Multiple sequence alignment - TraesCS1D01G261300

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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 TraesCS1D01G261300 chr1D 100.000 5448 0 0 1 5448 355436234 355430787 0.000000e+00 10061.0
1 TraesCS1D01G261300 chr1D 91.927 991 67 5 3537 4515 355319634 355320623 0.000000e+00 1375.0
2 TraesCS1D01G261300 chr1D 86.187 1209 114 26 3389 4575 355320728 355321905 0.000000e+00 1258.0
3 TraesCS1D01G261300 chr1D 90.083 484 44 3 1741 2220 355317979 355318462 4.630000e-175 625.0
4 TraesCS1D01G261300 chr1D 82.997 594 53 20 1856 2416 355317314 355317892 1.360000e-135 494.0
5 TraesCS1D01G261300 chr1D 82.143 616 58 30 4860 5448 434034255 434034845 1.060000e-131 481.0
6 TraesCS1D01G261300 chr1D 84.257 451 42 16 1042 1480 355316829 355317262 3.930000e-111 412.0
7 TraesCS1D01G261300 chr1D 84.651 430 38 17 5025 5448 433979452 433979859 2.360000e-108 403.0
8 TraesCS1D01G261300 chr1D 86.313 358 32 10 4575 4918 355321859 355322213 1.850000e-99 374.0
9 TraesCS1D01G261300 chr1D 87.826 230 23 4 2887 3115 355319231 355319456 1.160000e-66 265.0
10 TraesCS1D01G261300 chr1D 89.796 147 15 0 3389 3535 355319439 355319585 7.200000e-44 189.0
11 TraesCS1D01G261300 chr1D 96.364 55 1 1 1769 1823 355317261 355317314 7.520000e-14 89.8
12 TraesCS1D01G261300 chr1B 94.731 4764 171 37 719 5448 478059825 478055108 0.000000e+00 7334.0
13 TraesCS1D01G261300 chr1B 86.719 1521 115 38 1048 2517 477943652 477945136 0.000000e+00 1609.0
14 TraesCS1D01G261300 chr1B 91.935 992 66 6 3537 4515 477946777 477947767 0.000000e+00 1376.0
15 TraesCS1D01G261300 chr1B 85.773 1209 121 24 3389 4575 477947872 477949051 0.000000e+00 1232.0
16 TraesCS1D01G261300 chr1B 83.089 1023 115 26 1741 2732 477945138 477946133 0.000000e+00 878.0
17 TraesCS1D01G261300 chr1B 88.920 713 60 13 1 709 478061046 478060349 0.000000e+00 861.0
18 TraesCS1D01G261300 chr1B 83.373 421 51 9 5035 5448 587526516 587526924 6.660000e-99 372.0
19 TraesCS1D01G261300 chr1B 85.475 358 34 11 4575 4918 477949005 477949358 1.870000e-94 357.0
20 TraesCS1D01G261300 chr1B 89.565 230 22 2 2887 3115 477946371 477946599 1.920000e-74 291.0
21 TraesCS1D01G261300 chr1B 89.116 147 16 0 3389 3535 477946582 477946728 3.350000e-42 183.0
22 TraesCS1D01G261300 chr1A 93.637 4762 188 38 719 5448 455611070 455606392 0.000000e+00 7009.0
23 TraesCS1D01G261300 chr1A 90.691 709 57 6 4 709 455612396 455611694 0.000000e+00 935.0
24 TraesCS1D01G261300 chr1A 82.267 344 37 10 4860 5187 532264177 532264512 5.380000e-70 276.0
25 TraesCS1D01G261300 chr1A 89.899 99 5 3 4 102 455612547 455612454 7.410000e-24 122.0
26 TraesCS1D01G261300 chr7A 95.122 205 9 1 1118 1322 20685091 20684888 6.810000e-84 322.0
27 TraesCS1D01G261300 chr7A 92.893 197 14 0 1466 1662 454493555 454493751 2.480000e-73 287.0
28 TraesCS1D01G261300 chr7A 92.784 194 14 0 1469 1662 20684889 20684696 1.160000e-71 281.0
29 TraesCS1D01G261300 chr4A 94.146 205 11 1 1118 1322 603348258 603348461 1.470000e-80 311.0
30 TraesCS1D01G261300 chr4A 93.659 205 12 1 1118 1322 728411712 728411915 6.860000e-79 305.0
31 TraesCS1D01G261300 chr4A 93.401 197 13 0 1466 1662 603348457 603348653 5.340000e-75 292.0
32 TraesCS1D01G261300 chr4A 92.893 197 14 0 1466 1662 728411911 728412107 2.480000e-73 287.0
33 TraesCS1D01G261300 chr4A 89.333 225 18 4 3855 4073 67514492 67514716 1.490000e-70 278.0
34 TraesCS1D01G261300 chr6A 94.359 195 11 0 1118 1312 60063016 60062822 3.190000e-77 300.0
35 TraesCS1D01G261300 chr2A 93.171 205 13 1 1118 1322 680893915 680893712 3.190000e-77 300.0
36 TraesCS1D01G261300 chr2A 92.784 194 14 0 1469 1662 680893713 680893520 1.160000e-71 281.0
37 TraesCS1D01G261300 chr6B 92.386 197 15 0 1466 1662 104568100 104568296 1.160000e-71 281.0
38 TraesCS1D01G261300 chr7B 88.889 225 19 4 3855 4073 52983548 52983772 6.950000e-69 272.0
39 TraesCS1D01G261300 chr7B 89.401 217 19 2 3855 4067 52956882 52956666 2.500000e-68 270.0
40 TraesCS1D01G261300 chrUn 78.307 378 52 20 4973 5331 42300901 42301267 3.300000e-52 217.0
41 TraesCS1D01G261300 chrUn 78.307 378 52 18 4973 5331 319477182 319476816 3.300000e-52 217.0
42 TraesCS1D01G261300 chr5B 100.000 36 0 0 3331 3366 64309944 64309909 3.520000e-07 67.6


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 TraesCS1D01G261300 chr1D 355430787 355436234 5447 True 10061.000000 10061 100.000000 1 5448 1 chr1D.!!$R1 5447
1 TraesCS1D01G261300 chr1D 355316829 355322213 5384 False 564.644444 1375 88.416667 1042 4918 9 chr1D.!!$F3 3876
2 TraesCS1D01G261300 chr1D 434034255 434034845 590 False 481.000000 481 82.143000 4860 5448 1 chr1D.!!$F2 588
3 TraesCS1D01G261300 chr1B 478055108 478061046 5938 True 4097.500000 7334 91.825500 1 5448 2 chr1B.!!$R1 5447
4 TraesCS1D01G261300 chr1B 477943652 477949358 5706 False 846.571429 1609 87.381714 1048 4918 7 chr1B.!!$F2 3870
5 TraesCS1D01G261300 chr1A 455606392 455612547 6155 True 2688.666667 7009 91.409000 4 5448 3 chr1A.!!$R1 5444

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
574 735 0.178955 TGTGACCCCACCTCGAACTA 60.179 55.0 0.00 0.0 42.53 2.24 F
1356 2171 0.466007 TCCATGGATCATTGGTGCGG 60.466 55.0 11.44 0.0 0.00 5.69 F
2788 4929 0.392336 GGCAAACATGGGCTCAAACA 59.608 50.0 0.00 0.0 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1651 2477 0.374758 CGATGTTGATGAGGCCAACG 59.625 55.000 5.01 0.0 44.92 4.10 R
2867 5010 1.065102 GCTTTGCATCATCATGACGCT 59.935 47.619 7.31 0.0 36.42 5.07 R
4716 8300 0.179000 GTCACCGAATGGGCTGATCT 59.821 55.000 0.00 0.0 40.62 2.75 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
46 200 7.415229 GTCCTTTCACTTCTAATGTCGTTTTT 58.585 34.615 0.00 0.00 0.00 1.94
47 201 8.553696 GTCCTTTCACTTCTAATGTCGTTTTTA 58.446 33.333 0.00 0.00 0.00 1.52
48 202 9.280174 TCCTTTCACTTCTAATGTCGTTTTTAT 57.720 29.630 0.00 0.00 0.00 1.40
65 219 9.263538 TCGTTTTTATACTAGTGTGTGTTGATT 57.736 29.630 5.39 0.00 0.00 2.57
77 231 5.046529 TGTGTGTTGATTTGTTACAATGGC 58.953 37.500 0.00 0.00 0.00 4.40
78 232 5.163468 TGTGTGTTGATTTGTTACAATGGCT 60.163 36.000 0.00 0.00 0.00 4.75
136 293 4.779993 AAATCTCCTATTCACCACCTCC 57.220 45.455 0.00 0.00 0.00 4.30
137 294 2.940514 TCTCCTATTCACCACCTCCA 57.059 50.000 0.00 0.00 0.00 3.86
203 361 6.127451 ACCGAACAATGAAGAAACCTCTTTTT 60.127 34.615 0.00 0.00 42.19 1.94
212 370 8.340618 TGAAGAAACCTCTTTTTATCATGGAG 57.659 34.615 0.00 0.00 42.19 3.86
308 466 2.214387 GCTGCTGCAACTTTTGAACT 57.786 45.000 11.11 0.00 39.41 3.01
318 476 3.553828 ACTTTTGAACTTCCCACTCGA 57.446 42.857 0.00 0.00 0.00 4.04
319 477 3.203716 ACTTTTGAACTTCCCACTCGAC 58.796 45.455 0.00 0.00 0.00 4.20
331 489 1.166129 CACTCGACCGAGGAAGAGAA 58.834 55.000 21.42 0.00 45.88 2.87
401 559 2.127708 CCCCTTCTAGGTAGCCATTGT 58.872 52.381 0.00 0.00 31.93 2.71
404 562 3.199946 CCCTTCTAGGTAGCCATTGTTCA 59.800 47.826 0.00 0.00 31.93 3.18
405 563 4.141390 CCCTTCTAGGTAGCCATTGTTCAT 60.141 45.833 0.00 0.00 31.93 2.57
406 564 5.440610 CCTTCTAGGTAGCCATTGTTCATT 58.559 41.667 0.00 0.00 0.00 2.57
407 565 5.888161 CCTTCTAGGTAGCCATTGTTCATTT 59.112 40.000 0.00 0.00 0.00 2.32
458 619 0.734889 CCCGTGTCCATTGCTCATTC 59.265 55.000 0.00 0.00 0.00 2.67
461 622 2.868583 CCGTGTCCATTGCTCATTCTAG 59.131 50.000 0.00 0.00 0.00 2.43
509 670 8.787852 CCTATCCTCTTAATAAATCCTTGTTGC 58.212 37.037 0.00 0.00 0.00 4.17
532 693 2.686558 ACACATTTGTCATGCACGAC 57.313 45.000 5.84 5.84 36.40 4.34
550 711 3.066621 ACGACAGCATGACAAATTTGTGT 59.933 39.130 27.85 17.55 42.43 3.72
560 721 2.167487 ACAAATTTGTGTGGGGTGTGAC 59.833 45.455 22.71 0.00 40.49 3.67
574 735 0.178955 TGTGACCCCACCTCGAACTA 60.179 55.000 0.00 0.00 42.53 2.24
578 739 2.242965 TGACCCCACCTCGAACTATAGA 59.757 50.000 6.78 0.00 0.00 1.98
638 799 3.973425 AGCACCAATCTATCAGGCTTTT 58.027 40.909 0.00 0.00 0.00 2.27
648 809 5.385198 TCTATCAGGCTTTTGACCAGTTTT 58.615 37.500 0.00 0.00 0.00 2.43
658 819 8.094548 GGCTTTTGACCAGTTTTCCTTATAAAT 58.905 33.333 0.00 0.00 0.00 1.40
716 877 8.549338 AAAAAGAAGAGAGTTTCCCTTATACG 57.451 34.615 0.00 0.00 0.00 3.06
718 879 5.270794 AGAAGAGAGTTTCCCTTATACGGT 58.729 41.667 0.00 0.00 0.00 4.83
720 881 6.212993 AGAAGAGAGTTTCCCTTATACGGTTT 59.787 38.462 0.00 0.00 0.00 3.27
721 882 6.370186 AGAGAGTTTCCCTTATACGGTTTT 57.630 37.500 0.00 0.00 0.00 2.43
722 883 6.776744 AGAGAGTTTCCCTTATACGGTTTTT 58.223 36.000 0.00 0.00 0.00 1.94
884 1676 2.307098 CCTTTTCCTCCATCCTCACTGT 59.693 50.000 0.00 0.00 0.00 3.55
911 1703 3.805307 CTCGAGTCTGCGGCGAGT 61.805 66.667 12.98 0.00 44.59 4.18
912 1704 3.726631 CTCGAGTCTGCGGCGAGTC 62.727 68.421 12.98 15.14 44.59 3.36
913 1705 4.838486 CGAGTCTGCGGCGAGTCC 62.838 72.222 12.98 0.00 31.15 3.85
914 1706 3.749064 GAGTCTGCGGCGAGTCCA 61.749 66.667 12.98 0.00 34.01 4.02
1047 1840 2.023532 CCTCCTCCTCCTCCTCCTT 58.976 63.158 0.00 0.00 0.00 3.36
1301 2099 2.813908 CTACCTCGGTGCGTTGCC 60.814 66.667 0.00 0.00 0.00 4.52
1318 2116 4.477975 CCGCGACCTCGGTGTCTC 62.478 72.222 8.23 0.00 44.18 3.36
1346 2152 2.695666 TCTCTCGGTTTCTCCATGGATC 59.304 50.000 16.63 6.38 35.57 3.36
1347 2153 2.432146 CTCTCGGTTTCTCCATGGATCA 59.568 50.000 16.63 1.58 35.57 2.92
1348 2154 3.041211 TCTCGGTTTCTCCATGGATCAT 58.959 45.455 16.63 0.00 35.57 2.45
1356 2171 0.466007 TCCATGGATCATTGGTGCGG 60.466 55.000 11.44 0.00 0.00 5.69
1418 2233 3.060070 CGGATCGTTTCGGTTTATTAGGC 60.060 47.826 0.00 0.00 0.00 3.93
1458 2282 7.411264 CGTGACTACTGATGATTGTTTCTTCTG 60.411 40.741 0.00 0.00 35.13 3.02
1687 2513 1.146041 CGGCGGAATGATCCAAGGA 59.854 57.895 0.00 0.00 46.97 3.36
1745 3026 2.267324 GTGGCTCTGAGCTGGTCC 59.733 66.667 27.09 12.10 41.99 4.46
1892 3180 2.139917 GGGGTTTTTGCGATTTTGGTC 58.860 47.619 0.00 0.00 0.00 4.02
1996 3285 1.316706 GGAGGCAGCTACAGTCGACT 61.317 60.000 13.58 13.58 0.00 4.18
2003 3292 3.381045 CAGCTACAGTCGACTTGTTCAA 58.619 45.455 17.26 2.57 0.00 2.69
2013 3302 2.030540 CGACTTGTTCAAGAGGTCGGTA 60.031 50.000 17.75 0.00 43.69 4.02
2169 4250 3.815401 GCTTCTTGCTCCTCAGTTTGTTA 59.185 43.478 0.00 0.00 38.95 2.41
2209 4290 5.183904 GCCTCCTTTTTGATTATCAGTGTGT 59.816 40.000 0.00 0.00 0.00 3.72
2395 4532 5.008613 TGTTGGTTTGCAGTTCTAGAACATC 59.991 40.000 31.80 23.26 43.47 3.06
2400 4537 3.325870 TGCAGTTCTAGAACATCAACGG 58.674 45.455 31.80 15.41 43.47 4.44
2416 4553 1.821216 ACGGCTTCACCTATGGTTTG 58.179 50.000 0.00 0.00 31.02 2.93
2419 4556 1.474077 GGCTTCACCTATGGTTTGCAG 59.526 52.381 0.00 0.00 31.02 4.41
2420 4557 2.162681 GCTTCACCTATGGTTTGCAGT 58.837 47.619 0.00 0.00 31.02 4.40
2421 4558 2.558359 GCTTCACCTATGGTTTGCAGTT 59.442 45.455 0.00 0.00 31.02 3.16
2422 4559 3.366374 GCTTCACCTATGGTTTGCAGTTC 60.366 47.826 0.00 0.00 31.02 3.01
2424 4561 3.146066 TCACCTATGGTTTGCAGTTCAC 58.854 45.455 0.00 0.00 31.02 3.18
2425 4562 2.884012 CACCTATGGTTTGCAGTTCACA 59.116 45.455 0.00 0.00 31.02 3.58
2426 4563 3.058016 CACCTATGGTTTGCAGTTCACAG 60.058 47.826 0.00 0.00 31.02 3.66
2427 4564 3.181445 ACCTATGGTTTGCAGTTCACAGA 60.181 43.478 0.00 0.00 27.29 3.41
2428 4565 4.012374 CCTATGGTTTGCAGTTCACAGAT 58.988 43.478 0.00 0.00 0.00 2.90
2429 4566 3.928727 ATGGTTTGCAGTTCACAGATG 57.071 42.857 0.00 0.00 0.00 2.90
2430 4567 1.955778 TGGTTTGCAGTTCACAGATGG 59.044 47.619 0.00 0.00 0.00 3.51
2431 4568 2.229792 GGTTTGCAGTTCACAGATGGA 58.770 47.619 0.00 0.00 0.00 3.41
2432 4569 2.622942 GGTTTGCAGTTCACAGATGGAA 59.377 45.455 0.00 0.00 0.00 3.53
2433 4570 3.256631 GGTTTGCAGTTCACAGATGGAAT 59.743 43.478 0.00 0.00 0.00 3.01
2434 4571 4.458989 GGTTTGCAGTTCACAGATGGAATA 59.541 41.667 0.00 0.00 0.00 1.75
2435 4572 5.048083 GGTTTGCAGTTCACAGATGGAATAA 60.048 40.000 0.00 0.00 0.00 1.40
2436 4573 6.350445 GGTTTGCAGTTCACAGATGGAATAAT 60.350 38.462 0.00 0.00 0.00 1.28
2437 4574 6.441093 TTGCAGTTCACAGATGGAATAATC 57.559 37.500 0.00 0.00 0.00 1.75
2438 4575 4.883585 TGCAGTTCACAGATGGAATAATCC 59.116 41.667 0.00 0.00 46.76 3.01
2439 4576 4.276926 GCAGTTCACAGATGGAATAATCCC 59.723 45.833 0.00 0.00 45.95 3.85
2474 4611 6.266786 ACTGTCGAATTTGGGGTTATTTCTTT 59.733 34.615 0.00 0.00 0.00 2.52
2603 4740 5.452078 ACAATGAGGTGTAATGGTGTTTG 57.548 39.130 0.00 0.00 0.00 2.93
2608 4745 2.364002 AGGTGTAATGGTGTTTGGTTGC 59.636 45.455 0.00 0.00 0.00 4.17
2674 4815 3.413846 TTTTTGCATGCCAATAGCCAA 57.586 38.095 16.68 0.00 42.71 4.52
2676 4817 4.750021 TTTTGCATGCCAATAGCCAATA 57.250 36.364 16.68 0.00 42.71 1.90
2677 4818 4.959560 TTTGCATGCCAATAGCCAATAT 57.040 36.364 16.68 0.00 42.71 1.28
2678 4819 4.959560 TTGCATGCCAATAGCCAATATT 57.040 36.364 16.68 0.00 42.71 1.28
2699 4840 5.705609 TTGGCCAACTCTAGTTCATTTTC 57.294 39.130 16.05 0.00 35.83 2.29
2788 4929 0.392336 GGCAAACATGGGCTCAAACA 59.608 50.000 0.00 0.00 0.00 2.83
2913 5205 3.989817 GCAAATACAACCCTGAAAAGCAG 59.010 43.478 0.00 0.00 44.49 4.24
3028 5321 7.494625 GCTACACCACAGCATACTATCTTAAAA 59.505 37.037 0.00 0.00 38.93 1.52
3198 5493 5.560722 TTCACTGGTCTGTAATTTCTGGA 57.439 39.130 0.00 0.00 0.00 3.86
3370 5665 1.137086 GATGAGGAGGCTCGTTGCTTA 59.863 52.381 11.50 0.00 42.39 3.09
3694 6043 4.921470 TCGGTTTCTTTATTCTTCGCAG 57.079 40.909 0.00 0.00 0.00 5.18
4134 6486 8.482429 GCATCATTAGTACTGCATTTAAATTGC 58.518 33.333 5.39 12.76 34.77 3.56
4196 6551 5.489792 TGGAGTGCTAAGTCTTCTCATTT 57.510 39.130 0.00 0.00 0.00 2.32
4205 6560 5.774498 AAGTCTTCTCATTTTTGGTGGAC 57.226 39.130 0.00 0.00 0.00 4.02
4540 8124 2.476619 GAGTCGGACAGTGAAATGTGTG 59.523 50.000 11.27 0.00 32.25 3.82
4543 8127 2.159028 TCGGACAGTGAAATGTGTGTCA 60.159 45.455 0.00 0.00 40.96 3.58
4663 8247 1.832883 ATTCGCCTGTAAATGCACCA 58.167 45.000 0.00 0.00 0.00 4.17
4695 8279 9.726438 AATCTATATGGCCAAACTGTTAGATAC 57.274 33.333 10.96 0.00 0.00 2.24
4707 8291 9.546909 CAAACTGTTAGATACTGCAAATGTAAG 57.453 33.333 0.00 0.00 0.00 2.34
4716 8300 8.918116 AGATACTGCAAATGTAAGTATGAGAGA 58.082 33.333 12.59 0.00 37.27 3.10
4742 8326 3.192422 CAGCCCATTCGGTGACAAAATAA 59.808 43.478 0.00 0.00 0.00 1.40
4743 8327 3.829601 AGCCCATTCGGTGACAAAATAAA 59.170 39.130 0.00 0.00 0.00 1.40
4744 8328 4.466015 AGCCCATTCGGTGACAAAATAAAT 59.534 37.500 0.00 0.00 0.00 1.40
4785 8369 3.064545 GCTGATGTGTACCATTTCTCAGC 59.935 47.826 15.55 15.55 39.22 4.26
5192 8817 4.458295 CCTGCTTGAATGTCTGTCAGAATT 59.542 41.667 3.51 6.99 0.00 2.17
5193 8818 5.366829 TGCTTGAATGTCTGTCAGAATTG 57.633 39.130 3.51 0.00 0.00 2.32
5234 8859 5.530519 TTCATAGTGTCAACGATTCTTGC 57.469 39.130 0.00 0.00 0.00 4.01
5370 8995 0.865111 TGCATGAACGACCAGTTTCG 59.135 50.000 0.00 0.00 44.35 3.46
5396 9021 4.675510 AGTGCTCAAACTGTCAAATTGTG 58.324 39.130 0.00 0.00 0.00 3.33
5432 9058 6.128282 GCGTGCTATACTTGGTGCATATAATT 60.128 38.462 0.00 0.00 37.76 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 200 9.984190 TGTAACAAATCAACACACACTAGTATA 57.016 29.630 0.00 0.00 0.00 1.47
47 201 8.896320 TGTAACAAATCAACACACACTAGTAT 57.104 30.769 0.00 0.00 0.00 2.12
48 202 8.719560 TTGTAACAAATCAACACACACTAGTA 57.280 30.769 0.00 0.00 0.00 1.82
49 203 7.618502 TTGTAACAAATCAACACACACTAGT 57.381 32.000 0.00 0.00 0.00 2.57
50 204 7.591057 CCATTGTAACAAATCAACACACACTAG 59.409 37.037 0.00 0.00 0.00 2.57
51 205 7.421599 CCATTGTAACAAATCAACACACACTA 58.578 34.615 0.00 0.00 0.00 2.74
52 206 6.272318 CCATTGTAACAAATCAACACACACT 58.728 36.000 0.00 0.00 0.00 3.55
53 207 5.051106 GCCATTGTAACAAATCAACACACAC 60.051 40.000 0.00 0.00 0.00 3.82
54 208 5.046529 GCCATTGTAACAAATCAACACACA 58.953 37.500 0.00 0.00 0.00 3.72
65 219 6.707440 TCAAAGAAAGAGCCATTGTAACAA 57.293 33.333 0.00 0.00 0.00 2.83
136 293 5.986004 GGTAGGACCAAAGTTATCGATTG 57.014 43.478 1.71 0.00 38.42 2.67
203 361 0.925558 TTGGGCTTGGCTCCATGATA 59.074 50.000 6.04 0.00 31.26 2.15
212 370 4.163458 CAAAATGATTTTTGGGCTTGGC 57.837 40.909 0.00 0.00 45.18 4.52
308 466 1.228644 TTCCTCGGTCGAGTGGGAA 60.229 57.895 17.50 12.51 40.44 3.97
318 476 4.625607 AGTTCATTTTCTCTTCCTCGGT 57.374 40.909 0.00 0.00 0.00 4.69
319 477 4.378874 GCAAGTTCATTTTCTCTTCCTCGG 60.379 45.833 0.00 0.00 0.00 4.63
331 489 2.095059 GCGATGGTGAGCAAGTTCATTT 60.095 45.455 0.00 0.00 0.00 2.32
363 521 1.472728 GGGGCATTTCAGTCGATACGT 60.473 52.381 0.00 0.00 0.00 3.57
418 579 3.495193 GAACGTCTACTGCGATTGTACA 58.505 45.455 0.00 0.00 0.00 2.90
445 606 7.129457 AGTAACATCTAGAATGAGCAATGGA 57.871 36.000 0.00 0.00 0.00 3.41
458 619 6.533367 GGACAAGAGAGCAAAGTAACATCTAG 59.467 42.308 0.00 0.00 0.00 2.43
461 622 4.393371 GGGACAAGAGAGCAAAGTAACATC 59.607 45.833 0.00 0.00 0.00 3.06
509 670 2.975193 CGTGCATGACAAATGTGTTCTG 59.025 45.455 0.00 0.00 38.41 3.02
532 693 3.061322 CCCACACAAATTTGTCATGCTG 58.939 45.455 20.85 11.21 39.91 4.41
537 698 2.167281 CACACCCCACACAAATTTGTCA 59.833 45.455 20.85 0.00 39.91 3.58
560 721 4.748277 TTTTCTATAGTTCGAGGTGGGG 57.252 45.455 0.00 0.00 0.00 4.96
569 730 6.201234 GCCCGAGAGTTGATTTTCTATAGTTC 59.799 42.308 0.00 0.00 0.00 3.01
574 735 4.487714 TGCCCGAGAGTTGATTTTCTAT 57.512 40.909 0.00 0.00 0.00 1.98
578 739 4.636206 GTCTATTGCCCGAGAGTTGATTTT 59.364 41.667 0.00 0.00 0.00 1.82
638 799 7.726291 TGGTCAATTTATAAGGAAAACTGGTCA 59.274 33.333 0.00 0.00 0.00 4.02
658 819 8.292444 TCAAAAAGAAGAAGAGAATTGGTCAA 57.708 30.769 0.00 0.00 0.00 3.18
770 1548 2.583472 CCCCTTGGCCTGTTTCATC 58.417 57.895 3.32 0.00 0.00 2.92
911 1703 4.104738 GGTTTATGGAAGAGGATGGATGGA 59.895 45.833 0.00 0.00 0.00 3.41
912 1704 4.141181 TGGTTTATGGAAGAGGATGGATGG 60.141 45.833 0.00 0.00 0.00 3.51
913 1705 5.052693 TGGTTTATGGAAGAGGATGGATG 57.947 43.478 0.00 0.00 0.00 3.51
914 1706 4.977739 TCTGGTTTATGGAAGAGGATGGAT 59.022 41.667 0.00 0.00 0.00 3.41
1047 1840 0.470766 GTAGAGCGGAGAGGAGGAGA 59.529 60.000 0.00 0.00 0.00 3.71
1312 2110 0.098025 CGAGAGAAGCGAGGAGACAC 59.902 60.000 0.00 0.00 0.00 3.67
1313 2111 1.027255 CCGAGAGAAGCGAGGAGACA 61.027 60.000 0.00 0.00 0.00 3.41
1314 2112 1.027792 ACCGAGAGAAGCGAGGAGAC 61.028 60.000 0.00 0.00 0.00 3.36
1318 2116 0.528470 AGAAACCGAGAGAAGCGAGG 59.472 55.000 0.00 0.00 0.00 4.63
1346 2152 2.086251 AAACCAGCACCGCACCAATG 62.086 55.000 0.00 0.00 0.00 2.82
1347 2153 1.805428 GAAACCAGCACCGCACCAAT 61.805 55.000 0.00 0.00 0.00 3.16
1348 2154 2.441164 AAACCAGCACCGCACCAA 60.441 55.556 0.00 0.00 0.00 3.67
1356 2171 2.319472 GCAAAATCGAGAAACCAGCAC 58.681 47.619 0.00 0.00 0.00 4.40
1418 2233 1.208052 AGTCACGATGAACCATGGAGG 59.792 52.381 21.47 2.90 45.67 4.30
1458 2282 4.946784 AGATTACACGGAACAATCAAGC 57.053 40.909 0.00 0.00 32.27 4.01
1651 2477 0.374758 CGATGTTGATGAGGCCAACG 59.625 55.000 5.01 0.00 44.92 4.10
1662 2488 1.581934 GATCATTCCGCCGATGTTGA 58.418 50.000 0.00 0.00 0.00 3.18
1745 3026 4.452733 GGGAGCGGTGGGAGAACG 62.453 72.222 0.00 0.00 0.00 3.95
1996 3285 4.884668 AGAATACCGACCTCTTGAACAA 57.115 40.909 0.00 0.00 0.00 2.83
2003 3292 3.367087 CGACACAAAGAATACCGACCTCT 60.367 47.826 0.00 0.00 0.00 3.69
2013 3302 2.893637 CTCCCGATCGACACAAAGAAT 58.106 47.619 18.66 0.00 0.00 2.40
2209 4290 5.126222 TCTCCACAAGTAAAACAATGCACAA 59.874 36.000 0.00 0.00 0.00 3.33
2395 4532 1.821216 AACCATAGGTGAAGCCGTTG 58.179 50.000 0.00 0.00 43.70 4.10
2400 4537 2.162681 ACTGCAAACCATAGGTGAAGC 58.837 47.619 0.00 0.00 35.34 3.86
2416 4553 4.276926 GGGATTATTCCATCTGTGAACTGC 59.723 45.833 6.03 0.00 44.60 4.40
2419 4556 6.322201 ACAATGGGATTATTCCATCTGTGAAC 59.678 38.462 5.34 0.00 43.61 3.18
2420 4557 6.434302 ACAATGGGATTATTCCATCTGTGAA 58.566 36.000 5.34 0.00 43.61 3.18
2421 4558 6.017211 ACAATGGGATTATTCCATCTGTGA 57.983 37.500 5.34 0.00 43.61 3.58
2422 4559 6.548622 AGAACAATGGGATTATTCCATCTGTG 59.451 38.462 15.83 9.86 43.61 3.66
2424 4561 7.592885 AAGAACAATGGGATTATTCCATCTG 57.407 36.000 5.34 8.85 43.61 2.90
2425 4562 8.506083 AGTAAGAACAATGGGATTATTCCATCT 58.494 33.333 5.34 0.00 43.61 2.90
2426 4563 8.571336 CAGTAAGAACAATGGGATTATTCCATC 58.429 37.037 5.34 0.00 43.61 3.51
2427 4564 8.061304 ACAGTAAGAACAATGGGATTATTCCAT 58.939 33.333 0.00 0.00 46.11 3.41
2428 4565 7.410174 ACAGTAAGAACAATGGGATTATTCCA 58.590 34.615 0.00 0.00 44.60 3.53
2429 4566 7.254795 CGACAGTAAGAACAATGGGATTATTCC 60.255 40.741 0.00 0.00 41.77 3.01
2430 4567 7.494625 TCGACAGTAAGAACAATGGGATTATTC 59.505 37.037 0.00 0.00 0.00 1.75
2431 4568 7.335627 TCGACAGTAAGAACAATGGGATTATT 58.664 34.615 0.00 0.00 0.00 1.40
2432 4569 6.884832 TCGACAGTAAGAACAATGGGATTAT 58.115 36.000 0.00 0.00 0.00 1.28
2433 4570 6.288941 TCGACAGTAAGAACAATGGGATTA 57.711 37.500 0.00 0.00 0.00 1.75
2434 4571 5.160607 TCGACAGTAAGAACAATGGGATT 57.839 39.130 0.00 0.00 0.00 3.01
2435 4572 4.819105 TCGACAGTAAGAACAATGGGAT 57.181 40.909 0.00 0.00 0.00 3.85
2436 4573 4.610605 TTCGACAGTAAGAACAATGGGA 57.389 40.909 0.00 0.00 0.00 4.37
2437 4574 5.880054 AATTCGACAGTAAGAACAATGGG 57.120 39.130 0.00 0.00 0.00 4.00
2438 4575 6.086222 CCAAATTCGACAGTAAGAACAATGG 58.914 40.000 0.00 0.80 0.00 3.16
2439 4576 6.086222 CCCAAATTCGACAGTAAGAACAATG 58.914 40.000 0.00 0.00 0.00 2.82
2474 4611 4.195416 TCGCAATACCTGTGCAATATTGA 58.805 39.130 19.73 1.75 42.33 2.57
2603 4740 5.067283 CCAAACATACCCTTACATAGCAACC 59.933 44.000 0.00 0.00 0.00 3.77
2608 4745 6.601332 ACCATCCAAACATACCCTTACATAG 58.399 40.000 0.00 0.00 0.00 2.23
2672 4813 6.949352 ATGAACTAGAGTTGGCCAATATTG 57.051 37.500 23.66 13.51 38.56 1.90
2673 4814 7.961326 AAATGAACTAGAGTTGGCCAATATT 57.039 32.000 23.66 10.74 38.56 1.28
2674 4815 7.068716 GGAAAATGAACTAGAGTTGGCCAATAT 59.931 37.037 23.66 14.01 38.56 1.28
2676 4817 5.185828 GGAAAATGAACTAGAGTTGGCCAAT 59.814 40.000 23.66 10.87 38.56 3.16
2677 4818 4.522789 GGAAAATGAACTAGAGTTGGCCAA 59.477 41.667 16.05 16.05 38.56 4.52
2678 4819 4.079253 GGAAAATGAACTAGAGTTGGCCA 58.921 43.478 0.00 0.00 38.56 5.36
2679 4820 4.336280 AGGAAAATGAACTAGAGTTGGCC 58.664 43.478 0.00 0.00 38.56 5.36
2680 4821 5.966742 AAGGAAAATGAACTAGAGTTGGC 57.033 39.130 0.00 0.00 38.56 4.52
2867 5010 1.065102 GCTTTGCATCATCATGACGCT 59.935 47.619 7.31 0.00 36.42 5.07
2913 5205 7.745155 GCTTCGTTTTCAATAGTTTAGGACTTC 59.255 37.037 0.00 0.00 39.86 3.01
3385 5680 4.770795 AGCTGAAAGTACAACAGACTGTT 58.229 39.130 15.23 15.23 37.39 3.16
3386 5681 4.408182 AGCTGAAAGTACAACAGACTGT 57.592 40.909 1.07 1.07 35.30 3.55
4196 6551 0.459489 GCAGTTGCAAGTCCACCAAA 59.541 50.000 3.08 0.00 41.59 3.28
4540 8124 6.402222 ACTATTGAACTCCATGACTCTTGAC 58.598 40.000 0.00 0.00 0.00 3.18
4543 8127 6.611613 TGACTATTGAACTCCATGACTCTT 57.388 37.500 0.00 0.00 0.00 2.85
4663 8247 7.293073 ACAGTTTGGCCATATAGATTCTTCAT 58.707 34.615 6.09 0.00 0.00 2.57
4695 8279 7.924947 TGATCTCTCTCATACTTACATTTGCAG 59.075 37.037 0.00 0.00 0.00 4.41
4707 8291 4.617995 CGAATGGGCTGATCTCTCTCATAC 60.618 50.000 0.00 0.00 0.00 2.39
4716 8300 0.179000 GTCACCGAATGGGCTGATCT 59.821 55.000 0.00 0.00 40.62 2.75
4742 8326 4.460948 CTCAACAGCTGGGCAATTTATT 57.539 40.909 19.93 0.00 0.00 1.40
4905 8508 1.489481 TGTAGCAGTAGCAGCCATCT 58.511 50.000 0.00 0.00 45.49 2.90
5077 8702 2.886081 CTGAAGAACATGACTCTCCCG 58.114 52.381 0.00 0.00 0.00 5.14
5210 8835 5.961843 GCAAGAATCGTTGACACTATGAATG 59.038 40.000 0.00 0.00 0.00 2.67
5213 8838 3.612423 CGCAAGAATCGTTGACACTATGA 59.388 43.478 0.00 0.00 43.02 2.15
5222 8847 0.385849 TTGCTGCGCAAGAATCGTTG 60.386 50.000 13.05 0.00 43.99 4.10
5234 8859 1.469703 TCCAGATGAAATGTTGCTGCG 59.530 47.619 0.00 0.00 0.00 5.18
5370 8995 4.893424 TTTGACAGTTTGAGCACTTACC 57.107 40.909 0.00 0.00 0.00 2.85
5396 9021 2.295253 ATAGCACGCACACTACCTTC 57.705 50.000 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.