Multiple sequence alignment - TraesCS4D01G333000

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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 TraesCS4D01G333000 chr4D 100.000 3525 0 0 1 3525 490374757 490378281 0.000000e+00 6510.0
1 TraesCS4D01G333000 chr4D 90.546 952 57 13 1898 2844 490412201 490411278 0.000000e+00 1229.0
2 TraesCS4D01G333000 chr4D 86.476 525 37 8 1213 1719 490412781 490412273 2.390000e-151 545.0
3 TraesCS4D01G333000 chr4D 83.694 509 50 21 3039 3525 490411247 490410750 1.930000e-122 449.0
4 TraesCS4D01G333000 chr4D 79.742 543 84 17 3004 3525 490403222 490402685 1.550000e-98 370.0
5 TraesCS4D01G333000 chr4D 80.046 436 70 5 1213 1647 490404599 490404180 1.230000e-79 307.0
6 TraesCS4D01G333000 chr5A 96.533 2336 54 7 1213 3525 671955409 671957740 0.000000e+00 3840.0
7 TraesCS4D01G333000 chr5A 93.158 950 43 8 1 946 671952728 671953659 0.000000e+00 1375.0
8 TraesCS4D01G333000 chr5A 90.710 732 42 9 2113 2844 671988868 671988163 0.000000e+00 952.0
9 TraesCS4D01G333000 chr5A 90.974 698 33 9 255 948 675732128 675732799 0.000000e+00 913.0
10 TraesCS4D01G333000 chr5A 86.667 525 36 8 1213 1719 671989632 671989124 5.140000e-153 551.0
11 TraesCS4D01G333000 chr5A 83.465 508 52 19 3039 3525 671988129 671987633 8.980000e-121 444.0
12 TraesCS4D01G333000 chr5A 80.325 554 75 23 2997 3525 671976682 671976138 4.270000e-104 388.0
13 TraesCS4D01G333000 chr5A 96.711 152 4 1 1070 1220 671953953 671954104 5.840000e-63 252.0
14 TraesCS4D01G333000 chr5A 96.711 152 4 1 1070 1220 675733091 675733242 5.840000e-63 252.0
15 TraesCS4D01G333000 chr5A 91.011 178 16 0 1898 2075 671989052 671988875 1.260000e-59 241.0
16 TraesCS4D01G333000 chr5A 98.507 67 1 0 939 1005 671953841 671953907 6.180000e-23 119.0
17 TraesCS4D01G333000 chr5A 97.015 67 2 0 939 1005 675732979 675733045 2.880000e-21 113.0
18 TraesCS4D01G333000 chr4B 90.605 958 65 14 1898 2844 630043148 630042205 0.000000e+00 1247.0
19 TraesCS4D01G333000 chr4B 83.992 531 36 9 1213 1719 630043725 630043220 6.890000e-127 464.0
20 TraesCS4D01G333000 chr4B 84.458 489 49 15 3039 3507 630042106 630041625 1.150000e-124 457.0
21 TraesCS4D01G333000 chr4B 80.183 545 80 14 3004 3525 630013818 630013279 1.990000e-102 383.0
22 TraesCS4D01G333000 chr4B 80.275 436 69 11 1213 1647 630015206 630014787 2.640000e-81 313.0
23 TraesCS4D01G333000 chr5B 77.181 986 143 46 1915 2884 505777999 505777080 1.890000e-137 499.0
24 TraesCS4D01G333000 chr6B 93.388 242 15 1 1669 1910 482764708 482764948 1.200000e-94 357.0
25 TraesCS4D01G333000 chr6B 90.541 74 4 1 1436 1506 8423878 8423951 1.040000e-15 95.3
26 TraesCS4D01G333000 chrUn 91.228 114 9 1 1768 1881 71401253 71401365 1.690000e-33 154.0
27 TraesCS4D01G333000 chrUn 91.228 114 9 1 1768 1881 71495972 71496084 1.690000e-33 154.0
28 TraesCS4D01G333000 chrUn 91.228 114 9 1 1768 1881 71557296 71557408 1.690000e-33 154.0
29 TraesCS4D01G333000 chr3B 89.474 114 11 1 1768 1881 792802373 792802485 3.670000e-30 143.0
30 TraesCS4D01G333000 chr2D 81.457 151 26 2 268 417 410176669 410176818 4.780000e-24 122.0
31 TraesCS4D01G333000 chr7D 94.737 76 4 0 1819 1894 632329384 632329309 6.180000e-23 119.0
32 TraesCS4D01G333000 chr2A 94.444 72 4 0 1810 1881 177669044 177669115 1.030000e-20 111.0
33 TraesCS4D01G333000 chr4A 89.412 85 7 2 1810 1893 665186827 665186744 4.810000e-19 106.0
34 TraesCS4D01G333000 chr6D 87.500 80 7 1 1436 1512 4266596 4266517 4.850000e-14 89.8
35 TraesCS4D01G333000 chr6A 89.189 74 5 1 1436 1506 3001744 3001817 4.850000e-14 89.8


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 TraesCS4D01G333000 chr4D 490374757 490378281 3524 False 6510.000000 6510 100.000000 1 3525 1 chr4D.!!$F1 3524
1 TraesCS4D01G333000 chr4D 490410750 490412781 2031 True 741.000000 1229 86.905333 1213 3525 3 chr4D.!!$R2 2312
2 TraesCS4D01G333000 chr4D 490402685 490404599 1914 True 338.500000 370 79.894000 1213 3525 2 chr4D.!!$R1 2312
3 TraesCS4D01G333000 chr5A 671952728 671957740 5012 False 1396.500000 3840 96.227250 1 3525 4 chr5A.!!$F1 3524
4 TraesCS4D01G333000 chr5A 671987633 671989632 1999 True 547.000000 952 87.963250 1213 3525 4 chr5A.!!$R2 2312
5 TraesCS4D01G333000 chr5A 675732128 675733242 1114 False 426.000000 913 94.900000 255 1220 3 chr5A.!!$F2 965
6 TraesCS4D01G333000 chr5A 671976138 671976682 544 True 388.000000 388 80.325000 2997 3525 1 chr5A.!!$R1 528
7 TraesCS4D01G333000 chr4B 630041625 630043725 2100 True 722.666667 1247 86.351667 1213 3507 3 chr4B.!!$R2 2294
8 TraesCS4D01G333000 chr4B 630013279 630015206 1927 True 348.000000 383 80.229000 1213 3525 2 chr4B.!!$R1 2312
9 TraesCS4D01G333000 chr5B 505777080 505777999 919 True 499.000000 499 77.181000 1915 2884 1 chr5B.!!$R1 969

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
279 280 0.326238 GGGGAGGTGATGGTGTCCTA 60.326 60.0 0.00 0.0 0.00 2.94 F
1003 1213 0.032815 CCAATCCCGGCAAACGTTTT 59.967 50.0 11.66 0.0 42.24 2.43 F
1348 2877 0.539986 TTTACATGGAGCTCCCGACC 59.460 55.0 29.95 5.8 37.93 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1241 2764 0.543749 GGCACCTCCAGACATAAGCT 59.456 55.000 0.00 0.0 34.01 3.74 R
1850 3410 1.139095 GTTCTGGGGTAGCGACTCG 59.861 63.158 0.00 0.0 0.00 4.18 R
3114 4794 2.167075 GCATCTGAATTCCCCAAAGTGG 59.833 50.000 2.27 0.0 37.25 4.00 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
46 47 0.605589 CAAGAGTCGCCAGAGGAAGT 59.394 55.000 0.00 0.00 0.00 3.01
68 69 0.834687 TAGAAGAACACAGCGGGGGT 60.835 55.000 0.00 0.00 0.00 4.95
102 103 2.390599 CGACGTCCATTGCCACCAG 61.391 63.158 10.58 0.00 0.00 4.00
184 185 1.001641 GCCCTTGCATGAGGTCACT 60.002 57.895 0.00 0.00 37.47 3.41
240 241 3.771160 ATCGGCCTGGTCGTGGAC 61.771 66.667 21.33 0.00 30.45 4.02
249 250 4.115270 GTCGTGGACCTTCCTCCT 57.885 61.111 0.00 0.00 37.46 3.69
279 280 0.326238 GGGGAGGTGATGGTGTCCTA 60.326 60.000 0.00 0.00 0.00 2.94
298 299 3.254657 CCTAGCTAGGAATTCTCTCACCG 59.745 52.174 32.79 1.75 46.63 4.94
299 300 2.741145 AGCTAGGAATTCTCTCACCGT 58.259 47.619 5.23 0.00 0.00 4.83
305 306 2.251893 GAATTCTCTCACCGTGTCGTC 58.748 52.381 0.00 0.00 0.00 4.20
342 343 3.399181 GCCGAGGACCCCATGTCA 61.399 66.667 0.00 0.00 46.38 3.58
351 352 2.618053 GACCCCATGTCAGTTAACGAG 58.382 52.381 0.00 0.00 43.85 4.18
408 409 1.722034 AGGCTCCTGAAGTCTTGTCA 58.278 50.000 0.00 0.00 36.13 3.58
423 424 5.887035 AGTCTTGTCATGTACTCCTAGGTAC 59.113 44.000 9.08 5.63 41.51 3.34
425 426 4.596354 TGTCATGTACTCCTAGGTACCA 57.404 45.455 15.94 2.26 40.72 3.25
447 448 3.320673 AATCGTCAAGGACTTGGTCTC 57.679 47.619 11.76 1.26 40.78 3.36
477 478 6.304922 CACGTAGCCGACTATGATGTTATAAC 59.695 42.308 8.75 8.75 38.55 1.89
544 545 7.330946 CGTAGAAATACAACAACAATCTCAGGA 59.669 37.037 0.00 0.00 0.00 3.86
611 612 7.040686 ACAAGCAAGATGTACGGTTTTATCTTT 60.041 33.333 9.87 0.00 37.68 2.52
637 638 5.179533 GGAGAGTCTGAATCTGGGTAAAAC 58.820 45.833 12.89 0.00 0.00 2.43
640 641 5.310857 AGAGTCTGAATCTGGGTAAAACCTT 59.689 40.000 6.86 0.00 38.64 3.50
668 669 9.481340 TGTCTTTGTATTGTCATATCTAGATGC 57.519 33.333 15.79 3.86 0.00 3.91
677 678 7.745620 TGTCATATCTAGATGCTTAGTTCGA 57.254 36.000 15.79 0.00 0.00 3.71
682 683 4.190001 TCTAGATGCTTAGTTCGAGACGT 58.810 43.478 0.00 0.00 0.00 4.34
763 765 2.832498 GGTAGGGAGCAGGCCATC 59.168 66.667 5.01 0.00 0.00 3.51
764 766 2.823758 GGTAGGGAGCAGGCCATCC 61.824 68.421 5.01 9.52 34.64 3.51
765 767 1.768077 GTAGGGAGCAGGCCATCCT 60.768 63.158 18.10 12.73 45.66 3.24
845 847 3.402691 ATCTCCTCAGCGTCGCACG 62.403 63.158 21.09 10.24 45.88 5.34
858 860 4.719369 GCACGCGTCCTCGACCTT 62.719 66.667 9.86 0.00 39.71 3.50
863 865 0.942410 CGCGTCCTCGACCTTGAAAA 60.942 55.000 0.00 0.00 39.71 2.29
864 866 1.223187 GCGTCCTCGACCTTGAAAAA 58.777 50.000 0.00 0.00 39.71 1.94
1003 1213 0.032815 CCAATCCCGGCAAACGTTTT 59.967 50.000 11.66 0.00 42.24 2.43
1021 1231 2.172851 TTTTATCCGACGTGGCAACT 57.827 45.000 0.00 0.00 37.80 3.16
1028 1238 1.071814 GACGTGGCAACTAACCCCA 59.928 57.895 0.00 0.00 37.61 4.96
1029 1239 1.228033 ACGTGGCAACTAACCCCAC 60.228 57.895 0.00 0.00 44.28 4.61
1031 1241 1.151908 GTGGCAACTAACCCCACCA 59.848 57.895 0.00 0.00 42.44 4.17
1034 1244 1.004979 TGGCAACTAACCCCACCATAC 59.995 52.381 0.00 0.00 37.61 2.39
1035 1245 1.004979 GGCAACTAACCCCACCATACA 59.995 52.381 0.00 0.00 0.00 2.29
1036 1246 2.555670 GGCAACTAACCCCACCATACAA 60.556 50.000 0.00 0.00 0.00 2.41
1037 1247 2.490509 GCAACTAACCCCACCATACAAC 59.509 50.000 0.00 0.00 0.00 3.32
1038 1248 2.745281 CAACTAACCCCACCATACAACG 59.255 50.000 0.00 0.00 0.00 4.10
1039 1249 1.980036 ACTAACCCCACCATACAACGT 59.020 47.619 0.00 0.00 0.00 3.99
1040 1250 2.372837 ACTAACCCCACCATACAACGTT 59.627 45.455 0.00 0.00 0.00 3.99
1041 1251 2.368311 AACCCCACCATACAACGTTT 57.632 45.000 0.00 0.00 0.00 3.60
1042 1252 2.368311 ACCCCACCATACAACGTTTT 57.632 45.000 0.00 0.00 0.00 2.43
1043 1253 2.668625 ACCCCACCATACAACGTTTTT 58.331 42.857 0.00 0.00 0.00 1.94
1044 1254 2.362717 ACCCCACCATACAACGTTTTTG 59.637 45.455 0.00 0.00 0.00 2.44
1045 1255 2.399448 CCCACCATACAACGTTTTTGC 58.601 47.619 0.00 0.00 0.00 3.68
1046 1256 2.035321 CCCACCATACAACGTTTTTGCT 59.965 45.455 0.00 0.00 0.00 3.91
1047 1257 3.253677 CCCACCATACAACGTTTTTGCTA 59.746 43.478 0.00 0.00 0.00 3.49
1048 1258 4.472286 CCACCATACAACGTTTTTGCTAG 58.528 43.478 0.00 0.00 0.00 3.42
1049 1259 3.911964 CACCATACAACGTTTTTGCTAGC 59.088 43.478 8.10 8.10 0.00 3.42
1050 1260 3.566322 ACCATACAACGTTTTTGCTAGCA 59.434 39.130 14.93 14.93 0.00 3.49
1051 1261 4.036971 ACCATACAACGTTTTTGCTAGCAA 59.963 37.500 26.06 26.06 0.00 3.91
1052 1262 4.616802 CCATACAACGTTTTTGCTAGCAAG 59.383 41.667 27.82 19.33 37.24 4.01
1053 1263 3.775661 ACAACGTTTTTGCTAGCAAGT 57.224 38.095 27.82 19.95 37.24 3.16
1054 1264 4.886247 ACAACGTTTTTGCTAGCAAGTA 57.114 36.364 27.82 18.15 37.24 2.24
1055 1265 4.594136 ACAACGTTTTTGCTAGCAAGTAC 58.406 39.130 27.82 25.34 37.24 2.73
1056 1266 3.515071 ACGTTTTTGCTAGCAAGTACG 57.485 42.857 37.48 37.48 43.44 3.67
1057 1267 3.125316 ACGTTTTTGCTAGCAAGTACGA 58.875 40.909 41.40 25.54 42.00 3.43
1058 1268 3.556775 ACGTTTTTGCTAGCAAGTACGAA 59.443 39.130 41.40 28.48 42.00 3.85
1059 1269 4.212636 ACGTTTTTGCTAGCAAGTACGAAT 59.787 37.500 41.40 29.72 42.00 3.34
1060 1270 5.406175 ACGTTTTTGCTAGCAAGTACGAATA 59.594 36.000 41.40 23.87 42.00 1.75
1061 1271 5.952064 CGTTTTTGCTAGCAAGTACGAATAG 59.048 40.000 37.00 20.87 42.00 1.73
1062 1272 5.464965 TTTTGCTAGCAAGTACGAATAGC 57.535 39.130 27.82 12.58 39.41 2.97
1063 1273 3.793797 TGCTAGCAAGTACGAATAGCA 57.206 42.857 16.84 16.17 44.77 3.49
1064 1274 4.118093 TGCTAGCAAGTACGAATAGCAA 57.882 40.909 16.84 6.58 44.20 3.91
1065 1275 4.500127 TGCTAGCAAGTACGAATAGCAAA 58.500 39.130 16.84 2.34 44.20 3.68
1066 1276 4.328983 TGCTAGCAAGTACGAATAGCAAAC 59.671 41.667 16.84 2.13 44.20 2.93
1067 1277 4.567159 GCTAGCAAGTACGAATAGCAAACT 59.433 41.667 10.63 0.00 38.92 2.66
1068 1278 4.928661 AGCAAGTACGAATAGCAAACTG 57.071 40.909 0.00 0.00 0.00 3.16
1163 1374 5.633830 ATTGGATAGTTCAGTTTGTGCAG 57.366 39.130 0.00 0.00 0.00 4.41
1241 2764 8.469200 CATCCTGGTTAAGAATTCATTTTGCTA 58.531 33.333 8.44 0.00 0.00 3.49
1342 2871 4.380531 TCATCCGATTTTACATGGAGCTC 58.619 43.478 4.71 4.71 33.21 4.09
1348 2877 0.539986 TTTACATGGAGCTCCCGACC 59.460 55.000 29.95 5.80 37.93 4.79
1478 3007 1.674359 AACTGCGATGGTGTTGTTGA 58.326 45.000 0.00 0.00 0.00 3.18
1512 3041 3.751698 AGAAAACCATTCAACTAGACGGC 59.248 43.478 0.00 0.00 0.00 5.68
1850 3410 2.179517 CCAGGCTCGACTCGTCAC 59.820 66.667 0.00 0.00 0.00 3.67
1923 3483 6.594159 ACAACTGCGCTAAAACTATATTGTCT 59.406 34.615 9.73 0.00 0.00 3.41
1925 3485 7.695869 ACTGCGCTAAAACTATATTGTCTAC 57.304 36.000 9.73 0.00 0.00 2.59
2079 3651 7.414222 TGAACCCGAATAGTAGTGAGTATTT 57.586 36.000 0.00 0.00 32.33 1.40
2364 3969 7.968405 CGAATTTTCTTCGGTTTATTGGATTCT 59.032 33.333 0.00 0.00 38.19 2.40
2867 4493 7.121759 AGGAATCAGGATATTGTTCACTTGTTG 59.878 37.037 0.00 0.00 0.00 3.33
2900 4579 6.260050 ACAGTGTACATGACAAAGGTAAACAG 59.740 38.462 0.00 3.80 40.66 3.16
2952 4631 7.357303 ACTTAAAAATGTACACATGTCGGTTC 58.643 34.615 0.00 0.00 36.56 3.62
3045 4724 3.025978 CCAAGCTCAAGGCCATTGATTA 58.974 45.455 5.01 0.00 46.71 1.75
3114 4794 2.175715 ACATCCCCTTATTCCAGGCTTC 59.824 50.000 0.00 0.00 31.69 3.86
3313 5015 6.544928 TGGAGCTTGTAGACTGAAATATGA 57.455 37.500 0.00 0.00 0.00 2.15
3317 5019 9.717942 GGAGCTTGTAGACTGAAATATGATAAT 57.282 33.333 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 1.270625 CCCCGCTGTGTTCTTCTACAA 60.271 52.381 0.00 0.00 0.00 2.41
91 92 1.318158 GCCTCTTCCTGGTGGCAATG 61.318 60.000 14.26 0.00 44.34 2.82
102 103 3.731653 GAGCGGCTCAGCCTCTTCC 62.732 68.421 24.42 0.00 44.36 3.46
116 117 0.167470 TTGACGACGTCCTTAGAGCG 59.833 55.000 24.33 0.00 0.00 5.03
279 280 2.428890 CACGGTGAGAGAATTCCTAGCT 59.571 50.000 0.74 0.00 0.00 3.32
287 288 1.469308 GAGACGACACGGTGAGAGAAT 59.531 52.381 16.29 0.00 0.00 2.40
298 299 2.262915 CAGGCTGGGAGACGACAC 59.737 66.667 6.61 0.00 0.00 3.67
299 300 2.997315 CCAGGCTGGGAGACGACA 60.997 66.667 26.34 0.00 32.67 4.35
342 343 3.596214 CAACATAGCCCACTCGTTAACT 58.404 45.455 3.71 0.00 0.00 2.24
351 352 1.032114 GGCAGTCCAACATAGCCCAC 61.032 60.000 0.00 0.00 39.42 4.61
408 409 5.659971 ACGATTTTGGTACCTAGGAGTACAT 59.340 40.000 17.98 0.00 43.66 2.29
423 424 2.884639 ACCAAGTCCTTGACGATTTTGG 59.115 45.455 8.59 9.95 42.93 3.28
425 426 4.065789 GAGACCAAGTCCTTGACGATTTT 58.934 43.478 8.59 0.00 42.93 1.82
477 478 5.649970 ATATAGATACCGAGGGTCTAGGG 57.350 47.826 10.67 0.00 37.09 3.53
513 514 4.633175 TGTTGTTGTATTTCTACGAGCCA 58.367 39.130 0.00 0.00 0.00 4.75
611 612 3.251484 ACCCAGATTCAGACTCTCCAAA 58.749 45.455 0.00 0.00 0.00 3.28
637 638 8.498054 AGATATGACAATACAAAGACACAAGG 57.502 34.615 0.00 0.00 0.00 3.61
668 669 3.931468 TCAGTAGGACGTCTCGAACTAAG 59.069 47.826 16.46 4.70 0.00 2.18
677 678 1.951424 GCAGGTCTCAGTAGGACGTCT 60.951 57.143 16.46 4.12 34.82 4.18
682 683 1.379977 CCGGCAGGTCTCAGTAGGA 60.380 63.158 0.00 0.00 0.00 2.94
739 741 1.108132 CCTGCTCCCTACCGACTACC 61.108 65.000 0.00 0.00 0.00 3.18
748 750 2.705410 AGGATGGCCTGCTCCCTA 59.295 61.111 3.32 0.00 44.90 3.53
845 847 1.223187 TTTTTCAAGGTCGAGGACGC 58.777 50.000 0.00 0.00 39.58 5.19
858 860 1.658931 CGCGTTGCTGTCGATTTTTCA 60.659 47.619 0.00 0.00 0.00 2.69
863 865 1.709760 CATCGCGTTGCTGTCGATT 59.290 52.632 5.77 0.00 40.48 3.34
864 866 2.802667 GCATCGCGTTGCTGTCGAT 61.803 57.895 29.70 0.00 42.82 3.59
1003 1213 2.995258 GTTAGTTGCCACGTCGGATAAA 59.005 45.455 8.04 0.00 36.56 1.40
1005 1215 1.135024 GGTTAGTTGCCACGTCGGATA 60.135 52.381 8.04 0.00 36.56 2.59
1007 1217 1.005867 GGTTAGTTGCCACGTCGGA 60.006 57.895 8.04 0.00 36.56 4.55
1021 1231 3.505480 AAACGTTGTATGGTGGGGTTA 57.495 42.857 0.00 0.00 0.00 2.85
1028 1238 3.566322 TGCTAGCAAAAACGTTGTATGGT 59.434 39.130 16.84 9.67 0.00 3.55
1029 1239 4.153958 TGCTAGCAAAAACGTTGTATGG 57.846 40.909 16.84 0.00 0.00 2.74
1031 1241 5.432885 ACTTGCTAGCAAAAACGTTGTAT 57.567 34.783 28.95 0.70 35.33 2.29
1034 1244 3.657625 CGTACTTGCTAGCAAAAACGTTG 59.342 43.478 34.22 23.67 38.34 4.10
1035 1245 3.556775 TCGTACTTGCTAGCAAAAACGTT 59.443 39.130 37.14 21.12 41.12 3.99
1036 1246 3.125316 TCGTACTTGCTAGCAAAAACGT 58.875 40.909 37.14 29.82 41.12 3.99
1037 1247 3.781341 TCGTACTTGCTAGCAAAAACG 57.219 42.857 35.54 35.54 41.41 3.60
1038 1248 5.733109 GCTATTCGTACTTGCTAGCAAAAAC 59.267 40.000 28.95 25.43 35.88 2.43
1039 1249 5.410132 TGCTATTCGTACTTGCTAGCAAAAA 59.590 36.000 28.95 17.73 41.17 1.94
1040 1250 4.932799 TGCTATTCGTACTTGCTAGCAAAA 59.067 37.500 28.95 20.35 41.17 2.44
1041 1251 4.500127 TGCTATTCGTACTTGCTAGCAAA 58.500 39.130 28.95 14.34 41.17 3.68
1042 1252 4.118093 TGCTATTCGTACTTGCTAGCAA 57.882 40.909 27.67 27.67 41.17 3.91
1043 1253 3.793797 TGCTATTCGTACTTGCTAGCA 57.206 42.857 14.93 14.93 41.69 3.49
1044 1254 4.567159 AGTTTGCTATTCGTACTTGCTAGC 59.433 41.667 8.10 8.10 36.26 3.42
1045 1255 5.805486 TCAGTTTGCTATTCGTACTTGCTAG 59.195 40.000 0.00 0.00 0.00 3.42
1046 1256 5.716094 TCAGTTTGCTATTCGTACTTGCTA 58.284 37.500 0.00 0.00 0.00 3.49
1047 1257 4.566004 TCAGTTTGCTATTCGTACTTGCT 58.434 39.130 0.00 0.00 0.00 3.91
1048 1258 4.625742 TCTCAGTTTGCTATTCGTACTTGC 59.374 41.667 0.00 0.00 0.00 4.01
1049 1259 6.893958 ATCTCAGTTTGCTATTCGTACTTG 57.106 37.500 0.00 0.00 0.00 3.16
1050 1260 6.253727 CGAATCTCAGTTTGCTATTCGTACTT 59.746 38.462 0.00 0.00 42.27 2.24
1051 1261 5.744345 CGAATCTCAGTTTGCTATTCGTACT 59.256 40.000 0.00 0.00 42.27 2.73
1052 1262 5.952816 CGAATCTCAGTTTGCTATTCGTAC 58.047 41.667 0.00 0.00 42.27 3.67
1056 1266 7.394872 CAAGTACGAATCTCAGTTTGCTATTC 58.605 38.462 0.00 0.00 0.00 1.75
1057 1267 6.183360 GCAAGTACGAATCTCAGTTTGCTATT 60.183 38.462 0.00 0.00 37.34 1.73
1058 1268 5.292101 GCAAGTACGAATCTCAGTTTGCTAT 59.708 40.000 0.00 0.00 37.34 2.97
1059 1269 4.625742 GCAAGTACGAATCTCAGTTTGCTA 59.374 41.667 0.00 0.00 37.34 3.49
1060 1270 3.433615 GCAAGTACGAATCTCAGTTTGCT 59.566 43.478 0.00 0.00 37.34 3.91
1061 1271 3.186409 TGCAAGTACGAATCTCAGTTTGC 59.814 43.478 0.00 3.08 39.89 3.68
1062 1272 4.990543 TGCAAGTACGAATCTCAGTTTG 57.009 40.909 0.00 0.00 0.00 2.93
1063 1273 4.631813 GGATGCAAGTACGAATCTCAGTTT 59.368 41.667 0.00 0.00 0.00 2.66
1064 1274 4.184629 GGATGCAAGTACGAATCTCAGTT 58.815 43.478 0.00 0.00 0.00 3.16
1065 1275 3.195610 TGGATGCAAGTACGAATCTCAGT 59.804 43.478 0.00 0.00 0.00 3.41
1066 1276 3.785486 TGGATGCAAGTACGAATCTCAG 58.215 45.455 0.00 0.00 0.00 3.35
1067 1277 3.885724 TGGATGCAAGTACGAATCTCA 57.114 42.857 0.00 0.00 0.00 3.27
1068 1278 4.024556 CCATTGGATGCAAGTACGAATCTC 60.025 45.833 5.69 0.00 0.00 2.75
1134 1344 7.596248 CACAAACTGAACTATCCAATTTCCTTG 59.404 37.037 0.00 0.00 34.42 3.61
1163 1374 4.772100 TGGAGGGGAAATTGATTTGACTTC 59.228 41.667 0.00 0.00 0.00 3.01
1241 2764 0.543749 GGCACCTCCAGACATAAGCT 59.456 55.000 0.00 0.00 34.01 3.74
1326 2855 2.872858 GTCGGGAGCTCCATGTAAAATC 59.127 50.000 33.29 12.11 37.91 2.17
1348 2877 1.990563 CGCGTAAAAGGACCAGTAGTG 59.009 52.381 0.00 0.00 0.00 2.74
1403 2932 8.506437 TGCTTACATAATCTGTTTCTGACAAAG 58.494 33.333 0.00 0.00 39.39 2.77
1478 3007 1.260544 GGTTTTCTGCAGCTCCCATT 58.739 50.000 9.47 0.00 0.00 3.16
1512 3041 1.699634 TCTGGTCCTGGTGAAAAGAGG 59.300 52.381 0.00 0.00 0.00 3.69
1850 3410 1.139095 GTTCTGGGGTAGCGACTCG 59.861 63.158 0.00 0.00 0.00 4.18
1859 3419 2.623915 CGACGAGTCGTTCTGGGGT 61.624 63.158 20.91 0.00 46.99 4.95
1881 3441 6.441274 GCAGTTGTTCTCATCAAGATTTTCA 58.559 36.000 0.00 0.00 32.82 2.69
1887 3447 1.800586 GCGCAGTTGTTCTCATCAAGA 59.199 47.619 0.30 0.00 0.00 3.02
2079 3651 5.136828 TGAGAAACTTAAGTGGCAAATGGA 58.863 37.500 9.34 0.00 0.00 3.41
2120 3705 7.339466 GGATTCCCTTCAGTAATACACAAATGT 59.661 37.037 0.00 0.00 43.30 2.71
2127 3712 5.602978 GGAGAGGATTCCCTTCAGTAATACA 59.397 44.000 0.00 0.00 44.53 2.29
2676 4288 7.703197 GGAGAAACAAAATAAGGAAACGAACAA 59.297 33.333 0.00 0.00 0.00 2.83
2867 4493 4.055360 TGTCATGTACACTGTAGCAACAC 58.945 43.478 0.00 0.00 31.43 3.32
2952 4631 7.101700 TCATGCATGACTATTTCTGCTATAGG 58.898 38.462 25.42 0.00 35.66 2.57
3045 4724 6.150976 TGACAAACATTTCACTGTGAGAAACT 59.849 34.615 10.77 0.00 37.76 2.66
3114 4794 2.167075 GCATCTGAATTCCCCAAAGTGG 59.833 50.000 2.27 0.00 37.25 4.00
3225 4915 7.540055 GCTTAGAGAAAATGAAATTGTCAGGTG 59.460 37.037 0.00 0.00 43.21 4.00


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

AutoCloner maintained by Alex Coulton.