Multiple sequence alignment - TraesCS3B01G226500

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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 TraesCS3B01G226500 chr3B 100.000 2441 0 0 1 2441 315427445 315425005 0.000000e+00 4508.0
1 TraesCS3B01G226500 chr3B 88.142 1948 197 13 2 1925 661025747 661027684 0.000000e+00 2287.0
2 TraesCS3B01G226500 chr3B 85.923 547 59 10 1395 1925 826329688 826329144 3.520000e-158 568.0
3 TraesCS3B01G226500 chr3B 86.127 519 58 6 1395 1899 189420956 189420438 4.590000e-152 547.0
4 TraesCS3B01G226500 chr1D 88.568 1732 177 9 2 1725 485625497 485627215 0.000000e+00 2082.0
5 TraesCS3B01G226500 chr2D 88.347 1416 146 9 1 1413 35333677 35335076 0.000000e+00 1683.0
6 TraesCS3B01G226500 chr2D 80.767 1513 267 18 10 1515 360440844 360442339 0.000000e+00 1160.0
7 TraesCS3B01G226500 chr2B 82.215 1923 295 34 24 1926 492973463 492975358 0.000000e+00 1613.0
8 TraesCS3B01G226500 chr2B 89.093 1036 101 7 1 1035 374433106 374434130 0.000000e+00 1277.0
9 TraesCS3B01G226500 chr2B 88.102 353 40 2 1090 1442 374434456 374434806 3.750000e-113 418.0
10 TraesCS3B01G226500 chr7D 81.865 1930 295 27 24 1927 457537053 457535153 0.000000e+00 1574.0
11 TraesCS3B01G226500 chr1B 87.629 1261 125 22 635 1889 452518951 452517716 0.000000e+00 1435.0
12 TraesCS3B01G226500 chr1B 91.706 639 53 0 1 639 452563404 452562766 0.000000e+00 887.0
13 TraesCS3B01G226500 chr1B 86.972 545 56 7 1395 1925 235509515 235508972 1.250000e-167 599.0
14 TraesCS3B01G226500 chr3D 87.638 1181 118 9 589 1763 565998325 565997167 0.000000e+00 1347.0
15 TraesCS3B01G226500 chr3D 81.031 1513 264 16 10 1515 567865286 567866782 0.000000e+00 1182.0
16 TraesCS3B01G226500 chr3D 87.745 816 95 5 1 814 560719544 560720356 0.000000e+00 948.0
17 TraesCS3B01G226500 chr3D 86.069 524 51 8 1924 2441 266632823 266633330 5.940000e-151 544.0
18 TraesCS3B01G226500 chr3D 87.835 411 50 0 1305 1715 16585529 16585119 1.310000e-132 483.0
19 TraesCS3B01G226500 chr3D 76.068 117 28 0 950 1066 275654058 275653942 7.290000e-06 62.1
20 TraesCS3B01G226500 chr5B 86.422 464 50 6 1395 1845 345513027 345513490 1.690000e-136 496.0
21 TraesCS3B01G226500 chr3A 87.812 320 26 7 2005 2323 309336945 309337252 1.780000e-96 363.0
22 TraesCS3B01G226500 chr3A 79.508 122 9 6 1924 2040 309336781 309336891 3.370000e-09 73.1
23 TraesCS3B01G226500 chr5A 100.000 35 0 0 2006 2040 485708469 485708435 5.630000e-07 65.8


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 TraesCS3B01G226500 chr3B 315425005 315427445 2440 True 4508.0 4508 100.0000 1 2441 1 chr3B.!!$R2 2440
1 TraesCS3B01G226500 chr3B 661025747 661027684 1937 False 2287.0 2287 88.1420 2 1925 1 chr3B.!!$F1 1923
2 TraesCS3B01G226500 chr3B 826329144 826329688 544 True 568.0 568 85.9230 1395 1925 1 chr3B.!!$R3 530
3 TraesCS3B01G226500 chr3B 189420438 189420956 518 True 547.0 547 86.1270 1395 1899 1 chr3B.!!$R1 504
4 TraesCS3B01G226500 chr1D 485625497 485627215 1718 False 2082.0 2082 88.5680 2 1725 1 chr1D.!!$F1 1723
5 TraesCS3B01G226500 chr2D 35333677 35335076 1399 False 1683.0 1683 88.3470 1 1413 1 chr2D.!!$F1 1412
6 TraesCS3B01G226500 chr2D 360440844 360442339 1495 False 1160.0 1160 80.7670 10 1515 1 chr2D.!!$F2 1505
7 TraesCS3B01G226500 chr2B 492973463 492975358 1895 False 1613.0 1613 82.2150 24 1926 1 chr2B.!!$F1 1902
8 TraesCS3B01G226500 chr2B 374433106 374434806 1700 False 847.5 1277 88.5975 1 1442 2 chr2B.!!$F2 1441
9 TraesCS3B01G226500 chr7D 457535153 457537053 1900 True 1574.0 1574 81.8650 24 1927 1 chr7D.!!$R1 1903
10 TraesCS3B01G226500 chr1B 452517716 452518951 1235 True 1435.0 1435 87.6290 635 1889 1 chr1B.!!$R2 1254
11 TraesCS3B01G226500 chr1B 452562766 452563404 638 True 887.0 887 91.7060 1 639 1 chr1B.!!$R3 638
12 TraesCS3B01G226500 chr1B 235508972 235509515 543 True 599.0 599 86.9720 1395 1925 1 chr1B.!!$R1 530
13 TraesCS3B01G226500 chr3D 565997167 565998325 1158 True 1347.0 1347 87.6380 589 1763 1 chr3D.!!$R3 1174
14 TraesCS3B01G226500 chr3D 567865286 567866782 1496 False 1182.0 1182 81.0310 10 1515 1 chr3D.!!$F3 1505
15 TraesCS3B01G226500 chr3D 560719544 560720356 812 False 948.0 948 87.7450 1 814 1 chr3D.!!$F2 813
16 TraesCS3B01G226500 chr3D 266632823 266633330 507 False 544.0 544 86.0690 1924 2441 1 chr3D.!!$F1 517

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
150 151 2.629617 CCTGAAGAAAATGGTTGGCTGT 59.37 45.455 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1970 2307 0.10852 TCGGGTATTCACTCAACCGC 60.109 55.0 0.0 0.0 40.99 5.68 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
30 31 8.503428 AGGTTGTATCCTTCTCTGATATCATT 57.497 34.615 5.72 0.00 33.52 2.57
33 34 7.250032 TGTATCCTTCTCTGATATCATTGGG 57.750 40.000 5.72 5.16 0.00 4.12
42 43 3.949754 CTGATATCATTGGGTGCACTGTT 59.050 43.478 17.98 4.79 0.00 3.16
150 151 2.629617 CCTGAAGAAAATGGTTGGCTGT 59.370 45.455 0.00 0.00 0.00 4.40
169 170 5.104900 GGCTGTAGAGGAAAATTACTCTCCA 60.105 44.000 11.14 5.89 45.31 3.86
232 233 4.222145 GTGTTCCTGTCTACCTGTTATCCA 59.778 45.833 0.00 0.00 0.00 3.41
311 312 4.036852 CCTTTGGAGTGACTTTGAAGGAAC 59.963 45.833 13.27 0.00 35.36 3.62
328 329 3.653352 AGGAACTAGGAAGCTTCACCTTT 59.347 43.478 27.02 14.31 36.02 3.11
347 348 4.262894 CCTTTCTAACTGGCACTTGGTCTA 60.263 45.833 0.00 0.00 0.00 2.59
446 447 8.424918 GGTTAAGAGATACATCAAAGATGAGGA 58.575 37.037 13.46 0.00 39.70 3.71
640 641 6.315714 TGGGAAGATATTTTGTTTGGTACCA 58.684 36.000 11.60 11.60 0.00 3.25
656 657 2.762535 ACCACACCTTTATCTGTCCG 57.237 50.000 0.00 0.00 0.00 4.79
772 776 4.640771 TTTACCCCTATCATGATGGAGC 57.359 45.455 19.78 0.00 0.00 4.70
823 827 9.973661 TTACTAGTACCCAATACACAAGTAGTA 57.026 33.333 0.91 0.00 36.09 1.82
888 892 7.686434 ACACAACTGGGTCTTTGTATAGTATT 58.314 34.615 0.00 0.00 34.12 1.89
979 983 5.422331 CCTATAGTCCAAGTCTTTCTGTGGA 59.578 44.000 0.00 0.00 37.83 4.02
1192 1469 8.040727 ACCTTTCCATTGCTAAATTTTGGATAC 58.959 33.333 8.92 0.00 36.42 2.24
1342 1620 0.692419 GGGGCTCTTGAGGAGATGGA 60.692 60.000 0.00 0.00 44.45 3.41
1415 1693 3.055240 AGAGCTTCCTTGATCCTGAACAG 60.055 47.826 0.00 0.00 0.00 3.16
1451 1729 0.175073 GCGGGGTAGTCGAACTTGAT 59.825 55.000 0.00 0.00 0.00 2.57
1459 1737 6.373495 GGGGTAGTCGAACTTGATAAAAACAT 59.627 38.462 0.00 0.00 0.00 2.71
1535 1813 0.817654 CTCCATCGTCTAGCACCACA 59.182 55.000 0.00 0.00 0.00 4.17
1536 1814 1.204704 CTCCATCGTCTAGCACCACAA 59.795 52.381 0.00 0.00 0.00 3.33
1581 1859 1.202336 GCAGTTTCACTTGCAAGCACT 60.202 47.619 26.27 18.52 0.00 4.40
1605 1884 2.910479 TGAGTCCTGTGACGCCGT 60.910 61.111 0.00 0.00 46.51 5.68
1622 1901 2.528127 TTGGACCTTCCGGGCTCA 60.528 61.111 0.00 0.00 40.17 4.26
1704 1989 0.458543 GAAGATCTTGCAGCCGACGA 60.459 55.000 14.00 0.00 0.00 4.20
1707 1992 0.458543 GATCTTGCAGCCGACGAAGA 60.459 55.000 0.00 0.00 0.00 2.87
1729 2014 2.037772 AGACCAAGCAAGACAATCTCGT 59.962 45.455 0.00 0.00 0.00 4.18
1750 2035 3.961408 GTTGTCCTAGAGATTCCAGCCTA 59.039 47.826 0.00 0.00 0.00 3.93
1787 2084 3.891049 AGCTAGGCTTTATGGTCTTTGG 58.109 45.455 0.00 0.00 33.89 3.28
1788 2085 2.359214 GCTAGGCTTTATGGTCTTTGGC 59.641 50.000 0.00 0.00 0.00 4.52
1791 2088 2.580783 AGGCTTTATGGTCTTTGGCCTA 59.419 45.455 3.32 0.00 45.32 3.93
1794 2091 5.103686 AGGCTTTATGGTCTTTGGCCTATAA 60.104 40.000 3.32 0.00 45.32 0.98
1802 2099 5.534654 TGGTCTTTGGCCTATAATAATGTGC 59.465 40.000 3.32 0.00 0.00 4.57
1804 2101 6.294176 GGTCTTTGGCCTATAATAATGTGCAG 60.294 42.308 3.32 0.00 0.00 4.41
1805 2102 6.263168 GTCTTTGGCCTATAATAATGTGCAGT 59.737 38.462 3.32 0.00 0.00 4.40
1807 2133 6.389830 TTGGCCTATAATAATGTGCAGTTG 57.610 37.500 3.32 0.00 0.00 3.16
1824 2150 3.319122 CAGTTGTTCCCTTTCTTTCCTGG 59.681 47.826 0.00 0.00 0.00 4.45
1837 2163 1.321474 TTCCTGGACTTGCTTTGCAG 58.679 50.000 0.00 0.00 40.61 4.41
1863 2191 4.879545 TGTTTGACACCTAAACTCTGGTTC 59.120 41.667 0.00 0.00 38.50 3.62
1945 2282 7.835634 AAAAACAACCAAAAACATACGACAT 57.164 28.000 0.00 0.00 0.00 3.06
1955 2292 5.759506 AAACATACGACATGTTTGGTTCA 57.240 34.783 22.85 0.00 46.67 3.18
1993 2335 2.434702 GGTTGAGTGAATACCCGATCCT 59.565 50.000 0.00 0.00 0.00 3.24
1998 2340 3.279434 AGTGAATACCCGATCCTTTTGC 58.721 45.455 0.00 0.00 0.00 3.68
1999 2341 3.054361 AGTGAATACCCGATCCTTTTGCT 60.054 43.478 0.00 0.00 0.00 3.91
2000 2342 3.694566 GTGAATACCCGATCCTTTTGCTT 59.305 43.478 0.00 0.00 0.00 3.91
2001 2343 3.945285 TGAATACCCGATCCTTTTGCTTC 59.055 43.478 0.00 0.00 0.00 3.86
2002 2344 2.413310 TACCCGATCCTTTTGCTTCC 57.587 50.000 0.00 0.00 0.00 3.46
2003 2345 0.323451 ACCCGATCCTTTTGCTTCCC 60.323 55.000 0.00 0.00 0.00 3.97
2004 2346 0.034089 CCCGATCCTTTTGCTTCCCT 60.034 55.000 0.00 0.00 0.00 4.20
2005 2347 1.616994 CCCGATCCTTTTGCTTCCCTT 60.617 52.381 0.00 0.00 0.00 3.95
2006 2348 2.171003 CCGATCCTTTTGCTTCCCTTT 58.829 47.619 0.00 0.00 0.00 3.11
2007 2349 2.562738 CCGATCCTTTTGCTTCCCTTTT 59.437 45.455 0.00 0.00 0.00 2.27
2008 2350 3.578688 CGATCCTTTTGCTTCCCTTTTG 58.421 45.455 0.00 0.00 0.00 2.44
2009 2351 2.908688 TCCTTTTGCTTCCCTTTTGC 57.091 45.000 0.00 0.00 0.00 3.68
2040 2382 6.555463 ATGGGATGCTTTCTCAATTCAAAT 57.445 33.333 0.00 0.00 38.67 2.32
2089 2431 9.860650 ATTAAGCCATATATAAGTGAACACCAA 57.139 29.630 1.11 0.00 0.00 3.67
2102 2444 2.067365 ACACCAAAAGAACAGGGTCC 57.933 50.000 0.00 0.00 0.00 4.46
2103 2445 1.569072 ACACCAAAAGAACAGGGTCCT 59.431 47.619 0.00 0.00 0.00 3.85
2115 2457 3.728373 GGTCCTTCCGGCCACCAT 61.728 66.667 2.24 0.00 29.61 3.55
2120 2462 2.609299 TTCCGGCCACCATGAGGA 60.609 61.111 2.24 0.00 38.69 3.71
2121 2463 2.196997 CTTCCGGCCACCATGAGGAA 62.197 60.000 2.24 4.58 38.51 3.36
2122 2464 2.438434 CCGGCCACCATGAGGAAC 60.438 66.667 2.24 0.19 38.69 3.62
2123 2465 2.438434 CGGCCACCATGAGGAACC 60.438 66.667 2.24 0.74 38.69 3.62
2124 2466 2.763215 GGCCACCATGAGGAACCA 59.237 61.111 0.00 0.00 38.69 3.67
2128 2470 1.538047 CCACCATGAGGAACCAAGTG 58.462 55.000 0.00 0.00 38.69 3.16
2139 2481 3.717294 CCAAGTGGGGGAGGGACG 61.717 72.222 0.00 0.00 0.00 4.79
2154 2496 3.616721 ACGAGGCAAGGTGCTCGT 61.617 61.111 16.49 16.49 45.21 4.18
2156 2498 2.743928 GAGGCAAGGTGCTCGTGG 60.744 66.667 0.00 0.00 44.28 4.94
2157 2499 3.537206 GAGGCAAGGTGCTCGTGGT 62.537 63.158 0.00 0.00 44.28 4.16
2174 2516 1.203376 TGGTGGATAAGGGTGAGGTCA 60.203 52.381 0.00 0.00 0.00 4.02
2175 2517 1.209747 GGTGGATAAGGGTGAGGTCAC 59.790 57.143 1.17 1.17 45.72 3.67
2215 2557 2.069776 CACAGGAGGTCATGGTGGT 58.930 57.895 0.00 0.00 30.95 4.16
2221 2563 0.909610 GAGGTCATGGTGGTGAGGGA 60.910 60.000 0.00 0.00 0.00 4.20
2252 2595 2.152016 GAAAAGGGGAGTCGGACAAAG 58.848 52.381 11.27 0.00 0.00 2.77
2257 2600 0.109226 GGGAGTCGGACAAAGAGACG 60.109 60.000 11.27 0.00 39.65 4.18
2260 2603 1.268899 GAGTCGGACAAAGAGACGGAA 59.731 52.381 11.27 0.00 39.65 4.30
2266 2609 2.070028 GACAAAGAGACGGAAAGGAGC 58.930 52.381 0.00 0.00 0.00 4.70
2271 2614 1.891150 AGAGACGGAAAGGAGCGTTTA 59.109 47.619 0.00 0.00 0.00 2.01
2288 2631 2.812011 GTTTACGCTTCCCACTCAATGT 59.188 45.455 0.00 0.00 0.00 2.71
2324 2667 1.305219 TGCAAAGCGGTGTATCAGGC 61.305 55.000 0.00 0.00 0.00 4.85
2333 2676 2.414559 CGGTGTATCAGGCTTTGCAAAG 60.415 50.000 30.70 30.70 39.03 2.77
2334 2677 2.558359 GGTGTATCAGGCTTTGCAAAGT 59.442 45.455 33.47 19.62 38.28 2.66
2336 2679 2.557924 TGTATCAGGCTTTGCAAAGTGG 59.442 45.455 33.47 24.09 38.28 4.00
2344 2687 3.568538 GCTTTGCAAAGTGGTGTATCAG 58.431 45.455 33.47 10.94 38.28 2.90
2347 2690 5.123820 GCTTTGCAAAGTGGTGTATCAGATA 59.876 40.000 33.47 0.00 38.28 1.98
2349 2692 6.494893 TTGCAAAGTGGTGTATCAGATAAC 57.505 37.500 0.00 0.00 0.00 1.89
2389 2732 0.738389 AGCCGAAACAAACACCTGTG 59.262 50.000 0.00 0.00 0.00 3.66
2392 2735 1.267832 CCGAAACAAACACCTGTGACG 60.268 52.381 3.94 0.00 0.00 4.35
2397 2740 4.545823 AACAAACACCTGTGACGTATTG 57.454 40.909 3.94 4.24 0.00 1.90
2398 2741 2.875933 ACAAACACCTGTGACGTATTGG 59.124 45.455 3.94 0.00 0.00 3.16
2413 2756 4.103469 ACGTATTGGGGAGGCAATGTAATA 59.897 41.667 0.00 0.00 0.00 0.98
2415 2758 6.013206 ACGTATTGGGGAGGCAATGTAATATA 60.013 38.462 0.00 0.00 0.00 0.86
2420 2763 8.405971 TTGGGGAGGCAATGTAATATATAGAT 57.594 34.615 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
150 151 7.579723 GCAGAGTTGGAGAGTAATTTTCCTCTA 60.580 40.741 2.94 0.00 38.15 2.43
261 262 2.356069 GGCTAGCTGGCTGTTAATCAAC 59.644 50.000 22.23 0.00 38.32 3.18
311 312 5.872070 CAGTTAGAAAGGTGAAGCTTCCTAG 59.128 44.000 23.42 2.13 33.27 3.02
328 329 5.897250 TCATATAGACCAAGTGCCAGTTAGA 59.103 40.000 0.00 0.00 0.00 2.10
473 474 9.944079 TGTTGGGGGAATTATTAAGATATTTCA 57.056 29.630 0.00 0.00 33.11 2.69
640 641 3.782656 AAACCGGACAGATAAAGGTGT 57.217 42.857 9.46 0.00 35.08 4.16
656 657 3.306472 TGACATATAGGGGCCAAAACC 57.694 47.619 4.39 0.00 0.00 3.27
761 765 0.104855 GTACCAGCGCTCCATCATGA 59.895 55.000 7.13 0.00 0.00 3.07
772 776 0.037326 TTCTCAAGGCAGTACCAGCG 60.037 55.000 2.26 0.00 43.14 5.18
823 827 3.896888 TGTTGCCAAATCAAGGAGTCATT 59.103 39.130 0.00 0.00 0.00 2.57
888 892 7.934354 TGGCTATACACCCCTAAAGTTAATA 57.066 36.000 0.00 0.00 0.00 0.98
900 904 5.830991 TGGAATGTAAATTGGCTATACACCC 59.169 40.000 0.00 0.00 32.80 4.61
907 911 7.363705 CCAAACTGATGGAATGTAAATTGGCTA 60.364 37.037 0.00 0.00 43.54 3.93
909 913 5.581874 CCAAACTGATGGAATGTAAATTGGC 59.418 40.000 0.00 0.00 43.54 4.52
952 956 4.101741 CAGAAAGACTTGGACTATAGGGGG 59.898 50.000 4.43 0.00 0.00 5.40
953 957 4.717280 ACAGAAAGACTTGGACTATAGGGG 59.283 45.833 4.43 0.00 0.00 4.79
954 958 5.395768 CCACAGAAAGACTTGGACTATAGGG 60.396 48.000 4.43 0.00 32.50 3.53
955 959 5.422331 TCCACAGAAAGACTTGGACTATAGG 59.578 44.000 4.43 0.00 33.91 2.57
959 963 5.544176 AGAATCCACAGAAAGACTTGGACTA 59.456 40.000 0.00 0.00 38.02 2.59
969 973 5.144692 TGTGAGAGAGAATCCACAGAAAG 57.855 43.478 0.00 0.00 35.49 2.62
979 983 6.985645 GTCATCAGCTTATTGTGAGAGAGAAT 59.014 38.462 0.00 0.00 0.00 2.40
1105 1382 4.685924 AGAATTCCATATTTGCTTTGCCG 58.314 39.130 0.65 0.00 0.00 5.69
1139 1416 4.019321 CAGATCCCAGGGTACAAGAGAAAA 60.019 45.833 5.01 0.00 0.00 2.29
1192 1469 2.927553 GCAGTGTGCTTCTTATTGGG 57.072 50.000 0.00 0.00 40.96 4.12
1287 1565 5.007430 CCAGATCTGTTTCAAATCGATCCAG 59.993 44.000 21.11 0.00 32.87 3.86
1293 1571 4.697352 AGGTTCCAGATCTGTTTCAAATCG 59.303 41.667 21.11 2.94 0.00 3.34
1342 1620 4.404073 AGCTACGTCCTTGAGAAGAATCAT 59.596 41.667 0.00 0.00 0.00 2.45
1415 1693 1.294659 CGCTGTGAGCTGGAAAGGAC 61.295 60.000 0.00 0.00 39.60 3.85
1459 1737 3.383185 CACTTGGCTAAAAACACCCTCAA 59.617 43.478 0.00 0.00 0.00 3.02
1498 1776 0.329596 AGTTGACATCCTTCCCAGGC 59.670 55.000 0.00 0.00 40.58 4.85
1535 1813 2.671070 CTGGGTGGAGATGGCGTT 59.329 61.111 0.00 0.00 0.00 4.84
1536 1814 3.402681 CCTGGGTGGAGATGGCGT 61.403 66.667 0.00 0.00 38.35 5.68
1581 1859 1.903404 TCACAGGACTCAGCAGCGA 60.903 57.895 0.00 0.00 0.00 4.93
1622 1901 0.178975 TTTTTGTCGGATGGGCAGGT 60.179 50.000 0.00 0.00 0.00 4.00
1667 1952 4.978099 TCTTCATCTTCCATATTCCAGCC 58.022 43.478 0.00 0.00 0.00 4.85
1693 1978 1.372997 GTCTTCTTCGTCGGCTGCA 60.373 57.895 0.50 0.00 0.00 4.41
1704 1989 4.723309 AGATTGTCTTGCTTGGTCTTCTT 58.277 39.130 0.00 0.00 0.00 2.52
1707 1992 3.070018 CGAGATTGTCTTGCTTGGTCTT 58.930 45.455 0.00 0.00 0.00 3.01
1729 2014 3.121929 AGGCTGGAATCTCTAGGACAA 57.878 47.619 0.00 0.00 0.00 3.18
1787 2084 6.438763 GGAACAACTGCACATTATTATAGGC 58.561 40.000 0.00 0.00 0.00 3.93
1788 2085 6.772716 AGGGAACAACTGCACATTATTATAGG 59.227 38.462 0.00 0.00 0.00 2.57
1791 2088 7.397192 AGAAAGGGAACAACTGCACATTATTAT 59.603 33.333 0.00 0.00 0.00 1.28
1794 2091 5.079643 AGAAAGGGAACAACTGCACATTAT 58.920 37.500 0.00 0.00 0.00 1.28
1802 2099 3.319122 CCAGGAAAGAAAGGGAACAACTG 59.681 47.826 0.00 0.00 0.00 3.16
1804 2101 3.318275 GTCCAGGAAAGAAAGGGAACAAC 59.682 47.826 0.00 0.00 0.00 3.32
1805 2102 3.204382 AGTCCAGGAAAGAAAGGGAACAA 59.796 43.478 0.00 0.00 0.00 2.83
1807 2133 3.510531 AGTCCAGGAAAGAAAGGGAAC 57.489 47.619 0.00 0.00 0.00 3.62
1824 2150 3.054878 CAAACATCCTGCAAAGCAAGTC 58.945 45.455 0.00 0.00 38.41 3.01
1837 2163 4.455877 CCAGAGTTTAGGTGTCAAACATCC 59.544 45.833 0.00 0.00 38.16 3.51
1863 2191 4.023536 CCCGGTTCCATTATTGAATAACGG 60.024 45.833 12.64 12.64 36.74 4.44
1931 2268 6.565234 TGAACCAAACATGTCGTATGTTTTT 58.435 32.000 21.96 17.23 46.45 1.94
1955 2292 9.772973 TCACTCAACCGCTATATAATACAAATT 57.227 29.630 0.00 0.00 0.00 1.82
1970 2307 0.108520 TCGGGTATTCACTCAACCGC 60.109 55.000 0.00 0.00 40.99 5.68
1971 2308 2.470821 GATCGGGTATTCACTCAACCG 58.529 52.381 0.00 0.00 42.45 4.44
1993 2335 3.795877 CTGAAGCAAAAGGGAAGCAAAA 58.204 40.909 0.00 0.00 0.00 2.44
2040 2382 8.701908 AATCCTACGATCTAGGTTTGTACATA 57.298 34.615 14.29 0.00 36.16 2.29
2050 2392 5.923733 ATGGCTTAATCCTACGATCTAGG 57.076 43.478 10.42 10.42 36.06 3.02
2102 2444 2.124570 CCTCATGGTGGCCGGAAG 60.125 66.667 5.05 0.00 0.00 3.46
2103 2445 2.227757 TTCCTCATGGTGGCCGGAA 61.228 57.895 5.05 0.00 34.23 4.30
2115 2457 1.073319 TCCCCCACTTGGTTCCTCA 60.073 57.895 0.00 0.00 0.00 3.86
2120 2462 2.160853 GTCCCTCCCCCACTTGGTT 61.161 63.158 0.00 0.00 0.00 3.67
2121 2463 2.531942 GTCCCTCCCCCACTTGGT 60.532 66.667 0.00 0.00 0.00 3.67
2122 2464 3.717294 CGTCCCTCCCCCACTTGG 61.717 72.222 0.00 0.00 0.00 3.61
2123 2465 2.606519 TCGTCCCTCCCCCACTTG 60.607 66.667 0.00 0.00 0.00 3.16
2124 2466 2.284699 CTCGTCCCTCCCCCACTT 60.285 66.667 0.00 0.00 0.00 3.16
2139 2481 2.743928 CCACGAGCACCTTGCCTC 60.744 66.667 0.00 0.00 46.52 4.70
2154 2496 1.203376 TGACCTCACCCTTATCCACCA 60.203 52.381 0.00 0.00 0.00 4.17
2156 2498 2.693267 GTGACCTCACCCTTATCCAC 57.307 55.000 0.00 0.00 40.85 4.02
2195 2537 1.681666 CACCATGACCTCCTGTGCT 59.318 57.895 0.00 0.00 0.00 4.40
2200 2542 0.911525 CCTCACCACCATGACCTCCT 60.912 60.000 0.00 0.00 0.00 3.69
2252 2595 1.991264 GTAAACGCTCCTTTCCGTCTC 59.009 52.381 0.00 0.00 36.56 3.36
2266 2609 1.504359 TTGAGTGGGAAGCGTAAACG 58.496 50.000 0.00 0.00 43.27 3.60
2271 2614 2.932663 CACATTGAGTGGGAAGCGT 58.067 52.632 0.00 0.00 44.69 5.07
2324 2667 5.633830 ATCTGATACACCACTTTGCAAAG 57.366 39.130 32.53 32.53 41.73 2.77
2333 2676 4.122776 CCTGCTGTTATCTGATACACCAC 58.877 47.826 0.00 0.00 0.00 4.16
2334 2677 4.030216 TCCTGCTGTTATCTGATACACCA 58.970 43.478 0.00 0.00 0.00 4.17
2336 2679 4.920340 CGATCCTGCTGTTATCTGATACAC 59.080 45.833 0.00 0.86 0.00 2.90
2366 2709 1.299850 GTGTTTGTTTCGGCTGGGC 60.300 57.895 0.00 0.00 0.00 5.36
2368 2711 0.030638 CAGGTGTTTGTTTCGGCTGG 59.969 55.000 0.00 0.00 0.00 4.85
2369 2712 0.738389 ACAGGTGTTTGTTTCGGCTG 59.262 50.000 0.00 0.00 0.00 4.85
2389 2732 1.308998 CATTGCCTCCCCAATACGTC 58.691 55.000 0.00 0.00 33.86 4.34
2392 2735 9.561069 CTATATATTACATTGCCTCCCCAATAC 57.439 37.037 0.00 0.00 33.86 1.89
2397 2740 9.381038 TCTATCTATATATTACATTGCCTCCCC 57.619 37.037 0.00 0.00 0.00 4.81
2413 2756 7.868415 GGTTCGTGACTTTTGCTCTATCTATAT 59.132 37.037 0.00 0.00 0.00 0.86
2415 2758 6.043411 GGTTCGTGACTTTTGCTCTATCTAT 58.957 40.000 0.00 0.00 0.00 1.98
2420 2763 3.462483 TGGTTCGTGACTTTTGCTCTA 57.538 42.857 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.