Multiple sequence alignment - TraesCS7D01G082100

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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 TraesCS7D01G082100 chr7D 100.000 2822 0 0 1 2822 49186232 49189053 0.000000e+00 5212.0
1 TraesCS7D01G082100 chr7D 97.967 1771 31 4 1057 2822 12160926 12159156 0.000000e+00 3066.0
2 TraesCS7D01G082100 chr7D 93.558 1009 54 7 1057 2060 49171418 49172420 0.000000e+00 1493.0
3 TraesCS7D01G082100 chr7D 82.423 751 109 21 275 1018 12168925 12168191 3.970000e-178 634.0
4 TraesCS7D01G082100 chr7D 91.923 260 19 2 761 1019 49163947 49164205 2.070000e-96 363.0
5 TraesCS7D01G082100 chr7D 87.829 304 14 4 2071 2366 49172534 49172822 4.500000e-88 335.0
6 TraesCS7D01G082100 chr7D 88.827 179 19 1 2642 2820 16321360 16321183 4.730000e-53 219.0
7 TraesCS7D01G082100 chr7D 94.828 58 3 0 1013 1070 49164232 49164289 1.080000e-14 91.6
8 TraesCS7D01G082100 chrUn 97.648 978 21 1 904 1881 455117250 455118225 0.000000e+00 1677.0
9 TraesCS7D01G082100 chrUn 94.404 554 25 3 131 678 416275390 416274837 0.000000e+00 846.0
10 TraesCS7D01G082100 chrUn 96.907 485 12 3 1883 2366 360089781 360089299 0.000000e+00 809.0
11 TraesCS7D01G082100 chrUn 96.907 485 12 3 1883 2366 416058833 416058351 0.000000e+00 809.0
12 TraesCS7D01G082100 chrUn 94.455 523 23 3 162 678 474454787 474455309 0.000000e+00 800.0
13 TraesCS7D01G082100 chr4A 91.862 897 65 3 1136 2032 725878220 725879108 0.000000e+00 1245.0
14 TraesCS7D01G082100 chr4A 80.984 752 77 33 275 1007 725872123 725872827 1.150000e-148 536.0
15 TraesCS7D01G082100 chr4A 91.089 303 19 2 2071 2366 725880175 725880476 1.220000e-108 403.0
16 TraesCS7D01G082100 chr4A 82.135 431 64 10 537 957 726107486 726107913 9.610000e-95 357.0
17 TraesCS7D01G082100 chr4A 81.853 259 33 8 1964 2209 726109173 726109430 3.680000e-49 206.0
18 TraesCS7D01G082100 chr4A 87.730 163 18 1 1768 1928 726086510 726086348 3.710000e-44 189.0
19 TraesCS7D01G082100 chr4A 90.511 137 13 0 1007 1143 725872860 725872996 6.210000e-42 182.0
20 TraesCS7D01G082100 chr4A 76.382 199 41 5 1516 1713 703564510 703564703 4.970000e-18 102.0
21 TraesCS7D01G082100 chr7A 92.891 633 45 0 531 1163 11452458 11451826 0.000000e+00 920.0
22 TraesCS7D01G082100 chr7A 79.832 357 64 7 619 974 11230321 11229972 1.300000e-63 254.0
23 TraesCS7D01G082100 chr7B 77.591 714 146 11 1013 1722 750116184 750115481 1.210000e-113 420.0
24 TraesCS7D01G082100 chr3A 73.833 1093 228 34 649 1715 730851538 730850478 5.700000e-102 381.0
25 TraesCS7D01G082100 chr3D 73.228 1016 211 35 649 1626 602235221 602236213 2.110000e-81 313.0
26 TraesCS7D01G082100 chr3D 91.758 182 11 4 2639 2820 458607658 458607481 1.680000e-62 250.0
27 TraesCS7D01G082100 chr3D 88.950 181 14 6 2642 2821 1063202 1063027 4.730000e-53 219.0
28 TraesCS7D01G082100 chr3B 72.736 1016 216 38 649 1626 809437941 809438933 4.600000e-73 285.0
29 TraesCS7D01G082100 chr2D 91.160 181 13 2 2640 2820 637586708 637586531 2.810000e-60 243.0
30 TraesCS7D01G082100 chr1D 90.503 179 13 2 2642 2820 9914201 9914027 1.690000e-57 233.0
31 TraesCS7D01G082100 chr1D 89.385 179 15 2 2642 2820 10046790 10046964 3.660000e-54 222.0
32 TraesCS7D01G082100 chr5D 89.674 184 16 3 2638 2820 434423984 434423803 6.080000e-57 231.0
33 TraesCS7D01G082100 chr5D 88.525 183 18 3 2639 2820 324352667 324352487 4.730000e-53 219.0
34 TraesCS7D01G082100 chr5B 87.117 163 19 1 1768 1928 672822764 672822602 1.730000e-42 183.0


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 TraesCS7D01G082100 chr7D 49186232 49189053 2821 False 5212.0 5212 100.0000 1 2822 1 chr7D.!!$F1 2821
1 TraesCS7D01G082100 chr7D 12159156 12160926 1770 True 3066.0 3066 97.9670 1057 2822 1 chr7D.!!$R1 1765
2 TraesCS7D01G082100 chr7D 49171418 49172822 1404 False 914.0 1493 90.6935 1057 2366 2 chr7D.!!$F3 1309
3 TraesCS7D01G082100 chr7D 12168191 12168925 734 True 634.0 634 82.4230 275 1018 1 chr7D.!!$R2 743
4 TraesCS7D01G082100 chrUn 455117250 455118225 975 False 1677.0 1677 97.6480 904 1881 1 chrUn.!!$F1 977
5 TraesCS7D01G082100 chrUn 416274837 416275390 553 True 846.0 846 94.4040 131 678 1 chrUn.!!$R3 547
6 TraesCS7D01G082100 chrUn 474454787 474455309 522 False 800.0 800 94.4550 162 678 1 chrUn.!!$F2 516
7 TraesCS7D01G082100 chr4A 725878220 725880476 2256 False 824.0 1245 91.4755 1136 2366 2 chr4A.!!$F3 1230
8 TraesCS7D01G082100 chr4A 725872123 725872996 873 False 359.0 536 85.7475 275 1143 2 chr4A.!!$F2 868
9 TraesCS7D01G082100 chr4A 726107486 726109430 1944 False 281.5 357 81.9940 537 2209 2 chr4A.!!$F4 1672
10 TraesCS7D01G082100 chr7A 11451826 11452458 632 True 920.0 920 92.8910 531 1163 1 chr7A.!!$R2 632
11 TraesCS7D01G082100 chr7B 750115481 750116184 703 True 420.0 420 77.5910 1013 1722 1 chr7B.!!$R1 709
12 TraesCS7D01G082100 chr3A 730850478 730851538 1060 True 381.0 381 73.8330 649 1715 1 chr3A.!!$R1 1066
13 TraesCS7D01G082100 chr3D 602235221 602236213 992 False 313.0 313 73.2280 649 1626 1 chr3D.!!$F1 977
14 TraesCS7D01G082100 chr3B 809437941 809438933 992 False 285.0 285 72.7360 649 1626 1 chr3B.!!$F1 977

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
90 91 0.316689 GCGCGCTACAAAGTTGTTGT 60.317 50.0 26.67 0.00 42.35 3.32 F
294 295 0.327576 ACTCCCCCATGAACCCTAGG 60.328 60.0 0.06 0.06 0.00 3.02 F
737 778 0.327924 TCCTTCCGCCACATCATTGT 59.672 50.0 0.00 0.00 36.15 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1023 1124 0.741915 TGATATAGCGACGGTGCACA 59.258 50.000 20.43 0.00 37.31 4.57 R
1745 1887 1.129811 GGTTTGGGAAATCAGCGTACG 59.870 52.381 11.84 11.84 0.00 3.67 R
2465 3925 3.118408 ACCTAATTATCCTGACGCTGCAA 60.118 43.478 0.00 0.00 0.00 4.08 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
25 26 8.443953 ACTGATAAAAGTTCTAAGATGCATCC 57.556 34.615 23.06 6.67 0.00 3.51
26 27 8.049117 ACTGATAAAAGTTCTAAGATGCATCCA 58.951 33.333 23.06 10.54 0.00 3.41
27 28 8.806429 TGATAAAAGTTCTAAGATGCATCCAA 57.194 30.769 23.06 10.52 0.00 3.53
28 29 8.677300 TGATAAAAGTTCTAAGATGCATCCAAC 58.323 33.333 23.06 18.53 0.00 3.77
29 30 6.899393 AAAAGTTCTAAGATGCATCCAACA 57.101 33.333 23.06 5.13 0.00 3.33
30 31 6.899393 AAAGTTCTAAGATGCATCCAACAA 57.101 33.333 23.06 8.67 0.00 2.83
31 32 6.506500 AAGTTCTAAGATGCATCCAACAAG 57.493 37.500 23.06 12.83 0.00 3.16
32 33 4.946157 AGTTCTAAGATGCATCCAACAAGG 59.054 41.667 23.06 7.01 39.47 3.61
47 48 7.475137 TCCAACAAGGAGAAAAGAAAGAAAA 57.525 32.000 0.00 0.00 43.07 2.29
48 49 7.902087 TCCAACAAGGAGAAAAGAAAGAAAAA 58.098 30.769 0.00 0.00 43.07 1.94
49 50 8.539544 TCCAACAAGGAGAAAAGAAAGAAAAAT 58.460 29.630 0.00 0.00 43.07 1.82
50 51 8.606602 CCAACAAGGAGAAAAGAAAGAAAAATG 58.393 33.333 0.00 0.00 41.22 2.32
51 52 9.154847 CAACAAGGAGAAAAGAAAGAAAAATGT 57.845 29.630 0.00 0.00 0.00 2.71
52 53 8.932945 ACAAGGAGAAAAGAAAGAAAAATGTC 57.067 30.769 0.00 0.00 0.00 3.06
53 54 8.531146 ACAAGGAGAAAAGAAAGAAAAATGTCA 58.469 29.630 0.00 0.00 0.00 3.58
54 55 9.028185 CAAGGAGAAAAGAAAGAAAAATGTCAG 57.972 33.333 0.00 0.00 0.00 3.51
55 56 8.525290 AGGAGAAAAGAAAGAAAAATGTCAGA 57.475 30.769 0.00 0.00 0.00 3.27
56 57 8.409371 AGGAGAAAAGAAAGAAAAATGTCAGAC 58.591 33.333 0.00 0.00 0.00 3.51
57 58 7.377131 GGAGAAAAGAAAGAAAAATGTCAGACG 59.623 37.037 0.00 0.00 0.00 4.18
58 59 7.985476 AGAAAAGAAAGAAAAATGTCAGACGA 58.015 30.769 0.00 0.00 0.00 4.20
59 60 8.624776 AGAAAAGAAAGAAAAATGTCAGACGAT 58.375 29.630 0.00 0.00 0.00 3.73
60 61 9.237846 GAAAAGAAAGAAAAATGTCAGACGATT 57.762 29.630 0.00 0.00 0.00 3.34
61 62 8.566008 AAAGAAAGAAAAATGTCAGACGATTG 57.434 30.769 0.00 0.00 0.00 2.67
62 63 7.264373 AGAAAGAAAAATGTCAGACGATTGT 57.736 32.000 0.00 0.00 0.00 2.71
63 64 7.707104 AGAAAGAAAAATGTCAGACGATTGTT 58.293 30.769 0.00 0.00 0.00 2.83
64 65 7.645340 AGAAAGAAAAATGTCAGACGATTGTTG 59.355 33.333 0.00 0.00 0.00 3.33
65 66 6.377327 AGAAAAATGTCAGACGATTGTTGT 57.623 33.333 0.00 0.00 0.00 3.32
66 67 7.490962 AGAAAAATGTCAGACGATTGTTGTA 57.509 32.000 0.00 0.00 0.00 2.41
67 68 7.576236 AGAAAAATGTCAGACGATTGTTGTAG 58.424 34.615 0.00 0.00 0.00 2.74
68 69 6.861065 AAAATGTCAGACGATTGTTGTAGT 57.139 33.333 0.00 0.00 0.00 2.73
69 70 6.467723 AAATGTCAGACGATTGTTGTAGTC 57.532 37.500 0.00 0.00 0.00 2.59
70 71 3.561503 TGTCAGACGATTGTTGTAGTCG 58.438 45.455 0.00 0.00 43.33 4.18
71 72 2.915463 GTCAGACGATTGTTGTAGTCGG 59.085 50.000 0.00 0.00 42.17 4.79
72 73 1.654105 CAGACGATTGTTGTAGTCGGC 59.346 52.381 0.00 0.00 45.99 5.54
73 74 0.638746 GACGATTGTTGTAGTCGGCG 59.361 55.000 0.00 0.00 42.17 6.46
74 75 1.343821 CGATTGTTGTAGTCGGCGC 59.656 57.895 0.00 0.00 35.18 6.53
75 76 1.343821 GATTGTTGTAGTCGGCGCG 59.656 57.895 0.00 0.00 0.00 6.86
76 77 2.612335 GATTGTTGTAGTCGGCGCGC 62.612 60.000 25.94 25.94 0.00 6.86
77 78 3.851845 TTGTTGTAGTCGGCGCGCT 62.852 57.895 32.29 14.07 0.00 5.92
78 79 2.202518 GTTGTAGTCGGCGCGCTA 60.203 61.111 32.29 17.14 0.00 4.26
79 80 2.202518 TTGTAGTCGGCGCGCTAC 60.203 61.111 32.29 27.19 37.17 3.58
80 81 2.980378 TTGTAGTCGGCGCGCTACA 61.980 57.895 32.29 26.55 41.03 2.74
81 82 2.202518 GTAGTCGGCGCGCTACAA 60.203 61.111 32.29 11.14 36.90 2.41
82 83 1.802715 GTAGTCGGCGCGCTACAAA 60.803 57.895 32.29 17.51 36.90 2.83
83 84 1.515519 TAGTCGGCGCGCTACAAAG 60.516 57.895 32.29 14.97 0.00 2.77
84 85 2.203972 TAGTCGGCGCGCTACAAAGT 62.204 55.000 32.29 16.09 0.00 2.66
85 86 2.356553 TCGGCGCGCTACAAAGTT 60.357 55.556 32.29 0.00 0.00 2.66
86 87 2.202171 CGGCGCGCTACAAAGTTG 60.202 61.111 32.29 5.80 0.00 3.16
87 88 2.943653 GGCGCGCTACAAAGTTGT 59.056 55.556 32.29 1.75 44.86 3.32
88 89 1.281656 GGCGCGCTACAAAGTTGTT 59.718 52.632 32.29 0.00 42.35 2.83
89 90 0.996727 GGCGCGCTACAAAGTTGTTG 60.997 55.000 32.29 1.63 42.35 3.33
90 91 0.316689 GCGCGCTACAAAGTTGTTGT 60.317 50.000 26.67 0.00 42.35 3.32
91 92 1.858399 GCGCGCTACAAAGTTGTTGTT 60.858 47.619 26.67 0.00 42.35 2.83
92 93 2.034076 CGCGCTACAAAGTTGTTGTTC 58.966 47.619 5.56 0.00 42.35 3.18
93 94 2.537931 CGCGCTACAAAGTTGTTGTTCA 60.538 45.455 5.56 0.00 42.35 3.18
94 95 3.628017 GCGCTACAAAGTTGTTGTTCAT 58.372 40.909 0.00 0.00 42.35 2.57
95 96 3.421888 GCGCTACAAAGTTGTTGTTCATG 59.578 43.478 0.00 0.00 42.35 3.07
96 97 3.974401 CGCTACAAAGTTGTTGTTCATGG 59.026 43.478 1.35 0.00 42.35 3.66
97 98 4.260990 CGCTACAAAGTTGTTGTTCATGGA 60.261 41.667 1.35 0.00 42.35 3.41
98 99 5.587289 GCTACAAAGTTGTTGTTCATGGAA 58.413 37.500 1.35 0.00 42.35 3.53
99 100 6.039616 GCTACAAAGTTGTTGTTCATGGAAA 58.960 36.000 1.35 0.00 42.35 3.13
100 101 6.701400 GCTACAAAGTTGTTGTTCATGGAAAT 59.299 34.615 1.35 0.00 42.35 2.17
101 102 7.096065 GCTACAAAGTTGTTGTTCATGGAAATC 60.096 37.037 1.35 0.00 42.35 2.17
102 103 6.638610 ACAAAGTTGTTGTTCATGGAAATCA 58.361 32.000 0.00 0.00 38.47 2.57
103 104 6.757947 ACAAAGTTGTTGTTCATGGAAATCAG 59.242 34.615 0.00 0.00 38.47 2.90
104 105 6.713762 AAGTTGTTGTTCATGGAAATCAGA 57.286 33.333 0.00 0.00 0.00 3.27
105 106 6.713762 AGTTGTTGTTCATGGAAATCAGAA 57.286 33.333 0.00 0.00 0.00 3.02
106 107 6.507023 AGTTGTTGTTCATGGAAATCAGAAC 58.493 36.000 0.00 0.00 40.45 3.01
107 108 6.322201 AGTTGTTGTTCATGGAAATCAGAACT 59.678 34.615 0.00 0.00 40.62 3.01
108 109 6.075762 TGTTGTTCATGGAAATCAGAACTG 57.924 37.500 0.00 0.00 40.62 3.16
109 110 4.771590 TGTTCATGGAAATCAGAACTGC 57.228 40.909 0.00 0.00 40.62 4.40
110 111 4.401022 TGTTCATGGAAATCAGAACTGCT 58.599 39.130 0.00 0.00 40.62 4.24
111 112 4.828939 TGTTCATGGAAATCAGAACTGCTT 59.171 37.500 0.00 0.00 40.62 3.91
112 113 5.302568 TGTTCATGGAAATCAGAACTGCTTT 59.697 36.000 3.79 3.79 40.62 3.51
113 114 5.381174 TCATGGAAATCAGAACTGCTTTG 57.619 39.130 8.09 0.00 30.17 2.77
114 115 3.648339 TGGAAATCAGAACTGCTTTGC 57.352 42.857 12.97 12.97 37.48 3.68
115 116 2.957680 TGGAAATCAGAACTGCTTTGCA 59.042 40.909 16.70 16.70 42.00 4.08
116 117 3.575256 TGGAAATCAGAACTGCTTTGCAT 59.425 39.130 16.70 0.00 40.35 3.96
117 118 3.924686 GGAAATCAGAACTGCTTTGCATG 59.075 43.478 14.30 0.00 37.12 4.06
118 119 2.649331 ATCAGAACTGCTTTGCATGC 57.351 45.000 11.82 11.82 38.13 4.06
119 120 1.320507 TCAGAACTGCTTTGCATGCA 58.679 45.000 18.46 18.46 38.13 3.96
120 121 1.890489 TCAGAACTGCTTTGCATGCAT 59.110 42.857 23.37 3.89 38.13 3.96
121 122 3.083293 TCAGAACTGCTTTGCATGCATA 58.917 40.909 23.37 16.39 38.13 3.14
122 123 3.128068 TCAGAACTGCTTTGCATGCATAG 59.872 43.478 27.72 27.72 38.13 2.23
123 124 3.128068 CAGAACTGCTTTGCATGCATAGA 59.872 43.478 33.67 20.41 38.13 1.98
124 125 3.952323 AGAACTGCTTTGCATGCATAGAT 59.048 39.130 33.67 19.05 38.13 1.98
125 126 3.984508 ACTGCTTTGCATGCATAGATC 57.015 42.857 33.67 20.71 38.13 2.75
126 127 2.621998 ACTGCTTTGCATGCATAGATCC 59.378 45.455 33.67 20.12 38.13 3.36
127 128 1.958579 TGCTTTGCATGCATAGATCCC 59.041 47.619 33.67 19.82 35.31 3.85
128 129 1.068748 GCTTTGCATGCATAGATCCCG 60.069 52.381 33.67 13.73 0.00 5.14
129 130 2.497138 CTTTGCATGCATAGATCCCGA 58.503 47.619 27.99 5.57 0.00 5.14
243 244 4.844349 AATATCGTGGGCTAGCCAATAT 57.156 40.909 34.09 24.25 37.98 1.28
262 263 5.864418 ATATTCTGGTAAGGTCAGCGTTA 57.136 39.130 0.00 0.00 32.63 3.18
294 295 0.327576 ACTCCCCCATGAACCCTAGG 60.328 60.000 0.06 0.06 0.00 3.02
556 588 2.506438 CGCCGTTCCCGAGAGAAC 60.506 66.667 3.66 3.66 42.25 3.01
575 607 0.679640 CAAAAGCTCCACGGGCCATA 60.680 55.000 4.39 0.00 0.00 2.74
699 740 4.821589 GCCGAAGACCTCGCCCTG 62.822 72.222 0.00 0.00 46.71 4.45
728 769 3.393970 CTGCCTCTCCTTCCGCCA 61.394 66.667 0.00 0.00 0.00 5.69
735 776 0.911769 TCTCCTTCCGCCACATCATT 59.088 50.000 0.00 0.00 0.00 2.57
737 778 0.327924 TCCTTCCGCCACATCATTGT 59.672 50.000 0.00 0.00 36.15 2.71
920 964 3.542676 CACCGCCGGCCATACCTA 61.543 66.667 23.46 0.00 35.61 3.08
962 1006 4.988716 ACGTGTCCTCCTGGCCGA 62.989 66.667 0.00 0.00 0.00 5.54
998 1042 1.816074 TTTGTTGGTAGACGCATCCC 58.184 50.000 0.00 0.00 0.00 3.85
1023 1124 3.515316 CTTCACGGTGTGCGACCCT 62.515 63.158 8.17 0.00 42.62 4.34
1117 1221 3.307059 CCTCGATGTGGAGACTTTCCTTT 60.307 47.826 0.00 0.00 46.92 3.11
1281 1411 4.990426 GCCACACTTGCTTCATTTGTAAAT 59.010 37.500 0.00 0.00 0.00 1.40
1745 1887 0.984995 AAGCACTTACCTGGAGGACC 59.015 55.000 0.00 0.00 38.94 4.46
2157 3599 5.998981 CAGATAGTTCGTCTACTAGGTCCAT 59.001 44.000 0.00 0.00 34.32 3.41
2660 4122 3.728864 CGAAAATCCAAATCGGTGCTCAG 60.729 47.826 0.00 0.00 35.57 3.35
2674 4136 1.067749 CTCAGGCTCATCTGCTCCG 59.932 63.158 0.00 0.00 34.91 4.63
2755 4218 8.744568 TTATGTGTGGTAGATAATTTGATGCA 57.255 30.769 0.00 0.00 0.00 3.96
2765 4228 2.425143 ATTTGATGCATGAGGTCCGT 57.575 45.000 2.46 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.049117 TGGATGCATCTTAGAACTTTTATCAGT 58.951 33.333 25.28 0.00 0.00 3.41
1 2 8.442632 TGGATGCATCTTAGAACTTTTATCAG 57.557 34.615 25.28 0.00 0.00 2.90
2 3 8.677300 GTTGGATGCATCTTAGAACTTTTATCA 58.323 33.333 25.28 7.45 0.00 2.15
3 4 8.677300 TGTTGGATGCATCTTAGAACTTTTATC 58.323 33.333 25.28 4.91 0.00 1.75
4 5 8.579850 TGTTGGATGCATCTTAGAACTTTTAT 57.420 30.769 25.28 0.00 0.00 1.40
5 6 7.994425 TGTTGGATGCATCTTAGAACTTTTA 57.006 32.000 25.28 6.05 0.00 1.52
6 7 6.899393 TGTTGGATGCATCTTAGAACTTTT 57.101 33.333 25.28 0.00 0.00 2.27
7 8 6.071728 CCTTGTTGGATGCATCTTAGAACTTT 60.072 38.462 25.28 0.00 38.35 2.66
8 9 5.416952 CCTTGTTGGATGCATCTTAGAACTT 59.583 40.000 25.28 0.00 38.35 2.66
9 10 4.946157 CCTTGTTGGATGCATCTTAGAACT 59.054 41.667 25.28 0.00 38.35 3.01
10 11 4.943705 TCCTTGTTGGATGCATCTTAGAAC 59.056 41.667 25.28 20.38 40.56 3.01
11 12 5.045651 TCTCCTTGTTGGATGCATCTTAGAA 60.046 40.000 25.28 16.13 45.16 2.10
12 13 4.471025 TCTCCTTGTTGGATGCATCTTAGA 59.529 41.667 25.28 10.05 45.16 2.10
13 14 4.774124 TCTCCTTGTTGGATGCATCTTAG 58.226 43.478 25.28 14.48 45.16 2.18
14 15 4.842531 TCTCCTTGTTGGATGCATCTTA 57.157 40.909 25.28 12.71 45.16 2.10
15 16 3.726557 TCTCCTTGTTGGATGCATCTT 57.273 42.857 25.28 0.00 45.16 2.40
16 17 3.726557 TTCTCCTTGTTGGATGCATCT 57.273 42.857 25.28 0.00 45.16 2.90
17 18 4.460382 TCTTTTCTCCTTGTTGGATGCATC 59.540 41.667 18.81 18.81 45.16 3.91
18 19 4.410099 TCTTTTCTCCTTGTTGGATGCAT 58.590 39.130 0.00 0.00 45.16 3.96
19 20 3.831323 TCTTTTCTCCTTGTTGGATGCA 58.169 40.909 0.00 0.00 45.16 3.96
20 21 4.853924 TTCTTTTCTCCTTGTTGGATGC 57.146 40.909 0.00 0.00 45.16 3.91
21 22 6.639632 TCTTTCTTTTCTCCTTGTTGGATG 57.360 37.500 0.00 0.00 45.16 3.51
22 23 7.660030 TTTCTTTCTTTTCTCCTTGTTGGAT 57.340 32.000 0.00 0.00 45.16 3.41
23 24 7.475137 TTTTCTTTCTTTTCTCCTTGTTGGA 57.525 32.000 0.00 0.00 43.86 3.53
24 25 8.606602 CATTTTTCTTTCTTTTCTCCTTGTTGG 58.393 33.333 0.00 0.00 37.10 3.77
25 26 9.154847 ACATTTTTCTTTCTTTTCTCCTTGTTG 57.845 29.630 0.00 0.00 0.00 3.33
26 27 9.371136 GACATTTTTCTTTCTTTTCTCCTTGTT 57.629 29.630 0.00 0.00 0.00 2.83
27 28 8.531146 TGACATTTTTCTTTCTTTTCTCCTTGT 58.469 29.630 0.00 0.00 0.00 3.16
28 29 8.931385 TGACATTTTTCTTTCTTTTCTCCTTG 57.069 30.769 0.00 0.00 0.00 3.61
29 30 8.971073 TCTGACATTTTTCTTTCTTTTCTCCTT 58.029 29.630 0.00 0.00 0.00 3.36
30 31 8.409371 GTCTGACATTTTTCTTTCTTTTCTCCT 58.591 33.333 2.24 0.00 0.00 3.69
31 32 7.377131 CGTCTGACATTTTTCTTTCTTTTCTCC 59.623 37.037 8.73 0.00 0.00 3.71
32 33 8.122952 TCGTCTGACATTTTTCTTTCTTTTCTC 58.877 33.333 8.73 0.00 0.00 2.87
33 34 7.985476 TCGTCTGACATTTTTCTTTCTTTTCT 58.015 30.769 8.73 0.00 0.00 2.52
34 35 8.788409 ATCGTCTGACATTTTTCTTTCTTTTC 57.212 30.769 8.73 0.00 0.00 2.29
35 36 9.023967 CAATCGTCTGACATTTTTCTTTCTTTT 57.976 29.630 8.73 0.00 0.00 2.27
36 37 8.190784 ACAATCGTCTGACATTTTTCTTTCTTT 58.809 29.630 8.73 0.00 0.00 2.52
37 38 7.707104 ACAATCGTCTGACATTTTTCTTTCTT 58.293 30.769 8.73 0.00 0.00 2.52
38 39 7.264373 ACAATCGTCTGACATTTTTCTTTCT 57.736 32.000 8.73 0.00 0.00 2.52
39 40 7.432252 ACAACAATCGTCTGACATTTTTCTTTC 59.568 33.333 8.73 0.00 0.00 2.62
40 41 7.257722 ACAACAATCGTCTGACATTTTTCTTT 58.742 30.769 8.73 0.00 0.00 2.52
41 42 6.795399 ACAACAATCGTCTGACATTTTTCTT 58.205 32.000 8.73 0.00 0.00 2.52
42 43 6.377327 ACAACAATCGTCTGACATTTTTCT 57.623 33.333 8.73 0.00 0.00 2.52
43 44 7.352739 ACTACAACAATCGTCTGACATTTTTC 58.647 34.615 8.73 0.00 0.00 2.29
44 45 7.259290 ACTACAACAATCGTCTGACATTTTT 57.741 32.000 8.73 4.14 0.00 1.94
45 46 6.346598 CGACTACAACAATCGTCTGACATTTT 60.347 38.462 8.73 0.00 0.00 1.82
46 47 5.118664 CGACTACAACAATCGTCTGACATTT 59.881 40.000 8.73 0.00 0.00 2.32
47 48 4.621460 CGACTACAACAATCGTCTGACATT 59.379 41.667 8.73 4.42 0.00 2.71
48 49 4.166523 CGACTACAACAATCGTCTGACAT 58.833 43.478 8.73 0.00 0.00 3.06
49 50 3.561503 CGACTACAACAATCGTCTGACA 58.438 45.455 8.73 0.00 0.00 3.58
50 51 2.915463 CCGACTACAACAATCGTCTGAC 59.085 50.000 0.00 0.00 34.02 3.51
51 52 2.670229 GCCGACTACAACAATCGTCTGA 60.670 50.000 0.00 0.00 34.02 3.27
52 53 1.654105 GCCGACTACAACAATCGTCTG 59.346 52.381 0.00 0.00 34.02 3.51
53 54 1.731424 CGCCGACTACAACAATCGTCT 60.731 52.381 0.00 0.00 34.02 4.18
54 55 0.638746 CGCCGACTACAACAATCGTC 59.361 55.000 0.00 0.00 34.02 4.20
55 56 1.349259 GCGCCGACTACAACAATCGT 61.349 55.000 0.00 0.00 34.02 3.73
56 57 1.343821 GCGCCGACTACAACAATCG 59.656 57.895 0.00 0.00 35.62 3.34
57 58 1.343821 CGCGCCGACTACAACAATC 59.656 57.895 0.00 0.00 0.00 2.67
58 59 2.736682 GCGCGCCGACTACAACAAT 61.737 57.895 23.24 0.00 0.00 2.71
59 60 2.475098 TAGCGCGCCGACTACAACAA 62.475 55.000 30.33 0.00 0.00 2.83
60 61 2.980378 TAGCGCGCCGACTACAACA 61.980 57.895 30.33 0.00 0.00 3.33
61 62 2.202518 TAGCGCGCCGACTACAAC 60.203 61.111 30.33 0.00 0.00 3.32
62 63 2.202518 GTAGCGCGCCGACTACAA 60.203 61.111 30.33 0.00 36.90 2.41
63 64 2.475098 TTTGTAGCGCGCCGACTACA 62.475 55.000 30.33 25.56 41.03 2.74
64 65 1.740043 CTTTGTAGCGCGCCGACTAC 61.740 60.000 30.33 23.18 37.17 2.73
65 66 1.515519 CTTTGTAGCGCGCCGACTA 60.516 57.895 30.33 20.01 0.00 2.59
66 67 2.809601 CTTTGTAGCGCGCCGACT 60.810 61.111 30.33 12.34 0.00 4.18
67 68 2.664436 AACTTTGTAGCGCGCCGAC 61.664 57.895 30.33 26.01 0.00 4.79
68 69 2.356553 AACTTTGTAGCGCGCCGA 60.357 55.556 30.33 14.32 0.00 5.54
69 70 2.202171 CAACTTTGTAGCGCGCCG 60.202 61.111 30.33 11.84 0.00 6.46
70 71 0.996727 CAACAACTTTGTAGCGCGCC 60.997 55.000 30.33 14.69 41.31 6.53
71 72 0.316689 ACAACAACTTTGTAGCGCGC 60.317 50.000 26.66 26.66 41.31 6.86
72 73 2.034076 GAACAACAACTTTGTAGCGCG 58.966 47.619 0.00 0.00 41.31 6.86
73 74 3.059634 TGAACAACAACTTTGTAGCGC 57.940 42.857 0.00 0.00 41.31 5.92
74 75 3.974401 CCATGAACAACAACTTTGTAGCG 59.026 43.478 0.00 0.00 41.31 4.26
75 76 5.181690 TCCATGAACAACAACTTTGTAGC 57.818 39.130 0.00 0.00 41.31 3.58
76 77 7.920151 TGATTTCCATGAACAACAACTTTGTAG 59.080 33.333 0.00 0.00 41.31 2.74
77 78 7.776107 TGATTTCCATGAACAACAACTTTGTA 58.224 30.769 0.00 0.00 41.31 2.41
78 79 6.638610 TGATTTCCATGAACAACAACTTTGT 58.361 32.000 0.00 0.00 44.72 2.83
79 80 6.979817 TCTGATTTCCATGAACAACAACTTTG 59.020 34.615 0.00 0.00 0.00 2.77
80 81 7.111247 TCTGATTTCCATGAACAACAACTTT 57.889 32.000 0.00 0.00 0.00 2.66
81 82 6.713762 TCTGATTTCCATGAACAACAACTT 57.286 33.333 0.00 0.00 0.00 2.66
82 83 6.322201 AGTTCTGATTTCCATGAACAACAACT 59.678 34.615 0.00 0.00 40.62 3.16
83 84 6.418819 CAGTTCTGATTTCCATGAACAACAAC 59.581 38.462 0.00 0.00 40.62 3.32
84 85 6.506147 CAGTTCTGATTTCCATGAACAACAA 58.494 36.000 0.00 0.00 40.62 2.83
85 86 5.507817 GCAGTTCTGATTTCCATGAACAACA 60.508 40.000 3.84 0.00 40.62 3.33
86 87 4.919754 GCAGTTCTGATTTCCATGAACAAC 59.080 41.667 3.84 0.00 40.62 3.32
87 88 4.828939 AGCAGTTCTGATTTCCATGAACAA 59.171 37.500 3.84 0.00 40.62 2.83
88 89 4.401022 AGCAGTTCTGATTTCCATGAACA 58.599 39.130 3.84 0.00 40.62 3.18
89 90 5.382618 AAGCAGTTCTGATTTCCATGAAC 57.617 39.130 3.84 0.00 39.06 3.18
90 91 5.775686 CAAAGCAGTTCTGATTTCCATGAA 58.224 37.500 12.16 0.00 0.00 2.57
91 92 4.321452 GCAAAGCAGTTCTGATTTCCATGA 60.321 41.667 12.16 0.00 0.00 3.07
92 93 3.924686 GCAAAGCAGTTCTGATTTCCATG 59.075 43.478 12.16 4.88 0.00 3.66
93 94 3.575256 TGCAAAGCAGTTCTGATTTCCAT 59.425 39.130 12.16 0.00 33.32 3.41
94 95 2.957680 TGCAAAGCAGTTCTGATTTCCA 59.042 40.909 12.16 7.88 33.32 3.53
95 96 3.648339 TGCAAAGCAGTTCTGATTTCC 57.352 42.857 12.16 5.46 33.32 3.13
96 97 3.367025 GCATGCAAAGCAGTTCTGATTTC 59.633 43.478 14.21 8.72 43.65 2.17
97 98 3.243941 TGCATGCAAAGCAGTTCTGATTT 60.244 39.130 20.30 9.75 43.65 2.17
98 99 2.297880 TGCATGCAAAGCAGTTCTGATT 59.702 40.909 20.30 0.44 43.65 2.57
99 100 1.890489 TGCATGCAAAGCAGTTCTGAT 59.110 42.857 20.30 0.00 43.65 2.90
100 101 1.320507 TGCATGCAAAGCAGTTCTGA 58.679 45.000 20.30 0.00 43.65 3.27
101 102 2.363788 ATGCATGCAAAGCAGTTCTG 57.636 45.000 26.68 0.00 46.36 3.02
102 103 3.349927 TCTATGCATGCAAAGCAGTTCT 58.650 40.909 26.68 7.21 46.36 3.01
103 104 3.770263 TCTATGCATGCAAAGCAGTTC 57.230 42.857 26.68 0.00 46.36 3.01
104 105 3.067742 GGATCTATGCATGCAAAGCAGTT 59.932 43.478 26.68 13.70 46.36 3.16
105 106 2.621998 GGATCTATGCATGCAAAGCAGT 59.378 45.455 26.68 9.68 46.36 4.40
106 107 2.030185 GGGATCTATGCATGCAAAGCAG 60.030 50.000 26.68 18.31 46.36 4.24
108 109 1.068748 CGGGATCTATGCATGCAAAGC 60.069 52.381 26.68 15.52 0.00 3.51
109 110 2.225019 GTCGGGATCTATGCATGCAAAG 59.775 50.000 26.68 9.73 0.00 2.77
110 111 2.158769 AGTCGGGATCTATGCATGCAAA 60.159 45.455 26.68 13.80 0.00 3.68
111 112 1.417517 AGTCGGGATCTATGCATGCAA 59.582 47.619 26.68 9.06 0.00 4.08
112 113 1.051008 AGTCGGGATCTATGCATGCA 58.949 50.000 25.04 25.04 0.00 3.96
113 114 2.175878 AAGTCGGGATCTATGCATGC 57.824 50.000 11.82 11.82 0.00 4.06
114 115 4.790765 TCTAAGTCGGGATCTATGCATG 57.209 45.455 10.16 0.00 0.00 4.06
115 116 4.221703 CCTTCTAAGTCGGGATCTATGCAT 59.778 45.833 3.79 3.79 0.00 3.96
116 117 3.574396 CCTTCTAAGTCGGGATCTATGCA 59.426 47.826 0.00 0.00 0.00 3.96
117 118 3.056465 CCCTTCTAAGTCGGGATCTATGC 60.056 52.174 0.00 0.00 40.55 3.14
118 119 4.408276 TCCCTTCTAAGTCGGGATCTATG 58.592 47.826 0.00 0.00 41.95 2.23
119 120 4.743705 TCCCTTCTAAGTCGGGATCTAT 57.256 45.455 0.00 0.00 41.95 1.98
125 126 1.269998 CGCTATCCCTTCTAAGTCGGG 59.730 57.143 0.00 0.00 39.41 5.14
126 127 2.228059 TCGCTATCCCTTCTAAGTCGG 58.772 52.381 0.00 0.00 0.00 4.79
127 128 4.506886 AATCGCTATCCCTTCTAAGTCG 57.493 45.455 0.00 0.00 0.00 4.18
128 129 5.404096 GCTAATCGCTATCCCTTCTAAGTC 58.596 45.833 0.00 0.00 35.14 3.01
129 130 4.082679 CGCTAATCGCTATCCCTTCTAAGT 60.083 45.833 0.00 0.00 36.13 2.24
170 171 1.302383 CCACGTAATTTCCGGCAGCA 61.302 55.000 0.00 0.00 0.00 4.41
175 176 2.466140 CCGCCCACGTAATTTCCGG 61.466 63.158 0.00 0.00 37.70 5.14
204 205 5.049060 CGATATTTGGTGGTTGTTTGTCTCA 60.049 40.000 0.00 0.00 0.00 3.27
243 244 2.895404 ACTAACGCTGACCTTACCAGAA 59.105 45.455 0.00 0.00 33.65 3.02
262 263 1.209747 GGGGGAGTTTAGATTGCGACT 59.790 52.381 0.00 0.00 0.00 4.18
294 295 1.227973 GTTCATGGAGGATCGGGGC 60.228 63.158 0.00 0.00 34.37 5.80
378 389 2.521958 CTTCGACAGGGGCCGACATT 62.522 60.000 0.00 0.00 34.26 2.71
380 391 3.691342 CTTCGACAGGGGCCGACA 61.691 66.667 0.00 0.00 34.26 4.35
381 392 2.837371 CTTCTTCGACAGGGGCCGAC 62.837 65.000 0.00 0.00 34.26 4.79
395 406 3.330720 CTCCCCCGTGCCCTTCTT 61.331 66.667 0.00 0.00 0.00 2.52
469 489 2.192861 CCACAAAGCTCGCCCAACA 61.193 57.895 0.00 0.00 0.00 3.33
556 588 0.679640 TATGGCCCGTGGAGCTTTTG 60.680 55.000 0.00 0.00 0.00 2.44
716 757 0.911769 AATGATGTGGCGGAAGGAGA 59.088 50.000 0.00 0.00 0.00 3.71
728 769 4.948004 AGAAGTCATGATGCACAATGATGT 59.052 37.500 14.41 7.26 41.61 3.06
735 776 1.465777 CGCAAGAAGTCATGATGCACA 59.534 47.619 16.26 0.00 43.02 4.57
737 778 0.448990 GCGCAAGAAGTCATGATGCA 59.551 50.000 16.26 0.00 43.02 3.96
738 779 0.248377 GGCGCAAGAAGTCATGATGC 60.248 55.000 10.83 7.96 43.02 3.91
741 782 2.390599 GCGGCGCAAGAAGTCATGA 61.391 57.895 29.21 0.00 43.02 3.07
746 787 2.434359 GGTAGCGGCGCAAGAAGT 60.434 61.111 35.02 14.87 43.02 3.01
962 1006 5.221501 CCAACAAAATTTCTGACCAGGATGT 60.222 40.000 0.00 0.00 0.00 3.06
1023 1124 0.741915 TGATATAGCGACGGTGCACA 59.258 50.000 20.43 0.00 37.31 4.57
1281 1411 1.280133 CTTGACAGCCCAGGATCAGAA 59.720 52.381 0.00 0.00 0.00 3.02
1745 1887 1.129811 GGTTTGGGAAATCAGCGTACG 59.870 52.381 11.84 11.84 0.00 3.67
2157 3599 8.706322 TGACTAAGGCAATCTACAGTCATATA 57.294 34.615 0.00 0.00 40.13 0.86
2465 3925 3.118408 ACCTAATTATCCTGACGCTGCAA 60.118 43.478 0.00 0.00 0.00 4.08
2605 4065 3.332783 TCCTTTACTTTCTCCCCCTTTCC 59.667 47.826 0.00 0.00 0.00 3.13
2660 4122 3.453070 GACCCGGAGCAGATGAGCC 62.453 68.421 0.73 0.00 34.23 4.70
2732 4195 7.503230 TCATGCATCAAATTATCTACCACACAT 59.497 33.333 0.00 0.00 0.00 3.21
2755 4218 3.761897 TGAAATTTGGAACGGACCTCAT 58.238 40.909 0.00 0.00 0.00 2.90
2786 4249 1.934399 GCCGAGAGCTGCTCACATATC 60.934 57.143 29.49 17.18 44.15 1.63


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

AutoCloner maintained by Alex Coulton.