Multiple sequence alignment - TraesCS6A01G166000

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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 TraesCS6A01G166000 chr6A 100.000 5227 0 0 1 5227 168114098 168119324 0.000000e+00 9653.0
1 TraesCS6A01G166000 chr6B 93.156 5260 212 66 43 5227 228238468 228243654 0.000000e+00 7583.0
2 TraesCS6A01G166000 chr6B 76.025 317 59 16 3526 3834 671166177 671165870 1.170000e-31 148.0
3 TraesCS6A01G166000 chr6B 98.214 56 1 0 4352 4407 228242812 228242867 1.200000e-16 99.0
4 TraesCS6A01G166000 chr6D 93.237 4924 213 65 357 5227 129780336 129785192 0.000000e+00 7138.0
5 TraesCS6A01G166000 chr6D 86.111 252 20 6 1 238 129779975 129780225 1.870000e-64 257.0
6 TraesCS6A01G166000 chr6D 88.764 89 7 1 238 326 129780249 129780334 7.160000e-19 106.0
7 TraesCS6A01G166000 chr6D 96.296 54 2 0 4352 4405 129784350 129784403 7.210000e-14 89.8
8 TraesCS6A01G166000 chr5A 79.388 980 176 23 2889 3852 4957895 4956926 0.000000e+00 667.0
9 TraesCS6A01G166000 chr5A 91.111 45 3 1 4185 4228 576084920 576084876 5.650000e-05 60.2
10 TraesCS6A01G166000 chr5A 91.111 45 3 1 4185 4228 576272511 576272555 5.650000e-05 60.2
11 TraesCS6A01G166000 chr5A 90.909 44 3 1 4185 4227 575706082 575706039 2.030000e-04 58.4
12 TraesCS6A01G166000 chr5B 78.163 980 188 21 2889 3852 7707664 7706695 7.490000e-168 601.0
13 TraesCS6A01G166000 chr5B 90.909 44 3 1 4185 4227 560441483 560441440 2.030000e-04 58.4
14 TraesCS6A01G166000 chr5B 88.889 45 4 1 4185 4228 561061827 561061783 3.000000e-03 54.7
15 TraesCS6A01G166000 chr7A 77.737 274 45 8 3206 3468 15525081 15524813 2.520000e-33 154.0
16 TraesCS6A01G166000 chr5D 72.347 311 68 16 3521 3822 458180772 458180471 1.210000e-11 82.4
17 TraesCS6A01G166000 chr5D 90.909 44 3 1 4185 4227 458094833 458094790 2.030000e-04 58.4
18 TraesCS6A01G166000 chr5D 100.000 31 0 0 4198 4228 458180083 458180053 2.030000e-04 58.4


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 TraesCS6A01G166000 chr6A 168114098 168119324 5226 False 9653.0 9653 100.000 1 5227 1 chr6A.!!$F1 5226
1 TraesCS6A01G166000 chr6B 228238468 228243654 5186 False 3841.0 7583 95.685 43 5227 2 chr6B.!!$F1 5184
2 TraesCS6A01G166000 chr6D 129779975 129785192 5217 False 1897.7 7138 91.102 1 5227 4 chr6D.!!$F1 5226
3 TraesCS6A01G166000 chr5A 4956926 4957895 969 True 667.0 667 79.388 2889 3852 1 chr5A.!!$R1 963
4 TraesCS6A01G166000 chr5B 7706695 7707664 969 True 601.0 601 78.163 2889 3852 1 chr5B.!!$R1 963

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
867 975 0.248907 CATACTACCACGGACGCAGG 60.249 60.0 2.76 2.76 0.00 4.85 F
1393 1504 0.248215 GCTACAACGATGGCATGCAC 60.248 55.0 21.36 9.64 0.00 4.57 F
1395 1506 0.322008 TACAACGATGGCATGCACCA 60.322 50.0 21.36 9.76 45.82 4.17 F
2592 2765 0.383124 GTGACGTGACTTTGCGCTTC 60.383 55.0 9.73 0.01 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1814 1950 0.037139 ACGCACGCCATGGTTAGTTA 60.037 50.0 14.67 0.00 0.00 2.24 R
2578 2751 0.385223 CTGCAGAAGCGCAAAGTCAC 60.385 55.0 8.42 0.00 46.23 3.67 R
2782 2958 1.044790 GGGGAATTCCTGCACCATGG 61.045 60.0 23.63 11.19 35.95 3.66 R
4334 4516 0.885196 CTAGTAGATGCCTCTCCCGC 59.115 60.0 0.00 0.00 32.66 6.13 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
22 23 2.069165 GACAAGCCCTGGGTCACCTT 62.069 60.000 15.56 6.04 37.76 3.50
30 31 0.252467 CTGGGTCACCTTCTCCCTCT 60.252 60.000 0.00 0.00 41.58 3.69
32 33 0.615850 GGGTCACCTTCTCCCTCTTG 59.384 60.000 0.00 0.00 38.29 3.02
41 46 2.830651 TCTCCCTCTTGGTCTCCTAC 57.169 55.000 0.00 0.00 34.77 3.18
57 62 5.945191 GTCTCCTACCCTAGTGATGTATACC 59.055 48.000 0.00 0.00 0.00 2.73
61 66 3.155501 ACCCTAGTGATGTATACCTCGC 58.844 50.000 12.28 12.28 0.00 5.03
137 151 1.282875 GGTGGAACGTGCTTCAAGC 59.717 57.895 1.04 1.04 39.05 4.01
146 160 1.536766 CGTGCTTCAAGCTTCCAATGA 59.463 47.619 11.57 0.00 42.97 2.57
158 172 1.831286 CCAATGATGCCCTCCTGCC 60.831 63.158 0.00 0.00 0.00 4.85
194 208 0.472471 TGTGGTTTTCTCGAGCCCTT 59.528 50.000 7.81 0.00 0.00 3.95
220 234 3.509740 GTCGACTAGCCAACTTTCTACC 58.490 50.000 8.70 0.00 0.00 3.18
221 235 3.057033 GTCGACTAGCCAACTTTCTACCA 60.057 47.826 8.70 0.00 0.00 3.25
232 246 6.458615 GCCAACTTTCTACCACGTAAGAAAAA 60.459 38.462 16.19 3.88 43.62 1.94
254 292 3.998341 ACTTTCCAGCGACGCTTATTTTA 59.002 39.130 21.97 2.86 36.40 1.52
260 298 4.518217 CAGCGACGCTTATTTTAAGATGG 58.482 43.478 21.97 0.00 36.40 3.51
319 357 2.981805 CACAAAGATCAAATGTGGCGTG 59.018 45.455 14.35 0.00 40.51 5.34
338 376 1.529438 TGCGCTCAAACTTTTCGTAGG 59.471 47.619 9.73 0.00 0.00 3.18
351 389 9.720769 AAACTTTTCGTAGGAGAAAATATCTGA 57.279 29.630 5.51 0.00 45.50 3.27
358 397 5.378230 AGGAGAAAATATCTGATGCACCA 57.622 39.130 0.00 0.00 38.96 4.17
368 407 2.568509 TCTGATGCACCAGTCTCAATCA 59.431 45.455 8.25 0.00 35.71 2.57
434 474 4.884458 TGCAAACAATGAGTAACGACAA 57.116 36.364 0.00 0.00 0.00 3.18
450 490 8.842280 AGTAACGACAATGGAAAGTATTCAAAA 58.158 29.630 0.00 0.00 37.29 2.44
451 491 9.620660 GTAACGACAATGGAAAGTATTCAAAAT 57.379 29.630 0.00 0.00 37.29 1.82
453 493 8.110860 ACGACAATGGAAAGTATTCAAAATCT 57.889 30.769 0.00 0.00 37.29 2.40
534 637 6.830114 AGATTAGCTTACTATTCAACACGC 57.170 37.500 0.00 0.00 33.19 5.34
539 642 4.267928 AGCTTACTATTCAACACGCGATTC 59.732 41.667 15.93 0.00 0.00 2.52
638 744 3.838244 AACTTCTAGACAAGTGCACCA 57.162 42.857 14.63 0.00 36.69 4.17
639 745 3.838244 ACTTCTAGACAAGTGCACCAA 57.162 42.857 14.63 0.00 35.18 3.67
671 777 2.781681 GCCATATACCATAGGGCGTT 57.218 50.000 6.14 0.00 37.90 4.84
682 790 2.965572 TAGGGCGTTATGTACACACC 57.034 50.000 0.00 0.00 0.00 4.16
686 794 1.206371 GGCGTTATGTACACACCCTCT 59.794 52.381 0.00 0.00 0.00 3.69
687 795 2.354403 GGCGTTATGTACACACCCTCTT 60.354 50.000 0.00 0.00 0.00 2.85
688 796 2.928116 GCGTTATGTACACACCCTCTTC 59.072 50.000 0.00 0.00 0.00 2.87
689 797 3.615592 GCGTTATGTACACACCCTCTTCA 60.616 47.826 0.00 0.00 0.00 3.02
690 798 4.562082 CGTTATGTACACACCCTCTTCAA 58.438 43.478 0.00 0.00 0.00 2.69
691 799 4.992319 CGTTATGTACACACCCTCTTCAAA 59.008 41.667 0.00 0.00 0.00 2.69
692 800 5.120208 CGTTATGTACACACCCTCTTCAAAG 59.880 44.000 0.00 0.00 0.00 2.77
746 854 5.578157 AATTTGGTTAGATAGCCGGGTAT 57.422 39.130 25.69 25.69 0.00 2.73
749 857 1.403780 GGTTAGATAGCCGGGTATGCG 60.404 57.143 29.96 0.00 0.00 4.73
760 868 0.537143 GGGTATGCGGCCAATCATCA 60.537 55.000 2.24 0.00 0.00 3.07
795 903 1.068816 TCACGACTGACACACATACGG 60.069 52.381 0.00 0.00 33.78 4.02
799 907 1.198408 GACTGACACACATACGGACGA 59.802 52.381 0.00 0.00 0.00 4.20
816 924 1.787847 GAGAAACACATCGCCGTGG 59.212 57.895 8.60 0.00 41.38 4.94
843 951 4.338118 ACCGCATCCAACAATATAAACTGG 59.662 41.667 0.00 0.00 0.00 4.00
867 975 0.248907 CATACTACCACGGACGCAGG 60.249 60.000 2.76 2.76 0.00 4.85
912 1022 1.470996 CCTGCCCTCCTAGCTAGCTG 61.471 65.000 27.68 16.13 0.00 4.24
913 1023 0.468958 CTGCCCTCCTAGCTAGCTGA 60.469 60.000 27.68 15.54 0.00 4.26
917 1027 1.327303 CCTCCTAGCTAGCTGACTGG 58.673 60.000 27.68 21.06 0.00 4.00
1393 1504 0.248215 GCTACAACGATGGCATGCAC 60.248 55.000 21.36 9.64 0.00 4.57
1394 1505 0.378257 CTACAACGATGGCATGCACC 59.622 55.000 21.36 3.15 0.00 5.01
1395 1506 0.322008 TACAACGATGGCATGCACCA 60.322 50.000 21.36 9.76 45.82 4.17
1438 1565 3.670359 GCATGCTACAGCGTTTGATTTGA 60.670 43.478 11.37 0.00 45.83 2.69
1467 1594 4.036734 TCACATGGCTGAGAAAAGTTGTTC 59.963 41.667 0.00 0.00 0.00 3.18
1498 1625 2.444895 CGGGAAGGGAGAGGGAGG 60.445 72.222 0.00 0.00 0.00 4.30
1499 1626 2.040359 GGGAAGGGAGAGGGAGGG 60.040 72.222 0.00 0.00 0.00 4.30
1645 1772 2.897436 TCAAGGACATCAAGCTCATCG 58.103 47.619 0.00 0.00 0.00 3.84
1799 1935 4.121669 GCTCTCTCCGTGCTCGCA 62.122 66.667 1.89 0.00 35.54 5.10
1807 1943 2.780643 CGTGCTCGCATGGAACTG 59.219 61.111 3.21 0.00 0.00 3.16
1808 1944 2.029288 CGTGCTCGCATGGAACTGT 61.029 57.895 3.21 0.00 0.00 3.55
1809 1945 1.499056 GTGCTCGCATGGAACTGTG 59.501 57.895 0.00 0.00 0.00 3.66
1811 1947 2.401766 GCTCGCATGGAACTGTGGG 61.402 63.158 0.00 0.00 0.00 4.61
1812 1948 1.296392 CTCGCATGGAACTGTGGGA 59.704 57.895 0.00 0.00 35.98 4.37
1813 1949 1.003839 TCGCATGGAACTGTGGGAC 60.004 57.895 0.00 0.00 33.60 4.46
1814 1950 1.003355 CGCATGGAACTGTGGGACT 60.003 57.895 0.00 0.00 31.77 3.85
2012 2148 1.439679 GGACAAGAACATCGACCACC 58.560 55.000 0.00 0.00 0.00 4.61
2020 2156 4.404098 ATCGACCACCAACGCCCC 62.404 66.667 0.00 0.00 0.00 5.80
2104 2245 2.560861 GGTACGTACGCACACCGA 59.439 61.111 19.66 0.00 41.02 4.69
2119 2260 2.509336 CGACCTTGCTACCTGGCG 60.509 66.667 0.00 0.00 34.52 5.69
2120 2261 2.125106 GACCTTGCTACCTGGCGG 60.125 66.667 0.00 0.00 34.52 6.13
2122 2263 2.351276 CCTTGCTACCTGGCGGTT 59.649 61.111 6.35 0.00 42.13 4.44
2123 2264 1.196104 ACCTTGCTACCTGGCGGTTA 61.196 55.000 6.35 0.00 42.13 2.85
2124 2265 0.462047 CCTTGCTACCTGGCGGTTAG 60.462 60.000 6.35 0.00 42.13 2.34
2125 2266 1.078708 TTGCTACCTGGCGGTTAGC 60.079 57.895 15.28 15.28 42.13 3.09
2329 2478 0.461870 TGCTCAACAACTCGCAGTGT 60.462 50.000 0.00 0.00 34.88 3.55
2374 2523 1.141881 CCTCTACAGCGACGGCATT 59.858 57.895 0.00 0.00 43.41 3.56
2511 2660 1.558741 GAGATGCTTGAGAGTGAGCG 58.441 55.000 0.00 0.00 41.75 5.03
2551 2719 1.153765 CCAGAGCACGATCGAGCAA 60.154 57.895 33.40 0.00 34.21 3.91
2552 2720 1.416813 CCAGAGCACGATCGAGCAAC 61.417 60.000 33.40 26.09 34.21 4.17
2562 2730 5.034797 CACGATCGAGCAACTAATTACTGA 58.965 41.667 24.34 0.00 0.00 3.41
2565 2733 5.396947 CGATCGAGCAACTAATTACTGAGAC 59.603 44.000 10.26 0.00 0.00 3.36
2578 2751 1.199327 ACTGAGACCACATACGTGACG 59.801 52.381 2.24 2.24 46.80 4.35
2592 2765 0.383124 GTGACGTGACTTTGCGCTTC 60.383 55.000 9.73 0.01 0.00 3.86
2703 2876 8.032451 CCTCACGGTAATTAATCAACCATTTTT 58.968 33.333 16.25 0.00 32.55 1.94
2765 2941 9.978044 AAGTTCACTTAGTTAATTAACGAGAGT 57.022 29.630 27.14 23.36 40.96 3.24
3938 4120 2.586245 CTCCCCTCGCAGATGCAA 59.414 61.111 5.55 0.00 42.21 4.08
4067 4249 1.782181 GGCGTTCGAGAAGTTCAGC 59.218 57.895 5.50 0.91 0.00 4.26
4136 4318 0.868406 CGGAGAACAAGAACAGGTGC 59.132 55.000 0.00 0.00 0.00 5.01
4227 4409 2.158652 CCCAACAGCATCTCCATCTGAT 60.159 50.000 0.00 0.00 0.00 2.90
4228 4410 3.072038 CCCAACAGCATCTCCATCTGATA 59.928 47.826 0.00 0.00 0.00 2.15
4230 4412 4.316645 CAACAGCATCTCCATCTGATAGG 58.683 47.826 0.00 0.00 0.00 2.57
4232 4414 2.905085 CAGCATCTCCATCTGATAGGGT 59.095 50.000 0.00 0.00 0.00 4.34
4246 4428 3.181406 TGATAGGGTCCCCAGGATAAGAG 60.181 52.174 3.51 0.00 38.92 2.85
4268 4450 9.584008 AAGAGATCATTGCATGTAGGATTATTT 57.416 29.630 0.00 0.00 0.00 1.40
4387 4600 5.880054 AGGTTATTTGAATTGTGACCTCG 57.120 39.130 0.00 0.00 30.59 4.63
4405 4618 5.380043 ACCTCGTCGAATCCTAATTAGGTA 58.620 41.667 27.14 16.25 44.02 3.08
4406 4619 5.829924 ACCTCGTCGAATCCTAATTAGGTAA 59.170 40.000 27.14 12.65 44.02 2.85
4407 4620 6.492772 ACCTCGTCGAATCCTAATTAGGTAAT 59.507 38.462 27.14 14.27 44.02 1.89
4408 4621 7.015001 ACCTCGTCGAATCCTAATTAGGTAATT 59.985 37.037 27.14 20.77 44.02 1.40
4409 4622 7.541437 CCTCGTCGAATCCTAATTAGGTAATTC 59.459 40.741 27.14 25.22 44.02 2.17
4413 4626 7.416154 CGAATCCTAATTAGGTAATTCGCAA 57.584 36.000 33.22 16.39 45.11 4.85
4414 4627 7.288672 CGAATCCTAATTAGGTAATTCGCAAC 58.711 38.462 33.22 16.59 45.11 4.17
4415 4628 7.506328 AATCCTAATTAGGTAATTCGCAACC 57.494 36.000 27.14 0.00 44.02 3.77
4416 4629 5.991861 TCCTAATTAGGTAATTCGCAACCA 58.008 37.500 27.14 4.27 44.02 3.67
4417 4630 6.416415 TCCTAATTAGGTAATTCGCAACCAA 58.584 36.000 27.14 3.86 44.02 3.67
4418 4631 6.885376 TCCTAATTAGGTAATTCGCAACCAAA 59.115 34.615 27.14 3.25 44.02 3.28
4419 4632 7.393796 TCCTAATTAGGTAATTCGCAACCAAAA 59.606 33.333 27.14 2.89 44.02 2.44
4420 4633 8.030106 CCTAATTAGGTAATTCGCAACCAAAAA 58.970 33.333 21.62 0.00 38.30 1.94
4455 4668 4.783227 AGGTAAGAAAGAGTGGGCATCTAA 59.217 41.667 0.00 0.00 0.00 2.10
4456 4669 5.430089 AGGTAAGAAAGAGTGGGCATCTAAT 59.570 40.000 0.00 0.00 0.00 1.73
4614 4827 0.520404 GTGTCGACTGGCTAACGAGA 59.480 55.000 17.92 0.00 36.74 4.04
4646 4859 5.768164 CCACACATTTACAAGACTTAAGGGT 59.232 40.000 7.53 2.35 0.00 4.34
4647 4860 6.264518 CCACACATTTACAAGACTTAAGGGTT 59.735 38.462 7.53 0.00 0.00 4.11
4866 5079 4.404640 AGTTTACTTTGCTTACTTCCCCC 58.595 43.478 0.00 0.00 0.00 5.40
4964 5177 6.128282 GGCATCGACAGAAAATTGTAAAGAGA 60.128 38.462 0.00 0.00 0.00 3.10
5093 5306 0.392193 CACCCTGGCTGACTGATCAC 60.392 60.000 0.00 0.00 0.00 3.06
5113 5326 8.668353 TGATCACAGCAATCAAATTAAGACTAC 58.332 33.333 0.00 0.00 30.37 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.229658 AGGGAGAAGGTGACCCAGG 60.230 63.158 0.00 0.00 45.43 4.45
11 12 0.252467 AGAGGGAGAAGGTGACCCAG 60.252 60.000 0.00 0.00 45.43 4.45
12 13 0.193574 AAGAGGGAGAAGGTGACCCA 59.806 55.000 0.00 0.00 45.43 4.51
14 15 0.615850 CCAAGAGGGAGAAGGTGACC 59.384 60.000 0.00 0.00 40.01 4.02
22 23 2.830651 GTAGGAGACCAAGAGGGAGA 57.169 55.000 0.00 0.00 41.15 3.71
41 46 2.161808 CGCGAGGTATACATCACTAGGG 59.838 54.545 17.02 5.74 0.00 3.53
46 51 0.317603 ACGCGCGAGGTATACATCAC 60.318 55.000 39.36 6.89 0.00 3.06
108 113 4.263572 TTCCACCACACCCGGCAG 62.264 66.667 0.00 0.00 0.00 4.85
109 114 4.572571 GTTCCACCACACCCGGCA 62.573 66.667 0.00 0.00 0.00 5.69
137 151 1.688772 CAGGAGGGCATCATTGGAAG 58.311 55.000 0.08 0.00 0.00 3.46
146 160 4.115199 GAACGGGCAGGAGGGCAT 62.115 66.667 0.00 0.00 45.66 4.40
158 172 6.836577 AACCACATAAAATTTGTTGAACGG 57.163 33.333 7.43 7.06 0.00 4.44
194 208 0.892358 AGTTGGCTAGTCGACCGACA 60.892 55.000 22.26 9.59 46.76 4.35
220 234 3.966218 CGCTGGAAAGTTTTTCTTACGTG 59.034 43.478 0.00 0.00 35.02 4.49
221 235 3.872771 TCGCTGGAAAGTTTTTCTTACGT 59.127 39.130 0.00 0.00 35.02 3.57
232 246 2.094762 AATAAGCGTCGCTGGAAAGT 57.905 45.000 22.50 6.27 39.62 2.66
260 298 7.125053 AGCAGCCTAAAGAATATATACTCCCTC 59.875 40.741 0.00 0.00 0.00 4.30
319 357 1.796459 TCCTACGAAAAGTTTGAGCGC 59.204 47.619 0.00 0.00 0.00 5.92
338 376 6.054295 AGACTGGTGCATCAGATATTTTCTC 58.946 40.000 33.21 16.83 38.11 2.87
351 389 3.639672 TGATGATTGAGACTGGTGCAT 57.360 42.857 0.00 0.00 0.00 3.96
358 397 9.504708 GAATTCCTGAATATGATGATTGAGACT 57.495 33.333 0.00 0.00 0.00 3.24
391 430 5.757808 GCATGCCCTTTGTTTCTTTTTAGAA 59.242 36.000 6.36 0.00 0.00 2.10
450 490 6.882610 TCACAATTGTGCTTTCAGTTAGAT 57.117 33.333 29.84 0.00 45.25 1.98
451 491 6.691754 TTCACAATTGTGCTTTCAGTTAGA 57.308 33.333 29.84 8.66 45.25 2.10
453 493 6.625362 TGTTTCACAATTGTGCTTTCAGTTA 58.375 32.000 29.84 9.86 45.25 2.24
590 693 6.908870 AAAAAGTGCTGGAAAGAATTGAAC 57.091 33.333 0.00 0.00 0.00 3.18
671 777 5.818678 ACTTTGAAGAGGGTGTGTACATA 57.181 39.130 0.00 0.00 0.00 2.29
682 790 6.396829 AAGTCCATTTGAACTTTGAAGAGG 57.603 37.500 0.00 0.00 0.00 3.69
689 797 9.898152 TGGAAATAAAAAGTCCATTTGAACTTT 57.102 25.926 0.00 0.00 36.51 2.66
690 798 9.898152 TTGGAAATAAAAAGTCCATTTGAACTT 57.102 25.926 0.00 0.00 41.05 2.66
691 799 9.546428 CTTGGAAATAAAAAGTCCATTTGAACT 57.454 29.630 0.00 0.00 41.05 3.01
692 800 9.541143 TCTTGGAAATAAAAAGTCCATTTGAAC 57.459 29.630 0.00 0.00 41.05 3.18
724 832 3.945640 ACCCGGCTATCTAACCAAATT 57.054 42.857 0.00 0.00 0.00 1.82
741 849 0.537143 TGATGATTGGCCGCATACCC 60.537 55.000 0.00 0.00 0.00 3.69
746 854 0.456628 CAACATGATGATTGGCCGCA 59.543 50.000 0.00 0.00 0.00 5.69
749 857 1.799917 CGTGCAACATGATGATTGGCC 60.800 52.381 7.22 0.00 35.74 5.36
752 860 1.552226 GCCGTGCAACATGATGATTG 58.448 50.000 7.22 1.52 35.74 2.67
760 868 2.035469 TGATGGGCCGTGCAACAT 59.965 55.556 1.02 0.00 35.74 2.71
795 903 1.007336 ACGGCGATGTGTTTCTCGTC 61.007 55.000 16.62 0.00 37.23 4.20
799 907 0.670546 CTCCACGGCGATGTGTTTCT 60.671 55.000 16.62 0.00 38.20 2.52
816 924 1.378531 TATTGTTGGATGCGGTGCTC 58.621 50.000 0.00 0.00 0.00 4.26
826 934 5.073428 TGTGTGCCAGTTTATATTGTTGGA 58.927 37.500 0.00 0.00 0.00 3.53
843 951 1.636988 GTCCGTGGTAGTATGTGTGC 58.363 55.000 0.00 0.00 0.00 4.57
875 983 2.904866 CCCCTCTCTCGGCTCTCG 60.905 72.222 0.00 0.00 40.90 4.04
895 1005 0.757188 GTCAGCTAGCTAGGAGGGCA 60.757 60.000 18.86 0.00 0.00 5.36
928 1038 4.150359 TCGACCTCTACCTTCTGTTCTTT 58.850 43.478 0.00 0.00 0.00 2.52
1393 1504 0.464870 CTCTCTCCTGTCCTGCATGG 59.535 60.000 0.00 0.00 37.10 3.66
1394 1505 0.179078 GCTCTCTCCTGTCCTGCATG 60.179 60.000 0.00 0.00 0.00 4.06
1395 1506 0.616964 TGCTCTCTCCTGTCCTGCAT 60.617 55.000 0.00 0.00 0.00 3.96
1396 1507 0.616964 ATGCTCTCTCCTGTCCTGCA 60.617 55.000 0.00 0.00 0.00 4.41
1397 1508 0.179078 CATGCTCTCTCCTGTCCTGC 60.179 60.000 0.00 0.00 0.00 4.85
1398 1509 0.179078 GCATGCTCTCTCCTGTCCTG 60.179 60.000 11.37 0.00 0.00 3.86
1399 1510 0.616964 TGCATGCTCTCTCCTGTCCT 60.617 55.000 20.33 0.00 0.00 3.85
1429 1556 7.498239 TCAGCCATGTGAAAAATTCAAATCAAA 59.502 29.630 0.00 0.00 42.15 2.69
1498 1625 2.434359 CGCGAACCCCTTCACTCC 60.434 66.667 0.00 0.00 0.00 3.85
1499 1626 3.119096 GCGCGAACCCCTTCACTC 61.119 66.667 12.10 0.00 0.00 3.51
1776 1912 4.803426 CACGGAGAGAGCGTGGGC 62.803 72.222 0.00 0.00 40.37 5.36
1777 1913 4.803426 GCACGGAGAGAGCGTGGG 62.803 72.222 0.00 0.00 34.60 4.61
1796 1932 0.249120 TAGTCCCACAGTTCCATGCG 59.751 55.000 0.00 0.00 0.00 4.73
1799 1935 4.019591 GGTTAGTTAGTCCCACAGTTCCAT 60.020 45.833 0.00 0.00 0.00 3.41
1803 1939 4.263331 CCATGGTTAGTTAGTCCCACAGTT 60.263 45.833 2.57 0.00 0.00 3.16
1805 1941 3.873910 CCATGGTTAGTTAGTCCCACAG 58.126 50.000 2.57 0.00 0.00 3.66
1807 1943 2.640184 GCCATGGTTAGTTAGTCCCAC 58.360 52.381 14.67 0.00 0.00 4.61
1808 1944 1.208535 CGCCATGGTTAGTTAGTCCCA 59.791 52.381 14.67 0.00 0.00 4.37
1809 1945 1.208776 ACGCCATGGTTAGTTAGTCCC 59.791 52.381 14.67 0.00 0.00 4.46
1811 1947 1.664151 GCACGCCATGGTTAGTTAGTC 59.336 52.381 14.67 0.00 0.00 2.59
1812 1948 1.734163 GCACGCCATGGTTAGTTAGT 58.266 50.000 14.67 0.00 0.00 2.24
1813 1949 0.650512 CGCACGCCATGGTTAGTTAG 59.349 55.000 14.67 4.30 0.00 2.34
1814 1950 0.037139 ACGCACGCCATGGTTAGTTA 60.037 50.000 14.67 0.00 0.00 2.24
2329 2478 2.358247 GCCGGGAAGTGCGAGAAA 60.358 61.111 2.18 0.00 0.00 2.52
2551 2719 6.376299 TCACGTATGTGGTCTCAGTAATTAGT 59.624 38.462 15.02 0.00 46.42 2.24
2552 2720 6.691818 GTCACGTATGTGGTCTCAGTAATTAG 59.308 42.308 15.02 0.00 46.42 1.73
2562 2730 1.068748 GTCACGTCACGTATGTGGTCT 60.069 52.381 15.02 0.00 46.42 3.85
2565 2733 2.060326 AAGTCACGTCACGTATGTGG 57.940 50.000 15.02 2.70 46.42 4.17
2578 2751 0.385223 CTGCAGAAGCGCAAAGTCAC 60.385 55.000 8.42 0.00 46.23 3.67
2592 2765 1.369091 CGAAAATCGGTCCCCTGCAG 61.369 60.000 6.78 6.78 36.00 4.41
2703 2876 7.725251 ACTTGATCAAAGGCTGTGAAAAATAA 58.275 30.769 12.21 2.44 40.51 1.40
2704 2877 7.288810 ACTTGATCAAAGGCTGTGAAAAATA 57.711 32.000 12.21 0.00 40.51 1.40
2705 2878 6.165700 ACTTGATCAAAGGCTGTGAAAAAT 57.834 33.333 12.21 0.00 40.51 1.82
2706 2879 5.596836 ACTTGATCAAAGGCTGTGAAAAA 57.403 34.783 12.21 8.20 40.51 1.94
2707 2880 5.350633 CAACTTGATCAAAGGCTGTGAAAA 58.649 37.500 12.21 8.55 40.51 2.29
2708 2881 4.737352 GCAACTTGATCAAAGGCTGTGAAA 60.737 41.667 12.21 1.37 40.51 2.69
2772 2948 1.745890 GCACCATGGATGCATGCAT 59.254 52.632 32.66 32.66 42.88 3.96
2773 2949 3.212275 GCACCATGGATGCATGCA 58.788 55.556 25.04 25.04 42.88 3.96
2782 2958 1.044790 GGGGAATTCCTGCACCATGG 61.045 60.000 23.63 11.19 35.95 3.66
4052 4234 0.944311 TGCCGCTGAACTTCTCGAAC 60.944 55.000 0.00 0.62 0.00 3.95
4084 4266 4.530857 GGTCGATGGTGCCCTCCG 62.531 72.222 0.00 0.00 0.00 4.63
4232 4414 3.328931 GCAATGATCTCTTATCCTGGGGA 59.671 47.826 0.00 0.00 35.55 4.81
4282 4464 1.003839 CTGGGTGCGTACATGGTGT 60.004 57.895 5.86 0.00 0.00 4.16
4334 4516 0.885196 CTAGTAGATGCCTCTCCCGC 59.115 60.000 0.00 0.00 32.66 6.13
4425 4638 7.110155 TGCCCACTCTTTCTTACCTTAATTAG 58.890 38.462 0.00 0.00 0.00 1.73
4426 4639 7.023171 TGCCCACTCTTTCTTACCTTAATTA 57.977 36.000 0.00 0.00 0.00 1.40
4427 4640 5.887754 TGCCCACTCTTTCTTACCTTAATT 58.112 37.500 0.00 0.00 0.00 1.40
4428 4641 5.514500 TGCCCACTCTTTCTTACCTTAAT 57.486 39.130 0.00 0.00 0.00 1.40
4429 4642 4.986054 TGCCCACTCTTTCTTACCTTAA 57.014 40.909 0.00 0.00 0.00 1.85
4430 4643 4.783227 AGATGCCCACTCTTTCTTACCTTA 59.217 41.667 0.00 0.00 0.00 2.69
4431 4644 3.589288 AGATGCCCACTCTTTCTTACCTT 59.411 43.478 0.00 0.00 0.00 3.50
4432 4645 3.185455 AGATGCCCACTCTTTCTTACCT 58.815 45.455 0.00 0.00 0.00 3.08
4433 4646 3.636153 AGATGCCCACTCTTTCTTACC 57.364 47.619 0.00 0.00 0.00 2.85
4434 4647 6.458888 GCAATTAGATGCCCACTCTTTCTTAC 60.459 42.308 0.00 0.00 40.49 2.34
4455 4668 3.657398 TGATCTGTCCAGGAATGCAAT 57.343 42.857 0.00 0.00 0.00 3.56
4456 4669 3.657398 ATGATCTGTCCAGGAATGCAA 57.343 42.857 0.00 0.00 0.00 4.08
4541 4754 3.311871 GTCCTGATCTTACAATGCTGCTG 59.688 47.826 0.00 0.00 0.00 4.41
4640 4853 8.792830 ATGTAGTTCTGTCCATATAACCCTTA 57.207 34.615 0.00 0.00 0.00 2.69
4646 4859 9.429109 TCCACTTATGTAGTTCTGTCCATATAA 57.571 33.333 0.00 0.00 33.85 0.98
4647 4860 9.078990 CTCCACTTATGTAGTTCTGTCCATATA 57.921 37.037 0.00 0.00 33.85 0.86
4652 4865 5.916661 TCTCCACTTATGTAGTTCTGTCC 57.083 43.478 0.00 0.00 33.85 4.02
4866 5079 2.290916 ACTATGTGATGCTCGACTACGG 59.709 50.000 0.00 0.00 40.21 4.02
4867 5080 3.242772 ACACTATGTGATGCTCGACTACG 60.243 47.826 4.61 0.00 36.96 3.51
4868 5081 4.035792 AGACACTATGTGATGCTCGACTAC 59.964 45.833 4.61 0.00 36.96 2.73
4964 5177 3.568430 TCCGAGTATATGAAGCGTCACAT 59.432 43.478 3.91 0.68 36.31 3.21
5052 5265 0.616964 ACTGAGAGCTGCATCTCCCA 60.617 55.000 13.81 7.75 44.30 4.37
5093 5306 7.637519 CACATCGTAGTCTTAATTTGATTGCTG 59.362 37.037 0.00 0.00 0.00 4.41
5130 5343 5.368256 CACTTGATAGTGCAGCTTCTTTT 57.632 39.130 0.00 0.00 44.81 2.27


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

AutoCloner maintained by Alex Coulton.