Multiple sequence alignment - TraesCS4D01G336700

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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 TraesCS4D01G336700 chr4D 100.000 5575 0 0 1 5575 494274143 494268569 0.000000e+00 10296
1 TraesCS4D01G336700 chr5A 92.351 5151 205 61 537 5575 673779503 673774430 0.000000e+00 7155
2 TraesCS4D01G336700 chr5A 87.243 243 9 4 19 261 673779908 673779688 1.990000e-64 257
3 TraesCS4D01G336700 chr5A 86.093 151 18 3 264 412 414421180 414421031 5.780000e-35 159
4 TraesCS4D01G336700 chr4B 91.387 5062 172 76 5 4888 633767079 633762104 0.000000e+00 6689
5 TraesCS4D01G336700 chr4B 92.910 677 27 10 4918 5575 633762108 633761434 0.000000e+00 965
6 TraesCS4D01G336700 chr3A 96.460 113 4 0 300 412 64085283 64085395 2.650000e-43 187
7 TraesCS4D01G336700 chr2D 96.460 113 4 0 300 412 5672136 5672248 2.650000e-43 187
8 TraesCS4D01G336700 chr2D 96.460 113 4 0 300 412 579754409 579754521 2.650000e-43 187
9 TraesCS4D01G336700 chr2A 96.460 113 4 0 300 412 3002394 3002506 2.650000e-43 187
10 TraesCS4D01G336700 chr1B 96.460 113 4 0 300 412 384211013 384211125 2.650000e-43 187
11 TraesCS4D01G336700 chr1A 96.460 113 4 0 300 412 355717964 355717852 2.650000e-43 187
12 TraesCS4D01G336700 chr6D 95.614 114 5 0 298 411 388330732 388330845 3.430000e-42 183
13 TraesCS4D01G336700 chr5D 94.068 118 7 0 300 417 296366760 296366643 4.440000e-41 180


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 TraesCS4D01G336700 chr4D 494268569 494274143 5574 True 10296 10296 100.0000 1 5575 1 chr4D.!!$R1 5574
1 TraesCS4D01G336700 chr5A 673774430 673779908 5478 True 3706 7155 89.7970 19 5575 2 chr5A.!!$R2 5556
2 TraesCS4D01G336700 chr4B 633761434 633767079 5645 True 3827 6689 92.1485 5 5575 2 chr4B.!!$R1 5570

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
127 129 0.179045 GACCCGCTAACTCCATGCAT 60.179 55.0 0.0 0.0 0.00 3.96 F
128 130 0.255890 ACCCGCTAACTCCATGCATT 59.744 50.0 0.0 0.0 0.00 3.56 F
1955 2130 0.170116 GCCATGCGAAATCCGTCAAA 59.830 50.0 0.0 0.0 41.15 2.69 F
3317 3586 0.870393 CAACGAGACACTTGCAGCAT 59.130 50.0 0.0 0.0 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1646 1812 0.249615 CATGCACGGACGGATGAGAT 60.250 55.0 0.0 0.0 36.90 2.75 R
1974 2158 0.469917 ATCAACGGCTGGGATGGTAG 59.530 55.0 0.0 0.0 0.00 3.18 R
3336 3605 0.033503 TATGCTGGTCTCTCCGGTCA 60.034 55.0 0.0 0.0 44.16 4.02 R
4907 5186 0.035458 CTTCCACGCCTTGTTCTCCT 59.965 55.0 0.0 0.0 0.00 3.69 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
124 126 0.527817 GTCGACCCGCTAACTCCATG 60.528 60.000 3.51 0.00 0.00 3.66
125 127 1.883084 CGACCCGCTAACTCCATGC 60.883 63.158 0.00 0.00 0.00 4.06
126 128 1.220749 GACCCGCTAACTCCATGCA 59.779 57.895 0.00 0.00 0.00 3.96
127 129 0.179045 GACCCGCTAACTCCATGCAT 60.179 55.000 0.00 0.00 0.00 3.96
128 130 0.255890 ACCCGCTAACTCCATGCATT 59.744 50.000 0.00 0.00 0.00 3.56
129 131 1.340991 ACCCGCTAACTCCATGCATTT 60.341 47.619 0.00 0.00 0.00 2.32
130 132 1.334869 CCCGCTAACTCCATGCATTTC 59.665 52.381 0.00 0.00 0.00 2.17
131 133 1.334869 CCGCTAACTCCATGCATTTCC 59.665 52.381 0.00 0.00 0.00 3.13
132 134 1.334869 CGCTAACTCCATGCATTTCCC 59.665 52.381 0.00 0.00 0.00 3.97
133 135 1.683385 GCTAACTCCATGCATTTCCCC 59.317 52.381 0.00 0.00 0.00 4.81
134 136 1.949525 CTAACTCCATGCATTTCCCCG 59.050 52.381 0.00 0.00 0.00 5.73
135 137 0.331278 AACTCCATGCATTTCCCCGA 59.669 50.000 0.00 0.00 0.00 5.14
136 138 0.552848 ACTCCATGCATTTCCCCGAT 59.447 50.000 0.00 0.00 0.00 4.18
137 139 1.774254 ACTCCATGCATTTCCCCGATA 59.226 47.619 0.00 0.00 0.00 2.92
138 140 2.154462 CTCCATGCATTTCCCCGATAC 58.846 52.381 0.00 0.00 0.00 2.24
139 141 1.202879 TCCATGCATTTCCCCGATACC 60.203 52.381 0.00 0.00 0.00 2.73
140 142 1.202927 CCATGCATTTCCCCGATACCT 60.203 52.381 0.00 0.00 0.00 3.08
141 143 2.154462 CATGCATTTCCCCGATACCTC 58.846 52.381 0.00 0.00 0.00 3.85
190 192 8.388103 GCGTAATCACAACAGTAATAATCAACT 58.612 33.333 0.00 0.00 0.00 3.16
253 262 5.723405 CCATCATCCAGATTATCACTCCCTA 59.277 44.000 0.00 0.00 33.72 3.53
347 366 5.470047 AATTACATCCAGATCCGTAGACC 57.530 43.478 0.00 0.00 0.00 3.85
374 393 1.979469 CGACGACTACAAGCACTGAAG 59.021 52.381 0.00 0.00 0.00 3.02
580 671 4.335400 AATCATTGAACGCCAAAAGGTT 57.665 36.364 0.00 0.00 38.43 3.50
728 827 5.114081 GGTTAATTCAGTTCCGCTAGCTAA 58.886 41.667 13.93 4.14 0.00 3.09
729 828 5.234543 GGTTAATTCAGTTCCGCTAGCTAAG 59.765 44.000 13.93 1.32 0.00 2.18
761 862 4.606457 ATCAGCTTTAGTCGTTGATTGC 57.394 40.909 0.00 0.00 0.00 3.56
879 986 3.157881 CCCTTTTGACCCTTCTTCTTCC 58.842 50.000 0.00 0.00 0.00 3.46
880 987 3.181428 CCCTTTTGACCCTTCTTCTTCCT 60.181 47.826 0.00 0.00 0.00 3.36
881 988 4.075682 CCTTTTGACCCTTCTTCTTCCTC 58.924 47.826 0.00 0.00 0.00 3.71
882 989 3.790089 TTTGACCCTTCTTCTTCCTCC 57.210 47.619 0.00 0.00 0.00 4.30
971 1080 5.874810 TCTTCAATTCACCACTAGATTTCCG 59.125 40.000 0.00 0.00 0.00 4.30
972 1081 5.414789 TCAATTCACCACTAGATTTCCGA 57.585 39.130 0.00 0.00 0.00 4.55
988 1097 1.341156 CCGAATCTCCAGCCCCTTCT 61.341 60.000 0.00 0.00 0.00 2.85
990 1099 1.474143 CGAATCTCCAGCCCCTTCTTC 60.474 57.143 0.00 0.00 0.00 2.87
991 1100 1.561542 GAATCTCCAGCCCCTTCTTCA 59.438 52.381 0.00 0.00 0.00 3.02
992 1101 1.904440 ATCTCCAGCCCCTTCTTCAT 58.096 50.000 0.00 0.00 0.00 2.57
993 1102 2.568546 TCTCCAGCCCCTTCTTCATA 57.431 50.000 0.00 0.00 0.00 2.15
999 1134 1.211457 AGCCCCTTCTTCATAGCACAG 59.789 52.381 0.00 0.00 0.00 3.66
1007 1142 5.697178 CCTTCTTCATAGCACAGATGATGAG 59.303 44.000 0.00 0.00 38.19 2.90
1072 1207 1.000385 GCATTGTAAGCACACAAGCCA 60.000 47.619 8.78 0.00 41.48 4.75
1074 1210 2.340210 TTGTAAGCACACAAGCCAGA 57.660 45.000 0.00 0.00 33.55 3.86
1092 1228 6.779860 AGCCAGACTCTTCAACCTTAATTTA 58.220 36.000 0.00 0.00 0.00 1.40
1133 1269 6.410942 TCCGCTGCATGCTTCTATATATAT 57.589 37.500 20.33 0.00 40.11 0.86
1134 1270 7.524717 TCCGCTGCATGCTTCTATATATATA 57.475 36.000 20.33 2.49 40.11 0.86
1135 1271 8.127150 TCCGCTGCATGCTTCTATATATATAT 57.873 34.615 20.33 10.10 40.11 0.86
1136 1272 9.243105 TCCGCTGCATGCTTCTATATATATATA 57.757 33.333 20.33 11.21 40.11 0.86
1181 1317 0.673644 TCTCGCTTGCCTTGCTTACC 60.674 55.000 0.00 0.00 0.00 2.85
1189 1325 1.247567 GCCTTGCTTACCTTGCTTCA 58.752 50.000 0.00 0.00 0.00 3.02
1199 1335 6.658816 TGCTTACCTTGCTTCATTCAAATCTA 59.341 34.615 0.00 0.00 0.00 1.98
1200 1336 6.969473 GCTTACCTTGCTTCATTCAAATCTAC 59.031 38.462 0.00 0.00 0.00 2.59
1201 1337 7.148171 GCTTACCTTGCTTCATTCAAATCTACT 60.148 37.037 0.00 0.00 0.00 2.57
1236 1374 2.309693 TCGCTAACGTAACGTGTCTTG 58.690 47.619 0.00 0.00 39.99 3.02
1332 1475 9.820725 TGGCTTCTTGATTTTATTTATCCATTG 57.179 29.630 0.00 0.00 0.00 2.82
1357 1500 9.932699 TGCTTGAAAAATTATCATGTTTGTTTG 57.067 25.926 0.00 0.00 0.00 2.93
1496 1657 2.612212 GACTTGACGTCCTTTTCTTGCA 59.388 45.455 14.12 0.00 36.62 4.08
1520 1681 4.959839 TGGTAAAGCCTCTTCCAAAGTTTT 59.040 37.500 0.00 0.00 38.35 2.43
1527 1688 4.142160 GCCTCTTCCAAAGTTTTGACAGTT 60.142 41.667 6.18 0.00 40.55 3.16
1639 1805 0.594796 CTTGCACTTTGTTCACCGGC 60.595 55.000 0.00 0.00 0.00 6.13
1646 1812 4.513692 GCACTTTGTTCACCGGCATATATA 59.486 41.667 0.00 0.00 0.00 0.86
1677 1850 4.057224 TGCATGACACAACCGACC 57.943 55.556 0.00 0.00 0.00 4.79
1751 1924 4.440103 CGCTTCTATTTCATCTGCAAATGC 59.560 41.667 0.00 0.00 42.50 3.56
1953 2128 3.496711 GCCATGCGAAATCCGTCA 58.503 55.556 0.00 0.00 41.15 4.35
1954 2129 1.800032 GCCATGCGAAATCCGTCAA 59.200 52.632 0.00 0.00 41.15 3.18
1955 2130 0.170116 GCCATGCGAAATCCGTCAAA 59.830 50.000 0.00 0.00 41.15 2.69
1974 2158 5.460419 GTCAAATGATCAGAGACGACCATAC 59.540 44.000 0.09 0.00 0.00 2.39
2148 2362 2.306255 TAACCCATCTTCCTCGCCGC 62.306 60.000 0.00 0.00 0.00 6.53
2228 2442 5.200483 ACAGAACAGTTCCAAGGAATTTGA 58.800 37.500 9.85 0.00 39.21 2.69
2232 2446 3.758554 ACAGTTCCAAGGAATTTGATCCG 59.241 43.478 17.66 1.20 44.60 4.18
2372 2587 2.787473 TGTAGAAACATGCTCCAGGG 57.213 50.000 0.00 0.00 0.00 4.45
2445 2706 3.620488 TCCTTGGGTGATAACTCAATGC 58.380 45.455 0.00 0.00 31.85 3.56
2582 2844 6.718454 CCCGAGGAAGTACCAGACTATAATTA 59.282 42.308 0.00 0.00 37.44 1.40
2583 2845 7.094291 CCCGAGGAAGTACCAGACTATAATTAG 60.094 44.444 0.00 0.00 37.44 1.73
2584 2846 7.447853 CCGAGGAAGTACCAGACTATAATTAGT 59.552 40.741 0.00 0.00 40.26 2.24
2585 2847 8.848182 CGAGGAAGTACCAGACTATAATTAGTT 58.152 37.037 0.00 0.00 38.81 2.24
2614 2876 6.007076 ACCAAAATCCCAGTGTTTTTGTTTT 58.993 32.000 15.93 3.02 40.01 2.43
2915 3181 8.135382 ACCTTAGTACTCAAGAACATACATGT 57.865 34.615 2.69 2.69 44.20 3.21
2916 3182 8.035394 ACCTTAGTACTCAAGAACATACATGTG 58.965 37.037 9.11 0.00 41.61 3.21
2917 3183 8.251026 CCTTAGTACTCAAGAACATACATGTGA 58.749 37.037 9.11 0.00 41.61 3.58
2918 3184 8.981724 TTAGTACTCAAGAACATACATGTGAC 57.018 34.615 9.11 0.00 41.61 3.67
2920 3186 7.671302 AGTACTCAAGAACATACATGTGACTT 58.329 34.615 9.11 4.08 41.61 3.01
2921 3187 8.150945 AGTACTCAAGAACATACATGTGACTTT 58.849 33.333 9.11 0.00 41.61 2.66
2922 3188 9.419297 GTACTCAAGAACATACATGTGACTTTA 57.581 33.333 9.11 0.00 41.61 1.85
2923 3189 8.311650 ACTCAAGAACATACATGTGACTTTAC 57.688 34.615 9.11 0.00 41.61 2.01
2924 3190 8.150945 ACTCAAGAACATACATGTGACTTTACT 58.849 33.333 9.11 0.00 41.61 2.24
2925 3191 8.310406 TCAAGAACATACATGTGACTTTACTG 57.690 34.615 9.11 0.00 41.61 2.74
2926 3192 8.147704 TCAAGAACATACATGTGACTTTACTGA 58.852 33.333 9.11 0.00 41.61 3.41
2927 3193 8.939929 CAAGAACATACATGTGACTTTACTGAT 58.060 33.333 9.11 0.00 41.61 2.90
3124 3390 2.550699 CTACCTCCGGCCCATTTGCA 62.551 60.000 0.00 0.00 0.00 4.08
3250 3519 1.359474 TCCACTCTCTCAGCCCTACTT 59.641 52.381 0.00 0.00 0.00 2.24
3317 3586 0.870393 CAACGAGACACTTGCAGCAT 59.130 50.000 0.00 0.00 0.00 3.79
3347 3616 0.539669 TCAAGCTGTGACCGGAGAGA 60.540 55.000 9.46 0.00 0.00 3.10
3371 3640 1.268743 GCATAGAGCAATTCGGCCAAC 60.269 52.381 2.24 0.00 44.79 3.77
3469 3738 1.211457 GCTCCAGGGTGTGATGAAGAT 59.789 52.381 0.00 0.00 0.00 2.40
3715 3984 3.066704 AGATTCCATGAAGGGGGCTTAT 58.933 45.455 0.00 0.00 38.24 1.73
3797 4067 5.424757 TGCTTAACTGCGATAGTACCAAAT 58.575 37.500 0.00 0.00 39.18 2.32
3809 4079 3.164268 AGTACCAAATTTCCATGCAGCA 58.836 40.909 0.00 0.00 0.00 4.41
3812 4082 2.369532 ACCAAATTTCCATGCAGCACTT 59.630 40.909 0.00 0.00 0.00 3.16
3824 4094 5.050837 CCATGCAGCACTTGTAAAAGAAAAC 60.051 40.000 0.00 0.00 0.00 2.43
3888 4158 5.078411 TCTCTGACCTCTAAACAGAATGC 57.922 43.478 0.00 0.00 42.53 3.56
4095 4367 5.011533 AGGTAATATGGAGCATCTCAGACAC 59.988 44.000 0.00 0.00 33.73 3.67
4128 4400 5.368256 GCATAGGCATCTTACCAATTCAG 57.632 43.478 0.00 0.00 40.72 3.02
4438 4711 8.460831 AATGCAATCGTGTAATTTTCTAAACC 57.539 30.769 0.00 0.00 0.00 3.27
4595 4868 2.436542 ACTACCACACCTGCACAAACTA 59.563 45.455 0.00 0.00 0.00 2.24
4608 4881 4.095782 TGCACAAACTAAAGTCTGTGTTCC 59.904 41.667 15.86 3.04 0.00 3.62
4619 4892 1.939934 TCTGTGTTCCGCTTTCAGTTG 59.060 47.619 0.00 0.00 0.00 3.16
4651 4924 7.465116 CATAATCCATAGTTTCCCCTTGATCT 58.535 38.462 0.00 0.00 0.00 2.75
4652 4925 8.605947 CATAATCCATAGTTTCCCCTTGATCTA 58.394 37.037 0.00 0.00 0.00 1.98
4653 4926 6.694445 ATCCATAGTTTCCCCTTGATCTAG 57.306 41.667 0.00 0.00 0.00 2.43
4654 4927 4.348168 TCCATAGTTTCCCCTTGATCTAGC 59.652 45.833 0.00 0.00 0.00 3.42
4701 4975 2.036475 TCTGTCACAGGAGAAGTGCTTC 59.964 50.000 4.57 3.89 36.93 3.86
4721 4995 7.982354 GTGCTTCTAGTTCAAGTTATGGTAGAT 59.018 37.037 0.00 0.00 0.00 1.98
4882 5161 2.436173 CCATTCTAAGGTCTCCCCACTC 59.564 54.545 0.00 0.00 34.66 3.51
4907 5186 8.468399 TCGGTGTACATAATAACAGTATTCACA 58.532 33.333 0.00 0.00 32.10 3.58
5001 5280 1.497991 CGTAACATCTGGCCGTATGG 58.502 55.000 18.44 0.00 38.77 2.74
5237 5533 4.502950 GGATAGCAGAAATGGAGGACTCAG 60.503 50.000 1.32 0.00 0.00 3.35
5320 5616 9.487442 AATTAGGCCAAGAACTCCATATTTTAA 57.513 29.630 5.01 0.00 0.00 1.52
5321 5617 6.775594 AGGCCAAGAACTCCATATTTTAAC 57.224 37.500 5.01 0.00 0.00 2.01
5403 5699 5.276820 CCGCAGAAAATGAGAAAAACAAACC 60.277 40.000 0.00 0.00 0.00 3.27
5444 5742 9.753674 CTCCTAGAGGATTCTGAACTATTCTAT 57.246 37.037 0.00 0.00 44.46 1.98
5476 5774 4.445452 TGTAGATCGGGTCAGTTACAAC 57.555 45.455 0.00 0.00 0.00 3.32
5531 5831 4.895297 CCATTGTACAGGCCCAAGATAAAT 59.105 41.667 0.00 0.00 0.00 1.40
5542 5842 9.883142 CAGGCCCAAGATAAATAAATAACAAAA 57.117 29.630 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 19 1.254954 CCCATAGCCCTCTACGTACC 58.745 60.000 0.00 0.00 0.00 3.34
21 23 1.546961 CCTACCCATAGCCCTCTACG 58.453 60.000 0.00 0.00 0.00 3.51
27 29 1.054406 TGTCAGCCTACCCATAGCCC 61.054 60.000 0.00 0.00 0.00 5.19
124 126 1.947456 GTTGAGGTATCGGGGAAATGC 59.053 52.381 0.00 0.00 0.00 3.56
125 127 2.172717 AGGTTGAGGTATCGGGGAAATG 59.827 50.000 0.00 0.00 0.00 2.32
126 128 2.488836 AGGTTGAGGTATCGGGGAAAT 58.511 47.619 0.00 0.00 0.00 2.17
127 129 1.961133 AGGTTGAGGTATCGGGGAAA 58.039 50.000 0.00 0.00 0.00 3.13
128 130 1.961133 AAGGTTGAGGTATCGGGGAA 58.039 50.000 0.00 0.00 0.00 3.97
129 131 1.835531 GAAAGGTTGAGGTATCGGGGA 59.164 52.381 0.00 0.00 0.00 4.81
130 132 1.134189 GGAAAGGTTGAGGTATCGGGG 60.134 57.143 0.00 0.00 0.00 5.73
131 133 1.134189 GGGAAAGGTTGAGGTATCGGG 60.134 57.143 0.00 0.00 0.00 5.14
132 134 1.472728 CGGGAAAGGTTGAGGTATCGG 60.473 57.143 0.00 0.00 0.00 4.18
133 135 1.935933 CGGGAAAGGTTGAGGTATCG 58.064 55.000 0.00 0.00 0.00 2.92
134 136 1.664873 GCGGGAAAGGTTGAGGTATC 58.335 55.000 0.00 0.00 0.00 2.24
135 137 0.255033 GGCGGGAAAGGTTGAGGTAT 59.745 55.000 0.00 0.00 0.00 2.73
136 138 1.681076 GGCGGGAAAGGTTGAGGTA 59.319 57.895 0.00 0.00 0.00 3.08
137 139 2.434774 GGCGGGAAAGGTTGAGGT 59.565 61.111 0.00 0.00 0.00 3.85
138 140 2.361230 GGGCGGGAAAGGTTGAGG 60.361 66.667 0.00 0.00 0.00 3.86
139 141 1.377333 GAGGGCGGGAAAGGTTGAG 60.377 63.158 0.00 0.00 0.00 3.02
140 142 2.754375 GAGGGCGGGAAAGGTTGA 59.246 61.111 0.00 0.00 0.00 3.18
141 143 2.361230 GGAGGGCGGGAAAGGTTG 60.361 66.667 0.00 0.00 0.00 3.77
190 192 2.682856 GGCACAGTGAGTTTGAGTTTGA 59.317 45.455 4.15 0.00 0.00 2.69
193 195 1.680338 GGGCACAGTGAGTTTGAGTT 58.320 50.000 4.15 0.00 0.00 3.01
274 283 9.847224 ACCAATACAAATAGATCGGAAGTTTAT 57.153 29.630 0.00 0.00 0.00 1.40
276 285 9.106070 GTACCAATACAAATAGATCGGAAGTTT 57.894 33.333 0.00 0.00 0.00 2.66
277 286 8.262227 TGTACCAATACAAATAGATCGGAAGTT 58.738 33.333 0.00 0.00 38.40 2.66
278 287 7.788026 TGTACCAATACAAATAGATCGGAAGT 58.212 34.615 0.00 0.00 38.40 3.01
279 288 8.657074 TTGTACCAATACAAATAGATCGGAAG 57.343 34.615 0.00 0.00 46.12 3.46
292 301 8.734218 TTTCTAGTGTTTGTTGTACCAATACA 57.266 30.769 0.00 0.00 39.63 2.29
329 348 2.032620 GTGGTCTACGGATCTGGATGT 58.967 52.381 6.47 0.00 0.00 3.06
347 366 1.794437 GCTTGTAGTCGTCGCTAGGTG 60.794 57.143 0.00 0.00 0.00 4.00
390 409 3.219928 GAGGGGCGATGAGAGCGA 61.220 66.667 0.00 0.00 35.00 4.93
395 414 1.341156 AAAGAGGGAGGGGCGATGAG 61.341 60.000 0.00 0.00 0.00 2.90
481 531 9.182214 AGGTACACTCGTATCTAGACAAATAAA 57.818 33.333 0.00 0.00 37.29 1.40
530 584 6.157211 GTCAGGATGTTAATCTATGTACGGG 58.843 44.000 0.00 0.00 37.40 5.28
629 722 1.137825 GAGCTCCACGGAACTCGAG 59.862 63.158 11.84 11.84 42.43 4.04
728 827 8.744652 ACGACTAAAGCTGATATATCATTAGCT 58.255 33.333 22.96 20.62 37.41 3.32
729 828 8.918961 ACGACTAAAGCTGATATATCATTAGC 57.081 34.615 22.96 19.23 33.43 3.09
733 832 9.935241 AATCAACGACTAAAGCTGATATATCAT 57.065 29.630 15.71 4.00 36.02 2.45
734 833 9.196552 CAATCAACGACTAAAGCTGATATATCA 57.803 33.333 14.64 14.64 35.16 2.15
735 834 8.165428 GCAATCAACGACTAAAGCTGATATATC 58.835 37.037 5.73 5.73 0.00 1.63
737 836 6.143919 CGCAATCAACGACTAAAGCTGATATA 59.856 38.462 0.00 0.00 0.00 0.86
774 875 3.821306 GGGAACCGCCTCCATATTT 57.179 52.632 3.70 0.00 40.86 1.40
879 986 1.541672 GGAGGAGGAGGAGGAGGAG 59.458 68.421 0.00 0.00 0.00 3.69
880 987 2.015726 GGGAGGAGGAGGAGGAGGA 61.016 68.421 0.00 0.00 0.00 3.71
881 988 2.018086 AGGGAGGAGGAGGAGGAGG 61.018 68.421 0.00 0.00 0.00 4.30
882 989 1.541672 GAGGGAGGAGGAGGAGGAG 59.458 68.421 0.00 0.00 0.00 3.69
971 1080 1.561542 TGAAGAAGGGGCTGGAGATTC 59.438 52.381 0.00 0.00 0.00 2.52
972 1081 1.673767 TGAAGAAGGGGCTGGAGATT 58.326 50.000 0.00 0.00 0.00 2.40
988 1097 5.071384 ACATCCTCATCATCTGTGCTATGAA 59.929 40.000 0.00 0.00 36.95 2.57
990 1099 4.895961 ACATCCTCATCATCTGTGCTATG 58.104 43.478 0.00 0.00 0.00 2.23
991 1100 5.307456 AGAACATCCTCATCATCTGTGCTAT 59.693 40.000 0.00 0.00 0.00 2.97
992 1101 4.652881 AGAACATCCTCATCATCTGTGCTA 59.347 41.667 0.00 0.00 0.00 3.49
993 1102 3.455177 AGAACATCCTCATCATCTGTGCT 59.545 43.478 0.00 0.00 0.00 4.40
999 1134 4.038522 TCCTCGAAGAACATCCTCATCATC 59.961 45.833 0.00 0.00 34.09 2.92
1007 1142 1.202313 CGTCCTCCTCGAAGAACATCC 60.202 57.143 0.00 0.00 34.09 3.51
1062 1197 2.245159 TGAAGAGTCTGGCTTGTGTG 57.755 50.000 0.00 0.00 0.00 3.82
1072 1207 8.030106 CGAGAGTAAATTAAGGTTGAAGAGTCT 58.970 37.037 0.00 0.00 0.00 3.24
1074 1210 7.097834 CCGAGAGTAAATTAAGGTTGAAGAGT 58.902 38.462 0.00 0.00 0.00 3.24
1092 1228 2.097142 CGGATCGAACTAAACCGAGAGT 59.903 50.000 0.00 0.00 45.31 3.24
1135 1271 9.887862 TGGATCATCTATCTCCTTGCATATATA 57.112 33.333 0.00 0.00 34.75 0.86
1136 1272 8.794364 TGGATCATCTATCTCCTTGCATATAT 57.206 34.615 0.00 0.00 34.75 0.86
1137 1273 8.794364 ATGGATCATCTATCTCCTTGCATATA 57.206 34.615 0.00 0.00 34.75 0.86
1138 1274 7.693533 ATGGATCATCTATCTCCTTGCATAT 57.306 36.000 0.00 0.00 34.75 1.78
1139 1275 7.122138 GATGGATCATCTATCTCCTTGCATA 57.878 40.000 3.75 0.00 37.82 3.14
1140 1276 5.991861 GATGGATCATCTATCTCCTTGCAT 58.008 41.667 3.75 0.00 37.82 3.96
1199 1335 7.966204 ACGTTAGCGATGCAAAAATTTATAAGT 59.034 29.630 5.81 0.00 42.00 2.24
1200 1336 8.322906 ACGTTAGCGATGCAAAAATTTATAAG 57.677 30.769 5.81 0.00 42.00 1.73
1201 1337 9.770503 TTACGTTAGCGATGCAAAAATTTATAA 57.229 25.926 5.81 0.00 42.00 0.98
1236 1374 8.792538 CAATTTCATTCTATCAAGTTTTCGCTC 58.207 33.333 0.00 0.00 0.00 5.03
1279 1417 3.449018 AGCGTCTCATCTTTCATGGTAGT 59.551 43.478 0.00 0.00 0.00 2.73
1296 1438 1.333619 TCAAGAAGCCAAACAAGCGTC 59.666 47.619 0.00 0.00 38.77 5.19
1341 1484 7.447374 TTCGTCCTCAAACAAACATGATAAT 57.553 32.000 0.00 0.00 0.00 1.28
1344 1487 4.320494 GCTTCGTCCTCAAACAAACATGAT 60.320 41.667 0.00 0.00 0.00 2.45
1346 1489 3.243035 TGCTTCGTCCTCAAACAAACATG 60.243 43.478 0.00 0.00 0.00 3.21
1350 1493 3.629855 TGATTGCTTCGTCCTCAAACAAA 59.370 39.130 0.00 0.00 0.00 2.83
1357 1500 1.798813 ACGTTTGATTGCTTCGTCCTC 59.201 47.619 0.00 0.00 0.00 3.71
1496 1657 4.388577 ACTTTGGAAGAGGCTTTACCAT 57.611 40.909 7.96 0.00 43.14 3.55
1520 1681 2.806745 GCACCTACTGCTTGAACTGTCA 60.807 50.000 0.00 0.00 43.33 3.58
1639 1805 5.215903 GCACGGACGGATGAGATATATATG 58.784 45.833 0.00 0.00 0.00 1.78
1646 1812 0.249615 CATGCACGGACGGATGAGAT 60.250 55.000 0.00 0.00 36.90 2.75
1677 1850 7.038659 GGATTGATCTGGAAGTATCCTATTCG 58.961 42.308 0.00 0.00 46.70 3.34
1792 1965 5.250200 TGGCTTTGTACAATCCGTTATCTT 58.750 37.500 9.56 0.00 0.00 2.40
1947 2122 2.752903 TCGTCTCTGATCATTTGACGGA 59.247 45.455 28.30 19.13 46.82 4.69
1948 2123 2.854777 GTCGTCTCTGATCATTTGACGG 59.145 50.000 28.30 17.90 46.82 4.79
1950 2125 3.849911 TGGTCGTCTCTGATCATTTGAC 58.150 45.455 0.00 4.47 0.00 3.18
1951 2126 4.743057 ATGGTCGTCTCTGATCATTTGA 57.257 40.909 0.00 0.00 36.28 2.69
1952 2127 5.595885 AGTATGGTCGTCTCTGATCATTTG 58.404 41.667 0.00 0.00 40.18 2.32
1953 2128 5.860941 AGTATGGTCGTCTCTGATCATTT 57.139 39.130 0.00 0.00 40.18 2.32
1954 2129 5.241949 GGTAGTATGGTCGTCTCTGATCATT 59.758 44.000 0.00 0.00 40.18 2.57
1955 2130 4.762765 GGTAGTATGGTCGTCTCTGATCAT 59.237 45.833 0.00 0.00 42.26 2.45
1974 2158 0.469917 ATCAACGGCTGGGATGGTAG 59.530 55.000 0.00 0.00 0.00 3.18
2085 2286 2.343625 AGAAGAAGCCTGTTTCTCCCT 58.656 47.619 0.00 0.00 36.42 4.20
2086 2287 2.869101 AGAAGAAGCCTGTTTCTCCC 57.131 50.000 0.00 0.00 36.42 4.30
2087 2288 3.504134 GGAAAGAAGAAGCCTGTTTCTCC 59.496 47.826 0.00 0.00 36.42 3.71
2088 2289 4.393834 AGGAAAGAAGAAGCCTGTTTCTC 58.606 43.478 0.00 0.00 36.42 2.87
2228 2442 2.816958 CGCTGCAGCTTGTCGGAT 60.817 61.111 34.22 0.00 39.32 4.18
2372 2587 5.051574 GCAATTGAAAATGCTTGGTTTTTGC 60.052 36.000 10.34 0.00 39.46 3.68
2445 2706 4.422073 TGCAGTTATCACCTAAGATGGG 57.578 45.455 0.00 0.00 0.00 4.00
2559 2821 8.393671 ACTAATTATAGTCTGGTACTTCCTCG 57.606 38.462 0.00 0.00 37.90 4.63
2582 2844 7.849322 AACACTGGGATTTTGGTAATTAACT 57.151 32.000 1.50 0.00 0.00 2.24
2583 2845 8.896320 AAAACACTGGGATTTTGGTAATTAAC 57.104 30.769 0.00 0.00 0.00 2.01
2584 2846 9.331282 CAAAAACACTGGGATTTTGGTAATTAA 57.669 29.630 15.24 0.00 39.29 1.40
2585 2847 8.487028 ACAAAAACACTGGGATTTTGGTAATTA 58.513 29.630 23.49 0.00 44.37 1.40
2586 2848 7.342581 ACAAAAACACTGGGATTTTGGTAATT 58.657 30.769 23.49 5.33 44.37 1.40
2587 2849 6.894682 ACAAAAACACTGGGATTTTGGTAAT 58.105 32.000 23.49 5.63 44.37 1.89
2588 2850 6.301169 ACAAAAACACTGGGATTTTGGTAA 57.699 33.333 23.49 0.00 44.37 2.85
2589 2851 5.941555 ACAAAAACACTGGGATTTTGGTA 57.058 34.783 23.49 0.00 44.37 3.25
2873 3138 6.418101 ACTAAGGTTGACAAGCATACATGAT 58.582 36.000 18.93 0.00 0.00 2.45
3169 3435 0.875040 CATCGCTGTAGCTGCAGAGG 60.875 60.000 32.74 22.73 38.70 3.69
3317 3586 4.342378 GGTCACAGCTTGATAGTATCCTGA 59.658 45.833 17.02 3.93 36.32 3.86
3336 3605 0.033503 TATGCTGGTCTCTCCGGTCA 60.034 55.000 0.00 0.00 44.16 4.02
3347 3616 1.959042 CCGAATTGCTCTATGCTGGT 58.041 50.000 0.00 0.00 43.37 4.00
3371 3640 1.338136 ATACTCTGGGGAAGCCGTGG 61.338 60.000 0.00 0.00 0.00 4.94
3664 3933 2.751166 ATGTTCTGGTCAGTCCTTCG 57.249 50.000 0.00 0.00 37.07 3.79
3797 4067 4.340666 TCTTTTACAAGTGCTGCATGGAAA 59.659 37.500 5.27 7.61 27.86 3.13
3888 4158 0.889186 CAGGTCTTGGTTGTTCCCCG 60.889 60.000 0.00 0.00 34.77 5.73
4128 4400 3.332761 TTTGTTGCGTGTCATCAGAAC 57.667 42.857 0.00 0.00 0.00 3.01
4438 4711 6.680810 TGAGAAAATACAAGCATGAACCTTG 58.319 36.000 9.28 9.28 43.98 3.61
4595 4868 2.614057 CTGAAAGCGGAACACAGACTTT 59.386 45.455 0.00 0.00 33.45 2.66
4608 4881 0.100325 TGGTTGCACAACTGAAAGCG 59.900 50.000 12.87 0.00 40.94 4.68
4619 4892 5.221244 GGGAAACTATGGATTATGGTTGCAC 60.221 44.000 0.00 0.00 39.27 4.57
4651 4924 6.882140 TGTAAAGCTGTAGCCTTATTTTGCTA 59.118 34.615 0.00 0.00 43.38 3.49
4652 4925 5.710099 TGTAAAGCTGTAGCCTTATTTTGCT 59.290 36.000 0.00 0.00 43.38 3.91
4653 4926 5.949735 TGTAAAGCTGTAGCCTTATTTTGC 58.050 37.500 0.00 0.00 43.38 3.68
4654 4927 6.151144 ACCTGTAAAGCTGTAGCCTTATTTTG 59.849 38.462 0.00 0.00 43.38 2.44
4701 4975 8.883731 CACCAAATCTACCATAACTTGAACTAG 58.116 37.037 0.00 0.00 0.00 2.57
4715 4989 9.561069 ACAGATTGATAATACACCAAATCTACC 57.439 33.333 0.00 0.00 0.00 3.18
4721 4995 9.747898 AAGGTAACAGATTGATAATACACCAAA 57.252 29.630 0.00 0.00 41.41 3.28
4748 5027 3.067106 CACTCACTGTTAAGAACGGCAT 58.933 45.455 0.00 0.00 41.56 4.40
4882 5161 8.637281 TGTGAATACTGTTATTATGTACACCG 57.363 34.615 0.00 0.00 0.00 4.94
4907 5186 0.035458 CTTCCACGCCTTGTTCTCCT 59.965 55.000 0.00 0.00 0.00 3.69
4962 5241 2.755655 CGGATTCTCTGTACTGGAGTGT 59.244 50.000 13.31 6.32 33.06 3.55
5001 5280 8.246180 TGGATTCTAATTTGTCAATCTTCTTGC 58.754 33.333 0.00 0.00 0.00 4.01
5101 5380 7.062605 GTCTTGTGCATTTCCAGTATTTGATTG 59.937 37.037 0.00 0.00 0.00 2.67
5228 5524 3.126831 CAACCGCATTATCTGAGTCCTC 58.873 50.000 0.00 0.00 0.00 3.71
5237 5533 5.830912 TCAAATGAATCCAACCGCATTATC 58.169 37.500 0.00 0.00 31.30 1.75
5320 5616 3.492102 TGCTCTCTTTTTGCCACTAGT 57.508 42.857 0.00 0.00 0.00 2.57
5321 5617 3.817647 AGTTGCTCTCTTTTTGCCACTAG 59.182 43.478 0.00 0.00 32.19 2.57
5361 5657 0.257039 GGTGCTCTTGATGGATGGGT 59.743 55.000 0.00 0.00 0.00 4.51
5444 5742 0.174845 CGATCTACAAGGGTTCGGCA 59.825 55.000 0.00 0.00 0.00 5.69
5468 5766 4.338400 GCTTTTGGGTTCTCTGTTGTAACT 59.662 41.667 0.00 0.00 0.00 2.24
5476 5774 4.227864 AGATAGGCTTTTGGGTTCTCTG 57.772 45.455 0.00 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.