAAGGGTGGACG 58.216 55.000 0.00 0.00 0.00 4.79
3241 3505 2.027073 TGGACGTCGACATGCTTGC 61.027 57.895 17.16 0.00 0.00 4.01
3243 3507 1.291877 GGACGTCGACATGCTTGCTT 61.292 55.000 17.16 0.00 0.00 3.91
3289 3553 0.745845 GACGGCCTCATTCATGCTGT 60.746 55.000 0.00 0.00 46.73 4.40
3306 3570 3.251729 TGCTGTGAAAGATGTTGAGCTTC 59.748 43.478 0.00 0.00 0.00 3.86
3312 3576 5.008019 GTGAAAGATGTTGAGCTTCTTGTCA 59.992 40.000 0.00 3.24 40.23 3.58
3316 3580 4.391216 AGATGTTGAGCTTCTTGTCAATCG 59.609 41.667 0.00 0.00 35.22 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 57 6.398234 TGGAAAAAGTTCATCGGATTTGAA 57.602 33.333 0.00 0.00 35.25 2.69
37 58 6.398234 TTGGAAAAAGTTCATCGGATTTGA 57.602 33.333 0.00 0.00 35.25 2.69
488 687 1.671850 CGCGAGAACCACTACACCAAT 60.672 52.381 0.00 0.00 0.00 3.16
494 693 1.200948 ACCTAACGCGAGAACCACTAC 59.799 52.381 15.93 0.00 0.00 2.73
667 884 0.680061 CGGTATGGGAGCTCCTAACC 59.320 60.000 31.36 29.29 37.54 2.85
668 885 1.340568 GACGGTATGGGAGCTCCTAAC 59.659 57.143 31.36 23.97 36.20 2.34
669 886 1.700955 GACGGTATGGGAGCTCCTAA 58.299 55.000 31.36 20.51 36.20 2.69
670 887 0.178970 GGACGGTATGGGAGCTCCTA 60.179 60.000 31.36 27.17 36.20 2.94
671 888 1.457831 GGACGGTATGGGAGCTCCT 60.458 63.158 31.36 16.10 36.20 3.69
672 889 1.122019 ATGGACGGTATGGGAGCTCC 61.122 60.000 25.59 25.59 0.00 4.70
673 890 0.318762 GATGGACGGTATGGGAGCTC 59.681 60.000 4.71 4.71 0.00 4.09
674 891 1.464376 CGATGGACGGTATGGGAGCT 61.464 60.000 0.00 0.00 38.46 4.09
675 892 1.006102 CGATGGACGGTATGGGAGC 60.006 63.158 0.00 0.00 38.46 4.70
676 893 1.006102 GCGATGGACGGTATGGGAG 60.006 63.158 0.00 0.00 42.83 4.30
677 894 2.504274 GGCGATGGACGGTATGGGA 61.504 63.158 0.00 0.00 42.83 4.37
678 895 2.030562 GGCGATGGACGGTATGGG 59.969 66.667 0.00 0.00 42.83 4.00
679 896 2.030562 GGGCGATGGACGGTATGG 59.969 66.667 0.00 0.00 42.83 2.74
680 897 0.880278 CAAGGGCGATGGACGGTATG 60.880 60.000 0.00 0.00 42.83 2.39
681 898 1.046472 TCAAGGGCGATGGACGGTAT 61.046 55.000 0.00 0.00 42.83 2.73
682 899 1.672854 CTCAAGGGCGATGGACGGTA 61.673 60.000 0.00 0.00 42.83 4.02
683 900 3.000819 TCAAGGGCGATGGACGGT 61.001 61.111 0.00 0.00 42.83 4.83
684 901 2.202932 CTCAAGGGCGATGGACGG 60.203 66.667 0.00 0.00 42.83 4.79
685 902 1.079127 AACTCAAGGGCGATGGACG 60.079 57.895 0.00 0.00 45.66 4.79
686 903 1.648467 GCAACTCAAGGGCGATGGAC 61.648 60.000 0.00 0.00 0.00 4.02
687 904 1.377202 GCAACTCAAGGGCGATGGA 60.377 57.895 0.00 0.00 0.00 3.41
688 905 1.377725 AGCAACTCAAGGGCGATGG 60.378 57.895 0.00 0.00 0.00 3.51
689 906 0.674581 TCAGCAACTCAAGGGCGATG 60.675 55.000 0.00 0.00 0.00 3.84
690 907 0.674895 GTCAGCAACTCAAGGGCGAT 60.675 55.000 0.00 0.00 0.00 4.58
691 908 1.301716 GTCAGCAACTCAAGGGCGA 60.302 57.895 0.00 0.00 0.00 5.54
692 909 1.572085 CTGTCAGCAACTCAAGGGCG 61.572 60.000 0.00 0.00 0.00 6.13
693 910 0.250467 TCTGTCAGCAACTCAAGGGC 60.250 55.000 0.00 0.00 0.00 5.19
694 911 1.202687 TGTCTGTCAGCAACTCAAGGG 60.203 52.381 0.00 0.00 0.00 3.95
695 912 1.869767 GTGTCTGTCAGCAACTCAAGG 59.130 52.381 0.00 0.00 0.00 3.61
696 913 2.554142 TGTGTCTGTCAGCAACTCAAG 58.446 47.619 0.00 0.00 0.00 3.02
697 914 2.689553 TGTGTCTGTCAGCAACTCAA 57.310 45.000 0.00 0.00 0.00 3.02
698 915 2.689553 TTGTGTCTGTCAGCAACTCA 57.310 45.000 0.00 0.00 0.00 3.41
699 916 5.673337 TTATTTGTGTCTGTCAGCAACTC 57.327 39.130 0.00 0.00 0.00 3.01
700 917 6.639632 ATTTATTTGTGTCTGTCAGCAACT 57.360 33.333 0.00 0.00 0.00 3.16
701 918 6.801862 GGTATTTATTTGTGTCTGTCAGCAAC 59.198 38.462 0.00 0.00 0.00 4.17
702 919 6.714810 AGGTATTTATTTGTGTCTGTCAGCAA 59.285 34.615 0.00 0.00 0.00 3.91
703 920 6.237901 AGGTATTTATTTGTGTCTGTCAGCA 58.762 36.000 0.00 0.00 0.00 4.41
704 921 6.743575 AGGTATTTATTTGTGTCTGTCAGC 57.256 37.500 0.00 0.00 0.00 4.26
710 927 8.522830 CCATTGTGAAGGTATTTATTTGTGTCT 58.477 33.333 0.00 0.00 0.00 3.41
713 930 6.534793 GCCCATTGTGAAGGTATTTATTTGTG 59.465 38.462 0.00 0.00 0.00 3.33
720 937 4.019174 CTGAGCCCATTGTGAAGGTATTT 58.981 43.478 0.00 0.00 0.00 1.40
721 938 3.624777 CTGAGCCCATTGTGAAGGTATT 58.375 45.455 0.00 0.00 0.00 1.89
722 939 2.092212 CCTGAGCCCATTGTGAAGGTAT 60.092 50.000 0.00 0.00 0.00 2.73
723 940 1.281867 CCTGAGCCCATTGTGAAGGTA 59.718 52.381 0.00 0.00 0.00 3.08
809 1026 2.483013 CGGCCCATTTGATCTACGAAGA 60.483 50.000 0.00 0.00 35.80 2.87
878 1095 1.927895 CCTCTGTGTCTCGTATTGGC 58.072 55.000 0.00 0.00 0.00 4.52
1173 1390 9.131791 GTAATAAGAATTAGCAAGGGGAAATCA 57.868 33.333 0.00 0.00 31.76 2.57
1195 1412 4.207891 AGAAGACAATCACAGCGGTAAT 57.792 40.909 0.00 0.00 0.00 1.89
1236 1453 1.675641 ACCCCAGAAAGCGACATGC 60.676 57.895 0.00 0.00 46.98 4.06
1240 1457 0.250513 ATCTCACCCCAGAAAGCGAC 59.749 55.000 0.00 0.00 0.00 5.19
1250 1467 1.067582 CTTACGGCGATCTCACCCC 59.932 63.158 16.62 0.00 0.00 4.95
1253 1470 1.132588 GCATCTTACGGCGATCTCAC 58.867 55.000 16.62 0.00 0.00 3.51
1292 1509 3.009253 TCCTGGAATTAACTAAACGGGCA 59.991 43.478 0.00 0.00 0.00 5.36
1342 1563 6.145696 GCTAGTTAAACGAAAGCTCTTGAAGA 59.854 38.462 0.00 0.00 0.00 2.87
1344 1565 5.756347 TGCTAGTTAAACGAAAGCTCTTGAA 59.244 36.000 0.00 0.00 34.28 2.69
1355 1576 4.304110 CACAGTTCCTGCTAGTTAAACGA 58.696 43.478 0.00 0.00 34.37 3.85
1356 1577 3.120649 GCACAGTTCCTGCTAGTTAAACG 60.121 47.826 0.00 0.00 34.37 3.60
1357 1578 3.120649 CGCACAGTTCCTGCTAGTTAAAC 60.121 47.826 0.00 0.00 34.37 2.01
1358 1579 3.064207 CGCACAGTTCCTGCTAGTTAAA 58.936 45.455 0.00 0.00 34.37 1.52
1361 1582 0.393077 ACGCACAGTTCCTGCTAGTT 59.607 50.000 0.00 0.00 34.37 2.24
1365 1586 1.893808 CCAACGCACAGTTCCTGCT 60.894 57.895 0.00 0.00 42.02 4.24
1366 1587 2.639286 CCAACGCACAGTTCCTGC 59.361 61.111 0.00 0.00 42.02 4.85
1367 1588 1.447317 AAGCCAACGCACAGTTCCTG 61.447 55.000 0.00 0.00 42.02 3.86
1390 1611 2.490509 CAAGACAGCAGCATCAATTCCA 59.509 45.455 0.00 0.00 0.00 3.53
1432 1654 5.108517 GGCAGACAAAATGAAGTTGACAAA 58.891 37.500 0.00 0.00 0.00 2.83
1449 1671 5.007682 TCCTATGGTTTAAGTTTGGCAGAC 58.992 41.667 0.00 0.00 0.00 3.51
2007 2236 6.535508 AGAGTGGAGAAGCGTGAAATATTAAC 59.464 38.462 0.00 0.00 0.00 2.01
2128 2360 4.395625 TCTCGACATAACGGTATGGATCT 58.604 43.478 23.77 3.11 41.37 2.75
2216 2448 5.412594 GTGAATGGAATAGCTTGTTGTCTGA 59.587 40.000 0.00 0.00 0.00 3.27
2238 2470 1.531423 ATCAACTTGCAGAGCCAGTG 58.469 50.000 0.00 0.00 34.75 3.66
2244 2476 7.271511 AGTAGATAAGGAATCAACTTGCAGAG 58.728 38.462 0.00 0.00 37.03 3.35
2296 2528 3.438183 TCTTCTTCCCGTAAGTTAGGCT 58.562 45.455 0.00 0.00 36.51 4.58
2496 2728 6.692232 AATTACTCAAAACGAAGAGACTCG 57.308 37.500 0.00 0.00 44.50 4.18
2523 2757 3.498397 GCAGGAAACTCGAAAGATGAACA 59.502 43.478 0.00 0.00 40.21 3.18
2662 2896 0.811915 AGTAGCAGTAGCAGTGACGG 59.188 55.000 0.00 0.00 45.49 4.79
2663 2897 1.200252 ACAGTAGCAGTAGCAGTGACG 59.800 52.381 0.00 0.00 45.49 4.35
2664 2898 2.600731 CACAGTAGCAGTAGCAGTGAC 58.399 52.381 0.00 0.00 45.49 3.67
2665 2899 1.067565 GCACAGTAGCAGTAGCAGTGA 60.068 52.381 0.00 0.00 45.49 3.41
2666 2900 1.067283 AGCACAGTAGCAGTAGCAGTG 60.067 52.381 0.00 0.00 45.49 3.66
2667 2901 1.261480 AGCACAGTAGCAGTAGCAGT 58.739 50.000 0.00 0.00 45.49 4.40
2669 2903 2.164422 CACTAGCACAGTAGCAGTAGCA 59.836 50.000 0.00 0.00 38.31 3.49
2670 2904 2.164624 ACACTAGCACAGTAGCAGTAGC 59.835 50.000 0.00 0.00 34.98 3.58
2671 2905 4.442375 AACACTAGCACAGTAGCAGTAG 57.558 45.455 0.00 0.00 34.98 2.57
2672 2906 4.321750 GGAAACACTAGCACAGTAGCAGTA 60.322 45.833 0.00 0.00 34.98 2.74
2932 3172 6.627508 CGGTATATGCTAACTGTAGGGGAATC 60.628 46.154 0.00 0.00 0.00 2.52
2977 3217 2.318908 AGGGCTTGAAAATTGTGCTGA 58.681 42.857 0.00 0.00 0.00 4.26
3048 3298 8.821687 TTGTCTGGCAAACACTACTACTAGTGA 61.822 40.741 14.30 0.00 41.98 3.41
3125 3389 1.470098 CTGGACAATAGTGCACAAGGC 59.530 52.381 21.04 7.39 41.46 4.35
3157 3421 0.532573 TGAGGTTCTGATGACGGCTC 59.467 55.000 0.00 0.00 0.00 4.70
3189 3453 4.458397 ACAATGTCATCATGGAGCTAAGG 58.542 43.478 0.00 0.00 34.19 2.69
3228 3492 0.169009 GGGAAAGCAAGCATGTCGAC 59.831 55.000 9.11 9.11 0.00 4.20
3241 3505 2.947448 GCAACTGCCATTAGGGAAAG 57.053 50.000 0.00 0.00 40.01 2.62
3289 3553 5.125356 TGACAAGAAGCTCAACATCTTTCA 58.875 37.500 0.00 0.00 34.14 2.69
3306 3570 3.697045 AGAGGAGAGGTACGATTGACAAG 59.303 47.826 0.00 0.00 0.00 3.16
3312 3576 3.203487 AGAGGAAGAGGAGAGGTACGATT 59.797 47.826 0.00 0.00 0.00 3.34
3316 3580 3.053170 AGGAAGAGGAAGAGGAGAGGTAC 60.053 52.174 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.