Multiple sequence alignment - TraesCS6D01G380400

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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 TraesCS6D01G380400 chr6D 100.000 7954 0 0 1 7954 461457569 461449616 0.000000e+00 14689.0
1 TraesCS6D01G380400 chr6A 94.275 8070 226 90 1 7954 608121198 608113249 0.000000e+00 12126.0
2 TraesCS6D01G380400 chr6A 71.936 563 122 31 11 555 63098297 63097753 1.800000e-26 132.0
3 TraesCS6D01G380400 chr6B 94.236 6298 193 63 1743 7932 703289728 703283493 0.000000e+00 9463.0
4 TraesCS6D01G380400 chr6B 86.613 493 38 16 838 1324 703290764 703290294 3.290000e-143 520.0
5 TraesCS6D01G380400 chr6B 79.762 252 38 11 307 550 8097541 8097787 3.820000e-38 171.0
6 TraesCS6D01G380400 chrUn 84.848 297 45 0 3430 3726 93449000 93449296 4.670000e-77 300.0
7 TraesCS6D01G380400 chrUn 81.206 282 50 2 4255 4536 93450181 93450459 2.890000e-54 224.0
8 TraesCS6D01G380400 chrUn 84.507 213 30 3 6869 7078 93453337 93453549 2.910000e-49 207.0
9 TraesCS6D01G380400 chrUn 82.031 128 17 5 316 439 62957047 62957172 3.930000e-18 104.0
10 TraesCS6D01G380400 chr7B 84.512 297 46 0 3430 3726 743145887 743145591 2.170000e-75 294.0
11 TraesCS6D01G380400 chr7B 83.099 213 33 2 6869 7078 743142283 743142071 2.930000e-44 191.0
12 TraesCS6D01G380400 chr7B 79.558 181 30 5 338 512 741398440 741398619 1.080000e-23 122.0
13 TraesCS6D01G380400 chr1A 82.014 278 32 13 302 565 128640566 128640293 3.740000e-53 220.0
14 TraesCS6D01G380400 chr1A 79.825 114 17 5 409 519 515591692 515591582 2.380000e-10 78.7
15 TraesCS6D01G380400 chr1D 80.876 251 36 7 505 747 291102031 291101785 3.790000e-43 187.0
16 TraesCS6D01G380400 chr7A 84.375 192 24 6 551 737 584112574 584112384 4.900000e-42 183.0
17 TraesCS6D01G380400 chr7A 73.843 562 90 31 7 549 276923499 276924022 3.820000e-38 171.0
18 TraesCS6D01G380400 chr2B 85.714 175 20 5 2 173 39705554 39705382 6.340000e-41 180.0
19 TraesCS6D01G380400 chr5D 80.784 255 25 16 528 765 544289725 544289972 2.280000e-40 178.0
20 TraesCS6D01G380400 chr5D 80.995 221 23 14 528 736 548794386 548794173 2.970000e-34 158.0
21 TraesCS6D01G380400 chr5D 78.947 152 17 7 364 511 65857269 65857409 1.100000e-13 89.8
22 TraesCS6D01G380400 chr4A 82.028 217 24 12 529 736 569852728 569852518 3.820000e-38 171.0
23 TraesCS6D01G380400 chr2D 84.971 173 21 4 2 171 488062437 488062267 3.820000e-38 171.0
24 TraesCS6D01G380400 chr3A 79.087 263 38 13 1 257 16684314 16684063 1.780000e-36 165.0
25 TraesCS6D01G380400 chr3A 81.000 200 30 7 2 197 42021929 42022124 1.380000e-32 152.0
26 TraesCS6D01G380400 chr3A 79.654 231 32 10 528 747 464482833 464482607 1.380000e-32 152.0
27 TraesCS6D01G380400 chr3D 83.523 176 23 6 1 171 135047068 135047242 8.260000e-35 159.0
28 TraesCS6D01G380400 chr1B 83.721 172 24 4 2 171 640225119 640224950 8.260000e-35 159.0
29 TraesCS6D01G380400 chr4D 78.800 250 29 15 521 759 434528095 434527859 6.430000e-31 147.0
30 TraesCS6D01G380400 chr4B 79.452 219 29 11 528 734 524656475 524656261 2.990000e-29 141.0
31 TraesCS6D01G380400 chr4B 74.242 396 67 24 58 442 66190704 66191075 5.010000e-27 134.0
32 TraesCS6D01G380400 chr7D 78.112 233 41 9 8 236 408740743 408740969 1.080000e-28 139.0
33 TraesCS6D01G380400 chr3B 73.077 416 73 27 61 446 296195814 296195408 2.350000e-20 111.0
34 TraesCS6D01G380400 chr2A 81.379 145 17 9 372 507 4834369 4834512 8.440000e-20 110.0


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 TraesCS6D01G380400 chr6D 461449616 461457569 7953 True 14689.000000 14689 100.000000 1 7954 1 chr6D.!!$R1 7953
1 TraesCS6D01G380400 chr6A 608113249 608121198 7949 True 12126.000000 12126 94.275000 1 7954 1 chr6A.!!$R2 7953
2 TraesCS6D01G380400 chr6B 703283493 703290764 7271 True 4991.500000 9463 90.424500 838 7932 2 chr6B.!!$R1 7094
3 TraesCS6D01G380400 chrUn 93449000 93453549 4549 False 243.666667 300 83.520333 3430 7078 3 chrUn.!!$F2 3648
4 TraesCS6D01G380400 chr7B 743142071 743145887 3816 True 242.500000 294 83.805500 3430 7078 2 chr7B.!!$R1 3648

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
948 960 1.523758 GCCTCTTTCTTTCTTCGCCA 58.476 50.000 0.00 0.0 0.00 5.69 F
1205 1218 0.328258 GGTGGCTGGGATTGTACTGT 59.672 55.000 0.00 0.0 0.00 3.55 F
1670 2016 0.475906 AGTTCCTGCAAAGACTGGCT 59.524 50.000 0.00 0.0 0.00 4.75 F
2484 2860 0.894141 TTGCCCAATCATGTTTCCGG 59.106 50.000 0.00 0.0 0.00 5.14 F
3199 3601 1.298157 GGCATACGCACTTGTGAGCA 61.298 55.000 4.79 0.0 41.24 4.26 F
3798 4201 1.519246 CAGATTCAGGGCTCGCTCA 59.481 57.895 0.00 0.0 0.00 4.26 F
4995 5822 1.651737 TGGCTAACTCTACTTGGGCA 58.348 50.000 0.00 0.0 35.23 5.36 F
5316 6158 0.721718 CCTTGAACGCGACCTCAATC 59.278 55.000 15.93 0.0 31.40 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2468 2844 0.732571 CGACCGGAAACATGATTGGG 59.267 55.000 9.46 0.00 0.00 4.12 R
2677 3057 2.105477 AGCACATGTCAGAGGAACTTGT 59.895 45.455 0.00 0.00 41.55 3.16 R
2678 3058 2.775890 AGCACATGTCAGAGGAACTTG 58.224 47.619 0.00 0.00 41.55 3.16 R
3798 4201 0.617935 GCCTGCCTTCTCTTCCTCTT 59.382 55.000 0.00 0.00 0.00 2.85 R
4012 4749 3.851976 TGAAGATCTCATTTCCTGGGGAA 59.148 43.478 0.00 0.00 40.27 3.97 R
5316 6158 0.736325 AAGTCGGTTCGAGAATGCCG 60.736 55.000 8.12 8.12 44.95 5.69 R
6095 7527 1.363744 CAGTCTTCTTGATCCGTGCC 58.636 55.000 0.00 0.00 0.00 5.01 R
7187 8822 0.665298 GATGCCGCCTTTCAAGATCC 59.335 55.000 0.00 0.00 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
372 374 6.908284 CACACTGAAAAATTTCCAAATGCTTG 59.092 34.615 3.60 0.00 36.36 4.01
458 462 7.707624 ATGATCAACTTTCCACACATATTGT 57.292 32.000 0.00 0.00 39.97 2.71
461 465 9.898152 TGATCAACTTTCCACACATATTGTATA 57.102 29.630 0.00 0.00 35.67 1.47
581 587 7.359595 TCAACTTTTCACACACATTGTATAGC 58.640 34.615 0.00 0.00 35.67 2.97
600 606 1.652124 GCTTTTGCATGCATCTTCGTG 59.348 47.619 23.37 8.83 46.58 4.35
613 619 5.912396 TGCATCTTCGTGTACATTTGAAAAC 59.088 36.000 0.00 0.00 0.00 2.43
621 628 8.373048 TCGTGTACATTTGAAAACAACTCTAT 57.627 30.769 0.00 0.00 0.00 1.98
792 799 2.351706 ATAGGTCCTGTCGAGAGTCC 57.648 55.000 8.95 10.36 0.00 3.85
796 803 3.827898 CCTGTCGAGAGTCCCCGC 61.828 72.222 8.95 0.00 0.00 6.13
948 960 1.523758 GCCTCTTTCTTTCTTCGCCA 58.476 50.000 0.00 0.00 0.00 5.69
1119 1132 1.229984 CCTCCCCCTTCTTGGTCCT 60.230 63.158 0.00 0.00 0.00 3.85
1120 1133 0.846870 CCTCCCCCTTCTTGGTCCTT 60.847 60.000 0.00 0.00 0.00 3.36
1135 1148 1.064134 CCTTGCCGCTTAAATCCGC 59.936 57.895 0.00 0.00 0.00 5.54
1174 1187 3.866582 GGCCAGGATACCGCAGCT 61.867 66.667 0.00 0.00 34.11 4.24
1201 1214 2.994699 CCGGTGGCTGGGATTGTA 59.005 61.111 0.00 0.00 0.00 2.41
1202 1215 1.451387 CCGGTGGCTGGGATTGTAC 60.451 63.158 0.00 0.00 0.00 2.90
1203 1216 1.602237 CGGTGGCTGGGATTGTACT 59.398 57.895 0.00 0.00 0.00 2.73
1204 1217 0.744414 CGGTGGCTGGGATTGTACTG 60.744 60.000 0.00 0.00 0.00 2.74
1205 1218 0.328258 GGTGGCTGGGATTGTACTGT 59.672 55.000 0.00 0.00 0.00 3.55
1325 1341 1.313091 GCCGGTGGGAGTTGAAATCC 61.313 60.000 2.50 2.50 35.99 3.01
1394 1410 4.696455 ACAGGCCATGTTTTCTTTTCTTG 58.304 39.130 5.01 0.00 39.96 3.02
1406 1422 5.403897 TTCTTTTCTTGACGCTGTGTTAG 57.596 39.130 0.00 0.00 0.00 2.34
1421 1441 5.505324 GCTGTGTTAGAATGATTGATGGCTC 60.505 44.000 0.00 0.00 0.00 4.70
1585 1931 1.268899 GCATCTCAGCTGTTTGCACTT 59.731 47.619 23.65 0.08 45.94 3.16
1586 1932 2.485426 GCATCTCAGCTGTTTGCACTTA 59.515 45.455 23.65 0.64 45.94 2.24
1604 1950 4.452114 CACTTATGCAACACAACTGAGCTA 59.548 41.667 0.00 0.00 0.00 3.32
1670 2016 0.475906 AGTTCCTGCAAAGACTGGCT 59.524 50.000 0.00 0.00 0.00 4.75
1681 2028 4.034975 GCAAAGACTGGCTATAAGCTGAAG 59.965 45.833 0.00 0.00 41.99 3.02
1720 2067 8.746922 ATTTCATTTTATCATGTGTGTGTCAC 57.253 30.769 0.00 0.00 46.31 3.67
1798 2146 2.819608 TGCAGGAATTTTCTTCCCTTCG 59.180 45.455 0.44 0.00 39.39 3.79
1801 2149 3.440522 CAGGAATTTTCTTCCCTTCGACC 59.559 47.826 0.44 0.00 39.39 4.79
1837 2185 1.123928 GGTCCCTCCAGACGATCATT 58.876 55.000 0.00 0.00 37.66 2.57
1965 2319 1.913451 AAGGTCAGAGACGCGTCGAG 61.913 60.000 31.56 24.19 32.65 4.04
2116 2470 1.604308 CAACCTGCACCTGATGGCA 60.604 57.895 0.00 0.00 38.52 4.92
2305 2659 5.366768 ACTGCTGTAATATCTTGGCCTTCTA 59.633 40.000 3.32 0.00 0.00 2.10
2340 2697 7.103641 CAGCTATAAAACTGTCACCTCCTTAA 58.896 38.462 0.00 0.00 0.00 1.85
2354 2711 3.249080 CCTCCTTAACGAAACTTTGCGAA 59.751 43.478 0.00 0.00 0.00 4.70
2394 2751 2.777094 GCTTCTCAAGGCTTCTCAAGT 58.223 47.619 0.00 0.00 0.00 3.16
2395 2752 2.483491 GCTTCTCAAGGCTTCTCAAGTG 59.517 50.000 0.00 0.00 0.00 3.16
2418 2794 5.098211 GGCTGCAATAGTGAAGTGAATTTC 58.902 41.667 0.50 0.00 32.15 2.17
2468 2844 7.814587 AGTATTTTGTGCTTTATCCTTTCTTGC 59.185 33.333 0.00 0.00 0.00 4.01
2473 2849 4.081476 GTGCTTTATCCTTTCTTGCCCAAT 60.081 41.667 0.00 0.00 0.00 3.16
2484 2860 0.894141 TTGCCCAATCATGTTTCCGG 59.106 50.000 0.00 0.00 0.00 5.14
2489 2868 2.288666 CCAATCATGTTTCCGGTCGAT 58.711 47.619 0.00 0.00 0.00 3.59
2636 3016 5.995565 TGTAGTACAGTACAGCCAGAAAT 57.004 39.130 13.37 0.00 0.00 2.17
2653 3033 7.123247 AGCCAGAAATAATTAGACATTTGCACT 59.877 33.333 0.00 0.00 0.00 4.40
2655 3035 9.079833 CCAGAAATAATTAGACATTTGCACTTG 57.920 33.333 0.00 0.00 0.00 3.16
2677 3057 5.924356 TGAAATGTTACACTGACTGAAGGA 58.076 37.500 0.00 0.00 0.00 3.36
2678 3058 5.758296 TGAAATGTTACACTGACTGAAGGAC 59.242 40.000 0.00 0.00 0.00 3.85
2680 3060 4.746535 TGTTACACTGACTGAAGGACAA 57.253 40.909 0.00 0.00 0.00 3.18
2706 3095 4.591924 TCCTCTGACATGTGCTATCATCAT 59.408 41.667 1.15 0.00 0.00 2.45
2707 3096 4.930405 CCTCTGACATGTGCTATCATCATC 59.070 45.833 1.15 0.00 0.00 2.92
2708 3097 5.510861 CCTCTGACATGTGCTATCATCATCA 60.511 44.000 1.15 0.00 0.00 3.07
2809 3199 4.756642 TGCTCTTTACATCTCCACAACAAG 59.243 41.667 0.00 0.00 0.00 3.16
3199 3601 1.298157 GGCATACGCACTTGTGAGCA 61.298 55.000 4.79 0.00 41.24 4.26
3376 3778 2.224402 ACAAGGGAGTGTCAAGAGCTTC 60.224 50.000 0.00 0.00 0.00 3.86
3798 4201 1.519246 CAGATTCAGGGCTCGCTCA 59.481 57.895 0.00 0.00 0.00 4.26
4001 4738 5.869344 TGAAGACATAAACACCGAGATGAAG 59.131 40.000 0.00 0.00 0.00 3.02
4008 4745 2.461695 ACACCGAGATGAAGTGGAGAT 58.538 47.619 0.00 0.00 35.79 2.75
4012 4749 3.708631 ACCGAGATGAAGTGGAGATGAAT 59.291 43.478 0.00 0.00 0.00 2.57
4995 5822 1.651737 TGGCTAACTCTACTTGGGCA 58.348 50.000 0.00 0.00 35.23 5.36
5292 6134 2.179517 CCCGTCAGCGTCAGAGTC 59.820 66.667 0.00 0.00 36.15 3.36
5316 6158 0.721718 CCTTGAACGCGACCTCAATC 59.278 55.000 15.93 0.00 31.40 2.67
5471 6313 2.894387 GCTCCGGCTGTGCATCTC 60.894 66.667 0.00 0.00 33.65 2.75
5568 6410 2.603021 TCTAGGGAGCTCATCATGTCC 58.397 52.381 17.19 5.39 0.00 4.02
5757 6629 3.793144 GCCTGCGCCGTCTCTTTG 61.793 66.667 4.18 0.00 0.00 2.77
5944 6816 5.221048 CGGCTTCCAAAAGGATAATAACCAG 60.221 44.000 0.00 0.00 32.79 4.00
6095 7527 1.002134 AAGGCCACATTCAGGACGG 60.002 57.895 5.01 0.00 39.93 4.79
6181 7613 1.774639 TACTGGTTTGCGAAGTCGAC 58.225 50.000 7.70 7.70 43.02 4.20
6218 7650 0.031178 CCTGCAAAAGCACACCTGAC 59.969 55.000 0.00 0.00 0.00 3.51
6291 7727 4.827284 AGCATGCCAACTAAATATACCACC 59.173 41.667 15.66 0.00 0.00 4.61
6314 7750 3.581755 GCGCAGGGTATATGATTACGAA 58.418 45.455 0.30 0.00 0.00 3.85
6752 8376 5.643664 TGCTTGCATTTGAGTTAGCATAAG 58.356 37.500 1.41 0.00 36.80 1.73
6776 8405 9.797642 AAGTGCATATATCCTGAAACATATTCA 57.202 29.630 0.00 0.00 0.00 2.57
6794 8423 8.248945 ACATATTCAATTTGGCTTCTTTCTGAG 58.751 33.333 0.00 0.00 0.00 3.35
6798 8427 4.942761 ATTTGGCTTCTTTCTGAGCAAA 57.057 36.364 0.00 0.00 0.00 3.68
6800 8429 3.928727 TGGCTTCTTTCTGAGCAAATG 57.071 42.857 0.00 0.00 0.00 2.32
6813 8442 7.053316 TCTGAGCAAATGAGAAATGGAAAAA 57.947 32.000 0.00 0.00 0.00 1.94
6862 8494 0.883153 TGTCAGTGATGTTGGCATGC 59.117 50.000 9.90 9.90 35.07 4.06
7178 8813 0.321122 GGTCACCTGCCACAGAGAAG 60.321 60.000 0.00 0.00 32.44 2.85
7187 8822 1.941294 GCCACAGAGAAGCATGATCTG 59.059 52.381 13.09 13.09 44.81 2.90
7276 8914 4.644103 AAATGCTACCATGCAGAATGTC 57.356 40.909 0.00 0.00 46.71 3.06
7297 8935 2.947652 CCTAAGAATGTGGATGTGGCTG 59.052 50.000 0.00 0.00 0.00 4.85
7298 8936 1.180029 AAGAATGTGGATGTGGCTGC 58.820 50.000 0.00 0.00 0.00 5.25
7425 9067 0.741326 CGGAGATCACCACACGAGAT 59.259 55.000 9.99 0.00 0.00 2.75
7463 9106 1.880027 CCACTGGAAAAACGGAGAAGG 59.120 52.381 0.00 0.00 0.00 3.46
7718 9392 4.821589 GGCGTGCTCCTCGAAGGG 62.822 72.222 0.00 0.00 35.59 3.95
7936 9610 4.064768 TGGCTGGCATTGGGAGGG 62.065 66.667 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 9.719279 AGCATTTGAAAATGTTTAAAATGTGTG 57.281 25.926 18.39 3.03 45.77 3.82
581 587 2.937591 ACACGAAGATGCATGCAAAAG 58.062 42.857 26.68 16.21 0.00 2.27
594 600 7.186804 AGAGTTGTTTTCAAATGTACACGAAG 58.813 34.615 0.00 0.00 41.76 3.79
810 817 1.604378 CGGATCTCCATATGGGCCC 59.396 63.158 21.78 17.59 36.21 5.80
904 912 0.108709 GAGCAGAGCAGACAGACAGG 60.109 60.000 0.00 0.00 0.00 4.00
948 960 1.423395 CGCGTCTTCTTCTTCTTGCT 58.577 50.000 0.00 0.00 0.00 3.91
1135 1148 2.956964 GATCCGAGGACAAGCGCG 60.957 66.667 0.00 0.00 0.00 6.86
1201 1214 7.651808 CATCAAATCAGAAAAACACCTACAGT 58.348 34.615 0.00 0.00 0.00 3.55
1202 1215 6.583806 GCATCAAATCAGAAAAACACCTACAG 59.416 38.462 0.00 0.00 0.00 2.74
1203 1216 6.265196 AGCATCAAATCAGAAAAACACCTACA 59.735 34.615 0.00 0.00 0.00 2.74
1204 1217 6.583806 CAGCATCAAATCAGAAAAACACCTAC 59.416 38.462 0.00 0.00 0.00 3.18
1205 1218 6.265196 ACAGCATCAAATCAGAAAAACACCTA 59.735 34.615 0.00 0.00 0.00 3.08
1249 1265 1.656652 ATCAAATCCCGCGACAGAAG 58.343 50.000 8.23 0.00 0.00 2.85
1308 1324 1.812571 CAAGGATTTCAACTCCCACCG 59.187 52.381 0.00 0.00 32.89 4.94
1325 1341 4.005650 ACAGTGCTGGAATCATACACAAG 58.994 43.478 4.11 0.00 34.32 3.16
1394 1410 5.496387 CATCAATCATTCTAACACAGCGTC 58.504 41.667 0.00 0.00 0.00 5.19
1406 1422 3.057456 GCATCCTGAGCCATCAATCATTC 60.057 47.826 0.00 0.00 34.23 2.67
1421 1441 0.729116 CCTGCGTTTACAGCATCCTG 59.271 55.000 0.00 0.00 44.26 3.86
1585 1931 5.294306 GCTATTAGCTCAGTTGTGTTGCATA 59.706 40.000 8.47 0.00 38.45 3.14
1586 1932 4.095483 GCTATTAGCTCAGTTGTGTTGCAT 59.905 41.667 8.47 0.00 38.45 3.96
1595 1941 4.826274 TCAGTTGGCTATTAGCTCAGTT 57.174 40.909 15.02 2.41 41.99 3.16
1604 1950 2.751806 GCTTCAGCTTCAGTTGGCTATT 59.248 45.455 0.00 0.00 37.00 1.73
1720 2067 2.902484 GCGTCGCAGAAGTAAAAACATG 59.098 45.455 13.44 0.00 39.69 3.21
1885 2233 2.032071 GGGGTGTCGGTCTTGTGG 59.968 66.667 0.00 0.00 0.00 4.17
1996 2350 2.744202 GACCTTGCACGTGAAGATCATT 59.256 45.455 22.23 3.35 0.00 2.57
2116 2470 2.520536 AAACCAGCCGAGCCTGTCT 61.521 57.895 0.00 0.00 0.00 3.41
2276 2630 4.757149 GCCAAGATATTACAGCAGTAAGGG 59.243 45.833 7.79 3.85 43.02 3.95
2354 2711 4.265073 AGCCTTGAAACTGAGCGAATAAT 58.735 39.130 0.00 0.00 0.00 1.28
2372 2729 1.356124 TGAGAAGCCTTGAGAAGCCT 58.644 50.000 0.00 0.00 0.00 4.58
2385 2742 3.126514 CACTATTGCAGCCACTTGAGAAG 59.873 47.826 0.00 0.00 0.00 2.85
2386 2743 3.076621 CACTATTGCAGCCACTTGAGAA 58.923 45.455 0.00 0.00 0.00 2.87
2387 2744 2.302733 TCACTATTGCAGCCACTTGAGA 59.697 45.455 0.00 0.00 0.00 3.27
2388 2745 2.703416 TCACTATTGCAGCCACTTGAG 58.297 47.619 0.00 0.00 0.00 3.02
2390 2747 2.816087 ACTTCACTATTGCAGCCACTTG 59.184 45.455 0.00 0.00 0.00 3.16
2391 2748 2.816087 CACTTCACTATTGCAGCCACTT 59.184 45.455 0.00 0.00 0.00 3.16
2393 2750 2.426522 TCACTTCACTATTGCAGCCAC 58.573 47.619 0.00 0.00 0.00 5.01
2394 2751 2.857186 TCACTTCACTATTGCAGCCA 57.143 45.000 0.00 0.00 0.00 4.75
2395 2752 4.708726 AATTCACTTCACTATTGCAGCC 57.291 40.909 0.00 0.00 0.00 4.85
2468 2844 0.732571 CGACCGGAAACATGATTGGG 59.267 55.000 9.46 0.00 0.00 4.12
2473 2849 3.193903 TGTTCTATCGACCGGAAACATGA 59.806 43.478 9.46 0.00 0.00 3.07
2484 2860 9.469807 ACATCTCAATATCTTTGTTCTATCGAC 57.530 33.333 0.00 0.00 0.00 4.20
2489 2868 8.762645 AGGTCACATCTCAATATCTTTGTTCTA 58.237 33.333 0.00 0.00 0.00 2.10
2653 3033 6.260050 GTCCTTCAGTCAGTGTAACATTTCAA 59.740 38.462 0.00 0.00 41.43 2.69
2655 3035 5.758296 TGTCCTTCAGTCAGTGTAACATTTC 59.242 40.000 0.00 0.00 41.43 2.17
2677 3057 2.105477 AGCACATGTCAGAGGAACTTGT 59.895 45.455 0.00 0.00 41.55 3.16
2678 3058 2.775890 AGCACATGTCAGAGGAACTTG 58.224 47.619 0.00 0.00 41.55 3.16
2680 3060 4.408270 ATGATAGCACATGTCAGAGGAACT 59.592 41.667 0.00 0.00 33.39 3.01
2707 3096 5.334414 GGCGTTATCCATTTCAGATTAGCTG 60.334 44.000 0.00 0.00 46.31 4.24
2708 3097 4.757149 GGCGTTATCCATTTCAGATTAGCT 59.243 41.667 0.00 0.00 0.00 3.32
3199 3601 3.089784 GCGTTCGTGATCGCCAAT 58.910 55.556 12.92 0.00 45.54 3.16
3319 3721 5.900865 TTGCTCATGATACATGCTTTTGA 57.099 34.783 0.00 0.00 0.00 2.69
3501 3904 2.941453 ACTATGTCGTCATCGTTGCT 57.059 45.000 0.00 0.00 38.33 3.91
3798 4201 0.617935 GCCTGCCTTCTCTTCCTCTT 59.382 55.000 0.00 0.00 0.00 2.85
4008 4745 4.479796 AGATCTCATTTCCTGGGGAATTCA 59.520 41.667 7.93 0.00 41.71 2.57
4012 4749 3.851976 TGAAGATCTCATTTCCTGGGGAA 59.148 43.478 0.00 0.00 40.27 3.97
5292 6134 2.027625 GGTCGCGTTCAAGGACCTG 61.028 63.158 5.77 0.00 45.34 4.00
5316 6158 0.736325 AAGTCGGTTCGAGAATGCCG 60.736 55.000 8.12 8.12 44.95 5.69
5721 6593 3.580904 TCGTGAGAGGTGGAAAACG 57.419 52.632 0.00 0.00 34.84 3.60
5944 6816 2.924290 GCCACTAAGCGAATCGATATCC 59.076 50.000 6.91 0.00 0.00 2.59
6095 7527 1.363744 CAGTCTTCTTGATCCGTGCC 58.636 55.000 0.00 0.00 0.00 5.01
6181 7613 2.127708 AGGTATTACTGCAGGAAGGGG 58.872 52.381 18.11 0.00 0.00 4.79
6218 7650 4.659111 ATCTGTTCAGATGCTGAGAGAG 57.341 45.455 13.57 6.17 41.75 3.20
6276 7712 2.158928 TGCGCCGGTGGTATATTTAGTT 60.159 45.455 18.41 0.00 0.00 2.24
6291 7727 2.268298 GTAATCATATACCCTGCGCCG 58.732 52.381 4.18 0.00 0.00 6.46
6314 7750 2.341846 AGTTCCATCACAACCGTTGT 57.658 45.000 11.24 11.24 46.75 3.32
6716 8340 5.934935 AATGCAAGCAGAAAGGAAATTTG 57.065 34.783 0.00 0.00 0.00 2.32
6717 8341 6.056884 TCAAATGCAAGCAGAAAGGAAATTT 58.943 32.000 0.00 0.00 0.00 1.82
6772 8401 5.011329 TGCTCAGAAAGAAGCCAAATTGAAT 59.989 36.000 0.00 0.00 0.00 2.57
6773 8402 4.341806 TGCTCAGAAAGAAGCCAAATTGAA 59.658 37.500 0.00 0.00 0.00 2.69
6774 8403 3.890756 TGCTCAGAAAGAAGCCAAATTGA 59.109 39.130 0.00 0.00 0.00 2.57
6775 8404 4.247267 TGCTCAGAAAGAAGCCAAATTG 57.753 40.909 0.00 0.00 0.00 2.32
6776 8405 4.942761 TTGCTCAGAAAGAAGCCAAATT 57.057 36.364 0.00 0.00 0.00 1.82
6781 8410 3.755378 TCTCATTTGCTCAGAAAGAAGCC 59.245 43.478 0.00 0.00 0.00 4.35
6813 8442 2.831526 ACCACTGTTTTCCAGCAAACTT 59.168 40.909 0.00 0.00 45.68 2.66
6814 8443 2.166254 CACCACTGTTTTCCAGCAAACT 59.834 45.455 0.00 0.00 45.68 2.66
6815 8444 2.094234 ACACCACTGTTTTCCAGCAAAC 60.094 45.455 0.00 0.00 45.68 2.93
6816 8445 2.175202 ACACCACTGTTTTCCAGCAAA 58.825 42.857 0.00 0.00 45.68 3.68
6817 8446 1.846007 ACACCACTGTTTTCCAGCAA 58.154 45.000 0.00 0.00 45.68 3.91
6818 8447 1.748493 GAACACCACTGTTTTCCAGCA 59.252 47.619 0.00 0.00 45.68 4.41
6819 8448 2.024414 AGAACACCACTGTTTTCCAGC 58.976 47.619 0.00 0.00 45.68 4.85
6821 8450 5.221541 ACAAAAAGAACACCACTGTTTTCCA 60.222 36.000 0.00 0.00 40.93 3.53
6822 8451 5.234752 ACAAAAAGAACACCACTGTTTTCC 58.765 37.500 0.00 0.00 40.93 3.13
6823 8452 5.923684 TGACAAAAAGAACACCACTGTTTTC 59.076 36.000 0.00 0.00 40.93 2.29
6824 8453 5.848406 TGACAAAAAGAACACCACTGTTTT 58.152 33.333 0.00 0.00 40.93 2.43
6825 8454 5.010617 ACTGACAAAAAGAACACCACTGTTT 59.989 36.000 0.00 0.00 40.93 2.83
6826 8455 4.522789 ACTGACAAAAAGAACACCACTGTT 59.477 37.500 0.00 0.00 43.71 3.16
6827 8456 4.079253 ACTGACAAAAAGAACACCACTGT 58.921 39.130 0.00 0.00 0.00 3.55
6828 8457 4.155826 TCACTGACAAAAAGAACACCACTG 59.844 41.667 0.00 0.00 0.00 3.66
6829 8458 4.331968 TCACTGACAAAAAGAACACCACT 58.668 39.130 0.00 0.00 0.00 4.00
6830 8459 4.695217 TCACTGACAAAAAGAACACCAC 57.305 40.909 0.00 0.00 0.00 4.16
6831 8460 4.704540 ACATCACTGACAAAAAGAACACCA 59.295 37.500 0.00 0.00 0.00 4.17
6832 8461 5.248870 ACATCACTGACAAAAAGAACACC 57.751 39.130 0.00 0.00 0.00 4.16
6833 8462 5.516339 CCAACATCACTGACAAAAAGAACAC 59.484 40.000 0.00 0.00 0.00 3.32
6834 8463 5.649557 CCAACATCACTGACAAAAAGAACA 58.350 37.500 0.00 0.00 0.00 3.18
6835 8464 4.504097 GCCAACATCACTGACAAAAAGAAC 59.496 41.667 0.00 0.00 0.00 3.01
7178 8813 3.004524 GCCTTTCAAGATCCAGATCATGC 59.995 47.826 10.17 0.00 40.22 4.06
7187 8822 0.665298 GATGCCGCCTTTCAAGATCC 59.335 55.000 0.00 0.00 0.00 3.36
7243 8878 4.880759 TGGTAGCATTTTGAACCATTGTG 58.119 39.130 0.00 0.00 37.09 3.33
7276 8914 2.947652 CAGCCACATCCACATTCTTAGG 59.052 50.000 0.00 0.00 0.00 2.69
7439 9082 2.084546 CTCCGTTTTTCCAGTGGGATC 58.915 52.381 9.92 0.00 44.48 3.36
7447 9090 3.496160 CCTTCTCCTTCTCCGTTTTTCCA 60.496 47.826 0.00 0.00 0.00 3.53
7463 9106 2.941720 GTGCATGTCCATTCTCCTTCTC 59.058 50.000 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.