Multiple sequence alignment - TraesCS2B01G190700

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 TraesCS2B01G190700 chr2B 100.000 2799 0 0 932 3730 166292901 166290103 0.000000e+00 5169
1 TraesCS2B01G190700 chr2B 100.000 348 0 0 1 348 166293832 166293485 0.000000e+00 643
2 TraesCS2B01G190700 chr2D 93.747 2303 86 29 932 3215 115626980 115624717 0.000000e+00 3402
3 TraesCS2B01G190700 chr2D 92.410 527 25 4 3218 3730 115624551 115624026 0.000000e+00 737
4 TraesCS2B01G190700 chr2D 96.269 268 9 1 81 348 115627339 115627073 4.420000e-119 438
5 TraesCS2B01G190700 chr2A 94.598 2203 79 15 932 3117 117182577 117180398 0.000000e+00 3373
6 TraesCS2B01G190700 chr2A 88.324 531 26 15 3212 3730 117180097 117179591 4.120000e-169 604
7 TraesCS2B01G190700 chr2A 93.704 270 14 3 81 348 117182939 117182671 5.800000e-108 401
8 TraesCS2B01G190700 chr2A 95.699 93 2 2 3124 3215 117180353 117180262 8.350000e-32 148
9 TraesCS2B01G190700 chr3B 77.158 556 65 31 2322 2864 42170981 42170475 2.210000e-67 267


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 TraesCS2B01G190700 chr2B 166290103 166293832 3729 True 2906.000000 5169 100.00000 1 3730 2 chr2B.!!$R1 3729
1 TraesCS2B01G190700 chr2D 115624026 115627339 3313 True 1525.666667 3402 94.14200 81 3730 3 chr2D.!!$R1 3649
2 TraesCS2B01G190700 chr2A 117179591 117182939 3348 True 1131.500000 3373 93.08125 81 3730 4 chr2A.!!$R1 3649
3 TraesCS2B01G190700 chr3B 42170475 42170981 506 True 267.000000 267 77.15800 2322 2864 1 chr3B.!!$R1 542

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
62 63 0.034767 ATGGGATCACTGCCACACTG 60.035 55.0 0.0 0.0 46.73 3.66 F
129 130 0.627451 TGGATGCTCCCAAATCTGCT 59.373 50.0 0.0 0.0 35.03 4.24 F
1463 1473 0.957395 CGTCCTTGCATCTTGTGGCT 60.957 55.0 0.0 0.0 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1475 1485 0.187117 TGGCCAAAACTGGATGGTGA 59.813 50.0 0.61 0.00 39.0 4.02 R
1476 1486 1.047002 TTGGCCAAAACTGGATGGTG 58.953 50.0 17.98 0.00 39.0 4.17 R
3143 3219 0.037139 TGGAATGCAATGCAGGCAAC 60.037 50.0 18.29 14.66 45.6 4.17 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
23 24 6.552859 CATCCACACAATTACTGTACAACA 57.447 37.500 0.00 0.00 36.10 3.33
24 25 7.144722 CATCCACACAATTACTGTACAACAT 57.855 36.000 0.00 0.00 36.10 2.71
25 26 8.262715 CATCCACACAATTACTGTACAACATA 57.737 34.615 0.00 0.00 36.10 2.29
26 27 8.726068 CATCCACACAATTACTGTACAACATAA 58.274 33.333 0.00 0.00 36.10 1.90
27 28 8.678593 TCCACACAATTACTGTACAACATAAA 57.321 30.769 0.00 0.00 36.10 1.40
28 29 9.290988 TCCACACAATTACTGTACAACATAAAT 57.709 29.630 0.00 0.00 36.10 1.40
29 30 9.340695 CCACACAATTACTGTACAACATAAATG 57.659 33.333 0.00 2.88 36.10 2.32
36 37 6.662414 ACTGTACAACATAAATGATGGACG 57.338 37.500 10.04 7.90 44.59 4.79
37 38 6.048073 CTGTACAACATAAATGATGGACGG 57.952 41.667 9.28 9.28 44.59 4.79
38 39 4.334203 TGTACAACATAAATGATGGACGGC 59.666 41.667 10.04 0.00 44.59 5.68
39 40 3.620488 ACAACATAAATGATGGACGGCT 58.380 40.909 5.38 0.00 40.18 5.52
40 41 3.378112 ACAACATAAATGATGGACGGCTG 59.622 43.478 5.38 0.00 40.18 4.85
41 42 3.281727 ACATAAATGATGGACGGCTGT 57.718 42.857 0.00 0.00 40.18 4.40
42 43 2.945008 ACATAAATGATGGACGGCTGTG 59.055 45.455 0.80 0.00 40.18 3.66
43 44 3.205338 CATAAATGATGGACGGCTGTGA 58.795 45.455 0.80 0.00 31.20 3.58
44 45 2.425143 AAATGATGGACGGCTGTGAT 57.575 45.000 0.80 0.00 0.00 3.06
45 46 1.671979 AATGATGGACGGCTGTGATG 58.328 50.000 0.80 0.00 0.00 3.07
46 47 0.179037 ATGATGGACGGCTGTGATGG 60.179 55.000 0.80 0.00 0.00 3.51
47 48 1.524621 GATGGACGGCTGTGATGGG 60.525 63.158 0.80 0.00 0.00 4.00
48 49 1.971505 GATGGACGGCTGTGATGGGA 61.972 60.000 0.80 0.00 0.00 4.37
49 50 1.348008 ATGGACGGCTGTGATGGGAT 61.348 55.000 0.80 0.00 0.00 3.85
50 51 1.227674 GGACGGCTGTGATGGGATC 60.228 63.158 0.80 0.00 0.00 3.36
51 52 1.522092 GACGGCTGTGATGGGATCA 59.478 57.895 0.80 0.00 36.84 2.92
59 60 2.385777 TGATGGGATCACTGCCACA 58.614 52.632 0.00 0.00 46.73 4.17
60 61 0.035152 TGATGGGATCACTGCCACAC 60.035 55.000 0.00 0.00 46.73 3.82
61 62 0.254178 GATGGGATCACTGCCACACT 59.746 55.000 0.00 0.00 46.73 3.55
62 63 0.034767 ATGGGATCACTGCCACACTG 60.035 55.000 0.00 0.00 46.73 3.66
63 64 2.042831 GGGATCACTGCCACACTGC 61.043 63.158 0.00 0.00 31.98 4.40
64 65 2.042831 GGATCACTGCCACACTGCC 61.043 63.158 0.00 0.00 0.00 4.85
65 66 1.302752 GATCACTGCCACACTGCCA 60.303 57.895 0.00 0.00 0.00 4.92
66 67 1.580845 GATCACTGCCACACTGCCAC 61.581 60.000 0.00 0.00 0.00 5.01
67 68 2.342073 ATCACTGCCACACTGCCACA 62.342 55.000 0.00 0.00 0.00 4.17
68 69 2.120282 CACTGCCACACTGCCACAA 61.120 57.895 0.00 0.00 0.00 3.33
69 70 1.152694 ACTGCCACACTGCCACAAT 60.153 52.632 0.00 0.00 0.00 2.71
70 71 1.287815 CTGCCACACTGCCACAATG 59.712 57.895 0.00 0.00 0.00 2.82
71 72 1.455402 TGCCACACTGCCACAATGT 60.455 52.632 0.00 0.00 0.00 2.71
72 73 1.007038 GCCACACTGCCACAATGTG 60.007 57.895 6.37 6.37 42.75 3.21
73 74 1.737355 GCCACACTGCCACAATGTGT 61.737 55.000 12.79 0.00 44.52 3.72
83 84 1.522668 CACAATGTGTGGACCGATGT 58.477 50.000 5.00 0.00 44.27 3.06
117 118 1.066605 GCAAAATGCTCGATGGATGCT 59.933 47.619 0.00 0.00 40.96 3.79
129 130 0.627451 TGGATGCTCCCAAATCTGCT 59.373 50.000 0.00 0.00 35.03 4.24
173 174 5.848833 ATTGCCTGATCATTTTTCTCCTC 57.151 39.130 0.00 0.00 0.00 3.71
228 229 1.304617 CCCCTTTCTCTTCCCCAGC 59.695 63.158 0.00 0.00 0.00 4.85
269 271 5.048434 CCACATCTTGTCTTTCTTTCCCTTC 60.048 44.000 0.00 0.00 0.00 3.46
332 335 1.153086 CGCCTTCTCCTCCATTGGG 60.153 63.158 2.09 0.00 0.00 4.12
1315 1325 3.878699 GGTACGGTGAGAAACAAAAAGGA 59.121 43.478 0.00 0.00 0.00 3.36
1368 1378 2.228822 CAGTTTCCTTTTCCGTGATGGG 59.771 50.000 0.00 0.00 38.76 4.00
1434 1444 6.238374 CGTTTGACTCTTGTGTAAATCCAGTT 60.238 38.462 0.00 0.00 0.00 3.16
1462 1472 1.503542 CGTCCTTGCATCTTGTGGC 59.496 57.895 0.00 0.00 0.00 5.01
1463 1473 0.957395 CGTCCTTGCATCTTGTGGCT 60.957 55.000 0.00 0.00 0.00 4.75
1467 1477 1.401931 CCTTGCATCTTGTGGCTTTCG 60.402 52.381 0.00 0.00 0.00 3.46
1470 1480 1.739466 TGCATCTTGTGGCTTTCGATC 59.261 47.619 0.00 0.00 0.00 3.69
1471 1481 1.739466 GCATCTTGTGGCTTTCGATCA 59.261 47.619 0.00 0.00 0.00 2.92
1472 1482 2.476854 GCATCTTGTGGCTTTCGATCAC 60.477 50.000 0.00 0.00 0.00 3.06
1473 1483 1.808411 TCTTGTGGCTTTCGATCACC 58.192 50.000 0.00 0.00 0.00 4.02
1474 1484 1.071542 TCTTGTGGCTTTCGATCACCA 59.928 47.619 0.00 0.00 0.00 4.17
1475 1485 2.086869 CTTGTGGCTTTCGATCACCAT 58.913 47.619 4.36 0.00 34.04 3.55
1476 1486 1.737838 TGTGGCTTTCGATCACCATC 58.262 50.000 4.36 0.80 34.04 3.51
1477 1487 1.003003 TGTGGCTTTCGATCACCATCA 59.997 47.619 4.36 2.92 34.04 3.07
1478 1488 1.398390 GTGGCTTTCGATCACCATCAC 59.602 52.381 4.36 0.00 34.04 3.06
1479 1489 1.017387 GGCTTTCGATCACCATCACC 58.983 55.000 0.00 0.00 0.00 4.02
1480 1490 1.678728 GGCTTTCGATCACCATCACCA 60.679 52.381 0.00 0.00 0.00 4.17
1481 1491 2.292267 GCTTTCGATCACCATCACCAT 58.708 47.619 0.00 0.00 0.00 3.55
1482 1492 2.289002 GCTTTCGATCACCATCACCATC 59.711 50.000 0.00 0.00 0.00 3.51
1483 1493 2.620251 TTCGATCACCATCACCATCC 57.380 50.000 0.00 0.00 0.00 3.51
1484 1494 1.494960 TCGATCACCATCACCATCCA 58.505 50.000 0.00 0.00 0.00 3.41
1485 1495 1.413812 TCGATCACCATCACCATCCAG 59.586 52.381 0.00 0.00 0.00 3.86
1486 1496 1.139654 CGATCACCATCACCATCCAGT 59.860 52.381 0.00 0.00 0.00 4.00
1487 1497 2.420547 CGATCACCATCACCATCCAGTT 60.421 50.000 0.00 0.00 0.00 3.16
1488 1498 3.624777 GATCACCATCACCATCCAGTTT 58.375 45.455 0.00 0.00 0.00 2.66
1489 1499 3.524095 TCACCATCACCATCCAGTTTT 57.476 42.857 0.00 0.00 0.00 2.43
1490 1500 3.156293 TCACCATCACCATCCAGTTTTG 58.844 45.455 0.00 0.00 0.00 2.44
1503 1513 2.230992 CCAGTTTTGGCCAATTCGATCA 59.769 45.455 21.26 0.00 37.73 2.92
1558 1568 1.066430 CCTTTCCTCGATCCGGACAAA 60.066 52.381 6.12 0.00 0.00 2.83
1628 1638 2.679716 GGCTGCAGGTCCATTCCT 59.320 61.111 17.12 0.00 38.51 3.36
1654 1664 2.558359 CAATTTTGGACCACTGACCCTC 59.442 50.000 0.00 0.00 0.00 4.30
1693 1703 2.366640 TGGATAGGTTCCTCTCCTCG 57.633 55.000 19.34 0.00 45.68 4.63
1745 1755 5.298026 TCTGCATTGCTAACAACTGTGTAAA 59.702 36.000 10.49 0.00 38.99 2.01
1746 1756 6.016360 TCTGCATTGCTAACAACTGTGTAAAT 60.016 34.615 10.49 0.00 38.99 1.40
1747 1757 6.148948 TGCATTGCTAACAACTGTGTAAATC 58.851 36.000 10.49 0.00 38.99 2.17
1761 1771 6.807230 ACTGTGTAAATCGATCTGTTACTGAC 59.193 38.462 15.80 9.53 0.00 3.51
1840 1850 3.004024 CAACAGTTGATGTCAGTTGCC 57.996 47.619 7.61 0.00 43.00 4.52
1952 1962 8.469309 AATCGATAATTGTTTGATGATCCCTT 57.531 30.769 0.00 0.00 0.00 3.95
2009 2019 2.218759 GGTTTGCGATGAGTACTATGCG 59.781 50.000 0.00 0.55 0.00 4.73
2129 2139 5.047566 TCTTGGACAAGTTCAATGAAGGA 57.952 39.130 11.44 0.00 39.38 3.36
2138 2148 1.533625 TCAATGAAGGAAAGCCACCG 58.466 50.000 0.00 0.00 36.29 4.94
2153 2163 1.078709 CACCGAGTTACATGCTGGTG 58.921 55.000 0.00 0.00 40.68 4.17
2198 2208 0.535102 CCACTGTGAAAGGTTCGGCT 60.535 55.000 9.86 0.00 0.00 5.52
2343 2360 4.927782 TCGCTGCCGCAGTGGTTT 62.928 61.111 28.93 0.00 41.68 3.27
2350 2367 1.944234 GCCGCAGTGGTTTTATGGGG 61.944 60.000 0.89 3.37 46.69 4.96
2356 2373 1.149077 AGTGGTTTTATGGGGGCTTGT 59.851 47.619 0.00 0.00 0.00 3.16
2411 2428 2.097825 GCAGCATCTGAAATCCCTGTT 58.902 47.619 0.00 0.00 32.44 3.16
2522 2539 2.072298 GAGATGATTGCGGGATGCTAC 58.928 52.381 0.00 0.00 46.63 3.58
2546 2563 2.224402 GCTGTTGGTGAAGAAGAGAGGT 60.224 50.000 0.00 0.00 0.00 3.85
2809 2844 0.321830 TTTCTTACCCCGAAAGCCCG 60.322 55.000 0.00 0.00 0.00 6.13
2867 2902 5.991328 ACAGTAATTATCGAGCATTGTGG 57.009 39.130 0.00 0.00 0.00 4.17
2879 2914 1.747206 GCATTGTGGCGGTTAGAGGAT 60.747 52.381 0.00 0.00 0.00 3.24
2881 2916 3.804036 CATTGTGGCGGTTAGAGGATTA 58.196 45.455 0.00 0.00 0.00 1.75
2956 2991 0.560688 GATGGGAGGAGGGAGAGTCT 59.439 60.000 0.00 0.00 0.00 3.24
3003 3038 8.053355 TCTCCCCTTCTTCATTTTAGGTATTTC 58.947 37.037 0.00 0.00 0.00 2.17
3040 3078 3.652581 CCTTCTCCGAGGGCTTTTT 57.347 52.632 0.00 0.00 32.94 1.94
3046 3084 2.239654 TCTCCGAGGGCTTTTTGATGAT 59.760 45.455 0.00 0.00 0.00 2.45
3120 3196 8.865001 TGGATTTTCGTTTTGTTTCTTTACAAG 58.135 29.630 0.00 0.00 39.06 3.16
3173 3249 3.374220 TTGCATTCCAGTGCTCAAAAG 57.626 42.857 0.00 0.00 45.27 2.27
3215 3295 4.577693 TCATCAATGCATTCCTCTTACTGC 59.422 41.667 9.53 0.00 35.21 4.40
3237 3486 4.204012 CGCTCCCCATTTTTCCATTAGTA 58.796 43.478 0.00 0.00 0.00 1.82
3349 3598 2.983192 TCTGGTGGAGTTGTTTATCCCA 59.017 45.455 0.00 0.00 34.47 4.37
3607 3865 2.421073 TGCAGCTGTATGATTTGAGTGC 59.579 45.455 16.64 0.00 0.00 4.40
3626 3884 7.441836 TGAGTGCTAATCTCACTTTCACTAAA 58.558 34.615 0.00 0.00 44.09 1.85
3628 3886 7.445945 AGTGCTAATCTCACTTTCACTAAACT 58.554 34.615 0.00 0.00 41.61 2.66
3660 3918 3.118223 TGTGTGTGTGAATGAAGGTGGTA 60.118 43.478 0.00 0.00 0.00 3.25
3662 3920 3.074412 GTGTGTGAATGAAGGTGGTAGG 58.926 50.000 0.00 0.00 0.00 3.18
3663 3921 2.039746 TGTGTGAATGAAGGTGGTAGGG 59.960 50.000 0.00 0.00 0.00 3.53
3664 3922 1.004277 TGTGAATGAAGGTGGTAGGGC 59.996 52.381 0.00 0.00 0.00 5.19
3665 3923 1.004277 GTGAATGAAGGTGGTAGGGCA 59.996 52.381 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.552859 TGTTGTACAGTAATTGTGTGGATG 57.447 37.500 0.00 0.00 41.10 3.51
1 2 8.856153 TTATGTTGTACAGTAATTGTGTGGAT 57.144 30.769 0.00 0.00 41.10 3.41
2 3 8.678593 TTTATGTTGTACAGTAATTGTGTGGA 57.321 30.769 0.00 0.00 41.10 4.02
3 4 9.340695 CATTTATGTTGTACAGTAATTGTGTGG 57.659 33.333 0.00 0.00 41.10 4.17
10 11 8.826710 CGTCCATCATTTATGTTGTACAGTAAT 58.173 33.333 0.00 0.00 33.34 1.89
11 12 7.279090 CCGTCCATCATTTATGTTGTACAGTAA 59.721 37.037 0.00 0.00 33.34 2.24
12 13 6.759356 CCGTCCATCATTTATGTTGTACAGTA 59.241 38.462 0.00 0.00 33.34 2.74
13 14 5.584649 CCGTCCATCATTTATGTTGTACAGT 59.415 40.000 0.00 0.00 33.34 3.55
14 15 5.504010 GCCGTCCATCATTTATGTTGTACAG 60.504 44.000 0.00 0.00 33.34 2.74
15 16 4.334203 GCCGTCCATCATTTATGTTGTACA 59.666 41.667 0.00 0.00 33.34 2.90
16 17 4.574828 AGCCGTCCATCATTTATGTTGTAC 59.425 41.667 0.00 0.00 33.34 2.90
17 18 4.574421 CAGCCGTCCATCATTTATGTTGTA 59.426 41.667 0.00 0.00 33.34 2.41
18 19 3.378112 CAGCCGTCCATCATTTATGTTGT 59.622 43.478 0.00 0.00 33.34 3.32
19 20 3.378112 ACAGCCGTCCATCATTTATGTTG 59.622 43.478 0.00 0.00 33.34 3.33
20 21 3.378112 CACAGCCGTCCATCATTTATGTT 59.622 43.478 0.00 0.00 33.34 2.71
21 22 2.945008 CACAGCCGTCCATCATTTATGT 59.055 45.455 0.00 0.00 33.34 2.29
22 23 3.205338 TCACAGCCGTCCATCATTTATG 58.795 45.455 0.00 0.00 35.15 1.90
23 24 3.558931 TCACAGCCGTCCATCATTTAT 57.441 42.857 0.00 0.00 0.00 1.40
24 25 3.205338 CATCACAGCCGTCCATCATTTA 58.795 45.455 0.00 0.00 0.00 1.40
25 26 2.019249 CATCACAGCCGTCCATCATTT 58.981 47.619 0.00 0.00 0.00 2.32
26 27 1.671979 CATCACAGCCGTCCATCATT 58.328 50.000 0.00 0.00 0.00 2.57
27 28 0.179037 CCATCACAGCCGTCCATCAT 60.179 55.000 0.00 0.00 0.00 2.45
28 29 1.221566 CCATCACAGCCGTCCATCA 59.778 57.895 0.00 0.00 0.00 3.07
29 30 1.524621 CCCATCACAGCCGTCCATC 60.525 63.158 0.00 0.00 0.00 3.51
30 31 1.348008 ATCCCATCACAGCCGTCCAT 61.348 55.000 0.00 0.00 0.00 3.41
31 32 1.971505 GATCCCATCACAGCCGTCCA 61.972 60.000 0.00 0.00 0.00 4.02
32 33 1.227674 GATCCCATCACAGCCGTCC 60.228 63.158 0.00 0.00 0.00 4.79
33 34 1.522092 TGATCCCATCACAGCCGTC 59.478 57.895 0.00 0.00 33.59 4.79
34 35 3.726004 TGATCCCATCACAGCCGT 58.274 55.556 0.00 0.00 33.59 5.68
41 42 0.035152 GTGTGGCAGTGATCCCATCA 60.035 55.000 0.00 0.00 36.84 3.07
42 43 0.254178 AGTGTGGCAGTGATCCCATC 59.746 55.000 0.00 0.00 32.95 3.51
43 44 0.034767 CAGTGTGGCAGTGATCCCAT 60.035 55.000 0.00 0.00 36.99 4.00
44 45 1.376086 CAGTGTGGCAGTGATCCCA 59.624 57.895 0.00 0.00 36.99 4.37
45 46 2.042831 GCAGTGTGGCAGTGATCCC 61.043 63.158 8.01 0.00 36.99 3.85
46 47 2.042831 GGCAGTGTGGCAGTGATCC 61.043 63.158 8.01 0.00 43.14 3.36
47 48 3.583383 GGCAGTGTGGCAGTGATC 58.417 61.111 8.01 0.00 43.14 2.92
54 55 1.007038 CACATTGTGGCAGTGTGGC 60.007 57.895 15.85 0.00 44.53 5.01
65 66 1.522668 CACATCGGTCCACACATTGT 58.477 50.000 0.00 0.00 0.00 2.71
66 67 0.168788 GCACATCGGTCCACACATTG 59.831 55.000 0.00 0.00 0.00 2.82
67 68 1.298157 CGCACATCGGTCCACACATT 61.298 55.000 0.00 0.00 33.78 2.71
68 69 1.741401 CGCACATCGGTCCACACAT 60.741 57.895 0.00 0.00 33.78 3.21
69 70 2.356913 CGCACATCGGTCCACACA 60.357 61.111 0.00 0.00 33.78 3.72
78 79 0.947660 CTCCATCCATCCGCACATCG 60.948 60.000 0.00 0.00 38.08 3.84
79 80 1.233285 GCTCCATCCATCCGCACATC 61.233 60.000 0.00 0.00 0.00 3.06
80 81 1.228063 GCTCCATCCATCCGCACAT 60.228 57.895 0.00 0.00 0.00 3.21
81 82 2.190313 GCTCCATCCATCCGCACA 59.810 61.111 0.00 0.00 0.00 4.57
82 83 1.031571 TTTGCTCCATCCATCCGCAC 61.032 55.000 0.00 0.00 0.00 5.34
83 84 0.323269 TTTTGCTCCATCCATCCGCA 60.323 50.000 0.00 0.00 0.00 5.69
117 118 2.041620 AGGTTTAGCAGCAGATTTGGGA 59.958 45.455 0.00 0.00 0.00 4.37
129 130 1.590525 CGCCGCGATAGGTTTAGCA 60.591 57.895 8.23 0.00 0.00 3.49
163 164 4.401202 GGTCTGTGGTTTTGAGGAGAAAAA 59.599 41.667 0.00 0.00 0.00 1.94
173 174 6.072119 GGAGTTTTATAGGGTCTGTGGTTTTG 60.072 42.308 0.00 0.00 0.00 2.44
269 271 1.227823 TGTGTCTTGGGAAGTGGCG 60.228 57.895 0.00 0.00 0.00 5.69
1035 1042 3.443925 CTGTCCTCGCCGCAGAGA 61.444 66.667 12.07 0.00 40.57 3.10
1158 1168 1.517257 CATGACCTCGTCGCTGTCC 60.517 63.158 10.26 0.00 34.95 4.02
1245 1255 0.397254 TCCAGGAGGACTCGAATCCC 60.397 60.000 9.77 0.85 39.61 3.85
1368 1378 7.574404 GCAACAACCTACCTAGAACCAATTAAC 60.574 40.741 0.00 0.00 0.00 2.01
1462 1472 2.874701 GGATGGTGATGGTGATCGAAAG 59.125 50.000 0.00 0.00 0.00 2.62
1463 1473 2.238395 TGGATGGTGATGGTGATCGAAA 59.762 45.455 0.00 0.00 0.00 3.46
1467 1477 3.287867 AACTGGATGGTGATGGTGATC 57.712 47.619 0.00 0.00 0.00 2.92
1470 1480 2.231964 CCAAAACTGGATGGTGATGGTG 59.768 50.000 0.00 0.00 31.84 4.17
1471 1481 2.528564 CCAAAACTGGATGGTGATGGT 58.471 47.619 0.00 0.00 31.84 3.55
1472 1482 1.205417 GCCAAAACTGGATGGTGATGG 59.795 52.381 0.00 0.00 39.00 3.51
1473 1483 1.205417 GGCCAAAACTGGATGGTGATG 59.795 52.381 0.00 0.00 39.00 3.07
1474 1484 1.203162 TGGCCAAAACTGGATGGTGAT 60.203 47.619 0.61 0.00 39.00 3.06
1475 1485 0.187117 TGGCCAAAACTGGATGGTGA 59.813 50.000 0.61 0.00 39.00 4.02
1476 1486 1.047002 TTGGCCAAAACTGGATGGTG 58.953 50.000 17.98 0.00 39.00 4.17
1477 1487 2.028561 ATTGGCCAAAACTGGATGGT 57.971 45.000 24.71 0.00 39.00 3.55
1478 1488 2.674747 CGAATTGGCCAAAACTGGATGG 60.675 50.000 24.71 2.13 39.80 3.51
1479 1489 2.230992 TCGAATTGGCCAAAACTGGATG 59.769 45.455 24.71 6.85 0.00 3.51
1480 1490 2.524306 TCGAATTGGCCAAAACTGGAT 58.476 42.857 24.71 0.00 0.00 3.41
1481 1491 1.988293 TCGAATTGGCCAAAACTGGA 58.012 45.000 24.71 13.62 0.00 3.86
1482 1492 2.230992 TGATCGAATTGGCCAAAACTGG 59.769 45.455 24.71 11.44 0.00 4.00
1483 1493 3.244976 GTGATCGAATTGGCCAAAACTG 58.755 45.455 24.71 12.87 0.00 3.16
1484 1494 2.231235 GGTGATCGAATTGGCCAAAACT 59.769 45.455 24.71 10.23 0.00 2.66
1485 1495 2.029470 TGGTGATCGAATTGGCCAAAAC 60.029 45.455 24.71 17.75 0.00 2.43
1486 1496 2.242926 TGGTGATCGAATTGGCCAAAA 58.757 42.857 24.71 8.99 0.00 2.44
1487 1497 1.916506 TGGTGATCGAATTGGCCAAA 58.083 45.000 24.71 6.07 0.00 3.28
1488 1498 2.023673 GATGGTGATCGAATTGGCCAA 58.976 47.619 23.00 23.00 0.00 4.52
1489 1499 1.064832 TGATGGTGATCGAATTGGCCA 60.065 47.619 0.00 0.00 0.00 5.36
1490 1500 1.334869 GTGATGGTGATCGAATTGGCC 59.665 52.381 0.00 0.00 0.00 5.36
1503 1513 3.746751 GCTCATTGCTATCTGGTGATGGT 60.747 47.826 0.00 0.00 38.95 3.55
1558 1568 4.643334 GGACAGGTTCCACTTAAAACAAGT 59.357 41.667 0.00 0.00 45.10 3.16
1628 1638 5.310451 GGTCAGTGGTCCAAAATTGTAGTA 58.690 41.667 0.00 0.00 0.00 1.82
1693 1703 6.644347 TGAGATTCTTACTGGGAGATCAAAC 58.356 40.000 0.00 0.00 0.00 2.93
1745 1755 4.122776 GCAATGGTCAGTAACAGATCGAT 58.877 43.478 0.00 0.00 0.00 3.59
1746 1756 3.521560 GCAATGGTCAGTAACAGATCGA 58.478 45.455 0.00 0.00 0.00 3.59
1747 1757 2.282555 CGCAATGGTCAGTAACAGATCG 59.717 50.000 0.00 0.00 0.00 3.69
1761 1771 4.856115 ACAAAAACAAGAAACGCAATGG 57.144 36.364 0.00 0.00 0.00 3.16
1840 1850 2.975732 TGACAGCAAGAGATAGGCAG 57.024 50.000 0.00 0.00 0.00 4.85
1937 1947 9.656040 CAAAATTTATCAAGGGATCATCAAACA 57.344 29.630 0.00 0.00 34.89 2.83
1941 1951 7.664552 AGCAAAATTTATCAAGGGATCATCA 57.335 32.000 0.00 0.00 34.89 3.07
1971 1981 3.973206 AACCTGTCGTACATTCATCCA 57.027 42.857 0.00 0.00 0.00 3.41
2009 2019 5.507985 CCTCTTGATGTTCCTTGGTTCAAAC 60.508 44.000 0.00 0.00 0.00 2.93
2129 2139 1.165270 GCATGTAACTCGGTGGCTTT 58.835 50.000 0.00 0.00 0.00 3.51
2138 2148 1.726791 CGTGACACCAGCATGTAACTC 59.273 52.381 0.00 0.00 32.38 3.01
2198 2208 9.896263 GGTAAAACTTTTGGTTAATTCATCGTA 57.104 29.630 0.00 0.00 37.12 3.43
2206 2223 9.483916 GCAATGTAGGTAAAACTTTTGGTTAAT 57.516 29.630 0.00 0.00 37.12 1.40
2266 2283 1.170442 TGCACATCACAGGAATGCTG 58.830 50.000 0.00 0.00 39.02 4.41
2343 2360 3.011144 TGATTCTCAACAAGCCCCCATAA 59.989 43.478 0.00 0.00 0.00 1.90
2350 2367 2.783135 TGACCTGATTCTCAACAAGCC 58.217 47.619 0.00 0.00 0.00 4.35
2356 2373 1.833630 AGCCGATGACCTGATTCTCAA 59.166 47.619 0.00 0.00 0.00 3.02
2522 2539 1.205064 CTTCTTCACCAACAGCGCG 59.795 57.895 0.00 0.00 0.00 6.86
2546 2563 1.796459 GAAAGGCTCGCGTTGAAGTTA 59.204 47.619 5.77 0.00 0.00 2.24
2809 2844 3.185188 CGTTTCCATGATGATCGATGGAC 59.815 47.826 19.35 12.35 46.33 4.02
2867 2902 1.071699 TGCCCATAATCCTCTAACCGC 59.928 52.381 0.00 0.00 0.00 5.68
2879 2914 3.364549 AGCTTATTGTTGCTGCCCATAA 58.635 40.909 0.00 0.00 38.21 1.90
2881 2916 1.856629 AGCTTATTGTTGCTGCCCAT 58.143 45.000 0.00 0.00 38.21 4.00
2956 2991 8.047310 GGGAGACAAAATTGTATAGAGGAAGAA 58.953 37.037 0.00 0.00 42.43 2.52
2966 3001 6.552008 TGAAGAAGGGGAGACAAAATTGTAT 58.448 36.000 0.00 0.00 42.43 2.29
3003 3038 7.287927 GGAGAAGGGAAAGGGGAAATAAATAAG 59.712 40.741 0.00 0.00 0.00 1.73
3040 3078 9.317827 TCTCTCATATCCACAAAGATATCATCA 57.682 33.333 5.32 0.00 37.35 3.07
3046 3084 8.539117 TTCAGTCTCTCATATCCACAAAGATA 57.461 34.615 0.00 0.00 33.38 1.98
3143 3219 0.037139 TGGAATGCAATGCAGGCAAC 60.037 50.000 18.29 14.66 45.60 4.17
3146 3222 0.459585 CACTGGAATGCAATGCAGGC 60.460 55.000 24.80 7.81 43.65 4.85
3215 3295 3.023832 ACTAATGGAAAAATGGGGAGCG 58.976 45.455 0.00 0.00 0.00 5.03
3310 3559 5.868801 CACCAGAAAAACAAAACACAGACAT 59.131 36.000 0.00 0.00 0.00 3.06
3518 3776 7.394359 TCCAGAAGAAAGAATAATCACTTTGGG 59.606 37.037 0.00 0.00 36.63 4.12
3581 3839 3.119388 TCAAATCATACAGCTGCAAAGCC 60.119 43.478 15.27 0.00 34.90 4.35
3636 3894 2.682352 CACCTTCATTCACACACACACA 59.318 45.455 0.00 0.00 0.00 3.72
3640 3898 2.727123 ACCACCTTCATTCACACACA 57.273 45.000 0.00 0.00 0.00 3.72
3642 3900 2.039746 CCCTACCACCTTCATTCACACA 59.960 50.000 0.00 0.00 0.00 3.72
3660 3918 2.447408 TCAATCAATCATGCTGCCCT 57.553 45.000 0.00 0.00 0.00 5.19
3662 3920 4.202121 ACTCATTCAATCAATCATGCTGCC 60.202 41.667 0.00 0.00 0.00 4.85
3663 3921 4.740205 CACTCATTCAATCAATCATGCTGC 59.260 41.667 0.00 0.00 0.00 5.25
3664 3922 5.891451 ACACTCATTCAATCAATCATGCTG 58.109 37.500 0.00 0.00 0.00 4.41
3665 3923 6.152154 TGAACACTCATTCAATCAATCATGCT 59.848 34.615 0.00 0.00 35.65 3.79


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

AutoCloner maintained by Alex Coulton.