Multiple sequence alignment - TraesCS2D01G456200

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 TraesCS2D01G456200 chr2D 100.000 5105 0 0 1 5105 564089061 564083957 0 9428
1 TraesCS2D01G456200 chr2B 94.339 5158 202 39 1 5105 675349740 675344620 0 7825
2 TraesCS2D01G456200 chr2A 95.660 3710 127 17 1419 5105 704768994 704765296 0 5928
3 TraesCS2D01G456200 chr2A 93.410 1396 69 13 1 1380 704770383 704768995 0 2047


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 TraesCS2D01G456200 chr2D 564083957 564089061 5104 True 9428.0 9428 100.000 1 5105 1 chr2D.!!$R1 5104
1 TraesCS2D01G456200 chr2B 675344620 675349740 5120 True 7825.0 7825 94.339 1 5105 1 chr2B.!!$R1 5104
2 TraesCS2D01G456200 chr2A 704765296 704770383 5087 True 3987.5 5928 94.535 1 5105 2 chr2A.!!$R1 5104

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
802 803 0.106217 CTGGGTGTGGACCAAAAGGT 60.106 55.0 0.00 0.00 45.25 3.50 F
1282 1292 0.042731 ACGGGGGAGGAGAGAATCAA 59.957 55.0 0.00 0.00 37.82 2.57 F
1743 1785 0.107459 GCTCCCTCATCTGGACCAAC 60.107 60.0 0.00 0.00 0.00 3.77 F
2064 2106 1.779025 GCCATGGTGCGCATGTAGAG 61.779 60.0 15.91 2.29 0.00 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2498 2543 0.827089 TGGCACCCCAAAGTGTGATG 60.827 55.000 0.00 0.0 38.46 3.07 R
2731 2776 2.791158 CGGTTCCGCTACATGCATTTTC 60.791 50.000 0.00 0.0 43.06 2.29 R
3423 3468 0.878416 TCACAAAACCATGGCGCTAC 59.122 50.000 13.04 0.0 0.00 3.58 R
4107 4158 8.579850 AATCCTGTGTGAAGATAAGCAATTTA 57.420 30.769 0.00 0.0 0.00 1.40 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
222 223 1.652563 GCCGAAAGTGAAGGCGTTT 59.347 52.632 0.00 0.00 41.53 3.60
238 239 3.860930 TTTGGCAAGGAGTCCCCGC 62.861 63.158 5.25 8.81 40.87 6.13
244 245 4.698625 AGGAGTCCCCGCTTCGGT 62.699 66.667 5.25 0.00 46.80 4.69
267 268 1.279496 TGGACATGAAGGTCTCCAGG 58.721 55.000 0.00 0.00 37.91 4.45
330 331 1.625818 GTGTTCCAGGAGGTGACATCT 59.374 52.381 0.00 0.00 35.58 2.90
429 430 2.100631 GGTGATGACGTTGGGCTCG 61.101 63.158 0.00 0.00 0.00 5.03
430 431 1.374252 GTGATGACGTTGGGCTCGT 60.374 57.895 0.00 3.18 44.27 4.18
711 712 1.154488 CGTCGCCACCATTCAAACG 60.154 57.895 0.00 0.00 0.00 3.60
742 743 1.587054 GAGGTGAGGTGGACGTGAG 59.413 63.158 0.00 0.00 0.00 3.51
800 801 1.463553 GCCTGGGTGTGGACCAAAAG 61.464 60.000 0.00 0.00 45.25 2.27
802 803 0.106217 CTGGGTGTGGACCAAAAGGT 60.106 55.000 0.00 0.00 45.25 3.50
803 804 1.144093 CTGGGTGTGGACCAAAAGGTA 59.856 52.381 0.00 0.00 45.25 3.08
804 805 1.133730 TGGGTGTGGACCAAAAGGTAC 60.134 52.381 0.00 0.00 45.25 3.34
815 816 1.010419 AAAAGGTACGTACTGGCGCG 61.010 55.000 24.07 0.00 34.88 6.86
854 855 3.942748 TGTGAAAGCGTAAAGTGTTCCTT 59.057 39.130 0.00 0.00 33.79 3.36
868 869 3.437795 CCTTGCCTTGCCTGCTCG 61.438 66.667 0.00 0.00 0.00 5.03
882 884 2.885861 CTCGCCGCCTTCTGTAGT 59.114 61.111 0.00 0.00 0.00 2.73
911 913 1.135731 CGTCTGCGTCTCTCTGACC 59.864 63.158 0.00 0.00 42.49 4.02
1148 1151 4.194640 ACATCTGTACATGTCCTGATTGC 58.805 43.478 0.00 0.00 30.76 3.56
1150 1153 1.935873 CTGTACATGTCCTGATTGCGG 59.064 52.381 0.00 0.00 0.00 5.69
1152 1155 1.665679 GTACATGTCCTGATTGCGGTG 59.334 52.381 0.00 0.00 0.00 4.94
1162 1165 1.358725 GATTGCGGTGCGTGCTTAGA 61.359 55.000 0.00 0.00 0.00 2.10
1241 1246 6.206634 GGTCTGTTGGTGATTACTGATTTCAA 59.793 38.462 0.00 0.00 0.00 2.69
1243 1248 8.946085 GTCTGTTGGTGATTACTGATTTCAATA 58.054 33.333 0.00 0.00 0.00 1.90
1246 1251 7.888021 TGTTGGTGATTACTGATTTCAATAGGT 59.112 33.333 0.00 0.00 0.00 3.08
1247 1252 8.739972 GTTGGTGATTACTGATTTCAATAGGTT 58.260 33.333 0.00 0.00 0.00 3.50
1249 1254 9.613428 TGGTGATTACTGATTTCAATAGGTTAG 57.387 33.333 0.00 0.00 0.00 2.34
1269 1279 1.142060 TAATATGGGGTTGACGGGGG 58.858 55.000 0.00 0.00 0.00 5.40
1277 1287 1.305046 GTTGACGGGGGAGGAGAGA 60.305 63.158 0.00 0.00 0.00 3.10
1281 1291 0.397254 GACGGGGGAGGAGAGAATCA 60.397 60.000 0.00 0.00 37.82 2.57
1282 1292 0.042731 ACGGGGGAGGAGAGAATCAA 59.957 55.000 0.00 0.00 37.82 2.57
1283 1293 0.755686 CGGGGGAGGAGAGAATCAAG 59.244 60.000 0.00 0.00 37.82 3.02
1284 1294 1.886422 GGGGGAGGAGAGAATCAAGT 58.114 55.000 0.00 0.00 37.82 3.16
1285 1295 1.488393 GGGGGAGGAGAGAATCAAGTG 59.512 57.143 0.00 0.00 37.82 3.16
1286 1296 2.192263 GGGGAGGAGAGAATCAAGTGT 58.808 52.381 0.00 0.00 37.82 3.55
1288 1298 3.604582 GGGAGGAGAGAATCAAGTGTTG 58.395 50.000 0.00 0.00 37.82 3.33
1289 1299 3.008485 GGGAGGAGAGAATCAAGTGTTGT 59.992 47.826 0.00 0.00 37.82 3.32
1346 1364 3.569701 TCACTGGCTTGACAAATTCCTTC 59.430 43.478 0.00 0.00 0.00 3.46
1368 1394 7.767198 CCTTCGTGGAGTTTTAGGTTTATATGA 59.233 37.037 0.00 0.00 38.35 2.15
1380 1406 9.729023 TTTAGGTTTATATGATTTTGCACATCG 57.271 29.630 0.00 0.00 0.00 3.84
1398 1424 7.881516 CACATCGTGTGTATTTATTCACATG 57.118 36.000 12.72 12.72 46.54 3.21
1404 1430 7.725610 GTGTGTATTTATTCACATGAACTGC 57.274 36.000 0.00 0.00 44.48 4.40
1405 1431 7.304735 GTGTGTATTTATTCACATGAACTGCA 58.695 34.615 0.00 0.00 44.48 4.41
1406 1432 7.482743 GTGTGTATTTATTCACATGAACTGCAG 59.517 37.037 13.48 13.48 44.48 4.41
1407 1433 6.968904 GTGTATTTATTCACATGAACTGCAGG 59.031 38.462 19.93 1.54 36.80 4.85
1408 1434 5.587388 ATTTATTCACATGAACTGCAGGG 57.413 39.130 19.93 4.42 36.80 4.45
1409 1435 2.592102 ATTCACATGAACTGCAGGGT 57.408 45.000 19.93 5.09 36.80 4.34
1410 1436 2.363306 TTCACATGAACTGCAGGGTT 57.637 45.000 19.93 4.61 31.20 4.11
1411 1437 1.608055 TCACATGAACTGCAGGGTTG 58.392 50.000 19.93 12.10 31.20 3.77
1412 1438 5.174120 ATTCACATGAACTGCAGGGTTGC 62.174 47.826 19.93 0.00 42.83 4.17
1428 1454 3.421844 GGTTGCTTGGACACCTCTTATT 58.578 45.455 0.00 0.00 0.00 1.40
1439 1465 8.964476 TGGACACCTCTTATTTTCTTATCATC 57.036 34.615 0.00 0.00 0.00 2.92
1505 1531 0.608640 ACACATCCGACTTGTCCTCC 59.391 55.000 0.00 0.00 0.00 4.30
1514 1540 0.830444 ACTTGTCCTCCGGTGTGCTA 60.830 55.000 0.00 0.00 0.00 3.49
1700 1742 2.715046 TCCATTTGGACAGCACATCTC 58.285 47.619 0.00 0.00 39.78 2.75
1701 1743 2.040145 TCCATTTGGACAGCACATCTCA 59.960 45.455 0.00 0.00 39.78 3.27
1718 1760 5.163045 ACATCTCAAGGAAGGGTTTTCTCTT 60.163 40.000 0.00 0.00 44.26 2.85
1743 1785 0.107459 GCTCCCTCATCTGGACCAAC 60.107 60.000 0.00 0.00 0.00 3.77
1929 1971 5.068591 TCAATTCTGCAGTAGGCTAATCGTA 59.931 40.000 14.67 0.00 45.15 3.43
1971 2013 3.069158 CGTCCTTACATACCCTCCGAAAT 59.931 47.826 0.00 0.00 0.00 2.17
1992 2034 7.647715 CGAAATTGGGTTGGTAATATTGATGTC 59.352 37.037 0.00 0.00 0.00 3.06
2008 2050 4.136796 TGATGTCCAGAGGTTTGAAGTTG 58.863 43.478 0.00 0.00 0.00 3.16
2061 2103 2.828095 GGCCATGGTGCGCATGTA 60.828 61.111 15.91 3.03 0.00 2.29
2064 2106 1.779025 GCCATGGTGCGCATGTAGAG 61.779 60.000 15.91 2.29 0.00 2.43
2225 2267 8.229028 ACTTTGAAGTGGTGCATTGAGCATAG 62.229 42.308 0.00 0.00 46.65 2.23
2331 2373 9.751542 TGTTCGACAAAACCACATTATTTTTAT 57.248 25.926 0.00 0.00 0.00 1.40
2437 2480 5.319453 TCATCTTCAAGTCAATTGGCTCTT 58.681 37.500 14.03 9.00 39.54 2.85
2454 2497 6.100004 TGGCTCTTTTATGACTTCTTACTCG 58.900 40.000 0.00 0.00 0.00 4.18
2456 2499 6.253942 GGCTCTTTTATGACTTCTTACTCGTC 59.746 42.308 0.00 0.00 0.00 4.20
2599 2644 3.709987 GCACTGTGCTTCTTTTTGACAT 58.290 40.909 24.68 0.00 40.96 3.06
2688 2733 4.727507 TCTTAGTGAAGCTCTGGACATC 57.272 45.455 0.00 0.00 32.21 3.06
2731 2776 5.123027 GGTCATGAAGCTTAAACTTCTCTGG 59.877 44.000 17.22 6.61 45.20 3.86
2823 2868 3.876309 TTTGGCCTATGTAGATTCCCC 57.124 47.619 3.32 0.00 0.00 4.81
2824 2869 2.505672 TGGCCTATGTAGATTCCCCA 57.494 50.000 3.32 0.00 0.00 4.96
2827 2872 3.726859 TGGCCTATGTAGATTCCCCATTT 59.273 43.478 3.32 0.00 0.00 2.32
4158 4209 4.887655 AGGTTATGGCAAGCCTATTTGTAC 59.112 41.667 12.96 1.44 36.94 2.90
4218 4271 2.376695 ATCCTGATGCCATTTCCCAG 57.623 50.000 0.00 0.00 0.00 4.45
4244 4298 7.114811 GCAACACAAATTTTGTACCTCATAGTG 59.885 37.037 14.13 1.73 43.23 2.74
4435 4490 5.619132 TGAGTGATAAATGAGAGCATCCA 57.381 39.130 0.00 0.00 33.66 3.41
4517 4572 7.439157 TCGGGCAAAGAAAATATCAGATATG 57.561 36.000 3.51 0.00 0.00 1.78
4567 4622 5.920840 CCCATATCATGTGTTCAGTACGTAG 59.079 44.000 0.00 0.00 0.00 3.51
4568 4623 5.920840 CCATATCATGTGTTCAGTACGTAGG 59.079 44.000 0.00 0.00 0.00 3.18
4659 4716 5.714806 CCAAGGGGTTTATACAATTCACACT 59.285 40.000 0.00 0.00 0.00 3.55
4667 4724 7.749126 GGTTTATACAATTCACACTGTTACTGC 59.251 37.037 0.00 0.00 0.00 4.40
4694 4751 5.136828 TCCAAGCTTTTTGATAGTGAACCA 58.863 37.500 0.00 0.00 0.00 3.67
4709 4772 2.266554 GAACCATTGTCAGAGCTCTCG 58.733 52.381 14.96 9.98 34.09 4.04
4710 4773 0.534412 ACCATTGTCAGAGCTCTCGG 59.466 55.000 14.96 9.95 34.09 4.63
4711 4774 0.179089 CCATTGTCAGAGCTCTCGGG 60.179 60.000 14.96 2.79 34.09 5.14
4712 4775 0.809241 CATTGTCAGAGCTCTCGGGC 60.809 60.000 14.96 5.93 34.09 6.13
4713 4776 0.975040 ATTGTCAGAGCTCTCGGGCT 60.975 55.000 14.96 0.00 46.11 5.19
4908 4971 3.024547 TCAGGGAGAGTTATTCCAGACG 58.975 50.000 0.00 0.00 36.40 4.18
5005 5068 0.825410 CTGCCTGCAGAGAGATCTGT 59.175 55.000 17.39 0.00 46.30 3.41
5076 5141 5.438761 GCATCGGGCAAATTAAGAATACT 57.561 39.130 0.00 0.00 43.97 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 6.121776 TCAGTCAGATTAAAAGGCCAACTA 57.878 37.500 5.01 0.00 0.00 2.24
238 239 1.399440 CTTCATGTCCATGCACCGAAG 59.601 52.381 2.33 2.62 38.65 3.79
244 245 1.065199 GGAGACCTTCATGTCCATGCA 60.065 52.381 2.33 0.00 38.65 3.96
393 394 5.895636 TCACCCACAACATAATGATGAAC 57.104 39.130 0.00 0.00 36.48 3.18
429 430 3.918220 CTGCGCGGCGAGATCAAC 61.918 66.667 28.54 6.77 0.00 3.18
742 743 0.462047 CCCACTTGTCATACTCCGCC 60.462 60.000 0.00 0.00 0.00 6.13
800 801 1.785041 TATCCGCGCCAGTACGTACC 61.785 60.000 21.80 6.26 34.88 3.34
802 803 1.648720 GTATCCGCGCCAGTACGTA 59.351 57.895 0.00 0.00 34.88 3.57
803 804 2.410469 GTATCCGCGCCAGTACGT 59.590 61.111 0.00 0.00 34.88 3.57
804 805 2.354305 GGTATCCGCGCCAGTACG 60.354 66.667 0.00 0.00 0.00 3.67
815 816 5.379732 TTCACATTTGGAAAACGGTATCC 57.620 39.130 6.06 6.06 36.21 2.59
868 869 1.362406 GCAGAACTACAGAAGGCGGC 61.362 60.000 0.00 0.00 0.00 6.53
882 884 2.258591 GCAGACGACGGAGCAGAA 59.741 61.111 0.00 0.00 0.00 3.02
911 913 2.507992 CTCGCGAGCAAGGACAGG 60.508 66.667 25.07 0.00 0.00 4.00
934 936 3.147595 CGTGGGATCGAGCTGGGA 61.148 66.667 0.00 0.00 0.00 4.37
954 956 4.214327 CGCTCCTCTTCCTCGCCC 62.214 72.222 0.00 0.00 0.00 6.13
1148 1151 1.674611 CGAACTCTAAGCACGCACCG 61.675 60.000 0.00 0.00 0.00 4.94
1150 1153 1.415374 TTCGAACTCTAAGCACGCAC 58.585 50.000 0.00 0.00 0.00 5.34
1152 1155 1.588861 GGATTCGAACTCTAAGCACGC 59.411 52.381 0.00 0.00 0.00 5.34
1162 1165 1.017701 GGAAACGGCGGATTCGAACT 61.018 55.000 13.24 0.00 39.00 3.01
1241 1246 6.013984 CCGTCAACCCCATATTACTAACCTAT 60.014 42.308 0.00 0.00 0.00 2.57
1243 1248 4.102054 CCGTCAACCCCATATTACTAACCT 59.898 45.833 0.00 0.00 0.00 3.50
1246 1251 3.391955 CCCCGTCAACCCCATATTACTAA 59.608 47.826 0.00 0.00 0.00 2.24
1247 1252 2.974099 CCCCGTCAACCCCATATTACTA 59.026 50.000 0.00 0.00 0.00 1.82
1249 1254 1.202842 CCCCCGTCAACCCCATATTAC 60.203 57.143 0.00 0.00 0.00 1.89
1258 1268 2.284405 TCTCCTCCCCCGTCAACC 60.284 66.667 0.00 0.00 0.00 3.77
1269 1279 6.031751 ACTACAACACTTGATTCTCTCCTC 57.968 41.667 0.00 0.00 0.00 3.71
1273 1283 6.209589 TCAGCTACTACAACACTTGATTCTCT 59.790 38.462 0.00 0.00 0.00 3.10
1277 1287 9.672673 AATTATCAGCTACTACAACACTTGATT 57.327 29.630 0.00 0.00 0.00 2.57
1284 1294 9.595823 GGAACTAAATTATCAGCTACTACAACA 57.404 33.333 0.00 0.00 0.00 3.33
1285 1295 9.595823 TGGAACTAAATTATCAGCTACTACAAC 57.404 33.333 0.00 0.00 0.00 3.32
1384 1410 6.095440 ACCCTGCAGTTCATGTGAATAAATAC 59.905 38.462 13.81 0.00 36.33 1.89
1390 1416 2.559668 CAACCCTGCAGTTCATGTGAAT 59.440 45.455 13.81 0.00 36.33 2.57
1404 1430 0.890996 GAGGTGTCCAAGCAACCCTG 60.891 60.000 0.00 0.00 0.00 4.45
1405 1431 1.062488 AGAGGTGTCCAAGCAACCCT 61.062 55.000 0.00 0.00 0.00 4.34
1406 1432 0.178990 AAGAGGTGTCCAAGCAACCC 60.179 55.000 0.00 0.00 0.00 4.11
1407 1433 2.561478 TAAGAGGTGTCCAAGCAACC 57.439 50.000 0.00 0.00 0.00 3.77
1408 1434 5.241728 AGAAAATAAGAGGTGTCCAAGCAAC 59.758 40.000 0.00 0.00 0.00 4.17
1409 1435 5.385198 AGAAAATAAGAGGTGTCCAAGCAA 58.615 37.500 0.00 0.00 0.00 3.91
1410 1436 4.985538 AGAAAATAAGAGGTGTCCAAGCA 58.014 39.130 0.00 0.00 0.00 3.91
1411 1437 5.966742 AAGAAAATAAGAGGTGTCCAAGC 57.033 39.130 0.00 0.00 0.00 4.01
1412 1438 8.792830 TGATAAGAAAATAAGAGGTGTCCAAG 57.207 34.615 0.00 0.00 0.00 3.61
1413 1439 9.396022 GATGATAAGAAAATAAGAGGTGTCCAA 57.604 33.333 0.00 0.00 0.00 3.53
1417 1443 8.772250 TGGAGATGATAAGAAAATAAGAGGTGT 58.228 33.333 0.00 0.00 0.00 4.16
1439 1465 4.695928 CCTGCAGTTCATGATGATATGGAG 59.304 45.833 13.81 16.65 33.52 3.86
1505 1531 1.153369 CCCCTGACATAGCACACCG 60.153 63.158 0.00 0.00 0.00 4.94
1514 1540 1.915489 TCAAGCACATACCCCTGACAT 59.085 47.619 0.00 0.00 0.00 3.06
1554 1580 2.700722 TCTGCAAGTACACCACACAA 57.299 45.000 0.00 0.00 33.76 3.33
1700 1742 2.297315 GCCAAGAGAAAACCCTTCCTTG 59.703 50.000 0.00 0.00 32.01 3.61
1701 1743 2.177888 AGCCAAGAGAAAACCCTTCCTT 59.822 45.455 0.00 0.00 0.00 3.36
1718 1760 2.042537 AGATGAGGGAGCGAGCCA 60.043 61.111 0.00 0.00 0.00 4.75
1743 1785 2.012673 GACCATAACAAGAGCAGCCAG 58.987 52.381 0.00 0.00 0.00 4.85
1859 1901 9.450807 CAGTAATTACAAGGTTCAAAAGAGTTG 57.549 33.333 17.65 0.00 0.00 3.16
1971 2013 5.832221 TGGACATCAATATTACCAACCCAA 58.168 37.500 0.00 0.00 0.00 4.12
1992 2034 2.033801 CAGCACAACTTCAAACCTCTGG 59.966 50.000 0.00 0.00 0.00 3.86
2008 2050 3.429085 CTTTATTTCCGATGCACAGCAC 58.571 45.455 0.00 0.00 43.04 4.40
2061 2103 1.819229 CATGCGCCTCCTGTACTCT 59.181 57.895 4.18 0.00 0.00 3.24
2064 2106 1.305219 TTTGCATGCGCCTCCTGTAC 61.305 55.000 14.09 0.00 37.32 2.90
2331 2373 5.130477 GGTAGGGTGAGATGATGGTAAAAGA 59.870 44.000 0.00 0.00 0.00 2.52
2437 2480 8.882415 AAAACAGACGAGTAAGAAGTCATAAA 57.118 30.769 0.00 0.00 37.36 1.40
2498 2543 0.827089 TGGCACCCCAAAGTGTGATG 60.827 55.000 0.00 0.00 38.46 3.07
2599 2644 7.890127 AGAAGGATCATAATCACCACAGAAAAA 59.110 33.333 0.00 0.00 33.21 1.94
2637 2682 4.319911 GCTTACGATGCCACTAACAAAACA 60.320 41.667 0.00 0.00 0.00 2.83
2688 2733 5.710984 TGACCTTTTCTACTAAGAAGCTCG 58.289 41.667 0.00 0.00 42.60 5.03
2731 2776 2.791158 CGGTTCCGCTACATGCATTTTC 60.791 50.000 0.00 0.00 43.06 2.29
3004 3049 7.057264 TGGTGTATGGCATTTAATACTAAGCA 58.943 34.615 4.78 0.00 31.75 3.91
3423 3468 0.878416 TCACAAAACCATGGCGCTAC 59.122 50.000 13.04 0.00 0.00 3.58
4107 4158 8.579850 AATCCTGTGTGAAGATAAGCAATTTA 57.420 30.769 0.00 0.00 0.00 1.40
4158 4209 0.954449 GCATGATGCCGATCTCCCTG 60.954 60.000 6.04 0.00 37.42 4.45
4218 4271 7.114811 CACTATGAGGTACAAAATTTGTGTTGC 59.885 37.037 20.40 8.66 45.03 4.17
4244 4298 9.343539 AGGTAAAATGACTAAATATCTGGAAGC 57.656 33.333 0.00 0.00 0.00 3.86
4387 4441 6.926280 TTTTGCGCAATTCAATAGTAACAG 57.074 33.333 25.64 0.00 0.00 3.16
4395 4449 6.331845 TCACTCATATTTTGCGCAATTCAAT 58.668 32.000 25.64 21.80 0.00 2.57
4458 4513 2.353889 CACCATCTCATTTTCAGCCTCG 59.646 50.000 0.00 0.00 0.00 4.63
4517 4572 5.343058 CACTGTTATTGTTATGTGCTGTTGC 59.657 40.000 0.00 0.00 40.20 4.17
4543 4598 4.693283 ACGTACTGAACACATGATATGGG 58.307 43.478 0.00 0.00 40.30 4.00
4659 4716 0.771127 AGCTTGGAAGGGCAGTAACA 59.229 50.000 0.00 0.00 0.00 2.41
4667 4724 4.766891 TCACTATCAAAAAGCTTGGAAGGG 59.233 41.667 0.00 1.32 0.00 3.95
4694 4751 0.975040 AGCCCGAGAGCTCTGACAAT 60.975 55.000 23.91 0.74 39.48 2.71
4712 4775 4.598894 CATGAGCCCGAGCCCGAG 62.599 72.222 0.00 0.00 41.25 4.63
4728 4791 0.902516 GGCCAACCAATGTTAGGGCA 60.903 55.000 0.00 0.00 42.49 5.36
4863 4926 4.020928 TCTCTACCATGTTTCGCAGGTAAA 60.021 41.667 0.00 0.00 36.28 2.01
4908 4971 8.442384 CAATAGTTTGATTTGTTTTACCATGCC 58.558 33.333 0.00 0.00 34.60 4.40
5076 5141 7.935520 TGATGTGAGTGTTTGCAATTAACTTA 58.064 30.769 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.