Multiple sequence alignment - TraesCS6D01G204200

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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 TraesCS6D01G204200 chr6D 100.000 4098 0 0 1 4098 289358171 289354074 0.000000e+00 7568.0
1 TraesCS6D01G204200 chr6B 93.210 2548 127 20 1581 4098 450139636 450137105 0.000000e+00 3705.0
2 TraesCS6D01G204200 chr6B 94.762 630 31 2 916 1544 450140618 450139990 0.000000e+00 979.0
3 TraesCS6D01G204200 chr6B 82.407 108 12 5 3831 3938 658802089 658801989 2.030000e-13 87.9
4 TraesCS6D01G204200 chr6A 93.779 2122 76 22 1943 4038 435593798 435595889 0.000000e+00 3136.0
5 TraesCS6D01G204200 chr6A 97.619 630 15 0 856 1485 435590402 435591031 0.000000e+00 1081.0
6 TraesCS6D01G204200 chr6A 96.509 487 16 1 1472 1957 435592177 435592663 0.000000e+00 804.0
7 TraesCS6D01G204200 chr6A 81.621 876 120 21 1 856 435588920 435589774 0.000000e+00 688.0
8 TraesCS6D01G204200 chr6A 94.416 197 11 0 3900 4096 435595953 435596149 1.850000e-78 303.0
9 TraesCS6D01G204200 chr6A 90.667 75 7 0 3719 3793 435595671 435595597 2.610000e-17 100.0
10 TraesCS6D01G204200 chr1D 82.178 505 86 4 354 855 196099730 196099227 8.140000e-117 431.0
11 TraesCS6D01G204200 chr1D 81.046 306 41 12 63 355 200095635 200095936 1.150000e-55 228.0
12 TraesCS6D01G204200 chr1D 87.013 77 8 2 3719 3794 428611404 428611479 7.300000e-13 86.1
13 TraesCS6D01G204200 chr1B 81.980 505 87 4 354 855 269204563 269205066 3.790000e-115 425.0
14 TraesCS6D01G204200 chr1A 81.542 493 86 5 354 843 245124276 245123786 6.380000e-108 401.0
15 TraesCS6D01G204200 chr7D 84.457 341 44 7 19 355 47259316 47259651 1.100000e-85 327.0
16 TraesCS6D01G204200 chr7D 85.200 250 35 2 109 357 368887627 368887379 5.260000e-64 255.0
17 TraesCS6D01G204200 chrUn 83.381 349 56 2 508 855 303564751 303565098 5.110000e-84 322.0
18 TraesCS6D01G204200 chrUn 80.435 138 20 7 5 139 99836374 99836507 9.370000e-17 99.0
19 TraesCS6D01G204200 chr2B 82.961 358 55 6 1 355 14313669 14314023 6.610000e-83 318.0
20 TraesCS6D01G204200 chr2B 78.330 503 98 11 360 855 457334421 457333923 8.550000e-82 315.0
21 TraesCS6D01G204200 chr2B 86.538 104 14 0 3691 3794 768404560 768404663 9.310000e-22 115.0
22 TraesCS6D01G204200 chr2B 84.270 89 13 1 3706 3794 207058714 207058627 7.300000e-13 86.1
23 TraesCS6D01G204200 chr2B 80.702 114 19 3 33 144 746686510 746686622 7.300000e-13 86.1
24 TraesCS6D01G204200 chr2D 77.953 508 103 9 354 855 153051047 153050543 3.980000e-80 309.0
25 TraesCS6D01G204200 chr2D 79.085 459 83 10 354 804 497921200 497921653 1.850000e-78 303.0
26 TraesCS6D01G204200 chr2D 78.512 121 21 5 41 158 169985016 169985134 1.580000e-09 75.0
27 TraesCS6D01G204200 chr7A 75.292 684 135 23 34 698 286870647 286871315 3.100000e-76 296.0
28 TraesCS6D01G204200 chr7A 86.667 90 7 3 3849 3938 653656389 653656305 1.210000e-15 95.3
29 TraesCS6D01G204200 chr7A 83.133 83 8 4 3849 3931 562286921 562286997 2.040000e-08 71.3
30 TraesCS6D01G204200 chr5D 81.793 368 49 10 1 355 353517737 353517375 4.010000e-75 292.0
31 TraesCS6D01G204200 chr5D 76.023 171 28 10 194 355 38977894 38978060 4.390000e-10 76.8
32 TraesCS6D01G204200 chr5D 83.333 90 8 6 3849 3937 207256562 207256479 4.390000e-10 76.8
33 TraesCS6D01G204200 chr2A 77.439 492 103 7 368 855 148020638 148021125 1.860000e-73 287.0
34 TraesCS6D01G204200 chr2A 84.404 109 15 2 32 139 114680228 114680335 5.600000e-19 106.0
35 TraesCS6D01G204200 chr4A 80.444 225 36 8 29 251 597730939 597730721 9.110000e-37 165.0
36 TraesCS6D01G204200 chr5A 77.350 234 46 7 103 333 674662715 674662944 9.240000e-27 132.0
37 TraesCS6D01G204200 chr5A 86.364 66 7 2 3714 3777 697854162 697854227 2.040000e-08 71.3
38 TraesCS6D01G204200 chr4B 92.045 88 7 0 3707 3794 600919973 600920060 1.550000e-24 124.0
39 TraesCS6D01G204200 chr3B 84.677 124 14 5 3814 3937 623655790 623655908 7.200000e-23 119.0
40 TraesCS6D01G204200 chr3B 85.217 115 9 6 3825 3937 662539067 662539175 1.200000e-20 111.0
41 TraesCS6D01G204200 chr3D 95.161 62 3 0 3817 3878 553872143 553872082 9.370000e-17 99.0
42 TraesCS6D01G204200 chr3D 86.957 69 7 2 3727 3794 611672894 611672961 4.390000e-10 76.8


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 TraesCS6D01G204200 chr6D 289354074 289358171 4097 True 7568.0 7568 100.0000 1 4098 1 chr6D.!!$R1 4097
1 TraesCS6D01G204200 chr6B 450137105 450140618 3513 True 2342.0 3705 93.9860 916 4098 2 chr6B.!!$R2 3182
2 TraesCS6D01G204200 chr6A 435588920 435596149 7229 False 1202.4 3136 92.7888 1 4096 5 chr6A.!!$F1 4095
3 TraesCS6D01G204200 chr1D 196099227 196099730 503 True 431.0 431 82.1780 354 855 1 chr1D.!!$R1 501
4 TraesCS6D01G204200 chr1B 269204563 269205066 503 False 425.0 425 81.9800 354 855 1 chr1B.!!$F1 501
5 TraesCS6D01G204200 chr2D 153050543 153051047 504 True 309.0 309 77.9530 354 855 1 chr2D.!!$R1 501
6 TraesCS6D01G204200 chr7A 286870647 286871315 668 False 296.0 296 75.2920 34 698 1 chr7A.!!$F1 664

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
242 253 0.039180 TCCGAACCCTAGCTCACTCA 59.961 55.000 0.00 0.0 0.00 3.41 F
593 622 0.907704 ATAGGCACCAGACACGGGAA 60.908 55.000 0.00 0.0 0.00 3.97 F
761 790 1.089481 CGCTCCGGCTTGCTATTGAA 61.089 55.000 0.00 0.0 36.09 2.69 F
1839 3986 1.203758 CTGCAATGCTGATTCAAGCCA 59.796 47.619 6.82 0.0 42.83 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1488 3306 0.177141 TAGCTGAACCATACCGGCAC 59.823 55.0 0.0 0.00 39.03 5.01 R
1780 3927 0.610174 ACGAGTCATGGTCATGCACT 59.390 50.0 6.1 9.89 38.65 4.40 R
1877 4024 1.825090 ATGAAGGCGATGCAAGACAA 58.175 45.0 0.0 0.00 0.00 3.18 R
3815 7140 0.394352 CCCCCGGTGATTCCTCAAAG 60.394 60.0 0.0 0.00 31.85 2.77 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
21 22 2.433436 GTTTCAAATGCCCGAGTAGGT 58.567 47.619 0.00 0.00 38.74 3.08
32 33 0.447011 CGAGTAGGTCGTCCAGTCAC 59.553 60.000 0.51 0.00 44.20 3.67
74 75 2.637872 CCCAACTAGACCTCTCAAACCA 59.362 50.000 0.00 0.00 0.00 3.67
75 76 3.264450 CCCAACTAGACCTCTCAAACCAT 59.736 47.826 0.00 0.00 0.00 3.55
83 84 4.082125 GACCTCTCAAACCATGGACAAAT 58.918 43.478 21.47 0.00 0.00 2.32
189 200 2.751731 CCACCACTGACCCCACACA 61.752 63.158 0.00 0.00 0.00 3.72
205 216 3.831911 CCACACATATCCCACAAAAACCT 59.168 43.478 0.00 0.00 0.00 3.50
206 217 4.082245 CCACACATATCCCACAAAAACCTC 60.082 45.833 0.00 0.00 0.00 3.85
213 224 1.960689 CCCACAAAAACCTCAATCCGT 59.039 47.619 0.00 0.00 0.00 4.69
242 253 0.039180 TCCGAACCCTAGCTCACTCA 59.961 55.000 0.00 0.00 0.00 3.41
267 278 2.684104 CCCGTCCTCTCCTCTCCA 59.316 66.667 0.00 0.00 0.00 3.86
271 282 1.410932 CCGTCCTCTCCTCTCCATCTT 60.411 57.143 0.00 0.00 0.00 2.40
275 286 2.242452 TCCTCTCCTCTCCATCTTCGAA 59.758 50.000 0.00 0.00 0.00 3.71
278 289 4.261994 CCTCTCCTCTCCATCTTCGAATTC 60.262 50.000 0.00 0.00 0.00 2.17
279 290 3.639094 TCTCCTCTCCATCTTCGAATTCC 59.361 47.826 0.00 0.00 0.00 3.01
282 293 4.410228 TCCTCTCCATCTTCGAATTCCATT 59.590 41.667 0.00 0.00 0.00 3.16
293 304 3.199727 TCGAATTCCATTCCATCCACTCA 59.800 43.478 0.00 0.00 35.89 3.41
294 305 3.313526 CGAATTCCATTCCATCCACTCAC 59.686 47.826 0.00 0.00 35.89 3.51
300 311 3.371273 CCATTCCATCCACTCACATGTCT 60.371 47.826 0.00 0.00 0.00 3.41
306 317 4.262377 CCATCCACTCACATGTCTAGATCC 60.262 50.000 10.93 0.00 0.00 3.36
309 320 1.683917 ACTCACATGTCTAGATCCGGC 59.316 52.381 10.93 0.00 0.00 6.13
330 341 3.069318 GACTCCGGCTCCGACCTT 61.069 66.667 10.28 0.00 42.83 3.50
411 429 2.685380 CTCCGGAGCTGGACCCTT 60.685 66.667 20.67 0.00 33.48 3.95
445 463 1.614241 GCTCCACCAGGACCGTGTAT 61.614 60.000 0.00 0.00 39.61 2.29
469 489 3.322466 CCGCCCCCAACTGTCTCT 61.322 66.667 0.00 0.00 0.00 3.10
550 572 1.647545 CGCATGTGCACTCCGGAATT 61.648 55.000 19.41 0.00 42.21 2.17
559 581 4.830765 TCCGGAATTGGAGGCGCG 62.831 66.667 0.00 0.00 33.05 6.86
562 584 4.179579 GGAATTGGAGGCGCGCAC 62.180 66.667 34.42 24.73 0.00 5.34
593 622 0.907704 ATAGGCACCAGACACGGGAA 60.908 55.000 0.00 0.00 0.00 3.97
602 631 3.524648 GACACGGGAAAGGGACGCA 62.525 63.158 0.00 0.00 0.00 5.24
683 712 2.125326 CCTCGCATGGGTCTACCGA 61.125 63.158 9.86 0.00 44.64 4.69
701 730 3.461773 CGGTCCCTCATGACGGCT 61.462 66.667 5.90 0.00 36.07 5.52
708 737 1.657751 CCTCATGACGGCTGAGACGA 61.658 60.000 17.64 0.00 42.22 4.20
737 766 2.352032 CCTCCGAGGGAAGAACGCT 61.352 63.158 6.53 0.00 44.45 5.07
761 790 1.089481 CGCTCCGGCTTGCTATTGAA 61.089 55.000 0.00 0.00 36.09 2.69
810 839 4.020617 CTGAGGCGGCTTGGGTCA 62.021 66.667 14.76 5.19 0.00 4.02
823 852 1.337118 TGGGTCACCAAATTGAAGCC 58.663 50.000 0.00 0.00 45.87 4.35
872 1529 3.389329 TGAAGAGATGCTCCAAGGATACC 59.611 47.826 0.00 0.00 37.17 2.73
873 1530 2.334023 AGAGATGCTCCAAGGATACCC 58.666 52.381 0.00 0.00 37.17 3.69
1081 1738 1.682684 CACCCTGAGTACTCCGCCT 60.683 63.158 20.11 0.00 0.00 5.52
1488 3306 2.224917 TGGTTACTTAAGTTGCAGGGGG 60.225 50.000 14.49 0.00 0.00 5.40
1546 3364 5.048504 GCATGTTTCTGGAGAATGAACTGAA 60.049 40.000 0.00 0.00 33.54 3.02
1579 3714 2.703007 AGTGGTCTGAAGTTTCTGAGCT 59.297 45.455 22.58 10.98 46.81 4.09
1588 3723 6.201044 TCTGAAGTTTCTGAGCTCTTTTTACG 59.799 38.462 16.19 0.00 32.42 3.18
1779 3926 6.206634 TGATTTGGTCTACATGACTTTGGTTC 59.793 38.462 0.00 0.00 44.74 3.62
1780 3927 4.698201 TGGTCTACATGACTTTGGTTCA 57.302 40.909 0.00 0.00 44.74 3.18
1808 3955 4.250464 TGACCATGACTCGTATTTTGGAC 58.750 43.478 0.00 0.00 0.00 4.02
1839 3986 1.203758 CTGCAATGCTGATTCAAGCCA 59.796 47.619 6.82 0.00 42.83 4.75
1861 4008 6.986817 GCCATATCGTTAATGCCATATACTCT 59.013 38.462 0.00 0.00 0.00 3.24
1925 4072 6.990349 TGTATTCTTCCCTCGACCAAATTATC 59.010 38.462 0.00 0.00 0.00 1.75
2327 5629 9.473640 CTTTATTTTCCTAGATACCGAACTACC 57.526 37.037 0.00 0.00 0.00 3.18
2354 5656 3.845781 TGTTTATCTCCTGATCTGCCC 57.154 47.619 0.00 0.00 34.32 5.36
2371 5673 3.411446 TGCCCATTCTGTTTGTAGACTG 58.589 45.455 0.00 0.00 0.00 3.51
2406 5708 4.023193 ACGATTAAGGTGGACTTTGCAAAG 60.023 41.667 32.53 32.53 40.64 2.77
2768 6080 0.940833 CACACCACGCACACACATTA 59.059 50.000 0.00 0.00 0.00 1.90
2772 6084 4.006989 ACACCACGCACACACATTATTAT 58.993 39.130 0.00 0.00 0.00 1.28
2843 6155 0.445436 CACTGAAAGCTCATGGACGC 59.555 55.000 0.00 0.00 37.60 5.19
3101 6413 5.825679 TCTGAGGAGAGTGATAGCTAAGAAC 59.174 44.000 0.00 0.00 0.00 3.01
3110 6422 8.301002 AGAGTGATAGCTAAGAACGGATTATTC 58.699 37.037 0.00 0.00 0.00 1.75
3124 6436 5.129485 ACGGATTATTCTGAGAACCACAGAT 59.871 40.000 0.00 0.00 42.68 2.90
3317 6633 6.037172 AGCATGTCTGTTTATTTAACTAGCGG 59.963 38.462 0.00 0.00 37.64 5.52
3459 6775 5.460646 ACTTGCCGAAAAATGACTACAATG 58.539 37.500 0.00 0.00 0.00 2.82
3573 6898 7.064866 ACATGGACATTCATACCAATCTTCAT 58.935 34.615 0.00 0.00 37.24 2.57
3582 6907 6.973642 TCATACCAATCTTCATCTTTCCCTT 58.026 36.000 0.00 0.00 0.00 3.95
3611 6936 3.203710 TCCTTGTCCCTCGGAGTTATCTA 59.796 47.826 4.02 0.00 29.39 1.98
3612 6937 3.958798 CCTTGTCCCTCGGAGTTATCTAA 59.041 47.826 4.02 0.00 29.39 2.10
3749 7074 3.881089 TCGCTCAAACGGATGTATCTAGA 59.119 43.478 0.00 0.00 0.00 2.43
3750 7075 4.519350 TCGCTCAAACGGATGTATCTAGAT 59.481 41.667 10.73 10.73 0.00 1.98
3751 7076 5.704053 TCGCTCAAACGGATGTATCTAGATA 59.296 40.000 8.44 8.44 0.00 1.98
3753 7078 7.551617 TCGCTCAAACGGATGTATCTAGATATA 59.448 37.037 15.43 13.22 0.00 0.86
3754 7079 8.346300 CGCTCAAACGGATGTATCTAGATATAT 58.654 37.037 18.82 18.82 0.00 0.86
3779 7104 6.387041 TCAGTACTAGATACATCCGTTTGG 57.613 41.667 0.00 0.00 36.09 3.28
3784 7109 0.935196 GATACATCCGTTTGGGCGAC 59.065 55.000 0.00 0.00 35.24 5.19
3797 7122 6.189567 CGTTTGGGCGACAAGTAATATTAAG 58.810 40.000 0.00 0.00 40.82 1.85
3800 7125 9.048446 GTTTGGGCGACAAGTAATATTAAGATA 57.952 33.333 0.00 0.00 40.82 1.98
3891 7216 1.882623 GCCAAAAGTCAAGAGGGAGTG 59.117 52.381 0.00 0.00 0.00 3.51
3908 7233 1.215423 AGTGCCCTCTTGAAGTTTGGT 59.785 47.619 0.00 0.00 0.00 3.67
4063 7590 3.810941 AGCGAACGGTCTTCATTTTGTAA 59.189 39.130 0.00 0.00 0.00 2.41
4073 7600 9.139174 CGGTCTTCATTTTGTAATTTTGCTAAT 57.861 29.630 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.404986 CGACCTACTCGGGCATTTGAA 60.405 52.381 0.00 0.00 43.06 2.69
15 16 1.073444 TCAGTGACTGGACGACCTACT 59.927 52.381 13.33 2.17 37.04 2.57
17 18 1.531423 GTCAGTGACTGGACGACCTA 58.469 55.000 16.26 0.00 37.04 3.08
21 22 3.351450 CGGTCAGTGACTGGACGA 58.649 61.111 22.38 0.00 35.49 4.20
27 28 2.702592 TTTTTGACCGGTCAGTGACT 57.297 45.000 34.25 3.05 41.13 3.41
59 60 3.516586 TGTCCATGGTTTGAGAGGTCTA 58.483 45.455 12.58 0.00 0.00 2.59
63 64 3.367703 GCATTTGTCCATGGTTTGAGAGG 60.368 47.826 12.58 0.00 0.00 3.69
74 75 4.039042 GCCCAGGCATTTGTCCAT 57.961 55.556 3.12 0.00 41.49 3.41
92 93 0.178929 GATATGAGGGGTCCCGGTCT 60.179 60.000 0.48 0.00 41.95 3.85
93 94 1.192803 GGATATGAGGGGTCCCGGTC 61.193 65.000 0.48 1.62 41.95 4.79
189 200 4.644685 CGGATTGAGGTTTTTGTGGGATAT 59.355 41.667 0.00 0.00 0.00 1.63
242 253 3.999297 GAGAGGACGGGGCGAGAGT 62.999 68.421 0.00 0.00 0.00 3.24
275 286 4.212716 CATGTGAGTGGATGGAATGGAAT 58.787 43.478 0.00 0.00 0.00 3.01
278 289 2.947652 GACATGTGAGTGGATGGAATGG 59.052 50.000 1.15 0.00 0.00 3.16
279 290 3.882444 AGACATGTGAGTGGATGGAATG 58.118 45.455 1.15 0.00 0.00 2.67
282 293 3.981212 TCTAGACATGTGAGTGGATGGA 58.019 45.455 1.15 0.00 0.00 3.41
293 304 0.390860 GCTGCCGGATCTAGACATGT 59.609 55.000 5.05 0.00 0.00 3.21
294 305 0.665670 CGCTGCCGGATCTAGACATG 60.666 60.000 5.05 0.00 0.00 3.21
300 311 2.194212 GGAGTCGCTGCCGGATCTA 61.194 63.158 5.05 0.00 34.56 1.98
330 341 2.365617 GGCCATCTTCTCCTCGTAATCA 59.634 50.000 0.00 0.00 0.00 2.57
343 354 2.739996 CGCTCCAGAGGGCCATCTT 61.740 63.158 19.33 0.00 34.59 2.40
431 449 1.895238 CGGAATACACGGTCCTGGT 59.105 57.895 0.00 0.00 0.00 4.00
683 712 3.771160 GCCGTCATGAGGGACCGT 61.771 66.667 33.29 0.00 38.58 4.83
794 823 4.329545 GTGACCCAAGCCGCCTCA 62.330 66.667 0.00 0.00 0.00 3.86
804 833 1.337118 GGCTTCAATTTGGTGACCCA 58.663 50.000 0.00 0.00 39.65 4.51
810 839 0.404040 TCCTCCGGCTTCAATTTGGT 59.596 50.000 0.00 0.00 0.00 3.67
815 844 0.984230 TGTTCTCCTCCGGCTTCAAT 59.016 50.000 0.00 0.00 0.00 2.57
823 852 2.202932 CCGCCATGTTCTCCTCCG 60.203 66.667 0.00 0.00 0.00 4.63
828 857 1.810030 GACGGACCGCCATGTTCTC 60.810 63.158 15.39 0.00 0.00 2.87
831 860 1.899437 ATCTGACGGACCGCCATGTT 61.899 55.000 15.39 0.00 0.00 2.71
835 864 2.225791 CTTCATCTGACGGACCGCCA 62.226 60.000 15.39 8.60 0.00 5.69
847 876 3.382278 TCCTTGGAGCATCTCTTCATCT 58.618 45.455 0.00 0.00 33.73 2.90
872 1529 1.519408 ACGTCCGAAATCAGTTTGGG 58.481 50.000 0.00 0.00 42.61 4.12
873 1530 2.916111 CAACGTCCGAAATCAGTTTGG 58.084 47.619 0.00 0.00 41.77 3.28
954 1611 3.078594 GCAACGGCGAAATATCCAAAT 57.921 42.857 16.62 0.00 0.00 2.32
1081 1738 4.314440 GTGGCTGTGGCGAGGTGA 62.314 66.667 0.00 0.00 39.81 4.02
1199 1856 4.161295 CCTCCGCATCCGCCTGAA 62.161 66.667 0.00 0.00 33.11 3.02
1488 3306 0.177141 TAGCTGAACCATACCGGCAC 59.823 55.000 0.00 0.00 39.03 5.01
1579 3714 2.220593 CGGCGTAACAACCGTAAAAAGA 59.779 45.455 0.00 0.00 44.46 2.52
1588 3723 2.349722 CCTTTTGTACGGCGTAACAACC 60.350 50.000 22.77 9.50 0.00 3.77
1779 3926 1.004595 CGAGTCATGGTCATGCACTG 58.995 55.000 15.43 0.00 38.65 3.66
1780 3927 0.610174 ACGAGTCATGGTCATGCACT 59.390 50.000 6.10 9.89 38.65 4.40
1839 3986 9.601217 GGAAAGAGTATATGGCATTAACGATAT 57.399 33.333 4.78 0.00 0.00 1.63
1861 4008 3.803340 AGACAAGTCTCCCCTATGGAAA 58.197 45.455 0.00 0.00 44.57 3.13
1877 4024 1.825090 ATGAAGGCGATGCAAGACAA 58.175 45.000 0.00 0.00 0.00 3.18
1925 4072 7.041721 TGTATCTAAATGCTAGACACAACCAG 58.958 38.462 0.00 0.00 29.15 4.00
2327 5629 5.464722 CAGATCAGGAGATAAACAATGACCG 59.535 44.000 0.00 0.00 33.72 4.79
2354 5656 5.462068 TCGTTCACAGTCTACAAACAGAATG 59.538 40.000 0.00 0.00 44.23 2.67
2371 5673 5.231568 CCACCTTAATCGTTCTATCGTTCAC 59.768 44.000 0.00 0.00 0.00 3.18
2406 5708 2.677199 GCAGGTTGCTTCTTTTTAGGC 58.323 47.619 0.00 0.00 40.96 3.93
2622 5924 5.128919 CCATTGAAGGTAGAAATAGCAGCT 58.871 41.667 0.00 0.00 0.00 4.24
2768 6080 9.768662 GATGTTGCCTCCAATATTTTTCATAAT 57.231 29.630 0.00 0.00 33.59 1.28
2772 6084 6.211184 ACAGATGTTGCCTCCAATATTTTTCA 59.789 34.615 0.00 0.00 33.59 2.69
2998 6310 4.129380 CAGTGTCCTCTTTGAACATCACA 58.871 43.478 0.00 0.00 0.00 3.58
3101 6413 5.011090 TCTGTGGTTCTCAGAATAATCCG 57.989 43.478 0.00 0.00 38.71 4.18
3110 6422 6.030548 TGAACTTCTATCTGTGGTTCTCAG 57.969 41.667 0.00 0.00 37.66 3.35
3226 6538 7.116948 CACACATTTATATAGCTTCCTCCTTCG 59.883 40.741 0.00 0.00 0.00 3.79
3317 6633 2.363038 TGCGTACATATGTAGGTCACCC 59.637 50.000 27.52 15.96 38.32 4.61
3573 6898 3.720002 ACAAGGAGTGGTTAAGGGAAAGA 59.280 43.478 0.00 0.00 0.00 2.52
3582 6907 1.263356 CGAGGGACAAGGAGTGGTTA 58.737 55.000 0.00 0.00 0.00 2.85
3753 7078 7.926555 CCAAACGGATGTATCTAGTACTGAAAT 59.073 37.037 5.39 0.00 34.27 2.17
3754 7079 7.262772 CCAAACGGATGTATCTAGTACTGAAA 58.737 38.462 5.39 0.00 34.27 2.69
3755 7080 6.183360 CCCAAACGGATGTATCTAGTACTGAA 60.183 42.308 5.39 0.00 34.27 3.02
3756 7081 5.301045 CCCAAACGGATGTATCTAGTACTGA 59.699 44.000 5.39 1.42 34.27 3.41
3757 7082 5.529791 CCCAAACGGATGTATCTAGTACTG 58.470 45.833 5.39 0.00 34.27 2.74
3759 7084 4.304939 GCCCAAACGGATGTATCTAGTAC 58.695 47.826 0.00 0.00 0.00 2.73
3760 7085 3.005050 CGCCCAAACGGATGTATCTAGTA 59.995 47.826 0.00 0.00 0.00 1.82
3761 7086 2.223971 CGCCCAAACGGATGTATCTAGT 60.224 50.000 0.00 0.00 0.00 2.57
3779 7104 9.856488 TGATCTATCTTAATATTACTTGTCGCC 57.144 33.333 0.00 0.00 0.00 5.54
3797 7122 6.239289 CCTCAAAGAACTCCCTCTGATCTATC 60.239 46.154 0.00 0.00 0.00 2.08
3800 7125 3.774216 CCTCAAAGAACTCCCTCTGATCT 59.226 47.826 0.00 0.00 0.00 2.75
3815 7140 0.394352 CCCCCGGTGATTCCTCAAAG 60.394 60.000 0.00 0.00 31.85 2.77
3845 7170 5.277974 GCTTTTGAGCAATATATTCAGGCGA 60.278 40.000 0.00 0.00 34.41 5.54
3847 7172 5.919141 CAGCTTTTGAGCAATATATTCAGGC 59.081 40.000 0.00 0.00 37.25 4.85
3891 7216 2.306847 TCAACCAAACTTCAAGAGGGC 58.693 47.619 0.00 0.00 0.00 5.19
3908 7233 7.938140 CAGTTTCCCTTATTAACTGGATCAA 57.062 36.000 0.00 0.00 43.03 2.57
3919 7244 3.136626 CCTCCGATCCAGTTTCCCTTATT 59.863 47.826 0.00 0.00 0.00 1.40
4063 7590 7.836183 AGGTCAGAAGGAACATATTAGCAAAAT 59.164 33.333 0.00 0.00 34.85 1.82
4073 7600 5.544176 AGTTCAAGAGGTCAGAAGGAACATA 59.456 40.000 0.00 0.00 34.85 2.29


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

AutoCloner maintained by Alex Coulton.