Multiple sequence alignment - TraesCS2B01G520200

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 TraesCS2B01G520200 chr2B 100.000 1664 0 0 670 2333 714784873 714786536 0.000000e+00 3073
1 TraesCS2B01G520200 chr2B 100.000 382 0 0 1 382 714784204 714784585 0.000000e+00 706
2 TraesCS2B01G520200 chr2A 87.662 1694 115 49 670 2333 724522653 724524282 0.000000e+00 1884
3 TraesCS2B01G520200 chr2A 90.909 231 10 5 156 382 724522411 724522634 1.360000e-77 300
4 TraesCS2B01G520200 chr2A 91.071 112 3 1 11 115 724522289 724522400 6.720000e-31 145
5 TraesCS2B01G520200 chr2D 84.885 999 75 33 1339 2328 590155969 590156900 0.000000e+00 939
6 TraesCS2B01G520200 chr2D 90.801 674 44 9 676 1346 590155268 590155926 0.000000e+00 885
7 TraesCS2B01G520200 chr7A 90.462 346 32 1 987 1331 556102889 556102544 2.730000e-124 455


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 TraesCS2B01G520200 chr2B 714784204 714786536 2332 False 1889.500000 3073 100.000000 1 2333 2 chr2B.!!$F1 2332
1 TraesCS2B01G520200 chr2A 724522289 724524282 1993 False 776.333333 1884 89.880667 11 2333 3 chr2A.!!$F1 2322
2 TraesCS2B01G520200 chr2D 590155268 590156900 1632 False 912.000000 939 87.843000 676 2328 2 chr2D.!!$F1 1652

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
981 999 2.727123 TGCTTCTGGTTTTCACAGGA 57.273 45.0 0.0 0.0 36.62 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2108 2198 0.387929 TGACAGGGACTTGTGACGAC 59.612 55.0 0.0 0.0 34.6 4.34 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
47 55 8.362639 GTGCTTTTATGATGGAATATGATTGGT 58.637 33.333 0.00 0.00 0.00 3.67
55 63 6.944290 TGATGGAATATGATTGGTGAGATTCC 59.056 38.462 4.80 4.80 41.73 3.01
115 123 5.337491 GGAATTTGCAGTCATACCCATTGTT 60.337 40.000 0.00 0.00 0.00 2.83
116 124 4.517952 TTTGCAGTCATACCCATTGTTG 57.482 40.909 0.00 0.00 0.00 3.33
120 128 5.995446 TGCAGTCATACCCATTGTTGTATA 58.005 37.500 0.00 0.00 0.00 1.47
121 129 6.054941 TGCAGTCATACCCATTGTTGTATAG 58.945 40.000 0.00 0.00 0.00 1.31
122 130 6.126911 TGCAGTCATACCCATTGTTGTATAGA 60.127 38.462 0.00 0.00 0.00 1.98
124 132 7.445402 GCAGTCATACCCATTGTTGTATAGATT 59.555 37.037 0.00 0.00 0.00 2.40
125 133 8.993121 CAGTCATACCCATTGTTGTATAGATTC 58.007 37.037 0.00 0.00 0.00 2.52
126 134 8.938883 AGTCATACCCATTGTTGTATAGATTCT 58.061 33.333 0.00 0.00 0.00 2.40
152 160 8.862325 AAAAACATAGTATCTCACCAATCACA 57.138 30.769 0.00 0.00 0.00 3.58
153 161 8.862325 AAAACATAGTATCTCACCAATCACAA 57.138 30.769 0.00 0.00 0.00 3.33
154 162 8.862325 AAACATAGTATCTCACCAATCACAAA 57.138 30.769 0.00 0.00 0.00 2.83
188 196 6.845302 TGATGACAGTAAATGAAGACATTGC 58.155 36.000 0.00 0.00 44.67 3.56
192 200 4.997395 ACAGTAAATGAAGACATTGCGACT 59.003 37.500 0.00 0.00 44.67 4.18
211 220 5.394115 GCGACTATGGGGTTGAATTTGAAAT 60.394 40.000 0.00 0.00 0.00 2.17
238 247 9.897744 CATACTGTATTTTTGTCAATGTTGAGT 57.102 29.630 0.00 0.00 37.98 3.41
274 286 7.803279 ATACTTCCTTTTCTTTATAAGGGCG 57.197 36.000 0.00 0.00 41.05 6.13
299 311 6.358974 TCTGTTCTTGTCACCTTGATGATA 57.641 37.500 0.00 0.00 0.00 2.15
301 313 7.397221 TCTGTTCTTGTCACCTTGATGATATT 58.603 34.615 0.00 0.00 0.00 1.28
369 381 9.686683 AGGAATGTTATATTGTTTGCTTCTACT 57.313 29.630 0.00 0.00 0.00 2.57
375 387 8.836413 GTTATATTGTTTGCTTCTACTATGCCA 58.164 33.333 0.00 0.00 0.00 4.92
720 732 8.386606 GTTCAACAAATAAAGTGCATCAACAAA 58.613 29.630 0.00 0.00 0.00 2.83
777 789 8.644374 TCCAGTAACCTAATTAACAATTTGCT 57.356 30.769 0.00 0.00 32.38 3.91
796 808 3.071312 TGCTTTTTGTTGGGATGCTTCAT 59.929 39.130 1.64 0.00 0.00 2.57
881 898 3.667960 GCTGCAGTCAACTGAATTAACCG 60.668 47.826 16.64 0.00 46.59 4.44
882 899 3.472652 TGCAGTCAACTGAATTAACCGT 58.527 40.909 14.20 0.00 46.59 4.83
905 922 5.091261 TCTGTTTCTCTTAGGGATGCTTC 57.909 43.478 0.00 0.00 0.00 3.86
913 931 4.934356 TCTTAGGGATGCTTCACCATTTT 58.066 39.130 0.00 0.00 0.00 1.82
930 948 7.652909 TCACCATTTTATTTCTTTTGCTGACAG 59.347 33.333 0.00 0.00 0.00 3.51
932 950 6.647895 CCATTTTATTTCTTTTGCTGACAGCT 59.352 34.615 26.94 7.82 42.97 4.24
939 957 6.639632 TTCTTTTGCTGACAGCTTAAGATT 57.360 33.333 28.95 0.00 42.97 2.40
953 971 8.703743 ACAGCTTAAGATTGACTAGATTCTGAT 58.296 33.333 6.67 0.00 0.00 2.90
961 979 5.859205 TGACTAGATTCTGATAAGCAGCA 57.141 39.130 0.00 0.00 44.52 4.41
981 999 2.727123 TGCTTCTGGTTTTCACAGGA 57.273 45.000 0.00 0.00 36.62 3.86
1348 1417 1.594862 GATAGACGAACATGCTGGCAC 59.405 52.381 0.00 0.00 0.00 5.01
1349 1418 0.391130 TAGACGAACATGCTGGCACC 60.391 55.000 0.00 0.00 0.00 5.01
1350 1419 1.965930 GACGAACATGCTGGCACCA 60.966 57.895 0.00 0.00 0.00 4.17
1351 1420 1.303561 ACGAACATGCTGGCACCAT 60.304 52.632 0.00 0.00 0.00 3.55
1352 1421 0.895100 ACGAACATGCTGGCACCATT 60.895 50.000 0.00 0.00 0.00 3.16
1354 1423 1.717194 GAACATGCTGGCACCATTTG 58.283 50.000 0.00 0.00 0.00 2.32
1355 1424 1.273048 GAACATGCTGGCACCATTTGA 59.727 47.619 0.00 0.00 0.00 2.69
1356 1425 1.563924 ACATGCTGGCACCATTTGAT 58.436 45.000 0.00 0.00 0.00 2.57
1357 1426 1.206132 ACATGCTGGCACCATTTGATG 59.794 47.619 0.00 0.00 0.00 3.07
1373 1442 4.689612 TTGATGGATACCAAGAGTAGGC 57.310 45.455 0.00 0.00 36.95 3.93
1375 1444 3.643320 TGATGGATACCAAGAGTAGGCTG 59.357 47.826 0.00 0.00 36.95 4.85
1380 1449 2.187946 CAAGAGTAGGCTGGCCGG 59.812 66.667 7.41 7.41 41.95 6.13
1396 1465 2.434134 CGGACGAACAGCGCTGTAC 61.434 63.158 40.76 28.83 44.13 2.90
1398 1467 1.344942 GGACGAACAGCGCTGTACTG 61.345 60.000 40.76 32.10 44.13 2.74
1404 1473 2.010145 ACAGCGCTGTACTGTATTGG 57.990 50.000 40.15 11.49 46.32 3.16
1405 1474 1.275291 ACAGCGCTGTACTGTATTGGT 59.725 47.619 40.15 12.28 46.32 3.67
1406 1475 1.660607 CAGCGCTGTACTGTATTGGTG 59.339 52.381 29.24 0.00 0.00 4.17
1407 1476 1.275291 AGCGCTGTACTGTATTGGTGT 59.725 47.619 10.39 0.00 0.00 4.16
1408 1477 2.073816 GCGCTGTACTGTATTGGTGTT 58.926 47.619 0.00 0.00 0.00 3.32
1409 1478 3.056393 AGCGCTGTACTGTATTGGTGTTA 60.056 43.478 10.39 0.00 0.00 2.41
1428 1497 9.303116 TGGTGTTATTATGGTTTTGTACTGATT 57.697 29.630 0.00 0.00 0.00 2.57
1439 1508 7.888021 TGGTTTTGTACTGATTGGAGAATACAT 59.112 33.333 0.00 0.00 0.00 2.29
1445 1514 4.103785 ACTGATTGGAGAATACATCCCTGG 59.896 45.833 0.00 0.00 35.86 4.45
1446 1515 4.047166 TGATTGGAGAATACATCCCTGGT 58.953 43.478 0.00 0.00 35.86 4.00
1447 1516 3.931907 TTGGAGAATACATCCCTGGTG 57.068 47.619 0.00 0.00 35.86 4.17
1448 1517 3.129262 TGGAGAATACATCCCTGGTGA 57.871 47.619 0.00 0.00 35.86 4.02
1449 1518 3.668821 TGGAGAATACATCCCTGGTGAT 58.331 45.455 0.00 0.00 35.86 3.06
1457 1529 4.428294 ACATCCCTGGTGATTATCTGTG 57.572 45.455 0.00 0.00 0.00 3.66
1465 1537 5.468072 CCTGGTGATTATCTGTGATAACTGC 59.532 44.000 2.60 0.00 0.00 4.40
1468 1540 6.763135 TGGTGATTATCTGTGATAACTGCTTC 59.237 38.462 2.60 0.00 0.00 3.86
1482 1554 4.833478 ACTGCTTCTGATGTATGGTCTT 57.167 40.909 0.00 0.00 0.00 3.01
1483 1555 5.939764 ACTGCTTCTGATGTATGGTCTTA 57.060 39.130 0.00 0.00 0.00 2.10
1484 1556 6.299805 ACTGCTTCTGATGTATGGTCTTAA 57.700 37.500 0.00 0.00 0.00 1.85
1485 1557 6.109359 ACTGCTTCTGATGTATGGTCTTAAC 58.891 40.000 0.00 0.00 0.00 2.01
1486 1558 6.070538 ACTGCTTCTGATGTATGGTCTTAACT 60.071 38.462 0.00 0.00 0.00 2.24
1487 1559 6.341316 TGCTTCTGATGTATGGTCTTAACTC 58.659 40.000 0.00 0.00 0.00 3.01
1488 1560 6.155221 TGCTTCTGATGTATGGTCTTAACTCT 59.845 38.462 0.00 0.00 0.00 3.24
1489 1561 7.044798 GCTTCTGATGTATGGTCTTAACTCTT 58.955 38.462 0.00 0.00 0.00 2.85
1504 1576 9.165035 GTCTTAACTCTTAAGTGAGTCTAGCTA 57.835 37.037 11.37 0.00 45.49 3.32
1517 1589 4.893424 GTCTAGCTAGACTCTCAACTGG 57.107 50.000 36.20 4.24 46.99 4.00
1529 1601 0.398696 TCAACTGGTTATGCGGTGGT 59.601 50.000 0.00 0.00 0.00 4.16
1530 1602 0.521291 CAACTGGTTATGCGGTGGTG 59.479 55.000 0.00 0.00 0.00 4.17
1531 1603 0.398696 AACTGGTTATGCGGTGGTGA 59.601 50.000 0.00 0.00 0.00 4.02
1572 1644 4.648762 TGTTGTTGACTTGGAATGTGGATT 59.351 37.500 0.00 0.00 0.00 3.01
1574 1646 3.005684 TGTTGACTTGGAATGTGGATTGC 59.994 43.478 0.00 0.00 0.00 3.56
1693 1765 1.079405 GCGCCCAGTAGTGTGCTTA 60.079 57.895 0.00 0.00 35.20 3.09
1701 1773 5.453339 GCCCAGTAGTGTGCTTATCATAGAA 60.453 44.000 0.00 0.00 0.00 2.10
1714 1786 6.463049 GCTTATCATAGAACCAGCTGGAAGTA 60.463 42.308 39.19 24.11 38.94 2.24
1715 1787 5.543507 ATCATAGAACCAGCTGGAAGTAG 57.456 43.478 39.19 21.75 38.94 2.57
1716 1788 4.353777 TCATAGAACCAGCTGGAAGTAGT 58.646 43.478 39.19 13.13 38.94 2.73
1717 1789 5.516044 TCATAGAACCAGCTGGAAGTAGTA 58.484 41.667 39.19 19.42 38.94 1.82
1718 1790 5.594725 TCATAGAACCAGCTGGAAGTAGTAG 59.405 44.000 39.19 19.54 38.94 2.57
1719 1791 2.498078 AGAACCAGCTGGAAGTAGTAGC 59.502 50.000 39.19 15.24 38.94 3.58
1720 1792 1.938585 ACCAGCTGGAAGTAGTAGCA 58.061 50.000 39.19 0.00 39.84 3.49
1736 1808 1.800805 AGCACTTTGATCAGTGTCCG 58.199 50.000 14.52 1.61 45.31 4.79
1795 1867 3.209410 CGCTTAGGCATTTCCAGAATCT 58.791 45.455 0.00 0.00 38.60 2.40
1799 1871 5.678107 GCTTAGGCATTTCCAGAATCTTGTG 60.678 44.000 0.00 0.00 38.54 3.33
1804 1876 1.428448 TTCCAGAATCTTGTGTCGCG 58.572 50.000 0.00 0.00 0.00 5.87
1832 1904 4.313282 CAGAACTCTGAAGATGCTTCACA 58.687 43.478 5.81 1.54 46.59 3.58
1937 2018 4.022935 AGCAAAGCATTCGAAAGTTGATGA 60.023 37.500 0.00 0.00 0.00 2.92
2096 2186 3.001634 ACTGTGCGCTTTTATCATCATCG 59.998 43.478 9.73 0.00 0.00 3.84
2098 2188 3.001228 TGTGCGCTTTTATCATCATCGTC 59.999 43.478 9.73 0.00 0.00 4.20
2099 2189 2.218530 TGCGCTTTTATCATCATCGTCG 59.781 45.455 9.73 0.00 0.00 5.12
2100 2190 2.218759 GCGCTTTTATCATCATCGTCGT 59.781 45.455 0.00 0.00 0.00 4.34
2102 2192 3.419275 CGCTTTTATCATCATCGTCGTCG 60.419 47.826 0.00 0.00 38.55 5.12
2103 2193 3.486108 GCTTTTATCATCATCGTCGTCGT 59.514 43.478 1.33 0.00 38.33 4.34
2104 2194 4.374112 GCTTTTATCATCATCGTCGTCGTC 60.374 45.833 1.33 0.00 38.33 4.20
2105 2195 2.572173 TATCATCATCGTCGTCGTCG 57.428 50.000 5.50 5.50 38.33 5.12
2106 2196 0.656259 ATCATCATCGTCGTCGTCGT 59.344 50.000 11.41 0.00 38.33 4.34
2107 2197 0.025898 TCATCATCGTCGTCGTCGTC 59.974 55.000 11.41 0.00 38.33 4.20
2108 2198 1.012562 ATCATCGTCGTCGTCGTCG 60.013 57.895 14.18 14.18 46.06 5.12
2109 2199 1.690283 ATCATCGTCGTCGTCGTCGT 61.690 55.000 18.44 6.36 45.27 4.34
2110 2200 1.922220 CATCGTCGTCGTCGTCGTC 60.922 63.158 18.44 5.52 45.27 4.20
2111 2201 3.397649 ATCGTCGTCGTCGTCGTCG 62.398 63.158 20.39 20.39 45.27 5.12
2112 2202 4.400776 CGTCGTCGTCGTCGTCGT 62.401 66.667 18.87 0.00 45.27 4.34
2113 2203 2.566765 GTCGTCGTCGTCGTCGTC 60.567 66.667 18.44 11.28 45.27 4.20
2114 2204 3.029735 TCGTCGTCGTCGTCGTCA 61.030 61.111 18.44 1.12 45.27 4.35
2117 2207 1.368019 GTCGTCGTCGTCGTCACAA 60.368 57.895 11.41 0.00 38.33 3.33
2171 2262 3.079578 GCCTCCTTAAAACGCTAACCTT 58.920 45.455 0.00 0.00 0.00 3.50
2180 2271 5.526010 AAAACGCTAACCTTCGACTAATG 57.474 39.130 0.00 0.00 0.00 1.90
2181 2272 2.537401 ACGCTAACCTTCGACTAATGC 58.463 47.619 0.00 0.00 0.00 3.56
2183 2274 2.537401 GCTAACCTTCGACTAATGCGT 58.463 47.619 0.00 0.00 0.00 5.24
2186 2277 4.142966 GCTAACCTTCGACTAATGCGTTTT 60.143 41.667 0.00 0.00 0.00 2.43
2192 2283 4.123276 TCGACTAATGCGTTTTTGTCAC 57.877 40.909 0.00 0.00 0.00 3.67
2193 2284 3.556365 TCGACTAATGCGTTTTTGTCACA 59.444 39.130 0.00 0.00 0.00 3.58
2194 2285 4.034163 TCGACTAATGCGTTTTTGTCACAA 59.966 37.500 0.00 0.00 0.00 3.33
2199 2290 5.942325 AATGCGTTTTTGTCACAAAGTAC 57.058 34.783 2.58 5.44 0.00 2.73
2200 2291 3.418094 TGCGTTTTTGTCACAAAGTACG 58.582 40.909 24.50 24.50 0.00 3.67
2201 2292 3.120269 TGCGTTTTTGTCACAAAGTACGT 60.120 39.130 26.95 0.00 0.00 3.57
2202 2293 4.092529 TGCGTTTTTGTCACAAAGTACGTA 59.907 37.500 26.95 23.36 0.00 3.57
2203 2294 4.663091 GCGTTTTTGTCACAAAGTACGTAG 59.337 41.667 26.95 11.36 0.00 3.51
2205 2296 6.507771 GCGTTTTTGTCACAAAGTACGTAGTA 60.508 38.462 26.95 2.63 45.11 1.82
2242 2333 4.217118 ACTTTGCTCAATCTGCTAACCAAG 59.783 41.667 0.00 0.00 0.00 3.61
2248 2339 6.127925 TGCTCAATCTGCTAACCAAGTTTATG 60.128 38.462 0.00 0.00 0.00 1.90
2258 2349 8.533657 TGCTAACCAAGTTTATGCTACTAGTAA 58.466 33.333 3.76 0.00 0.00 2.24
2259 2350 9.374838 GCTAACCAAGTTTATGCTACTAGTAAA 57.625 33.333 3.76 0.00 0.00 2.01
2309 2409 4.858433 TTACGGATCGTGGCGGCG 62.858 66.667 0.51 0.51 41.39 6.46
2332 2432 6.755380 CGTGATTACGTATTTGCCCTTAGGG 61.755 48.000 14.11 14.11 44.81 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.336433 GCACAAAGACATGTAGGCATATGT 59.664 41.667 0.00 1.70 39.01 2.29
2 3 4.577693 AGCACAAAGACATGTAGGCATATG 59.422 41.667 0.00 0.00 33.30 1.78
3 4 4.785301 AGCACAAAGACATGTAGGCATAT 58.215 39.130 0.00 0.00 33.30 1.78
4 5 4.220693 AGCACAAAGACATGTAGGCATA 57.779 40.909 0.00 0.00 33.30 3.14
5 6 3.077484 AGCACAAAGACATGTAGGCAT 57.923 42.857 0.00 0.00 35.32 4.40
6 7 2.566833 AGCACAAAGACATGTAGGCA 57.433 45.000 0.00 0.00 30.84 4.75
7 8 3.923017 AAAGCACAAAGACATGTAGGC 57.077 42.857 0.00 0.00 30.84 3.93
8 9 7.144722 TCATAAAAGCACAAAGACATGTAGG 57.855 36.000 0.00 0.00 30.84 3.18
9 10 7.699391 CCATCATAAAAGCACAAAGACATGTAG 59.301 37.037 0.00 0.00 30.84 2.74
126 134 9.952030 TGTGATTGGTGAGATACTATGTTTTTA 57.048 29.630 0.00 0.00 0.00 1.52
127 135 8.862325 TGTGATTGGTGAGATACTATGTTTTT 57.138 30.769 0.00 0.00 0.00 1.94
128 136 8.862325 TTGTGATTGGTGAGATACTATGTTTT 57.138 30.769 0.00 0.00 0.00 2.43
129 137 8.862325 TTTGTGATTGGTGAGATACTATGTTT 57.138 30.769 0.00 0.00 0.00 2.83
130 138 8.862325 TTTTGTGATTGGTGAGATACTATGTT 57.138 30.769 0.00 0.00 0.00 2.71
131 139 8.862325 TTTTTGTGATTGGTGAGATACTATGT 57.138 30.769 0.00 0.00 0.00 2.29
132 140 8.400947 CCTTTTTGTGATTGGTGAGATACTATG 58.599 37.037 0.00 0.00 0.00 2.23
133 141 7.557719 CCCTTTTTGTGATTGGTGAGATACTAT 59.442 37.037 0.00 0.00 0.00 2.12
134 142 6.884295 CCCTTTTTGTGATTGGTGAGATACTA 59.116 38.462 0.00 0.00 0.00 1.82
135 143 5.711976 CCCTTTTTGTGATTGGTGAGATACT 59.288 40.000 0.00 0.00 0.00 2.12
136 144 5.710099 TCCCTTTTTGTGATTGGTGAGATAC 59.290 40.000 0.00 0.00 0.00 2.24
137 145 5.710099 GTCCCTTTTTGTGATTGGTGAGATA 59.290 40.000 0.00 0.00 0.00 1.98
138 146 4.524328 GTCCCTTTTTGTGATTGGTGAGAT 59.476 41.667 0.00 0.00 0.00 2.75
139 147 3.888930 GTCCCTTTTTGTGATTGGTGAGA 59.111 43.478 0.00 0.00 0.00 3.27
140 148 3.005791 GGTCCCTTTTTGTGATTGGTGAG 59.994 47.826 0.00 0.00 0.00 3.51
141 149 2.962421 GGTCCCTTTTTGTGATTGGTGA 59.038 45.455 0.00 0.00 0.00 4.02
142 150 2.037121 GGGTCCCTTTTTGTGATTGGTG 59.963 50.000 0.00 0.00 0.00 4.17
143 151 2.090775 AGGGTCCCTTTTTGTGATTGGT 60.091 45.455 3.85 0.00 0.00 3.67
144 152 2.299867 CAGGGTCCCTTTTTGTGATTGG 59.700 50.000 8.08 0.00 0.00 3.16
145 153 3.230134 TCAGGGTCCCTTTTTGTGATTG 58.770 45.455 8.08 0.00 0.00 2.67
146 154 3.611025 TCAGGGTCCCTTTTTGTGATT 57.389 42.857 8.08 0.00 0.00 2.57
147 155 3.075882 TCATCAGGGTCCCTTTTTGTGAT 59.924 43.478 8.08 4.88 0.00 3.06
148 156 2.445145 TCATCAGGGTCCCTTTTTGTGA 59.555 45.455 8.08 2.22 0.00 3.58
149 157 2.558359 GTCATCAGGGTCCCTTTTTGTG 59.442 50.000 8.08 3.16 0.00 3.33
150 158 2.176798 TGTCATCAGGGTCCCTTTTTGT 59.823 45.455 8.08 0.00 0.00 2.83
151 159 2.821969 CTGTCATCAGGGTCCCTTTTTG 59.178 50.000 8.08 6.43 37.97 2.44
152 160 2.447047 ACTGTCATCAGGGTCCCTTTTT 59.553 45.455 8.08 0.00 45.14 1.94
153 161 2.065799 ACTGTCATCAGGGTCCCTTTT 58.934 47.619 8.08 0.00 45.14 2.27
154 162 1.747444 ACTGTCATCAGGGTCCCTTT 58.253 50.000 8.08 0.00 45.14 3.11
188 196 5.637006 TTTCAAATTCAACCCCATAGTCG 57.363 39.130 0.00 0.00 0.00 4.18
192 200 8.694540 CAGTATGATTTCAAATTCAACCCCATA 58.305 33.333 0.00 0.00 39.69 2.74
274 286 5.240891 TCATCAAGGTGACAAGAACAGATC 58.759 41.667 0.00 0.00 0.00 2.75
343 355 9.686683 AGTAGAAGCAAACAATATAACATTCCT 57.313 29.630 0.00 0.00 0.00 3.36
354 366 4.641989 CCTGGCATAGTAGAAGCAAACAAT 59.358 41.667 0.00 0.00 0.00 2.71
777 789 4.344679 AGTGATGAAGCATCCCAACAAAAA 59.655 37.500 5.08 0.00 39.87 1.94
796 808 7.094508 TGCACTCACAAAAGAAATAAAGTGA 57.905 32.000 0.00 0.00 35.95 3.41
881 898 4.837972 AGCATCCCTAAGAGAAACAGAAC 58.162 43.478 0.00 0.00 0.00 3.01
882 899 5.013079 TGAAGCATCCCTAAGAGAAACAGAA 59.987 40.000 0.00 0.00 0.00 3.02
905 922 7.569957 GCTGTCAGCAAAAGAAATAAAATGGTG 60.570 37.037 20.16 0.00 41.89 4.17
913 931 7.744087 TCTTAAGCTGTCAGCAAAAGAAATA 57.256 32.000 26.92 13.27 45.56 1.40
939 957 5.859205 TGCTGCTTATCAGAATCTAGTCA 57.141 39.130 0.00 0.00 45.72 3.41
959 977 2.608752 CCTGTGAAAACCAGAAGCATGC 60.609 50.000 10.51 10.51 31.38 4.06
961 979 3.228188 TCCTGTGAAAACCAGAAGCAT 57.772 42.857 0.00 0.00 31.38 3.79
966 984 3.869912 GCTGCTATCCTGTGAAAACCAGA 60.870 47.826 0.00 0.00 31.38 3.86
981 999 1.070445 GGCTGTCGGATGCTGCTAT 59.930 57.895 0.00 0.00 0.00 2.97
1155 1173 2.663196 CACCTCCCCTGGAACGAC 59.337 66.667 0.00 0.00 0.00 4.34
1349 1418 5.471456 GCCTACTCTTGGTATCCATCAAATG 59.529 44.000 0.00 0.00 31.53 2.32
1350 1419 5.370880 AGCCTACTCTTGGTATCCATCAAAT 59.629 40.000 0.00 0.00 31.53 2.32
1351 1420 4.721776 AGCCTACTCTTGGTATCCATCAAA 59.278 41.667 0.00 0.00 31.53 2.69
1352 1421 4.101585 CAGCCTACTCTTGGTATCCATCAA 59.898 45.833 0.00 0.00 31.53 2.57
1354 1423 3.007398 CCAGCCTACTCTTGGTATCCATC 59.993 52.174 0.00 0.00 31.53 3.51
1355 1424 2.975489 CCAGCCTACTCTTGGTATCCAT 59.025 50.000 0.00 0.00 31.53 3.41
1356 1425 2.398588 CCAGCCTACTCTTGGTATCCA 58.601 52.381 0.00 0.00 0.00 3.41
1357 1426 1.070914 GCCAGCCTACTCTTGGTATCC 59.929 57.143 0.00 0.00 0.00 2.59
1380 1449 0.663568 ACAGTACAGCGCTGTTCGTC 60.664 55.000 44.31 29.73 43.87 4.20
1400 1469 9.303116 TCAGTACAAAACCATAATAACACCAAT 57.697 29.630 0.00 0.00 0.00 3.16
1401 1470 8.693120 TCAGTACAAAACCATAATAACACCAA 57.307 30.769 0.00 0.00 0.00 3.67
1402 1471 8.871629 ATCAGTACAAAACCATAATAACACCA 57.128 30.769 0.00 0.00 0.00 4.17
1403 1472 9.567848 CAATCAGTACAAAACCATAATAACACC 57.432 33.333 0.00 0.00 0.00 4.16
1404 1473 9.567848 CCAATCAGTACAAAACCATAATAACAC 57.432 33.333 0.00 0.00 0.00 3.32
1405 1474 9.521841 TCCAATCAGTACAAAACCATAATAACA 57.478 29.630 0.00 0.00 0.00 2.41
1407 1476 9.967451 TCTCCAATCAGTACAAAACCATAATAA 57.033 29.630 0.00 0.00 0.00 1.40
1408 1477 9.967451 TTCTCCAATCAGTACAAAACCATAATA 57.033 29.630 0.00 0.00 0.00 0.98
1409 1478 8.877864 TTCTCCAATCAGTACAAAACCATAAT 57.122 30.769 0.00 0.00 0.00 1.28
1419 1488 5.905331 AGGGATGTATTCTCCAATCAGTACA 59.095 40.000 0.00 0.00 34.24 2.90
1428 1497 3.129262 TCACCAGGGATGTATTCTCCA 57.871 47.619 0.00 0.00 34.24 3.86
1439 1508 5.905331 AGTTATCACAGATAATCACCAGGGA 59.095 40.000 3.10 0.00 0.00 4.20
1445 1514 7.708322 TCAGAAGCAGTTATCACAGATAATCAC 59.292 37.037 3.10 0.00 0.00 3.06
1446 1515 7.785033 TCAGAAGCAGTTATCACAGATAATCA 58.215 34.615 3.10 0.00 0.00 2.57
1447 1516 8.710551 CATCAGAAGCAGTTATCACAGATAATC 58.289 37.037 3.10 0.00 0.00 1.75
1448 1517 8.209584 ACATCAGAAGCAGTTATCACAGATAAT 58.790 33.333 3.10 0.00 0.00 1.28
1449 1518 7.559486 ACATCAGAAGCAGTTATCACAGATAA 58.441 34.615 0.00 0.00 0.00 1.75
1457 1529 6.520272 AGACCATACATCAGAAGCAGTTATC 58.480 40.000 0.00 0.00 0.00 1.75
1468 1540 9.307121 CACTTAAGAGTTAAGACCATACATCAG 57.693 37.037 10.09 0.00 44.19 2.90
1504 1576 2.093973 CCGCATAACCAGTTGAGAGTCT 60.094 50.000 0.00 0.00 0.00 3.24
1517 1589 1.194547 CGCATATCACCACCGCATAAC 59.805 52.381 0.00 0.00 0.00 1.89
1529 1601 0.108377 AACAGTCACGGCGCATATCA 60.108 50.000 10.83 0.00 0.00 2.15
1530 1602 1.006832 AAACAGTCACGGCGCATATC 58.993 50.000 10.83 0.00 0.00 1.63
1531 1603 0.726827 CAAACAGTCACGGCGCATAT 59.273 50.000 10.83 0.00 0.00 1.78
1572 1644 2.268920 GGGAAGCCAGTCATCGCA 59.731 61.111 0.00 0.00 0.00 5.10
1574 1646 1.811266 CACGGGAAGCCAGTCATCG 60.811 63.158 0.00 0.00 27.46 3.84
1600 1672 0.594796 CTTGCAACGGCCAAGACAAC 60.595 55.000 2.24 0.00 40.13 3.32
1681 1753 6.684111 GCTGGTTCTATGATAAGCACACTACT 60.684 42.308 0.00 0.00 31.53 2.57
1682 1754 5.463724 GCTGGTTCTATGATAAGCACACTAC 59.536 44.000 0.00 0.00 31.53 2.73
1693 1765 4.965532 ACTACTTCCAGCTGGTTCTATGAT 59.034 41.667 31.58 12.33 36.34 2.45
1701 1773 1.550976 GTGCTACTACTTCCAGCTGGT 59.449 52.381 31.58 16.00 36.26 4.00
1720 1792 1.971357 AGACCGGACACTGATCAAAGT 59.029 47.619 9.46 0.00 0.00 2.66
1736 1808 3.050275 GGCTCAACCACGCAGACC 61.050 66.667 0.00 0.00 38.86 3.85
1769 1841 0.945099 GGAAATGCCTAAGCGCTACC 59.055 55.000 12.05 0.00 44.31 3.18
1795 1867 0.812014 TTCTGAAAGCCGCGACACAA 60.812 50.000 8.23 0.00 0.00 3.33
1799 1871 0.667792 AGAGTTCTGAAAGCCGCGAC 60.668 55.000 8.23 0.00 0.00 5.19
1852 1932 3.551846 TCCACCTGAAGAAACCAGAAAC 58.448 45.455 0.00 0.00 33.65 2.78
1853 1933 3.435026 CCTCCACCTGAAGAAACCAGAAA 60.435 47.826 0.00 0.00 33.65 2.52
1854 1934 2.106511 CCTCCACCTGAAGAAACCAGAA 59.893 50.000 0.00 0.00 33.65 3.02
1855 1935 1.699634 CCTCCACCTGAAGAAACCAGA 59.300 52.381 0.00 0.00 33.65 3.86
1856 1936 1.421646 ACCTCCACCTGAAGAAACCAG 59.578 52.381 0.00 0.00 0.00 4.00
1857 1937 1.518367 ACCTCCACCTGAAGAAACCA 58.482 50.000 0.00 0.00 0.00 3.67
1858 1938 2.658807 AACCTCCACCTGAAGAAACC 57.341 50.000 0.00 0.00 0.00 3.27
2017 2104 3.565482 ACTGTATTTTCAGTGTGCCTGTG 59.435 43.478 0.00 0.00 45.40 3.66
2018 2105 3.820557 ACTGTATTTTCAGTGTGCCTGT 58.179 40.909 0.00 0.00 45.40 4.00
2019 2106 5.237815 TCTACTGTATTTTCAGTGTGCCTG 58.762 41.667 9.21 0.00 46.36 4.85
2020 2107 5.482908 CTCTACTGTATTTTCAGTGTGCCT 58.517 41.667 9.21 0.00 46.36 4.75
2040 2127 1.524002 CCATCATCACGGTGGCTCT 59.476 57.895 8.50 0.00 0.00 4.09
2041 2128 4.131376 CCATCATCACGGTGGCTC 57.869 61.111 8.50 0.00 0.00 4.70
2099 2189 1.319010 CTTGTGACGACGACGACGAC 61.319 60.000 25.15 19.21 42.66 4.34
2100 2190 1.083209 CTTGTGACGACGACGACGA 60.083 57.895 25.15 1.77 42.66 4.20
2102 2192 0.995731 GGACTTGTGACGACGACGAC 60.996 60.000 15.32 8.68 42.66 4.34
2103 2193 1.280746 GGACTTGTGACGACGACGA 59.719 57.895 15.32 0.00 42.66 4.20
2104 2194 1.728426 GGGACTTGTGACGACGACG 60.728 63.158 5.58 5.58 45.75 5.12
2105 2195 0.663568 CAGGGACTTGTGACGACGAC 60.664 60.000 0.00 0.00 34.60 4.34
2106 2196 1.105167 ACAGGGACTTGTGACGACGA 61.105 55.000 0.00 0.00 34.60 4.20
2107 2197 0.663568 GACAGGGACTTGTGACGACG 60.664 60.000 0.00 0.00 34.60 5.12
2108 2198 0.387929 TGACAGGGACTTGTGACGAC 59.612 55.000 0.00 0.00 34.60 4.34
2109 2199 1.068588 CTTGACAGGGACTTGTGACGA 59.931 52.381 0.00 0.00 34.60 4.20
2110 2200 1.502231 CTTGACAGGGACTTGTGACG 58.498 55.000 0.00 0.00 34.60 4.35
2111 2201 1.416401 TCCTTGACAGGGACTTGTGAC 59.584 52.381 1.35 0.00 41.25 3.67
2112 2202 1.694150 CTCCTTGACAGGGACTTGTGA 59.306 52.381 1.35 0.00 41.25 3.58
2113 2203 1.271054 CCTCCTTGACAGGGACTTGTG 60.271 57.143 1.35 0.00 41.25 3.33
2114 2204 1.059913 CCTCCTTGACAGGGACTTGT 58.940 55.000 1.35 0.00 41.25 3.16
2117 2207 0.907230 GCTCCTCCTTGACAGGGACT 60.907 60.000 1.35 0.00 41.25 3.85
2136 2227 1.668101 GGAGGCGTACTGGACAGGAG 61.668 65.000 4.14 0.00 0.00 3.69
2171 2262 3.556365 TGTGACAAAAACGCATTAGTCGA 59.444 39.130 0.00 0.00 32.01 4.20
2180 2271 3.419004 ACGTACTTTGTGACAAAAACGC 58.581 40.909 29.55 14.44 32.65 4.84
2181 2272 5.788467 ACTACGTACTTTGTGACAAAAACG 58.212 37.500 28.70 28.70 35.38 3.60
2183 2274 9.019764 GTACTACTACGTACTTTGTGACAAAAA 57.980 33.333 12.26 0.60 37.39 1.94
2186 2277 6.362686 CGTACTACTACGTACTTTGTGACAA 58.637 40.000 0.00 0.00 40.83 3.18
2248 2339 7.386978 GGCACGTAATAGTTTTACTAGTAGC 57.613 40.000 2.23 0.00 32.71 3.58
2309 2409 4.514066 CCCTAAGGGCAAATACGTAATCAC 59.486 45.833 0.00 0.00 35.35 3.06
2310 2410 4.710324 CCCTAAGGGCAAATACGTAATCA 58.290 43.478 0.00 0.00 35.35 2.57


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

AutoCloner maintained by Alex Coulton.