Multiple sequence alignment - TraesCS1D01G216600

Loading Multiple Alignment...

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 TraesCS1D01G216600 chr1D 100.000 6789 0 0 1 6789 302383896 302377108 0.000000e+00 12538.0
1 TraesCS1D01G216600 chr1B 97.849 4927 69 8 1454 6368 409250568 409245667 0.000000e+00 8477.0
2 TraesCS1D01G216600 chr1B 87.113 1389 107 33 3 1370 409251922 409250585 0.000000e+00 1507.0
3 TraesCS1D01G216600 chr1B 89.391 443 27 5 6367 6789 409245637 409245195 2.150000e-149 540.0
4 TraesCS1D01G216600 chr1A 96.732 4927 144 12 1454 6368 377019780 377014859 0.000000e+00 8191.0
5 TraesCS1D01G216600 chr1A 88.567 1417 102 26 3 1370 377021202 377019797 0.000000e+00 1664.0
6 TraesCS1D01G216600 chr1A 88.182 220 11 9 6367 6584 377014829 377014623 1.460000e-61 248.0
7 TraesCS1D01G216600 chr6B 92.815 1197 81 3 1454 2650 346733570 346732379 0.000000e+00 1729.0
8 TraesCS1D01G216600 chr6B 92.793 333 17 5 2646 2974 346711766 346711437 6.160000e-130 475.0
9 TraesCS1D01G216600 chr6B 92.381 315 21 3 3002 3315 346626891 346626579 4.830000e-121 446.0
10 TraesCS1D01G216600 chr6B 87.958 382 37 5 1031 1411 346733944 346733571 6.250000e-120 442.0
11 TraesCS1D01G216600 chr6B 94.681 188 10 0 3347 3534 346625971 346625784 6.660000e-75 292.0
12 TraesCS1D01G216600 chr6B 92.958 71 4 1 4368 4437 346625406 346625336 1.200000e-17 102.0
13 TraesCS1D01G216600 chr7A 89.182 379 41 0 1977 2355 529327642 529328020 2.220000e-129 473.0
14 TraesCS1D01G216600 chr7A 90.047 211 21 0 993 1203 529325852 529326062 2.410000e-69 274.0
15 TraesCS1D01G216600 chr7A 81.091 275 41 8 2476 2746 529328578 529328845 6.900000e-50 209.0
16 TraesCS1D01G216600 chr7D 89.702 369 34 4 1989 2355 469841752 469841386 1.030000e-127 468.0
17 TraesCS1D01G216600 chr7D 90.952 210 18 1 994 1203 469843633 469843425 1.440000e-71 281.0
18 TraesCS1D01G216600 chr7D 90.909 55 4 1 1403 1457 88485960 88486013 9.440000e-09 73.1
19 TraesCS1D01G216600 chr7B 89.373 367 39 0 1989 2355 493525205 493524839 4.800000e-126 462.0
20 TraesCS1D01G216600 chr7B 91.429 210 17 1 994 1203 493527076 493526868 3.100000e-73 287.0
21 TraesCS1D01G216600 chr7B 82.182 275 38 8 2476 2746 493524241 493523974 6.850000e-55 226.0
22 TraesCS1D01G216600 chr4A 95.745 47 2 0 1406 1452 514068719 514068765 7.300000e-10 76.8
23 TraesCS1D01G216600 chr4A 95.556 45 2 0 3026 3070 744387367 744387323 9.440000e-09 73.1
24 TraesCS1D01G216600 chr3D 90.741 54 5 0 4319 4372 556952211 556952158 9.440000e-09 73.1
25 TraesCS1D01G216600 chr3D 90.385 52 4 1 4323 4374 583611374 583611324 4.390000e-07 67.6
26 TraesCS1D01G216600 chr3B 90.741 54 5 0 4323 4376 157768303 157768250 9.440000e-09 73.1
27 TraesCS1D01G216600 chr5B 88.889 54 6 0 4317 4370 319332950 319333003 4.390000e-07 67.6
28 TraesCS1D01G216600 chr3A 89.091 55 5 1 4317 4370 605881365 605881419 4.390000e-07 67.6
29 TraesCS1D01G216600 chr2B 91.667 48 4 0 4323 4370 777628045 777627998 4.390000e-07 67.6
30 TraesCS1D01G216600 chr4D 91.489 47 4 0 4323 4369 465607302 465607256 1.580000e-06 65.8
31 TraesCS1D01G216600 chr6D 93.023 43 3 0 3025 3067 23637214 23637256 5.680000e-06 63.9
32 TraesCS1D01G216600 chr5A 91.111 45 4 0 6542 6586 332644122 332644078 2.040000e-05 62.1


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 TraesCS1D01G216600 chr1D 302377108 302383896 6788 True 12538.000000 12538 100.000000 1 6789 1 chr1D.!!$R1 6788
1 TraesCS1D01G216600 chr1B 409245195 409251922 6727 True 3508.000000 8477 91.451000 3 6789 3 chr1B.!!$R1 6786
2 TraesCS1D01G216600 chr1A 377014623 377021202 6579 True 3367.666667 8191 91.160333 3 6584 3 chr1A.!!$R1 6581
3 TraesCS1D01G216600 chr6B 346732379 346733944 1565 True 1085.500000 1729 90.386500 1031 2650 2 chr6B.!!$R3 1619
4 TraesCS1D01G216600 chr6B 346625336 346626891 1555 True 280.000000 446 93.340000 3002 4437 3 chr6B.!!$R2 1435
5 TraesCS1D01G216600 chr7A 529325852 529328845 2993 False 318.666667 473 86.773333 993 2746 3 chr7A.!!$F1 1753
6 TraesCS1D01G216600 chr7D 469841386 469843633 2247 True 374.500000 468 90.327000 994 2355 2 chr7D.!!$R1 1361
7 TraesCS1D01G216600 chr7B 493523974 493527076 3102 True 325.000000 462 87.661333 994 2746 3 chr7B.!!$R1 1752

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
112 124 0.823356 ATCACACCAAGCCACCACAC 60.823 55.000 0.00 0.00 0.00 3.82 F
330 355 1.035932 TTAGGGTTCCCGCTCGAGAG 61.036 60.000 18.75 13.89 35.22 3.20 F
338 363 1.067084 CCGCTCGAGAGTGATGCAT 59.933 57.895 18.75 0.00 41.24 3.96 F
1361 1517 0.179073 CCTTGCAGTATCTGTCCGGG 60.179 60.000 0.00 0.00 33.43 5.73 F
1972 2931 3.581332 TCTCCGTTTGTCTAATTGGACCT 59.419 43.478 18.14 0.00 35.54 3.85 F
4245 6573 2.158534 TGGTATGGTGTGAGGCAGTTTT 60.159 45.455 0.00 0.00 0.00 2.43 F
5662 8000 1.374125 CTGCAATGACGTCGGGACA 60.374 57.895 11.62 6.05 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1280 1328 0.179037 GGCCAGATCACATGCTAGCA 60.179 55.000 21.85 21.85 0.00 3.49 R
1343 1499 0.179073 CCCCGGACAGATACTGCAAG 60.179 60.000 0.73 0.00 42.29 4.01 R
1487 1643 0.322546 CCCGGACCTCCCTTCTTTTG 60.323 60.000 0.73 0.00 0.00 2.44 R
3109 4584 1.202879 TCACCCTCACAAACCCACATC 60.203 52.381 0.00 0.00 0.00 3.06 R
5259 7596 5.005740 TGCTGAGATTTTACTGCAGTCAAT 58.994 37.500 25.56 21.77 36.41 2.57 R
5677 8015 0.317854 GGGTTTCAAAGACGTGCTGC 60.318 55.000 0.00 0.00 0.00 5.25 R
6627 9041 0.460284 GGGTCATACGTGCACCTCAG 60.460 60.000 12.15 0.00 0.00 3.35 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
95 107 4.147322 CCGTTGCCGCACGTGATC 62.147 66.667 22.23 7.47 38.57 2.92
98 110 2.280457 TTGCCGCACGTGATCACA 60.280 55.556 24.93 8.35 0.00 3.58
100 112 3.788766 GCCGCACGTGATCACACC 61.789 66.667 24.93 11.26 43.34 4.16
106 118 0.884259 CACGTGATCACACCAAGCCA 60.884 55.000 24.93 0.00 43.34 4.75
112 124 0.823356 ATCACACCAAGCCACCACAC 60.823 55.000 0.00 0.00 0.00 3.82
154 166 1.200716 CAACATTCGCCAGAGCAACAT 59.799 47.619 0.00 0.00 39.83 2.71
158 170 1.159285 TTCGCCAGAGCAACATTCTG 58.841 50.000 0.00 0.00 41.34 3.02
200 212 3.041940 GGTCACCACGGCGAACAG 61.042 66.667 16.62 0.72 0.00 3.16
250 262 2.226437 ACGCTCGCATGAGAAACAAATT 59.774 40.909 0.00 0.00 45.57 1.82
264 276 7.090953 AGAAACAAATTCAGTAACCGTCAAA 57.909 32.000 0.00 0.00 40.72 2.69
268 293 2.600470 TTCAGTAACCGTCAAACCGT 57.400 45.000 0.00 0.00 0.00 4.83
271 296 1.523934 CAGTAACCGTCAAACCGTCAC 59.476 52.381 0.00 0.00 0.00 3.67
275 300 1.068417 CCGTCAAACCGTCACTGGA 59.932 57.895 0.00 0.00 0.00 3.86
284 309 2.317609 CGTCACTGGACTTTGCCCG 61.318 63.158 0.00 0.00 42.05 6.13
286 311 1.070786 TCACTGGACTTTGCCCGAC 59.929 57.895 0.00 0.00 0.00 4.79
290 315 3.110178 GGACTTTGCCCGACGACG 61.110 66.667 0.00 0.00 39.43 5.12
320 345 4.432859 GGCGACGATTAGGGTTCC 57.567 61.111 0.00 0.00 0.00 3.62
330 355 1.035932 TTAGGGTTCCCGCTCGAGAG 61.036 60.000 18.75 13.89 35.22 3.20
331 356 2.207501 TAGGGTTCCCGCTCGAGAGT 62.208 60.000 18.75 0.00 35.22 3.24
334 359 1.668101 GGTTCCCGCTCGAGAGTGAT 61.668 60.000 18.75 0.00 41.24 3.06
338 363 1.067084 CCGCTCGAGAGTGATGCAT 59.933 57.895 18.75 0.00 41.24 3.96
364 389 5.007626 GTCTTCTTTTGTTCCCCAATTTTGC 59.992 40.000 0.00 0.00 31.81 3.68
429 462 1.206371 GTGTAGACGCAATACCCAGGT 59.794 52.381 0.00 0.00 0.00 4.00
431 464 2.303600 TGTAGACGCAATACCCAGGTTT 59.696 45.455 0.00 0.00 0.00 3.27
440 479 1.278537 TACCCAGGTTTAGTTCCCCG 58.721 55.000 0.00 0.00 0.00 5.73
441 480 1.378119 CCCAGGTTTAGTTCCCCGC 60.378 63.158 0.00 0.00 0.00 6.13
449 488 3.068448 GGTTTAGTTCCCCGCAAAAAGAA 59.932 43.478 0.00 0.00 0.00 2.52
451 490 5.110598 GTTTAGTTCCCCGCAAAAAGAAAA 58.889 37.500 0.00 0.00 0.00 2.29
452 491 3.897141 AGTTCCCCGCAAAAAGAAAAA 57.103 38.095 0.00 0.00 0.00 1.94
453 492 3.792401 AGTTCCCCGCAAAAAGAAAAAG 58.208 40.909 0.00 0.00 0.00 2.27
454 493 3.449377 AGTTCCCCGCAAAAAGAAAAAGA 59.551 39.130 0.00 0.00 0.00 2.52
455 494 4.081365 AGTTCCCCGCAAAAAGAAAAAGAA 60.081 37.500 0.00 0.00 0.00 2.52
456 495 4.473477 TCCCCGCAAAAAGAAAAAGAAA 57.527 36.364 0.00 0.00 0.00 2.52
457 496 4.833390 TCCCCGCAAAAAGAAAAAGAAAA 58.167 34.783 0.00 0.00 0.00 2.29
458 497 5.246307 TCCCCGCAAAAAGAAAAAGAAAAA 58.754 33.333 0.00 0.00 0.00 1.94
480 519 3.216187 TGAAACCGGATCAGTTTGGAA 57.784 42.857 9.46 2.02 37.55 3.53
631 676 6.877855 GGTACAAGGGTAGTTTAGGAAGAAAG 59.122 42.308 0.00 0.00 0.00 2.62
894 942 4.890158 TGTCTAAGCCTCACAAAGATCA 57.110 40.909 0.00 0.00 0.00 2.92
943 991 4.400251 CTCCTCCTCCCCCGGTGT 62.400 72.222 0.00 0.00 0.00 4.16
1210 1258 1.204704 TCACCATCAGTAACTGCTCCG 59.795 52.381 0.00 0.00 0.00 4.63
1280 1328 7.172190 GCCTAACTTAAGGTTCTTTAGTCGTTT 59.828 37.037 7.53 0.00 39.02 3.60
1321 1477 2.448926 TGCATTCGTTTCTTCGAGGA 57.551 45.000 0.00 0.00 40.86 3.71
1331 1487 4.381718 CGTTTCTTCGAGGACTAGGGATTT 60.382 45.833 0.00 0.00 0.00 2.17
1343 1499 0.831711 AGGGATTTTGGGTGTGTGCC 60.832 55.000 0.00 0.00 0.00 5.01
1344 1500 0.831711 GGGATTTTGGGTGTGTGCCT 60.832 55.000 0.00 0.00 0.00 4.75
1361 1517 0.179073 CCTTGCAGTATCTGTCCGGG 60.179 60.000 0.00 0.00 33.43 5.73
1380 1536 3.602483 GGGGTTCTAGAATTTGCGTGTA 58.398 45.455 8.75 0.00 0.00 2.90
1383 1539 4.495844 GGGTTCTAGAATTTGCGTGTATGC 60.496 45.833 8.75 0.00 0.00 3.14
1384 1540 4.094294 GGTTCTAGAATTTGCGTGTATGCA 59.906 41.667 8.75 0.00 44.61 3.96
1404 1560 4.081642 TGCACTAGCCTAACTTAAGGTCTG 60.082 45.833 7.53 0.00 41.13 3.51
1408 1564 6.935208 CACTAGCCTAACTTAAGGTCTGTTTT 59.065 38.462 7.53 0.00 39.02 2.43
1462 1618 9.214957 CAAATAATAGCCATATCAGTTCCGTTA 57.785 33.333 0.00 0.00 0.00 3.18
1523 1682 4.577693 GTCCGGGTTTCTGAATAATTACCC 59.422 45.833 14.58 14.58 41.43 3.69
1532 1784 9.197306 GTTTCTGAATAATTACCCCCTTTATGT 57.803 33.333 0.00 0.00 0.00 2.29
1533 1785 9.777008 TTTCTGAATAATTACCCCCTTTATGTT 57.223 29.630 0.00 0.00 0.00 2.71
1972 2931 3.581332 TCTCCGTTTGTCTAATTGGACCT 59.419 43.478 18.14 0.00 35.54 3.85
2948 4423 8.650143 ATTTGTGGGAGTTTTTGTCTGTATAT 57.350 30.769 0.00 0.00 0.00 0.86
3109 4584 3.309954 GTCCGCTGACTTTAATTAGCCAG 59.690 47.826 0.37 0.00 38.53 4.85
3853 6181 9.793259 TTAGTCATTACAGGAGTTTTTGAAGAT 57.207 29.630 0.00 0.00 0.00 2.40
4245 6573 2.158534 TGGTATGGTGTGAGGCAGTTTT 60.159 45.455 0.00 0.00 0.00 2.43
4466 6795 7.039313 TGTCGAATCTAGTGTACTTGCATAT 57.961 36.000 0.00 0.00 0.00 1.78
5537 7874 4.977963 GCGTCAATGCAGCATATTTTATGT 59.022 37.500 8.75 0.00 34.15 2.29
5570 7908 3.484229 GCTGATTTGGATGTCTCGTTTCG 60.484 47.826 0.00 0.00 0.00 3.46
5662 8000 1.374125 CTGCAATGACGTCGGGACA 60.374 57.895 11.62 6.05 0.00 4.02
5677 8015 3.315470 TCGGGACAAACGATATGAGAGAG 59.685 47.826 0.00 0.00 35.12 3.20
6145 8483 1.133915 TCACTTGGTGGGGTTCACTTC 60.134 52.381 0.00 0.00 45.38 3.01
6254 8592 8.807948 ATACATTTAGAATTGTGCTAGTTGGT 57.192 30.769 0.00 0.00 0.00 3.67
6497 8894 7.766278 ACAACCTCTCATATGAGTTATTGTGTC 59.234 37.037 29.43 0.00 42.60 3.67
6627 9041 8.999431 TGTCTACATGTTAGACCTTTTGAATTC 58.001 33.333 22.07 0.00 42.32 2.17
6643 9057 3.056179 TGAATTCTGAGGTGCACGTATGA 60.056 43.478 12.81 10.57 0.00 2.15
6679 9093 1.221781 TGGTTGTTGGGGAGGGAAAAT 59.778 47.619 0.00 0.00 0.00 1.82
6681 9095 1.899814 GTTGTTGGGGAGGGAAAATCC 59.100 52.381 0.00 0.00 35.99 3.01
6695 9109 3.952323 GGAAAATCCAGGGTAGTAAAGCC 59.048 47.826 0.00 0.00 46.88 4.35
6733 9147 1.830477 GTGCTCATGAGGTCCTCTCTT 59.170 52.381 23.89 2.33 42.86 2.85
6751 9165 4.600547 TCTCTTGCAATGGGGAGATATCAT 59.399 41.667 11.04 0.00 31.02 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.159156 CGGTGGTTCCTCGTTATGATGA 60.159 50.000 0.00 0.00 0.00 2.92
11 12 4.410400 CCCAGGCGGTGGTTCCTC 62.410 72.222 3.23 0.00 46.37 3.71
40 41 0.535335 GGTCCTATGCTTCGTGGTGA 59.465 55.000 0.00 0.00 0.00 4.02
93 105 0.823356 GTGTGGTGGCTTGGTGTGAT 60.823 55.000 0.00 0.00 0.00 3.06
94 106 1.453015 GTGTGGTGGCTTGGTGTGA 60.453 57.895 0.00 0.00 0.00 3.58
95 107 2.489275 GGTGTGGTGGCTTGGTGTG 61.489 63.158 0.00 0.00 0.00 3.82
130 142 1.986575 GCTCTGGCGAATGTTGAGGC 61.987 60.000 0.00 0.00 0.00 4.70
154 166 2.583441 CGTGGGACTGGCCTCAGAA 61.583 63.158 3.32 0.00 43.49 3.02
158 170 4.459089 GCTCGTGGGACTGGCCTC 62.459 72.222 3.32 0.00 36.66 4.70
200 212 4.154347 CAGCCCTCTCGGTGGAGC 62.154 72.222 0.00 0.00 40.26 4.70
237 249 6.485313 TGACGGTTACTGAATTTGTTTCTCAT 59.515 34.615 0.00 0.00 35.23 2.90
250 262 1.408340 TGACGGTTTGACGGTTACTGA 59.592 47.619 0.00 0.00 38.39 3.41
264 276 1.227853 GGCAAAGTCCAGTGACGGT 60.228 57.895 0.00 0.00 46.51 4.83
268 293 1.070786 GTCGGGCAAAGTCCAGTGA 59.929 57.895 0.00 0.00 0.00 3.41
271 296 2.027625 GTCGTCGGGCAAAGTCCAG 61.028 63.158 0.00 0.00 0.00 3.86
275 300 2.660552 CACGTCGTCGGGCAAAGT 60.661 61.111 7.05 0.00 41.85 2.66
296 321 1.997227 CTAATCGTCGCCGTCGTCG 60.997 63.158 3.41 0.00 45.67 5.12
298 323 2.406401 CCTAATCGTCGCCGTCGT 59.594 61.111 3.41 0.00 36.96 4.34
299 324 2.353145 CCCTAATCGTCGCCGTCG 60.353 66.667 0.00 0.00 35.01 5.12
300 325 0.869028 GAACCCTAATCGTCGCCGTC 60.869 60.000 0.00 0.00 35.01 4.79
301 326 1.140375 GAACCCTAATCGTCGCCGT 59.860 57.895 0.00 0.00 35.01 5.68
319 344 2.279120 GCATCACTCTCGAGCGGG 60.279 66.667 7.81 1.91 0.00 6.13
320 345 1.067084 ATGCATCACTCTCGAGCGG 59.933 57.895 7.81 5.61 0.00 5.52
330 355 4.510038 ACAAAAGAAGACCATGCATCAC 57.490 40.909 0.00 0.00 0.00 3.06
331 356 4.022068 GGAACAAAAGAAGACCATGCATCA 60.022 41.667 0.00 0.00 0.00 3.07
334 359 2.627699 GGGAACAAAAGAAGACCATGCA 59.372 45.455 0.00 0.00 0.00 3.96
338 363 3.390175 TTGGGGAACAAAAGAAGACCA 57.610 42.857 0.00 0.00 35.79 4.02
364 389 4.690748 ACAATAGTGTGACTGAACAATCGG 59.309 41.667 0.00 0.00 36.31 4.18
399 424 2.063266 TGCGTCTACACGGACAAAATC 58.937 47.619 0.00 0.00 46.80 2.17
400 425 2.157834 TGCGTCTACACGGACAAAAT 57.842 45.000 0.00 0.00 46.80 1.82
429 462 5.340439 TTTTCTTTTTGCGGGGAACTAAA 57.660 34.783 0.00 0.00 0.00 1.85
431 464 4.645588 TCTTTTTCTTTTTGCGGGGAACTA 59.354 37.500 0.00 0.00 0.00 2.24
455 494 5.069781 TCCAAACTGATCCGGTTTCATTTTT 59.930 36.000 16.74 12.87 40.45 1.94
456 495 4.586841 TCCAAACTGATCCGGTTTCATTTT 59.413 37.500 14.86 14.86 40.45 1.82
457 496 4.148838 TCCAAACTGATCCGGTTTCATTT 58.851 39.130 0.00 4.21 40.45 2.32
458 497 3.761897 TCCAAACTGATCCGGTTTCATT 58.238 40.909 0.00 0.00 40.45 2.57
459 498 3.433306 TCCAAACTGATCCGGTTTCAT 57.567 42.857 0.00 0.00 40.45 2.57
460 499 2.940994 TCCAAACTGATCCGGTTTCA 57.059 45.000 0.00 5.47 40.45 2.69
461 500 4.577834 TTTTCCAAACTGATCCGGTTTC 57.422 40.909 0.00 0.09 40.45 2.78
462 501 6.658188 TTATTTTCCAAACTGATCCGGTTT 57.342 33.333 0.00 7.73 42.78 3.27
463 502 6.658188 TTTATTTTCCAAACTGATCCGGTT 57.342 33.333 0.00 0.00 34.04 4.44
464 503 6.435904 TGATTTATTTTCCAAACTGATCCGGT 59.564 34.615 0.00 0.00 0.00 5.28
465 504 6.862209 TGATTTATTTTCCAAACTGATCCGG 58.138 36.000 0.00 0.00 0.00 5.14
466 505 6.974622 CCTGATTTATTTTCCAAACTGATCCG 59.025 38.462 0.00 0.00 0.00 4.18
469 508 7.486407 AGCCTGATTTATTTTCCAAACTGAT 57.514 32.000 0.00 0.00 0.00 2.90
480 519 9.383519 CGACCATATATGTAGCCTGATTTATTT 57.616 33.333 11.73 0.00 0.00 1.40
574 616 5.163723 CCAAGCATGATAAGTGTTACACCTG 60.164 44.000 12.28 2.30 34.49 4.00
575 620 4.943705 CCAAGCATGATAAGTGTTACACCT 59.056 41.667 12.28 1.31 34.49 4.00
757 802 3.058983 ACGAATAAAACCCGAAACCGTTC 60.059 43.478 0.00 0.00 0.00 3.95
875 923 3.368427 CGGTGATCTTTGTGAGGCTTAGA 60.368 47.826 0.00 0.00 0.00 2.10
943 991 2.032620 GCTTCTAGAAGGGTCGGATCA 58.967 52.381 29.22 0.00 38.80 2.92
1210 1258 4.863925 GGAGCGAGAGAGTGCGGC 62.864 72.222 0.00 0.00 35.87 6.53
1240 1288 5.622346 AAGTTAGGCTAAGATCAGGAAGG 57.378 43.478 7.33 0.00 0.00 3.46
1280 1328 0.179037 GGCCAGATCACATGCTAGCA 60.179 55.000 21.85 21.85 0.00 3.49
1321 1477 2.817839 GCACACACCCAAAATCCCTAGT 60.818 50.000 0.00 0.00 0.00 2.57
1331 1487 2.043551 TGCAAGGCACACACCCAA 60.044 55.556 0.00 0.00 31.71 4.12
1343 1499 0.179073 CCCCGGACAGATACTGCAAG 60.179 60.000 0.73 0.00 42.29 4.01
1344 1500 0.907704 ACCCCGGACAGATACTGCAA 60.908 55.000 0.73 0.00 34.37 4.08
1361 1517 4.094294 TGCATACACGCAAATTCTAGAACC 59.906 41.667 7.48 0.00 39.45 3.62
1380 1536 4.717280 AGACCTTAAGTTAGGCTAGTGCAT 59.283 41.667 0.97 0.00 41.91 3.96
1383 1539 5.662674 ACAGACCTTAAGTTAGGCTAGTG 57.337 43.478 0.97 0.00 38.99 2.74
1384 1540 6.683312 AAACAGACCTTAAGTTAGGCTAGT 57.317 37.500 0.97 0.00 38.99 2.57
1433 1589 8.393366 CGGAACTGATATGGCTATTATTTGATG 58.607 37.037 0.00 0.00 0.00 3.07
1434 1590 8.103305 ACGGAACTGATATGGCTATTATTTGAT 58.897 33.333 0.00 0.00 0.00 2.57
1435 1591 7.450074 ACGGAACTGATATGGCTATTATTTGA 58.550 34.615 0.00 0.00 0.00 2.69
1436 1592 7.672983 ACGGAACTGATATGGCTATTATTTG 57.327 36.000 0.00 0.00 0.00 2.32
1437 1593 9.436957 CTAACGGAACTGATATGGCTATTATTT 57.563 33.333 0.00 0.00 0.00 1.40
1438 1594 8.812972 TCTAACGGAACTGATATGGCTATTATT 58.187 33.333 0.00 0.00 0.00 1.40
1441 1597 6.665992 TCTAACGGAACTGATATGGCTATT 57.334 37.500 0.00 0.00 0.00 1.73
1442 1598 6.665992 TTCTAACGGAACTGATATGGCTAT 57.334 37.500 0.00 0.00 0.00 2.97
1443 1599 6.474140 TTTCTAACGGAACTGATATGGCTA 57.526 37.500 0.00 0.00 33.13 3.93
1444 1600 5.353394 TTTCTAACGGAACTGATATGGCT 57.647 39.130 0.00 0.00 33.13 4.75
1445 1601 6.619801 AATTTCTAACGGAACTGATATGGC 57.380 37.500 0.00 0.00 33.13 4.40
1446 1602 8.888579 AGTAATTTCTAACGGAACTGATATGG 57.111 34.615 0.00 0.00 33.13 2.74
1449 1605 9.932207 TTGAAGTAATTTCTAACGGAACTGATA 57.068 29.630 0.00 0.00 36.71 2.15
1450 1606 8.842358 TTGAAGTAATTTCTAACGGAACTGAT 57.158 30.769 0.00 0.00 36.71 2.90
1487 1643 0.322546 CCCGGACCTCCCTTCTTTTG 60.323 60.000 0.73 0.00 0.00 2.44
1499 1658 4.577693 GGTAATTATTCAGAAACCCGGACC 59.422 45.833 0.73 0.00 0.00 4.46
1750 2002 5.435291 AGGTGATCAAAAGCTATCTTGGAG 58.565 41.667 0.00 0.00 31.78 3.86
1972 2931 7.414436 GTTAACACTGCAGTTTAAGAATGACA 58.586 34.615 18.94 0.00 33.07 3.58
3109 4584 1.202879 TCACCCTCACAAACCCACATC 60.203 52.381 0.00 0.00 0.00 3.06
5259 7596 5.005740 TGCTGAGATTTTACTGCAGTCAAT 58.994 37.500 25.56 21.77 36.41 2.57
5570 7908 3.129113 TCACATGCATGTTACTCCAATGC 59.871 43.478 29.48 0.01 39.39 3.56
5662 8000 3.452474 GTGCTGCTCTCTCATATCGTTT 58.548 45.455 0.00 0.00 0.00 3.60
5677 8015 0.317854 GGGTTTCAAAGACGTGCTGC 60.318 55.000 0.00 0.00 0.00 5.25
6121 8459 0.537371 GAACCCCACCAAGTGACCAG 60.537 60.000 0.00 0.00 35.23 4.00
6145 8483 4.880537 CACCTGAGCGGCTAGGCG 62.881 72.222 32.23 32.23 37.61 5.52
6179 8517 2.175202 TCATGGCCTTTTAAATGGCGT 58.825 42.857 28.87 20.79 46.88 5.68
6181 8519 5.003160 ACTTTTCATGGCCTTTTAAATGGC 58.997 37.500 28.51 28.51 45.63 4.40
6232 8570 7.383102 AGACCAACTAGCACAATTCTAAATG 57.617 36.000 0.00 0.00 0.00 2.32
6233 8571 9.686683 ATTAGACCAACTAGCACAATTCTAAAT 57.313 29.630 0.00 0.00 30.35 1.40
6234 8572 8.946085 CATTAGACCAACTAGCACAATTCTAAA 58.054 33.333 0.00 0.00 30.35 1.85
6235 8573 8.318412 TCATTAGACCAACTAGCACAATTCTAA 58.682 33.333 0.00 0.00 32.30 2.10
6236 8574 7.847096 TCATTAGACCAACTAGCACAATTCTA 58.153 34.615 0.00 0.00 32.30 2.10
6237 8575 6.711277 TCATTAGACCAACTAGCACAATTCT 58.289 36.000 0.00 0.00 32.30 2.40
6238 8576 6.985188 TCATTAGACCAACTAGCACAATTC 57.015 37.500 0.00 0.00 32.30 2.17
6239 8577 6.942576 AGTTCATTAGACCAACTAGCACAATT 59.057 34.615 0.00 0.00 32.30 2.32
6240 8578 6.372659 CAGTTCATTAGACCAACTAGCACAAT 59.627 38.462 0.00 0.00 32.30 2.71
6241 8579 5.700832 CAGTTCATTAGACCAACTAGCACAA 59.299 40.000 0.00 0.00 32.30 3.33
6242 8580 5.011635 TCAGTTCATTAGACCAACTAGCACA 59.988 40.000 0.00 0.00 32.30 4.57
6243 8581 5.479306 TCAGTTCATTAGACCAACTAGCAC 58.521 41.667 0.00 0.00 32.30 4.40
6244 8582 5.738619 TCAGTTCATTAGACCAACTAGCA 57.261 39.130 0.00 0.00 32.30 3.49
6245 8583 6.595716 ACATTCAGTTCATTAGACCAACTAGC 59.404 38.462 0.00 0.00 32.30 3.42
6246 8584 8.553459 AACATTCAGTTCATTAGACCAACTAG 57.447 34.615 0.00 0.00 34.74 2.57
6247 8585 8.918202 AAACATTCAGTTCATTAGACCAACTA 57.082 30.769 0.00 0.00 40.26 2.24
6248 8586 7.823745 AAACATTCAGTTCATTAGACCAACT 57.176 32.000 0.00 0.00 40.26 3.16
6249 8587 9.559958 CATAAACATTCAGTTCATTAGACCAAC 57.440 33.333 0.00 0.00 40.26 3.77
6250 8588 9.295825 ACATAAACATTCAGTTCATTAGACCAA 57.704 29.630 0.00 0.00 40.26 3.67
6251 8589 8.862325 ACATAAACATTCAGTTCATTAGACCA 57.138 30.769 0.00 0.00 40.26 4.02
6410 8804 7.958053 AAGTAATGAAAGGCCGTATACATAC 57.042 36.000 3.32 0.00 0.00 2.39
6420 8814 9.699703 TTATTGTGTTTAAAGTAATGAAAGGCC 57.300 29.630 0.00 0.00 0.00 5.19
6497 8894 6.137794 ACTCACCTCGAGAATTGTGTATAG 57.862 41.667 15.71 9.17 45.45 1.31
6502 8912 4.998788 TCATACTCACCTCGAGAATTGTG 58.001 43.478 15.71 13.39 45.45 3.33
6603 9017 9.219603 CAGAATTCAAAAGGTCTAACATGTAGA 57.780 33.333 8.44 0.00 0.00 2.59
6617 9031 3.003689 ACGTGCACCTCAGAATTCAAAAG 59.996 43.478 12.15 1.73 0.00 2.27
6627 9041 0.460284 GGGTCATACGTGCACCTCAG 60.460 60.000 12.15 0.00 0.00 3.35
6643 9057 3.116900 ACAACCAAATAAGTCCCAAGGGT 60.117 43.478 4.80 0.00 36.47 4.34
6695 9109 5.033589 AGCACATGAAAATCTCTCCTAGG 57.966 43.478 0.82 0.82 0.00 3.02
6733 9147 3.140707 ACCAATGATATCTCCCCATTGCA 59.859 43.478 3.98 0.00 43.30 4.08


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

AutoCloner maintained by Alex Coulton.