Multiple sequence alignment - TraesCS3A01G523300

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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 TraesCS3A01G523300 chr3A 100.000 3420 0 0 1 3420 738731217 738727798 0.000000e+00 6316.0
1 TraesCS3A01G523300 chr3A 100.000 366 0 0 3810 4175 738727408 738727043 0.000000e+00 676.0
2 TraesCS3A01G523300 chr3D 97.467 2487 49 3 869 3344 605478871 605481354 0.000000e+00 4231.0
3 TraesCS3A01G523300 chr3D 97.386 2487 51 3 869 3344 605521780 605524263 0.000000e+00 4220.0
4 TraesCS3A01G523300 chr3D 97.553 2411 45 3 869 3268 605565289 605567696 0.000000e+00 4113.0
5 TraesCS3A01G523300 chr3D 97.052 1662 38 2 869 2519 605544650 605546311 0.000000e+00 2787.0
6 TraesCS3A01G523300 chr3D 95.363 647 28 1 869 1513 605500924 605501570 0.000000e+00 1027.0
7 TraesCS3A01G523300 chr3D 95.957 371 10 1 3810 4175 605524458 605524828 7.730000e-167 597.0
8 TraesCS3A01G523300 chr3D 95.935 369 10 1 3810 4173 605481549 605481917 9.990000e-166 593.0
9 TraesCS3A01G523300 chr3D 94.879 371 14 1 3810 4175 605567873 605568243 3.620000e-160 575.0
10 TraesCS3A01G523300 chr3D 95.440 307 9 1 3874 4175 605546310 605546616 6.280000e-133 484.0
11 TraesCS3A01G523300 chr3D 96.040 101 4 0 3168 3268 605481272 605481372 9.290000e-37 165.0
12 TraesCS3A01G523300 chr3D 96.040 101 4 0 3168 3268 605524181 605524281 9.290000e-37 165.0
13 TraesCS3A01G523300 chr3D 95.181 83 4 0 3262 3344 605481178 605481260 9.420000e-27 132.0
14 TraesCS3A01G523300 chr3D 95.181 83 4 0 3262 3344 605524087 605524169 9.420000e-27 132.0
15 TraesCS3A01G523300 chr3D 95.181 83 4 0 3262 3344 605567596 605567678 9.420000e-27 132.0
16 TraesCS3A01G523300 chr3D 95.775 71 2 1 3350 3420 605481428 605481497 3.410000e-21 113.0
17 TraesCS3A01G523300 chr3D 95.775 71 2 1 3350 3420 605524337 605524406 3.410000e-21 113.0
18 TraesCS3A01G523300 chr3D 95.775 71 2 1 3350 3420 605567752 605567821 3.410000e-21 113.0
19 TraesCS3A01G523300 chr2D 93.274 892 37 4 1 869 65529663 65530554 0.000000e+00 1293.0
20 TraesCS3A01G523300 chr2D 81.511 887 138 10 7 869 78680649 78679765 0.000000e+00 706.0
21 TraesCS3A01G523300 chr2D 79.707 887 156 10 7 869 20327835 20326949 1.650000e-173 619.0
22 TraesCS3A01G523300 chr4D 91.974 623 27 4 271 870 426619088 426619710 0.000000e+00 852.0
23 TraesCS3A01G523300 chr3B 78.460 831 151 23 6 816 605300809 605299987 6.190000e-143 518.0
24 TraesCS3A01G523300 chr6B 77.679 896 162 22 5 869 630454387 630453499 2.880000e-141 512.0
25 TraesCS3A01G523300 chr6B 81.633 98 14 3 4081 4175 607680834 607680738 1.240000e-10 78.7
26 TraesCS3A01G523300 chr5B 76.047 931 182 28 1128 2039 590371917 590372825 2.960000e-121 446.0
27 TraesCS3A01G523300 chr4B 77.794 680 117 18 224 873 9537516 9536841 5.060000e-104 388.0
28 TraesCS3A01G523300 chr4B 78.934 394 47 23 498 869 484775382 484775003 6.980000e-58 235.0
29 TraesCS3A01G523300 chr5D 78.554 401 51 19 497 868 410441962 410442356 9.030000e-57 231.0
30 TraesCS3A01G523300 chr5D 85.417 96 13 1 4081 4175 33110390 33110295 9.550000e-17 99.0
31 TraesCS3A01G523300 chr5A 80.882 204 33 4 2935 3132 521933640 521933843 5.590000e-34 156.0
32 TraesCS3A01G523300 chr4A 74.634 205 42 9 608 807 485387023 485387222 9.620000e-12 82.4
33 TraesCS3A01G523300 chr1A 80.220 91 18 0 717 807 474220949 474221039 7.490000e-08 69.4


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 TraesCS3A01G523300 chr3A 738727043 738731217 4174 True 3496.00 6316 100.0000 1 4175 2 chr3A.!!$R1 4174
1 TraesCS3A01G523300 chr3D 605544650 605546616 1966 False 1635.50 2787 96.2460 869 4175 2 chr3D.!!$F4 3306
2 TraesCS3A01G523300 chr3D 605565289 605568243 2954 False 1233.25 4113 95.8470 869 4175 4 chr3D.!!$F5 3306
3 TraesCS3A01G523300 chr3D 605478871 605481917 3046 False 1046.80 4231 96.0796 869 4173 5 chr3D.!!$F2 3304
4 TraesCS3A01G523300 chr3D 605521780 605524828 3048 False 1045.40 4220 96.0678 869 4175 5 chr3D.!!$F3 3306
5 TraesCS3A01G523300 chr3D 605500924 605501570 646 False 1027.00 1027 95.3630 869 1513 1 chr3D.!!$F1 644
6 TraesCS3A01G523300 chr2D 65529663 65530554 891 False 1293.00 1293 93.2740 1 869 1 chr2D.!!$F1 868
7 TraesCS3A01G523300 chr2D 78679765 78680649 884 True 706.00 706 81.5110 7 869 1 chr2D.!!$R2 862
8 TraesCS3A01G523300 chr2D 20326949 20327835 886 True 619.00 619 79.7070 7 869 1 chr2D.!!$R1 862
9 TraesCS3A01G523300 chr4D 426619088 426619710 622 False 852.00 852 91.9740 271 870 1 chr4D.!!$F1 599
10 TraesCS3A01G523300 chr3B 605299987 605300809 822 True 518.00 518 78.4600 6 816 1 chr3B.!!$R1 810
11 TraesCS3A01G523300 chr6B 630453499 630454387 888 True 512.00 512 77.6790 5 869 1 chr6B.!!$R2 864
12 TraesCS3A01G523300 chr5B 590371917 590372825 908 False 446.00 446 76.0470 1128 2039 1 chr5B.!!$F1 911
13 TraesCS3A01G523300 chr4B 9536841 9537516 675 True 388.00 388 77.7940 224 873 1 chr4B.!!$R1 649

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
231 232 0.536233 TGCAGTTACATTGTGGGCGT 60.536 50.0 0.0 0.0 0.00 5.68 F
603 615 0.615331 TGCAGATCTCCAGGGTTGTC 59.385 55.0 0.0 0.0 0.00 3.18 F
1714 1749 0.099436 GCGACCCGAGTACGTGTTAT 59.901 55.0 0.0 0.0 37.88 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1242 1268 0.036952 ACGTGGAAGACTGCATCAGG 60.037 55.0 0.00 0.0 35.51 3.86 R
2118 2174 0.107081 TGGTAGTGGTCAACAACGGG 59.893 55.0 0.00 0.0 0.00 5.28 R
3284 3434 0.454957 GCGCGTGCACTGATTGAATT 60.455 50.0 17.66 0.0 42.15 2.17 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
176 177 2.480419 GAGACGATGGTTGTTTGTCCTG 59.520 50.000 0.00 0.00 0.00 3.86
231 232 0.536233 TGCAGTTACATTGTGGGCGT 60.536 50.000 0.00 0.00 0.00 5.68
355 356 1.454479 CCAAGGCGATGCAAGGGAT 60.454 57.895 0.00 0.00 0.00 3.85
442 443 1.303317 GAGTGGACGGGGCAACAAT 60.303 57.895 0.00 0.00 39.74 2.71
560 563 1.758440 TTGCGACTGGAAGCTCTGGT 61.758 55.000 0.00 0.00 37.60 4.00
566 569 1.344763 ACTGGAAGCTCTGGTGTGTAC 59.655 52.381 0.00 0.00 37.60 2.90
603 615 0.615331 TGCAGATCTCCAGGGTTGTC 59.385 55.000 0.00 0.00 0.00 3.18
632 644 1.229625 ACTGCCAGGGAGTGATCCA 60.230 57.895 13.91 0.00 0.00 3.41
648 660 5.310068 AGTGATCCAGGATATCAAAGATGCT 59.690 40.000 0.32 1.79 35.23 3.79
690 702 5.046376 TGCTGTAATCAAGGAGATCACTGAA 60.046 40.000 0.00 0.00 35.39 3.02
695 707 4.963318 TCAAGGAGATCACTGAAACAGT 57.037 40.909 0.00 0.00 46.51 3.55
919 945 1.413118 CAAAGAAAAGGGGCACACCT 58.587 50.000 0.00 0.00 44.56 4.00
920 946 1.069049 CAAAGAAAAGGGGCACACCTG 59.931 52.381 0.00 0.00 40.87 4.00
952 978 6.014242 TGCAAGGATATATAGGAGTGAGGTTG 60.014 42.308 0.00 0.00 0.00 3.77
1025 1051 1.809207 CCGACATGAACCAATGCCC 59.191 57.895 0.00 0.00 0.00 5.36
1056 1082 1.611936 GCTCCCAGTCCTTTTCCAGAC 60.612 57.143 0.00 0.00 0.00 3.51
1074 1100 9.706691 TTTCCAGACACAAATAGTAACTTAGAG 57.293 33.333 0.00 0.00 0.00 2.43
1081 1107 7.332182 ACACAAATAGTAACTTAGAGAAGCTGC 59.668 37.037 0.00 0.00 35.97 5.25
1090 1116 5.423886 ACTTAGAGAAGCTGCTACCATTTC 58.576 41.667 0.90 0.00 35.97 2.17
1092 1118 1.936547 GAGAAGCTGCTACCATTTCGG 59.063 52.381 0.90 0.00 42.50 4.30
1115 1141 1.062845 GAGCTCTGGTCGTCGTAGC 59.937 63.158 6.43 0.00 0.00 3.58
1119 1145 2.202440 CTGGTCGTCGTAGCCGTG 60.202 66.667 0.00 0.00 35.01 4.94
1242 1268 2.184579 GTCAGCTACACCCTCGGC 59.815 66.667 0.00 0.00 0.00 5.54
1316 1342 2.815211 GCTCATGCTCGTCGGCAA 60.815 61.111 11.52 0.00 45.68 4.52
1714 1749 0.099436 GCGACCCGAGTACGTGTTAT 59.901 55.000 0.00 0.00 37.88 1.89
2118 2174 4.051922 TGCTCTTCGAGAAGAACAAGTTC 58.948 43.478 14.36 4.82 45.75 3.01
2120 2176 3.991121 CTCTTCGAGAAGAACAAGTTCCC 59.009 47.826 15.37 2.68 45.75 3.97
2286 2342 0.322975 ACGGCTTCTGTCAGATGCTT 59.677 50.000 29.48 19.05 42.83 3.91
2663 2719 1.023513 AGCCTCGATGAGCAAGCAAC 61.024 55.000 5.21 0.00 0.00 4.17
2895 2951 3.455177 AGAAGCTCATGGACATCAGTGAT 59.545 43.478 0.00 0.00 0.00 3.06
2897 2953 2.770232 AGCTCATGGACATCAGTGATGA 59.230 45.455 34.38 16.44 42.09 2.92
2898 2954 2.871022 GCTCATGGACATCAGTGATGAC 59.129 50.000 34.38 28.19 42.09 3.06
2904 2960 1.478510 GACATCAGTGATGACCGGTCT 59.521 52.381 34.38 19.82 42.09 3.85
3196 3252 3.824133 TCCATCCATCGCTTCAATTCAT 58.176 40.909 0.00 0.00 0.00 2.57
3227 3377 2.177977 CGCGCGGCATTGTTAATTTAA 58.822 42.857 24.84 0.00 0.00 1.52
3268 3418 2.289631 CCACGGCCATGCATCTATCTAA 60.290 50.000 2.24 0.00 0.00 2.10
3269 3419 3.603532 CACGGCCATGCATCTATCTAAT 58.396 45.455 2.24 0.00 0.00 1.73
3271 3421 3.201290 CGGCCATGCATCTATCTAATCC 58.799 50.000 2.24 0.00 0.00 3.01
3272 3422 3.369787 CGGCCATGCATCTATCTAATCCA 60.370 47.826 2.24 0.00 0.00 3.41
3274 3424 4.820716 GGCCATGCATCTATCTAATCCATC 59.179 45.833 0.00 0.00 0.00 3.51
3275 3425 4.510711 GCCATGCATCTATCTAATCCATCG 59.489 45.833 0.00 0.00 0.00 3.84
3278 3428 6.645827 CCATGCATCTATCTAATCCATCGATC 59.354 42.308 0.00 0.00 0.00 3.69
3279 3429 5.825507 TGCATCTATCTAATCCATCGATCG 58.174 41.667 9.36 9.36 0.00 3.69
3280 3430 4.679197 GCATCTATCTAATCCATCGATCGC 59.321 45.833 11.09 0.00 0.00 4.58
3281 3431 5.507149 GCATCTATCTAATCCATCGATCGCT 60.507 44.000 11.09 0.00 0.00 4.93
3283 3433 6.125327 TCTATCTAATCCATCGATCGCTTC 57.875 41.667 11.09 0.00 0.00 3.86
3284 3434 4.790765 ATCTAATCCATCGATCGCTTCA 57.209 40.909 11.09 0.00 0.00 3.02
3285 3435 4.584327 TCTAATCCATCGATCGCTTCAA 57.416 40.909 11.09 0.00 0.00 2.69
3287 3437 5.541845 TCTAATCCATCGATCGCTTCAATT 58.458 37.500 11.09 8.70 0.00 2.32
3289 3439 3.177997 TCCATCGATCGCTTCAATTCA 57.822 42.857 11.09 0.00 0.00 2.57
3291 3441 4.129380 TCCATCGATCGCTTCAATTCAAT 58.871 39.130 11.09 0.00 0.00 2.57
3292 3442 4.212004 TCCATCGATCGCTTCAATTCAATC 59.788 41.667 11.09 0.00 0.00 2.67
3293 3443 4.024641 CCATCGATCGCTTCAATTCAATCA 60.025 41.667 11.09 0.00 0.00 2.57
3294 3444 4.783959 TCGATCGCTTCAATTCAATCAG 57.216 40.909 11.09 0.00 0.00 2.90
3295 3445 4.183865 TCGATCGCTTCAATTCAATCAGT 58.816 39.130 11.09 0.00 0.00 3.41
3296 3446 4.033243 TCGATCGCTTCAATTCAATCAGTG 59.967 41.667 11.09 0.00 0.00 3.66
3297 3447 3.476295 TCGCTTCAATTCAATCAGTGC 57.524 42.857 0.00 0.00 0.00 4.40
3299 3449 2.912967 CGCTTCAATTCAATCAGTGCAC 59.087 45.455 9.40 9.40 0.00 4.57
3300 3450 2.912967 GCTTCAATTCAATCAGTGCACG 59.087 45.455 12.01 6.78 0.00 5.34
3301 3451 2.617250 TCAATTCAATCAGTGCACGC 57.383 45.000 12.01 0.00 0.00 5.34
3302 3452 1.136000 TCAATTCAATCAGTGCACGCG 60.136 47.619 12.01 3.53 0.00 6.01
3304 3454 2.567470 ATTCAATCAGTGCACGCGCG 62.567 55.000 30.96 30.96 42.97 6.86
3316 3466 4.802972 CGCGCGCGGCATTGTTTA 62.803 61.111 43.28 0.00 43.84 2.01
3318 3468 1.871789 GCGCGCGGCATTGTTTATT 60.872 52.632 33.06 0.00 42.87 1.40
3319 3469 1.409982 GCGCGCGGCATTGTTTATTT 61.410 50.000 33.06 0.00 42.87 1.40
3320 3470 1.816370 CGCGCGGCATTGTTTATTTA 58.184 45.000 24.84 0.00 0.00 1.40
3321 3471 2.380660 CGCGCGGCATTGTTTATTTAT 58.619 42.857 24.84 0.00 0.00 1.40
3322 3472 2.786578 CGCGCGGCATTGTTTATTTATT 59.213 40.909 24.84 0.00 0.00 1.40
3323 3473 3.241784 CGCGCGGCATTGTTTATTTATTT 59.758 39.130 24.84 0.00 0.00 1.40
3324 3474 4.438145 CGCGCGGCATTGTTTATTTATTTA 59.562 37.500 24.84 0.00 0.00 1.40
3325 3475 5.116377 CGCGCGGCATTGTTTATTTATTTAT 59.884 36.000 24.84 0.00 0.00 1.40
3326 3476 6.513317 GCGCGGCATTGTTTATTTATTTATC 58.487 36.000 8.83 0.00 0.00 1.75
3327 3477 6.664128 GCGCGGCATTGTTTATTTATTTATCG 60.664 38.462 8.83 0.00 0.00 2.92
3328 3478 6.358558 CGCGGCATTGTTTATTTATTTATCGT 59.641 34.615 0.00 0.00 0.00 3.73
3329 3479 7.490055 GCGGCATTGTTTATTTATTTATCGTG 58.510 34.615 0.00 0.00 0.00 4.35
3330 3480 7.166804 GCGGCATTGTTTATTTATTTATCGTGT 59.833 33.333 0.00 0.00 0.00 4.49
3331 3481 9.015577 CGGCATTGTTTATTTATTTATCGTGTT 57.984 29.630 0.00 0.00 0.00 3.32
3342 3492 9.940166 ATTTATTTATCGTGTTTATTTCCGTCC 57.060 29.630 0.00 0.00 0.00 4.79
3343 3493 6.988622 ATTTATCGTGTTTATTTCCGTCCA 57.011 33.333 0.00 0.00 0.00 4.02
3344 3494 6.988622 TTTATCGTGTTTATTTCCGTCCAT 57.011 33.333 0.00 0.00 0.00 3.41
3345 3495 6.592798 TTATCGTGTTTATTTCCGTCCATC 57.407 37.500 0.00 0.00 0.00 3.51
3346 3496 4.196626 TCGTGTTTATTTCCGTCCATCT 57.803 40.909 0.00 0.00 0.00 2.90
3347 3497 5.327616 TCGTGTTTATTTCCGTCCATCTA 57.672 39.130 0.00 0.00 0.00 1.98
3348 3498 5.909477 TCGTGTTTATTTCCGTCCATCTAT 58.091 37.500 0.00 0.00 0.00 1.98
3875 4025 0.877071 AGTGACTACGTGGTGTACCG 59.123 55.000 10.14 0.00 39.43 4.02
4001 4156 5.789643 AATAATGATGCGGGTAAATTGCT 57.210 34.783 0.00 0.00 0.00 3.91
4043 4198 5.278709 CCTCACTACTACTATCATGCCACAG 60.279 48.000 0.00 0.00 0.00 3.66
4054 4209 6.828273 ACTATCATGCCACAGCTAAAATGTTA 59.172 34.615 0.00 0.00 40.80 2.41
4070 4225 3.478175 TGTTAGTAGAAGCCTGGGGTA 57.522 47.619 0.00 0.00 0.00 3.69
4117 4272 5.506815 GCGTCTGTAGTACCATGTGCTATTA 60.507 44.000 0.00 0.00 33.76 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.098934 GTGTGCTTGTGGTCATGTTTCA 59.901 45.455 0.00 0.00 0.00 2.69
12 13 2.112198 CACACCGTGTGCTTGTGGT 61.112 57.895 18.38 0.00 41.89 4.16
31 32 2.129555 ATCTTCTGCCCCGCACAAGT 62.130 55.000 2.30 0.00 36.29 3.16
194 195 1.892474 GCAACCTGGGTAAATTCTGCA 59.108 47.619 0.00 0.00 0.00 4.41
355 356 3.642503 CCGGGGTTGGGTGCACTA 61.643 66.667 17.98 3.30 0.00 2.74
541 542 1.004560 CCAGAGCTTCCAGTCGCAA 60.005 57.895 0.00 0.00 0.00 4.85
560 563 1.074072 ATTGCAAGGGCGGTACACA 59.926 52.632 4.94 0.00 45.35 3.72
566 569 1.978617 AAGTCCATTGCAAGGGCGG 60.979 57.895 25.10 12.40 45.35 6.13
603 615 0.809385 CCTGGCAGTCTGAAGCAATG 59.191 55.000 14.43 0.00 0.00 2.82
632 644 5.248020 CCTCCTGTAGCATCTTTGATATCCT 59.752 44.000 0.00 0.00 0.00 3.24
648 660 3.612251 GCGTAGTGCCCTCCTGTA 58.388 61.111 0.00 0.00 37.76 2.74
690 702 5.564259 GCATTGCTCAAAATCTCTCACTGTT 60.564 40.000 0.16 0.00 0.00 3.16
695 707 3.192001 GGTGCATTGCTCAAAATCTCTCA 59.808 43.478 10.49 0.00 0.00 3.27
919 945 4.405680 CCTATATATCCTTGCATCCGGTCA 59.594 45.833 0.00 0.00 0.00 4.02
920 946 4.649674 TCCTATATATCCTTGCATCCGGTC 59.350 45.833 0.00 0.00 0.00 4.79
924 950 6.183360 CCTCACTCCTATATATCCTTGCATCC 60.183 46.154 0.00 0.00 0.00 3.51
973 999 2.043450 CCCCTGCTCTCCTCTCGT 60.043 66.667 0.00 0.00 0.00 4.18
1033 1059 2.034221 AAAAGGACTGGGAGCGGC 59.966 61.111 0.00 0.00 0.00 6.53
1045 1071 7.745620 AGTTACTATTTGTGTCTGGAAAAGG 57.254 36.000 0.00 0.00 0.00 3.11
1056 1082 7.547370 AGCAGCTTCTCTAAGTTACTATTTGTG 59.453 37.037 0.00 0.00 34.99 3.33
1073 1099 1.555075 TCCGAAATGGTAGCAGCTTCT 59.445 47.619 0.00 0.00 39.52 2.85
1074 1100 2.024176 TCCGAAATGGTAGCAGCTTC 57.976 50.000 0.00 5.23 39.52 3.86
1081 1107 1.341531 AGCTCCGATCCGAAATGGTAG 59.658 52.381 0.00 0.00 39.52 3.18
1090 1116 2.725008 GACCAGAGCTCCGATCCG 59.275 66.667 10.93 0.00 0.00 4.18
1092 1118 1.357334 GACGACCAGAGCTCCGATC 59.643 63.158 10.93 4.34 0.00 3.69
1115 1141 1.626654 GACGAACAGCATGACCACGG 61.627 60.000 0.00 0.00 39.69 4.94
1119 1145 1.639298 GCAGGACGAACAGCATGACC 61.639 60.000 0.00 0.00 39.69 4.02
1242 1268 0.036952 ACGTGGAAGACTGCATCAGG 60.037 55.000 0.00 0.00 35.51 3.86
2118 2174 0.107081 TGGTAGTGGTCAACAACGGG 59.893 55.000 0.00 0.00 0.00 5.28
2120 2176 1.942677 TGTGGTAGTGGTCAACAACG 58.057 50.000 0.00 0.00 0.00 4.10
2286 2342 7.338710 CCTTCAACCTCAATAGAAGACCAATA 58.661 38.462 0.00 0.00 39.78 1.90
3227 3377 4.035909 GTGGCCGGAAATAAACACGATAAT 59.964 41.667 5.05 0.00 0.00 1.28
3268 3418 3.732212 TGAATTGAAGCGATCGATGGAT 58.268 40.909 21.57 1.07 32.16 3.41
3269 3419 3.177997 TGAATTGAAGCGATCGATGGA 57.822 42.857 21.57 2.33 32.16 3.41
3271 3421 5.086888 TGATTGAATTGAAGCGATCGATG 57.913 39.130 21.57 0.00 32.16 3.84
3272 3422 4.813161 ACTGATTGAATTGAAGCGATCGAT 59.187 37.500 21.57 10.64 33.24 3.59
3274 3424 4.269312 CACTGATTGAATTGAAGCGATCG 58.731 43.478 11.69 11.69 0.00 3.69
3275 3425 4.033684 GCACTGATTGAATTGAAGCGATC 58.966 43.478 0.00 0.00 0.00 3.69
3278 3428 2.912967 GTGCACTGATTGAATTGAAGCG 59.087 45.455 10.32 0.00 0.00 4.68
3279 3429 2.912967 CGTGCACTGATTGAATTGAAGC 59.087 45.455 16.19 0.00 0.00 3.86
3280 3430 2.912967 GCGTGCACTGATTGAATTGAAG 59.087 45.455 16.19 0.00 0.00 3.02
3281 3431 2.665245 CGCGTGCACTGATTGAATTGAA 60.665 45.455 16.19 0.00 0.00 2.69
3283 3433 1.253116 CGCGTGCACTGATTGAATTG 58.747 50.000 16.19 0.00 0.00 2.32
3284 3434 0.454957 GCGCGTGCACTGATTGAATT 60.455 50.000 17.66 0.00 42.15 2.17
3285 3435 1.135315 GCGCGTGCACTGATTGAAT 59.865 52.632 17.66 0.00 42.15 2.57
3287 3437 3.776849 CGCGCGTGCACTGATTGA 61.777 61.111 24.19 0.00 42.97 2.57
3299 3449 4.802972 TAAACAATGCCGCGCGCG 62.803 61.111 43.73 43.73 42.08 6.86
3300 3450 1.409982 AAATAAACAATGCCGCGCGC 61.410 50.000 27.36 23.91 38.31 6.86
3301 3451 1.816370 TAAATAAACAATGCCGCGCG 58.184 45.000 25.67 25.67 0.00 6.86
3302 3452 4.770351 AAATAAATAAACAATGCCGCGC 57.230 36.364 0.00 0.00 0.00 6.86
3304 3454 7.166804 ACACGATAAATAAATAAACAATGCCGC 59.833 33.333 0.00 0.00 0.00 6.53
3305 3455 8.555166 ACACGATAAATAAATAAACAATGCCG 57.445 30.769 0.00 0.00 0.00 5.69
3316 3466 9.940166 GGACGGAAATAAACACGATAAATAAAT 57.060 29.630 0.00 0.00 0.00 1.40
3318 3468 8.489990 TGGACGGAAATAAACACGATAAATAA 57.510 30.769 0.00 0.00 0.00 1.40
3319 3469 8.665643 ATGGACGGAAATAAACACGATAAATA 57.334 30.769 0.00 0.00 0.00 1.40
3320 3470 6.988622 TGGACGGAAATAAACACGATAAAT 57.011 33.333 0.00 0.00 0.00 1.40
3321 3471 6.819649 AGATGGACGGAAATAAACACGATAAA 59.180 34.615 0.00 0.00 0.00 1.40
3322 3472 6.342906 AGATGGACGGAAATAAACACGATAA 58.657 36.000 0.00 0.00 0.00 1.75
3323 3473 5.909477 AGATGGACGGAAATAAACACGATA 58.091 37.500 0.00 0.00 0.00 2.92
3324 3474 4.766375 AGATGGACGGAAATAAACACGAT 58.234 39.130 0.00 0.00 0.00 3.73
3325 3475 4.196626 AGATGGACGGAAATAAACACGA 57.803 40.909 0.00 0.00 0.00 4.35
3326 3476 5.983720 AGATAGATGGACGGAAATAAACACG 59.016 40.000 0.00 0.00 0.00 4.49
3327 3477 8.142551 AGTAGATAGATGGACGGAAATAAACAC 58.857 37.037 0.00 0.00 0.00 3.32
3328 3478 8.246430 AGTAGATAGATGGACGGAAATAAACA 57.754 34.615 0.00 0.00 0.00 2.83
3331 3481 9.749340 TGATAGTAGATAGATGGACGGAAATAA 57.251 33.333 0.00 0.00 0.00 1.40
3332 3482 9.749340 TTGATAGTAGATAGATGGACGGAAATA 57.251 33.333 0.00 0.00 0.00 1.40
3333 3483 8.651589 TTGATAGTAGATAGATGGACGGAAAT 57.348 34.615 0.00 0.00 0.00 2.17
3334 3484 8.473358 TTTGATAGTAGATAGATGGACGGAAA 57.527 34.615 0.00 0.00 0.00 3.13
3335 3485 8.651589 ATTTGATAGTAGATAGATGGACGGAA 57.348 34.615 0.00 0.00 0.00 4.30
3336 3486 8.651589 AATTTGATAGTAGATAGATGGACGGA 57.348 34.615 0.00 0.00 0.00 4.69
3337 3487 9.360093 GAAATTTGATAGTAGATAGATGGACGG 57.640 37.037 0.00 0.00 0.00 4.79
3338 3488 9.914131 TGAAATTTGATAGTAGATAGATGGACG 57.086 33.333 0.00 0.00 0.00 4.79
3376 3526 4.081142 TGCTCATTCCATCGAAACCTAAGA 60.081 41.667 0.00 0.00 0.00 2.10
3844 3994 3.139850 CGTAGTCACTCCGTCCATCTAT 58.860 50.000 0.00 0.00 0.00 1.98
3875 4025 0.811281 CGCTGGGGGTCTGAAATTTC 59.189 55.000 11.41 11.41 0.00 2.17
4001 4156 1.304879 GGCCCCATGCTGTTACCAA 60.305 57.895 0.00 0.00 40.92 3.67
4043 4198 5.297029 CCCAGGCTTCTACTAACATTTTAGC 59.703 44.000 0.00 0.00 38.71 3.09
4054 4209 2.399580 GTGATACCCCAGGCTTCTACT 58.600 52.381 0.00 0.00 0.00 2.57
4070 4225 5.278858 GCGCTACTACTATTTAGGTGGTGAT 60.279 44.000 0.00 0.00 31.26 3.06


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

AutoCloner maintained by Alex Coulton.