Multiple sequence alignment - TraesCS5B01G478400

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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 TraesCS5B01G478400 chr5B 100.000 4871 0 0 1 4871 650137463 650132593 0.000000e+00 8996.0
1 TraesCS5B01G478400 chr5B 87.054 448 37 11 4054 4484 650125227 650124784 2.040000e-133 486.0
2 TraesCS5B01G478400 chr5B 84.416 231 14 8 4596 4810 650124735 650124511 1.780000e-49 207.0
3 TraesCS5B01G478400 chr5B 86.029 136 19 0 1796 1931 650135390 650135255 3.930000e-31 147.0
4 TraesCS5B01G478400 chr5B 86.029 136 19 0 2074 2209 650135668 650135533 3.930000e-31 147.0
5 TraesCS5B01G478400 chr5B 93.182 44 3 0 1888 1931 650135254 650135211 1.130000e-06 65.8
6 TraesCS5B01G478400 chr5B 97.222 36 1 0 4009 4044 650125259 650125224 1.460000e-05 62.1
7 TraesCS5B01G478400 chr5D 94.998 2439 93 15 2167 4591 517603124 517600701 0.000000e+00 3801.0
8 TraesCS5B01G478400 chr5D 95.238 1554 66 6 870 2417 517604962 517603411 0.000000e+00 2453.0
9 TraesCS5B01G478400 chr5D 89.598 846 49 15 29 852 517605779 517604951 0.000000e+00 1038.0
10 TraesCS5B01G478400 chr5D 85.682 447 31 16 1891 2330 517603541 517603121 1.610000e-119 440.0
11 TraesCS5B01G478400 chr5D 85.219 433 50 9 4009 4437 517591977 517591555 2.690000e-117 433.0
12 TraesCS5B01G478400 chr5D 92.308 273 20 1 4599 4871 517600503 517600232 2.130000e-103 387.0
13 TraesCS5B01G478400 chr5D 88.688 221 14 6 4596 4810 517591296 517591081 4.840000e-65 259.0
14 TraesCS5B01G478400 chr5D 90.964 166 14 1 2166 2330 517603247 517603082 6.350000e-54 222.0
15 TraesCS5B01G478400 chr5D 82.589 224 15 12 4625 4839 517521783 517521575 5.010000e-40 176.0
16 TraesCS5B01G478400 chr5D 87.586 145 18 0 2065 2209 517604045 517603901 8.380000e-38 169.0
17 TraesCS5B01G478400 chr5A 95.088 2056 77 15 2166 4198 645003375 645001321 0.000000e+00 3216.0
18 TraesCS5B01G478400 chr5A 91.481 1573 82 16 767 2330 645005273 645003744 0.000000e+00 2115.0
19 TraesCS5B01G478400 chr5A 86.995 792 57 21 1 767 645006002 645005232 0.000000e+00 850.0
20 TraesCS5B01G478400 chr5A 87.605 476 45 9 4009 4479 644921160 644920694 1.540000e-149 540.0
21 TraesCS5B01G478400 chr5A 86.230 443 29 9 1891 2327 645003668 645003252 7.430000e-123 451.0
22 TraesCS5B01G478400 chr5A 87.241 290 22 5 4596 4870 644923378 644923089 2.830000e-82 316.0
23 TraesCS5B01G478400 chr5A 90.795 239 10 8 4361 4591 644923780 644923546 4.740000e-80 309.0
24 TraesCS5B01G478400 chr5A 88.976 254 19 3 2167 2416 645003786 645003538 6.130000e-79 305.0
25 TraesCS5B01G478400 chr5A 94.410 161 8 1 2171 2330 645003865 645003705 3.770000e-61 246.0
26 TraesCS5B01G478400 chr5A 86.331 139 19 0 2065 2203 645004264 645004126 8.440000e-33 152.0
27 TraesCS5B01G478400 chr5A 86.260 131 17 1 1801 1931 645004000 645003871 1.830000e-29 141.0
28 TraesCS5B01G478400 chr5A 93.182 44 3 0 1888 1931 645003331 645003288 1.130000e-06 65.8
29 TraesCS5B01G478400 chr5A 93.182 44 3 0 1888 1931 645003826 645003783 1.130000e-06 65.8


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 TraesCS5B01G478400 chr5B 650132593 650137463 4870 True 2338.950000 8996 91.310000 1 4871 4 chr5B.!!$R2 4870
1 TraesCS5B01G478400 chr5B 650124511 650125259 748 True 251.700000 486 89.564000 4009 4810 3 chr5B.!!$R1 801
2 TraesCS5B01G478400 chr5D 517600232 517605779 5547 True 1215.714286 3801 90.910571 29 4871 7 chr5D.!!$R3 4842
3 TraesCS5B01G478400 chr5D 517591081 517591977 896 True 346.000000 433 86.953500 4009 4810 2 chr5D.!!$R2 801
4 TraesCS5B01G478400 chr5A 645001321 645006002 4681 True 760.760000 3216 90.213500 1 4198 10 chr5A.!!$R2 4197
5 TraesCS5B01G478400 chr5A 644920694 644923780 3086 True 388.333333 540 88.547000 4009 4870 3 chr5A.!!$R1 861

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
485 515 0.467659 CTCCCCTCCGAGGTAACGAT 60.468 60.0 13.62 0.0 46.39 3.73 F
1362 1396 0.178981 ATGGTGTTCTTGCACTGGCT 60.179 50.0 0.00 0.0 41.91 4.75 F
2434 3133 0.108615 CGTGCTCTAAGTGGGTCCTG 60.109 60.0 0.00 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2415 3114 0.108615 CAGGACCCACTTAGAGCACG 60.109 60.000 0.00 0.00 0.00 5.34 R
3288 3998 2.302733 TCATTGCTTCAGCCTGTACAGA 59.697 45.455 24.68 0.93 41.18 3.41 R
4357 5210 0.177604 CAGACCACAGAGATGGAGCC 59.822 60.000 0.00 0.00 43.02 4.70 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
39 40 2.584835 TGGCTAGTGTGGCAAGAAAT 57.415 45.000 0.00 0.00 39.58 2.17
170 178 3.519930 GCGGAGGAGGGAGACGAC 61.520 72.222 0.00 0.00 0.00 4.34
231 239 1.033574 CCCGTTCCGCTAGAAGAGAT 58.966 55.000 0.00 0.00 34.29 2.75
233 241 1.269309 CCGTTCCGCTAGAAGAGATGG 60.269 57.143 0.00 0.00 34.29 3.51
236 244 2.630580 GTTCCGCTAGAAGAGATGGGAT 59.369 50.000 0.00 0.00 34.29 3.85
237 245 2.242926 TCCGCTAGAAGAGATGGGATG 58.757 52.381 0.00 0.00 0.00 3.51
238 246 1.274728 CCGCTAGAAGAGATGGGATGG 59.725 57.143 0.00 0.00 0.00 3.51
389 419 1.893588 AATACCCTCCCGACCCTCCA 61.894 60.000 0.00 0.00 0.00 3.86
390 420 2.600735 ATACCCTCCCGACCCTCCAC 62.601 65.000 0.00 0.00 0.00 4.02
485 515 0.467659 CTCCCCTCCGAGGTAACGAT 60.468 60.000 13.62 0.00 46.39 3.73
494 524 2.740981 CCGAGGTAACGATACGCTCTAT 59.259 50.000 14.63 0.00 46.39 1.98
496 526 3.679025 CGAGGTAACGATACGCTCTATCT 59.321 47.826 14.63 0.00 46.39 1.98
498 528 5.220191 CGAGGTAACGATACGCTCTATCTAC 60.220 48.000 14.63 0.00 46.39 2.59
508 538 1.000052 GCTCTATCTACGGTTCCTGCC 60.000 57.143 0.00 0.00 0.00 4.85
509 539 1.614413 CTCTATCTACGGTTCCTGCCC 59.386 57.143 0.00 0.00 0.00 5.36
662 694 4.767255 GCTCGTGGGTGCTCAGGG 62.767 72.222 0.00 0.00 0.00 4.45
663 695 4.767255 CTCGTGGGTGCTCAGGGC 62.767 72.222 0.00 0.00 42.22 5.19
665 697 4.767255 CGTGGGTGCTCAGGGCTC 62.767 72.222 0.00 0.00 42.39 4.70
666 698 4.767255 GTGGGTGCTCAGGGCTCG 62.767 72.222 0.00 0.00 42.39 5.03
669 701 4.459089 GGTGCTCAGGGCTCGTCC 62.459 72.222 0.00 0.00 42.39 4.79
670 702 3.386237 GTGCTCAGGGCTCGTCCT 61.386 66.667 0.00 0.00 42.39 3.85
709 741 3.691342 AACCTGCTGTCGCCGCTA 61.691 61.111 0.00 0.00 34.43 4.26
710 742 3.019003 AACCTGCTGTCGCCGCTAT 62.019 57.895 0.00 0.00 34.43 2.97
718 750 1.143183 GTCGCCGCTATTTCTCCCA 59.857 57.895 0.00 0.00 0.00 4.37
754 786 1.263484 CTTGCTGCGCTATCCTGATTG 59.737 52.381 9.73 0.00 0.00 2.67
757 789 1.563435 CTGCGCTATCCTGATTGGCG 61.563 60.000 9.73 16.92 41.27 5.69
832 864 2.029073 CTCGCAGTTCGTGGTGGT 59.971 61.111 0.00 0.00 39.67 4.16
839 871 1.069513 CAGTTCGTGGTGGTCTGGTTA 59.930 52.381 0.00 0.00 0.00 2.85
854 886 4.514066 GTCTGGTTACTCGGTTGATTGTTT 59.486 41.667 0.00 0.00 0.00 2.83
856 888 5.591067 TCTGGTTACTCGGTTGATTGTTTTT 59.409 36.000 0.00 0.00 0.00 1.94
884 916 2.932614 AGCGTACTCTGTTGATTGATGC 59.067 45.455 0.00 0.00 0.00 3.91
889 921 5.276726 CGTACTCTGTTGATTGATGCATCTG 60.277 44.000 26.32 4.25 0.00 2.90
890 922 3.377485 ACTCTGTTGATTGATGCATCTGC 59.623 43.478 26.32 15.71 42.50 4.26
891 923 3.617284 TCTGTTGATTGATGCATCTGCT 58.383 40.909 26.32 11.54 42.66 4.24
892 924 3.377172 TCTGTTGATTGATGCATCTGCTG 59.623 43.478 26.32 13.23 42.66 4.41
893 925 2.425668 TGTTGATTGATGCATCTGCTGG 59.574 45.455 26.32 0.00 42.66 4.85
894 926 1.029681 TGATTGATGCATCTGCTGGC 58.970 50.000 26.32 10.92 42.66 4.85
895 927 1.319541 GATTGATGCATCTGCTGGCT 58.680 50.000 26.32 4.39 42.66 4.75
896 928 2.158726 TGATTGATGCATCTGCTGGCTA 60.159 45.455 26.32 1.49 42.66 3.93
938 972 2.358898 GGTACCATGATTGTGATGTGGC 59.641 50.000 7.15 0.00 33.24 5.01
939 973 2.219080 ACCATGATTGTGATGTGGCA 57.781 45.000 0.00 0.00 33.24 4.92
998 1032 3.547513 GGGATAGGCGCCTTCCGT 61.548 66.667 37.74 18.63 39.71 4.69
1362 1396 0.178981 ATGGTGTTCTTGCACTGGCT 60.179 50.000 0.00 0.00 41.91 4.75
1383 1417 4.512484 CTTCCTCAAGAAACTCTGGATCC 58.488 47.826 4.20 4.20 32.88 3.36
1587 1621 3.830755 TCTACTTAACGGAGAAACCTGCT 59.169 43.478 0.00 0.00 36.31 4.24
1788 1822 9.672673 AAATAAGACTGATACAGCTGTAACAAT 57.327 29.630 29.57 23.78 33.81 2.71
1817 1851 3.380004 TCTTTTGTCGCTTGTTGGAATGT 59.620 39.130 0.00 0.00 0.00 2.71
1819 1853 2.772568 TGTCGCTTGTTGGAATGTTG 57.227 45.000 0.00 0.00 0.00 3.33
1966 2000 7.402054 TGACTGAAATGGTAAATATGAGGTGT 58.598 34.615 0.00 0.00 0.00 4.16
2092 2623 1.525619 CTCTTTTGTCGGTTGTCGGAC 59.474 52.381 0.00 0.00 41.97 4.79
2117 2648 7.871463 ACTGGTAGTATTTGTTGTAGTGAAGTC 59.129 37.037 0.00 0.00 0.00 3.01
2132 2663 7.710907 TGTAGTGAAGTCATCTTATATGCCAAC 59.289 37.037 0.00 0.00 33.64 3.77
2152 2683 5.270083 CAACGAGTCAATGTTGTTTTGCTA 58.730 37.500 0.00 0.00 40.37 3.49
2156 2687 5.343058 CGAGTCAATGTTGTTTTGCTATTGG 59.657 40.000 0.00 0.00 31.47 3.16
2288 2986 6.329496 CAAAATGCCGTGTTATGGTTTATCT 58.671 36.000 0.00 0.00 0.00 1.98
2433 3132 0.251653 TCGTGCTCTAAGTGGGTCCT 60.252 55.000 0.00 0.00 0.00 3.85
2434 3133 0.108615 CGTGCTCTAAGTGGGTCCTG 60.109 60.000 0.00 0.00 0.00 3.86
2483 3182 2.936202 ACATCACAGCACAAGAAAGGT 58.064 42.857 0.00 0.00 0.00 3.50
2618 3317 7.799081 TCTGATGATGAAGATGGTGAATTACT 58.201 34.615 0.00 0.00 0.00 2.24
2867 3569 2.383338 AGGAGGAATTTGGGTTGGATGT 59.617 45.455 0.00 0.00 0.00 3.06
3233 3943 5.793817 AGCAACAGGTTTGTTTTTCTTCTT 58.206 33.333 0.00 0.00 45.01 2.52
3288 3998 4.530553 GTGACCCAATTTTAATGGTCCCTT 59.469 41.667 5.17 0.00 45.36 3.95
3332 4042 5.842339 AGGAAAATATTGGGGATTGACACT 58.158 37.500 0.00 0.00 0.00 3.55
3352 4062 5.600484 ACACTGAGAAGAAGAAGGAAGAGAA 59.400 40.000 0.00 0.00 0.00 2.87
3622 4332 5.240623 TCAGGTTAAACACAATGCCTACTTG 59.759 40.000 0.00 0.00 0.00 3.16
3636 4348 3.127030 GCCTACTTGTGGCTATTTCACAC 59.873 47.826 0.00 0.00 46.38 3.82
3705 4417 2.621055 GTGTGCTTACATTCAACACCCA 59.379 45.455 0.00 0.00 0.00 4.51
3884 4596 0.457443 TGCTGATGCTACAGAGTCGG 59.543 55.000 13.22 0.00 39.94 4.79
3895 4607 0.317160 CAGAGTCGGTGGTGCAAGTA 59.683 55.000 0.00 0.00 0.00 2.24
3901 4613 1.777030 CGGTGGTGCAAGTAAACGCA 61.777 55.000 0.00 0.00 35.30 5.24
3908 4620 0.028374 GCAAGTAAACGCACAACCGT 59.972 50.000 0.00 0.00 44.41 4.83
4011 4723 2.417933 CTGAGGATTGAAAACTGAGCGG 59.582 50.000 0.00 0.00 0.00 5.52
4087 4801 5.480772 GGATGTATGTATGTAGTAGCTGGGT 59.519 44.000 0.00 0.00 0.00 4.51
4111 4825 4.229876 GTGCAAAAGAGTCTGGTTTATGC 58.770 43.478 0.00 0.00 0.00 3.14
4199 4931 4.960938 TGGCTATGATGGTATGAGTTGAC 58.039 43.478 0.00 0.00 0.00 3.18
4256 4988 2.163818 TGTTCCGGTGTTGTGATCTC 57.836 50.000 0.00 0.00 0.00 2.75
4275 5007 2.125350 CTCTGGAAGCAGCCGTCC 60.125 66.667 5.86 5.86 39.71 4.79
4276 5008 2.922503 TCTGGAAGCAGCCGTCCA 60.923 61.111 13.60 13.60 45.53 4.02
4277 5009 2.743928 CTGGAAGCAGCCGTCCAC 60.744 66.667 10.80 0.00 43.36 4.02
4299 5139 1.451028 GTCCATCTCTGTGGGCTGC 60.451 63.158 0.00 0.00 40.74 5.25
4305 5146 4.314440 TCTGTGGGCTGCCGTGAC 62.314 66.667 13.40 9.70 0.00 3.67
4309 5150 2.359850 TGGGCTGCCGTGACAATC 60.360 61.111 13.40 0.00 0.00 2.67
4316 5161 2.345991 CCGTGACAATCCACCGGT 59.654 61.111 0.00 0.00 33.67 5.28
4333 5179 1.428869 GGTAGCCCATCTCTGTGGAT 58.571 55.000 0.00 0.00 42.02 3.41
4336 5182 0.549950 AGCCCATCTCTGTGGATTGG 59.450 55.000 0.00 0.00 42.02 3.16
4337 5183 0.548031 GCCCATCTCTGTGGATTGGA 59.452 55.000 0.00 0.00 42.02 3.53
4357 5210 2.673368 GAGTGGTAATTCACTGGAAGCG 59.327 50.000 4.62 0.00 46.76 4.68
4373 5226 3.023949 GCGGCTCCATCTCTGTGGT 62.024 63.158 0.00 0.00 40.27 4.16
4378 5231 1.405256 GCTCCATCTCTGTGGTCTGTG 60.405 57.143 0.00 0.00 40.27 3.66
4445 5302 1.538047 TTCATTGGAAGCAGCTGTCC 58.462 50.000 16.64 15.68 0.00 4.02
4505 5366 2.647297 GGTTGTGCTGCAGCCTTC 59.353 61.111 34.64 23.85 44.03 3.46
4507 5368 1.458639 GGTTGTGCTGCAGCCTTCTT 61.459 55.000 34.64 0.00 44.03 2.52
4508 5369 0.039708 GTTGTGCTGCAGCCTTCTTC 60.040 55.000 34.64 17.61 41.18 2.87
4509 5370 0.179009 TTGTGCTGCAGCCTTCTTCT 60.179 50.000 34.64 0.00 41.18 2.85
4510 5371 0.686789 TGTGCTGCAGCCTTCTTCTA 59.313 50.000 34.64 11.80 41.18 2.10
4511 5372 1.338484 TGTGCTGCAGCCTTCTTCTAG 60.338 52.381 34.64 0.00 41.18 2.43
4512 5373 1.066573 GTGCTGCAGCCTTCTTCTAGA 60.067 52.381 34.64 10.20 41.18 2.43
4513 5374 1.836166 TGCTGCAGCCTTCTTCTAGAT 59.164 47.619 34.64 0.00 41.18 1.98
4536 5397 2.270352 TTGTGCTGGAACCTGGTAAG 57.730 50.000 0.00 0.00 0.00 2.34
4554 5415 2.251642 GGATAATGACCACGGGCGC 61.252 63.158 0.00 0.00 0.00 6.53
4562 5423 2.748251 CCACGGGCGCCATGTTAA 60.748 61.111 30.85 0.00 0.00 2.01
4568 5429 0.885196 GGGCGCCATGTTAACTTTGA 59.115 50.000 30.85 0.00 0.00 2.69
4572 5433 3.612423 GGCGCCATGTTAACTTTGATTTC 59.388 43.478 24.80 0.00 0.00 2.17
4573 5434 3.612423 GCGCCATGTTAACTTTGATTTCC 59.388 43.478 7.22 0.00 0.00 3.13
4615 5668 4.051237 TCATTGATAGATGACGCCGAAAG 58.949 43.478 0.00 0.00 31.35 2.62
4636 5691 7.223582 CGAAAGTTGGCATGCTATATATAGAGG 59.776 40.741 21.65 11.32 32.05 3.69
4666 5721 1.266989 GTAGCTTTGGGCAGACACAAC 59.733 52.381 0.00 0.00 44.79 3.32
4677 5734 1.327460 CAGACACAACCACGACACAAG 59.673 52.381 0.00 0.00 0.00 3.16
4740 5812 3.222603 AGTTTAGGAGCAACCAACCAAG 58.777 45.455 2.96 0.00 42.04 3.61
4817 5889 0.459237 GATCCTCGCACACTCACAGG 60.459 60.000 0.00 0.00 0.00 4.00
4819 5891 2.029518 CTCGCACACTCACAGGCA 59.970 61.111 0.00 0.00 0.00 4.75
4826 5898 3.233980 ACTCACAGGCAGCGGACA 61.234 61.111 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.530946 ACACTAGCCATACAACCTTGTAGT 59.469 41.667 4.32 0.00 45.80 2.73
14 15 2.107950 TGCCACACTAGCCATACAAC 57.892 50.000 0.00 0.00 0.00 3.32
18 19 3.712016 TTTCTTGCCACACTAGCCATA 57.288 42.857 0.00 0.00 0.00 2.74
19 20 2.584835 TTTCTTGCCACACTAGCCAT 57.415 45.000 0.00 0.00 0.00 4.40
39 40 3.161866 GTTTGGCTCCTTGGACCAATTA 58.838 45.455 7.54 0.00 42.77 1.40
231 239 1.474320 CGCGTAATTTCTCCCATCCCA 60.474 52.381 0.00 0.00 0.00 4.37
233 241 1.865340 GACGCGTAATTTCTCCCATCC 59.135 52.381 13.97 0.00 0.00 3.51
236 244 1.079875 GCGACGCGTAATTTCTCCCA 61.080 55.000 13.97 0.00 0.00 4.37
237 245 1.634753 GCGACGCGTAATTTCTCCC 59.365 57.895 13.97 0.00 0.00 4.30
238 246 1.634753 GGCGACGCGTAATTTCTCC 59.365 57.895 13.97 0.00 0.00 3.71
389 419 4.699522 GTTTGCGGCGAGAGGGGT 62.700 66.667 12.98 0.00 0.00 4.95
392 422 2.515996 TTAGGGTTTGCGGCGAGAGG 62.516 60.000 12.98 0.00 0.00 3.69
485 515 3.136763 CAGGAACCGTAGATAGAGCGTA 58.863 50.000 0.00 0.00 0.00 4.42
709 741 4.763793 GCATATGCATACACTGGGAGAAAT 59.236 41.667 22.84 0.00 41.59 2.17
710 742 4.136796 GCATATGCATACACTGGGAGAAA 58.863 43.478 22.84 0.00 41.59 2.52
718 750 3.813724 CAGCAAGAGCATATGCATACACT 59.186 43.478 28.62 16.78 44.95 3.55
757 789 4.740822 AGCATGTGCCCGAACCCC 62.741 66.667 0.57 0.00 43.38 4.95
769 801 0.250209 AGGATAGCGGCAAGAGCATG 60.250 55.000 1.45 0.00 44.61 4.06
832 864 4.345859 AACAATCAACCGAGTAACCAGA 57.654 40.909 0.00 0.00 0.00 3.86
866 898 5.503683 GCAGATGCATCAATCAACAGAGTAC 60.504 44.000 27.81 0.00 41.59 2.73
867 899 4.573607 GCAGATGCATCAATCAACAGAGTA 59.426 41.667 27.81 0.00 41.59 2.59
868 900 3.377485 GCAGATGCATCAATCAACAGAGT 59.623 43.478 27.81 0.00 41.59 3.24
869 901 3.628032 AGCAGATGCATCAATCAACAGAG 59.372 43.478 27.81 6.04 45.16 3.35
872 904 2.425668 CCAGCAGATGCATCAATCAACA 59.574 45.455 27.81 0.00 45.16 3.33
884 916 0.393402 TTGCAGGTAGCCAGCAGATG 60.393 55.000 9.23 0.00 46.13 2.90
889 921 1.672881 CAGTAATTGCAGGTAGCCAGC 59.327 52.381 0.00 0.40 44.83 4.85
890 922 2.991250 ACAGTAATTGCAGGTAGCCAG 58.009 47.619 0.00 0.00 44.83 4.85
891 923 3.433306 AACAGTAATTGCAGGTAGCCA 57.567 42.857 0.00 0.00 44.83 4.75
892 924 7.308589 CCATATAAACAGTAATTGCAGGTAGCC 60.309 40.741 0.00 0.00 44.83 3.93
893 925 7.228706 ACCATATAAACAGTAATTGCAGGTAGC 59.771 37.037 0.00 0.00 45.96 3.58
894 926 8.677148 ACCATATAAACAGTAATTGCAGGTAG 57.323 34.615 0.00 0.00 0.00 3.18
895 927 9.550406 GTACCATATAAACAGTAATTGCAGGTA 57.450 33.333 0.00 0.00 0.00 3.08
896 928 7.501225 GGTACCATATAAACAGTAATTGCAGGT 59.499 37.037 7.15 0.00 0.00 4.00
938 972 3.061563 CCTGCGTGCATTGAAATGAAATG 59.938 43.478 7.21 1.58 38.70 2.32
939 973 3.255725 CCTGCGTGCATTGAAATGAAAT 58.744 40.909 7.21 0.00 38.70 2.17
982 1016 2.100879 ATCACGGAAGGCGCCTATCC 62.101 60.000 33.07 32.13 0.00 2.59
998 1032 1.692395 TTCCCGAGCCCATCCATCA 60.692 57.895 0.00 0.00 0.00 3.07
1182 1216 2.678934 TACAGCTCCTTCCGCCGT 60.679 61.111 0.00 0.00 0.00 5.68
1188 1222 1.404315 CCGTTGAGGTACAGCTCCTTC 60.404 57.143 6.01 0.00 35.20 3.46
1362 1396 3.909995 TGGATCCAGAGTTTCTTGAGGAA 59.090 43.478 11.44 0.00 0.00 3.36
1383 1417 2.356313 AACTGCGAGGCGTCAGTG 60.356 61.111 7.26 0.00 40.82 3.66
1485 1519 2.365582 ACGTCAACAGGCTCTTGTTTT 58.634 42.857 2.38 0.00 39.17 2.43
1722 1756 4.044065 TGGATGGGGTTGAGTTATTTCAGT 59.956 41.667 0.00 0.00 0.00 3.41
1723 1757 4.599041 TGGATGGGGTTGAGTTATTTCAG 58.401 43.478 0.00 0.00 0.00 3.02
1788 1822 6.016693 TCCAACAAGCGACAAAAGAATAATCA 60.017 34.615 0.00 0.00 0.00 2.57
1817 1851 9.182214 AGATTACGTCACTAGAGTAAATACCAA 57.818 33.333 0.00 0.00 34.55 3.67
2092 2623 7.870954 TGACTTCACTACAACAAATACTACCAG 59.129 37.037 0.00 0.00 0.00 4.00
2117 2648 6.203530 ACATTGACTCGTTGGCATATAAGATG 59.796 38.462 0.00 0.00 31.11 2.90
2132 2663 5.343058 CCAATAGCAAAACAACATTGACTCG 59.657 40.000 0.00 0.00 0.00 4.18
2152 2683 5.645497 GCATAGACAAGAGAGTTGAACCAAT 59.355 40.000 0.00 0.00 0.00 3.16
2156 2687 4.826556 AGGCATAGACAAGAGAGTTGAAC 58.173 43.478 0.00 0.00 0.00 3.18
2415 3114 0.108615 CAGGACCCACTTAGAGCACG 60.109 60.000 0.00 0.00 0.00 5.34
2433 3132 6.823689 GCTCACCAGAATCCTATAAAAAGACA 59.176 38.462 0.00 0.00 0.00 3.41
2434 3133 6.823689 TGCTCACCAGAATCCTATAAAAAGAC 59.176 38.462 0.00 0.00 0.00 3.01
2483 3182 5.815222 CCATCAACGTGATTACCATGACTAA 59.185 40.000 0.00 0.00 34.28 2.24
2628 3327 5.163457 TGCAGCTTTAGCCACTTTAAGTTTT 60.163 36.000 0.00 0.00 43.38 2.43
2867 3569 9.842775 AATCAGCTTCAATTAATCTATCAGACA 57.157 29.630 0.00 0.00 0.00 3.41
3078 3786 7.716799 ACCAAGACCATTTAGCATTTTATCA 57.283 32.000 0.00 0.00 0.00 2.15
3288 3998 2.302733 TCATTGCTTCAGCCTGTACAGA 59.697 45.455 24.68 0.93 41.18 3.41
3332 4042 6.518200 GCTTCTTCTCTTCCTTCTTCTTCTCA 60.518 42.308 0.00 0.00 0.00 3.27
3352 4062 3.804873 GTCTTCACGTTCTTTCTGCTTCT 59.195 43.478 0.00 0.00 0.00 2.85
3468 4178 0.743688 TTTGCTTGCTTTTCCTGCGA 59.256 45.000 0.00 0.00 0.00 5.10
3622 4332 1.737236 TGATGCGTGTGAAATAGCCAC 59.263 47.619 0.00 0.00 35.23 5.01
3636 4348 3.928992 ACTAGTCACTCACAAATGATGCG 59.071 43.478 0.00 0.00 33.22 4.73
3705 4417 2.498885 GGAGAAATGAAAGCCAAGCCAT 59.501 45.455 0.00 0.00 0.00 4.40
3895 4607 3.894947 GCCCACGGTTGTGCGTTT 61.895 61.111 0.00 0.00 45.04 3.60
3908 4620 3.083349 CTCCTCCATGTCCGCCCA 61.083 66.667 0.00 0.00 0.00 5.36
4011 4723 2.002586 CACCTCAACATCATCCGTCAC 58.997 52.381 0.00 0.00 0.00 3.67
4087 4801 2.325583 AACCAGACTCTTTTGCACGA 57.674 45.000 0.00 0.00 0.00 4.35
4111 4825 0.606401 AATCCTCCACTTGCCACACG 60.606 55.000 0.00 0.00 0.00 4.49
4181 4904 5.069119 AGCGAAGTCAACTCATACCATCATA 59.931 40.000 0.00 0.00 0.00 2.15
4199 4931 3.804325 ACAATGATGGATAACGAGCGAAG 59.196 43.478 0.00 0.00 0.00 3.79
4256 4988 1.153667 GACGGCTGCTTCCAGAGAG 60.154 63.158 0.00 0.00 41.77 3.20
4275 5007 3.729356 CACAGAGATGGACTCCGTG 57.271 57.895 0.00 0.00 44.20 4.94
4276 5008 0.972983 CCCACAGAGATGGACTCCGT 60.973 60.000 0.00 0.00 45.96 4.69
4277 5009 1.819229 CCCACAGAGATGGACTCCG 59.181 63.158 0.00 0.00 45.96 4.63
4299 5139 0.459585 CTACCGGTGGATTGTCACGG 60.460 60.000 19.93 0.00 38.46 4.94
4305 5146 0.535102 GATGGGCTACCGGTGGATTG 60.535 60.000 23.78 5.61 40.75 2.67
4309 5150 1.762460 AGAGATGGGCTACCGGTGG 60.762 63.158 19.93 17.17 40.75 4.61
4316 5161 1.770658 CCAATCCACAGAGATGGGCTA 59.229 52.381 0.00 0.00 40.49 3.93
4333 5179 4.651778 CTTCCAGTGAATTACCACTCCAA 58.348 43.478 0.00 0.00 44.87 3.53
4336 5182 2.673368 CGCTTCCAGTGAATTACCACTC 59.327 50.000 0.00 0.00 44.87 3.51
4357 5210 0.177604 CAGACCACAGAGATGGAGCC 59.822 60.000 0.00 0.00 43.02 4.70
4412 5269 6.792250 GCTTCCAATGAATTATTATCACGACG 59.208 38.462 0.00 0.00 0.00 5.12
4445 5302 0.972983 ACCACAGAGATGGACTCCCG 60.973 60.000 0.00 0.00 45.96 5.14
4505 5366 5.065731 GGTTCCAGCACAATTCATCTAGAAG 59.934 44.000 0.00 0.00 40.15 2.85
4507 5368 4.225942 AGGTTCCAGCACAATTCATCTAGA 59.774 41.667 0.00 0.00 0.00 2.43
4508 5369 4.334759 CAGGTTCCAGCACAATTCATCTAG 59.665 45.833 0.00 0.00 0.00 2.43
4509 5370 4.264253 CAGGTTCCAGCACAATTCATCTA 58.736 43.478 0.00 0.00 0.00 1.98
4510 5371 3.087031 CAGGTTCCAGCACAATTCATCT 58.913 45.455 0.00 0.00 0.00 2.90
4511 5372 2.165030 CCAGGTTCCAGCACAATTCATC 59.835 50.000 0.00 0.00 0.00 2.92
4512 5373 2.173519 CCAGGTTCCAGCACAATTCAT 58.826 47.619 0.00 0.00 0.00 2.57
4513 5374 1.133513 ACCAGGTTCCAGCACAATTCA 60.134 47.619 0.00 0.00 0.00 2.57
4536 5397 2.251642 GCGCCCGTGGTCATTATCC 61.252 63.158 0.00 0.00 0.00 2.59
4554 5415 8.773645 GGAAAAAGGAAATCAAAGTTAACATGG 58.226 33.333 8.61 0.00 0.00 3.66
4591 5452 3.578688 TCGGCGTCATCTATCAATGATG 58.421 45.455 6.85 0.00 42.89 3.07
4592 5453 3.942130 TCGGCGTCATCTATCAATGAT 57.058 42.857 6.85 0.00 37.93 2.45
4593 5454 3.726291 TTCGGCGTCATCTATCAATGA 57.274 42.857 6.85 0.00 33.30 2.57
4594 5455 3.804325 ACTTTCGGCGTCATCTATCAATG 59.196 43.478 6.85 0.00 0.00 2.82
4615 5668 6.098982 ACTCCCTCTATATATAGCATGCCAAC 59.901 42.308 15.66 0.00 0.00 3.77
4636 5691 1.541588 CCCAAAGCTACAAGCAACTCC 59.458 52.381 1.22 0.00 45.56 3.85
4666 5721 2.099141 ATGATGGTCTTGTGTCGTGG 57.901 50.000 0.00 0.00 0.00 4.94
4677 5734 1.134699 TCTGCTCGTGGAATGATGGTC 60.135 52.381 0.00 0.00 0.00 4.02
4706 5763 1.087501 CTAAACTTGCTCTTCCCGGC 58.912 55.000 0.00 0.00 0.00 6.13
4740 5812 1.565305 CAGCGTGCTACTCTTCATCC 58.435 55.000 0.00 0.00 0.00 3.51
4781 5853 2.343475 ATCCCCATGACCATGACGGC 62.343 60.000 11.28 0.00 41.20 5.68
4819 5891 3.741476 GTACCGTCCGTGTCCGCT 61.741 66.667 0.00 0.00 0.00 5.52
4826 5898 2.369870 CGTAGTACGTACCGTCCGT 58.630 57.895 21.80 5.15 41.54 4.69


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

AutoCloner maintained by Alex Coulton.