Multiple sequence alignment - TraesCS1B01G325400

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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 TraesCS1B01G325400 chr1B 100.000 2882 0 0 1 2882 551118171 551115290 0.000000e+00 5323.0
1 TraesCS1B01G325400 chr1D 91.981 2918 152 48 1 2882 409350026 409347155 0.000000e+00 4017.0
2 TraesCS1B01G325400 chr1D 78.261 115 24 1 2404 2518 482501198 482501085 3.980000e-09 73.1
3 TraesCS1B01G325400 chr1A 91.285 2926 178 42 1 2882 505339975 505337083 0.000000e+00 3919.0
4 TraesCS1B01G325400 chr7A 81.301 123 18 5 2397 2518 160982020 160982138 8.500000e-16 95.3
5 TraesCS1B01G325400 chr7A 79.167 120 19 4 2391 2507 39272346 39272230 8.560000e-11 78.7
6 TraesCS1B01G325400 chr4B 81.633 98 13 4 2421 2518 568368800 568368892 3.080000e-10 76.8
7 TraesCS1B01G325400 chr7D 80.583 103 14 6 2405 2506 58893096 58892999 1.110000e-09 75.0
8 TraesCS1B01G325400 chr7D 100.000 32 0 0 1241 1272 543739902 543739871 3.100000e-05 60.2
9 TraesCS1B01G325400 chr5D 78.947 114 18 3 2412 2525 528310158 528310265 3.980000e-09 73.1
10 TraesCS1B01G325400 chr4A 78.070 114 22 2 2411 2524 622214647 622214537 5.150000e-08 69.4


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 TraesCS1B01G325400 chr1B 551115290 551118171 2881 True 5323 5323 100.000 1 2882 1 chr1B.!!$R1 2881
1 TraesCS1B01G325400 chr1D 409347155 409350026 2871 True 4017 4017 91.981 1 2882 1 chr1D.!!$R1 2881
2 TraesCS1B01G325400 chr1A 505337083 505339975 2892 True 3919 3919 91.285 1 2882 1 chr1A.!!$R1 2881

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
246 248 0.111832 CCCTGGTCATGGATCATGGG 59.888 60.0 7.88 0.0 41.66 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1984 2001 0.240145 GCAAGCCAACGTTTCTACCC 59.76 55.0 0.0 0.0 0.0 3.69 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
30 31 0.822121 ACCTTTCCAACTTCCGTGGC 60.822 55.000 0.00 0.00 0.00 5.01
42 43 2.727392 CCGTGGCATCGAACCCCTA 61.727 63.158 10.33 0.00 0.00 3.53
126 128 1.142060 TCCAACCGAACCAACATCAGT 59.858 47.619 0.00 0.00 0.00 3.41
191 193 3.443045 CCGTCCCAGCCAACATGC 61.443 66.667 0.00 0.00 0.00 4.06
193 195 2.672996 GTCCCAGCCAACATGCGT 60.673 61.111 0.00 0.00 36.02 5.24
202 204 1.129624 GCCAACATGCGTATTTCGACA 59.870 47.619 0.00 0.00 42.86 4.35
206 208 4.856487 CCAACATGCGTATTTCGACATTTT 59.144 37.500 0.00 0.00 42.86 1.82
207 209 5.344665 CCAACATGCGTATTTCGACATTTTT 59.655 36.000 0.00 0.00 42.86 1.94
218 220 2.803956 TCGACATTTTTGACTTCCGGAC 59.196 45.455 1.83 0.00 0.00 4.79
231 233 3.134804 ACTTCCGGACTATCAAATCCCTG 59.865 47.826 1.83 0.00 0.00 4.45
246 248 0.111832 CCCTGGTCATGGATCATGGG 59.888 60.000 7.88 0.00 41.66 4.00
305 307 3.181397 CAACATGGGCATTTCGACATTC 58.819 45.455 0.00 0.00 0.00 2.67
315 318 2.823924 TTCGACATTCCGACTTCCAA 57.176 45.000 0.00 0.00 38.39 3.53
363 366 5.887598 TCATGGATCCGTCTTTCATGATTTT 59.112 36.000 2.53 0.00 39.15 1.82
418 421 0.324091 ACCAACTCTCGGGGTATCGT 60.324 55.000 0.00 0.00 31.89 3.73
576 579 4.383602 CCCTTTCGTTGCCGTGCG 62.384 66.667 0.00 0.00 35.01 5.34
688 691 3.591023 TCGTTTCAGAAACAGTCACACA 58.409 40.909 23.02 0.43 41.44 3.72
689 692 3.369756 TCGTTTCAGAAACAGTCACACAC 59.630 43.478 23.02 0.00 41.44 3.82
690 693 3.370978 CGTTTCAGAAACAGTCACACACT 59.629 43.478 23.02 0.00 41.44 3.55
691 694 4.492570 CGTTTCAGAAACAGTCACACACTC 60.493 45.833 23.02 0.00 41.44 3.51
928 931 1.389609 CCATCAAGCACCTCCCATGC 61.390 60.000 0.00 0.00 43.74 4.06
950 961 2.189594 TTGACATCCCAGAGCACTTG 57.810 50.000 0.00 0.00 0.00 3.16
951 962 1.059098 TGACATCCCAGAGCACTTGT 58.941 50.000 0.00 0.00 0.00 3.16
952 963 2.256306 TGACATCCCAGAGCACTTGTA 58.744 47.619 0.00 0.00 0.00 2.41
953 964 2.028112 TGACATCCCAGAGCACTTGTAC 60.028 50.000 0.00 0.00 0.00 2.90
974 985 2.030701 CGTAGTAGTCAAGAGGAGTCGC 59.969 54.545 0.00 0.00 0.00 5.19
985 996 0.394488 AGGAGTCGCAGCTAGTAGCA 60.394 55.000 23.77 0.00 45.56 3.49
1059 1070 2.892425 GGTGATCAGAAGGCGCCG 60.892 66.667 23.20 6.78 0.00 6.46
1194 1205 4.746309 GGCTGCATCTGGCCACCA 62.746 66.667 0.00 0.00 46.84 4.17
1239 1250 3.441290 CGAGAGTTCCGGTCGGCT 61.441 66.667 0.00 0.00 34.68 5.52
1302 1313 2.604686 AGGCTCAAGCTGTCCGGA 60.605 61.111 0.00 0.00 41.70 5.14
1447 1458 2.058798 CAGTACGCAGCTTTCTTTCGA 58.941 47.619 0.00 0.00 0.00 3.71
1503 1514 1.693606 AGAACCATTTGGGGCAAACAG 59.306 47.619 0.96 0.00 42.91 3.16
1577 1588 3.753294 AGAGGTGTTTCTTCACGATGT 57.247 42.857 0.00 0.00 39.00 3.06
1641 1652 2.289320 GCTGAAGCTGAGTCTTCTTGGA 60.289 50.000 14.49 0.00 42.15 3.53
1653 1664 0.882927 TTCTTGGACGCCGAACAAGG 60.883 55.000 19.38 6.98 41.35 3.61
1661 1672 0.242825 CGCCGAACAAGGAGTGTCTA 59.757 55.000 0.00 0.00 40.60 2.59
1710 1724 6.741992 AAGATTGTTCATCTATGTCGCAAA 57.258 33.333 0.00 0.00 41.93 3.68
1745 1759 2.104530 GGAGGCTACCGAGTTCGC 59.895 66.667 0.00 0.00 38.18 4.70
1764 1778 2.223479 CGCTCTGTCTTCTTCCTCTAGC 60.223 54.545 0.00 0.00 0.00 3.42
1782 1796 1.417592 CGAGCATCTGCAACGTGAC 59.582 57.895 4.79 0.00 45.16 3.67
1785 1799 1.130613 GCATCTGCAACGTGACGAC 59.869 57.895 13.70 0.73 41.59 4.34
1850 1867 1.536907 TTTGTCCTAGCACCCCGGA 60.537 57.895 0.73 0.00 0.00 5.14
1909 1926 7.997803 ACTATCCAAAACTATACTAGAGTCCGT 59.002 37.037 0.00 0.00 0.00 4.69
1910 1927 6.446781 TCCAAAACTATACTAGAGTCCGTG 57.553 41.667 0.00 0.00 0.00 4.94
1911 1928 5.041940 CCAAAACTATACTAGAGTCCGTGC 58.958 45.833 0.00 0.00 0.00 5.34
1912 1929 5.393787 CCAAAACTATACTAGAGTCCGTGCA 60.394 44.000 0.00 0.00 0.00 4.57
2003 2020 0.240145 GGGTAGAAACGTTGGCTTGC 59.760 55.000 0.00 0.00 0.00 4.01
2005 2022 1.607148 GGTAGAAACGTTGGCTTGCTT 59.393 47.619 0.00 0.00 0.00 3.91
2068 2087 2.892852 TGGGCAAGTCAATTCTCTTTGG 59.107 45.455 0.00 0.00 0.00 3.28
2075 2094 6.145048 GCAAGTCAATTCTCTTTGGAAATGTG 59.855 38.462 0.00 0.00 30.66 3.21
2076 2095 5.776744 AGTCAATTCTCTTTGGAAATGTGC 58.223 37.500 0.00 0.00 30.66 4.57
2097 2116 4.591498 TGCAAAGGTGTACTCTAGAGGAAA 59.409 41.667 23.50 7.87 0.00 3.13
2183 2205 6.921914 TGCATACATGTGTGAAATTCAATGA 58.078 32.000 24.94 0.00 0.00 2.57
2192 2214 8.713737 TGTGTGAAATTCAATGACATTTTTCA 57.286 26.923 16.96 16.96 32.41 2.69
2234 2256 4.819105 TCACCTAGTTGTTTCATCGGAT 57.181 40.909 0.00 0.00 0.00 4.18
2379 2407 1.203928 CGTGGATCATCGTTGCTCTC 58.796 55.000 0.00 0.00 0.00 3.20
2381 2409 2.468831 GTGGATCATCGTTGCTCTCTC 58.531 52.381 0.00 0.00 0.00 3.20
2414 2448 7.862873 CCTTTCTTCTTTGTATTTTCTTTCGCT 59.137 33.333 0.00 0.00 0.00 4.93
2447 2481 6.434028 AGCTTTGGTCTTGTATGATTTTGCTA 59.566 34.615 0.00 0.00 0.00 3.49
2453 2487 7.720957 TGGTCTTGTATGATTTTGCTATATGCT 59.279 33.333 0.00 0.00 43.37 3.79
2476 2510 2.294233 ACATGATCCTTTGTGTGTGTGC 59.706 45.455 0.00 0.00 0.00 4.57
2480 2514 3.018428 CTTTGTGTGTGTGCGCGC 61.018 61.111 27.26 27.26 36.27 6.86
2481 2515 4.544689 TTTGTGTGTGTGCGCGCC 62.545 61.111 30.77 20.33 34.96 6.53
2502 2536 2.396601 GTGGTGTTGAATGTGTGCATG 58.603 47.619 0.00 0.00 35.15 4.06
2506 2543 3.495193 GTGTTGAATGTGTGCATGCTAG 58.505 45.455 20.33 0.00 35.15 3.42
2512 2549 0.033366 TGTGTGCATGCTAGTCGTGT 59.967 50.000 20.33 0.00 34.19 4.49
2519 2556 2.541999 GCATGCTAGTCGTGTAGAGGTC 60.542 54.545 11.37 0.00 34.19 3.85
2520 2557 2.484742 TGCTAGTCGTGTAGAGGTCA 57.515 50.000 0.00 0.00 0.00 4.02
2521 2558 2.786777 TGCTAGTCGTGTAGAGGTCAA 58.213 47.619 0.00 0.00 0.00 3.18
2526 2563 1.000607 GTCGTGTAGAGGTCAAGTGCA 60.001 52.381 0.00 0.00 0.00 4.57
2529 2566 3.699538 TCGTGTAGAGGTCAAGTGCATAT 59.300 43.478 0.00 0.00 0.00 1.78
2531 2568 4.504461 CGTGTAGAGGTCAAGTGCATATTC 59.496 45.833 0.00 0.00 0.00 1.75
2533 2570 3.895232 AGAGGTCAAGTGCATATTCGT 57.105 42.857 0.00 0.00 0.00 3.85
2535 2572 3.935203 AGAGGTCAAGTGCATATTCGTTG 59.065 43.478 0.00 0.00 0.00 4.10
2536 2573 3.674997 AGGTCAAGTGCATATTCGTTGT 58.325 40.909 0.00 0.00 0.00 3.32
2537 2574 3.436704 AGGTCAAGTGCATATTCGTTGTG 59.563 43.478 0.00 0.00 0.00 3.33
2543 2580 8.172484 GTCAAGTGCATATTCGTTGTGTTTATA 58.828 33.333 0.00 0.00 0.00 0.98
2544 2581 8.722394 TCAAGTGCATATTCGTTGTGTTTATAA 58.278 29.630 0.00 0.00 0.00 0.98
2545 2582 8.785101 CAAGTGCATATTCGTTGTGTTTATAAC 58.215 33.333 0.00 0.00 0.00 1.89
2547 2584 8.726988 AGTGCATATTCGTTGTGTTTATAACTT 58.273 29.630 0.00 0.00 0.00 2.66
2577 2614 9.664332 ATCCACTCAGTTTGATGCTATATTATC 57.336 33.333 0.00 0.00 0.00 1.75
2601 2638 7.534282 TCAGTCAATAAAAATGCGCTTTATCA 58.466 30.769 9.73 0.00 30.41 2.15
2602 2639 7.697710 TCAGTCAATAAAAATGCGCTTTATCAG 59.302 33.333 9.73 7.62 30.41 2.90
2605 2642 8.859156 GTCAATAAAAATGCGCTTTATCAGAAA 58.141 29.630 9.73 0.00 30.41 2.52
2650 2693 5.246203 ACTGAGCTCACAACTAATTACTCCA 59.754 40.000 13.74 0.00 0.00 3.86
2653 2696 5.352284 AGCTCACAACTAATTACTCCATCG 58.648 41.667 0.00 0.00 0.00 3.84
2654 2697 4.508124 GCTCACAACTAATTACTCCATCGG 59.492 45.833 0.00 0.00 0.00 4.18
2655 2698 4.439057 TCACAACTAATTACTCCATCGGC 58.561 43.478 0.00 0.00 0.00 5.54
2656 2699 4.161565 TCACAACTAATTACTCCATCGGCT 59.838 41.667 0.00 0.00 0.00 5.52
2657 2700 4.508124 CACAACTAATTACTCCATCGGCTC 59.492 45.833 0.00 0.00 0.00 4.70
2658 2701 4.406003 ACAACTAATTACTCCATCGGCTCT 59.594 41.667 0.00 0.00 0.00 4.09
2669 2712 2.352960 CCATCGGCTCTTGCTTTAGAAC 59.647 50.000 0.00 0.00 39.59 3.01
2673 2716 0.448197 GCTCTTGCTTTAGAACCGGC 59.552 55.000 0.00 0.00 36.03 6.13
2693 2739 6.042093 ACCGGCATATATATGGATAGGACAAG 59.958 42.308 21.50 3.98 34.32 3.16
2699 2745 9.486497 CATATATATGGATAGGACAAGACATGC 57.514 37.037 14.04 0.00 0.00 4.06
2712 2758 6.400303 GGACAAGACATGCAATTCATTTTTCG 60.400 38.462 0.00 0.00 31.79 3.46
2744 2794 7.287235 ACCTATAGTGTACTACTGGAATTCCAC 59.713 40.741 23.63 12.85 42.01 4.02
2755 2810 8.220559 ACTACTGGAATTCCACATAGCAAATAT 58.779 33.333 27.05 13.32 42.01 1.28
2759 2814 8.853077 TGGAATTCCACATAGCAAATATAGAG 57.147 34.615 23.63 0.00 42.01 2.43
2760 2815 8.659527 TGGAATTCCACATAGCAAATATAGAGA 58.340 33.333 23.63 0.00 42.01 3.10
2761 2816 9.678260 GGAATTCCACATAGCAAATATAGAGAT 57.322 33.333 20.04 0.00 35.64 2.75
2763 2818 8.939201 ATTCCACATAGCAAATATAGAGATCG 57.061 34.615 0.00 0.00 0.00 3.69
2764 2819 7.703058 TCCACATAGCAAATATAGAGATCGA 57.297 36.000 0.00 0.00 0.00 3.59
2781 2836 6.929049 AGAGATCGAATCTGTTGTGTAAAACA 59.071 34.615 2.93 0.00 40.38 2.83
2872 2933 7.695201 GCAAAGAGTAAACGTGTAAAGAACTTT 59.305 33.333 5.18 5.18 36.63 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.057526 GGAAGTTGGAAAGGTCGAAATGG 60.058 47.826 0.00 0.00 0.00 3.16
30 31 1.473434 GCCAAGACTAGGGGTTCGATG 60.473 57.143 0.00 0.00 0.00 3.84
42 43 0.467384 CGGATCCATGAGCCAAGACT 59.533 55.000 13.41 0.00 38.11 3.24
126 128 6.874278 TCCAAGACTAAGGATTCAAGATCA 57.126 37.500 0.00 0.00 0.00 2.92
164 166 3.002583 TGGGACGGCTGATGCTCA 61.003 61.111 0.00 0.00 39.59 4.26
191 193 5.503376 CGGAAGTCAAAAATGTCGAAATACG 59.497 40.000 0.00 0.00 44.09 3.06
193 195 5.701750 TCCGGAAGTCAAAAATGTCGAAATA 59.298 36.000 0.00 0.00 0.00 1.40
202 204 7.148069 GGATTTGATAGTCCGGAAGTCAAAAAT 60.148 37.037 28.78 20.39 40.75 1.82
206 208 4.383770 GGGATTTGATAGTCCGGAAGTCAA 60.384 45.833 18.29 18.29 35.28 3.18
207 209 3.134081 GGGATTTGATAGTCCGGAAGTCA 59.866 47.826 5.23 8.25 35.28 3.41
218 220 4.712051 TCCATGACCAGGGATTTGATAG 57.288 45.455 0.00 0.00 36.20 2.08
231 233 3.496870 GGTTAGACCCATGATCCATGACC 60.497 52.174 8.38 3.62 43.81 4.02
246 248 5.423015 TGCTCAGAATCATGAAGGTTAGAC 58.577 41.667 0.00 0.00 0.00 2.59
305 307 2.064014 GTTCGTTACCTTGGAAGTCGG 58.936 52.381 0.00 0.00 0.00 4.79
315 318 0.042281 AGGCTAGGGGTTCGTTACCT 59.958 55.000 8.88 0.00 46.86 3.08
418 421 1.918293 CAGTCCAGCACCAGGGGTA 60.918 63.158 0.00 0.00 32.11 3.69
459 462 3.620427 AATTACGGTCACTGCCACATA 57.380 42.857 0.00 0.00 0.00 2.29
460 463 2.489938 AATTACGGTCACTGCCACAT 57.510 45.000 0.00 0.00 0.00 3.21
576 579 6.913873 TTAACGATATTTAACCTGAGTGCC 57.086 37.500 0.00 0.00 0.00 5.01
688 691 1.507140 TCCAGTTTGTCACAGGGAGT 58.493 50.000 0.00 0.00 32.68 3.85
689 692 2.224621 ACATCCAGTTTGTCACAGGGAG 60.225 50.000 0.00 0.00 35.30 4.30
690 693 1.774254 ACATCCAGTTTGTCACAGGGA 59.226 47.619 0.00 0.00 36.03 4.20
691 694 1.881973 CACATCCAGTTTGTCACAGGG 59.118 52.381 0.00 0.00 32.68 4.45
928 931 2.787994 AGTGCTCTGGGATGTCAAAAG 58.212 47.619 0.00 0.00 0.00 2.27
930 933 2.158623 ACAAGTGCTCTGGGATGTCAAA 60.159 45.455 0.00 0.00 0.00 2.69
950 961 4.267452 CGACTCCTCTTGACTACTACGTAC 59.733 50.000 0.00 0.00 0.00 3.67
951 962 4.428209 CGACTCCTCTTGACTACTACGTA 58.572 47.826 0.00 0.00 0.00 3.57
952 963 3.260740 CGACTCCTCTTGACTACTACGT 58.739 50.000 0.00 0.00 0.00 3.57
953 964 2.030701 GCGACTCCTCTTGACTACTACG 59.969 54.545 0.00 0.00 0.00 3.51
974 985 0.457851 ACGCTCCTTGCTACTAGCTG 59.542 55.000 9.49 2.78 42.97 4.24
985 996 1.489481 TCCATGAGATGACGCTCCTT 58.511 50.000 0.00 0.00 33.95 3.36
1116 1127 1.487976 TCCCACGACTCGTAGTAGGAT 59.512 52.381 3.20 0.00 38.32 3.24
1117 1128 0.904649 TCCCACGACTCGTAGTAGGA 59.095 55.000 3.20 5.83 38.32 2.94
1169 1180 3.005539 AGATGCAGCCACCGAGGT 61.006 61.111 0.00 0.00 40.61 3.85
1191 1202 1.478510 CTGCACGAGTAGGATCTTGGT 59.521 52.381 0.00 0.00 0.00 3.67
1194 1205 1.479709 AGCTGCACGAGTAGGATCTT 58.520 50.000 1.02 0.00 0.00 2.40
1251 1262 2.358125 TGGACGTTCATGTGCCCG 60.358 61.111 0.00 0.00 0.00 6.13
1284 1295 2.125350 CCGGACAGCTTGAGCCTC 60.125 66.667 0.00 0.00 43.38 4.70
1296 1307 1.522569 CTCCTCCACCATTCCGGAC 59.477 63.158 1.83 0.00 38.63 4.79
1380 1391 1.619977 GCACTAGGTCTTGGAGGAGGA 60.620 57.143 0.00 0.00 0.00 3.71
1447 1458 1.210478 CACCAACGATCTCCCTGGATT 59.790 52.381 0.00 0.00 32.97 3.01
1530 1541 1.156736 CATGTTCTTGGGTGTCCGAC 58.843 55.000 0.00 0.00 35.24 4.79
1533 1544 1.247567 CACCATGTTCTTGGGTGTCC 58.752 55.000 0.00 0.00 45.48 4.02
1577 1588 1.199327 CTTGCTCTGAACGTACCTCGA 59.801 52.381 0.00 0.00 42.86 4.04
1636 1647 1.291877 CTCCTTGTTCGGCGTCCAAG 61.292 60.000 24.13 24.13 36.26 3.61
1638 1649 2.342279 CTCCTTGTTCGGCGTCCA 59.658 61.111 6.85 1.44 0.00 4.02
1641 1652 1.300697 GACACTCCTTGTTCGGCGT 60.301 57.895 6.85 0.00 39.17 5.68
1653 1664 8.855110 TCTTCTTTATCATCCTCATAGACACTC 58.145 37.037 0.00 0.00 0.00 3.51
1661 1672 7.295322 TCATCGTCTTCTTTATCATCCTCAT 57.705 36.000 0.00 0.00 0.00 2.90
1710 1724 3.316501 CTCCAGATCAATCCTCCTCCTT 58.683 50.000 0.00 0.00 0.00 3.36
1745 1759 3.275143 TCGCTAGAGGAAGAAGACAGAG 58.725 50.000 0.00 0.00 0.00 3.35
1764 1778 1.417592 GTCACGTTGCAGATGCTCG 59.582 57.895 16.53 16.53 42.66 5.03
1782 1796 4.738198 CCATCATCACGAGGGTCG 57.262 61.111 0.00 0.00 46.93 4.79
1850 1867 3.626930 AGCTCAAGATCTAGTTCCTCGT 58.373 45.455 0.00 0.00 0.00 4.18
1984 2001 0.240145 GCAAGCCAACGTTTCTACCC 59.760 55.000 0.00 0.00 0.00 3.69
1985 2002 1.235724 AGCAAGCCAACGTTTCTACC 58.764 50.000 0.00 0.00 0.00 3.18
2018 2037 9.767228 TCAATAAAATCGACCGAAATAGGATTA 57.233 29.630 0.00 0.00 34.73 1.75
2039 2058 6.664816 AGAGAATTGACTTGCCCAAATCAATA 59.335 34.615 15.38 0.00 40.13 1.90
2068 2087 5.932303 TCTAGAGTACACCTTTGCACATTTC 59.068 40.000 0.00 0.00 0.00 2.17
2075 2094 4.803098 TTCCTCTAGAGTACACCTTTGC 57.197 45.455 18.42 0.00 0.00 3.68
2076 2095 6.097915 TGTTTCCTCTAGAGTACACCTTTG 57.902 41.667 18.42 0.06 0.00 2.77
2097 2116 9.850628 CAAAATATGACAAATCAGTTGAGATGT 57.149 29.630 0.00 3.19 39.87 3.06
2192 2214 7.779798 AGGTGAACAAATATAAGCCATACACAT 59.220 33.333 0.00 0.00 0.00 3.21
2361 2389 2.100584 AGAGAGAGCAACGATGATCCAC 59.899 50.000 7.36 2.78 43.02 4.02
2389 2423 8.788409 AGCGAAAGAAAATACAAAGAAGAAAG 57.212 30.769 0.00 0.00 0.00 2.62
2392 2426 8.504005 CCTAAGCGAAAGAAAATACAAAGAAGA 58.496 33.333 0.00 0.00 0.00 2.87
2393 2427 7.271438 GCCTAAGCGAAAGAAAATACAAAGAAG 59.729 37.037 0.00 0.00 0.00 2.85
2394 2428 7.081976 GCCTAAGCGAAAGAAAATACAAAGAA 58.918 34.615 0.00 0.00 0.00 2.52
2396 2430 6.378582 TGCCTAAGCGAAAGAAAATACAAAG 58.621 36.000 0.00 0.00 44.31 2.77
2397 2431 6.320494 TGCCTAAGCGAAAGAAAATACAAA 57.680 33.333 0.00 0.00 44.31 2.83
2398 2432 5.950758 TGCCTAAGCGAAAGAAAATACAA 57.049 34.783 0.00 0.00 44.31 2.41
2399 2433 6.238374 GCTATGCCTAAGCGAAAGAAAATACA 60.238 38.462 0.00 0.00 44.31 2.29
2400 2434 6.017852 AGCTATGCCTAAGCGAAAGAAAATAC 60.018 38.462 0.00 0.00 44.87 1.89
2401 2435 6.055588 AGCTATGCCTAAGCGAAAGAAAATA 58.944 36.000 0.00 0.00 44.87 1.40
2402 2436 4.884164 AGCTATGCCTAAGCGAAAGAAAAT 59.116 37.500 0.00 0.00 44.87 1.82
2414 2448 4.301072 ACAAGACCAAAGCTATGCCTAA 57.699 40.909 0.00 0.00 0.00 2.69
2447 2481 6.830324 ACACACAAAGGATCATGTTAGCATAT 59.170 34.615 0.00 0.00 33.30 1.78
2453 2487 4.023279 GCACACACACAAAGGATCATGTTA 60.023 41.667 0.00 0.00 0.00 2.41
2476 2510 3.722295 ATTCAACACCACGGCGCG 61.722 61.111 6.90 0.00 0.00 6.86
2480 2514 0.317770 GCACACATTCAACACCACGG 60.318 55.000 0.00 0.00 0.00 4.94
2481 2515 0.380024 TGCACACATTCAACACCACG 59.620 50.000 0.00 0.00 0.00 4.94
2482 2516 2.396601 CATGCACACATTCAACACCAC 58.603 47.619 0.00 0.00 32.87 4.16
2502 2536 2.748532 ACTTGACCTCTACACGACTAGC 59.251 50.000 0.00 0.00 0.00 3.42
2506 2543 1.000607 TGCACTTGACCTCTACACGAC 60.001 52.381 0.00 0.00 0.00 4.34
2512 2549 5.109210 CAACGAATATGCACTTGACCTCTA 58.891 41.667 0.00 0.00 0.00 2.43
2519 2556 8.785101 GTTATAAACACAACGAATATGCACTTG 58.215 33.333 0.00 0.00 0.00 3.16
2520 2557 8.726988 AGTTATAAACACAACGAATATGCACTT 58.273 29.630 0.00 0.00 0.00 3.16
2521 2558 8.263940 AGTTATAAACACAACGAATATGCACT 57.736 30.769 0.00 0.00 0.00 4.40
2543 2580 7.831193 AGCATCAAACTGAGTGGATATAAAGTT 59.169 33.333 0.46 0.00 0.00 2.66
2544 2581 7.341805 AGCATCAAACTGAGTGGATATAAAGT 58.658 34.615 0.46 0.00 0.00 2.66
2545 2582 7.798596 AGCATCAAACTGAGTGGATATAAAG 57.201 36.000 0.46 0.00 0.00 1.85
2551 2588 9.664332 GATAATATAGCATCAAACTGAGTGGAT 57.336 33.333 0.00 0.00 0.00 3.41
2552 2589 8.650490 TGATAATATAGCATCAAACTGAGTGGA 58.350 33.333 0.00 0.00 0.00 4.02
2553 2590 8.837788 TGATAATATAGCATCAAACTGAGTGG 57.162 34.615 0.00 0.00 0.00 4.00
2554 2591 9.486497 ACTGATAATATAGCATCAAACTGAGTG 57.514 33.333 0.00 0.00 31.04 3.51
2555 2592 9.703892 GACTGATAATATAGCATCAAACTGAGT 57.296 33.333 0.00 0.00 31.04 3.41
2556 2593 9.702494 TGACTGATAATATAGCATCAAACTGAG 57.298 33.333 0.00 0.00 31.04 3.35
2576 2613 7.534282 TGATAAAGCGCATTTTTATTGACTGA 58.466 30.769 11.47 0.00 32.42 3.41
2577 2614 7.697710 TCTGATAAAGCGCATTTTTATTGACTG 59.302 33.333 11.47 4.67 32.42 3.51
2611 2648 2.219674 GCTCAGTTCAACAGAGTCGTTG 59.780 50.000 11.28 16.68 46.21 4.10
2612 2649 2.101582 AGCTCAGTTCAACAGAGTCGTT 59.898 45.455 11.28 0.00 34.64 3.85
2613 2650 1.683917 AGCTCAGTTCAACAGAGTCGT 59.316 47.619 11.28 0.00 34.64 4.34
2614 2651 2.287849 TGAGCTCAGTTCAACAGAGTCG 60.288 50.000 13.74 0.00 34.64 4.18
2615 2652 3.056304 GTGAGCTCAGTTCAACAGAGTC 58.944 50.000 18.89 8.21 34.64 3.36
2617 2654 3.103447 TGTGAGCTCAGTTCAACAGAG 57.897 47.619 18.89 5.58 35.19 3.35
2629 2672 5.460419 CGATGGAGTAATTAGTTGTGAGCTC 59.540 44.000 6.82 6.82 0.00 4.09
2650 2693 2.633488 GGTTCTAAAGCAAGAGCCGAT 58.367 47.619 1.83 0.00 43.56 4.18
2653 2696 1.087501 CCGGTTCTAAAGCAAGAGCC 58.912 55.000 0.00 6.57 41.94 4.70
2654 2697 0.448197 GCCGGTTCTAAAGCAAGAGC 59.552 55.000 1.90 0.00 42.56 4.09
2655 2698 1.808411 TGCCGGTTCTAAAGCAAGAG 58.192 50.000 1.90 0.00 30.97 2.85
2656 2699 2.489938 ATGCCGGTTCTAAAGCAAGA 57.510 45.000 1.90 0.00 38.99 3.02
2657 2700 7.201644 CCATATATATGCCGGTTCTAAAGCAAG 60.202 40.741 16.08 0.00 38.99 4.01
2658 2701 6.597672 CCATATATATGCCGGTTCTAAAGCAA 59.402 38.462 16.08 0.00 38.99 3.91
2669 2712 6.267699 TCTTGTCCTATCCATATATATGCCGG 59.732 42.308 16.08 12.30 32.40 6.13
2673 2716 9.486497 GCATGTCTTGTCCTATCCATATATATG 57.514 37.037 14.78 14.78 0.00 1.78
2693 2739 7.566858 ACTAACGAAAAATGAATTGCATGTC 57.433 32.000 0.00 0.00 37.28 3.06
2744 2794 9.800433 ACAGATTCGATCTCTATATTTGCTATG 57.200 33.333 0.00 0.00 37.58 2.23
2755 2810 8.085909 TGTTTTACACAACAGATTCGATCTCTA 58.914 33.333 0.00 0.00 32.11 2.43
2759 2814 8.728088 ATTTGTTTTACACAACAGATTCGATC 57.272 30.769 0.00 0.00 45.54 3.69


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

AutoCloner maintained by Alex Coulton.