Multiple sequence alignment - TraesCS1B01G173100

Loading Multiple Alignment...

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 TraesCS1B01G173100 chr1B 100.000 4887 0 0 1 4887 308902014 308906900 0.000000e+00 9025
1 TraesCS1B01G173100 chr1D 96.835 3254 89 3 734 3985 216012928 216016169 0.000000e+00 5426
2 TraesCS1B01G173100 chr1D 85.806 155 18 3 584 736 271228522 271228370 1.410000e-35 161
3 TraesCS1B01G173100 chr1A 97.313 3126 83 1 815 3940 276569295 276572419 0.000000e+00 5306
4 TraesCS1B01G173100 chr1A 92.774 429 22 2 4457 4885 276572422 276572841 3.230000e-171 612
5 TraesCS1B01G173100 chr1A 94.118 68 3 1 728 794 276569230 276569297 8.650000e-18 102
6 TraesCS1B01G173100 chr5D 92.822 613 40 2 3997 4609 508283855 508284463 0.000000e+00 885
7 TraesCS1B01G173100 chr2D 82.148 745 103 23 1 736 148288708 148289431 3.230000e-171 612
8 TraesCS1B01G173100 chr2D 83.412 633 81 14 109 736 322470546 322469933 2.550000e-157 566
9 TraesCS1B01G173100 chr2D 76.247 762 114 41 8 739 335682966 335682242 4.680000e-90 342
10 TraesCS1B01G173100 chr2D 90.110 182 12 3 3997 4178 170614183 170614358 1.060000e-56 231
11 TraesCS1B01G173100 chr2D 85.897 156 22 0 581 736 176940446 176940601 3.030000e-37 167
12 TraesCS1B01G173100 chr3B 81.769 746 109 21 1 737 254102721 254103448 2.520000e-167 599
13 TraesCS1B01G173100 chr3B 81.203 133 25 0 3992 4124 797725749 797725617 1.860000e-19 108
14 TraesCS1B01G173100 chr2B 84.272 604 76 12 139 736 390579589 390578999 5.490000e-159 571
15 TraesCS1B01G173100 chr2B 77.519 903 191 11 3986 4884 296018080 296017186 2.590000e-147 532
16 TraesCS1B01G173100 chr2B 92.818 181 13 0 3998 4178 226699666 226699486 3.750000e-66 263
17 TraesCS1B01G173100 chr2B 81.988 161 24 5 1 158 489918747 489918905 1.100000e-26 132
18 TraesCS1B01G173100 chr3A 78.241 887 165 17 3997 4881 725065784 725064924 1.200000e-150 544
19 TraesCS1B01G173100 chr3A 76.504 349 73 8 3987 4331 290447731 290448074 1.080000e-41 182
20 TraesCS1B01G173100 chr7A 86.290 496 33 15 3987 4470 735949067 735949539 1.570000e-139 507
21 TraesCS1B01G173100 chr7D 86.981 361 36 7 108 463 169812352 169812706 3.540000e-106 396
22 TraesCS1B01G173100 chr7B 80.123 488 78 12 21 497 443855867 443856346 3.620000e-91 346
23 TraesCS1B01G173100 chr7B 91.129 124 9 2 3991 4113 744023888 744024010 3.030000e-37 167
24 TraesCS1B01G173100 chr2A 83.125 320 42 8 418 736 156664772 156664464 1.040000e-71 281
25 TraesCS1B01G173100 chr2A 74.800 750 99 47 8 739 446065672 446064995 6.280000e-64 255
26 TraesCS1B01G173100 chr4A 85.161 155 19 3 584 736 434739107 434738955 6.550000e-34 156
27 TraesCS1B01G173100 chr4A 81.095 201 31 6 540 736 169827786 169827589 2.360000e-33 154


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 TraesCS1B01G173100 chr1B 308902014 308906900 4886 False 9025.000000 9025 100.000 1 4887 1 chr1B.!!$F1 4886
1 TraesCS1B01G173100 chr1D 216012928 216016169 3241 False 5426.000000 5426 96.835 734 3985 1 chr1D.!!$F1 3251
2 TraesCS1B01G173100 chr1A 276569230 276572841 3611 False 2006.666667 5306 94.735 728 4885 3 chr1A.!!$F1 4157
3 TraesCS1B01G173100 chr5D 508283855 508284463 608 False 885.000000 885 92.822 3997 4609 1 chr5D.!!$F1 612
4 TraesCS1B01G173100 chr2D 148288708 148289431 723 False 612.000000 612 82.148 1 736 1 chr2D.!!$F1 735
5 TraesCS1B01G173100 chr2D 322469933 322470546 613 True 566.000000 566 83.412 109 736 1 chr2D.!!$R1 627
6 TraesCS1B01G173100 chr2D 335682242 335682966 724 True 342.000000 342 76.247 8 739 1 chr2D.!!$R2 731
7 TraesCS1B01G173100 chr3B 254102721 254103448 727 False 599.000000 599 81.769 1 737 1 chr3B.!!$F1 736
8 TraesCS1B01G173100 chr2B 390578999 390579589 590 True 571.000000 571 84.272 139 736 1 chr2B.!!$R3 597
9 TraesCS1B01G173100 chr2B 296017186 296018080 894 True 532.000000 532 77.519 3986 4884 1 chr2B.!!$R2 898
10 TraesCS1B01G173100 chr3A 725064924 725065784 860 True 544.000000 544 78.241 3997 4881 1 chr3A.!!$R1 884
11 TraesCS1B01G173100 chr2A 446064995 446065672 677 True 255.000000 255 74.800 8 739 1 chr2A.!!$R2 731

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
137 139 0.105246 AACCCATCAGGCAACCCAAA 60.105 50.000 0.00 0.0 40.58 3.28 F
879 925 0.254178 CTCCCTCCTCCCATGTTGTG 59.746 60.000 0.00 0.0 0.00 3.33 F
1087 1133 2.091278 CCTCCCGCATATATCCCTAGGA 60.091 54.545 11.48 0.0 35.55 2.94 F
1677 1723 4.011698 TGACATGTGCAGCAACATAGAAT 58.988 39.130 1.15 0.0 38.75 2.40 F
3098 3144 2.075338 GCACTCTCTGAAGCTGGAAAG 58.925 52.381 0.00 0.0 0.00 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1723 1769 0.032515 TGCAGACCCGGATCCTAGAA 60.033 55.000 10.75 0.0 0.00 2.10 R
1936 1982 1.951895 GCTCCAATGCCATGTCTGTCA 60.952 52.381 0.00 0.0 0.00 3.58 R
2495 2541 2.435805 CTGCAGCCCTTTGTCTAGGATA 59.564 50.000 0.00 0.0 37.50 2.59 R
3317 3363 2.872245 ACAGCATAACATACGGTCATGC 59.128 45.455 0.00 0.0 41.78 4.06 R
4599 4649 0.032515 TTCGAGGGATCCACCAGCTA 60.033 55.000 15.23 0.0 41.20 3.32 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
22 23 2.360726 AATCGGGTCGGGTTTGGC 60.361 61.111 0.00 0.00 0.00 4.52
28 29 4.019312 GTCGGGTTTGGCCGGGTA 62.019 66.667 2.18 0.00 38.06 3.69
53 54 0.986019 TTACCAGACCCATGCCCGAT 60.986 55.000 0.00 0.00 0.00 4.18
54 55 0.986019 TACCAGACCCATGCCCGATT 60.986 55.000 0.00 0.00 0.00 3.34
55 56 0.986019 ACCAGACCCATGCCCGATTA 60.986 55.000 0.00 0.00 0.00 1.75
58 60 2.039746 CCAGACCCATGCCCGATTAATA 59.960 50.000 0.00 0.00 0.00 0.98
77 79 8.953368 ATTAATAATCGGGTCGTTTCTAAACT 57.047 30.769 4.24 0.00 36.77 2.66
135 137 1.076549 GAACCCATCAGGCAACCCA 59.923 57.895 0.00 0.00 40.58 4.51
137 139 0.105246 AACCCATCAGGCAACCCAAA 60.105 50.000 0.00 0.00 40.58 3.28
140 142 1.543944 CCATCAGGCAACCCAAACCC 61.544 60.000 0.00 0.00 37.17 4.11
144 146 0.831288 CAGGCAACCCAAACCCATCA 60.831 55.000 0.00 0.00 37.17 3.07
216 220 1.207488 TACTGGGGCCATGCACTTCT 61.207 55.000 4.39 0.00 29.71 2.85
229 236 3.149196 TGCACTTCTGAACCAAGGATTC 58.851 45.455 0.00 0.00 0.00 2.52
245 252 2.749621 GGATTCCTACTGGCAAACTGTG 59.250 50.000 0.00 0.00 33.02 3.66
254 261 4.319177 ACTGGCAAACTGTGTCTTCTATC 58.681 43.478 0.00 0.00 30.97 2.08
270 277 8.394822 TGTCTTCTATCCTCTTATATAGGCAGT 58.605 37.037 0.00 0.00 33.84 4.40
272 279 7.836685 TCTTCTATCCTCTTATATAGGCAGTGG 59.163 40.741 0.00 0.00 33.84 4.00
315 322 1.406341 GGCGAGGTGGTACTAATGCAA 60.406 52.381 0.00 0.00 0.00 4.08
330 337 2.723746 CAACTGGCAAGCTGCGTT 59.276 55.556 0.00 0.00 46.21 4.84
463 483 5.862924 TGCTTTTGTCTATCTACAGCAAC 57.137 39.130 0.00 0.00 28.61 4.17
489 509 1.661197 CAACGTGGGTGCATGTTGC 60.661 57.895 0.00 0.00 42.68 4.17
490 510 1.827789 AACGTGGGTGCATGTTGCT 60.828 52.632 0.00 0.00 45.31 3.91
493 513 0.673333 CGTGGGTGCATGTTGCTCTA 60.673 55.000 0.00 0.00 45.31 2.43
520 541 7.775397 AAAATCTCACCAAAATTGTTCACAG 57.225 32.000 0.00 0.00 0.00 3.66
525 546 4.097741 TCACCAAAATTGTTCACAGGTCAG 59.902 41.667 0.00 0.00 0.00 3.51
538 559 6.548441 TCACAGGTCAGGTAAAATAAAACG 57.452 37.500 0.00 0.00 0.00 3.60
543 564 9.154847 ACAGGTCAGGTAAAATAAAACGTATAC 57.845 33.333 0.00 0.00 0.00 1.47
545 566 9.895138 AGGTCAGGTAAAATAAAACGTATACAT 57.105 29.630 3.32 0.00 0.00 2.29
572 594 7.736447 AGTACTTACTAATATTAGTCGGCGT 57.264 36.000 27.40 20.79 42.66 5.68
574 596 6.874288 ACTTACTAATATTAGTCGGCGTCT 57.126 37.500 27.40 11.93 42.66 4.18
579 601 4.585955 AATATTAGTCGGCGTCTCATGT 57.414 40.909 10.44 0.70 0.00 3.21
595 617 2.511637 TCATGTGTAACCCATGGGCATA 59.488 45.455 31.73 20.84 40.07 3.14
599 621 2.429250 GTGTAACCCATGGGCATAAACC 59.571 50.000 31.73 12.53 39.32 3.27
600 622 2.313342 TGTAACCCATGGGCATAAACCT 59.687 45.455 31.73 5.43 39.32 3.50
612 634 3.490348 GCATAAACCTGCATCCATACCT 58.510 45.455 0.00 0.00 41.87 3.08
620 642 3.587061 CCTGCATCCATACCTTACCCATA 59.413 47.826 0.00 0.00 0.00 2.74
630 652 8.014263 TCCATACCTTACCCATAACTAATCAGA 58.986 37.037 0.00 0.00 0.00 3.27
636 658 8.881262 CCTTACCCATAACTAATCAGATTACCT 58.119 37.037 0.00 0.00 0.00 3.08
640 662 9.615660 ACCCATAACTAATCAGATTACCTATCA 57.384 33.333 0.00 0.00 35.59 2.15
648 670 7.863901 AATCAGATTACCTATCAGGCTTACT 57.136 36.000 0.00 0.00 39.63 2.24
654 676 3.928754 ACCTATCAGGCTTACTCATGGA 58.071 45.455 0.00 0.00 39.63 3.41
665 711 5.363101 GCTTACTCATGGATGAAGATGACA 58.637 41.667 0.00 0.00 36.18 3.58
668 714 5.432680 ACTCATGGATGAAGATGACAACT 57.567 39.130 0.00 0.00 36.18 3.16
678 724 6.867519 TGAAGATGACAACTCATACCCTAA 57.132 37.500 0.00 0.00 37.24 2.69
679 725 7.437713 TGAAGATGACAACTCATACCCTAAT 57.562 36.000 0.00 0.00 37.24 1.73
742 788 2.463589 ATTGCCGGGTTGAAGCGAGA 62.464 55.000 2.18 0.00 0.00 4.04
810 856 3.173965 CTCCTCCTCAGTTGAAAGGGTA 58.826 50.000 9.24 0.00 33.21 3.69
811 857 3.583086 CTCCTCCTCAGTTGAAAGGGTAA 59.417 47.826 9.24 0.00 33.21 2.85
812 858 3.326880 TCCTCCTCAGTTGAAAGGGTAAC 59.673 47.826 9.24 0.00 33.21 2.50
879 925 0.254178 CTCCCTCCTCCCATGTTGTG 59.746 60.000 0.00 0.00 0.00 3.33
1087 1133 2.091278 CCTCCCGCATATATCCCTAGGA 60.091 54.545 11.48 0.00 35.55 2.94
1397 1443 4.326826 TGGCACTTTCTCTTTGGATAGTG 58.673 43.478 9.52 9.52 43.27 2.74
1400 1446 4.154918 GCACTTTCTCTTTGGATAGTGTGG 59.845 45.833 13.41 0.00 42.77 4.17
1563 1609 7.822334 TCTGTTCGTGAATAAATGGATACTGTT 59.178 33.333 0.00 0.00 37.61 3.16
1581 1627 5.005740 ACTGTTGTCATGCATACACAGATT 58.994 37.500 23.38 8.11 33.76 2.40
1616 1662 7.652524 TGCCTTTAACAATATAATTGCCAGA 57.347 32.000 0.00 0.00 0.00 3.86
1677 1723 4.011698 TGACATGTGCAGCAACATAGAAT 58.988 39.130 1.15 0.00 38.75 2.40
1722 1768 6.532657 CACATTTCATTGTATTGCCCTTTCTC 59.467 38.462 0.00 0.00 0.00 2.87
1723 1769 6.438425 ACATTTCATTGTATTGCCCTTTCTCT 59.562 34.615 0.00 0.00 0.00 3.10
1936 1982 9.085645 TGATAGTTTATTGTATGGTCTACGGAT 57.914 33.333 0.00 0.00 0.00 4.18
2205 2251 5.192927 TGCTGAAGTATGGATTAAACCCTG 58.807 41.667 0.00 0.00 0.00 4.45
2495 2541 7.704359 AGAAGGGATGAAGATAAGAAAGGAT 57.296 36.000 0.00 0.00 0.00 3.24
2555 2601 3.072184 ACAGTGTCCTTCTCAATGCTCTT 59.928 43.478 0.00 0.00 34.83 2.85
2978 3024 7.928706 ACATGTAATTCTCTTCTGTATGGCTAC 59.071 37.037 0.00 0.00 0.00 3.58
3098 3144 2.075338 GCACTCTCTGAAGCTGGAAAG 58.925 52.381 0.00 0.00 0.00 2.62
3102 3148 3.904339 ACTCTCTGAAGCTGGAAAGGTTA 59.096 43.478 0.00 0.00 0.00 2.85
3107 3153 3.219281 TGAAGCTGGAAAGGTTAACACC 58.781 45.455 8.10 5.78 44.67 4.16
3245 3291 3.047857 TCTGGACAATATGGATGGAGCA 58.952 45.455 0.00 0.00 0.00 4.26
3317 3363 1.758936 TCCAGATGGCTTTCTGCATG 58.241 50.000 11.16 0.00 45.15 4.06
3477 3523 8.659925 ATTGAGAAAATTTGCATACACAACAA 57.340 26.923 0.00 0.00 0.00 2.83
3605 3651 4.681025 GCAATCAATCGACTTTGCAAAAGA 59.319 37.500 13.84 12.84 43.00 2.52
3623 3669 7.986889 TGCAAAAGAAAATTTCCTAAAGAAGCT 59.013 29.630 1.57 0.00 35.40 3.74
3625 3671 7.953158 AAAGAAAATTTCCTAAAGAAGCTGC 57.047 32.000 1.57 0.00 35.40 5.25
3670 3716 0.382873 GTTGGTGTTTTCCCGGACAC 59.617 55.000 14.19 14.19 44.09 3.67
3703 3749 1.070601 TGTGCTTGTTAGAGCTCTGCA 59.929 47.619 26.78 22.32 43.11 4.41
3767 3813 8.726988 GCACTTTCTGTCAAAACTGGTATATAA 58.273 33.333 0.00 0.00 0.00 0.98
3775 3821 8.215050 TGTCAAAACTGGTATATAATACCCTGG 58.785 37.037 12.43 6.50 36.79 4.45
3976 4024 1.202651 ACCACAGGACAGTGCAGTTAC 60.203 52.381 0.00 0.00 38.18 2.50
3985 4033 2.112087 TGCAGTTACGCCAAGGCA 59.888 55.556 12.19 0.00 42.06 4.75
3986 4034 1.303236 TGCAGTTACGCCAAGGCAT 60.303 52.632 12.19 0.00 42.06 4.40
3987 4035 0.893270 TGCAGTTACGCCAAGGCATT 60.893 50.000 12.19 0.00 42.06 3.56
3988 4036 0.243636 GCAGTTACGCCAAGGCATTT 59.756 50.000 12.19 0.00 42.06 2.32
3989 4037 1.470890 GCAGTTACGCCAAGGCATTTA 59.529 47.619 12.19 0.00 42.06 1.40
3990 4038 2.099098 GCAGTTACGCCAAGGCATTTAT 59.901 45.455 12.19 0.00 42.06 1.40
3995 4043 2.971307 ACGCCAAGGCATTTATTTTGG 58.029 42.857 12.19 0.00 42.30 3.28
4030 4078 6.507023 AGACTTTGCGTTTCTTTTCATTGAT 58.493 32.000 0.00 0.00 0.00 2.57
4040 4088 4.609301 TCTTTTCATTGATAAGGTGGGGG 58.391 43.478 14.39 0.00 0.00 5.40
4200 4248 3.569827 TGTCAAGAGGGGGACAGAA 57.430 52.632 0.00 0.00 39.00 3.02
4228 4276 2.053638 CATCGAAGACGCATGCGC 60.054 61.111 38.15 28.98 42.51 6.09
4263 4311 3.779183 AGATCATCCATCCTGTCAACAGT 59.221 43.478 9.19 0.00 42.27 3.55
4286 4334 4.021925 GGTGGCGAGTCCCTTGCT 62.022 66.667 3.64 0.00 40.49 3.91
4352 4401 3.998672 GGGAGTTGTCGCGGTCCA 61.999 66.667 6.13 0.00 0.00 4.02
4398 4447 1.089920 GAGAGTGCATCGTGCCAAAT 58.910 50.000 7.38 0.00 44.23 2.32
4447 4496 0.036732 GGTGGTGCATTGTCTCAGGA 59.963 55.000 0.00 0.00 0.00 3.86
4470 4519 1.376037 GGTCGCAAAGTAGGCAGCT 60.376 57.895 0.00 0.00 0.00 4.24
4506 4556 2.255252 GCGGCGTTGCAATCTGTT 59.745 55.556 9.37 0.00 34.15 3.16
4508 4558 1.573932 CGGCGTTGCAATCTGTTGA 59.426 52.632 0.59 0.00 37.53 3.18
4589 4639 4.039609 CCCAGTTCTTCCAAATGAGCTTTT 59.960 41.667 0.00 0.00 0.00 2.27
4634 4684 3.585862 CTCGAAAGTAGCAAGGTAGCAA 58.414 45.455 0.00 0.00 36.85 3.91
4681 4731 1.759445 GCTCCACTTCCAGATCAGCTA 59.241 52.381 0.00 0.00 0.00 3.32
4711 4761 0.764369 TCTGAGAGGGTGGTGTGCTT 60.764 55.000 0.00 0.00 0.00 3.91
4754 4804 1.296392 CTGCCCAATCTCGTGGACA 59.704 57.895 0.00 0.00 41.65 4.02
4769 4819 2.770904 ACACCCAGGTTCCCGTGT 60.771 61.111 0.00 0.00 34.69 4.49
4777 4827 1.079681 GGTTCCCGTGTATGTCGCA 60.080 57.895 0.00 0.00 0.00 5.10
4785 4835 0.109458 GTGTATGTCGCACGTCCAGA 60.109 55.000 0.00 0.00 0.00 3.86
4831 4881 2.736721 CCGATTGAAGCTTTCGTCTTCA 59.263 45.455 15.71 1.72 45.62 3.02
4885 4935 1.377725 CGCTCACAGATTTGCCCCT 60.378 57.895 0.00 0.00 0.00 4.79
4886 4936 1.651240 CGCTCACAGATTTGCCCCTG 61.651 60.000 0.00 0.00 36.53 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.479730 GTCTGGTAAAGGTCTACCCGG 59.520 57.143 0.00 0.00 40.71 5.73
28 29 1.282157 GCATGGGTCTGGTAAAGGTCT 59.718 52.381 0.00 0.00 0.00 3.85
53 54 8.034215 TGAGTTTAGAAACGACCCGATTATTAA 58.966 33.333 0.00 0.00 43.51 1.40
54 55 7.546358 TGAGTTTAGAAACGACCCGATTATTA 58.454 34.615 0.00 0.00 43.51 0.98
55 56 6.400568 TGAGTTTAGAAACGACCCGATTATT 58.599 36.000 0.00 0.00 43.51 1.40
58 60 4.261578 TGAGTTTAGAAACGACCCGATT 57.738 40.909 0.00 0.00 43.51 3.34
67 69 5.183969 GGGTAGGGTCATGAGTTTAGAAAC 58.816 45.833 0.00 0.00 39.17 2.78
68 70 4.847512 TGGGTAGGGTCATGAGTTTAGAAA 59.152 41.667 0.00 0.00 0.00 2.52
70 72 4.069312 TGGGTAGGGTCATGAGTTTAGA 57.931 45.455 0.00 0.00 0.00 2.10
71 73 4.444876 CCATGGGTAGGGTCATGAGTTTAG 60.445 50.000 2.85 0.00 42.25 1.85
72 74 3.458118 CCATGGGTAGGGTCATGAGTTTA 59.542 47.826 2.85 0.00 42.25 2.01
77 79 2.944231 CCCATGGGTAGGGTCATGA 58.056 57.895 23.93 0.00 42.25 3.07
97 99 1.660167 GGGCGTGGGTCTAATAACAC 58.340 55.000 0.00 0.00 0.00 3.32
99 101 0.461135 TCGGGCGTGGGTCTAATAAC 59.539 55.000 0.00 0.00 0.00 1.89
100 102 1.134729 GTTCGGGCGTGGGTCTAATAA 60.135 52.381 0.00 0.00 0.00 1.40
102 104 1.219935 GTTCGGGCGTGGGTCTAAT 59.780 57.895 0.00 0.00 0.00 1.73
104 106 3.384532 GGTTCGGGCGTGGGTCTA 61.385 66.667 0.00 0.00 0.00 2.59
129 131 0.831288 TGCCTGATGGGTTTGGGTTG 60.831 55.000 0.00 0.00 37.43 3.77
130 132 0.831711 GTGCCTGATGGGTTTGGGTT 60.832 55.000 0.00 0.00 37.43 4.11
135 137 0.324645 GATGGGTGCCTGATGGGTTT 60.325 55.000 0.00 0.00 37.43 3.27
137 139 3.010144 GATGGGTGCCTGATGGGT 58.990 61.111 0.00 0.00 37.43 4.51
140 142 2.203252 CCCGATGGGTGCCTGATG 60.203 66.667 0.00 0.00 38.25 3.07
144 146 1.719063 ATTATGCCCGATGGGTGCCT 61.719 55.000 3.40 0.00 46.51 4.75
195 199 2.124151 GTGCATGGCCCCAGTAGG 60.124 66.667 0.00 0.00 0.00 3.18
198 202 2.036256 GAAGTGCATGGCCCCAGT 59.964 61.111 0.00 0.00 0.00 4.00
216 220 2.026262 GCCAGTAGGAATCCTTGGTTCA 60.026 50.000 18.47 0.00 34.80 3.18
229 236 2.550830 AGACACAGTTTGCCAGTAGG 57.449 50.000 0.00 0.00 38.23 3.18
245 252 8.682710 CACTGCCTATATAAGAGGATAGAAGAC 58.317 40.741 8.00 0.00 35.99 3.01
254 261 4.021016 GTGGACCACTGCCTATATAAGAGG 60.021 50.000 17.84 0.52 37.12 3.69
270 277 1.220749 GCGCATAGGAAGTGGACCA 59.779 57.895 0.30 0.00 0.00 4.02
272 279 0.872021 CGAGCGCATAGGAAGTGGAC 60.872 60.000 11.47 0.00 0.00 4.02
315 322 1.815866 AAAAACGCAGCTTGCCAGT 59.184 47.368 3.09 0.00 41.12 4.00
394 410 5.051891 AGTAGCATCAATGAAGCAACAAC 57.948 39.130 13.09 5.42 0.00 3.32
440 460 5.939883 TGTTGCTGTAGATAGACAAAAGCAT 59.060 36.000 0.00 0.00 30.80 3.79
441 461 5.304778 TGTTGCTGTAGATAGACAAAAGCA 58.695 37.500 0.00 0.00 0.00 3.91
452 472 4.610945 GTTGCTTTGTTGTTGCTGTAGAT 58.389 39.130 0.00 0.00 0.00 1.98
463 483 1.145162 GCACCCACGTTGCTTTGTTG 61.145 55.000 3.46 0.00 0.00 3.33
511 532 7.883391 TTTATTTTACCTGACCTGTGAACAA 57.117 32.000 0.00 0.00 0.00 2.83
546 567 9.442047 ACGCCGACTAATATTAGTAAGTACTAT 57.558 33.333 24.69 2.57 43.64 2.12
547 568 8.833231 ACGCCGACTAATATTAGTAAGTACTA 57.167 34.615 24.69 0.00 43.64 1.82
548 569 7.659390 AGACGCCGACTAATATTAGTAAGTACT 59.341 37.037 24.69 16.86 43.64 2.73
549 570 7.801752 AGACGCCGACTAATATTAGTAAGTAC 58.198 38.462 24.69 12.96 43.64 2.73
556 577 5.569441 CACATGAGACGCCGACTAATATTAG 59.431 44.000 18.99 18.99 36.82 1.73
565 586 0.989890 GTTACACATGAGACGCCGAC 59.010 55.000 0.00 0.00 0.00 4.79
572 594 1.064758 GCCCATGGGTTACACATGAGA 60.065 52.381 31.58 0.00 46.60 3.27
574 596 0.701147 TGCCCATGGGTTACACATGA 59.299 50.000 31.58 6.27 46.60 3.07
579 601 2.313342 AGGTTTATGCCCATGGGTTACA 59.687 45.455 31.58 21.24 37.65 2.41
595 617 3.372675 GGGTAAGGTATGGATGCAGGTTT 60.373 47.826 0.00 0.00 0.00 3.27
599 621 3.795688 ATGGGTAAGGTATGGATGCAG 57.204 47.619 0.00 0.00 0.00 4.41
600 622 4.663120 AGTTATGGGTAAGGTATGGATGCA 59.337 41.667 0.00 0.00 0.00 3.96
620 642 7.863901 AGCCTGATAGGTAATCTGATTAGTT 57.136 36.000 10.26 4.92 37.80 2.24
630 652 6.084738 TCCATGAGTAAGCCTGATAGGTAAT 58.915 40.000 0.00 0.00 37.80 1.89
636 658 5.840693 TCTTCATCCATGAGTAAGCCTGATA 59.159 40.000 0.00 0.00 38.19 2.15
640 662 4.657504 TCATCTTCATCCATGAGTAAGCCT 59.342 41.667 0.00 0.00 38.19 4.58
648 670 5.425196 TGAGTTGTCATCTTCATCCATGA 57.575 39.130 0.00 0.00 34.44 3.07
654 676 5.965033 AGGGTATGAGTTGTCATCTTCAT 57.035 39.130 0.00 0.00 42.80 2.57
665 711 5.228945 CCCGAATGATTAGGGTATGAGTT 57.771 43.478 14.46 0.00 40.27 3.01
678 724 2.189521 GCACCCGACCCGAATGAT 59.810 61.111 0.00 0.00 0.00 2.45
679 725 4.090588 GGCACCCGACCCGAATGA 62.091 66.667 0.00 0.00 0.00 2.57
810 856 0.251474 GGGGTTTAAGCGAAGGGGTT 60.251 55.000 0.00 0.00 40.10 4.11
811 857 1.381463 GGGGTTTAAGCGAAGGGGT 59.619 57.895 0.00 0.00 0.00 4.95
812 858 1.747745 CGGGGTTTAAGCGAAGGGG 60.748 63.158 0.00 0.00 0.00 4.79
813 859 1.022982 GTCGGGGTTTAAGCGAAGGG 61.023 60.000 0.00 0.00 0.00 3.95
818 864 1.301874 TGTGGTCGGGGTTTAAGCG 60.302 57.895 0.00 0.00 0.00 4.68
855 901 2.731461 ATGGGAGGAGGGAGGAGGG 61.731 68.421 0.00 0.00 0.00 4.30
899 945 3.959991 GAGCTTCCGTGTGCCTCCC 62.960 68.421 0.00 0.00 0.00 4.30
940 986 1.372997 CTACTGTGTGGAGCGCGTT 60.373 57.895 8.43 0.00 0.00 4.84
945 991 2.125512 CGGGCTACTGTGTGGAGC 60.126 66.667 0.00 0.00 35.39 4.70
972 1018 4.115199 AAGGTCTCATGGCGGGGC 62.115 66.667 0.00 0.00 0.00 5.80
1087 1133 3.647636 CGGAGGGATATGAGGATATGGT 58.352 50.000 0.00 0.00 0.00 3.55
1397 1443 4.946784 AGATGAATAAGCGTGTTTCCAC 57.053 40.909 0.00 0.00 38.27 4.02
1400 1446 7.851822 TTCAAAAGATGAATAAGCGTGTTTC 57.148 32.000 0.00 0.00 43.08 2.78
1563 1609 6.656270 AGAAGAAAATCTGTGTATGCATGACA 59.344 34.615 10.16 11.06 0.00 3.58
1641 1687 1.812571 CATGTCAAGGCAACAGGTACC 59.187 52.381 2.73 2.73 41.41 3.34
1677 1723 6.156748 TGTGAGAACTGTGAGCTTTAACTA 57.843 37.500 0.00 0.00 0.00 2.24
1722 1768 0.676736 GCAGACCCGGATCCTAGAAG 59.323 60.000 10.75 0.00 0.00 2.85
1723 1769 0.032515 TGCAGACCCGGATCCTAGAA 60.033 55.000 10.75 0.00 0.00 2.10
1936 1982 1.951895 GCTCCAATGCCATGTCTGTCA 60.952 52.381 0.00 0.00 0.00 3.58
2089 2135 4.044065 AGGACATTCCCAATGGTCTAAACA 59.956 41.667 0.00 0.00 43.21 2.83
2495 2541 2.435805 CTGCAGCCCTTTGTCTAGGATA 59.564 50.000 0.00 0.00 37.50 2.59
2555 2601 6.041523 CCTCATAGACCAAACCCTTTTTGAAA 59.958 38.462 0.00 0.00 0.00 2.69
2864 2910 3.257873 CACCAACCTTTGCATAACCATCA 59.742 43.478 0.00 0.00 0.00 3.07
2978 3024 3.925913 CGTGTAAATCCCCAAATTTGCAG 59.074 43.478 12.92 6.04 40.40 4.41
3245 3291 5.985911 AGCGTATTGTAAGTTATTGGGTCT 58.014 37.500 0.00 0.00 0.00 3.85
3317 3363 2.872245 ACAGCATAACATACGGTCATGC 59.128 45.455 0.00 0.00 41.78 4.06
3477 3523 5.710513 TTTGCACACTGAGCTTTGATTAT 57.289 34.783 0.00 0.00 0.00 1.28
3605 3651 5.806654 TGGCAGCTTCTTTAGGAAATTTT 57.193 34.783 0.00 0.00 33.07 1.82
3623 3669 4.206375 ACATAATCGGAATGAACATGGCA 58.794 39.130 0.00 0.00 0.00 4.92
3625 3671 8.232513 CAGATAACATAATCGGAATGAACATGG 58.767 37.037 0.00 0.00 0.00 3.66
3679 3725 4.498009 GCAGAGCTCTAACAAGCACAAAAA 60.498 41.667 17.75 0.00 45.00 1.94
3723 3769 4.002982 AGTGCGTGCAATATGGGTATATG 58.997 43.478 0.00 0.00 30.00 1.78
3767 3813 4.620723 TCTCACTTACATGACCAGGGTAT 58.379 43.478 0.00 0.00 0.00 2.73
3857 3905 5.247337 TCTCAATACCTGTACATCACCAACA 59.753 40.000 0.00 0.00 0.00 3.33
3976 4024 2.093764 TCCCAAAATAAATGCCTTGGCG 60.094 45.455 7.18 0.00 37.57 5.69
3985 4033 6.989759 AGTCTTTGCGTTTTCCCAAAATAAAT 59.010 30.769 0.00 0.00 31.29 1.40
3986 4034 6.342111 AGTCTTTGCGTTTTCCCAAAATAAA 58.658 32.000 0.00 0.00 31.29 1.40
3987 4035 5.908341 AGTCTTTGCGTTTTCCCAAAATAA 58.092 33.333 0.00 0.00 31.29 1.40
3988 4036 5.523438 AGTCTTTGCGTTTTCCCAAAATA 57.477 34.783 0.00 0.00 31.29 1.40
3989 4037 4.400529 AGTCTTTGCGTTTTCCCAAAAT 57.599 36.364 0.00 0.00 31.29 1.82
3990 4038 3.878160 AGTCTTTGCGTTTTCCCAAAA 57.122 38.095 0.00 0.00 31.29 2.44
4030 4078 4.668636 CATGTAACTTTTCCCCCACCTTA 58.331 43.478 0.00 0.00 0.00 2.69
4040 4088 5.099042 TCCTAGGAGGCATGTAACTTTTC 57.901 43.478 7.62 0.00 34.61 2.29
4228 4276 3.574445 GATCTGGCAGCAGCGCAG 61.574 66.667 11.47 1.31 43.41 5.18
4238 4286 1.419012 TGACAGGATGGATGATCTGGC 59.581 52.381 0.00 0.00 43.62 4.85
4263 4311 2.731571 GGGACTCGCCACCATAGCA 61.732 63.158 0.00 0.00 38.95 3.49
4301 4350 2.811317 CGCTGCCAAGGAGACGAC 60.811 66.667 0.00 0.00 0.00 4.34
4352 4401 1.356124 AGGATGACTTGCAGACCACT 58.644 50.000 0.00 0.00 31.87 4.00
4398 4447 2.899900 TCTTGCACTTTCTCTAGGCAGA 59.100 45.455 0.00 0.00 35.68 4.26
4447 4496 1.003118 TGCCTACTTTGCGACCAAGAT 59.997 47.619 0.00 0.00 31.52 2.40
4470 4519 1.993391 GGCCTACAGCACCACCCTA 60.993 63.158 0.00 0.00 46.50 3.53
4506 4556 3.970332 ACAGGTGCTGGACTGTCA 58.030 55.556 10.38 0.00 44.08 3.58
4599 4649 0.032515 TTCGAGGGATCCACCAGCTA 60.033 55.000 15.23 0.00 41.20 3.32
4634 4684 1.134965 GGCACATACTCTGCTCGTTCT 60.135 52.381 0.00 0.00 34.84 3.01
4661 4711 0.540923 AGCTGATCTGGAAGTGGAGC 59.459 55.000 1.46 0.00 33.76 4.70
4681 4731 1.388065 CCTCTCAGACGAGCCGGATT 61.388 60.000 5.05 0.00 39.30 3.01
4711 4761 2.033911 TGCTTTGGCGAGCCATCA 59.966 55.556 18.32 12.89 46.64 3.07
4831 4881 2.847327 ATATGCCTGCATCGCTAAGT 57.153 45.000 8.09 0.00 37.82 2.24


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

AutoCloner maintained by Alex Coulton.