Multiple sequence alignment - TraesCS2D01G395800

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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 TraesCS2D01G395800 chr2D 100.000 6105 0 0 1 6105 506798687 506792583 0.000000e+00 11274.0
1 TraesCS2D01G395800 chr2A 93.135 3059 153 26 1 3019 651616055 651613014 0.000000e+00 4433.0
2 TraesCS2D01G395800 chr2A 98.149 1459 26 1 3018 4476 651612910 651611453 0.000000e+00 2543.0
3 TraesCS2D01G395800 chr2A 91.163 1573 75 31 4555 6105 651611374 651609844 0.000000e+00 2076.0
4 TraesCS2D01G395800 chr2A 96.667 60 2 0 4459 4518 651611441 651611382 3.890000e-17 100.0
5 TraesCS2D01G395800 chr2B 96.063 2489 76 9 1739 4209 594851575 594849091 0.000000e+00 4034.0
6 TraesCS2D01G395800 chr2B 94.538 1538 50 14 4576 6105 594848328 594846817 0.000000e+00 2344.0
7 TraesCS2D01G395800 chr2B 93.697 825 30 7 832 1640 594852402 594851584 0.000000e+00 1216.0
8 TraesCS2D01G395800 chr2B 96.957 230 6 1 4183 4411 594848925 594848696 9.600000e-103 385.0
9 TraesCS2D01G395800 chr2B 97.101 69 2 0 4408 4476 594848581 594848513 3.870000e-22 117.0
10 TraesCS2D01G395800 chr2B 96.610 59 2 0 4459 4517 594848502 594848444 1.400000e-16 99.0
11 TraesCS2D01G395800 chr5D 93.478 46 3 0 707 752 556546755 556546800 1.100000e-07 69.4
12 TraesCS2D01G395800 chr5D 97.297 37 1 0 706 742 346884142 346884106 5.110000e-06 63.9
13 TraesCS2D01G395800 chr3B 90.196 51 2 2 706 756 493117253 493117300 5.110000e-06 63.9


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 TraesCS2D01G395800 chr2D 506792583 506798687 6104 True 11274.000000 11274 100.000000 1 6105 1 chr2D.!!$R1 6104
1 TraesCS2D01G395800 chr2A 651609844 651616055 6211 True 2288.000000 4433 94.778500 1 6105 4 chr2A.!!$R1 6104
2 TraesCS2D01G395800 chr2B 594846817 594852402 5585 True 1365.833333 4034 95.827667 832 6105 6 chr2B.!!$R1 5273

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
262 264 0.034337 TACTTGCCTTCACCACCGAC 59.966 55.000 0.00 0.0 0.00 4.79 F
699 703 0.167470 TGAGTCGGCGAGAACTAACG 59.833 55.000 11.20 0.0 0.00 3.18 F
710 714 0.175073 GAACTAACGATCTGCCGGGT 59.825 55.000 2.18 0.0 0.00 5.28 F
1224 1246 0.249826 GGTTCCGGTGGACGTGTAAA 60.250 55.000 0.00 0.0 42.24 2.01 F
1876 1918 0.930310 CTTACATCCACATGGCGTCG 59.070 55.000 0.00 0.0 33.82 5.12 F
2682 2729 0.247814 GTGAACCTCGCAATGCATCG 60.248 55.000 5.91 0.0 0.00 3.84 F
4105 4273 1.734137 GGATTGGCATGCTGCTGAG 59.266 57.895 18.92 0.0 44.28 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1735 1772 0.318120 CCATGTCAAGTTTGTGGGGC 59.682 55.000 0.00 0.00 0.00 5.80 R
2178 2225 1.344065 TAACAACAGCGGGAGGAGAA 58.656 50.000 0.00 0.00 0.00 2.87 R
2600 2647 3.004419 CACATACGATGTAGACCCGTGAT 59.996 47.826 0.00 0.00 42.70 3.06 R
2616 2663 8.543862 TTATCATCTCATCTTCATGCACATAC 57.456 34.615 0.00 0.00 0.00 2.39 R
3870 4038 0.803380 GGCCATTGCTTCATGCGAAC 60.803 55.000 0.00 0.00 46.63 3.95 R
4592 5182 5.223382 AGGATTAAATATCAGACGTGAGCG 58.777 41.667 0.00 0.00 44.93 5.03 R
5710 6325 0.319383 CATCCCGCAGCTAGCTACTG 60.319 60.000 18.86 8.27 42.61 2.74 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
31 32 6.606234 AATAACCGGCGAAAAACAAAATTT 57.394 29.167 9.30 0.00 0.00 1.82
37 38 4.903016 CGGCGAAAAACAAAATTTCATTGG 59.097 37.500 0.00 0.00 36.75 3.16
47 48 9.625747 AAACAAAATTTCATTGGAAACCATACT 57.374 25.926 0.00 0.00 45.22 2.12
49 50 9.927668 ACAAAATTTCATTGGAAACCATACTAG 57.072 29.630 0.00 0.00 45.22 2.57
54 55 5.132502 TCATTGGAAACCATACTAGCCATG 58.867 41.667 0.00 0.00 31.53 3.66
55 56 4.584638 TTGGAAACCATACTAGCCATGT 57.415 40.909 0.00 0.00 31.53 3.21
87 88 0.602638 TGTGTGCCACTTGACGGATC 60.603 55.000 0.00 0.00 35.11 3.36
132 133 1.839994 CAAGAGGAGGGGATACTTGCA 59.160 52.381 0.00 0.00 33.13 4.08
144 146 4.076394 GGATACTTGCAAACACCCTTGTA 58.924 43.478 0.00 0.00 33.55 2.41
149 151 4.022329 ACTTGCAAACACCCTTGTAATAGC 60.022 41.667 0.00 0.00 33.55 2.97
151 153 3.891977 TGCAAACACCCTTGTAATAGCAA 59.108 39.130 0.00 0.00 33.55 3.91
167 169 5.772825 ATAGCAAACTTTGAAGAGTGCAA 57.227 34.783 18.42 0.00 39.82 4.08
168 170 4.660789 AGCAAACTTTGAAGAGTGCAAT 57.339 36.364 18.42 0.00 39.82 3.56
176 178 3.138884 TGAAGAGTGCAATGCTAACCA 57.861 42.857 6.82 0.00 0.00 3.67
179 181 2.283298 AGAGTGCAATGCTAACCATCG 58.717 47.619 6.82 0.00 31.43 3.84
181 183 0.734889 GTGCAATGCTAACCATCGCT 59.265 50.000 6.82 0.00 34.90 4.93
188 190 3.763097 TGCTAACCATCGCTTGAAATG 57.237 42.857 0.00 0.00 0.00 2.32
189 191 2.423185 TGCTAACCATCGCTTGAAATGG 59.577 45.455 0.00 0.00 46.53 3.16
201 203 8.798153 CATCGCTTGAAATGGTATTTAGAAAAC 58.202 33.333 0.00 0.00 0.00 2.43
202 204 7.018826 TCGCTTGAAATGGTATTTAGAAAACG 58.981 34.615 0.00 0.00 0.00 3.60
220 222 8.173321 AGAAAACGTTGAAAGAATTTTGACTG 57.827 30.769 0.00 0.00 39.27 3.51
256 258 5.065218 CAGATAACACATACTTGCCTTCACC 59.935 44.000 0.00 0.00 0.00 4.02
261 263 0.981183 ATACTTGCCTTCACCACCGA 59.019 50.000 0.00 0.00 0.00 4.69
262 264 0.034337 TACTTGCCTTCACCACCGAC 59.966 55.000 0.00 0.00 0.00 4.79
265 267 3.948719 GCCTTCACCACCGACCCA 61.949 66.667 0.00 0.00 0.00 4.51
294 296 3.620488 TGGAGAAATAGGACCATGCAAC 58.380 45.455 0.00 0.00 0.00 4.17
295 297 3.010027 TGGAGAAATAGGACCATGCAACA 59.990 43.478 0.00 0.00 0.00 3.33
312 315 7.201626 CCATGCAACAGAACAAATCAAAAGAAA 60.202 33.333 0.00 0.00 0.00 2.52
337 340 1.468520 CGGAGTCATCGCACCAAAATT 59.531 47.619 0.00 0.00 0.00 1.82
342 345 3.317711 AGTCATCGCACCAAAATTCAACA 59.682 39.130 0.00 0.00 0.00 3.33
356 359 7.201478 CCAAAATTCAACAAACAACTTCGCTTA 60.201 33.333 0.00 0.00 0.00 3.09
365 368 5.493133 AACAACTTCGCTTAATTGACACA 57.507 34.783 0.00 0.00 0.00 3.72
392 396 2.266554 GCCAAGATCGAAGAGACACAG 58.733 52.381 0.00 0.00 43.63 3.66
407 411 3.750130 AGACACAGCAAATCTGATGACAC 59.250 43.478 0.00 0.00 45.72 3.67
423 427 0.258774 ACACATACCCTCATTGGCCC 59.741 55.000 0.00 0.00 0.00 5.80
426 430 1.645919 ACATACCCTCATTGGCCCTTT 59.354 47.619 0.00 0.00 0.00 3.11
440 444 2.619074 GGCCCTTTGCTAGTGTCAGATT 60.619 50.000 0.00 0.00 40.92 2.40
447 451 5.386958 TTGCTAGTGTCAGATTAGACGTT 57.613 39.130 0.00 0.00 41.41 3.99
463 467 1.340795 ACGTTGTCGAGGTAGGGAGAT 60.341 52.381 0.00 0.00 40.62 2.75
465 469 1.112113 TTGTCGAGGTAGGGAGATGC 58.888 55.000 0.00 0.00 0.00 3.91
488 492 4.142816 CCTTATTCCAACTCGTCTTTGCAG 60.143 45.833 0.00 0.00 0.00 4.41
495 499 0.957395 CTCGTCTTTGCAGCCACCAT 60.957 55.000 0.00 0.00 0.00 3.55
499 503 1.068055 GTCTTTGCAGCCACCATCTTG 60.068 52.381 0.00 0.00 0.00 3.02
500 504 0.389426 CTTTGCAGCCACCATCTTGC 60.389 55.000 0.00 0.00 0.00 4.01
505 509 1.452651 AGCCACCATCTTGCCATCG 60.453 57.895 0.00 0.00 0.00 3.84
507 511 2.484062 CCACCATCTTGCCATCGCC 61.484 63.158 0.00 0.00 0.00 5.54
509 513 3.957535 CCATCTTGCCATCGCCGC 61.958 66.667 0.00 0.00 0.00 6.53
510 514 4.303603 CATCTTGCCATCGCCGCG 62.304 66.667 6.39 6.39 0.00 6.46
528 532 1.922570 CGGAGGAAACACGACCATAG 58.077 55.000 0.00 0.00 35.36 2.23
532 536 4.618927 CGGAGGAAACACGACCATAGTAAA 60.619 45.833 0.00 0.00 35.36 2.01
575 579 1.150992 TCCCTACTCCTCTAGCCGC 59.849 63.158 0.00 0.00 0.00 6.53
592 596 1.448013 GCTAACGAGGCCACCAGAC 60.448 63.158 5.01 0.00 0.00 3.51
600 604 1.216710 GGCCACCAGACGAGAGAAG 59.783 63.158 0.00 0.00 0.00 2.85
668 672 2.952310 AGGGTTGACAAAAGAGCAAGTC 59.048 45.455 0.00 0.00 0.00 3.01
687 691 4.369182 AGTCACTTAACAAGTTGAGTCGG 58.631 43.478 10.54 0.00 40.46 4.79
688 692 3.059800 GTCACTTAACAAGTTGAGTCGGC 60.060 47.826 10.54 2.88 40.46 5.54
694 698 0.784778 CAAGTTGAGTCGGCGAGAAC 59.215 55.000 11.20 13.76 0.00 3.01
699 703 0.167470 TGAGTCGGCGAGAACTAACG 59.833 55.000 11.20 0.00 0.00 3.18
704 708 1.063616 TCGGCGAGAACTAACGATCTG 59.936 52.381 4.99 0.00 0.00 2.90
710 714 0.175073 GAACTAACGATCTGCCGGGT 59.825 55.000 2.18 0.00 0.00 5.28
743 747 5.644644 GGTTAGCAATCTCAAACCTTGATG 58.355 41.667 0.00 0.00 39.30 3.07
924 936 2.028748 ACGGCAAACCTATCGTACAAGT 60.029 45.455 0.00 0.00 33.89 3.16
1224 1246 0.249826 GGTTCCGGTGGACGTGTAAA 60.250 55.000 0.00 0.00 42.24 2.01
1348 1370 2.930040 ACATCGCATCTTCCTTTGTACG 59.070 45.455 0.00 0.00 0.00 3.67
1357 1379 8.922676 CGCATCTTCCTTTGTACGTATATAATT 58.077 33.333 0.00 0.00 0.00 1.40
1384 1406 5.609423 CCTCTAGATTGATGTGGGAAGAAG 58.391 45.833 0.00 0.00 0.00 2.85
1401 1423 6.333416 GGAAGAAGCAACTGAAGAAAAAGTT 58.667 36.000 0.00 0.00 37.09 2.66
1427 1449 5.789643 ATTGTGTTTAGATGCTGGTGTTT 57.210 34.783 0.00 0.00 0.00 2.83
1428 1450 4.566545 TGTGTTTAGATGCTGGTGTTTG 57.433 40.909 0.00 0.00 0.00 2.93
1433 1455 5.048782 TGTTTAGATGCTGGTGTTTGATCAC 60.049 40.000 0.00 0.00 37.57 3.06
1498 1520 1.269569 TGTGCTGTTCAGTGGAGTACG 60.270 52.381 1.78 0.00 0.00 3.67
1573 1595 6.656632 TTCAGTGATACCTAGGAATAGCTG 57.343 41.667 17.98 16.56 0.00 4.24
1588 1610 4.935352 ATAGCTGACTAGAAGCCTCTTG 57.065 45.455 15.54 0.00 41.82 3.02
1634 1656 7.311092 TCTAGATGTTAGAACTTGAAACCCA 57.689 36.000 0.00 0.00 0.00 4.51
1725 1762 6.716628 ACTATAAATTGGGTGCCATCACATAG 59.283 38.462 0.00 0.00 44.87 2.23
1734 1771 5.454755 GGGTGCCATCACATAGTATAACTGT 60.455 44.000 0.00 0.00 44.87 3.55
1735 1772 5.466728 GGTGCCATCACATAGTATAACTGTG 59.533 44.000 2.68 2.68 44.87 3.66
1736 1773 5.050091 GTGCCATCACATAGTATAACTGTGC 60.050 44.000 4.00 0.00 40.45 4.57
1737 1774 4.452455 GCCATCACATAGTATAACTGTGCC 59.548 45.833 4.00 0.00 40.45 5.01
1876 1918 0.930310 CTTACATCCACATGGCGTCG 59.070 55.000 0.00 0.00 33.82 5.12
1902 1944 4.376920 CGTATCAACAGCGAAATGTTCACA 60.377 41.667 0.00 0.00 41.41 3.58
1951 1993 3.686016 ACTGGAAATGTTTATGCCGTCT 58.314 40.909 0.00 0.00 0.00 4.18
2025 2071 3.063510 GGTTACCCACCTGACTAAACC 57.936 52.381 0.00 0.00 43.29 3.27
2134 2181 8.547967 TTTCTACTTGCTACATACTTGAAAGG 57.452 34.615 0.00 0.00 0.00 3.11
2178 2225 7.603784 GTGGAACTTTGGATTTAAAAGCATGAT 59.396 33.333 0.00 0.00 38.03 2.45
2274 2321 8.627403 CCATGCTACATGTTTCTCATCTTATTT 58.373 33.333 2.30 0.00 34.09 1.40
2600 2647 6.355747 ACTGCAAATCTGGAAAAATGGAAAA 58.644 32.000 0.00 0.00 0.00 2.29
2616 2663 2.864343 GGAAAATCACGGGTCTACATCG 59.136 50.000 0.00 0.00 0.00 3.84
2682 2729 0.247814 GTGAACCTCGCAATGCATCG 60.248 55.000 5.91 0.00 0.00 3.84
2926 2989 6.687604 ACAACATTCAGTAATTTTGCCCTAC 58.312 36.000 0.00 0.00 36.60 3.18
3001 3064 5.865085 ACAGTAAGAAATGCTCCTACACAA 58.135 37.500 0.00 0.00 0.00 3.33
3002 3065 6.476378 ACAGTAAGAAATGCTCCTACACAAT 58.524 36.000 0.00 0.00 0.00 2.71
3003 3066 6.595716 ACAGTAAGAAATGCTCCTACACAATC 59.404 38.462 0.00 0.00 0.00 2.67
3199 3367 5.466058 TGTCAAGCAAAATTAGTTGGCAATG 59.534 36.000 1.92 0.00 31.80 2.82
3381 3549 5.861251 CAGCATTGAAAAAGGTAATACGCAA 59.139 36.000 0.00 0.00 0.00 4.85
3408 3576 4.402474 AGAGCATAAGTTTATTTGGGTGCC 59.598 41.667 0.00 0.00 32.06 5.01
3804 3972 8.482578 CCTTGTGGAAAATGTGACAAAGTTTGT 61.483 37.037 21.00 21.00 40.63 2.83
3870 4038 4.811557 GGAACCTATTTTGGACTCATCGAG 59.188 45.833 0.00 0.00 35.52 4.04
4105 4273 1.734137 GGATTGGCATGCTGCTGAG 59.266 57.895 18.92 0.00 44.28 3.35
4178 4346 3.251004 GGTGAGTTTCATGTCCTGTGAAC 59.749 47.826 0.00 0.00 35.47 3.18
4209 4570 3.216187 TGTTCTCGTTGAATGGGGAAA 57.784 42.857 0.00 0.00 36.99 3.13
4223 4584 1.970640 GGGGAAAAAGATGGCTGTGTT 59.029 47.619 0.00 0.00 0.00 3.32
4508 5016 2.586258 TTGCTTTGCTGGCGTTTAAA 57.414 40.000 0.00 0.00 0.00 1.52
4568 5158 6.594744 TGGTGAGCATTATACATTCATCACT 58.405 36.000 0.00 0.00 36.81 3.41
4592 5182 8.371699 ACTCCTAGATATGTTTTTGATCTAGCC 58.628 37.037 11.12 0.00 44.05 3.93
4596 5186 5.698545 AGATATGTTTTTGATCTAGCCGCTC 59.301 40.000 0.00 0.00 0.00 5.03
4598 5188 2.742053 TGTTTTTGATCTAGCCGCTCAC 59.258 45.455 0.00 0.00 0.00 3.51
4624 5214 8.818057 CGTCTGATATTTAATCCTTCGAAACTT 58.182 33.333 0.00 0.00 0.00 2.66
4703 5293 1.134946 GCAAACCAACTGCTTCTGTGT 59.865 47.619 0.00 0.00 36.84 3.72
4744 5334 0.251077 CCCAGGCTGTTGCTCTTTCT 60.251 55.000 14.43 0.00 39.59 2.52
4762 5353 7.495934 GCTCTTTCTATGCAGGTATGTTCTAAA 59.504 37.037 0.00 0.00 0.00 1.85
4793 5384 3.440173 TCTTAGGCTTAGCACATGTTTGC 59.560 43.478 6.53 0.00 43.34 3.68
4822 5415 7.663043 TCCACACCACACACATACTTATATA 57.337 36.000 0.00 0.00 0.00 0.86
4823 5416 7.494211 TCCACACCACACACATACTTATATAC 58.506 38.462 0.00 0.00 0.00 1.47
4825 5418 7.418597 CCACACCACACACATACTTATATACCT 60.419 40.741 0.00 0.00 0.00 3.08
4826 5419 7.985184 CACACCACACACATACTTATATACCTT 59.015 37.037 0.00 0.00 0.00 3.50
4827 5420 8.545472 ACACCACACACATACTTATATACCTTT 58.455 33.333 0.00 0.00 0.00 3.11
4828 5421 8.826710 CACCACACACATACTTATATACCTTTG 58.173 37.037 0.00 0.00 0.00 2.77
4858 5451 0.034380 ATCAGGAGGAACGAGACCGA 60.034 55.000 0.00 0.00 39.50 4.69
4867 5460 4.554163 CGAGACCGAAAACTCGCT 57.446 55.556 0.00 0.00 46.54 4.93
4937 5542 1.000396 GCAGTTCAATCAGGGCCCT 60.000 57.895 22.28 22.28 0.00 5.19
4940 5545 0.909610 AGTTCAATCAGGGCCCTCGA 60.910 55.000 25.77 23.11 0.00 4.04
4942 5547 1.910580 TTCAATCAGGGCCCTCGACC 61.911 60.000 25.77 0.00 0.00 4.79
4970 5575 1.146041 AGCTCCACGCAGACAACAA 59.854 52.632 0.00 0.00 42.61 2.83
5106 5711 2.328819 ATGCTGGAAGATGACTGAGC 57.671 50.000 0.00 0.00 34.07 4.26
5200 5805 2.224354 CCCATCTGCCAGTTTTTGCTTT 60.224 45.455 0.00 0.00 0.00 3.51
5222 5827 6.811253 TTATGTTTTTACGCCATCTGAACT 57.189 33.333 0.00 0.00 0.00 3.01
5223 5828 4.742438 TGTTTTTACGCCATCTGAACTC 57.258 40.909 0.00 0.00 0.00 3.01
5229 5834 1.135373 ACGCCATCTGAACTCGTAGTG 60.135 52.381 0.79 0.00 0.00 2.74
5230 5835 1.799181 CGCCATCTGAACTCGTAGTGG 60.799 57.143 0.00 0.00 0.00 4.00
5232 5837 2.353803 GCCATCTGAACTCGTAGTGGTT 60.354 50.000 0.00 0.00 0.00 3.67
5234 5839 4.315803 CCATCTGAACTCGTAGTGGTTTT 58.684 43.478 0.00 0.00 0.00 2.43
5235 5840 4.389077 CCATCTGAACTCGTAGTGGTTTTC 59.611 45.833 0.00 0.00 0.00 2.29
5237 5842 4.617959 TCTGAACTCGTAGTGGTTTTCTG 58.382 43.478 0.00 0.00 0.00 3.02
5246 5855 4.500887 CGTAGTGGTTTTCTGGTTCTGAGA 60.501 45.833 0.00 0.00 0.00 3.27
5450 6065 1.676635 CACACCCAGTGGATGCCAG 60.677 63.158 11.95 0.00 44.69 4.85
5707 6322 0.535780 CACCTGAGTTCTTGCTGCCA 60.536 55.000 0.00 0.00 0.00 4.92
5710 6325 1.093159 CTGAGTTCTTGCTGCCATCC 58.907 55.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 5.753921 TGAAATTTTGTTTTTCGCCGGTTAT 59.246 32.000 1.90 0.00 36.16 1.89
14 15 4.903016 CCAATGAAATTTTGTTTTTCGCCG 59.097 37.500 0.00 0.00 36.16 6.46
15 16 6.054035 TCCAATGAAATTTTGTTTTTCGCC 57.946 33.333 0.00 0.00 36.16 5.54
31 32 4.853468 TGGCTAGTATGGTTTCCAATGA 57.147 40.909 0.00 0.00 36.95 2.57
71 72 0.798776 CAAGATCCGTCAAGTGGCAC 59.201 55.000 10.29 10.29 0.00 5.01
76 77 4.278170 TGCAATTTTCAAGATCCGTCAAGT 59.722 37.500 0.00 0.00 0.00 3.16
87 88 7.809331 TGCTATCACTTAAGTGCAATTTTCAAG 59.191 33.333 27.49 13.01 45.25 3.02
116 117 1.992557 TGTTTGCAAGTATCCCCTCCT 59.007 47.619 0.00 0.00 0.00 3.69
132 133 6.724893 AAGTTTGCTATTACAAGGGTGTTT 57.275 33.333 0.00 0.00 39.30 2.83
144 146 5.772825 TGCACTCTTCAAAGTTTGCTATT 57.227 34.783 10.90 0.00 36.49 1.73
149 151 4.365723 AGCATTGCACTCTTCAAAGTTTG 58.634 39.130 11.91 9.44 0.00 2.93
151 153 5.507985 GGTTAGCATTGCACTCTTCAAAGTT 60.508 40.000 11.91 0.00 0.00 2.66
167 169 3.067180 CCATTTCAAGCGATGGTTAGCAT 59.933 43.478 0.00 0.00 38.38 3.79
168 170 2.423185 CCATTTCAAGCGATGGTTAGCA 59.577 45.455 0.00 0.00 38.38 3.49
176 178 7.696453 CGTTTTCTAAATACCATTTCAAGCGAT 59.304 33.333 0.00 0.00 0.00 4.58
179 181 8.424731 CAACGTTTTCTAAATACCATTTCAAGC 58.575 33.333 0.00 0.00 0.00 4.01
196 198 7.391016 CCAGTCAAAATTCTTTCAACGTTTTC 58.609 34.615 0.00 0.00 0.00 2.29
201 203 4.298332 CCCCAGTCAAAATTCTTTCAACG 58.702 43.478 0.00 0.00 0.00 4.10
202 204 4.058124 GCCCCAGTCAAAATTCTTTCAAC 58.942 43.478 0.00 0.00 0.00 3.18
213 215 4.841441 GGTGATGCCCCAGTCAAA 57.159 55.556 0.00 0.00 0.00 2.69
235 237 4.700213 GTGGTGAAGGCAAGTATGTGTTAT 59.300 41.667 0.00 0.00 0.00 1.89
236 238 4.069304 GTGGTGAAGGCAAGTATGTGTTA 58.931 43.478 0.00 0.00 0.00 2.41
256 258 0.316841 CCAACCATTTTGGGTCGGTG 59.683 55.000 0.00 0.00 43.37 4.94
261 263 4.777366 CCTATTTCTCCAACCATTTTGGGT 59.223 41.667 3.25 0.00 43.37 4.51
262 264 5.022787 TCCTATTTCTCCAACCATTTTGGG 58.977 41.667 3.25 0.00 43.37 4.12
265 267 5.650283 TGGTCCTATTTCTCCAACCATTTT 58.350 37.500 0.00 0.00 32.08 1.82
294 296 6.198966 CCGACCTTTTCTTTTGATTTGTTCTG 59.801 38.462 0.00 0.00 0.00 3.02
295 297 6.096282 TCCGACCTTTTCTTTTGATTTGTTCT 59.904 34.615 0.00 0.00 0.00 3.01
312 315 1.215647 GTGCGATGACTCCGACCTT 59.784 57.895 0.00 0.00 0.00 3.50
337 340 6.470877 GTCAATTAAGCGAAGTTGTTTGTTGA 59.529 34.615 0.00 0.00 0.00 3.18
342 345 5.885881 TGTGTCAATTAAGCGAAGTTGTTT 58.114 33.333 0.00 0.00 0.00 2.83
365 368 3.196469 TCTCTTCGATCTTGGCACTTGAT 59.804 43.478 0.00 0.00 0.00 2.57
370 373 1.996191 GTGTCTCTTCGATCTTGGCAC 59.004 52.381 0.00 0.00 0.00 5.01
392 396 4.202441 AGGGTATGTGTCATCAGATTTGC 58.798 43.478 0.00 0.00 0.00 3.68
407 411 2.034124 CAAAGGGCCAATGAGGGTATG 58.966 52.381 6.18 0.00 38.09 2.39
423 427 5.403246 ACGTCTAATCTGACACTAGCAAAG 58.597 41.667 0.00 0.00 36.82 2.77
426 430 4.217767 ACAACGTCTAATCTGACACTAGCA 59.782 41.667 0.00 0.00 36.82 3.49
440 444 1.278985 TCCCTACCTCGACAACGTCTA 59.721 52.381 0.00 0.00 40.69 2.59
447 451 0.755698 GGCATCTCCCTACCTCGACA 60.756 60.000 0.00 0.00 0.00 4.35
463 467 3.695830 AAGACGAGTTGGAATAAGGCA 57.304 42.857 0.00 0.00 0.00 4.75
465 469 3.751175 TGCAAAGACGAGTTGGAATAAGG 59.249 43.478 0.00 0.00 0.00 2.69
488 492 3.113745 CGATGGCAAGATGGTGGC 58.886 61.111 0.00 0.00 44.09 5.01
500 504 4.830765 TTTCCTCCGCGGCGATGG 62.831 66.667 25.92 23.23 0.00 3.51
507 511 3.110178 GGTCGTGTTTCCTCCGCG 61.110 66.667 0.00 0.00 37.17 6.46
509 513 1.203994 ACTATGGTCGTGTTTCCTCCG 59.796 52.381 0.00 0.00 0.00 4.63
510 514 4.460948 TTACTATGGTCGTGTTTCCTCC 57.539 45.455 0.00 0.00 0.00 4.30
512 516 5.861727 AGTTTTACTATGGTCGTGTTTCCT 58.138 37.500 0.00 0.00 0.00 3.36
520 524 7.842721 GCGTTGTTATTAGTTTTACTATGGTCG 59.157 37.037 0.00 0.00 29.64 4.79
528 532 5.564882 CCCGTTGCGTTGTTATTAGTTTTAC 59.435 40.000 0.00 0.00 0.00 2.01
532 536 3.058777 CACCCGTTGCGTTGTTATTAGTT 60.059 43.478 0.00 0.00 0.00 2.24
575 579 1.153823 CGTCTGGTGGCCTCGTTAG 60.154 63.158 3.32 0.00 0.00 2.34
588 592 0.820871 CCCTTCCCTTCTCTCGTCTG 59.179 60.000 0.00 0.00 0.00 3.51
592 596 1.331399 GGTCCCCTTCCCTTCTCTCG 61.331 65.000 0.00 0.00 0.00 4.04
615 619 2.470983 AAAATTTCCCATGCCGTTGG 57.529 45.000 0.00 0.00 36.46 3.77
633 637 1.950909 CAACCCTAGCCGTCACAAAAA 59.049 47.619 0.00 0.00 0.00 1.94
641 645 1.418637 TCTTTTGTCAACCCTAGCCGT 59.581 47.619 0.00 0.00 0.00 5.68
668 672 2.096909 CGCCGACTCAACTTGTTAAGTG 60.097 50.000 0.00 0.00 41.91 3.16
687 691 1.201343 GGCAGATCGTTAGTTCTCGC 58.799 55.000 0.00 0.00 0.00 5.03
688 692 1.467875 CGGCAGATCGTTAGTTCTCG 58.532 55.000 0.00 0.00 0.00 4.04
694 698 1.227263 CCACCCGGCAGATCGTTAG 60.227 63.158 0.00 0.00 0.00 2.34
714 718 1.271840 TGAGATTGCTAACCGGGCCT 61.272 55.000 6.32 0.00 0.00 5.19
716 720 1.132453 GTTTGAGATTGCTAACCGGGC 59.868 52.381 6.32 0.00 0.00 6.13
719 723 3.751175 TCAAGGTTTGAGATTGCTAACCG 59.249 43.478 0.00 0.00 44.71 4.44
721 725 6.259550 ACATCAAGGTTTGAGATTGCTAAC 57.740 37.500 0.00 0.00 43.98 2.34
924 936 5.356190 GCTTCATCAATCAGTCATCCAAAGA 59.644 40.000 0.00 0.00 0.00 2.52
1323 1345 3.005554 CAAAGGAAGATGCGATGTCAGT 58.994 45.455 0.00 0.00 0.00 3.41
1357 1379 2.702478 CCCACATCAATCTAGAGGCTCA 59.298 50.000 18.26 1.80 0.00 4.26
1384 1406 9.476761 CACAATTTAAACTTTTTCTTCAGTTGC 57.523 29.630 0.00 0.00 33.38 4.17
1401 1423 7.283625 ACACCAGCATCTAAACACAATTTAA 57.716 32.000 0.00 0.00 0.00 1.52
1407 1429 4.203226 TCAAACACCAGCATCTAAACACA 58.797 39.130 0.00 0.00 0.00 3.72
1421 1443 2.571212 TGTGTCCTGTGATCAAACACC 58.429 47.619 20.35 2.39 38.46 4.16
1427 1449 4.572909 CTGAAGAATGTGTCCTGTGATCA 58.427 43.478 0.00 0.00 0.00 2.92
1428 1450 3.373439 GCTGAAGAATGTGTCCTGTGATC 59.627 47.826 0.00 0.00 0.00 2.92
1433 1455 3.049708 TCTGCTGAAGAATGTGTCCTG 57.950 47.619 0.00 0.00 29.54 3.86
1498 1520 3.495670 ACTATCTGCTGTCGTTCTCAC 57.504 47.619 0.00 0.00 0.00 3.51
1557 1579 6.661805 GCTTCTAGTCAGCTATTCCTAGGTAT 59.338 42.308 9.08 7.47 33.97 2.73
1573 1595 4.568760 GTGCAATACAAGAGGCTTCTAGTC 59.431 45.833 0.00 0.00 31.96 2.59
1588 1610 0.323360 TTGGGGCTCCAGTGCAATAC 60.323 55.000 4.89 0.00 45.04 1.89
1634 1656 6.948309 ACAGCAATTCTAAACTCACCCTAATT 59.052 34.615 0.00 0.00 0.00 1.40
1650 1672 1.981533 GCTTTCGCAGAACAGCAATTC 59.018 47.619 14.15 0.00 45.90 2.17
1713 1750 5.056480 GCACAGTTATACTATGTGATGGCA 58.944 41.667 12.92 0.00 45.67 4.92
1725 1762 3.418047 AGTTTGTGGGGCACAGTTATAC 58.582 45.455 0.00 0.00 45.39 1.47
1734 1771 1.039068 CATGTCAAGTTTGTGGGGCA 58.961 50.000 0.00 0.00 0.00 5.36
1735 1772 0.318120 CCATGTCAAGTTTGTGGGGC 59.682 55.000 0.00 0.00 0.00 5.80
1736 1773 1.993956 TCCATGTCAAGTTTGTGGGG 58.006 50.000 0.00 0.00 0.00 4.96
1737 1774 4.399004 TTTTCCATGTCAAGTTTGTGGG 57.601 40.909 0.00 0.00 0.00 4.61
1817 1859 3.333680 AGGAAGGGCAATAAAGAGTGGAA 59.666 43.478 0.00 0.00 0.00 3.53
1828 1870 1.829222 CAATGCAAGAGGAAGGGCAAT 59.171 47.619 0.00 0.00 40.02 3.56
1876 1918 2.348666 ACATTTCGCTGTTGATACGAGC 59.651 45.455 0.00 0.00 37.11 5.03
1911 1953 5.542635 TCCAGTTAGTAGGACATGAACAGTT 59.457 40.000 0.00 0.00 0.00 3.16
1951 1993 4.469657 AGAATGCAAAGTGGACCAGTAAA 58.530 39.130 1.14 0.00 0.00 2.01
2008 2054 2.307496 TCGGTTTAGTCAGGTGGGTA 57.693 50.000 0.00 0.00 0.00 3.69
2134 2181 7.420002 AGTTCCACTTAACAATAACCGTTTTC 58.580 34.615 0.00 0.00 0.00 2.29
2178 2225 1.344065 TAACAACAGCGGGAGGAGAA 58.656 50.000 0.00 0.00 0.00 2.87
2274 2321 6.017109 GCCAGAAAAACAGATTCAAGAGTGTA 60.017 38.462 0.00 0.00 0.00 2.90
2600 2647 3.004419 CACATACGATGTAGACCCGTGAT 59.996 47.826 0.00 0.00 42.70 3.06
2616 2663 8.543862 TTATCATCTCATCTTCATGCACATAC 57.456 34.615 0.00 0.00 0.00 2.39
3381 3549 8.197439 GCACCCAAATAAACTTATGCTCTAAAT 58.803 33.333 0.00 0.00 0.00 1.40
3408 3576 7.607250 ACATCTACTAGACTTCCAGTGAAAAG 58.393 38.462 0.00 0.00 0.00 2.27
3804 3972 2.158682 TCCCTTGCTTCTGTACTTTGCA 60.159 45.455 0.00 0.00 0.00 4.08
3870 4038 0.803380 GGCCATTGCTTCATGCGAAC 60.803 55.000 0.00 0.00 46.63 3.95
4178 4346 7.253750 CCATTCAACGAGAACAAGAAAACTTTG 60.254 37.037 0.00 0.00 39.49 2.77
4209 4570 6.435277 ACAGATCAATTAACACAGCCATCTTT 59.565 34.615 0.00 0.00 0.00 2.52
4539 5129 6.128486 TGAATGTATAATGCTCACCAACCAT 58.872 36.000 0.00 0.00 0.00 3.55
4568 5158 7.378966 CGGCTAGATCAAAAACATATCTAGGA 58.621 38.462 16.33 0.00 44.84 2.94
4592 5182 5.223382 AGGATTAAATATCAGACGTGAGCG 58.777 41.667 0.00 0.00 44.93 5.03
4596 5186 7.694388 TTCGAAGGATTAAATATCAGACGTG 57.306 36.000 0.00 0.00 0.00 4.49
4598 5188 8.354011 AGTTTCGAAGGATTAAATATCAGACG 57.646 34.615 0.00 0.00 0.00 4.18
4703 5293 4.526970 GGATTCTTATGTTTCAGGCCTGA 58.473 43.478 32.00 32.00 37.91 3.86
4744 5334 5.366482 TGCCTTTAGAACATACCTGCATA 57.634 39.130 0.00 0.00 0.00 3.14
4762 5353 2.422093 GCTAAGCCTAAGATGGTTGCCT 60.422 50.000 0.00 0.00 0.00 4.75
4793 5384 5.245531 AGTATGTGTGTGGTGTGGAAATAG 58.754 41.667 0.00 0.00 0.00 1.73
4822 5415 6.715264 CCTCCTGATTAACAGTAAACAAAGGT 59.285 38.462 0.00 0.00 44.40 3.50
4823 5416 6.940298 TCCTCCTGATTAACAGTAAACAAAGG 59.060 38.462 0.00 0.00 44.40 3.11
4825 5418 7.041644 CGTTCCTCCTGATTAACAGTAAACAAA 60.042 37.037 0.00 0.00 44.40 2.83
4826 5419 6.425721 CGTTCCTCCTGATTAACAGTAAACAA 59.574 38.462 0.00 0.00 44.40 2.83
4827 5420 5.929992 CGTTCCTCCTGATTAACAGTAAACA 59.070 40.000 0.00 0.00 44.40 2.83
4828 5421 6.161381 TCGTTCCTCCTGATTAACAGTAAAC 58.839 40.000 0.00 0.00 44.40 2.01
4867 5460 4.302455 CTGCTCTTTTCTCTCTTTCGTCA 58.698 43.478 0.00 0.00 0.00 4.35
5106 5711 4.728534 TGTTTCTCCACGACAACAAAAAG 58.271 39.130 0.00 0.00 0.00 2.27
5200 5805 5.062934 CGAGTTCAGATGGCGTAAAAACATA 59.937 40.000 0.00 0.00 0.00 2.29
5222 5827 3.385433 TCAGAACCAGAAAACCACTACGA 59.615 43.478 0.00 0.00 0.00 3.43
5223 5828 3.724374 TCAGAACCAGAAAACCACTACG 58.276 45.455 0.00 0.00 0.00 3.51
5229 5834 4.389374 TGTGATCTCAGAACCAGAAAACC 58.611 43.478 0.00 0.00 0.00 3.27
5230 5835 5.618640 GCATGTGATCTCAGAACCAGAAAAC 60.619 44.000 3.58 0.00 0.00 2.43
5232 5837 4.005650 GCATGTGATCTCAGAACCAGAAA 58.994 43.478 3.58 0.00 0.00 2.52
5234 5839 2.093288 GGCATGTGATCTCAGAACCAGA 60.093 50.000 3.58 0.00 0.00 3.86
5235 5840 2.286872 GGCATGTGATCTCAGAACCAG 58.713 52.381 3.58 0.00 0.00 4.00
5237 5842 2.408271 TGGCATGTGATCTCAGAACC 57.592 50.000 3.58 5.33 0.00 3.62
5246 5855 0.324645 GAACCCCCTTGGCATGTGAT 60.325 55.000 0.00 0.00 37.83 3.06
5430 6045 2.034687 GCATCCACTGGGTGTGCT 59.965 61.111 10.18 0.00 44.92 4.40
5476 6091 1.754107 CCTTTTGCACCAAAGGGGG 59.246 57.895 18.56 0.00 43.76 5.40
5496 6111 0.467474 CATGGATCACTGCCAGCCAT 60.467 55.000 0.00 0.00 39.11 4.40
5507 6122 1.971505 GCCGAGGACACCATGGATCA 61.972 60.000 21.47 0.00 0.00 2.92
5645 6260 1.862201 CGTCCAGCGCCGATATAAAAA 59.138 47.619 2.29 0.00 0.00 1.94
5707 6322 1.467678 CCCGCAGCTAGCTACTGGAT 61.468 60.000 18.86 0.00 42.61 3.41
5710 6325 0.319383 CATCCCGCAGCTAGCTACTG 60.319 60.000 18.86 8.27 42.61 2.74
5946 6561 3.211963 GTCCATGCCCATCACCGC 61.212 66.667 0.00 0.00 0.00 5.68


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

AutoCloner maintained by Alex Coulton.