Multiple sequence alignment - TraesCS7D01G188300

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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 TraesCS7D01G188300 chr7D 100.000 4791 0 0 1 4791 140806926 140802136 0.000000e+00 8848.0
1 TraesCS7D01G188300 chr7D 92.188 64 5 0 3636 3699 511117079 511117016 1.840000e-14 91.6
2 TraesCS7D01G188300 chr7D 92.982 57 3 1 241 296 582130435 582130379 1.110000e-11 82.4
3 TraesCS7D01G188300 chr7A 94.891 4463 151 28 77 4507 142987081 142982664 0.000000e+00 6907.0
4 TraesCS7D01G188300 chr7A 94.915 59 2 1 240 297 398270164 398270222 1.840000e-14 91.6
5 TraesCS7D01G188300 chr7B 95.697 4253 130 19 552 4786 105884858 105880641 0.000000e+00 6791.0
6 TraesCS7D01G188300 chr6A 77.660 1231 213 40 1072 2278 541229219 541228027 0.000000e+00 693.0
7 TraesCS7D01G188300 chr6A 91.525 59 3 2 238 295 492096236 492096179 3.970000e-11 80.5
8 TraesCS7D01G188300 chr6D 77.713 1198 206 40 1072 2246 394724180 394725339 0.000000e+00 676.0
9 TraesCS7D01G188300 chr6D 88.487 304 34 1 3441 3744 73792611 73792913 2.720000e-97 366.0
10 TraesCS7D01G188300 chr6D 95.745 47 0 2 238 283 351233433 351233478 1.850000e-09 75.0
11 TraesCS7D01G188300 chr6B 77.483 1208 213 40 1071 2256 590913622 590912452 0.000000e+00 669.0
12 TraesCS7D01G188300 chr6B 90.000 60 2 3 302 357 228695799 228695858 1.850000e-09 75.0
13 TraesCS7D01G188300 chr5B 80.137 584 71 27 3450 4019 2053846 2053294 1.250000e-105 394.0
14 TraesCS7D01G188300 chr5B 84.507 71 7 4 298 364 27316303 27316233 3.090000e-07 67.6
15 TraesCS7D01G188300 chr2D 79.664 595 74 30 3447 4028 81653498 81654058 7.520000e-103 385.0
16 TraesCS7D01G188300 chr1B 85.849 212 20 5 3441 3652 577972142 577972343 2.900000e-52 217.0
17 TraesCS7D01G188300 chr1B 87.097 62 4 3 298 355 177835830 177835891 3.090000e-07 67.6
18 TraesCS7D01G188300 chr5D 84.651 215 23 4 3441 3655 277314234 277314030 6.290000e-49 206.0
19 TraesCS7D01G188300 chr5D 97.917 48 1 0 244 291 371443544 371443497 3.070000e-12 84.2
20 TraesCS7D01G188300 chr4A 94.340 53 0 2 296 345 714441670 714441618 1.430000e-10 78.7
21 TraesCS7D01G188300 chr4A 91.228 57 3 2 240 295 52607347 52607292 5.140000e-10 76.8
22 TraesCS7D01G188300 chr3D 89.062 64 3 4 295 355 475546255 475546317 5.140000e-10 76.8
23 TraesCS7D01G188300 chr3D 91.071 56 2 3 298 350 333287704 333287649 6.650000e-09 73.1
24 TraesCS7D01G188300 chr2A 91.228 57 4 1 240 295 670457897 670457841 5.140000e-10 76.8
25 TraesCS7D01G188300 chr1A 91.071 56 4 1 240 295 513494406 513494460 1.850000e-09 75.0
26 TraesCS7D01G188300 chrUn 90.909 55 2 3 299 350 243337327 243337273 2.390000e-08 71.3
27 TraesCS7D01G188300 chrUn 90.909 55 2 3 299 350 248708732 248708678 2.390000e-08 71.3


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 TraesCS7D01G188300 chr7D 140802136 140806926 4790 True 8848 8848 100.000 1 4791 1 chr7D.!!$R1 4790
1 TraesCS7D01G188300 chr7A 142982664 142987081 4417 True 6907 6907 94.891 77 4507 1 chr7A.!!$R1 4430
2 TraesCS7D01G188300 chr7B 105880641 105884858 4217 True 6791 6791 95.697 552 4786 1 chr7B.!!$R1 4234
3 TraesCS7D01G188300 chr6A 541228027 541229219 1192 True 693 693 77.660 1072 2278 1 chr6A.!!$R2 1206
4 TraesCS7D01G188300 chr6D 394724180 394725339 1159 False 676 676 77.713 1072 2246 1 chr6D.!!$F3 1174
5 TraesCS7D01G188300 chr6B 590912452 590913622 1170 True 669 669 77.483 1071 2256 1 chr6B.!!$R1 1185
6 TraesCS7D01G188300 chr5B 2053294 2053846 552 True 394 394 80.137 3450 4019 1 chr5B.!!$R1 569
7 TraesCS7D01G188300 chr2D 81653498 81654058 560 False 385 385 79.664 3447 4028 1 chr2D.!!$F1 581

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
690 701 0.321122 CGGCAAGCCTCTTCTCACTT 60.321 55.0 9.73 0.0 0.00 3.16 F
1024 1038 0.106619 CTACTCGGCTACTCCCCAGT 60.107 60.0 0.00 0.0 36.55 4.00 F
1309 1327 1.599606 GCAGTCGCTCTCCTTCTCCA 61.600 60.0 0.00 0.0 34.30 3.86 F
2807 2851 0.806868 CAATGGATGTGCTCACGCTT 59.193 50.0 0.00 0.0 36.97 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2441 2485 4.215613 CCATGATGAGCATAATGACAGTGG 59.784 45.833 9.01 0.0 34.82 4.00 R
2522 2566 6.035843 CCAAGATAAATGATGTTTGGGAACG 58.964 40.000 0.00 0.0 38.65 3.95 R
3093 3146 3.820557 AGGCCATACCACATACAACATC 58.179 45.455 5.01 0.0 43.14 3.06 R
4448 4523 0.877071 AAGTCAGCAAGCAATGGACG 59.123 50.000 0.00 0.0 33.84 4.79 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
28 29 8.970691 AGAAAAATGATTTCACTACAAATCGG 57.029 30.769 4.01 0.00 43.19 4.18
29 30 8.792633 AGAAAAATGATTTCACTACAAATCGGA 58.207 29.630 4.01 0.00 43.19 4.55
30 31 9.573133 GAAAAATGATTTCACTACAAATCGGAT 57.427 29.630 0.00 0.00 43.19 4.18
31 32 8.915871 AAAATGATTTCACTACAAATCGGATG 57.084 30.769 0.00 0.00 43.19 3.51
32 33 7.630242 AATGATTTCACTACAAATCGGATGT 57.370 32.000 0.00 0.00 43.19 3.06
33 34 6.662414 TGATTTCACTACAAATCGGATGTC 57.338 37.500 0.00 0.00 43.19 3.06
34 35 6.169800 TGATTTCACTACAAATCGGATGTCA 58.830 36.000 0.00 0.00 43.19 3.58
35 36 6.313658 TGATTTCACTACAAATCGGATGTCAG 59.686 38.462 0.00 0.00 43.19 3.51
36 37 5.400066 TTCACTACAAATCGGATGTCAGA 57.600 39.130 0.00 0.00 32.27 3.27
37 38 5.598416 TCACTACAAATCGGATGTCAGAT 57.402 39.130 0.00 0.00 32.22 2.90
38 39 5.977635 TCACTACAAATCGGATGTCAGATT 58.022 37.500 3.08 3.08 41.35 2.40
39 40 6.406370 TCACTACAAATCGGATGTCAGATTT 58.594 36.000 13.09 13.09 46.44 2.17
40 41 6.878923 TCACTACAAATCGGATGTCAGATTTT 59.121 34.615 15.33 10.94 44.34 1.82
41 42 7.390440 TCACTACAAATCGGATGTCAGATTTTT 59.610 33.333 15.33 12.79 44.34 1.94
42 43 8.664798 CACTACAAATCGGATGTCAGATTTTTA 58.335 33.333 15.33 13.13 44.34 1.52
43 44 9.226606 ACTACAAATCGGATGTCAGATTTTTAA 57.773 29.630 15.33 6.38 44.34 1.52
44 45 9.708222 CTACAAATCGGATGTCAGATTTTTAAG 57.292 33.333 15.33 10.58 44.34 1.85
45 46 7.029563 ACAAATCGGATGTCAGATTTTTAAGC 58.970 34.615 15.33 0.00 44.34 3.09
46 47 6.757897 AATCGGATGTCAGATTTTTAAGCA 57.242 33.333 3.08 0.00 37.46 3.91
47 48 6.949352 ATCGGATGTCAGATTTTTAAGCAT 57.051 33.333 0.00 0.00 0.00 3.79
48 49 6.122850 TCGGATGTCAGATTTTTAAGCATG 57.877 37.500 0.00 0.00 0.00 4.06
49 50 4.736793 CGGATGTCAGATTTTTAAGCATGC 59.263 41.667 10.51 10.51 0.00 4.06
50 51 5.045872 GGATGTCAGATTTTTAAGCATGCC 58.954 41.667 15.66 0.00 0.00 4.40
51 52 5.394443 GGATGTCAGATTTTTAAGCATGCCA 60.394 40.000 15.66 0.00 0.00 4.92
52 53 5.465532 TGTCAGATTTTTAAGCATGCCAA 57.534 34.783 15.66 6.11 0.00 4.52
53 54 5.851720 TGTCAGATTTTTAAGCATGCCAAA 58.148 33.333 15.66 12.43 0.00 3.28
54 55 6.465948 TGTCAGATTTTTAAGCATGCCAAAT 58.534 32.000 15.66 13.50 0.00 2.32
55 56 6.591062 TGTCAGATTTTTAAGCATGCCAAATC 59.409 34.615 22.60 22.60 35.11 2.17
56 57 6.591062 GTCAGATTTTTAAGCATGCCAAATCA 59.409 34.615 27.24 15.40 36.64 2.57
57 58 7.118101 GTCAGATTTTTAAGCATGCCAAATCAA 59.882 33.333 27.24 18.81 36.64 2.57
58 59 7.660617 TCAGATTTTTAAGCATGCCAAATCAAA 59.339 29.630 27.24 18.60 36.64 2.69
59 60 8.455682 CAGATTTTTAAGCATGCCAAATCAAAT 58.544 29.630 27.24 19.37 36.64 2.32
60 61 8.455682 AGATTTTTAAGCATGCCAAATCAAATG 58.544 29.630 27.24 0.00 36.64 2.32
61 62 7.741027 TTTTTAAGCATGCCAAATCAAATGA 57.259 28.000 15.66 0.00 0.00 2.57
62 63 7.925043 TTTTAAGCATGCCAAATCAAATGAT 57.075 28.000 15.66 0.00 36.07 2.45
63 64 7.925043 TTTAAGCATGCCAAATCAAATGATT 57.075 28.000 15.66 2.83 45.91 2.57
117 118 1.147473 GCCAAAATTTCCCGTGCTTG 58.853 50.000 0.00 0.00 0.00 4.01
131 132 2.088969 CGTGCTTGCTAAACGAAATTGC 59.911 45.455 0.00 0.00 39.64 3.56
133 134 2.035193 TGCTTGCTAAACGAAATTGCCA 59.965 40.909 0.00 0.00 0.00 4.92
138 139 2.477863 GCTAAACGAAATTGCCATCGCT 60.478 45.455 0.00 0.00 42.61 4.93
139 140 2.723124 AAACGAAATTGCCATCGCTT 57.277 40.000 0.00 0.00 42.61 4.68
140 141 1.981254 AACGAAATTGCCATCGCTTG 58.019 45.000 0.00 0.00 42.61 4.01
157 158 3.376859 CGCTTGGATAACATAACTTGCCA 59.623 43.478 0.00 0.00 0.00 4.92
188 189 6.705825 AGTTTTGATTTGTCATGCTTTAACCC 59.294 34.615 0.00 0.00 0.00 4.11
207 208 9.765795 TTTAACCCGTGATGAATTTTTAACATT 57.234 25.926 0.00 0.00 0.00 2.71
208 209 7.650834 AACCCGTGATGAATTTTTAACATTG 57.349 32.000 0.00 0.00 0.00 2.82
209 210 6.987386 ACCCGTGATGAATTTTTAACATTGA 58.013 32.000 0.00 0.00 0.00 2.57
244 245 9.833917 AATTAGATACTTGGTTTTAGCTACTCC 57.166 33.333 0.00 0.00 0.00 3.85
245 246 8.605325 TTAGATACTTGGTTTTAGCTACTCCT 57.395 34.615 0.00 0.00 0.00 3.69
249 250 2.532843 TGGTTTTAGCTACTCCTCCGT 58.467 47.619 0.00 0.00 0.00 4.69
339 343 5.970501 ATTTAGGAACGGAGGGAGTATTT 57.029 39.130 0.00 0.00 0.00 1.40
380 384 9.321562 AGATGATTAACCAATGATGAATTTTGC 57.678 29.630 0.00 0.00 0.00 3.68
381 385 7.846644 TGATTAACCAATGATGAATTTTGCC 57.153 32.000 0.00 0.00 0.00 4.52
410 414 3.744940 AGATCATCAGGAGGGCAAAAA 57.255 42.857 0.00 0.00 0.00 1.94
411 415 3.629087 AGATCATCAGGAGGGCAAAAAG 58.371 45.455 0.00 0.00 0.00 2.27
501 507 4.638865 ACCAAACTGTTAAGCCGATAATCC 59.361 41.667 0.00 0.00 0.00 3.01
514 520 4.095782 GCCGATAATCCACTGCAACTAAAA 59.904 41.667 0.00 0.00 0.00 1.52
521 527 3.876914 TCCACTGCAACTAAAACACAGAG 59.123 43.478 0.00 0.00 32.67 3.35
533 539 6.831868 ACTAAAACACAGAGGCCTAAAGAAAA 59.168 34.615 4.42 0.00 0.00 2.29
592 599 8.468399 TGTCGACACTAAATTTTAAACCCTTTT 58.532 29.630 15.76 0.00 0.00 2.27
636 646 5.641209 GTGATACTGGAATATCAGCATGTCC 59.359 44.000 0.00 0.00 41.23 4.02
675 686 1.002624 GGATTTGTCCAGTCCGGCA 60.003 57.895 0.00 0.00 33.14 5.69
690 701 0.321122 CGGCAAGCCTCTTCTCACTT 60.321 55.000 9.73 0.00 0.00 3.16
691 702 1.163554 GGCAAGCCTCTTCTCACTTG 58.836 55.000 3.29 0.00 41.89 3.16
694 705 2.421619 CAAGCCTCTTCTCACTTGGAC 58.578 52.381 0.00 0.00 36.67 4.02
707 718 2.038426 CACTTGGACACATCACACCCTA 59.962 50.000 0.00 0.00 0.00 3.53
710 721 3.866703 TGGACACATCACACCCTAAAA 57.133 42.857 0.00 0.00 0.00 1.52
738 749 1.656587 TGGGCTCACCACTAATGAGT 58.343 50.000 4.10 0.00 46.80 3.41
755 766 3.613030 TGAGTCCCACATGTCATTGATG 58.387 45.455 0.00 0.00 0.00 3.07
759 770 1.407618 CCCACATGTCATTGATGGCAG 59.592 52.381 0.00 0.15 46.62 4.85
765 776 1.026182 GTCATTGATGGCAGGCGACA 61.026 55.000 0.00 0.00 31.41 4.35
812 824 3.801114 AACCAAAAGCAAAGAGTCCAC 57.199 42.857 0.00 0.00 0.00 4.02
852 865 4.715523 TGCTACTGGGCCCAACGC 62.716 66.667 28.29 26.36 0.00 4.84
1021 1035 1.531128 CCCTACTCGGCTACTCCCC 60.531 68.421 0.00 0.00 0.00 4.81
1022 1036 1.229359 CCTACTCGGCTACTCCCCA 59.771 63.158 0.00 0.00 0.00 4.96
1023 1037 0.824182 CCTACTCGGCTACTCCCCAG 60.824 65.000 0.00 0.00 0.00 4.45
1024 1038 0.106619 CTACTCGGCTACTCCCCAGT 60.107 60.000 0.00 0.00 36.55 4.00
1026 1040 2.043248 TCGGCTACTCCCCAGTCC 60.043 66.667 0.00 0.00 33.62 3.85
1027 1041 3.155167 CGGCTACTCCCCAGTCCC 61.155 72.222 0.00 0.00 33.62 4.46
1309 1327 1.599606 GCAGTCGCTCTCCTTCTCCA 61.600 60.000 0.00 0.00 34.30 3.86
2367 2411 9.128107 CATCAGTTATTTGTTATGTTTGGTGTC 57.872 33.333 0.00 0.00 0.00 3.67
2441 2485 6.143496 GCAAGTCCTACTTAAGTTTCTTTGC 58.857 40.000 14.49 17.72 36.03 3.68
2593 2637 4.079253 GGGAAACAACTCCATTAAGCTCA 58.921 43.478 0.00 0.00 37.20 4.26
2807 2851 0.806868 CAATGGATGTGCTCACGCTT 59.193 50.000 0.00 0.00 36.97 4.68
2847 2891 2.124411 GGAGTGGTTAGGGATGCCTTA 58.876 52.381 12.53 0.00 0.00 2.69
2952 2996 9.736414 TTTTCTTCTCTTTGAGAATCTCATGAT 57.264 29.630 14.31 0.00 45.84 2.45
3008 3057 7.035612 GTGCCATTACCTTATTTTCCTTCTTG 58.964 38.462 0.00 0.00 0.00 3.02
3058 3111 9.196552 GCAAAATATAAAGTCTAAATGATGCCC 57.803 33.333 0.00 0.00 0.00 5.36
3678 3732 1.953686 GCTTTCAACCAGTACAAGGCA 59.046 47.619 4.43 0.00 0.00 4.75
3717 3771 4.278975 AGACACTGAAATGGAGTTCCTC 57.721 45.455 0.00 0.00 36.82 3.71
4020 4091 7.027874 TCCAACTGTATTTATGGAAAGGAGT 57.972 36.000 0.00 0.00 38.95 3.85
4021 4092 7.110155 TCCAACTGTATTTATGGAAAGGAGTC 58.890 38.462 0.00 0.00 38.95 3.36
4069 4140 9.030301 ACAATTTATGCTTTTTATTATGTCGCC 57.970 29.630 0.00 0.00 0.00 5.54
4070 4141 9.248291 CAATTTATGCTTTTTATTATGTCGCCT 57.752 29.630 0.00 0.00 0.00 5.52
4071 4142 9.816354 AATTTATGCTTTTTATTATGTCGCCTT 57.184 25.926 0.00 0.00 0.00 4.35
4095 4169 8.844441 TTCTTATTTTGTTTCACTAACGGTTG 57.156 30.769 3.07 0.00 39.72 3.77
4153 4227 1.987770 GCCATGTTGTGAGCGAAATTG 59.012 47.619 0.00 0.00 0.00 2.32
4201 4275 9.196552 CAATTCCTTCTAAAAGTTGTTCATTCC 57.803 33.333 0.00 0.00 0.00 3.01
4233 4307 3.320541 CCTACCTAGATTCTCACCTGCTG 59.679 52.174 0.00 0.00 0.00 4.41
4259 4333 3.391296 GGAATCCCAGGTATGCTAACTGA 59.609 47.826 9.10 0.00 46.42 3.41
4269 4343 7.095910 CAGGTATGCTAACTGATTCCTCTATG 58.904 42.308 3.02 0.00 46.42 2.23
4283 4357 5.015813 TCCTCTATGCCTGAAGATGGATA 57.984 43.478 0.00 0.00 0.00 2.59
4335 4409 6.586751 CATTTAGTGTGAATGCTTGCTTTTG 58.413 36.000 0.00 0.00 0.00 2.44
4341 4415 4.060205 GTGAATGCTTGCTTTTGTTCCAT 58.940 39.130 0.00 0.00 0.00 3.41
4363 4437 7.295672 TCCATGTATTTGATTATCTTCCCCTCT 59.704 37.037 0.00 0.00 0.00 3.69
4394 4469 9.760077 CTAAATACTTTGGTACTTATCACGGAT 57.240 33.333 0.00 0.00 0.00 4.18
4398 4473 7.356089 ACTTTGGTACTTATCACGGATATCA 57.644 36.000 4.83 0.00 0.00 2.15
4400 4475 6.971726 TTGGTACTTATCACGGATATCAGT 57.028 37.500 4.83 3.55 0.00 3.41
4401 4476 8.467963 TTTGGTACTTATCACGGATATCAGTA 57.532 34.615 8.24 0.93 0.00 2.74
4402 4477 8.467963 TTGGTACTTATCACGGATATCAGTAA 57.532 34.615 8.24 0.00 27.02 2.24
4403 4478 8.645814 TGGTACTTATCACGGATATCAGTAAT 57.354 34.615 8.24 2.53 27.02 1.89
4404 4479 9.743581 TGGTACTTATCACGGATATCAGTAATA 57.256 33.333 8.24 1.51 27.02 0.98
4603 4679 8.927721 CCTTAAGCAAGTTTCTTCTTCTAGTAC 58.072 37.037 0.00 0.00 0.00 2.73
4604 4680 8.516811 TTAAGCAAGTTTCTTCTTCTAGTACG 57.483 34.615 0.00 0.00 0.00 3.67
4610 4686 9.279904 CAAGTTTCTTCTTCTAGTACGTATCTG 57.720 37.037 0.00 0.00 0.00 2.90
4623 4699 1.740380 CGTATCTGTGAGCAGGTTGGG 60.740 57.143 0.00 0.00 42.78 4.12
4696 4772 2.238521 TCCAAGAATGCCCACAACTTC 58.761 47.619 0.00 0.00 0.00 3.01
4703 4779 2.957402 TGCCCACAACTTCTGAATCT 57.043 45.000 0.00 0.00 0.00 2.40
4706 4782 3.245016 TGCCCACAACTTCTGAATCTCAT 60.245 43.478 0.00 0.00 0.00 2.90
4707 4783 3.760684 GCCCACAACTTCTGAATCTCATT 59.239 43.478 0.00 0.00 0.00 2.57
4745 4821 2.894387 GGGCGAGTGAGCAGATGC 60.894 66.667 0.00 0.00 39.27 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 8.792633 TCCGATTTGTAGTGAAATCATTTTTCT 58.207 29.630 0.00 0.00 40.83 2.52
4 5 8.964420 TCCGATTTGTAGTGAAATCATTTTTC 57.036 30.769 0.00 0.00 40.83 2.29
5 6 9.357652 CATCCGATTTGTAGTGAAATCATTTTT 57.642 29.630 0.00 0.00 40.83 1.94
6 7 8.522830 ACATCCGATTTGTAGTGAAATCATTTT 58.477 29.630 0.00 0.00 40.83 1.82
7 8 8.055279 ACATCCGATTTGTAGTGAAATCATTT 57.945 30.769 0.00 0.00 40.83 2.32
8 9 7.336679 TGACATCCGATTTGTAGTGAAATCATT 59.663 33.333 0.00 0.00 40.83 2.57
9 10 6.823182 TGACATCCGATTTGTAGTGAAATCAT 59.177 34.615 0.00 0.00 40.83 2.45
10 11 6.169800 TGACATCCGATTTGTAGTGAAATCA 58.830 36.000 0.00 0.00 40.83 2.57
11 12 6.535150 TCTGACATCCGATTTGTAGTGAAATC 59.465 38.462 0.00 0.00 38.47 2.17
12 13 6.406370 TCTGACATCCGATTTGTAGTGAAAT 58.594 36.000 0.00 0.00 0.00 2.17
13 14 5.789521 TCTGACATCCGATTTGTAGTGAAA 58.210 37.500 0.00 0.00 0.00 2.69
14 15 5.400066 TCTGACATCCGATTTGTAGTGAA 57.600 39.130 0.00 0.00 0.00 3.18
15 16 5.598416 ATCTGACATCCGATTTGTAGTGA 57.402 39.130 0.00 0.00 0.00 3.41
16 17 6.668541 AAATCTGACATCCGATTTGTAGTG 57.331 37.500 9.62 0.00 38.16 2.74
17 18 7.687941 AAAAATCTGACATCCGATTTGTAGT 57.312 32.000 10.78 0.00 39.18 2.73
18 19 9.708222 CTTAAAAATCTGACATCCGATTTGTAG 57.292 33.333 10.78 6.43 39.18 2.74
19 20 8.181573 GCTTAAAAATCTGACATCCGATTTGTA 58.818 33.333 10.78 7.86 39.18 2.41
20 21 7.029563 GCTTAAAAATCTGACATCCGATTTGT 58.970 34.615 10.78 8.66 39.18 2.83
21 22 7.028962 TGCTTAAAAATCTGACATCCGATTTG 58.971 34.615 10.78 2.37 39.18 2.32
22 23 7.156876 TGCTTAAAAATCTGACATCCGATTT 57.843 32.000 5.68 5.68 40.50 2.17
23 24 6.757897 TGCTTAAAAATCTGACATCCGATT 57.242 33.333 0.00 0.00 0.00 3.34
24 25 6.732154 CATGCTTAAAAATCTGACATCCGAT 58.268 36.000 0.00 0.00 0.00 4.18
25 26 5.449041 GCATGCTTAAAAATCTGACATCCGA 60.449 40.000 11.37 0.00 0.00 4.55
26 27 4.736793 GCATGCTTAAAAATCTGACATCCG 59.263 41.667 11.37 0.00 0.00 4.18
27 28 5.045872 GGCATGCTTAAAAATCTGACATCC 58.954 41.667 18.92 0.00 0.00 3.51
28 29 5.653507 TGGCATGCTTAAAAATCTGACATC 58.346 37.500 18.92 0.00 0.00 3.06
29 30 5.664294 TGGCATGCTTAAAAATCTGACAT 57.336 34.783 18.92 0.00 0.00 3.06
30 31 5.465532 TTGGCATGCTTAAAAATCTGACA 57.534 34.783 18.92 0.00 0.00 3.58
31 32 6.591062 TGATTTGGCATGCTTAAAAATCTGAC 59.409 34.615 28.13 15.94 37.85 3.51
32 33 6.699366 TGATTTGGCATGCTTAAAAATCTGA 58.301 32.000 28.13 17.63 37.85 3.27
33 34 6.971527 TGATTTGGCATGCTTAAAAATCTG 57.028 33.333 28.13 0.00 37.85 2.90
34 35 7.982761 TTTGATTTGGCATGCTTAAAAATCT 57.017 28.000 28.13 15.07 37.85 2.40
35 36 8.452534 TCATTTGATTTGGCATGCTTAAAAATC 58.547 29.630 25.09 25.09 37.62 2.17
36 37 8.338072 TCATTTGATTTGGCATGCTTAAAAAT 57.662 26.923 18.92 16.98 0.00 1.82
37 38 7.741027 TCATTTGATTTGGCATGCTTAAAAA 57.259 28.000 18.92 13.21 0.00 1.94
38 39 7.925043 ATCATTTGATTTGGCATGCTTAAAA 57.075 28.000 18.92 15.60 0.00 1.52
39 40 7.925043 AATCATTTGATTTGGCATGCTTAAA 57.075 28.000 18.92 18.51 41.64 1.52
99 100 1.147473 GCAAGCACGGGAAATTTTGG 58.853 50.000 0.00 0.00 0.00 3.28
102 103 3.649073 GTTTAGCAAGCACGGGAAATTT 58.351 40.909 0.00 0.00 0.00 1.82
117 118 1.846175 GCGATGGCAATTTCGTTTAGC 59.154 47.619 10.31 0.00 39.62 3.09
133 134 4.275936 GGCAAGTTATGTTATCCAAGCGAT 59.724 41.667 0.00 0.00 34.73 4.58
165 166 5.694006 CGGGTTAAAGCATGACAAATCAAAA 59.306 36.000 0.00 0.00 38.69 2.44
176 177 4.637483 ATTCATCACGGGTTAAAGCATG 57.363 40.909 0.00 0.00 0.00 4.06
242 243 6.742559 AGGCTTATATTTAGAAACGGAGGA 57.257 37.500 0.00 0.00 0.00 3.71
313 314 8.912614 AATACTCCCTCCGTTCCTAAATATAT 57.087 34.615 0.00 0.00 0.00 0.86
327 331 8.172070 ACTACTCTATTCCTAAATACTCCCTCC 58.828 40.741 0.00 0.00 0.00 4.30
367 371 8.125978 TCTAAAGACTTGGCAAAATTCATCAT 57.874 30.769 0.00 0.00 0.00 2.45
380 384 5.454471 CCCTCCTGATGATCTAAAGACTTGG 60.454 48.000 0.00 0.00 0.00 3.61
381 385 5.609423 CCCTCCTGATGATCTAAAGACTTG 58.391 45.833 0.00 0.00 0.00 3.16
410 414 0.634465 ATAAAATGGAACCGGGGGCT 59.366 50.000 6.32 0.00 0.00 5.19
411 415 2.368311 TATAAAATGGAACCGGGGGC 57.632 50.000 6.32 0.00 0.00 5.80
444 448 4.448732 GCTTGGATGATGTTGGTTTTGTTC 59.551 41.667 0.00 0.00 0.00 3.18
449 453 3.579586 ACATGCTTGGATGATGTTGGTTT 59.420 39.130 9.03 0.00 0.00 3.27
501 507 3.548818 GCCTCTGTGTTTTAGTTGCAGTG 60.549 47.826 0.00 0.00 0.00 3.66
514 520 4.532834 TGTTTTTCTTTAGGCCTCTGTGT 58.467 39.130 9.68 0.00 0.00 3.72
521 527 7.709182 ACATGTAGTTTTGTTTTTCTTTAGGCC 59.291 33.333 0.00 0.00 0.00 5.19
533 539 9.553418 GCAAAATTTTGAACATGTAGTTTTGTT 57.447 25.926 30.40 0.00 41.51 2.83
549 555 2.973224 CGACAGACTCGGCAAAATTTTG 59.027 45.455 23.74 23.74 38.87 2.44
592 599 9.383519 GTATCACCTGTTAATTTTGATCAGAGA 57.616 33.333 0.00 0.00 0.00 3.10
675 686 2.050144 TGTCCAAGTGAGAAGAGGCTT 58.950 47.619 0.00 0.00 0.00 4.35
690 701 3.866703 TTTTAGGGTGTGATGTGTCCA 57.133 42.857 0.00 0.00 0.00 4.02
691 702 4.522789 ACATTTTTAGGGTGTGATGTGTCC 59.477 41.667 0.00 0.00 0.00 4.02
694 705 5.703978 TGACATTTTTAGGGTGTGATGTG 57.296 39.130 0.00 0.00 0.00 3.21
707 718 2.299867 GGTGAGCCCACATGACATTTTT 59.700 45.455 0.00 0.00 44.93 1.94
710 721 0.405198 TGGTGAGCCCACATGACATT 59.595 50.000 0.00 0.00 44.93 2.71
729 740 5.045651 TCAATGACATGTGGGACTCATTAGT 60.046 40.000 1.15 0.00 40.87 2.24
738 749 1.005687 TGCCATCAATGACATGTGGGA 59.994 47.619 1.15 9.68 0.00 4.37
759 770 1.152383 GATAAACGGGAGCTGTCGCC 61.152 60.000 0.00 0.00 36.60 5.54
852 865 2.233676 GAGGGTTGCTGGGGTTTTAATG 59.766 50.000 0.00 0.00 0.00 1.90
1027 1041 3.797353 CATCGGGTGGAGTGGGGG 61.797 72.222 0.00 0.00 0.00 5.40
1309 1327 1.928714 GAGAGGTCGGAGGAGAGGGT 61.929 65.000 0.00 0.00 0.00 4.34
2367 2411 5.674525 ACCACAATACATGACACCTATCAG 58.325 41.667 0.00 0.00 30.46 2.90
2441 2485 4.215613 CCATGATGAGCATAATGACAGTGG 59.784 45.833 9.01 0.00 34.82 4.00
2522 2566 6.035843 CCAAGATAAATGATGTTTGGGAACG 58.964 40.000 0.00 0.00 38.65 3.95
3008 3057 9.577110 TGCATATTCTGAGAAAATGAATGAAAC 57.423 29.630 0.00 0.00 33.24 2.78
3078 3131 8.494433 ACATACAACATCTACCATTAGTCCATT 58.506 33.333 0.00 0.00 0.00 3.16
3079 3132 7.933577 CACATACAACATCTACCATTAGTCCAT 59.066 37.037 0.00 0.00 0.00 3.41
3080 3133 7.272244 CACATACAACATCTACCATTAGTCCA 58.728 38.462 0.00 0.00 0.00 4.02
3081 3134 6.706270 CCACATACAACATCTACCATTAGTCC 59.294 42.308 0.00 0.00 0.00 3.85
3082 3135 7.272978 ACCACATACAACATCTACCATTAGTC 58.727 38.462 0.00 0.00 0.00 2.59
3083 3136 7.195374 ACCACATACAACATCTACCATTAGT 57.805 36.000 0.00 0.00 0.00 2.24
3084 3137 9.208022 CATACCACATACAACATCTACCATTAG 57.792 37.037 0.00 0.00 0.00 1.73
3085 3138 8.154203 CCATACCACATACAACATCTACCATTA 58.846 37.037 0.00 0.00 0.00 1.90
3093 3146 3.820557 AGGCCATACCACATACAACATC 58.179 45.455 5.01 0.00 43.14 3.06
3678 3732 1.977854 TCTACATGCTTGGTCCACAGT 59.022 47.619 4.44 0.00 0.00 3.55
3717 3771 6.455647 TCAGAGACCAAAGTTACATAGTGTG 58.544 40.000 0.00 0.00 0.00 3.82
4067 4138 6.581166 CCGTTAGTGAAACAAAATAAGAAGGC 59.419 38.462 0.00 0.00 41.43 4.35
4069 4140 8.953990 CAACCGTTAGTGAAACAAAATAAGAAG 58.046 33.333 0.00 0.00 41.43 2.85
4070 4141 7.432838 GCAACCGTTAGTGAAACAAAATAAGAA 59.567 33.333 0.00 0.00 41.43 2.52
4071 4142 6.913673 GCAACCGTTAGTGAAACAAAATAAGA 59.086 34.615 0.00 0.00 41.43 2.10
4122 4196 2.026641 ACAACATGGCAGCATCATACC 58.973 47.619 0.00 0.00 0.00 2.73
4153 4227 2.279741 TGATGAAGTGCCAATCTACGC 58.720 47.619 0.00 0.00 0.00 4.42
4201 4275 4.892934 AGAATCTAGGTAGGAGCAGTCTTG 59.107 45.833 0.00 0.00 0.00 3.02
4259 4333 4.237843 TCCATCTTCAGGCATAGAGGAAT 58.762 43.478 0.00 0.00 0.00 3.01
4335 4409 7.725844 AGGGGAAGATAATCAAATACATGGAAC 59.274 37.037 0.00 0.00 0.00 3.62
4341 4415 8.016652 TCCTAGAGGGGAAGATAATCAAATACA 58.983 37.037 0.00 0.00 35.41 2.29
4448 4523 0.877071 AAGTCAGCAAGCAATGGACG 59.123 50.000 0.00 0.00 33.84 4.79
4449 4524 2.294233 TGAAAGTCAGCAAGCAATGGAC 59.706 45.455 0.00 0.00 0.00 4.02
4581 4657 6.514063 ACGTACTAGAAGAAGAAACTTGCTT 58.486 36.000 0.00 0.00 0.00 3.91
4610 4686 1.620822 ATCAAACCCAACCTGCTCAC 58.379 50.000 0.00 0.00 0.00 3.51
4623 4699 7.808856 AGTTCTCAGACTCGTAGTAAATCAAAC 59.191 37.037 0.00 0.00 0.00 2.93
4763 4841 1.005512 ATGGTGCGCAACGTAGACA 60.006 52.632 20.83 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.