Multiple sequence alignment - TraesCS3D01G264000

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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 TraesCS3D01G264000 chr3D 100.000 3954 0 0 1 3954 365908094 365904141 0.000000e+00 7302.0
1 TraesCS3D01G264000 chr3D 82.245 383 59 9 3494 3869 113670560 113670940 4.930000e-84 322.0
2 TraesCS3D01G264000 chr3A 93.344 3095 141 33 75 3124 487856174 487853100 0.000000e+00 4514.0
3 TraesCS3D01G264000 chr3A 91.498 494 35 5 3465 3954 487850419 487849929 0.000000e+00 673.0
4 TraesCS3D01G264000 chr3A 95.238 63 2 1 1 62 487856294 487856232 9.040000e-17 99.0
5 TraesCS3D01G264000 chr3A 91.667 48 4 0 3505 3552 573676422 573676469 2.550000e-07 67.6
6 TraesCS3D01G264000 chr3B 92.635 1901 86 26 682 2558 476946613 476944743 0.000000e+00 2686.0
7 TraesCS3D01G264000 chr3B 95.098 714 21 11 2600 3308 476944741 476944037 0.000000e+00 1112.0
8 TraesCS3D01G264000 chr3B 88.752 649 48 14 3326 3954 476943993 476943350 0.000000e+00 771.0
9 TraesCS3D01G264000 chr3B 86.901 313 27 8 383 690 476947099 476946796 4.890000e-89 339.0
10 TraesCS3D01G264000 chr1A 84.597 857 122 9 1122 1970 550972057 550971203 0.000000e+00 843.0
11 TraesCS3D01G264000 chr1B 83.897 857 128 9 1122 1970 629942592 629941738 0.000000e+00 809.0
12 TraesCS3D01G264000 chr1D 84.459 785 112 8 1194 1970 458486190 458485408 0.000000e+00 765.0
13 TraesCS3D01G264000 chr4B 81.319 364 59 6 3513 3869 58236711 58237072 1.800000e-73 287.0
14 TraesCS3D01G264000 chr5A 76.887 212 43 6 3535 3742 573596962 573597171 8.980000e-22 115.0
15 TraesCS3D01G264000 chr2D 81.148 122 20 3 3569 3688 73016256 73016376 1.170000e-15 95.3
16 TraesCS3D01G264000 chr4D 93.220 59 4 0 3505 3563 291724548 291724490 1.960000e-13 87.9
17 TraesCS3D01G264000 chr6A 91.228 57 5 0 3496 3552 399877143 399877199 1.180000e-10 78.7
18 TraesCS3D01G264000 chr6D 84.722 72 11 0 3496 3567 276134288 276134217 5.480000e-09 73.1


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 TraesCS3D01G264000 chr3D 365904141 365908094 3953 True 7302 7302 100.0000 1 3954 1 chr3D.!!$R1 3953
1 TraesCS3D01G264000 chr3A 487849929 487856294 6365 True 1762 4514 93.3600 1 3954 3 chr3A.!!$R1 3953
2 TraesCS3D01G264000 chr3B 476943350 476947099 3749 True 1227 2686 90.8465 383 3954 4 chr3B.!!$R1 3571
3 TraesCS3D01G264000 chr1A 550971203 550972057 854 True 843 843 84.5970 1122 1970 1 chr1A.!!$R1 848
4 TraesCS3D01G264000 chr1B 629941738 629942592 854 True 809 809 83.8970 1122 1970 1 chr1B.!!$R1 848
5 TraesCS3D01G264000 chr1D 458485408 458486190 782 True 765 765 84.4590 1194 1970 1 chr1D.!!$R1 776


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
709 968 0.033781 TCACCCAAGCAAAAGCATGC 59.966 50.0 10.51 10.51 46.78 4.06 F
1703 1983 0.737219 GCACTCTTGATGGTCATGGC 59.263 55.0 0.00 0.00 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2598 2895 1.140816 GAAGCCACTCAACAGACGAC 58.859 55.0 0.00 0.00 0.0 4.34 R
3475 3825 0.031857 TGTTTTCATTGCGCAGGTGG 59.968 50.0 20.29 8.72 0.0 4.61 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
42 44 0.729140 GCAGAACGCCGGTTGATTTG 60.729 55.000 1.90 0.00 36.24 2.32
53 55 2.481795 CGGTTGATTTGATTCATGGGGC 60.482 50.000 0.00 0.00 0.00 5.80
62 64 3.624777 TGATTCATGGGGCTCTTTCTTC 58.375 45.455 0.00 0.00 0.00 2.87
64 66 2.496899 TCATGGGGCTCTTTCTTCAC 57.503 50.000 0.00 0.00 0.00 3.18
65 67 1.988107 TCATGGGGCTCTTTCTTCACT 59.012 47.619 0.00 0.00 0.00 3.41
66 68 2.089980 CATGGGGCTCTTTCTTCACTG 58.910 52.381 0.00 0.00 0.00 3.66
67 69 0.250901 TGGGGCTCTTTCTTCACTGC 60.251 55.000 0.00 0.00 0.00 4.40
68 70 0.037447 GGGGCTCTTTCTTCACTGCT 59.963 55.000 0.00 0.00 0.00 4.24
69 71 1.546548 GGGGCTCTTTCTTCACTGCTT 60.547 52.381 0.00 0.00 0.00 3.91
70 72 2.234143 GGGCTCTTTCTTCACTGCTTT 58.766 47.619 0.00 0.00 0.00 3.51
98 145 4.718940 AAACAATTGGGATGTCCGATTC 57.281 40.909 10.83 0.00 44.45 2.52
100 147 1.603802 CAATTGGGATGTCCGATTCGG 59.396 52.381 19.16 19.16 44.45 4.30
129 176 4.707030 TGATTTTGCTTGCACCATAGAG 57.293 40.909 0.00 0.00 0.00 2.43
189 238 2.414594 GCAATCCCAGCGAATGCC 59.585 61.111 0.00 0.00 40.91 4.40
190 239 3.122850 CAATCCCAGCGAATGCCC 58.877 61.111 0.00 0.00 44.31 5.36
191 240 1.454479 CAATCCCAGCGAATGCCCT 60.454 57.895 0.00 0.00 44.31 5.19
192 241 1.039233 CAATCCCAGCGAATGCCCTT 61.039 55.000 0.00 0.00 44.31 3.95
193 242 0.550914 AATCCCAGCGAATGCCCTTA 59.449 50.000 0.00 0.00 44.31 2.69
197 246 0.109342 CCAGCGAATGCCCTTAGGAT 59.891 55.000 0.00 0.00 44.31 3.24
231 280 5.121611 CCAATTGAACGCATGACAGTTACTA 59.878 40.000 7.12 0.00 0.00 1.82
238 287 2.545526 GCATGACAGTTACTATGCGCAT 59.454 45.455 28.23 28.23 36.89 4.73
244 293 2.216488 CAGTTACTATGCGCATCGTGAC 59.784 50.000 30.48 30.48 0.00 3.67
278 336 6.266558 TGCCAGTTTTCTACATGGTAATTGTT 59.733 34.615 0.00 0.00 35.17 2.83
282 340 7.538678 CAGTTTTCTACATGGTAATTGTTGCTC 59.461 37.037 0.00 0.00 0.00 4.26
305 363 7.914427 TCTAGAGCATAACAAATCCCTTAGA 57.086 36.000 0.00 0.00 0.00 2.10
314 372 6.780457 AACAAATCCCTTAGAACATCATGG 57.220 37.500 0.00 0.00 0.00 3.66
332 390 9.499479 ACATCATGGCAATTTTATTTGTTTACA 57.501 25.926 0.00 0.00 0.00 2.41
340 398 7.745594 GCAATTTTATTTGTTTACACATGGCAG 59.254 33.333 0.00 0.00 31.06 4.85
344 402 4.314740 TTTGTTTACACATGGCAGTTCC 57.685 40.909 0.00 0.00 31.06 3.62
360 420 1.852157 TTCCAGGCTCGCTGGGAAAT 61.852 55.000 7.54 0.00 42.03 2.17
483 545 9.001542 TGCAATGAATTTCTTAGGAAAAATTGG 57.998 29.630 21.72 12.14 43.51 3.16
646 714 6.716173 TGTCATGACATGATCCTTTTCTTGAA 59.284 34.615 24.56 0.00 42.04 2.69
702 961 4.407296 ACCTAAATGTTTCACCCAAGCAAA 59.593 37.500 0.00 0.00 0.00 3.68
708 967 2.529780 TTCACCCAAGCAAAAGCATG 57.470 45.000 0.00 0.00 0.00 4.06
709 968 0.033781 TCACCCAAGCAAAAGCATGC 59.966 50.000 10.51 10.51 46.78 4.06
734 993 4.039042 GCATTTCCTGCCCCATGT 57.961 55.556 0.00 0.00 45.66 3.21
735 994 1.518774 GCATTTCCTGCCCCATGTG 59.481 57.895 0.00 0.00 45.66 3.21
800 1059 2.983791 CCCATGGGGCAGCAAAAG 59.016 61.111 24.53 0.00 35.35 2.27
812 1081 2.684881 GCAGCAAAAGAAGCTATAGGCA 59.315 45.455 1.04 0.00 41.14 4.75
813 1082 3.243002 GCAGCAAAAGAAGCTATAGGCAG 60.243 47.826 1.04 0.00 41.14 4.85
814 1083 3.314635 CAGCAAAAGAAGCTATAGGCAGG 59.685 47.826 1.04 0.00 41.14 4.85
941 1212 2.488153 GCACAAAGTCCACTAATCCACC 59.512 50.000 0.00 0.00 0.00 4.61
1646 1926 3.474570 GGCTCATGGGACCGCTCT 61.475 66.667 0.00 0.00 0.00 4.09
1703 1983 0.737219 GCACTCTTGATGGTCATGGC 59.263 55.000 0.00 0.00 0.00 4.40
2000 2283 8.102484 ACCTATTACCACCATCACTTATTTCT 57.898 34.615 0.00 0.00 0.00 2.52
2161 2446 9.221933 ACGTGTTAGTTTTATGTTGGAATGATA 57.778 29.630 0.00 0.00 0.00 2.15
2192 2479 6.493458 AGCATAGGTTTTGAACATTACCAGTT 59.507 34.615 0.00 0.00 33.02 3.16
2194 2481 8.466798 GCATAGGTTTTGAACATTACCAGTTAT 58.533 33.333 0.00 0.00 33.02 1.89
2217 2504 4.302455 TGGTTTTGGTTCAACGCATTATG 58.698 39.130 0.00 0.00 0.00 1.90
2297 2584 6.146021 GGTTGACTTAAGTTGCCAAATTGATG 59.854 38.462 10.02 0.00 0.00 3.07
2339 2626 8.359642 AGCAGAAAAATAAATAGCAAGTTCACA 58.640 29.630 0.00 0.00 0.00 3.58
2352 2639 5.185056 AGCAAGTTCACAACCAGTACTTTTT 59.815 36.000 0.00 0.00 28.83 1.94
2458 2746 1.303155 GCCTCCTGCCCATCTATGC 60.303 63.158 0.00 0.00 0.00 3.14
2469 2757 2.487805 CCCATCTATGCTAAGGCTGCAA 60.488 50.000 3.45 0.00 44.01 4.08
2499 2789 4.523173 TGTCAAGCGAGGTATATAGGAAGG 59.477 45.833 0.00 0.00 0.00 3.46
2501 2791 5.243283 GTCAAGCGAGGTATATAGGAAGGAA 59.757 44.000 0.00 0.00 0.00 3.36
2502 2792 5.477291 TCAAGCGAGGTATATAGGAAGGAAG 59.523 44.000 0.00 0.00 0.00 3.46
2503 2793 3.764972 AGCGAGGTATATAGGAAGGAAGC 59.235 47.826 0.00 0.00 0.00 3.86
2504 2794 3.510360 GCGAGGTATATAGGAAGGAAGCA 59.490 47.826 0.00 0.00 0.00 3.91
2507 2797 5.336055 CGAGGTATATAGGAAGGAAGCACAG 60.336 48.000 0.00 0.00 0.00 3.66
2629 2926 6.719370 TGTTGAGTGGCTTCTTAATATGGTTT 59.281 34.615 0.00 0.00 0.00 3.27
2737 3034 5.073428 ACTATCCGCATCTACAAGATCTCA 58.927 41.667 0.00 0.00 31.32 3.27
2960 3258 9.730705 AATATATTGTCTCGTGAATCATGGAAT 57.269 29.630 2.27 0.26 0.00 3.01
3141 3444 6.295180 GCTAGGTTCTAGTACCACTCAAAAGT 60.295 42.308 19.53 0.00 40.82 2.66
3160 3463 2.044135 GTTTTTGCTTAGCTGTGCGTC 58.956 47.619 5.60 0.00 0.00 5.19
3174 3477 1.226128 GCGTCAAAAGGAGCGCATC 60.226 57.895 11.47 4.01 42.02 3.91
3308 3616 1.261619 GTCTAAGAATTCATGCCGGCG 59.738 52.381 23.90 8.74 0.00 6.46
3356 3690 1.068753 CAGTCCTAGCTCATGCCGG 59.931 63.158 0.00 0.00 40.80 6.13
3368 3702 2.164219 CTCATGCCGGCTTACAAAATGT 59.836 45.455 29.70 0.00 0.00 2.71
3370 3704 2.430546 TGCCGGCTTACAAAATGTTG 57.569 45.000 29.70 0.00 40.84 3.33
3409 3743 4.024218 GCTCAATCATTTAGCTCGAGCATT 60.024 41.667 36.87 23.43 42.99 3.56
3410 3744 5.413969 TCAATCATTTAGCTCGAGCATTG 57.586 39.130 36.87 31.25 45.16 2.82
3413 3747 1.945394 CATTTAGCTCGAGCATTGCCT 59.055 47.619 36.87 19.08 45.16 4.75
3414 3748 2.113860 TTTAGCTCGAGCATTGCCTT 57.886 45.000 36.87 18.34 45.16 4.35
3439 3773 3.881220 TGTTTCTTCTCGAACCAAACCT 58.119 40.909 0.00 0.00 0.00 3.50
3446 3780 3.991367 TCTCGAACCAAACCTTTCTCTC 58.009 45.455 0.00 0.00 0.00 3.20
3447 3781 3.386726 TCTCGAACCAAACCTTTCTCTCA 59.613 43.478 0.00 0.00 0.00 3.27
3448 3782 3.463944 TCGAACCAAACCTTTCTCTCAC 58.536 45.455 0.00 0.00 0.00 3.51
3449 3783 2.548480 CGAACCAAACCTTTCTCTCACC 59.452 50.000 0.00 0.00 0.00 4.02
3471 3821 1.746615 CTCAACTCCACCGCCATGG 60.747 63.158 7.63 7.63 46.41 3.66
3481 6259 2.124983 CGCCATGGTCTCCACCTG 60.125 66.667 14.67 0.00 44.17 4.00
3569 6347 0.974383 TCCTCCTTTTGACGGTCTCC 59.026 55.000 9.88 0.00 0.00 3.71
3571 6349 1.066787 CCTCCTTTTGACGGTCTCCTC 60.067 57.143 9.88 0.00 0.00 3.71
3578 6356 0.331616 TGACGGTCTCCTCCATCTCA 59.668 55.000 9.88 0.00 0.00 3.27
3588 6366 3.176411 TCCTCCATCTCAAGCTTCTTCA 58.824 45.455 0.00 0.00 0.00 3.02
3596 6374 6.294899 CCATCTCAAGCTTCTTCATTTGGAAA 60.295 38.462 0.00 0.00 34.44 3.13
3598 6376 7.294017 TCTCAAGCTTCTTCATTTGGAAATT 57.706 32.000 0.00 0.00 34.44 1.82
3623 6401 4.579869 TGTAGACCTTCATTTGCTTCTCC 58.420 43.478 0.00 0.00 0.00 3.71
3649 6429 1.524008 TTGCGCTTCCTCTCGTCTCA 61.524 55.000 9.73 0.00 0.00 3.27
3697 6478 2.472816 CAAGTTTGTTGCAAGGCGAAT 58.527 42.857 0.00 0.00 0.00 3.34
3774 6556 1.929836 CTCCTTCATGCTCAACTACGC 59.070 52.381 0.00 0.00 0.00 4.42
3802 6584 2.823152 GCCCTCCATTCTTCTTTTGGGT 60.823 50.000 0.00 0.00 36.00 4.51
3814 6596 2.496871 TCTTTTGGGTGGCATATTGCTG 59.503 45.455 0.00 0.00 44.28 4.41
3919 6701 1.746171 CGAGACATGGGAGTCGGAGTA 60.746 57.143 0.00 0.00 43.24 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 44 3.379688 GTGAAGAAAGAGCCCCATGAATC 59.620 47.826 0.00 0.00 0.00 2.52
69 71 6.037610 CGGACATCCCAATTGTTTTTGAAAAA 59.962 34.615 4.43 0.00 34.14 1.94
70 72 5.525378 CGGACATCCCAATTGTTTTTGAAAA 59.475 36.000 4.43 0.00 34.14 2.29
73 120 3.891977 TCGGACATCCCAATTGTTTTTGA 59.108 39.130 4.43 0.00 34.14 2.69
98 145 3.688272 CAAGCAAAATCATGTAGAGCCG 58.312 45.455 0.00 0.00 0.00 5.52
100 147 3.855950 GTGCAAGCAAAATCATGTAGAGC 59.144 43.478 0.00 0.00 0.00 4.09
150 198 3.058501 CCTAAAAATGACGTTCGCTGGTT 60.059 43.478 0.00 0.00 0.00 3.67
152 200 2.727916 GCCTAAAAATGACGTTCGCTGG 60.728 50.000 0.00 0.00 0.00 4.85
189 238 4.778213 TTGGGATCTGACAATCCTAAGG 57.222 45.455 13.15 0.00 44.06 2.69
190 239 6.359804 TCAATTGGGATCTGACAATCCTAAG 58.640 40.000 5.42 7.79 45.84 2.18
191 240 6.325993 TCAATTGGGATCTGACAATCCTAA 57.674 37.500 5.42 13.68 46.43 2.69
192 241 5.974156 TCAATTGGGATCTGACAATCCTA 57.026 39.130 5.42 7.31 44.06 2.94
193 242 4.868172 TCAATTGGGATCTGACAATCCT 57.132 40.909 5.42 0.00 44.06 3.24
197 246 2.487762 GCGTTCAATTGGGATCTGACAA 59.512 45.455 5.42 0.00 0.00 3.18
231 280 0.726827 AAAATCGTCACGATGCGCAT 59.273 45.000 25.66 25.66 46.30 4.73
238 287 1.798223 CTGGCAGAAAAATCGTCACGA 59.202 47.619 9.42 0.28 41.13 4.35
244 293 5.757886 TGTAGAAAACTGGCAGAAAAATCG 58.242 37.500 23.66 0.00 0.00 3.34
247 296 5.362430 ACCATGTAGAAAACTGGCAGAAAAA 59.638 36.000 23.66 0.00 32.60 1.94
282 340 7.987458 TGTTCTAAGGGATTTGTTATGCTCTAG 59.013 37.037 0.00 0.00 0.00 2.43
314 372 7.579726 TGCCATGTGTAAACAAATAAAATTGC 58.420 30.769 0.00 0.00 33.52 3.56
344 402 0.393537 AAGATTTCCCAGCGAGCCTG 60.394 55.000 0.00 0.00 41.41 4.85
506 568 9.927668 AGTTTTCCTATGTTGGTTATTTGATTG 57.072 29.630 0.00 0.00 0.00 2.67
646 714 8.127327 CACAAGAAAATTCGAGCATAAGATGAT 58.873 33.333 0.00 0.00 0.00 2.45
734 993 2.892852 CAAGAAATGCTTTGGTCCTCCA 59.107 45.455 0.00 0.00 42.66 3.86
735 994 3.582714 CAAGAAATGCTTTGGTCCTCC 57.417 47.619 0.00 0.00 33.60 4.30
765 1024 0.106149 GGCCTAATCACCGGTACAGG 59.894 60.000 6.87 12.56 37.30 4.00
767 1026 0.618107 TGGGCCTAATCACCGGTACA 60.618 55.000 6.87 0.00 0.00 2.90
771 1030 1.228245 CCATGGGCCTAATCACCGG 60.228 63.158 2.85 0.00 0.00 5.28
774 1033 4.929807 CCCCATGGGCCTAATCAC 57.070 61.111 26.87 0.00 35.35 3.06
795 1054 2.620585 GGCCTGCCTATAGCTTCTTTTG 59.379 50.000 0.00 0.00 44.23 2.44
796 1055 2.242196 TGGCCTGCCTATAGCTTCTTTT 59.758 45.455 9.97 0.00 44.23 2.27
799 1058 1.350351 CATGGCCTGCCTATAGCTTCT 59.650 52.381 9.97 0.00 44.23 2.85
800 1059 1.818642 CATGGCCTGCCTATAGCTTC 58.181 55.000 9.97 0.00 44.23 3.86
812 1081 2.749044 CTCACTTGCGCATGGCCT 60.749 61.111 24.99 3.77 42.61 5.19
813 1082 2.747460 TCTCACTTGCGCATGGCC 60.747 61.111 24.99 0.00 42.61 5.36
814 1083 2.482374 GTCTCACTTGCGCATGGC 59.518 61.111 24.99 6.05 43.96 4.40
941 1212 1.068474 CGTGAGACGCTAGGGTTTTG 58.932 55.000 14.33 0.00 33.65 2.44
1975 2255 7.993183 CAGAAATAAGTGATGGTGGTAATAGGT 59.007 37.037 0.00 0.00 0.00 3.08
1982 2262 4.985538 ACACAGAAATAAGTGATGGTGGT 58.014 39.130 0.00 0.00 39.03 4.16
1987 2267 9.903682 ATCAAAGAAACACAGAAATAAGTGATG 57.096 29.630 0.00 0.00 39.03 3.07
2000 2283 9.743057 CCAATAGTAAACAATCAAAGAAACACA 57.257 29.630 0.00 0.00 0.00 3.72
2036 2321 4.917415 GCTGGTCATACAAACAACACATTC 59.083 41.667 0.00 0.00 0.00 2.67
2192 2479 4.592485 ATGCGTTGAACCAAAACCAATA 57.408 36.364 0.00 0.00 0.00 1.90
2194 2481 2.969628 ATGCGTTGAACCAAAACCAA 57.030 40.000 0.00 0.00 0.00 3.67
2195 2482 2.969628 AATGCGTTGAACCAAAACCA 57.030 40.000 0.00 0.00 0.00 3.67
2317 2604 9.255304 TGGTTGTGAACTTGCTATTTATTTTTC 57.745 29.630 0.00 0.00 0.00 2.29
2366 2653 6.127925 CCAACAGAACAAGCACATACATGTAT 60.128 38.462 12.75 12.75 39.39 2.29
2373 2660 6.892658 AATAACCAACAGAACAAGCACATA 57.107 33.333 0.00 0.00 0.00 2.29
2458 2746 5.565592 TGACAATACAATTGCAGCCTTAG 57.434 39.130 5.05 0.00 0.00 2.18
2469 2757 8.035394 CCTATATACCTCGCTTGACAATACAAT 58.965 37.037 0.00 0.00 0.00 2.71
2499 2789 4.503741 TTAGAACAAATGCCTGTGCTTC 57.496 40.909 0.00 0.00 36.53 3.86
2501 2791 4.445452 CATTAGAACAAATGCCTGTGCT 57.555 40.909 0.00 0.00 38.78 4.40
2598 2895 1.140816 GAAGCCACTCAACAGACGAC 58.859 55.000 0.00 0.00 0.00 4.34
2629 2926 3.808728 GAGCATCTGGGCAAACAGTATA 58.191 45.455 2.82 0.00 39.48 1.47
3141 3444 1.673400 TGACGCACAGCTAAGCAAAAA 59.327 42.857 9.84 0.00 0.00 1.94
3160 3463 0.305922 GATCGGATGCGCTCCTTTTG 59.694 55.000 19.30 7.80 42.47 2.44
3285 3593 1.261619 CGGCATGAATTCTTAGACGCC 59.738 52.381 7.05 8.40 34.91 5.68
3291 3599 0.746204 TGCGCCGGCATGAATTCTTA 60.746 50.000 28.98 0.00 46.21 2.10
3323 3631 3.027412 AGGACTGCGAGACATGAACTAT 58.973 45.455 0.00 0.00 0.00 2.12
3324 3632 2.447443 AGGACTGCGAGACATGAACTA 58.553 47.619 0.00 0.00 0.00 2.24
3356 3690 5.050837 CCAAGAGCAACAACATTTTGTAAGC 60.051 40.000 11.90 11.90 45.69 3.09
3368 3702 1.234615 GCTACGGCCAAGAGCAACAA 61.235 55.000 14.10 0.00 46.50 2.83
3370 3704 1.362406 GAGCTACGGCCAAGAGCAAC 61.362 60.000 19.53 11.01 46.50 4.17
3439 3773 3.495100 GGAGTTGAGCAAGGTGAGAGAAA 60.495 47.826 0.00 0.00 0.00 2.52
3446 3780 1.230635 CGGTGGAGTTGAGCAAGGTG 61.231 60.000 0.00 0.00 0.00 4.00
3447 3781 1.071471 CGGTGGAGTTGAGCAAGGT 59.929 57.895 0.00 0.00 0.00 3.50
3448 3782 2.328099 GCGGTGGAGTTGAGCAAGG 61.328 63.158 0.00 0.00 0.00 3.61
3449 3783 2.328099 GGCGGTGGAGTTGAGCAAG 61.328 63.158 0.00 0.00 0.00 4.01
3471 3821 0.955428 TTCATTGCGCAGGTGGAGAC 60.955 55.000 20.29 0.00 0.00 3.36
3473 3823 0.597568 TTTTCATTGCGCAGGTGGAG 59.402 50.000 20.29 5.92 0.00 3.86
3474 3824 0.313672 GTTTTCATTGCGCAGGTGGA 59.686 50.000 20.29 12.24 0.00 4.02
3475 3825 0.031857 TGTTTTCATTGCGCAGGTGG 59.968 50.000 20.29 8.72 0.00 4.61
3533 6311 1.178276 GGAAGCTCGAGACTGAGGAA 58.822 55.000 18.75 0.00 36.47 3.36
3569 6347 5.163642 CCAAATGAAGAAGCTTGAGATGGAG 60.164 44.000 2.10 0.00 0.00 3.86
3571 6349 4.703575 TCCAAATGAAGAAGCTTGAGATGG 59.296 41.667 2.10 3.32 0.00 3.51
3578 6356 7.447594 ACATCAATTTCCAAATGAAGAAGCTT 58.552 30.769 0.00 0.00 33.63 3.74
3588 6366 8.599624 ATGAAGGTCTACATCAATTTCCAAAT 57.400 30.769 0.00 0.00 0.00 2.32
3596 6374 6.888632 AGAAGCAAATGAAGGTCTACATCAAT 59.111 34.615 0.00 0.00 0.00 2.57
3598 6376 5.809001 AGAAGCAAATGAAGGTCTACATCA 58.191 37.500 0.00 0.00 0.00 3.07
3649 6429 4.622220 GCATGATGACCCAAAAGAAAGCAT 60.622 41.667 0.00 0.00 0.00 3.79
3802 6584 5.477510 CCAAGTTTAAACAGCAATATGCCA 58.522 37.500 20.06 0.00 46.52 4.92
3814 6596 5.606505 TCAAAGATTGCCCCAAGTTTAAAC 58.393 37.500 10.47 10.47 0.00 2.01
3888 6670 0.378962 CATGTCTCGACGTCCTCCTC 59.621 60.000 10.58 0.00 0.00 3.71
3919 6701 4.755266 AGGACATCGGCTACATAAAACT 57.245 40.909 0.00 0.00 0.00 2.66



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

AutoCloner maintained by Alex Coulton.