Multiple sequence alignment - TraesCS1B01G149900

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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 TraesCS1B01G149900 chr1B 100.000 3328 0 0 1 3328 226359478 226356151 0.000000e+00 6146.0
1 TraesCS1B01G149900 chr1D 91.736 2057 149 9 1273 3328 171163158 171161122 0.000000e+00 2837.0
2 TraesCS1B01G149900 chr1D 94.157 1181 46 10 1 1167 171164789 171163618 0.000000e+00 1777.0
3 TraesCS1B01G149900 chr1D 100.000 31 0 0 1177 1207 171163202 171163172 1.290000e-04 58.4
4 TraesCS1B01G149900 chr1D 100.000 29 0 0 1221 1249 171163186 171163158 2.000000e-03 54.7
5 TraesCS1B01G149900 chr1A 91.465 1898 152 8 1221 3116 229170240 229168351 0.000000e+00 2599.0
6 TraesCS1B01G149900 chr1A 94.683 1166 46 9 16 1167 229171589 229170426 0.000000e+00 1796.0
7 TraesCS1B01G149900 chr1A 83.946 299 38 8 3034 3327 222594646 222594353 9.090000e-71 278.0
8 TraesCS1B01G149900 chr1A 100.000 31 0 0 1177 1207 229170256 229170226 1.290000e-04 58.4
9 TraesCS1B01G149900 chr4D 87.987 308 33 4 1903 2208 443521033 443521338 8.780000e-96 361.0
10 TraesCS1B01G149900 chr4D 83.946 299 40 8 3033 3327 455351624 455351918 2.530000e-71 279.0
11 TraesCS1B01G149900 chr4D 82.759 319 42 11 3016 3327 206691949 206691637 4.230000e-69 272.0
12 TraesCS1B01G149900 chr4D 82.812 128 18 2 1607 1731 116270842 116270968 9.760000e-21 111.0
13 TraesCS1B01G149900 chr4A 87.582 306 38 0 1903 2208 24216812 24216507 4.080000e-94 355.0
14 TraesCS1B01G149900 chr4A 89.256 121 13 0 1691 1811 24217020 24216900 5.750000e-33 152.0
15 TraesCS1B01G149900 chr4B 86.928 306 40 0 1903 2208 552846179 552846484 8.840000e-91 344.0
16 TraesCS1B01G149900 chr4B 82.812 128 18 2 1607 1731 178071773 178071899 9.760000e-21 111.0
17 TraesCS1B01G149900 chr6D 84.385 301 35 10 3033 3327 192077669 192077375 5.430000e-73 285.0
18 TraesCS1B01G149900 chr3A 84.281 299 40 7 3033 3327 260027275 260027570 5.430000e-73 285.0
19 TraesCS1B01G149900 chr6A 83.077 325 41 12 3012 3327 283775080 283775399 1.950000e-72 283.0
20 TraesCS1B01G149900 chr3B 84.642 293 36 7 3039 3326 337297937 337297649 1.950000e-72 283.0
21 TraesCS1B01G149900 chr6B 82.812 320 41 12 3016 3327 325760119 325759806 1.180000e-69 274.0
22 TraesCS1B01G149900 chr2B 79.375 160 33 0 1640 1799 78072106 78072265 2.710000e-21 113.0
23 TraesCS1B01G149900 chr2B 77.301 163 37 0 1640 1802 77995060 77994898 2.730000e-16 97.1
24 TraesCS1B01G149900 chr2B 89.474 57 6 0 1913 1969 3292169 3292225 4.610000e-09 73.1
25 TraesCS1B01G149900 chr2B 90.000 50 5 0 1910 1959 66560803 66560852 7.710000e-07 65.8
26 TraesCS1B01G149900 chr2B 100.000 29 0 0 965 993 551634260 551634232 2.000000e-03 54.7
27 TraesCS1B01G149900 chr2D 78.750 160 34 0 1640 1799 39320897 39320738 1.260000e-19 108.0
28 TraesCS1B01G149900 chr2D 78.750 160 34 0 1640 1799 50238186 50238345 1.260000e-19 108.0
29 TraesCS1B01G149900 chr2D 90.000 50 5 0 1910 1959 38095021 38095070 7.710000e-07 65.8
30 TraesCS1B01G149900 chr2A 78.125 160 35 0 1640 1799 51945269 51945428 5.870000e-18 102.0
31 TraesCS1B01G149900 chr2A 87.755 49 6 0 1921 1969 4978857 4978809 1.290000e-04 58.4
32 TraesCS1B01G149900 chr2A 100.000 29 0 0 965 993 613988747 613988719 2.000000e-03 54.7


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 TraesCS1B01G149900 chr1B 226356151 226359478 3327 True 6146.000000 6146 100.000000 1 3328 1 chr1B.!!$R1 3327
1 TraesCS1B01G149900 chr1D 171161122 171164789 3667 True 1181.775000 2837 96.473250 1 3328 4 chr1D.!!$R1 3327
2 TraesCS1B01G149900 chr1A 229168351 229171589 3238 True 1484.466667 2599 95.382667 16 3116 3 chr1A.!!$R2 3100
3 TraesCS1B01G149900 chr4A 24216507 24217020 513 True 253.500000 355 88.419000 1691 2208 2 chr4A.!!$R1 517

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
137 143 0.108963 AGTACCGATCCTCCTCCTCG 59.891 60.0 0.0 0.0 0.00 4.63 F
277 289 0.605589 CTCGTCAACTCTTGAGCCCT 59.394 55.0 0.0 0.0 41.01 5.19 F
802 820 0.984961 CTCCCAAGATCCAGAGCCCA 60.985 60.0 0.0 0.0 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1234 1686 0.037697 CTGCACCTACCACGCTTACA 60.038 55.000 0.00 0.0 0.00 2.41 R
1357 1809 0.321653 CCGCTAGCTTCACCAGGTTT 60.322 55.000 13.93 0.0 34.13 3.27 R
2466 2973 1.354368 TGCCCAAGGAACTAAGGAAGG 59.646 52.381 0.00 0.0 38.49 3.46 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
112 118 7.039644 TCCTTTCTCCTCTTGTTGAAGTAGTAG 60.040 40.741 0.00 0.00 0.00 2.57
137 143 0.108963 AGTACCGATCCTCCTCCTCG 59.891 60.000 0.00 0.00 0.00 4.63
163 175 5.182950 GTCTCTCTCTCTCTGTGTTCATTCA 59.817 44.000 0.00 0.00 0.00 2.57
164 176 5.951148 TCTCTCTCTCTCTGTGTTCATTCAT 59.049 40.000 0.00 0.00 0.00 2.57
165 177 6.436847 TCTCTCTCTCTCTGTGTTCATTCATT 59.563 38.462 0.00 0.00 0.00 2.57
166 178 6.629128 TCTCTCTCTCTGTGTTCATTCATTC 58.371 40.000 0.00 0.00 0.00 2.67
176 188 5.179368 TGTGTTCATTCATTCCTCTTTCGTC 59.821 40.000 0.00 0.00 0.00 4.20
223 235 1.344438 CTTTGGCCCTTTCCCTGTTTC 59.656 52.381 0.00 0.00 0.00 2.78
277 289 0.605589 CTCGTCAACTCTTGAGCCCT 59.394 55.000 0.00 0.00 41.01 5.19
289 301 3.906218 TCTTGAGCCCTGCATATAGACAT 59.094 43.478 0.00 0.00 0.00 3.06
415 433 2.119495 GTGGCAGAAATAGGGGAGAGA 58.881 52.381 0.00 0.00 0.00 3.10
417 435 2.023015 TGGCAGAAATAGGGGAGAGAGA 60.023 50.000 0.00 0.00 0.00 3.10
453 471 6.655425 GGGAATAAATACTCTGTCTTATGGGC 59.345 42.308 0.00 0.00 0.00 5.36
635 653 2.254152 AGTCCTGATTGGGCACTCTA 57.746 50.000 0.00 0.00 44.59 2.43
649 667 7.618019 TGGGCACTCTATTTCAGTATTCTAT 57.382 36.000 0.00 0.00 0.00 1.98
650 668 8.721133 TGGGCACTCTATTTCAGTATTCTATA 57.279 34.615 0.00 0.00 0.00 1.31
714 732 4.883585 CACTAGCTCCAGCAAAATCCATTA 59.116 41.667 0.48 0.00 45.16 1.90
717 735 5.945144 AGCTCCAGCAAAATCCATTATTT 57.055 34.783 0.48 0.00 45.16 1.40
802 820 0.984961 CTCCCAAGATCCAGAGCCCA 60.985 60.000 0.00 0.00 0.00 5.36
829 847 2.026879 GACCGGAGCGATGAGAGC 59.973 66.667 9.46 0.00 0.00 4.09
867 885 3.731728 GGAGGTGGAGGCCATGCA 61.732 66.667 5.01 0.00 35.28 3.96
880 898 4.862092 ATGCAGCTCGACTCGGCG 62.862 66.667 0.00 0.00 0.00 6.46
999 1017 4.692475 GTACAAGGGCGCCGTGGT 62.692 66.667 30.43 30.43 37.32 4.16
1000 1018 2.996153 TACAAGGGCGCCGTGGTA 60.996 61.111 28.30 28.30 37.32 3.25
1001 1019 2.360767 TACAAGGGCGCCGTGGTAT 61.361 57.895 28.30 11.62 37.32 2.73
1050 1069 2.742372 GCCGTCAAGGTGCACGAT 60.742 61.111 11.45 0.00 43.70 3.73
1080 1099 2.935481 TTCCAGGGCCACAGGGAG 60.935 66.667 6.18 0.00 35.59 4.30
1114 1137 4.634883 GTCTCTCTAATCGTGACACCTACA 59.365 45.833 0.00 0.00 0.00 2.74
1119 1145 6.811665 TCTCTAATCGTGACACCTACATTTTG 59.188 38.462 0.00 0.00 0.00 2.44
1123 1149 5.821516 TCGTGACACCTACATTTTGTTTT 57.178 34.783 0.00 0.00 0.00 2.43
1140 1166 4.688021 TGTTTTCAAATTGGCACCTACAC 58.312 39.130 0.00 0.00 0.00 2.90
1149 1175 8.301002 TCAAATTGGCACCTACACTAATTAAAC 58.699 33.333 0.00 0.00 0.00 2.01
1173 1199 8.880991 ACTCTCACAAATCTTTACTACTCCTA 57.119 34.615 0.00 0.00 0.00 2.94
1175 1201 8.880991 TCTCACAAATCTTTACTACTCCTACT 57.119 34.615 0.00 0.00 0.00 2.57
1259 1711 1.135689 GCGTGGTAGGTGCAGATTTTG 60.136 52.381 0.00 0.00 0.00 2.44
1262 1714 2.890945 GTGGTAGGTGCAGATTTTGGTT 59.109 45.455 0.00 0.00 0.00 3.67
1264 1716 2.890945 GGTAGGTGCAGATTTTGGTTGT 59.109 45.455 0.00 0.00 0.00 3.32
1266 1718 4.082949 GGTAGGTGCAGATTTTGGTTGTAC 60.083 45.833 0.00 0.00 0.00 2.90
1268 1720 2.315901 GTGCAGATTTTGGTTGTACGC 58.684 47.619 0.00 0.00 0.00 4.42
1292 1744 3.806380 AGCCTGACAAGCATCTATCTTG 58.194 45.455 0.00 1.63 44.71 3.02
1309 1761 4.503741 TCTTGCTATGCCTTTTTGTGTC 57.496 40.909 0.00 0.00 0.00 3.67
1313 1765 2.742053 GCTATGCCTTTTTGTGTCGAGA 59.258 45.455 0.00 0.00 0.00 4.04
1323 1775 6.594159 CCTTTTTGTGTCGAGATTATGTAGGT 59.406 38.462 0.00 0.00 0.00 3.08
1328 1780 4.338682 GTGTCGAGATTATGTAGGTGGAGT 59.661 45.833 0.00 0.00 0.00 3.85
1351 1803 1.672356 CTTCTTGGGCCACCTGTCG 60.672 63.158 5.23 0.00 37.76 4.35
1432 1884 2.494918 GAGTACATGCCGCTCGGT 59.505 61.111 10.24 0.00 37.65 4.69
1494 1946 5.659079 ACCACCTTCATTTTCCACACTTTTA 59.341 36.000 0.00 0.00 0.00 1.52
1510 1962 2.039818 TTTAGTTTGGTGCGTGTCCA 57.960 45.000 0.00 0.00 0.00 4.02
1515 1967 2.601194 TTTGGTGCGTGTCCAGAGCA 62.601 55.000 0.00 0.00 38.71 4.26
1533 1985 1.671979 CAGGTGCGATTGATGGATGT 58.328 50.000 0.00 0.00 0.00 3.06
1589 2041 0.385751 GGCGACGAGGATGAAGATCA 59.614 55.000 0.00 0.00 0.00 2.92
1824 2276 1.002315 GACAGGTGCCATGCCAAAAAT 59.998 47.619 0.00 0.00 0.00 1.82
1860 2312 9.113838 ACAAACTCAAATTAAGCTCGATCATAT 57.886 29.630 0.00 0.00 0.00 1.78
1901 2408 7.274250 GCTAAATTGATTTGACTGAAAGCGATT 59.726 33.333 0.00 0.00 43.14 3.34
1951 2458 4.016706 GCTACGGGGTGGTGCTGT 62.017 66.667 0.00 0.00 0.00 4.40
2039 2546 3.204827 GGCGTTGCCGATGCTGAT 61.205 61.111 0.00 0.00 39.62 2.90
2218 2725 2.357881 TGCAGCAACTGGAGCTCG 60.358 61.111 7.83 0.00 41.14 5.03
2253 2760 8.463930 ACTTGTGATCCTCATTTCAAGTTTTA 57.536 30.769 0.00 0.00 41.31 1.52
2267 2774 1.425448 AGTTTTAGTCCAGGCCTTGCT 59.575 47.619 0.00 3.84 0.00 3.91
2272 2779 3.177884 TCCAGGCCTTGCTGGTGT 61.178 61.111 0.00 0.00 41.28 4.16
2302 2809 1.406898 CATCGCCTCTACTTCAGCTCA 59.593 52.381 0.00 0.00 0.00 4.26
2304 2811 2.932261 TCGCCTCTACTTCAGCTCATA 58.068 47.619 0.00 0.00 0.00 2.15
2312 2819 5.196695 TCTACTTCAGCTCATAGAAGCAGA 58.803 41.667 10.57 9.94 45.00 4.26
2371 2878 0.690744 TATAGCAGGCAGGCAGGTGA 60.691 55.000 0.92 0.00 35.83 4.02
2387 2894 4.318332 CAGGTGAAGTGTTCTTGATGCTA 58.682 43.478 0.00 0.00 33.64 3.49
2444 2951 3.656045 GTGTGCGGGTGGAAACGG 61.656 66.667 0.00 0.00 0.00 4.44
2445 2952 3.862991 TGTGCGGGTGGAAACGGA 61.863 61.111 0.00 0.00 0.00 4.69
2463 2970 5.407407 ACGGACTCTGATAGTTTGTCAAT 57.593 39.130 0.00 0.00 39.07 2.57
2465 2972 7.113658 ACGGACTCTGATAGTTTGTCAATAT 57.886 36.000 0.00 0.00 39.07 1.28
2466 2973 7.203910 ACGGACTCTGATAGTTTGTCAATATC 58.796 38.462 0.00 0.88 39.07 1.63
2478 2985 8.794335 AGTTTGTCAATATCCTTCCTTAGTTC 57.206 34.615 0.00 0.00 0.00 3.01
2491 2998 2.555227 CCTTAGTTCCTTGGGCACACAT 60.555 50.000 0.00 0.00 0.00 3.21
2518 3025 5.584551 AAGACCTGTAAAACCCTCTTGAT 57.415 39.130 0.00 0.00 0.00 2.57
2546 3053 6.291067 TGTTACTCGTAGGTGTGTATATCG 57.709 41.667 0.60 0.00 0.00 2.92
2594 3102 1.303309 CCAACATGAAGCCGATCCTC 58.697 55.000 0.00 0.00 0.00 3.71
2624 3132 0.249398 GAGGCAAGTCGGGAAGCTAA 59.751 55.000 0.00 0.00 0.00 3.09
2682 3190 7.428826 AGCAAGTTAGAGTCCTTTTGAAATTG 58.571 34.615 0.00 0.00 0.00 2.32
2685 3193 9.237846 CAAGTTAGAGTCCTTTTGAAATTGAAC 57.762 33.333 0.00 0.00 0.00 3.18
2704 3212 3.004752 ACTGGAACTGTTGAACAAGCT 57.995 42.857 0.00 0.00 37.12 3.74
2711 3219 6.096141 TGGAACTGTTGAACAAGCTAAATGAA 59.904 34.615 0.00 0.00 0.00 2.57
2765 3273 5.901552 AGCTGAAACGGATCTTTTGAAAAA 58.098 33.333 0.00 0.00 0.00 1.94
2768 3276 6.420604 GCTGAAACGGATCTTTTGAAAAATGA 59.579 34.615 0.00 0.00 0.00 2.57
2776 3284 9.624697 CGGATCTTTTGAAAAATGAACTCAATA 57.375 29.630 0.00 0.00 0.00 1.90
2830 3338 7.696981 TGAAACTAGAGAGTCCTTCCTAAGTA 58.303 38.462 0.00 0.00 33.58 2.24
2937 3445 0.463654 AGCCAAACGTTGTCAGAGCA 60.464 50.000 0.00 0.00 0.00 4.26
2956 3464 7.831690 TCAGAGCATGGGTTAACATTTACAATA 59.168 33.333 8.10 0.00 0.00 1.90
2958 3466 8.850156 AGAGCATGGGTTAACATTTACAATATC 58.150 33.333 8.10 0.00 0.00 1.63
2965 3473 7.343574 GGGTTAACATTTACAATATCAAGGGGT 59.656 37.037 8.10 0.00 0.00 4.95
2977 3485 9.862149 ACAATATCAAGGGGTATAACTAAAAGG 57.138 33.333 0.00 0.00 0.00 3.11
3001 3509 6.874134 GGTAGAGAAGTAAAGTTCATTGCAGA 59.126 38.462 0.68 0.00 0.00 4.26
3061 3569 7.472100 CGATCTTTCAATGAGGGGTAACTATCT 60.472 40.741 0.00 0.00 0.00 1.98
3066 3574 7.938140 TCAATGAGGGGTAACTATCTTTTTG 57.062 36.000 0.00 0.00 0.00 2.44
3075 3584 6.822170 GGGTAACTATCTTTTTGGTGGAGTAG 59.178 42.308 0.00 0.00 0.00 2.57
3116 3625 2.645510 CGTGTGAAGACGTCGTGCC 61.646 63.158 9.23 0.00 34.56 5.01
3117 3626 1.299926 GTGTGAAGACGTCGTGCCT 60.300 57.895 9.23 0.00 0.00 4.75
3141 3650 7.170828 CCTTAGCAATTGTTAAACCAACTTTCC 59.829 37.037 14.60 0.00 38.05 3.13
3145 3654 6.500041 CAATTGTTAAACCAACTTTCCGAGA 58.500 36.000 0.00 0.00 38.05 4.04
3156 3665 6.426025 ACCAACTTTCCGAGATTACTAACAAC 59.574 38.462 0.00 0.00 0.00 3.32
3158 3667 7.041644 CCAACTTTCCGAGATTACTAACAACAA 60.042 37.037 0.00 0.00 0.00 2.83
3174 3683 3.256631 ACAACAAAGGAGCATGATCAACC 59.743 43.478 13.85 1.46 0.00 3.77
3182 3691 0.729116 GCATGATCAACCTGACCACG 59.271 55.000 0.00 0.00 0.00 4.94
3185 3694 2.455674 TGATCAACCTGACCACGAAG 57.544 50.000 0.00 0.00 0.00 3.79
3187 3696 0.321653 ATCAACCTGACCACGAAGGC 60.322 55.000 0.00 0.00 43.14 4.35
3265 3774 9.111702 GATATTGCGAATTAAGATGAAAGCTTC 57.888 33.333 0.00 0.00 38.98 3.86
3269 3778 6.748658 TGCGAATTAAGATGAAAGCTTCATTG 59.251 34.615 0.00 0.00 38.98 2.82
3297 3806 1.588674 TGCGGTTTCGTGAACATCTT 58.411 45.000 6.73 0.00 40.13 2.40
3320 3829 2.773487 CCTGGTCGTTGGACACAAATA 58.227 47.619 0.00 0.00 45.28 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 7.272144 ACCATCACTTTCTTCCCTTTATACT 57.728 36.000 0.00 0.00 0.00 2.12
112 118 2.622470 GAGGAGGATCGGTACTTGGTAC 59.378 54.545 0.00 0.00 38.19 3.34
137 143 2.507407 ACACAGAGAGAGAGAGACCC 57.493 55.000 0.00 0.00 0.00 4.46
163 175 2.632996 TGGTCACAGACGAAAGAGGAAT 59.367 45.455 0.00 0.00 32.65 3.01
164 176 2.036387 TGGTCACAGACGAAAGAGGAA 58.964 47.619 0.00 0.00 32.65 3.36
165 177 1.699730 TGGTCACAGACGAAAGAGGA 58.300 50.000 0.00 0.00 32.65 3.71
166 178 2.135933 GTTGGTCACAGACGAAAGAGG 58.864 52.381 0.00 0.00 32.60 3.69
176 188 2.802816 CGGAGAGAAAAGTTGGTCACAG 59.197 50.000 0.00 0.00 0.00 3.66
244 256 1.078637 ACGAGAGTCCGGACGATCA 60.079 57.895 29.60 0.00 44.19 2.92
277 289 7.391833 AGAAGACGATCACTATGTCTATATGCA 59.608 37.037 0.00 0.00 41.88 3.96
289 301 6.591750 AAGAAAGGAAGAAGACGATCACTA 57.408 37.500 0.00 0.00 0.00 2.74
441 459 1.741706 CAGCAGTTGCCCATAAGACAG 59.258 52.381 0.00 0.00 43.38 3.51
453 471 2.268076 CCCCCGAAACCAGCAGTTG 61.268 63.158 0.00 0.00 39.19 3.16
609 627 0.328258 CCCAATCAGGACTTCCGGTT 59.672 55.000 0.00 0.00 41.22 4.44
663 681 4.657969 TGGGTGGTCAAAATTTCAGGAAAT 59.342 37.500 1.50 1.50 42.35 2.17
680 698 0.824759 GAGCTAGTGGTAGTGGGTGG 59.175 60.000 0.00 0.00 0.00 4.61
714 732 8.616076 CGCCAACTGAATTATCTCTCTTTAAAT 58.384 33.333 0.00 0.00 0.00 1.40
717 735 6.535150 CACGCCAACTGAATTATCTCTCTTTA 59.465 38.462 0.00 0.00 0.00 1.85
739 757 2.972625 ACTGTCAATACCATCACCACG 58.027 47.619 0.00 0.00 0.00 4.94
1050 1069 0.918983 CCTGGAAGCTGTTATCCCCA 59.081 55.000 0.00 0.00 34.68 4.96
1080 1099 1.840737 TAGAGAGACTGACCAGCCAC 58.159 55.000 0.00 0.00 0.00 5.01
1114 1137 6.825721 TGTAGGTGCCAATTTGAAAACAAAAT 59.174 30.769 0.00 0.00 0.00 1.82
1119 1145 4.944048 AGTGTAGGTGCCAATTTGAAAAC 58.056 39.130 0.00 0.00 0.00 2.43
1123 1149 8.301002 GTTTAATTAGTGTAGGTGCCAATTTGA 58.699 33.333 0.00 0.00 0.00 2.69
1131 1157 6.872020 TGTGAGAGTTTAATTAGTGTAGGTGC 59.128 38.462 0.00 0.00 0.00 5.01
1149 1175 8.962679 AGTAGGAGTAGTAAAGATTTGTGAGAG 58.037 37.037 0.00 0.00 0.00 3.20
1217 1669 9.982291 CACGCTTACAATTACTACATTTATGTT 57.018 29.630 0.02 0.00 41.97 2.71
1218 1670 8.609176 CCACGCTTACAATTACTACATTTATGT 58.391 33.333 0.53 0.53 44.48 2.29
1219 1671 8.609176 ACCACGCTTACAATTACTACATTTATG 58.391 33.333 0.00 0.00 0.00 1.90
1220 1672 8.726870 ACCACGCTTACAATTACTACATTTAT 57.273 30.769 0.00 0.00 0.00 1.40
1221 1673 9.304731 CTACCACGCTTACAATTACTACATTTA 57.695 33.333 0.00 0.00 0.00 1.40
1222 1674 7.279313 CCTACCACGCTTACAATTACTACATTT 59.721 37.037 0.00 0.00 0.00 2.32
1223 1675 6.759827 CCTACCACGCTTACAATTACTACATT 59.240 38.462 0.00 0.00 0.00 2.71
1224 1676 6.127253 ACCTACCACGCTTACAATTACTACAT 60.127 38.462 0.00 0.00 0.00 2.29
1225 1677 5.185635 ACCTACCACGCTTACAATTACTACA 59.814 40.000 0.00 0.00 0.00 2.74
1226 1678 5.517770 CACCTACCACGCTTACAATTACTAC 59.482 44.000 0.00 0.00 0.00 2.73
1227 1679 5.653507 CACCTACCACGCTTACAATTACTA 58.346 41.667 0.00 0.00 0.00 1.82
1228 1680 4.501071 CACCTACCACGCTTACAATTACT 58.499 43.478 0.00 0.00 0.00 2.24
1229 1681 3.063045 GCACCTACCACGCTTACAATTAC 59.937 47.826 0.00 0.00 0.00 1.89
1230 1682 3.264104 GCACCTACCACGCTTACAATTA 58.736 45.455 0.00 0.00 0.00 1.40
1231 1683 2.081462 GCACCTACCACGCTTACAATT 58.919 47.619 0.00 0.00 0.00 2.32
1232 1684 1.002659 TGCACCTACCACGCTTACAAT 59.997 47.619 0.00 0.00 0.00 2.71
1233 1685 0.393448 TGCACCTACCACGCTTACAA 59.607 50.000 0.00 0.00 0.00 2.41
1234 1686 0.037697 CTGCACCTACCACGCTTACA 60.038 55.000 0.00 0.00 0.00 2.41
1259 1711 0.459759 GTCAGGCTAGGCGTACAACC 60.460 60.000 11.10 0.00 0.00 3.77
1262 1714 0.530744 CTTGTCAGGCTAGGCGTACA 59.469 55.000 18.49 18.49 0.00 2.90
1264 1716 1.254975 TGCTTGTCAGGCTAGGCGTA 61.255 55.000 11.10 0.00 0.00 4.42
1266 1718 1.153289 ATGCTTGTCAGGCTAGGCG 60.153 57.895 11.10 6.24 0.00 5.52
1268 1720 3.577848 AGATAGATGCTTGTCAGGCTAGG 59.422 47.826 8.55 0.00 0.00 3.02
1292 1744 2.742053 TCTCGACACAAAAAGGCATAGC 59.258 45.455 0.00 0.00 0.00 2.97
1309 1761 5.515797 TCAACTCCACCTACATAATCTCG 57.484 43.478 0.00 0.00 0.00 4.04
1313 1765 7.682787 AGAAGATCAACTCCACCTACATAAT 57.317 36.000 0.00 0.00 0.00 1.28
1323 1775 1.004745 GGCCCAAGAAGATCAACTCCA 59.995 52.381 0.00 0.00 0.00 3.86
1328 1780 1.075601 AGGTGGCCCAAGAAGATCAA 58.924 50.000 0.00 0.00 0.00 2.57
1357 1809 0.321653 CCGCTAGCTTCACCAGGTTT 60.322 55.000 13.93 0.00 34.13 3.27
1494 1946 0.532862 CTCTGGACACGCACCAAACT 60.533 55.000 0.00 0.00 36.95 2.66
1510 1962 0.463295 CCATCAATCGCACCTGCTCT 60.463 55.000 0.00 0.00 39.32 4.09
1515 1967 1.671979 CACATCCATCAATCGCACCT 58.328 50.000 0.00 0.00 0.00 4.00
1524 1976 5.047164 CCTGAAATGAAAACCACATCCATCA 60.047 40.000 0.00 0.00 0.00 3.07
1529 1981 3.578282 ACCCCTGAAATGAAAACCACATC 59.422 43.478 0.00 0.00 0.00 3.06
1533 1985 3.320610 TCACCCCTGAAATGAAAACCA 57.679 42.857 0.00 0.00 0.00 3.67
1602 2054 3.661648 GGAAAGCCAGGCCCCTCA 61.662 66.667 8.22 0.00 0.00 3.86
1780 2232 2.362760 TACTCTGGGGCGGCGTAA 60.363 61.111 9.37 0.00 0.00 3.18
1824 2276 9.640963 GCTTAATTTGAGTTTGTAGTCTCTCTA 57.359 33.333 0.00 0.00 0.00 2.43
1860 2312 6.953101 TCAATTTAGCCACCAGACAAGTATA 58.047 36.000 0.00 0.00 0.00 1.47
1865 2317 5.538053 TCAAATCAATTTAGCCACCAGACAA 59.462 36.000 0.00 0.00 0.00 3.18
1866 2318 5.048083 GTCAAATCAATTTAGCCACCAGACA 60.048 40.000 0.00 0.00 0.00 3.41
1951 2458 3.074281 CCCCGTAACCAGCTCCAA 58.926 61.111 0.00 0.00 0.00 3.53
1962 2469 3.307906 AGTGACTTGCGCCCCGTA 61.308 61.111 4.18 0.00 0.00 4.02
1977 2484 1.525995 CGGCCAACACTTGTCCAGT 60.526 57.895 2.24 0.00 35.35 4.00
2039 2546 2.571212 CCAACACCTACTTCTTGTGCA 58.429 47.619 0.00 0.00 33.30 4.57
2050 2557 2.359994 GGTCTAGGATCCCCAACACCTA 60.360 54.545 8.55 0.00 34.42 3.08
2218 2725 2.200170 GATCACAAGTTGGCGGGCAC 62.200 60.000 2.73 0.00 0.00 5.01
2267 2774 1.675714 GCGATGGATCTGACAACACCA 60.676 52.381 0.00 0.00 35.09 4.17
2272 2779 1.489481 AGAGGCGATGGATCTGACAA 58.511 50.000 0.00 0.00 0.00 3.18
2302 2809 8.016301 TCACATGAATTCTAGTCTGCTTCTAT 57.984 34.615 7.05 0.00 0.00 1.98
2304 2811 6.291648 TCACATGAATTCTAGTCTGCTTCT 57.708 37.500 7.05 0.00 0.00 2.85
2333 2840 5.760253 GCTATACTAGGCAATCACACACAAT 59.240 40.000 0.00 0.00 0.00 2.71
2334 2841 5.116180 GCTATACTAGGCAATCACACACAA 58.884 41.667 0.00 0.00 0.00 3.33
2387 2894 8.964476 ACTCGGAAGAATGTACAATCATTTAT 57.036 30.769 13.30 0.00 41.32 1.40
2399 2906 2.550208 GGTCCACAACTCGGAAGAATGT 60.550 50.000 0.00 0.00 41.32 2.71
2430 2937 3.524648 GAGTCCGTTTCCACCCGCA 62.525 63.158 0.00 0.00 0.00 5.69
2444 2951 9.255304 GAAGGATATTGACAAACTATCAGAGTC 57.745 37.037 9.81 0.00 37.44 3.36
2445 2952 8.207545 GGAAGGATATTGACAAACTATCAGAGT 58.792 37.037 9.81 0.00 41.56 3.24
2463 2970 3.458487 GCCCAAGGAACTAAGGAAGGATA 59.542 47.826 0.00 0.00 38.49 2.59
2465 2972 1.633945 GCCCAAGGAACTAAGGAAGGA 59.366 52.381 0.00 0.00 38.49 3.36
2466 2973 1.354368 TGCCCAAGGAACTAAGGAAGG 59.646 52.381 0.00 0.00 38.49 3.46
2478 2985 2.364970 TCTTTTTGATGTGTGCCCAAGG 59.635 45.455 0.00 0.00 0.00 3.61
2491 2998 5.762279 AGAGGGTTTTACAGGTCTTTTTGA 58.238 37.500 0.00 0.00 0.00 2.69
2524 3031 5.466728 TCCGATATACACACCTACGAGTAAC 59.533 44.000 0.00 0.00 0.00 2.50
2573 3081 1.837439 AGGATCGGCTTCATGTTGGTA 59.163 47.619 0.00 0.00 0.00 3.25
2581 3089 3.206150 GCAAATTAGAGGATCGGCTTCA 58.794 45.455 0.00 0.00 42.67 3.02
2615 3123 3.570125 ACAAAAGAGCACTTTAGCTTCCC 59.430 43.478 9.64 0.00 46.75 3.97
2645 3153 5.061721 TCTAACTTGCTTTCCCCTTCTTT 57.938 39.130 0.00 0.00 0.00 2.52
2646 3154 4.104897 ACTCTAACTTGCTTTCCCCTTCTT 59.895 41.667 0.00 0.00 0.00 2.52
2647 3155 3.653352 ACTCTAACTTGCTTTCCCCTTCT 59.347 43.478 0.00 0.00 0.00 2.85
2648 3156 4.004314 GACTCTAACTTGCTTTCCCCTTC 58.996 47.826 0.00 0.00 0.00 3.46
2649 3157 3.244946 GGACTCTAACTTGCTTTCCCCTT 60.245 47.826 0.00 0.00 0.00 3.95
2650 3158 2.306219 GGACTCTAACTTGCTTTCCCCT 59.694 50.000 0.00 0.00 0.00 4.79
2682 3190 3.378427 AGCTTGTTCAACAGTTCCAGTTC 59.622 43.478 0.00 0.00 0.00 3.01
2685 3193 5.499139 TTTAGCTTGTTCAACAGTTCCAG 57.501 39.130 0.00 0.00 0.00 3.86
2830 3338 2.285368 TGGGTGCCGGATCCTCTT 60.285 61.111 5.05 0.00 0.00 2.85
2886 3394 5.725338 AGAGGATATCAGGCATGTATGATGT 59.275 40.000 19.18 14.74 36.81 3.06
2937 3445 8.923270 CCCTTGATATTGTAAATGTTAACCCAT 58.077 33.333 2.48 0.00 0.00 4.00
2956 3464 8.865244 TCTACCTTTTAGTTATACCCCTTGAT 57.135 34.615 0.00 0.00 0.00 2.57
2958 3466 8.315220 TCTCTACCTTTTAGTTATACCCCTTG 57.685 38.462 0.00 0.00 0.00 3.61
2977 3485 7.815068 TCTCTGCAATGAACTTTACTTCTCTAC 59.185 37.037 0.00 0.00 0.00 2.59
3001 3509 7.336427 CCTGCTCTATCAAAATCTGTCTTTTCT 59.664 37.037 0.00 0.00 0.00 2.52
3061 3569 4.573201 CGTGAAAGTCTACTCCACCAAAAA 59.427 41.667 8.89 0.00 0.00 1.94
3066 3574 3.429135 GGATCGTGAAAGTCTACTCCACC 60.429 52.174 8.89 0.00 0.00 4.61
3075 3584 2.094894 TCGTAGTCGGATCGTGAAAGTC 59.905 50.000 0.00 0.00 37.69 3.01
3116 3625 7.096230 CGGAAAGTTGGTTTAACAATTGCTAAG 60.096 37.037 5.05 0.00 41.88 2.18
3117 3626 6.697892 CGGAAAGTTGGTTTAACAATTGCTAA 59.302 34.615 5.05 0.63 41.88 3.09
3125 3634 6.993902 AGTAATCTCGGAAAGTTGGTTTAACA 59.006 34.615 0.00 0.00 41.88 2.41
3126 3635 7.430992 AGTAATCTCGGAAAGTTGGTTTAAC 57.569 36.000 0.00 0.00 39.65 2.01
3127 3636 8.992073 GTTAGTAATCTCGGAAAGTTGGTTTAA 58.008 33.333 0.00 0.00 0.00 1.52
3128 3637 8.149647 TGTTAGTAATCTCGGAAAGTTGGTTTA 58.850 33.333 0.00 0.00 0.00 2.01
3133 3642 7.416154 TGTTGTTAGTAATCTCGGAAAGTTG 57.584 36.000 0.00 0.00 0.00 3.16
3141 3650 5.637810 TGCTCCTTTGTTGTTAGTAATCTCG 59.362 40.000 0.00 0.00 0.00 4.04
3145 3654 7.611467 TGATCATGCTCCTTTGTTGTTAGTAAT 59.389 33.333 0.00 0.00 0.00 1.89
3156 3665 3.128242 GTCAGGTTGATCATGCTCCTTTG 59.872 47.826 0.00 0.00 0.00 2.77
3158 3667 2.356535 GGTCAGGTTGATCATGCTCCTT 60.357 50.000 0.00 0.00 0.00 3.36
3174 3683 2.280628 GAATTAGGCCTTCGTGGTCAG 58.719 52.381 12.58 0.00 44.59 3.51
3182 3691 1.339291 GCATGCAGGAATTAGGCCTTC 59.661 52.381 12.58 1.33 32.12 3.46
3185 3694 1.113788 TTGCATGCAGGAATTAGGCC 58.886 50.000 21.50 0.00 0.00 5.19
3187 3696 4.659111 TCATTTGCATGCAGGAATTAGG 57.341 40.909 21.50 7.42 0.00 2.69
3265 3774 4.915085 ACGAAACCGCAAACTTTATCAATG 59.085 37.500 0.00 0.00 0.00 2.82
3269 3778 4.136517 TCACGAAACCGCAAACTTTATC 57.863 40.909 0.00 0.00 0.00 1.75
3297 3806 3.164977 TGTCCAACGACCAGGCCA 61.165 61.111 5.01 0.00 38.32 5.36


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

AutoCloner maintained by Alex Coulton.