Multiple sequence alignment - TraesCS6D01G318900

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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 TraesCS6D01G318900 chr6D 100.000 6793 0 0 1 6793 427128749 427121957 0.000000e+00 12545.0
1 TraesCS6D01G318900 chr6D 88.312 77 9 0 1706 1782 283796466 283796390 7.250000e-15 93.5
2 TraesCS6D01G318900 chr6A 94.143 4422 148 35 2348 6741 571848413 571844075 0.000000e+00 6628.0
3 TraesCS6D01G318900 chr6A 97.831 1614 30 3 602 2214 571850021 571848412 0.000000e+00 2782.0
4 TraesCS6D01G318900 chr6A 95.413 545 24 1 1 545 571850748 571850205 0.000000e+00 867.0
5 TraesCS6D01G318900 chr6A 87.500 96 7 3 2964 3059 268970413 268970323 9.320000e-19 106.0
6 TraesCS6D01G318900 chr6B 95.111 2557 85 15 3867 6400 642965352 642962813 0.000000e+00 3993.0
7 TraesCS6D01G318900 chr6B 94.785 1630 61 13 2220 3841 642972195 642970582 0.000000e+00 2518.0
8 TraesCS6D01G318900 chr6B 96.007 1177 35 7 2 1172 642974362 642973192 0.000000e+00 1903.0
9 TraesCS6D01G318900 chr6B 90.806 1055 41 13 1173 2222 642973161 642972158 0.000000e+00 1360.0
10 TraesCS6D01G318900 chr6B 94.052 269 15 1 6525 6792 642962819 642962551 2.280000e-109 407.0
11 TraesCS6D01G318900 chr6B 95.082 61 3 0 1725 1785 77881320 77881380 5.610000e-16 97.1
12 TraesCS6D01G318900 chr6B 92.063 63 5 0 1588 1650 679656445 679656507 9.380000e-14 89.8
13 TraesCS6D01G318900 chr6B 87.013 77 10 0 1706 1782 444683499 444683423 3.370000e-13 87.9
14 TraesCS6D01G318900 chr6B 96.875 32 1 0 943 974 642973154 642973185 3.000000e-03 54.7
15 TraesCS6D01G318900 chr5A 88.593 1464 99 26 2263 3684 706823978 706825415 0.000000e+00 1716.0
16 TraesCS6D01G318900 chr5A 87.654 972 91 23 3720 4678 706825419 706826374 0.000000e+00 1103.0
17 TraesCS6D01G318900 chr5A 93.040 704 36 8 628 1326 706780978 706781673 0.000000e+00 1016.0
18 TraesCS6D01G318900 chr5A 88.204 746 86 2 5065 5809 503532657 503533401 0.000000e+00 889.0
19 TraesCS6D01G318900 chr5A 90.498 442 40 2 143 584 706780536 706780975 3.530000e-162 582.0
20 TraesCS6D01G318900 chr5A 85.823 395 40 12 1650 2040 706821699 706822081 8.200000e-109 405.0
21 TraesCS6D01G318900 chr5A 81.902 326 12 6 4744 5058 706826401 706826690 1.470000e-56 231.0
22 TraesCS6D01G318900 chr5D 84.145 1047 138 24 5065 6099 398539767 398540797 0.000000e+00 989.0
23 TraesCS6D01G318900 chr5D 80.769 286 39 10 1872 2152 398537263 398537537 6.900000e-50 209.0
24 TraesCS6D01G318900 chr5D 89.320 103 8 3 2165 2265 369429228 369429127 7.150000e-25 126.0
25 TraesCS6D01G318900 chr5D 89.899 99 7 3 2169 2265 212467764 212467667 2.570000e-24 124.0
26 TraesCS6D01G318900 chr5D 76.371 237 45 8 3846 4081 398538512 398538738 4.300000e-22 117.0
27 TraesCS6D01G318900 chr5D 93.651 63 3 1 1588 1650 138454500 138454439 7.250000e-15 93.5
28 TraesCS6D01G318900 chr5B 83.222 1049 142 29 5065 6098 478491180 478492209 0.000000e+00 931.0
29 TraesCS6D01G318900 chr5B 80.714 280 38 11 1872 2146 478488669 478488937 3.210000e-48 204.0
30 TraesCS6D01G318900 chr5B 87.000 100 13 0 2964 3063 289706137 289706038 5.570000e-21 113.0
31 TraesCS6D01G318900 chrUn 92.250 400 31 0 5152 5551 30169809 30170208 9.890000e-158 568.0
32 TraesCS6D01G318900 chrUn 90.444 293 25 3 5549 5839 30182680 30182971 3.840000e-102 383.0
33 TraesCS6D01G318900 chr4B 89.655 290 21 4 5524 5805 666802089 666801801 1.800000e-95 361.0
34 TraesCS6D01G318900 chr4B 91.509 212 18 0 5092 5303 666803227 666803016 6.660000e-75 292.0
35 TraesCS6D01G318900 chr4B 86.975 238 25 4 5290 5523 666802799 666802564 5.220000e-66 263.0
36 TraesCS6D01G318900 chr4B 89.109 101 8 3 2169 2267 664775714 664775615 9.250000e-24 122.0
37 TraesCS6D01G318900 chr4B 77.455 275 16 9 4670 4944 666803453 666803225 9.250000e-24 122.0
38 TraesCS6D01G318900 chr4B 91.803 61 5 0 1590 1650 415511057 415510997 1.210000e-12 86.1
39 TraesCS6D01G318900 chr4B 78.723 141 13 11 6320 6456 666801231 666801104 2.030000e-10 78.7
40 TraesCS6D01G318900 chr2D 89.941 169 15 1 1650 1818 582545100 582545266 4.130000e-52 217.0
41 TraesCS6D01G318900 chr2D 89.899 99 7 3 2169 2265 389095026 389094929 2.570000e-24 124.0
42 TraesCS6D01G318900 chr2B 86.145 166 21 1 1650 1815 701505306 701505469 1.950000e-40 178.0
43 TraesCS6D01G318900 chr2B 88.350 103 9 3 2169 2269 9735946 9735845 3.330000e-23 121.0
44 TraesCS6D01G318900 chr2B 95.000 40 2 0 6284 6323 729957159 729957120 5.690000e-06 63.9
45 TraesCS6D01G318900 chr1B 90.741 108 7 3 2163 2268 572529353 572529459 2.550000e-29 141.0
46 TraesCS6D01G318900 chr1B 90.625 96 9 0 2964 3059 345320512 345320607 1.990000e-25 128.0
47 TraesCS6D01G318900 chr1D 90.909 99 9 0 2964 3062 267794582 267794484 4.270000e-27 134.0
48 TraesCS6D01G318900 chr1D 93.651 63 4 0 1588 1650 257695980 257696042 2.020000e-15 95.3
49 TraesCS6D01G318900 chr1D 85.526 76 4 6 6252 6322 480528430 480528503 9.450000e-09 73.1
50 TraesCS6D01G318900 chr1D 100.000 36 0 0 6290 6325 246951962 246951997 4.400000e-07 67.6
51 TraesCS6D01G318900 chr1D 84.932 73 4 6 6252 6319 480527823 480527893 4.400000e-07 67.6
52 TraesCS6D01G318900 chr1A 91.667 96 8 0 2964 3059 335028607 335028702 4.270000e-27 134.0
53 TraesCS6D01G318900 chr7D 87.500 112 9 5 2168 2275 190163216 190163106 2.570000e-24 124.0
54 TraesCS6D01G318900 chr7D 95.455 44 2 0 6282 6325 550241512 550241469 3.400000e-08 71.3
55 TraesCS6D01G318900 chr2A 89.899 99 7 3 2169 2265 762011814 762011911 2.570000e-24 124.0
56 TraesCS6D01G318900 chr3D 81.366 161 20 6 2903 3059 126396099 126396253 9.250000e-24 122.0
57 TraesCS6D01G318900 chr3D 92.063 63 5 0 1588 1650 221900541 221900603 9.380000e-14 89.8
58 TraesCS6D01G318900 chr3D 94.737 57 3 0 1595 1651 291973695 291973639 9.380000e-14 89.8
59 TraesCS6D01G318900 chr3D 97.619 42 1 0 6281 6322 136055771 136055812 9.450000e-09 73.1
60 TraesCS6D01G318900 chr3D 97.561 41 1 0 6284 6324 250931531 250931491 3.400000e-08 71.3
61 TraesCS6D01G318900 chr7B 92.308 65 4 1 1583 1647 611691979 611692042 2.610000e-14 91.6


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 TraesCS6D01G318900 chr6D 427121957 427128749 6792 True 12545.000000 12545 100.000000 1 6793 1 chr6D.!!$R2 6792
1 TraesCS6D01G318900 chr6A 571844075 571850748 6673 True 3425.666667 6628 95.795667 1 6741 3 chr6A.!!$R2 6740
2 TraesCS6D01G318900 chr6B 642962551 642965352 2801 True 2200.000000 3993 94.581500 3867 6792 2 chr6B.!!$R2 2925
3 TraesCS6D01G318900 chr6B 642970582 642974362 3780 True 1927.000000 2518 93.866000 2 3841 3 chr6B.!!$R3 3839
4 TraesCS6D01G318900 chr5A 503532657 503533401 744 False 889.000000 889 88.204000 5065 5809 1 chr5A.!!$F1 744
5 TraesCS6D01G318900 chr5A 706821699 706826690 4991 False 863.750000 1716 85.993000 1650 5058 4 chr5A.!!$F3 3408
6 TraesCS6D01G318900 chr5A 706780536 706781673 1137 False 799.000000 1016 91.769000 143 1326 2 chr5A.!!$F2 1183
7 TraesCS6D01G318900 chr5D 398537263 398540797 3534 False 438.333333 989 80.428333 1872 6099 3 chr5D.!!$F1 4227
8 TraesCS6D01G318900 chr5B 478488669 478492209 3540 False 567.500000 931 81.968000 1872 6098 2 chr5B.!!$F1 4226
9 TraesCS6D01G318900 chr4B 666801104 666803453 2349 True 223.340000 361 84.863400 4670 6456 5 chr4B.!!$R3 1786

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
27 28 0.323725 AACCTACCTTCCGGTCGCTA 60.324 55.000 0.00 0.00 44.21 4.26 F
745 881 1.280133 CACCATTGCCTCTCCTTCAGA 59.720 52.381 0.00 0.00 0.00 3.27 F
750 886 1.734655 TGCCTCTCCTTCAGACCTTT 58.265 50.000 0.00 0.00 0.00 3.11 F
1600 1772 2.437359 ATGAGCGAACAGGCCTGC 60.437 61.111 33.06 18.93 0.00 4.85 F
2691 4660 0.465097 CATCACCCCCTCTCACATGC 60.465 60.000 0.00 0.00 0.00 4.06 F
3845 5839 0.319083 TCGAGCGCCTTTTCCTGTTA 59.681 50.000 2.29 0.00 0.00 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1600 1772 0.035317 TCACTGCAACCACTAGGCTG 59.965 55.000 0.00 0.00 39.06 4.85 R
2238 4187 2.233922 CCCTCCGTCACAGAATAAGTGT 59.766 50.000 0.00 0.00 38.16 3.55 R
2257 4206 6.603201 TCCATGATCTCAAAACAAATAGTCCC 59.397 38.462 0.00 0.00 0.00 4.46 R
3147 5120 1.040339 GCACCACCCAAACCTGACAA 61.040 55.000 0.00 0.00 0.00 3.18 R
4530 6551 1.801178 GTTCTCTCCCTCAGCAAAACG 59.199 52.381 0.00 0.00 0.00 3.60 R
5817 8708 0.527385 TTTTGCAGCAAGTTGCCGAC 60.527 50.000 24.02 13.98 46.52 4.79 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 0.323725 AACCTACCTTCCGGTCGCTA 60.324 55.000 0.00 0.00 44.21 4.26
67 68 1.667724 CGTATTCCTGAAAGCCTGCAG 59.332 52.381 6.78 6.78 0.00 4.41
197 203 8.370493 TGCTAATCATCAGATGCTTTAGTAAC 57.630 34.615 21.86 13.05 33.90 2.50
207 213 3.873910 TGCTTTAGTAACCAGGAGATGC 58.126 45.455 0.00 0.00 0.00 3.91
217 223 1.676746 CAGGAGATGCCCTTGATGTG 58.323 55.000 0.00 0.00 37.37 3.21
422 428 2.480037 TGACTTTGTTGCTACGCATCAG 59.520 45.455 0.00 0.00 39.04 2.90
483 489 3.295093 TGGAAGCAGTGGAAATTTCACA 58.705 40.909 19.49 11.95 37.58 3.58
520 526 2.687935 TCAGACAAGTTTTCCTGCCAAC 59.312 45.455 0.00 0.00 0.00 3.77
524 530 4.162131 AGACAAGTTTTCCTGCCAACAAAT 59.838 37.500 0.00 0.00 0.00 2.32
569 685 6.267471 TGGTCATTTCTAAATTGGAACAGCTT 59.733 34.615 0.00 0.00 42.39 3.74
584 701 3.421844 ACAGCTTCTCAATGGGTAAACC 58.578 45.455 0.00 0.00 40.81 3.27
711 847 1.821136 GAAGACCAAATCCAAGGCCAG 59.179 52.381 5.01 0.00 0.00 4.85
745 881 1.280133 CACCATTGCCTCTCCTTCAGA 59.720 52.381 0.00 0.00 0.00 3.27
750 886 1.734655 TGCCTCTCCTTCAGACCTTT 58.265 50.000 0.00 0.00 0.00 3.11
851 987 6.367969 CAGCACAATTAGGTACTTTCGTTAGT 59.632 38.462 0.00 0.00 41.75 2.24
900 1036 3.202906 CCTTTTCGTGTTTGAGGTGAGA 58.797 45.455 0.00 0.00 0.00 3.27
1303 1475 9.772973 ACTTGTGTGTGAATAGAAAGTAATACA 57.227 29.630 0.00 0.00 0.00 2.29
1600 1772 2.437359 ATGAGCGAACAGGCCTGC 60.437 61.111 33.06 18.93 0.00 4.85
1716 1889 4.436998 GCACCCTGTAGCGCGTCT 62.437 66.667 8.43 8.22 0.00 4.18
2212 4161 8.788325 AAGTGTCTCAACTTTAGTACAACTTT 57.212 30.769 0.00 0.00 37.05 2.66
2213 4162 8.197988 AGTGTCTCAACTTTAGTACAACTTTG 57.802 34.615 0.00 0.00 0.00 2.77
2214 4163 7.822822 AGTGTCTCAACTTTAGTACAACTTTGT 59.177 33.333 0.00 0.00 44.86 2.83
2215 4164 9.090692 GTGTCTCAACTTTAGTACAACTTTGTA 57.909 33.333 0.00 0.00 42.35 2.41
2257 4206 4.082733 TGAGACACTTATTCTGTGACGGAG 60.083 45.833 0.00 0.00 38.65 4.63
2261 4210 2.496470 ACTTATTCTGTGACGGAGGGAC 59.504 50.000 0.00 0.00 0.00 4.46
2298 4260 4.780815 TCATGGATGAACCCAGACATAAC 58.219 43.478 0.00 0.00 39.97 1.89
2307 4269 6.177610 TGAACCCAGACATAACCAGAATAAC 58.822 40.000 0.00 0.00 0.00 1.89
2691 4660 0.465097 CATCACCCCCTCTCACATGC 60.465 60.000 0.00 0.00 0.00 4.06
2804 4773 5.758784 GGCCTTGATACCATAGTAAGTTCAC 59.241 44.000 0.00 0.00 30.59 3.18
2805 4774 6.346096 GCCTTGATACCATAGTAAGTTCACA 58.654 40.000 0.00 0.00 30.59 3.58
2817 4786 1.717032 AGTTCACAGACCAGCCACTA 58.283 50.000 0.00 0.00 0.00 2.74
3006 4976 3.561143 AGTTTCATGCACCAACCAGTAA 58.439 40.909 0.00 0.00 0.00 2.24
3147 5120 1.808945 CAAGAGGAGCTTCGCAAATGT 59.191 47.619 0.00 0.00 33.60 2.71
3203 5176 7.113658 ACATGTCCACTAGGTATAGTTTCTG 57.886 40.000 0.00 0.00 40.38 3.02
3412 5402 7.286775 ACACCACCAAGTGATTTTGTAAGTAAT 59.713 33.333 0.00 0.00 40.34 1.89
3512 5505 4.764172 AGTTCATGACTATGGTTCAGAGC 58.236 43.478 0.00 0.00 36.65 4.09
3845 5839 0.319083 TCGAGCGCCTTTTCCTGTTA 59.681 50.000 2.29 0.00 0.00 2.41
4452 6473 4.188247 TGTACAGGACGAAATGGAGAAG 57.812 45.455 0.00 0.00 0.00 2.85
4599 6620 6.602406 AGCTGCATATTCCAGATCATATTTCC 59.398 38.462 1.02 0.00 32.03 3.13
5288 7694 2.311854 CCACTCCAGCTTCCCCCAT 61.312 63.158 0.00 0.00 0.00 4.00
5317 7723 2.185350 CGCGGACCTGAAGCTGAT 59.815 61.111 0.00 0.00 0.00 2.90
5393 7803 0.815734 GCATTGTGCAGATGAAGCCT 59.184 50.000 12.86 0.00 44.26 4.58
5394 7804 1.203994 GCATTGTGCAGATGAAGCCTT 59.796 47.619 12.86 0.00 44.26 4.35
5511 7921 3.933900 GACGTCTACGCGTTCGGCA 62.934 63.158 20.78 0.00 45.79 5.69
5569 8453 0.179171 AACATCGTCGAGCAGGTACG 60.179 55.000 0.00 0.00 37.96 3.67
5839 8730 1.585297 GGCAACTTGCTGCAAAATGT 58.415 45.000 16.74 8.18 44.28 2.71
5881 8773 5.738619 TTCTCTTGTGAACCTGCACTATA 57.261 39.130 0.00 0.00 39.49 1.31
5882 8774 5.330455 TCTCTTGTGAACCTGCACTATAG 57.670 43.478 0.00 0.00 39.49 1.31
5883 8775 4.772624 TCTCTTGTGAACCTGCACTATAGT 59.227 41.667 0.00 0.00 39.49 2.12
5909 8801 5.895636 TGGGTTTAGTTTGTGATGCTATG 57.104 39.130 0.00 0.00 0.00 2.23
5910 8802 4.704540 TGGGTTTAGTTTGTGATGCTATGG 59.295 41.667 0.00 0.00 0.00 2.74
6069 9164 0.322816 AGCGCCCACAAACATCTCAT 60.323 50.000 2.29 0.00 0.00 2.90
6172 9269 7.524717 AAGCATCACAAACTAAACCAAGTAT 57.475 32.000 0.00 0.00 0.00 2.12
6243 9344 1.770658 CATCCTGATTGGCACTCCCTA 59.229 52.381 2.13 0.00 35.26 3.53
6244 9345 1.965414 TCCTGATTGGCACTCCCTAA 58.035 50.000 2.13 0.00 35.26 2.69
6339 9441 3.679389 AGTAATAAGCAGCACAAGCACT 58.321 40.909 0.00 0.00 45.49 4.40
6342 9444 1.965935 TAAGCAGCACAAGCACTCAA 58.034 45.000 0.00 0.00 45.49 3.02
6365 9470 1.153353 GAGCAACGAACCGGATCAAA 58.847 50.000 9.46 0.00 0.00 2.69
6378 9483 3.126171 CCGGATCAAACTAATGCGTGAAA 59.874 43.478 0.00 0.00 36.38 2.69
6400 9505 3.306206 CAAATCGCTTGCCGGTAAC 57.694 52.632 0.00 0.00 37.59 2.50
6401 9506 0.519519 CAAATCGCTTGCCGGTAACA 59.480 50.000 0.00 0.00 37.59 2.41
6430 9535 1.299541 CGGTTACATCAGGATGCACC 58.700 55.000 16.16 16.16 42.39 5.01
6432 9537 1.299541 GTTACATCAGGATGCACCCG 58.700 55.000 9.12 0.00 42.39 5.28
6448 9553 0.591170 CCCGCGTTCACATGAAGTTT 59.409 50.000 4.92 0.00 34.27 2.66
6457 9562 5.554636 GTTCACATGAAGTTTAGATCAGCG 58.445 41.667 0.00 0.00 34.27 5.18
6468 9573 2.125912 ATCAGCGTCGACACAGCC 60.126 61.111 17.16 0.00 0.00 4.85
6502 9607 1.557443 GCGCAACTACGTCACAGCTT 61.557 55.000 0.30 0.00 34.88 3.74
6503 9608 0.859232 CGCAACTACGTCACAGCTTT 59.141 50.000 0.00 0.00 0.00 3.51
6504 9609 1.136611 CGCAACTACGTCACAGCTTTC 60.137 52.381 0.00 0.00 0.00 2.62
6505 9610 1.864711 GCAACTACGTCACAGCTTTCA 59.135 47.619 0.00 0.00 0.00 2.69
6521 9626 4.164988 AGCTTTCATTCTAGGGCAGTACAT 59.835 41.667 0.00 0.00 0.00 2.29
6528 9633 2.037144 CTAGGGCAGTACATAACGGGT 58.963 52.381 0.00 0.00 0.00 5.28
6544 9649 9.252962 ACATAACGGGTAATCTAATAAGTTTCG 57.747 33.333 0.00 0.00 0.00 3.46
6605 9710 0.801251 GGTGACAGATTGTGCTCAGC 59.199 55.000 0.00 0.00 31.88 4.26
6618 9723 2.627221 GTGCTCAGCCATCATCTCTAGA 59.373 50.000 0.00 0.00 0.00 2.43
6624 9729 4.824537 TCAGCCATCATCTCTAGACAGTAC 59.175 45.833 0.00 0.00 0.00 2.73
6751 9856 4.693283 TGTCTAATTGTCTATCCTTGCCG 58.307 43.478 0.00 0.00 0.00 5.69
6752 9857 4.404394 TGTCTAATTGTCTATCCTTGCCGA 59.596 41.667 0.00 0.00 0.00 5.54
6767 9872 3.557577 TGCCGAGATCAAACACAAATG 57.442 42.857 0.00 0.00 0.00 2.32
6778 9883 4.024133 TCAAACACAAATGGATCGACACAG 60.024 41.667 0.00 0.00 0.00 3.66
6780 9885 3.329386 ACACAAATGGATCGACACAGAG 58.671 45.455 0.00 0.00 0.00 3.35
6781 9886 2.674852 CACAAATGGATCGACACAGAGG 59.325 50.000 0.00 0.00 0.00 3.69
6782 9887 2.567169 ACAAATGGATCGACACAGAGGA 59.433 45.455 0.00 0.00 0.00 3.71
6783 9888 3.193263 CAAATGGATCGACACAGAGGAG 58.807 50.000 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.119495 GGTATCCCAGTGTGAGGACAT 58.881 52.381 0.00 0.00 34.20 3.06
67 68 2.354821 ACGGAAGTGCTTGTTGAGAAAC 59.645 45.455 0.00 0.00 46.97 2.78
194 200 1.965414 TCAAGGGCATCTCCTGGTTA 58.035 50.000 0.00 0.00 37.20 2.85
197 203 0.549950 ACATCAAGGGCATCTCCTGG 59.450 55.000 0.00 0.00 37.20 4.45
207 213 7.445096 TGTCAATATAGTAATGCACATCAAGGG 59.555 37.037 0.00 0.00 0.00 3.95
217 223 4.697352 CCCAGGCTGTCAATATAGTAATGC 59.303 45.833 14.43 0.00 0.00 3.56
422 428 0.606673 GCCCCTGGTTGACTGACTTC 60.607 60.000 0.00 0.00 0.00 3.01
483 489 3.071023 TGTCTGATTCGGGTGAACTTTCT 59.929 43.478 0.00 0.00 36.81 2.52
569 685 5.245075 GGAAACATTGGTTTACCCATTGAGA 59.755 40.000 9.52 0.00 46.84 3.27
711 847 4.932799 GGCAATGGTGGTGGTTTTAAATAC 59.067 41.667 0.00 0.00 0.00 1.89
745 881 4.042187 AGGAAGTGTCAGCTCATAAAAGGT 59.958 41.667 0.00 0.00 0.00 3.50
750 886 4.610333 TCCTAGGAAGTGTCAGCTCATAA 58.390 43.478 9.71 0.00 0.00 1.90
778 914 4.835284 TCTTTTCCCTTTTGTGCCTTTT 57.165 36.364 0.00 0.00 0.00 2.27
900 1036 3.584848 AGCAGAACCTGAACCATAGAAGT 59.415 43.478 0.00 0.00 32.44 3.01
987 1123 4.226846 TCTTGATCCATCTTTCTTGCTCCT 59.773 41.667 0.00 0.00 0.00 3.69
1600 1772 0.035317 TCACTGCAACCACTAGGCTG 59.965 55.000 0.00 0.00 39.06 4.85
2215 4164 8.827677 GTGTCTCAATTTTAGTACAACTTCAGT 58.172 33.333 0.00 0.00 0.00 3.41
2216 4165 9.046296 AGTGTCTCAATTTTAGTACAACTTCAG 57.954 33.333 0.00 0.00 0.00 3.02
2217 4166 8.958119 AGTGTCTCAATTTTAGTACAACTTCA 57.042 30.769 0.00 0.00 0.00 3.02
2226 4175 9.778741 TCACAGAATAAGTGTCTCAATTTTAGT 57.221 29.630 0.00 0.00 38.16 2.24
2228 4177 8.708742 CGTCACAGAATAAGTGTCTCAATTTTA 58.291 33.333 0.00 0.00 38.16 1.52
2229 4178 7.307989 CCGTCACAGAATAAGTGTCTCAATTTT 60.308 37.037 0.00 0.00 38.16 1.82
2230 4179 6.147821 CCGTCACAGAATAAGTGTCTCAATTT 59.852 38.462 0.00 0.00 38.16 1.82
2231 4180 5.639506 CCGTCACAGAATAAGTGTCTCAATT 59.360 40.000 0.00 0.00 38.16 2.32
2238 4187 2.233922 CCCTCCGTCACAGAATAAGTGT 59.766 50.000 0.00 0.00 38.16 3.55
2247 4196 2.233922 ACAAATAGTCCCTCCGTCACAG 59.766 50.000 0.00 0.00 0.00 3.66
2257 4206 6.603201 TCCATGATCTCAAAACAAATAGTCCC 59.397 38.462 0.00 0.00 0.00 4.46
2261 4210 9.512435 GTTCATCCATGATCTCAAAACAAATAG 57.488 33.333 0.00 0.00 36.56 1.73
2783 4752 7.707035 GGTCTGTGAACTTACTATGGTATCAAG 59.293 40.741 0.00 0.00 0.00 3.02
2804 4773 1.496060 TGGGTATAGTGGCTGGTCTG 58.504 55.000 0.00 0.00 0.00 3.51
2805 4774 2.263895 TTGGGTATAGTGGCTGGTCT 57.736 50.000 0.00 0.00 0.00 3.85
2817 4786 3.007182 TCGTTCTTCGGTCTTTTGGGTAT 59.993 43.478 0.00 0.00 40.32 2.73
3006 4976 4.405358 TCCATCAGTTCAGGCTTTTGTTTT 59.595 37.500 0.00 0.00 0.00 2.43
3147 5120 1.040339 GCACCACCCAAACCTGACAA 61.040 55.000 0.00 0.00 0.00 3.18
3412 5402 7.744087 ATGTGTGTAATGCTTTACTGAAAGA 57.256 32.000 19.69 5.70 44.23 2.52
3512 5505 2.224209 ACACCACGAGTTAGGACCAAAG 60.224 50.000 0.00 0.00 0.00 2.77
3582 5575 3.141398 CACCATCCATCTGAATAACCCG 58.859 50.000 0.00 0.00 0.00 5.28
3711 5705 6.038603 CCCTGGATATTGTTTCTGTATGTGTG 59.961 42.308 0.00 0.00 0.00 3.82
3712 5706 6.122277 CCCTGGATATTGTTTCTGTATGTGT 58.878 40.000 0.00 0.00 0.00 3.72
3713 5707 6.122277 ACCCTGGATATTGTTTCTGTATGTG 58.878 40.000 0.00 0.00 0.00 3.21
3956 5950 6.803154 AGTCATAGGTAGCACTTGTTTTTC 57.197 37.500 0.00 0.00 0.00 2.29
4028 6023 2.236893 TCAGCTTCCTGCACATCATACA 59.763 45.455 0.00 0.00 45.94 2.29
4452 6473 6.533012 GCAGATCTTTTAATTTCCTTTGGAGC 59.467 38.462 0.00 0.00 31.21 4.70
4530 6551 1.801178 GTTCTCTCCCTCAGCAAAACG 59.199 52.381 0.00 0.00 0.00 3.60
4599 6620 2.274232 TACGCGACATGGGGAACTCG 62.274 60.000 15.93 0.00 34.15 4.18
4803 6836 9.775854 CTCAGATAGTTAAATGAATGACCTGAT 57.224 33.333 0.00 0.00 0.00 2.90
4869 6902 8.335532 TGCTTATTGCTCTGTATTAAGTTTGT 57.664 30.769 0.00 0.00 43.37 2.83
5010 7101 6.346477 TGCAAGTCTGTTATCTACTTCTGT 57.654 37.500 0.00 0.00 31.21 3.41
5225 7401 1.235281 CGGCGAGGATCCTGATACGA 61.235 60.000 22.02 0.00 0.00 3.43
5288 7694 3.780173 TCCGCGTGGATGATGGCA 61.780 61.111 15.21 0.00 40.17 4.92
5317 7723 1.511305 GCGTCGAGGAGGATGTTCA 59.489 57.895 9.75 0.00 0.00 3.18
5393 7803 4.016444 GGCATATTGTGTCCTCCTTCAAA 58.984 43.478 0.00 0.00 0.00 2.69
5394 7804 3.620488 GGCATATTGTGTCCTCCTTCAA 58.380 45.455 0.00 0.00 0.00 2.69
5511 7921 1.077212 GCACCTGCAGGATCACCAT 60.077 57.895 39.19 12.29 41.59 3.55
5817 8708 0.527385 TTTTGCAGCAAGTTGCCGAC 60.527 50.000 24.02 13.98 46.52 4.79
5881 8773 5.183140 GCATCACAAACTAAACCCATGTACT 59.817 40.000 0.00 0.00 0.00 2.73
5882 8774 5.183140 AGCATCACAAACTAAACCCATGTAC 59.817 40.000 0.00 0.00 0.00 2.90
5883 8775 5.321102 AGCATCACAAACTAAACCCATGTA 58.679 37.500 0.00 0.00 0.00 2.29
5909 8801 5.886960 ATGTACATTCACAAGAGAAAGCC 57.113 39.130 1.41 0.00 30.84 4.35
5910 8802 9.846248 AATTAATGTACATTCACAAGAGAAAGC 57.154 29.630 24.00 0.00 32.50 3.51
5966 8866 8.443953 AAATTACAATGATAGAGAGGAACTGC 57.556 34.615 0.00 0.00 41.55 4.40
6069 9164 2.684630 GCTCATGTGGGTCATTGGATCA 60.685 50.000 0.00 0.00 34.09 2.92
6172 9269 7.665559 GGCCCATTGATCTGATTGTTATACTAA 59.334 37.037 0.00 0.00 0.00 2.24
6339 9441 0.934496 CGGTTCGTTGCTCTGTTTGA 59.066 50.000 0.00 0.00 0.00 2.69
6342 9444 0.034896 ATCCGGTTCGTTGCTCTGTT 59.965 50.000 0.00 0.00 0.00 3.16
6354 9456 2.418628 CACGCATTAGTTTGATCCGGTT 59.581 45.455 0.00 0.00 0.00 4.44
6395 9500 2.826277 CCGTGTTACCGGTGTTACC 58.174 57.895 19.93 6.13 43.07 2.85
6430 9535 2.734606 TCTAAACTTCATGTGAACGCGG 59.265 45.455 12.47 0.00 0.00 6.46
6432 9537 5.530519 TGATCTAAACTTCATGTGAACGC 57.469 39.130 0.00 0.00 0.00 4.84
6448 9553 0.098905 GCTGTGTCGACGCTGATCTA 59.901 55.000 32.07 11.53 0.00 1.98
6457 9562 1.227263 ATATGGCGGCTGTGTCGAC 60.227 57.895 9.11 9.11 40.10 4.20
6492 9597 2.932614 CCCTAGAATGAAAGCTGTGACG 59.067 50.000 0.00 0.00 0.00 4.35
6502 9607 5.452776 CCGTTATGTACTGCCCTAGAATGAA 60.453 44.000 0.00 0.00 0.00 2.57
6503 9608 4.038763 CCGTTATGTACTGCCCTAGAATGA 59.961 45.833 0.00 0.00 0.00 2.57
6504 9609 4.307432 CCGTTATGTACTGCCCTAGAATG 58.693 47.826 0.00 0.00 0.00 2.67
6505 9610 3.323979 CCCGTTATGTACTGCCCTAGAAT 59.676 47.826 0.00 0.00 0.00 2.40
6521 9626 9.301153 GTTCGAAACTTATTAGATTACCCGTTA 57.699 33.333 0.00 0.00 0.00 3.18
6544 9649 4.754114 AGAATTGAGCTTCACTGTCAGTTC 59.246 41.667 1.67 0.00 37.26 3.01
6605 9710 3.565902 TGCGTACTGTCTAGAGATGATGG 59.434 47.826 0.00 0.00 0.00 3.51
6618 9723 1.037493 TCTCAAGTGGTGCGTACTGT 58.963 50.000 3.01 0.00 0.00 3.55
6624 9729 1.845809 GCTGGTTCTCAAGTGGTGCG 61.846 60.000 0.00 0.00 0.00 5.34
6751 9856 5.122239 TGTCGATCCATTTGTGTTTGATCTC 59.878 40.000 0.00 0.00 31.76 2.75
6752 9857 5.003160 TGTCGATCCATTTGTGTTTGATCT 58.997 37.500 0.00 0.00 31.76 2.75
6767 9872 1.395826 CCCCTCCTCTGTGTCGATCC 61.396 65.000 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.