Multiple sequence alignment - TraesCS2B01G350900

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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 TraesCS2B01G350900 chr2B 100.000 4414 0 0 1 4414 497879441 497875028 0.000000e+00 8152
1 TraesCS2B01G350900 chr2A 91.042 2534 187 23 1902 4410 564265091 564267609 0.000000e+00 3386
2 TraesCS2B01G350900 chr2A 87.561 619 41 20 157 751 564263299 564263905 0.000000e+00 684
3 TraesCS2B01G350900 chr2A 86.644 599 39 15 796 1356 564263906 564264501 3.750000e-175 625
4 TraesCS2B01G350900 chr2A 85.784 204 12 5 1395 1596 564264501 564264689 2.690000e-47 200
5 TraesCS2B01G350900 chr2A 90.511 137 11 2 7 143 564262468 564262602 3.510000e-41 180
6 TraesCS2B01G350900 chr2A 96.296 81 2 1 1819 1899 564264907 564264986 9.960000e-27 132
7 TraesCS2B01G350900 chr2D 94.919 2027 64 22 1856 3872 424000600 423998603 0.000000e+00 3136
8 TraesCS2B01G350900 chr2D 88.198 1898 117 57 55 1867 424007894 424006019 0.000000e+00 2165
9 TraesCS2B01G350900 chr2D 86.082 388 38 10 3907 4292 423998600 423998227 1.910000e-108 403
10 TraesCS2B01G350900 chr2D 92.405 79 6 0 4336 4414 423997467 423997389 3.610000e-21 113


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 TraesCS2B01G350900 chr2B 497875028 497879441 4413 True 8152.000000 8152 100.000000 1 4414 1 chr2B.!!$R1 4413
1 TraesCS2B01G350900 chr2A 564262468 564267609 5141 False 867.833333 3386 89.639667 7 4410 6 chr2A.!!$F1 4403
2 TraesCS2B01G350900 chr2D 424006019 424007894 1875 True 2165.000000 2165 88.198000 55 1867 1 chr2D.!!$R1 1812
3 TraesCS2B01G350900 chr2D 423997389 424000600 3211 True 1217.333333 3136 91.135333 1856 4414 3 chr2D.!!$R2 2558

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
31 32 0.243636 AGGTGCTACAAATTTGCGGC 59.756 50.0 18.12 20.16 0.00 6.53 F
130 134 0.532115 ATTTTGGGCACGGCAGATTC 59.468 50.0 0.00 0.00 0.00 2.52 F
1624 2404 0.599558 TCGTTCTTGTACCAGTCGGG 59.400 55.0 11.61 0.00 44.81 5.14 F
2173 3113 0.321346 TCAGATCAAGCAGGCGAACA 59.679 50.0 0.00 0.00 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1414 2194 0.034380 GGAAAACTCCCCTGCTACCC 60.034 60.000 0.00 0.00 0.00 3.69 R
1923 2863 0.322816 TCTTGTGGAAGAGCATGGCC 60.323 55.000 0.00 0.00 32.98 5.36 R
3397 4345 0.104855 GCTCTACGATGATGGTGCCA 59.895 55.000 0.00 0.00 0.00 4.92 R
3992 4948 2.027460 CCGCCTGTTGGTTGCAAC 59.973 61.111 21.59 21.59 35.27 4.17 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
29 30 2.318578 CACAGGTGCTACAAATTTGCG 58.681 47.619 18.12 10.48 0.00 4.85
31 32 0.243636 AGGTGCTACAAATTTGCGGC 59.756 50.000 18.12 20.16 0.00 6.53
34 35 1.516169 GCTACAAATTTGCGGCGGG 60.516 57.895 18.12 3.70 0.00 6.13
91 92 4.905429 TGTTGGAGCACTATCTTTTAGCA 58.095 39.130 0.00 0.00 0.00 3.49
127 128 1.102154 CATATTTTGGGCACGGCAGA 58.898 50.000 0.00 0.00 0.00 4.26
130 134 0.532115 ATTTTGGGCACGGCAGATTC 59.468 50.000 0.00 0.00 0.00 2.52
164 168 6.992123 TCTGTTGAAGATGAGCTAAGAAAACA 59.008 34.615 0.00 0.00 0.00 2.83
185 878 3.692257 TGAGGAGGAAAGAAGAAGCAG 57.308 47.619 0.00 0.00 0.00 4.24
198 897 1.001641 AAGCAGGGCAAGGTAGCAG 60.002 57.895 0.00 0.00 35.83 4.24
214 919 1.589716 GCAGGCGTGGCAAAGAAGAT 61.590 55.000 8.72 0.00 0.00 2.40
222 927 1.283029 TGGCAAAGAAGATGGGAGAGG 59.717 52.381 0.00 0.00 0.00 3.69
230 935 1.690633 GATGGGAGAGGAGGGCACA 60.691 63.158 0.00 0.00 0.00 4.57
231 936 1.229951 ATGGGAGAGGAGGGCACAA 60.230 57.895 0.00 0.00 0.00 3.33
233 938 1.301293 GGGAGAGGAGGGCACAAAG 59.699 63.158 0.00 0.00 0.00 2.77
253 973 2.800096 TCGCACTTTAACGACCGTC 58.200 52.632 0.00 0.00 32.45 4.79
276 997 3.979911 TGTGGCACATTCCTTGGATAAT 58.020 40.909 17.96 0.00 44.52 1.28
277 998 5.122707 TGTGGCACATTCCTTGGATAATA 57.877 39.130 17.96 0.00 44.52 0.98
430 1151 4.862823 CCTCCCTCCGACCCTCCC 62.863 77.778 0.00 0.00 0.00 4.30
433 1154 3.756783 CCCTCCGACCCTCCCTCT 61.757 72.222 0.00 0.00 0.00 3.69
458 1179 2.488545 TCTCTCGTTTCCCTCTCTTTCG 59.511 50.000 0.00 0.00 0.00 3.46
539 1260 2.212327 CAAGGTATGCTCCGTCCCT 58.788 57.895 0.00 0.00 0.00 4.20
552 1273 4.285260 GCTCCGTCCCTCCCTTATATTTTA 59.715 45.833 0.00 0.00 0.00 1.52
554 1275 4.594491 TCCGTCCCTCCCTTATATTTTACC 59.406 45.833 0.00 0.00 0.00 2.85
558 1279 5.013913 GTCCCTCCCTTATATTTTACCCTCC 59.986 48.000 0.00 0.00 0.00 4.30
559 1280 5.101904 TCCCTCCCTTATATTTTACCCTCCT 60.102 44.000 0.00 0.00 0.00 3.69
582 1303 3.564225 ACGAGTTCCTTGATTGGTTGAAC 59.436 43.478 0.00 0.00 36.45 3.18
588 1309 2.171003 CTTGATTGGTTGAACCCCTCC 58.829 52.381 12.53 0.00 37.50 4.30
590 1311 1.786441 TGATTGGTTGAACCCCTCCTT 59.214 47.619 12.53 0.00 37.50 3.36
629 1350 7.481642 AGAAACTCGTTATTCGACATAGATGT 58.518 34.615 0.00 0.00 44.01 3.06
630 1351 7.974501 AGAAACTCGTTATTCGACATAGATGTT 59.025 33.333 0.00 0.00 44.01 2.71
634 1355 6.327154 TCGTTATTCGACATAGATGTTGTGT 58.673 36.000 9.27 3.44 44.01 3.72
635 1356 6.471198 TCGTTATTCGACATAGATGTTGTGTC 59.529 38.462 9.27 0.00 44.01 3.67
654 1378 7.444558 TGTGTCAAAAATTCTTAGCGTTTTC 57.555 32.000 0.00 0.00 0.00 2.29
655 1379 6.474102 TGTGTCAAAAATTCTTAGCGTTTTCC 59.526 34.615 0.00 0.00 0.00 3.13
656 1380 6.695713 GTGTCAAAAATTCTTAGCGTTTTCCT 59.304 34.615 0.00 0.00 0.00 3.36
673 1397 8.080417 GCGTTTTCCTTTTCTAATTTAAGGAGT 58.920 33.333 0.00 0.00 45.86 3.85
678 1402 9.668497 TTCCTTTTCTAATTTAAGGAGTAGCTC 57.332 33.333 0.00 0.00 45.86 4.09
815 1540 4.082523 GCTCCTGGTGCGTGGCTA 62.083 66.667 4.83 0.00 0.00 3.93
978 1732 7.337436 ACCAATTTGGCCAAATAAATCATCAAG 59.663 33.333 37.45 20.12 42.67 3.02
1026 1780 3.277142 AAAAGTCCTGTTTCACCGTCT 57.723 42.857 0.00 0.00 0.00 4.18
1082 1836 3.356639 GATCAGCCACGGTCGCTCA 62.357 63.158 0.00 0.00 33.17 4.26
1091 1845 2.581354 GGTCGCTCAGAGGCATGT 59.419 61.111 0.00 0.00 0.00 3.21
1192 1957 9.823647 CCAGACAGTAAACACTATCTATTCATT 57.176 33.333 0.00 0.00 0.00 2.57
1218 1983 7.507616 TCCCTGTTATATTTTCTTGTGTTTGGT 59.492 33.333 0.00 0.00 0.00 3.67
1259 2030 9.299963 TCTGAAGAACATGTTATTGTTGTTTTG 57.700 29.630 22.36 4.55 41.52 2.44
1271 2042 8.603181 GTTATTGTTGTTTTGCAAGTTCTTGAT 58.397 29.630 15.52 0.00 37.83 2.57
1299 2070 9.747898 ATTGACCACTAGAATATTTGGTTGTTA 57.252 29.630 10.23 0.00 42.60 2.41
1302 2073 7.996385 ACCACTAGAATATTTGGTTGTTATGC 58.004 34.615 4.05 0.00 39.41 3.14
1309 2080 9.777297 AGAATATTTGGTTGTTATGCAAAAGTT 57.223 25.926 0.00 0.00 39.03 2.66
1316 2087 6.975772 TGGTTGTTATGCAAAAGTTAACAGTC 59.024 34.615 8.61 7.48 39.03 3.51
1317 2088 6.975772 GGTTGTTATGCAAAAGTTAACAGTCA 59.024 34.615 8.61 0.00 39.03 3.41
1369 2143 5.078411 AGTTTATGTACAGTCTGCCTGAG 57.922 43.478 0.33 0.00 44.49 3.35
1389 2163 4.065088 GAGGCACTATGAAACAACACTGA 58.935 43.478 0.00 0.00 41.55 3.41
1393 2167 4.273480 GCACTATGAAACAACACTGACAGT 59.727 41.667 1.07 1.07 0.00 3.55
1414 2194 6.017109 ACAGTTGCACTTGACAATTTAGTAGG 60.017 38.462 3.77 0.00 0.00 3.18
1415 2195 5.473504 AGTTGCACTTGACAATTTAGTAGGG 59.526 40.000 0.00 0.00 0.00 3.53
1416 2196 4.331968 TGCACTTGACAATTTAGTAGGGG 58.668 43.478 0.00 0.00 0.00 4.79
1417 2197 4.202524 TGCACTTGACAATTTAGTAGGGGT 60.203 41.667 0.00 0.00 0.00 4.95
1418 2198 5.013287 TGCACTTGACAATTTAGTAGGGGTA 59.987 40.000 0.00 0.00 0.00 3.69
1420 2200 5.585047 CACTTGACAATTTAGTAGGGGTAGC 59.415 44.000 0.00 0.00 0.00 3.58
1422 2202 5.353394 TGACAATTTAGTAGGGGTAGCAG 57.647 43.478 0.00 0.00 0.00 4.24
1423 2203 4.163458 TGACAATTTAGTAGGGGTAGCAGG 59.837 45.833 0.00 0.00 0.00 4.85
1424 2204 3.458487 ACAATTTAGTAGGGGTAGCAGGG 59.542 47.826 0.00 0.00 0.00 4.45
1425 2205 2.185663 TTTAGTAGGGGTAGCAGGGG 57.814 55.000 0.00 0.00 0.00 4.79
1529 2309 1.135972 CGAGAAAATGGTTCTGCGGTG 60.136 52.381 0.00 0.00 0.00 4.94
1596 2376 9.199982 CATTTGAATTCATGCTTCTGTAGTTTT 57.800 29.630 9.40 0.00 0.00 2.43
1613 2393 9.793245 CTGTAGTTTTAAGTGTTATCGTTCTTG 57.207 33.333 0.00 0.00 0.00 3.02
1624 2404 0.599558 TCGTTCTTGTACCAGTCGGG 59.400 55.000 11.61 0.00 44.81 5.14
1648 2428 3.251729 TCATGAAGAGTTGAAGCTGTTGC 59.748 43.478 0.00 0.00 40.05 4.17
1650 2430 2.225467 GAAGAGTTGAAGCTGTTGCCT 58.775 47.619 0.00 0.00 40.80 4.75
1684 2464 1.945394 GATGTGCTAGCATGGACCAAG 59.055 52.381 22.51 0.00 0.00 3.61
1715 2497 8.750515 TCACATGATCAAGCTATCCAATTTTA 57.249 30.769 0.00 0.00 0.00 1.52
1737 2535 8.677148 TTTAATAGAGTCAAGTGTTTTCTGCT 57.323 30.769 0.00 0.00 0.00 4.24
1754 2553 3.052109 TCTGCTCTTATTGGGAGGACCTA 60.052 47.826 0.00 0.00 41.11 3.08
1774 2573 5.136828 CCTAGAGATGAGAACCTAAGCTGA 58.863 45.833 0.00 0.00 0.00 4.26
1779 2578 7.725251 AGAGATGAGAACCTAAGCTGATTTAG 58.275 38.462 0.00 0.00 0.00 1.85
1923 2863 4.913335 ACATTATTTCCTGCAGCATCAG 57.087 40.909 8.66 0.00 0.00 2.90
2091 3031 1.682323 GTGGGAAGCCGTTTGGTTTTA 59.318 47.619 0.00 0.00 39.01 1.52
2133 3073 2.143122 GTGCAAATGAGAACACTCGGA 58.857 47.619 0.00 0.00 33.80 4.55
2173 3113 0.321346 TCAGATCAAGCAGGCGAACA 59.679 50.000 0.00 0.00 0.00 3.18
2203 3143 1.630878 AGTTGAAGATGTGACTCCCCC 59.369 52.381 0.00 0.00 0.00 5.40
2249 3189 8.631797 CATGATTTTTGTTTTGGGATTCCTTTT 58.368 29.630 2.01 0.00 0.00 2.27
2292 3232 4.886579 ACAAAGGCAAAATCCTGTCATTC 58.113 39.130 0.00 0.00 36.38 2.67
2329 3269 6.279513 TCATGTGGGTGAATGTAAAATTCC 57.720 37.500 0.00 0.00 0.00 3.01
2335 3275 2.088423 TGAATGTAAAATTCCGCCGCT 58.912 42.857 0.00 0.00 0.00 5.52
2349 3289 1.739035 CGCCGCTGAAGTTTCCTGATA 60.739 52.381 0.00 0.00 0.00 2.15
2350 3290 2.356135 GCCGCTGAAGTTTCCTGATAA 58.644 47.619 0.00 0.00 0.00 1.75
2355 3295 4.181578 GCTGAAGTTTCCTGATAAGCGTA 58.818 43.478 0.00 0.00 0.00 4.42
2363 3303 4.893424 TCCTGATAAGCGTAATTTTGCC 57.107 40.909 0.00 0.00 0.00 4.52
2507 3451 8.322828 TCACTGCATAATTACCCAAACTTACTA 58.677 33.333 0.00 0.00 0.00 1.82
2640 3586 3.568007 CCCAAACCAGTCGAAAATGAGAA 59.432 43.478 0.00 0.00 0.00 2.87
2649 3595 6.456584 CCAGTCGAAAATGAGAATGTCATGAG 60.457 42.308 0.00 0.00 45.89 2.90
2707 3653 6.704512 TGTTCCTTATTACGTTAACGGTTC 57.295 37.500 29.81 9.75 44.95 3.62
2930 3878 6.665695 TCTTGGTACCCTCAGTTTAAACTTT 58.334 36.000 18.25 3.73 37.08 2.66
3064 4012 3.940209 TGACATGTTCAATTTGCTCCC 57.060 42.857 0.00 0.00 0.00 4.30
3246 4194 3.851098 CTTCACTGAGGTACCTTACTGC 58.149 50.000 17.53 2.92 0.00 4.40
3282 4230 5.417580 CCCCTTCATTTTTCTCGTGGAAATA 59.582 40.000 7.02 4.12 42.63 1.40
3374 4322 1.174712 TGCTGCTTGCTGGAGGAAAC 61.175 55.000 0.00 0.00 43.37 2.78
3482 4430 1.672363 TGCTCCATAAAATGCTGCGAG 59.328 47.619 0.00 0.00 32.36 5.03
3567 4515 1.541588 GCGAGCTCTTGGATTTTTGGT 59.458 47.619 12.85 0.00 0.00 3.67
3606 4555 4.796110 ATACTGGCAGGATGGTTGTAAT 57.204 40.909 20.34 0.00 35.86 1.89
3664 4618 6.375174 TGAACATGATGAAGGATAACCAGTTG 59.625 38.462 0.00 0.00 38.94 3.16
3796 4750 5.505286 GTGTATTCAGGCGATGATTCTTTG 58.495 41.667 0.00 0.00 37.89 2.77
3799 4753 1.281867 TCAGGCGATGATTCTTTGGGT 59.718 47.619 0.00 0.00 31.12 4.51
3800 4754 2.503765 TCAGGCGATGATTCTTTGGGTA 59.496 45.455 0.00 0.00 31.12 3.69
3808 4764 6.294176 GCGATGATTCTTTGGGTAGCAAATAT 60.294 38.462 0.00 0.00 0.00 1.28
3813 4769 4.854173 TCTTTGGGTAGCAAATATGAGCA 58.146 39.130 0.00 0.00 0.00 4.26
3836 4792 1.813859 CCACCTGCTCCATTGCATG 59.186 57.895 0.00 0.00 42.48 4.06
3839 4795 1.035932 ACCTGCTCCATTGCATGAGC 61.036 55.000 20.47 20.47 42.48 4.26
3847 4803 2.492881 TCCATTGCATGAGCGAAACAAT 59.507 40.909 0.00 0.00 46.23 2.71
3869 4825 8.537858 ACAATAGTTCGGGAGTAGAGTTTTAAT 58.462 33.333 0.00 0.00 0.00 1.40
3890 4846 3.659786 TGGGAACACACGAGTTATCAAG 58.340 45.455 0.00 0.00 33.40 3.02
3891 4847 2.415512 GGGAACACACGAGTTATCAAGC 59.584 50.000 0.00 0.00 0.00 4.01
3892 4848 3.326747 GGAACACACGAGTTATCAAGCT 58.673 45.455 0.00 0.00 0.00 3.74
3893 4849 3.123621 GGAACACACGAGTTATCAAGCTG 59.876 47.826 0.00 0.00 0.00 4.24
3894 4850 3.386768 ACACACGAGTTATCAAGCTGT 57.613 42.857 0.00 0.00 0.00 4.40
3895 4851 3.728845 ACACACGAGTTATCAAGCTGTT 58.271 40.909 0.00 0.00 0.00 3.16
3896 4852 4.127171 ACACACGAGTTATCAAGCTGTTT 58.873 39.130 0.00 0.00 0.00 2.83
3897 4853 4.574828 ACACACGAGTTATCAAGCTGTTTT 59.425 37.500 0.00 0.00 0.00 2.43
3898 4854 5.065988 ACACACGAGTTATCAAGCTGTTTTT 59.934 36.000 0.00 0.00 0.00 1.94
3901 4857 6.038271 ACACGAGTTATCAAGCTGTTTTTCTT 59.962 34.615 0.00 0.00 0.00 2.52
3902 4858 6.912591 CACGAGTTATCAAGCTGTTTTTCTTT 59.087 34.615 0.00 0.00 0.00 2.52
3905 4861 8.472236 CGAGTTATCAAGCTGTTTTTCTTTTTC 58.528 33.333 0.00 0.00 0.00 2.29
3968 4924 9.337396 CATAGGGTTACAATCTGCTAATACAAA 57.663 33.333 0.00 0.00 0.00 2.83
3979 4935 9.976511 AATCTGCTAATACAAAATCATGAATGG 57.023 29.630 0.00 0.00 0.00 3.16
3981 4937 9.358406 TCTGCTAATACAAAATCATGAATGGAT 57.642 29.630 0.00 0.00 0.00 3.41
3992 4948 1.529244 GAATGGATTGGGGGCCTCG 60.529 63.158 0.84 0.00 0.00 4.63
4058 5015 4.631813 AGCGAGACAATGTGAAACCTATTC 59.368 41.667 0.00 0.00 34.36 1.75
4073 5030 8.177456 TGAAACCTATTCTGGGATCTAGCTATA 58.823 37.037 0.00 0.00 0.00 1.31
4079 5036 6.859112 TTCTGGGATCTAGCTATATCAACC 57.141 41.667 17.94 12.29 0.00 3.77
4104 5061 5.122869 GGTTTAAACTCCCGTTCTACCATTC 59.877 44.000 17.50 0.00 32.47 2.67
4121 5078 6.442513 ACCATTCGATTCTTGATTTCCTTC 57.557 37.500 0.00 0.00 0.00 3.46
4160 5117 2.027285 TGATTTGACGAGGGAAGCATCA 60.027 45.455 0.00 0.00 0.00 3.07
4166 5123 3.126831 GACGAGGGAAGCATCAACATAG 58.873 50.000 0.00 0.00 0.00 2.23
4191 5150 3.561143 AGAGCTATCATTGAGTCCGACT 58.439 45.455 0.00 0.00 0.00 4.18
4193 5152 4.517453 AGAGCTATCATTGAGTCCGACTAC 59.483 45.833 0.00 0.00 0.00 2.73
4194 5153 4.207955 AGCTATCATTGAGTCCGACTACA 58.792 43.478 0.00 0.00 0.00 2.74
4196 5155 3.802948 ATCATTGAGTCCGACTACACC 57.197 47.619 0.00 0.00 0.00 4.16
4197 5156 2.521126 TCATTGAGTCCGACTACACCA 58.479 47.619 0.00 0.00 0.00 4.17
4203 5162 1.758280 AGTCCGACTACACCACAACAA 59.242 47.619 0.00 0.00 0.00 2.83
4262 5304 5.816449 TCATTATTGCTTGAATCTTCGCA 57.184 34.783 0.00 0.00 0.00 5.10
4263 5305 5.813717 TCATTATTGCTTGAATCTTCGCAG 58.186 37.500 0.00 0.00 33.48 5.18
4345 6020 0.883814 CTCAAGATCATGCCCGCTCC 60.884 60.000 0.00 0.00 0.00 4.70
4402 6077 2.014128 CGATAAAGCCAACCAATCCGT 58.986 47.619 0.00 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.138671 CCCCGCCGCAAATTTGTAG 59.861 57.895 19.03 13.10 0.00 2.74
34 35 1.067821 TCACGTGTCAAAATTTGCCCC 59.932 47.619 16.51 0.00 0.00 5.80
37 38 8.841444 ATATCTTATCACGTGTCAAAATTTGC 57.159 30.769 16.51 0.00 0.00 3.68
111 112 0.532115 GAATCTGCCGTGCCCAAAAT 59.468 50.000 0.00 0.00 0.00 1.82
152 156 5.505181 TTCCTCCTCATGTTTTCTTAGCT 57.495 39.130 0.00 0.00 0.00 3.32
155 159 7.745717 TCTTCTTTCCTCCTCATGTTTTCTTA 58.254 34.615 0.00 0.00 0.00 2.10
159 163 5.242615 GCTTCTTCTTTCCTCCTCATGTTTT 59.757 40.000 0.00 0.00 0.00 2.43
164 168 3.054508 CCTGCTTCTTCTTTCCTCCTCAT 60.055 47.826 0.00 0.00 0.00 2.90
185 878 4.410400 ACGCCTGCTACCTTGCCC 62.410 66.667 0.00 0.00 0.00 5.36
198 897 1.508088 CCATCTTCTTTGCCACGCC 59.492 57.895 0.00 0.00 0.00 5.68
214 919 1.463214 TTTGTGCCCTCCTCTCCCA 60.463 57.895 0.00 0.00 0.00 4.37
222 927 2.281484 TGCGACCTTTGTGCCCTC 60.281 61.111 0.00 0.00 0.00 4.30
253 973 1.548081 TCCAAGGAATGTGCCACATG 58.452 50.000 11.79 0.00 37.97 3.21
276 997 4.889409 GCAATTGATCCTCTGGACCAAATA 59.111 41.667 10.34 0.00 32.98 1.40
277 998 3.703052 GCAATTGATCCTCTGGACCAAAT 59.297 43.478 10.34 0.00 32.98 2.32
350 1071 1.133199 TGTGGGCAGACCTGGAAATTT 60.133 47.619 0.00 0.00 41.11 1.82
379 1100 4.135493 GTTCGCGGCGAGTCAAGC 62.135 66.667 25.02 8.89 37.14 4.01
381 1102 2.486636 ATCTGTTCGCGGCGAGTCAA 62.487 55.000 25.02 16.87 37.14 3.18
382 1103 2.867333 GATCTGTTCGCGGCGAGTCA 62.867 60.000 25.02 23.81 37.14 3.41
383 1104 2.202623 ATCTGTTCGCGGCGAGTC 60.203 61.111 25.02 20.86 37.14 3.36
386 1107 3.449227 AGGATCTGTTCGCGGCGA 61.449 61.111 22.69 22.69 0.00 5.54
430 1151 1.813786 AGGGAAACGAGAGACGAAGAG 59.186 52.381 0.00 0.00 45.77 2.85
433 1154 1.811359 GAGAGGGAAACGAGAGACGAA 59.189 52.381 0.00 0.00 45.77 3.85
539 1260 6.623329 TCGTAGGAGGGTAAAATATAAGGGA 58.377 40.000 0.00 0.00 0.00 4.20
552 1273 1.076677 TCAAGGAACTCGTAGGAGGGT 59.923 52.381 16.38 4.19 44.93 4.34
554 1275 3.430929 CCAATCAAGGAACTCGTAGGAGG 60.431 52.174 16.38 0.00 44.93 4.30
558 1279 4.566004 TCAACCAATCAAGGAACTCGTAG 58.434 43.478 0.00 0.00 38.49 3.51
559 1280 4.610605 TCAACCAATCAAGGAACTCGTA 57.389 40.909 0.00 0.00 38.49 3.43
582 1303 1.966845 TCTAGGGTTTCAAGGAGGGG 58.033 55.000 0.00 0.00 0.00 4.79
588 1309 5.578727 CGAGTTTCTCATCTAGGGTTTCAAG 59.421 44.000 0.00 0.00 0.00 3.02
590 1311 4.527038 ACGAGTTTCTCATCTAGGGTTTCA 59.473 41.667 0.00 0.00 0.00 2.69
629 1350 7.009723 GGAAAACGCTAAGAATTTTTGACACAA 59.990 33.333 0.00 0.00 0.00 3.33
630 1351 6.474102 GGAAAACGCTAAGAATTTTTGACACA 59.526 34.615 0.00 0.00 0.00 3.72
634 1355 8.710835 AAAAGGAAAACGCTAAGAATTTTTGA 57.289 26.923 0.00 0.00 0.00 2.69
635 1356 8.817100 AGAAAAGGAAAACGCTAAGAATTTTTG 58.183 29.630 0.00 0.00 0.00 2.44
654 1378 8.439993 GGAGCTACTCCTTAAATTAGAAAAGG 57.560 38.462 6.38 0.00 46.41 3.11
805 1530 2.356553 TGAACGGTAGCCACGCAC 60.357 61.111 0.00 0.00 34.00 5.34
1026 1780 0.180171 CTACCGCCATGTGGGATTGA 59.820 55.000 6.30 0.00 40.01 2.57
1068 1822 3.753434 CTCTGAGCGACCGTGGCT 61.753 66.667 7.88 7.88 45.00 4.75
1091 1845 1.930914 AGGAGGGTACTCTGAAGGCTA 59.069 52.381 0.00 0.00 43.46 3.93
1192 1957 7.507616 ACCAAACACAAGAAAATATAACAGGGA 59.492 33.333 0.00 0.00 0.00 4.20
1218 1983 8.581253 TGTTCTTCAGATGAGTAGAGTATCAA 57.419 34.615 0.00 0.00 37.82 2.57
1222 1993 7.946381 ACATGTTCTTCAGATGAGTAGAGTA 57.054 36.000 0.00 0.00 0.00 2.59
1259 2030 4.217118 AGTGGTCAATGATCAAGAACTTGC 59.783 41.667 15.13 7.68 40.24 4.01
1271 2042 7.888021 ACAACCAAATATTCTAGTGGTCAATGA 59.112 33.333 9.47 0.00 43.62 2.57
1292 2063 6.975772 TGACTGTTAACTTTTGCATAACAACC 59.024 34.615 7.22 6.46 38.61 3.77
1299 2070 6.389830 TCACATGACTGTTAACTTTTGCAT 57.610 33.333 7.22 1.38 31.62 3.96
1302 2073 9.299963 TGAAAATCACATGACTGTTAACTTTTG 57.700 29.630 7.22 0.85 31.62 2.44
1311 2082 9.288576 TCTTCTTTATGAAAATCACATGACTGT 57.711 29.630 0.00 0.00 33.79 3.55
1341 2115 9.547753 CAGGCAGACTGTACATAAACTTAATAT 57.452 33.333 3.99 0.00 42.42 1.28
1369 2143 3.563808 TGTCAGTGTTGTTTCATAGTGCC 59.436 43.478 0.00 0.00 0.00 5.01
1379 2153 2.919666 GTGCAACTGTCAGTGTTGTT 57.080 45.000 6.18 0.00 44.54 2.83
1393 2167 4.764823 CCCCTACTAAATTGTCAAGTGCAA 59.235 41.667 0.00 0.00 0.00 4.08
1414 2194 0.034380 GGAAAACTCCCCTGCTACCC 60.034 60.000 0.00 0.00 0.00 3.69
1415 2195 0.696501 TGGAAAACTCCCCTGCTACC 59.303 55.000 0.00 0.00 0.00 3.18
1416 2196 2.808906 ATGGAAAACTCCCCTGCTAC 57.191 50.000 0.00 0.00 0.00 3.58
1417 2197 3.430453 CAAATGGAAAACTCCCCTGCTA 58.570 45.455 0.00 0.00 0.00 3.49
1418 2198 2.250924 CAAATGGAAAACTCCCCTGCT 58.749 47.619 0.00 0.00 0.00 4.24
1420 2200 1.969923 TGCAAATGGAAAACTCCCCTG 59.030 47.619 0.00 0.00 0.00 4.45
1422 2202 1.336795 CGTGCAAATGGAAAACTCCCC 60.337 52.381 0.00 0.00 0.00 4.81
1423 2203 1.934849 GCGTGCAAATGGAAAACTCCC 60.935 52.381 0.00 0.00 0.00 4.30
1424 2204 1.269517 TGCGTGCAAATGGAAAACTCC 60.270 47.619 0.00 0.00 0.00 3.85
1425 2205 2.132740 TGCGTGCAAATGGAAAACTC 57.867 45.000 0.00 0.00 0.00 3.01
1487 2267 7.987458 TCTCGCCTCTTTGTGATATAATTTTCT 59.013 33.333 0.00 0.00 0.00 2.52
1529 2309 1.068055 CAAGCAGATTCACCAACCAGC 60.068 52.381 0.00 0.00 0.00 4.85
1596 2376 6.985117 ACTGGTACAAGAACGATAACACTTA 58.015 36.000 3.64 0.00 38.70 2.24
1624 2404 5.210715 CAACAGCTTCAACTCTTCATGAAC 58.789 41.667 3.38 0.00 32.46 3.18
1625 2405 4.261322 GCAACAGCTTCAACTCTTCATGAA 60.261 41.667 8.12 8.12 34.57 2.57
1626 2406 3.251729 GCAACAGCTTCAACTCTTCATGA 59.748 43.478 0.00 0.00 0.00 3.07
1631 2411 2.355010 AGGCAACAGCTTCAACTCTT 57.645 45.000 0.00 0.00 41.41 2.85
1648 2428 2.106566 ACATCAGAGCACAGGAGTAGG 58.893 52.381 0.00 0.00 0.00 3.18
1650 2430 1.205655 GCACATCAGAGCACAGGAGTA 59.794 52.381 0.00 0.00 0.00 2.59
1684 2464 9.440773 TTGGATAGCTTGATCATGTGATTATAC 57.559 33.333 10.05 5.57 34.37 1.47
1715 2497 6.529220 AGAGCAGAAAACACTTGACTCTATT 58.471 36.000 0.00 0.00 31.74 1.73
1727 2509 4.042809 TCCTCCCAATAAGAGCAGAAAACA 59.957 41.667 0.00 0.00 0.00 2.83
1737 2535 5.136220 TCATCTCTAGGTCCTCCCAATAAGA 59.864 44.000 0.00 0.00 34.66 2.10
1754 2553 6.558488 AAATCAGCTTAGGTTCTCATCTCT 57.442 37.500 0.00 0.00 0.00 3.10
1821 2659 7.422465 AATGCATTTACTACCAATGGTGATT 57.578 32.000 16.41 1.19 36.19 2.57
1923 2863 0.322816 TCTTGTGGAAGAGCATGGCC 60.323 55.000 0.00 0.00 32.98 5.36
2036 2976 3.494332 AGAAACTGAAAGCTGAGGCAAT 58.506 40.909 0.00 0.00 41.70 3.56
2091 3031 4.398673 ACATTTTGTTGCAATTTTGGCACT 59.601 33.333 0.59 0.00 41.75 4.40
2133 3073 4.520874 TGATCTCGAGTTCAACTCTTCAGT 59.479 41.667 21.07 0.00 42.92 3.41
2173 3113 5.641209 GTCACATCTTCAACTGCTTCTACAT 59.359 40.000 0.00 0.00 0.00 2.29
2203 3143 4.478206 TGGATCTTAGCACTCCTCTTTG 57.522 45.455 0.00 0.00 0.00 2.77
2249 3189 9.843334 CTTTGTTGTAAAAACAGTTACTTACCA 57.157 29.630 12.51 3.30 35.41 3.25
2329 3269 1.021390 ATCAGGAAACTTCAGCGGCG 61.021 55.000 0.51 0.51 40.21 6.46
2335 3275 7.681939 AAATTACGCTTATCAGGAAACTTCA 57.318 32.000 0.00 0.00 40.21 3.02
2349 3289 3.093057 TGGTATGGGCAAAATTACGCTT 58.907 40.909 0.00 0.00 0.00 4.68
2350 3290 2.687935 CTGGTATGGGCAAAATTACGCT 59.312 45.455 0.00 0.00 0.00 5.07
2355 3295 5.071653 ACAAGAAACTGGTATGGGCAAAATT 59.928 36.000 0.00 0.00 0.00 1.82
2363 3303 6.472887 TCTCCTAAACAAGAAACTGGTATGG 58.527 40.000 0.00 0.00 0.00 2.74
2427 3371 6.183360 CGACCTACAGCTTCAGTTTCATTAAG 60.183 42.308 0.00 0.00 0.00 1.85
2437 3381 3.057456 ACAGTTACGACCTACAGCTTCAG 60.057 47.826 0.00 0.00 0.00 3.02
2507 3451 6.620877 TGTAGGGTCAATCAACACTCTAAT 57.379 37.500 0.00 0.00 34.00 1.73
2524 3468 5.763204 TGTAGCTTTTCTGAAACTTGTAGGG 59.237 40.000 1.58 0.00 0.00 3.53
2576 3520 1.019673 CAAGGGCAATCTGACATCCG 58.980 55.000 0.00 0.00 0.00 4.18
2640 3586 4.038282 TGCAAAAGAAAGCACTCATGACAT 59.962 37.500 0.00 0.00 35.51 3.06
2649 3595 5.113502 AGTATGACTGCAAAAGAAAGCAC 57.886 39.130 0.00 0.00 36.62 4.40
2695 3641 1.942586 GCCTGATGGAACCGTTAACGT 60.943 52.381 25.15 9.05 34.52 3.99
2707 3653 3.152341 GGATACCATTCAAGCCTGATGG 58.848 50.000 10.48 10.48 36.80 3.51
2930 3878 2.191400 CTGGATCTTCCACTCCTCCAA 58.809 52.381 0.00 0.00 42.67 3.53
3246 4194 7.561356 AGAAAAATGAAGGGGGTTATACATCAG 59.439 37.037 0.00 0.00 0.00 2.90
3282 4230 8.140112 AGAGTAACAATACATCAAGGTCTTCT 57.860 34.615 0.00 0.00 34.29 2.85
3374 4322 0.827507 CCAACTTCTTGGGTGGTGGG 60.828 60.000 0.00 0.00 43.19 4.61
3397 4345 0.104855 GCTCTACGATGATGGTGCCA 59.895 55.000 0.00 0.00 0.00 4.92
3482 4430 3.381949 ACAAACTCTTCTGTGCTCGTAC 58.618 45.455 0.00 0.00 0.00 3.67
3567 4515 5.527214 CCAGTATTATTTGCTCGATGTTCCA 59.473 40.000 0.00 0.00 0.00 3.53
3750 4704 4.088496 CGACCAAATCGTTCAAAATTCTGC 59.912 41.667 0.00 0.00 46.25 4.26
3796 4750 3.251972 GCTTCTGCTCATATTTGCTACCC 59.748 47.826 0.00 0.00 36.03 3.69
3799 4753 3.879295 GTGGCTTCTGCTCATATTTGCTA 59.121 43.478 0.00 0.00 39.59 3.49
3800 4754 2.686915 GTGGCTTCTGCTCATATTTGCT 59.313 45.455 0.00 0.00 39.59 3.91
3836 4792 2.603560 CTCCCGAACTATTGTTTCGCTC 59.396 50.000 0.00 0.00 36.39 5.03
3839 4795 4.990257 TCTACTCCCGAACTATTGTTTCG 58.010 43.478 0.00 0.00 36.39 3.46
3847 4803 6.127253 CCCATTAAAACTCTACTCCCGAACTA 60.127 42.308 0.00 0.00 0.00 2.24
3869 4825 3.659786 CTTGATAACTCGTGTGTTCCCA 58.340 45.455 0.00 0.00 0.00 4.37
3881 4837 9.875691 AAGAAAAAGAAAAACAGCTTGATAACT 57.124 25.926 0.00 0.00 0.00 2.24
3912 4868 6.260050 TGGAATAGAACTTTGTGATTATCCGC 59.740 38.462 0.00 0.00 0.00 5.54
3916 4872 7.014615 GGCCATGGAATAGAACTTTGTGATTAT 59.985 37.037 18.40 0.00 0.00 1.28
3924 4880 5.388654 CCTATGGCCATGGAATAGAACTTT 58.611 41.667 29.26 0.32 0.00 2.66
3930 4886 3.814504 AACCCTATGGCCATGGAATAG 57.185 47.619 29.26 19.76 33.59 1.73
3968 4924 2.332117 GCCCCCAATCCATTCATGATT 58.668 47.619 0.00 0.00 0.00 2.57
3979 4935 3.140814 GCAACGAGGCCCCCAATC 61.141 66.667 0.00 0.00 0.00 2.67
3981 4937 4.211330 TTGCAACGAGGCCCCCAA 62.211 61.111 0.00 0.00 0.00 4.12
3992 4948 2.027460 CCGCCTGTTGGTTGCAAC 59.973 61.111 21.59 21.59 35.27 4.17
4058 5015 4.098654 CCGGTTGATATAGCTAGATCCCAG 59.901 50.000 22.37 14.24 0.00 4.45
4073 5030 2.429478 CGGGAGTTTAAACCGGTTGAT 58.571 47.619 23.08 8.92 43.69 2.57
4104 5061 4.937620 TCTGGTGAAGGAAATCAAGAATCG 59.062 41.667 0.00 0.00 0.00 3.34
4160 5117 8.248904 ACTCAATGATAGCTCTCTTCTATGTT 57.751 34.615 0.00 0.00 0.00 2.71
4166 5123 4.277174 TCGGACTCAATGATAGCTCTCTTC 59.723 45.833 0.00 0.00 0.00 2.87
4191 5150 3.644265 TCTAGCCTTCTTGTTGTGGTGTA 59.356 43.478 0.00 0.00 0.00 2.90
4193 5152 2.808543 GTCTAGCCTTCTTGTTGTGGTG 59.191 50.000 0.00 0.00 0.00 4.17
4194 5153 2.706190 AGTCTAGCCTTCTTGTTGTGGT 59.294 45.455 0.00 0.00 0.00 4.16
4196 5155 6.166279 TCAATAGTCTAGCCTTCTTGTTGTG 58.834 40.000 0.00 0.00 0.00 3.33
4197 5156 6.360370 TCAATAGTCTAGCCTTCTTGTTGT 57.640 37.500 0.00 0.00 0.00 3.32
4203 5162 3.389656 GCCCTTCAATAGTCTAGCCTTCT 59.610 47.826 0.00 0.00 0.00 2.85
4292 5334 6.591062 GTGAGATTATTTTTGCTTCATGCCAA 59.409 34.615 0.00 0.00 42.00 4.52
4312 5354 2.036387 TCTTGAGGAACAACGGTGAGA 58.964 47.619 7.88 0.00 34.56 3.27
4345 6020 1.345089 CCTCAGAGGATGGATCAGCAG 59.655 57.143 11.62 0.00 37.67 4.24


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

AutoCloner maintained by Alex Coulton.