Multiple sequence alignment - TraesCS4A01G262500

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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 TraesCS4A01G262500 chr4A 100.000 3418 0 0 1 3418 574843011 574839594 0.000000e+00 6312.0
1 TraesCS4A01G262500 chr4D 92.370 3329 128 50 3 3249 28880262 28883546 0.000000e+00 4625.0
2 TraesCS4A01G262500 chr4D 81.818 198 36 0 1535 1732 80836572 80836769 2.110000e-37 167.0
3 TraesCS4A01G262500 chr4D 87.500 96 9 3 3319 3414 28883569 28883661 1.300000e-19 108.0
4 TraesCS4A01G262500 chr4B 91.306 2450 94 67 3 2405 41196204 41198581 0.000000e+00 3234.0
5 TraesCS4A01G262500 chr4B 86.134 851 65 16 2443 3250 41199269 41200109 0.000000e+00 869.0
6 TraesCS4A01G262500 chr3D 98.529 136 2 0 2120 2255 569929255 569929390 1.230000e-59 241.0
7 TraesCS4A01G262500 chr3D 83.412 211 33 2 1534 1743 180470744 180470535 9.680000e-46 195.0
8 TraesCS4A01G262500 chr3D 83.249 197 33 0 1534 1730 546198932 546198736 7.530000e-42 182.0
9 TraesCS4A01G262500 chr3B 83.886 211 32 2 1534 1743 258721284 258721075 2.080000e-47 200.0
10 TraesCS4A01G262500 chr3B 83.756 197 32 0 1534 1730 722590912 722590716 1.620000e-43 187.0
11 TraesCS4A01G262500 chr3A 83.886 211 32 2 1534 1743 225894569 225894360 2.080000e-47 200.0
12 TraesCS4A01G262500 chr7A 76.882 186 33 9 1532 1712 708319219 708319399 2.810000e-16 97.1
13 TraesCS4A01G262500 chr1D 93.750 48 3 0 428 475 413357406 413357453 4.730000e-09 73.1


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 TraesCS4A01G262500 chr4A 574839594 574843011 3417 True 6312.0 6312 100.000 1 3418 1 chr4A.!!$R1 3417
1 TraesCS4A01G262500 chr4D 28880262 28883661 3399 False 2366.5 4625 89.935 3 3414 2 chr4D.!!$F2 3411
2 TraesCS4A01G262500 chr4B 41196204 41200109 3905 False 2051.5 3234 88.720 3 3250 2 chr4B.!!$F1 3247

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
823 853 0.689080 TCATCTCTCTCCAGTGGCCC 60.689 60.000 3.51 0.0 0.0 5.80 F
1434 1478 2.029918 TCATCTATCGCGCACAAGCTAT 60.030 45.455 8.75 0.0 39.1 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1819 1872 0.391263 CCGTGGTGTTCTTAGGGCTC 60.391 60.0 0.0 0.0 0.00 4.70 R
3309 4105 0.320596 CCGTTGTGGTAAAGGCGGTA 60.321 55.0 0.0 0.0 35.11 4.02 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
68 70 6.324770 TGATCTCTCTGAAAGGCACATATGTA 59.675 38.462 8.32 0.00 0.00 2.29
330 341 1.165907 ACACGTCACACATGCTTGGG 61.166 55.000 0.00 0.00 0.00 4.12
415 427 5.590530 TTTGTTGAGCAAATGTAACTGGT 57.409 34.783 0.00 0.00 41.68 4.00
416 428 4.566545 TGTTGAGCAAATGTAACTGGTG 57.433 40.909 0.00 0.00 0.00 4.17
417 429 3.317711 TGTTGAGCAAATGTAACTGGTGG 59.682 43.478 0.00 0.00 0.00 4.61
649 669 1.376812 CGGGGTTGGCCAGTTAGAC 60.377 63.158 5.11 0.00 36.17 2.59
690 716 2.168272 ATCACTTTCCCTTGGCCCCC 62.168 60.000 0.00 0.00 0.00 5.40
728 754 9.493830 TTCTATCTATCTATATATCCCCCACCT 57.506 37.037 0.00 0.00 0.00 4.00
793 823 5.015178 TCTCTTCTCTTCCCTTCTCTCTCTT 59.985 44.000 0.00 0.00 0.00 2.85
795 825 5.480073 TCTTCTCTTCCCTTCTCTCTCTTTG 59.520 44.000 0.00 0.00 0.00 2.77
796 826 3.513515 TCTCTTCCCTTCTCTCTCTTTGC 59.486 47.826 0.00 0.00 0.00 3.68
797 827 3.242867 TCTTCCCTTCTCTCTCTTTGCA 58.757 45.455 0.00 0.00 0.00 4.08
798 828 3.843027 TCTTCCCTTCTCTCTCTTTGCAT 59.157 43.478 0.00 0.00 0.00 3.96
799 829 3.902881 TCCCTTCTCTCTCTTTGCATC 57.097 47.619 0.00 0.00 0.00 3.91
823 853 0.689080 TCATCTCTCTCCAGTGGCCC 60.689 60.000 3.51 0.00 0.00 5.80
850 880 6.830114 AATCGATCGATCTTGGTCTTAAAC 57.170 37.500 29.48 0.00 33.08 2.01
854 884 5.399892 CGATCGATCTTGGTCTTAAACTAGC 59.600 44.000 22.43 0.00 0.00 3.42
857 887 6.698380 TCGATCTTGGTCTTAAACTAGCTTT 58.302 36.000 0.00 0.00 0.00 3.51
858 888 7.833786 TCGATCTTGGTCTTAAACTAGCTTTA 58.166 34.615 0.00 0.00 0.00 1.85
859 889 7.974501 TCGATCTTGGTCTTAAACTAGCTTTAG 59.025 37.037 0.00 0.00 0.00 1.85
861 891 9.438228 GATCTTGGTCTTAAACTAGCTTTAGTT 57.562 33.333 0.00 0.00 41.63 2.24
863 893 9.924650 TCTTGGTCTTAAACTAGCTTTAGTTAG 57.075 33.333 2.32 0.00 39.18 2.34
905 935 5.051891 CTGTTTATGTGCAGCTAGCTTTT 57.948 39.130 16.46 0.64 45.94 2.27
949 983 4.166144 AGAGATAGCTAGCTAGAGGGATCC 59.834 50.000 27.42 14.19 31.45 3.36
963 997 4.923236 AGAGGGATCCATAGAGGTTAGAGA 59.077 45.833 15.23 0.00 39.02 3.10
970 1004 7.234577 GGATCCATAGAGGTTAGAGAGATTTGT 59.765 40.741 6.95 0.00 39.02 2.83
976 1019 7.246171 AGAGGTTAGAGAGATTTGTTGCTTA 57.754 36.000 0.00 0.00 0.00 3.09
977 1020 7.856415 AGAGGTTAGAGAGATTTGTTGCTTAT 58.144 34.615 0.00 0.00 0.00 1.73
982 1025 6.521151 AGAGAGATTTGTTGCTTATTTGGG 57.479 37.500 0.00 0.00 0.00 4.12
983 1026 5.077134 AGAGATTTGTTGCTTATTTGGGC 57.923 39.130 0.00 0.00 0.00 5.36
1266 1310 3.897505 CTGACTTTTGGGGGATTTCTTGT 59.102 43.478 0.00 0.00 0.00 3.16
1267 1311 4.294347 TGACTTTTGGGGGATTTCTTGTT 58.706 39.130 0.00 0.00 0.00 2.83
1268 1312 5.459505 TGACTTTTGGGGGATTTCTTGTTA 58.540 37.500 0.00 0.00 0.00 2.41
1269 1313 5.900123 TGACTTTTGGGGGATTTCTTGTTAA 59.100 36.000 0.00 0.00 0.00 2.01
1359 1403 8.213518 TCTATCACTTGTGGAGCAATTTTATC 57.786 34.615 0.64 0.00 36.36 1.75
1360 1404 8.049117 TCTATCACTTGTGGAGCAATTTTATCT 58.951 33.333 0.64 0.00 36.36 1.98
1361 1405 9.330063 CTATCACTTGTGGAGCAATTTTATCTA 57.670 33.333 0.64 0.00 36.36 1.98
1368 1412 7.338710 TGTGGAGCAATTTTATCTACTAGCTT 58.661 34.615 0.00 0.00 0.00 3.74
1434 1478 2.029918 TCATCTATCGCGCACAAGCTAT 60.030 45.455 8.75 0.00 39.10 2.97
1453 1497 2.309528 TCTATCCATGGTGTCGTTGC 57.690 50.000 12.58 0.00 0.00 4.17
1522 1572 4.549458 CATGGAAAATGACCTGTTGTGTC 58.451 43.478 0.00 0.00 0.00 3.67
1523 1573 3.897239 TGGAAAATGACCTGTTGTGTCT 58.103 40.909 0.00 0.00 33.83 3.41
1524 1574 3.631686 TGGAAAATGACCTGTTGTGTCTG 59.368 43.478 0.00 0.00 33.83 3.51
1526 1576 4.498009 GGAAAATGACCTGTTGTGTCTGTG 60.498 45.833 0.00 0.00 33.83 3.66
1527 1577 3.558931 AATGACCTGTTGTGTCTGTGA 57.441 42.857 0.00 0.00 33.83 3.58
1528 1578 3.777106 ATGACCTGTTGTGTCTGTGAT 57.223 42.857 0.00 0.00 33.83 3.06
1529 1579 3.558931 TGACCTGTTGTGTCTGTGATT 57.441 42.857 0.00 0.00 33.83 2.57
1530 1580 3.884895 TGACCTGTTGTGTCTGTGATTT 58.115 40.909 0.00 0.00 33.83 2.17
1531 1581 3.876914 TGACCTGTTGTGTCTGTGATTTC 59.123 43.478 0.00 0.00 33.83 2.17
1819 1872 1.801913 CGGTGCCGAGAAAGACGAG 60.802 63.158 4.35 0.00 42.83 4.18
1827 1880 1.743958 CGAGAAAGACGAGAGCCCTAA 59.256 52.381 0.00 0.00 0.00 2.69
1837 1890 0.608640 AGAGCCCTAAGAACACCACG 59.391 55.000 0.00 0.00 0.00 4.94
1891 1944 4.133373 ATGGCCGCCTTGCTCCAT 62.133 61.111 11.61 4.56 35.74 3.41
2021 2074 5.777802 CATGCAGGGTTCTAGTATACAGAG 58.222 45.833 5.50 2.12 0.00 3.35
2026 2079 4.579753 AGGGTTCTAGTATACAGAGCGTTC 59.420 45.833 5.50 0.00 0.00 3.95
2029 2082 5.277925 GGTTCTAGTATACAGAGCGTTCTCC 60.278 48.000 5.50 0.00 40.22 3.71
2033 2086 3.570550 AGTATACAGAGCGTTCTCCCATC 59.429 47.826 5.50 0.00 40.22 3.51
2059 2112 6.820656 AGTTTAGCTTGTATGTCTGGAATGAG 59.179 38.462 0.00 0.00 0.00 2.90
2662 3409 9.142014 TCTGTTTGATTATTGGTTATTATGGGG 57.858 33.333 0.00 0.00 0.00 4.96
2683 3430 7.282585 TGGGGTTTTAATCAGTCATGAGATAG 58.717 38.462 0.00 0.00 39.29 2.08
2694 3441 6.672218 TCAGTCATGAGATAGTTTTTCCCCTA 59.328 38.462 0.00 0.00 0.00 3.53
2707 3454 0.042731 TCCCCTAGGACCTTCCACTG 59.957 60.000 11.48 0.00 39.61 3.66
2730 3477 6.650120 TGTCAAAGATAACAGAATAGTCCCC 58.350 40.000 0.00 0.00 0.00 4.81
2732 3479 7.037586 TGTCAAAGATAACAGAATAGTCCCCTT 60.038 37.037 0.00 0.00 0.00 3.95
2735 3482 7.989947 AAGATAACAGAATAGTCCCCTTGTA 57.010 36.000 0.00 0.00 0.00 2.41
2748 3495 2.409975 CCCTTGTATATTGTACCCGCG 58.590 52.381 0.00 0.00 0.00 6.46
2800 3547 0.912006 AGAGCCCCCTCTCCACTTTC 60.912 60.000 0.00 0.00 45.21 2.62
2868 3616 8.421002 ACTAGAAGCAGCAAAAGGAAATAAAAA 58.579 29.630 0.00 0.00 0.00 1.94
2968 3716 5.123227 GGCATAGCTGTTGATAACCTACAA 58.877 41.667 0.00 0.00 30.56 2.41
2986 3734 5.851177 CCTACAAACAGTTAAAATGACTGCG 59.149 40.000 4.30 0.00 46.53 5.18
3080 3853 6.778821 TCATTAAAGATGGAGGTGACTTTCA 58.221 36.000 0.00 0.00 44.43 2.69
3114 3887 0.108992 CACGGAGCCTTTAGTACGCA 60.109 55.000 0.00 0.00 0.00 5.24
3150 3923 4.161377 TGTGTGTGCTTATGTATGCTAGGA 59.839 41.667 0.00 0.00 0.00 2.94
3153 3926 5.070313 TGTGTGCTTATGTATGCTAGGATCA 59.930 40.000 0.00 0.00 0.00 2.92
3156 3929 7.984050 GTGTGCTTATGTATGCTAGGATCATAT 59.016 37.037 0.00 0.00 0.00 1.78
3197 3971 8.586879 TTATCATATGTGGTTTGTTGATTCCA 57.413 30.769 1.90 0.00 0.00 3.53
3198 3972 6.513806 TCATATGTGGTTTGTTGATTCCAG 57.486 37.500 1.90 0.00 0.00 3.86
3224 3998 2.036217 CCGGTATAGGCGTTTATGACCA 59.964 50.000 0.00 0.00 0.00 4.02
3225 3999 3.054878 CGGTATAGGCGTTTATGACCAC 58.945 50.000 0.00 0.00 0.00 4.16
3236 4010 3.431411 TTATGACCACCCCCTCTATGT 57.569 47.619 0.00 0.00 0.00 2.29
3268 4064 2.282110 CCACAACGGTGCCATCCA 60.282 61.111 0.00 0.00 43.88 3.41
3291 4087 6.860080 CATAGATTGGATTTCACTTGCTTGT 58.140 36.000 0.00 0.00 0.00 3.16
3292 4088 7.988737 CATAGATTGGATTTCACTTGCTTGTA 58.011 34.615 0.00 0.00 0.00 2.41
3293 4089 6.899393 AGATTGGATTTCACTTGCTTGTAA 57.101 33.333 0.00 0.00 0.00 2.41
3294 4090 7.472334 AGATTGGATTTCACTTGCTTGTAAT 57.528 32.000 0.00 0.00 0.00 1.89
3295 4091 7.318141 AGATTGGATTTCACTTGCTTGTAATG 58.682 34.615 0.00 0.00 0.00 1.90
3296 4092 6.647334 TTGGATTTCACTTGCTTGTAATGA 57.353 33.333 0.00 0.00 0.00 2.57
3297 4093 6.258230 TGGATTTCACTTGCTTGTAATGAG 57.742 37.500 0.00 0.00 0.00 2.90
3298 4094 5.769662 TGGATTTCACTTGCTTGTAATGAGT 59.230 36.000 0.00 0.00 0.00 3.41
3299 4095 6.265196 TGGATTTCACTTGCTTGTAATGAGTT 59.735 34.615 0.00 0.00 0.00 3.01
3300 4096 6.803807 GGATTTCACTTGCTTGTAATGAGTTC 59.196 38.462 0.00 0.00 0.00 3.01
3301 4097 6.942532 TTTCACTTGCTTGTAATGAGTTCT 57.057 33.333 0.00 0.00 0.00 3.01
3302 4098 6.545504 TTCACTTGCTTGTAATGAGTTCTC 57.454 37.500 0.00 0.00 0.00 2.87
3303 4099 5.858381 TCACTTGCTTGTAATGAGTTCTCT 58.142 37.500 1.53 0.00 0.00 3.10
3304 4100 6.993079 TCACTTGCTTGTAATGAGTTCTCTA 58.007 36.000 1.53 0.00 0.00 2.43
3305 4101 7.441836 TCACTTGCTTGTAATGAGTTCTCTAA 58.558 34.615 1.53 0.00 0.00 2.10
3306 4102 7.931407 TCACTTGCTTGTAATGAGTTCTCTAAA 59.069 33.333 1.53 0.00 0.00 1.85
3307 4103 8.559536 CACTTGCTTGTAATGAGTTCTCTAAAA 58.440 33.333 1.53 0.00 0.00 1.52
3308 4104 9.289782 ACTTGCTTGTAATGAGTTCTCTAAAAT 57.710 29.630 1.53 0.00 0.00 1.82
3312 4108 9.989869 GCTTGTAATGAGTTCTCTAAAATTACC 57.010 33.333 13.28 2.18 0.00 2.85
3314 4110 8.193250 TGTAATGAGTTCTCTAAAATTACCGC 57.807 34.615 13.28 0.00 0.00 5.68
3315 4111 6.679327 AATGAGTTCTCTAAAATTACCGCC 57.321 37.500 1.53 0.00 0.00 6.13
3316 4112 5.416271 TGAGTTCTCTAAAATTACCGCCT 57.584 39.130 1.53 0.00 0.00 5.52
3317 4113 5.801380 TGAGTTCTCTAAAATTACCGCCTT 58.199 37.500 1.53 0.00 0.00 4.35
3318 4114 6.235664 TGAGTTCTCTAAAATTACCGCCTTT 58.764 36.000 1.53 0.00 0.00 3.11
3319 4115 7.388437 TGAGTTCTCTAAAATTACCGCCTTTA 58.612 34.615 1.53 0.00 0.00 1.85
3320 4116 7.332678 TGAGTTCTCTAAAATTACCGCCTTTAC 59.667 37.037 1.53 0.00 0.00 2.01
3321 4117 6.596888 AGTTCTCTAAAATTACCGCCTTTACC 59.403 38.462 0.00 0.00 0.00 2.85
3322 4118 6.052405 TCTCTAAAATTACCGCCTTTACCA 57.948 37.500 0.00 0.00 0.00 3.25
3323 4119 5.876460 TCTCTAAAATTACCGCCTTTACCAC 59.124 40.000 0.00 0.00 0.00 4.16
3324 4120 5.558818 TCTAAAATTACCGCCTTTACCACA 58.441 37.500 0.00 0.00 0.00 4.17
3325 4121 6.002704 TCTAAAATTACCGCCTTTACCACAA 58.997 36.000 0.00 0.00 0.00 3.33
3326 4122 4.508461 AAATTACCGCCTTTACCACAAC 57.492 40.909 0.00 0.00 0.00 3.32
3327 4123 1.510776 TTACCGCCTTTACCACAACG 58.489 50.000 0.00 0.00 0.00 4.10
3328 4124 0.320596 TACCGCCTTTACCACAACGG 60.321 55.000 0.00 0.00 45.86 4.44
3345 4141 1.508632 CGGTATTGCCCGTAGATTGG 58.491 55.000 0.00 0.00 43.07 3.16
3346 4142 1.069513 CGGTATTGCCCGTAGATTGGA 59.930 52.381 0.00 0.00 43.07 3.53
3360 4156 4.119442 AGATTGGATTTCACTTGCATGC 57.881 40.909 11.82 11.82 0.00 4.06
3364 4160 2.563620 TGGATTTCACTTGCATGCATGT 59.436 40.909 28.16 28.16 35.16 3.21
3366 4162 4.403113 TGGATTTCACTTGCATGCATGTAT 59.597 37.500 31.58 23.58 33.79 2.29
3367 4163 4.743151 GGATTTCACTTGCATGCATGTATG 59.257 41.667 31.58 24.79 33.79 2.39
3410 4206 5.524281 TCGCGATAGGTGTTTTGCATAAATA 59.476 36.000 3.71 0.00 0.00 1.40
3414 4210 9.030301 GCGATAGGTGTTTTGCATAAATATTTT 57.970 29.630 5.91 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.961277 GTGAGCCGGTCTTGGTGTG 60.961 63.158 1.90 0.00 0.00 3.82
1 2 2.426023 GTGAGCCGGTCTTGGTGT 59.574 61.111 1.90 0.00 0.00 4.16
68 70 4.747931 GCCTGCAGGTTGGATCACTATATT 60.748 45.833 32.81 0.00 37.57 1.28
330 341 3.840890 TTCTTGTGTGTGTTTGTGTCC 57.159 42.857 0.00 0.00 0.00 4.02
364 375 5.784578 ACGGAAAAGAAACCATTTAAGCT 57.215 34.783 0.00 0.00 0.00 3.74
371 382 6.399639 AACAACATACGGAAAAGAAACCAT 57.600 33.333 0.00 0.00 0.00 3.55
415 427 0.894835 TAATCTGCAGTGTCTCGCCA 59.105 50.000 14.67 0.00 0.00 5.69
416 428 1.134965 ACTAATCTGCAGTGTCTCGCC 60.135 52.381 14.67 0.00 0.00 5.54
417 429 2.285827 ACTAATCTGCAGTGTCTCGC 57.714 50.000 14.67 0.00 0.00 5.03
502 518 0.456312 ACGTTAAGCTTCGCGAGAGG 60.456 55.000 23.40 5.14 43.69 3.69
631 651 1.376812 GTCTAACTGGCCAACCCCG 60.377 63.158 7.01 0.00 33.59 5.73
649 669 1.275856 AGCAGGCAGTTTCTCTCTCTG 59.724 52.381 0.00 0.00 0.00 3.35
690 716 5.650283 AGATAGATAGAAAGGTGGGGAGAG 58.350 45.833 0.00 0.00 0.00 3.20
728 754 6.438741 TGAGAAGAGGCAAGAGAAAGATAAGA 59.561 38.462 0.00 0.00 0.00 2.10
793 823 4.019950 TGGAGAGAGATGAACAAGATGCAA 60.020 41.667 0.00 0.00 0.00 4.08
795 825 4.121317 CTGGAGAGAGATGAACAAGATGC 58.879 47.826 0.00 0.00 0.00 3.91
796 826 5.110598 CACTGGAGAGAGATGAACAAGATG 58.889 45.833 0.00 0.00 0.00 2.90
797 827 4.161942 CCACTGGAGAGAGATGAACAAGAT 59.838 45.833 0.00 0.00 0.00 2.40
798 828 3.513119 CCACTGGAGAGAGATGAACAAGA 59.487 47.826 0.00 0.00 0.00 3.02
799 829 3.859443 CCACTGGAGAGAGATGAACAAG 58.141 50.000 0.00 0.00 0.00 3.16
857 887 8.504005 GCAGCAAAAGAATGAACTAACTAACTA 58.496 33.333 0.00 0.00 0.00 2.24
858 888 7.229506 AGCAGCAAAAGAATGAACTAACTAACT 59.770 33.333 0.00 0.00 0.00 2.24
859 889 7.324616 CAGCAGCAAAAGAATGAACTAACTAAC 59.675 37.037 0.00 0.00 0.00 2.34
861 891 6.486657 ACAGCAGCAAAAGAATGAACTAACTA 59.513 34.615 0.00 0.00 0.00 2.24
862 892 5.300286 ACAGCAGCAAAAGAATGAACTAACT 59.700 36.000 0.00 0.00 0.00 2.24
863 893 5.523369 ACAGCAGCAAAAGAATGAACTAAC 58.477 37.500 0.00 0.00 0.00 2.34
870 900 5.389098 GCACATAAACAGCAGCAAAAGAATG 60.389 40.000 0.00 0.00 0.00 2.67
949 983 7.271511 AGCAACAAATCTCTCTAACCTCTATG 58.728 38.462 0.00 0.00 0.00 2.23
963 997 3.509575 TCGCCCAAATAAGCAACAAATCT 59.490 39.130 0.00 0.00 0.00 2.40
970 1004 2.031258 TCGATCGCCCAAATAAGCAA 57.969 45.000 11.09 0.00 0.00 3.91
994 1037 1.222936 CTCTGGTGCACATCCTCCC 59.777 63.158 20.43 0.00 0.00 4.30
995 1038 1.222936 CCTCTGGTGCACATCCTCC 59.777 63.158 20.43 0.00 0.00 4.30
1266 1310 7.541162 TCGAAATTCTCTCGTGGACTAATTAA 58.459 34.615 0.00 0.00 37.56 1.40
1267 1311 7.092137 TCGAAATTCTCTCGTGGACTAATTA 57.908 36.000 0.00 0.00 37.56 1.40
1268 1312 5.962433 TCGAAATTCTCTCGTGGACTAATT 58.038 37.500 0.00 0.00 37.56 1.40
1269 1313 5.578005 TCGAAATTCTCTCGTGGACTAAT 57.422 39.130 0.00 0.00 37.56 1.73
1337 1381 7.831193 AGTAGATAAAATTGCTCCACAAGTGAT 59.169 33.333 0.94 0.00 42.87 3.06
1368 1412 6.546428 AATTAACTCTCTAAGTGGCTAGCA 57.454 37.500 18.24 0.00 38.58 3.49
1404 1448 3.987868 TGCGCGATAGATGAATTAGGAAC 59.012 43.478 12.10 0.00 39.76 3.62
1434 1478 1.552792 TGCAACGACACCATGGATAGA 59.447 47.619 21.47 0.00 0.00 1.98
1453 1497 1.063174 GAAGCTTAGGCGATGTGCTTG 59.937 52.381 0.00 0.00 42.95 4.01
1491 1535 4.528206 AGGTCATTTTCCATGGGTTTTCTC 59.472 41.667 13.02 0.00 0.00 2.87
1492 1536 4.284234 CAGGTCATTTTCCATGGGTTTTCT 59.716 41.667 13.02 0.00 0.00 2.52
1493 1537 4.040339 ACAGGTCATTTTCCATGGGTTTTC 59.960 41.667 13.02 0.00 0.00 2.29
1494 1538 3.973305 ACAGGTCATTTTCCATGGGTTTT 59.027 39.130 13.02 0.00 0.00 2.43
1495 1539 3.586429 ACAGGTCATTTTCCATGGGTTT 58.414 40.909 13.02 0.00 0.00 3.27
1522 1572 3.055240 AGCTCTTCCCTGAGAAATCACAG 60.055 47.826 1.41 1.41 36.23 3.66
1523 1573 2.909006 AGCTCTTCCCTGAGAAATCACA 59.091 45.455 0.00 0.00 36.23 3.58
1524 1574 3.269178 CAGCTCTTCCCTGAGAAATCAC 58.731 50.000 0.00 0.00 36.23 3.06
1526 1576 2.287769 GCAGCTCTTCCCTGAGAAATC 58.712 52.381 0.00 0.00 36.23 2.17
1527 1577 1.632409 TGCAGCTCTTCCCTGAGAAAT 59.368 47.619 0.00 0.00 36.23 2.17
1528 1578 1.002888 CTGCAGCTCTTCCCTGAGAAA 59.997 52.381 0.00 0.00 36.23 2.52
1529 1579 0.612229 CTGCAGCTCTTCCCTGAGAA 59.388 55.000 0.00 0.00 36.23 2.87
1530 1580 1.263342 CCTGCAGCTCTTCCCTGAGA 61.263 60.000 8.66 0.00 36.23 3.27
1531 1581 1.221293 CCTGCAGCTCTTCCCTGAG 59.779 63.158 8.66 0.00 37.16 3.35
1819 1872 0.391263 CCGTGGTGTTCTTAGGGCTC 60.391 60.000 0.00 0.00 0.00 4.70
1865 1918 2.203153 GGCGGCCATGGTATTCGT 60.203 61.111 15.62 0.00 0.00 3.85
1891 1944 3.932710 CAGCAAATTCTCTGCGGTACTTA 59.067 43.478 0.00 0.00 44.75 2.24
2021 2074 1.666189 GCTAAACTGATGGGAGAACGC 59.334 52.381 0.00 0.00 0.00 4.84
2026 2079 5.431765 ACATACAAGCTAAACTGATGGGAG 58.568 41.667 0.00 0.00 0.00 4.30
2029 2082 5.295292 CCAGACATACAAGCTAAACTGATGG 59.705 44.000 0.00 0.00 0.00 3.51
2033 2086 6.595326 TCATTCCAGACATACAAGCTAAACTG 59.405 38.462 0.00 0.00 0.00 3.16
2059 2112 5.596845 TCTGCAAAACAAACCCTAATTGAC 58.403 37.500 0.00 0.00 0.00 3.18
2268 2334 7.713942 CCCTAGTTAAATACTGACCCATAACAC 59.286 40.741 0.00 0.00 37.73 3.32
2427 2505 7.430793 GCATGTGTGCGTACATCAATAAATTAA 59.569 33.333 10.21 0.00 42.28 1.40
2580 3309 5.194740 TCCCATGACTGATTAAAACCCCATA 59.805 40.000 0.00 0.00 0.00 2.74
2581 3310 4.016666 TCCCATGACTGATTAAAACCCCAT 60.017 41.667 0.00 0.00 0.00 4.00
2583 3312 3.976015 TCCCATGACTGATTAAAACCCC 58.024 45.455 0.00 0.00 0.00 4.95
2683 3430 2.377531 TGGAAGGTCCTAGGGGAAAAAC 59.622 50.000 9.46 0.00 44.15 2.43
2694 3441 2.408565 TCTTTGACAGTGGAAGGTCCT 58.591 47.619 0.00 0.00 37.46 3.85
2707 3454 6.890293 AGGGGACTATTCTGTTATCTTTGAC 58.110 40.000 0.00 0.00 40.61 3.18
2730 3477 3.973657 ACTCGCGGGTACAATATACAAG 58.026 45.455 11.59 0.00 0.00 3.16
2732 3479 2.294233 GGACTCGCGGGTACAATATACA 59.706 50.000 18.74 0.00 0.00 2.29
2735 3482 1.405872 TGGACTCGCGGGTACAATAT 58.594 50.000 24.81 0.00 0.00 1.28
2786 3533 4.846367 TGATATATGGAAAGTGGAGAGGGG 59.154 45.833 0.00 0.00 0.00 4.79
2794 3541 7.554118 ACAAGTGGTTCTGATATATGGAAAGTG 59.446 37.037 0.00 0.00 0.00 3.16
2795 3542 7.633789 ACAAGTGGTTCTGATATATGGAAAGT 58.366 34.615 0.00 0.00 0.00 2.66
2800 3547 8.400947 CAAAAGACAAGTGGTTCTGATATATGG 58.599 37.037 0.00 0.00 0.00 2.74
2868 3616 0.622136 TCTGCCAGGATTGTGCATCT 59.378 50.000 0.00 0.00 32.55 2.90
2951 3699 5.941948 ACTGTTTGTAGGTTATCAACAGC 57.058 39.130 9.68 0.00 32.08 4.40
2968 3716 2.621055 TGCCGCAGTCATTTTAACTGTT 59.379 40.909 0.00 0.00 44.79 3.16
2979 3727 1.804151 GAGTTTATGTTGCCGCAGTCA 59.196 47.619 0.00 0.00 0.00 3.41
2984 3732 1.398390 CTGGAGAGTTTATGTTGCCGC 59.602 52.381 0.00 0.00 0.00 6.53
2986 3734 2.026262 TCCCTGGAGAGTTTATGTTGCC 60.026 50.000 0.00 0.00 0.00 4.52
3080 3853 3.799232 GCTCCGTGAGTGTCAAGTTTAGT 60.799 47.826 3.38 0.00 31.39 2.24
3114 3887 5.683876 AGCACACACATCCTTCTAGTAAT 57.316 39.130 0.00 0.00 0.00 1.89
3181 3955 5.619086 CGGAATACTGGAATCAACAAACCAC 60.619 44.000 0.00 0.00 0.00 4.16
3184 3958 4.457949 ACCGGAATACTGGAATCAACAAAC 59.542 41.667 9.46 0.00 44.87 2.93
3185 3959 4.658063 ACCGGAATACTGGAATCAACAAA 58.342 39.130 9.46 0.00 44.87 2.83
3197 3971 5.477984 TCATAAACGCCTATACCGGAATACT 59.522 40.000 9.46 0.00 0.00 2.12
3198 3972 5.574443 GTCATAAACGCCTATACCGGAATAC 59.426 44.000 9.46 0.00 0.00 1.89
3224 3998 1.274416 ACCACATGACATAGAGGGGGT 60.274 52.381 0.00 0.00 0.00 4.95
3225 3999 1.511613 ACCACATGACATAGAGGGGG 58.488 55.000 0.00 0.00 0.00 5.40
3268 4064 8.579850 TTACAAGCAAGTGAAATCCAATCTAT 57.420 30.769 0.00 0.00 0.00 1.98
3277 4073 7.446625 AGAGAACTCATTACAAGCAAGTGAAAT 59.553 33.333 4.64 0.00 0.00 2.17
3278 4074 6.767902 AGAGAACTCATTACAAGCAAGTGAAA 59.232 34.615 4.64 0.00 0.00 2.69
3279 4075 6.291377 AGAGAACTCATTACAAGCAAGTGAA 58.709 36.000 4.64 0.00 0.00 3.18
3280 4076 5.858381 AGAGAACTCATTACAAGCAAGTGA 58.142 37.500 4.64 0.00 0.00 3.41
3281 4077 7.658179 TTAGAGAACTCATTACAAGCAAGTG 57.342 36.000 4.64 0.00 0.00 3.16
3282 4078 8.677148 TTTTAGAGAACTCATTACAAGCAAGT 57.323 30.769 4.64 0.00 0.00 3.16
3286 4082 9.989869 GGTAATTTTAGAGAACTCATTACAAGC 57.010 33.333 16.78 0.00 31.90 4.01
3288 4084 8.662141 GCGGTAATTTTAGAGAACTCATTACAA 58.338 33.333 16.78 1.33 31.90 2.41
3289 4085 7.279313 GGCGGTAATTTTAGAGAACTCATTACA 59.721 37.037 16.78 0.00 31.90 2.41
3290 4086 7.494952 AGGCGGTAATTTTAGAGAACTCATTAC 59.505 37.037 4.64 8.68 0.00 1.89
3291 4087 7.562135 AGGCGGTAATTTTAGAGAACTCATTA 58.438 34.615 4.64 0.00 0.00 1.90
3292 4088 6.415573 AGGCGGTAATTTTAGAGAACTCATT 58.584 36.000 4.64 0.00 0.00 2.57
3293 4089 5.990668 AGGCGGTAATTTTAGAGAACTCAT 58.009 37.500 4.64 0.00 0.00 2.90
3294 4090 5.416271 AGGCGGTAATTTTAGAGAACTCA 57.584 39.130 4.64 0.00 0.00 3.41
3295 4091 6.738832 AAAGGCGGTAATTTTAGAGAACTC 57.261 37.500 0.00 0.00 0.00 3.01
3296 4092 6.596888 GGTAAAGGCGGTAATTTTAGAGAACT 59.403 38.462 0.00 0.00 0.00 3.01
3297 4093 6.372381 TGGTAAAGGCGGTAATTTTAGAGAAC 59.628 38.462 0.00 0.00 0.00 3.01
3298 4094 6.372381 GTGGTAAAGGCGGTAATTTTAGAGAA 59.628 38.462 0.00 0.00 0.00 2.87
3299 4095 5.876460 GTGGTAAAGGCGGTAATTTTAGAGA 59.124 40.000 0.00 0.00 0.00 3.10
3300 4096 5.644636 TGTGGTAAAGGCGGTAATTTTAGAG 59.355 40.000 0.00 0.00 0.00 2.43
3301 4097 5.558818 TGTGGTAAAGGCGGTAATTTTAGA 58.441 37.500 0.00 0.00 0.00 2.10
3302 4098 5.883503 TGTGGTAAAGGCGGTAATTTTAG 57.116 39.130 0.00 0.00 0.00 1.85
3303 4099 5.334724 CGTTGTGGTAAAGGCGGTAATTTTA 60.335 40.000 0.00 0.00 0.00 1.52
3304 4100 4.557097 CGTTGTGGTAAAGGCGGTAATTTT 60.557 41.667 0.00 0.00 0.00 1.82
3305 4101 3.058085 CGTTGTGGTAAAGGCGGTAATTT 60.058 43.478 0.00 0.00 0.00 1.82
3306 4102 2.485038 CGTTGTGGTAAAGGCGGTAATT 59.515 45.455 0.00 0.00 0.00 1.40
3307 4103 2.078392 CGTTGTGGTAAAGGCGGTAAT 58.922 47.619 0.00 0.00 0.00 1.89
3308 4104 1.510776 CGTTGTGGTAAAGGCGGTAA 58.489 50.000 0.00 0.00 0.00 2.85
3309 4105 0.320596 CCGTTGTGGTAAAGGCGGTA 60.321 55.000 0.00 0.00 35.11 4.02
3310 4106 1.598685 CCGTTGTGGTAAAGGCGGT 60.599 57.895 0.00 0.00 35.11 5.68
3311 4107 3.259930 CCGTTGTGGTAAAGGCGG 58.740 61.111 0.00 0.00 0.00 6.13
3327 4123 2.922740 TCCAATCTACGGGCAATACC 57.077 50.000 0.00 0.00 37.93 2.73
3328 4124 4.819630 TGAAATCCAATCTACGGGCAATAC 59.180 41.667 0.00 0.00 0.00 1.89
3329 4125 4.819630 GTGAAATCCAATCTACGGGCAATA 59.180 41.667 0.00 0.00 0.00 1.90
3330 4126 3.632145 GTGAAATCCAATCTACGGGCAAT 59.368 43.478 0.00 0.00 0.00 3.56
3331 4127 3.013921 GTGAAATCCAATCTACGGGCAA 58.986 45.455 0.00 0.00 0.00 4.52
3332 4128 2.238646 AGTGAAATCCAATCTACGGGCA 59.761 45.455 0.00 0.00 0.00 5.36
3333 4129 2.919228 AGTGAAATCCAATCTACGGGC 58.081 47.619 0.00 0.00 0.00 6.13
3334 4130 3.065371 GCAAGTGAAATCCAATCTACGGG 59.935 47.826 0.00 0.00 0.00 5.28
3335 4131 3.689161 TGCAAGTGAAATCCAATCTACGG 59.311 43.478 0.00 0.00 0.00 4.02
3336 4132 4.944962 TGCAAGTGAAATCCAATCTACG 57.055 40.909 0.00 0.00 0.00 3.51
3337 4133 5.039333 GCATGCAAGTGAAATCCAATCTAC 58.961 41.667 14.21 0.00 0.00 2.59
3338 4134 4.705991 TGCATGCAAGTGAAATCCAATCTA 59.294 37.500 20.30 0.00 0.00 1.98
3339 4135 3.512329 TGCATGCAAGTGAAATCCAATCT 59.488 39.130 20.30 0.00 0.00 2.40
3340 4136 3.852286 TGCATGCAAGTGAAATCCAATC 58.148 40.909 20.30 0.00 0.00 2.67
3341 4137 3.965379 TGCATGCAAGTGAAATCCAAT 57.035 38.095 20.30 0.00 0.00 3.16
3342 4138 3.007074 ACATGCATGCAAGTGAAATCCAA 59.993 39.130 26.39 0.00 0.00 3.53
3343 4139 2.563620 ACATGCATGCAAGTGAAATCCA 59.436 40.909 26.39 0.00 0.00 3.41
3344 4140 3.241067 ACATGCATGCAAGTGAAATCC 57.759 42.857 26.39 0.00 0.00 3.01
3345 4141 5.883328 CATACATGCATGCAAGTGAAATC 57.117 39.130 32.61 0.00 0.00 2.17
3360 4156 4.022935 ACACACAAGGAAACTGCATACATG 60.023 41.667 0.00 0.00 42.68 3.21
3364 4160 2.293122 GCACACACAAGGAAACTGCATA 59.707 45.455 0.00 0.00 42.68 3.14
3366 4162 0.455410 GCACACACAAGGAAACTGCA 59.545 50.000 0.00 0.00 42.68 4.41
3367 4163 0.740737 AGCACACACAAGGAAACTGC 59.259 50.000 0.00 0.00 42.68 4.40
3368 4164 1.003545 CGAGCACACACAAGGAAACTG 60.004 52.381 0.00 0.00 42.68 3.16
3375 4171 0.642291 CTATCGCGAGCACACACAAG 59.358 55.000 16.66 0.00 0.00 3.16
3379 4175 1.153842 CACCTATCGCGAGCACACA 60.154 57.895 16.66 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.