Multiple sequence alignment - TraesCS2A01G398400

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 TraesCS2A01G398400 chr2A 100.000 3254 0 0 1 3254 651801689 651798436 0.000000e+00 6010.0
1 TraesCS2A01G398400 chr2A 98.187 1103 16 1 2150 3248 4901670 4900568 0.000000e+00 1923.0
2 TraesCS2A01G398400 chr7A 97.919 2211 40 3 1047 3253 59429870 59432078 0.000000e+00 3823.0
3 TraesCS2A01G398400 chr7A 98.178 2195 31 3 1058 3247 704616228 704614038 0.000000e+00 3823.0
4 TraesCS2A01G398400 chr3B 97.458 2203 52 3 1050 3248 503981224 503979022 0.000000e+00 3755.0
5 TraesCS2A01G398400 chr6B 94.279 2185 101 7 1072 3252 41563786 41561622 0.000000e+00 3321.0
6 TraesCS2A01G398400 chr6B 86.001 1593 193 17 1679 3250 50462307 50463890 0.000000e+00 1679.0
7 TraesCS2A01G398400 chr6B 78.169 142 29 2 1262 1402 41563539 41563399 4.470000e-14 89.8
8 TraesCS2A01G398400 chr1B 96.802 1501 43 2 1752 3248 402043404 402041905 0.000000e+00 2501.0
9 TraesCS2A01G398400 chr1B 85.705 1595 203 13 1675 3248 643252947 643254537 0.000000e+00 1659.0
10 TraesCS2A01G398400 chr1B 78.723 188 32 5 1117 1299 585531644 585531460 5.700000e-23 119.0
11 TraesCS2A01G398400 chr7B 88.173 1784 184 7 1470 3247 641064207 641062445 0.000000e+00 2100.0
12 TraesCS2A01G398400 chr7B 97.346 1055 22 3 2198 3248 720348716 720349768 0.000000e+00 1788.0
13 TraesCS2A01G398400 chr3D 89.892 1484 139 4 1772 3248 431835875 431834396 0.000000e+00 1899.0
14 TraesCS2A01G398400 chr3D 90.219 593 51 5 1083 1672 431836516 431835928 0.000000e+00 767.0
15 TraesCS2A01G398400 chr4B 94.388 784 42 2 1088 1870 659527359 659528141 0.000000e+00 1203.0
16 TraesCS2A01G398400 chr2D 86.587 671 49 8 7 672 507049452 507048818 0.000000e+00 702.0
17 TraesCS2A01G398400 chr2D 89.766 342 24 8 668 1004 507048713 507048378 8.340000e-116 427.0
18 TraesCS2A01G398400 chr2D 85.714 63 6 1 997 1056 507048353 507048291 2.710000e-06 63.9
19 TraesCS2A01G398400 chr7D 85.497 593 86 0 1079 1671 266212689 266212097 1.280000e-173 619.0
20 TraesCS2A01G398400 chr4D 83.882 577 88 4 1101 1676 406647687 406647115 2.210000e-151 545.0
21 TraesCS2A01G398400 chr2B 88.535 314 24 8 669 976 595124583 595124276 1.430000e-98 370.0
22 TraesCS2A01G398400 chr2B 90.526 285 7 9 7 271 595125445 595125161 3.090000e-95 359.0
23 TraesCS2A01G398400 chr2B 82.462 325 39 9 348 672 595124968 595124662 5.350000e-68 268.0
24 TraesCS2A01G398400 chr2B 75.092 273 58 7 1092 1358 755013439 755013171 5.700000e-23 119.0


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 TraesCS2A01G398400 chr2A 651798436 651801689 3253 True 6010.000000 6010 100.000000 1 3254 1 chr2A.!!$R2 3253
1 TraesCS2A01G398400 chr2A 4900568 4901670 1102 True 1923.000000 1923 98.187000 2150 3248 1 chr2A.!!$R1 1098
2 TraesCS2A01G398400 chr7A 59429870 59432078 2208 False 3823.000000 3823 97.919000 1047 3253 1 chr7A.!!$F1 2206
3 TraesCS2A01G398400 chr7A 704614038 704616228 2190 True 3823.000000 3823 98.178000 1058 3247 1 chr7A.!!$R1 2189
4 TraesCS2A01G398400 chr3B 503979022 503981224 2202 True 3755.000000 3755 97.458000 1050 3248 1 chr3B.!!$R1 2198
5 TraesCS2A01G398400 chr6B 41561622 41563786 2164 True 1705.400000 3321 86.224000 1072 3252 2 chr6B.!!$R1 2180
6 TraesCS2A01G398400 chr6B 50462307 50463890 1583 False 1679.000000 1679 86.001000 1679 3250 1 chr6B.!!$F1 1571
7 TraesCS2A01G398400 chr1B 402041905 402043404 1499 True 2501.000000 2501 96.802000 1752 3248 1 chr1B.!!$R1 1496
8 TraesCS2A01G398400 chr1B 643252947 643254537 1590 False 1659.000000 1659 85.705000 1675 3248 1 chr1B.!!$F1 1573
9 TraesCS2A01G398400 chr7B 641062445 641064207 1762 True 2100.000000 2100 88.173000 1470 3247 1 chr7B.!!$R1 1777
10 TraesCS2A01G398400 chr7B 720348716 720349768 1052 False 1788.000000 1788 97.346000 2198 3248 1 chr7B.!!$F1 1050
11 TraesCS2A01G398400 chr3D 431834396 431836516 2120 True 1333.000000 1899 90.055500 1083 3248 2 chr3D.!!$R1 2165
12 TraesCS2A01G398400 chr4B 659527359 659528141 782 False 1203.000000 1203 94.388000 1088 1870 1 chr4B.!!$F1 782
13 TraesCS2A01G398400 chr2D 507048291 507049452 1161 True 397.633333 702 87.355667 7 1056 3 chr2D.!!$R1 1049
14 TraesCS2A01G398400 chr7D 266212097 266212689 592 True 619.000000 619 85.497000 1079 1671 1 chr7D.!!$R1 592
15 TraesCS2A01G398400 chr4D 406647115 406647687 572 True 545.000000 545 83.882000 1101 1676 1 chr4D.!!$R1 575
16 TraesCS2A01G398400 chr2B 595124276 595125445 1169 True 332.333333 370 87.174333 7 976 3 chr2B.!!$R2 969

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
136 142 0.106116 TGGGTTGGGTTGGGTTACAC 60.106 55.0 0.00 0.0 0.00 2.90 F
271 277 0.250234 CCTCAAGATTGGCCTCGTCA 59.750 55.0 3.32 0.0 0.00 4.35 F
926 1044 0.316689 AAAAAGAAACGGAGCGTGCG 60.317 50.0 0.00 0.0 39.99 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1043 1196 0.835941 TTTTGCATTTGCCCAGTGGT 59.164 45.000 8.74 0.0 41.18 4.16 R
1219 1373 1.140407 GACGAATGAACGGAGAGGCG 61.140 60.000 0.00 0.0 37.61 5.52 R
2579 2783 1.869767 GAAGCAGGGCTCGAACATATG 59.130 52.381 0.00 0.0 38.25 1.78 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
101 107 1.341913 GGGTTTTTGGCCTGTGGGTT 61.342 55.000 3.32 0.00 34.45 4.11
102 108 0.179059 GGTTTTTGGCCTGTGGGTTG 60.179 55.000 3.32 0.00 34.45 3.77
103 109 0.179059 GTTTTTGGCCTGTGGGTTGG 60.179 55.000 3.32 0.00 34.45 3.77
136 142 0.106116 TGGGTTGGGTTGGGTTACAC 60.106 55.000 0.00 0.00 0.00 2.90
152 158 2.859165 ACACTGACCATGGTTAGGTG 57.141 50.000 33.08 30.36 40.09 4.00
153 159 2.054799 ACACTGACCATGGTTAGGTGT 58.945 47.619 33.08 30.87 40.09 4.16
207 213 2.047465 AGCGCCTTGAGAGCTGTG 60.047 61.111 2.29 0.00 40.07 3.66
268 274 3.819188 GCCTCAAGATTGGCCTCG 58.181 61.111 3.32 0.00 43.11 4.63
269 275 1.078143 GCCTCAAGATTGGCCTCGT 60.078 57.895 3.32 0.00 43.11 4.18
270 276 1.092345 GCCTCAAGATTGGCCTCGTC 61.092 60.000 3.32 0.00 43.11 4.20
271 277 0.250234 CCTCAAGATTGGCCTCGTCA 59.750 55.000 3.32 0.00 0.00 4.35
272 278 1.339055 CCTCAAGATTGGCCTCGTCAA 60.339 52.381 3.32 0.00 0.00 3.18
273 279 2.426522 CTCAAGATTGGCCTCGTCAAA 58.573 47.619 3.32 0.00 28.60 2.69
274 280 2.813754 CTCAAGATTGGCCTCGTCAAAA 59.186 45.455 3.32 0.00 28.60 2.44
275 281 3.420893 TCAAGATTGGCCTCGTCAAAAT 58.579 40.909 3.32 0.00 28.60 1.82
276 282 3.826157 TCAAGATTGGCCTCGTCAAAATT 59.174 39.130 3.32 0.00 28.60 1.82
277 283 4.082787 TCAAGATTGGCCTCGTCAAAATTC 60.083 41.667 3.32 0.00 28.60 2.17
278 284 3.420893 AGATTGGCCTCGTCAAAATTCA 58.579 40.909 3.32 0.00 28.60 2.57
279 285 3.826157 AGATTGGCCTCGTCAAAATTCAA 59.174 39.130 3.32 0.00 28.60 2.69
280 286 4.280677 AGATTGGCCTCGTCAAAATTCAAA 59.719 37.500 3.32 0.00 28.60 2.69
281 287 4.392921 TTGGCCTCGTCAAAATTCAAAA 57.607 36.364 3.32 0.00 0.00 2.44
282 288 4.392921 TGGCCTCGTCAAAATTCAAAAA 57.607 36.364 3.32 0.00 0.00 1.94
283 289 4.367450 TGGCCTCGTCAAAATTCAAAAAG 58.633 39.130 3.32 0.00 0.00 2.27
284 290 4.098654 TGGCCTCGTCAAAATTCAAAAAGA 59.901 37.500 3.32 0.00 0.00 2.52
285 291 5.221422 TGGCCTCGTCAAAATTCAAAAAGAT 60.221 36.000 3.32 0.00 0.00 2.40
286 292 5.696270 GGCCTCGTCAAAATTCAAAAAGATT 59.304 36.000 0.00 0.00 0.00 2.40
287 293 6.202762 GGCCTCGTCAAAATTCAAAAAGATTT 59.797 34.615 0.00 0.00 0.00 2.17
288 294 7.065283 GCCTCGTCAAAATTCAAAAAGATTTG 58.935 34.615 0.00 0.00 45.92 2.32
289 295 7.566709 CCTCGTCAAAATTCAAAAAGATTTGG 58.433 34.615 1.86 0.00 44.88 3.28
290 296 7.224557 CCTCGTCAAAATTCAAAAAGATTTGGT 59.775 33.333 1.86 0.00 44.88 3.67
321 327 8.690884 TCTTTTAAAATTCATTCACCACTGTCA 58.309 29.630 0.09 0.00 0.00 3.58
331 337 7.648142 TCATTCACCACTGTCAAAATAGAAAC 58.352 34.615 0.00 0.00 0.00 2.78
337 343 5.983118 CCACTGTCAAAATAGAAACCAAACC 59.017 40.000 0.00 0.00 0.00 3.27
340 346 7.169645 CACTGTCAAAATAGAAACCAAACCATG 59.830 37.037 0.00 0.00 0.00 3.66
345 351 5.743636 AATAGAAACCAAACCATGTGCAT 57.256 34.783 0.00 0.00 0.00 3.96
350 356 7.238486 AGAAACCAAACCATGTGCATATTTA 57.762 32.000 0.00 0.00 0.00 1.40
382 388 8.773645 CATTTTAGCACGTGGATATGATTTCTA 58.226 33.333 18.88 2.95 0.00 2.10
387 393 5.909610 GCACGTGGATATGATTTCTAAAAGC 59.090 40.000 18.88 0.00 0.00 3.51
392 398 7.095649 CGTGGATATGATTTCTAAAAGCGATGA 60.096 37.037 0.00 0.00 0.00 2.92
400 406 7.692291 TGATTTCTAAAAGCGATGATTTTCGAC 59.308 33.333 0.00 0.00 41.62 4.20
401 407 5.464965 TCTAAAAGCGATGATTTTCGACC 57.535 39.130 0.00 0.00 41.62 4.79
408 414 3.370978 GCGATGATTTTCGACCTTTCTCA 59.629 43.478 0.00 0.00 41.62 3.27
414 420 9.278734 GATGATTTTCGACCTTTCTCAATAAAC 57.721 33.333 0.00 0.00 0.00 2.01
416 422 9.496873 TGATTTTCGACCTTTCTCAATAAACTA 57.503 29.630 0.00 0.00 0.00 2.24
422 428 7.042335 CGACCTTTCTCAATAAACTATGGACT 58.958 38.462 0.00 0.00 0.00 3.85
426 432 8.391106 CCTTTCTCAATAAACTATGGACTTTCG 58.609 37.037 0.00 0.00 0.00 3.46
448 454 3.185797 GGAACGGTGAACAGACAATACAC 59.814 47.826 0.00 0.00 0.00 2.90
449 455 2.762745 ACGGTGAACAGACAATACACC 58.237 47.619 0.00 0.00 44.90 4.16
467 473 8.872845 CAATACACCAAAATCAAAGAAATAGGC 58.127 33.333 0.00 0.00 0.00 3.93
469 475 5.306678 ACACCAAAATCAAAGAAATAGGCCA 59.693 36.000 5.01 0.00 0.00 5.36
470 476 5.639082 CACCAAAATCAAAGAAATAGGCCAC 59.361 40.000 5.01 0.00 0.00 5.01
472 478 5.279910 CCAAAATCAAAGAAATAGGCCACCA 60.280 40.000 5.01 0.00 0.00 4.17
473 479 5.405935 AAATCAAAGAAATAGGCCACCAC 57.594 39.130 5.01 0.00 0.00 4.16
543 549 6.624352 ACAGTATAACATAGGCATTTGCTG 57.376 37.500 2.12 0.00 41.70 4.41
544 550 6.122277 ACAGTATAACATAGGCATTTGCTGT 58.878 36.000 2.12 0.00 41.70 4.40
545 551 6.603201 ACAGTATAACATAGGCATTTGCTGTT 59.397 34.615 11.72 11.72 39.32 3.16
571 577 1.766494 TGTGGGATAGGCATTTGCTG 58.234 50.000 2.12 0.00 41.70 4.41
580 586 5.302823 GGATAGGCATTTGCTGGTTCTATTT 59.697 40.000 2.12 0.00 41.70 1.40
584 590 7.186570 AGGCATTTGCTGGTTCTATTTAAAT 57.813 32.000 5.89 5.89 41.70 1.40
591 597 7.695480 TGCTGGTTCTATTTAAATACTTGCA 57.305 32.000 3.71 9.01 0.00 4.08
623 629 6.038714 GCATTGGTTTACTAGGAGAAATGAGG 59.961 42.308 0.00 0.00 0.00 3.86
626 632 5.189145 TGGTTTACTAGGAGAAATGAGGGAC 59.811 44.000 0.00 0.00 0.00 4.46
695 810 7.287696 TCAAATCTTAAAATTCCCTATCCTGGC 59.712 37.037 0.00 0.00 0.00 4.85
697 812 4.165372 TCTTAAAATTCCCTATCCTGGCGT 59.835 41.667 0.00 0.00 0.00 5.68
699 814 2.348411 AATTCCCTATCCTGGCGTTG 57.652 50.000 0.00 0.00 0.00 4.10
700 815 1.507140 ATTCCCTATCCTGGCGTTGA 58.493 50.000 0.00 0.00 0.00 3.18
701 816 0.830648 TTCCCTATCCTGGCGTTGAG 59.169 55.000 0.00 0.00 0.00 3.02
706 821 3.370103 CCCTATCCTGGCGTTGAGTTTTA 60.370 47.826 0.00 0.00 0.00 1.52
741 859 4.699522 GTTTGGACGCGCCTCCCT 62.700 66.667 20.73 0.00 37.63 4.20
762 880 5.529060 CCCTTGTGTAAGCTGATATTTCCTC 59.471 44.000 0.00 0.00 32.40 3.71
765 883 4.058817 GTGTAAGCTGATATTTCCTCGGG 58.941 47.826 0.00 0.00 0.00 5.14
770 888 2.772287 CTGATATTTCCTCGGGCTTCC 58.228 52.381 0.00 0.00 0.00 3.46
784 902 0.807667 GCTTCCGCAGACGATCATGT 60.808 55.000 0.00 0.00 43.93 3.21
788 906 2.422597 TCCGCAGACGATCATGTTTTT 58.577 42.857 0.00 0.00 43.93 1.94
790 908 2.508867 CGCAGACGATCATGTTTTTGG 58.491 47.619 0.00 0.00 43.93 3.28
791 909 2.253603 GCAGACGATCATGTTTTTGGC 58.746 47.619 0.00 0.00 0.00 4.52
832 950 1.285641 GCTACAGCGCTGCCAAAAA 59.714 52.632 36.28 14.17 0.00 1.94
843 961 2.648318 GCCAAAAAGTGCTTCGCGC 61.648 57.895 0.00 0.00 39.59 6.86
869 987 2.813908 CTCGTCCGGCCGAAAAGG 60.814 66.667 30.73 16.93 44.97 3.11
924 1042 3.334272 AAGAAAAAGAAACGGAGCGTG 57.666 42.857 0.00 0.00 39.99 5.34
925 1043 1.002792 AGAAAAAGAAACGGAGCGTGC 60.003 47.619 0.00 0.00 39.99 5.34
926 1044 0.316689 AAAAAGAAACGGAGCGTGCG 60.317 50.000 0.00 0.00 39.99 5.34
931 1049 0.569349 GAAACGGAGCGTGCGTATAC 59.431 55.000 5.17 0.00 45.62 1.47
976 1094 3.181451 TGATGATTGATGGGTAGTGCCTC 60.181 47.826 0.00 0.00 37.43 4.70
983 1101 2.543037 TGGGTAGTGCCTCAGTGATA 57.457 50.000 0.00 0.00 37.43 2.15
988 1106 4.122776 GGTAGTGCCTCAGTGATACAATG 58.877 47.826 0.00 0.00 0.00 2.82
1004 1122 7.746034 GTGATACAATGTATCCATTTACATGCG 59.254 37.037 25.36 0.00 40.94 4.73
1006 1124 6.304356 ACAATGTATCCATTTACATGCGAG 57.696 37.500 0.00 0.00 40.94 5.03
1007 1125 5.822519 ACAATGTATCCATTTACATGCGAGT 59.177 36.000 0.00 0.00 40.94 4.18
1036 1189 2.614481 GGGCAAGAGACATGTAAACGGA 60.614 50.000 0.00 0.00 0.00 4.69
1043 1196 5.607477 AGAGACATGTAAACGGAAAGACAA 58.393 37.500 0.00 0.00 0.00 3.18
1219 1373 2.654863 CTCTCTCCTCTCCTTCAGTCC 58.345 57.143 0.00 0.00 0.00 3.85
1237 1391 1.153823 CGCCTCTCCGTTCATTCGT 60.154 57.895 0.00 0.00 0.00 3.85
1741 1898 2.525629 TGTCGTGGGCTTCCCTCA 60.526 61.111 3.27 0.00 45.70 3.86
1754 1911 1.348064 TCCCTCATGGACAACGTCTT 58.652 50.000 0.00 0.00 38.61 3.01
2224 2400 1.519455 CGTGGATCTTGGGCGTCTC 60.519 63.158 0.00 0.00 0.00 3.36
2493 2694 5.759763 CGGGACAATTCATCATTGATGTCTA 59.240 40.000 22.64 12.11 44.78 2.59
2912 3892 0.758685 CAAGTGGTTGCCTCCCCAAA 60.759 55.000 0.00 0.00 31.17 3.28
2991 3971 0.442699 GAAGACGCCCACGATTTCAC 59.557 55.000 0.00 0.00 43.93 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 99 1.903404 GCCTCAACCCAACCCACAG 60.903 63.158 0.00 0.00 0.00 3.66
101 107 3.970410 CAGCCTGGCCTCAACCCA 61.970 66.667 16.57 0.00 0.00 4.51
102 108 4.748144 CCAGCCTGGCCTCAACCC 62.748 72.222 16.57 0.00 0.00 4.11
103 109 4.748144 CCCAGCCTGGCCTCAACC 62.748 72.222 16.57 0.00 35.79 3.77
136 142 1.351017 ACCACACCTAACCATGGTCAG 59.649 52.381 20.07 13.96 41.76 3.51
152 158 4.514585 TGCCCCACACCACACCAC 62.515 66.667 0.00 0.00 0.00 4.16
153 159 4.514585 GTGCCCCACACCACACCA 62.515 66.667 0.00 0.00 44.02 4.17
207 213 0.533755 CCCCACCGCAGAAGATCATC 60.534 60.000 0.00 0.00 0.00 2.92
265 271 8.130307 ACCAAATCTTTTTGAATTTTGACGAG 57.870 30.769 0.00 0.00 44.11 4.18
266 272 7.978975 AGACCAAATCTTTTTGAATTTTGACGA 59.021 29.630 0.00 0.00 44.11 4.20
267 273 8.130307 AGACCAAATCTTTTTGAATTTTGACG 57.870 30.769 0.19 0.00 44.11 4.35
268 274 8.268738 CGAGACCAAATCTTTTTGAATTTTGAC 58.731 33.333 0.19 0.00 44.11 3.18
269 275 7.978975 ACGAGACCAAATCTTTTTGAATTTTGA 59.021 29.630 0.00 0.00 44.11 2.69
270 276 8.130307 ACGAGACCAAATCTTTTTGAATTTTG 57.870 30.769 0.00 0.00 44.11 2.44
271 277 8.197439 AGACGAGACCAAATCTTTTTGAATTTT 58.803 29.630 0.00 0.00 44.11 1.82
272 278 7.716612 AGACGAGACCAAATCTTTTTGAATTT 58.283 30.769 0.00 0.00 44.11 1.82
273 279 7.277174 AGACGAGACCAAATCTTTTTGAATT 57.723 32.000 0.00 0.00 44.11 2.17
274 280 6.884280 AGACGAGACCAAATCTTTTTGAAT 57.116 33.333 0.00 0.00 44.11 2.57
275 281 6.693315 AAGACGAGACCAAATCTTTTTGAA 57.307 33.333 0.00 0.00 44.11 2.69
276 282 6.693315 AAAGACGAGACCAAATCTTTTTGA 57.307 33.333 0.00 0.00 44.11 2.69
277 283 8.850454 TTAAAAGACGAGACCAAATCTTTTTG 57.150 30.769 14.08 0.00 44.87 2.44
278 284 9.863845 TTTTAAAAGACGAGACCAAATCTTTTT 57.136 25.926 14.08 0.00 44.87 1.94
281 287 9.678941 GAATTTTAAAAGACGAGACCAAATCTT 57.321 29.630 6.79 0.00 38.00 2.40
282 288 8.846211 TGAATTTTAAAAGACGAGACCAAATCT 58.154 29.630 6.79 0.00 41.91 2.40
283 289 9.626045 ATGAATTTTAAAAGACGAGACCAAATC 57.374 29.630 6.79 0.00 0.00 2.17
284 290 9.981114 AATGAATTTTAAAAGACGAGACCAAAT 57.019 25.926 6.79 0.00 0.00 2.32
285 291 9.458374 GAATGAATTTTAAAAGACGAGACCAAA 57.542 29.630 6.79 0.00 0.00 3.28
286 292 8.625651 TGAATGAATTTTAAAAGACGAGACCAA 58.374 29.630 6.79 0.00 0.00 3.67
287 293 8.073768 GTGAATGAATTTTAAAAGACGAGACCA 58.926 33.333 6.79 0.00 0.00 4.02
288 294 7.537649 GGTGAATGAATTTTAAAAGACGAGACC 59.462 37.037 6.79 3.93 0.00 3.85
289 295 8.073768 TGGTGAATGAATTTTAAAAGACGAGAC 58.926 33.333 6.79 0.00 0.00 3.36
290 296 8.073768 GTGGTGAATGAATTTTAAAAGACGAGA 58.926 33.333 6.79 0.00 0.00 4.04
306 312 7.255451 GGTTTCTATTTTGACAGTGGTGAATGA 60.255 37.037 0.00 0.00 0.00 2.57
321 327 5.923204 TGCACATGGTTTGGTTTCTATTTT 58.077 33.333 0.00 0.00 0.00 1.82
331 337 7.927092 TGAATGATAAATATGCACATGGTTTGG 59.073 33.333 0.00 0.00 0.00 3.28
345 351 9.114952 TCCACGTGCTAAAATGAATGATAAATA 57.885 29.630 10.91 0.00 0.00 1.40
350 356 7.445096 TCATATCCACGTGCTAAAATGAATGAT 59.555 33.333 10.91 5.45 0.00 2.45
382 388 4.766404 AAGGTCGAAAATCATCGCTTTT 57.234 36.364 0.00 0.00 42.44 2.27
387 393 5.530519 TTGAGAAAGGTCGAAAATCATCG 57.469 39.130 0.00 0.00 44.04 3.84
400 406 8.391106 CGAAAGTCCATAGTTTATTGAGAAAGG 58.609 37.037 0.00 0.00 0.00 3.11
401 407 8.391106 CCGAAAGTCCATAGTTTATTGAGAAAG 58.609 37.037 0.00 0.00 0.00 2.62
408 414 5.583457 CCGTTCCGAAAGTCCATAGTTTATT 59.417 40.000 0.00 0.00 0.00 1.40
414 420 2.094390 TCACCGTTCCGAAAGTCCATAG 60.094 50.000 0.00 0.00 0.00 2.23
416 422 0.682852 TCACCGTTCCGAAAGTCCAT 59.317 50.000 0.00 0.00 0.00 3.41
422 428 1.134759 TGTCTGTTCACCGTTCCGAAA 60.135 47.619 0.00 0.00 0.00 3.46
426 432 3.185797 GTGTATTGTCTGTTCACCGTTCC 59.814 47.826 0.00 0.00 0.00 3.62
436 442 7.581213 TCTTTGATTTTGGTGTATTGTCTGT 57.419 32.000 0.00 0.00 0.00 3.41
437 443 8.870160 TTTCTTTGATTTTGGTGTATTGTCTG 57.130 30.769 0.00 0.00 0.00 3.51
445 451 5.306678 TGGCCTATTTCTTTGATTTTGGTGT 59.693 36.000 3.32 0.00 0.00 4.16
448 454 5.178061 GGTGGCCTATTTCTTTGATTTTGG 58.822 41.667 3.32 0.00 0.00 3.28
449 455 5.639082 GTGGTGGCCTATTTCTTTGATTTTG 59.361 40.000 3.32 0.00 0.00 2.44
469 475 1.503347 AGGGGAATCCACAAAAGTGGT 59.497 47.619 3.57 0.00 44.53 4.16
470 476 2.309136 AGGGGAATCCACAAAAGTGG 57.691 50.000 3.57 8.32 45.53 4.00
472 478 3.655777 TGTCTAGGGGAATCCACAAAAGT 59.344 43.478 3.57 0.00 38.24 2.66
473 479 4.301072 TGTCTAGGGGAATCCACAAAAG 57.699 45.455 3.57 0.00 38.24 2.27
490 496 9.950496 AGTATAACTTTCACATTTCTGATGTCT 57.050 29.630 0.00 0.00 0.00 3.41
517 523 7.442364 CAGCAAATGCCTATGTTATACTGTACT 59.558 37.037 0.94 0.00 43.38 2.73
518 524 7.226720 ACAGCAAATGCCTATGTTATACTGTAC 59.773 37.037 0.94 0.00 43.38 2.90
519 525 7.279615 ACAGCAAATGCCTATGTTATACTGTA 58.720 34.615 0.94 0.00 43.38 2.74
520 526 6.122277 ACAGCAAATGCCTATGTTATACTGT 58.878 36.000 0.94 0.00 43.38 3.55
521 527 6.624352 ACAGCAAATGCCTATGTTATACTG 57.376 37.500 0.94 0.00 43.38 2.74
522 528 7.645058 AAACAGCAAATGCCTATGTTATACT 57.355 32.000 10.64 0.00 43.38 2.12
549 555 3.055963 CAGCAAATGCCTATCCCACAAAA 60.056 43.478 0.94 0.00 43.38 2.44
561 567 8.197439 AGTATTTAAATAGAACCAGCAAATGCC 58.803 33.333 8.18 0.00 43.38 4.40
562 568 9.586435 AAGTATTTAAATAGAACCAGCAAATGC 57.414 29.630 8.18 0.00 42.49 3.56
591 597 7.630082 TCTCCTAGTAAACCAATGCATACTTT 58.370 34.615 0.00 0.49 31.46 2.66
598 604 6.038714 CCTCATTTCTCCTAGTAAACCAATGC 59.961 42.308 0.00 0.00 0.00 3.56
608 614 5.843019 TTTTGTCCCTCATTTCTCCTAGT 57.157 39.130 0.00 0.00 0.00 2.57
666 672 9.997172 AGGATAGGGAATTTTAAGATTTGAAGT 57.003 29.630 0.00 0.00 0.00 3.01
688 803 5.010282 AGAAATAAAACTCAACGCCAGGAT 58.990 37.500 0.00 0.00 0.00 3.24
689 804 4.215399 CAGAAATAAAACTCAACGCCAGGA 59.785 41.667 0.00 0.00 0.00 3.86
690 805 4.023193 ACAGAAATAAAACTCAACGCCAGG 60.023 41.667 0.00 0.00 0.00 4.45
691 806 5.108385 ACAGAAATAAAACTCAACGCCAG 57.892 39.130 0.00 0.00 0.00 4.85
693 808 8.448615 ACTAATACAGAAATAAAACTCAACGCC 58.551 33.333 0.00 0.00 0.00 5.68
706 821 9.458374 CGTCCAAACAAAAACTAATACAGAAAT 57.542 29.630 0.00 0.00 0.00 2.17
724 842 4.699522 AGGGAGGCGCGTCCAAAC 62.700 66.667 40.50 27.46 38.52 2.93
741 859 5.116180 CCGAGGAAATATCAGCTTACACAA 58.884 41.667 0.00 0.00 0.00 3.33
770 888 2.508867 CCAAAAACATGATCGTCTGCG 58.491 47.619 0.00 0.00 39.92 5.18
784 902 1.739707 GCCATCGATGCATGCCAAAAA 60.740 47.619 20.25 0.00 0.00 1.94
788 906 1.895231 GAGCCATCGATGCATGCCA 60.895 57.895 20.25 3.52 0.00 4.92
790 908 1.600076 AGGAGCCATCGATGCATGC 60.600 57.895 20.25 17.25 0.00 4.06
791 909 0.534427 ACAGGAGCCATCGATGCATG 60.534 55.000 20.25 15.79 0.00 4.06
894 1012 5.004061 CCGTTTCTTTTTCTTTTCCGTGTTC 59.996 40.000 0.00 0.00 0.00 3.18
955 1073 3.181451 TGAGGCACTACCCATCAATCATC 60.181 47.826 0.00 0.00 41.55 2.92
967 1085 4.759782 ACATTGTATCACTGAGGCACTAC 58.240 43.478 0.00 0.00 41.55 2.73
988 1106 7.866393 ACTACTAACTCGCATGTAAATGGATAC 59.134 37.037 0.00 0.00 0.00 2.24
1004 1122 3.510360 TGTCTCTTGCCCACTACTAACTC 59.490 47.826 0.00 0.00 0.00 3.01
1006 1124 3.955650 TGTCTCTTGCCCACTACTAAC 57.044 47.619 0.00 0.00 0.00 2.34
1007 1125 3.838317 ACATGTCTCTTGCCCACTACTAA 59.162 43.478 0.00 0.00 0.00 2.24
1036 1189 1.859302 TTTGCCCAGTGGTTGTCTTT 58.141 45.000 8.74 0.00 0.00 2.52
1043 1196 0.835941 TTTTGCATTTGCCCAGTGGT 59.164 45.000 8.74 0.00 41.18 4.16
1219 1373 1.140407 GACGAATGAACGGAGAGGCG 61.140 60.000 0.00 0.00 37.61 5.52
1337 1494 4.082523 CAGGAGGCGCCCGAAAGA 62.083 66.667 26.15 0.00 37.37 2.52
1741 1898 2.479566 ATGCTGAAGACGTTGTCCAT 57.520 45.000 0.00 0.00 32.18 3.41
1754 1911 4.117685 CTCGTCTTCATCATCAATGCTGA 58.882 43.478 0.00 0.00 35.17 4.26
1803 1961 2.930562 ACCCCACTGGAGCACCTC 60.931 66.667 0.71 0.00 38.00 3.85
2579 2783 1.869767 GAAGCAGGGCTCGAACATATG 59.130 52.381 0.00 0.00 38.25 1.78
2832 3811 9.552114 GTCAAGAAAATCATAGAACTCATTGTG 57.448 33.333 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.