Multiple sequence alignment - TraesCS7D01G251500

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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 TraesCS7D01G251500 chr7D 100.000 6312 0 0 634 6945 224460771 224454460 0.000000e+00 11657
1 TraesCS7D01G251500 chr7D 100.000 257 0 0 1 257 224461404 224461148 6.300000e-130 475
2 TraesCS7D01G251500 chr7D 82.909 275 25 13 1067 1329 541968916 541969180 1.950000e-55 228
3 TraesCS7D01G251500 chr7D 78.713 404 35 17 3298 3677 224458038 224457662 9.070000e-54 222
4 TraesCS7D01G251500 chr7D 78.713 404 35 17 3367 3743 224458107 224457728 9.070000e-54 222
5 TraesCS7D01G251500 chr7A 96.241 4416 92 28 1836 6201 237941609 237937218 0.000000e+00 7167
6 TraesCS7D01G251500 chr7A 89.400 1217 68 29 636 1836 237943152 237941981 0.000000e+00 1476
7 TraesCS7D01G251500 chr7A 89.593 442 42 2 6237 6675 237936819 237936379 6.080000e-155 558
8 TraesCS7D01G251500 chr7A 92.029 276 17 3 6675 6945 237936349 237936074 3.930000e-102 383
9 TraesCS7D01G251500 chr7A 91.566 249 12 5 11 257 237943951 237943710 1.120000e-87 335
10 TraesCS7D01G251500 chr7A 78.465 404 36 17 3367 3743 237940123 237939744 4.220000e-52 217
11 TraesCS7D01G251500 chr7A 77.970 404 38 14 3298 3677 237940054 237939678 9.130000e-49 206
12 TraesCS7D01G251500 chr7B 95.884 3644 113 9 2573 6201 172587416 172591037 0.000000e+00 5864
13 TraesCS7D01G251500 chr7B 86.851 1985 121 57 636 2586 172585573 172587451 0.000000e+00 2091
14 TraesCS7D01G251500 chr7B 91.956 721 48 6 6233 6945 172591432 172592150 0.000000e+00 1002
15 TraesCS7D01G251500 chr7B 92.917 240 12 2 11 249 172585171 172585406 1.850000e-90 344
16 TraesCS7D01G251500 chr7B 77.510 498 60 21 832 1304 585577728 585578198 1.160000e-62 252
17 TraesCS7D01G251500 chr7B 78.960 404 37 15 3367 3743 172588124 172588506 1.510000e-56 231
18 TraesCS7D01G251500 chr7B 77.519 387 41 24 943 1329 585629108 585629448 2.560000e-44 191
19 TraesCS7D01G251500 chr7B 79.562 274 34 12 1067 1329 585517192 585517454 7.160000e-40 176
20 TraesCS7D01G251500 chr7B 79.134 254 45 6 6678 6925 585469085 585468834 1.200000e-37 169
21 TraesCS7D01G251500 chr7B 75.567 397 63 20 3298 3677 172588193 172588572 1.550000e-36 165
22 TraesCS7D01G251500 chr2A 79.636 275 51 3 6675 6945 40478599 40478872 7.110000e-45 193
23 TraesCS7D01G251500 chr6B 79.528 254 44 6 6678 6925 691026118 691026369 2.570000e-39 174
24 TraesCS7D01G251500 chr4A 79.528 254 44 6 6678 6925 720805524 720805775 2.570000e-39 174
25 TraesCS7D01G251500 chr3B 79.134 254 48 5 6696 6945 82341611 82341863 3.330000e-38 171
26 TraesCS7D01G251500 chr2B 78.491 265 52 5 6685 6945 184386226 184385963 1.200000e-37 169
27 TraesCS7D01G251500 chr5B 77.536 276 56 6 6675 6945 682814650 682814376 2.000000e-35 161


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 TraesCS7D01G251500 chr7D 224454460 224461404 6944 True 3144.000000 11657 89.356500 1 6945 4 chr7D.!!$R1 6944
1 TraesCS7D01G251500 chr7A 237936074 237943951 7877 True 1477.428571 7167 87.894857 11 6945 7 chr7A.!!$R1 6934
2 TraesCS7D01G251500 chr7B 172585171 172592150 6979 False 1616.166667 5864 87.022500 11 6945 6 chr7B.!!$F4 6934

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
908 1133 2.495669 AGTAGAGAGAGAAAGTGCTGCC 59.504 50.000 0.00 0.00 0.00 4.85 F
1735 1999 0.113190 CTCTTTCCCCTTGTGGCCTT 59.887 55.000 3.32 0.00 0.00 4.35 F
1736 2000 0.178964 TCTTTCCCCTTGTGGCCTTG 60.179 55.000 3.32 0.00 0.00 3.61 F
2297 2960 0.250234 AAGGAATGTCGCTGCTAGCA 59.750 50.000 18.22 18.22 42.58 3.49 F
2822 3486 0.250901 GCCCGGGCATGACATATTCT 60.251 55.000 40.73 0.00 41.49 2.40 F
3237 3901 0.764890 TACCCTGTGGATGGCTATGC 59.235 55.000 0.00 0.00 34.81 3.14 F
4656 5329 3.242867 TGGAAGTCATCACTCCACTCTT 58.757 45.455 0.00 0.00 29.70 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1940 2583 0.329596 GGTGAAATGAGGGGTCAGCT 59.670 55.000 0.00 0.00 36.94 4.24 R
2822 3486 1.211703 TCCAGAGCCTTGTGTTGTCAA 59.788 47.619 0.00 0.00 0.00 3.18 R
3237 3901 3.135348 TGGGAAGAATCTATCTGTGCCAG 59.865 47.826 0.00 0.00 38.79 4.85 R
3562 4229 3.802948 ACGTAGTTTGGCCTCTCATAG 57.197 47.619 3.32 0.00 37.78 2.23 R
4656 5329 7.526918 TCTTCTCCCATGTATACAGTCTATCA 58.473 38.462 11.91 0.00 0.00 2.15 R
5194 5879 5.649602 TTGTTTGCTGAAAATTTTAGCGG 57.350 34.783 15.96 9.62 40.24 5.52 R
6227 6925 1.065928 CACTACTCCGGCGTCATCC 59.934 63.158 0.00 0.00 0.00 3.51 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
18 19 3.398365 AAAACACCCCCACCCCCAC 62.398 63.158 0.00 0.00 0.00 4.61
90 91 4.442706 GTGTGAGAAAAGACAGTTCTCCA 58.557 43.478 10.74 6.51 46.98 3.86
91 92 4.509600 GTGTGAGAAAAGACAGTTCTCCAG 59.490 45.833 10.74 0.00 46.98 3.86
132 133 3.880490 TGCACAAACAAACCTACTACTGG 59.120 43.478 0.00 0.00 0.00 4.00
908 1133 2.495669 AGTAGAGAGAGAAAGTGCTGCC 59.504 50.000 0.00 0.00 0.00 4.85
1050 1294 4.399303 CCTGGTTTCTTCTCTCTCTCTCTC 59.601 50.000 0.00 0.00 0.00 3.20
1053 1297 4.640647 GGTTTCTTCTCTCTCTCTCTCTCC 59.359 50.000 0.00 0.00 0.00 3.71
1055 1299 2.777692 TCTTCTCTCTCTCTCTCTCCCC 59.222 54.545 0.00 0.00 0.00 4.81
1192 1437 4.622701 ATTTCGCCTGCTCTTTAATGTC 57.377 40.909 0.00 0.00 0.00 3.06
1214 1459 0.737367 CAGACGAGAATTCAGCGGCA 60.737 55.000 23.00 0.00 35.00 5.69
1357 1604 2.478134 GCATCAGAATCAGATACCGTGC 59.522 50.000 0.00 0.00 0.00 5.34
1397 1644 1.068679 GTAGCGGATAACGGAGGTAGC 60.069 57.143 0.00 0.00 44.51 3.58
1398 1645 1.371389 GCGGATAACGGAGGTAGCG 60.371 63.158 0.00 0.00 44.51 4.26
1419 1666 1.075601 AATGCACTTCCCTCTTCCCA 58.924 50.000 0.00 0.00 0.00 4.37
1518 1769 1.986210 GCCAGGATTGCCTTGCCTT 60.986 57.895 0.00 0.00 44.94 4.35
1559 1812 4.799715 TGGGGTCCGTAATTTATCCATT 57.200 40.909 0.00 0.00 0.00 3.16
1560 1813 4.721132 TGGGGTCCGTAATTTATCCATTC 58.279 43.478 0.00 0.00 0.00 2.67
1568 1821 5.691305 CCGTAATTTATCCATTCGTTCCGTA 59.309 40.000 0.00 0.00 0.00 4.02
1569 1822 6.366877 CCGTAATTTATCCATTCGTTCCGTAT 59.633 38.462 0.00 0.00 0.00 3.06
1577 1830 3.308866 CCATTCGTTCCGTATCTTGGTTC 59.691 47.826 0.00 0.00 0.00 3.62
1638 1897 5.185828 GTCCTGTCCAGCAAATCCTTAATTT 59.814 40.000 0.00 0.00 38.11 1.82
1677 1936 3.052082 CCACTCGCAGGTTGGCAG 61.052 66.667 0.00 0.00 0.00 4.85
1686 1945 0.529378 CAGGTTGGCAGGAGCAATTC 59.471 55.000 0.00 0.00 44.61 2.17
1688 1947 0.968405 GGTTGGCAGGAGCAATTCAA 59.032 50.000 0.00 0.00 44.61 2.69
1722 1986 6.154706 TGGAGGATTGGAACTAGTACTCTTTC 59.845 42.308 0.00 3.13 0.00 2.62
1732 1996 1.351350 AGTACTCTTTCCCCTTGTGGC 59.649 52.381 0.00 0.00 0.00 5.01
1734 1998 1.068352 ACTCTTTCCCCTTGTGGCCT 61.068 55.000 3.32 0.00 0.00 5.19
1735 1999 0.113190 CTCTTTCCCCTTGTGGCCTT 59.887 55.000 3.32 0.00 0.00 4.35
1736 2000 0.178964 TCTTTCCCCTTGTGGCCTTG 60.179 55.000 3.32 0.00 0.00 3.61
1737 2001 0.469892 CTTTCCCCTTGTGGCCTTGT 60.470 55.000 3.32 0.00 0.00 3.16
1738 2002 0.758685 TTTCCCCTTGTGGCCTTGTG 60.759 55.000 3.32 0.00 0.00 3.33
1739 2003 2.601367 CCCCTTGTGGCCTTGTGG 60.601 66.667 3.32 0.99 0.00 4.17
1740 2004 2.601367 CCCTTGTGGCCTTGTGGG 60.601 66.667 3.32 7.20 38.36 4.61
1741 2005 2.198426 CCTTGTGGCCTTGTGGGT 59.802 61.111 3.32 0.00 37.43 4.51
1786 2050 9.739276 TGTTATTATTACCCATCATCATCTTCC 57.261 33.333 0.00 0.00 0.00 3.46
1787 2051 9.178758 GTTATTATTACCCATCATCATCTTCCC 57.821 37.037 0.00 0.00 0.00 3.97
1820 2084 9.515020 CTTGTAATTTTCTTCTTGTTACAGCAA 57.485 29.630 0.00 0.00 36.82 3.91
1851 2484 2.769095 ACCTTTTGCCCAACTGCTTAAA 59.231 40.909 0.00 0.00 0.00 1.52
1856 2489 1.036707 GCCCAACTGCTTAAACACCA 58.963 50.000 0.00 0.00 0.00 4.17
1874 2507 4.042809 ACACCAGAAAATCAGTCCACCATA 59.957 41.667 0.00 0.00 0.00 2.74
1903 2536 2.783510 GGGAATTTAGTCCATCCAGGGA 59.216 50.000 0.00 0.00 39.70 4.20
1940 2583 1.959226 GCGGTGCACTTCTTCGGAA 60.959 57.895 17.98 0.00 0.00 4.30
1965 2608 2.820197 GACCCCTCATTTCACCTTCAAC 59.180 50.000 0.00 0.00 0.00 3.18
1982 2625 5.290158 CCTTCAACATATCTTTGCATTGTGC 59.710 40.000 0.00 0.00 45.29 4.57
1991 2634 3.132646 TCTTTGCATTGTGCTTTTCTGGT 59.867 39.130 3.41 0.00 45.31 4.00
2050 2693 2.031769 TGCTGATTTCACTGCACGAAAG 60.032 45.455 11.17 1.45 39.16 2.62
2053 2696 4.789481 GCTGATTTCACTGCACGAAAGAAA 60.789 41.667 11.17 5.18 35.91 2.52
2054 2697 4.847633 TGATTTCACTGCACGAAAGAAAG 58.152 39.130 11.17 0.00 35.91 2.62
2218 2881 2.093658 AGGCAGTAGGACCGTTTATGTG 60.094 50.000 0.00 0.00 0.00 3.21
2297 2960 0.250234 AAGGAATGTCGCTGCTAGCA 59.750 50.000 18.22 18.22 42.58 3.49
2321 2984 3.692593 ACCGAAAAATGTGTAGGGTATGC 59.307 43.478 0.00 0.00 0.00 3.14
2434 3097 4.065088 TGTGAGAGGTAGTTGCATTTCAC 58.935 43.478 0.00 0.00 35.48 3.18
2501 3164 3.199727 TGTTGCTGGTGATTAGCCTATCA 59.800 43.478 0.00 0.00 40.42 2.15
2537 3200 5.469373 TGATACACAATTTGATCGCTCAC 57.531 39.130 2.79 0.00 0.00 3.51
2538 3201 4.934602 TGATACACAATTTGATCGCTCACA 59.065 37.500 2.79 0.00 0.00 3.58
2578 3241 8.677300 TCTGGAATTTGCTACTGAATAAATGTC 58.323 33.333 0.00 0.00 0.00 3.06
2760 3423 0.438830 GCTGAAACTTACCTGTCGCG 59.561 55.000 0.00 0.00 0.00 5.87
2769 3433 1.787012 TACCTGTCGCGTTCCTTTTC 58.213 50.000 5.77 0.00 0.00 2.29
2822 3486 0.250901 GCCCGGGCATGACATATTCT 60.251 55.000 40.73 0.00 41.49 2.40
3237 3901 0.764890 TACCCTGTGGATGGCTATGC 59.235 55.000 0.00 0.00 34.81 3.14
3562 4229 5.140454 AGGAATTCTTATTACATGCCACCC 58.860 41.667 5.23 0.00 0.00 4.61
4263 4936 4.594123 TCACTGTGTATCTGAACCGAAA 57.406 40.909 7.79 0.00 0.00 3.46
4656 5329 3.242867 TGGAAGTCATCACTCCACTCTT 58.757 45.455 0.00 0.00 29.70 2.85
5224 5909 3.799281 TTTCAGCAAACAAAGGGTGAG 57.201 42.857 0.00 0.00 41.86 3.51
5282 5967 4.418013 TGTAGGAATGCACGTGAATTTG 57.582 40.909 22.62 0.00 0.00 2.32
5315 6000 4.153117 GCCTGATCGTAGCCTTTGATAATG 59.847 45.833 0.00 0.00 0.00 1.90
5422 6107 0.321122 ACGCCAAGCTTCTCTTCCTG 60.321 55.000 0.00 0.00 31.27 3.86
5676 6361 3.402681 CATGGAGTGGGGGCTCGT 61.403 66.667 0.00 0.00 36.41 4.18
5689 6374 4.462417 CTCGTCGTCGAAGCGGCT 62.462 66.667 6.19 0.00 45.61 5.52
5692 6377 2.430244 GTCGTCGAAGCGGCTTCA 60.430 61.111 34.29 21.97 40.17 3.02
5737 6422 3.636313 CTTCTTCGTGGCCGGCGTA 62.636 63.158 22.54 9.49 33.95 4.42
6082 6770 3.247948 TGCATGGCTGATTATTGGGAT 57.752 42.857 0.00 0.00 0.00 3.85
6116 6804 5.290386 CCCAGTTTATACTAGCAGCAGTAC 58.710 45.833 0.00 0.00 33.94 2.73
6145 6841 1.427753 CCTTACCCCTGGTGGTTTTCT 59.572 52.381 11.39 0.00 39.91 2.52
6150 6846 0.951558 CCCTGGTGGTTTTCTTCGTG 59.048 55.000 0.00 0.00 0.00 4.35
6209 6907 9.933723 TTCTTTTCTACTGTATAAACTGGTACC 57.066 33.333 4.43 4.43 0.00 3.34
6211 6909 9.939802 CTTTTCTACTGTATAAACTGGTACCTT 57.060 33.333 14.36 1.43 0.00 3.50
6224 6922 2.121948 GGTACCTTACCTTACCCCTGG 58.878 57.143 4.06 0.00 45.52 4.45
6226 6924 2.265526 ACCTTACCTTACCCCTGGAG 57.734 55.000 0.00 0.00 0.00 3.86
6227 6925 1.274242 ACCTTACCTTACCCCTGGAGG 60.274 57.143 0.00 0.00 36.62 4.30
6260 7341 4.281435 GGAGTAGTGCCCTAGGATTAGAAC 59.719 50.000 11.48 0.00 0.00 3.01
6288 7369 0.035317 ACATGGTGAGTGTGCGTCAT 59.965 50.000 0.00 0.00 0.00 3.06
6335 7416 1.664873 GAATTCAAGGGTAGCGGGAC 58.335 55.000 0.00 0.00 0.00 4.46
6488 7572 1.382522 TGCTTTGGGCGATGATTCTC 58.617 50.000 0.00 0.00 45.43 2.87
6492 7576 0.464373 TTGGGCGATGATTCTCAGGC 60.464 55.000 0.00 0.00 0.00 4.85
6493 7577 1.599240 GGGCGATGATTCTCAGGCC 60.599 63.158 0.00 0.00 44.44 5.19
6533 7617 1.482182 AGCCATACGATGCTCTTCACA 59.518 47.619 0.00 0.00 30.33 3.58
6611 7695 8.709386 ATGACTACACATTCATAACTGAGTTC 57.291 34.615 0.00 0.00 30.41 3.01
6623 7707 3.356529 ACTGAGTTCCTATGCTTTGGG 57.643 47.619 0.41 0.00 0.00 4.12
6652 7736 1.855295 ATTGCAATGCATGAGGACCA 58.145 45.000 12.09 0.00 38.76 4.02
6677 7791 1.069978 TGTTCAGTCATCAGCCGACAA 59.930 47.619 0.00 0.00 35.77 3.18
6797 7914 8.442374 TGGTGAGGGTTTATTTAGTTTTCTAGT 58.558 33.333 0.00 0.00 33.61 2.57
6853 7973 1.079197 TGCCGTAGTGCACCATCAG 60.079 57.895 14.63 0.00 36.04 2.90
6871 7991 6.869913 ACCATCAGTTTCATGCTTGTTATTTG 59.130 34.615 0.00 0.00 0.00 2.32
6876 7996 7.594758 TCAGTTTCATGCTTGTTATTTGCTTAC 59.405 33.333 0.00 0.00 0.00 2.34
6881 8001 5.277601 TGCTTGTTATTTGCTTACGACTC 57.722 39.130 0.00 0.00 0.00 3.36
6888 8008 7.784037 TGTTATTTGCTTACGACTCCCTAATA 58.216 34.615 0.00 0.00 0.00 0.98
6893 8013 6.085555 TGCTTACGACTCCCTAATATTGAG 57.914 41.667 0.00 0.00 0.00 3.02
6927 8047 1.003839 GAATGCCACGACACTCCCA 60.004 57.895 0.00 0.00 0.00 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.036959 TGGGGGTGGGGGTGTTTT 61.037 61.111 0.00 0.00 0.00 2.43
1 2 3.840132 GTGGGGGTGGGGGTGTTT 61.840 66.667 0.00 0.00 0.00 2.83
42 43 9.250624 CGGGAATTTTGACATTTTTGTTACTTA 57.749 29.630 0.00 0.00 0.00 2.24
58 59 4.976116 GTCTTTTCTCACACGGGAATTTTG 59.024 41.667 0.00 0.00 0.00 2.44
633 635 0.996762 GGGGAGGGAGAGAGAGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
634 636 1.292941 TGGGGAGGGAGAGAGAGAGG 61.293 65.000 0.00 0.00 0.00 3.69
723 935 6.099269 GTCTATACCTGTTACCTGGGATTGAA 59.901 42.308 0.00 0.00 36.83 2.69
756 968 9.859152 AAGAAGAGATTAAAAATAGGATCAGGG 57.141 33.333 0.00 0.00 0.00 4.45
908 1133 1.368019 CGAGCACACAAACACGCAG 60.368 57.895 0.00 0.00 0.00 5.18
940 1165 6.439487 TCTCTCTCTAGGGATGAAGAACATT 58.561 40.000 0.00 0.00 39.56 2.71
1022 1247 0.402121 AGAGAAGAAACCAGGGGCAC 59.598 55.000 0.00 0.00 0.00 5.01
1050 1294 3.086600 GACTGCTGGGAGGGGGAG 61.087 72.222 0.00 0.00 0.00 4.30
1053 1297 3.086600 GGAGACTGCTGGGAGGGG 61.087 72.222 0.00 0.00 0.00 4.79
1055 1299 2.040278 AGGGAGACTGCTGGGAGG 59.960 66.667 0.00 0.00 0.00 4.30
1192 1437 1.746727 CGCTGAATTCTCGTCTGGCG 61.747 60.000 7.05 0.00 43.01 5.69
1214 1459 5.010922 TGGCAGCAATAATCAAACAGAAACT 59.989 36.000 0.00 0.00 0.00 2.66
1316 1563 2.657066 GGACGGGAAGGTGGAGACC 61.657 68.421 0.00 0.00 43.52 3.85
1331 1578 4.314121 GGTATCTGATTCTGATGCAGGAC 58.686 47.826 18.43 8.57 31.51 3.85
1357 1604 5.573669 GCTACAGAACCGAAAGAAACTAGAG 59.426 44.000 0.00 0.00 0.00 2.43
1397 1644 2.280628 GGAAGAGGGAAGTGCATTACG 58.719 52.381 0.00 0.00 0.00 3.18
1398 1645 2.026262 TGGGAAGAGGGAAGTGCATTAC 60.026 50.000 0.00 0.00 0.00 1.89
1413 1660 2.702478 TCATGGAGCAGATACTGGGAAG 59.298 50.000 0.00 0.00 31.21 3.46
1446 1693 7.907389 AGGAGAATTGAAGGGGAAATAAAAAC 58.093 34.615 0.00 0.00 0.00 2.43
1502 1751 1.203994 CTTGAAGGCAAGGCAATCCTG 59.796 52.381 0.00 0.00 46.13 3.86
1518 1769 2.989840 CAACCAAAAACACAACGCTTGA 59.010 40.909 5.01 0.00 0.00 3.02
1577 1830 4.759564 GCTCGTTGCATCTTGCTG 57.240 55.556 0.75 0.00 45.31 4.41
1655 1914 2.030562 AACCTGCGAGTGGAACCG 59.969 61.111 0.00 0.00 37.80 4.44
1688 1947 3.541242 TCCAATCCTCCAACCAAATGT 57.459 42.857 0.00 0.00 0.00 2.71
1722 1986 2.601367 CCACAAGGCCACAAGGGG 60.601 66.667 5.01 0.00 37.04 4.79
1740 2004 5.211174 ACACTTGTCTCTGGGTAAACTAC 57.789 43.478 0.00 0.00 0.00 2.73
1741 2005 5.881923 AACACTTGTCTCTGGGTAAACTA 57.118 39.130 0.00 0.00 0.00 2.24
1750 2014 8.964476 ATGGGTAATAATAACACTTGTCTCTG 57.036 34.615 0.00 0.00 0.00 3.35
1786 2050 7.922811 ACAAGAAGAAAATTACAAGAAAGCTGG 59.077 33.333 0.00 0.00 0.00 4.85
1787 2051 8.862550 ACAAGAAGAAAATTACAAGAAAGCTG 57.137 30.769 0.00 0.00 0.00 4.24
1851 2484 2.174639 TGGTGGACTGATTTTCTGGTGT 59.825 45.455 0.00 0.00 0.00 4.16
1856 2489 4.472833 AGCTCTATGGTGGACTGATTTTCT 59.527 41.667 0.00 0.00 0.00 2.52
1874 2507 2.912956 TGGACTAAATTCCCACAGCTCT 59.087 45.455 0.00 0.00 34.33 4.09
1903 2536 2.226437 CGCAGGCAAACAGAAGTATTGT 59.774 45.455 0.00 0.00 0.00 2.71
1907 2540 2.927004 CCGCAGGCAAACAGAAGTA 58.073 52.632 0.00 0.00 46.14 2.24
1940 2583 0.329596 GGTGAAATGAGGGGTCAGCT 59.670 55.000 0.00 0.00 36.94 4.24
1982 2625 5.005971 CACAAATCACAAGCAACCAGAAAAG 59.994 40.000 0.00 0.00 0.00 2.27
1991 2634 1.336440 CCGTCCACAAATCACAAGCAA 59.664 47.619 0.00 0.00 0.00 3.91
2050 2693 5.460646 TGGAATTCGAAACAGCATTCTTTC 58.539 37.500 0.00 0.00 0.00 2.62
2053 2696 5.047802 ACATTGGAATTCGAAACAGCATTCT 60.048 36.000 7.00 0.00 0.00 2.40
2054 2697 5.163513 ACATTGGAATTCGAAACAGCATTC 58.836 37.500 7.00 0.00 0.00 2.67
2218 2881 1.228737 TAACCCTTGGCCCAGCAAC 60.229 57.895 0.00 0.00 0.00 4.17
2297 2960 5.336134 GCATACCCTACACATTTTTCGGTTT 60.336 40.000 0.00 0.00 0.00 3.27
2321 2984 5.982890 AATGAAATACCCCACTGACAAAG 57.017 39.130 0.00 0.00 0.00 2.77
2419 3082 4.217754 TCAAACGTGAAATGCAACTACC 57.782 40.909 0.00 0.00 0.00 3.18
2434 3097 5.178797 AGATTGACTACTTGGGATCAAACG 58.821 41.667 0.00 0.00 34.88 3.60
2501 3164 5.304686 TGTGTATCAAAAGGGAACTCAGT 57.695 39.130 0.00 0.00 42.68 3.41
2537 3200 5.578005 ATTCCAGACATTTCAGAAGCATG 57.422 39.130 0.00 0.00 0.00 4.06
2538 3201 6.395629 CAAATTCCAGACATTTCAGAAGCAT 58.604 36.000 0.00 0.00 0.00 3.79
2578 3241 4.394300 AGACATTTCAGAAGCGAATTCCAG 59.606 41.667 0.00 0.00 38.84 3.86
2760 3423 6.099341 ACATGTCAAAACACAGAAAAGGAAC 58.901 36.000 0.00 0.00 38.48 3.62
2769 3433 6.430451 GGAGTCTTAACATGTCAAAACACAG 58.570 40.000 0.00 0.00 38.48 3.66
2822 3486 1.211703 TCCAGAGCCTTGTGTTGTCAA 59.788 47.619 0.00 0.00 0.00 3.18
3237 3901 3.135348 TGGGAAGAATCTATCTGTGCCAG 59.865 47.826 0.00 0.00 38.79 4.85
3562 4229 3.802948 ACGTAGTTTGGCCTCTCATAG 57.197 47.619 3.32 0.00 37.78 2.23
4656 5329 7.526918 TCTTCTCCCATGTATACAGTCTATCA 58.473 38.462 11.91 0.00 0.00 2.15
5194 5879 5.649602 TTGTTTGCTGAAAATTTTAGCGG 57.350 34.783 15.96 9.62 40.24 5.52
5224 5909 6.992715 ACTATGATCAATAACCCAACAGCTAC 59.007 38.462 0.00 0.00 0.00 3.58
5282 5967 0.755686 ACGATCAGGCAAGATCCCTC 59.244 55.000 12.47 0.00 41.03 4.30
5315 6000 2.033801 ACAATGCAACAACAGCTCTGTC 59.966 45.455 2.68 0.00 44.13 3.51
5676 6361 2.126463 CTGAAGCCGCTTCGACGA 60.126 61.111 24.52 9.22 42.78 4.20
5689 6374 3.390521 ATCACCCGCGCCTCTGAA 61.391 61.111 0.00 0.00 0.00 3.02
6116 6804 1.280998 CCAGGGGTAAGGTAACACTGG 59.719 57.143 7.21 7.21 38.70 4.00
6145 6841 3.804036 ACCATTCAGACTTCAACACGAA 58.196 40.909 0.00 0.00 0.00 3.85
6150 6846 5.660460 ACCAAAAACCATTCAGACTTCAAC 58.340 37.500 0.00 0.00 0.00 3.18
6206 6904 2.022722 CCTCCAGGGGTAAGGTAAGGTA 60.023 54.545 0.00 0.00 0.00 3.08
6207 6905 1.274242 CCTCCAGGGGTAAGGTAAGGT 60.274 57.143 0.00 0.00 0.00 3.50
6208 6906 1.508256 CCTCCAGGGGTAAGGTAAGG 58.492 60.000 0.00 0.00 0.00 2.69
6220 6918 4.227134 CGGCGTCATCCCTCCAGG 62.227 72.222 0.00 0.00 0.00 4.45
6221 6919 4.227134 CCGGCGTCATCCCTCCAG 62.227 72.222 6.01 0.00 0.00 3.86
6222 6920 4.770362 TCCGGCGTCATCCCTCCA 62.770 66.667 6.01 0.00 0.00 3.86
6224 6922 1.797211 CTACTCCGGCGTCATCCCTC 61.797 65.000 0.00 0.00 0.00 4.30
6226 6924 2.125961 ACTACTCCGGCGTCATCCC 61.126 63.158 0.00 0.00 0.00 3.85
6227 6925 1.065928 CACTACTCCGGCGTCATCC 59.934 63.158 0.00 0.00 0.00 3.51
6228 6926 1.589196 GCACTACTCCGGCGTCATC 60.589 63.158 0.00 0.00 0.00 2.92
6229 6927 2.494918 GCACTACTCCGGCGTCAT 59.505 61.111 0.00 0.00 0.00 3.06
6231 6929 4.509737 GGGCACTACTCCGGCGTC 62.510 72.222 0.00 0.00 0.00 5.19
6260 7341 1.462283 CACTCACCATGTGCGAAGAAG 59.538 52.381 0.00 0.00 32.98 2.85
6288 7369 1.527433 CGATAGAGATGCGGCCCAGA 61.527 60.000 0.00 0.00 39.76 3.86
6335 7416 1.228429 TTTGTTGAGGCTTCCCCCG 60.228 57.895 0.00 0.00 0.00 5.73
6338 7419 2.306847 TGTTCTTTGTTGAGGCTTCCC 58.693 47.619 0.00 0.00 0.00 3.97
6348 7429 4.280929 GCTGGGTTTCCTATGTTCTTTGTT 59.719 41.667 0.00 0.00 0.00 2.83
6462 7546 2.947938 ATCGCCCAAAGCATCTCCCG 62.948 60.000 0.00 0.00 44.04 5.14
6488 7572 1.517242 GAGTTCAGACACAAGGCCTG 58.483 55.000 5.69 2.82 0.00 4.85
6492 7576 2.104792 TGAAGGGAGTTCAGACACAAGG 59.895 50.000 0.00 0.00 40.45 3.61
6493 7577 3.475566 TGAAGGGAGTTCAGACACAAG 57.524 47.619 0.00 0.00 40.45 3.16
6611 7695 2.806945 TCCACTTCCCAAAGCATAGG 57.193 50.000 0.00 0.00 35.81 2.57
6623 7707 5.593968 TCATGCATTGCAATATTCCACTTC 58.406 37.500 16.46 0.00 43.62 3.01
6652 7736 2.440409 GGCTGATGACTGAACAACCAT 58.560 47.619 0.00 0.00 0.00 3.55
6726 7840 2.761465 GGGATCCCCTTGCCTGAGG 61.761 68.421 21.42 0.00 41.34 3.86
6797 7914 0.467474 ACCGCCGATCTCCTCATGTA 60.467 55.000 0.00 0.00 0.00 2.29
6853 7973 6.580791 TCGTAAGCAAATAACAAGCATGAAAC 59.419 34.615 0.00 0.00 37.18 2.78
6871 7991 5.243283 TCCTCAATATTAGGGAGTCGTAAGC 59.757 44.000 9.66 0.00 34.66 3.09
6876 7996 4.082463 GCTCTCCTCAATATTAGGGAGTCG 60.082 50.000 23.67 19.06 43.97 4.18
6881 8001 3.165875 TCCGCTCTCCTCAATATTAGGG 58.834 50.000 9.66 5.66 34.66 3.53
6888 8008 1.068753 CGCATCCGCTCTCCTCAAT 59.931 57.895 0.00 0.00 35.30 2.57
6893 8013 2.685387 ATTCGACGCATCCGCTCTCC 62.685 60.000 0.00 0.00 38.22 3.71


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

AutoCloner maintained by Alex Coulton.