Multiple sequence alignment - TraesCS4D01G191200

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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 TraesCS4D01G191200 chr4D 100.000 2675 0 0 1 2675 334631132 334633806 0.000000e+00 4940
1 TraesCS4D01G191200 chr4A 92.835 1926 71 31 492 2377 138833668 138831770 0.000000e+00 2730
2 TraesCS4D01G191200 chr4A 92.668 491 17 13 3 478 138834140 138833654 0.000000e+00 689
3 TraesCS4D01G191200 chr4A 94.958 238 10 2 2439 2675 138831763 138831527 3.250000e-99 372
4 TraesCS4D01G191200 chr4B 93.584 1730 59 28 489 2199 412590114 412591810 0.000000e+00 2532
5 TraesCS4D01G191200 chr4B 92.791 430 22 5 2 422 412588389 412588818 4.890000e-172 614
6 TraesCS4D01G191200 chr4B 97.009 234 7 0 2442 2675 412592068 412592301 6.940000e-106 394
7 TraesCS4D01G191200 chr4B 81.461 178 14 6 2197 2374 412591896 412592054 7.770000e-26 128
8 TraesCS4D01G191200 chr2B 84.270 534 75 7 1139 1667 65883477 65882948 1.840000e-141 512
9 TraesCS4D01G191200 chr2D 84.142 536 72 10 1139 1667 37646346 37645817 8.540000e-140 507
10 TraesCS4D01G191200 chr2A 83.426 537 74 12 1139 1667 42495221 42494692 4.000000e-133 484
11 TraesCS4D01G191200 chr1D 79.882 507 85 9 1162 1664 392697011 392697504 3.280000e-94 355
12 TraesCS4D01G191200 chr1A 79.644 506 86 9 1162 1663 492652782 492652290 5.480000e-92 348
13 TraesCS4D01G191200 chr1B 79.290 507 88 9 1162 1664 529998581 529998088 3.300000e-89 339
14 TraesCS4D01G191200 chr3D 77.953 508 89 14 1147 1638 454904066 454904566 2.010000e-76 296


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 TraesCS4D01G191200 chr4D 334631132 334633806 2674 False 4940.000000 4940 100.00000 1 2675 1 chr4D.!!$F1 2674
1 TraesCS4D01G191200 chr4A 138831527 138834140 2613 True 1263.666667 2730 93.48700 3 2675 3 chr4A.!!$R1 2672
2 TraesCS4D01G191200 chr4B 412588389 412592301 3912 False 917.000000 2532 91.21125 2 2675 4 chr4B.!!$F1 2673
3 TraesCS4D01G191200 chr2B 65882948 65883477 529 True 512.000000 512 84.27000 1139 1667 1 chr2B.!!$R1 528
4 TraesCS4D01G191200 chr2D 37645817 37646346 529 True 507.000000 507 84.14200 1139 1667 1 chr2D.!!$R1 528
5 TraesCS4D01G191200 chr2A 42494692 42495221 529 True 484.000000 484 83.42600 1139 1667 1 chr2A.!!$R1 528
6 TraesCS4D01G191200 chr3D 454904066 454904566 500 False 296.000000 296 77.95300 1147 1638 1 chr3D.!!$F1 491

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
940 2220 0.179029 AAAGATATTCCACCGGCCGG 60.179 55.0 42.17 42.17 42.03 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2396 3793 0.098025 CTGCTCTTCTCGACCTCGTC 59.902 60.0 0.0 0.0 40.8 4.2 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
167 168 2.078665 GGATAGGGCAAGAGGGGCA 61.079 63.158 0.00 0.00 34.52 5.36
201 202 1.407979 GAAATGAGCATCCAGGGCAAG 59.592 52.381 0.00 0.00 0.00 4.01
202 203 1.041447 AATGAGCATCCAGGGCAAGC 61.041 55.000 0.00 0.00 0.00 4.01
215 216 2.842256 GCAAGCACAGCACAGCACT 61.842 57.895 0.00 0.00 0.00 4.40
301 310 5.642063 CCGGCCACTCGTATCATTAATTAAT 59.358 40.000 2.24 4.81 0.00 1.40
303 312 7.332430 CCGGCCACTCGTATCATTAATTAATAA 59.668 37.037 10.34 0.00 0.00 1.40
304 313 8.380644 CGGCCACTCGTATCATTAATTAATAAG 58.619 37.037 10.34 0.26 0.00 1.73
365 376 0.384669 CCGGCGTAGGAGTTAGAAGG 59.615 60.000 6.01 0.00 0.00 3.46
371 382 3.857756 GCGTAGGAGTTAGAAGGCATAGC 60.858 52.174 0.00 0.00 0.00 2.97
422 440 2.365617 ACCCAGTATTGAGCTACATCCG 59.634 50.000 0.00 0.00 0.00 4.18
469 1744 5.190925 ACCCTAGTAGCATGTGGTGAAATAA 59.809 40.000 0.00 0.00 0.00 1.40
470 1745 6.126478 ACCCTAGTAGCATGTGGTGAAATAAT 60.126 38.462 0.00 0.00 0.00 1.28
471 1746 6.205464 CCCTAGTAGCATGTGGTGAAATAATG 59.795 42.308 0.00 0.00 0.00 1.90
472 1747 6.205464 CCTAGTAGCATGTGGTGAAATAATGG 59.795 42.308 0.00 0.00 0.00 3.16
473 1748 5.754782 AGTAGCATGTGGTGAAATAATGGA 58.245 37.500 0.00 0.00 0.00 3.41
474 1749 6.186957 AGTAGCATGTGGTGAAATAATGGAA 58.813 36.000 0.00 0.00 0.00 3.53
475 1750 6.835488 AGTAGCATGTGGTGAAATAATGGAAT 59.165 34.615 0.00 0.00 0.00 3.01
476 1751 6.549433 AGCATGTGGTGAAATAATGGAATT 57.451 33.333 0.00 0.00 41.28 2.17
477 1752 6.949715 AGCATGTGGTGAAATAATGGAATTT 58.050 32.000 0.00 0.00 37.87 1.82
478 1753 7.396418 AGCATGTGGTGAAATAATGGAATTTT 58.604 30.769 0.00 0.00 37.87 1.82
479 1754 7.884354 AGCATGTGGTGAAATAATGGAATTTTT 59.116 29.630 0.00 0.00 37.87 1.94
576 1851 9.884465 CTTTATTAGCAAGTGTAATAATGGAGC 57.116 33.333 0.00 0.00 34.07 4.70
727 2002 5.318630 TGCTCCGGAATTTAAACCTTTAGT 58.681 37.500 5.23 0.00 0.00 2.24
939 2219 1.226746 GAAAGATATTCCACCGGCCG 58.773 55.000 21.04 21.04 0.00 6.13
940 2220 0.179029 AAAGATATTCCACCGGCCGG 60.179 55.000 42.17 42.17 42.03 6.13
941 2221 2.668550 GATATTCCACCGGCCGGC 60.669 66.667 43.58 21.18 39.32 6.13
1071 2351 2.490217 CACCACCGAGTCCTAGCG 59.510 66.667 0.00 0.00 0.00 4.26
1077 2357 3.823330 CGAGTCCTAGCGGGCGTT 61.823 66.667 0.00 0.00 40.84 4.84
1551 2843 3.360340 ACCGTCGTCGTGGAGTCC 61.360 66.667 0.73 0.73 35.01 3.85
1698 2990 1.307343 CCTCCACCTCCCTGGATGT 60.307 63.158 0.00 0.00 39.72 3.06
1703 2995 1.206878 CACCTCCCTGGATGTGATCA 58.793 55.000 14.31 0.00 41.24 2.92
1739 3032 1.094785 CGGGATGGATGTGTGTTTCC 58.905 55.000 0.00 0.00 0.00 3.13
2037 3336 6.349611 CCTTGTGTTGTTGAGCATAGCTAATT 60.350 38.462 0.00 0.00 39.88 1.40
2040 3339 8.279970 TGTGTTGTTGAGCATAGCTAATTAAT 57.720 30.769 0.00 0.00 39.88 1.40
2041 3340 8.397906 TGTGTTGTTGAGCATAGCTAATTAATC 58.602 33.333 0.00 0.00 39.88 1.75
2043 3342 8.955388 TGTTGTTGAGCATAGCTAATTAATCAA 58.045 29.630 0.00 2.10 39.88 2.57
2044 3343 9.443283 GTTGTTGAGCATAGCTAATTAATCAAG 57.557 33.333 0.00 0.00 39.88 3.02
2046 3345 9.394767 TGTTGAGCATAGCTAATTAATCAAGAA 57.605 29.630 0.00 0.00 39.88 2.52
2047 3346 9.657121 GTTGAGCATAGCTAATTAATCAAGAAC 57.343 33.333 0.00 0.00 39.88 3.01
2049 3348 9.394767 TGAGCATAGCTAATTAATCAAGAACAA 57.605 29.630 0.00 0.00 39.88 2.83
2066 3369 5.109903 AGAACAATACAGTCTTATCGTGGC 58.890 41.667 0.00 0.00 0.00 5.01
2074 3377 1.026584 TCTTATCGTGGCGGATCGAA 58.973 50.000 0.00 0.00 39.45 3.71
2081 3384 0.165944 GTGGCGGATCGAACTTGTTG 59.834 55.000 0.00 0.00 0.00 3.33
2082 3385 0.250124 TGGCGGATCGAACTTGTTGT 60.250 50.000 0.00 0.00 0.00 3.32
2083 3386 0.872388 GGCGGATCGAACTTGTTGTT 59.128 50.000 0.00 0.00 42.38 2.83
2084 3387 2.070783 GGCGGATCGAACTTGTTGTTA 58.929 47.619 0.00 0.00 39.30 2.41
2085 3388 2.481185 GGCGGATCGAACTTGTTGTTAA 59.519 45.455 0.00 0.00 39.30 2.01
2086 3389 3.058777 GGCGGATCGAACTTGTTGTTAAA 60.059 43.478 0.00 0.00 39.30 1.52
2087 3390 4.379082 GGCGGATCGAACTTGTTGTTAAAT 60.379 41.667 0.00 0.00 39.30 1.40
2088 3391 5.151389 GCGGATCGAACTTGTTGTTAAATT 58.849 37.500 0.00 0.00 39.30 1.82
2089 3392 5.059221 GCGGATCGAACTTGTTGTTAAATTG 59.941 40.000 0.00 0.00 39.30 2.32
2090 3393 5.059221 CGGATCGAACTTGTTGTTAAATTGC 59.941 40.000 0.00 0.00 39.30 3.56
2091 3394 5.059221 GGATCGAACTTGTTGTTAAATTGCG 59.941 40.000 0.00 0.00 39.30 4.85
2092 3395 3.726730 TCGAACTTGTTGTTAAATTGCGC 59.273 39.130 0.00 0.00 39.30 6.09
2093 3396 3.483922 CGAACTTGTTGTTAAATTGCGCA 59.516 39.130 5.66 5.66 39.30 6.09
2094 3397 4.602957 CGAACTTGTTGTTAAATTGCGCAC 60.603 41.667 11.12 0.00 39.30 5.34
2095 3398 3.775202 ACTTGTTGTTAAATTGCGCACA 58.225 36.364 11.12 0.00 0.00 4.57
2096 3399 4.367450 ACTTGTTGTTAAATTGCGCACAT 58.633 34.783 11.12 4.17 0.00 3.21
2097 3400 5.524284 ACTTGTTGTTAAATTGCGCACATA 58.476 33.333 11.12 0.00 0.00 2.29
2098 3401 5.401079 ACTTGTTGTTAAATTGCGCACATAC 59.599 36.000 11.12 4.91 0.00 2.39
2099 3402 4.230657 TGTTGTTAAATTGCGCACATACC 58.769 39.130 11.12 0.00 0.00 2.73
2100 3403 3.124316 TGTTAAATTGCGCACATACCG 57.876 42.857 11.12 0.00 0.00 4.02
2101 3404 2.484651 TGTTAAATTGCGCACATACCGT 59.515 40.909 11.12 0.00 0.00 4.83
2102 3405 3.683340 TGTTAAATTGCGCACATACCGTA 59.317 39.130 11.12 0.00 0.00 4.02
2108 3413 0.808453 GCGCACATACCGTACCACAT 60.808 55.000 0.30 0.00 0.00 3.21
2109 3414 1.205657 CGCACATACCGTACCACATC 58.794 55.000 0.00 0.00 0.00 3.06
2119 3424 7.225931 ACATACCGTACCACATCAAATAATGAC 59.774 37.037 0.00 0.00 41.93 3.06
2122 3427 5.051039 CCGTACCACATCAAATAATGACGAG 60.051 44.000 0.00 0.00 41.93 4.18
2156 3461 5.592104 TGGTATGGTACTCTATGTGTGTG 57.408 43.478 0.00 0.00 0.00 3.82
2168 3473 0.392706 TGTGTGTGTCCTAGCTGGTG 59.607 55.000 0.00 0.00 37.07 4.17
2193 3498 7.746526 GTCAGATGACCAAATTTATTGCTTC 57.253 36.000 1.33 0.00 39.07 3.86
2194 3499 7.315142 GTCAGATGACCAAATTTATTGCTTCA 58.685 34.615 1.33 0.00 39.07 3.02
2195 3500 7.274250 GTCAGATGACCAAATTTATTGCTTCAC 59.726 37.037 1.33 0.00 39.07 3.18
2263 3655 3.671716 ACCGATAACTTTGGTCACTTCC 58.328 45.455 0.00 0.00 37.60 3.46
2266 3658 4.700213 CCGATAACTTTGGTCACTTCCATT 59.300 41.667 0.00 0.00 37.33 3.16
2267 3659 5.183140 CCGATAACTTTGGTCACTTCCATTT 59.817 40.000 0.00 0.00 37.33 2.32
2314 3706 2.342650 GCCGGCAGATGCTCCAAAA 61.343 57.895 24.80 0.00 41.70 2.44
2316 3708 0.819582 CCGGCAGATGCTCCAAAATT 59.180 50.000 4.59 0.00 41.70 1.82
2319 3711 3.820467 CCGGCAGATGCTCCAAAATTATA 59.180 43.478 4.59 0.00 41.70 0.98
2321 3713 5.047802 CCGGCAGATGCTCCAAAATTATAAT 60.048 40.000 4.59 0.00 41.70 1.28
2343 3740 2.005451 CTATAAGCAGCCGATCCATGC 58.995 52.381 3.82 3.82 40.29 4.06
2370 3767 3.170791 TGATCTCTCCTTCGACAATGC 57.829 47.619 0.00 0.00 0.00 3.56
2374 3771 4.313277 TCTCTCCTTCGACAATGCATAG 57.687 45.455 0.00 0.00 0.00 2.23
2377 3774 3.447229 TCTCCTTCGACAATGCATAGACA 59.553 43.478 0.00 0.00 0.00 3.41
2378 3775 4.100035 TCTCCTTCGACAATGCATAGACAT 59.900 41.667 0.00 0.00 0.00 3.06
2380 3777 5.185454 TCCTTCGACAATGCATAGACATTT 58.815 37.500 0.00 0.00 38.19 2.32
2381 3778 5.647658 TCCTTCGACAATGCATAGACATTTT 59.352 36.000 0.00 0.00 38.19 1.82
2402 3799 3.889196 TTGATTTCCAAAACGACGAGG 57.111 42.857 0.00 0.00 0.00 4.63
2403 3800 2.841215 TGATTTCCAAAACGACGAGGT 58.159 42.857 0.00 0.00 0.00 3.85
2404 3801 2.803956 TGATTTCCAAAACGACGAGGTC 59.196 45.455 0.00 0.00 0.00 3.85
2418 3815 2.878429 GGTCGAGAAGAGCAGCGA 59.122 61.111 0.00 0.00 46.08 4.93
2419 3816 1.226547 GGTCGAGAAGAGCAGCGAG 60.227 63.158 0.00 0.00 46.08 5.03
2420 3817 1.871789 GTCGAGAAGAGCAGCGAGC 60.872 63.158 0.00 0.00 46.19 5.03
2431 3828 2.551355 GCAGCGAGCTATATCATCGA 57.449 50.000 0.00 0.00 41.15 3.59
2432 3829 3.077229 GCAGCGAGCTATATCATCGAT 57.923 47.619 0.00 0.00 41.15 3.59
2454 3851 8.487970 TCGATGATAAGAAAATAGAACGAATGC 58.512 33.333 0.00 0.00 0.00 3.56
2474 3871 6.949352 ATGCTATGAATCCACGAAGAAATT 57.051 33.333 0.00 0.00 0.00 1.82
2533 3930 4.612943 GCTCTATAGGAGAAGGACGTTTG 58.387 47.826 0.00 0.00 44.45 2.93
2581 3978 2.281761 AGCGGGAAGGTGCAGTTG 60.282 61.111 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
167 168 7.387397 GGATGCTCATTTCTTTCTCTATCGATT 59.613 37.037 1.71 0.00 0.00 3.34
187 188 2.362120 GTGCTTGCCCTGGATGCT 60.362 61.111 0.00 0.00 0.00 3.79
215 216 0.468226 GCGATGAGGTTATCCCCACA 59.532 55.000 0.00 0.00 0.00 4.17
449 1724 6.894682 TCCATTATTTCACCACATGCTACTA 58.105 36.000 0.00 0.00 0.00 1.82
453 1728 6.549433 AATTCCATTATTTCACCACATGCT 57.451 33.333 0.00 0.00 0.00 3.79
480 1755 3.161067 TCCATCATTTCGCCCTCAAAAA 58.839 40.909 0.00 0.00 0.00 1.94
481 1756 2.801483 TCCATCATTTCGCCCTCAAAA 58.199 42.857 0.00 0.00 0.00 2.44
482 1757 2.505650 TCCATCATTTCGCCCTCAAA 57.494 45.000 0.00 0.00 0.00 2.69
483 1758 2.505650 TTCCATCATTTCGCCCTCAA 57.494 45.000 0.00 0.00 0.00 3.02
484 1759 2.734755 ATTCCATCATTTCGCCCTCA 57.265 45.000 0.00 0.00 0.00 3.86
485 1760 4.580580 ACTAAATTCCATCATTTCGCCCTC 59.419 41.667 0.00 0.00 0.00 4.30
486 1761 4.536765 ACTAAATTCCATCATTTCGCCCT 58.463 39.130 0.00 0.00 0.00 5.19
487 1762 4.918810 ACTAAATTCCATCATTTCGCCC 57.081 40.909 0.00 0.00 0.00 6.13
488 1763 7.648142 TGATTACTAAATTCCATCATTTCGCC 58.352 34.615 0.00 0.00 0.00 5.54
489 1764 9.683069 AATGATTACTAAATTCCATCATTTCGC 57.317 29.630 0.00 0.00 40.20 4.70
527 1802 2.026262 GGACTAATCCACACCCACACAT 60.026 50.000 0.00 0.00 45.47 3.21
576 1851 3.611057 GCCTCTTGCTTGTTTGATCTGTG 60.611 47.826 0.00 0.00 36.87 3.66
771 2047 2.871633 CCCACTTGTGTTTTCCAAATGC 59.128 45.455 0.00 0.00 0.00 3.56
939 2219 2.348605 TTTTCTTGCCGTGTGCTGCC 62.349 55.000 0.00 0.00 42.00 4.85
940 2220 0.936297 CTTTTCTTGCCGTGTGCTGC 60.936 55.000 0.00 0.00 42.00 5.25
941 2221 0.318107 CCTTTTCTTGCCGTGTGCTG 60.318 55.000 0.00 0.00 42.00 4.41
974 2254 0.542333 TCGAGTCTCGGTGATCTCCT 59.458 55.000 21.63 0.00 40.88 3.69
1739 3032 2.513065 AAAAATGCTCACGCGCCGAG 62.513 55.000 18.97 18.97 39.65 4.63
1820 3118 1.135199 GGGCATGCATCTCACAACAAG 60.135 52.381 21.36 0.00 0.00 3.16
1882 3181 5.784750 TGCAGTGAATTTGAAGTCTATCG 57.215 39.130 0.00 0.00 0.00 2.92
2040 3339 6.811665 CCACGATAAGACTGTATTGTTCTTGA 59.188 38.462 0.00 0.00 0.00 3.02
2041 3340 6.455646 GCCACGATAAGACTGTATTGTTCTTG 60.456 42.308 0.00 0.00 0.00 3.02
2043 3342 5.109903 GCCACGATAAGACTGTATTGTTCT 58.890 41.667 0.00 0.00 0.00 3.01
2044 3343 4.026804 CGCCACGATAAGACTGTATTGTTC 60.027 45.833 0.00 0.00 0.00 3.18
2046 3345 3.444916 CGCCACGATAAGACTGTATTGT 58.555 45.455 0.00 0.00 0.00 2.71
2047 3346 2.794910 CCGCCACGATAAGACTGTATTG 59.205 50.000 0.00 0.00 0.00 1.90
2049 3348 2.304092 TCCGCCACGATAAGACTGTAT 58.696 47.619 0.00 0.00 0.00 2.29
2054 3353 0.309922 TCGATCCGCCACGATAAGAC 59.690 55.000 0.00 0.00 33.62 3.01
2056 3355 1.129326 GTTCGATCCGCCACGATAAG 58.871 55.000 0.00 0.00 38.30 1.73
2062 3365 0.165944 CAACAAGTTCGATCCGCCAC 59.834 55.000 0.00 0.00 0.00 5.01
2066 3369 5.059221 GCAATTTAACAACAAGTTCGATCCG 59.941 40.000 0.00 0.00 41.64 4.18
2074 3377 3.775202 TGTGCGCAATTTAACAACAAGT 58.225 36.364 14.00 0.00 0.00 3.16
2081 3384 3.125698 ACGGTATGTGCGCAATTTAAC 57.874 42.857 14.00 6.04 0.00 2.01
2082 3385 3.063725 GGTACGGTATGTGCGCAATTTAA 59.936 43.478 14.00 0.00 33.41 1.52
2083 3386 2.608546 GGTACGGTATGTGCGCAATTTA 59.391 45.455 14.00 0.58 33.41 1.40
2084 3387 1.399089 GGTACGGTATGTGCGCAATTT 59.601 47.619 14.00 1.76 33.41 1.82
2085 3388 1.011333 GGTACGGTATGTGCGCAATT 58.989 50.000 14.00 4.86 33.41 2.32
2086 3389 0.108089 TGGTACGGTATGTGCGCAAT 60.108 50.000 14.00 11.02 33.41 3.56
2087 3390 1.015085 GTGGTACGGTATGTGCGCAA 61.015 55.000 14.00 2.60 33.41 4.85
2088 3391 1.446445 GTGGTACGGTATGTGCGCA 60.446 57.895 5.66 5.66 33.41 6.09
2089 3392 0.808453 ATGTGGTACGGTATGTGCGC 60.808 55.000 0.00 0.00 33.41 6.09
2090 3393 1.205657 GATGTGGTACGGTATGTGCG 58.794 55.000 0.00 0.00 33.41 5.34
2091 3394 2.303163 TGATGTGGTACGGTATGTGC 57.697 50.000 0.00 0.00 0.00 4.57
2092 3395 6.912203 TTATTTGATGTGGTACGGTATGTG 57.088 37.500 0.00 0.00 0.00 3.21
2093 3396 7.225931 GTCATTATTTGATGTGGTACGGTATGT 59.774 37.037 0.00 0.00 36.54 2.29
2094 3397 7.568679 CGTCATTATTTGATGTGGTACGGTATG 60.569 40.741 0.00 0.00 36.72 2.39
2095 3398 6.422701 CGTCATTATTTGATGTGGTACGGTAT 59.577 38.462 0.00 0.00 36.72 2.73
2096 3399 5.749588 CGTCATTATTTGATGTGGTACGGTA 59.250 40.000 0.00 0.00 36.72 4.02
2097 3400 4.569162 CGTCATTATTTGATGTGGTACGGT 59.431 41.667 0.00 0.00 36.72 4.83
2098 3401 4.806775 TCGTCATTATTTGATGTGGTACGG 59.193 41.667 0.00 0.00 41.38 4.02
2099 3402 5.518847 ACTCGTCATTATTTGATGTGGTACG 59.481 40.000 0.00 0.00 41.38 3.67
2100 3403 6.903883 ACTCGTCATTATTTGATGTGGTAC 57.096 37.500 0.00 0.00 41.38 3.34
2101 3404 7.915293 AAACTCGTCATTATTTGATGTGGTA 57.085 32.000 0.00 0.00 41.38 3.25
2102 3405 6.817765 AAACTCGTCATTATTTGATGTGGT 57.182 33.333 0.00 0.00 41.38 4.16
2108 3413 6.592220 TGGATCGAAAACTCGTCATTATTTGA 59.408 34.615 0.00 0.00 0.00 2.69
2109 3414 6.771076 TGGATCGAAAACTCGTCATTATTTG 58.229 36.000 0.00 0.00 0.00 2.32
2119 3424 4.715520 CATACCATGGATCGAAAACTCG 57.284 45.455 21.47 0.00 0.00 4.18
2142 3447 4.640647 CAGCTAGGACACACACATAGAGTA 59.359 45.833 0.00 0.00 0.00 2.59
2143 3448 3.445450 CAGCTAGGACACACACATAGAGT 59.555 47.826 0.00 0.00 0.00 3.24
2144 3449 3.181482 CCAGCTAGGACACACACATAGAG 60.181 52.174 0.00 0.00 41.22 2.43
2145 3450 2.760650 CCAGCTAGGACACACACATAGA 59.239 50.000 0.00 0.00 41.22 1.98
2146 3451 2.497675 ACCAGCTAGGACACACACATAG 59.502 50.000 8.91 0.00 41.22 2.23
2156 3461 1.137872 CATCTGACCACCAGCTAGGAC 59.862 57.143 8.91 2.52 42.62 3.85
2188 3493 9.265901 GCTAGATTAAGATTTCTATGTGAAGCA 57.734 33.333 0.00 0.00 35.89 3.91
2189 3494 8.716909 GGCTAGATTAAGATTTCTATGTGAAGC 58.283 37.037 0.00 0.00 35.89 3.86
2190 3495 9.770097 TGGCTAGATTAAGATTTCTATGTGAAG 57.230 33.333 0.00 0.00 35.89 3.02
2263 3655 1.002576 TGCGCGGCAGATCATAAAATG 60.003 47.619 8.83 0.00 33.32 2.32
2266 3658 4.530581 TGCGCGGCAGATCATAAA 57.469 50.000 8.83 0.00 33.32 1.40
2314 3706 8.924303 TGGATCGGCTGCTTATAGTATTATAAT 58.076 33.333 2.97 2.97 32.70 1.28
2316 3708 7.891498 TGGATCGGCTGCTTATAGTATTATA 57.109 36.000 0.00 0.00 0.00 0.98
2319 3711 5.423015 CATGGATCGGCTGCTTATAGTATT 58.577 41.667 0.00 0.00 0.00 1.89
2321 3713 3.368427 GCATGGATCGGCTGCTTATAGTA 60.368 47.826 0.00 0.00 33.15 1.82
2326 3718 1.047801 TAGCATGGATCGGCTGCTTA 58.952 50.000 17.10 4.96 43.44 3.09
2327 3719 0.181114 TTAGCATGGATCGGCTGCTT 59.819 50.000 17.10 5.69 43.44 3.91
2330 3722 0.179048 TGGTTAGCATGGATCGGCTG 60.179 55.000 13.49 0.00 41.25 4.85
2331 3723 0.767375 ATGGTTAGCATGGATCGGCT 59.233 50.000 9.64 9.64 43.94 5.52
2332 3724 0.877071 CATGGTTAGCATGGATCGGC 59.123 55.000 15.75 0.00 0.00 5.54
2333 3725 2.549064 TCATGGTTAGCATGGATCGG 57.451 50.000 21.89 0.00 0.00 4.18
2334 3726 3.931468 GAGATCATGGTTAGCATGGATCG 59.069 47.826 21.89 0.00 0.00 3.69
2337 3734 3.326006 GGAGAGATCATGGTTAGCATGGA 59.674 47.826 21.89 10.79 0.00 3.41
2343 3740 4.339530 TGTCGAAGGAGAGATCATGGTTAG 59.660 45.833 0.00 0.00 0.00 2.34
2381 3778 3.628487 ACCTCGTCGTTTTGGAAATCAAA 59.372 39.130 0.00 0.00 42.98 2.69
2383 3780 2.803956 GACCTCGTCGTTTTGGAAATCA 59.196 45.455 0.00 0.00 0.00 2.57
2384 3781 3.450893 GACCTCGTCGTTTTGGAAATC 57.549 47.619 0.00 0.00 0.00 2.17
2396 3793 0.098025 CTGCTCTTCTCGACCTCGTC 59.902 60.000 0.00 0.00 40.80 4.20
2397 3794 1.928706 GCTGCTCTTCTCGACCTCGT 61.929 60.000 0.00 0.00 40.80 4.18
2398 3795 1.226547 GCTGCTCTTCTCGACCTCG 60.227 63.158 0.00 0.00 41.45 4.63
2399 3796 1.226547 CGCTGCTCTTCTCGACCTC 60.227 63.158 0.00 0.00 0.00 3.85
2400 3797 1.653094 CTCGCTGCTCTTCTCGACCT 61.653 60.000 0.00 0.00 0.00 3.85
2401 3798 1.226547 CTCGCTGCTCTTCTCGACC 60.227 63.158 0.00 0.00 0.00 4.79
2402 3799 1.871789 GCTCGCTGCTCTTCTCGAC 60.872 63.158 0.00 0.00 38.95 4.20
2403 3800 2.487428 GCTCGCTGCTCTTCTCGA 59.513 61.111 0.00 0.00 38.95 4.04
2410 3807 8.646414 ATCATCGATGATATAGCTCGCTGCTC 62.646 46.154 34.01 0.00 46.50 4.26
2412 3809 2.551355 TCGATGATATAGCTCGCTGC 57.449 50.000 0.85 0.00 43.29 5.25
2413 3810 4.284378 TCATCGATGATATAGCTCGCTG 57.716 45.455 23.99 0.00 31.74 5.18
2414 3811 6.484977 TCTTATCATCGATGATATAGCTCGCT 59.515 38.462 36.41 18.85 45.99 4.93
2415 3812 6.663565 TCTTATCATCGATGATATAGCTCGC 58.336 40.000 36.41 0.00 45.99 5.03
2416 3813 9.508567 TTTTCTTATCATCGATGATATAGCTCG 57.491 33.333 36.41 23.43 45.99 5.03
2425 3822 9.744468 TTCGTTCTATTTTCTTATCATCGATGA 57.256 29.630 29.09 29.09 41.70 2.92
2428 3825 8.487970 GCATTCGTTCTATTTTCTTATCATCGA 58.512 33.333 0.00 0.00 0.00 3.59
2429 3826 8.491152 AGCATTCGTTCTATTTTCTTATCATCG 58.509 33.333 0.00 0.00 0.00 3.84
2437 3834 8.778358 GGATTCATAGCATTCGTTCTATTTTCT 58.222 33.333 0.00 0.00 0.00 2.52
2438 3835 8.559536 TGGATTCATAGCATTCGTTCTATTTTC 58.440 33.333 0.00 0.00 0.00 2.29
2439 3836 8.345565 GTGGATTCATAGCATTCGTTCTATTTT 58.654 33.333 0.00 0.00 0.00 1.82
2440 3837 7.307396 CGTGGATTCATAGCATTCGTTCTATTT 60.307 37.037 0.00 0.00 0.00 1.40
2447 3844 3.452755 TCGTGGATTCATAGCATTCGT 57.547 42.857 0.00 0.00 0.00 3.85
2449 3846 5.991328 TTCTTCGTGGATTCATAGCATTC 57.009 39.130 0.00 0.00 0.00 2.67
2454 3851 7.482743 CACACAAATTTCTTCGTGGATTCATAG 59.517 37.037 10.18 0.00 33.62 2.23
2533 3930 4.743644 CCGGGACTATATTTTTCGTCTCAC 59.256 45.833 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.