Multiple sequence alignment - TraesCS7A01G565600

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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 TraesCS7A01G565600 chr7A 100.000 3357 0 0 1 3357 735167024 735170380 0.000000e+00 6200.0
1 TraesCS7A01G565600 chr7A 83.246 191 15 6 625 815 735038024 735037851 3.470000e-35 159.0
2 TraesCS7A01G565600 chr7B 90.639 1816 100 25 282 2072 744563363 744561593 0.000000e+00 2348.0
3 TraesCS7A01G565600 chr7B 97.127 1288 33 4 2073 3357 744561550 744560264 0.000000e+00 2170.0
4 TraesCS7A01G565600 chr7D 94.036 1157 61 7 2073 3225 632398108 632396956 0.000000e+00 1748.0
5 TraesCS7A01G565600 chr7D 86.700 1188 87 21 344 1501 632401124 632399978 0.000000e+00 1253.0
6 TraesCS7A01G565600 chr7D 93.567 171 5 6 1557 1725 632399695 632399529 2.000000e-62 250.0
7 TraesCS7A01G565600 chr7D 88.038 209 19 4 1865 2072 632398354 632398151 3.350000e-60 243.0
8 TraesCS7A01G565600 chr7D 86.826 167 9 4 186 345 632401518 632401358 1.240000e-39 174.0
9 TraesCS7A01G565600 chr7D 84.270 178 11 10 1744 1905 632399484 632399308 1.250000e-34 158.0
10 TraesCS7A01G565600 chr7D 97.368 38 1 0 74 111 632401588 632401551 7.770000e-07 65.8
11 TraesCS7A01G565600 chr4B 82.522 904 147 7 2073 2974 663105887 663106781 0.000000e+00 784.0
12 TraesCS7A01G565600 chr4B 82.822 489 70 7 990 1469 663102590 663103073 3.100000e-115 425.0
13 TraesCS7A01G565600 chr3B 83.678 821 126 6 2073 2890 11467197 11468012 0.000000e+00 767.0
14 TraesCS7A01G565600 chr3B 79.863 437 76 9 1007 1443 11466446 11466870 3.250000e-80 309.0
15 TraesCS7A01G565600 chr3D 80.811 740 134 6 2071 2807 9118140 9118874 1.040000e-159 573.0
16 TraesCS7A01G565600 chr3D 84.436 257 37 3 1187 1443 9117572 9117825 2.000000e-62 250.0
17 TraesCS7A01G565600 chr4A 77.536 138 31 0 1202 1339 685322234 685322097 2.150000e-12 84.2
18 TraesCS7A01G565600 chrUn 79.646 113 17 5 1202 1311 110785243 110785134 3.590000e-10 76.8


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 TraesCS7A01G565600 chr7A 735167024 735170380 3356 False 6200.000000 6200 100.0000 1 3357 1 chr7A.!!$F1 3356
1 TraesCS7A01G565600 chr7B 744560264 744563363 3099 True 2259.000000 2348 93.8830 282 3357 2 chr7B.!!$R1 3075
2 TraesCS7A01G565600 chr7D 632396956 632401588 4632 True 555.971429 1748 90.1150 74 3225 7 chr7D.!!$R1 3151
3 TraesCS7A01G565600 chr4B 663102590 663106781 4191 False 604.500000 784 82.6720 990 2974 2 chr4B.!!$F1 1984
4 TraesCS7A01G565600 chr3B 11466446 11468012 1566 False 538.000000 767 81.7705 1007 2890 2 chr3B.!!$F1 1883
5 TraesCS7A01G565600 chr3D 9117572 9118874 1302 False 411.500000 573 82.6235 1187 2807 2 chr3D.!!$F1 1620

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
673 923 0.179000 ATCATGTGGGGAGAAGACGC 59.821 55.0 0.00 0.00 0.00 5.19 F
825 1087 0.179067 TCTTGTCAACACGTGGACCC 60.179 55.0 21.57 5.57 33.09 4.46 F
835 1097 0.688418 ACGTGGACCCGGGATAATCA 60.688 55.0 32.02 14.36 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1623 3485 1.369091 CGCCCAGTGGTTGCATACTC 61.369 60.000 8.74 0.0 0.00 2.59 R
2258 6105 2.019984 GCCAAAGATGAAGAAGCGGAT 58.980 47.619 0.00 0.0 0.00 4.18 R
2609 6457 2.528673 TGCCATGAAATCCACCATGA 57.471 45.000 0.00 0.0 41.88 3.07 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
24 25 5.883661 AGTCCATATGCAATCAAAAACTCG 58.116 37.500 0.00 0.00 0.00 4.18
25 26 5.415701 AGTCCATATGCAATCAAAAACTCGT 59.584 36.000 0.00 0.00 0.00 4.18
26 27 6.597672 AGTCCATATGCAATCAAAAACTCGTA 59.402 34.615 0.00 0.00 0.00 3.43
27 28 7.283127 AGTCCATATGCAATCAAAAACTCGTAT 59.717 33.333 0.00 0.00 0.00 3.06
28 29 8.556194 GTCCATATGCAATCAAAAACTCGTATA 58.444 33.333 0.00 0.00 0.00 1.47
29 30 9.283768 TCCATATGCAATCAAAAACTCGTATAT 57.716 29.630 0.00 0.00 0.00 0.86
30 31 9.333497 CCATATGCAATCAAAAACTCGTATATG 57.667 33.333 0.00 0.00 0.00 1.78
31 32 9.882996 CATATGCAATCAAAAACTCGTATATGT 57.117 29.630 0.00 0.00 0.00 2.29
34 35 9.638239 ATGCAATCAAAAACTCGTATATGTTTT 57.362 25.926 0.00 0.00 44.91 2.43
36 37 9.937577 GCAATCAAAAACTCGTATATGTTTTTC 57.062 29.630 16.71 8.05 46.72 2.29
40 41 9.887406 TCAAAAACTCGTATATGTTTTTCCTTC 57.113 29.630 16.71 0.00 46.72 3.46
41 42 9.893305 CAAAAACTCGTATATGTTTTTCCTTCT 57.107 29.630 16.71 2.33 46.72 2.85
42 43 9.893305 AAAAACTCGTATATGTTTTTCCTTCTG 57.107 29.630 15.10 0.00 46.72 3.02
43 44 8.842358 AAACTCGTATATGTTTTTCCTTCTGA 57.158 30.769 0.00 0.00 33.21 3.27
44 45 8.842358 AACTCGTATATGTTTTTCCTTCTGAA 57.158 30.769 0.00 0.00 0.00 3.02
45 46 8.842358 ACTCGTATATGTTTTTCCTTCTGAAA 57.158 30.769 0.00 0.00 41.18 2.69
58 59 8.463930 TTTCCTTCTGAAAAACTGATGTATGT 57.536 30.769 0.00 0.00 39.98 2.29
59 60 9.567776 TTTCCTTCTGAAAAACTGATGTATGTA 57.432 29.630 0.00 0.00 39.98 2.29
60 61 8.547967 TCCTTCTGAAAAACTGATGTATGTAC 57.452 34.615 0.00 0.00 0.00 2.90
61 62 7.330946 TCCTTCTGAAAAACTGATGTATGTACG 59.669 37.037 0.00 0.00 0.00 3.67
62 63 7.117812 CCTTCTGAAAAACTGATGTATGTACGT 59.882 37.037 0.00 0.00 0.00 3.57
63 64 7.956420 TCTGAAAAACTGATGTATGTACGTT 57.044 32.000 0.00 0.00 0.00 3.99
64 65 8.373048 TCTGAAAAACTGATGTATGTACGTTT 57.627 30.769 0.00 0.00 0.00 3.60
65 66 8.279800 TCTGAAAAACTGATGTATGTACGTTTG 58.720 33.333 0.00 0.00 0.00 2.93
66 67 7.921787 TGAAAAACTGATGTATGTACGTTTGT 58.078 30.769 0.00 0.00 0.00 2.83
67 68 9.043079 TGAAAAACTGATGTATGTACGTTTGTA 57.957 29.630 0.00 0.00 0.00 2.41
114 115 8.702819 ACTTGTTAACAATACTATCTACTCCCC 58.297 37.037 20.83 0.00 35.02 4.81
115 116 8.849543 TTGTTAACAATACTATCTACTCCCCT 57.150 34.615 17.01 0.00 0.00 4.79
116 117 8.474710 TGTTAACAATACTATCTACTCCCCTC 57.525 38.462 5.64 0.00 0.00 4.30
117 118 8.287350 TGTTAACAATACTATCTACTCCCCTCT 58.713 37.037 5.64 0.00 0.00 3.69
118 119 9.145442 GTTAACAATACTATCTACTCCCCTCTT 57.855 37.037 0.00 0.00 0.00 2.85
119 120 9.725206 TTAACAATACTATCTACTCCCCTCTTT 57.275 33.333 0.00 0.00 0.00 2.52
121 122 8.709272 ACAATACTATCTACTCCCCTCTTTAC 57.291 38.462 0.00 0.00 0.00 2.01
122 123 7.729431 ACAATACTATCTACTCCCCTCTTTACC 59.271 40.741 0.00 0.00 0.00 2.85
123 124 5.745988 ACTATCTACTCCCCTCTTTACCA 57.254 43.478 0.00 0.00 0.00 3.25
124 125 5.456779 ACTATCTACTCCCCTCTTTACCAC 58.543 45.833 0.00 0.00 0.00 4.16
125 126 3.839323 TCTACTCCCCTCTTTACCACA 57.161 47.619 0.00 0.00 0.00 4.17
126 127 4.136341 TCTACTCCCCTCTTTACCACAA 57.864 45.455 0.00 0.00 0.00 3.33
127 128 4.695606 TCTACTCCCCTCTTTACCACAAT 58.304 43.478 0.00 0.00 0.00 2.71
128 129 5.845734 TCTACTCCCCTCTTTACCACAATA 58.154 41.667 0.00 0.00 0.00 1.90
129 130 4.838904 ACTCCCCTCTTTACCACAATAC 57.161 45.455 0.00 0.00 0.00 1.89
130 131 4.436079 ACTCCCCTCTTTACCACAATACT 58.564 43.478 0.00 0.00 0.00 2.12
131 132 4.850386 ACTCCCCTCTTTACCACAATACTT 59.150 41.667 0.00 0.00 0.00 2.24
132 133 5.174037 TCCCCTCTTTACCACAATACTTG 57.826 43.478 0.00 0.00 0.00 3.16
133 134 4.600111 TCCCCTCTTTACCACAATACTTGT 59.400 41.667 0.00 0.00 46.75 3.16
134 135 5.786457 TCCCCTCTTTACCACAATACTTGTA 59.214 40.000 0.00 0.00 43.23 2.41
135 136 6.070424 TCCCCTCTTTACCACAATACTTGTAG 60.070 42.308 0.00 0.00 43.23 2.74
136 137 5.585047 CCCTCTTTACCACAATACTTGTAGC 59.415 44.000 0.00 0.00 43.23 3.58
137 138 6.407202 CCTCTTTACCACAATACTTGTAGCT 58.593 40.000 0.00 0.00 43.23 3.32
138 139 6.313905 CCTCTTTACCACAATACTTGTAGCTG 59.686 42.308 0.00 0.00 43.23 4.24
139 140 6.170506 TCTTTACCACAATACTTGTAGCTGG 58.829 40.000 0.00 0.00 43.23 4.85
140 141 3.350219 ACCACAATACTTGTAGCTGGG 57.650 47.619 0.00 0.00 43.23 4.45
141 142 2.026262 ACCACAATACTTGTAGCTGGGG 60.026 50.000 0.00 10.59 43.23 4.96
142 143 2.643551 CACAATACTTGTAGCTGGGGG 58.356 52.381 0.00 0.00 43.23 5.40
143 144 2.238646 CACAATACTTGTAGCTGGGGGA 59.761 50.000 0.00 0.00 43.23 4.81
144 145 2.916934 ACAATACTTGTAGCTGGGGGAA 59.083 45.455 0.00 0.00 43.27 3.97
145 146 3.279434 CAATACTTGTAGCTGGGGGAAC 58.721 50.000 0.00 0.00 0.00 3.62
146 147 6.397977 ACAATACTTGTAGCTGGGGGAACC 62.398 50.000 0.00 0.00 46.76 3.62
171 172 8.925338 CCAGAGGGAGTACTTAATTACAATACT 58.075 37.037 0.00 3.30 35.59 2.12
246 252 6.942532 TTTGCAGGGCTAATATTAACTCTG 57.057 37.500 17.87 17.87 0.00 3.35
253 266 6.881602 AGGGCTAATATTAACTCTGCTAATGC 59.118 38.462 0.00 0.00 40.20 3.56
306 319 2.969950 TGCATTTACCCTCTACCGCTAT 59.030 45.455 0.00 0.00 0.00 2.97
342 590 4.116238 GTTCTGCTAGTTAGAGTGGATGC 58.884 47.826 0.00 0.00 0.00 3.91
348 596 5.163509 TGCTAGTTAGAGTGGATGCAGTTAG 60.164 44.000 0.00 0.00 0.00 2.34
378 626 0.396974 ACACTTGCCCACACCATGTT 60.397 50.000 0.00 0.00 0.00 2.71
380 628 0.752054 ACTTGCCCACACCATGTTTG 59.248 50.000 0.00 0.00 0.00 2.93
381 629 0.752054 CTTGCCCACACCATGTTTGT 59.248 50.000 0.00 0.00 0.00 2.83
448 698 4.289410 TGGTCAATGCTATATATGGTGCCT 59.711 41.667 0.00 0.00 0.00 4.75
449 699 5.487131 TGGTCAATGCTATATATGGTGCCTA 59.513 40.000 0.00 0.00 0.00 3.93
450 700 6.158520 TGGTCAATGCTATATATGGTGCCTAT 59.841 38.462 0.00 0.00 0.00 2.57
451 701 7.346960 TGGTCAATGCTATATATGGTGCCTATA 59.653 37.037 0.00 0.00 0.00 1.31
452 702 8.378565 GGTCAATGCTATATATGGTGCCTATAT 58.621 37.037 0.00 0.00 0.00 0.86
491 741 2.029244 GTGTCAAGTATCGGCAATGTCG 59.971 50.000 0.00 0.00 0.00 4.35
495 745 0.454600 AGTATCGGCAATGTCGTCGT 59.545 50.000 7.25 0.00 30.45 4.34
497 747 1.777461 GTATCGGCAATGTCGTCGTAC 59.223 52.381 7.25 5.87 30.45 3.67
498 748 0.454600 ATCGGCAATGTCGTCGTACT 59.545 50.000 7.25 0.00 30.45 2.73
499 749 0.179181 TCGGCAATGTCGTCGTACTC 60.179 55.000 7.25 0.00 30.45 2.59
500 750 0.179171 CGGCAATGTCGTCGTACTCT 60.179 55.000 0.00 0.00 0.00 3.24
501 751 1.546834 GGCAATGTCGTCGTACTCTC 58.453 55.000 0.00 0.00 0.00 3.20
502 752 1.546834 GCAATGTCGTCGTACTCTCC 58.453 55.000 0.00 0.00 0.00 3.71
503 753 1.135489 GCAATGTCGTCGTACTCTCCA 60.135 52.381 0.00 0.00 0.00 3.86
504 754 2.516923 CAATGTCGTCGTACTCTCCAC 58.483 52.381 0.00 0.00 0.00 4.02
505 755 2.110901 ATGTCGTCGTACTCTCCACT 57.889 50.000 0.00 0.00 0.00 4.00
516 766 3.359695 ACTCTCCACTCTCTCCACTAC 57.640 52.381 0.00 0.00 0.00 2.73
547 797 6.374333 GGCTTGATGACAGTTAAGGTTGAATA 59.626 38.462 0.00 0.00 0.00 1.75
567 817 6.828785 TGAATATTTTAGCAGAGGTTCCTTCC 59.171 38.462 0.00 0.00 0.00 3.46
589 839 1.077501 CGGGCAATGGTCTGGACAT 60.078 57.895 3.10 0.00 0.00 3.06
618 868 9.326413 GATTTGGGGAAGATATATATTACGTGG 57.674 37.037 0.00 0.00 0.00 4.94
619 869 6.229936 TGGGGAAGATATATATTACGTGGC 57.770 41.667 0.00 0.00 0.00 5.01
620 870 5.962031 TGGGGAAGATATATATTACGTGGCT 59.038 40.000 0.00 0.00 0.00 4.75
621 871 7.127405 TGGGGAAGATATATATTACGTGGCTA 58.873 38.462 0.00 0.00 0.00 3.93
622 872 7.287005 TGGGGAAGATATATATTACGTGGCTAG 59.713 40.741 0.00 0.00 0.00 3.42
635 885 0.400525 TGGCTAGGGGGATCCTTCAG 60.401 60.000 12.58 5.36 45.47 3.02
637 887 1.512735 GCTAGGGGGATCCTTCAGTT 58.487 55.000 12.58 0.00 45.47 3.16
638 888 2.690840 GCTAGGGGGATCCTTCAGTTA 58.309 52.381 12.58 0.00 45.47 2.24
641 891 1.082194 AGGGGGATCCTTCAGTTACCA 59.918 52.381 12.58 0.00 45.47 3.25
663 913 7.577303 ACCAAGCCTATATAATATCATGTGGG 58.423 38.462 0.00 0.00 0.00 4.61
673 923 0.179000 ATCATGTGGGGAGAAGACGC 59.821 55.000 0.00 0.00 0.00 5.19
718 968 2.365823 CGTGTCCGTTGGTTATCGG 58.634 57.895 0.00 0.00 46.93 4.18
724 974 0.722848 CCGTTGGTTATCGGGTTTCG 59.277 55.000 0.00 0.00 42.61 3.46
741 991 0.829990 TCGATGCATGCTTACTGGGA 59.170 50.000 20.33 3.83 0.00 4.37
760 1010 4.961099 TGGGAATAAATGAATGGCATGTGA 59.039 37.500 0.00 0.00 37.28 3.58
775 1025 4.802039 GGCATGTGAATCAACTTATTGCAG 59.198 41.667 0.00 0.00 35.63 4.41
776 1026 5.404946 GCATGTGAATCAACTTATTGCAGT 58.595 37.500 0.00 0.00 35.63 4.40
780 1031 6.804677 TGTGAATCAACTTATTGCAGTGTTT 58.195 32.000 0.00 0.00 35.63 2.83
788 1039 4.518970 ACTTATTGCAGTGTTTCGTTGGAT 59.481 37.500 0.00 0.00 0.00 3.41
813 1064 3.194861 GCATACTTGCGGTATCTTGTCA 58.805 45.455 0.05 0.00 38.92 3.58
814 1065 3.621268 GCATACTTGCGGTATCTTGTCAA 59.379 43.478 0.05 0.00 38.92 3.18
815 1066 4.494199 GCATACTTGCGGTATCTTGTCAAC 60.494 45.833 0.05 0.00 38.92 3.18
825 1087 0.179067 TCTTGTCAACACGTGGACCC 60.179 55.000 21.57 5.57 33.09 4.46
835 1097 0.688418 ACGTGGACCCGGGATAATCA 60.688 55.000 32.02 14.36 0.00 2.57
845 1107 1.334059 CGGGATAATCATGCAACACGC 60.334 52.381 0.00 0.00 42.89 5.34
889 1151 6.405176 GCAAAGCTGAAGCCTATAAATTGAGT 60.405 38.462 0.00 0.00 43.38 3.41
896 1158 6.599244 TGAAGCCTATAAATTGAGTGTCCTTG 59.401 38.462 0.00 0.00 0.00 3.61
957 1219 5.705905 ACATAAGTAGAAGAACAAACCAGCC 59.294 40.000 0.00 0.00 0.00 4.85
963 1225 2.664402 AGAACAAACCAGCCACTCAT 57.336 45.000 0.00 0.00 0.00 2.90
1042 1307 1.004918 AGAAAACCCGAGCTCGTGG 60.005 57.895 32.41 31.18 37.74 4.94
1044 1309 1.566018 GAAAACCCGAGCTCGTGGTG 61.566 60.000 34.80 23.23 40.80 4.17
1101 1366 2.537214 CTCCGACGTTGATGATGACATG 59.463 50.000 3.74 0.00 36.82 3.21
1183 1472 2.049433 CTGCCACTGCTGCAAAGC 60.049 61.111 3.02 7.50 38.46 3.51
1398 1687 4.015406 TTGTGCGAGGTGGGCGAT 62.015 61.111 0.00 0.00 0.00 4.58
1486 2772 7.038302 ACTCTTCACCTCATTATTCCACACTAA 60.038 37.037 0.00 0.00 0.00 2.24
1623 3485 6.313744 ACAACATTTTCTCTAAAAGGGTCG 57.686 37.500 0.00 0.00 39.95 4.79
1672 3534 4.082895 GGCCAATCAGATTCTACATGCATC 60.083 45.833 0.00 0.00 0.00 3.91
1988 5789 2.486592 AGCCACCGCTTTACAACATTAC 59.513 45.455 0.00 0.00 45.55 1.89
2203 6050 2.603075 TTGTGGGATTCCTCCAAAGG 57.397 50.000 2.01 0.00 44.08 3.11
2258 6105 1.376683 CCGCCGGAAGAAATGGTCA 60.377 57.895 5.05 0.00 0.00 4.02
2439 6287 6.064717 GGGCCTAATGTTCTCTATGAATGTT 58.935 40.000 0.84 0.00 36.99 2.71
2464 6312 4.424711 GTGGGAAGCGCCATGGGA 62.425 66.667 15.13 0.00 38.95 4.37
2609 6457 2.102420 TGACAGACGACAACATGGAGTT 59.898 45.455 0.00 0.00 42.42 3.01
2976 6824 2.962142 TAAACCCCGGCGCACAAGTT 62.962 55.000 10.83 4.34 0.00 2.66
3185 7034 7.013369 TCTGCTTTAAAGAAGGAAGGAAAGAAC 59.987 37.037 21.01 0.00 32.18 3.01
3231 7082 1.955778 CAACTGATTTGGCACACCTCA 59.044 47.619 0.00 0.00 39.29 3.86
3247 7098 4.079730 ACACCTCAAAGGAAAGAAGGAAGT 60.080 41.667 0.00 0.00 37.67 3.01
3271 7122 3.118531 AGAGATGGGAGTAAATGGCAGT 58.881 45.455 0.00 0.00 0.00 4.40
3303 7154 5.356470 TCATGTATGTTTTGGCATGATTCGA 59.644 36.000 0.00 0.00 41.60 3.71
3351 7202 1.674651 GGAACAGCCTTCGAACCCC 60.675 63.158 0.00 0.00 0.00 4.95
3352 7203 2.032071 AACAGCCTTCGAACCCCG 59.968 61.111 0.00 0.00 40.25 5.73
3353 7204 2.444700 GAACAGCCTTCGAACCCCGA 62.445 60.000 0.00 0.00 46.94 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.415701 ACGAGTTTTTGATTGCATATGGACT 59.584 36.000 4.56 0.00 0.00 3.85
2 3 5.640732 ACGAGTTTTTGATTGCATATGGAC 58.359 37.500 4.56 0.00 0.00 4.02
4 5 9.333497 CATATACGAGTTTTTGATTGCATATGG 57.667 33.333 4.56 0.00 0.00 2.74
5 6 9.882996 ACATATACGAGTTTTTGATTGCATATG 57.117 29.630 0.00 0.00 0.00 1.78
17 18 9.280174 TCAGAAGGAAAAACATATACGAGTTTT 57.720 29.630 0.00 0.00 46.53 2.43
18 19 8.842358 TCAGAAGGAAAAACATATACGAGTTT 57.158 30.769 0.00 0.00 39.46 2.66
19 20 8.842358 TTCAGAAGGAAAAACATATACGAGTT 57.158 30.769 0.00 0.00 30.98 3.01
20 21 8.842358 TTTCAGAAGGAAAAACATATACGAGT 57.158 30.769 0.00 0.00 42.37 4.18
33 34 8.463930 ACATACATCAGTTTTTCAGAAGGAAA 57.536 30.769 0.00 0.00 43.59 3.13
34 35 8.999431 GTACATACATCAGTTTTTCAGAAGGAA 58.001 33.333 0.00 0.00 0.00 3.36
35 36 7.330946 CGTACATACATCAGTTTTTCAGAAGGA 59.669 37.037 0.00 0.00 0.00 3.36
36 37 7.117812 ACGTACATACATCAGTTTTTCAGAAGG 59.882 37.037 0.00 0.00 0.00 3.46
37 38 8.018677 ACGTACATACATCAGTTTTTCAGAAG 57.981 34.615 0.00 0.00 0.00 2.85
38 39 7.956420 ACGTACATACATCAGTTTTTCAGAA 57.044 32.000 0.00 0.00 0.00 3.02
39 40 7.956420 AACGTACATACATCAGTTTTTCAGA 57.044 32.000 0.00 0.00 0.00 3.27
40 41 8.067784 ACAAACGTACATACATCAGTTTTTCAG 58.932 33.333 0.00 0.00 30.56 3.02
41 42 7.921787 ACAAACGTACATACATCAGTTTTTCA 58.078 30.769 0.00 0.00 30.56 2.69
72 73 9.952188 TGTTAACAAGTAGATCGATGAAGATAG 57.048 33.333 5.64 0.00 0.00 2.08
105 106 3.839323 TGTGGTAAAGAGGGGAGTAGA 57.161 47.619 0.00 0.00 0.00 2.59
107 108 5.596763 AGTATTGTGGTAAAGAGGGGAGTA 58.403 41.667 0.00 0.00 0.00 2.59
108 109 4.436079 AGTATTGTGGTAAAGAGGGGAGT 58.564 43.478 0.00 0.00 0.00 3.85
109 110 5.186198 CAAGTATTGTGGTAAAGAGGGGAG 58.814 45.833 0.00 0.00 42.34 4.30
110 111 5.174037 CAAGTATTGTGGTAAAGAGGGGA 57.826 43.478 0.00 0.00 42.34 4.81
124 125 6.396762 TGGTTCCCCCAGCTACAAGTATTG 62.397 50.000 0.00 0.00 45.89 1.90
125 126 2.241430 GGTTCCCCCAGCTACAAGTATT 59.759 50.000 0.00 0.00 0.00 1.89
126 127 1.844497 GGTTCCCCCAGCTACAAGTAT 59.156 52.381 0.00 0.00 0.00 2.12
127 128 1.282382 GGTTCCCCCAGCTACAAGTA 58.718 55.000 0.00 0.00 0.00 2.24
128 129 0.770557 TGGTTCCCCCAGCTACAAGT 60.771 55.000 0.00 0.00 38.72 3.16
129 130 2.074967 TGGTTCCCCCAGCTACAAG 58.925 57.895 0.00 0.00 38.72 3.16
130 131 4.341199 TGGTTCCCCCAGCTACAA 57.659 55.556 0.00 0.00 38.72 2.41
137 138 1.457380 TACTCCCTCTGGTTCCCCCA 61.457 60.000 0.00 0.00 42.51 4.96
138 139 0.981801 GTACTCCCTCTGGTTCCCCC 60.982 65.000 0.00 0.00 0.00 5.40
139 140 0.042881 AGTACTCCCTCTGGTTCCCC 59.957 60.000 0.00 0.00 0.00 4.81
140 141 1.954035 AAGTACTCCCTCTGGTTCCC 58.046 55.000 0.00 0.00 0.00 3.97
141 142 5.695424 AATTAAGTACTCCCTCTGGTTCC 57.305 43.478 0.00 0.00 0.00 3.62
142 143 7.179076 TGTAATTAAGTACTCCCTCTGGTTC 57.821 40.000 13.68 0.00 0.00 3.62
143 144 7.563724 TTGTAATTAAGTACTCCCTCTGGTT 57.436 36.000 13.68 0.00 0.00 3.67
144 145 7.750947 ATTGTAATTAAGTACTCCCTCTGGT 57.249 36.000 13.68 0.00 0.00 4.00
145 146 8.925338 AGTATTGTAATTAAGTACTCCCTCTGG 58.075 37.037 13.68 0.00 0.00 3.86
171 172 7.884877 AGAGGTCAAAATTGTTGATGATCTGTA 59.115 33.333 0.00 0.00 33.56 2.74
175 176 6.810182 CCAAGAGGTCAAAATTGTTGATGATC 59.190 38.462 0.00 0.00 0.00 2.92
177 178 5.832595 TCCAAGAGGTCAAAATTGTTGATGA 59.167 36.000 0.00 0.00 35.89 2.92
178 179 6.088016 TCCAAGAGGTCAAAATTGTTGATG 57.912 37.500 0.00 0.00 35.89 3.07
179 180 6.239402 CCTTCCAAGAGGTCAAAATTGTTGAT 60.239 38.462 0.00 0.00 35.89 2.57
180 181 5.068987 CCTTCCAAGAGGTCAAAATTGTTGA 59.931 40.000 0.00 0.00 35.89 3.18
181 182 5.291971 CCTTCCAAGAGGTCAAAATTGTTG 58.708 41.667 0.00 0.00 35.89 3.33
182 183 5.535753 CCTTCCAAGAGGTCAAAATTGTT 57.464 39.130 0.00 0.00 35.89 2.83
218 224 8.078060 AGTTAATATTAGCCCTGCAAAATTGT 57.922 30.769 5.77 0.00 0.00 2.71
253 266 4.352039 CGCCGGTATAGAAGCAGTATATG 58.648 47.826 1.90 0.00 0.00 1.78
255 268 2.751259 CCGCCGGTATAGAAGCAGTATA 59.249 50.000 1.90 0.00 0.00 1.47
263 276 0.675633 GTTAGCCCGCCGGTATAGAA 59.324 55.000 1.90 0.00 0.00 2.10
264 277 1.181098 GGTTAGCCCGCCGGTATAGA 61.181 60.000 1.90 0.00 0.00 1.98
348 596 2.265683 GGGCAAGTGTACTAGTTACGC 58.734 52.381 0.00 4.43 40.95 4.42
350 598 3.992427 GTGTGGGCAAGTGTACTAGTTAC 59.008 47.826 0.00 0.90 0.00 2.50
448 698 8.935614 ACACAGTGTCTTAGGTGCTATATATA 57.064 34.615 0.00 0.00 34.69 0.86
449 699 7.841282 ACACAGTGTCTTAGGTGCTATATAT 57.159 36.000 0.00 0.00 34.69 0.86
450 700 7.273320 GACACAGTGTCTTAGGTGCTATATA 57.727 40.000 24.23 0.00 43.73 0.86
451 701 6.150396 GACACAGTGTCTTAGGTGCTATAT 57.850 41.667 24.23 0.00 43.73 0.86
452 702 5.578005 GACACAGTGTCTTAGGTGCTATA 57.422 43.478 24.23 0.00 43.73 1.31
479 729 0.454600 AGTACGACGACATTGCCGAT 59.545 50.000 0.00 0.00 0.00 4.18
491 741 2.282407 GGAGAGAGTGGAGAGTACGAC 58.718 57.143 0.00 0.00 0.00 4.34
495 745 3.118702 CGTAGTGGAGAGAGTGGAGAGTA 60.119 52.174 0.00 0.00 0.00 2.59
497 747 2.285083 CGTAGTGGAGAGAGTGGAGAG 58.715 57.143 0.00 0.00 0.00 3.20
498 748 1.065345 CCGTAGTGGAGAGAGTGGAGA 60.065 57.143 0.00 0.00 42.00 3.71
499 749 1.065345 TCCGTAGTGGAGAGAGTGGAG 60.065 57.143 0.00 0.00 43.74 3.86
500 750 0.989602 TCCGTAGTGGAGAGAGTGGA 59.010 55.000 0.00 0.00 43.74 4.02
501 751 3.571748 TCCGTAGTGGAGAGAGTGG 57.428 57.895 0.00 0.00 43.74 4.00
516 766 0.036010 ACTGTCATCAAGCCCTTCCG 60.036 55.000 0.00 0.00 0.00 4.30
547 797 3.333680 TGGGAAGGAACCTCTGCTAAAAT 59.666 43.478 0.00 0.00 0.00 1.82
567 817 3.136123 CAGACCATTGCCCGCTGG 61.136 66.667 0.00 0.00 38.55 4.85
611 861 0.761702 GGATCCCCCTAGCCACGTAA 60.762 60.000 0.00 0.00 0.00 3.18
612 862 1.152398 GGATCCCCCTAGCCACGTA 60.152 63.158 0.00 0.00 0.00 3.57
613 863 2.446036 GGATCCCCCTAGCCACGT 60.446 66.667 0.00 0.00 0.00 4.49
614 864 2.122813 AGGATCCCCCTAGCCACG 60.123 66.667 8.55 0.00 45.48 4.94
619 869 3.632645 TGGTAACTGAAGGATCCCCCTAG 60.633 52.174 8.55 4.77 41.02 3.02
620 870 2.319747 TGGTAACTGAAGGATCCCCCTA 59.680 50.000 8.55 0.00 41.02 3.53
621 871 1.082194 TGGTAACTGAAGGATCCCCCT 59.918 52.381 8.55 0.00 43.18 4.79
622 872 1.591768 TGGTAACTGAAGGATCCCCC 58.408 55.000 8.55 0.49 37.61 5.40
637 887 8.713971 CCCACATGATATTATATAGGCTTGGTA 58.286 37.037 0.00 0.00 0.00 3.25
638 888 7.366823 CCCCACATGATATTATATAGGCTTGGT 60.367 40.741 0.00 0.00 0.00 3.67
641 891 7.851451 TCTCCCCACATGATATTATATAGGCTT 59.149 37.037 0.00 0.00 0.00 4.35
673 923 0.798776 CACCTAGCAGGCAACGAAAG 59.201 55.000 0.00 0.00 39.63 2.62
718 968 2.223340 CCAGTAAGCATGCATCGAAACC 60.223 50.000 21.98 0.00 0.00 3.27
724 974 5.772825 TTTATTCCCAGTAAGCATGCATC 57.227 39.130 21.98 9.49 0.00 3.91
728 978 7.149973 CCATTCATTTATTCCCAGTAAGCATG 58.850 38.462 0.00 0.00 0.00 4.06
729 979 6.239402 GCCATTCATTTATTCCCAGTAAGCAT 60.239 38.462 0.00 0.00 0.00 3.79
730 980 5.068987 GCCATTCATTTATTCCCAGTAAGCA 59.931 40.000 0.00 0.00 0.00 3.91
741 991 8.262227 AGTTGATTCACATGCCATTCATTTATT 58.738 29.630 0.00 0.00 31.79 1.40
760 1010 6.072112 ACGAAACACTGCAATAAGTTGATT 57.928 33.333 0.00 0.00 37.53 2.57
775 1025 2.483583 TGCAACATCCAACGAAACAC 57.516 45.000 0.00 0.00 0.00 3.32
776 1026 3.818210 AGTATGCAACATCCAACGAAACA 59.182 39.130 0.00 0.00 0.00 2.83
813 1064 1.193462 TTATCCCGGGTCCACGTGTT 61.193 55.000 22.86 0.00 0.00 3.32
814 1065 0.979187 ATTATCCCGGGTCCACGTGT 60.979 55.000 22.86 0.19 0.00 4.49
815 1066 0.249741 GATTATCCCGGGTCCACGTG 60.250 60.000 22.86 9.08 0.00 4.49
825 1087 1.334059 GCGTGTTGCATGATTATCCCG 60.334 52.381 0.00 0.00 45.45 5.14
845 1107 0.996462 CTGCAAAAGCATTCGCCATG 59.004 50.000 0.00 0.00 39.83 3.66
846 1108 3.429043 CTGCAAAAGCATTCGCCAT 57.571 47.368 0.00 0.00 39.83 4.40
889 1151 0.463654 GTGGATATGGCGCAAGGACA 60.464 55.000 10.83 0.00 38.71 4.02
896 1158 1.265095 CTTGTCATGTGGATATGGCGC 59.735 52.381 0.00 0.00 35.46 6.53
957 1219 3.217599 AGTGTAGTGCGTACATGAGTG 57.782 47.619 6.38 0.00 43.70 3.51
963 1225 1.129251 GCGTCTAGTGTAGTGCGTACA 59.871 52.381 6.38 0.00 39.47 2.90
1101 1366 4.301505 TGCAGAAATCGCAGGTCC 57.698 55.556 0.00 0.00 33.55 4.46
1163 1452 4.591399 TTGCAGCAGTGGCAGGCT 62.591 61.111 7.71 7.71 43.05 4.58
1183 1472 2.990479 AAGGGCCGCCTTGACTAG 59.010 61.111 9.86 0.00 0.00 2.57
1356 1645 1.498865 CTTCGATGCATGGGTACGGC 61.499 60.000 2.46 0.00 0.00 5.68
1369 1658 2.061773 CTCGCACAACAGTTCTTCGAT 58.938 47.619 0.00 0.00 0.00 3.59
1398 1687 2.414612 ACTCCAACAACAACCCTAGGA 58.585 47.619 11.48 0.00 0.00 2.94
1610 3472 4.386867 TGCATACTCGACCCTTTTAGAG 57.613 45.455 0.00 0.00 36.83 2.43
1623 3485 1.369091 CGCCCAGTGGTTGCATACTC 61.369 60.000 8.74 0.00 0.00 2.59
1809 4604 9.575868 TGGTTTTCTTTGGTATTGTAGATGTTA 57.424 29.630 0.00 0.00 0.00 2.41
2203 6050 2.671619 TTGCCGGTGCTGCCTAAC 60.672 61.111 1.90 0.00 38.71 2.34
2258 6105 2.019984 GCCAAAGATGAAGAAGCGGAT 58.980 47.619 0.00 0.00 0.00 4.18
2358 6206 3.049674 CAACGCCACATGACCGCT 61.050 61.111 0.00 0.00 0.00 5.52
2609 6457 2.528673 TGCCATGAAATCCACCATGA 57.471 45.000 0.00 0.00 41.88 3.07
3102 6951 3.058983 GCCCAAAAGCAAGTGCAAATTAC 60.059 43.478 6.00 0.00 45.16 1.89
3231 7082 7.310983 CCATCTCTCTACTTCCTTCTTTCCTTT 60.311 40.741 0.00 0.00 0.00 3.11
3247 7098 4.556697 TGCCATTTACTCCCATCTCTCTA 58.443 43.478 0.00 0.00 0.00 2.43
3271 7122 4.455533 GCCAAAACATACATGACTCACTCA 59.544 41.667 0.00 0.00 0.00 3.41
3303 7154 5.680619 TCCGGTAACTATGAAGCAAATGAT 58.319 37.500 0.00 0.00 0.00 2.45
3311 7162 3.736252 CAGCGAATCCGGTAACTATGAAG 59.264 47.826 0.00 0.00 45.57 3.02


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

AutoCloner maintained by Alex Coulton.