Multiple sequence alignment - TraesCS4A01G425000

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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 TraesCS4A01G425000 chr4A 100.000 3213 0 0 1 3213 696007398 696004186 0.000000e+00 5934.0
1 TraesCS4A01G425000 chr4A 79.299 628 86 23 19 625 632369746 632369142 1.800000e-107 399.0
2 TraesCS4A01G425000 chr7A 92.386 1878 129 10 1346 3213 32025073 32026946 0.000000e+00 2663.0
3 TraesCS4A01G425000 chr7A 87.475 495 30 16 856 1345 32024571 32025038 2.820000e-150 542.0
4 TraesCS4A01G425000 chr7A 81.215 708 72 34 244 915 32013228 32013910 6.150000e-142 514.0
5 TraesCS4A01G425000 chr7A 95.706 163 6 1 3052 3213 32302702 32302864 8.840000e-66 261.0
6 TraesCS4A01G425000 chr7D 91.198 1636 118 15 1344 2976 31948066 31949678 0.000000e+00 2200.0
7 TraesCS4A01G425000 chr7D 88.372 1290 102 22 81 1356 31946792 31948047 0.000000e+00 1507.0
8 TraesCS4A01G425000 chr7D 87.703 431 32 8 310 731 109950232 109949814 1.730000e-132 483.0
9 TraesCS4A01G425000 chr7D 93.802 242 12 3 2973 3213 31949791 31950030 8.470000e-96 361.0
10 TraesCS4A01G425000 chr7D 96.552 58 2 0 3 60 31946741 31946798 2.640000e-16 97.1
11 TraesCS4A01G425000 chr2D 88.973 662 50 8 81 731 477991494 477990845 0.000000e+00 797.0
12 TraesCS4A01G425000 chr2D 85.279 197 19 5 544 731 477991687 477991882 9.090000e-46 195.0
13 TraesCS4A01G425000 chr2D 84.746 177 19 5 551 721 73456025 73456199 1.530000e-38 171.0
14 TraesCS4A01G425000 chr2D 96.552 58 2 0 3 60 477991545 477991488 2.640000e-16 97.1
15 TraesCS4A01G425000 chr6D 87.585 443 34 5 298 731 276588330 276587900 8.010000e-136 494.0
16 TraesCS4A01G425000 chr6D 89.535 172 17 1 1843 2014 298139491 298139321 1.940000e-52 217.0
17 TraesCS4A01G425000 chr6D 86.316 190 17 4 551 731 415403042 415403231 7.030000e-47 198.0
18 TraesCS4A01G425000 chr5A 78.846 624 92 25 19 625 707685841 707685241 5.030000e-103 385.0
19 TraesCS4A01G425000 chr5B 79.930 573 71 22 16 567 460195435 460195984 6.500000e-102 381.0
20 TraesCS4A01G425000 chrUn 91.636 275 21 1 81 353 477296453 477296179 2.340000e-101 379.0
21 TraesCS4A01G425000 chrUn 86.752 234 27 2 1809 2038 235799088 235799321 1.140000e-64 257.0
22 TraesCS4A01G425000 chrUn 96.552 58 2 0 3 60 477296504 477296447 2.640000e-16 97.1
23 TraesCS4A01G425000 chrUn 81.416 113 12 3 1235 1347 356835344 356835241 2.050000e-12 84.2
24 TraesCS4A01G425000 chr4B 79.443 574 72 25 16 567 116355463 116356012 6.550000e-97 364.0
25 TraesCS4A01G425000 chr1B 78.984 571 75 22 19 567 27092188 27091641 6.600000e-92 348.0
26 TraesCS4A01G425000 chr1B 78.883 573 77 22 16 567 637312984 637313533 6.600000e-92 348.0
27 TraesCS4A01G425000 chr6B 84.709 327 31 14 250 565 180391251 180390933 3.110000e-80 309.0
28 TraesCS4A01G425000 chr6A 85.532 235 29 4 1809 2038 48549945 48550179 1.150000e-59 241.0
29 TraesCS4A01G425000 chr6A 79.487 156 23 6 1193 1347 48549385 48549532 5.670000e-18 102.0
30 TraesCS4A01G425000 chr2B 84.746 118 14 3 1809 1922 745508314 745508431 7.280000e-22 115.0
31 TraesCS4A01G425000 chr2B 88.060 67 8 0 1959 2025 745508434 745508500 2.660000e-11 80.5


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 TraesCS4A01G425000 chr4A 696004186 696007398 3212 True 5934.000 5934 100.0000 1 3213 1 chr4A.!!$R2 3212
1 TraesCS4A01G425000 chr4A 632369142 632369746 604 True 399.000 399 79.2990 19 625 1 chr4A.!!$R1 606
2 TraesCS4A01G425000 chr7A 32024571 32026946 2375 False 1602.500 2663 89.9305 856 3213 2 chr7A.!!$F3 2357
3 TraesCS4A01G425000 chr7A 32013228 32013910 682 False 514.000 514 81.2150 244 915 1 chr7A.!!$F1 671
4 TraesCS4A01G425000 chr7D 31946741 31950030 3289 False 1041.275 2200 92.4810 3 3213 4 chr7D.!!$F1 3210
5 TraesCS4A01G425000 chr2D 477990845 477991545 700 True 447.050 797 92.7625 3 731 2 chr2D.!!$R1 728
6 TraesCS4A01G425000 chr5A 707685241 707685841 600 True 385.000 385 78.8460 19 625 1 chr5A.!!$R1 606
7 TraesCS4A01G425000 chr5B 460195435 460195984 549 False 381.000 381 79.9300 16 567 1 chr5B.!!$F1 551
8 TraesCS4A01G425000 chr4B 116355463 116356012 549 False 364.000 364 79.4430 16 567 1 chr4B.!!$F1 551
9 TraesCS4A01G425000 chr1B 27091641 27092188 547 True 348.000 348 78.9840 19 567 1 chr1B.!!$R1 548
10 TraesCS4A01G425000 chr1B 637312984 637313533 549 False 348.000 348 78.8830 16 567 1 chr1B.!!$F1 551

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
959 1025 0.1023 GCGGAAACAAACCAAGCAGT 59.898 50.0 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2464 2601 0.386858 CGTCCAGTTCTCGCGAAGAA 60.387 55.0 11.33 13.22 41.81 2.52 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 1.603633 TATCCCAGCTCCTCCCCTGT 61.604 60.000 0.00 0.00 0.00 4.00
43 44 2.905676 ATCCCAGCTCCTCCCCTGTC 62.906 65.000 0.00 0.00 0.00 3.51
63 71 4.411869 TGTCCTATCCTATTTGCACCATGA 59.588 41.667 0.00 0.00 0.00 3.07
68 76 5.579753 ATCCTATTTGCACCATGATCTCT 57.420 39.130 0.00 0.00 0.00 3.10
75 83 4.672587 TGCACCATGATCTCTACTTACC 57.327 45.455 0.00 0.00 0.00 2.85
79 87 5.545588 CACCATGATCTCTACTTACCCATG 58.454 45.833 0.00 0.00 0.00 3.66
80 88 5.070981 CACCATGATCTCTACTTACCCATGT 59.929 44.000 0.00 0.00 0.00 3.21
82 90 5.994054 CCATGATCTCTACTTACCCATGTTG 59.006 44.000 0.00 0.00 0.00 3.33
83 91 5.023533 TGATCTCTACTTACCCATGTTGC 57.976 43.478 0.00 0.00 0.00 4.17
84 92 4.716784 TGATCTCTACTTACCCATGTTGCT 59.283 41.667 0.00 0.00 0.00 3.91
85 93 4.737855 TCTCTACTTACCCATGTTGCTC 57.262 45.455 0.00 0.00 0.00 4.26
135 145 5.881443 TCCTAACAGAGAACTAGCTAGACAC 59.119 44.000 27.45 17.06 0.00 3.67
160 170 2.907910 AGTCGCATGCATTTCAGTTC 57.092 45.000 19.57 0.00 0.00 3.01
162 172 2.161012 AGTCGCATGCATTTCAGTTCAG 59.839 45.455 19.57 0.00 0.00 3.02
208 220 5.073311 TCAGACTGTTACTACTGCCAATC 57.927 43.478 1.59 0.00 0.00 2.67
214 226 4.575885 TGTTACTACTGCCAATCAAGTCC 58.424 43.478 0.00 0.00 0.00 3.85
268 280 1.002134 ATCACCTTGGCCTTGGTCG 60.002 57.895 15.72 11.95 33.75 4.79
345 357 4.415150 ACCCCCTGCACGCATCAG 62.415 66.667 0.00 0.00 0.00 2.90
433 460 1.604915 GGAGAAAGAGGGGAGCACC 59.395 63.158 0.00 0.00 39.11 5.01
436 463 1.377856 GAAAGAGGGGAGCACCAGC 60.378 63.158 1.58 0.00 42.91 4.85
437 464 2.828480 GAAAGAGGGGAGCACCAGCC 62.828 65.000 1.58 0.00 43.56 4.85
516 543 3.333219 CCCCTGCAGGCTCTCCAA 61.333 66.667 28.39 0.00 33.74 3.53
520 547 1.376942 CTGCAGGCTCTCCAACCAG 60.377 63.158 5.57 0.00 33.74 4.00
818 876 1.745115 GCGAGCCATGTGCCACTTA 60.745 57.895 0.00 0.00 42.71 2.24
830 888 1.531748 CCACTTATCATGGGCCGGT 59.468 57.895 1.90 0.00 33.18 5.28
865 927 0.813821 GAAGCCCAGAGTGCCAATTC 59.186 55.000 0.00 0.00 0.00 2.17
910 976 0.251653 TGTAACCTCGCCTCCTCTGT 60.252 55.000 0.00 0.00 0.00 3.41
917 983 1.135333 CTCGCCTCCTCTGTTCTAACC 59.865 57.143 0.00 0.00 0.00 2.85
924 990 0.736325 CTCTGTTCTAACCCCGCGTG 60.736 60.000 4.92 0.00 0.00 5.34
931 997 2.901051 CTAACCCCGCGTGGCAGTAG 62.901 65.000 7.81 3.33 0.00 2.57
955 1021 1.660264 GCGGCGGAAACAAACCAAG 60.660 57.895 9.78 0.00 0.00 3.61
959 1025 0.102300 GCGGAAACAAACCAAGCAGT 59.898 50.000 0.00 0.00 0.00 4.40
961 1027 2.604614 GCGGAAACAAACCAAGCAGTAG 60.605 50.000 0.00 0.00 0.00 2.57
962 1028 2.616842 CGGAAACAAACCAAGCAGTAGT 59.383 45.455 0.00 0.00 0.00 2.73
1198 1264 0.739112 CGCTTCCTCAGGTGAGCTTC 60.739 60.000 16.46 0.00 40.75 3.86
1229 1296 0.112801 ATACCTCCTCTCCTACGGCC 59.887 60.000 0.00 0.00 0.00 6.13
1382 1517 4.848299 CGTCTTGCAAAATTAGCTTCTGTC 59.152 41.667 0.00 0.00 0.00 3.51
1384 1519 3.201726 TGCAAAATTAGCTTCTGTCGC 57.798 42.857 0.00 0.00 0.00 5.19
1397 1532 2.191354 CTGTCGCCTGTGCCATTGTG 62.191 60.000 0.00 0.00 0.00 3.33
1405 1540 3.674138 GCCTGTGCCATTGTGATTTAGTG 60.674 47.826 0.00 0.00 0.00 2.74
1439 1574 1.408702 TGTGCAGAAAACCAAGAAGCC 59.591 47.619 0.00 0.00 0.00 4.35
1441 1576 0.039165 GCAGAAAACCAAGAAGCCGG 60.039 55.000 0.00 0.00 0.00 6.13
1443 1578 0.467290 AGAAAACCAAGAAGCCGGCA 60.467 50.000 31.54 0.00 0.00 5.69
1512 1647 3.824510 GAGAACGCGAACGCCGAC 61.825 66.667 15.93 5.09 45.53 4.79
1619 1754 4.791088 GCAGAAAAGGAAGAAGTGAGTTGC 60.791 45.833 0.00 0.00 0.00 4.17
1623 1758 3.971245 AGGAAGAAGTGAGTTGCCTAG 57.029 47.619 0.00 0.00 0.00 3.02
1633 1768 3.018856 TGAGTTGCCTAGCCATTTGATG 58.981 45.455 0.00 0.00 0.00 3.07
1645 1780 3.509575 GCCATTTGATGTGTCCTGGTTTA 59.490 43.478 0.00 0.00 0.00 2.01
1647 1782 4.082245 CCATTTGATGTGTCCTGGTTTACC 60.082 45.833 0.00 0.00 0.00 2.85
1669 1804 0.595310 GCTCGGATCGTGTAGCCTTC 60.595 60.000 0.00 0.00 0.00 3.46
1679 1814 2.679837 CGTGTAGCCTTCTGCATCAATT 59.320 45.455 0.00 0.00 44.83 2.32
1680 1815 3.127548 CGTGTAGCCTTCTGCATCAATTT 59.872 43.478 0.00 0.00 44.83 1.82
1681 1816 4.418392 GTGTAGCCTTCTGCATCAATTTG 58.582 43.478 0.00 0.00 44.83 2.32
1720 1855 3.623960 CCTGGTGCAAATAAAATGCCATG 59.376 43.478 0.00 0.00 43.16 3.66
1725 1860 5.063312 GGTGCAAATAAAATGCCATGTACAC 59.937 40.000 0.00 0.00 43.16 2.90
1764 1899 5.402568 AGTGATGCTAAGTTAATCGCATACG 59.597 40.000 7.80 0.00 42.60 3.06
1769 1904 6.244999 TGCTAAGTTAATCGCATACGTTTTG 58.755 36.000 0.00 0.00 41.18 2.44
1778 1913 2.350498 CGCATACGTTTTGGAACTAGGG 59.650 50.000 0.00 0.00 33.51 3.53
1858 1994 9.283768 AGCAACGTATAATGAATGGATGATAAA 57.716 29.630 0.00 0.00 0.00 1.40
1948 2084 1.849039 ACTCATCTGGAATTCCCTGGG 59.151 52.381 21.90 17.39 34.88 4.45
1954 2090 1.001393 GGAATTCCCTGGGCGTGAA 60.001 57.895 14.03 0.00 0.00 3.18
2018 2154 0.786435 ATTCCCAAAGGTGCCCTCTT 59.214 50.000 0.00 0.00 30.89 2.85
2030 2166 1.004745 TGCCCTCTTTTCTCATGTCCC 59.995 52.381 0.00 0.00 0.00 4.46
2084 2220 7.757526 TCGTGGATTAAATGTATTGTTCTTGG 58.242 34.615 0.00 0.00 0.00 3.61
2085 2221 6.472163 CGTGGATTAAATGTATTGTTCTTGGC 59.528 38.462 0.00 0.00 0.00 4.52
2171 2307 3.228188 ACAGAAACATCAAAGGCTGGA 57.772 42.857 0.00 0.00 0.00 3.86
2216 2352 5.086104 TCCCACTCTAGCTGAATAAACAC 57.914 43.478 0.00 0.00 0.00 3.32
2218 2354 4.192317 CCACTCTAGCTGAATAAACACCC 58.808 47.826 0.00 0.00 0.00 4.61
2237 2373 4.698304 CACCCGTGTAACCATTTATCTTGT 59.302 41.667 0.00 0.00 0.00 3.16
2238 2374 4.698304 ACCCGTGTAACCATTTATCTTGTG 59.302 41.667 0.00 0.00 0.00 3.33
2249 2385 6.183360 ACCATTTATCTTGTGCCTTCTTATGC 60.183 38.462 0.00 0.00 0.00 3.14
2281 2417 9.869844 CAGAGTTGCTTATATATAACAACTTGC 57.130 33.333 29.49 23.60 40.44 4.01
2285 2421 6.655062 TGCTTATATATAACAACTTGCGCAC 58.345 36.000 11.12 0.00 0.00 5.34
2308 2444 6.634436 CACTCTCTTGTAAGCAATTGTGAAAC 59.366 38.462 7.40 1.81 33.65 2.78
2337 2473 4.285807 TGTTGTTTGATTCGAGGTTGTG 57.714 40.909 0.00 0.00 0.00 3.33
2403 2540 5.246307 GGTAATCGGGAATTCTGGGATTAG 58.754 45.833 18.20 0.00 32.13 1.73
2409 2546 4.338400 CGGGAATTCTGGGATTAGGAAAAC 59.662 45.833 5.23 0.00 0.00 2.43
2432 2569 6.337356 ACGTATTATTTGCTTTTGGAATGGG 58.663 36.000 0.00 0.00 0.00 4.00
2463 2600 6.859715 GCATAAACTCATGCTACTTTGTTG 57.140 37.500 0.92 0.00 46.35 3.33
2464 2601 6.381801 GCATAAACTCATGCTACTTTGTTGT 58.618 36.000 0.92 0.00 46.35 3.32
2466 2603 7.061094 GCATAAACTCATGCTACTTTGTTGTTC 59.939 37.037 0.92 0.00 46.35 3.18
2467 2604 6.699575 AAACTCATGCTACTTTGTTGTTCT 57.300 33.333 0.00 0.00 0.00 3.01
2469 2606 6.305693 ACTCATGCTACTTTGTTGTTCTTC 57.694 37.500 0.00 0.00 0.00 2.87
2483 2625 0.386858 TTCTTCGCGAGAACTGGACG 60.387 55.000 9.59 0.00 46.92 4.79
2523 2665 5.121454 GTCAAAAGAGTAGCTGTTGGAGATG 59.879 44.000 0.00 0.00 41.38 2.90
2537 2679 7.654022 TGTTGGAGATGTACATATGACAGTA 57.346 36.000 7.92 0.00 0.00 2.74
2540 2682 5.154932 GGAGATGTACATATGACAGTACGC 58.845 45.833 7.92 7.20 42.62 4.42
2560 2702 4.642885 ACGCTCAGAAAAGATCTAGTAGCT 59.357 41.667 0.00 0.00 36.32 3.32
2566 2708 7.030165 TCAGAAAAGATCTAGTAGCTTGTTCG 58.970 38.462 0.00 0.00 36.32 3.95
2604 2746 7.396623 TGAAATATTACGGGGGTACACAAAAAT 59.603 33.333 0.00 0.00 0.00 1.82
2774 2916 3.877450 GGCCCGCCTGATCATGGA 61.877 66.667 13.48 0.00 0.00 3.41
2874 3016 5.462068 TGACTTGAGAACTGATGTTAACACG 59.538 40.000 11.22 5.19 36.39 4.49
2984 3243 9.357161 ACCATGTTGTTTCCTACTTTATTTGTA 57.643 29.630 0.00 0.00 0.00 2.41
3036 3295 8.903820 AGCAACAGAAGGGTCATATTTAAATAC 58.096 33.333 10.07 0.82 0.00 1.89
3057 3316 9.777297 AAATACCAGCAATGTGACTTTTTAATT 57.223 25.926 0.00 0.00 0.00 1.40
3059 3318 9.777297 ATACCAGCAATGTGACTTTTTAATTTT 57.223 25.926 0.00 0.00 0.00 1.82
3060 3319 8.504812 ACCAGCAATGTGACTTTTTAATTTTT 57.495 26.923 0.00 0.00 0.00 1.94
3106 3365 0.107456 ATATTCTCGCCTGTGCCTGG 59.893 55.000 0.00 0.00 0.00 4.45
3138 3398 1.693606 TGTCAGAGTTGGACATGCTCA 59.306 47.619 0.00 0.00 40.16 4.26
3158 3418 7.290061 TGCTCACTGAATAAAATTATAGGCCT 58.710 34.615 11.78 11.78 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.507140 CAAGGTGGGTATAGGCTGGA 58.493 55.000 0.00 0.00 0.00 3.86
1 2 0.474184 CCAAGGTGGGTATAGGCTGG 59.526 60.000 0.00 0.00 32.67 4.85
8 9 2.021441 TGGGATAGACCAAGGTGGGTAT 60.021 50.000 0.00 0.00 43.37 2.73
42 43 5.549228 AGATCATGGTGCAAATAGGATAGGA 59.451 40.000 0.00 0.00 0.00 2.94
43 44 5.813383 AGATCATGGTGCAAATAGGATAGG 58.187 41.667 0.00 0.00 0.00 2.57
63 71 4.101741 GGAGCAACATGGGTAAGTAGAGAT 59.898 45.833 0.00 0.00 0.00 2.75
68 76 2.270858 TGGGAGCAACATGGGTAAGTA 58.729 47.619 0.00 0.00 0.00 2.24
75 83 1.080569 GCGTTTGGGAGCAACATGG 60.081 57.895 0.00 0.00 0.00 3.66
79 87 0.102300 AAACAGCGTTTGGGAGCAAC 59.898 50.000 5.99 0.00 35.48 4.17
80 88 0.102120 CAAACAGCGTTTGGGAGCAA 59.898 50.000 19.67 0.00 35.48 3.91
82 90 0.102300 AACAAACAGCGTTTGGGAGC 59.898 50.000 26.31 0.00 33.92 4.70
83 91 2.099098 AGAAACAAACAGCGTTTGGGAG 59.901 45.455 26.31 11.07 36.72 4.30
84 92 2.096248 AGAAACAAACAGCGTTTGGGA 58.904 42.857 26.31 0.00 36.72 4.37
85 93 2.577449 AGAAACAAACAGCGTTTGGG 57.423 45.000 26.31 11.83 36.72 4.12
135 145 2.159667 TGAAATGCATGCGACTTTCTCG 60.160 45.455 26.67 0.00 45.97 4.04
149 159 3.319122 AGGTGTTTCCTGAACTGAAATGC 59.681 43.478 0.00 0.00 46.19 3.56
160 170 9.218440 AATTATGCAATTTTAAGGTGTTTCCTG 57.782 29.630 0.00 0.00 37.58 3.86
162 172 9.213799 TGAATTATGCAATTTTAAGGTGTTTCC 57.786 29.630 0.00 0.00 34.44 3.13
184 196 5.483685 TTGGCAGTAGTAACAGTCTGAAT 57.516 39.130 6.91 0.00 0.00 2.57
186 198 4.526650 TGATTGGCAGTAGTAACAGTCTGA 59.473 41.667 6.91 0.00 0.00 3.27
208 220 3.270877 CTTTTATGACCCTCCGGACTTG 58.729 50.000 0.00 0.00 0.00 3.16
214 226 7.441458 CCTTAATTCTACTTTTATGACCCTCCG 59.559 40.741 0.00 0.00 0.00 4.63
219 231 6.831868 TGCCCCTTAATTCTACTTTTATGACC 59.168 38.462 0.00 0.00 0.00 4.02
228 240 4.307259 TCTGGATGCCCCTTAATTCTACT 58.693 43.478 0.00 0.00 35.38 2.57
314 326 2.045340 GGGTGGACATGTTCGGGG 60.045 66.667 0.00 0.00 0.00 5.73
433 460 4.415150 ATCCAGGTGCGGTGGCTG 62.415 66.667 0.00 0.00 40.82 4.85
436 463 2.124983 CTCATCCAGGTGCGGTGG 60.125 66.667 0.00 0.00 36.28 4.61
437 464 1.976132 ATCCTCATCCAGGTGCGGTG 61.976 60.000 0.00 0.00 43.95 4.94
500 527 2.045536 GTTGGAGAGCCTGCAGGG 60.046 66.667 33.46 15.81 32.58 4.45
686 722 4.089757 TCTCCTCCCCTTCCCCGG 62.090 72.222 0.00 0.00 0.00 5.73
840 898 3.394836 ACTCTGGGCTTCCTCGGC 61.395 66.667 0.00 0.00 0.00 5.54
841 899 2.581354 CACTCTGGGCTTCCTCGG 59.419 66.667 0.00 0.00 0.00 4.63
842 900 2.125350 GCACTCTGGGCTTCCTCG 60.125 66.667 0.00 0.00 0.00 4.63
845 903 0.613012 AATTGGCACTCTGGGCTTCC 60.613 55.000 0.00 0.00 0.00 3.46
910 976 3.599285 CTGCCACGCGGGGTTAGAA 62.599 63.158 31.19 8.97 37.04 2.10
946 1012 3.733337 CTCTCACTACTGCTTGGTTTGT 58.267 45.455 0.00 0.00 0.00 2.83
955 1021 2.580867 CGCCGCTCTCACTACTGC 60.581 66.667 0.00 0.00 0.00 4.40
981 1047 4.144727 TCCTCCTCCTCCTCCGCC 62.145 72.222 0.00 0.00 0.00 6.13
982 1048 2.366153 ATCTCCTCCTCCTCCTCCGC 62.366 65.000 0.00 0.00 0.00 5.54
983 1049 0.539438 CATCTCCTCCTCCTCCTCCG 60.539 65.000 0.00 0.00 0.00 4.63
984 1050 0.856982 TCATCTCCTCCTCCTCCTCC 59.143 60.000 0.00 0.00 0.00 4.30
985 1051 1.817740 CGTCATCTCCTCCTCCTCCTC 60.818 61.905 0.00 0.00 0.00 3.71
986 1052 0.184933 CGTCATCTCCTCCTCCTCCT 59.815 60.000 0.00 0.00 0.00 3.69
987 1053 0.825840 CCGTCATCTCCTCCTCCTCC 60.826 65.000 0.00 0.00 0.00 4.30
988 1054 0.825840 CCCGTCATCTCCTCCTCCTC 60.826 65.000 0.00 0.00 0.00 3.71
989 1055 1.231641 CCCGTCATCTCCTCCTCCT 59.768 63.158 0.00 0.00 0.00 3.69
990 1056 1.834822 CCCCGTCATCTCCTCCTCC 60.835 68.421 0.00 0.00 0.00 4.30
991 1057 0.397254 TTCCCCGTCATCTCCTCCTC 60.397 60.000 0.00 0.00 0.00 3.71
1313 1380 3.204467 TTCCCCGCCTTGTCCTTGG 62.204 63.158 0.00 0.00 0.00 3.61
1314 1381 1.675641 CTTCCCCGCCTTGTCCTTG 60.676 63.158 0.00 0.00 0.00 3.61
1397 1532 5.126061 ACAATCATTCACCAGCCACTAAATC 59.874 40.000 0.00 0.00 0.00 2.17
1405 1540 0.889994 TGCACAATCATTCACCAGCC 59.110 50.000 0.00 0.00 0.00 4.85
1512 1647 3.330267 CTTCCTCTTCTTCTTTCCACCG 58.670 50.000 0.00 0.00 0.00 4.94
1590 1725 5.297776 TCACTTCTTCCTTTTCTGCTTCTTG 59.702 40.000 0.00 0.00 0.00 3.02
1619 1754 2.947652 CAGGACACATCAAATGGCTAGG 59.052 50.000 0.00 0.00 33.60 3.02
1623 1758 1.549203 ACCAGGACACATCAAATGGC 58.451 50.000 0.00 0.00 31.04 4.40
1633 1768 0.400594 AGCCAGGTAAACCAGGACAC 59.599 55.000 14.34 0.00 44.73 3.67
1645 1780 1.379443 TACACGATCCGAGCCAGGT 60.379 57.895 0.00 0.00 0.00 4.00
1647 1782 1.299468 GCTACACGATCCGAGCCAG 60.299 63.158 0.00 0.00 0.00 4.85
1666 1801 7.912383 AGAAACAAAACAAATTGATGCAGAAG 58.088 30.769 0.00 0.00 34.38 2.85
1669 1804 8.767085 ACATAGAAACAAAACAAATTGATGCAG 58.233 29.630 0.00 0.00 34.38 4.41
1679 1814 5.105146 ACCAGGCAACATAGAAACAAAACAA 60.105 36.000 0.00 0.00 41.41 2.83
1680 1815 4.404073 ACCAGGCAACATAGAAACAAAACA 59.596 37.500 0.00 0.00 41.41 2.83
1681 1816 4.744631 CACCAGGCAACATAGAAACAAAAC 59.255 41.667 0.00 0.00 41.41 2.43
1720 1855 5.926542 TCACTTGAAGCAAGATACTGTGTAC 59.073 40.000 13.56 0.00 43.42 2.90
1725 1860 4.634883 AGCATCACTTGAAGCAAGATACTG 59.365 41.667 13.56 2.35 43.42 2.74
1764 1899 3.006859 AGCATTTGCCCTAGTTCCAAAAC 59.993 43.478 0.00 0.00 43.38 2.43
1769 1904 2.426842 AGAGCATTTGCCCTAGTTCC 57.573 50.000 0.00 0.00 43.38 3.62
1778 1913 3.804873 GCCTACTACACTAGAGCATTTGC 59.195 47.826 0.00 0.00 42.49 3.68
1858 1994 7.122501 TGTCTGCAACCAATGACACAATATATT 59.877 33.333 0.44 0.00 34.94 1.28
1863 1999 2.957680 TGTCTGCAACCAATGACACAAT 59.042 40.909 0.44 0.00 34.94 2.71
1948 2084 3.245048 CACCAAATTTGACCTTTTCACGC 59.755 43.478 19.86 0.00 32.26 5.34
1954 2090 8.428063 TCAACAATATCACCAAATTTGACCTTT 58.572 29.630 19.86 3.04 0.00 3.11
2018 2154 5.485353 AGTTCACATAGAGGGACATGAGAAA 59.515 40.000 0.00 0.00 34.82 2.52
2074 2210 2.228822 CCGCTACAAAGCCAAGAACAAT 59.771 45.455 0.00 0.00 46.68 2.71
2084 2220 2.080286 TGACTCTTCCGCTACAAAGC 57.920 50.000 0.00 0.00 45.86 3.51
2085 2221 4.142816 CCAAATGACTCTTCCGCTACAAAG 60.143 45.833 0.00 0.00 0.00 2.77
2171 2307 2.670148 GGAGACCGGGCCTTGATGT 61.670 63.158 1.76 0.00 0.00 3.06
2182 2318 2.232298 GAGTGGGAAGCTGGAGACCG 62.232 65.000 0.00 0.00 0.00 4.79
2216 2352 4.438200 GCACAAGATAAATGGTTACACGGG 60.438 45.833 0.00 0.00 0.00 5.28
2218 2354 4.394920 AGGCACAAGATAAATGGTTACACG 59.605 41.667 0.00 0.00 0.00 4.49
2237 2373 4.898265 ACTCTGATCTAGCATAAGAAGGCA 59.102 41.667 0.00 0.00 33.96 4.75
2238 2374 5.467035 ACTCTGATCTAGCATAAGAAGGC 57.533 43.478 0.00 0.00 0.00 4.35
2277 2413 1.127582 GCTTACAAGAGAGTGCGCAAG 59.872 52.381 14.00 2.19 43.44 4.01
2281 2417 3.187227 ACAATTGCTTACAAGAGAGTGCG 59.813 43.478 5.05 0.00 39.69 5.34
2285 2421 5.848036 CGTTTCACAATTGCTTACAAGAGAG 59.152 40.000 5.05 0.00 39.69 3.20
2308 2444 7.461107 ACCTCGAATCAAACAACAATATAACG 58.539 34.615 0.00 0.00 0.00 3.18
2337 2473 4.911514 TTAGGGAAGCAAAACAGAACAC 57.088 40.909 0.00 0.00 0.00 3.32
2377 2513 2.108250 CCCAGAATTCCCGATTACCCAT 59.892 50.000 0.65 0.00 0.00 4.00
2386 2523 3.857157 TTCCTAATCCCAGAATTCCCG 57.143 47.619 0.65 0.00 0.00 5.14
2403 2540 7.876896 TCCAAAAGCAAATAATACGTTTTCC 57.123 32.000 0.00 0.00 0.00 3.13
2409 2546 6.568869 TCCCATTCCAAAAGCAAATAATACG 58.431 36.000 0.00 0.00 0.00 3.06
2464 2601 0.386858 CGTCCAGTTCTCGCGAAGAA 60.387 55.000 11.33 13.22 41.81 2.52
2466 2603 0.663568 AACGTCCAGTTCTCGCGAAG 60.664 55.000 11.33 4.62 39.16 3.79
2467 2604 0.592637 TAACGTCCAGTTCTCGCGAA 59.407 50.000 11.33 0.00 43.06 4.70
2469 2606 1.625616 AATAACGTCCAGTTCTCGCG 58.374 50.000 0.00 0.00 43.06 5.87
2523 2665 5.419760 TCTGAGCGTACTGTCATATGTAC 57.580 43.478 1.90 0.80 36.59 2.90
2537 2679 4.642885 AGCTACTAGATCTTTTCTGAGCGT 59.357 41.667 0.00 0.00 39.30 5.07
2540 2682 7.219917 CGAACAAGCTACTAGATCTTTTCTGAG 59.780 40.741 0.00 0.00 35.79 3.35
2560 2702 1.021202 CAGCTTGAACACCCGAACAA 58.979 50.000 0.00 0.00 0.00 2.83
2566 2708 5.448632 CCGTAATATTTCAGCTTGAACACCC 60.449 44.000 0.00 0.00 35.89 4.61
2604 2746 4.851540 TCCATATGGATCAAGGCCTTCATA 59.148 41.667 20.98 19.59 39.78 2.15
2905 3048 4.898320 AGTACTGCAACTGACATCAATCA 58.102 39.130 0.00 0.00 0.00 2.57
2907 3050 6.000219 AGAAAGTACTGCAACTGACATCAAT 59.000 36.000 0.00 0.00 0.00 2.57
3011 3270 8.135529 GGTATTTAAATATGACCCTTCTGTTGC 58.864 37.037 11.00 0.00 0.00 4.17
3021 3280 8.629158 TCACATTGCTGGTATTTAAATATGACC 58.371 33.333 11.00 10.73 0.00 4.02
3022 3281 9.450807 GTCACATTGCTGGTATTTAAATATGAC 57.549 33.333 11.00 12.27 0.00 3.06
3060 3319 8.842280 CACTATAAGTTGGTACTTGGTGAAAAA 58.158 33.333 0.00 0.00 44.22 1.94
3071 3330 7.541437 GGCGAGAATATCACTATAAGTTGGTAC 59.459 40.741 0.00 0.00 0.00 3.34
3106 3365 4.321230 CCAACTCTGACAAATTGGGTTAGC 60.321 45.833 0.00 0.00 38.36 3.09


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

AutoCloner maintained by Alex Coulton.