Multiple sequence alignment - TraesCS4B01G138500

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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 TraesCS4B01G138500 chr4B 100.000 2623 0 0 1 2623 182271752 182269130 0.000000e+00 4844
1 TraesCS4B01G138500 chr4B 99.222 900 7 0 1724 2623 182263163 182262264 0.000000e+00 1624
2 TraesCS4B01G138500 chr4A 87.283 1557 100 34 191 1705 450767415 450765915 0.000000e+00 1688
3 TraesCS4B01G138500 chr3B 99.333 900 6 0 1724 2623 763460874 763461773 0.000000e+00 1629
4 TraesCS4B01G138500 chr2A 99.225 903 7 0 1721 2623 467216537 467215635 0.000000e+00 1629
5 TraesCS4B01G138500 chr6B 99.222 900 7 0 1724 2623 635253116 635254015 0.000000e+00 1624
6 TraesCS4B01G138500 chr3A 99.222 900 7 0 1724 2623 460977748 460978647 0.000000e+00 1624
7 TraesCS4B01G138500 chr3A 99.113 902 8 0 1722 2623 726868495 726869396 0.000000e+00 1622
8 TraesCS4B01G138500 chr2B 99.222 900 7 0 1724 2623 781230824 781231723 0.000000e+00 1624
9 TraesCS4B01G138500 chr1A 99.114 903 8 0 1721 2623 558338171 558339073 0.000000e+00 1624
10 TraesCS4B01G138500 chr6A 99.113 902 8 0 1722 2623 117627027 117627928 0.000000e+00 1622
11 TraesCS4B01G138500 chr4D 92.012 1014 38 16 735 1723 119807604 119806609 0.000000e+00 1384
12 TraesCS4B01G138500 chr4D 81.654 387 40 11 300 675 119810023 119809657 2.550000e-75 292
13 TraesCS4B01G138500 chr4D 87.607 234 24 5 16 246 119810259 119810028 1.550000e-67 267
14 TraesCS4B01G138500 chr4D 93.023 86 3 2 663 745 119809517 119809432 3.550000e-24 122


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 TraesCS4B01G138500 chr4B 182269130 182271752 2622 True 4844.00 4844 100.000 1 2623 1 chr4B.!!$R2 2622
1 TraesCS4B01G138500 chr4B 182262264 182263163 899 True 1624.00 1624 99.222 1724 2623 1 chr4B.!!$R1 899
2 TraesCS4B01G138500 chr4A 450765915 450767415 1500 True 1688.00 1688 87.283 191 1705 1 chr4A.!!$R1 1514
3 TraesCS4B01G138500 chr3B 763460874 763461773 899 False 1629.00 1629 99.333 1724 2623 1 chr3B.!!$F1 899
4 TraesCS4B01G138500 chr2A 467215635 467216537 902 True 1629.00 1629 99.225 1721 2623 1 chr2A.!!$R1 902
5 TraesCS4B01G138500 chr6B 635253116 635254015 899 False 1624.00 1624 99.222 1724 2623 1 chr6B.!!$F1 899
6 TraesCS4B01G138500 chr3A 460977748 460978647 899 False 1624.00 1624 99.222 1724 2623 1 chr3A.!!$F1 899
7 TraesCS4B01G138500 chr3A 726868495 726869396 901 False 1622.00 1622 99.113 1722 2623 1 chr3A.!!$F2 901
8 TraesCS4B01G138500 chr2B 781230824 781231723 899 False 1624.00 1624 99.222 1724 2623 1 chr2B.!!$F1 899
9 TraesCS4B01G138500 chr1A 558338171 558339073 902 False 1624.00 1624 99.114 1721 2623 1 chr1A.!!$F1 902
10 TraesCS4B01G138500 chr6A 117627027 117627928 901 False 1622.00 1622 99.113 1722 2623 1 chr6A.!!$F1 901
11 TraesCS4B01G138500 chr4D 119806609 119810259 3650 True 516.25 1384 88.574 16 1723 4 chr4D.!!$R1 1707

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
562 576 0.038983 TCATGGACGGTACACACACG 60.039 55.0 0.0 0.0 0.00 4.49 F
1303 3341 0.105964 CTCCTACCCTGCTAGGCTGA 60.106 60.0 0.0 0.0 34.25 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1579 3618 1.064463 CAAAGAGGCCATGCTTCCCTA 60.064 52.381 5.01 0.0 35.17 3.53 R
2472 4521 1.983691 CTGGATACCCATGATGGCTCT 59.016 52.381 5.79 0.0 42.59 4.09 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
35 36 5.437289 TCATGTGTGATGAACTTTCCAAC 57.563 39.130 0.00 0.00 0.00 3.77
44 45 2.091610 TGAACTTTCCAACCCCACATGA 60.092 45.455 0.00 0.00 0.00 3.07
47 48 3.586429 ACTTTCCAACCCCACATGATTT 58.414 40.909 0.00 0.00 0.00 2.17
76 77 5.891451 TCTAATCGTGTGTGATAAGAGGTG 58.109 41.667 0.00 0.00 0.00 4.00
78 79 1.893137 TCGTGTGTGATAAGAGGTGCT 59.107 47.619 0.00 0.00 0.00 4.40
80 81 3.128764 TCGTGTGTGATAAGAGGTGCTAG 59.871 47.826 0.00 0.00 0.00 3.42
95 96 2.593336 GTGCTAGCGTAGACGTTTCTTC 59.407 50.000 10.77 0.00 42.22 2.87
96 97 2.183636 GCTAGCGTAGACGTTTCTTCC 58.816 52.381 0.00 0.00 42.22 3.46
99 100 1.617357 AGCGTAGACGTTTCTTCCCTT 59.383 47.619 3.73 0.00 42.22 3.95
110 111 5.156355 CGTTTCTTCCCTTCAAATCATGTG 58.844 41.667 0.00 0.00 0.00 3.21
111 112 5.473039 GTTTCTTCCCTTCAAATCATGTGG 58.527 41.667 0.00 0.00 0.00 4.17
115 116 5.193527 TCTTCCCTTCAAATCATGTGGGATA 59.806 40.000 0.00 0.00 45.29 2.59
143 144 1.735571 GACCTCACACGTGTGTTGTTT 59.264 47.619 39.25 23.88 45.76 2.83
146 147 1.656594 CTCACACGTGTGTTGTTTCGA 59.343 47.619 39.25 21.83 45.76 3.71
158 159 5.005203 TGTGTTGTTTCGATTGATTGTTTGC 59.995 36.000 0.00 0.00 0.00 3.68
159 160 5.005203 GTGTTGTTTCGATTGATTGTTTGCA 59.995 36.000 0.00 0.00 0.00 4.08
160 161 5.752472 TGTTGTTTCGATTGATTGTTTGCAT 59.248 32.000 0.00 0.00 0.00 3.96
162 163 7.436376 TGTTGTTTCGATTGATTGTTTGCATTA 59.564 29.630 0.00 0.00 0.00 1.90
166 167 5.953183 TCGATTGATTGTTTGCATTAGCTT 58.047 33.333 0.00 0.00 42.74 3.74
170 171 7.253750 CGATTGATTGTTTGCATTAGCTTAACC 60.254 37.037 0.00 0.00 42.74 2.85
171 172 5.398169 TGATTGTTTGCATTAGCTTAACCG 58.602 37.500 0.00 0.00 42.74 4.44
172 173 4.839668 TTGTTTGCATTAGCTTAACCGT 57.160 36.364 0.00 0.00 42.74 4.83
173 174 4.413495 TGTTTGCATTAGCTTAACCGTC 57.587 40.909 0.00 0.00 42.74 4.79
175 176 4.276183 TGTTTGCATTAGCTTAACCGTCAA 59.724 37.500 0.00 0.00 42.74 3.18
176 177 4.413495 TTGCATTAGCTTAACCGTCAAC 57.587 40.909 0.00 0.00 42.74 3.18
178 179 2.096980 GCATTAGCTTAACCGTCAACCC 59.903 50.000 0.00 0.00 37.91 4.11
179 180 3.340034 CATTAGCTTAACCGTCAACCCA 58.660 45.455 0.00 0.00 0.00 4.51
181 182 2.109425 AGCTTAACCGTCAACCCATC 57.891 50.000 0.00 0.00 0.00 3.51
197 198 5.284861 ACCCATCGCACATATTTACTACA 57.715 39.130 0.00 0.00 0.00 2.74
223 224 3.006859 CCTATCGACCTATTGCACATGGA 59.993 47.826 0.00 0.00 0.00 3.41
247 250 0.095245 CCTTAACGTGTGCGATGCAG 59.905 55.000 0.00 0.00 40.08 4.41
248 251 1.067693 CTTAACGTGTGCGATGCAGA 58.932 50.000 0.00 0.00 40.08 4.26
258 261 3.010144 GATGCAGACCCCACCCAT 58.990 61.111 0.00 0.00 0.00 4.00
279 282 4.002256 TCTCCCCTTATCACACACCATA 57.998 45.455 0.00 0.00 0.00 2.74
280 283 4.367166 TCTCCCCTTATCACACACCATAA 58.633 43.478 0.00 0.00 0.00 1.90
309 312 1.203313 GTTCGCAACTACGTGTGCC 59.797 57.895 13.10 0.00 0.00 5.01
322 325 0.813184 GTGTGCCATGACCCAATCTG 59.187 55.000 0.00 0.00 0.00 2.90
323 326 0.323633 TGTGCCATGACCCAATCTGG 60.324 55.000 0.00 0.00 37.25 3.86
340 343 4.703645 TCTGGAGTAGTGATTCAAGACG 57.296 45.455 0.00 0.00 0.00 4.18
350 355 3.066380 TGATTCAAGACGACCATGTGTG 58.934 45.455 0.00 0.00 0.00 3.82
357 362 2.094182 AGACGACCATGTGTGATGTACC 60.094 50.000 0.00 0.00 0.00 3.34
359 364 1.742411 CGACCATGTGTGATGTACCCC 60.742 57.143 0.00 0.00 0.00 4.95
385 390 3.769739 TTAGCCTGACACTTCACACAT 57.230 42.857 0.00 0.00 0.00 3.21
393 398 0.877071 CACTTCACACATGGCCACTC 59.123 55.000 8.16 0.00 0.00 3.51
398 403 1.151221 ACACATGGCCACTCTTGCA 59.849 52.632 8.16 0.00 0.00 4.08
406 411 3.495331 TGGCCACTCTTGCAATTAGAAA 58.505 40.909 0.00 0.00 0.00 2.52
407 412 3.255642 TGGCCACTCTTGCAATTAGAAAC 59.744 43.478 0.00 4.46 0.00 2.78
430 436 4.323417 CACACACATTTCAGCCCTAACTA 58.677 43.478 0.00 0.00 0.00 2.24
448 461 5.789574 AACTATGGGGAAGGTGTGAATAA 57.210 39.130 0.00 0.00 0.00 1.40
494 508 2.987149 GACATGTCATCGAAGTCGTTGT 59.013 45.455 21.07 0.00 39.36 3.32
505 519 4.266029 TCGAAGTCGTTGTTGTACTTTGTC 59.734 41.667 0.00 0.00 40.80 3.18
513 527 9.525007 GTCGTTGTTGTACTTTGTCTTATAATG 57.475 33.333 0.00 0.00 0.00 1.90
515 529 9.872757 CGTTGTTGTACTTTGTCTTATAATGTT 57.127 29.630 0.00 0.00 0.00 2.71
524 538 9.950680 ACTTTGTCTTATAATGTTTTGACACAG 57.049 29.630 11.78 11.78 37.87 3.66
525 539 9.398170 CTTTGTCTTATAATGTTTTGACACAGG 57.602 33.333 3.26 0.00 34.73 4.00
526 540 7.447374 TGTCTTATAATGTTTTGACACAGGG 57.553 36.000 0.00 0.00 30.78 4.45
527 541 7.227873 TGTCTTATAATGTTTTGACACAGGGA 58.772 34.615 0.00 0.00 30.78 4.20
528 542 7.174253 TGTCTTATAATGTTTTGACACAGGGAC 59.826 37.037 0.00 0.00 30.78 4.46
529 543 6.370442 TCTTATAATGTTTTGACACAGGGACG 59.630 38.462 0.00 0.00 0.00 4.79
530 544 1.604604 ATGTTTTGACACAGGGACGG 58.395 50.000 0.00 0.00 0.00 4.79
531 545 0.542333 TGTTTTGACACAGGGACGGA 59.458 50.000 0.00 0.00 0.00 4.69
532 546 1.226746 GTTTTGACACAGGGACGGAG 58.773 55.000 0.00 0.00 0.00 4.63
533 547 0.107831 TTTTGACACAGGGACGGAGG 59.892 55.000 0.00 0.00 0.00 4.30
534 548 1.764571 TTTGACACAGGGACGGAGGG 61.765 60.000 0.00 0.00 0.00 4.30
535 549 2.283676 GACACAGGGACGGAGGGA 60.284 66.667 0.00 0.00 0.00 4.20
536 550 2.283966 ACACAGGGACGGAGGGAG 60.284 66.667 0.00 0.00 0.00 4.30
549 563 2.158652 CGGAGGGAGTAGTACTCATGGA 60.159 54.545 27.41 0.00 46.79 3.41
562 576 0.038983 TCATGGACGGTACACACACG 60.039 55.000 0.00 0.00 0.00 4.49
577 591 6.462073 ACACACACGTTGATAGAACATTAC 57.538 37.500 5.01 0.00 0.00 1.89
598 612 4.652822 ACAAGAAGGTGGTAGAATTGTCC 58.347 43.478 0.00 0.00 0.00 4.02
631 645 8.918202 TTGAGACGATAAATTAATTAGGGCAT 57.082 30.769 0.01 0.00 0.00 4.40
672 838 5.517770 ACGTGCGAATAATCAAGTTAGGTAC 59.482 40.000 0.00 0.00 0.00 3.34
726 892 6.516739 TTCTATTTGTCGAGATGAGACACT 57.483 37.500 0.00 0.00 46.81 3.55
732 898 3.942115 TGTCGAGATGAGACACTAGAAGG 59.058 47.826 0.00 0.00 42.91 3.46
773 2787 8.394971 TGGAATATGTTCGATCTTGCAATATT 57.605 30.769 0.00 0.00 35.10 1.28
774 2788 8.849168 TGGAATATGTTCGATCTTGCAATATTT 58.151 29.630 0.00 0.00 35.10 1.40
819 2833 1.753903 TGGAATCCCACCAAAGGAGA 58.246 50.000 0.00 0.00 37.58 3.71
823 2837 0.332972 ATCCCACCAAAGGAGAAGCC 59.667 55.000 0.00 0.00 36.67 4.35
866 2880 2.061028 CCGTCCATTGAAAGCAAAAGC 58.939 47.619 0.00 0.00 37.59 3.51
868 2882 3.057596 CCGTCCATTGAAAGCAAAAGCTA 60.058 43.478 0.00 0.00 37.59 3.32
903 2917 3.782046 TCCGATCGAGAAGGAATTTCAC 58.218 45.455 18.66 0.00 38.31 3.18
945 2959 1.871080 CCTCGCCAAGGCTATAAGTG 58.129 55.000 9.73 0.00 38.67 3.16
946 2960 1.412710 CCTCGCCAAGGCTATAAGTGA 59.587 52.381 9.73 0.00 38.67 3.41
948 2962 3.126831 CTCGCCAAGGCTATAAGTGAAG 58.873 50.000 9.73 0.00 39.32 3.02
972 2987 2.865119 AGCACATGACAGGATGAACA 57.135 45.000 0.00 0.00 39.69 3.18
973 2988 2.430465 AGCACATGACAGGATGAACAC 58.570 47.619 0.00 0.00 39.69 3.32
974 2989 1.470098 GCACATGACAGGATGAACACC 59.530 52.381 0.00 0.00 39.69 4.16
975 2990 2.781923 CACATGACAGGATGAACACCA 58.218 47.619 0.00 0.00 39.69 4.17
1027 3065 1.371558 GGACACAAGGAGAGCGGTT 59.628 57.895 0.00 0.00 0.00 4.44
1083 3121 2.045242 AGCGCCTACTCGTCTCCA 60.045 61.111 2.29 0.00 0.00 3.86
1270 3308 4.396478 CGTATCTATCCATCGATCACCACT 59.604 45.833 0.00 0.00 0.00 4.00
1285 3323 6.017605 CGATCACCACTTACCTAACGTATACT 60.018 42.308 0.56 0.00 0.00 2.12
1286 3324 6.683974 TCACCACTTACCTAACGTATACTC 57.316 41.667 0.56 0.00 0.00 2.59
1287 3325 5.590259 TCACCACTTACCTAACGTATACTCC 59.410 44.000 0.56 0.00 0.00 3.85
1288 3326 5.591877 CACCACTTACCTAACGTATACTCCT 59.408 44.000 0.56 0.00 0.00 3.69
1289 3327 6.767902 CACCACTTACCTAACGTATACTCCTA 59.232 42.308 0.56 0.00 0.00 2.94
1290 3328 6.768381 ACCACTTACCTAACGTATACTCCTAC 59.232 42.308 0.56 0.00 0.00 3.18
1291 3329 6.205658 CCACTTACCTAACGTATACTCCTACC 59.794 46.154 0.56 0.00 0.00 3.18
1292 3330 6.205658 CACTTACCTAACGTATACTCCTACCC 59.794 46.154 0.56 0.00 0.00 3.69
1293 3331 6.101881 ACTTACCTAACGTATACTCCTACCCT 59.898 42.308 0.56 0.00 0.00 4.34
1294 3332 4.723309 ACCTAACGTATACTCCTACCCTG 58.277 47.826 0.56 0.00 0.00 4.45
1295 3333 3.505293 CCTAACGTATACTCCTACCCTGC 59.495 52.174 0.56 0.00 0.00 4.85
1296 3334 3.309600 AACGTATACTCCTACCCTGCT 57.690 47.619 0.56 0.00 0.00 4.24
1297 3335 4.443978 AACGTATACTCCTACCCTGCTA 57.556 45.455 0.56 0.00 0.00 3.49
1298 3336 4.018484 ACGTATACTCCTACCCTGCTAG 57.982 50.000 0.56 0.00 0.00 3.42
1299 3337 3.244840 ACGTATACTCCTACCCTGCTAGG 60.245 52.174 0.56 0.00 35.43 3.02
1300 3338 2.312424 ATACTCCTACCCTGCTAGGC 57.688 55.000 0.00 0.00 34.25 3.93
1301 3339 1.232909 TACTCCTACCCTGCTAGGCT 58.767 55.000 0.00 0.00 34.25 4.58
1302 3340 0.397816 ACTCCTACCCTGCTAGGCTG 60.398 60.000 0.00 0.00 34.25 4.85
1303 3341 0.105964 CTCCTACCCTGCTAGGCTGA 60.106 60.000 0.00 0.00 34.25 4.26
1304 3342 0.563173 TCCTACCCTGCTAGGCTGAT 59.437 55.000 0.00 0.00 34.25 2.90
1305 3343 1.787058 TCCTACCCTGCTAGGCTGATA 59.213 52.381 0.00 0.00 34.25 2.15
1306 3344 2.179204 TCCTACCCTGCTAGGCTGATAA 59.821 50.000 0.00 0.00 34.25 1.75
1307 3345 2.300437 CCTACCCTGCTAGGCTGATAAC 59.700 54.545 0.00 0.00 32.73 1.89
1308 3346 2.182516 ACCCTGCTAGGCTGATAACT 57.817 50.000 0.00 0.00 32.73 2.24
1309 3347 3.330126 ACCCTGCTAGGCTGATAACTA 57.670 47.619 0.00 0.00 32.73 2.24
1341 3379 4.851843 TCCATGGATCTATCATGAATGGC 58.148 43.478 11.44 0.00 43.25 4.40
1379 3418 4.083862 GCAGGTCACGGAGGGTCC 62.084 72.222 0.00 0.00 0.00 4.46
1431 3470 2.588596 CCTATGGCGCGCATCACA 60.589 61.111 34.42 21.88 0.00 3.58
1451 3490 3.704231 GAGCCATGGCCATCACGGT 62.704 63.158 33.14 12.23 43.17 4.83
1579 3618 2.956987 GCACATGCGCCTCTTTGT 59.043 55.556 4.18 0.00 0.00 2.83
1656 3704 1.946768 GGATCTGTCGAGAGGAGTGAG 59.053 57.143 10.02 0.00 0.00 3.51
2029 4078 4.807304 ACAAAGATCGTGTAGTTCGTTTGT 59.193 37.500 3.52 0.85 32.13 2.83
2171 4220 3.512329 TGCACTACAGGTATCTCCGAAAA 59.488 43.478 0.00 0.00 41.99 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 7.825761 AGTTCATCACACATGATTTGTCAGATA 59.174 33.333 0.00 0.00 43.40 1.98
3 4 6.657966 AGTTCATCACACATGATTTGTCAGAT 59.342 34.615 0.00 0.00 43.40 2.90
4 5 5.999600 AGTTCATCACACATGATTTGTCAGA 59.000 36.000 0.00 0.00 43.40 3.27
5 6 6.250344 AGTTCATCACACATGATTTGTCAG 57.750 37.500 0.00 0.00 43.40 3.51
6 7 6.638096 AAGTTCATCACACATGATTTGTCA 57.362 33.333 0.00 0.00 43.40 3.58
7 8 6.583806 GGAAAGTTCATCACACATGATTTGTC 59.416 38.462 0.00 0.00 43.40 3.18
8 9 6.040729 TGGAAAGTTCATCACACATGATTTGT 59.959 34.615 0.00 0.00 43.40 2.83
9 10 6.448852 TGGAAAGTTCATCACACATGATTTG 58.551 36.000 0.00 0.00 43.40 2.32
10 11 6.653526 TGGAAAGTTCATCACACATGATTT 57.346 33.333 0.00 0.00 43.40 2.17
11 12 6.449698 GTTGGAAAGTTCATCACACATGATT 58.550 36.000 0.00 0.00 43.40 2.57
13 14 4.278170 GGTTGGAAAGTTCATCACACATGA 59.722 41.667 0.00 0.00 39.83 3.07
14 15 4.549458 GGTTGGAAAGTTCATCACACATG 58.451 43.478 0.00 0.00 0.00 3.21
35 36 2.528564 AGAACACCAAATCATGTGGGG 58.471 47.619 0.00 0.00 45.79 4.96
44 45 5.060506 TCACACACGATTAGAACACCAAAT 58.939 37.500 0.00 0.00 0.00 2.32
47 48 3.737032 TCACACACGATTAGAACACCA 57.263 42.857 0.00 0.00 0.00 4.17
76 77 2.183636 GGAAGAAACGTCTACGCTAGC 58.816 52.381 4.06 4.06 44.43 3.42
78 79 2.440409 AGGGAAGAAACGTCTACGCTA 58.560 47.619 1.74 0.00 44.43 4.26
80 81 1.991264 GAAGGGAAGAAACGTCTACGC 59.009 52.381 1.74 0.00 44.43 4.42
95 96 7.121759 GTCATATATCCCACATGATTTGAAGGG 59.878 40.741 0.00 0.00 42.15 3.95
96 97 7.666804 TGTCATATATCCCACATGATTTGAAGG 59.333 37.037 0.00 0.00 31.74 3.46
99 100 7.879677 GTCTGTCATATATCCCACATGATTTGA 59.120 37.037 0.00 0.00 31.74 2.69
110 111 4.321304 CGTGTGAGGTCTGTCATATATCCC 60.321 50.000 0.00 0.00 0.00 3.85
111 112 4.278669 ACGTGTGAGGTCTGTCATATATCC 59.721 45.833 0.00 0.00 0.00 2.59
115 116 2.826128 ACACGTGTGAGGTCTGTCATAT 59.174 45.455 22.71 0.00 0.00 1.78
143 144 5.565592 AGCTAATGCAAACAATCAATCGA 57.434 34.783 0.00 0.00 42.74 3.59
146 147 6.531240 CGGTTAAGCTAATGCAAACAATCAAT 59.469 34.615 2.76 0.00 42.74 2.57
158 159 3.340034 TGGGTTGACGGTTAAGCTAATG 58.660 45.455 13.42 0.00 0.00 1.90
159 160 3.706600 TGGGTTGACGGTTAAGCTAAT 57.293 42.857 13.42 0.00 0.00 1.73
160 161 3.602483 GATGGGTTGACGGTTAAGCTAA 58.398 45.455 13.42 4.54 0.00 3.09
162 163 1.674817 CGATGGGTTGACGGTTAAGCT 60.675 52.381 13.42 0.00 0.00 3.74
166 167 0.671163 GTGCGATGGGTTGACGGTTA 60.671 55.000 0.00 0.00 0.00 2.85
170 171 1.581934 ATATGTGCGATGGGTTGACG 58.418 50.000 0.00 0.00 0.00 4.35
171 172 4.574828 AGTAAATATGTGCGATGGGTTGAC 59.425 41.667 0.00 0.00 0.00 3.18
172 173 4.776349 AGTAAATATGTGCGATGGGTTGA 58.224 39.130 0.00 0.00 0.00 3.18
173 174 5.525745 TGTAGTAAATATGTGCGATGGGTTG 59.474 40.000 0.00 0.00 0.00 3.77
175 176 5.284861 TGTAGTAAATATGTGCGATGGGT 57.715 39.130 0.00 0.00 0.00 4.51
176 177 6.612247 TTTGTAGTAAATATGTGCGATGGG 57.388 37.500 0.00 0.00 0.00 4.00
178 179 6.017934 AGGCTTTGTAGTAAATATGTGCGATG 60.018 38.462 0.00 0.00 0.00 3.84
179 180 6.055588 AGGCTTTGTAGTAAATATGTGCGAT 58.944 36.000 0.00 0.00 0.00 4.58
181 182 5.734855 AGGCTTTGTAGTAAATATGTGCG 57.265 39.130 0.00 0.00 0.00 5.34
197 198 3.118408 TGTGCAATAGGTCGATAGGCTTT 60.118 43.478 0.00 0.00 43.22 3.51
223 224 0.601576 TCGCACACGTTAAGGCACAT 60.602 50.000 0.00 0.00 41.18 3.21
247 250 3.097162 GGGGAGATGGGTGGGGTC 61.097 72.222 0.00 0.00 0.00 4.46
248 251 1.844296 TAAGGGGAGATGGGTGGGGT 61.844 60.000 0.00 0.00 0.00 4.95
258 261 2.335681 TGGTGTGTGATAAGGGGAGA 57.664 50.000 0.00 0.00 0.00 3.71
309 312 3.452264 TCACTACTCCAGATTGGGTCATG 59.548 47.826 0.00 0.00 38.32 3.07
322 325 3.192844 TGGTCGTCTTGAATCACTACTCC 59.807 47.826 0.00 0.00 0.00 3.85
323 326 4.436242 TGGTCGTCTTGAATCACTACTC 57.564 45.455 0.00 0.00 0.00 2.59
340 343 1.280710 TGGGGTACATCACACATGGTC 59.719 52.381 0.00 0.00 29.07 4.02
350 355 3.694566 CAGGCTAAAAGTTGGGGTACATC 59.305 47.826 0.00 0.00 0.00 3.06
357 362 2.863809 AGTGTCAGGCTAAAAGTTGGG 58.136 47.619 0.00 0.00 0.00 4.12
359 364 4.335315 TGTGAAGTGTCAGGCTAAAAGTTG 59.665 41.667 0.00 0.00 33.27 3.16
385 390 2.877097 TCTAATTGCAAGAGTGGCCA 57.123 45.000 0.00 0.00 0.00 5.36
393 398 4.930963 TGTGTGTGGTTTCTAATTGCAAG 58.069 39.130 4.94 0.00 0.00 4.01
398 403 6.215845 GCTGAAATGTGTGTGGTTTCTAATT 58.784 36.000 0.00 0.00 33.99 1.40
406 411 0.185901 AGGGCTGAAATGTGTGTGGT 59.814 50.000 0.00 0.00 0.00 4.16
407 412 2.198827 TAGGGCTGAAATGTGTGTGG 57.801 50.000 0.00 0.00 0.00 4.17
430 436 4.344104 CAACTTATTCACACCTTCCCCAT 58.656 43.478 0.00 0.00 0.00 4.00
437 450 7.504238 TGTTATGAAACCAACTTATTCACACCT 59.496 33.333 0.00 0.00 36.03 4.00
448 461 5.703592 TGTAATCGCTGTTATGAAACCAACT 59.296 36.000 0.00 0.00 34.49 3.16
484 498 5.713822 AGACAAAGTACAACAACGACTTC 57.286 39.130 0.00 0.00 32.27 3.01
505 519 6.403200 CCGTCCCTGTGTCAAAACATTATAAG 60.403 42.308 0.00 0.00 37.81 1.73
513 527 1.226746 CTCCGTCCCTGTGTCAAAAC 58.773 55.000 0.00 0.00 0.00 2.43
515 529 1.752198 CCTCCGTCCCTGTGTCAAA 59.248 57.895 0.00 0.00 0.00 2.69
518 532 2.283676 TCCCTCCGTCCCTGTGTC 60.284 66.667 0.00 0.00 0.00 3.67
520 534 1.000019 TACTCCCTCCGTCCCTGTG 60.000 63.158 0.00 0.00 0.00 3.66
521 535 1.306970 CTACTCCCTCCGTCCCTGT 59.693 63.158 0.00 0.00 0.00 4.00
522 536 0.549950 TACTACTCCCTCCGTCCCTG 59.450 60.000 0.00 0.00 0.00 4.45
523 537 0.550432 GTACTACTCCCTCCGTCCCT 59.450 60.000 0.00 0.00 0.00 4.20
524 538 0.550432 AGTACTACTCCCTCCGTCCC 59.450 60.000 0.00 0.00 0.00 4.46
525 539 1.211457 TGAGTACTACTCCCTCCGTCC 59.789 57.143 12.79 0.00 44.44 4.79
526 540 2.706339 TGAGTACTACTCCCTCCGTC 57.294 55.000 12.79 0.00 44.44 4.79
527 541 2.423088 CCATGAGTACTACTCCCTCCGT 60.423 54.545 12.79 0.00 44.44 4.69
528 542 2.158652 TCCATGAGTACTACTCCCTCCG 60.159 54.545 12.79 0.00 44.44 4.63
529 543 3.224269 GTCCATGAGTACTACTCCCTCC 58.776 54.545 12.79 0.00 44.44 4.30
530 544 2.879646 CGTCCATGAGTACTACTCCCTC 59.120 54.545 12.79 0.00 44.44 4.30
531 545 2.423088 CCGTCCATGAGTACTACTCCCT 60.423 54.545 12.79 0.00 44.44 4.20
532 546 1.955080 CCGTCCATGAGTACTACTCCC 59.045 57.143 12.79 0.00 44.44 4.30
533 547 2.652590 ACCGTCCATGAGTACTACTCC 58.347 52.381 12.79 0.00 44.44 3.85
534 548 4.034975 GTGTACCGTCCATGAGTACTACTC 59.965 50.000 9.04 9.04 45.26 2.59
535 549 3.944015 GTGTACCGTCCATGAGTACTACT 59.056 47.826 0.00 0.00 37.76 2.57
536 550 3.691118 TGTGTACCGTCCATGAGTACTAC 59.309 47.826 0.00 0.00 37.76 2.73
549 563 2.553602 TCTATCAACGTGTGTGTACCGT 59.446 45.455 0.00 0.00 35.98 4.83
562 576 7.390718 ACCACCTTCTTGTAATGTTCTATCAAC 59.609 37.037 0.00 0.00 0.00 3.18
577 591 4.651778 TGGACAATTCTACCACCTTCTTG 58.348 43.478 0.00 0.00 0.00 3.02
598 612 9.716507 AATTAATTTATCGTCTCAAACCGAATG 57.283 29.630 0.00 0.00 36.57 2.67
631 645 3.635331 CACGTACTCTCGACCTTTTTCA 58.365 45.455 0.00 0.00 34.70 2.69
672 838 3.135348 TCCACTTTCTCTATGGCCTCATG 59.865 47.826 3.32 0.00 34.96 3.07
726 892 8.473358 TCCATCTCGTTTTACATATCCTTCTA 57.527 34.615 0.00 0.00 0.00 2.10
773 2787 8.821686 TTGATATCCTTCTTTAATGCCAGAAA 57.178 30.769 0.00 0.00 0.00 2.52
774 2788 8.821686 TTTGATATCCTTCTTTAATGCCAGAA 57.178 30.769 0.00 0.00 0.00 3.02
819 2833 2.752322 TAACTGCGTACGTGCGGCTT 62.752 55.000 26.86 12.51 45.31 4.35
823 2837 0.780002 AAGTTAACTGCGTACGTGCG 59.220 50.000 22.15 22.15 37.81 5.34
866 2880 2.077627 TCGGAATCGCTAGCTAGCTAG 58.922 52.381 37.09 37.09 46.85 3.42
868 2882 1.470890 GATCGGAATCGCTAGCTAGCT 59.529 52.381 36.02 23.12 46.85 3.32
903 2917 0.242825 CACACCCAGCAAGCATCTTG 59.757 55.000 2.40 2.40 0.00 3.02
945 2959 3.273434 TCCTGTCATGTGCTAATGCTTC 58.727 45.455 0.00 0.00 40.48 3.86
946 2960 3.354948 TCCTGTCATGTGCTAATGCTT 57.645 42.857 0.00 0.00 40.48 3.91
948 2962 3.208594 TCATCCTGTCATGTGCTAATGC 58.791 45.455 0.00 0.00 40.20 3.56
1012 3050 2.671177 CGCAACCGCTCTCCTTGTG 61.671 63.158 0.00 0.00 35.30 3.33
1027 3065 1.159713 CCTCTGCTGTTTGTGTCGCA 61.160 55.000 0.00 0.00 0.00 5.10
1065 3103 2.113433 TGGAGACGAGTAGGCGCTC 61.113 63.158 7.64 0.00 35.34 5.03
1083 3121 4.157120 GCAGGGTACGCGATGGGT 62.157 66.667 15.93 0.00 0.00 4.51
1270 3308 6.299141 CAGGGTAGGAGTATACGTTAGGTAA 58.701 44.000 0.00 0.00 34.09 2.85
1285 3323 0.563173 ATCAGCCTAGCAGGGTAGGA 59.437 55.000 24.65 7.64 45.88 2.94
1286 3324 2.300437 GTTATCAGCCTAGCAGGGTAGG 59.700 54.545 17.99 17.99 45.88 3.18
1287 3325 3.235200 AGTTATCAGCCTAGCAGGGTAG 58.765 50.000 6.58 0.00 45.88 3.18
1288 3326 3.330126 AGTTATCAGCCTAGCAGGGTA 57.670 47.619 6.58 0.00 45.88 3.69
1290 3328 3.951775 CTAGTTATCAGCCTAGCAGGG 57.048 52.381 4.65 0.00 35.37 4.45
1295 3333 5.239351 TCGAGTAGCTAGTTATCAGCCTAG 58.761 45.833 1.78 0.00 39.99 3.02
1296 3334 5.224821 TCGAGTAGCTAGTTATCAGCCTA 57.775 43.478 1.78 0.00 39.99 3.93
1297 3335 4.088056 TCGAGTAGCTAGTTATCAGCCT 57.912 45.455 1.78 0.00 39.99 4.58
1298 3336 4.142556 GGATCGAGTAGCTAGTTATCAGCC 60.143 50.000 19.00 7.47 39.99 4.85
1299 3337 4.456222 TGGATCGAGTAGCTAGTTATCAGC 59.544 45.833 19.00 9.08 39.41 4.26
1300 3338 6.404184 CCATGGATCGAGTAGCTAGTTATCAG 60.404 46.154 5.56 11.82 0.00 2.90
1301 3339 5.416013 CCATGGATCGAGTAGCTAGTTATCA 59.584 44.000 5.56 9.05 0.00 2.15
1302 3340 5.648526 TCCATGGATCGAGTAGCTAGTTATC 59.351 44.000 11.44 8.99 0.00 1.75
1303 3341 5.571285 TCCATGGATCGAGTAGCTAGTTAT 58.429 41.667 11.44 0.00 0.00 1.89
1304 3342 4.981812 TCCATGGATCGAGTAGCTAGTTA 58.018 43.478 11.44 0.00 0.00 2.24
1305 3343 3.833732 TCCATGGATCGAGTAGCTAGTT 58.166 45.455 11.44 0.00 0.00 2.24
1306 3344 3.510531 TCCATGGATCGAGTAGCTAGT 57.489 47.619 11.44 0.00 0.00 2.57
1307 3345 4.630894 GATCCATGGATCGAGTAGCTAG 57.369 50.000 33.48 0.00 41.09 3.42
1341 3379 5.803118 TGCACGATCGATATTATACCGTAG 58.197 41.667 24.34 0.00 0.00 3.51
1431 3470 1.527611 CGTGATGGCCATGGCTCAT 60.528 57.895 34.70 31.78 41.60 2.90
1451 3490 1.386525 GGTGGTAGTATCCGCCGTGA 61.387 60.000 0.00 0.00 46.21 4.35
1579 3618 1.064463 CAAAGAGGCCATGCTTCCCTA 60.064 52.381 5.01 0.00 35.17 3.53
1656 3704 7.147976 GGATTTATTCCCAACATCACATTAGC 58.852 38.462 0.00 0.00 38.75 3.09
2029 4078 4.144297 ACTTGACATTGGCAAAGCTCTAA 58.856 39.130 6.37 0.00 0.00 2.10
2171 4220 8.251026 TCTCGATCCGCATAAAACAATAGATAT 58.749 33.333 0.00 0.00 0.00 1.63
2472 4521 1.983691 CTGGATACCCATGATGGCTCT 59.016 52.381 5.79 0.00 42.59 4.09


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

AutoCloner maintained by Alex Coulton.