Multiple sequence alignment - TraesCS2D01G436000

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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 TraesCS2D01G436000 chr2D 100.000 3072 0 0 1 3072 546864971 546868042 0.000000e+00 5674.0
1 TraesCS2D01G436000 chr2D 100.000 2580 0 0 3452 6031 546868422 546871001 0.000000e+00 4765.0
2 TraesCS2D01G436000 chr4A 93.406 2290 96 27 786 3050 33025271 33027530 0.000000e+00 3341.0
3 TraesCS2D01G436000 chr4A 93.137 1763 62 18 3453 5206 33027743 33029455 0.000000e+00 2531.0
4 TraesCS2D01G436000 chr4A 80.784 510 82 8 1 498 33024440 33024945 9.480000e-103 385.0
5 TraesCS2D01G436000 chr4A 88.288 222 23 3 1909 2130 33027869 33028087 4.640000e-66 263.0
6 TraesCS2D01G436000 chr4A 87.387 222 26 2 3579 3798 33026392 33026613 2.790000e-63 254.0
7 TraesCS2D01G436000 chr2B 93.295 2237 82 26 789 3004 653603645 653605834 0.000000e+00 3238.0
8 TraesCS2D01G436000 chr2B 89.886 1137 77 17 4533 5659 653607483 653608591 0.000000e+00 1428.0
9 TraesCS2D01G436000 chr2B 90.847 590 35 9 3452 4035 653606162 653606738 0.000000e+00 773.0
10 TraesCS2D01G436000 chr2B 94.395 446 24 1 4089 4534 653606739 653607183 0.000000e+00 684.0
11 TraesCS2D01G436000 chr2B 87.023 262 19 7 5777 6023 653609588 653609849 1.280000e-71 281.0
12 TraesCS2D01G436000 chr2B 89.189 222 22 2 3579 3798 653604746 653604967 5.950000e-70 276.0
13 TraesCS2D01G436000 chr2B 82.432 222 29 5 1909 2130 653606286 653606497 1.030000e-42 185.0
14 TraesCS2D01G436000 chr2A 94.805 1540 58 9 1496 3025 689716427 689714900 0.000000e+00 2381.0
15 TraesCS2D01G436000 chr2A 95.248 1473 46 8 1 1454 689717890 689716423 0.000000e+00 2311.0
16 TraesCS2D01G436000 chr2A 91.939 1253 64 17 4054 5289 689713783 689712551 0.000000e+00 1720.0
17 TraesCS2D01G436000 chr2A 98.350 606 8 1 3452 4055 689714482 689713877 0.000000e+00 1062.0
18 TraesCS2D01G436000 chr2A 83.519 449 45 11 5600 6023 689711886 689711442 5.670000e-105 392.0
19 TraesCS2D01G436000 chr2A 90.179 224 18 3 3579 3798 689716023 689715800 7.650000e-74 289.0
20 TraesCS2D01G436000 chr2A 93.333 45 3 0 3823 3867 689715799 689715755 3.900000e-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 TraesCS2D01G436000 chr2D 546864971 546871001 6030 False 5219.500000 5674 100.000000 1 6031 2 chr2D.!!$F1 6030
1 TraesCS2D01G436000 chr4A 33024440 33029455 5015 False 1354.800000 3341 88.600400 1 5206 5 chr4A.!!$F1 5205
2 TraesCS2D01G436000 chr2B 653603645 653609849 6204 False 980.714286 3238 89.581000 789 6023 7 chr2B.!!$F1 5234
3 TraesCS2D01G436000 chr2A 689711442 689717890 6448 True 1174.657143 2381 92.481857 1 6023 7 chr2A.!!$R1 6022

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
704 801 0.534412 AAGTGATCGCCAGAGGTCAG 59.466 55.000 1.76 0.0 0.00 3.51 F
871 1015 1.078848 CTCCACCGAAGCCCAAGAG 60.079 63.158 0.00 0.0 0.00 2.85 F
1262 1406 1.602771 GGCCACAGTACCTTCCCTC 59.397 63.158 0.00 0.0 0.00 4.30 F
2243 2412 0.104671 GGCCATGTGTGTGCAAAACT 59.895 50.000 0.00 0.0 0.00 2.66 F
2985 3161 0.179045 GTAACGCTGATGGCTGGGAT 60.179 55.000 0.00 0.0 39.13 3.85 F
3051 3286 0.673644 CGTTCTCTGATTGGGGCGTT 60.674 55.000 0.00 0.0 0.00 4.84 F
4161 4570 3.563808 TGCCCTTTGCGTATATCATGTTC 59.436 43.478 0.00 0.0 45.60 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1996 2161 0.391130 TGTGGGAGTTGATAGCACGC 60.391 55.000 0.00 0.00 0.00 5.34 R
2118 2284 1.278637 GAAAGACGTGCACAACCGG 59.721 57.895 18.64 0.00 0.00 5.28 R
2405 2574 1.357258 CGATGGTCTGCTGCTGACAC 61.357 60.000 31.51 23.21 34.69 3.67 R
4222 4631 0.904649 TCCCCAGTGTGTATCTGCAG 59.095 55.000 7.63 7.63 0.00 4.41 R
4606 5316 1.072648 TGACCCTTTTACCAACCCGAG 59.927 52.381 0.00 0.00 0.00 4.63 R
4607 5317 1.138568 TGACCCTTTTACCAACCCGA 58.861 50.000 0.00 0.00 0.00 5.14 R
5944 7991 0.179084 GCGCCACCTGCTTCATACTA 60.179 55.000 0.00 0.00 38.05 1.82 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
46 47 4.360964 TGGCGTTGTACCGGACGG 62.361 66.667 9.46 9.56 39.52 4.79
53 54 2.480073 CGTTGTACCGGACGGACATATT 60.480 50.000 18.80 0.00 38.96 1.28
191 192 1.577328 CGGCATTGCTTTCTCCACGT 61.577 55.000 8.82 0.00 0.00 4.49
350 351 9.955208 CTTAATTAATACAATCCCGTTTTACCC 57.045 33.333 0.00 0.00 0.00 3.69
400 406 8.100164 TGTTTCTTAGGACATGTACAATGATCA 58.900 33.333 11.55 0.00 0.00 2.92
444 450 6.740110 AGCCTTACACATAATCTAGAGAACG 58.260 40.000 0.00 0.00 0.00 3.95
468 480 7.642194 ACGCAATAAAAATACGATGTACAATGG 59.358 33.333 0.00 0.00 0.00 3.16
656 750 7.181143 CATCATTGCATATGCCCTTAAAAAC 57.819 36.000 24.54 0.00 41.18 2.43
704 801 0.534412 AAGTGATCGCCAGAGGTCAG 59.466 55.000 1.76 0.00 0.00 3.51
764 865 3.782443 ACGGTTGAGATCGGGGGC 61.782 66.667 0.00 0.00 0.00 5.80
854 998 2.982130 GATCGTCCCAGTGGCACT 59.018 61.111 15.88 15.88 0.00 4.40
871 1015 1.078848 CTCCACCGAAGCCCAAGAG 60.079 63.158 0.00 0.00 0.00 2.85
934 1078 3.604582 CAATTCCACCTTCACCTCTCTC 58.395 50.000 0.00 0.00 0.00 3.20
935 1079 2.704190 TTCCACCTTCACCTCTCTCT 57.296 50.000 0.00 0.00 0.00 3.10
1152 1296 3.516615 CGTGTCATTCCTCTTCTCCTTC 58.483 50.000 0.00 0.00 0.00 3.46
1250 1394 3.066190 CTCTACCGGTCGGCCACA 61.066 66.667 12.40 0.00 39.32 4.17
1262 1406 1.602771 GGCCACAGTACCTTCCCTC 59.397 63.158 0.00 0.00 0.00 4.30
1301 1459 2.093128 TGTTTCCCGAGCTTAGGAATCC 60.093 50.000 16.60 11.82 41.69 3.01
1337 1495 5.240713 AGTTAGCATGCAAATTAGCTGTC 57.759 39.130 21.98 0.00 37.94 3.51
1357 1515 2.103432 TCTTGGTGTTTAGCGTGGAGAA 59.897 45.455 0.00 0.00 0.00 2.87
1362 1520 4.251268 GGTGTTTAGCGTGGAGAACTTAT 58.749 43.478 0.00 0.00 0.00 1.73
1378 1540 9.638239 GGAGAACTTATTGCAAATTTTGTGATA 57.362 29.630 1.71 6.71 0.00 2.15
1448 1610 1.669265 GCTTACGTATTCCCCACTTGC 59.331 52.381 0.00 0.00 0.00 4.01
1489 1651 2.408050 GATGCGCTATCACTTGGGTAG 58.592 52.381 9.73 0.00 35.78 3.18
1863 2028 5.940470 ACTTGCTTTATCTTCTTGTACCAGG 59.060 40.000 0.00 0.00 0.00 4.45
1864 2029 4.261801 TGCTTTATCTTCTTGTACCAGGC 58.738 43.478 0.00 0.00 0.00 4.85
1865 2030 4.019321 TGCTTTATCTTCTTGTACCAGGCT 60.019 41.667 0.00 0.00 0.00 4.58
1866 2031 5.188948 TGCTTTATCTTCTTGTACCAGGCTA 59.811 40.000 0.00 0.00 0.00 3.93
1867 2032 5.524281 GCTTTATCTTCTTGTACCAGGCTAC 59.476 44.000 0.00 0.00 0.00 3.58
1868 2033 5.609533 TTATCTTCTTGTACCAGGCTACC 57.390 43.478 0.00 0.00 0.00 3.18
1869 2034 2.897350 TCTTCTTGTACCAGGCTACCA 58.103 47.619 0.00 0.00 0.00 3.25
1870 2035 2.832129 TCTTCTTGTACCAGGCTACCAG 59.168 50.000 0.00 0.00 0.00 4.00
1884 2049 2.616960 CTACCAGCACAGCGACATTTA 58.383 47.619 0.00 0.00 0.00 1.40
1968 2133 7.910683 GGCTGTCTAATGCTTTTAACTGATAAC 59.089 37.037 0.00 0.00 0.00 1.89
1969 2134 8.450964 GCTGTCTAATGCTTTTAACTGATAACA 58.549 33.333 0.00 0.00 0.00 2.41
1996 2161 3.996150 ACAGACCTTTCATGCTTTGTG 57.004 42.857 0.00 0.00 0.00 3.33
2036 2201 6.638063 CCACATAAGGCAATAAATGATGAACG 59.362 38.462 0.00 0.00 0.00 3.95
2106 2272 7.658525 AAGGGCATGACATATTTACATTTCA 57.341 32.000 0.00 0.00 0.00 2.69
2123 2289 2.270352 TCAAACATCAGCTTCCGGTT 57.730 45.000 0.00 0.00 0.00 4.44
2243 2412 0.104671 GGCCATGTGTGTGCAAAACT 59.895 50.000 0.00 0.00 0.00 2.66
2405 2574 6.086222 CCACAAACCTCATAAGAAAATGACG 58.914 40.000 0.00 0.00 32.51 4.35
2985 3161 0.179045 GTAACGCTGATGGCTGGGAT 60.179 55.000 0.00 0.00 39.13 3.85
3043 3278 0.732880 CACCGTCGCGTTCTCTGATT 60.733 55.000 5.77 0.00 0.00 2.57
3044 3279 0.732880 ACCGTCGCGTTCTCTGATTG 60.733 55.000 5.77 0.00 0.00 2.67
3045 3280 1.413767 CCGTCGCGTTCTCTGATTGG 61.414 60.000 5.77 0.00 0.00 3.16
3046 3281 1.413767 CGTCGCGTTCTCTGATTGGG 61.414 60.000 5.77 0.00 0.00 4.12
3047 3282 1.084370 GTCGCGTTCTCTGATTGGGG 61.084 60.000 5.77 0.00 0.00 4.96
3048 3283 2.464459 CGCGTTCTCTGATTGGGGC 61.464 63.158 0.00 0.00 0.00 5.80
3049 3284 2.464459 GCGTTCTCTGATTGGGGCG 61.464 63.158 0.00 0.00 0.00 6.13
3050 3285 1.079127 CGTTCTCTGATTGGGGCGT 60.079 57.895 0.00 0.00 0.00 5.68
3051 3286 0.673644 CGTTCTCTGATTGGGGCGTT 60.674 55.000 0.00 0.00 0.00 4.84
3713 3983 9.807649 AAGGCAATAAATGATGAACAATTCTAC 57.192 29.630 0.00 0.00 0.00 2.59
3725 3995 9.220767 GATGAACAATTCTACCTGTAGTTTCTT 57.779 33.333 4.36 1.17 34.84 2.52
3774 4044 6.751514 AAGACACGCCATATTTACATTTCA 57.248 33.333 0.00 0.00 0.00 2.69
4049 4332 6.932947 AGTTCAAGGTACACTACTATGGAAC 58.067 40.000 0.00 0.00 0.00 3.62
4114 4523 5.604758 TCCATAATGTTCTCTCCAGTGAG 57.395 43.478 0.00 0.00 40.17 3.51
4161 4570 3.563808 TGCCCTTTGCGTATATCATGTTC 59.436 43.478 0.00 0.00 45.60 3.18
4222 4631 8.492673 TCTTGTAGGTCAATGAATCATACAAC 57.507 34.615 6.91 0.00 34.84 3.32
4502 4911 5.300539 TCTGACTAGCTCTAGTGCTTTATGG 59.699 44.000 23.23 11.91 45.63 2.74
4524 4933 6.454795 TGGTTATCAATTGGCTTTGTTTCTC 58.545 36.000 5.42 0.00 0.00 2.87
4527 5236 8.250332 GGTTATCAATTGGCTTTGTTTCTCATA 58.750 33.333 5.42 0.00 0.00 2.15
4530 5239 6.913170 TCAATTGGCTTTGTTTCTCATACTC 58.087 36.000 5.42 0.00 0.00 2.59
4531 5240 6.716628 TCAATTGGCTTTGTTTCTCATACTCT 59.283 34.615 5.42 0.00 0.00 3.24
4592 5302 9.146586 TGTAAACACTAGGAACTTAAGAACCTA 57.853 33.333 21.45 21.45 41.75 3.08
4629 5339 2.750471 CGGGTTGGTAAAAGGGTCACTT 60.750 50.000 0.00 0.00 42.52 3.16
4830 5540 5.528043 ACTCATCACCATAGCAGTAAGAG 57.472 43.478 0.00 0.00 0.00 2.85
4892 5602 1.133976 AGCAACCATAGCATCAGGGTC 60.134 52.381 0.00 0.00 32.01 4.46
5013 5723 1.967319 TGTGCTGGACTTCAAACTCC 58.033 50.000 0.00 0.00 0.00 3.85
5219 5938 2.536803 GCAGTGCAACATGTGTCAAAAG 59.463 45.455 11.09 0.00 41.43 2.27
5224 5943 2.733026 GCAACATGTGTCAAAAGCATCC 59.267 45.455 0.00 0.00 0.00 3.51
5270 5990 6.038714 GGAAATATGGTCTAACTTTCTGGCTG 59.961 42.308 0.00 0.00 0.00 4.85
5278 5998 1.985473 ACTTTCTGGCTGTGAATGCA 58.015 45.000 0.00 0.00 0.00 3.96
5279 5999 1.884579 ACTTTCTGGCTGTGAATGCAG 59.115 47.619 0.00 0.00 39.37 4.41
5294 6042 0.251916 TGCAGATCACGGTTAAGGGG 59.748 55.000 0.00 0.00 0.00 4.79
5300 6048 0.611714 TCACGGTTAAGGGGCTCTTC 59.388 55.000 1.00 0.00 36.93 2.87
5327 6075 4.093408 TCGCTGGAATTTTTCTCTGAATCG 59.907 41.667 0.00 0.00 0.00 3.34
5381 6130 9.874205 ACATTCTTTCAAACTGAATCTTTTTGA 57.126 25.926 5.96 5.96 36.11 2.69
5402 6426 0.103208 GGGATCAGAGGTACGTGCTG 59.897 60.000 3.01 3.59 0.00 4.41
5421 6445 3.469008 TGGACGAACCATGCCTAATAG 57.531 47.619 0.00 0.00 44.64 1.73
5430 6454 4.130118 ACCATGCCTAATAGAGCTTTTCG 58.870 43.478 0.00 0.00 0.00 3.46
5434 6458 4.585879 TGCCTAATAGAGCTTTTCGGTTT 58.414 39.130 0.00 0.00 0.00 3.27
5484 6512 1.652947 TTTACTCCGGGAGCCTTCTT 58.347 50.000 23.84 5.90 32.04 2.52
5511 6551 5.011329 AGCTGCTTGGAATTCAGAAATTTCA 59.989 36.000 19.99 0.00 38.37 2.69
5536 6576 4.703897 TGGAACAACAGTACTTCCAGAAG 58.296 43.478 8.84 5.85 38.83 2.85
5586 6681 8.373981 AGTGCAGCTCTCATGATACTTTTATAT 58.626 33.333 0.00 0.00 0.00 0.86
5587 6682 9.645059 GTGCAGCTCTCATGATACTTTTATATA 57.355 33.333 0.00 0.00 0.00 0.86
5588 6683 9.645059 TGCAGCTCTCATGATACTTTTATATAC 57.355 33.333 0.00 0.00 0.00 1.47
5624 6719 8.732746 AAATATGGTGGTACATAGAAACTGTC 57.267 34.615 0.00 0.00 44.52 3.51
5702 7724 3.075148 GTTTCTGGAGCCCTTTAGACAC 58.925 50.000 0.00 0.00 0.00 3.67
5707 7729 1.347320 GAGCCCTTTAGACACGAACG 58.653 55.000 0.00 0.00 0.00 3.95
5738 7777 1.273606 ACTGGACATGACCAAGTCTCG 59.726 52.381 17.60 7.70 39.59 4.04
5739 7778 0.608130 TGGACATGACCAAGTCTCGG 59.392 55.000 14.77 0.00 36.96 4.63
5743 7782 2.753452 GACATGACCAAGTCTCGGACTA 59.247 50.000 0.00 0.00 42.59 2.59
5751 7790 3.181485 CCAAGTCTCGGACTATTCCACTC 60.181 52.174 6.93 0.00 42.59 3.51
5766 7805 1.541889 CCACTCAGCACTCAAGCTCAA 60.542 52.381 0.00 0.00 44.54 3.02
5772 7811 0.590195 GCACTCAAGCTCAACACCTG 59.410 55.000 0.00 0.00 0.00 4.00
5799 7845 2.749076 CCTCGTCTTCCATTTTGATGCA 59.251 45.455 0.00 0.00 0.00 3.96
5889 7935 2.042333 TCGTCCCCATCATCCCGT 60.042 61.111 0.00 0.00 0.00 5.28
5895 7941 3.911698 CCATCATCCCGTCCGCGA 61.912 66.667 8.23 0.00 41.33 5.87
5896 7942 2.340078 CATCATCCCGTCCGCGAT 59.660 61.111 8.23 0.00 41.33 4.58
5938 7985 2.603473 GGTTGACCCCCAAAGGCC 60.603 66.667 0.00 0.00 36.36 5.19
5944 7991 2.081585 GACCCCCAAAGGCCAAGACT 62.082 60.000 5.01 0.00 0.00 3.24
5949 7996 2.509964 CCCCAAAGGCCAAGACTAGTAT 59.490 50.000 5.01 0.00 0.00 2.12
5950 7997 3.545703 CCCAAAGGCCAAGACTAGTATG 58.454 50.000 5.01 0.00 0.00 2.39
5952 7999 4.324254 CCCAAAGGCCAAGACTAGTATGAA 60.324 45.833 5.01 0.00 0.00 2.57
5953 8000 4.878397 CCAAAGGCCAAGACTAGTATGAAG 59.122 45.833 5.01 0.00 0.00 3.02
6019 8074 2.253452 CAGCACGGCAAGTCAAGC 59.747 61.111 0.00 0.00 0.00 4.01
6023 8078 2.357517 ACGGCAAGTCAAGCTCGG 60.358 61.111 0.00 0.00 32.52 4.63
6024 8079 3.793144 CGGCAAGTCAAGCTCGGC 61.793 66.667 0.00 0.00 0.00 5.54
6025 8080 2.359230 GGCAAGTCAAGCTCGGCT 60.359 61.111 0.00 0.00 42.56 5.52
6026 8081 2.394563 GGCAAGTCAAGCTCGGCTC 61.395 63.158 0.00 0.00 38.25 4.70
6027 8082 2.734673 GCAAGTCAAGCTCGGCTCG 61.735 63.158 0.00 0.00 38.25 5.03
6028 8083 2.433318 AAGTCAAGCTCGGCTCGC 60.433 61.111 0.00 0.00 38.25 5.03
6029 8084 3.226429 AAGTCAAGCTCGGCTCGCA 62.226 57.895 0.00 0.00 38.25 5.10
6030 8085 2.715532 AAGTCAAGCTCGGCTCGCAA 62.716 55.000 0.00 0.00 38.25 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 7.362315 CCTTGCAATCTAGTTCATTGATCAACA 60.362 37.037 11.07 0.00 33.69 3.33
254 255 0.175073 GCACCTAACCAGACTACCGG 59.825 60.000 0.00 0.00 0.00 5.28
444 450 8.850454 ACCATTGTACATCGTATTTTTATTGC 57.150 30.769 0.00 0.00 0.00 3.56
635 729 5.426504 TGGTTTTTAAGGGCATATGCAATG 58.573 37.500 28.07 0.00 44.36 2.82
646 740 6.800072 TTAAGGGCATATGGTTTTTAAGGG 57.200 37.500 4.56 0.00 0.00 3.95
656 750 6.405538 TCTTTTGCTTTTTAAGGGCATATGG 58.594 36.000 4.56 0.00 35.84 2.74
704 801 3.645687 AGCAGAGATGGGTTAGATCTTCC 59.354 47.826 0.00 4.24 29.97 3.46
854 998 1.125093 TTCTCTTGGGCTTCGGTGGA 61.125 55.000 0.00 0.00 0.00 4.02
1152 1296 2.587194 CCAGCGATGCCGAAGAGG 60.587 66.667 0.00 0.00 44.97 3.69
1262 1406 1.134098 ACAGCATGGGAGTAAATCGGG 60.134 52.381 0.00 0.00 43.62 5.14
1301 1459 1.156736 CTAACTTCAGCACCCGGTTG 58.843 55.000 0.00 0.00 0.00 3.77
1337 1495 2.163818 TCTCCACGCTAAACACCAAG 57.836 50.000 0.00 0.00 0.00 3.61
1448 1610 2.221749 CGAAATCCACACAGTGACACAG 59.778 50.000 7.81 1.82 35.23 3.66
1489 1651 0.031994 GCATCCAACACACACCCAAC 59.968 55.000 0.00 0.00 0.00 3.77
1863 2028 1.021390 AATGTCGCTGTGCTGGTAGC 61.021 55.000 0.00 0.00 42.82 3.58
1864 2029 1.442769 AAATGTCGCTGTGCTGGTAG 58.557 50.000 0.00 0.00 0.00 3.18
1865 2030 2.753055 TAAATGTCGCTGTGCTGGTA 57.247 45.000 0.00 0.00 0.00 3.25
1866 2031 1.890876 TTAAATGTCGCTGTGCTGGT 58.109 45.000 0.00 0.00 0.00 4.00
1867 2032 3.373748 TGTATTAAATGTCGCTGTGCTGG 59.626 43.478 0.00 0.00 0.00 4.85
1868 2033 4.598406 TGTATTAAATGTCGCTGTGCTG 57.402 40.909 0.00 0.00 0.00 4.41
1869 2034 5.118990 AGATGTATTAAATGTCGCTGTGCT 58.881 37.500 0.00 0.00 0.00 4.40
1870 2035 5.409643 AGATGTATTAAATGTCGCTGTGC 57.590 39.130 0.00 0.00 0.00 4.57
1968 2133 9.888878 CAAAGCATGAAAGGTCTGTATATATTG 57.111 33.333 0.00 0.00 0.00 1.90
1969 2134 9.632638 ACAAAGCATGAAAGGTCTGTATATATT 57.367 29.630 0.00 0.00 0.00 1.28
1996 2161 0.391130 TGTGGGAGTTGATAGCACGC 60.391 55.000 0.00 0.00 0.00 5.34
2036 2201 8.989653 ACAAACTAGAAACTACAGCTAGAATC 57.010 34.615 0.00 0.00 36.12 2.52
2106 2272 1.608590 CACAACCGGAAGCTGATGTTT 59.391 47.619 9.46 0.00 0.00 2.83
2118 2284 1.278637 GAAAGACGTGCACAACCGG 59.721 57.895 18.64 0.00 0.00 5.28
2123 2289 3.263261 TGTAAACTGAAAGACGTGCACA 58.737 40.909 18.64 0.00 37.43 4.57
2351 2520 8.429493 TGAACATGTTCATGATCTTCTGTATC 57.571 34.615 32.36 6.26 43.90 2.24
2405 2574 1.357258 CGATGGTCTGCTGCTGACAC 61.357 60.000 31.51 23.21 34.69 3.67
3513 3783 1.915078 CTTCCGTCCCCTTCCAGCAT 61.915 60.000 0.00 0.00 0.00 3.79
3713 3983 9.450807 CTTTATGAACAAACAAGAAACTACAGG 57.549 33.333 0.00 0.00 0.00 4.00
3774 4044 2.031157 GCACGACCACAAGCTAATGTTT 60.031 45.455 0.00 0.00 0.00 2.83
4049 4332 7.895975 TGTTCTTTCTCATGTGAACTAGATG 57.104 36.000 9.65 0.00 39.38 2.90
4050 4333 8.538701 AGATGTTCTTTCTCATGTGAACTAGAT 58.461 33.333 9.65 3.20 39.38 1.98
4051 4334 7.901029 AGATGTTCTTTCTCATGTGAACTAGA 58.099 34.615 9.65 8.42 39.38 2.43
4052 4335 9.299963 CTAGATGTTCTTTCTCATGTGAACTAG 57.700 37.037 9.65 10.77 39.38 2.57
4053 4336 8.807118 ACTAGATGTTCTTTCTCATGTGAACTA 58.193 33.333 9.65 5.85 39.38 2.24
4054 4337 7.675062 ACTAGATGTTCTTTCTCATGTGAACT 58.325 34.615 9.65 5.07 39.38 3.01
4055 4338 7.897575 ACTAGATGTTCTTTCTCATGTGAAC 57.102 36.000 9.65 9.55 39.18 3.18
4070 4353 7.397221 TGGATTTCTCATGTGAACTAGATGTT 58.603 34.615 9.65 0.00 42.38 2.71
4071 4354 6.950842 TGGATTTCTCATGTGAACTAGATGT 58.049 36.000 9.65 0.00 32.20 3.06
4093 4502 5.350504 ACTCACTGGAGAGAACATTATGG 57.649 43.478 6.42 0.00 44.26 2.74
4114 4523 7.059448 TGCAAACAACTGAAGATTCAAAAAC 57.941 32.000 0.00 0.00 36.64 2.43
4222 4631 0.904649 TCCCCAGTGTGTATCTGCAG 59.095 55.000 7.63 7.63 0.00 4.41
4437 4846 5.500234 AGCAATGAGTACTTTTGGCTATCA 58.500 37.500 16.66 1.04 0.00 2.15
4502 4911 9.076596 GTATGAGAAACAAAGCCAATTGATAAC 57.923 33.333 7.12 0.00 34.38 1.89
4524 4933 5.878332 TGCAACAATACAACCAGAGTATG 57.122 39.130 0.00 0.00 32.78 2.39
4527 5236 4.216257 GTGATGCAACAATACAACCAGAGT 59.784 41.667 0.00 0.00 0.00 3.24
4530 5239 3.255395 TGGTGATGCAACAATACAACCAG 59.745 43.478 0.00 0.00 0.00 4.00
4531 5240 3.005261 GTGGTGATGCAACAATACAACCA 59.995 43.478 0.00 0.00 30.77 3.67
4592 5302 6.608922 ACCAACCCGAGTACTATAAGATACT 58.391 40.000 0.00 0.00 34.28 2.12
4593 5303 6.890979 ACCAACCCGAGTACTATAAGATAC 57.109 41.667 0.00 0.00 0.00 2.24
4594 5304 8.995027 TTTACCAACCCGAGTACTATAAGATA 57.005 34.615 0.00 0.00 0.00 1.98
4595 5305 7.902920 TTTACCAACCCGAGTACTATAAGAT 57.097 36.000 0.00 0.00 0.00 2.40
4596 5306 7.147846 CCTTTTACCAACCCGAGTACTATAAGA 60.148 40.741 0.00 0.00 0.00 2.10
4597 5307 6.982724 CCTTTTACCAACCCGAGTACTATAAG 59.017 42.308 0.00 0.00 0.00 1.73
4598 5308 6.127083 CCCTTTTACCAACCCGAGTACTATAA 60.127 42.308 0.00 0.00 0.00 0.98
4599 5309 5.363580 CCCTTTTACCAACCCGAGTACTATA 59.636 44.000 0.00 0.00 0.00 1.31
4600 5310 4.162888 CCCTTTTACCAACCCGAGTACTAT 59.837 45.833 0.00 0.00 0.00 2.12
4601 5311 3.515104 CCCTTTTACCAACCCGAGTACTA 59.485 47.826 0.00 0.00 0.00 1.82
4602 5312 2.303890 CCCTTTTACCAACCCGAGTACT 59.696 50.000 0.00 0.00 0.00 2.73
4603 5313 2.038952 ACCCTTTTACCAACCCGAGTAC 59.961 50.000 0.00 0.00 0.00 2.73
4604 5314 2.302733 GACCCTTTTACCAACCCGAGTA 59.697 50.000 0.00 0.00 0.00 2.59
4605 5315 1.072806 GACCCTTTTACCAACCCGAGT 59.927 52.381 0.00 0.00 0.00 4.18
4606 5316 1.072648 TGACCCTTTTACCAACCCGAG 59.927 52.381 0.00 0.00 0.00 4.63
4607 5317 1.138568 TGACCCTTTTACCAACCCGA 58.861 50.000 0.00 0.00 0.00 5.14
4608 5318 1.202842 AGTGACCCTTTTACCAACCCG 60.203 52.381 0.00 0.00 0.00 5.28
4609 5319 2.670019 AGTGACCCTTTTACCAACCC 57.330 50.000 0.00 0.00 0.00 4.11
4629 5339 7.953493 ACCATTATAAGAAGTGAAGGGGAAAAA 59.047 33.333 0.00 0.00 0.00 1.94
4674 5384 7.716123 TCTCAAGTTAAACGGAAGGAAATGTTA 59.284 33.333 0.00 0.00 0.00 2.41
4687 5397 7.855409 TGTCATGTTTCAATCTCAAGTTAAACG 59.145 33.333 0.00 0.00 31.19 3.60
4797 5507 5.720371 ATGGTGATGAGTATAGAGCTCAC 57.280 43.478 17.77 5.45 44.52 3.51
4830 5540 1.891616 GGAACACTCCTCGGAGGAC 59.108 63.158 22.70 12.33 45.88 3.85
5013 5723 7.979444 TTACATTTTACAAGAACCTCTCCAG 57.021 36.000 0.00 0.00 0.00 3.86
5219 5938 2.301346 CCCCAACTGTCATTAGGATGC 58.699 52.381 0.00 0.00 33.14 3.91
5244 5964 5.007724 GCCAGAAAGTTAGACCATATTTCCG 59.992 44.000 0.00 0.00 31.69 4.30
5251 5971 3.327757 TCACAGCCAGAAAGTTAGACCAT 59.672 43.478 0.00 0.00 0.00 3.55
5270 5990 3.063997 CCTTAACCGTGATCTGCATTCAC 59.936 47.826 16.22 16.22 40.06 3.18
5278 5998 0.831307 GAGCCCCTTAACCGTGATCT 59.169 55.000 0.00 0.00 0.00 2.75
5279 5999 0.831307 AGAGCCCCTTAACCGTGATC 59.169 55.000 0.00 0.00 0.00 2.92
5294 6042 1.576356 ATTCCAGCGAATCGAAGAGC 58.424 50.000 6.91 0.00 43.63 4.09
5300 6048 4.093408 TCAGAGAAAAATTCCAGCGAATCG 59.907 41.667 0.00 0.00 37.76 3.34
5327 6075 4.168291 CCTCGCTGGGGCCTCTTC 62.168 72.222 3.07 0.00 34.44 2.87
5374 6123 4.572389 CGTACCTCTGATCCCATCAAAAAG 59.428 45.833 0.00 0.00 39.11 2.27
5379 6128 2.031870 CACGTACCTCTGATCCCATCA 58.968 52.381 0.00 0.00 37.76 3.07
5380 6129 1.269831 GCACGTACCTCTGATCCCATC 60.270 57.143 0.00 0.00 0.00 3.51
5381 6130 0.753262 GCACGTACCTCTGATCCCAT 59.247 55.000 0.00 0.00 0.00 4.00
5382 6131 0.324368 AGCACGTACCTCTGATCCCA 60.324 55.000 0.00 0.00 0.00 4.37
5402 6426 3.654414 CTCTATTAGGCATGGTTCGTCC 58.346 50.000 0.00 0.00 0.00 4.79
5410 6434 4.130118 ACCGAAAAGCTCTATTAGGCATG 58.870 43.478 0.00 0.00 0.00 4.06
5459 6487 0.462225 GCTCCCGGAGTAAAAGAGCC 60.462 60.000 16.09 0.00 43.27 4.70
5484 6512 3.144657 TCTGAATTCCAAGCAGCTCAA 57.855 42.857 2.27 0.00 0.00 3.02
5511 6551 4.974645 TGGAAGTACTGTTGTTCCAGAT 57.025 40.909 15.73 0.00 43.87 2.90
5598 6693 9.826574 GACAGTTTCTATGTACCACCATATTTA 57.173 33.333 0.00 0.00 0.00 1.40
5608 6703 4.392138 GGCAACAGACAGTTTCTATGTACC 59.608 45.833 0.00 0.00 38.74 3.34
5611 6706 4.085357 TGGCAACAGACAGTTTCTATGT 57.915 40.909 0.00 0.00 46.17 2.29
5672 6769 3.635836 AGGGCTCCAGAAACGTACTATAC 59.364 47.826 0.00 0.00 0.00 1.47
5673 6770 3.907221 AGGGCTCCAGAAACGTACTATA 58.093 45.455 0.00 0.00 0.00 1.31
5674 6771 2.748388 AGGGCTCCAGAAACGTACTAT 58.252 47.619 0.00 0.00 0.00 2.12
5675 6772 2.226962 AGGGCTCCAGAAACGTACTA 57.773 50.000 0.00 0.00 0.00 1.82
5676 6773 1.349067 AAGGGCTCCAGAAACGTACT 58.651 50.000 0.00 0.00 0.00 2.73
5677 6774 2.180432 AAAGGGCTCCAGAAACGTAC 57.820 50.000 0.00 0.00 0.00 3.67
5687 6784 1.723220 GTTCGTGTCTAAAGGGCTCC 58.277 55.000 0.00 0.00 0.00 4.70
5690 6787 1.632948 GCCGTTCGTGTCTAAAGGGC 61.633 60.000 3.42 3.42 45.71 5.19
5707 7729 1.690219 ATGTCCAGTCGGAGATGGCC 61.690 60.000 0.00 0.00 43.53 5.36
5717 7739 2.672478 CGAGACTTGGTCATGTCCAGTC 60.672 54.545 21.94 21.94 38.80 3.51
5718 7740 1.273606 CGAGACTTGGTCATGTCCAGT 59.726 52.381 11.57 11.61 38.80 4.00
5738 7777 2.497675 TGAGTGCTGAGTGGAATAGTCC 59.502 50.000 1.18 1.18 45.21 3.85
5739 7778 3.876274 TGAGTGCTGAGTGGAATAGTC 57.124 47.619 0.00 0.00 0.00 2.59
5743 7782 1.350351 AGCTTGAGTGCTGAGTGGAAT 59.650 47.619 0.00 0.00 42.33 3.01
5751 7790 0.590195 GGTGTTGAGCTTGAGTGCTG 59.410 55.000 0.00 0.00 44.17 4.41
5766 7805 3.537206 GACGAGGCCAAGCAGGTGT 62.537 63.158 5.01 0.00 40.61 4.16
5772 7811 0.678048 AATGGAAGACGAGGCCAAGC 60.678 55.000 5.01 0.00 34.95 4.01
5799 7845 0.469144 GTTTGACATGGTGGGTGGGT 60.469 55.000 0.00 0.00 0.00 4.51
5889 7935 0.534873 TGACCATTCTTCATCGCGGA 59.465 50.000 6.13 0.00 0.00 5.54
5895 7941 2.026822 AGGCGACTTGACCATTCTTCAT 60.027 45.455 0.00 0.00 37.44 2.57
5896 7942 1.347707 AGGCGACTTGACCATTCTTCA 59.652 47.619 0.00 0.00 37.44 3.02
5938 7985 4.437239 CCACCTGCTTCATACTAGTCTTG 58.563 47.826 0.00 0.00 0.00 3.02
5944 7991 0.179084 GCGCCACCTGCTTCATACTA 60.179 55.000 0.00 0.00 38.05 1.82
5999 8054 2.453773 CTTGACTTGCCGTGCTGCTG 62.454 60.000 0.00 0.00 0.00 4.41
6008 8063 2.359230 AGCCGAGCTTGACTTGCC 60.359 61.111 1.22 0.00 33.89 4.52
6012 8067 3.226429 TTGCGAGCCGAGCTTGACT 62.226 57.895 15.00 0.00 42.27 3.41


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

AutoCloner maintained by Alex Coulton.