Multiple sequence alignment - TraesCS6D01G270900

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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 TraesCS6D01G270900 chr6D 100.000 4596 0 0 1 4596 380443429 380448024 0.000000e+00 8488
1 TraesCS6D01G270900 chr6A 92.377 4631 188 64 1 4596 520543946 520539446 0.000000e+00 6444
2 TraesCS6D01G270900 chr6B 95.266 2535 98 9 2066 4596 565420791 565418275 0.000000e+00 3997
3 TraesCS6D01G270900 chr6B 88.859 754 40 16 514 1257 565422395 565421676 0.000000e+00 887
4 TraesCS6D01G270900 chr6B 89.431 492 19 15 1 480 565422868 565422398 1.420000e-164 590
5 TraesCS6D01G270900 chr6B 86.089 496 46 13 1325 1810 565421566 565421084 3.170000e-141 512
6 TraesCS6D01G270900 chr6B 95.082 183 9 0 1827 2009 565420971 565420789 5.820000e-74 289


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 TraesCS6D01G270900 chr6D 380443429 380448024 4595 False 8488 8488 100.0000 1 4596 1 chr6D.!!$F1 4595
1 TraesCS6D01G270900 chr6A 520539446 520543946 4500 True 6444 6444 92.3770 1 4596 1 chr6A.!!$R1 4595
2 TraesCS6D01G270900 chr6B 565418275 565422868 4593 True 1255 3997 90.9454 1 4596 5 chr6B.!!$R1 4595

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
21 22 0.317519 CGGCTGTTTTGACGGTTTCC 60.318 55.0 0.00 0.0 34.33 3.13 F
1052 1091 0.320508 GAAACTCCGCCGTCTTCCTT 60.321 55.0 0.00 0.0 0.00 3.36 F
2042 2245 0.036952 GCAGAGTGCACAGGCTAGAA 60.037 55.0 21.04 0.0 44.26 2.10 F
2447 2650 0.259647 ACTGCATGCCATGGGTATGT 59.740 50.0 16.68 0.0 45.41 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1657 1766 0.248825 CCATTCTCGAGCCGTGAGAG 60.249 60.000 7.81 0.0 42.97 3.20 R
2311 2514 1.234821 TCCACGTGGTGAGAATTTGC 58.765 50.000 32.74 0.0 35.23 3.68 R
3580 3794 2.651361 CTTCAGTCGCACCGGAGT 59.349 61.111 9.46 0.0 0.00 3.85 R
4110 4328 2.009774 CTTGCTCCAATCTTACCCACG 58.990 52.381 0.00 0.0 0.00 4.94 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 0.317519 CGGCTGTTTTGACGGTTTCC 60.318 55.000 0.00 0.00 34.33 3.13
76 77 3.184683 CGCTTGCGCTCCTCTCAC 61.185 66.667 9.73 0.00 0.00 3.51
77 78 2.264166 GCTTGCGCTCCTCTCACT 59.736 61.111 9.73 0.00 0.00 3.41
78 79 2.099431 GCTTGCGCTCCTCTCACTG 61.099 63.158 9.73 0.00 0.00 3.66
82 88 1.181741 TGCGCTCCTCTCACTGTCTT 61.182 55.000 9.73 0.00 0.00 3.01
214 220 2.438254 GCCGGGCACATGACATGA 60.438 61.111 22.19 0.00 0.00 3.07
215 221 2.764314 GCCGGGCACATGACATGAC 61.764 63.158 22.19 12.65 0.00 3.06
216 222 1.377072 CCGGGCACATGACATGACA 60.377 57.895 22.19 0.00 0.00 3.58
217 223 0.749091 CCGGGCACATGACATGACAT 60.749 55.000 22.19 4.76 0.00 3.06
227 233 1.202405 TGACATGACATGGGATCGTCG 60.202 52.381 19.39 0.00 34.78 5.12
229 235 1.688735 ACATGACATGGGATCGTCGAT 59.311 47.619 19.39 7.63 34.78 3.59
380 397 1.021390 CACCACAACGCCTCTCATCC 61.021 60.000 0.00 0.00 0.00 3.51
540 564 2.994995 ATCCACCGTGCGTCTCCA 60.995 61.111 0.00 0.00 0.00 3.86
616 640 2.324330 CCACGCCGATGTCTTTGCA 61.324 57.895 0.00 0.00 0.00 4.08
621 645 1.064505 CGCCGATGTCTTTGCATCAAT 59.935 47.619 6.83 0.00 43.92 2.57
633 657 3.114668 TGCATCAATTTGCTTGCTGTT 57.885 38.095 18.63 0.00 43.18 3.16
635 659 3.989167 TGCATCAATTTGCTTGCTGTTAC 59.011 39.130 18.63 0.00 43.18 2.50
636 660 3.368843 GCATCAATTTGCTTGCTGTTACC 59.631 43.478 13.60 0.00 39.57 2.85
637 661 3.658757 TCAATTTGCTTGCTGTTACCC 57.341 42.857 0.00 0.00 34.66 3.69
638 662 3.230134 TCAATTTGCTTGCTGTTACCCT 58.770 40.909 0.00 0.00 34.66 4.34
639 663 4.402829 TCAATTTGCTTGCTGTTACCCTA 58.597 39.130 0.00 0.00 34.66 3.53
640 664 4.830046 TCAATTTGCTTGCTGTTACCCTAA 59.170 37.500 0.00 0.00 34.66 2.69
642 666 6.014669 TCAATTTGCTTGCTGTTACCCTAATT 60.015 34.615 0.00 0.00 34.66 1.40
643 667 5.799827 TTTGCTTGCTGTTACCCTAATTT 57.200 34.783 0.00 0.00 0.00 1.82
645 669 7.475137 TTTGCTTGCTGTTACCCTAATTTAT 57.525 32.000 0.00 0.00 0.00 1.40
646 670 7.475137 TTGCTTGCTGTTACCCTAATTTATT 57.525 32.000 0.00 0.00 0.00 1.40
654 679 8.869897 GCTGTTACCCTAATTTATTTTTGCTTC 58.130 33.333 0.00 0.00 0.00 3.86
693 718 1.843851 AGACGTGGAGGAGAGAGAGAT 59.156 52.381 0.00 0.00 0.00 2.75
694 719 2.241176 AGACGTGGAGGAGAGAGAGATT 59.759 50.000 0.00 0.00 0.00 2.40
725 750 5.339611 GCTGTTGTGCGTATAAACTTTTGAG 59.660 40.000 4.25 0.00 0.00 3.02
818 857 1.762957 CCCGACTCTCTCTCTCTCTCT 59.237 57.143 0.00 0.00 0.00 3.10
819 858 2.224066 CCCGACTCTCTCTCTCTCTCTC 60.224 59.091 0.00 0.00 0.00 3.20
820 859 2.695666 CCGACTCTCTCTCTCTCTCTCT 59.304 54.545 0.00 0.00 0.00 3.10
943 982 1.376424 ACCGTCATTCCTGCTGCTG 60.376 57.895 0.00 0.00 0.00 4.41
944 983 2.758089 CCGTCATTCCTGCTGCTGC 61.758 63.158 8.89 8.89 40.20 5.25
945 984 1.744368 CGTCATTCCTGCTGCTGCT 60.744 57.895 17.00 0.00 40.48 4.24
1027 1066 3.821033 GCTCTTCCAAGGTAAACACATGT 59.179 43.478 0.00 0.00 0.00 3.21
1030 1069 5.441500 TCTTCCAAGGTAAACACATGTCAA 58.558 37.500 0.00 0.00 0.00 3.18
1031 1070 5.888724 TCTTCCAAGGTAAACACATGTCAAA 59.111 36.000 0.00 0.00 0.00 2.69
1052 1091 0.320508 GAAACTCCGCCGTCTTCCTT 60.321 55.000 0.00 0.00 0.00 3.36
1078 1117 4.020128 TGTCTCTTTTAGCTTCTCCCTTCC 60.020 45.833 0.00 0.00 0.00 3.46
1079 1118 3.195825 TCTCTTTTAGCTTCTCCCTTCCG 59.804 47.826 0.00 0.00 0.00 4.30
1080 1119 2.904434 TCTTTTAGCTTCTCCCTTCCGT 59.096 45.455 0.00 0.00 0.00 4.69
1107 1146 3.117175 GATGCTGACCATGGCGTGC 62.117 63.158 13.04 13.78 33.29 5.34
1231 1274 2.663196 GCCAGCAAGGTACCGTCT 59.337 61.111 6.18 1.90 40.61 4.18
1308 1380 0.461961 GCTGTATCTCCGTTCAGGCT 59.538 55.000 0.00 0.00 40.77 4.58
1309 1381 1.134670 GCTGTATCTCCGTTCAGGCTT 60.135 52.381 0.00 0.00 40.77 4.35
1467 1561 2.353889 AGACATGACATTTCGATGCAGC 59.646 45.455 0.00 0.00 0.00 5.25
1469 1563 1.402613 CATGACATTTCGATGCAGCCA 59.597 47.619 0.00 0.00 0.00 4.75
1484 1578 0.322975 AGCCATGAAGTCGCTTGAGT 59.677 50.000 0.00 0.00 0.00 3.41
1663 1772 1.666311 CCGTCTGTTTCGGTCTCTCAC 60.666 57.143 0.00 0.00 42.62 3.51
1699 1808 3.121030 GCGCATGAAGCACGGTCT 61.121 61.111 0.30 0.00 46.13 3.85
1713 1822 3.605634 CACGGTCTGGAATTATGGTTCA 58.394 45.455 0.00 0.00 0.00 3.18
1714 1823 3.374058 CACGGTCTGGAATTATGGTTCAC 59.626 47.826 0.00 0.00 0.00 3.18
1726 1835 1.148273 GGTTCACAGTGCTCCACCA 59.852 57.895 0.00 0.00 34.49 4.17
1735 1844 2.978010 GCTCCACCAACACCCACG 60.978 66.667 0.00 0.00 0.00 4.94
1782 1891 7.390440 CGACAATAAGAGATCTAGAGGTGAGAT 59.610 40.741 0.00 0.00 36.33 2.75
1790 1899 6.857848 AGATCTAGAGGTGAGATGATTGGTA 58.142 40.000 0.00 0.00 33.71 3.25
1852 2055 4.171754 GTTATACGGGTTCAGACACTGAC 58.828 47.826 0.74 0.00 40.46 3.51
1933 2136 3.473647 CCCAGCAGCCCGAGATCA 61.474 66.667 0.00 0.00 0.00 2.92
1988 2191 4.439700 CCAAGATAAATGACAGGCAAGCTG 60.440 45.833 0.00 0.00 0.00 4.24
1991 2194 2.283145 AAATGACAGGCAAGCTGACT 57.717 45.000 0.00 0.00 34.86 3.41
2006 2209 3.133691 GCTGACTGCGATCATAATTCCA 58.866 45.455 0.00 0.00 0.00 3.53
2009 2212 5.163913 GCTGACTGCGATCATAATTCCATAC 60.164 44.000 0.00 0.00 0.00 2.39
2040 2243 4.198625 GCAGAGTGCACAGGCTAG 57.801 61.111 21.04 8.96 44.26 3.42
2041 2244 1.593787 GCAGAGTGCACAGGCTAGA 59.406 57.895 21.04 0.00 44.26 2.43
2042 2245 0.036952 GCAGAGTGCACAGGCTAGAA 60.037 55.000 21.04 0.00 44.26 2.10
2043 2246 1.719600 CAGAGTGCACAGGCTAGAAC 58.280 55.000 21.04 0.00 41.91 3.01
2044 2247 0.610687 AGAGTGCACAGGCTAGAACC 59.389 55.000 21.04 0.00 41.91 3.62
2045 2248 0.610687 GAGTGCACAGGCTAGAACCT 59.389 55.000 21.04 0.00 42.30 3.50
2046 2249 1.002544 GAGTGCACAGGCTAGAACCTT 59.997 52.381 21.04 0.00 38.26 3.50
2047 2250 2.233922 GAGTGCACAGGCTAGAACCTTA 59.766 50.000 21.04 0.00 38.26 2.69
2048 2251 2.840651 AGTGCACAGGCTAGAACCTTAT 59.159 45.455 21.04 0.00 38.26 1.73
2049 2252 4.030913 AGTGCACAGGCTAGAACCTTATA 58.969 43.478 21.04 0.00 38.26 0.98
2050 2253 4.469945 AGTGCACAGGCTAGAACCTTATAA 59.530 41.667 21.04 0.00 38.26 0.98
2051 2254 4.571176 GTGCACAGGCTAGAACCTTATAAC 59.429 45.833 13.17 0.00 38.26 1.89
2052 2255 4.224147 TGCACAGGCTAGAACCTTATAACA 59.776 41.667 0.00 0.00 38.26 2.41
2053 2256 4.571176 GCACAGGCTAGAACCTTATAACAC 59.429 45.833 0.00 0.00 38.26 3.32
2054 2257 5.730550 CACAGGCTAGAACCTTATAACACA 58.269 41.667 0.00 0.00 38.26 3.72
2055 2258 6.349300 CACAGGCTAGAACCTTATAACACAT 58.651 40.000 0.00 0.00 38.26 3.21
2056 2259 6.823689 CACAGGCTAGAACCTTATAACACATT 59.176 38.462 0.00 0.00 38.26 2.71
2057 2260 7.985184 CACAGGCTAGAACCTTATAACACATTA 59.015 37.037 0.00 0.00 38.26 1.90
2058 2261 8.204836 ACAGGCTAGAACCTTATAACACATTAG 58.795 37.037 0.00 0.00 38.26 1.73
2059 2262 7.171678 CAGGCTAGAACCTTATAACACATTAGC 59.828 40.741 0.00 0.00 38.26 3.09
2060 2263 6.990349 GGCTAGAACCTTATAACACATTAGCA 59.010 38.462 0.00 0.00 33.35 3.49
2061 2264 7.497909 GGCTAGAACCTTATAACACATTAGCAA 59.502 37.037 0.00 0.00 33.35 3.91
2062 2265 9.057089 GCTAGAACCTTATAACACATTAGCAAT 57.943 33.333 0.00 0.00 32.32 3.56
2079 2282 8.924691 CATTAGCAATAGATAGAAAGAGTGAGC 58.075 37.037 0.00 0.00 0.00 4.26
2090 2293 9.139174 GATAGAAAGAGTGAGCTAAGCATAATC 57.861 37.037 0.00 0.00 0.00 1.75
2106 2309 7.239166 AGCATAATCTGTTCATGAGTAAACG 57.761 36.000 0.00 0.00 0.00 3.60
2185 2388 5.782893 AGAAGTGTCTATCCATGCTCTAC 57.217 43.478 0.00 0.00 29.93 2.59
2270 2473 5.309543 TCTTTCCTTCTGGAGGTTCATACAA 59.690 40.000 0.97 0.00 46.39 2.41
2291 2494 5.984926 ACAACATCTTGTAAATTTGGCACAG 59.015 36.000 0.00 1.97 38.21 3.66
2324 2527 6.150976 CAGGTTATACTTGCAAATTCTCACCA 59.849 38.462 0.00 0.00 0.00 4.17
2328 2531 2.033299 ACTTGCAAATTCTCACCACGTG 59.967 45.455 9.08 9.08 34.45 4.49
2329 2532 0.950836 TGCAAATTCTCACCACGTGG 59.049 50.000 32.83 32.83 42.17 4.94
2338 2541 3.283751 TCTCACCACGTGGAACATTTTT 58.716 40.909 40.21 13.26 44.52 1.94
2341 2544 5.180492 TCTCACCACGTGGAACATTTTTATC 59.820 40.000 40.21 0.00 44.52 1.75
2342 2545 4.822350 TCACCACGTGGAACATTTTTATCA 59.178 37.500 40.21 0.00 44.52 2.15
2348 2551 5.048991 ACGTGGAACATTTTTATCACAGGTC 60.049 40.000 0.00 0.00 44.52 3.85
2446 2649 1.067974 CAACTGCATGCCATGGGTATG 59.932 52.381 16.68 10.46 46.19 2.39
2447 2650 0.259647 ACTGCATGCCATGGGTATGT 59.740 50.000 16.68 0.00 45.41 2.29
2448 2651 1.494296 ACTGCATGCCATGGGTATGTA 59.506 47.619 16.68 9.08 45.41 2.29
2449 2652 1.881973 CTGCATGCCATGGGTATGTAC 59.118 52.381 16.68 0.00 45.41 2.90
2450 2653 1.494296 TGCATGCCATGGGTATGTACT 59.506 47.619 16.68 0.00 45.41 2.73
2451 2654 2.708325 TGCATGCCATGGGTATGTACTA 59.292 45.455 16.68 0.00 45.41 1.82
2452 2655 3.330405 TGCATGCCATGGGTATGTACTAT 59.670 43.478 16.68 0.00 45.41 2.12
2502 2705 5.845391 TTTTACCAGAAACAAAGACAGGG 57.155 39.130 0.00 0.00 0.00 4.45
2541 2744 6.042437 ACCTTACTTTCTCCTTCGACCTTTTA 59.958 38.462 0.00 0.00 0.00 1.52
2655 2858 8.345565 CAGAGAGCACAAAGTTGTATTTTACTT 58.654 33.333 0.00 0.00 39.91 2.24
2703 2907 3.127548 CCCATCGTATATCAATGCCAAGC 59.872 47.826 0.00 0.00 0.00 4.01
2719 2926 3.366374 GCCAAGCGCCTTCATTTATATCC 60.366 47.826 2.29 0.00 0.00 2.59
2985 3196 7.696992 TTTAAATAGGCAGGGTTCTTTGTAG 57.303 36.000 0.00 0.00 0.00 2.74
3180 3391 2.337359 AGTGCTTACTCCCAAGGGTA 57.663 50.000 4.80 0.00 36.47 3.69
3207 3418 5.925969 CCCCTAAACTGTTTTTGCTTACATG 59.074 40.000 11.48 0.00 0.00 3.21
3235 3446 9.877178 AGCTACCATTAGAAATGTATATAGTGC 57.123 33.333 0.00 0.00 0.00 4.40
3277 3489 1.937899 ACTTGCGACAGGTTGTTACAC 59.062 47.619 0.00 0.00 0.00 2.90
3307 3519 1.135333 GAAGCTCTACAGAAGTCGGGG 59.865 57.143 0.00 0.00 0.00 5.73
3420 3632 5.798132 ACAATGATGCATCGATGTACCTAT 58.202 37.500 26.57 13.63 0.00 2.57
3435 3647 9.261180 CGATGTACCTATGTTTACTGATCAAAT 57.739 33.333 0.00 0.00 0.00 2.32
3580 3794 1.561643 CTGTCCAGGTAGCCAAGAGA 58.438 55.000 0.00 0.00 0.00 3.10
3608 3822 1.135139 GCGACTGAAGCTACATCTCCA 59.865 52.381 0.00 0.00 0.00 3.86
3776 3990 2.355513 GGAGAGCAGCAGAATTCTTCCA 60.356 50.000 4.86 0.00 0.00 3.53
3855 4069 6.825721 GTGTATTTCTCCCTCATTCAACTCAT 59.174 38.462 0.00 0.00 0.00 2.90
3972 4190 7.551974 GTGATCTATAATGCCATTGTATCAGCT 59.448 37.037 0.00 0.00 0.00 4.24
4110 4328 3.818773 TCAGATTCCGTTTCCCTTTTGTC 59.181 43.478 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 3.379688 TCCATCGATCAAGACAGTGAGAG 59.620 47.826 0.00 0.00 0.00 3.20
71 72 3.356290 TCCATCGATCAAGACAGTGAGA 58.644 45.455 0.00 0.00 0.00 3.27
72 73 3.490590 CCTCCATCGATCAAGACAGTGAG 60.491 52.174 0.00 0.00 0.00 3.51
73 74 2.428530 CCTCCATCGATCAAGACAGTGA 59.571 50.000 0.00 0.00 0.00 3.41
74 75 2.167281 ACCTCCATCGATCAAGACAGTG 59.833 50.000 0.00 0.00 0.00 3.66
75 76 2.461695 ACCTCCATCGATCAAGACAGT 58.538 47.619 0.00 0.00 0.00 3.55
76 77 3.193263 CAACCTCCATCGATCAAGACAG 58.807 50.000 0.00 0.00 0.00 3.51
77 78 2.567169 ACAACCTCCATCGATCAAGACA 59.433 45.455 0.00 0.00 0.00 3.41
78 79 3.252974 ACAACCTCCATCGATCAAGAC 57.747 47.619 0.00 0.00 0.00 3.01
82 88 3.531538 GCTTTACAACCTCCATCGATCA 58.468 45.455 0.00 0.00 0.00 2.92
106 112 0.463474 CTCTGGCTCTGGCTTTAGGC 60.463 60.000 0.00 0.00 38.73 3.93
107 113 0.463474 GCTCTGGCTCTGGCTTTAGG 60.463 60.000 0.00 0.00 38.73 2.69
108 114 0.251354 TGCTCTGGCTCTGGCTTTAG 59.749 55.000 0.00 0.00 39.59 1.85
121 127 0.250166 TCGCCATGATGGATGCTCTG 60.250 55.000 17.22 0.00 40.96 3.35
122 128 0.250209 GTCGCCATGATGGATGCTCT 60.250 55.000 17.22 0.00 40.96 4.09
214 220 2.097629 CGCTATATCGACGATCCCATGT 59.902 50.000 14.80 0.00 0.00 3.21
215 221 2.354821 TCGCTATATCGACGATCCCATG 59.645 50.000 14.80 3.44 33.02 3.66
216 222 2.614520 CTCGCTATATCGACGATCCCAT 59.385 50.000 14.80 5.22 34.94 4.00
217 223 2.007608 CTCGCTATATCGACGATCCCA 58.992 52.381 14.80 0.00 34.94 4.37
218 224 1.331138 CCTCGCTATATCGACGATCCC 59.669 57.143 14.80 0.60 34.94 3.85
278 284 1.592939 GAGGCGGCAGCTAAGCTAC 60.593 63.158 13.08 0.00 44.37 3.58
281 287 3.764160 ATGGAGGCGGCAGCTAAGC 62.764 63.158 13.08 0.00 44.37 3.09
282 288 1.596477 GATGGAGGCGGCAGCTAAG 60.596 63.158 13.08 0.00 44.37 2.18
283 289 2.505982 GATGGAGGCGGCAGCTAA 59.494 61.111 13.08 0.00 44.37 3.09
284 290 3.916544 CGATGGAGGCGGCAGCTA 61.917 66.667 13.08 0.24 44.37 3.32
380 397 4.498520 ATCACGTGCTCCGCCGAG 62.499 66.667 11.67 0.00 41.42 4.63
429 453 1.697432 TCTGGAGGAGCGAAAGGAAAA 59.303 47.619 0.00 0.00 0.00 2.29
458 482 3.106407 GATAGATCCCGTGCGCGC 61.106 66.667 27.26 27.26 36.67 6.86
459 483 2.430921 GGATAGATCCCGTGCGCG 60.431 66.667 13.88 13.88 41.20 6.86
616 640 3.834231 AGGGTAACAGCAAGCAAATTGAT 59.166 39.130 0.00 0.00 38.28 2.57
621 645 5.799827 AAATTAGGGTAACAGCAAGCAAA 57.200 34.783 0.00 0.00 39.74 3.68
643 667 9.337091 GCTCAACGTAAATAAGAAGCAAAAATA 57.663 29.630 0.00 0.00 0.00 1.40
645 669 7.197017 TGCTCAACGTAAATAAGAAGCAAAAA 58.803 30.769 0.00 0.00 0.00 1.94
646 670 6.730175 TGCTCAACGTAAATAAGAAGCAAAA 58.270 32.000 0.00 0.00 0.00 2.44
654 679 4.265556 CGTCTCCTGCTCAACGTAAATAAG 59.734 45.833 0.00 0.00 0.00 1.73
657 682 2.029290 ACGTCTCCTGCTCAACGTAAAT 60.029 45.455 0.00 0.00 45.59 1.40
667 692 1.680651 CTCCTCCACGTCTCCTGCT 60.681 63.158 0.00 0.00 0.00 4.24
693 718 0.464735 ACGCACAACAGCAAGGGTAA 60.465 50.000 0.00 0.00 0.00 2.85
694 719 0.393448 TACGCACAACAGCAAGGGTA 59.607 50.000 0.00 0.00 0.00 3.69
725 750 3.433615 GTCTGTCTGCTTGTGTTGTATCC 59.566 47.826 0.00 0.00 0.00 2.59
818 857 0.179043 ATAGTCGGCAGAGCGAGAGA 60.179 55.000 0.00 0.00 0.00 3.10
819 858 1.514003 TATAGTCGGCAGAGCGAGAG 58.486 55.000 0.00 0.00 0.00 3.20
820 859 1.963172 TTATAGTCGGCAGAGCGAGA 58.037 50.000 0.00 0.00 0.00 4.04
888 927 3.283751 CTGGCTGCTACTCTGTACTAGT 58.716 50.000 0.00 0.00 0.00 2.57
902 941 2.772691 GGATCTTGCTGCTGGCTGC 61.773 63.158 15.66 15.66 42.39 5.25
1027 1066 1.202604 AGACGGCGGAGTTTCTTTTGA 60.203 47.619 13.24 0.00 0.00 2.69
1030 1069 1.509703 GAAGACGGCGGAGTTTCTTT 58.490 50.000 13.24 0.00 0.00 2.52
1031 1070 0.320508 GGAAGACGGCGGAGTTTCTT 60.321 55.000 13.24 10.83 0.00 2.52
1052 1091 3.056749 GGGAGAAGCTAAAAGAGACACGA 60.057 47.826 0.00 0.00 0.00 4.35
1114 1153 4.743975 TTACGCGTGCATGGCCGA 62.744 61.111 24.59 0.00 0.00 5.54
1115 1154 2.964924 GAATTACGCGTGCATGGCCG 62.965 60.000 24.59 6.22 0.00 6.13
1116 1155 1.298339 GAATTACGCGTGCATGGCC 60.298 57.895 24.59 0.00 0.00 5.36
1117 1156 1.651132 CGAATTACGCGTGCATGGC 60.651 57.895 24.59 5.30 34.51 4.40
1118 1157 4.569399 CGAATTACGCGTGCATGG 57.431 55.556 24.59 4.39 34.51 3.66
1231 1274 0.693049 GTGGAAAGGCAAGGAGAGGA 59.307 55.000 0.00 0.00 0.00 3.71
1461 1555 0.679002 AAGCGACTTCATGGCTGCAT 60.679 50.000 0.50 0.00 42.38 3.96
1467 1561 1.998315 CTGACTCAAGCGACTTCATGG 59.002 52.381 0.00 0.00 0.00 3.66
1469 1563 1.674221 GGCTGACTCAAGCGACTTCAT 60.674 52.381 0.00 0.00 44.52 2.57
1574 1683 0.467384 CTGATGCTGAAGGTCCCGAT 59.533 55.000 0.00 0.00 0.00 4.18
1657 1766 0.248825 CCATTCTCGAGCCGTGAGAG 60.249 60.000 7.81 0.00 42.97 3.20
1663 1772 1.495878 CAATCTCCATTCTCGAGCCG 58.504 55.000 7.81 0.00 0.00 5.52
1699 1808 4.009675 GAGCACTGTGAACCATAATTCCA 58.990 43.478 12.86 0.00 0.00 3.53
1713 1822 1.152963 GGTGTTGGTGGAGCACTGT 60.153 57.895 0.00 0.00 34.40 3.55
1714 1823 1.898574 GGGTGTTGGTGGAGCACTG 60.899 63.158 0.00 0.00 34.40 3.66
1735 1844 2.615912 GGTGCTAGAATCTTGCCACATC 59.384 50.000 13.62 0.00 31.70 3.06
1796 1905 5.989477 TGCTATCTGGTACTACAAAGCATT 58.011 37.500 8.12 0.00 34.05 3.56
1797 1906 5.614324 TGCTATCTGGTACTACAAAGCAT 57.386 39.130 8.12 0.00 34.05 3.79
1799 1908 5.064834 GGTTTGCTATCTGGTACTACAAAGC 59.935 44.000 5.95 5.95 37.03 3.51
1800 1909 6.170506 TGGTTTGCTATCTGGTACTACAAAG 58.829 40.000 0.00 0.00 0.00 2.77
1802 1911 5.338056 CCTGGTTTGCTATCTGGTACTACAA 60.338 44.000 0.00 0.00 0.00 2.41
1804 1913 4.161754 ACCTGGTTTGCTATCTGGTACTAC 59.838 45.833 0.00 0.00 32.25 2.73
1805 1914 4.359105 ACCTGGTTTGCTATCTGGTACTA 58.641 43.478 0.00 0.00 32.25 1.82
1806 1915 3.182152 ACCTGGTTTGCTATCTGGTACT 58.818 45.455 0.00 0.00 32.25 2.73
1852 2055 1.808945 GACCCTGAACATTCACAGCAG 59.191 52.381 0.00 0.00 32.90 4.24
1903 2106 2.341543 CTGGGATCCTGATCGGCG 59.658 66.667 12.58 0.00 38.69 6.46
1988 2191 6.159293 TCAGTATGGAATTATGATCGCAGTC 58.841 40.000 0.00 0.00 36.16 3.51
1991 2194 7.573656 GCAATTCAGTATGGAATTATGATCGCA 60.574 37.037 0.00 0.00 43.66 5.10
1993 2196 7.809665 TGCAATTCAGTATGGAATTATGATCG 58.190 34.615 0.00 0.00 43.66 3.69
1999 2202 6.979817 GCACAATGCAATTCAGTATGGAATTA 59.020 34.615 0.00 0.00 43.66 1.40
2030 2233 4.571176 GTGTTATAAGGTTCTAGCCTGTGC 59.429 45.833 0.00 0.00 39.17 4.57
2035 2238 6.990349 TGCTAATGTGTTATAAGGTTCTAGCC 59.010 38.462 10.83 0.00 0.00 3.93
2036 2239 8.433421 TTGCTAATGTGTTATAAGGTTCTAGC 57.567 34.615 8.08 8.08 0.00 3.42
2050 2253 9.539825 CACTCTTTCTATCTATTGCTAATGTGT 57.460 33.333 0.00 0.00 0.00 3.72
2051 2254 9.755804 TCACTCTTTCTATCTATTGCTAATGTG 57.244 33.333 0.00 0.00 0.00 3.21
2052 2255 9.979578 CTCACTCTTTCTATCTATTGCTAATGT 57.020 33.333 0.00 0.00 0.00 2.71
2053 2256 8.924691 GCTCACTCTTTCTATCTATTGCTAATG 58.075 37.037 0.00 0.00 0.00 1.90
2054 2257 8.869109 AGCTCACTCTTTCTATCTATTGCTAAT 58.131 33.333 0.00 0.00 0.00 1.73
2055 2258 8.243961 AGCTCACTCTTTCTATCTATTGCTAA 57.756 34.615 0.00 0.00 0.00 3.09
2056 2259 7.831691 AGCTCACTCTTTCTATCTATTGCTA 57.168 36.000 0.00 0.00 0.00 3.49
2057 2260 6.729690 AGCTCACTCTTTCTATCTATTGCT 57.270 37.500 0.00 0.00 0.00 3.91
2058 2261 7.116233 GCTTAGCTCACTCTTTCTATCTATTGC 59.884 40.741 0.00 0.00 0.00 3.56
2059 2262 8.140628 TGCTTAGCTCACTCTTTCTATCTATTG 58.859 37.037 5.60 0.00 0.00 1.90
2060 2263 8.243961 TGCTTAGCTCACTCTTTCTATCTATT 57.756 34.615 5.60 0.00 0.00 1.73
2061 2264 7.831691 TGCTTAGCTCACTCTTTCTATCTAT 57.168 36.000 5.60 0.00 0.00 1.98
2062 2265 7.831691 ATGCTTAGCTCACTCTTTCTATCTA 57.168 36.000 5.60 0.00 0.00 1.98
2063 2266 6.729690 ATGCTTAGCTCACTCTTTCTATCT 57.270 37.500 5.60 0.00 0.00 1.98
2064 2267 9.139174 GATTATGCTTAGCTCACTCTTTCTATC 57.861 37.037 5.60 0.00 0.00 2.08
2072 2275 6.045318 TGAACAGATTATGCTTAGCTCACTC 58.955 40.000 5.60 0.00 0.00 3.51
2090 2293 2.721797 GCACGCGTTTACTCATGAACAG 60.722 50.000 10.22 0.00 0.00 3.16
2106 2309 1.528586 CTGGAATAGTATGCAGCACGC 59.471 52.381 0.00 0.00 42.89 5.34
2185 2388 2.166459 TCGGAGTATGTCAAGCCTGAAG 59.834 50.000 0.00 0.00 31.88 3.02
2270 2473 4.039004 TGCTGTGCCAAATTTACAAGATGT 59.961 37.500 0.00 0.00 0.00 3.06
2291 2494 2.352960 GCAAGTATAACCTGCTGACTGC 59.647 50.000 0.00 0.00 43.25 4.40
2311 2514 1.234821 TCCACGTGGTGAGAATTTGC 58.765 50.000 32.74 0.00 35.23 3.68
2312 2515 2.616376 TGTTCCACGTGGTGAGAATTTG 59.384 45.455 32.74 4.60 35.23 2.32
2324 2527 4.825085 ACCTGTGATAAAAATGTTCCACGT 59.175 37.500 0.00 0.00 0.00 4.49
2328 2531 7.601856 TCAATGACCTGTGATAAAAATGTTCC 58.398 34.615 0.00 0.00 0.00 3.62
2329 2532 9.643693 ATTCAATGACCTGTGATAAAAATGTTC 57.356 29.630 0.00 0.00 0.00 3.18
2338 2541 7.151976 CCGTATGTATTCAATGACCTGTGATA 58.848 38.462 0.00 0.00 0.00 2.15
2341 2544 4.024893 GCCGTATGTATTCAATGACCTGTG 60.025 45.833 0.00 0.00 0.00 3.66
2342 2545 4.127171 GCCGTATGTATTCAATGACCTGT 58.873 43.478 0.00 0.00 0.00 4.00
2348 2551 4.273235 TGCAAGAGCCGTATGTATTCAATG 59.727 41.667 0.00 0.00 41.13 2.82
2452 2655 9.139174 CATCGCATATTGTACAATGTCTATACA 57.861 33.333 27.62 8.42 40.69 2.29
2476 2679 7.264947 CCTGTCTTTGTTTCTGGTAAAAACAT 58.735 34.615 2.62 0.00 43.85 2.71
2541 2744 3.299503 ACACTTTGTCCTGCCAAGAATT 58.700 40.909 0.00 0.00 0.00 2.17
2627 2830 6.699575 AAATACAACTTTGTGCTCTCTGTT 57.300 33.333 4.82 0.00 42.31 3.16
2673 2876 6.649141 GCATTGATATACGATGGGTTCACTTA 59.351 38.462 0.00 0.00 39.93 2.24
2687 2890 2.154462 AGGCGCTTGGCATTGATATAC 58.846 47.619 7.64 0.00 46.16 1.47
2703 2907 9.166173 TCATGATAAAGGATATAAATGAAGGCG 57.834 33.333 0.00 0.00 0.00 5.52
2719 2926 9.717892 CTGATGTTCTGTGAAATCATGATAAAG 57.282 33.333 9.04 0.00 0.00 1.85
2970 3181 2.749621 CACCATCTACAAAGAACCCTGC 59.250 50.000 0.00 0.00 34.73 4.85
2985 3196 6.314896 GCATGGTAAATATAGCTCTCACCATC 59.685 42.308 10.62 5.26 42.02 3.51
3180 3391 3.038280 AGCAAAAACAGTTTAGGGGCTT 58.962 40.909 0.00 0.00 0.00 4.35
3235 3446 5.065218 AGTCAAAGCAGTGTTCAGTTAGTTG 59.935 40.000 0.00 0.00 0.00 3.16
3277 3489 6.481644 ACTTCTGTAGAGCTTCTTTCAGTTTG 59.518 38.462 0.00 0.00 32.86 2.93
3307 3519 9.274206 GATATTTTAGTTTGAGATGGGTCTACC 57.726 37.037 0.00 0.00 33.97 3.18
3420 3632 7.595819 ACTTTTCCCATTTGATCAGTAAACA 57.404 32.000 0.00 0.00 0.00 2.83
3435 3647 4.885325 ACTTTCTTAAGCGAACTTTTCCCA 59.115 37.500 0.00 0.00 37.33 4.37
3507 3721 4.335594 AGCGAAAATACTGGGTAAATGCTC 59.664 41.667 0.00 0.00 0.00 4.26
3580 3794 2.651361 CTTCAGTCGCACCGGAGT 59.349 61.111 9.46 0.00 0.00 3.85
3608 3822 3.845781 ATGAATTGTCTAGTGCGGGAT 57.154 42.857 0.00 0.00 0.00 3.85
4060 4278 3.313526 CCGAACATCTCCATGGTTCATTC 59.686 47.826 12.58 9.56 33.82 2.67
4110 4328 2.009774 CTTGCTCCAATCTTACCCACG 58.990 52.381 0.00 0.00 0.00 4.94
4288 4507 4.821589 CAGTCCTTCGCGCCCTCC 62.822 72.222 0.00 0.00 0.00 4.30
4489 4708 3.110178 CCGGTCTTCAACGCCGTC 61.110 66.667 0.00 0.00 43.56 4.79


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

AutoCloner maintained by Alex Coulton.