Multiple sequence alignment - TraesCS2D01G149300

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 TraesCS2D01G149300 chr2D 100.000 4435 0 0 1 4435 90717711 90713277 0.000000e+00 8191.0
1 TraesCS2D01G149300 chr2D 89.283 1437 87 24 2323 3745 90506764 90505381 0.000000e+00 1738.0
2 TraesCS2D01G149300 chr2D 88.627 765 49 14 1159 1903 90521301 90520555 0.000000e+00 896.0
3 TraesCS2D01G149300 chr2D 86.642 539 41 15 3811 4334 90505387 90504865 6.440000e-158 568.0
4 TraesCS2D01G149300 chr2D 89.706 340 23 6 1990 2318 90508121 90507783 1.470000e-114 424.0
5 TraesCS2D01G149300 chr2D 91.883 308 14 6 754 1056 90521605 90521304 1.910000e-113 420.0
6 TraesCS2D01G149300 chr2D 88.506 87 7 3 3879 3965 142662456 142662539 7.850000e-18 102.0
7 TraesCS2D01G149300 chr2D 91.228 57 5 0 1 57 506584499 506584443 1.320000e-10 78.7
8 TraesCS2D01G149300 chr2B 96.825 2803 57 13 1172 3951 143776351 143773558 0.000000e+00 4654.0
9 TraesCS2D01G149300 chr2B 90.900 978 56 15 48 1006 143777578 143776615 0.000000e+00 1282.0
10 TraesCS2D01G149300 chr2B 88.462 650 28 14 766 1393 143280439 143279815 0.000000e+00 741.0
11 TraesCS2D01G149300 chr2B 85.431 707 65 17 3182 3864 143278392 143277700 0.000000e+00 701.0
12 TraesCS2D01G149300 chr2B 90.361 498 28 16 3950 4435 143754744 143754255 1.740000e-178 636.0
13 TraesCS2D01G149300 chr2B 82.330 515 54 19 3945 4435 143277557 143277056 3.190000e-111 412.0
14 TraesCS2D01G149300 chr2A 89.669 1936 149 29 1961 3868 90523725 90521813 0.000000e+00 2420.0
15 TraesCS2D01G149300 chr2A 89.426 1967 116 47 765 2681 90427344 90425420 0.000000e+00 2396.0
16 TraesCS2D01G149300 chr2A 94.242 1042 39 11 48 1078 90526244 90525213 0.000000e+00 1572.0
17 TraesCS2D01G149300 chr2A 93.390 469 21 2 3257 3715 90425416 90424948 0.000000e+00 686.0
18 TraesCS2D01G149300 chr2A 89.474 475 28 7 3979 4435 90521666 90521196 8.270000e-162 580.0
19 TraesCS2D01G149300 chr2A 89.953 428 39 4 1478 1903 90524362 90523937 2.330000e-152 549.0
20 TraesCS2D01G149300 chr2A 91.057 369 15 5 1140 1494 90524911 90524547 2.400000e-132 483.0
21 TraesCS2D01G149300 chr2A 97.959 49 1 0 1 49 164618056 164618008 7.900000e-13 86.1
22 TraesCS2D01G149300 chr4D 78.876 587 95 15 2415 2980 505242199 505241621 1.950000e-98 370.0
23 TraesCS2D01G149300 chr4D 83.774 265 34 5 2716 2980 490417351 490417096 4.430000e-60 243.0
24 TraesCS2D01G149300 chr4D 100.000 46 0 0 1 46 163168013 163167968 7.900000e-13 86.1
25 TraesCS2D01G149300 chr5A 78.571 532 87 18 2468 2980 689432071 689431548 4.280000e-85 326.0
26 TraesCS2D01G149300 chr1A 80.603 232 29 11 4086 4304 572020073 572020301 9.870000e-37 165.0
27 TraesCS2D01G149300 chr7B 89.362 94 5 2 3879 3971 153326846 153326935 3.630000e-21 113.0
28 TraesCS2D01G149300 chr4A 88.421 95 5 3 3871 3965 565436119 565436207 4.690000e-20 110.0
29 TraesCS2D01G149300 chr7A 87.500 96 6 2 3871 3966 574129412 574129323 6.070000e-19 106.0
30 TraesCS2D01G149300 chr6D 86.458 96 9 2 3879 3974 338696211 338696120 7.850000e-18 102.0
31 TraesCS2D01G149300 chr6D 100.000 46 0 0 1 46 337917367 337917412 7.900000e-13 86.1
32 TraesCS2D01G149300 chr6D 100.000 46 0 0 1 46 337967723 337967768 7.900000e-13 86.1
33 TraesCS2D01G149300 chr5D 88.506 87 6 2 3879 3965 134916576 134916494 7.850000e-18 102.0
34 TraesCS2D01G149300 chr5D 100.000 46 0 0 1 46 130313548 130313503 7.900000e-13 86.1
35 TraesCS2D01G149300 chr3D 88.506 87 6 2 3879 3965 326696958 326697040 7.850000e-18 102.0
36 TraesCS2D01G149300 chr6A 84.158 101 14 1 3864 3964 511034416 511034318 3.650000e-16 97.1
37 TraesCS2D01G149300 chr7D 82.203 118 11 7 3868 3984 475193965 475193857 4.720000e-15 93.5
38 TraesCS2D01G149300 chr7D 100.000 46 0 0 1 46 215546034 215545989 7.900000e-13 86.1
39 TraesCS2D01G149300 chr1B 92.727 55 4 0 1 55 412909941 412909887 3.680000e-11 80.5
40 TraesCS2D01G149300 chr3A 86.567 67 6 3 1 65 64499720 64499785 2.210000e-08 71.3
41 TraesCS2D01G149300 chr4B 91.304 46 3 1 428 472 139063907 139063862 1.330000e-05 62.1


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 TraesCS2D01G149300 chr2D 90713277 90717711 4434 True 8191.0 8191 100.000000 1 4435 1 chr2D.!!$R1 4434
1 TraesCS2D01G149300 chr2D 90504865 90508121 3256 True 910.0 1738 88.543667 1990 4334 3 chr2D.!!$R3 2344
2 TraesCS2D01G149300 chr2D 90520555 90521605 1050 True 658.0 896 90.255000 754 1903 2 chr2D.!!$R4 1149
3 TraesCS2D01G149300 chr2B 143773558 143777578 4020 True 2968.0 4654 93.862500 48 3951 2 chr2B.!!$R3 3903
4 TraesCS2D01G149300 chr2B 143277056 143280439 3383 True 618.0 741 85.407667 766 4435 3 chr2B.!!$R2 3669
5 TraesCS2D01G149300 chr2A 90424948 90427344 2396 True 1541.0 2396 91.408000 765 3715 2 chr2A.!!$R2 2950
6 TraesCS2D01G149300 chr2A 90521196 90526244 5048 True 1120.8 2420 90.879000 48 4435 5 chr2A.!!$R3 4387
7 TraesCS2D01G149300 chr4D 505241621 505242199 578 True 370.0 370 78.876000 2415 2980 1 chr4D.!!$R3 565
8 TraesCS2D01G149300 chr5A 689431548 689432071 523 True 326.0 326 78.571000 2468 2980 1 chr5A.!!$R1 512

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
185 186 0.698818 AAAGTCCCAGATTCCCGCTT 59.301 50.0 0.00 0.0 0.00 4.68 F
1136 1174 0.518636 CGCTGATCTGGTTGTGTTGG 59.481 55.0 1.46 0.0 0.00 3.77 F
1933 2606 1.078709 ATGAACGCTCAATGTGTCCG 58.921 50.0 0.00 0.0 38.63 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1741 2236 1.901085 CCGTCCCTCTTTCCTCCAG 59.099 63.158 0.0 0.0 0.00 3.86 R
2457 4159 0.986527 TTGCAGAAGAGAGGGCATGA 59.013 50.000 0.0 0.0 35.98 3.07 R
3441 5893 0.902531 CGGAAGAGCTACCCCTTGAA 59.097 55.000 0.0 0.0 0.00 2.69 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
27 28 6.560253 CCATTAACATGGGATTACTGTAGC 57.440 41.667 0.00 0.00 45.99 3.58
28 29 6.299141 CCATTAACATGGGATTACTGTAGCT 58.701 40.000 0.00 0.00 45.99 3.32
29 30 6.772716 CCATTAACATGGGATTACTGTAGCTT 59.227 38.462 0.00 0.00 45.99 3.74
30 31 7.936847 CCATTAACATGGGATTACTGTAGCTTA 59.063 37.037 0.00 0.00 45.99 3.09
31 32 9.337396 CATTAACATGGGATTACTGTAGCTTAA 57.663 33.333 0.00 0.00 0.00 1.85
33 34 9.914834 TTAACATGGGATTACTGTAGCTTAATT 57.085 29.630 0.00 0.00 0.00 1.40
36 37 9.726438 ACATGGGATTACTGTAGCTTAATTATC 57.274 33.333 0.00 0.00 0.00 1.75
37 38 9.167311 CATGGGATTACTGTAGCTTAATTATCC 57.833 37.037 0.00 0.00 0.00 2.59
38 39 7.383687 TGGGATTACTGTAGCTTAATTATCCG 58.616 38.462 0.00 0.00 31.87 4.18
39 40 6.817140 GGGATTACTGTAGCTTAATTATCCGG 59.183 42.308 0.00 0.00 31.87 5.14
40 41 6.817140 GGATTACTGTAGCTTAATTATCCGGG 59.183 42.308 0.00 0.00 0.00 5.73
41 42 4.004196 ACTGTAGCTTAATTATCCGGGC 57.996 45.455 0.00 0.00 0.00 6.13
42 43 2.993899 CTGTAGCTTAATTATCCGGGCG 59.006 50.000 0.00 0.00 0.00 6.13
43 44 2.366266 TGTAGCTTAATTATCCGGGCGT 59.634 45.455 0.00 0.00 0.00 5.68
44 45 2.632987 AGCTTAATTATCCGGGCGTT 57.367 45.000 0.00 0.00 0.00 4.84
45 46 3.756933 AGCTTAATTATCCGGGCGTTA 57.243 42.857 0.00 0.00 0.00 3.18
46 47 4.281898 AGCTTAATTATCCGGGCGTTAT 57.718 40.909 0.00 0.00 0.00 1.89
79 80 0.904865 AACCTCGTGGGATCAGAGCA 60.905 55.000 8.63 0.00 38.76 4.26
99 100 3.675225 GCAGCATAATTTCGCTCTATCGA 59.325 43.478 0.00 0.00 35.96 3.59
129 130 0.748367 CCTCTCCGGTGTCATCGAGA 60.748 60.000 7.17 7.21 0.00 4.04
136 137 2.223805 CCGGTGTCATCGAGATTCATGA 60.224 50.000 7.17 0.00 0.00 3.07
185 186 0.698818 AAAGTCCCAGATTCCCGCTT 59.301 50.000 0.00 0.00 0.00 4.68
229 230 4.503910 TGGAATTCACAAGGAGATACACG 58.496 43.478 7.93 0.00 0.00 4.49
362 372 1.764723 AGCTCATCGATCATCCACCAA 59.235 47.619 0.00 0.00 0.00 3.67
428 439 3.096092 GGCCAAGTTTATCATTGACCCA 58.904 45.455 0.00 0.00 0.00 4.51
626 640 7.326305 CGGAAGATGAAACTAGACATATAACGG 59.674 40.741 0.00 0.00 0.00 4.44
640 656 8.162085 AGACATATAACGGTAAGAGAGGTATCA 58.838 37.037 0.00 0.00 0.00 2.15
832 853 4.772886 ATGGGCCGTTCTACTCTTTTAT 57.227 40.909 0.00 0.00 0.00 1.40
833 854 4.563140 TGGGCCGTTCTACTCTTTTATT 57.437 40.909 0.00 0.00 0.00 1.40
834 855 4.913784 TGGGCCGTTCTACTCTTTTATTT 58.086 39.130 0.00 0.00 0.00 1.40
835 856 5.318630 TGGGCCGTTCTACTCTTTTATTTT 58.681 37.500 0.00 0.00 0.00 1.82
836 857 6.474630 TGGGCCGTTCTACTCTTTTATTTTA 58.525 36.000 0.00 0.00 0.00 1.52
1136 1174 0.518636 CGCTGATCTGGTTGTGTTGG 59.481 55.000 1.46 0.00 0.00 3.77
1138 1407 1.267806 GCTGATCTGGTTGTGTTGGTG 59.732 52.381 1.46 0.00 0.00 4.17
1310 1584 4.020307 TGAGAAACTGCTGATGTGATGGTA 60.020 41.667 0.00 0.00 0.00 3.25
1339 1613 8.814931 CATTTGAGGGATCAGATCTAGAAGTAT 58.185 37.037 10.36 0.00 0.00 2.12
1502 1990 5.879237 TGTGTGTGAACAGAAGATTGTTTC 58.121 37.500 0.00 0.00 41.15 2.78
1504 1992 6.095300 TGTGTGTGAACAGAAGATTGTTTCAT 59.905 34.615 0.00 0.00 41.15 2.57
1599 2088 2.074230 ATTGTTGGTGTGGCAGCACG 62.074 55.000 12.01 0.00 41.66 5.34
1741 2236 5.709164 AGGAATTATAGCCATGCATCACTTC 59.291 40.000 0.00 0.00 0.00 3.01
1743 2238 6.349115 GGAATTATAGCCATGCATCACTTCTG 60.349 42.308 0.00 0.00 0.00 3.02
1831 2334 9.930693 ACTATGGTTGCTAGTTTATAGCTTATC 57.069 33.333 8.24 0.00 40.95 1.75
1852 2355 3.648067 TCTGGTGAATTGACTCTCAAGGT 59.352 43.478 0.00 0.00 40.05 3.50
1932 2605 3.623060 ACATATGAACGCTCAATGTGTCC 59.377 43.478 10.38 0.00 38.63 4.02
1933 2606 1.078709 ATGAACGCTCAATGTGTCCG 58.921 50.000 0.00 0.00 38.63 4.79
2028 2702 6.398234 TGCTGTATTTTAACTTTGCTTGGA 57.602 33.333 0.00 0.00 0.00 3.53
2457 4159 2.307496 TGCACCATTCAGGGACATTT 57.693 45.000 0.00 0.00 43.89 2.32
2493 4203 7.488150 TCTTCTGCAAATTCTGTATGTAGTACG 59.512 37.037 0.00 0.00 36.01 3.67
2527 4240 8.915654 CATTTCTTTTTATACACCTCAACTTGC 58.084 33.333 0.00 0.00 0.00 4.01
2624 4350 1.008938 ACTCATCCCCTAGCTGGTTCT 59.991 52.381 0.00 0.00 0.00 3.01
3278 5730 7.458397 ACCAGTTTCAGAAGTCATTTACCATA 58.542 34.615 0.00 0.00 0.00 2.74
3279 5731 7.942341 ACCAGTTTCAGAAGTCATTTACCATAA 59.058 33.333 0.00 0.00 0.00 1.90
3441 5893 7.989741 CCTACAAGGATGATGACTAGTTTCATT 59.010 37.037 18.14 8.79 37.67 2.57
3507 5968 2.361119 GGATATCCGTTTTGCTTTCCCC 59.639 50.000 5.86 0.00 0.00 4.81
3529 5991 3.938963 CGTGGCTGTAATTCTGGTACAAT 59.061 43.478 0.00 0.00 38.70 2.71
3542 6005 6.032956 TCTGGTACAATCGTCATGTTTACT 57.967 37.500 0.00 0.00 38.70 2.24
3817 6294 7.174946 TGTCCTATGTCAGACCTTTTGAAATTC 59.825 37.037 0.00 0.00 31.76 2.17
3917 6477 5.554822 AAGTGTCGCAGTTTTGAACTAAA 57.445 34.783 0.00 0.00 40.46 1.85
3919 6479 4.634443 AGTGTCGCAGTTTTGAACTAAACT 59.366 37.500 8.14 8.14 46.42 2.66
4034 6597 5.375417 TTGGTGTTGAAGTAGCATTCATG 57.625 39.130 0.61 0.00 38.90 3.07
4196 6773 0.918983 ATCTTTCCCGCCATCCTTGA 59.081 50.000 0.00 0.00 0.00 3.02
4226 6806 1.048601 TGAAGCCAGACCTTTCGACT 58.951 50.000 0.00 0.00 0.00 4.18
4229 6809 1.004440 GCCAGACCTTTCGACTGCT 60.004 57.895 0.00 0.00 0.00 4.24
4250 6830 2.777114 TGGCTGGGCATAGAGTTCAATA 59.223 45.455 0.00 0.00 0.00 1.90
4358 6958 3.307906 TGCTTACGCACCCTCCGT 61.308 61.111 0.00 0.00 42.25 4.69
4403 7008 4.043200 GTTCCTTGTGGCTGCGGC 62.043 66.667 9.72 9.72 37.82 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 7.807977 AAGCTACAGTAATCCCATGTTAATG 57.192 36.000 0.00 0.00 34.37 1.90
7 8 9.914834 AATTAAGCTACAGTAATCCCATGTTAA 57.085 29.630 0.00 0.00 0.00 2.01
10 11 9.726438 GATAATTAAGCTACAGTAATCCCATGT 57.274 33.333 0.00 0.00 0.00 3.21
11 12 9.167311 GGATAATTAAGCTACAGTAATCCCATG 57.833 37.037 0.00 0.00 0.00 3.66
12 13 8.041323 CGGATAATTAAGCTACAGTAATCCCAT 58.959 37.037 0.00 0.00 0.00 4.00
13 14 7.383687 CGGATAATTAAGCTACAGTAATCCCA 58.616 38.462 0.00 0.00 0.00 4.37
14 15 6.817140 CCGGATAATTAAGCTACAGTAATCCC 59.183 42.308 0.00 0.00 0.00 3.85
15 16 6.817140 CCCGGATAATTAAGCTACAGTAATCC 59.183 42.308 0.73 0.00 0.00 3.01
16 17 6.313164 GCCCGGATAATTAAGCTACAGTAATC 59.687 42.308 0.73 0.00 0.00 1.75
17 18 6.171213 GCCCGGATAATTAAGCTACAGTAAT 58.829 40.000 0.73 0.00 0.00 1.89
18 19 5.544650 GCCCGGATAATTAAGCTACAGTAA 58.455 41.667 0.73 0.00 0.00 2.24
19 20 4.321452 CGCCCGGATAATTAAGCTACAGTA 60.321 45.833 0.73 0.00 0.00 2.74
20 21 3.554337 CGCCCGGATAATTAAGCTACAGT 60.554 47.826 0.73 0.00 0.00 3.55
21 22 2.993899 CGCCCGGATAATTAAGCTACAG 59.006 50.000 0.73 0.00 0.00 2.74
22 23 2.366266 ACGCCCGGATAATTAAGCTACA 59.634 45.455 0.73 0.00 0.00 2.74
23 24 3.036075 ACGCCCGGATAATTAAGCTAC 57.964 47.619 0.73 0.00 0.00 3.58
24 25 3.756933 AACGCCCGGATAATTAAGCTA 57.243 42.857 0.73 0.00 0.00 3.32
25 26 2.632987 AACGCCCGGATAATTAAGCT 57.367 45.000 0.73 0.00 0.00 3.74
26 27 5.173664 ACTATAACGCCCGGATAATTAAGC 58.826 41.667 0.73 0.00 0.00 3.09
27 28 6.647895 ACAACTATAACGCCCGGATAATTAAG 59.352 38.462 0.73 0.00 0.00 1.85
28 29 6.424509 CACAACTATAACGCCCGGATAATTAA 59.575 38.462 0.73 0.00 0.00 1.40
29 30 5.927689 CACAACTATAACGCCCGGATAATTA 59.072 40.000 0.73 0.00 0.00 1.40
30 31 4.753107 CACAACTATAACGCCCGGATAATT 59.247 41.667 0.73 0.00 0.00 1.40
31 32 4.202284 ACACAACTATAACGCCCGGATAAT 60.202 41.667 0.73 0.00 0.00 1.28
32 33 3.132646 ACACAACTATAACGCCCGGATAA 59.867 43.478 0.73 0.00 0.00 1.75
33 34 2.694628 ACACAACTATAACGCCCGGATA 59.305 45.455 0.73 0.00 0.00 2.59
34 35 1.483415 ACACAACTATAACGCCCGGAT 59.517 47.619 0.73 0.00 0.00 4.18
35 36 0.896923 ACACAACTATAACGCCCGGA 59.103 50.000 0.73 0.00 0.00 5.14
36 37 1.283736 GACACAACTATAACGCCCGG 58.716 55.000 0.00 0.00 0.00 5.73
37 38 1.924524 CTGACACAACTATAACGCCCG 59.075 52.381 0.00 0.00 0.00 6.13
38 39 2.928116 GACTGACACAACTATAACGCCC 59.072 50.000 0.00 0.00 0.00 6.13
39 40 3.581755 TGACTGACACAACTATAACGCC 58.418 45.455 0.00 0.00 0.00 5.68
40 41 4.143179 GGTTGACTGACACAACTATAACGC 60.143 45.833 0.00 0.00 44.50 4.84
41 42 5.227908 AGGTTGACTGACACAACTATAACG 58.772 41.667 0.00 0.00 44.50 3.18
42 43 5.345202 CGAGGTTGACTGACACAACTATAAC 59.655 44.000 0.00 0.00 44.50 1.89
43 44 5.010314 ACGAGGTTGACTGACACAACTATAA 59.990 40.000 0.00 0.00 44.50 0.98
44 45 4.521639 ACGAGGTTGACTGACACAACTATA 59.478 41.667 0.00 0.00 44.50 1.31
45 46 3.321111 ACGAGGTTGACTGACACAACTAT 59.679 43.478 0.00 0.00 44.50 2.12
46 47 2.691526 ACGAGGTTGACTGACACAACTA 59.308 45.455 0.00 0.00 44.50 2.24
99 100 3.263425 ACACCGGAGAGGAACAATATGTT 59.737 43.478 9.46 0.00 44.37 2.71
129 130 8.571461 AAATATCCACGAGCATATTCATGAAT 57.429 30.769 23.75 23.75 33.67 2.57
136 137 9.593134 GAATCTAGAAATATCCACGAGCATATT 57.407 33.333 0.00 0.00 0.00 1.28
252 253 1.002857 CTTGAATCCCCCTGTCCCTT 58.997 55.000 0.00 0.00 0.00 3.95
331 341 2.216046 TCGATGAGCTTTGATGATGCC 58.784 47.619 0.00 0.00 0.00 4.40
440 451 4.262463 CCTTCCCTACGCATAGCTTTGATA 60.262 45.833 8.49 0.00 0.00 2.15
487 501 5.319453 ACATATGAATCTTGGCCGATCAAT 58.681 37.500 10.38 0.00 0.00 2.57
640 656 8.017418 TCCCAGATGAAACAAAAAGTTACATT 57.983 30.769 0.00 0.00 40.26 2.71
652 668 9.270640 CAAACAATAAAATTCCCAGATGAAACA 57.729 29.630 0.00 0.00 0.00 2.83
743 760 9.855021 CAACAACGATCTTTCCCTTAATATTTT 57.145 29.630 0.00 0.00 0.00 1.82
744 761 7.973944 GCAACAACGATCTTTCCCTTAATATTT 59.026 33.333 0.00 0.00 0.00 1.40
763 780 5.018539 AGGTTCCCTTTTAAAGCAACAAC 57.981 39.130 15.10 8.11 0.00 3.32
802 823 1.654023 GAACGGCCCATTCTTTCCCG 61.654 60.000 0.00 0.00 44.19 5.14
832 853 1.487558 GTAGTCCATCGGCCCCTAAAA 59.512 52.381 0.00 0.00 0.00 1.52
833 854 1.125633 GTAGTCCATCGGCCCCTAAA 58.874 55.000 0.00 0.00 0.00 1.85
834 855 0.031917 TGTAGTCCATCGGCCCCTAA 60.032 55.000 0.00 0.00 0.00 2.69
835 856 0.469331 CTGTAGTCCATCGGCCCCTA 60.469 60.000 0.00 0.00 0.00 3.53
836 857 1.762460 CTGTAGTCCATCGGCCCCT 60.762 63.158 0.00 0.00 0.00 4.79
1094 1123 4.830765 TGCAGATGTACGGGCGCC 62.831 66.667 21.18 21.18 0.00 6.53
1095 1124 3.564027 GTGCAGATGTACGGGCGC 61.564 66.667 0.00 0.00 0.00 6.53
1289 1561 3.430042 ACCATCACATCAGCAGTTTCT 57.570 42.857 0.00 0.00 0.00 2.52
1310 1584 6.329404 TCTAGATCTGATCCCTCAAATGGAT 58.671 40.000 13.83 0.00 45.32 3.41
1339 1613 5.734140 TCCCTAGGTAAAATTCCCAGATTCA 59.266 40.000 8.29 0.00 0.00 2.57
1500 1988 8.352137 AGATGATACAACATCACCAAAATGAA 57.648 30.769 0.00 0.00 46.11 2.57
1502 1990 8.464404 AGAAGATGATACAACATCACCAAAATG 58.536 33.333 0.00 0.00 46.11 2.32
1504 1992 7.148423 CGAGAAGATGATACAACATCACCAAAA 60.148 37.037 0.00 0.00 46.11 2.44
1599 2088 5.856126 TTGAACAATGGAACGTAGATGAC 57.144 39.130 0.00 0.00 0.00 3.06
1741 2236 1.901085 CCGTCCCTCTTTCCTCCAG 59.099 63.158 0.00 0.00 0.00 3.86
1743 2238 2.585153 GCCGTCCCTCTTTCCTCC 59.415 66.667 0.00 0.00 0.00 4.30
1831 2334 4.013267 ACCTTGAGAGTCAATTCACCAG 57.987 45.455 0.00 0.00 35.59 4.00
1852 2355 7.312154 CAAACATAGTAATAACTGCCAGCAAA 58.688 34.615 0.00 0.00 36.36 3.68
1932 2605 5.176958 GCTATAAACCAGCAACCATAGTACG 59.823 44.000 0.00 0.00 38.93 3.67
1933 2606 6.289064 AGCTATAAACCAGCAACCATAGTAC 58.711 40.000 0.00 0.00 41.66 2.73
2249 2935 8.902806 TCAAAACATTTTGTCTCACAAGTCTAT 58.097 29.630 14.95 0.00 45.77 1.98
2321 4021 3.409570 ACTGCTACACTGTCGACTTCTA 58.590 45.455 17.92 0.00 0.00 2.10
2457 4159 0.986527 TTGCAGAAGAGAGGGCATGA 59.013 50.000 0.00 0.00 35.98 3.07
2527 4240 3.561725 GTCTTGGGCCTTCGATTAATGAG 59.438 47.826 4.53 0.00 0.00 2.90
2624 4350 2.877154 AGGAGGATAAGCAGAAGGGA 57.123 50.000 0.00 0.00 0.00 4.20
3226 5678 1.065491 ACAGCACTGGGATCGCAATTA 60.065 47.619 14.01 0.00 34.19 1.40
3278 5730 7.330208 GCAACATCAATTAAACTTGATCAGCTT 59.670 33.333 0.00 0.00 42.52 3.74
3279 5731 6.810182 GCAACATCAATTAAACTTGATCAGCT 59.190 34.615 0.00 0.00 42.52 4.24
3441 5893 0.902531 CGGAAGAGCTACCCCTTGAA 59.097 55.000 0.00 0.00 0.00 2.69
3507 5968 2.967362 TGTACCAGAATTACAGCCACG 58.033 47.619 0.00 0.00 0.00 4.94
3529 5991 3.064207 GTGCCTCAAGTAAACATGACGA 58.936 45.455 0.00 0.00 0.00 4.20
3542 6005 2.363306 ACAATGAACAGGTGCCTCAA 57.637 45.000 0.00 0.00 0.00 3.02
3691 6161 3.432890 GCTCCGGAAGATCTTTTCCAGAT 60.433 47.826 9.87 0.00 45.66 2.90
3883 6443 5.670485 ACTGCGACACTTATTATGGATCAA 58.330 37.500 0.00 0.00 0.00 2.57
3917 6477 2.583143 GCAGTTTTGAACTACCCCAGT 58.417 47.619 0.00 0.00 40.46 4.00
3919 6479 1.141254 TCGCAGTTTTGAACTACCCCA 59.859 47.619 0.00 0.00 40.46 4.96
3920 6480 1.534163 GTCGCAGTTTTGAACTACCCC 59.466 52.381 0.00 0.00 40.46 4.95
3921 6481 2.032290 GTGTCGCAGTTTTGAACTACCC 60.032 50.000 0.00 0.00 40.46 3.69
3922 6482 2.870411 AGTGTCGCAGTTTTGAACTACC 59.130 45.455 0.00 0.00 40.46 3.18
3923 6483 4.531659 AAGTGTCGCAGTTTTGAACTAC 57.468 40.909 0.00 0.00 40.46 2.73
4008 6571 4.685169 ATGCTACTTCAACACCAAATCG 57.315 40.909 0.00 0.00 0.00 3.34
4065 6635 3.139025 AGGGAATGTAATATGCTGGCACT 59.861 43.478 0.00 0.00 0.00 4.40
4154 6725 3.866651 AGCCGGCATGTCTATATCAATC 58.133 45.455 31.54 0.00 0.00 2.67
4196 6773 0.539051 CTGGCTTCAAGGAGGTCGAT 59.461 55.000 0.00 0.00 0.00 3.59
4226 6806 1.565390 AACTCTATGCCCAGCCAGCA 61.565 55.000 0.00 0.00 45.94 4.41
4229 6809 0.991146 TTGAACTCTATGCCCAGCCA 59.009 50.000 0.00 0.00 0.00 4.75
4358 6958 2.868583 CGAGTTCCGAGTAATACCGAGA 59.131 50.000 3.50 0.00 41.76 4.04
4396 7001 1.709147 ATCAATCTTGACGCCGCAGC 61.709 55.000 0.00 0.00 40.49 5.25
4403 7008 5.862924 AACCTGTACAATCAATCTTGACG 57.137 39.130 0.00 0.00 40.49 4.35


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

AutoCloner maintained by Alex Coulton.