Multiple sequence alignment - TraesCS4D01G243600

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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 TraesCS4D01G243600 chr4D 100.000 4292 0 0 1 4292 406234635 406230344 0.000000e+00 7926.0
1 TraesCS4D01G243600 chr4D 77.612 402 60 17 159 559 406234606 406234978 2.600000e-52 217.0
2 TraesCS4D01G243600 chr4B 95.854 2412 82 12 893 3300 505546468 505544071 0.000000e+00 3884.0
3 TraesCS4D01G243600 chr4B 89.107 560 28 14 3340 3882 505543943 505543400 0.000000e+00 665.0
4 TraesCS4D01G243600 chr4B 91.667 336 13 6 553 884 505546838 505546514 6.540000e-123 451.0
5 TraesCS4D01G243600 chr4B 85.581 430 30 14 3869 4285 505539911 505539501 5.130000e-114 422.0
6 TraesCS4D01G243600 chr4A 90.587 1806 102 32 410 2183 63827944 63826175 0.000000e+00 2331.0
7 TraesCS4D01G243600 chr4A 90.048 1256 44 25 2225 3423 63826173 63824942 0.000000e+00 1552.0
8 TraesCS4D01G243600 chr4A 88.889 810 33 21 3488 4281 63824438 63823670 0.000000e+00 944.0
9 TraesCS4D01G243600 chr4A 90.663 407 19 11 1 403 63828383 63827992 1.370000e-144 523.0
10 TraesCS4D01G243600 chr4A 78.673 422 62 22 145 561 63828340 63828738 5.510000e-64 255.0
11 TraesCS4D01G243600 chrUn 89.552 335 30 4 1495 1827 316220296 316219965 1.850000e-113 420.0
12 TraesCS4D01G243600 chrUn 91.064 235 19 1 1903 2137 316219960 316219728 2.490000e-82 316.0
13 TraesCS4D01G243600 chr6D 89.552 335 30 4 1495 1827 216943129 216943460 1.850000e-113 420.0
14 TraesCS4D01G243600 chr6D 90.756 238 20 1 1900 2137 216943462 216943697 2.490000e-82 316.0
15 TraesCS4D01G243600 chr5D 89.552 335 30 4 1495 1827 285500871 285501202 1.850000e-113 420.0
16 TraesCS4D01G243600 chr5D 81.336 434 55 16 1 430 454832135 454832546 3.200000e-86 329.0
17 TraesCS4D01G243600 chr5D 80.876 434 61 13 1 430 455601769 455602184 5.350000e-84 322.0
18 TraesCS4D01G243600 chr5D 90.756 238 20 1 1900 2137 285501204 285501439 2.490000e-82 316.0
19 TraesCS4D01G243600 chr5D 80.781 333 44 13 226 554 455601752 455601436 4.290000e-60 243.0
20 TraesCS4D01G243600 chr5D 77.844 334 40 21 257 563 389004173 389003847 4.410000e-40 176.0
21 TraesCS4D01G243600 chr5D 77.778 189 29 5 3 189 498311142 498310965 2.110000e-18 104.0
22 TraesCS4D01G243600 chr5D 83.951 81 7 2 3405 3479 285542971 285543051 5.950000e-09 73.1
23 TraesCS4D01G243600 chr5A 81.250 432 54 15 3 430 572215711 572216119 1.490000e-84 324.0
24 TraesCS4D01G243600 chr2B 76.965 369 61 17 3 353 743698833 743698471 5.670000e-44 189.0
25 TraesCS4D01G243600 chr7A 84.393 173 19 7 391 557 182859293 182859463 3.430000e-36 163.0
26 TraesCS4D01G243600 chr7A 84.848 99 12 3 114 209 735479308 735479406 3.530000e-16 97.1
27 TraesCS4D01G243600 chr6B 83.243 185 23 7 381 559 42575263 42575081 3.430000e-36 163.0
28 TraesCS4D01G243600 chr7D 84.568 162 21 3 398 555 591483596 591483757 1.600000e-34 158.0
29 TraesCS4D01G243600 chr7D 87.218 133 13 4 429 559 567338208 567338338 9.620000e-32 148.0
30 TraesCS4D01G243600 chr7D 83.810 105 15 2 147 249 634722500 634722396 9.820000e-17 99.0
31 TraesCS4D01G243600 chr3B 88.148 135 13 3 429 562 82825337 82825469 1.600000e-34 158.0
32 TraesCS4D01G243600 chr2D 90.833 120 6 4 436 554 484379182 484379067 5.750000e-34 156.0
33 TraesCS4D01G243600 chr5B 83.000 100 16 1 109 208 617635618 617635520 5.910000e-14 89.8


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 TraesCS4D01G243600 chr4D 406230344 406234635 4291 True 7926.0 7926 100.00000 1 4292 1 chr4D.!!$R1 4291
1 TraesCS4D01G243600 chr4B 505539501 505546838 7337 True 1355.5 3884 90.55225 553 4285 4 chr4B.!!$R1 3732
2 TraesCS4D01G243600 chr4A 63823670 63828383 4713 True 1337.5 2331 90.04675 1 4281 4 chr4A.!!$R1 4280
3 TraesCS4D01G243600 chrUn 316219728 316220296 568 True 368.0 420 90.30800 1495 2137 2 chrUn.!!$R1 642
4 TraesCS4D01G243600 chr6D 216943129 216943697 568 False 368.0 420 90.15400 1495 2137 2 chr6D.!!$F1 642
5 TraesCS4D01G243600 chr5D 285500871 285501439 568 False 368.0 420 90.15400 1495 2137 2 chr5D.!!$F4 642

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
946 1044 0.251832 TCTGCTCGTCCCTTCCTCTT 60.252 55.0 0.00 0.0 0.0 2.85 F
1544 1649 0.027586 GTGATGTTTATGTCGCGGGC 59.972 55.0 6.13 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1807 1919 0.820871 CTGACGGAAGAGGGAGAAGG 59.179 60.0 0.0 0.0 0.0 3.46 R
3531 4235 0.870393 TGTGTCTGTACGTCCGTCTC 59.130 55.0 0.0 0.0 0.0 3.36 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 3.751767 AGCAAGATTCTTGGGTGCA 57.248 47.368 24.09 0.00 37.68 4.57
42 43 8.382030 CACTAGGTGCATGAATATTTGTATGA 57.618 34.615 0.00 0.00 0.00 2.15
72 73 3.251004 ACATTCAAGGAGCTCGTGAAAAC 59.749 43.478 26.16 5.80 44.50 2.43
76 77 3.692101 TCAAGGAGCTCGTGAAAACAAAA 59.308 39.130 10.16 0.00 31.17 2.44
77 78 4.156922 TCAAGGAGCTCGTGAAAACAAAAA 59.843 37.500 10.16 0.00 31.17 1.94
78 79 4.028852 AGGAGCTCGTGAAAACAAAAAC 57.971 40.909 8.40 0.00 0.00 2.43
79 80 3.442273 AGGAGCTCGTGAAAACAAAAACA 59.558 39.130 8.40 0.00 0.00 2.83
80 81 4.082463 AGGAGCTCGTGAAAACAAAAACAA 60.082 37.500 8.40 0.00 0.00 2.83
81 82 4.623595 GGAGCTCGTGAAAACAAAAACAAA 59.376 37.500 7.83 0.00 0.00 2.83
82 83 5.119434 GGAGCTCGTGAAAACAAAAACAAAA 59.881 36.000 7.83 0.00 0.00 2.44
84 85 7.127917 AGCTCGTGAAAACAAAAACAAAATT 57.872 28.000 0.00 0.00 0.00 1.82
85 86 7.580600 AGCTCGTGAAAACAAAAACAAAATTT 58.419 26.923 0.00 0.00 0.00 1.82
86 87 7.533561 AGCTCGTGAAAACAAAAACAAAATTTG 59.466 29.630 3.89 3.89 42.18 2.32
87 88 7.532209 GCTCGTGAAAACAAAAACAAAATTTGA 59.468 29.630 13.19 0.00 39.56 2.69
88 89 8.700994 TCGTGAAAACAAAAACAAAATTTGAC 57.299 26.923 13.19 0.00 39.56 3.18
89 90 8.552034 TCGTGAAAACAAAAACAAAATTTGACT 58.448 25.926 13.19 0.00 39.56 3.41
90 91 8.826658 CGTGAAAACAAAAACAAAATTTGACTC 58.173 29.630 13.19 1.16 39.56 3.36
91 92 9.657121 GTGAAAACAAAAACAAAATTTGACTCA 57.343 25.926 13.19 3.28 39.56 3.41
255 259 8.484641 TTGAATTTACAGTTCATCTAGAGCAG 57.515 34.615 0.00 0.00 35.68 4.24
258 262 8.854614 AATTTACAGTTCATCTAGAGCAGTTT 57.145 30.769 0.00 0.00 30.29 2.66
260 264 7.658179 TTACAGTTCATCTAGAGCAGTTTTG 57.342 36.000 0.00 0.00 30.29 2.44
262 266 6.759272 ACAGTTCATCTAGAGCAGTTTTGTA 58.241 36.000 0.00 0.00 0.00 2.41
263 267 7.390027 ACAGTTCATCTAGAGCAGTTTTGTAT 58.610 34.615 0.00 0.00 0.00 2.29
266 270 9.289782 AGTTCATCTAGAGCAGTTTTGTATTTT 57.710 29.630 0.00 0.00 0.00 1.82
318 322 8.409371 TGTTCAAACACTATGAAAATTAGCACA 58.591 29.630 0.00 0.00 38.44 4.57
418 462 0.400213 TCCATCAGCGAAACCTGGTT 59.600 50.000 6.18 6.18 33.64 3.67
424 468 2.035704 TCAGCGAAACCTGGTTAACGTA 59.964 45.455 26.95 16.77 33.64 3.57
442 488 6.481954 AACGTAGTCAATCTGATTTTGGAC 57.518 37.500 0.00 5.79 45.00 4.02
447 493 6.089249 AGTCAATCTGATTTTGGACCAAAC 57.911 37.500 19.42 9.67 32.79 2.93
512 558 4.957327 AGTCTTGAGGGACCAAGTCTATAC 59.043 45.833 0.00 0.00 42.95 1.47
525 571 6.890268 ACCAAGTCTATACTTTTGGGGAATTC 59.110 38.462 0.00 0.00 43.60 2.17
526 572 6.038271 CCAAGTCTATACTTTTGGGGAATTCG 59.962 42.308 0.00 0.00 43.60 3.34
538 584 2.092323 GGGAATTCGAGGGACCAAAAG 58.908 52.381 0.00 0.00 0.00 2.27
542 588 2.286365 TTCGAGGGACCAAAAGCATT 57.714 45.000 0.00 0.00 0.00 3.56
543 589 2.286365 TCGAGGGACCAAAAGCATTT 57.714 45.000 0.00 0.00 42.41 2.32
813 864 9.057911 TCTCTCCCTTAGATTTCCTTTATCAAA 57.942 33.333 0.00 0.00 32.41 2.69
815 866 9.462606 TCTCCCTTAGATTTCCTTTATCAAAAC 57.537 33.333 0.00 0.00 0.00 2.43
890 951 5.403766 GTCATATACATGCAAGAGGAACGAG 59.596 44.000 0.00 0.00 31.73 4.18
908 1006 9.862371 AGGAACGAGTTATATATTTATCTGCAG 57.138 33.333 7.63 7.63 0.00 4.41
946 1044 0.251832 TCTGCTCGTCCCTTCCTCTT 60.252 55.000 0.00 0.00 0.00 2.85
982 1080 2.667470 CGAGTTAATCTCCTCCCCTGA 58.333 52.381 0.00 0.00 39.84 3.86
1027 1125 1.202927 CCAGGAAGTTTCTCTTGGCCA 60.203 52.381 0.00 0.00 36.40 5.36
1069 1167 4.385825 TCTTCTTTACATGTTTCCGCACT 58.614 39.130 2.30 0.00 0.00 4.40
1244 1342 2.840651 AGGTATGTGAAACCAGCTAGCT 59.159 45.455 12.68 12.68 39.64 3.32
1272 1371 1.337260 GCTGCTCTGTTTCTTCCGAGA 60.337 52.381 0.00 0.00 0.00 4.04
1328 1432 0.584396 TGCGTTTACAGGCGTTTCTG 59.416 50.000 0.00 0.00 40.40 3.02
1367 1471 1.609501 CAACTCCTCCTCCGACCCA 60.610 63.158 0.00 0.00 0.00 4.51
1460 1564 1.167851 CCACGATCACAGCAATGGTT 58.832 50.000 0.00 0.00 0.00 3.67
1480 1584 3.770040 TCAGGCCACCGGTGATCG 61.770 66.667 36.07 20.06 38.88 3.69
1481 1585 3.770040 CAGGCCACCGGTGATCGA 61.770 66.667 36.07 0.00 42.43 3.59
1482 1586 2.764128 AGGCCACCGGTGATCGAT 60.764 61.111 36.07 13.60 42.43 3.59
1483 1587 2.280186 GGCCACCGGTGATCGATC 60.280 66.667 36.07 18.72 42.43 3.69
1544 1649 0.027586 GTGATGTTTATGTCGCGGGC 59.972 55.000 6.13 0.00 0.00 6.13
1807 1919 1.227205 CTCACCGAGCCTGCATCTC 60.227 63.158 6.15 6.15 0.00 2.75
2020 2137 3.248171 GCACGTCGTGATCGCCTC 61.248 66.667 28.83 5.36 35.23 4.70
2158 2275 1.806542 CACAGGTACACTCCAATGCAC 59.193 52.381 0.00 0.00 0.00 4.57
2200 2317 6.652481 ACATCATCCGATTCATTTATCCAGTC 59.348 38.462 0.00 0.00 0.00 3.51
2203 2320 5.777850 TCCGATTCATTTATCCAGTCGTA 57.222 39.130 0.00 0.00 0.00 3.43
2237 2354 1.452145 TTGGCGAGCTTTGGTTGGTC 61.452 55.000 0.00 0.00 0.00 4.02
2243 2360 2.805295 CGAGCTTTGGTTGGTCACTGTA 60.805 50.000 0.00 0.00 32.79 2.74
2244 2361 3.412386 GAGCTTTGGTTGGTCACTGTAT 58.588 45.455 0.00 0.00 32.79 2.29
2245 2362 3.821033 GAGCTTTGGTTGGTCACTGTATT 59.179 43.478 0.00 0.00 32.79 1.89
2246 2363 4.215109 AGCTTTGGTTGGTCACTGTATTT 58.785 39.130 0.00 0.00 0.00 1.40
2250 2367 5.523438 TTGGTTGGTCACTGTATTTTTCC 57.477 39.130 0.00 0.00 0.00 3.13
2251 2372 4.798882 TGGTTGGTCACTGTATTTTTCCT 58.201 39.130 0.00 0.00 0.00 3.36
2256 2377 5.690865 TGGTCACTGTATTTTTCCTCTTGT 58.309 37.500 0.00 0.00 0.00 3.16
2258 2379 6.605594 TGGTCACTGTATTTTTCCTCTTGTTT 59.394 34.615 0.00 0.00 0.00 2.83
2272 2393 7.931578 TCCTCTTGTTTTTGTGAACTTTCTA 57.068 32.000 0.00 0.00 0.00 2.10
2307 2428 3.812262 CATATCCATTGTGTCTGGCTCA 58.188 45.455 0.00 0.00 33.56 4.26
2425 2546 4.599047 AATTTGAATTTGACGCCTCCAA 57.401 36.364 0.00 0.00 0.00 3.53
2426 2547 4.806640 ATTTGAATTTGACGCCTCCAAT 57.193 36.364 0.00 0.00 0.00 3.16
2702 2846 0.460311 AGCACCATGGTACTCTACGC 59.540 55.000 19.28 15.01 0.00 4.42
2710 2854 0.027848 GGTACTCTACGCGCTCTCAC 59.972 60.000 5.73 0.00 0.00 3.51
2931 3092 1.089920 CCAAGAAACCATGCTCCGAG 58.910 55.000 0.00 0.00 0.00 4.63
3012 3184 7.336931 TCTTTCTAGCAGTTGACAAGTTTCTTT 59.663 33.333 0.00 0.00 0.00 2.52
3053 3225 8.537049 AAAGTTTTTAACACACAGTAAAACCC 57.463 30.769 0.00 0.00 38.53 4.11
3207 3383 2.159170 TGTTTCTTTGGTCGGGCAAAAG 60.159 45.455 2.98 2.98 39.05 2.27
3266 3442 7.278868 CAGAGTTATAACACCAGGATTCAACTC 59.721 40.741 17.65 17.26 39.59 3.01
3300 3476 3.549221 CCGCGGACATGTAGTTTGTTTTT 60.549 43.478 24.07 0.00 0.00 1.94
3302 3478 4.553938 CGCGGACATGTAGTTTGTTTTTCT 60.554 41.667 0.00 0.00 0.00 2.52
3443 3880 3.054655 ACCCCCATGTACTGACATACAAC 60.055 47.826 0.00 0.00 44.82 3.32
3447 3884 5.106317 CCCCATGTACTGACATACAACAAAC 60.106 44.000 0.00 0.00 44.82 2.93
3482 3939 1.872952 TGCGGAGACTTTTCACATGTG 59.127 47.619 20.18 20.18 0.00 3.21
3486 3943 3.607775 CGGAGACTTTTCACATGTGCTTG 60.608 47.826 21.38 12.58 0.00 4.01
3492 4196 0.385029 TTCACATGTGCTTGTGTGGC 59.615 50.000 21.38 0.00 45.73 5.01
3514 4218 6.151985 TGGCTAATTGTATGTCGGTTTGAAAT 59.848 34.615 0.00 0.00 0.00 2.17
3531 4235 7.148490 GGTTTGAAATTTTGAATATGAACGGGG 60.148 37.037 0.00 0.00 0.00 5.73
3545 4249 2.758089 CGGGGAGACGGACGTACAG 61.758 68.421 0.00 0.00 0.00 2.74
3660 4364 4.651503 ACGACTGTGAGAAGGAATATGGAT 59.348 41.667 0.00 0.00 0.00 3.41
3695 4399 4.812403 ATCCATCCATCCATTGGTGTAA 57.188 40.909 1.86 0.00 46.52 2.41
3697 4401 4.940483 TCCATCCATCCATTGGTGTAAAA 58.060 39.130 1.86 0.00 46.52 1.52
3699 4403 5.421693 TCCATCCATCCATTGGTGTAAAAAG 59.578 40.000 1.86 0.00 46.52 2.27
3700 4404 5.395546 CCATCCATCCATTGGTGTAAAAAGG 60.396 44.000 1.86 0.00 46.52 3.11
3701 4405 4.746466 TCCATCCATTGGTGTAAAAAGGT 58.254 39.130 1.86 0.00 46.52 3.50
3780 4487 3.998341 TCCTGAAAAAGATAACCGTTCCG 59.002 43.478 0.00 0.00 0.00 4.30
3887 8099 9.309516 GTATCAGAACCAGTTTTATATCGTTGA 57.690 33.333 0.00 0.00 0.00 3.18
3890 8102 7.279981 TCAGAACCAGTTTTATATCGTTGATGG 59.720 37.037 0.00 0.00 0.00 3.51
3919 8131 4.883006 AGTTTCCGGTGCTAAAGTTTTGTA 59.117 37.500 0.00 0.00 0.00 2.41
3920 8132 5.008316 AGTTTCCGGTGCTAAAGTTTTGTAG 59.992 40.000 0.00 0.00 0.00 2.74
3921 8133 4.075963 TCCGGTGCTAAAGTTTTGTAGT 57.924 40.909 0.00 0.00 0.00 2.73
3922 8134 5.212532 TCCGGTGCTAAAGTTTTGTAGTA 57.787 39.130 0.00 0.00 0.00 1.82
3923 8135 4.990426 TCCGGTGCTAAAGTTTTGTAGTAC 59.010 41.667 0.00 0.00 33.61 2.73
3924 8136 4.992951 CCGGTGCTAAAGTTTTGTAGTACT 59.007 41.667 0.00 0.00 34.48 2.73
3925 8137 6.015519 TCCGGTGCTAAAGTTTTGTAGTACTA 60.016 38.462 0.00 0.00 34.48 1.82
3926 8138 6.309737 CCGGTGCTAAAGTTTTGTAGTACTAG 59.690 42.308 1.87 0.00 34.48 2.57
3927 8139 6.865205 CGGTGCTAAAGTTTTGTAGTACTAGT 59.135 38.462 1.87 0.00 34.48 2.57
3928 8140 8.023128 CGGTGCTAAAGTTTTGTAGTACTAGTA 58.977 37.037 1.87 0.00 34.48 1.82
3929 8141 9.133627 GGTGCTAAAGTTTTGTAGTACTAGTAC 57.866 37.037 23.03 23.03 34.48 2.73
4004 8216 2.165167 TCCGCGGTGATTATACTAGGG 58.835 52.381 27.15 0.00 0.00 3.53
4222 8457 0.391927 TGCAATTAACGGACCCCTCG 60.392 55.000 0.00 0.00 0.00 4.63
4245 8480 1.433879 CACATCCTCGTCGTCCTCC 59.566 63.158 0.00 0.00 0.00 4.30
4289 8526 4.790962 CCTGCTGCCGCTCCACAT 62.791 66.667 0.70 0.00 36.97 3.21
4290 8527 3.506096 CTGCTGCCGCTCCACATG 61.506 66.667 0.70 0.00 36.97 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 9.006839 CATCATACAAATATTCATGCACCTAGT 57.993 33.333 0.00 0.00 0.00 2.57
39 40 5.479375 AGCTCCTTGAATGTCAAAACATCAT 59.521 36.000 0.00 0.00 45.48 2.45
49 50 2.370281 TCACGAGCTCCTTGAATGTC 57.630 50.000 8.47 0.00 0.00 3.06
119 120 8.304596 GTCAAATAACATCCGAGGTGATCTATA 58.695 37.037 0.00 0.00 0.00 1.31
127 128 3.008594 TGTGGTCAAATAACATCCGAGGT 59.991 43.478 0.00 0.00 0.00 3.85
228 230 9.283768 TGCTCTAGATGAACTGTAAATTCAAAA 57.716 29.630 0.00 0.00 39.43 2.44
269 273 2.656560 GAGGAGCTCGTAGCAAGAAA 57.343 50.000 9.29 0.00 45.56 2.52
279 283 5.933286 TGTTTGAACACTCGAGGAGCTCG 62.933 52.174 18.41 0.00 43.42 5.03
318 322 0.181114 TGCTCAAGTGCTCAAGGTGT 59.819 50.000 0.00 0.00 0.00 4.16
399 403 0.400213 AACCAGGTTTCGCTGATGGA 59.600 50.000 0.00 0.00 34.99 3.41
401 405 2.159707 CGTTAACCAGGTTTCGCTGATG 60.160 50.000 11.02 0.00 0.00 3.07
402 406 2.073816 CGTTAACCAGGTTTCGCTGAT 58.926 47.619 11.02 0.00 0.00 2.90
403 407 1.202557 ACGTTAACCAGGTTTCGCTGA 60.203 47.619 21.71 0.00 0.00 4.26
404 408 1.223187 ACGTTAACCAGGTTTCGCTG 58.777 50.000 21.71 8.24 0.00 5.18
405 409 2.036346 ACTACGTTAACCAGGTTTCGCT 59.964 45.455 21.71 14.55 0.00 4.93
406 410 2.407090 ACTACGTTAACCAGGTTTCGC 58.593 47.619 21.71 9.06 0.00 4.70
407 411 3.641648 TGACTACGTTAACCAGGTTTCG 58.358 45.455 11.02 17.39 0.00 3.46
408 412 5.930569 AGATTGACTACGTTAACCAGGTTTC 59.069 40.000 11.02 0.18 0.00 2.78
418 462 6.592607 GGTCCAAAATCAGATTGACTACGTTA 59.407 38.462 0.00 0.00 0.00 3.18
424 468 5.835280 AGTTTGGTCCAAAATCAGATTGACT 59.165 36.000 18.74 5.59 35.03 3.41
442 488 4.814771 AGTCTCAAAACCGAGTAAGTTTGG 59.185 41.667 0.00 0.00 37.50 3.28
447 493 5.634020 CCTACAAGTCTCAAAACCGAGTAAG 59.366 44.000 0.00 0.00 34.46 2.34
512 558 2.092323 GTCCCTCGAATTCCCCAAAAG 58.908 52.381 0.00 0.00 0.00 2.27
525 571 3.385193 AAAAATGCTTTTGGTCCCTCG 57.615 42.857 0.00 0.00 33.39 4.63
606 652 3.693578 TCTTGTCATAATGCGATGCCAAA 59.306 39.130 0.00 0.00 25.29 3.28
689 740 4.085357 ACTTAGCATCCGATGGCAATTA 57.915 40.909 10.41 0.00 0.00 1.40
754 805 3.187637 GCCATTCACGTGCTAAGTGTTTA 59.812 43.478 11.67 0.00 40.28 2.01
813 864 6.219417 GATCATCATCCGATCCTAGATGTT 57.781 41.667 12.35 5.59 40.63 2.71
925 1023 0.681564 GAGGAAGGGACGAGCAGAGA 60.682 60.000 0.00 0.00 0.00 3.10
946 1044 3.314307 ACTCGGTGATTATGGAGGAGA 57.686 47.619 0.00 0.00 0.00 3.71
1027 1125 6.606395 AGAAGAACTGATACGGTAGTAATGGT 59.394 38.462 0.00 0.00 36.29 3.55
1272 1371 2.159043 CGGAGTGCTGTTACATGGAGAT 60.159 50.000 0.00 0.00 0.00 2.75
1367 1471 2.670148 GGGCACGAGGAACAGGGAT 61.670 63.158 0.00 0.00 0.00 3.85
1460 1564 1.305802 ATCACCGGTGGCCTGACTA 60.306 57.895 33.40 12.86 0.00 2.59
1480 1584 4.543692 ACGGTATGCGTAGTATTGTGATC 58.456 43.478 0.00 0.00 32.95 2.92
1481 1585 4.579454 ACGGTATGCGTAGTATTGTGAT 57.421 40.909 0.00 0.00 32.95 3.06
1482 1586 4.096833 AGAACGGTATGCGTAGTATTGTGA 59.903 41.667 0.00 0.00 32.95 3.58
1483 1587 4.357142 AGAACGGTATGCGTAGTATTGTG 58.643 43.478 0.00 0.00 32.95 3.33
1544 1649 0.598680 GCGTTCCCCTGATCTGATCG 60.599 60.000 12.65 7.63 0.00 3.69
1797 1909 1.148048 GGGAGAAGGAGATGCAGGC 59.852 63.158 0.00 0.00 0.00 4.85
1807 1919 0.820871 CTGACGGAAGAGGGAGAAGG 59.179 60.000 0.00 0.00 0.00 3.46
1938 2055 3.077359 GGTTGCAGCTTCTGAAGTACAT 58.923 45.455 17.97 0.79 32.44 2.29
2200 2317 3.725356 CCAAAATCGATCGCATGATACG 58.275 45.455 11.09 0.00 34.09 3.06
2203 2320 1.069703 CGCCAAAATCGATCGCATGAT 60.070 47.619 11.09 0.00 37.60 2.45
2237 2354 8.594687 CACAAAAACAAGAGGAAAAATACAGTG 58.405 33.333 0.00 0.00 0.00 3.66
2243 2360 8.846943 AAGTTCACAAAAACAAGAGGAAAAAT 57.153 26.923 0.00 0.00 0.00 1.82
2244 2361 8.669946 AAAGTTCACAAAAACAAGAGGAAAAA 57.330 26.923 0.00 0.00 0.00 1.94
2245 2362 8.147704 AGAAAGTTCACAAAAACAAGAGGAAAA 58.852 29.630 0.00 0.00 0.00 2.29
2246 2363 7.666623 AGAAAGTTCACAAAAACAAGAGGAAA 58.333 30.769 0.00 0.00 0.00 3.13
2250 2367 7.698130 CCTGTAGAAAGTTCACAAAAACAAGAG 59.302 37.037 0.00 0.00 0.00 2.85
2251 2372 7.175990 ACCTGTAGAAAGTTCACAAAAACAAGA 59.824 33.333 0.00 0.00 0.00 3.02
2256 2377 7.338196 TCATCACCTGTAGAAAGTTCACAAAAA 59.662 33.333 0.00 0.00 0.00 1.94
2258 2379 6.260050 GTCATCACCTGTAGAAAGTTCACAAA 59.740 38.462 0.00 0.00 0.00 2.83
2272 2393 2.773661 TGGATATGCAGTCATCACCTGT 59.226 45.455 0.00 0.00 34.22 4.00
2307 2428 0.957395 CTGATGCCCGCACAAACTCT 60.957 55.000 0.00 0.00 0.00 3.24
2536 2672 1.913262 ACGTCAGAGACATGGGCCA 60.913 57.895 9.61 9.61 32.09 5.36
2702 2846 5.161358 TGAACTGTATTTGTAGTGAGAGCG 58.839 41.667 0.00 0.00 0.00 5.03
2931 3092 7.046652 GGATTTACTGTAGGAAAAGTACCTCC 58.953 42.308 0.00 0.00 38.76 4.30
3207 3383 2.662866 GAACATTTAAGGTAGGCCCCC 58.337 52.381 0.00 0.00 34.57 5.40
3266 3442 3.209097 CCGCGGTGCAATAAGGGG 61.209 66.667 19.50 0.00 0.00 4.79
3300 3476 7.373493 GGCAAAACTTGTGTACTACTACTAGA 58.627 38.462 0.00 0.00 0.00 2.43
3302 3478 6.041865 TGGGCAAAACTTGTGTACTACTACTA 59.958 38.462 0.00 0.00 0.00 1.82
3310 3486 8.085909 AGTATAAAATGGGCAAAACTTGTGTAC 58.914 33.333 0.00 0.00 0.00 2.90
3392 3656 7.704047 CGAGGGTACTTTTGGACTAGTAAATAC 59.296 40.741 0.00 0.00 0.00 1.89
3443 3880 4.201513 CCGCACGATGATTTGATTTGTTTG 60.202 41.667 0.00 0.00 0.00 2.93
3447 3884 3.063861 TCTCCGCACGATGATTTGATTTG 59.936 43.478 0.00 0.00 0.00 2.32
3482 3939 4.662145 GACATACAATTAGCCACACAAGC 58.338 43.478 0.00 0.00 0.00 4.01
3486 3943 3.267483 ACCGACATACAATTAGCCACAC 58.733 45.455 0.00 0.00 0.00 3.82
3514 4218 3.936453 CGTCTCCCCGTTCATATTCAAAA 59.064 43.478 0.00 0.00 0.00 2.44
3531 4235 0.870393 TGTGTCTGTACGTCCGTCTC 59.130 55.000 0.00 0.00 0.00 3.36
3545 4249 2.986306 GCCTGCCTGCACATGTGTC 61.986 63.158 26.01 18.27 0.00 3.67
3573 4277 8.255905 ACACAAGTACACAACTAAAGTCTAAGT 58.744 33.333 0.00 0.00 37.50 2.24
3641 4345 4.987285 CGTCATCCATATTCCTTCTCACAG 59.013 45.833 0.00 0.00 0.00 3.66
3660 4364 2.047655 GGATTGCACCGGACGTCA 60.048 61.111 18.91 0.00 0.00 4.35
3695 4399 3.465871 TGCGGACGTTTTACTACCTTTT 58.534 40.909 0.00 0.00 0.00 2.27
3697 4401 2.818130 TGCGGACGTTTTACTACCTT 57.182 45.000 0.00 0.00 0.00 3.50
3699 4403 3.364267 CCTTTTGCGGACGTTTTACTACC 60.364 47.826 0.00 0.00 0.00 3.18
3700 4404 3.364267 CCCTTTTGCGGACGTTTTACTAC 60.364 47.826 0.00 0.00 0.00 2.73
3701 4405 2.807392 CCCTTTTGCGGACGTTTTACTA 59.193 45.455 0.00 0.00 0.00 1.82
3780 4487 1.908483 GAGGGAGGACCACATGGAC 59.092 63.158 4.53 0.00 43.89 4.02
3851 4563 9.975218 AAAACTGGTTCTGATACATAAGGTTAT 57.025 29.630 0.00 0.00 0.00 1.89
3860 4572 9.093970 CAACGATATAAAACTGGTTCTGATACA 57.906 33.333 0.00 0.00 0.00 2.29
3861 4573 9.309516 TCAACGATATAAAACTGGTTCTGATAC 57.690 33.333 0.00 0.00 0.00 2.24
3887 8099 1.150536 ACCGGAAACTGTGCACCAT 59.849 52.632 15.69 0.00 0.00 3.55
3919 8131 9.202273 GTGCACGAAGTATATAGTACTAGTACT 57.798 37.037 32.39 32.39 44.39 2.73
3920 8132 8.439286 GGTGCACGAAGTATATAGTACTAGTAC 58.561 40.741 23.03 23.03 41.61 2.73
3921 8133 8.370940 AGGTGCACGAAGTATATAGTACTAGTA 58.629 37.037 11.45 0.00 41.61 1.82
3922 8134 7.222872 AGGTGCACGAAGTATATAGTACTAGT 58.777 38.462 11.45 0.00 41.61 2.57
3923 8135 7.670009 AGGTGCACGAAGTATATAGTACTAG 57.330 40.000 11.45 0.00 41.61 2.57
3924 8136 7.332926 GCTAGGTGCACGAAGTATATAGTACTA 59.667 40.741 11.45 4.77 41.61 1.82
3925 8137 6.149142 GCTAGGTGCACGAAGTATATAGTACT 59.851 42.308 11.45 0.00 41.61 2.73
3926 8138 6.149142 AGCTAGGTGCACGAAGTATATAGTAC 59.851 42.308 11.45 0.00 41.61 2.73
3927 8139 6.236409 AGCTAGGTGCACGAAGTATATAGTA 58.764 40.000 11.45 0.00 41.61 1.82
3928 8140 5.071370 AGCTAGGTGCACGAAGTATATAGT 58.929 41.667 11.45 0.00 41.61 2.12
3929 8141 5.630661 AGCTAGGTGCACGAAGTATATAG 57.369 43.478 11.45 4.12 41.61 1.31
3930 8142 5.123502 GCTAGCTAGGTGCACGAAGTATATA 59.876 44.000 22.10 2.96 41.61 0.86
3931 8143 4.082679 GCTAGCTAGGTGCACGAAGTATAT 60.083 45.833 22.10 2.01 41.61 0.86
4200 8427 0.956902 GGGGTCCGTTAATTGCACGT 60.957 55.000 10.15 0.00 35.81 4.49
4203 8430 0.391927 CGAGGGGTCCGTTAATTGCA 60.392 55.000 0.00 0.00 0.00 4.08
4222 8457 3.545481 CGACGAGGATGTGCGTGC 61.545 66.667 0.00 0.00 41.34 5.34


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

AutoCloner maintained by Alex Coulton.