Multiple sequence alignment - TraesCS3B01G470800

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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 TraesCS3B01G470800 chr3B 100.000 7298 0 0 939 8236 719092119 719084822 0.000000e+00 13477.0
1 TraesCS3B01G470800 chr3B 100.000 639 0 0 1 639 719093057 719092419 0.000000e+00 1181.0
2 TraesCS3B01G470800 chr3A 96.508 6758 181 28 967 7684 680359357 680352615 0.000000e+00 11121.0
3 TraesCS3B01G470800 chr3A 90.484 578 45 3 3 570 680360111 680359534 0.000000e+00 754.0
4 TraesCS3B01G470800 chr3A 92.637 421 20 5 7824 8236 680352373 680351956 5.500000e-166 595.0
5 TraesCS3B01G470800 chr3D 96.197 5785 155 25 939 6706 543509438 543503702 0.000000e+00 9404.0
6 TraesCS3B01G470800 chr3D 94.182 911 38 8 6734 7630 543503381 543502472 0.000000e+00 1375.0
7 TraesCS3B01G470800 chr3D 90.968 620 25 11 3 592 543510312 543509694 0.000000e+00 806.0
8 TraesCS3B01G470800 chr3D 93.750 416 21 3 7822 8236 543502214 543501803 3.270000e-173 619.0
9 TraesCS3B01G470800 chr7A 90.136 811 37 14 3411 4206 575280817 575280035 0.000000e+00 1014.0
10 TraesCS3B01G470800 chr7A 93.902 82 5 0 4703 4784 575275790 575275709 3.120000e-24 124.0
11 TraesCS3B01G470800 chr7A 96.552 58 2 0 943 1000 554935470 554935527 6.800000e-16 97.1
12 TraesCS3B01G470800 chr7A 94.444 54 3 0 3589 3642 35092043 35092096 5.300000e-12 84.2
13 TraesCS3B01G470800 chrUn 100.000 386 0 0 4272 4657 480633002 480632617 0.000000e+00 713.0
14 TraesCS3B01G470800 chr2B 80.781 973 105 31 2795 3754 32099875 32100778 0.000000e+00 686.0
15 TraesCS3B01G470800 chr6A 89.865 148 5 1 4733 4880 437967361 437967224 1.830000e-41 182.0
16 TraesCS3B01G470800 chr6A 98.276 58 1 0 943 1000 351963541 351963598 1.460000e-17 102.0
17 TraesCS3B01G470800 chr5A 89.865 148 5 1 4733 4880 515747092 515747229 1.830000e-41 182.0


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 TraesCS3B01G470800 chr3B 719084822 719093057 8235 True 7329.000000 13477 100.000000 1 8236 2 chr3B.!!$R1 8235
1 TraesCS3B01G470800 chr3A 680351956 680360111 8155 True 4156.666667 11121 93.209667 3 8236 3 chr3A.!!$R1 8233
2 TraesCS3B01G470800 chr3D 543501803 543510312 8509 True 3051.000000 9404 93.774250 3 8236 4 chr3D.!!$R1 8233
3 TraesCS3B01G470800 chr7A 575280035 575280817 782 True 1014.000000 1014 90.136000 3411 4206 1 chr7A.!!$R2 795
4 TraesCS3B01G470800 chr2B 32099875 32100778 903 False 686.000000 686 80.781000 2795 3754 1 chr2B.!!$F1 959

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
463 498 1.215647 CCGTCTCCTCCCAGAAACG 59.784 63.158 0.00 0.0 0.00 3.60 F
1371 1415 0.109723 ACCATGGCACGTAGGTTGTT 59.890 50.000 13.04 0.0 0.00 2.83 F
1988 2050 0.321387 GAAGGAAGTGGACCGGGAAC 60.321 60.000 6.32 0.0 0.00 3.62 F
3450 3519 0.693430 AGGCTCCAGATGATGCTCCA 60.693 55.000 0.00 0.0 0.00 3.86 F
5270 5357 0.034089 GCCTGGTGGTGCTCCTTTAT 60.034 55.000 6.34 0.0 35.27 1.40 F
5314 5401 0.541392 TAGCACGTCATCATGGCCTT 59.459 50.000 3.32 0.0 0.00 4.35 F
6151 6238 1.021968 AGCCACACAACGAACTTTCC 58.978 50.000 0.00 0.0 0.00 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1760 1811 0.182537 TGCTTGTAACAGCACCCAGT 59.817 50.000 0.00 0.00 45.14 4.00 R
2245 2307 0.896019 CACGGGAGTCTGACTCAGGT 60.896 60.000 32.16 25.96 46.79 4.00 R
3462 3531 0.753262 GGTACGGCATGAGGTCAGAT 59.247 55.000 0.00 0.00 0.00 2.90 R
5314 5401 2.108075 ACCATGTGTTTCCATCTGACCA 59.892 45.455 0.00 0.00 0.00 4.02 R
6482 6578 0.031449 GGGTTTGCTGTGCGCTTTAA 59.969 50.000 9.73 0.00 40.11 1.52 R
6524 6620 1.611977 TGAAGACAGATCCGTTGACGT 59.388 47.619 2.63 0.00 37.74 4.34 R
8048 8574 0.179056 ATACCAATTCTGTCCCGGCG 60.179 55.000 0.00 0.00 0.00 6.46 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
53 54 2.799488 TTTCGATGACACCGCGCGTA 62.799 55.000 29.95 9.69 0.00 4.42
131 136 1.604755 GCGACATGAGTATCCTCTCGT 59.395 52.381 0.00 0.00 36.09 4.18
132 137 2.350007 GCGACATGAGTATCCTCTCGTC 60.350 54.545 0.00 0.00 36.09 4.20
142 147 2.433868 TCCTCTCGTCCAAGTTTTCG 57.566 50.000 0.00 0.00 0.00 3.46
145 150 1.721926 CTCTCGTCCAAGTTTTCGCTC 59.278 52.381 0.00 0.00 0.00 5.03
148 153 1.866925 GTCCAAGTTTTCGCTCCGG 59.133 57.895 0.00 0.00 0.00 5.14
157 162 5.441709 AGTTTTCGCTCCGGAAATTTTAA 57.558 34.783 5.23 0.00 36.70 1.52
158 163 5.458015 AGTTTTCGCTCCGGAAATTTTAAG 58.542 37.500 5.23 0.00 36.70 1.85
169 194 6.324254 TCCGGAAATTTTAAGGTCCAGAAAAA 59.676 34.615 0.00 2.79 0.00 1.94
210 241 1.604278 GCACAAACAACTGAGGGAGAC 59.396 52.381 0.00 0.00 0.00 3.36
242 273 2.295909 CGAAAACCAGATCCAAAAGCCA 59.704 45.455 0.00 0.00 0.00 4.75
279 310 5.475719 ACAAGATCGACGTTTAGGATCAAA 58.524 37.500 16.71 0.00 39.17 2.69
307 338 3.970842 ACAACCTCCCTGTTTAACAACA 58.029 40.909 0.00 0.00 40.82 3.33
308 339 3.697542 ACAACCTCCCTGTTTAACAACAC 59.302 43.478 0.00 0.00 38.03 3.32
463 498 1.215647 CCGTCTCCTCCCAGAAACG 59.784 63.158 0.00 0.00 0.00 3.60
971 1006 2.189784 GCCCGAAACCCTAGCTCC 59.810 66.667 0.00 0.00 0.00 4.70
1151 1186 2.693591 CGTATGGGTAGATCTGTGTGGT 59.306 50.000 5.18 0.00 0.00 4.16
1159 1194 1.589716 GATCTGTGTGGTTGGCTGGC 61.590 60.000 0.00 0.00 0.00 4.85
1217 1252 2.634777 CTCTCGCTCGGGATCGAC 59.365 66.667 0.00 0.00 40.88 4.20
1290 1325 1.683365 TACCCTCGTTTCTCCCGGG 60.683 63.158 16.85 16.85 40.79 5.73
1313 1348 0.110056 CACATCAGTGTTGCTTCGGC 60.110 55.000 0.94 0.00 40.92 5.54
1317 1352 0.319900 TCAGTGTTGCTTCGGCTCTC 60.320 55.000 0.00 0.00 42.37 3.20
1322 1357 2.033424 GTGTTGCTTCGGCTCTCTTTTT 59.967 45.455 0.00 0.00 42.37 1.94
1349 1393 3.118261 TGTTCTTATTAGCTGCTGAGGGG 60.118 47.826 13.43 0.05 0.00 4.79
1367 1411 0.251073 GGTTACCATGGCACGTAGGT 59.749 55.000 13.04 7.71 38.14 3.08
1371 1415 0.109723 ACCATGGCACGTAGGTTGTT 59.890 50.000 13.04 0.00 0.00 2.83
1399 1443 4.688021 CTCTACTGTCTGTAGGATTTGGC 58.312 47.826 14.79 0.00 46.45 4.52
1459 1504 2.899838 TGCACGTGTGGACCTTGC 60.900 61.111 18.38 0.00 0.00 4.01
1511 1560 1.352622 TTGGGGTGGCAGTCTGAGTT 61.353 55.000 3.32 0.00 0.00 3.01
1512 1561 1.352622 TGGGGTGGCAGTCTGAGTTT 61.353 55.000 3.32 0.00 0.00 2.66
1514 1563 1.518903 GGGTGGCAGTCTGAGTTTGC 61.519 60.000 3.32 3.08 37.11 3.68
1547 1596 5.410132 TGTTATTGAGTACGTGTTTGATGGG 59.590 40.000 0.00 0.00 0.00 4.00
1548 1597 3.478857 TTGAGTACGTGTTTGATGGGT 57.521 42.857 0.00 0.00 0.00 4.51
1549 1598 4.603989 TTGAGTACGTGTTTGATGGGTA 57.396 40.909 0.00 0.00 0.00 3.69
1578 1627 3.133362 TGGTTTTACTGAGTCGTTGACCT 59.867 43.478 0.00 0.00 32.18 3.85
1622 1671 0.322277 CAGCAGCACCTGGAGAACAT 60.322 55.000 0.00 0.00 31.21 2.71
1675 1724 1.213537 CCAAGCGATGCCAAGGTTG 59.786 57.895 8.03 8.03 43.17 3.77
1760 1811 7.455638 AGTCAGTGTTATTTACCTAGGGTGTTA 59.544 37.037 14.81 0.00 36.19 2.41
1761 1812 7.547019 GTCAGTGTTATTTACCTAGGGTGTTAC 59.453 40.741 14.81 4.62 36.19 2.50
1771 1833 1.060163 AGGGTGTTACTGGGTGCTGT 61.060 55.000 0.00 0.00 0.00 4.40
1840 1902 1.681166 CCTCATGGGTCCTTGCTTGAG 60.681 57.143 0.00 0.00 0.00 3.02
1897 1959 2.704012 GCTAAGAAAGAGCGCCGC 59.296 61.111 2.29 0.00 0.00 6.53
1988 2050 0.321387 GAAGGAAGTGGACCGGGAAC 60.321 60.000 6.32 0.00 0.00 3.62
2170 2232 0.882474 ACGACAAGGAGAAGGACTCG 59.118 55.000 0.00 0.00 45.76 4.18
2311 2373 1.819903 GAGACTCAGACCAGTGGTACC 59.180 57.143 16.72 4.43 35.25 3.34
2709 2771 5.686753 TCTTTTAAAGTGGCTGTTCACCTA 58.313 37.500 4.53 0.00 38.34 3.08
2712 2774 6.569179 TTTAAAGTGGCTGTTCACCTATTC 57.431 37.500 0.00 0.00 38.34 1.75
2756 2818 6.305399 CAGTTTATTTATCCGTTTGTGTGCTG 59.695 38.462 0.00 0.00 0.00 4.41
2859 2925 7.118535 GGAGAGAAACAAAGATCTTGAAGGTAC 59.881 40.741 9.17 0.00 0.00 3.34
2887 2953 6.967135 CATCATGGGATGCATATATTACTGC 58.033 40.000 0.00 0.00 44.03 4.40
2982 3048 6.610075 ATTGATGCCAACAAGGATAAAAGT 57.390 33.333 0.00 0.00 41.22 2.66
3027 3093 1.676529 CATGAAGGATCTGCTGCCTTG 59.323 52.381 7.14 0.00 44.23 3.61
3042 3108 4.630111 CTGCCTTGATATCAGAGAAGGAC 58.370 47.826 20.75 13.68 37.74 3.85
3043 3109 3.389329 TGCCTTGATATCAGAGAAGGACC 59.611 47.826 20.75 8.08 37.74 4.46
3209 3278 7.664318 TGATATCGATCCTAGCACTAAGTTACA 59.336 37.037 0.00 0.00 0.00 2.41
3402 3471 7.821846 GTCTCCTGGTATGAAGATGGATATTTC 59.178 40.741 0.00 0.00 0.00 2.17
3450 3519 0.693430 AGGCTCCAGATGATGCTCCA 60.693 55.000 0.00 0.00 0.00 3.86
3462 3531 0.546122 ATGCTCCATTTCGCCCACTA 59.454 50.000 0.00 0.00 0.00 2.74
3755 3827 2.037136 GTCAGCAGCGCATTCCTGT 61.037 57.895 11.47 0.00 32.93 4.00
3764 3836 1.128692 GCGCATTCCTGTAACTGTGAC 59.871 52.381 0.30 0.00 0.00 3.67
3788 3860 4.287067 TCAGGATGCTGAAGGTTAGTTTCT 59.713 41.667 15.31 0.00 34.76 2.52
3830 3910 6.799512 AGTGTTTTTCTTCACATTCTCTTGG 58.200 36.000 0.00 0.00 37.07 3.61
4118 4205 5.164620 TCTCTCATCAAATGTGCTTGGTA 57.835 39.130 0.00 0.00 0.00 3.25
4132 4219 2.808543 GCTTGGTATAAATGAGCGGAGG 59.191 50.000 0.00 0.00 0.00 4.30
5119 5206 2.158475 TGCCTCCAGACTTGGTCAATTT 60.158 45.455 0.52 0.00 45.26 1.82
5176 5263 2.028294 GGAGCATCATGACCATCTCGAT 60.028 50.000 0.00 0.00 36.25 3.59
5224 5311 2.039084 GCATAGGGGAGGTCAAGGTATG 59.961 54.545 0.00 0.00 0.00 2.39
5270 5357 0.034089 GCCTGGTGGTGCTCCTTTAT 60.034 55.000 6.34 0.00 35.27 1.40
5314 5401 0.541392 TAGCACGTCATCATGGCCTT 59.459 50.000 3.32 0.00 0.00 4.35
5560 5647 4.666412 TGTGGAAATGAACCTTCCCATA 57.334 40.909 0.00 0.00 41.54 2.74
5713 5800 3.242413 CGGCATCATTTGGACGTAAAGAG 60.242 47.826 0.00 0.00 0.00 2.85
6151 6238 1.021968 AGCCACACAACGAACTTTCC 58.978 50.000 0.00 0.00 0.00 3.13
6229 6323 6.397272 CATCCAAGTTCTGATATCTAGGCTC 58.603 44.000 3.98 0.00 0.00 4.70
6275 6369 4.945246 TGTGTTCCTTCAGTACTCTGTTC 58.055 43.478 0.00 0.00 41.91 3.18
6321 6416 9.793259 TCTTTATTATGTTCACTTTTCCAGAGT 57.207 29.630 0.00 0.00 0.00 3.24
6323 6418 6.727824 ATTATGTTCACTTTTCCAGAGTCG 57.272 37.500 0.00 0.00 0.00 4.18
6346 6441 8.601476 GTCGATTAGGTATTTTACTTGTCCAAG 58.399 37.037 5.51 5.51 43.79 3.61
6482 6578 2.002625 GGAAGCTCCCATTCCCTGT 58.997 57.895 0.00 0.00 40.37 4.00
6612 6708 1.084289 GGTACGCCATGTTCAACCTC 58.916 55.000 0.00 0.00 34.09 3.85
6713 6810 7.433708 TGTTAAGTCCAATAATATCCATGCG 57.566 36.000 0.00 0.00 0.00 4.73
6740 7130 8.814038 AGCTAATTGAATTAACTGAAGACCAT 57.186 30.769 0.40 0.00 0.00 3.55
6858 7254 5.316987 ACTTGAGGATTCTACAAAAGGGTG 58.683 41.667 0.00 0.00 0.00 4.61
6953 7349 2.359230 GTCACCTCAGCAGCCCAC 60.359 66.667 0.00 0.00 0.00 4.61
7244 7640 1.671850 CCCGACGACTAACATGCTTGT 60.672 52.381 0.00 0.00 37.82 3.16
7403 7800 5.073144 TGTCAAGTTGAAATTAGGAGGGAGT 59.927 40.000 7.25 0.00 0.00 3.85
7466 7865 5.010112 AGGATACATGAATCTGTACAGGACG 59.990 44.000 22.48 8.25 34.59 4.79
7547 7950 6.256053 TCTTAATTCCTCAGGCCATTTCTTT 58.744 36.000 5.01 0.00 0.00 2.52
7581 7984 5.179452 TGAACAAGCCTAGCTTCCTTATT 57.821 39.130 0.00 0.00 46.77 1.40
7585 7988 6.253946 ACAAGCCTAGCTTCCTTATTATGT 57.746 37.500 0.00 0.00 46.77 2.29
7589 7992 8.470002 CAAGCCTAGCTTCCTTATTATGTTTTT 58.530 33.333 0.00 0.00 46.77 1.94
7590 7993 9.695155 AAGCCTAGCTTCCTTATTATGTTTTTA 57.305 29.630 0.00 0.00 46.77 1.52
7591 7994 9.695155 AGCCTAGCTTCCTTATTATGTTTTTAA 57.305 29.630 0.00 0.00 33.89 1.52
7616 8021 5.450688 GGTTAGAGGATATACATAGCAGCCG 60.451 48.000 0.00 0.00 0.00 5.52
7638 8043 2.779755 AACGTGGCATTATCCAGTCA 57.220 45.000 0.00 0.00 36.67 3.41
7639 8044 3.281727 AACGTGGCATTATCCAGTCAT 57.718 42.857 0.00 0.00 36.67 3.06
7640 8045 4.415881 AACGTGGCATTATCCAGTCATA 57.584 40.909 0.00 0.00 36.67 2.15
7641 8046 3.995199 ACGTGGCATTATCCAGTCATAG 58.005 45.455 0.00 0.00 36.67 2.23
7644 8049 4.816385 CGTGGCATTATCCAGTCATAGTTT 59.184 41.667 0.00 0.00 36.67 2.66
7645 8050 5.989168 CGTGGCATTATCCAGTCATAGTTTA 59.011 40.000 0.00 0.00 36.67 2.01
7650 8056 9.502091 GGCATTATCCAGTCATAGTTTAATGTA 57.498 33.333 0.00 0.00 31.46 2.29
7686 8146 4.413969 GTTTCTCGAGCTGTAGGACTAAC 58.586 47.826 7.81 0.00 0.00 2.34
7702 8162 6.206042 AGGACTAACCAGAGGATTATGAAGT 58.794 40.000 0.00 0.00 42.04 3.01
7726 8186 4.935205 CAGACATGGAATCCTAAACGAACA 59.065 41.667 0.00 0.00 0.00 3.18
7728 8188 5.586243 AGACATGGAATCCTAAACGAACATG 59.414 40.000 0.00 0.00 40.04 3.21
7740 8200 4.553330 AACGAACATGGTCAGATTAGGT 57.447 40.909 12.13 0.00 0.00 3.08
7748 8208 5.241506 ACATGGTCAGATTAGGTTGTTGTTG 59.758 40.000 0.00 0.00 0.00 3.33
7785 8245 3.382865 TCAGTTTGCCTTGTTTGTGCATA 59.617 39.130 0.00 0.00 34.51 3.14
7789 8249 2.591923 TGCCTTGTTTGTGCATAGGAA 58.408 42.857 0.00 0.00 0.00 3.36
7845 8365 8.955061 TCTCATTCTTTTGAATCGAAATGAAC 57.045 30.769 6.41 0.00 46.51 3.18
7909 8433 7.230466 TCTTCTTCTACGTTCTTGTGAAAAC 57.770 36.000 0.00 0.00 33.52 2.43
7914 8438 6.497785 TCTACGTTCTTGTGAAAACCAAAA 57.502 33.333 0.00 0.00 33.52 2.44
8188 8714 0.905357 AGGGATCTCAACGGTGAAGG 59.095 55.000 3.93 0.00 31.88 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.621526 CCCTAAAACAACTCGGTTGCTT 59.378 45.455 14.29 7.78 46.20 3.91
1 2 2.227194 CCCTAAAACAACTCGGTTGCT 58.773 47.619 14.29 2.60 46.20 3.91
53 54 2.406002 AAACGGACGGTGGATTGCCT 62.406 55.000 0.00 0.00 34.31 4.75
120 125 3.858238 CGAAAACTTGGACGAGAGGATAC 59.142 47.826 0.00 0.00 0.00 2.24
131 136 0.107081 TTCCGGAGCGAAAACTTGGA 59.893 50.000 3.34 0.00 0.00 3.53
132 137 0.948678 TTTCCGGAGCGAAAACTTGG 59.051 50.000 3.34 0.00 0.00 3.61
142 147 3.086282 TGGACCTTAAAATTTCCGGAGC 58.914 45.455 3.34 0.00 0.00 4.70
145 150 5.715434 TTTCTGGACCTTAAAATTTCCGG 57.285 39.130 0.00 0.00 36.03 5.14
192 217 1.843851 TGGTCTCCCTCAGTTGTTTGT 59.156 47.619 0.00 0.00 0.00 2.83
210 241 3.211045 TCTGGTTTTCGGAGAAAAGTGG 58.789 45.455 8.04 2.80 45.90 4.00
223 254 3.037549 TGTGGCTTTTGGATCTGGTTTT 58.962 40.909 0.00 0.00 0.00 2.43
242 273 6.797513 CGTCGATCTTGTATATTCGATTCTGT 59.202 38.462 0.00 0.00 41.96 3.41
279 310 0.475828 ACAGGGAGGTTGTTAGGGCT 60.476 55.000 0.00 0.00 0.00 5.19
308 339 9.578439 CCTGCTTTATTTCTTTCTTAATTGGAG 57.422 33.333 0.00 0.00 0.00 3.86
463 498 2.438434 CGGGGATGGGAACTGTGC 60.438 66.667 0.00 0.00 0.00 4.57
1169 1204 4.289342 CGAAACAAGCACACATCAAATCA 58.711 39.130 0.00 0.00 0.00 2.57
1217 1252 2.728817 GCGGTGGACCTATCCTCG 59.271 66.667 0.00 0.86 46.43 4.63
1278 1313 1.670083 GTGGTTCCCGGGAGAAACG 60.670 63.158 25.26 0.00 36.17 3.60
1290 1325 2.349817 CGAAGCAACACTGATGTGGTTC 60.350 50.000 5.06 5.06 42.21 3.62
1322 1357 6.072508 CCTCAGCAGCTAATAAGAACAACAAA 60.073 38.462 0.00 0.00 0.00 2.83
1325 1360 4.333926 CCCTCAGCAGCTAATAAGAACAAC 59.666 45.833 0.00 0.00 0.00 3.32
1326 1361 4.517285 CCCTCAGCAGCTAATAAGAACAA 58.483 43.478 0.00 0.00 0.00 2.83
1328 1363 3.118223 ACCCCTCAGCAGCTAATAAGAAC 60.118 47.826 0.00 0.00 0.00 3.01
1330 1365 2.764269 ACCCCTCAGCAGCTAATAAGA 58.236 47.619 0.00 0.00 0.00 2.10
1342 1386 0.394352 GTGCCATGGTAACCCCTCAG 60.394 60.000 14.67 0.00 0.00 3.35
1349 1393 1.735571 CAACCTACGTGCCATGGTAAC 59.264 52.381 14.67 11.41 31.82 2.50
1386 1430 4.437682 TCCCATAAGCCAAATCCTACAG 57.562 45.455 0.00 0.00 0.00 2.74
1399 1443 4.406649 AGCAACCATTCCATTTCCCATAAG 59.593 41.667 0.00 0.00 0.00 1.73
1459 1504 4.394941 CAGTCGCACGCACGAACG 62.395 66.667 1.58 0.00 44.93 3.95
1511 1560 2.480037 CTCAATAACAGCTCACACGCAA 59.520 45.455 0.00 0.00 0.00 4.85
1512 1561 2.068519 CTCAATAACAGCTCACACGCA 58.931 47.619 0.00 0.00 0.00 5.24
1514 1563 3.300853 CGTACTCAATAACAGCTCACACG 59.699 47.826 0.00 0.00 0.00 4.49
1547 1596 6.534079 ACGACTCAGTAAAACCATGCTATTAC 59.466 38.462 0.00 0.00 0.00 1.89
1548 1597 6.636705 ACGACTCAGTAAAACCATGCTATTA 58.363 36.000 0.00 0.00 0.00 0.98
1549 1598 5.488341 ACGACTCAGTAAAACCATGCTATT 58.512 37.500 0.00 0.00 0.00 1.73
1622 1671 1.079490 ACTGAGGGGACAGAGGAATGA 59.921 52.381 0.00 0.00 40.63 2.57
1675 1724 3.008049 ACAGAAATAGGACACCAGTGACC 59.992 47.826 10.75 10.75 43.96 4.02
1760 1811 0.182537 TGCTTGTAACAGCACCCAGT 59.817 50.000 0.00 0.00 45.14 4.00
1761 1812 3.019964 TGCTTGTAACAGCACCCAG 57.980 52.632 0.00 0.00 45.14 4.45
1771 1833 6.652900 TCTGCACAGTTAATACATGCTTGTAA 59.347 34.615 15.56 0.00 41.51 2.41
1840 1902 2.421248 CCTCCCATCTTTCTCAGAAGGC 60.421 54.545 0.00 0.00 38.86 4.35
1857 1919 0.545646 AGAGCCTTCAAGCATCCTCC 59.454 55.000 0.00 0.00 34.23 4.30
1882 1944 2.508439 CGGCGGCGCTCTTTCTTA 60.508 61.111 32.30 0.00 0.00 2.10
1988 2050 3.060363 CGATCGTTTTTACGGTTCTCCAG 59.940 47.826 7.03 0.00 0.00 3.86
2170 2232 5.047802 TGCATCCATCTTCTTTTCTGGTTTC 60.048 40.000 0.00 0.00 0.00 2.78
2224 2286 2.257207 AGCAGCCTTACAGGAAGTGTA 58.743 47.619 0.00 0.00 40.94 2.90
2245 2307 0.896019 CACGGGAGTCTGACTCAGGT 60.896 60.000 32.16 25.96 46.79 4.00
2311 2373 3.913573 GCAGCACGGTATGTCGCG 61.914 66.667 0.00 0.00 32.22 5.87
2670 2732 4.541973 AAAAGAAACCATGAAGGGCATC 57.458 40.909 0.00 0.00 43.89 3.91
2709 2771 9.975218 AACTGGGTAGTAGTGATAAAAATGAAT 57.025 29.630 0.00 0.00 35.69 2.57
2756 2818 6.759497 AATATCTTCCAAAACAGCCTGTAC 57.241 37.500 0.00 0.00 0.00 2.90
2887 2953 6.590068 AGGAACAGAAGAATCATATGACAGG 58.410 40.000 7.78 0.00 0.00 4.00
3048 3114 3.270027 TGCGAACATCCCTTCATTGTAG 58.730 45.455 0.00 0.00 0.00 2.74
3209 3278 6.769134 TGAACTGAGCATTTGAATCATCAT 57.231 33.333 0.00 0.00 34.96 2.45
3402 3471 0.811616 GCACAGGTAGCTCCAATCCG 60.812 60.000 0.00 0.00 39.02 4.18
3450 3519 2.103263 GAGGTCAGATAGTGGGCGAAAT 59.897 50.000 0.00 0.00 0.00 2.17
3462 3531 0.753262 GGTACGGCATGAGGTCAGAT 59.247 55.000 0.00 0.00 0.00 2.90
3755 3827 3.165071 TCAGCATCCTGAGTCACAGTTA 58.835 45.455 0.00 0.00 42.98 2.24
3830 3910 6.214191 TCAGAGTTTCAGACATGGATAGAC 57.786 41.667 0.00 0.00 0.00 2.59
4118 4205 2.711009 TGGGATTCCTCCGCTCATTTAT 59.289 45.455 2.01 0.00 43.11 1.40
4132 4219 1.087501 GAGCTGTCGGTTTGGGATTC 58.912 55.000 0.00 0.00 0.00 2.52
4270 4357 3.131046 GGGAAATTAGCCCTGACATGTTG 59.869 47.826 0.00 0.00 42.56 3.33
5119 5206 2.259917 TGAAGGGACTGCAGAAGATCA 58.740 47.619 23.35 14.35 40.52 2.92
5176 5263 4.560128 GTTCATGCATAGATAGGCTTCGA 58.440 43.478 0.00 0.00 33.54 3.71
5270 5357 5.105392 GGGCATTTACAACATCAGGATTTGA 60.105 40.000 9.56 0.00 40.85 2.69
5314 5401 2.108075 ACCATGTGTTTCCATCTGACCA 59.892 45.455 0.00 0.00 0.00 4.02
5560 5647 2.965805 CCATGCATGTGGGTTGTCT 58.034 52.632 24.58 0.00 35.55 3.41
5713 5800 1.949525 TGTGCAAAGAGTGAAGAAGGC 59.050 47.619 0.00 0.00 0.00 4.35
5899 5986 3.451526 CATTGTCGCAGAGCTTGATCTA 58.548 45.455 0.00 0.00 36.95 1.98
6194 6288 3.647590 AGAACTTGGATGGGTTTGCAAAT 59.352 39.130 16.21 0.00 0.00 2.32
6201 6295 5.983333 AGATATCAGAACTTGGATGGGTT 57.017 39.130 5.32 0.00 0.00 4.11
6321 6416 8.712285 CTTGGACAAGTAAAATACCTAATCGA 57.288 34.615 3.93 0.00 33.87 3.59
6346 6441 9.594038 CACTATGTGTAAACTGACAATAACAAC 57.406 33.333 0.00 0.00 0.00 3.32
6382 6478 4.323553 ACTAGAGAACCAACTGTGTGTC 57.676 45.455 0.00 0.00 0.00 3.67
6482 6578 0.031449 GGGTTTGCTGTGCGCTTTAA 59.969 50.000 9.73 0.00 40.11 1.52
6524 6620 1.611977 TGAAGACAGATCCGTTGACGT 59.388 47.619 2.63 0.00 37.74 4.34
6612 6708 4.790766 GCATGAGAAGAAAACCACACAGTG 60.791 45.833 0.00 0.00 0.00 3.66
6713 6810 9.162764 TGGTCTTCAGTTAATTCAATTAGCTAC 57.837 33.333 6.22 2.08 35.01 3.58
6816 7207 2.484264 AGTCAGTAAGCGGAACATTTGC 59.516 45.455 0.00 0.00 0.00 3.68
6953 7349 4.389576 GCAGTGGCTTCAACGGCG 62.390 66.667 4.80 4.80 36.96 6.46
7130 7526 7.147915 TGCTTTCCTTTCTTTGCTTTCTTCTTA 60.148 33.333 0.00 0.00 0.00 2.10
7244 7640 2.289565 TGTACACAAAATGGCACGACA 58.710 42.857 0.00 0.00 0.00 4.35
7466 7865 0.537143 TACATGCCCATGATTCCGGC 60.537 55.000 14.69 0.00 41.20 6.13
7547 7950 1.004745 GCTTGTTCAATCAGGGAGGGA 59.995 52.381 0.00 0.00 0.00 4.20
7589 7992 7.342284 GGCTGCTATGTATATCCTCTAACCTTA 59.658 40.741 0.00 0.00 0.00 2.69
7590 7993 6.155393 GGCTGCTATGTATATCCTCTAACCTT 59.845 42.308 0.00 0.00 0.00 3.50
7591 7994 5.659079 GGCTGCTATGTATATCCTCTAACCT 59.341 44.000 0.00 0.00 0.00 3.50
7597 8000 3.024547 TCCGGCTGCTATGTATATCCTC 58.975 50.000 0.00 0.00 0.00 3.71
7600 8003 3.612860 CGTTTCCGGCTGCTATGTATATC 59.387 47.826 0.00 0.00 0.00 1.63
7601 8004 3.006537 ACGTTTCCGGCTGCTATGTATAT 59.993 43.478 0.00 0.00 38.78 0.86
7603 8006 1.138266 ACGTTTCCGGCTGCTATGTAT 59.862 47.619 0.00 0.00 38.78 2.29
7606 8009 1.705337 CCACGTTTCCGGCTGCTATG 61.705 60.000 0.00 0.00 38.78 2.23
7616 8021 2.354821 GACTGGATAATGCCACGTTTCC 59.645 50.000 0.00 0.00 33.52 3.13
7639 8044 9.305555 ACCAGTACTGAGACTTACATTAAACTA 57.694 33.333 24.68 0.00 0.00 2.24
7640 8045 8.191534 ACCAGTACTGAGACTTACATTAAACT 57.808 34.615 24.68 0.00 0.00 2.66
7641 8046 8.828688 AACCAGTACTGAGACTTACATTAAAC 57.171 34.615 24.68 0.00 0.00 2.01
7644 8049 8.418597 AGAAACCAGTACTGAGACTTACATTA 57.581 34.615 24.68 0.00 0.00 1.90
7645 8050 7.304497 AGAAACCAGTACTGAGACTTACATT 57.696 36.000 24.68 5.32 0.00 2.71
7650 8056 4.142790 TCGAGAAACCAGTACTGAGACTT 58.857 43.478 24.68 10.84 0.00 3.01
7686 8146 5.604758 TGTCTGACTTCATAATCCTCTGG 57.395 43.478 9.51 0.00 0.00 3.86
7702 8162 5.175859 GTTCGTTTAGGATTCCATGTCTGA 58.824 41.667 5.29 0.00 0.00 3.27
7726 8186 4.218417 GCAACAACAACCTAATCTGACCAT 59.782 41.667 0.00 0.00 0.00 3.55
7728 8188 3.821033 AGCAACAACAACCTAATCTGACC 59.179 43.478 0.00 0.00 0.00 4.02
7758 8218 4.033129 CACAAACAAGGCAAACTGACATTG 59.967 41.667 0.00 0.00 0.00 2.82
7763 8223 1.547820 TGCACAAACAAGGCAAACTGA 59.452 42.857 0.00 0.00 34.05 3.41
7766 8226 3.059166 CCTATGCACAAACAAGGCAAAC 58.941 45.455 0.00 0.00 41.43 2.93
7785 8245 3.452878 TCAAATCCCCATTTGCATTCCT 58.547 40.909 3.05 0.00 46.01 3.36
7789 8249 3.839490 TCAACTCAAATCCCCATTTGCAT 59.161 39.130 3.05 0.00 46.01 3.96
7796 8256 6.985653 TTTTACAATCAACTCAAATCCCCA 57.014 33.333 0.00 0.00 0.00 4.96
7828 8348 7.042321 ACACTAGTCGTTCATTTCGATTCAAAA 60.042 33.333 0.00 0.00 39.45 2.44
7886 8410 6.036735 TGGTTTTCACAAGAACGTAGAAGAAG 59.963 38.462 0.00 0.00 32.39 2.85
7909 8433 2.159028 TCGTTTTTCAGGGCCTTTTTGG 60.159 45.455 1.32 0.00 39.35 3.28
7914 8438 1.318576 CTGTCGTTTTTCAGGGCCTT 58.681 50.000 1.32 0.00 0.00 4.35
8048 8574 0.179056 ATACCAATTCTGTCCCGGCG 60.179 55.000 0.00 0.00 0.00 6.46
8188 8714 4.828925 GCTGCTGCCGGTCTCTCC 62.829 72.222 1.90 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.