Multiple sequence alignment - TraesCS7D01G328900

Loading Multiple Alignment...

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 TraesCS7D01G328900 chr7D 100.000 3959 0 0 1 3959 420629764 420633722 0.000000e+00 7312.0
1 TraesCS7D01G328900 chr7D 80.749 187 31 4 3390 3574 634836686 634836869 1.480000e-29 141.0
2 TraesCS7D01G328900 chr7D 76.703 279 47 12 3393 3665 576102718 576102452 5.330000e-29 139.0
3 TraesCS7D01G328900 chr7B 94.671 3115 142 10 1 3102 436704834 436707937 0.000000e+00 4811.0
4 TraesCS7D01G328900 chr7B 89.247 465 43 6 3125 3583 436741433 436741896 3.430000e-160 575.0
5 TraesCS7D01G328900 chr7B 93.657 268 16 1 3690 3956 436744835 436745102 2.220000e-107 399.0
6 TraesCS7D01G328900 chr7B 85.027 187 23 5 3390 3574 741333389 741333206 6.760000e-43 185.0
7 TraesCS7D01G328900 chr7B 93.976 83 5 0 3613 3695 436741898 436741980 4.150000e-25 126.0
8 TraesCS7D01G328900 chr7A 93.582 3132 158 16 1 3112 512439875 512436767 0.000000e+00 4630.0
9 TraesCS7D01G328900 chr7A 79.845 258 45 6 3396 3649 666978027 666977773 8.740000e-42 182.0
10 TraesCS7D01G328900 chr7A 92.233 103 6 2 3114 3214 512436717 512436615 1.150000e-30 145.0
11 TraesCS7D01G328900 chr3D 79.918 244 38 8 3390 3631 432501208 432500974 6.800000e-38 169.0
12 TraesCS7D01G328900 chr3D 72.626 358 70 24 2175 2523 4077343 4077681 4.210000e-15 93.5
13 TraesCS7D01G328900 chr3D 72.423 359 69 26 2175 2523 4167910 4167572 1.960000e-13 87.9
14 TraesCS7D01G328900 chr2D 84.571 175 22 4 3390 3563 644023042 644022872 6.800000e-38 169.0
15 TraesCS7D01G328900 chr2D 78.736 174 26 9 3496 3665 638722277 638722443 5.410000e-19 106.0
16 TraesCS7D01G328900 chr5A 85.315 143 21 0 3401 3543 524746574 524746716 8.860000e-32 148.0
17 TraesCS7D01G328900 chr6D 79.787 188 28 8 3390 3574 296691976 296691796 1.150000e-25 128.0
18 TraesCS7D01G328900 chr5D 100.000 28 0 0 1021 1048 218995655 218995682 7.000000e-03 52.8


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 TraesCS7D01G328900 chr7D 420629764 420633722 3958 False 7312.000000 7312 100.000000 1 3959 1 chr7D.!!$F1 3958
1 TraesCS7D01G328900 chr7B 436704834 436707937 3103 False 4811.000000 4811 94.671000 1 3102 1 chr7B.!!$F1 3101
2 TraesCS7D01G328900 chr7B 436741433 436745102 3669 False 366.666667 575 92.293333 3125 3956 3 chr7B.!!$F2 831
3 TraesCS7D01G328900 chr7A 512436615 512439875 3260 True 2387.500000 4630 92.907500 1 3214 2 chr7A.!!$R2 3213

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
125 126 1.540146 GGGTGGCATTTTGCGAGTTTT 60.540 47.619 0.00 0.00 46.21 2.43 F
1101 1118 2.364186 GGGACCAAGGCCAATGGG 60.364 66.667 26.14 14.79 42.48 4.00 F
1437 1454 0.625849 ATGATGACGCCCCCTTCTTT 59.374 50.000 0.00 0.00 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1419 1436 0.322456 CAAAGAAGGGGGCGTCATCA 60.322 55.0 0.0 0.0 0.0 3.07 R
2226 2243 0.732571 CCAGCAGTGTGACAACGTTT 59.267 50.0 0.0 0.0 0.0 3.60 R
3180 3258 0.318955 GCACTTCAAACTGCCGCATT 60.319 50.0 0.0 0.0 0.0 3.56 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
125 126 1.540146 GGGTGGCATTTTGCGAGTTTT 60.540 47.619 0.00 0.00 46.21 2.43
275 284 4.250699 ACCAGGTATGTGGCTGGT 57.749 55.556 0.00 0.00 44.46 4.00
286 296 3.586470 TGTGGCTGGTTTTTCTCCTTA 57.414 42.857 0.00 0.00 0.00 2.69
289 299 3.753797 GTGGCTGGTTTTTCTCCTTAGAG 59.246 47.826 0.00 0.00 41.93 2.43
311 321 8.034058 AGAGTCTGCTGTTGTGATAAAATTAC 57.966 34.615 0.00 0.00 0.00 1.89
347 357 9.950496 ATCTTATTTGTTTCATAGTGACAGAGT 57.050 29.630 0.00 0.00 0.00 3.24
448 458 5.379706 AAATATCCCAGGACTTCAGAAGG 57.620 43.478 14.90 0.00 0.00 3.46
558 568 6.090628 CACTTGTTGAAGCTTCAGAGACTATC 59.909 42.308 28.46 15.78 38.61 2.08
559 569 5.728637 TGTTGAAGCTTCAGAGACTATCA 57.271 39.130 27.02 14.46 38.61 2.15
560 570 5.718146 TGTTGAAGCTTCAGAGACTATCAG 58.282 41.667 27.02 0.00 38.61 2.90
561 571 5.244851 TGTTGAAGCTTCAGAGACTATCAGT 59.755 40.000 27.02 0.00 38.61 3.41
562 572 5.574891 TGAAGCTTCAGAGACTATCAGTC 57.425 43.478 25.16 0.00 37.80 3.51
563 573 5.260424 TGAAGCTTCAGAGACTATCAGTCT 58.740 41.667 25.16 8.54 44.32 3.24
564 574 6.418946 TGAAGCTTCAGAGACTATCAGTCTA 58.581 40.000 25.16 0.00 42.94 2.59
565 575 7.059788 TGAAGCTTCAGAGACTATCAGTCTAT 58.940 38.462 25.16 3.29 46.69 1.98
625 636 8.630037 CCCATCCAACTTTTAATTATACACCTC 58.370 37.037 0.00 0.00 0.00 3.85
631 642 9.646336 CAACTTTTAATTATACACCTCGCATAC 57.354 33.333 0.00 0.00 0.00 2.39
1101 1118 2.364186 GGGACCAAGGCCAATGGG 60.364 66.667 26.14 14.79 42.48 4.00
1214 1231 3.069946 CCAACACATGGCCGCCAT 61.070 61.111 19.79 19.79 46.37 4.40
1245 1262 3.745797 GCTTCCTGAACTCCACTTTCACT 60.746 47.826 0.00 0.00 0.00 3.41
1248 1265 3.323979 TCCTGAACTCCACTTTCACTACC 59.676 47.826 0.00 0.00 0.00 3.18
1303 1320 2.741985 CCATGTGCTTCGCCGACA 60.742 61.111 0.00 0.00 0.00 4.35
1419 1436 2.202797 CACTGCCTCGTGCGCTAT 60.203 61.111 9.73 0.00 45.60 2.97
1437 1454 0.625849 ATGATGACGCCCCCTTCTTT 59.374 50.000 0.00 0.00 0.00 2.52
1799 1816 2.045045 CATGCCACCGTCCATGGT 60.045 61.111 12.58 0.00 45.21 3.55
1815 1832 2.132352 GGTACCCCTGCTACCTCCG 61.132 68.421 0.00 0.00 32.23 4.63
1816 1833 2.132352 GTACCCCTGCTACCTCCGG 61.132 68.421 0.00 0.00 0.00 5.14
1948 1965 7.756558 AGCATTTCTGTATTACAAGAAGAAGC 58.243 34.615 0.00 8.61 0.00 3.86
2037 2054 1.825474 CAACATCCGAGGAGGTACAGT 59.175 52.381 9.99 0.00 38.24 3.55
2043 2060 2.306805 TCCGAGGAGGTACAGTTACTCA 59.693 50.000 0.00 0.00 41.99 3.41
2054 2071 5.813672 GGTACAGTTACTCACAAGTGAAACA 59.186 40.000 15.97 0.00 41.43 2.83
2078 2095 2.731451 TGACGAAATCTTTCTCGCACAG 59.269 45.455 0.00 0.00 38.64 3.66
2082 2099 3.060098 CGAAATCTTTCTCGCACAGACTC 59.940 47.826 1.56 0.00 35.07 3.36
2088 2105 3.573772 CTCGCACAGACTCGGCCAA 62.574 63.158 2.24 0.00 0.00 4.52
2142 2159 1.525535 GGATGGCTGCGAGATTGCT 60.526 57.895 0.00 0.00 35.36 3.91
2165 2182 3.565482 GTGAAGATGCTCAAGGACAACAA 59.435 43.478 0.00 0.00 0.00 2.83
2172 2189 2.561569 CTCAAGGACAACAAGGACGTT 58.438 47.619 0.00 0.00 0.00 3.99
2226 2243 0.042581 TCAGCAGGACCTCCCATGTA 59.957 55.000 0.00 0.00 37.41 2.29
2232 2249 1.982958 AGGACCTCCCATGTAAACGTT 59.017 47.619 0.00 0.00 37.41 3.99
2262 2279 1.304282 GGGATTCTGCTTGCAGGGA 59.696 57.895 20.62 11.36 0.00 4.20
2272 2289 1.131315 GCTTGCAGGGAAGATCGAAAC 59.869 52.381 4.63 0.00 0.00 2.78
2274 2291 0.606096 TGCAGGGAAGATCGAAACGA 59.394 50.000 0.00 0.00 41.13 3.85
2316 2333 1.098050 CGAATGGCTCCCTTGAAAGG 58.902 55.000 1.81 1.81 46.06 3.11
2379 2399 0.235665 CGCTGTTCGACATTGCTGTT 59.764 50.000 0.00 0.00 41.67 3.16
2484 2505 2.801631 GGATCAGGACCTCCAGCCG 61.802 68.421 0.00 0.00 38.89 5.52
2516 2537 2.731691 TTCGGACTGGCCAAGCTGTC 62.732 60.000 7.01 10.84 35.94 3.51
2613 2634 4.475444 TCCAGGGGAGTAGGGGCG 62.475 72.222 0.00 0.00 0.00 6.13
2686 2707 0.694444 TGGGGCTAGGAGGAACATCC 60.694 60.000 0.00 0.00 39.89 3.51
2688 2709 0.470341 GGGCTAGGAGGAACATCCAC 59.530 60.000 8.19 0.00 42.26 4.02
2745 2766 1.077005 AGCAGCAAGTATTTCCCCCAA 59.923 47.619 0.00 0.00 0.00 4.12
2871 2898 0.918983 TGCAAATCTCCCCTTCGGAT 59.081 50.000 0.00 0.00 41.00 4.18
2954 2981 1.872234 CACATACTCCGCGTGGACG 60.872 63.158 15.21 12.87 40.17 4.79
2987 3016 5.344743 TGAAGACTCGGCTATCTTGAATT 57.655 39.130 0.23 0.00 35.29 2.17
2988 3017 6.465439 TGAAGACTCGGCTATCTTGAATTA 57.535 37.500 0.23 0.00 35.29 1.40
3066 3095 1.135199 GTGATGCATGCACTTCTTGGG 60.135 52.381 25.37 0.00 33.57 4.12
3089 3118 4.318831 GGTGTCGTTTCTCTGAATTCACAC 60.319 45.833 3.38 7.67 0.00 3.82
3095 3124 5.120208 CGTTTCTCTGAATTCACACGGTAAT 59.880 40.000 3.38 0.00 0.00 1.89
3112 3142 8.973378 ACACGGTAATTTTGAAATTGTTATGTG 58.027 29.630 11.02 12.68 38.90 3.21
3161 3239 4.942852 TGGTCATTTCCATTTGTGTCAAC 58.057 39.130 0.00 0.00 31.96 3.18
3177 3255 4.091509 GTGTCAACAGATAACCACGATGAC 59.908 45.833 0.00 0.00 37.15 3.06
3180 3258 5.178623 GTCAACAGATAACCACGATGACAAA 59.821 40.000 0.00 0.00 36.75 2.83
3184 3262 5.030295 CAGATAACCACGATGACAAAATGC 58.970 41.667 0.00 0.00 0.00 3.56
3214 3294 7.435192 AGTTTGAAGTGCCGAAAGAAAATTAAG 59.565 33.333 0.00 0.00 0.00 1.85
3220 3300 8.887036 AGTGCCGAAAGAAAATTAAGAAAATT 57.113 26.923 0.00 0.00 0.00 1.82
3221 3301 8.764287 AGTGCCGAAAGAAAATTAAGAAAATTG 58.236 29.630 0.00 0.00 0.00 2.32
3283 3363 4.630644 ATGACACTGAGTTGTGGAAGAT 57.369 40.909 0.00 0.00 41.84 2.40
3288 3370 0.321564 TGAGTTGTGGAAGATGGCCG 60.322 55.000 0.00 0.00 0.00 6.13
3292 3374 1.488705 TTGTGGAAGATGGCCGGACT 61.489 55.000 9.82 0.00 0.00 3.85
3303 3385 1.684734 GCCGGACTAGAGGTTGGGA 60.685 63.158 5.05 0.00 0.00 4.37
3308 3390 2.614734 CGGACTAGAGGTTGGGAAAACC 60.615 54.545 0.00 0.00 40.58 3.27
3312 3394 0.106419 AGAGGTTGGGAAAACCGCAA 60.106 50.000 12.52 0.00 44.82 4.85
3336 3418 4.304939 GGCACAACTCGTCCTATATAACC 58.695 47.826 0.00 0.00 0.00 2.85
3379 3463 6.442952 CACGAGTTGTGGGAATATTTTGAAA 58.557 36.000 2.16 0.00 45.21 2.69
3382 3466 8.458843 ACGAGTTGTGGGAATATTTTGAAATAG 58.541 33.333 0.00 0.00 34.62 1.73
3519 3603 9.529325 CAATAGAATGAAAATTCTCATGCATGT 57.471 29.630 25.43 4.94 40.91 3.21
3534 3618 1.798283 CATGTTTGCATGTTGGGGTG 58.202 50.000 0.00 0.00 45.48 4.61
3549 3633 1.393603 GGGTGAGCCTTTTCCTATGC 58.606 55.000 0.00 0.00 34.45 3.14
3552 3636 3.435026 GGGTGAGCCTTTTCCTATGCATA 60.435 47.826 6.20 6.20 34.45 3.14
3556 3640 4.883585 TGAGCCTTTTCCTATGCATAGTTG 59.116 41.667 27.75 16.15 0.00 3.16
3577 3661 5.601583 TGCATGTTATGATTGGCATTTCT 57.398 34.783 0.00 0.00 38.44 2.52
3583 3667 1.532523 TGATTGGCATTTCTCGTGCA 58.467 45.000 0.00 0.00 44.25 4.57
3584 3668 1.469703 TGATTGGCATTTCTCGTGCAG 59.530 47.619 0.00 0.00 44.25 4.41
3585 3669 1.470098 GATTGGCATTTCTCGTGCAGT 59.530 47.619 0.00 0.00 44.25 4.40
3586 3670 1.317613 TTGGCATTTCTCGTGCAGTT 58.682 45.000 0.00 0.00 44.25 3.16
3587 3671 0.592637 TGGCATTTCTCGTGCAGTTG 59.407 50.000 0.00 0.00 44.25 3.16
3588 3672 0.730494 GGCATTTCTCGTGCAGTTGC 60.730 55.000 0.00 0.00 44.25 4.17
3598 3682 3.578456 GCAGTTGCATGCGTAGGT 58.422 55.556 14.09 0.00 41.59 3.08
3599 3683 1.135315 GCAGTTGCATGCGTAGGTG 59.865 57.895 14.09 7.06 41.59 4.00
3600 3684 1.796151 CAGTTGCATGCGTAGGTGG 59.204 57.895 14.09 0.00 0.00 4.61
3601 3685 2.040544 AGTTGCATGCGTAGGTGGC 61.041 57.895 14.09 0.00 0.00 5.01
3602 3686 2.033294 TTGCATGCGTAGGTGGCA 59.967 55.556 14.09 0.00 45.71 4.92
3603 3687 1.602041 TTGCATGCGTAGGTGGCAA 60.602 52.632 14.09 0.00 44.66 4.52
3604 3688 0.964860 TTGCATGCGTAGGTGGCAAT 60.965 50.000 14.09 0.00 44.66 3.56
3605 3689 1.064621 GCATGCGTAGGTGGCAATG 59.935 57.895 0.00 0.00 44.66 2.82
3606 3690 1.064621 CATGCGTAGGTGGCAATGC 59.935 57.895 0.00 0.00 44.66 3.56
3607 3691 1.077501 ATGCGTAGGTGGCAATGCT 60.078 52.632 4.82 0.00 44.66 3.79
3608 3692 0.680921 ATGCGTAGGTGGCAATGCTT 60.681 50.000 4.82 0.00 44.66 3.91
3609 3693 1.137404 GCGTAGGTGGCAATGCTTG 59.863 57.895 4.82 0.00 0.00 4.01
3610 3694 1.802636 CGTAGGTGGCAATGCTTGG 59.197 57.895 4.82 0.00 0.00 3.61
3611 3695 0.676466 CGTAGGTGGCAATGCTTGGA 60.676 55.000 4.82 0.00 0.00 3.53
3618 3702 1.546923 TGGCAATGCTTGGATGTTGAG 59.453 47.619 4.82 0.00 0.00 3.02
3623 3707 4.151157 GCAATGCTTGGATGTTGAGAAAAC 59.849 41.667 0.00 0.00 0.00 2.43
3635 3719 8.956426 GGATGTTGAGAAAACTATGTTAATGGA 58.044 33.333 0.00 0.00 0.00 3.41
3804 6749 1.081892 CCTCAAGATGCAACCGAGTG 58.918 55.000 9.31 0.00 0.00 3.51
3818 6763 1.075542 CGAGTGCGCCTTTGAACATA 58.924 50.000 4.18 0.00 0.00 2.29
3837 6782 5.237815 ACATACACTAATCATGCCATACCG 58.762 41.667 0.00 0.00 0.00 4.02
3872 6817 7.275183 TGATTGATGTCATCCTCTAAATCGTT 58.725 34.615 10.36 0.00 0.00 3.85
3882 6827 3.941483 CCTCTAAATCGTTGATGCCACTT 59.059 43.478 0.00 0.00 0.00 3.16
3883 6828 4.396166 CCTCTAAATCGTTGATGCCACTTT 59.604 41.667 0.00 0.00 0.00 2.66
3884 6829 5.295431 TCTAAATCGTTGATGCCACTTTG 57.705 39.130 0.00 0.00 0.00 2.77
3886 6831 3.837213 AATCGTTGATGCCACTTTGAG 57.163 42.857 0.00 0.00 0.00 3.02
3912 6857 5.253096 AGGTACATAGACATGGGGAAAGTTT 59.747 40.000 0.00 0.00 36.39 2.66
3940 6885 3.007940 CCATTATTCCTATCTCCGCCACA 59.992 47.826 0.00 0.00 0.00 4.17
3941 6886 4.504864 CCATTATTCCTATCTCCGCCACAA 60.505 45.833 0.00 0.00 0.00 3.33
3956 6901 1.204467 CCACAACCCCAATTTCATCGG 59.796 52.381 0.00 0.00 0.00 4.18
3957 6902 0.894835 ACAACCCCAATTTCATCGGC 59.105 50.000 0.00 0.00 0.00 5.54
3958 6903 0.894141 CAACCCCAATTTCATCGGCA 59.106 50.000 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
125 126 7.178097 GGTAGAGTTACAAAGAAACCTCTCCTA 59.822 40.741 0.00 0.00 0.00 2.94
275 284 5.552870 ACAGCAGACTCTAAGGAGAAAAA 57.447 39.130 0.00 0.00 41.86 1.94
286 296 7.880195 AGTAATTTTATCACAACAGCAGACTCT 59.120 33.333 0.00 0.00 0.00 3.24
289 299 7.750903 GGAAGTAATTTTATCACAACAGCAGAC 59.249 37.037 0.00 0.00 0.00 3.51
311 321 7.149569 TGAAACAAATAAGATGCAGAGGAAG 57.850 36.000 0.00 0.00 0.00 3.46
448 458 4.636206 AGAATGAGAACTGAAATAACGGCC 59.364 41.667 0.00 0.00 0.00 6.13
559 569 1.977854 TGGTGGTTGCAGTGATAGACT 59.022 47.619 0.00 0.00 34.02 3.24
560 570 2.472695 TGGTGGTTGCAGTGATAGAC 57.527 50.000 0.00 0.00 0.00 2.59
561 571 3.517500 TGTATGGTGGTTGCAGTGATAGA 59.482 43.478 0.00 0.00 0.00 1.98
562 572 3.872696 TGTATGGTGGTTGCAGTGATAG 58.127 45.455 0.00 0.00 0.00 2.08
563 573 3.872696 CTGTATGGTGGTTGCAGTGATA 58.127 45.455 0.00 0.00 0.00 2.15
564 574 2.715046 CTGTATGGTGGTTGCAGTGAT 58.285 47.619 0.00 0.00 0.00 3.06
565 575 1.881925 GCTGTATGGTGGTTGCAGTGA 60.882 52.381 0.00 0.00 0.00 3.41
625 636 2.097629 TCTTTCTCTCTCCACGTATGCG 59.902 50.000 0.19 0.19 44.93 4.73
674 686 5.578157 ACTACTATTCCACCACAAAACCT 57.422 39.130 0.00 0.00 0.00 3.50
702 714 2.352421 GCTGACTACGTAGCAAAGGTCA 60.352 50.000 22.40 15.99 39.67 4.02
904 916 6.982141 GCAAATTATTCATGCAAGGAGAATCA 59.018 34.615 9.40 2.11 39.81 2.57
905 917 6.982141 TGCAAATTATTCATGCAAGGAGAATC 59.018 34.615 2.24 0.00 46.23 2.52
1101 1118 3.075005 TCAGGGCAGGCGTACCTC 61.075 66.667 0.00 0.00 46.34 3.85
1181 1198 2.042025 GGAGAGAGGCCTGGAGCT 60.042 66.667 12.00 0.00 43.05 4.09
1214 1231 2.515979 TTCAGGAAGCTGGCGTCCA 61.516 57.895 24.44 6.85 45.06 4.02
1370 1387 2.825836 CAATGTCCCTGCGGCCTC 60.826 66.667 0.00 0.00 0.00 4.70
1419 1436 0.322456 CAAAGAAGGGGGCGTCATCA 60.322 55.000 0.00 0.00 0.00 3.07
1575 1592 1.652012 CTCGGCGTCAAAGGCAAAA 59.348 52.632 6.85 0.00 36.37 2.44
1815 1832 2.047179 GGTTCAGACACCGGAGCC 60.047 66.667 9.46 0.00 31.81 4.70
1816 1833 1.374758 CTGGTTCAGACACCGGAGC 60.375 63.158 9.46 0.00 45.19 4.70
1823 1840 0.836400 GGGAGTCCCTGGTTCAGACA 60.836 60.000 22.04 0.00 41.34 3.41
1912 1929 4.313020 ACAGAAATGCTCCCAGAAGAAT 57.687 40.909 0.00 0.00 0.00 2.40
1948 1965 1.407989 GGGAGGAAGTGAGCCATGAAG 60.408 57.143 0.00 0.00 0.00 3.02
2037 2054 5.462068 CGTCATCTGTTTCACTTGTGAGTAA 59.538 40.000 3.61 0.00 33.90 2.24
2043 2060 5.760253 AGATTTCGTCATCTGTTTCACTTGT 59.240 36.000 0.00 0.00 31.88 3.16
2054 2071 3.614616 GTGCGAGAAAGATTTCGTCATCT 59.385 43.478 0.00 0.00 41.92 2.90
2131 2148 2.004733 CATCTTCACAGCAATCTCGCA 58.995 47.619 0.00 0.00 0.00 5.10
2142 2159 3.141398 GTTGTCCTTGAGCATCTTCACA 58.859 45.455 0.00 0.00 34.92 3.58
2165 2182 1.573108 ATCCTCACCATCAACGTCCT 58.427 50.000 0.00 0.00 0.00 3.85
2172 2189 4.225717 TCAGTCATGAAATCCTCACCATCA 59.774 41.667 0.00 0.00 36.69 3.07
2178 2195 3.118992 CGACCTCAGTCATGAAATCCTCA 60.119 47.826 0.00 0.00 43.73 3.86
2226 2243 0.732571 CCAGCAGTGTGACAACGTTT 59.267 50.000 0.00 0.00 0.00 3.60
2232 2249 1.059098 AGAATCCCAGCAGTGTGACA 58.941 50.000 0.00 0.00 0.00 3.58
2262 2279 3.697045 AGATGAGTCCTCGTTTCGATCTT 59.303 43.478 0.00 0.00 34.61 2.40
2316 2333 1.066787 GTGCCTCTCCCAGAAGTGTAC 60.067 57.143 0.00 0.00 0.00 2.90
2391 2411 2.283604 TGCAGGTACTCGAGGCCA 60.284 61.111 24.01 5.47 34.60 5.36
2439 2460 1.511850 TGTTGTGAGGCTTGATGTCG 58.488 50.000 0.00 0.00 0.00 4.35
2469 2490 1.984570 CTTCGGCTGGAGGTCCTGA 60.985 63.158 0.00 0.00 37.15 3.86
2484 2505 3.181491 CCAGTCCGAAGTCAGAGATCTTC 60.181 52.174 0.00 0.00 37.34 2.87
2516 2537 1.202927 TGGTGCTCTCTTTTTGGGAGG 60.203 52.381 0.00 0.00 0.00 4.30
2562 2583 1.440060 GATGTACCCGATCGTGCCA 59.560 57.895 15.09 3.64 0.00 4.92
2613 2634 1.668151 GTCGGACTTGCTGGTGACC 60.668 63.158 0.00 0.00 0.00 4.02
2686 2707 1.464608 ACCAGCAAAATCGTCATCGTG 59.535 47.619 0.00 0.00 38.33 4.35
2688 2709 2.159430 TGAACCAGCAAAATCGTCATCG 59.841 45.455 0.00 0.00 38.55 3.84
2871 2898 1.612146 TCTGGTCATGGAAGGCCGA 60.612 57.895 0.00 0.00 36.79 5.54
2954 2981 1.190323 CGAGTCTTCAGCGTGTTCAAC 59.810 52.381 0.00 0.00 0.00 3.18
3035 3064 2.415759 GCATGCATCACCGAATGAAACA 60.416 45.455 14.21 0.00 41.93 2.83
3066 3095 3.807622 TGTGAATTCAGAGAAACGACACC 59.192 43.478 8.80 0.00 0.00 4.16
3089 3118 8.012151 TGCACATAACAATTTCAAAATTACCG 57.988 30.769 0.63 0.00 36.52 4.02
3112 3142 4.571984 GGCTTATCCATGGTTGAATTTTGC 59.428 41.667 12.58 5.29 34.01 3.68
3161 3239 5.030295 GCATTTTGTCATCGTGGTTATCTG 58.970 41.667 0.00 0.00 0.00 2.90
3177 3255 2.219216 CACTTCAAACTGCCGCATTTTG 59.781 45.455 23.38 23.38 36.03 2.44
3180 3258 0.318955 GCACTTCAAACTGCCGCATT 60.319 50.000 0.00 0.00 0.00 3.56
3214 3294 9.759259 GCAAACCTTATTTCATTAGCAATTTTC 57.241 29.630 0.00 0.00 0.00 2.29
3220 3300 7.068593 AGCTATGCAAACCTTATTTCATTAGCA 59.931 33.333 8.42 0.00 0.00 3.49
3221 3301 7.380602 CAGCTATGCAAACCTTATTTCATTAGC 59.619 37.037 0.00 0.00 0.00 3.09
3268 3348 1.457346 GGCCATCTTCCACAACTCAG 58.543 55.000 0.00 0.00 0.00 3.35
3272 3352 1.002624 TCCGGCCATCTTCCACAAC 60.003 57.895 2.24 0.00 0.00 3.32
3283 3363 1.987855 CCAACCTCTAGTCCGGCCA 60.988 63.158 2.24 0.00 0.00 5.36
3288 3370 2.614734 CGGTTTTCCCAACCTCTAGTCC 60.615 54.545 2.39 0.00 38.15 3.85
3292 3374 0.766131 TGCGGTTTTCCCAACCTCTA 59.234 50.000 2.39 0.00 38.15 2.43
3303 3385 1.142965 GTTGTGCCCTTGCGGTTTT 59.857 52.632 0.00 0.00 41.78 2.43
3308 3390 2.954753 GACGAGTTGTGCCCTTGCG 61.955 63.158 0.00 0.00 41.78 4.85
3312 3394 2.154567 TATAGGACGAGTTGTGCCCT 57.845 50.000 0.00 0.00 40.31 5.19
3318 3400 8.627403 TCTAGTTTGGTTATATAGGACGAGTTG 58.373 37.037 0.00 0.00 0.00 3.16
3336 3418 3.131396 GTGCGGGGTATCATCTAGTTTG 58.869 50.000 0.00 0.00 0.00 2.93
3519 3603 1.470996 GGCTCACCCCAACATGCAAA 61.471 55.000 0.00 0.00 0.00 3.68
3534 3618 5.429957 CAACTATGCATAGGAAAAGGCTC 57.570 43.478 31.87 0.00 34.69 4.70
3549 3633 5.834169 TGCCAATCATAACATGCAACTATG 58.166 37.500 0.00 0.00 0.00 2.23
3552 3636 5.347620 AATGCCAATCATAACATGCAACT 57.652 34.783 0.00 0.00 34.33 3.16
3556 3640 4.678287 CGAGAAATGCCAATCATAACATGC 59.322 41.667 0.00 0.00 34.33 4.06
3563 3647 2.093890 TGCACGAGAAATGCCAATCAT 58.906 42.857 0.00 0.00 42.69 2.45
3564 3648 1.469703 CTGCACGAGAAATGCCAATCA 59.530 47.619 0.00 0.00 42.69 2.57
3568 3652 0.592637 CAACTGCACGAGAAATGCCA 59.407 50.000 0.00 0.00 42.69 4.92
3583 3667 2.040544 GCCACCTACGCATGCAACT 61.041 57.895 19.57 1.31 0.00 3.16
3584 3668 1.861542 TTGCCACCTACGCATGCAAC 61.862 55.000 19.57 0.00 37.04 4.17
3585 3669 0.964860 ATTGCCACCTACGCATGCAA 60.965 50.000 19.57 3.82 44.96 4.08
3586 3670 1.378382 ATTGCCACCTACGCATGCA 60.378 52.632 19.57 0.00 35.83 3.96
3587 3671 1.064621 CATTGCCACCTACGCATGC 59.935 57.895 7.91 7.91 35.83 4.06
3588 3672 1.064621 GCATTGCCACCTACGCATG 59.935 57.895 0.00 0.00 35.83 4.06
3589 3673 0.680921 AAGCATTGCCACCTACGCAT 60.681 50.000 4.70 0.00 35.83 4.73
3590 3674 1.303236 AAGCATTGCCACCTACGCA 60.303 52.632 4.70 0.00 0.00 5.24
3591 3675 1.137404 CAAGCATTGCCACCTACGC 59.863 57.895 4.70 0.00 40.39 4.42
3602 3686 5.796424 AGTTTTCTCAACATCCAAGCATT 57.204 34.783 0.00 0.00 0.00 3.56
3603 3687 6.435277 ACATAGTTTTCTCAACATCCAAGCAT 59.565 34.615 0.00 0.00 0.00 3.79
3604 3688 5.769662 ACATAGTTTTCTCAACATCCAAGCA 59.230 36.000 0.00 0.00 0.00 3.91
3605 3689 6.259550 ACATAGTTTTCTCAACATCCAAGC 57.740 37.500 0.00 0.00 0.00 4.01
3608 3692 8.739039 CCATTAACATAGTTTTCTCAACATCCA 58.261 33.333 0.00 0.00 0.00 3.41
3609 3693 8.956426 TCCATTAACATAGTTTTCTCAACATCC 58.044 33.333 0.00 0.00 0.00 3.51
3610 3694 9.994432 CTCCATTAACATAGTTTTCTCAACATC 57.006 33.333 0.00 0.00 0.00 3.06
3611 3695 8.960591 CCTCCATTAACATAGTTTTCTCAACAT 58.039 33.333 0.00 0.00 0.00 2.71
3618 3702 6.768381 AGCTAGCCTCCATTAACATAGTTTTC 59.232 38.462 12.13 0.00 0.00 2.29
3702 6647 5.920085 CATGTTGAGATTACATGTTTGCG 57.080 39.130 2.30 0.00 44.88 4.85
3725 6670 9.621629 ATGTGGATTTTTCCTCGTGTATAATTA 57.378 29.630 0.00 0.00 0.00 1.40
3732 6677 3.750371 TGATGTGGATTTTTCCTCGTGT 58.250 40.909 0.00 0.00 0.00 4.49
3804 6749 4.094294 TGATTAGTGTATGTTCAAAGGCGC 59.906 41.667 0.00 0.00 0.00 6.53
3809 6754 7.643569 ATGGCATGATTAGTGTATGTTCAAA 57.356 32.000 0.00 0.00 0.00 2.69
3818 6763 3.388024 ACTCGGTATGGCATGATTAGTGT 59.612 43.478 10.98 1.78 0.00 3.55
3837 6782 0.933097 ACATCAATCATCGCGCACTC 59.067 50.000 8.75 0.00 0.00 3.51
3872 6817 2.957402 ACCTTCTCAAAGTGGCATCA 57.043 45.000 0.00 0.00 0.00 3.07
3882 6827 4.408921 CCCCATGTCTATGTACCTTCTCAA 59.591 45.833 0.00 0.00 32.21 3.02
3883 6828 3.967326 CCCCATGTCTATGTACCTTCTCA 59.033 47.826 0.00 0.00 32.21 3.27
3884 6829 4.223953 TCCCCATGTCTATGTACCTTCTC 58.776 47.826 0.00 0.00 32.21 2.87
3886 6831 5.104485 ACTTTCCCCATGTCTATGTACCTTC 60.104 44.000 0.00 0.00 32.21 3.46
3912 6857 6.295688 GGCGGAGATAGGAATAATGGTTCTTA 60.296 42.308 0.00 0.00 0.00 2.10
3932 6877 1.152440 AAATTGGGGTTGTGGCGGA 60.152 52.632 0.00 0.00 0.00 5.54


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

AutoCloner maintained by Alex Coulton.