Multiple sequence alignment - TraesCS1D01G397700

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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 TraesCS1D01G397700 chr1D 100.000 5206 0 0 1 5206 465135768 465130563 0.000000e+00 9614.0
1 TraesCS1D01G397700 chr4B 94.133 2659 130 16 1843 4496 112041605 112038968 0.000000e+00 4023.0
2 TraesCS1D01G397700 chr4B 89.457 939 57 21 1 904 112043981 112043050 0.000000e+00 1147.0
3 TraesCS1D01G397700 chr4B 94.350 531 30 0 4676 5206 112038319 112037789 0.000000e+00 815.0
4 TraesCS1D01G397700 chr4B 95.105 429 17 3 3 430 112081383 112080958 0.000000e+00 673.0
5 TraesCS1D01G397700 chr4B 94.432 431 21 2 1 430 112078030 112077602 0.000000e+00 660.0
6 TraesCS1D01G397700 chr4B 83.724 682 73 18 900 1551 112042534 112041861 1.240000e-170 610.0
7 TraesCS1D01G397700 chr4B 92.111 431 29 4 1 430 112074913 112074487 2.070000e-168 603.0
8 TraesCS1D01G397700 chr4B 89.744 195 16 4 4497 4689 112038912 112038720 4.030000e-61 246.0
9 TraesCS1D01G397700 chr4B 90.196 153 14 1 1558 1710 112041818 112041667 1.140000e-46 198.0
10 TraesCS1D01G397700 chr3A 89.543 2802 178 54 1731 4496 22203620 22206342 0.000000e+00 3445.0
11 TraesCS1D01G397700 chr3A 90.439 889 53 11 3608 4496 22220951 22221807 0.000000e+00 1142.0
12 TraesCS1D01G397700 chr3A 89.865 888 57 8 3609 4496 22218424 22219278 0.000000e+00 1110.0
13 TraesCS1D01G397700 chr3A 89.944 716 56 12 4497 5206 22219333 22220038 0.000000e+00 909.0
14 TraesCS1D01G397700 chr3A 89.385 716 62 11 4497 5206 22221862 22222569 0.000000e+00 889.0
15 TraesCS1D01G397700 chr3A 90.280 679 47 13 4497 5170 22206397 22207061 0.000000e+00 870.0
16 TraesCS1D01G397700 chr3A 83.777 789 87 25 923 1687 22200013 22200784 0.000000e+00 710.0
17 TraesCS1D01G397700 chr3A 91.803 122 8 2 1138 1258 49520302 49520422 8.970000e-38 169.0
18 TraesCS1D01G397700 chr2B 91.483 1632 104 21 2873 4483 87919509 87921126 0.000000e+00 2211.0
19 TraesCS1D01G397700 chr2B 89.286 728 55 14 4497 5206 87921536 87922258 0.000000e+00 891.0
20 TraesCS1D01G397700 chr2B 81.541 753 68 35 2107 2824 87918574 87919290 5.890000e-154 555.0
21 TraesCS1D01G397700 chr2B 89.147 387 28 6 939 1316 87917889 87918270 2.190000e-128 470.0
22 TraesCS1D01G397700 chr2B 94.492 236 12 1 148 382 758259133 758258898 3.830000e-96 363.0
23 TraesCS1D01G397700 chr2B 81.057 227 23 8 486 694 87915806 87916030 4.170000e-36 163.0
24 TraesCS1D01G397700 chr2B 87.273 110 14 0 715 824 87916086 87916195 5.470000e-25 126.0
25 TraesCS1D01G397700 chr2B 100.000 29 0 0 870 898 87916209 87916237 3.000000e-03 54.7
26 TraesCS1D01G397700 chr1A 93.374 1464 79 7 1829 3286 557494431 557492980 0.000000e+00 2150.0
27 TraesCS1D01G397700 chr1A 93.355 918 38 9 1 903 557497592 557496683 0.000000e+00 1336.0
28 TraesCS1D01G397700 chr1A 95.840 649 20 3 942 1589 557495195 557494553 0.000000e+00 1042.0
29 TraesCS1D01G397700 chr1A 95.213 564 24 3 3271 3833 557492623 557492062 0.000000e+00 889.0
30 TraesCS1D01G397700 chr1A 91.981 636 28 10 3865 4496 557492063 557491447 0.000000e+00 870.0
31 TraesCS1D01G397700 chr1A 95.692 325 14 0 4882 5206 557491258 557490934 1.660000e-144 523.0
32 TraesCS1D01G397700 chr1A 92.063 126 9 1 4507 4631 557491387 557491262 5.360000e-40 176.0
33 TraesCS1D01G397700 chr1A 100.000 39 0 0 1612 1650 557494549 557494511 7.230000e-09 73.1
34 TraesCS1D01G397700 chr7B 90.414 1617 89 30 2907 4496 504193269 504191692 0.000000e+00 2067.0
35 TraesCS1D01G397700 chr7B 89.589 730 48 19 4497 5206 504191352 504190631 0.000000e+00 902.0
36 TraesCS1D01G397700 chr7B 82.953 745 62 29 2110 2824 504194223 504193514 3.450000e-171 612.0
37 TraesCS1D01G397700 chr7B 88.630 387 28 7 939 1316 504194909 504194530 1.710000e-124 457.0
38 TraesCS1D01G397700 chr7B 94.068 236 13 1 148 382 504088752 504088517 1.780000e-94 357.0
39 TraesCS1D01G397700 chr7B 86.381 257 22 9 4634 4880 322488455 322488708 8.590000e-68 268.0
40 TraesCS1D01G397700 chr7B 85.333 225 14 5 486 693 504208312 504208090 1.140000e-51 215.0
41 TraesCS1D01G397700 chr6D 89.558 498 23 12 47 519 274348716 274349209 5.770000e-169 604.0
42 TraesCS1D01G397700 chr6D 84.956 113 15 2 715 826 274350702 274350813 4.260000e-21 113.0
43 TraesCS1D01G397700 chr6D 91.837 49 3 1 1 48 274348630 274348678 3.360000e-07 67.6
44 TraesCS1D01G397700 chr7D 86.111 504 35 17 47 519 536981178 536981677 1.290000e-140 510.0
45 TraesCS1D01G397700 chr7D 88.073 109 12 1 715 822 466667737 466667629 1.520000e-25 128.0
46 TraesCS1D01G397700 chr7D 93.617 47 3 0 1 47 536981092 536981138 2.600000e-08 71.3
47 TraesCS1D01G397700 chr5B 91.327 196 17 0 4691 4886 447183430 447183235 8.590000e-68 268.0
48 TraesCS1D01G397700 chr2A 85.417 240 30 5 4632 4869 3580220 3580456 1.450000e-60 244.0
49 TraesCS1D01G397700 chr2A 91.525 118 10 0 1141 1258 708689560 708689443 4.170000e-36 163.0
50 TraesCS1D01G397700 chr4D 91.935 124 10 0 1135 1258 210025388 210025511 1.930000e-39 174.0
51 TraesCS1D01G397700 chr6A 90.909 121 11 0 1135 1255 616334583 616334703 4.170000e-36 163.0


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 TraesCS1D01G397700 chr1D 465130563 465135768 5205 True 9614.000000 9614 100.000000 1 5206 1 chr1D.!!$R1 5205
1 TraesCS1D01G397700 chr4B 112037789 112043981 6192 True 1173.166667 4023 90.267333 1 5206 6 chr4B.!!$R1 5205
2 TraesCS1D01G397700 chr4B 112074487 112081383 6896 True 645.333333 673 93.882667 1 430 3 chr4B.!!$R2 429
3 TraesCS1D01G397700 chr3A 22200013 22207061 7048 False 1675.000000 3445 87.866667 923 5170 3 chr3A.!!$F2 4247
4 TraesCS1D01G397700 chr3A 22218424 22222569 4145 False 1012.500000 1142 89.908250 3608 5206 4 chr3A.!!$F3 1598
5 TraesCS1D01G397700 chr2B 87915806 87922258 6452 False 638.671429 2211 88.541000 486 5206 7 chr2B.!!$F1 4720
6 TraesCS1D01G397700 chr1A 557490934 557497592 6658 True 882.387500 2150 94.689750 1 5206 8 chr1A.!!$R1 5205
7 TraesCS1D01G397700 chr7B 504190631 504194909 4278 True 1009.500000 2067 87.896500 939 5206 4 chr7B.!!$R3 4267
8 TraesCS1D01G397700 chr6D 274348630 274350813 2183 False 261.533333 604 88.783667 1 826 3 chr6D.!!$F1 825
9 TraesCS1D01G397700 chr7D 536981092 536981677 585 False 290.650000 510 89.864000 1 519 2 chr7D.!!$F1 518

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
810 2262 0.538287 GAATGGCTGGGTAGATGGGC 60.538 60.000 0.00 0.00 0.00 5.36 F
832 2292 1.149148 GGCGAGGAACTTCTGTGAAC 58.851 55.000 0.00 0.00 41.55 3.18 F
1377 8770 1.744872 TAGGGGAGGGGTTTTCGAAA 58.255 50.000 6.47 6.47 0.00 3.46 F
1807 12104 1.876156 CAACAAACAGTGAGGAGCTCC 59.124 52.381 26.22 26.22 0.00 4.70 F
2027 12325 2.202236 GATCAGTCAAGCCCCTGCCA 62.202 60.000 0.00 0.00 38.69 4.92 F
3804 17834 0.668401 CACGTCTCATCTGCAGCACA 60.668 55.000 9.47 0.00 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2479 12933 1.831106 TGAATCCACCATAGTCAGCGT 59.169 47.619 0.00 0.0 0.00 5.07 R
2540 13012 3.477530 AGAATAAGCCTGGAATAACGGC 58.522 45.455 0.00 0.0 44.09 5.68 R
2882 13814 4.613850 GCAGGAAGTAAAACAGCAAGTAGC 60.614 45.833 0.00 0.0 46.19 3.58 R
3783 17813 1.216444 GCTGCAGATGAGACGTGGA 59.784 57.895 20.43 0.0 0.00 4.02 R
3843 17873 0.790207 ATGTCGTGCAGCAAACTACG 59.210 50.000 0.00 0.0 37.85 3.51 R
5104 20264 0.674581 CTGTCGGGAATCAAGCAGCA 60.675 55.000 0.00 0.0 0.00 4.41 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
61 142 6.896021 TCTCTGCAAGTACTTTACTACTGT 57.104 37.500 5.07 0.00 38.26 3.55
80 161 8.379331 ACTACTGTCTGCTATAGATCTCACATA 58.621 37.037 3.21 0.00 37.83 2.29
81 162 9.394767 CTACTGTCTGCTATAGATCTCACATAT 57.605 37.037 3.21 0.00 37.83 1.78
132 213 2.464865 GAGTGTATACCTCGCTTGCTG 58.535 52.381 0.00 0.00 0.00 4.41
352 440 5.559148 AAGGTGAAAGCATCCCTCTATAG 57.441 43.478 0.00 0.00 36.26 1.31
466 578 3.067180 ACACACAAGCACTGAAATCCTTG 59.933 43.478 0.00 0.00 40.26 3.61
568 1772 5.915196 GTCTTGTTCAAATTTGTACTGCTCC 59.085 40.000 23.18 8.60 30.87 4.70
593 1797 2.538512 TCCATCGGATGAGCAATGAG 57.461 50.000 19.30 0.25 0.00 2.90
663 2057 3.077359 CTGGTCAAGGGAATGTGAAGTC 58.923 50.000 0.00 0.00 0.00 3.01
810 2262 0.538287 GAATGGCTGGGTAGATGGGC 60.538 60.000 0.00 0.00 0.00 5.36
826 2279 4.083862 GCCGGGCGAGGAACTTCT 62.084 66.667 1.81 0.00 41.55 2.85
832 2292 1.149148 GGCGAGGAACTTCTGTGAAC 58.851 55.000 0.00 0.00 41.55 3.18
1096 8460 2.726351 CCCTGTCTCGCCTTCCTCC 61.726 68.421 0.00 0.00 0.00 4.30
1308 8701 2.414559 CCAACTGTTCGATGCATTGTCC 60.415 50.000 13.73 6.29 0.00 4.02
1377 8770 1.744872 TAGGGGAGGGGTTTTCGAAA 58.255 50.000 6.47 6.47 0.00 3.46
1449 8842 7.883391 TTGTTTGTTGTTAGGTTCTGGATTA 57.117 32.000 0.00 0.00 0.00 1.75
1565 8994 3.131046 GGTTTGGGCATCTTTGTCTATGG 59.869 47.826 0.00 0.00 0.00 2.74
1710 12007 7.372451 TGGTACTGCAAATAACATGTTCTAC 57.628 36.000 15.85 2.37 0.00 2.59
1711 12008 6.373216 TGGTACTGCAAATAACATGTTCTACC 59.627 38.462 15.85 8.42 0.00 3.18
1712 12009 6.373216 GGTACTGCAAATAACATGTTCTACCA 59.627 38.462 15.85 6.54 0.00 3.25
1713 12010 7.067008 GGTACTGCAAATAACATGTTCTACCAT 59.933 37.037 15.85 0.00 0.00 3.55
1714 12011 7.466746 ACTGCAAATAACATGTTCTACCATT 57.533 32.000 15.85 6.03 0.00 3.16
1715 12012 7.538575 ACTGCAAATAACATGTTCTACCATTC 58.461 34.615 15.85 0.00 0.00 2.67
1716 12013 7.176515 ACTGCAAATAACATGTTCTACCATTCA 59.823 33.333 15.85 3.76 0.00 2.57
1717 12014 7.890515 TGCAAATAACATGTTCTACCATTCAA 58.109 30.769 15.85 0.00 0.00 2.69
1807 12104 1.876156 CAACAAACAGTGAGGAGCTCC 59.124 52.381 26.22 26.22 0.00 4.70
1812 12109 3.999285 AGTGAGGAGCTCCCCGGT 61.999 66.667 29.54 10.96 36.42 5.28
1829 12126 4.244862 CCCGGTTCCATTTCATTGAAAAG 58.755 43.478 15.34 11.09 35.11 2.27
1951 12249 3.357079 CTGTCCAACGCACAGCCC 61.357 66.667 0.00 0.00 35.15 5.19
1971 12269 4.240888 CCCTGATCTGACTATTACATGCG 58.759 47.826 0.38 0.00 0.00 4.73
2027 12325 2.202236 GATCAGTCAAGCCCCTGCCA 62.202 60.000 0.00 0.00 38.69 4.92
2069 12370 2.354259 CAGCATCAAGGGTTGAGACTC 58.646 52.381 0.00 0.00 43.98 3.36
2108 12409 5.213891 TGCTTGAGTCATCTGTTTGAGTA 57.786 39.130 0.00 0.00 29.40 2.59
2123 12424 5.305902 TGTTTGAGTACCAGTAGAACATGGA 59.694 40.000 0.00 0.00 39.02 3.41
2293 12728 5.111293 CAAAACAGGAGTCAGCAACAAAAT 58.889 37.500 0.00 0.00 0.00 1.82
2294 12729 4.574599 AACAGGAGTCAGCAACAAAATC 57.425 40.909 0.00 0.00 0.00 2.17
2311 12746 4.766404 AAATCGTAAAGAGGCTTTGGTG 57.234 40.909 2.85 0.00 0.00 4.17
2472 12908 4.288626 ACAGGTATGTTCCAGCTTAAGGAA 59.711 41.667 4.29 0.00 42.62 3.36
2479 12933 5.690865 TGTTCCAGCTTAAGGAAGAAGAAA 58.309 37.500 4.30 0.00 45.27 2.52
2810 13741 7.607991 AGTGCTAATGTGTAGCTTAGTTGATTT 59.392 33.333 6.88 0.00 40.95 2.17
2851 13783 2.642427 ACAACTGAACACACAGCATGA 58.358 42.857 0.00 0.00 39.69 3.07
2882 13814 8.671921 GGAATAACATGATGCATCAGTTATAGG 58.328 37.037 34.49 22.59 40.64 2.57
2892 13824 4.450419 GCATCAGTTATAGGCTACTTGCTG 59.550 45.833 0.00 3.80 42.39 4.41
2911 13843 3.181491 GCTGTTTTACTTCCTGCACAACA 60.181 43.478 0.00 0.00 0.00 3.33
3067 14175 2.349886 GCACTGCAAGAAACCTCTATCG 59.650 50.000 0.00 0.00 37.43 2.92
3072 14180 3.994392 TGCAAGAAACCTCTATCGTGAAC 59.006 43.478 0.00 0.00 0.00 3.18
3325 14826 3.859386 GCATTTTCTTGCTTCCATTACCG 59.141 43.478 0.00 0.00 39.57 4.02
3582 15083 4.336713 GGCCTATTTTCTGTTCTCACATCC 59.663 45.833 0.00 0.00 30.39 3.51
3804 17834 0.668401 CACGTCTCATCTGCAGCACA 60.668 55.000 9.47 0.00 0.00 4.57
3870 17900 1.667212 TGCTGCACGACATCATTCATC 59.333 47.619 0.00 0.00 0.00 2.92
4020 18050 1.549170 AGAACCGTTCCTTATGCTCGT 59.451 47.619 7.68 0.00 0.00 4.18
4028 18058 1.461091 CCTTATGCTCGTCCGCCCTA 61.461 60.000 0.00 0.00 0.00 3.53
4056 18086 8.408043 TCAATTACATCATCTCCAAACTTGTT 57.592 30.769 0.00 0.00 0.00 2.83
4069 18099 4.582656 CCAAACTTGTTGTCCTACCATTGA 59.417 41.667 0.00 0.00 0.00 2.57
4106 18136 7.094377 ACCTTATTGTTGTGTACACCAATGATC 60.094 37.037 27.22 10.81 36.21 2.92
4321 18351 4.575645 GCAGAGCTAGCATTGAGAGAAAAT 59.424 41.667 18.83 0.00 0.00 1.82
4329 18382 6.645790 AGCATTGAGAGAAAATTGACACTT 57.354 33.333 0.00 0.00 0.00 3.16
4346 18399 6.353323 TGACACTTAACCTGTCAAAGATTGA 58.647 36.000 8.25 0.00 43.99 2.57
4450 18503 6.653320 TGAACTTGGTATCCATGTTGTACTTC 59.347 38.462 19.61 8.86 46.89 3.01
4451 18504 5.497474 ACTTGGTATCCATGTTGTACTTCC 58.503 41.667 0.00 0.00 38.49 3.46
4465 18518 9.974980 ATGTTGTACTTCCGAAAATGTTTTAAT 57.025 25.926 0.00 0.00 0.00 1.40
4495 18968 8.575454 GTGCAAATTTAACTTAAATAGCAGACG 58.425 33.333 22.32 0.00 43.52 4.18
4529 19002 7.041916 TGGATGATGAAAAATTTGTTTGACTGC 60.042 33.333 0.00 0.00 0.00 4.40
4538 19011 6.651755 AATTTGTTTGACTGCAAAACTCTG 57.348 33.333 12.41 0.00 44.91 3.35
4604 19078 1.582968 CAAATGGCAACGCAGCTCT 59.417 52.632 0.00 0.00 42.51 4.09
4617 19091 2.286294 CGCAGCTCTATCACACCATTTC 59.714 50.000 0.00 0.00 0.00 2.17
4618 19092 3.273434 GCAGCTCTATCACACCATTTCA 58.727 45.455 0.00 0.00 0.00 2.69
4631 19105 2.639839 ACCATTTCACTGGCTGTAGTCT 59.360 45.455 0.00 0.00 40.15 3.24
4632 19106 3.005554 CCATTTCACTGGCTGTAGTCTG 58.994 50.000 0.00 0.00 0.00 3.51
4642 19116 3.301274 GGCTGTAGTCTGATACTCCCTT 58.699 50.000 0.00 0.00 39.80 3.95
4782 19669 8.780616 ATGAATCCAATGGTATTGATTTGGTA 57.219 30.769 0.00 0.00 39.67 3.25
4880 19767 7.981102 ACAAAGTAAATAAGAACAGAGGGAC 57.019 36.000 0.00 0.00 0.00 4.46
4901 20053 5.463724 GGACTATTATTCTGCCTTGAAGACG 59.536 44.000 0.00 0.00 0.00 4.18
4906 20058 1.229428 TCTGCCTTGAAGACGCAAAG 58.771 50.000 0.00 0.00 30.85 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 138 7.362834 GCATATGTGAGATCTATAGCAGACAGT 60.363 40.741 4.29 0.00 35.62 3.55
61 142 7.118060 AGAGCATATGTGAGATCTATAGCAGA 58.882 38.462 4.29 0.00 37.79 4.26
132 213 1.183549 ACTACACCGATGTGAGTCCC 58.816 55.000 0.00 0.00 45.76 4.46
352 440 2.128771 TAGGAAAGTGGGCTGAATGC 57.871 50.000 0.00 0.00 41.94 3.56
568 1772 0.657840 GCTCATCCGATGGAAAACCG 59.342 55.000 8.54 0.00 34.34 4.44
735 2187 1.069636 GCCAAAACACAGAAGAGAGCG 60.070 52.381 0.00 0.00 0.00 5.03
810 2262 2.125512 CAGAAGTTCCTCGCCCGG 60.126 66.667 0.00 0.00 0.00 5.73
826 2279 0.916086 AATATCCAGGCCCGTTCACA 59.084 50.000 0.00 0.00 0.00 3.58
832 2292 1.956477 CCAGAAAAATATCCAGGCCCG 59.044 52.381 0.00 0.00 0.00 6.13
1262 8626 3.550275 TGCACGAACTATATGCGAGAAAC 59.450 43.478 0.00 0.00 42.44 2.78
1308 8701 1.740296 CTCACGCCAACCCCTAACG 60.740 63.158 0.00 0.00 0.00 3.18
1449 8842 8.358582 AGTGCTCTTTGAAAAATATCATCCTT 57.641 30.769 0.00 0.00 0.00 3.36
1565 8994 4.688021 AGAAAGCTCACAATAGATCCGTC 58.312 43.478 0.00 0.00 0.00 4.79
1599 9047 2.555757 GTGCTCCATGCCATCTAATTCC 59.444 50.000 0.00 0.00 42.00 3.01
1606 9057 1.133790 GTTTCAGTGCTCCATGCCATC 59.866 52.381 0.00 0.00 42.00 3.51
1610 9061 1.503542 CCGTTTCAGTGCTCCATGC 59.496 57.895 0.00 0.00 43.25 4.06
1679 9149 5.593010 TGTTATTTGCAGTACCAAAACACC 58.407 37.500 2.07 0.00 38.12 4.16
1732 12029 4.895668 ACCGGTTTCCTAGAACATGTTA 57.104 40.909 11.95 0.00 0.00 2.41
1735 12032 3.431766 CCCTACCGGTTTCCTAGAACATG 60.432 52.174 15.04 0.00 0.00 3.21
1736 12033 2.770232 CCCTACCGGTTTCCTAGAACAT 59.230 50.000 15.04 0.00 0.00 2.71
1737 12034 2.181975 CCCTACCGGTTTCCTAGAACA 58.818 52.381 15.04 0.00 0.00 3.18
1738 12035 2.182827 ACCCTACCGGTTTCCTAGAAC 58.817 52.381 15.04 0.00 45.36 3.01
1739 12036 2.629017 ACCCTACCGGTTTCCTAGAA 57.371 50.000 15.04 0.00 45.36 2.10
1807 12104 3.951775 TTTCAATGAAATGGAACCGGG 57.048 42.857 6.32 0.00 35.58 5.73
1812 12109 5.550290 GGGCTTCTTTTCAATGAAATGGAA 58.450 37.500 17.73 17.39 33.50 3.53
1951 12249 5.632764 CCTTCGCATGTAATAGTCAGATCAG 59.367 44.000 0.00 0.00 0.00 2.90
1971 12269 2.270352 TGTGGTGTGGATTGTCCTTC 57.730 50.000 0.00 0.00 37.46 3.46
2123 12424 3.325135 CCTAGGTCCTGTGAGAAAACACT 59.675 47.826 0.00 0.00 40.87 3.55
2293 12728 2.367567 ACTCACCAAAGCCTCTTTACGA 59.632 45.455 0.00 0.00 0.00 3.43
2294 12729 2.767505 ACTCACCAAAGCCTCTTTACG 58.232 47.619 0.00 0.00 0.00 3.18
2311 12746 4.570772 TGATGCGCTTGGACTAATAAACTC 59.429 41.667 9.73 0.00 0.00 3.01
2357 12793 2.751259 ACACATTTCTCATGAGCGCATT 59.249 40.909 18.36 0.00 30.68 3.56
2472 12908 3.589988 CACCATAGTCAGCGTTTCTTCT 58.410 45.455 0.00 0.00 0.00 2.85
2479 12933 1.831106 TGAATCCACCATAGTCAGCGT 59.169 47.619 0.00 0.00 0.00 5.07
2540 13012 3.477530 AGAATAAGCCTGGAATAACGGC 58.522 45.455 0.00 0.00 44.09 5.68
2594 13073 9.220767 GTCCCCAATCTAGATAACAATAATGAC 57.779 37.037 5.46 0.92 0.00 3.06
2606 13283 6.831664 AATAACACTGTCCCCAATCTAGAT 57.168 37.500 0.00 0.00 0.00 1.98
2636 13313 7.829211 TCCCCTTTAAGAACAAATCAGACATAG 59.171 37.037 0.00 0.00 0.00 2.23
2810 13741 4.944317 TGTTCACCACAAAACACTGACATA 59.056 37.500 0.00 0.00 30.73 2.29
2851 13783 6.381994 ACTGATGCATCATGTTATTCCCTTTT 59.618 34.615 28.81 1.73 36.02 2.27
2882 13814 4.613850 GCAGGAAGTAAAACAGCAAGTAGC 60.614 45.833 0.00 0.00 46.19 3.58
2892 13824 5.348164 ACATTGTTGTGCAGGAAGTAAAAC 58.652 37.500 0.00 0.00 33.85 2.43
3067 14175 5.161943 AGTGGGTCCTGTTTATAGTTCAC 57.838 43.478 0.00 0.00 0.00 3.18
3072 14180 7.611855 AGAATTCAAAGTGGGTCCTGTTTATAG 59.388 37.037 8.44 0.00 0.00 1.31
3325 14826 4.927978 ATAGTATGTCACAGCAGGACTC 57.072 45.455 4.44 0.00 36.26 3.36
3582 15083 7.494952 TCTGAGATGATTCTTAGCTTTGTCATG 59.505 37.037 0.00 0.00 35.95 3.07
3652 15154 4.142491 CCTCCAGCGCTGTCTTCTATATAG 60.142 50.000 33.75 15.18 0.00 1.31
3783 17813 1.216444 GCTGCAGATGAGACGTGGA 59.784 57.895 20.43 0.00 0.00 4.02
3804 17834 4.836125 ATGTGTCGCATCAGAAAGTTTT 57.164 36.364 0.00 0.00 30.67 2.43
3843 17873 0.790207 ATGTCGTGCAGCAAACTACG 59.210 50.000 0.00 0.00 37.85 3.51
3844 17874 1.798223 TGATGTCGTGCAGCAAACTAC 59.202 47.619 0.00 0.00 40.93 2.73
3845 17875 2.162319 TGATGTCGTGCAGCAAACTA 57.838 45.000 0.00 0.00 40.93 2.24
3846 17876 3.005205 TGATGTCGTGCAGCAAACT 57.995 47.368 0.00 0.00 40.93 2.66
4015 18045 4.273257 GAGCTAGGGCGGACGAGC 62.273 72.222 0.00 0.00 44.37 5.03
4020 18050 1.491668 TGTAATTGAGCTAGGGCGGA 58.508 50.000 0.00 0.00 44.37 5.54
4028 18058 6.421485 AGTTTGGAGATGATGTAATTGAGCT 58.579 36.000 0.00 0.00 0.00 4.09
4056 18086 3.389656 TCAGTGTGTTCAATGGTAGGACA 59.610 43.478 0.00 0.00 39.67 4.02
4069 18099 6.071616 ACACAACAATAAGGTTTCAGTGTGTT 60.072 34.615 0.00 0.00 35.43 3.32
4329 18382 5.222027 TGGTCCATCAATCTTTGACAGGTTA 60.222 40.000 9.20 0.00 43.48 2.85
4346 18399 3.892031 AGGAGGGAATATGATGGTCCAT 58.108 45.455 3.26 3.26 32.70 3.41
4358 18411 4.080526 ACAGCATTTACGTTAGGAGGGAAT 60.081 41.667 0.00 0.00 0.00 3.01
4450 18503 7.588143 TTGCACCATATTAAAACATTTTCGG 57.412 32.000 0.00 0.00 0.00 4.30
4529 19002 8.725148 ACATATGCTTTCTTCTACAGAGTTTTG 58.275 33.333 1.58 0.00 31.12 2.44
4604 19078 3.244875 ACAGCCAGTGAAATGGTGTGATA 60.245 43.478 7.88 0.00 42.75 2.15
4617 19091 3.067461 GGAGTATCAGACTACAGCCAGTG 59.933 52.174 0.00 0.00 39.11 3.66
4618 19092 3.292460 GGAGTATCAGACTACAGCCAGT 58.708 50.000 0.00 0.00 39.11 4.00
4869 19756 5.071115 AGGCAGAATAATAGTCCCTCTGTTC 59.929 44.000 0.00 0.00 36.67 3.18
4873 19760 5.219739 TCAAGGCAGAATAATAGTCCCTCT 58.780 41.667 0.00 0.00 0.00 3.69
4874 19761 5.552870 TCAAGGCAGAATAATAGTCCCTC 57.447 43.478 0.00 0.00 0.00 4.30
4880 19767 4.811024 TGCGTCTTCAAGGCAGAATAATAG 59.189 41.667 0.00 0.00 43.50 1.73
4901 20053 9.231297 TGATGTATTTATTATAGCTCCCTTTGC 57.769 33.333 0.00 0.00 0.00 3.68
5104 20264 0.674581 CTGTCGGGAATCAAGCAGCA 60.675 55.000 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.