Multiple sequence alignment - TraesCS7D01G413500

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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 TraesCS7D01G413500 chr7D 100.000 2952 0 0 1 2952 531826089 531829040 0.000000e+00 5452.0
1 TraesCS7D01G413500 chr7B 90.247 2102 122 41 489 2533 572389618 572391693 0.000000e+00 2669.0
2 TraesCS7D01G413500 chr7B 90.809 544 38 6 1 534 572389164 572389705 0.000000e+00 717.0
3 TraesCS7D01G413500 chr7B 94.512 164 8 1 2790 2952 572391958 572392121 4.880000e-63 252.0
4 TraesCS7D01G413500 chr7A 89.459 1480 71 45 539 1962 612369178 612370628 0.000000e+00 1790.0
5 TraesCS7D01G413500 chr7A 88.337 523 34 13 1 500 612368704 612369222 1.170000e-168 603.0
6 TraesCS7D01G413500 chr7A 85.714 266 23 9 2009 2261 612370641 612370904 1.740000e-67 267.0
7 TraesCS7D01G413500 chr7A 92.715 151 10 1 2802 2951 612372235 612372385 1.780000e-52 217.0
8 TraesCS7D01G413500 chr1B 87.329 584 52 13 1082 1645 594863238 594862657 0.000000e+00 649.0
9 TraesCS7D01G413500 chrUn 89.840 187 12 6 1369 1554 38166661 38166481 1.770000e-57 233.0
10 TraesCS7D01G413500 chr4A 89.130 46 5 0 997 1042 740185394 740185439 1.140000e-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 TraesCS7D01G413500 chr7D 531826089 531829040 2951 False 5452.000000 5452 100.00000 1 2952 1 chr7D.!!$F1 2951
1 TraesCS7D01G413500 chr7B 572389164 572392121 2957 False 1212.666667 2669 91.85600 1 2952 3 chr7B.!!$F1 2951
2 TraesCS7D01G413500 chr7A 612368704 612372385 3681 False 719.250000 1790 89.05625 1 2951 4 chr7A.!!$F1 2950
3 TraesCS7D01G413500 chr1B 594862657 594863238 581 True 649.000000 649 87.32900 1082 1645 1 chr1B.!!$R1 563

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
684 717 0.250640 CAGCCAGCACCTTCTTCTGT 60.251 55.0 0.0 0.0 0.0 3.41 F
1063 1129 0.101579 GCTAGCTCTTCGTCAGGTCC 59.898 60.0 7.7 0.0 0.0 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1888 1985 0.039798 ATCACTGCAAGCAAGCAACG 60.040 50.0 4.63 0.0 45.13 4.10 R
1998 2098 0.315251 GAACAAGCAGCAGGGGAAAC 59.685 55.0 0.00 0.0 0.00 2.78 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
17 18 4.792087 ATCAAGCGGTCCGTGTTT 57.208 50.000 13.94 2.60 0.00 2.83
139 160 3.303791 GCCGTGTAAGAAAAGTTGGTCAG 60.304 47.826 0.00 0.00 0.00 3.51
210 234 4.260334 CGTAAAAACCTTTCGACCGTTTCT 60.260 41.667 4.65 0.00 0.00 2.52
239 263 6.915349 TCCAAGAACGAAAGAAAACAGAAAA 58.085 32.000 0.00 0.00 0.00 2.29
252 276 2.029844 AGAAAAGGAGAGCGTGCGC 61.030 57.895 8.67 8.67 42.33 6.09
275 300 2.478879 CGCTCACGGTTTTGGTTTTTCT 60.479 45.455 0.00 0.00 34.97 2.52
276 301 3.242804 CGCTCACGGTTTTGGTTTTTCTA 60.243 43.478 0.00 0.00 34.97 2.10
287 312 2.329614 TTTTTCTAGCGTGCCGGCC 61.330 57.895 26.77 14.70 0.00 6.13
414 447 5.344743 TCCATGACCTTATCTCTGTTGTC 57.655 43.478 0.00 0.00 0.00 3.18
489 522 4.038883 AGTTACAGAAGAAGCCACGTAACT 59.961 41.667 6.88 6.88 42.39 2.24
490 523 3.027974 ACAGAAGAAGCCACGTAACTC 57.972 47.619 0.00 0.00 0.00 3.01
491 524 2.628657 ACAGAAGAAGCCACGTAACTCT 59.371 45.455 0.00 0.00 0.00 3.24
492 525 3.825014 ACAGAAGAAGCCACGTAACTCTA 59.175 43.478 0.00 0.00 0.00 2.43
493 526 4.280174 ACAGAAGAAGCCACGTAACTCTAA 59.720 41.667 0.00 0.00 0.00 2.10
494 527 4.621886 CAGAAGAAGCCACGTAACTCTAAC 59.378 45.833 0.00 0.00 0.00 2.34
495 528 4.523558 AGAAGAAGCCACGTAACTCTAACT 59.476 41.667 0.00 0.00 0.00 2.24
496 529 4.437772 AGAAGCCACGTAACTCTAACTC 57.562 45.455 0.00 0.00 0.00 3.01
497 530 4.080687 AGAAGCCACGTAACTCTAACTCT 58.919 43.478 0.00 0.00 0.00 3.24
498 531 3.851976 AGCCACGTAACTCTAACTCTG 57.148 47.619 0.00 0.00 0.00 3.35
499 532 3.155501 AGCCACGTAACTCTAACTCTGT 58.844 45.455 0.00 0.00 0.00 3.41
500 533 3.057456 AGCCACGTAACTCTAACTCTGTG 60.057 47.826 0.00 0.00 0.00 3.66
537 570 3.589495 AGAAGCCACGTAACTCTAACC 57.411 47.619 0.00 0.00 0.00 2.85
542 575 2.929592 GCCACGTAACTCTAACCCTGTG 60.930 54.545 0.00 0.00 0.00 3.66
558 591 2.224042 CCTGTGCACAGTCAGTTACAGA 60.224 50.000 37.55 5.35 41.75 3.41
572 605 2.060326 TACAGAAAGAAGCCACGTCG 57.940 50.000 0.00 0.00 0.00 5.12
635 668 1.139058 ACGAGCGGCCTTGATTATCTT 59.861 47.619 0.00 0.00 0.00 2.40
647 680 5.067023 CCTTGATTATCTTGAACTTGGGCTC 59.933 44.000 0.00 0.00 0.00 4.70
654 687 1.896660 GAACTTGGGCTCGCCACAA 60.897 57.895 10.51 10.29 37.98 3.33
684 717 0.250640 CAGCCAGCACCTTCTTCTGT 60.251 55.000 0.00 0.00 0.00 3.41
692 725 1.889829 CACCTTCTTCTGTCCGTCTCT 59.110 52.381 0.00 0.00 0.00 3.10
750 783 5.127031 GCTAATGACAATTTGGTACCATGGT 59.873 40.000 23.55 23.55 0.00 3.55
756 789 5.636123 ACAATTTGGTACCATGGTCAGTTA 58.364 37.500 23.76 6.00 0.00 2.24
799 838 0.738389 GCGACAACATGGTAATGGGG 59.262 55.000 0.00 0.00 38.19 4.96
856 895 3.201930 TGATTAGGTGGATAAGCCTGCAA 59.798 43.478 0.00 0.00 36.38 4.08
901 940 8.078596 GCAATCTTATCTAAATCCGCAATCTTT 58.921 33.333 0.00 0.00 0.00 2.52
903 942 9.956720 AATCTTATCTAAATCCGCAATCTTTTG 57.043 29.630 0.00 0.00 35.85 2.44
948 988 4.755656 TTTTTCCCCTCGGCATCC 57.244 55.556 0.00 0.00 0.00 3.51
949 989 1.770985 TTTTTCCCCTCGGCATCCA 59.229 52.632 0.00 0.00 0.00 3.41
1060 1126 1.064946 CCGCTAGCTCTTCGTCAGG 59.935 63.158 13.93 0.00 0.00 3.86
1061 1127 1.658686 CCGCTAGCTCTTCGTCAGGT 61.659 60.000 13.93 0.00 0.00 4.00
1062 1128 0.248296 CGCTAGCTCTTCGTCAGGTC 60.248 60.000 13.93 0.00 0.00 3.85
1063 1129 0.101579 GCTAGCTCTTCGTCAGGTCC 59.898 60.000 7.70 0.00 0.00 4.46
1192 1262 3.991051 CACCACTCGTGCCGACCT 61.991 66.667 0.00 0.00 35.18 3.85
1202 1272 3.834799 GCCGACCTCCGACCGATT 61.835 66.667 0.00 0.00 41.76 3.34
1209 1300 0.527817 CCTCCGACCGATTTTCCTCG 60.528 60.000 0.00 0.00 38.37 4.63
1232 1323 1.732917 CTCCGCTTCGAGCTCAGAT 59.267 57.895 15.40 0.00 39.60 2.90
1789 1886 4.899239 GAGTCCATGGGCCGCTCG 62.899 72.222 14.18 0.00 0.00 5.03
1858 1955 1.269448 CTAGGATCTTCCTCTGCTCGC 59.731 57.143 0.00 0.00 45.66 5.03
1861 1958 0.875474 GATCTTCCTCTGCTCGCTGC 60.875 60.000 0.00 0.00 43.25 5.25
1888 1985 1.298488 TTGCCGCCGTTTCGTTTTC 60.298 52.632 0.00 0.00 0.00 2.29
1910 2007 2.143008 TGCTTGCTTGCAGTGATTTG 57.857 45.000 0.00 0.00 38.12 2.32
1911 2008 1.409790 TGCTTGCTTGCAGTGATTTGT 59.590 42.857 0.00 0.00 38.12 2.83
1912 2009 2.622470 TGCTTGCTTGCAGTGATTTGTA 59.378 40.909 0.00 0.00 38.12 2.41
1965 2065 4.706842 TTTTCTCCTTCTGTTAGTGCCT 57.293 40.909 0.00 0.00 0.00 4.75
1968 2068 2.231478 TCTCCTTCTGTTAGTGCCTTCG 59.769 50.000 0.00 0.00 0.00 3.79
1973 2073 2.791655 TCTGTTAGTGCCTTCGAGAGA 58.208 47.619 0.00 0.00 39.20 3.10
1974 2074 2.750166 TCTGTTAGTGCCTTCGAGAGAG 59.250 50.000 0.00 0.00 43.69 3.20
1989 2089 6.043854 TCGAGAGAGATATAGCTCTGCTTA 57.956 41.667 24.65 10.76 44.92 3.09
1991 2091 7.787028 TCGAGAGAGATATAGCTCTGCTTATA 58.213 38.462 24.65 8.52 44.92 0.98
1992 2092 8.428852 TCGAGAGAGATATAGCTCTGCTTATAT 58.571 37.037 24.65 0.00 44.92 0.86
1993 2093 8.712363 CGAGAGAGATATAGCTCTGCTTATATC 58.288 40.741 24.65 8.20 44.92 1.63
1995 2095 8.727149 AGAGAGATATAGCTCTGCTTATATCCT 58.273 37.037 24.65 9.38 44.92 3.24
1996 2096 8.924511 AGAGATATAGCTCTGCTTATATCCTC 57.075 38.462 19.47 6.07 43.35 3.71
1997 2097 7.944554 AGAGATATAGCTCTGCTTATATCCTCC 59.055 40.741 19.47 0.00 43.35 4.30
1998 2098 6.714810 AGATATAGCTCTGCTTATATCCTCCG 59.285 42.308 7.87 0.00 40.44 4.63
2001 2101 3.643792 AGCTCTGCTTATATCCTCCGTTT 59.356 43.478 0.00 0.00 33.89 3.60
2003 2103 4.561105 CTCTGCTTATATCCTCCGTTTCC 58.439 47.826 0.00 0.00 0.00 3.13
2004 2104 3.323979 TCTGCTTATATCCTCCGTTTCCC 59.676 47.826 0.00 0.00 0.00 3.97
2005 2105 2.370849 TGCTTATATCCTCCGTTTCCCC 59.629 50.000 0.00 0.00 0.00 4.81
2006 2106 2.638363 GCTTATATCCTCCGTTTCCCCT 59.362 50.000 0.00 0.00 0.00 4.79
2007 2107 3.557264 GCTTATATCCTCCGTTTCCCCTG 60.557 52.174 0.00 0.00 0.00 4.45
2042 2142 7.916977 TCATAATCAATCTGTACATTTTGCAGC 59.083 33.333 11.26 0.00 37.83 5.25
2083 2183 8.260818 TCAGAAACCAGATTTCCTACTATTCTG 58.739 37.037 0.00 0.00 46.94 3.02
2088 2188 7.106239 ACCAGATTTCCTACTATTCTGTTGTG 58.894 38.462 0.00 0.00 33.56 3.33
2096 2196 6.939730 TCCTACTATTCTGTTGTGCATTTTCA 59.060 34.615 0.00 0.00 0.00 2.69
2125 2244 8.996024 TTGTTCATCATTAATCTCTTCGTGTA 57.004 30.769 0.00 0.00 0.00 2.90
2126 2245 8.634475 TGTTCATCATTAATCTCTTCGTGTAG 57.366 34.615 0.00 0.00 0.00 2.74
2231 2361 2.282887 GGTGCCCCCATTGTCGTT 60.283 61.111 0.00 0.00 0.00 3.85
2237 2367 1.378762 CCCCATTGTCGTTCCACCT 59.621 57.895 0.00 0.00 0.00 4.00
2347 2859 3.702048 TCTGACTTTCGGGCGGGG 61.702 66.667 0.00 0.00 0.00 5.73
2355 2867 0.037877 TTTCGGGCGGGGTTAATTCA 59.962 50.000 0.00 0.00 0.00 2.57
2360 2872 2.888414 CGGGCGGGGTTAATTCATAATT 59.112 45.455 0.00 0.00 34.90 1.40
2361 2873 4.073549 CGGGCGGGGTTAATTCATAATTA 58.926 43.478 0.00 0.00 32.38 1.40
2362 2874 4.703093 CGGGCGGGGTTAATTCATAATTAT 59.297 41.667 0.00 0.00 33.64 1.28
2363 2875 5.392595 CGGGCGGGGTTAATTCATAATTATG 60.393 44.000 17.82 17.82 33.64 1.90
2415 2928 4.223953 GGTCACTCTCCCTCCATGTAATA 58.776 47.826 0.00 0.00 0.00 0.98
2450 2963 3.509967 CCTCAACAAACCCCTCATTAACC 59.490 47.826 0.00 0.00 0.00 2.85
2507 3059 3.194116 CCAAATGTCAAACCCCATCTCTG 59.806 47.826 0.00 0.00 0.00 3.35
2533 3085 5.412594 TCTCCTCGGTTTCATCTCAAATTTG 59.587 40.000 12.15 12.15 0.00 2.32
2534 3086 4.458989 TCCTCGGTTTCATCTCAAATTTGG 59.541 41.667 17.90 9.01 0.00 3.28
2535 3087 4.458989 CCTCGGTTTCATCTCAAATTTGGA 59.541 41.667 17.90 13.74 0.00 3.53
2536 3088 5.392380 CCTCGGTTTCATCTCAAATTTGGAG 60.392 44.000 17.90 13.26 0.00 3.86
2537 3089 5.070001 TCGGTTTCATCTCAAATTTGGAGT 58.930 37.500 17.90 1.74 34.04 3.85
2538 3090 6.234920 TCGGTTTCATCTCAAATTTGGAGTA 58.765 36.000 17.90 2.24 34.04 2.59
2539 3091 6.148811 TCGGTTTCATCTCAAATTTGGAGTAC 59.851 38.462 17.90 8.85 34.04 2.73
2540 3092 6.314784 GGTTTCATCTCAAATTTGGAGTACG 58.685 40.000 17.90 3.18 34.04 3.67
2541 3093 6.072673 GGTTTCATCTCAAATTTGGAGTACGT 60.073 38.462 17.90 0.00 34.04 3.57
2542 3094 7.118680 GGTTTCATCTCAAATTTGGAGTACGTA 59.881 37.037 17.90 0.00 34.04 3.57
2543 3095 7.591006 TTCATCTCAAATTTGGAGTACGTAC 57.409 36.000 18.10 18.10 34.04 3.67
2544 3096 6.693466 TCATCTCAAATTTGGAGTACGTACA 58.307 36.000 26.55 6.82 34.04 2.90
2545 3097 7.156000 TCATCTCAAATTTGGAGTACGTACAA 58.844 34.615 26.55 12.93 34.04 2.41
2546 3098 7.822334 TCATCTCAAATTTGGAGTACGTACAAT 59.178 33.333 26.55 14.57 34.04 2.71
2547 3099 7.972832 TCTCAAATTTGGAGTACGTACAATT 57.027 32.000 26.55 19.03 34.04 2.32
2548 3100 8.385898 TCTCAAATTTGGAGTACGTACAATTT 57.614 30.769 26.55 22.85 34.04 1.82
2549 3101 8.842280 TCTCAAATTTGGAGTACGTACAATTTT 58.158 29.630 26.55 16.45 34.04 1.82
2608 3166 2.552599 TTGAAGATACACCCACGCAA 57.447 45.000 0.00 0.00 0.00 4.85
2612 3170 0.036164 AGATACACCCACGCAAGCAA 59.964 50.000 0.00 0.00 45.62 3.91
2665 3223 5.414765 GGTTCCCGAGTCATTTTACAGAAAT 59.585 40.000 0.00 0.00 0.00 2.17
2666 3224 6.072119 GGTTCCCGAGTCATTTTACAGAAATT 60.072 38.462 0.00 0.00 0.00 1.82
2667 3225 6.737254 TCCCGAGTCATTTTACAGAAATTC 57.263 37.500 0.00 0.00 0.00 2.17
2668 3226 6.234920 TCCCGAGTCATTTTACAGAAATTCA 58.765 36.000 0.00 0.00 0.00 2.57
2669 3227 6.371548 TCCCGAGTCATTTTACAGAAATTCAG 59.628 38.462 0.00 0.00 0.00 3.02
2670 3228 6.371548 CCCGAGTCATTTTACAGAAATTCAGA 59.628 38.462 0.00 0.00 0.00 3.27
2673 3231 9.107367 CGAGTCATTTTACAGAAATTCAGAAAC 57.893 33.333 0.00 0.00 0.00 2.78
2674 3232 9.107367 GAGTCATTTTACAGAAATTCAGAAACG 57.893 33.333 0.00 0.00 0.00 3.60
2675 3233 8.621286 AGTCATTTTACAGAAATTCAGAAACGT 58.379 29.630 0.00 0.00 0.00 3.99
2676 3234 9.872757 GTCATTTTACAGAAATTCAGAAACGTA 57.127 29.630 0.00 0.00 0.00 3.57
2679 3237 8.665643 TTTTACAGAAATTCAGAAACGTAGGA 57.334 30.769 0.00 0.00 0.00 2.94
2680 3238 7.884816 TTACAGAAATTCAGAAACGTAGGAG 57.115 36.000 0.00 0.00 0.00 3.69
2681 3239 5.855045 ACAGAAATTCAGAAACGTAGGAGT 58.145 37.500 0.00 0.00 0.00 3.85
2682 3240 6.989659 ACAGAAATTCAGAAACGTAGGAGTA 58.010 36.000 0.00 0.00 0.00 2.59
2683 3241 7.612677 ACAGAAATTCAGAAACGTAGGAGTAT 58.387 34.615 0.00 0.00 0.00 2.12
2684 3242 7.545965 ACAGAAATTCAGAAACGTAGGAGTATG 59.454 37.037 0.00 0.00 0.00 2.39
2685 3243 7.545965 CAGAAATTCAGAAACGTAGGAGTATGT 59.454 37.037 0.00 0.00 0.00 2.29
2686 3244 8.746530 AGAAATTCAGAAACGTAGGAGTATGTA 58.253 33.333 0.00 0.00 0.00 2.29
2688 3246 5.475273 TCAGAAACGTAGGAGTATGTACG 57.525 43.478 0.00 0.57 45.96 3.67
2704 3618 3.592059 TGTACGTATTCCAAGCCTTGTC 58.408 45.455 3.37 0.00 0.00 3.18
2768 3696 3.067106 ACTAATTATCGCCTGCCATTCG 58.933 45.455 0.00 0.00 0.00 3.34
2856 3892 2.887568 GCAGACGCCCATCACTCG 60.888 66.667 0.00 0.00 0.00 4.18
2911 3948 0.042431 ATCTCTCTGGGCCACTCTGT 59.958 55.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 3.057104 TCGCTCGGTCAATCTTCTAAACA 60.057 43.478 0.00 0.00 0.00 2.83
17 18 2.097629 CACTCGCTCGGTCAATCTTCTA 59.902 50.000 0.00 0.00 0.00 2.10
123 126 2.289547 GCGTGCTGACCAACTTTTCTTA 59.710 45.455 0.00 0.00 0.00 2.10
139 160 2.649843 TTTGGTTCGTTTCGGCGTGC 62.650 55.000 6.85 0.00 0.00 5.34
210 234 5.358442 TGTTTTCTTTCGTTCTTGGATTGGA 59.642 36.000 0.00 0.00 0.00 3.53
252 276 2.655952 AAACCAAAACCGTGAGCGCG 62.656 55.000 0.00 0.00 36.67 6.86
257 281 3.242804 CGCTAGAAAAACCAAAACCGTGA 60.243 43.478 0.00 0.00 0.00 4.35
414 447 8.322906 TCCACAGTGTAACAAAGATGATAAAG 57.677 34.615 0.00 0.00 41.43 1.85
465 498 3.027974 ACGTGGCTTCTTCTGTAACTC 57.972 47.619 0.00 0.00 0.00 3.01
469 502 3.825014 AGAGTTACGTGGCTTCTTCTGTA 59.175 43.478 0.00 0.00 0.00 2.74
489 522 2.288457 GCTGACTGTGCACAGAGTTAGA 60.288 50.000 44.82 22.98 46.59 2.10
490 523 2.064762 GCTGACTGTGCACAGAGTTAG 58.935 52.381 44.82 33.33 46.59 2.34
491 524 1.688735 AGCTGACTGTGCACAGAGTTA 59.311 47.619 44.82 27.40 46.59 2.24
492 525 0.467384 AGCTGACTGTGCACAGAGTT 59.533 50.000 44.82 30.04 46.59 3.01
493 526 0.249784 CAGCTGACTGTGCACAGAGT 60.250 55.000 44.82 29.37 46.59 3.24
494 527 2.529925 CAGCTGACTGTGCACAGAG 58.470 57.895 44.82 33.99 46.59 3.35
495 528 4.764896 CAGCTGACTGTGCACAGA 57.235 55.556 44.82 27.13 46.59 3.41
542 575 4.319118 GCTTCTTTCTGTAACTGACTGTGC 60.319 45.833 0.00 0.00 0.00 4.57
558 591 0.946221 CAGAGCGACGTGGCTTCTTT 60.946 55.000 26.20 9.86 44.93 2.52
572 605 4.386049 TCGTTCGAAGAAAGAAATCAGAGC 59.614 41.667 0.00 0.00 45.90 4.09
609 642 4.421479 AAGGCCGCTCGTGAGTCG 62.421 66.667 0.00 3.18 41.41 4.18
684 717 1.751351 CACCAGCAATCTAGAGACGGA 59.249 52.381 0.00 0.00 0.00 4.69
740 773 5.655532 TCTCTAACTAACTGACCATGGTACC 59.344 44.000 19.80 7.05 0.00 3.34
750 783 3.935203 CGTACCCGTCTCTAACTAACTGA 59.065 47.826 0.00 0.00 0.00 3.41
756 789 4.142293 GGAAATTCGTACCCGTCTCTAACT 60.142 45.833 0.00 0.00 35.01 2.24
834 873 2.777114 TGCAGGCTTATCCACCTAATCA 59.223 45.455 0.00 0.00 37.29 2.57
856 895 2.911484 GCTTCTGCACAAGCCTATACT 58.089 47.619 15.11 0.00 42.68 2.12
901 940 9.213799 CTAAACCCTTAATTAATTTGCAAGCAA 57.786 29.630 5.91 2.89 0.00 3.91
903 942 8.655970 CACTAAACCCTTAATTAATTTGCAAGC 58.344 33.333 5.91 0.00 0.00 4.01
938 978 0.035458 GATAAGGGTGGATGCCGAGG 59.965 60.000 0.00 0.00 0.00 4.63
942 982 1.460699 GGGGATAAGGGTGGATGCC 59.539 63.158 0.00 0.00 33.00 4.40
943 983 1.073199 CGGGGATAAGGGTGGATGC 59.927 63.158 0.00 0.00 0.00 3.91
944 984 1.073199 GCGGGGATAAGGGTGGATG 59.927 63.158 0.00 0.00 0.00 3.51
945 985 2.154074 GGCGGGGATAAGGGTGGAT 61.154 63.158 0.00 0.00 0.00 3.41
948 988 1.064825 ATAAGGCGGGGATAAGGGTG 58.935 55.000 0.00 0.00 0.00 4.61
949 989 2.727429 TATAAGGCGGGGATAAGGGT 57.273 50.000 0.00 0.00 0.00 4.34
1042 1108 1.064946 CCTGACGAAGAGCTAGCGG 59.935 63.158 9.55 0.00 0.00 5.52
1218 1309 0.102844 AGCTGATCTGAGCTCGAAGC 59.897 55.000 9.64 14.63 46.85 3.86
1229 1320 1.679032 GGCGGTTAAACCAGCTGATCT 60.679 52.381 17.39 0.53 38.47 2.75
1232 1323 0.037590 ATGGCGGTTAAACCAGCTGA 59.962 50.000 17.39 0.00 39.88 4.26
1807 1904 2.662596 CTGCGGTTGCTCAGGGTA 59.337 61.111 0.00 0.00 43.34 3.69
1888 1985 0.039798 ATCACTGCAAGCAAGCAACG 60.040 50.000 4.63 0.00 45.13 4.10
1910 2007 4.497300 TGATGGCGGTACAAAACTACTAC 58.503 43.478 0.00 0.00 0.00 2.73
1911 2008 4.804868 TGATGGCGGTACAAAACTACTA 57.195 40.909 0.00 0.00 0.00 1.82
1912 2009 3.688694 TGATGGCGGTACAAAACTACT 57.311 42.857 0.00 0.00 0.00 2.57
1965 2065 4.905429 AGCAGAGCTATATCTCTCTCGAA 58.095 43.478 3.06 0.00 41.22 3.71
1968 2068 9.003658 GGATATAAGCAGAGCTATATCTCTCTC 57.996 40.741 3.06 0.00 41.22 3.20
1973 2073 6.714810 CGGAGGATATAAGCAGAGCTATATCT 59.285 42.308 17.64 0.00 38.25 1.98
1974 2074 6.488683 ACGGAGGATATAAGCAGAGCTATATC 59.511 42.308 13.80 13.80 38.25 1.63
1989 2089 0.765510 GCAGGGGAAACGGAGGATAT 59.234 55.000 0.00 0.00 0.00 1.63
1991 2091 1.616628 AGCAGGGGAAACGGAGGAT 60.617 57.895 0.00 0.00 0.00 3.24
1992 2092 2.203938 AGCAGGGGAAACGGAGGA 60.204 61.111 0.00 0.00 0.00 3.71
1993 2093 2.045926 CAGCAGGGGAAACGGAGG 60.046 66.667 0.00 0.00 0.00 4.30
1995 2095 2.829384 AAGCAGCAGGGGAAACGGA 61.829 57.895 0.00 0.00 0.00 4.69
1996 2096 2.282462 AAGCAGCAGGGGAAACGG 60.282 61.111 0.00 0.00 0.00 4.44
1997 2097 1.455383 AACAAGCAGCAGGGGAAACG 61.455 55.000 0.00 0.00 0.00 3.60
1998 2098 0.315251 GAACAAGCAGCAGGGGAAAC 59.685 55.000 0.00 0.00 0.00 2.78
2001 2101 0.991146 TATGAACAAGCAGCAGGGGA 59.009 50.000 0.00 0.00 0.00 4.81
2003 2103 3.018856 TGATTATGAACAAGCAGCAGGG 58.981 45.455 0.00 0.00 0.00 4.45
2004 2104 4.707030 TTGATTATGAACAAGCAGCAGG 57.293 40.909 0.00 0.00 0.00 4.85
2005 2105 5.971792 CAGATTGATTATGAACAAGCAGCAG 59.028 40.000 0.00 0.00 35.31 4.24
2006 2106 5.416639 ACAGATTGATTATGAACAAGCAGCA 59.583 36.000 0.00 0.00 35.31 4.41
2007 2107 5.888105 ACAGATTGATTATGAACAAGCAGC 58.112 37.500 0.00 0.00 35.31 5.25
2042 2142 8.188799 TCTGGTTTCTGATACTAGTACAAATCG 58.811 37.037 4.31 0.00 0.00 3.34
2096 2196 7.281774 ACGAAGAGATTAATGATGAACAAGCAT 59.718 33.333 0.00 0.00 0.00 3.79
2151 2275 6.159293 TCATTAGCCGCACTAATCTATCTTG 58.841 40.000 6.11 0.00 46.60 3.02
2224 2354 1.890876 CCATCAAGGTGGAACGACAA 58.109 50.000 0.00 0.00 42.02 3.18
2237 2367 0.528466 GACTCGCAGATCGCCATCAA 60.528 55.000 0.00 0.00 37.30 2.57
2347 2859 8.637986 TCCACTTGGGCATAATTATGAATTAAC 58.362 33.333 26.22 9.28 35.26 2.01
2363 2875 1.298014 CTCCTCTGTCCACTTGGGC 59.702 63.158 0.00 0.00 41.09 5.36
2403 2916 1.971357 AGCCTCGGTATTACATGGAGG 59.029 52.381 17.10 17.10 45.58 4.30
2433 2946 4.675063 ATGAGGTTAATGAGGGGTTTGT 57.325 40.909 0.00 0.00 0.00 2.83
2450 2963 5.519927 GGGTGTTGTTTTGTCTGAAAATGAG 59.480 40.000 0.00 0.00 0.00 2.90
2507 3059 1.478510 TGAGATGAAACCGAGGAGAGC 59.521 52.381 0.00 0.00 0.00 4.09
2556 3108 9.369904 GTAAGTACGTACTAAATCCCATCAAAA 57.630 33.333 27.59 0.00 34.99 2.44
2557 3109 8.530311 TGTAAGTACGTACTAAATCCCATCAAA 58.470 33.333 27.59 0.91 34.99 2.69
2558 3110 8.065473 TGTAAGTACGTACTAAATCCCATCAA 57.935 34.615 27.59 0.24 34.99 2.57
2559 3111 7.643569 TGTAAGTACGTACTAAATCCCATCA 57.356 36.000 27.59 12.96 34.99 3.07
2560 3112 9.538508 AATTGTAAGTACGTACTAAATCCCATC 57.461 33.333 27.59 10.92 34.99 3.51
2561 3113 9.321562 CAATTGTAAGTACGTACTAAATCCCAT 57.678 33.333 27.59 12.47 34.99 4.00
2562 3114 8.530311 TCAATTGTAAGTACGTACTAAATCCCA 58.470 33.333 27.59 14.59 34.99 4.37
2563 3115 8.931385 TCAATTGTAAGTACGTACTAAATCCC 57.069 34.615 27.59 12.46 34.99 3.85
2570 3122 9.871238 ATCTTCAATCAATTGTAAGTACGTACT 57.129 29.630 22.45 22.45 38.84 2.73
2573 3125 9.647797 TGTATCTTCAATCAATTGTAAGTACGT 57.352 29.630 5.13 0.00 38.84 3.57
2574 3126 9.901724 GTGTATCTTCAATCAATTGTAAGTACG 57.098 33.333 5.13 0.00 38.84 3.67
2612 3170 4.437794 CGTATCAAACTTCACATGCATGCT 60.438 41.667 26.53 11.04 0.00 3.79
2618 3176 5.343058 CCTTTTGCGTATCAAACTTCACATG 59.657 40.000 0.00 0.00 43.76 3.21
2619 3177 5.009610 ACCTTTTGCGTATCAAACTTCACAT 59.990 36.000 0.00 0.00 43.76 3.21
2620 3178 4.336993 ACCTTTTGCGTATCAAACTTCACA 59.663 37.500 0.00 0.00 43.76 3.58
2621 3179 4.855531 ACCTTTTGCGTATCAAACTTCAC 58.144 39.130 0.00 0.00 43.76 3.18
2622 3180 5.506649 GGAACCTTTTGCGTATCAAACTTCA 60.507 40.000 0.00 0.00 43.76 3.02
2623 3181 4.915667 GGAACCTTTTGCGTATCAAACTTC 59.084 41.667 0.00 0.00 43.76 3.01
2624 3182 4.866921 GGAACCTTTTGCGTATCAAACTT 58.133 39.130 0.00 0.00 43.76 2.66
2642 3200 5.934935 TTTCTGTAAAATGACTCGGGAAC 57.065 39.130 0.00 0.00 0.00 3.62
2665 3223 5.412594 ACGTACATACTCCTACGTTTCTGAA 59.587 40.000 0.00 0.00 45.05 3.02
2666 3224 4.937620 ACGTACATACTCCTACGTTTCTGA 59.062 41.667 0.00 0.00 45.05 3.27
2667 3225 5.227238 ACGTACATACTCCTACGTTTCTG 57.773 43.478 0.00 0.00 45.05 3.02
2668 3226 7.254932 GGAATACGTACATACTCCTACGTTTCT 60.255 40.741 8.04 0.00 45.05 2.52
2669 3227 6.853362 GGAATACGTACATACTCCTACGTTTC 59.147 42.308 8.04 10.56 45.05 2.78
2670 3228 6.318648 TGGAATACGTACATACTCCTACGTTT 59.681 38.462 8.04 0.00 45.05 3.60
2673 3231 5.929697 TGGAATACGTACATACTCCTACG 57.070 43.478 0.00 0.00 41.24 3.51
2674 3232 6.148264 GCTTGGAATACGTACATACTCCTAC 58.852 44.000 0.00 0.00 0.00 3.18
2675 3233 5.242393 GGCTTGGAATACGTACATACTCCTA 59.758 44.000 0.00 0.00 0.00 2.94
2676 3234 4.038883 GGCTTGGAATACGTACATACTCCT 59.961 45.833 0.00 0.00 0.00 3.69
2677 3235 4.038883 AGGCTTGGAATACGTACATACTCC 59.961 45.833 0.00 0.10 0.00 3.85
2679 3237 5.105064 ACAAGGCTTGGAATACGTACATACT 60.105 40.000 29.26 1.21 34.12 2.12
2680 3238 5.114081 ACAAGGCTTGGAATACGTACATAC 58.886 41.667 29.26 0.00 34.12 2.39
2681 3239 5.128171 AGACAAGGCTTGGAATACGTACATA 59.872 40.000 29.26 0.00 34.12 2.29
2682 3240 4.081087 AGACAAGGCTTGGAATACGTACAT 60.081 41.667 29.26 5.26 34.12 2.29
2683 3241 3.259876 AGACAAGGCTTGGAATACGTACA 59.740 43.478 29.26 0.00 34.12 2.90
2684 3242 3.858247 AGACAAGGCTTGGAATACGTAC 58.142 45.455 29.26 9.89 34.12 3.67
2685 3243 4.020928 TCAAGACAAGGCTTGGAATACGTA 60.021 41.667 29.26 0.00 44.14 3.57
2686 3244 3.074412 CAAGACAAGGCTTGGAATACGT 58.926 45.455 29.26 8.07 41.15 3.57
2688 3246 4.154918 CACTCAAGACAAGGCTTGGAATAC 59.845 45.833 29.26 15.05 44.14 1.89
2693 3607 1.972872 ACACTCAAGACAAGGCTTGG 58.027 50.000 29.26 13.83 44.14 3.61
2747 3670 3.067106 CGAATGGCAGGCGATAATTAGT 58.933 45.455 5.95 0.00 0.00 2.24
2786 3714 7.148623 CCGAAACTCAACCTACAAAACTAGATC 60.149 40.741 0.00 0.00 0.00 2.75
2911 3948 2.043752 TGGCGGGATGTAGACGGA 60.044 61.111 0.00 0.00 0.00 4.69


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

AutoCloner maintained by Alex Coulton.