Multiple sequence alignment - TraesCS5B01G297200

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 TraesCS5B01G297200 chr5B 100.000 2450 0 0 1 2450 479887183 479889632 0 4525
1 TraesCS5B01G297200 chr5B 90.305 1506 134 10 66 1561 38469418 38467915 0 1962
2 TraesCS5B01G297200 chr1B 91.744 1502 110 9 66 1558 599204157 599205653 0 2074
3 TraesCS5B01G297200 chr1D 91.218 1503 121 10 67 1561 468701518 468700019 0 2034
4 TraesCS5B01G297200 chr1D 94.754 896 47 0 1553 2448 45806245 45807140 0 1395
5 TraesCS5B01G297200 chr2A 90.696 1494 128 9 66 1553 709826712 709825224 0 1978
6 TraesCS5B01G297200 chr3A 90.546 1502 126 14 66 1558 58871768 58873262 0 1973
7 TraesCS5B01G297200 chr3A 94.978 896 45 0 1553 2448 58874387 58875282 0 1406
8 TraesCS5B01G297200 chr3B 90.333 1500 131 11 69 1558 485694904 485696399 0 1954
9 TraesCS5B01G297200 chr7B 90.247 1497 132 9 66 1558 687332179 687333665 0 1943
10 TraesCS5B01G297200 chr1A 90.013 1512 136 12 66 1567 281368079 281369585 0 1941
11 TraesCS5B01G297200 chr7A 89.894 1504 138 11 66 1558 26583398 26584898 0 1923
12 TraesCS5B01G297200 chr7A 95.647 896 39 0 1553 2448 435932324 435933219 0 1439
13 TraesCS5B01G297200 chr6B 95.424 896 41 0 1553 2448 55728570 55727675 0 1428
14 TraesCS5B01G297200 chr6B 95.312 896 42 0 1553 2448 623349281 623348386 0 1423
15 TraesCS5B01G297200 chr6B 95.089 896 44 0 1553 2448 624464320 624465215 0 1411
16 TraesCS5B01G297200 chr4D 95.424 896 41 0 1553 2448 467592735 467593630 0 1428
17 TraesCS5B01G297200 chr4B 95.095 897 43 1 1553 2448 13938689 13939585 0 1411
18 TraesCS5B01G297200 chr5A 94.883 899 45 1 1553 2450 391984439 391983541 0 1404


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 TraesCS5B01G297200 chr5B 479887183 479889632 2449 False 4525.0 4525 100.000 1 2450 1 chr5B.!!$F1 2449
1 TraesCS5B01G297200 chr5B 38467915 38469418 1503 True 1962.0 1962 90.305 66 1561 1 chr5B.!!$R1 1495
2 TraesCS5B01G297200 chr1B 599204157 599205653 1496 False 2074.0 2074 91.744 66 1558 1 chr1B.!!$F1 1492
3 TraesCS5B01G297200 chr1D 468700019 468701518 1499 True 2034.0 2034 91.218 67 1561 1 chr1D.!!$R1 1494
4 TraesCS5B01G297200 chr1D 45806245 45807140 895 False 1395.0 1395 94.754 1553 2448 1 chr1D.!!$F1 895
5 TraesCS5B01G297200 chr2A 709825224 709826712 1488 True 1978.0 1978 90.696 66 1553 1 chr2A.!!$R1 1487
6 TraesCS5B01G297200 chr3A 58871768 58875282 3514 False 1689.5 1973 92.762 66 2448 2 chr3A.!!$F1 2382
7 TraesCS5B01G297200 chr3B 485694904 485696399 1495 False 1954.0 1954 90.333 69 1558 1 chr3B.!!$F1 1489
8 TraesCS5B01G297200 chr7B 687332179 687333665 1486 False 1943.0 1943 90.247 66 1558 1 chr7B.!!$F1 1492
9 TraesCS5B01G297200 chr1A 281368079 281369585 1506 False 1941.0 1941 90.013 66 1567 1 chr1A.!!$F1 1501
10 TraesCS5B01G297200 chr7A 26583398 26584898 1500 False 1923.0 1923 89.894 66 1558 1 chr7A.!!$F1 1492
11 TraesCS5B01G297200 chr7A 435932324 435933219 895 False 1439.0 1439 95.647 1553 2448 1 chr7A.!!$F2 895
12 TraesCS5B01G297200 chr6B 55727675 55728570 895 True 1428.0 1428 95.424 1553 2448 1 chr6B.!!$R1 895
13 TraesCS5B01G297200 chr6B 623348386 623349281 895 True 1423.0 1423 95.312 1553 2448 1 chr6B.!!$R2 895
14 TraesCS5B01G297200 chr6B 624464320 624465215 895 False 1411.0 1411 95.089 1553 2448 1 chr6B.!!$F1 895
15 TraesCS5B01G297200 chr4D 467592735 467593630 895 False 1428.0 1428 95.424 1553 2448 1 chr4D.!!$F1 895
16 TraesCS5B01G297200 chr4B 13938689 13939585 896 False 1411.0 1411 95.095 1553 2448 1 chr4B.!!$F1 895
17 TraesCS5B01G297200 chr5A 391983541 391984439 898 True 1404.0 1404 94.883 1553 2450 1 chr5A.!!$R1 897

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
53 54 0.328592 AGAGTAGGTGCTCCAGTCGA 59.671 55.0 7.7 0.0 36.2 4.20 F
381 390 0.415429 TCCCCTCTCTGCTCTTTCCT 59.585 55.0 0.0 0.0 0.0 3.36 F
511 520 0.626382 CCTCCCTTTCCCCTCTTTCC 59.374 60.0 0.0 0.0 0.0 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1435 1451 0.178068 AGCGTTCACACCAGTCTGTT 59.822 50.000 0.0 0.0 0.00 3.16 R
1438 1454 0.249911 GGAAGCGTTCACACCAGTCT 60.250 55.000 0.0 0.0 0.00 3.24 R
1577 2724 1.336755 GGTGTTGAAAGCAATGTCGGT 59.663 47.619 0.0 0.0 36.22 4.69 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
18 19 3.877951 AGGGAGAGCAAATGCAGAG 57.122 52.632 8.28 0.00 45.16 3.35
19 20 0.394080 AGGGAGAGCAAATGCAGAGC 60.394 55.000 8.28 0.00 45.16 4.09
20 21 0.394080 GGGAGAGCAAATGCAGAGCT 60.394 55.000 9.73 9.73 45.16 4.09
21 22 1.461559 GGAGAGCAAATGCAGAGCTT 58.538 50.000 8.28 3.01 45.16 3.74
22 23 2.636830 GGAGAGCAAATGCAGAGCTTA 58.363 47.619 8.28 0.00 45.16 3.09
23 24 2.354199 GGAGAGCAAATGCAGAGCTTAC 59.646 50.000 8.28 8.48 45.16 2.34
24 25 3.269178 GAGAGCAAATGCAGAGCTTACT 58.731 45.455 8.28 5.51 45.16 2.24
25 26 3.269178 AGAGCAAATGCAGAGCTTACTC 58.731 45.455 8.28 3.13 45.16 2.59
26 27 3.005554 GAGCAAATGCAGAGCTTACTCA 58.994 45.455 8.28 0.00 45.16 3.41
27 28 2.746362 AGCAAATGCAGAGCTTACTCAC 59.254 45.455 8.28 0.00 45.16 3.51
28 29 2.159462 GCAAATGCAGAGCTTACTCACC 60.159 50.000 0.00 0.00 46.09 4.02
29 30 2.015736 AATGCAGAGCTTACTCACCG 57.984 50.000 0.00 0.00 46.09 4.94
30 31 1.186200 ATGCAGAGCTTACTCACCGA 58.814 50.000 0.00 0.00 46.09 4.69
31 32 1.186200 TGCAGAGCTTACTCACCGAT 58.814 50.000 0.00 0.00 46.09 4.18
32 33 1.135139 TGCAGAGCTTACTCACCGATC 59.865 52.381 0.00 0.00 46.09 3.69
33 34 1.407258 GCAGAGCTTACTCACCGATCT 59.593 52.381 0.00 0.00 46.09 2.75
34 35 2.619177 GCAGAGCTTACTCACCGATCTA 59.381 50.000 0.00 0.00 46.09 1.98
35 36 3.304391 GCAGAGCTTACTCACCGATCTAG 60.304 52.174 0.00 0.00 46.09 2.43
36 37 4.130857 CAGAGCTTACTCACCGATCTAGA 58.869 47.826 0.00 0.00 46.09 2.43
37 38 4.213270 CAGAGCTTACTCACCGATCTAGAG 59.787 50.000 0.00 4.88 46.09 2.43
38 39 4.131596 GAGCTTACTCACCGATCTAGAGT 58.868 47.826 13.65 13.65 42.93 3.24
39 40 5.070714 AGAGCTTACTCACCGATCTAGAGTA 59.929 44.000 12.13 12.13 46.09 2.59
40 41 5.302360 AGCTTACTCACCGATCTAGAGTAG 58.698 45.833 14.38 11.40 43.42 2.57
41 42 4.453136 GCTTACTCACCGATCTAGAGTAGG 59.547 50.000 16.70 16.70 43.42 3.18
42 43 5.613329 CTTACTCACCGATCTAGAGTAGGT 58.387 45.833 14.38 9.88 43.42 3.08
45 46 2.577700 CACCGATCTAGAGTAGGTGCT 58.422 52.381 22.73 0.00 44.56 4.40
46 47 2.550606 CACCGATCTAGAGTAGGTGCTC 59.449 54.545 22.73 3.98 44.56 4.26
47 48 2.156098 CCGATCTAGAGTAGGTGCTCC 58.844 57.143 0.00 0.00 36.20 4.70
48 49 2.487445 CCGATCTAGAGTAGGTGCTCCA 60.487 54.545 7.70 0.00 36.20 3.86
49 50 2.811431 CGATCTAGAGTAGGTGCTCCAG 59.189 54.545 7.70 0.00 36.20 3.86
50 51 3.746114 CGATCTAGAGTAGGTGCTCCAGT 60.746 52.174 7.70 0.00 36.20 4.00
51 52 3.284793 TCTAGAGTAGGTGCTCCAGTC 57.715 52.381 7.70 5.89 36.20 3.51
52 53 1.944024 CTAGAGTAGGTGCTCCAGTCG 59.056 57.143 7.70 0.00 36.20 4.18
53 54 0.328592 AGAGTAGGTGCTCCAGTCGA 59.671 55.000 7.70 0.00 36.20 4.20
54 55 0.452585 GAGTAGGTGCTCCAGTCGAC 59.547 60.000 7.70 7.70 35.89 4.20
55 56 1.136984 GTAGGTGCTCCAGTCGACG 59.863 63.158 10.46 5.16 35.89 5.12
56 57 2.697761 TAGGTGCTCCAGTCGACGC 61.698 63.158 10.46 8.09 35.89 5.19
58 59 4.357947 GTGCTCCAGTCGACGCCA 62.358 66.667 10.46 1.39 0.00 5.69
59 60 3.381983 TGCTCCAGTCGACGCCAT 61.382 61.111 10.46 0.00 0.00 4.40
60 61 2.583593 GCTCCAGTCGACGCCATC 60.584 66.667 10.46 0.00 0.00 3.51
61 62 3.069980 GCTCCAGTCGACGCCATCT 62.070 63.158 10.46 0.00 0.00 2.90
62 63 1.064946 CTCCAGTCGACGCCATCTC 59.935 63.158 10.46 0.00 0.00 2.75
63 64 1.657751 CTCCAGTCGACGCCATCTCA 61.658 60.000 10.46 0.00 0.00 3.27
64 65 1.037579 TCCAGTCGACGCCATCTCAT 61.038 55.000 10.46 0.00 0.00 2.90
122 123 2.562298 CAGCACAAAATGGCCCTCTTTA 59.438 45.455 0.00 0.00 0.00 1.85
153 154 0.536460 ATAAAATGGCCCTACCCGCG 60.536 55.000 0.00 0.00 37.83 6.46
198 199 1.621814 GCTAGATACCATAACGCCCCA 59.378 52.381 0.00 0.00 0.00 4.96
207 208 0.696501 ATAACGCCCCAGTCAAAGGT 59.303 50.000 0.00 0.00 0.00 3.50
217 218 0.610232 AGTCAAAGGTGCCATGCTCC 60.610 55.000 0.00 0.00 41.85 4.70
240 241 1.813513 GCACTGACTGCCACATAAGT 58.186 50.000 0.00 0.00 40.42 2.24
350 359 2.835895 GCCCGAGTCCTCCCTCTC 60.836 72.222 0.00 0.00 0.00 3.20
351 360 3.011885 CCCGAGTCCTCCCTCTCT 58.988 66.667 0.00 0.00 0.00 3.10
355 364 1.551452 CGAGTCCTCCCTCTCTGTTT 58.449 55.000 0.00 0.00 0.00 2.83
356 365 1.203523 CGAGTCCTCCCTCTCTGTTTG 59.796 57.143 0.00 0.00 0.00 2.93
365 374 3.149981 CCCTCTCTGTTTGTTCTTTCCC 58.850 50.000 0.00 0.00 0.00 3.97
381 390 0.415429 TCCCCTCTCTGCTCTTTCCT 59.585 55.000 0.00 0.00 0.00 3.36
410 419 3.508840 GCGCCCCTCAAATCACCG 61.509 66.667 0.00 0.00 0.00 4.94
511 520 0.626382 CCTCCCTTTCCCCTCTTTCC 59.374 60.000 0.00 0.00 0.00 3.13
785 801 7.286313 TGCACATATATGGTGTATGGAAGAAA 58.714 34.615 16.96 0.00 38.51 2.52
949 965 2.151202 GACGGTTCATGGCAGAAGAAA 58.849 47.619 0.00 0.00 0.00 2.52
950 966 1.880027 ACGGTTCATGGCAGAAGAAAC 59.120 47.619 0.00 0.00 0.00 2.78
984 1000 1.376553 GCTTCACCTGAGGTCTGGC 60.377 63.158 0.00 2.01 38.38 4.85
1072 1088 3.306364 CCCTTTCATCTCACTCGTGTCTT 60.306 47.826 0.00 0.00 0.00 3.01
1077 1093 1.610363 TCTCACTCGTGTCTTGCTCT 58.390 50.000 0.00 0.00 0.00 4.09
1100 1116 1.882352 GCCGAAGATGAACCCTTGTGT 60.882 52.381 0.00 0.00 0.00 3.72
1114 1130 2.429478 CTTGTGTGATCATGGCACTCA 58.571 47.619 14.06 16.12 37.80 3.41
1119 1135 3.630769 GTGTGATCATGGCACTCATTGAT 59.369 43.478 16.78 0.34 37.18 2.57
1121 1137 3.881089 GTGATCATGGCACTCATTGATCA 59.119 43.478 20.96 20.96 41.88 2.92
1127 1143 2.029623 GGCACTCATTGATCAATGGCT 58.970 47.619 36.26 23.69 46.08 4.75
1131 1147 2.242965 ACTCATTGATCAATGGCTCCCA 59.757 45.455 36.26 21.38 46.08 4.37
1170 1186 2.477104 TCTATGCTGGGGAGATGACA 57.523 50.000 0.00 0.00 0.00 3.58
1185 1201 2.708216 TGACAGTCACTTTGCAGGAA 57.292 45.000 0.00 0.00 0.00 3.36
1219 1235 2.040412 ACTGGACTTCCCATCAAAGGAC 59.960 50.000 0.00 0.00 45.57 3.85
1221 1237 2.649312 TGGACTTCCCATCAAAGGACAT 59.351 45.455 0.00 0.00 40.82 3.06
1256 1272 2.927028 CACAGATTCTGATGGATGGCA 58.073 47.619 20.33 0.00 35.18 4.92
1268 1284 4.290196 TGATGGATGGCATGAGATTATGGA 59.710 41.667 3.81 0.00 0.00 3.41
1311 1327 1.359168 GGGTACAAGGGAAGTCCACT 58.641 55.000 0.00 0.00 38.24 4.00
1333 1349 6.095300 CACTGGTGCAAGTTATCATTGGATTA 59.905 38.462 0.00 0.00 34.89 1.75
1353 1369 2.597455 ACTGAACACTTTGGGGAATGG 58.403 47.619 0.00 0.00 0.00 3.16
1438 1454 7.316544 GTCACTTGGACTCTTTTCTTTAACA 57.683 36.000 0.00 0.00 43.46 2.41
1505 1522 0.326264 GGGAGCATGGACTCAGTTGT 59.674 55.000 0.00 0.00 38.50 3.32
1518 1535 1.006832 CAGTTGTGGTATGGTAGCGC 58.993 55.000 0.00 0.00 37.21 5.92
1577 2724 7.824289 GCATATAGTACATGCCAGGATTTTCTA 59.176 37.037 1.71 0.00 42.41 2.10
1581 2728 2.238646 ACATGCCAGGATTTTCTACCGA 59.761 45.455 0.00 0.00 0.00 4.69
1602 2749 2.622942 ACATTGCTTTCAACACCATCGT 59.377 40.909 0.00 0.00 34.60 3.73
1750 2898 6.789268 CCAAATGGGATATGTTGGGAGTATA 58.211 40.000 0.00 0.00 40.01 1.47
1758 2906 7.998964 GGGATATGTTGGGAGTATATTTATGGG 59.001 40.741 0.00 0.00 0.00 4.00
1778 2926 2.821969 GGGGCTGAAAATCGATATGCAT 59.178 45.455 3.79 3.79 0.00 3.96
1780 2928 4.458989 GGGGCTGAAAATCGATATGCATTA 59.541 41.667 3.54 0.00 0.00 1.90
1827 2975 8.235226 GTGATCATCCTTTACATTAGCATCATG 58.765 37.037 0.00 0.00 0.00 3.07
1896 3044 1.978617 ATTGTGGCCCGCCTTTGAG 60.979 57.895 7.35 0.00 36.94 3.02
1939 3087 3.499338 AGGGCAATGATTCTTGTGTTCA 58.501 40.909 0.00 0.00 0.00 3.18
1960 3108 5.803552 TCATCACATCTGACCACATAACAA 58.196 37.500 0.00 0.00 0.00 2.83
1987 3135 4.703897 TCGAGTTTGACTTCTCCACAAAT 58.296 39.130 0.00 0.00 36.25 2.32
2045 3193 4.706476 CCCATATTTGAAGTTCTGCCAAGA 59.294 41.667 4.17 0.00 0.00 3.02
2050 3198 4.488126 TTGAAGTTCTGCCAAGATTTCG 57.512 40.909 4.17 0.00 32.80 3.46
2112 3260 4.331992 GGTATCTCGCTTTGAAGTTAACCC 59.668 45.833 0.88 0.00 0.00 4.11
2283 3431 2.285368 TGGGCCTTCATCCTCCGT 60.285 61.111 4.53 0.00 0.00 4.69
2305 3453 1.496001 TCCCACGCATAGGACCTACTA 59.504 52.381 2.46 0.00 0.00 1.82
2336 3484 0.833287 ATGGTCCATGTCCTCTTCCG 59.167 55.000 2.68 0.00 0.00 4.30
2418 3566 2.430465 CTCAAACTCACCACCATCCAG 58.570 52.381 0.00 0.00 0.00 3.86
2448 3596 9.941664 CAAGTATTCATTATCAACTTGGTCATC 57.058 33.333 5.77 0.00 41.99 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.394080 GCTCTGCATTTGCTCTCCCT 60.394 55.000 3.94 0.00 42.66 4.20
1 2 0.394080 AGCTCTGCATTTGCTCTCCC 60.394 55.000 3.94 0.00 42.66 4.30
3 4 3.269178 AGTAAGCTCTGCATTTGCTCTC 58.731 45.455 8.35 5.72 42.66 3.20
5 6 3.005554 TGAGTAAGCTCTGCATTTGCTC 58.994 45.455 8.35 9.16 42.13 4.26
6 7 2.746362 GTGAGTAAGCTCTGCATTTGCT 59.254 45.455 3.94 2.92 42.13 3.91
7 8 2.159462 GGTGAGTAAGCTCTGCATTTGC 60.159 50.000 0.00 0.00 42.13 3.68
8 9 2.094894 CGGTGAGTAAGCTCTGCATTTG 59.905 50.000 0.00 0.00 42.13 2.32
9 10 2.028112 TCGGTGAGTAAGCTCTGCATTT 60.028 45.455 0.00 0.00 42.13 2.32
10 11 1.550524 TCGGTGAGTAAGCTCTGCATT 59.449 47.619 0.00 0.00 42.13 3.56
11 12 1.186200 TCGGTGAGTAAGCTCTGCAT 58.814 50.000 0.00 0.00 42.13 3.96
12 13 1.135139 GATCGGTGAGTAAGCTCTGCA 59.865 52.381 0.00 0.00 42.13 4.41
13 14 1.407258 AGATCGGTGAGTAAGCTCTGC 59.593 52.381 0.00 0.00 42.13 4.26
14 15 4.130857 TCTAGATCGGTGAGTAAGCTCTG 58.869 47.826 0.00 0.00 42.13 3.35
15 16 4.141574 ACTCTAGATCGGTGAGTAAGCTCT 60.142 45.833 13.79 0.00 42.13 4.09
16 17 4.131596 ACTCTAGATCGGTGAGTAAGCTC 58.868 47.826 13.79 0.00 39.02 4.09
17 18 4.159244 ACTCTAGATCGGTGAGTAAGCT 57.841 45.455 13.79 0.00 39.02 3.74
18 19 4.453136 CCTACTCTAGATCGGTGAGTAAGC 59.547 50.000 18.75 0.00 41.09 3.09
19 20 5.467399 CACCTACTCTAGATCGGTGAGTAAG 59.533 48.000 21.65 16.47 46.11 2.34
20 21 5.366460 CACCTACTCTAGATCGGTGAGTAA 58.634 45.833 21.65 9.08 46.11 2.24
21 22 4.743045 GCACCTACTCTAGATCGGTGAGTA 60.743 50.000 26.70 16.76 46.11 2.59
22 23 3.811083 CACCTACTCTAGATCGGTGAGT 58.189 50.000 21.65 17.59 46.11 3.41
23 24 2.550606 GCACCTACTCTAGATCGGTGAG 59.449 54.545 26.70 12.52 46.11 3.51
24 25 2.172930 AGCACCTACTCTAGATCGGTGA 59.827 50.000 26.70 2.35 46.11 4.02
25 26 2.550606 GAGCACCTACTCTAGATCGGTG 59.449 54.545 21.77 21.77 45.99 4.94
26 27 2.487625 GGAGCACCTACTCTAGATCGGT 60.488 54.545 0.00 0.00 36.87 4.69
27 28 2.156098 GGAGCACCTACTCTAGATCGG 58.844 57.143 0.00 0.00 36.87 4.18
28 29 2.811431 CTGGAGCACCTACTCTAGATCG 59.189 54.545 0.71 0.00 45.41 3.69
29 30 3.818773 GACTGGAGCACCTACTCTAGATC 59.181 52.174 11.27 2.93 45.41 2.75
30 31 3.746114 CGACTGGAGCACCTACTCTAGAT 60.746 52.174 11.27 0.00 45.41 1.98
31 32 2.420269 CGACTGGAGCACCTACTCTAGA 60.420 54.545 11.27 0.00 45.41 2.43
33 34 1.558294 TCGACTGGAGCACCTACTCTA 59.442 52.381 0.71 0.00 36.87 2.43
34 35 0.328592 TCGACTGGAGCACCTACTCT 59.671 55.000 0.71 0.00 36.87 3.24
35 36 0.452585 GTCGACTGGAGCACCTACTC 59.547 60.000 8.70 0.00 37.04 2.59
36 37 1.306642 CGTCGACTGGAGCACCTACT 61.307 60.000 14.70 0.00 37.04 2.57
37 38 1.136984 CGTCGACTGGAGCACCTAC 59.863 63.158 14.70 0.00 37.04 3.18
38 39 2.697761 GCGTCGACTGGAGCACCTA 61.698 63.158 14.70 0.00 37.04 3.08
39 40 4.057428 GCGTCGACTGGAGCACCT 62.057 66.667 14.70 0.00 37.04 4.00
41 42 3.649277 ATGGCGTCGACTGGAGCAC 62.649 63.158 14.70 4.64 0.00 4.40
42 43 3.356639 GATGGCGTCGACTGGAGCA 62.357 63.158 14.70 1.43 0.00 4.26
43 44 2.583593 GATGGCGTCGACTGGAGC 60.584 66.667 14.70 9.31 0.00 4.70
44 45 1.064946 GAGATGGCGTCGACTGGAG 59.935 63.158 14.70 0.00 0.00 3.86
45 46 1.037579 ATGAGATGGCGTCGACTGGA 61.038 55.000 14.70 0.00 0.00 3.86
46 47 0.873312 CATGAGATGGCGTCGACTGG 60.873 60.000 14.70 0.00 0.00 4.00
47 48 0.179127 ACATGAGATGGCGTCGACTG 60.179 55.000 14.70 8.46 33.60 3.51
48 49 0.179127 CACATGAGATGGCGTCGACT 60.179 55.000 14.70 0.00 33.60 4.18
49 50 0.179137 TCACATGAGATGGCGTCGAC 60.179 55.000 5.18 5.18 33.60 4.20
50 51 0.530288 TTCACATGAGATGGCGTCGA 59.470 50.000 0.00 0.00 33.60 4.20
51 52 1.358877 TTTCACATGAGATGGCGTCG 58.641 50.000 0.00 0.00 33.60 5.12
52 53 3.829886 TTTTTCACATGAGATGGCGTC 57.170 42.857 0.00 0.00 33.60 5.19
53 54 3.758023 TGATTTTTCACATGAGATGGCGT 59.242 39.130 0.00 0.00 33.60 5.68
54 55 4.100529 GTGATTTTTCACATGAGATGGCG 58.899 43.478 0.00 0.00 40.16 5.69
55 56 5.063180 TGTGATTTTTCACATGAGATGGC 57.937 39.130 0.00 0.00 44.63 4.40
168 169 0.035458 GGTATCTAGCATGGCGCCTT 59.965 55.000 29.70 19.97 44.04 4.35
198 199 0.610232 GGAGCATGGCACCTTTGACT 60.610 55.000 0.00 0.00 36.40 3.41
309 311 1.579140 TATGGTGAAGGGGCATGGCA 61.579 55.000 22.06 0.00 0.00 4.92
315 317 1.961277 CGCGATATGGTGAAGGGGC 60.961 63.158 0.00 0.00 0.00 5.80
345 354 3.149981 GGGGAAAGAACAAACAGAGAGG 58.850 50.000 0.00 0.00 0.00 3.69
348 357 4.068599 GAGAGGGGAAAGAACAAACAGAG 58.931 47.826 0.00 0.00 0.00 3.35
350 359 3.817647 CAGAGAGGGGAAAGAACAAACAG 59.182 47.826 0.00 0.00 0.00 3.16
351 360 3.820557 CAGAGAGGGGAAAGAACAAACA 58.179 45.455 0.00 0.00 0.00 2.83
355 364 1.625818 GAGCAGAGAGGGGAAAGAACA 59.374 52.381 0.00 0.00 0.00 3.18
356 365 1.905894 AGAGCAGAGAGGGGAAAGAAC 59.094 52.381 0.00 0.00 0.00 3.01
365 374 1.206849 GTGGAGGAAAGAGCAGAGAGG 59.793 57.143 0.00 0.00 0.00 3.69
410 419 1.201429 TTTGAGTGGGGAGAGGGAGC 61.201 60.000 0.00 0.00 0.00 4.70
511 520 6.160684 TCAAATGCAGAGATTTCAACCAATG 58.839 36.000 0.00 0.00 0.00 2.82
694 704 6.432403 TCTTCCATACACCATATATGTGCA 57.568 37.500 11.73 2.12 0.00 4.57
785 801 9.762933 ACATGTGCAAAATTTCTACACTAATTT 57.237 25.926 15.17 0.00 35.95 1.82
949 965 3.960102 TGAAGCTGATCAAAAACCCTTGT 59.040 39.130 0.00 0.00 0.00 3.16
950 966 4.301628 GTGAAGCTGATCAAAAACCCTTG 58.698 43.478 0.00 0.00 0.00 3.61
984 1000 3.193263 CTCCATCTTGTCATGAACCGAG 58.807 50.000 0.00 0.00 0.00 4.63
1077 1093 2.238646 ACAAGGGTTCATCTTCGGCATA 59.761 45.455 0.00 0.00 0.00 3.14
1100 1116 4.159244 TGATCAATGAGTGCCATGATCA 57.841 40.909 11.97 11.97 41.67 2.92
1114 1130 2.781757 TCTCTGGGAGCCATTGATCAAT 59.218 45.455 15.36 15.36 30.82 2.57
1119 1135 0.615331 GTGTCTCTGGGAGCCATTGA 59.385 55.000 0.00 0.00 30.82 2.57
1121 1137 1.293062 ATGTGTCTCTGGGAGCCATT 58.707 50.000 0.00 0.00 30.82 3.16
1127 1143 4.593206 AGTGAAAAGTATGTGTCTCTGGGA 59.407 41.667 0.00 0.00 0.00 4.37
1131 1147 7.547370 GCATAGAAGTGAAAAGTATGTGTCTCT 59.453 37.037 0.00 0.00 0.00 3.10
1185 1201 3.168035 AGTCCAGTGATCAGAGACACT 57.832 47.619 17.44 7.09 46.32 3.55
1219 1235 8.680903 AGAATCTGTGCTAAAACAAATAGGATG 58.319 33.333 0.00 0.00 0.00 3.51
1221 1237 7.882791 TCAGAATCTGTGCTAAAACAAATAGGA 59.117 33.333 10.36 0.00 32.61 2.94
1256 1272 6.386342 CCCTATGAGTCCATCCATAATCTCAT 59.614 42.308 9.74 9.74 42.60 2.90
1268 1284 1.484065 GCTCCCTCCCTATGAGTCCAT 60.484 57.143 0.00 0.00 39.65 3.41
1311 1327 6.095300 CAGTAATCCAATGATAACTTGCACCA 59.905 38.462 0.00 0.00 0.00 4.17
1333 1349 2.597455 CCATTCCCCAAAGTGTTCAGT 58.403 47.619 0.00 0.00 0.00 3.41
1418 1434 7.254932 CCAGTCTGTTAAAGAAAAGAGTCCAAG 60.255 40.741 0.00 0.00 36.40 3.61
1420 1436 6.055588 CCAGTCTGTTAAAGAAAAGAGTCCA 58.944 40.000 0.00 0.00 36.40 4.02
1435 1451 0.178068 AGCGTTCACACCAGTCTGTT 59.822 50.000 0.00 0.00 0.00 3.16
1438 1454 0.249911 GGAAGCGTTCACACCAGTCT 60.250 55.000 0.00 0.00 0.00 3.24
1505 1522 2.063979 AGCCAGCGCTACCATACCA 61.064 57.895 10.99 0.00 46.08 3.25
1518 1535 4.442706 ACCTGACGATACAAATAAGCCAG 58.557 43.478 0.00 0.00 0.00 4.85
1577 2724 1.336755 GGTGTTGAAAGCAATGTCGGT 59.663 47.619 0.00 0.00 36.22 4.69
1581 2728 2.622942 ACGATGGTGTTGAAAGCAATGT 59.377 40.909 0.00 0.00 36.22 2.71
1602 2749 3.531538 GAAGAATCATACAACCGCCTCA 58.468 45.455 0.00 0.00 0.00 3.86
1672 2819 3.429960 GGTACGAGGTGAAGTATGGGAAC 60.430 52.174 0.00 0.00 0.00 3.62
1741 2889 3.591527 CAGCCCCCATAAATATACTCCCA 59.408 47.826 0.00 0.00 0.00 4.37
1750 2898 3.909732 TCGATTTTCAGCCCCCATAAAT 58.090 40.909 0.00 0.00 0.00 1.40
1758 2906 4.510038 AATGCATATCGATTTTCAGCCC 57.490 40.909 1.71 0.00 0.00 5.19
1778 2926 6.920758 CACCGTCAATTGACCTTGAAATTTAA 59.079 34.615 28.40 0.00 41.86 1.52
1780 2928 5.068460 TCACCGTCAATTGACCTTGAAATTT 59.932 36.000 28.40 0.00 41.86 1.82
1787 2935 3.417069 TGATCACCGTCAATTGACCTT 57.583 42.857 28.40 15.31 41.86 3.50
1827 2975 3.131396 CGGTGTAGTGGCAAGGATATTC 58.869 50.000 0.00 0.00 0.00 1.75
1896 3044 1.940613 GGGTTATCCGTGCAAGATGTC 59.059 52.381 10.10 4.09 33.83 3.06
1939 3087 6.240894 AGTTTGTTATGTGGTCAGATGTGAT 58.759 36.000 0.00 0.00 34.36 3.06
1987 3135 3.013921 GGTCAAGTTTCATCGGCCATTA 58.986 45.455 2.24 0.00 0.00 1.90
2045 3193 7.444183 TGTTAGTGAAGGAACAATCTTCGAAAT 59.556 33.333 0.00 0.00 42.43 2.17
2050 3198 5.763204 TGGTGTTAGTGAAGGAACAATCTTC 59.237 40.000 0.00 0.00 37.31 2.87
2112 3260 5.222631 GGACAAGTAAAATTCTTGCACCAG 58.777 41.667 5.52 0.00 43.97 4.00
2305 3453 5.280882 GGACATGGACCATGAGATTCCATAT 60.281 44.000 35.91 13.30 46.47 1.78
2418 3566 6.974622 CCAAGTTGATAATGAATACTTGCACC 59.025 38.462 3.87 0.00 42.55 5.01


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

AutoCloner maintained by Alex Coulton.