Multiple sequence alignment - TraesCS2A01G058600

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 TraesCS2A01G058600 chr2A 100.000 2376 0 0 1 2376 24531066 24528691 0.000000e+00 4388
1 TraesCS2A01G058600 chr2A 81.419 296 40 7 1089 1376 64043581 64043293 6.610000e-56 228
2 TraesCS2A01G058600 chr2D 85.259 1662 133 55 3 1609 22963157 22961553 0.000000e+00 1609
3 TraesCS2A01G058600 chr2D 86.981 1083 90 25 1130 2186 22927209 22926152 0.000000e+00 1171
4 TraesCS2A01G058600 chr2D 90.581 637 38 5 1617 2232 22961381 22960746 0.000000e+00 824
5 TraesCS2A01G058600 chr2D 76.766 538 77 25 1573 2077 22959131 22958609 8.430000e-65 257
6 TraesCS2A01G058600 chr2D 91.216 148 9 1 2229 2376 22959456 22959313 5.180000e-47 198
7 TraesCS2A01G058600 chr2D 84.375 128 14 1 967 1088 22952469 22952342 1.150000e-23 121
8 TraesCS2A01G058600 chr2B 84.600 1461 111 53 1 1380 37431210 37432637 0.000000e+00 1347
9 TraesCS2A01G058600 chr2B 81.612 397 60 9 1850 2241 73074018 73073630 1.370000e-82 316
10 TraesCS2A01G058600 chr2B 83.810 315 42 7 2044 2355 37433420 37433728 8.310000e-75 291
11 TraesCS2A01G058600 chr4B 83.544 395 56 6 1850 2241 327139608 327139220 6.240000e-96 361
12 TraesCS2A01G058600 chr7A 82.536 418 52 13 165 571 199440084 199440491 4.860000e-92 348
13 TraesCS2A01G058600 chr3A 84.807 362 37 9 165 516 689755022 689755375 4.860000e-92 348
14 TraesCS2A01G058600 chr3A 80.371 377 52 11 143 510 87733393 87733030 1.400000e-67 267
15 TraesCS2A01G058600 chrUn 82.297 418 52 13 165 571 295944470 295944876 2.260000e-90 342
16 TraesCS2A01G058600 chr4A 82.410 415 51 13 168 571 611288985 611288582 2.260000e-90 342
17 TraesCS2A01G058600 chr5B 76.500 600 76 38 84 655 39517529 39518091 1.400000e-67 267
18 TraesCS2A01G058600 chr1B 79.045 377 57 11 143 510 519432890 519433253 3.050000e-59 239
19 TraesCS2A01G058600 chr3B 79.063 363 59 13 155 510 446528942 446528590 1.420000e-57 233
20 TraesCS2A01G058600 chr6B 76.585 410 45 30 84 483 76042675 76042307 6.750000e-41 178


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 TraesCS2A01G058600 chr2A 24528691 24531066 2375 True 4388 4388 100.0000 1 2376 1 chr2A.!!$R1 2375
1 TraesCS2A01G058600 chr2D 22926152 22927209 1057 True 1171 1171 86.9810 1130 2186 1 chr2D.!!$R1 1056
2 TraesCS2A01G058600 chr2D 22958609 22963157 4548 True 722 1609 85.9555 3 2376 4 chr2D.!!$R3 2373
3 TraesCS2A01G058600 chr2B 37431210 37433728 2518 False 819 1347 84.2050 1 2355 2 chr2B.!!$F1 2354
4 TraesCS2A01G058600 chr5B 39517529 39518091 562 False 267 267 76.5000 84 655 1 chr5B.!!$F1 571

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
540 573 1.005924 CCCCCAAGCAACCTATGAACT 59.994 52.381 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1418 1562 0.108377 ATCACAAGATGCCGCGTACA 60.108 50.0 4.92 2.86 31.91 2.9 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
31 32 1.067635 CATGGCCCTTTTGGTTCTTCG 60.068 52.381 0.00 0.00 38.10 3.79
94 95 5.106948 GGTATCATACATCTGACATTTGCCG 60.107 44.000 0.00 0.00 0.00 5.69
156 157 9.586732 TTTGGAATCCTCTTTTCTGAGATAAAA 57.413 29.630 0.00 0.00 36.23 1.52
158 159 7.611855 TGGAATCCTCTTTTCTGAGATAAAACC 59.388 37.037 0.00 0.00 36.23 3.27
187 188 6.597832 AACAGGATATACATAGAGCCTGAC 57.402 41.667 21.38 0.00 44.27 3.51
209 210 5.189180 ACTGGAGCAGAATATTGGTTTCTC 58.811 41.667 0.00 0.00 35.18 2.87
252 253 4.080687 GGTTCTGACTGTCTACTACCACT 58.919 47.826 9.51 0.00 0.00 4.00
263 269 7.068839 ACTGTCTACTACCACTCCAAATATGAG 59.931 40.741 0.00 0.00 35.92 2.90
268 274 7.437713 ACTACCACTCCAAATATGAGATGAA 57.562 36.000 0.00 0.00 33.95 2.57
272 278 6.825721 ACCACTCCAAATATGAGATGAAAGTC 59.174 38.462 0.00 0.00 33.95 3.01
279 285 7.937942 CCAAATATGAGATGAAAGTCTCTCCAT 59.062 37.037 5.61 0.00 43.96 3.41
288 295 4.532126 TGAAAGTCTCTCCATCTTTGCCTA 59.468 41.667 0.00 0.00 32.59 3.93
305 312 3.973973 TGCCTAATCCACCTTATGCTAGT 59.026 43.478 0.00 0.00 0.00 2.57
307 314 5.605069 TGCCTAATCCACCTTATGCTAGTTA 59.395 40.000 0.00 0.00 0.00 2.24
310 317 7.310734 GCCTAATCCACCTTATGCTAGTTAGAT 60.311 40.741 0.00 0.00 0.00 1.98
311 318 8.037758 CCTAATCCACCTTATGCTAGTTAGATG 58.962 40.741 0.00 0.00 0.00 2.90
312 319 7.618019 AATCCACCTTATGCTAGTTAGATGA 57.382 36.000 0.00 0.00 0.00 2.92
313 320 7.618019 ATCCACCTTATGCTAGTTAGATGAA 57.382 36.000 0.00 0.00 0.00 2.57
314 321 7.618019 TCCACCTTATGCTAGTTAGATGAAT 57.382 36.000 0.00 0.00 0.00 2.57
382 390 1.153086 CCTTGGAATCGCTGGGAGG 60.153 63.158 0.00 0.00 0.00 4.30
407 415 1.323271 TTCTCGCGCAATCCTCCTCT 61.323 55.000 8.75 0.00 0.00 3.69
483 501 3.944015 ACATTCTCAGCACCTAATTCAGC 59.056 43.478 0.00 0.00 0.00 4.26
540 573 1.005924 CCCCCAAGCAACCTATGAACT 59.994 52.381 0.00 0.00 0.00 3.01
568 601 5.188434 CCAATTCTGCCTATCTGAAGAACA 58.812 41.667 0.00 0.00 36.33 3.18
575 620 7.624549 TCTGCCTATCTGAAGAACAAACTAAT 58.375 34.615 0.00 0.00 0.00 1.73
585 630 5.353394 AGAACAAACTAATATCGGAGCCA 57.647 39.130 0.00 0.00 0.00 4.75
624 670 3.086600 GAGCACTCCCCTCCCCTG 61.087 72.222 0.00 0.00 0.00 4.45
649 697 3.942115 GGGATAAAAGAACTCACCTCTGC 59.058 47.826 0.00 0.00 0.00 4.26
803 869 2.432628 GCGTTGTGAGGACCGGAG 60.433 66.667 9.46 0.00 0.00 4.63
863 933 3.823330 ACATCGCTCGGTCGGTCC 61.823 66.667 0.00 0.00 0.00 4.46
870 944 1.507174 CTCGGTCGGTCCTTCTGTC 59.493 63.158 0.00 0.00 0.00 3.51
878 952 4.332543 TCCTTCTGTCCGGGCCCT 62.333 66.667 22.43 0.00 0.00 5.19
917 995 4.484872 GGCTCGGCCCAACCCTAC 62.485 72.222 0.00 0.00 44.06 3.18
918 996 3.712907 GCTCGGCCCAACCCTACA 61.713 66.667 0.00 0.00 33.26 2.74
919 997 2.267961 CTCGGCCCAACCCTACAC 59.732 66.667 0.00 0.00 33.26 2.90
929 1010 5.487845 GGCCCAACCCTACACTATAATATCT 59.512 44.000 0.00 0.00 0.00 1.98
933 1014 5.916661 ACCCTACACTATAATATCTGCCG 57.083 43.478 0.00 0.00 0.00 5.69
953 1034 1.374758 GACCGCACAGGAAGACCAG 60.375 63.158 0.00 0.00 45.00 4.00
954 1035 2.100879 GACCGCACAGGAAGACCAGT 62.101 60.000 0.00 0.00 45.00 4.00
961 1042 1.837051 AGGAAGACCAGTGACGGCA 60.837 57.895 0.00 0.00 38.94 5.69
978 1059 1.932850 CATCCACCCACCCATCCAT 59.067 57.895 0.00 0.00 0.00 3.41
979 1060 1.148216 CATCCACCCACCCATCCATA 58.852 55.000 0.00 0.00 0.00 2.74
980 1061 1.074405 CATCCACCCACCCATCCATAG 59.926 57.143 0.00 0.00 0.00 2.23
981 1062 1.151450 CCACCCACCCATCCATAGC 59.849 63.158 0.00 0.00 0.00 2.97
1247 1365 2.118683 CCGCACGCATGGATTTATTTG 58.881 47.619 0.00 0.00 0.00 2.32
1417 1561 3.470888 CCCTGCCCCTCTGTACGG 61.471 72.222 0.00 0.00 0.00 4.02
1418 1562 2.683933 CCTGCCCCTCTGTACGGT 60.684 66.667 0.64 0.00 0.00 4.83
1419 1563 2.579201 CTGCCCCTCTGTACGGTG 59.421 66.667 0.64 0.00 0.00 4.94
1420 1564 2.203728 TGCCCCTCTGTACGGTGT 60.204 61.111 0.64 0.00 0.00 4.16
1421 1565 0.968901 CTGCCCCTCTGTACGGTGTA 60.969 60.000 0.64 0.00 0.00 2.90
1422 1566 1.252904 TGCCCCTCTGTACGGTGTAC 61.253 60.000 0.64 0.22 0.00 2.90
1439 1584 1.004927 GTACGCGGCATCTTGTGATTC 60.005 52.381 12.47 0.00 0.00 2.52
1440 1585 0.391661 ACGCGGCATCTTGTGATTCT 60.392 50.000 12.47 0.00 0.00 2.40
1450 1595 5.658468 CATCTTGTGATTCTCTCTGTGCTA 58.342 41.667 0.00 0.00 0.00 3.49
1467 1612 0.319900 CTACACCTGCGCTTCAGTGT 60.320 55.000 22.12 22.12 41.25 3.55
1469 1614 0.748005 ACACCTGCGCTTCAGTGTTT 60.748 50.000 9.73 0.00 41.25 2.83
1470 1615 0.317269 CACCTGCGCTTCAGTGTTTG 60.317 55.000 9.73 0.00 41.25 2.93
1471 1616 0.748005 ACCTGCGCTTCAGTGTTTGT 60.748 50.000 9.73 0.00 41.25 2.83
1472 1617 0.317269 CCTGCGCTTCAGTGTTTGTG 60.317 55.000 9.73 0.00 41.25 3.33
1474 1619 0.098552 TGCGCTTCAGTGTTTGTGTG 59.901 50.000 9.73 0.00 0.00 3.82
1477 1622 1.396648 CGCTTCAGTGTTTGTGTGTGA 59.603 47.619 0.00 0.00 0.00 3.58
1478 1623 2.159585 CGCTTCAGTGTTTGTGTGTGAA 60.160 45.455 0.00 0.00 0.00 3.18
1479 1624 3.171277 GCTTCAGTGTTTGTGTGTGAAC 58.829 45.455 0.00 0.00 0.00 3.18
1480 1625 3.119849 GCTTCAGTGTTTGTGTGTGAACT 60.120 43.478 0.00 0.00 0.00 3.01
1481 1626 4.094294 GCTTCAGTGTTTGTGTGTGAACTA 59.906 41.667 0.00 0.00 0.00 2.24
1482 1627 5.727791 GCTTCAGTGTTTGTGTGTGAACTAG 60.728 44.000 0.00 0.00 0.00 2.57
1483 1628 4.827692 TCAGTGTTTGTGTGTGAACTAGT 58.172 39.130 0.00 0.00 0.00 2.57
1484 1629 4.629634 TCAGTGTTTGTGTGTGAACTAGTG 59.370 41.667 0.00 0.00 0.00 2.74
1485 1630 4.629634 CAGTGTTTGTGTGTGAACTAGTGA 59.370 41.667 0.00 0.00 0.00 3.41
1491 1636 5.585820 TGTGTGTGAACTAGTGACTGTTA 57.414 39.130 0.00 0.00 0.00 2.41
1494 1658 6.040878 GTGTGTGAACTAGTGACTGTTAAGT 58.959 40.000 0.00 0.00 40.21 2.24
1524 1688 0.540365 CAGGGTTGTGTGGGCAGAAT 60.540 55.000 0.00 0.00 30.44 2.40
1551 1715 2.230992 TGTGTCCAACAATTAGGCATGC 59.769 45.455 9.90 9.90 35.24 4.06
1556 1720 2.187707 CAACAATTAGGCATGCTTCGC 58.812 47.619 18.92 0.00 0.00 4.70
1559 1723 0.940126 AATTAGGCATGCTTCGCTCG 59.060 50.000 18.92 0.00 0.00 5.03
1560 1724 0.179073 ATTAGGCATGCTTCGCTCGT 60.179 50.000 18.92 0.00 0.00 4.18
1568 1732 0.388134 TGCTTCGCTCGTTGTAGGTC 60.388 55.000 0.00 0.00 0.00 3.85
1569 1733 0.109226 GCTTCGCTCGTTGTAGGTCT 60.109 55.000 0.00 0.00 0.00 3.85
1570 1734 1.897641 CTTCGCTCGTTGTAGGTCTC 58.102 55.000 0.00 0.00 0.00 3.36
1614 1942 5.592282 TGGTCAAGCATGTCAACTAAGAAAA 59.408 36.000 0.00 0.00 0.00 2.29
1615 1943 6.096141 TGGTCAAGCATGTCAACTAAGAAAAA 59.904 34.615 0.00 0.00 0.00 1.94
1707 2037 3.574284 TGCTTAGCGTTGATGCAATTT 57.426 38.095 0.00 0.00 37.31 1.82
1733 2063 4.315803 ACAGTAGAAAATGGAACCGACAG 58.684 43.478 0.00 0.00 0.00 3.51
1751 2081 4.919168 CGACAGCATCATCATTTTGTTTGT 59.081 37.500 0.00 0.00 0.00 2.83
1811 2159 7.416022 ACCGTCTCACGAGTTCTTATTAATAG 58.584 38.462 0.00 0.00 46.05 1.73
1830 2186 2.813179 CTCGCATACAACTGGCCGC 61.813 63.158 0.00 0.00 0.00 6.53
1848 2204 2.536928 CCGCGCTACAAGTTTATTGCTC 60.537 50.000 5.56 0.00 0.00 4.26
1938 2456 4.212847 ACGCACCTACGTAGATACAGTATG 59.787 45.833 24.15 10.16 46.19 2.39
1945 2463 9.790344 ACCTACGTAGATACAGTATGAAACTAT 57.210 33.333 24.15 0.00 39.69 2.12
2024 2542 7.556275 AGGTGAGTTCACTTTATTTCAGACAAA 59.444 33.333 11.67 0.00 45.73 2.83
2094 2612 4.821805 CACTAGTCCAAAACAGTCCATTGT 59.178 41.667 0.00 0.00 0.00 2.71
2167 2686 1.476085 TGGAACCACTTTGCTGTGTTG 59.524 47.619 0.00 0.00 36.30 3.33
2186 2705 4.209080 TGTTGTCGAATATGACGATCATGC 59.791 41.667 9.77 0.00 41.87 4.06
2205 2724 2.224670 TGCGGAAGGTATGTCTTTTGGT 60.225 45.455 0.00 0.00 0.00 3.67
2246 4058 2.957680 TGACTCATGCTTTCTTTGCCAA 59.042 40.909 0.00 0.00 0.00 4.52
2254 4066 6.935771 TCATGCTTTCTTTGCCAATTTTACAT 59.064 30.769 0.00 0.00 0.00 2.29
2264 4076 8.485976 TTTGCCAATTTTACATAAATAGGCAC 57.514 30.769 17.45 0.00 41.73 5.01
2273 4085 3.275143 CATAAATAGGCACGGACCACAA 58.725 45.455 0.00 0.00 0.00 3.33
2274 4086 1.821216 AAATAGGCACGGACCACAAG 58.179 50.000 0.00 0.00 0.00 3.16
2275 4087 0.676782 AATAGGCACGGACCACAAGC 60.677 55.000 0.00 0.00 0.00 4.01
2276 4088 1.553690 ATAGGCACGGACCACAAGCT 61.554 55.000 0.00 0.00 0.00 3.74
2312 4124 7.616542 TGTAACTAGTGTGGTATATGGACTTGA 59.383 37.037 0.00 0.00 0.00 3.02
2333 4145 2.044353 ACCCATCTAGCCCAAACCAATT 59.956 45.455 0.00 0.00 0.00 2.32
2365 4177 0.612174 CCGAGTGAAGTGGGAGGAGA 60.612 60.000 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 0.596577 GACCGAAGAACCAAAAGGGC 59.403 55.000 0.00 0.00 42.05 5.19
72 73 5.610398 ACGGCAAATGTCAGATGTATGATA 58.390 37.500 0.00 0.00 0.00 2.15
126 127 9.933240 ATCTCAGAAAAGAGGATTCCAAATTAT 57.067 29.630 5.29 0.00 36.30 1.28
134 135 8.672815 CAGGTTTTATCTCAGAAAAGAGGATTC 58.327 37.037 0.00 0.00 36.30 2.52
158 159 7.613801 AGGCTCTATGTATATCCTGTTAGTCAG 59.386 40.741 0.00 0.00 43.27 3.51
181 182 2.877168 CAATATTCTGCTCCAGTCAGGC 59.123 50.000 0.00 0.00 37.29 4.85
187 188 5.188434 TGAGAAACCAATATTCTGCTCCAG 58.812 41.667 0.00 0.00 37.26 3.86
209 210 3.120199 CCTTACGGTCTTGCAACATCTTG 60.120 47.826 0.00 0.00 0.00 3.02
252 253 7.126268 TGGAGAGACTTTCATCTCATATTTGGA 59.874 37.037 5.63 0.00 46.51 3.53
263 269 4.335037 GGCAAAGATGGAGAGACTTTCATC 59.665 45.833 0.00 0.00 37.02 2.92
268 274 5.397334 GGATTAGGCAAAGATGGAGAGACTT 60.397 44.000 0.00 0.00 0.00 3.01
272 278 4.133078 GTGGATTAGGCAAAGATGGAGAG 58.867 47.826 0.00 0.00 0.00 3.20
279 285 4.079787 AGCATAAGGTGGATTAGGCAAAGA 60.080 41.667 5.99 0.00 43.13 2.52
288 295 7.618019 TCATCTAACTAGCATAAGGTGGATT 57.382 36.000 0.00 0.00 32.57 3.01
305 312 8.347004 TGTTTCAGCCATACAAATTCATCTAA 57.653 30.769 0.00 0.00 0.00 2.10
307 314 6.660521 TCTGTTTCAGCCATACAAATTCATCT 59.339 34.615 0.00 0.00 0.00 2.90
310 317 6.003326 TCTCTGTTTCAGCCATACAAATTCA 58.997 36.000 0.00 0.00 0.00 2.57
311 318 6.072508 TGTCTCTGTTTCAGCCATACAAATTC 60.073 38.462 0.00 0.00 0.00 2.17
312 319 5.769662 TGTCTCTGTTTCAGCCATACAAATT 59.230 36.000 0.00 0.00 0.00 1.82
313 320 5.316167 TGTCTCTGTTTCAGCCATACAAAT 58.684 37.500 0.00 0.00 0.00 2.32
314 321 4.713553 TGTCTCTGTTTCAGCCATACAAA 58.286 39.130 0.00 0.00 0.00 2.83
370 378 4.537433 GCGAGCCTCCCAGCGATT 62.537 66.667 0.00 0.00 38.01 3.34
407 415 2.034939 CAGTTGCTGCTCCAACAATTCA 59.965 45.455 17.93 0.00 45.73 2.57
523 556 4.156008 GGTTGTAGTTCATAGGTTGCTTGG 59.844 45.833 0.00 0.00 0.00 3.61
540 573 5.692115 TCAGATAGGCAGAATTGGTTGTA 57.308 39.130 0.00 0.00 0.00 2.41
568 601 2.775384 TGGGTGGCTCCGATATTAGTTT 59.225 45.455 0.00 0.00 37.00 2.66
575 620 2.021723 GCAAATTGGGTGGCTCCGATA 61.022 52.381 0.00 0.00 37.00 2.92
585 630 2.996734 CGGGGCTGCAAATTGGGT 60.997 61.111 0.50 0.00 0.00 4.51
624 670 3.942115 GAGGTGAGTTCTTTTATCCCTGC 59.058 47.826 0.00 0.00 0.00 4.85
629 677 3.942115 GGGCAGAGGTGAGTTCTTTTATC 59.058 47.826 0.00 0.00 0.00 1.75
725 782 1.372683 GTCAGCTGCCACTTCCTCA 59.627 57.895 9.47 0.00 0.00 3.86
765 822 3.191539 CAGAAGCGAGCGGAAGGC 61.192 66.667 0.00 0.00 44.05 4.35
863 933 2.732619 GGTAGGGCCCGGACAGAAG 61.733 68.421 25.82 0.00 0.00 2.85
917 995 3.179830 GGTCGCGGCAGATATTATAGTG 58.820 50.000 14.93 0.00 0.00 2.74
918 996 2.159421 CGGTCGCGGCAGATATTATAGT 60.159 50.000 14.93 0.00 0.00 2.12
919 997 2.451132 CGGTCGCGGCAGATATTATAG 58.549 52.381 14.93 0.00 0.00 1.31
933 1014 3.112709 GTCTTCCTGTGCGGTCGC 61.113 66.667 8.54 8.54 42.35 5.19
948 1029 1.741770 GTGGATGCCGTCACTGGTC 60.742 63.158 0.00 0.00 0.00 4.02
953 1034 2.746277 GTGGGTGGATGCCGTCAC 60.746 66.667 0.00 0.00 0.00 3.67
954 1035 4.028490 GGTGGGTGGATGCCGTCA 62.028 66.667 0.00 0.00 0.00 4.35
955 1036 4.796495 GGGTGGGTGGATGCCGTC 62.796 72.222 0.00 0.00 0.00 4.79
961 1042 1.449271 CTATGGATGGGTGGGTGGAT 58.551 55.000 0.00 0.00 0.00 3.41
991 1097 2.358125 TGCCGACATGGTCAACCG 60.358 61.111 0.00 0.00 41.21 4.44
992 1098 2.040544 CCTGCCGACATGGTCAACC 61.041 63.158 0.00 0.00 41.21 3.77
1237 1355 5.156804 ACGATTCAGCGACAAATAAATCC 57.843 39.130 0.00 0.00 34.83 3.01
1247 1365 0.389948 ACCAGGAACGATTCAGCGAC 60.390 55.000 0.00 0.00 34.83 5.19
1331 1458 4.459089 GGCCTGCTCGGTCTCCAC 62.459 72.222 0.00 0.00 33.40 4.02
1417 1561 1.011968 TCACAAGATGCCGCGTACAC 61.012 55.000 4.92 0.00 0.00 2.90
1418 1562 0.108377 ATCACAAGATGCCGCGTACA 60.108 50.000 4.92 2.86 31.91 2.90
1419 1563 1.004927 GAATCACAAGATGCCGCGTAC 60.005 52.381 4.92 0.00 33.90 3.67
1420 1564 1.134818 AGAATCACAAGATGCCGCGTA 60.135 47.619 4.92 0.00 33.90 4.42
1421 1565 0.391661 AGAATCACAAGATGCCGCGT 60.392 50.000 4.92 0.00 33.90 6.01
1422 1566 0.302890 GAGAATCACAAGATGCCGCG 59.697 55.000 0.00 0.00 33.90 6.46
1423 1567 1.596727 GAGAGAATCACAAGATGCCGC 59.403 52.381 0.00 0.00 37.82 6.53
1424 1568 2.864946 CAGAGAGAATCACAAGATGCCG 59.135 50.000 0.00 0.00 37.82 5.69
1425 1569 3.622163 CACAGAGAGAATCACAAGATGCC 59.378 47.826 0.00 0.00 37.82 4.40
1439 1584 0.457509 CGCAGGTGTAGCACAGAGAG 60.458 60.000 1.61 0.00 35.86 3.20
1440 1585 1.586541 CGCAGGTGTAGCACAGAGA 59.413 57.895 1.61 0.00 35.86 3.10
1467 1612 4.827692 ACAGTCACTAGTTCACACACAAA 58.172 39.130 0.00 0.00 0.00 2.83
1469 1614 4.465632 AACAGTCACTAGTTCACACACA 57.534 40.909 0.00 0.00 0.00 3.72
1470 1615 6.040878 ACTTAACAGTCACTAGTTCACACAC 58.959 40.000 0.00 0.00 0.00 3.82
1471 1616 6.216801 ACTTAACAGTCACTAGTTCACACA 57.783 37.500 0.00 0.00 0.00 3.72
1485 1630 5.337894 CCCTGATCACTCATGACTTAACAGT 60.338 44.000 0.00 0.00 37.79 3.55
1491 1636 3.328931 ACAACCCTGATCACTCATGACTT 59.671 43.478 0.00 0.00 37.79 3.01
1494 1658 2.639347 ACACAACCCTGATCACTCATGA 59.361 45.455 0.00 0.00 39.83 3.07
1524 1688 5.948758 TGCCTAATTGTTGGACACATGATTA 59.051 36.000 0.00 0.00 34.43 1.75
1551 1715 1.467713 GGAGACCTACAACGAGCGAAG 60.468 57.143 0.00 0.00 0.00 3.79
1556 1720 2.680841 CAGAGAGGAGACCTACAACGAG 59.319 54.545 0.00 0.00 31.76 4.18
1559 1723 2.452505 AGCAGAGAGGAGACCTACAAC 58.547 52.381 0.00 0.00 31.76 3.32
1560 1724 2.909504 AGCAGAGAGGAGACCTACAA 57.090 50.000 0.00 0.00 31.76 2.41
1568 1732 6.432472 ACCAAAAATCTAAAAGCAGAGAGGAG 59.568 38.462 0.00 0.00 0.00 3.69
1569 1733 6.306987 ACCAAAAATCTAAAAGCAGAGAGGA 58.693 36.000 0.00 0.00 0.00 3.71
1570 1734 6.207417 TGACCAAAAATCTAAAAGCAGAGAGG 59.793 38.462 0.00 0.00 0.00 3.69
1614 1942 5.882557 CAGAGGCACAAAATGTACTCCTATT 59.117 40.000 9.42 0.00 35.46 1.73
1615 1943 5.431765 CAGAGGCACAAAATGTACTCCTAT 58.568 41.667 9.42 1.01 35.46 2.57
1707 2037 7.613585 TGTCGGTTCCATTTTCTACTGTAATA 58.386 34.615 0.00 0.00 0.00 0.98
1733 2063 8.075593 ACAACTTACAAACAAAATGATGATGC 57.924 30.769 0.00 0.00 0.00 3.91
1751 2081 1.202510 ACACACGGCGGTTACAACTTA 60.203 47.619 13.24 0.00 0.00 2.24
1796 2144 8.744008 TGTATGCGAGCTATTAATAAGAACTC 57.256 34.615 0.00 1.60 0.00 3.01
1811 2159 2.813179 CGGCCAGTTGTATGCGAGC 61.813 63.158 2.24 0.00 0.00 5.03
1830 2186 2.030457 CCCGAGCAATAAACTTGTAGCG 59.970 50.000 0.00 0.00 0.00 4.26
1848 2204 8.967918 TCCTATATCTAAGTATGTTGATTCCCG 58.032 37.037 0.00 0.00 0.00 5.14
1872 2228 1.541233 CCGCTCTTCCACCATACATCC 60.541 57.143 0.00 0.00 0.00 3.51
1876 2394 2.622064 ATTCCGCTCTTCCACCATAC 57.378 50.000 0.00 0.00 0.00 2.39
1881 2399 5.949735 TGAATTTTAATTCCGCTCTTCCAC 58.050 37.500 11.54 0.00 43.19 4.02
1938 2456 7.442666 CAGATCCCTTTAGCCTGTTATAGTTTC 59.557 40.741 0.00 0.00 0.00 2.78
1945 2463 6.013379 CCATATCAGATCCCTTTAGCCTGTTA 60.013 42.308 0.00 0.00 0.00 2.41
1956 2474 4.471386 CGATAAACCCCATATCAGATCCCT 59.529 45.833 0.00 0.00 31.47 4.20
2117 2635 2.497675 GACCCTGTGAGCTGACTAATCA 59.502 50.000 4.57 0.00 0.00 2.57
2167 2686 2.342651 CCGCATGATCGTCATATTCGAC 59.657 50.000 0.00 0.00 40.07 4.20
2186 2705 5.646360 ACAATACCAAAAGACATACCTTCCG 59.354 40.000 0.00 0.00 0.00 4.30
2246 4058 6.038936 GTGGTCCGTGCCTATTTATGTAAAAT 59.961 38.462 0.00 0.00 0.00 1.82
2254 4066 2.937873 GCTTGTGGTCCGTGCCTATTTA 60.938 50.000 0.00 0.00 0.00 1.40
2264 4076 2.509336 CGCCTAGCTTGTGGTCCG 60.509 66.667 0.00 0.00 0.00 4.79
2275 4087 3.116300 CACTAGTTACACATGCGCCTAG 58.884 50.000 4.18 8.23 0.00 3.02
2276 4088 2.494471 ACACTAGTTACACATGCGCCTA 59.506 45.455 4.18 0.00 0.00 3.93
2312 4124 1.080638 TTGGTTTGGGCTAGATGGGT 58.919 50.000 0.00 0.00 0.00 4.51
2333 4145 7.093902 CCCACTTCACTCGGCTAATAAGATATA 60.094 40.741 0.00 0.00 0.00 0.86


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

AutoCloner maintained by Alex Coulton.