Multiple sequence alignment - TraesCS7D01G187600

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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 TraesCS7D01G187600 chr7D 100.000 2585 0 0 619 3203 140232146 140234730 0.000000e+00 4774.0
1 TraesCS7D01G187600 chr7D 100.000 292 0 0 1 292 140231528 140231819 1.010000e-149 540.0
2 TraesCS7D01G187600 chr7A 96.378 1960 54 8 619 2571 140536182 140538131 0.000000e+00 3210.0
3 TraesCS7D01G187600 chr7A 89.434 530 52 3 2674 3203 140538198 140538723 0.000000e+00 665.0
4 TraesCS7D01G187600 chr7A 96.371 248 9 0 2822 3069 120950374 120950127 2.970000e-110 409.0
5 TraesCS7D01G187600 chr7A 96.371 248 9 0 2822 3069 671984741 671984494 2.970000e-110 409.0
6 TraesCS7D01G187600 chr7A 95.610 205 4 5 91 292 140535894 140536096 1.110000e-84 324.0
7 TraesCS7D01G187600 chr7B 94.493 1816 58 17 619 2429 105322814 105324592 0.000000e+00 2761.0
8 TraesCS7D01G187600 chr7B 87.122 761 73 9 2459 3203 105324592 105325343 0.000000e+00 839.0
9 TraesCS7D01G187600 chr7B 94.231 208 6 4 86 292 105322524 105322726 2.400000e-81 313.0
10 TraesCS7D01G187600 chr6A 78.171 1159 133 71 969 2052 540145874 540144761 2.100000e-176 628.0
11 TraesCS7D01G187600 chr6B 77.807 1158 133 73 969 2052 589129458 589128351 4.570000e-168 601.0
12 TraesCS7D01G187600 chr6D 77.768 1156 134 70 969 2052 393936422 393935318 5.910000e-167 597.0
13 TraesCS7D01G187600 chr5B 96.371 248 9 0 2822 3069 713137974 713138221 2.970000e-110 409.0
14 TraesCS7D01G187600 chr4D 96.371 248 9 0 2822 3069 123627967 123627720 2.970000e-110 409.0
15 TraesCS7D01G187600 chr2A 96.371 248 9 0 2822 3069 735148270 735148517 2.970000e-110 409.0
16 TraesCS7D01G187600 chr1B 96.371 248 9 0 2822 3069 338903901 338904148 2.970000e-110 409.0
17 TraesCS7D01G187600 chr1B 96.371 248 9 0 2822 3069 683722665 683722418 2.970000e-110 409.0
18 TraesCS7D01G187600 chr2D 89.873 79 7 1 2749 2827 77375507 77375430 2.030000e-17 100.0
19 TraesCS7D01G187600 chr4A 84.091 88 13 1 2560 2647 665724631 665724545 2.050000e-12 84.2
20 TraesCS7D01G187600 chr1D 85.185 81 11 1 2560 2640 54014245 54014324 7.360000e-12 82.4
21 TraesCS7D01G187600 chr3B 100.000 31 0 0 2560 2590 237109372 237109402 1.240000e-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 TraesCS7D01G187600 chr7D 140231528 140234730 3202 False 2657.000000 4774 100.000000 1 3203 2 chr7D.!!$F1 3202
1 TraesCS7D01G187600 chr7A 140535894 140538723 2829 False 1399.666667 3210 93.807333 91 3203 3 chr7A.!!$F1 3112
2 TraesCS7D01G187600 chr7B 105322524 105325343 2819 False 1304.333333 2761 91.948667 86 3203 3 chr7B.!!$F1 3117
3 TraesCS7D01G187600 chr6A 540144761 540145874 1113 True 628.000000 628 78.171000 969 2052 1 chr6A.!!$R1 1083
4 TraesCS7D01G187600 chr6B 589128351 589129458 1107 True 601.000000 601 77.807000 969 2052 1 chr6B.!!$R1 1083
5 TraesCS7D01G187600 chr6D 393935318 393936422 1104 True 597.000000 597 77.768000 969 2052 1 chr6D.!!$R1 1083

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
66 67 0.035881 CGTAGGAGCCCATGCATCAT 59.964 55.0 0.00 0.00 41.13 2.45 F
888 897 0.610174 TCACCTAACCAGCTGAGCAG 59.390 55.0 17.39 8.32 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2103 2190 1.142097 GCGAGTAGTCCCTTCAGCC 59.858 63.158 0.0 0.0 0.0 4.85 R
2714 2855 0.036306 GCCTTGACCCCTTTCTCGAA 59.964 55.000 0.0 0.0 0.0 3.71 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
23 24 5.288543 ACTTCATCAATCTCAAAACTCGC 57.711 39.130 0.00 0.00 0.00 5.03
24 25 4.154918 ACTTCATCAATCTCAAAACTCGCC 59.845 41.667 0.00 0.00 0.00 5.54
25 26 2.672874 TCATCAATCTCAAAACTCGCCG 59.327 45.455 0.00 0.00 0.00 6.46
26 27 1.438651 TCAATCTCAAAACTCGCCGG 58.561 50.000 0.00 0.00 0.00 6.13
27 28 0.179189 CAATCTCAAAACTCGCCGGC 60.179 55.000 19.07 19.07 0.00 6.13
28 29 0.321653 AATCTCAAAACTCGCCGGCT 60.322 50.000 26.68 1.82 0.00 5.52
29 30 0.741221 ATCTCAAAACTCGCCGGCTC 60.741 55.000 26.68 0.00 0.00 4.70
30 31 1.667830 CTCAAAACTCGCCGGCTCA 60.668 57.895 26.68 10.09 0.00 4.26
31 32 1.630244 CTCAAAACTCGCCGGCTCAG 61.630 60.000 26.68 21.86 0.00 3.35
32 33 1.961277 CAAAACTCGCCGGCTCAGT 60.961 57.895 26.68 22.56 0.00 3.41
33 34 1.668151 AAAACTCGCCGGCTCAGTC 60.668 57.895 26.68 0.00 0.00 3.51
34 35 3.591254 AAACTCGCCGGCTCAGTCC 62.591 63.158 26.68 0.00 0.00 3.85
36 37 3.842923 CTCGCCGGCTCAGTCCAT 61.843 66.667 26.68 0.00 0.00 3.41
37 38 4.147449 TCGCCGGCTCAGTCCATG 62.147 66.667 26.68 5.22 0.00 3.66
38 39 4.147449 CGCCGGCTCAGTCCATGA 62.147 66.667 26.68 0.00 36.21 3.07
57 58 2.429478 GAGAGATACTCGTAGGAGCCC 58.571 57.143 12.30 2.33 44.48 5.19
58 59 1.775459 AGAGATACTCGTAGGAGCCCA 59.225 52.381 12.30 0.00 44.48 5.36
59 60 2.377193 AGAGATACTCGTAGGAGCCCAT 59.623 50.000 12.30 3.76 44.48 4.00
60 61 2.490115 GAGATACTCGTAGGAGCCCATG 59.510 54.545 12.30 0.00 44.48 3.66
61 62 0.969894 ATACTCGTAGGAGCCCATGC 59.030 55.000 12.30 0.00 44.48 4.06
62 63 0.396556 TACTCGTAGGAGCCCATGCA 60.397 55.000 12.30 0.00 44.48 3.96
63 64 1.050988 ACTCGTAGGAGCCCATGCAT 61.051 55.000 12.30 0.00 44.48 3.96
64 65 0.320247 CTCGTAGGAGCCCATGCATC 60.320 60.000 0.00 0.00 41.13 3.91
65 66 1.048160 TCGTAGGAGCCCATGCATCA 61.048 55.000 0.00 0.00 41.13 3.07
66 67 0.035881 CGTAGGAGCCCATGCATCAT 59.964 55.000 0.00 0.00 41.13 2.45
67 68 1.544093 CGTAGGAGCCCATGCATCATT 60.544 52.381 0.00 0.00 41.13 2.57
68 69 2.590821 GTAGGAGCCCATGCATCATTT 58.409 47.619 0.00 0.00 41.13 2.32
69 70 2.170012 AGGAGCCCATGCATCATTTT 57.830 45.000 0.00 0.00 41.13 1.82
70 71 1.760613 AGGAGCCCATGCATCATTTTG 59.239 47.619 0.00 0.00 41.13 2.44
71 72 1.483415 GGAGCCCATGCATCATTTTGT 59.517 47.619 0.00 0.00 41.13 2.83
72 73 2.694628 GGAGCCCATGCATCATTTTGTA 59.305 45.455 0.00 0.00 41.13 2.41
73 74 3.132646 GGAGCCCATGCATCATTTTGTAA 59.867 43.478 0.00 0.00 41.13 2.41
74 75 4.382901 GGAGCCCATGCATCATTTTGTAAA 60.383 41.667 0.00 0.00 41.13 2.01
75 76 5.163281 AGCCCATGCATCATTTTGTAAAA 57.837 34.783 0.00 0.00 41.13 1.52
76 77 5.558818 AGCCCATGCATCATTTTGTAAAAA 58.441 33.333 0.00 0.00 41.13 1.94
77 78 5.644636 AGCCCATGCATCATTTTGTAAAAAG 59.355 36.000 0.00 0.00 41.13 2.27
78 79 5.642919 GCCCATGCATCATTTTGTAAAAAGA 59.357 36.000 0.00 0.00 37.47 2.52
79 80 6.316890 GCCCATGCATCATTTTGTAAAAAGAT 59.683 34.615 0.00 2.89 36.94 2.40
80 81 7.495279 GCCCATGCATCATTTTGTAAAAAGATA 59.505 33.333 0.00 0.00 35.02 1.98
81 82 9.381033 CCCATGCATCATTTTGTAAAAAGATAA 57.619 29.630 0.00 1.82 35.02 1.75
125 126 6.554334 TGTGTGAAACCTATACAAAGAAGC 57.446 37.500 0.00 0.00 34.36 3.86
728 733 5.715753 CCCATCTCTCTCTCATCATCATACA 59.284 44.000 0.00 0.00 0.00 2.29
760 769 5.500645 AAAATATTTCTCGCCAACCTAGC 57.499 39.130 0.10 0.00 0.00 3.42
761 770 4.423625 AATATTTCTCGCCAACCTAGCT 57.576 40.909 0.00 0.00 0.00 3.32
762 771 5.546621 AATATTTCTCGCCAACCTAGCTA 57.453 39.130 0.00 0.00 0.00 3.32
763 772 2.961526 TTTCTCGCCAACCTAGCTAG 57.038 50.000 14.20 14.20 0.00 3.42
789 798 0.637195 TCCCTAACAGCTAGCTCCCT 59.363 55.000 16.15 4.55 0.00 4.20
791 800 1.412361 CCCTAACAGCTAGCTCCCTCT 60.412 57.143 16.15 0.00 0.00 3.69
792 801 1.960689 CCTAACAGCTAGCTCCCTCTC 59.039 57.143 16.15 0.00 0.00 3.20
793 802 2.424234 CCTAACAGCTAGCTCCCTCTCT 60.424 54.545 16.15 0.00 0.00 3.10
888 897 0.610174 TCACCTAACCAGCTGAGCAG 59.390 55.000 17.39 8.32 0.00 4.24
910 919 2.328099 CCCACAAGAACAGCTCGGC 61.328 63.158 0.00 0.00 0.00 5.54
1554 1587 2.203938 TCCACCACCACCTCCTCC 60.204 66.667 0.00 0.00 0.00 4.30
2120 2207 1.433879 CGGCTGAAGGGACTACTCG 59.566 63.158 0.00 0.00 38.49 4.18
2318 2405 2.095969 TCGCTTGTTATGGCTTTGTTCG 60.096 45.455 0.00 0.00 0.00 3.95
2319 2406 2.095969 CGCTTGTTATGGCTTTGTTCGA 60.096 45.455 0.00 0.00 0.00 3.71
2320 2407 3.426159 CGCTTGTTATGGCTTTGTTCGAT 60.426 43.478 0.00 0.00 0.00 3.59
2321 2408 4.098416 GCTTGTTATGGCTTTGTTCGATC 58.902 43.478 0.00 0.00 0.00 3.69
2408 2503 5.331902 TGCTATAAAATCTTTGCAAGCGAC 58.668 37.500 0.00 0.00 0.00 5.19
2445 2570 8.965986 GCCAAACGATCTAAAGAACTTTATTT 57.034 30.769 7.35 3.33 34.86 1.40
2446 2571 9.406828 GCCAAACGATCTAAAGAACTTTATTTT 57.593 29.630 7.35 1.94 34.86 1.82
2479 2604 9.555727 CTTTTAATTTGTATCCTCCGGATCTTA 57.444 33.333 3.57 0.00 42.11 2.10
2527 2652 5.883685 TGGAGAGAAGAGACATTATGCAT 57.116 39.130 3.79 3.79 0.00 3.96
2572 2697 1.822990 TGTTTGCTACTCCCTCCGTAG 59.177 52.381 0.00 0.00 37.88 3.51
2590 2731 8.077386 CCTCCGTAGAGAAATATAAGAGTGTTC 58.923 40.741 0.00 0.00 43.39 3.18
2605 2746 6.995511 AGAGTGTTCAGATCACTAGAGTAC 57.004 41.667 13.22 1.87 44.68 2.73
2612 2753 7.831690 TGTTCAGATCACTAGAGTACTGATCTT 59.168 37.037 17.46 5.51 42.39 2.40
2625 2766 9.509956 AGAGTACTGATCTTAACGCTCTTATAT 57.490 33.333 0.00 0.00 0.00 0.86
2699 2840 2.063979 TCGATTCCTCCCCACGCAT 61.064 57.895 0.00 0.00 0.00 4.73
2729 2870 2.176889 CTAGGTTCGAGAAAGGGGTCA 58.823 52.381 0.00 0.00 0.00 4.02
2730 2871 1.430992 AGGTTCGAGAAAGGGGTCAA 58.569 50.000 0.00 0.00 0.00 3.18
2737 2878 1.128188 AGAAAGGGGTCAAGGCGTCT 61.128 55.000 0.00 0.00 0.00 4.18
2774 2915 4.574674 AATAGTGGATTCAGCAGGAACA 57.425 40.909 0.00 0.00 38.60 3.18
2804 2945 7.011202 ACAACTCATCATTCATTTCTCGATCAG 59.989 37.037 0.00 0.00 0.00 2.90
2818 2959 7.421530 TTCTCGATCAGTTTGAAACCTTAAG 57.578 36.000 4.14 0.00 0.00 1.85
2819 2960 6.755206 TCTCGATCAGTTTGAAACCTTAAGA 58.245 36.000 3.36 0.00 0.00 2.10
2875 3016 1.843851 ACCACCTCTGACTTCACCAAA 59.156 47.619 0.00 0.00 0.00 3.28
2985 3126 3.648339 TGGAAGTGCAAGAAGAAATGC 57.352 42.857 0.00 0.00 42.86 3.56
2986 3127 2.297033 TGGAAGTGCAAGAAGAAATGCC 59.703 45.455 0.00 0.00 41.87 4.40
3011 3152 6.802348 CGTAAATAGGAGTTCCATCTATCACG 59.198 42.308 0.28 0.00 38.89 4.35
3041 3182 3.496331 CCACACCCCAACTAACTTCAAT 58.504 45.455 0.00 0.00 0.00 2.57
3045 3186 5.064707 CACACCCCAACTAACTTCAATATCG 59.935 44.000 0.00 0.00 0.00 2.92
3069 3210 0.041833 TCAGCTAGGAGGAAGGTGCT 59.958 55.000 0.00 0.00 41.22 4.40
3077 3218 1.757699 GGAGGAAGGTGCTAACGAGAT 59.242 52.381 0.00 0.00 0.00 2.75
3084 3225 0.872021 GTGCTAACGAGATGGAGCCG 60.872 60.000 0.00 0.00 33.87 5.52
3092 3233 0.600557 GAGATGGAGCCGATGACGAT 59.399 55.000 0.00 0.00 42.66 3.73
3100 3241 2.226674 GAGCCGATGACGATGTGATAGA 59.773 50.000 0.00 0.00 42.66 1.98
3101 3242 2.030717 AGCCGATGACGATGTGATAGAC 60.031 50.000 0.00 0.00 42.66 2.59
3102 3243 2.575363 CCGATGACGATGTGATAGACG 58.425 52.381 0.00 0.00 42.66 4.18
3103 3244 2.223377 CCGATGACGATGTGATAGACGA 59.777 50.000 0.00 0.00 42.66 4.20
3108 3249 1.063616 ACGATGTGATAGACGACCACG 59.936 52.381 0.00 0.00 45.75 4.94
3141 3282 1.628846 AGGCTTGATTAGTTCGGGTGT 59.371 47.619 0.00 0.00 0.00 4.16
3147 3288 1.832998 GATTAGTTCGGGTGTGGGGTA 59.167 52.381 0.00 0.00 0.00 3.69
3197 3338 4.468689 GGAAGGTCGGAAGGCGGG 62.469 72.222 0.00 0.00 35.76 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.319931 GCGAGTTTTGAGATTGATGAAGTC 58.680 41.667 0.00 0.00 0.00 3.01
2 3 4.656041 GGCGAGTTTTGAGATTGATGAAG 58.344 43.478 0.00 0.00 0.00 3.02
8 9 0.179189 GCCGGCGAGTTTTGAGATTG 60.179 55.000 12.58 0.00 0.00 2.67
9 10 0.321653 AGCCGGCGAGTTTTGAGATT 60.322 50.000 23.20 0.00 0.00 2.40
14 15 1.901650 GACTGAGCCGGCGAGTTTTG 61.902 60.000 28.23 15.58 0.00 2.44
15 16 1.668151 GACTGAGCCGGCGAGTTTT 60.668 57.895 28.23 9.44 0.00 2.43
16 17 2.048127 GACTGAGCCGGCGAGTTT 60.048 61.111 28.23 10.20 0.00 2.66
19 20 3.842923 ATGGACTGAGCCGGCGAG 61.843 66.667 23.20 22.90 0.00 5.03
20 21 4.147449 CATGGACTGAGCCGGCGA 62.147 66.667 23.20 11.27 0.00 5.54
21 22 4.147449 TCATGGACTGAGCCGGCG 62.147 66.667 23.20 9.91 0.00 6.46
22 23 2.202987 CTCATGGACTGAGCCGGC 60.203 66.667 21.89 21.89 44.73 6.13
28 29 4.157849 ACGAGTATCTCTCATGGACTGA 57.842 45.455 0.00 0.00 42.88 3.41
29 30 4.454161 CCTACGAGTATCTCTCATGGACTG 59.546 50.000 0.00 0.00 42.88 3.51
30 31 4.348461 TCCTACGAGTATCTCTCATGGACT 59.652 45.833 0.00 0.00 42.88 3.85
31 32 4.643463 TCCTACGAGTATCTCTCATGGAC 58.357 47.826 0.00 0.00 42.88 4.02
32 33 4.804597 GCTCCTACGAGTATCTCTCATGGA 60.805 50.000 0.00 0.00 42.88 3.41
33 34 3.438781 GCTCCTACGAGTATCTCTCATGG 59.561 52.174 0.00 0.00 42.88 3.66
34 35 3.438781 GGCTCCTACGAGTATCTCTCATG 59.561 52.174 0.00 0.00 42.88 3.07
35 36 3.560453 GGGCTCCTACGAGTATCTCTCAT 60.560 52.174 0.00 0.00 42.88 2.90
36 37 2.224572 GGGCTCCTACGAGTATCTCTCA 60.225 54.545 0.00 0.00 42.88 3.27
37 38 2.224572 TGGGCTCCTACGAGTATCTCTC 60.225 54.545 0.00 0.00 38.49 3.20
38 39 1.775459 TGGGCTCCTACGAGTATCTCT 59.225 52.381 0.00 0.00 38.49 3.10
39 40 2.273538 TGGGCTCCTACGAGTATCTC 57.726 55.000 0.00 0.00 38.49 2.75
40 41 2.520069 CATGGGCTCCTACGAGTATCT 58.480 52.381 0.00 0.00 38.49 1.98
41 42 1.067495 GCATGGGCTCCTACGAGTATC 60.067 57.143 0.00 0.00 38.49 2.24
42 43 0.969894 GCATGGGCTCCTACGAGTAT 59.030 55.000 0.00 0.00 38.49 2.12
43 44 0.396556 TGCATGGGCTCCTACGAGTA 60.397 55.000 0.00 0.00 41.91 2.59
44 45 1.050988 ATGCATGGGCTCCTACGAGT 61.051 55.000 0.00 0.00 41.91 4.18
45 46 0.320247 GATGCATGGGCTCCTACGAG 60.320 60.000 2.46 0.00 41.91 4.18
46 47 1.048160 TGATGCATGGGCTCCTACGA 61.048 55.000 2.46 0.00 41.91 3.43
47 48 0.035881 ATGATGCATGGGCTCCTACG 59.964 55.000 2.46 0.00 41.91 3.51
48 49 2.283145 AATGATGCATGGGCTCCTAC 57.717 50.000 2.46 0.00 41.91 3.18
49 50 2.960384 CAAAATGATGCATGGGCTCCTA 59.040 45.455 2.46 0.00 41.91 2.94
50 51 1.760613 CAAAATGATGCATGGGCTCCT 59.239 47.619 2.46 0.00 41.91 3.69
51 52 1.483415 ACAAAATGATGCATGGGCTCC 59.517 47.619 2.46 0.00 41.91 4.70
52 53 2.973694 ACAAAATGATGCATGGGCTC 57.026 45.000 2.46 0.00 41.91 4.70
53 54 4.822685 TTTACAAAATGATGCATGGGCT 57.177 36.364 2.46 0.00 41.91 5.19
54 55 5.642919 TCTTTTTACAAAATGATGCATGGGC 59.357 36.000 2.46 0.00 32.92 5.36
55 56 7.852971 ATCTTTTTACAAAATGATGCATGGG 57.147 32.000 2.46 0.00 39.69 4.00
87 88 8.691797 AGGTTTCACACATACATGTAACTTTTT 58.308 29.630 10.14 0.00 39.39 1.94
88 89 8.232913 AGGTTTCACACATACATGTAACTTTT 57.767 30.769 10.14 0.00 39.39 2.27
89 90 7.817418 AGGTTTCACACATACATGTAACTTT 57.183 32.000 10.14 0.00 39.39 2.66
91 92 9.595823 GTATAGGTTTCACACATACATGTAACT 57.404 33.333 10.14 0.00 39.39 2.24
92 93 9.373603 TGTATAGGTTTCACACATACATGTAAC 57.626 33.333 10.14 2.48 39.39 2.50
93 94 9.945904 TTGTATAGGTTTCACACATACATGTAA 57.054 29.630 10.14 0.00 39.39 2.41
94 95 9.945904 TTTGTATAGGTTTCACACATACATGTA 57.054 29.630 8.27 8.27 39.39 2.29
95 96 8.856153 TTTGTATAGGTTTCACACATACATGT 57.144 30.769 2.69 2.69 42.84 3.21
96 97 9.161629 TCTTTGTATAGGTTTCACACATACATG 57.838 33.333 0.00 0.00 33.42 3.21
97 98 9.733556 TTCTTTGTATAGGTTTCACACATACAT 57.266 29.630 0.00 0.00 33.42 2.29
98 99 9.214957 CTTCTTTGTATAGGTTTCACACATACA 57.785 33.333 0.00 0.00 31.91 2.29
99 100 8.175716 GCTTCTTTGTATAGGTTTCACACATAC 58.824 37.037 0.00 0.00 0.00 2.39
100 101 7.064134 CGCTTCTTTGTATAGGTTTCACACATA 59.936 37.037 0.00 0.00 0.00 2.29
101 102 6.128282 CGCTTCTTTGTATAGGTTTCACACAT 60.128 38.462 0.00 0.00 0.00 3.21
102 103 5.178623 CGCTTCTTTGTATAGGTTTCACACA 59.821 40.000 0.00 0.00 0.00 3.72
103 104 5.407387 TCGCTTCTTTGTATAGGTTTCACAC 59.593 40.000 0.00 0.00 0.00 3.82
135 136 2.740506 ACGAAAAGGACCCCAGAAAA 57.259 45.000 0.00 0.00 0.00 2.29
136 137 2.740506 AACGAAAAGGACCCCAGAAA 57.259 45.000 0.00 0.00 0.00 2.52
728 733 8.006298 TGGCGAGAAATATTTTTCATATGGTT 57.994 30.769 16.45 0.00 43.09 3.67
760 769 4.810191 AGCTGTTAGGGAAACACTCTAG 57.190 45.455 0.00 0.00 43.22 2.43
761 770 4.159879 GCTAGCTGTTAGGGAAACACTCTA 59.840 45.833 7.70 0.00 43.22 2.43
762 771 3.055747 GCTAGCTGTTAGGGAAACACTCT 60.056 47.826 7.70 0.00 43.22 3.24
763 772 3.055747 AGCTAGCTGTTAGGGAAACACTC 60.056 47.826 18.57 0.00 43.22 3.51
789 798 2.022035 AGGAGAGAGAGAGAGGGAGAGA 60.022 54.545 0.00 0.00 0.00 3.10
791 800 2.126882 CAGGAGAGAGAGAGAGGGAGA 58.873 57.143 0.00 0.00 0.00 3.71
792 801 1.846439 ACAGGAGAGAGAGAGAGGGAG 59.154 57.143 0.00 0.00 0.00 4.30
793 802 1.979809 ACAGGAGAGAGAGAGAGGGA 58.020 55.000 0.00 0.00 0.00 4.20
888 897 1.239347 GAGCTGTTCTTGTGGGGTTC 58.761 55.000 0.00 0.00 0.00 3.62
930 939 0.833949 TTTTGGTTGGGGGAAGTTGC 59.166 50.000 0.00 0.00 0.00 4.17
2103 2190 1.142097 GCGAGTAGTCCCTTCAGCC 59.858 63.158 0.00 0.00 0.00 4.85
2120 2207 1.133790 GCTGGTTCTGATGTTGATGGC 59.866 52.381 0.00 0.00 0.00 4.40
2318 2405 4.437930 CGTGCAAGAATTTGGAGAAGGATC 60.438 45.833 0.00 0.00 35.16 3.36
2319 2406 3.441572 CGTGCAAGAATTTGGAGAAGGAT 59.558 43.478 0.00 0.00 35.16 3.24
2320 2407 2.813754 CGTGCAAGAATTTGGAGAAGGA 59.186 45.455 0.00 0.00 35.16 3.36
2321 2408 2.095059 CCGTGCAAGAATTTGGAGAAGG 60.095 50.000 0.00 0.00 35.16 3.46
2408 2503 0.937304 CGTTTGGCGATCCACCTATG 59.063 55.000 1.42 0.00 43.33 2.23
2445 2570 9.020731 GGAGGATACAAATTAAAAGGTGAGAAA 57.979 33.333 0.00 0.00 41.41 2.52
2446 2571 7.335924 CGGAGGATACAAATTAAAAGGTGAGAA 59.664 37.037 0.00 0.00 41.41 2.87
2447 2572 6.821665 CGGAGGATACAAATTAAAAGGTGAGA 59.178 38.462 0.00 0.00 41.41 3.27
2448 2573 7.016361 CGGAGGATACAAATTAAAAGGTGAG 57.984 40.000 0.00 0.00 41.41 3.51
2449 2574 6.995511 CGGAGGATACAAATTAAAAGGTGA 57.004 37.500 0.00 0.00 41.41 4.02
2479 2604 8.679344 AGAATTTGGATAAAACCCTAATTGGT 57.321 30.769 0.00 0.00 38.54 3.67
2629 2770 5.503002 GTGCTTATTACCCCCTCTGTAAAA 58.497 41.667 0.00 0.00 32.37 1.52
2641 2782 0.377203 GCAGGTGCGTGCTTATTACC 59.623 55.000 9.30 0.00 40.54 2.85
2667 2808 3.056749 AGGAATCGACTAGCGTGTCTTTT 60.057 43.478 9.70 4.22 41.80 2.27
2668 2809 2.492484 AGGAATCGACTAGCGTGTCTTT 59.508 45.455 9.70 4.50 41.80 2.52
2669 2810 2.093106 AGGAATCGACTAGCGTGTCTT 58.907 47.619 9.70 0.10 41.80 3.01
2670 2811 1.671845 GAGGAATCGACTAGCGTGTCT 59.328 52.381 9.70 2.15 41.80 3.41
2678 2819 1.389609 GCGTGGGGAGGAATCGACTA 61.390 60.000 0.00 0.00 0.00 2.59
2714 2855 0.036306 GCCTTGACCCCTTTCTCGAA 59.964 55.000 0.00 0.00 0.00 3.71
2715 2856 1.677552 GCCTTGACCCCTTTCTCGA 59.322 57.895 0.00 0.00 0.00 4.04
2729 2870 0.684805 AGCTGTAGCCTAGACGCCTT 60.685 55.000 0.00 0.00 43.38 4.35
2730 2871 1.076632 AGCTGTAGCCTAGACGCCT 60.077 57.895 0.00 0.00 43.38 5.52
2737 2878 4.700692 CCACTATTATCGAGCTGTAGCCTA 59.299 45.833 0.00 0.00 43.38 3.93
2744 2885 4.624882 GCTGAATCCACTATTATCGAGCTG 59.375 45.833 0.00 0.00 0.00 4.24
2745 2886 4.281941 TGCTGAATCCACTATTATCGAGCT 59.718 41.667 0.00 0.00 0.00 4.09
2774 2915 9.166173 TCGAGAAATGAATGATGAGTTGTTTAT 57.834 29.630 0.00 0.00 0.00 1.40
2804 2945 8.981724 ACTTTTTGACTCTTAAGGTTTCAAAC 57.018 30.769 18.66 0.00 36.24 2.93
2818 2959 6.432472 AGATTCATGGAAGGACTTTTTGACTC 59.568 38.462 0.00 0.00 0.00 3.36
2819 2960 6.310149 AGATTCATGGAAGGACTTTTTGACT 58.690 36.000 0.00 0.00 0.00 3.41
2875 3016 3.307762 CCTTCGACCAAAGAAAGGGAGAT 60.308 47.826 0.00 0.00 0.00 2.75
2936 3077 5.760484 AGAGGAAGAAGCATCTCTCTTTT 57.240 39.130 4.76 0.00 34.74 2.27
2985 3126 7.091443 GTGATAGATGGAACTCCTATTTACGG 58.909 42.308 0.00 0.00 36.82 4.02
2986 3127 6.802348 CGTGATAGATGGAACTCCTATTTACG 59.198 42.308 0.00 0.00 36.82 3.18
3026 3167 8.141909 TGAGTATCGATATTGAAGTTAGTTGGG 58.858 37.037 8.66 0.00 38.61 4.12
3041 3182 5.492895 CTTCCTCCTAGCTGAGTATCGATA 58.507 45.833 0.00 0.00 38.61 2.92
3045 3186 3.572255 CACCTTCCTCCTAGCTGAGTATC 59.428 52.174 0.00 0.00 0.00 2.24
3069 3210 1.337071 GTCATCGGCTCCATCTCGTTA 59.663 52.381 0.00 0.00 0.00 3.18
3077 3218 1.141665 CACATCGTCATCGGCTCCA 59.858 57.895 0.00 0.00 37.69 3.86
3084 3225 3.003378 TGGTCGTCTATCACATCGTCATC 59.997 47.826 0.00 0.00 0.00 2.92
3092 3233 1.092348 CTCCGTGGTCGTCTATCACA 58.908 55.000 0.00 0.00 35.01 3.58
3117 3258 1.571919 CGAACTAATCAAGCCTCCGG 58.428 55.000 0.00 0.00 0.00 5.14
3131 3272 1.152183 ACTACCCCACACCCGAACT 60.152 57.895 0.00 0.00 0.00 3.01
3141 3282 2.282674 ACGTCAGCGACTACCCCA 60.283 61.111 7.03 0.00 42.00 4.96
3147 3288 2.282251 TCCTCCACGTCAGCGACT 60.282 61.111 7.03 0.00 42.00 4.18
3168 3309 0.540454 GACCTTCCCTCTAAACCCCG 59.460 60.000 0.00 0.00 0.00 5.73


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

AutoCloner maintained by Alex Coulton.