Multiple sequence alignment - TraesCS7A01G124600

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 TraesCS7A01G124600 chr7A 100.000 4220 0 0 1 4220 80312909 80317128 0.000000e+00 7793
1 TraesCS7A01G124600 chr7A 90.884 2183 193 3 1190 3372 82155452 82153276 0.000000e+00 2924
2 TraesCS7A01G124600 chr7A 86.650 397 44 4 790 1179 82156791 82156397 8.380000e-117 431
3 TraesCS7A01G124600 chr7A 89.222 334 27 6 3839 4164 82129847 82129515 3.930000e-110 409
4 TraesCS7A01G124600 chr7A 93.939 99 3 2 1 96 323098906 323098808 3.400000e-31 147
5 TraesCS7A01G124600 chr7A 91.509 106 6 3 1 104 634718352 634718248 4.400000e-30 143
6 TraesCS7A01G124600 chr7D 97.632 4138 91 7 86 4219 76396028 76400162 0.000000e+00 7092
7 TraesCS7A01G124600 chr7D 90.168 2319 208 9 1181 3493 79360859 79358555 0.000000e+00 3001
8 TraesCS7A01G124600 chr7D 89.876 1452 147 0 785 2236 79208600 79207149 0.000000e+00 1868
9 TraesCS7A01G124600 chr7D 90.254 985 96 0 785 1769 79265334 79264350 0.000000e+00 1288
10 TraesCS7A01G124600 chr7D 89.362 658 56 10 540 1187 79376635 79375982 0.000000e+00 815
11 TraesCS7A01G124600 chr7D 87.603 605 56 14 3610 4205 79177764 79177170 0.000000e+00 684
12 TraesCS7A01G124600 chr7D 90.435 460 41 2 82 539 25170349 25170807 1.680000e-168 603
13 TraesCS7A01G124600 chr7D 92.571 175 9 4 3787 3958 79358556 79358383 9.060000e-62 248
14 TraesCS7A01G124600 chr7D 86.916 214 22 3 3956 4164 79321590 79321378 7.050000e-58 235
15 TraesCS7A01G124600 chr3B 89.734 2484 238 8 1017 3493 703922187 703924660 0.000000e+00 3158
16 TraesCS7A01G124600 chr3B 90.588 425 32 7 3787 4205 703924659 703925081 1.330000e-154 556
17 TraesCS7A01G124600 chr7B 91.379 2285 186 9 763 3043 26654449 26652172 0.000000e+00 3118
18 TraesCS7A01G124600 chr7B 91.726 423 29 6 3787 4205 26650449 26650029 2.190000e-162 582
19 TraesCS7A01G124600 chr7B 85.135 444 46 10 3050 3493 26650871 26650448 1.800000e-118 436
20 TraesCS7A01G124600 chr2D 81.928 2479 416 24 747 3206 51160418 51157953 0.000000e+00 2067
21 TraesCS7A01G124600 chr2D 82.270 2414 401 23 875 3272 51253154 51255556 0.000000e+00 2061
22 TraesCS7A01G124600 chr2A 81.569 2485 424 25 747 3206 52573402 52570927 0.000000e+00 2021
23 TraesCS7A01G124600 chr2A 81.935 2408 396 32 880 3264 52756527 52758918 0.000000e+00 2001
24 TraesCS7A01G124600 chr2A 81.499 1854 322 18 745 2586 52541074 52539230 0.000000e+00 1504
25 TraesCS7A01G124600 chr2A 89.032 465 48 3 82 544 692020795 692021258 1.320000e-159 573
26 TraesCS7A01G124600 chr2A 97.727 88 2 0 1 88 505832223 505832136 7.310000e-33 152
27 TraesCS7A01G124600 chr2B 81.924 2401 403 26 875 3257 80200438 80202825 0.000000e+00 2001
28 TraesCS7A01G124600 chr4D 90.672 461 40 3 82 540 463709386 463708927 1.000000e-170 610
29 TraesCS7A01G124600 chr4D 89.588 461 45 3 82 540 110324944 110325403 2.190000e-162 582
30 TraesCS7A01G124600 chr1B 90.435 460 39 5 82 539 362303013 362303469 6.040000e-168 601
31 TraesCS7A01G124600 chr6D 90.022 461 42 4 82 540 429215752 429215294 1.010000e-165 593
32 TraesCS7A01G124600 chr6B 89.371 461 46 3 82 540 10233887 10233428 1.020000e-160 577
33 TraesCS7A01G124600 chr4B 89.032 465 47 4 82 544 587005388 587005850 1.320000e-159 573
34 TraesCS7A01G124600 chr6A 97.727 88 2 0 1 88 31308843 31308756 7.310000e-33 152
35 TraesCS7A01G124600 chr6A 97.727 88 2 0 1 88 516278761 516278674 7.310000e-33 152
36 TraesCS7A01G124600 chr4A 97.727 88 2 0 1 88 201783294 201783207 7.310000e-33 152
37 TraesCS7A01G124600 chr1A 93.204 103 6 1 1 103 532839175 532839074 2.630000e-32 150
38 TraesCS7A01G124600 chr5A 94.737 95 5 0 1 95 396051363 396051269 9.450000e-32 148
39 TraesCS7A01G124600 chr5A 92.308 104 5 2 1 102 290440789 290440687 1.220000e-30 145


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 TraesCS7A01G124600 chr7A 80312909 80317128 4219 False 7793.000000 7793 100.000000 1 4220 1 chr7A.!!$F1 4219
1 TraesCS7A01G124600 chr7A 82153276 82156791 3515 True 1677.500000 2924 88.767000 790 3372 2 chr7A.!!$R4 2582
2 TraesCS7A01G124600 chr7D 76396028 76400162 4134 False 7092.000000 7092 97.632000 86 4219 1 chr7D.!!$F2 4133
3 TraesCS7A01G124600 chr7D 79207149 79208600 1451 True 1868.000000 1868 89.876000 785 2236 1 chr7D.!!$R2 1451
4 TraesCS7A01G124600 chr7D 79358383 79360859 2476 True 1624.500000 3001 91.369500 1181 3958 2 chr7D.!!$R6 2777
5 TraesCS7A01G124600 chr7D 79264350 79265334 984 True 1288.000000 1288 90.254000 785 1769 1 chr7D.!!$R3 984
6 TraesCS7A01G124600 chr7D 79375982 79376635 653 True 815.000000 815 89.362000 540 1187 1 chr7D.!!$R5 647
7 TraesCS7A01G124600 chr7D 79177170 79177764 594 True 684.000000 684 87.603000 3610 4205 1 chr7D.!!$R1 595
8 TraesCS7A01G124600 chr3B 703922187 703925081 2894 False 1857.000000 3158 90.161000 1017 4205 2 chr3B.!!$F1 3188
9 TraesCS7A01G124600 chr7B 26650029 26654449 4420 True 1378.666667 3118 89.413333 763 4205 3 chr7B.!!$R1 3442
10 TraesCS7A01G124600 chr2D 51157953 51160418 2465 True 2067.000000 2067 81.928000 747 3206 1 chr2D.!!$R1 2459
11 TraesCS7A01G124600 chr2D 51253154 51255556 2402 False 2061.000000 2061 82.270000 875 3272 1 chr2D.!!$F1 2397
12 TraesCS7A01G124600 chr2A 52570927 52573402 2475 True 2021.000000 2021 81.569000 747 3206 1 chr2A.!!$R2 2459
13 TraesCS7A01G124600 chr2A 52756527 52758918 2391 False 2001.000000 2001 81.935000 880 3264 1 chr2A.!!$F1 2384
14 TraesCS7A01G124600 chr2A 52539230 52541074 1844 True 1504.000000 1504 81.499000 745 2586 1 chr2A.!!$R1 1841
15 TraesCS7A01G124600 chr2B 80200438 80202825 2387 False 2001.000000 2001 81.924000 875 3257 1 chr2B.!!$F1 2382

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
23 24 0.598562 TCACACTCTCCTCTCGTTGC 59.401 55.000 0.0 0.0 0.00 4.17 F
1179 1223 0.531532 CCTCGAATGCAGGCGAAGAT 60.532 55.000 13.6 0.0 35.95 2.40 F
1313 2291 1.445410 CCGATGCCGAACTCGACAA 60.445 57.895 0.0 0.0 43.02 3.18 F
3120 5413 0.389391 CCTTCAGTGTGTCCGTGAGT 59.611 55.000 0.0 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1951 2946 0.737715 GCTTCATTCGTGACGGAGCT 60.738 55.0 4.7 0.0 0.00 4.09 R
2994 3993 0.326264 ATGTTGACTCTGCTGGACCC 59.674 55.0 0.0 0.0 0.00 4.46 R
3123 5416 0.600057 GCTCTTTGCCCAGTTCAAGG 59.400 55.0 0.0 0.0 35.15 3.61 R
4027 6335 5.179555 GTGGAGCCTTGTTACTTTAGACTTG 59.820 44.0 0.0 0.0 0.00 3.16 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
20 21 2.799126 AGATCACACTCTCCTCTCGT 57.201 50.000 0.00 0.00 0.00 4.18
21 22 3.080300 AGATCACACTCTCCTCTCGTT 57.920 47.619 0.00 0.00 0.00 3.85
22 23 2.752354 AGATCACACTCTCCTCTCGTTG 59.248 50.000 0.00 0.00 0.00 4.10
23 24 0.598562 TCACACTCTCCTCTCGTTGC 59.401 55.000 0.00 0.00 0.00 4.17
24 25 0.600557 CACACTCTCCTCTCGTTGCT 59.399 55.000 0.00 0.00 0.00 3.91
25 26 1.813178 CACACTCTCCTCTCGTTGCTA 59.187 52.381 0.00 0.00 0.00 3.49
26 27 2.425312 CACACTCTCCTCTCGTTGCTAT 59.575 50.000 0.00 0.00 0.00 2.97
27 28 2.425312 ACACTCTCCTCTCGTTGCTATG 59.575 50.000 0.00 0.00 0.00 2.23
28 29 1.407258 ACTCTCCTCTCGTTGCTATGC 59.593 52.381 0.00 0.00 0.00 3.14
29 30 1.406898 CTCTCCTCTCGTTGCTATGCA 59.593 52.381 0.00 0.00 36.47 3.96
30 31 2.034878 TCTCCTCTCGTTGCTATGCAT 58.965 47.619 3.79 3.79 38.76 3.96
31 32 2.035193 TCTCCTCTCGTTGCTATGCATC 59.965 50.000 0.19 0.00 38.76 3.91
32 33 1.756538 TCCTCTCGTTGCTATGCATCA 59.243 47.619 0.19 0.00 38.76 3.07
33 34 1.863454 CCTCTCGTTGCTATGCATCAC 59.137 52.381 0.19 0.00 38.76 3.06
34 35 1.863454 CTCTCGTTGCTATGCATCACC 59.137 52.381 0.19 0.00 38.76 4.02
35 36 1.206849 TCTCGTTGCTATGCATCACCA 59.793 47.619 0.19 0.00 38.76 4.17
36 37 2.158914 TCTCGTTGCTATGCATCACCAT 60.159 45.455 0.19 0.00 38.76 3.55
37 38 1.941975 TCGTTGCTATGCATCACCATG 59.058 47.619 0.19 0.00 38.76 3.66
38 39 1.941975 CGTTGCTATGCATCACCATGA 59.058 47.619 0.19 0.00 38.76 3.07
39 40 2.551032 CGTTGCTATGCATCACCATGAT 59.449 45.455 0.19 0.00 38.76 2.45
40 41 3.364664 CGTTGCTATGCATCACCATGATC 60.365 47.826 0.19 0.00 38.76 2.92
41 42 3.782656 TGCTATGCATCACCATGATCT 57.217 42.857 0.19 0.00 34.28 2.75
42 43 4.094830 TGCTATGCATCACCATGATCTT 57.905 40.909 0.19 0.00 34.28 2.40
43 44 3.818773 TGCTATGCATCACCATGATCTTG 59.181 43.478 0.19 1.60 34.28 3.02
44 45 3.366070 GCTATGCATCACCATGATCTTGC 60.366 47.826 0.19 0.00 34.28 4.01
45 46 2.131776 TGCATCACCATGATCTTGCA 57.868 45.000 3.07 8.61 37.51 4.08
46 47 2.661718 TGCATCACCATGATCTTGCAT 58.338 42.857 3.07 0.00 35.67 3.96
47 48 2.360801 TGCATCACCATGATCTTGCATG 59.639 45.455 3.07 0.00 44.05 4.06
48 49 2.361119 GCATCACCATGATCTTGCATGT 59.639 45.455 3.07 0.00 43.16 3.21
49 50 3.795488 GCATCACCATGATCTTGCATGTG 60.795 47.826 3.07 6.61 43.16 3.21
50 51 1.746787 TCACCATGATCTTGCATGTGC 59.253 47.619 3.07 0.00 43.16 4.57
51 52 0.736636 ACCATGATCTTGCATGTGCG 59.263 50.000 3.07 0.00 43.16 5.34
52 53 0.736636 CCATGATCTTGCATGTGCGT 59.263 50.000 3.07 0.00 43.16 5.24
53 54 1.941975 CCATGATCTTGCATGTGCGTA 59.058 47.619 3.07 0.00 43.16 4.42
54 55 2.032290 CCATGATCTTGCATGTGCGTAG 60.032 50.000 3.07 1.03 43.16 3.51
55 56 1.655484 TGATCTTGCATGTGCGTAGG 58.345 50.000 0.01 0.00 45.83 3.18
56 57 1.206849 TGATCTTGCATGTGCGTAGGA 59.793 47.619 0.01 0.00 45.83 2.94
57 58 2.279741 GATCTTGCATGTGCGTAGGAA 58.720 47.619 0.01 0.00 45.83 3.36
58 59 2.177394 TCTTGCATGTGCGTAGGAAA 57.823 45.000 0.01 0.00 45.83 3.13
59 60 2.499197 TCTTGCATGTGCGTAGGAAAA 58.501 42.857 0.01 0.00 45.83 2.29
60 61 3.081061 TCTTGCATGTGCGTAGGAAAAT 58.919 40.909 0.01 0.00 45.83 1.82
61 62 3.505680 TCTTGCATGTGCGTAGGAAAATT 59.494 39.130 0.01 0.00 45.83 1.82
62 63 3.932545 TGCATGTGCGTAGGAAAATTT 57.067 38.095 0.01 0.00 45.83 1.82
63 64 4.250116 TGCATGTGCGTAGGAAAATTTT 57.750 36.364 2.28 2.28 45.83 1.82
64 65 3.986572 TGCATGTGCGTAGGAAAATTTTG 59.013 39.130 8.47 0.00 45.83 2.44
65 66 4.233789 GCATGTGCGTAGGAAAATTTTGA 58.766 39.130 8.47 0.00 0.00 2.69
66 67 4.683781 GCATGTGCGTAGGAAAATTTTGAA 59.316 37.500 8.47 0.00 0.00 2.69
67 68 5.176590 GCATGTGCGTAGGAAAATTTTGAAA 59.823 36.000 8.47 0.00 0.00 2.69
68 69 6.128580 GCATGTGCGTAGGAAAATTTTGAAAT 60.129 34.615 8.47 0.00 0.00 2.17
69 70 7.571059 GCATGTGCGTAGGAAAATTTTGAAATT 60.571 33.333 8.47 0.00 40.15 1.82
70 71 8.920665 CATGTGCGTAGGAAAATTTTGAAATTA 58.079 29.630 8.47 0.00 37.62 1.40
71 72 8.288217 TGTGCGTAGGAAAATTTTGAAATTAC 57.712 30.769 8.47 3.20 37.62 1.89
72 73 8.138712 TGTGCGTAGGAAAATTTTGAAATTACT 58.861 29.630 8.47 0.00 37.62 2.24
73 74 9.615295 GTGCGTAGGAAAATTTTGAAATTACTA 57.385 29.630 8.47 0.00 37.62 1.82
74 75 9.615295 TGCGTAGGAAAATTTTGAAATTACTAC 57.385 29.630 8.47 17.54 37.62 2.73
75 76 9.615295 GCGTAGGAAAATTTTGAAATTACTACA 57.385 29.630 21.89 0.00 38.47 2.74
84 85 9.719355 AATTTTGAAATTACTACATTCCCCAAC 57.281 29.630 0.05 0.00 36.88 3.77
141 142 4.051237 GGTGCCTTCAAATCTTGACAAAC 58.949 43.478 0.00 0.00 39.87 2.93
147 148 6.572519 CCTTCAAATCTTGACAAACTTTGGA 58.427 36.000 16.29 10.53 39.87 3.53
196 197 6.096673 AGAGAAAGAAAACAGAGAGGAGAC 57.903 41.667 0.00 0.00 0.00 3.36
202 203 3.669251 AAACAGAGAGGAGACGAAAGG 57.331 47.619 0.00 0.00 0.00 3.11
204 205 1.075698 ACAGAGAGGAGACGAAAGGGA 59.924 52.381 0.00 0.00 0.00 4.20
210 211 3.841255 AGAGGAGACGAAAGGGAAAGAAT 59.159 43.478 0.00 0.00 0.00 2.40
287 288 5.105228 TGGTTATACGAACCAGGACTAAAGG 60.105 44.000 5.05 0.00 44.74 3.11
288 289 5.105187 GGTTATACGAACCAGGACTAAAGGT 60.105 44.000 0.00 0.00 40.03 3.50
290 291 2.322658 ACGAACCAGGACTAAAGGTGA 58.677 47.619 0.00 0.00 35.42 4.02
389 394 2.426024 CTCTTTAGTCCCGATTCGTGGA 59.574 50.000 10.91 10.91 0.00 4.02
415 420 2.295885 CCGGTACTAGAGGTTCGACAT 58.704 52.381 0.00 0.00 0.00 3.06
433 438 2.838202 ACATGAACCGGGACTAATGAGT 59.162 45.455 6.32 0.00 39.20 3.41
459 464 2.975536 CCTAGCCGTTGGAACCGA 59.024 61.111 0.00 0.00 0.00 4.69
492 497 4.634004 TCACATTAGTGCCGGTTCATTTAG 59.366 41.667 1.90 0.00 45.49 1.85
501 506 1.741145 CGGTTCATTTAGAAACCGGGG 59.259 52.381 16.66 0.00 41.01 5.73
555 560 8.753133 TCTACTAGTGTCACTTGATTTCATCAT 58.247 33.333 19.40 0.00 39.39 2.45
558 563 9.071276 ACTAGTGTCACTTGATTTCATCATTTT 57.929 29.630 19.40 0.00 39.39 1.82
724 732 7.007313 GTATTTACGAACATCGGGAAAATCA 57.993 36.000 4.66 0.00 45.59 2.57
756 768 4.920245 CCCCAATCCCGCCCCATG 62.920 72.222 0.00 0.00 0.00 3.66
956 981 3.057104 ACGCGGTATCGATCATATTCCAA 60.057 43.478 12.47 0.00 39.00 3.53
994 1021 2.591429 TGTTCCTGTGTGCGGCTG 60.591 61.111 0.00 0.00 0.00 4.85
1179 1223 0.531532 CCTCGAATGCAGGCGAAGAT 60.532 55.000 13.60 0.00 35.95 2.40
1313 2291 1.445410 CCGATGCCGAACTCGACAA 60.445 57.895 0.00 0.00 43.02 3.18
1341 2319 2.912025 AAGCCAGGGTTTGTGCGG 60.912 61.111 0.00 0.00 0.00 5.69
1620 2604 2.292292 TCATGACTCTGACGACGAACAA 59.708 45.455 0.00 0.00 0.00 2.83
1893 2888 1.497991 TATCTATTGGCGCGTTCAGC 58.502 50.000 8.43 0.00 43.95 4.26
1951 2946 1.790755 CAACAACGGTCCGATTCAGA 58.209 50.000 20.51 0.00 0.00 3.27
2150 3145 7.330946 GCGGTACTGCAATTATGACTATGATAA 59.669 37.037 21.95 0.00 34.15 1.75
2360 3356 2.545952 CCCTCATAGCTTACATCGCGTT 60.546 50.000 5.77 0.00 0.00 4.84
2757 3756 2.913578 TACGACACAGGTGCCGGT 60.914 61.111 12.51 4.80 40.76 5.28
2770 3769 2.757056 GCCGGTCATGTAAACCCGC 61.757 63.158 1.90 0.00 39.12 6.13
2958 3957 2.845752 TAACCGTGCCGCTCACATCC 62.846 60.000 6.75 0.00 45.92 3.51
2994 3993 3.064682 TGAACCGAACTGTGACAAATGTG 59.935 43.478 0.00 0.00 0.00 3.21
3120 5413 0.389391 CCTTCAGTGTGTCCGTGAGT 59.611 55.000 0.00 0.00 0.00 3.41
3123 5416 0.596577 TCAGTGTGTCCGTGAGTAGC 59.403 55.000 0.00 0.00 0.00 3.58
3372 5670 5.500645 ACAAGAATGTGCATCATCTCATG 57.499 39.130 0.00 3.29 38.69 3.07
3393 5691 3.627123 TGTGTACCAATACATGATGCTGC 59.373 43.478 0.00 0.00 43.21 5.25
3509 5811 5.880332 GTGTCTGTATGTAATCACCACCATT 59.120 40.000 0.00 0.00 0.00 3.16
3517 5819 1.075601 ATCACCACCATTCCACCACT 58.924 50.000 0.00 0.00 0.00 4.00
3758 6061 5.164620 TGGATTCAAGCTCAGTTGTGATA 57.835 39.130 0.00 0.00 30.18 2.15
3929 6234 6.952773 TTGTAGCATGGTAAACTTCAAAGT 57.047 33.333 6.12 0.00 42.04 2.66
4027 6335 6.610741 CAGAACTGCCACTATCTAAATTCC 57.389 41.667 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.916359 ACGAGAGGAGAGTGTGATCTA 57.084 47.619 0.00 0.00 0.00 1.98
1 2 2.752354 CAACGAGAGGAGAGTGTGATCT 59.248 50.000 0.00 0.00 0.00 2.75
3 4 1.203523 GCAACGAGAGGAGAGTGTGAT 59.796 52.381 0.00 0.00 0.00 3.06
5 6 0.600557 AGCAACGAGAGGAGAGTGTG 59.399 55.000 0.00 0.00 0.00 3.82
6 7 2.201921 TAGCAACGAGAGGAGAGTGT 57.798 50.000 0.00 0.00 0.00 3.55
7 8 2.797792 GCATAGCAACGAGAGGAGAGTG 60.798 54.545 0.00 0.00 0.00 3.51
8 9 1.407258 GCATAGCAACGAGAGGAGAGT 59.593 52.381 0.00 0.00 0.00 3.24
9 10 1.406898 TGCATAGCAACGAGAGGAGAG 59.593 52.381 0.00 0.00 34.76 3.20
10 11 1.474330 TGCATAGCAACGAGAGGAGA 58.526 50.000 0.00 0.00 34.76 3.71
11 12 2.223900 TGATGCATAGCAACGAGAGGAG 60.224 50.000 0.00 0.00 43.62 3.69
12 13 1.756538 TGATGCATAGCAACGAGAGGA 59.243 47.619 0.00 0.00 43.62 3.71
13 14 1.863454 GTGATGCATAGCAACGAGAGG 59.137 52.381 0.00 0.00 43.62 3.69
14 15 1.863454 GGTGATGCATAGCAACGAGAG 59.137 52.381 0.00 0.00 43.62 3.20
15 16 1.206849 TGGTGATGCATAGCAACGAGA 59.793 47.619 0.00 0.00 43.62 4.04
16 17 1.655484 TGGTGATGCATAGCAACGAG 58.345 50.000 0.00 0.00 43.62 4.18
17 18 1.941975 CATGGTGATGCATAGCAACGA 59.058 47.619 0.00 0.00 43.62 3.85
18 19 1.941975 TCATGGTGATGCATAGCAACG 59.058 47.619 0.00 1.35 43.62 4.10
19 20 3.819337 AGATCATGGTGATGCATAGCAAC 59.181 43.478 0.00 0.00 43.62 4.17
20 21 4.094830 AGATCATGGTGATGCATAGCAA 57.905 40.909 0.00 0.00 43.62 3.91
21 22 3.782656 AGATCATGGTGATGCATAGCA 57.217 42.857 0.00 4.86 44.86 3.49
22 23 3.366070 GCAAGATCATGGTGATGCATAGC 60.366 47.826 0.00 0.00 37.20 2.97
23 24 3.818773 TGCAAGATCATGGTGATGCATAG 59.181 43.478 10.42 0.00 35.67 2.23
24 25 3.822940 TGCAAGATCATGGTGATGCATA 58.177 40.909 10.42 0.00 35.67 3.14
25 26 2.661718 TGCAAGATCATGGTGATGCAT 58.338 42.857 10.42 0.00 35.67 3.96
26 27 2.131776 TGCAAGATCATGGTGATGCA 57.868 45.000 10.42 10.42 37.51 3.96
27 28 2.361119 ACATGCAAGATCATGGTGATGC 59.639 45.455 5.77 5.77 46.02 3.91
28 29 3.795488 GCACATGCAAGATCATGGTGATG 60.795 47.826 9.18 0.66 46.02 3.07
29 30 2.361119 GCACATGCAAGATCATGGTGAT 59.639 45.455 9.18 0.00 46.02 3.06
30 31 1.746787 GCACATGCAAGATCATGGTGA 59.253 47.619 9.18 0.00 46.02 4.02
31 32 1.533129 CGCACATGCAAGATCATGGTG 60.533 52.381 4.49 1.26 46.02 4.17
32 33 0.736636 CGCACATGCAAGATCATGGT 59.263 50.000 4.49 0.00 46.02 3.55
33 34 0.736636 ACGCACATGCAAGATCATGG 59.263 50.000 4.49 0.00 46.02 3.66
34 35 2.032290 CCTACGCACATGCAAGATCATG 60.032 50.000 4.49 0.00 46.86 3.07
35 36 2.158914 TCCTACGCACATGCAAGATCAT 60.159 45.455 4.49 0.00 42.21 2.45
36 37 1.206849 TCCTACGCACATGCAAGATCA 59.793 47.619 4.49 0.00 42.21 2.92
37 38 1.939974 TCCTACGCACATGCAAGATC 58.060 50.000 4.49 0.00 42.21 2.75
38 39 2.401583 TTCCTACGCACATGCAAGAT 57.598 45.000 4.49 0.00 42.21 2.40
39 40 2.177394 TTTCCTACGCACATGCAAGA 57.823 45.000 4.49 0.00 42.21 3.02
40 41 2.987413 TTTTCCTACGCACATGCAAG 57.013 45.000 4.49 0.69 42.21 4.01
41 42 3.932545 AATTTTCCTACGCACATGCAA 57.067 38.095 4.49 0.00 42.21 4.08
42 43 3.932545 AAATTTTCCTACGCACATGCA 57.067 38.095 4.49 0.00 42.21 3.96
43 44 4.233789 TCAAAATTTTCCTACGCACATGC 58.766 39.130 0.00 0.00 37.78 4.06
44 45 6.761731 TTTCAAAATTTTCCTACGCACATG 57.238 33.333 0.00 0.00 0.00 3.21
45 46 7.961325 AATTTCAAAATTTTCCTACGCACAT 57.039 28.000 0.00 0.00 35.16 3.21
46 47 8.138712 AGTAATTTCAAAATTTTCCTACGCACA 58.861 29.630 0.00 0.00 39.24 4.57
47 48 8.515473 AGTAATTTCAAAATTTTCCTACGCAC 57.485 30.769 0.00 0.00 39.24 5.34
48 49 9.615295 GTAGTAATTTCAAAATTTTCCTACGCA 57.385 29.630 0.00 0.00 39.24 5.24
49 50 9.615295 TGTAGTAATTTCAAAATTTTCCTACGC 57.385 29.630 0.00 0.09 39.24 4.42
58 59 9.719355 GTTGGGGAATGTAGTAATTTCAAAATT 57.281 29.630 6.04 6.04 41.24 1.82
59 60 8.875168 TGTTGGGGAATGTAGTAATTTCAAAAT 58.125 29.630 0.00 0.00 0.00 1.82
60 61 8.251383 TGTTGGGGAATGTAGTAATTTCAAAA 57.749 30.769 0.00 0.00 0.00 2.44
61 62 7.507616 ACTGTTGGGGAATGTAGTAATTTCAAA 59.492 33.333 0.00 0.00 0.00 2.69
62 63 7.007723 ACTGTTGGGGAATGTAGTAATTTCAA 58.992 34.615 0.00 0.00 0.00 2.69
63 64 6.548321 ACTGTTGGGGAATGTAGTAATTTCA 58.452 36.000 0.00 0.00 0.00 2.69
64 65 7.362660 GGAACTGTTGGGGAATGTAGTAATTTC 60.363 40.741 0.00 0.00 0.00 2.17
65 66 6.436218 GGAACTGTTGGGGAATGTAGTAATTT 59.564 38.462 0.00 0.00 0.00 1.82
66 67 5.949952 GGAACTGTTGGGGAATGTAGTAATT 59.050 40.000 0.00 0.00 0.00 1.40
67 68 5.253096 AGGAACTGTTGGGGAATGTAGTAAT 59.747 40.000 0.00 0.00 37.18 1.89
68 69 4.600111 AGGAACTGTTGGGGAATGTAGTAA 59.400 41.667 0.00 0.00 37.18 2.24
69 70 4.172807 AGGAACTGTTGGGGAATGTAGTA 58.827 43.478 0.00 0.00 37.18 1.82
70 71 2.986728 AGGAACTGTTGGGGAATGTAGT 59.013 45.455 0.00 0.00 37.18 2.73
71 72 3.721087 AGGAACTGTTGGGGAATGTAG 57.279 47.619 0.00 0.00 37.18 2.74
72 73 4.263594 GGTTAGGAACTGTTGGGGAATGTA 60.264 45.833 0.00 0.00 41.52 2.29
73 74 3.499745 GGTTAGGAACTGTTGGGGAATGT 60.500 47.826 0.00 0.00 41.52 2.71
74 75 3.089284 GGTTAGGAACTGTTGGGGAATG 58.911 50.000 0.00 0.00 41.52 2.67
75 76 2.993863 AGGTTAGGAACTGTTGGGGAAT 59.006 45.455 0.00 0.00 41.52 3.01
76 77 2.424793 AGGTTAGGAACTGTTGGGGAA 58.575 47.619 0.00 0.00 41.52 3.97
77 78 2.127651 AGGTTAGGAACTGTTGGGGA 57.872 50.000 0.00 0.00 41.52 4.81
78 79 2.890945 CAAAGGTTAGGAACTGTTGGGG 59.109 50.000 0.00 0.00 41.52 4.96
79 80 3.317993 CACAAAGGTTAGGAACTGTTGGG 59.682 47.826 0.00 3.46 41.52 4.12
80 81 4.204012 TCACAAAGGTTAGGAACTGTTGG 58.796 43.478 0.00 0.00 41.52 3.77
81 82 5.530915 TGATCACAAAGGTTAGGAACTGTTG 59.469 40.000 0.00 0.00 41.52 3.33
82 83 5.531287 GTGATCACAAAGGTTAGGAACTGTT 59.469 40.000 21.07 0.00 41.52 3.16
83 84 5.063880 GTGATCACAAAGGTTAGGAACTGT 58.936 41.667 21.07 0.00 41.52 3.55
84 85 5.308825 AGTGATCACAAAGGTTAGGAACTG 58.691 41.667 27.02 0.00 41.52 3.16
154 155 0.843309 TCCTCTCGAGCTCATCCTCT 59.157 55.000 15.40 0.00 0.00 3.69
196 197 5.017294 AGCTCTCTATTCTTTCCCTTTCG 57.983 43.478 0.00 0.00 0.00 3.46
202 203 2.547007 GCCCGAGCTCTCTATTCTTTCC 60.547 54.545 12.85 0.00 35.50 3.13
204 205 2.900716 GCCCGAGCTCTCTATTCTTT 57.099 50.000 12.85 0.00 35.50 2.52
225 226 9.566331 AGATCATCCTATATAAACCCTTCATCA 57.434 33.333 0.00 0.00 0.00 3.07
277 278 5.022122 GGTACTAGGTTCACCTTTAGTCCT 58.978 45.833 3.18 0.00 46.09 3.85
306 311 1.546589 TTAGTCCCGGTTCGTGGCAT 61.547 55.000 0.00 0.00 0.00 4.40
389 394 2.206576 ACCTCTAGTACCGGTTCGTT 57.793 50.000 15.04 0.00 0.00 3.85
410 415 2.159156 TCATTAGTCCCGGTTCATGTCG 60.159 50.000 0.00 0.00 0.00 4.35
415 420 2.232941 GACACTCATTAGTCCCGGTTCA 59.767 50.000 0.00 0.00 31.97 3.18
492 497 2.405143 GCTCATTAGCCCCGGTTTC 58.595 57.895 0.00 0.00 43.40 2.78
501 506 6.292150 AGGACCTAATGTTTAGCTCATTAGC 58.708 40.000 20.53 12.19 46.17 3.09
683 691 7.979037 CGTAAATACGCACACTGTAATACTAG 58.021 38.462 0.00 0.00 43.14 2.57
684 692 7.897153 CGTAAATACGCACACTGTAATACTA 57.103 36.000 0.00 0.00 43.14 1.82
685 693 6.801367 CGTAAATACGCACACTGTAATACT 57.199 37.500 0.00 0.00 43.14 2.12
724 732 3.181282 GGGGGCAGGGTCTCTTTT 58.819 61.111 0.00 0.00 0.00 2.27
756 768 4.657039 TGGGTAATGTATCTACCTGGGTTC 59.343 45.833 0.00 0.00 39.11 3.62
899 923 6.573434 TGGCACAAACAATTAATGTGTTGTA 58.427 32.000 14.95 0.00 44.79 2.41
956 981 4.264083 ACACAAGGAAGATGATGGGAATGT 60.264 41.667 0.00 0.00 0.00 2.71
1195 2173 4.668431 CGATGTCGACAAGAAAGACTCGTA 60.668 45.833 24.13 0.00 43.02 3.43
1313 2291 1.763770 CCTGGCTTCTTGGACACCT 59.236 57.895 0.00 0.00 0.00 4.00
1341 2319 1.883021 CGTTTGGTCTGGGAATGCC 59.117 57.895 0.00 0.00 0.00 4.40
1620 2604 1.228552 GGTGTGTGTTCCATGCCCT 60.229 57.895 0.00 0.00 0.00 5.19
1951 2946 0.737715 GCTTCATTCGTGACGGAGCT 60.738 55.000 4.70 0.00 0.00 4.09
2150 3145 4.530161 GGAGGATCTTACCAGTGATGCTAT 59.470 45.833 0.00 0.00 40.54 2.97
2360 3356 3.243535 CGCCATAGAGCTATTGTCTGTCA 60.244 47.826 0.00 0.00 0.00 3.58
2434 3430 0.966370 CCCCGAGAAGAGAACGAGGT 60.966 60.000 0.00 0.00 0.00 3.85
2757 3756 1.948611 GCTCTTGGCGGGTTTACATGA 60.949 52.381 0.00 0.00 0.00 3.07
2770 3769 3.710722 AGGGTCGGCAGCTCTTGG 61.711 66.667 0.00 0.00 0.00 3.61
2958 3957 1.660052 CGGTTCACAGTGAATTGCGTG 60.660 52.381 19.04 2.78 38.79 5.34
2994 3993 0.326264 ATGTTGACTCTGCTGGACCC 59.674 55.000 0.00 0.00 0.00 4.46
3123 5416 0.600057 GCTCTTTGCCCAGTTCAAGG 59.400 55.000 0.00 0.00 35.15 3.61
3372 5670 3.627123 TGCAGCATCATGTATTGGTACAC 59.373 43.478 0.00 0.00 43.21 2.90
3509 5811 1.913419 GAATGGGGAAGTAGTGGTGGA 59.087 52.381 0.00 0.00 0.00 4.02
3517 5819 1.856920 GGAATGGGGAATGGGGAAGTA 59.143 52.381 0.00 0.00 0.00 2.24
3758 6061 3.806949 TCCAGTAAAACCAGCCAATCT 57.193 42.857 0.00 0.00 0.00 2.40
4027 6335 5.179555 GTGGAGCCTTGTTACTTTAGACTTG 59.820 44.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.