Multiple sequence alignment - TraesCS6A01G234000

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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 TraesCS6A01G234000 chr6A 100.000 3806 0 0 1 3806 441502656 441498851 0.000000e+00 7029.0
1 TraesCS6A01G234000 chr6A 96.341 82 3 0 1199 1280 441501419 441501338 6.630000e-28 135.0
2 TraesCS6A01G234000 chr6A 96.341 82 3 0 1238 1319 441501458 441501377 6.630000e-28 135.0
3 TraesCS6A01G234000 chr6A 95.349 43 2 0 1199 1241 441501380 441501338 6.820000e-08 69.4
4 TraesCS6A01G234000 chr6A 95.349 43 2 0 1277 1319 441501458 441501416 6.820000e-08 69.4
5 TraesCS6A01G234000 chr6D 94.357 3491 165 19 1 3483 306140627 306137161 0.000000e+00 5326.0
6 TraesCS6A01G234000 chr6D 87.768 327 28 4 3484 3806 306137105 306136787 4.640000e-99 372.0
7 TraesCS6A01G234000 chr6D 95.122 82 4 0 1199 1280 306139406 306139325 3.090000e-26 130.0
8 TraesCS6A01G234000 chr6D 95.122 82 4 0 1238 1319 306139445 306139364 3.090000e-26 130.0
9 TraesCS6A01G234000 chr6D 95.349 43 2 0 1199 1241 306139367 306139325 6.820000e-08 69.4
10 TraesCS6A01G234000 chr6D 95.349 43 2 0 1277 1319 306139445 306139403 6.820000e-08 69.4
11 TraesCS6A01G234000 chr6B 94.937 2785 115 7 720 3483 473070049 473067270 0.000000e+00 4338.0
12 TraesCS6A01G234000 chr6B 87.569 362 30 11 228 584 473070762 473070411 4.580000e-109 405.0
13 TraesCS6A01G234000 chr6B 92.222 180 13 1 3484 3662 473067202 473067023 1.750000e-63 254.0
14 TraesCS6A01G234000 chr6B 84.483 232 22 7 1 232 473074903 473074686 2.300000e-52 217.0
15 TraesCS6A01G234000 chr6B 86.111 144 14 3 3667 3806 473062921 473062780 2.370000e-32 150.0
16 TraesCS6A01G234000 chr6B 95.122 82 4 0 1199 1280 473069531 473069450 3.090000e-26 130.0
17 TraesCS6A01G234000 chr6B 93.902 82 4 1 1238 1319 473069570 473069490 5.160000e-24 122.0
18 TraesCS6A01G234000 chr6B 95.238 42 2 0 1200 1241 473069491 473069450 2.450000e-07 67.6
19 TraesCS6A01G234000 chr6B 93.023 43 3 0 1277 1319 473069570 473069528 3.170000e-06 63.9
20 TraesCS6A01G234000 chr5A 98.795 83 1 0 3249 3331 510463983 510463901 8.520000e-32 148.0
21 TraesCS6A01G234000 chr5A 97.590 83 2 0 3249 3331 510464098 510464180 3.960000e-30 143.0
22 TraesCS6A01G234000 chr7D 98.780 82 1 0 3249 3330 252062995 252063076 3.060000e-31 147.0
23 TraesCS6A01G234000 chr7B 97.647 85 2 0 3247 3331 228827639 228827723 3.060000e-31 147.0
24 TraesCS6A01G234000 chr5D 98.765 81 1 0 3252 3332 402976802 402976882 1.100000e-30 145.0
25 TraesCS6A01G234000 chr5D 98.734 79 1 0 3252 3330 402976694 402976616 1.430000e-29 141.0
26 TraesCS6A01G234000 chr7A 98.750 80 1 0 3251 3330 269102297 269102218 3.960000e-30 143.0


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 TraesCS6A01G234000 chr6A 441498851 441502656 3805 True 1487.560000 7029 96.6760 1 3806 5 chr6A.!!$R1 3805
1 TraesCS6A01G234000 chr6D 306136787 306140627 3840 True 1016.133333 5326 93.8445 1 3806 6 chr6D.!!$R1 3805
2 TraesCS6A01G234000 chr6B 473067023 473074903 7880 True 699.687500 4338 92.0620 1 3662 8 chr6B.!!$R2 3661

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
552 4486 0.898326 CTACCCAAACCCCAACCAGC 60.898 60.0 0.0 0.0 0.0 4.85 F
1156 5316 0.034337 GCGGGGTAGTCAAACTGTCA 59.966 55.0 0.0 0.0 0.0 3.58 F
2085 6245 0.037326 CACTTGCTAGGCGGTCTGAA 60.037 55.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1440 5600 0.179124 AAGCCTCGTCGATCTTCAGC 60.179 55.0 0.0 0.0 0.00 4.26 R
2580 6740 0.517316 GGTTGATCACAAGGTCGCAC 59.483 55.0 0.0 0.0 36.64 5.34 R
3664 7916 0.034059 CCTCTCTCTGCCACAACGTT 59.966 55.0 0.0 0.0 0.00 3.99 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
54 55 2.186903 CACTGGCGGCGGTAAGAT 59.813 61.111 24.40 0.00 0.00 2.40
60 61 1.144496 GCGGCGGTAAGATGGGTTA 59.856 57.895 9.78 0.00 0.00 2.85
69 70 2.588034 GATGGGTTAGCGACGGGC 60.588 66.667 0.00 0.00 44.05 6.13
82 83 4.162690 CGGGCAGTGGCTAGGGTC 62.163 72.222 17.16 0.00 40.87 4.46
91 92 2.439883 GCTAGGGTCCGGTCGACT 60.440 66.667 16.46 0.11 41.64 4.18
106 107 2.203640 ACTGCCTCGACCCTGTCA 60.204 61.111 0.00 0.00 32.09 3.58
107 108 2.219325 GACTGCCTCGACCCTGTCAG 62.219 65.000 10.71 0.00 32.09 3.51
142 143 7.009815 AGGTTTATGTGTGTTATGTTATCGTCG 59.990 37.037 0.00 0.00 0.00 5.12
143 144 7.201461 GGTTTATGTGTGTTATGTTATCGTCGT 60.201 37.037 0.00 0.00 0.00 4.34
144 145 5.944049 ATGTGTGTTATGTTATCGTCGTC 57.056 39.130 0.00 0.00 0.00 4.20
162 163 3.119065 TCGTCGAATATGTTACCTTGGCA 60.119 43.478 0.00 0.00 0.00 4.92
213 214 8.865090 ACCATGATCAATACAAGGTTGTTTAAA 58.135 29.630 0.00 0.00 42.35 1.52
225 226 4.966168 AGGTTGTTTAAACCCTTCCACATT 59.034 37.500 15.59 0.00 41.18 2.71
232 4161 4.600692 AAACCCTTCCACATTTGCTTAC 57.399 40.909 0.00 0.00 0.00 2.34
249 4178 4.724697 CGCAGGCGTCAACAAGCG 62.725 66.667 5.34 0.00 39.17 4.68
336 4268 4.037222 TGGACCTTGAGCCATTATCTACA 58.963 43.478 0.00 0.00 0.00 2.74
343 4275 8.754080 ACCTTGAGCCATTATCTACATCTATAC 58.246 37.037 0.00 0.00 0.00 1.47
376 4308 8.609478 TCGTGAGAAGAAAAACATTGTAAAAC 57.391 30.769 0.00 0.00 37.03 2.43
456 4389 2.225267 ACCGTCAAAAATCCATCCCCTT 60.225 45.455 0.00 0.00 0.00 3.95
457 4390 3.010808 ACCGTCAAAAATCCATCCCCTTA 59.989 43.478 0.00 0.00 0.00 2.69
458 4391 3.632145 CCGTCAAAAATCCATCCCCTTAG 59.368 47.826 0.00 0.00 0.00 2.18
459 4392 4.523083 CGTCAAAAATCCATCCCCTTAGA 58.477 43.478 0.00 0.00 0.00 2.10
460 4393 4.576463 CGTCAAAAATCCATCCCCTTAGAG 59.424 45.833 0.00 0.00 0.00 2.43
461 4394 4.339530 GTCAAAAATCCATCCCCTTAGAGC 59.660 45.833 0.00 0.00 0.00 4.09
462 4395 4.017591 TCAAAAATCCATCCCCTTAGAGCA 60.018 41.667 0.00 0.00 0.00 4.26
465 4398 2.568546 TCCATCCCCTTAGAGCAAGA 57.431 50.000 0.00 0.00 36.22 3.02
466 4399 3.066208 TCCATCCCCTTAGAGCAAGAT 57.934 47.619 0.00 0.00 36.22 2.40
552 4486 0.898326 CTACCCAAACCCCAACCAGC 60.898 60.000 0.00 0.00 0.00 4.85
591 4525 2.125229 CAGTCCAGCAGCATCGCT 60.125 61.111 0.00 0.00 45.21 4.93
603 4537 1.153489 CATCGCTGTGACCTGGAGG 60.153 63.158 0.00 0.00 42.17 4.30
604 4538 3.023949 ATCGCTGTGACCTGGAGGC 62.024 63.158 0.00 0.00 39.32 4.70
605 4539 3.699894 CGCTGTGACCTGGAGGCT 61.700 66.667 0.00 0.00 39.32 4.58
606 4540 2.046507 GCTGTGACCTGGAGGCTG 60.047 66.667 0.00 0.00 39.32 4.85
607 4541 2.667418 CTGTGACCTGGAGGCTGG 59.333 66.667 0.00 0.00 39.32 4.85
608 4542 1.915266 CTGTGACCTGGAGGCTGGA 60.915 63.158 0.00 0.00 39.32 3.86
609 4543 1.897225 CTGTGACCTGGAGGCTGGAG 61.897 65.000 0.00 0.00 39.32 3.86
610 4544 3.005539 TGACCTGGAGGCTGGAGC 61.006 66.667 0.00 0.00 39.32 4.70
632 4566 2.047560 GCCGTCCGGTAGCTTTGT 60.048 61.111 7.66 0.00 37.65 2.83
688 4622 4.452733 CCAGAACCCTCCCGCGTC 62.453 72.222 4.92 0.00 0.00 5.19
715 4649 4.035102 GCCGTCCCCTTTCTGCCT 62.035 66.667 0.00 0.00 0.00 4.75
737 4897 2.890474 CCCGTTCTCAATCCCGCG 60.890 66.667 0.00 0.00 0.00 6.46
870 5030 1.208706 TTTGTGACTCACCTGACCCA 58.791 50.000 6.72 0.00 32.73 4.51
1071 5231 3.057969 TCTCGGTCATGCTTTGTCATT 57.942 42.857 0.00 0.00 0.00 2.57
1102 5262 0.389817 CCCGTTCAGAATGCTGTCGA 60.390 55.000 17.76 0.00 42.84 4.20
1156 5316 0.034337 GCGGGGTAGTCAAACTGTCA 59.966 55.000 0.00 0.00 0.00 3.58
1254 5414 3.258872 TGCCACAAAGCAAAGCTGATTAT 59.741 39.130 0.00 0.00 40.56 1.28
1271 5431 6.387192 TGATTATGTGAAGAAGGAAAGGGA 57.613 37.500 0.00 0.00 0.00 4.20
1325 5485 3.319198 GGGGCCACGAACTGGAGA 61.319 66.667 4.39 0.00 43.95 3.71
1352 5512 2.015587 GCCAAGCTCAAGAGATTCTGG 58.984 52.381 0.32 1.58 34.42 3.86
1410 5570 1.669115 GAAGCCAGCGAAGAGTGCA 60.669 57.895 0.00 0.00 33.85 4.57
1473 5633 3.174375 CGAGGCTTTATTTTCTGCAAGC 58.826 45.455 0.00 0.00 40.85 4.01
1611 5771 6.706295 TGATGCGGTTATCCAATCATATACA 58.294 36.000 2.45 0.00 33.96 2.29
1629 5789 0.605589 CAGGGTCGGGGAAAACACTC 60.606 60.000 0.00 0.00 0.00 3.51
1779 5939 3.357203 AGTGCGAGAAGTGGAGAAGATA 58.643 45.455 0.00 0.00 0.00 1.98
1896 6056 2.203294 GTTGGAACACCTGGCCGT 60.203 61.111 0.00 0.00 39.29 5.68
1920 6080 2.202610 GAAATTTCAGCGGCGGGC 60.203 61.111 13.40 0.00 44.05 6.13
1935 6095 0.517316 CGGGCAAGCTACAAACTCAC 59.483 55.000 0.00 0.00 0.00 3.51
1983 6143 6.240894 TGAAGTTGACCAGCTCTTATCATTT 58.759 36.000 0.00 0.00 0.00 2.32
1992 6152 6.204882 ACCAGCTCTTATCATTTAATTACCGC 59.795 38.462 0.00 0.00 0.00 5.68
2064 6224 3.895232 TCTTCTAGTCACATCCTTGGC 57.105 47.619 0.00 0.00 0.00 4.52
2085 6245 0.037326 CACTTGCTAGGCGGTCTGAA 60.037 55.000 0.00 0.00 0.00 3.02
2133 6293 2.414138 AGTGCCGTTTTCAGTTATACGC 59.586 45.455 0.00 0.00 32.97 4.42
2292 6452 1.882912 CTGCAGTTGACAGCTTACCA 58.117 50.000 5.25 0.00 0.00 3.25
2298 6458 2.084546 GTTGACAGCTTACCACCATCC 58.915 52.381 0.00 0.00 0.00 3.51
2430 6590 2.030805 GCCACTGAAGGATGTTGTGTTC 60.031 50.000 0.00 0.00 0.00 3.18
2502 6662 1.312815 AGCTTGCAAGGTCAACAGTC 58.687 50.000 24.96 6.09 29.15 3.51
2505 6665 1.605710 CTTGCAAGGTCAACAGTCCTG 59.394 52.381 19.14 0.00 33.97 3.86
2520 6680 2.959030 AGTCCTGAAAAAGTTCAAGGCC 59.041 45.455 0.00 0.00 43.18 5.19
2536 6696 0.898326 GGCCGGTGAATTCAGGGTTT 60.898 55.000 20.85 0.00 0.00 3.27
2556 6716 0.464036 TGGTCACAAACGAGCTGTCT 59.536 50.000 0.00 0.00 34.46 3.41
2622 6782 3.245622 TGGATCTTCCCACAGACTCTACA 60.246 47.826 0.00 0.00 35.03 2.74
2643 6803 2.283604 TACGCCCACAGAGCTGGA 60.284 61.111 0.00 0.00 32.30 3.86
2697 6857 6.017933 CGTTGTCTCAATATGTGAAGAAAGC 58.982 40.000 0.00 0.00 35.22 3.51
2748 6908 0.105760 AGTTGGGTGTGGCCATCAAA 60.106 50.000 9.72 0.00 39.65 2.69
2808 6968 8.893727 CATAAAGAGGAAGACGTGGAATAAAAT 58.106 33.333 0.00 0.00 0.00 1.82
2815 6975 4.250464 AGACGTGGAATAAAATTCTGCGA 58.750 39.130 16.64 0.00 0.00 5.10
2828 6988 6.741992 AAATTCTGCGATGTTCAACTATCA 57.258 33.333 0.00 0.00 0.00 2.15
3011 7175 9.965824 TTGAAATCTGAAAATTACCAGTCTTTC 57.034 29.630 17.90 17.90 35.83 2.62
3033 7197 3.185797 CCTGGTGACGTTTAGCTGTTTAC 59.814 47.826 0.00 0.00 0.00 2.01
3042 7206 8.828644 TGACGTTTAGCTGTTTACTTTTCAATA 58.171 29.630 0.00 0.00 0.00 1.90
3089 7253 3.252554 TGTTTTGGTGCCCCTCTTATT 57.747 42.857 0.00 0.00 0.00 1.40
3096 7260 4.464262 CCCCTCTTATTGAGCGGC 57.536 61.111 0.00 0.00 41.35 6.53
3102 7266 0.036483 TCTTATTGAGCGGCACTGCA 60.036 50.000 1.45 0.00 37.31 4.41
3122 7286 5.748402 TGCAATTTGTGAGATGACTCCTAT 58.252 37.500 0.00 0.00 41.99 2.57
3128 7292 6.737720 TTGTGAGATGACTCCTATAATGCT 57.262 37.500 0.00 0.00 41.99 3.79
3129 7293 6.094193 TGTGAGATGACTCCTATAATGCTG 57.906 41.667 0.00 0.00 41.99 4.41
3131 7295 5.925397 GTGAGATGACTCCTATAATGCTGTG 59.075 44.000 0.00 0.00 41.99 3.66
3132 7296 5.835280 TGAGATGACTCCTATAATGCTGTGA 59.165 40.000 0.00 0.00 41.99 3.58
3133 7297 6.095432 AGATGACTCCTATAATGCTGTGAC 57.905 41.667 0.00 0.00 0.00 3.67
3134 7298 4.672587 TGACTCCTATAATGCTGTGACC 57.327 45.455 0.00 0.00 0.00 4.02
3135 7299 4.290093 TGACTCCTATAATGCTGTGACCT 58.710 43.478 0.00 0.00 0.00 3.85
3136 7300 4.716784 TGACTCCTATAATGCTGTGACCTT 59.283 41.667 0.00 0.00 0.00 3.50
3140 7304 6.554982 ACTCCTATAATGCTGTGACCTTATGA 59.445 38.462 0.00 0.00 0.00 2.15
3190 7354 2.460757 ATGCGAAAAGGCTTGCAAAT 57.539 40.000 13.76 0.00 41.22 2.32
3197 7361 1.345063 AAGGCTTGCAAATTCCTGCT 58.655 45.000 13.36 0.00 43.07 4.24
3208 7372 4.448732 GCAAATTCCTGCTCATTTTCGTTT 59.551 37.500 0.00 0.00 39.34 3.60
3216 7380 4.109050 TGCTCATTTTCGTTTGTTTGGAC 58.891 39.130 0.00 0.00 0.00 4.02
3235 7399 3.565902 GGACATAAGTAAAGCTGGATGCC 59.434 47.826 0.00 0.00 44.23 4.40
3247 7411 4.929198 GATGCCATCCATTTCGCG 57.071 55.556 0.00 0.00 33.29 5.87
3372 7555 3.490439 TCTCAGCAACACAATCCTTCA 57.510 42.857 0.00 0.00 0.00 3.02
3381 7564 5.702209 GCAACACAATCCTTCAATCCATTTT 59.298 36.000 0.00 0.00 0.00 1.82
3506 7757 4.827284 TCCTTTGGACATTCAGGAAAAGAC 59.173 41.667 0.00 0.00 32.19 3.01
3507 7758 4.320494 CCTTTGGACATTCAGGAAAAGACG 60.320 45.833 0.00 0.00 0.00 4.18
3631 7883 1.067916 GTTGGTGTTGCAGCCTTGG 59.932 57.895 0.00 0.00 0.00 3.61
3632 7884 2.795110 TTGGTGTTGCAGCCTTGGC 61.795 57.895 2.97 2.97 0.00 4.52
3648 7900 1.306296 GGCAAAGCCTGGGGACATA 59.694 57.895 0.00 0.00 46.69 2.29
3661 7913 0.464452 GGACATACCCTCCTGAACCG 59.536 60.000 0.00 0.00 0.00 4.44
3662 7914 1.481871 GACATACCCTCCTGAACCGA 58.518 55.000 0.00 0.00 0.00 4.69
3663 7915 2.040178 GACATACCCTCCTGAACCGAT 58.960 52.381 0.00 0.00 0.00 4.18
3664 7916 3.228453 GACATACCCTCCTGAACCGATA 58.772 50.000 0.00 0.00 0.00 2.92
3665 7917 3.640029 GACATACCCTCCTGAACCGATAA 59.360 47.826 0.00 0.00 0.00 1.75
3666 7918 3.387050 ACATACCCTCCTGAACCGATAAC 59.613 47.826 0.00 0.00 0.00 1.89
3681 7933 2.415491 CGATAACGTTGTGGCAGAGAGA 60.415 50.000 11.99 0.00 34.56 3.10
3695 7947 1.617839 AGAGAGGGGGCCAAAGAGG 60.618 63.158 4.39 0.00 41.84 3.69
3698 7950 2.009302 GAGGGGGCCAAAGAGGGAT 61.009 63.158 4.39 0.00 38.09 3.85
3707 7959 1.547372 CCAAAGAGGGATTGCCAACTG 59.453 52.381 0.00 0.00 35.15 3.16
3715 7967 2.305635 GGGATTGCCAACTGGGATTTTT 59.694 45.455 0.00 0.00 40.01 1.94
3716 7968 3.599343 GGATTGCCAACTGGGATTTTTC 58.401 45.455 0.00 0.00 40.01 2.29
3718 7970 3.749665 TTGCCAACTGGGATTTTTCAG 57.250 42.857 0.00 0.00 40.01 3.02
3721 7973 2.353109 GCCAACTGGGATTTTTCAGAGC 60.353 50.000 0.00 0.00 40.01 4.09
3731 7983 5.106357 GGGATTTTTCAGAGCTTGAGAGTTC 60.106 44.000 0.00 0.00 37.07 3.01
3738 7990 2.230266 AGAGCTTGAGAGTTCGAGTTCC 59.770 50.000 5.38 0.00 42.83 3.62
3745 7997 2.422127 GAGAGTTCGAGTTCCTCCAGAG 59.578 54.545 0.00 0.00 0.00 3.35
3746 7998 2.164338 GAGTTCGAGTTCCTCCAGAGT 58.836 52.381 0.00 0.00 0.00 3.24
3749 8001 3.388350 AGTTCGAGTTCCTCCAGAGTTTT 59.612 43.478 0.00 0.00 0.00 2.43
3764 8020 6.095440 TCCAGAGTTTTGATTATGCTTAAGCC 59.905 38.462 24.30 9.21 41.18 4.35
3792 8048 3.641648 CCATCAAACACAGAAAATGCGT 58.358 40.909 0.00 0.00 0.00 5.24
3793 8049 4.793071 CCATCAAACACAGAAAATGCGTA 58.207 39.130 0.00 0.00 0.00 4.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 4.077184 CTGCCCGTCGCTAACCCA 62.077 66.667 0.00 0.00 38.78 4.51
69 70 2.683933 ACCGGACCCTAGCCACTG 60.684 66.667 9.46 0.00 0.00 3.66
70 71 2.363925 GACCGGACCCTAGCCACT 60.364 66.667 9.46 0.00 0.00 4.00
91 92 2.997315 CCTGACAGGGTCGAGGCA 60.997 66.667 14.26 0.00 34.95 4.75
106 107 2.238521 CACATAAACCTTGGTGTGCCT 58.761 47.619 0.00 0.00 36.01 4.75
107 108 1.960689 ACACATAAACCTTGGTGTGCC 59.039 47.619 4.43 0.00 44.27 5.01
142 143 5.065988 ACAATGCCAAGGTAACATATTCGAC 59.934 40.000 0.00 0.00 41.41 4.20
143 144 5.065859 CACAATGCCAAGGTAACATATTCGA 59.934 40.000 0.00 0.00 41.41 3.71
144 145 5.163663 ACACAATGCCAAGGTAACATATTCG 60.164 40.000 0.00 0.00 41.41 3.34
162 163 1.882912 TGCTCTCGCTTGAACACAAT 58.117 45.000 0.00 0.00 36.97 2.71
213 214 2.159382 CGTAAGCAAATGTGGAAGGGT 58.841 47.619 0.00 0.00 0.00 4.34
232 4161 4.724697 CGCTTGTTGACGCCTGCG 62.725 66.667 10.40 10.40 46.03 5.18
249 4178 4.813235 TGCCATTGGTAGCCCGCC 62.813 66.667 4.26 0.00 0.00 6.13
256 4185 3.509575 GGATGTTTGACTTGCCATTGGTA 59.490 43.478 4.26 0.00 0.00 3.25
307 4238 8.448008 AGATAATGGCTCAAGGTCCATATTTTA 58.552 33.333 0.00 0.00 41.92 1.52
343 4275 9.884465 AATGTTTTTCTTCTCACGAAAAGATAG 57.116 29.630 0.00 0.00 40.30 2.08
456 4389 4.759782 CGGAGAGGAAAAATCTTGCTCTA 58.240 43.478 8.29 0.00 45.29 2.43
458 4391 2.096657 GCGGAGAGGAAAAATCTTGCTC 59.903 50.000 0.00 0.00 37.18 4.26
459 4392 2.087646 GCGGAGAGGAAAAATCTTGCT 58.912 47.619 0.00 0.00 0.00 3.91
460 4393 1.133216 GGCGGAGAGGAAAAATCTTGC 59.867 52.381 0.00 0.00 0.00 4.01
461 4394 2.680339 GAGGCGGAGAGGAAAAATCTTG 59.320 50.000 0.00 0.00 0.00 3.02
462 4395 2.356227 GGAGGCGGAGAGGAAAAATCTT 60.356 50.000 0.00 0.00 0.00 2.40
465 4398 1.210722 GAGGAGGCGGAGAGGAAAAAT 59.789 52.381 0.00 0.00 0.00 1.82
466 4399 0.613777 GAGGAGGCGGAGAGGAAAAA 59.386 55.000 0.00 0.00 0.00 1.94
520 4453 0.909610 TGGGTAGGTCAGGCAGGAAG 60.910 60.000 0.00 0.00 0.00 3.46
521 4454 0.474854 TTGGGTAGGTCAGGCAGGAA 60.475 55.000 0.00 0.00 0.00 3.36
552 4486 1.032114 GGTGAGATTTTGGAGCCGGG 61.032 60.000 2.18 0.00 0.00 5.73
591 4525 1.915266 CTCCAGCCTCCAGGTCACA 60.915 63.158 0.00 0.00 37.57 3.58
622 4556 3.767287 GTGGCGAAACAAAGCTACC 57.233 52.632 0.00 0.00 38.64 3.18
629 4563 3.641986 GCGTCGGTGGCGAAACAA 61.642 61.111 0.00 0.00 0.00 2.83
662 4596 2.991540 GGGTTCTGGGGCTGTTGC 60.992 66.667 0.00 0.00 38.76 4.17
663 4597 1.303643 GAGGGTTCTGGGGCTGTTG 60.304 63.158 0.00 0.00 0.00 3.33
665 4599 2.936032 GGAGGGTTCTGGGGCTGT 60.936 66.667 0.00 0.00 0.00 4.40
666 4600 3.732849 GGGAGGGTTCTGGGGCTG 61.733 72.222 0.00 0.00 0.00 4.85
715 4649 1.559065 GGGATTGAGAACGGGGTGGA 61.559 60.000 0.00 0.00 0.00 4.02
902 5062 1.531602 GCAAGTTCAGGGCAGGGTT 60.532 57.895 0.00 0.00 0.00 4.11
1071 5231 0.834261 TGAACGGGAGATGGTCACCA 60.834 55.000 0.00 0.00 38.19 4.17
1156 5316 4.254709 TGTGCTGCCGCTGTCCTT 62.255 61.111 0.70 0.00 36.97 3.36
1254 5414 1.073923 GGCTCCCTTTCCTTCTTCACA 59.926 52.381 0.00 0.00 0.00 3.58
1271 5431 1.335145 ATCAGCTTTGCTTTGTGGCT 58.665 45.000 0.00 0.00 36.40 4.75
1325 5485 1.673665 CTTGAGCTTGGCTTCGGCT 60.674 57.895 0.00 0.00 39.88 5.52
1410 5570 1.923356 CCACTGGTGGCTTTGGTAAT 58.077 50.000 6.84 0.00 44.73 1.89
1440 5600 0.179124 AAGCCTCGTCGATCTTCAGC 60.179 55.000 0.00 0.00 0.00 4.26
1473 5633 2.928757 CAGACCGAGCTCTTCAAATGAG 59.071 50.000 12.85 0.00 34.87 2.90
1611 5771 1.759236 GAGTGTTTTCCCCGACCCT 59.241 57.895 0.00 0.00 0.00 4.34
1629 5789 1.955080 AGAATAGGGAGAAGGTACGCG 59.045 52.381 3.53 3.53 0.00 6.01
1779 5939 3.964031 GTCTCTTATCATCAGGACCCAGT 59.036 47.826 0.00 0.00 0.00 4.00
1896 6056 2.223157 CGCCGCTGAAATTTCCGAAATA 60.223 45.455 15.48 0.00 0.00 1.40
1920 6080 3.548818 GGCAGTTGTGAGTTTGTAGCTTG 60.549 47.826 0.00 0.00 0.00 4.01
1935 6095 3.548014 CCAGTACAAGAAAACGGCAGTTG 60.548 47.826 2.10 0.00 41.05 3.16
1983 6143 3.945981 TGCATATCCTCGCGGTAATTA 57.054 42.857 6.13 0.00 0.00 1.40
1992 6152 4.889995 TCCAGTATCCTATGCATATCCTCG 59.110 45.833 6.92 0.00 0.00 4.63
2007 6167 3.118261 TCCTTCCAACATGCTCCAGTATC 60.118 47.826 0.00 0.00 0.00 2.24
2019 6179 2.441750 AGTGCTAGGTTTCCTTCCAACA 59.558 45.455 0.00 0.00 34.61 3.33
2064 6224 2.125106 GACCGCCTAGCAAGTGGG 60.125 66.667 5.40 0.00 39.30 4.61
2085 6245 3.804036 TGAAACCAAGATTGTCTGACGT 58.196 40.909 2.98 0.00 0.00 4.34
2292 6452 9.256317 GTACAGTAGTAATGCTCCAAGGATGGT 62.256 44.444 0.00 0.00 38.79 3.55
2298 6458 5.581085 GGTTGTACAGTAGTAATGCTCCAAG 59.419 44.000 0.00 0.00 30.67 3.61
2430 6590 2.672996 CCACGGGCCTCCAACTTG 60.673 66.667 0.84 0.00 0.00 3.16
2502 6662 1.000274 CCGGCCTTGAACTTTTTCAGG 60.000 52.381 0.00 0.00 42.79 3.86
2505 6665 1.679153 TCACCGGCCTTGAACTTTTTC 59.321 47.619 0.00 0.00 0.00 2.29
2520 6680 1.960689 ACCAAAACCCTGAATTCACCG 59.039 47.619 3.38 0.00 0.00 4.94
2536 6696 1.134521 AGACAGCTCGTTTGTGACCAA 60.135 47.619 0.00 0.00 0.00 3.67
2580 6740 0.517316 GGTTGATCACAAGGTCGCAC 59.483 55.000 0.00 0.00 36.64 5.34
2622 6782 1.908793 AGCTCTGTGGGCGTAGTGT 60.909 57.895 0.00 0.00 34.52 3.55
2676 6836 5.478407 TCGCTTTCTTCACATATTGAGACA 58.522 37.500 0.00 0.00 34.94 3.41
2697 6857 5.756195 TTTTCCTCATGATAAATGCCTCG 57.244 39.130 0.00 0.00 0.00 4.63
2733 6893 0.904394 ATGGTTTGATGGCCACACCC 60.904 55.000 8.16 11.31 43.37 4.61
2748 6908 2.086869 CCTTCAGTGAATTCGCATGGT 58.913 47.619 20.55 0.00 0.00 3.55
2808 6968 6.741992 AAATGATAGTTGAACATCGCAGAA 57.258 33.333 0.00 0.00 43.58 3.02
2828 6988 9.946165 GCAGTACAACTTAAGACAAACTAAAAT 57.054 29.630 10.09 0.00 0.00 1.82
2847 7007 2.356665 TGCCAAGGAAAAGCAGTACA 57.643 45.000 0.00 0.00 31.65 2.90
2961 7124 1.026182 TGCACTCCTGCTAAATGCCG 61.026 55.000 0.00 0.00 44.57 5.69
3011 7175 1.878953 AACAGCTAAACGTCACCAGG 58.121 50.000 0.00 0.00 0.00 4.45
3033 7197 9.241317 GCTGAACATCAACCATATATTGAAAAG 57.759 33.333 5.85 3.22 39.43 2.27
3042 7206 4.508551 TCCAGCTGAACATCAACCATAT 57.491 40.909 17.39 0.00 0.00 1.78
3089 7253 1.286570 CAAATTGCAGTGCCGCTCA 59.713 52.632 13.72 0.00 0.00 4.26
3096 7260 4.379186 GGAGTCATCTCACAAATTGCAGTG 60.379 45.833 0.00 0.00 42.05 3.66
3102 7266 8.216423 AGCATTATAGGAGTCATCTCACAAATT 58.784 33.333 0.00 0.00 42.05 1.82
3122 7286 5.744171 ACACATCATAAGGTCACAGCATTA 58.256 37.500 0.00 0.00 0.00 1.90
3128 7292 9.898152 TTCAAATATACACATCATAAGGTCACA 57.102 29.630 0.00 0.00 0.00 3.58
3135 7299 9.179552 GCGCAATTTCAAATATACACATCATAA 57.820 29.630 0.30 0.00 0.00 1.90
3136 7300 7.533561 CGCGCAATTTCAAATATACACATCATA 59.466 33.333 8.75 0.00 0.00 2.15
3140 7304 5.455201 CACGCGCAATTTCAAATATACACAT 59.545 36.000 5.73 0.00 0.00 3.21
3160 7324 0.300491 TTTTCGCATATCTCGCACGC 59.700 50.000 0.00 0.00 0.00 5.34
3174 7338 2.733026 CAGGAATTTGCAAGCCTTTTCG 59.267 45.455 13.08 1.81 0.00 3.46
3190 7354 4.647424 AACAAACGAAAATGAGCAGGAA 57.353 36.364 0.00 0.00 0.00 3.36
3197 7361 7.484975 ACTTATGTCCAAACAAACGAAAATGA 58.515 30.769 0.00 0.00 39.30 2.57
3208 7372 5.626142 TCCAGCTTTACTTATGTCCAAACA 58.374 37.500 0.00 0.00 40.38 2.83
3216 7380 5.368256 GATGGCATCCAGCTTTACTTATG 57.632 43.478 16.75 0.00 44.79 1.90
3235 7399 1.197721 GGGCTATTCGCGAAATGGATG 59.802 52.381 27.23 12.69 40.44 3.51
3245 7409 3.056465 ACTGAGCTATAAGGGCTATTCGC 60.056 47.826 0.00 0.00 40.40 4.70
3247 7411 4.284746 ACCACTGAGCTATAAGGGCTATTC 59.715 45.833 0.00 0.00 40.40 1.75
3332 7496 5.300034 TGAGAAGATCAAAAACATGTGCACT 59.700 36.000 19.41 0.15 34.02 4.40
3347 7529 4.260170 AGGATTGTGTTGCTGAGAAGATC 58.740 43.478 0.00 0.00 0.00 2.75
3372 7555 1.137479 CGCATCAGGGCAAAATGGATT 59.863 47.619 0.00 0.00 0.00 3.01
3381 7564 3.942377 ATTGGCACGCATCAGGGCA 62.942 57.895 0.00 0.00 43.62 5.36
3420 7604 3.998099 TTTGTGTCGCATTTGGATTGA 57.002 38.095 0.00 0.00 0.00 2.57
3424 7608 2.228582 CTGGATTTGTGTCGCATTTGGA 59.771 45.455 0.00 0.00 0.00 3.53
3472 7656 0.473755 TCCAAAGGAACTGCTGAGCA 59.526 50.000 7.05 7.05 40.86 4.26
3631 7883 1.037579 GGTATGTCCCCAGGCTTTGC 61.038 60.000 0.00 0.00 0.00 3.68
3632 7884 3.191182 GGTATGTCCCCAGGCTTTG 57.809 57.895 0.00 0.00 0.00 2.77
3648 7900 0.822164 CGTTATCGGTTCAGGAGGGT 59.178 55.000 0.00 0.00 0.00 4.34
3656 7908 1.127951 CTGCCACAACGTTATCGGTTC 59.872 52.381 0.00 0.00 41.85 3.62
3661 7913 3.182967 CTCTCTCTGCCACAACGTTATC 58.817 50.000 0.00 0.00 0.00 1.75
3662 7914 2.093973 CCTCTCTCTGCCACAACGTTAT 60.094 50.000 0.00 0.00 0.00 1.89
3663 7915 1.272490 CCTCTCTCTGCCACAACGTTA 59.728 52.381 0.00 0.00 0.00 3.18
3664 7916 0.034059 CCTCTCTCTGCCACAACGTT 59.966 55.000 0.00 0.00 0.00 3.99
3665 7917 1.668294 CCTCTCTCTGCCACAACGT 59.332 57.895 0.00 0.00 0.00 3.99
3666 7918 1.079543 CCCTCTCTCTGCCACAACG 60.080 63.158 0.00 0.00 0.00 4.10
3681 7933 1.547495 AATCCCTCTTTGGCCCCCT 60.547 57.895 0.00 0.00 0.00 4.79
3695 7947 3.007831 TGAAAAATCCCAGTTGGCAATCC 59.992 43.478 1.92 0.00 0.00 3.01
3698 7950 3.303938 TCTGAAAAATCCCAGTTGGCAA 58.696 40.909 0.00 0.00 0.00 4.52
3707 7959 4.331108 ACTCTCAAGCTCTGAAAAATCCC 58.669 43.478 0.00 0.00 32.17 3.85
3715 7967 2.509569 ACTCGAACTCTCAAGCTCTGA 58.490 47.619 0.00 0.00 0.00 3.27
3716 7968 3.241701 GAACTCGAACTCTCAAGCTCTG 58.758 50.000 0.00 0.00 0.00 3.35
3718 7970 2.230266 AGGAACTCGAACTCTCAAGCTC 59.770 50.000 0.00 0.00 0.00 4.09
3738 7990 7.192232 GCTTAAGCATAATCAAAACTCTGGAG 58.808 38.462 22.59 0.00 41.59 3.86
3764 8020 7.569957 GCATTTTCTGTGTTTGATGGCTTAAAG 60.570 37.037 0.00 0.00 0.00 1.85
3776 8032 3.880490 TCCAGTACGCATTTTCTGTGTTT 59.120 39.130 0.00 0.00 46.34 2.83


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

AutoCloner maintained by Alex Coulton.