Multiple sequence alignment - TraesCS7A01G482400

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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 TraesCS7A01G482400 chr7A 100.000 2937 0 0 1 2937 674507213 674504277 0.000000e+00 5424.0
1 TraesCS7A01G482400 chr7A 88.869 1698 133 26 20 1694 674738787 674737123 0.000000e+00 2037.0
2 TraesCS7A01G482400 chr7A 91.555 1338 91 10 363 1694 674753178 674751857 0.000000e+00 1825.0
3 TraesCS7A01G482400 chr7A 87.607 815 56 14 1873 2672 547687408 547686624 0.000000e+00 904.0
4 TraesCS7A01G482400 chr7A 87.402 762 65 13 144 882 674527607 674526854 0.000000e+00 846.0
5 TraesCS7A01G482400 chr7A 88.924 632 50 5 264 881 674523210 674522585 0.000000e+00 761.0
6 TraesCS7A01G482400 chr7A 82.692 364 45 12 256 612 674684108 674683756 1.020000e-79 307.0
7 TraesCS7A01G482400 chr7D 93.243 1184 73 4 532 1711 582748406 582747226 0.000000e+00 1736.0
8 TraesCS7A01G482400 chr7D 85.880 1636 156 42 267 1874 582651578 582649990 0.000000e+00 1672.0
9 TraesCS7A01G482400 chr7D 91.790 1084 67 11 1873 2936 62166770 62165689 0.000000e+00 1489.0
10 TraesCS7A01G482400 chr7D 89.988 869 82 4 835 1699 582557228 582556361 0.000000e+00 1118.0
11 TraesCS7A01G482400 chr7D 85.310 565 52 16 75 612 582745632 582745072 3.310000e-154 555.0
12 TraesCS7A01G482400 chr7D 80.583 103 11 6 1777 1870 582542977 582542875 1.460000e-08 71.3
13 TraesCS7A01G482400 chr7D 80.583 103 11 6 1777 1870 582648432 582648330 1.460000e-08 71.3
14 TraesCS7A01G482400 chr7B 87.794 1401 135 28 491 1874 650362463 650361082 0.000000e+00 1607.0
15 TraesCS7A01G482400 chr7B 87.723 1401 135 28 491 1874 650409446 650408066 0.000000e+00 1600.0
16 TraesCS7A01G482400 chr7B 87.580 1401 138 29 491 1874 650318191 650316810 0.000000e+00 1591.0
17 TraesCS7A01G482400 chr7B 87.266 1390 132 32 498 1874 650456179 650454822 0.000000e+00 1544.0
18 TraesCS7A01G482400 chr7B 81.553 103 10 4 1777 1870 650246381 650246279 3.140000e-10 76.8
19 TraesCS7A01G482400 chr7B 81.553 103 10 4 1777 1870 650260955 650260853 3.140000e-10 76.8
20 TraesCS7A01G482400 chr7B 81.553 103 10 4 1777 1870 650273316 650273214 3.140000e-10 76.8
21 TraesCS7A01G482400 chr4D 92.500 1080 57 10 1873 2937 151987881 151986811 0.000000e+00 1524.0
22 TraesCS7A01G482400 chr4D 88.858 1086 86 20 1873 2935 489335943 489337016 0.000000e+00 1303.0
23 TraesCS7A01G482400 chr5D 92.193 1076 68 7 1876 2937 495363213 495364286 0.000000e+00 1507.0
24 TraesCS7A01G482400 chr5D 90.481 1061 67 13 1874 2907 99922392 99923445 0.000000e+00 1369.0
25 TraesCS7A01G482400 chr3A 91.897 1086 66 11 1870 2937 12633120 12634201 0.000000e+00 1498.0
26 TraesCS7A01G482400 chr3A 92.154 803 38 8 2150 2937 12706997 12707789 0.000000e+00 1110.0
27 TraesCS7A01G482400 chr1D 88.695 1088 92 21 1873 2937 478575955 478577034 0.000000e+00 1299.0
28 TraesCS7A01G482400 chr1D 88.116 791 67 14 1873 2640 89233049 89232263 0.000000e+00 915.0
29 TraesCS7A01G482400 chr2D 88.043 1104 90 16 1873 2937 172990231 172991331 0.000000e+00 1269.0
30 TraesCS7A01G482400 chr2D 92.218 771 40 7 2184 2936 640280394 640281162 0.000000e+00 1074.0
31 TraesCS7A01G482400 chr2A 90.505 653 51 3 1881 2522 690533517 690532865 0.000000e+00 852.0
32 TraesCS7A01G482400 chr4A 90.484 620 40 8 1873 2478 21043139 21042525 0.000000e+00 800.0


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 TraesCS7A01G482400 chr7A 674504277 674507213 2936 True 5424.00 5424 100.0000 1 2937 1 chr7A.!!$R2 2936
1 TraesCS7A01G482400 chr7A 674737123 674738787 1664 True 2037.00 2037 88.8690 20 1694 1 chr7A.!!$R4 1674
2 TraesCS7A01G482400 chr7A 674751857 674753178 1321 True 1825.00 1825 91.5550 363 1694 1 chr7A.!!$R5 1331
3 TraesCS7A01G482400 chr7A 547686624 547687408 784 True 904.00 904 87.6070 1873 2672 1 chr7A.!!$R1 799
4 TraesCS7A01G482400 chr7A 674522585 674527607 5022 True 803.50 846 88.1630 144 882 2 chr7A.!!$R6 738
5 TraesCS7A01G482400 chr7D 62165689 62166770 1081 True 1489.00 1489 91.7900 1873 2936 1 chr7D.!!$R1 1063
6 TraesCS7A01G482400 chr7D 582745072 582748406 3334 True 1145.50 1736 89.2765 75 1711 2 chr7D.!!$R5 1636
7 TraesCS7A01G482400 chr7D 582556361 582557228 867 True 1118.00 1118 89.9880 835 1699 1 chr7D.!!$R3 864
8 TraesCS7A01G482400 chr7D 582648330 582651578 3248 True 871.65 1672 83.2315 267 1874 2 chr7D.!!$R4 1607
9 TraesCS7A01G482400 chr7B 650361082 650362463 1381 True 1607.00 1607 87.7940 491 1874 1 chr7B.!!$R5 1383
10 TraesCS7A01G482400 chr7B 650408066 650409446 1380 True 1600.00 1600 87.7230 491 1874 1 chr7B.!!$R6 1383
11 TraesCS7A01G482400 chr7B 650316810 650318191 1381 True 1591.00 1591 87.5800 491 1874 1 chr7B.!!$R4 1383
12 TraesCS7A01G482400 chr7B 650454822 650456179 1357 True 1544.00 1544 87.2660 498 1874 1 chr7B.!!$R7 1376
13 TraesCS7A01G482400 chr4D 151986811 151987881 1070 True 1524.00 1524 92.5000 1873 2937 1 chr4D.!!$R1 1064
14 TraesCS7A01G482400 chr4D 489335943 489337016 1073 False 1303.00 1303 88.8580 1873 2935 1 chr4D.!!$F1 1062
15 TraesCS7A01G482400 chr5D 495363213 495364286 1073 False 1507.00 1507 92.1930 1876 2937 1 chr5D.!!$F2 1061
16 TraesCS7A01G482400 chr5D 99922392 99923445 1053 False 1369.00 1369 90.4810 1874 2907 1 chr5D.!!$F1 1033
17 TraesCS7A01G482400 chr3A 12633120 12634201 1081 False 1498.00 1498 91.8970 1870 2937 1 chr3A.!!$F1 1067
18 TraesCS7A01G482400 chr3A 12706997 12707789 792 False 1110.00 1110 92.1540 2150 2937 1 chr3A.!!$F2 787
19 TraesCS7A01G482400 chr1D 478575955 478577034 1079 False 1299.00 1299 88.6950 1873 2937 1 chr1D.!!$F1 1064
20 TraesCS7A01G482400 chr1D 89232263 89233049 786 True 915.00 915 88.1160 1873 2640 1 chr1D.!!$R1 767
21 TraesCS7A01G482400 chr2D 172990231 172991331 1100 False 1269.00 1269 88.0430 1873 2937 1 chr2D.!!$F1 1064
22 TraesCS7A01G482400 chr2D 640280394 640281162 768 False 1074.00 1074 92.2180 2184 2936 1 chr2D.!!$F2 752
23 TraesCS7A01G482400 chr2A 690532865 690533517 652 True 852.00 852 90.5050 1881 2522 1 chr2A.!!$R1 641
24 TraesCS7A01G482400 chr4A 21042525 21043139 614 True 800.00 800 90.4840 1873 2478 1 chr4A.!!$R1 605

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
63 64 0.096976 GTTGTTGGATGGCACGATCG 59.903 55.0 14.88 14.88 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2020 6502 0.036164 TCACTTGTGTTCGGATGGGG 59.964 55.0 0.46 0.0 0.0 4.96 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
42 43 6.473455 GGAAATCTGCATTAGTCAATTTTCCG 59.527 38.462 0.00 0.00 32.81 4.30
43 44 6.757897 AATCTGCATTAGTCAATTTTCCGA 57.242 33.333 0.00 0.00 0.00 4.55
45 46 5.245531 TCTGCATTAGTCAATTTTCCGAGT 58.754 37.500 0.00 0.00 0.00 4.18
46 47 5.705441 TCTGCATTAGTCAATTTTCCGAGTT 59.295 36.000 0.00 0.00 0.00 3.01
58 59 0.605319 TCCGAGTTGTTGGATGGCAC 60.605 55.000 0.00 0.00 30.21 5.01
63 64 0.096976 GTTGTTGGATGGCACGATCG 59.903 55.000 14.88 14.88 0.00 3.69
65 66 0.533032 TGTTGGATGGCACGATCGTA 59.467 50.000 22.26 5.97 0.00 3.43
81 82 0.319727 CGTACCGCCACCTGTTAACA 60.320 55.000 8.28 8.28 0.00 2.41
87 88 2.556622 CCGCCACCTGTTAACATTCTTT 59.443 45.455 9.13 0.00 0.00 2.52
113 115 1.762460 ATCTTCCTCCCCGTGCGAT 60.762 57.895 0.00 0.00 0.00 4.58
118 120 2.819595 CTCCCCGTGCGATGGTTG 60.820 66.667 0.00 0.00 0.00 3.77
142 147 0.629596 TCCTCCCACGTGATCTACCT 59.370 55.000 19.30 0.00 0.00 3.08
148 153 0.249120 CACGTGATCTACCTTGCCCA 59.751 55.000 10.90 0.00 0.00 5.36
151 156 1.737793 CGTGATCTACCTTGCCCAAAC 59.262 52.381 0.00 0.00 0.00 2.93
166 171 0.321653 CAAACCGGCAGCCTACTTCT 60.322 55.000 10.54 0.00 0.00 2.85
223 229 4.101448 CAGCCCTGAACCTCCCCG 62.101 72.222 0.00 0.00 0.00 5.73
281 294 2.271800 GTGATCTGCAGTAAACTCCGG 58.728 52.381 14.67 0.00 0.00 5.14
320 333 2.507484 CCTCAACCTGCATCAGTCAAA 58.493 47.619 0.00 0.00 0.00 2.69
328 341 4.021719 ACCTGCATCAGTCAAATTTTGGAG 60.022 41.667 9.18 0.00 0.00 3.86
331 344 4.022068 TGCATCAGTCAAATTTTGGAGTCC 60.022 41.667 0.73 0.73 0.00 3.85
366 393 0.605319 GTCATTGTCACCCGCCTTCA 60.605 55.000 0.00 0.00 0.00 3.02
368 395 0.606401 CATTGTCACCCGCCTTCAGT 60.606 55.000 0.00 0.00 0.00 3.41
427 454 9.498176 GAAAATTTCAGGTACCTAGTGTTTAGA 57.502 33.333 15.80 1.74 0.00 2.10
462 489 0.533085 TTCGTCGGCACAACCAATGA 60.533 50.000 0.00 0.00 39.03 2.57
479 506 8.849168 CAACCAATGATGCTGGATTAACTAATA 58.151 33.333 0.00 0.00 37.40 0.98
511 539 0.522180 CGAGCTGAACGTAGGTGTCT 59.478 55.000 0.00 0.00 0.00 3.41
515 543 2.355132 AGCTGAACGTAGGTGTCTATCG 59.645 50.000 0.00 0.00 0.00 2.92
530 558 0.463654 TATCGGTGCCAATGAGCCAC 60.464 55.000 0.00 0.00 0.00 5.01
587 618 7.178983 AGACACATGGAATCAAAACCATACAAT 59.821 33.333 0.00 0.00 43.89 2.71
605 636 7.256655 CCATACAATTCCTATATGTGTCTCCCA 60.257 40.741 0.00 0.00 0.00 4.37
612 643 1.507140 TATGTGTCTCCCATGACCCC 58.493 55.000 0.00 0.00 36.21 4.95
632 4932 1.270305 CGATGATCAGGGTTACGCCAT 60.270 52.381 0.09 0.00 39.65 4.40
636 4936 1.412710 GATCAGGGTTACGCCATCTCA 59.587 52.381 0.00 0.00 39.65 3.27
673 4973 6.212589 TGCCAGATATATTCCTTTGTCCGATA 59.787 38.462 0.00 0.00 0.00 2.92
694 4998 8.417106 CCGATACTATGCTCCAGATTATTATGT 58.583 37.037 0.00 0.00 0.00 2.29
776 5081 7.509659 AGGAGTACTCTTCTTGGAAACTAAAGA 59.490 37.037 21.88 0.00 0.00 2.52
876 5185 5.835113 AACATGCCAGTACAATAATGGTC 57.165 39.130 4.42 0.00 45.25 4.02
882 5191 3.063452 CCAGTACAATAATGGTCGCACAC 59.937 47.826 0.00 0.00 39.00 3.82
884 5193 3.682858 AGTACAATAATGGTCGCACACAC 59.317 43.478 0.00 0.00 0.00 3.82
975 5286 6.875195 GCACACTATAACCGGCCTATAAATAA 59.125 38.462 0.00 0.00 0.00 1.40
1037 5351 2.898705 CCTACAAGCTTAGCCACAGAG 58.101 52.381 0.00 0.00 0.00 3.35
1045 5359 2.354203 GCTTAGCCACAGAGCAGTAAGT 60.354 50.000 0.00 0.00 36.45 2.24
1103 5417 2.046892 CTCGCCCTGAACCTGGTG 60.047 66.667 0.00 0.00 0.00 4.17
1115 5429 4.711949 CTGGTGCTCCTTGCCGCT 62.712 66.667 6.34 0.00 42.00 5.52
1140 5454 4.154347 GCTGCGAGCCCTACTGCT 62.154 66.667 0.00 0.00 46.37 4.24
1512 5835 8.631676 TGCATAATCGTTGTATTCGTAACTAA 57.368 30.769 0.00 0.00 0.00 2.24
1540 5863 2.761767 TGCCATACGTACACACCATACT 59.238 45.455 0.00 0.00 0.00 2.12
1570 5894 5.854010 TCTATGTTCCAGTCCATGTACTC 57.146 43.478 0.00 0.00 0.00 2.59
1613 5937 1.592400 CCTCGCTCGTGCATGCATA 60.592 57.895 25.64 14.37 39.64 3.14
1622 5946 4.083643 GCTCGTGCATGCATACTTGATAAT 60.084 41.667 25.64 0.00 39.41 1.28
1624 5948 4.150451 TCGTGCATGCATACTTGATAATCG 59.850 41.667 25.64 17.23 0.00 3.34
1637 5962 7.474398 ACTTGATAATCGTGTGATTGATCAG 57.526 36.000 0.00 0.00 44.46 2.90
1644 5969 5.014808 TCGTGTGATTGATCAGTGATCAT 57.985 39.130 31.24 21.95 46.52 2.45
1652 5977 7.660617 GTGATTGATCAGTGATCATTGTATCCT 59.339 37.037 31.24 12.20 46.52 3.24
1662 5987 8.150945 AGTGATCATTGTATCCTGTTATGGTAC 58.849 37.037 0.00 0.00 0.00 3.34
1663 5988 8.150945 GTGATCATTGTATCCTGTTATGGTACT 58.849 37.037 0.00 0.00 0.00 2.73
1665 5990 9.209175 GATCATTGTATCCTGTTATGGTACTTC 57.791 37.037 0.00 0.00 0.00 3.01
1695 6020 7.221452 GCATGATTCATGTATTTGTGAAAGGAC 59.779 37.037 23.86 2.23 43.10 3.85
1701 6026 8.806429 TCATGTATTTGTGAAAGGACATACAT 57.194 30.769 0.00 0.00 34.52 2.29
1708 6033 9.733556 ATTTGTGAAAGGACATACATACTTGTA 57.266 29.630 0.00 0.00 42.35 2.41
1711 6036 8.536175 TGTGAAAGGACATACATACTTGTATCA 58.464 33.333 0.00 0.00 45.27 2.15
1712 6037 9.547753 GTGAAAGGACATACATACTTGTATCAT 57.452 33.333 0.00 0.00 45.27 2.45
1737 6094 5.585445 TGTATGTGTACGTGAAAGGTTTGTT 59.415 36.000 0.00 0.00 35.89 2.83
1741 6098 4.789629 GTGTACGTGAAAGGTTTGTTCAAC 59.210 41.667 0.00 0.00 36.77 3.18
1752 6109 4.773149 AGGTTTGTTCAACTTGGGTTAACA 59.227 37.500 8.10 0.00 35.46 2.41
1753 6110 4.865925 GGTTTGTTCAACTTGGGTTAACAC 59.134 41.667 8.10 3.98 35.46 3.32
1762 6119 2.862738 GGGTTAACACATCACCCGG 58.137 57.895 8.10 0.00 41.00 5.73
1766 6123 2.486592 GGTTAACACATCACCCGGAAAG 59.513 50.000 0.73 0.00 0.00 2.62
1767 6124 3.404899 GTTAACACATCACCCGGAAAGA 58.595 45.455 0.73 0.00 0.00 2.52
1771 6128 3.496331 ACACATCACCCGGAAAGAAAAT 58.504 40.909 0.73 0.00 0.00 1.82
1806 6164 2.224606 CCGTGATATGCCAGCTTGAAT 58.775 47.619 0.00 0.00 0.00 2.57
1808 6166 3.814842 CCGTGATATGCCAGCTTGAATTA 59.185 43.478 0.00 0.00 0.00 1.40
1852 6324 5.589050 ACATGATTGTGTCAATCCTGATCAG 59.411 40.000 23.60 16.24 40.97 2.90
1858 6330 5.181009 TGTGTCAATCCTGATCAGATTCAC 58.819 41.667 24.62 21.05 33.05 3.18
1861 6333 6.988580 GTGTCAATCCTGATCAGATTCACATA 59.011 38.462 24.62 1.97 33.05 2.29
1867 6339 9.863650 AATCCTGATCAGATTCACATATTTTCT 57.136 29.630 24.62 0.00 0.00 2.52
1895 6367 2.315925 TACTTATCAGTGCAGCTGCC 57.684 50.000 34.64 24.89 44.66 4.85
1913 6385 2.115510 CCTAATTGGGCTTTCCGGC 58.884 57.895 0.00 0.00 38.76 6.13
2020 6502 1.757699 AGGAAACTATCTGGTCCTCGC 59.242 52.381 0.00 0.00 40.61 5.03
2112 6769 8.771920 AGTCATAACTTTTGATTCGTGTATCA 57.228 30.769 0.00 0.00 29.81 2.15
2134 6791 6.827641 TCAGAATTTAGATTCGTTTTCACCG 58.172 36.000 0.65 0.00 45.10 4.94
2178 6835 8.552296 AGTTCTTCAAAACTAGATCCCATATGT 58.448 33.333 0.00 0.00 37.71 2.29
2219 6879 2.435372 TTCTGAGCAACTTTGGGTGT 57.565 45.000 0.00 0.00 0.00 4.16
2383 7059 4.091509 GCCAACACTATGTTTCAGAGTACG 59.908 45.833 0.00 0.00 38.77 3.67
2408 7084 1.404181 GCATGAGCTACACCGACAGAA 60.404 52.381 0.00 0.00 37.91 3.02
2438 7114 6.206243 TGTCCTAGTATCGTAGCCAACTAATC 59.794 42.308 0.00 0.00 0.00 1.75
2467 7143 3.272925 TGCAAACCGGGCATCATTA 57.727 47.368 6.32 0.00 36.11 1.90
2708 9099 2.103263 GGGGTAAGATAGCTGTCCACAG 59.897 54.545 6.88 2.06 46.40 3.66
2713 9104 0.826715 GATAGCTGTCCACAGAGGCA 59.173 55.000 11.04 0.00 46.59 4.75
2736 9127 6.345723 GCAATTCAAGTTGGTCATACGTTTTG 60.346 38.462 2.34 0.00 0.00 2.44
2888 10084 4.891168 TGTAGGATAGTTGCTCGGTTATGA 59.109 41.667 0.00 0.00 0.00 2.15
2926 10122 8.309656 TGCATTGATGTTTGGTAATACATTTGA 58.690 29.630 0.00 0.00 35.24 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.297134 TGACTAATGCAGATTTCCCCC 57.703 47.619 0.00 0.00 0.00 5.40
15 16 5.859205 AATTGACTAATGCAGATTTCCCC 57.141 39.130 0.00 0.00 0.00 4.81
16 17 6.758416 GGAAAATTGACTAATGCAGATTTCCC 59.242 38.462 0.00 0.00 36.66 3.97
17 18 6.473455 CGGAAAATTGACTAATGCAGATTTCC 59.527 38.462 0.00 0.00 37.85 3.13
18 19 7.250569 TCGGAAAATTGACTAATGCAGATTTC 58.749 34.615 0.00 0.00 0.00 2.17
29 30 5.369833 TCCAACAACTCGGAAAATTGACTA 58.630 37.500 3.99 0.00 0.00 2.59
42 43 1.398390 GATCGTGCCATCCAACAACTC 59.602 52.381 0.00 0.00 0.00 3.01
43 44 1.453155 GATCGTGCCATCCAACAACT 58.547 50.000 0.00 0.00 0.00 3.16
45 46 0.321210 ACGATCGTGCCATCCAACAA 60.321 50.000 22.06 0.00 0.00 2.83
46 47 0.533032 TACGATCGTGCCATCCAACA 59.467 50.000 30.23 3.26 0.00 3.33
63 64 2.103537 ATGTTAACAGGTGGCGGTAC 57.896 50.000 14.65 0.00 0.00 3.34
65 66 1.073284 AGAATGTTAACAGGTGGCGGT 59.927 47.619 14.65 0.00 0.00 5.68
81 82 4.080072 GGAGGAAGATGTGAGGGAAAGAAT 60.080 45.833 0.00 0.00 0.00 2.40
87 88 0.326618 GGGGAGGAAGATGTGAGGGA 60.327 60.000 0.00 0.00 0.00 4.20
113 115 2.206900 TGGGAGGAGGAGCAACCA 59.793 61.111 2.96 0.00 42.04 3.67
118 120 2.022240 GATCACGTGGGAGGAGGAGC 62.022 65.000 17.00 0.00 0.00 4.70
148 153 0.321653 CAGAAGTAGGCTGCCGGTTT 60.322 55.000 13.96 8.61 0.00 3.27
151 156 2.187946 CCAGAAGTAGGCTGCCGG 59.812 66.667 13.96 0.00 32.06 6.13
257 270 0.247301 GTTTACTGCAGATCACGCGC 60.247 55.000 23.35 0.00 0.00 6.86
295 308 1.379044 GATGCAGGTTGAGGGTGGG 60.379 63.158 0.00 0.00 0.00 4.61
328 341 2.363147 AGGACGAGCAGGAGGGAC 60.363 66.667 0.00 0.00 0.00 4.46
331 344 2.752238 ACGAGGACGAGCAGGAGG 60.752 66.667 0.00 0.00 42.66 4.30
366 393 0.179045 AGCCTGTTTTGTGCGAGACT 60.179 50.000 0.00 0.00 0.00 3.24
368 395 0.463654 ACAGCCTGTTTTGTGCGAGA 60.464 50.000 0.00 0.00 0.00 4.04
427 454 4.320202 CCGACGAAGAATTCCACACATTTT 60.320 41.667 0.65 0.00 43.81 1.82
479 506 9.504710 CTACGTTCAGCTCGCTATATAATAATT 57.495 33.333 0.00 0.00 0.00 1.40
485 512 4.153655 CACCTACGTTCAGCTCGCTATATA 59.846 45.833 0.00 0.00 0.00 0.86
486 513 3.058155 CACCTACGTTCAGCTCGCTATAT 60.058 47.826 0.00 0.00 0.00 0.86
487 514 2.289820 CACCTACGTTCAGCTCGCTATA 59.710 50.000 0.00 0.00 0.00 1.31
488 515 1.065701 CACCTACGTTCAGCTCGCTAT 59.934 52.381 0.00 0.00 0.00 2.97
489 516 0.450583 CACCTACGTTCAGCTCGCTA 59.549 55.000 0.00 0.00 0.00 4.26
511 539 1.911471 TGGCTCATTGGCACCGATA 59.089 52.632 0.00 0.00 46.76 2.92
587 618 4.593206 GGTCATGGGAGACACATATAGGAA 59.407 45.833 0.00 0.00 40.29 3.36
612 643 0.104120 TGGCGTAACCCTGATCATCG 59.896 55.000 0.00 0.00 37.83 3.84
632 4932 1.895131 TGGCATGATAGCGCTATGAGA 59.105 47.619 33.54 17.31 34.64 3.27
636 4936 4.952071 ATATCTGGCATGATAGCGCTAT 57.048 40.909 29.38 29.38 33.12 2.97
644 4944 6.888632 GGACAAAGGAATATATCTGGCATGAT 59.111 38.462 0.00 0.00 0.00 2.45
673 4973 9.314133 TGTAGACATAATAATCTGGAGCATAGT 57.686 33.333 0.00 0.00 0.00 2.12
694 4998 7.458397 AGATTTGATGGGTTTACAAGTGTAGA 58.542 34.615 0.00 0.00 0.00 2.59
776 5081 1.968540 GCTGCGCCAGGAGACTTTT 60.969 57.895 4.18 0.00 40.21 2.27
876 5185 0.919981 AATTGCAAAACGTGTGTGCG 59.080 45.000 1.71 0.00 41.27 5.34
882 5191 2.906161 GCCGTAGTAATTGCAAAACGTG 59.094 45.455 1.71 4.90 0.00 4.49
884 5193 3.190314 TGCCGTAGTAATTGCAAAACG 57.810 42.857 1.71 8.75 0.00 3.60
975 5286 0.550914 TCTTGGGCTGTTTGAGGTGT 59.449 50.000 0.00 0.00 0.00 4.16
1037 5351 3.770666 TGCTACTGATCGAACTTACTGC 58.229 45.455 0.00 0.00 0.00 4.40
1045 5359 1.570813 CGCCATTGCTACTGATCGAA 58.429 50.000 0.00 0.00 34.43 3.71
1140 5454 0.838987 GGGGTAGGGACAACTGGTGA 60.839 60.000 0.00 0.00 0.00 4.02
1148 5462 4.468769 ATCGGCGGGGTAGGGACA 62.469 66.667 7.21 0.00 0.00 4.02
1349 5666 0.107017 CGAGGATGTTGGCCCTGATT 60.107 55.000 0.00 0.00 31.84 2.57
1436 5753 0.842030 AGATGGGGCAGGTGAAGTCA 60.842 55.000 0.00 0.00 0.00 3.41
1512 5835 3.013219 TGTGTACGTATGGCATGCAAAT 58.987 40.909 21.36 14.75 0.00 2.32
1561 5885 2.362397 ACGCCTGACATAGAGTACATGG 59.638 50.000 0.00 0.00 0.00 3.66
1570 5894 1.064505 CCATGCAAACGCCTGACATAG 59.935 52.381 0.00 0.00 0.00 2.23
1613 5937 7.010830 CACTGATCAATCACACGATTATCAAGT 59.989 37.037 0.00 0.00 39.96 3.16
1622 5946 4.454728 TGATCACTGATCAATCACACGA 57.545 40.909 17.80 0.00 44.70 4.35
1637 5962 8.150945 AGTACCATAACAGGATACAATGATCAC 58.849 37.037 0.00 0.00 41.41 3.06
1644 5969 7.282224 GCATTGAAGTACCATAACAGGATACAA 59.718 37.037 0.00 0.00 41.41 2.41
1652 5977 7.338957 TGAATCATGCATTGAAGTACCATAACA 59.661 33.333 0.00 0.00 38.03 2.41
1662 5987 8.539674 CACAAATACATGAATCATGCATTGAAG 58.460 33.333 27.51 19.72 44.80 3.02
1663 5988 8.251721 TCACAAATACATGAATCATGCATTGAA 58.748 29.630 27.51 18.21 44.80 2.69
1665 5990 7.995463 TCACAAATACATGAATCATGCATTG 57.005 32.000 21.92 22.55 44.80 2.82
1701 6026 8.460428 TCACGTACACATACAATGATACAAGTA 58.540 33.333 0.00 0.00 0.00 2.24
1708 6033 6.170506 ACCTTTCACGTACACATACAATGAT 58.829 36.000 0.00 0.00 30.18 2.45
1711 6036 6.261381 ACAAACCTTTCACGTACACATACAAT 59.739 34.615 0.00 0.00 0.00 2.71
1712 6037 5.585445 ACAAACCTTTCACGTACACATACAA 59.415 36.000 0.00 0.00 0.00 2.41
1723 6048 3.857093 CCAAGTTGAACAAACCTTTCACG 59.143 43.478 3.87 0.00 39.85 4.35
1737 6094 3.886505 GGTGATGTGTTAACCCAAGTTGA 59.113 43.478 3.87 0.00 36.68 3.18
1752 6109 2.825532 CCATTTTCTTTCCGGGTGATGT 59.174 45.455 0.00 0.00 0.00 3.06
1753 6110 2.166254 CCCATTTTCTTTCCGGGTGATG 59.834 50.000 0.00 0.00 31.80 3.07
1762 6119 7.709269 GGTCAAGTTAAACCCATTTTCTTTC 57.291 36.000 0.00 0.00 0.00 2.62
1775 6132 3.942748 GGCATATCACGGGTCAAGTTAAA 59.057 43.478 0.00 0.00 0.00 1.52
1833 6192 6.318144 GTGAATCTGATCAGGATTGACACAAT 59.682 38.462 22.42 1.77 37.30 2.71
1837 6196 5.425196 TGTGAATCTGATCAGGATTGACA 57.575 39.130 23.01 23.01 41.99 3.58
1838 6197 8.618702 AATATGTGAATCTGATCAGGATTGAC 57.381 34.615 22.42 20.95 37.64 3.18
1861 6333 9.988350 CACTGATAAGTATTTGCGTTAGAAAAT 57.012 29.630 0.00 0.00 38.99 1.82
1867 6339 5.220586 GCTGCACTGATAAGTATTTGCGTTA 60.221 40.000 0.00 0.00 32.49 3.18
1870 6342 3.310774 AGCTGCACTGATAAGTATTTGCG 59.689 43.478 1.02 0.00 32.49 4.85
1895 6367 2.115510 GCCGGAAAGCCCAATTAGG 58.884 57.895 5.05 0.00 34.14 2.69
1967 6447 3.691049 AACGATGACACACACCTTTTG 57.309 42.857 0.00 0.00 0.00 2.44
1971 6451 2.364324 ACTGTAACGATGACACACACCT 59.636 45.455 0.00 0.00 0.00 4.00
2020 6502 0.036164 TCACTTGTGTTCGGATGGGG 59.964 55.000 0.46 0.00 0.00 4.96
2053 6537 9.875675 TTTTGTAAAACTCAAATAAATGCATGC 57.124 25.926 11.82 11.82 35.25 4.06
2112 6769 6.796705 ACGGTGAAAACGAATCTAAATTCT 57.203 33.333 0.00 0.00 39.36 2.40
2134 6791 1.404035 ACTCGCAGTGAAAAACCCAAC 59.596 47.619 0.00 0.00 0.00 3.77
2148 6805 4.929808 GGATCTAGTTTTGAAGAACTCGCA 59.070 41.667 0.00 0.00 40.24 5.10
2408 7084 4.708421 TGGCTACGATACTAGGACAAGTTT 59.292 41.667 0.00 0.00 0.00 2.66
2438 7114 0.521867 CGGTTTGCATGTCATCGCTG 60.522 55.000 0.00 0.00 0.00 5.18
2708 9099 4.437390 CGTATGACCAACTTGAATTGCCTC 60.437 45.833 0.00 0.00 0.00 4.70
2713 9104 6.801575 ACAAAACGTATGACCAACTTGAATT 58.198 32.000 8.14 0.00 0.00 2.17
2815 9982 8.116651 TCCAAGCAACTGCATTACTAAATAAA 57.883 30.769 4.22 0.00 45.16 1.40


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

AutoCloner maintained by Alex Coulton.