Multiple sequence alignment - TraesCS7D01G314000

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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 TraesCS7D01G314000 chr7D 100.000 2062 0 0 2385 4446 398719748 398717687 0.000000e+00 3808
1 TraesCS7D01G314000 chr7D 100.000 1923 0 0 1 1923 398722132 398720210 0.000000e+00 3552
2 TraesCS7D01G314000 chr7D 87.137 241 31 0 1525 1765 34151394 34151154 1.580000e-69 274
3 TraesCS7D01G314000 chr7D 86.640 247 27 4 1525 1765 33754892 33755138 7.330000e-68 268
4 TraesCS7D01G314000 chr7D 85.830 247 29 5 1525 1765 34445267 34445513 1.590000e-64 257
5 TraesCS7D01G314000 chr7D 85.425 247 30 4 1525 1765 34011496 34011250 7.380000e-63 252
6 TraesCS7D01G314000 chr7D 85.425 247 30 4 1525 1765 34076887 34076641 7.380000e-63 252
7 TraesCS7D01G314000 chr7D 82.114 246 38 4 1525 1764 420742658 420742413 5.830000e-49 206
8 TraesCS7D01G314000 chr7A 95.707 2073 57 14 2385 4446 455395104 455393053 0.000000e+00 3306
9 TraesCS7D01G314000 chr7A 91.462 1956 132 14 1 1923 455397142 455395189 0.000000e+00 2654
10 TraesCS7D01G314000 chr7A 86.235 247 28 2 1525 1765 34106282 34106036 3.410000e-66 263
11 TraesCS7D01G314000 chr7A 85.425 247 30 4 1525 1765 34519311 34519065 7.380000e-63 252
12 TraesCS7D01G314000 chr7A 84.146 246 33 4 1525 1764 512328944 512329189 2.670000e-57 233
13 TraesCS7D01G314000 chr1B 82.197 528 79 13 24 544 25227640 25227121 1.470000e-119 440
14 TraesCS7D01G314000 chr5D 81.748 515 83 8 36 544 61484933 61485442 1.910000e-113 420
15 TraesCS7D01G314000 chr5D 81.165 515 89 7 35 544 220674049 220674560 1.490000e-109 407
16 TraesCS7D01G314000 chr6B 81.395 516 87 8 35 544 43320040 43319528 3.200000e-111 412
17 TraesCS7D01G314000 chr3D 81.431 517 84 9 35 544 401012240 401011729 3.200000e-111 412
18 TraesCS7D01G314000 chr3D 81.055 512 85 11 41 544 447592755 447593262 8.960000e-107 398
19 TraesCS7D01G314000 chr5B 81.188 505 87 5 35 536 311547772 311547273 2.490000e-107 399
20 TraesCS7D01G314000 chr3A 81.225 506 85 8 35 534 693124939 693124438 2.490000e-107 399
21 TraesCS7D01G314000 chr4A 85.425 247 30 4 1525 1765 691166777 691167023 7.380000e-63 252
22 TraesCS7D01G314000 chr4A 85.020 247 31 2 1525 1765 690937943 690937697 3.430000e-61 246
23 TraesCS7D01G314000 chr4A 86.286 175 22 2 1070 1243 690881558 690881385 5.870000e-44 189
24 TraesCS7D01G314000 chr4A 85.326 184 26 1 1060 1243 691246754 691246936 5.870000e-44 189
25 TraesCS7D01G314000 chr4A 81.223 229 36 6 1541 1766 739587226 739587450 1.270000e-40 178
26 TraesCS7D01G314000 chr6D 83.843 229 28 8 1541 1765 310888063 310887840 4.510000e-50 209
27 TraesCS7D01G314000 chr7B 82.114 246 38 4 1525 1764 436787601 436787356 5.830000e-49 206
28 TraesCS7D01G314000 chr6A 83.260 227 33 5 1541 1765 447178890 447178667 2.100000e-48 204


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 TraesCS7D01G314000 chr7D 398717687 398722132 4445 True 3680 3808 100.0000 1 4446 2 chr7D.!!$R5 4445
1 TraesCS7D01G314000 chr7A 455393053 455397142 4089 True 2980 3306 93.5845 1 4446 2 chr7A.!!$R3 4445
2 TraesCS7D01G314000 chr1B 25227121 25227640 519 True 440 440 82.1970 24 544 1 chr1B.!!$R1 520
3 TraesCS7D01G314000 chr5D 61484933 61485442 509 False 420 420 81.7480 36 544 1 chr5D.!!$F1 508
4 TraesCS7D01G314000 chr5D 220674049 220674560 511 False 407 407 81.1650 35 544 1 chr5D.!!$F2 509
5 TraesCS7D01G314000 chr6B 43319528 43320040 512 True 412 412 81.3950 35 544 1 chr6B.!!$R1 509
6 TraesCS7D01G314000 chr3D 401011729 401012240 511 True 412 412 81.4310 35 544 1 chr3D.!!$R1 509
7 TraesCS7D01G314000 chr3D 447592755 447593262 507 False 398 398 81.0550 41 544 1 chr3D.!!$F1 503
8 TraesCS7D01G314000 chr3A 693124438 693124939 501 True 399 399 81.2250 35 534 1 chr3A.!!$R1 499

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
25 26 0.179018 ATCTTCGGTGGCATTAGGGC 60.179 55.000 0.00 0.00 43.73 5.19 F
942 979 0.756442 CCTCCTCTCCTCCTCAGCTG 60.756 65.000 7.63 7.63 0.00 4.24 F
1710 1749 0.896940 TCGTCTTCTACAAGGGCCGT 60.897 55.000 0.00 0.00 0.00 5.68 F
1776 1815 1.080025 CGACGACCCTTCTTCCACC 60.080 63.158 0.00 0.00 0.00 4.61 F
2657 2696 1.655654 CTACTCCAGCGACGATGCG 60.656 63.158 7.77 3.32 40.67 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1008 1045 0.324091 TCTTCCAGGGACCGGTAGAC 60.324 60.0 7.34 0.0 0.00 2.59 R
2657 2696 0.035630 AGTGCAGGATCTGGTCAAGC 60.036 55.0 0.00 0.0 31.21 4.01 R
2948 2987 0.319040 CGACTAGCCGGTCCATCATG 60.319 60.0 1.90 0.0 33.07 3.07 R
3248 3287 0.508641 CACCTTTCGTGTCTTCAGCG 59.491 55.0 0.00 0.0 37.73 5.18 R
4186 4233 0.261991 TCTAGATCGACCTTGGCCCT 59.738 55.0 0.00 0.0 0.00 5.19 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 1.296392 CACCTCATCTTCGGTGGCA 59.704 57.895 0.00 0.00 45.39 4.92
25 26 0.179018 ATCTTCGGTGGCATTAGGGC 60.179 55.000 0.00 0.00 43.73 5.19
32 33 3.141449 GGCATTAGGGCAATGGGC 58.859 61.111 0.45 0.00 43.70 5.36
53 56 1.202675 ACGGTGAAAGGGCTCGTTTTA 60.203 47.619 0.00 0.00 0.00 1.52
54 57 1.463444 CGGTGAAAGGGCTCGTTTTAG 59.537 52.381 0.00 0.00 0.00 1.85
57 60 3.127030 GGTGAAAGGGCTCGTTTTAGATG 59.873 47.826 0.00 0.00 0.00 2.90
108 112 2.430610 GCTCAGGGAGGCGAGACAT 61.431 63.158 0.00 0.00 0.00 3.06
153 157 1.133419 AGTTTTTCCCCGTTTAGCCCA 60.133 47.619 0.00 0.00 0.00 5.36
232 238 2.942804 TCTGTCTTTGGTGGATTTGCA 58.057 42.857 0.00 0.00 0.00 4.08
250 256 2.433970 TGCACGGATCTGGTCATCATTA 59.566 45.455 6.47 0.00 0.00 1.90
266 272 5.347635 TCATCATTAGTCTACGTTTGTGTGC 59.652 40.000 0.00 0.00 0.00 4.57
313 320 2.273370 TTACTCTTCATCGGCGACAC 57.727 50.000 13.76 0.00 0.00 3.67
327 334 1.864711 GCGACACTTGTTGTTCTGCTA 59.135 47.619 0.00 0.00 39.17 3.49
370 377 1.030457 ACGACGACTTCCTGACTGTT 58.970 50.000 0.00 0.00 0.00 3.16
371 378 2.031420 CACGACGACTTCCTGACTGTTA 60.031 50.000 0.00 0.00 0.00 2.41
464 472 2.352421 GCTTGTAGTCGTTGCTAGGTGA 60.352 50.000 0.00 0.00 0.00 4.02
474 482 8.582657 AGTCGTTGCTAGGTGATATATAGATT 57.417 34.615 0.00 0.00 0.00 2.40
567 582 3.317603 AAAAAGGGCATTCATGAACCG 57.682 42.857 11.07 6.31 33.37 4.44
569 584 1.322538 AAGGGCATTCATGAACCGCC 61.323 55.000 30.09 30.09 39.95 6.13
576 591 3.741388 GCATTCATGAACCGCCTACTAGT 60.741 47.826 11.07 0.00 0.00 2.57
586 601 8.277490 TGAACCGCCTACTAGTAATAGATATG 57.723 38.462 3.83 0.00 0.00 1.78
803 820 1.041447 TCCGATCGTTTCTCCCTCCC 61.041 60.000 15.09 0.00 0.00 4.30
842 863 4.895889 CACCTCTCTCTCTCTCTCTCTCTA 59.104 50.000 0.00 0.00 0.00 2.43
942 979 0.756442 CCTCCTCTCCTCCTCAGCTG 60.756 65.000 7.63 7.63 0.00 4.24
972 1009 5.574740 GCTAGCTCCAATCTATCTCCCTCTA 60.575 48.000 7.70 0.00 0.00 2.43
981 1018 2.022718 ATCTCCCTCTATCTGCCCAC 57.977 55.000 0.00 0.00 0.00 4.61
985 1022 2.630580 CTCCCTCTATCTGCCCACTTAC 59.369 54.545 0.00 0.00 0.00 2.34
1008 1045 3.059597 CAGCCTTTAACACACGAACTCAG 60.060 47.826 0.00 0.00 0.00 3.35
1045 1082 4.988598 ACCACTTCACGCAGGCCG 62.989 66.667 0.00 0.00 44.21 6.13
1056 1093 2.539338 GCAGGCCGTCGTTTTGTCA 61.539 57.895 0.00 0.00 0.00 3.58
1066 1103 4.027621 CCGTCGTTTTGTCAATCGATCTAG 60.028 45.833 13.63 0.00 36.69 2.43
1098 1135 0.942410 CGGTGAACGGTCAATCGTGT 60.942 55.000 3.77 0.00 43.07 4.49
1252 1289 7.074653 TGGGATATCCAAGGTACAACTATTC 57.925 40.000 23.27 0.68 43.84 1.75
1256 1293 9.057089 GGATATCCAAGGTACAACTATTCTTTG 57.943 37.037 17.34 0.00 35.64 2.77
1266 1303 7.387948 GGTACAACTATTCTTTGCTTCTTCTCA 59.612 37.037 0.00 0.00 0.00 3.27
1348 1385 6.961554 CGGTTCATGAAGCAAATAGTAGTTTC 59.038 38.462 30.87 5.85 38.62 2.78
1446 1483 3.836365 AATTTCTTGGGTGGGTTGTTG 57.164 42.857 0.00 0.00 0.00 3.33
1449 1486 1.040339 TCTTGGGTGGGTTGTTGTGC 61.040 55.000 0.00 0.00 0.00 4.57
1450 1487 1.305297 TTGGGTGGGTTGTTGTGCA 60.305 52.632 0.00 0.00 0.00 4.57
1453 1490 1.608717 GGGTGGGTTGTTGTGCACAA 61.609 55.000 27.96 27.96 43.55 3.33
1584 1623 2.105821 CCACAAGGACAAGAAGTACCCA 59.894 50.000 0.00 0.00 36.89 4.51
1710 1749 0.896940 TCGTCTTCTACAAGGGCCGT 60.897 55.000 0.00 0.00 0.00 5.68
1764 1803 2.402787 GAGTACCGCCTCGACGAC 59.597 66.667 0.00 0.00 34.06 4.34
1776 1815 1.080025 CGACGACCCTTCTTCCACC 60.080 63.158 0.00 0.00 0.00 4.61
1851 1890 3.686622 GGAGCTAATGCACCGATCA 57.313 52.632 0.00 0.00 39.93 2.92
2657 2696 1.655654 CTACTCCAGCGACGATGCG 60.656 63.158 7.77 3.32 40.67 4.73
2948 2987 4.176752 GGGATCACGGACTGGGCC 62.177 72.222 0.00 0.00 0.00 5.80
2963 3002 2.818169 GGCCATGATGGACCGGCTA 61.818 63.158 17.22 0.00 40.64 3.93
3225 3264 4.032900 CGTAACAACTGTAGCTGCTATTGG 59.967 45.833 19.83 12.87 0.00 3.16
3226 3265 3.703001 ACAACTGTAGCTGCTATTGGT 57.297 42.857 19.83 13.36 0.00 3.67
3241 3280 1.929745 TGGTATGGCCAATGGAGGG 59.070 57.895 10.96 0.00 45.94 4.30
3321 3360 8.938906 ACAGTAAAAAGACTACAACGAGAAAAA 58.061 29.630 0.00 0.00 0.00 1.94
3408 3447 5.874093 AGATTGATGTGTGGAGAGAAAACT 58.126 37.500 0.00 0.00 0.00 2.66
3466 3505 1.202313 GGAGTATCACTGTCACCGCTC 60.202 57.143 0.00 0.00 36.25 5.03
3608 3647 0.610509 TTGTGGTGTGTGCAAGGTGT 60.611 50.000 0.00 0.00 0.00 4.16
3610 3649 1.001517 TGGTGTGTGCAAGGTGTGT 60.002 52.632 0.00 0.00 0.00 3.72
3617 3656 3.696548 TGTGTGCAAGGTGTGTAATTCAA 59.303 39.130 0.00 0.00 0.00 2.69
3671 3710 7.178983 TCTCTTCAAATTGTTGCCTGGAAATAT 59.821 33.333 0.00 0.00 34.50 1.28
3672 3711 7.098477 TCTTCAAATTGTTGCCTGGAAATATG 58.902 34.615 0.00 0.00 34.50 1.78
3673 3712 6.602410 TCAAATTGTTGCCTGGAAATATGA 57.398 33.333 0.00 0.00 34.50 2.15
3698 3741 5.296283 CAGATGGCCAAACTTTCTCATAGAG 59.704 44.000 10.96 0.00 0.00 2.43
3706 3749 9.384764 GCCAAACTTTCTCATAGAGTAGTAATT 57.615 33.333 0.00 0.00 30.40 1.40
3720 3763 5.789535 AGTAGTAATTGGGGTGGAGACTAT 58.210 41.667 0.00 0.00 0.00 2.12
3735 3778 6.364706 GTGGAGACTATCGATTTAGCTTCATG 59.635 42.308 1.71 0.00 0.00 3.07
3759 3802 8.213518 TGCTTTTTGCCATACAATTTGTTTAA 57.786 26.923 7.45 0.00 42.00 1.52
3800 3843 9.461312 TGCAGTTGATTAGTTAGGTGATTAATT 57.539 29.630 0.00 0.00 0.00 1.40
3893 3938 2.375766 CGCTTGTCGTGACAGGAGC 61.376 63.158 15.34 14.59 42.94 4.70
3922 3969 8.702163 AGGCAAATGAATTTAATTAAAGTCGG 57.298 30.769 25.09 17.82 41.59 4.79
4083 4130 1.036707 CACCTCCTCTGCCTAGCTAC 58.963 60.000 0.00 0.00 0.00 3.58
4114 4161 1.941294 GAGTCGCTGATCTCCGTTCTA 59.059 52.381 0.00 0.00 0.00 2.10
4128 4175 5.413213 TCTCCGTTCTAGAGAGAGAAAACAG 59.587 44.000 13.22 0.00 37.20 3.16
4186 4233 5.069318 TGCTACATCATGGACACAGAAAAA 58.931 37.500 0.00 0.00 0.00 1.94
4189 4236 3.828451 ACATCATGGACACAGAAAAAGGG 59.172 43.478 0.00 0.00 0.00 3.95
4190 4237 2.238521 TCATGGACACAGAAAAAGGGC 58.761 47.619 0.00 0.00 0.00 5.19
4191 4238 1.273327 CATGGACACAGAAAAAGGGCC 59.727 52.381 0.00 0.00 0.00 5.80
4253 4300 6.011981 GGGAGAGAGATCTTTAGATAGGGAGA 60.012 46.154 0.00 0.00 34.37 3.71
4384 4431 2.287644 CGAGACATGCACAAGTCAACAA 59.712 45.455 15.53 0.00 37.23 2.83
4386 4433 4.671377 GAGACATGCACAAGTCAACAAAA 58.329 39.130 15.53 0.00 37.23 2.44
4397 4444 1.335496 GTCAACAAAAGGCGGCAACTA 59.665 47.619 13.08 0.00 0.00 2.24
4402 4449 1.130561 CAAAAGGCGGCAACTAGCTAC 59.869 52.381 13.08 0.00 44.79 3.58
4403 4450 0.613777 AAAGGCGGCAACTAGCTACT 59.386 50.000 13.08 0.00 44.79 2.57
4404 4451 1.481871 AAGGCGGCAACTAGCTACTA 58.518 50.000 13.08 0.00 44.79 1.82
4405 4452 1.033574 AGGCGGCAACTAGCTACTAG 58.966 55.000 13.08 0.08 44.79 2.57
4408 4458 2.287487 GGCGGCAACTAGCTACTAGTAC 60.287 54.545 3.07 3.96 45.28 2.73
4413 4463 4.828387 GGCAACTAGCTACTAGTACCTGAT 59.172 45.833 7.66 0.00 45.28 2.90
4424 4474 2.893637 AGTACCTGATTCATGCACGTC 58.106 47.619 0.00 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.179018 GCCCTAATGCCACCGAAGAT 60.179 55.000 0.00 0.00 0.00 2.40
15 16 1.761667 TGCCCATTGCCCTAATGCC 60.762 57.895 0.00 0.00 43.90 4.40
16 17 1.442987 GTGCCCATTGCCCTAATGC 59.557 57.895 0.00 0.00 43.90 3.56
18 19 1.455587 CCGTGCCCATTGCCCTAAT 60.456 57.895 0.00 0.00 40.16 1.73
25 26 1.586028 CCTTTCACCGTGCCCATTG 59.414 57.895 0.00 0.00 0.00 2.82
32 33 1.164041 AAACGAGCCCTTTCACCGTG 61.164 55.000 0.00 0.00 33.48 4.94
33 34 0.464916 AAAACGAGCCCTTTCACCGT 60.465 50.000 0.00 0.00 34.74 4.83
39 41 5.784578 AAAACATCTAAAACGAGCCCTTT 57.215 34.783 0.00 0.00 0.00 3.11
97 101 4.933064 CCGCCGATGTCTCGCCTC 62.933 72.222 0.00 0.00 43.66 4.70
153 157 0.386476 TAGACACACCGCAAGAACGT 59.614 50.000 0.00 0.00 43.02 3.99
232 238 4.219115 AGACTAATGATGACCAGATCCGT 58.781 43.478 0.00 0.00 0.00 4.69
250 256 2.159014 TGAAGGCACACAAACGTAGACT 60.159 45.455 0.00 0.00 0.00 3.24
266 272 2.362397 TCGAAAGGATCCGATCTGAAGG 59.638 50.000 5.98 0.00 0.00 3.46
313 320 2.816087 ACCAGCATAGCAGAACAACAAG 59.184 45.455 0.00 0.00 0.00 3.16
327 334 4.202305 GCTAAGACCTCATAGAACCAGCAT 60.202 45.833 0.00 0.00 0.00 3.79
394 402 3.976490 ATCGCCCCTCCCTCGTCAA 62.976 63.158 0.00 0.00 0.00 3.18
552 567 0.465460 TAGGCGGTTCATGAATGCCC 60.465 55.000 33.65 23.32 42.23 5.36
553 568 0.663153 GTAGGCGGTTCATGAATGCC 59.337 55.000 31.89 31.89 41.85 4.40
557 572 5.864418 ATTACTAGTAGGCGGTTCATGAA 57.136 39.130 3.38 3.38 0.00 2.57
586 601 6.327279 TCATGCATGAATCATGATTCCTTC 57.673 37.500 34.65 24.20 43.81 3.46
637 653 0.672342 GAGAAGAGCGGCCGGTATTA 59.328 55.000 34.21 0.00 0.00 0.98
643 659 0.816018 TAGAGAGAGAAGAGCGGCCG 60.816 60.000 24.05 24.05 0.00 6.13
803 820 0.689412 GGTGAGGAGGAAGAGGAGGG 60.689 65.000 0.00 0.00 0.00 4.30
842 863 5.127031 GGTTGCAAAGTAGAGAGAGAGAGAT 59.873 44.000 0.00 0.00 0.00 2.75
972 1009 0.916358 AGGCTGGTAAGTGGGCAGAT 60.916 55.000 0.00 0.00 0.00 2.90
981 1018 3.395639 TCGTGTGTTAAAGGCTGGTAAG 58.604 45.455 0.00 0.00 0.00 2.34
985 1022 2.218603 AGTTCGTGTGTTAAAGGCTGG 58.781 47.619 0.00 0.00 0.00 4.85
1008 1045 0.324091 TCTTCCAGGGACCGGTAGAC 60.324 60.000 7.34 0.00 0.00 2.59
1045 1082 4.326278 TGCTAGATCGATTGACAAAACGAC 59.674 41.667 18.17 13.50 42.39 4.34
1056 1093 5.149973 AGATGCTCATTGCTAGATCGATT 57.850 39.130 0.00 0.00 43.37 3.34
1066 1103 1.063174 GTTCACCGAGATGCTCATTGC 59.937 52.381 0.00 0.00 43.25 3.56
1252 1289 1.229428 TGGCGTGAGAAGAAGCAAAG 58.771 50.000 0.00 0.00 0.00 2.77
1256 1293 1.986575 GCCATGGCGTGAGAAGAAGC 61.987 60.000 23.48 0.00 0.00 3.86
1348 1385 1.135024 AGTTTGCCACTTTGCACTGTG 60.135 47.619 2.76 2.76 41.88 3.66
1436 1473 0.530288 ACTTGTGCACAACAACCCAC 59.470 50.000 27.96 0.00 43.96 4.61
1446 1483 0.796312 CATCACGGGTACTTGTGCAC 59.204 55.000 10.75 10.75 35.36 4.57
1449 1486 2.761559 TGTTCATCACGGGTACTTGTG 58.238 47.619 10.54 10.54 36.36 3.33
1450 1487 3.478857 TTGTTCATCACGGGTACTTGT 57.521 42.857 0.00 0.00 0.00 3.16
1453 1490 4.280436 TGATTTGTTCATCACGGGTACT 57.720 40.909 0.00 0.00 0.00 2.73
1584 1623 4.283403 TTCGTCCGCGTTCCCGTT 62.283 61.111 4.92 0.00 39.49 4.44
1695 1734 0.741221 GAGCACGGCCCTTGTAGAAG 60.741 60.000 0.00 0.00 0.00 2.85
1710 1749 2.940467 TTCTGGCCATGGGGAGCA 60.940 61.111 15.13 0.00 35.59 4.26
1764 1803 3.478780 TCCGTGGTGGAAGAAGGG 58.521 61.111 0.00 0.00 46.38 3.95
1814 1853 2.439507 TCCCCAATTGAGCTAGGTGATC 59.560 50.000 7.12 0.00 0.00 2.92
1849 1888 3.613671 CGGCAGCAAACAATTAATGGTGA 60.614 43.478 16.20 0.00 43.34 4.02
1851 1890 2.298729 ACGGCAGCAAACAATTAATGGT 59.701 40.909 0.00 0.00 0.00 3.55
2598 2637 2.370445 CCTTGCCCCCATCGTCTCT 61.370 63.158 0.00 0.00 0.00 3.10
2657 2696 0.035630 AGTGCAGGATCTGGTCAAGC 60.036 55.000 0.00 0.00 31.21 4.01
2774 2813 1.501741 CTTCATGAAACCGTGGCCG 59.498 57.895 9.88 0.00 0.00 6.13
2859 2898 0.811616 ACATTTCCATCTCCGCTCGC 60.812 55.000 0.00 0.00 0.00 5.03
2863 2902 1.212616 CTCGACATTTCCATCTCCGC 58.787 55.000 0.00 0.00 0.00 5.54
2864 2903 1.212616 GCTCGACATTTCCATCTCCG 58.787 55.000 0.00 0.00 0.00 4.63
2870 2909 1.805539 CTCGCGCTCGACATTTCCA 60.806 57.895 5.56 0.00 40.21 3.53
2927 2966 4.873129 CAGTCCGTGATCCCGCCG 62.873 72.222 0.00 0.00 0.00 6.46
2948 2987 0.319040 CGACTAGCCGGTCCATCATG 60.319 60.000 1.90 0.00 33.07 3.07
2963 3002 2.283529 ATTGAGGTGGGACGCGACT 61.284 57.895 15.93 0.00 41.51 4.18
3104 3143 3.403558 GCCCCTCCGAGAAGCCTT 61.404 66.667 0.00 0.00 0.00 4.35
3225 3264 4.181051 GCCCTCCATTGGCCATAC 57.819 61.111 6.09 0.00 43.33 2.39
3241 3280 2.047844 TGTCTTCAGCGGCTCAGC 60.048 61.111 0.00 0.00 37.41 4.26
3242 3281 2.091112 CGTGTCTTCAGCGGCTCAG 61.091 63.158 0.00 0.00 0.00 3.35
3243 3282 2.049156 CGTGTCTTCAGCGGCTCA 60.049 61.111 0.00 0.00 0.00 4.26
3244 3283 0.944311 TTTCGTGTCTTCAGCGGCTC 60.944 55.000 0.00 0.00 0.00 4.70
3245 3284 0.946221 CTTTCGTGTCTTCAGCGGCT 60.946 55.000 0.00 0.00 0.00 5.52
3246 3285 1.493311 CTTTCGTGTCTTCAGCGGC 59.507 57.895 0.00 0.00 0.00 6.53
3247 3286 0.600255 ACCTTTCGTGTCTTCAGCGG 60.600 55.000 0.00 0.00 0.00 5.52
3248 3287 0.508641 CACCTTTCGTGTCTTCAGCG 59.491 55.000 0.00 0.00 37.73 5.18
3321 3360 9.495572 CGCTCTCCTTTATTATTATTTTCTCCT 57.504 33.333 0.00 0.00 0.00 3.69
3408 3447 7.308951 CGCTTTAATCCCCTTTTCTTTCACTTA 60.309 37.037 0.00 0.00 0.00 2.24
3466 3505 1.860950 CAATAAGAGACGGGTGCGATG 59.139 52.381 0.00 0.00 0.00 3.84
3535 3574 8.703604 ATATCACCGGTCGATCTTAATTATTG 57.296 34.615 18.79 0.00 0.00 1.90
3572 3611 5.974751 CACCACAACAAACTGTGTAATTACC 59.025 40.000 13.01 5.32 44.35 2.85
3582 3621 1.067985 TGCACACACCACAACAAACTG 60.068 47.619 0.00 0.00 0.00 3.16
3637 3676 7.719633 AGGCAACAATTTGAAGAGAAGTTACTA 59.280 33.333 2.79 0.00 41.41 1.82
3671 3710 3.149196 GAGAAAGTTTGGCCATCTGTCA 58.851 45.455 22.55 0.36 0.00 3.58
3672 3711 3.149196 TGAGAAAGTTTGGCCATCTGTC 58.851 45.455 6.09 13.17 0.00 3.51
3673 3712 3.228188 TGAGAAAGTTTGGCCATCTGT 57.772 42.857 6.09 3.11 0.00 3.41
3698 3741 5.278858 CGATAGTCTCCACCCCAATTACTAC 60.279 48.000 0.00 0.00 0.00 2.73
3706 3749 2.471815 AATCGATAGTCTCCACCCCA 57.528 50.000 0.00 0.00 37.40 4.96
3735 3778 8.952979 GTTTAAACAAATTGTATGGCAAAAAGC 58.047 29.630 13.51 0.00 40.91 3.51
3928 3975 5.479724 TCCATCGATCTATGCATCTTCTTCT 59.520 40.000 0.19 0.00 0.00 2.85
3929 3976 5.718146 TCCATCGATCTATGCATCTTCTTC 58.282 41.667 0.19 0.00 0.00 2.87
3930 3977 5.735285 TCCATCGATCTATGCATCTTCTT 57.265 39.130 0.19 0.00 0.00 2.52
3931 3978 5.395435 CCATCCATCGATCTATGCATCTTCT 60.395 44.000 0.19 0.00 0.00 2.85
3932 3979 4.809958 CCATCCATCGATCTATGCATCTTC 59.190 45.833 0.19 0.00 0.00 2.87
3933 3980 4.468868 TCCATCCATCGATCTATGCATCTT 59.531 41.667 0.19 0.00 0.00 2.40
3937 3984 4.397481 GATCCATCCATCGATCTATGCA 57.603 45.455 9.92 0.00 33.53 3.96
4099 4146 3.472652 TCTCTCTAGAACGGAGATCAGC 58.527 50.000 6.17 0.00 38.85 4.26
4114 4161 3.482156 TGCTTGCTGTTTTCTCTCTCT 57.518 42.857 0.00 0.00 0.00 3.10
4128 4175 2.989166 GTCCAGCTTTTATGTTGCTTGC 59.011 45.455 0.00 0.00 34.51 4.01
4186 4233 0.261991 TCTAGATCGACCTTGGCCCT 59.738 55.000 0.00 0.00 0.00 5.19
4189 4236 2.552315 CTCTCTCTAGATCGACCTTGGC 59.448 54.545 0.00 0.00 0.00 4.52
4190 4237 4.079980 TCTCTCTCTAGATCGACCTTGG 57.920 50.000 0.00 0.00 0.00 3.61
4191 4238 5.820423 TCTTTCTCTCTCTAGATCGACCTTG 59.180 44.000 0.00 0.00 0.00 3.61
4223 4270 6.786843 ATCTAAAGATCTCTCTCCCTCTCT 57.213 41.667 0.00 0.00 0.00 3.10
4253 4300 1.829533 CCACTTGCCAGTTGCCACT 60.830 57.895 0.00 0.00 40.16 4.00
4312 4359 0.965439 ATATCGCACTGGCTCCTCTC 59.035 55.000 0.00 0.00 38.10 3.20
4313 4360 0.678395 CATATCGCACTGGCTCCTCT 59.322 55.000 0.00 0.00 38.10 3.69
4314 4361 0.676184 TCATATCGCACTGGCTCCTC 59.324 55.000 0.00 0.00 38.10 3.71
4315 4362 1.346062 ATCATATCGCACTGGCTCCT 58.654 50.000 0.00 0.00 38.10 3.69
4316 4363 2.611518 GTATCATATCGCACTGGCTCC 58.388 52.381 0.00 0.00 38.10 4.70
4317 4364 2.254459 CGTATCATATCGCACTGGCTC 58.746 52.381 0.00 0.00 38.10 4.70
4384 4431 0.613777 AGTAGCTAGTTGCCGCCTTT 59.386 50.000 0.00 0.00 44.23 3.11
4386 4433 1.033574 CTAGTAGCTAGTTGCCGCCT 58.966 55.000 6.36 0.00 44.23 5.52
4397 4444 4.895889 TGCATGAATCAGGTACTAGTAGCT 59.104 41.667 25.40 25.40 43.88 3.32
4402 4449 4.045104 GACGTGCATGAATCAGGTACTAG 58.955 47.826 14.17 2.62 36.02 2.57
4403 4450 3.488553 CGACGTGCATGAATCAGGTACTA 60.489 47.826 14.17 0.00 36.02 1.82
4404 4451 2.735444 CGACGTGCATGAATCAGGTACT 60.735 50.000 14.17 1.93 43.88 2.73
4405 4452 1.588404 CGACGTGCATGAATCAGGTAC 59.412 52.381 14.17 6.07 33.35 3.34
4408 4458 0.647410 GTCGACGTGCATGAATCAGG 59.353 55.000 14.17 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.