Multiple sequence alignment - TraesCS2B01G415500

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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 TraesCS2B01G415500 chr2B 100.000 4542 0 0 969 5510 594100360 594095819 0.000000e+00 8388.0
1 TraesCS2B01G415500 chr2B 100.000 638 0 0 1 638 594101328 594100691 0.000000e+00 1179.0
2 TraesCS2B01G415500 chr2B 83.578 408 43 15 4935 5319 402120331 402120737 1.460000e-95 361.0
3 TraesCS2B01G415500 chr2A 94.723 4605 168 36 969 5510 651085269 651080677 0.000000e+00 7088.0
4 TraesCS2B01G415500 chr2A 89.954 219 17 3 198 416 651085903 651085690 1.510000e-70 278.0
5 TraesCS2B01G415500 chr2A 84.127 126 1 7 450 574 651085465 651085358 2.720000e-18 104.0
6 TraesCS2B01G415500 chr2D 95.151 4372 146 33 987 5319 506406496 506402152 0.000000e+00 6839.0
7 TraesCS2B01G415500 chr2D 97.126 174 5 0 49 222 506406707 506406534 1.500000e-75 294.0
8 TraesCS2B01G415500 chr2D 91.176 170 11 3 5345 5510 506402155 506401986 1.540000e-55 228.0
9 TraesCS2B01G415500 chr4B 100.000 37 0 0 1 37 397241080 397241044 9.900000e-08 69.4
10 TraesCS2B01G415500 chr4A 100.000 37 0 0 1 37 666278310 666278274 9.900000e-08 69.4
11 TraesCS2B01G415500 chr3B 100.000 37 0 0 1 37 110763056 110763020 9.900000e-08 69.4
12 TraesCS2B01G415500 chrUn 100.000 36 0 0 1 36 40418353 40418318 3.560000e-07 67.6
13 TraesCS2B01G415500 chrUn 100.000 36 0 0 1 36 79439990 79440025 3.560000e-07 67.6
14 TraesCS2B01G415500 chrUn 100.000 36 0 0 1 36 240107901 240107936 3.560000e-07 67.6
15 TraesCS2B01G415500 chrUn 100.000 36 0 0 1 36 294342733 294342698 3.560000e-07 67.6
16 TraesCS2B01G415500 chrUn 100.000 36 0 0 1 36 344975541 344975576 3.560000e-07 67.6
17 TraesCS2B01G415500 chr1D 100.000 36 0 0 1 36 342116095 342116060 3.560000e-07 67.6


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 TraesCS2B01G415500 chr2B 594095819 594101328 5509 True 4783.500000 8388 100.000000 1 5510 2 chr2B.!!$R1 5509
1 TraesCS2B01G415500 chr2A 651080677 651085903 5226 True 2490.000000 7088 89.601333 198 5510 3 chr2A.!!$R1 5312
2 TraesCS2B01G415500 chr2D 506401986 506406707 4721 True 2453.666667 6839 94.484333 49 5510 3 chr2D.!!$R1 5461

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
568 761 0.103390 CACCCAAACCCGTCCAAAAC 59.897 55.0 0.00 0.00 0.0 2.43 F
1089 1375 0.247460 TCTTCCTGCTCGTCATGGTG 59.753 55.0 0.00 0.00 0.0 4.17 F
2570 2862 0.322098 ATTCCGTCGACCATTGGCAA 60.322 50.0 10.58 0.68 0.0 4.52 F
3819 4111 0.172578 CGGATGTTCGTCTGCTGGTA 59.827 55.0 0.00 0.00 0.0 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2316 2608 0.320771 TCTGGCCTGCGAAAGAGTTC 60.321 55.0 3.32 0.0 0.00 3.01 R
2767 3059 0.324943 CCATAGGTAGCCGGGATTGG 59.675 60.0 2.18 0.0 0.00 3.16 R
4098 4390 0.244450 GTGATCCAACCGGTGTCGTA 59.756 55.0 8.52 0.0 33.95 3.43 R
5188 5516 0.039618 TCATTTCCTCCCCCAGTTGC 59.960 55.0 0.00 0.0 0.00 4.17 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
23 24 6.720112 ATATGCAATAGACATGGCAACTTT 57.280 33.333 0.00 0.00 44.38 2.66
24 25 4.870123 TGCAATAGACATGGCAACTTTT 57.130 36.364 0.00 0.00 38.19 2.27
25 26 5.973899 TGCAATAGACATGGCAACTTTTA 57.026 34.783 0.00 0.00 38.19 1.52
26 27 6.338214 TGCAATAGACATGGCAACTTTTAA 57.662 33.333 0.00 0.00 38.19 1.52
27 28 6.934056 TGCAATAGACATGGCAACTTTTAAT 58.066 32.000 0.00 0.00 38.19 1.40
28 29 7.035004 TGCAATAGACATGGCAACTTTTAATC 58.965 34.615 0.00 0.00 38.19 1.75
29 30 6.476706 GCAATAGACATGGCAACTTTTAATCC 59.523 38.462 0.00 0.00 30.66 3.01
30 31 7.546358 CAATAGACATGGCAACTTTTAATCCA 58.454 34.615 0.00 0.00 37.61 3.41
31 32 7.716799 ATAGACATGGCAACTTTTAATCCAA 57.283 32.000 0.00 0.00 37.61 3.53
32 33 6.418057 AGACATGGCAACTTTTAATCCAAA 57.582 33.333 0.00 0.00 37.61 3.28
33 34 6.825610 AGACATGGCAACTTTTAATCCAAAA 58.174 32.000 0.00 0.00 34.89 2.44
34 35 7.278875 AGACATGGCAACTTTTAATCCAAAAA 58.721 30.769 0.00 0.00 35.71 1.94
70 71 6.701145 TTTATGTGCACACTAAAAAGGACA 57.299 33.333 24.37 3.03 36.77 4.02
82 83 2.350863 AAAGGACAGGAGGGAGTGAT 57.649 50.000 0.00 0.00 0.00 3.06
167 168 4.512198 AGCTCAGTGTAGTACTATAGCACG 59.488 45.833 5.75 6.72 44.26 5.34
227 228 2.753966 GCCCGCGTCTGACGTACTA 61.754 63.158 28.38 0.00 44.73 1.82
228 229 1.061570 CCCGCGTCTGACGTACTAC 59.938 63.158 28.38 12.48 44.73 2.73
295 296 1.201825 GAGCGACGTCAAAGTGCAC 59.798 57.895 17.16 9.40 0.00 4.57
307 308 0.321298 AAGTGCACCGCGGTAGAAAT 60.321 50.000 33.70 16.58 0.00 2.17
311 312 2.202837 ACCGCGGTAGAAATCGGC 60.203 61.111 33.34 0.00 45.23 5.54
312 313 2.202824 CCGCGGTAGAAATCGGCA 60.203 61.111 19.50 0.00 35.20 5.69
385 386 2.730928 AGCGCGCTTAACGTTAACTAAA 59.269 40.909 31.32 0.00 46.11 1.85
424 448 1.737838 CTCCATGCTTTAACGCCAGA 58.262 50.000 0.99 0.00 0.00 3.86
425 449 1.398390 CTCCATGCTTTAACGCCAGAC 59.602 52.381 0.99 0.00 0.00 3.51
437 461 3.469564 GCCAGACGAGAGAGAGAGA 57.530 57.895 0.00 0.00 0.00 3.10
438 462 1.299541 GCCAGACGAGAGAGAGAGAG 58.700 60.000 0.00 0.00 0.00 3.20
439 463 1.134521 GCCAGACGAGAGAGAGAGAGA 60.135 57.143 0.00 0.00 0.00 3.10
440 464 2.826428 CCAGACGAGAGAGAGAGAGAG 58.174 57.143 0.00 0.00 0.00 3.20
443 467 4.503910 CAGACGAGAGAGAGAGAGAGAAA 58.496 47.826 0.00 0.00 0.00 2.52
445 469 3.270877 ACGAGAGAGAGAGAGAGAAAGC 58.729 50.000 0.00 0.00 0.00 3.51
446 470 3.270027 CGAGAGAGAGAGAGAGAAAGCA 58.730 50.000 0.00 0.00 0.00 3.91
447 471 3.310774 CGAGAGAGAGAGAGAGAAAGCAG 59.689 52.174 0.00 0.00 0.00 4.24
448 472 3.019564 AGAGAGAGAGAGAGAAAGCAGC 58.980 50.000 0.00 0.00 0.00 5.25
449 473 2.754552 GAGAGAGAGAGAGAAAGCAGCA 59.245 50.000 0.00 0.00 0.00 4.41
450 474 2.756760 AGAGAGAGAGAGAAAGCAGCAG 59.243 50.000 0.00 0.00 0.00 4.24
451 475 2.754552 GAGAGAGAGAGAAAGCAGCAGA 59.245 50.000 0.00 0.00 0.00 4.26
510 703 4.710695 CGCGCACACACCCGAGTA 62.711 66.667 8.75 0.00 0.00 2.59
511 704 3.110178 GCGCACACACCCGAGTAC 61.110 66.667 0.30 0.00 0.00 2.73
512 705 2.803670 CGCACACACCCGAGTACG 60.804 66.667 0.00 0.00 39.43 3.67
513 706 2.646719 GCACACACCCGAGTACGA 59.353 61.111 0.00 0.00 42.66 3.43
514 707 1.443872 GCACACACCCGAGTACGAG 60.444 63.158 0.00 0.00 42.66 4.18
515 708 1.954528 CACACACCCGAGTACGAGT 59.045 57.895 0.00 0.00 42.66 4.18
516 709 1.159285 CACACACCCGAGTACGAGTA 58.841 55.000 0.00 0.00 42.66 2.59
517 710 1.135859 CACACACCCGAGTACGAGTAC 60.136 57.143 5.32 5.32 42.66 2.73
519 712 2.028112 ACACACCCGAGTACGAGTACTA 60.028 50.000 15.03 0.00 45.63 1.82
520 713 2.349886 CACACCCGAGTACGAGTACTAC 59.650 54.545 15.03 8.69 45.63 2.73
521 714 1.936547 CACCCGAGTACGAGTACTACC 59.063 57.143 15.03 4.36 45.63 3.18
522 715 1.555075 ACCCGAGTACGAGTACTACCA 59.445 52.381 15.03 0.00 45.63 3.25
523 716 2.027192 ACCCGAGTACGAGTACTACCAA 60.027 50.000 15.03 0.00 45.63 3.67
568 761 0.103390 CACCCAAACCCGTCCAAAAC 59.897 55.000 0.00 0.00 0.00 2.43
569 762 1.044231 ACCCAAACCCGTCCAAAACC 61.044 55.000 0.00 0.00 0.00 3.27
570 763 1.743391 CCAAACCCGTCCAAAACCC 59.257 57.895 0.00 0.00 0.00 4.11
571 764 1.743391 CAAACCCGTCCAAAACCCC 59.257 57.895 0.00 0.00 0.00 4.95
572 765 1.829096 AAACCCGTCCAAAACCCCG 60.829 57.895 0.00 0.00 0.00 5.73
573 766 4.960866 ACCCGTCCAAAACCCCGC 62.961 66.667 0.00 0.00 0.00 6.13
574 767 4.958897 CCCGTCCAAAACCCCGCA 62.959 66.667 0.00 0.00 0.00 5.69
575 768 3.666253 CCGTCCAAAACCCCGCAC 61.666 66.667 0.00 0.00 0.00 5.34
576 769 4.020378 CGTCCAAAACCCCGCACG 62.020 66.667 0.00 0.00 0.00 5.34
577 770 4.337060 GTCCAAAACCCCGCACGC 62.337 66.667 0.00 0.00 0.00 5.34
578 771 4.877619 TCCAAAACCCCGCACGCA 62.878 61.111 0.00 0.00 0.00 5.24
579 772 4.639171 CCAAAACCCCGCACGCAC 62.639 66.667 0.00 0.00 0.00 5.34
580 773 3.893763 CAAAACCCCGCACGCACA 61.894 61.111 0.00 0.00 0.00 4.57
581 774 3.894947 AAAACCCCGCACGCACAC 61.895 61.111 0.00 0.00 0.00 3.82
631 914 3.732849 CCCTCCCTTCCCCTGCAC 61.733 72.222 0.00 0.00 0.00 4.57
632 915 2.935481 CCTCCCTTCCCCTGCACA 60.935 66.667 0.00 0.00 0.00 4.57
633 916 2.352805 CTCCCTTCCCCTGCACAC 59.647 66.667 0.00 0.00 0.00 3.82
634 917 3.612247 CTCCCTTCCCCTGCACACG 62.612 68.421 0.00 0.00 0.00 4.49
1051 1334 2.284405 GAACCTCCTCCCCCGTGA 60.284 66.667 0.00 0.00 0.00 4.35
1089 1375 0.247460 TCTTCCTGCTCGTCATGGTG 59.753 55.000 0.00 0.00 0.00 4.17
1094 1380 4.760047 GCTCGTCATGGTGGCGGT 62.760 66.667 4.01 0.00 46.79 5.68
1458 1750 2.811317 CAGGACAACGCGCTCTCC 60.811 66.667 5.73 7.29 0.00 3.71
2112 2404 2.232941 CCTTTCTGGCAATGCATTCACT 59.767 45.455 9.53 0.00 0.00 3.41
2265 2557 2.044252 AGCTTCTCCGGCGAGGTA 60.044 61.111 9.30 0.00 41.99 3.08
2316 2608 2.697751 CAGAGAGGTCTATCTTGGTGGG 59.302 54.545 0.00 0.00 0.00 4.61
2319 2611 3.108376 AGAGGTCTATCTTGGTGGGAAC 58.892 50.000 0.00 0.00 0.00 3.62
2537 2829 2.367030 TTGAATTTGAGCGGCAATGG 57.633 45.000 1.45 0.00 36.15 3.16
2570 2862 0.322098 ATTCCGTCGACCATTGGCAA 60.322 50.000 10.58 0.68 0.00 4.52
2763 3055 7.219322 TCAACATCTCAGTCAATTCTTTCTCA 58.781 34.615 0.00 0.00 0.00 3.27
2767 3059 3.679389 TCAGTCAATTCTTTCTCAGGGC 58.321 45.455 0.00 0.00 0.00 5.19
2892 3184 0.250038 TCACTGTGCTTGACCTCAGC 60.250 55.000 2.12 0.00 0.00 4.26
2914 3206 0.679002 CAACCATCTGACTGGCCCAG 60.679 60.000 9.83 9.83 40.15 4.45
3096 3388 1.181741 ACCTCTCGAAGCTGCAGACA 61.182 55.000 20.43 0.00 0.00 3.41
3102 3394 1.001293 TCGAAGCTGCAGACACTTGAT 59.999 47.619 20.43 0.00 0.00 2.57
3351 3643 1.302285 CCTGGCTCTGCTGATTGGT 59.698 57.895 0.00 0.00 0.00 3.67
3354 3646 2.758089 GGCTCTGCTGATTGGTGCG 61.758 63.158 0.00 0.00 0.00 5.34
3684 3976 3.787001 CGGCTCCCTTCCACCTCC 61.787 72.222 0.00 0.00 0.00 4.30
3687 3979 2.685380 CTCCCTTCCACCTCCGCT 60.685 66.667 0.00 0.00 0.00 5.52
3819 4111 0.172578 CGGATGTTCGTCTGCTGGTA 59.827 55.000 0.00 0.00 0.00 3.25
4137 4429 3.151906 GGCTATGTCGCCCCAGAT 58.848 61.111 0.00 0.00 44.41 2.90
4512 4804 3.048602 CCATCCCCGGCGTAGTAG 58.951 66.667 6.01 0.00 0.00 2.57
4572 4865 6.406692 TTCAGTTCAGTAGCTTGTACTCTT 57.593 37.500 0.00 0.00 0.00 2.85
4573 4866 7.520451 TTCAGTTCAGTAGCTTGTACTCTTA 57.480 36.000 0.00 0.00 0.00 2.10
4574 4867 7.147143 TCAGTTCAGTAGCTTGTACTCTTAG 57.853 40.000 0.00 0.00 0.00 2.18
4575 4868 6.715718 TCAGTTCAGTAGCTTGTACTCTTAGT 59.284 38.462 0.00 0.00 0.00 2.24
4658 4951 3.994853 GCCAAGCAAGTGGGTGGC 61.995 66.667 0.00 0.00 39.26 5.01
4695 4989 4.161001 GGGGTTTCTAATCTCGTGGTTAGA 59.839 45.833 14.58 14.58 35.69 2.10
4823 5125 1.341531 GCTACTGATGCAGGATACGGT 59.658 52.381 0.00 0.00 46.39 4.83
4828 5130 1.299541 GATGCAGGATACGGTTGTGG 58.700 55.000 0.00 0.00 46.39 4.17
4958 5272 1.139095 GCTGCTGCCAGATCTTTGC 59.861 57.895 3.85 6.99 41.77 3.68
5014 5329 9.109246 TGTTATCTATCTCCATTGATCCAAGAT 57.891 33.333 0.00 0.00 0.00 2.40
5016 5331 5.802465 TCTATCTCCATTGATCCAAGATGC 58.198 41.667 0.00 0.00 0.00 3.91
5044 5371 3.955771 TGACCGTTAGCTTGTTGTTTC 57.044 42.857 0.00 0.00 0.00 2.78
5107 5435 5.836358 TGTTGGAGTATTTAACTTTGCCCTT 59.164 36.000 0.00 0.00 39.07 3.95
5108 5436 6.325286 TGTTGGAGTATTTAACTTTGCCCTTT 59.675 34.615 0.00 0.00 39.07 3.11
5112 5440 9.403583 TGGAGTATTTAACTTTGCCCTTTATAG 57.596 33.333 0.00 0.00 39.07 1.31
5136 5464 4.271016 GGGGCCCCTGCTTATCCG 62.271 72.222 35.49 0.00 37.74 4.18
5186 5514 6.704493 TCTGTTAGTGCACCTTGTTTTACTAG 59.296 38.462 14.63 0.00 0.00 2.57
5188 5516 3.751518 AGTGCACCTTGTTTTACTAGGG 58.248 45.455 14.63 3.06 43.89 3.53
5192 5520 3.305131 GCACCTTGTTTTACTAGGGCAAC 60.305 47.826 11.09 0.00 43.89 4.17
5213 5544 1.008206 TGGGGGAGGAAATGATTTGGG 59.992 52.381 0.00 0.00 0.00 4.12
5215 5546 1.290732 GGGGAGGAAATGATTTGGGGA 59.709 52.381 0.00 0.00 0.00 4.81
5216 5547 2.670939 GGGAGGAAATGATTTGGGGAG 58.329 52.381 0.00 0.00 0.00 4.30
5217 5548 2.034878 GGAGGAAATGATTTGGGGAGC 58.965 52.381 0.00 0.00 0.00 4.70
5218 5549 2.624029 GGAGGAAATGATTTGGGGAGCA 60.624 50.000 0.00 0.00 0.00 4.26
5239 5587 4.675029 GCCACCACCGCTGTACGT 62.675 66.667 0.00 0.00 41.42 3.57
5269 5617 2.874701 CAATTAGCGGGAGATCTTGGTG 59.125 50.000 0.00 0.00 0.00 4.17
5294 5642 1.007336 GCACTCCACCGTCGTACTTG 61.007 60.000 0.00 0.00 0.00 3.16
5322 5670 4.066490 AGCATCTAAATCTCATCAGCAGC 58.934 43.478 0.00 0.00 0.00 5.25
5352 5700 1.341531 GGTGAGATACGGTCAGATGGG 59.658 57.143 0.00 0.00 0.00 4.00
5410 5760 8.956426 TGTATCAGTTAATGAAATCTGGAAACC 58.044 33.333 0.00 0.00 42.53 3.27
5455 5805 1.856265 GAGGACGGCCAGTTTTGCAG 61.856 60.000 11.69 0.00 36.29 4.41
5503 5856 6.676456 GCTGAAATGAGCCACAATAAGTAGTG 60.676 42.308 0.00 0.00 32.35 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.720112 AAAGTTGCCATGTCTATTGCATAT 57.280 33.333 0.00 0.00 35.21 1.78
1 2 6.528537 AAAAGTTGCCATGTCTATTGCATA 57.471 33.333 0.00 0.00 35.21 3.14
2 3 5.410355 AAAAGTTGCCATGTCTATTGCAT 57.590 34.783 0.00 0.00 35.21 3.96
3 4 4.870123 AAAAGTTGCCATGTCTATTGCA 57.130 36.364 0.00 0.00 33.58 4.08
4 5 6.476706 GGATTAAAAGTTGCCATGTCTATTGC 59.523 38.462 0.00 0.00 0.00 3.56
5 6 7.546358 TGGATTAAAAGTTGCCATGTCTATTG 58.454 34.615 0.00 0.00 0.00 1.90
6 7 7.716799 TGGATTAAAAGTTGCCATGTCTATT 57.283 32.000 0.00 0.00 0.00 1.73
7 8 7.716799 TTGGATTAAAAGTTGCCATGTCTAT 57.283 32.000 0.00 0.00 0.00 1.98
8 9 7.531857 TTTGGATTAAAAGTTGCCATGTCTA 57.468 32.000 0.00 0.00 0.00 2.59
9 10 6.418057 TTTGGATTAAAAGTTGCCATGTCT 57.582 33.333 0.00 0.00 0.00 3.41
10 11 7.489574 TTTTTGGATTAAAAGTTGCCATGTC 57.510 32.000 0.00 0.00 39.29 3.06
31 32 3.249917 CATAAATTGGGTCGCGCTTTTT 58.750 40.909 5.56 0.00 0.00 1.94
32 33 2.230266 ACATAAATTGGGTCGCGCTTTT 59.770 40.909 5.56 0.00 0.00 2.27
33 34 1.816224 ACATAAATTGGGTCGCGCTTT 59.184 42.857 5.56 0.00 0.00 3.51
34 35 1.132262 CACATAAATTGGGTCGCGCTT 59.868 47.619 5.56 0.00 0.00 4.68
35 36 0.732571 CACATAAATTGGGTCGCGCT 59.267 50.000 5.56 0.00 0.00 5.92
36 37 0.865639 GCACATAAATTGGGTCGCGC 60.866 55.000 0.00 0.00 0.00 6.86
37 38 0.449786 TGCACATAAATTGGGTCGCG 59.550 50.000 0.00 0.00 0.00 5.87
38 39 1.201181 TGTGCACATAAATTGGGTCGC 59.799 47.619 17.42 0.00 0.00 5.19
39 40 2.487762 AGTGTGCACATAAATTGGGTCG 59.512 45.455 24.69 0.00 0.00 4.79
40 41 5.637006 TTAGTGTGCACATAAATTGGGTC 57.363 39.130 24.69 5.70 0.00 4.46
41 42 6.412362 TTTTAGTGTGCACATAAATTGGGT 57.588 33.333 24.69 2.24 0.00 4.51
42 43 6.368516 CCTTTTTAGTGTGCACATAAATTGGG 59.631 38.462 24.69 20.41 0.00 4.12
43 44 7.116233 GTCCTTTTTAGTGTGCACATAAATTGG 59.884 37.037 24.69 24.36 0.00 3.16
44 45 7.651304 TGTCCTTTTTAGTGTGCACATAAATTG 59.349 33.333 24.69 18.82 0.00 2.32
45 46 7.721402 TGTCCTTTTTAGTGTGCACATAAATT 58.279 30.769 24.69 9.16 0.00 1.82
46 47 7.283625 TGTCCTTTTTAGTGTGCACATAAAT 57.716 32.000 24.69 12.02 0.00 1.40
47 48 6.238897 CCTGTCCTTTTTAGTGTGCACATAAA 60.239 38.462 24.69 22.13 0.00 1.40
70 71 4.273318 GCAAAAACATATCACTCCCTCCT 58.727 43.478 0.00 0.00 0.00 3.69
82 83 2.873472 ACACTCGAACCGCAAAAACATA 59.127 40.909 0.00 0.00 0.00 2.29
121 122 1.776667 CCAAATGGCCTCTCCCTCATA 59.223 52.381 3.32 0.00 0.00 2.15
167 168 1.201647 AGCTGATGAAATGTGTGCAGC 59.798 47.619 0.00 0.00 46.58 5.25
219 220 2.680339 GGTGGACCTACAGTAGTACGTC 59.320 54.545 6.84 6.84 36.28 4.34
227 228 2.119832 AGCGGGTGGACCTACAGT 59.880 61.111 0.00 0.00 36.97 3.55
228 229 2.579201 CAGCGGGTGGACCTACAG 59.421 66.667 0.00 0.00 36.97 2.74
276 277 1.954146 TGCACTTTGACGTCGCTCC 60.954 57.895 11.62 0.00 0.00 4.70
279 280 2.248431 GGTGCACTTTGACGTCGC 59.752 61.111 17.98 8.25 0.00 5.19
286 287 1.225376 TTCTACCGCGGTGCACTTTG 61.225 55.000 40.02 19.33 0.00 2.77
291 292 1.807981 CGATTTCTACCGCGGTGCA 60.808 57.895 40.02 23.42 0.00 4.57
295 296 1.157870 AATGCCGATTTCTACCGCGG 61.158 55.000 26.86 26.86 46.14 6.46
325 326 4.994471 CAGGCTGTCACTGCGGCA 62.994 66.667 6.28 1.29 42.25 5.69
326 327 4.996434 ACAGGCTGTCACTGCGGC 62.996 66.667 15.88 0.00 39.55 6.53
385 386 3.649986 GCGCGCTTTGTGAGGTGT 61.650 61.111 26.67 0.00 0.00 4.16
424 448 3.270877 GCTTTCTCTCTCTCTCTCTCGT 58.729 50.000 0.00 0.00 0.00 4.18
425 449 3.270027 TGCTTTCTCTCTCTCTCTCTCG 58.730 50.000 0.00 0.00 0.00 4.04
427 451 3.019564 GCTGCTTTCTCTCTCTCTCTCT 58.980 50.000 0.00 0.00 0.00 3.10
428 452 2.754552 TGCTGCTTTCTCTCTCTCTCTC 59.245 50.000 0.00 0.00 0.00 3.20
432 456 3.591196 TTCTGCTGCTTTCTCTCTCTC 57.409 47.619 0.00 0.00 0.00 3.20
433 457 4.348863 TTTTCTGCTGCTTTCTCTCTCT 57.651 40.909 0.00 0.00 0.00 3.10
434 458 4.083377 CCTTTTTCTGCTGCTTTCTCTCTC 60.083 45.833 0.00 0.00 0.00 3.20
435 459 3.819902 CCTTTTTCTGCTGCTTTCTCTCT 59.180 43.478 0.00 0.00 0.00 3.10
436 460 3.611293 GCCTTTTTCTGCTGCTTTCTCTC 60.611 47.826 0.00 0.00 0.00 3.20
437 461 2.295629 GCCTTTTTCTGCTGCTTTCTCT 59.704 45.455 0.00 0.00 0.00 3.10
438 462 2.670479 GCCTTTTTCTGCTGCTTTCTC 58.330 47.619 0.00 0.00 0.00 2.87
439 463 1.000938 CGCCTTTTTCTGCTGCTTTCT 60.001 47.619 0.00 0.00 0.00 2.52
440 464 1.412387 CGCCTTTTTCTGCTGCTTTC 58.588 50.000 0.00 0.00 0.00 2.62
443 467 2.270986 CCCGCCTTTTTCTGCTGCT 61.271 57.895 0.00 0.00 0.00 4.24
445 469 1.589716 CTCCCCGCCTTTTTCTGCTG 61.590 60.000 0.00 0.00 0.00 4.41
446 470 1.303643 CTCCCCGCCTTTTTCTGCT 60.304 57.895 0.00 0.00 0.00 4.24
447 471 1.303317 TCTCCCCGCCTTTTTCTGC 60.303 57.895 0.00 0.00 0.00 4.26
448 472 1.298859 CGTCTCCCCGCCTTTTTCTG 61.299 60.000 0.00 0.00 0.00 3.02
449 473 1.003718 CGTCTCCCCGCCTTTTTCT 60.004 57.895 0.00 0.00 0.00 2.52
450 474 0.604511 TTCGTCTCCCCGCCTTTTTC 60.605 55.000 0.00 0.00 0.00 2.29
451 475 0.179012 TTTCGTCTCCCCGCCTTTTT 60.179 50.000 0.00 0.00 0.00 1.94
497 690 4.861883 CTCGTACTCGGGTGTGTG 57.138 61.111 0.00 0.00 37.69 3.82
506 699 6.589830 TTACGATTGGTAGTACTCGTACTC 57.410 41.667 17.83 5.79 43.79 2.59
507 700 6.985188 TTTACGATTGGTAGTACTCGTACT 57.015 37.500 17.83 13.63 43.79 2.73
508 701 9.716507 TTTATTTACGATTGGTAGTACTCGTAC 57.283 33.333 17.83 0.00 43.79 3.67
510 703 9.076596 GTTTTATTTACGATTGGTAGTACTCGT 57.923 33.333 17.03 17.03 45.40 4.18
511 704 8.255143 CGTTTTATTTACGATTGGTAGTACTCG 58.745 37.037 0.00 8.43 41.33 4.18
512 705 8.534778 CCGTTTTATTTACGATTGGTAGTACTC 58.465 37.037 0.00 0.00 41.33 2.59
513 706 7.010460 GCCGTTTTATTTACGATTGGTAGTACT 59.990 37.037 0.00 0.00 41.33 2.73
514 707 7.119360 GCCGTTTTATTTACGATTGGTAGTAC 58.881 38.462 0.00 0.00 41.33 2.73
515 708 6.257630 GGCCGTTTTATTTACGATTGGTAGTA 59.742 38.462 0.00 0.00 41.33 1.82
516 709 5.065090 GGCCGTTTTATTTACGATTGGTAGT 59.935 40.000 0.00 0.00 41.33 2.73
517 710 5.295045 AGGCCGTTTTATTTACGATTGGTAG 59.705 40.000 0.00 0.00 41.33 3.18
518 711 5.184711 AGGCCGTTTTATTTACGATTGGTA 58.815 37.500 0.00 0.00 41.33 3.25
519 712 4.011698 AGGCCGTTTTATTTACGATTGGT 58.988 39.130 0.00 0.00 41.33 3.67
520 713 4.594136 GAGGCCGTTTTATTTACGATTGG 58.406 43.478 0.00 0.00 41.33 3.16
521 714 4.033129 TCGAGGCCGTTTTATTTACGATTG 59.967 41.667 0.00 0.00 41.33 2.67
522 715 4.183101 TCGAGGCCGTTTTATTTACGATT 58.817 39.130 0.00 0.00 41.33 3.34
523 716 3.784338 TCGAGGCCGTTTTATTTACGAT 58.216 40.909 0.00 0.00 41.33 3.73
589 782 3.040414 GAAGAAAAGGAGCGCGGGC 62.040 63.158 17.92 17.92 40.37 6.13
590 783 1.362406 GAGAAGAAAAGGAGCGCGGG 61.362 60.000 8.83 0.00 0.00 6.13
593 786 1.027255 GGGGAGAAGAAAAGGAGCGC 61.027 60.000 0.00 0.00 0.00 5.92
615 898 2.935481 TGTGCAGGGGAAGGGAGG 60.935 66.667 0.00 0.00 0.00 4.30
616 899 2.352805 GTGTGCAGGGGAAGGGAG 59.647 66.667 0.00 0.00 0.00 4.30
617 900 3.636231 CGTGTGCAGGGGAAGGGA 61.636 66.667 0.00 0.00 0.00 4.20
972 1255 1.103398 CGAGGGCCTTGGCATTTAGG 61.103 60.000 13.46 0.00 34.54 2.69
973 1256 0.107214 TCGAGGGCCTTGGCATTTAG 60.107 55.000 20.82 1.07 0.00 1.85
974 1257 0.107214 CTCGAGGGCCTTGGCATTTA 60.107 55.000 20.82 0.00 0.00 1.40
975 1258 1.379044 CTCGAGGGCCTTGGCATTT 60.379 57.895 20.82 0.00 0.00 2.32
976 1259 2.273449 CTCGAGGGCCTTGGCATT 59.727 61.111 20.82 0.30 0.00 3.56
977 1260 4.496336 GCTCGAGGGCCTTGGCAT 62.496 66.667 20.82 0.97 0.00 4.40
980 1263 3.393970 TCAGCTCGAGGGCCTTGG 61.394 66.667 20.82 12.26 0.00 3.61
981 1264 2.125350 GTCAGCTCGAGGGCCTTG 60.125 66.667 15.18 15.18 0.00 3.61
982 1265 1.557269 ATTGTCAGCTCGAGGGCCTT 61.557 55.000 15.58 0.00 0.00 4.35
983 1266 1.992277 ATTGTCAGCTCGAGGGCCT 60.992 57.895 15.58 5.25 0.00 5.19
984 1267 1.817099 CATTGTCAGCTCGAGGGCC 60.817 63.158 15.58 0.00 0.00 5.80
985 1268 1.086634 GTCATTGTCAGCTCGAGGGC 61.087 60.000 15.58 0.66 0.00 5.19
986 1269 0.803768 CGTCATTGTCAGCTCGAGGG 60.804 60.000 15.58 0.00 0.00 4.30
987 1270 0.171231 TCGTCATTGTCAGCTCGAGG 59.829 55.000 15.58 0.00 0.00 4.63
988 1271 1.851053 CATCGTCATTGTCAGCTCGAG 59.149 52.381 8.45 8.45 0.00 4.04
2316 2608 0.320771 TCTGGCCTGCGAAAGAGTTC 60.321 55.000 3.32 0.00 0.00 3.01
2319 2611 1.012841 GAATCTGGCCTGCGAAAGAG 58.987 55.000 3.32 0.00 0.00 2.85
2443 2735 1.273886 GTTGTCAGAGAGGTCCAGGAC 59.726 57.143 11.70 11.70 0.00 3.85
2537 2829 1.803289 GGAATGCGGCCTGAGAAAC 59.197 57.895 0.00 0.00 0.00 2.78
2570 2862 1.122019 AACTCGGAGGTTCAGCAGGT 61.122 55.000 10.23 0.00 0.00 4.00
2767 3059 0.324943 CCATAGGTAGCCGGGATTGG 59.675 60.000 2.18 0.00 0.00 3.16
2892 3184 1.021390 GGCCAGTCAGATGGTTGTCG 61.021 60.000 0.00 0.00 42.75 4.35
2914 3206 1.473278 CCTCGAGAGGTCACTTGGTAC 59.527 57.143 15.71 0.00 43.61 3.34
3096 3388 4.717877 TGTTGTTGGATGACAGATCAAGT 58.282 39.130 0.00 0.00 38.69 3.16
3102 3394 4.067192 CTGTGATGTTGTTGGATGACAGA 58.933 43.478 0.00 0.00 36.29 3.41
3250 3542 0.105964 CCACACAAGTCTCGGTTGGA 59.894 55.000 0.00 0.00 0.00 3.53
3346 3638 4.666253 AGCAGCCACCGCACCAAT 62.666 61.111 0.00 0.00 37.52 3.16
3354 3646 2.360852 AGTGATGCAGCAGCCACC 60.361 61.111 20.88 5.72 41.13 4.61
3378 3670 2.549198 GCAGCAGCACAGCAACAGA 61.549 57.895 0.00 0.00 41.58 3.41
3402 3694 2.554636 CCACCGCAGCAAGCTGAAA 61.555 57.895 25.03 0.00 46.30 2.69
3807 4099 2.034104 AGTCGTATACCAGCAGACGA 57.966 50.000 0.00 0.00 39.61 4.20
3819 4111 3.126001 CCATTGGGCATGTAGTCGTAT 57.874 47.619 0.00 0.00 0.00 3.06
4098 4390 0.244450 GTGATCCAACCGGTGTCGTA 59.756 55.000 8.52 0.00 33.95 3.43
4392 4684 4.570663 CGATCCAGCGGGTCGGAC 62.571 72.222 18.58 0.00 35.46 4.79
4497 4789 1.902432 GAGCTACTACGCCGGGGAT 60.902 63.158 27.23 11.98 0.00 3.85
4544 4837 4.573900 ACAAGCTACTGAACTGAATCTGG 58.426 43.478 0.00 0.00 0.00 3.86
4695 4989 3.586225 ATGGCCACCTGACCTCCCT 62.586 63.158 8.16 0.00 0.00 4.20
4823 5125 0.178921 ACAGAGGAGAGGAGCCACAA 60.179 55.000 0.00 0.00 0.00 3.33
4828 5130 2.172717 AGAGAGTACAGAGGAGAGGAGC 59.827 54.545 0.00 0.00 0.00 4.70
4900 5207 7.943413 ATGATGAGTATTGAAGACAAGATCG 57.057 36.000 0.00 0.00 39.46 3.69
4945 5259 1.469703 CGACATTGCAAAGATCTGGCA 59.530 47.619 16.08 16.08 35.41 4.92
4958 5272 1.717113 CAAATGCACAGCACGACATTG 59.283 47.619 0.00 0.00 43.04 2.82
5014 5329 1.725641 CTAACGGTCATGAAGCAGCA 58.274 50.000 0.00 0.00 0.00 4.41
5016 5331 2.015736 AGCTAACGGTCATGAAGCAG 57.984 50.000 16.54 7.79 35.63 4.24
5044 5371 4.990257 CACTAATCATTTTGTGCAGAGGG 58.010 43.478 0.00 0.00 33.10 4.30
5107 5435 1.297141 AGGGGCCCCTTCTCACTATAA 59.703 52.381 39.79 0.00 45.70 0.98
5108 5436 0.949582 AGGGGCCCCTTCTCACTATA 59.050 55.000 39.79 0.00 45.70 1.31
5112 5440 4.432741 GCAGGGGCCCCTTCTCAC 62.433 72.222 42.71 23.36 45.70 3.51
5123 5451 0.541863 AGACAACGGATAAGCAGGGG 59.458 55.000 0.00 0.00 0.00 4.79
5136 5464 2.565841 GTATCCATCCAGCCAGACAAC 58.434 52.381 0.00 0.00 0.00 3.32
5186 5514 2.168272 ATTTCCTCCCCCAGTTGCCC 62.168 60.000 0.00 0.00 0.00 5.36
5188 5516 0.039618 TCATTTCCTCCCCCAGTTGC 59.960 55.000 0.00 0.00 0.00 4.17
5192 5520 2.391678 CCAAATCATTTCCTCCCCCAG 58.608 52.381 0.00 0.00 0.00 4.45
5231 5579 5.229260 GCTAATTGCCAAATAAACGTACAGC 59.771 40.000 0.00 0.00 35.15 4.40
5239 5587 4.274147 TCTCCCGCTAATTGCCAAATAAA 58.726 39.130 0.00 0.00 38.78 1.40
5294 5642 5.061853 TGATGAGATTTAGATGCTCAAGGC 58.938 41.667 0.00 0.00 41.48 4.35
5322 5670 3.076258 TATCTCACCGTGCGCCCAG 62.076 63.158 4.18 0.00 0.00 4.45
5410 5760 4.919168 CAGTGGACACAAATGCACATTTAG 59.081 41.667 8.22 7.11 38.84 1.85
5442 5792 1.662044 CACTCCTGCAAAACTGGCC 59.338 57.895 0.00 0.00 37.30 5.36


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

AutoCloner maintained by Alex Coulton.