Multiple sequence alignment - TraesCS7B01G226900

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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 TraesCS7B01G226900 chr7B 100.000 5130 0 0 1 5130 427297748 427302877 0.000000e+00 9474.0
1 TraesCS7B01G226900 chr7A 92.893 3194 106 32 468 3575 474291401 474294559 0.000000e+00 4529.0
2 TraesCS7B01G226900 chr7A 92.816 1573 46 23 3575 5130 474294737 474296259 0.000000e+00 2217.0
3 TraesCS7B01G226900 chr7A 85.616 438 35 12 43 467 474290944 474291366 7.890000e-118 435.0
4 TraesCS7B01G226900 chr7D 95.070 2434 68 23 1187 3575 412881594 412884020 0.000000e+00 3783.0
5 TraesCS7B01G226900 chr7D 96.471 1020 26 6 3575 4585 412884198 412885216 0.000000e+00 1676.0
6 TraesCS7B01G226900 chr7D 89.755 693 22 17 468 1139 412880932 412881596 0.000000e+00 841.0
7 TraesCS7B01G226900 chr7D 93.487 476 29 1 4657 5130 412885221 412885696 0.000000e+00 706.0
8 TraesCS7B01G226900 chr7D 87.616 323 29 8 156 467 412880578 412880900 1.050000e-96 364.0
9 TraesCS7B01G226900 chr1A 89.516 124 13 0 4833 4956 466927361 466927484 1.910000e-34 158.0
10 TraesCS7B01G226900 chr1A 91.837 49 4 0 156 204 535039700 535039748 9.220000e-08 69.4
11 TraesCS7B01G226900 chr1D 88.710 124 14 0 4833 4956 367429177 367429300 8.900000e-33 152.0
12 TraesCS7B01G226900 chr1B 88.710 124 14 0 4833 4956 491982666 491982789 8.900000e-33 152.0
13 TraesCS7B01G226900 chr1B 88.525 61 7 0 134 194 363632829 363632889 1.980000e-09 75.0
14 TraesCS7B01G226900 chr5A 90.141 71 7 0 134 204 584453490 584453420 5.470000e-15 93.5
15 TraesCS7B01G226900 chr3A 90.141 71 7 0 134 204 466057048 466056978 5.470000e-15 93.5
16 TraesCS7B01G226900 chr4D 89.394 66 7 0 134 199 29833580 29833645 3.290000e-12 84.2
17 TraesCS7B01G226900 chr3B 88.333 60 7 0 136 195 678447723 678447664 7.130000e-09 73.1
18 TraesCS7B01G226900 chr5B 97.500 40 1 0 156 195 622390251 622390212 9.220000e-08 69.4


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 TraesCS7B01G226900 chr7B 427297748 427302877 5129 False 9474.000000 9474 100.000000 1 5130 1 chr7B.!!$F1 5129
1 TraesCS7B01G226900 chr7A 474290944 474296259 5315 False 2393.666667 4529 90.441667 43 5130 3 chr7A.!!$F1 5087
2 TraesCS7B01G226900 chr7D 412880578 412885696 5118 False 1474.000000 3783 92.479800 156 5130 5 chr7D.!!$F1 4974

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
461 479 0.249784 CTCCAGCACCGGATGATCTG 60.250 60.0 9.46 7.31 33.56 2.90 F
737 804 0.471211 ACACCGAGGAAGAAGACCCA 60.471 55.0 0.00 0.00 0.00 4.51 F
1379 1490 0.323360 GGAGCTTGGGTGCCATTGTA 60.323 55.0 0.00 0.00 31.53 2.41 F
2527 2683 0.821711 TTGGAAAACCCACGCCTCAG 60.822 55.0 0.00 0.00 46.62 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1376 1487 0.108520 GAGGACGGTCGCCATTTACA 60.109 55.000 1.43 0.0 0.00 2.41 R
1541 1674 2.652348 TCTAAATTGCCCTTCCCTTCCA 59.348 45.455 0.00 0.0 0.00 3.53 R
3066 3222 1.134670 CAGTAAGGGCTGTCAGGTAGC 60.135 57.143 1.14 0.0 40.41 3.58 R
4474 4843 0.745845 CAGATGGCCGGTGGAAGAAG 60.746 60.000 1.90 0.0 0.00 2.85 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
17 18 2.274760 AGTACTCCCTCCGTCCCG 59.725 66.667 0.00 0.00 0.00 5.14
18 19 2.273449 GTACTCCCTCCGTCCCGA 59.727 66.667 0.00 0.00 0.00 5.14
19 20 1.379044 GTACTCCCTCCGTCCCGAA 60.379 63.158 0.00 0.00 0.00 4.30
20 21 1.379044 TACTCCCTCCGTCCCGAAC 60.379 63.158 0.00 0.00 0.00 3.95
29 30 3.426008 CGTCCCGAACGTTTTTGAC 57.574 52.632 0.46 8.45 46.42 3.18
30 31 0.651551 CGTCCCGAACGTTTTTGACA 59.348 50.000 18.69 0.00 46.42 3.58
31 32 1.592830 CGTCCCGAACGTTTTTGACAC 60.593 52.381 18.69 6.11 46.42 3.67
32 33 1.667212 GTCCCGAACGTTTTTGACACT 59.333 47.619 0.46 0.00 0.00 3.55
33 34 2.865551 GTCCCGAACGTTTTTGACACTA 59.134 45.455 0.46 0.00 0.00 2.74
34 35 3.060070 GTCCCGAACGTTTTTGACACTAG 60.060 47.826 0.46 0.00 0.00 2.57
35 36 2.222445 CCCGAACGTTTTTGACACTAGG 59.778 50.000 0.46 0.00 0.00 3.02
36 37 3.125316 CCGAACGTTTTTGACACTAGGA 58.875 45.455 0.46 0.00 0.00 2.94
37 38 3.183775 CCGAACGTTTTTGACACTAGGAG 59.816 47.826 0.46 0.00 0.00 3.69
38 39 3.183775 CGAACGTTTTTGACACTAGGAGG 59.816 47.826 0.46 0.00 0.00 4.30
39 40 4.374399 GAACGTTTTTGACACTAGGAGGA 58.626 43.478 0.46 0.00 0.00 3.71
40 41 4.411256 ACGTTTTTGACACTAGGAGGAA 57.589 40.909 0.00 0.00 0.00 3.36
41 42 4.377897 ACGTTTTTGACACTAGGAGGAAG 58.622 43.478 0.00 0.00 0.00 3.46
42 43 4.141779 ACGTTTTTGACACTAGGAGGAAGT 60.142 41.667 0.00 0.00 0.00 3.01
43 44 5.069516 ACGTTTTTGACACTAGGAGGAAGTA 59.930 40.000 0.00 0.00 0.00 2.24
44 45 5.987347 CGTTTTTGACACTAGGAGGAAGTAA 59.013 40.000 0.00 0.00 0.00 2.24
45 46 6.073927 CGTTTTTGACACTAGGAGGAAGTAAC 60.074 42.308 0.00 0.00 0.00 2.50
46 47 6.742559 TTTTGACACTAGGAGGAAGTAACT 57.257 37.500 0.00 0.00 0.00 2.24
47 48 5.723672 TTGACACTAGGAGGAAGTAACTG 57.276 43.478 0.00 0.00 0.00 3.16
48 49 4.994282 TGACACTAGGAGGAAGTAACTGA 58.006 43.478 0.00 0.00 0.00 3.41
49 50 5.580998 TGACACTAGGAGGAAGTAACTGAT 58.419 41.667 0.00 0.00 0.00 2.90
50 51 6.728411 TGACACTAGGAGGAAGTAACTGATA 58.272 40.000 0.00 0.00 0.00 2.15
51 52 7.179966 TGACACTAGGAGGAAGTAACTGATAA 58.820 38.462 0.00 0.00 0.00 1.75
52 53 7.839705 TGACACTAGGAGGAAGTAACTGATAAT 59.160 37.037 0.00 0.00 0.00 1.28
53 54 8.611051 ACACTAGGAGGAAGTAACTGATAATT 57.389 34.615 0.00 0.00 0.00 1.40
54 55 9.047947 ACACTAGGAGGAAGTAACTGATAATTT 57.952 33.333 0.00 0.00 0.00 1.82
130 134 0.765510 GAGGCGTGGGGAAGGATTAT 59.234 55.000 0.00 0.00 0.00 1.28
137 141 1.975680 TGGGGAAGGATTATACGAGGC 59.024 52.381 0.00 0.00 0.00 4.70
141 145 2.613223 GGAAGGATTATACGAGGCTGCC 60.613 54.545 11.65 11.65 0.00 4.85
151 155 3.249189 AGGCTGCCTCGAACCCAA 61.249 61.111 17.22 0.00 0.00 4.12
152 156 2.282180 GGCTGCCTCGAACCCAAA 60.282 61.111 12.43 0.00 0.00 3.28
154 158 1.460273 GGCTGCCTCGAACCCAAAAA 61.460 55.000 12.43 0.00 0.00 1.94
161 165 3.211045 CCTCGAACCCAAAAACTCTTGA 58.789 45.455 0.00 0.00 0.00 3.02
194 202 0.892755 TACTTCACCACTACGCCAGG 59.107 55.000 0.00 0.00 0.00 4.45
213 221 1.967779 GGCCTGCCCTTTCTAACAAAA 59.032 47.619 0.00 0.00 0.00 2.44
216 224 3.258123 GCCTGCCCTTTCTAACAAAATGA 59.742 43.478 0.00 0.00 0.00 2.57
221 229 7.095102 CCTGCCCTTTCTAACAAAATGAAAATG 60.095 37.037 0.00 0.00 30.67 2.32
299 314 4.653341 ACATGGATCCTAACCAAGAGAGAG 59.347 45.833 14.23 0.00 40.93 3.20
300 315 3.647636 TGGATCCTAACCAAGAGAGAGG 58.352 50.000 14.23 0.00 34.25 3.69
329 346 5.940192 TGAATAGTTGTTGACACATGGAC 57.060 39.130 0.00 0.00 31.06 4.02
395 412 2.037251 CCCCACTCCAATAGTACCATCG 59.963 54.545 0.00 0.00 35.76 3.84
398 415 4.322049 CCCACTCCAATAGTACCATCGATC 60.322 50.000 0.00 0.00 35.76 3.69
426 444 2.310538 CTGCTATTTTTAGGGGCCTGG 58.689 52.381 0.84 0.00 0.00 4.45
460 478 0.689080 ACTCCAGCACCGGATGATCT 60.689 55.000 9.46 0.00 33.56 2.75
461 479 0.249784 CTCCAGCACCGGATGATCTG 60.250 60.000 9.46 7.31 33.56 2.90
478 530 9.208022 GGATGATCTGTCGAATATTATGAACAA 57.792 33.333 0.00 0.00 0.00 2.83
547 606 9.271828 GAAAGAGAAAGAAAAAGAGAGAGACAT 57.728 33.333 0.00 0.00 0.00 3.06
549 608 9.705290 AAGAGAAAGAAAAAGAGAGAGACATAC 57.295 33.333 0.00 0.00 0.00 2.39
645 709 3.071892 CCTCGTCTAGAGTCTAGACCCAT 59.928 52.174 37.45 8.16 45.44 4.00
737 804 0.471211 ACACCGAGGAAGAAGACCCA 60.471 55.000 0.00 0.00 0.00 4.51
851 918 1.454847 CGAGAGAGGGAGAGGTGGG 60.455 68.421 0.00 0.00 0.00 4.61
855 922 1.547755 AGAGGGAGAGGTGGGGAGA 60.548 63.158 0.00 0.00 0.00 3.71
966 1033 4.403752 GGATTCCATTTCTTCCCTTCTTGG 59.596 45.833 0.00 0.00 0.00 3.61
1137 1238 1.645034 CGTGTTGCTCTGGATCGATT 58.355 50.000 0.00 0.00 0.00 3.34
1167 1271 4.827087 CGCCGCAGTGCCATCTCT 62.827 66.667 10.11 0.00 0.00 3.10
1184 1288 2.909006 TCTCTGCCACTCCTTCTGATTT 59.091 45.455 0.00 0.00 0.00 2.17
1214 1318 1.629043 TTCTGTCTAACCTGGCGAGT 58.371 50.000 0.00 0.00 0.00 4.18
1374 1485 1.832167 GTTTGGAGCTTGGGTGCCA 60.832 57.895 0.00 0.00 0.00 4.92
1376 1487 0.471591 TTTGGAGCTTGGGTGCCATT 60.472 50.000 0.00 0.00 31.53 3.16
1379 1490 0.323360 GGAGCTTGGGTGCCATTGTA 60.323 55.000 0.00 0.00 31.53 2.41
1402 1514 3.450115 CGACCGTCCTCTCCCCAC 61.450 72.222 0.00 0.00 0.00 4.61
1403 1515 3.075641 GACCGTCCTCTCCCCACC 61.076 72.222 0.00 0.00 0.00 4.61
1404 1516 3.899545 GACCGTCCTCTCCCCACCA 62.900 68.421 0.00 0.00 0.00 4.17
1483 1599 2.505364 AATCCAACCAGGGCTCAGGC 62.505 60.000 0.00 0.00 38.24 4.85
1541 1674 5.892348 ACTCCATCAGTTCAAGGGTTTAAT 58.108 37.500 0.00 0.00 26.56 1.40
1632 1769 4.806640 TCACTCTGCTCATGATGTTGTA 57.193 40.909 0.00 0.00 0.00 2.41
1633 1770 4.752146 TCACTCTGCTCATGATGTTGTAG 58.248 43.478 0.00 0.00 0.00 2.74
1634 1771 4.221482 TCACTCTGCTCATGATGTTGTAGT 59.779 41.667 0.00 0.00 0.00 2.73
1635 1772 4.329256 CACTCTGCTCATGATGTTGTAGTG 59.671 45.833 0.00 2.57 0.00 2.74
1642 1786 5.626543 GCTCATGATGTTGTAGTGTTTTGTG 59.373 40.000 0.00 0.00 0.00 3.33
1643 1787 6.691754 TCATGATGTTGTAGTGTTTTGTGT 57.308 33.333 0.00 0.00 0.00 3.72
1645 1789 6.317391 TCATGATGTTGTAGTGTTTTGTGTCA 59.683 34.615 0.00 0.00 0.00 3.58
1653 1797 4.297299 AGTGTTTTGTGTCATGAAGCTG 57.703 40.909 0.00 0.00 0.00 4.24
1736 1880 2.440980 GGACCAGATGCCAAGGCC 60.441 66.667 8.89 0.00 41.09 5.19
1808 1952 5.549742 TCTTTGTGGGCAAAAATCTCATT 57.450 34.783 0.00 0.00 43.17 2.57
1951 2095 4.998051 AGGTTGGTAGGATTTGTGTTCAT 58.002 39.130 0.00 0.00 0.00 2.57
2064 2211 8.441608 GCAAGATGCAAGATATCATGTAACTAG 58.558 37.037 8.73 0.00 44.26 2.57
2133 2280 3.762407 TTGTGGCTAGCAGTTAGTTCA 57.238 42.857 18.24 0.00 0.00 3.18
2136 2283 3.003480 GTGGCTAGCAGTTAGTTCAAGG 58.997 50.000 18.24 0.00 0.00 3.61
2195 2342 4.878397 GTGCACTAAGCCATCACTATCTTT 59.122 41.667 10.32 0.00 44.83 2.52
2198 2345 5.220931 GCACTAAGCCATCACTATCTTTTGG 60.221 44.000 0.00 0.00 37.23 3.28
2251 2402 6.147821 GTGGATATAGTTGCGAACATGCTAAT 59.852 38.462 0.00 0.00 35.36 1.73
2252 2403 6.147656 TGGATATAGTTGCGAACATGCTAATG 59.852 38.462 0.00 0.00 39.89 1.90
2366 2522 8.386606 TCAATTGAATTTTGTTTGTAACTGCAC 58.613 29.630 5.45 0.00 0.00 4.57
2432 2588 2.826128 TGTACTTGGCTCTACTGGTCAG 59.174 50.000 0.00 0.00 0.00 3.51
2506 2662 8.995027 TGCATGGTTCTATATTTATTTCCTGT 57.005 30.769 0.00 0.00 0.00 4.00
2523 2679 1.066752 GTGTTGGAAAACCCACGCC 59.933 57.895 0.00 0.00 46.62 5.68
2527 2683 0.821711 TTGGAAAACCCACGCCTCAG 60.822 55.000 0.00 0.00 46.62 3.35
2640 2796 7.276658 CCATGAGTTATGTTCTCTCAACAGTAC 59.723 40.741 0.00 0.00 40.73 2.73
2964 3120 2.267426 TGTGATAATTGTGTCGAGCGG 58.733 47.619 0.00 0.00 0.00 5.52
3424 3580 4.215399 CCTCACACGAAAACATTGGTACAT 59.785 41.667 0.00 0.00 39.30 2.29
3484 3647 9.979578 ATGTTCAGCTATCTACTCTCAAATAAG 57.020 33.333 0.00 0.00 0.00 1.73
3485 3648 8.417106 TGTTCAGCTATCTACTCTCAAATAAGG 58.583 37.037 0.00 0.00 0.00 2.69
3486 3649 8.634444 GTTCAGCTATCTACTCTCAAATAAGGA 58.366 37.037 0.00 0.00 0.00 3.36
3487 3650 8.948401 TCAGCTATCTACTCTCAAATAAGGAT 57.052 34.615 0.00 0.00 0.00 3.24
3591 3947 9.709495 TGCATTGCTGAAATAATAAGAACTTTT 57.291 25.926 10.49 0.00 0.00 2.27
3708 4065 0.673437 CAACCCAATGCGTTTGACCT 59.327 50.000 1.04 0.00 37.53 3.85
3932 4289 2.203070 GGCGCCGGTCAGATGAAT 60.203 61.111 12.58 0.00 0.00 2.57
3947 4304 6.255453 GTCAGATGAATTGAGTGACTTAGAGC 59.745 42.308 3.76 0.00 35.64 4.09
4268 4626 3.758554 TGCTGCCTTCTTTTTGTAGGATC 59.241 43.478 0.00 0.00 35.50 3.36
4354 4715 9.681062 TTATGAAGGTTTTAAGAGATTGTAGGG 57.319 33.333 0.00 0.00 0.00 3.53
4467 4836 8.677148 TGAACTGTATAATTATTTCTCCTGCC 57.323 34.615 2.68 0.00 0.00 4.85
4468 4837 8.494433 TGAACTGTATAATTATTTCTCCTGCCT 58.506 33.333 2.68 0.00 0.00 4.75
4469 4838 9.998106 GAACTGTATAATTATTTCTCCTGCCTA 57.002 33.333 2.68 0.00 0.00 3.93
4475 4844 8.946797 ATAATTATTTCTCCTGCCTAAATGCT 57.053 30.769 0.00 0.00 0.00 3.79
4476 4845 7.666063 AATTATTTCTCCTGCCTAAATGCTT 57.334 32.000 0.00 0.00 0.00 3.91
4477 4846 6.699575 TTATTTCTCCTGCCTAAATGCTTC 57.300 37.500 0.00 0.00 0.00 3.86
4478 4847 4.307032 TTTCTCCTGCCTAAATGCTTCT 57.693 40.909 0.00 0.00 0.00 2.85
4479 4848 4.307032 TTCTCCTGCCTAAATGCTTCTT 57.693 40.909 0.00 0.00 0.00 2.52
4552 4942 6.920210 GCAGAATTTTAATCCCTATTGACTGC 59.080 38.462 0.00 0.00 37.81 4.40
4585 4975 7.795734 CACGATTTATTACAGATGACTTCATGC 59.204 37.037 0.00 0.00 36.57 4.06
4626 5017 2.362077 GGGGAGAAAAATGCACGCATAT 59.638 45.455 4.68 0.00 35.31 1.78
4628 5019 4.044426 GGGAGAAAAATGCACGCATATTC 58.956 43.478 16.70 16.70 35.31 1.75
4629 5020 4.439974 GGGAGAAAAATGCACGCATATTCA 60.440 41.667 22.26 0.00 36.08 2.57
4632 5023 6.237648 GGAGAAAAATGCACGCATATTCAAAG 60.238 38.462 22.26 0.00 36.08 2.77
4633 5024 6.389091 AGAAAAATGCACGCATATTCAAAGA 58.611 32.000 22.26 0.00 36.08 2.52
4634 5025 7.037438 AGAAAAATGCACGCATATTCAAAGAT 58.963 30.769 22.26 7.67 36.08 2.40
4635 5026 6.578020 AAAATGCACGCATATTCAAAGATG 57.422 33.333 4.68 0.00 35.31 2.90
4637 5028 4.700268 TGCACGCATATTCAAAGATGTT 57.300 36.364 0.00 0.00 30.58 2.71
4639 5030 6.188400 TGCACGCATATTCAAAGATGTTTA 57.812 33.333 0.00 0.00 30.58 2.01
4669 5060 8.615878 TTTTGCTGATACTTACAATGTACAGT 57.384 30.769 0.33 0.00 0.00 3.55
4700 5091 4.523943 AGAGGCATGAAAAACATAGCAACA 59.476 37.500 0.00 0.00 37.46 3.33
4703 5094 4.143347 GGCATGAAAAACATAGCAACAACG 60.143 41.667 0.00 0.00 37.46 4.10
4773 5164 8.292448 ACAAGTAAATCAACAACAGCAATAGAG 58.708 33.333 0.00 0.00 0.00 2.43
4803 5194 7.545362 AAAAGATCTTGATGGACTTATCACG 57.455 36.000 9.17 0.00 36.84 4.35
4804 5195 5.860941 AGATCTTGATGGACTTATCACGT 57.139 39.130 0.00 0.00 36.84 4.49
4806 5197 7.348080 AGATCTTGATGGACTTATCACGTAA 57.652 36.000 0.00 0.00 36.84 3.18
4808 5199 7.707035 AGATCTTGATGGACTTATCACGTAAAC 59.293 37.037 0.00 0.00 36.84 2.01
4822 5215 1.668751 CGTAAACACTTGTGCCACTGT 59.331 47.619 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.667212 AGTGTCAAAAACGTTCGGGAC 59.333 47.619 0.00 10.00 0.00 4.46
15 16 3.125316 TCCTAGTGTCAAAAACGTTCGG 58.875 45.455 0.00 0.00 0.00 4.30
16 17 3.183775 CCTCCTAGTGTCAAAAACGTTCG 59.816 47.826 0.00 0.00 0.00 3.95
17 18 4.374399 TCCTCCTAGTGTCAAAAACGTTC 58.626 43.478 0.00 0.00 0.00 3.95
18 19 4.411256 TCCTCCTAGTGTCAAAAACGTT 57.589 40.909 0.00 0.00 0.00 3.99
19 20 4.141779 ACTTCCTCCTAGTGTCAAAAACGT 60.142 41.667 0.00 0.00 0.00 3.99
20 21 4.377897 ACTTCCTCCTAGTGTCAAAAACG 58.622 43.478 0.00 0.00 0.00 3.60
21 22 6.990939 AGTTACTTCCTCCTAGTGTCAAAAAC 59.009 38.462 0.00 0.00 0.00 2.43
22 23 6.990349 CAGTTACTTCCTCCTAGTGTCAAAAA 59.010 38.462 0.00 0.00 0.00 1.94
23 24 6.325545 TCAGTTACTTCCTCCTAGTGTCAAAA 59.674 38.462 0.00 0.00 0.00 2.44
24 25 5.836898 TCAGTTACTTCCTCCTAGTGTCAAA 59.163 40.000 0.00 0.00 0.00 2.69
25 26 5.391256 TCAGTTACTTCCTCCTAGTGTCAA 58.609 41.667 0.00 0.00 0.00 3.18
26 27 4.994282 TCAGTTACTTCCTCCTAGTGTCA 58.006 43.478 0.00 0.00 0.00 3.58
27 28 7.642082 TTATCAGTTACTTCCTCCTAGTGTC 57.358 40.000 0.00 0.00 0.00 3.67
28 29 8.611051 AATTATCAGTTACTTCCTCCTAGTGT 57.389 34.615 0.00 0.00 0.00 3.55
29 30 9.892130 AAAATTATCAGTTACTTCCTCCTAGTG 57.108 33.333 0.00 0.00 0.00 2.74
81 82 0.035915 GAAGCTTCTCACAGGGGGTC 60.036 60.000 19.44 0.00 0.00 4.46
86 87 0.034059 ACGTGGAAGCTTCTCACAGG 59.966 55.000 30.46 24.32 32.34 4.00
87 88 1.871080 AACGTGGAAGCTTCTCACAG 58.129 50.000 30.46 26.12 32.34 3.66
89 90 2.288886 ACCTAACGTGGAAGCTTCTCAC 60.289 50.000 25.05 25.53 0.00 3.51
93 97 2.338500 CTCACCTAACGTGGAAGCTTC 58.662 52.381 18.54 18.54 43.23 3.86
112 116 1.697982 GTATAATCCTTCCCCACGCCT 59.302 52.381 0.00 0.00 0.00 5.52
137 141 1.266989 GAGTTTTTGGGTTCGAGGCAG 59.733 52.381 0.00 0.00 0.00 4.85
141 145 3.625764 TGTCAAGAGTTTTTGGGTTCGAG 59.374 43.478 0.00 0.00 0.00 4.04
151 155 3.023832 CCCCACTTGTGTCAAGAGTTTT 58.976 45.455 15.04 0.00 0.00 2.43
152 156 2.241176 TCCCCACTTGTGTCAAGAGTTT 59.759 45.455 15.04 0.00 0.00 2.66
154 158 1.417890 CTCCCCACTTGTGTCAAGAGT 59.582 52.381 15.04 0.28 0.00 3.24
161 165 2.104281 GTGAAGTACTCCCCACTTGTGT 59.896 50.000 12.85 0.00 36.38 3.72
194 202 3.258123 TCATTTTGTTAGAAAGGGCAGGC 59.742 43.478 0.00 0.00 0.00 4.85
279 294 3.012959 ACCTCTCTCTTGGTTAGGATCCA 59.987 47.826 15.82 0.00 31.62 3.41
289 304 4.750021 TTCATGATGACCTCTCTCTTGG 57.250 45.455 0.00 0.00 0.00 3.61
299 314 6.149308 TGTGTCAACAACTATTCATGATGACC 59.851 38.462 15.58 9.71 44.19 4.02
300 315 7.132694 TGTGTCAACAACTATTCATGATGAC 57.867 36.000 12.69 12.69 44.71 3.06
426 444 5.576774 GTGCTGGAGTAAAATGGCAATTTAC 59.423 40.000 24.09 24.09 41.42 2.01
547 606 2.561419 CCTGGGACACTTTTCTCTCGTA 59.439 50.000 0.00 0.00 0.00 3.43
549 608 1.338200 CCCTGGGACACTTTTCTCTCG 60.338 57.143 7.01 0.00 0.00 4.04
590 649 1.006832 TCGTTACGCCGGAGTACTAC 58.993 55.000 18.33 13.25 0.00 2.73
591 650 1.006832 GTCGTTACGCCGGAGTACTA 58.993 55.000 18.33 1.10 0.00 1.82
592 651 1.796796 GTCGTTACGCCGGAGTACT 59.203 57.895 18.33 0.00 0.00 2.73
645 709 5.093677 TGATCTTTAGATGGGCTATGCCTA 58.906 41.667 8.56 2.52 44.78 3.93
801 868 1.075600 GAGAGGGTGAGGGAGAGGG 60.076 68.421 0.00 0.00 0.00 4.30
802 869 1.144913 CTAGAGAGGGTGAGGGAGAGG 59.855 61.905 0.00 0.00 0.00 3.69
803 870 2.131854 TCTAGAGAGGGTGAGGGAGAG 58.868 57.143 0.00 0.00 0.00 3.20
804 871 1.847737 GTCTAGAGAGGGTGAGGGAGA 59.152 57.143 0.00 0.00 0.00 3.71
805 872 1.476110 CGTCTAGAGAGGGTGAGGGAG 60.476 61.905 0.00 0.00 0.00 4.30
806 873 0.547075 CGTCTAGAGAGGGTGAGGGA 59.453 60.000 0.00 0.00 0.00 4.20
1123 1224 1.227350 CGCCAATCGATCCAGAGCA 60.227 57.895 0.00 0.00 41.67 4.26
1167 1271 2.886523 CAACAAATCAGAAGGAGTGGCA 59.113 45.455 0.00 0.00 0.00 4.92
1170 1274 5.762218 AGAAGACAACAAATCAGAAGGAGTG 59.238 40.000 0.00 0.00 0.00 3.51
1184 1288 6.049149 CAGGTTAGACAGAAAGAAGACAACA 58.951 40.000 0.00 0.00 0.00 3.33
1214 1318 2.302733 GTTACCCCGTTCCCACTTCTTA 59.697 50.000 0.00 0.00 0.00 2.10
1374 1485 1.065709 AGGACGGTCGCCATTTACAAT 60.066 47.619 1.43 0.00 0.00 2.71
1376 1487 0.108520 GAGGACGGTCGCCATTTACA 60.109 55.000 1.43 0.00 0.00 2.41
1379 1490 1.218316 GAGAGGACGGTCGCCATTT 59.782 57.895 1.43 0.00 0.00 2.32
1402 1514 7.012607 ACCTCCCAATTGGATTATCTTATTGG 58.987 38.462 26.60 21.02 44.07 3.16
1403 1515 7.177392 GGACCTCCCAATTGGATTATCTTATTG 59.823 40.741 26.60 4.36 44.07 1.90
1404 1516 7.146960 TGGACCTCCCAATTGGATTATCTTATT 60.147 37.037 26.60 0.00 44.07 1.40
1483 1599 4.439700 CCCTGTGCATGATTTTCTAAGCAG 60.440 45.833 0.00 0.00 32.43 4.24
1541 1674 2.652348 TCTAAATTGCCCTTCCCTTCCA 59.348 45.455 0.00 0.00 0.00 3.53
1586 1719 6.658831 AGATGTCAACAAAGTTTATGTCGTG 58.341 36.000 0.00 0.00 0.00 4.35
1591 1724 8.562892 AGAGTGAAGATGTCAACAAAGTTTATG 58.437 33.333 0.00 0.00 38.23 1.90
1632 1769 3.696051 ACAGCTTCATGACACAAAACACT 59.304 39.130 0.00 0.00 0.00 3.55
1633 1770 4.032703 ACAGCTTCATGACACAAAACAC 57.967 40.909 0.00 0.00 0.00 3.32
1634 1771 3.242706 CGACAGCTTCATGACACAAAACA 60.243 43.478 0.00 0.00 0.00 2.83
1635 1772 3.002246 TCGACAGCTTCATGACACAAAAC 59.998 43.478 0.00 0.00 0.00 2.43
1642 1786 4.083855 TGAAACATTCGACAGCTTCATGAC 60.084 41.667 0.00 0.00 0.00 3.06
1643 1787 4.064388 TGAAACATTCGACAGCTTCATGA 58.936 39.130 0.00 0.00 0.00 3.07
1645 1789 5.181811 TCATTGAAACATTCGACAGCTTCAT 59.818 36.000 3.75 0.00 0.00 2.57
1653 1797 4.386049 AGAGACGTCATTGAAACATTCGAC 59.614 41.667 19.50 0.00 0.00 4.20
1736 1880 5.743026 TCAGCGAGAAAGATAGTAGAGTG 57.257 43.478 0.00 0.00 0.00 3.51
1808 1952 4.511454 GCGTTATATGCAGGAAAGATGTGA 59.489 41.667 0.00 0.00 0.00 3.58
1861 2005 4.937620 GCTTACTCACATGAATTGTCAGGA 59.062 41.667 0.00 0.00 37.78 3.86
1957 2101 5.266733 ACTGAACAAAGCAAACACATGAT 57.733 34.783 0.00 0.00 0.00 2.45
1972 2116 4.080582 TCAGGACTTTTCTCCAACTGAACA 60.081 41.667 0.00 0.00 31.30 3.18
2004 2148 4.130118 ACGTTGAAGCTCTCAGAAAATGT 58.870 39.130 0.00 0.00 34.81 2.71
2005 2149 4.739046 ACGTTGAAGCTCTCAGAAAATG 57.261 40.909 0.00 0.00 34.81 2.32
2133 2280 4.989277 TGCTGTATGATCATAATGGCCTT 58.011 39.130 16.97 0.00 0.00 4.35
2136 2283 3.754850 TGCTGCTGTATGATCATAATGGC 59.245 43.478 16.97 18.82 0.00 4.40
2195 2342 4.467082 AGTCTTAAATGCAATCATGGCCAA 59.533 37.500 10.96 0.00 32.23 4.52
2198 2345 5.870978 ACAAAGTCTTAAATGCAATCATGGC 59.129 36.000 0.00 0.00 32.23 4.40
2251 2402 6.296259 GGTTCCCTTGATAAGAAACTAGGTCA 60.296 42.308 0.00 0.00 0.00 4.02
2252 2403 6.070136 AGGTTCCCTTGATAAGAAACTAGGTC 60.070 42.308 0.00 0.00 35.82 3.85
2432 2588 7.275123 GGAAGATGAAAAGATCACAAAATGCTC 59.725 37.037 0.00 0.00 41.93 4.26
2451 2607 6.207417 ACATGTGTAGGTGAAAAAGGAAGATG 59.793 38.462 0.00 0.00 0.00 2.90
2523 2679 4.565022 ACCAAACCAACAACAAAACTGAG 58.435 39.130 0.00 0.00 0.00 3.35
2527 2683 6.814146 TGAATAGACCAAACCAACAACAAAAC 59.186 34.615 0.00 0.00 0.00 2.43
2802 2958 6.424883 AGGAGCTGAAGAATCATGAGAAAAT 58.575 36.000 0.09 0.00 34.37 1.82
2964 3120 1.270550 CAAGGGCAGTGGTGATCAAAC 59.729 52.381 0.00 0.00 0.00 2.93
3066 3222 1.134670 CAGTAAGGGCTGTCAGGTAGC 60.135 57.143 1.14 0.00 40.41 3.58
3220 3376 4.403752 ACTGAACGATGATCCTTCATGAGA 59.596 41.667 7.20 0.00 42.73 3.27
3235 3391 1.691195 TTGCCTCCACCACTGAACGA 61.691 55.000 0.00 0.00 0.00 3.85
3408 3564 4.722194 CAGTCCATGTACCAATGTTTTCG 58.278 43.478 0.00 0.00 0.00 3.46
3424 3580 3.264193 ACATTGTATCTCAAGGCAGTCCA 59.736 43.478 0.00 0.00 40.88 4.02
3483 3646 8.043710 GCCAGTGTAAGCATTATATCTTATCCT 58.956 37.037 0.00 0.00 30.46 3.24
3484 3647 8.043710 AGCCAGTGTAAGCATTATATCTTATCC 58.956 37.037 0.00 0.00 30.46 2.59
3708 4065 4.305769 GAAGCAATTGTGTATGCAACCAA 58.694 39.130 7.40 0.00 44.95 3.67
3932 4289 1.276421 GCCCAGCTCTAAGTCACTCAA 59.724 52.381 0.00 0.00 0.00 3.02
3947 4304 0.813184 CCATTGCTTGTAGTGCCCAG 59.187 55.000 0.00 0.00 0.00 4.45
4210 4568 6.857451 GCCAAATTCATCCAAATTTCAAACAC 59.143 34.615 0.00 0.00 36.86 3.32
4268 4626 3.770933 ACCAATCAATCAACATTCCCCAG 59.229 43.478 0.00 0.00 0.00 4.45
4362 4731 4.718774 AGATACTCTTCCTGGAATCTTGCA 59.281 41.667 10.03 0.00 0.00 4.08
4425 4794 5.483937 ACAGTTCAATGGTCTACACCTATGA 59.516 40.000 0.00 0.00 44.17 2.15
4460 4829 2.948315 GGAAGAAGCATTTAGGCAGGAG 59.052 50.000 0.00 0.00 35.83 3.69
4461 4830 2.308570 TGGAAGAAGCATTTAGGCAGGA 59.691 45.455 0.00 0.00 35.83 3.86
4462 4831 2.424956 GTGGAAGAAGCATTTAGGCAGG 59.575 50.000 0.00 0.00 35.83 4.85
4463 4832 2.424956 GGTGGAAGAAGCATTTAGGCAG 59.575 50.000 0.00 0.00 35.83 4.85
4464 4833 2.446435 GGTGGAAGAAGCATTTAGGCA 58.554 47.619 0.00 0.00 35.83 4.75
4465 4834 1.401905 CGGTGGAAGAAGCATTTAGGC 59.598 52.381 0.00 0.00 0.00 3.93
4466 4835 2.017049 CCGGTGGAAGAAGCATTTAGG 58.983 52.381 0.00 0.00 0.00 2.69
4467 4836 1.401905 GCCGGTGGAAGAAGCATTTAG 59.598 52.381 1.90 0.00 0.00 1.85
4468 4837 1.459450 GCCGGTGGAAGAAGCATTTA 58.541 50.000 1.90 0.00 0.00 1.40
4469 4838 1.250840 GGCCGGTGGAAGAAGCATTT 61.251 55.000 1.90 0.00 0.00 2.32
4470 4839 1.678970 GGCCGGTGGAAGAAGCATT 60.679 57.895 1.90 0.00 0.00 3.56
4471 4840 2.044946 GGCCGGTGGAAGAAGCAT 60.045 61.111 1.90 0.00 0.00 3.79
4472 4841 2.819984 GATGGCCGGTGGAAGAAGCA 62.820 60.000 1.90 0.00 0.00 3.91
4473 4842 2.044946 ATGGCCGGTGGAAGAAGC 60.045 61.111 1.90 0.00 0.00 3.86
4474 4843 0.745845 CAGATGGCCGGTGGAAGAAG 60.746 60.000 1.90 0.00 0.00 2.85
4475 4844 1.198094 TCAGATGGCCGGTGGAAGAA 61.198 55.000 1.90 0.00 0.00 2.52
4476 4845 0.982852 ATCAGATGGCCGGTGGAAGA 60.983 55.000 1.90 0.00 0.00 2.87
4477 4846 0.816825 CATCAGATGGCCGGTGGAAG 60.817 60.000 1.90 0.00 0.00 3.46
4478 4847 1.224315 CATCAGATGGCCGGTGGAA 59.776 57.895 1.90 0.00 0.00 3.53
4479 4848 1.056125 ATCATCAGATGGCCGGTGGA 61.056 55.000 10.67 0.00 31.91 4.02
4518 4907 7.325694 AGGGATTAAAATTCTGCATGTCAAAG 58.674 34.615 0.00 0.00 0.00 2.77
4552 4942 5.469373 TCTGTAATAAATCGTGCTGCAAG 57.531 39.130 2.77 6.57 0.00 4.01
4561 4951 7.005958 CGCATGAAGTCATCTGTAATAAATCG 58.994 38.462 0.00 0.00 33.61 3.34
4585 4975 3.089784 GCCAATGGCGTGTACTCG 58.910 61.111 9.14 12.77 39.62 4.18
4644 5035 8.615878 ACTGTACATTGTAAGTATCAGCAAAA 57.384 30.769 0.00 0.00 30.62 2.44
4646 5037 9.713713 TTTACTGTACATTGTAAGTATCAGCAA 57.286 29.630 14.24 6.42 31.46 3.91
4647 5038 9.366216 CTTTACTGTACATTGTAAGTATCAGCA 57.634 33.333 14.24 2.01 31.46 4.41
4648 5039 9.367444 ACTTTACTGTACATTGTAAGTATCAGC 57.633 33.333 11.36 0.00 31.46 4.26
4654 5045 9.477484 CTCTGAACTTTACTGTACATTGTAAGT 57.523 33.333 0.00 3.15 31.46 2.24
4655 5046 8.926710 CCTCTGAACTTTACTGTACATTGTAAG 58.073 37.037 0.00 2.53 31.46 2.34
4669 5060 6.707440 TGTTTTTCATGCCTCTGAACTTTA 57.293 33.333 0.00 0.00 34.96 1.85
4700 5091 7.222000 TGGCAAGAAATATAAAGGTTTCGTT 57.778 32.000 0.00 0.00 38.89 3.85
4703 5094 9.875691 AAGAATGGCAAGAAATATAAAGGTTTC 57.124 29.630 0.00 0.00 35.18 2.78
4803 5194 3.875134 AGTACAGTGGCACAAGTGTTTAC 59.125 43.478 21.41 11.14 44.16 2.01
4804 5195 3.874543 CAGTACAGTGGCACAAGTGTTTA 59.125 43.478 21.41 0.00 44.16 2.01
4806 5197 2.288666 CAGTACAGTGGCACAAGTGTT 58.711 47.619 21.41 7.76 44.16 3.32
4808 5199 1.229428 CCAGTACAGTGGCACAAGTG 58.771 55.000 21.41 16.16 44.16 3.16
4822 5215 4.141711 GGCCTGTGAATGAATAGACCAGTA 60.142 45.833 0.00 0.00 0.00 2.74
4944 5337 2.626840 GAGAAGGTGATCCTGCAGTTC 58.373 52.381 13.81 9.83 44.35 3.01
4980 5373 0.982673 CGTCAAGTTCATCGTCGTCC 59.017 55.000 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.