Multiple sequence alignment - TraesCS1D01G280100

Loading Multiple Alignment...

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 TraesCS1D01G280100 chr1D 100.000 2771 0 0 1 2771 378072992 378070222 0.000000e+00 5118.0
1 TraesCS1D01G280100 chr1D 100.000 37 0 0 2236 2272 378070694 378070658 4.950000e-08 69.4
2 TraesCS1D01G280100 chr1D 100.000 37 0 0 2299 2335 378070757 378070721 4.950000e-08 69.4
3 TraesCS1D01G280100 chr2D 84.742 1645 181 24 468 2110 182372469 182370893 0.000000e+00 1583.0
4 TraesCS1D01G280100 chr2D 93.038 158 10 1 2615 2771 182292995 182292838 2.150000e-56 230.0
5 TraesCS1D01G280100 chr2D 95.294 85 4 0 2536 2620 182370509 182370425 4.810000e-28 135.0
6 TraesCS1D01G280100 chr3D 90.765 1007 80 1 468 1474 26069304 26068311 0.000000e+00 1332.0
7 TraesCS1D01G280100 chr3D 88.275 597 32 13 2206 2771 26059682 26059093 0.000000e+00 680.0
8 TraesCS1D01G280100 chr3D 91.121 428 31 4 1472 1899 26060404 26059984 8.610000e-160 573.0
9 TraesCS1D01G280100 chr3D 93.141 277 19 0 1844 2120 26060005 26059729 9.240000e-110 407.0
10 TraesCS1D01G280100 chr2B 82.483 1313 188 24 468 1766 423899817 423901101 0.000000e+00 1112.0
11 TraesCS1D01G280100 chr2B 81.188 1313 217 23 467 1766 655906067 655904772 0.000000e+00 1029.0
12 TraesCS1D01G280100 chr2B 88.660 97 8 3 2437 2531 655904339 655904244 6.270000e-22 115.0
13 TraesCS1D01G280100 chr6B 82.241 1312 193 22 468 1766 551808400 551807116 0.000000e+00 1096.0
14 TraesCS1D01G280100 chr6B 88.542 96 10 1 2437 2531 551806736 551806641 6.270000e-22 115.0
15 TraesCS1D01G280100 chr4A 82.232 1317 190 26 464 1766 42260775 42259489 0.000000e+00 1096.0
16 TraesCS1D01G280100 chr1B 82.192 1314 192 24 467 1766 391583805 391582520 0.000000e+00 1092.0
17 TraesCS1D01G280100 chr1B 81.839 1316 202 25 462 1766 346965873 346967162 0.000000e+00 1072.0
18 TraesCS1D01G280100 chr3A 82.040 1314 193 25 467 1766 443994335 443993051 0.000000e+00 1079.0
19 TraesCS1D01G280100 chr3A 89.216 102 7 4 2422 2522 210241827 210241925 1.040000e-24 124.0
20 TraesCS1D01G280100 chr5D 95.309 405 18 1 24 427 458814083 458813679 2.330000e-180 641.0
21 TraesCS1D01G280100 chr6D 94.335 406 17 4 23 427 14914924 14914524 3.920000e-173 617.0
22 TraesCS1D01G280100 chr7D 96.346 301 10 1 24 323 32158830 32158530 6.890000e-136 494.0
23 TraesCS1D01G280100 chr7D 85.789 190 24 3 467 654 508831092 508830904 6.050000e-47 198.0
24 TraesCS1D01G280100 chr7D 93.750 112 7 0 316 427 32157458 32157347 4.750000e-38 169.0
25 TraesCS1D01G280100 chr6A 75.604 910 208 11 795 1701 353643240 353644138 3.280000e-119 438.0
26 TraesCS1D01G280100 chr1A 88.623 167 17 2 468 633 705776 705941 4.680000e-48 202.0
27 TraesCS1D01G280100 chr7B 88.623 167 16 3 468 633 179959180 179959016 1.680000e-47 200.0
28 TraesCS1D01G280100 chr7A 89.375 160 15 2 468 626 139792873 139792715 1.680000e-47 200.0
29 TraesCS1D01G280100 chrUn 82.949 217 34 3 468 683 102524949 102524735 2.820000e-45 193.0
30 TraesCS1D01G280100 chr5B 85.185 189 26 2 468 655 671294240 671294053 2.820000e-45 193.0
31 TraesCS1D01G280100 chr2A 91.765 85 6 1 793 877 710965674 710965757 1.740000e-22 117.0
32 TraesCS1D01G280100 chr5A 100.000 37 0 0 2437 2473 665954896 665954860 4.950000e-08 69.4


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 TraesCS1D01G280100 chr1D 378070222 378072992 2770 True 1752.266667 5118 100.000000 1 2771 3 chr1D.!!$R1 2770
1 TraesCS1D01G280100 chr2D 182370425 182372469 2044 True 859.000000 1583 90.018000 468 2620 2 chr2D.!!$R2 2152
2 TraesCS1D01G280100 chr3D 26068311 26069304 993 True 1332.000000 1332 90.765000 468 1474 1 chr3D.!!$R1 1006
3 TraesCS1D01G280100 chr3D 26059093 26060404 1311 True 553.333333 680 90.845667 1472 2771 3 chr3D.!!$R2 1299
4 TraesCS1D01G280100 chr2B 423899817 423901101 1284 False 1112.000000 1112 82.483000 468 1766 1 chr2B.!!$F1 1298
5 TraesCS1D01G280100 chr2B 655904244 655906067 1823 True 572.000000 1029 84.924000 467 2531 2 chr2B.!!$R1 2064
6 TraesCS1D01G280100 chr6B 551806641 551808400 1759 True 605.500000 1096 85.391500 468 2531 2 chr6B.!!$R1 2063
7 TraesCS1D01G280100 chr4A 42259489 42260775 1286 True 1096.000000 1096 82.232000 464 1766 1 chr4A.!!$R1 1302
8 TraesCS1D01G280100 chr1B 391582520 391583805 1285 True 1092.000000 1092 82.192000 467 1766 1 chr1B.!!$R1 1299
9 TraesCS1D01G280100 chr1B 346965873 346967162 1289 False 1072.000000 1072 81.839000 462 1766 1 chr1B.!!$F1 1304
10 TraesCS1D01G280100 chr3A 443993051 443994335 1284 True 1079.000000 1079 82.040000 467 1766 1 chr3A.!!$R1 1299
11 TraesCS1D01G280100 chr7D 32157347 32158830 1483 True 331.500000 494 95.048000 24 427 2 chr7D.!!$R2 403
12 TraesCS1D01G280100 chr6A 353643240 353644138 898 False 438.000000 438 75.604000 795 1701 1 chr6A.!!$F1 906

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
404 1485 0.752658 TGTACCTGATGATGGAGCCG 59.247 55.0 0.00 0.0 0.00 5.52 F
1217 2313 0.038166 ACGGTGGTGCTCCAATCATT 59.962 50.0 9.53 0.0 46.15 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1536 2632 0.940126 CACACGCAACAAGCTCTTCT 59.060 50.0 0.0 0.0 42.61 2.85 R
2653 3936 1.032014 GACTGAAGCCCAACAAGCAA 58.968 50.0 0.0 0.0 0.00 3.91 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
209 211 5.821516 ACTCCAGATCAGTAGTAAACTCG 57.178 43.478 0.00 0.00 35.76 4.18
255 257 2.002586 GTCCATGACAATCACAGGTCG 58.997 52.381 0.00 0.00 36.83 4.79
273 275 1.416401 TCGCATCCTCCTTATTCCCAC 59.584 52.381 0.00 0.00 0.00 4.61
274 276 1.140852 CGCATCCTCCTTATTCCCACA 59.859 52.381 0.00 0.00 0.00 4.17
284 286 4.288366 TCCTTATTCCCACACTGTTCATCA 59.712 41.667 0.00 0.00 0.00 3.07
360 1441 3.380320 GGTAACAAAGAGCAAACACACCT 59.620 43.478 0.00 0.00 0.00 4.00
386 1467 2.187958 TCTAGAGGTTCACCCCACATG 58.812 52.381 0.00 0.00 36.42 3.21
396 1477 1.559219 CACCCCACATGTACCTGATGA 59.441 52.381 5.05 0.00 0.00 2.92
404 1485 0.752658 TGTACCTGATGATGGAGCCG 59.247 55.000 0.00 0.00 0.00 5.52
407 1488 0.977627 ACCTGATGATGGAGCCGTCA 60.978 55.000 13.41 13.41 44.76 4.35
420 1501 4.758251 CGTCATGGGCTCGTGGCA 62.758 66.667 11.69 0.00 44.01 4.92
424 1505 2.360350 ATGGGCTCGTGGCACTTG 60.360 61.111 16.72 9.10 46.25 3.16
427 1508 3.730761 GGCTCGTGGCACTTGCTG 61.731 66.667 23.59 7.28 44.01 4.41
428 1509 2.974698 GCTCGTGGCACTTGCTGT 60.975 61.111 16.72 0.00 41.70 4.40
429 1510 2.959357 GCTCGTGGCACTTGCTGTC 61.959 63.158 16.72 0.00 41.70 3.51
430 1511 2.661537 TCGTGGCACTTGCTGTCG 60.662 61.111 16.72 0.00 41.70 4.35
431 1512 2.967076 CGTGGCACTTGCTGTCGT 60.967 61.111 16.72 0.00 41.70 4.34
432 1513 2.633657 GTGGCACTTGCTGTCGTG 59.366 61.111 11.13 0.00 41.70 4.35
433 1514 1.887242 GTGGCACTTGCTGTCGTGA 60.887 57.895 11.13 0.00 41.70 4.35
434 1515 1.595109 TGGCACTTGCTGTCGTGAG 60.595 57.895 0.38 0.00 41.70 3.51
435 1516 2.553268 GCACTTGCTGTCGTGAGC 59.447 61.111 0.00 2.01 39.62 4.26
436 1517 2.959357 GCACTTGCTGTCGTGAGCC 61.959 63.158 6.07 0.00 38.28 4.70
437 1518 2.356313 ACTTGCTGTCGTGAGCCG 60.356 61.111 6.07 1.19 38.28 5.52
438 1519 2.356313 CTTGCTGTCGTGAGCCGT 60.356 61.111 6.07 0.00 38.28 5.68
439 1520 2.355837 TTGCTGTCGTGAGCCGTC 60.356 61.111 6.07 0.00 38.28 4.79
440 1521 4.700365 TGCTGTCGTGAGCCGTCG 62.700 66.667 6.07 0.00 38.28 5.12
441 1522 4.702081 GCTGTCGTGAGCCGTCGT 62.702 66.667 0.00 0.00 37.94 4.34
442 1523 2.801162 CTGTCGTGAGCCGTCGTG 60.801 66.667 0.00 0.00 37.94 4.35
443 1524 4.337060 TGTCGTGAGCCGTCGTGG 62.337 66.667 0.00 0.00 42.50 4.94
461 1542 2.124860 GCTCGTGGCCCCGTTATT 60.125 61.111 7.70 0.00 34.27 1.40
462 1543 2.178235 GCTCGTGGCCCCGTTATTC 61.178 63.158 7.70 0.00 34.27 1.75
491 1572 6.515696 CGAGATAATTGCATCTACAGTCCTCA 60.516 42.308 0.00 0.00 35.37 3.86
514 1595 2.034879 CGCTGGCGACATCCACTTT 61.035 57.895 9.51 0.00 42.83 2.66
576 1657 8.708742 CGGTACATGAAAATATGTCGTCAATAT 58.291 33.333 0.00 0.00 41.31 1.28
661 1742 4.101448 GCCACGTCAGCCCAGGAT 62.101 66.667 0.00 0.00 0.00 3.24
662 1743 2.671070 CCACGTCAGCCCAGGATT 59.329 61.111 0.00 0.00 0.00 3.01
663 1744 1.002134 CCACGTCAGCCCAGGATTT 60.002 57.895 0.00 0.00 0.00 2.17
685 1766 2.434774 GTCAGGTTGGACCCACCC 59.565 66.667 11.16 2.91 39.75 4.61
698 1779 3.374402 CACCCGTCAGCTCGAGGT 61.374 66.667 12.24 12.24 35.80 3.85
740 1823 1.775962 GCTGCTCTGTTTCGTCGAC 59.224 57.895 5.18 5.18 0.00 4.20
743 1826 1.081641 GCTCTGTTTCGTCGACGGA 60.082 57.895 35.05 27.17 40.29 4.69
766 1849 2.629017 AATTCCCCAATTCCTGCACT 57.371 45.000 0.00 0.00 0.00 4.40
842 1938 2.501128 CATGTCCCTCGATGCGGT 59.499 61.111 0.00 0.00 0.00 5.68
1018 2114 1.000019 ATGGATGCAGTGCAGGCTT 60.000 52.632 24.20 6.27 43.65 4.35
1030 2126 1.296715 CAGGCTTGCTACCGAGGTT 59.703 57.895 0.00 0.00 0.00 3.50
1217 2313 0.038166 ACGGTGGTGCTCCAATCATT 59.962 50.000 9.53 0.00 46.15 2.57
1278 2374 1.395826 GGTGGGTGAGAGAGATCCGG 61.396 65.000 0.00 0.00 0.00 5.14
1359 2455 1.078759 CATGGTCGAGGCGTTCAGTC 61.079 60.000 0.00 0.00 0.00 3.51
1536 2632 2.660572 GATCTGCCTCCACAGTCTCTA 58.339 52.381 0.00 0.00 38.84 2.43
1543 2639 2.687935 CCTCCACAGTCTCTAGAAGAGC 59.312 54.545 0.00 0.00 42.04 4.09
1586 2682 1.712977 GAGTACGGACCATCGTCGCT 61.713 60.000 0.00 0.00 42.82 4.93
1602 2698 2.029828 GTCGCTGAGGAAGAAGAAGACA 60.030 50.000 0.00 0.00 0.00 3.41
1674 2775 2.659016 CTCGCTGAAGACCTGCCA 59.341 61.111 0.00 0.00 36.50 4.92
1710 2811 0.688087 ACGAAGGGGAGGATCTGACC 60.688 60.000 0.00 0.00 33.73 4.02
1754 2855 1.526575 CTTGGCAAAGTGGACGGCAT 61.527 55.000 0.00 0.00 34.92 4.40
1841 2953 8.251026 TGTCTATGTAGTTTCTGAACCAGTATG 58.749 37.037 0.00 0.00 36.39 2.39
1865 2977 5.968676 ATTTGGTATGTCTAGTGGCCTTA 57.031 39.130 3.32 0.00 0.00 2.69
1866 2978 4.748277 TTGGTATGTCTAGTGGCCTTAC 57.252 45.455 3.32 0.00 0.00 2.34
1894 3033 4.637276 TGTGAATTTGGTATGTCGAGTGT 58.363 39.130 0.00 0.00 0.00 3.55
1949 3088 7.808381 AGTTGACATATTATCTACGGATGAACG 59.192 37.037 0.00 0.00 40.31 3.95
2043 3183 6.648879 ATTATGTGGTGCTAACTGTTTGTT 57.351 33.333 0.00 0.00 42.31 2.83
2071 3211 5.454554 CAGAATAAGAATGCAATGCAGTTCG 59.545 40.000 14.98 0.00 43.65 3.95
2087 3227 6.391537 TGCAGTTCGTCATGTTATTGTACTA 58.608 36.000 0.00 0.00 0.00 1.82
2097 3237 9.066939 GTCATGTTATTGTACTATAGCTCATCG 57.933 37.037 11.21 7.14 0.00 3.84
2120 3260 2.350772 GCAACCACATTGTACAGAGCAC 60.351 50.000 0.00 0.00 40.77 4.40
2121 3261 3.141398 CAACCACATTGTACAGAGCACT 58.859 45.455 0.00 0.00 33.20 4.40
2122 3262 3.492102 ACCACATTGTACAGAGCACTT 57.508 42.857 0.00 0.00 0.00 3.16
2124 3264 3.181455 ACCACATTGTACAGAGCACTTCA 60.181 43.478 0.00 0.00 0.00 3.02
2126 3266 4.456911 CCACATTGTACAGAGCACTTCATT 59.543 41.667 0.00 0.00 0.00 2.57
2130 3270 9.049523 CACATTGTACAGAGCACTTCATTATAT 57.950 33.333 0.00 0.00 0.00 0.86
2138 3278 8.874156 ACAGAGCACTTCATTATATATTCTGGA 58.126 33.333 8.03 0.00 34.24 3.86
2139 3279 9.368674 CAGAGCACTTCATTATATATTCTGGAG 57.631 37.037 0.00 0.00 0.00 3.86
2140 3280 8.040132 AGAGCACTTCATTATATATTCTGGAGC 58.960 37.037 0.00 0.00 0.00 4.70
2141 3281 7.683578 AGCACTTCATTATATATTCTGGAGCA 58.316 34.615 0.00 0.00 0.00 4.26
2142 3282 8.327271 AGCACTTCATTATATATTCTGGAGCAT 58.673 33.333 0.00 0.00 0.00 3.79
2152 3292 8.757982 ATATATTCTGGAGCATTTCACAAACT 57.242 30.769 0.00 0.00 0.00 2.66
2153 3293 9.851686 ATATATTCTGGAGCATTTCACAAACTA 57.148 29.630 0.00 0.00 0.00 2.24
2154 3294 5.689383 TTCTGGAGCATTTCACAAACTAC 57.311 39.130 0.00 0.00 0.00 2.73
2155 3295 4.713553 TCTGGAGCATTTCACAAACTACA 58.286 39.130 0.00 0.00 0.00 2.74
2156 3296 4.756642 TCTGGAGCATTTCACAAACTACAG 59.243 41.667 0.00 0.00 40.11 2.74
2157 3297 4.460263 TGGAGCATTTCACAAACTACAGT 58.540 39.130 0.00 0.00 0.00 3.55
2158 3298 4.275689 TGGAGCATTTCACAAACTACAGTG 59.724 41.667 0.00 0.00 37.10 3.66
2159 3299 4.222114 GAGCATTTCACAAACTACAGTGC 58.778 43.478 0.00 0.00 35.76 4.40
2160 3300 3.631686 AGCATTTCACAAACTACAGTGCA 59.368 39.130 0.00 0.00 35.76 4.57
2161 3301 4.279169 AGCATTTCACAAACTACAGTGCAT 59.721 37.500 0.00 0.00 35.76 3.96
2162 3302 4.618489 GCATTTCACAAACTACAGTGCATC 59.382 41.667 0.00 0.00 35.76 3.91
2163 3303 5.563475 GCATTTCACAAACTACAGTGCATCT 60.563 40.000 0.00 0.00 35.76 2.90
2164 3304 5.673337 TTTCACAAACTACAGTGCATCTC 57.327 39.130 0.00 0.00 35.76 2.75
2165 3305 4.335400 TCACAAACTACAGTGCATCTCA 57.665 40.909 0.00 0.00 35.76 3.27
2166 3306 4.058124 TCACAAACTACAGTGCATCTCAC 58.942 43.478 0.00 0.00 45.98 3.51
2192 3332 8.933807 CACAAGAGCATTACAAGATCATATAGG 58.066 37.037 0.00 0.00 0.00 2.57
2244 3384 5.702670 TGGAGCATCTCACAAACTTTAGAAG 59.297 40.000 0.00 0.00 33.73 2.85
2300 3440 4.564041 CATCTCACAAAGTACAGAGCACT 58.436 43.478 0.00 0.00 0.00 4.40
2301 3441 4.672587 TCTCACAAAGTACAGAGCACTT 57.327 40.909 0.00 0.00 37.85 3.16
2310 3450 8.202137 ACAAAGTACAGAGCACTTTAGAAGTTA 58.798 33.333 0.00 0.00 42.79 2.24
2501 3724 6.882656 ACATGTTCTACAGCTGATCATAAGT 58.117 36.000 23.35 6.91 0.00 2.24
2614 3897 5.888724 TCTTCATTTGTGTTGGTTTGGACTA 59.111 36.000 0.00 0.00 0.00 2.59
2627 3910 5.245751 TGGTTTGGACTAACATGCAATCATT 59.754 36.000 0.00 0.00 29.29 2.57
2632 3915 5.819379 TGGACTAACATGCAATCATTCTCTC 59.181 40.000 0.00 0.00 0.00 3.20
2643 3926 2.114616 TCATTCTCTCTTCCTCTGCCC 58.885 52.381 0.00 0.00 0.00 5.36
2648 3931 1.077858 CTCTTCCTCTGCCCTTGCC 60.078 63.158 0.00 0.00 36.33 4.52
2653 3936 1.994507 CCTCTGCCCTTGCCTCTCT 60.995 63.158 0.00 0.00 36.33 3.10
2656 3939 2.034687 TGCCCTTGCCTCTCTTGC 59.965 61.111 0.00 0.00 36.33 4.01
2669 3952 1.133823 TCTCTTGCTTGTTGGGCTTCA 60.134 47.619 0.00 0.00 0.00 3.02
2670 3953 1.268899 CTCTTGCTTGTTGGGCTTCAG 59.731 52.381 0.00 0.00 0.00 3.02
2715 3999 4.279169 TGCCTCAATTCTTGTTTCTTCCTG 59.721 41.667 0.00 0.00 0.00 3.86
2716 4000 4.802999 CCTCAATTCTTGTTTCTTCCTGC 58.197 43.478 0.00 0.00 0.00 4.85
2725 4009 5.471456 TCTTGTTTCTTCCTGCTGATTTCTC 59.529 40.000 0.00 0.00 0.00 2.87
2728 4012 5.471456 TGTTTCTTCCTGCTGATTTCTCTTC 59.529 40.000 0.00 0.00 0.00 2.87
2767 4051 2.158623 TCTTGATGCCTCCTGTGTTTGT 60.159 45.455 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 9.631452 GTAAATGCAGAAAAGCTTCTTTTCTAT 57.369 29.630 25.17 17.19 44.30 1.98
117 119 1.764134 TGGGTAGTTGGTTCAGTTCGT 59.236 47.619 0.00 0.00 0.00 3.85
118 120 2.536761 TGGGTAGTTGGTTCAGTTCG 57.463 50.000 0.00 0.00 0.00 3.95
209 211 2.237392 AGGTGACACTGATAAGGAAGGC 59.763 50.000 5.39 0.00 0.00 4.35
255 257 2.173569 AGTGTGGGAATAAGGAGGATGC 59.826 50.000 0.00 0.00 0.00 3.91
273 275 5.089970 TCTAACAGGGATGATGAACAGTG 57.910 43.478 0.00 0.00 0.00 3.66
274 276 5.762179 TTCTAACAGGGATGATGAACAGT 57.238 39.130 0.00 0.00 0.00 3.55
306 308 8.826710 TGAATCACCATAATTTTACATCGAGAC 58.173 33.333 0.00 0.00 0.00 3.36
386 1467 0.753262 ACGGCTCCATCATCAGGTAC 59.247 55.000 0.00 0.00 0.00 3.34
404 1485 3.127533 GTGCCACGAGCCCATGAC 61.128 66.667 0.00 0.00 42.71 3.06
407 1488 2.360350 CAAGTGCCACGAGCCCAT 60.360 61.111 0.00 0.00 42.71 4.00
444 1525 2.124860 AATAACGGGGCCACGAGC 60.125 61.111 38.56 0.00 42.60 5.03
445 1526 0.107848 AAGAATAACGGGGCCACGAG 60.108 55.000 38.56 6.30 37.61 4.18
446 1527 1.134729 GTAAGAATAACGGGGCCACGA 60.135 52.381 38.56 14.41 37.61 4.35
447 1528 1.292992 GTAAGAATAACGGGGCCACG 58.707 55.000 29.60 29.60 40.31 4.94
448 1529 1.292992 CGTAAGAATAACGGGGCCAC 58.707 55.000 4.39 0.00 43.02 5.01
449 1530 3.764658 CGTAAGAATAACGGGGCCA 57.235 52.632 4.39 0.00 43.02 5.36
462 1543 7.327275 GGACTGTAGATGCAATTATCTCGTAAG 59.673 40.741 0.00 0.00 38.35 2.34
483 1564 0.249238 GCCAGCGAGTATGAGGACTG 60.249 60.000 0.00 0.00 0.00 3.51
545 1626 5.365619 GACATATTTTCATGTACCGGGACT 58.634 41.667 19.95 0.00 39.25 3.85
576 1657 0.107831 CGTTTCAACCTCAGGGACCA 59.892 55.000 0.00 0.00 36.25 4.02
661 1742 1.098712 GGTCCAACCTGACGTGCAAA 61.099 55.000 0.00 0.00 36.07 3.68
662 1743 1.525077 GGTCCAACCTGACGTGCAA 60.525 57.895 0.00 0.00 36.07 4.08
663 1744 2.110213 GGTCCAACCTGACGTGCA 59.890 61.111 0.00 0.00 36.07 4.57
685 1766 2.179517 GTGGACCTCGAGCTGACG 59.820 66.667 6.99 0.00 0.00 4.35
714 1795 2.550978 GAAACAGAGCAGCGCCTTATA 58.449 47.619 2.29 0.00 0.00 0.98
899 1995 0.322456 TGCCCTCGCAAGCAAACTAT 60.322 50.000 0.00 0.00 43.74 2.12
1012 2108 0.321653 AAACCTCGGTAGCAAGCCTG 60.322 55.000 0.00 0.00 0.00 4.85
1018 2114 0.834687 AGGACCAAACCTCGGTAGCA 60.835 55.000 0.00 0.00 36.69 3.49
1026 2122 2.116125 GCCAGCAGGACCAAACCT 59.884 61.111 0.00 0.00 41.43 3.50
1030 2126 3.177884 AGTGGCCAGCAGGACCAA 61.178 61.111 5.11 0.00 45.14 3.67
1117 2213 4.790962 CACCTCCGCCAGCAGCAT 62.791 66.667 0.00 0.00 44.04 3.79
1124 2220 4.147449 CGATGCTCACCTCCGCCA 62.147 66.667 0.00 0.00 0.00 5.69
1217 2313 1.162698 GCAGCACTTGAGCTTCATCA 58.837 50.000 0.00 0.00 43.70 3.07
1359 2455 4.319177 CCAAGTCCTTCAGTAGACCTTTG 58.681 47.826 0.00 0.00 33.29 2.77
1397 2493 2.544277 CGGTTCTTCGGCGGTATAATCA 60.544 50.000 7.21 0.00 0.00 2.57
1470 2566 2.238646 GGGTATCTCCATGTCAACCACA 59.761 50.000 0.00 0.00 40.18 4.17
1520 2616 2.041755 TCTTCTAGAGACTGTGGAGGCA 59.958 50.000 0.00 0.00 0.00 4.75
1536 2632 0.940126 CACACGCAACAAGCTCTTCT 59.060 50.000 0.00 0.00 42.61 2.85
1543 2639 1.191096 GTGCTTTCACACGCAACAAG 58.809 50.000 0.00 0.00 42.66 3.16
1552 2648 2.198406 GTACTCACACGTGCTTTCACA 58.802 47.619 17.22 0.00 43.28 3.58
1674 2775 1.486310 TCGTTAGGCAGCCATTCATCT 59.514 47.619 15.80 0.00 0.00 2.90
1710 2811 1.154225 GGTGAATTCGTGCTTGCGG 60.154 57.895 0.04 0.00 0.00 5.69
1785 2897 8.094548 TGACAAGTTCATAGCTAAACTACACAT 58.905 33.333 10.51 0.00 34.71 3.21
1808 2920 8.488764 GTTCAGAAACTACATAGACAAACTGAC 58.511 37.037 0.00 0.00 31.90 3.51
1841 2953 4.781934 AGGCCACTAGACATACCAAATTC 58.218 43.478 5.01 0.00 0.00 2.17
1865 2977 5.278266 CGACATACCAAATTCACAAACAGGT 60.278 40.000 0.00 0.00 0.00 4.00
1866 2978 5.049060 TCGACATACCAAATTCACAAACAGG 60.049 40.000 0.00 0.00 0.00 4.00
1894 3033 9.747898 ATATTACATACCAAGTTCACAAAAGGA 57.252 29.630 0.00 0.00 0.00 3.36
1940 3079 4.026062 CACATTACATACCACGTTCATCCG 60.026 45.833 0.00 0.00 0.00 4.18
1949 3088 7.279981 TGAGAATTACTGCACATTACATACCAC 59.720 37.037 0.00 0.00 0.00 4.16
2017 3156 8.172352 ACAAACAGTTAGCACCACATAATTTA 57.828 30.769 0.00 0.00 0.00 1.40
2040 3180 6.587226 GCATTGCATTCTTATTCTGACAAACA 59.413 34.615 3.15 0.00 0.00 2.83
2043 3183 6.071784 ACTGCATTGCATTCTTATTCTGACAA 60.072 34.615 12.53 0.00 38.13 3.18
2071 3211 9.066939 CGATGAGCTATAGTACAATAACATGAC 57.933 37.037 0.00 0.00 0.00 3.06
2097 3237 2.160417 GCTCTGTACAATGTGGTTGCTC 59.840 50.000 0.00 0.00 41.69 4.26
2126 3266 9.851686 AGTTTGTGAAATGCTCCAGAATATATA 57.148 29.630 0.00 0.00 0.00 0.86
2130 3270 6.939730 TGTAGTTTGTGAAATGCTCCAGAATA 59.060 34.615 0.00 0.00 0.00 1.75
2131 3271 5.769662 TGTAGTTTGTGAAATGCTCCAGAAT 59.230 36.000 0.00 0.00 0.00 2.40
2133 3273 4.713553 TGTAGTTTGTGAAATGCTCCAGA 58.286 39.130 0.00 0.00 0.00 3.86
2134 3274 4.516698 ACTGTAGTTTGTGAAATGCTCCAG 59.483 41.667 0.00 0.00 0.00 3.86
2135 3275 4.275689 CACTGTAGTTTGTGAAATGCTCCA 59.724 41.667 0.00 0.00 36.38 3.86
2136 3276 4.787598 CACTGTAGTTTGTGAAATGCTCC 58.212 43.478 0.00 0.00 36.38 4.70
2137 3277 4.222114 GCACTGTAGTTTGTGAAATGCTC 58.778 43.478 0.00 0.00 36.38 4.26
2138 3278 3.631686 TGCACTGTAGTTTGTGAAATGCT 59.368 39.130 0.00 0.00 36.38 3.79
2139 3279 3.963665 TGCACTGTAGTTTGTGAAATGC 58.036 40.909 0.00 0.00 36.38 3.56
2140 3280 6.005583 AGATGCACTGTAGTTTGTGAAATG 57.994 37.500 0.00 0.00 36.38 2.32
2141 3281 5.764686 TGAGATGCACTGTAGTTTGTGAAAT 59.235 36.000 0.00 0.00 36.38 2.17
2142 3282 5.007626 GTGAGATGCACTGTAGTTTGTGAAA 59.992 40.000 0.00 0.00 44.27 2.69
2144 3284 4.058124 GTGAGATGCACTGTAGTTTGTGA 58.942 43.478 0.00 0.00 44.27 3.58
2145 3285 4.395581 GTGAGATGCACTGTAGTTTGTG 57.604 45.455 0.00 0.00 44.27 3.33
2157 3297 2.484742 ATGCTCTTGTGTGAGATGCA 57.515 45.000 0.00 0.00 36.23 3.96
2158 3298 3.686241 TGTAATGCTCTTGTGTGAGATGC 59.314 43.478 0.00 0.00 36.23 3.91
2159 3299 5.640783 TCTTGTAATGCTCTTGTGTGAGATG 59.359 40.000 0.00 0.00 36.23 2.90
2160 3300 5.798132 TCTTGTAATGCTCTTGTGTGAGAT 58.202 37.500 0.00 0.00 36.23 2.75
2161 3301 5.213891 TCTTGTAATGCTCTTGTGTGAGA 57.786 39.130 0.00 0.00 36.23 3.27
2162 3302 5.640783 TGATCTTGTAATGCTCTTGTGTGAG 59.359 40.000 0.00 0.00 37.16 3.51
2163 3303 5.550290 TGATCTTGTAATGCTCTTGTGTGA 58.450 37.500 0.00 0.00 0.00 3.58
2164 3304 5.868043 TGATCTTGTAATGCTCTTGTGTG 57.132 39.130 0.00 0.00 0.00 3.82
2165 3305 9.486497 CTATATGATCTTGTAATGCTCTTGTGT 57.514 33.333 0.00 0.00 0.00 3.72
2166 3306 8.933807 CCTATATGATCTTGTAATGCTCTTGTG 58.066 37.037 0.00 0.00 0.00 3.33
2167 3307 8.654997 ACCTATATGATCTTGTAATGCTCTTGT 58.345 33.333 0.00 0.00 0.00 3.16
2168 3308 8.933807 CACCTATATGATCTTGTAATGCTCTTG 58.066 37.037 0.00 0.00 0.00 3.02
2198 3338 8.837788 TCCAGAATATATAATGAACTGCTGTG 57.162 34.615 0.00 0.00 0.00 3.66
2200 3340 7.605309 TGCTCCAGAATATATAATGAACTGCTG 59.395 37.037 0.00 0.00 0.00 4.41
2205 3345 9.881649 TGAGATGCTCCAGAATATATAATGAAC 57.118 33.333 0.00 0.00 0.00 3.18
2208 3348 9.662947 TTGTGAGATGCTCCAGAATATATAATG 57.337 33.333 0.00 0.00 0.00 1.90
2614 3897 5.507637 AGGAAGAGAGAATGATTGCATGTT 58.492 37.500 0.00 0.00 34.26 2.71
2627 3910 1.566211 CAAGGGCAGAGGAAGAGAGA 58.434 55.000 0.00 0.00 0.00 3.10
2632 3915 1.077858 GAGGCAAGGGCAGAGGAAG 60.078 63.158 0.00 0.00 43.71 3.46
2643 3926 1.268899 CCAACAAGCAAGAGAGGCAAG 59.731 52.381 0.00 0.00 0.00 4.01
2648 3931 1.538950 GAAGCCCAACAAGCAAGAGAG 59.461 52.381 0.00 0.00 0.00 3.20
2653 3936 1.032014 GACTGAAGCCCAACAAGCAA 58.968 50.000 0.00 0.00 0.00 3.91
2656 3939 4.391405 AAAAAGACTGAAGCCCAACAAG 57.609 40.909 0.00 0.00 0.00 3.16
2699 3983 6.492772 AGAAATCAGCAGGAAGAAACAAGAAT 59.507 34.615 0.00 0.00 0.00 2.40
2700 3984 5.829924 AGAAATCAGCAGGAAGAAACAAGAA 59.170 36.000 0.00 0.00 0.00 2.52
2715 3999 2.287769 GGGAGCAGAAGAGAAATCAGC 58.712 52.381 0.00 0.00 0.00 4.26
2716 4000 3.623906 TGGGAGCAGAAGAGAAATCAG 57.376 47.619 0.00 0.00 0.00 2.90
2743 4027 1.421268 ACACAGGAGGCATCAAGACAA 59.579 47.619 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.