Multiple sequence alignment - TraesCS1B01G117100

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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 TraesCS1B01G117100 chr1B 100.000 2681 0 0 1 2681 137445312 137442632 0.000000e+00 4951
1 TraesCS1B01G117100 chr1D 93.870 1615 82 3 1069 2681 84715498 84713899 0.000000e+00 2418
2 TraesCS1B01G117100 chr1D 92.171 1073 35 14 20 1069 84722934 84721888 0.000000e+00 1471
3 TraesCS1B01G117100 chr1A 91.429 210 8 8 77 280 78953299 78953094 2.030000e-71 279


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 TraesCS1B01G117100 chr1B 137442632 137445312 2680 True 4951 4951 100.000 1 2681 1 chr1B.!!$R1 2680
1 TraesCS1B01G117100 chr1D 84713899 84715498 1599 True 2418 2418 93.870 1069 2681 1 chr1D.!!$R1 1612
2 TraesCS1B01G117100 chr1D 84721888 84722934 1046 True 1471 1471 92.171 20 1069 1 chr1D.!!$R2 1049

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
470 492 0.251787 ATCCTTTTGAGGTGCCACCC 60.252 55.0 11.06 2.62 39.75 4.61 F
1175 1197 0.109781 CACTGGGTGCGCAATAACAC 60.110 55.0 14.00 0.00 36.03 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1279 1301 0.169672 CCTGCAATTTCTCCACGCTG 59.830 55.000 0.0 0.0 0.00 5.18 R
2177 2201 1.528586 CGGTGACAAGAACTTCAGCAG 59.471 52.381 0.0 0.0 39.69 4.24 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
146 150 1.618343 CACAACTTGGGCCCTTTTAGG 59.382 52.381 25.70 10.79 34.30 2.69
195 199 1.540146 CCATTCACTGTGTGTCGTCCA 60.540 52.381 7.79 0.00 34.79 4.02
204 208 4.846551 TGTCGTCCAACACAGTGG 57.153 55.556 5.31 0.00 40.33 4.00
257 279 1.113517 GCCCATAGTAGCCCTCACGA 61.114 60.000 0.00 0.00 0.00 4.35
316 338 1.408127 CCTTCCCTCAACACACACACA 60.408 52.381 0.00 0.00 0.00 3.72
317 339 1.670811 CTTCCCTCAACACACACACAC 59.329 52.381 0.00 0.00 0.00 3.82
318 340 0.615850 TCCCTCAACACACACACACA 59.384 50.000 0.00 0.00 0.00 3.72
459 481 1.321805 TGGCGGCATGGATCCTTTTG 61.322 55.000 14.23 9.23 0.00 2.44
467 489 0.776810 TGGATCCTTTTGAGGTGCCA 59.223 50.000 14.23 5.40 33.39 4.92
468 490 1.177401 GGATCCTTTTGAGGTGCCAC 58.823 55.000 3.84 0.00 0.00 5.01
469 491 1.177401 GATCCTTTTGAGGTGCCACC 58.823 55.000 5.50 5.50 38.99 4.61
470 492 0.251787 ATCCTTTTGAGGTGCCACCC 60.252 55.000 11.06 2.62 39.75 4.61
516 538 0.811281 CGTTTTTCTCATGGGCCTCC 59.189 55.000 4.53 0.00 0.00 4.30
530 552 2.561037 CCTCCGCACAAAACCCACC 61.561 63.158 0.00 0.00 0.00 4.61
562 584 5.837829 TCCTGGGCCTTAATCACTTTATTT 58.162 37.500 4.53 0.00 0.00 1.40
563 585 6.975949 TCCTGGGCCTTAATCACTTTATTTA 58.024 36.000 4.53 0.00 0.00 1.40
564 586 7.591821 TCCTGGGCCTTAATCACTTTATTTAT 58.408 34.615 4.53 0.00 0.00 1.40
565 587 8.065007 TCCTGGGCCTTAATCACTTTATTTATT 58.935 33.333 4.53 0.00 0.00 1.40
580 602 3.408288 TTTATTAATTGCGGTCCGTGC 57.592 42.857 13.94 0.00 0.00 5.34
634 656 0.748005 CCATCAAGTAGGGGGCGTTG 60.748 60.000 0.00 0.00 0.00 4.10
643 665 1.222661 GGGGGCGTTGGGTTAGTAG 59.777 63.158 0.00 0.00 0.00 2.57
781 803 2.816689 TGGGACGATATACAGCAAACG 58.183 47.619 0.00 0.00 0.00 3.60
866 888 2.684943 TGATGGGATCTTACGGCCTTA 58.315 47.619 0.00 0.00 0.00 2.69
867 889 3.042682 TGATGGGATCTTACGGCCTTAA 58.957 45.455 0.00 0.16 0.00 1.85
883 905 4.646492 GGCCTTAAACCATCTCATCAACAT 59.354 41.667 0.00 0.00 0.00 2.71
926 948 3.554934 TGATTGCATGGTTGGATCCTAC 58.445 45.455 17.01 17.01 0.00 3.18
930 952 1.871080 CATGGTTGGATCCTACGCTC 58.129 55.000 18.34 7.10 0.00 5.03
960 982 9.547753 TTATATAATCTTCACTTGCAGAACTCC 57.452 33.333 0.00 0.00 0.00 3.85
972 994 0.613777 AGAACTCCCCGACATTCCAC 59.386 55.000 0.00 0.00 0.00 4.02
999 1021 0.395862 TGGACGAGGATCCTGAGACC 60.396 60.000 22.02 21.21 39.75 3.85
1007 1029 1.070445 GGATCCTGAGACCATGAGCAG 59.930 57.143 3.84 0.00 0.00 4.24
1014 1036 5.604231 TCCTGAGACCATGAGCAGTAATTAT 59.396 40.000 0.00 0.00 0.00 1.28
1026 1048 3.557595 GCAGTAATTATGACGCTCTGCTT 59.442 43.478 12.35 0.00 42.00 3.91
1037 1059 4.877823 TGACGCTCTGCTTGATGAAATTAT 59.122 37.500 0.00 0.00 0.00 1.28
1063 1085 3.209410 CATATCAGACAGCTTTGGGGTC 58.791 50.000 0.00 0.00 0.00 4.46
1066 1088 1.202806 TCAGACAGCTTTGGGGTCAAG 60.203 52.381 4.19 0.00 33.98 3.02
1067 1089 0.846693 AGACAGCTTTGGGGTCAAGT 59.153 50.000 4.19 0.00 33.98 3.16
1086 1108 1.747355 GTGAATGGACAGCAGAATGGG 59.253 52.381 0.00 0.00 35.86 4.00
1110 1132 5.975693 TGGTGGAAGGTATTTTAAGCTTG 57.024 39.130 9.86 0.00 37.32 4.01
1139 1161 4.506758 GGTGCAGGCAAATTCATTATTGT 58.493 39.130 0.00 0.00 0.00 2.71
1140 1162 4.330620 GGTGCAGGCAAATTCATTATTGTG 59.669 41.667 0.00 0.00 0.00 3.33
1141 1163 3.933955 TGCAGGCAAATTCATTATTGTGC 59.066 39.130 0.00 0.00 33.39 4.57
1175 1197 0.109781 CACTGGGTGCGCAATAACAC 60.110 55.000 14.00 0.00 36.03 3.32
1188 1210 5.109210 CGCAATAACACTGATCCAGTTAGA 58.891 41.667 0.00 0.00 42.59 2.10
1251 1273 2.289819 CCGAAAAGGCAAGTGGTACCTA 60.290 50.000 14.36 0.00 32.08 3.08
1282 1304 7.999679 AGATATCTATCTAGAGATGCAACAGC 58.000 38.462 2.53 0.00 41.05 4.40
1306 1328 3.903090 TGGAGAAATTGCAGGAACCAATT 59.097 39.130 0.00 0.00 42.83 2.32
1332 1354 4.278419 AGATCACTTGGTTTTACTGGCAAC 59.722 41.667 0.00 0.00 0.00 4.17
1337 1359 6.999272 TCACTTGGTTTTACTGGCAACTATAA 59.001 34.615 0.00 0.00 37.61 0.98
1367 1389 6.480763 TGGGTTCTGAATTCAGTAGCATTAA 58.519 36.000 31.97 18.33 41.50 1.40
1368 1390 6.374333 TGGGTTCTGAATTCAGTAGCATTAAC 59.626 38.462 31.97 25.31 41.50 2.01
1383 1405 5.057149 AGCATTAACTTAGGAGGTTATGCG 58.943 41.667 9.05 0.00 37.92 4.73
1393 1415 2.356135 GAGGTTATGCGCTCTTCCAAA 58.644 47.619 9.73 0.00 0.00 3.28
1400 1422 4.782019 ATGCGCTCTTCCAAATTTACAA 57.218 36.364 9.73 0.00 0.00 2.41
1402 1424 4.545610 TGCGCTCTTCCAAATTTACAAAG 58.454 39.130 9.73 0.00 0.00 2.77
1408 1430 7.096551 GCTCTTCCAAATTTACAAAGGCATTA 58.903 34.615 0.00 0.00 0.00 1.90
1423 1445 2.026262 GGCATTACTGAGTTTCCTGGGA 60.026 50.000 0.00 0.00 0.00 4.37
1424 1446 3.561313 GGCATTACTGAGTTTCCTGGGAA 60.561 47.826 0.00 0.00 0.00 3.97
1440 1462 4.262164 CCTGGGAAAGAAATCAAACCACAG 60.262 45.833 0.00 0.00 0.00 3.66
1471 1493 2.435805 AGTGTGGTCAGCTTTTCAGAGA 59.564 45.455 0.00 0.00 0.00 3.10
1472 1494 2.805099 GTGTGGTCAGCTTTTCAGAGAG 59.195 50.000 0.00 0.00 0.00 3.20
1476 1498 2.419324 GGTCAGCTTTTCAGAGAGCATG 59.581 50.000 9.74 0.00 41.31 4.06
1486 1508 2.011947 CAGAGAGCATGCGATTTCCAA 58.988 47.619 13.01 0.00 0.00 3.53
1489 1511 1.066605 AGAGCATGCGATTTCCAATGC 59.933 47.619 13.01 0.00 35.47 3.56
1494 1516 2.570393 GCGATTTCCAATGCTTCGC 58.430 52.632 0.00 0.00 46.70 4.70
1495 1517 3.994729 CGATTTCCAATGCTTCGCA 57.005 47.368 0.00 0.00 44.86 5.10
1507 1529 1.989864 TGCTTCGCAAGTACATACGTG 59.010 47.619 0.00 1.14 38.45 4.49
1509 1531 2.027688 GCTTCGCAAGTACATACGTGAC 59.972 50.000 8.86 0.00 37.80 3.67
1531 1553 1.340405 GCATGTCCATGGGTCTGTCTT 60.340 52.381 13.02 0.00 39.16 3.01
1532 1554 2.636830 CATGTCCATGGGTCTGTCTTC 58.363 52.381 13.02 0.00 35.24 2.87
1540 1562 1.251527 GGGTCTGTCTTCCGCAGAGA 61.252 60.000 0.00 0.00 42.80 3.10
1543 1565 2.427453 GGTCTGTCTTCCGCAGAGAATA 59.573 50.000 0.00 0.00 42.80 1.75
1546 1568 4.505922 GTCTGTCTTCCGCAGAGAATATTG 59.494 45.833 0.00 0.00 42.80 1.90
1554 1576 4.576053 TCCGCAGAGAATATTGAATGGTTG 59.424 41.667 0.00 0.00 0.00 3.77
1558 1580 5.505286 CAGAGAATATTGAATGGTTGTCGC 58.495 41.667 0.00 0.00 0.00 5.19
1584 1606 6.493166 TCATTTCCAGGATTGGTCAGTTTAT 58.507 36.000 0.00 0.00 45.26 1.40
1619 1641 2.673368 GTGACGGTAGAGATGCTTTTGG 59.327 50.000 0.00 0.00 0.00 3.28
1640 1662 7.872061 TTGGAGCTATTCCTGGAATAGATAA 57.128 36.000 40.90 29.96 46.69 1.75
1665 1687 1.610522 GATGACCTGCTTGCACTTGTT 59.389 47.619 0.00 0.00 0.00 2.83
1667 1689 2.221169 TGACCTGCTTGCACTTGTTAG 58.779 47.619 0.00 0.00 0.00 2.34
1758 1780 1.880027 GGTGGCTTAACAGTTGACAGG 59.120 52.381 0.00 0.00 0.00 4.00
1787 1809 8.702438 CACAATGTAATCCTCATCAACAAAAAC 58.298 33.333 0.00 0.00 0.00 2.43
1800 1822 6.279513 TCAACAAAAACAAGGTCATCACTT 57.720 33.333 0.00 0.00 0.00 3.16
1917 1939 5.016831 TGAGCAAGTCATACTTACCTCTGA 58.983 41.667 15.05 0.00 36.03 3.27
1957 1979 8.753497 TCTATGTCTGAAGATAGAACTTGCTA 57.247 34.615 5.57 0.00 35.46 3.49
1967 1989 8.541133 AAGATAGAACTTGCTACAAAGAGTTC 57.459 34.615 6.92 6.92 45.11 3.01
1985 2007 7.437713 AGAGTTCCATATTCAGTGGATAACA 57.562 36.000 0.00 0.00 44.75 2.41
2017 2039 5.208503 GCAGAACTAAAGTGACAAAAGAGC 58.791 41.667 0.00 0.00 0.00 4.09
2041 2063 5.868258 CACAAATAACAATGTTATGGCTGCA 59.132 36.000 18.15 0.00 0.00 4.41
2042 2064 5.868801 ACAAATAACAATGTTATGGCTGCAC 59.131 36.000 18.15 0.00 0.00 4.57
2092 2114 5.298276 ACTGTGGTTTCATACAACGACATTT 59.702 36.000 2.46 0.00 42.37 2.32
2098 2120 7.133513 GGTTTCATACAACGACATTTGTAACA 58.866 34.615 1.09 0.00 43.47 2.41
2106 2128 7.357303 ACAACGACATTTGTAACATTTCTACC 58.643 34.615 0.00 0.00 37.96 3.18
2127 2149 3.741344 CCGAAGAAAACTGACTCAACGAT 59.259 43.478 0.00 0.00 0.00 3.73
2263 2287 6.620877 ACTTCATATTGGCCCGATAATCTA 57.379 37.500 0.00 0.00 0.00 1.98
2266 2290 7.770897 ACTTCATATTGGCCCGATAATCTATTC 59.229 37.037 0.00 0.00 0.00 1.75
2346 2370 2.892852 TCAGTTTCCATGCCCTTTTCTG 59.107 45.455 0.00 0.00 0.00 3.02
2424 2448 4.035675 GGCTTACACAAGATAGTGATTGGC 59.964 45.833 0.57 0.00 42.05 4.52
2470 2494 4.360889 AGTGGGGATTAAATGCCATCAAA 58.639 39.130 0.00 0.00 43.48 2.69
2478 2502 5.999205 TTAAATGCCATCAAACACCTCAT 57.001 34.783 0.00 0.00 0.00 2.90
2563 2587 5.356291 ACTCATGGAGAAAATCAGAGGAG 57.644 43.478 0.00 0.00 33.32 3.69
2621 2645 0.467384 GCTGGCAGATGGCTTCTCTA 59.533 55.000 20.86 0.00 44.01 2.43
2622 2646 1.540797 GCTGGCAGATGGCTTCTCTAG 60.541 57.143 20.86 4.83 44.01 2.43
2623 2647 1.761784 CTGGCAGATGGCTTCTCTAGT 59.238 52.381 9.42 0.00 44.01 2.57
2624 2648 1.759445 TGGCAGATGGCTTCTCTAGTC 59.241 52.381 7.95 0.00 44.01 2.59
2625 2649 1.069978 GGCAGATGGCTTCTCTAGTCC 59.930 57.143 0.00 0.00 44.01 3.85
2626 2650 2.038659 GCAGATGGCTTCTCTAGTCCT 58.961 52.381 0.00 0.00 40.25 3.85
2627 2651 2.433970 GCAGATGGCTTCTCTAGTCCTT 59.566 50.000 0.00 0.00 40.25 3.36
2628 2652 3.639094 GCAGATGGCTTCTCTAGTCCTTA 59.361 47.826 0.00 0.00 40.25 2.69
2629 2653 4.261994 GCAGATGGCTTCTCTAGTCCTTAG 60.262 50.000 0.00 0.00 40.25 2.18
2630 2654 5.136828 CAGATGGCTTCTCTAGTCCTTAGA 58.863 45.833 0.00 0.00 36.91 2.10
2631 2655 8.179368 GCAGATGGCTTCTCTAGTCCTTAGAG 62.179 50.000 0.00 5.11 46.37 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1 2 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2 3 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3 4 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
4 5 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5 6 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
6 7 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
7 8 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
8 9 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
9 10 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
10 11 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
11 12 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
12 13 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
13 14 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
14 15 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
15 16 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
16 17 5.476599 CCTAGAGAGAGAGAGAGAGAGAGAG 59.523 52.000 0.00 0.00 0.00 3.20
17 18 5.389520 CCTAGAGAGAGAGAGAGAGAGAGA 58.610 50.000 0.00 0.00 0.00 3.10
18 19 4.526262 CCCTAGAGAGAGAGAGAGAGAGAG 59.474 54.167 0.00 0.00 0.00 3.20
67 71 4.142665 CGACTCGTCCATCTTTCTCAACTA 60.143 45.833 0.00 0.00 0.00 2.24
154 158 1.451567 CTAGGCCTCTGACCGTCGA 60.452 63.158 9.68 0.00 0.00 4.20
155 159 2.482333 CCTAGGCCTCTGACCGTCG 61.482 68.421 9.68 0.00 0.00 5.12
195 199 0.036732 ACGATGATGCCCACTGTGTT 59.963 50.000 7.08 0.00 0.00 3.32
201 205 0.676466 TCCAACACGATGATGCCCAC 60.676 55.000 0.00 0.00 0.00 4.61
202 206 0.676466 GTCCAACACGATGATGCCCA 60.676 55.000 0.00 0.00 0.00 5.36
204 208 1.009829 GAGTCCAACACGATGATGCC 58.990 55.000 0.00 0.00 0.00 4.40
247 269 3.083997 GGGGTGATCGTGAGGGCT 61.084 66.667 0.00 0.00 0.00 5.19
432 454 3.454573 CATGCCGCCAATGCTGGT 61.455 61.111 0.00 0.00 45.53 4.00
488 510 0.690762 TGAGAAAAACGAGGAGGGGG 59.309 55.000 0.00 0.00 0.00 5.40
493 515 1.613255 GGCCCATGAGAAAAACGAGGA 60.613 52.381 0.00 0.00 0.00 3.71
494 516 0.811281 GGCCCATGAGAAAAACGAGG 59.189 55.000 0.00 0.00 0.00 4.63
495 517 1.740025 GAGGCCCATGAGAAAAACGAG 59.260 52.381 0.00 0.00 0.00 4.18
496 518 1.613255 GGAGGCCCATGAGAAAAACGA 60.613 52.381 0.00 0.00 0.00 3.85
497 519 0.811281 GGAGGCCCATGAGAAAAACG 59.189 55.000 0.00 0.00 0.00 3.60
498 520 0.811281 CGGAGGCCCATGAGAAAAAC 59.189 55.000 0.00 0.00 0.00 2.43
499 521 0.965363 GCGGAGGCCCATGAGAAAAA 60.965 55.000 0.00 0.00 0.00 1.94
516 538 0.744281 AGAAAGGTGGGTTTTGTGCG 59.256 50.000 0.00 0.00 0.00 5.34
530 552 6.039829 GTGATTAAGGCCCAGGATTAAGAAAG 59.960 42.308 0.00 0.00 0.00 2.62
562 584 0.931702 CGCACGGACCGCAATTAATA 59.068 50.000 15.39 0.00 0.00 0.98
563 585 1.711060 CCGCACGGACCGCAATTAAT 61.711 55.000 15.39 0.00 37.50 1.40
564 586 2.392181 CCGCACGGACCGCAATTAA 61.392 57.895 15.39 0.00 37.50 1.40
565 587 2.816083 CCGCACGGACCGCAATTA 60.816 61.111 15.39 0.00 37.50 1.40
580 602 2.819608 ACCATGAACTGATTCCAAACCG 59.180 45.455 0.00 0.00 33.49 4.44
584 606 2.304470 TCGGACCATGAACTGATTCCAA 59.696 45.455 0.00 0.00 33.49 3.53
634 656 1.527370 CAGCCAGCCCTACTAACCC 59.473 63.158 0.00 0.00 0.00 4.11
643 665 2.594365 AATCCAATCCCAGCCAGCCC 62.594 60.000 0.00 0.00 0.00 5.19
747 769 9.770097 GTATATCGTCCCAATCAATCATCATAT 57.230 33.333 0.00 0.00 0.00 1.78
748 770 8.757877 TGTATATCGTCCCAATCAATCATCATA 58.242 33.333 0.00 0.00 0.00 2.15
749 771 7.623630 TGTATATCGTCCCAATCAATCATCAT 58.376 34.615 0.00 0.00 0.00 2.45
750 772 7.003402 TGTATATCGTCCCAATCAATCATCA 57.997 36.000 0.00 0.00 0.00 3.07
751 773 6.036517 GCTGTATATCGTCCCAATCAATCATC 59.963 42.308 0.00 0.00 0.00 2.92
781 803 0.527385 TTCGTTTGCCAGCAACTTGC 60.527 50.000 4.18 5.55 45.46 4.01
866 888 8.137745 ACCAATTTATGTTGATGAGATGGTTT 57.862 30.769 0.00 0.00 33.92 3.27
867 889 7.722949 ACCAATTTATGTTGATGAGATGGTT 57.277 32.000 0.00 0.00 33.92 3.67
926 948 7.954248 GCAAGTGAAGATTATATAACATGAGCG 59.046 37.037 0.00 0.00 0.00 5.03
946 968 0.951040 GTCGGGGAGTTCTGCAAGTG 60.951 60.000 0.00 0.00 33.76 3.16
960 982 1.926511 GCTGCAAGTGGAATGTCGGG 61.927 60.000 0.00 0.00 35.30 5.14
972 994 0.809241 GATCCTCGTCCAGCTGCAAG 60.809 60.000 8.66 0.00 0.00 4.01
999 1021 5.261370 GAGCGTCATAATTACTGCTCATG 57.739 43.478 18.04 0.00 46.05 3.07
1007 1029 5.463392 TCATCAAGCAGAGCGTCATAATTAC 59.537 40.000 0.00 0.00 0.00 1.89
1014 1036 2.168326 TTTCATCAAGCAGAGCGTCA 57.832 45.000 0.00 0.00 0.00 4.35
1026 1048 8.158789 TGTCTGATATGCTGGATAATTTCATCA 58.841 33.333 0.00 0.00 0.00 3.07
1037 1059 3.538591 CAAAGCTGTCTGATATGCTGGA 58.461 45.455 0.00 0.00 35.79 3.86
1044 1066 2.265367 TGACCCCAAAGCTGTCTGATA 58.735 47.619 3.17 0.00 0.00 2.15
1063 1085 3.119602 CCATTCTGCTGTCCATTCACTTG 60.120 47.826 0.00 0.00 0.00 3.16
1066 1088 1.747355 CCCATTCTGCTGTCCATTCAC 59.253 52.381 0.00 0.00 0.00 3.18
1067 1089 1.634973 TCCCATTCTGCTGTCCATTCA 59.365 47.619 0.00 0.00 0.00 2.57
1086 1108 6.564328 CAAGCTTAAAATACCTTCCACCATC 58.436 40.000 0.00 0.00 0.00 3.51
1092 1114 3.132289 GGGGCAAGCTTAAAATACCTTCC 59.868 47.826 0.00 0.00 0.00 3.46
1141 1163 1.670087 CCAGTGTTGTGGAGCGAGTAG 60.670 57.143 0.00 0.00 40.44 2.57
1175 1197 8.043710 AGGAAAACAATAGTCTAACTGGATCAG 58.956 37.037 0.00 0.00 37.52 2.90
1217 1239 3.857010 GCCTTTTCGGTGAAAACCATCAG 60.857 47.826 0.81 0.00 36.73 2.90
1232 1254 5.977489 AAATAGGTACCACTTGCCTTTTC 57.023 39.130 15.94 0.00 36.84 2.29
1236 1258 6.382919 TCTTTAAATAGGTACCACTTGCCT 57.617 37.500 15.94 0.00 43.97 4.75
1270 1292 0.390340 TCTCCACGCTGTTGCATCTC 60.390 55.000 0.00 0.00 39.64 2.75
1272 1294 0.874390 TTTCTCCACGCTGTTGCATC 59.126 50.000 0.00 0.00 39.64 3.91
1279 1301 0.169672 CCTGCAATTTCTCCACGCTG 59.830 55.000 0.00 0.00 0.00 5.18
1282 1304 1.200020 GGTTCCTGCAATTTCTCCACG 59.800 52.381 0.00 0.00 0.00 4.94
1306 1328 6.065374 TGCCAGTAAAACCAAGTGATCTTAA 58.935 36.000 0.00 0.00 32.07 1.85
1337 1359 3.490348 CTGAATTCAGAACCCAGTTGGT 58.510 45.455 28.13 0.00 46.59 3.67
1348 1370 8.758829 TCCTAAGTTAATGCTACTGAATTCAGA 58.241 33.333 36.15 20.69 46.59 3.27
1352 1374 7.862675 ACCTCCTAAGTTAATGCTACTGAATT 58.137 34.615 0.00 0.00 0.00 2.17
1353 1375 7.439108 ACCTCCTAAGTTAATGCTACTGAAT 57.561 36.000 0.00 0.00 0.00 2.57
1367 1389 2.389715 AGAGCGCATAACCTCCTAAGT 58.610 47.619 11.47 0.00 0.00 2.24
1368 1390 3.385577 GAAGAGCGCATAACCTCCTAAG 58.614 50.000 11.47 0.00 0.00 2.18
1383 1405 4.881920 TGCCTTTGTAAATTTGGAAGAGC 58.118 39.130 0.00 8.17 0.00 4.09
1393 1415 7.451566 AGGAAACTCAGTAATGCCTTTGTAAAT 59.548 33.333 0.00 0.00 32.90 1.40
1400 1422 3.562176 CCCAGGAAACTCAGTAATGCCTT 60.562 47.826 0.00 0.00 40.21 4.35
1402 1424 2.026262 TCCCAGGAAACTCAGTAATGCC 60.026 50.000 0.00 0.00 40.21 4.40
1408 1430 4.519906 TTTCTTTCCCAGGAAACTCAGT 57.480 40.909 7.79 0.00 40.21 3.41
1423 1445 5.594926 CTTGAGCTGTGGTTTGATTTCTTT 58.405 37.500 0.00 0.00 0.00 2.52
1424 1446 4.500375 GCTTGAGCTGTGGTTTGATTTCTT 60.500 41.667 0.00 0.00 38.21 2.52
1450 1472 2.435805 TCTCTGAAAAGCTGACCACACT 59.564 45.455 0.00 0.00 0.00 3.55
1452 1474 2.808202 GCTCTCTGAAAAGCTGACCACA 60.808 50.000 0.00 0.00 35.60 4.17
1471 1493 1.108776 AGCATTGGAAATCGCATGCT 58.891 45.000 17.13 10.56 40.12 3.79
1472 1494 1.856597 GAAGCATTGGAAATCGCATGC 59.143 47.619 7.91 7.91 35.47 4.06
1489 1511 2.597305 GGTCACGTATGTACTTGCGAAG 59.403 50.000 22.51 14.97 0.00 3.79
1494 1516 1.985334 TGCGGTCACGTATGTACTTG 58.015 50.000 0.00 0.00 43.45 3.16
1495 1517 2.953466 ATGCGGTCACGTATGTACTT 57.047 45.000 0.00 0.00 43.81 2.24
1507 1529 1.819632 GACCCATGGACATGCGGTC 60.820 63.158 24.11 24.11 44.21 4.79
1509 1531 1.820906 CAGACCCATGGACATGCGG 60.821 63.158 15.22 11.32 37.49 5.69
1531 1553 4.422073 ACCATTCAATATTCTCTGCGGA 57.578 40.909 0.00 0.00 0.00 5.54
1532 1554 4.336433 ACAACCATTCAATATTCTCTGCGG 59.664 41.667 0.00 0.00 0.00 5.69
1540 1562 5.833406 TGATGCGACAACCATTCAATATT 57.167 34.783 0.00 0.00 0.00 1.28
1543 1565 4.724074 AATGATGCGACAACCATTCAAT 57.276 36.364 0.00 0.00 0.00 2.57
1546 1568 3.119531 TGGAAATGATGCGACAACCATTC 60.120 43.478 0.00 0.00 0.00 2.67
1554 1576 2.033801 CCAATCCTGGAAATGATGCGAC 59.966 50.000 12.85 0.00 46.92 5.19
1558 1580 4.275810 ACTGACCAATCCTGGAAATGATG 58.724 43.478 12.85 3.07 46.92 3.07
1584 1606 2.555325 ACCGTCACGTATCTTCTCACAA 59.445 45.455 0.00 0.00 0.00 3.33
1619 1641 9.213799 CAAAGTTATCTATTCCAGGAATAGCTC 57.786 37.037 32.81 23.58 46.36 4.09
1640 1662 1.610522 GTGCAAGCAGGTCATCAAAGT 59.389 47.619 0.00 0.00 0.00 2.66
1647 1669 2.221169 CTAACAAGTGCAAGCAGGTCA 58.779 47.619 0.00 0.00 0.00 4.02
1741 1763 1.266989 GCACCTGTCAACTGTTAAGCC 59.733 52.381 0.00 0.00 0.00 4.35
1742 1764 1.946768 TGCACCTGTCAACTGTTAAGC 59.053 47.619 0.00 0.00 0.00 3.09
1758 1780 5.106197 TGTTGATGAGGATTACATTGTGCAC 60.106 40.000 10.75 10.75 0.00 4.57
1787 1809 3.049708 TGCAGAGAAGTGATGACCTTG 57.950 47.619 0.00 0.00 0.00 3.61
1800 1822 6.103997 CGGTACCTATTTTAAGTTGCAGAGA 58.896 40.000 10.90 0.00 0.00 3.10
1917 1939 8.324191 TCAGACATAGAAGAACCCAAAGATAT 57.676 34.615 0.00 0.00 0.00 1.63
1957 1979 6.126863 TCCACTGAATATGGAACTCTTTGT 57.873 37.500 0.00 0.00 43.43 2.83
1967 1989 4.717877 TGCCTGTTATCCACTGAATATGG 58.282 43.478 0.00 0.00 38.71 2.74
1985 2007 3.755378 CACTTTAGTTCTGCATCTTGCCT 59.245 43.478 0.00 0.00 44.23 4.75
2017 2039 5.868258 TGCAGCCATAACATTGTTATTTGTG 59.132 36.000 17.42 14.80 0.00 3.33
2041 2063 7.833682 TCCTGACATCCATACATAAAACATTGT 59.166 33.333 0.00 0.00 0.00 2.71
2042 2064 8.224389 TCCTGACATCCATACATAAAACATTG 57.776 34.615 0.00 0.00 0.00 2.82
2106 2128 4.444388 TGATCGTTGAGTCAGTTTTCTTCG 59.556 41.667 0.00 0.00 0.00 3.79
2127 2149 6.071108 GCTAAATGCTATAGAGACCAGGATGA 60.071 42.308 3.21 0.00 37.11 2.92
2177 2201 1.528586 CGGTGACAAGAACTTCAGCAG 59.471 52.381 0.00 0.00 39.69 4.24
2263 2287 3.575256 TGCTTCTTCTGCAACCAATGAAT 59.425 39.130 0.00 0.00 37.51 2.57
2266 2290 3.374220 TTGCTTCTTCTGCAACCAATG 57.626 42.857 0.00 0.00 44.24 2.82
2346 2370 2.489938 TATGCTGGGTCACCTCAAAC 57.510 50.000 0.00 0.00 37.76 2.93
2399 2423 3.906720 TCACTATCTTGTGTAAGCCCC 57.093 47.619 0.00 0.00 38.90 5.80
2424 2448 2.746362 GTGGAAAATGGCAGTCAGAGAG 59.254 50.000 0.00 0.00 0.00 3.20
2470 2494 2.965831 AGCATACGTGGATATGAGGTGT 59.034 45.455 0.00 0.00 34.94 4.16
2478 2502 3.449377 TGTTTCCAGAGCATACGTGGATA 59.551 43.478 0.00 0.00 40.11 2.59
2544 2568 5.008811 GCATTCTCCTCTGATTTTCTCCATG 59.991 44.000 0.00 0.00 0.00 3.66
2563 2587 3.243334 GGCCTTGAGCTTATCTTGCATTC 60.243 47.826 0.00 0.00 43.05 2.67
2621 2645 3.390175 TGCTCTAAGCCTCTAAGGACT 57.610 47.619 0.00 0.00 41.51 3.85
2622 2646 4.681074 AATGCTCTAAGCCTCTAAGGAC 57.319 45.455 0.00 0.00 41.51 3.85
2623 2647 5.700402 AAAATGCTCTAAGCCTCTAAGGA 57.300 39.130 0.00 0.00 41.51 3.36
2624 2648 6.118852 AGAAAAATGCTCTAAGCCTCTAAGG 58.881 40.000 0.00 0.00 41.51 2.69
2625 2649 6.019156 CGAGAAAAATGCTCTAAGCCTCTAAG 60.019 42.308 0.00 0.00 41.51 2.18
2626 2650 5.812642 CGAGAAAAATGCTCTAAGCCTCTAA 59.187 40.000 0.00 0.00 41.51 2.10
2627 2651 5.105310 ACGAGAAAAATGCTCTAAGCCTCTA 60.105 40.000 0.00 0.00 41.51 2.43
2628 2652 4.187694 CGAGAAAAATGCTCTAAGCCTCT 58.812 43.478 0.00 0.00 41.51 3.69
2629 2653 3.935828 ACGAGAAAAATGCTCTAAGCCTC 59.064 43.478 0.00 0.00 41.51 4.70
2630 2654 3.686726 CACGAGAAAAATGCTCTAAGCCT 59.313 43.478 0.00 0.00 41.51 4.58
2631 2655 3.437049 ACACGAGAAAAATGCTCTAAGCC 59.563 43.478 0.00 0.00 41.51 4.35
2632 2656 4.083802 ACACACGAGAAAAATGCTCTAAGC 60.084 41.667 0.00 0.00 42.82 3.09
2633 2657 5.406780 AGACACACGAGAAAAATGCTCTAAG 59.593 40.000 0.00 0.00 0.00 2.18
2634 2658 5.297547 AGACACACGAGAAAAATGCTCTAA 58.702 37.500 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.