Multiple sequence alignment - TraesCS1A01G418400

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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 TraesCS1A01G418400 chr1A 100.000 2999 0 0 1 2999 575775690 575778688 0.000000e+00 5539
1 TraesCS1A01G418400 chr1D 94.840 1686 44 11 738 2418 479519290 479520937 0.000000e+00 2591
2 TraesCS1A01G418400 chr1D 91.349 578 29 9 2414 2972 479520994 479521569 0.000000e+00 771
3 TraesCS1A01G418400 chr1D 81.974 932 106 28 1 916 479518220 479519105 0.000000e+00 734
4 TraesCS1A01G418400 chr1B 93.554 1691 66 11 738 2418 667715762 667717419 0.000000e+00 2479
5 TraesCS1A01G418400 chr1B 89.184 564 32 13 2414 2957 667717485 667718039 0.000000e+00 676
6 TraesCS1A01G418400 chr1B 75.497 453 97 12 30 478 169667595 169668037 3.030000e-50 209
7 TraesCS1A01G418400 chr7D 78.698 507 91 13 23 522 8744616 8744120 3.730000e-84 322
8 TraesCS1A01G418400 chr7D 78.808 302 60 4 8 307 39518973 39519272 1.820000e-47 200
9 TraesCS1A01G418400 chr3B 73.953 645 120 33 38 654 53578294 53577670 1.810000e-52 217
10 TraesCS1A01G418400 chr3B 73.386 635 140 19 38 654 2182286 2181663 3.030000e-50 209
11 TraesCS1A01G418400 chr7B 75.435 460 102 9 21 477 204038251 204037800 2.340000e-51 213
12 TraesCS1A01G418400 chr5B 75.052 477 108 9 8 482 677803536 677804003 8.420000e-51 211
13 TraesCS1A01G418400 chr5B 75.162 463 102 8 23 482 181387945 181387493 3.920000e-49 206
14 TraesCS1A01G418400 chr5B 78.738 301 56 6 8 307 545154683 545154976 8.480000e-46 195
15 TraesCS1A01G418400 chr6B 75.162 463 102 11 23 482 33588760 33588308 3.920000e-49 206
16 TraesCS1A01G418400 chr4A 74.214 477 112 9 8 482 741816742 741816275 3.950000e-44 189


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 TraesCS1A01G418400 chr1A 575775690 575778688 2998 False 5539.000000 5539 100.000000 1 2999 1 chr1A.!!$F1 2998
1 TraesCS1A01G418400 chr1D 479518220 479521569 3349 False 1365.333333 2591 89.387667 1 2972 3 chr1D.!!$F1 2971
2 TraesCS1A01G418400 chr1B 667715762 667718039 2277 False 1577.500000 2479 91.369000 738 2957 2 chr1B.!!$F2 2219
3 TraesCS1A01G418400 chr3B 53577670 53578294 624 True 217.000000 217 73.953000 38 654 1 chr3B.!!$R2 616
4 TraesCS1A01G418400 chr3B 2181663 2182286 623 True 209.000000 209 73.386000 38 654 1 chr3B.!!$R1 616

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
357 368 0.029035 CTTGAGCTCATCATTGCCGC 59.971 55.0 19.04 0.0 37.89 6.53 F
497 509 0.183492 AGGAACAACAGCAGGAGCAA 59.817 50.0 0.00 0.0 45.49 3.91 F
881 1243 0.744414 AATGGTCGTGGATCGGCTTG 60.744 55.0 0.00 0.0 44.25 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1341 1703 0.818445 GCTGGTAGAGGACGGATCGA 60.818 60.000 0.0 0.0 0.00 3.59 R
1809 2171 1.227089 CGCCTTGGACTCGATGAGG 60.227 63.158 0.0 0.0 33.35 3.86 R
2503 2944 0.752658 TCAGATACCATCACGGCCTG 59.247 55.000 0.0 0.0 39.03 4.85 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
28 29 2.663196 GCAACTACGGTGCCCTCT 59.337 61.111 0.00 0.00 0.00 3.69
66 69 2.904866 TATGCCCCGAATTGCCGC 60.905 61.111 0.00 0.00 0.00 6.53
74 77 1.498166 CGAATTGCCGCGTACCAAA 59.502 52.632 4.92 0.00 0.00 3.28
75 78 0.098025 CGAATTGCCGCGTACCAAAT 59.902 50.000 4.92 0.00 0.00 2.32
89 92 5.390567 GCGTACCAAATAACACCTTCAAGAG 60.391 44.000 0.00 0.00 0.00 2.85
102 111 1.444553 CAAGAGGGACTGCGACGAC 60.445 63.158 0.00 0.00 41.55 4.34
103 112 1.901948 AAGAGGGACTGCGACGACA 60.902 57.895 0.00 0.00 41.55 4.35
105 114 1.215647 GAGGGACTGCGACGACAAT 59.784 57.895 0.00 0.00 41.55 2.71
109 118 0.666274 GGACTGCGACGACAATGACA 60.666 55.000 0.00 0.00 0.00 3.58
110 119 1.136690 GACTGCGACGACAATGACAA 58.863 50.000 0.00 0.00 0.00 3.18
111 120 1.525197 GACTGCGACGACAATGACAAA 59.475 47.619 0.00 0.00 0.00 2.83
112 121 1.526887 ACTGCGACGACAATGACAAAG 59.473 47.619 0.00 0.00 0.00 2.77
113 122 0.234625 TGCGACGACAATGACAAAGC 59.765 50.000 0.00 0.00 0.00 3.51
114 123 0.512952 GCGACGACAATGACAAAGCT 59.487 50.000 0.00 0.00 0.00 3.74
164 173 3.834799 CGGTACACGGAGGGGAGC 61.835 72.222 0.00 0.00 39.42 4.70
179 190 2.204029 AGCGGGGAAGGGGTACAA 60.204 61.111 0.00 0.00 0.00 2.41
180 191 1.618447 AGCGGGGAAGGGGTACAAT 60.618 57.895 0.00 0.00 0.00 2.71
186 197 0.819582 GGAAGGGGTACAATCGACGA 59.180 55.000 0.00 0.00 0.00 4.20
224 235 4.643387 GCCCACAAGCGTCACCCT 62.643 66.667 0.00 0.00 0.00 4.34
274 285 0.686789 CTCCTGACACCCACACATCA 59.313 55.000 0.00 0.00 0.00 3.07
278 289 1.603802 CTGACACCCACACATCAACAC 59.396 52.381 0.00 0.00 0.00 3.32
297 308 3.622826 CCAGGACCAACCGTCGGT 61.623 66.667 12.23 12.23 42.99 4.69
300 311 4.309950 GGACCAACCGTCGGTGCT 62.310 66.667 19.67 0.00 42.99 4.40
306 317 3.562779 AACCGTCGGTGCTACCACG 62.563 63.158 19.67 15.86 43.00 4.94
307 318 3.740397 CCGTCGGTGCTACCACGA 61.740 66.667 20.35 7.76 41.74 4.35
316 327 1.264749 TGCTACCACGATTGCCTCCT 61.265 55.000 0.00 0.00 0.00 3.69
321 332 0.179073 CCACGATTGCCTCCTACCAG 60.179 60.000 0.00 0.00 0.00 4.00
330 341 4.175337 TCCTACCAGCATGCGCCC 62.175 66.667 13.01 0.00 39.83 6.13
357 368 0.029035 CTTGAGCTCATCATTGCCGC 59.971 55.000 19.04 0.00 37.89 6.53
401 412 1.137404 CGCTCGGGCCAAAATGAAG 59.863 57.895 4.39 0.00 34.44 3.02
405 416 1.205417 CTCGGGCCAAAATGAAGCAAT 59.795 47.619 4.39 0.00 0.00 3.56
407 418 1.067000 CGGGCCAAAATGAAGCAATCA 60.067 47.619 4.39 0.00 43.67 2.57
419 430 4.903054 TGAAGCAATCATAGATAGGGCTG 58.097 43.478 0.00 0.00 31.50 4.85
420 431 4.594491 TGAAGCAATCATAGATAGGGCTGA 59.406 41.667 0.00 0.00 31.50 4.26
421 432 4.550076 AGCAATCATAGATAGGGCTGAC 57.450 45.455 0.00 0.00 0.00 3.51
422 433 3.906218 AGCAATCATAGATAGGGCTGACA 59.094 43.478 0.00 0.00 0.00 3.58
423 434 4.020396 AGCAATCATAGATAGGGCTGACAG 60.020 45.833 0.00 0.00 0.00 3.51
424 435 4.262808 GCAATCATAGATAGGGCTGACAGT 60.263 45.833 3.99 0.00 0.00 3.55
426 437 5.736951 ATCATAGATAGGGCTGACAGTTC 57.263 43.478 3.99 0.00 0.00 3.01
428 439 1.115467 AGATAGGGCTGACAGTTCCG 58.885 55.000 3.99 0.00 0.00 4.30
429 440 0.530870 GATAGGGCTGACAGTTCCGC 60.531 60.000 3.99 0.00 0.00 5.54
430 441 1.264749 ATAGGGCTGACAGTTCCGCA 61.265 55.000 3.99 1.47 33.78 5.69
432 443 2.617274 GGGCTGACAGTTCCGCAAC 61.617 63.158 3.99 0.00 33.78 4.17
433 444 1.598130 GGCTGACAGTTCCGCAACT 60.598 57.895 3.99 0.00 44.26 3.16
478 490 0.537188 GCTTAGGCAGTAGCAGACCA 59.463 55.000 0.00 0.00 44.61 4.02
481 493 0.335019 TAGGCAGTAGCAGACCAGGA 59.665 55.000 0.00 0.00 44.61 3.86
485 497 1.270839 GCAGTAGCAGACCAGGAACAA 60.271 52.381 0.00 0.00 41.58 2.83
497 509 0.183492 AGGAACAACAGCAGGAGCAA 59.817 50.000 0.00 0.00 45.49 3.91
507 519 1.304713 CAGGAGCAAACCAGGCCAT 60.305 57.895 5.01 0.00 0.00 4.40
514 526 1.228862 AAACCAGGCCATGTGTCCC 60.229 57.895 5.01 0.00 0.00 4.46
534 557 4.821589 CGGGCCCGTGAAGCTCTC 62.822 72.222 36.64 0.00 34.35 3.20
555 578 2.103934 GCCACGCTGCAACAAACA 59.896 55.556 0.00 0.00 0.00 2.83
558 581 1.061729 CACGCTGCAACAAACACGA 59.938 52.632 0.00 0.00 0.00 4.35
562 585 0.865639 GCTGCAACAAACACGACACC 60.866 55.000 0.00 0.00 0.00 4.16
564 587 1.065401 CTGCAACAAACACGACACCAT 59.935 47.619 0.00 0.00 0.00 3.55
566 589 2.683362 TGCAACAAACACGACACCATAA 59.317 40.909 0.00 0.00 0.00 1.90
611 635 2.125912 CCAGACCAGCCGAAGACG 60.126 66.667 0.00 0.00 39.43 4.18
632 659 1.874345 CTCGTCACAGCCCTAACCGT 61.874 60.000 0.00 0.00 0.00 4.83
673 700 4.693566 CGGGTTGCTTAATGTAAGAGTTGA 59.306 41.667 0.00 0.00 38.02 3.18
724 752 1.120530 ACAGTTTCAGACCTCACCGT 58.879 50.000 0.00 0.00 0.00 4.83
725 753 1.068741 ACAGTTTCAGACCTCACCGTC 59.931 52.381 0.00 0.00 0.00 4.79
729 757 1.996798 TTCAGACCTCACCGTCTCTT 58.003 50.000 0.00 0.00 41.23 2.85
735 763 2.801111 GACCTCACCGTCTCTTCAAAAC 59.199 50.000 0.00 0.00 0.00 2.43
748 777 8.289618 CGTCTCTTCAAAACTCCATAATCAAAA 58.710 33.333 0.00 0.00 0.00 2.44
871 1233 5.621197 TTTGGAAAGTGATAATGGTCGTG 57.379 39.130 0.00 0.00 0.00 4.35
881 1243 0.744414 AATGGTCGTGGATCGGCTTG 60.744 55.000 0.00 0.00 44.25 4.01
894 1256 2.203126 GCTTGAGATCCAGGCCGG 60.203 66.667 0.00 0.00 41.49 6.13
895 1257 2.203126 CTTGAGATCCAGGCCGGC 60.203 66.667 21.18 21.18 33.14 6.13
896 1258 3.764160 CTTGAGATCCAGGCCGGCC 62.764 68.421 39.29 39.29 33.14 6.13
898 1260 4.247380 GAGATCCAGGCCGGCCAG 62.247 72.222 45.13 37.69 38.92 4.85
921 1283 3.437213 GCCAACCCCACCTTAATAAGTT 58.563 45.455 0.00 0.00 0.00 2.66
1040 1402 3.355344 GCCCTTTCCCCATCCCCA 61.355 66.667 0.00 0.00 0.00 4.96
1041 1403 2.715125 GCCCTTTCCCCATCCCCAT 61.715 63.158 0.00 0.00 0.00 4.00
1042 1404 1.543690 CCCTTTCCCCATCCCCATC 59.456 63.158 0.00 0.00 0.00 3.51
1043 1405 1.543690 CCTTTCCCCATCCCCATCC 59.456 63.158 0.00 0.00 0.00 3.51
1044 1406 1.543690 CTTTCCCCATCCCCATCCC 59.456 63.158 0.00 0.00 0.00 3.85
1045 1407 2.018086 TTTCCCCATCCCCATCCCC 61.018 63.158 0.00 0.00 0.00 4.81
1046 1408 2.832672 TTTCCCCATCCCCATCCCCA 62.833 60.000 0.00 0.00 0.00 4.96
1047 1409 3.511610 CCCCATCCCCATCCCCAC 61.512 72.222 0.00 0.00 0.00 4.61
1048 1410 3.511610 CCCATCCCCATCCCCACC 61.512 72.222 0.00 0.00 0.00 4.61
1049 1411 3.511610 CCATCCCCATCCCCACCC 61.512 72.222 0.00 0.00 0.00 4.61
1050 1412 3.511610 CATCCCCATCCCCACCCC 61.512 72.222 0.00 0.00 0.00 4.95
1051 1413 4.883414 ATCCCCATCCCCACCCCC 62.883 72.222 0.00 0.00 0.00 5.40
1341 1703 1.918800 CCCCTTCCACTCCCTCGTT 60.919 63.158 0.00 0.00 0.00 3.85
1470 1832 4.140599 CTCTCCGCCGAGCAGCTT 62.141 66.667 0.00 0.00 35.94 3.74
1530 1892 1.686325 ATGACCTCGCCCGCAAGTAT 61.686 55.000 0.00 0.00 0.00 2.12
1629 1991 3.706373 ATCGGCGCCTGGAGTGTT 61.706 61.111 26.68 0.00 0.00 3.32
1653 2015 5.662657 TCACATGTTCATGATCTTCTCCCTA 59.337 40.000 17.96 0.00 0.00 3.53
2002 2367 3.444029 CTTCCAGGATTGGGGTGAATTT 58.556 45.455 0.00 0.00 45.10 1.82
2099 2464 6.403049 TGTGTATCATTGTTCTGTATCGGTT 58.597 36.000 0.00 0.00 0.00 4.44
2503 2944 1.865970 GCATCATACAGTCTGCTGAGC 59.134 52.381 0.00 0.00 45.28 4.26
2529 2970 3.119291 CGTGATGGTATCTGAAGCAGTC 58.881 50.000 0.00 0.00 32.61 3.51
2536 2977 4.284490 TGGTATCTGAAGCAGTCAAGTCTT 59.716 41.667 0.00 0.00 35.22 3.01
2540 2981 7.550906 GGTATCTGAAGCAGTCAAGTCTTTTAT 59.449 37.037 0.00 0.00 35.22 1.40
2562 3003 9.914131 TTTATAGTATCCTCACAAAGATCATCG 57.086 33.333 0.00 0.00 0.00 3.84
2572 3013 4.271776 CACAAAGATCATCGCATAGCTCAA 59.728 41.667 0.00 0.00 0.00 3.02
2729 3170 2.606587 CCAGGGCTGGTAGGTTGCT 61.607 63.158 0.00 0.00 45.53 3.91
2731 3172 0.678048 CAGGGCTGGTAGGTTGCTTC 60.678 60.000 0.00 0.00 0.00 3.86
2748 3189 3.030209 TCGGAGTCGAAGCAATTCG 57.970 52.632 4.08 4.08 43.03 3.34
2770 3211 2.667448 GCACCAATATGCTGATGATGCG 60.667 50.000 0.00 0.00 42.62 4.73
2811 3252 1.227089 CGCAAGACATCCTCGGAGG 60.227 63.158 18.25 18.25 43.02 4.30
2828 3291 2.045926 GCGAGGGTGATGCCTTGT 60.046 61.111 0.00 0.00 37.43 3.16
2843 3306 6.883756 TGATGCCTTGTGTTTCATAGTCAATA 59.116 34.615 0.00 0.00 0.00 1.90
2885 3348 8.631480 TCATCCATAATTTTGAGGAGATCATG 57.369 34.615 0.00 0.00 37.89 3.07
2961 3424 3.251972 GCTCAACTTCAGGAAACCAAGAG 59.748 47.826 0.00 0.00 0.00 2.85
2977 3440 5.674933 CCAAGAGGTGTTGAAGTAAACTC 57.325 43.478 0.00 0.00 0.00 3.01
2978 3441 5.123227 CCAAGAGGTGTTGAAGTAAACTCA 58.877 41.667 0.00 0.00 0.00 3.41
2979 3442 5.588648 CCAAGAGGTGTTGAAGTAAACTCAA 59.411 40.000 0.00 0.00 0.00 3.02
2980 3443 6.094881 CCAAGAGGTGTTGAAGTAAACTCAAA 59.905 38.462 0.00 0.00 0.00 2.69
2981 3444 6.927294 AGAGGTGTTGAAGTAAACTCAAAG 57.073 37.500 0.00 0.00 0.00 2.77
2982 3445 5.297029 AGAGGTGTTGAAGTAAACTCAAAGC 59.703 40.000 0.00 0.00 0.00 3.51
2983 3446 4.947388 AGGTGTTGAAGTAAACTCAAAGCA 59.053 37.500 0.00 0.00 0.00 3.91
2984 3447 5.594317 AGGTGTTGAAGTAAACTCAAAGCAT 59.406 36.000 0.00 0.00 0.00 3.79
2985 3448 5.687285 GGTGTTGAAGTAAACTCAAAGCATG 59.313 40.000 0.00 0.00 0.00 4.06
2986 3449 5.687285 GTGTTGAAGTAAACTCAAAGCATGG 59.313 40.000 0.00 0.00 0.00 3.66
2987 3450 5.592282 TGTTGAAGTAAACTCAAAGCATGGA 59.408 36.000 0.00 0.00 0.00 3.41
2988 3451 6.096141 TGTTGAAGTAAACTCAAAGCATGGAA 59.904 34.615 0.00 0.00 0.00 3.53
2989 3452 6.707440 TGAAGTAAACTCAAAGCATGGAAA 57.293 33.333 0.00 0.00 0.00 3.13
2990 3453 6.738114 TGAAGTAAACTCAAAGCATGGAAAG 58.262 36.000 0.00 0.00 0.00 2.62
2991 3454 5.712152 AGTAAACTCAAAGCATGGAAAGG 57.288 39.130 0.00 0.00 0.00 3.11
2992 3455 4.524328 AGTAAACTCAAAGCATGGAAAGGG 59.476 41.667 0.00 0.00 0.00 3.95
2993 3456 2.978156 ACTCAAAGCATGGAAAGGGA 57.022 45.000 0.00 0.00 0.00 4.20
2994 3457 3.243359 ACTCAAAGCATGGAAAGGGAA 57.757 42.857 0.00 0.00 0.00 3.97
2995 3458 3.160269 ACTCAAAGCATGGAAAGGGAAG 58.840 45.455 0.00 0.00 0.00 3.46
2996 3459 1.895131 TCAAAGCATGGAAAGGGAAGC 59.105 47.619 0.00 0.00 0.00 3.86
2997 3460 1.897802 CAAAGCATGGAAAGGGAAGCT 59.102 47.619 0.00 0.00 0.00 3.74
2998 3461 2.301009 CAAAGCATGGAAAGGGAAGCTT 59.699 45.455 0.00 0.00 43.43 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.485764 GGAATTCTCCAGAGGGCAC 57.514 57.895 5.23 0.00 41.96 5.01
66 69 5.121768 CCTCTTGAAGGTGTTATTTGGTACG 59.878 44.000 0.00 0.00 40.67 3.67
74 77 3.307762 GCAGTCCCTCTTGAAGGTGTTAT 60.308 47.826 0.00 0.00 44.56 1.89
75 78 2.038557 GCAGTCCCTCTTGAAGGTGTTA 59.961 50.000 0.00 0.00 44.56 2.41
89 92 1.080093 TCATTGTCGTCGCAGTCCC 60.080 57.895 0.00 0.00 0.00 4.46
93 96 1.722751 GCTTTGTCATTGTCGTCGCAG 60.723 52.381 0.00 0.00 0.00 5.18
129 138 2.292984 ACCGGGAGAAATCCTAGGAACT 60.293 50.000 17.30 15.14 46.37 3.01
164 173 1.145377 CGATTGTACCCCTTCCCCG 59.855 63.158 0.00 0.00 0.00 5.73
179 190 1.204941 CCCTTCTTGAAGGTCGTCGAT 59.795 52.381 23.12 0.00 38.28 3.59
180 191 0.601558 CCCTTCTTGAAGGTCGTCGA 59.398 55.000 23.12 0.00 38.28 4.20
186 197 1.700186 GTCACCTCCCTTCTTGAAGGT 59.300 52.381 23.12 7.18 38.28 3.50
248 259 2.303022 TGTGGGTGTCAGGAGAAATCTC 59.697 50.000 1.68 1.68 42.14 2.75
274 285 2.931921 GGTTGGTCCTGGGGTGTT 59.068 61.111 0.00 0.00 0.00 3.32
278 289 4.388499 CGACGGTTGGTCCTGGGG 62.388 72.222 0.00 0.00 42.99 4.96
297 308 1.220749 GGAGGCAATCGTGGTAGCA 59.779 57.895 0.00 0.00 0.00 3.49
300 311 1.117150 GGTAGGAGGCAATCGTGGTA 58.883 55.000 0.00 0.00 0.00 3.25
306 317 1.602311 CATGCTGGTAGGAGGCAATC 58.398 55.000 0.00 0.00 39.46 2.67
307 318 0.466922 GCATGCTGGTAGGAGGCAAT 60.467 55.000 11.37 0.00 42.91 3.56
330 341 0.042361 GATGAGCTCAAGATTGCGCG 60.042 55.000 22.50 0.00 43.25 6.86
333 344 3.372954 GCAATGATGAGCTCAAGATTGC 58.627 45.455 35.87 35.87 42.21 3.56
336 347 2.219458 CGGCAATGATGAGCTCAAGAT 58.781 47.619 22.50 12.62 37.44 2.40
357 368 0.525761 CGGTGTTTGCCATGGTAAGG 59.474 55.000 15.25 1.09 0.00 2.69
386 397 1.204467 GATTGCTTCATTTTGGCCCGA 59.796 47.619 0.00 0.00 0.00 5.14
390 401 7.088905 CCTATCTATGATTGCTTCATTTTGGC 58.911 38.462 7.82 0.00 42.62 4.52
391 402 7.600065 CCCTATCTATGATTGCTTCATTTTGG 58.400 38.462 7.82 5.22 42.62 3.28
397 408 4.594491 TCAGCCCTATCTATGATTGCTTCA 59.406 41.667 0.00 0.00 39.12 3.02
401 412 4.252073 CTGTCAGCCCTATCTATGATTGC 58.748 47.826 0.00 0.00 0.00 3.56
405 416 3.898123 GGAACTGTCAGCCCTATCTATGA 59.102 47.826 0.00 0.00 0.00 2.15
407 418 2.894126 CGGAACTGTCAGCCCTATCTAT 59.106 50.000 0.00 0.00 0.00 1.98
412 423 1.476845 TTGCGGAACTGTCAGCCCTA 61.477 55.000 0.00 0.00 43.56 3.53
417 428 1.060713 CGTAGTTGCGGAACTGTCAG 58.939 55.000 29.82 14.99 42.66 3.51
418 429 0.386476 ACGTAGTTGCGGAACTGTCA 59.614 50.000 29.82 9.60 37.78 3.58
419 430 0.782384 CACGTAGTTGCGGAACTGTC 59.218 55.000 29.82 20.68 41.61 3.51
420 431 0.599204 CCACGTAGTTGCGGAACTGT 60.599 55.000 29.82 18.26 41.61 3.55
421 432 1.289109 CCCACGTAGTTGCGGAACTG 61.289 60.000 29.82 17.62 41.61 3.16
422 433 1.005394 CCCACGTAGTTGCGGAACT 60.005 57.895 25.85 25.85 41.61 3.01
423 434 1.005867 TCCCACGTAGTTGCGGAAC 60.006 57.895 12.40 12.40 41.61 3.62
424 435 1.290955 CTCCCACGTAGTTGCGGAA 59.709 57.895 0.00 0.00 41.61 4.30
426 437 2.125673 CCTCCCACGTAGTTGCGG 60.126 66.667 0.00 0.00 41.61 5.69
428 439 0.672711 GTTCCCTCCCACGTAGTTGC 60.673 60.000 0.00 0.00 41.61 4.17
429 440 0.682852 TGTTCCCTCCCACGTAGTTG 59.317 55.000 0.00 0.00 41.61 3.16
430 441 1.553704 GATGTTCCCTCCCACGTAGTT 59.446 52.381 0.00 0.00 41.61 2.24
432 443 0.464452 GGATGTTCCCTCCCACGTAG 59.536 60.000 0.00 0.00 0.00 3.51
433 444 0.042131 AGGATGTTCCCTCCCACGTA 59.958 55.000 0.00 0.00 37.19 3.57
478 490 0.183492 TTGCTCCTGCTGTTGTTCCT 59.817 50.000 0.00 0.00 40.48 3.36
481 493 0.746659 GGTTTGCTCCTGCTGTTGTT 59.253 50.000 0.00 0.00 40.48 2.83
485 497 1.228367 CCTGGTTTGCTCCTGCTGT 60.228 57.895 0.00 0.00 40.48 4.40
497 509 2.440599 GGGACACATGGCCTGGTT 59.559 61.111 3.32 0.00 44.77 3.67
552 575 0.952010 GGCGGTTATGGTGTCGTGTT 60.952 55.000 0.00 0.00 0.00 3.32
555 578 2.125832 CGGCGGTTATGGTGTCGT 60.126 61.111 0.00 0.00 0.00 4.34
558 581 2.266689 GGACGGCGGTTATGGTGT 59.733 61.111 13.24 0.00 0.00 4.16
562 585 0.388134 CGATAGGGACGGCGGTTATG 60.388 60.000 13.24 0.00 0.00 1.90
564 587 2.848858 GCGATAGGGACGGCGGTTA 61.849 63.158 13.24 0.00 0.00 2.85
611 635 0.108756 GGTTAGGGCTGTGACGAGTC 60.109 60.000 0.00 0.00 0.00 3.36
632 659 4.414956 ATCTGGGTCAGGGCGGGA 62.415 66.667 0.00 0.00 31.51 5.14
829 1191 8.491331 TCCAAAAACAATTTCCAAAAAGAGAG 57.509 30.769 0.00 0.00 0.00 3.20
834 1196 8.850156 TCACTTTCCAAAAACAATTTCCAAAAA 58.150 25.926 0.00 0.00 0.00 1.94
847 1209 6.442952 CACGACCATTATCACTTTCCAAAAA 58.557 36.000 0.00 0.00 0.00 1.94
881 1243 4.247380 CTGGCCGGCCTGGATCTC 62.247 72.222 43.34 17.51 42.00 2.75
921 1283 0.323302 TGTGGTATTTCCGAGCTGCA 59.677 50.000 1.02 0.00 39.52 4.41
962 1324 4.097218 GGTTCTTGACCTTGGGGC 57.903 61.111 0.00 0.00 45.55 5.80
1040 1402 4.124126 GGGAGAGGGGGTGGGGAT 62.124 72.222 0.00 0.00 0.00 3.85
1341 1703 0.818445 GCTGGTAGAGGACGGATCGA 60.818 60.000 0.00 0.00 0.00 3.59
1377 1739 3.902086 GAGTAGACGGAGGCGGCC 61.902 72.222 12.11 12.11 0.00 6.13
1470 1832 2.582436 GAGACCCCGATTTGGCGA 59.418 61.111 0.00 0.00 35.87 5.54
1530 1892 2.833582 GAGAGGATCCCCGACGCA 60.834 66.667 8.55 0.00 37.58 5.24
1563 1925 4.451150 GAGCGGTCGTCCATGGCA 62.451 66.667 6.96 0.00 0.00 4.92
1626 1988 5.645067 GGAGAAGATCATGAACATGTGAACA 59.355 40.000 13.35 0.74 39.72 3.18
1629 1991 4.472470 AGGGAGAAGATCATGAACATGTGA 59.528 41.667 13.35 0.00 39.72 3.58
1794 2156 2.046314 AGGCGCCACATGTACCAC 60.046 61.111 31.54 0.00 0.00 4.16
1809 2171 1.227089 CGCCTTGGACTCGATGAGG 60.227 63.158 0.00 0.00 33.35 3.86
2002 2367 3.751518 TGAGCAGAGCGAGTATATACCA 58.248 45.455 9.32 0.00 0.00 3.25
2099 2464 3.306989 CCTGTCCAATGCTACACTTCTCA 60.307 47.826 0.00 0.00 0.00 3.27
2379 2750 8.129496 TGTCACTTGAGGTAGATGTATTAACA 57.871 34.615 0.00 0.00 40.69 2.41
2503 2944 0.752658 TCAGATACCATCACGGCCTG 59.247 55.000 0.00 0.00 39.03 4.85
2562 3003 7.953158 TTACATGAGTATCTTTGAGCTATGC 57.047 36.000 0.00 0.00 34.92 3.14
2572 3013 7.744087 TTGTGCAGTTTTACATGAGTATCTT 57.256 32.000 0.00 0.00 34.92 2.40
2740 3181 1.067516 GCATATTGGTGCCGAATTGCT 59.932 47.619 8.08 0.00 39.18 3.91
2748 3189 2.352421 GCATCATCAGCATATTGGTGCC 60.352 50.000 1.94 0.00 44.81 5.01
2764 3205 3.371097 GACGAAGAGGGCCGCATCA 62.371 63.158 10.70 0.00 0.00 3.07
2770 3211 2.046217 GGGTTGACGAAGAGGGCC 60.046 66.667 0.00 0.00 0.00 5.80
2811 3252 2.045926 ACAAGGCATCACCCTCGC 60.046 61.111 0.00 0.00 40.58 5.03
2843 3306 3.684788 GGATGAGCGACACACTTGTTTAT 59.315 43.478 0.00 0.00 35.47 1.40
2857 3320 5.059161 TCTCCTCAAAATTATGGATGAGCG 58.941 41.667 0.00 0.00 38.34 5.03
2885 3348 1.717194 CAGCACCACCAAAATCATGC 58.283 50.000 0.00 0.00 0.00 4.06
2961 3424 5.243426 TGCTTTGAGTTTACTTCAACACC 57.757 39.130 0.00 0.00 0.00 4.16
2965 3428 6.707440 TTCCATGCTTTGAGTTTACTTCAA 57.293 33.333 0.00 0.00 0.00 2.69
2972 3435 3.575805 TCCCTTTCCATGCTTTGAGTTT 58.424 40.909 0.00 0.00 0.00 2.66
2973 3436 3.243359 TCCCTTTCCATGCTTTGAGTT 57.757 42.857 0.00 0.00 0.00 3.01
2974 3437 2.978156 TCCCTTTCCATGCTTTGAGT 57.022 45.000 0.00 0.00 0.00 3.41
2975 3438 2.094338 GCTTCCCTTTCCATGCTTTGAG 60.094 50.000 0.00 0.00 0.00 3.02
2976 3439 1.895131 GCTTCCCTTTCCATGCTTTGA 59.105 47.619 0.00 0.00 0.00 2.69
2977 3440 1.897802 AGCTTCCCTTTCCATGCTTTG 59.102 47.619 0.00 0.00 0.00 2.77
2978 3441 2.315720 AGCTTCCCTTTCCATGCTTT 57.684 45.000 0.00 0.00 0.00 3.51
2979 3442 2.315720 AAGCTTCCCTTTCCATGCTT 57.684 45.000 0.00 0.00 36.16 3.91


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

AutoCloner maintained by Alex Coulton.