Multiple sequence alignment - TraesCS6A01G253600

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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 TraesCS6A01G253600 chr6A 100.000 5689 0 0 1 5689 469424953 469430641 0.000000e+00 10506.0
1 TraesCS6A01G253600 chr6D 93.437 4114 192 25 636 4732 330107360 330111412 0.000000e+00 6030.0
2 TraesCS6A01G253600 chr6D 92.765 622 32 8 1 615 330106672 330107287 0.000000e+00 887.0
3 TraesCS6A01G253600 chr6D 91.509 424 15 4 4738 5149 330111500 330111914 1.070000e-156 564.0
4 TraesCS6A01G253600 chr6D 88.446 251 20 7 5278 5519 330112046 330112296 1.550000e-75 294.0
5 TraesCS6A01G253600 chr6B 90.673 3506 216 47 2248 5689 490260768 490257310 0.000000e+00 4560.0
6 TraesCS6A01G253600 chr6B 93.869 1680 67 17 636 2300 490262428 490260770 0.000000e+00 2499.0
7 TraesCS6A01G253600 chr6B 91.369 672 20 16 1 648 490263179 490262522 0.000000e+00 885.0
8 TraesCS6A01G253600 chr2B 84.393 173 23 4 998 1168 608945942 608945772 3.530000e-37 167.0
9 TraesCS6A01G253600 chr1D 97.368 38 1 0 5149 5186 59876044 59876081 1.320000e-06 65.8
10 TraesCS6A01G253600 chr1D 96.970 33 0 1 5145 5176 319934897 319934929 3.000000e-03 54.7
11 TraesCS6A01G253600 chr2D 100.000 29 0 0 3655 3683 170277799 170277827 3.000000e-03 54.7
12 TraesCS6A01G253600 chr5B 100.000 28 0 0 3655 3682 661232239 661232212 1.000000e-02 52.8
13 TraesCS6A01G253600 chr3A 96.774 31 1 0 3652 3682 746355902 746355932 1.000000e-02 52.8
14 TraesCS6A01G253600 chr1B 100.000 28 0 0 5149 5176 432823725 432823752 1.000000e-02 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 TraesCS6A01G253600 chr6A 469424953 469430641 5688 False 10506.00 10506 100.000000 1 5689 1 chr6A.!!$F1 5688
1 TraesCS6A01G253600 chr6D 330106672 330112296 5624 False 1943.75 6030 91.539250 1 5519 4 chr6D.!!$F1 5518
2 TraesCS6A01G253600 chr6B 490257310 490263179 5869 True 2648.00 4560 91.970333 1 5689 3 chr6B.!!$R1 5688

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
725 870 0.036875 AAAGAAGGAAGGGGCGAGTG 59.963 55.0 0.00 0.0 0.00 3.51 F
981 1147 0.038526 CACTAGCGAACAACCGAGGT 60.039 55.0 0.00 0.0 0.00 3.85 F
2366 2588 0.109458 TTTCGTCTCGGATGGTGTCG 60.109 55.0 0.00 0.0 0.00 4.35 F
2739 2994 0.109827 TTGCGCAATGACAACATCCG 60.110 50.0 21.02 0.0 35.50 4.18 F
3382 3641 0.102120 AAGCTCAGAAGATCGAGGCG 59.898 55.0 0.00 0.0 0.00 5.52 F
4038 4313 0.108329 GGCGAAGAACCTGGATTCGA 60.108 55.0 25.71 0.0 46.57 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2124 2296 0.252197 ATTGGTAACTCCGCCTGTCC 59.748 55.0 0.00 0.0 39.52 4.02 R
2708 2963 0.521291 TTGCGCAAAGATGGCACTAC 59.479 50.0 22.78 0.0 34.07 2.73 R
3349 3608 0.600057 GAGCTTCAGCACCCTTTTGG 59.400 55.0 0.75 0.0 45.16 3.28 R
4253 4528 0.603707 ACCAGGTGTTGCAGATGACG 60.604 55.0 0.00 0.0 0.00 4.35 R
4274 4549 0.825010 AAATCCGATCCATGGCCTGC 60.825 55.0 6.96 0.0 0.00 4.85 R
5614 6063 0.178947 TCGGGGGCAATGTTTTTCCT 60.179 50.0 0.00 0.0 0.00 3.36 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
78 79 3.612251 CATGGGCTGCAAAGAGGG 58.388 61.111 0.50 0.00 0.00 4.30
147 149 0.873054 CATCATCTCATTCGGGCAGC 59.127 55.000 0.00 0.00 0.00 5.25
364 371 3.433319 GCGTATCCTCTCGCCAGA 58.567 61.111 0.00 0.00 45.54 3.86
365 372 1.284408 GCGTATCCTCTCGCCAGAG 59.716 63.158 0.65 0.65 45.44 3.35
374 381 3.719883 CTCGCCAGAGCAGAGCAGG 62.720 68.421 0.00 0.00 39.83 4.85
468 475 4.487412 GCGTCAATGCCTGCCTGC 62.487 66.667 0.00 0.00 0.00 4.85
595 624 5.241728 ACAAAACTGGTTAAATGGAGAGAGC 59.758 40.000 0.00 0.00 0.00 4.09
718 863 1.545841 CCCGGAAAAAGAAGGAAGGG 58.454 55.000 0.73 0.00 0.00 3.95
719 864 1.545841 CCGGAAAAAGAAGGAAGGGG 58.454 55.000 0.00 0.00 0.00 4.79
720 865 0.888619 CGGAAAAAGAAGGAAGGGGC 59.111 55.000 0.00 0.00 0.00 5.80
721 866 0.888619 GGAAAAAGAAGGAAGGGGCG 59.111 55.000 0.00 0.00 0.00 6.13
722 867 1.546998 GGAAAAAGAAGGAAGGGGCGA 60.547 52.381 0.00 0.00 0.00 5.54
723 868 1.813178 GAAAAAGAAGGAAGGGGCGAG 59.187 52.381 0.00 0.00 0.00 5.03
724 869 0.771755 AAAAGAAGGAAGGGGCGAGT 59.228 50.000 0.00 0.00 0.00 4.18
725 870 0.036875 AAAGAAGGAAGGGGCGAGTG 59.963 55.000 0.00 0.00 0.00 3.51
726 871 1.842381 AAGAAGGAAGGGGCGAGTGG 61.842 60.000 0.00 0.00 0.00 4.00
767 912 0.940991 CCAAGCAAAACGGCAAGAGC 60.941 55.000 0.00 0.00 41.10 4.09
782 933 2.204291 AGCAGATTCCCACCCCCA 60.204 61.111 0.00 0.00 0.00 4.96
813 973 0.393077 GCCTCCACTACACACACAGT 59.607 55.000 0.00 0.00 0.00 3.55
842 1008 2.353607 CTCCGCACGCCTCGATAC 60.354 66.667 0.00 0.00 0.00 2.24
920 1086 2.282251 GCTTATAAGCCCGGCCCC 60.282 66.667 24.34 0.00 46.20 5.80
969 1135 0.097674 GATTGGCAGTTGCACTAGCG 59.902 55.000 6.43 0.00 46.23 4.26
970 1136 0.321564 ATTGGCAGTTGCACTAGCGA 60.322 50.000 6.43 0.00 46.23 4.93
971 1137 0.533978 TTGGCAGTTGCACTAGCGAA 60.534 50.000 6.43 0.00 46.23 4.70
972 1138 1.227999 TGGCAGTTGCACTAGCGAAC 61.228 55.000 6.43 0.00 46.23 3.95
973 1139 1.227999 GGCAGTTGCACTAGCGAACA 61.228 55.000 6.43 0.00 46.23 3.18
980 1146 1.352156 GCACTAGCGAACAACCGAGG 61.352 60.000 0.00 0.00 0.00 4.63
981 1147 0.038526 CACTAGCGAACAACCGAGGT 60.039 55.000 0.00 0.00 0.00 3.85
1372 1538 1.954146 CACGACCAACTCCACCACG 60.954 63.158 0.00 0.00 0.00 4.94
1376 1548 4.988598 CCAACTCCACCACGCGCT 62.989 66.667 5.73 0.00 0.00 5.92
2070 2242 4.918201 GCCGGGGAGATCAAGGCG 62.918 72.222 2.18 0.00 38.28 5.52
2265 2437 9.277783 AGAACTGGCATATTTTCTGATATACAC 57.722 33.333 0.00 0.00 0.00 2.90
2271 2493 7.301054 GCATATTTTCTGATATACACTGTGGC 58.699 38.462 13.09 0.00 0.00 5.01
2366 2588 0.109458 TTTCGTCTCGGATGGTGTCG 60.109 55.000 0.00 0.00 0.00 4.35
2391 2613 3.492421 CTGCATTACCAAATTCAGCGT 57.508 42.857 0.00 0.00 31.17 5.07
2393 2615 4.342772 CTGCATTACCAAATTCAGCGTAC 58.657 43.478 0.00 0.00 31.17 3.67
2525 2747 7.120923 TGAGGTTAAGGTATGTATTCACCTC 57.879 40.000 10.10 10.10 44.55 3.85
2531 2753 5.470047 AGGTATGTATTCACCTCCGATTC 57.530 43.478 0.00 0.00 41.44 2.52
2583 2805 7.564793 TGTGCTGGAATGATATGTTAGTAACT 58.435 34.615 14.00 2.99 0.00 2.24
2584 2806 7.495606 TGTGCTGGAATGATATGTTAGTAACTG 59.504 37.037 14.00 0.00 0.00 3.16
2585 2807 6.483307 TGCTGGAATGATATGTTAGTAACTGC 59.517 38.462 14.00 0.00 0.00 4.40
2586 2808 6.708054 GCTGGAATGATATGTTAGTAACTGCT 59.292 38.462 14.00 2.32 0.00 4.24
2587 2809 7.095439 GCTGGAATGATATGTTAGTAACTGCTC 60.095 40.741 14.00 8.07 0.00 4.26
2588 2810 6.923508 TGGAATGATATGTTAGTAACTGCTCG 59.076 38.462 14.00 0.00 0.00 5.03
2609 2831 6.199937 TCGTAGGTATGTTGGAGTACTTTC 57.800 41.667 0.00 0.00 0.00 2.62
2631 2853 9.319143 CTTTCTCAAGTTAACTGATATGTAGGG 57.681 37.037 9.34 0.00 0.00 3.53
2708 2963 2.376808 AGCAGAGTGTCATCCTTTCG 57.623 50.000 0.00 0.00 0.00 3.46
2718 2973 2.866762 GTCATCCTTTCGTAGTGCCATC 59.133 50.000 0.00 0.00 0.00 3.51
2739 2994 0.109827 TTGCGCAATGACAACATCCG 60.110 50.000 21.02 0.00 35.50 4.18
2748 3003 1.346395 TGACAACATCCGTAAGCTGGT 59.654 47.619 0.00 0.00 0.00 4.00
2752 3007 1.221840 CATCCGTAAGCTGGTGCCT 59.778 57.895 0.00 0.00 40.80 4.75
2789 3044 6.094464 TGCAGTAAGATGAAATGTTGATCCTG 59.906 38.462 0.00 0.00 29.89 3.86
2834 3089 0.403271 ATGCCAGGTGTTCTGCTTCT 59.597 50.000 0.00 0.00 42.05 2.85
3070 3325 4.931002 TGCTACACACGGATACCTTTTTAC 59.069 41.667 0.00 0.00 0.00 2.01
3080 3335 7.605309 CACGGATACCTTTTTACTAGGTTTCTT 59.395 37.037 10.76 0.00 43.45 2.52
3264 3523 8.094548 TGTTAACTACTGTGCTACATCTGATTT 58.905 33.333 7.22 0.00 0.00 2.17
3349 3608 0.603975 AGCGGCTGAAGTTCTTGGAC 60.604 55.000 0.00 0.00 0.00 4.02
3382 3641 0.102120 AAGCTCAGAAGATCGAGGCG 59.898 55.000 0.00 0.00 0.00 5.52
3629 3888 7.217200 TGCTTGTCTAGTTTGTACAATCTTCT 58.783 34.615 21.12 13.73 33.01 2.85
3630 3889 8.364894 TGCTTGTCTAGTTTGTACAATCTTCTA 58.635 33.333 21.12 14.04 33.01 2.10
3631 3890 8.865001 GCTTGTCTAGTTTGTACAATCTTCTAG 58.135 37.037 21.12 20.30 33.01 2.43
3653 3912 2.449137 TTAGGAAGTACTCCCTCCGG 57.551 55.000 2.82 0.00 46.81 5.14
3668 3927 2.550208 CCTCCGGCTTATATTGTGGGAC 60.550 54.545 0.00 0.00 0.00 4.46
3933 4208 4.768968 ACAGAACCTAGCTTGCATCAAAAT 59.231 37.500 0.00 0.00 0.00 1.82
3942 4217 6.088016 AGCTTGCATCAAAATACTGACAAA 57.912 33.333 0.00 0.00 0.00 2.83
3943 4218 6.694447 AGCTTGCATCAAAATACTGACAAAT 58.306 32.000 0.00 0.00 0.00 2.32
3944 4219 6.810182 AGCTTGCATCAAAATACTGACAAATC 59.190 34.615 0.00 0.00 0.00 2.17
3945 4220 6.035327 GCTTGCATCAAAATACTGACAAATCC 59.965 38.462 0.00 0.00 0.00 3.01
3953 4228 5.904362 AATACTGACAAATCCCTCTTTGC 57.096 39.130 0.00 0.00 39.26 3.68
3962 4237 3.806949 ATCCCTCTTTGCAGGTTTGTA 57.193 42.857 0.00 0.00 0.00 2.41
4025 4300 1.795286 GAAGCAATATCGGAGGCGAAG 59.205 52.381 0.00 0.00 0.00 3.79
4038 4313 0.108329 GGCGAAGAACCTGGATTCGA 60.108 55.000 25.71 0.00 46.57 3.71
4040 4315 1.641577 CGAAGAACCTGGATTCGACC 58.358 55.000 20.56 0.00 46.57 4.79
4089 4364 1.815003 CAATGGAGCTTGAAGTGGACC 59.185 52.381 0.00 0.00 0.00 4.46
4106 4381 4.082245 GTGGACCTGGTTAAATGGATTGTG 60.082 45.833 0.00 0.00 0.00 3.33
4127 4402 5.009610 TGTGAATTTCTGCTCTTGGGTAAAC 59.990 40.000 0.00 0.00 0.00 2.01
4160 4435 2.317609 CGTGAAGGCACTGAACGGG 61.318 63.158 0.00 0.00 42.13 5.28
4226 4501 0.178973 GAGCTCCTCCCTACTCTCCC 60.179 65.000 0.87 0.00 0.00 4.30
4274 4549 0.320683 TCATCTGCAACACCTGGTCG 60.321 55.000 0.00 0.00 0.00 4.79
4277 4552 2.591429 TGCAACACCTGGTCGCAG 60.591 61.111 10.22 0.00 0.00 5.18
4322 4597 3.434319 GTGGTCACCGCCATGCAG 61.434 66.667 0.00 0.00 41.08 4.41
4547 4822 0.883833 ACCAGGCGCATTTTCTTGAG 59.116 50.000 10.83 0.00 0.00 3.02
4610 4885 2.569134 GAGAGCTTCGCGTCCAGT 59.431 61.111 5.77 0.00 0.00 4.00
4613 4888 2.430921 AGCTTCGCGTCCAGTTCG 60.431 61.111 5.77 0.00 0.00 3.95
4675 4950 1.935799 ATGCTGTCCAGAGAGAGTGT 58.064 50.000 0.00 0.00 35.81 3.55
4707 4986 2.097825 AGCCTGATTTTGCATCTGACC 58.902 47.619 0.00 0.00 0.00 4.02
4812 5173 6.385649 TGCTTCTGACGGATTTTAGTTTTT 57.614 33.333 0.00 0.00 0.00 1.94
4921 5299 4.788925 AGTAGCAGGTAAATATGGGCAA 57.211 40.909 0.00 0.00 0.00 4.52
4983 5361 0.034186 AGCGCATTGAATCCCTTGGA 60.034 50.000 11.47 0.00 35.55 3.53
4984 5362 0.817013 GCGCATTGAATCCCTTGGAA 59.183 50.000 0.30 0.00 34.34 3.53
5055 5434 3.911868 TGTTTGAATGTGCAATAGTGGC 58.088 40.909 0.00 0.00 0.00 5.01
5099 5479 4.848562 TGTTCTGTACATGTCGAGTCTT 57.151 40.909 0.00 0.00 0.00 3.01
5186 5566 2.311542 TGATGCAGAGGTTGGGGTAATT 59.688 45.455 0.00 0.00 0.00 1.40
5189 5569 1.616994 GCAGAGGTTGGGGTAATTGCT 60.617 52.381 0.00 0.00 0.00 3.91
5195 5575 3.970640 AGGTTGGGGTAATTGCTTTTTCA 59.029 39.130 0.00 0.00 0.00 2.69
5197 5577 5.782845 AGGTTGGGGTAATTGCTTTTTCATA 59.217 36.000 0.00 0.00 0.00 2.15
5198 5578 6.271159 AGGTTGGGGTAATTGCTTTTTCATAA 59.729 34.615 0.00 0.00 0.00 1.90
5241 5621 8.202811 GTGGGTTAGTAAATAAGGTTAGGAGAG 58.797 40.741 0.00 0.00 0.00 3.20
5341 5776 1.156645 GCTTAGGCTCACATGCTCCG 61.157 60.000 0.00 0.00 35.22 4.63
5358 5793 3.134458 CTCCGGGATGAGCACTAAATTC 58.866 50.000 0.00 0.00 0.00 2.17
5407 5844 6.804534 AAAACATGTTCATGTGTTTGTACG 57.195 33.333 12.39 0.00 45.05 3.67
5445 5882 7.459795 TTGTGAAGAAATGGCATATGTTGTA 57.540 32.000 0.00 0.00 0.00 2.41
5539 5981 6.560253 AAACTCGCATTTAGAAGACACAAT 57.440 33.333 0.00 0.00 0.00 2.71
5542 5984 5.877012 ACTCGCATTTAGAAGACACAATCAT 59.123 36.000 0.00 0.00 0.00 2.45
5553 5995 7.995289 AGAAGACACAATCATGTTTGTTGTAA 58.005 30.769 17.54 0.00 37.73 2.41
5556 5998 9.598517 AAGACACAATCATGTTTGTTGTAAAAT 57.401 25.926 17.54 6.31 37.73 1.82
5564 6006 9.859427 ATCATGTTTGTTGTAAAATCAGGTATG 57.141 29.630 0.00 0.00 0.00 2.39
5604 6053 2.549064 TTACTGTGAGCATGTGCACT 57.451 45.000 19.41 0.00 45.16 4.40
5606 6055 0.949397 ACTGTGAGCATGTGCACTTG 59.051 50.000 24.37 24.37 45.16 3.16
5608 6057 0.466007 TGTGAGCATGTGCACTTGGT 60.466 50.000 30.44 30.44 45.16 3.67
5609 6058 0.239347 GTGAGCATGTGCACTTGGTC 59.761 55.000 37.99 37.99 44.05 4.02
5610 6059 0.109153 TGAGCATGTGCACTTGGTCT 59.891 50.000 40.55 27.89 44.08 3.85
5611 6060 1.242076 GAGCATGTGCACTTGGTCTT 58.758 50.000 37.62 14.08 45.16 3.01
5612 6061 0.956633 AGCATGTGCACTTGGTCTTG 59.043 50.000 26.33 10.65 45.16 3.02
5613 6062 0.038892 GCATGTGCACTTGGTCTTGG 60.039 55.000 28.02 7.13 41.59 3.61
5614 6063 1.608055 CATGTGCACTTGGTCTTGGA 58.392 50.000 21.78 0.00 0.00 3.53
5615 6064 1.538512 CATGTGCACTTGGTCTTGGAG 59.461 52.381 21.78 0.00 0.00 3.86
5616 6065 0.179020 TGTGCACTTGGTCTTGGAGG 60.179 55.000 19.41 0.00 0.00 4.30
5632 6081 0.246360 GAGGAAAAACATTGCCCCCG 59.754 55.000 0.00 0.00 0.00 5.73
5640 6089 2.746279 ACATTGCCCCCGATATCAAA 57.254 45.000 3.12 0.00 0.00 2.69
5645 6094 5.418840 ACATTGCCCCCGATATCAAATATTC 59.581 40.000 3.12 0.00 0.00 1.75
5650 6099 6.015519 TGCCCCCGATATCAAATATTCAAAAG 60.016 38.462 3.12 0.00 0.00 2.27
5659 6108 7.656707 ATCAAATATTCAAAAGTGTTGCACC 57.343 32.000 0.00 0.00 34.49 5.01
5660 6109 6.577103 TCAAATATTCAAAAGTGTTGCACCA 58.423 32.000 0.00 0.00 34.49 4.17
5661 6110 7.044181 TCAAATATTCAAAAGTGTTGCACCAA 58.956 30.769 0.00 0.00 34.49 3.67
5668 6117 3.902881 AAGTGTTGCACCAAATCCAAA 57.097 38.095 0.00 0.00 34.49 3.28
5684 6133 4.038271 TCCAAACATCATCCTTGAAGCT 57.962 40.909 0.00 0.00 34.96 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 0.103390 TGTTGACGCTTCTTCCACGA 59.897 50.000 0.00 0.00 0.00 4.35
78 79 4.271049 GTCTTTTGCTTTGCCTTTTCTTCC 59.729 41.667 0.00 0.00 0.00 3.46
147 149 3.181546 CGAGTAAAAGAGCAAACGTACCG 60.182 47.826 0.00 0.00 0.00 4.02
154 156 3.067106 CTCAGCCGAGTAAAAGAGCAAA 58.933 45.455 0.00 0.00 34.29 3.68
158 160 5.672321 GCAAAATCTCAGCCGAGTAAAAGAG 60.672 44.000 0.00 0.00 40.44 2.85
276 283 1.992667 GGCTTAAGGTTTTCGCATTGC 59.007 47.619 4.29 0.00 0.00 3.56
361 368 2.125065 CTGCCCTGCTCTGCTCTG 60.125 66.667 0.00 0.00 0.00 3.35
362 369 3.400928 CCTGCCCTGCTCTGCTCT 61.401 66.667 0.00 0.00 0.00 4.09
363 370 4.486503 CCCTGCCCTGCTCTGCTC 62.487 72.222 0.00 0.00 0.00 4.26
441 448 2.033448 ATTGACGCCCGGCTTGAA 59.967 55.556 8.05 0.00 0.00 2.69
485 492 4.766088 CGCGCAGGCTTTGGCTTC 62.766 66.667 8.75 0.00 35.88 3.86
595 624 2.014128 AGGCCGTCATGTTATTTTCGG 58.986 47.619 0.00 0.00 40.72 4.30
692 828 2.084546 CTTCTTTTTCCGGGCTCGATT 58.915 47.619 8.08 0.00 39.00 3.34
719 864 4.724602 TGCACTCGCTCCACTCGC 62.725 66.667 0.00 0.00 39.64 5.03
720 865 1.664649 TTTGCACTCGCTCCACTCG 60.665 57.895 0.00 0.00 39.64 4.18
721 866 0.880278 TGTTTGCACTCGCTCCACTC 60.880 55.000 0.00 0.00 39.64 3.51
722 867 0.463654 TTGTTTGCACTCGCTCCACT 60.464 50.000 0.00 0.00 39.64 4.00
723 868 0.380378 TTTGTTTGCACTCGCTCCAC 59.620 50.000 0.00 0.00 39.64 4.02
724 869 1.317613 ATTTGTTTGCACTCGCTCCA 58.682 45.000 0.00 0.00 39.64 3.86
725 870 2.422276 AATTTGTTTGCACTCGCTCC 57.578 45.000 0.00 0.00 39.64 4.70
726 871 2.726241 GGAAATTTGTTTGCACTCGCTC 59.274 45.455 0.00 0.00 39.64 5.03
767 912 2.683475 GGTGGGGGTGGGAATCTG 59.317 66.667 0.00 0.00 0.00 2.90
842 1008 0.690744 GGGGGTTGATGGGGAAATGG 60.691 60.000 0.00 0.00 0.00 3.16
927 1093 0.103208 ACAGGCAGGAACGATCGATC 59.897 55.000 24.34 19.93 0.00 3.69
928 1094 0.179100 CACAGGCAGGAACGATCGAT 60.179 55.000 24.34 10.66 0.00 3.59
929 1095 1.215382 CACAGGCAGGAACGATCGA 59.785 57.895 24.34 0.00 0.00 3.59
936 1102 0.251297 CCAATCACCACAGGCAGGAA 60.251 55.000 0.00 0.00 0.00 3.36
939 1105 3.281240 GCCAATCACCACAGGCAG 58.719 61.111 0.00 0.00 46.26 4.85
969 1135 2.804527 GTCCTTGTTACCTCGGTTGTTC 59.195 50.000 0.00 0.00 0.00 3.18
970 1136 2.804212 CGTCCTTGTTACCTCGGTTGTT 60.804 50.000 0.00 0.00 0.00 2.83
971 1137 1.269936 CGTCCTTGTTACCTCGGTTGT 60.270 52.381 0.00 0.00 0.00 3.32
972 1138 1.425412 CGTCCTTGTTACCTCGGTTG 58.575 55.000 0.00 0.00 0.00 3.77
973 1139 0.320160 GCGTCCTTGTTACCTCGGTT 60.320 55.000 0.00 0.00 0.00 4.44
980 1146 3.484547 CCGGCGCGTCCTTGTTAC 61.485 66.667 4.51 0.00 0.00 2.50
1005 1171 2.116125 AGCTTGGACCCCTTGCAC 59.884 61.111 0.00 0.00 0.00 4.57
1354 1520 1.954146 CGTGGTGGAGTTGGTCGTG 60.954 63.158 0.00 0.00 0.00 4.35
1413 1585 3.107447 CCGTACCCGTACCCGTAC 58.893 66.667 6.95 6.95 32.61 3.67
2070 2242 2.127232 GCCGCTCGAACAAACTGC 60.127 61.111 0.00 0.00 0.00 4.40
2124 2296 0.252197 ATTGGTAACTCCGCCTGTCC 59.748 55.000 0.00 0.00 39.52 4.02
2264 2436 8.982091 ATATCAGAGTATATATACGCCACAGT 57.018 34.615 19.36 7.54 38.28 3.55
2296 2518 2.029380 TGACACCAAGAATCGACGACAT 60.029 45.455 0.00 0.00 0.00 3.06
2366 2588 2.163412 TGAATTTGGTAATGCAGCCGTC 59.837 45.455 0.00 0.00 0.00 4.79
2389 2611 1.402456 CCAACTCTTCACCTCCGTACG 60.402 57.143 8.69 8.69 0.00 3.67
2391 2613 2.297698 TCCAACTCTTCACCTCCGTA 57.702 50.000 0.00 0.00 0.00 4.02
2393 2615 1.276421 ACATCCAACTCTTCACCTCCG 59.724 52.381 0.00 0.00 0.00 4.63
2456 2678 9.770926 CAGATATAGAGTTTCTGCAGGGTGACC 62.771 48.148 15.13 0.00 39.70 4.02
2525 2747 6.338146 TCAGGTATTACTTCAACAGAATCGG 58.662 40.000 0.00 0.00 0.00 4.18
2583 2805 2.453521 ACTCCAACATACCTACGAGCA 58.546 47.619 0.00 0.00 0.00 4.26
2584 2806 3.631227 AGTACTCCAACATACCTACGAGC 59.369 47.826 0.00 0.00 0.00 5.03
2585 2807 5.831702 AAGTACTCCAACATACCTACGAG 57.168 43.478 0.00 0.00 0.00 4.18
2586 2808 5.948162 AGAAAGTACTCCAACATACCTACGA 59.052 40.000 0.00 0.00 0.00 3.43
2587 2809 6.127814 TGAGAAAGTACTCCAACATACCTACG 60.128 42.308 0.00 0.00 36.22 3.51
2588 2810 7.166691 TGAGAAAGTACTCCAACATACCTAC 57.833 40.000 0.00 0.00 36.22 3.18
2609 2831 6.480320 GCACCCTACATATCAGTTAACTTGAG 59.520 42.308 5.07 0.00 0.00 3.02
2631 2853 4.026886 GGAGTCGAACAAAAACAATTGCAC 60.027 41.667 5.05 0.00 33.52 4.57
2708 2963 0.521291 TTGCGCAAAGATGGCACTAC 59.479 50.000 22.78 0.00 34.07 2.73
2718 2973 1.987770 GGATGTTGTCATTGCGCAAAG 59.012 47.619 28.81 23.54 34.06 2.77
2759 3014 6.598850 TCAACATTTCATCTTACTGCATAGCA 59.401 34.615 0.00 0.00 36.92 3.49
2769 3024 5.508567 TGCCAGGATCAACATTTCATCTTA 58.491 37.500 0.00 0.00 0.00 2.10
2789 3044 1.453762 GATCTCAGCCTTGCCATGCC 61.454 60.000 0.00 0.00 0.00 4.40
3040 3295 4.574828 GGTATCCGTGTGTAGCATCATTTT 59.425 41.667 0.00 0.00 0.00 1.82
3041 3296 4.127171 GGTATCCGTGTGTAGCATCATTT 58.873 43.478 0.00 0.00 0.00 2.32
3043 3298 2.965831 AGGTATCCGTGTGTAGCATCAT 59.034 45.455 0.00 0.00 0.00 2.45
3044 3299 2.384828 AGGTATCCGTGTGTAGCATCA 58.615 47.619 0.00 0.00 0.00 3.07
3045 3300 3.454371 AAGGTATCCGTGTGTAGCATC 57.546 47.619 0.00 0.00 0.00 3.91
3046 3301 3.906720 AAAGGTATCCGTGTGTAGCAT 57.093 42.857 0.00 0.00 0.00 3.79
3047 3302 3.688694 AAAAGGTATCCGTGTGTAGCA 57.311 42.857 0.00 0.00 0.00 3.49
3048 3303 5.173664 AGTAAAAAGGTATCCGTGTGTAGC 58.826 41.667 0.00 0.00 0.00 3.58
3049 3304 6.976925 CCTAGTAAAAAGGTATCCGTGTGTAG 59.023 42.308 0.00 0.00 0.00 2.74
3050 3305 6.437162 ACCTAGTAAAAAGGTATCCGTGTGTA 59.563 38.462 0.00 0.00 45.69 2.90
3051 3306 5.246883 ACCTAGTAAAAAGGTATCCGTGTGT 59.753 40.000 0.00 0.00 45.69 3.72
3052 3307 5.727434 ACCTAGTAAAAAGGTATCCGTGTG 58.273 41.667 0.00 0.00 45.69 3.82
3053 3308 6.364568 AACCTAGTAAAAAGGTATCCGTGT 57.635 37.500 0.00 0.00 46.85 4.49
3054 3309 7.101700 AGAAACCTAGTAAAAAGGTATCCGTG 58.898 38.462 0.00 0.00 46.85 4.94
3055 3310 7.250032 AGAAACCTAGTAAAAAGGTATCCGT 57.750 36.000 0.00 0.00 46.85 4.69
3056 3311 9.828039 ATAAGAAACCTAGTAAAAAGGTATCCG 57.172 33.333 0.00 0.00 46.85 4.18
3059 3314 9.969001 TGCATAAGAAACCTAGTAAAAAGGTAT 57.031 29.630 0.00 0.00 46.85 2.73
3097 3352 9.423061 AGCCAACAACATAGTTTAAATGAAATC 57.577 29.630 0.00 0.00 0.00 2.17
3150 3405 5.933617 AGTGCTGCATAAGAGATTTCCATA 58.066 37.500 5.27 0.00 0.00 2.74
3154 3409 6.917217 AACTAGTGCTGCATAAGAGATTTC 57.083 37.500 17.64 0.00 0.00 2.17
3270 3529 6.837312 TCAGACTGGAAGAGGAAAACATAAA 58.163 36.000 1.81 0.00 37.43 1.40
3273 3532 4.982241 TCAGACTGGAAGAGGAAAACAT 57.018 40.909 1.81 0.00 37.43 2.71
3349 3608 0.600057 GAGCTTCAGCACCCTTTTGG 59.400 55.000 0.75 0.00 45.16 3.28
3379 3638 2.351738 CCTGACCAAATTTTGAGTCGCC 60.352 50.000 10.72 0.00 35.18 5.54
3382 3641 4.279420 AGCTTCCTGACCAAATTTTGAGTC 59.721 41.667 10.72 14.66 33.93 3.36
3629 3888 5.874093 CGGAGGGAGTACTTCCTAATACTA 58.126 45.833 23.53 0.00 45.98 1.82
3630 3889 4.727677 CGGAGGGAGTACTTCCTAATACT 58.272 47.826 23.53 0.00 45.98 2.12
3653 3912 2.550208 CCCTCCGTCCCACAATATAAGC 60.550 54.545 0.00 0.00 0.00 3.09
3668 3927 2.761208 ACTGAGAATGTTACTCCCTCCG 59.239 50.000 0.00 0.00 33.95 4.63
3933 4208 4.326826 CTGCAAAGAGGGATTTGTCAGTA 58.673 43.478 11.81 0.00 41.31 2.74
3942 4217 2.683211 ACAAACCTGCAAAGAGGGAT 57.317 45.000 0.00 0.00 37.45 3.85
3943 4218 3.586470 TTACAAACCTGCAAAGAGGGA 57.414 42.857 0.00 0.00 37.45 4.20
3944 4219 3.888930 TCTTTACAAACCTGCAAAGAGGG 59.111 43.478 0.00 0.00 39.15 4.30
3945 4220 5.010012 ACATCTTTACAAACCTGCAAAGAGG 59.990 40.000 9.70 9.70 44.44 3.69
3953 4228 4.278170 TCTTGCCACATCTTTACAAACCTG 59.722 41.667 0.00 0.00 0.00 4.00
3962 4237 3.243975 CCAGCTTTTCTTGCCACATCTTT 60.244 43.478 0.00 0.00 0.00 2.52
4025 4300 2.483889 GGAGATGGTCGAATCCAGGTTC 60.484 54.545 0.93 0.00 41.05 3.62
4038 4313 3.234730 GATCCCGCCGGAGATGGT 61.235 66.667 5.05 0.00 43.12 3.55
4040 4315 2.341543 CTGATCCCGCCGGAGATG 59.658 66.667 5.05 0.00 43.12 2.90
4089 4364 7.063780 GCAGAAATTCACAATCCATTTAACCAG 59.936 37.037 0.00 0.00 0.00 4.00
4106 4381 4.723248 CGTTTACCCAAGAGCAGAAATTC 58.277 43.478 0.00 0.00 0.00 2.17
4127 4402 3.414700 ACGAAGCTCCTTTGCGCG 61.415 61.111 0.00 0.00 39.85 6.86
4169 4444 1.012841 GCTGATAGTTGAGGCACAGC 58.987 55.000 0.00 0.00 42.44 4.40
4247 4522 0.858583 TGTTGCAGATGACGAACACG 59.141 50.000 0.00 0.00 0.00 4.49
4253 4528 0.603707 ACCAGGTGTTGCAGATGACG 60.604 55.000 0.00 0.00 0.00 4.35
4274 4549 0.825010 AAATCCGATCCATGGCCTGC 60.825 55.000 6.96 0.00 0.00 4.85
4277 4552 2.646121 GGAAATCCGATCCATGGCC 58.354 57.895 6.96 0.00 36.92 5.36
4514 4789 3.007070 CTGGTACGTTTGCGCCGTC 62.007 63.158 13.36 6.12 42.83 4.79
4562 4837 4.021925 ACCCGGCTCAAGCTCACC 62.022 66.667 0.00 0.00 41.70 4.02
4613 4888 2.672996 TCCCGGAAAGCTTGCAGC 60.673 61.111 6.80 0.47 42.84 5.25
4707 4986 2.887152 AGCTTTGTTTGTTGGCTCTAGG 59.113 45.455 0.00 0.00 0.00 3.02
4812 5173 5.070981 ACTCAGAAGTCAGAATTTCTCCACA 59.929 40.000 0.00 0.00 29.69 4.17
4837 5198 3.372954 CAAATCTCGGTCGGCTACTAAG 58.627 50.000 0.00 0.00 0.00 2.18
4870 5245 4.333926 GCTGTTCTATTCTGATGGACCAAC 59.666 45.833 0.00 0.00 0.00 3.77
5036 5415 4.220163 TCATGCCACTATTGCACATTCAAA 59.780 37.500 0.00 0.00 42.38 2.69
5069 5448 4.501071 ACATGTACAGAACAATACGACCC 58.499 43.478 0.00 0.00 42.70 4.46
5099 5479 7.811653 TGACAATTTCAACATAATTCACGCTA 58.188 30.769 0.00 0.00 0.00 4.26
5172 5552 4.039852 TGAAAAAGCAATTACCCCAACCTC 59.960 41.667 0.00 0.00 0.00 3.85
5176 5556 8.980481 TTTTTATGAAAAAGCAATTACCCCAA 57.020 26.923 0.00 0.00 36.02 4.12
5214 5594 7.679453 TCTCCTAACCTTATTTACTAACCCACA 59.321 37.037 0.00 0.00 0.00 4.17
5341 5776 6.515272 TTTTCTGAATTTAGTGCTCATCCC 57.485 37.500 0.00 0.00 0.00 3.85
5407 5844 7.804614 TTTCTTCACAAAACATAACACACAC 57.195 32.000 0.00 0.00 0.00 3.82
5522 5964 7.596248 ACAAACATGATTGTGTCTTCTAAATGC 59.404 33.333 19.31 0.00 41.78 3.56
5539 5981 8.855110 ACATACCTGATTTTACAACAAACATGA 58.145 29.630 0.00 0.00 0.00 3.07
5586 6028 2.145536 CAAGTGCACATGCTCACAGTA 58.854 47.619 21.04 0.00 42.66 2.74
5587 6029 0.949397 CAAGTGCACATGCTCACAGT 59.051 50.000 21.04 5.04 42.66 3.55
5588 6030 0.240145 CCAAGTGCACATGCTCACAG 59.760 55.000 21.04 0.00 42.66 3.66
5590 6032 0.239347 GACCAAGTGCACATGCTCAC 59.761 55.000 21.04 9.24 42.66 3.51
5604 6053 4.442753 GCAATGTTTTTCCTCCAAGACCAA 60.443 41.667 0.00 0.00 0.00 3.67
5606 6055 3.554960 GGCAATGTTTTTCCTCCAAGACC 60.555 47.826 0.00 0.00 0.00 3.85
5608 6057 2.632512 GGGCAATGTTTTTCCTCCAAGA 59.367 45.455 0.00 0.00 0.00 3.02
5609 6058 2.289631 GGGGCAATGTTTTTCCTCCAAG 60.290 50.000 0.00 0.00 0.00 3.61
5610 6059 1.696884 GGGGCAATGTTTTTCCTCCAA 59.303 47.619 0.00 0.00 0.00 3.53
5611 6060 1.347062 GGGGCAATGTTTTTCCTCCA 58.653 50.000 0.00 0.00 0.00 3.86
5612 6061 0.613260 GGGGGCAATGTTTTTCCTCC 59.387 55.000 0.00 0.00 31.05 4.30
5613 6062 0.246360 CGGGGGCAATGTTTTTCCTC 59.754 55.000 0.00 0.00 0.00 3.71
5614 6063 0.178947 TCGGGGGCAATGTTTTTCCT 60.179 50.000 0.00 0.00 0.00 3.36
5615 6064 0.901827 ATCGGGGGCAATGTTTTTCC 59.098 50.000 0.00 0.00 0.00 3.13
5616 6065 3.383185 TGATATCGGGGGCAATGTTTTTC 59.617 43.478 0.00 0.00 0.00 2.29
5640 6089 6.650390 GGATTTGGTGCAACACTTTTGAATAT 59.350 34.615 2.40 0.00 39.98 1.28
5645 6094 3.529533 TGGATTTGGTGCAACACTTTTG 58.470 40.909 2.40 0.00 39.98 2.44
5650 6099 2.898705 TGTTTGGATTTGGTGCAACAC 58.101 42.857 2.40 0.00 37.93 3.32
5658 6107 5.664294 TCAAGGATGATGTTTGGATTTGG 57.336 39.130 0.00 0.00 0.00 3.28
5659 6108 5.579511 GCTTCAAGGATGATGTTTGGATTTG 59.420 40.000 0.00 0.00 34.96 2.32
5660 6109 5.482878 AGCTTCAAGGATGATGTTTGGATTT 59.517 36.000 0.00 0.00 34.96 2.17
5661 6110 5.021458 AGCTTCAAGGATGATGTTTGGATT 58.979 37.500 0.00 0.00 34.96 3.01


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

AutoCloner maintained by Alex Coulton.