Multiple sequence alignment - TraesCS6B01G099700

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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 TraesCS6B01G099700 chr6B 100.000 5029 0 0 1 5029 77612651 77617679 0.000000e+00 9287.0
1 TraesCS6B01G099700 chr6B 83.598 567 85 6 3392 3955 63767621 63767060 4.460000e-145 525.0
2 TraesCS6B01G099700 chr6B 84.458 489 67 8 3389 3871 63997677 63997192 1.640000e-129 473.0
3 TraesCS6B01G099700 chr6B 77.255 787 132 29 1158 1919 63613526 63612762 7.790000e-113 418.0
4 TraesCS6B01G099700 chr6B 74.528 1060 208 47 1155 2191 83139612 83138592 6.060000e-109 405.0
5 TraesCS6B01G099700 chr6B 73.223 1027 210 41 1157 2162 64196276 64195294 3.780000e-81 313.0
6 TraesCS6B01G099700 chr6B 74.823 564 120 18 1601 2152 84566499 84567052 8.420000e-58 235.0
7 TraesCS6B01G099700 chrUn 94.096 4539 207 26 534 5029 113111756 113107236 0.000000e+00 6841.0
8 TraesCS6B01G099700 chrUn 94.115 2022 98 11 716 2726 113160399 113158388 0.000000e+00 3055.0
9 TraesCS6B01G099700 chrUn 94.718 1912 87 6 3125 5025 350654415 350652507 0.000000e+00 2959.0
10 TraesCS6B01G099700 chrUn 95.580 1629 59 3 3406 5029 113158393 113156773 0.000000e+00 2597.0
11 TraesCS6B01G099700 chrUn 83.715 829 115 15 3389 4205 102650881 102650061 0.000000e+00 765.0
12 TraesCS6B01G099700 chrUn 81.486 821 96 28 1 790 464846031 464846826 1.540000e-174 623.0
13 TraesCS6B01G099700 chrUn 75.142 1058 197 51 1155 2191 26726722 26727734 2.150000e-118 436.0
14 TraesCS6B01G099700 chrUn 81.524 525 63 17 1 501 113113402 113112888 7.840000e-108 401.0
15 TraesCS6B01G099700 chrUn 74.112 1070 222 38 1155 2204 102827630 102826596 1.700000e-104 390.0
16 TraesCS6B01G099700 chrUn 75.836 658 124 31 1552 2191 26573267 26572627 8.180000e-78 302.0
17 TraesCS6B01G099700 chrUn 88.583 254 22 3 792 1041 350654660 350654410 8.180000e-78 302.0
18 TraesCS6B01G099700 chrUn 72.523 1070 225 42 1159 2196 153378184 153379216 2.960000e-72 283.0
19 TraesCS6B01G099700 chrUn 79.710 414 44 18 290 667 113160798 113160389 3.860000e-66 263.0
20 TraesCS6B01G099700 chrUn 74.823 564 120 18 1601 2152 331176583 331177136 8.420000e-58 235.0
21 TraesCS6B01G099700 chrUn 86.301 73 7 3 4240 4310 102556161 102556090 5.400000e-10 76.8
22 TraesCS6B01G099700 chr6A 91.122 3289 204 46 269 3497 44695632 44698892 0.000000e+00 4375.0
23 TraesCS6B01G099700 chr6A 93.250 1674 81 7 3356 5029 44829149 44830790 0.000000e+00 2436.0
24 TraesCS6B01G099700 chr6A 83.754 1071 111 31 1 1035 44818119 44819162 0.000000e+00 955.0
25 TraesCS6B01G099700 chr6A 91.270 378 28 2 4653 5025 44266763 44267140 1.250000e-140 510.0
26 TraesCS6B01G099700 chr6A 90.871 241 11 3 3125 3354 44819163 44819403 3.780000e-81 313.0
27 TraesCS6B01G099700 chr6A 72.999 1037 209 48 1159 2159 48056944 48055943 1.060000e-76 298.0
28 TraesCS6B01G099700 chr6A 83.700 227 33 4 1 226 44695408 44695631 1.420000e-50 211.0
29 TraesCS6B01G099700 chr7B 74.749 1097 220 41 1129 2191 608183228 608184301 5.980000e-119 438.0
30 TraesCS6B01G099700 chr7B 75.316 316 64 10 114 424 385919630 385919936 6.790000e-29 139.0
31 TraesCS6B01G099700 chr7B 77.200 250 48 6 123 368 480682539 480682783 2.440000e-28 137.0
32 TraesCS6B01G099700 chr2D 80.625 320 48 7 108 424 355620507 355620815 8.420000e-58 235.0
33 TraesCS6B01G099700 chr1A 80.822 292 50 3 108 397 45780644 45780931 1.820000e-54 224.0
34 TraesCS6B01G099700 chr5B 77.603 317 48 12 108 414 534102419 534102722 2.410000e-38 171.0
35 TraesCS6B01G099700 chr5B 78.201 289 32 12 105 390 479395161 479395421 6.740000e-34 156.0
36 TraesCS6B01G099700 chr3D 79.352 247 45 3 113 357 549630217 549630459 8.660000e-38 169.0
37 TraesCS6B01G099700 chr5D 79.630 216 36 6 113 325 388049891 388049681 1.130000e-31 148.0
38 TraesCS6B01G099700 chr4D 79.630 216 32 11 113 324 469197887 469198094 1.460000e-30 145.0
39 TraesCS6B01G099700 chr1D 88.889 108 8 4 287 391 205131557 205131663 4.090000e-26 130.0
40 TraesCS6B01G099700 chr4B 84.783 92 14 0 11 102 626466079 626466170 5.360000e-15 93.5
41 TraesCS6B01G099700 chr2B 83.333 72 11 1 22 93 373112184 373112114 1.170000e-06 65.8


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 TraesCS6B01G099700 chr6B 77612651 77617679 5028 False 9287.000000 9287 100.000000 1 5029 1 chr6B.!!$F1 5028
1 TraesCS6B01G099700 chr6B 63767060 63767621 561 True 525.000000 525 83.598000 3392 3955 1 chr6B.!!$R2 563
2 TraesCS6B01G099700 chr6B 63612762 63613526 764 True 418.000000 418 77.255000 1158 1919 1 chr6B.!!$R1 761
3 TraesCS6B01G099700 chr6B 83138592 83139612 1020 True 405.000000 405 74.528000 1155 2191 1 chr6B.!!$R5 1036
4 TraesCS6B01G099700 chr6B 64195294 64196276 982 True 313.000000 313 73.223000 1157 2162 1 chr6B.!!$R4 1005
5 TraesCS6B01G099700 chr6B 84566499 84567052 553 False 235.000000 235 74.823000 1601 2152 1 chr6B.!!$F2 551
6 TraesCS6B01G099700 chrUn 113107236 113113402 6166 True 3621.000000 6841 87.810000 1 5029 2 chrUn.!!$R5 5028
7 TraesCS6B01G099700 chrUn 113156773 113160798 4025 True 1971.666667 3055 89.801667 290 5029 3 chrUn.!!$R6 4739
8 TraesCS6B01G099700 chrUn 350652507 350654660 2153 True 1630.500000 2959 91.650500 792 5025 2 chrUn.!!$R7 4233
9 TraesCS6B01G099700 chrUn 102650061 102650881 820 True 765.000000 765 83.715000 3389 4205 1 chrUn.!!$R3 816
10 TraesCS6B01G099700 chrUn 464846031 464846826 795 False 623.000000 623 81.486000 1 790 1 chrUn.!!$F4 789
11 TraesCS6B01G099700 chrUn 26726722 26727734 1012 False 436.000000 436 75.142000 1155 2191 1 chrUn.!!$F1 1036
12 TraesCS6B01G099700 chrUn 102826596 102827630 1034 True 390.000000 390 74.112000 1155 2204 1 chrUn.!!$R4 1049
13 TraesCS6B01G099700 chrUn 26572627 26573267 640 True 302.000000 302 75.836000 1552 2191 1 chrUn.!!$R1 639
14 TraesCS6B01G099700 chrUn 153378184 153379216 1032 False 283.000000 283 72.523000 1159 2196 1 chrUn.!!$F2 1037
15 TraesCS6B01G099700 chrUn 331176583 331177136 553 False 235.000000 235 74.823000 1601 2152 1 chrUn.!!$F3 551
16 TraesCS6B01G099700 chr6A 44829149 44830790 1641 False 2436.000000 2436 93.250000 3356 5029 1 chr6A.!!$F2 1673
17 TraesCS6B01G099700 chr6A 44695408 44698892 3484 False 2293.000000 4375 87.411000 1 3497 2 chr6A.!!$F3 3496
18 TraesCS6B01G099700 chr6A 44818119 44819403 1284 False 634.000000 955 87.312500 1 3354 2 chr6A.!!$F4 3353
19 TraesCS6B01G099700 chr6A 48055943 48056944 1001 True 298.000000 298 72.999000 1159 2159 1 chr6A.!!$R1 1000
20 TraesCS6B01G099700 chr7B 608183228 608184301 1073 False 438.000000 438 74.749000 1129 2191 1 chr7B.!!$F3 1062

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
634 1768 0.108329 AACGTAATCCCTGAGCCACG 60.108 55.0 0.0 0.0 35.62 4.94 F
999 2160 0.034089 CTCCCCACTTGATTCCCCAC 60.034 60.0 0.0 0.0 0.00 4.61 F
1208 2376 0.179092 TCTGCACCATCATCTCGCTG 60.179 55.0 0.0 0.0 0.00 5.18 F
1516 2702 0.249073 CGCTTCCCTGGATGTACTCG 60.249 60.0 0.0 0.0 0.00 4.18 F
1940 3152 0.883833 TCTTACCCGTCGTCTCCAAC 59.116 55.0 0.0 0.0 0.00 3.77 F
3108 4362 1.233285 GCAGCACAGCAGCAGTACTT 61.233 55.0 0.0 0.0 40.73 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1485 2671 0.517316 GGGAAGCGCTTGTAGTTGTG 59.483 55.000 30.47 0.00 0.00 3.33 R
2371 3612 0.530744 TGAGAACAGGGAATCGTCCG 59.469 55.000 0.00 0.00 46.04 4.79 R
3031 4285 2.284190 GTCAAAGTAGGGAGCATGCTC 58.716 52.381 34.99 34.99 42.04 4.26 R
3108 4362 3.772572 TCCACGATAAACTCTCCCAATCA 59.227 43.478 0.00 0.00 0.00 2.57 R
3627 4892 0.984829 CACCGATATAGCATCGCACG 59.015 55.000 1.20 0.00 39.95 5.34 R
4522 5801 1.277580 CCCCAGGCTGTTCAGGATCT 61.278 60.000 14.43 0.00 0.00 2.75 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
117 118 3.423154 CGCAGCGGTGAAGGTTCC 61.423 66.667 20.69 0.00 0.00 3.62
141 142 2.893215 TCCAACGAGGAAGAGTAGGA 57.107 50.000 0.00 0.00 45.65 2.94
154 155 1.043673 AGTAGGACATGGGAGACGGC 61.044 60.000 0.00 0.00 0.00 5.68
175 176 1.599047 CGCCTTGAGTCCCATGAGT 59.401 57.895 0.00 0.00 0.00 3.41
177 178 0.460987 GCCTTGAGTCCCATGAGTCG 60.461 60.000 0.00 0.00 42.83 4.18
178 179 1.186200 CCTTGAGTCCCATGAGTCGA 58.814 55.000 0.00 0.00 42.83 4.20
187 188 1.753649 CCCATGAGTCGATCTGTGTCT 59.246 52.381 0.00 0.00 0.00 3.41
216 217 3.129502 CTACCTCGACGGCGACCA 61.130 66.667 10.67 0.00 42.51 4.02
220 221 3.432588 CTCGACGGCGACCAGACT 61.433 66.667 10.67 0.00 42.51 3.24
229 230 2.089980 GGCGACCAGACTAACACTCTA 58.910 52.381 0.00 0.00 0.00 2.43
240 241 1.435256 AACACTCTAAGGGGCACAGT 58.565 50.000 0.00 0.00 0.00 3.55
241 242 0.687354 ACACTCTAAGGGGCACAGTG 59.313 55.000 3.61 3.61 40.33 3.66
253 254 1.079819 CACAGTGGGCCACTAGACG 60.080 63.158 37.13 26.52 43.43 4.18
361 364 4.808414 TGTTTGTGGTTGTGGAATCAAA 57.192 36.364 0.00 0.00 0.00 2.69
367 370 8.669243 GTTTGTGGTTGTGGAATCAAATTTTTA 58.331 29.630 0.00 0.00 0.00 1.52
383 386 6.773976 AATTTTTATGTGATGTCCGGTCAT 57.226 33.333 14.28 14.28 0.00 3.06
391 394 2.047655 GTCCGGTCATTGTCCGCA 60.048 61.111 15.60 0.00 45.71 5.69
442 469 0.907486 TGGCAGATGCACTTAGCTCT 59.093 50.000 7.19 0.00 45.94 4.09
543 1670 8.996024 ATTTTTAGCTAATGCGTAAAACCAAT 57.004 26.923 7.08 0.00 45.42 3.16
546 1673 8.455598 TTTAGCTAATGCGTAAAACCAATTTC 57.544 30.769 7.08 0.00 45.42 2.17
551 1678 7.739911 GCTAATGCGTAAAACCAATTTCTTTTG 59.260 33.333 1.60 0.00 32.27 2.44
558 1685 8.865001 CGTAAAACCAATTTCTTTTGAGAAACA 58.135 29.630 3.92 0.00 40.12 2.83
627 1761 0.463833 GAGGCCCAACGTAATCCCTG 60.464 60.000 0.00 0.00 0.00 4.45
634 1768 0.108329 AACGTAATCCCTGAGCCACG 60.108 55.000 0.00 0.00 35.62 4.94
701 1837 7.787725 AAAATAGATAAAACTCCGGTGCTAG 57.212 36.000 0.00 0.00 0.00 3.42
772 1912 0.608130 AGACAAGCATACGCCAGACA 59.392 50.000 0.00 0.00 39.83 3.41
783 1923 0.234884 CGCCAGACACGGAAAGAAAC 59.765 55.000 0.00 0.00 0.00 2.78
830 1970 2.936498 ACACTGACAAACGAGGAAAGTG 59.064 45.455 0.00 0.00 39.49 3.16
919 2072 2.023414 AACACCTCTCCGTCGTTGCA 62.023 55.000 0.00 0.00 0.00 4.08
972 2133 1.383799 CAGCCAGTTCCATTCCCCA 59.616 57.895 0.00 0.00 0.00 4.96
999 2160 0.034089 CTCCCCACTTGATTCCCCAC 60.034 60.000 0.00 0.00 0.00 4.61
1178 2346 0.254178 ATTTCATCAGCACGCTCCCT 59.746 50.000 0.00 0.00 0.00 4.20
1208 2376 0.179092 TCTGCACCATCATCTCGCTG 60.179 55.000 0.00 0.00 0.00 5.18
1485 2671 1.757699 AGGAGCTCGAATTCACCTACC 59.242 52.381 7.83 3.37 0.00 3.18
1516 2702 0.249073 CGCTTCCCTGGATGTACTCG 60.249 60.000 0.00 0.00 0.00 4.18
1655 2859 4.002982 TCTCCTTGATGTTCGTTTCCATG 58.997 43.478 0.00 0.00 0.00 3.66
1728 2937 5.590259 AGCTTATACATGGCTGAAATTCGTT 59.410 36.000 0.00 0.00 34.82 3.85
1793 3002 2.101750 TGGCTTCCGTAATAGCGATGAA 59.898 45.455 0.00 0.00 38.28 2.57
1866 3078 7.071196 TGCTACCTTATATTCACCACTCTGATT 59.929 37.037 0.00 0.00 0.00 2.57
1940 3152 0.883833 TCTTACCCGTCGTCTCCAAC 59.116 55.000 0.00 0.00 0.00 3.77
2204 3443 9.136323 AGTACTCATCTTTTCCTTTTGATTGTT 57.864 29.630 0.00 0.00 0.00 2.83
2242 3481 7.665690 TGTATTGTTGGTTGCATATTTTGAGT 58.334 30.769 0.00 0.00 0.00 3.41
2248 3487 5.263599 TGGTTGCATATTTTGAGTCTCCAT 58.736 37.500 0.00 0.00 0.00 3.41
2313 3554 9.107177 GTTGAATTATGTGATTGAGATCTGACT 57.893 33.333 0.00 0.00 33.28 3.41
2371 3612 4.444720 CAGACCTGAAAGTTTACGAGTCAC 59.555 45.833 0.00 0.00 0.00 3.67
2405 3646 6.884295 CCCTGTTCTCATATTTAGGTTCAACA 59.116 38.462 0.00 0.00 0.00 3.33
2569 3813 8.317679 TCTTCCTTATCTTTTCTCTCTTTCCTG 58.682 37.037 0.00 0.00 0.00 3.86
2661 3905 4.498177 CCCACAGATCTCACTATGTACACG 60.498 50.000 0.00 0.00 0.00 4.49
2695 3939 7.226523 GGTCATATATGCATTCACACTTACACA 59.773 37.037 3.54 0.00 0.00 3.72
2717 3961 9.308000 ACACAAATCTCCATAAAAATCAGGTAA 57.692 29.630 0.00 0.00 0.00 2.85
2842 4087 4.142403 GGCATCCATCAAATTCGAAGTTGA 60.142 41.667 34.58 34.58 45.47 3.18
2915 4160 4.392754 TGTGCAGTACAACTTGCAGATATG 59.607 41.667 7.69 0.00 36.06 1.78
3088 4342 4.979815 GTGTGGTTGGTATAAAAAGTGCAC 59.020 41.667 9.40 9.40 0.00 4.57
3108 4362 1.233285 GCAGCACAGCAGCAGTACTT 61.233 55.000 0.00 0.00 40.73 2.24
3162 4417 9.770097 TGATCAAAAGAGGATGTTCAGATATAC 57.230 33.333 0.00 0.00 0.00 1.47
3208 4467 9.194972 TGAAAACCATCAAAACATGCCTATATA 57.805 29.630 0.00 0.00 0.00 0.86
3294 4559 6.413783 TCTGGCGGATGTATTCACTAAATA 57.586 37.500 0.00 0.00 0.00 1.40
3322 4587 9.062524 CGAATATCCATATCAACCCACTTTAAA 57.937 33.333 0.00 0.00 0.00 1.52
3332 4597 7.296628 TCAACCCACTTTAAAAGCAATACAT 57.703 32.000 0.00 0.00 0.00 2.29
3443 4708 1.473258 TTTGCAGTTTGGCAGACACT 58.527 45.000 11.05 0.62 45.88 3.55
3634 4899 2.223947 TGAAGTATATGGTGCGTGCGAT 60.224 45.455 0.00 0.00 0.00 4.58
3635 4900 1.783284 AGTATATGGTGCGTGCGATG 58.217 50.000 0.00 0.00 0.00 3.84
3658 4923 5.188948 TGCTATATCGGTGGCTTATTACCAT 59.811 40.000 0.00 0.00 39.95 3.55
3912 5179 9.209175 TCAATTTCTAGTCTAAAGTTCTTCTGC 57.791 33.333 0.00 0.00 0.00 4.26
3956 5231 4.133820 GCCCCTGTTAAAATTGCAAAAGT 58.866 39.130 1.71 0.00 0.00 2.66
3959 5234 5.588246 CCCCTGTTAAAATTGCAAAAGTTGT 59.412 36.000 1.71 0.00 0.00 3.32
4152 5428 6.846325 TTTTCGTGTATGTGTGACATTACA 57.154 33.333 7.10 7.10 39.88 2.41
4155 5431 5.715070 TCGTGTATGTGTGACATTACATCA 58.285 37.500 12.41 7.33 39.88 3.07
4308 5584 8.984891 TGATCGGTTAGTAAAGTTCGATTTTA 57.015 30.769 10.73 0.00 37.46 1.52
4310 5586 7.581011 TCGGTTAGTAAAGTTCGATTTTACC 57.419 36.000 20.58 12.49 40.29 2.85
4313 5589 7.953710 CGGTTAGTAAAGTTCGATTTTACCAAG 59.046 37.037 20.58 10.51 40.29 3.61
4335 5611 7.256835 CCAAGATTGTCCTATTAGGCTAAGGAT 60.257 40.741 16.11 3.04 41.34 3.24
4457 5736 3.993081 TGCTTGCAAAACCGGAATATTTG 59.007 39.130 9.46 14.57 37.17 2.32
4517 5796 1.002011 GGGGCAGACTGAAGTTCCC 60.002 63.158 6.65 6.59 34.08 3.97
4522 5801 1.072331 GCAGACTGAAGTTCCCCTGAA 59.928 52.381 6.65 0.00 0.00 3.02
4544 5823 2.673523 CTGAACAGCCTGGGGGAG 59.326 66.667 0.00 0.00 33.58 4.30
4554 5833 1.534338 CCTGGGGGAGGGAATGTTAT 58.466 55.000 0.00 0.00 38.36 1.89
4647 5926 7.500559 GCTAAGGATCTGAAAATAGTGTTGGAT 59.499 37.037 0.00 0.00 0.00 3.41
4719 6003 2.224523 ACCCACACCATACACACTCTTG 60.225 50.000 0.00 0.00 0.00 3.02
4831 6115 9.683069 CAAGAAATTTTGTGAAACTAGTAGCAT 57.317 29.630 0.00 0.00 38.04 3.79
4841 6125 7.441760 TGTGAAACTAGTAGCATAACGGAAAAA 59.558 33.333 0.00 0.00 38.04 1.94
4886 6170 2.759191 AGCATATACTCGTGGCATGTG 58.241 47.619 6.60 6.92 0.00 3.21
4896 6180 0.801251 GTGGCATGTGCAAGAGAGAC 59.199 55.000 7.36 0.00 44.36 3.36
4931 6215 5.354234 CCATTAAGAAGGATTAAGCGTGTGT 59.646 40.000 0.00 0.00 0.00 3.72
5025 6309 4.563580 CCTCCGCTGTATATGCCTGTTTAT 60.564 45.833 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.799755 GCGGACACCCATGCGTTC 61.800 66.667 0.00 0.00 0.00 3.95
103 104 2.920912 TCCGGAACCTTCACCGCT 60.921 61.111 0.00 0.00 46.59 5.52
154 155 4.473520 ATGGGACTCAAGGCGCCG 62.474 66.667 23.20 9.47 0.00 6.46
167 168 1.753649 AGACACAGATCGACTCATGGG 59.246 52.381 0.00 0.00 0.00 4.00
170 171 3.698539 ACATGAGACACAGATCGACTCAT 59.301 43.478 0.00 6.62 45.26 2.90
175 176 2.728007 AGGACATGAGACACAGATCGA 58.272 47.619 0.00 0.00 0.00 3.59
177 178 4.887071 AGAGTAGGACATGAGACACAGATC 59.113 45.833 0.00 0.00 0.00 2.75
178 179 4.865905 AGAGTAGGACATGAGACACAGAT 58.134 43.478 0.00 0.00 0.00 2.90
187 188 3.740452 CGTCGAGGTAGAGTAGGACATGA 60.740 52.174 0.00 0.00 0.00 3.07
216 217 2.832733 GTGCCCCTTAGAGTGTTAGTCT 59.167 50.000 0.00 0.00 0.00 3.24
220 221 2.301870 CACTGTGCCCCTTAGAGTGTTA 59.698 50.000 0.00 0.00 35.43 2.41
253 254 3.423154 CGGCTCTTTCGTGCCCAC 61.423 66.667 0.00 0.00 44.87 4.61
281 282 5.889219 ACGTAAAACCTACTCTAAGCTAGC 58.111 41.667 6.62 6.62 0.00 3.42
282 283 7.081526 TGACGTAAAACCTACTCTAAGCTAG 57.918 40.000 0.00 0.00 0.00 3.42
283 284 7.121759 ACATGACGTAAAACCTACTCTAAGCTA 59.878 37.037 0.00 0.00 0.00 3.32
284 285 5.972107 TGACGTAAAACCTACTCTAAGCT 57.028 39.130 0.00 0.00 0.00 3.74
332 335 4.403752 TCCACAACCACAAACATCATTTCA 59.596 37.500 0.00 0.00 0.00 2.69
361 364 6.152661 ACAATGACCGGACATCACATAAAAAT 59.847 34.615 19.63 0.00 0.00 1.82
367 370 2.632377 GACAATGACCGGACATCACAT 58.368 47.619 19.63 5.95 0.00 3.21
383 386 2.274645 CCCAAATGCCTGCGGACAA 61.275 57.895 0.00 0.00 0.00 3.18
391 394 2.820899 AAATCCGCCCCCAAATGCCT 62.821 55.000 0.00 0.00 0.00 4.75
393 396 0.744057 CAAAATCCGCCCCCAAATGC 60.744 55.000 0.00 0.00 0.00 3.56
395 398 1.909459 GCCAAAATCCGCCCCCAAAT 61.909 55.000 0.00 0.00 0.00 2.32
421 448 0.742281 AGCTAAGTGCATCTGCCACG 60.742 55.000 0.00 0.00 45.94 4.94
424 451 1.580815 GAGAGCTAAGTGCATCTGCC 58.419 55.000 0.00 0.00 45.94 4.85
426 453 2.975732 TGGAGAGCTAAGTGCATCTG 57.024 50.000 0.00 0.00 45.94 2.90
433 460 4.853007 AGATTGCAAATGGAGAGCTAAGT 58.147 39.130 1.71 0.00 0.00 2.24
442 469 5.889289 TGAGATCATCAAGATTGCAAATGGA 59.111 36.000 1.71 0.00 37.00 3.41
516 1519 9.909644 TTGGTTTTACGCATTAGCTAAAAATAA 57.090 25.926 10.85 4.76 36.29 1.40
520 1523 8.819643 AAATTGGTTTTACGCATTAGCTAAAA 57.180 26.923 10.85 0.00 39.10 1.52
523 1526 7.385778 AGAAATTGGTTTTACGCATTAGCTA 57.614 32.000 0.00 0.00 39.10 3.32
525 1528 6.944557 AAGAAATTGGTTTTACGCATTAGC 57.055 33.333 0.00 0.00 37.42 3.09
634 1768 3.255642 TGTATTCTTTTCTTGCCCTGTGC 59.744 43.478 0.00 0.00 41.77 4.57
681 1817 5.927281 AACTAGCACCGGAGTTTTATCTA 57.073 39.130 9.46 0.00 31.83 1.98
683 1819 5.874895 AAAACTAGCACCGGAGTTTTATC 57.125 39.130 23.13 0.00 38.42 1.75
735 1874 2.936498 GTCTGCCGCAGTGTGTAATAAT 59.064 45.455 19.77 0.00 32.61 1.28
736 1875 2.289133 TGTCTGCCGCAGTGTGTAATAA 60.289 45.455 19.77 0.00 32.61 1.40
737 1876 1.273886 TGTCTGCCGCAGTGTGTAATA 59.726 47.619 19.77 0.00 32.61 0.98
741 1880 1.889105 CTTGTCTGCCGCAGTGTGT 60.889 57.895 19.77 0.00 32.61 3.72
772 1912 0.883370 GAGCCGTGGTTTCTTTCCGT 60.883 55.000 0.00 0.00 0.00 4.69
783 1923 1.084370 GTTCGATTCCTGAGCCGTGG 61.084 60.000 0.00 0.00 0.00 4.94
830 1970 0.539986 TTCTGATCCCCGTACTTGCC 59.460 55.000 0.00 0.00 0.00 4.52
972 2133 1.852626 CAAGTGGGGAGGGGAGGTT 60.853 63.158 0.00 0.00 0.00 3.50
1178 2346 2.265739 GTGCAGAGGATGGCGTCA 59.734 61.111 9.27 0.00 0.00 4.35
1208 2376 4.410400 CCGTCCTTGGTGGGGAGC 62.410 72.222 0.00 0.00 36.20 4.70
1485 2671 0.517316 GGGAAGCGCTTGTAGTTGTG 59.483 55.000 30.47 0.00 0.00 3.33
1516 2702 1.267121 TGGTGGCAGTAGGTTCTCTC 58.733 55.000 0.00 0.00 0.00 3.20
1655 2859 1.094785 CATGAAACACATCCCCCGAC 58.905 55.000 0.00 0.00 37.07 4.79
1770 2979 2.676632 TCGCTATTACGGAAGCCAAA 57.323 45.000 0.00 0.00 35.22 3.28
1866 3078 8.777413 CCTAACTACACGTATAGTAGCACAATA 58.223 37.037 6.99 0.00 42.04 1.90
1940 3152 6.872547 TGCTACGTACCTGAGATACTAGTATG 59.127 42.308 20.13 7.76 0.00 2.39
2041 3280 2.170607 GCTGAGGTGAGTGGGCTTATTA 59.829 50.000 0.00 0.00 0.00 0.98
2348 3589 4.444720 GTGACTCGTAAACTTTCAGGTCTG 59.555 45.833 0.00 0.00 0.00 3.51
2371 3612 0.530744 TGAGAACAGGGAATCGTCCG 59.469 55.000 0.00 0.00 46.04 4.79
2405 3646 5.483811 TGTCATACGTGTTGTGGTTATGAT 58.516 37.500 0.00 0.00 0.00 2.45
2470 3713 7.565398 ACTCCACATGTCTATTGTACCTCTAAT 59.435 37.037 0.00 0.00 0.00 1.73
2595 3839 9.821662 CTTATTTACAACAACTTGCCTAAGTAC 57.178 33.333 0.00 0.00 46.14 2.73
2640 3884 4.038361 GCGTGTACATAGTGAGATCTGTG 58.962 47.826 0.00 0.00 33.76 3.66
2641 3885 3.694566 TGCGTGTACATAGTGAGATCTGT 59.305 43.478 0.00 0.00 0.00 3.41
2661 3905 3.313012 TGCATATATGACCGGTACTGC 57.687 47.619 17.10 11.09 0.00 4.40
2795 4040 7.201504 GCCTCTTGTACCGAGTTAGTAATTTTC 60.202 40.741 8.06 0.00 0.00 2.29
2813 4058 3.379372 CGAATTTGATGGATGCCTCTTGT 59.621 43.478 0.00 0.00 0.00 3.16
2965 4210 8.429641 TGACACTTCTTTTGGTTACTATTCTCT 58.570 33.333 0.00 0.00 0.00 3.10
3031 4285 2.284190 GTCAAAGTAGGGAGCATGCTC 58.716 52.381 34.99 34.99 42.04 4.26
3066 4320 4.261238 CGTGCACTTTTTATACCAACCACA 60.261 41.667 16.19 0.00 0.00 4.17
3108 4362 3.772572 TCCACGATAAACTCTCCCAATCA 59.227 43.478 0.00 0.00 0.00 2.57
3162 4417 6.795098 TTCATCCGAAACATTATTATCCCG 57.205 37.500 0.00 0.00 0.00 5.14
3208 4467 7.643123 AGTTTGATATCTCCCCACTTGTATTT 58.357 34.615 3.98 0.00 0.00 1.40
3294 4559 6.627087 AGTGGGTTGATATGGATATTCGAT 57.373 37.500 0.00 0.00 0.00 3.59
3322 4587 9.618890 ACATATAGACTTGACAATGTATTGCTT 57.381 29.630 4.58 0.00 41.38 3.91
3332 4597 6.154534 ACAGGCTACACATATAGACTTGACAA 59.845 38.462 0.00 0.00 37.21 3.18
3443 4708 6.825721 GGCTCATTTTTCTTATTCTCCTCTGA 59.174 38.462 0.00 0.00 0.00 3.27
3627 4892 0.984829 CACCGATATAGCATCGCACG 59.015 55.000 1.20 0.00 39.95 5.34
3634 4899 4.528987 TGGTAATAAGCCACCGATATAGCA 59.471 41.667 0.00 0.00 37.66 3.49
3635 4900 5.080969 TGGTAATAAGCCACCGATATAGC 57.919 43.478 0.00 0.00 37.66 2.97
3658 4923 5.538813 TCTCTTTTCCACTTGTAGCAGACTA 59.461 40.000 0.00 0.00 0.00 2.59
3742 5007 3.129813 CCACAGACAAATCATGGACATGG 59.870 47.826 11.98 0.00 39.24 3.66
3794 5059 3.144506 ACAGTGCAATCTTCAGGTTCAG 58.855 45.455 0.00 0.00 0.00 3.02
3875 5142 7.055667 AGACTAGAAATTGAGCGGATTCATA 57.944 36.000 0.00 0.00 0.00 2.15
3912 5179 5.220931 GGCAAGCTCATAAGTACTGGAATTG 60.221 44.000 0.00 4.81 0.00 2.32
3956 5231 5.186797 ACAAACCATTTGAACTTCTCCACAA 59.813 36.000 8.24 0.00 43.26 3.33
3959 5234 6.801575 GTTACAAACCATTTGAACTTCTCCA 58.198 36.000 8.24 0.00 43.26 3.86
4308 5584 6.183361 CCTTAGCCTAATAGGACAATCTTGGT 60.183 42.308 11.13 0.00 37.67 3.67
4310 5586 7.067496 TCCTTAGCCTAATAGGACAATCTTG 57.933 40.000 11.13 0.00 37.67 3.02
4313 5589 7.179338 TCAGATCCTTAGCCTAATAGGACAATC 59.821 40.741 11.13 3.93 40.68 2.67
4457 5736 2.783135 TCCCAGTCTGAAATTCACAGC 58.217 47.619 0.00 4.35 35.61 4.40
4517 5796 1.558756 AGGCTGTTCAGGATCTTCAGG 59.441 52.381 1.97 0.00 0.00 3.86
4522 5801 1.277580 CCCCAGGCTGTTCAGGATCT 61.278 60.000 14.43 0.00 0.00 2.75
4608 5887 3.536956 TCCTTAGCCCAATAGAACGTG 57.463 47.619 0.00 0.00 0.00 4.49
4673 5952 4.486090 CCCATACGCACTGATACAGATAC 58.514 47.826 5.76 0.00 35.18 2.24
4719 6003 7.031226 TCATAATCTCAAGCCAGTTTTATGC 57.969 36.000 0.00 0.00 0.00 3.14
4841 6125 3.615496 CGATAATTGTCGTCCGGAAAACT 59.385 43.478 15.61 0.00 36.88 2.66
4886 6170 4.116238 GGTATTAGCAGTGTCTCTCTTGC 58.884 47.826 0.00 0.00 0.00 4.01
4896 6180 8.682936 AATCCTTCTTAATGGTATTAGCAGTG 57.317 34.615 6.12 0.00 0.00 3.66
4955 6239 1.405463 TCCTCGTCAAGACATGATCCG 59.595 52.381 0.00 0.00 40.97 4.18
4957 6241 3.629855 TCTCTCCTCGTCAAGACATGATC 59.370 47.826 0.00 0.00 40.97 2.92


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

AutoCloner maintained by Alex Coulton.