Multiple sequence alignment - TraesCS5B01G002800

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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 TraesCS5B01G002800 chr5B 100.000 2363 0 0 1 2363 4060095 4062457 0.000000e+00 4364
1 TraesCS5B01G002800 chr5A 87.196 1437 95 41 2 1378 1202293 1200886 0.000000e+00 1552
2 TraesCS5B01G002800 chr5A 80.627 1275 157 36 988 2255 1114453 1113262 0.000000e+00 904
3 TraesCS5B01G002800 chr5D 86.485 1465 99 45 1 1399 2121868 2120437 0.000000e+00 1517
4 TraesCS5B01G002800 chr5D 85.290 775 80 20 1494 2260 2119397 2118649 0.000000e+00 769
5 TraesCS5B01G002800 chr5D 81.913 481 71 12 1414 1881 2120453 2119976 2.200000e-105 392
6 TraesCS5B01G002800 chr5D 86.220 254 33 2 1947 2199 2119765 2119513 8.320000e-70 274
7 TraesCS5B01G002800 chr5D 80.377 265 41 5 1053 1317 2118491 2118238 8.620000e-45 191
8 TraesCS5B01G002800 chr5D 89.524 105 10 1 2257 2361 2118616 2118513 5.300000e-27 132


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 TraesCS5B01G002800 chr5B 4060095 4062457 2362 False 4364.000000 4364 100.000000 1 2363 1 chr5B.!!$F1 2362
1 TraesCS5B01G002800 chr5A 1200886 1202293 1407 True 1552.000000 1552 87.196000 2 1378 1 chr5A.!!$R2 1376
2 TraesCS5B01G002800 chr5A 1113262 1114453 1191 True 904.000000 904 80.627000 988 2255 1 chr5A.!!$R1 1267
3 TraesCS5B01G002800 chr5D 2118238 2121868 3630 True 545.833333 1517 84.968167 1 2361 6 chr5D.!!$R1 2360

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
525 576 0.44231 CGAAATACTGCACCACGTGG 59.558 55.0 32.83 32.83 42.17 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1568 1680 0.03213 ATCGAGACAACACGTGCACT 59.968 50.0 17.22 9.69 0.0 4.4 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
168 169 2.507452 CGCCATCATGCTCCCAGA 59.493 61.111 0.00 0.00 0.00 3.86
227 234 3.664025 CTCACCGCCGATGAAGCCA 62.664 63.158 0.00 0.00 0.00 4.75
228 235 2.514592 CACCGCCGATGAAGCCAT 60.515 61.111 0.00 0.00 35.29 4.40
229 236 1.227527 CACCGCCGATGAAGCCATA 60.228 57.895 0.00 0.00 32.09 2.74
250 257 8.371699 GCCATAATAACTGTTCTTCTATCTCCT 58.628 37.037 0.00 0.00 0.00 3.69
265 272 0.615331 CTCCTGCCCTATGTGTGTGT 59.385 55.000 0.00 0.00 0.00 3.72
308 322 5.111989 TCTCGATCTTATCAAGTTGCAAGG 58.888 41.667 0.00 0.00 0.00 3.61
311 325 4.272018 CGATCTTATCAAGTTGCAAGGGAG 59.728 45.833 0.00 0.00 0.00 4.30
416 459 3.052081 GTGTCTGTCACGGAGGCT 58.948 61.111 0.00 0.00 37.31 4.58
417 460 1.367840 GTGTCTGTCACGGAGGCTT 59.632 57.895 0.00 0.00 37.31 4.35
435 486 4.382114 CGACGTGGCGCATGCAAA 62.382 61.111 19.57 0.00 45.35 3.68
498 549 0.941542 GTACGTGTCCTGCTTTGCAA 59.058 50.000 0.00 0.00 38.41 4.08
503 554 3.659092 TCCTGCTTTGCAACCGCG 61.659 61.111 13.40 0.00 42.97 6.46
517 568 0.668096 ACCGCGAACGAAATACTGCA 60.668 50.000 8.23 0.00 43.93 4.41
524 575 1.144969 ACGAAATACTGCACCACGTG 58.855 50.000 9.08 9.08 36.51 4.49
525 576 0.442310 CGAAATACTGCACCACGTGG 59.558 55.000 32.83 32.83 42.17 4.94
545 596 2.175184 CTTCTCGCAACCAACAGCCG 62.175 60.000 0.00 0.00 0.00 5.52
589 640 1.227263 CAACGAGCCCCCATCTACG 60.227 63.158 0.00 0.00 0.00 3.51
621 672 1.340211 ACACCTCTACTCGCTAGCACT 60.340 52.381 16.45 0.00 0.00 4.40
650 713 3.226347 GCACGACCAAAAGAATTTCTCG 58.774 45.455 0.00 0.99 37.28 4.04
693 772 2.893895 CGATCGTCCGTCCGAGGA 60.894 66.667 7.03 0.00 40.68 3.71
723 802 8.242085 TCATTATTTTATGTTTGTTGCTGCTG 57.758 30.769 0.00 0.00 0.00 4.41
724 803 4.996062 ATTTTATGTTTGTTGCTGCTGC 57.004 36.364 8.89 8.89 40.20 5.25
813 902 1.596934 GGCCATGACCGAGAAGACA 59.403 57.895 0.00 0.00 0.00 3.41
832 921 2.434884 AGCTGGTCCGTTCATGCG 60.435 61.111 0.00 0.00 0.00 4.73
834 923 3.027170 GCTGGTCCGTTCATGCGTG 62.027 63.158 0.00 0.00 0.00 5.34
905 994 1.136363 CGTCCGCGCATAAATATGGTG 60.136 52.381 8.75 0.60 34.32 4.17
964 1053 0.940126 CAGCAGAACCACACACACTC 59.060 55.000 0.00 0.00 0.00 3.51
965 1054 0.541392 AGCAGAACCACACACACTCA 59.459 50.000 0.00 0.00 0.00 3.41
966 1055 0.657840 GCAGAACCACACACACTCAC 59.342 55.000 0.00 0.00 0.00 3.51
967 1056 2.011548 GCAGAACCACACACACTCACA 61.012 52.381 0.00 0.00 0.00 3.58
973 1062 1.437625 CACACACACTCACACACACA 58.562 50.000 0.00 0.00 0.00 3.72
1063 1164 3.583276 CTAGTGGCCGTTGCGTGGA 62.583 63.158 0.00 0.00 38.85 4.02
1108 1209 2.678934 TGGAGAAGGGGTCCGACG 60.679 66.667 0.00 0.00 36.82 5.12
1145 1246 2.299013 TGCAGATCAAGTACGACAAGGT 59.701 45.455 0.00 0.00 0.00 3.50
1182 1283 0.036022 AGGTGGAGCTGAAGCAGAAC 59.964 55.000 4.90 0.00 45.16 3.01
1241 1342 0.532573 TGGGAGATCAAGAGCGACAC 59.467 55.000 0.00 0.00 0.00 3.67
1305 1406 2.094659 CCAGCGCAACGTCTTCGAT 61.095 57.895 11.47 0.00 40.62 3.59
1309 1410 1.614227 GCGCAACGTCTTCGATGACA 61.614 55.000 25.61 0.00 41.24 3.58
1364 1468 2.496817 GCCAGAGGCGTACTGAGG 59.503 66.667 10.02 0.00 39.62 3.86
1369 1473 1.478510 CAGAGGCGTACTGAGGTTCAT 59.521 52.381 0.00 0.00 37.54 2.57
1397 1502 2.922740 TGGTTCCGCCATTATCTACC 57.077 50.000 0.00 0.00 43.61 3.18
1398 1503 2.404559 TGGTTCCGCCATTATCTACCT 58.595 47.619 0.00 0.00 43.61 3.08
1399 1504 2.775384 TGGTTCCGCCATTATCTACCTT 59.225 45.455 0.00 0.00 43.61 3.50
1400 1505 3.201266 TGGTTCCGCCATTATCTACCTTT 59.799 43.478 0.00 0.00 43.61 3.11
1401 1506 3.813724 GGTTCCGCCATTATCTACCTTTC 59.186 47.826 0.00 0.00 37.17 2.62
1402 1507 4.444449 GGTTCCGCCATTATCTACCTTTCT 60.444 45.833 0.00 0.00 37.17 2.52
1403 1508 5.123936 GTTCCGCCATTATCTACCTTTCTT 58.876 41.667 0.00 0.00 0.00 2.52
1404 1509 5.367945 TCCGCCATTATCTACCTTTCTTT 57.632 39.130 0.00 0.00 0.00 2.52
1405 1510 5.751586 TCCGCCATTATCTACCTTTCTTTT 58.248 37.500 0.00 0.00 0.00 2.27
1406 1511 6.184789 TCCGCCATTATCTACCTTTCTTTTT 58.815 36.000 0.00 0.00 0.00 1.94
1407 1512 6.094881 TCCGCCATTATCTACCTTTCTTTTTG 59.905 38.462 0.00 0.00 0.00 2.44
1408 1513 6.094881 CCGCCATTATCTACCTTTCTTTTTGA 59.905 38.462 0.00 0.00 0.00 2.69
1409 1514 7.201821 CCGCCATTATCTACCTTTCTTTTTGAT 60.202 37.037 0.00 0.00 0.00 2.57
1410 1515 8.836413 CGCCATTATCTACCTTTCTTTTTGATA 58.164 33.333 0.00 0.00 0.00 2.15
1417 1522 7.758495 TCTACCTTTCTTTTTGATAAATCCGC 58.242 34.615 0.00 0.00 0.00 5.54
1418 1523 5.720202 ACCTTTCTTTTTGATAAATCCGCC 58.280 37.500 0.00 0.00 0.00 6.13
1419 1524 5.245075 ACCTTTCTTTTTGATAAATCCGCCA 59.755 36.000 0.00 0.00 0.00 5.69
1420 1525 6.070824 ACCTTTCTTTTTGATAAATCCGCCAT 60.071 34.615 0.00 0.00 0.00 4.40
1421 1526 6.818142 CCTTTCTTTTTGATAAATCCGCCATT 59.182 34.615 0.00 0.00 0.00 3.16
1422 1527 7.978975 CCTTTCTTTTTGATAAATCCGCCATTA 59.021 33.333 0.00 0.00 0.00 1.90
1423 1528 8.696410 TTTCTTTTTGATAAATCCGCCATTAC 57.304 30.769 0.00 0.00 0.00 1.89
1432 1537 2.493030 CGCCATTACCGACCTCGT 59.507 61.111 0.00 0.00 37.74 4.18
1435 1540 1.269413 CGCCATTACCGACCTCGTAAT 60.269 52.381 0.00 0.00 37.74 1.89
1439 1544 4.992951 GCCATTACCGACCTCGTAATTAAT 59.007 41.667 0.00 0.00 37.74 1.40
1441 1546 6.646240 GCCATTACCGACCTCGTAATTAATAA 59.354 38.462 0.00 0.00 37.74 1.40
1442 1547 7.332678 GCCATTACCGACCTCGTAATTAATAAT 59.667 37.037 0.00 0.00 37.74 1.28
1449 1554 6.563381 CGACCTCGTAATTAATAATGTGCCAC 60.563 42.308 0.00 0.00 34.11 5.01
1463 1568 2.872557 CCACAAGGCGCACAGATG 59.127 61.111 10.83 2.44 0.00 2.90
1501 1606 8.848182 AGTAGTATTACCTCCGTTCTGAATTAG 58.152 37.037 0.00 0.00 0.00 1.73
1510 1617 7.664318 ACCTCCGTTCTGAATTAGTTGTAATTT 59.336 33.333 0.00 0.00 38.70 1.82
1511 1618 8.512138 CCTCCGTTCTGAATTAGTTGTAATTTT 58.488 33.333 0.00 0.00 38.70 1.82
1515 1622 9.840427 CGTTCTGAATTAGTTGTAATTTTGGAT 57.160 29.630 0.00 0.00 38.70 3.41
1526 1638 7.393515 AGTTGTAATTTTGGATGAAGGGAGTAC 59.606 37.037 0.00 0.00 0.00 2.73
1542 1654 2.099427 GAGTACTAGGAGAAGCAACGGG 59.901 54.545 0.00 0.00 0.00 5.28
1568 1680 2.158957 GGTCGGATGTATTTGCTCTCCA 60.159 50.000 0.00 0.00 0.00 3.86
1575 1687 1.394917 GTATTTGCTCTCCAGTGCACG 59.605 52.381 12.01 6.45 43.16 5.34
1576 1688 0.250467 ATTTGCTCTCCAGTGCACGT 60.250 50.000 12.01 0.00 43.16 4.49
1592 1704 1.122501 CACGTGTTGTCTCGATTGACG 59.877 52.381 7.58 0.00 39.64 4.35
1594 1706 1.382419 CGTGTTGTCTCGATTGACGAC 59.618 52.381 15.12 15.12 46.45 4.34
1597 1709 3.049912 TGTTGTCTCGATTGACGACTTG 58.950 45.455 20.09 0.00 46.30 3.16
1602 1715 4.208460 TGTCTCGATTGACGACTTGTTTTC 59.792 41.667 11.49 0.00 46.45 2.29
1607 1720 6.210796 TCGATTGACGACTTGTTTTCTTCTA 58.789 36.000 0.00 0.00 46.45 2.10
1612 1725 8.827177 TTGACGACTTGTTTTCTTCTATGTAT 57.173 30.769 0.00 0.00 0.00 2.29
1763 2824 3.008049 GGATTATGCTCTACCCCACGATT 59.992 47.826 0.00 0.00 0.00 3.34
1768 2829 0.541863 CTCTACCCCACGATTGCCTT 59.458 55.000 0.00 0.00 0.00 4.35
1782 2843 2.972505 CCTTGGTGCGCGTTGACT 60.973 61.111 8.43 0.00 0.00 3.41
1801 2862 7.675962 TTGACTACAACCATATGTAACCAAC 57.324 36.000 1.24 0.00 35.48 3.77
1802 2863 6.770542 TGACTACAACCATATGTAACCAACA 58.229 36.000 1.24 0.00 43.86 3.33
1803 2864 7.225011 TGACTACAACCATATGTAACCAACAA 58.775 34.615 1.24 0.00 42.70 2.83
1832 2896 4.655963 AGAGAACACAACAGCCATATGTT 58.344 39.130 1.24 0.00 44.12 2.71
1851 2915 8.906867 CATATGTTGTCCCTTTGTCTTGATAAT 58.093 33.333 0.00 0.00 0.00 1.28
1863 2927 7.936496 TTGTCTTGATAATATGTCCTTGCAA 57.064 32.000 0.00 0.00 0.00 4.08
1868 2932 6.544038 TGATAATATGTCCTTGCAATGACG 57.456 37.500 24.01 3.68 34.18 4.35
1897 2963 2.087857 TTTTTGACGCCCCTCCCCAT 62.088 55.000 0.00 0.00 0.00 4.00
1943 3009 4.646945 TCTCAATCTCCCATGTAGTCACTC 59.353 45.833 0.00 0.00 0.00 3.51
1944 3010 4.352893 TCAATCTCCCATGTAGTCACTCA 58.647 43.478 0.00 0.00 0.00 3.41
1979 3045 1.134907 ACCAGTGTAAGGCGTATTCCG 60.135 52.381 0.00 0.00 40.40 4.30
2018 3084 2.589540 CCCATGAAGGCGCCAGTA 59.410 61.111 31.54 14.49 35.39 2.74
2026 3092 0.965363 AAGGCGCCAGTACCAAATGG 60.965 55.000 31.54 0.00 39.73 3.16
2036 3102 4.832741 CCAAATGGTTCCCCGACA 57.167 55.556 0.00 0.00 0.00 4.35
2056 3122 5.612351 GACACCTTTCTAATAGACCCATCC 58.388 45.833 0.00 0.00 0.00 3.51
2061 3127 7.561356 CACCTTTCTAATAGACCCATCCAAAAT 59.439 37.037 0.00 0.00 0.00 1.82
2066 3132 8.519799 TCTAATAGACCCATCCAAAATGTTTC 57.480 34.615 0.00 0.00 0.00 2.78
2067 3133 5.835113 ATAGACCCATCCAAAATGTTTCG 57.165 39.130 0.00 0.00 0.00 3.46
2074 3140 5.508825 CCCATCCAAAATGTTTCGAAAGTGA 60.509 40.000 11.66 0.00 0.00 3.41
2083 3150 8.472683 AAATGTTTCGAAAGTGAAATTTGTGA 57.527 26.923 11.66 0.00 39.80 3.58
2100 3167 0.669318 TGAGGTTGCTAGCGGTTTCG 60.669 55.000 10.77 0.00 39.81 3.46
2101 3168 0.389426 GAGGTTGCTAGCGGTTTCGA 60.389 55.000 10.77 0.00 39.00 3.71
2102 3169 0.389948 AGGTTGCTAGCGGTTTCGAG 60.390 55.000 10.77 0.00 39.00 4.04
2119 3186 6.203723 GGTTTCGAGGAAGGAGATATGATTTG 59.796 42.308 0.00 0.00 0.00 2.32
2145 3213 1.068474 GTTGTTCGACTCCACCATCG 58.932 55.000 0.00 0.00 39.72 3.84
2149 3217 2.494471 TGTTCGACTCCACCATCGTAAT 59.506 45.455 0.00 0.00 39.38 1.89
2153 3221 4.139038 TCGACTCCACCATCGTAATGATA 58.861 43.478 0.00 0.00 39.38 2.15
2158 3226 7.009179 ACTCCACCATCGTAATGATATCAAT 57.991 36.000 9.99 3.69 34.83 2.57
2182 3250 4.158949 GGCGAACCACCCTAAACAATAAAT 59.841 41.667 0.00 0.00 35.26 1.40
2212 3280 2.258755 CATGCATGCACACATTCACTG 58.741 47.619 25.37 10.28 32.09 3.66
2213 3281 1.320507 TGCATGCACACATTCACTGT 58.679 45.000 18.46 0.00 39.20 3.55
2222 3290 0.106769 ACATTCACTGTGGTGGTGCA 60.107 50.000 8.11 0.00 43.17 4.57
2228 3296 1.303074 CTGTGGTGGTGCAGCATCT 60.303 57.895 27.91 0.00 43.70 2.90
2250 3318 6.851318 TCTCAATGGGATTTTGCCTATATGA 58.149 36.000 0.00 0.00 0.00 2.15
2271 3375 7.818997 ATGAAGAGCACATCATCACATTAAT 57.181 32.000 0.00 0.00 38.39 1.40
2304 3408 4.806247 CCGACTTAGAATGATTGGTCTCAC 59.194 45.833 0.00 0.00 0.00 3.51
2342 3446 1.349026 AGTGACCCATCTTCACCAGTG 59.651 52.381 0.00 0.00 43.85 3.66
2344 3448 0.678048 GACCCATCTTCACCAGTGGC 60.678 60.000 9.78 0.00 0.00 5.01
2352 3456 0.179020 TTCACCAGTGGCTTCACCTG 60.179 55.000 9.78 0.00 42.13 4.00
2354 3458 1.770110 ACCAGTGGCTTCACCTGGA 60.770 57.895 9.78 0.00 42.13 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 1.883732 CACCCTGTCATCGTCGTCT 59.116 57.895 0.00 0.00 0.00 4.18
227 234 8.371699 GGCAGGAGATAGAAGAACAGTTATTAT 58.628 37.037 0.00 0.00 0.00 1.28
228 235 7.202011 GGGCAGGAGATAGAAGAACAGTTATTA 60.202 40.741 0.00 0.00 0.00 0.98
229 236 6.408662 GGGCAGGAGATAGAAGAACAGTTATT 60.409 42.308 0.00 0.00 0.00 1.40
250 257 1.670730 CGCACACACACATAGGGCA 60.671 57.895 0.00 0.00 0.00 5.36
282 289 7.439356 CCTTGCAACTTGATAAGATCGAGATAA 59.561 37.037 10.14 0.93 42.34 1.75
415 458 4.505217 GCATGCGCCACGTCGAAG 62.505 66.667 4.18 0.00 0.00 3.79
498 549 0.668096 TGCAGTATTTCGTTCGCGGT 60.668 50.000 6.13 0.00 41.70 5.68
503 554 1.796459 ACGTGGTGCAGTATTTCGTTC 59.204 47.619 0.00 0.00 0.00 3.95
572 623 3.090219 GCGTAGATGGGGGCTCGTT 62.090 63.158 0.00 0.00 0.00 3.85
621 672 0.978151 TTTTGGTCGTGCCCTAGCTA 59.022 50.000 0.00 0.00 40.80 3.32
624 675 2.178912 TTCTTTTGGTCGTGCCCTAG 57.821 50.000 0.00 0.00 36.04 3.02
625 676 2.871096 ATTCTTTTGGTCGTGCCCTA 57.129 45.000 0.00 0.00 36.04 3.53
629 692 3.226347 CGAGAAATTCTTTTGGTCGTGC 58.774 45.455 0.00 0.00 0.00 5.34
693 772 9.492973 AGCAACAAACATAAAATAATGAGCTTT 57.507 25.926 0.00 0.00 0.00 3.51
723 802 5.245531 TGCCTGCCTAATTATACACATAGC 58.754 41.667 0.00 0.00 0.00 2.97
724 803 6.183360 GCATGCCTGCCTAATTATACACATAG 60.183 42.308 6.36 0.00 42.88 2.23
803 892 0.172352 GACCAGCTCTGTCTTCTCGG 59.828 60.000 5.79 0.00 0.00 4.63
813 902 1.078848 GCATGAACGGACCAGCTCT 60.079 57.895 0.00 0.00 0.00 4.09
905 994 1.805428 GATGGGTTGTGTGGTGTGGC 61.805 60.000 0.00 0.00 0.00 5.01
919 1008 1.747355 GGATTGTGAGCTTGTGATGGG 59.253 52.381 0.00 0.00 0.00 4.00
964 1053 1.803555 TCTTGTGTGTGTGTGTGTGTG 59.196 47.619 0.00 0.00 0.00 3.82
965 1054 2.177394 TCTTGTGTGTGTGTGTGTGT 57.823 45.000 0.00 0.00 0.00 3.72
966 1055 3.126686 TGATTCTTGTGTGTGTGTGTGTG 59.873 43.478 0.00 0.00 0.00 3.82
967 1056 3.342719 TGATTCTTGTGTGTGTGTGTGT 58.657 40.909 0.00 0.00 0.00 3.72
973 1062 2.612212 GTCGGTTGATTCTTGTGTGTGT 59.388 45.455 0.00 0.00 0.00 3.72
1047 1148 4.988598 CTCCACGCAACGGCCACT 62.989 66.667 2.24 0.00 36.38 4.00
1084 1185 1.229529 ACCCCTTCTCCACCGTGAT 60.230 57.895 0.00 0.00 0.00 3.06
1145 1246 2.125552 CCTTCATGCTGTCGCCGA 60.126 61.111 0.00 0.00 34.43 5.54
1305 1406 1.275666 AATCTGTGGGGACGATGTCA 58.724 50.000 0.00 0.00 33.68 3.58
1309 1410 2.305927 ACTTGAAATCTGTGGGGACGAT 59.694 45.455 0.00 0.00 0.00 3.73
1393 1498 6.972901 GGCGGATTTATCAAAAAGAAAGGTAG 59.027 38.462 0.00 0.00 0.00 3.18
1394 1499 6.434652 TGGCGGATTTATCAAAAAGAAAGGTA 59.565 34.615 0.00 0.00 0.00 3.08
1395 1500 5.245075 TGGCGGATTTATCAAAAAGAAAGGT 59.755 36.000 0.00 0.00 0.00 3.50
1396 1501 5.719173 TGGCGGATTTATCAAAAAGAAAGG 58.281 37.500 0.00 0.00 0.00 3.11
1397 1502 7.832503 AATGGCGGATTTATCAAAAAGAAAG 57.167 32.000 0.00 0.00 0.00 2.62
1398 1503 7.762159 GGTAATGGCGGATTTATCAAAAAGAAA 59.238 33.333 0.00 0.00 0.00 2.52
1399 1504 7.262048 GGTAATGGCGGATTTATCAAAAAGAA 58.738 34.615 0.00 0.00 0.00 2.52
1400 1505 6.459024 CGGTAATGGCGGATTTATCAAAAAGA 60.459 38.462 0.00 0.00 0.00 2.52
1401 1506 5.685511 CGGTAATGGCGGATTTATCAAAAAG 59.314 40.000 0.00 0.00 0.00 2.27
1402 1507 5.357314 TCGGTAATGGCGGATTTATCAAAAA 59.643 36.000 0.00 0.00 0.00 1.94
1403 1508 4.882427 TCGGTAATGGCGGATTTATCAAAA 59.118 37.500 0.00 0.00 0.00 2.44
1404 1509 4.273969 GTCGGTAATGGCGGATTTATCAAA 59.726 41.667 0.00 0.00 0.00 2.69
1405 1510 3.810941 GTCGGTAATGGCGGATTTATCAA 59.189 43.478 0.00 0.00 0.00 2.57
1406 1511 3.395639 GTCGGTAATGGCGGATTTATCA 58.604 45.455 0.00 0.00 0.00 2.15
1407 1512 2.740447 GGTCGGTAATGGCGGATTTATC 59.260 50.000 0.00 0.00 0.00 1.75
1408 1513 2.370849 AGGTCGGTAATGGCGGATTTAT 59.629 45.455 0.00 0.00 0.00 1.40
1409 1514 1.764134 AGGTCGGTAATGGCGGATTTA 59.236 47.619 0.00 0.00 0.00 1.40
1410 1515 0.544697 AGGTCGGTAATGGCGGATTT 59.455 50.000 0.00 0.00 0.00 2.17
1411 1516 0.106149 GAGGTCGGTAATGGCGGATT 59.894 55.000 0.00 0.00 0.00 3.01
1412 1517 1.746517 GAGGTCGGTAATGGCGGAT 59.253 57.895 0.00 0.00 0.00 4.18
1413 1518 2.777972 CGAGGTCGGTAATGGCGGA 61.778 63.158 0.00 0.00 35.37 5.54
1414 1519 1.727511 TACGAGGTCGGTAATGGCGG 61.728 60.000 4.13 0.00 44.95 6.13
1415 1520 0.101040 TTACGAGGTCGGTAATGGCG 59.899 55.000 4.13 0.00 44.95 5.69
1416 1521 2.521105 ATTACGAGGTCGGTAATGGC 57.479 50.000 4.13 0.00 44.95 4.40
1417 1522 8.653338 CATTATTAATTACGAGGTCGGTAATGG 58.347 37.037 4.13 0.00 44.95 3.16
1418 1523 9.199982 ACATTATTAATTACGAGGTCGGTAATG 57.800 33.333 4.13 8.59 44.95 1.90
1419 1524 9.199982 CACATTATTAATTACGAGGTCGGTAAT 57.800 33.333 4.13 3.49 44.95 1.89
1420 1525 7.169645 GCACATTATTAATTACGAGGTCGGTAA 59.830 37.037 4.13 1.35 44.95 2.85
1421 1526 6.642131 GCACATTATTAATTACGAGGTCGGTA 59.358 38.462 4.13 0.00 44.95 4.02
1422 1527 5.464389 GCACATTATTAATTACGAGGTCGGT 59.536 40.000 4.13 0.00 44.95 4.69
1423 1528 5.107220 GGCACATTATTAATTACGAGGTCGG 60.107 44.000 4.13 0.00 44.95 4.79
1476 1581 8.628280 ACTAATTCAGAACGGAGGTAATACTAC 58.372 37.037 0.00 0.00 0.00 2.73
1479 1584 7.763071 ACAACTAATTCAGAACGGAGGTAATAC 59.237 37.037 0.00 0.00 0.00 1.89
1488 1593 8.293867 TCCAAAATTACAACTAATTCAGAACGG 58.706 33.333 0.00 0.00 32.29 4.44
1501 1606 6.590234 ACTCCCTTCATCCAAAATTACAAC 57.410 37.500 0.00 0.00 0.00 3.32
1510 1617 4.232122 TCTCCTAGTACTCCCTTCATCCAA 59.768 45.833 0.00 0.00 0.00 3.53
1511 1618 3.792114 TCTCCTAGTACTCCCTTCATCCA 59.208 47.826 0.00 0.00 0.00 3.41
1515 1622 3.011369 TGCTTCTCCTAGTACTCCCTTCA 59.989 47.826 0.00 0.00 0.00 3.02
1526 1638 1.519455 CGCCCGTTGCTTCTCCTAG 60.519 63.158 0.00 0.00 38.05 3.02
1542 1654 1.885850 AAATACATCCGACCGCCGC 60.886 57.895 0.00 0.00 36.84 6.53
1568 1680 0.032130 ATCGAGACAACACGTGCACT 59.968 50.000 17.22 9.69 0.00 4.40
1734 2795 4.080687 GGGTAGAGCATAATCCGACTACT 58.919 47.826 0.00 0.00 33.26 2.57
1740 2801 1.336887 CGTGGGGTAGAGCATAATCCG 60.337 57.143 0.00 0.00 0.00 4.18
1747 2808 1.220749 GCAATCGTGGGGTAGAGCA 59.779 57.895 0.00 0.00 0.00 4.26
1768 2829 1.227292 TTGTAGTCAACGCGCACCA 60.227 52.632 5.73 0.00 0.00 4.17
1819 2880 3.456380 AAGGGACAACATATGGCTGTT 57.544 42.857 7.80 0.00 39.91 3.16
1823 2884 3.356290 AGACAAAGGGACAACATATGGC 58.644 45.455 7.80 0.00 35.73 4.40
1832 2896 7.054124 GGACATATTATCAAGACAAAGGGACA 58.946 38.462 0.00 0.00 0.00 4.02
1851 2915 2.016604 GCCCGTCATTGCAAGGACATA 61.017 52.381 35.09 5.61 39.51 2.29
1852 2916 1.315257 GCCCGTCATTGCAAGGACAT 61.315 55.000 35.09 4.30 39.51 3.06
1863 2927 2.099405 CAAAAATAGGGTGCCCGTCAT 58.901 47.619 0.98 0.00 41.95 3.06
1868 2932 0.172578 GCGTCAAAAATAGGGTGCCC 59.827 55.000 0.00 0.00 0.00 5.36
1883 2947 0.541863 CATATATGGGGAGGGGCGTC 59.458 60.000 4.68 0.00 0.00 5.19
1897 2963 2.705658 CTCCTTGTGAGCACCCCATATA 59.294 50.000 0.00 0.00 33.47 0.86
1908 2974 3.784338 GAGATTGAGAGCTCCTTGTGAG 58.216 50.000 10.93 0.00 44.47 3.51
1925 2991 4.550669 TCATGAGTGACTACATGGGAGAT 58.449 43.478 18.27 0.00 42.53 2.75
1943 3009 5.618236 ACACTGGTCTCCATTCATATCATG 58.382 41.667 0.00 0.00 30.82 3.07
1944 3010 5.901413 ACACTGGTCTCCATTCATATCAT 57.099 39.130 0.00 0.00 30.82 2.45
1979 3045 2.433970 CCCCTTCTCTGATCTCCTTGTC 59.566 54.545 0.00 0.00 0.00 3.18
1982 3048 1.506025 GCCCCTTCTCTGATCTCCTT 58.494 55.000 0.00 0.00 0.00 3.36
2026 3092 2.845363 TTAGAAAGGTGTCGGGGAAC 57.155 50.000 0.00 0.00 0.00 3.62
2029 3095 3.181468 GGTCTATTAGAAAGGTGTCGGGG 60.181 52.174 0.00 0.00 0.00 5.73
2031 3097 3.449737 TGGGTCTATTAGAAAGGTGTCGG 59.550 47.826 0.00 0.00 0.00 4.79
2036 3102 6.652205 TTTGGATGGGTCTATTAGAAAGGT 57.348 37.500 0.00 0.00 0.00 3.50
2056 3122 8.987729 CACAAATTTCACTTTCGAAACATTTTG 58.012 29.630 6.47 12.54 37.85 2.44
2061 3127 6.033341 CCTCACAAATTTCACTTTCGAAACA 58.967 36.000 6.47 0.00 37.69 2.83
2066 3132 4.207019 GCAACCTCACAAATTTCACTTTCG 59.793 41.667 0.00 0.00 0.00 3.46
2067 3133 5.351458 AGCAACCTCACAAATTTCACTTTC 58.649 37.500 0.00 0.00 0.00 2.62
2074 3140 2.228822 CCGCTAGCAACCTCACAAATTT 59.771 45.455 16.45 0.00 0.00 1.82
2083 3150 0.389948 CTCGAAACCGCTAGCAACCT 60.390 55.000 16.45 0.00 0.00 3.50
2100 3167 5.280419 CCTCCCAAATCATATCTCCTTCCTC 60.280 48.000 0.00 0.00 0.00 3.71
2101 3168 4.600983 CCTCCCAAATCATATCTCCTTCCT 59.399 45.833 0.00 0.00 0.00 3.36
2102 3169 4.263683 CCCTCCCAAATCATATCTCCTTCC 60.264 50.000 0.00 0.00 0.00 3.46
2119 3186 1.295746 GAGTCGAACAACCCCTCCC 59.704 63.158 0.00 0.00 0.00 4.30
2145 3213 5.940192 TGGTTCGCCATTGATATCATTAC 57.060 39.130 6.17 0.00 43.56 1.89
2158 3226 0.183014 TTGTTTAGGGTGGTTCGCCA 59.817 50.000 0.00 0.00 46.87 5.69
2188 3256 2.036089 TGAATGTGTGCATGCATGTGTT 59.964 40.909 25.64 16.31 35.78 3.32
2212 3280 0.890542 TTGAGATGCTGCACCACCAC 60.891 55.000 3.57 0.00 0.00 4.16
2213 3281 0.038599 ATTGAGATGCTGCACCACCA 59.961 50.000 3.57 0.00 0.00 4.17
2222 3290 2.433239 GGCAAAATCCCATTGAGATGCT 59.567 45.455 0.00 0.00 33.00 3.79
2228 3296 7.296856 TCTTCATATAGGCAAAATCCCATTGA 58.703 34.615 0.00 0.00 0.00 2.57
2280 3384 4.709886 TGAGACCAATCATTCTAAGTCGGA 59.290 41.667 0.00 0.00 0.00 4.55
2281 3385 4.806247 GTGAGACCAATCATTCTAAGTCGG 59.194 45.833 0.00 0.00 0.00 4.79
2282 3386 5.410924 TGTGAGACCAATCATTCTAAGTCG 58.589 41.667 0.00 0.00 0.00 4.18
2283 3387 7.361286 GGTTTGTGAGACCAATCATTCTAAGTC 60.361 40.741 0.00 0.00 37.14 3.01
2297 3401 4.258543 TCGGATTAATGGTTTGTGAGACC 58.741 43.478 0.00 0.00 37.69 3.85
2304 3408 6.238648 GGGTCACTAATCGGATTAATGGTTTG 60.239 42.308 16.49 4.84 0.00 2.93
2342 3446 1.303643 CCCTTGTCCAGGTGAAGCC 60.304 63.158 0.00 0.00 42.02 4.35


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

AutoCloner maintained by Alex Coulton.