Multiple sequence alignment - TraesCS1A01G150500

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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 TraesCS1A01G150500 chr1A 100.000 3568 0 0 1 3568 258182512 258178945 0.000000e+00 6589.0
1 TraesCS1A01G150500 chr1A 92.371 852 52 6 1 851 506642182 506643021 0.000000e+00 1201.0
2 TraesCS1A01G150500 chr1D 95.414 1897 65 10 1689 3568 203536320 203534429 0.000000e+00 3001.0
3 TraesCS1A01G150500 chr1D 95.853 651 26 1 1040 1690 203537018 203536369 0.000000e+00 1051.0
4 TraesCS1A01G150500 chr3A 92.840 852 52 3 1 851 164565269 164566112 0.000000e+00 1227.0
5 TraesCS1A01G150500 chr3A 96.875 32 1 0 3083 3114 660197038 660197069 2.000000e-03 54.7
6 TraesCS1A01G150500 chr5A 92.606 852 48 5 1 851 493169380 493170217 0.000000e+00 1210.0
7 TraesCS1A01G150500 chrUn 91.735 859 53 4 1 851 5571463 5570615 0.000000e+00 1177.0
8 TraesCS1A01G150500 chr2A 91.667 852 59 4 1 851 91005239 91006079 0.000000e+00 1170.0
9 TraesCS1A01G150500 chr2A 87.288 118 15 0 922 1039 275928503 275928620 6.210000e-28 135.0
10 TraesCS1A01G150500 chr3B 91.385 859 56 5 1 850 10169434 10168585 0.000000e+00 1160.0
11 TraesCS1A01G150500 chr4A 91.432 852 59 6 1 850 244689051 244689890 0.000000e+00 1157.0
12 TraesCS1A01G150500 chr4A 85.460 729 103 3 1748 2474 137541259 137541986 0.000000e+00 756.0
13 TraesCS1A01G150500 chr4A 86.196 326 35 9 1066 1384 137540432 137540754 9.480000e-91 344.0
14 TraesCS1A01G150500 chr2B 91.289 861 54 8 1 851 597873836 597874685 0.000000e+00 1155.0
15 TraesCS1A01G150500 chr6B 91.173 861 58 6 1 851 147955045 147954193 0.000000e+00 1153.0
16 TraesCS1A01G150500 chr1B 93.417 638 35 3 1689 2325 297477587 297476956 0.000000e+00 939.0
17 TraesCS1A01G150500 chr1B 95.116 430 16 2 1216 1645 297480459 297480035 0.000000e+00 673.0
18 TraesCS1A01G150500 chr1B 90.343 321 25 3 2279 2599 297476950 297476636 1.980000e-112 416.0
19 TraesCS1A01G150500 chr1B 85.390 308 27 11 2753 3052 297476362 297476065 1.610000e-78 303.0
20 TraesCS1A01G150500 chr1B 90.741 216 15 2 1810 2025 297475298 297475088 2.100000e-72 283.0
21 TraesCS1A01G150500 chr1B 92.670 191 14 0 1044 1234 297486566 297486376 3.510000e-70 276.0
22 TraesCS1A01G150500 chr4D 85.517 725 102 3 1752 2474 335334999 335334276 0.000000e+00 754.0
23 TraesCS1A01G150500 chr4B 85.322 729 105 2 1748 2474 413448031 413447303 0.000000e+00 752.0
24 TraesCS1A01G150500 chr4B 84.091 352 42 12 1040 1384 413448890 413448546 9.550000e-86 327.0
25 TraesCS1A01G150500 chr4B 80.524 267 42 7 2738 2996 413447298 413447034 2.810000e-46 196.0
26 TraesCS1A01G150500 chr7D 93.750 112 6 1 929 1040 189329455 189329565 2.200000e-37 167.0
27 TraesCS1A01G150500 chr6A 82.143 168 19 6 881 1041 85283536 85283373 2.230000e-27 134.0
28 TraesCS1A01G150500 chr2D 87.209 86 9 2 901 984 206695806 206695721 2.930000e-16 97.1


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 TraesCS1A01G150500 chr1A 258178945 258182512 3567 True 6589.0 6589 100.000000 1 3568 1 chr1A.!!$R1 3567
1 TraesCS1A01G150500 chr1A 506642182 506643021 839 False 1201.0 1201 92.371000 1 851 1 chr1A.!!$F1 850
2 TraesCS1A01G150500 chr1D 203534429 203537018 2589 True 2026.0 3001 95.633500 1040 3568 2 chr1D.!!$R1 2528
3 TraesCS1A01G150500 chr3A 164565269 164566112 843 False 1227.0 1227 92.840000 1 851 1 chr3A.!!$F1 850
4 TraesCS1A01G150500 chr5A 493169380 493170217 837 False 1210.0 1210 92.606000 1 851 1 chr5A.!!$F1 850
5 TraesCS1A01G150500 chrUn 5570615 5571463 848 True 1177.0 1177 91.735000 1 851 1 chrUn.!!$R1 850
6 TraesCS1A01G150500 chr2A 91005239 91006079 840 False 1170.0 1170 91.667000 1 851 1 chr2A.!!$F1 850
7 TraesCS1A01G150500 chr3B 10168585 10169434 849 True 1160.0 1160 91.385000 1 850 1 chr3B.!!$R1 849
8 TraesCS1A01G150500 chr4A 244689051 244689890 839 False 1157.0 1157 91.432000 1 850 1 chr4A.!!$F1 849
9 TraesCS1A01G150500 chr4A 137540432 137541986 1554 False 550.0 756 85.828000 1066 2474 2 chr4A.!!$F2 1408
10 TraesCS1A01G150500 chr2B 597873836 597874685 849 False 1155.0 1155 91.289000 1 851 1 chr2B.!!$F1 850
11 TraesCS1A01G150500 chr6B 147954193 147955045 852 True 1153.0 1153 91.173000 1 851 1 chr6B.!!$R1 850
12 TraesCS1A01G150500 chr1B 297475088 297480459 5371 True 522.8 939 91.001400 1216 3052 5 chr1B.!!$R2 1836
13 TraesCS1A01G150500 chr4D 335334276 335334999 723 True 754.0 754 85.517000 1752 2474 1 chr4D.!!$R1 722
14 TraesCS1A01G150500 chr4B 413447034 413448890 1856 True 425.0 752 83.312333 1040 2996 3 chr4B.!!$R1 1956

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
957 985 0.828022 TAACAGGCTGGTGTATCCCG 59.172 55.0 17.03 0.0 34.77 5.14 F
1859 4570 0.462581 TTGATCTGCAGCCATCCGTC 60.463 55.0 9.47 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2062 4773 0.580104 GTGTTAACGCAACGAGCAGT 59.420 50.0 14.22 0.0 46.13 4.40 R
3200 6670 1.166531 AGGCTTCTGTGACGTTTGCC 61.167 55.0 0.00 0.0 39.19 4.52 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
141 146 5.294356 TGATACACCGTACTAATTGATGGC 58.706 41.667 0.00 0.00 0.00 4.40
142 147 3.620427 ACACCGTACTAATTGATGGCA 57.380 42.857 0.00 0.00 0.00 4.92
143 148 3.531538 ACACCGTACTAATTGATGGCAG 58.468 45.455 0.00 0.00 0.00 4.85
144 149 2.287915 CACCGTACTAATTGATGGCAGC 59.712 50.000 0.00 0.00 0.00 5.25
145 150 1.873591 CCGTACTAATTGATGGCAGCC 59.126 52.381 3.66 3.66 0.00 4.85
146 151 2.485479 CCGTACTAATTGATGGCAGCCT 60.485 50.000 14.15 0.00 0.00 4.58
147 152 2.545526 CGTACTAATTGATGGCAGCCTG 59.454 50.000 14.15 0.00 0.00 4.85
148 153 2.062971 ACTAATTGATGGCAGCCTGG 57.937 50.000 14.15 0.00 0.00 4.45
157 162 2.914097 GCAGCCTGGCAGGTTTGT 60.914 61.111 32.80 13.96 37.80 2.83
185 192 4.734398 AAAATGTGCCAACTCAAACTGA 57.266 36.364 0.00 0.00 0.00 3.41
218 227 6.596888 TCGCAAGAGAGAGAAAATGATCAATT 59.403 34.615 0.00 0.00 45.01 2.32
226 235 7.011857 AGAGAGAAAATGATCAATTAGTTCGCC 59.988 37.037 0.00 0.00 0.00 5.54
243 252 4.974645 TCGCCACCTGATTAAATAGGAT 57.025 40.909 13.57 0.00 37.52 3.24
315 342 2.354821 GTCTTGAAGACAAACAAGGCGT 59.645 45.455 19.73 0.00 44.45 5.68
317 344 1.305201 TGAAGACAAACAAGGCGTCC 58.695 50.000 0.00 0.00 0.00 4.79
362 389 4.040829 TGAAGTGTGTGTCTCATTCATCCT 59.959 41.667 0.00 0.00 0.00 3.24
629 657 5.931294 TCCGAATAATGCCTTGGTATGTAA 58.069 37.500 0.00 0.00 0.00 2.41
637 665 6.949352 ATGCCTTGGTATGTAAGATTTGAG 57.051 37.500 0.00 0.00 0.00 3.02
660 688 7.888021 TGAGATGAGGCCTTTTAAATAACAGAA 59.112 33.333 6.77 0.00 0.00 3.02
707 735 8.733128 CAAAAATATCATACGTGATGGTTTTCG 58.267 33.333 0.00 0.00 44.62 3.46
753 781 2.244651 GCGTTTGTCTCACTGCCGT 61.245 57.895 0.00 0.00 0.00 5.68
798 826 2.289565 TGTTATGCCGTGTTGTTGTGA 58.710 42.857 0.00 0.00 0.00 3.58
897 925 8.948853 CACACACGTGTAGAATATTTTCAATT 57.051 30.769 22.90 0.00 42.83 2.32
949 977 2.748209 AAAACAGGTAACAGGCTGGT 57.252 45.000 20.34 16.10 41.41 4.00
950 978 1.981256 AAACAGGTAACAGGCTGGTG 58.019 50.000 17.03 8.29 41.41 4.17
951 979 0.843984 AACAGGTAACAGGCTGGTGT 59.156 50.000 17.03 8.94 41.41 4.16
952 980 1.724545 ACAGGTAACAGGCTGGTGTA 58.275 50.000 17.03 2.85 41.41 2.90
953 981 2.266279 ACAGGTAACAGGCTGGTGTAT 58.734 47.619 17.03 0.00 41.41 2.29
954 982 2.236395 ACAGGTAACAGGCTGGTGTATC 59.764 50.000 17.03 6.30 41.41 2.24
955 983 1.838077 AGGTAACAGGCTGGTGTATCC 59.162 52.381 17.03 12.02 41.41 2.59
956 984 1.134189 GGTAACAGGCTGGTGTATCCC 60.134 57.143 17.03 3.32 34.77 3.85
957 985 0.828022 TAACAGGCTGGTGTATCCCG 59.172 55.000 17.03 0.00 34.77 5.14
958 986 2.203070 CAGGCTGGTGTATCCCGC 60.203 66.667 6.61 0.00 44.11 6.13
959 987 2.687200 AGGCTGGTGTATCCCGCA 60.687 61.111 0.00 0.00 46.16 5.69
960 988 2.513897 GGCTGGTGTATCCCGCAC 60.514 66.667 3.11 0.00 46.16 5.34
961 989 2.890474 GCTGGTGTATCCCGCACG 60.890 66.667 0.00 0.00 44.23 5.34
962 990 2.890474 CTGGTGTATCCCGCACGC 60.890 66.667 0.00 0.00 37.70 5.34
963 991 4.805231 TGGTGTATCCCGCACGCG 62.805 66.667 3.53 3.53 37.70 6.01
964 992 4.807039 GGTGTATCCCGCACGCGT 62.807 66.667 5.58 5.58 37.70 6.01
965 993 3.550992 GTGTATCCCGCACGCGTG 61.551 66.667 34.01 34.01 37.81 5.34
966 994 4.805231 TGTATCCCGCACGCGTGG 62.805 66.667 37.47 26.73 42.94 4.94
1011 1039 2.728817 CGAGGTGTCGCCCCTATC 59.271 66.667 0.00 0.00 39.88 2.08
1012 1040 1.828660 CGAGGTGTCGCCCCTATCT 60.829 63.158 0.00 0.00 39.88 1.98
1013 1041 1.797211 CGAGGTGTCGCCCCTATCTC 61.797 65.000 0.00 0.00 39.88 2.75
1014 1042 1.797211 GAGGTGTCGCCCCTATCTCG 61.797 65.000 0.00 0.00 38.26 4.04
1015 1043 2.027751 GTGTCGCCCCTATCTCGC 59.972 66.667 0.00 0.00 0.00 5.03
1016 1044 2.123854 TGTCGCCCCTATCTCGCT 60.124 61.111 0.00 0.00 0.00 4.93
1017 1045 2.336809 GTCGCCCCTATCTCGCTG 59.663 66.667 0.00 0.00 0.00 5.18
1018 1046 2.194212 GTCGCCCCTATCTCGCTGA 61.194 63.158 0.00 0.00 0.00 4.26
1019 1047 1.455032 TCGCCCCTATCTCGCTGAA 60.455 57.895 0.00 0.00 0.00 3.02
1020 1048 1.300233 CGCCCCTATCTCGCTGAAC 60.300 63.158 0.00 0.00 0.00 3.18
1021 1049 1.300233 GCCCCTATCTCGCTGAACG 60.300 63.158 0.00 0.00 45.62 3.95
1022 1050 1.300233 CCCCTATCTCGCTGAACGC 60.300 63.158 0.00 0.00 43.23 4.84
1032 1060 3.347411 GCTGAACGCGAGGAATAGT 57.653 52.632 15.93 0.00 0.00 2.12
1033 1061 1.201343 GCTGAACGCGAGGAATAGTC 58.799 55.000 15.93 0.00 0.00 2.59
1034 1062 1.467875 CTGAACGCGAGGAATAGTCG 58.532 55.000 15.93 0.00 40.50 4.18
1061 1089 2.273179 CCCGACGTTGTCTCCTCCA 61.273 63.158 1.30 0.00 0.00 3.86
1069 1097 4.131088 GTCTCCTCCACCGTCCGC 62.131 72.222 0.00 0.00 0.00 5.54
1366 1401 4.020039 TGGTGTAAGTATCGTCCCAAACAT 60.020 41.667 0.00 0.00 0.00 2.71
1374 1409 1.418342 CGTCCCAAACATCGGTAGCG 61.418 60.000 8.29 8.29 0.00 4.26
1465 1532 9.388506 CCTTGGTGGCTATATAATCTTCAATAG 57.611 37.037 0.00 0.00 0.00 1.73
1681 4114 5.818678 ATTATTTCCGTCCATAGCTACCA 57.181 39.130 0.00 0.00 0.00 3.25
1682 4115 3.753294 ATTTCCGTCCATAGCTACCAG 57.247 47.619 0.00 0.00 0.00 4.00
1685 4118 2.307768 TCCGTCCATAGCTACCAGAAG 58.692 52.381 0.00 0.00 0.00 2.85
1857 4568 0.745486 TGTTGATCTGCAGCCATCCG 60.745 55.000 9.47 0.00 0.00 4.18
1859 4570 0.462581 TTGATCTGCAGCCATCCGTC 60.463 55.000 9.47 0.00 0.00 4.79
2007 4718 8.131455 TCTTTGTTATCTCGAGCAATATTGTC 57.869 34.615 16.61 11.41 0.00 3.18
2051 4762 0.673644 GTGGTCACCTCAATCCACGG 60.674 60.000 0.00 0.00 40.36 4.94
2052 4763 0.834261 TGGTCACCTCAATCCACGGA 60.834 55.000 0.00 0.00 0.00 4.69
2062 4773 2.369203 TCAATCCACGGACACTGGTTTA 59.631 45.455 0.00 0.00 0.00 2.01
2121 4832 8.940952 GGTGAAGGAGTTATAATTATGCAGATC 58.059 37.037 8.28 0.04 0.00 2.75
2247 4961 9.595823 CTTGATCTGCCAGAATTAATTTGATTT 57.404 29.630 0.00 0.00 0.00 2.17
2354 5120 6.143278 GCACTTTAACCGGAAAACACATTAAG 59.857 38.462 9.46 0.00 0.00 1.85
2432 5198 0.254178 ATCTTGCTGCTGTACTGGGG 59.746 55.000 0.00 0.00 0.00 4.96
2433 5199 2.034066 TTGCTGCTGTACTGGGGC 59.966 61.111 0.00 0.00 0.00 5.80
2447 5213 1.344763 CTGGGGCTAGTAGGCATGTAC 59.655 57.143 23.73 7.16 43.44 2.90
2492 5258 1.160137 GGACTGAGTTCACATGGCAC 58.840 55.000 0.00 0.00 0.00 5.01
2582 5348 6.036517 GCACAGTGTAGAATGAGTGGAATTAG 59.963 42.308 1.61 0.00 0.00 1.73
2647 5413 4.133856 CTGACGAAACAGGTGAATTCAC 57.866 45.455 27.16 27.16 45.72 3.18
2648 5414 3.804036 TGACGAAACAGGTGAATTCACT 58.196 40.909 31.81 18.40 45.73 3.41
2683 5450 5.866207 ACCGAAGAAACAGGTCTCTTTATT 58.134 37.500 0.00 0.00 32.01 1.40
2709 5476 0.314935 AAAATGTGGCTTGCTGGTCG 59.685 50.000 0.00 0.00 0.00 4.79
2731 5511 4.508065 CCATCTTGGGGGAGGAGT 57.492 61.111 0.00 0.00 32.67 3.85
2732 5512 1.918253 CCATCTTGGGGGAGGAGTG 59.082 63.158 0.00 0.00 32.67 3.51
2917 5809 7.576750 TGAAGATGTCATAGAAACGTTGTAC 57.423 36.000 0.00 0.00 0.00 2.90
2920 5812 9.517609 GAAGATGTCATAGAAACGTTGTACTAT 57.482 33.333 0.00 9.07 0.00 2.12
3054 5949 4.627467 CGCTCACTAAGATAAGCAACAGTT 59.373 41.667 0.00 0.00 34.39 3.16
3055 5950 5.120830 CGCTCACTAAGATAAGCAACAGTTT 59.879 40.000 0.00 0.00 34.39 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
141 146 0.825010 AAGACAAACCTGCCAGGCTG 60.825 55.000 11.63 12.69 39.63 4.85
142 147 0.771127 TAAGACAAACCTGCCAGGCT 59.229 50.000 11.63 0.00 39.63 4.58
143 148 1.616159 TTAAGACAAACCTGCCAGGC 58.384 50.000 11.63 3.66 39.63 4.85
144 149 4.664150 TTTTTAAGACAAACCTGCCAGG 57.336 40.909 9.83 9.83 42.49 4.45
218 227 5.364446 TCCTATTTAATCAGGTGGCGAACTA 59.636 40.000 0.00 0.00 33.37 2.24
226 235 6.488006 CCAAGGTGATCCTATTTAATCAGGTG 59.512 42.308 0.00 0.00 44.35 4.00
243 252 6.926630 AATTTGGTATAAAAGCCAAGGTGA 57.073 33.333 0.00 0.00 44.43 4.02
315 342 7.728083 TCATCCTTTTTGTTCTTATTCTTGGGA 59.272 33.333 0.00 0.00 0.00 4.37
317 344 9.415544 CTTCATCCTTTTTGTTCTTATTCTTGG 57.584 33.333 0.00 0.00 0.00 3.61
362 389 8.608185 AATTTCTCTTTCCTTTTATGCCCATA 57.392 30.769 0.00 0.00 0.00 2.74
566 594 0.673333 ATGCGCACGGAGTCATGAAA 60.673 50.000 14.90 0.00 41.61 2.69
629 657 7.968014 ATTTAAAAGGCCTCATCTCAAATCT 57.032 32.000 5.23 0.00 0.00 2.40
677 705 8.918202 ACCATCACGTATGATATTTTTGGTAT 57.082 30.769 0.00 0.00 44.13 2.73
707 735 6.366332 CCAGAAATGCCTATAAGACGTACATC 59.634 42.308 0.00 0.00 0.00 3.06
753 781 0.975135 CAAATGGTGCCACCCAATGA 59.025 50.000 12.25 0.00 37.50 2.57
798 826 6.043243 ACGGGAGAGATAAATAACATGTCCAT 59.957 38.462 0.00 0.00 0.00 3.41
869 897 6.480651 TGAAAATATTCTACACGTGTGTGTGT 59.519 34.615 30.83 14.69 45.47 3.72
870 898 6.883129 TGAAAATATTCTACACGTGTGTGTG 58.117 36.000 30.83 17.02 45.47 3.82
871 899 7.485418 TTGAAAATATTCTACACGTGTGTGT 57.515 32.000 30.83 15.70 45.88 3.72
872 900 8.948853 AATTGAAAATATTCTACACGTGTGTG 57.051 30.769 30.83 21.77 42.82 3.82
929 957 2.693074 CACCAGCCTGTTACCTGTTTTT 59.307 45.455 0.00 0.00 0.00 1.94
930 958 2.306847 CACCAGCCTGTTACCTGTTTT 58.693 47.619 0.00 0.00 0.00 2.43
931 959 1.214424 ACACCAGCCTGTTACCTGTTT 59.786 47.619 0.00 0.00 0.00 2.83
932 960 0.843984 ACACCAGCCTGTTACCTGTT 59.156 50.000 0.00 0.00 0.00 3.16
933 961 1.724545 TACACCAGCCTGTTACCTGT 58.275 50.000 0.00 0.00 0.00 4.00
934 962 2.420129 GGATACACCAGCCTGTTACCTG 60.420 54.545 0.00 0.00 38.79 4.00
935 963 1.838077 GGATACACCAGCCTGTTACCT 59.162 52.381 0.00 0.00 38.79 3.08
936 964 1.134189 GGGATACACCAGCCTGTTACC 60.134 57.143 0.00 0.00 41.20 2.85
937 965 1.472728 CGGGATACACCAGCCTGTTAC 60.473 57.143 0.00 0.00 41.20 2.50
938 966 0.828022 CGGGATACACCAGCCTGTTA 59.172 55.000 0.00 0.00 41.20 2.41
939 967 1.602237 CGGGATACACCAGCCTGTT 59.398 57.895 0.00 0.00 41.20 3.16
940 968 3.309582 CGGGATACACCAGCCTGT 58.690 61.111 0.00 0.00 41.20 4.00
945 973 2.890474 GCGTGCGGGATACACCAG 60.890 66.667 0.00 0.00 41.20 4.00
946 974 4.805231 CGCGTGCGGGATACACCA 62.805 66.667 6.30 0.00 41.20 4.17
947 975 4.807039 ACGCGTGCGGGATACACC 62.807 66.667 12.93 0.00 44.69 4.16
968 996 3.591835 AAACGCCACTTGCACCGG 61.592 61.111 0.00 0.00 41.33 5.28
969 997 2.353376 CAAACGCCACTTGCACCG 60.353 61.111 0.00 0.00 41.33 4.94
970 998 2.658268 GCAAACGCCACTTGCACC 60.658 61.111 7.07 0.00 46.78 5.01
980 1008 2.174349 CTCGCTGAAGGCAAACGC 59.826 61.111 0.00 0.00 41.91 4.84
981 1009 1.961277 ACCTCGCTGAAGGCAAACG 60.961 57.895 0.00 0.00 40.34 3.60
982 1010 1.166531 ACACCTCGCTGAAGGCAAAC 61.167 55.000 0.00 0.00 40.34 2.93
983 1011 0.884704 GACACCTCGCTGAAGGCAAA 60.885 55.000 0.00 0.00 40.34 3.68
984 1012 1.301716 GACACCTCGCTGAAGGCAA 60.302 57.895 0.00 0.00 40.34 4.52
985 1013 2.343758 GACACCTCGCTGAAGGCA 59.656 61.111 0.00 0.00 40.34 4.75
986 1014 2.811317 CGACACCTCGCTGAAGGC 60.811 66.667 0.00 0.00 40.34 4.35
995 1023 1.797211 CGAGATAGGGGCGACACCTC 61.797 65.000 3.80 0.00 40.54 3.85
996 1024 1.828660 CGAGATAGGGGCGACACCT 60.829 63.158 5.94 5.94 42.15 4.00
997 1025 2.728817 CGAGATAGGGGCGACACC 59.271 66.667 0.00 0.00 37.93 4.16
998 1026 2.027751 GCGAGATAGGGGCGACAC 59.972 66.667 0.00 0.00 0.00 3.67
999 1027 2.123854 AGCGAGATAGGGGCGACA 60.124 61.111 0.00 0.00 0.00 4.35
1000 1028 1.735376 TTCAGCGAGATAGGGGCGAC 61.735 60.000 0.00 0.00 0.00 5.19
1001 1029 1.455032 TTCAGCGAGATAGGGGCGA 60.455 57.895 0.00 0.00 0.00 5.54
1002 1030 1.300233 GTTCAGCGAGATAGGGGCG 60.300 63.158 0.00 0.00 0.00 6.13
1003 1031 1.300233 CGTTCAGCGAGATAGGGGC 60.300 63.158 0.00 0.00 44.77 5.80
1004 1032 1.300233 GCGTTCAGCGAGATAGGGG 60.300 63.158 0.00 0.00 44.77 4.79
1005 1033 4.327885 GCGTTCAGCGAGATAGGG 57.672 61.111 0.00 0.00 44.77 3.53
1014 1042 1.201343 GACTATTCCTCGCGTTCAGC 58.799 55.000 5.77 0.00 43.95 4.26
1015 1043 1.467875 CGACTATTCCTCGCGTTCAG 58.532 55.000 5.77 0.00 0.00 3.02
1016 1044 0.524816 GCGACTATTCCTCGCGTTCA 60.525 55.000 5.77 0.00 46.32 3.18
1017 1045 2.205385 GCGACTATTCCTCGCGTTC 58.795 57.895 5.77 0.00 46.32 3.95
1018 1046 4.396854 GCGACTATTCCTCGCGTT 57.603 55.556 5.77 0.00 46.32 4.84
1022 1050 2.354773 GGGCGCGACTATTCCTCG 60.355 66.667 13.91 0.00 0.00 4.63
1023 1051 1.300233 CTGGGCGCGACTATTCCTC 60.300 63.158 13.91 0.00 0.00 3.71
1024 1052 2.017559 GACTGGGCGCGACTATTCCT 62.018 60.000 13.91 0.00 0.00 3.36
1025 1053 1.591863 GACTGGGCGCGACTATTCC 60.592 63.158 13.91 0.00 0.00 3.01
1026 1054 1.591863 GGACTGGGCGCGACTATTC 60.592 63.158 13.91 10.11 0.00 1.75
1027 1055 2.499685 GGACTGGGCGCGACTATT 59.500 61.111 13.91 0.00 0.00 1.73
1028 1056 3.537874 GGGACTGGGCGCGACTAT 61.538 66.667 13.91 0.00 0.00 2.12
1036 1064 4.309950 ACAACGTCGGGACTGGGC 62.310 66.667 0.00 0.00 0.00 5.36
1037 1065 2.048503 GACAACGTCGGGACTGGG 60.049 66.667 0.00 0.00 0.00 4.45
1038 1066 1.080705 GAGACAACGTCGGGACTGG 60.081 63.158 0.00 0.00 37.67 4.00
1366 1401 3.961838 AAATTGCCCGCGCTACCGA 62.962 57.895 5.56 0.00 36.29 4.69
1465 1532 0.961019 TTCTGCAGTCCAATTGCCAC 59.039 50.000 14.67 0.00 40.81 5.01
1568 1647 8.137437 CCAATGACATTACTACCAAATTCATCC 58.863 37.037 0.00 0.00 0.00 3.51
1668 4101 3.493524 GGCTTCTTCTGGTAGCTATGGAC 60.494 52.174 0.00 0.00 35.30 4.02
1681 4114 3.616076 CGTCTGTGATTCAGGCTTCTTCT 60.616 47.826 0.00 0.00 45.61 2.85
1682 4115 2.670414 CGTCTGTGATTCAGGCTTCTTC 59.330 50.000 0.00 0.00 45.61 2.87
1685 4118 2.086054 ACGTCTGTGATTCAGGCTTC 57.914 50.000 0.00 0.00 45.61 3.86
1702 4191 1.468908 GGCACTGAGATCTCTGTCACG 60.469 57.143 27.00 18.86 39.29 4.35
1954 4665 9.462606 AACTTGGTTTAACTATCCCTAAATCAG 57.537 33.333 0.00 0.00 31.55 2.90
1982 4693 7.763985 TGACAATATTGCTCGAGATAACAAAGA 59.236 33.333 18.75 4.03 0.00 2.52
2026 4737 3.197766 TGGATTGAGGTGACCACATCTAC 59.802 47.826 14.59 0.00 42.11 2.59
2051 4762 2.150397 ACGAGCAGTAAACCAGTGTC 57.850 50.000 0.00 0.00 0.00 3.67
2052 4763 2.210116 CAACGAGCAGTAAACCAGTGT 58.790 47.619 0.00 0.00 0.00 3.55
2062 4773 0.580104 GTGTTAACGCAACGAGCAGT 59.420 50.000 14.22 0.00 46.13 4.40
2121 4832 4.640789 AGAGACTAACAAGTATGCTCCG 57.359 45.455 0.00 0.00 0.00 4.63
2247 4961 6.468333 ACCTATGCATCAATAACAATTGCA 57.532 33.333 0.19 0.00 46.22 4.08
2354 5120 5.648092 GGCCATGGGTCTACATCATAATAAC 59.352 44.000 15.13 0.00 0.00 1.89
2432 5198 7.659186 AGTTATTACAGTACATGCCTACTAGC 58.341 38.462 0.00 0.00 0.00 3.42
2476 5242 1.229428 AACGTGCCATGTGAACTCAG 58.771 50.000 0.00 0.00 0.00 3.35
2499 5265 5.122519 TCAGCGCAATCTGTAAATTATGGA 58.877 37.500 11.47 0.00 35.63 3.41
2683 5450 3.005684 CAGCAAGCCACATTTTGAGGTTA 59.994 43.478 0.00 0.00 30.35 2.85
3031 5926 4.177026 ACTGTTGCTTATCTTAGTGAGCG 58.823 43.478 0.00 0.00 37.94 5.03
3064 5959 6.935208 ACCAATAGTTCTACAGTTCAGGTTTC 59.065 38.462 0.00 0.00 0.00 2.78
3200 6670 1.166531 AGGCTTCTGTGACGTTTGCC 61.167 55.000 0.00 0.00 39.19 4.52


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

AutoCloner maintained by Alex Coulton.