Multiple sequence alignment - TraesCS1D01G339600

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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 TraesCS1D01G339600 chr1D 100.000 3867 0 0 1 3867 429598432 429602298 0.000000e+00 7142.0
1 TraesCS1D01G339600 chr1D 94.118 102 6 0 2029 2130 425476829 425476930 5.170000e-34 156.0
2 TraesCS1D01G339600 chr1B 90.426 1410 64 29 741 2129 580622205 580623564 0.000000e+00 1790.0
3 TraesCS1D01G339600 chr1B 87.791 1245 95 30 2238 3462 580623876 580625083 0.000000e+00 1404.0
4 TraesCS1D01G339600 chr1B 86.647 674 26 18 1 659 580621230 580621854 0.000000e+00 688.0
5 TraesCS1D01G339600 chr1B 92.822 404 27 1 3464 3867 580625245 580625646 5.570000e-163 584.0
6 TraesCS1D01G339600 chr1A 93.601 797 26 12 759 1545 527101075 527101856 0.000000e+00 1166.0
7 TraesCS1D01G339600 chr1A 92.547 644 25 6 98 738 527100232 527100855 0.000000e+00 902.0
8 TraesCS1D01G339600 chr1A 91.390 662 35 7 2444 3101 527103041 527103684 0.000000e+00 887.0
9 TraesCS1D01G339600 chr1A 91.773 547 31 8 1593 2130 527101857 527102398 0.000000e+00 749.0
10 TraesCS1D01G339600 chr1A 84.153 366 47 4 3502 3867 527104302 527104656 1.030000e-90 344.0
11 TraesCS1D01G339600 chr1A 96.512 172 6 0 2238 2409 527102697 527102868 6.320000e-73 285.0
12 TraesCS1D01G339600 chr1A 81.053 190 24 1 3464 3641 96315104 96314915 1.450000e-29 141.0
13 TraesCS1D01G339600 chr1A 94.286 35 2 0 1 35 527100147 527100181 2.000000e-03 54.7
14 TraesCS1D01G339600 chr7B 90.511 548 38 6 1593 2130 125077235 125077778 0.000000e+00 712.0
15 TraesCS1D01G339600 chr7B 90.909 154 14 0 1509 1662 515592021 515592174 1.410000e-49 207.0
16 TraesCS1D01G339600 chr7B 90.152 132 13 0 3503 3634 417872721 417872852 5.140000e-39 172.0
17 TraesCS1D01G339600 chr6B 90.656 503 42 3 1633 2130 691469253 691468751 0.000000e+00 664.0
18 TraesCS1D01G339600 chr4D 89.501 381 33 4 1756 2130 407023122 407022743 3.500000e-130 475.0
19 TraesCS1D01G339600 chr4D 92.562 121 9 0 1509 1629 437506439 437506559 1.430000e-39 174.0
20 TraesCS1D01G339600 chr2D 88.601 386 35 7 1753 2130 584515402 584515786 9.790000e-126 460.0
21 TraesCS1D01G339600 chr2D 92.208 154 12 0 1509 1662 645429608 645429761 6.500000e-53 219.0
22 TraesCS1D01G339600 chr7D 91.600 250 21 0 1413 1662 486202528 486202279 2.860000e-91 346.0
23 TraesCS1D01G339600 chr7D 92.857 154 11 0 1509 1662 41752288 41752135 1.400000e-54 224.0
24 TraesCS1D01G339600 chr7D 79.464 224 36 9 3464 3677 93778089 93778312 2.410000e-32 150.0
25 TraesCS1D01G339600 chr5B 86.851 289 28 6 1756 2036 81632366 81632080 8.060000e-82 315.0
26 TraesCS1D01G339600 chr5B 85.764 288 34 4 1756 2036 687948621 687948334 8.120000e-77 298.0
27 TraesCS1D01G339600 chr3D 80.312 320 48 9 3502 3817 11374980 11374672 1.080000e-55 228.0
28 TraesCS1D01G339600 chr3D 77.709 323 47 14 3502 3817 419463023 419463327 1.430000e-39 174.0
29 TraesCS1D01G339600 chr3D 89.041 73 8 0 2481 2553 400311574 400311502 1.480000e-14 91.6
30 TraesCS1D01G339600 chr3A 89.610 154 16 0 1509 1662 629106614 629106767 3.050000e-46 196.0
31 TraesCS1D01G339600 chr3A 75.076 329 65 13 2240 2553 519245166 519244840 1.870000e-28 137.0
32 TraesCS1D01G339600 chr7A 83.978 181 25 4 3502 3678 96551633 96551813 1.850000e-38 171.0
33 TraesCS1D01G339600 chr3B 85.714 154 15 4 1509 1662 749193015 749192869 5.170000e-34 156.0
34 TraesCS1D01G339600 chr3B 75.493 355 55 19 3482 3818 16401553 16401213 1.120000e-30 145.0
35 TraesCS1D01G339600 chr3B 79.213 178 35 2 2240 2416 525990859 525990683 5.250000e-24 122.0
36 TraesCS1D01G339600 chr4B 90.517 116 11 0 2015 2130 397900881 397900996 1.860000e-33 154.0
37 TraesCS1D01G339600 chr2A 83.436 163 27 0 3502 3664 666980088 666979926 6.690000e-33 152.0
38 TraesCS1D01G339600 chr4A 89.655 116 12 0 2015 2130 26835080 26835195 8.660000e-32 148.0


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 TraesCS1D01G339600 chr1D 429598432 429602298 3866 False 7142.000000 7142 100.000000 1 3867 1 chr1D.!!$F2 3866
1 TraesCS1D01G339600 chr1B 580621230 580625646 4416 False 1116.500000 1790 89.421500 1 3867 4 chr1B.!!$F1 3866
2 TraesCS1D01G339600 chr1A 527100147 527104656 4509 False 626.814286 1166 92.037429 1 3867 7 chr1A.!!$F1 3866
3 TraesCS1D01G339600 chr7B 125077235 125077778 543 False 712.000000 712 90.511000 1593 2130 1 chr7B.!!$F1 537
4 TraesCS1D01G339600 chr6B 691468751 691469253 502 True 664.000000 664 90.656000 1633 2130 1 chr6B.!!$R1 497

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
51 67 1.175983 CCCTGCTCCTCCTAGCGTAG 61.176 65.0 0.0 0.0 45.85 3.51 F
1796 2292 0.532573 TCGGAGTGTGATGGAGCTTC 59.467 55.0 0.0 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1852 2348 0.179094 CCCGCGTAGAAACATGGCTA 60.179 55.0 4.92 0.0 0.0 3.93 R
3737 4874 0.037697 AAGTCATCGCACGCCTTGTA 60.038 50.0 0.00 0.0 0.0 2.41 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
51 67 1.175983 CCCTGCTCCTCCTAGCGTAG 61.176 65.000 0.00 0.00 45.85 3.51
95 111 2.743928 GGAGCACCGCCTTCACTG 60.744 66.667 0.00 0.00 0.00 3.66
96 112 2.743928 GAGCACCGCCTTCACTGG 60.744 66.667 0.00 0.00 0.00 4.00
103 119 1.296392 CGCCTTCACTGGATCCACA 59.704 57.895 11.44 0.00 0.00 4.17
159 175 1.585267 GCCACCGCATTCATCACACA 61.585 55.000 0.00 0.00 34.03 3.72
218 234 1.375523 GGTGTTCGTGATCGCCCTT 60.376 57.895 0.00 0.00 36.96 3.95
355 374 2.804167 CCGGTGCAACAGCAACAA 59.196 55.556 0.98 0.00 46.26 2.83
458 477 3.127533 GTCTGGTCGCATGGCACC 61.128 66.667 0.00 0.00 32.96 5.01
459 478 3.635191 TCTGGTCGCATGGCACCA 61.635 61.111 10.54 10.54 37.38 4.17
460 479 2.438975 CTGGTCGCATGGCACCAT 60.439 61.111 11.15 0.00 38.36 3.55
577 602 2.921121 TGTTGTGCGATGATACGAGAAC 59.079 45.455 0.00 0.00 35.09 3.01
738 1011 4.860352 TGTGAATGTACACGAAGGATTACG 59.140 41.667 0.00 0.00 42.86 3.18
739 1012 4.860907 GTGAATGTACACGAAGGATTACGT 59.139 41.667 0.00 0.00 43.50 3.57
752 1050 2.159747 GGATTACGTGTTTTCTGTCGGC 60.160 50.000 0.00 0.00 0.00 5.54
872 1359 6.642683 TTTTTCGTCACTAATCCTCGATTC 57.357 37.500 0.00 0.00 33.95 2.52
873 1360 5.578005 TTTCGTCACTAATCCTCGATTCT 57.422 39.130 0.00 0.00 33.95 2.40
883 1370 7.377397 CACTAATCCTCGATTCTTTCTAACTCG 59.623 40.741 0.00 0.00 33.95 4.18
952 1439 4.050934 TGACGTCGTCGCAGGCAT 62.051 61.111 19.81 0.00 41.18 4.40
1526 2014 2.261671 CTGTAAGTCGCGGCCTGT 59.738 61.111 7.31 0.00 0.00 4.00
1548 2038 3.643320 TCTCTGCTTTCTCCTTCAGTTCA 59.357 43.478 0.00 0.00 0.00 3.18
1549 2039 3.995705 CTCTGCTTTCTCCTTCAGTTCAG 59.004 47.826 0.00 0.00 0.00 3.02
1551 2041 3.995705 CTGCTTTCTCCTTCAGTTCAGAG 59.004 47.826 0.00 0.00 0.00 3.35
1552 2042 3.389329 TGCTTTCTCCTTCAGTTCAGAGT 59.611 43.478 0.00 0.00 0.00 3.24
1553 2043 4.141620 TGCTTTCTCCTTCAGTTCAGAGTT 60.142 41.667 0.00 0.00 0.00 3.01
1554 2044 4.450757 GCTTTCTCCTTCAGTTCAGAGTTC 59.549 45.833 0.00 0.00 0.00 3.01
1555 2045 5.741673 GCTTTCTCCTTCAGTTCAGAGTTCT 60.742 44.000 0.00 0.00 0.00 3.01
1556 2046 4.862902 TCTCCTTCAGTTCAGAGTTCTG 57.137 45.455 2.69 2.69 45.08 3.02
1578 2068 3.857052 AGATGGCATGCTTGATTTTGTG 58.143 40.909 18.92 0.00 0.00 3.33
1581 2071 2.070783 GGCATGCTTGATTTTGTGGTG 58.929 47.619 18.92 0.00 0.00 4.17
1582 2072 2.070783 GCATGCTTGATTTTGTGGTGG 58.929 47.619 11.37 0.00 0.00 4.61
1584 2074 3.803021 GCATGCTTGATTTTGTGGTGGAA 60.803 43.478 11.37 0.00 0.00 3.53
1590 2080 5.350504 TTGATTTTGTGGTGGAATTGTGT 57.649 34.783 0.00 0.00 0.00 3.72
1605 2097 4.970662 ATTGTGTCACTAATGATGCACC 57.029 40.909 4.27 0.00 37.14 5.01
1606 2098 2.345876 TGTGTCACTAATGATGCACCG 58.654 47.619 4.27 0.00 37.14 4.94
1607 2099 2.289382 TGTGTCACTAATGATGCACCGT 60.289 45.455 4.27 0.00 37.14 4.83
1621 2117 1.752694 ACCGTTGTTGCACTGCCTT 60.753 52.632 0.00 0.00 0.00 4.35
1732 2228 2.671070 GCCCAAGGTAAAAATGCACGAG 60.671 50.000 0.00 0.00 0.00 4.18
1751 2247 3.613193 CGAGGAGATCACGTTGTTTGGTA 60.613 47.826 0.00 0.00 0.00 3.25
1754 2250 3.556423 GGAGATCACGTTGTTTGGTAGGT 60.556 47.826 0.00 0.00 0.00 3.08
1764 2260 8.761497 CACGTTGTTTGGTAGGTAGATATATTG 58.239 37.037 0.00 0.00 0.00 1.90
1796 2292 0.532573 TCGGAGTGTGATGGAGCTTC 59.467 55.000 0.00 0.00 0.00 3.86
1956 2455 5.163622 CCTGACCTGAATAAAACGCAATGAT 60.164 40.000 0.00 0.00 0.00 2.45
1957 2456 6.038161 CCTGACCTGAATAAAACGCAATGATA 59.962 38.462 0.00 0.00 0.00 2.15
2135 2702 3.971305 TGGTCTCTTGGGTGAGTTTTCTA 59.029 43.478 0.00 0.00 35.68 2.10
2144 2711 4.578928 TGGGTGAGTTTTCTAAAGTTCAGC 59.421 41.667 9.87 9.87 33.59 4.26
2146 2713 5.049336 GGGTGAGTTTTCTAAAGTTCAGCTC 60.049 44.000 14.49 0.00 34.21 4.09
2151 2718 6.525629 AGTTTTCTAAAGTTCAGCTCAGCTA 58.474 36.000 0.00 0.00 36.40 3.32
2152 2719 6.425417 AGTTTTCTAAAGTTCAGCTCAGCTAC 59.575 38.462 0.00 0.00 36.40 3.58
2153 2720 4.457834 TCTAAAGTTCAGCTCAGCTACC 57.542 45.455 0.00 0.00 36.40 3.18
2157 2724 0.461961 GTTCAGCTCAGCTACCGGAT 59.538 55.000 9.46 0.00 36.40 4.18
2158 2725 0.461548 TTCAGCTCAGCTACCGGATG 59.538 55.000 9.46 0.23 36.40 3.51
2171 2738 0.603707 CCGGATGAACACTGTGCAGT 60.604 55.000 7.90 0.00 43.61 4.40
2172 2739 1.229428 CGGATGAACACTGTGCAGTT 58.771 50.000 7.90 0.00 40.20 3.16
2176 2743 1.667236 TGAACACTGTGCAGTTCAGG 58.333 50.000 13.51 3.36 46.46 3.86
2178 2745 2.288666 GAACACTGTGCAGTTCAGGAA 58.711 47.619 7.90 0.00 42.72 3.36
2179 2746 2.418368 ACACTGTGCAGTTCAGGAAA 57.582 45.000 7.90 0.00 40.20 3.13
2186 2918 5.146010 TGTGCAGTTCAGGAAAACTTTTT 57.854 34.783 0.00 0.00 37.38 1.94
2193 2925 2.620251 AGGAAAACTTTTTGCTGGCC 57.380 45.000 7.58 0.00 45.30 5.36
2215 2947 6.238130 GGCCTCTTCGTCTGATTATTTTGTAC 60.238 42.308 0.00 0.00 0.00 2.90
2218 2950 7.253684 CCTCTTCGTCTGATTATTTTGTACGTC 60.254 40.741 0.00 0.00 0.00 4.34
2219 2951 7.310664 TCTTCGTCTGATTATTTTGTACGTCT 58.689 34.615 0.00 0.00 0.00 4.18
2220 2952 8.453320 TCTTCGTCTGATTATTTTGTACGTCTA 58.547 33.333 0.00 0.00 0.00 2.59
2221 2953 8.969121 TTCGTCTGATTATTTTGTACGTCTAA 57.031 30.769 0.00 0.00 0.00 2.10
2222 2954 9.577110 TTCGTCTGATTATTTTGTACGTCTAAT 57.423 29.630 0.00 0.00 0.00 1.73
2223 2955 9.577110 TCGTCTGATTATTTTGTACGTCTAATT 57.423 29.630 0.00 0.00 0.00 1.40
2272 3004 0.319900 TGCTGACGAAAGCTCTGGAC 60.320 55.000 13.68 0.00 43.90 4.02
2409 3141 1.080230 CACGAGTGAGCCAGGTGAG 60.080 63.158 0.00 0.00 0.00 3.51
2410 3142 1.531840 ACGAGTGAGCCAGGTGAGT 60.532 57.895 0.00 0.00 0.00 3.41
2411 3143 1.080230 CGAGTGAGCCAGGTGAGTG 60.080 63.158 0.00 0.00 0.00 3.51
2412 3144 1.810606 CGAGTGAGCCAGGTGAGTGT 61.811 60.000 0.00 0.00 0.00 3.55
2415 3147 1.459348 TGAGCCAGGTGAGTGTCCA 60.459 57.895 0.00 0.00 0.00 4.02
2417 3149 0.392193 GAGCCAGGTGAGTGTCCATG 60.392 60.000 0.00 0.00 0.00 3.66
2419 3151 1.377725 CCAGGTGAGTGTCCATGCC 60.378 63.158 0.00 0.00 0.00 4.40
2421 3153 2.436646 GGTGAGTGTCCATGCCCG 60.437 66.667 0.00 0.00 0.00 6.13
2422 3154 3.127533 GTGAGTGTCCATGCCCGC 61.128 66.667 0.00 0.00 0.00 6.13
2423 3155 3.321648 TGAGTGTCCATGCCCGCT 61.322 61.111 0.00 0.00 0.00 5.52
2424 3156 2.512515 GAGTGTCCATGCCCGCTC 60.513 66.667 7.41 7.41 0.00 5.03
2425 3157 4.101448 AGTGTCCATGCCCGCTCC 62.101 66.667 0.00 0.00 0.00 4.70
2427 3159 3.329889 TGTCCATGCCCGCTCCTT 61.330 61.111 0.00 0.00 0.00 3.36
2429 3161 4.161295 TCCATGCCCGCTCCTTCG 62.161 66.667 0.00 0.00 0.00 3.79
2432 3164 4.514577 ATGCCCGCTCCTTCGACG 62.515 66.667 0.00 0.00 0.00 5.12
2435 3167 3.744719 CCCGCTCCTTCGACGACA 61.745 66.667 0.00 0.00 0.00 4.35
2437 3169 1.153823 CCGCTCCTTCGACGACATT 60.154 57.895 0.00 0.00 0.00 2.71
2439 3171 0.179161 CGCTCCTTCGACGACATTCT 60.179 55.000 0.00 0.00 0.00 2.40
2441 3173 1.656095 GCTCCTTCGACGACATTCTTG 59.344 52.381 0.00 0.00 0.00 3.02
2442 3174 2.263077 CTCCTTCGACGACATTCTTGG 58.737 52.381 0.00 0.00 0.00 3.61
2448 3318 4.188247 TCGACGACATTCTTGGAGAAAT 57.812 40.909 0.00 0.00 37.82 2.17
2449 3319 3.926527 TCGACGACATTCTTGGAGAAATG 59.073 43.478 0.00 0.00 37.82 2.32
2457 3327 5.180117 ACATTCTTGGAGAAATGAACTGACG 59.820 40.000 2.36 0.00 37.82 4.35
2459 3329 4.307432 TCTTGGAGAAATGAACTGACGAC 58.693 43.478 0.00 0.00 0.00 4.34
2462 3332 1.057847 GAGAAATGAACTGACGACGCG 59.942 52.381 3.53 3.53 0.00 6.01
2947 3819 3.202906 TGCTACGTATTGCCTTTGGATC 58.797 45.455 0.00 0.00 0.00 3.36
2956 3828 6.967199 CGTATTGCCTTTGGATCTTAGTTTTC 59.033 38.462 0.00 0.00 0.00 2.29
2961 3833 7.209475 TGCCTTTGGATCTTAGTTTTCTTTTG 58.791 34.615 0.00 0.00 0.00 2.44
2964 3836 6.664428 TTGGATCTTAGTTTTCTTTTGGGG 57.336 37.500 0.00 0.00 0.00 4.96
2965 3837 4.526650 TGGATCTTAGTTTTCTTTTGGGGC 59.473 41.667 0.00 0.00 0.00 5.80
3041 3915 8.232913 ACTTCTTTAGTGTTTGCCATTTCTTA 57.767 30.769 0.00 0.00 35.19 2.10
3096 3970 8.687824 AAAACAAAACAGTTGTGATGTTAGAG 57.312 30.769 10.70 0.00 39.91 2.43
3140 4014 0.544697 TTTTGTATCTCCGAGGCCCC 59.455 55.000 0.00 0.00 0.00 5.80
3170 4044 5.009510 CCTCTCGAACAGATGATGTAGATGT 59.990 44.000 0.00 0.00 43.00 3.06
3171 4045 6.205658 CCTCTCGAACAGATGATGTAGATGTA 59.794 42.308 0.00 0.00 43.00 2.29
3204 4108 4.708177 ACATCTTCGCCTGCAAATATACT 58.292 39.130 0.00 0.00 0.00 2.12
3205 4109 4.512944 ACATCTTCGCCTGCAAATATACTG 59.487 41.667 0.00 0.00 0.00 2.74
3206 4110 4.137116 TCTTCGCCTGCAAATATACTGT 57.863 40.909 0.00 0.00 0.00 3.55
3207 4111 5.270893 TCTTCGCCTGCAAATATACTGTA 57.729 39.130 0.00 0.00 0.00 2.74
3208 4112 5.666462 TCTTCGCCTGCAAATATACTGTAA 58.334 37.500 0.00 0.00 0.00 2.41
3252 4174 0.251209 GCCGTTTCCTTTCCTTCCCT 60.251 55.000 0.00 0.00 0.00 4.20
3367 4333 2.158959 GTGTCCGCCACTCGATTCG 61.159 63.158 0.00 0.00 41.11 3.34
3417 4383 2.508439 CACCGGACGATTCCACCG 60.508 66.667 9.46 0.00 43.00 4.94
3423 4389 3.687102 ACGATTCCACCGCCGTCA 61.687 61.111 0.00 0.00 0.00 4.35
3500 4626 4.284746 GGAAATTCGGATGGAGGAGATACT 59.715 45.833 0.00 0.00 0.00 2.12
3526 4663 2.306847 AGAAGCCGACCATTGTTGTTT 58.693 42.857 0.00 0.00 0.00 2.83
3645 4782 2.093235 CGAGCAGAAGAAGAAGGGGATT 60.093 50.000 0.00 0.00 0.00 3.01
3648 4785 5.501156 GAGCAGAAGAAGAAGGGGATTAAA 58.499 41.667 0.00 0.00 0.00 1.52
3682 4819 1.227468 GGCCCCTCGACGGTAAATC 60.227 63.158 0.00 0.00 0.00 2.17
3690 4827 2.514267 GACGGTAAATCGGCGATCC 58.486 57.895 24.20 18.53 0.00 3.36
3691 4828 0.031721 GACGGTAAATCGGCGATCCT 59.968 55.000 24.20 15.59 0.00 3.24
3697 4834 1.968050 AAATCGGCGATCCTCCCGTT 61.968 55.000 24.20 8.91 44.63 4.44
3702 4839 1.389609 GGCGATCCTCCCGTTGAGTA 61.390 60.000 0.00 0.00 39.65 2.59
3737 4874 1.613785 GGTGTGACTCGGAGTAGGAGT 60.614 57.143 11.27 0.00 46.91 3.85
3740 4877 2.303890 TGTGACTCGGAGTAGGAGTACA 59.696 50.000 11.27 7.09 44.41 2.90
3744 4881 1.677052 CTCGGAGTAGGAGTACAAGGC 59.323 57.143 0.00 0.00 0.00 4.35
3755 4892 0.736325 GTACAAGGCGTGCGATGACT 60.736 55.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 93 4.021925 AGTGAAGGCGGTGCTCCC 62.022 66.667 0.00 0.00 0.00 4.30
92 108 3.402681 CCCGGCTGTGGATCCAGT 61.403 66.667 16.81 0.00 34.84 4.00
95 111 0.746923 GTAAACCCGGCTGTGGATCC 60.747 60.000 4.20 4.20 0.00 3.36
96 112 0.746923 GGTAAACCCGGCTGTGGATC 60.747 60.000 0.00 0.00 0.00 3.36
159 175 1.742761 CCGATCACTGCTTTGGATGT 58.257 50.000 0.00 0.00 0.00 3.06
218 234 2.925706 TAGAACAGCCCGGCCACA 60.926 61.111 5.55 0.00 0.00 4.17
278 297 0.965866 TACCTGACGAGCTGGACTGG 60.966 60.000 18.56 18.56 38.83 4.00
280 299 2.569183 GTACCTGACGAGCTGGACT 58.431 57.895 1.44 0.00 38.83 3.85
320 339 2.256158 CAACGACGAGGGTGCGTA 59.744 61.111 0.00 0.00 45.72 4.42
355 374 1.220206 CCTCTTGATGCCAGCTCGT 59.780 57.895 0.00 0.00 0.00 4.18
362 381 1.134670 ACGCTCTAACCTCTTGATGCC 60.135 52.381 0.00 0.00 0.00 4.40
510 529 4.201679 TCGCCGTCGATCGCCAAT 62.202 61.111 11.09 0.00 40.21 3.16
577 602 0.521867 CATGCACATTTCCACTCGCG 60.522 55.000 0.00 0.00 0.00 5.87
683 956 6.656693 AGCAGTACTACTAACTTTTACTCGGA 59.343 38.462 0.00 0.00 0.00 4.55
738 1011 2.943653 CCGGCCGACAGAAAACAC 59.056 61.111 30.73 0.00 0.00 3.32
739 1012 2.951475 AAGCCGGCCGACAGAAAACA 62.951 55.000 30.73 0.00 0.00 2.83
752 1050 3.578688 AGTAAACACGTAACTAAGCCGG 58.421 45.455 0.00 0.00 0.00 6.13
827 1314 0.396435 TCAGTGCCACCGAAGTCAAT 59.604 50.000 0.00 0.00 0.00 2.57
854 1341 5.583495 AGAAAGAATCGAGGATTAGTGACG 58.417 41.667 0.00 0.00 31.89 4.35
855 1342 8.192110 AGTTAGAAAGAATCGAGGATTAGTGAC 58.808 37.037 0.00 0.00 31.89 3.67
856 1343 8.294954 AGTTAGAAAGAATCGAGGATTAGTGA 57.705 34.615 0.00 0.00 31.89 3.41
858 1345 7.067251 ACGAGTTAGAAAGAATCGAGGATTAGT 59.933 37.037 0.90 0.00 37.16 2.24
859 1346 7.377397 CACGAGTTAGAAAGAATCGAGGATTAG 59.623 40.741 0.90 0.00 37.16 1.73
860 1347 7.066645 TCACGAGTTAGAAAGAATCGAGGATTA 59.933 37.037 0.90 0.00 37.16 1.75
862 1349 5.357314 TCACGAGTTAGAAAGAATCGAGGAT 59.643 40.000 0.90 0.00 37.16 3.24
863 1350 4.698780 TCACGAGTTAGAAAGAATCGAGGA 59.301 41.667 0.90 0.00 37.16 3.71
864 1351 4.982999 TCACGAGTTAGAAAGAATCGAGG 58.017 43.478 0.90 0.00 37.16 4.63
865 1352 6.087522 AGTTCACGAGTTAGAAAGAATCGAG 58.912 40.000 0.90 0.00 37.16 4.04
866 1353 6.010294 AGTTCACGAGTTAGAAAGAATCGA 57.990 37.500 0.90 0.00 37.16 3.59
867 1354 6.144080 ACAAGTTCACGAGTTAGAAAGAATCG 59.856 38.462 0.00 0.00 39.22 3.34
868 1355 7.409465 ACAAGTTCACGAGTTAGAAAGAATC 57.591 36.000 0.00 0.00 0.00 2.52
869 1356 7.787725 AACAAGTTCACGAGTTAGAAAGAAT 57.212 32.000 0.00 0.00 0.00 2.40
870 1357 7.461107 CAAACAAGTTCACGAGTTAGAAAGAA 58.539 34.615 0.00 0.00 0.00 2.52
871 1358 6.456449 GCAAACAAGTTCACGAGTTAGAAAGA 60.456 38.462 0.00 0.00 0.00 2.52
872 1359 5.677178 GCAAACAAGTTCACGAGTTAGAAAG 59.323 40.000 0.00 0.00 0.00 2.62
873 1360 5.448089 GGCAAACAAGTTCACGAGTTAGAAA 60.448 40.000 0.00 0.00 0.00 2.52
952 1439 2.687805 CCGAGAAGGACGAGCGTGA 61.688 63.158 0.00 0.00 45.00 4.35
978 1465 1.693083 GCGGTATGGTTGACAGCGAC 61.693 60.000 0.00 0.00 35.31 5.19
979 1466 1.447140 GCGGTATGGTTGACAGCGA 60.447 57.895 0.00 0.00 35.31 4.93
980 1467 2.461110 GGCGGTATGGTTGACAGCG 61.461 63.158 0.00 0.00 38.68 5.18
981 1468 0.958382 TTGGCGGTATGGTTGACAGC 60.958 55.000 0.00 0.00 37.29 4.40
982 1469 1.401552 CATTGGCGGTATGGTTGACAG 59.598 52.381 0.00 0.00 0.00 3.51
983 1470 1.271652 ACATTGGCGGTATGGTTGACA 60.272 47.619 0.00 0.00 0.00 3.58
984 1471 1.459450 ACATTGGCGGTATGGTTGAC 58.541 50.000 0.00 0.00 0.00 3.18
1431 1918 4.363990 CAGTCCAGCAGCGTCGGT 62.364 66.667 0.00 0.00 0.00 4.69
1494 1981 2.139323 TACAGTCCTCGTGCAGGTAT 57.861 50.000 6.26 0.00 43.95 2.73
1519 2006 0.739112 GAGAAAGCAGAGACAGGCCG 60.739 60.000 0.00 0.00 0.00 6.13
1520 2007 0.392327 GGAGAAAGCAGAGACAGGCC 60.392 60.000 0.00 0.00 0.00 5.19
1521 2008 0.612744 AGGAGAAAGCAGAGACAGGC 59.387 55.000 0.00 0.00 0.00 4.85
1522 2009 2.301296 TGAAGGAGAAAGCAGAGACAGG 59.699 50.000 0.00 0.00 0.00 4.00
1526 2014 3.643320 TGAACTGAAGGAGAAAGCAGAGA 59.357 43.478 0.00 0.00 32.86 3.10
1548 2038 1.838715 AGCATGCCATCTCAGAACTCT 59.161 47.619 15.66 0.00 0.00 3.24
1549 2039 2.328819 AGCATGCCATCTCAGAACTC 57.671 50.000 15.66 0.00 0.00 3.01
1551 2041 2.362736 TCAAGCATGCCATCTCAGAAC 58.637 47.619 15.66 0.00 0.00 3.01
1552 2042 2.793288 TCAAGCATGCCATCTCAGAA 57.207 45.000 15.66 0.00 0.00 3.02
1553 2043 3.292492 AATCAAGCATGCCATCTCAGA 57.708 42.857 15.66 2.45 0.00 3.27
1554 2044 4.112634 CAAAATCAAGCATGCCATCTCAG 58.887 43.478 15.66 0.00 0.00 3.35
1555 2045 3.512329 ACAAAATCAAGCATGCCATCTCA 59.488 39.130 15.66 0.00 0.00 3.27
1556 2046 3.863424 CACAAAATCAAGCATGCCATCTC 59.137 43.478 15.66 0.00 0.00 2.75
1557 2047 3.369052 CCACAAAATCAAGCATGCCATCT 60.369 43.478 15.66 0.00 0.00 2.90
1558 2048 2.933906 CCACAAAATCAAGCATGCCATC 59.066 45.455 15.66 0.00 0.00 3.51
1559 2049 2.303600 ACCACAAAATCAAGCATGCCAT 59.696 40.909 15.66 0.00 0.00 4.40
1560 2050 1.693062 ACCACAAAATCAAGCATGCCA 59.307 42.857 15.66 0.00 0.00 4.92
1561 2051 2.070783 CACCACAAAATCAAGCATGCC 58.929 47.619 15.66 0.00 0.00 4.40
1562 2052 2.070783 CCACCACAAAATCAAGCATGC 58.929 47.619 10.51 10.51 0.00 4.06
1578 2068 5.677091 GCATCATTAGTGACACAATTCCACC 60.677 44.000 8.59 0.00 37.14 4.61
1581 2071 5.335127 GTGCATCATTAGTGACACAATTCC 58.665 41.667 8.59 0.00 37.14 3.01
1582 2072 5.335127 GGTGCATCATTAGTGACACAATTC 58.665 41.667 8.59 0.00 37.14 2.17
1584 2074 3.374988 CGGTGCATCATTAGTGACACAAT 59.625 43.478 8.59 3.17 37.14 2.71
1590 2080 3.052455 ACAACGGTGCATCATTAGTGA 57.948 42.857 0.00 0.00 39.04 3.41
1605 2097 0.592247 GACAAGGCAGTGCAACAACG 60.592 55.000 18.61 1.09 41.43 4.10
1606 2098 0.740737 AGACAAGGCAGTGCAACAAC 59.259 50.000 18.61 5.14 41.43 3.32
1607 2099 1.134753 CAAGACAAGGCAGTGCAACAA 59.865 47.619 18.61 0.00 41.43 2.83
1621 2117 6.758254 TGACAAGATACATTCAGTCAAGACA 58.242 36.000 2.72 0.00 38.15 3.41
1682 2178 2.567169 TGTCATCGAGAAGGATGTTGGT 59.433 45.455 0.00 0.00 43.39 3.67
1732 2228 3.000727 CCTACCAAACAACGTGATCTCC 58.999 50.000 0.00 0.00 0.00 3.71
1754 2250 9.860898 CCGAGATGAACATTCACAATATATCTA 57.139 33.333 0.00 0.00 40.49 1.98
1764 2260 3.369147 CACACTCCGAGATGAACATTCAC 59.631 47.826 1.33 0.00 40.49 3.18
1796 2292 1.287730 GCGACCTGCACAAGACAGAG 61.288 60.000 0.00 0.00 45.45 3.35
1852 2348 0.179094 CCCGCGTAGAAACATGGCTA 60.179 55.000 4.92 0.00 0.00 3.93
1956 2455 2.640332 TGTACCTGCCAAACCAGTCATA 59.360 45.455 0.00 0.00 0.00 2.15
1957 2456 1.423541 TGTACCTGCCAAACCAGTCAT 59.576 47.619 0.00 0.00 0.00 3.06
2099 2603 2.843669 GACCAGAGTCTCGTCGTCT 58.156 57.895 1.94 0.00 40.10 4.18
2135 2702 1.338200 CCGGTAGCTGAGCTGAACTTT 60.338 52.381 18.79 0.00 40.10 2.66
2144 2711 1.478510 AGTGTTCATCCGGTAGCTGAG 59.521 52.381 0.00 0.00 0.00 3.35
2146 2713 1.066858 ACAGTGTTCATCCGGTAGCTG 60.067 52.381 0.00 4.52 0.00 4.24
2151 2718 0.603707 CTGCACAGTGTTCATCCGGT 60.604 55.000 0.00 0.00 0.00 5.28
2152 2719 0.603707 ACTGCACAGTGTTCATCCGG 60.604 55.000 1.71 0.00 40.75 5.14
2153 2720 1.195448 GAACTGCACAGTGTTCATCCG 59.805 52.381 3.64 0.00 41.58 4.18
2157 2724 1.209261 TCCTGAACTGCACAGTGTTCA 59.791 47.619 15.85 15.85 46.73 3.18
2158 2725 1.953559 TCCTGAACTGCACAGTGTTC 58.046 50.000 3.64 9.08 41.58 3.18
2171 2738 3.530535 GCCAGCAAAAAGTTTTCCTGAA 58.469 40.909 21.44 0.00 38.00 3.02
2172 2739 2.158971 GGCCAGCAAAAAGTTTTCCTGA 60.159 45.455 21.44 0.00 38.00 3.86
2175 2742 2.103094 AGAGGCCAGCAAAAAGTTTTCC 59.897 45.455 5.01 0.00 0.00 3.13
2176 2743 3.459232 AGAGGCCAGCAAAAAGTTTTC 57.541 42.857 5.01 0.00 0.00 2.29
2178 2745 2.223805 CGAAGAGGCCAGCAAAAAGTTT 60.224 45.455 5.01 0.00 0.00 2.66
2179 2746 1.338020 CGAAGAGGCCAGCAAAAAGTT 59.662 47.619 5.01 0.00 0.00 2.66
2186 2918 1.260538 ATCAGACGAAGAGGCCAGCA 61.261 55.000 5.01 0.00 0.00 4.41
2190 2922 4.636206 ACAAAATAATCAGACGAAGAGGCC 59.364 41.667 0.00 0.00 0.00 5.19
2193 2925 7.485277 AGACGTACAAAATAATCAGACGAAGAG 59.515 37.037 0.00 0.00 33.30 2.85
2229 2961 0.824182 CCGTGCCTGTACCCCAAAAA 60.824 55.000 0.00 0.00 0.00 1.94
2230 2962 1.228306 CCGTGCCTGTACCCCAAAA 60.228 57.895 0.00 0.00 0.00 2.44
2231 2963 2.432563 CCGTGCCTGTACCCCAAA 59.567 61.111 0.00 0.00 0.00 3.28
2232 2964 4.338710 GCCGTGCCTGTACCCCAA 62.339 66.667 0.00 0.00 0.00 4.12
2260 2992 1.219393 CTCCCCGTCCAGAGCTTTC 59.781 63.158 0.00 0.00 0.00 2.62
2409 3141 3.628646 AAGGAGCGGGCATGGACAC 62.629 63.158 0.00 0.00 0.00 3.67
2410 3142 3.329542 GAAGGAGCGGGCATGGACA 62.330 63.158 0.00 0.00 0.00 4.02
2411 3143 2.514824 GAAGGAGCGGGCATGGAC 60.515 66.667 0.00 0.00 0.00 4.02
2412 3144 4.161295 CGAAGGAGCGGGCATGGA 62.161 66.667 0.00 0.00 0.00 3.41
2415 3147 4.514577 CGTCGAAGGAGCGGGCAT 62.515 66.667 0.00 0.00 0.00 4.40
2419 3151 1.140407 GAATGTCGTCGAAGGAGCGG 61.140 60.000 0.00 0.00 0.00 5.52
2421 3153 1.656095 CAAGAATGTCGTCGAAGGAGC 59.344 52.381 0.00 0.00 0.00 4.70
2422 3154 2.094700 TCCAAGAATGTCGTCGAAGGAG 60.095 50.000 0.00 0.00 0.00 3.69
2423 3155 1.890489 TCCAAGAATGTCGTCGAAGGA 59.110 47.619 0.00 0.00 0.00 3.36
2424 3156 2.094700 TCTCCAAGAATGTCGTCGAAGG 60.095 50.000 0.00 0.00 0.00 3.46
2425 3157 3.217599 TCTCCAAGAATGTCGTCGAAG 57.782 47.619 0.00 0.00 0.00 3.79
2427 3159 3.653539 TTTCTCCAAGAATGTCGTCGA 57.346 42.857 0.00 0.00 33.67 4.20
2429 3161 5.409826 AGTTCATTTCTCCAAGAATGTCGTC 59.590 40.000 0.00 0.00 33.67 4.20
2432 3164 6.606768 GTCAGTTCATTTCTCCAAGAATGTC 58.393 40.000 0.00 0.00 33.67 3.06
2433 3165 5.180117 CGTCAGTTCATTTCTCCAAGAATGT 59.820 40.000 0.00 0.00 33.67 2.71
2434 3166 5.409520 TCGTCAGTTCATTTCTCCAAGAATG 59.590 40.000 0.00 0.00 33.67 2.67
2435 3167 5.409826 GTCGTCAGTTCATTTCTCCAAGAAT 59.590 40.000 0.00 0.00 33.67 2.40
2437 3169 4.307432 GTCGTCAGTTCATTTCTCCAAGA 58.693 43.478 0.00 0.00 0.00 3.02
2439 3171 3.057019 CGTCGTCAGTTCATTTCTCCAA 58.943 45.455 0.00 0.00 0.00 3.53
2441 3173 1.390463 GCGTCGTCAGTTCATTTCTCC 59.610 52.381 0.00 0.00 0.00 3.71
2442 3174 1.057847 CGCGTCGTCAGTTCATTTCTC 59.942 52.381 0.00 0.00 0.00 2.87
2462 3332 2.720750 CGTTTGTCGTTGCCACGC 60.721 61.111 5.28 1.77 46.70 5.34
2689 3559 4.074526 TCGCTGCTGGAGCTGGAC 62.075 66.667 19.01 0.00 46.64 4.02
2905 3777 6.818233 AGCAGTATTTTACTAGCCTAACTCC 58.182 40.000 0.00 0.00 37.23 3.85
2947 3819 2.301870 GGGGCCCCAAAAGAAAACTAAG 59.698 50.000 37.61 0.00 35.81 2.18
2961 3833 3.825623 CTCCAATGAGGGGGCCCC 61.826 72.222 35.78 35.78 45.90 5.80
3110 3984 8.033626 CCTCGGAGATACAAAAGTTAGTTACTT 58.966 37.037 6.58 0.00 42.59 2.24
3111 3985 7.545489 CCTCGGAGATACAAAAGTTAGTTACT 58.455 38.462 6.58 0.00 34.92 2.24
3112 3986 6.255237 GCCTCGGAGATACAAAAGTTAGTTAC 59.745 42.308 6.58 0.00 33.89 2.50
3113 3987 6.335777 GCCTCGGAGATACAAAAGTTAGTTA 58.664 40.000 6.58 0.00 33.89 2.24
3114 3988 5.176592 GCCTCGGAGATACAAAAGTTAGTT 58.823 41.667 6.58 0.00 33.89 2.24
3115 3989 4.382793 GGCCTCGGAGATACAAAAGTTAGT 60.383 45.833 6.58 0.00 33.89 2.24
3116 3990 4.120589 GGCCTCGGAGATACAAAAGTTAG 58.879 47.826 6.58 0.00 33.89 2.34
3117 3991 3.118519 GGGCCTCGGAGATACAAAAGTTA 60.119 47.826 6.58 0.00 33.89 2.24
3118 3992 2.355818 GGGCCTCGGAGATACAAAAGTT 60.356 50.000 6.58 0.00 33.89 2.66
3119 3993 1.209747 GGGCCTCGGAGATACAAAAGT 59.790 52.381 6.58 0.00 33.89 2.66
3120 3994 1.475213 GGGGCCTCGGAGATACAAAAG 60.475 57.143 6.58 0.00 33.89 2.27
3121 3995 0.544697 GGGGCCTCGGAGATACAAAA 59.455 55.000 6.58 0.00 33.89 2.44
3122 3996 0.619255 TGGGGCCTCGGAGATACAAA 60.619 55.000 6.58 0.00 33.89 2.83
3123 3997 0.619255 TTGGGGCCTCGGAGATACAA 60.619 55.000 6.58 3.72 33.89 2.41
3124 3998 0.619255 TTTGGGGCCTCGGAGATACA 60.619 55.000 6.58 0.00 33.89 2.29
3125 3999 0.179054 GTTTGGGGCCTCGGAGATAC 60.179 60.000 6.58 0.00 33.89 2.24
3126 4000 1.342672 GGTTTGGGGCCTCGGAGATA 61.343 60.000 6.58 0.00 33.89 1.98
3127 4001 2.680370 GGTTTGGGGCCTCGGAGAT 61.680 63.158 6.58 0.00 33.89 2.75
3128 4002 3.327404 GGTTTGGGGCCTCGGAGA 61.327 66.667 6.58 0.00 0.00 3.71
3129 4003 4.426313 GGGTTTGGGGCCTCGGAG 62.426 72.222 0.84 0.00 0.00 4.63
3140 4014 2.028112 TCATCTGTTCGAGAGGGGTTTG 60.028 50.000 0.00 0.00 33.04 2.93
3232 4152 1.583495 GGGAAGGAAAGGAAACGGCG 61.583 60.000 4.80 4.80 0.00 6.46
3252 4174 2.436911 GCGGGAGGAAAAAGATAGGGTA 59.563 50.000 0.00 0.00 0.00 3.69
3394 4360 2.358247 AATCGTCCGGTGGTGCAC 60.358 61.111 8.80 8.80 0.00 4.57
3408 4374 2.818274 GGTGACGGCGGTGGAATC 60.818 66.667 13.24 0.00 0.00 2.52
3420 4386 2.511600 CGAATCAGGGCGGGTGAC 60.512 66.667 0.00 0.00 0.00 3.67
3423 4389 3.782443 GGACGAATCAGGGCGGGT 61.782 66.667 0.00 0.00 0.00 5.28
3451 4417 2.272146 GAGGAAAGGCCGGATGCA 59.728 61.111 5.05 0.00 43.89 3.96
3500 4626 2.224523 ACAATGGTCGGCTTCTTCTTCA 60.225 45.455 0.00 0.00 0.00 3.02
3645 4782 1.547372 CCGACCTCGTCCTCCTTTTTA 59.453 52.381 0.00 0.00 37.74 1.52
3648 4785 2.647158 GCCGACCTCGTCCTCCTTT 61.647 63.158 0.00 0.00 37.74 3.11
3690 4827 1.065701 CCGAGTCATACTCAACGGGAG 59.934 57.143 7.75 4.98 45.30 4.30
3691 4828 1.100510 CCGAGTCATACTCAACGGGA 58.899 55.000 7.75 0.00 45.30 5.14
3697 4834 2.644676 CAGTCCTCCGAGTCATACTCA 58.355 52.381 7.75 0.00 45.30 3.41
3702 4839 0.251832 ACACCAGTCCTCCGAGTCAT 60.252 55.000 0.00 0.00 0.00 3.06
3737 4874 0.037697 AAGTCATCGCACGCCTTGTA 60.038 50.000 0.00 0.00 0.00 2.41
3740 4877 2.034879 CCAAGTCATCGCACGCCTT 61.035 57.895 0.00 0.00 0.00 4.35
3744 4881 0.439985 CTTGTCCAAGTCATCGCACG 59.560 55.000 0.00 0.00 33.87 5.34
3755 4892 2.978978 TCCAGAACTCATCCTTGTCCAA 59.021 45.455 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.