Multiple sequence alignment - TraesCS4D01G193400

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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 TraesCS4D01G193400 chr4D 100.000 7991 0 0 1 7991 336656878 336664868 0.000000e+00 14757.0
1 TraesCS4D01G193400 chr4D 82.094 363 45 15 1325 1682 145529178 145528831 7.840000e-75 292.0
2 TraesCS4D01G193400 chr4D 82.184 348 45 12 1325 1669 145494151 145493818 4.720000e-72 283.0
3 TraesCS4D01G193400 chr4A 96.261 7461 187 38 174 7587 136760649 136753234 0.000000e+00 12148.0
4 TraesCS4D01G193400 chr4A 90.000 460 40 4 2 456 136761102 136760644 2.480000e-164 590.0
5 TraesCS4D01G193400 chr4A 89.880 415 26 4 7577 7991 136752986 136752588 3.310000e-143 520.0
6 TraesCS4D01G193400 chr4A 75.194 258 44 11 7749 7991 648312961 648312709 3.940000e-18 104.0
7 TraesCS4D01G193400 chr4B 96.086 5697 159 27 2326 7991 414860847 414866510 0.000000e+00 9226.0
8 TraesCS4D01G193400 chr4B 95.763 1652 57 7 504 2143 414858874 414860524 0.000000e+00 2651.0
9 TraesCS4D01G193400 chr4B 90.816 196 8 4 2140 2332 414860559 414860747 3.700000e-63 254.0
10 TraesCS4D01G193400 chr4B 89.785 186 14 2 1 181 414858686 414858871 4.820000e-57 233.0
11 TraesCS4D01G193400 chr1A 91.570 1459 74 18 4505 5953 35507257 35508676 0.000000e+00 1967.0
12 TraesCS4D01G193400 chr1A 96.424 783 27 1 4300 5082 35532925 35533706 0.000000e+00 1290.0
13 TraesCS4D01G193400 chr1A 89.431 861 62 21 5990 6842 35512816 35513655 0.000000e+00 1059.0
14 TraesCS4D01G193400 chr1A 90.028 361 31 5 6485 6842 35483745 35484103 5.650000e-126 462.0
15 TraesCS4D01G193400 chr1A 85.246 366 36 7 6131 6483 35438751 35439111 2.120000e-95 361.0
16 TraesCS4D01G193400 chr1A 98.068 207 4 0 4300 4506 35500635 35500841 2.120000e-95 361.0
17 TraesCS4D01G193400 chr1A 82.915 398 30 18 6885 7276 35484105 35484470 2.780000e-84 324.0
18 TraesCS4D01G193400 chr1A 90.043 231 16 6 6885 7113 35513657 35513882 7.840000e-75 292.0
19 TraesCS4D01G193400 chr1A 87.970 133 12 4 7112 7244 35534721 35534849 3.860000e-33 154.0
20 TraesCS4D01G193400 chr1A 97.403 77 2 0 6462 6538 35534358 35534434 1.810000e-26 132.0
21 TraesCS4D01G193400 chr1A 88.462 104 8 4 7145 7248 35513885 35513984 1.090000e-23 122.0
22 TraesCS4D01G193400 chr1B 91.395 1441 84 18 4503 5939 55971373 55972777 0.000000e+00 1938.0
23 TraesCS4D01G193400 chr1B 92.759 1312 83 9 4647 5953 55953601 55954905 0.000000e+00 1886.0
24 TraesCS4D01G193400 chr1B 92.460 1313 86 10 4647 5953 55942347 55943652 0.000000e+00 1864.0
25 TraesCS4D01G193400 chr1B 89.463 1471 87 35 4488 5954 56014322 56015728 0.000000e+00 1796.0
26 TraesCS4D01G193400 chr1B 91.390 1115 70 11 4829 5939 55993410 55994502 0.000000e+00 1504.0
27 TraesCS4D01G193400 chr1B 97.283 184 5 0 4300 4483 56014094 56014277 6.020000e-81 313.0
28 TraesCS4D01G193400 chr1B 96.739 184 6 0 4300 4483 55970923 55971106 2.800000e-79 307.0
29 TraesCS4D01G193400 chr1B 85.890 163 18 2 5956 6116 56015889 56016048 1.380000e-37 169.0
30 TraesCS4D01G193400 chr1B 85.714 161 20 3 5956 6116 55943739 55943896 4.960000e-37 167.0
31 TraesCS4D01G193400 chr1B 85.714 161 20 3 5956 6116 55954992 55955149 4.960000e-37 167.0
32 TraesCS4D01G193400 chr1B 96.226 53 2 0 7018 7070 55976292 55976344 3.970000e-13 87.9
33 TraesCS4D01G193400 chr1B 94.340 53 3 0 7018 7070 56016046 56016098 1.850000e-11 82.4
34 TraesCS4D01G193400 chr1B 74.654 217 34 9 7758 7965 439449673 439449877 8.600000e-10 76.8
35 TraesCS4D01G193400 chr1D 93.986 1247 53 9 4300 5539 36312649 36313880 0.000000e+00 1868.0
36 TraesCS4D01G193400 chr1D 94.479 163 8 1 6903 7065 36314338 36314499 4.790000e-62 250.0
37 TraesCS4D01G193400 chr1D 89.683 126 9 4 7112 7237 36314501 36314622 2.990000e-34 158.0
38 TraesCS4D01G193400 chr1D 96.104 77 2 1 6462 6538 36314134 36314209 3.030000e-24 124.0
39 TraesCS4D01G193400 chr1D 73.200 250 44 8 7725 7965 326169145 326169380 1.440000e-07 69.4
40 TraesCS4D01G193400 chrUn 91.390 1115 70 11 4829 5939 319316023 319317115 0.000000e+00 1504.0
41 TraesCS4D01G193400 chrUn 83.694 785 64 36 1185 1946 178689254 178688511 0.000000e+00 682.0
42 TraesCS4D01G193400 chrUn 85.714 161 20 3 5956 6116 480727093 480726936 4.960000e-37 167.0
43 TraesCS4D01G193400 chr2D 81.629 1780 298 24 3384 5150 37259302 37257539 0.000000e+00 1448.0
44 TraesCS4D01G193400 chr2D 83.916 143 21 2 1125 1266 37260911 37260770 1.400000e-27 135.0
45 TraesCS4D01G193400 chr2B 81.598 1777 304 23 3384 5150 64995724 64993961 0.000000e+00 1448.0
46 TraesCS4D01G193400 chr2B 83.439 157 24 2 1111 1266 64997042 64996887 2.320000e-30 145.0
47 TraesCS4D01G193400 chr2A 81.475 1776 307 22 3384 5150 42160234 42158472 0.000000e+00 1437.0
48 TraesCS4D01G193400 chr2A 89.145 304 21 8 174 472 122146924 122147220 1.270000e-97 368.0
49 TraesCS4D01G193400 chr2A 86.344 227 31 0 2607 2833 42160614 42160388 1.720000e-61 248.0
50 TraesCS4D01G193400 chr2A 83.893 149 21 3 1119 1266 42161807 42161661 1.080000e-28 139.0
51 TraesCS4D01G193400 chr2A 81.301 123 19 4 7749 7868 98453706 98453585 6.600000e-16 97.1
52 TraesCS4D01G193400 chr3D 91.003 289 23 2 184 470 255424678 255424391 3.500000e-103 387.0
53 TraesCS4D01G193400 chr5A 90.345 290 25 2 183 470 313313746 313313458 2.110000e-100 377.0
54 TraesCS4D01G193400 chr5A 82.933 375 43 13 1325 1697 268024658 268024303 1.290000e-82 318.0
55 TraesCS4D01G193400 chr3B 90.311 289 24 3 184 470 377115405 377115119 7.570000e-100 375.0
56 TraesCS4D01G193400 chr5D 89.180 305 26 6 170 470 7559693 7559994 2.720000e-99 374.0
57 TraesCS4D01G193400 chr3A 90.000 290 25 3 184 470 319962599 319962311 9.790000e-99 372.0
58 TraesCS4D01G193400 chr6A 89.037 301 25 5 174 468 374422960 374422662 4.560000e-97 366.0
59 TraesCS4D01G193400 chr6D 85.429 350 36 14 184 526 3743964 3744305 4.590000e-92 350.0


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 TraesCS4D01G193400 chr4D 336656878 336664868 7990 False 14757.000000 14757 100.000000 1 7991 1 chr4D.!!$F1 7990
1 TraesCS4D01G193400 chr4A 136752588 136761102 8514 True 4419.333333 12148 92.047000 2 7991 3 chr4A.!!$R2 7989
2 TraesCS4D01G193400 chr4B 414858686 414866510 7824 False 3091.000000 9226 93.112500 1 7991 4 chr4B.!!$F1 7990
3 TraesCS4D01G193400 chr1A 35507257 35508676 1419 False 1967.000000 1967 91.570000 4505 5953 1 chr1A.!!$F3 1448
4 TraesCS4D01G193400 chr1A 35532925 35534849 1924 False 525.333333 1290 93.932333 4300 7244 3 chr1A.!!$F6 2944
5 TraesCS4D01G193400 chr1A 35512816 35513984 1168 False 491.000000 1059 89.312000 5990 7248 3 chr1A.!!$F5 1258
6 TraesCS4D01G193400 chr1A 35483745 35484470 725 False 393.000000 462 86.471500 6485 7276 2 chr1A.!!$F4 791
7 TraesCS4D01G193400 chr1B 55993410 55994502 1092 False 1504.000000 1504 91.390000 4829 5939 1 chr1B.!!$F1 1110
8 TraesCS4D01G193400 chr1B 55953601 55955149 1548 False 1026.500000 1886 89.236500 4647 6116 2 chr1B.!!$F4 1469
9 TraesCS4D01G193400 chr1B 55942347 55943896 1549 False 1015.500000 1864 89.087000 4647 6116 2 chr1B.!!$F3 1469
10 TraesCS4D01G193400 chr1B 55970923 55976344 5421 False 777.633333 1938 94.786667 4300 7070 3 chr1B.!!$F5 2770
11 TraesCS4D01G193400 chr1B 56014094 56016098 2004 False 590.100000 1796 91.744000 4300 7070 4 chr1B.!!$F6 2770
12 TraesCS4D01G193400 chr1D 36312649 36314622 1973 False 600.000000 1868 93.563000 4300 7237 4 chr1D.!!$F2 2937
13 TraesCS4D01G193400 chrUn 319316023 319317115 1092 False 1504.000000 1504 91.390000 4829 5939 1 chrUn.!!$F1 1110
14 TraesCS4D01G193400 chrUn 178688511 178689254 743 True 682.000000 682 83.694000 1185 1946 1 chrUn.!!$R1 761
15 TraesCS4D01G193400 chr2D 37257539 37260911 3372 True 791.500000 1448 82.772500 1125 5150 2 chr2D.!!$R1 4025
16 TraesCS4D01G193400 chr2B 64993961 64997042 3081 True 796.500000 1448 82.518500 1111 5150 2 chr2B.!!$R1 4039
17 TraesCS4D01G193400 chr2A 42158472 42161807 3335 True 608.000000 1437 83.904000 1119 5150 3 chr2A.!!$R2 4031

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
616 894 0.252835 AGGCTTGCCCATCCCAAAAT 60.253 50.000 8.17 0.0 35.39 1.82 F
637 915 0.673644 CAACGGCCAAGATTCCTCGT 60.674 55.000 2.24 0.0 0.00 4.18 F
2080 2566 1.134670 CCTTTTAGAGGGGAGTGAGCG 60.135 57.143 0.00 0.0 42.26 5.03 F
3527 4477 2.151502 TTTGTGACTTTGGGCCTGAA 57.848 45.000 4.53 0.0 0.00 3.02 F
4614 5812 2.102252 GCTGCTAGTGCTATCAACTCCT 59.898 50.000 0.00 0.0 40.48 3.69 F
5539 6764 2.027625 CGGACTGGGCGAAGAACAC 61.028 63.158 0.00 0.0 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2080 2566 0.179034 ATTCCTCAGAATCGCTGGGC 60.179 55.000 0.00 0.0 44.16 5.36 R
2221 2745 1.158007 TTTCCCTTTCCAGGAGGCTT 58.842 50.000 0.00 0.0 44.19 4.35 R
3934 4884 0.102300 GCGCCCAAACTTTTGTCTGT 59.898 50.000 0.00 0.0 36.45 3.41 R
5498 6721 1.988015 GGGGATCCCGAAAGACACA 59.012 57.895 24.90 0.0 36.85 3.72 R
6585 11268 0.393077 AGTCTTCAACTGGGTGGTCG 59.607 55.000 0.00 0.0 36.65 4.79 R
7170 11859 0.032403 GGCATGCAACAAACAGAGCA 59.968 50.000 21.36 0.0 41.73 4.26 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
24 25 5.393678 GGTGCTCTTGTTTCAAGTTTACCAA 60.394 40.000 17.31 0.00 0.00 3.67
36 37 4.439253 AGTTTACCAACTCCAAGCTTCT 57.561 40.909 0.00 0.00 39.15 2.85
210 216 4.340019 TGCCCGTGCATTGCAACG 62.340 61.111 13.94 17.64 44.23 4.10
231 237 9.017669 GCAACGGGATATAAATATTCTAGTACG 57.982 37.037 0.00 0.00 0.00 3.67
248 256 9.731819 TTCTAGTACGTTAGCTTGATTTATCTG 57.268 33.333 0.00 0.00 0.00 2.90
251 259 7.544622 AGTACGTTAGCTTGATTTATCTGTCA 58.455 34.615 0.00 0.00 0.00 3.58
427 435 0.938192 AAGGGGTGGTGGGAAGAAAA 59.062 50.000 0.00 0.00 0.00 2.29
428 436 0.938192 AGGGGTGGTGGGAAGAAAAA 59.062 50.000 0.00 0.00 0.00 1.94
436 444 5.221621 GGTGGTGGGAAGAAAAATGAAATGA 60.222 40.000 0.00 0.00 0.00 2.57
616 894 0.252835 AGGCTTGCCCATCCCAAAAT 60.253 50.000 8.17 0.00 35.39 1.82
637 915 0.673644 CAACGGCCAAGATTCCTCGT 60.674 55.000 2.24 0.00 0.00 4.18
943 1240 1.831106 CCATTTCTGGGGTTTTAGGGC 59.169 52.381 0.00 0.00 39.04 5.19
1078 1375 2.108362 CACGGGTAGGGGAATCGC 59.892 66.667 0.00 0.00 0.00 4.58
1433 1873 3.753272 TGCTTAGTTGCTGGATTGAGAAC 59.247 43.478 0.00 0.00 0.00 3.01
1495 1937 1.673665 CAGGGCTGAGTTGCTGGAC 60.674 63.158 0.00 0.00 0.00 4.02
1567 2010 5.674933 GTTCAAACAGAGTGAACCCTTAG 57.325 43.478 6.10 0.00 45.99 2.18
1813 2293 7.144661 TCATGTTTACATTGGTAGCTTTTGTG 58.855 34.615 0.00 0.00 33.61 3.33
1894 2379 3.426695 GCAAACTGTGATAAGCGCTGAAT 60.427 43.478 12.58 8.18 0.00 2.57
1955 2440 4.559862 ATGGAGCTGCAGTTACTAGTTT 57.440 40.909 14.98 0.00 0.00 2.66
2080 2566 1.134670 CCTTTTAGAGGGGAGTGAGCG 60.135 57.143 0.00 0.00 42.26 5.03
2123 2609 2.764128 TGAGATGTCCGAGGGGCC 60.764 66.667 0.00 0.00 0.00 5.80
2235 2817 2.172293 AGCAGATAAGCCTCCTGGAAAG 59.828 50.000 0.00 0.00 34.57 2.62
2465 3155 5.850557 TGGGCAAAGTAATATGGTCATTG 57.149 39.130 0.00 0.00 0.00 2.82
2467 3157 5.359576 TGGGCAAAGTAATATGGTCATTGAC 59.640 40.000 8.34 8.34 0.00 3.18
2491 3181 5.337169 CGAGCAATTATTTTCCCTTTTCCCA 60.337 40.000 0.00 0.00 0.00 4.37
2748 3689 2.270047 GCTGCTGCTTGTGTTGAAAAA 58.730 42.857 8.53 0.00 36.03 1.94
2943 3884 2.158623 ACTGTGCCTGAAATCAAGTGGA 60.159 45.455 0.00 0.00 0.00 4.02
2953 3894 7.682021 GCCTGAAATCAAGTGGAATGGTATTAC 60.682 40.741 0.00 0.00 0.00 1.89
3093 4042 6.039415 TCATAATACCCAGTAGAACTCCCT 57.961 41.667 0.00 0.00 0.00 4.20
3254 4204 7.985476 TGAAGCTAATGTGAATAAGTAAAGCC 58.015 34.615 0.00 0.00 0.00 4.35
3369 4319 3.324846 TCCTTCCTGCGTATATGCTGATT 59.675 43.478 21.59 0.00 36.04 2.57
3527 4477 2.151502 TTTGTGACTTTGGGCCTGAA 57.848 45.000 4.53 0.00 0.00 3.02
3934 4884 6.530120 TCGCATTTCTAGCCTTGGATAATTA 58.470 36.000 0.00 0.00 0.00 1.40
4140 5090 3.886505 TGGTGGTATTGTTGGTCAAGAAC 59.113 43.478 0.00 0.00 39.55 3.01
4614 5812 2.102252 GCTGCTAGTGCTATCAACTCCT 59.898 50.000 0.00 0.00 40.48 3.69
4895 6101 2.124011 CACCAATGTGCACAGTTCAC 57.876 50.000 25.84 0.00 35.31 3.18
5498 6721 3.453717 TGTCTGCTTCCATATTGAGAGCT 59.546 43.478 0.00 0.00 34.56 4.09
5539 6764 2.027625 CGGACTGGGCGAAGAACAC 61.028 63.158 0.00 0.00 0.00 3.32
5711 6965 2.608752 GGAAGCATGTGCCAAGAAACTG 60.609 50.000 0.57 0.00 43.38 3.16
5834 7095 6.819397 GGCTGTTTAAGAACATCCTTACTT 57.181 37.500 5.23 0.00 44.73 2.24
5903 7164 6.309980 TGCATATTTGGTAAGCAAAAACATCG 59.690 34.615 0.00 0.00 34.36 3.84
5968 10570 6.603095 CATTGAGTTACAGAACTTAGTTGCC 58.397 40.000 0.93 0.00 46.23 4.52
6005 10607 5.544650 TCCCTTGTTGTTGCTAGTAGTAAC 58.455 41.667 20.55 20.55 40.55 2.50
6168 10772 4.435121 GCTGGTACCGTAAAGATGTTTTCG 60.435 45.833 7.57 7.28 36.50 3.46
6269 10896 5.279406 GGCATGCAATTATAACTGGGCATTA 60.279 40.000 21.36 0.00 39.73 1.90
6470 11098 5.581085 GTGCGAGAAACTATGGTATTCAAGT 59.419 40.000 0.00 0.00 0.00 3.16
6585 11268 0.250727 TGTACAAGGTTCTGGCAGGC 60.251 55.000 15.73 8.02 0.00 4.85
6827 11513 2.158682 TGCTGTACAACACCATGTTCCT 60.159 45.455 0.00 0.00 38.77 3.36
7095 11784 4.282703 ACTCTTCTTAGTCGGCTTGGTTTA 59.717 41.667 0.00 0.00 0.00 2.01
7170 11859 1.011333 CGTTTTGTGTGGGTCGTTCT 58.989 50.000 0.00 0.00 0.00 3.01
7303 11998 6.202954 GGTTACATGCATATGGTAGTTCAGTC 59.797 42.308 0.00 0.00 38.66 3.51
7335 12030 4.398358 CCTCATCATCAGTTTCACTTGCAT 59.602 41.667 0.00 0.00 0.00 3.96
7337 12032 6.238402 CCTCATCATCAGTTTCACTTGCATAG 60.238 42.308 0.00 0.00 0.00 2.23
7338 12033 6.175471 TCATCATCAGTTTCACTTGCATAGT 58.825 36.000 0.00 0.00 37.68 2.12
7379 12078 7.663493 AGAAAGCTTGCTAGTTATCCCATTATC 59.337 37.037 4.67 0.00 0.00 1.75
7454 12153 4.836736 TGCATAGATAGGTTAGGGTACACC 59.163 45.833 0.00 0.00 40.67 4.16
7455 12154 4.836736 GCATAGATAGGTTAGGGTACACCA 59.163 45.833 0.00 0.00 43.89 4.17
7484 12183 5.772521 CTGGCAGTTTTAGTTTTGCTACAT 58.227 37.500 6.28 0.00 36.79 2.29
7524 12228 4.566004 CATCTCGAACTCCCAAACAGTTA 58.434 43.478 0.00 0.00 34.10 2.24
7574 12279 2.028020 AGTGAGGTCAATTCTCCCGAAC 60.028 50.000 0.00 0.00 30.67 3.95
7580 12544 4.120589 GGTCAATTCTCCCGAACATACTC 58.879 47.826 0.00 0.00 30.67 2.59
7677 12641 1.613836 GCCATAATGGAGAGGCAAGG 58.386 55.000 0.00 0.00 46.26 3.61
7711 12675 4.954970 CCAACCACTGCCGCTGGT 62.955 66.667 0.00 0.00 44.39 4.00
7746 12710 3.325753 GACCCCTGCTCCACTGCT 61.326 66.667 0.00 0.00 0.00 4.24
7747 12711 2.856000 ACCCCTGCTCCACTGCTT 60.856 61.111 0.00 0.00 0.00 3.91
7944 12909 3.326297 AGGTGGTGAAGAAGAGGAAGAAG 59.674 47.826 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.164843 AGCTTGGAGTTGGTAAACTTGA 57.835 40.909 0.00 0.00 46.84 3.02
24 25 5.407407 TCTTCGAATAAGAAGCTTGGAGT 57.593 39.130 2.10 0.00 45.28 3.85
36 37 5.444744 TCCCCCAATTCTTCTTCGAATAA 57.555 39.130 0.00 0.00 33.47 1.40
196 202 1.372838 TATCCCGTTGCAATGCACGG 61.373 55.000 28.95 28.95 45.37 4.94
197 203 0.662619 ATATCCCGTTGCAATGCACG 59.337 50.000 7.72 14.71 38.71 5.34
202 208 9.959721 ACTAGAATATTTATATCCCGTTGCAAT 57.040 29.630 0.59 0.00 0.00 3.56
245 253 5.983118 ACACGATCGCATTATTATTGACAGA 59.017 36.000 16.60 0.00 0.00 3.41
395 403 3.181437 ACCACCCCTTCGTCTAACATTTT 60.181 43.478 0.00 0.00 0.00 1.82
399 407 0.682852 CACCACCCCTTCGTCTAACA 59.317 55.000 0.00 0.00 0.00 2.41
403 411 2.928396 CCCACCACCCCTTCGTCT 60.928 66.667 0.00 0.00 0.00 4.18
410 418 1.623311 CATTTTTCTTCCCACCACCCC 59.377 52.381 0.00 0.00 0.00 4.95
412 420 4.681074 TTTCATTTTTCTTCCCACCACC 57.319 40.909 0.00 0.00 0.00 4.61
604 882 0.823460 CCGTTGGATTTTGGGATGGG 59.177 55.000 0.00 0.00 0.00 4.00
616 894 0.035439 GAGGAATCTTGGCCGTTGGA 60.035 55.000 0.00 0.00 0.00 3.53
637 915 4.541648 GGAGAGGGCGGAGGGCTA 62.542 72.222 0.00 0.00 42.94 3.93
652 930 2.610859 GAGAGGCTTGGGGGTGGA 60.611 66.667 0.00 0.00 0.00 4.02
1433 1873 3.732212 TGAAGTAATCGCAGATCCATGG 58.268 45.455 4.97 4.97 45.12 3.66
1567 2010 7.763071 TGATCATAGCAGCATATGTCAGTAATC 59.237 37.037 4.29 0.52 35.16 1.75
1813 2293 3.728845 TCGCCTATTTCTAGTGGCAATC 58.271 45.455 0.00 0.00 45.13 2.67
1931 2416 3.639094 ACTAGTAACTGCAGCTCCATAGG 59.361 47.826 15.27 0.15 0.00 2.57
1955 2440 5.644977 ATGTCAGTCAGTCGATAAGTCAA 57.355 39.130 0.00 0.00 0.00 3.18
2080 2566 0.179034 ATTCCTCAGAATCGCTGGGC 60.179 55.000 0.00 0.00 44.16 5.36
2217 2741 2.131023 CCCTTTCCAGGAGGCTTATCT 58.869 52.381 0.00 0.00 44.19 1.98
2221 2745 1.158007 TTTCCCTTTCCAGGAGGCTT 58.842 50.000 0.00 0.00 44.19 4.35
2339 3029 8.444783 ACCATATTACTTGCCCAATTAGACATA 58.555 33.333 0.00 0.00 0.00 2.29
2385 3075 1.736612 CTGAGCAGGAGAAGAAAGGC 58.263 55.000 0.00 0.00 0.00 4.35
2465 3155 5.805486 GGAAAAGGGAAAATAATTGCTCGTC 59.195 40.000 0.00 0.00 0.00 4.20
2467 3157 5.109210 GGGAAAAGGGAAAATAATTGCTCG 58.891 41.667 0.00 0.00 0.00 5.03
2748 3689 4.339247 ACAGCATTGTTAAGTTCTTGCAGT 59.661 37.500 0.00 0.00 32.28 4.40
2906 3847 7.934665 TCAGGCACAGTTCAAATAAGTAAAGTA 59.065 33.333 0.00 0.00 0.00 2.24
2953 3894 7.646130 TCCAAAACAGAAATTAGCTTAAACACG 59.354 33.333 0.00 0.00 0.00 4.49
3254 4204 4.577283 TGCATGATGATGACCAACTATGTG 59.423 41.667 0.00 0.00 0.00 3.21
3369 4319 3.009033 ACAGCCTGCAAATAAGAGGTACA 59.991 43.478 0.00 0.00 0.00 2.90
3527 4477 7.448161 TCACCATCAACATCAAGAACAGTAAAT 59.552 33.333 0.00 0.00 0.00 1.40
3934 4884 0.102300 GCGCCCAAACTTTTGTCTGT 59.898 50.000 0.00 0.00 36.45 3.41
4140 5090 1.610522 CCCAGAACAAGCCTTCACAAG 59.389 52.381 0.00 0.00 0.00 3.16
4614 5812 3.136992 TGAAGAGCATCAATATGGAGGCA 59.863 43.478 18.49 0.00 46.34 4.75
4895 6101 6.573664 TGGTCAATATTGTGTGGAAAAGAG 57.426 37.500 14.97 0.00 0.00 2.85
5498 6721 1.988015 GGGGATCCCGAAAGACACA 59.012 57.895 24.90 0.00 36.85 3.72
5539 6764 6.153000 ACTTACTATATCAGCCAGATTACCCG 59.847 42.308 0.00 0.00 38.19 5.28
5711 6965 3.429960 GCTTCATTTGGAATCCTGAAGGC 60.430 47.826 22.94 15.07 42.99 4.35
5903 7164 7.047891 TGTGACTGAATTACATAATCCCTGTC 58.952 38.462 12.18 12.18 33.33 3.51
5968 10570 5.174395 CAACAAGGGAGAAGACAGATACTG 58.826 45.833 0.00 0.00 37.52 2.74
6005 10607 3.135348 TCTGGGCAGAAGTGGAGAATATG 59.865 47.826 0.00 0.00 33.91 1.78
6168 10772 3.599343 TGACACAGGCAATCACAGTATC 58.401 45.455 0.00 0.00 0.00 2.24
6470 11098 1.165907 CGCCTTCAGCTTGTCAACCA 61.166 55.000 0.00 0.00 40.39 3.67
6585 11268 0.393077 AGTCTTCAACTGGGTGGTCG 59.607 55.000 0.00 0.00 36.65 4.79
6827 11513 0.247460 CAGTCGATCCTTGTGCCTCA 59.753 55.000 0.00 0.00 0.00 3.86
7071 11758 2.231721 ACCAAGCCGACTAAGAAGAGTC 59.768 50.000 0.00 0.00 42.13 3.36
7095 11784 6.364701 TCACTAGGCTACCAATGCATAAAAT 58.635 36.000 0.00 0.00 0.00 1.82
7170 11859 0.032403 GGCATGCAACAAACAGAGCA 59.968 50.000 21.36 0.00 41.73 4.26
7303 11998 6.368791 TGAAACTGATGATGAGGTAAAAGACG 59.631 38.462 0.00 0.00 0.00 4.18
7379 12078 1.813513 AGAGTTGCGAGGACAAATGG 58.186 50.000 0.00 0.00 0.00 3.16
7454 12153 2.498167 ACTAAAACTGCCAGCTGACTG 58.502 47.619 17.39 10.73 44.05 3.51
7455 12154 2.938956 ACTAAAACTGCCAGCTGACT 57.061 45.000 17.39 0.00 0.00 3.41
7484 12183 2.248280 TGCTCTAAACACGCAAAGGA 57.752 45.000 0.00 0.00 0.00 3.36
7524 12228 4.470304 GCCGAGGGGTATAATTTATCCTCT 59.530 45.833 15.42 11.44 38.78 3.69
7638 12602 1.458777 AGAATCGGGGGCATCGGTA 60.459 57.895 0.00 0.00 0.00 4.02
7746 12710 1.691196 CAACCTCTTCCTTGGTGCAA 58.309 50.000 0.00 0.00 36.57 4.08
7747 12711 0.178992 CCAACCTCTTCCTTGGTGCA 60.179 55.000 0.00 0.00 36.57 4.57
7918 12883 1.981495 CCTCTTCTTCACCACCTCCTT 59.019 52.381 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.