Multiple sequence alignment - TraesCS1A01G131900

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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 TraesCS1A01G131900 chr1A 100.000 9156 0 0 1 9156 177464418 177473573 0.000000e+00 16909
1 TraesCS1A01G131900 chr5D 97.986 6404 112 7 1466 7861 45661546 45655152 0.000000e+00 11095
2 TraesCS1A01G131900 chr5D 97.584 6416 139 8 1459 7864 73406882 73400473 0.000000e+00 10975
3 TraesCS1A01G131900 chr5D 90.498 1305 113 4 7863 9156 154610901 154612205 0.000000e+00 1712
4 TraesCS1A01G131900 chr5D 89.310 580 56 3 887 1463 154610328 154610904 0.000000e+00 723
5 TraesCS1A01G131900 chr5D 83.624 574 70 9 324 890 154609626 154610182 1.360000e-142 518
6 TraesCS1A01G131900 chr3D 97.830 6407 121 8 1466 7860 67009958 67003558 0.000000e+00 11045
7 TraesCS1A01G131900 chr3D 97.578 6441 101 25 1466 7864 437763040 437756613 0.000000e+00 10979
8 TraesCS1A01G131900 chr1D 97.700 6434 102 23 1463 7860 315624343 315630766 0.000000e+00 11020
9 TraesCS1A01G131900 chrUn 97.473 6410 144 10 1466 7862 175492138 175485734 0.000000e+00 10924
10 TraesCS1A01G131900 chrUn 86.575 581 72 5 887 1463 136438812 136438234 3.610000e-178 636
11 TraesCS1A01G131900 chrUn 88.672 256 29 0 7861 8116 136438239 136437984 6.900000e-81 313
12 TraesCS1A01G131900 chr2D 97.473 6411 138 15 1463 7860 624904369 624910768 0.000000e+00 10920
13 TraesCS1A01G131900 chr2D 97.034 6439 153 16 1463 7867 410491711 410498145 0.000000e+00 10798
14 TraesCS1A01G131900 chr6B 96.990 6412 168 13 1466 7860 543737648 543731245 0.000000e+00 10748
15 TraesCS1A01G131900 chr2A 92.646 1455 103 2 12 1463 133645160 133643707 0.000000e+00 2091
16 TraesCS1A01G131900 chr2A 95.223 1298 59 3 7861 9156 133643712 133642416 0.000000e+00 2050
17 TraesCS1A01G131900 chr2A 88.739 444 50 0 8137 8580 744806116 744805673 2.250000e-150 544
18 TraesCS1A01G131900 chr3A 96.039 1237 39 1 7861 9097 637957177 637958403 0.000000e+00 2004
19 TraesCS1A01G131900 chr3A 94.213 1296 73 1 7861 9156 98514024 98512731 0.000000e+00 1977
20 TraesCS1A01G131900 chr3A 92.180 1023 55 4 465 1463 98515040 98514019 0.000000e+00 1423
21 TraesCS1A01G131900 chr3A 95.000 540 21 1 279 812 637946569 637947108 0.000000e+00 843
22 TraesCS1A01G131900 chr3A 96.956 427 13 0 1037 1463 637956756 637957182 0.000000e+00 717
23 TraesCS1A01G131900 chr3A 90.302 464 42 2 12 473 98516279 98515817 1.020000e-168 604
24 TraesCS1A01G131900 chr3A 94.700 283 14 1 1 282 637921552 637921834 1.090000e-118 438
25 TraesCS1A01G131900 chr3A 92.793 111 5 1 936 1043 637947105 637947215 3.420000e-34 158
26 TraesCS1A01G131900 chr7B 92.677 1270 93 0 7863 9132 415325917 415327186 0.000000e+00 1831
27 TraesCS1A01G131900 chr7B 90.706 581 49 4 887 1463 415325341 415325920 0.000000e+00 769
28 TraesCS1A01G131900 chr7A 94.133 392 13 4 1466 1848 701455831 701455441 1.020000e-163 588
29 TraesCS1A01G131900 chr7A 77.244 624 124 10 7862 8475 259560221 259559606 5.260000e-92 350
30 TraesCS1A01G131900 chr2B 89.051 411 27 7 1466 1858 546631736 546631326 2.300000e-135 494
31 TraesCS1A01G131900 chr6A 86.774 310 41 0 8131 8440 121670765 121671074 6.810000e-91 346
32 TraesCS1A01G131900 chr5A 75.730 651 138 11 7861 8495 635470288 635469642 8.930000e-80 309


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 TraesCS1A01G131900 chr1A 177464418 177473573 9155 False 16909.000000 16909 100.000000 1 9156 1 chr1A.!!$F1 9155
1 TraesCS1A01G131900 chr5D 45655152 45661546 6394 True 11095.000000 11095 97.986000 1466 7861 1 chr5D.!!$R1 6395
2 TraesCS1A01G131900 chr5D 73400473 73406882 6409 True 10975.000000 10975 97.584000 1459 7864 1 chr5D.!!$R2 6405
3 TraesCS1A01G131900 chr5D 154609626 154612205 2579 False 984.333333 1712 87.810667 324 9156 3 chr5D.!!$F1 8832
4 TraesCS1A01G131900 chr3D 67003558 67009958 6400 True 11045.000000 11045 97.830000 1466 7860 1 chr3D.!!$R1 6394
5 TraesCS1A01G131900 chr3D 437756613 437763040 6427 True 10979.000000 10979 97.578000 1466 7864 1 chr3D.!!$R2 6398
6 TraesCS1A01G131900 chr1D 315624343 315630766 6423 False 11020.000000 11020 97.700000 1463 7860 1 chr1D.!!$F1 6397
7 TraesCS1A01G131900 chrUn 175485734 175492138 6404 True 10924.000000 10924 97.473000 1466 7862 1 chrUn.!!$R1 6396
8 TraesCS1A01G131900 chrUn 136437984 136438812 828 True 474.500000 636 87.623500 887 8116 2 chrUn.!!$R2 7229
9 TraesCS1A01G131900 chr2D 624904369 624910768 6399 False 10920.000000 10920 97.473000 1463 7860 1 chr2D.!!$F2 6397
10 TraesCS1A01G131900 chr2D 410491711 410498145 6434 False 10798.000000 10798 97.034000 1463 7867 1 chr2D.!!$F1 6404
11 TraesCS1A01G131900 chr6B 543731245 543737648 6403 True 10748.000000 10748 96.990000 1466 7860 1 chr6B.!!$R1 6394
12 TraesCS1A01G131900 chr2A 133642416 133645160 2744 True 2070.500000 2091 93.934500 12 9156 2 chr2A.!!$R2 9144
13 TraesCS1A01G131900 chr3A 637956756 637958403 1647 False 1360.500000 2004 96.497500 1037 9097 2 chr3A.!!$F3 8060
14 TraesCS1A01G131900 chr3A 98512731 98516279 3548 True 1334.666667 1977 92.231667 12 9156 3 chr3A.!!$R1 9144
15 TraesCS1A01G131900 chr3A 637946569 637947215 646 False 500.500000 843 93.896500 279 1043 2 chr3A.!!$F2 764
16 TraesCS1A01G131900 chr7B 415325341 415327186 1845 False 1300.000000 1831 91.691500 887 9132 2 chr7B.!!$F1 8245
17 TraesCS1A01G131900 chr7A 259559606 259560221 615 True 350.000000 350 77.244000 7862 8475 1 chr7A.!!$R1 613
18 TraesCS1A01G131900 chr5A 635469642 635470288 646 True 309.000000 309 75.730000 7861 8495 1 chr5A.!!$R1 634

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
556 1347 2.203538 CCCAGCCAGCCAAGTTGT 60.204 61.111 1.45 0.00 0.00 3.32 F
1755 2765 0.955428 CCTTGCAGGAGCGCAGTTTA 60.955 55.000 11.47 0.00 44.14 2.01 F
2192 3207 0.452585 TCGTCGCCAACATCGTCATA 59.547 50.000 0.00 0.00 0.00 2.15 F
3372 4388 0.610174 TGTGTGCTGACATCTCCCTC 59.390 55.000 0.00 0.00 33.63 4.30 F
3409 4425 0.984230 TGCAAGGGATTCTTCCGTCT 59.016 50.000 0.00 0.00 43.63 4.18 F
5484 6504 2.680312 TGAAAGATCTGGGAGAAGCG 57.320 50.000 0.00 0.00 0.00 4.68 F
5964 6984 1.271054 GCAGTGTCATGGAGGTCTTGT 60.271 52.381 0.00 0.00 0.00 3.16 F
7519 8589 0.404040 ATCCTGCACCGGAAAAGGAA 59.596 50.000 21.76 10.16 41.99 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1899 2914 0.179234 TTTTCGGTGTGTCTCTGGCA 59.821 50.000 0.00 0.0 0.00 4.92 R
3390 4406 0.984230 AGACGGAAGAATCCCTTGCA 59.016 50.000 0.00 0.0 42.57 4.08 R
3842 4859 1.021390 ATGAGGCTTTCGAGGTTGCG 61.021 55.000 0.00 0.0 0.00 4.85 R
5320 6340 0.818296 ACACACCTATCAGCCTCGTC 59.182 55.000 0.00 0.0 0.00 4.20 R
5669 6689 4.024048 ACATGAGTGAACCGACAATTTGAC 60.024 41.667 0.00 0.0 0.00 3.18 R
6589 7609 2.212869 ACTGCGACGTTTACAGTCAA 57.787 45.000 11.81 0.0 40.56 3.18 R
7924 8996 1.278985 CACATTGAGGTAGCAGGGTCA 59.721 52.381 0.00 0.0 0.00 4.02 R
9023 10121 0.874390 CCACACGTGCATAAGCTGTT 59.126 50.000 17.22 0.0 42.74 3.16 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
83 84 6.838198 TCACAATACAGCAATTACCGTATC 57.162 37.500 0.00 0.00 0.00 2.24
95 96 9.120538 AGCAATTACCGTATCTAAACATCAAAT 57.879 29.630 0.00 0.00 0.00 2.32
358 364 4.030314 TCCTATCGATCCATAACCGAGT 57.970 45.455 0.00 0.00 35.70 4.18
398 404 3.458118 CACATCCACCCAACCTTATCCTA 59.542 47.826 0.00 0.00 0.00 2.94
405 411 3.785887 ACCCAACCTTATCCTATTGCTCA 59.214 43.478 0.00 0.00 0.00 4.26
556 1347 2.203538 CCCAGCCAGCCAAGTTGT 60.204 61.111 1.45 0.00 0.00 3.32
677 1492 6.949352 TTGATTTCTTGCATCTTAGATCCC 57.051 37.500 0.00 0.00 0.00 3.85
748 1563 9.408648 CAGGACAAATCTAATTACCAAGGTATT 57.591 33.333 0.00 0.00 0.00 1.89
771 1586 7.605410 TTTTCTTATACTTTAACTCCAGCCG 57.395 36.000 0.00 0.00 0.00 5.52
777 1592 3.163467 ACTTTAACTCCAGCCGTACTCT 58.837 45.455 0.00 0.00 0.00 3.24
860 1675 3.118408 CGGTTGGAGGAATGGTCTGATAA 60.118 47.826 0.00 0.00 0.00 1.75
913 1877 3.157881 TCTCCCGATGTCCTCATGATAC 58.842 50.000 0.00 0.00 34.06 2.24
921 1886 7.118390 CCCGATGTCCTCATGATACTAAAATTC 59.882 40.741 0.00 0.00 34.06 2.17
922 1887 7.875041 CCGATGTCCTCATGATACTAAAATTCT 59.125 37.037 0.00 0.00 34.06 2.40
1108 2076 1.610038 CACTGGCTGAAGCAATGTTCA 59.390 47.619 4.43 0.00 44.36 3.18
1109 2077 2.230508 CACTGGCTGAAGCAATGTTCAT 59.769 45.455 4.43 0.00 44.36 2.57
1182 2152 8.754096 CAAGATCGATTTAGAACAGAGATTCAG 58.246 37.037 0.00 0.00 0.00 3.02
1220 2190 1.745115 GGTACCATGCTTCAGCGCA 60.745 57.895 11.47 0.00 45.83 6.09
1250 2220 7.572759 ACAAAATTATCAAGCCGTATATGTCG 58.427 34.615 0.00 0.00 0.00 4.35
1251 2221 5.779806 AATTATCAAGCCGTATATGTCGC 57.220 39.130 0.00 0.00 0.00 5.19
1371 2341 7.656397 GCTAGAGCAAATGAAGATGGCACAC 62.656 48.000 0.00 0.00 41.21 3.82
1461 2431 5.741040 GCAGATAACTAAAGAAGCATGCAAC 59.259 40.000 21.98 13.09 0.00 4.17
1464 2434 6.881065 AGATAACTAAAGAAGCATGCAACTGA 59.119 34.615 21.98 9.15 0.00 3.41
1752 2762 3.630013 TCCTTGCAGGAGCGCAGT 61.630 61.111 11.47 0.00 40.06 4.40
1755 2765 0.955428 CCTTGCAGGAGCGCAGTTTA 60.955 55.000 11.47 0.00 44.14 2.01
1756 2766 1.089920 CTTGCAGGAGCGCAGTTTAT 58.910 50.000 11.47 0.00 44.14 1.40
1761 2771 3.504134 TGCAGGAGCGCAGTTTATTTTTA 59.496 39.130 11.47 0.00 46.23 1.52
1762 2772 4.157656 TGCAGGAGCGCAGTTTATTTTTAT 59.842 37.500 11.47 0.00 46.23 1.40
1867 2882 2.098233 CGCGACACAATACCGCCTT 61.098 57.895 0.00 0.00 45.39 4.35
1978 2993 2.251409 TCGTAGTCTACTCCATCCCG 57.749 55.000 8.37 0.00 0.00 5.14
2048 3063 1.741401 CTTTGCGATCCTGCACCGA 60.741 57.895 0.00 0.00 46.25 4.69
2049 3064 1.298157 CTTTGCGATCCTGCACCGAA 61.298 55.000 0.00 0.00 46.25 4.30
2098 3113 1.225854 GTGCGCGACTGCTCAAATC 60.226 57.895 12.10 0.00 37.61 2.17
2192 3207 0.452585 TCGTCGCCAACATCGTCATA 59.547 50.000 0.00 0.00 0.00 2.15
2262 3277 6.826231 TCCTTTGTTCATGTCTGTTTCTACAA 59.174 34.615 0.00 0.00 32.92 2.41
2276 3291 6.879962 TGTTTCTACAACTATTGTTACGTGC 58.120 36.000 0.00 0.00 42.22 5.34
2522 3538 1.004440 GAAGACCACGCTCTGGCTT 60.004 57.895 0.00 2.87 45.32 4.35
2572 3588 0.842635 GGTGCTCCAGAGGGAATGAT 59.157 55.000 0.00 0.00 44.38 2.45
2649 3665 1.134521 TGAGTGTTCTTGCTGACCGTT 60.135 47.619 0.00 0.00 0.00 4.44
2760 3776 6.998074 TGAACTGTACATCATGGAGAGTTTTT 59.002 34.615 13.55 0.00 43.85 1.94
2960 3976 7.911651 AGAGACAGGAGATATCAGTTGAAAAA 58.088 34.615 5.32 0.00 0.00 1.94
2961 3977 8.547173 AGAGACAGGAGATATCAGTTGAAAAAT 58.453 33.333 5.32 0.00 0.00 1.82
2962 3978 9.171877 GAGACAGGAGATATCAGTTGAAAAATT 57.828 33.333 5.32 0.00 0.00 1.82
3024 4040 3.956744 AGATACCACTGAAAAAGGAGGC 58.043 45.455 0.00 0.00 0.00 4.70
3086 4102 4.640647 ACAGAACAAGAACAAAGGGAAGAC 59.359 41.667 0.00 0.00 0.00 3.01
3098 4114 2.945456 AGGGAAGACCAAACCTGTTTC 58.055 47.619 0.00 0.00 43.89 2.78
3165 4181 2.364970 CAAGGCTGAGCTAGAGTGCTAT 59.635 50.000 3.72 0.00 44.17 2.97
3289 4305 9.243105 GCAATACTGATGGGTATGGTAATTTAT 57.757 33.333 0.00 0.00 33.31 1.40
3372 4388 0.610174 TGTGTGCTGACATCTCCCTC 59.390 55.000 0.00 0.00 33.63 4.30
3390 4406 6.960542 TCTCCCTCTTTACTTCTTATCAGGTT 59.039 38.462 0.00 0.00 0.00 3.50
3409 4425 0.984230 TGCAAGGGATTCTTCCGTCT 59.016 50.000 0.00 0.00 43.63 4.18
3473 4489 4.755123 CACGGTGGATCTGAAGTTTACTTT 59.245 41.667 0.00 0.00 36.11 2.66
3475 4491 4.994852 CGGTGGATCTGAAGTTTACTTTGA 59.005 41.667 0.00 0.15 36.11 2.69
3561 4577 3.226777 CTCCCTTCTATGTCGAGATGGT 58.773 50.000 5.12 0.00 38.52 3.55
3842 4859 3.689161 TGCCATAGTTGTGTGCAATCTAC 59.311 43.478 0.00 0.00 36.92 2.59
3946 4963 4.950475 TGAATGGTGTGTTGACAAAAGGTA 59.050 37.500 0.00 0.00 32.49 3.08
4278 5295 3.554934 TGCTGGTTTATCTAAGGCATGG 58.445 45.455 0.00 0.00 0.00 3.66
4279 5296 3.053693 TGCTGGTTTATCTAAGGCATGGT 60.054 43.478 0.00 0.00 0.00 3.55
4280 5297 3.316308 GCTGGTTTATCTAAGGCATGGTG 59.684 47.826 0.00 0.00 0.00 4.17
4681 5701 9.820229 GTACAACTGATGAATATTTCGAACAAA 57.180 29.630 0.00 0.00 0.00 2.83
4892 5912 8.454894 GGACTCAATTCTTTCTAATGGAACTTC 58.545 37.037 0.00 0.00 33.13 3.01
4965 5985 4.745125 GTGTTCAAAAAGAAGCTAAAGCCC 59.255 41.667 0.00 0.00 43.38 5.19
5320 6340 4.216902 TGACTTCTGCAGGATTTGTCATTG 59.783 41.667 15.13 0.00 30.39 2.82
5408 6428 4.219725 TGTGGACGACATACTGATCTTTGA 59.780 41.667 0.00 0.00 0.00 2.69
5484 6504 2.680312 TGAAAGATCTGGGAGAAGCG 57.320 50.000 0.00 0.00 0.00 4.68
5669 6689 9.743057 AGAAACGAGAGATCAATTAAGATACTG 57.257 33.333 0.00 0.00 0.00 2.74
5854 6874 6.757173 TTACTTATTTAGGGCATCCTGCTA 57.243 37.500 0.00 0.00 44.61 3.49
5964 6984 1.271054 GCAGTGTCATGGAGGTCTTGT 60.271 52.381 0.00 0.00 0.00 3.16
6267 7287 2.222227 AAAACCTGGCAGATCCCTTC 57.778 50.000 17.94 0.00 0.00 3.46
6312 7332 5.423290 TGTGATAGATATTGCATCGAGGGAT 59.577 40.000 0.00 0.00 0.00 3.85
6589 7609 8.918202 TTGAAAGAACACACCTATATGAGTTT 57.082 30.769 0.00 0.00 34.13 2.66
6770 7790 5.625197 GCAATTCAAGGCATAGTCCATTGTT 60.625 40.000 0.00 0.00 0.00 2.83
6797 7817 5.818136 TGTGAATGGATGTAGCTTAAAGC 57.182 39.130 0.00 0.00 42.84 3.51
7047 8068 7.456269 CCTCTTTATATAGTGGGTTCTCTCCAT 59.544 40.741 3.99 0.00 36.58 3.41
7376 8446 3.231889 CTGCGGCCAGAGACACACT 62.232 63.158 2.24 0.00 41.77 3.55
7424 8494 3.736100 CAACTTGCGCCGCCATCA 61.736 61.111 6.63 0.00 0.00 3.07
7512 8582 3.247056 TTTGCGATCCTGCACCGGA 62.247 57.895 9.46 0.00 46.25 5.14
7514 8584 2.435938 GCGATCCTGCACCGGAAA 60.436 61.111 9.46 0.00 36.49 3.13
7519 8589 0.404040 ATCCTGCACCGGAAAAGGAA 59.596 50.000 21.76 10.16 41.99 3.36
7688 8758 4.994852 GCACCCATAATAGCTAACGATCAA 59.005 41.667 0.00 0.00 0.00 2.57
7704 8774 4.119862 CGATCAATACGTCCAACATCCTT 58.880 43.478 0.00 0.00 0.00 3.36
7739 8809 5.119588 TGTTTCTACAGCTATTGTTACGTGC 59.880 40.000 0.00 0.00 41.29 5.34
7918 8989 2.328099 CCAAGACCTTGCTGCCGTC 61.328 63.158 4.31 0.14 39.16 4.79
7924 8996 0.179018 ACCTTGCTGCCGTCTTCTTT 60.179 50.000 0.00 0.00 0.00 2.52
8023 9095 5.048294 TCAAAGCTCTACAACTACGACATCA 60.048 40.000 0.00 0.00 0.00 3.07
8082 9154 1.694150 AGTGCCTGAACAGAGCTACAA 59.306 47.619 3.19 0.00 0.00 2.41
8139 9221 3.271055 TCACCACATGGATGATGACTG 57.729 47.619 4.53 0.00 38.94 3.51
8189 9280 1.269778 CCTGCTGAACTGTCTCGTTGA 60.270 52.381 0.00 0.00 0.00 3.18
8325 9419 9.417561 TCGACCTAGAAATCTTTATCCTTTCTA 57.582 33.333 0.00 0.00 39.34 2.10
8403 9497 5.981315 GTGTTATTTATCTGTGCTACGCCTA 59.019 40.000 0.00 0.00 0.00 3.93
8932 10028 1.072505 ACGTCACGCCCCTCATTTT 59.927 52.632 0.00 0.00 0.00 1.82
8964 10060 8.149631 TCTTCATCTGCCATATCAACCATATA 57.850 34.615 0.00 0.00 0.00 0.86
8981 10077 9.993454 CAACCATATATGTATCCTCCATATGAG 57.007 37.037 11.73 0.00 36.45 2.90
9016 10114 5.393027 GGTTGGTGCGAGATTTAATGAATGT 60.393 40.000 0.00 0.00 0.00 2.71
9018 10116 4.940654 TGGTGCGAGATTTAATGAATGTGA 59.059 37.500 0.00 0.00 0.00 3.58
9023 10121 7.325821 GTGCGAGATTTAATGAATGTGACAAAA 59.674 33.333 0.00 0.00 0.00 2.44
9097 10195 5.091552 TGGGACTGAAGTTCTATGTTACCT 58.908 41.667 4.17 0.00 0.00 3.08
9132 10230 2.431782 GGTGTGCCAATGGAAGCAATAT 59.568 45.455 2.05 0.00 41.48 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 8.220755 ACGGTAATTGCTGTATTGTGATAAAT 57.779 30.769 6.18 0.00 0.00 1.40
338 341 3.128938 GGACTCGGTTATGGATCGATAGG 59.871 52.174 0.00 0.00 32.32 2.57
358 364 0.252696 TGGCAGGCTAGAAGAAGGGA 60.253 55.000 0.00 0.00 0.00 4.20
427 433 2.395619 GGAAGGAGATAAGAACGGGGA 58.604 52.381 0.00 0.00 0.00 4.81
513 1304 4.424711 TGCTTGCGGGGGATCCAC 62.425 66.667 15.23 10.58 34.36 4.02
748 1563 6.704310 ACGGCTGGAGTTAAAGTATAAGAAA 58.296 36.000 0.00 0.00 0.00 2.52
750 1565 5.927281 ACGGCTGGAGTTAAAGTATAAGA 57.073 39.130 0.00 0.00 0.00 2.10
771 1586 5.347907 ACAGCGTATTGTAAAGCAAGAGTAC 59.652 40.000 0.00 0.00 40.86 2.73
777 1592 3.403968 TGGACAGCGTATTGTAAAGCAA 58.596 40.909 0.00 0.00 41.89 3.91
827 1642 3.013921 TCCTCCAACCGATTTTATGTGC 58.986 45.455 0.00 0.00 0.00 4.57
860 1675 1.489230 ACCAGGACAGGAAACGAAACT 59.511 47.619 0.00 0.00 0.00 2.66
913 1877 8.802267 TGAACCTATGGGAAAACAGAATTTTAG 58.198 33.333 0.25 0.00 36.25 1.85
921 1886 5.556915 TGTACTGAACCTATGGGAAAACAG 58.443 41.667 0.25 7.90 36.25 3.16
922 1887 5.570205 TGTACTGAACCTATGGGAAAACA 57.430 39.130 0.25 0.00 36.25 2.83
996 1961 8.823220 AAGGTATAAACACAGCTTCCATTAAT 57.177 30.769 0.00 0.00 0.00 1.40
1182 2152 0.920664 GTGCTTTTGTGCGGTGAAAC 59.079 50.000 0.00 0.00 35.36 2.78
1220 2190 2.422127 CGGCTTGATAATTTTGTCCGGT 59.578 45.455 0.00 0.00 32.75 5.28
1227 2197 6.203915 TGCGACATATACGGCTTGATAATTTT 59.796 34.615 0.00 0.00 0.00 1.82
1250 2220 2.309613 TCATTGATGCTACCCCATTGC 58.690 47.619 0.00 0.00 0.00 3.56
1251 2221 4.585581 TGATTCATTGATGCTACCCCATTG 59.414 41.667 0.00 0.00 0.00 2.82
1371 2341 3.005554 CAACCTGGCTGATACTCTTGTG 58.994 50.000 0.00 0.00 0.00 3.33
1461 2431 5.189180 GGCCTAGCCCATTAATTCTATCAG 58.811 45.833 0.00 0.00 44.06 2.90
1867 2882 9.128404 CGGTAGCTGTATATATATTAGGACCAA 57.872 37.037 0.00 0.00 0.00 3.67
1899 2914 0.179234 TTTTCGGTGTGTCTCTGGCA 59.821 50.000 0.00 0.00 0.00 4.92
2048 3063 5.243060 CCCAAAAACCTAATTCGTCCTCTTT 59.757 40.000 0.00 0.00 0.00 2.52
2049 3064 4.765339 CCCAAAAACCTAATTCGTCCTCTT 59.235 41.667 0.00 0.00 0.00 2.85
2192 3207 2.264005 TTATGGGTGCGACAGTGTTT 57.736 45.000 0.00 0.00 0.00 2.83
2262 3277 2.159627 GCAGCAAGCACGTAACAATAGT 59.840 45.455 0.00 0.00 44.79 2.12
2522 3538 3.807622 CGTGGAAAACTTTCAGAGCAGTA 59.192 43.478 4.67 0.00 38.92 2.74
2572 3588 3.777465 ATTTTCTCCGATCTTCGTCGA 57.223 42.857 0.00 0.00 44.06 4.20
2649 3665 3.209410 TGTGCATGTACACATCACACAA 58.791 40.909 13.02 8.19 45.36 3.33
3098 4114 2.568623 AGTCTTGGTAGGCTTGTTGG 57.431 50.000 0.00 0.00 30.27 3.77
3165 4181 3.970410 CCAGGCTTCCCACAGGCA 61.970 66.667 0.00 0.00 41.89 4.75
3289 4305 9.230122 TGATTGAAATACTGAAAGCACAATAGA 57.770 29.630 0.00 0.00 37.60 1.98
3372 4388 6.127897 CCCTTGCAACCTGATAAGAAGTAAAG 60.128 42.308 0.00 0.00 0.00 1.85
3390 4406 0.984230 AGACGGAAGAATCCCTTGCA 59.016 50.000 0.00 0.00 42.57 4.08
3409 4425 3.641046 CATGTGACCCATTCCCCATTAA 58.359 45.455 0.00 0.00 0.00 1.40
3473 4489 4.021456 TCCTTAGTTGCACGATCTTTCTCA 60.021 41.667 0.00 0.00 0.00 3.27
3475 4491 4.537135 TCCTTAGTTGCACGATCTTTCT 57.463 40.909 0.00 0.00 0.00 2.52
3842 4859 1.021390 ATGAGGCTTTCGAGGTTGCG 61.021 55.000 0.00 0.00 0.00 4.85
4179 5196 6.377996 CCACTCCATTTGATTGAGGTGAATAA 59.622 38.462 0.00 0.00 0.00 1.40
4441 5461 2.426738 CTGTCTTTGGTCCAAGTTTGCA 59.573 45.455 4.09 1.16 0.00 4.08
4892 5912 6.390721 CCATATGGTCTATCAGTTAGTTCCG 58.609 44.000 14.09 0.00 0.00 4.30
4965 5985 7.328737 GCCTTGTACTTATCAATAGTACCATCG 59.671 40.741 9.83 0.00 44.65 3.84
5320 6340 0.818296 ACACACCTATCAGCCTCGTC 59.182 55.000 0.00 0.00 0.00 4.20
5669 6689 4.024048 ACATGAGTGAACCGACAATTTGAC 60.024 41.667 0.00 0.00 0.00 3.18
5864 6884 9.224267 CGGAGATCCAATTTGAATCACTATATT 57.776 33.333 0.00 0.00 35.14 1.28
5964 6984 4.839121 ACCTCGTCAATATGGTTTGCTTA 58.161 39.130 0.00 0.00 0.00 3.09
6120 7140 7.907214 AGAATTGTTCACTTTAGCGATAACT 57.093 32.000 0.00 0.00 0.00 2.24
6191 7211 4.451900 GGAGTTTCTCAACTTCCTGACAA 58.548 43.478 0.00 0.00 43.79 3.18
6267 7287 4.695455 ACATTTCGTGATAGTCCCTTTGTG 59.305 41.667 0.00 0.00 0.00 3.33
6589 7609 2.212869 ACTGCGACGTTTACAGTCAA 57.787 45.000 11.81 0.00 40.56 3.18
6770 7790 8.856153 TTTAAGCTACATCCATTCACAACTTA 57.144 30.769 0.00 0.00 0.00 2.24
6797 7817 6.223852 TGTTAAGTTGAACTTCTGCCTAGAG 58.776 40.000 14.64 0.00 39.51 2.43
6895 7915 6.136155 CCATTAATTCTAACAATCCCCCACT 58.864 40.000 0.00 0.00 0.00 4.00
7376 8446 3.133183 GGCAAAACCCTAGGTGTTTTTCA 59.867 43.478 25.98 0.00 42.38 2.69
7424 8494 3.069729 GCGTTTGGGATGGAGTAGACTAT 59.930 47.826 0.00 0.00 0.00 2.12
7512 8582 7.684317 TCCCAAAAACCTAATTCTTCCTTTT 57.316 32.000 0.00 0.00 0.00 2.27
7514 8584 6.239600 GCTTCCCAAAAACCTAATTCTTCCTT 60.240 38.462 0.00 0.00 0.00 3.36
7519 8589 3.056821 GCGCTTCCCAAAAACCTAATTCT 60.057 43.478 0.00 0.00 0.00 2.40
7688 8758 4.647611 TGAACAAAGGATGTTGGACGTAT 58.352 39.130 0.00 0.00 45.86 3.06
7918 8989 2.303022 TGAGGTAGCAGGGTCAAAGAAG 59.697 50.000 0.00 0.00 0.00 2.85
7924 8996 1.278985 CACATTGAGGTAGCAGGGTCA 59.721 52.381 0.00 0.00 0.00 4.02
8082 9154 5.672503 CTGAATCTTCATCTGAGTGACCAT 58.327 41.667 0.00 0.00 36.46 3.55
8122 9195 1.674441 GCACAGTCATCATCCATGTGG 59.326 52.381 5.85 0.00 41.17 4.17
8139 9221 2.196776 CTCATGGGGATGGGGCAC 59.803 66.667 0.00 0.00 0.00 5.01
8189 9280 7.282585 AGCCATACATATACAGTTTCACATGT 58.717 34.615 0.00 0.00 0.00 3.21
8198 9289 4.799586 GCGGTGAAGCCATACATATACAGT 60.800 45.833 0.00 0.00 36.97 3.55
8234 9325 5.123344 AGGAGACTAAACACAACAAACACAC 59.877 40.000 0.00 0.00 40.61 3.82
8325 9419 8.950210 CACTTATACATGTCCAGATTGAAGTTT 58.050 33.333 0.00 0.00 0.00 2.66
8403 9497 2.425143 ATCACAGCGGATGAAACCAT 57.575 45.000 0.00 0.00 0.00 3.55
8525 9620 6.610830 ACAAGGAGAATTGAGTAAAAAGGGA 58.389 36.000 0.00 0.00 34.20 4.20
8659 9754 6.258160 GCACTTGGTGTAGCATTAGTAAATG 58.742 40.000 0.00 0.00 39.55 2.32
8924 10020 6.561614 CAGATGAAGATGTTCCAAAATGAGG 58.438 40.000 0.00 0.00 0.00 3.86
8932 10028 3.657398 ATGGCAGATGAAGATGTTCCA 57.343 42.857 0.00 0.00 0.00 3.53
8964 10060 4.528206 TGCGTTCTCATATGGAGGATACAT 59.472 41.667 2.13 0.00 44.19 2.29
8981 10077 1.875963 CACCAACCAGGATGCGTTC 59.124 57.895 0.00 0.00 41.22 3.95
9016 10114 3.066064 ACGTGCATAAGCTGTTTTTGTCA 59.934 39.130 0.00 0.00 42.74 3.58
9018 10116 3.181491 ACACGTGCATAAGCTGTTTTTGT 60.181 39.130 17.22 0.00 42.74 2.83
9023 10121 0.874390 CCACACGTGCATAAGCTGTT 59.126 50.000 17.22 0.00 42.74 3.16
9097 10195 3.265791 GGCACACCAACATTTTTCACAA 58.734 40.909 0.00 0.00 35.26 3.33


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

AutoCloner maintained by Alex Coulton.