Multiple sequence alignment - TraesCS2D01G543200

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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 TraesCS2D01G543200 chr2D 100.000 3746 0 0 1 3746 621160026 621156281 0.000000e+00 6918.0
1 TraesCS2D01G543200 chr2D 92.764 691 47 1 1335 2025 621331818 621331131 0.000000e+00 996.0
2 TraesCS2D01G543200 chr2D 90.590 712 56 9 2 706 526522104 526522811 0.000000e+00 933.0
3 TraesCS2D01G543200 chr2D 89.747 712 61 11 1 706 580020465 580019760 0.000000e+00 900.0
4 TraesCS2D01G543200 chr2D 96.604 530 15 2 2023 2549 621318991 621318462 0.000000e+00 876.0
5 TraesCS2D01G543200 chr2D 92.970 569 35 4 2561 3128 621316842 621316278 0.000000e+00 824.0
6 TraesCS2D01G543200 chr2D 89.003 582 39 19 765 1337 621341659 621341094 0.000000e+00 697.0
7 TraesCS2D01G543200 chr2D 87.500 56 6 1 715 769 95664636 95664581 3.120000e-06 63.9
8 TraesCS2D01G543200 chr2A 91.671 2029 137 14 1102 3128 753013413 753011415 0.000000e+00 2782.0
9 TraesCS2D01G543200 chr2A 87.554 1607 148 12 1104 2697 753064306 753062739 0.000000e+00 1812.0
10 TraesCS2D01G543200 chr2A 76.516 1154 204 43 1172 2290 753084449 753085570 5.430000e-158 568.0
11 TraesCS2D01G543200 chr2A 91.358 405 34 1 3123 3526 589749800 589750204 1.520000e-153 553.0
12 TraesCS2D01G543200 chr2A 83.296 449 47 7 2682 3128 753061986 753061564 4.540000e-104 388.0
13 TraesCS2D01G543200 chr2A 89.333 150 6 3 765 904 753064593 753064444 2.970000e-41 180.0
14 TraesCS2D01G543200 chr2A 88.667 150 7 3 765 904 753015959 753015810 1.380000e-39 174.0
15 TraesCS2D01G543200 chr2A 87.826 115 9 2 893 1003 753015780 753015667 3.040000e-26 130.0
16 TraesCS2D01G543200 chr2A 89.831 59 5 1 712 769 51655148 51655206 1.440000e-09 75.0
17 TraesCS2D01G543200 chr6D 89.918 734 64 8 1 729 8159373 8158645 0.000000e+00 937.0
18 TraesCS2D01G543200 chr7D 89.835 728 65 8 1 722 91741767 91742491 0.000000e+00 926.0
19 TraesCS2D01G543200 chr7D 89.660 706 61 11 1 696 164532697 164531994 0.000000e+00 889.0
20 TraesCS2D01G543200 chr1D 88.402 776 76 10 1 769 354461895 354461127 0.000000e+00 922.0
21 TraesCS2D01G543200 chrUn 91.896 654 50 3 1 651 98134316 98133663 0.000000e+00 911.0
22 TraesCS2D01G543200 chrUn 87.895 380 40 4 2748 3125 23360243 23360618 3.430000e-120 442.0
23 TraesCS2D01G543200 chrUn 92.883 281 16 3 2012 2289 389709619 389709898 4.510000e-109 405.0
24 TraesCS2D01G543200 chrUn 88.424 311 35 1 1700 2010 475540044 475539735 1.270000e-99 374.0
25 TraesCS2D01G543200 chr6B 89.266 736 65 11 1 729 683982447 683981719 0.000000e+00 909.0
26 TraesCS2D01G543200 chr7B 88.736 728 74 7 1 722 563472441 563473166 0.000000e+00 883.0
27 TraesCS2D01G543200 chr7B 89.047 493 48 6 3123 3613 193305880 193306368 1.150000e-169 606.0
28 TraesCS2D01G543200 chr2B 94.030 402 20 1 1104 1505 762074238 762073841 1.150000e-169 606.0
29 TraesCS2D01G543200 chr2B 76.598 970 182 27 1172 2120 762091580 762092525 3.360000e-135 492.0
30 TraesCS2D01G543200 chr2B 91.026 78 2 1 1002 1079 762074308 762074236 2.380000e-17 100.0
31 TraesCS2D01G543200 chr5B 83.163 683 59 29 1 648 539199738 539199077 1.170000e-159 573.0
32 TraesCS2D01G543200 chr5B 90.406 271 17 3 3351 3613 81198471 81198740 7.700000e-92 348.0
33 TraesCS2D01G543200 chr5B 92.105 228 17 1 3130 3356 81197778 81198005 1.680000e-83 320.0
34 TraesCS2D01G543200 chr5B 85.000 60 6 3 712 769 508340868 508340926 1.450000e-04 58.4
35 TraesCS2D01G543200 chr5B 100.000 30 0 0 741 770 427234432 427234403 5.230000e-04 56.5
36 TraesCS2D01G543200 chr1A 90.370 405 38 1 3123 3526 574644837 574645241 7.120000e-147 531.0
37 TraesCS2D01G543200 chr1A 89.975 399 39 1 3129 3526 447163528 447163130 7.170000e-142 514.0
38 TraesCS2D01G543200 chr1A 94.030 134 6 2 3613 3746 447162991 447162860 6.340000e-48 202.0
39 TraesCS2D01G543200 chr1A 94.030 134 7 1 3613 3746 574645380 574645512 6.340000e-48 202.0
40 TraesCS2D01G543200 chr7A 90.493 284 27 0 3243 3526 251251816 251251533 3.530000e-100 375.0
41 TraesCS2D01G543200 chr7A 87.937 315 25 3 3212 3526 625611101 625611402 3.560000e-95 359.0
42 TraesCS2D01G543200 chr7A 96.269 134 4 1 3613 3746 625611544 625611676 6.300000e-53 219.0
43 TraesCS2D01G543200 chr3B 93.617 94 5 1 3653 3746 402467561 402467469 5.050000e-29 139.0
44 TraesCS2D01G543200 chr5A 89.831 59 5 1 712 769 480484723 480484781 1.440000e-09 75.0
45 TraesCS2D01G543200 chr6A 100.000 28 0 0 740 767 3308600 3308627 7.000000e-03 52.8


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 TraesCS2D01G543200 chr2D 621156281 621160026 3745 True 6918.000000 6918 100.000000 1 3746 1 chr2D.!!$R3 3745
1 TraesCS2D01G543200 chr2D 621331131 621331818 687 True 996.000000 996 92.764000 1335 2025 1 chr2D.!!$R4 690
2 TraesCS2D01G543200 chr2D 526522104 526522811 707 False 933.000000 933 90.590000 2 706 1 chr2D.!!$F1 704
3 TraesCS2D01G543200 chr2D 580019760 580020465 705 True 900.000000 900 89.747000 1 706 1 chr2D.!!$R2 705
4 TraesCS2D01G543200 chr2D 621316278 621318991 2713 True 850.000000 876 94.787000 2023 3128 2 chr2D.!!$R6 1105
5 TraesCS2D01G543200 chr2D 621341094 621341659 565 True 697.000000 697 89.003000 765 1337 1 chr2D.!!$R5 572
6 TraesCS2D01G543200 chr2A 753011415 753015959 4544 True 1028.666667 2782 89.388000 765 3128 3 chr2A.!!$R1 2363
7 TraesCS2D01G543200 chr2A 753061564 753064593 3029 True 793.333333 1812 86.727667 765 3128 3 chr2A.!!$R2 2363
8 TraesCS2D01G543200 chr2A 753084449 753085570 1121 False 568.000000 568 76.516000 1172 2290 1 chr2A.!!$F3 1118
9 TraesCS2D01G543200 chr6D 8158645 8159373 728 True 937.000000 937 89.918000 1 729 1 chr6D.!!$R1 728
10 TraesCS2D01G543200 chr7D 91741767 91742491 724 False 926.000000 926 89.835000 1 722 1 chr7D.!!$F1 721
11 TraesCS2D01G543200 chr7D 164531994 164532697 703 True 889.000000 889 89.660000 1 696 1 chr7D.!!$R1 695
12 TraesCS2D01G543200 chr1D 354461127 354461895 768 True 922.000000 922 88.402000 1 769 1 chr1D.!!$R1 768
13 TraesCS2D01G543200 chrUn 98133663 98134316 653 True 911.000000 911 91.896000 1 651 1 chrUn.!!$R1 650
14 TraesCS2D01G543200 chr6B 683981719 683982447 728 True 909.000000 909 89.266000 1 729 1 chr6B.!!$R1 728
15 TraesCS2D01G543200 chr7B 563472441 563473166 725 False 883.000000 883 88.736000 1 722 1 chr7B.!!$F2 721
16 TraesCS2D01G543200 chr2B 762091580 762092525 945 False 492.000000 492 76.598000 1172 2120 1 chr2B.!!$F1 948
17 TraesCS2D01G543200 chr5B 539199077 539199738 661 True 573.000000 573 83.163000 1 648 1 chr5B.!!$R2 647
18 TraesCS2D01G543200 chr5B 81197778 81198740 962 False 334.000000 348 91.255500 3130 3613 2 chr5B.!!$F2 483
19 TraesCS2D01G543200 chr1A 574644837 574645512 675 False 366.500000 531 92.200000 3123 3746 2 chr1A.!!$F1 623
20 TraesCS2D01G543200 chr1A 447162860 447163528 668 True 358.000000 514 92.002500 3129 3746 2 chr1A.!!$R1 617
21 TraesCS2D01G543200 chr7A 625611101 625611676 575 False 289.000000 359 92.103000 3212 3746 2 chr7A.!!$F1 534

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
732 779 0.322636 TCCCCAAGCGGCGATTTTTA 60.323 50.0 12.98 0.0 0.0 1.52 F
1043 1166 0.181824 ACACCATAATACACCCGGCC 59.818 55.0 0.00 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2324 4650 0.322546 AGTTCAAACCCATCTCCGCC 60.323 55.0 0.0 0.0 0.00 6.13 R
3037 7749 0.258774 CCGGAATGGTTTCATCCCCT 59.741 55.0 0.0 0.0 33.23 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
84 85 1.939934 CTCAAACGTTGTGCCAAGAGA 59.060 47.619 0.00 0.00 0.00 3.10
89 90 0.588252 CGTTGTGCCAAGAGACAAGG 59.412 55.000 0.00 0.00 32.81 3.61
159 160 1.824230 GGCATTTGGTGTGCTCCAATA 59.176 47.619 6.56 0.31 45.30 1.90
172 173 3.561310 TGCTCCAATATCGATTTGCTGTC 59.439 43.478 1.71 0.00 0.00 3.51
220 222 3.684788 CGAAAGATCAAACGTGGGAGATT 59.315 43.478 0.00 0.00 0.00 2.40
288 290 3.496130 CAGTAAGAGCCAGTGTTTGACAG 59.504 47.826 0.00 0.00 0.00 3.51
324 326 4.943373 GGGTCCTCTTGCCCAAAA 57.057 55.556 0.00 0.00 44.23 2.44
372 374 1.137513 GCGTACCTCAATATGCGTCC 58.862 55.000 0.00 0.00 0.00 4.79
435 437 2.763039 TCTGATGGAGCACCTATGGAA 58.237 47.619 0.71 0.00 37.04 3.53
463 465 1.493950 GCGACGCCTAGCTCTACGTA 61.494 60.000 9.14 0.00 39.16 3.57
472 474 4.918583 GCCTAGCTCTACGTATGATGAAAC 59.081 45.833 0.00 0.00 0.00 2.78
647 692 1.419381 ACCGAAAGTGGGCCAAAAAT 58.581 45.000 8.40 0.00 0.00 1.82
677 723 0.801836 GCGTCGAAAATGGGCCAATG 60.802 55.000 11.89 0.00 0.00 2.82
729 776 2.750237 GTCCCCAAGCGGCGATTT 60.750 61.111 12.98 0.04 0.00 2.17
730 777 2.034999 TCCCCAAGCGGCGATTTT 59.965 55.556 12.98 0.00 0.00 1.82
731 778 1.605165 TCCCCAAGCGGCGATTTTT 60.605 52.632 12.98 0.00 0.00 1.94
732 779 0.322636 TCCCCAAGCGGCGATTTTTA 60.323 50.000 12.98 0.00 0.00 1.52
734 781 1.535860 CCCCAAGCGGCGATTTTTATG 60.536 52.381 12.98 0.00 0.00 1.90
735 782 1.199624 CCAAGCGGCGATTTTTATGC 58.800 50.000 12.98 0.00 0.00 3.14
736 783 1.199624 CAAGCGGCGATTTTTATGCC 58.800 50.000 12.98 0.00 45.39 4.40
737 784 1.102978 AAGCGGCGATTTTTATGCCT 58.897 45.000 12.98 0.00 46.67 4.75
738 785 1.961793 AGCGGCGATTTTTATGCCTA 58.038 45.000 12.98 0.00 46.67 3.93
740 787 1.602377 GCGGCGATTTTTATGCCTACT 59.398 47.619 12.98 0.00 46.67 2.57
741 788 2.602217 GCGGCGATTTTTATGCCTACTG 60.602 50.000 12.98 0.00 46.67 2.74
742 789 2.032030 CGGCGATTTTTATGCCTACTGG 60.032 50.000 0.00 0.00 46.67 4.00
743 790 3.211045 GGCGATTTTTATGCCTACTGGA 58.789 45.455 0.00 0.00 45.40 3.86
744 791 3.251004 GGCGATTTTTATGCCTACTGGAG 59.749 47.826 0.00 0.00 45.40 3.86
799 846 3.547249 GACGACGGCAGGTTCGACA 62.547 63.158 0.00 0.00 0.00 4.35
801 848 2.338984 GACGGCAGGTTCGACACT 59.661 61.111 0.00 0.00 0.00 3.55
893 950 1.937546 GAGGGGCGCAAATCACTTGG 61.938 60.000 10.83 0.00 35.38 3.61
904 1001 4.751098 GCAAATCACTTGGCTTGATTTTGA 59.249 37.500 15.24 0.00 46.76 2.69
1003 1110 5.221303 CCGATGATTTACATGGAAGGCAAAT 60.221 40.000 0.00 0.00 39.56 2.32
1013 1130 1.527311 GGAAGGCAAATATCGAGTCGC 59.473 52.381 7.92 0.00 0.00 5.19
1030 1153 3.388024 AGTCGCTGATAATACCACACCAT 59.612 43.478 0.00 0.00 0.00 3.55
1032 1155 5.069914 AGTCGCTGATAATACCACACCATAA 59.930 40.000 0.00 0.00 0.00 1.90
1033 1156 5.932303 GTCGCTGATAATACCACACCATAAT 59.068 40.000 0.00 0.00 0.00 1.28
1034 1157 7.039293 AGTCGCTGATAATACCACACCATAATA 60.039 37.037 0.00 0.00 0.00 0.98
1035 1158 7.063074 GTCGCTGATAATACCACACCATAATAC 59.937 40.741 0.00 0.00 0.00 1.89
1037 1160 7.148639 CGCTGATAATACCACACCATAATACAC 60.149 40.741 0.00 0.00 0.00 2.90
1038 1161 7.119262 GCTGATAATACCACACCATAATACACC 59.881 40.741 0.00 0.00 0.00 4.16
1040 1163 2.702592 ACCACACCATAATACACCCG 57.297 50.000 0.00 0.00 0.00 5.28
1041 1164 1.210967 ACCACACCATAATACACCCGG 59.789 52.381 0.00 0.00 0.00 5.73
1042 1165 1.305201 CACACCATAATACACCCGGC 58.695 55.000 0.00 0.00 0.00 6.13
1043 1166 0.181824 ACACCATAATACACCCGGCC 59.818 55.000 0.00 0.00 0.00 6.13
1044 1167 0.536460 CACCATAATACACCCGGCCC 60.536 60.000 0.00 0.00 0.00 5.80
1045 1168 1.302192 CCATAATACACCCGGCCCG 60.302 63.158 0.00 0.00 0.00 6.13
1047 1170 3.186656 ATAATACACCCGGCCCGGC 62.187 63.158 19.21 0.00 46.86 6.13
1098 3392 8.991275 AGCGGTAATATATACTACTCCTAGAGT 58.009 37.037 2.38 2.38 45.54 3.24
1111 3405 6.745794 ACTCCTAGAGTACTAGTACCGATT 57.254 41.667 25.97 10.44 41.51 3.34
1327 3622 0.251341 GGCAACTCCACCACCTCAAT 60.251 55.000 0.00 0.00 34.01 2.57
1385 3684 3.379445 TGGCCGTCTTCCTCGTCC 61.379 66.667 0.00 0.00 0.00 4.79
1647 3953 1.183030 TTCATCGACGTGGAGGTGGT 61.183 55.000 11.92 0.00 0.00 4.16
1676 3982 2.185310 ATTGCCGGCGAAGGTCTTCT 62.185 55.000 22.97 0.00 37.44 2.85
1677 3983 2.047179 GCCGGCGAAGGTCTTCTT 60.047 61.111 12.58 0.00 37.44 2.52
1889 4204 1.235989 AGGGACTGGGTGTCTGTCA 59.764 57.895 0.00 0.00 44.74 3.58
2014 4335 2.668550 GACCACGACAACCCTGCC 60.669 66.667 0.00 0.00 0.00 4.85
2121 4442 1.550524 CCACCTCCGACTGATCAAGAA 59.449 52.381 0.00 0.00 0.00 2.52
2202 4523 1.600023 GACGGGTTGAAACACCATCA 58.400 50.000 0.00 0.00 38.79 3.07
2219 4540 4.643387 ACAAGGTGCCCGCCAGAC 62.643 66.667 0.17 0.00 0.00 3.51
2220 4541 4.335647 CAAGGTGCCCGCCAGACT 62.336 66.667 0.17 0.00 0.00 3.24
2234 4559 1.067142 CCAGACTCGAAATCGTGGGAA 60.067 52.381 9.35 0.00 40.80 3.97
2240 4565 3.071479 CTCGAAATCGTGGGAAAAAGGA 58.929 45.455 2.41 0.00 40.80 3.36
2477 4804 5.968167 TGTCCAATAAGTATGGTAAGTCCCT 59.032 40.000 0.00 0.00 39.09 4.20
2486 4813 6.579865 AGTATGGTAAGTCCCTACATTTTCG 58.420 40.000 0.00 0.00 38.98 3.46
2922 7634 2.914097 GCACTTGGGCTGTTGGCT 60.914 61.111 0.00 0.00 41.46 4.75
2941 7653 4.148825 GGGCAGGCGATGACGAGT 62.149 66.667 0.00 0.00 38.10 4.18
2959 7671 4.703575 ACGAGTAGTAGTTAGGCATGACAA 59.296 41.667 0.00 0.00 0.00 3.18
2961 7673 4.995124 AGTAGTAGTTAGGCATGACAACG 58.005 43.478 0.00 0.00 0.00 4.10
2965 7677 3.895232 AGTTAGGCATGACAACGATCT 57.105 42.857 0.00 0.00 0.00 2.75
2983 7695 0.518636 CTTGACCTTCATGCCACACG 59.481 55.000 0.00 0.00 0.00 4.49
3006 7718 2.939640 GCAATGGCGAGAGGGAAGTTAA 60.940 50.000 0.00 0.00 0.00 2.01
3015 7727 5.163844 GCGAGAGGGAAGTTAAAGATGAAAC 60.164 44.000 0.00 0.00 0.00 2.78
3017 7729 6.595716 CGAGAGGGAAGTTAAAGATGAAACAT 59.404 38.462 0.00 0.00 0.00 2.71
3024 7736 5.313712 AGTTAAAGATGAAACATCGGGTGT 58.686 37.500 0.00 0.00 44.84 4.16
3037 7749 4.081142 ACATCGGGTGTCTGTGATAATGAA 60.081 41.667 0.00 0.00 35.77 2.57
3041 7753 3.545703 GGTGTCTGTGATAATGAAGGGG 58.454 50.000 0.00 0.00 0.00 4.79
3046 7758 5.191522 TGTCTGTGATAATGAAGGGGATGAA 59.808 40.000 0.00 0.00 0.00 2.57
3048 7760 6.038714 GTCTGTGATAATGAAGGGGATGAAAC 59.961 42.308 0.00 0.00 0.00 2.78
3049 7761 5.200483 TGTGATAATGAAGGGGATGAAACC 58.800 41.667 0.00 0.00 0.00 3.27
3055 7767 2.024414 GAAGGGGATGAAACCATTCCG 58.976 52.381 0.00 0.00 41.57 4.30
3059 7771 1.064685 GGGATGAAACCATTCCGGAGT 60.065 52.381 3.34 0.00 38.63 3.85
3076 7788 2.615747 GGAGTTGAGGGTGGCTTCTTAC 60.616 54.545 0.00 0.00 0.00 2.34
3080 7792 0.108281 GAGGGTGGCTTCTTACGGTC 60.108 60.000 0.00 0.00 0.00 4.79
3084 7796 2.263540 GGCTTCTTACGGTCGGCA 59.736 61.111 0.00 0.00 0.00 5.69
3151 7864 2.099756 ACACGATCTCATCAAGCGATCA 59.900 45.455 0.00 0.00 38.16 2.92
3186 7900 4.838152 CCCAGGCACCCACGATCG 62.838 72.222 14.88 14.88 0.00 3.69
3199 7913 1.340248 CACGATCGCCACCTACCTATT 59.660 52.381 16.60 0.00 0.00 1.73
3266 7980 3.941188 CACACCAGTCCGTGCCCT 61.941 66.667 0.00 0.00 37.25 5.19
3267 7981 3.941188 ACACCAGTCCGTGCCCTG 61.941 66.667 0.00 0.00 37.25 4.45
3287 8001 2.045926 GCTCGACACCCTTGCCAT 60.046 61.111 0.00 0.00 0.00 4.40
3327 8041 1.221840 CCCTGTTGATCCACTCCGG 59.778 63.158 0.00 0.00 0.00 5.14
3391 8575 0.321564 CGTGTGCTTCCCCATCTCAA 60.322 55.000 0.00 0.00 0.00 3.02
3403 8587 3.412386 CCCATCTCAACGAACTTCCTTT 58.588 45.455 0.00 0.00 0.00 3.11
3496 8680 2.343163 CTAGAAGTGAGGCGGCGAGG 62.343 65.000 12.98 0.00 0.00 4.63
3543 8727 2.892425 CGGAATCCGGTGCTCAGC 60.892 66.667 14.91 0.00 44.15 4.26
3544 8728 2.514824 GGAATCCGGTGCTCAGCC 60.515 66.667 0.00 0.00 0.00 4.85
3660 8983 2.124193 TGTTGCTGCTGGTGCTGT 60.124 55.556 0.00 0.00 39.81 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 0.178990 GGCAAAGTGGGACTCCTTGT 60.179 55.000 0.00 0.00 0.00 3.16
89 90 0.178990 ACCTTGGCAAAGTGGGACTC 60.179 55.000 9.94 0.00 0.00 3.36
159 160 0.806102 CCGGACGACAGCAAATCGAT 60.806 55.000 0.00 0.00 42.25 3.59
288 290 2.420129 CCCTGCCTGTAGTATGGTTCAC 60.420 54.545 0.00 0.00 0.00 3.18
323 325 0.179045 GCCGGTAGCTGGTGATCATT 60.179 55.000 1.90 0.00 38.99 2.57
324 326 1.337384 TGCCGGTAGCTGGTGATCAT 61.337 55.000 1.90 0.00 44.23 2.45
355 357 1.338973 TCCGGACGCATATTGAGGTAC 59.661 52.381 0.00 0.00 0.00 3.34
384 386 1.462731 TTGTTGATGCACCTGTGGGC 61.463 55.000 0.00 0.00 35.63 5.36
564 605 2.032799 TGGTTCAGCGTGAATTGTCAAC 59.967 45.455 4.21 0.00 38.79 3.18
569 610 0.725784 GCGTGGTTCAGCGTGAATTG 60.726 55.000 4.21 0.00 38.79 2.32
624 667 2.296073 TTGGCCCACTTTCGGTAAAT 57.704 45.000 0.00 0.00 0.00 1.40
661 707 0.808125 CGACATTGGCCCATTTTCGA 59.192 50.000 8.14 0.00 0.00 3.71
722 769 3.211045 TCCAGTAGGCATAAAAATCGCC 58.789 45.455 0.00 0.00 46.62 5.54
723 770 3.251004 CCTCCAGTAGGCATAAAAATCGC 59.749 47.826 0.00 0.00 38.97 4.58
724 771 3.815401 CCCTCCAGTAGGCATAAAAATCG 59.185 47.826 0.00 0.00 45.03 3.34
735 782 2.584608 CGTTGGCCCTCCAGTAGG 59.415 66.667 0.00 0.00 44.53 3.18
736 783 2.584608 CCGTTGGCCCTCCAGTAG 59.415 66.667 0.00 0.00 44.53 2.57
737 784 3.712907 GCCGTTGGCCCTCCAGTA 61.713 66.667 0.00 0.00 44.06 2.74
799 846 2.591072 CCCTCAGCAGCCACTCAGT 61.591 63.158 0.00 0.00 0.00 3.41
801 848 2.527624 ACCCTCAGCAGCCACTCA 60.528 61.111 0.00 0.00 0.00 3.41
893 950 5.095490 CGGTATGGAAAGTCAAAATCAAGC 58.905 41.667 0.00 0.00 0.00 4.01
904 1001 2.552315 CACAAAGCACGGTATGGAAAGT 59.448 45.455 0.00 0.00 0.00 2.66
1003 1110 4.758165 TGTGGTATTATCAGCGACTCGATA 59.242 41.667 1.63 0.00 0.00 2.92
1013 1130 7.606456 GGGTGTATTATGGTGTGGTATTATCAG 59.394 40.741 0.00 0.00 0.00 2.90
1043 1166 2.290071 ACTGAAATATATTCCCGGCCGG 60.290 50.000 37.99 37.99 0.00 6.13
1044 1167 3.053831 ACTGAAATATATTCCCGGCCG 57.946 47.619 21.04 21.04 0.00 6.13
1045 1168 5.161943 AGTACTGAAATATATTCCCGGCC 57.838 43.478 0.00 0.00 0.00 6.13
1047 1170 9.587772 CTATTGAGTACTGAAATATATTCCCGG 57.412 37.037 0.00 0.00 0.00 5.73
1048 1171 9.088512 GCTATTGAGTACTGAAATATATTCCCG 57.911 37.037 0.00 0.00 0.00 5.14
1049 1172 9.088512 CGCTATTGAGTACTGAAATATATTCCC 57.911 37.037 0.00 0.00 0.00 3.97
1050 1173 9.088512 CCGCTATTGAGTACTGAAATATATTCC 57.911 37.037 0.00 0.00 0.00 3.01
1051 1174 9.640963 ACCGCTATTGAGTACTGAAATATATTC 57.359 33.333 0.00 0.00 0.00 1.75
1085 3379 6.369629 TCGGTACTAGTACTCTAGGAGTAGT 58.630 44.000 27.71 13.12 44.42 2.73
1086 3380 6.892658 TCGGTACTAGTACTCTAGGAGTAG 57.107 45.833 27.71 2.96 44.42 2.57
1087 3381 7.847711 AATCGGTACTAGTACTCTAGGAGTA 57.152 40.000 27.71 0.00 45.60 2.59
1088 3382 6.745794 AATCGGTACTAGTACTCTAGGAGT 57.254 41.667 27.71 15.53 45.60 3.85
1089 3383 6.650390 GGAAATCGGTACTAGTACTCTAGGAG 59.350 46.154 27.71 13.21 45.60 3.69
1090 3384 6.100279 TGGAAATCGGTACTAGTACTCTAGGA 59.900 42.308 27.71 18.25 45.60 2.94
1091 3385 6.294473 TGGAAATCGGTACTAGTACTCTAGG 58.706 44.000 27.71 14.56 45.60 3.02
1092 3386 7.518052 CGTTGGAAATCGGTACTAGTACTCTAG 60.518 44.444 27.71 17.95 46.43 2.43
1093 3387 6.258727 CGTTGGAAATCGGTACTAGTACTCTA 59.741 42.308 27.71 14.86 36.36 2.43
1094 3388 5.065731 CGTTGGAAATCGGTACTAGTACTCT 59.934 44.000 27.71 13.06 36.36 3.24
1095 3389 5.269313 CGTTGGAAATCGGTACTAGTACTC 58.731 45.833 27.71 18.30 36.36 2.59
1096 3390 4.096984 CCGTTGGAAATCGGTACTAGTACT 59.903 45.833 27.71 11.54 41.58 2.73
1097 3391 4.354587 CCGTTGGAAATCGGTACTAGTAC 58.645 47.826 22.53 22.53 41.58 2.73
1098 3392 4.637483 CCGTTGGAAATCGGTACTAGTA 57.363 45.455 0.00 0.00 41.58 1.82
1099 3393 3.515330 CCGTTGGAAATCGGTACTAGT 57.485 47.619 0.00 0.00 41.58 2.57
1200 3495 3.668226 CGTCATGGAATCTATCGTCTCGG 60.668 52.174 0.00 0.00 0.00 4.63
1520 3820 2.359975 CCTTCCGTTGCCCCAGAC 60.360 66.667 0.00 0.00 0.00 3.51
1529 3829 2.653087 GGACGTAGCCCCTTCCGTT 61.653 63.158 0.00 0.00 33.03 4.44
1647 3953 1.083489 CGCCGGCAATTTTCTCACTA 58.917 50.000 28.98 0.00 0.00 2.74
1696 4002 4.400961 GCCACTGGCTTCGAGGCT 62.401 66.667 19.65 0.00 46.69 4.58
1714 4029 2.818274 GACGTGCCGATTGTCCCC 60.818 66.667 0.00 0.00 0.00 4.81
1885 4200 3.822192 CCGCGACCGAGGATGACA 61.822 66.667 8.23 0.00 37.24 3.58
2014 4335 4.047125 AAGCACCGGGACCCATGG 62.047 66.667 12.15 4.14 0.00 3.66
2219 4540 3.071479 TCCTTTTTCCCACGATTTCGAG 58.929 45.455 7.01 0.00 43.02 4.04
2220 4541 3.128852 TCCTTTTTCCCACGATTTCGA 57.871 42.857 7.01 0.00 43.02 3.71
2234 4559 4.383552 CCTCGTCTCTTCATCCATCCTTTT 60.384 45.833 0.00 0.00 0.00 2.27
2240 4565 2.461300 TCCCTCGTCTCTTCATCCAT 57.539 50.000 0.00 0.00 0.00 3.41
2273 4598 1.770294 AGCTAGTACCTGAGGCTCAC 58.230 55.000 14.43 3.68 0.00 3.51
2324 4650 0.322546 AGTTCAAACCCATCTCCGCC 60.323 55.000 0.00 0.00 0.00 6.13
2477 4804 5.182487 TGAAATAGAGGCAGCGAAAATGTA 58.818 37.500 0.00 0.00 0.00 2.29
2486 4813 1.398390 CGGTGTTGAAATAGAGGCAGC 59.602 52.381 0.00 0.00 0.00 5.25
2670 6612 1.330234 TGGTTGCATGCATGTTGTCT 58.670 45.000 26.79 0.00 0.00 3.41
2713 7423 9.863650 ACTAGTAACTGTATATGTGTATGGTCT 57.136 33.333 0.00 0.00 0.00 3.85
2934 7646 4.334759 GTCATGCCTAACTACTACTCGTCA 59.665 45.833 0.00 0.00 0.00 4.35
2938 7650 5.035443 CGTTGTCATGCCTAACTACTACTC 58.965 45.833 0.00 0.00 0.00 2.59
2941 7653 5.593095 AGATCGTTGTCATGCCTAACTACTA 59.407 40.000 0.00 0.00 0.00 1.82
2959 7671 1.278985 TGGCATGAAGGTCAAGATCGT 59.721 47.619 0.00 0.00 0.00 3.73
2961 7673 2.421424 GTGTGGCATGAAGGTCAAGATC 59.579 50.000 0.00 0.00 0.00 2.75
2965 7677 1.514678 GCGTGTGGCATGAAGGTCAA 61.515 55.000 0.00 0.00 42.87 3.18
2996 7708 5.648092 CCGATGTTTCATCTTTAACTTCCCT 59.352 40.000 7.89 0.00 0.00 4.20
2997 7709 5.163652 CCCGATGTTTCATCTTTAACTTCCC 60.164 44.000 7.89 0.00 0.00 3.97
3006 7718 3.244561 ACAGACACCCGATGTTTCATCTT 60.245 43.478 7.89 0.00 43.56 2.40
3015 7727 4.058721 TCATTATCACAGACACCCGATG 57.941 45.455 0.00 0.00 0.00 3.84
3017 7729 3.118775 CCTTCATTATCACAGACACCCGA 60.119 47.826 0.00 0.00 0.00 5.14
3024 7736 5.974156 TTCATCCCCTTCATTATCACAGA 57.026 39.130 0.00 0.00 0.00 3.41
3037 7749 0.258774 CCGGAATGGTTTCATCCCCT 59.741 55.000 0.00 0.00 33.23 4.79
3041 7753 3.343617 TCAACTCCGGAATGGTTTCATC 58.656 45.455 5.23 0.00 39.52 2.92
3046 7758 0.328258 CCCTCAACTCCGGAATGGTT 59.672 55.000 5.23 3.26 39.52 3.67
3048 7760 0.392998 CACCCTCAACTCCGGAATGG 60.393 60.000 5.23 0.00 40.09 3.16
3049 7761 0.392998 CCACCCTCAACTCCGGAATG 60.393 60.000 5.23 8.19 0.00 2.67
3055 7767 0.402121 AAGAAGCCACCCTCAACTCC 59.598 55.000 0.00 0.00 0.00 3.85
3059 7771 0.323629 CCGTAAGAAGCCACCCTCAA 59.676 55.000 0.00 0.00 43.02 3.02
3076 7788 0.724453 CGAAACATGTTTGCCGACCG 60.724 55.000 27.85 18.81 32.11 4.79
3080 7792 0.386731 GTCCCGAAACATGTTTGCCG 60.387 55.000 27.85 23.25 32.11 5.69
3084 7796 6.754193 ACAATATTTGTCCCGAAACATGTTT 58.246 32.000 23.49 23.49 40.56 2.83
3151 7864 1.147600 GTGGGTGGGTTTGACGAGT 59.852 57.895 0.00 0.00 0.00 4.18
3186 7900 0.874607 CGACGCAATAGGTAGGTGGC 60.875 60.000 0.00 0.00 0.00 5.01
3252 7966 2.847234 TTCAGGGCACGGACTGGT 60.847 61.111 0.00 0.00 35.47 4.00
3266 7980 1.301716 GCAAGGGTGTCGAGCTTCA 60.302 57.895 0.00 0.00 0.00 3.02
3267 7981 2.035442 GGCAAGGGTGTCGAGCTTC 61.035 63.158 0.00 0.00 0.00 3.86
3287 8001 2.212794 GACCTCGACCCAGGGAGAGA 62.213 65.000 27.01 16.11 37.96 3.10
3374 8558 0.321564 CGTTGAGATGGGGAAGCACA 60.322 55.000 0.00 0.00 0.00 4.57
3391 8575 1.226746 CGCCTGAAAAGGAAGTTCGT 58.773 50.000 0.00 0.00 0.00 3.85
3403 8587 2.264480 CCATCACGACCGCCTGAA 59.736 61.111 0.00 0.00 0.00 3.02
3524 8708 4.467084 TGAGCACCGGATTCCGCC 62.467 66.667 19.80 9.68 46.86 6.13
3525 8709 2.892425 CTGAGCACCGGATTCCGC 60.892 66.667 19.80 6.27 46.86 5.54
3527 8711 2.514824 GGCTGAGCACCGGATTCC 60.515 66.667 9.46 0.00 0.00 3.01
3642 8965 2.191513 ACAGCACCAGCAGCAACAG 61.192 57.895 0.00 0.00 45.49 3.16


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

AutoCloner maintained by Alex Coulton.