Multiple sequence alignment - TraesCS1D01G239000

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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 TraesCS1D01G239000 chr1D 100.000 2871 0 0 1 2871 328799303 328796433 0.000000e+00 5302.0
1 TraesCS1D01G239000 chr1A 88.114 2953 133 84 1 2853 425682836 425680002 0.000000e+00 3308.0
2 TraesCS1D01G239000 chr1A 100.000 29 0 0 2842 2870 425679982 425679954 1.000000e-03 54.7
3 TraesCS1D01G239000 chr1B 88.169 2037 93 68 1 2007 442971968 442970050 0.000000e+00 2290.0
4 TraesCS1D01G239000 chr1B 89.734 526 29 12 2351 2870 442969597 442969091 0.000000e+00 649.0
5 TraesCS1D01G239000 chr1B 91.364 220 8 7 2044 2254 442970049 442969832 1.010000e-74 291.0
6 TraesCS1D01G239000 chr3B 86.098 410 55 2 1191 1599 776195217 776195625 9.440000e-120 440.0
7 TraesCS1D01G239000 chr3B 85.337 416 59 2 1191 1605 777997583 777997169 2.040000e-116 429.0
8 TraesCS1D01G239000 chr3D 85.922 412 52 3 1191 1599 580713774 580714182 4.390000e-118 435.0
9 TraesCS1D01G239000 chr3D 85.203 419 54 5 1191 1605 581834193 581833779 9.510000e-115 424.0
10 TraesCS1D01G239000 chr3A 85.194 412 55 4 1191 1599 716258966 716259374 4.420000e-113 418.0


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 TraesCS1D01G239000 chr1D 328796433 328799303 2870 True 5302.000000 5302 100.000000 1 2871 1 chr1D.!!$R1 2870
1 TraesCS1D01G239000 chr1A 425679954 425682836 2882 True 1681.350000 3308 94.057000 1 2870 2 chr1A.!!$R1 2869
2 TraesCS1D01G239000 chr1B 442969091 442971968 2877 True 1076.666667 2290 89.755667 1 2870 3 chr1B.!!$R1 2869

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
147 158 0.030369 ACGACGACAGACACCTTGAC 59.970 55.0 0.00 0.0 0.00 3.18 F
1010 1085 0.237498 GCCTGTTAACCTCGCAACAC 59.763 55.0 2.48 0.0 31.61 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1058 1142 0.178932 CCATGGACGGGAGAGGGATA 60.179 60.0 5.56 0.0 0.0 2.59 R
2707 2992 0.396060 CTGAAGATGAGGGGCTAGGC 59.604 60.0 8.00 8.0 0.0 3.93 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
137 148 1.120714 CATGACGACGACGACGACAG 61.121 60.000 25.15 14.43 42.66 3.51
138 149 1.287041 ATGACGACGACGACGACAGA 61.287 55.000 25.15 5.78 42.66 3.41
139 150 1.506686 GACGACGACGACGACAGAC 60.507 63.158 25.15 7.94 42.66 3.51
140 151 2.150809 GACGACGACGACGACAGACA 62.151 60.000 25.15 0.00 42.66 3.41
141 152 1.787438 CGACGACGACGACAGACAC 60.787 63.158 15.32 0.00 42.66 3.67
142 153 1.440023 GACGACGACGACAGACACC 60.440 63.158 15.32 0.00 42.66 4.16
143 154 1.839598 GACGACGACGACAGACACCT 61.840 60.000 15.32 0.00 42.66 4.00
144 155 1.281960 CGACGACGACAGACACCTT 59.718 57.895 0.00 0.00 42.66 3.50
147 158 0.030369 ACGACGACAGACACCTTGAC 59.970 55.000 0.00 0.00 0.00 3.18
154 165 0.319900 CAGACACCTTGACAGGACGG 60.320 60.000 0.00 0.00 44.19 4.79
184 195 2.675423 TCCCCCGTCGTCTCACAG 60.675 66.667 0.00 0.00 0.00 3.66
185 196 2.989824 CCCCCGTCGTCTCACAGT 60.990 66.667 0.00 0.00 0.00 3.55
186 197 1.676635 CCCCCGTCGTCTCACAGTA 60.677 63.158 0.00 0.00 0.00 2.74
187 198 1.654954 CCCCCGTCGTCTCACAGTAG 61.655 65.000 0.00 0.00 0.00 2.57
188 199 0.675837 CCCCGTCGTCTCACAGTAGA 60.676 60.000 0.00 0.00 0.00 2.59
189 200 0.447011 CCCGTCGTCTCACAGTAGAC 59.553 60.000 0.00 0.00 42.09 2.59
190 201 1.440708 CCGTCGTCTCACAGTAGACT 58.559 55.000 0.00 0.00 43.11 3.24
191 202 1.394227 CCGTCGTCTCACAGTAGACTC 59.606 57.143 0.00 0.00 43.11 3.36
192 203 2.067013 CGTCGTCTCACAGTAGACTCA 58.933 52.381 0.00 0.00 43.11 3.41
193 204 2.159814 CGTCGTCTCACAGTAGACTCAC 60.160 54.545 0.00 0.00 43.11 3.51
194 205 2.806818 GTCGTCTCACAGTAGACTCACA 59.193 50.000 0.00 0.00 43.11 3.58
195 206 3.067833 TCGTCTCACAGTAGACTCACAG 58.932 50.000 0.00 0.00 43.11 3.66
329 340 4.906792 GCGGCAGCTAGGCAGAGG 62.907 72.222 0.00 0.00 44.47 3.69
347 358 2.278661 GCGTACGGAGCACCTAGC 60.279 66.667 18.39 0.00 46.19 3.42
453 496 1.429148 GATCATGGCCACGTCGGTTC 61.429 60.000 8.16 0.00 36.97 3.62
476 519 1.061411 GCGTACGGCCGATTTTTCC 59.939 57.895 35.90 9.12 34.80 3.13
491 534 1.153353 TTTCCACCGCTTGATTCGTC 58.847 50.000 0.00 0.00 0.00 4.20
545 591 1.367665 GCTGCGTGTGACAAACGAC 60.368 57.895 22.24 13.03 43.68 4.34
547 593 1.476235 CTGCGTGTGACAAACGACGA 61.476 55.000 22.24 3.78 43.68 4.20
549 595 0.448861 GCGTGTGACAAACGACGATG 60.449 55.000 22.24 2.61 43.68 3.84
550 596 0.448861 CGTGTGACAAACGACGATGC 60.449 55.000 13.04 0.00 43.68 3.91
551 597 0.859232 GTGTGACAAACGACGATGCT 59.141 50.000 0.00 0.00 0.00 3.79
552 598 1.260561 GTGTGACAAACGACGATGCTT 59.739 47.619 0.00 0.00 0.00 3.91
553 599 1.937223 TGTGACAAACGACGATGCTTT 59.063 42.857 0.00 0.00 0.00 3.51
554 600 2.033236 TGTGACAAACGACGATGCTTTC 60.033 45.455 0.00 0.00 0.00 2.62
605 651 2.797850 GCGCCGCGGTAAACAAAC 60.798 61.111 28.70 5.98 0.00 2.93
618 664 6.951530 GCGGTAAACAAACAAAGAAAGAAAAC 59.048 34.615 0.00 0.00 0.00 2.43
620 666 8.652463 CGGTAAACAAACAAAGAAAGAAAACAT 58.348 29.630 0.00 0.00 0.00 2.71
688 739 2.751436 GCCGCAAAGCTCCATCCA 60.751 61.111 0.00 0.00 0.00 3.41
690 741 2.768492 CCGCAAAGCTCCATCCAGC 61.768 63.158 0.00 0.00 39.99 4.85
770 844 4.138665 TCCGTATGGGAGCAACCA 57.861 55.556 0.00 1.61 46.24 3.67
771 845 2.378211 TCCGTATGGGAGCAACCAA 58.622 52.632 0.00 0.00 45.13 3.67
933 1007 1.449726 AACCCAAAAACCGCGTCCTC 61.450 55.000 4.92 0.00 0.00 3.71
937 1011 1.302271 AAAAACCGCGTCCTCCCTC 60.302 57.895 4.92 0.00 0.00 4.30
984 1059 2.709934 CCTCCAACATCCAGATCCTCAT 59.290 50.000 0.00 0.00 0.00 2.90
985 1060 3.244491 CCTCCAACATCCAGATCCTCATC 60.244 52.174 0.00 0.00 0.00 2.92
986 1061 3.387012 TCCAACATCCAGATCCTCATCA 58.613 45.455 0.00 0.00 0.00 3.07
1004 1079 1.004200 AACCCGCCTGTTAACCTCG 60.004 57.895 2.48 3.91 0.00 4.63
1010 1085 0.237498 GCCTGTTAACCTCGCAACAC 59.763 55.000 2.48 0.00 31.61 3.32
1060 1144 2.279252 GCGACACCACCGCGATAT 60.279 61.111 8.23 0.00 43.28 1.63
1062 1146 1.660575 CGACACCACCGCGATATCC 60.661 63.158 8.23 0.00 0.00 2.59
1335 1423 2.502492 ATGATGGAGGAGGCCGACG 61.502 63.158 0.00 0.00 0.00 5.12
1645 1733 3.342627 CAACGTCCGCGCCTGAAA 61.343 61.111 0.00 0.00 42.83 2.69
1646 1734 3.041940 AACGTCCGCGCCTGAAAG 61.042 61.111 0.00 0.00 42.83 2.62
1648 1736 3.479269 CGTCCGCGCCTGAAAGAC 61.479 66.667 0.00 0.00 34.07 3.01
1649 1737 3.479269 GTCCGCGCCTGAAAGACG 61.479 66.667 0.00 0.00 34.07 4.18
1650 1738 3.986006 TCCGCGCCTGAAAGACGT 61.986 61.111 0.00 0.00 34.07 4.34
1651 1739 2.126228 CCGCGCCTGAAAGACGTA 60.126 61.111 0.00 0.00 34.07 3.57
1653 1741 2.774951 CGCGCCTGAAAGACGTACG 61.775 63.158 15.01 15.01 34.07 3.67
1654 1742 3.067846 GCGCCTGAAAGACGTACGC 62.068 63.158 16.72 8.42 34.07 4.42
1656 1744 3.067846 GCCTGAAAGACGTACGCGC 62.068 63.158 16.72 7.97 42.83 6.86
1657 1745 1.731613 CCTGAAAGACGTACGCGCA 60.732 57.895 16.72 5.62 42.83 6.09
1734 1831 2.510594 CGACCCACCGCGAAATACG 61.511 63.158 8.23 2.14 45.66 3.06
1739 1836 1.632422 CCACCGCGAAATACGTACTT 58.368 50.000 8.23 0.00 44.60 2.24
1740 1837 2.479389 CCCACCGCGAAATACGTACTTA 60.479 50.000 8.23 0.00 44.60 2.24
1741 1838 2.531508 CCACCGCGAAATACGTACTTAC 59.468 50.000 8.23 0.00 44.60 2.34
1743 1840 4.495679 CCACCGCGAAATACGTACTTACTA 60.496 45.833 8.23 0.00 44.60 1.82
1744 1841 4.434588 CACCGCGAAATACGTACTTACTAC 59.565 45.833 8.23 0.00 44.60 2.73
1812 1910 4.173256 GGTGTGCCATTATTTTGCTGTAC 58.827 43.478 0.00 0.00 34.09 2.90
1842 1940 0.949397 TATCGGAACTGTCGGATCGG 59.051 55.000 0.64 0.00 41.50 4.18
1899 2003 2.031245 CAGCTTGTGTATTTGGCGTCAA 60.031 45.455 0.00 0.00 0.00 3.18
1901 2005 3.067461 AGCTTGTGTATTTGGCGTCAAAA 59.933 39.130 20.41 6.28 44.83 2.44
1930 2038 4.248691 TCTGCTCATCAGATAATGTCCG 57.751 45.455 0.00 0.00 46.34 4.79
1942 2058 4.512198 AGATAATGTCCGTGAGTCTCGTAG 59.488 45.833 13.08 0.00 0.00 3.51
1943 2059 2.110901 ATGTCCGTGAGTCTCGTAGT 57.889 50.000 13.08 0.00 0.00 2.73
1944 2060 2.749280 TGTCCGTGAGTCTCGTAGTA 57.251 50.000 13.08 0.00 0.00 1.82
1945 2061 3.257469 TGTCCGTGAGTCTCGTAGTAT 57.743 47.619 13.08 0.00 0.00 2.12
1946 2062 4.391405 TGTCCGTGAGTCTCGTAGTATA 57.609 45.455 13.08 0.00 0.00 1.47
1947 2063 4.758688 TGTCCGTGAGTCTCGTAGTATAA 58.241 43.478 13.08 0.00 0.00 0.98
1948 2064 5.178061 TGTCCGTGAGTCTCGTAGTATAAA 58.822 41.667 13.08 0.00 0.00 1.40
1949 2065 5.819379 TGTCCGTGAGTCTCGTAGTATAAAT 59.181 40.000 13.08 0.00 0.00 1.40
2031 2147 6.402550 CGGATGACTTTGTGAAGTTATGAAGG 60.403 42.308 1.91 0.00 45.88 3.46
2081 2198 4.998051 ACCTGTAAATGAAAGGGACATGT 58.002 39.130 0.00 0.00 35.24 3.21
2134 2260 1.372582 TGACAATCATTCTGCCGAGC 58.627 50.000 0.00 0.00 0.00 5.03
2197 2323 6.604396 TGCAATACCTCTGATGAAATTGACAT 59.396 34.615 12.80 0.00 0.00 3.06
2388 2660 2.209315 GGTGCCCTGGTGCAATTGT 61.209 57.895 7.40 0.00 44.11 2.71
2460 2739 2.951726 ACTTTCGAAGCTTACCGGTAC 58.048 47.619 15.53 3.62 0.00 3.34
2461 2740 2.560105 ACTTTCGAAGCTTACCGGTACT 59.440 45.455 15.53 6.34 0.00 2.73
2462 2741 3.758554 ACTTTCGAAGCTTACCGGTACTA 59.241 43.478 15.53 0.00 0.00 1.82
2613 2898 2.905880 GCTACCGCGCTAGGAGGA 60.906 66.667 5.56 0.00 37.92 3.71
2614 2899 2.269529 GCTACCGCGCTAGGAGGAT 61.270 63.158 5.56 0.00 37.92 3.24
2615 2900 0.959372 GCTACCGCGCTAGGAGGATA 60.959 60.000 5.56 0.00 37.92 2.59
2616 2901 1.752683 CTACCGCGCTAGGAGGATAT 58.247 55.000 5.56 0.00 37.92 1.63
2617 2902 1.671845 CTACCGCGCTAGGAGGATATC 59.328 57.143 5.56 0.00 37.92 1.63
2705 2990 1.481871 GGGACAGATAACCCACGAGA 58.518 55.000 0.00 0.00 44.96 4.04
2706 2991 1.409427 GGGACAGATAACCCACGAGAG 59.591 57.143 0.00 0.00 44.96 3.20
2707 2992 1.409427 GGACAGATAACCCACGAGAGG 59.591 57.143 0.00 0.00 0.00 3.69
2807 3097 1.400846 GCATGCAGTGTCTCATTCCAG 59.599 52.381 14.21 0.00 0.00 3.86
2823 3113 6.957631 TCATTCCAGAGGCAATTAGTAGAAA 58.042 36.000 0.00 0.00 0.00 2.52
2824 3114 7.402054 TCATTCCAGAGGCAATTAGTAGAAAA 58.598 34.615 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
137 148 1.004918 CCCGTCCTGTCAAGGTGTC 60.005 63.158 0.00 0.00 44.82 3.67
138 149 2.516888 CCCCGTCCTGTCAAGGTGT 61.517 63.158 0.00 0.00 44.82 4.16
139 150 2.347490 CCCCGTCCTGTCAAGGTG 59.653 66.667 0.00 0.00 44.82 4.00
140 151 3.637273 GCCCCGTCCTGTCAAGGT 61.637 66.667 0.00 0.00 44.82 3.50
141 152 4.760047 CGCCCCGTCCTGTCAAGG 62.760 72.222 0.00 0.00 46.06 3.61
184 195 0.037232 GGTGGTGGCTGTGAGTCTAC 60.037 60.000 0.00 0.00 0.00 2.59
185 196 0.471022 TGGTGGTGGCTGTGAGTCTA 60.471 55.000 0.00 0.00 0.00 2.59
186 197 1.344953 TTGGTGGTGGCTGTGAGTCT 61.345 55.000 0.00 0.00 0.00 3.24
187 198 1.148273 TTGGTGGTGGCTGTGAGTC 59.852 57.895 0.00 0.00 0.00 3.36
188 199 1.152963 GTTGGTGGTGGCTGTGAGT 60.153 57.895 0.00 0.00 0.00 3.41
189 200 2.253758 CGTTGGTGGTGGCTGTGAG 61.254 63.158 0.00 0.00 0.00 3.51
190 201 2.203139 CGTTGGTGGTGGCTGTGA 60.203 61.111 0.00 0.00 0.00 3.58
191 202 3.286751 CCGTTGGTGGTGGCTGTG 61.287 66.667 0.00 0.00 0.00 3.66
192 203 4.579384 CCCGTTGGTGGTGGCTGT 62.579 66.667 0.00 0.00 0.00 4.40
323 334 4.874977 GCTCCGTACGCCCTCTGC 62.875 72.222 10.49 3.39 0.00 4.26
329 340 2.412112 CTAGGTGCTCCGTACGCC 59.588 66.667 10.49 5.16 39.05 5.68
347 358 1.283181 CGGGCGCTAGCACTAGTAG 59.717 63.158 16.45 0.00 46.73 2.57
348 359 2.191513 CCGGGCGCTAGCACTAGTA 61.192 63.158 16.45 0.00 46.73 1.82
349 360 3.528370 CCGGGCGCTAGCACTAGT 61.528 66.667 16.45 0.00 46.73 2.57
350 361 4.951963 GCCGGGCGCTAGCACTAG 62.952 72.222 16.45 2.90 46.73 2.57
355 366 4.476410 GTTTTGCCGGGCGCTAGC 62.476 66.667 15.40 4.06 44.18 3.42
432 454 2.202743 CGACGTGGCCATGATCGT 60.203 61.111 31.74 24.62 39.21 3.73
476 519 1.148310 ACAAGACGAATCAAGCGGTG 58.852 50.000 0.00 0.00 0.00 4.94
491 534 1.136446 CCGCGACGACCTTTTTACAAG 60.136 52.381 8.23 0.00 0.00 3.16
545 591 0.179215 GCCAAGTCGTGAAAGCATCG 60.179 55.000 0.00 0.00 0.00 3.84
547 593 1.267806 CAAGCCAAGTCGTGAAAGCAT 59.732 47.619 0.00 0.00 0.00 3.79
549 595 0.661483 GCAAGCCAAGTCGTGAAAGC 60.661 55.000 0.00 0.00 0.00 3.51
550 596 0.662619 TGCAAGCCAAGTCGTGAAAG 59.337 50.000 0.00 0.00 0.00 2.62
551 597 0.380378 GTGCAAGCCAAGTCGTGAAA 59.620 50.000 0.00 0.00 0.00 2.69
552 598 1.444119 GGTGCAAGCCAAGTCGTGAA 61.444 55.000 0.00 0.00 0.00 3.18
553 599 1.891919 GGTGCAAGCCAAGTCGTGA 60.892 57.895 0.00 0.00 0.00 4.35
554 600 2.639286 GGTGCAAGCCAAGTCGTG 59.361 61.111 0.00 0.00 0.00 4.35
618 664 4.891992 ATCGGGACTCCTTTGGTATATG 57.108 45.455 0.00 0.00 0.00 1.78
620 666 4.413760 CCTATCGGGACTCCTTTGGTATA 58.586 47.826 0.00 0.00 37.23 1.47
622 668 2.674420 CCTATCGGGACTCCTTTGGTA 58.326 52.381 0.00 0.00 37.23 3.25
623 669 1.497161 CCTATCGGGACTCCTTTGGT 58.503 55.000 0.00 0.00 37.23 3.67
685 736 1.335132 GGGGAATACCGACTGCTGGA 61.335 60.000 0.00 0.00 41.60 3.86
688 739 3.643398 GGGGGAATACCGACTGCT 58.357 61.111 0.00 0.00 41.60 4.24
746 820 0.905337 GCTCCCATACGGATAGGGCT 60.905 60.000 9.61 0.00 41.00 5.19
768 842 2.796735 CGTCTTTTCCGTTGGGTTTTGG 60.797 50.000 0.00 0.00 33.83 3.28
769 843 2.456010 CGTCTTTTCCGTTGGGTTTTG 58.544 47.619 0.00 0.00 33.83 2.44
770 844 1.202325 GCGTCTTTTCCGTTGGGTTTT 60.202 47.619 0.00 0.00 33.83 2.43
771 845 0.382873 GCGTCTTTTCCGTTGGGTTT 59.617 50.000 0.00 0.00 33.83 3.27
937 1011 2.922950 TACTTATAGGCGCGCGGGG 61.923 63.158 33.06 13.62 0.00 5.73
941 1015 3.144605 GCGTACTTATAGGCGCGC 58.855 61.111 25.94 25.94 40.46 6.86
945 1019 1.373873 GCGGGGCGTACTTATAGGC 60.374 63.158 0.00 0.00 40.72 3.93
971 1046 1.696336 CGGGTTGATGAGGATCTGGAT 59.304 52.381 0.00 0.00 34.92 3.41
984 1059 0.035739 GAGGTTAACAGGCGGGTTGA 59.964 55.000 8.10 0.00 32.29 3.18
985 1060 1.296056 CGAGGTTAACAGGCGGGTTG 61.296 60.000 8.10 0.00 32.29 3.77
986 1061 1.004200 CGAGGTTAACAGGCGGGTT 60.004 57.895 8.10 3.25 34.81 4.11
1004 1079 2.612721 GGTTTGGATTGGATGGTGTTGC 60.613 50.000 0.00 0.00 0.00 4.17
1010 1085 1.006998 TGGGAGGTTTGGATTGGATGG 59.993 52.381 0.00 0.00 0.00 3.51
1049 1124 1.587054 GAGAGGGATATCGCGGTGG 59.413 63.158 6.13 0.00 0.00 4.61
1056 1140 1.827969 CATGGACGGGAGAGGGATATC 59.172 57.143 0.00 0.00 0.00 1.63
1058 1142 0.178932 CCATGGACGGGAGAGGGATA 60.179 60.000 5.56 0.00 0.00 2.59
1059 1143 1.460305 CCATGGACGGGAGAGGGAT 60.460 63.158 5.56 0.00 0.00 3.85
1060 1144 2.041922 CCATGGACGGGAGAGGGA 60.042 66.667 5.56 0.00 0.00 4.20
1292 1380 2.281345 ACCTCGTCGTCCGTGACT 60.281 61.111 0.00 0.00 36.71 3.41
1311 1399 2.446848 CCTCCTCCATCATGCGGGT 61.447 63.158 1.61 0.00 0.00 5.28
1337 1425 4.547905 ATGTAGCCGTCGCCGTCG 62.548 66.667 0.00 0.00 34.57 5.12
1364 1452 2.435938 TTGATGGCGGCGAACTCC 60.436 61.111 12.98 1.84 0.00 3.85
1645 1733 4.337060 TGCACTGCGCGTACGTCT 62.337 61.111 17.90 0.00 46.97 4.18
1646 1734 4.117372 GTGCACTGCGCGTACGTC 62.117 66.667 17.90 9.76 46.97 4.34
1649 1737 3.479269 GAGGTGCACTGCGCGTAC 61.479 66.667 17.98 0.00 46.97 3.67
1650 1738 4.735132 GGAGGTGCACTGCGCGTA 62.735 66.667 17.98 0.71 46.97 4.42
1739 1836 8.415950 AGCTAATAGAGTAGGAGTACGTAGTA 57.584 38.462 2.11 0.00 45.11 1.82
1740 1837 8.522830 CTAGCTAATAGAGTAGGAGTACGTAGT 58.477 40.741 1.62 1.62 38.01 2.73
1741 1838 8.522830 ACTAGCTAATAGAGTAGGAGTACGTAG 58.477 40.741 0.00 0.00 35.30 3.51
1743 1840 7.301868 ACTAGCTAATAGAGTAGGAGTACGT 57.698 40.000 0.00 0.00 35.30 3.57
1744 1841 6.527722 CGACTAGCTAATAGAGTAGGAGTACG 59.472 46.154 0.00 0.00 35.30 3.67
1745 1842 6.311200 GCGACTAGCTAATAGAGTAGGAGTAC 59.689 46.154 0.00 0.00 44.04 2.73
1746 1843 6.397272 GCGACTAGCTAATAGAGTAGGAGTA 58.603 44.000 0.00 0.00 44.04 2.59
1747 1844 5.240121 GCGACTAGCTAATAGAGTAGGAGT 58.760 45.833 0.00 0.00 44.04 3.85
1748 1845 5.789710 GCGACTAGCTAATAGAGTAGGAG 57.210 47.826 0.00 0.00 44.04 3.69
1812 1910 8.403236 TCCGACAGTTCCGATACATTATATATG 58.597 37.037 0.00 0.00 0.00 1.78
1842 1940 5.128919 ACATGGAGGATTATTCTTCAGTGC 58.871 41.667 0.00 0.00 29.78 4.40
1991 2107 1.991167 TCCGGCCGGGAGTTGTAAT 60.991 57.895 42.36 0.00 40.94 1.89
1992 2108 2.604079 TCCGGCCGGGAGTTGTAA 60.604 61.111 42.36 19.62 40.94 2.41
2031 2147 1.817099 CACATGAAGCTCGCTCCCC 60.817 63.158 0.00 0.00 0.00 4.81
2081 2198 1.296392 CAGCCTGGGTCACATCGAA 59.704 57.895 0.00 0.00 0.00 3.71
2134 2260 2.159448 TGAGGTTTTGTTGTTCACGCTG 60.159 45.455 0.00 0.00 0.00 5.18
2372 2644 1.255882 CTTACAATTGCACCAGGGCA 58.744 50.000 5.05 0.00 43.19 5.36
2388 2660 5.716703 GGGGTACTACAAGTCTACAACCTTA 59.283 44.000 0.00 0.00 0.00 2.69
2460 2739 5.043903 CAGTGTCAAACCGTCTATCCATAG 58.956 45.833 0.00 0.00 0.00 2.23
2461 2740 4.707934 TCAGTGTCAAACCGTCTATCCATA 59.292 41.667 0.00 0.00 0.00 2.74
2462 2741 3.513912 TCAGTGTCAAACCGTCTATCCAT 59.486 43.478 0.00 0.00 0.00 3.41
2495 2774 6.662865 TGTTGGTATCCATCAATTTGTTGT 57.337 33.333 6.69 0.00 31.25 3.32
2613 2898 4.096532 CCTACGCGTGGTCTGATATGATAT 59.903 45.833 24.59 0.00 0.00 1.63
2614 2899 3.439129 CCTACGCGTGGTCTGATATGATA 59.561 47.826 24.59 0.00 0.00 2.15
2615 2900 2.229062 CCTACGCGTGGTCTGATATGAT 59.771 50.000 24.59 0.00 0.00 2.45
2616 2901 1.607148 CCTACGCGTGGTCTGATATGA 59.393 52.381 24.59 0.00 0.00 2.15
2617 2902 1.335964 CCCTACGCGTGGTCTGATATG 60.336 57.143 24.59 2.91 0.00 1.78
2707 2992 0.396060 CTGAAGATGAGGGGCTAGGC 59.604 60.000 8.00 8.00 0.00 3.93
2740 3025 1.466856 TCTGAAGGCATGCATGTTCC 58.533 50.000 26.79 19.96 0.00 3.62
2807 3097 5.897377 TGCCTTTTTCTACTAATTGCCTC 57.103 39.130 0.00 0.00 0.00 4.70
2823 3113 3.297620 CAGCCGCCACTTGCCTTT 61.298 61.111 0.00 0.00 36.24 3.11


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

AutoCloner maintained by Alex Coulton.