Multiple sequence alignment - TraesCS5A01G157700

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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 TraesCS5A01G157700 chr5A 100.000 4204 0 0 1 4204 337940095 337944298 0.000000e+00 7764
1 TraesCS5A01G157700 chr5B 91.519 3679 165 74 226 3823 288179118 288175506 0.000000e+00 4929
2 TraesCS5A01G157700 chr5B 91.456 316 22 4 3827 4140 288175150 288174838 3.000000e-116 429
3 TraesCS5A01G157700 chr5D 89.513 2794 155 60 13 2771 254585489 254588179 0.000000e+00 3410
4 TraesCS5A01G157700 chr5D 95.698 1046 42 3 2779 3823 254588221 254589264 0.000000e+00 1679
5 TraesCS5A01G157700 chr5D 92.950 383 20 6 3827 4203 254589620 254590001 6.140000e-153 551
6 TraesCS5A01G157700 chr4A 78.850 539 89 18 1034 1558 450765569 450765042 1.450000e-89 340
7 TraesCS5A01G157700 chr4A 80.000 210 42 0 2898 3107 450764805 450764596 5.630000e-34 156
8 TraesCS5A01G157700 chr4A 82.090 134 18 2 3489 3616 92744214 92744347 4.440000e-20 110
9 TraesCS5A01G157700 chr4D 78.131 535 91 22 1041 1558 119806273 119805748 2.440000e-82 316
10 TraesCS5A01G157700 chr4D 78.114 297 47 15 3459 3743 371133037 371132747 5.590000e-39 172
11 TraesCS5A01G157700 chr4D 79.524 210 43 0 2898 3107 119805511 119805302 2.620000e-32 150
12 TraesCS5A01G157700 chr4B 77.861 533 97 15 1041 1558 182260977 182260451 1.130000e-80 311
13 TraesCS5A01G157700 chr2B 86.458 96 13 0 1465 1560 560459351 560459256 5.750000e-19 106
14 TraesCS5A01G157700 chr2D 85.417 96 14 0 1465 1560 478119049 478118954 2.670000e-17 100
15 TraesCS5A01G157700 chr2A 85.417 96 14 0 1465 1560 621268652 621268557 2.670000e-17 100


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 TraesCS5A01G157700 chr5A 337940095 337944298 4203 False 7764 7764 100.000000 1 4204 1 chr5A.!!$F1 4203
1 TraesCS5A01G157700 chr5B 288174838 288179118 4280 True 2679 4929 91.487500 226 4140 2 chr5B.!!$R1 3914
2 TraesCS5A01G157700 chr5D 254585489 254590001 4512 False 1880 3410 92.720333 13 4203 3 chr5D.!!$F1 4190
3 TraesCS5A01G157700 chr4A 450764596 450765569 973 True 248 340 79.425000 1034 3107 2 chr4A.!!$R1 2073
4 TraesCS5A01G157700 chr4D 119805302 119806273 971 True 233 316 78.827500 1041 3107 2 chr4D.!!$R2 2066
5 TraesCS5A01G157700 chr4B 182260451 182260977 526 True 311 311 77.861000 1041 1558 1 chr4B.!!$R1 517

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
79 82 0.452987 CCGTCATGGTGAAGCATTGG 59.547 55.0 0.00 0.00 0.0 3.16 F
85 88 0.609957 TGGTGAAGCATTGGGAGCAG 60.610 55.0 0.00 0.00 0.0 4.24 F
426 438 0.827507 TTTTGTGAGGAAGGGCTGCC 60.828 55.0 11.05 11.05 0.0 4.85 F
1581 1650 0.742990 GCGTGCATGCTTACCCACTA 60.743 55.0 23.72 0.00 0.0 2.74 F
1807 1885 1.014352 GGCCGTTAGTGATTTCGCAT 58.986 50.0 0.00 0.00 0.0 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1164 1211 0.176910 CGAGGAGGAAGGAAGGAAGC 59.823 60.0 0.0 0.0 0.00 3.86 R
1165 1212 0.176910 GCGAGGAGGAAGGAAGGAAG 59.823 60.0 0.0 0.0 0.00 3.46 R
1818 1896 0.467844 TCCGGCATGGATTGGAATGG 60.468 55.0 0.0 0.0 43.74 3.16 R
2611 2714 0.445436 CACACGAGCAAATCAGCCTC 59.555 55.0 0.0 0.0 34.23 4.70 R
3685 3823 0.326618 ACTACCCCACTCCATCCCTG 60.327 60.0 0.0 0.0 0.00 4.45 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
42 45 4.634443 ACGCCACATAGATAAAAACCTGAC 59.366 41.667 0.00 0.00 0.00 3.51
58 61 2.271800 CTGACATGGCGACCTAAGAAC 58.728 52.381 0.00 0.00 0.00 3.01
63 66 1.291272 GGCGACCTAAGAACACCGT 59.709 57.895 0.00 0.00 0.00 4.83
79 82 0.452987 CCGTCATGGTGAAGCATTGG 59.547 55.000 0.00 0.00 0.00 3.16
85 88 0.609957 TGGTGAAGCATTGGGAGCAG 60.610 55.000 0.00 0.00 0.00 4.24
93 96 2.157738 GCATTGGGAGCAGCCTTATAG 58.842 52.381 0.00 0.00 36.66 1.31
94 97 2.157738 CATTGGGAGCAGCCTTATAGC 58.842 52.381 0.00 0.00 36.66 2.97
97 100 1.051812 GGGAGCAGCCTTATAGCAGA 58.948 55.000 0.00 0.00 36.66 4.26
108 111 5.366768 AGCCTTATAGCAGAACAACTGGATA 59.633 40.000 0.00 0.00 45.82 2.59
117 120 8.353423 AGCAGAACAACTGGATAAATTGTTAT 57.647 30.769 1.82 0.00 44.45 1.89
121 124 9.661563 AGAACAACTGGATAAATTGTTATACGA 57.338 29.630 1.82 0.00 44.45 3.43
142 145 6.053005 ACGATTTTTGGTTGAGTTAGAGTCA 58.947 36.000 0.00 0.00 0.00 3.41
144 147 7.228706 ACGATTTTTGGTTGAGTTAGAGTCATT 59.771 33.333 0.00 0.00 0.00 2.57
148 151 4.713553 TGGTTGAGTTAGAGTCATTTGCA 58.286 39.130 0.00 0.00 0.00 4.08
151 154 5.334414 GGTTGAGTTAGAGTCATTTGCACAG 60.334 44.000 0.00 0.00 0.00 3.66
157 160 6.939163 AGTTAGAGTCATTTGCACAGATTTCT 59.061 34.615 0.00 0.00 0.00 2.52
189 192 5.471797 TCGTCTAATCCAAACAAAATGCAGA 59.528 36.000 0.00 0.00 0.00 4.26
194 197 6.790285 AATCCAAACAAAATGCAGATTCAC 57.210 33.333 0.00 0.00 0.00 3.18
245 248 9.712305 TTTTGAGAACCAAACAAAATTTACTCA 57.288 25.926 0.00 0.00 43.82 3.41
246 249 8.696410 TTGAGAACCAAACAAAATTTACTCAC 57.304 30.769 0.00 0.00 31.90 3.51
261 264 8.732746 AATTTACTCACTACACAAACACTTCT 57.267 30.769 0.00 0.00 0.00 2.85
264 267 4.081087 ACTCACTACACAAACACTTCTGGT 60.081 41.667 0.00 0.00 0.00 4.00
287 290 3.788227 AGCTCCACCAGTGTTAAATCA 57.212 42.857 0.00 0.00 0.00 2.57
293 296 6.182507 TCCACCAGTGTTAAATCAACTACT 57.817 37.500 0.00 0.00 38.05 2.57
294 297 5.995282 TCCACCAGTGTTAAATCAACTACTG 59.005 40.000 0.00 0.00 41.24 2.74
307 310 5.160607 TCAACTACTGGTGGAAATACAGG 57.839 43.478 0.00 0.00 36.57 4.00
321 324 1.264749 TACAGGTGTAGCCAGGCAGG 61.265 60.000 15.80 0.00 40.61 4.85
341 344 3.199727 AGGGTGAATGGCAGTTTGTTTTT 59.800 39.130 0.00 0.00 0.00 1.94
372 375 3.841643 CGTACACACTTAAATCCTCGGT 58.158 45.455 0.00 0.00 0.00 4.69
425 437 1.039856 TTTTTGTGAGGAAGGGCTGC 58.960 50.000 0.00 0.00 0.00 5.25
426 438 0.827507 TTTTGTGAGGAAGGGCTGCC 60.828 55.000 11.05 11.05 0.00 4.85
427 439 1.719063 TTTGTGAGGAAGGGCTGCCT 61.719 55.000 19.68 0.00 37.18 4.75
428 440 2.045536 GTGAGGAAGGGCTGCCTG 60.046 66.667 19.68 0.00 33.84 4.85
440 452 1.065418 GGCTGCCTGTATACTTGGTGT 60.065 52.381 12.43 0.00 0.00 4.16
441 453 2.280628 GCTGCCTGTATACTTGGTGTC 58.719 52.381 4.17 0.00 0.00 3.67
467 479 5.237236 AGCTTTTGGGTAGCTGTAGTAAA 57.763 39.130 0.00 0.00 46.71 2.01
511 523 2.379005 AGGTGACACGATAGATGAGCA 58.621 47.619 0.00 0.00 41.38 4.26
514 526 4.022762 AGGTGACACGATAGATGAGCATAC 60.023 45.833 0.00 0.00 41.38 2.39
623 635 3.302675 GGTGAACGGACGTTAACTGAAAC 60.303 47.826 20.75 4.33 39.00 2.78
672 697 3.691498 GCACCAATTAACATTACGGAGC 58.309 45.455 0.00 0.00 0.00 4.70
850 887 5.344066 CGTCCACATATATAGCTGTCATCC 58.656 45.833 0.00 0.00 0.00 3.51
852 889 6.406288 CGTCCACATATATAGCTGTCATCCAT 60.406 42.308 0.00 0.00 0.00 3.41
877 914 3.610669 CCCTGATCCTCCTCGCCG 61.611 72.222 0.00 0.00 0.00 6.46
944 990 3.863424 CGCTCTTTAATTTCTCGTGGCTA 59.137 43.478 0.00 0.00 0.00 3.93
1003 1050 1.490574 AGAAGAGAAGGGGTCGATGG 58.509 55.000 0.00 0.00 0.00 3.51
1070 1117 1.939769 GAGGAGGAGTCGGTGCAGAC 61.940 65.000 0.00 0.00 41.23 3.51
1164 1211 2.202636 TGCCATGGTACGTACGCG 60.203 61.111 16.72 3.53 44.93 6.01
1165 1212 3.623330 GCCATGGTACGTACGCGC 61.623 66.667 16.72 13.10 42.83 6.86
1175 1222 1.445582 CGTACGCGCTTCCTTCCTT 60.446 57.895 5.73 0.00 0.00 3.36
1177 1224 1.082679 GTACGCGCTTCCTTCCTTCC 61.083 60.000 5.73 0.00 0.00 3.46
1371 1440 2.386935 GGGGCTCCAGGGCTACATT 61.387 63.158 0.00 0.00 40.65 2.71
1401 1470 2.202362 CTCCTCGTCAGCGACACG 60.202 66.667 8.91 4.50 42.81 4.49
1562 1631 1.748879 CCCCCATGTGCAAGGTACG 60.749 63.158 0.00 0.00 0.00 3.67
1580 1649 2.040544 GCGTGCATGCTTACCCACT 61.041 57.895 23.72 0.00 0.00 4.00
1581 1650 0.742990 GCGTGCATGCTTACCCACTA 60.743 55.000 23.72 0.00 0.00 2.74
1616 1687 2.435805 CCCTCCGAATCATCTTCCAGAA 59.564 50.000 0.00 0.00 0.00 3.02
1621 1692 3.812053 CCGAATCATCTTCCAGAATCCAC 59.188 47.826 0.00 0.00 0.00 4.02
1658 1732 1.224075 CTAGCTACTAGTACGCGGCA 58.776 55.000 12.47 0.00 30.16 5.69
1692 1770 2.022346 CGAGATGCATGCACGCAC 59.978 61.111 25.37 15.37 46.56 5.34
1693 1771 2.022346 GAGATGCATGCACGCACG 59.978 61.111 25.37 0.00 46.56 5.34
1694 1772 4.170062 AGATGCATGCACGCACGC 62.170 61.111 25.37 5.32 46.56 5.34
1807 1885 1.014352 GGCCGTTAGTGATTTCGCAT 58.986 50.000 0.00 0.00 0.00 4.73
1810 1888 3.064271 GGCCGTTAGTGATTTCGCATTTA 59.936 43.478 0.00 0.00 0.00 1.40
1816 1894 7.958567 CCGTTAGTGATTTCGCATTTAGTTTAA 59.041 33.333 0.00 0.00 0.00 1.52
1819 1897 9.997482 TTAGTGATTTCGCATTTAGTTTAATCC 57.003 29.630 0.00 0.00 0.00 3.01
1821 1899 8.686334 AGTGATTTCGCATTTAGTTTAATCCAT 58.314 29.630 0.00 0.00 0.00 3.41
1884 1962 2.438583 CTTCTCGACCGATAACGACAC 58.561 52.381 0.00 0.00 42.66 3.67
1904 1995 9.993454 ACGACACATATTCTAGTAGTAGTATCA 57.007 33.333 4.51 0.00 0.00 2.15
1960 2051 9.927668 CATTAATTTGGACCAATTCAAAGTAGT 57.072 29.630 7.99 0.00 35.71 2.73
1963 2054 6.548441 TTTGGACCAATTCAAAGTAGTACG 57.452 37.500 7.99 0.00 0.00 3.67
1964 2055 5.217978 TGGACCAATTCAAAGTAGTACGT 57.782 39.130 0.00 0.00 0.00 3.57
1965 2056 6.343716 TGGACCAATTCAAAGTAGTACGTA 57.656 37.500 0.00 0.00 0.00 3.57
1966 2057 6.392354 TGGACCAATTCAAAGTAGTACGTAG 58.608 40.000 0.00 0.00 0.00 3.51
1968 2059 7.176515 TGGACCAATTCAAAGTAGTACGTAGTA 59.823 37.037 6.02 6.02 45.11 1.82
1986 2077 5.450412 CGTAGTACATAAAACTAAGGGCGGA 60.450 44.000 0.38 0.00 31.48 5.54
1988 2079 3.994931 ACATAAAACTAAGGGCGGAGT 57.005 42.857 0.00 0.00 0.00 3.85
1989 2080 5.658190 AGTACATAAAACTAAGGGCGGAGTA 59.342 40.000 0.00 0.00 0.00 2.59
1990 2081 5.625568 ACATAAAACTAAGGGCGGAGTAT 57.374 39.130 0.00 0.00 0.00 2.12
1991 2082 5.997843 ACATAAAACTAAGGGCGGAGTATT 58.002 37.500 0.00 0.00 0.00 1.89
1992 2083 6.420638 ACATAAAACTAAGGGCGGAGTATTT 58.579 36.000 0.00 0.00 0.00 1.40
1993 2084 6.888088 ACATAAAACTAAGGGCGGAGTATTTT 59.112 34.615 0.00 0.00 0.00 1.82
1994 2085 7.395206 ACATAAAACTAAGGGCGGAGTATTTTT 59.605 33.333 0.00 0.00 0.00 1.94
2241 2332 1.540363 GCCTCAACCTCGAGAACAACA 60.540 52.381 15.71 0.00 34.79 3.33
2259 2350 5.238583 ACAACATACTCTCAAAGGTGCTAC 58.761 41.667 0.00 0.00 0.00 3.58
2363 2454 9.823647 TCACTCATTTCAATCTTTATCTAGTCC 57.176 33.333 0.00 0.00 0.00 3.85
2456 2550 4.698201 TTCCCATTGTCTCCGCATATAA 57.302 40.909 0.00 0.00 0.00 0.98
2467 2561 6.156083 TGTCTCCGCATATAATATTCCATGGA 59.844 38.462 11.44 11.44 0.00 3.41
2504 2607 2.659016 CACGCTTGCAGAGGGAGA 59.341 61.111 16.04 0.00 40.59 3.71
2516 2619 4.100653 TGCAGAGGGAGAGAGATATGTTTG 59.899 45.833 0.00 0.00 0.00 2.93
2566 2669 3.637911 TCTTAATGGTAATGTGCCCGT 57.362 42.857 0.00 0.00 0.00 5.28
2567 2670 3.275143 TCTTAATGGTAATGTGCCCGTG 58.725 45.455 0.00 0.00 0.00 4.94
2605 2708 8.604035 CGATCGATCTCTTTTTCTCCAATTAAA 58.396 33.333 22.43 0.00 0.00 1.52
2606 2709 9.709600 GATCGATCTCTTTTTCTCCAATTAAAC 57.290 33.333 18.29 0.00 0.00 2.01
2611 2714 8.396272 TCTCTTTTTCTCCAATTAAACTCAGG 57.604 34.615 0.00 0.00 0.00 3.86
2615 2718 4.222124 TCTCCAATTAAACTCAGGAGGC 57.778 45.455 6.91 0.00 44.65 4.70
2627 2730 0.392193 CAGGAGGCTGATTTGCTCGT 60.392 55.000 0.00 0.00 0.00 4.18
2724 2827 9.653287 CTGTTTAGATCACACTCAAGGTATTTA 57.347 33.333 0.00 0.00 0.00 1.40
2760 2863 4.438744 CCCGTTCAATGAATTCCAGTTAGC 60.439 45.833 2.27 0.00 0.00 3.09
2764 2867 3.696051 TCAATGAATTCCAGTTAGCAGCC 59.304 43.478 2.27 0.00 0.00 4.85
2771 2874 1.483827 TCCAGTTAGCAGCCTGATGAG 59.516 52.381 0.00 0.00 0.00 2.90
2773 2876 2.432146 CCAGTTAGCAGCCTGATGAGTA 59.568 50.000 0.00 0.00 0.00 2.59
2774 2877 3.070734 CCAGTTAGCAGCCTGATGAGTAT 59.929 47.826 0.00 0.00 0.00 2.12
2775 2878 4.281941 CCAGTTAGCAGCCTGATGAGTATA 59.718 45.833 0.00 0.00 0.00 1.47
2777 2880 6.153510 CCAGTTAGCAGCCTGATGAGTATATA 59.846 42.308 0.00 0.00 0.00 0.86
2781 2918 6.864151 AGCAGCCTGATGAGTATATATCAA 57.136 37.500 0.00 0.00 33.30 2.57
2807 2944 4.065789 ACAACGACTTTTCCCTCATCTTC 58.934 43.478 0.00 0.00 0.00 2.87
2809 2946 2.271800 CGACTTTTCCCTCATCTTCCG 58.728 52.381 0.00 0.00 0.00 4.30
2918 3055 1.890510 GGTGTCGTTGCCGTTCCTT 60.891 57.895 0.00 0.00 35.01 3.36
2966 3103 3.823330 GACCCGTCGGTGAGCGAT 61.823 66.667 10.76 0.00 44.88 4.58
3011 3148 2.487986 CCAGGACAAGAAGCTCAACCTT 60.488 50.000 0.00 0.00 0.00 3.50
3179 3316 1.166531 AACAGAAGGCCAAGCACGAC 61.167 55.000 5.01 0.00 0.00 4.34
3268 3405 2.846206 ACAGCTGGGACTTGGAATCATA 59.154 45.455 19.93 0.00 0.00 2.15
3270 3407 4.070716 CAGCTGGGACTTGGAATCATATC 58.929 47.826 5.57 0.00 0.00 1.63
3273 3411 4.202398 GCTGGGACTTGGAATCATATCAGA 60.202 45.833 0.00 0.00 0.00 3.27
3306 3444 6.242396 TGGCTACAAGTGTGGTGTATTAATT 58.758 36.000 0.00 0.00 31.27 1.40
3351 3489 5.406780 AGCTAGTTCGTCAATTTCTGTCTTG 59.593 40.000 0.00 0.00 0.00 3.02
3425 3563 6.824305 AGCAGTGCTATTTCAGTTTTACAT 57.176 33.333 18.11 0.00 36.99 2.29
3427 3565 8.335532 AGCAGTGCTATTTCAGTTTTACATAA 57.664 30.769 18.11 0.00 36.99 1.90
3428 3566 8.960591 AGCAGTGCTATTTCAGTTTTACATAAT 58.039 29.630 18.11 0.00 36.99 1.28
3470 3608 1.376609 CTGACTTGCATAACGCCCCC 61.377 60.000 0.00 0.00 41.33 5.40
3485 3623 1.594293 CCCCGCGTTGCTATCGATT 60.594 57.895 1.71 0.00 0.00 3.34
3499 3637 8.526681 GTTGCTATCGATTCACAAAAATGATTC 58.473 33.333 1.71 0.00 0.00 2.52
3606 3744 1.393196 TGTGTAATTGCGTCAGCGATG 59.607 47.619 0.00 0.00 46.35 3.84
3681 3819 5.033589 AGCAGTTTCAAGATAGATGAGGG 57.966 43.478 0.00 0.00 0.00 4.30
3685 3823 4.410555 AGTTTCAAGATAGATGAGGGGGAC 59.589 45.833 0.00 0.00 0.00 4.46
3686 3824 3.706389 TCAAGATAGATGAGGGGGACA 57.294 47.619 0.00 0.00 0.00 4.02
3744 3883 7.778382 ACCACCAACTCCAATTTATAAGATACC 59.222 37.037 0.00 0.00 0.00 2.73
3812 3951 3.607741 CAGTCATGGATCTGAGCACTTT 58.392 45.455 0.00 0.00 34.02 2.66
3911 4402 5.640732 TCAGTGTTGTCTTTCTTTTTCTGC 58.359 37.500 0.00 0.00 0.00 4.26
3921 4412 9.651913 TGTCTTTCTTTTTCTGCTTGTTATTTT 57.348 25.926 0.00 0.00 0.00 1.82
4100 4592 9.982291 AACAATGAATATATTTACACACACGTC 57.018 29.630 0.00 0.00 0.00 4.34
4144 4637 9.702494 TGTCATGACATTTTTAAAATACATGCA 57.298 25.926 24.56 23.87 36.21 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 5.007682 AGGTTTTTATCTATGTGGCGTGTT 58.992 37.500 0.00 0.00 0.00 3.32
21 22 6.460123 CCATGTCAGGTTTTTATCTATGTGGC 60.460 42.308 0.00 0.00 0.00 5.01
30 31 2.752903 GGTCGCCATGTCAGGTTTTTAT 59.247 45.455 0.00 0.00 0.00 1.40
35 36 0.981183 TTAGGTCGCCATGTCAGGTT 59.019 50.000 0.00 0.00 0.00 3.50
37 38 0.824109 TCTTAGGTCGCCATGTCAGG 59.176 55.000 0.00 0.00 0.00 3.86
42 45 1.369625 GGTGTTCTTAGGTCGCCATG 58.630 55.000 0.00 0.00 0.00 3.66
63 66 1.956636 GCTCCCAATGCTTCACCATGA 60.957 52.381 0.00 0.00 0.00 3.07
71 74 0.332632 TAAGGCTGCTCCCAATGCTT 59.667 50.000 0.00 0.00 34.51 3.91
79 82 2.158900 TGTTCTGCTATAAGGCTGCTCC 60.159 50.000 0.00 0.00 0.00 4.70
85 88 3.873910 TCCAGTTGTTCTGCTATAAGGC 58.126 45.455 0.00 0.00 42.38 4.35
93 96 9.503427 GTATAACAATTTATCCAGTTGTTCTGC 57.497 33.333 6.04 0.00 42.97 4.26
94 97 9.702726 CGTATAACAATTTATCCAGTTGTTCTG 57.297 33.333 6.04 0.00 42.97 3.02
108 111 9.974980 ACTCAACCAAAAATCGTATAACAATTT 57.025 25.926 0.00 0.00 0.00 1.82
117 120 7.211573 TGACTCTAACTCAACCAAAAATCGTA 58.788 34.615 0.00 0.00 0.00 3.43
121 124 7.653311 GCAAATGACTCTAACTCAACCAAAAAT 59.347 33.333 0.00 0.00 0.00 1.82
151 154 5.520649 GGATTAGACGAGTTCCACAGAAATC 59.479 44.000 0.00 0.00 42.35 2.17
157 160 4.202274 TGTTTGGATTAGACGAGTTCCACA 60.202 41.667 0.00 0.00 37.97 4.17
158 161 4.312443 TGTTTGGATTAGACGAGTTCCAC 58.688 43.478 0.00 0.00 37.97 4.02
163 166 5.240623 TGCATTTTGTTTGGATTAGACGAGT 59.759 36.000 0.00 0.00 0.00 4.18
169 172 7.201376 CGTGAATCTGCATTTTGTTTGGATTAG 60.201 37.037 0.00 0.00 0.00 1.73
189 192 6.660887 AAGAAAAATGTTTGCAACGTGAAT 57.339 29.167 0.00 0.00 0.00 2.57
194 197 8.433585 AAAGAAAAAGAAAAATGTTTGCAACG 57.566 26.923 0.00 0.00 0.00 4.10
219 222 9.712305 TGAGTAAATTTTGTTTGGTTCTCAAAA 57.288 25.926 0.00 0.00 45.74 2.44
220 223 9.145865 GTGAGTAAATTTTGTTTGGTTCTCAAA 57.854 29.630 0.00 0.00 42.50 2.69
221 224 8.527810 AGTGAGTAAATTTTGTTTGGTTCTCAA 58.472 29.630 0.00 0.00 31.64 3.02
222 225 8.062065 AGTGAGTAAATTTTGTTTGGTTCTCA 57.938 30.769 0.00 0.00 0.00 3.27
223 226 9.447040 GTAGTGAGTAAATTTTGTTTGGTTCTC 57.553 33.333 0.00 0.00 0.00 2.87
224 227 8.962679 TGTAGTGAGTAAATTTTGTTTGGTTCT 58.037 29.630 0.00 0.00 0.00 3.01
225 228 9.016623 GTGTAGTGAGTAAATTTTGTTTGGTTC 57.983 33.333 0.00 0.00 0.00 3.62
226 229 8.524487 TGTGTAGTGAGTAAATTTTGTTTGGTT 58.476 29.630 0.00 0.00 0.00 3.67
227 230 8.057536 TGTGTAGTGAGTAAATTTTGTTTGGT 57.942 30.769 0.00 0.00 0.00 3.67
228 231 8.918961 TTGTGTAGTGAGTAAATTTTGTTTGG 57.081 30.769 0.00 0.00 0.00 3.28
242 245 4.442706 ACCAGAAGTGTTTGTGTAGTGAG 58.557 43.478 0.00 0.00 0.00 3.51
243 246 4.481368 ACCAGAAGTGTTTGTGTAGTGA 57.519 40.909 0.00 0.00 0.00 3.41
244 247 6.671614 TTAACCAGAAGTGTTTGTGTAGTG 57.328 37.500 0.00 0.00 0.00 2.74
245 248 5.296035 GCTTAACCAGAAGTGTTTGTGTAGT 59.704 40.000 0.00 0.00 0.00 2.73
246 249 5.527582 AGCTTAACCAGAAGTGTTTGTGTAG 59.472 40.000 0.00 0.00 0.00 2.74
261 264 1.136828 ACACTGGTGGAGCTTAACCA 58.863 50.000 17.70 17.70 44.20 3.67
264 267 5.626142 TGATTTAACACTGGTGGAGCTTAA 58.374 37.500 5.70 0.00 34.19 1.85
278 281 9.005777 GTATTTCCACCAGTAGTTGATTTAACA 57.994 33.333 0.00 0.00 41.88 2.41
287 290 4.349930 ACACCTGTATTTCCACCAGTAGTT 59.650 41.667 0.00 0.00 0.00 2.24
293 296 2.026636 GGCTACACCTGTATTTCCACCA 60.027 50.000 0.00 0.00 34.51 4.17
294 297 2.026636 TGGCTACACCTGTATTTCCACC 60.027 50.000 0.00 0.00 40.22 4.61
307 310 2.045926 CACCCTGCCTGGCTACAC 60.046 66.667 21.03 0.00 0.00 2.90
321 324 3.559655 GGAAAAACAAACTGCCATTCACC 59.440 43.478 0.00 0.00 0.00 4.02
425 437 5.918608 AGCTAATGACACCAAGTATACAGG 58.081 41.667 5.50 9.09 0.00 4.00
426 438 7.849804 AAAGCTAATGACACCAAGTATACAG 57.150 36.000 5.50 0.00 0.00 2.74
427 439 7.120579 CCAAAAGCTAATGACACCAAGTATACA 59.879 37.037 5.50 0.00 0.00 2.29
428 440 7.415206 CCCAAAAGCTAATGACACCAAGTATAC 60.415 40.741 0.00 0.00 0.00 1.47
511 523 2.350484 CGTCTCACATATGTCGCCGTAT 60.350 50.000 5.07 0.00 0.00 3.06
514 526 1.540607 GCGTCTCACATATGTCGCCG 61.541 60.000 22.30 15.37 36.42 6.46
672 697 9.234384 GCTAAATCTTGAATCAATCAATCACTG 57.766 33.333 0.00 0.00 46.62 3.66
850 887 3.958860 GATCAGGGCCGGGGGATG 61.959 72.222 2.18 0.00 0.00 3.51
889 926 0.879090 AATTTTTGCGAGACGGGGAC 59.121 50.000 0.00 0.00 0.00 4.46
890 927 1.161843 GAATTTTTGCGAGACGGGGA 58.838 50.000 0.00 0.00 0.00 4.81
891 928 0.878416 TGAATTTTTGCGAGACGGGG 59.122 50.000 0.00 0.00 0.00 5.73
944 990 2.046507 CGCAGGAAGGAAGCAGCT 60.047 61.111 0.00 0.00 0.00 4.24
1023 1070 4.758251 CTGCCATCGTCCGCCACA 62.758 66.667 0.00 0.00 0.00 4.17
1122 1169 1.404843 AGACGAGGGCCTTGACTATC 58.595 55.000 27.80 13.91 0.00 2.08
1164 1211 0.176910 CGAGGAGGAAGGAAGGAAGC 59.823 60.000 0.00 0.00 0.00 3.86
1165 1212 0.176910 GCGAGGAGGAAGGAAGGAAG 59.823 60.000 0.00 0.00 0.00 3.46
1175 1222 1.152735 ATTAGAGCGGCGAGGAGGA 60.153 57.895 12.98 0.00 0.00 3.71
1177 1224 1.006805 CCATTAGAGCGGCGAGGAG 60.007 63.158 12.98 0.00 0.00 3.69
1371 1440 0.614979 CGAGGAGGTCAAAGGAGGGA 60.615 60.000 0.00 0.00 0.00 4.20
1380 1449 2.033602 TCGCTGACGAGGAGGTCA 59.966 61.111 0.00 0.00 45.12 4.02
1401 1470 3.119096 GCGGTGAAGAAGGCGTCC 61.119 66.667 0.00 0.00 0.00 4.79
1434 1503 4.717313 GGGAGGTCCGTGTTGGCC 62.717 72.222 0.00 0.00 37.80 5.36
1562 1631 0.742990 TAGTGGGTAAGCATGCACGC 60.743 55.000 21.98 18.28 0.00 5.34
1616 1687 2.561478 AAAGTTGCGGTAGTGTGGAT 57.439 45.000 0.00 0.00 0.00 3.41
1621 1692 3.858238 GCTAGTCTAAAGTTGCGGTAGTG 59.142 47.826 0.00 0.00 0.00 2.74
1658 1732 0.518636 TCGTTTCCGTCTCGATCGTT 59.481 50.000 15.94 0.00 35.01 3.85
1692 1770 2.321060 GGATTGATCGTGCGTGCG 59.679 61.111 0.00 0.00 0.00 5.34
1693 1771 2.321060 CGGATTGATCGTGCGTGC 59.679 61.111 4.10 0.00 0.00 5.34
1694 1772 3.005898 CCGGATTGATCGTGCGTG 58.994 61.111 0.00 0.43 0.00 5.34
1695 1773 2.890474 GCCGGATTGATCGTGCGT 60.890 61.111 5.05 0.00 0.00 5.24
1696 1774 3.640000 GGCCGGATTGATCGTGCG 61.640 66.667 5.05 5.10 0.00 5.34
1697 1775 3.640000 CGGCCGGATTGATCGTGC 61.640 66.667 20.10 0.00 0.00 5.34
1698 1776 3.640000 GCGGCCGGATTGATCGTG 61.640 66.667 29.38 0.00 0.00 4.35
1807 1885 8.203485 GCATGGATTGGAATGGATTAAACTAAA 58.797 33.333 0.00 0.00 0.00 1.85
1810 1888 5.070847 GGCATGGATTGGAATGGATTAAACT 59.929 40.000 0.00 0.00 0.00 2.66
1816 1894 1.624336 CGGCATGGATTGGAATGGAT 58.376 50.000 0.00 0.00 0.00 3.41
1818 1896 0.467844 TCCGGCATGGATTGGAATGG 60.468 55.000 0.00 0.00 43.74 3.16
1819 1897 3.114527 TCCGGCATGGATTGGAATG 57.885 52.632 0.00 0.00 43.74 2.67
1871 1949 6.630444 ACTAGAATATGTGTCGTTATCGGT 57.370 37.500 0.00 0.00 37.69 4.69
1904 1995 9.241317 GCAAATATTCATCGATCAACAAAGAAT 57.759 29.630 0.00 2.55 0.00 2.40
1905 1996 8.461222 AGCAAATATTCATCGATCAACAAAGAA 58.539 29.630 0.00 0.00 0.00 2.52
1959 2050 6.414987 CGCCCTTAGTTTTATGTACTACGTAC 59.585 42.308 0.00 0.00 39.24 3.67
1960 2051 6.459573 CCGCCCTTAGTTTTATGTACTACGTA 60.460 42.308 0.00 0.00 0.00 3.57
1961 2052 5.343249 CGCCCTTAGTTTTATGTACTACGT 58.657 41.667 0.00 0.00 0.00 3.57
1962 2053 4.741676 CCGCCCTTAGTTTTATGTACTACG 59.258 45.833 0.00 0.00 0.00 3.51
1963 2054 5.906073 TCCGCCCTTAGTTTTATGTACTAC 58.094 41.667 0.00 0.00 0.00 2.73
1964 2055 5.658190 ACTCCGCCCTTAGTTTTATGTACTA 59.342 40.000 0.00 0.00 0.00 1.82
1965 2056 4.468868 ACTCCGCCCTTAGTTTTATGTACT 59.531 41.667 0.00 0.00 0.00 2.73
1966 2057 4.763073 ACTCCGCCCTTAGTTTTATGTAC 58.237 43.478 0.00 0.00 0.00 2.90
1967 2058 6.736110 ATACTCCGCCCTTAGTTTTATGTA 57.264 37.500 0.00 0.00 0.00 2.29
1968 2059 3.994931 ACTCCGCCCTTAGTTTTATGT 57.005 42.857 0.00 0.00 0.00 2.29
1969 2060 6.937436 AAATACTCCGCCCTTAGTTTTATG 57.063 37.500 0.00 0.00 0.00 1.90
1970 2061 7.949690 AAAAATACTCCGCCCTTAGTTTTAT 57.050 32.000 0.00 0.00 0.00 1.40
1992 2083 8.902806 AGCGATCTGAAATATAATGACCAAAAA 58.097 29.630 0.00 0.00 0.00 1.94
1993 2084 8.344831 CAGCGATCTGAAATATAATGACCAAAA 58.655 33.333 0.00 0.00 42.95 2.44
1994 2085 7.714813 TCAGCGATCTGAAATATAATGACCAAA 59.285 33.333 0.00 0.00 45.69 3.28
1995 2086 7.216494 TCAGCGATCTGAAATATAATGACCAA 58.784 34.615 0.00 0.00 45.69 3.67
1996 2087 6.758254 TCAGCGATCTGAAATATAATGACCA 58.242 36.000 0.00 0.00 45.69 4.02
2387 2478 6.006449 GTGCTCCCTCCATTCACAAATATAT 58.994 40.000 0.00 0.00 0.00 0.86
2440 2534 7.500227 CCATGGAATATTATATGCGGAGACAAT 59.500 37.037 5.56 0.00 0.00 2.71
2467 2561 6.787225 GCGTGCTAGCTAGTTGATATATACT 58.213 40.000 21.62 0.00 0.00 2.12
2539 2642 8.956426 CGGGCACATTACCATTAAGAAATATAT 58.044 33.333 0.00 0.00 0.00 0.86
2543 2646 4.953579 ACGGGCACATTACCATTAAGAAAT 59.046 37.500 0.00 0.00 0.00 2.17
2566 2669 2.000429 TCGATCGAGACGTGTAGACA 58.000 50.000 15.15 0.00 0.00 3.41
2567 2670 2.796031 AGATCGATCGAGACGTGTAGAC 59.204 50.000 23.84 4.67 0.00 2.59
2575 2678 4.973663 GGAGAAAAAGAGATCGATCGAGAC 59.026 45.833 23.84 18.54 0.00 3.36
2580 2683 9.709600 GTTTAATTGGAGAAAAAGAGATCGATC 57.290 33.333 17.91 17.91 0.00 3.69
2610 2713 0.674895 ACACGAGCAAATCAGCCTCC 60.675 55.000 0.00 0.00 34.23 4.30
2611 2714 0.445436 CACACGAGCAAATCAGCCTC 59.555 55.000 0.00 0.00 34.23 4.70
2615 2718 1.125021 GACGTCACACGAGCAAATCAG 59.875 52.381 11.55 0.00 46.05 2.90
2627 2730 1.678598 AACCGAACAGGGACGTCACA 61.679 55.000 22.01 0.00 46.96 3.58
2724 2827 2.227089 GAACGGGCCACTCACGAGAT 62.227 60.000 4.39 0.00 0.00 2.75
2774 2877 9.675464 AGGGAAAAGTCGTTGTTATTTGATATA 57.325 29.630 0.00 0.00 0.00 0.86
2775 2878 8.575649 AGGGAAAAGTCGTTGTTATTTGATAT 57.424 30.769 0.00 0.00 0.00 1.63
2777 2880 6.488683 TGAGGGAAAAGTCGTTGTTATTTGAT 59.511 34.615 0.00 0.00 0.00 2.57
2781 2918 6.238648 AGATGAGGGAAAAGTCGTTGTTATT 58.761 36.000 0.00 0.00 0.00 1.40
2797 2934 9.226606 GTATATATCTATCTCGGAAGATGAGGG 57.773 40.741 1.78 0.00 42.36 4.30
2918 3055 1.430632 GTCGCCTCCGTGAACGATA 59.569 57.895 4.03 0.00 43.02 2.92
2966 3103 2.124403 GCCGACCGGTAGAGGAGA 60.124 66.667 22.83 0.00 37.65 3.71
3011 3148 3.652013 TGCCACATGCCCGGGTAA 61.652 61.111 24.63 11.92 40.16 2.85
3053 3190 2.631160 AGACGGTGTGGATGTTTTCA 57.369 45.000 0.00 0.00 0.00 2.69
3179 3316 1.460743 TGCTTGTCGAAATTCTGCTCG 59.539 47.619 0.00 0.00 36.39 5.03
3268 3405 3.041211 TGTAGCCAGCCAGTTATCTGAT 58.959 45.455 2.20 0.00 43.76 2.90
3270 3407 2.988010 TGTAGCCAGCCAGTTATCTG 57.012 50.000 0.00 0.00 41.01 2.90
3273 3411 2.305927 ACACTTGTAGCCAGCCAGTTAT 59.694 45.455 0.00 0.00 0.00 1.89
3306 3444 9.967346 CTAGCTAGCAAGTTAGTACAATAATGA 57.033 33.333 18.83 0.00 33.21 2.57
3470 3608 0.920664 TGTGAATCGATAGCAACGCG 59.079 50.000 3.53 3.53 0.00 6.01
3485 3623 8.637099 TCCAATACAACTGAATCATTTTTGTGA 58.363 29.630 12.49 2.66 32.73 3.58
3606 3744 6.645790 ATCATATCTTTCATTGGTGCTTCC 57.354 37.500 0.00 0.00 0.00 3.46
3642 3780 6.420913 AACTGCTAGACTCCTTTAGTTTGA 57.579 37.500 0.00 0.00 39.07 2.69
3660 3798 4.133078 CCCCTCATCTATCTTGAAACTGC 58.867 47.826 0.00 0.00 0.00 4.40
3681 3819 2.378634 CCCACTCCATCCCTGTCCC 61.379 68.421 0.00 0.00 0.00 4.46
3685 3823 0.326618 ACTACCCCACTCCATCCCTG 60.327 60.000 0.00 0.00 0.00 4.45
3686 3824 1.326055 TACTACCCCACTCCATCCCT 58.674 55.000 0.00 0.00 0.00 4.20
3744 3883 8.997323 CCTTTGCCTTTGATTATCTCTACTATG 58.003 37.037 0.00 0.00 0.00 2.23
3819 3958 3.406764 AGAGAGAAAACTGCGCAGAAAT 58.593 40.909 42.03 26.00 0.00 2.17
3823 3962 2.805099 AGAAAGAGAGAAAACTGCGCAG 59.195 45.455 34.89 34.89 0.00 5.18
3824 3963 2.838736 AGAAAGAGAGAAAACTGCGCA 58.161 42.857 10.98 10.98 0.00 6.09
3825 3964 3.887339 AAGAAAGAGAGAAAACTGCGC 57.113 42.857 0.00 0.00 0.00 6.09
3852 4343 7.760340 ACCGATGAAAAATAGTAGAGACAACTC 59.240 37.037 0.00 0.00 42.90 3.01


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

AutoCloner maintained by Alex Coulton.