Multiple sequence alignment - TraesCS1B01G129200

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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 TraesCS1B01G129200 chr1B 100.000 2865 0 0 1 2865 159205267 159202403 0.000000e+00 5291
1 TraesCS1B01G129200 chr1A 91.723 2356 127 30 2 2333 110072004 110074315 0.000000e+00 3208
2 TraesCS1B01G129200 chr1A 90.000 320 30 2 2548 2865 110079853 110080172 2.050000e-111 412
3 TraesCS1B01G129200 chr1D 92.585 1942 77 17 224 2139 107501640 107503540 0.000000e+00 2726
4 TraesCS1B01G129200 chr1D 86.290 744 70 14 2135 2865 107509075 107509799 0.000000e+00 780
5 TraesCS1B01G129200 chr4B 78.261 207 35 9 2624 2827 134953089 134953288 1.080000e-24 124
6 TraesCS1B01G129200 chr4A 77.143 210 34 9 2623 2830 484537143 484536946 3.020000e-20 110


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 TraesCS1B01G129200 chr1B 159202403 159205267 2864 True 5291 5291 100.000 1 2865 1 chr1B.!!$R1 2864
1 TraesCS1B01G129200 chr1A 110072004 110074315 2311 False 3208 3208 91.723 2 2333 1 chr1A.!!$F1 2331
2 TraesCS1B01G129200 chr1D 107501640 107503540 1900 False 2726 2726 92.585 224 2139 1 chr1D.!!$F1 1915
3 TraesCS1B01G129200 chr1D 107509075 107509799 724 False 780 780 86.290 2135 2865 1 chr1D.!!$F2 730

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
82 83 0.246360 TCACAGTGTGGCATCCGTAG 59.754 55.0 22.79 0.0 33.87 3.51 F
104 105 2.863137 GCAACTGGCTTCGATCTCTTAG 59.137 50.0 0.00 0.0 40.25 2.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1207 1239 0.173481 TCGAAACGGATCTCTGGCTG 59.827 55.0 0.0 0.0 0.00 4.85 R
1976 2014 1.281419 TGGCAATACCTTCCCTCGAA 58.719 50.0 0.0 0.0 40.22 3.71 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
21 22 1.170290 AGCTGGCCGTACAAACAACC 61.170 55.000 0.00 0.00 0.00 3.77
28 29 2.496111 CCGTACAAACAACCTAGGCAA 58.504 47.619 9.30 0.00 0.00 4.52
42 43 6.252599 ACCTAGGCAATCAATCATGTTCTA 57.747 37.500 9.30 0.00 0.00 2.10
61 62 5.468540 TCTATGTGGGATTTCTCATACCG 57.531 43.478 0.00 0.00 0.00 4.02
68 69 4.202253 TGGGATTTCTCATACCGATCACAG 60.202 45.833 0.00 0.00 0.00 3.66
74 75 1.134818 TCATACCGATCACAGTGTGGC 60.135 52.381 22.79 14.01 33.87 5.01
77 78 0.391661 ACCGATCACAGTGTGGCATC 60.392 55.000 22.79 17.10 33.87 3.91
79 80 1.423721 CGATCACAGTGTGGCATCCG 61.424 60.000 22.79 14.30 33.87 4.18
82 83 0.246360 TCACAGTGTGGCATCCGTAG 59.754 55.000 22.79 0.00 33.87 3.51
104 105 2.863137 GCAACTGGCTTCGATCTCTTAG 59.137 50.000 0.00 0.00 40.25 2.18
107 108 4.379339 ACTGGCTTCGATCTCTTAGAAC 57.621 45.455 0.00 0.00 0.00 3.01
140 141 6.751514 AGGATGATGTAGACGAGCTATAAG 57.248 41.667 0.00 0.00 0.00 1.73
145 146 9.320352 GATGATGTAGACGAGCTATAAGAGATA 57.680 37.037 0.00 0.00 0.00 1.98
149 150 8.481974 TGTAGACGAGCTATAAGAGATATCAC 57.518 38.462 5.32 0.00 0.00 3.06
154 155 8.341892 ACGAGCTATAAGAGATATCACATCAA 57.658 34.615 5.32 0.00 0.00 2.57
182 183 6.817765 TTGCCTAGTTGAAATAGGAAACAG 57.182 37.500 21.63 0.00 42.15 3.16
185 186 5.586643 GCCTAGTTGAAATAGGAAACAGAGG 59.413 44.000 21.63 0.00 42.15 3.69
195 196 4.632327 AGGAAACAGAGGAAAGAGAAGG 57.368 45.455 0.00 0.00 0.00 3.46
349 374 6.940739 AGCTATTACATTGGCTATACCTGAG 58.059 40.000 0.00 0.00 40.22 3.35
418 443 5.504173 GCTCTTAGGCATCGTTTGGATAAAC 60.504 44.000 0.00 0.00 42.14 2.01
434 459 9.968870 TTTGGATAAACTTTTGGTTGTATACAC 57.031 29.630 4.68 1.11 38.29 2.90
443 468 6.582677 TTTGGTTGTATACACCAAATCAGG 57.417 37.500 29.26 0.00 45.30 3.86
456 481 4.766891 ACCAAATCAGGTAGATGGTTGTTG 59.233 41.667 0.00 0.00 36.44 3.33
800 827 5.956068 AAATGAGACAAGCTCTTTTCCTC 57.044 39.130 0.00 0.00 43.53 3.71
825 855 2.924290 GCACAGCTGCACTAGTTAGTAC 59.076 50.000 15.27 0.00 43.62 2.73
941 971 4.260985 TCATTTGTATGTTCCACTGCGAT 58.739 39.130 0.00 0.00 33.34 4.58
1053 1085 3.279116 TTGTCGTCGTCGTCGGGT 61.279 61.111 11.74 0.00 38.33 5.28
1207 1239 9.567848 TTCTTGTTTTGTTCATACTGAAAAGTC 57.432 29.630 0.00 0.00 38.22 3.01
1261 1293 2.939103 CAGATGACGAAACCAATCCCTC 59.061 50.000 0.00 0.00 0.00 4.30
1281 1313 3.815401 CTCAAACCAAGTTGACAGGGTAG 59.185 47.826 3.87 0.00 33.92 3.18
1488 1523 1.024271 ACACGATTGCAAGCAACAGT 58.976 45.000 15.98 10.01 38.88 3.55
1525 1560 0.037697 CCAACGAGATCACCGTCCAA 60.038 55.000 12.46 0.00 39.57 3.53
1541 1576 4.402528 AATGCTACACCGCCGCCA 62.403 61.111 0.00 0.00 0.00 5.69
1560 1595 3.033764 CGACAACCGGACCACGTG 61.034 66.667 9.46 9.08 42.24 4.49
1566 1601 2.358125 CCGGACCACGTGCATTCA 60.358 61.111 10.91 0.00 42.24 2.57
1582 1617 3.807538 CATGCCACCGTCAGCTGC 61.808 66.667 9.47 3.23 0.00 5.25
1613 1648 2.283529 GGCCTCTTCGTGGGTCTGA 61.284 63.158 0.00 0.00 0.00 3.27
1621 1656 3.311110 GTGGGTCTGACCGGAGCA 61.311 66.667 19.98 9.81 39.83 4.26
1712 1747 2.203480 TGTTGTGCAAGGAGGGCC 60.203 61.111 0.00 0.00 0.00 5.80
1835 1873 4.444164 GCAAGAGGGAGAGGATTTTAGAGG 60.444 50.000 0.00 0.00 0.00 3.69
1836 1874 3.935172 AGAGGGAGAGGATTTTAGAGGG 58.065 50.000 0.00 0.00 0.00 4.30
1837 1875 2.976185 GAGGGAGAGGATTTTAGAGGGG 59.024 54.545 0.00 0.00 0.00 4.79
1838 1876 1.422024 GGGAGAGGATTTTAGAGGGGC 59.578 57.143 0.00 0.00 0.00 5.80
1903 1941 7.201938 GGGAAGAATATTTTCAGATGGAATGCA 60.202 37.037 0.00 0.00 34.91 3.96
1964 2002 0.537188 CAGTCGAGCCAGGGTATTGT 59.463 55.000 0.00 0.00 0.00 2.71
1966 2004 0.535335 GTCGAGCCAGGGTATTGTGA 59.465 55.000 0.00 0.00 0.00 3.58
1967 2005 1.139058 GTCGAGCCAGGGTATTGTGAT 59.861 52.381 0.00 0.00 0.00 3.06
1968 2006 2.364324 GTCGAGCCAGGGTATTGTGATA 59.636 50.000 0.00 0.00 0.00 2.15
1969 2007 2.364324 TCGAGCCAGGGTATTGTGATAC 59.636 50.000 0.00 0.00 37.90 2.24
1994 2032 2.413310 TTTCGAGGGAAGGTATTGCC 57.587 50.000 0.00 0.00 46.85 4.52
2053 2091 3.973206 TGGTATGTCATGGTCTCGTTT 57.027 42.857 0.00 0.00 0.00 3.60
2056 2094 2.010145 ATGTCATGGTCTCGTTTCGG 57.990 50.000 0.00 0.00 0.00 4.30
2058 2096 1.341852 TGTCATGGTCTCGTTTCGGAA 59.658 47.619 0.00 0.00 0.00 4.30
2059 2097 1.993370 GTCATGGTCTCGTTTCGGAAG 59.007 52.381 0.00 0.00 0.00 3.46
2123 2161 2.901192 TGTCACGGGTTCTTCATTCCTA 59.099 45.455 0.00 0.00 0.00 2.94
2127 2165 4.712829 TCACGGGTTCTTCATTCCTATGTA 59.287 41.667 0.00 0.00 33.34 2.29
2133 2171 6.833933 GGGTTCTTCATTCCTATGTATGGTTT 59.166 38.462 0.00 0.00 33.34 3.27
2209 2248 6.406288 CCTCGCATATCCATGTCATGTAGTAT 60.406 42.308 11.84 4.52 34.40 2.12
2210 2249 6.935167 TCGCATATCCATGTCATGTAGTATT 58.065 36.000 11.84 0.00 34.40 1.89
2211 2250 8.062065 TCGCATATCCATGTCATGTAGTATTA 57.938 34.615 11.84 0.00 34.40 0.98
2263 2311 9.606631 TTAAACAATAACTTCCAGCAACATTTT 57.393 25.926 0.00 0.00 0.00 1.82
2274 2322 8.674263 TTCCAGCAACATTTTCATTGTATTTT 57.326 26.923 0.00 0.00 0.00 1.82
2319 2367 3.243839 ACAATGTCAAGCAAAATTCGGCT 60.244 39.130 0.00 0.00 43.46 5.52
2327 2375 3.642705 AGCAAAATTCGGCTGAAAGAAC 58.357 40.909 12.96 1.47 39.30 3.01
2337 2385 2.254671 CTGAAAGAACGAGCGCGACG 62.255 60.000 19.05 23.29 37.19 5.12
2338 2386 2.050714 AAAGAACGAGCGCGACGA 60.051 55.556 29.23 0.00 41.64 4.20
2339 2387 1.988696 GAAAGAACGAGCGCGACGAG 61.989 60.000 29.23 11.95 41.64 4.18
2340 2388 3.948086 AAGAACGAGCGCGACGAGG 62.948 63.158 29.23 8.57 41.64 4.63
2341 2389 4.755614 GAACGAGCGCGACGAGGT 62.756 66.667 29.23 16.97 41.64 3.85
2350 2398 4.415332 CGACGAGGTGTGGTCCGG 62.415 72.222 0.00 0.00 0.00 5.14
2351 2399 3.300765 GACGAGGTGTGGTCCGGT 61.301 66.667 0.00 0.00 0.00 5.28
2352 2400 3.569049 GACGAGGTGTGGTCCGGTG 62.569 68.421 0.00 0.00 0.00 4.94
2385 2434 2.262915 GAGCAGTGAGACGGGGTG 59.737 66.667 0.00 0.00 0.00 4.61
2422 2472 7.798710 TTATCCATAGGAGAGGAATAACCAG 57.201 40.000 0.00 0.00 36.66 4.00
2429 2479 4.410555 AGGAGAGGAATAACCAGGTGATTC 59.589 45.833 18.90 18.90 42.04 2.52
2447 2497 6.154363 GGTGATTCCTTTGATTTGGTGGAATA 59.846 38.462 5.66 0.00 44.57 1.75
2490 2540 3.330998 GGAATATTCCTTCCCCGAGGATT 59.669 47.826 24.74 0.00 44.98 3.01
2493 2543 1.503800 TTCCTTCCCCGAGGATTACC 58.496 55.000 0.00 0.00 44.98 2.85
2512 2562 1.916181 CCTGGTTCCTGTACCATCCTT 59.084 52.381 0.00 0.00 46.63 3.36
2515 2565 4.514401 CTGGTTCCTGTACCATCCTTAAC 58.486 47.826 0.00 0.00 46.63 2.01
2525 2575 6.469410 TGTACCATCCTTAACTAAACACTGG 58.531 40.000 0.00 0.00 0.00 4.00
2539 2589 0.911769 CACTGGAATGGTGGGCTAGA 59.088 55.000 0.00 0.00 0.00 2.43
2540 2590 1.134280 CACTGGAATGGTGGGCTAGAG 60.134 57.143 0.00 0.00 0.00 2.43
2543 2593 1.204146 GGAATGGTGGGCTAGAGACA 58.796 55.000 0.00 0.00 0.00 3.41
2544 2594 1.559682 GGAATGGTGGGCTAGAGACAA 59.440 52.381 0.00 0.00 0.00 3.18
2546 2596 3.274288 GAATGGTGGGCTAGAGACAAAG 58.726 50.000 0.00 0.00 0.00 2.77
2552 2602 2.972713 TGGGCTAGAGACAAAGTCAACT 59.027 45.455 0.00 1.83 34.60 3.16
2554 2604 3.246619 GGCTAGAGACAAAGTCAACTCG 58.753 50.000 0.00 0.00 34.60 4.18
2571 2621 5.475909 TCAACTCGTCTAGTTCCACTGTATT 59.524 40.000 0.00 0.00 45.64 1.89
2588 2638 5.181690 TGTATTCTCAAAGCAAACACACC 57.818 39.130 0.00 0.00 0.00 4.16
2596 2646 3.577805 AAGCAAACACACCCTTAGAGT 57.422 42.857 0.00 0.00 0.00 3.24
2598 2648 1.880027 GCAAACACACCCTTAGAGTGG 59.120 52.381 0.00 0.00 39.63 4.00
2612 2662 9.004231 ACCCTTAGAGTGGAGAACAAATATATT 57.996 33.333 0.00 0.00 0.00 1.28
2618 2668 9.965902 AGAGTGGAGAACAAATATATTTTCTGT 57.034 29.630 14.41 6.35 0.00 3.41
2619 2669 9.994432 GAGTGGAGAACAAATATATTTTCTGTG 57.006 33.333 14.41 5.19 0.00 3.66
2660 2712 4.082354 GCTCTGCCAAGTTCATTCAAAGAT 60.082 41.667 0.00 0.00 0.00 2.40
2682 2734 8.668510 AGATGAATACGAAAATACAGATTGCT 57.331 30.769 0.00 0.00 0.00 3.91
2702 2754 3.057946 GCTCTGCTTACAAGGGAAACAAG 60.058 47.826 0.00 0.00 0.00 3.16
2728 2780 5.009210 TCGAAAACCACAACATTAGGAAAGG 59.991 40.000 0.00 0.00 0.00 3.11
2733 2785 5.393866 ACCACAACATTAGGAAAGGACAAT 58.606 37.500 0.00 0.00 0.00 2.71
2735 2787 6.158598 CCACAACATTAGGAAAGGACAATTG 58.841 40.000 3.24 3.24 0.00 2.32
2743 2795 2.802247 GGAAAGGACAATTGTGCAAAGC 59.198 45.455 28.72 15.71 38.96 3.51
2747 2799 0.681175 GACAATTGTGCAAAGCCCCT 59.319 50.000 17.58 0.00 0.00 4.79
2749 2801 0.037046 CAATTGTGCAAAGCCCCTCC 60.037 55.000 0.00 0.00 0.00 4.30
2766 2818 4.446311 CCCCTCCAAAAGAAGAGAAACAGA 60.446 45.833 0.00 0.00 31.43 3.41
2769 2821 6.096846 CCCTCCAAAAGAAGAGAAACAGAAAA 59.903 38.462 0.00 0.00 31.43 2.29
2789 2841 2.888834 AGAAACAACAATGGCCACAC 57.111 45.000 8.16 0.00 0.00 3.82
2840 2892 3.055719 ACAATCCGGTGCTTGGCG 61.056 61.111 0.00 0.00 0.00 5.69
2841 2893 4.481112 CAATCCGGTGCTTGGCGC 62.481 66.667 0.00 0.00 38.45 6.53
2848 2900 2.173382 GTGCTTGGCGCGTAGTTG 59.827 61.111 8.43 0.00 43.27 3.16
2858 2910 2.350498 GGCGCGTAGTTGATAATGTTGT 59.650 45.455 8.43 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.081462 GTTGTTTGTACGGCCAGCTAT 58.919 47.619 2.24 0.00 0.00 2.97
21 22 7.308408 CCACATAGAACATGATTGATTGCCTAG 60.308 40.741 0.00 0.00 0.00 3.02
28 29 8.003044 AGAAATCCCACATAGAACATGATTGAT 58.997 33.333 0.00 0.00 0.00 2.57
42 43 4.347876 TGATCGGTATGAGAAATCCCACAT 59.652 41.667 0.00 0.00 0.00 3.21
61 62 0.391661 ACGGATGCCACACTGTGATC 60.392 55.000 15.86 6.72 35.23 2.92
68 69 1.376683 TTGCCTACGGATGCCACAC 60.377 57.895 0.00 0.00 0.00 3.82
74 75 0.392998 AAGCCAGTTGCCTACGGATG 60.393 55.000 0.00 0.00 42.71 3.51
77 78 2.100631 CGAAGCCAGTTGCCTACGG 61.101 63.158 0.00 0.00 42.71 4.02
79 80 1.134670 AGATCGAAGCCAGTTGCCTAC 60.135 52.381 0.00 0.00 42.71 3.18
82 83 0.107945 AGAGATCGAAGCCAGTTGCC 60.108 55.000 0.00 0.00 42.71 4.52
88 89 4.220821 ACTTGTTCTAAGAGATCGAAGCCA 59.779 41.667 0.00 0.00 0.00 4.75
107 108 9.995957 CTCGTCTACATCATCCTATTATACTTG 57.004 37.037 0.00 0.00 0.00 3.16
145 146 8.523915 TCAACTAGGCAAATATTTGATGTGAT 57.476 30.769 28.33 9.55 40.55 3.06
176 177 6.944234 TTTTCCTTCTCTTTCCTCTGTTTC 57.056 37.500 0.00 0.00 0.00 2.78
207 208 3.568538 CAGCCAGCTGTAAATTCACAAC 58.431 45.455 13.81 0.00 39.10 3.32
208 209 3.921119 CAGCCAGCTGTAAATTCACAA 57.079 42.857 13.81 0.00 39.10 3.33
434 459 4.766891 ACAACAACCATCTACCTGATTTGG 59.233 41.667 0.00 0.00 30.88 3.28
443 468 3.660865 ACTTCCGACAACAACCATCTAC 58.339 45.455 0.00 0.00 0.00 2.59
456 481 3.328237 TTTTGCGAGAAAACTTCCGAC 57.672 42.857 0.00 0.00 0.00 4.79
488 513 4.312443 TCCTACAAACTGGTTTCGACATC 58.688 43.478 0.00 0.00 0.00 3.06
847 877 1.971695 GGTGAACAAAGCGAGGGGG 60.972 63.158 0.00 0.00 0.00 5.40
941 971 5.303078 AGAAGCAAAGTCTCTACTCACTCAA 59.697 40.000 0.00 0.00 33.75 3.02
1036 1068 1.900585 CTACCCGACGACGACGACAA 61.901 60.000 20.63 4.76 42.66 3.18
1053 1085 4.790962 ACCTCCGTCGCGCTCCTA 62.791 66.667 5.56 0.00 0.00 2.94
1207 1239 0.173481 TCGAAACGGATCTCTGGCTG 59.827 55.000 0.00 0.00 0.00 4.85
1244 1276 2.882137 GTTTGAGGGATTGGTTTCGTCA 59.118 45.455 0.00 0.00 0.00 4.35
1261 1293 2.293399 GCTACCCTGTCAACTTGGTTTG 59.707 50.000 0.00 0.00 32.27 2.93
1281 1313 2.746269 TGTTTCAGCAGCAAATTCAGC 58.254 42.857 0.00 0.00 0.00 4.26
1525 1560 4.838152 CTGGCGGCGGTGTAGCAT 62.838 66.667 9.78 0.00 39.27 3.79
1541 1576 4.657824 CGTGGTCCGGTTGTCGCT 62.658 66.667 0.00 0.00 37.59 4.93
1597 1632 1.592223 GGTCAGACCCACGAAGAGG 59.408 63.158 8.65 0.00 38.25 3.69
1637 1672 1.345741 CTCTGTTCTCAGCACCCTCAA 59.654 52.381 0.00 0.00 41.10 3.02
1774 1809 2.041265 ACCATCTCCGGGAAGGCT 59.959 61.111 12.41 0.00 40.77 4.58
1837 1875 4.830765 TACATGACCGGGCAGCGC 62.831 66.667 18.96 0.00 0.00 5.92
1838 1876 2.890474 GTACATGACCGGGCAGCG 60.890 66.667 18.96 12.75 0.00 5.18
1903 1941 2.604373 CGACGTGTGTGGATTTGCAATT 60.604 45.455 0.00 0.00 0.00 2.32
1973 2011 3.086282 GGCAATACCTTCCCTCGAAAAA 58.914 45.455 0.00 0.00 34.51 1.94
1974 2012 2.040545 TGGCAATACCTTCCCTCGAAAA 59.959 45.455 0.00 0.00 40.22 2.29
1975 2013 1.631388 TGGCAATACCTTCCCTCGAAA 59.369 47.619 0.00 0.00 40.22 3.46
1976 2014 1.281419 TGGCAATACCTTCCCTCGAA 58.719 50.000 0.00 0.00 40.22 3.71
1977 2015 1.507140 ATGGCAATACCTTCCCTCGA 58.493 50.000 0.00 0.00 40.22 4.04
1978 2016 2.767505 GTATGGCAATACCTTCCCTCG 58.232 52.381 0.00 0.00 40.22 4.63
1994 2032 3.430453 ACCAAACACATCCCAAGGTATG 58.570 45.455 0.00 0.00 0.00 2.39
2053 2091 2.158740 TGACACCAACCATTTCTTCCGA 60.159 45.455 0.00 0.00 0.00 4.55
2056 2094 5.712152 AGAATGACACCAACCATTTCTTC 57.288 39.130 0.00 0.00 33.57 2.87
2058 2096 4.895297 ACAAGAATGACACCAACCATTTCT 59.105 37.500 0.00 0.00 33.57 2.52
2059 2097 4.984161 CACAAGAATGACACCAACCATTTC 59.016 41.667 0.00 0.00 33.57 2.17
2062 2100 3.565307 ACACAAGAATGACACCAACCAT 58.435 40.909 0.00 0.00 0.00 3.55
2063 2101 3.011566 ACACAAGAATGACACCAACCA 57.988 42.857 0.00 0.00 0.00 3.67
2071 2109 2.875933 TCCAACCGAACACAAGAATGAC 59.124 45.455 0.00 0.00 0.00 3.06
2148 2187 6.934645 ACAAGGTGAGTCGAATCAGATTTTTA 59.065 34.615 17.01 0.00 0.00 1.52
2227 2266 9.553064 TGGAAGTTATTGTTTAATGCAAATTGT 57.447 25.926 0.00 0.00 0.00 2.71
2243 2282 7.933033 ACAATGAAAATGTTGCTGGAAGTTATT 59.067 29.630 0.00 0.00 35.30 1.40
2247 2286 5.280654 ACAATGAAAATGTTGCTGGAAGT 57.719 34.783 0.00 0.00 35.30 3.01
2248 2287 7.894376 AATACAATGAAAATGTTGCTGGAAG 57.106 32.000 0.00 0.00 32.27 3.46
2274 2322 9.817809 TTGTACATTGCTAATTGTTAAAACCAA 57.182 25.926 0.00 0.00 0.00 3.67
2319 2367 2.362047 CGTCGCGCTCGTTCTTTCA 61.362 57.895 5.56 0.00 36.96 2.69
2337 2385 4.016706 CCCACCGGACCACACCTC 62.017 72.222 9.46 0.00 0.00 3.85
2340 2388 4.636435 CACCCCACCGGACCACAC 62.636 72.222 9.46 0.00 34.64 3.82
2372 2420 0.108019 GGAAAACACCCCGTCTCACT 59.892 55.000 0.00 0.00 0.00 3.41
2373 2421 0.108019 AGGAAAACACCCCGTCTCAC 59.892 55.000 0.00 0.00 0.00 3.51
2403 2453 4.901849 TCACCTGGTTATTCCTCTCCTATG 59.098 45.833 0.00 0.00 37.07 2.23
2407 2457 4.445019 GGAATCACCTGGTTATTCCTCTCC 60.445 50.000 31.80 15.79 40.88 3.71
2422 2472 3.831911 TCCACCAAATCAAAGGAATCACC 59.168 43.478 0.00 0.00 39.35 4.02
2429 2479 5.185635 TCAAGCTATTCCACCAAATCAAAGG 59.814 40.000 0.00 0.00 0.00 3.11
2433 2483 5.508567 TCATCAAGCTATTCCACCAAATCA 58.491 37.500 0.00 0.00 0.00 2.57
2481 2531 0.468648 GGAACCAGGTAATCCTCGGG 59.531 60.000 3.23 0.00 43.07 5.14
2504 2554 5.836024 TCCAGTGTTTAGTTAAGGATGGT 57.164 39.130 0.00 0.00 0.00 3.55
2505 2555 6.095440 CCATTCCAGTGTTTAGTTAAGGATGG 59.905 42.308 0.00 0.00 0.00 3.51
2512 2562 4.658063 CCCACCATTCCAGTGTTTAGTTA 58.342 43.478 0.00 0.00 33.20 2.24
2515 2565 1.818674 GCCCACCATTCCAGTGTTTAG 59.181 52.381 0.00 0.00 33.20 1.85
2525 2575 3.274288 CTTTGTCTCTAGCCCACCATTC 58.726 50.000 0.00 0.00 0.00 2.67
2571 2621 2.435372 AGGGTGTGTTTGCTTTGAGA 57.565 45.000 0.00 0.00 0.00 3.27
2612 2662 4.389374 CTGCCTTTCTCCTTACACAGAAA 58.611 43.478 0.00 0.00 34.17 2.52
2615 2665 2.303022 TCCTGCCTTTCTCCTTACACAG 59.697 50.000 0.00 0.00 0.00 3.66
2617 2667 2.937433 GCTCCTGCCTTTCTCCTTACAC 60.937 54.545 0.00 0.00 0.00 2.90
2618 2668 1.279271 GCTCCTGCCTTTCTCCTTACA 59.721 52.381 0.00 0.00 0.00 2.41
2619 2669 1.557371 AGCTCCTGCCTTTCTCCTTAC 59.443 52.381 0.00 0.00 40.80 2.34
2660 2712 7.465916 GCAGAGCAATCTGTATTTTCGTATTCA 60.466 37.037 7.07 0.00 39.76 2.57
2682 2734 3.117663 ACCTTGTTTCCCTTGTAAGCAGA 60.118 43.478 0.00 0.00 0.00 4.26
2686 2738 3.735591 TCGACCTTGTTTCCCTTGTAAG 58.264 45.455 0.00 0.00 0.00 2.34
2691 2743 2.691526 GGTTTTCGACCTTGTTTCCCTT 59.308 45.455 0.00 0.00 45.55 3.95
2716 2768 4.832266 TGCACAATTGTCCTTTCCTAATGT 59.168 37.500 8.48 0.00 0.00 2.71
2717 2769 5.389859 TGCACAATTGTCCTTTCCTAATG 57.610 39.130 8.48 0.00 0.00 1.90
2721 2773 3.493176 GCTTTGCACAATTGTCCTTTCCT 60.493 43.478 8.48 0.00 0.00 3.36
2722 2774 2.802247 GCTTTGCACAATTGTCCTTTCC 59.198 45.455 8.48 0.00 0.00 3.13
2728 2780 0.681175 AGGGGCTTTGCACAATTGTC 59.319 50.000 8.48 4.68 30.93 3.18
2733 2785 0.689080 TTTGGAGGGGCTTTGCACAA 60.689 50.000 0.00 0.00 30.93 3.33
2735 2787 0.033920 CTTTTGGAGGGGCTTTGCAC 59.966 55.000 0.00 0.00 0.00 4.57
2743 2795 3.823304 CTGTTTCTCTTCTTTTGGAGGGG 59.177 47.826 0.00 0.00 0.00 4.79
2747 2799 8.348285 TCTTTTTCTGTTTCTCTTCTTTTGGA 57.652 30.769 0.00 0.00 0.00 3.53
2766 2818 4.394610 GTGTGGCCATTGTTGTTTCTTTTT 59.605 37.500 9.72 0.00 0.00 1.94
2769 2821 2.158971 GGTGTGGCCATTGTTGTTTCTT 60.159 45.455 9.72 0.00 37.17 2.52
2789 2841 2.033194 GGAGTTTCGAGTTGGCCGG 61.033 63.158 0.00 0.00 0.00 6.13
2840 2892 4.963953 GCATGACAACATTATCAACTACGC 59.036 41.667 0.00 0.00 34.15 4.42
2841 2893 5.190342 CGCATGACAACATTATCAACTACG 58.810 41.667 0.00 0.00 34.15 3.51


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

AutoCloner maintained by Alex Coulton.