Multiple sequence alignment - TraesCS6D01G032400

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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 TraesCS6D01G032400 chr6D 100.000 3990 0 0 1 3990 13602985 13606974 0.000000e+00 7369.0
1 TraesCS6D01G032400 chr6D 94.828 58 3 0 3113 3170 13606065 13606122 1.530000e-14 91.6
2 TraesCS6D01G032400 chr6D 94.828 58 3 0 3081 3138 13606097 13606154 1.530000e-14 91.6
3 TraesCS6D01G032400 chr6D 76.404 178 27 11 1781 1952 21701227 21701395 9.190000e-12 82.4
4 TraesCS6D01G032400 chr6D 76.224 143 25 7 1902 2041 21053239 21053375 2.570000e-07 67.6
5 TraesCS6D01G032400 chr6D 87.273 55 7 0 1183 1237 26249885 26249939 3.330000e-06 63.9
6 TraesCS6D01G032400 chr6B 94.782 3162 104 18 1 3138 25258446 25261570 0.000000e+00 4868.0
7 TraesCS6D01G032400 chr6B 91.201 591 18 6 3113 3670 25261513 25262102 0.000000e+00 773.0
8 TraesCS6D01G032400 chr6B 94.964 139 7 0 3852 3990 25262102 25262240 6.710000e-53 219.0
9 TraesCS6D01G032400 chr6B 73.333 345 85 7 1613 1952 33700401 33700059 1.950000e-23 121.0
10 TraesCS6D01G032400 chr6B 74.766 214 44 8 1830 2041 36132311 36132516 1.980000e-13 87.9
11 TraesCS6D01G032400 chrUn 95.086 2218 72 12 950 3138 71302979 71300770 0.000000e+00 3458.0
12 TraesCS6D01G032400 chrUn 91.009 912 41 11 1 884 71304021 71303123 0.000000e+00 1192.0
13 TraesCS6D01G032400 chrUn 91.030 903 40 20 3113 3990 71300827 71299941 0.000000e+00 1181.0
14 TraesCS6D01G032400 chrUn 85.714 56 6 1 3506 3559 71300602 71300547 1.550000e-04 58.4
15 TraesCS6D01G032400 chr4A 72.506 1233 293 40 1057 2264 45149891 45148680 1.360000e-94 357.0
16 TraesCS6D01G032400 chr4B 72.493 1007 239 32 1059 2044 517429759 517430748 1.400000e-74 291.0
17 TraesCS6D01G032400 chr2A 76.395 466 97 10 1048 1511 758583314 758583768 5.150000e-59 239.0
18 TraesCS6D01G032400 chr2A 76.977 430 84 10 1079 1502 758596608 758597028 8.620000e-57 231.0
19 TraesCS6D01G032400 chr2D 75.647 464 93 16 1054 1511 628581721 628581272 3.120000e-51 213.0
20 TraesCS6D01G032400 chr2D 74.364 472 98 18 1062 1523 628587839 628587381 3.170000e-41 180.0
21 TraesCS6D01G032400 chr2D 89.474 76 7 1 1436 1511 628307261 628307335 1.180000e-15 95.3
22 TraesCS6D01G032400 chr6A 76.608 342 72 6 1060 1396 19890238 19889900 8.810000e-42 182.0
23 TraesCS6D01G032400 chr6A 88.462 52 4 2 1902 1952 21316443 21316493 1.200000e-05 62.1
24 TraesCS6D01G032400 chr6A 88.462 52 4 2 1902 1952 21321838 21321888 1.200000e-05 62.1
25 TraesCS6D01G032400 chr6A 88.462 52 4 2 1902 1952 21328084 21328134 1.200000e-05 62.1
26 TraesCS6D01G032400 chr2B 74.640 347 69 13 1173 1511 771380326 771380661 6.960000e-28 135.0
27 TraesCS6D01G032400 chr2B 91.549 71 5 1 1437 1506 771048513 771048443 3.280000e-16 97.1
28 TraesCS6D01G032400 chr7A 74.257 303 64 10 1098 1396 704451974 704452266 9.060000e-22 115.0
29 TraesCS6D01G032400 chr5D 88.000 50 6 0 1188 1237 441239028 441238979 4.310000e-05 60.2


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 TraesCS6D01G032400 chr6D 13602985 13606974 3989 False 2517.400000 7369 96.55200 1 3990 3 chr6D.!!$F4 3989
1 TraesCS6D01G032400 chr6B 25258446 25262240 3794 False 1953.333333 4868 93.64900 1 3990 3 chr6B.!!$F2 3989
2 TraesCS6D01G032400 chrUn 71299941 71304021 4080 True 1472.350000 3458 90.70975 1 3990 4 chrUn.!!$R1 3989
3 TraesCS6D01G032400 chr4A 45148680 45149891 1211 True 357.000000 357 72.50600 1057 2264 1 chr4A.!!$R1 1207
4 TraesCS6D01G032400 chr4B 517429759 517430748 989 False 291.000000 291 72.49300 1059 2044 1 chr4B.!!$F1 985

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
697 726 1.411246 TGCACGTTGGAGTGTTACTCT 59.589 47.619 8.68 0.0 44.46 3.24 F
1429 1551 0.105039 GGCTGGTATCGGTCAGAAGG 59.895 60.000 0.00 0.0 33.11 3.46 F
2410 2560 0.251121 ATTGTGATTGGGGTGCGTCA 60.251 50.000 0.00 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2392 2542 0.466372 TTGACGCACCCCAATCACAA 60.466 50.000 0.0 0.0 0.00 3.33 R
2927 3078 0.813184 CCAGCATCAACACCATCACC 59.187 55.000 0.0 0.0 0.00 4.02 R
3946 4136 1.004200 CGTTGGCCGAACCCTAGTT 60.004 57.895 0.0 0.0 39.56 2.24 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
101 102 2.774007 CGAAGGTGAGCTAATTTTGCG 58.226 47.619 0.00 0.00 35.28 4.85
121 122 3.535561 CGTCCCAGCATTTCATTAGACT 58.464 45.455 0.00 0.00 0.00 3.24
175 179 1.626321 TCTGCCGTCTGGGTTGATTTA 59.374 47.619 0.00 0.00 38.44 1.40
212 216 1.815408 GCAGCTCAGGTTTGTCCTTGA 60.815 52.381 0.00 0.00 45.67 3.02
316 320 9.853177 CCTTCACATCTATTTAGAAAAGGGTAT 57.147 33.333 10.55 0.00 35.69 2.73
512 540 4.130118 ACGAGAAGCTGAACTGATTTTGT 58.870 39.130 0.00 0.00 0.00 2.83
513 541 4.024556 ACGAGAAGCTGAACTGATTTTGTG 60.025 41.667 0.00 0.00 0.00 3.33
518 546 3.002656 AGCTGAACTGATTTTGTGTCACG 59.997 43.478 0.00 0.00 0.00 4.35
542 570 3.206150 CATTGATTAGACCGGTGAAGGG 58.794 50.000 14.63 0.00 35.02 3.95
692 721 2.143122 CACTATGCACGTTGGAGTGTT 58.857 47.619 0.00 0.00 43.61 3.32
696 725 1.860676 TGCACGTTGGAGTGTTACTC 58.139 50.000 0.39 0.39 44.32 2.59
697 726 1.411246 TGCACGTTGGAGTGTTACTCT 59.589 47.619 8.68 0.00 44.46 3.24
818 850 7.867403 ACAAAACATGAAAGCACCATAAGTTAG 59.133 33.333 0.00 0.00 0.00 2.34
891 923 3.558321 GGACTTGGTGTGTATACTTGGCA 60.558 47.826 4.17 0.00 0.00 4.92
1122 1238 0.543410 TCTTCCTTCGCCTACCCACA 60.543 55.000 0.00 0.00 0.00 4.17
1165 1281 1.519719 GTCGGCTGCATCTCCTTCT 59.480 57.895 0.50 0.00 0.00 2.85
1429 1551 0.105039 GGCTGGTATCGGTCAGAAGG 59.895 60.000 0.00 0.00 33.11 3.46
1587 1710 1.379044 CCTTTTGCCTCCCTGCGAT 60.379 57.895 0.00 0.00 0.00 4.58
1595 1718 1.947678 GCCTCCCTGCGATAATGATGG 60.948 57.143 0.00 0.00 0.00 3.51
1689 1812 5.047235 TGCCTTTGTCTTCTCTTCTAGTACC 60.047 44.000 0.00 0.00 0.00 3.34
1813 1939 5.294552 GGCTGTTTCTACTGGATGTTACATC 59.705 44.000 16.30 16.30 0.00 3.06
1851 1977 3.232213 GTGCTTGACACTCGGAAGATA 57.768 47.619 0.00 0.00 46.41 1.98
1889 2015 1.986882 CCCCCACCTCAAGCAATATC 58.013 55.000 0.00 0.00 0.00 1.63
2143 2273 5.337652 GGCTATGGTTGTTTCTCACTAGACT 60.338 44.000 0.00 0.00 0.00 3.24
2410 2560 0.251121 ATTGTGATTGGGGTGCGTCA 60.251 50.000 0.00 0.00 0.00 4.35
2578 2729 3.694072 CCTTTGTGACAACCTTTCTGTGA 59.306 43.478 0.00 0.00 0.00 3.58
2623 2774 2.306847 GCAATATGAAATGGGACCGGT 58.693 47.619 6.92 6.92 0.00 5.28
2691 2842 3.255642 CCAACTTGTATGTGGTCCTTTGG 59.744 47.826 0.00 0.00 0.00 3.28
2810 2961 7.493499 AGCTCCAGAATATATATCTGCAACT 57.507 36.000 14.51 10.05 42.36 3.16
2830 2981 4.985538 ACTTGAGTATGTTCATGTTGGGT 58.014 39.130 0.00 0.00 33.24 4.51
2831 2982 6.121776 ACTTGAGTATGTTCATGTTGGGTA 57.878 37.500 0.00 0.00 33.24 3.69
2832 2983 6.721318 ACTTGAGTATGTTCATGTTGGGTAT 58.279 36.000 0.00 0.00 33.24 2.73
2871 3022 2.909006 AGAAGGAGATGCTGGAACAAGA 59.091 45.455 0.00 0.00 38.70 3.02
2873 3024 1.980765 AGGAGATGCTGGAACAAGACA 59.019 47.619 0.00 0.00 38.70 3.41
2876 3027 0.798776 GATGCTGGAACAAGACACGG 59.201 55.000 0.00 0.00 38.70 4.94
3059 3210 0.736325 CGGCTCTGTTTGGTCCGTAG 60.736 60.000 0.00 0.00 35.75 3.51
3118 3269 7.271438 GCTTTCGATTTGACTTGAAGTTTATCC 59.729 37.037 0.00 0.00 0.00 2.59
3123 3274 7.307989 CGATTTGACTTGAAGTTTATCCTGTGT 60.308 37.037 0.00 0.00 0.00 3.72
3124 3275 6.618287 TTGACTTGAAGTTTATCCTGTGTG 57.382 37.500 0.00 0.00 0.00 3.82
3125 3276 4.515191 TGACTTGAAGTTTATCCTGTGTGC 59.485 41.667 0.00 0.00 0.00 4.57
3126 3277 4.718961 ACTTGAAGTTTATCCTGTGTGCT 58.281 39.130 0.00 0.00 0.00 4.40
3127 3278 5.133221 ACTTGAAGTTTATCCTGTGTGCTT 58.867 37.500 0.00 0.00 0.00 3.91
3128 3279 5.594317 ACTTGAAGTTTATCCTGTGTGCTTT 59.406 36.000 0.00 0.00 0.00 3.51
3129 3280 5.689383 TGAAGTTTATCCTGTGTGCTTTC 57.311 39.130 0.00 0.00 0.00 2.62
3130 3281 5.129634 TGAAGTTTATCCTGTGTGCTTTCA 58.870 37.500 0.00 0.00 0.00 2.69
3131 3282 5.592282 TGAAGTTTATCCTGTGTGCTTTCAA 59.408 36.000 0.00 0.00 0.00 2.69
3132 3283 6.265196 TGAAGTTTATCCTGTGTGCTTTCAAT 59.735 34.615 0.00 0.00 0.00 2.57
3133 3284 6.655078 AGTTTATCCTGTGTGCTTTCAATT 57.345 33.333 0.00 0.00 0.00 2.32
3134 3285 7.054491 AGTTTATCCTGTGTGCTTTCAATTT 57.946 32.000 0.00 0.00 0.00 1.82
3135 3286 6.925165 AGTTTATCCTGTGTGCTTTCAATTTG 59.075 34.615 0.00 0.00 0.00 2.32
3136 3287 6.647334 TTATCCTGTGTGCTTTCAATTTGA 57.353 33.333 0.00 0.00 0.00 2.69
3137 3288 4.305989 TCCTGTGTGCTTTCAATTTGAC 57.694 40.909 0.00 0.00 0.00 3.18
3138 3289 3.953612 TCCTGTGTGCTTTCAATTTGACT 59.046 39.130 0.00 0.00 0.00 3.41
3139 3290 4.402155 TCCTGTGTGCTTTCAATTTGACTT 59.598 37.500 0.00 0.00 0.00 3.01
3140 3291 4.505191 CCTGTGTGCTTTCAATTTGACTTG 59.495 41.667 0.00 0.00 0.00 3.16
3141 3292 5.321959 TGTGTGCTTTCAATTTGACTTGA 57.678 34.783 0.00 0.00 33.42 3.02
3142 3293 5.718146 TGTGTGCTTTCAATTTGACTTGAA 58.282 33.333 0.00 0.00 41.97 2.69
3143 3294 5.806502 TGTGTGCTTTCAATTTGACTTGAAG 59.193 36.000 0.00 1.74 43.80 3.02
3144 3295 5.807011 GTGTGCTTTCAATTTGACTTGAAGT 59.193 36.000 0.00 0.00 43.80 3.01
3145 3296 6.311200 GTGTGCTTTCAATTTGACTTGAAGTT 59.689 34.615 0.00 0.00 43.80 2.66
3146 3297 6.873076 TGTGCTTTCAATTTGACTTGAAGTTT 59.127 30.769 0.00 0.00 43.80 2.66
3147 3298 8.031864 TGTGCTTTCAATTTGACTTGAAGTTTA 58.968 29.630 0.00 0.00 43.80 2.01
3148 3299 9.034544 GTGCTTTCAATTTGACTTGAAGTTTAT 57.965 29.630 0.00 0.00 43.80 1.40
3149 3300 9.248291 TGCTTTCAATTTGACTTGAAGTTTATC 57.752 29.630 0.00 0.00 43.80 1.75
3150 3301 8.703336 GCTTTCAATTTGACTTGAAGTTTATCC 58.297 33.333 0.00 0.00 43.80 2.59
3151 3302 9.971922 CTTTCAATTTGACTTGAAGTTTATCCT 57.028 29.630 0.00 0.00 43.80 3.24
3152 3303 9.748708 TTTCAATTTGACTTGAAGTTTATCCTG 57.251 29.630 0.00 0.00 43.80 3.86
3153 3304 8.463930 TCAATTTGACTTGAAGTTTATCCTGT 57.536 30.769 0.00 0.00 32.35 4.00
3154 3305 8.352201 TCAATTTGACTTGAAGTTTATCCTGTG 58.648 33.333 0.00 0.00 32.35 3.66
3199 3350 1.268352 TGTGTTTGCCGCATAAAGACC 59.732 47.619 0.00 0.00 32.24 3.85
3220 3371 5.869579 ACCATGTGAGTAGTCAAAAGTGAT 58.130 37.500 0.69 0.00 35.80 3.06
3258 3409 5.181245 TGAGGTATTTGCAACTAAGCAGAAC 59.819 40.000 0.00 0.00 46.54 3.01
3369 3526 1.268692 TGCTGCTCTTTTTCTTGCACG 60.269 47.619 0.00 0.00 0.00 5.34
3491 3676 1.662629 CGAGCTTGTGATGCCTGTTAG 59.337 52.381 0.00 0.00 0.00 2.34
3510 3695 5.188359 TGTTAGTGTTGTACCCTAAGGATCC 59.812 44.000 2.48 2.48 36.73 3.36
3532 3717 3.800506 CCTTTGTGCTGCTCTTTTTCTTG 59.199 43.478 0.00 0.00 0.00 3.02
3533 3718 2.497107 TGTGCTGCTCTTTTTCTTGC 57.503 45.000 0.00 0.00 0.00 4.01
3535 3720 2.122564 GTGCTGCTCTTTTTCTTGCAC 58.877 47.619 0.00 0.00 41.53 4.57
3569 3754 7.707624 ACATGTGGTTATGTTTGATCTCATT 57.292 32.000 0.00 0.00 38.05 2.57
3709 3894 1.066605 CAGCCTTATGCACTCCATTGC 59.933 52.381 0.00 0.00 44.83 3.56
3728 3913 7.938490 TCCATTGCTAAGATCATATGCAAGTTA 59.062 33.333 16.24 5.96 44.94 2.24
3733 3918 9.123902 TGCTAAGATCATATGCAAGTTATTGTT 57.876 29.630 0.00 0.00 38.76 2.83
3744 3929 5.140177 GCAAGTTATTGTTCAACAGACTCG 58.860 41.667 4.39 0.00 38.76 4.18
3763 3948 1.919600 GCACCCCTCCTGCTCAAGAT 61.920 60.000 0.00 0.00 0.00 2.40
3765 3950 0.252881 ACCCCTCCTGCTCAAGATCA 60.253 55.000 0.00 0.00 0.00 2.92
3881 4071 2.256461 CGGCCTTGCTGCTGAAAC 59.744 61.111 0.00 0.00 40.15 2.78
3894 4084 2.288666 GCTGAAACTGGATATTGCCGA 58.711 47.619 0.00 0.00 0.00 5.54
3946 4136 2.159184 GCTCGAACTCATGTCCAGATCA 60.159 50.000 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 94 2.036992 TGAAATGCTGGGACGCAAAATT 59.963 40.909 0.00 0.00 40.56 1.82
101 102 3.629398 CCAGTCTAATGAAATGCTGGGAC 59.371 47.826 0.00 0.00 39.65 4.46
121 122 6.270219 GGGAATAATCCTAACCCTTTACCA 57.730 41.667 0.00 0.00 45.77 3.25
212 216 5.415701 ACAGAAAATTGGTCGAGCATACATT 59.584 36.000 19.37 12.38 0.00 2.71
267 271 8.631480 AGGTAGTAATTTTTCCCTGTAACAAG 57.369 34.615 0.00 0.00 0.00 3.16
316 320 2.616524 ACACAGGTAGTCCTTGCCTTA 58.383 47.619 0.00 0.00 43.07 2.69
385 407 0.809636 CACATGCGACGGCCATAAGA 60.810 55.000 2.24 0.00 38.85 2.10
450 472 1.748403 GCAGTGAGGACAGGTGTCA 59.252 57.895 12.09 0.00 46.47 3.58
451 473 1.004440 GGCAGTGAGGACAGGTGTC 60.004 63.158 1.17 1.17 44.04 3.67
457 479 0.179076 CGCATATGGCAGTGAGGACA 60.179 55.000 4.56 0.00 45.17 4.02
512 540 2.627945 GTCTAATCAATGGCCGTGACA 58.372 47.619 10.92 2.36 0.00 3.58
513 541 1.940613 GGTCTAATCAATGGCCGTGAC 59.059 52.381 10.92 6.69 0.00 3.67
518 546 1.134220 TCACCGGTCTAATCAATGGCC 60.134 52.381 2.59 0.00 0.00 5.36
542 570 6.712547 CCAAGGGATTCACAGAATAACCTATC 59.287 42.308 12.85 0.00 0.00 2.08
742 774 7.488150 CGAATAATCCTTTACTTTGCCCTTTTC 59.512 37.037 0.00 0.00 0.00 2.29
818 850 1.068194 CCAAGATCTATCGAGCGGGAC 60.068 57.143 0.00 0.00 29.88 4.46
891 923 3.238597 TGCAGGGCCTTCTTAAAAATGT 58.761 40.909 1.32 0.00 0.00 2.71
1122 1238 3.461773 CGGATGAGGTCGGCTGGT 61.462 66.667 0.00 0.00 0.00 4.00
1165 1281 2.080693 GCGGTTGGTGATGATGTTGTA 58.919 47.619 0.00 0.00 0.00 2.41
1412 1534 0.753262 CCCCTTCTGACCGATACCAG 59.247 60.000 0.00 0.00 0.00 4.00
1429 1551 2.298729 CCATCTCCTCGAAGATTCTCCC 59.701 54.545 0.00 0.00 33.68 4.30
1473 1596 2.737830 GGGAGCAGGAGATACCGC 59.262 66.667 0.00 0.00 44.74 5.68
1538 1661 5.995282 TGGTACAAATAATATGCCTCTTCCG 59.005 40.000 0.00 0.00 31.92 4.30
1587 1710 1.410083 GCTGTTGCCTCCCCATCATTA 60.410 52.381 0.00 0.00 0.00 1.90
1595 1718 2.674380 CCACAGCTGTTGCCTCCC 60.674 66.667 18.94 0.00 40.80 4.30
1786 1912 3.614092 ACATCCAGTAGAAACAGCCATG 58.386 45.455 0.00 0.00 0.00 3.66
1813 1939 4.813027 AGCACCAATATTTTCTTGCACAG 58.187 39.130 9.03 0.00 32.24 3.66
1851 1977 3.200165 GGGGGTTAGCAATGTAGAACTCT 59.800 47.826 0.00 0.00 0.00 3.24
1889 2015 9.525409 CAATGGCTATATCCAGAAAAGAAAAAG 57.475 33.333 1.21 0.00 39.89 2.27
2143 2273 5.243730 CCCTTTTAAGCTGGAATGTCTTGAA 59.756 40.000 0.00 0.00 0.00 2.69
2392 2542 0.466372 TTGACGCACCCCAATCACAA 60.466 50.000 0.00 0.00 0.00 3.33
2410 2560 5.362430 ACAGAACATAACCACCACAATGTTT 59.638 36.000 1.52 0.00 41.37 2.83
2578 2729 7.576236 CATGACAAAGATAAAGACAAAGTCGT 58.424 34.615 0.00 0.00 37.67 4.34
2691 2842 7.804129 CAGTAAGAAGCATAATAGACGAGGTAC 59.196 40.741 0.00 0.00 0.00 3.34
2725 2876 8.527810 ACAACACTTGGTAAATTTCTTTTGAGA 58.472 29.630 0.00 0.00 34.12 3.27
2810 2961 7.092623 ACCTATACCCAACATGAACATACTCAA 60.093 37.037 0.00 0.00 0.00 3.02
2821 2972 4.899457 TCCTGAGTACCTATACCCAACATG 59.101 45.833 0.00 0.00 30.88 3.21
2830 2981 5.988865 TCTCACCTTCCTGAGTACCTATA 57.011 43.478 0.00 0.00 39.08 1.31
2831 2982 4.883021 TCTCACCTTCCTGAGTACCTAT 57.117 45.455 0.00 0.00 39.08 2.57
2832 2983 4.570079 CCTTCTCACCTTCCTGAGTACCTA 60.570 50.000 0.00 0.00 39.08 3.08
2871 3022 3.022287 CTTGCTGCGTTTCCGTGT 58.978 55.556 0.00 0.00 36.15 4.49
2924 3075 1.802636 CATCAACACCATCACCGGC 59.197 57.895 0.00 0.00 0.00 6.13
2927 3078 0.813184 CCAGCATCAACACCATCACC 59.187 55.000 0.00 0.00 0.00 4.02
3027 3178 1.041437 AGAGCCGCCTATTACAGACC 58.959 55.000 0.00 0.00 0.00 3.85
3028 3179 1.409427 ACAGAGCCGCCTATTACAGAC 59.591 52.381 0.00 0.00 0.00 3.51
3118 3269 5.342433 TCAAGTCAAATTGAAAGCACACAG 58.658 37.500 0.00 0.00 36.28 3.66
3123 3274 9.248291 GATAAACTTCAAGTCAAATTGAAAGCA 57.752 29.630 0.00 0.00 45.80 3.91
3124 3275 8.703336 GGATAAACTTCAAGTCAAATTGAAAGC 58.297 33.333 0.00 0.00 45.80 3.51
3125 3276 9.971922 AGGATAAACTTCAAGTCAAATTGAAAG 57.028 29.630 0.00 0.36 45.80 2.62
3126 3277 9.748708 CAGGATAAACTTCAAGTCAAATTGAAA 57.251 29.630 0.00 0.00 45.80 2.69
3127 3278 8.912988 ACAGGATAAACTTCAAGTCAAATTGAA 58.087 29.630 0.00 5.61 44.72 2.69
3128 3279 8.352201 CACAGGATAAACTTCAAGTCAAATTGA 58.648 33.333 0.00 0.00 37.41 2.57
3129 3280 8.137437 ACACAGGATAAACTTCAAGTCAAATTG 58.863 33.333 0.00 0.00 0.00 2.32
3130 3281 8.137437 CACACAGGATAAACTTCAAGTCAAATT 58.863 33.333 0.00 0.00 0.00 1.82
3131 3282 7.651808 CACACAGGATAAACTTCAAGTCAAAT 58.348 34.615 0.00 0.00 0.00 2.32
3132 3283 6.459573 GCACACAGGATAAACTTCAAGTCAAA 60.460 38.462 0.00 0.00 0.00 2.69
3133 3284 5.008613 GCACACAGGATAAACTTCAAGTCAA 59.991 40.000 0.00 0.00 0.00 3.18
3134 3285 4.515191 GCACACAGGATAAACTTCAAGTCA 59.485 41.667 0.00 0.00 0.00 3.41
3135 3286 4.757149 AGCACACAGGATAAACTTCAAGTC 59.243 41.667 0.00 0.00 0.00 3.01
3136 3287 4.718961 AGCACACAGGATAAACTTCAAGT 58.281 39.130 0.00 0.00 0.00 3.16
3137 3288 5.695851 AAGCACACAGGATAAACTTCAAG 57.304 39.130 0.00 0.00 0.00 3.02
3138 3289 5.592282 TGAAAGCACACAGGATAAACTTCAA 59.408 36.000 0.00 0.00 0.00 2.69
3139 3290 5.129634 TGAAAGCACACAGGATAAACTTCA 58.870 37.500 0.00 0.00 0.00 3.02
3140 3291 5.689383 TGAAAGCACACAGGATAAACTTC 57.311 39.130 0.00 0.00 0.00 3.01
3141 3292 6.655078 ATTGAAAGCACACAGGATAAACTT 57.345 33.333 0.00 0.00 0.00 2.66
3142 3293 7.611467 TCATATTGAAAGCACACAGGATAAACT 59.389 33.333 0.00 0.00 0.00 2.66
3143 3294 7.698130 GTCATATTGAAAGCACACAGGATAAAC 59.302 37.037 0.00 0.00 0.00 2.01
3144 3295 7.413988 CGTCATATTGAAAGCACACAGGATAAA 60.414 37.037 0.00 0.00 0.00 1.40
3145 3296 6.037062 CGTCATATTGAAAGCACACAGGATAA 59.963 38.462 0.00 0.00 0.00 1.75
3146 3297 5.523552 CGTCATATTGAAAGCACACAGGATA 59.476 40.000 0.00 0.00 0.00 2.59
3147 3298 4.333649 CGTCATATTGAAAGCACACAGGAT 59.666 41.667 0.00 0.00 0.00 3.24
3148 3299 3.684305 CGTCATATTGAAAGCACACAGGA 59.316 43.478 0.00 0.00 0.00 3.86
3149 3300 3.684305 TCGTCATATTGAAAGCACACAGG 59.316 43.478 0.00 0.00 0.00 4.00
3150 3301 4.926860 TCGTCATATTGAAAGCACACAG 57.073 40.909 0.00 0.00 0.00 3.66
3151 3302 4.094739 CCATCGTCATATTGAAAGCACACA 59.905 41.667 0.00 0.00 0.00 3.72
3152 3303 4.094887 ACCATCGTCATATTGAAAGCACAC 59.905 41.667 0.00 0.00 0.00 3.82
3153 3304 4.260985 ACCATCGTCATATTGAAAGCACA 58.739 39.130 0.00 0.00 0.00 4.57
3154 3305 4.882671 ACCATCGTCATATTGAAAGCAC 57.117 40.909 0.00 0.00 0.00 4.40
3199 3350 7.425577 TTGATCACTTTTGACTACTCACATG 57.574 36.000 0.00 0.00 33.38 3.21
3220 3371 6.922957 GCAAATACCTCACAAACTCAAATTGA 59.077 34.615 0.00 0.00 0.00 2.57
3258 3409 9.507280 CAACACAAATAGATTATAAGCCAACAG 57.493 33.333 0.00 0.00 0.00 3.16
3369 3526 4.212214 CACAGAACTTCAAGTAGCTTCACC 59.788 45.833 0.00 0.00 0.00 4.02
3471 3632 1.662629 CTAACAGGCATCACAAGCTCG 59.337 52.381 0.00 0.00 0.00 5.03
3491 3676 3.113043 AGGGATCCTTAGGGTACAACAC 58.887 50.000 12.58 0.00 0.00 3.32
3510 3695 3.722728 AGAAAAAGAGCAGCACAAAGG 57.277 42.857 0.00 0.00 0.00 3.11
3532 3717 2.878406 ACCACATGTAACTTCACTGTGC 59.122 45.455 0.00 0.00 36.69 4.57
3533 3718 6.204688 ACATAACCACATGTAACTTCACTGTG 59.795 38.462 0.00 0.17 37.37 3.66
3535 3720 6.801539 ACATAACCACATGTAACTTCACTG 57.198 37.500 0.00 0.00 37.37 3.66
3569 3754 2.363306 ACAACTGATTGAGGGTGCAA 57.637 45.000 0.00 0.00 39.30 4.08
3728 3913 1.873591 GGTGCGAGTCTGTTGAACAAT 59.126 47.619 0.00 0.00 0.00 2.71
3733 3918 1.816863 GAGGGGTGCGAGTCTGTTGA 61.817 60.000 0.00 0.00 0.00 3.18
3744 3929 1.919600 ATCTTGAGCAGGAGGGGTGC 61.920 60.000 0.00 0.00 41.54 5.01
3881 4071 1.299541 AAAGCGTCGGCAATATCCAG 58.700 50.000 0.00 0.00 43.41 3.86
3894 4084 4.759693 TCCAAGACACATTATCAAAAGCGT 59.240 37.500 0.00 0.00 0.00 5.07
3946 4136 1.004200 CGTTGGCCGAACCCTAGTT 60.004 57.895 0.00 0.00 39.56 2.24


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

AutoCloner maintained by Alex Coulton.