Multiple sequence alignment - TraesCS1B01G297600

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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 TraesCS1B01G297600 chr1B 100.000 5103 0 0 1 5103 517903902 517909004 0.000000e+00 9424
1 TraesCS1B01G297600 chr1D 92.471 4768 206 54 1 4685 385617588 385622285 0.000000e+00 6674
2 TraesCS1B01G297600 chr1D 78.374 615 129 3 1436 2048 385803870 385804482 3.700000e-106 396
3 TraesCS1B01G297600 chr1D 89.954 219 7 3 4896 5101 385623742 385623958 8.420000e-68 268
4 TraesCS1B01G297600 chr1A 93.548 3038 146 18 1 2999 485339820 485342846 0.000000e+00 4479
5 TraesCS1B01G297600 chr1A 92.342 888 38 11 2997 3856 485342949 485343834 0.000000e+00 1236
6 TraesCS1B01G297600 chr1A 89.587 605 35 11 4085 4685 485343955 485344535 0.000000e+00 743
7 TraesCS1B01G297600 chr1A 91.905 420 24 3 4687 5103 485344699 485345111 3.430000e-161 579
8 TraesCS1B01G297600 chr1A 97.581 124 3 0 3900 4023 485343828 485343951 4.000000e-51 213
9 TraesCS1B01G297600 chr3A 83.333 438 36 13 4687 5093 629014592 629014161 2.240000e-98 370
10 TraesCS1B01G297600 chr3A 82.648 438 39 17 4687 5093 696243868 696243437 2.260000e-93 353
11 TraesCS1B01G297600 chr3A 90.110 91 6 2 4689 4779 181115758 181115671 1.160000e-21 115
12 TraesCS1B01G297600 chr3A 89.011 91 7 2 4689 4779 180540034 180540121 5.400000e-20 110
13 TraesCS1B01G297600 chr3D 83.032 442 34 19 4687 5093 560110288 560109853 3.760000e-96 363
14 TraesCS1B01G297600 chr3D 86.641 262 19 7 4845 5093 259362972 259363230 5.030000e-70 276
15 TraesCS1B01G297600 chr7A 87.023 262 18 7 4845 5093 671907835 671908093 1.080000e-71 281
16 TraesCS1B01G297600 chr3B 80.309 259 42 8 4699 4952 747495660 747495914 2.430000e-43 187
17 TraesCS1B01G297600 chr4D 77.075 253 34 13 4325 4566 416766750 416766511 1.930000e-24 124
18 TraesCS1B01G297600 chr4A 90.000 90 6 2 4689 4778 738304001 738304087 4.180000e-21 113
19 TraesCS1B01G297600 chr2B 89.011 91 7 2 4689 4779 480430326 480430239 5.400000e-20 110
20 TraesCS1B01G297600 chrUn 88.889 90 7 2 4689 4778 417727881 417727795 1.940000e-19 108
21 TraesCS1B01G297600 chr4B 88.889 90 7 2 4689 4778 101491034 101490948 1.940000e-19 108
22 TraesCS1B01G297600 chr4B 88.889 90 7 2 4689 4778 276890907 276890821 1.940000e-19 108
23 TraesCS1B01G297600 chr4B 88.889 90 7 2 4689 4778 463531704 463531790 1.940000e-19 108


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 TraesCS1B01G297600 chr1B 517903902 517909004 5102 False 9424 9424 100.0000 1 5103 1 chr1B.!!$F1 5102
1 TraesCS1B01G297600 chr1D 385617588 385623958 6370 False 3471 6674 91.2125 1 5101 2 chr1D.!!$F2 5100
2 TraesCS1B01G297600 chr1D 385803870 385804482 612 False 396 396 78.3740 1436 2048 1 chr1D.!!$F1 612
3 TraesCS1B01G297600 chr1A 485339820 485345111 5291 False 1450 4479 92.9926 1 5103 5 chr1A.!!$F1 5102

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
164 188 0.679321 CCTGCTTGCCTTCCTTCTCC 60.679 60.000 0.0 0.0 0.0 3.71 F
1183 1254 0.106519 GATGGTGGAATCTGGTGGGG 60.107 60.000 0.0 0.0 0.0 4.96 F
1713 1793 1.266989 GCCTTCACCAGTGCAGTTAAC 59.733 52.381 0.0 0.0 0.0 2.01 F
3079 3268 0.107945 GCTTGTAGGCTGTCTGGAGG 60.108 60.000 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1204 1284 0.757188 ATCTGCGCCAGGCTACTACT 60.757 55.0 10.54 0.0 44.05 2.57 R
2424 2504 0.114364 TCAGTCCAGACCAGTAGGCA 59.886 55.0 0.00 0.0 39.06 4.75 R
3592 3804 0.676466 CAAATGCAGTAGTCGGGCCA 60.676 55.0 4.39 0.0 0.00 5.36 R
4945 6422 0.251354 AGATGCCAGCACGTGATCTT 59.749 50.0 22.23 0.0 0.00 2.40 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
71 72 2.174319 GCCGGCTTCTTGGATCGAC 61.174 63.158 22.15 0.00 0.00 4.20
91 96 2.100252 ACAACATCGATACGGATCGGTT 59.900 45.455 28.78 21.81 46.94 4.44
98 103 4.559906 ATCGATACGGATCGGTTATTTGCA 60.560 41.667 28.78 7.46 46.94 4.08
121 126 3.192633 TCGACTGGAATTCGATGAAGACA 59.807 43.478 0.00 0.00 40.51 3.41
122 127 3.926527 CGACTGGAATTCGATGAAGACAA 59.073 43.478 0.00 0.00 38.85 3.18
129 134 6.536582 TGGAATTCGATGAAGACAAGAGAATC 59.463 38.462 0.00 0.00 32.04 2.52
153 177 1.069227 CGGTTTCAGTTACCTGCTTGC 60.069 52.381 0.00 0.00 38.66 4.01
164 188 0.679321 CCTGCTTGCCTTCCTTCTCC 60.679 60.000 0.00 0.00 0.00 3.71
184 208 2.488355 GCGATCAGGTTCCGACGA 59.512 61.111 0.00 0.00 0.00 4.20
264 288 1.437986 GCTCTTCGCCTATCGGTGT 59.562 57.895 0.00 0.00 41.65 4.16
305 330 7.771927 AATCATCAAGAACAAGTGGAAATCT 57.228 32.000 0.00 0.00 0.00 2.40
384 430 7.360776 GCAAAACAAAAATGTGAACCTCTTTCA 60.361 33.333 0.00 0.00 42.26 2.69
741 799 3.878667 CCTCCCAATCGGCTCCCC 61.879 72.222 0.00 0.00 0.00 4.81
835 893 1.227664 CCTAGAGCCTCCGTCTCCA 59.772 63.158 0.00 0.00 0.00 3.86
986 1057 2.783288 CGACTAACCTCTCCGCCCC 61.783 68.421 0.00 0.00 0.00 5.80
1009 1080 2.820728 TCCACAGATTCGAGTAGGGA 57.179 50.000 0.00 0.00 0.00 4.20
1146 1217 2.345991 CAGGGGAGTTTCGGCGAA 59.654 61.111 19.83 19.83 0.00 4.70
1183 1254 0.106519 GATGGTGGAATCTGGTGGGG 60.107 60.000 0.00 0.00 0.00 4.96
1191 1271 2.142292 AATCTGGTGGGGTGCAGGAC 62.142 60.000 0.00 0.00 0.00 3.85
1202 1282 3.151022 GCAGGACGAGGAGGAGGG 61.151 72.222 0.00 0.00 0.00 4.30
1204 1284 2.617538 AGGACGAGGAGGAGGGGA 60.618 66.667 0.00 0.00 0.00 4.81
1309 1389 2.224066 GCCGGTAAGCATACTCTGACAT 60.224 50.000 1.90 0.00 32.36 3.06
1343 1423 6.371548 GGTTAGTTTGATCTACTGCATGTTGA 59.628 38.462 10.23 0.00 35.14 3.18
1389 1469 4.415881 TGTATGGCATCACGGACTAATT 57.584 40.909 1.65 0.00 0.00 1.40
1391 1471 3.558931 ATGGCATCACGGACTAATTGA 57.441 42.857 0.00 0.00 0.00 2.57
1424 1504 4.996758 TCTTGCAGAATTGAACGAAGATGA 59.003 37.500 0.00 0.00 0.00 2.92
1432 1512 3.775661 TGAACGAAGATGATCAGCGTA 57.224 42.857 5.12 0.00 34.46 4.42
1433 1513 3.435566 TGAACGAAGATGATCAGCGTAC 58.564 45.455 5.12 0.48 34.46 3.67
1442 1522 5.561679 AGATGATCAGCGTACTAGATACCA 58.438 41.667 5.12 0.00 0.00 3.25
1629 1709 1.336755 GGTTCTTTTGCGTGGTGTCAT 59.663 47.619 0.00 0.00 0.00 3.06
1663 1743 3.788227 AGCCTTTCATGGACAACTGTA 57.212 42.857 0.00 0.00 0.00 2.74
1713 1793 1.266989 GCCTTCACCAGTGCAGTTAAC 59.733 52.381 0.00 0.00 0.00 2.01
1817 1897 3.417101 TGTGTTATCTGCGTGGGAATTT 58.583 40.909 0.00 0.00 0.00 1.82
1989 2069 6.074569 GCTCTCAACTTATGTCTTTCTATCGC 60.075 42.308 0.00 0.00 0.00 4.58
2346 2426 5.128205 TCTACTGAAATGAGCATGATTGGG 58.872 41.667 0.00 0.00 0.00 4.12
2380 2460 3.181454 GGACAGGAGTGAAGAGTGGAAAA 60.181 47.826 0.00 0.00 0.00 2.29
2424 2504 1.490490 ACAACGGACCATATGCAGGAT 59.510 47.619 0.00 0.00 0.00 3.24
2460 2540 5.185249 TGGACTGAGTTTACATACTGTCTCC 59.815 44.000 0.00 0.00 33.79 3.71
2583 2663 3.689347 ACAGAATATGCAGCCTGAAACA 58.311 40.909 12.40 0.00 0.00 2.83
2674 2754 1.417145 ACGTAAACCCCACTGCACTTA 59.583 47.619 0.00 0.00 0.00 2.24
2728 2808 8.766994 TCCTTCAGAAATGGATTTTATTAGGG 57.233 34.615 0.00 0.00 0.00 3.53
2757 2837 4.113354 GTCGCTATGGACCACTAAAAGAG 58.887 47.826 0.00 0.00 0.00 2.85
2776 2856 1.004277 GACCGAGACTGAAGTGCACG 61.004 60.000 12.01 0.00 0.00 5.34
2783 2863 2.036475 AGACTGAAGTGCACGAGAACAT 59.964 45.455 12.01 0.00 0.00 2.71
2792 2872 5.479306 AGTGCACGAGAACATAAATACTGT 58.521 37.500 12.01 0.00 0.00 3.55
2876 2956 3.951680 GGTTCTTTTGGACCTTCACTTCA 59.048 43.478 0.00 0.00 0.00 3.02
2917 2997 6.867662 ATATGCCATTTTCTCTAAGAACGG 57.132 37.500 0.00 0.00 33.26 4.44
2942 3022 9.120538 GGCTGAATTGAATTATCCTAAGTTACA 57.879 33.333 0.00 0.00 0.00 2.41
2953 3033 9.670442 ATTATCCTAAGTTACACCCTGAAGATA 57.330 33.333 0.00 0.00 0.00 1.98
2956 3036 7.645942 TCCTAAGTTACACCCTGAAGATAGTA 58.354 38.462 0.00 0.00 0.00 1.82
3011 3197 8.106247 TCTTAAATTTGTAAAATCCAGCGAGT 57.894 30.769 0.00 0.00 0.00 4.18
3044 3230 4.830826 AGTTGCTTACAGTACCTTTTGC 57.169 40.909 0.00 0.00 0.00 3.68
3069 3258 6.737254 TGTGTTTTCTTATAGCTTGTAGGC 57.263 37.500 0.00 0.00 0.00 3.93
3079 3268 0.107945 GCTTGTAGGCTGTCTGGAGG 60.108 60.000 0.00 0.00 0.00 4.30
3094 3283 0.326264 GGAGGTGCACTGGATTCTGT 59.674 55.000 17.98 0.00 0.00 3.41
3108 3297 4.523558 TGGATTCTGTGCAAATTGACATCA 59.476 37.500 0.00 0.00 0.00 3.07
3121 3310 2.349590 TGACATCATCGACAAAGCTGG 58.650 47.619 0.00 0.00 0.00 4.85
3139 3328 3.181480 GCTGGCAAAGGTGAAACTGTAAA 60.181 43.478 0.00 0.00 36.74 2.01
3222 3411 3.975992 CGTGCTTTACATGCTGGAC 57.024 52.632 0.00 0.00 0.00 4.02
3288 3477 5.505181 AACTGGAATTGTAGATGACACCT 57.495 39.130 0.00 0.00 37.96 4.00
3331 3520 0.606401 CATGGTGTTGTCGAGGCCTT 60.606 55.000 6.77 0.00 0.00 4.35
3417 3627 5.183228 CCGGATATGTACCAAAACAGTCTT 58.817 41.667 0.00 0.00 31.70 3.01
3432 3642 1.831736 AGTCTTTGGGGGATGAGTACG 59.168 52.381 0.00 0.00 0.00 3.67
3435 3645 1.546589 TTTGGGGGATGAGTACGCGT 61.547 55.000 19.17 19.17 0.00 6.01
3452 3662 1.527370 GTTCCAGGGAATCGAGGGG 59.473 63.158 3.73 0.00 36.45 4.79
3534 3744 2.031465 GGAAACCGCGGAAGGTGA 59.969 61.111 35.90 0.00 45.21 4.02
3547 3757 2.097825 GAAGGTGAGATTGCAGCCAAT 58.902 47.619 0.00 0.00 44.11 3.16
3592 3804 0.534412 CTGACAAGACTCTGGGCGAT 59.466 55.000 0.00 0.00 0.00 4.58
3841 4056 2.846193 ACCGTGCACAACTGATTACTT 58.154 42.857 18.64 0.00 0.00 2.24
3845 4060 4.457810 CGTGCACAACTGATTACTTGAAG 58.542 43.478 18.64 0.00 0.00 3.02
3852 4067 8.119226 GCACAACTGATTACTTGAAGATCATAC 58.881 37.037 0.00 0.00 0.00 2.39
3853 4068 9.376075 CACAACTGATTACTTGAAGATCATACT 57.624 33.333 0.00 0.00 0.00 2.12
3960 4175 4.566545 TTTGACTGCCATGTAGTGTTTG 57.433 40.909 4.75 0.00 0.00 2.93
3993 4208 8.900781 ACCAAGATAGTGAAAAATGATCATGAG 58.099 33.333 9.46 0.00 0.00 2.90
4028 4243 7.036863 TGGTGAGAAAATAGGAAATACTCCCTT 60.037 37.037 0.00 0.00 46.81 3.95
4030 4245 7.224949 GTGAGAAAATAGGAAATACTCCCTTCG 59.775 40.741 0.00 0.00 46.81 3.79
4060 4275 7.923344 AGGAATATGAGAACGTTTAGATCACTG 59.077 37.037 0.46 0.00 0.00 3.66
4062 4277 9.302345 GAATATGAGAACGTTTAGATCACTGAA 57.698 33.333 0.46 0.00 0.00 3.02
4063 4278 8.864069 ATATGAGAACGTTTAGATCACTGAAG 57.136 34.615 0.46 0.00 0.00 3.02
4064 4279 6.327279 TGAGAACGTTTAGATCACTGAAGA 57.673 37.500 0.46 0.00 0.00 2.87
4065 4280 6.150318 TGAGAACGTTTAGATCACTGAAGAC 58.850 40.000 0.46 0.00 0.00 3.01
4066 4281 5.154932 AGAACGTTTAGATCACTGAAGACG 58.845 41.667 0.46 0.00 0.00 4.18
4067 4282 3.834610 ACGTTTAGATCACTGAAGACGG 58.165 45.455 0.00 0.00 0.00 4.79
4068 4283 3.179830 CGTTTAGATCACTGAAGACGGG 58.820 50.000 0.00 0.00 0.00 5.28
4069 4284 3.522553 GTTTAGATCACTGAAGACGGGG 58.477 50.000 0.00 0.00 0.00 5.73
4070 4285 2.526888 TAGATCACTGAAGACGGGGT 57.473 50.000 0.00 0.00 0.00 4.95
4071 4286 2.526888 AGATCACTGAAGACGGGGTA 57.473 50.000 0.00 0.00 0.00 3.69
4072 4287 2.100989 AGATCACTGAAGACGGGGTAC 58.899 52.381 0.00 0.00 0.00 3.34
4073 4288 1.822990 GATCACTGAAGACGGGGTACA 59.177 52.381 0.00 0.00 0.00 2.90
4074 4289 1.707106 TCACTGAAGACGGGGTACAA 58.293 50.000 0.00 0.00 0.00 2.41
4075 4290 2.253610 TCACTGAAGACGGGGTACAAT 58.746 47.619 0.00 0.00 0.00 2.71
4076 4291 3.433343 TCACTGAAGACGGGGTACAATA 58.567 45.455 0.00 0.00 0.00 1.90
4077 4292 4.028131 TCACTGAAGACGGGGTACAATAT 58.972 43.478 0.00 0.00 0.00 1.28
4078 4293 5.202765 TCACTGAAGACGGGGTACAATATA 58.797 41.667 0.00 0.00 0.00 0.86
4079 4294 5.836898 TCACTGAAGACGGGGTACAATATAT 59.163 40.000 0.00 0.00 0.00 0.86
4080 4295 6.325545 TCACTGAAGACGGGGTACAATATATT 59.674 38.462 0.00 0.00 0.00 1.28
4081 4296 6.423905 CACTGAAGACGGGGTACAATATATTG 59.576 42.308 21.42 21.42 43.26 1.90
4140 4355 2.866762 GGTATGAGTCGCATCTCAAACC 59.133 50.000 11.01 0.00 45.65 3.27
4145 4360 1.816835 AGTCGCATCTCAAACCGAGTA 59.183 47.619 0.00 0.00 42.88 2.59
4151 4366 3.129638 GCATCTCAAACCGAGTAGACTCT 59.870 47.826 8.01 0.00 42.88 3.24
4166 4381 2.900546 AGACTCTGGTTTCTCATCCGTT 59.099 45.455 0.00 0.00 0.00 4.44
4195 4410 4.436113 AATTCTTTGGGTGCAATGGTTT 57.564 36.364 0.00 0.00 0.00 3.27
4203 4418 3.763360 TGGGTGCAATGGTTTCTCTAATG 59.237 43.478 0.00 0.00 0.00 1.90
4211 4426 6.374333 GCAATGGTTTCTCTAATGGTAGTGAA 59.626 38.462 0.00 0.00 37.82 3.18
4275 4490 8.887036 AATTGTTTTTAGGCGAAAAGAGATTT 57.113 26.923 5.68 0.00 38.27 2.17
4374 4592 2.191641 GCTCCACTGCCATCTCCC 59.808 66.667 0.00 0.00 0.00 4.30
4376 4594 1.692042 CTCCACTGCCATCTCCCCT 60.692 63.158 0.00 0.00 0.00 4.79
4377 4595 1.229951 TCCACTGCCATCTCCCCTT 60.230 57.895 0.00 0.00 0.00 3.95
4379 4597 1.225704 CACTGCCATCTCCCCTTCC 59.774 63.158 0.00 0.00 0.00 3.46
4418 4640 2.297895 CCTCCACCATGGTCGGGAA 61.298 63.158 21.18 9.13 39.03 3.97
4419 4641 1.078426 CTCCACCATGGTCGGGAAC 60.078 63.158 21.18 0.00 39.03 3.62
4458 4680 2.034879 CATTGACTGGACGGCGCTT 61.035 57.895 6.90 0.00 0.00 4.68
4524 4746 4.344865 AACATTGCCCTCCGCCGT 62.345 61.111 0.00 0.00 36.24 5.68
4526 4748 3.061848 CATTGCCCTCCGCCGTTT 61.062 61.111 0.00 0.00 36.24 3.60
4697 5090 1.237285 GCTCGTGCCAGGACATTGTT 61.237 55.000 0.00 0.00 0.00 2.83
4743 5136 6.488769 AGATTGAGATCTCATTCTGCTTCT 57.511 37.500 33.76 20.66 44.12 2.85
4757 5150 1.813192 CTTCTCGGTGCTCCTCTCC 59.187 63.158 2.85 0.00 0.00 3.71
4780 5173 7.881142 TCCGAAGAATGCTTCTAAATTTCAAA 58.119 30.769 11.79 0.00 46.64 2.69
4827 5220 5.679906 ACAAAAACGATCATTCAGTCTTCG 58.320 37.500 0.00 0.00 35.99 3.79
4843 5236 0.529378 TTCGTTCTCCGGAAGCTACC 59.471 55.000 5.23 0.00 37.11 3.18
4844 5237 0.323178 TCGTTCTCCGGAAGCTACCT 60.323 55.000 5.23 0.00 37.11 3.08
4845 5238 1.065199 TCGTTCTCCGGAAGCTACCTA 60.065 52.381 5.23 0.00 37.11 3.08
4846 5239 1.065251 CGTTCTCCGGAAGCTACCTAC 59.935 57.143 5.23 0.00 31.46 3.18
4860 5256 0.251354 ACCTACACTCAGGCAGCATG 59.749 55.000 0.00 0.00 39.53 4.06
4945 6422 4.583907 TGGTGATCACAAATCTTCAAGCAA 59.416 37.500 26.47 0.00 0.00 3.91
5014 6491 4.436332 TGATTCATGTCGAGGTCTGAATG 58.564 43.478 13.36 0.00 38.19 2.67
5032 6509 2.849880 TGCAAACACAGTTTCTGCTC 57.150 45.000 7.73 0.00 34.37 4.26
5062 6551 5.001874 CCCTGGTTTTCTGACCTTAGTTAC 58.998 45.833 0.00 0.00 40.47 2.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 86 1.864711 CGATGCAAATAACCGATCCGT 59.135 47.619 0.00 0.00 0.00 4.69
91 96 4.438148 TCGAATTCCAGTCGATGCAAATA 58.562 39.130 0.00 0.00 42.31 1.40
121 126 2.372172 ACTGAAACCGTGGGATTCTCTT 59.628 45.455 6.28 0.00 35.83 2.85
122 127 1.978580 ACTGAAACCGTGGGATTCTCT 59.021 47.619 6.28 0.00 35.83 3.10
153 177 0.031449 GATCGCGAGGAGAAGGAAGG 59.969 60.000 16.66 0.00 0.00 3.46
164 188 1.586564 GTCGGAACCTGATCGCGAG 60.587 63.158 16.66 2.71 0.00 5.03
184 208 1.674764 CGTGCAGAGGATCCTGAGCT 61.675 60.000 26.69 14.31 36.29 4.09
261 285 6.946165 TGATTTTTGCATTTTGTCATCACAC 58.054 32.000 0.00 0.00 29.76 3.82
264 288 7.964604 TGATGATTTTTGCATTTTGTCATCA 57.035 28.000 19.56 19.56 44.60 3.07
305 330 5.048364 AGTTTTGCTGCCGTAAACATCATTA 60.048 36.000 18.06 0.00 34.93 1.90
384 430 4.640364 CAGAAGACAGAAGAAGGCTCTTT 58.360 43.478 0.00 0.00 42.19 2.52
629 681 3.670377 GGTTGGTTCGTGGGCTGC 61.670 66.667 0.00 0.00 0.00 5.25
675 727 2.195956 GGGCTTATGGGCTGGACC 59.804 66.667 0.00 0.00 40.65 4.46
741 799 0.941463 GTGGTGATATCGGCGAGCTG 60.941 60.000 17.22 0.00 0.00 4.24
808 866 1.574263 GAGGCTCTAGGGTTTGGTCT 58.426 55.000 7.40 0.00 0.00 3.85
810 868 1.265454 CGGAGGCTCTAGGGTTTGGT 61.265 60.000 15.23 0.00 0.00 3.67
986 1057 4.122776 CCCTACTCGAATCTGTGGAATTG 58.877 47.826 0.00 0.00 0.00 2.32
1107 1178 4.511246 ATCGCCTCCCCGTCCGTA 62.511 66.667 0.00 0.00 0.00 4.02
1146 1217 3.069586 CCATCATGGCATCAAAATCTGCT 59.930 43.478 0.00 0.00 38.45 4.24
1183 1254 2.716017 CCTCCTCCTCGTCCTGCAC 61.716 68.421 0.00 0.00 0.00 4.57
1191 1271 1.072648 CTACTACTCCCCTCCTCCTCG 59.927 61.905 0.00 0.00 0.00 4.63
1202 1282 2.356818 CTGCGCCAGGCTACTACTCC 62.357 65.000 10.54 0.00 44.05 3.85
1204 1284 0.757188 ATCTGCGCCAGGCTACTACT 60.757 55.000 10.54 0.00 44.05 2.57
1309 1389 6.948886 AGTAGATCAAACTAACCAGAGTCTGA 59.051 38.462 22.09 0.46 32.44 3.27
1343 1423 1.077169 GAAGGAACAAGGGGGTGGAAT 59.923 52.381 0.00 0.00 0.00 3.01
1389 1469 9.761504 TTCAATTCTGCAAGATTACAAAAATCA 57.238 25.926 0.00 0.00 46.36 2.57
1391 1471 8.702438 CGTTCAATTCTGCAAGATTACAAAAAT 58.298 29.630 0.00 0.00 46.36 1.82
1412 1492 2.654749 ACGCTGATCATCTTCGTTCA 57.345 45.000 0.00 0.00 0.00 3.18
1424 1504 5.416326 GGAAGATGGTATCTAGTACGCTGAT 59.584 44.000 0.00 4.32 39.08 2.90
1432 1512 3.735442 AGGGGAGGAAGATGGTATCTAGT 59.265 47.826 0.00 0.00 39.08 2.57
1433 1513 4.412060 AGGGGAGGAAGATGGTATCTAG 57.588 50.000 0.00 0.00 39.08 2.43
1442 1522 5.074239 CCATCTTTATCAAGGGGAGGAAGAT 59.926 44.000 0.00 0.00 39.63 2.40
1629 1709 2.978156 AAGGCTTCAACTGGGATTCA 57.022 45.000 0.00 0.00 0.00 2.57
1663 1743 5.441718 TTGCCTTGTTTCTCCATCTCTAT 57.558 39.130 0.00 0.00 0.00 1.98
1713 1793 1.991965 GAGAGTTCTTGAAGCGCAGAG 59.008 52.381 11.47 1.13 0.00 3.35
1817 1897 1.719063 AACTCCAGCCTTGAGCCCAA 61.719 55.000 0.00 0.00 45.47 4.12
1909 1989 2.600729 AAGGGGACAGAGCCAGCAG 61.601 63.158 0.00 0.00 0.00 4.24
1910 1990 2.530151 AAGGGGACAGAGCCAGCA 60.530 61.111 0.00 0.00 0.00 4.41
1989 2069 4.511826 GCAATTTCACCGTATCCCTTAGAG 59.488 45.833 0.00 0.00 0.00 2.43
2205 2285 4.133820 CACCACACTCTGTTTCACCAATA 58.866 43.478 0.00 0.00 0.00 1.90
2346 2426 2.106684 ACTCCTGTCCCCTTCAGTTTTC 59.893 50.000 0.00 0.00 0.00 2.29
2380 2460 4.998051 TCTTCCTTAGGACAAGGCAAAAT 58.002 39.130 0.00 0.00 37.34 1.82
2424 2504 0.114364 TCAGTCCAGACCAGTAGGCA 59.886 55.000 0.00 0.00 39.06 4.75
2460 2540 2.338577 CCCCTTTGAGGCTATGAGTG 57.661 55.000 0.00 0.00 32.73 3.51
2583 2663 8.552296 ACTTCTATCTTCCTGTTAACATCCAAT 58.448 33.333 9.13 2.80 0.00 3.16
2728 2808 1.067142 TGGTCCATAGCGACTGAACAC 60.067 52.381 0.00 0.00 33.07 3.32
2757 2837 1.004277 CGTGCACTTCAGTCTCGGTC 61.004 60.000 16.19 0.00 0.00 4.79
2792 2872 5.644636 ACACGTTTCCTGAAGACAACTTTAA 59.355 36.000 0.00 0.00 36.39 1.52
2856 2936 5.714806 ACTTTGAAGTGAAGGTCCAAAAGAA 59.285 36.000 0.00 0.00 37.98 2.52
2917 2997 9.937175 GTGTAACTTAGGATAATTCAATTCAGC 57.063 33.333 0.00 0.00 0.00 4.26
2942 3022 3.900601 CTCCATGCTACTATCTTCAGGGT 59.099 47.826 0.00 0.00 32.74 4.34
2953 3033 2.769209 ACCAGGAATCTCCATGCTACT 58.231 47.619 0.00 0.00 39.61 2.57
2956 3036 3.266772 TGTTTACCAGGAATCTCCATGCT 59.733 43.478 0.00 0.00 39.61 3.79
3007 3193 8.600625 TGTAAGCAACTAAGCATATTTAACTCG 58.399 33.333 0.00 0.00 36.85 4.18
3044 3230 7.066284 AGCCTACAAGCTATAAGAAAACACATG 59.934 37.037 0.00 0.00 42.70 3.21
3069 3258 1.004080 CCAGTGCACCTCCAGACAG 60.004 63.158 14.63 0.00 0.00 3.51
3094 3283 4.762956 TTGTCGATGATGTCAATTTGCA 57.237 36.364 0.00 0.00 0.00 4.08
3108 3297 0.883833 CCTTTGCCAGCTTTGTCGAT 59.116 50.000 0.00 0.00 0.00 3.59
3121 3310 5.920840 GGATTCTTTACAGTTTCACCTTTGC 59.079 40.000 0.00 0.00 0.00 3.68
3139 3328 4.758674 CAGTGTGTTCAACTGATGGATTCT 59.241 41.667 0.00 0.00 33.65 2.40
3218 3407 2.037121 TGACTCTTCATTTCTGCGTCCA 59.963 45.455 0.00 0.00 0.00 4.02
3222 3411 2.414481 CAGGTGACTCTTCATTTCTGCG 59.586 50.000 0.00 0.00 40.21 5.18
3331 3520 5.715439 ATCAACTTCCATGGTATCTTCCA 57.285 39.130 12.58 0.00 42.01 3.53
3395 3605 6.542852 CAAAGACTGTTTTGGTACATATCCG 58.457 40.000 0.00 0.00 39.30 4.18
3417 3627 1.546589 AACGCGTACTCATCCCCCAA 61.547 55.000 14.46 0.00 0.00 4.12
3432 3642 1.521681 CCTCGATTCCCTGGAACGC 60.522 63.158 0.00 0.00 36.91 4.84
3435 3645 1.692749 CCCCCTCGATTCCCTGGAA 60.693 63.158 0.22 0.22 38.59 3.53
3452 3662 2.362077 ACAGGCATTTCAACTGTTGACC 59.638 45.455 21.95 18.62 42.38 4.02
3534 3744 1.381928 CGCTGGATTGGCTGCAATCT 61.382 55.000 17.82 0.00 40.42 2.40
3547 3757 4.468510 TCTTTAGTTTCCTAATCCGCTGGA 59.531 41.667 0.00 0.00 33.27 3.86
3592 3804 0.676466 CAAATGCAGTAGTCGGGCCA 60.676 55.000 4.39 0.00 0.00 5.36
3598 3810 4.437930 GCTTGTCCATCAAATGCAGTAGTC 60.438 45.833 0.00 0.00 35.48 2.59
3602 3814 2.230508 CAGCTTGTCCATCAAATGCAGT 59.769 45.455 0.00 0.00 35.48 4.40
3603 3815 2.490509 TCAGCTTGTCCATCAAATGCAG 59.509 45.455 0.00 0.00 35.48 4.41
3735 3950 6.183360 GCCAGAAAAATGACAGTATGGTACTC 60.183 42.308 0.00 0.00 43.62 2.59
3822 4037 2.805671 TCAAGTAATCAGTTGTGCACGG 59.194 45.455 13.13 1.69 36.60 4.94
3841 4056 3.515104 TCACTGCACCAGTATGATCTTCA 59.485 43.478 0.00 0.00 43.43 3.02
3845 4060 4.056740 CTGATCACTGCACCAGTATGATC 58.943 47.826 14.19 14.19 43.43 2.92
3852 4067 0.322648 TCCACTGATCACTGCACCAG 59.677 55.000 0.00 0.00 37.52 4.00
3853 4068 0.322648 CTCCACTGATCACTGCACCA 59.677 55.000 0.00 0.00 0.00 4.17
3960 4175 3.281727 TTCACTATCTTGGTGATGGGC 57.718 47.619 0.00 0.00 42.26 5.36
3993 4208 4.156739 CCTATTTTCTCACCAGGCAGAAAC 59.843 45.833 12.12 0.00 38.16 2.78
4028 4243 8.461222 TCTAAACGTTCTCATATTCCTTTACGA 58.539 33.333 0.00 0.00 0.00 3.43
4036 4251 8.858003 TCAGTGATCTAAACGTTCTCATATTC 57.142 34.615 0.00 0.00 0.00 1.75
4038 4253 8.687242 TCTTCAGTGATCTAAACGTTCTCATAT 58.313 33.333 0.00 0.00 0.00 1.78
4042 4257 5.284188 CGTCTTCAGTGATCTAAACGTTCTC 59.716 44.000 0.00 0.00 0.00 2.87
4046 4261 3.367087 CCCGTCTTCAGTGATCTAAACGT 60.367 47.826 0.00 0.00 0.00 3.99
4076 4291 8.752187 ACAGGAGCAAACAATTTATCACAATAT 58.248 29.630 0.00 0.00 0.00 1.28
4077 4292 8.121305 ACAGGAGCAAACAATTTATCACAATA 57.879 30.769 0.00 0.00 0.00 1.90
4078 4293 6.996509 ACAGGAGCAAACAATTTATCACAAT 58.003 32.000 0.00 0.00 0.00 2.71
4079 4294 6.403866 ACAGGAGCAAACAATTTATCACAA 57.596 33.333 0.00 0.00 0.00 3.33
4080 4295 6.403866 AACAGGAGCAAACAATTTATCACA 57.596 33.333 0.00 0.00 0.00 3.58
4081 4296 6.701400 ACAAACAGGAGCAAACAATTTATCAC 59.299 34.615 0.00 0.00 0.00 3.06
4082 4297 6.815089 ACAAACAGGAGCAAACAATTTATCA 58.185 32.000 0.00 0.00 0.00 2.15
4083 4298 7.713764 AACAAACAGGAGCAAACAATTTATC 57.286 32.000 0.00 0.00 0.00 1.75
4087 4302 7.552330 ACAATAAACAAACAGGAGCAAACAATT 59.448 29.630 0.00 0.00 0.00 2.32
4098 4313 9.840427 CATACCTCTAAACAATAAACAAACAGG 57.160 33.333 0.00 0.00 0.00 4.00
4145 4360 2.530701 ACGGATGAGAAACCAGAGTCT 58.469 47.619 0.00 0.00 0.00 3.24
4151 4366 8.801882 ATTTAGAATAAACGGATGAGAAACCA 57.198 30.769 0.00 0.00 0.00 3.67
4166 4381 8.040132 CCATTGCACCCAAAGAATTTAGAATAA 58.960 33.333 0.00 0.00 35.03 1.40
4211 4426 5.336372 CCAATAACCGATCACAATGGTGTTT 60.336 40.000 0.00 0.00 45.45 2.83
4329 4545 3.119779 GGTCGAGAGTGAGGTTTGACTAG 60.120 52.174 0.00 0.00 0.00 2.57
4332 4548 1.614413 AGGTCGAGAGTGAGGTTTGAC 59.386 52.381 0.00 0.00 0.00 3.18
4368 4586 2.287251 CGGGAGGGAAGGGGAGAT 59.713 66.667 0.00 0.00 0.00 2.75
4419 4641 4.933064 GACTCGCTGCCGGATCCG 62.933 72.222 27.65 27.65 39.44 4.18
4524 4746 1.304381 GCCCCTGTCCATCTGCAAA 60.304 57.895 0.00 0.00 0.00 3.68
4526 4748 4.100084 CGCCCCTGTCCATCTGCA 62.100 66.667 0.00 0.00 0.00 4.41
4606 4828 3.083349 CCCCTGCCACCTGATCGA 61.083 66.667 0.00 0.00 0.00 3.59
4685 4907 1.955778 TGCAACTGAACAATGTCCTGG 59.044 47.619 0.00 0.00 0.00 4.45
4712 5105 6.550481 AGAATGAGATCTCAATCTACTGCAGA 59.450 38.462 32.69 7.19 45.22 4.26
4716 5109 6.751157 AGCAGAATGAGATCTCAATCTACTG 58.249 40.000 32.94 28.65 45.27 2.74
4827 5220 2.097825 TGTAGGTAGCTTCCGGAGAAC 58.902 52.381 3.34 1.48 0.00 3.01
4843 5236 1.066645 TCACATGCTGCCTGAGTGTAG 60.067 52.381 11.93 0.00 0.00 2.74
4844 5237 0.975887 TCACATGCTGCCTGAGTGTA 59.024 50.000 11.93 0.00 0.00 2.90
4845 5238 0.327259 ATCACATGCTGCCTGAGTGT 59.673 50.000 11.93 0.00 0.00 3.55
4846 5239 1.938577 GTATCACATGCTGCCTGAGTG 59.061 52.381 11.93 8.01 0.00 3.51
4860 5256 3.201266 TGTGGATGGGTAAAGGGTATCAC 59.799 47.826 0.00 0.00 0.00 3.06
4945 6422 0.251354 AGATGCCAGCACGTGATCTT 59.749 50.000 22.23 0.00 0.00 2.40
5014 6491 2.098117 ACTGAGCAGAAACTGTGTTTGC 59.902 45.455 5.39 5.39 33.43 3.68
5032 6509 0.675633 CAGAAAACCAGGGCCAACTG 59.324 55.000 6.18 3.06 38.21 3.16
5062 6551 2.185350 CCAGCAGCGAGTGGGTAG 59.815 66.667 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.