Multiple sequence alignment - TraesCS4B01G271800

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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 TraesCS4B01G271800 chr4B 100.000 2633 0 0 1 2633 548119604 548122236 0.000000e+00 4863.0
1 TraesCS4B01G271800 chr4B 95.711 816 23 5 1829 2633 1075803 1074989 0.000000e+00 1303.0
2 TraesCS4B01G271800 chr4B 95.000 820 32 7 1820 2633 122467056 122467872 0.000000e+00 1279.0
3 TraesCS4B01G271800 chr4B 82.014 884 92 32 833 1683 548184933 548185782 0.000000e+00 689.0
4 TraesCS4B01G271800 chr4D 93.644 1715 74 17 139 1829 441652130 441653833 0.000000e+00 2531.0
5 TraesCS4B01G271800 chr4D 89.616 886 63 15 958 1829 441809775 441810645 0.000000e+00 1099.0
6 TraesCS4B01G271800 chr4D 81.786 851 108 18 958 1781 441836798 441837628 0.000000e+00 669.0
7 TraesCS4B01G271800 chr4D 90.385 52 5 0 208 259 441638042 441638093 4.700000e-08 69.4
8 TraesCS4B01G271800 chr4A 92.720 1717 96 14 139 1829 25787041 25785328 0.000000e+00 2451.0
9 TraesCS4B01G271800 chr4A 80.806 844 101 27 970 1781 25700742 25699928 2.900000e-169 604.0
10 TraesCS4B01G271800 chr4A 82.055 730 102 13 1061 1781 676781709 676782418 1.740000e-166 595.0
11 TraesCS4B01G271800 chr4A 96.377 138 5 0 1 138 704794331 704794468 7.330000e-56 228.0
12 TraesCS4B01G271800 chr4A 93.478 46 3 0 214 259 25804217 25804172 4.700000e-08 69.4
13 TraesCS4B01G271800 chr3B 96.054 811 23 7 1829 2633 741701504 741700697 0.000000e+00 1312.0
14 TraesCS4B01G271800 chr3B 95.604 819 30 4 1821 2633 249988798 249987980 0.000000e+00 1308.0
15 TraesCS4B01G271800 chr5B 95.488 820 23 6 1826 2633 456331279 456330462 0.000000e+00 1297.0
16 TraesCS4B01G271800 chr5B 95.320 812 26 8 1826 2633 159923660 159924463 0.000000e+00 1279.0
17 TraesCS4B01G271800 chr7B 95.232 818 25 9 1829 2633 586573842 586573026 0.000000e+00 1282.0
18 TraesCS4B01G271800 chr7B 96.377 138 5 0 1 138 73180679 73180816 7.330000e-56 228.0
19 TraesCS4B01G271800 chr2B 95.221 816 27 8 1828 2633 562156883 562157696 0.000000e+00 1280.0
20 TraesCS4B01G271800 chr2B 96.296 135 5 0 4 138 353560203 353560069 3.410000e-54 222.0
21 TraesCS4B01G271800 chr2B 96.296 135 5 0 4 138 675367693 675367559 3.410000e-54 222.0
22 TraesCS4B01G271800 chr2B 95.652 138 6 0 1 138 795059904 795060041 3.410000e-54 222.0
23 TraesCS4B01G271800 chr2B 77.143 210 31 4 206 400 676193448 676193655 3.580000e-19 106.0
24 TraesCS4B01G271800 chr2B 74.163 209 37 7 206 399 676589712 676589918 1.310000e-08 71.3
25 TraesCS4B01G271800 chr1B 94.293 841 33 13 1807 2633 32687444 32688283 0.000000e+00 1273.0
26 TraesCS4B01G271800 chr7D 84.748 636 82 10 1061 1683 58925509 58924876 8.000000e-175 623.0
27 TraesCS4B01G271800 chr6B 97.037 135 4 0 4 138 715074145 715074011 7.330000e-56 228.0
28 TraesCS4B01G271800 chr6B 95.652 138 6 0 1 138 450605836 450605699 3.410000e-54 222.0
29 TraesCS4B01G271800 chrUn 95.652 138 6 0 1 138 84677009 84677146 3.410000e-54 222.0
30 TraesCS4B01G271800 chrUn 76.573 286 60 5 1155 1435 307394491 307394774 1.630000e-32 150.0
31 TraesCS4B01G271800 chr7A 96.296 135 5 0 4 138 14507939 14507805 3.410000e-54 222.0
32 TraesCS4B01G271800 chr2A 77.143 210 31 4 206 400 705526658 705526865 3.580000e-19 106.0
33 TraesCS4B01G271800 chr2D 74.641 209 36 7 206 399 564922364 564922570 2.810000e-10 76.8
34 TraesCS4B01G271800 chr2D 88.889 54 6 0 206 259 564702234 564702287 1.690000e-07 67.6


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 TraesCS4B01G271800 chr4B 548119604 548122236 2632 False 4863 4863 100.000 1 2633 1 chr4B.!!$F2 2632
1 TraesCS4B01G271800 chr4B 1074989 1075803 814 True 1303 1303 95.711 1829 2633 1 chr4B.!!$R1 804
2 TraesCS4B01G271800 chr4B 122467056 122467872 816 False 1279 1279 95.000 1820 2633 1 chr4B.!!$F1 813
3 TraesCS4B01G271800 chr4B 548184933 548185782 849 False 689 689 82.014 833 1683 1 chr4B.!!$F3 850
4 TraesCS4B01G271800 chr4D 441652130 441653833 1703 False 2531 2531 93.644 139 1829 1 chr4D.!!$F2 1690
5 TraesCS4B01G271800 chr4D 441809775 441810645 870 False 1099 1099 89.616 958 1829 1 chr4D.!!$F3 871
6 TraesCS4B01G271800 chr4D 441836798 441837628 830 False 669 669 81.786 958 1781 1 chr4D.!!$F4 823
7 TraesCS4B01G271800 chr4A 25785328 25787041 1713 True 2451 2451 92.720 139 1829 1 chr4A.!!$R2 1690
8 TraesCS4B01G271800 chr4A 25699928 25700742 814 True 604 604 80.806 970 1781 1 chr4A.!!$R1 811
9 TraesCS4B01G271800 chr4A 676781709 676782418 709 False 595 595 82.055 1061 1781 1 chr4A.!!$F1 720
10 TraesCS4B01G271800 chr3B 741700697 741701504 807 True 1312 1312 96.054 1829 2633 1 chr3B.!!$R2 804
11 TraesCS4B01G271800 chr3B 249987980 249988798 818 True 1308 1308 95.604 1821 2633 1 chr3B.!!$R1 812
12 TraesCS4B01G271800 chr5B 456330462 456331279 817 True 1297 1297 95.488 1826 2633 1 chr5B.!!$R1 807
13 TraesCS4B01G271800 chr5B 159923660 159924463 803 False 1279 1279 95.320 1826 2633 1 chr5B.!!$F1 807
14 TraesCS4B01G271800 chr7B 586573026 586573842 816 True 1282 1282 95.232 1829 2633 1 chr7B.!!$R1 804
15 TraesCS4B01G271800 chr2B 562156883 562157696 813 False 1280 1280 95.221 1828 2633 1 chr2B.!!$F1 805
16 TraesCS4B01G271800 chr1B 32687444 32688283 839 False 1273 1273 94.293 1807 2633 1 chr1B.!!$F1 826
17 TraesCS4B01G271800 chr7D 58924876 58925509 633 True 623 623 84.748 1061 1683 1 chr7D.!!$R1 622

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
757 768 0.398696 ACCAACGTACTTCCATGCCA 59.601 50.0 0.0 0.0 0.0 4.92 F
1362 1417 0.313672 GCGCCATCAACACCTTCAAA 59.686 50.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1617 1678 0.955428 GCGTTCAAGCCATGAGACCA 60.955 55.000 0.0 0.0 39.77 4.02 R
2589 2695 2.207924 CGGGGGTAGGGGAATCTCG 61.208 68.421 0.0 0.0 0.00 4.04 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
26 27 8.757982 AGAAATATGGTGAGACAAATTATGCT 57.242 30.769 0.00 0.00 0.00 3.79
27 28 9.851686 AGAAATATGGTGAGACAAATTATGCTA 57.148 29.630 0.00 0.00 0.00 3.49
30 31 9.851686 AATATGGTGAGACAAATTATGCTAAGA 57.148 29.630 0.00 0.00 0.00 2.10
31 32 7.798596 ATGGTGAGACAAATTATGCTAAGAG 57.201 36.000 0.00 0.00 0.00 2.85
32 33 6.946340 TGGTGAGACAAATTATGCTAAGAGA 58.054 36.000 0.00 0.00 0.00 3.10
33 34 7.568349 TGGTGAGACAAATTATGCTAAGAGAT 58.432 34.615 0.00 0.00 0.00 2.75
34 35 7.712639 TGGTGAGACAAATTATGCTAAGAGATC 59.287 37.037 0.00 0.00 0.00 2.75
35 36 7.712639 GGTGAGACAAATTATGCTAAGAGATCA 59.287 37.037 0.00 0.00 0.00 2.92
36 37 9.270640 GTGAGACAAATTATGCTAAGAGATCAT 57.729 33.333 0.00 0.00 0.00 2.45
37 38 9.486497 TGAGACAAATTATGCTAAGAGATCATC 57.514 33.333 0.00 0.00 0.00 2.92
38 39 9.709495 GAGACAAATTATGCTAAGAGATCATCT 57.291 33.333 0.00 0.00 41.27 2.90
39 40 9.709495 AGACAAATTATGCTAAGAGATCATCTC 57.291 33.333 6.55 6.55 43.70 2.75
80 81 5.897050 AGAGAAGACAAGCCTTATCTTACG 58.103 41.667 0.00 0.00 40.60 3.18
81 82 5.652891 AGAGAAGACAAGCCTTATCTTACGA 59.347 40.000 0.00 0.00 40.60 3.43
82 83 6.322712 AGAGAAGACAAGCCTTATCTTACGAT 59.677 38.462 0.00 0.00 40.60 3.73
83 84 6.879400 AGAAGACAAGCCTTATCTTACGATT 58.121 36.000 0.00 0.00 32.83 3.34
84 85 7.331791 AGAAGACAAGCCTTATCTTACGATTT 58.668 34.615 0.00 0.00 32.83 2.17
85 86 7.492994 AGAAGACAAGCCTTATCTTACGATTTC 59.507 37.037 0.00 0.00 32.83 2.17
86 87 6.879400 AGACAAGCCTTATCTTACGATTTCT 58.121 36.000 0.00 0.00 0.00 2.52
87 88 6.981559 AGACAAGCCTTATCTTACGATTTCTC 59.018 38.462 0.00 0.00 0.00 2.87
88 89 6.879400 ACAAGCCTTATCTTACGATTTCTCT 58.121 36.000 0.00 0.00 0.00 3.10
89 90 6.981559 ACAAGCCTTATCTTACGATTTCTCTC 59.018 38.462 0.00 0.00 0.00 3.20
90 91 6.969993 AGCCTTATCTTACGATTTCTCTCT 57.030 37.500 0.00 0.00 0.00 3.10
91 92 7.354751 AGCCTTATCTTACGATTTCTCTCTT 57.645 36.000 0.00 0.00 0.00 2.85
92 93 7.430441 AGCCTTATCTTACGATTTCTCTCTTC 58.570 38.462 0.00 0.00 0.00 2.87
93 94 7.286775 AGCCTTATCTTACGATTTCTCTCTTCT 59.713 37.037 0.00 0.00 0.00 2.85
94 95 7.593644 GCCTTATCTTACGATTTCTCTCTTCTC 59.406 40.741 0.00 0.00 0.00 2.87
95 96 8.079809 CCTTATCTTACGATTTCTCTCTTCTCC 58.920 40.741 0.00 0.00 0.00 3.71
96 97 8.521170 TTATCTTACGATTTCTCTCTTCTCCA 57.479 34.615 0.00 0.00 0.00 3.86
97 98 6.197364 TCTTACGATTTCTCTCTTCTCCAC 57.803 41.667 0.00 0.00 0.00 4.02
98 99 3.878160 ACGATTTCTCTCTTCTCCACC 57.122 47.619 0.00 0.00 0.00 4.61
99 100 3.436243 ACGATTTCTCTCTTCTCCACCT 58.564 45.455 0.00 0.00 0.00 4.00
100 101 3.445805 ACGATTTCTCTCTTCTCCACCTC 59.554 47.826 0.00 0.00 0.00 3.85
101 102 3.445450 CGATTTCTCTCTTCTCCACCTCA 59.555 47.826 0.00 0.00 0.00 3.86
102 103 4.099266 CGATTTCTCTCTTCTCCACCTCAT 59.901 45.833 0.00 0.00 0.00 2.90
103 104 5.600696 GATTTCTCTCTTCTCCACCTCATC 58.399 45.833 0.00 0.00 0.00 2.92
104 105 3.746792 TCTCTCTTCTCCACCTCATCA 57.253 47.619 0.00 0.00 0.00 3.07
105 106 4.262891 TCTCTCTTCTCCACCTCATCAT 57.737 45.455 0.00 0.00 0.00 2.45
106 107 4.618635 TCTCTCTTCTCCACCTCATCATT 58.381 43.478 0.00 0.00 0.00 2.57
107 108 5.028802 TCTCTCTTCTCCACCTCATCATTT 58.971 41.667 0.00 0.00 0.00 2.32
108 109 6.197903 TCTCTCTTCTCCACCTCATCATTTA 58.802 40.000 0.00 0.00 0.00 1.40
109 110 6.843333 TCTCTCTTCTCCACCTCATCATTTAT 59.157 38.462 0.00 0.00 0.00 1.40
110 111 7.015098 TCTCTCTTCTCCACCTCATCATTTATC 59.985 40.741 0.00 0.00 0.00 1.75
111 112 6.042552 TCTCTTCTCCACCTCATCATTTATCC 59.957 42.308 0.00 0.00 0.00 2.59
112 113 5.907662 TCTTCTCCACCTCATCATTTATCCT 59.092 40.000 0.00 0.00 0.00 3.24
113 114 7.075797 TCTTCTCCACCTCATCATTTATCCTA 58.924 38.462 0.00 0.00 0.00 2.94
114 115 6.672266 TCTCCACCTCATCATTTATCCTAC 57.328 41.667 0.00 0.00 0.00 3.18
115 116 5.243954 TCTCCACCTCATCATTTATCCTACG 59.756 44.000 0.00 0.00 0.00 3.51
116 117 4.899457 TCCACCTCATCATTTATCCTACGT 59.101 41.667 0.00 0.00 0.00 3.57
117 118 4.991056 CCACCTCATCATTTATCCTACGTG 59.009 45.833 0.00 0.00 0.00 4.49
118 119 4.991056 CACCTCATCATTTATCCTACGTGG 59.009 45.833 0.00 0.00 37.10 4.94
119 120 3.997021 CCTCATCATTTATCCTACGTGGC 59.003 47.826 0.00 0.00 35.26 5.01
120 121 4.503123 CCTCATCATTTATCCTACGTGGCA 60.503 45.833 0.00 0.00 35.26 4.92
121 122 5.227569 TCATCATTTATCCTACGTGGCAT 57.772 39.130 0.00 0.00 35.26 4.40
122 123 5.620206 TCATCATTTATCCTACGTGGCATT 58.380 37.500 0.00 0.00 35.26 3.56
123 124 5.700832 TCATCATTTATCCTACGTGGCATTC 59.299 40.000 0.00 0.00 35.26 2.67
124 125 5.290493 TCATTTATCCTACGTGGCATTCT 57.710 39.130 0.00 0.00 35.26 2.40
125 126 5.680619 TCATTTATCCTACGTGGCATTCTT 58.319 37.500 0.00 0.00 35.26 2.52
126 127 6.822442 TCATTTATCCTACGTGGCATTCTTA 58.178 36.000 0.00 0.00 35.26 2.10
127 128 7.276658 TCATTTATCCTACGTGGCATTCTTAA 58.723 34.615 0.00 0.00 35.26 1.85
128 129 7.441157 TCATTTATCCTACGTGGCATTCTTAAG 59.559 37.037 0.00 0.00 35.26 1.85
129 130 6.474140 TTATCCTACGTGGCATTCTTAAGA 57.526 37.500 0.00 0.00 35.26 2.10
130 131 5.552870 ATCCTACGTGGCATTCTTAAGAT 57.447 39.130 5.89 0.00 35.26 2.40
131 132 6.665992 ATCCTACGTGGCATTCTTAAGATA 57.334 37.500 5.89 0.00 35.26 1.98
132 133 6.085555 TCCTACGTGGCATTCTTAAGATAG 57.914 41.667 5.89 3.24 35.26 2.08
133 134 5.831525 TCCTACGTGGCATTCTTAAGATAGA 59.168 40.000 5.89 0.00 35.26 1.98
134 135 6.322969 TCCTACGTGGCATTCTTAAGATAGAA 59.677 38.462 5.89 0.00 35.78 2.10
135 136 6.421202 CCTACGTGGCATTCTTAAGATAGAAC 59.579 42.308 5.89 1.47 37.00 3.01
136 137 5.116882 ACGTGGCATTCTTAAGATAGAACC 58.883 41.667 5.89 4.99 37.00 3.62
137 138 5.116180 CGTGGCATTCTTAAGATAGAACCA 58.884 41.667 5.89 7.45 37.00 3.67
180 181 1.533625 ATCCCCAATGTCACAACGTG 58.466 50.000 0.00 0.00 34.45 4.49
196 197 8.440059 GTCACAACGTGTCAATCAAATTAGATA 58.560 33.333 0.00 0.00 34.79 1.98
212 213 8.510505 CAAATTAGATAAAGAGGGAAGCATAGC 58.489 37.037 0.00 0.00 0.00 2.97
271 272 2.288666 TGTCGAAAGTGCAAAAGAGCT 58.711 42.857 0.00 0.00 34.99 4.09
447 453 7.755582 AGCAGTTAAGAACAACATTCAAAAC 57.244 32.000 0.00 0.00 0.00 2.43
448 454 7.319646 AGCAGTTAAGAACAACATTCAAAACA 58.680 30.769 0.00 0.00 0.00 2.83
449 455 7.816995 AGCAGTTAAGAACAACATTCAAAACAA 59.183 29.630 0.00 0.00 0.00 2.83
592 602 1.472480 GGACAACGGCTGCAATATTGT 59.528 47.619 16.61 5.90 36.24 2.71
654 665 2.180204 CAAACCCGGCCTATGCTCG 61.180 63.158 0.00 0.00 37.74 5.03
688 699 2.689983 CCTGGAGCCGCTTAATTTGAAT 59.310 45.455 0.00 0.00 0.00 2.57
693 704 4.380444 GGAGCCGCTTAATTTGAATTGTCA 60.380 41.667 0.00 0.00 0.00 3.58
694 705 5.329035 AGCCGCTTAATTTGAATTGTCAT 57.671 34.783 0.00 0.00 32.48 3.06
710 721 2.037902 TGTCATTTGTCAACTAGCCGGA 59.962 45.455 5.05 0.00 0.00 5.14
736 747 5.688224 GCTAGCTAGCTCGATGGTGACAG 62.688 56.522 33.71 10.00 45.08 3.51
757 768 0.398696 ACCAACGTACTTCCATGCCA 59.601 50.000 0.00 0.00 0.00 4.92
766 777 4.024893 CGTACTTCCATGCCATATTGTGAC 60.025 45.833 0.00 0.00 0.00 3.67
818 829 0.672711 GTGAAGGTGGAACGGTAGCC 60.673 60.000 0.00 0.00 38.12 3.93
1098 1132 0.404040 TGCATTCCTCCTTCCGGTTT 59.596 50.000 0.00 0.00 0.00 3.27
1153 1205 4.418328 TTGCCGTGGCCGCCTTAT 62.418 61.111 11.56 0.00 41.09 1.73
1282 1337 4.001652 TGAGATCGTCTTCAAGTACTCGT 58.998 43.478 0.00 0.00 0.00 4.18
1287 1342 0.524862 TCTTCAAGTACTCGTCCGCC 59.475 55.000 0.00 0.00 0.00 6.13
1362 1417 0.313672 GCGCCATCAACACCTTCAAA 59.686 50.000 0.00 0.00 0.00 2.69
1365 1420 2.489329 CGCCATCAACACCTTCAAATCT 59.511 45.455 0.00 0.00 0.00 2.40
1388 1443 1.605058 AACGACGTCATCCCCCTCAG 61.605 60.000 17.16 0.00 0.00 3.35
1497 1558 4.761058 TCGGGCTCCTCTTCGCCT 62.761 66.667 0.00 0.00 45.57 5.52
1500 1561 2.188207 GGCTCCTCTTCGCCTTCC 59.812 66.667 0.00 0.00 42.98 3.46
1655 1729 3.004862 CGCATATATTGATCAGCTGCCA 58.995 45.455 9.47 6.69 0.00 4.92
1785 1870 6.877611 TCACGTCTATATGTAATCTGCAGA 57.122 37.500 20.79 20.79 0.00 4.26
1855 1941 3.931130 CGTCCGTGCGTTGCAACA 61.931 61.111 28.01 8.05 41.47 3.33
1933 2024 2.827800 ATCCTCACACACACACTCTG 57.172 50.000 0.00 0.00 0.00 3.35
1973 2066 2.774234 ACTCTCTCTCCCTCTCTCTCTG 59.226 54.545 0.00 0.00 0.00 3.35
2155 2258 3.155501 AGTCGTTAGCTACAGTGACCTT 58.844 45.455 0.00 0.00 0.00 3.50
2466 2572 6.605194 TGTGCCACCTAAAAATATTATGCTCA 59.395 34.615 0.00 0.00 0.00 4.26
2589 2695 6.656314 AAAACCAAAAGGACGATGAAAAAC 57.344 33.333 0.00 0.00 0.00 2.43
2591 2697 3.628487 ACCAAAAGGACGATGAAAAACGA 59.372 39.130 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.757982 AGCATAATTTGTCTCACCATATTTCT 57.242 30.769 0.00 0.00 0.00 2.52
4 5 9.851686 TCTTAGCATAATTTGTCTCACCATATT 57.148 29.630 0.00 0.00 0.00 1.28
5 6 9.499479 CTCTTAGCATAATTTGTCTCACCATAT 57.501 33.333 0.00 0.00 0.00 1.78
6 7 8.704668 TCTCTTAGCATAATTTGTCTCACCATA 58.295 33.333 0.00 0.00 0.00 2.74
7 8 7.568349 TCTCTTAGCATAATTTGTCTCACCAT 58.432 34.615 0.00 0.00 0.00 3.55
8 9 6.946340 TCTCTTAGCATAATTTGTCTCACCA 58.054 36.000 0.00 0.00 0.00 4.17
10 11 8.654230 TGATCTCTTAGCATAATTTGTCTCAC 57.346 34.615 0.00 0.00 0.00 3.51
11 12 9.486497 GATGATCTCTTAGCATAATTTGTCTCA 57.514 33.333 0.00 0.00 33.33 3.27
12 13 9.709495 AGATGATCTCTTAGCATAATTTGTCTC 57.291 33.333 0.00 0.00 33.33 3.36
13 14 9.709495 GAGATGATCTCTTAGCATAATTTGTCT 57.291 33.333 14.98 0.00 40.30 3.41
53 54 9.825109 GTAAGATAAGGCTTGTCTTCTCTTATT 57.175 33.333 33.45 16.25 40.83 1.40
54 55 8.138712 CGTAAGATAAGGCTTGTCTTCTCTTAT 58.861 37.037 33.45 16.87 40.83 1.73
55 56 7.338703 TCGTAAGATAAGGCTTGTCTTCTCTTA 59.661 37.037 33.45 18.62 45.01 2.10
56 57 6.153000 TCGTAAGATAAGGCTTGTCTTCTCTT 59.847 38.462 33.45 18.08 45.01 2.85
57 58 5.652891 TCGTAAGATAAGGCTTGTCTTCTCT 59.347 40.000 33.45 18.40 45.01 3.10
58 59 5.892568 TCGTAAGATAAGGCTTGTCTTCTC 58.107 41.667 33.45 26.15 45.01 2.87
59 60 5.916661 TCGTAAGATAAGGCTTGTCTTCT 57.083 39.130 33.45 19.32 45.01 2.85
75 76 5.126384 AGGTGGAGAAGAGAGAAATCGTAAG 59.874 44.000 0.00 0.00 0.00 2.34
76 77 5.017490 AGGTGGAGAAGAGAGAAATCGTAA 58.983 41.667 0.00 0.00 0.00 3.18
77 78 4.601084 AGGTGGAGAAGAGAGAAATCGTA 58.399 43.478 0.00 0.00 0.00 3.43
78 79 3.436243 AGGTGGAGAAGAGAGAAATCGT 58.564 45.455 0.00 0.00 0.00 3.73
79 80 3.445450 TGAGGTGGAGAAGAGAGAAATCG 59.555 47.826 0.00 0.00 0.00 3.34
80 81 5.128499 TGATGAGGTGGAGAAGAGAGAAATC 59.872 44.000 0.00 0.00 0.00 2.17
81 82 5.028802 TGATGAGGTGGAGAAGAGAGAAAT 58.971 41.667 0.00 0.00 0.00 2.17
82 83 4.420206 TGATGAGGTGGAGAAGAGAGAAA 58.580 43.478 0.00 0.00 0.00 2.52
83 84 4.053009 TGATGAGGTGGAGAAGAGAGAA 57.947 45.455 0.00 0.00 0.00 2.87
84 85 3.746792 TGATGAGGTGGAGAAGAGAGA 57.253 47.619 0.00 0.00 0.00 3.10
85 86 5.356291 AAATGATGAGGTGGAGAAGAGAG 57.644 43.478 0.00 0.00 0.00 3.20
86 87 6.042552 GGATAAATGATGAGGTGGAGAAGAGA 59.957 42.308 0.00 0.00 0.00 3.10
87 88 6.043012 AGGATAAATGATGAGGTGGAGAAGAG 59.957 42.308 0.00 0.00 0.00 2.85
88 89 5.907662 AGGATAAATGATGAGGTGGAGAAGA 59.092 40.000 0.00 0.00 0.00 2.87
89 90 6.185114 AGGATAAATGATGAGGTGGAGAAG 57.815 41.667 0.00 0.00 0.00 2.85
90 91 6.239317 CGTAGGATAAATGATGAGGTGGAGAA 60.239 42.308 0.00 0.00 0.00 2.87
91 92 5.243954 CGTAGGATAAATGATGAGGTGGAGA 59.756 44.000 0.00 0.00 0.00 3.71
92 93 5.011125 ACGTAGGATAAATGATGAGGTGGAG 59.989 44.000 0.00 0.00 0.00 3.86
93 94 4.899457 ACGTAGGATAAATGATGAGGTGGA 59.101 41.667 0.00 0.00 0.00 4.02
94 95 4.991056 CACGTAGGATAAATGATGAGGTGG 59.009 45.833 0.00 0.00 0.00 4.61
95 96 4.991056 CCACGTAGGATAAATGATGAGGTG 59.009 45.833 0.00 0.00 41.22 4.00
96 97 4.503296 GCCACGTAGGATAAATGATGAGGT 60.503 45.833 8.04 0.00 41.22 3.85
97 98 3.997021 GCCACGTAGGATAAATGATGAGG 59.003 47.826 8.04 0.00 41.22 3.86
98 99 4.631131 TGCCACGTAGGATAAATGATGAG 58.369 43.478 8.04 0.00 41.22 2.90
99 100 4.681074 TGCCACGTAGGATAAATGATGA 57.319 40.909 8.04 0.00 41.22 2.92
100 101 5.702670 AGAATGCCACGTAGGATAAATGATG 59.297 40.000 8.04 0.00 41.22 3.07
101 102 5.869579 AGAATGCCACGTAGGATAAATGAT 58.130 37.500 8.04 0.00 41.22 2.45
102 103 5.290493 AGAATGCCACGTAGGATAAATGA 57.710 39.130 8.04 0.00 41.22 2.57
103 104 7.441157 TCTTAAGAATGCCACGTAGGATAAATG 59.559 37.037 1.68 0.00 41.22 2.32
104 105 7.506114 TCTTAAGAATGCCACGTAGGATAAAT 58.494 34.615 1.68 0.00 41.22 1.40
105 106 6.880484 TCTTAAGAATGCCACGTAGGATAAA 58.120 36.000 1.68 0.00 41.22 1.40
106 107 6.474140 TCTTAAGAATGCCACGTAGGATAA 57.526 37.500 1.68 0.00 41.22 1.75
107 108 6.665992 ATCTTAAGAATGCCACGTAGGATA 57.334 37.500 9.71 0.00 41.22 2.59
108 109 5.552870 ATCTTAAGAATGCCACGTAGGAT 57.447 39.130 9.71 0.00 41.22 3.24
109 110 5.831525 TCTATCTTAAGAATGCCACGTAGGA 59.168 40.000 9.71 0.00 41.22 2.94
110 111 6.085555 TCTATCTTAAGAATGCCACGTAGG 57.914 41.667 9.71 0.00 41.84 3.18
111 112 6.421202 GGTTCTATCTTAAGAATGCCACGTAG 59.579 42.308 9.71 4.38 37.78 3.51
112 113 6.127281 TGGTTCTATCTTAAGAATGCCACGTA 60.127 38.462 9.71 0.00 37.78 3.57
113 114 5.116882 GGTTCTATCTTAAGAATGCCACGT 58.883 41.667 9.71 0.00 37.78 4.49
114 115 5.116180 TGGTTCTATCTTAAGAATGCCACG 58.884 41.667 9.71 0.00 37.78 4.94
115 116 5.008118 GCTGGTTCTATCTTAAGAATGCCAC 59.992 44.000 9.71 3.30 37.78 5.01
116 117 5.104360 AGCTGGTTCTATCTTAAGAATGCCA 60.104 40.000 9.71 12.05 37.78 4.92
117 118 5.372373 AGCTGGTTCTATCTTAAGAATGCC 58.628 41.667 9.71 8.32 37.78 4.40
118 119 6.317391 ACAAGCTGGTTCTATCTTAAGAATGC 59.683 38.462 9.71 5.49 37.78 3.56
119 120 7.856145 ACAAGCTGGTTCTATCTTAAGAATG 57.144 36.000 9.71 5.56 37.78 2.67
120 121 7.554476 GGAACAAGCTGGTTCTATCTTAAGAAT 59.446 37.037 28.79 1.22 45.07 2.40
121 122 6.879458 GGAACAAGCTGGTTCTATCTTAAGAA 59.121 38.462 28.79 0.00 45.07 2.52
122 123 6.407202 GGAACAAGCTGGTTCTATCTTAAGA 58.593 40.000 28.79 7.82 45.07 2.10
123 124 5.292101 CGGAACAAGCTGGTTCTATCTTAAG 59.708 44.000 28.79 10.12 45.07 1.85
124 125 5.175859 CGGAACAAGCTGGTTCTATCTTAA 58.824 41.667 28.79 0.00 45.07 1.85
125 126 4.382685 CCGGAACAAGCTGGTTCTATCTTA 60.383 45.833 28.79 0.00 45.07 2.10
126 127 3.600388 CGGAACAAGCTGGTTCTATCTT 58.400 45.455 28.79 0.00 45.07 2.40
127 128 2.093447 CCGGAACAAGCTGGTTCTATCT 60.093 50.000 28.79 0.00 45.07 1.98
128 129 2.280628 CCGGAACAAGCTGGTTCTATC 58.719 52.381 28.79 14.56 45.07 2.08
129 130 1.628846 ACCGGAACAAGCTGGTTCTAT 59.371 47.619 28.79 14.64 45.15 1.98
130 131 1.053424 ACCGGAACAAGCTGGTTCTA 58.947 50.000 28.79 0.00 45.15 2.10
131 132 0.535102 CACCGGAACAAGCTGGTTCT 60.535 55.000 28.79 10.72 45.15 3.01
132 133 1.515521 CCACCGGAACAAGCTGGTTC 61.516 60.000 23.65 23.65 45.15 3.62
133 134 1.528309 CCACCGGAACAAGCTGGTT 60.528 57.895 9.46 6.07 45.15 3.67
135 136 1.966451 GACCACCGGAACAAGCTGG 60.966 63.158 9.46 5.84 40.29 4.85
136 137 1.966451 GGACCACCGGAACAAGCTG 60.966 63.158 9.46 0.00 0.00 4.24
137 138 2.430367 GGACCACCGGAACAAGCT 59.570 61.111 9.46 0.00 0.00 3.74
196 197 3.746792 AAAGGCTATGCTTCCCTCTTT 57.253 42.857 0.00 0.00 0.00 2.52
212 213 4.461198 CCCTACATTTACCAGGCTAAAGG 58.539 47.826 0.00 0.00 0.00 3.11
271 272 7.255836 CGGTCAACAGGTTCCTAATATGATCTA 60.256 40.741 0.00 0.00 0.00 1.98
592 602 1.160946 TTCTGCGGCTTTGCGTGTTA 61.161 50.000 0.00 0.00 37.81 2.41
688 699 2.811431 CCGGCTAGTTGACAAATGACAA 59.189 45.455 0.00 0.00 0.00 3.18
693 704 3.679083 GCTACTCCGGCTAGTTGACAAAT 60.679 47.826 8.58 0.00 0.00 2.32
694 705 2.353406 GCTACTCCGGCTAGTTGACAAA 60.353 50.000 8.58 0.00 0.00 2.83
730 741 1.525619 GAAGTACGTTGGTGCTGTCAC 59.474 52.381 0.00 0.00 39.20 3.67
736 747 0.168128 GCATGGAAGTACGTTGGTGC 59.832 55.000 0.00 0.00 0.00 5.01
738 749 0.398696 TGGCATGGAAGTACGTTGGT 59.601 50.000 0.00 0.00 0.00 3.67
757 768 0.461339 GCCGTGGACCGTCACAATAT 60.461 55.000 0.00 0.00 37.50 1.28
818 829 1.246737 GGCTGACCTTTTCTGGCCTG 61.247 60.000 3.32 2.92 41.40 4.85
1098 1132 0.527113 CAGCCATTGATTGCGGTTGA 59.473 50.000 0.00 0.00 33.21 3.18
1362 1417 0.460284 GGATGACGTCGTTGCCAGAT 60.460 55.000 12.40 0.00 0.00 2.90
1365 1420 2.047655 GGGATGACGTCGTTGCCA 60.048 61.111 19.57 0.00 0.00 4.92
1449 1504 2.112898 CATGACCTTCATGCTGGCC 58.887 57.895 0.00 0.00 46.37 5.36
1491 1546 1.299648 CATGGGTGAGGAAGGCGAA 59.700 57.895 0.00 0.00 0.00 4.70
1497 1558 2.356278 GCTGGCATGGGTGAGGAA 59.644 61.111 0.00 0.00 0.00 3.36
1617 1678 0.955428 GCGTTCAAGCCATGAGACCA 60.955 55.000 0.00 0.00 39.77 4.02
1655 1729 2.154854 ATAAGCTCATATGTGCGCGT 57.845 45.000 20.69 13.90 40.89 6.01
1690 1767 3.123804 CACCCGTGATAATGACTACAGC 58.876 50.000 0.00 0.00 0.00 4.40
1698 1777 7.905604 ATACATGTATTCACCCGTGATAATG 57.094 36.000 12.75 3.86 39.64 1.90
1855 1941 5.256806 ACTCTTAAAGTTAATGTGGCCCT 57.743 39.130 0.00 0.00 33.03 5.19
1895 1981 8.522830 GTGAGGATTTGATGGTAAAAAGATCAA 58.477 33.333 0.00 0.00 34.94 2.57
1933 2024 1.383386 GAGGAAGAGGGAGGGGGAC 60.383 68.421 0.00 0.00 0.00 4.46
1973 2066 5.753921 GGAGAATAGGCTATGTGTGTGTTAC 59.246 44.000 7.99 0.00 0.00 2.50
2155 2258 2.134354 TGACATGGCATCATTAGGGGA 58.866 47.619 0.00 0.00 0.00 4.81
2314 2420 4.162131 GGGTCAAATAATGTTGGGCTCAAT 59.838 41.667 0.27 0.00 35.10 2.57
2589 2695 2.207924 CGGGGGTAGGGGAATCTCG 61.208 68.421 0.00 0.00 0.00 4.04
2591 2697 2.289341 CCGGGGGTAGGGGAATCT 59.711 66.667 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.