Multiple sequence alignment - TraesCS4A01G098500

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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 TraesCS4A01G098500 chr4A 100.000 3758 0 0 580 4337 110378632 110382389 0.000000e+00 6940
1 TraesCS4A01G098500 chr4A 100.000 336 0 0 1 336 110378053 110378388 4.760000e-174 621
2 TraesCS4A01G098500 chr4D 92.793 3802 140 37 580 4337 354147115 354143404 0.000000e+00 5380
3 TraesCS4A01G098500 chr4D 95.385 325 7 3 20 336 354147429 354147105 1.080000e-140 510
4 TraesCS4A01G098500 chr4B 95.230 2977 89 22 587 3534 438227883 438224931 0.000000e+00 4662
5 TraesCS4A01G098500 chr4B 88.151 768 25 13 3584 4335 438224932 438224215 0.000000e+00 854
6 TraesCS4A01G098500 chr4B 91.277 321 5 4 20 322 438228594 438228279 2.410000e-112 416
7 TraesCS4A01G098500 chr3B 80.153 393 76 2 1608 1999 59186335 59186726 4.240000e-75 292
8 TraesCS4A01G098500 chr3B 78.462 390 78 6 1612 1999 616182900 616183285 2.590000e-62 250
9 TraesCS4A01G098500 chr3A 78.961 385 77 4 1617 1999 606425501 606425883 4.300000e-65 259
10 TraesCS4A01G098500 chr3D 78.442 385 79 4 1617 1999 463082335 463081953 9.310000e-62 248


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 TraesCS4A01G098500 chr4A 110378053 110382389 4336 False 3780.500000 6940 100.000000 1 4337 2 chr4A.!!$F1 4336
1 TraesCS4A01G098500 chr4D 354143404 354147429 4025 True 2945.000000 5380 94.089000 20 4337 2 chr4D.!!$R1 4317
2 TraesCS4A01G098500 chr4B 438224215 438228594 4379 True 1977.333333 4662 91.552667 20 4335 3 chr4B.!!$R1 4315

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
78 81 1.532728 TCGACTAGAGAGGAGGGCC 59.467 63.158 0.0 0.0 0.0 5.80 F
1318 1491 0.911525 AGACCACCACCCTCCATGAG 60.912 60.000 0.0 0.0 0.0 2.90 F
1879 2052 1.198759 TAGTGGGTGTTCCTGAGGCC 61.199 60.000 0.0 0.0 36.2 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1489 1662 0.035881 ATGCACCCCAGATGCTATCG 59.964 55.0 0.0 0.0 43.77 2.92 R
2428 2601 0.107214 TCAAGAATGGCATCCGTCCC 60.107 55.0 0.0 0.0 0.00 4.46 R
3532 3716 0.107897 ACAAGGTGTTGCGTGAGACA 60.108 50.0 0.0 0.0 37.14 3.41 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
78 81 1.532728 TCGACTAGAGAGGAGGGCC 59.467 63.158 0.00 0.00 0.00 5.80
99 112 2.833582 GAGAGCCCGTCGATCCCA 60.834 66.667 0.00 0.00 0.00 4.37
120 133 4.664267 ACCCTCCTCTGGCTGGCA 62.664 66.667 3.18 3.18 0.00 4.92
331 351 4.776322 CCACCCGCCGCTCATCAA 62.776 66.667 0.00 0.00 0.00 2.57
332 352 3.499737 CACCCGCCGCTCATCAAC 61.500 66.667 0.00 0.00 0.00 3.18
333 353 4.015406 ACCCGCCGCTCATCAACA 62.015 61.111 0.00 0.00 0.00 3.33
334 354 2.514592 CCCGCCGCTCATCAACAT 60.515 61.111 0.00 0.00 0.00 2.71
335 355 2.114670 CCCGCCGCTCATCAACATT 61.115 57.895 0.00 0.00 0.00 2.71
618 773 6.968904 CAGGAATTCGATTTGATTTCGATTGT 59.031 34.615 0.00 0.00 44.32 2.71
644 799 2.047465 AACTCTGCTCTGCTGCGG 60.047 61.111 0.95 0.95 40.46 5.69
662 822 4.459089 GAGAGGCCTCCACCACGC 62.459 72.222 29.54 1.86 33.30 5.34
666 826 4.459089 GGCCTCCACCACGCTCTC 62.459 72.222 0.00 0.00 0.00 3.20
692 852 2.747446 GGGCAGCTGTTCTTCGATTTTA 59.253 45.455 16.64 0.00 0.00 1.52
693 853 3.181506 GGGCAGCTGTTCTTCGATTTTAG 60.182 47.826 16.64 0.00 0.00 1.85
696 856 4.003648 CAGCTGTTCTTCGATTTTAGGGT 58.996 43.478 5.25 0.00 0.00 4.34
702 862 3.666274 TCTTCGATTTTAGGGTTTGCGA 58.334 40.909 0.00 0.00 0.00 5.10
755 924 2.049063 CGGGCCGGATCTCGAATC 60.049 66.667 20.56 0.00 42.43 2.52
777 946 5.611374 TCCGTGGGATTTCTCATTAGATTC 58.389 41.667 0.00 0.00 0.00 2.52
784 953 6.238759 GGGATTTCTCATTAGATTCGGGTTTG 60.239 42.308 0.00 0.00 0.00 2.93
804 973 5.840243 TTGGAATGCGAGATTGATTGATT 57.160 34.783 0.00 0.00 0.00 2.57
805 974 5.177725 TGGAATGCGAGATTGATTGATTG 57.822 39.130 0.00 0.00 0.00 2.67
807 976 4.037208 GGAATGCGAGATTGATTGATTGGT 59.963 41.667 0.00 0.00 0.00 3.67
808 977 5.450965 GGAATGCGAGATTGATTGATTGGTT 60.451 40.000 0.00 0.00 0.00 3.67
809 978 4.359971 TGCGAGATTGATTGATTGGTTG 57.640 40.909 0.00 0.00 0.00 3.77
810 979 4.009002 TGCGAGATTGATTGATTGGTTGA 58.991 39.130 0.00 0.00 0.00 3.18
811 980 4.641541 TGCGAGATTGATTGATTGGTTGAT 59.358 37.500 0.00 0.00 0.00 2.57
812 981 4.974275 GCGAGATTGATTGATTGGTTGATG 59.026 41.667 0.00 0.00 0.00 3.07
813 982 5.449588 GCGAGATTGATTGATTGGTTGATGT 60.450 40.000 0.00 0.00 0.00 3.06
814 983 5.969435 CGAGATTGATTGATTGGTTGATGTG 59.031 40.000 0.00 0.00 0.00 3.21
815 984 6.216801 AGATTGATTGATTGGTTGATGTGG 57.783 37.500 0.00 0.00 0.00 4.17
816 985 5.718130 AGATTGATTGATTGGTTGATGTGGT 59.282 36.000 0.00 0.00 0.00 4.16
1318 1491 0.911525 AGACCACCACCCTCCATGAG 60.912 60.000 0.00 0.00 0.00 2.90
1577 1750 3.423154 GCAAGACGAAGGCACCCG 61.423 66.667 0.00 0.00 0.00 5.28
1729 1902 2.125512 AATGGTCACTCGCGCCTC 60.126 61.111 0.00 0.00 0.00 4.70
1879 2052 1.198759 TAGTGGGTGTTCCTGAGGCC 61.199 60.000 0.00 0.00 36.20 5.19
2077 2250 1.439679 GTTCTGGCCTTAACCTGTCG 58.560 55.000 3.32 0.00 0.00 4.35
2092 2265 2.226200 CCTGTCGACACATGCATCAAAA 59.774 45.455 15.76 0.00 0.00 2.44
2124 2297 2.289945 GGGATGGTATGGACATCTCAGC 60.290 54.545 5.52 0.00 43.66 4.26
2125 2298 2.636893 GGATGGTATGGACATCTCAGCT 59.363 50.000 5.52 0.00 43.25 4.24
2128 2301 2.432146 TGGTATGGACATCTCAGCTGTC 59.568 50.000 14.67 0.00 41.83 3.51
2209 2382 5.634118 TCAAATTCAGACAAGGTTCAGGAT 58.366 37.500 0.00 0.00 0.00 3.24
2245 2418 2.821378 CACTTTTGAGCCATCATGGACA 59.179 45.455 8.30 3.68 40.96 4.02
2425 2598 5.059832 CGTCGTTAAGATATCATGCACTAGC 59.940 44.000 5.32 0.00 42.57 3.42
2728 2901 7.484975 AGATGTTCATGTAGTAGTTAGAGTGC 58.515 38.462 0.00 0.00 0.00 4.40
2938 3111 0.254178 ATGCTACAGGCCACAAGGAG 59.746 55.000 5.01 0.00 40.92 3.69
3066 3241 1.822990 CCTGCTCAATGTGCTTCCATT 59.177 47.619 8.78 0.00 35.45 3.16
3067 3242 2.159282 CCTGCTCAATGTGCTTCCATTC 60.159 50.000 8.78 0.00 32.81 2.67
3068 3243 1.820519 TGCTCAATGTGCTTCCATTCC 59.179 47.619 8.78 0.00 32.81 3.01
3069 3244 1.820519 GCTCAATGTGCTTCCATTCCA 59.179 47.619 0.00 0.00 32.81 3.53
3070 3245 2.429610 GCTCAATGTGCTTCCATTCCAT 59.570 45.455 0.00 0.00 32.81 3.41
3087 3262 1.945394 CCATCTGTGCATTACTCTGGC 59.055 52.381 0.00 0.00 0.00 4.85
3114 3289 7.112779 AGCAGTCTGTTTAGGCATTTATAGTT 58.887 34.615 0.93 0.00 0.00 2.24
3163 3338 1.104577 TTGTGGGCGTTCCTGGAAAC 61.105 55.000 11.40 5.99 36.20 2.78
3288 3464 1.401539 GGAGGCGAGTGCAATTGTTTC 60.402 52.381 7.40 1.46 45.35 2.78
3392 3568 9.590451 AATTCACTTTCATATGCTTTGGTATTG 57.410 29.630 0.00 0.00 0.00 1.90
3396 3572 7.485913 CACTTTCATATGCTTTGGTATTGTGTC 59.514 37.037 0.00 0.00 0.00 3.67
3417 3594 0.822121 AGTTCAACTTCAACCCCGCC 60.822 55.000 0.00 0.00 0.00 6.13
3470 3648 7.425577 AGTTTATCTGCATTTTTCTTTTGCC 57.574 32.000 0.00 0.00 35.51 4.52
3490 3673 3.005897 GCCGAAGTATCTGCAAGGATAGA 59.994 47.826 0.00 0.00 36.00 1.98
3494 3677 6.708054 CCGAAGTATCTGCAAGGATAGAATTT 59.292 38.462 0.00 0.00 0.00 1.82
3509 3692 0.620030 AATTTGCCCCATTTGGAGGC 59.380 50.000 17.37 17.37 45.76 4.70
3532 3716 6.465894 GGCATTTACCTATTCTGGTGTCCTAT 60.466 42.308 0.00 0.00 41.05 2.57
3554 3738 2.610374 GTCTCACGCAACACCTTGTTAA 59.390 45.455 0.00 0.00 38.77 2.01
3566 3750 5.258051 ACACCTTGTTAACAACCAGAGAAA 58.742 37.500 17.01 0.00 0.00 2.52
3620 3804 2.003937 TAAGTTTTTGCCCTGGGACC 57.996 50.000 19.27 0.00 0.00 4.46
3663 3847 6.076981 TGCATCTTCTTTTGAGAACCTTTC 57.923 37.500 0.00 0.00 0.00 2.62
3669 3853 9.809096 ATCTTCTTTTGAGAACCTTTCTTTTTC 57.191 29.630 0.00 0.00 40.87 2.29
3670 3854 9.025041 TCTTCTTTTGAGAACCTTTCTTTTTCT 57.975 29.630 0.00 0.00 40.87 2.52
3671 3855 8.986477 TTCTTTTGAGAACCTTTCTTTTTCTG 57.014 30.769 0.00 0.00 40.87 3.02
3726 3910 2.045634 GATGCAGGGTGAGCAGCA 60.046 61.111 3.64 3.64 46.81 4.41
3727 3911 2.681591 ATGCAGGGTGAGCAGCAT 59.318 55.556 7.78 7.78 46.36 3.79
3728 3912 1.453379 ATGCAGGGTGAGCAGCATC 60.453 57.895 7.78 0.00 43.67 3.91
3791 3975 3.323403 TGGTGTGTTCCATGATTTTTCCC 59.677 43.478 0.00 0.00 31.96 3.97
3794 3978 5.454613 GGTGTGTTCCATGATTTTTCCCTTT 60.455 40.000 0.00 0.00 0.00 3.11
3897 4081 2.599408 TACTCCCTCCGTCCCATATC 57.401 55.000 0.00 0.00 0.00 1.63
3954 4138 1.154225 CGATGTTTGTTCCTGCGCC 60.154 57.895 4.18 0.00 0.00 6.53
3971 4155 1.152567 CCGAGGCCTGAGGATCTCT 60.153 63.158 12.00 0.00 34.92 3.10
3975 4159 2.334653 GCCTGAGGATCTCTCGCG 59.665 66.667 0.65 0.00 45.32 5.87
4004 4188 1.273455 GCGATTAGCGTTATCGGCGT 61.273 55.000 6.85 0.00 43.75 5.68
4024 4208 5.679792 GGCGTTAATCATTTGTTAATCCGAC 59.320 40.000 0.00 0.00 0.00 4.79
4029 4213 3.616219 TCATTTGTTAATCCGACCCTGG 58.384 45.455 0.00 0.00 0.00 4.45
4038 4222 2.214216 CCGACCCTGGTTGACCTGA 61.214 63.158 5.07 0.00 37.15 3.86
4125 4311 2.359354 TTGCTGGGCGTGCGTATT 60.359 55.556 0.00 0.00 0.00 1.89
4126 4312 1.969064 TTGCTGGGCGTGCGTATTT 60.969 52.632 0.00 0.00 0.00 1.40
4127 4313 2.100216 GCTGGGCGTGCGTATTTG 59.900 61.111 0.00 0.00 0.00 2.32
4128 4314 2.100216 CTGGGCGTGCGTATTTGC 59.900 61.111 0.00 0.00 0.00 3.68
4129 4315 2.359354 TGGGCGTGCGTATTTGCT 60.359 55.556 0.00 0.00 35.36 3.91
4130 4316 2.100216 GGGCGTGCGTATTTGCTG 59.900 61.111 0.00 0.00 35.36 4.41
4131 4317 2.686816 GGGCGTGCGTATTTGCTGT 61.687 57.895 0.00 0.00 35.36 4.40
4132 4318 1.209127 GGCGTGCGTATTTGCTGTT 59.791 52.632 0.00 0.00 35.36 3.16
4133 4319 1.065031 GGCGTGCGTATTTGCTGTTG 61.065 55.000 0.00 0.00 35.36 3.33
4134 4320 1.664643 GCGTGCGTATTTGCTGTTGC 61.665 55.000 0.00 0.00 40.20 4.17
4135 4321 0.110238 CGTGCGTATTTGCTGTTGCT 60.110 50.000 0.00 0.00 40.48 3.91
4136 4322 1.330306 GTGCGTATTTGCTGTTGCTG 58.670 50.000 0.00 0.00 40.48 4.41
4137 4323 0.240678 TGCGTATTTGCTGTTGCTGG 59.759 50.000 0.00 0.00 40.48 4.85
4138 4324 0.456653 GCGTATTTGCTGTTGCTGGG 60.457 55.000 0.00 0.00 40.48 4.45
4139 4325 0.456653 CGTATTTGCTGTTGCTGGGC 60.457 55.000 0.00 0.00 40.48 5.36
4140 4326 0.456653 GTATTTGCTGTTGCTGGGCG 60.457 55.000 0.00 0.00 40.48 6.13
4141 4327 0.893270 TATTTGCTGTTGCTGGGCGT 60.893 50.000 0.00 0.00 40.48 5.68
4164 4350 2.073816 GTATGTTTATATGCGCGCCCT 58.926 47.619 30.77 18.71 0.00 5.19
4229 4428 2.317149 ATAAGGTGCGCCTCCTCTGC 62.317 60.000 21.49 0.00 46.33 4.26
4257 4456 1.228894 ACCCACAGAAGAGCTCCGA 60.229 57.895 10.93 0.00 0.00 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 47 6.755206 TCTAGTCGAGTTTGGATTCTTTTGA 58.245 36.000 0.00 0.00 0.00 2.69
78 81 2.899044 GATCGACGGGCTCTCCTCG 61.899 68.421 0.00 0.00 37.45 4.63
99 112 4.928981 AGCCAGAGGAGGGTGAAT 57.071 55.556 0.00 0.00 38.13 2.57
120 133 1.447643 CTCGCCTTGGATCGGGAAT 59.552 57.895 2.75 0.00 0.00 3.01
674 834 4.003648 ACCCTAAAATCGAAGAACAGCTG 58.996 43.478 13.48 13.48 43.58 4.24
675 835 4.287766 ACCCTAAAATCGAAGAACAGCT 57.712 40.909 0.00 0.00 43.58 4.24
677 837 5.154222 GCAAACCCTAAAATCGAAGAACAG 58.846 41.667 0.00 0.00 43.58 3.16
679 839 4.083696 TCGCAAACCCTAAAATCGAAGAAC 60.084 41.667 0.00 0.00 43.58 3.01
693 853 2.650778 CAAGGGCTTCGCAAACCC 59.349 61.111 0.00 0.00 44.62 4.11
696 856 1.272212 GAAATCCAAGGGCTTCGCAAA 59.728 47.619 0.00 0.00 0.00 3.68
702 862 0.035820 TACGCGAAATCCAAGGGCTT 60.036 50.000 15.93 0.00 0.00 4.35
733 893 3.299190 GAGATCCGGCCCGAGGAG 61.299 72.222 3.71 0.00 41.66 3.69
755 924 4.449068 CGAATCTAATGAGAAATCCCACGG 59.551 45.833 0.00 0.00 34.61 4.94
769 938 3.315191 CGCATTCCAAACCCGAATCTAAT 59.685 43.478 0.00 0.00 0.00 1.73
777 946 1.094785 AATCTCGCATTCCAAACCCG 58.905 50.000 0.00 0.00 0.00 5.28
784 953 4.037208 ACCAATCAATCAATCTCGCATTCC 59.963 41.667 0.00 0.00 0.00 3.01
1318 1491 1.135489 TCTAGCATGTCGACGTTGGAC 60.135 52.381 7.76 12.27 34.99 4.02
1489 1662 0.035881 ATGCACCCCAGATGCTATCG 59.964 55.000 0.00 0.00 43.77 2.92
1577 1750 3.697439 TACCATTCCCGGCAGCAGC 62.697 63.158 0.00 0.00 41.10 5.25
1585 1758 2.218603 GTGGCACTATTACCATTCCCG 58.781 52.381 11.13 0.00 38.46 5.14
1729 1902 2.359975 GGAAACTGTGGCTCCCCG 60.360 66.667 0.00 0.00 0.00 5.73
1879 2052 3.633235 CTCGAACCACCTCTTCATATCG 58.367 50.000 0.00 0.00 0.00 2.92
1906 2079 2.216898 GAGAAATTGGCATCTCTCCCG 58.783 52.381 8.92 0.00 39.18 5.14
1927 2100 3.019003 ATCCGCCTCAGTGGGAACG 62.019 63.158 0.00 0.00 44.41 3.95
2077 2250 3.916761 ACCATGTTTTGATGCATGTGTC 58.083 40.909 2.46 0.00 40.42 3.67
2092 2265 1.979809 TACCATCCCCAGAACCATGT 58.020 50.000 0.00 0.00 0.00 3.21
2124 2297 1.148310 CCTACGTTTGTGGCAGACAG 58.852 55.000 0.00 0.00 35.44 3.51
2125 2298 0.753867 TCCTACGTTTGTGGCAGACA 59.246 50.000 0.00 0.00 0.00 3.41
2128 2301 1.156736 CCTTCCTACGTTTGTGGCAG 58.843 55.000 0.00 0.00 0.00 4.85
2209 2382 3.719268 AAAGTGTGGCTCACATCCATA 57.281 42.857 20.49 0.00 46.32 2.74
2425 2598 2.124736 AATGGCATCCGTCCCACG 60.125 61.111 0.00 0.00 42.11 4.94
2428 2601 0.107214 TCAAGAATGGCATCCGTCCC 60.107 55.000 0.00 0.00 0.00 4.46
2728 2901 2.928334 AGAGCAGCTGACAATAATGGG 58.072 47.619 20.43 0.00 0.00 4.00
2938 3111 3.923461 GCGAGTGAGTAATCCAGATATGC 59.077 47.826 0.00 0.00 0.00 3.14
3066 3241 2.420547 GCCAGAGTAATGCACAGATGGA 60.421 50.000 8.28 0.00 31.34 3.41
3067 3242 1.945394 GCCAGAGTAATGCACAGATGG 59.055 52.381 0.00 0.00 32.33 3.51
3068 3243 1.596260 CGCCAGAGTAATGCACAGATG 59.404 52.381 0.00 0.00 0.00 2.90
3069 3244 1.482182 TCGCCAGAGTAATGCACAGAT 59.518 47.619 0.00 0.00 0.00 2.90
3070 3245 0.894835 TCGCCAGAGTAATGCACAGA 59.105 50.000 0.00 0.00 0.00 3.41
3087 3262 2.015736 ATGCCTAAACAGACTGCTCG 57.984 50.000 1.25 0.00 0.00 5.03
3114 3289 7.016268 AGACTTCTCACCAACCTATGAAAACTA 59.984 37.037 0.00 0.00 0.00 2.24
3163 3338 4.292186 TGAACTCCTTTCCTGGATGAAG 57.708 45.455 0.00 0.00 35.30 3.02
3265 3441 1.675641 AATTGCACTCGCCTCCCAC 60.676 57.895 0.00 0.00 37.32 4.61
3269 3445 1.266718 TGAAACAATTGCACTCGCCTC 59.733 47.619 5.05 0.00 37.32 4.70
3288 3464 5.763204 ACAGATTGTTTACACTGGTACCTTG 59.237 40.000 14.36 12.62 35.08 3.61
3392 3568 2.357952 GGGTTGAAGTTGAACTGGACAC 59.642 50.000 0.00 0.00 0.00 3.67
3396 3572 0.951558 CGGGGTTGAAGTTGAACTGG 59.048 55.000 0.00 0.00 0.00 4.00
3436 3613 1.075542 CAGATAAACTCGGCGTTGCA 58.924 50.000 6.85 0.00 35.61 4.08
3470 3648 7.571026 CAAATTCTATCCTTGCAGATACTTCG 58.429 38.462 0.00 0.00 0.00 3.79
3490 3673 0.620030 GCCTCCAAATGGGGCAAATT 59.380 50.000 20.46 0.00 45.24 1.82
3509 3692 7.509546 ACATAGGACACCAGAATAGGTAAATG 58.490 38.462 0.00 0.00 40.77 2.32
3532 3716 0.107897 ACAAGGTGTTGCGTGAGACA 60.108 50.000 0.00 0.00 37.14 3.41
3566 3750 6.925165 CAGTTGCCACTTTGTTATGAGAAAAT 59.075 34.615 0.00 0.00 0.00 1.82
3663 3847 3.202906 TCGTGAGTGGTTCCAGAAAAAG 58.797 45.455 0.00 0.00 0.00 2.27
3669 3853 1.432514 CACATCGTGAGTGGTTCCAG 58.567 55.000 0.00 0.00 35.23 3.86
3670 3854 3.605013 CACATCGTGAGTGGTTCCA 57.395 52.632 0.00 0.00 35.23 3.53
3725 3909 6.565435 GCAAGATAAGATGACAACGATGGATG 60.565 42.308 0.00 0.00 0.00 3.51
3726 3910 5.468072 GCAAGATAAGATGACAACGATGGAT 59.532 40.000 0.00 0.00 0.00 3.41
3727 3911 4.811024 GCAAGATAAGATGACAACGATGGA 59.189 41.667 0.00 0.00 0.00 3.41
3728 3912 4.571984 TGCAAGATAAGATGACAACGATGG 59.428 41.667 0.00 0.00 0.00 3.51
3791 3975 2.225491 TGAAACCGAATCGCCTCAAAAG 59.775 45.455 0.00 0.00 0.00 2.27
3794 3978 1.153353 GTGAAACCGAATCGCCTCAA 58.847 50.000 0.00 0.00 0.00 3.02
3835 4019 2.125512 CCGGTGCTGGCTGTCTAC 60.126 66.667 0.00 0.00 0.00 2.59
3897 4081 1.860950 CATGCGTCCAGGAATTACTCG 59.139 52.381 0.00 0.00 0.00 4.18
3954 4138 1.514678 CGAGAGATCCTCAGGCCTCG 61.515 65.000 0.00 9.24 42.06 4.63
3975 4159 2.470821 ACGCTAATCGCAAGTGGATAC 58.529 47.619 0.00 0.00 43.23 2.24
4004 4188 6.320164 CCAGGGTCGGATTAACAAATGATTAA 59.680 38.462 0.00 0.00 0.00 1.40
4024 4208 0.326264 CCTTCTCAGGTCAACCAGGG 59.674 60.000 1.33 0.00 38.89 4.45
4029 4213 1.743996 GCCATCCTTCTCAGGTCAAC 58.256 55.000 0.00 0.00 41.69 3.18
4038 4222 1.091771 CATCGCAACGCCATCCTTCT 61.092 55.000 0.00 0.00 0.00 2.85
4125 4311 3.594775 CACGCCCAGCAACAGCAA 61.595 61.111 0.00 0.00 0.00 3.91
4129 4315 3.892740 ATACGCACGCCCAGCAACA 62.893 57.895 0.00 0.00 0.00 3.33
4130 4316 3.124921 ATACGCACGCCCAGCAAC 61.125 61.111 0.00 0.00 0.00 4.17
4131 4317 3.124270 CATACGCACGCCCAGCAA 61.124 61.111 0.00 0.00 0.00 3.91
4132 4318 3.892740 AACATACGCACGCCCAGCA 62.893 57.895 0.00 0.00 0.00 4.41
4133 4319 1.363145 TAAACATACGCACGCCCAGC 61.363 55.000 0.00 0.00 0.00 4.85
4134 4320 1.295792 ATAAACATACGCACGCCCAG 58.704 50.000 0.00 0.00 0.00 4.45
4135 4321 2.598686 TATAAACATACGCACGCCCA 57.401 45.000 0.00 0.00 0.00 5.36
4136 4322 2.412325 GCATATAAACATACGCACGCCC 60.412 50.000 0.00 0.00 0.00 6.13
4137 4323 2.720590 CGCATATAAACATACGCACGCC 60.721 50.000 0.00 0.00 0.00 5.68
4138 4324 2.482235 CGCATATAAACATACGCACGC 58.518 47.619 0.00 0.00 0.00 5.34
4139 4325 2.482235 GCGCATATAAACATACGCACG 58.518 47.619 0.30 0.00 45.25 5.34
4140 4326 2.482235 CGCGCATATAAACATACGCAC 58.518 47.619 8.75 0.00 46.16 5.34
4141 4327 1.136474 GCGCGCATATAAACATACGCA 60.136 47.619 29.10 0.00 46.16 5.24
4164 4350 3.842732 TCGAAACGTGCAGATAAGAGA 57.157 42.857 0.00 0.00 0.00 3.10
4229 4428 2.669569 CTGTGGGTGGAGCAACCG 60.670 66.667 0.00 0.00 45.71 4.44
4232 4431 0.397941 CTCTTCTGTGGGTGGAGCAA 59.602 55.000 0.00 0.00 0.00 3.91
4257 4456 3.028098 TCCTCCTACTCCCGGCCT 61.028 66.667 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.