Multiple sequence alignment - TraesCS2A01G398900

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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 TraesCS2A01G398900 chr2A 100.000 4334 0 0 1 4334 652287362 652291695 0.000000e+00 8004.0
1 TraesCS2A01G398900 chr2D 95.103 3921 119 23 47 3942 507748467 507752339 0.000000e+00 6109.0
2 TraesCS2A01G398900 chr2D 96.667 240 8 0 4095 4334 507752393 507752632 2.430000e-107 399.0
3 TraesCS2A01G398900 chr2B 94.446 3961 149 27 398 4334 596409821 596413734 0.000000e+00 6030.0
4 TraesCS2A01G398900 chr2B 92.941 170 6 4 62 230 596409649 596409813 4.330000e-60 243.0
5 TraesCS2A01G398900 chr1A 80.677 502 62 16 3378 3876 551490690 551490221 1.480000e-94 357.0
6 TraesCS2A01G398900 chr5A 75.175 713 149 26 1428 2126 593089878 593089180 1.170000e-80 311.0
7 TraesCS2A01G398900 chr4D 73.637 899 187 42 1243 2119 50641483 50642353 7.040000e-78 302.0
8 TraesCS2A01G398900 chr4D 74.865 370 66 24 2548 2902 387756418 387756775 4.520000e-30 143.0
9 TraesCS2A01G398900 chr5B 73.253 916 189 47 1236 2126 580515270 580514386 2.550000e-72 283.0
10 TraesCS2A01G398900 chr5D 74.468 705 154 24 1435 2126 473117336 473116645 9.180000e-72 281.0
11 TraesCS2A01G398900 chr6D 73.178 686 147 32 2237 2902 427569345 427568677 3.400000e-51 213.0
12 TraesCS2A01G398900 chr7A 89.474 133 13 1 3750 3881 65461698 65461566 2.680000e-37 167.0
13 TraesCS2A01G398900 chr7A 76.923 221 41 8 2559 2774 556299617 556299832 2.740000e-22 117.0
14 TraesCS2A01G398900 chr7A 87.037 54 7 0 2550 2603 33606952 33606899 1.300000e-05 62.1
15 TraesCS2A01G398900 chr7B 78.281 221 38 8 2559 2774 517394136 517394351 2.720000e-27 134.0
16 TraesCS2A01G398900 chr7D 77.376 221 40 8 2559 2774 489114491 489114706 5.890000e-24 122.0
17 TraesCS2A01G398900 chr6B 83.846 130 17 4 2642 2769 219570954 219571081 2.120000e-23 121.0
18 TraesCS2A01G398900 chr6A 75.966 233 46 9 2548 2775 156751796 156751569 1.270000e-20 111.0


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 TraesCS2A01G398900 chr2A 652287362 652291695 4333 False 8004.0 8004 100.0000 1 4334 1 chr2A.!!$F1 4333
1 TraesCS2A01G398900 chr2D 507748467 507752632 4165 False 3254.0 6109 95.8850 47 4334 2 chr2D.!!$F1 4287
2 TraesCS2A01G398900 chr2B 596409649 596413734 4085 False 3136.5 6030 93.6935 62 4334 2 chr2B.!!$F1 4272
3 TraesCS2A01G398900 chr5A 593089180 593089878 698 True 311.0 311 75.1750 1428 2126 1 chr5A.!!$R1 698
4 TraesCS2A01G398900 chr4D 50641483 50642353 870 False 302.0 302 73.6370 1243 2119 1 chr4D.!!$F1 876
5 TraesCS2A01G398900 chr5B 580514386 580515270 884 True 283.0 283 73.2530 1236 2126 1 chr5B.!!$R1 890
6 TraesCS2A01G398900 chr5D 473116645 473117336 691 True 281.0 281 74.4680 1435 2126 1 chr5D.!!$R1 691
7 TraesCS2A01G398900 chr6D 427568677 427569345 668 True 213.0 213 73.1780 2237 2902 1 chr6D.!!$R1 665

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
185 186 0.039437 CGTACCGTCAAGTCAGCAGT 60.039 55.0 0.00 0.0 0.00 4.40 F
969 1004 0.530288 GAGCTCTCCACACTCACTCC 59.470 60.0 6.43 0.0 0.00 3.85 F
983 1018 0.967887 CACTCCCCTCTCGCTTCTCA 60.968 60.0 0.00 0.0 0.00 3.27 F
2798 2850 0.665369 GTCCACGACAACACCTACCG 60.665 60.0 0.00 0.0 32.09 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1215 1253 0.249447 CGATCCTCGCATAAGCACCA 60.249 55.000 0.00 0.0 42.27 4.17 R
2185 2234 3.714001 GGACCTGGGGTTCGGGAC 61.714 72.222 0.00 0.0 44.90 4.46 R
3036 3088 1.218316 GGTGAAGACGGCGGAGATT 59.782 57.895 13.24 0.0 0.00 2.40 R
4055 4108 0.244721 GAATTTGAGCACTGGTGGGC 59.755 55.000 2.84 0.0 0.00 5.36 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 8.503458 CATGGAAGATGGAACCATAGATAATC 57.497 38.462 6.31 0.00 41.68 1.75
26 27 7.631510 TGGAAGATGGAACCATAGATAATCA 57.368 36.000 6.31 0.00 36.70 2.57
27 28 8.044574 TGGAAGATGGAACCATAGATAATCAA 57.955 34.615 6.31 0.00 36.70 2.57
28 29 7.939039 TGGAAGATGGAACCATAGATAATCAAC 59.061 37.037 6.31 0.00 36.70 3.18
29 30 8.160106 GGAAGATGGAACCATAGATAATCAACT 58.840 37.037 6.31 0.00 36.70 3.16
30 31 9.566432 GAAGATGGAACCATAGATAATCAACTT 57.434 33.333 6.31 2.25 36.70 2.66
31 32 9.566432 AAGATGGAACCATAGATAATCAACTTC 57.434 33.333 6.31 0.00 36.70 3.01
32 33 8.160106 AGATGGAACCATAGATAATCAACTTCC 58.840 37.037 6.31 0.00 36.70 3.46
33 34 7.451731 TGGAACCATAGATAATCAACTTCCT 57.548 36.000 0.00 0.00 0.00 3.36
34 35 7.282585 TGGAACCATAGATAATCAACTTCCTG 58.717 38.462 0.00 0.00 0.00 3.86
35 36 7.092444 TGGAACCATAGATAATCAACTTCCTGT 60.092 37.037 0.00 0.00 0.00 4.00
36 37 7.775561 GGAACCATAGATAATCAACTTCCTGTT 59.224 37.037 0.00 0.00 39.92 3.16
37 38 9.178758 GAACCATAGATAATCAACTTCCTGTTT 57.821 33.333 0.00 0.00 36.63 2.83
38 39 9.533831 AACCATAGATAATCAACTTCCTGTTTT 57.466 29.630 0.00 0.00 36.63 2.43
39 40 9.533831 ACCATAGATAATCAACTTCCTGTTTTT 57.466 29.630 0.00 0.00 36.63 1.94
98 99 2.468015 AGGCACACCTCAATCCTGT 58.532 52.632 0.00 0.00 46.34 4.00
107 108 3.997021 CACCTCAATCCTGTTGTGTACTC 59.003 47.826 0.00 0.00 0.00 2.59
185 186 0.039437 CGTACCGTCAAGTCAGCAGT 60.039 55.000 0.00 0.00 0.00 4.40
187 188 2.593257 GTACCGTCAAGTCAGCAGTAC 58.407 52.381 0.00 0.00 0.00 2.73
188 189 1.329256 ACCGTCAAGTCAGCAGTACT 58.671 50.000 0.00 0.00 0.00 2.73
189 190 1.687123 ACCGTCAAGTCAGCAGTACTT 59.313 47.619 0.00 0.00 37.67 2.24
219 220 2.997986 GACGCTCCCGATGAAACTTTTA 59.002 45.455 0.00 0.00 38.29 1.52
220 221 2.740447 ACGCTCCCGATGAAACTTTTAC 59.260 45.455 0.00 0.00 38.29 2.01
221 222 2.739913 CGCTCCCGATGAAACTTTTACA 59.260 45.455 0.00 0.00 36.29 2.41
222 223 3.374058 CGCTCCCGATGAAACTTTTACAT 59.626 43.478 0.00 0.00 36.29 2.29
223 224 4.569162 CGCTCCCGATGAAACTTTTACATA 59.431 41.667 0.00 0.00 36.29 2.29
224 225 5.501897 CGCTCCCGATGAAACTTTTACATAC 60.502 44.000 0.00 0.00 36.29 2.39
225 226 5.585047 GCTCCCGATGAAACTTTTACATACT 59.415 40.000 0.00 0.00 0.00 2.12
226 227 6.238130 GCTCCCGATGAAACTTTTACATACTC 60.238 42.308 0.00 0.00 0.00 2.59
227 228 6.110707 TCCCGATGAAACTTTTACATACTCC 58.889 40.000 0.00 0.00 0.00 3.85
228 229 5.878116 CCCGATGAAACTTTTACATACTCCA 59.122 40.000 0.00 0.00 0.00 3.86
229 230 6.542370 CCCGATGAAACTTTTACATACTCCAT 59.458 38.462 0.00 0.00 0.00 3.41
230 231 7.409697 CCGATGAAACTTTTACATACTCCATG 58.590 38.462 0.00 0.00 40.78 3.66
232 233 8.331022 CGATGAAACTTTTACATACTCCATGAG 58.669 37.037 0.00 0.00 38.10 2.90
233 234 7.377766 TGAAACTTTTACATACTCCATGAGC 57.622 36.000 0.00 0.00 38.10 4.26
234 235 6.374333 TGAAACTTTTACATACTCCATGAGCC 59.626 38.462 0.00 0.00 38.10 4.70
236 237 6.006275 ACTTTTACATACTCCATGAGCCAT 57.994 37.500 0.00 0.00 38.10 4.40
237 238 5.824624 ACTTTTACATACTCCATGAGCCATG 59.175 40.000 0.00 7.88 41.10 3.66
238 239 2.267174 ACATACTCCATGAGCCATGC 57.733 50.000 9.04 0.00 40.20 4.06
239 240 1.773052 ACATACTCCATGAGCCATGCT 59.227 47.619 9.04 0.00 43.88 3.79
263 264 3.560989 GAGCCCTCCTCCCTCATG 58.439 66.667 0.00 0.00 34.35 3.07
381 382 5.278463 CGTACAATCCATTTCCATTCCATCC 60.278 44.000 0.00 0.00 0.00 3.51
386 387 5.419239 TCCATTTCCATTCCATCCAAAAC 57.581 39.130 0.00 0.00 0.00 2.43
394 395 0.674269 TCCATCCAAAACCGTACGGC 60.674 55.000 33.62 0.00 39.32 5.68
426 427 0.701147 CCCTTTCCTTGAAGGAGGCT 59.299 55.000 14.40 0.00 46.73 4.58
441 442 2.421424 GGAGGCTGTGTCATTGTCAATC 59.579 50.000 0.00 0.00 0.00 2.67
442 443 3.341823 GAGGCTGTGTCATTGTCAATCT 58.658 45.455 0.00 0.00 0.00 2.40
443 444 3.341823 AGGCTGTGTCATTGTCAATCTC 58.658 45.455 0.00 0.00 0.00 2.75
448 452 4.264253 TGTGTCATTGTCAATCTCCCATC 58.736 43.478 0.00 0.00 0.00 3.51
458 462 5.185635 TGTCAATCTCCCATCACCAAATTTC 59.814 40.000 0.00 0.00 0.00 2.17
499 503 3.431725 GCCACTGCCTGCCGTTAC 61.432 66.667 0.00 0.00 0.00 2.50
565 589 2.860735 GAGACGAATCAATGCGCTAACT 59.139 45.455 9.73 0.00 0.00 2.24
596 620 4.835927 CCGCTGGCAGGTAGTAAG 57.164 61.111 17.64 0.00 0.00 2.34
597 621 1.898154 CCGCTGGCAGGTAGTAAGT 59.102 57.895 17.64 0.00 0.00 2.24
598 622 1.108776 CCGCTGGCAGGTAGTAAGTA 58.891 55.000 17.64 0.00 0.00 2.24
623 647 1.152383 GCCGCGTTAATGTCCTCCTC 61.152 60.000 4.92 0.00 0.00 3.71
663 687 1.744741 GCAGCTGGAGCAGAGGAAC 60.745 63.158 17.12 0.00 45.16 3.62
679 703 1.153329 AACAAGACACGGGCGTCAA 60.153 52.632 0.00 0.00 38.43 3.18
680 704 1.157870 AACAAGACACGGGCGTCAAG 61.158 55.000 0.00 0.00 38.43 3.02
681 705 2.030562 AAGACACGGGCGTCAAGG 59.969 61.111 0.00 0.00 38.43 3.61
682 706 4.681978 AGACACGGGCGTCAAGGC 62.682 66.667 0.00 0.00 45.91 4.35
683 707 4.681978 GACACGGGCGTCAAGGCT 62.682 66.667 0.00 0.00 45.89 4.58
684 708 4.681978 ACACGGGCGTCAAGGCTC 62.682 66.667 0.00 0.00 45.89 4.70
685 709 4.680237 CACGGGCGTCAAGGCTCA 62.680 66.667 0.00 0.00 45.89 4.26
752 776 2.599973 GTGTGTGACAAGCAAAGCAAAG 59.400 45.455 0.00 0.00 0.00 2.77
753 777 1.589779 GTGTGACAAGCAAAGCAAAGC 59.410 47.619 0.00 0.00 0.00 3.51
754 778 1.204231 TGTGACAAGCAAAGCAAAGCA 59.796 42.857 0.00 0.00 0.00 3.91
755 779 2.270047 GTGACAAGCAAAGCAAAGCAA 58.730 42.857 0.00 0.00 0.00 3.91
756 780 2.672381 GTGACAAGCAAAGCAAAGCAAA 59.328 40.909 0.00 0.00 0.00 3.68
780 804 2.507992 CCAACAGCTCTCCTCGCG 60.508 66.667 0.00 0.00 0.00 5.87
827 851 2.588146 CTTCAATGCGGCCAGAAGCG 62.588 60.000 2.24 0.00 45.17 4.68
851 875 3.495753 CCACCGTATTTTATTACCGCTCC 59.504 47.826 0.00 0.00 0.00 4.70
878 902 1.134521 TCACTGTTCAGCGGTTCAACT 60.135 47.619 7.51 0.00 33.66 3.16
960 995 1.020333 CAGCAAGCAGAGCTCTCCAC 61.020 60.000 14.96 6.54 41.14 4.02
965 1000 0.541530 AGCAGAGCTCTCCACACTCA 60.542 55.000 14.96 0.00 30.62 3.41
969 1004 0.530288 GAGCTCTCCACACTCACTCC 59.470 60.000 6.43 0.00 0.00 3.85
976 1011 1.599606 CCACACTCACTCCCCTCTCG 61.600 65.000 0.00 0.00 0.00 4.04
978 1013 1.680651 CACTCACTCCCCTCTCGCT 60.681 63.158 0.00 0.00 0.00 4.93
983 1018 0.967887 CACTCCCCTCTCGCTTCTCA 60.968 60.000 0.00 0.00 0.00 3.27
984 1019 0.968393 ACTCCCCTCTCGCTTCTCAC 60.968 60.000 0.00 0.00 0.00 3.51
1104 1142 1.285078 GGAGCCCCCAAGACTTACATT 59.715 52.381 0.00 0.00 34.14 2.71
1107 1145 2.110011 AGCCCCCAAGACTTACATTGTT 59.890 45.455 0.00 0.00 0.00 2.83
1110 1148 3.758554 CCCCCAAGACTTACATTGTTCAG 59.241 47.826 0.00 0.00 0.00 3.02
1212 1250 1.349026 CAGGTTGAAGCTGAGGAGGAA 59.651 52.381 18.81 0.00 45.98 3.36
1215 1253 2.238395 GGTTGAAGCTGAGGAGGAAGAT 59.762 50.000 0.00 0.00 0.00 2.40
1217 1255 1.836166 TGAAGCTGAGGAGGAAGATGG 59.164 52.381 0.00 0.00 0.00 3.51
1224 1262 3.387962 TGAGGAGGAAGATGGTGCTTAT 58.612 45.455 0.00 0.00 0.00 1.73
1974 2023 2.456119 CGTGTTCATCGCCTGCTCC 61.456 63.158 0.00 0.00 0.00 4.70
2439 2488 2.152016 GCAAAGAAGTACACCAGGACC 58.848 52.381 0.00 0.00 0.00 4.46
2798 2850 0.665369 GTCCACGACAACACCTACCG 60.665 60.000 0.00 0.00 32.09 4.02
2950 3002 2.355837 GCACGCAGAACCTGACGA 60.356 61.111 14.20 0.00 35.69 4.20
3036 3088 2.642254 CGACCTCAACTACCCGGCA 61.642 63.158 0.00 0.00 0.00 5.69
3303 3355 2.754658 CACGTAGTCCGGAGCCCT 60.755 66.667 3.06 0.09 41.61 5.19
3354 3406 6.072064 TGTGAGCTTTTCTCCTAGTACTGTAC 60.072 42.308 9.93 9.93 41.18 2.90
3435 3487 3.938963 GGTAAGCGAGGTTGATGAATCAA 59.061 43.478 1.55 1.55 43.94 2.57
3494 3546 2.160417 GCCGGAAGAAAGATGTTGTGAG 59.840 50.000 5.05 0.00 0.00 3.51
3499 3551 3.064900 AGAAAGATGTTGTGAGGCTCC 57.935 47.619 12.86 4.00 0.00 4.70
3500 3552 2.373169 AGAAAGATGTTGTGAGGCTCCA 59.627 45.455 12.86 6.82 0.00 3.86
3501 3553 2.957402 AAGATGTTGTGAGGCTCCAA 57.043 45.000 12.86 12.64 0.00 3.53
3502 3554 3.446442 AAGATGTTGTGAGGCTCCAAT 57.554 42.857 12.86 2.15 0.00 3.16
3503 3555 2.996631 AGATGTTGTGAGGCTCCAATC 58.003 47.619 12.86 10.66 0.00 2.67
3504 3556 2.575279 AGATGTTGTGAGGCTCCAATCT 59.425 45.455 12.86 12.49 0.00 2.40
3505 3557 2.957402 TGTTGTGAGGCTCCAATCTT 57.043 45.000 12.86 0.00 0.00 2.40
3614 3667 4.155280 GTGTGTGTACAACATATTGGGGTC 59.845 45.833 0.00 0.00 41.97 4.46
3847 3900 1.202927 CCTGAAAACTGGGCTTCTCCA 60.203 52.381 0.00 0.00 36.21 3.86
3850 3903 3.157087 TGAAAACTGGGCTTCTCCATTC 58.843 45.455 0.00 0.00 36.05 2.67
3894 3947 0.178992 TCACCAAGGGGCTGTTTCAG 60.179 55.000 0.00 0.00 37.90 3.02
3966 4019 6.228273 ACAACAGTACTGTCGAAATCAATG 57.772 37.500 28.04 20.09 44.13 2.82
3977 4030 6.898041 TGTCGAAATCAATGTTAAGTGAAGG 58.102 36.000 0.00 0.00 33.43 3.46
3978 4031 6.485313 TGTCGAAATCAATGTTAAGTGAAGGT 59.515 34.615 0.00 0.00 33.43 3.50
4003 4056 6.140786 GGTCTTTCAGTTTTACCAACGATTC 58.859 40.000 0.00 0.00 0.00 2.52
4031 4084 6.909909 AGAACAATTTAAAGGATCGAACACC 58.090 36.000 0.00 0.00 0.00 4.16
4032 4085 6.715264 AGAACAATTTAAAGGATCGAACACCT 59.285 34.615 0.00 0.00 38.23 4.00
4033 4086 6.254281 ACAATTTAAAGGATCGAACACCTG 57.746 37.500 9.35 0.94 36.56 4.00
4097 4150 7.117285 TCATCAAATCTCAGCTACACATACT 57.883 36.000 0.00 0.00 0.00 2.12
4138 4191 5.694231 TCAACTGTCATTTTCACCAGATG 57.306 39.130 0.00 0.00 0.00 2.90
4142 4195 6.748333 ACTGTCATTTTCACCAGATGTATG 57.252 37.500 0.00 0.00 0.00 2.39
4209 4262 4.756642 TGAGCTACAGTTGTTCAATTCTGG 59.243 41.667 0.00 0.00 32.92 3.86
4290 4345 3.504863 CAGTGTGTCAATATTTGCAGCC 58.495 45.455 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.105197 TGATTATCTATGGTTCCATCTTCCATG 58.895 37.037 7.67 0.00 41.34 3.66
2 3 7.631510 TGATTATCTATGGTTCCATCTTCCA 57.368 36.000 7.67 0.00 35.64 3.53
3 4 8.160106 AGTTGATTATCTATGGTTCCATCTTCC 58.840 37.037 7.67 0.00 0.00 3.46
4 5 9.566432 AAGTTGATTATCTATGGTTCCATCTTC 57.434 33.333 7.67 0.00 0.00 2.87
5 6 9.566432 GAAGTTGATTATCTATGGTTCCATCTT 57.434 33.333 7.67 1.91 0.00 2.40
6 7 8.160106 GGAAGTTGATTATCTATGGTTCCATCT 58.840 37.037 7.67 0.00 32.75 2.90
7 8 8.160106 AGGAAGTTGATTATCTATGGTTCCATC 58.840 37.037 7.67 0.00 34.57 3.51
9 10 7.092444 ACAGGAAGTTGATTATCTATGGTTCCA 60.092 37.037 13.33 0.00 34.57 3.53
10 11 7.283329 ACAGGAAGTTGATTATCTATGGTTCC 58.717 38.462 0.00 1.52 32.67 3.62
11 12 8.738645 AACAGGAAGTTGATTATCTATGGTTC 57.261 34.615 0.00 0.00 39.49 3.62
13 14 9.533831 AAAAACAGGAAGTTGATTATCTATGGT 57.466 29.630 0.00 0.00 41.19 3.55
39 40 9.778741 CACAGGAGTTAATATATCTTGCCTAAA 57.221 33.333 0.00 0.00 0.00 1.85
40 41 9.154632 TCACAGGAGTTAATATATCTTGCCTAA 57.845 33.333 0.00 0.00 0.00 2.69
41 42 8.585881 GTCACAGGAGTTAATATATCTTGCCTA 58.414 37.037 0.00 0.00 0.00 3.93
42 43 7.445945 GTCACAGGAGTTAATATATCTTGCCT 58.554 38.462 0.00 0.00 0.00 4.75
43 44 6.366332 CGTCACAGGAGTTAATATATCTTGCC 59.634 42.308 0.00 0.00 0.00 4.52
44 45 6.924060 ACGTCACAGGAGTTAATATATCTTGC 59.076 38.462 0.00 0.00 0.00 4.01
45 46 7.921214 ACACGTCACAGGAGTTAATATATCTTG 59.079 37.037 0.00 0.00 0.00 3.02
46 47 7.921214 CACACGTCACAGGAGTTAATATATCTT 59.079 37.037 0.00 0.00 0.00 2.40
47 48 7.426410 CACACGTCACAGGAGTTAATATATCT 58.574 38.462 0.00 0.00 0.00 1.98
48 49 6.144080 GCACACGTCACAGGAGTTAATATATC 59.856 42.308 0.00 0.00 0.00 1.63
49 50 5.983720 GCACACGTCACAGGAGTTAATATAT 59.016 40.000 0.00 0.00 0.00 0.86
50 51 5.105675 TGCACACGTCACAGGAGTTAATATA 60.106 40.000 0.00 0.00 0.00 0.86
51 52 4.181578 GCACACGTCACAGGAGTTAATAT 58.818 43.478 0.00 0.00 0.00 1.28
52 53 3.006003 TGCACACGTCACAGGAGTTAATA 59.994 43.478 0.00 0.00 0.00 0.98
53 54 2.224185 TGCACACGTCACAGGAGTTAAT 60.224 45.455 0.00 0.00 0.00 1.40
54 55 1.137282 TGCACACGTCACAGGAGTTAA 59.863 47.619 0.00 0.00 0.00 2.01
55 56 0.747852 TGCACACGTCACAGGAGTTA 59.252 50.000 0.00 0.00 0.00 2.24
56 57 0.107897 TTGCACACGTCACAGGAGTT 60.108 50.000 0.00 0.00 0.00 3.01
57 58 0.106708 ATTGCACACGTCACAGGAGT 59.893 50.000 0.00 0.00 0.00 3.85
58 59 0.792640 GATTGCACACGTCACAGGAG 59.207 55.000 0.00 0.00 0.00 3.69
59 60 0.392706 AGATTGCACACGTCACAGGA 59.607 50.000 0.00 0.00 0.00 3.86
60 61 2.078849 TAGATTGCACACGTCACAGG 57.921 50.000 0.00 0.00 0.00 4.00
98 99 3.788227 AAATCTGGCAGGAGTACACAA 57.212 42.857 15.73 0.00 0.00 3.33
107 108 2.821378 TGTCACATGAAAATCTGGCAGG 59.179 45.455 15.73 0.00 0.00 4.85
185 186 1.404391 GGAGCGTCGGATGAAGAAGTA 59.596 52.381 0.33 0.00 0.00 2.24
187 188 0.528684 GGGAGCGTCGGATGAAGAAG 60.529 60.000 0.33 0.00 0.00 2.85
188 189 1.515954 GGGAGCGTCGGATGAAGAA 59.484 57.895 0.33 0.00 0.00 2.52
189 190 2.771639 CGGGAGCGTCGGATGAAGA 61.772 63.158 0.33 0.00 0.00 2.87
219 220 1.773052 AGCATGGCTCATGGAGTATGT 59.227 47.619 14.50 1.47 41.64 2.29
220 221 2.152016 CAGCATGGCTCATGGAGTATG 58.848 52.381 14.50 0.00 41.64 2.39
221 222 1.544982 GCAGCATGGCTCATGGAGTAT 60.545 52.381 14.50 0.00 41.64 2.12
222 223 0.179037 GCAGCATGGCTCATGGAGTA 60.179 55.000 14.50 0.00 41.64 2.59
223 224 1.453379 GCAGCATGGCTCATGGAGT 60.453 57.895 14.50 0.00 41.64 3.85
224 225 3.433319 GCAGCATGGCTCATGGAG 58.567 61.111 14.50 0.00 41.64 3.86
234 235 3.224324 GGGCTCCATGGCAGCATG 61.224 66.667 26.93 8.65 43.83 4.06
236 237 4.119363 GAGGGCTCCATGGCAGCA 62.119 66.667 26.93 4.86 43.83 4.41
263 264 0.320247 CCTCGCCCAGCTGTATCATC 60.320 60.000 13.81 0.00 0.00 2.92
304 305 1.086067 GCTGCGCTGCTATCACAAGA 61.086 55.000 29.28 0.00 0.00 3.02
305 306 1.088340 AGCTGCGCTGCTATCACAAG 61.088 55.000 36.28 9.84 42.10 3.16
306 307 1.078918 AGCTGCGCTGCTATCACAA 60.079 52.632 36.28 0.00 42.10 3.33
307 308 1.520120 GAGCTGCGCTGCTATCACA 60.520 57.895 36.96 0.00 44.17 3.58
334 335 3.649843 TGATTAGGGTAATCTGGGACGT 58.350 45.455 7.90 0.00 43.79 4.34
381 382 1.082366 GCTGTGCCGTACGGTTTTG 60.082 57.895 33.34 21.74 37.99 2.44
394 395 1.372087 GAAAGGGATGCGAGGCTGTG 61.372 60.000 0.00 0.00 0.00 3.66
426 427 3.786368 TGGGAGATTGACAATGACACA 57.214 42.857 5.14 3.87 0.00 3.72
441 442 2.110578 GGGGAAATTTGGTGATGGGAG 58.889 52.381 0.00 0.00 0.00 4.30
442 443 1.273552 GGGGGAAATTTGGTGATGGGA 60.274 52.381 0.00 0.00 0.00 4.37
443 444 1.203237 GGGGGAAATTTGGTGATGGG 58.797 55.000 0.00 0.00 0.00 4.00
448 452 0.897621 GCTGAGGGGGAAATTTGGTG 59.102 55.000 0.00 0.00 0.00 4.17
458 462 2.115910 TGCTTTGTGCTGAGGGGG 59.884 61.111 0.00 0.00 43.37 5.40
499 503 1.705337 CGTCTTTATGGCGCCACTGG 61.705 60.000 35.50 21.56 36.81 4.00
595 619 0.672342 ATTAACGCGGCGGATCTACT 59.328 50.000 27.37 0.00 0.00 2.57
596 620 0.782384 CATTAACGCGGCGGATCTAC 59.218 55.000 27.37 0.00 0.00 2.59
597 621 0.386476 ACATTAACGCGGCGGATCTA 59.614 50.000 27.37 9.29 0.00 1.98
598 622 0.874607 GACATTAACGCGGCGGATCT 60.875 55.000 27.37 10.30 0.00 2.75
623 647 0.172352 GGCGTCTCTCTGTTCCTCAG 59.828 60.000 0.00 0.00 44.85 3.35
663 687 2.317609 CCTTGACGCCCGTGTCTTG 61.318 63.158 9.61 2.97 39.64 3.02
752 776 1.807142 GAGCTGTTGGAGTAGGTTTGC 59.193 52.381 0.00 0.00 0.00 3.68
753 777 3.330267 GAGAGCTGTTGGAGTAGGTTTG 58.670 50.000 0.00 0.00 0.00 2.93
754 778 2.303311 GGAGAGCTGTTGGAGTAGGTTT 59.697 50.000 0.00 0.00 0.00 3.27
755 779 1.903183 GGAGAGCTGTTGGAGTAGGTT 59.097 52.381 0.00 0.00 0.00 3.50
756 780 1.077993 AGGAGAGCTGTTGGAGTAGGT 59.922 52.381 0.00 0.00 0.00 3.08
827 851 2.031769 GCGGTAATAAAATACGGTGGCC 60.032 50.000 0.00 0.00 0.00 5.36
835 859 6.322969 TGAGACTGAGGAGCGGTAATAAAATA 59.677 38.462 0.00 0.00 35.85 1.40
878 902 1.270907 GAGTTGAAGAGGAGCAGGGA 58.729 55.000 0.00 0.00 0.00 4.20
960 995 1.254284 AAGCGAGAGGGGAGTGAGTG 61.254 60.000 0.00 0.00 0.00 3.51
965 1000 0.968393 GTGAGAAGCGAGAGGGGAGT 60.968 60.000 0.00 0.00 0.00 3.85
969 1004 1.671901 GAGGGTGAGAAGCGAGAGGG 61.672 65.000 0.00 0.00 0.00 4.30
976 1011 1.893919 AAGAGGCGAGGGTGAGAAGC 61.894 60.000 0.00 0.00 0.00 3.86
978 1013 1.595993 CGAAGAGGCGAGGGTGAGAA 61.596 60.000 0.00 0.00 0.00 2.87
1104 1142 2.434185 GACGCGGCCATCTGAACA 60.434 61.111 12.47 0.00 0.00 3.18
1195 1233 3.269178 CATCTTCCTCCTCAGCTTCAAC 58.731 50.000 0.00 0.00 0.00 3.18
1212 1250 1.123077 TCCTCGCATAAGCACCATCT 58.877 50.000 0.00 0.00 42.27 2.90
1215 1253 0.249447 CGATCCTCGCATAAGCACCA 60.249 55.000 0.00 0.00 42.27 4.17
1217 1255 1.132588 GACGATCCTCGCATAAGCAC 58.867 55.000 0.00 0.00 45.12 4.40
1224 1262 1.460504 AGTTGTAGACGATCCTCGCA 58.539 50.000 0.00 0.00 45.12 5.10
2185 2234 3.714001 GGACCTGGGGTTCGGGAC 61.714 72.222 0.00 0.00 44.90 4.46
3036 3088 1.218316 GGTGAAGACGGCGGAGATT 59.782 57.895 13.24 0.00 0.00 2.40
3303 3355 1.985614 CAGCCATGTGAGGACCAGA 59.014 57.895 0.00 0.00 0.00 3.86
3327 3379 6.039616 CAGTACTAGGAGAAAAGCTCACATC 58.960 44.000 0.00 0.00 45.81 3.06
3354 3406 3.325870 TCTGACTAATGCAGAACAACGG 58.674 45.455 0.00 0.00 39.29 4.44
3435 3487 2.046023 TGCCTGCTGCTACGCAAT 60.046 55.556 0.00 0.00 39.80 3.56
3450 3502 2.105466 GCTACTCCTGTGCTGCTGC 61.105 63.158 8.89 8.89 40.20 5.25
3494 3546 4.037923 TGTTTTGAGTTGAAGATTGGAGCC 59.962 41.667 0.00 0.00 0.00 4.70
3499 3551 7.529880 AAAGCTTGTTTTGAGTTGAAGATTG 57.470 32.000 0.00 0.00 0.00 2.67
3500 3552 9.822185 ATAAAAGCTTGTTTTGAGTTGAAGATT 57.178 25.926 0.00 0.00 0.00 2.40
3501 3553 9.822185 AATAAAAGCTTGTTTTGAGTTGAAGAT 57.178 25.926 0.00 0.00 0.00 2.40
3502 3554 9.301153 GAATAAAAGCTTGTTTTGAGTTGAAGA 57.699 29.630 0.00 0.00 0.00 2.87
3503 3555 8.542953 GGAATAAAAGCTTGTTTTGAGTTGAAG 58.457 33.333 0.00 0.00 0.00 3.02
3504 3556 8.037758 TGGAATAAAAGCTTGTTTTGAGTTGAA 58.962 29.630 0.00 0.00 0.00 2.69
3505 3557 7.491048 GTGGAATAAAAGCTTGTTTTGAGTTGA 59.509 33.333 0.00 0.00 0.00 3.18
3619 3672 4.966005 GGAGTTTTCCGCAAAGCC 57.034 55.556 0.00 0.00 32.79 4.35
3847 3900 4.161377 GGAACACTAGAAGCTGGAGAGAAT 59.839 45.833 0.00 0.00 0.00 2.40
3850 3903 2.167487 GGGAACACTAGAAGCTGGAGAG 59.833 54.545 0.00 0.00 0.00 3.20
3900 3953 4.439700 GCAGCAAGTTAAGATGACATGCAT 60.440 41.667 0.00 0.00 42.39 3.96
3966 4019 5.123936 ACTGAAAGACCACCTTCACTTAAC 58.876 41.667 0.00 0.00 37.43 2.01
3977 4030 4.333372 TCGTTGGTAAAACTGAAAGACCAC 59.667 41.667 0.00 0.00 36.91 4.16
3978 4031 4.515361 TCGTTGGTAAAACTGAAAGACCA 58.485 39.130 0.00 0.00 35.56 4.02
4003 4056 9.151471 TGTTCGATCCTTTAAATTGTTCTCTAG 57.849 33.333 0.00 0.00 0.00 2.43
4031 4084 1.341080 ACCATCCTGTTTTTGCCCAG 58.659 50.000 0.00 0.00 0.00 4.45
4032 4085 1.799933 AACCATCCTGTTTTTGCCCA 58.200 45.000 0.00 0.00 0.00 5.36
4033 4086 2.897326 AGTAACCATCCTGTTTTTGCCC 59.103 45.455 0.00 0.00 0.00 5.36
4055 4108 0.244721 GAATTTGAGCACTGGTGGGC 59.755 55.000 2.84 0.00 0.00 5.36
4097 4150 1.888512 GATTGCAAAGTGAAGGCCAGA 59.111 47.619 5.01 0.00 0.00 3.86
4162 4215 4.564769 CCTCACTTCTTTCGTTAGATCTGC 59.435 45.833 5.18 0.00 0.00 4.26
4209 4262 4.058124 TGTGCTGTCAGAACATAACAGAC 58.942 43.478 9.82 0.00 42.37 3.51
4290 4345 6.573664 TGACCAGATTCACCAAACTAAATG 57.426 37.500 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.