Multiple sequence alignment - TraesCS2B01G132800

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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 TraesCS2B01G132800 chr2B 100.000 2730 0 0 1 2730 99265180 99267909 0.000000e+00 5042.0
1 TraesCS2B01G132800 chr2A 85.650 1324 76 59 3 1261 65181637 65182911 0.000000e+00 1288.0
2 TraesCS2B01G132800 chr2A 94.730 740 25 5 1312 2046 65182995 65183725 0.000000e+00 1138.0
3 TraesCS2B01G132800 chr2A 84.775 578 35 22 2177 2730 65183786 65184334 5.180000e-147 531.0
4 TraesCS2B01G132800 chr2A 88.406 69 6 2 2301 2369 551321462 551321528 6.270000e-12 82.4
5 TraesCS2B01G132800 chr2A 81.000 100 18 1 2246 2344 610997896 610997995 8.100000e-11 78.7
6 TraesCS2B01G132800 chr2D 97.243 544 13 1 1312 1855 63569714 63570255 0.000000e+00 920.0
7 TraesCS2B01G132800 chr2D 90.803 685 35 16 595 1261 63568955 63569629 0.000000e+00 891.0
8 TraesCS2B01G132800 chr2D 93.515 478 17 8 1929 2402 63570254 63570721 0.000000e+00 699.0
9 TraesCS2B01G132800 chr2D 89.871 543 31 15 1 528 63568111 63568644 0.000000e+00 676.0
10 TraesCS2B01G132800 chr2D 97.490 239 6 0 2492 2730 63570738 63570976 2.530000e-110 409.0
11 TraesCS2B01G132800 chr4D 81.944 144 25 1 1073 1216 293380799 293380941 1.330000e-23 121.0
12 TraesCS2B01G132800 chr4B 81.944 144 25 1 1073 1216 278411725 278411867 1.330000e-23 121.0
13 TraesCS2B01G132800 chr4A 81.944 144 25 1 1073 1216 231019716 231019858 1.330000e-23 121.0


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 TraesCS2B01G132800 chr2B 99265180 99267909 2729 False 5042.000000 5042 100.0000 1 2730 1 chr2B.!!$F1 2729
1 TraesCS2B01G132800 chr2A 65181637 65184334 2697 False 985.666667 1288 88.3850 3 2730 3 chr2A.!!$F3 2727
2 TraesCS2B01G132800 chr2D 63568111 63570976 2865 False 719.000000 920 93.7844 1 2730 5 chr2D.!!$F1 2729

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
103 113 0.179089 CGAGTGCTTATCTGCAGCCT 60.179 55.0 9.47 0.84 44.2 4.58 F
531 553 0.179200 GGCCGTTGTAAATGTCGCTG 60.179 55.0 0.00 0.00 0.0 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1277 1567 0.249073 GCGATCGAGCTTCTTGGCTA 60.249 55.000 21.57 0.0 43.2 3.93 R
2094 2424 1.269051 GGGAAGGCGAAACAACACTTG 60.269 52.381 0.00 0.0 0.0 3.16 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
24 26 7.588497 GCCTAAAAACAATGGAGATATCCTT 57.412 36.000 8.09 0.00 0.00 3.36
25 27 8.691661 GCCTAAAAACAATGGAGATATCCTTA 57.308 34.615 8.09 0.00 0.00 2.69
26 28 8.568794 GCCTAAAAACAATGGAGATATCCTTAC 58.431 37.037 8.09 0.00 0.00 2.34
29 31 7.553881 AAAACAATGGAGATATCCTTACACG 57.446 36.000 8.09 0.00 0.00 4.49
64 74 4.697352 ACAATAGAAGCATGTGTGTCCTTC 59.303 41.667 0.00 0.00 0.00 3.46
103 113 0.179089 CGAGTGCTTATCTGCAGCCT 60.179 55.000 9.47 0.84 44.20 4.58
126 136 1.522355 CTGAACCGGCTCGCATCAT 60.522 57.895 0.00 0.00 0.00 2.45
135 145 1.658717 CTCGCATCATCGTCGACCC 60.659 63.158 10.58 0.00 0.00 4.46
164 174 9.589461 ACCTACTACTATGCAGACTAACATATT 57.411 33.333 0.00 0.00 0.00 1.28
199 209 1.947013 CATCAGCTGCCAATAGCCG 59.053 57.895 9.47 0.00 44.76 5.52
377 389 5.700832 CACTTCTAATCCGCATTATTGCCTA 59.299 40.000 4.10 0.00 46.57 3.93
378 390 5.701290 ACTTCTAATCCGCATTATTGCCTAC 59.299 40.000 4.10 0.00 46.57 3.18
382 394 5.941948 AATCCGCATTATTGCCTACTAAC 57.058 39.130 4.10 0.00 46.57 2.34
439 460 2.545106 GCAGTTCCAAACCATGCAAAAG 59.455 45.455 0.00 0.00 34.00 2.27
487 508 6.060028 TGCACTTTTCTTGCTACTACTTTG 57.940 37.500 0.00 0.00 40.86 2.77
490 512 6.366630 CACTTTTCTTGCTACTACTTTGAGC 58.633 40.000 0.00 0.00 36.72 4.26
528 550 1.135803 CAAGGGCCGTTGTAAATGTCG 60.136 52.381 26.50 1.27 0.00 4.35
529 551 1.135939 GGGCCGTTGTAAATGTCGC 59.864 57.895 0.00 0.00 0.00 5.19
530 552 1.303091 GGGCCGTTGTAAATGTCGCT 61.303 55.000 0.00 0.00 0.00 4.93
531 553 0.179200 GGCCGTTGTAAATGTCGCTG 60.179 55.000 0.00 0.00 0.00 5.18
533 555 1.463528 GCCGTTGTAAATGTCGCTGTC 60.464 52.381 0.00 0.00 0.00 3.51
534 556 1.795872 CCGTTGTAAATGTCGCTGTCA 59.204 47.619 0.00 0.00 0.00 3.58
535 557 2.415168 CCGTTGTAAATGTCGCTGTCAT 59.585 45.455 0.00 0.00 0.00 3.06
536 558 3.407252 CGTTGTAAATGTCGCTGTCATG 58.593 45.455 0.00 0.00 0.00 3.07
537 559 3.163594 GTTGTAAATGTCGCTGTCATGC 58.836 45.455 0.00 0.00 0.00 4.06
539 561 3.073678 TGTAAATGTCGCTGTCATGCTT 58.926 40.909 0.00 0.00 0.00 3.91
541 563 2.105006 AATGTCGCTGTCATGCTTCT 57.895 45.000 0.00 0.00 0.00 2.85
542 564 2.967599 ATGTCGCTGTCATGCTTCTA 57.032 45.000 0.00 0.00 0.00 2.10
543 565 2.284263 TGTCGCTGTCATGCTTCTAG 57.716 50.000 0.00 0.00 0.00 2.43
545 567 2.029020 TGTCGCTGTCATGCTTCTAGTT 60.029 45.455 0.00 0.00 0.00 2.24
546 568 2.996621 GTCGCTGTCATGCTTCTAGTTT 59.003 45.455 0.00 0.00 0.00 2.66
548 570 2.995939 CGCTGTCATGCTTCTAGTTTGA 59.004 45.455 0.00 0.00 0.00 2.69
549 571 3.061831 CGCTGTCATGCTTCTAGTTTGAG 59.938 47.826 0.00 0.00 0.00 3.02
550 572 3.373439 GCTGTCATGCTTCTAGTTTGAGG 59.627 47.826 0.00 0.00 0.00 3.86
552 574 4.973168 TGTCATGCTTCTAGTTTGAGGTT 58.027 39.130 0.00 0.00 0.00 3.50
553 575 6.109156 TGTCATGCTTCTAGTTTGAGGTTA 57.891 37.500 0.00 0.00 0.00 2.85
554 576 6.711277 TGTCATGCTTCTAGTTTGAGGTTAT 58.289 36.000 0.00 0.00 0.00 1.89
556 578 8.318412 TGTCATGCTTCTAGTTTGAGGTTATTA 58.682 33.333 0.00 0.00 0.00 0.98
557 579 8.821894 GTCATGCTTCTAGTTTGAGGTTATTAG 58.178 37.037 0.00 0.00 0.00 1.73
575 623 5.803237 ATTAGTACTAATTAGGCACGGCT 57.197 39.130 20.27 0.00 32.21 5.52
584 632 3.620427 TTAGGCACGGCTATTTTGAGA 57.380 42.857 0.68 0.00 0.00 3.27
586 634 2.292267 AGGCACGGCTATTTTGAGATG 58.708 47.619 0.00 0.00 0.00 2.90
597 645 5.803967 GCTATTTTGAGATGGCTTTGTCTTG 59.196 40.000 0.00 0.00 31.56 3.02
618 884 1.593265 CTGAAATGGTTGGCCTGCC 59.407 57.895 3.32 6.77 35.27 4.85
634 900 1.282875 GCCGTTGGTTTCAGTGCTC 59.717 57.895 0.00 0.00 0.00 4.26
636 902 1.157870 CCGTTGGTTTCAGTGCTCGT 61.158 55.000 0.00 0.00 0.00 4.18
637 903 0.655733 CGTTGGTTTCAGTGCTCGTT 59.344 50.000 0.00 0.00 0.00 3.85
638 904 1.594518 CGTTGGTTTCAGTGCTCGTTG 60.595 52.381 0.00 0.00 0.00 4.10
639 905 1.021202 TTGGTTTCAGTGCTCGTTGG 58.979 50.000 0.00 0.00 0.00 3.77
640 906 1.282875 GGTTTCAGTGCTCGTTGGC 59.717 57.895 0.00 0.00 0.00 4.52
657 923 3.644966 TGGCGAGATGAAAATTAGGGT 57.355 42.857 0.00 0.00 0.00 4.34
659 925 4.703897 TGGCGAGATGAAAATTAGGGTAG 58.296 43.478 0.00 0.00 0.00 3.18
660 926 4.407621 TGGCGAGATGAAAATTAGGGTAGA 59.592 41.667 0.00 0.00 0.00 2.59
663 929 6.317893 GGCGAGATGAAAATTAGGGTAGAAAA 59.682 38.462 0.00 0.00 0.00 2.29
675 948 0.947180 GTAGAAAACCGCACGCAGGA 60.947 55.000 6.86 0.00 0.00 3.86
676 949 0.249953 TAGAAAACCGCACGCAGGAA 60.250 50.000 6.86 0.00 0.00 3.36
693 966 0.868406 GAAGCACTGGAACTTGGACG 59.132 55.000 0.00 0.00 0.00 4.79
696 969 2.030562 ACTGGAACTTGGACGCGG 59.969 61.111 12.47 0.00 0.00 6.46
699 972 0.673644 CTGGAACTTGGACGCGGATT 60.674 55.000 12.47 0.00 0.00 3.01
777 1050 9.907229 ATAAATGTGTTTCAAGGGGTTTTTAAA 57.093 25.926 0.00 0.00 0.00 1.52
778 1051 8.815565 AAATGTGTTTCAAGGGGTTTTTAAAT 57.184 26.923 0.00 0.00 0.00 1.40
779 1052 9.907229 AAATGTGTTTCAAGGGGTTTTTAAATA 57.093 25.926 0.00 0.00 0.00 1.40
781 1054 9.719355 ATGTGTTTCAAGGGGTTTTTAAATATC 57.281 29.630 0.00 0.00 0.00 1.63
782 1055 8.705594 TGTGTTTCAAGGGGTTTTTAAATATCA 58.294 29.630 0.00 0.00 0.00 2.15
783 1056 9.719355 GTGTTTCAAGGGGTTTTTAAATATCAT 57.281 29.630 0.00 0.00 0.00 2.45
784 1057 9.936759 TGTTTCAAGGGGTTTTTAAATATCATC 57.063 29.630 0.00 0.00 0.00 2.92
787 1060 9.540538 TTCAAGGGGTTTTTAAATATCATCTGA 57.459 29.630 0.00 0.00 0.00 3.27
825 1098 4.355549 TCCAAAAAGAGCATCATCCCAAT 58.644 39.130 0.00 0.00 37.82 3.16
844 1118 4.444022 CCAATTTGTCCTCTCTCGATCCAT 60.444 45.833 0.00 0.00 0.00 3.41
879 1153 3.660111 GCAACCACGTCACCAGCC 61.660 66.667 0.00 0.00 0.00 4.85
980 1264 0.511221 TAGCGCGCAGACAGAAAAAC 59.489 50.000 35.10 0.00 0.00 2.43
981 1265 1.160329 AGCGCGCAGACAGAAAAACT 61.160 50.000 35.10 3.94 0.00 2.66
982 1266 0.317020 GCGCGCAGACAGAAAAACTT 60.317 50.000 29.10 0.00 0.00 2.66
983 1267 1.070175 GCGCGCAGACAGAAAAACTTA 60.070 47.619 29.10 0.00 0.00 2.24
984 1268 2.601266 GCGCGCAGACAGAAAAACTTAA 60.601 45.455 29.10 0.00 0.00 1.85
993 1277 7.477733 GCAGACAGAAAAACTTAATTAGTACGC 59.522 37.037 0.00 0.00 35.54 4.42
1030 1314 0.938168 ACACTCTTCGCCGTCGTTTC 60.938 55.000 0.00 0.00 36.96 2.78
1270 1560 2.719426 GGTGTGTACAGCGTACTTCT 57.281 50.000 16.13 0.00 34.50 2.85
1271 1561 3.022607 GGTGTGTACAGCGTACTTCTT 57.977 47.619 16.13 0.00 34.50 2.52
1273 1563 3.805971 GGTGTGTACAGCGTACTTCTTTT 59.194 43.478 16.13 0.00 34.50 2.27
1274 1564 4.084693 GGTGTGTACAGCGTACTTCTTTTC 60.085 45.833 16.13 4.57 34.50 2.29
1275 1565 4.743644 GTGTGTACAGCGTACTTCTTTTCT 59.256 41.667 16.13 0.00 0.00 2.52
1277 1567 6.585322 GTGTGTACAGCGTACTTCTTTTCTAT 59.415 38.462 16.13 0.00 0.00 1.98
1278 1568 7.752239 GTGTGTACAGCGTACTTCTTTTCTATA 59.248 37.037 16.13 0.00 0.00 1.31
1279 1569 7.966753 TGTGTACAGCGTACTTCTTTTCTATAG 59.033 37.037 16.13 0.00 0.00 1.31
1280 1570 6.971184 TGTACAGCGTACTTCTTTTCTATAGC 59.029 38.462 16.13 0.00 0.00 2.97
1283 1573 5.810587 CAGCGTACTTCTTTTCTATAGCCAA 59.189 40.000 0.00 0.00 0.00 4.52
1284 1574 6.019479 CAGCGTACTTCTTTTCTATAGCCAAG 60.019 42.308 0.00 0.00 0.00 3.61
1296 1621 0.249073 TAGCCAAGAAGCTCGATCGC 60.249 55.000 11.09 0.00 43.67 4.58
1297 1622 2.864931 GCCAAGAAGCTCGATCGCG 61.865 63.158 11.09 5.24 39.35 5.87
1298 1623 1.517257 CCAAGAAGCTCGATCGCGT 60.517 57.895 11.09 0.00 38.98 6.01
1305 1630 1.078759 AGCTCGATCGCGTTTTCTGG 61.079 55.000 11.09 0.00 38.98 3.86
1307 1632 1.351430 CTCGATCGCGTTTTCTGGCA 61.351 55.000 11.09 0.00 38.98 4.92
1308 1633 0.946700 TCGATCGCGTTTTCTGGCAA 60.947 50.000 11.09 0.00 38.98 4.52
1312 1637 0.736053 TCGCGTTTTCTGGCAAGTTT 59.264 45.000 5.77 0.00 0.00 2.66
1313 1638 1.941294 TCGCGTTTTCTGGCAAGTTTA 59.059 42.857 5.77 0.00 0.00 2.01
1314 1639 2.041244 CGCGTTTTCTGGCAAGTTTAC 58.959 47.619 0.00 0.00 0.00 2.01
1316 1641 3.702330 GCGTTTTCTGGCAAGTTTACTT 58.298 40.909 0.00 0.00 36.45 2.24
1317 1642 4.553156 CGCGTTTTCTGGCAAGTTTACTTA 60.553 41.667 0.00 0.00 34.28 2.24
1318 1643 5.458015 GCGTTTTCTGGCAAGTTTACTTAT 58.542 37.500 0.00 0.00 34.28 1.73
1319 1644 5.342259 GCGTTTTCTGGCAAGTTTACTTATG 59.658 40.000 0.00 0.00 34.28 1.90
1327 1652 5.184864 TGGCAAGTTTACTTATGATTGTGGG 59.815 40.000 0.00 0.00 34.28 4.61
1331 1656 7.523052 GCAAGTTTACTTATGATTGTGGGTTCA 60.523 37.037 0.00 0.00 34.28 3.18
1792 2121 5.369685 TCGTGTGAATTACCGTGTAACTA 57.630 39.130 0.00 0.00 31.75 2.24
1806 2135 4.143326 CGTGTAACTACGAGTAGAACGACA 60.143 45.833 16.27 10.72 46.46 4.35
1862 2192 4.096231 TGATTTTGATTCCATGTAGTGCGG 59.904 41.667 0.00 0.00 0.00 5.69
1880 2210 1.737838 GGCACGACATCTCCATCAAA 58.262 50.000 0.00 0.00 0.00 2.69
1885 2215 3.748048 CACGACATCTCCATCAAACTTGT 59.252 43.478 0.00 0.00 0.00 3.16
1899 2229 5.361427 TCAAACTTGTGATGACTCCGTTAA 58.639 37.500 0.00 0.00 0.00 2.01
1910 2240 6.980978 TGATGACTCCGTTAATCTCAAGATTC 59.019 38.462 8.48 0.00 43.17 2.52
1948 2278 3.528597 TGGGTTTGTACTGCCAAAAAC 57.471 42.857 0.00 0.00 36.17 2.43
2147 2477 1.136329 AACTCTCCACCAGGGCATGT 61.136 55.000 0.00 0.00 36.21 3.21
2159 2489 0.098728 GGGCATGTGATTCCGTTTCG 59.901 55.000 0.00 0.00 0.00 3.46
2359 2701 0.615850 AGCACCTCTTCTAAGCACCC 59.384 55.000 0.00 0.00 0.00 4.61
2372 2714 2.772739 GCACCCTGCACTGTATCTG 58.227 57.895 0.00 0.00 44.26 2.90
2373 2715 0.036010 GCACCCTGCACTGTATCTGT 60.036 55.000 0.00 0.00 44.26 3.41
2374 2716 1.207089 GCACCCTGCACTGTATCTGTA 59.793 52.381 0.00 0.00 44.26 2.74
2375 2717 2.158900 GCACCCTGCACTGTATCTGTAT 60.159 50.000 0.00 0.00 44.26 2.29
2402 2744 4.289672 AGACCTAAATGGATTCACACTGGT 59.710 41.667 0.00 0.00 39.71 4.00
2403 2745 4.589908 ACCTAAATGGATTCACACTGGTC 58.410 43.478 0.00 0.00 39.71 4.02
2404 2746 4.289672 ACCTAAATGGATTCACACTGGTCT 59.710 41.667 0.00 0.00 39.71 3.85
2405 2747 5.487488 ACCTAAATGGATTCACACTGGTCTA 59.513 40.000 0.00 0.00 39.71 2.59
2407 2749 6.540189 CCTAAATGGATTCACACTGGTCTAAG 59.460 42.308 0.00 0.00 38.35 2.18
2410 2752 3.003480 GGATTCACACTGGTCTAAGCAC 58.997 50.000 0.00 0.00 0.00 4.40
2500 2854 1.134560 ACGCTATCTGTCGAAACTCCC 59.865 52.381 0.00 0.00 0.00 4.30
2675 3029 3.066900 TCTTCTTTCTAGATCCGCCTTCG 59.933 47.826 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 15 2.228343 CCGACCGTGTAAGGATATCTCC 59.772 54.545 2.05 0.00 42.43 3.71
22 24 4.159377 TGTTAAGTACCGACCGTGTAAG 57.841 45.455 0.00 0.00 0.00 2.34
23 25 4.576216 TTGTTAAGTACCGACCGTGTAA 57.424 40.909 0.00 0.00 0.00 2.41
24 26 4.782019 ATTGTTAAGTACCGACCGTGTA 57.218 40.909 0.00 0.00 0.00 2.90
25 27 3.665745 ATTGTTAAGTACCGACCGTGT 57.334 42.857 0.00 0.00 0.00 4.49
26 28 4.985413 TCTATTGTTAAGTACCGACCGTG 58.015 43.478 0.00 0.00 0.00 4.94
28 30 4.501921 GCTTCTATTGTTAAGTACCGACCG 59.498 45.833 0.00 0.00 0.00 4.79
29 31 5.413499 TGCTTCTATTGTTAAGTACCGACC 58.587 41.667 0.00 0.00 0.00 4.79
135 145 3.478509 AGTCTGCATAGTAGTAGGTCGG 58.521 50.000 0.00 0.00 0.00 4.79
164 174 2.858941 TGATGCGCGCGTACTTAAATAA 59.141 40.909 32.35 3.29 0.00 1.40
166 176 1.257936 CTGATGCGCGCGTACTTAAAT 59.742 47.619 32.35 11.35 0.00 1.40
167 177 0.643310 CTGATGCGCGCGTACTTAAA 59.357 50.000 32.35 5.73 0.00 1.52
168 178 1.748647 GCTGATGCGCGCGTACTTAA 61.749 55.000 32.35 6.65 0.00 1.85
169 179 2.228241 GCTGATGCGCGCGTACTTA 61.228 57.895 32.35 15.42 0.00 2.24
377 389 6.287589 AGCAACAGCAATACTCTAGTTAGT 57.712 37.500 0.00 0.00 0.00 2.24
378 390 6.020281 CGAAGCAACAGCAATACTCTAGTTAG 60.020 42.308 0.00 0.00 0.00 2.34
382 394 4.177026 ACGAAGCAACAGCAATACTCTAG 58.823 43.478 0.00 0.00 0.00 2.43
439 460 1.300542 GAGATGCTAGCCAGTCGCC 60.301 63.158 13.29 2.56 38.78 5.54
449 470 0.871592 GTGCATGCGTCGAGATGCTA 60.872 55.000 22.60 11.70 44.46 3.49
487 508 2.231721 GGTACTTCATAGGATCGGGCTC 59.768 54.545 0.00 0.00 0.00 4.70
490 512 3.006967 CCTTGGTACTTCATAGGATCGGG 59.993 52.174 0.00 0.00 0.00 5.14
528 550 3.373439 CCTCAAACTAGAAGCATGACAGC 59.627 47.826 0.00 0.00 0.00 4.40
529 551 4.573900 ACCTCAAACTAGAAGCATGACAG 58.426 43.478 0.00 0.00 0.00 3.51
530 552 4.623932 ACCTCAAACTAGAAGCATGACA 57.376 40.909 0.00 0.00 0.00 3.58
531 553 7.617041 AATAACCTCAAACTAGAAGCATGAC 57.383 36.000 0.00 0.00 0.00 3.06
533 555 8.723942 ACTAATAACCTCAAACTAGAAGCATG 57.276 34.615 0.00 0.00 0.00 4.06
534 556 9.819267 GTACTAATAACCTCAAACTAGAAGCAT 57.181 33.333 0.00 0.00 0.00 3.79
535 557 9.032624 AGTACTAATAACCTCAAACTAGAAGCA 57.967 33.333 0.00 0.00 0.00 3.91
546 568 8.355169 CGTGCCTAATTAGTACTAATAACCTCA 58.645 37.037 24.86 16.64 34.90 3.86
548 570 7.664758 CCGTGCCTAATTAGTACTAATAACCT 58.335 38.462 24.86 13.86 34.90 3.50
549 571 6.367149 GCCGTGCCTAATTAGTACTAATAACC 59.633 42.308 24.86 15.11 34.90 2.85
550 572 7.150640 AGCCGTGCCTAATTAGTACTAATAAC 58.849 38.462 24.86 16.92 34.90 1.89
552 574 6.906157 AGCCGTGCCTAATTAGTACTAATA 57.094 37.500 24.86 13.85 34.90 0.98
553 575 5.803237 AGCCGTGCCTAATTAGTACTAAT 57.197 39.130 20.27 20.27 37.36 1.73
554 576 6.906157 ATAGCCGTGCCTAATTAGTACTAA 57.094 37.500 17.41 17.41 0.00 2.24
556 578 5.803237 AATAGCCGTGCCTAATTAGTACT 57.197 39.130 11.50 0.00 0.00 2.73
557 579 6.480981 TCAAAATAGCCGTGCCTAATTAGTAC 59.519 38.462 11.50 8.90 0.00 2.73
567 615 1.334869 CCATCTCAAAATAGCCGTGCC 59.665 52.381 0.00 0.00 0.00 5.01
575 623 5.619757 CGCAAGACAAAGCCATCTCAAAATA 60.620 40.000 0.00 0.00 43.02 1.40
584 632 0.890542 TCAGCGCAAGACAAAGCCAT 60.891 50.000 11.47 0.00 43.02 4.40
586 634 0.030638 TTTCAGCGCAAGACAAAGCC 59.969 50.000 11.47 0.00 43.02 4.35
597 645 2.125952 GGCCAACCATTTCAGCGC 60.126 61.111 0.00 0.00 35.26 5.92
618 884 0.655733 AACGAGCACTGAAACCAACG 59.344 50.000 0.00 0.00 0.00 4.10
634 900 3.242739 CCCTAATTTTCATCTCGCCAACG 60.243 47.826 0.00 0.00 42.01 4.10
636 902 3.963129 ACCCTAATTTTCATCTCGCCAA 58.037 40.909 0.00 0.00 0.00 4.52
637 903 3.644966 ACCCTAATTTTCATCTCGCCA 57.355 42.857 0.00 0.00 0.00 5.69
638 904 4.957296 TCTACCCTAATTTTCATCTCGCC 58.043 43.478 0.00 0.00 0.00 5.54
639 905 6.920569 TTTCTACCCTAATTTTCATCTCGC 57.079 37.500 0.00 0.00 0.00 5.03
640 906 7.465513 CGGTTTTCTACCCTAATTTTCATCTCG 60.466 40.741 0.00 0.00 44.70 4.04
643 909 6.127842 TGCGGTTTTCTACCCTAATTTTCATC 60.128 38.462 0.00 0.00 44.70 2.92
650 916 2.624636 CGTGCGGTTTTCTACCCTAAT 58.375 47.619 0.00 0.00 44.70 1.73
651 917 1.940752 GCGTGCGGTTTTCTACCCTAA 60.941 52.381 0.00 0.00 44.70 2.69
657 923 0.249953 TTCCTGCGTGCGGTTTTCTA 60.250 50.000 0.00 0.00 0.00 2.10
659 925 1.082104 CTTCCTGCGTGCGGTTTTC 60.082 57.895 0.00 0.00 0.00 2.29
660 926 3.030652 CTTCCTGCGTGCGGTTTT 58.969 55.556 0.00 0.00 0.00 2.43
665 931 4.081030 CAGTGCTTCCTGCGTGCG 62.081 66.667 0.00 0.00 46.63 5.34
666 932 3.730761 CCAGTGCTTCCTGCGTGC 61.731 66.667 0.00 0.00 46.63 5.34
667 933 1.597854 TTCCAGTGCTTCCTGCGTG 60.598 57.895 0.00 0.00 46.63 5.34
668 934 1.598130 GTTCCAGTGCTTCCTGCGT 60.598 57.895 0.00 0.00 46.63 5.24
669 935 0.886490 AAGTTCCAGTGCTTCCTGCG 60.886 55.000 0.00 0.00 46.63 5.18
675 948 1.166531 GCGTCCAAGTTCCAGTGCTT 61.167 55.000 0.00 0.00 0.00 3.91
676 949 1.598130 GCGTCCAAGTTCCAGTGCT 60.598 57.895 0.00 0.00 0.00 4.40
693 966 5.438761 AATTAGGCAAATAGTCAATCCGC 57.561 39.130 0.00 0.00 0.00 5.54
699 972 7.704472 CGGCAATTTTAATTAGGCAAATAGTCA 59.296 33.333 0.00 0.00 0.00 3.41
844 1118 3.812156 TGCTGGCTCGCTTAAACTATA 57.188 42.857 1.45 0.00 0.00 1.31
879 1153 1.000938 AGAGAGCAAAAGCGCAAAAGG 60.001 47.619 11.47 0.00 0.00 3.11
980 1264 4.383052 CCATCTCTGCGCGTACTAATTAAG 59.617 45.833 8.43 0.00 0.00 1.85
981 1265 4.295870 CCATCTCTGCGCGTACTAATTAA 58.704 43.478 8.43 0.00 0.00 1.40
982 1266 3.855895 GCCATCTCTGCGCGTACTAATTA 60.856 47.826 8.43 0.00 0.00 1.40
983 1267 2.743938 CCATCTCTGCGCGTACTAATT 58.256 47.619 8.43 0.00 0.00 1.40
984 1268 1.603172 GCCATCTCTGCGCGTACTAAT 60.603 52.381 8.43 0.00 0.00 1.73
1077 1367 2.030562 AGCGTGAACACCTTCCCG 59.969 61.111 0.00 0.00 31.13 5.14
1228 1518 3.302555 TCTTGTGTATGTTGACGACGAC 58.697 45.455 0.00 0.00 0.00 4.34
1261 1551 6.040878 TCTTGGCTATAGAAAAGAAGTACGC 58.959 40.000 3.21 0.00 0.00 4.42
1262 1552 8.121167 CTTCTTGGCTATAGAAAAGAAGTACG 57.879 38.462 28.65 16.65 45.40 3.67
1269 1559 5.352284 TCGAGCTTCTTGGCTATAGAAAAG 58.648 41.667 3.21 6.25 43.20 2.27
1270 1560 5.339008 TCGAGCTTCTTGGCTATAGAAAA 57.661 39.130 3.21 0.00 43.20 2.29
1271 1561 5.533482 GATCGAGCTTCTTGGCTATAGAAA 58.467 41.667 3.21 0.00 43.20 2.52
1273 1563 3.189495 CGATCGAGCTTCTTGGCTATAGA 59.811 47.826 10.26 0.00 43.20 1.98
1274 1564 3.497118 CGATCGAGCTTCTTGGCTATAG 58.503 50.000 10.26 0.00 43.20 1.31
1275 1565 2.351835 GCGATCGAGCTTCTTGGCTATA 60.352 50.000 21.57 0.00 43.20 1.31
1277 1567 0.249073 GCGATCGAGCTTCTTGGCTA 60.249 55.000 21.57 0.00 43.20 3.93
1278 1568 1.520342 GCGATCGAGCTTCTTGGCT 60.520 57.895 21.57 0.00 46.11 4.75
1279 1569 2.864931 CGCGATCGAGCTTCTTGGC 61.865 63.158 21.57 0.00 38.10 4.52
1280 1570 1.078759 AACGCGATCGAGCTTCTTGG 61.079 55.000 21.57 0.00 39.41 3.61
1283 1573 0.992802 GAAAACGCGATCGAGCTTCT 59.007 50.000 21.57 4.47 39.41 2.85
1284 1574 0.992802 AGAAAACGCGATCGAGCTTC 59.007 50.000 21.57 20.40 39.41 3.86
1288 1578 1.345176 GCCAGAAAACGCGATCGAG 59.655 57.895 21.57 19.49 39.41 4.04
1296 1621 6.664515 TCATAAGTAAACTTGCCAGAAAACG 58.335 36.000 5.62 0.00 37.40 3.60
1297 1622 8.915654 CAATCATAAGTAAACTTGCCAGAAAAC 58.084 33.333 5.62 0.00 37.40 2.43
1298 1623 8.637986 ACAATCATAAGTAAACTTGCCAGAAAA 58.362 29.630 5.62 0.00 37.40 2.29
1305 1630 6.267496 ACCCACAATCATAAGTAAACTTGC 57.733 37.500 5.62 0.00 37.40 4.01
1307 1632 8.522830 CATGAACCCACAATCATAAGTAAACTT 58.477 33.333 0.39 0.39 39.85 2.66
1308 1633 7.362920 GCATGAACCCACAATCATAAGTAAACT 60.363 37.037 0.00 0.00 34.61 2.66
1312 1637 5.504853 TGCATGAACCCACAATCATAAGTA 58.495 37.500 0.00 0.00 34.61 2.24
1313 1638 4.343231 TGCATGAACCCACAATCATAAGT 58.657 39.130 0.00 0.00 34.61 2.24
1314 1639 4.641541 TCTGCATGAACCCACAATCATAAG 59.358 41.667 0.00 0.00 34.61 1.73
1316 1641 4.233632 TCTGCATGAACCCACAATCATA 57.766 40.909 0.00 0.00 34.61 2.15
1317 1642 3.090210 TCTGCATGAACCCACAATCAT 57.910 42.857 0.00 0.00 36.74 2.45
1318 1643 2.583024 TCTGCATGAACCCACAATCA 57.417 45.000 0.00 0.00 0.00 2.57
1319 1644 2.416431 GCTTCTGCATGAACCCACAATC 60.416 50.000 0.00 0.00 39.41 2.67
1327 1652 1.059994 CGCGAGCTTCTGCATGAAC 59.940 57.895 0.00 0.00 42.74 3.18
1331 1656 1.499056 CAAACGCGAGCTTCTGCAT 59.501 52.632 15.93 0.00 42.74 3.96
1627 1952 4.361971 AGCACGTCCTCCCCGAGA 62.362 66.667 0.00 0.00 0.00 4.04
1806 2135 3.759086 AGTCATCTGTGTCACACTACGAT 59.241 43.478 9.90 5.87 35.11 3.73
1862 2192 2.350522 AGTTTGATGGAGATGTCGTGC 58.649 47.619 0.00 0.00 0.00 5.34
1880 2210 5.047306 TGAGATTAACGGAGTCATCACAAGT 60.047 40.000 0.00 0.00 45.00 3.16
1885 2215 5.914898 TCTTGAGATTAACGGAGTCATCA 57.085 39.130 0.00 0.00 45.00 3.07
1893 2223 2.858344 ACGCGAATCTTGAGATTAACGG 59.142 45.455 15.93 12.72 44.14 4.44
1894 2224 5.807730 ATACGCGAATCTTGAGATTAACG 57.192 39.130 15.93 18.58 44.14 3.18
1922 2252 3.505386 TGGCAGTACAAACCCAAATGAT 58.495 40.909 0.00 0.00 0.00 2.45
1925 2255 4.762289 TTTTGGCAGTACAAACCCAAAT 57.238 36.364 15.35 0.00 44.22 2.32
1926 2256 4.254492 GTTTTTGGCAGTACAAACCCAAA 58.746 39.130 12.37 12.37 43.44 3.28
1927 2257 3.676324 CGTTTTTGGCAGTACAAACCCAA 60.676 43.478 0.00 0.00 39.82 4.12
1928 2258 2.159226 CGTTTTTGGCAGTACAAACCCA 60.159 45.455 0.00 0.00 39.82 4.51
1929 2259 2.159212 ACGTTTTTGGCAGTACAAACCC 60.159 45.455 0.00 0.00 39.82 4.11
1930 2260 3.153676 ACGTTTTTGGCAGTACAAACC 57.846 42.857 0.00 0.00 39.82 3.27
1996 2326 1.872952 CAACTTGCACTGATCGAACCA 59.127 47.619 0.00 0.00 0.00 3.67
2087 2417 3.543852 GGCGAAACAACACTTGCAATTTG 60.544 43.478 0.00 6.81 0.00 2.32
2094 2424 1.269051 GGGAAGGCGAAACAACACTTG 60.269 52.381 0.00 0.00 0.00 3.16
2159 2489 2.100879 AACTGTCCAGCGACCTGACC 62.101 60.000 0.00 0.00 41.77 4.02
2195 2526 2.684001 TGCGGTATGTTCCTTAGTGG 57.316 50.000 0.00 0.00 37.10 4.00
2200 2531 2.092429 ACATGGATGCGGTATGTTCCTT 60.092 45.455 0.00 0.00 31.38 3.36
2280 2622 2.696526 TGTCTCTGTAGAAGGGGTGT 57.303 50.000 0.00 0.00 32.16 4.16
2359 2701 5.980116 GGTCTTGTATACAGATACAGTGCAG 59.020 44.000 5.56 0.00 46.69 4.41
2370 2712 9.046296 GTGAATCCATTTAGGTCTTGTATACAG 57.954 37.037 5.56 1.19 39.02 2.74
2371 2713 8.544622 TGTGAATCCATTTAGGTCTTGTATACA 58.455 33.333 0.08 0.08 39.02 2.29
2372 2714 8.827677 GTGTGAATCCATTTAGGTCTTGTATAC 58.172 37.037 0.00 0.00 39.02 1.47
2373 2715 8.768397 AGTGTGAATCCATTTAGGTCTTGTATA 58.232 33.333 0.00 0.00 39.02 1.47
2374 2716 7.554118 CAGTGTGAATCCATTTAGGTCTTGTAT 59.446 37.037 0.00 0.00 39.02 2.29
2375 2717 6.878923 CAGTGTGAATCCATTTAGGTCTTGTA 59.121 38.462 0.00 0.00 39.02 2.41
2402 2744 4.777896 AGAATACAGTTCAGGGTGCTTAGA 59.222 41.667 0.00 0.00 0.00 2.10
2403 2745 4.872691 CAGAATACAGTTCAGGGTGCTTAG 59.127 45.833 0.00 0.00 0.00 2.18
2404 2746 4.530553 TCAGAATACAGTTCAGGGTGCTTA 59.469 41.667 0.00 0.00 0.00 3.09
2405 2747 3.327757 TCAGAATACAGTTCAGGGTGCTT 59.672 43.478 0.00 0.00 0.00 3.91
2407 2749 3.334583 TCAGAATACAGTTCAGGGTGC 57.665 47.619 0.00 0.00 0.00 5.01
2410 2752 4.125703 GAGCATCAGAATACAGTTCAGGG 58.874 47.826 0.00 0.00 33.17 4.45
2500 2854 8.633075 AGTCAATTGTTTTGTAATGTCAGTTG 57.367 30.769 5.13 0.00 0.00 3.16
2651 3005 2.359531 AGGCGGATCTAGAAAGAAGACG 59.640 50.000 0.00 0.00 34.73 4.18
2675 3029 0.669625 AGTGGAACGAGCTTTACGGC 60.670 55.000 0.00 0.00 45.86 5.68


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

AutoCloner maintained by Alex Coulton.