Multiple sequence alignment - TraesCS2A01G261800

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 TraesCS2A01G261800 chr2A 100.000 6636 0 0 1 6636 412517263 412510628 0.000000e+00 12255.0
1 TraesCS2A01G261800 chr2A 84.211 76 8 1 1459 1530 113898929 113898854 3.320000e-08 71.3
2 TraesCS2A01G261800 chr2B 95.013 2607 71 20 734 3297 387069370 387071960 0.000000e+00 4039.0
3 TraesCS2A01G261800 chr2B 96.427 1987 56 5 4653 6636 387076269 387078243 0.000000e+00 3262.0
4 TraesCS2A01G261800 chr2B 96.847 888 25 2 3349 4234 387074840 387075726 0.000000e+00 1482.0
5 TraesCS2A01G261800 chr2B 87.749 702 63 11 1 693 387068701 387069388 0.000000e+00 798.0
6 TraesCS2A01G261800 chr2B 94.988 419 20 1 4235 4652 387075772 387076190 0.000000e+00 656.0
7 TraesCS2A01G261800 chr2B 85.034 147 20 2 3292 3437 98566795 98566940 1.490000e-31 148.0
8 TraesCS2A01G261800 chr2B 84.211 76 8 1 1459 1530 161359454 161359379 3.320000e-08 71.3
9 TraesCS2A01G261800 chr2D 95.702 2187 57 4 4451 6636 318553232 318555382 0.000000e+00 3483.0
10 TraesCS2A01G261800 chr2D 95.855 1906 49 10 707 2589 318546391 318548289 0.000000e+00 3055.0
11 TraesCS2A01G261800 chr2D 96.163 1199 36 6 3262 4455 318551729 318552922 0.000000e+00 1951.0
12 TraesCS2A01G261800 chr2D 94.490 726 30 7 1 722 318545717 318546436 0.000000e+00 1110.0
13 TraesCS2A01G261800 chr2D 96.117 618 16 6 2660 3277 318548286 318548895 0.000000e+00 1002.0
14 TraesCS2A01G261800 chr2D 92.523 107 7 1 4384 4490 636776245 636776350 1.150000e-32 152.0
15 TraesCS2A01G261800 chr6A 90.323 155 12 2 4832 4985 613277339 613277187 4.060000e-47 200.0
16 TraesCS2A01G261800 chr6A 80.220 91 13 3 2472 2558 29758256 29758345 5.560000e-06 63.9
17 TraesCS2A01G261800 chr7D 94.231 104 6 0 4394 4497 474338818 474338715 6.890000e-35 159.0
18 TraesCS2A01G261800 chr1D 94.231 104 6 0 4393 4496 490538213 490538110 6.890000e-35 159.0
19 TraesCS2A01G261800 chr1D 91.071 112 9 1 4391 4501 354518917 354519028 4.150000e-32 150.0
20 TraesCS2A01G261800 chr1D 100.000 31 0 0 2656 2686 21448347 21448317 2.580000e-04 58.4
21 TraesCS2A01G261800 chr4D 95.000 100 5 0 4393 4492 205963441 205963540 2.480000e-34 158.0
22 TraesCS2A01G261800 chr1B 95.000 100 5 0 4393 4492 572529358 572529457 2.480000e-34 158.0
23 TraesCS2A01G261800 chr1B 78.652 89 17 2 2597 2684 329485217 329485304 2.580000e-04 58.4
24 TraesCS2A01G261800 chr5D 91.071 112 9 1 4381 4492 558970543 558970433 4.150000e-32 150.0
25 TraesCS2A01G261800 chr1A 95.652 46 2 0 1494 1539 30498004 30497959 2.570000e-09 75.0
26 TraesCS2A01G261800 chr3A 84.211 76 8 1 1459 1530 493706438 493706513 3.320000e-08 71.3


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 TraesCS2A01G261800 chr2A 412510628 412517263 6635 True 12255.0 12255 100.0000 1 6636 1 chr2A.!!$R2 6635
1 TraesCS2A01G261800 chr2B 387068701 387078243 9542 False 2047.4 4039 94.2048 1 6636 5 chr2B.!!$F2 6635
2 TraesCS2A01G261800 chr2D 318545717 318555382 9665 False 2120.2 3483 95.6654 1 6636 5 chr2D.!!$F2 6635

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
286 289 0.763035 AGTACAAACCCCTCGCTGTT 59.237 50.000 0.00 0.00 0.00 3.16 F
391 395 1.004080 GCAGAAGGAGTCAGCAGCA 60.004 57.895 0.00 0.00 38.58 4.41 F
1052 1065 1.306141 CACTAGGCACTCCTCCCCA 60.306 63.158 0.00 0.00 43.06 4.96 F
1162 1175 1.792006 CGGACAAGAACCGCTACTTT 58.208 50.000 0.00 0.00 43.74 2.66 F
1248 1261 2.363018 CTCGCCTCCTCCCACAGA 60.363 66.667 0.00 0.00 0.00 3.41 F
2963 3018 1.066908 TGTACCAGCTTTGCAAGTTGC 59.933 47.619 21.17 21.17 45.29 4.17 F
3603 9336 2.432444 CGGGAAAGGCACAGTAATCAA 58.568 47.619 0.00 0.00 0.00 2.57 F
5147 11324 1.391577 TGCTTGTTCATGCAGTGTGT 58.608 45.000 8.85 0.00 34.84 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1378 1391 0.463295 AAGCTCGGATCAGCACCATG 60.463 55.000 7.7 0.0 42.40 3.66 R
2375 2413 0.232303 GTGAAACCGTTGCAGAGTCG 59.768 55.000 0.0 0.0 0.00 4.18 R
2642 2682 2.526304 AGTGTCGCAGCTTGAACTAA 57.474 45.000 0.0 0.0 0.00 2.24 R
2644 2684 2.526304 TAAGTGTCGCAGCTTGAACT 57.474 45.000 0.0 0.0 0.00 3.01 R
3127 3182 2.664402 ACAGCCATGATAATGTCCCC 57.336 50.000 0.0 0.0 0.00 4.81 R
4205 9941 2.099405 CATCTTGTTACCCCCGCAAAT 58.901 47.619 0.0 0.0 0.00 2.32 R
5353 11530 3.365832 CCATGCACGTTCATAAAGATGC 58.634 45.455 0.0 0.0 32.62 3.91 R
6285 12466 1.308998 CGACAAACAGCAAAGAGGGT 58.691 50.000 0.0 0.0 0.00 4.34 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
92 94 2.425668 CGAACCATAATCCCAACAACCC 59.574 50.000 0.00 0.00 0.00 4.11
286 289 0.763035 AGTACAAACCCCTCGCTGTT 59.237 50.000 0.00 0.00 0.00 3.16
354 357 3.605634 AGCGTAGATGTTGTTGGCATTA 58.394 40.909 0.00 0.00 0.00 1.90
391 395 1.004080 GCAGAAGGAGTCAGCAGCA 60.004 57.895 0.00 0.00 38.58 4.41
410 414 2.680221 GCAATGGAGCTGACAGAGATGT 60.680 50.000 6.65 0.00 0.00 3.06
419 423 4.774726 AGCTGACAGAGATGTAAAAGGAGA 59.225 41.667 6.65 0.00 0.00 3.71
454 458 8.757164 TCTTTTCCTTTTCAGTTTTTCTTCAC 57.243 30.769 0.00 0.00 0.00 3.18
458 462 7.181569 TCCTTTTCAGTTTTTCTTCACCAAT 57.818 32.000 0.00 0.00 0.00 3.16
720 730 7.906199 TTTTTAGGGGAAAAGAAACATCAGA 57.094 32.000 0.00 0.00 38.27 3.27
721 731 8.491045 TTTTTAGGGGAAAAGAAACATCAGAT 57.509 30.769 0.00 0.00 38.27 2.90
839 849 2.428960 AATTGGCCCGTTTCGCAACC 62.429 55.000 0.00 0.00 0.00 3.77
1052 1065 1.306141 CACTAGGCACTCCTCCCCA 60.306 63.158 0.00 0.00 43.06 4.96
1060 1073 1.897647 GCACTCCTCCCCACTACTTCT 60.898 57.143 0.00 0.00 0.00 2.85
1162 1175 1.792006 CGGACAAGAACCGCTACTTT 58.208 50.000 0.00 0.00 43.74 2.66
1248 1261 2.363018 CTCGCCTCCTCCCACAGA 60.363 66.667 0.00 0.00 0.00 3.41
1291 1304 2.437895 GAGCTGCTGCATGCCAGA 60.438 61.111 23.23 2.21 44.64 3.86
1822 1857 9.962783 CAATTTCTCTTTTCTTGAAGACAGAAT 57.037 29.630 0.00 0.00 32.50 2.40
1843 1881 8.190122 CAGAATGTGCATGGCTTTATAAGTTTA 58.810 33.333 0.00 0.00 0.00 2.01
1893 1931 6.586463 TCAGTTGTTCTCTTTGAGTATAAGCG 59.414 38.462 0.00 0.00 0.00 4.68
2059 2097 4.921515 CAGTGAATTCTCCACTTGCAAATG 59.078 41.667 7.05 0.00 42.44 2.32
2160 2198 3.869272 GCCAGCGCCAACTCATCG 61.869 66.667 2.29 0.00 0.00 3.84
2192 2230 6.808212 CGAGCATTGTATCCTCAAAATTGTTT 59.192 34.615 0.00 0.00 0.00 2.83
2642 2682 3.045601 AGTGTCGCAGCTTTGAACTAT 57.954 42.857 0.00 0.00 0.00 2.12
2643 2683 3.403038 AGTGTCGCAGCTTTGAACTATT 58.597 40.909 0.00 0.00 0.00 1.73
2644 2684 4.566004 AGTGTCGCAGCTTTGAACTATTA 58.434 39.130 0.00 0.00 0.00 0.98
2645 2685 4.627467 AGTGTCGCAGCTTTGAACTATTAG 59.373 41.667 0.00 0.00 0.00 1.73
2647 2687 4.994852 TGTCGCAGCTTTGAACTATTAGTT 59.005 37.500 8.81 8.81 41.95 2.24
2668 2723 6.338146 AGTTCAAGCTGCGACACTTATTATA 58.662 36.000 0.00 0.00 0.00 0.98
2931 2986 6.113411 AGTAACTTGTTGTCACAACTTAGCT 58.887 36.000 21.23 12.01 38.03 3.32
2963 3018 1.066908 TGTACCAGCTTTGCAAGTTGC 59.933 47.619 21.17 21.17 45.29 4.17
3026 3081 2.561209 TATGGGAGTAGGCAGTGGAA 57.439 50.000 0.00 0.00 0.00 3.53
3127 3182 4.475944 CTGGTTTGCTTAATTTGGAGACG 58.524 43.478 0.00 0.00 0.00 4.18
3169 3224 8.014322 TGTATCGTTGTAAAAGTGACATTCTC 57.986 34.615 0.00 0.00 0.00 2.87
3268 6170 4.876107 CCAATGGTCTGTTAGGTGTGTATC 59.124 45.833 0.00 0.00 0.00 2.24
3330 6309 4.897670 AGCTGAATAAATGCCTAATGCCTT 59.102 37.500 0.00 0.00 40.16 4.35
3338 6317 4.622260 ATGCCTAATGCCTTTGTTTTGT 57.378 36.364 0.00 0.00 40.16 2.83
3340 6319 4.125703 TGCCTAATGCCTTTGTTTTGTTG 58.874 39.130 0.00 0.00 40.16 3.33
3482 9215 4.706476 TGGCGTAGTTACTACAACATACCT 59.294 41.667 20.62 0.00 36.83 3.08
3549 9282 2.620367 GGGAAATGTGGTGCTATGTGGA 60.620 50.000 0.00 0.00 0.00 4.02
3603 9336 2.432444 CGGGAAAGGCACAGTAATCAA 58.568 47.619 0.00 0.00 0.00 2.57
3941 9676 3.865700 GCAGTTTGCAGGTAACCAC 57.134 52.632 0.00 0.00 44.26 4.16
3980 9715 4.561530 GCTGACACTCTAGTTTGGACATGA 60.562 45.833 0.00 0.00 0.00 3.07
4062 9797 5.422650 GGATGAACACTACTTCTTAGGGAGT 59.577 44.000 0.00 0.00 34.39 3.85
4161 9896 5.263599 TCACAGGATTGATTTGCCACTAAT 58.736 37.500 0.00 0.00 0.00 1.73
4205 9941 7.282224 ACTCAGTGCAGTTTAACAAGATGTTTA 59.718 33.333 0.54 0.00 41.45 2.01
4384 10168 3.117663 GGTTATTGCCCAGTTCCCAGATA 60.118 47.826 0.00 0.00 0.00 1.98
4417 10201 3.452878 TCCCTCCGTCCCAAAATAACTA 58.547 45.455 0.00 0.00 0.00 2.24
4504 10603 7.967303 ACGGAGAGAGTATTAGTTAAAGTTTCG 59.033 37.037 0.00 0.00 0.00 3.46
4531 10630 8.236586 TGTGTTAGCAGCATAATGAGTTAAAAG 58.763 33.333 0.00 0.00 0.00 2.27
4533 10632 7.609918 TGTTAGCAGCATAATGAGTTAAAAGGA 59.390 33.333 0.00 0.00 0.00 3.36
4534 10633 8.624776 GTTAGCAGCATAATGAGTTAAAAGGAT 58.375 33.333 0.00 0.00 0.00 3.24
4598 10697 9.586150 CATAATGAGTTGACGCTTTATTGTATC 57.414 33.333 4.19 0.00 0.00 2.24
4727 10904 4.464069 AGTGAGGAAAGTACAGAGCATC 57.536 45.455 0.00 0.00 0.00 3.91
5009 11186 5.640147 TGAGGTTACCCATTGAAACTGAAT 58.360 37.500 0.00 0.00 0.00 2.57
5147 11324 1.391577 TGCTTGTTCATGCAGTGTGT 58.608 45.000 8.85 0.00 34.84 3.72
5241 11418 3.430790 GGCTTTGGCATTCCTGGAATTAC 60.431 47.826 19.12 14.62 40.87 1.89
5247 11424 3.385755 GGCATTCCTGGAATTACTGCAAT 59.614 43.478 25.66 2.04 28.94 3.56
5265 11442 6.317140 ACTGCAATATCGAATCATGAGTTTGT 59.683 34.615 0.09 0.00 0.00 2.83
5353 11530 4.761739 ACAGGACAATGAACAACATAGTGG 59.238 41.667 0.00 0.00 38.38 4.00
5702 11882 3.756117 ACTGCTTTTTCTTCGGGAAGAT 58.244 40.909 11.60 0.00 45.78 2.40
5728 11908 2.604914 CGAAGACGATTGATCCTGTTGG 59.395 50.000 0.00 0.00 42.66 3.77
5729 11909 3.600388 GAAGACGATTGATCCTGTTGGT 58.400 45.455 0.00 0.00 34.23 3.67
5730 11910 3.703001 AGACGATTGATCCTGTTGGTT 57.297 42.857 0.00 0.00 34.23 3.67
5731 11911 3.338249 AGACGATTGATCCTGTTGGTTG 58.662 45.455 0.00 0.00 34.23 3.77
5770 11950 3.245668 AAGCTGGTGTCGCTGGAGG 62.246 63.158 0.00 0.00 37.87 4.30
5780 11960 2.420890 GCTGGAGGGATCTCAGCG 59.579 66.667 12.35 0.00 41.69 5.18
5840 12020 5.022227 AGTTATATGGGATCTGCTCCTCT 57.978 43.478 0.00 0.00 44.28 3.69
5934 12114 4.591498 TGAGTTACCTTAGGAAAGCAGACA 59.409 41.667 4.77 0.00 0.00 3.41
5997 12178 7.916977 GTCAGCAATGTGATATTTTCTGCAATA 59.083 33.333 0.00 0.00 0.00 1.90
6079 12260 2.673368 CAAACACTGCTTCGGAGGTATC 59.327 50.000 0.00 0.00 0.00 2.24
6122 12303 0.515127 TATCACACAAAACTGGCGCG 59.485 50.000 0.00 0.00 0.00 6.86
6207 12388 6.526526 TGCTTGGTACTGTCTACATTTACAA 58.473 36.000 0.00 0.00 0.00 2.41
6213 12394 7.439955 TGGTACTGTCTACATTTACAACACTTG 59.560 37.037 0.00 0.00 0.00 3.16
6231 12412 4.153835 CACTTGATCTCTCAAACTTCCAGC 59.846 45.833 0.00 0.00 40.78 4.85
6232 12413 3.340814 TGATCTCTCAAACTTCCAGCC 57.659 47.619 0.00 0.00 0.00 4.85
6255 12436 5.536916 CCCCATGTTCAAGTTAAACCTAACA 59.463 40.000 0.00 0.00 40.03 2.41
6393 12574 1.280133 CCGCATATCTGACCCATCCAT 59.720 52.381 0.00 0.00 0.00 3.41
6396 12577 4.384537 CCGCATATCTGACCCATCCATAAT 60.385 45.833 0.00 0.00 0.00 1.28
6488 12669 3.191162 GCACAACAAACATGCCTGAGATA 59.809 43.478 0.00 0.00 33.06 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.959535 AATCATTGGCAACCGTTCATT 57.040 38.095 0.00 0.00 0.00 2.57
7 8 3.380004 GGATAATCATTGGCAACCGTTCA 59.620 43.478 0.00 0.00 0.00 3.18
10 11 1.946768 CGGATAATCATTGGCAACCGT 59.053 47.619 13.21 0.00 35.40 4.83
230 233 5.360714 TCTGCTTTCCCATATCCAATTTCAC 59.639 40.000 0.00 0.00 0.00 3.18
286 289 0.178992 CTCCACCCCAGCAAGTTCAA 60.179 55.000 0.00 0.00 0.00 2.69
354 357 2.029073 CTCGTCCACGCCACAGTT 59.971 61.111 0.00 0.00 39.60 3.16
391 395 5.426689 TTTACATCTCTGTCAGCTCCATT 57.573 39.130 0.00 0.00 36.79 3.16
410 414 8.630037 GGAAAAGAAAGATGTTGTCTCCTTTTA 58.370 33.333 13.27 0.00 42.85 1.52
419 423 7.840931 ACTGAAAAGGAAAAGAAAGATGTTGT 58.159 30.769 0.00 0.00 0.00 3.32
697 707 8.491045 AATCTGATGTTTCTTTTCCCCTAAAA 57.509 30.769 0.00 0.00 35.74 1.52
698 708 8.367156 CAAATCTGATGTTTCTTTTCCCCTAAA 58.633 33.333 0.00 0.00 0.00 1.85
699 709 7.508977 ACAAATCTGATGTTTCTTTTCCCCTAA 59.491 33.333 0.00 0.00 0.00 2.69
700 710 7.010160 ACAAATCTGATGTTTCTTTTCCCCTA 58.990 34.615 0.00 0.00 0.00 3.53
701 711 5.840693 ACAAATCTGATGTTTCTTTTCCCCT 59.159 36.000 0.00 0.00 0.00 4.79
702 712 6.101650 ACAAATCTGATGTTTCTTTTCCCC 57.898 37.500 0.00 0.00 0.00 4.81
712 722 8.729805 TTTTGCCTAAAAACAAATCTGATGTT 57.270 26.923 0.00 0.00 42.56 2.71
713 723 8.729805 TTTTTGCCTAAAAACAAATCTGATGT 57.270 26.923 0.00 0.00 39.99 3.06
792 802 3.299503 GCCCACCCACATTGATAGATTT 58.700 45.455 0.00 0.00 0.00 2.17
793 803 2.424812 GGCCCACCCACATTGATAGATT 60.425 50.000 0.00 0.00 0.00 2.40
795 805 0.550914 GGCCCACCCACATTGATAGA 59.449 55.000 0.00 0.00 0.00 1.98
796 806 0.819259 CGGCCCACCCACATTGATAG 60.819 60.000 0.00 0.00 0.00 2.08
797 807 1.225983 CGGCCCACCCACATTGATA 59.774 57.895 0.00 0.00 0.00 2.15
1019 1032 3.369997 GCCTAGTGGAGAAGAGGAAAAGG 60.370 52.174 0.00 0.00 34.57 3.11
1052 1065 0.666577 GCCGTTCGTGCAGAAGTAGT 60.667 55.000 0.00 0.00 39.95 2.73
1060 1073 2.515057 AAGTTGGCCGTTCGTGCA 60.515 55.556 0.00 0.00 0.00 4.57
1126 1139 0.680921 CCGGGTCGTAGTAGAACCCA 60.681 60.000 16.61 0.00 45.03 4.51
1291 1304 1.681327 ACCACCGCCGTACATCTCT 60.681 57.895 0.00 0.00 0.00 3.10
1378 1391 0.463295 AAGCTCGGATCAGCACCATG 60.463 55.000 7.70 0.00 42.40 3.66
2059 2097 3.051081 AGCTGTTTCAGATGACCAGAC 57.949 47.619 11.13 4.85 32.44 3.51
2121 2159 1.548081 CATCATGGAAGTTGTGCCCA 58.452 50.000 0.00 0.00 0.00 5.36
2149 2187 1.796796 GCTGAACCGATGAGTTGGC 59.203 57.895 0.00 0.00 31.34 4.52
2160 2198 1.599542 GGATACAATGCTCGCTGAACC 59.400 52.381 0.00 0.00 0.00 3.62
2227 2265 2.755836 ATGCACAAGTCGAAACACAC 57.244 45.000 0.00 0.00 0.00 3.82
2375 2413 0.232303 GTGAAACCGTTGCAGAGTCG 59.768 55.000 0.00 0.00 0.00 4.18
2642 2682 2.526304 AGTGTCGCAGCTTGAACTAA 57.474 45.000 0.00 0.00 0.00 2.24
2643 2683 2.526304 AAGTGTCGCAGCTTGAACTA 57.474 45.000 0.00 0.00 0.00 2.24
2644 2684 2.526304 TAAGTGTCGCAGCTTGAACT 57.474 45.000 0.00 0.00 0.00 3.01
2645 2685 3.813529 AATAAGTGTCGCAGCTTGAAC 57.186 42.857 0.00 0.00 0.00 3.18
2647 2687 6.144078 TCTATAATAAGTGTCGCAGCTTGA 57.856 37.500 0.00 0.00 0.00 3.02
2648 2688 6.183359 CGATCTATAATAAGTGTCGCAGCTTG 60.183 42.308 0.00 0.00 0.00 4.01
2668 2723 5.769162 GTGTTATTACTACTCCCTCCGATCT 59.231 44.000 0.00 0.00 0.00 2.75
2963 3018 8.903820 CCTTCCACTTTCCTTGTATAAAATAGG 58.096 37.037 0.00 0.00 0.00 2.57
3026 3081 9.732130 AAGCTTAATTGATACAGAAGAAGTTCT 57.268 29.630 0.00 0.00 44.40 3.01
3127 3182 2.664402 ACAGCCATGATAATGTCCCC 57.336 50.000 0.00 0.00 0.00 4.81
3228 3283 7.347222 AGACCATTGGACATATGAAACCTACTA 59.653 37.037 10.37 0.00 0.00 1.82
3229 3284 6.158695 AGACCATTGGACATATGAAACCTACT 59.841 38.462 10.37 0.00 0.00 2.57
3230 3285 6.260936 CAGACCATTGGACATATGAAACCTAC 59.739 42.308 10.37 0.00 0.00 3.18
3268 6170 2.135933 GTTTTGGTGACTCTCCTGACG 58.864 52.381 0.00 0.00 0.00 4.35
3323 6302 6.868339 GCTCTATACAACAAAACAAAGGCATT 59.132 34.615 0.00 0.00 0.00 3.56
3330 6309 7.541091 CGTCTAGAGCTCTATACAACAAAACAA 59.459 37.037 28.65 6.51 0.00 2.83
3338 6317 5.922053 TGTACCGTCTAGAGCTCTATACAA 58.078 41.667 28.65 16.31 0.00 2.41
3340 6319 9.985730 ATATATGTACCGTCTAGAGCTCTATAC 57.014 37.037 23.48 23.20 0.00 1.47
3482 9215 1.630369 AGCATAGTGGAGACAGGCAAA 59.370 47.619 0.00 0.00 44.46 3.68
3549 9282 2.628657 GACTATGCTCCCATTCCGTAGT 59.371 50.000 0.00 0.00 34.84 2.73
3576 9309 2.433888 TGCCTTTCCCGCACATCA 59.566 55.556 0.00 0.00 0.00 3.07
3706 9439 4.709250 TGGCTACATTAAACACACTGTGA 58.291 39.130 16.30 0.00 36.96 3.58
3941 9676 5.587844 AGTGTCAGCAAGCCAAGAATAATAG 59.412 40.000 0.00 0.00 0.00 1.73
3980 9715 8.203485 TCAATTTTTAGCACCAAGAAACTTGAT 58.797 29.630 12.25 0.00 30.68 2.57
4205 9941 2.099405 CATCTTGTTACCCCCGCAAAT 58.901 47.619 0.00 0.00 0.00 2.32
4243 10024 2.728007 GCTACCCTCAGCCTCATTTTT 58.272 47.619 0.00 0.00 35.40 1.94
4300 10084 5.889289 GGGGCAAATAAACCAGTGTATCTTA 59.111 40.000 0.00 0.00 0.00 2.10
4384 10168 4.837298 GGGACGGAGGGAGTATTAGTTAAT 59.163 45.833 0.00 0.00 0.00 1.40
4504 10603 5.551760 AACTCATTATGCTGCTAACACAC 57.448 39.130 0.00 0.00 0.00 3.82
4531 10630 5.357878 TGAAGATGCAGGAAACATGTAATCC 59.642 40.000 18.52 18.52 0.00 3.01
4533 10632 7.414222 AATGAAGATGCAGGAAACATGTAAT 57.586 32.000 0.00 0.00 0.00 1.89
4534 10633 6.839124 AATGAAGATGCAGGAAACATGTAA 57.161 33.333 0.00 0.00 0.00 2.41
4598 10697 7.760131 ATTGTATCAATTTGAAATTCGCTGG 57.240 32.000 2.68 0.00 0.00 4.85
4727 10904 4.763073 TGTTACCATCTCAGAGAAGCATG 58.237 43.478 3.63 0.00 0.00 4.06
5147 11324 8.800370 TTTAATACCAATGCATCTGTTACTGA 57.200 30.769 0.00 0.00 0.00 3.41
5241 11418 6.631636 CACAAACTCATGATTCGATATTGCAG 59.368 38.462 0.00 0.00 0.00 4.41
5247 11424 6.595326 AGCTTTCACAAACTCATGATTCGATA 59.405 34.615 0.00 0.00 0.00 2.92
5265 11442 9.825972 CATAGTTTTCTCGAAATTTAGCTTTCA 57.174 29.630 0.00 0.00 35.32 2.69
5353 11530 3.365832 CCATGCACGTTCATAAAGATGC 58.634 45.455 0.00 0.00 32.62 3.91
5728 11908 2.792749 CACACTTTTCGGTGAACCAAC 58.207 47.619 0.00 0.00 40.13 3.77
5729 11909 1.133407 GCACACTTTTCGGTGAACCAA 59.867 47.619 0.00 0.00 40.13 3.67
5730 11910 0.736053 GCACACTTTTCGGTGAACCA 59.264 50.000 0.00 0.00 40.13 3.67
5731 11911 1.002792 GAGCACACTTTTCGGTGAACC 60.003 52.381 1.52 0.00 40.13 3.62
5770 11950 0.739561 AACTACGACCGCTGAGATCC 59.260 55.000 0.00 0.00 0.00 3.36
5780 11960 2.028385 ACCAACAGGATCAACTACGACC 60.028 50.000 0.00 0.00 0.00 4.79
6079 12260 3.543680 AAGATCTGGAATGGTGTACCG 57.456 47.619 0.00 0.00 39.43 4.02
6119 12300 3.933155 AGAGCTGAATAAAATGTCGCG 57.067 42.857 0.00 0.00 0.00 5.87
6122 12303 8.394121 CAAGTAGGAAGAGCTGAATAAAATGTC 58.606 37.037 0.00 0.00 0.00 3.06
6207 12388 5.296151 TGGAAGTTTGAGAGATCAAGTGT 57.704 39.130 0.00 0.00 0.00 3.55
6213 12394 2.637947 GGGCTGGAAGTTTGAGAGATC 58.362 52.381 0.00 0.00 35.30 2.75
6231 12412 5.536916 TGTTAGGTTTAACTTGAACATGGGG 59.463 40.000 0.00 0.00 39.90 4.96
6232 12413 6.642707 TGTTAGGTTTAACTTGAACATGGG 57.357 37.500 0.00 0.00 39.90 4.00
6285 12466 1.308998 CGACAAACAGCAAAGAGGGT 58.691 50.000 0.00 0.00 0.00 4.34
6488 12669 6.433404 ACATGTCTTTCTGAAATTCAGCATCT 59.567 34.615 17.58 1.13 43.95 2.90


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

AutoCloner maintained by Alex Coulton.