Multiple sequence alignment - TraesCS2A01G039800

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 TraesCS2A01G039800 chr2A 100.000 2792 0 0 1 2792 16497786 16494995 0.000000e+00 5156.0
1 TraesCS2A01G039800 chr2D 89.599 2192 131 36 385 2501 14128144 14125975 0.000000e+00 2695.0
2 TraesCS2A01G039800 chr2D 90.659 364 17 4 1 348 14128880 14128518 4.210000e-128 468.0
3 TraesCS2A01G039800 chr2D 91.892 296 16 2 2505 2792 14125884 14125589 9.310000e-110 407.0
4 TraesCS2A01G039800 chr2B 87.695 2056 180 22 492 2501 25844290 25842262 0.000000e+00 2327.0
5 TraesCS2A01G039800 chr2B 90.876 833 64 3 976 1805 25787936 25787113 0.000000e+00 1107.0
6 TraesCS2A01G039800 chr2B 88.985 581 44 7 1925 2500 25779406 25778841 0.000000e+00 701.0
7 TraesCS2A01G039800 chr2B 87.680 487 30 6 521 978 25794359 25793874 8.800000e-150 540.0
8 TraesCS2A01G039800 chr2B 93.772 289 17 1 2505 2792 25842169 25841881 1.540000e-117 433.0
9 TraesCS2A01G039800 chr2B 91.216 296 17 3 2505 2792 25778749 25778455 7.250000e-106 394.0
10 TraesCS2A01G039800 chr4B 81.399 1301 186 20 542 1805 665975901 665974620 0.000000e+00 1011.0
11 TraesCS2A01G039800 chr4B 80.000 255 46 4 1555 1805 665972931 665972678 1.710000e-42 183.0
12 TraesCS2A01G039800 chr4B 93.443 61 4 0 2371 2431 665974348 665974288 1.060000e-14 91.6
13 TraesCS2A01G039800 chr4B 89.394 66 6 1 2372 2436 665921771 665921836 6.410000e-12 82.4
14 TraesCS2A01G039800 chrUn 80.941 1296 194 22 540 1805 108250657 108251929 0.000000e+00 976.0
15 TraesCS2A01G039800 chrUn 78.638 1292 194 37 567 1805 108254985 108256247 0.000000e+00 782.0
16 TraesCS2A01G039800 chrUn 81.362 558 76 16 1904 2441 108256474 108257023 1.990000e-116 429.0
17 TraesCS2A01G039800 chrUn 81.646 158 14 10 2340 2486 108252494 108252647 1.760000e-22 117.0
18 TraesCS2A01G039800 chr7D 80.453 1325 206 23 515 1805 45858097 45856792 0.000000e+00 963.0
19 TraesCS2A01G039800 chr7D 79.919 1235 195 33 604 1805 45838790 45837576 0.000000e+00 857.0
20 TraesCS2A01G039800 chr7D 85.542 249 28 5 521 765 503942017 503941773 1.280000e-63 254.0
21 TraesCS2A01G039800 chr6A 75.800 1281 228 38 521 1755 617803743 617804987 8.670000e-160 573.0
22 TraesCS2A01G039800 chr6A 75.758 1221 204 44 598 1776 610477923 610476753 5.300000e-147 531.0
23 TraesCS2A01G039800 chr6D 75.499 1302 223 46 521 1785 471820028 471818786 1.460000e-152 549.0
24 TraesCS2A01G039800 chr1D 75.139 1255 242 36 598 1805 461143012 461144243 2.460000e-145 525.0
25 TraesCS2A01G039800 chr6B 74.904 1307 218 60 521 1776 707307739 707306492 1.930000e-136 496.0
26 TraesCS2A01G039800 chr1A 74.701 1253 245 34 597 1805 552216704 552217928 2.500000e-135 492.0
27 TraesCS2A01G039800 chr5A 78.205 234 22 16 2512 2728 296678419 296678640 3.780000e-24 122.0
28 TraesCS2A01G039800 chr5A 77.824 239 24 16 2507 2728 12880711 12880937 1.360000e-23 121.0
29 TraesCS2A01G039800 chr5A 85.246 122 10 6 2507 2628 591608541 591608654 4.890000e-23 119.0
30 TraesCS2A01G039800 chr5A 86.869 99 8 4 2340 2437 705953112 705953018 3.800000e-19 106.0
31 TraesCS2A01G039800 chr5A 76.496 234 24 16 2512 2728 52524658 52524877 6.360000e-17 99.0
32 TraesCS2A01G039800 chr3A 77.824 239 24 16 2507 2728 458178565 458178339 1.360000e-23 121.0
33 TraesCS2A01G039800 chr7A 82.075 106 7 6 2507 2612 704645942 704645849 2.310000e-11 80.5
34 TraesCS2A01G039800 chr5D 75.269 186 34 9 1638 1816 441233832 441234012 8.290000e-11 78.7


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 TraesCS2A01G039800 chr2A 16494995 16497786 2791 True 5156.000000 5156 100.000000 1 2792 1 chr2A.!!$R1 2791
1 TraesCS2A01G039800 chr2D 14125589 14128880 3291 True 1190.000000 2695 90.716667 1 2792 3 chr2D.!!$R1 2791
2 TraesCS2A01G039800 chr2B 25841881 25844290 2409 True 1380.000000 2327 90.733500 492 2792 2 chr2B.!!$R4 2300
3 TraesCS2A01G039800 chr2B 25787113 25787936 823 True 1107.000000 1107 90.876000 976 1805 1 chr2B.!!$R1 829
4 TraesCS2A01G039800 chr2B 25778455 25779406 951 True 547.500000 701 90.100500 1925 2792 2 chr2B.!!$R3 867
5 TraesCS2A01G039800 chr4B 665972678 665975901 3223 True 428.533333 1011 84.947333 542 2431 3 chr4B.!!$R1 1889
6 TraesCS2A01G039800 chrUn 108250657 108257023 6366 False 576.000000 976 80.646750 540 2486 4 chrUn.!!$F1 1946
7 TraesCS2A01G039800 chr7D 45856792 45858097 1305 True 963.000000 963 80.453000 515 1805 1 chr7D.!!$R2 1290
8 TraesCS2A01G039800 chr7D 45837576 45838790 1214 True 857.000000 857 79.919000 604 1805 1 chr7D.!!$R1 1201
9 TraesCS2A01G039800 chr6A 617803743 617804987 1244 False 573.000000 573 75.800000 521 1755 1 chr6A.!!$F1 1234
10 TraesCS2A01G039800 chr6A 610476753 610477923 1170 True 531.000000 531 75.758000 598 1776 1 chr6A.!!$R1 1178
11 TraesCS2A01G039800 chr6D 471818786 471820028 1242 True 549.000000 549 75.499000 521 1785 1 chr6D.!!$R1 1264
12 TraesCS2A01G039800 chr1D 461143012 461144243 1231 False 525.000000 525 75.139000 598 1805 1 chr1D.!!$F1 1207
13 TraesCS2A01G039800 chr6B 707306492 707307739 1247 True 496.000000 496 74.904000 521 1776 1 chr6B.!!$R1 1255
14 TraesCS2A01G039800 chr1A 552216704 552217928 1224 False 492.000000 492 74.701000 597 1805 1 chr1A.!!$F1 1208

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
519 873 0.108898 CTCTCCGCTGACTTCCACTG 60.109 60.0 0.00 0.0 0.00 3.66 F
809 1203 0.313043 TTCCTCGAGGTCGACAACAC 59.687 55.0 30.17 0.0 44.22 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1747 2200 0.393402 GCAGTGCCCTCATCATCACA 60.393 55.0 2.85 0.0 32.25 3.58 R
2703 7762 0.034670 AATCTCCCCTGCTGCTGTTC 60.035 55.0 0.00 0.0 0.00 3.18 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
110 112 2.841442 ACACAGAGGTTGCTAAGGTC 57.159 50.000 0.00 0.00 0.00 3.85
136 138 5.980715 ACATTTAAAACGTGCTAACAAAGGG 59.019 36.000 0.00 0.00 0.00 3.95
205 221 9.906660 GACATTGTAAATGGAGTTTGAATAACA 57.093 29.630 5.08 0.00 0.00 2.41
206 222 9.691362 ACATTGTAAATGGAGTTTGAATAACAC 57.309 29.630 5.08 0.00 0.00 3.32
214 230 3.469739 AGTTTGAATAACACGTCGGGTT 58.530 40.909 18.27 18.27 0.00 4.11
306 322 7.883311 ACAGATTATTATATGTTTTCCCCTCCG 59.117 37.037 0.00 0.00 32.46 4.63
308 324 9.108111 AGATTATTATATGTTTTCCCCTCCGTA 57.892 33.333 0.00 0.00 0.00 4.02
348 365 5.237779 CACATAGTTTTACCGTCAACCAGTT 59.762 40.000 0.00 0.00 0.00 3.16
349 366 5.824097 ACATAGTTTTACCGTCAACCAGTTT 59.176 36.000 0.00 0.00 0.00 2.66
350 367 6.991531 ACATAGTTTTACCGTCAACCAGTTTA 59.008 34.615 0.00 0.00 0.00 2.01
353 370 5.824097 AGTTTTACCGTCAACCAGTTTACAT 59.176 36.000 0.00 0.00 0.00 2.29
354 371 5.676532 TTTACCGTCAACCAGTTTACATG 57.323 39.130 0.00 0.00 0.00 3.21
355 372 2.500229 ACCGTCAACCAGTTTACATGG 58.500 47.619 0.00 0.00 43.87 3.66
357 374 2.482721 CCGTCAACCAGTTTACATGGAC 59.517 50.000 0.00 0.00 40.51 4.02
358 375 3.399330 CGTCAACCAGTTTACATGGACT 58.601 45.455 0.00 0.00 40.51 3.85
360 377 4.387862 CGTCAACCAGTTTACATGGACTAC 59.612 45.833 0.00 0.00 40.51 2.73
361 378 5.548406 GTCAACCAGTTTACATGGACTACT 58.452 41.667 0.00 0.00 40.51 2.57
362 379 5.995897 GTCAACCAGTTTACATGGACTACTT 59.004 40.000 0.00 0.00 40.51 2.24
363 380 5.995282 TCAACCAGTTTACATGGACTACTTG 59.005 40.000 0.00 3.83 40.51 3.16
364 381 4.906618 ACCAGTTTACATGGACTACTTGG 58.093 43.478 0.00 2.65 40.51 3.61
366 383 4.935808 CCAGTTTACATGGACTACTTGGAC 59.064 45.833 0.00 0.00 40.51 4.02
367 384 5.280011 CCAGTTTACATGGACTACTTGGACT 60.280 44.000 0.00 0.00 40.51 3.85
369 386 6.812160 CAGTTTACATGGACTACTTGGACTAC 59.188 42.308 0.00 0.00 0.00 2.73
370 387 5.927281 TTACATGGACTACTTGGACTACC 57.073 43.478 0.00 0.00 0.00 3.18
371 388 2.758979 ACATGGACTACTTGGACTACCG 59.241 50.000 0.00 0.00 39.42 4.02
372 389 1.843368 TGGACTACTTGGACTACCGG 58.157 55.000 0.00 0.00 39.42 5.28
373 390 1.076024 TGGACTACTTGGACTACCGGT 59.924 52.381 13.98 13.98 39.42 5.28
374 391 2.174360 GGACTACTTGGACTACCGGTT 58.826 52.381 15.04 0.00 39.42 4.44
375 392 2.564504 GGACTACTTGGACTACCGGTTT 59.435 50.000 15.04 0.00 39.42 3.27
377 394 4.220602 GGACTACTTGGACTACCGGTTTTA 59.779 45.833 15.04 0.00 39.42 1.52
378 395 5.397142 ACTACTTGGACTACCGGTTTTAG 57.603 43.478 15.04 6.92 39.42 1.85
379 396 3.690475 ACTTGGACTACCGGTTTTAGG 57.310 47.619 15.04 0.71 39.42 2.69
380 397 3.242011 ACTTGGACTACCGGTTTTAGGA 58.758 45.455 15.04 0.00 39.42 2.94
383 400 5.128335 ACTTGGACTACCGGTTTTAGGATAG 59.872 44.000 15.04 3.26 39.42 2.08
429 783 2.300723 ACTACTTGGACCATTGCGTACA 59.699 45.455 0.00 0.00 0.00 2.90
465 819 4.780815 TGAAGTCTATAATGGGCTTGGTG 58.219 43.478 0.00 0.00 0.00 4.17
479 833 3.194861 GCTTGGTGCATTCGTACTATGA 58.805 45.455 8.52 0.00 42.31 2.15
480 834 3.621268 GCTTGGTGCATTCGTACTATGAA 59.379 43.478 8.52 0.00 42.31 2.57
481 835 4.494199 GCTTGGTGCATTCGTACTATGAAC 60.494 45.833 8.52 7.84 42.31 3.18
494 848 5.284660 CGTACTATGAACAACAACTACGGAC 59.715 44.000 0.00 0.00 31.58 4.79
519 873 0.108898 CTCTCCGCTGACTTCCACTG 60.109 60.000 0.00 0.00 0.00 3.66
809 1203 0.313043 TTCCTCGAGGTCGACAACAC 59.687 55.000 30.17 0.00 44.22 3.32
962 1369 1.589196 GCGACGGCTACATCCTCAC 60.589 63.158 0.00 0.00 35.83 3.51
1066 1480 2.046217 GGAGCCTCACCGGTTTCC 60.046 66.667 2.97 3.56 33.49 3.13
1246 1666 1.675552 CCTAAATTACGGTGCTGGGG 58.324 55.000 0.00 0.00 0.00 4.96
1338 1761 2.151502 TGGATGTCTCCTCTCTGGAC 57.848 55.000 0.00 0.00 42.59 4.02
1341 1764 2.031120 GATGTCTCCTCTCTGGACCTG 58.969 57.143 0.00 0.00 40.56 4.00
1493 1919 1.476488 CGGTGATGGAATTGGGGTTTC 59.524 52.381 0.00 0.00 0.00 2.78
1597 2047 1.067212 CTAGGTCTGGATGCGTGTACC 59.933 57.143 0.00 0.00 0.00 3.34
1625 2078 2.710471 TGATATGCATAACCCCTGCTGA 59.290 45.455 11.13 0.00 40.34 4.26
1747 2200 1.247567 CTGGCCTCCGTGTTTGATTT 58.752 50.000 3.32 0.00 0.00 2.17
1766 6561 0.393402 TGTGATGATGAGGGCACTGC 60.393 55.000 0.00 0.00 32.69 4.40
1869 6707 9.903682 CAAAGAAATATCTATAGTTGGCATTGG 57.096 33.333 0.00 0.00 33.77 3.16
1897 6735 4.586421 TGGAAGATAGTGCCTCTGTATCTG 59.414 45.833 0.00 0.00 0.00 2.90
1902 6826 3.883830 AGTGCCTCTGTATCTGAAGTG 57.116 47.619 0.00 0.00 0.00 3.16
1923 6851 6.893583 AGTGATGGTTATGCTCATAGAAACT 58.106 36.000 0.00 0.00 0.00 2.66
1974 6902 9.064706 ACAAATCTGGAGCTAATGAATCTTATG 57.935 33.333 0.00 0.00 0.00 1.90
1976 6904 5.555017 TCTGGAGCTAATGAATCTTATGGC 58.445 41.667 0.00 0.00 0.00 4.40
2014 6947 6.258230 TCTGTTGCAACTTTCTATGGAATG 57.742 37.500 28.61 3.52 34.19 2.67
2026 6959 8.052748 ACTTTCTATGGAATGCTGTTATGGTAA 58.947 33.333 4.82 0.00 32.09 2.85
2032 6965 5.184864 TGGAATGCTGTTATGGTAACTTTGG 59.815 40.000 2.04 0.00 37.61 3.28
2036 6969 3.254657 GCTGTTATGGTAACTTTGGTGCA 59.745 43.478 2.04 0.00 37.61 4.57
2064 6997 6.891908 AGTCCCATTGCTTAATTTGTGTCTAT 59.108 34.615 0.00 0.00 0.00 1.98
2065 6998 8.052748 AGTCCCATTGCTTAATTTGTGTCTATA 58.947 33.333 0.00 0.00 0.00 1.31
2101 7038 8.397906 TGTGTTTGTCATTTACAGAGAGAAAAG 58.602 33.333 0.00 0.00 39.87 2.27
2183 7120 4.025396 GGACATGCATCTGTGATTCTAACG 60.025 45.833 0.00 0.00 0.00 3.18
2215 7157 7.013846 CCCTTCATACACTTGTTCTTTTTACCA 59.986 37.037 0.00 0.00 0.00 3.25
2238 7180 6.094603 CCACACAATCTCTTCATCTTTTAGGG 59.905 42.308 0.00 0.00 0.00 3.53
2245 7187 6.068010 TCTCTTCATCTTTTAGGGTGCAAAA 58.932 36.000 0.00 0.00 0.00 2.44
2282 7227 2.529151 CTTTGTTGTTCTTTGCTGCGT 58.471 42.857 0.00 0.00 0.00 5.24
2283 7228 2.187351 TTGTTGTTCTTTGCTGCGTC 57.813 45.000 0.00 0.00 0.00 5.19
2285 7230 0.380378 GTTGTTCTTTGCTGCGTCCA 59.620 50.000 0.00 0.00 0.00 4.02
2286 7231 0.380378 TTGTTCTTTGCTGCGTCCAC 59.620 50.000 0.00 0.00 0.00 4.02
2287 7232 0.746204 TGTTCTTTGCTGCGTCCACA 60.746 50.000 0.00 0.00 0.00 4.17
2288 7233 0.040958 GTTCTTTGCTGCGTCCACAG 60.041 55.000 0.00 0.00 40.80 3.66
2289 7234 1.165907 TTCTTTGCTGCGTCCACAGG 61.166 55.000 0.00 0.00 38.16 4.00
2371 7317 6.257193 CCGACCTAACTTTAATGGTGATGTAC 59.743 42.308 0.00 0.00 32.30 2.90
2436 7394 1.915141 CAGTTGGTCCCTTGCTTGAT 58.085 50.000 0.00 0.00 0.00 2.57
2442 7400 0.804989 GTCCCTTGCTTGATTGGACG 59.195 55.000 0.00 0.00 36.47 4.79
2443 7401 0.960364 TCCCTTGCTTGATTGGACGC 60.960 55.000 0.00 0.00 0.00 5.19
2444 7402 1.135315 CCTTGCTTGATTGGACGCG 59.865 57.895 3.53 3.53 0.00 6.01
2445 7403 1.298157 CCTTGCTTGATTGGACGCGA 61.298 55.000 15.93 0.00 0.00 5.87
2446 7404 0.095935 CTTGCTTGATTGGACGCGAG 59.904 55.000 15.93 0.00 0.00 5.03
2497 7460 3.449227 CTGGTGTAGCTCGGCGGA 61.449 66.667 7.21 0.00 0.00 5.54
2501 7464 1.660560 GGTGTAGCTCGGCGGAACTA 61.661 60.000 7.21 3.58 0.00 2.24
2502 7465 0.525029 GTGTAGCTCGGCGGAACTAC 60.525 60.000 21.57 21.57 40.61 2.73
2533 7585 5.465390 TGTCAACTATGTTCCAGTTTCTTCG 59.535 40.000 0.00 0.00 33.99 3.79
2634 7693 3.431207 GCATCCTAAAGCATTGCACCAAT 60.431 43.478 11.91 0.00 34.04 3.16
2658 7717 7.716799 TGGGTAGAATTTGCACAAGATTAAT 57.283 32.000 0.00 0.00 0.00 1.40
2703 7762 2.159338 ACACTGCTTTTGTGACAGCAAG 60.159 45.455 0.00 1.53 45.36 4.01
2705 7764 2.754552 ACTGCTTTTGTGACAGCAAGAA 59.245 40.909 9.93 0.13 45.36 2.52
2746 7806 2.353269 CGTGTAAACTGCAAGGTTGTCA 59.647 45.455 0.00 0.00 46.40 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 86 6.183361 ACCTTAGCAACCTCTGTGTACTAAAA 60.183 38.462 0.00 0.00 0.00 1.52
95 97 1.629043 TGTCGACCTTAGCAACCTCT 58.371 50.000 14.12 0.00 0.00 3.69
110 112 6.129561 CCTTTGTTAGCACGTTTTAAATGTCG 60.130 38.462 0.00 0.00 0.00 4.35
136 138 0.894835 AAATCATGGTTTCCGGCCAC 59.105 50.000 2.24 0.00 39.03 5.01
205 221 8.897872 ATAAAATTCTTATATGAACCCGACGT 57.102 30.769 3.35 0.00 0.00 4.34
280 296 7.883311 CGGAGGGGAAAACATATAATAATCTGT 59.117 37.037 0.00 0.00 0.00 3.41
295 311 1.557832 CACCATCTACGGAGGGGAAAA 59.442 52.381 12.56 0.00 46.58 2.29
299 315 1.200519 TTTCACCATCTACGGAGGGG 58.799 55.000 0.00 0.00 46.58 4.79
303 319 3.389656 TGGCATATTTCACCATCTACGGA 59.610 43.478 0.00 0.00 0.00 4.69
304 320 3.498397 GTGGCATATTTCACCATCTACGG 59.502 47.826 0.00 0.00 35.53 4.02
306 322 6.936900 ACTATGTGGCATATTTCACCATCTAC 59.063 38.462 0.94 0.00 35.53 2.59
308 324 5.945310 ACTATGTGGCATATTTCACCATCT 58.055 37.500 0.94 0.00 35.53 2.90
348 365 4.400251 CGGTAGTCCAAGTAGTCCATGTAA 59.600 45.833 0.00 0.00 0.00 2.41
349 366 3.949754 CGGTAGTCCAAGTAGTCCATGTA 59.050 47.826 0.00 0.00 0.00 2.29
350 367 2.758979 CGGTAGTCCAAGTAGTCCATGT 59.241 50.000 0.00 0.00 0.00 3.21
353 370 1.076024 ACCGGTAGTCCAAGTAGTCCA 59.924 52.381 4.49 0.00 0.00 4.02
354 371 1.844687 ACCGGTAGTCCAAGTAGTCC 58.155 55.000 4.49 0.00 0.00 3.85
355 372 3.949842 AAACCGGTAGTCCAAGTAGTC 57.050 47.619 8.00 0.00 0.00 2.59
357 374 4.463891 TCCTAAAACCGGTAGTCCAAGTAG 59.536 45.833 8.00 0.89 0.00 2.57
358 375 4.415596 TCCTAAAACCGGTAGTCCAAGTA 58.584 43.478 8.00 0.00 0.00 2.24
360 377 3.967332 TCCTAAAACCGGTAGTCCAAG 57.033 47.619 8.00 0.00 0.00 3.61
361 378 4.406649 CCTATCCTAAAACCGGTAGTCCAA 59.593 45.833 8.00 0.00 0.00 3.53
362 379 3.962718 CCTATCCTAAAACCGGTAGTCCA 59.037 47.826 8.00 0.00 0.00 4.02
363 380 3.323115 CCCTATCCTAAAACCGGTAGTCC 59.677 52.174 8.00 0.00 0.00 3.85
364 381 3.244009 GCCCTATCCTAAAACCGGTAGTC 60.244 52.174 8.00 0.00 0.00 2.59
366 383 2.970640 AGCCCTATCCTAAAACCGGTAG 59.029 50.000 8.00 0.43 0.00 3.18
367 384 2.967887 GAGCCCTATCCTAAAACCGGTA 59.032 50.000 8.00 0.00 0.00 4.02
369 386 1.071857 GGAGCCCTATCCTAAAACCGG 59.928 57.143 0.00 0.00 36.35 5.28
370 387 2.545537 GGAGCCCTATCCTAAAACCG 57.454 55.000 0.00 0.00 36.35 4.44
378 395 7.724061 TGTAAATTTATTTCAGGAGCCCTATCC 59.276 37.037 0.31 0.00 39.89 2.59
379 396 8.691661 TGTAAATTTATTTCAGGAGCCCTATC 57.308 34.615 0.31 0.00 29.64 2.08
380 397 9.082313 CATGTAAATTTATTTCAGGAGCCCTAT 57.918 33.333 0.31 0.00 29.64 2.57
383 400 6.323739 TCCATGTAAATTTATTTCAGGAGCCC 59.676 38.462 0.31 0.00 0.00 5.19
429 783 2.097825 GACTTCATGCTTTCAGCCCAT 58.902 47.619 0.00 0.00 41.51 4.00
453 807 0.899717 ACGAATGCACCAAGCCCATT 60.900 50.000 0.00 0.00 44.83 3.16
465 819 6.165659 AGTTGTTGTTCATAGTACGAATGC 57.834 37.500 6.42 0.00 0.00 3.56
479 833 1.764134 TCTGGGTCCGTAGTTGTTGTT 59.236 47.619 0.00 0.00 0.00 2.83
480 834 1.069668 GTCTGGGTCCGTAGTTGTTGT 59.930 52.381 0.00 0.00 0.00 3.32
481 835 1.343465 AGTCTGGGTCCGTAGTTGTTG 59.657 52.381 0.00 0.00 0.00 3.33
494 848 1.254284 AAGTCAGCGGAGAGTCTGGG 61.254 60.000 0.00 0.00 0.00 4.45
519 873 1.354337 TTCGCTGCTCATTGCTCGAC 61.354 55.000 0.00 0.00 42.91 4.20
557 911 4.626081 AGGTTTCGCTGGCGCAGT 62.626 61.111 10.83 0.00 39.59 4.40
831 1225 4.212913 GGATCTGAGCGGCGCAGA 62.213 66.667 32.86 32.86 43.61 4.26
917 1321 4.961511 TGACGGTCCAGCACGTGC 62.962 66.667 32.79 32.79 44.24 5.34
962 1369 2.125912 CCCAGAGCGAGTTCCACG 60.126 66.667 0.00 0.00 0.00 4.94
1066 1480 2.641305 CAGATGGAAGCCAAGGAAGAG 58.359 52.381 0.00 0.00 36.95 2.85
1175 1592 2.104331 CGACCCAATCCCTCGTCG 59.896 66.667 0.00 0.00 41.70 5.12
1246 1666 2.437359 AGAGCCATTCACCAGCGC 60.437 61.111 0.00 0.00 0.00 5.92
1338 1761 1.143813 ATGAGGGTAATGAGGGCAGG 58.856 55.000 0.00 0.00 0.00 4.85
1341 1764 1.140312 TCCATGAGGGTAATGAGGGC 58.860 55.000 0.00 0.00 38.11 5.19
1493 1919 3.264897 GTATGAGCAGCGGCACCG 61.265 66.667 12.44 4.30 44.61 4.94
1625 2078 2.411628 TAACCAGCTGTGTTGTGTGT 57.588 45.000 22.99 6.52 0.00 3.72
1662 2115 8.089625 TGATCATTAACTCAATCTCCTTGGTA 57.910 34.615 0.00 0.00 35.43 3.25
1747 2200 0.393402 GCAGTGCCCTCATCATCACA 60.393 55.000 2.85 0.00 32.25 3.58
1766 6561 2.807967 TGAGAACCTTCAACTTCATGCG 59.192 45.455 0.00 0.00 0.00 4.73
1839 6675 9.547753 TGCCAACTATAGATATTTCTTTGAGAC 57.452 33.333 6.78 0.00 33.17 3.36
1843 6679 9.903682 CCAATGCCAACTATAGATATTTCTTTG 57.096 33.333 6.78 0.00 33.17 2.77
1850 6686 8.051535 CCAGATTCCAATGCCAACTATAGATAT 58.948 37.037 6.78 0.00 0.00 1.63
1869 6707 4.100808 ACAGAGGCACTATCTTCCAGATTC 59.899 45.833 0.00 0.00 41.55 2.52
1889 6727 6.286758 AGCATAACCATCACTTCAGATACAG 58.713 40.000 0.00 0.00 0.00 2.74
1897 6735 7.497249 AGTTTCTATGAGCATAACCATCACTTC 59.503 37.037 0.00 0.00 0.00 3.01
1974 6902 4.996788 ACAGATGAAAATCCAATCTGCC 57.003 40.909 10.91 0.00 41.62 4.85
1976 6904 5.716094 TGCAACAGATGAAAATCCAATCTG 58.284 37.500 9.70 9.70 43.04 2.90
2014 6947 3.254657 TGCACCAAAGTTACCATAACAGC 59.745 43.478 1.84 0.00 0.00 4.40
2026 6959 1.859302 TGGGACTTTTGCACCAAAGT 58.141 45.000 14.82 14.82 34.72 2.66
2032 6965 2.531522 AAGCAATGGGACTTTTGCAC 57.468 45.000 9.94 0.00 45.62 4.57
2036 6969 6.591001 ACACAAATTAAGCAATGGGACTTTT 58.409 32.000 0.00 0.00 0.00 2.27
2064 6997 9.130312 GTAAATGACAAACACAAACACAAACTA 57.870 29.630 0.00 0.00 0.00 2.24
2065 6998 7.653713 TGTAAATGACAAACACAAACACAAACT 59.346 29.630 0.00 0.00 34.15 2.66
2101 7038 1.674221 CCAGAACTAGCAGTCCTGTGC 60.674 57.143 2.85 0.00 44.35 4.57
2143 7080 6.091034 TGCATGTCCGAAAATTCATTTCATTG 59.909 34.615 0.00 0.00 46.42 2.82
2183 7120 6.410540 AGAACAAGTGTATGAAGGGATTCTC 58.589 40.000 0.00 0.00 0.00 2.87
2198 7135 7.257722 AGATTGTGTGGTAAAAAGAACAAGTG 58.742 34.615 0.00 0.00 31.67 3.16
2215 7157 6.656693 CACCCTAAAAGATGAAGAGATTGTGT 59.343 38.462 0.00 0.00 0.00 3.72
2238 7180 7.751732 AGGTTGAAAGAAAAGAAATTTTGCAC 58.248 30.769 0.00 0.00 0.00 4.57
2282 7227 1.578897 TATTAGCTGTGGCCTGTGGA 58.421 50.000 3.32 0.00 39.73 4.02
2283 7228 2.418368 TTATTAGCTGTGGCCTGTGG 57.582 50.000 3.32 0.00 39.73 4.17
2285 7230 8.163408 TGATTTATATTATTAGCTGTGGCCTGT 58.837 33.333 3.32 0.00 39.73 4.00
2286 7231 8.565896 TGATTTATATTATTAGCTGTGGCCTG 57.434 34.615 3.32 0.00 39.73 4.85
2287 7232 7.337942 GCTGATTTATATTATTAGCTGTGGCCT 59.662 37.037 3.32 0.00 39.73 5.19
2288 7233 7.337942 AGCTGATTTATATTATTAGCTGTGGCC 59.662 37.037 12.89 0.00 41.64 5.36
2289 7234 8.273780 AGCTGATTTATATTATTAGCTGTGGC 57.726 34.615 12.89 0.00 41.64 5.01
2334 7279 7.895975 AAAGTTAGGTCGGAAACATACTAAC 57.104 36.000 0.00 0.00 0.00 2.34
2345 7290 5.046159 ACATCACCATTAAAGTTAGGTCGGA 60.046 40.000 0.00 0.00 30.44 4.55
2451 7409 7.518211 GCAGAAAGAATGCAAATAACCGTTTTT 60.518 33.333 0.00 0.00 43.31 1.94
2452 7410 6.073819 GCAGAAAGAATGCAAATAACCGTTTT 60.074 34.615 0.00 0.00 43.31 2.43
2453 7411 5.405269 GCAGAAAGAATGCAAATAACCGTTT 59.595 36.000 0.00 0.00 43.31 3.60
2454 7412 4.923281 GCAGAAAGAATGCAAATAACCGTT 59.077 37.500 0.00 0.00 43.31 4.44
2455 7413 4.485163 GCAGAAAGAATGCAAATAACCGT 58.515 39.130 0.00 0.00 43.31 4.83
2497 7460 7.441458 GGAACATAGTTGACACTTGAAGTAGTT 59.559 37.037 0.00 0.00 34.06 2.24
2501 7464 5.680619 TGGAACATAGTTGACACTTGAAGT 58.319 37.500 0.00 0.00 34.06 3.01
2502 7465 5.760253 ACTGGAACATAGTTGACACTTGAAG 59.240 40.000 0.00 0.00 38.20 3.02
2533 7585 8.150945 TCTTGCAATAAGGTGATCTTATACTCC 58.849 37.037 0.00 0.00 45.24 3.85
2634 7693 7.716799 ATTAATCTTGTGCAAATTCTACCCA 57.283 32.000 0.00 0.00 0.00 4.51
2658 7717 1.486310 AGTCTCCATCAAAGCGGCATA 59.514 47.619 1.45 0.00 0.00 3.14
2703 7762 0.034670 AATCTCCCCTGCTGCTGTTC 60.035 55.000 0.00 0.00 0.00 3.18
2705 7764 0.323178 CAAATCTCCCCTGCTGCTGT 60.323 55.000 0.00 0.00 0.00 4.40
2746 7806 2.809601 GCGTTCGACACCGAGCAT 60.810 61.111 2.80 0.00 46.39 3.79


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

AutoCloner maintained by Alex Coulton.