Multiple sequence alignment - TraesCS5B01G079200

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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 TraesCS5B01G079200 chr5B 100.000 4412 0 0 1 4412 96560069 96555658 0.000000e+00 8148.0
1 TraesCS5B01G079200 chr5B 93.293 984 64 2 1030 2011 493402037 493403020 0.000000e+00 1450.0
2 TraesCS5B01G079200 chr5B 90.426 752 45 10 285 1035 100709969 100710694 0.000000e+00 965.0
3 TraesCS5B01G079200 chr5B 96.082 485 15 1 2833 3317 100711648 100712128 0.000000e+00 787.0
4 TraesCS5B01G079200 chr5B 94.027 519 20 2 2328 2835 100711103 100711621 0.000000e+00 776.0
5 TraesCS5B01G079200 chr5B 92.079 303 15 5 2007 2302 100710690 100710990 6.830000e-113 418.0
6 TraesCS5B01G079200 chr5B 94.361 266 14 1 1 265 100709533 100709798 1.480000e-109 407.0
7 TraesCS5B01G079200 chr5B 79.812 213 32 10 1806 2012 340599251 340599458 1.280000e-30 145.0
8 TraesCS5B01G079200 chr7D 93.797 1064 54 8 3358 4412 175770406 175769346 0.000000e+00 1589.0
9 TraesCS5B01G079200 chr7D 91.414 396 32 2 1601 1996 574801931 574801538 3.880000e-150 542.0
10 TraesCS5B01G079200 chr7D 83.471 605 56 20 1034 1603 574802585 574801990 1.410000e-144 523.0
11 TraesCS5B01G079200 chr7D 81.481 189 25 9 1821 2004 91711898 91711715 3.560000e-31 147.0
12 TraesCS5B01G079200 chr5D 94.313 932 46 5 3485 4412 416793678 416792750 0.000000e+00 1421.0
13 TraesCS5B01G079200 chr5D 89.623 848 62 11 2007 2836 91356895 91356056 0.000000e+00 1055.0
14 TraesCS5B01G079200 chr5D 82.790 767 83 25 303 1035 91357642 91356891 1.340000e-179 640.0
15 TraesCS5B01G079200 chr5D 92.481 266 16 1 3047 3312 91355844 91355583 1.160000e-100 377.0
16 TraesCS5B01G079200 chr5D 92.973 185 13 0 2829 3013 91356035 91355851 2.020000e-68 270.0
17 TraesCS5B01G079200 chr5D 94.059 101 4 2 3358 3456 416793772 416793672 7.640000e-33 152.0
18 TraesCS5B01G079200 chr5D 76.895 277 46 16 3359 3627 107792573 107792839 1.650000e-29 141.0
19 TraesCS5B01G079200 chr7B 83.224 608 58 18 1031 1603 634769062 634768464 6.540000e-143 518.0
20 TraesCS5B01G079200 chr7B 89.313 393 35 7 1619 2007 634768405 634768016 1.840000e-133 486.0
21 TraesCS5B01G079200 chr7B 82.143 168 26 4 1029 1194 475645353 475645188 1.650000e-29 141.0
22 TraesCS5B01G079200 chr7A 82.890 602 59 23 1037 1603 664433361 664432769 6.590000e-138 501.0
23 TraesCS5B01G079200 chr7A 86.747 249 32 1 1764 2011 664432529 664432281 4.350000e-70 276.0
24 TraesCS5B01G079200 chr7A 89.412 170 16 2 1602 1771 664432719 664432552 3.460000e-51 213.0
25 TraesCS5B01G079200 chrUn 82.479 234 34 7 3359 3587 77474062 77473831 9.680000e-47 198.0
26 TraesCS5B01G079200 chr4B 82.418 182 22 9 1831 2007 439193022 439193198 2.750000e-32 150.0
27 TraesCS5B01G079200 chr2D 80.214 187 32 5 1827 2011 348614712 348614529 7.700000e-28 135.0
28 TraesCS5B01G079200 chr2D 80.000 170 26 7 1031 1196 380407848 380408013 7.750000e-23 119.0
29 TraesCS5B01G079200 chr2D 100.000 28 0 0 669 696 608483210 608483237 8.000000e-03 52.8
30 TraesCS5B01G079200 chr1D 78.008 241 35 13 1786 2014 460460704 460460470 7.700000e-28 135.0
31 TraesCS5B01G079200 chr1D 81.481 162 23 7 1036 1195 461001391 461001235 4.630000e-25 126.0
32 TraesCS5B01G079200 chr6B 81.212 165 25 6 1034 1195 80856521 80856360 1.290000e-25 128.0
33 TraesCS5B01G079200 chr6B 100.000 28 0 0 668 695 239293060 239293033 8.000000e-03 52.8
34 TraesCS5B01G079200 chr6D 80.588 170 27 6 1029 1195 101503430 101503596 4.630000e-25 126.0


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 TraesCS5B01G079200 chr5B 96555658 96560069 4411 True 8148.0 8148 100.000000 1 4412 1 chr5B.!!$R1 4411
1 TraesCS5B01G079200 chr5B 493402037 493403020 983 False 1450.0 1450 93.293000 1030 2011 1 chr5B.!!$F2 981
2 TraesCS5B01G079200 chr5B 100709533 100712128 2595 False 670.6 965 93.395000 1 3317 5 chr5B.!!$F3 3316
3 TraesCS5B01G079200 chr7D 175769346 175770406 1060 True 1589.0 1589 93.797000 3358 4412 1 chr7D.!!$R2 1054
4 TraesCS5B01G079200 chr7D 574801538 574802585 1047 True 532.5 542 87.442500 1034 1996 2 chr7D.!!$R3 962
5 TraesCS5B01G079200 chr5D 416792750 416793772 1022 True 786.5 1421 94.186000 3358 4412 2 chr5D.!!$R2 1054
6 TraesCS5B01G079200 chr5D 91355583 91357642 2059 True 585.5 1055 89.466750 303 3312 4 chr5D.!!$R1 3009
7 TraesCS5B01G079200 chr7B 634768016 634769062 1046 True 502.0 518 86.268500 1031 2007 2 chr7B.!!$R2 976
8 TraesCS5B01G079200 chr7A 664432281 664433361 1080 True 330.0 501 86.349667 1037 2011 3 chr7A.!!$R1 974

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
267 269 0.033796 AGGTGGCATGGGTCTTGATG 60.034 55.0 0.00 0.0 0.0 3.07 F
937 1137 0.179029 CTCCTCCTCGTCTCCTCCTC 60.179 65.0 0.00 0.0 0.0 3.71 F
2027 2359 1.049289 AAGTATCTCCCAGTCCGCCC 61.049 60.0 0.00 0.0 0.0 6.13 F
2417 2854 0.382158 TCGTCTAGATGCTGGCTTCG 59.618 55.0 7.11 0.0 0.0 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1784 2115 0.261696 GCCTCTCCCTCTCTCCTTCT 59.738 60.0 0.00 0.00 0.0 2.85 R
2417 2854 0.530870 GCTCCGTATGCAGAAGGGAC 60.531 60.0 13.47 2.33 0.0 4.46 R
2907 3377 0.608856 TGGTGGACGATGCATTGCTT 60.609 50.0 14.18 3.11 0.0 3.91 R
4194 4672 0.740737 GGGCAAGATTTCCATCCGTG 59.259 55.0 0.00 0.00 0.0 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
35 36 0.518636 TTGAGCATTGAAGCTGCGAC 59.481 50.000 0.00 0.00 46.75 5.19
48 49 1.406887 GCTGCGACCATCCTCCTTTTA 60.407 52.381 0.00 0.00 0.00 1.52
56 57 2.420022 CCATCCTCCTTTTACTTGTGCG 59.580 50.000 0.00 0.00 0.00 5.34
84 85 1.402511 CTTTTCTGCTTGCGCTTGAC 58.597 50.000 9.73 0.00 36.97 3.18
201 203 2.668212 TTTGAGGACGCGGCCTTG 60.668 61.111 38.50 0.00 38.73 3.61
208 210 3.100862 GACGCGGCCTTGAATGAGC 62.101 63.158 12.47 0.00 0.00 4.26
213 215 1.298157 CGGCCTTGAATGAGCGACAA 61.298 55.000 0.00 0.00 0.00 3.18
214 216 0.169009 GGCCTTGAATGAGCGACAAC 59.831 55.000 0.00 0.00 0.00 3.32
225 227 0.463654 AGCGACAACAGCTTGTTCCA 60.464 50.000 0.00 0.00 43.24 3.53
265 267 0.618458 GTAGGTGGCATGGGTCTTGA 59.382 55.000 0.00 0.00 0.00 3.02
266 268 1.212935 GTAGGTGGCATGGGTCTTGAT 59.787 52.381 0.00 0.00 0.00 2.57
267 269 0.033796 AGGTGGCATGGGTCTTGATG 60.034 55.000 0.00 0.00 0.00 3.07
268 270 1.039233 GGTGGCATGGGTCTTGATGG 61.039 60.000 0.00 0.00 0.00 3.51
269 271 1.380246 TGGCATGGGTCTTGATGGC 60.380 57.895 0.00 0.00 43.61 4.40
270 272 2.484062 GGCATGGGTCTTGATGGCG 61.484 63.158 0.00 0.00 35.67 5.69
271 273 2.484062 GCATGGGTCTTGATGGCGG 61.484 63.158 0.00 0.00 0.00 6.13
272 274 1.825191 CATGGGTCTTGATGGCGGG 60.825 63.158 0.00 0.00 0.00 6.13
273 275 3.060614 ATGGGTCTTGATGGCGGGG 62.061 63.158 0.00 0.00 0.00 5.73
274 276 4.506255 GGGTCTTGATGGCGGGGG 62.506 72.222 0.00 0.00 0.00 5.40
300 453 1.301637 CATGTGGACCACGTCTGCA 60.302 57.895 16.79 0.00 37.14 4.41
372 525 3.649277 CTCGGACGAGGCAAGGTGG 62.649 68.421 13.59 0.00 38.51 4.61
545 717 7.713764 AGAAACTTAATTTGCGCAATCTTTT 57.286 28.000 25.64 16.23 0.00 2.27
625 807 9.772973 ATTACGACATGAGTATTTGGCTATTTA 57.227 29.630 0.00 0.00 0.00 1.40
681 866 9.102757 CATGCTAATCCGCTAGAATATTTATGT 57.897 33.333 0.00 0.00 0.00 2.29
682 867 9.672673 ATGCTAATCCGCTAGAATATTTATGTT 57.327 29.630 0.00 0.00 0.00 2.71
685 870 7.596749 AATCCGCTAGAATATTTATGTTCCG 57.403 36.000 0.00 0.00 0.00 4.30
701 886 1.661197 CCGTTGCAACACATGTGCC 60.661 57.895 28.01 14.32 0.00 5.01
730 915 3.258372 TGATCGGATTAGTGGTAGATGCC 59.742 47.826 0.00 0.00 0.00 4.40
744 929 3.376935 ATGCCGAGTCTTCGCCCTG 62.377 63.158 0.00 0.00 45.38 4.45
753 938 3.751518 AGTCTTCGCCCTGTTTTAATGT 58.248 40.909 0.00 0.00 0.00 2.71
928 1128 0.256464 AATCCTCGTCTCCTCCTCGT 59.744 55.000 0.00 0.00 0.00 4.18
934 1134 0.812412 CGTCTCCTCCTCGTCTCCTC 60.812 65.000 0.00 0.00 0.00 3.71
935 1135 0.464916 GTCTCCTCCTCGTCTCCTCC 60.465 65.000 0.00 0.00 0.00 4.30
936 1136 0.622154 TCTCCTCCTCGTCTCCTCCT 60.622 60.000 0.00 0.00 0.00 3.69
937 1137 0.179029 CTCCTCCTCGTCTCCTCCTC 60.179 65.000 0.00 0.00 0.00 3.71
938 1138 1.525077 CCTCCTCGTCTCCTCCTCG 60.525 68.421 0.00 0.00 0.00 4.63
939 1139 2.124653 TCCTCGTCTCCTCCTCGC 60.125 66.667 0.00 0.00 0.00 5.03
940 1140 3.213402 CCTCGTCTCCTCCTCGCC 61.213 72.222 0.00 0.00 0.00 5.54
941 1141 2.124487 CTCGTCTCCTCCTCGCCT 60.124 66.667 0.00 0.00 0.00 5.52
942 1142 2.124653 TCGTCTCCTCCTCGCCTC 60.125 66.667 0.00 0.00 0.00 4.70
943 1143 3.213402 CGTCTCCTCCTCGCCTCC 61.213 72.222 0.00 0.00 0.00 4.30
944 1144 2.277404 GTCTCCTCCTCGCCTCCT 59.723 66.667 0.00 0.00 0.00 3.69
1103 1308 1.633432 TCCACTGGAATGGGTCGATTT 59.367 47.619 0.00 0.00 40.49 2.17
1120 1326 4.452795 TCGATTTCATTCTTGCGTTTGGTA 59.547 37.500 0.00 0.00 0.00 3.25
1314 1520 5.880054 ACATAATAATTGCTATGTCCGGC 57.120 39.130 0.00 0.00 34.37 6.13
1421 1660 7.562454 TCAAAGATAAGGACGGAAGGATTAGTA 59.438 37.037 0.00 0.00 0.00 1.82
1477 1716 3.138625 ACGGAGTGTGGAGTGTGG 58.861 61.111 0.00 0.00 42.51 4.17
1514 1753 2.285368 ACTCCGATGAAGGGGCCA 60.285 61.111 4.39 0.00 34.28 5.36
1517 1756 3.727258 CCGATGAAGGGGCCACCA 61.727 66.667 0.00 0.00 43.89 4.17
1898 2230 4.487714 TCTTGGTGGAATATTCGCTCTT 57.512 40.909 9.32 0.00 0.00 2.85
1982 2314 1.354101 TGGACCCGTTACATTCCAGT 58.646 50.000 0.00 0.00 33.02 4.00
2027 2359 1.049289 AAGTATCTCCCAGTCCGCCC 61.049 60.000 0.00 0.00 0.00 6.13
2058 2390 1.449601 GCTTAAGGCCTAGTGCGCA 60.450 57.895 5.16 5.66 42.61 6.09
2133 2466 7.011295 CCCACAAGTACGTACTTTGTTTTAGAA 59.989 37.037 32.93 0.00 43.57 2.10
2135 2468 8.598075 CACAAGTACGTACTTTGTTTTAGAAGT 58.402 33.333 32.93 21.67 43.57 3.01
2228 2568 4.830046 TGCTATGCTTTCTGGTGGTTTTTA 59.170 37.500 0.00 0.00 0.00 1.52
2302 2642 5.131784 ACACCCATCAAAATGCATGTTTTT 58.868 33.333 0.00 0.00 29.78 1.94
2397 2834 1.686587 ACGTCTGTGGTGATTGTCTGA 59.313 47.619 0.00 0.00 0.00 3.27
2417 2854 0.382158 TCGTCTAGATGCTGGCTTCG 59.618 55.000 7.11 0.00 0.00 3.79
2531 2968 1.218047 CGGATGGCTTCTGTTCGGA 59.782 57.895 1.17 0.00 0.00 4.55
2725 3165 1.135199 GGAGGTCAATCTGTTACGCGA 60.135 52.381 15.93 0.00 0.00 5.87
2830 3270 0.729116 CTTGATAAGTGGCTGCACCG 59.271 55.000 0.50 0.00 43.94 4.94
2857 3327 3.706373 ACCGCTGAACTGGCCGAT 61.706 61.111 0.00 0.00 0.00 4.18
2907 3377 2.592993 GGGCTGTCCTACCTGCACA 61.593 63.158 0.00 0.00 33.36 4.57
2979 3449 0.677731 TGCCTTCAAGCCCAAGATCG 60.678 55.000 0.00 0.00 0.00 3.69
3156 3626 5.859205 TTCTGCTAGCATATGACTTCAGA 57.141 39.130 19.72 14.36 0.00 3.27
3157 3627 5.193663 TCTGCTAGCATATGACTTCAGAC 57.806 43.478 19.72 0.00 0.00 3.51
3158 3628 4.646492 TCTGCTAGCATATGACTTCAGACA 59.354 41.667 19.72 0.00 0.00 3.41
3159 3629 4.941657 TGCTAGCATATGACTTCAGACAG 58.058 43.478 14.93 0.00 0.00 3.51
3169 3639 4.765273 TGACTTCAGACAGTTGCTTAACA 58.235 39.130 0.00 0.00 0.00 2.41
3171 3641 5.822519 TGACTTCAGACAGTTGCTTAACAAT 59.177 36.000 0.00 0.00 41.27 2.71
3279 3749 3.463585 CTAGTAACCGGGCGGGCA 61.464 66.667 11.50 0.00 40.62 5.36
3313 3783 0.531532 CATCACTGACGATGGAGGCC 60.532 60.000 0.00 0.00 39.33 5.19
3317 3787 3.144120 CTGACGATGGAGGCCGAGG 62.144 68.421 0.00 0.00 0.00 4.63
3318 3788 2.833582 GACGATGGAGGCCGAGGA 60.834 66.667 0.00 0.00 0.00 3.71
3319 3789 3.140225 GACGATGGAGGCCGAGGAC 62.140 68.421 0.00 0.00 0.00 3.85
3320 3790 3.917760 CGATGGAGGCCGAGGACC 61.918 72.222 0.00 0.00 0.00 4.46
3321 3791 3.551407 GATGGAGGCCGAGGACCC 61.551 72.222 0.00 0.00 0.00 4.46
3322 3792 4.095400 ATGGAGGCCGAGGACCCT 62.095 66.667 0.00 0.00 0.00 4.34
3325 3795 4.779733 GAGGCCGAGGACCCTGGA 62.780 72.222 0.00 0.00 0.00 3.86
3326 3796 4.095400 AGGCCGAGGACCCTGGAT 62.095 66.667 0.00 0.00 0.00 3.41
3327 3797 3.090532 GGCCGAGGACCCTGGATT 61.091 66.667 3.77 0.00 0.00 3.01
3328 3798 2.680370 GGCCGAGGACCCTGGATTT 61.680 63.158 3.77 0.00 0.00 2.17
3329 3799 1.303282 GCCGAGGACCCTGGATTTT 59.697 57.895 3.77 0.00 0.00 1.82
3330 3800 0.323451 GCCGAGGACCCTGGATTTTT 60.323 55.000 3.77 0.00 0.00 1.94
3354 3824 8.450780 TTTTAATCTTTTACCTCTCCCTCTCT 57.549 34.615 0.00 0.00 0.00 3.10
3355 3825 7.663043 TTAATCTTTTACCTCTCCCTCTCTC 57.337 40.000 0.00 0.00 0.00 3.20
3356 3826 4.957606 TCTTTTACCTCTCCCTCTCTCT 57.042 45.455 0.00 0.00 0.00 3.10
3357 3827 4.862371 TCTTTTACCTCTCCCTCTCTCTC 58.138 47.826 0.00 0.00 0.00 3.20
3358 3828 3.673543 TTTACCTCTCCCTCTCTCTCC 57.326 52.381 0.00 0.00 0.00 3.71
3359 3829 1.525175 TACCTCTCCCTCTCTCTCCC 58.475 60.000 0.00 0.00 0.00 4.30
3360 3830 1.293683 ACCTCTCCCTCTCTCTCCCC 61.294 65.000 0.00 0.00 0.00 4.81
3361 3831 1.541672 CTCTCCCTCTCTCTCCCCC 59.458 68.421 0.00 0.00 0.00 5.40
3552 4026 4.373116 GCGGAGGTGAGGCGTCAA 62.373 66.667 11.28 0.00 33.27 3.18
3589 4063 4.619227 CTTCCGGTGTGGTGGCGT 62.619 66.667 0.00 0.00 39.52 5.68
3653 4127 0.111061 TTGCAGTTGAGGCTCATGGT 59.889 50.000 19.50 2.83 0.00 3.55
3724 4198 1.817099 GGCTGGAGCAAGATGGTCG 60.817 63.158 0.20 0.00 45.17 4.79
3865 4340 2.833121 TGGATCTGAGGCGCGCTA 60.833 61.111 32.29 16.55 0.00 4.26
3866 4341 2.152297 CTGGATCTGAGGCGCGCTAT 62.152 60.000 32.29 20.41 0.00 2.97
3889 4364 1.522569 GCTCCGGGTATGTGAGCTT 59.477 57.895 0.00 0.00 46.19 3.74
3969 4446 3.727258 TTGGTGGCTGGCGGCTAT 61.727 61.111 19.30 0.00 41.46 2.97
4043 4520 0.948678 CTTTTTCTTGGCCGAACGGA 59.051 50.000 17.63 0.00 37.50 4.69
4096 4574 0.821517 TAGGGTGGTGTACTGCATCG 59.178 55.000 0.00 0.00 0.00 3.84
4107 4585 0.035534 ACTGCATCGTTATGGCCACA 60.036 50.000 8.16 0.00 33.38 4.17
4165 4643 0.036732 TGGACAGTGTGCCTCAATCC 59.963 55.000 12.66 0.00 0.00 3.01
4184 4662 1.135915 CCGATGAGGAGTGTTGGAGAG 59.864 57.143 0.00 0.00 45.00 3.20
4192 4670 2.022129 GTGTTGGAGAGGTGCGACG 61.022 63.158 0.00 0.00 30.89 5.12
4193 4671 2.197605 TGTTGGAGAGGTGCGACGA 61.198 57.895 0.00 0.00 30.89 4.20
4194 4672 1.733399 GTTGGAGAGGTGCGACGAC 60.733 63.158 0.00 0.00 0.00 4.34
4202 4680 3.179265 GTGCGACGACACGGATGG 61.179 66.667 0.00 0.00 35.93 3.51
4221 4699 0.887933 GAAATCTTGCCCGGCTTTGA 59.112 50.000 11.61 6.50 0.00 2.69
4228 4706 3.508840 CCCGGCTTTGATCGGTGC 61.509 66.667 0.00 0.00 44.32 5.01
4276 4754 2.449967 TACCCTCCTTGGAGGCGTCA 62.450 60.000 26.16 10.43 40.95 4.35
4302 4780 2.285368 TGTCGGCATCTCCCCCTT 60.285 61.111 0.00 0.00 0.00 3.95
4324 4802 1.675552 AGTTTGGGTTGTTGTCTCCG 58.324 50.000 0.00 0.00 0.00 4.63
4325 4803 1.210967 AGTTTGGGTTGTTGTCTCCGA 59.789 47.619 0.00 0.00 0.00 4.55
4383 4861 0.728466 CGTCTTGACGTCGTTCCTCC 60.728 60.000 11.62 0.00 0.00 4.30
4397 4875 1.880340 CCTCCGTTGAGAGCATCGC 60.880 63.158 0.00 0.00 41.42 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 2.420022 CGCACAAGTAAAAGGAGGATGG 59.580 50.000 0.00 0.00 0.00 3.51
201 203 1.532868 ACAAGCTGTTGTCGCTCATTC 59.467 47.619 0.00 0.00 43.88 2.67
208 210 0.307760 GGTGGAACAAGCTGTTGTCG 59.692 55.000 6.31 0.00 46.68 4.35
213 215 0.178981 AGCATGGTGGAACAAGCTGT 60.179 50.000 0.00 0.00 44.16 4.40
214 216 0.524862 GAGCATGGTGGAACAAGCTG 59.475 55.000 0.00 0.00 44.16 4.24
218 220 1.883638 GCTCAGAGCATGGTGGAACAA 60.884 52.381 18.17 0.00 40.52 2.83
244 246 2.513897 GACCCATGCCACCTACGC 60.514 66.667 0.00 0.00 0.00 4.42
280 282 1.291877 GCAGACGTGGTCCACATGAC 61.292 60.000 21.91 7.00 43.67 3.06
281 283 1.005037 GCAGACGTGGTCCACATGA 60.005 57.895 21.91 0.00 39.46 3.07
282 284 0.674581 ATGCAGACGTGGTCCACATG 60.675 55.000 21.91 16.59 41.98 3.21
283 285 0.901827 TATGCAGACGTGGTCCACAT 59.098 50.000 21.91 6.55 34.50 3.21
288 441 1.539065 CCATCCTATGCAGACGTGGTC 60.539 57.143 0.00 0.00 0.00 4.02
300 453 0.618968 GGGATCCCTCGCCATCCTAT 60.619 60.000 24.69 0.00 38.98 2.57
320 473 1.596934 GACATGGGGTCTCGCTTCA 59.403 57.895 0.00 0.00 43.46 3.02
350 503 1.587054 CTTGCCTCGTCCGAGAAGT 59.413 57.895 17.73 0.00 44.53 3.01
396 549 2.611971 CGTCCCTCAATCCGAGACAAAA 60.612 50.000 0.00 0.00 45.45 2.44
469 639 2.676471 CCAAACAAGGAGCCCCCG 60.676 66.667 0.00 0.00 40.87 5.73
472 642 4.423231 CTCCCAAACAAGGAGCCC 57.577 61.111 0.00 0.00 44.30 5.19
545 717 1.341852 TGGTGTAAGTGTAAGCTCGCA 59.658 47.619 0.00 0.00 0.00 5.10
590 772 7.925703 ATACTCATGTCGTAATCGGTAAAAG 57.074 36.000 0.00 0.00 37.69 2.27
635 817 8.951787 AGCATGTGATTGCATGTTTATTTTAT 57.048 26.923 7.71 0.00 45.75 1.40
657 842 9.151471 GAACATAAATATTCTAGCGGATTAGCA 57.849 33.333 0.00 0.00 40.15 3.49
681 866 0.248825 GCACATGTGTTGCAACGGAA 60.249 50.000 26.01 12.52 0.00 4.30
682 867 1.358402 GCACATGTGTTGCAACGGA 59.642 52.632 26.01 13.42 0.00 4.69
701 886 4.887748 ACCACTAATCCGATCAGCTAATG 58.112 43.478 0.00 0.00 0.00 1.90
744 929 4.965119 AGAGATGCCCGAACATTAAAAC 57.035 40.909 0.00 0.00 0.00 2.43
753 938 8.117813 AGTTTTTAATTAAAGAGATGCCCGAA 57.882 30.769 10.40 0.00 0.00 4.30
928 1128 2.277072 CAGGAGGCGAGGAGGAGA 59.723 66.667 0.00 0.00 0.00 3.71
938 1138 4.828925 GGACGAGCAGCAGGAGGC 62.829 72.222 0.00 0.00 45.30 4.70
939 1139 4.504916 CGGACGAGCAGCAGGAGG 62.505 72.222 0.00 0.00 0.00 4.30
940 1140 3.753434 ACGGACGAGCAGCAGGAG 61.753 66.667 0.00 0.00 0.00 3.69
941 1141 4.056125 CACGGACGAGCAGCAGGA 62.056 66.667 0.00 0.00 0.00 3.86
1019 1219 0.107459 CACCCTTAGAGGCAGCTTCC 60.107 60.000 0.00 0.00 32.73 3.46
1059 1259 3.635591 GGAACCATGACATTCCATTCCT 58.364 45.455 14.88 0.00 43.40 3.36
1120 1326 4.487714 TCCATTCCATCTTTTAGCTCGT 57.512 40.909 0.00 0.00 0.00 4.18
1123 1329 4.843728 TCGTTCCATTCCATCTTTTAGCT 58.156 39.130 0.00 0.00 0.00 3.32
1314 1520 5.751243 ACTGTTAGTTTTAGTTGCAGTGG 57.249 39.130 0.00 0.00 34.87 4.00
1421 1660 5.711976 AGTCCATTTGCTGCTTGTAGTTAAT 59.288 36.000 0.00 0.00 0.00 1.40
1477 1716 1.156645 GCCTCGTCTGGATGTGCATC 61.157 60.000 3.71 3.71 37.11 3.91
1514 1753 3.077556 CCTAGACGCCTGGCTGGT 61.078 66.667 17.92 8.12 38.35 4.00
1583 1823 5.799827 AGAGATAAGTTCATGGCTACCTC 57.200 43.478 0.00 0.00 0.00 3.85
1738 2039 2.504681 GCCACGGCAATGAAAGCG 60.505 61.111 2.36 0.00 41.49 4.68
1784 2115 0.261696 GCCTCTCCCTCTCTCCTTCT 59.738 60.000 0.00 0.00 0.00 2.85
1898 2230 2.029964 GAACCCACGCGTTCCTCA 59.970 61.111 10.22 0.00 36.87 3.86
1917 2249 3.765505 GTTCGGTTGACAAGTAGAACG 57.234 47.619 11.90 0.00 0.00 3.95
1963 2295 1.276989 GACTGGAATGTAACGGGTCCA 59.723 52.381 0.00 0.00 37.83 4.02
1982 2314 3.252215 GTGTGTTTGGTTTCGATCATGGA 59.748 43.478 0.00 0.00 0.00 3.41
2027 2359 5.667466 AGGCCTTAAGCAAATGAATTGATG 58.333 37.500 0.00 0.00 46.50 3.07
2058 2390 4.202264 CGGGACTTTTACAGAGCCAGATAT 60.202 45.833 0.00 0.00 0.00 1.63
2133 2466 3.092301 GCCTAAAAAGGATGCCTTCACT 58.908 45.455 0.00 0.00 43.92 3.41
2135 2468 2.091541 CGCCTAAAAAGGATGCCTTCA 58.908 47.619 0.00 0.00 43.92 3.02
2263 2603 5.543507 TGGGTGTTTAATGACTTTTGCAT 57.456 34.783 0.00 0.00 0.00 3.96
2355 2782 2.415168 CACGGCATGTCGAGTAAATTGT 59.585 45.455 28.94 0.00 0.00 2.71
2397 2834 1.000827 CGAAGCCAGCATCTAGACGAT 60.001 52.381 0.00 0.00 0.00 3.73
2417 2854 0.530870 GCTCCGTATGCAGAAGGGAC 60.531 60.000 13.47 2.33 0.00 4.46
2531 2968 2.058675 CCCAAGTCTCCAGGTTCGT 58.941 57.895 0.00 0.00 0.00 3.85
2538 2975 1.227823 CAACGTGCCCAAGTCTCCA 60.228 57.895 0.00 0.00 0.00 3.86
2576 3013 1.250328 CTTGCCCTGCTTCATCACAA 58.750 50.000 0.00 0.00 0.00 3.33
2725 3165 1.069513 TGATGTTTTCGTGACGGAGGT 59.930 47.619 4.70 0.00 0.00 3.85
2848 3318 2.765807 CCCTCCTCATCGGCCAGT 60.766 66.667 2.24 0.00 0.00 4.00
2907 3377 0.608856 TGGTGGACGATGCATTGCTT 60.609 50.000 14.18 3.11 0.00 3.91
2984 3454 1.533625 TCTTTTGGGCATGACCGAAG 58.466 50.000 20.02 21.02 37.45 3.79
3041 3511 4.379143 GGTTGAAACGTCGGCGGC 62.379 66.667 16.39 3.25 43.45 6.53
3130 3600 9.247861 TCTGAAGTCATATGCTAGCAGAATATA 57.752 33.333 23.89 10.47 25.38 0.86
3156 3626 9.338622 AGTAGACTTAAATTGTTAAGCAACTGT 57.661 29.630 6.21 0.00 46.98 3.55
3159 3629 8.902735 GCAAGTAGACTTAAATTGTTAAGCAAC 58.097 33.333 6.21 3.33 46.98 4.17
3279 3749 1.067635 GTGATGGCAAATTCAACGGCT 60.068 47.619 0.00 0.00 0.00 5.52
3328 3798 8.891501 AGAGAGGGAGAGGTAAAAGATTAAAAA 58.108 33.333 0.00 0.00 0.00 1.94
3329 3799 8.450780 AGAGAGGGAGAGGTAAAAGATTAAAA 57.549 34.615 0.00 0.00 0.00 1.52
3330 3800 7.901861 AGAGAGAGGGAGAGGTAAAAGATTAAA 59.098 37.037 0.00 0.00 0.00 1.52
3331 3801 7.423341 AGAGAGAGGGAGAGGTAAAAGATTAA 58.577 38.462 0.00 0.00 0.00 1.40
3332 3802 6.987557 AGAGAGAGGGAGAGGTAAAAGATTA 58.012 40.000 0.00 0.00 0.00 1.75
3333 3803 5.849140 AGAGAGAGGGAGAGGTAAAAGATT 58.151 41.667 0.00 0.00 0.00 2.40
3334 3804 5.454966 GAGAGAGAGGGAGAGGTAAAAGAT 58.545 45.833 0.00 0.00 0.00 2.40
3335 3805 4.325501 GGAGAGAGAGGGAGAGGTAAAAGA 60.326 50.000 0.00 0.00 0.00 2.52
3336 3806 3.958147 GGAGAGAGAGGGAGAGGTAAAAG 59.042 52.174 0.00 0.00 0.00 2.27
3337 3807 3.309994 GGGAGAGAGAGGGAGAGGTAAAA 60.310 52.174 0.00 0.00 0.00 1.52
3338 3808 2.245287 GGGAGAGAGAGGGAGAGGTAAA 59.755 54.545 0.00 0.00 0.00 2.01
3339 3809 1.854280 GGGAGAGAGAGGGAGAGGTAA 59.146 57.143 0.00 0.00 0.00 2.85
3340 3810 1.525175 GGGAGAGAGAGGGAGAGGTA 58.475 60.000 0.00 0.00 0.00 3.08
3341 3811 1.293683 GGGGAGAGAGAGGGAGAGGT 61.294 65.000 0.00 0.00 0.00 3.85
3342 3812 1.541672 GGGGAGAGAGAGGGAGAGG 59.458 68.421 0.00 0.00 0.00 3.69
3343 3813 0.998945 AGGGGGAGAGAGAGGGAGAG 60.999 65.000 0.00 0.00 0.00 3.20
3344 3814 0.996762 GAGGGGGAGAGAGAGGGAGA 60.997 65.000 0.00 0.00 0.00 3.71
3345 3815 1.541672 GAGGGGGAGAGAGAGGGAG 59.458 68.421 0.00 0.00 0.00 4.30
3346 3816 2.015726 GGAGGGGGAGAGAGAGGGA 61.016 68.421 0.00 0.00 0.00 4.20
3347 3817 2.018086 AGGAGGGGGAGAGAGAGGG 61.018 68.421 0.00 0.00 0.00 4.30
3348 3818 1.541672 GAGGAGGGGGAGAGAGAGG 59.458 68.421 0.00 0.00 0.00 3.69
3349 3819 0.998945 AGGAGGAGGGGGAGAGAGAG 60.999 65.000 0.00 0.00 0.00 3.20
3350 3820 0.996762 GAGGAGGAGGGGGAGAGAGA 60.997 65.000 0.00 0.00 0.00 3.10
3351 3821 1.541672 GAGGAGGAGGGGGAGAGAG 59.458 68.421 0.00 0.00 0.00 3.20
3352 3822 2.015726 GGAGGAGGAGGGGGAGAGA 61.016 68.421 0.00 0.00 0.00 3.10
3353 3823 2.612251 GGAGGAGGAGGGGGAGAG 59.388 72.222 0.00 0.00 0.00 3.20
3354 3824 3.036959 GGGAGGAGGAGGGGGAGA 61.037 72.222 0.00 0.00 0.00 3.71
3355 3825 4.548513 CGGGAGGAGGAGGGGGAG 62.549 77.778 0.00 0.00 0.00 4.30
3402 3872 3.324108 TCGCGGGGCTAGGGTTTT 61.324 61.111 6.13 0.00 0.00 2.43
3589 4063 1.978455 CTGCAACTACCCCCGCCATA 61.978 60.000 0.00 0.00 0.00 2.74
3641 4115 2.580815 CGAGCACCATGAGCCTCA 59.419 61.111 0.00 0.00 0.00 3.86
3653 4127 3.797353 GGATCCCAAGCCCGAGCA 61.797 66.667 0.00 0.00 43.56 4.26
3705 4179 1.817099 GACCATCTTGCTCCAGCCG 60.817 63.158 0.00 0.00 41.18 5.52
3794 4269 4.662961 CGCGCAGAGGACACCACA 62.663 66.667 8.75 0.00 0.00 4.17
3843 4318 1.372748 GCGCCTCAGATCCAGATCG 60.373 63.158 0.00 0.00 42.48 3.69
3865 4340 2.072487 ACATACCCGGAGCAGCCAT 61.072 57.895 0.73 0.00 35.94 4.40
3866 4341 2.687200 ACATACCCGGAGCAGCCA 60.687 61.111 0.73 0.00 35.94 4.75
3889 4364 2.598394 GCCAGCCACCAAGCAGAA 60.598 61.111 0.00 0.00 34.23 3.02
3935 4410 1.091771 CAACTCCAGATTGCGCGGAT 61.092 55.000 8.83 0.00 0.00 4.18
4022 4499 1.334689 CCGTTCGGCCAAGAAAAAGTC 60.335 52.381 2.24 0.00 0.00 3.01
4043 4520 1.455383 CGCAGCCCAACTTCCAACTT 61.455 55.000 0.00 0.00 0.00 2.66
4070 4547 1.228956 TACACCACCCTACACGGCT 60.229 57.895 0.00 0.00 0.00 5.52
4077 4554 0.821517 CGATGCAGTACACCACCCTA 59.178 55.000 0.00 0.00 0.00 3.53
4165 4643 1.135915 CCTCTCCAACACTCCTCATCG 59.864 57.143 0.00 0.00 0.00 3.84
4184 4662 3.179265 CATCCGTGTCGTCGCACC 61.179 66.667 12.18 0.00 36.08 5.01
4192 4670 1.401905 GGCAAGATTTCCATCCGTGTC 59.598 52.381 0.00 0.00 0.00 3.67
4193 4671 1.463674 GGCAAGATTTCCATCCGTGT 58.536 50.000 0.00 0.00 0.00 4.49
4194 4672 0.740737 GGGCAAGATTTCCATCCGTG 59.259 55.000 0.00 0.00 0.00 4.94
4202 4680 0.887933 TCAAAGCCGGGCAAGATTTC 59.112 50.000 23.09 0.00 0.00 2.17
4276 4754 1.204941 GAGATGCCGACACACCTTAGT 59.795 52.381 0.00 0.00 0.00 2.24
4302 4780 3.493699 CGGAGACAACAACCCAAACTAGA 60.494 47.826 0.00 0.00 0.00 2.43
4324 4802 1.228657 ACGAACCAAGGCTTTCGCTC 61.229 55.000 17.19 2.80 46.83 5.03
4325 4803 0.818040 AACGAACCAAGGCTTTCGCT 60.818 50.000 17.19 5.03 46.83 4.93
4383 4861 2.088763 ACACGCGATGCTCTCAACG 61.089 57.895 15.93 0.00 40.78 4.10


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

AutoCloner maintained by Alex Coulton.