Multiple sequence alignment - TraesCS6B01G002700

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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 TraesCS6B01G002700 chr6B 100.000 4759 0 0 1 4759 2071182 2075940 0.000000e+00 8789.0
1 TraesCS6B01G002700 chr6B 95.702 1815 66 3 2052 3857 5791410 5793221 0.000000e+00 2909.0
2 TraesCS6B01G002700 chr6B 95.789 1805 65 3 2052 3847 5794828 5796630 0.000000e+00 2902.0
3 TraesCS6B01G002700 chr6B 87.835 1529 77 42 517 2041 5789917 5791340 0.000000e+00 1692.0
4 TraesCS6B01G002700 chr6B 88.051 1498 76 39 517 2010 5793335 5794733 0.000000e+00 1679.0
5 TraesCS6B01G002700 chr6B 82.590 471 77 5 1496 1965 646745242 646744776 1.230000e-110 411.0
6 TraesCS6B01G002700 chr6B 79.724 217 35 7 2478 2690 35722429 35722218 1.070000e-31 148.0
7 TraesCS6B01G002700 chr6B 96.591 88 3 0 395 482 5793252 5793339 3.840000e-31 147.0
8 TraesCS6B01G002700 chr6D 94.753 2344 110 4 2052 4384 1489805 1492146 0.000000e+00 3635.0
9 TraesCS6B01G002700 chr6D 90.476 1113 85 9 870 1970 606360 605257 0.000000e+00 1448.0
10 TraesCS6B01G002700 chr6D 92.850 965 54 6 1045 1997 1488728 1489689 0.000000e+00 1386.0
11 TraesCS6B01G002700 chr6D 86.945 1172 146 6 2973 4141 604137 602970 0.000000e+00 1310.0
12 TraesCS6B01G002700 chr6D 89.647 821 63 15 1 819 1487879 1488679 0.000000e+00 1026.0
13 TraesCS6B01G002700 chr6D 86.329 929 101 15 1 927 1479619 1480523 0.000000e+00 989.0
14 TraesCS6B01G002700 chr6D 82.200 691 76 26 2130 2791 605077 604405 6.960000e-153 551.0
15 TraesCS6B01G002700 chr6D 82.759 377 35 13 4395 4759 1492204 1492562 4.630000e-80 309.0
16 TraesCS6B01G002700 chr6D 92.965 199 14 0 2785 2983 604367 604169 1.680000e-74 291.0
17 TraesCS6B01G002700 chr6D 86.777 242 21 9 4317 4548 527633 527393 4.720000e-65 259.0
18 TraesCS6B01G002700 chr6D 93.233 133 9 0 1 133 636036 635904 3.760000e-46 196.0
19 TraesCS6B01G002700 chr6D 96.970 33 1 0 1022 1054 1488693 1488725 6.650000e-04 56.5
20 TraesCS6B01G002700 chr2B 83.522 2027 249 52 1000 2983 755591294 755593278 0.000000e+00 1814.0
21 TraesCS6B01G002700 chr2B 86.510 1579 182 22 2991 4548 755628650 755630218 0.000000e+00 1707.0
22 TraesCS6B01G002700 chr2B 87.522 1162 137 7 2973 4130 755593310 755594467 0.000000e+00 1336.0
23 TraesCS6B01G002700 chr2B 89.868 227 18 4 4536 4759 755630236 755630460 2.170000e-73 287.0
24 TraesCS6B01G002700 chr4D 87.162 1589 122 29 263 1815 19773567 19775109 0.000000e+00 1729.0
25 TraesCS6B01G002700 chr4D 89.714 1118 82 13 877 1970 19756017 19754909 0.000000e+00 1397.0
26 TraesCS6B01G002700 chr4D 87.009 1170 149 3 2973 4141 19753338 19752171 0.000000e+00 1315.0
27 TraesCS6B01G002700 chr4D 92.844 559 40 0 2233 2791 19782493 19783051 0.000000e+00 811.0
28 TraesCS6B01G002700 chr4D 92.665 559 41 0 2233 2791 19754168 19753610 0.000000e+00 806.0
29 TraesCS6B01G002700 chr4D 92.118 203 12 1 2785 2983 19753572 19753370 2.800000e-72 283.0
30 TraesCS6B01G002700 chr4D 92.118 203 12 1 2785 2983 19783089 19783291 2.800000e-72 283.0
31 TraesCS6B01G002700 chrUn 85.897 1560 191 23 2997 4548 228625083 228626621 0.000000e+00 1635.0
32 TraesCS6B01G002700 chrUn 75.943 769 146 33 1066 1825 426377989 426377251 4.530000e-95 359.0
33 TraesCS6B01G002700 chr4A 87.650 1166 139 4 2973 4133 744537207 744536042 0.000000e+00 1351.0
34 TraesCS6B01G002700 chr4A 97.674 43 1 0 753 795 72586645 72586603 1.840000e-09 75.0
35 TraesCS6B01G002700 chr3D 79.049 988 158 39 995 1965 1655939 1656894 2.420000e-177 632.0
36 TraesCS6B01G002700 chr3A 79.571 886 147 28 1088 1968 7388969 7388113 1.890000e-168 603.0
37 TraesCS6B01G002700 chr3B 77.632 912 165 33 1066 1968 3803483 3804364 7.060000e-143 518.0
38 TraesCS6B01G002700 chr3B 77.303 912 167 34 1066 1968 4701962 4702842 7.110000e-138 501.0
39 TraesCS6B01G002700 chr6A 80.645 217 33 7 2478 2690 3328080 3327869 4.930000e-35 159.0
40 TraesCS6B01G002700 chr6A 75.598 209 34 12 2914 3108 594278615 594278820 2.360000e-13 87.9
41 TraesCS6B01G002700 chr6A 91.304 46 4 0 97 142 180925722 180925677 3.980000e-06 63.9
42 TraesCS6B01G002700 chr7B 86.567 134 16 2 2286 2419 123844449 123844318 3.840000e-31 147.0
43 TraesCS6B01G002700 chr7A 83.582 134 20 2 2286 2419 162919296 162919165 1.800000e-24 124.0
44 TraesCS6B01G002700 chr7A 81.250 96 11 4 740 828 589837524 589837619 2.380000e-08 71.3
45 TraesCS6B01G002700 chr5D 74.897 243 46 9 2878 3108 450171124 450170885 3.920000e-16 97.1
46 TraesCS6B01G002700 chr1A 92.500 40 3 0 2161 2200 285429411 285429450 1.850000e-04 58.4


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 TraesCS6B01G002700 chr6B 2071182 2075940 4758 False 8789.00 8789 100.0000 1 4759 1 chr6B.!!$F1 4758
1 TraesCS6B01G002700 chr6B 5789917 5796630 6713 False 1865.80 2909 92.7936 395 3857 5 chr6B.!!$F2 3462
2 TraesCS6B01G002700 chr6D 1487879 1492562 4683 False 1282.50 3635 91.3958 1 4759 5 chr6D.!!$F2 4758
3 TraesCS6B01G002700 chr6D 1479619 1480523 904 False 989.00 989 86.3290 1 927 1 chr6D.!!$F1 926
4 TraesCS6B01G002700 chr6D 602970 606360 3390 True 900.00 1448 88.1465 870 4141 4 chr6D.!!$R3 3271
5 TraesCS6B01G002700 chr2B 755591294 755594467 3173 False 1575.00 1814 85.5220 1000 4130 2 chr2B.!!$F1 3130
6 TraesCS6B01G002700 chr2B 755628650 755630460 1810 False 997.00 1707 88.1890 2991 4759 2 chr2B.!!$F2 1768
7 TraesCS6B01G002700 chr4D 19773567 19775109 1542 False 1729.00 1729 87.1620 263 1815 1 chr4D.!!$F1 1552
8 TraesCS6B01G002700 chr4D 19752171 19756017 3846 True 950.25 1397 90.3765 877 4141 4 chr4D.!!$R1 3264
9 TraesCS6B01G002700 chr4D 19782493 19783291 798 False 547.00 811 92.4810 2233 2983 2 chr4D.!!$F2 750
10 TraesCS6B01G002700 chrUn 228625083 228626621 1538 False 1635.00 1635 85.8970 2997 4548 1 chrUn.!!$F1 1551
11 TraesCS6B01G002700 chrUn 426377251 426377989 738 True 359.00 359 75.9430 1066 1825 1 chrUn.!!$R1 759
12 TraesCS6B01G002700 chr4A 744536042 744537207 1165 True 1351.00 1351 87.6500 2973 4133 1 chr4A.!!$R2 1160
13 TraesCS6B01G002700 chr3D 1655939 1656894 955 False 632.00 632 79.0490 995 1965 1 chr3D.!!$F1 970
14 TraesCS6B01G002700 chr3A 7388113 7388969 856 True 603.00 603 79.5710 1088 1968 1 chr3A.!!$R1 880
15 TraesCS6B01G002700 chr3B 3803483 3804364 881 False 518.00 518 77.6320 1066 1968 1 chr3B.!!$F1 902
16 TraesCS6B01G002700 chr3B 4701962 4702842 880 False 501.00 501 77.3030 1066 1968 1 chr3B.!!$F2 902

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
521 541 0.236711 CTTGCGTCCTTTGTCTGCTG 59.763 55.000 0.00 0.0 0.00 4.41 F
1158 1219 0.463620 TCGGCATCGTCCATTCATCA 59.536 50.000 0.00 0.0 37.69 3.07 F
1672 1778 0.247736 GGAGATCCACAACGTCAGCT 59.752 55.000 0.00 0.0 35.64 4.24 F
2574 6686 2.032681 GCGGGGTCTGCAGAAACT 59.967 61.111 20.19 0.0 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1485 1582 0.246910 TGTACTTGCCGCCGTAATCA 59.753 50.000 0.00 0.0 0.00 2.57 R
2574 6686 1.003442 AGTCATAGCCTCCCAGCCA 59.997 57.895 0.00 0.0 0.00 4.75 R
3569 7771 0.807496 GTGCATCCAAGTTGAGAGCC 59.193 55.000 3.87 0.0 0.00 4.70 R
4516 8771 0.112995 TTCCTGAATGTGCCAAGGCT 59.887 50.000 12.96 0.0 42.51 4.58 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
41 42 2.563179 TCTCTCTACACTGCCTTGGTTC 59.437 50.000 0.00 0.00 0.00 3.62
86 87 0.469144 TCAGGGTCTTTGTTTGCCCC 60.469 55.000 0.00 0.00 41.99 5.80
88 89 0.469892 AGGGTCTTTGTTTGCCCCAG 60.470 55.000 0.00 0.00 41.99 4.45
126 127 7.917003 TCCTTCCGATCCATATTAATTGATGA 58.083 34.615 0.00 0.00 0.00 2.92
189 190 5.168569 GCGTCAATAAATATGGATCGGAGA 58.831 41.667 0.00 0.00 45.75 3.71
219 220 3.613877 TTTGCGGCGGCCATGTAGA 62.614 57.895 20.71 0.00 38.85 2.59
221 222 2.591715 GCGGCGGCCATGTAGAAT 60.592 61.111 20.71 0.00 0.00 2.40
368 369 5.360714 ACTGTTCATTGTCACACTCCAAAAT 59.639 36.000 0.00 0.00 0.00 1.82
370 371 6.041511 TGTTCATTGTCACACTCCAAAATTG 58.958 36.000 0.00 0.00 0.00 2.32
470 480 1.441738 CAACATCGGTGCATGAGTGA 58.558 50.000 0.00 0.00 0.00 3.41
521 541 0.236711 CTTGCGTCCTTTGTCTGCTG 59.763 55.000 0.00 0.00 0.00 4.41
699 721 0.980423 GCCAAGAGGGTGTTCTCTCT 59.020 55.000 0.00 0.00 42.75 3.10
704 727 3.760580 AGAGGGTGTTCTCTCTTGTTG 57.239 47.619 0.00 0.00 39.75 3.33
767 791 8.215050 TGATTCAAAACTACTCCCTCTGTAAAA 58.785 33.333 0.00 0.00 0.00 1.52
827 853 5.887035 ACTAAGGTAGTGATCTAAACGCTCT 59.113 40.000 0.00 0.00 37.69 4.09
828 854 4.904253 AGGTAGTGATCTAAACGCTCTC 57.096 45.455 0.00 0.00 0.00 3.20
829 855 3.312973 AGGTAGTGATCTAAACGCTCTCG 59.687 47.826 0.00 0.00 42.43 4.04
830 856 2.196295 AGTGATCTAAACGCTCTCGC 57.804 50.000 0.00 0.00 39.84 5.03
839 866 2.882742 AACGCTCTCGCAATTTCTTC 57.117 45.000 0.00 0.00 39.84 2.87
867 894 6.956435 TGAGGGAGTAGTTATCATGAGCATAT 59.044 38.462 0.09 0.00 0.00 1.78
885 912 5.474532 AGCATATATACACCCGAACGTTCTA 59.525 40.000 24.80 11.21 0.00 2.10
886 913 6.152323 AGCATATATACACCCGAACGTTCTAT 59.848 38.462 24.80 16.92 0.00 1.98
931 958 2.119484 TAAAGCCACCCAGACCACGG 62.119 60.000 0.00 0.00 0.00 4.94
1013 1044 1.656818 CCATCCATGCCGTTCCACAC 61.657 60.000 0.00 0.00 0.00 3.82
1119 1168 1.015607 GCCAAAGAAAATGCGGCAGG 61.016 55.000 9.25 2.34 42.50 4.85
1156 1217 1.875514 CATTCGGCATCGTCCATTCAT 59.124 47.619 0.00 0.00 37.69 2.57
1157 1218 1.581934 TTCGGCATCGTCCATTCATC 58.418 50.000 0.00 0.00 37.69 2.92
1158 1219 0.463620 TCGGCATCGTCCATTCATCA 59.536 50.000 0.00 0.00 37.69 3.07
1171 1244 1.239296 TTCATCACCCGACGACGACT 61.239 55.000 9.28 0.00 42.66 4.18
1217 1293 1.301716 GCCTGACCTGCAACGAGAA 60.302 57.895 0.00 0.00 0.00 2.87
1544 1650 2.797278 GCCGGGGAGACGATGTGAT 61.797 63.158 2.18 0.00 35.47 3.06
1617 1723 3.099170 CCCAGGGGGCTGCAGTAT 61.099 66.667 16.64 0.00 35.35 2.12
1672 1778 0.247736 GGAGATCCACAACGTCAGCT 59.752 55.000 0.00 0.00 35.64 4.24
1857 1963 3.244105 GCGTGTGTCAGCGACAAT 58.756 55.556 11.92 0.00 44.49 2.71
2010 5534 4.617253 TCCACATGGTAATCCTTATCCG 57.383 45.455 0.00 0.00 36.34 4.18
2016 5540 2.371841 TGGTAATCCTTATCCGCATGCT 59.628 45.455 17.13 0.00 34.23 3.79
2049 5573 9.327628 CATGCATGTTCCATAATTAATCCAAAA 57.672 29.630 18.91 0.00 0.00 2.44
2050 5574 9.902684 ATGCATGTTCCATAATTAATCCAAAAA 57.097 25.926 0.00 0.00 0.00 1.94
2101 5848 7.870509 TCATTAGCAAGCAAGATTAACTGAT 57.129 32.000 0.00 0.00 0.00 2.90
2165 5918 9.807649 AATATGATGCACTTCCTTTAATGTTTC 57.192 29.630 0.00 0.00 0.00 2.78
2221 5974 8.784043 GTTCTACGCTATTTTCCCATTAATCAT 58.216 33.333 0.00 0.00 0.00 2.45
2265 6334 5.578336 ACAACAAGAAAAGAAAGAGCAAAGC 59.422 36.000 0.00 0.00 0.00 3.51
2388 6476 7.469181 GCACTAATCCATCCTTTCAAGGTATTG 60.469 40.741 5.48 3.02 46.54 1.90
2429 6517 2.621055 TGTGTTCCAACGCTTGCTTTAT 59.379 40.909 4.71 0.00 40.01 1.40
2474 6586 6.627395 AAACGTGTTGGAGAAATTGTCATA 57.373 33.333 0.00 0.00 0.00 2.15
2574 6686 2.032681 GCGGGGTCTGCAGAAACT 59.967 61.111 20.19 0.00 0.00 2.66
2667 6779 3.264193 TCATTTCCCTCTAGCAGCAAAGA 59.736 43.478 0.00 0.00 0.00 2.52
2745 6857 7.770433 AGCTCATAGTGCAATGAACATTAGTAA 59.230 33.333 0.00 0.00 35.51 2.24
2856 7012 6.095860 CAGGACATATGATTGCTTCAAAGGAA 59.904 38.462 10.38 0.00 40.68 3.36
2859 7015 7.437267 GGACATATGATTGCTTCAAAGGAATTG 59.563 37.037 10.38 7.58 45.40 2.32
2978 7138 9.807921 TTCCTTGAAGTTGTTCTAAGGATTTAT 57.192 29.630 14.42 0.00 42.82 1.40
3151 7353 4.947388 TCTAGGTACAATTGTTGGCATTCC 59.053 41.667 17.78 8.20 34.12 3.01
3170 7372 7.611467 GGCATTCCTATCATGGTGATTATAACA 59.389 37.037 0.00 0.00 38.26 2.41
3206 7408 7.553881 TCTTCACAACGAGAAAAAGAAGATT 57.446 32.000 0.00 0.00 36.18 2.40
3305 7507 9.750125 GACCTCAAGTCATTTCTAAACAAAAAT 57.250 29.630 0.00 0.00 45.55 1.82
3557 7759 5.184479 CCTCCATGACATTCTTCACAACAAT 59.816 40.000 0.00 0.00 0.00 2.71
3569 7771 9.912634 ATTCTTCACAACAATAATAACAAGGTG 57.087 29.630 0.00 0.00 0.00 4.00
3737 7940 6.874288 ATTTCAGACTTTGGCATATCTAGC 57.126 37.500 0.00 0.00 0.00 3.42
3756 7959 2.101917 AGCTTGCTTGCAACAGACAAAT 59.898 40.909 3.70 0.00 34.99 2.32
3761 7964 5.199024 TGCTTGCAACAGACAAATAACAT 57.801 34.783 0.00 0.00 0.00 2.71
3827 8030 2.753452 TCTACAAGAAGGCCTACTCACG 59.247 50.000 5.16 0.00 0.00 4.35
3863 8066 4.386049 GTCTACAGTTTCGGAGTTGTGATG 59.614 45.833 2.61 0.00 0.00 3.07
3894 8097 2.422939 TAGCAGGAGGAAGGCCATAT 57.577 50.000 5.01 0.00 36.29 1.78
3954 8157 4.336280 AGCCCATAAGGAACAGAAGAAAC 58.664 43.478 0.00 0.00 38.24 2.78
3989 8192 3.058450 TGACAAGGAAATTGCAATTGCG 58.942 40.909 24.74 12.86 45.83 4.85
4016 8219 9.248291 GAAGATTTAGAGCTTCTTGATAGTCTG 57.752 37.037 4.13 0.00 43.30 3.51
4025 8228 5.686124 GCTTCTTGATAGTCTGGCAGGTATT 60.686 44.000 15.73 0.55 0.00 1.89
4089 8292 1.342374 TGATGGAGGTAGCTGAGCAGA 60.342 52.381 7.39 0.00 0.00 4.26
4100 8303 3.594134 AGCTGAGCAGATACACAAACTC 58.406 45.455 7.39 0.00 0.00 3.01
4163 8367 4.469586 ACATTTGACAAAACCCTCCTTTGT 59.530 37.500 4.41 0.79 46.89 2.83
4171 8375 0.549469 ACCCTCCTTTGTTTCCGTGT 59.451 50.000 0.00 0.00 0.00 4.49
4173 8377 2.224450 ACCCTCCTTTGTTTCCGTGTAG 60.224 50.000 0.00 0.00 0.00 2.74
4177 8382 4.577283 CCTCCTTTGTTTCCGTGTAGAAAA 59.423 41.667 0.00 0.00 37.49 2.29
4180 8385 4.679654 CCTTTGTTTCCGTGTAGAAAATGC 59.320 41.667 0.00 0.00 37.49 3.56
4185 8390 5.527951 TGTTTCCGTGTAGAAAATGCAACTA 59.472 36.000 0.00 0.00 37.49 2.24
4188 8393 5.242434 TCCGTGTAGAAAATGCAACTATGT 58.758 37.500 0.00 0.00 0.00 2.29
4198 8403 7.604927 AGAAAATGCAACTATGTTTCTACGGTA 59.395 33.333 0.00 0.00 0.00 4.02
4241 8446 8.925161 TGCATTTGTAATTATGTTTCTAAGGC 57.075 30.769 0.00 0.00 0.00 4.35
4259 8466 5.796350 AAGGCTTTGTAACGATATGTCAC 57.204 39.130 0.00 0.00 0.00 3.67
4394 8613 2.542907 AAACTTGTGGTCCAGCGCG 61.543 57.895 0.00 0.00 0.00 6.86
4397 8616 4.980805 TTGTGGTCCAGCGCGGTC 62.981 66.667 8.38 11.38 35.57 4.79
4497 8752 3.134458 AGTTGAAGTGCAGTAGCTTGAC 58.866 45.455 0.00 0.00 42.74 3.18
4500 8755 2.295070 TGAAGTGCAGTAGCTTGACGTA 59.705 45.455 0.00 0.00 42.74 3.57
4515 8770 2.101249 TGACGTAAAGACTTGGGTCGTT 59.899 45.455 0.00 0.00 46.29 3.85
4516 8771 3.317711 TGACGTAAAGACTTGGGTCGTTA 59.682 43.478 0.00 0.00 46.29 3.18
4518 8773 2.665052 CGTAAAGACTTGGGTCGTTAGC 59.335 50.000 5.17 0.00 43.26 3.09
4529 8784 1.165270 GTCGTTAGCCTTGGCACATT 58.835 50.000 14.54 0.00 39.30 2.71
4533 8788 1.474077 GTTAGCCTTGGCACATTCAGG 59.526 52.381 14.54 0.00 39.30 3.86
4548 8836 2.620251 TCAGGAACACCACTTCACTG 57.380 50.000 0.00 0.00 0.00 3.66
4558 8846 0.533531 CACTTCACTGGTGCTGCAGA 60.534 55.000 20.43 0.00 0.00 4.26
4627 8924 5.711506 TCCTCGAAATACAACCACTGTACTA 59.288 40.000 0.00 0.00 43.35 1.82
4629 8926 6.127814 CCTCGAAATACAACCACTGTACTAGA 60.128 42.308 0.00 0.00 43.35 2.43
4647 8944 1.141053 AGAACTTGACTTGGCCTCGTT 59.859 47.619 3.32 0.00 0.00 3.85
4650 8947 1.072331 ACTTGACTTGGCCTCGTTGAT 59.928 47.619 3.32 0.00 0.00 2.57
4718 9016 0.109532 TTTTGCCGACATGGAGACCA 59.890 50.000 0.00 0.00 42.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 9.981460 AAAGAGGGCTAAATATTATCCATTAGG 57.019 33.333 0.00 0.00 0.00 2.69
88 89 4.516365 TCGGAAGGAGTACAGAGTTTTC 57.484 45.455 0.00 0.00 0.00 2.29
164 165 4.929211 TCCGATCCATATTTATTGACGCAG 59.071 41.667 0.00 0.00 0.00 5.18
174 175 4.963318 TTGCTCTCTCCGATCCATATTT 57.037 40.909 0.00 0.00 0.00 1.40
219 220 3.007635 CGGAAAGCGTTTAGGAGGAATT 58.992 45.455 0.00 0.00 0.00 2.17
221 222 1.338389 CCGGAAAGCGTTTAGGAGGAA 60.338 52.381 0.00 0.00 0.00 3.36
521 541 8.495949 CGAACCACCAAACTACAATGATATATC 58.504 37.037 5.73 5.73 0.00 1.63
656 678 1.284982 GCATCGAGTGACGCACAACT 61.285 55.000 11.58 0.00 42.26 3.16
679 701 0.687354 GAGAGAACACCCTCTTGGCA 59.313 55.000 0.00 0.00 43.11 4.92
739 763 6.784031 ACAGAGGGAGTAGTTTTGAATCATT 58.216 36.000 0.00 0.00 0.00 2.57
740 764 6.380079 ACAGAGGGAGTAGTTTTGAATCAT 57.620 37.500 0.00 0.00 0.00 2.45
741 765 5.825593 ACAGAGGGAGTAGTTTTGAATCA 57.174 39.130 0.00 0.00 0.00 2.57
745 769 7.369551 TCTTTTACAGAGGGAGTAGTTTTGA 57.630 36.000 0.00 0.00 0.00 2.69
767 791 8.611051 AGTGGTCTAAACACTCCTATATTTCT 57.389 34.615 0.00 0.00 45.50 2.52
776 800 7.224522 TCTAAACTAGTGGTCTAAACACTCC 57.775 40.000 0.00 0.00 45.50 3.85
827 853 2.038426 TCCCTCAGTGAAGAAATTGCGA 59.962 45.455 0.00 0.00 0.00 5.10
828 854 2.417933 CTCCCTCAGTGAAGAAATTGCG 59.582 50.000 0.00 0.00 0.00 4.85
829 855 3.416156 ACTCCCTCAGTGAAGAAATTGC 58.584 45.455 0.00 0.00 32.26 3.56
830 856 5.799213 ACTACTCCCTCAGTGAAGAAATTG 58.201 41.667 0.00 0.00 36.43 2.32
839 866 5.508825 GCTCATGATAACTACTCCCTCAGTG 60.509 48.000 0.00 0.00 36.43 3.66
867 894 3.876914 ACGATAGAACGTTCGGGTGTATA 59.123 43.478 21.87 8.02 44.14 1.47
1013 1044 4.392921 ACTACAGGTACAGCAGCTAATG 57.607 45.455 0.00 0.00 32.37 1.90
1119 1168 3.244112 CGAATGGGTAAGGGATGTCTACC 60.244 52.174 0.00 0.00 0.00 3.18
1156 1217 2.382746 CGTAGTCGTCGTCGGGTGA 61.383 63.158 1.55 0.00 37.69 4.02
1157 1218 2.097160 CGTAGTCGTCGTCGGGTG 59.903 66.667 1.55 0.00 37.69 4.61
1158 1219 3.121030 CCGTAGTCGTCGTCGGGT 61.121 66.667 1.55 0.00 39.41 5.28
1217 1293 2.755469 GGCCACCATCAATGCCGT 60.755 61.111 0.00 0.00 33.59 5.68
1485 1582 0.246910 TGTACTTGCCGCCGTAATCA 59.753 50.000 0.00 0.00 0.00 2.57
1544 1650 2.338620 CGTTGCTCAGGGTCGACA 59.661 61.111 18.91 0.00 0.00 4.35
1617 1723 1.267806 GAGTCGAACTCCACGTGGTAA 59.732 52.381 32.74 15.11 39.28 2.85
1803 1909 3.254654 CGGGCTACGTCGCATGTG 61.255 66.667 14.50 0.00 37.93 3.21
2257 6326 6.074142 CCAACTTTCACTTTATTGCTTTGCTC 60.074 38.462 0.00 0.00 0.00 4.26
2265 6334 5.452078 TGAGCCCAACTTTCACTTTATTG 57.548 39.130 0.00 0.00 0.00 1.90
2388 6476 7.412137 ACACAGAATAAAAGCAAAGCATTTC 57.588 32.000 0.00 0.00 35.03 2.17
2429 6517 9.146984 CGTTTTCAACTACCATTTCATCTAGTA 57.853 33.333 0.00 0.00 0.00 1.82
2474 6586 5.305902 ACTTGGGGATTTTAACGAATTGGTT 59.694 36.000 10.80 10.80 0.00 3.67
2574 6686 1.003442 AGTCATAGCCTCCCAGCCA 59.997 57.895 0.00 0.00 0.00 4.75
2667 6779 8.260818 TGTAGTAGAGTACTTACCGACTACAAT 58.739 37.037 22.53 8.11 39.45 2.71
2745 6857 2.116983 ATCTCACCCAGCGTGCTGTT 62.117 55.000 19.58 4.40 42.69 3.16
3025 7227 8.621532 AATAGTTTCTTTTGCTCATGTACTCA 57.378 30.769 0.00 0.00 0.00 3.41
3170 7372 8.378172 TCTCGTTGTGAAGAATAACAAGAAAT 57.622 30.769 0.00 0.00 36.98 2.17
3191 7393 7.303998 AGAATTCTGCAATCTTCTTTTTCTCG 58.696 34.615 7.30 0.00 0.00 4.04
3305 7507 7.659390 CCAAAGGAACCATTTGCAATTAAGTTA 59.341 33.333 0.00 0.00 36.52 2.24
3557 7759 5.499004 AGTTGAGAGCCACCTTGTTATTA 57.501 39.130 0.00 0.00 0.00 0.98
3569 7771 0.807496 GTGCATCCAAGTTGAGAGCC 59.193 55.000 3.87 0.00 0.00 4.70
3737 7940 5.042593 TGTTATTTGTCTGTTGCAAGCAAG 58.957 37.500 7.88 0.00 36.52 4.01
3756 7959 4.452114 GCCGATGATTGATGCAGTATGTTA 59.548 41.667 0.00 0.00 39.31 2.41
3761 7964 1.068434 TCGCCGATGATTGATGCAGTA 59.932 47.619 0.00 0.00 0.00 2.74
3908 8111 4.338118 TCAAGGAAACACTTTACCAAGCTG 59.662 41.667 0.00 0.00 32.57 4.24
3989 8192 8.421002 AGACTATCAAGAAGCTCTAAATCTTCC 58.579 37.037 0.00 0.00 39.48 3.46
4025 8228 2.699768 GCTAAGGCATTGCACGGCA 61.700 57.895 11.39 0.00 38.54 5.69
4089 8292 4.156190 ACGAGATCGACTGAGTTTGTGTAT 59.844 41.667 9.58 0.00 43.02 2.29
4100 8303 4.331992 TCTTACACCTTACGAGATCGACTG 59.668 45.833 9.58 0.00 43.02 3.51
4163 8367 6.205853 ACATAGTTGCATTTTCTACACGGAAA 59.794 34.615 0.00 0.00 33.98 3.13
4171 8375 7.604927 ACCGTAGAAACATAGTTGCATTTTCTA 59.395 33.333 0.00 0.00 37.60 2.10
4173 8377 6.608610 ACCGTAGAAACATAGTTGCATTTTC 58.391 36.000 0.00 0.00 0.00 2.29
4177 8382 4.809426 GCTACCGTAGAAACATAGTTGCAT 59.191 41.667 9.88 0.00 0.00 3.96
4180 8385 3.795101 CGGCTACCGTAGAAACATAGTTG 59.205 47.826 9.88 0.00 42.73 3.16
4206 8411 0.251297 TACAAATGCAGCCTGCCAGT 60.251 50.000 15.29 9.66 44.23 4.00
4209 8414 2.678471 AATTACAAATGCAGCCTGCC 57.322 45.000 15.29 0.00 44.23 4.85
4229 8434 8.612619 CATATCGTTACAAAGCCTTAGAAACAT 58.387 33.333 0.00 0.00 0.00 2.71
4241 8446 5.348724 AGTGCTGTGACATATCGTTACAAAG 59.651 40.000 0.00 0.00 42.92 2.77
4250 8455 8.122952 GGTAAAAATGTAGTGCTGTGACATATC 58.877 37.037 0.00 0.00 33.48 1.63
4324 8531 8.049117 TGGATCTGTTTCTTGCACTCTATTTAT 58.951 33.333 0.00 0.00 0.00 1.40
4394 8613 3.055094 TCTTGATTAGACAAGGCCTGACC 60.055 47.826 5.69 0.00 44.84 4.02
4397 8616 4.478206 TCTCTTGATTAGACAAGGCCTG 57.522 45.455 5.69 2.82 44.84 4.85
4398 8617 4.685575 GCATCTCTTGATTAGACAAGGCCT 60.686 45.833 0.00 0.00 44.84 5.19
4399 8618 3.563390 GCATCTCTTGATTAGACAAGGCC 59.437 47.826 0.00 0.00 44.84 5.19
4400 8619 4.272991 CAGCATCTCTTGATTAGACAAGGC 59.727 45.833 0.00 0.00 44.84 4.35
4497 8752 2.665052 GCTAACGACCCAAGTCTTTACG 59.335 50.000 0.00 0.00 41.16 3.18
4500 8755 1.697982 AGGCTAACGACCCAAGTCTTT 59.302 47.619 0.00 0.00 41.16 2.52
4515 8770 0.991146 TCCTGAATGTGCCAAGGCTA 59.009 50.000 12.96 1.85 42.51 3.93
4516 8771 0.112995 TTCCTGAATGTGCCAAGGCT 59.887 50.000 12.96 0.00 42.51 4.58
4518 8773 1.270550 GTGTTCCTGAATGTGCCAAGG 59.729 52.381 0.00 0.00 0.00 3.61
4529 8784 1.140852 CCAGTGAAGTGGTGTTCCTGA 59.859 52.381 0.00 0.00 31.51 3.86
4548 8836 2.730672 CGCGTAACTCTGCAGCACC 61.731 63.158 9.47 0.00 0.00 5.01
4558 8846 0.892358 TGGAGGACACTCGCGTAACT 60.892 55.000 5.77 0.00 44.93 2.24
4576 8872 2.292569 GCAGGTGCATGAATGGTATCTG 59.707 50.000 0.00 0.00 41.59 2.90
4627 8924 0.759346 ACGAGGCCAAGTCAAGTTCT 59.241 50.000 5.01 0.00 0.00 3.01
4629 8926 1.134220 TCAACGAGGCCAAGTCAAGTT 60.134 47.619 5.01 0.00 0.00 2.66
4647 8944 4.951715 AGTTGCTTAATGAAGATGCCATCA 59.048 37.500 7.56 0.00 34.25 3.07
4650 8947 4.523943 ACAAGTTGCTTAATGAAGATGCCA 59.476 37.500 1.81 0.00 34.25 4.92
4718 9016 1.945394 GATGCGCAAAGACCATCTCAT 59.055 47.619 17.11 0.00 34.12 2.90
4724 9022 0.036732 AGGAAGATGCGCAAAGACCA 59.963 50.000 17.11 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.