Multiple sequence alignment - TraesCS7D01G143100

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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 TraesCS7D01G143100 chr7D 100.000 3066 0 0 1 3066 91144821 91141756 0.000000e+00 5662
1 TraesCS7D01G143100 chr7D 82.927 451 66 9 2519 2968 532897699 532897259 2.220000e-106 396
2 TraesCS7D01G143100 chr7D 80.088 226 29 13 1036 1253 611135669 611135886 1.470000e-33 154
3 TraesCS7D01G143100 chr7B 91.653 1833 103 29 653 2467 43755002 43753202 0.000000e+00 2492
4 TraesCS7D01G143100 chr7B 87.070 611 73 4 2456 3065 43749650 43749045 0.000000e+00 686
5 TraesCS7D01G143100 chr7B 81.221 655 115 4 1 652 41274536 41275185 3.500000e-144 521
6 TraesCS7D01G143100 chr7B 78.659 656 127 9 1 653 24121786 24122431 1.020000e-114 424
7 TraesCS7D01G143100 chr7B 80.093 216 27 13 1055 1262 700184177 700184384 2.460000e-31 147
8 TraesCS7D01G143100 chr7A 89.365 1749 86 48 796 2490 93081643 93083345 0.000000e+00 2108
9 TraesCS7D01G143100 chr7A 88.376 585 63 3 2482 3065 93083451 93084031 0.000000e+00 699
10 TraesCS7D01G143100 chr7A 84.296 433 63 3 2536 2968 694104117 694104544 4.730000e-113 418
11 TraesCS7D01G143100 chr7A 77.224 281 41 20 1044 1313 701149407 701149675 3.190000e-30 143
12 TraesCS7D01G143100 chr5D 90.447 649 60 2 4 651 465089668 465089021 0.000000e+00 854
13 TraesCS7D01G143100 chr6A 88.532 654 71 4 1 653 510882581 510883231 0.000000e+00 789
14 TraesCS7D01G143100 chr6A 84.340 447 65 3 2522 2968 11128674 11128233 1.690000e-117 433
15 TraesCS7D01G143100 chr5A 87.250 651 83 0 1 651 123129837 123130487 0.000000e+00 743
16 TraesCS7D01G143100 chr1D 86.381 514 69 1 139 651 410789634 410790147 7.420000e-156 560
17 TraesCS7D01G143100 chr1A 80.213 657 116 12 1 652 10236281 10235634 5.950000e-132 481
18 TraesCS7D01G143100 chr3A 79.878 656 119 10 1 652 674254928 674254282 4.630000e-128 468
19 TraesCS7D01G143100 chr3D 85.202 446 59 5 2523 2968 529837890 529838328 4.660000e-123 451
20 TraesCS7D01G143100 chr4D 84.581 454 59 8 2505 2955 477906329 477906774 1.010000e-119 440
21 TraesCS7D01G143100 chr4D 82.151 465 72 9 2506 2968 460664889 460665344 3.710000e-104 388
22 TraesCS7D01G143100 chr4D 81.720 465 74 9 2506 2968 460656137 460656592 8.020000e-101 377
23 TraesCS7D01G143100 chr6D 82.880 368 62 1 285 652 295307068 295306702 2.280000e-86 329
24 TraesCS7D01G143100 chr2B 81.081 185 29 6 1056 1237 744058437 744058256 3.190000e-30 143
25 TraesCS7D01G143100 chr2D 80.645 186 28 8 1056 1237 609515761 609515580 1.480000e-28 137
26 TraesCS7D01G143100 chr2A 80.645 186 28 8 1056 1237 742293582 742293401 1.480000e-28 137


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 TraesCS7D01G143100 chr7D 91141756 91144821 3065 True 5662.0 5662 100.0000 1 3066 1 chr7D.!!$R1 3065
1 TraesCS7D01G143100 chr7B 43749045 43755002 5957 True 1589.0 2492 89.3615 653 3065 2 chr7B.!!$R1 2412
2 TraesCS7D01G143100 chr7B 41274536 41275185 649 False 521.0 521 81.2210 1 652 1 chr7B.!!$F2 651
3 TraesCS7D01G143100 chr7B 24121786 24122431 645 False 424.0 424 78.6590 1 653 1 chr7B.!!$F1 652
4 TraesCS7D01G143100 chr7A 93081643 93084031 2388 False 1403.5 2108 88.8705 796 3065 2 chr7A.!!$F3 2269
5 TraesCS7D01G143100 chr5D 465089021 465089668 647 True 854.0 854 90.4470 4 651 1 chr5D.!!$R1 647
6 TraesCS7D01G143100 chr6A 510882581 510883231 650 False 789.0 789 88.5320 1 653 1 chr6A.!!$F1 652
7 TraesCS7D01G143100 chr5A 123129837 123130487 650 False 743.0 743 87.2500 1 651 1 chr5A.!!$F1 650
8 TraesCS7D01G143100 chr1D 410789634 410790147 513 False 560.0 560 86.3810 139 651 1 chr1D.!!$F1 512
9 TraesCS7D01G143100 chr1A 10235634 10236281 647 True 481.0 481 80.2130 1 652 1 chr1A.!!$R1 651
10 TraesCS7D01G143100 chr3A 674254282 674254928 646 True 468.0 468 79.8780 1 652 1 chr3A.!!$R1 651

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
964 975 0.467384 CCCTGCTACTGTGCTAGCAT 59.533 55.0 22.51 7.71 46.35 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2597 6367 0.334676 CCTCCTATGGCCCCAAAACA 59.665 55.0 0.0 0.0 0.0 2.83 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
66 67 1.228245 GTGAAGGGCAAGCAGGTGA 60.228 57.895 0.00 0.00 0.00 4.02
171 174 2.032681 GGGCCAAGCTGAACGTCT 59.967 61.111 4.39 0.00 0.00 4.18
277 280 3.715854 GTCAACTACGGAGATGCGT 57.284 52.632 0.00 4.47 0.00 5.24
334 337 1.227586 GCCTAAACCTAGCGCTCCC 60.228 63.158 16.34 0.00 0.00 4.30
412 415 2.662596 GGGCGACACTGTGGATCA 59.337 61.111 13.09 0.00 0.00 2.92
419 422 1.929836 GACACTGTGGATCAATCTCGC 59.070 52.381 13.09 0.00 0.00 5.03
421 424 2.027745 ACACTGTGGATCAATCTCGCTT 60.028 45.455 13.09 0.00 0.00 4.68
480 483 4.446023 GGGGAGGAAGAGATACGAGACTAA 60.446 50.000 0.00 0.00 0.00 2.24
582 586 2.267961 GTTCCGGTCCAGGCGATT 59.732 61.111 0.00 0.00 0.00 3.34
587 591 1.376683 CGGTCCAGGCGATTTTCCA 60.377 57.895 0.00 0.00 0.00 3.53
588 592 0.748005 CGGTCCAGGCGATTTTCCAT 60.748 55.000 0.00 0.00 0.00 3.41
609 613 9.905713 TTCCATATCTTTGTAAGCAAGACTATT 57.094 29.630 0.00 0.00 35.82 1.73
616 620 9.555727 TCTTTGTAAGCAAGACTATTAGTTTGT 57.444 29.630 14.56 0.00 35.82 2.83
643 647 6.555463 ATCAATAGAAACTTTACCCTCCGA 57.445 37.500 0.00 0.00 0.00 4.55
667 671 3.615224 AAAAAGGTATCGCTCCGGTAA 57.385 42.857 0.00 0.00 0.00 2.85
675 679 2.243602 TCGCTCCGGTAAACAACTTT 57.756 45.000 0.00 0.00 0.00 2.66
743 747 3.876198 CGCGGCAGCAACATACCC 61.876 66.667 10.08 0.00 45.49 3.69
747 751 2.406616 GGCAGCAACATACCCGGTG 61.407 63.158 0.00 0.00 0.00 4.94
767 771 3.751698 GTGAAAACCGGTTCAGCTAGAAT 59.248 43.478 22.53 0.00 38.17 2.40
774 778 5.010282 ACCGGTTCAGCTAGAATTTCATTT 58.990 37.500 0.00 0.00 38.76 2.32
849 853 3.003173 CTCGCTCCCCTCCAACCA 61.003 66.667 0.00 0.00 0.00 3.67
886 890 1.954382 CCCCAATCATGCTCACATCAG 59.046 52.381 0.00 0.00 32.87 2.90
914 918 0.885879 TTCGTACATCGCTCCACACT 59.114 50.000 0.00 0.00 39.67 3.55
917 921 1.841450 GTACATCGCTCCACACTAGC 58.159 55.000 0.00 0.00 36.60 3.42
920 924 0.807667 CATCGCTCCACACTAGCCAC 60.808 60.000 0.00 0.00 36.60 5.01
921 925 1.961180 ATCGCTCCACACTAGCCACC 61.961 60.000 0.00 0.00 36.60 4.61
922 926 2.942796 CGCTCCACACTAGCCACCA 61.943 63.158 0.00 0.00 36.60 4.17
923 927 1.078848 GCTCCACACTAGCCACCAG 60.079 63.158 0.00 0.00 33.73 4.00
924 928 1.078848 CTCCACACTAGCCACCAGC 60.079 63.158 0.00 0.00 44.25 4.85
963 974 1.617018 CCCCTGCTACTGTGCTAGCA 61.617 60.000 14.93 14.93 45.58 3.49
964 975 0.467384 CCCTGCTACTGTGCTAGCAT 59.533 55.000 22.51 7.71 46.35 3.79
965 976 1.688735 CCCTGCTACTGTGCTAGCATA 59.311 52.381 22.51 17.95 46.35 3.14
966 977 2.288702 CCCTGCTACTGTGCTAGCATAG 60.289 54.545 32.58 32.58 46.35 2.23
1022 1033 3.755628 GCTCGTGCGTCCCACCTA 61.756 66.667 0.00 0.00 41.53 3.08
1034 1045 1.194781 CCCACCTACACACCTGAGCT 61.195 60.000 0.00 0.00 0.00 4.09
1541 1559 2.811317 CTCTCACGAACAGCGCCC 60.811 66.667 2.29 0.00 46.04 6.13
1542 1563 3.573772 CTCTCACGAACAGCGCCCA 62.574 63.158 2.29 0.00 46.04 5.36
1547 1568 2.429069 CGAACAGCGCCCAAAAGC 60.429 61.111 2.29 0.00 0.00 3.51
1548 1569 2.049156 GAACAGCGCCCAAAAGCC 60.049 61.111 2.29 0.00 0.00 4.35
1549 1570 2.837291 AACAGCGCCCAAAAGCCA 60.837 55.556 2.29 0.00 0.00 4.75
1554 1575 2.243957 GCGCCCAAAAGCCAACAAC 61.244 57.895 0.00 0.00 0.00 3.32
1558 1579 1.851658 CCCAAAAGCCAACAACGAAG 58.148 50.000 0.00 0.00 0.00 3.79
1559 1580 1.407258 CCCAAAAGCCAACAACGAAGA 59.593 47.619 0.00 0.00 0.00 2.87
1560 1581 2.159170 CCCAAAAGCCAACAACGAAGAA 60.159 45.455 0.00 0.00 0.00 2.52
1561 1582 3.516615 CCAAAAGCCAACAACGAAGAAA 58.483 40.909 0.00 0.00 0.00 2.52
1562 1583 3.551485 CCAAAAGCCAACAACGAAGAAAG 59.449 43.478 0.00 0.00 0.00 2.62
1563 1584 3.436700 AAAGCCAACAACGAAGAAAGG 57.563 42.857 0.00 0.00 0.00 3.11
1564 1585 0.668535 AGCCAACAACGAAGAAAGGC 59.331 50.000 0.00 0.00 40.85 4.35
1565 1586 0.660300 GCCAACAACGAAGAAAGGCG 60.660 55.000 0.00 0.00 0.00 5.52
1566 1587 0.660300 CCAACAACGAAGAAAGGCGC 60.660 55.000 0.00 0.00 0.00 6.53
1567 1588 0.660300 CAACAACGAAGAAAGGCGCC 60.660 55.000 21.89 21.89 0.00 6.53
1568 1589 2.113131 AACAACGAAGAAAGGCGCCG 62.113 55.000 23.20 9.85 0.00 6.46
1569 1590 2.280592 AACGAAGAAAGGCGCCGT 60.281 55.556 23.20 16.90 34.74 5.68
1686 1707 4.271816 CGAGGACGCCGAGATGGG 62.272 72.222 0.00 0.00 38.63 4.00
1805 1826 1.072806 CACGTCCATCCATCCATCCAT 59.927 52.381 0.00 0.00 0.00 3.41
1983 2029 7.329962 TGCATATTTGAGCTCATTTTGTTTGAG 59.670 33.333 19.04 1.81 42.83 3.02
1991 2037 3.575687 CTCATTTTGTTTGAGCCCCTTCT 59.424 43.478 0.00 0.00 34.68 2.85
1993 2039 3.817709 TTTTGTTTGAGCCCCTTCTTG 57.182 42.857 0.00 0.00 0.00 3.02
1994 2040 2.746279 TTGTTTGAGCCCCTTCTTGA 57.254 45.000 0.00 0.00 0.00 3.02
1997 2043 3.157087 TGTTTGAGCCCCTTCTTGATTC 58.843 45.455 0.00 0.00 0.00 2.52
1998 2044 3.181429 TGTTTGAGCCCCTTCTTGATTCT 60.181 43.478 0.00 0.00 0.00 2.40
1999 2045 2.795231 TGAGCCCCTTCTTGATTCTG 57.205 50.000 0.00 0.00 0.00 3.02
2000 2046 2.269023 TGAGCCCCTTCTTGATTCTGA 58.731 47.619 0.00 0.00 0.00 3.27
2001 2047 2.644299 TGAGCCCCTTCTTGATTCTGAA 59.356 45.455 0.00 0.00 0.00 3.02
2002 2048 3.277715 GAGCCCCTTCTTGATTCTGAAG 58.722 50.000 10.79 10.79 39.32 3.02
2003 2049 1.747924 GCCCCTTCTTGATTCTGAAGC 59.252 52.381 0.00 0.00 38.55 3.86
2004 2050 2.620108 GCCCCTTCTTGATTCTGAAGCT 60.620 50.000 7.22 0.00 38.55 3.74
2005 2051 3.370953 GCCCCTTCTTGATTCTGAAGCTA 60.371 47.826 7.22 0.00 38.55 3.32
2006 2052 4.450053 CCCCTTCTTGATTCTGAAGCTAG 58.550 47.826 10.19 10.19 38.55 3.42
2007 2053 4.450053 CCCTTCTTGATTCTGAAGCTAGG 58.550 47.826 15.08 11.50 38.55 3.02
2008 2054 4.163078 CCCTTCTTGATTCTGAAGCTAGGA 59.837 45.833 15.08 7.45 38.55 2.94
2009 2055 5.163216 CCCTTCTTGATTCTGAAGCTAGGAT 60.163 44.000 15.08 0.00 38.55 3.24
2010 2056 5.990996 CCTTCTTGATTCTGAAGCTAGGATC 59.009 44.000 15.08 0.00 38.55 3.36
2011 2057 5.543507 TCTTGATTCTGAAGCTAGGATCC 57.456 43.478 15.08 2.48 32.62 3.36
2012 2058 5.215069 TCTTGATTCTGAAGCTAGGATCCT 58.785 41.667 20.48 20.48 32.62 3.24
2068 2151 7.786178 TTGGATGTAGCACATTAATACAGTC 57.214 36.000 3.76 0.00 39.27 3.51
2069 2152 5.983118 TGGATGTAGCACATTAATACAGTCG 59.017 40.000 3.76 0.00 39.27 4.18
2071 2154 6.074302 GGATGTAGCACATTAATACAGTCGTG 60.074 42.308 3.76 0.00 39.27 4.35
2251 2341 3.392882 CACTGTGTTGACTAGTGCATCA 58.607 45.455 0.00 1.30 35.87 3.07
2276 2366 0.834612 TGGTTGAGTGGACGAAAGGT 59.165 50.000 0.00 0.00 0.00 3.50
2343 2434 2.037251 TGCAAAGATAGATCTACCGGCC 59.963 50.000 4.10 0.00 35.76 6.13
2425 2517 4.452455 CCTACTCTGCTTGATTTTGAACGT 59.548 41.667 0.00 0.00 0.00 3.99
2440 2532 5.657470 TTGAACGTCTGTCTCTTGAAATG 57.343 39.130 0.00 0.00 0.00 2.32
2520 6290 4.201695 GGCGATCGTTTTCTTTCTTCCTAC 60.202 45.833 17.81 0.00 0.00 3.18
2534 6304 3.399952 TTCCTACGGAAGAAGGAGGAT 57.600 47.619 0.00 0.00 42.74 3.24
2554 6324 1.278127 TCCTTTGGCTAGGGTTTCTCG 59.722 52.381 6.43 0.00 35.90 4.04
2597 6367 1.743958 CGGTCTACCTCGTCTCATGTT 59.256 52.381 0.00 0.00 0.00 2.71
2603 6373 4.988540 TCTACCTCGTCTCATGTTGTTTTG 59.011 41.667 0.00 0.00 0.00 2.44
2627 6397 1.338107 CATAGGAGGCGTGGTGGATA 58.662 55.000 0.00 0.00 0.00 2.59
2738 6508 2.549778 GCAACAGCTCTCTGAAGAAGGT 60.550 50.000 0.00 0.00 42.95 3.50
2805 6575 1.001269 ATCGGAGGACGTGTGGAGA 60.001 57.895 0.00 0.00 44.69 3.71
2816 6586 3.199677 ACGTGTGGAGATTTGTTTTCGA 58.800 40.909 0.00 0.00 0.00 3.71
2833 6603 0.949397 CGACGGATCTCACGGGATTA 59.051 55.000 0.00 0.00 35.23 1.75
2834 6604 1.069159 CGACGGATCTCACGGGATTAG 60.069 57.143 0.00 0.00 35.23 1.73
2895 6665 1.330213 TCGTTCGTCTGTGTTCGTGTA 59.670 47.619 0.00 0.00 0.00 2.90
2900 6670 4.332186 TCGTCTGTGTTCGTGTATCTAC 57.668 45.455 0.00 0.00 0.00 2.59
2932 6702 3.181485 CCTTCCGATCTACGCTTCTCTTT 60.181 47.826 0.00 0.00 41.07 2.52
2942 6712 0.810031 GCTTCTCTTTATCGGCGGCA 60.810 55.000 10.53 0.00 0.00 5.69
2958 6728 1.103398 GGCAGTTGCTGTTCTGGTGT 61.103 55.000 3.88 0.00 41.70 4.16
2959 6729 0.029834 GCAGTTGCTGTTCTGGTGTG 59.970 55.000 0.00 0.00 38.21 3.82
2960 6730 1.382522 CAGTTGCTGTTCTGGTGTGT 58.617 50.000 0.00 0.00 0.00 3.72
2975 6745 3.181453 TGGTGTGTTGGTCCTTTCGATTA 60.181 43.478 0.00 0.00 0.00 1.75
2998 6768 1.202582 CACGTCTCGACATCCTCCTTT 59.797 52.381 0.00 0.00 0.00 3.11
3065 6835 0.902531 CCCACCCACTTCGTAGACAT 59.097 55.000 0.00 0.00 34.32 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 3.058160 GGTGTGCAGCGCTTCCAT 61.058 61.111 7.50 0.00 0.00 3.41
149 152 1.531602 GTTCAGCTTGGCCCAACCT 60.532 57.895 0.00 0.00 40.22 3.50
277 280 1.817357 CTCAGCTTCAAGTGCATCCA 58.183 50.000 0.00 0.00 0.00 3.41
412 415 2.910199 TCAGCATAGCAAAGCGAGATT 58.090 42.857 0.00 0.00 35.48 2.40
419 422 4.749099 GTCTGGTCTATCAGCATAGCAAAG 59.251 45.833 0.00 0.00 33.10 2.77
421 424 3.070159 GGTCTGGTCTATCAGCATAGCAA 59.930 47.826 0.00 0.00 33.10 3.91
480 483 1.298713 GATCGCGCGAGATGTGAGT 60.299 57.895 36.99 18.66 0.00 3.41
491 494 3.724257 GGCTAACTTTATTTTGATCGCGC 59.276 43.478 0.00 0.00 0.00 6.86
582 586 9.905713 ATAGTCTTGCTTACAAAGATATGGAAA 57.094 29.630 0.00 0.00 34.74 3.13
616 620 7.767198 CGGAGGGTAAAGTTTCTATTGATTACA 59.233 37.037 0.00 0.00 0.00 2.41
655 659 2.467566 AAGTTGTTTACCGGAGCGAT 57.532 45.000 9.46 0.00 0.00 4.58
675 679 2.531103 CGACAGTCAACGTGTACGAAAA 59.469 45.455 11.79 0.00 43.02 2.29
678 682 0.936600 TCGACAGTCAACGTGTACGA 59.063 50.000 11.79 0.00 43.02 3.43
680 684 4.221342 TGTATTCGACAGTCAACGTGTAC 58.779 43.478 0.41 0.00 32.86 2.90
692 696 3.435566 GAGATTCGTGCTGTATTCGACA 58.564 45.455 0.00 0.00 36.35 4.35
747 751 5.048991 TGAAATTCTAGCTGAACCGGTTTTC 60.049 40.000 23.22 16.46 37.52 2.29
759 763 4.878397 CCGTGGAGAAATGAAATTCTAGCT 59.122 41.667 0.00 0.00 39.70 3.32
761 765 5.428253 TCCCGTGGAGAAATGAAATTCTAG 58.572 41.667 0.00 0.00 39.70 2.43
849 853 1.619669 GGGGAGGAGGTTGGTGGAT 60.620 63.158 0.00 0.00 0.00 3.41
886 890 1.138047 CGATGTACGAAGGTGCGTCC 61.138 60.000 0.00 0.00 44.39 4.79
899 903 0.744874 GGCTAGTGTGGAGCGATGTA 59.255 55.000 0.00 0.00 41.06 2.29
914 918 4.415150 GCTGGCTGCTGGTGGCTA 62.415 66.667 9.31 0.00 42.39 3.93
925 929 3.899545 AAATGGCTGGCTGCTGGCT 62.900 57.895 17.87 0.00 42.39 4.75
926 930 3.366739 GAAATGGCTGGCTGCTGGC 62.367 63.158 16.14 10.40 42.39 4.85
963 974 4.099113 GGACGAGGGTTTAGTACAAGCTAT 59.901 45.833 0.00 0.00 0.00 2.97
964 975 3.445096 GGACGAGGGTTTAGTACAAGCTA 59.555 47.826 0.00 0.00 0.00 3.32
965 976 2.233186 GGACGAGGGTTTAGTACAAGCT 59.767 50.000 0.00 0.00 0.00 3.74
966 977 2.614779 GGACGAGGGTTTAGTACAAGC 58.385 52.381 0.00 0.00 0.00 4.01
967 978 3.242549 GGGACGAGGGTTTAGTACAAG 57.757 52.381 0.00 0.00 0.00 3.16
1022 1033 1.261238 GCTCCCTAGCTCAGGTGTGT 61.261 60.000 0.00 0.00 45.85 3.72
1034 1045 3.776347 CTCCCTCGCTCGCTCCCTA 62.776 68.421 0.00 0.00 0.00 3.53
1045 1063 2.136878 CCAGTCCATCCCTCCCTCG 61.137 68.421 0.00 0.00 0.00 4.63
1467 1485 0.605589 CAGCTTCCTCTTCGTGACCT 59.394 55.000 0.00 0.00 0.00 3.85
1525 1543 2.652382 TTTGGGCGCTGTTCGTGAGA 62.652 55.000 7.64 0.00 41.07 3.27
1541 1559 3.551485 CCTTTCTTCGTTGTTGGCTTTTG 59.449 43.478 0.00 0.00 0.00 2.44
1542 1563 3.780902 CCTTTCTTCGTTGTTGGCTTTT 58.219 40.909 0.00 0.00 0.00 2.27
1547 1568 0.660300 GCGCCTTTCTTCGTTGTTGG 60.660 55.000 0.00 0.00 0.00 3.77
1548 1569 0.660300 GGCGCCTTTCTTCGTTGTTG 60.660 55.000 22.15 0.00 0.00 3.33
1549 1570 1.652563 GGCGCCTTTCTTCGTTGTT 59.347 52.632 22.15 0.00 0.00 2.83
1554 1575 3.838795 CGACGGCGCCTTTCTTCG 61.839 66.667 26.68 19.10 0.00 3.79
1574 1595 2.098871 CATGTACGTCGTCGGCGA 59.901 61.111 27.88 8.66 45.79 5.54
1663 1684 4.710167 TCGGCGTCCTCGTCCTCA 62.710 66.667 6.85 0.00 38.56 3.86
1983 2029 1.747924 GCTTCAGAATCAAGAAGGGGC 59.252 52.381 14.31 1.72 41.13 5.80
1984 2030 3.362870 AGCTTCAGAATCAAGAAGGGG 57.637 47.619 14.31 0.00 41.13 4.79
1985 2031 4.163078 TCCTAGCTTCAGAATCAAGAAGGG 59.837 45.833 14.31 9.04 41.13 3.95
1986 2032 5.350504 TCCTAGCTTCAGAATCAAGAAGG 57.649 43.478 14.31 6.68 41.13 3.46
1987 2033 5.990996 GGATCCTAGCTTCAGAATCAAGAAG 59.009 44.000 3.84 9.98 43.12 2.85
1988 2034 5.664908 AGGATCCTAGCTTCAGAATCAAGAA 59.335 40.000 14.27 0.00 0.00 2.52
1989 2035 5.070180 CAGGATCCTAGCTTCAGAATCAAGA 59.930 44.000 15.67 0.00 0.00 3.02
1991 2037 4.718774 ACAGGATCCTAGCTTCAGAATCAA 59.281 41.667 15.67 0.00 0.00 2.57
1993 2039 4.953940 ACAGGATCCTAGCTTCAGAATC 57.046 45.455 15.67 0.00 0.00 2.52
1994 2040 4.283212 GCTACAGGATCCTAGCTTCAGAAT 59.717 45.833 23.92 0.00 33.15 2.40
1997 2043 2.961741 TGCTACAGGATCCTAGCTTCAG 59.038 50.000 28.68 13.30 36.58 3.02
1998 2044 3.032265 TGCTACAGGATCCTAGCTTCA 57.968 47.619 28.68 15.39 36.58 3.02
1999 2045 4.615588 AATGCTACAGGATCCTAGCTTC 57.384 45.455 28.68 13.39 36.58 3.86
2000 2046 5.128919 CAAAATGCTACAGGATCCTAGCTT 58.871 41.667 28.68 22.42 36.58 3.74
2001 2047 4.164988 ACAAAATGCTACAGGATCCTAGCT 59.835 41.667 28.68 16.29 36.58 3.32
2002 2048 4.455606 ACAAAATGCTACAGGATCCTAGC 58.544 43.478 24.29 24.29 36.20 3.42
2003 2049 5.220931 GCAACAAAATGCTACAGGATCCTAG 60.221 44.000 15.67 10.77 43.06 3.02
2004 2050 4.640201 GCAACAAAATGCTACAGGATCCTA 59.360 41.667 15.67 0.00 43.06 2.94
2005 2051 3.445096 GCAACAAAATGCTACAGGATCCT 59.555 43.478 9.02 9.02 43.06 3.24
2006 2052 3.774066 GCAACAAAATGCTACAGGATCC 58.226 45.455 2.48 2.48 43.06 3.36
2030 2081 6.777091 TGCTACATCCAATACCATTAAAGCAT 59.223 34.615 0.00 0.00 30.73 3.79
2068 2151 4.043750 TCGTACTTAAAACCACACTCACG 58.956 43.478 0.00 0.00 0.00 4.35
2069 2152 5.045872 ACTCGTACTTAAAACCACACTCAC 58.954 41.667 0.00 0.00 0.00 3.51
2071 2154 7.141363 TCTTACTCGTACTTAAAACCACACTC 58.859 38.462 0.00 0.00 0.00 3.51
2251 2341 3.417069 TCGTCCACTCAACCAATGAAT 57.583 42.857 0.00 0.00 37.67 2.57
2276 2366 5.185056 TCGATGGATGAAAAGACTGTCAGTA 59.815 40.000 5.21 0.00 0.00 2.74
2392 2484 3.623906 AGCAGAGTAGGACACGTAGTA 57.376 47.619 0.00 0.00 41.61 1.82
2425 2517 8.795513 TGATTATTTTGCATTTCAAGAGACAGA 58.204 29.630 0.00 0.00 35.84 3.41
2534 6304 1.278127 CGAGAAACCCTAGCCAAAGGA 59.722 52.381 0.00 0.00 39.15 3.36
2573 6343 2.821366 GACGAGGTAGACCGGCGA 60.821 66.667 9.30 0.00 42.08 5.54
2597 6367 0.334676 CCTCCTATGGCCCCAAAACA 59.665 55.000 0.00 0.00 0.00 2.83
2682 6452 5.686753 TCTAAGCAGAACACAAACCCTAAA 58.313 37.500 0.00 0.00 0.00 1.85
2719 6489 6.859112 TTATACCTTCTTCAGAGAGCTGTT 57.141 37.500 0.00 0.00 42.84 3.16
2738 6508 5.042827 AGGACTAGGTGGGGAGAACTTTATA 60.043 44.000 0.00 0.00 0.00 0.98
2805 6575 3.122948 CGTGAGATCCGTCGAAAACAAAT 59.877 43.478 0.00 0.00 0.00 2.32
2816 6586 1.329256 CCTAATCCCGTGAGATCCGT 58.671 55.000 0.00 0.00 0.00 4.69
2833 6603 1.064979 ACCAAAGACAAACACCGACCT 60.065 47.619 0.00 0.00 0.00 3.85
2834 6604 1.064952 CACCAAAGACAAACACCGACC 59.935 52.381 0.00 0.00 0.00 4.79
2862 6632 3.131223 AGACGAACGAAGACATGATCCAT 59.869 43.478 0.00 0.00 0.00 3.41
2895 6665 2.700897 CGGAAGGATCCAACCTGTAGAT 59.299 50.000 15.82 0.00 46.97 1.98
2900 6670 2.246719 GATCGGAAGGATCCAACCTG 57.753 55.000 15.82 12.25 46.97 4.00
2932 6702 2.511373 CAGCAACTGCCGCCGATA 60.511 61.111 0.00 0.00 43.38 2.92
2942 6712 1.745087 CAACACACCAGAACAGCAACT 59.255 47.619 0.00 0.00 0.00 3.16
2958 6728 2.372504 TGGGTAATCGAAAGGACCAACA 59.627 45.455 9.69 0.00 33.33 3.33
2959 6729 2.745821 GTGGGTAATCGAAAGGACCAAC 59.254 50.000 9.69 5.72 33.33 3.77
2960 6730 2.613474 CGTGGGTAATCGAAAGGACCAA 60.613 50.000 9.69 0.00 33.33 3.67
2975 6745 1.304217 AGGATGTCGAGACGTGGGT 60.304 57.895 2.30 0.00 0.00 4.51


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

AutoCloner maintained by Alex Coulton.