Multiple sequence alignment - TraesCS2A01G118900

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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 TraesCS2A01G118900 chr2A 100.000 3161 0 0 1 3161 69268320 69265160 0.000000e+00 5838.0
1 TraesCS2A01G118900 chr2D 95.280 1822 65 11 693 2506 65535702 65537510 0.000000e+00 2868.0
2 TraesCS2A01G118900 chr2D 94.055 656 36 3 2506 3159 602692102 602692756 0.000000e+00 992.0
3 TraesCS2A01G118900 chr2D 85.000 740 73 22 1 713 65534960 65535688 0.000000e+00 717.0
4 TraesCS2A01G118900 chr2D 82.075 106 16 2 34 139 307042864 307042762 1.560000e-13 87.9
5 TraesCS2A01G118900 chr2B 92.978 1538 78 17 741 2262 105765188 105763665 0.000000e+00 2215.0
6 TraesCS2A01G118900 chr5B 98.366 673 10 1 2490 3161 451179272 451178600 0.000000e+00 1181.0
7 TraesCS2A01G118900 chr7A 99.233 652 5 0 2508 3159 219859106 219858455 0.000000e+00 1177.0
8 TraesCS2A01G118900 chr1B 99.084 655 6 0 2507 3161 533405658 533405004 0.000000e+00 1177.0
9 TraesCS2A01G118900 chr1B 87.010 485 40 11 2507 2983 551720064 551719595 2.790000e-145 525.0
10 TraesCS2A01G118900 chr1D 95.245 652 29 2 2509 3159 204385068 204385718 0.000000e+00 1031.0
11 TraesCS2A01G118900 chr1D 94.360 656 34 3 2508 3161 345275823 345276477 0.000000e+00 1003.0
12 TraesCS2A01G118900 chr1D 86.385 213 23 5 214 425 318665601 318665394 8.820000e-56 228.0
13 TraesCS2A01G118900 chr5D 93.740 655 38 3 2507 3159 367408921 367408268 0.000000e+00 979.0
14 TraesCS2A01G118900 chr5D 82.060 563 77 16 2508 3058 119495105 119495655 2.870000e-125 459.0
15 TraesCS2A01G118900 chr3B 87.383 214 19 5 214 425 201514222 201514015 4.070000e-59 239.0
16 TraesCS2A01G118900 chr3B 86.916 214 20 5 214 425 201514759 201514552 1.900000e-57 233.0
17 TraesCS2A01G118900 chr3B 86.916 214 20 5 214 425 201515801 201515594 1.900000e-57 233.0
18 TraesCS2A01G118900 chrUn 87.805 205 17 5 214 416 445811942 445812140 1.900000e-57 233.0
19 TraesCS2A01G118900 chr7B 87.805 205 17 5 214 416 45215068 45215266 1.900000e-57 233.0
20 TraesCS2A01G118900 chr3D 86.792 212 22 5 215 425 21905747 21905541 6.820000e-57 231.0
21 TraesCS2A01G118900 chr6B 85.981 214 22 6 214 425 22427065 22426858 4.100000e-54 222.0
22 TraesCS2A01G118900 chr6D 78.231 147 27 5 1701 1843 67384935 67384790 4.340000e-14 89.8


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 TraesCS2A01G118900 chr2A 69265160 69268320 3160 True 5838.0 5838 100.000000 1 3161 1 chr2A.!!$R1 3160
1 TraesCS2A01G118900 chr2D 65534960 65537510 2550 False 1792.5 2868 90.140000 1 2506 2 chr2D.!!$F2 2505
2 TraesCS2A01G118900 chr2D 602692102 602692756 654 False 992.0 992 94.055000 2506 3159 1 chr2D.!!$F1 653
3 TraesCS2A01G118900 chr2B 105763665 105765188 1523 True 2215.0 2215 92.978000 741 2262 1 chr2B.!!$R1 1521
4 TraesCS2A01G118900 chr5B 451178600 451179272 672 True 1181.0 1181 98.366000 2490 3161 1 chr5B.!!$R1 671
5 TraesCS2A01G118900 chr7A 219858455 219859106 651 True 1177.0 1177 99.233000 2508 3159 1 chr7A.!!$R1 651
6 TraesCS2A01G118900 chr1B 533405004 533405658 654 True 1177.0 1177 99.084000 2507 3161 1 chr1B.!!$R1 654
7 TraesCS2A01G118900 chr1D 204385068 204385718 650 False 1031.0 1031 95.245000 2509 3159 1 chr1D.!!$F1 650
8 TraesCS2A01G118900 chr1D 345275823 345276477 654 False 1003.0 1003 94.360000 2508 3161 1 chr1D.!!$F2 653
9 TraesCS2A01G118900 chr5D 367408268 367408921 653 True 979.0 979 93.740000 2507 3159 1 chr5D.!!$R1 652
10 TraesCS2A01G118900 chr5D 119495105 119495655 550 False 459.0 459 82.060000 2508 3058 1 chr5D.!!$F1 550
11 TraesCS2A01G118900 chr3B 201514015 201515801 1786 True 235.0 239 87.071667 214 425 3 chr3B.!!$R1 211

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
619 653 0.244721 CTTTGGTAAGGCAGGCAAGC 59.755 55.0 0.0 0.0 0.0 4.01 F
1503 2096 0.179189 CGTCCTTCAAGAAATGGCGC 60.179 55.0 0.0 0.0 0.0 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1785 2378 0.039165 GCGAAAAGCCAAACCAGAGG 60.039 55.0 0.0 0.0 40.81 3.69 R
2328 2922 2.054232 TTCCAACGGCAACTAACCAA 57.946 45.0 0.0 0.0 0.00 3.67 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
32 33 9.979578 AGTTCTAGACTTGATATTGATGATCAC 57.020 33.333 0.00 0.00 33.92 3.06
103 104 1.741706 GAGATGTTCCGGTCGACTACA 59.258 52.381 16.46 14.28 0.00 2.74
135 136 6.934645 TCTGTGGTAACTTGGTCAATCTTAAG 59.065 38.462 0.00 0.00 37.61 1.85
144 145 9.911788 AACTTGGTCAATCTTAAGATGATGTAT 57.088 29.630 18.61 0.00 34.49 2.29
147 148 7.951591 TGGTCAATCTTAAGATGATGTATCGA 58.048 34.615 18.61 0.00 40.86 3.59
149 150 7.329717 GGTCAATCTTAAGATGATGTATCGACC 59.670 40.741 18.61 17.11 40.86 4.79
150 151 8.085296 GTCAATCTTAAGATGATGTATCGACCT 58.915 37.037 18.61 0.00 40.86 3.85
172 173 5.705441 CCTAGTCTCTCAGAGGTGCTTATAG 59.295 48.000 0.57 0.00 0.00 1.31
175 176 3.463704 TCTCTCAGAGGTGCTTATAGGGA 59.536 47.826 0.57 0.00 0.00 4.20
184 185 4.043812 AGGTGCTTATAGGGATACGTAGGA 59.956 45.833 0.08 0.00 40.84 2.94
206 207 0.467804 TGCATGCGTTCATAGGGCTA 59.532 50.000 14.09 0.00 0.00 3.93
210 211 2.596904 TGCGTTCATAGGGCTAACTC 57.403 50.000 0.00 0.00 0.00 3.01
212 213 3.293337 TGCGTTCATAGGGCTAACTCTA 58.707 45.455 0.00 0.00 0.00 2.43
218 219 6.015688 CGTTCATAGGGCTAACTCTAATACCA 60.016 42.308 0.00 0.00 0.00 3.25
225 226 6.157994 AGGGCTAACTCTAATACCATGTTTGA 59.842 38.462 0.00 0.00 0.00 2.69
228 229 6.017852 GCTAACTCTAATACCATGTTTGAGCC 60.018 42.308 6.10 0.00 33.60 4.70
263 264 6.940298 ACAATTAAGAGGTCCATTCGAAGAAA 59.060 34.615 3.35 0.00 45.90 2.52
269 270 5.008712 AGAGGTCCATTCGAAGAAAACAAAC 59.991 40.000 3.35 0.00 45.90 2.93
294 295 9.293404 ACACTAATTTAAGTAAGAAGTTTCCCC 57.707 33.333 0.00 0.00 0.00 4.81
386 387 5.119694 GGTTCTCGGAAGAAGATAGCAAAT 58.880 41.667 0.00 0.00 42.14 2.32
388 389 6.422400 GGTTCTCGGAAGAAGATAGCAAATAG 59.578 42.308 0.00 0.00 42.14 1.73
389 390 6.961360 TCTCGGAAGAAGATAGCAAATAGA 57.039 37.500 0.00 0.00 41.32 1.98
390 391 6.976088 TCTCGGAAGAAGATAGCAAATAGAG 58.024 40.000 0.00 0.00 41.32 2.43
393 394 7.957002 TCGGAAGAAGATAGCAAATAGAGAAT 58.043 34.615 0.00 0.00 37.03 2.40
394 395 8.424918 TCGGAAGAAGATAGCAAATAGAGAATT 58.575 33.333 0.00 0.00 37.03 2.17
523 557 7.898014 AATTCCTTTAAAAGTGAGACACCTT 57.102 32.000 0.00 0.00 34.49 3.50
524 558 7.898014 ATTCCTTTAAAAGTGAGACACCTTT 57.102 32.000 0.00 0.00 34.49 3.11
525 559 6.693315 TCCTTTAAAAGTGAGACACCTTTG 57.307 37.500 8.21 0.00 34.49 2.77
526 560 5.592688 TCCTTTAAAAGTGAGACACCTTTGG 59.407 40.000 8.21 3.05 34.49 3.28
528 562 6.544564 CCTTTAAAAGTGAGACACCTTTGGTA 59.455 38.462 8.21 0.00 34.49 3.25
529 563 6.930667 TTAAAAGTGAGACACCTTTGGTAC 57.069 37.500 8.21 0.00 34.49 3.34
530 564 4.772886 AAAGTGAGACACCTTTGGTACT 57.227 40.909 0.00 0.00 34.49 2.73
532 566 4.868314 AGTGAGACACCTTTGGTACTAC 57.132 45.455 0.00 0.00 34.49 2.73
533 567 3.255149 AGTGAGACACCTTTGGTACTACG 59.745 47.826 0.00 0.00 34.49 3.51
538 572 4.343239 AGACACCTTTGGTACTACGAAAGT 59.657 41.667 17.56 5.34 40.74 2.66
539 573 4.374399 ACACCTTTGGTACTACGAAAGTG 58.626 43.478 17.56 16.70 40.74 3.16
540 574 4.099881 ACACCTTTGGTACTACGAAAGTGA 59.900 41.667 17.56 0.00 40.74 3.41
541 575 5.051816 CACCTTTGGTACTACGAAAGTGAA 58.948 41.667 17.56 0.00 40.74 3.18
542 576 5.524646 CACCTTTGGTACTACGAAAGTGAAA 59.475 40.000 17.56 2.54 40.74 2.69
543 577 6.037391 CACCTTTGGTACTACGAAAGTGAAAA 59.963 38.462 17.56 3.59 40.74 2.29
544 578 6.769341 ACCTTTGGTACTACGAAAGTGAAAAT 59.231 34.615 17.56 0.48 40.74 1.82
545 579 7.933033 ACCTTTGGTACTACGAAAGTGAAAATA 59.067 33.333 17.56 0.00 40.74 1.40
616 650 4.841441 CCTTTGGTAAGGCAGGCA 57.159 55.556 0.00 0.00 44.27 4.75
617 651 3.050089 CCTTTGGTAAGGCAGGCAA 57.950 52.632 0.00 0.00 44.27 4.52
618 652 0.890683 CCTTTGGTAAGGCAGGCAAG 59.109 55.000 0.00 0.00 44.27 4.01
619 653 0.244721 CTTTGGTAAGGCAGGCAAGC 59.755 55.000 0.00 0.00 0.00 4.01
631 665 3.889227 GCAAGCTATGCGACCACA 58.111 55.556 5.35 0.00 46.87 4.17
662 697 7.646922 CCTTGTCAAATCAACAAAGAAGAAGAG 59.353 37.037 0.00 0.00 36.27 2.85
664 699 6.095300 TGTCAAATCAACAAAGAAGAAGAGCA 59.905 34.615 0.00 0.00 0.00 4.26
671 706 3.893813 ACAAAGAAGAAGAGCAAAGGCAT 59.106 39.130 0.00 0.00 44.61 4.40
676 711 4.586001 AGAAGAAGAGCAAAGGCATGAAAA 59.414 37.500 0.00 0.00 44.61 2.29
724 795 2.990740 TGGCCCATAAACTTGAAGGT 57.009 45.000 0.00 0.00 0.00 3.50
728 799 2.524306 CCCATAAACTTGAAGGTGCCA 58.476 47.619 0.00 0.00 0.00 4.92
783 854 2.125326 CGGCAGGACGGAGATGGTA 61.125 63.158 0.00 0.00 0.00 3.25
787 858 1.043116 CAGGACGGAGATGGTAGGCA 61.043 60.000 0.00 0.00 0.00 4.75
878 959 9.399403 GTTATTGTCTTGGTTCTTTCATTTCTC 57.601 33.333 0.00 0.00 0.00 2.87
896 977 1.821753 CTCGGAGAAGAAGAGGCTGAA 59.178 52.381 0.00 0.00 34.09 3.02
897 978 2.430332 CTCGGAGAAGAAGAGGCTGAAT 59.570 50.000 0.00 0.00 34.09 2.57
898 979 2.167281 TCGGAGAAGAAGAGGCTGAATG 59.833 50.000 0.00 0.00 0.00 2.67
899 980 2.741228 CGGAGAAGAAGAGGCTGAATGG 60.741 54.545 0.00 0.00 0.00 3.16
900 981 2.287769 GAGAAGAAGAGGCTGAATGGC 58.712 52.381 0.00 0.00 42.15 4.40
984 1073 5.235186 ACACAAATCAGATTTCGATCGATCC 59.765 40.000 20.18 10.89 0.00 3.36
1176 1449 4.093408 ACGACAATGATGAAATCTCGGTTG 59.907 41.667 0.00 0.00 45.81 3.77
1249 1577 0.236711 CGGGCAGATCGATTTCATGC 59.763 55.000 14.02 14.02 36.16 4.06
1476 2069 2.370445 CCTCCTCCGGGACAGCAAT 61.370 63.158 0.00 0.00 36.57 3.56
1503 2096 0.179189 CGTCCTTCAAGAAATGGCGC 60.179 55.000 0.00 0.00 0.00 6.53
1624 2217 1.006102 ACTGAGTTCCAAGACGCCG 60.006 57.895 0.00 0.00 0.00 6.46
1779 2372 4.783734 GCGGTGTACGTCCCCGAC 62.784 72.222 20.54 10.44 44.41 4.79
1900 2493 2.764128 GGGACGATCTGGCCTGGA 60.764 66.667 10.07 5.61 0.00 3.86
2124 2717 2.972505 CGGCACAAGTCCAAGCGT 60.973 61.111 0.00 0.00 0.00 5.07
2133 2726 0.677842 AGTCCAAGCGTTACGACCTT 59.322 50.000 9.62 0.00 0.00 3.50
2163 2756 0.539438 TCGCCAAAGCCCTGTGAATT 60.539 50.000 0.00 0.00 34.57 2.17
2180 2773 3.452990 TGAATTAATGGTACGGAGGAGCA 59.547 43.478 0.00 0.00 0.00 4.26
2183 2776 1.276622 AATGGTACGGAGGAGCACTT 58.723 50.000 0.00 0.00 0.00 3.16
2210 2804 0.786581 CTTCTGCGCCGTGCTATATG 59.213 55.000 4.18 0.00 46.63 1.78
2216 2810 1.564622 GCCGTGCTATATGTGTGCG 59.435 57.895 0.00 0.00 0.00 5.34
2242 2836 3.693085 TGCTTGTGTTTTTGTTACGGGTA 59.307 39.130 0.00 0.00 0.00 3.69
2328 2922 1.399440 CACTGCATTGTCGCTGCTTAT 59.601 47.619 0.00 0.00 40.34 1.73
2339 2933 2.418628 TCGCTGCTTATTGGTTAGTTGC 59.581 45.455 0.00 0.00 0.00 4.17
2403 2997 6.798959 GGTGAATCTTGCAATAATAATCTCGC 59.201 38.462 0.00 0.00 0.00 5.03
2488 3082 2.047151 AAAGTTGACGGCTGCGTGTG 62.047 55.000 0.68 0.00 0.00 3.82
2975 3587 2.105128 CTAGCCCGTTCCAGCTCG 59.895 66.667 0.00 0.00 40.56 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 3.315470 GCCGGAAAGTCTGGAATAAATCC 59.685 47.826 5.05 0.00 45.95 3.01
50 51 2.464459 GCATCGCCGGAAAGTCTGG 61.464 63.158 5.05 0.00 45.82 3.86
59 60 2.587194 CTGAAGGAGCATCGCCGG 60.587 66.667 0.00 0.00 34.37 6.13
103 104 1.000955 CAAGTTACCACAGACGCCTCT 59.999 52.381 0.00 0.00 0.00 3.69
110 111 4.974645 AGATTGACCAAGTTACCACAGA 57.025 40.909 0.00 0.00 0.00 3.41
111 112 6.934645 TCTTAAGATTGACCAAGTTACCACAG 59.065 38.462 0.00 0.00 0.00 3.66
116 117 9.167311 ACATCATCTTAAGATTGACCAAGTTAC 57.833 33.333 19.47 0.00 31.21 2.50
118 119 9.911788 ATACATCATCTTAAGATTGACCAAGTT 57.088 29.630 19.47 3.05 31.21 2.66
135 136 5.935206 TGAGAGACTAGGTCGATACATCATC 59.065 44.000 0.00 0.00 37.67 2.92
143 144 2.775384 ACCTCTGAGAGACTAGGTCGAT 59.225 50.000 11.82 0.00 37.87 3.59
144 145 2.093394 CACCTCTGAGAGACTAGGTCGA 60.093 54.545 11.82 0.00 40.39 4.20
147 148 1.638589 AGCACCTCTGAGAGACTAGGT 59.361 52.381 11.82 0.00 43.15 3.08
149 150 5.705441 CCTATAAGCACCTCTGAGAGACTAG 59.295 48.000 11.82 0.00 0.00 2.57
150 151 5.456907 CCCTATAAGCACCTCTGAGAGACTA 60.457 48.000 11.82 0.00 0.00 2.59
172 173 2.688507 CATGCACATCCTACGTATCCC 58.311 52.381 0.00 0.00 0.00 3.85
175 176 1.068588 ACGCATGCACATCCTACGTAT 59.931 47.619 19.57 0.00 0.00 3.06
184 185 1.311859 CCCTATGAACGCATGCACAT 58.688 50.000 19.57 19.93 35.94 3.21
206 207 5.648092 GTGGCTCAAACATGGTATTAGAGTT 59.352 40.000 0.00 0.00 0.00 3.01
210 211 3.632145 GGGTGGCTCAAACATGGTATTAG 59.368 47.826 0.00 0.00 0.00 1.73
212 213 2.042979 AGGGTGGCTCAAACATGGTATT 59.957 45.455 0.00 0.00 0.00 1.89
218 219 1.067295 TGAGAGGGTGGCTCAAACAT 58.933 50.000 0.00 0.00 39.29 2.71
225 226 3.330701 TCTTAATTGTTGAGAGGGTGGCT 59.669 43.478 0.00 0.00 0.00 4.75
269 270 9.292195 TGGGGAAACTTCTTACTTAAATTAGTG 57.708 33.333 0.00 0.00 0.00 2.74
294 295 9.967346 TCATTTAAGTAAGAAGTCTCCGATATG 57.033 33.333 0.00 0.00 0.00 1.78
332 333 2.875933 TCCAGCAACTCCAACTAAAACG 59.124 45.455 0.00 0.00 0.00 3.60
333 334 4.911514 TTCCAGCAACTCCAACTAAAAC 57.088 40.909 0.00 0.00 0.00 2.43
498 532 7.898014 AGGTGTCTCACTTTTAAAGGAATTT 57.102 32.000 9.64 0.00 34.40 1.82
501 535 6.096282 CCAAAGGTGTCTCACTTTTAAAGGAA 59.904 38.462 9.64 0.00 40.69 3.36
503 537 5.359860 ACCAAAGGTGTCTCACTTTTAAAGG 59.640 40.000 9.64 9.12 40.69 3.11
512 546 3.254166 TCGTAGTACCAAAGGTGTCTCAC 59.746 47.826 0.00 0.00 36.19 3.51
513 547 3.489355 TCGTAGTACCAAAGGTGTCTCA 58.511 45.455 0.00 0.00 36.19 3.27
515 549 4.343239 ACTTTCGTAGTACCAAAGGTGTCT 59.657 41.667 20.18 1.31 36.19 3.41
516 550 4.446719 CACTTTCGTAGTACCAAAGGTGTC 59.553 45.833 20.18 0.00 36.19 3.67
517 551 4.099881 TCACTTTCGTAGTACCAAAGGTGT 59.900 41.667 20.18 2.65 36.19 4.16
518 552 4.624015 TCACTTTCGTAGTACCAAAGGTG 58.376 43.478 20.18 17.08 36.19 4.00
519 553 4.942761 TCACTTTCGTAGTACCAAAGGT 57.057 40.909 20.18 8.19 40.16 3.50
520 554 6.607735 TTTTCACTTTCGTAGTACCAAAGG 57.392 37.500 20.18 11.67 34.56 3.11
521 555 9.755064 CATATTTTCACTTTCGTAGTACCAAAG 57.245 33.333 16.13 16.13 34.56 2.77
523 557 7.148373 GGCATATTTTCACTTTCGTAGTACCAA 60.148 37.037 0.00 0.00 34.56 3.67
524 558 6.314400 GGCATATTTTCACTTTCGTAGTACCA 59.686 38.462 0.00 0.00 34.56 3.25
525 559 6.238293 GGGCATATTTTCACTTTCGTAGTACC 60.238 42.308 0.00 0.00 34.56 3.34
526 560 6.238293 GGGGCATATTTTCACTTTCGTAGTAC 60.238 42.308 0.00 0.00 34.56 2.73
528 562 4.638865 GGGGCATATTTTCACTTTCGTAGT 59.361 41.667 0.00 0.00 37.68 2.73
529 563 4.638421 TGGGGCATATTTTCACTTTCGTAG 59.362 41.667 0.00 0.00 0.00 3.51
530 564 4.590918 TGGGGCATATTTTCACTTTCGTA 58.409 39.130 0.00 0.00 0.00 3.43
532 566 4.082245 ACTTGGGGCATATTTTCACTTTCG 60.082 41.667 0.00 0.00 0.00 3.46
533 567 5.047377 TCACTTGGGGCATATTTTCACTTTC 60.047 40.000 0.00 0.00 0.00 2.62
538 572 5.815233 TTTTCACTTGGGGCATATTTTCA 57.185 34.783 0.00 0.00 0.00 2.69
539 573 6.643388 AGATTTTCACTTGGGGCATATTTTC 58.357 36.000 0.00 0.00 0.00 2.29
540 574 6.625532 AGATTTTCACTTGGGGCATATTTT 57.374 33.333 0.00 0.00 0.00 1.82
541 575 7.619302 TCTTAGATTTTCACTTGGGGCATATTT 59.381 33.333 0.00 0.00 0.00 1.40
542 576 7.125391 TCTTAGATTTTCACTTGGGGCATATT 58.875 34.615 0.00 0.00 0.00 1.28
543 577 6.672593 TCTTAGATTTTCACTTGGGGCATAT 58.327 36.000 0.00 0.00 0.00 1.78
544 578 6.073447 TCTTAGATTTTCACTTGGGGCATA 57.927 37.500 0.00 0.00 0.00 3.14
545 579 4.934356 TCTTAGATTTTCACTTGGGGCAT 58.066 39.130 0.00 0.00 0.00 4.40
546 580 4.380843 TCTTAGATTTTCACTTGGGGCA 57.619 40.909 0.00 0.00 0.00 5.36
577 611 9.649167 AAAGGTGTGTCACTTTGTAGTATATAC 57.351 33.333 4.60 4.60 34.04 1.47
579 613 7.606456 CCAAAGGTGTGTCACTTTGTAGTATAT 59.394 37.037 13.92 0.00 34.04 0.86
580 614 6.932400 CCAAAGGTGTGTCACTTTGTAGTATA 59.068 38.462 13.92 0.00 34.04 1.47
581 615 5.763204 CCAAAGGTGTGTCACTTTGTAGTAT 59.237 40.000 13.92 0.00 34.04 2.12
582 616 5.120399 CCAAAGGTGTGTCACTTTGTAGTA 58.880 41.667 13.92 0.00 34.04 1.82
583 617 3.945285 CCAAAGGTGTGTCACTTTGTAGT 59.055 43.478 13.92 0.00 34.04 2.73
588 622 3.951680 CCTTACCAAAGGTGTGTCACTTT 59.048 43.478 4.27 0.00 46.34 2.66
616 650 1.599047 AGCTGTGGTCGCATAGCTT 59.401 52.632 8.17 0.00 45.30 3.74
617 651 3.303189 AGCTGTGGTCGCATAGCT 58.697 55.556 8.17 8.17 43.31 3.32
618 652 1.884926 GGAGCTGTGGTCGCATAGC 60.885 63.158 0.00 4.05 39.22 2.97
619 653 1.227380 GGGAGCTGTGGTCGCATAG 60.227 63.158 0.00 0.00 41.49 2.23
624 658 1.374758 GACAAGGGAGCTGTGGTCG 60.375 63.158 0.00 0.00 0.00 4.79
631 665 3.228188 TGTTGATTTGACAAGGGAGCT 57.772 42.857 0.00 0.00 0.00 4.09
724 795 2.371841 ACATCTGGTGAGTAGTTTGGCA 59.628 45.455 0.00 0.00 0.00 4.92
728 799 6.365970 AGATCAACATCTGGTGAGTAGTTT 57.634 37.500 4.04 0.00 46.01 2.66
773 844 1.869754 CGTGAATGCCTACCATCTCCG 60.870 57.143 0.00 0.00 31.43 4.63
783 854 2.011741 TATCGCCGACGTGAATGCCT 62.012 55.000 0.00 0.00 41.18 4.75
787 858 0.868602 CCGTTATCGCCGACGTGAAT 60.869 55.000 0.00 0.00 41.18 2.57
878 959 2.548875 CATTCAGCCTCTTCTTCTCCG 58.451 52.381 0.00 0.00 0.00 4.63
896 977 4.277672 GCTCATATTGTTGACATCAGCCAT 59.722 41.667 0.00 0.00 0.00 4.40
897 978 3.628942 GCTCATATTGTTGACATCAGCCA 59.371 43.478 0.00 0.00 0.00 4.75
898 979 3.004106 GGCTCATATTGTTGACATCAGCC 59.996 47.826 0.00 0.00 0.00 4.85
899 980 3.881688 AGGCTCATATTGTTGACATCAGC 59.118 43.478 0.00 0.00 0.00 4.26
900 981 4.880120 ACAGGCTCATATTGTTGACATCAG 59.120 41.667 0.00 0.00 0.00 2.90
901 982 4.637091 CACAGGCTCATATTGTTGACATCA 59.363 41.667 0.00 0.00 0.00 3.07
902 983 4.637534 ACACAGGCTCATATTGTTGACATC 59.362 41.667 0.00 0.00 0.00 3.06
903 984 4.592942 ACACAGGCTCATATTGTTGACAT 58.407 39.130 0.00 0.00 0.00 3.06
959 1047 5.454736 TCGATCGAAATCTGATTTGTGTG 57.545 39.130 19.59 7.45 31.47 3.82
963 1051 5.693555 TCTGGATCGATCGAAATCTGATTTG 59.306 40.000 23.50 11.89 31.47 2.32
984 1073 3.119065 TGCTCATGCTCTCTCTTTCTCTG 60.119 47.826 0.00 0.00 40.48 3.35
1144 1417 3.534554 TCATCATTGTCGTTGGATCTGG 58.465 45.455 0.00 0.00 0.00 3.86
1272 1600 1.514087 GTTGTCCACGGCGAGGATA 59.486 57.895 27.98 22.90 37.52 2.59
1445 2038 2.194326 GGAGGGCCTGGAAGCATC 59.806 66.667 12.95 0.00 0.00 3.91
1476 2069 1.612676 TCTTGAAGGACGAGGACGAA 58.387 50.000 0.00 0.00 42.66 3.85
1624 2217 2.126346 GTGGGCGCAGATTGCAAC 60.126 61.111 10.83 0.00 45.36 4.17
1779 2372 2.027625 GCCAAACCAGAGGTCGTCG 61.028 63.158 0.00 0.00 33.12 5.12
1785 2378 0.039165 GCGAAAAGCCAAACCAGAGG 60.039 55.000 0.00 0.00 40.81 3.69
1895 2488 3.465403 CCCAGCTCTCCGTCCAGG 61.465 72.222 0.00 0.00 42.97 4.45
2124 2717 1.225376 CGTTGCAGCCAAGGTCGTAA 61.225 55.000 0.00 0.00 33.38 3.18
2163 2756 2.154567 AGTGCTCCTCCGTACCATTA 57.845 50.000 0.00 0.00 0.00 1.90
2180 2773 1.560860 GCGCAGAAGCACGAGAAAGT 61.561 55.000 0.30 0.00 42.27 2.66
2183 2776 2.738521 GGCGCAGAAGCACGAGAA 60.739 61.111 10.83 0.00 42.27 2.87
2210 2804 2.024588 CACAAGCACCACGCACAC 59.975 61.111 0.00 0.00 46.13 3.82
2216 2810 3.302170 CGTAACAAAAACACAAGCACCAC 59.698 43.478 0.00 0.00 0.00 4.16
2292 2886 5.405935 TGCAGTGCTATGAGTTCTAAGAA 57.594 39.130 17.60 0.00 0.00 2.52
2293 2887 5.604758 ATGCAGTGCTATGAGTTCTAAGA 57.395 39.130 17.60 0.00 0.00 2.10
2328 2922 2.054232 TTCCAACGGCAACTAACCAA 57.946 45.000 0.00 0.00 0.00 3.67
2339 2933 5.043248 GCAAAATATTCTCCATTCCAACGG 58.957 41.667 0.00 0.00 0.00 4.44
2378 2972 6.798959 GCGAGATTATTATTGCAAGATTCACC 59.201 38.462 4.94 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.