Multiple sequence alignment - TraesCS2A01G586400

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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 TraesCS2A01G586400 chr2A 100.000 3189 0 0 1 3189 777067143 777063955 0.000000e+00 5890
1 TraesCS2A01G586400 chr2A 80.496 282 39 8 118 391 777066605 777066332 5.390000e-48 202
2 TraesCS2A01G586400 chr2D 94.186 2597 112 22 622 3189 650962442 650965028 0.000000e+00 3923
3 TraesCS2A01G586400 chr2D 83.077 195 21 7 204 391 650962449 650962638 1.970000e-37 167
4 TraesCS2A01G586400 chr2D 90.984 122 8 2 487 608 650962271 650962389 9.150000e-36 161
5 TraesCS2A01G586400 chr2D 91.743 109 6 2 3084 3189 651110128 651110236 7.130000e-32 148
6 TraesCS2A01G586400 chrUn 90.553 2371 124 40 483 2808 23530404 23532719 0.000000e+00 3046
7 TraesCS2A01G586400 chrUn 84.965 286 42 1 83 368 23529383 23529667 4.020000e-74 289
8 TraesCS2A01G586400 chrUn 83.333 240 23 8 164 391 23530515 23530749 4.170000e-49 206


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 TraesCS2A01G586400 chr2A 777063955 777067143 3188 True 3046.000000 5890 90.248000 1 3189 2 chr2A.!!$R1 3188
1 TraesCS2A01G586400 chr2D 650962271 650965028 2757 False 1417.000000 3923 89.415667 204 3189 3 chr2D.!!$F2 2985
2 TraesCS2A01G586400 chrUn 23529383 23532719 3336 False 1180.333333 3046 86.283667 83 2808 3 chrUn.!!$F1 2725

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
28 29 0.103390 TTTGCCACTGAGACGTTCGA 59.897 50.0 0.00 0.00 0.00 3.71 F
40 41 0.109781 ACGTTCGATTTGCCATGTGC 60.110 50.0 0.00 0.00 41.77 4.57 F
261 262 0.184933 CTGATCCCCTCTCCTCTCGT 59.815 60.0 0.00 0.00 0.00 4.18 F
1424 2117 0.531200 CCGGTCTACCAGGTGACTTC 59.469 60.0 16.95 5.69 40.21 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1424 2117 1.163420 TGTGCTACAACTGCAACCGG 61.163 55.000 0.00 0.0 42.41 5.28 R
1459 2156 1.599542 GGCTGAGTTGATTATGACCGC 59.400 52.381 0.00 0.0 0.00 5.68 R
2169 2866 1.269309 CCTATACAGAGTCACGCTGGC 60.269 57.143 13.61 0.0 35.65 4.85 R
3022 3737 0.666880 TGCATGTTGTTGCGAATGCC 60.667 50.000 5.98 0.0 45.77 4.40 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
22 23 5.886960 ATCACTAAATTTGCCACTGAGAC 57.113 39.130 0.00 0.00 0.00 3.36
23 24 3.745975 TCACTAAATTTGCCACTGAGACG 59.254 43.478 0.00 0.00 0.00 4.18
24 25 3.498397 CACTAAATTTGCCACTGAGACGT 59.502 43.478 0.00 0.00 0.00 4.34
25 26 4.024048 CACTAAATTTGCCACTGAGACGTT 60.024 41.667 0.00 0.00 0.00 3.99
26 27 3.626028 AAATTTGCCACTGAGACGTTC 57.374 42.857 0.00 0.00 0.00 3.95
27 28 1.148310 ATTTGCCACTGAGACGTTCG 58.852 50.000 0.00 0.00 0.00 3.95
28 29 0.103390 TTTGCCACTGAGACGTTCGA 59.897 50.000 0.00 0.00 0.00 3.71
29 30 0.317160 TTGCCACTGAGACGTTCGAT 59.683 50.000 0.00 0.00 0.00 3.59
30 31 0.317160 TGCCACTGAGACGTTCGATT 59.683 50.000 0.00 0.00 0.00 3.34
31 32 1.270094 TGCCACTGAGACGTTCGATTT 60.270 47.619 0.00 0.00 0.00 2.17
32 33 1.126846 GCCACTGAGACGTTCGATTTG 59.873 52.381 0.00 0.00 0.00 2.32
33 34 1.126846 CCACTGAGACGTTCGATTTGC 59.873 52.381 0.00 0.00 0.00 3.68
34 35 1.126846 CACTGAGACGTTCGATTTGCC 59.873 52.381 0.00 0.00 0.00 4.52
35 36 1.270094 ACTGAGACGTTCGATTTGCCA 60.270 47.619 0.00 0.00 0.00 4.92
36 37 2.002586 CTGAGACGTTCGATTTGCCAT 58.997 47.619 0.00 0.00 0.00 4.40
37 38 1.731709 TGAGACGTTCGATTTGCCATG 59.268 47.619 0.00 0.00 0.00 3.66
38 39 1.732259 GAGACGTTCGATTTGCCATGT 59.268 47.619 0.00 0.00 0.00 3.21
39 40 1.464608 AGACGTTCGATTTGCCATGTG 59.535 47.619 0.00 0.00 0.00 3.21
40 41 0.109781 ACGTTCGATTTGCCATGTGC 60.110 50.000 0.00 0.00 41.77 4.57
51 52 2.389713 GCCATGTGCACATATCGTTC 57.610 50.000 30.92 12.86 40.77 3.95
52 53 1.333169 GCCATGTGCACATATCGTTCG 60.333 52.381 30.92 16.77 40.77 3.95
53 54 1.261354 CCATGTGCACATATCGTTCGG 59.739 52.381 30.92 21.48 34.26 4.30
54 55 1.261354 CATGTGCACATATCGTTCGGG 59.739 52.381 30.92 12.36 34.26 5.14
55 56 1.087202 TGTGCACATATCGTTCGGGC 61.087 55.000 17.42 0.00 0.00 6.13
56 57 1.880796 TGCACATATCGTTCGGGCG 60.881 57.895 0.00 0.00 0.00 6.13
57 58 1.881252 GCACATATCGTTCGGGCGT 60.881 57.895 0.14 0.00 0.00 5.68
58 59 1.426041 GCACATATCGTTCGGGCGTT 61.426 55.000 0.14 0.00 0.00 4.84
59 60 1.842720 CACATATCGTTCGGGCGTTA 58.157 50.000 0.14 0.00 0.00 3.18
60 61 2.400399 CACATATCGTTCGGGCGTTAT 58.600 47.619 0.14 0.00 0.00 1.89
61 62 2.407361 CACATATCGTTCGGGCGTTATC 59.593 50.000 0.14 0.00 0.00 1.75
62 63 2.034939 ACATATCGTTCGGGCGTTATCA 59.965 45.455 0.14 0.00 0.00 2.15
63 64 2.410785 TATCGTTCGGGCGTTATCAG 57.589 50.000 0.14 0.00 0.00 2.90
64 65 0.458669 ATCGTTCGGGCGTTATCAGT 59.541 50.000 0.14 0.00 0.00 3.41
65 66 0.244450 TCGTTCGGGCGTTATCAGTT 59.756 50.000 0.14 0.00 0.00 3.16
66 67 1.073177 CGTTCGGGCGTTATCAGTTT 58.927 50.000 0.00 0.00 0.00 2.66
67 68 1.461897 CGTTCGGGCGTTATCAGTTTT 59.538 47.619 0.00 0.00 0.00 2.43
68 69 2.096119 CGTTCGGGCGTTATCAGTTTTT 60.096 45.455 0.00 0.00 0.00 1.94
123 124 8.887036 AAAAAGAAGGGCTTAGTATTTGTTTG 57.113 30.769 0.00 0.00 35.24 2.93
129 130 5.880887 AGGGCTTAGTATTTGTTTGAGTAGC 59.119 40.000 0.00 0.00 0.00 3.58
132 133 5.646360 GCTTAGTATTTGTTTGAGTAGCCCA 59.354 40.000 0.00 0.00 0.00 5.36
171 172 3.645884 GCAAAGTGTTGTACTCGGACTA 58.354 45.455 0.00 0.00 39.18 2.59
197 198 2.185350 CCGGCACTGACTAGGCAG 59.815 66.667 24.63 24.63 41.63 4.85
199 200 2.985456 GGCACTGACTAGGCAGCT 59.015 61.111 26.12 10.12 39.51 4.24
215 216 4.082354 AGGCAGCTGAAAAATAAAGAGCAG 60.082 41.667 20.43 0.00 31.80 4.24
217 218 4.741342 CAGCTGAAAAATAAAGAGCAGGG 58.259 43.478 8.42 0.00 31.80 4.45
219 220 3.056607 GCTGAAAAATAAAGAGCAGGGCA 60.057 43.478 0.00 0.00 0.00 5.36
220 221 4.741342 CTGAAAAATAAAGAGCAGGGCAG 58.259 43.478 0.00 0.00 0.00 4.85
222 223 4.218417 TGAAAAATAAAGAGCAGGGCAGAC 59.782 41.667 0.00 0.00 0.00 3.51
223 224 2.426842 AATAAAGAGCAGGGCAGACC 57.573 50.000 0.00 0.00 40.67 3.85
243 244 0.609131 CCCCATTGCTTCACCGTTCT 60.609 55.000 0.00 0.00 0.00 3.01
246 247 2.086869 CCATTGCTTCACCGTTCTGAT 58.913 47.619 0.00 0.00 0.00 2.90
259 260 2.316108 GTTCTGATCCCCTCTCCTCTC 58.684 57.143 0.00 0.00 0.00 3.20
261 262 0.184933 CTGATCCCCTCTCCTCTCGT 59.815 60.000 0.00 0.00 0.00 4.18
265 266 2.123640 CCCTCTCCTCTCGTCCCC 60.124 72.222 0.00 0.00 0.00 4.81
272 273 2.829458 CTCTCGTCCCCCGACTCC 60.829 72.222 0.00 0.00 41.60 3.85
344 345 0.682855 CTCCTCCTCTCTGCGACCTT 60.683 60.000 0.00 0.00 0.00 3.50
356 357 4.856607 GACCTTCGCCCGCTCTCG 62.857 72.222 0.00 0.00 0.00 4.04
390 391 3.847602 CGAGAGCTGAGCCCCCTG 61.848 72.222 0.00 0.00 0.00 4.45
391 392 2.364842 GAGAGCTGAGCCCCCTGA 60.365 66.667 0.00 0.00 0.00 3.86
392 393 1.765657 GAGAGCTGAGCCCCCTGAT 60.766 63.158 0.00 0.00 0.00 2.90
393 394 2.042404 GAGAGCTGAGCCCCCTGATG 62.042 65.000 0.00 0.00 0.00 3.07
394 395 3.771110 GAGCTGAGCCCCCTGATGC 62.771 68.421 0.00 0.00 0.00 3.91
451 651 8.352942 AGAAATGCCATATCTTAAAATCCGAAC 58.647 33.333 0.00 0.00 0.00 3.95
452 652 5.666969 TGCCATATCTTAAAATCCGAACG 57.333 39.130 0.00 0.00 0.00 3.95
453 653 5.361427 TGCCATATCTTAAAATCCGAACGA 58.639 37.500 0.00 0.00 0.00 3.85
454 654 5.465390 TGCCATATCTTAAAATCCGAACGAG 59.535 40.000 0.00 0.00 0.00 4.18
470 1055 4.608951 GAACGAGTAGCATTTCCGACTAT 58.391 43.478 0.00 0.00 0.00 2.12
471 1056 4.226113 ACGAGTAGCATTTCCGACTATC 57.774 45.455 0.00 0.00 0.00 2.08
473 1058 4.222886 CGAGTAGCATTTCCGACTATCTG 58.777 47.826 0.00 0.00 0.00 2.90
480 1065 2.225382 TTCCGACTATCTGTGGGTCA 57.775 50.000 0.00 0.00 43.83 4.02
510 1133 9.299963 CTGACACAACAATTGTTTTTCATTAGA 57.700 29.630 21.10 1.87 43.23 2.10
550 1175 1.095807 GGGGGCATTGTTCGAGTAGC 61.096 60.000 0.00 0.00 0.00 3.58
584 1209 1.148310 CCACGCAGGAAGTGTTGTAG 58.852 55.000 0.00 0.00 39.40 2.74
598 1223 1.397692 GTTGTAGTCGGAGTCTCGGAG 59.602 57.143 10.19 0.00 0.00 4.63
1101 1794 2.105466 GTCGCCGTCGGTCTACTCT 61.105 63.158 13.94 0.00 36.13 3.24
1156 1849 2.747460 CGTCCCCGTCGACCTACA 60.747 66.667 10.58 0.00 0.00 2.74
1424 2117 0.531200 CCGGTCTACCAGGTGACTTC 59.469 60.000 16.95 5.69 40.21 3.01
1466 2163 7.701924 CACAGTTTTATTTATCATTGCGGTCAT 59.298 33.333 0.00 0.00 0.00 3.06
1480 2177 2.743183 GCGGTCATAATCAACTCAGCCT 60.743 50.000 0.00 0.00 0.00 4.58
1503 2200 1.368641 TCTTGATACATGGTGTGCGC 58.631 50.000 0.00 0.00 0.00 6.09
1687 2384 2.044946 GCCTTCCTTCCGCACCAT 60.045 61.111 0.00 0.00 0.00 3.55
1741 2438 1.488393 GAGCCTATCTTCTGCCCTGTT 59.512 52.381 0.00 0.00 0.00 3.16
1870 2567 1.630148 CCTTCACGTCGACCATCTTC 58.370 55.000 10.58 0.00 0.00 2.87
1934 2631 4.684134 AGGGCCGTGGCATTGCTT 62.684 61.111 13.76 0.00 44.11 3.91
2169 2866 2.823829 GCATCCGTAAGCTTGGCCG 61.824 63.158 9.86 8.54 0.00 6.13
2195 2892 3.631227 GCGTGACTCTGTATAGGTTAGGT 59.369 47.826 0.00 0.00 0.00 3.08
2254 2953 5.663106 AGGATTACTGCTAGTTGATTCCAGA 59.337 40.000 0.00 0.00 0.00 3.86
2321 3021 2.363306 ATGCTTGGTCTGTTGTGGAA 57.637 45.000 0.00 0.00 0.00 3.53
2357 3057 0.623723 ATGGGGAATGTAAGCACCGT 59.376 50.000 0.00 0.00 0.00 4.83
2403 3103 7.281324 CAGCTATATGTAGATACTCGTAGGCTT 59.719 40.741 0.00 0.00 0.00 4.35
2457 3157 2.430332 TGATGGTCTCGCACATGTCATA 59.570 45.455 0.00 0.00 0.00 2.15
2485 3185 3.587797 TTCGTCAGGTAACACATCTCC 57.412 47.619 0.00 0.00 41.41 3.71
2553 3253 6.169094 CCAGATGTTTCTCTATGTTCAGTGT 58.831 40.000 0.00 0.00 0.00 3.55
2556 3256 7.814587 CAGATGTTTCTCTATGTTCAGTGTGTA 59.185 37.037 0.00 0.00 0.00 2.90
2560 3260 5.659440 TCTCTATGTTCAGTGTGTATGCA 57.341 39.130 0.00 0.00 0.00 3.96
2561 3261 6.225981 TCTCTATGTTCAGTGTGTATGCAT 57.774 37.500 3.79 3.79 0.00 3.96
2578 3279 4.420522 TGCATTTTTCCCTTGCTTTCTT 57.579 36.364 0.00 0.00 37.28 2.52
2699 3412 4.697352 AGTTTGTTCACCTGTGCTGATATC 59.303 41.667 0.00 0.00 0.00 1.63
2702 3415 2.939103 GTTCACCTGTGCTGATATCACC 59.061 50.000 0.00 0.00 33.71 4.02
2720 3433 5.100344 TCACCAACCCTTTTGCGTATATA 57.900 39.130 0.00 0.00 0.00 0.86
2733 3446 9.341899 CTTTTGCGTATATAAAGAGTTTGCTTT 57.658 29.630 0.00 0.00 40.85 3.51
2825 3538 1.710809 ACCATGTAACCCAGCTTTCCT 59.289 47.619 0.00 0.00 0.00 3.36
2834 3547 2.158696 ACCCAGCTTTCCTGCATCTATC 60.159 50.000 0.00 0.00 40.36 2.08
2850 3563 6.709145 CATCTATCTTGTAGAGATGCAAGC 57.291 41.667 0.00 0.00 44.58 4.01
2851 3564 5.859205 TCTATCTTGTAGAGATGCAAGCA 57.141 39.130 0.00 0.00 44.80 3.91
2874 3587 6.293571 GCAAGCAATGTCTAAATTTTGGCTTT 60.294 34.615 5.84 3.13 0.00 3.51
2875 3588 7.293018 CAAGCAATGTCTAAATTTTGGCTTTC 58.707 34.615 5.84 1.73 0.00 2.62
2881 3594 5.102313 GTCTAAATTTTGGCTTTCCGATGG 58.898 41.667 0.00 0.00 34.14 3.51
2890 3603 3.192422 TGGCTTTCCGATGGTTAATTGTG 59.808 43.478 0.00 0.00 34.14 3.33
2893 3606 4.621034 GCTTTCCGATGGTTAATTGTGTTG 59.379 41.667 0.00 0.00 0.00 3.33
2899 3612 6.655425 TCCGATGGTTAATTGTGTTGTGATTA 59.345 34.615 0.00 0.00 0.00 1.75
2912 3627 6.934083 TGTGTTGTGATTAGTGAGCTTATGAA 59.066 34.615 0.00 0.00 0.00 2.57
2919 3634 9.334693 GTGATTAGTGAGCTTATGAAACAAAAG 57.665 33.333 0.00 0.00 0.00 2.27
2922 3637 8.677148 TTAGTGAGCTTATGAAACAAAAGTCT 57.323 30.769 0.00 0.00 0.00 3.24
2967 3682 5.789643 AACATTAGCACAACAATGGAAGT 57.210 34.783 0.00 0.00 36.63 3.01
2980 3695 2.798976 TGGAAGTTCATTGTTGCAGC 57.201 45.000 5.01 0.00 0.00 5.25
2981 3696 2.030371 TGGAAGTTCATTGTTGCAGCA 58.970 42.857 0.00 0.00 0.00 4.41
2982 3697 2.629137 TGGAAGTTCATTGTTGCAGCAT 59.371 40.909 3.36 0.00 0.00 3.79
3022 3737 5.267776 CAAATGCAGCAAAACCAGAAAAAG 58.732 37.500 0.00 0.00 0.00 2.27
3024 3739 1.599071 GCAGCAAAACCAGAAAAAGGC 59.401 47.619 0.00 0.00 0.00 4.35
3025 3740 2.903798 CAGCAAAACCAGAAAAAGGCA 58.096 42.857 0.00 0.00 0.00 4.75
3026 3741 3.469739 CAGCAAAACCAGAAAAAGGCAT 58.530 40.909 0.00 0.00 0.00 4.40
3028 3743 4.024641 CAGCAAAACCAGAAAAAGGCATTC 60.025 41.667 0.00 0.00 0.00 2.67
3029 3744 3.059665 GCAAAACCAGAAAAAGGCATTCG 60.060 43.478 0.00 0.00 32.04 3.34
3030 3745 2.438868 AACCAGAAAAAGGCATTCGC 57.561 45.000 0.00 0.00 37.44 4.70
3031 3746 1.327303 ACCAGAAAAAGGCATTCGCA 58.673 45.000 0.00 0.00 41.24 5.10
3033 3748 2.061028 CCAGAAAAAGGCATTCGCAAC 58.939 47.619 0.00 0.00 41.24 4.17
3034 3749 2.545532 CCAGAAAAAGGCATTCGCAACA 60.546 45.455 0.00 0.00 41.24 3.33
3036 3751 3.060339 CAGAAAAAGGCATTCGCAACAAC 60.060 43.478 0.00 0.00 41.24 3.32
3039 3754 2.068837 AAGGCATTCGCAACAACATG 57.931 45.000 0.00 0.00 41.24 3.21
3040 3755 0.388907 AGGCATTCGCAACAACATGC 60.389 50.000 0.00 0.00 41.17 4.06
3041 3756 0.666880 GGCATTCGCAACAACATGCA 60.667 50.000 5.42 0.00 46.76 3.96
3042 3757 1.138337 GCATTCGCAACAACATGCAA 58.862 45.000 0.00 0.00 46.76 4.08
3043 3758 1.136557 GCATTCGCAACAACATGCAAC 60.137 47.619 0.00 0.00 46.76 4.17
3045 3760 2.284263 TTCGCAACAACATGCAACAA 57.716 40.000 0.00 0.00 46.76 2.83
3046 3761 2.505628 TCGCAACAACATGCAACAAT 57.494 40.000 0.00 0.00 46.76 2.71
3047 3762 2.819115 TCGCAACAACATGCAACAATT 58.181 38.095 0.00 0.00 46.76 2.32
3048 3763 2.538861 TCGCAACAACATGCAACAATTG 59.461 40.909 3.24 3.24 46.76 2.32
3051 3768 3.059461 GCAACAACATGCAACAATTGGAG 60.059 43.478 10.83 2.65 45.70 3.86
3087 3804 1.847328 TGCTACTGGATCCTTCGTGA 58.153 50.000 14.23 0.00 0.00 4.35
3090 3807 2.362397 GCTACTGGATCCTTCGTGATCA 59.638 50.000 14.23 0.00 42.41 2.92
3091 3808 3.006323 GCTACTGGATCCTTCGTGATCAT 59.994 47.826 14.23 0.00 42.41 2.45
3144 3875 0.178909 ATTGCCATGGGTCCCAACAA 60.179 50.000 16.55 19.16 36.95 2.83
3162 3893 4.361827 CGTCCACGTCTTCTAGCG 57.638 61.111 0.00 0.00 34.11 4.26
3167 3898 1.068748 TCCACGTCTTCTAGCGACAAC 60.069 52.381 11.08 0.00 0.00 3.32
3168 3899 0.975544 CACGTCTTCTAGCGACAACG 59.024 55.000 11.08 6.98 42.93 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.393062 CGTCTCAGTGGCAAATTTAGTGAT 59.607 41.667 0.00 0.00 0.00 3.06
1 2 3.745975 CGTCTCAGTGGCAAATTTAGTGA 59.254 43.478 0.00 0.00 0.00 3.41
5 6 3.185594 CGAACGTCTCAGTGGCAAATTTA 59.814 43.478 0.00 0.00 0.00 1.40
6 7 2.032030 CGAACGTCTCAGTGGCAAATTT 60.032 45.455 0.00 0.00 0.00 1.82
7 8 1.531149 CGAACGTCTCAGTGGCAAATT 59.469 47.619 0.00 0.00 0.00 1.82
8 9 1.148310 CGAACGTCTCAGTGGCAAAT 58.852 50.000 0.00 0.00 0.00 2.32
9 10 0.103390 TCGAACGTCTCAGTGGCAAA 59.897 50.000 0.00 0.00 0.00 3.68
10 11 0.317160 ATCGAACGTCTCAGTGGCAA 59.683 50.000 0.00 0.00 0.00 4.52
11 12 0.317160 AATCGAACGTCTCAGTGGCA 59.683 50.000 0.00 0.00 0.00 4.92
12 13 1.126846 CAAATCGAACGTCTCAGTGGC 59.873 52.381 0.00 0.00 0.00 5.01
13 14 1.126846 GCAAATCGAACGTCTCAGTGG 59.873 52.381 0.00 0.00 0.00 4.00
14 15 1.126846 GGCAAATCGAACGTCTCAGTG 59.873 52.381 0.00 0.00 0.00 3.66
15 16 1.270094 TGGCAAATCGAACGTCTCAGT 60.270 47.619 0.00 0.00 0.00 3.41
16 17 1.428448 TGGCAAATCGAACGTCTCAG 58.572 50.000 0.00 0.00 0.00 3.35
17 18 1.731709 CATGGCAAATCGAACGTCTCA 59.268 47.619 0.00 0.00 0.00 3.27
18 19 1.732259 ACATGGCAAATCGAACGTCTC 59.268 47.619 0.00 0.00 0.00 3.36
19 20 1.464608 CACATGGCAAATCGAACGTCT 59.535 47.619 0.00 0.00 0.00 4.18
20 21 1.882198 CACATGGCAAATCGAACGTC 58.118 50.000 0.00 0.00 0.00 4.34
21 22 0.109781 GCACATGGCAAATCGAACGT 60.110 50.000 0.00 0.00 43.97 3.99
22 23 2.640684 GCACATGGCAAATCGAACG 58.359 52.632 0.00 0.00 43.97 3.95
32 33 1.333169 CGAACGATATGTGCACATGGC 60.333 52.381 36.72 26.74 45.13 4.40
33 34 1.261354 CCGAACGATATGTGCACATGG 59.739 52.381 36.72 27.18 37.15 3.66
34 35 1.261354 CCCGAACGATATGTGCACATG 59.739 52.381 36.72 24.53 37.15 3.21
35 36 1.581934 CCCGAACGATATGTGCACAT 58.418 50.000 33.20 33.20 40.22 3.21
36 37 1.087202 GCCCGAACGATATGTGCACA 61.087 55.000 24.08 24.08 0.00 4.57
37 38 1.641677 GCCCGAACGATATGTGCAC 59.358 57.895 10.75 10.75 0.00 4.57
38 39 1.880796 CGCCCGAACGATATGTGCA 60.881 57.895 0.00 0.00 34.06 4.57
39 40 1.426041 AACGCCCGAACGATATGTGC 61.426 55.000 4.02 0.00 36.70 4.57
40 41 1.842720 TAACGCCCGAACGATATGTG 58.157 50.000 4.02 0.00 36.70 3.21
41 42 2.034939 TGATAACGCCCGAACGATATGT 59.965 45.455 4.02 0.00 32.09 2.29
42 43 2.661675 CTGATAACGCCCGAACGATATG 59.338 50.000 4.02 0.00 32.09 1.78
43 44 2.295349 ACTGATAACGCCCGAACGATAT 59.705 45.455 4.02 2.22 34.26 1.63
44 45 1.677576 ACTGATAACGCCCGAACGATA 59.322 47.619 4.02 0.00 36.70 2.92
45 46 0.458669 ACTGATAACGCCCGAACGAT 59.541 50.000 4.02 0.00 36.70 3.73
46 47 0.244450 AACTGATAACGCCCGAACGA 59.756 50.000 4.02 0.00 36.70 3.85
47 48 1.073177 AAACTGATAACGCCCGAACG 58.927 50.000 0.00 0.00 39.50 3.95
48 49 3.547649 AAAAACTGATAACGCCCGAAC 57.452 42.857 0.00 0.00 0.00 3.95
69 70 5.007034 TGATAACGCCCAGATTCTCAAAAA 58.993 37.500 0.00 0.00 0.00 1.94
70 71 4.584874 TGATAACGCCCAGATTCTCAAAA 58.415 39.130 0.00 0.00 0.00 2.44
71 72 4.081142 TCTGATAACGCCCAGATTCTCAAA 60.081 41.667 0.00 0.00 34.78 2.69
72 73 3.450817 TCTGATAACGCCCAGATTCTCAA 59.549 43.478 0.00 0.00 34.78 3.02
73 74 3.031013 TCTGATAACGCCCAGATTCTCA 58.969 45.455 0.00 0.00 34.78 3.27
74 75 3.735237 TCTGATAACGCCCAGATTCTC 57.265 47.619 0.00 0.00 34.78 2.87
75 76 5.808366 TTATCTGATAACGCCCAGATTCT 57.192 39.130 6.01 0.00 45.01 2.40
76 77 6.861065 TTTTATCTGATAACGCCCAGATTC 57.139 37.500 9.54 0.00 45.01 2.52
108 109 5.646360 TGGGCTACTCAAACAAATACTAAGC 59.354 40.000 0.00 0.00 0.00 3.09
110 111 6.177610 CCTGGGCTACTCAAACAAATACTAA 58.822 40.000 0.00 0.00 0.00 2.24
187 188 6.237901 TCTTTATTTTTCAGCTGCCTAGTCA 58.762 36.000 9.47 0.00 0.00 3.41
188 189 6.676700 GCTCTTTATTTTTCAGCTGCCTAGTC 60.677 42.308 9.47 0.00 0.00 2.59
197 198 3.056607 TGCCCTGCTCTTTATTTTTCAGC 60.057 43.478 0.00 0.00 0.00 4.26
199 200 4.218417 GTCTGCCCTGCTCTTTATTTTTCA 59.782 41.667 0.00 0.00 0.00 2.69
223 224 1.595093 GAACGGTGAAGCAATGGGGG 61.595 60.000 0.00 0.00 0.00 5.40
230 231 0.036388 GGGATCAGAACGGTGAAGCA 60.036 55.000 0.00 0.00 0.00 3.91
236 237 0.688087 GGAGAGGGGATCAGAACGGT 60.688 60.000 0.00 0.00 0.00 4.83
239 240 2.316108 GAGAGGAGAGGGGATCAGAAC 58.684 57.143 0.00 0.00 0.00 3.01
243 244 0.183971 GACGAGAGGAGAGGGGATCA 59.816 60.000 0.00 0.00 0.00 2.92
246 247 2.691779 GGGACGAGAGGAGAGGGGA 61.692 68.421 0.00 0.00 0.00 4.81
325 326 0.682855 AAGGTCGCAGAGAGGAGGAG 60.683 60.000 0.00 0.00 36.95 3.69
368 369 4.828925 GGCTCAGCTCTCGCCCAC 62.829 72.222 0.00 0.00 37.86 4.61
373 374 3.847602 CAGGGGGCTCAGCTCTCG 61.848 72.222 0.00 0.00 32.78 4.04
375 376 2.071262 CATCAGGGGGCTCAGCTCT 61.071 63.158 0.00 0.00 0.00 4.09
376 377 2.509916 CATCAGGGGGCTCAGCTC 59.490 66.667 0.00 0.00 0.00 4.09
377 378 3.806667 GCATCAGGGGGCTCAGCT 61.807 66.667 0.00 0.00 0.00 4.24
378 379 4.891037 GGCATCAGGGGGCTCAGC 62.891 72.222 0.00 0.00 0.00 4.26
382 383 1.004758 TAAGAGGCATCAGGGGGCT 59.995 57.895 0.00 0.00 44.69 5.19
383 384 1.348775 ACTAAGAGGCATCAGGGGGC 61.349 60.000 0.00 0.00 0.00 5.80
385 386 5.825593 TTATTACTAAGAGGCATCAGGGG 57.174 43.478 0.00 0.00 0.00 4.79
389 390 7.779798 AGGCATTTTTATTACTAAGAGGCATCA 59.220 33.333 0.00 0.00 0.00 3.07
390 391 8.171164 AGGCATTTTTATTACTAAGAGGCATC 57.829 34.615 0.00 0.00 0.00 3.91
391 392 8.539117 AAGGCATTTTTATTACTAAGAGGCAT 57.461 30.769 0.00 0.00 0.00 4.40
392 393 7.954666 AAGGCATTTTTATTACTAAGAGGCA 57.045 32.000 0.00 0.00 0.00 4.75
423 485 8.912988 TCGGATTTTAAGATATGGCATTTCTTT 58.087 29.630 29.48 16.84 33.56 2.52
426 626 7.323656 CGTTCGGATTTTAAGATATGGCATTTC 59.676 37.037 4.78 7.67 0.00 2.17
436 636 5.657474 TGCTACTCGTTCGGATTTTAAGAT 58.343 37.500 0.00 0.00 0.00 2.40
442 642 3.621715 GGAAATGCTACTCGTTCGGATTT 59.378 43.478 0.00 0.00 32.53 2.17
446 646 0.921347 CGGAAATGCTACTCGTTCGG 59.079 55.000 0.00 0.00 0.00 4.30
447 647 1.582502 GTCGGAAATGCTACTCGTTCG 59.417 52.381 0.00 0.00 0.00 3.95
448 648 2.877335 AGTCGGAAATGCTACTCGTTC 58.123 47.619 0.00 0.00 0.00 3.95
451 651 4.222886 CAGATAGTCGGAAATGCTACTCG 58.777 47.826 0.00 0.00 0.00 4.18
452 652 4.979197 CACAGATAGTCGGAAATGCTACTC 59.021 45.833 0.00 0.00 0.00 2.59
453 653 4.202161 CCACAGATAGTCGGAAATGCTACT 60.202 45.833 0.00 0.00 0.00 2.57
454 654 4.051922 CCACAGATAGTCGGAAATGCTAC 58.948 47.826 0.00 0.00 0.00 3.58
480 1065 7.151308 TGAAAAACAATTGTTGTGTCAGAGTT 58.849 30.769 23.93 8.70 44.59 3.01
510 1133 0.875059 CTTTTCCGCTCTCGCCTTTT 59.125 50.000 0.00 0.00 0.00 2.27
531 1154 1.095807 GCTACTCGAACAATGCCCCC 61.096 60.000 0.00 0.00 0.00 5.40
584 1209 2.408241 CCCACTCCGAGACTCCGAC 61.408 68.421 1.33 0.00 0.00 4.79
619 1253 5.539955 TGCCCTGCTCTTTATTTTTCTTTCT 59.460 36.000 0.00 0.00 0.00 2.52
620 1254 5.783111 TGCCCTGCTCTTTATTTTTCTTTC 58.217 37.500 0.00 0.00 0.00 2.62
621 1255 5.539955 TCTGCCCTGCTCTTTATTTTTCTTT 59.460 36.000 0.00 0.00 0.00 2.52
622 1256 5.079643 TCTGCCCTGCTCTTTATTTTTCTT 58.920 37.500 0.00 0.00 0.00 2.52
751 1426 4.144727 GGCTCGGGGAGAGGAGGA 62.145 72.222 0.00 0.00 46.91 3.71
836 1520 1.224870 GGGCCTTCTTACCTGAGCC 59.775 63.158 0.84 0.00 39.73 4.70
1424 2117 1.163420 TGTGCTACAACTGCAACCGG 61.163 55.000 0.00 0.00 42.41 5.28
1459 2156 1.599542 GGCTGAGTTGATTATGACCGC 59.400 52.381 0.00 0.00 0.00 5.68
1466 2163 5.620206 TCAAGAACAAGGCTGAGTTGATTA 58.380 37.500 9.95 0.00 0.00 1.75
1480 2177 3.188254 CGCACACCATGTATCAAGAACAA 59.812 43.478 0.00 0.00 0.00 2.83
1934 2631 1.957668 CGGATGCAGATCATGGACAA 58.042 50.000 0.00 0.00 35.05 3.18
2169 2866 1.269309 CCTATACAGAGTCACGCTGGC 60.269 57.143 13.61 0.00 35.65 4.85
2195 2892 2.307496 ATTGCCATCAACCAAGGTCA 57.693 45.000 0.00 0.00 34.60 4.02
2254 2953 6.379133 ACCTCAACATAACATTCAGCAATGAT 59.621 34.615 3.92 0.00 41.97 2.45
2321 3021 3.290710 CCCATCTCAACCATCCGAAAAT 58.709 45.455 0.00 0.00 0.00 1.82
2403 3103 8.857694 ATAAAGGTTTCGTCCTCAGATAAAAA 57.142 30.769 0.00 0.00 36.74 1.94
2423 3123 9.599322 GTGCGAGACCATCATAAATAAATAAAG 57.401 33.333 0.00 0.00 0.00 1.85
2457 3157 5.487433 TGTGTTACCTGACGAATTCATGAT 58.513 37.500 6.22 0.00 32.17 2.45
2485 3185 2.616376 TCAACAATCAGTGTGAAACCCG 59.384 45.455 0.00 0.00 40.60 5.28
2553 3253 4.888326 AAGCAAGGGAAAAATGCATACA 57.112 36.364 0.00 0.00 42.45 2.29
2556 3256 4.628963 AGAAAGCAAGGGAAAAATGCAT 57.371 36.364 0.00 0.00 42.45 3.96
2560 3260 5.628797 TCCAAAGAAAGCAAGGGAAAAAT 57.371 34.783 0.00 0.00 0.00 1.82
2561 3261 5.104569 ACATCCAAAGAAAGCAAGGGAAAAA 60.105 36.000 0.00 0.00 0.00 1.94
2578 3279 4.096833 GCAGCAATTCATACTGACATCCAA 59.903 41.667 0.00 0.00 33.10 3.53
2699 3412 5.821516 TTATATACGCAAAAGGGTTGGTG 57.178 39.130 0.00 0.00 0.00 4.17
2702 3415 7.316544 ACTCTTTATATACGCAAAAGGGTTG 57.683 36.000 0.00 0.00 40.20 3.77
2733 3446 9.276590 ACTCAATCGCAAATATTGATAAGATGA 57.723 29.630 0.00 0.00 41.28 2.92
2765 3478 1.405256 CCAAGCAACCAAAACTGCACA 60.405 47.619 0.00 0.00 41.17 4.57
2834 3547 2.745821 TGCTTGCTTGCATCTCTACAAG 59.254 45.455 0.00 0.00 44.88 3.16
2848 3561 4.692155 GCCAAAATTTAGACATTGCTTGCT 59.308 37.500 0.00 0.00 0.00 3.91
2849 3562 4.692155 AGCCAAAATTTAGACATTGCTTGC 59.308 37.500 0.00 0.00 0.00 4.01
2850 3563 6.790285 AAGCCAAAATTTAGACATTGCTTG 57.210 33.333 0.00 0.00 0.00 4.01
2851 3564 6.427853 GGAAAGCCAAAATTTAGACATTGCTT 59.572 34.615 0.00 0.00 0.00 3.91
2855 3568 6.339587 TCGGAAAGCCAAAATTTAGACATT 57.660 33.333 0.00 0.00 0.00 2.71
2864 3577 5.675684 ATTAACCATCGGAAAGCCAAAAT 57.324 34.783 0.00 0.00 0.00 1.82
2874 3587 4.390264 TCACAACACAATTAACCATCGGA 58.610 39.130 0.00 0.00 0.00 4.55
2875 3588 4.757799 TCACAACACAATTAACCATCGG 57.242 40.909 0.00 0.00 0.00 4.18
2881 3594 7.584987 AGCTCACTAATCACAACACAATTAAC 58.415 34.615 0.00 0.00 0.00 2.01
2890 3603 7.806690 TGTTTCATAAGCTCACTAATCACAAC 58.193 34.615 0.00 0.00 0.00 3.32
2893 3606 9.334693 CTTTTGTTTCATAAGCTCACTAATCAC 57.665 33.333 0.00 0.00 0.00 3.06
2899 3612 7.573968 AAGACTTTTGTTTCATAAGCTCACT 57.426 32.000 0.00 0.00 0.00 3.41
2939 3654 7.215789 TCCATTGTTGTGCTAATGTTTCAATT 58.784 30.769 0.00 0.00 33.52 2.32
2967 3682 3.061322 GCTTTGATGCTGCAACAATGAA 58.939 40.909 29.56 15.51 0.00 2.57
3022 3737 0.666880 TGCATGTTGTTGCGAATGCC 60.667 50.000 5.98 0.00 45.77 4.40
3024 3739 2.125685 TGTTGCATGTTGTTGCGAATG 58.874 42.857 0.00 0.00 45.77 2.67
3025 3740 2.505628 TGTTGCATGTTGTTGCGAAT 57.494 40.000 0.00 0.00 45.77 3.34
3026 3741 2.284263 TTGTTGCATGTTGTTGCGAA 57.716 40.000 0.00 0.00 45.77 4.70
3028 3743 2.348685 CCAATTGTTGCATGTTGTTGCG 60.349 45.455 4.43 0.00 45.77 4.85
3029 3744 2.871022 TCCAATTGTTGCATGTTGTTGC 59.129 40.909 4.43 0.00 43.07 4.17
3030 3745 4.209703 GTCTCCAATTGTTGCATGTTGTTG 59.790 41.667 4.43 0.00 0.00 3.33
3031 3746 4.141981 TGTCTCCAATTGTTGCATGTTGTT 60.142 37.500 4.43 0.00 0.00 2.83
3033 3748 3.979948 TGTCTCCAATTGTTGCATGTTG 58.020 40.909 4.43 0.00 0.00 3.33
3034 3749 4.341806 TCTTGTCTCCAATTGTTGCATGTT 59.658 37.500 4.43 0.00 0.00 2.71
3036 3751 4.508461 TCTTGTCTCCAATTGTTGCATG 57.492 40.909 4.43 0.00 0.00 4.06
3039 3754 4.936891 AGTTTCTTGTCTCCAATTGTTGC 58.063 39.130 4.43 0.00 0.00 4.17
3040 3755 6.254157 CACAAGTTTCTTGTCTCCAATTGTTG 59.746 38.462 11.47 0.31 30.34 3.33
3041 3756 6.152661 TCACAAGTTTCTTGTCTCCAATTGTT 59.847 34.615 11.47 0.00 30.34 2.83
3042 3757 5.652014 TCACAAGTTTCTTGTCTCCAATTGT 59.348 36.000 11.47 0.00 32.01 2.71
3043 3758 6.135290 TCACAAGTTTCTTGTCTCCAATTG 57.865 37.500 11.47 0.00 0.00 2.32
3045 3760 6.736794 GCAATCACAAGTTTCTTGTCTCCAAT 60.737 38.462 11.47 0.69 0.00 3.16
3046 3761 5.450412 GCAATCACAAGTTTCTTGTCTCCAA 60.450 40.000 11.47 0.00 0.00 3.53
3047 3762 4.036734 GCAATCACAAGTTTCTTGTCTCCA 59.963 41.667 11.47 0.00 0.00 3.86
3048 3763 4.276926 AGCAATCACAAGTTTCTTGTCTCC 59.723 41.667 11.47 1.42 0.00 3.71
3051 3768 6.138761 CAGTAGCAATCACAAGTTTCTTGTC 58.861 40.000 11.47 2.18 0.00 3.18
3060 3777 4.148128 AGGATCCAGTAGCAATCACAAG 57.852 45.455 15.82 0.00 0.00 3.16
3162 3893 7.160633 AGAAAATTAAAACATGTGCGTTGTC 57.839 32.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.