Multiple sequence alignment - TraesCS6D01G113300

Loading Multiple Alignment...

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 TraesCS6D01G113300 chr6D 100.000 2648 0 0 1 2648 79935234 79932587 0.000000e+00 4891.0
1 TraesCS6D01G113300 chr6D 89.442 1345 88 37 673 2001 80061026 80062332 0.000000e+00 1648.0
2 TraesCS6D01G113300 chr6D 83.409 657 78 18 2008 2648 80088263 80088904 4.910000e-162 580.0
3 TraesCS6D01G113300 chr6D 81.835 534 75 17 9 532 80059689 80060210 1.880000e-116 429.0
4 TraesCS6D01G113300 chr6D 86.379 301 28 5 30 319 80060231 80060529 1.530000e-82 316.0
5 TraesCS6D01G113300 chr6D 90.233 215 19 2 433 646 80060540 80060753 2.010000e-71 279.0
6 TraesCS6D01G113300 chr6A 90.789 1357 73 26 380 1712 96771686 96773014 0.000000e+00 1766.0
7 TraesCS6D01G113300 chr6A 82.151 902 106 27 1769 2648 96773021 96773889 0.000000e+00 723.0
8 TraesCS6D01G113300 chr6B 92.557 1048 47 13 688 1712 152631484 152630445 0.000000e+00 1474.0
9 TraesCS6D01G113300 chr6B 92.060 403 21 4 574 970 152696863 152696466 8.280000e-155 556.0
10 TraesCS6D01G113300 chr6B 93.510 339 19 1 962 1297 152696006 152695668 3.930000e-138 501.0
11 TraesCS6D01G113300 chr6B 92.063 189 14 1 2096 2284 152629967 152629780 5.620000e-67 265.0
12 TraesCS6D01G113300 chr6B 74.131 259 57 7 1113 1366 696099798 696099545 6.030000e-17 99.0
13 TraesCS6D01G113300 chr2D 86.314 548 68 6 1096 1641 102725400 102725942 8.160000e-165 590.0
14 TraesCS6D01G113300 chr2D 96.970 33 1 0 1982 2014 291082716 291082684 3.680000e-04 56.5
15 TraesCS6D01G113300 chr2A 85.949 548 70 6 1096 1641 101836458 101837000 1.770000e-161 579.0
16 TraesCS6D01G113300 chr2B 85.219 548 74 6 1096 1641 153903597 153904139 8.280000e-155 556.0
17 TraesCS6D01G113300 chr2B 94.915 59 3 0 1267 1325 74359081 74359139 2.810000e-15 93.5
18 TraesCS6D01G113300 chr7B 75.111 225 53 2 1098 1322 665534976 665535197 4.660000e-18 102.0
19 TraesCS6D01G113300 chr4B 91.525 59 5 0 1267 1325 636684407 636684465 6.070000e-12 82.4
20 TraesCS6D01G113300 chr5D 84.337 83 10 3 1937 2017 558237912 558237831 7.860000e-11 78.7
21 TraesCS6D01G113300 chr1B 86.667 60 6 2 2293 2351 623540631 623540573 6.120000e-07 65.8


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 TraesCS6D01G113300 chr6D 79932587 79935234 2647 True 4891.0 4891 100.00000 1 2648 1 chr6D.!!$R1 2647
1 TraesCS6D01G113300 chr6D 80059689 80062332 2643 False 668.0 1648 86.97225 9 2001 4 chr6D.!!$F2 1992
2 TraesCS6D01G113300 chr6D 80088263 80088904 641 False 580.0 580 83.40900 2008 2648 1 chr6D.!!$F1 640
3 TraesCS6D01G113300 chr6A 96771686 96773889 2203 False 1244.5 1766 86.47000 380 2648 2 chr6A.!!$F1 2268
4 TraesCS6D01G113300 chr6B 152629780 152631484 1704 True 869.5 1474 92.31000 688 2284 2 chr6B.!!$R2 1596
5 TraesCS6D01G113300 chr6B 152695668 152696863 1195 True 528.5 556 92.78500 574 1297 2 chr6B.!!$R3 723
6 TraesCS6D01G113300 chr2D 102725400 102725942 542 False 590.0 590 86.31400 1096 1641 1 chr2D.!!$F1 545
7 TraesCS6D01G113300 chr2A 101836458 101837000 542 False 579.0 579 85.94900 1096 1641 1 chr2A.!!$F1 545
8 TraesCS6D01G113300 chr2B 153903597 153904139 542 False 556.0 556 85.21900 1096 1641 1 chr2B.!!$F2 545

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
36 37 0.615544 CACTGGCATTGGAATGGGGT 60.616 55.0 0.00 0.0 36.9 4.95 F
37 38 1.006813 ACTGGCATTGGAATGGGGTA 58.993 50.0 1.67 0.0 36.9 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1388 2593 0.247736 CCTGGAGAGGTCCTTGAACG 59.752 60.0 0.0 0.0 44.3 3.95 R
1670 2885 1.909700 TGACAAGACCAAGGGAATGC 58.090 50.0 0.0 0.0 0.0 3.56 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
22 23 3.196469 TCTGAGCTAAGGATTGACACTGG 59.804 47.826 0.00 0.00 0.00 4.00
28 29 1.843368 AGGATTGACACTGGCATTGG 58.157 50.000 9.77 0.00 0.00 3.16
33 34 1.548081 TGACACTGGCATTGGAATGG 58.452 50.000 9.77 0.00 36.90 3.16
34 35 0.819582 GACACTGGCATTGGAATGGG 59.180 55.000 9.77 0.00 36.90 4.00
36 37 0.615544 CACTGGCATTGGAATGGGGT 60.616 55.000 0.00 0.00 36.90 4.95
37 38 1.006813 ACTGGCATTGGAATGGGGTA 58.993 50.000 1.67 0.00 36.90 3.69
52 53 2.256117 GGGTATTCTCCCAATCCACG 57.744 55.000 0.00 0.00 46.30 4.94
90 91 7.139392 GTCTAGAAATTGTGGACCTTTTGAAC 58.861 38.462 0.00 0.00 0.00 3.18
95 96 7.495606 AGAAATTGTGGACCTTTTGAACAAATC 59.504 33.333 0.82 0.00 34.67 2.17
101 102 6.015434 GTGGACCTTTTGAACAAATCAGGTAT 60.015 38.462 17.90 3.51 40.02 2.73
120 121 1.801242 TGGATAGATCCCGCTTTGGA 58.199 50.000 6.09 0.00 46.59 3.53
132 133 2.159338 CCGCTTTGGATTCATGGTTCAG 60.159 50.000 0.00 0.00 42.00 3.02
153 154 8.772705 GTTCAGGAGATTAAATCACTGATGATC 58.227 37.037 0.00 0.00 45.26 2.92
154 155 7.150640 TCAGGAGATTAAATCACTGATGATCG 58.849 38.462 0.00 0.00 45.26 3.69
158 159 7.358765 GGAGATTAAATCACTGATGATCGAACG 60.359 40.741 0.00 0.00 45.26 3.95
160 161 6.569228 TTAAATCACTGATGATCGAACGAC 57.431 37.500 0.00 0.00 45.26 4.34
162 163 2.863739 TCACTGATGATCGAACGACAC 58.136 47.619 0.00 0.00 0.00 3.67
181 182 7.152645 ACGACACTCTTGTATTACTCATGTTT 58.847 34.615 0.00 0.00 35.47 2.83
182 183 7.116376 ACGACACTCTTGTATTACTCATGTTTG 59.884 37.037 0.00 0.00 35.47 2.93
184 185 9.155975 GACACTCTTGTATTACTCATGTTTGAT 57.844 33.333 0.00 0.00 35.47 2.57
185 186 8.939929 ACACTCTTGTATTACTCATGTTTGATG 58.060 33.333 0.00 0.00 32.60 3.07
192 193 7.833682 TGTATTACTCATGTTTGATGGAACCAT 59.166 33.333 6.00 6.00 39.69 3.55
196 197 9.913310 TTACTCATGTTTGATGGAACCATAATA 57.087 29.630 6.31 0.00 36.70 0.98
198 199 9.425248 ACTCATGTTTGATGGAACCATAATATT 57.575 29.630 6.31 0.00 36.70 1.28
206 207 9.474313 TTGATGGAACCATAATATTATTAGCCC 57.526 33.333 5.18 6.13 36.70 5.19
208 209 9.700831 GATGGAACCATAATATTATTAGCCCTT 57.299 33.333 5.18 4.23 36.70 3.95
210 211 9.528489 TGGAACCATAATATTATTAGCCCTTTC 57.472 33.333 5.18 1.61 0.00 2.62
253 260 4.082408 CGTAGTGGGAGAACTATTGTGTGA 60.082 45.833 0.00 0.00 35.20 3.58
258 265 4.003648 GGGAGAACTATTGTGTGACTTGG 58.996 47.826 0.00 0.00 0.00 3.61
259 266 4.262894 GGGAGAACTATTGTGTGACTTGGA 60.263 45.833 0.00 0.00 0.00 3.53
294 301 9.661563 AGATGGTATTGTCGAACTTTGTAATTA 57.338 29.630 0.00 0.00 0.00 1.40
332 339 4.514781 ACGTGAGTAATACAAGTCTGCA 57.485 40.909 0.00 0.00 46.88 4.41
333 340 4.878439 ACGTGAGTAATACAAGTCTGCAA 58.122 39.130 0.00 0.00 46.88 4.08
443 470 6.381801 CGGGACAAGCATATTTTATGGATTC 58.618 40.000 0.00 0.00 0.00 2.52
477 932 9.504708 TCTATCTAGTGCTATTTCTAGTGGTAC 57.495 37.037 0.00 0.00 36.17 3.34
480 935 6.996879 TCTAGTGCTATTTCTAGTGGTACGAT 59.003 38.462 0.00 0.00 36.17 3.73
487 942 3.076079 TCTAGTGGTACGATGTGTCCA 57.924 47.619 0.00 0.00 0.00 4.02
498 953 1.200716 GATGTGTCCACCGACTACGAA 59.799 52.381 0.00 0.00 42.66 3.85
506 961 2.982470 CCACCGACTACGAAGTGTTTAC 59.018 50.000 0.00 0.00 45.73 2.01
508 963 2.290641 ACCGACTACGAAGTGTTTACGT 59.709 45.455 0.00 0.00 45.73 3.57
515 970 4.720530 ACGAAGTGTTTACGTCAATTCC 57.279 40.909 9.44 0.00 42.51 3.01
520 975 6.510478 CGAAGTGTTTACGTCAATTCCTCAAA 60.510 38.462 9.44 0.00 36.83 2.69
532 987 7.009999 CGTCAATTCCTCAAACTCAAGATCTAG 59.990 40.741 0.00 0.00 0.00 2.43
533 988 6.820656 TCAATTCCTCAAACTCAAGATCTAGC 59.179 38.462 0.00 0.00 0.00 3.42
537 992 2.497675 TCAAACTCAAGATCTAGCGGCT 59.502 45.455 7.98 7.98 0.00 5.52
554 1009 1.882311 CTCAGTCTCTCGCAGCTGT 59.118 57.895 16.64 0.00 31.66 4.40
602 1057 2.672478 CGTTCATGAGGGTGAGTGTCTC 60.672 54.545 0.00 0.00 0.00 3.36
609 1064 2.024319 GGTGAGTGTCTCTGCGTGC 61.024 63.158 0.00 0.00 0.00 5.34
640 1096 6.577427 GCGTATTGTAGTGTTTCCAAAAGAAG 59.423 38.462 0.00 0.00 35.40 2.85
644 1100 7.931578 TTGTAGTGTTTCCAAAAGAAGAAGA 57.068 32.000 0.00 0.00 35.40 2.87
645 1101 7.931578 TGTAGTGTTTCCAAAAGAAGAAGAA 57.068 32.000 0.00 0.00 35.40 2.52
768 1478 3.058224 GTGACCAAAACTACATGAGCCAC 60.058 47.826 0.00 0.00 0.00 5.01
769 1479 2.151202 ACCAAAACTACATGAGCCACG 58.849 47.619 0.00 0.00 0.00 4.94
796 1508 2.669229 CATGTGCGAGTGGCCACA 60.669 61.111 36.39 16.40 42.61 4.17
805 1517 2.680841 GCGAGTGGCCACAAATATACAA 59.319 45.455 36.39 0.00 34.80 2.41
936 1662 3.358993 GGTTCGCGCACGTACTATATAAC 59.641 47.826 8.75 0.00 39.30 1.89
1005 2207 1.084289 GTAAGGTCGTTGCCATGGAC 58.916 55.000 18.40 7.64 0.00 4.02
1044 2249 3.486685 ATCCAGATGCCTGCGCCT 61.487 61.111 4.18 0.00 39.07 5.52
1470 2675 2.872557 CTCGTGTTCCTCGCCGTA 59.127 61.111 0.00 0.00 0.00 4.02
1667 2882 2.108157 ACGCTCAGCAAACGTGGA 59.892 55.556 0.00 0.00 38.85 4.02
1670 2885 2.328099 GCTCAGCAAACGTGGAGGG 61.328 63.158 0.00 0.00 0.00 4.30
1688 2910 1.177401 GGCATTCCCTTGGTCTTGTC 58.823 55.000 0.00 0.00 0.00 3.18
1689 2911 1.547675 GGCATTCCCTTGGTCTTGTCA 60.548 52.381 0.00 0.00 0.00 3.58
1691 2913 3.620488 GCATTCCCTTGGTCTTGTCATA 58.380 45.455 0.00 0.00 0.00 2.15
1692 2914 4.016444 GCATTCCCTTGGTCTTGTCATAA 58.984 43.478 0.00 0.00 0.00 1.90
1693 2915 4.096984 GCATTCCCTTGGTCTTGTCATAAG 59.903 45.833 0.00 0.00 0.00 1.73
1694 2916 3.350219 TCCCTTGGTCTTGTCATAAGC 57.650 47.619 0.00 0.00 0.00 3.09
1695 2917 2.026262 TCCCTTGGTCTTGTCATAAGCC 60.026 50.000 0.00 0.00 0.00 4.35
1697 2919 3.420893 CCTTGGTCTTGTCATAAGCCAA 58.579 45.455 8.86 8.86 34.60 4.52
1698 2920 4.019174 CCTTGGTCTTGTCATAAGCCAAT 58.981 43.478 9.41 0.00 34.98 3.16
1699 2921 4.096984 CCTTGGTCTTGTCATAAGCCAATC 59.903 45.833 9.41 0.00 34.98 2.67
1700 2922 3.620488 TGGTCTTGTCATAAGCCAATCC 58.380 45.455 0.00 0.00 0.00 3.01
1701 2923 3.010027 TGGTCTTGTCATAAGCCAATCCA 59.990 43.478 0.00 0.00 0.00 3.41
1702 2924 4.210331 GGTCTTGTCATAAGCCAATCCAT 58.790 43.478 0.00 0.00 0.00 3.41
1703 2925 4.646492 GGTCTTGTCATAAGCCAATCCATT 59.354 41.667 0.00 0.00 0.00 3.16
1704 2926 5.127682 GGTCTTGTCATAAGCCAATCCATTT 59.872 40.000 0.00 0.00 0.00 2.32
1705 2927 6.268566 GTCTTGTCATAAGCCAATCCATTTC 58.731 40.000 0.00 0.00 0.00 2.17
1706 2928 5.951148 TCTTGTCATAAGCCAATCCATTTCA 59.049 36.000 0.00 0.00 0.00 2.69
1707 2929 6.436847 TCTTGTCATAAGCCAATCCATTTCAA 59.563 34.615 0.00 0.00 0.00 2.69
1708 2930 6.602410 TGTCATAAGCCAATCCATTTCAAA 57.398 33.333 0.00 0.00 0.00 2.69
1709 2931 6.397272 TGTCATAAGCCAATCCATTTCAAAC 58.603 36.000 0.00 0.00 0.00 2.93
1710 2932 6.211184 TGTCATAAGCCAATCCATTTCAAACT 59.789 34.615 0.00 0.00 0.00 2.66
1711 2933 7.099120 GTCATAAGCCAATCCATTTCAAACTT 58.901 34.615 0.00 0.00 0.00 2.66
1712 2934 7.603784 GTCATAAGCCAATCCATTTCAAACTTT 59.396 33.333 0.00 0.00 0.00 2.66
1713 2935 8.156165 TCATAAGCCAATCCATTTCAAACTTTT 58.844 29.630 0.00 0.00 0.00 2.27
1714 2936 8.785946 CATAAGCCAATCCATTTCAAACTTTTT 58.214 29.630 0.00 0.00 0.00 1.94
1753 2975 8.550376 CAATCCATTTTAAACTTGACCAAACTG 58.450 33.333 0.00 0.00 0.00 3.16
1902 3129 2.736721 TGCGTGACTTTTAGACATGAGC 59.263 45.455 0.00 0.00 30.32 4.26
1964 3194 7.980099 ACTACCTCAATTCAGGTTTATTAGTCG 59.020 37.037 6.25 0.00 45.24 4.18
1969 3199 7.103641 TCAATTCAGGTTTATTAGTCGCTCTT 58.896 34.615 0.00 0.00 0.00 2.85
1980 3210 2.790433 AGTCGCTCTTTTATTTGGGCA 58.210 42.857 0.00 0.00 0.00 5.36
2132 3490 8.665685 GTTTAATAGATGGTCGAAGTTTGACAT 58.334 33.333 22.09 14.23 38.10 3.06
2137 3495 7.504924 AGATGGTCGAAGTTTGACATAAAAA 57.495 32.000 22.09 3.77 38.10 1.94
2167 3525 1.006639 GCCAAATAAACCCCTCCCTCA 59.993 52.381 0.00 0.00 0.00 3.86
2221 3579 3.181489 GGTTCGATCACCCACTAGTGTAG 60.181 52.174 21.18 14.30 38.91 2.74
2225 3583 3.314635 CGATCACCCACTAGTGTAGGTAC 59.685 52.174 21.18 14.09 38.91 3.34
2316 3674 2.945456 GGAAGGTTCCTGACAGGTTTT 58.055 47.619 21.06 10.97 44.11 2.43
2320 3678 1.328279 GTTCCTGACAGGTTTTGGGG 58.672 55.000 21.06 0.00 36.53 4.96
2372 3730 7.628769 TTTTCTGTACTACTTTTTCGGGTTT 57.371 32.000 0.00 0.00 0.00 3.27
2375 3733 7.250445 TCTGTACTACTTTTTCGGGTTTTTC 57.750 36.000 0.00 0.00 0.00 2.29
2381 3739 8.962884 ACTACTTTTTCGGGTTTTTCTAGTTA 57.037 30.769 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.196469 CCAGTGTCAATCCTTAGCTCAGA 59.804 47.826 0.00 0.00 0.00 3.27
1 2 3.529533 CCAGTGTCAATCCTTAGCTCAG 58.470 50.000 0.00 0.00 0.00 3.35
2 3 2.355108 GCCAGTGTCAATCCTTAGCTCA 60.355 50.000 0.00 0.00 0.00 4.26
3 4 2.284190 GCCAGTGTCAATCCTTAGCTC 58.716 52.381 0.00 0.00 0.00 4.09
4 5 1.630369 TGCCAGTGTCAATCCTTAGCT 59.370 47.619 0.00 0.00 0.00 3.32
5 6 2.113860 TGCCAGTGTCAATCCTTAGC 57.886 50.000 0.00 0.00 0.00 3.09
6 7 3.379372 CCAATGCCAGTGTCAATCCTTAG 59.621 47.826 0.00 0.00 0.00 2.18
7 8 3.010027 TCCAATGCCAGTGTCAATCCTTA 59.990 43.478 0.00 0.00 0.00 2.69
17 18 0.615544 ACCCCATTCCAATGCCAGTG 60.616 55.000 0.00 0.00 35.08 3.66
20 21 2.247111 AGAATACCCCATTCCAATGCCA 59.753 45.455 0.00 0.00 43.63 4.92
22 23 2.893489 GGAGAATACCCCATTCCAATGC 59.107 50.000 0.00 0.00 43.63 3.56
34 35 2.943033 CAACGTGGATTGGGAGAATACC 59.057 50.000 0.00 0.00 0.00 2.73
36 37 3.772572 TCTCAACGTGGATTGGGAGAATA 59.227 43.478 0.00 0.00 34.03 1.75
37 38 2.571653 TCTCAACGTGGATTGGGAGAAT 59.428 45.455 0.00 0.00 34.03 2.40
73 74 6.232581 TGATTTGTTCAAAAGGTCCACAAT 57.767 33.333 2.11 0.00 0.00 2.71
79 80 6.208599 TCCATACCTGATTTGTTCAAAAGGTC 59.791 38.462 18.82 7.38 36.99 3.85
101 102 2.711009 AATCCAAAGCGGGATCTATCCA 59.289 45.455 11.06 0.00 46.96 3.41
120 121 8.057623 AGTGATTTAATCTCCTGAACCATGAAT 58.942 33.333 6.50 0.00 0.00 2.57
132 133 7.358765 CGTTCGATCATCAGTGATTTAATCTCC 60.359 40.741 1.86 0.00 44.96 3.71
152 153 5.179929 TGAGTAATACAAGAGTGTCGTTCGA 59.820 40.000 0.00 0.00 39.30 3.71
153 154 5.388111 TGAGTAATACAAGAGTGTCGTTCG 58.612 41.667 0.00 0.00 39.30 3.95
154 155 6.807230 ACATGAGTAATACAAGAGTGTCGTTC 59.193 38.462 0.00 0.00 39.30 3.95
158 159 8.534333 TCAAACATGAGTAATACAAGAGTGTC 57.466 34.615 0.00 0.00 39.30 3.67
160 161 8.393366 CCATCAAACATGAGTAATACAAGAGTG 58.607 37.037 0.00 0.00 0.00 3.51
162 163 8.722480 TCCATCAAACATGAGTAATACAAGAG 57.278 34.615 0.00 0.00 0.00 2.85
181 182 8.845793 AGGGCTAATAATATTATGGTTCCATCA 58.154 33.333 8.74 0.00 0.00 3.07
182 183 9.700831 AAGGGCTAATAATATTATGGTTCCATC 57.299 33.333 8.74 0.00 0.00 3.51
184 185 9.528489 GAAAGGGCTAATAATATTATGGTTCCA 57.472 33.333 8.74 0.00 0.00 3.53
185 186 9.755122 AGAAAGGGCTAATAATATTATGGTTCC 57.245 33.333 8.74 8.77 0.00 3.62
198 199 9.998106 CATAAGTAGCTAAAGAAAGGGCTAATA 57.002 33.333 0.00 0.00 38.70 0.98
203 204 5.437946 ACCATAAGTAGCTAAAGAAAGGGC 58.562 41.667 0.00 0.00 0.00 5.19
204 205 7.927092 GTCTACCATAAGTAGCTAAAGAAAGGG 59.073 40.741 0.00 0.00 46.98 3.95
205 206 7.648510 CGTCTACCATAAGTAGCTAAAGAAAGG 59.351 40.741 0.00 0.00 46.98 3.11
206 207 8.189460 ACGTCTACCATAAGTAGCTAAAGAAAG 58.811 37.037 0.00 0.00 46.98 2.62
208 209 7.636150 ACGTCTACCATAAGTAGCTAAAGAA 57.364 36.000 0.00 0.00 46.98 2.52
209 210 7.989741 ACTACGTCTACCATAAGTAGCTAAAGA 59.010 37.037 0.00 0.00 46.98 2.52
210 211 8.068977 CACTACGTCTACCATAAGTAGCTAAAG 58.931 40.741 0.00 0.00 46.98 1.85
215 222 4.023365 CCCACTACGTCTACCATAAGTAGC 60.023 50.000 0.00 0.00 46.98 3.58
230 237 4.082408 TCACACAATAGTTCTCCCACTACG 60.082 45.833 0.00 0.00 31.92 3.51
238 245 6.312426 CAGATCCAAGTCACACAATAGTTCTC 59.688 42.308 0.00 0.00 0.00 2.87
245 252 3.679389 GACCAGATCCAAGTCACACAAT 58.321 45.455 3.22 0.00 0.00 2.71
258 265 4.636249 GACAATACCATCTGGACCAGATC 58.364 47.826 30.57 16.21 46.83 2.75
294 301 0.391661 CGTTGCAGAGCTACACCCAT 60.392 55.000 4.65 0.00 34.26 4.00
372 383 9.695526 CCATTTCAAAACATAAGACATTCAAGA 57.304 29.630 0.00 0.00 0.00 3.02
373 384 9.695526 TCCATTTCAAAACATAAGACATTCAAG 57.304 29.630 0.00 0.00 0.00 3.02
374 385 9.695526 CTCCATTTCAAAACATAAGACATTCAA 57.304 29.630 0.00 0.00 0.00 2.69
375 386 8.306038 CCTCCATTTCAAAACATAAGACATTCA 58.694 33.333 0.00 0.00 0.00 2.57
376 387 8.522830 TCCTCCATTTCAAAACATAAGACATTC 58.477 33.333 0.00 0.00 0.00 2.67
377 388 8.421249 TCCTCCATTTCAAAACATAAGACATT 57.579 30.769 0.00 0.00 0.00 2.71
408 419 0.174845 CTTGTCCCGCCAACTATCGA 59.825 55.000 0.00 0.00 0.00 3.59
410 421 0.392461 TGCTTGTCCCGCCAACTATC 60.392 55.000 0.00 0.00 0.00 2.08
415 442 1.846007 AAATATGCTTGTCCCGCCAA 58.154 45.000 0.00 0.00 0.00 4.52
468 923 3.146618 GTGGACACATCGTACCACTAG 57.853 52.381 0.00 0.00 46.14 2.57
480 935 0.594602 CTTCGTAGTCGGTGGACACA 59.405 55.000 4.69 0.00 45.92 3.72
487 942 2.290641 ACGTAAACACTTCGTAGTCGGT 59.709 45.455 0.00 0.00 36.05 4.69
498 953 5.820947 AGTTTGAGGAATTGACGTAAACACT 59.179 36.000 7.34 0.00 0.00 3.55
506 961 5.641209 AGATCTTGAGTTTGAGGAATTGACG 59.359 40.000 0.00 0.00 0.00 4.35
508 963 6.820656 GCTAGATCTTGAGTTTGAGGAATTGA 59.179 38.462 8.45 0.00 0.00 2.57
515 970 2.863137 GCCGCTAGATCTTGAGTTTGAG 59.137 50.000 8.45 0.00 0.00 3.02
520 975 1.680735 CTGAGCCGCTAGATCTTGAGT 59.319 52.381 8.45 0.00 0.00 3.41
532 987 4.121669 TGCGAGAGACTGAGCCGC 62.122 66.667 0.00 0.00 45.28 6.53
533 988 2.101965 CTGCGAGAGACTGAGCCG 59.898 66.667 0.00 0.00 0.00 5.52
537 992 0.242286 GAACAGCTGCGAGAGACTGA 59.758 55.000 15.27 0.00 32.92 3.41
554 1009 5.810074 CACACGTACATCATATTCCTGTGAA 59.190 40.000 0.00 0.00 34.33 3.18
602 1057 1.354337 AATACGCTCACAGCACGCAG 61.354 55.000 0.00 0.00 42.58 5.18
609 1064 4.091509 GGAAACACTACAATACGCTCACAG 59.908 45.833 0.00 0.00 0.00 3.66
640 1096 9.803315 ACTCAATTAACAAACTCCTTTTTCTTC 57.197 29.630 0.00 0.00 0.00 2.87
644 1100 9.161629 CCAAACTCAATTAACAAACTCCTTTTT 57.838 29.630 0.00 0.00 0.00 1.94
645 1101 7.279981 GCCAAACTCAATTAACAAACTCCTTTT 59.720 33.333 0.00 0.00 0.00 2.27
686 1392 0.320073 CCAGACAACGGCCGAACTAA 60.320 55.000 35.90 0.00 0.00 2.24
923 1643 7.661968 TGTCTACCTCTCGTTATATAGTACGT 58.338 38.462 6.81 0.00 38.79 3.57
926 1646 8.530311 CCTCTGTCTACCTCTCGTTATATAGTA 58.470 40.741 0.00 0.00 0.00 1.82
936 1662 0.736053 GTGCCTCTGTCTACCTCTCG 59.264 60.000 0.00 0.00 0.00 4.04
1005 2207 1.586028 CACAGCATTGGAAACGGGG 59.414 57.895 0.00 0.00 0.00 5.73
1044 2249 1.691219 GGGAGAGGATTGTTGGGCA 59.309 57.895 0.00 0.00 0.00 5.36
1263 2468 1.260538 TGAAGGAGAGGAGCACGCAT 61.261 55.000 0.00 0.00 0.00 4.73
1388 2593 0.247736 CCTGGAGAGGTCCTTGAACG 59.752 60.000 0.00 0.00 44.30 3.95
1446 2651 3.909258 GAGGAACACGAGCGCCGAA 62.909 63.158 22.10 0.00 41.76 4.30
1670 2885 1.909700 TGACAAGACCAAGGGAATGC 58.090 50.000 0.00 0.00 0.00 3.56
1688 2910 7.910441 AAAGTTTGAAATGGATTGGCTTATG 57.090 32.000 0.00 0.00 0.00 1.90
1689 2911 8.922931 AAAAAGTTTGAAATGGATTGGCTTAT 57.077 26.923 0.00 0.00 0.00 1.73
1715 2937 4.599047 AAATGGATTGTCCTCGCAAAAA 57.401 36.364 0.00 0.00 37.46 1.94
1716 2938 4.599047 AAAATGGATTGTCCTCGCAAAA 57.401 36.364 0.00 0.00 37.46 2.44
1717 2939 5.713792 TTAAAATGGATTGTCCTCGCAAA 57.286 34.783 0.00 0.00 37.46 3.68
1718 2940 5.242838 AGTTTAAAATGGATTGTCCTCGCAA 59.757 36.000 0.00 0.00 37.46 4.85
1719 2941 4.764823 AGTTTAAAATGGATTGTCCTCGCA 59.235 37.500 0.00 0.00 37.46 5.10
1720 2942 5.310720 AGTTTAAAATGGATTGTCCTCGC 57.689 39.130 0.00 0.00 37.46 5.03
1721 2943 6.801862 GTCAAGTTTAAAATGGATTGTCCTCG 59.198 38.462 0.00 0.00 37.46 4.63
1722 2944 7.090808 GGTCAAGTTTAAAATGGATTGTCCTC 58.909 38.462 0.00 0.00 37.46 3.71
1723 2945 6.553100 TGGTCAAGTTTAAAATGGATTGTCCT 59.447 34.615 0.00 0.00 37.46 3.85
1724 2946 6.754193 TGGTCAAGTTTAAAATGGATTGTCC 58.246 36.000 0.00 2.97 36.96 4.02
1725 2947 8.547894 GTTTGGTCAAGTTTAAAATGGATTGTC 58.452 33.333 0.00 0.00 0.00 3.18
1726 2948 8.264347 AGTTTGGTCAAGTTTAAAATGGATTGT 58.736 29.630 0.00 0.00 0.00 2.71
1866 3093 3.189287 GTCACGCACTTTGAAATGGAGAT 59.811 43.478 0.00 0.00 0.00 2.75
1870 3097 3.354089 AAGTCACGCACTTTGAAATGG 57.646 42.857 0.00 0.00 43.38 3.16
1964 3194 7.591057 GTCAAATTTTTGCCCAAATAAAAGAGC 59.409 33.333 0.00 0.00 38.05 4.09
2099 3457 9.715121 ACTTCGACCATCTATTAAACTAACAAA 57.285 29.630 0.00 0.00 0.00 2.83
2132 3490 9.232473 GGTTTATTTGGCCCAATTGTATTTTTA 57.768 29.630 7.46 0.00 0.00 1.52
2137 3495 4.165180 GGGGTTTATTTGGCCCAATTGTAT 59.835 41.667 7.46 0.00 44.07 2.29
2304 3662 0.539669 GGTCCCCAAAACCTGTCAGG 60.540 60.000 17.88 17.88 42.49 3.86
2311 3669 3.687125 CTTCTAGAAGGTCCCCAAAACC 58.313 50.000 22.67 0.00 34.87 3.27
2515 3894 9.639563 ACCTTAACAAATTTTGAAATCCCAATT 57.360 25.926 15.81 0.00 0.00 2.32
2516 3895 9.639563 AACCTTAACAAATTTTGAAATCCCAAT 57.360 25.926 15.81 0.00 0.00 3.16
2517 3896 9.467796 AAACCTTAACAAATTTTGAAATCCCAA 57.532 25.926 15.81 0.00 0.00 4.12
2518 3897 9.467796 AAAACCTTAACAAATTTTGAAATCCCA 57.532 25.926 15.81 0.00 0.00 4.37
2519 3898 9.944663 GAAAACCTTAACAAATTTTGAAATCCC 57.055 29.630 15.81 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.