Multiple sequence alignment - TraesCS7A01G137200

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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 TraesCS7A01G137200 chr7A 100.000 2273 0 0 1 2273 89899856 89902128 0.000000e+00 4198
1 TraesCS7A01G137200 chr2D 91.787 1242 102 0 1 1242 155000641 155001882 0.000000e+00 1729
2 TraesCS7A01G137200 chr7D 86.647 996 76 19 1299 2273 88316043 88317002 0.000000e+00 1050
3 TraesCS7A01G137200 chr2A 80.122 1308 229 25 1 1297 750367480 750368767 0.000000e+00 946
4 TraesCS7A01G137200 chr7B 87.500 840 78 10 1430 2247 38372518 38373352 0.000000e+00 944
5 TraesCS7A01G137200 chr7B 88.618 123 4 3 1299 1421 38321603 38321715 8.460000e-30 141
6 TraesCS7A01G137200 chr3B 80.367 1253 232 14 57 1302 674434923 674433678 0.000000e+00 939
7 TraesCS7A01G137200 chr3B 80.637 1193 218 12 113 1299 636870256 636871441 0.000000e+00 911
8 TraesCS7A01G137200 chr6A 80.177 1246 238 9 57 1297 463580360 463581601 0.000000e+00 924
9 TraesCS7A01G137200 chr5B 81.556 1041 183 9 263 1298 642054256 642053220 0.000000e+00 850


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 TraesCS7A01G137200 chr7A 89899856 89902128 2272 False 4198 4198 100.000 1 2273 1 chr7A.!!$F1 2272
1 TraesCS7A01G137200 chr2D 155000641 155001882 1241 False 1729 1729 91.787 1 1242 1 chr2D.!!$F1 1241
2 TraesCS7A01G137200 chr7D 88316043 88317002 959 False 1050 1050 86.647 1299 2273 1 chr7D.!!$F1 974
3 TraesCS7A01G137200 chr2A 750367480 750368767 1287 False 946 946 80.122 1 1297 1 chr2A.!!$F1 1296
4 TraesCS7A01G137200 chr7B 38372518 38373352 834 False 944 944 87.500 1430 2247 1 chr7B.!!$F2 817
5 TraesCS7A01G137200 chr3B 674433678 674434923 1245 True 939 939 80.367 57 1302 1 chr3B.!!$R1 1245
6 TraesCS7A01G137200 chr3B 636870256 636871441 1185 False 911 911 80.637 113 1299 1 chr3B.!!$F1 1186
7 TraesCS7A01G137200 chr6A 463580360 463581601 1241 False 924 924 80.177 57 1297 1 chr6A.!!$F1 1240
8 TraesCS7A01G137200 chr5B 642053220 642054256 1036 True 850 850 81.556 263 1298 1 chr5B.!!$R1 1035

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
717 726 0.107456 AGTCCATGATCATGACCCGC 59.893 55.0 32.71 18.03 41.2 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2128 2161 0.252284 GGGAGAACAGGGGTCAGAGA 60.252 60.0 0.0 0.0 0.0 3.1 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
31 32 3.923648 ACTGTGGCCATGATACCTACTA 58.076 45.455 9.72 0.00 0.00 1.82
99 100 8.627208 ATGATGATATTGGTATGTGGAAAGTC 57.373 34.615 0.00 0.00 0.00 3.01
116 117 6.878923 TGGAAAGTCGATGTTATCAGACAAAT 59.121 34.615 12.60 3.32 36.21 2.32
117 118 8.038351 TGGAAAGTCGATGTTATCAGACAAATA 58.962 33.333 12.60 0.00 36.21 1.40
132 133 6.073314 CAGACAAATATTCATTCCCCCTGAT 58.927 40.000 0.00 0.00 0.00 2.90
172 181 1.153628 CCGATCAGAACGGGTGGAC 60.154 63.158 11.28 0.00 45.65 4.02
206 215 1.628846 GGCCTGGGAGTTTGAGAAGTA 59.371 52.381 0.00 0.00 0.00 2.24
243 252 6.631016 TGTAAAATCTGTGTATCGCTCTCTT 58.369 36.000 0.00 0.00 0.00 2.85
283 292 0.753848 AGCTCTAGAGGAAGGGACGC 60.754 60.000 21.23 4.36 0.00 5.19
284 293 1.740332 GCTCTAGAGGAAGGGACGCC 61.740 65.000 21.23 0.00 0.00 5.68
393 402 0.901827 TGCTGCGAGGAATTCTACCA 59.098 50.000 5.23 0.00 0.00 3.25
471 480 2.174363 TGCACACTGATGAGACCTTG 57.826 50.000 0.00 0.00 0.00 3.61
546 555 2.948979 AGAGTGGTTGCAAATCAAACGA 59.051 40.909 0.00 0.00 39.64 3.85
549 558 1.268794 TGGTTGCAAATCAAACGACCG 60.269 47.619 0.00 0.00 45.29 4.79
609 618 2.033927 TGATCCTCGCTTCTCTGAATCG 59.966 50.000 0.00 0.00 0.00 3.34
675 684 3.487376 CCCGCAATAACATCACACATGAC 60.487 47.826 0.00 0.00 37.79 3.06
717 726 0.107456 AGTCCATGATCATGACCCGC 59.893 55.000 32.71 18.03 41.20 6.13
744 753 5.709631 TGCACTTGCTTTACTTGATATTCCA 59.290 36.000 2.33 0.00 42.66 3.53
813 822 6.360618 GGATGAGAACTGGGTGAAGATTAAT 58.639 40.000 0.00 0.00 0.00 1.40
822 831 4.410883 TGGGTGAAGATTAATACCGATGGT 59.589 41.667 0.00 0.00 40.16 3.55
886 895 1.468908 CGAGAACTCGCTCTGCATTCT 60.469 52.381 11.13 0.00 46.50 2.40
935 944 3.007398 GGGATCTCAGATCCGCTAATTGT 59.993 47.826 24.94 0.00 39.07 2.71
993 1002 0.108585 AGCTGCGAGGTTTCTCCAAA 59.891 50.000 0.00 0.00 39.02 3.28
994 1003 0.951558 GCTGCGAGGTTTCTCCAAAA 59.048 50.000 0.00 0.00 39.02 2.44
1005 1014 6.018469 AGGTTTCTCCAAAATCATCATGGAA 58.982 36.000 0.00 0.00 42.41 3.53
1014 1023 4.978083 AATCATCATGGAAACTGACTGC 57.022 40.909 0.00 0.00 0.00 4.40
1048 1057 4.278170 TCAACTTCTGGAATTTGCGTCAAT 59.722 37.500 8.05 0.00 32.91 2.57
1053 1062 4.326826 TCTGGAATTTGCGTCAATCTTCT 58.673 39.130 11.40 0.00 0.00 2.85
1056 1065 3.485877 GGAATTTGCGTCAATCTTCTCGG 60.486 47.826 11.40 0.00 0.00 4.63
1057 1066 2.448926 TTTGCGTCAATCTTCTCGGA 57.551 45.000 0.00 0.00 0.00 4.55
1062 1071 2.159421 GCGTCAATCTTCTCGGACAGTA 60.159 50.000 0.00 0.00 0.00 2.74
1075 1084 1.033574 GACAGTAGTGGCGCCTATCT 58.966 55.000 29.70 23.39 0.00 1.98
1079 1088 2.885266 CAGTAGTGGCGCCTATCTTAGA 59.115 50.000 29.70 0.07 0.00 2.10
1120 1129 6.811170 TGCCTTGTCTTTTACTTCTTTTGTTG 59.189 34.615 0.00 0.00 0.00 3.33
1129 1138 7.754069 TTTACTTCTTTTGTTGTTCAGCATG 57.246 32.000 0.00 0.00 37.54 4.06
1236 1245 6.867293 CGAAACCTAGCTTTCTTGTAACTAGT 59.133 38.462 8.52 0.00 30.56 2.57
1249 1258 6.890268 TCTTGTAACTAGTCTCTTGGCAGATA 59.110 38.462 0.00 0.00 0.00 1.98
1265 1275 1.440145 GATACTGCCGGAGCCTTTGC 61.440 60.000 5.05 0.00 38.69 3.68
1281 1291 3.119495 CCTTTGCTGAATAAAACTCCCCG 60.119 47.826 0.00 0.00 0.00 5.73
1341 1351 2.103537 CCCCCTAACAACAAGTACGG 57.896 55.000 0.00 0.00 0.00 4.02
1342 1352 1.624813 CCCCCTAACAACAAGTACGGA 59.375 52.381 0.00 0.00 0.00 4.69
1343 1353 2.613725 CCCCCTAACAACAAGTACGGAC 60.614 54.545 0.00 0.00 0.00 4.79
1344 1354 2.613725 CCCCTAACAACAAGTACGGACC 60.614 54.545 0.00 0.00 0.00 4.46
1345 1355 2.301009 CCCTAACAACAAGTACGGACCT 59.699 50.000 0.00 0.00 0.00 3.85
1346 1356 3.244318 CCCTAACAACAAGTACGGACCTT 60.244 47.826 0.00 0.00 0.00 3.50
1347 1357 3.992427 CCTAACAACAAGTACGGACCTTC 59.008 47.826 0.00 0.00 0.00 3.46
1348 1358 2.538512 ACAACAAGTACGGACCTTCC 57.461 50.000 0.00 0.00 0.00 3.46
1349 1359 2.044758 ACAACAAGTACGGACCTTCCT 58.955 47.619 0.00 0.00 33.30 3.36
1350 1360 2.224209 ACAACAAGTACGGACCTTCCTG 60.224 50.000 0.00 0.00 33.30 3.86
1351 1361 1.713297 ACAAGTACGGACCTTCCTGT 58.287 50.000 0.00 0.00 33.30 4.00
1354 1364 3.836562 ACAAGTACGGACCTTCCTGTAAT 59.163 43.478 0.00 0.00 33.30 1.89
1379 1389 1.499007 GGGGATGGGGAATCAAGCTAA 59.501 52.381 0.00 0.00 36.98 3.09
1387 1397 5.271598 TGGGGAATCAAGCTAAATGAACAT 58.728 37.500 0.00 0.00 0.00 2.71
1421 1431 6.933521 AGATTTAGCAACACTAGCTCCATATG 59.066 38.462 0.00 0.00 42.32 1.78
1428 1438 6.346919 GCAACACTAGCTCCATATGAAATACG 60.347 42.308 3.65 0.00 0.00 3.06
1469 1479 4.747810 ACAATCGAAGCAAAAATCCATCC 58.252 39.130 0.00 0.00 0.00 3.51
1470 1480 4.220382 ACAATCGAAGCAAAAATCCATCCA 59.780 37.500 0.00 0.00 0.00 3.41
1473 1483 3.571828 TCGAAGCAAAAATCCATCCACAA 59.428 39.130 0.00 0.00 0.00 3.33
1490 1500 0.809385 CAAGCCTGGATCAGCAACTG 59.191 55.000 0.00 0.00 0.00 3.16
1498 1508 1.251251 GATCAGCAACTGCAAACCCT 58.749 50.000 4.22 0.00 45.16 4.34
1500 1510 0.746063 TCAGCAACTGCAAACCCTTG 59.254 50.000 4.22 0.00 45.16 3.61
1526 1542 1.354368 TCTAACAAGCAAAGGGGAGGG 59.646 52.381 0.00 0.00 0.00 4.30
1550 1566 3.165071 ACCACCTGAATGAAAATCCCAC 58.835 45.455 0.00 0.00 0.00 4.61
1551 1567 2.497273 CCACCTGAATGAAAATCCCACC 59.503 50.000 0.00 0.00 0.00 4.61
1552 1568 3.434309 CACCTGAATGAAAATCCCACCT 58.566 45.455 0.00 0.00 0.00 4.00
1553 1569 3.445096 CACCTGAATGAAAATCCCACCTC 59.555 47.826 0.00 0.00 0.00 3.85
1563 1579 4.625225 AAATCCCACCTCCCATACAAAT 57.375 40.909 0.00 0.00 0.00 2.32
1588 1604 7.848128 TCACCTAAACAACTAGGAATAGGAAG 58.152 38.462 13.14 7.63 41.02 3.46
1629 1645 0.047802 AATTGGAGGATGGAGGGGGA 59.952 55.000 0.00 0.00 0.00 4.81
1634 1650 0.999712 GAGGATGGAGGGGGAAAACA 59.000 55.000 0.00 0.00 0.00 2.83
1685 1702 9.734620 CTAGAGATGAACAAAAACAAACAATCA 57.265 29.630 0.00 0.00 0.00 2.57
1692 1709 7.172190 TGAACAAAAACAAACAATCAAGAGCAA 59.828 29.630 0.00 0.00 0.00 3.91
1695 1712 8.513774 ACAAAAACAAACAATCAAGAGCAAAAT 58.486 25.926 0.00 0.00 0.00 1.82
1708 1726 2.632512 GAGCAAAATGGGGAAGGTTGAA 59.367 45.455 0.00 0.00 0.00 2.69
1738 1757 0.535553 GACAAACCGCTACACCCCAA 60.536 55.000 0.00 0.00 0.00 4.12
1746 1765 2.643551 CGCTACACCCCAAATGAATCT 58.356 47.619 0.00 0.00 0.00 2.40
1831 1850 9.281371 GGTTAGGTTTTTAGAGTCATAAAGTGT 57.719 33.333 0.00 0.00 0.00 3.55
1854 1873 7.225734 GTGTGGCAAACCTTGTTATGTTTAAAT 59.774 33.333 0.00 0.00 33.57 1.40
1858 1877 7.655732 GGCAAACCTTGTTATGTTTAAATGACT 59.344 33.333 0.00 0.00 33.57 3.41
1860 1879 8.487176 CAAACCTTGTTATGTTTAAATGACTGC 58.513 33.333 0.00 0.00 33.57 4.40
1890 1910 1.539827 GGTGGCATGTAGTTTTTCGCT 59.460 47.619 0.00 0.00 0.00 4.93
1894 1914 4.506288 GTGGCATGTAGTTTTTCGCTTTTT 59.494 37.500 0.00 0.00 0.00 1.94
1920 1940 0.754957 TTGTGGCACCTTGAACCTGG 60.755 55.000 16.26 0.00 0.00 4.45
1939 1959 2.544480 GCGTTTTAGCCCAGATGTTC 57.456 50.000 0.00 0.00 0.00 3.18
1942 1962 3.334691 CGTTTTAGCCCAGATGTTCTCA 58.665 45.455 0.00 0.00 0.00 3.27
1973 1993 8.364142 TGTAAGGTTTTGGTTTCATTTCTATGG 58.636 33.333 0.00 0.00 32.40 2.74
1983 2003 4.794311 TCATTTCTATGGAATGGAGCCA 57.206 40.909 0.00 0.00 34.41 4.75
2015 2036 6.127479 CCCCTTTGATTGAAATTTGATACCGA 60.127 38.462 0.00 0.00 0.00 4.69
2019 2040 5.505780 TGATTGAAATTTGATACCGAGGGT 58.494 37.500 0.00 0.00 40.16 4.34
2026 2048 2.077687 TGATACCGAGGGTAGGAACC 57.922 55.000 0.62 0.00 41.83 3.62
2032 2054 3.592546 GAGGGTAGGAACCTCGAGT 57.407 57.895 12.31 0.00 44.50 4.18
2033 2055 1.849977 GAGGGTAGGAACCTCGAGTT 58.150 55.000 12.31 5.83 44.50 3.01
2045 2067 4.073293 ACCTCGAGTTCAAACACTCAAT 57.927 40.909 12.31 0.00 43.11 2.57
2074 2107 3.791320 TGGGAAGAAGATGAGGTAGTGT 58.209 45.455 0.00 0.00 0.00 3.55
2079 2112 3.108376 AGAAGATGAGGTAGTGTTCCCC 58.892 50.000 0.00 0.00 0.00 4.81
2113 2146 9.768215 CTATTATCTATTCTCCCTCTCTTTCCT 57.232 37.037 0.00 0.00 0.00 3.36
2128 2161 4.421131 TCTTTCCTTGTAGCTTCTCTCCT 58.579 43.478 0.00 0.00 0.00 3.69
2136 2169 2.143876 AGCTTCTCTCCTCTCTGACC 57.856 55.000 0.00 0.00 0.00 4.02
2137 2170 1.111277 GCTTCTCTCCTCTCTGACCC 58.889 60.000 0.00 0.00 0.00 4.46
2138 2171 1.775385 CTTCTCTCCTCTCTGACCCC 58.225 60.000 0.00 0.00 0.00 4.95
2164 2197 1.587043 CCCTGTCTCTCGAGCGACAA 61.587 60.000 31.45 18.91 39.01 3.18
2187 2220 7.329226 ACAAGAAATGAACAAACAGACAAACAG 59.671 33.333 0.00 0.00 0.00 3.16
2193 2226 1.734388 AAACAGACAAACAGGCGGGC 61.734 55.000 0.00 0.00 0.00 6.13
2194 2227 2.594303 CAGACAAACAGGCGGGCA 60.594 61.111 3.78 0.00 0.00 5.36
2222 2255 1.213926 AGCAGGAGGGGAAGCAATTAG 59.786 52.381 0.00 0.00 0.00 1.73
2259 2292 2.774799 CCACTATTGGGCGGCTTGC 61.775 63.158 9.56 0.00 39.57 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.641906 AGTAGGTATCATGGCCACAGTAC 59.358 47.826 8.16 11.15 0.00 2.73
16 17 4.463186 ACCGATTCTAGTAGGTATCATGGC 59.537 45.833 0.00 0.00 34.83 4.40
31 32 5.488341 ACTTACTTGTGCATTACCGATTCT 58.512 37.500 0.00 0.00 0.00 2.40
99 100 9.817365 GGAATGAATATTTGTCTGATAACATCG 57.183 33.333 0.00 0.00 0.00 3.84
116 117 3.055328 TCTGCATCAGGGGGAATGAATA 58.945 45.455 0.00 0.00 31.51 1.75
117 118 1.854939 TCTGCATCAGGGGGAATGAAT 59.145 47.619 0.00 0.00 31.51 2.57
156 157 1.207089 TCATGTCCACCCGTTCTGATC 59.793 52.381 0.00 0.00 0.00 2.92
172 181 5.183530 TCCCAGGCCAATATATCTTCATG 57.816 43.478 5.01 0.00 0.00 3.07
206 215 5.250774 ACAGATTTTACAGTGTAGGTCCCAT 59.749 40.000 2.68 0.00 0.00 4.00
243 252 4.093408 GCTTTATGCTCGTTCTGATTCACA 59.907 41.667 0.00 0.00 38.95 3.58
284 293 3.082548 TCTGTCTCTGAGGTTTCCGTAG 58.917 50.000 4.59 0.00 0.00 3.51
423 432 4.330250 ACTTGCATGTGCTTTCAGTAGAT 58.670 39.130 4.14 0.00 42.66 1.98
489 498 5.399858 CAGAATTTCCTTGCATGAGAACAG 58.600 41.667 0.00 0.00 0.00 3.16
546 555 2.244252 AGTAAGAGGATGTAGGTCCGGT 59.756 50.000 0.00 0.00 43.27 5.28
549 558 4.287552 TCCAAGTAAGAGGATGTAGGTCC 58.712 47.826 0.00 0.00 38.62 4.46
609 618 1.613925 GAGACCAACTTTGCCCTTTCC 59.386 52.381 0.00 0.00 0.00 3.13
675 684 0.393537 CAGGGCTGGTAGCTCCTTTG 60.394 60.000 0.00 0.00 44.67 2.77
717 726 3.811722 TCAAGTAAAGCAAGTGCATCG 57.188 42.857 6.00 0.00 45.16 3.84
744 753 0.807667 GAATCCGAGCATGCTCACGT 60.808 55.000 38.97 24.46 42.86 4.49
786 795 1.221840 CACCCAGTTCTCATCCCGG 59.778 63.158 0.00 0.00 0.00 5.73
788 797 1.909302 TCTTCACCCAGTTCTCATCCC 59.091 52.381 0.00 0.00 0.00 3.85
813 822 3.699538 CCATAGCTATGCTACCATCGGTA 59.300 47.826 25.60 0.00 44.24 4.02
852 861 4.180946 CTCGCGACTCCTCCACCG 62.181 72.222 3.71 0.00 0.00 4.94
882 891 2.584835 TACACCAAGCTGCCAAGAAT 57.415 45.000 0.00 0.00 0.00 2.40
886 895 1.036707 GGTTTACACCAAGCTGCCAA 58.963 50.000 0.00 0.00 43.61 4.52
919 928 3.623060 GCTTCAACAATTAGCGGATCTGA 59.377 43.478 5.48 0.00 0.00 3.27
993 1002 3.698040 GGCAGTCAGTTTCCATGATGATT 59.302 43.478 0.00 0.00 0.00 2.57
994 1003 3.285484 GGCAGTCAGTTTCCATGATGAT 58.715 45.455 0.00 0.00 0.00 2.45
1005 1014 1.212935 ACAAGGTCTTGGCAGTCAGTT 59.787 47.619 14.29 0.00 44.45 3.16
1014 1023 2.880890 CCAGAAGTTGACAAGGTCTTGG 59.119 50.000 14.29 0.00 44.45 3.61
1048 1057 1.174783 GCCACTACTGTCCGAGAAGA 58.825 55.000 0.00 0.00 0.00 2.87
1053 1062 2.825075 TAGGCGCCACTACTGTCCGA 62.825 60.000 31.54 0.00 0.00 4.55
1056 1065 1.033574 AGATAGGCGCCACTACTGTC 58.966 55.000 31.54 15.26 0.00 3.51
1057 1066 1.486211 AAGATAGGCGCCACTACTGT 58.514 50.000 31.54 8.51 0.00 3.55
1062 1071 2.598565 TCATCTAAGATAGGCGCCACT 58.401 47.619 31.54 21.25 0.00 4.00
1075 1084 4.507335 GGCATGCTCCCCTATTTCATCTAA 60.507 45.833 18.92 0.00 0.00 2.10
1079 1088 1.785208 AGGCATGCTCCCCTATTTCAT 59.215 47.619 18.92 0.00 0.00 2.57
1120 1129 4.633126 TGCTGATCTAGAAACATGCTGAAC 59.367 41.667 0.00 0.00 0.00 3.18
1129 1138 4.393371 GGAGGTGTTTGCTGATCTAGAAAC 59.607 45.833 0.00 0.00 32.16 2.78
1265 1275 5.298527 GGGAAATACGGGGAGTTTTATTCAG 59.701 44.000 0.00 0.00 0.00 3.02
1323 1333 2.613725 GGTCCGTACTTGTTGTTAGGGG 60.614 54.545 0.00 0.00 0.00 4.79
1324 1334 2.301009 AGGTCCGTACTTGTTGTTAGGG 59.699 50.000 0.00 0.00 0.00 3.53
1344 1354 4.042187 CCCATCCCCTTCTATTACAGGAAG 59.958 50.000 0.00 0.00 38.76 3.46
1345 1355 3.980698 CCCATCCCCTTCTATTACAGGAA 59.019 47.826 0.00 0.00 30.81 3.36
1346 1356 3.598264 CCCATCCCCTTCTATTACAGGA 58.402 50.000 0.00 0.00 30.81 3.86
1347 1357 2.644798 CCCCATCCCCTTCTATTACAGG 59.355 54.545 0.00 0.00 0.00 4.00
1348 1358 3.598264 TCCCCATCCCCTTCTATTACAG 58.402 50.000 0.00 0.00 0.00 2.74
1349 1359 3.736227 TCCCCATCCCCTTCTATTACA 57.264 47.619 0.00 0.00 0.00 2.41
1350 1360 4.601857 TGATTCCCCATCCCCTTCTATTAC 59.398 45.833 0.00 0.00 0.00 1.89
1351 1361 4.850328 TGATTCCCCATCCCCTTCTATTA 58.150 43.478 0.00 0.00 0.00 0.98
1354 1364 2.908263 TGATTCCCCATCCCCTTCTA 57.092 50.000 0.00 0.00 0.00 2.10
1379 1389 4.895668 AATCTTGTGGGCAATGTTCATT 57.104 36.364 0.00 0.00 33.65 2.57
1387 1397 2.961741 TGTTGCTAAATCTTGTGGGCAA 59.038 40.909 0.00 0.00 37.35 4.52
1421 1431 3.252458 AGTTTTGGTGTGCTCCGTATTTC 59.748 43.478 0.00 0.00 0.00 2.17
1428 1438 2.685897 TGTACAAGTTTTGGTGTGCTCC 59.314 45.455 0.00 0.00 32.28 4.70
1469 1479 0.524862 GTTGCTGATCCAGGCTTGTG 59.475 55.000 0.00 0.00 31.21 3.33
1470 1480 0.403271 AGTTGCTGATCCAGGCTTGT 59.597 50.000 0.00 0.00 31.21 3.16
1473 1483 1.378250 GCAGTTGCTGATCCAGGCT 60.378 57.895 0.00 0.00 38.21 4.58
1490 1500 6.524101 TTGTTAGATATTCCAAGGGTTTGC 57.476 37.500 0.00 0.00 32.79 3.68
1498 1508 5.656416 CCCCTTTGCTTGTTAGATATTCCAA 59.344 40.000 0.00 0.00 0.00 3.53
1500 1510 5.445964 TCCCCTTTGCTTGTTAGATATTCC 58.554 41.667 0.00 0.00 0.00 3.01
1526 1542 3.588955 GGATTTTCATTCAGGTGGTTGC 58.411 45.455 0.00 0.00 0.00 4.17
1535 1551 2.381618 TGGGAGGTGGGATTTTCATTCA 59.618 45.455 0.00 0.00 0.00 2.57
1539 1555 2.922955 TGTATGGGAGGTGGGATTTTCA 59.077 45.455 0.00 0.00 0.00 2.69
1540 1556 3.662759 TGTATGGGAGGTGGGATTTTC 57.337 47.619 0.00 0.00 0.00 2.29
1541 1557 4.412060 TTTGTATGGGAGGTGGGATTTT 57.588 40.909 0.00 0.00 0.00 1.82
1550 1566 5.505780 TGTTTAGGTGATTTGTATGGGAGG 58.494 41.667 0.00 0.00 0.00 4.30
1551 1567 6.659242 AGTTGTTTAGGTGATTTGTATGGGAG 59.341 38.462 0.00 0.00 0.00 4.30
1552 1568 6.548321 AGTTGTTTAGGTGATTTGTATGGGA 58.452 36.000 0.00 0.00 0.00 4.37
1553 1569 6.834168 AGTTGTTTAGGTGATTTGTATGGG 57.166 37.500 0.00 0.00 0.00 4.00
1563 1579 7.093024 CCTTCCTATTCCTAGTTGTTTAGGTGA 60.093 40.741 0.00 0.00 40.91 4.02
1629 1645 8.962884 AGATTTTGGTTTGCTTAGATTGTTTT 57.037 26.923 0.00 0.00 0.00 2.43
1634 1650 7.890655 AGGTCTAGATTTTGGTTTGCTTAGATT 59.109 33.333 0.00 0.00 0.00 2.40
1685 1702 2.634453 CAACCTTCCCCATTTTGCTCTT 59.366 45.455 0.00 0.00 0.00 2.85
1692 1709 3.777522 TGTTTGTTCAACCTTCCCCATTT 59.222 39.130 0.00 0.00 33.97 2.32
1695 1712 2.534042 TGTTTGTTCAACCTTCCCCA 57.466 45.000 0.00 0.00 33.97 4.96
1708 1726 1.135228 GCGGTTTGTCACCTTGTTTGT 60.135 47.619 0.00 0.00 44.69 2.83
1738 1757 2.418669 ACCCCCGGTATCAGATTCATT 58.581 47.619 0.00 0.00 32.11 2.57
1746 1765 1.963464 GCGAAGAACCCCCGGTATCA 61.963 60.000 0.00 0.00 33.12 2.15
1815 1834 5.472137 GGTTTGCCACACTTTATGACTCTAA 59.528 40.000 0.00 0.00 34.09 2.10
1831 1850 7.439655 GTCATTTAAACATAACAAGGTTTGCCA 59.560 33.333 0.00 0.00 37.73 4.92
1854 1873 2.203280 CCAAACCGGTGGCAGTCA 60.203 61.111 8.52 0.00 0.00 3.41
1894 1914 1.110442 CAAGGTGCCACAAAGGACAA 58.890 50.000 0.00 0.00 41.22 3.18
1902 1922 1.152777 CCAGGTTCAAGGTGCCACA 60.153 57.895 0.00 0.00 0.00 4.17
1920 1940 2.084546 AGAACATCTGGGCTAAAACGC 58.915 47.619 0.00 0.00 0.00 4.84
1939 1959 7.093992 TGAAACCAAAACCTTACAAAAGTGAG 58.906 34.615 0.00 0.00 0.00 3.51
1942 1962 8.856153 AAATGAAACCAAAACCTTACAAAAGT 57.144 26.923 0.00 0.00 0.00 2.66
2000 2021 4.717778 TCCTACCCTCGGTATCAAATTTCA 59.282 41.667 0.00 0.00 37.56 2.69
2015 2036 1.849977 GAACTCGAGGTTCCTACCCT 58.150 55.000 18.41 0.00 46.28 4.34
2032 2054 4.096231 CCATGGCGATATTGAGTGTTTGAA 59.904 41.667 0.00 0.00 0.00 2.69
2033 2055 3.627123 CCATGGCGATATTGAGTGTTTGA 59.373 43.478 0.00 0.00 0.00 2.69
2045 2067 2.972021 TCATCTTCTTCCCATGGCGATA 59.028 45.455 6.09 0.00 0.00 2.92
2074 2107 7.894364 AGAATAGATAATAGAAGCTACGGGGAA 59.106 37.037 0.00 0.00 0.00 3.97
2079 2112 8.514330 AGGGAGAATAGATAATAGAAGCTACG 57.486 38.462 0.00 0.00 0.00 3.51
2113 2146 4.013728 GTCAGAGAGGAGAGAAGCTACAA 58.986 47.826 0.00 0.00 0.00 2.41
2128 2161 0.252284 GGGAGAACAGGGGTCAGAGA 60.252 60.000 0.00 0.00 0.00 3.10
2136 2169 1.190643 GAGAGACAGGGAGAACAGGG 58.809 60.000 0.00 0.00 0.00 4.45
2137 2170 0.814457 CGAGAGACAGGGAGAACAGG 59.186 60.000 0.00 0.00 0.00 4.00
2138 2171 1.742831 CTCGAGAGACAGGGAGAACAG 59.257 57.143 6.58 0.00 35.39 3.16
2164 2197 6.332630 CCTGTTTGTCTGTTTGTTCATTTCT 58.667 36.000 0.00 0.00 0.00 2.52
2201 2234 0.411058 AATTGCTTCCCCTCCTGCTT 59.589 50.000 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.