Multiple sequence alignment - TraesCS5B01G461200

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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 TraesCS5B01G461200 chr5B 100.000 3729 0 0 1 3729 636927525 636931253 0.000000e+00 6887.0
1 TraesCS5B01G461200 chr5B 85.185 945 66 19 2523 3419 654086253 654085335 0.000000e+00 902.0
2 TraesCS5B01G461200 chr5B 84.908 709 61 17 2726 3391 600120725 600120020 0.000000e+00 675.0
3 TraesCS5B01G461200 chr5B 94.928 276 14 0 2252 2527 654091878 654091603 2.060000e-117 433.0
4 TraesCS5B01G461200 chr5B 76.682 669 138 14 1497 2162 578826642 578827295 4.580000e-94 355.0
5 TraesCS5B01G461200 chr5D 90.767 2437 158 28 1336 3729 506167159 506169571 0.000000e+00 3192.0
6 TraesCS5B01G461200 chr5D 93.137 816 54 2 1381 2195 506210049 506210863 0.000000e+00 1195.0
7 TraesCS5B01G461200 chr5D 88.644 951 75 7 2191 3115 506210944 506211887 0.000000e+00 1127.0
8 TraesCS5B01G461200 chr5D 91.124 845 48 16 50 886 506164803 506165628 0.000000e+00 1120.0
9 TraesCS5B01G461200 chr5D 88.641 449 41 9 3164 3605 506212316 506212761 4.240000e-149 538.0
10 TraesCS5B01G461200 chr5D 85.227 440 43 10 50 475 506207295 506207726 2.060000e-117 433.0
11 TraesCS5B01G461200 chr5D 77.539 512 53 27 884 1374 506208399 506208869 6.180000e-63 252.0
12 TraesCS5B01G461200 chr4A 84.318 829 117 10 1381 2200 531105350 531104526 0.000000e+00 798.0
13 TraesCS5B01G461200 chr4A 86.667 675 71 11 2204 2871 531104131 531103469 0.000000e+00 730.0
14 TraesCS5B01G461200 chr4A 84.160 625 94 3 1571 2191 698310715 698311338 5.330000e-168 601.0
15 TraesCS5B01G461200 chr4A 83.752 597 82 5 1571 2164 698491774 698492358 5.440000e-153 551.0
16 TraesCS5B01G461200 chr4A 86.842 76 5 3 2 75 98531861 98531933 3.090000e-11 80.5
17 TraesCS5B01G461200 chr5A 85.661 802 64 18 2557 3315 633978802 633979595 0.000000e+00 797.0
18 TraesCS5B01G461200 chr5A 90.204 245 13 5 3491 3729 633979593 633979832 3.620000e-80 309.0
19 TraesCS5B01G461200 chr5A 92.188 64 3 2 2 64 658704432 658704494 5.130000e-14 89.8
20 TraesCS5B01G461200 chr4B 85.279 754 107 2 1440 2191 95710291 95709540 0.000000e+00 774.0
21 TraesCS5B01G461200 chr4B 87.202 672 77 6 2207 2871 95709080 95708411 0.000000e+00 756.0
22 TraesCS5B01G461200 chr2D 84.282 808 109 8 1381 2187 114539837 114539047 0.000000e+00 773.0
23 TraesCS5B01G461200 chr2D 85.905 525 64 6 2204 2723 114538616 114538097 5.440000e-153 551.0
24 TraesCS5B01G461200 chr2D 73.126 707 156 27 2023 2712 476849210 476849899 4.850000e-54 222.0
25 TraesCS5B01G461200 chr2D 74.225 516 120 11 2207 2717 476913703 476914210 1.760000e-48 204.0
26 TraesCS5B01G461200 chr2D 87.324 71 9 0 2 72 422712445 422712375 8.580000e-12 82.4
27 TraesCS5B01G461200 chr2A 82.797 715 117 5 1477 2187 115788016 115787304 5.250000e-178 634.0
28 TraesCS5B01G461200 chr2A 74.455 505 99 20 2223 2717 619239156 619239640 1.370000e-44 191.0
29 TraesCS5B01G461200 chr7D 84.076 628 97 1 1571 2195 30395349 30395976 1.480000e-168 603.0
30 TraesCS5B01G461200 chr7D 91.045 67 4 2 2 67 566815269 566815204 5.130000e-14 89.8
31 TraesCS5B01G461200 chr7B 79.103 847 129 32 2870 3688 652131184 652132010 1.180000e-149 540.0
32 TraesCS5B01G461200 chr2B 82.392 602 97 6 1445 2040 165072364 165071766 1.990000e-142 516.0
33 TraesCS5B01G461200 chr2B 75.767 326 75 4 2207 2530 558284034 558284357 1.070000e-35 161.0
34 TraesCS5B01G461200 chr6B 91.935 62 5 0 2 63 73523994 73523933 1.850000e-13 87.9
35 TraesCS5B01G461200 chr6B 91.045 67 2 4 2 67 415849620 415849683 1.850000e-13 87.9
36 TraesCS5B01G461200 chr6A 92.063 63 4 1 2 64 39698993 39698932 1.850000e-13 87.9
37 TraesCS5B01G461200 chr6A 89.855 69 4 3 2 70 217117191 217117256 6.640000e-13 86.1
38 TraesCS5B01G461200 chr3A 91.935 62 5 0 2 63 46585873 46585812 1.850000e-13 87.9
39 TraesCS5B01G461200 chr3D 95.122 41 2 0 2229 2269 45403556 45403516 8.640000e-07 65.8
40 TraesCS5B01G461200 chr3B 95.122 41 2 0 2229 2269 70980987 70980947 8.640000e-07 65.8


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 TraesCS5B01G461200 chr5B 636927525 636931253 3728 False 6887 6887 100.0000 1 3729 1 chr5B.!!$F2 3728
1 TraesCS5B01G461200 chr5B 654085335 654086253 918 True 902 902 85.1850 2523 3419 1 chr5B.!!$R2 896
2 TraesCS5B01G461200 chr5B 600120020 600120725 705 True 675 675 84.9080 2726 3391 1 chr5B.!!$R1 665
3 TraesCS5B01G461200 chr5B 578826642 578827295 653 False 355 355 76.6820 1497 2162 1 chr5B.!!$F1 665
4 TraesCS5B01G461200 chr5D 506164803 506169571 4768 False 2156 3192 90.9455 50 3729 2 chr5D.!!$F1 3679
5 TraesCS5B01G461200 chr5D 506207295 506212761 5466 False 709 1195 86.6376 50 3605 5 chr5D.!!$F2 3555
6 TraesCS5B01G461200 chr4A 531103469 531105350 1881 True 764 798 85.4925 1381 2871 2 chr4A.!!$R1 1490
7 TraesCS5B01G461200 chr4A 698310715 698311338 623 False 601 601 84.1600 1571 2191 1 chr4A.!!$F2 620
8 TraesCS5B01G461200 chr4A 698491774 698492358 584 False 551 551 83.7520 1571 2164 1 chr4A.!!$F3 593
9 TraesCS5B01G461200 chr5A 633978802 633979832 1030 False 553 797 87.9325 2557 3729 2 chr5A.!!$F2 1172
10 TraesCS5B01G461200 chr4B 95708411 95710291 1880 True 765 774 86.2405 1440 2871 2 chr4B.!!$R1 1431
11 TraesCS5B01G461200 chr2D 114538097 114539837 1740 True 662 773 85.0935 1381 2723 2 chr2D.!!$R2 1342
12 TraesCS5B01G461200 chr2D 476849210 476849899 689 False 222 222 73.1260 2023 2712 1 chr2D.!!$F1 689
13 TraesCS5B01G461200 chr2D 476913703 476914210 507 False 204 204 74.2250 2207 2717 1 chr2D.!!$F2 510
14 TraesCS5B01G461200 chr2A 115787304 115788016 712 True 634 634 82.7970 1477 2187 1 chr2A.!!$R1 710
15 TraesCS5B01G461200 chr7D 30395349 30395976 627 False 603 603 84.0760 1571 2195 1 chr7D.!!$F1 624
16 TraesCS5B01G461200 chr7B 652131184 652132010 826 False 540 540 79.1030 2870 3688 1 chr7B.!!$F1 818
17 TraesCS5B01G461200 chr2B 165071766 165072364 598 True 516 516 82.3920 1445 2040 1 chr2B.!!$R1 595

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
693 903 0.321996 GATCGGATGGTAAGGGAGGC 59.678 60.0 0.0 0.0 0.00 4.70 F
1012 2476 0.396695 TCGAGGGAGGCCGAATAAGT 60.397 55.0 0.0 0.0 0.00 2.24 F
1808 4478 0.315568 GACGAGGTGTCTGAAGCTGT 59.684 55.0 0.0 0.0 44.58 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1796 4466 0.318441 CGGAAGGACAGCTTCAGACA 59.682 55.000 0.0 0.0 32.84 3.41 R
2395 5617 1.004560 CAGCTTCTTGAGGACGGCA 60.005 57.895 0.0 0.0 0.00 5.69 R
2995 6253 1.135575 CGCAAGAAAACCCTGCATCTC 60.136 52.381 0.0 0.0 43.02 2.75 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
37 38 9.627123 AATAACTTTATTATTGCCTGTAGAGCA 57.373 29.630 0.00 0.00 33.39 4.26
38 39 9.799106 ATAACTTTATTATTGCCTGTAGAGCAT 57.201 29.630 0.00 0.00 40.59 3.79
40 41 9.799106 AACTTTATTATTGCCTGTAGAGCATAT 57.201 29.630 0.00 0.00 40.59 1.78
41 42 9.799106 ACTTTATTATTGCCTGTAGAGCATATT 57.201 29.630 0.00 0.00 40.59 1.28
44 45 7.693969 ATTATTGCCTGTAGAGCATATTTCC 57.306 36.000 0.00 0.00 40.59 3.13
45 46 4.778213 TTGCCTGTAGAGCATATTTCCT 57.222 40.909 0.00 0.00 40.59 3.36
46 47 4.778213 TGCCTGTAGAGCATATTTCCTT 57.222 40.909 0.00 0.00 34.69 3.36
47 48 4.708177 TGCCTGTAGAGCATATTTCCTTC 58.292 43.478 0.00 0.00 34.69 3.46
48 49 4.164030 TGCCTGTAGAGCATATTTCCTTCA 59.836 41.667 0.00 0.00 34.69 3.02
64 65 4.074970 TCCTTCAAGGATGAGAACAAAGC 58.925 43.478 0.34 0.00 40.06 3.51
67 68 1.470098 CAAGGATGAGAACAAAGCGGG 59.530 52.381 0.00 0.00 0.00 6.13
191 202 6.834969 AGGAACTCCTACTACTATTCCAGAAC 59.165 42.308 0.00 0.00 46.48 3.01
348 359 4.275936 ACAACTTCAACATGTGCTAGTTCC 59.724 41.667 13.68 0.00 32.66 3.62
428 443 2.920912 TCACCTCGACCACCCACC 60.921 66.667 0.00 0.00 0.00 4.61
436 451 1.144093 TCGACCACCCACCTCAATTTT 59.856 47.619 0.00 0.00 0.00 1.82
452 467 1.048601 TTTTGCCGAGGAGAGAGTGT 58.951 50.000 0.00 0.00 0.00 3.55
509 524 0.605319 CAACGCCTCTTGCCACCTTA 60.605 55.000 0.00 0.00 36.24 2.69
576 745 1.226773 GCAATGCGGGAGATTGTGC 60.227 57.895 0.00 0.00 33.96 4.57
598 767 4.473520 AGGAGGCCATGCGTTCGG 62.474 66.667 5.01 0.00 0.00 4.30
638 848 8.075574 TGTAGTTGCACACATTAGAATTTGAAG 58.924 33.333 0.00 0.00 0.00 3.02
640 850 7.715657 AGTTGCACACATTAGAATTTGAAGAA 58.284 30.769 0.00 0.00 0.00 2.52
664 874 5.733226 AAAATTACACAGGTTTTGCTTGC 57.267 34.783 0.00 0.00 0.00 4.01
665 875 4.670896 AATTACACAGGTTTTGCTTGCT 57.329 36.364 0.00 0.00 0.00 3.91
683 893 2.061773 GCTACGTTGATGATCGGATGG 58.938 52.381 0.00 0.00 0.00 3.51
693 903 0.321996 GATCGGATGGTAAGGGAGGC 59.678 60.000 0.00 0.00 0.00 4.70
731 941 6.897259 GCTCAACATTTTGTGCATGATATT 57.103 33.333 12.48 0.00 46.81 1.28
734 944 7.583860 TCAACATTTTGTGCATGATATTGTG 57.416 32.000 0.00 0.00 34.02 3.33
752 965 9.793252 GATATTGTGTTTGCATAGATGAAACTT 57.207 29.630 13.66 5.02 33.28 2.66
768 981 9.383519 AGATGAAACTTGACAATATATCAACGT 57.616 29.630 0.00 0.00 32.67 3.99
854 1067 1.134401 CATAGGCGAGGGAGCTTTGAA 60.134 52.381 0.00 0.00 37.29 2.69
880 1299 4.157656 GCACCAAATAGATGCAAAGGTACA 59.842 41.667 0.00 0.00 39.23 2.90
929 2393 1.534729 AGGGAAATGCGAAGGTGTTC 58.465 50.000 0.00 0.00 0.00 3.18
991 2455 1.286248 AAAACTGGGCCGTAGAGGAT 58.714 50.000 12.15 0.00 45.00 3.24
1012 2476 0.396695 TCGAGGGAGGCCGAATAAGT 60.397 55.000 0.00 0.00 0.00 2.24
1156 2643 3.883631 AAAAAGCGAAACCGACGTTAT 57.116 38.095 0.00 0.00 0.00 1.89
1157 2644 4.988708 AAAAAGCGAAACCGACGTTATA 57.011 36.364 0.00 0.00 0.00 0.98
1158 2645 4.988708 AAAAGCGAAACCGACGTTATAA 57.011 36.364 0.00 0.00 0.00 0.98
1174 2661 9.933175 CGACGTTATAATTATAACTCCAAATCG 57.067 33.333 31.29 25.58 43.54 3.34
1215 2702 3.295734 CGATGCACGGATGGATTCT 57.704 52.632 0.00 0.00 36.94 2.40
1216 2703 1.586422 CGATGCACGGATGGATTCTT 58.414 50.000 0.00 0.00 36.94 2.52
1217 2704 2.754472 CGATGCACGGATGGATTCTTA 58.246 47.619 0.00 0.00 36.94 2.10
1218 2705 3.329386 CGATGCACGGATGGATTCTTAT 58.671 45.455 0.00 0.00 36.94 1.73
1219 2706 3.748048 CGATGCACGGATGGATTCTTATT 59.252 43.478 0.00 0.00 36.94 1.40
1220 2707 4.143030 CGATGCACGGATGGATTCTTATTC 60.143 45.833 0.00 0.00 36.94 1.75
1221 2708 4.422073 TGCACGGATGGATTCTTATTCT 57.578 40.909 0.00 0.00 0.00 2.40
1222 2709 4.380531 TGCACGGATGGATTCTTATTCTC 58.619 43.478 0.00 0.00 0.00 2.87
1223 2710 4.101585 TGCACGGATGGATTCTTATTCTCT 59.898 41.667 0.00 0.00 0.00 3.10
1224 2711 5.304357 TGCACGGATGGATTCTTATTCTCTA 59.696 40.000 0.00 0.00 0.00 2.43
1225 2712 6.014242 TGCACGGATGGATTCTTATTCTCTAT 60.014 38.462 0.00 0.00 0.00 1.98
1226 2713 6.312426 GCACGGATGGATTCTTATTCTCTATG 59.688 42.308 0.00 0.00 0.00 2.23
1227 2714 6.312426 CACGGATGGATTCTTATTCTCTATGC 59.688 42.308 0.00 0.00 0.00 3.14
1229 2716 6.534436 CGGATGGATTCTTATTCTCTATGCAG 59.466 42.308 0.00 0.00 0.00 4.41
1230 2717 6.822676 GGATGGATTCTTATTCTCTATGCAGG 59.177 42.308 0.00 0.00 0.00 4.85
1408 4075 1.081892 CGAAACAGAGGGATGCACTG 58.918 55.000 8.57 8.57 37.62 3.66
1410 4077 2.679059 CGAAACAGAGGGATGCACTGAT 60.679 50.000 15.06 3.37 35.85 2.90
1420 4087 3.810812 GCACTGATGGAGCAGAGC 58.189 61.111 0.00 0.00 43.26 4.09
1474 4144 1.720694 AAAACCCGTCGGTGCAGTTG 61.721 55.000 11.06 0.00 43.71 3.16
1793 4463 1.378646 ATCTGGAGCGACCTGACGA 60.379 57.895 12.74 2.58 46.51 4.20
1808 4478 0.315568 GACGAGGTGTCTGAAGCTGT 59.684 55.000 0.00 0.00 44.58 4.40
1902 4572 2.202932 CCGGAGCCAGATCAACGG 60.203 66.667 0.00 0.00 35.01 4.44
2011 4684 2.102578 GCCATGTACTTCAAGGGCAAT 58.897 47.619 2.05 0.00 44.55 3.56
2059 4732 1.098712 ACACCGCACACGAACCATTT 61.099 50.000 0.00 0.00 43.93 2.32
2110 4791 0.809241 CCTTCATGCAGAGCTCGGAC 60.809 60.000 18.66 9.43 0.00 4.79
2195 4888 1.207089 CAGATTACCAGGAACAGGCGA 59.793 52.381 0.00 0.00 39.28 5.54
2395 5617 1.956170 CTTCCACAGCAGCGTCGTT 60.956 57.895 0.00 0.00 0.00 3.85
2579 5801 2.108425 ACTATGGTCATCTCGGCTCCTA 59.892 50.000 0.00 0.00 0.00 2.94
2621 5843 2.425592 CACCGCCTCCACAAGTGA 59.574 61.111 0.94 0.00 0.00 3.41
2758 5985 3.425625 GCTGTTGAGTTGAACGAACACAA 60.426 43.478 10.58 0.00 41.23 3.33
2886 6118 8.250332 TCTTTGTGCTTTCTTGAAGTGTAATTT 58.750 29.630 0.00 0.00 37.69 1.82
2995 6253 2.492088 TCATGGTTACTGTCCAGAGTCG 59.508 50.000 0.40 0.00 38.42 4.18
3005 6263 1.039785 TCCAGAGTCGAGATGCAGGG 61.040 60.000 0.00 0.00 0.00 4.45
3058 6325 6.035843 TGAATCAAAACAAAGAACTGCTCAC 58.964 36.000 0.00 0.00 0.00 3.51
3081 6348 0.598065 AACCTGCAAACGATCTTGGC 59.402 50.000 0.00 0.00 0.00 4.52
3115 6382 7.386299 ACTGAAATGTGTAGTTTTTGTTTTGCA 59.614 29.630 0.00 0.00 0.00 4.08
3116 6383 7.737395 TGAAATGTGTAGTTTTTGTTTTGCAG 58.263 30.769 0.00 0.00 0.00 4.41
3117 6384 7.386299 TGAAATGTGTAGTTTTTGTTTTGCAGT 59.614 29.630 0.00 0.00 0.00 4.40
3144 6773 8.902806 TGACATTTTATATTTTCAGTAGGCAGG 58.097 33.333 0.00 0.00 0.00 4.85
3261 6913 4.281941 AGTGTGAGATCAGTTCTGCAAGTA 59.718 41.667 0.00 0.00 33.74 2.24
3268 6920 8.097038 TGAGATCAGTTCTGCAAGTAAGTTATT 58.903 33.333 0.00 0.00 33.74 1.40
3326 6987 2.926586 GCAGCATGTGTGTCGTTAGAGA 60.927 50.000 0.00 0.00 39.31 3.10
3331 6992 4.921515 GCATGTGTGTCGTTAGAGAGTTTA 59.078 41.667 0.00 0.00 0.00 2.01
3336 6997 8.428186 TGTGTGTCGTTAGAGAGTTTATTTTT 57.572 30.769 0.00 0.00 0.00 1.94
3393 7056 5.441500 TGTGTAGGGATGTTTTTGTTCAGA 58.558 37.500 0.00 0.00 0.00 3.27
3676 7345 9.191479 TCAAGTCTGAAATTTTTAGTTGGGTAA 57.809 29.630 12.32 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 9.627123 TGCTCTACAGGCAATAATAAAGTTATT 57.373 29.630 2.11 2.11 36.71 1.40
12 13 9.799106 ATGCTCTACAGGCAATAATAAAGTTAT 57.201 29.630 0.00 0.00 43.14 1.89
14 15 9.799106 ATATGCTCTACAGGCAATAATAAAGTT 57.201 29.630 0.00 0.00 43.14 2.66
15 16 9.799106 AATATGCTCTACAGGCAATAATAAAGT 57.201 29.630 0.00 0.00 43.14 2.66
18 19 9.231297 GGAAATATGCTCTACAGGCAATAATAA 57.769 33.333 0.00 0.00 43.14 1.40
19 20 8.605947 AGGAAATATGCTCTACAGGCAATAATA 58.394 33.333 0.00 0.00 43.14 0.98
20 21 7.465116 AGGAAATATGCTCTACAGGCAATAAT 58.535 34.615 0.00 0.00 43.14 1.28
21 22 6.841601 AGGAAATATGCTCTACAGGCAATAA 58.158 36.000 0.00 0.00 43.14 1.40
22 23 6.439636 AGGAAATATGCTCTACAGGCAATA 57.560 37.500 0.00 0.00 43.14 1.90
23 24 5.316158 AGGAAATATGCTCTACAGGCAAT 57.684 39.130 0.00 0.00 43.14 3.56
24 25 4.778213 AGGAAATATGCTCTACAGGCAA 57.222 40.909 0.00 0.00 43.14 4.52
25 26 4.164030 TGAAGGAAATATGCTCTACAGGCA 59.836 41.667 0.00 0.00 44.05 4.75
26 27 4.708177 TGAAGGAAATATGCTCTACAGGC 58.292 43.478 0.00 0.00 0.00 4.85
27 28 5.762218 CCTTGAAGGAAATATGCTCTACAGG 59.238 44.000 4.95 0.00 37.67 4.00
28 29 6.586344 TCCTTGAAGGAAATATGCTCTACAG 58.414 40.000 12.35 0.00 42.51 2.74
29 30 6.560003 TCCTTGAAGGAAATATGCTCTACA 57.440 37.500 12.35 0.00 42.51 2.74
43 44 3.120060 CGCTTTGTTCTCATCCTTGAAGG 60.120 47.826 4.45 4.45 36.46 3.46
44 45 3.120060 CCGCTTTGTTCTCATCCTTGAAG 60.120 47.826 0.00 0.00 0.00 3.02
45 46 2.813754 CCGCTTTGTTCTCATCCTTGAA 59.186 45.455 0.00 0.00 0.00 2.69
46 47 2.426522 CCGCTTTGTTCTCATCCTTGA 58.573 47.619 0.00 0.00 0.00 3.02
47 48 1.470098 CCCGCTTTGTTCTCATCCTTG 59.530 52.381 0.00 0.00 0.00 3.61
48 49 1.614317 CCCCGCTTTGTTCTCATCCTT 60.614 52.381 0.00 0.00 0.00 3.36
64 65 2.740826 CGGTAGTGTTGCACCCCG 60.741 66.667 11.60 11.60 40.83 5.73
67 68 2.032071 AGGCGGTAGTGTTGCACC 59.968 61.111 0.00 0.00 34.49 5.01
74 75 0.532573 ATGTCAGTGAGGCGGTAGTG 59.467 55.000 0.00 0.00 0.00 2.74
77 78 1.897423 CCATGTCAGTGAGGCGGTA 59.103 57.895 0.00 0.00 0.00 4.02
191 202 4.012374 AGTGGTATGATGGCTCACTTTTG 58.988 43.478 0.00 0.00 35.44 2.44
348 359 7.466805 CACACAGTCATACTAAATTGGTCATG 58.533 38.462 0.00 0.00 0.00 3.07
428 443 2.935201 CTCTCTCCTCGGCAAAATTGAG 59.065 50.000 0.00 0.00 0.00 3.02
436 451 1.967535 CAACACTCTCTCCTCGGCA 59.032 57.895 0.00 0.00 0.00 5.69
452 467 0.389817 CAAGATGACGGTCGAGGCAA 60.390 55.000 3.34 0.00 0.00 4.52
484 499 1.503542 GCAAGAGGCGTTGGTCATG 59.496 57.895 5.03 0.00 0.00 3.07
509 524 2.108976 CGACGCACATAGGCCCAT 59.891 61.111 0.00 0.00 0.00 4.00
533 702 2.590007 GCGCTAGGTGGCATCTGG 60.590 66.667 11.36 8.98 0.00 3.86
546 715 2.580276 CATTGCATTTGGGGCGCT 59.420 55.556 7.64 0.00 0.00 5.92
547 716 3.197092 GCATTGCATTTGGGGCGC 61.197 61.111 0.00 0.00 0.00 6.53
598 767 1.156736 ACTACACAATTCAGGCGTGC 58.843 50.000 0.35 0.00 33.89 5.34
651 861 2.032799 TCAACGTAGCAAGCAAAACCTG 59.967 45.455 0.00 0.00 0.00 4.00
652 862 2.294074 TCAACGTAGCAAGCAAAACCT 58.706 42.857 0.00 0.00 0.00 3.50
664 874 3.371102 ACCATCCGATCATCAACGTAG 57.629 47.619 0.00 0.00 0.00 3.51
665 875 4.261867 CCTTACCATCCGATCATCAACGTA 60.262 45.833 0.00 0.00 0.00 3.57
683 893 1.887854 GATAGAGTCCGCCTCCCTTAC 59.112 57.143 0.00 0.00 41.47 2.34
693 903 3.182967 GTTGAGCTTGTGATAGAGTCCG 58.817 50.000 0.00 0.00 0.00 4.79
723 933 9.738832 TTTCATCTATGCAAACACAATATCATG 57.261 29.630 0.00 0.00 0.00 3.07
731 941 6.039159 TGTCAAGTTTCATCTATGCAAACACA 59.961 34.615 14.62 10.18 33.89 3.72
734 944 9.793252 ATATTGTCAAGTTTCATCTATGCAAAC 57.207 29.630 0.00 0.00 32.77 2.93
752 965 4.518249 TGGCCAACGTTGATATATTGTCA 58.482 39.130 29.35 15.03 0.00 3.58
763 976 6.183360 ACCAAAGTATTATATGGCCAACGTTG 60.183 38.462 21.47 21.47 36.37 4.10
768 981 6.892456 TCACAACCAAAGTATTATATGGCCAA 59.108 34.615 10.96 0.00 36.37 4.52
825 1038 1.876156 CCCTCGCCTATGCTGATTTTC 59.124 52.381 0.00 0.00 34.43 2.29
854 1067 3.133362 CCTTTGCATCTATTTGGTGCCAT 59.867 43.478 0.90 0.00 38.06 4.40
903 2367 5.712917 ACACCTTCGCATTTCCCTATAAAAA 59.287 36.000 0.00 0.00 0.00 1.94
968 2432 3.385755 TCCTCTACGGCCCAGTTTTATAC 59.614 47.826 0.00 0.00 0.00 1.47
991 2455 2.168496 CTTATTCGGCCTCCCTCGATA 58.832 52.381 0.00 0.00 35.25 2.92
1012 2476 4.164843 AGTTTGAGTTAGCCAGTTTGGA 57.835 40.909 0.00 0.00 40.96 3.53
1140 2627 7.777425 GTTATAATTATAACGTCGGTTTCGCT 58.223 34.615 25.17 0.00 38.80 4.93
1141 2628 7.961325 GTTATAATTATAACGTCGGTTTCGC 57.039 36.000 25.17 5.74 38.80 4.70
1174 2661 3.251972 GCCTCCGATCTGATTTGGATTTC 59.748 47.826 11.51 3.25 0.00 2.17
1199 2686 4.978099 AGAATAAGAATCCATCCGTGCAT 58.022 39.130 0.00 0.00 0.00 3.96
1203 2690 6.014242 TGCATAGAGAATAAGAATCCATCCGT 60.014 38.462 0.00 0.00 0.00 4.69
1205 2692 6.822676 CCTGCATAGAGAATAAGAATCCATCC 59.177 42.308 0.00 0.00 0.00 3.51
1206 2693 7.619050 TCCTGCATAGAGAATAAGAATCCATC 58.381 38.462 0.00 0.00 0.00 3.51
1207 2694 7.565190 TCCTGCATAGAGAATAAGAATCCAT 57.435 36.000 0.00 0.00 0.00 3.41
1208 2695 7.379059 TTCCTGCATAGAGAATAAGAATCCA 57.621 36.000 0.00 0.00 0.00 3.41
1209 2696 8.099537 TGATTCCTGCATAGAGAATAAGAATCC 58.900 37.037 0.00 0.00 30.52 3.01
1210 2697 9.499479 TTGATTCCTGCATAGAGAATAAGAATC 57.501 33.333 0.00 0.00 30.52 2.52
1213 2700 8.654094 TGATTGATTCCTGCATAGAGAATAAGA 58.346 33.333 0.00 0.00 30.52 2.10
1214 2701 8.843885 TGATTGATTCCTGCATAGAGAATAAG 57.156 34.615 0.00 0.00 30.52 1.73
1215 2702 9.445878 GATGATTGATTCCTGCATAGAGAATAA 57.554 33.333 0.00 0.00 30.52 1.40
1216 2703 8.599792 TGATGATTGATTCCTGCATAGAGAATA 58.400 33.333 0.00 0.00 30.52 1.75
1217 2704 7.459234 TGATGATTGATTCCTGCATAGAGAAT 58.541 34.615 0.00 0.00 33.01 2.40
1218 2705 6.834107 TGATGATTGATTCCTGCATAGAGAA 58.166 36.000 0.00 0.00 0.00 2.87
1219 2706 6.429521 TGATGATTGATTCCTGCATAGAGA 57.570 37.500 0.00 0.00 0.00 3.10
1220 2707 7.390718 TGATTGATGATTGATTCCTGCATAGAG 59.609 37.037 0.00 0.00 0.00 2.43
1221 2708 7.228590 TGATTGATGATTGATTCCTGCATAGA 58.771 34.615 0.00 0.00 0.00 1.98
1222 2709 7.448748 TGATTGATGATTGATTCCTGCATAG 57.551 36.000 0.00 0.00 0.00 2.23
1223 2710 7.826918 TTGATTGATGATTGATTCCTGCATA 57.173 32.000 0.00 0.00 0.00 3.14
1224 2711 6.724893 TTGATTGATGATTGATTCCTGCAT 57.275 33.333 0.00 0.00 0.00 3.96
1225 2712 6.532988 TTTGATTGATGATTGATTCCTGCA 57.467 33.333 0.00 0.00 0.00 4.41
1226 2713 5.462398 GCTTTGATTGATGATTGATTCCTGC 59.538 40.000 0.00 0.00 0.00 4.85
1227 2714 6.569780 TGCTTTGATTGATGATTGATTCCTG 58.430 36.000 0.00 0.00 0.00 3.86
1229 2716 6.018994 GCTTGCTTTGATTGATGATTGATTCC 60.019 38.462 0.00 0.00 0.00 3.01
1230 2717 6.533723 TGCTTGCTTTGATTGATGATTGATTC 59.466 34.615 0.00 0.00 0.00 2.52
1277 2766 1.136057 GCTTCGTGGTTTCATCGTTCC 60.136 52.381 0.00 0.00 0.00 3.62
1278 2767 1.529438 TGCTTCGTGGTTTCATCGTTC 59.471 47.619 0.00 0.00 0.00 3.95
1337 2826 3.181967 CTTCTTGCGCGGACGAGG 61.182 66.667 8.83 4.74 43.93 4.63
1375 4042 2.482333 TTTCGGTTGCCCAACACGG 61.482 57.895 12.65 2.49 42.85 4.94
1408 4075 2.237393 CAGGTAAGCTCTGCTCCATC 57.763 55.000 0.00 0.00 38.25 3.51
1429 4096 1.134401 ACCGGCAACTCATATCCTGTG 60.134 52.381 0.00 0.00 0.00 3.66
1431 4098 1.138859 TCACCGGCAACTCATATCCTG 59.861 52.381 0.00 0.00 0.00 3.86
1474 4144 1.658673 CGTCGGCCCTACTACATCC 59.341 63.158 0.00 0.00 0.00 3.51
1793 4463 1.346068 GAAGGACAGCTTCAGACACCT 59.654 52.381 0.00 0.00 0.00 4.00
1796 4466 0.318441 CGGAAGGACAGCTTCAGACA 59.682 55.000 0.00 0.00 32.84 3.41
1808 4478 3.379445 GACGGCCTCACGGAAGGA 61.379 66.667 9.36 0.00 38.87 3.36
1885 4555 2.202932 CCGTTGATCTGGCTCCGG 60.203 66.667 0.00 0.00 0.00 5.14
2011 4684 2.852075 AACGGCTGGTCCTCCCAA 60.852 61.111 0.00 0.00 44.65 4.12
2195 4888 2.814919 CGCTATGATCGGAGTTAGAGGT 59.185 50.000 0.00 0.00 0.00 3.85
2331 5553 1.953231 CTCGCTGAGGGTGATCTGCA 61.953 60.000 0.00 0.00 42.43 4.41
2395 5617 1.004560 CAGCTTCTTGAGGACGGCA 60.005 57.895 0.00 0.00 0.00 5.69
2450 5672 1.448540 CGTCCTCCACCATGTCAGC 60.449 63.158 0.00 0.00 0.00 4.26
2579 5801 4.473520 CCCCCTTCGTGCGCATCT 62.474 66.667 15.91 0.00 0.00 2.90
2621 5843 1.308998 GGATGGTCGGCGATGAAATT 58.691 50.000 14.79 0.00 0.00 1.82
2844 6076 6.041296 AGCACAAAGAAGATTTTCATGAGGTT 59.959 34.615 0.00 0.00 35.70 3.50
2860 6092 6.751514 TTACACTTCAAGAAAGCACAAAGA 57.248 33.333 0.00 0.00 38.67 2.52
2886 6118 7.090953 ACAAACCAATAAAACTCACTCGAAA 57.909 32.000 0.00 0.00 0.00 3.46
2922 6154 6.069331 ACTGAAACTCACTCCTACTAGTTGA 58.931 40.000 0.00 0.00 32.69 3.18
2995 6253 1.135575 CGCAAGAAAACCCTGCATCTC 60.136 52.381 0.00 0.00 43.02 2.75
3005 6263 2.544267 AGTCTGTGCTACGCAAGAAAAC 59.456 45.455 0.00 0.00 41.47 2.43
3058 6325 3.558505 CAAGATCGTTTGCAGGTTTCTG 58.441 45.455 0.00 0.00 43.64 3.02
3081 6348 8.801715 AAAACTACACATTTCAGTGCTATTTG 57.198 30.769 0.00 0.00 43.23 2.32
3165 6813 2.568623 AACAATCTGGACCTCACACC 57.431 50.000 0.00 0.00 0.00 4.16
3225 6875 7.121168 ACTGATCTCACACTTTCAAACAAAAGA 59.879 33.333 3.56 0.00 38.30 2.52
3226 6876 7.253422 ACTGATCTCACACTTTCAAACAAAAG 58.747 34.615 0.00 0.00 41.15 2.27
3232 6884 5.008019 GCAGAACTGATCTCACACTTTCAAA 59.992 40.000 5.97 0.00 35.73 2.69
3299 6951 2.034532 CACACATGCTGCCCCTGA 59.965 61.111 0.00 0.00 0.00 3.86
3326 6987 9.830975 ACAAAAATGAGCAGGTAAAAATAAACT 57.169 25.926 0.00 0.00 0.00 2.66
3331 6992 7.442062 CCTTCACAAAAATGAGCAGGTAAAAAT 59.558 33.333 0.00 0.00 0.00 1.82
3336 6997 4.469657 ACCTTCACAAAAATGAGCAGGTA 58.530 39.130 0.00 0.00 37.83 3.08
3393 7056 2.774351 GCCCCCTCCCAGTGCTAT 60.774 66.667 0.00 0.00 0.00 2.97
3701 7372 5.480772 ACCTACCGAAGAAAGAAAGATGAGA 59.519 40.000 0.00 0.00 0.00 3.27
3702 7373 5.725362 ACCTACCGAAGAAAGAAAGATGAG 58.275 41.667 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.