Multiple sequence alignment - TraesCS2D01G102100

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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 TraesCS2D01G102100 chr2D 100.000 7189 0 0 1 7189 55159917 55152729 0.000000e+00 13276.0
1 TraesCS2D01G102100 chr2D 89.680 281 20 4 4707 4986 406278272 406278544 4.130000e-92 350.0
2 TraesCS2D01G102100 chr2D 90.323 124 5 2 4550 4666 406278067 406278190 9.660000e-34 156.0
3 TraesCS2D01G102100 chr2B 94.990 6727 167 57 321 6953 87356832 87350182 0.000000e+00 10399.0
4 TraesCS2D01G102100 chr2B 92.285 337 24 1 1 335 87357308 87356972 1.810000e-130 477.0
5 TraesCS2D01G102100 chr2A 95.679 6248 155 44 956 7144 55948548 55942357 0.000000e+00 9936.0
6 TraesCS2D01G102100 chr2A 100.000 49 0 0 7134 7182 55941658 55941610 2.760000e-14 91.6
7 TraesCS2D01G102100 chr5A 82.319 1035 167 13 5160 6191 640169359 640168338 0.000000e+00 883.0
8 TraesCS2D01G102100 chr5A 79.600 951 154 32 2651 3591 640172197 640171277 0.000000e+00 645.0
9 TraesCS2D01G102100 chr5A 82.444 450 71 5 3704 4150 640171209 640170765 3.150000e-103 387.0
10 TraesCS2D01G102100 chr5A 87.629 194 23 1 1152 1345 640173492 640173300 2.610000e-54 224.0
11 TraesCS2D01G102100 chr5B 82.212 1040 169 14 5160 6196 642832774 642831748 0.000000e+00 881.0
12 TraesCS2D01G102100 chr5B 78.632 950 165 32 2651 3591 642835200 642834280 4.800000e-166 595.0
13 TraesCS2D01G102100 chr5B 82.889 450 69 5 3704 4150 642834194 642833750 1.450000e-106 398.0
14 TraesCS2D01G102100 chr5B 88.968 281 24 4 4707 4986 311558701 311558427 2.480000e-89 340.0
15 TraesCS2D01G102100 chr5B 87.755 196 23 1 1152 1347 642836492 642836298 2.020000e-55 228.0
16 TraesCS2D01G102100 chr5B 90.678 118 4 2 4556 4666 311558900 311558783 4.490000e-32 150.0
17 TraesCS2D01G102100 chr5D 81.844 1041 171 16 5160 6196 511879538 511878512 0.000000e+00 859.0
18 TraesCS2D01G102100 chr5D 79.285 951 157 31 2651 3591 511881948 511881028 4.730000e-176 628.0
19 TraesCS2D01G102100 chr5D 82.222 450 72 5 3704 4150 511880942 511880498 1.460000e-101 381.0
20 TraesCS2D01G102100 chr5D 87.069 232 20 5 1106 1331 289560204 289560431 3.330000e-63 254.0
21 TraesCS2D01G102100 chr5D 87.755 196 23 1 1152 1347 511883247 511883053 2.020000e-55 228.0
22 TraesCS2D01G102100 chr6B 89.324 281 23 4 4707 4986 126698062 126697788 5.340000e-91 346.0
23 TraesCS2D01G102100 chr6B 88.983 118 6 2 4556 4666 126698261 126698144 9.720000e-29 139.0
24 TraesCS2D01G102100 chrUn 88.968 281 24 4 4707 4986 77288759 77288485 2.480000e-89 340.0
25 TraesCS2D01G102100 chrUn 88.983 118 6 2 4556 4666 77288959 77288842 9.720000e-29 139.0
26 TraesCS2D01G102100 chr4A 96.569 204 7 0 2471 2674 353126406 353126203 8.930000e-89 339.0
27 TraesCS2D01G102100 chr4A 81.481 189 27 3 2883 3064 697816872 697817059 1.620000e-31 148.0
28 TraesCS2D01G102100 chr7A 93.578 218 9 3 2456 2673 269093046 269092834 3.240000e-83 320.0
29 TraesCS2D01G102100 chr7A 86.087 230 22 7 1106 1329 627405814 627406039 9.320000e-59 239.0
30 TraesCS2D01G102100 chr4B 92.035 226 14 2 1106 1331 153306305 153306526 1.510000e-81 315.0
31 TraesCS2D01G102100 chr3B 89.474 209 17 3 1105 1313 705447702 705447499 7.150000e-65 259.0
32 TraesCS2D01G102100 chr6A 96.491 57 2 0 1260 1316 4929430 4929374 2.140000e-15 95.3


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 TraesCS2D01G102100 chr2D 55152729 55159917 7188 True 13276.00 13276 100.0000 1 7189 1 chr2D.!!$R1 7188
1 TraesCS2D01G102100 chr2B 87350182 87357308 7126 True 5438.00 10399 93.6375 1 6953 2 chr2B.!!$R1 6952
2 TraesCS2D01G102100 chr2A 55941610 55948548 6938 True 5013.80 9936 97.8395 956 7182 2 chr2A.!!$R1 6226
3 TraesCS2D01G102100 chr5A 640168338 640173492 5154 True 534.75 883 82.9980 1152 6191 4 chr5A.!!$R1 5039
4 TraesCS2D01G102100 chr5B 642831748 642836492 4744 True 525.50 881 82.8720 1152 6196 4 chr5B.!!$R2 5044
5 TraesCS2D01G102100 chr5D 511878512 511883247 4735 True 524.00 859 82.7765 1152 6196 4 chr5D.!!$R1 5044

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
196 197 0.250989 TGTTTGGTCCCCGATTGGTC 60.251 55.000 0.00 0.00 0.00 4.02 F
527 691 0.401356 TTCCACTCAGCCTGATTGCA 59.599 50.000 6.54 0.00 0.00 4.08 F
1355 1579 0.249398 AGGTAACGCTCACCATCCAC 59.751 55.000 3.79 0.00 46.39 4.02 F
1429 1680 1.002868 AATTGAGCTGAGCGCACCT 60.003 52.632 11.17 0.00 38.19 4.00 F
1966 2222 1.529244 AACAGCCAGGTTGGTGCTC 60.529 57.895 8.37 0.00 40.46 4.26 F
3821 4162 1.619654 CTGGATTCCAGCACCACAAA 58.380 50.000 19.49 0.00 45.13 2.83 F
4210 4556 1.280982 AGCGTAACATGTGATGCTCG 58.719 50.000 22.36 5.39 0.00 5.03 F
4798 5170 0.321671 ATGGTGGTGTTCCTCAGTCG 59.678 55.000 0.00 0.00 34.23 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1344 1568 0.035056 GTGGGGAAGTGGATGGTGAG 60.035 60.000 0.0 0.0 0.00 3.51 R
1842 2098 0.251564 CAACATTGCCACTACCCCCA 60.252 55.000 0.0 0.0 0.00 4.96 R
3130 3467 4.012374 CCACAGGATAATCAACAGCAAGT 58.988 43.478 0.0 0.0 0.00 3.16 R
3322 3659 7.504238 TCTTTAACAAATGAAGGCTGGACTTTA 59.496 33.333 0.0 0.0 0.00 1.85 R
3957 4298 6.421377 TCAAGATTCAACATGTATTGTCCG 57.579 37.500 0.0 0.0 37.68 4.79 R
4666 5016 0.323725 ACCCAGCACCTGCCAAATAG 60.324 55.000 0.0 0.0 43.38 1.73 R
5203 6101 1.470098 GCGTGCATCTTGAATCCAGTT 59.530 47.619 0.0 0.0 0.00 3.16 R
6547 7450 1.613925 GAAAAACTCCTGGACTTGCCC 59.386 52.381 0.0 0.0 34.97 5.36 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
43 44 3.255888 TGGATGACCGTCATGCTATCTAC 59.744 47.826 27.18 8.75 44.27 2.59
52 53 2.623416 TCATGCTATCTACTGTCCGTGG 59.377 50.000 0.00 0.00 0.00 4.94
85 86 7.019418 GGACGTGTTGGTAGACATTTTATTTC 58.981 38.462 0.00 0.00 0.00 2.17
86 87 7.094933 GGACGTGTTGGTAGACATTTTATTTCT 60.095 37.037 0.00 0.00 0.00 2.52
162 163 5.445964 AGTTGCCCAAATTATAGATCGGTT 58.554 37.500 0.00 0.00 0.00 4.44
196 197 0.250989 TGTTTGGTCCCCGATTGGTC 60.251 55.000 0.00 0.00 0.00 4.02
198 199 1.427895 TTTGGTCCCCGATTGGTCCA 61.428 55.000 0.00 1.18 35.36 4.02
211 212 3.885976 TTGGTCCAGGTGTTTCCAATA 57.114 42.857 0.00 0.00 39.02 1.90
212 213 4.396357 TTGGTCCAGGTGTTTCCAATAT 57.604 40.909 0.00 0.00 39.02 1.28
255 256 1.609208 AAAACTGGGCTGTGCTAGTG 58.391 50.000 0.00 0.00 0.00 2.74
266 269 3.436704 GCTGTGCTAGTGTTTTGCTATGA 59.563 43.478 0.00 0.00 0.00 2.15
295 298 9.561270 GTATCTTTTGATTCTAGTTTTGGCTTC 57.439 33.333 0.00 0.00 40.19 3.86
309 312 7.154656 AGTTTTGGCTTCCATTATCTTTTGAC 58.845 34.615 0.00 0.00 31.53 3.18
317 320 5.639757 TCCATTATCTTTTGACGCAATGTG 58.360 37.500 0.00 0.00 0.00 3.21
328 331 0.447801 CGCAATGTGCTACAGAACCC 59.552 55.000 0.00 0.00 42.25 4.11
347 504 2.756760 CCCAAGGATCTGAACCATGTTG 59.243 50.000 6.74 2.63 0.00 3.33
351 508 5.476599 CCAAGGATCTGAACCATGTTGTTAA 59.523 40.000 6.74 0.00 0.00 2.01
397 554 1.289160 TGGAGGCAATGCTCCTTAGT 58.711 50.000 19.21 0.00 40.28 2.24
401 558 3.347216 GAGGCAATGCTCCTTAGTTTGA 58.653 45.455 4.82 0.00 33.24 2.69
405 562 4.686091 GGCAATGCTCCTTAGTTTGAAAAC 59.314 41.667 4.82 0.00 39.17 2.43
493 654 3.242248 CGCCTTGCTACAGTATCGTTTAC 59.758 47.826 0.00 0.00 0.00 2.01
519 683 1.517242 CACTTCACTTCCACTCAGCC 58.483 55.000 0.00 0.00 0.00 4.85
527 691 0.401356 TTCCACTCAGCCTGATTGCA 59.599 50.000 6.54 0.00 0.00 4.08
541 705 3.678289 TGATTGCACAGCAGTAGTTGAT 58.322 40.909 0.00 0.00 40.61 2.57
571 735 3.784412 ATTTTCCGTGCGCGTCCG 61.784 61.111 19.61 10.43 36.15 4.79
586 750 3.470888 CCGACCTACCAGGGGCAG 61.471 72.222 0.00 0.00 40.58 4.85
587 751 3.470888 CGACCTACCAGGGGCAGG 61.471 72.222 0.00 0.00 40.58 4.85
738 915 7.452880 TCTCATCCAGAATAAACAAAACAGG 57.547 36.000 0.00 0.00 0.00 4.00
780 957 5.279156 CCAATGGCCTCCTAATTAATCAAGC 60.279 44.000 3.32 0.00 0.00 4.01
839 1021 2.539081 GGCCTGTCCCTTTCACCCT 61.539 63.158 0.00 0.00 0.00 4.34
842 1024 0.842467 CCTGTCCCTTTCACCCTCCT 60.842 60.000 0.00 0.00 0.00 3.69
843 1025 0.615850 CTGTCCCTTTCACCCTCCTC 59.384 60.000 0.00 0.00 0.00 3.71
861 1043 2.767073 CCCCCTCCCGGTAGTTCC 60.767 72.222 0.00 0.00 0.00 3.62
862 1044 2.039951 CCCCTCCCGGTAGTTCCA 59.960 66.667 0.00 0.00 35.57 3.53
865 1047 1.611261 CCTCCCGGTAGTTCCACCA 60.611 63.158 0.00 0.00 38.61 4.17
866 1048 1.595357 CTCCCGGTAGTTCCACCAC 59.405 63.158 0.00 0.00 38.61 4.16
867 1049 1.896122 CTCCCGGTAGTTCCACCACC 61.896 65.000 0.00 0.00 38.61 4.61
1043 1252 3.155167 GAGTCCCCCGCGGATCTT 61.155 66.667 30.73 7.89 44.66 2.40
1044 1253 2.687566 AGTCCCCCGCGGATCTTT 60.688 61.111 30.73 6.11 44.66 2.52
1045 1254 2.253403 GAGTCCCCCGCGGATCTTTT 62.253 60.000 30.73 7.28 44.66 2.27
1046 1255 1.378119 GTCCCCCGCGGATCTTTTT 60.378 57.895 30.73 0.00 44.66 1.94
1047 1256 1.078001 TCCCCCGCGGATCTTTTTC 60.078 57.895 30.73 0.00 34.86 2.29
1048 1257 1.077716 CCCCCGCGGATCTTTTTCT 60.078 57.895 30.73 0.00 0.00 2.52
1093 1302 4.096003 CGGGCCGGATCTGTGGTT 62.096 66.667 20.56 0.00 0.00 3.67
1094 1303 2.124695 GGGCCGGATCTGTGGTTC 60.125 66.667 5.05 0.00 0.00 3.62
1102 1311 1.009829 GATCTGTGGTTCGTGGATGC 58.990 55.000 0.00 0.00 0.00 3.91
1343 1567 1.374252 AAGCGCCACAGAGGTAACG 60.374 57.895 2.29 0.00 46.39 3.18
1344 1568 3.488090 GCGCCACAGAGGTAACGC 61.488 66.667 0.00 0.00 41.31 4.84
1353 1577 3.364277 GAGGTAACGCTCACCATCC 57.636 57.895 3.79 0.00 46.39 3.51
1354 1578 0.535335 GAGGTAACGCTCACCATCCA 59.465 55.000 3.79 0.00 46.39 3.41
1355 1579 0.249398 AGGTAACGCTCACCATCCAC 59.751 55.000 3.79 0.00 46.39 4.02
1356 1580 0.249398 GGTAACGCTCACCATCCACT 59.751 55.000 0.00 0.00 36.01 4.00
1357 1581 1.338769 GGTAACGCTCACCATCCACTT 60.339 52.381 0.00 0.00 36.01 3.16
1429 1680 1.002868 AATTGAGCTGAGCGCACCT 60.003 52.632 11.17 0.00 38.19 4.00
1497 1748 4.534500 TCCCCTTTTGTAGATCTTGCTACA 59.466 41.667 0.00 0.00 46.52 2.74
1519 1770 2.998670 ACATCATTCTTGTCGTGAGCTG 59.001 45.455 0.00 0.00 0.00 4.24
1656 1912 4.142315 CCTGGTCATTGACTGCAATTTAGG 60.142 45.833 16.02 7.72 41.87 2.69
1746 2002 1.733399 GGAAGGCGACGACACTGAC 60.733 63.158 2.19 0.00 0.00 3.51
1842 2098 2.033141 AGCTGGCGCATGAACACT 59.967 55.556 10.83 0.00 39.10 3.55
1966 2222 1.529244 AACAGCCAGGTTGGTGCTC 60.529 57.895 8.37 0.00 40.46 4.26
2415 2712 4.228317 CTGACATCGATGCATCTACTGAG 58.772 47.826 25.11 7.83 0.00 3.35
2464 2761 1.814429 TCCAACACCCTCCTCTTCAA 58.186 50.000 0.00 0.00 0.00 2.69
2553 2851 5.256474 AGATTGCCTTTATACTTGCACAGT 58.744 37.500 6.74 6.74 39.87 3.55
2638 2967 6.264067 AGCCTATTGTCTTCCAGCATTAATTC 59.736 38.462 0.00 0.00 0.00 2.17
2721 3056 7.049133 CCATTGCTTCATCCAAAATAAATCCA 58.951 34.615 0.00 0.00 0.00 3.41
2940 3275 7.001674 TGGCTTTAAGGTGATCTTCTTAACAA 58.998 34.615 15.59 6.59 35.83 2.83
3130 3467 2.238395 TGCCAACACTGTGCTATCCATA 59.762 45.455 7.90 0.00 0.00 2.74
3322 3659 7.178983 TGCCAGAAAATTGATTACCTGAAAGAT 59.821 33.333 0.00 0.00 34.07 2.40
3380 3717 3.229276 TGAAGGTGTGTTTGCTTTGTG 57.771 42.857 0.00 0.00 0.00 3.33
3782 4123 2.027837 TGAGCTCCCCCGTTTAGTTTAC 60.028 50.000 12.15 0.00 0.00 2.01
3821 4162 1.619654 CTGGATTCCAGCACCACAAA 58.380 50.000 19.49 0.00 45.13 2.83
3957 4298 4.487019 GTGTCTCAGCTGTCCTTACTAAC 58.513 47.826 14.67 1.18 0.00 2.34
4095 4436 2.698274 GTTCCCACAAAGGTTTGATGGT 59.302 45.455 9.42 0.00 40.55 3.55
4210 4556 1.280982 AGCGTAACATGTGATGCTCG 58.719 50.000 22.36 5.39 0.00 5.03
4304 4650 2.086094 CCAATGATTTTTGGGCTTGCC 58.914 47.619 2.49 2.49 42.09 4.52
4637 4983 4.690184 TTGTCATCTGCAGCAGTTATTG 57.310 40.909 22.10 14.71 32.61 1.90
4639 4985 4.831107 TGTCATCTGCAGCAGTTATTGTA 58.169 39.130 22.10 0.88 32.61 2.41
4640 4986 4.631377 TGTCATCTGCAGCAGTTATTGTAC 59.369 41.667 22.10 11.70 32.61 2.90
4641 4987 4.631377 GTCATCTGCAGCAGTTATTGTACA 59.369 41.667 22.10 0.00 32.61 2.90
4666 5016 6.870971 TCTGGAGTTTTAACCAACATGTAC 57.129 37.500 0.00 0.00 35.67 2.90
4798 5170 0.321671 ATGGTGGTGTTCCTCAGTCG 59.678 55.000 0.00 0.00 34.23 4.18
4979 5351 4.943705 AGTGAGGTACCAGTATGCAAAATG 59.056 41.667 15.94 0.00 31.97 2.32
5203 6101 8.718158 ATGGATCTGTCACAGAAGATATTCTA 57.282 34.615 12.63 1.76 44.04 2.10
5789 6687 1.597742 GTCTTCTGAAGGTGCTTGCA 58.402 50.000 16.83 0.00 0.00 4.08
5882 6780 0.387929 TCAAGTGGACGACGCTTCTT 59.612 50.000 7.51 0.00 46.56 2.52
6525 7428 6.821665 TGGAGGAGTTTTTAAATATGAGGTCG 59.178 38.462 0.00 0.00 0.00 4.79
6558 7461 3.321682 TGAAATTTCTTGGGCAAGTCCAG 59.678 43.478 18.64 0.00 39.38 3.86
6577 7480 4.168088 TCCAGGAGTTTTTCTTTCCCTTCT 59.832 41.667 0.00 0.00 0.00 2.85
6682 7588 2.712984 TGCAGAAATCGGCAACACA 58.287 47.368 5.76 0.00 43.64 3.72
6683 7589 1.028130 TGCAGAAATCGGCAACACAA 58.972 45.000 5.76 0.00 43.64 3.33
6684 7590 1.268999 TGCAGAAATCGGCAACACAAC 60.269 47.619 5.76 0.00 43.64 3.32
6685 7591 1.001378 GCAGAAATCGGCAACACAACT 60.001 47.619 0.54 0.00 37.03 3.16
6718 7624 8.958119 ACACTGAACTCATGTACTTCTTTTAA 57.042 30.769 0.00 0.00 0.00 1.52
6721 7627 9.046296 ACTGAACTCATGTACTTCTTTTAACTG 57.954 33.333 0.00 0.00 0.00 3.16
6931 7837 5.258051 TGGGTTCGTTAGGATAAGCATTTT 58.742 37.500 0.00 0.00 0.00 1.82
7014 7920 5.331876 AGTTACAGCTTGGCTCTACTTAG 57.668 43.478 0.00 0.00 36.40 2.18
7015 7921 4.160626 AGTTACAGCTTGGCTCTACTTAGG 59.839 45.833 0.00 0.00 36.40 2.69
7129 8035 4.505039 GGAGTTGTAGATGTCACCCAAACT 60.505 45.833 0.00 0.00 0.00 2.66
7182 8797 3.875727 GGTCTAATTTTAGTCCTTCGGCC 59.124 47.826 0.00 0.00 36.46 6.13
7183 8798 4.383880 GGTCTAATTTTAGTCCTTCGGCCT 60.384 45.833 0.00 0.00 36.46 5.19
7184 8799 5.183969 GTCTAATTTTAGTCCTTCGGCCTT 58.816 41.667 0.00 0.00 32.61 4.35
7185 8800 5.293814 GTCTAATTTTAGTCCTTCGGCCTTC 59.706 44.000 0.00 0.00 32.61 3.46
7186 8801 2.088950 TTTTAGTCCTTCGGCCTTCG 57.911 50.000 0.00 0.00 40.90 3.79
7187 8802 0.248289 TTTAGTCCTTCGGCCTTCGG 59.752 55.000 0.00 0.00 39.77 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.402528 CGGTCATCCAACCCGGCA 62.403 66.667 0.00 0.00 38.09 5.69
58 59 1.250328 ATGTCTACCAACACGTCCGA 58.750 50.000 0.00 0.00 30.55 4.55
61 62 7.744715 CAGAAATAAAATGTCTACCAACACGTC 59.255 37.037 0.00 0.00 30.55 4.34
63 64 7.533900 CACAGAAATAAAATGTCTACCAACACG 59.466 37.037 0.00 0.00 30.55 4.49
69 70 7.390718 ACCTCACACAGAAATAAAATGTCTACC 59.609 37.037 0.00 0.00 0.00 3.18
85 86 1.068472 GTCTACGGACACCTCACACAG 60.068 57.143 0.00 0.00 41.75 3.66
86 87 0.956633 GTCTACGGACACCTCACACA 59.043 55.000 0.00 0.00 41.75 3.72
117 118 5.067153 ACTCCAACATCGTGAATCAAAACAA 59.933 36.000 0.00 0.00 0.00 2.83
121 122 4.556501 GCAACTCCAACATCGTGAATCAAA 60.557 41.667 0.00 0.00 0.00 2.69
162 163 5.885912 GGACCAAACATAGCTTCTGGAAATA 59.114 40.000 0.00 0.00 0.00 1.40
211 212 2.291209 TGAACACAGCACATCCCAAT 57.709 45.000 0.00 0.00 0.00 3.16
212 213 2.064434 TTGAACACAGCACATCCCAA 57.936 45.000 0.00 0.00 0.00 4.12
223 224 4.020662 AGCCCAGTTTTTCTTTTGAACACA 60.021 37.500 0.00 0.00 38.30 3.72
255 256 9.846248 AATCAAAAGATACACTCATAGCAAAAC 57.154 29.630 0.00 0.00 0.00 2.43
266 269 8.515414 GCCAAAACTAGAATCAAAAGATACACT 58.485 33.333 0.00 0.00 0.00 3.55
295 298 4.266029 GCACATTGCGTCAAAAGATAATGG 59.734 41.667 0.00 0.00 31.71 3.16
317 320 2.501723 TCAGATCCTTGGGTTCTGTAGC 59.498 50.000 18.41 0.00 45.01 3.58
328 331 6.573664 TTAACAACATGGTTCAGATCCTTG 57.426 37.500 10.57 10.57 36.56 3.61
347 504 9.013490 CATTGAGATTGAAACAATCGGATTAAC 57.987 33.333 15.54 0.00 32.92 2.01
351 508 7.395190 TTCATTGAGATTGAAACAATCGGAT 57.605 32.000 15.54 9.94 32.92 4.18
397 554 8.202745 ACGAGGCAAATTATTTTGTTTTCAAA 57.797 26.923 10.80 0.00 46.39 2.69
428 585 9.296400 GTAGAAGAGAATAAACAGATGTCAGAC 57.704 37.037 0.00 0.00 0.00 3.51
472 633 3.554731 GGTAAACGATACTGTAGCAAGGC 59.445 47.826 3.80 0.00 0.00 4.35
473 634 4.117685 GGGTAAACGATACTGTAGCAAGG 58.882 47.826 3.80 0.00 0.00 3.61
474 635 3.795101 CGGGTAAACGATACTGTAGCAAG 59.205 47.826 3.80 0.00 35.47 4.01
475 636 3.193267 ACGGGTAAACGATACTGTAGCAA 59.807 43.478 3.80 0.00 37.61 3.91
477 638 3.427161 ACGGGTAAACGATACTGTAGC 57.573 47.619 0.00 0.00 37.61 3.58
479 640 4.095782 GTGGTACGGGTAAACGATACTGTA 59.904 45.833 0.00 0.00 37.61 2.74
480 641 3.088532 TGGTACGGGTAAACGATACTGT 58.911 45.455 0.00 0.00 37.61 3.55
493 654 0.682852 TGGAAGTGAAGTGGTACGGG 59.317 55.000 0.00 0.00 0.00 5.28
519 683 3.069289 TCAACTACTGCTGTGCAATCAG 58.931 45.455 6.48 8.91 38.41 2.90
527 691 8.883731 GTGTGATTATTTATCAACTACTGCTGT 58.116 33.333 0.66 0.66 44.62 4.40
586 750 1.841103 GGAGGAGGAGATCTGCCCC 60.841 68.421 11.06 8.87 33.99 5.80
587 751 0.831711 GAGGAGGAGGAGATCTGCCC 60.832 65.000 11.06 11.63 33.99 5.36
780 957 0.392998 CTGTCGGTTTCCATGAGGGG 60.393 60.000 0.00 0.00 37.22 4.79
825 1007 0.840722 GGAGGAGGGTGAAAGGGACA 60.841 60.000 0.00 0.00 0.00 4.02
830 1012 3.416351 GGGGGAGGAGGGTGAAAG 58.584 66.667 0.00 0.00 0.00 2.62
848 1030 1.595357 GTGGTGGAACTACCGGGAG 59.405 63.158 13.79 13.79 43.21 4.30
849 1031 3.795905 GTGGTGGAACTACCGGGA 58.204 61.111 6.32 0.00 43.21 5.14
854 1036 8.065974 GCTACTAGTAGTGGTGGTGGAACTAC 62.066 50.000 26.76 4.43 44.28 2.73
855 1037 4.393239 ACTAGTAGTGGTGGTGGAACTA 57.607 45.455 0.85 0.00 36.74 2.24
856 1038 3.255634 ACTAGTAGTGGTGGTGGAACT 57.744 47.619 0.85 0.00 36.74 3.01
857 1039 3.119209 GCTACTAGTAGTGGTGGTGGAAC 60.119 52.174 26.76 6.00 35.65 3.62
859 1041 2.042026 TGCTACTAGTAGTGGTGGTGGA 59.958 50.000 26.76 2.12 35.65 4.02
861 1043 2.159226 GCTGCTACTAGTAGTGGTGGTG 60.159 54.545 26.76 12.61 35.65 4.17
862 1044 2.100989 GCTGCTACTAGTAGTGGTGGT 58.899 52.381 26.76 0.00 35.65 4.16
867 1049 0.317103 CGCCGCTGCTACTAGTAGTG 60.317 60.000 26.76 20.79 38.03 2.74
1043 1252 3.951680 AGCGAGGTTCTTGGAAAAGAAAA 59.048 39.130 2.63 0.00 40.15 2.29
1044 1253 3.551846 AGCGAGGTTCTTGGAAAAGAAA 58.448 40.909 2.63 0.00 40.15 2.52
1045 1254 3.208747 AGCGAGGTTCTTGGAAAAGAA 57.791 42.857 0.00 0.00 36.52 2.52
1046 1255 2.930826 AGCGAGGTTCTTGGAAAAGA 57.069 45.000 0.00 0.00 0.00 2.52
1047 1256 3.632189 CAAAGCGAGGTTCTTGGAAAAG 58.368 45.455 0.00 0.00 0.00 2.27
1048 1257 2.223711 GCAAAGCGAGGTTCTTGGAAAA 60.224 45.455 0.00 0.00 0.00 2.29
1093 1302 1.741401 CGAGGCTTTGCATCCACGA 60.741 57.895 12.24 0.00 38.43 4.35
1094 1303 1.091771 ATCGAGGCTTTGCATCCACG 61.092 55.000 11.65 11.65 35.86 4.94
1102 1311 1.729149 GCGGTCAAAATCGAGGCTTTG 60.729 52.381 9.87 9.87 34.49 2.77
1343 1567 1.077429 GGGGAAGTGGATGGTGAGC 60.077 63.158 0.00 0.00 0.00 4.26
1344 1568 0.035056 GTGGGGAAGTGGATGGTGAG 60.035 60.000 0.00 0.00 0.00 3.51
1345 1569 1.836999 CGTGGGGAAGTGGATGGTGA 61.837 60.000 0.00 0.00 0.00 4.02
1346 1570 1.377202 CGTGGGGAAGTGGATGGTG 60.377 63.158 0.00 0.00 0.00 4.17
1347 1571 2.602676 CCGTGGGGAAGTGGATGGT 61.603 63.158 0.00 0.00 34.06 3.55
1348 1572 2.272146 CCGTGGGGAAGTGGATGG 59.728 66.667 0.00 0.00 34.06 3.51
1349 1573 1.078426 GTCCGTGGGGAAGTGGATG 60.078 63.158 0.00 0.00 46.08 3.51
1350 1574 2.656069 CGTCCGTGGGGAAGTGGAT 61.656 63.158 0.00 0.00 46.08 3.41
1351 1575 3.307906 CGTCCGTGGGGAAGTGGA 61.308 66.667 0.00 0.00 46.08 4.02
1352 1576 4.388499 CCGTCCGTGGGGAAGTGG 62.388 72.222 0.00 0.00 46.08 4.00
1353 1577 2.573609 GATCCGTCCGTGGGGAAGTG 62.574 65.000 0.00 0.00 46.08 3.16
1354 1578 2.284405 ATCCGTCCGTGGGGAAGT 60.284 61.111 0.00 0.00 46.08 3.01
1355 1579 2.017559 GAGATCCGTCCGTGGGGAAG 62.018 65.000 0.00 0.00 46.08 3.46
1356 1580 2.038329 AGATCCGTCCGTGGGGAA 59.962 61.111 0.00 0.00 46.08 3.97
1357 1581 2.441532 GAGATCCGTCCGTGGGGA 60.442 66.667 0.00 0.00 41.08 4.81
1429 1680 6.263516 ACTACTCGTAGCATAAACTTGTCA 57.736 37.500 4.08 0.00 36.66 3.58
1497 1748 3.434641 CAGCTCACGACAAGAATGATGTT 59.565 43.478 0.00 0.00 0.00 2.71
1519 1770 0.533951 ACCGTCCGACCTTCATTACC 59.466 55.000 0.00 0.00 0.00 2.85
1629 1880 1.028868 GCAGTCAATGACCAGGAGGC 61.029 60.000 10.12 1.33 39.06 4.70
1636 1892 3.763897 ACCCTAAATTGCAGTCAATGACC 59.236 43.478 10.12 0.00 41.77 4.02
1656 1912 5.169836 AGACTCGACAAAATGTTTCAACC 57.830 39.130 0.00 0.00 0.00 3.77
1842 2098 0.251564 CAACATTGCCACTACCCCCA 60.252 55.000 0.00 0.00 0.00 4.96
2415 2712 4.689345 AGTAAAGCGTCTTCCATGTTGTAC 59.311 41.667 0.00 0.00 0.00 2.90
2464 2761 7.436430 CAGATGCTGCTGTAAGATATGAATT 57.564 36.000 0.00 0.00 34.07 2.17
2940 3275 8.150945 TCTGCTTCAACTAAGTACAGAAGAAAT 58.849 33.333 0.00 0.00 38.30 2.17
2990 3327 5.046910 ACAGAAATGAAATGGTAGCAACG 57.953 39.130 0.00 0.00 0.00 4.10
3130 3467 4.012374 CCACAGGATAATCAACAGCAAGT 58.988 43.478 0.00 0.00 0.00 3.16
3322 3659 7.504238 TCTTTAACAAATGAAGGCTGGACTTTA 59.496 33.333 0.00 0.00 0.00 1.85
3957 4298 6.421377 TCAAGATTCAACATGTATTGTCCG 57.579 37.500 0.00 0.00 37.68 4.79
4095 4436 9.889128 TTTGCATATCGATCATTCCTATCAATA 57.111 29.630 0.00 0.00 0.00 1.90
4150 4491 3.999663 GTGAATTCAGGAGAGAACTGTGG 59.000 47.826 8.80 0.00 37.25 4.17
4152 4493 4.262808 CCAGTGAATTCAGGAGAGAACTGT 60.263 45.833 8.80 0.00 37.25 3.55
4304 4650 1.017387 GCCCCTCAAGTTAATCTGCG 58.983 55.000 0.00 0.00 0.00 5.18
4438 4784 2.291540 CCTTCTTCTTGCCCCCACATAA 60.292 50.000 0.00 0.00 0.00 1.90
4637 4983 7.266922 TGTTGGTTAAAACTCCAGAATGTAC 57.733 36.000 0.00 0.00 35.05 2.90
4639 4985 6.323739 ACATGTTGGTTAAAACTCCAGAATGT 59.676 34.615 0.00 0.00 37.07 2.71
4640 4986 6.748132 ACATGTTGGTTAAAACTCCAGAATG 58.252 36.000 0.00 0.00 35.93 2.67
4641 4987 6.976934 ACATGTTGGTTAAAACTCCAGAAT 57.023 33.333 0.00 0.00 35.05 2.40
4666 5016 0.323725 ACCCAGCACCTGCCAAATAG 60.324 55.000 0.00 0.00 43.38 1.73
4798 5170 4.899502 TCAAAAGAGATTCTGGAGTGGAC 58.100 43.478 0.00 0.00 0.00 4.02
4979 5351 4.202111 ACAAAAACACTAGTTGCATCCACC 60.202 41.667 0.00 0.00 38.17 4.61
5203 6101 1.470098 GCGTGCATCTTGAATCCAGTT 59.530 47.619 0.00 0.00 0.00 3.16
5789 6687 2.897969 AGTGAAGTTGGTGTCGATACCT 59.102 45.455 28.64 11.40 41.43 3.08
5882 6780 1.784358 AAATGGTCGTCGGAGGGATA 58.216 50.000 0.00 0.00 0.00 2.59
6339 7237 6.759827 GCTTAACCTCATGAAAACGGTAGATA 59.240 38.462 4.89 0.00 0.00 1.98
6547 7450 1.613925 GAAAAACTCCTGGACTTGCCC 59.386 52.381 0.00 0.00 34.97 5.36
6558 7461 4.730966 AGGAGAAGGGAAAGAAAAACTCC 58.269 43.478 0.00 0.00 41.74 3.85
6577 7480 5.779241 AATGGTTTCTTACATGGAGAGGA 57.221 39.130 0.00 0.00 0.00 3.71
6678 7584 4.465632 TCAGTGTCTTGTGTAGTTGTGT 57.534 40.909 0.00 0.00 0.00 3.72
6679 7585 4.870426 AGTTCAGTGTCTTGTGTAGTTGTG 59.130 41.667 0.00 0.00 0.00 3.33
6680 7586 5.086104 AGTTCAGTGTCTTGTGTAGTTGT 57.914 39.130 0.00 0.00 0.00 3.32
6681 7587 5.109210 TGAGTTCAGTGTCTTGTGTAGTTG 58.891 41.667 0.00 0.00 0.00 3.16
6682 7588 5.339008 TGAGTTCAGTGTCTTGTGTAGTT 57.661 39.130 0.00 0.00 0.00 2.24
6683 7589 5.163405 ACATGAGTTCAGTGTCTTGTGTAGT 60.163 40.000 0.00 0.00 31.73 2.73
6684 7590 5.292765 ACATGAGTTCAGTGTCTTGTGTAG 58.707 41.667 0.00 0.00 31.73 2.74
6685 7591 5.276461 ACATGAGTTCAGTGTCTTGTGTA 57.724 39.130 0.00 0.00 31.73 2.90
6718 7624 6.270064 CAAAAACCGAAAACATAGGAACAGT 58.730 36.000 0.00 0.00 0.00 3.55
6721 7627 5.044558 TGCAAAAACCGAAAACATAGGAAC 58.955 37.500 0.00 0.00 0.00 3.62
6795 7701 5.817816 ACAGGGAGAGAAAATAAACTATGCG 59.182 40.000 0.00 0.00 0.00 4.73
6815 7721 3.056821 TGATGACCGACAACTTCTACAGG 60.057 47.826 0.00 0.00 0.00 4.00
6931 7837 5.772672 ACTTTGGCATAGTAATTGTTGGTCA 59.227 36.000 8.93 0.00 0.00 4.02
7014 7920 4.932146 AGTGCATTGTGTTTTTCTGTACC 58.068 39.130 0.00 0.00 0.00 3.34
7015 7921 6.636850 CCTTAGTGCATTGTGTTTTTCTGTAC 59.363 38.462 0.00 0.00 0.00 2.90
7129 8035 9.923143 TCTTCATCGAGAACATACTTTAGAAAA 57.077 29.630 0.00 0.00 31.61 2.29


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

AutoCloner maintained by Alex Coulton.