Multiple sequence alignment - TraesCS4A01G095900

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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 TraesCS4A01G095900 chr4A 100.000 3344 0 0 1 3344 103783522 103786865 0.000000e+00 6176.0
1 TraesCS4A01G095900 chr4B 93.315 1855 86 22 721 2540 446202109 446200258 0.000000e+00 2704.0
2 TraesCS4A01G095900 chr4B 85.750 800 81 18 2545 3344 446196869 446196103 0.000000e+00 815.0
3 TraesCS4A01G095900 chr4B 90.936 342 19 6 345 686 446202441 446202112 1.830000e-122 449.0
4 TraesCS4A01G095900 chr4B 96.196 184 6 1 1 184 446202719 446202537 1.950000e-77 300.0
5 TraesCS4A01G095900 chr4D 92.561 1882 72 26 721 2545 360913919 360912049 0.000000e+00 2638.0
6 TraesCS4A01G095900 chr4D 89.373 734 74 4 2614 3344 360866997 360866265 0.000000e+00 920.0
7 TraesCS4A01G095900 chr4D 91.586 309 16 5 1 308 360914627 360914328 5.160000e-113 418.0
8 TraesCS4A01G095900 chr4D 89.130 322 18 6 372 688 360914229 360913920 5.230000e-103 385.0
9 TraesCS4A01G095900 chr3D 76.289 776 131 43 1579 2332 466754740 466753996 6.820000e-97 364.0
10 TraesCS4A01G095900 chr3A 75.907 772 139 36 1580 2332 609828415 609827672 5.310000e-93 351.0
11 TraesCS4A01G095900 chr3B 75.809 773 140 39 1579 2332 620665496 620664752 6.870000e-92 348.0
12 TraesCS4A01G095900 chr3B 90.566 53 5 0 2786 2838 709817 709765 1.660000e-08 71.3
13 TraesCS4A01G095900 chr6B 76.862 376 71 11 2765 3134 638439126 638438761 7.320000e-47 198.0
14 TraesCS4A01G095900 chr5B 73.103 435 102 15 2774 3199 633269955 633270383 1.250000e-29 141.0
15 TraesCS4A01G095900 chr5B 72.644 435 104 15 2774 3199 633273566 633273994 2.710000e-26 130.0
16 TraesCS4A01G095900 chr5B 95.349 43 2 0 2787 2829 699562556 699562598 5.990000e-08 69.4
17 TraesCS4A01G095900 chr1B 100.000 28 0 0 3309 3336 670610640 670610667 6.000000e-03 52.8


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 TraesCS4A01G095900 chr4A 103783522 103786865 3343 False 6176 6176 100.000000 1 3344 1 chr4A.!!$F1 3343
1 TraesCS4A01G095900 chr4B 446196103 446202719 6616 True 1067 2704 91.549250 1 3344 4 chr4B.!!$R1 3343
2 TraesCS4A01G095900 chr4D 360912049 360914627 2578 True 1147 2638 91.092333 1 2545 3 chr4D.!!$R2 2544
3 TraesCS4A01G095900 chr4D 360866265 360866997 732 True 920 920 89.373000 2614 3344 1 chr4D.!!$R1 730
4 TraesCS4A01G095900 chr3D 466753996 466754740 744 True 364 364 76.289000 1579 2332 1 chr3D.!!$R1 753
5 TraesCS4A01G095900 chr3A 609827672 609828415 743 True 351 351 75.907000 1580 2332 1 chr3A.!!$R1 752
6 TraesCS4A01G095900 chr3B 620664752 620665496 744 True 348 348 75.809000 1579 2332 1 chr3B.!!$R2 753

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
403 453 0.037326 GGTGAGTTCTCGCCATGTGA 60.037 55.0 22.59 0.0 39.90 3.58 F
846 918 0.038526 GACGACGGGTCAGATGTTGT 60.039 55.0 0.00 0.0 45.36 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1311 1413 0.025001 CGCCGTATGTGAAAGAAGCG 59.975 55.0 0.0 0.0 36.06 4.68 R
2744 6258 0.179067 TTCTGTCGCCGTGGTTCTTT 60.179 50.0 0.0 0.0 0.00 2.52 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
43 44 4.678622 AGTTCGCAAAGGTAAAAGGTTTG 58.321 39.130 0.00 0.00 34.83 2.93
49 50 5.047847 GCAAAGGTAAAAGGTTTGGAGTTC 58.952 41.667 0.00 0.00 32.78 3.01
150 151 1.512996 CGCCATCCCATGATCACTGC 61.513 60.000 0.00 0.00 0.00 4.40
187 188 2.652313 TCCGTTTGGAAGGGCATTG 58.348 52.632 0.00 0.00 42.85 2.82
188 189 0.897863 TCCGTTTGGAAGGGCATTGG 60.898 55.000 0.00 0.00 42.85 3.16
189 190 0.897863 CCGTTTGGAAGGGCATTGGA 60.898 55.000 0.00 0.00 37.49 3.53
190 191 0.527565 CGTTTGGAAGGGCATTGGAG 59.472 55.000 0.00 0.00 0.00 3.86
191 192 1.632589 GTTTGGAAGGGCATTGGAGT 58.367 50.000 0.00 0.00 0.00 3.85
192 193 1.546029 GTTTGGAAGGGCATTGGAGTC 59.454 52.381 0.00 0.00 0.00 3.36
193 194 0.039618 TTGGAAGGGCATTGGAGTCC 59.960 55.000 0.73 0.73 0.00 3.85
194 195 0.846427 TGGAAGGGCATTGGAGTCCT 60.846 55.000 11.33 0.00 0.00 3.85
195 196 0.332972 GGAAGGGCATTGGAGTCCTT 59.667 55.000 11.33 0.00 41.78 3.36
200 201 1.341383 GGGCATTGGAGTCCTTCACAT 60.341 52.381 11.33 0.00 0.00 3.21
208 209 1.198637 GAGTCCTTCACATGTTGCTGC 59.801 52.381 0.00 0.00 0.00 5.25
239 240 2.309136 ACTGGTTTGAAATGGGGGAG 57.691 50.000 0.00 0.00 0.00 4.30
264 265 4.619336 GCGAAATTTACCGATTTCTGCAAA 59.381 37.500 15.36 0.00 41.61 3.68
288 289 1.069296 CGTGCACTGTAAACATGGGTG 60.069 52.381 16.19 0.00 0.00 4.61
312 355 0.523072 CGGGCAAAATGTCCTGTCAG 59.477 55.000 0.00 0.00 40.79 3.51
315 358 1.815003 GGCAAAATGTCCTGTCAGAGG 59.185 52.381 0.00 0.00 44.45 3.69
324 374 4.451900 TGTCCTGTCAGAGGTTTTTCTTC 58.548 43.478 0.00 0.00 43.37 2.87
329 379 5.590259 CCTGTCAGAGGTTTTTCTTCTTTGA 59.410 40.000 0.00 0.00 37.02 2.69
330 380 6.238593 CCTGTCAGAGGTTTTTCTTCTTTGAG 60.239 42.308 0.00 0.00 37.02 3.02
332 382 5.066505 GTCAGAGGTTTTTCTTCTTTGAGCA 59.933 40.000 0.00 0.00 29.81 4.26
335 385 5.298026 AGAGGTTTTTCTTCTTTGAGCAGAC 59.702 40.000 0.00 0.00 0.00 3.51
353 403 1.683917 GACGCATAGAGTCCCTGTGAT 59.316 52.381 9.41 0.00 36.24 3.06
385 435 0.603065 GGCAACTAGGCACAAAAGGG 59.397 55.000 0.00 0.00 43.51 3.95
403 453 0.037326 GGTGAGTTCTCGCCATGTGA 60.037 55.000 22.59 0.00 39.90 3.58
421 471 0.396060 GATCCAGTCATCCTCCAGCC 59.604 60.000 0.00 0.00 0.00 4.85
434 484 0.846015 TCCAGCCATTATCACCAGGG 59.154 55.000 0.00 0.00 0.00 4.45
435 485 0.846015 CCAGCCATTATCACCAGGGA 59.154 55.000 0.00 0.00 0.00 4.20
436 486 1.426598 CCAGCCATTATCACCAGGGAT 59.573 52.381 0.00 0.00 0.00 3.85
437 487 2.158415 CCAGCCATTATCACCAGGGATT 60.158 50.000 0.00 0.00 0.00 3.01
466 516 0.693049 ACCGCAGACAGGGAGATTTT 59.307 50.000 0.00 0.00 0.00 1.82
470 520 2.637947 GCAGACAGGGAGATTTTCCTC 58.362 52.381 0.00 0.00 45.98 3.71
480 530 1.351017 AGATTTTCCTCCCGACAAGCA 59.649 47.619 0.00 0.00 0.00 3.91
489 539 1.021202 CCCGACAAGCACAACAAGAA 58.979 50.000 0.00 0.00 0.00 2.52
515 565 1.895238 CAATGCCTTGCCCCTGAAG 59.105 57.895 0.00 0.00 0.00 3.02
570 620 0.664761 AAAGTCTTGGTCGACGACGA 59.335 50.000 20.92 15.24 46.56 4.20
667 722 2.898729 ACGTATTCATGAGCTCCCTG 57.101 50.000 12.15 9.14 0.00 4.45
688 743 1.609794 GACCCTGTCCCCTTCTCGT 60.610 63.158 0.00 0.00 0.00 4.18
689 744 1.605971 GACCCTGTCCCCTTCTCGTC 61.606 65.000 0.00 0.00 0.00 4.20
690 745 1.305381 CCCTGTCCCCTTCTCGTCT 60.305 63.158 0.00 0.00 0.00 4.18
691 746 0.905337 CCCTGTCCCCTTCTCGTCTT 60.905 60.000 0.00 0.00 0.00 3.01
692 747 0.247736 CCTGTCCCCTTCTCGTCTTG 59.752 60.000 0.00 0.00 0.00 3.02
693 748 0.390472 CTGTCCCCTTCTCGTCTTGC 60.390 60.000 0.00 0.00 0.00 4.01
694 749 1.079057 GTCCCCTTCTCGTCTTGCC 60.079 63.158 0.00 0.00 0.00 4.52
695 750 1.535444 TCCCCTTCTCGTCTTGCCA 60.535 57.895 0.00 0.00 0.00 4.92
696 751 1.078848 CCCCTTCTCGTCTTGCCAG 60.079 63.158 0.00 0.00 0.00 4.85
697 752 1.674057 CCCTTCTCGTCTTGCCAGT 59.326 57.895 0.00 0.00 0.00 4.00
698 753 0.390472 CCCTTCTCGTCTTGCCAGTC 60.390 60.000 0.00 0.00 0.00 3.51
699 754 0.734253 CCTTCTCGTCTTGCCAGTCG 60.734 60.000 0.00 0.00 33.39 4.18
700 755 0.734253 CTTCTCGTCTTGCCAGTCGG 60.734 60.000 4.74 0.00 33.00 4.79
710 765 2.281761 CCAGTCGGCACCTTGCTT 60.282 61.111 0.00 0.00 44.28 3.91
711 766 1.898574 CCAGTCGGCACCTTGCTTT 60.899 57.895 0.00 0.00 44.28 3.51
712 767 1.576421 CAGTCGGCACCTTGCTTTC 59.424 57.895 0.00 0.00 44.28 2.62
713 768 1.148273 AGTCGGCACCTTGCTTTCA 59.852 52.632 0.00 0.00 44.28 2.69
714 769 0.250901 AGTCGGCACCTTGCTTTCAT 60.251 50.000 0.00 0.00 44.28 2.57
715 770 0.109597 GTCGGCACCTTGCTTTCATG 60.110 55.000 0.00 0.00 44.28 3.07
716 771 1.444895 CGGCACCTTGCTTTCATGC 60.445 57.895 0.00 0.00 44.28 4.06
717 772 1.444895 GGCACCTTGCTTTCATGCG 60.445 57.895 0.00 0.00 44.28 4.73
718 773 2.090524 GCACCTTGCTTTCATGCGC 61.091 57.895 0.00 0.00 40.96 6.09
719 774 1.286570 CACCTTGCTTTCATGCGCA 59.713 52.632 14.96 14.96 35.36 6.09
813 885 1.135402 GCTTATGGAAAACACGCCAGG 60.135 52.381 0.00 0.00 37.64 4.45
845 917 1.071019 CGACGACGGGTCAGATGTTG 61.071 60.000 0.00 0.00 46.42 3.33
846 918 0.038526 GACGACGGGTCAGATGTTGT 60.039 55.000 0.00 0.00 45.36 3.32
848 920 1.201647 ACGACGGGTCAGATGTTGTAG 59.798 52.381 0.00 0.00 0.00 2.74
851 923 1.201647 ACGGGTCAGATGTTGTAGACG 59.798 52.381 0.00 0.00 31.93 4.18
852 924 1.201647 CGGGTCAGATGTTGTAGACGT 59.798 52.381 0.00 0.00 31.93 4.34
853 925 2.607187 GGGTCAGATGTTGTAGACGTG 58.393 52.381 0.00 0.00 31.93 4.49
854 926 2.607187 GGTCAGATGTTGTAGACGTGG 58.393 52.381 0.00 0.00 31.93 4.94
855 927 2.230508 GGTCAGATGTTGTAGACGTGGA 59.769 50.000 0.00 0.00 31.93 4.02
857 929 3.921021 GTCAGATGTTGTAGACGTGGAAG 59.079 47.826 0.00 0.00 0.00 3.46
858 930 3.824443 TCAGATGTTGTAGACGTGGAAGA 59.176 43.478 0.00 0.00 0.00 2.87
859 931 3.921021 CAGATGTTGTAGACGTGGAAGAC 59.079 47.826 0.00 0.00 0.00 3.01
896 985 1.354506 GTAGACGTGGATCGGACCG 59.645 63.158 7.84 7.84 44.69 4.79
943 1032 0.249031 GCAGTTGGTTGACAGTTGCC 60.249 55.000 0.00 0.00 35.48 4.52
948 1037 0.465460 TGGTTGACAGTTGCCCACTC 60.465 55.000 0.00 0.00 30.92 3.51
1014 1116 1.097547 CGCCAATGGACATGGACTCC 61.098 60.000 2.05 0.00 40.56 3.85
1085 1187 0.321298 GGCGTTGGTAGAGAAGGCAA 60.321 55.000 0.00 0.00 36.21 4.52
1123 1225 4.399395 TTCCGCTCAGGCTGCAGG 62.399 66.667 17.12 12.59 40.77 4.85
1185 1287 2.401766 CCGCCACAATGTGAGCCTC 61.402 63.158 15.91 0.00 35.23 4.70
1320 1422 1.154654 CAACGCGTCCGCTTCTTTC 60.155 57.895 14.44 0.00 39.32 2.62
1323 1425 2.307309 CGCGTCCGCTTCTTTCACA 61.307 57.895 10.21 0.00 39.32 3.58
1549 1651 2.978452 CTATTCCTCCAGCACGGCCG 62.978 65.000 26.86 26.86 33.14 6.13
1566 1668 2.804856 GCCAACAACAACGCCACT 59.195 55.556 0.00 0.00 0.00 4.00
1749 1854 0.747255 ACACGCCGCTGATAGAGATT 59.253 50.000 0.00 0.00 0.00 2.40
2235 2343 2.279252 GCGTACGTGATCGGGCAT 60.279 61.111 17.90 0.00 41.85 4.40
2374 2500 2.478894 AGTGGCATTTCGTCGTGTAAAG 59.521 45.455 0.00 0.00 0.00 1.85
2576 6089 5.856126 AGTAAGCGACATTTCAATTTCGA 57.144 34.783 11.36 0.00 40.09 3.71
2661 6175 4.832823 AGTGAGGGTCAAGTTTAAATTGGG 59.167 41.667 5.31 0.00 0.00 4.12
2665 6179 4.966168 AGGGTCAAGTTTAAATTGGGTTGT 59.034 37.500 5.31 0.00 0.00 3.32
2698 6212 1.449601 CAACGCTAAGGGTCGCCAT 60.450 57.895 0.00 0.00 0.00 4.40
2712 6226 0.031857 CGCCATTGCCAAGTCAACAA 59.968 50.000 0.00 0.00 0.00 2.83
2736 6250 0.622665 CAAAGGTCCTGAGCCCTGAT 59.377 55.000 0.00 0.00 0.00 2.90
2744 6258 3.054361 GTCCTGAGCCCTGATAAGGAAAA 60.054 47.826 0.00 0.00 38.73 2.29
2745 6259 3.591527 TCCTGAGCCCTGATAAGGAAAAA 59.408 43.478 0.00 0.00 34.11 1.94
2800 6314 4.999939 GTTGGCGCCAAAGCACGG 63.000 66.667 41.60 0.00 39.83 4.94
2834 6348 4.248842 CTCACCCGTGCCACCACA 62.249 66.667 0.00 0.00 42.17 4.17
2963 6477 1.207089 CCGCCTACATGACAAAGAGGA 59.793 52.381 0.00 0.00 0.00 3.71
3008 6523 4.003788 CCGGAGAGCCAACCACGT 62.004 66.667 0.00 0.00 0.00 4.49
3022 6537 1.226974 CACGTAGACCGCCATCCAG 60.227 63.158 0.00 0.00 41.42 3.86
3072 6588 0.884704 GACCAACCGTGCACATCACT 60.885 55.000 18.64 0.00 43.46 3.41
3103 6619 5.243207 CAACCACGGTAGGAAGAGTAAAAT 58.757 41.667 4.04 0.00 0.00 1.82
3105 6621 4.285260 ACCACGGTAGGAAGAGTAAAATGT 59.715 41.667 4.04 0.00 0.00 2.71
3114 6630 7.913674 AGGAAGAGTAAAATGTGACATCTTC 57.086 36.000 13.26 13.26 40.12 2.87
3126 6642 5.734720 TGTGACATCTTCCATTCCTAACTC 58.265 41.667 0.00 0.00 0.00 3.01
3203 6719 0.481567 ATACCCAGCTAGTCCCGCTA 59.518 55.000 0.00 0.00 35.63 4.26
3212 6728 0.478942 TAGTCCCGCTAGAGAGGCAT 59.521 55.000 0.00 0.00 33.34 4.40
3233 6749 0.246635 GACACGCCACATGACTACCT 59.753 55.000 0.00 0.00 0.00 3.08
3243 6759 0.458669 ATGACTACCTACGGCCGTTG 59.541 55.000 38.94 33.61 0.00 4.10
3271 6787 1.080501 CTCACACGACGCCATGTCT 60.081 57.895 0.00 0.00 45.87 3.41
3290 6806 1.375523 GTGGCCTTCGACACCGATT 60.376 57.895 3.32 0.00 45.10 3.34
3295 6811 1.405121 GCCTTCGACACCGATTTACCT 60.405 52.381 0.00 0.00 45.10 3.08
3296 6812 2.268298 CCTTCGACACCGATTTACCTG 58.732 52.381 0.00 0.00 45.10 4.00
3306 6822 2.612972 CCGATTTACCTGACAGTGCAGT 60.613 50.000 0.93 0.00 34.06 4.40
3335 6851 2.747022 CACCACCATCGACCACCA 59.253 61.111 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 0.721718 CTTTGCGAACTCCGGTGATC 59.278 55.000 11.17 7.14 39.04 2.92
43 44 1.450312 CCATGGACCTGCGAACTCC 60.450 63.158 5.56 0.00 0.00 3.85
150 151 3.134458 GGACTAATGATTCCGGAAGCTG 58.866 50.000 30.75 19.92 0.00 4.24
184 185 2.821969 GCAACATGTGAAGGACTCCAAT 59.178 45.455 0.00 0.00 0.00 3.16
186 187 1.421268 AGCAACATGTGAAGGACTCCA 59.579 47.619 0.00 0.00 0.00 3.86
187 188 1.808945 CAGCAACATGTGAAGGACTCC 59.191 52.381 0.00 0.00 0.00 3.85
188 189 1.198637 GCAGCAACATGTGAAGGACTC 59.801 52.381 0.00 0.00 0.00 3.36
189 190 1.242076 GCAGCAACATGTGAAGGACT 58.758 50.000 0.00 0.00 0.00 3.85
190 191 0.242017 GGCAGCAACATGTGAAGGAC 59.758 55.000 0.00 0.00 0.00 3.85
191 192 0.111061 AGGCAGCAACATGTGAAGGA 59.889 50.000 0.00 0.00 0.00 3.36
192 193 0.524862 GAGGCAGCAACATGTGAAGG 59.475 55.000 0.00 0.00 0.00 3.46
193 194 0.524862 GGAGGCAGCAACATGTGAAG 59.475 55.000 0.00 0.00 0.00 3.02
194 195 1.236616 CGGAGGCAGCAACATGTGAA 61.237 55.000 0.00 0.00 0.00 3.18
195 196 1.672030 CGGAGGCAGCAACATGTGA 60.672 57.895 0.00 0.00 0.00 3.58
200 201 4.254709 ACAGCGGAGGCAGCAACA 62.255 61.111 0.00 0.00 43.41 3.33
208 209 0.535102 AAACCAGTTCACAGCGGAGG 60.535 55.000 0.00 0.00 0.00 4.30
239 240 3.542310 GCAGAAATCGGTAAATTTCGCAC 59.458 43.478 14.92 0.00 45.92 5.34
264 265 3.057596 CCCATGTTTACAGTGCACGATTT 60.058 43.478 12.01 0.00 0.00 2.17
269 270 2.226330 TCACCCATGTTTACAGTGCAC 58.774 47.619 9.40 9.40 0.00 4.57
288 289 2.223947 ACAGGACATTTTGCCCGTTTTC 60.224 45.455 0.00 0.00 0.00 2.29
312 355 5.515184 GTCTGCTCAAAGAAGAAAAACCTC 58.485 41.667 0.00 0.00 30.01 3.85
315 358 3.726235 GCGTCTGCTCAAAGAAGAAAAAC 59.274 43.478 0.00 0.00 30.01 2.43
324 374 2.857152 GACTCTATGCGTCTGCTCAAAG 59.143 50.000 0.00 0.00 43.34 2.77
329 379 0.396417 AGGGACTCTATGCGTCTGCT 60.396 55.000 0.00 0.00 43.34 4.24
330 380 0.249238 CAGGGACTCTATGCGTCTGC 60.249 60.000 0.00 0.00 34.60 4.26
332 382 1.107114 CACAGGGACTCTATGCGTCT 58.893 55.000 0.00 0.00 34.60 4.18
335 385 1.269988 CCATCACAGGGACTCTATGCG 60.270 57.143 0.00 0.00 34.60 4.73
353 403 2.512692 AGTTGCCAGCATTACATCCA 57.487 45.000 0.00 0.00 0.00 3.41
378 428 0.875059 GGCGAGAACTCACCCTTTTG 59.125 55.000 2.78 0.00 0.00 2.44
385 435 1.929836 GATCACATGGCGAGAACTCAC 59.070 52.381 0.00 0.00 0.00 3.51
403 453 0.326904 TGGCTGGAGGATGACTGGAT 60.327 55.000 0.00 0.00 0.00 3.41
421 471 6.774170 TGAGAAATCAATCCCTGGTGATAATG 59.226 38.462 0.00 0.00 33.31 1.90
434 484 3.436704 TGTCTGCGGTTGAGAAATCAATC 59.563 43.478 0.00 0.00 31.79 2.67
435 485 3.411446 TGTCTGCGGTTGAGAAATCAAT 58.589 40.909 0.00 0.00 31.79 2.57
436 486 2.807967 CTGTCTGCGGTTGAGAAATCAA 59.192 45.455 0.00 0.00 0.00 2.57
437 487 2.416747 CTGTCTGCGGTTGAGAAATCA 58.583 47.619 0.00 0.00 0.00 2.57
466 516 1.070786 GTTGTGCTTGTCGGGAGGA 59.929 57.895 0.00 0.00 0.00 3.71
470 520 1.002468 CTTCTTGTTGTGCTTGTCGGG 60.002 52.381 0.00 0.00 0.00 5.14
480 530 1.034838 TTGCCACGGCTTCTTGTTGT 61.035 50.000 9.92 0.00 42.51 3.32
509 559 1.805345 CTTTCAGTGCAGCTCTTCAGG 59.195 52.381 0.00 0.00 0.00 3.86
515 565 0.888285 AGTGGCTTTCAGTGCAGCTC 60.888 55.000 12.37 7.52 36.20 4.09
591 641 7.384660 GCTCACCAGAGACAAGAATATAGAATG 59.615 40.741 0.00 0.00 44.98 2.67
592 642 7.441017 GCTCACCAGAGACAAGAATATAGAAT 58.559 38.462 0.00 0.00 44.98 2.40
593 643 6.810911 GCTCACCAGAGACAAGAATATAGAA 58.189 40.000 0.00 0.00 44.98 2.10
594 644 6.398234 GCTCACCAGAGACAAGAATATAGA 57.602 41.667 0.00 0.00 44.98 1.98
646 701 3.570125 TCAGGGAGCTCATGAATACGTAG 59.430 47.826 17.19 0.00 0.00 3.51
693 748 1.856265 GAAAGCAAGGTGCCGACTGG 61.856 60.000 0.00 0.00 46.52 4.00
694 749 1.165907 TGAAAGCAAGGTGCCGACTG 61.166 55.000 0.00 0.00 46.52 3.51
695 750 0.250901 ATGAAAGCAAGGTGCCGACT 60.251 50.000 0.00 0.00 46.52 4.18
696 751 0.109597 CATGAAAGCAAGGTGCCGAC 60.110 55.000 0.00 0.00 46.52 4.79
697 752 1.865788 GCATGAAAGCAAGGTGCCGA 61.866 55.000 0.00 0.00 46.52 5.54
698 753 1.444895 GCATGAAAGCAAGGTGCCG 60.445 57.895 0.00 0.00 46.52 5.69
699 754 1.444895 CGCATGAAAGCAAGGTGCC 60.445 57.895 0.00 0.00 46.52 5.01
700 755 2.090524 GCGCATGAAAGCAAGGTGC 61.091 57.895 0.30 0.00 45.46 5.01
701 756 0.731514 CTGCGCATGAAAGCAAGGTG 60.732 55.000 12.24 0.00 43.31 4.00
702 757 0.890542 TCTGCGCATGAAAGCAAGGT 60.891 50.000 12.24 0.00 43.31 3.50
703 758 0.179171 CTCTGCGCATGAAAGCAAGG 60.179 55.000 12.24 0.00 43.31 3.61
704 759 0.797249 GCTCTGCGCATGAAAGCAAG 60.797 55.000 12.24 0.00 43.31 4.01
705 760 1.210931 GCTCTGCGCATGAAAGCAA 59.789 52.632 12.24 0.00 43.31 3.91
706 761 2.693762 GGCTCTGCGCATGAAAGCA 61.694 57.895 25.49 3.67 41.67 3.91
707 762 2.101770 GGCTCTGCGCATGAAAGC 59.898 61.111 12.24 17.32 41.67 3.51
708 763 2.042259 TGGGCTCTGCGCATGAAAG 61.042 57.895 12.24 7.73 46.09 2.62
709 764 2.033911 TGGGCTCTGCGCATGAAA 59.966 55.556 12.24 0.00 46.09 2.69
717 772 2.167398 TTACTCCGTGTGGGCTCTGC 62.167 60.000 0.00 0.00 35.24 4.26
718 773 0.320374 TTTACTCCGTGTGGGCTCTG 59.680 55.000 0.00 0.00 35.24 3.35
719 774 0.608640 CTTTACTCCGTGTGGGCTCT 59.391 55.000 0.00 0.00 35.24 4.09
813 885 0.179184 GTCGTCGTCTCCTCTGCTTC 60.179 60.000 0.00 0.00 0.00 3.86
851 923 0.033504 TCTGCTTCCACGTCTTCCAC 59.966 55.000 0.00 0.00 0.00 4.02
852 924 0.756294 TTCTGCTTCCACGTCTTCCA 59.244 50.000 0.00 0.00 0.00 3.53
853 925 1.149148 GTTCTGCTTCCACGTCTTCC 58.851 55.000 0.00 0.00 0.00 3.46
854 926 1.527311 GTGTTCTGCTTCCACGTCTTC 59.473 52.381 0.00 0.00 0.00 2.87
855 927 1.583054 GTGTTCTGCTTCCACGTCTT 58.417 50.000 0.00 0.00 0.00 3.01
857 929 1.853319 CGTGTTCTGCTTCCACGTC 59.147 57.895 0.00 0.00 45.00 4.34
858 930 4.027755 CGTGTTCTGCTTCCACGT 57.972 55.556 0.00 0.00 45.00 4.49
860 932 0.814010 ACACCGTGTTCTGCTTCCAC 60.814 55.000 0.00 0.00 0.00 4.02
896 985 2.639327 GCATGGACCTGCAACCACC 61.639 63.158 8.72 1.33 41.87 4.61
943 1032 2.440409 CTGGGGTTGAAATGAGAGTGG 58.560 52.381 0.00 0.00 0.00 4.00
948 1037 1.180029 CTGCCTGGGGTTGAAATGAG 58.820 55.000 0.00 0.00 0.00 2.90
1014 1116 5.845391 AGAGGAAGAGGAGAACGATAAAG 57.155 43.478 0.00 0.00 0.00 1.85
1101 1203 3.780173 AGCCTGAGCGGAAGGAGC 61.780 66.667 6.56 0.00 46.67 4.70
1104 1206 4.399395 TGCAGCCTGAGCGGAAGG 62.399 66.667 0.00 0.00 46.67 3.46
1185 1287 4.602259 ACAGCCACCGACACCGTG 62.602 66.667 0.00 0.00 0.00 4.94
1311 1413 0.025001 CGCCGTATGTGAAAGAAGCG 59.975 55.000 0.00 0.00 36.06 4.68
1549 1651 1.588667 CAGTGGCGTTGTTGTTGGC 60.589 57.895 0.00 0.00 0.00 4.52
1725 1830 1.065102 TCTATCAGCGGCGTGTAGTTC 59.935 52.381 9.37 0.00 0.00 3.01
2235 2343 2.842462 ACGTCCTGCTGGTGGTGA 60.842 61.111 9.73 0.00 34.23 4.02
2374 2500 2.391879 CCGCTAGTATTTCGCTGTACC 58.608 52.381 0.00 0.00 0.00 3.34
2409 2535 3.976701 ATACGTGCCCTGCCACTGC 62.977 63.158 0.00 0.00 33.60 4.40
2410 2536 1.815421 GATACGTGCCCTGCCACTG 60.815 63.158 0.00 0.00 33.60 3.66
2547 6060 7.792374 ATTGAAATGTCGCTTACTATGTCAT 57.208 32.000 0.00 0.00 0.00 3.06
2576 6089 1.557099 TGAGTGAGTTACTGCCCGAT 58.443 50.000 0.00 0.00 40.53 4.18
2646 6160 8.527810 GGATATGACAACCCAATTTAAACTTGA 58.472 33.333 10.22 0.00 0.00 3.02
2661 6175 5.390613 CGTTGTTCTTTGGGATATGACAAC 58.609 41.667 0.00 0.00 38.01 3.32
2665 6179 3.950397 AGCGTTGTTCTTTGGGATATGA 58.050 40.909 0.00 0.00 0.00 2.15
2675 6189 1.792006 CGACCCTTAGCGTTGTTCTT 58.208 50.000 0.00 0.00 0.00 2.52
2698 6212 2.382882 TGTCCATTGTTGACTTGGCAA 58.617 42.857 0.00 0.00 33.83 4.52
2744 6258 0.179067 TTCTGTCGCCGTGGTTCTTT 60.179 50.000 0.00 0.00 0.00 2.52
2745 6259 0.600255 CTTCTGTCGCCGTGGTTCTT 60.600 55.000 0.00 0.00 0.00 2.52
2800 6314 2.177778 GCTGCCGAGCAAAAGCTC 59.822 61.111 7.39 7.39 45.46 4.09
2834 6348 3.246936 GTCGCGTTTGTTTTAGAGACCTT 59.753 43.478 5.77 0.00 0.00 3.50
2842 6356 6.104439 TCTAAACTTGTCGCGTTTGTTTTA 57.896 33.333 19.82 12.86 36.18 1.52
2844 6358 4.603231 TCTAAACTTGTCGCGTTTGTTT 57.397 36.364 5.77 15.07 36.18 2.83
2926 6440 2.345991 GCGGGAGGTGTAGCAACA 59.654 61.111 0.00 0.00 0.00 3.33
2927 6441 2.436115 GGCGGGAGGTGTAGCAAC 60.436 66.667 0.00 0.00 0.00 4.17
2952 6466 2.306847 GGTGGCTTTTCCTCTTTGTCA 58.693 47.619 0.00 0.00 35.26 3.58
2963 6477 0.105760 TGGTGATGGTGGTGGCTTTT 60.106 50.000 0.00 0.00 0.00 2.27
2992 6507 1.153823 CTACGTGGTTGGCTCTCCG 60.154 63.158 0.00 0.00 34.14 4.63
3072 6588 2.668185 CTACCGTGGTTGGTGCACCA 62.668 60.000 34.74 34.74 45.13 4.17
3103 6619 5.624509 CGAGTTAGGAATGGAAGATGTCACA 60.625 44.000 0.00 0.00 0.00 3.58
3105 6621 4.141937 CCGAGTTAGGAATGGAAGATGTCA 60.142 45.833 0.00 0.00 0.00 3.58
3114 6630 2.487934 CTGATGCCGAGTTAGGAATGG 58.512 52.381 0.00 0.00 26.92 3.16
3184 6700 0.481567 TAGCGGGACTAGCTGGGTAT 59.518 55.000 0.85 0.00 45.60 2.73
3212 6728 1.475280 GGTAGTCATGTGGCGTGTCTA 59.525 52.381 0.00 0.00 0.00 2.59
3233 6749 3.523087 TTGCTCAGCAACGGCCGTA 62.523 57.895 34.44 15.21 43.99 4.02
3271 6787 3.228017 TCGGTGTCGAAGGCCACA 61.228 61.111 5.01 0.00 43.03 4.17
3290 6806 1.128200 ACCACTGCACTGTCAGGTAA 58.872 50.000 4.53 0.00 38.36 2.85
3295 6811 1.146041 GGACACCACTGCACTGTCA 59.854 57.895 9.92 0.00 36.76 3.58
3296 6812 1.598130 GGGACACCACTGCACTGTC 60.598 63.158 0.00 0.00 36.50 3.51


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

AutoCloner maintained by Alex Coulton.