Multiple sequence alignment - TraesCS2B01G440500

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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 TraesCS2B01G440500 chr2B 100.000 3165 0 0 1 3165 632514433 632511269 0.000000e+00 5845
1 TraesCS2B01G440500 chr2B 87.393 817 62 16 1738 2518 632563812 632563001 0.000000e+00 900
2 TraesCS2B01G440500 chr2D 85.724 2809 239 61 1 2713 532500866 532498124 0.000000e+00 2817
3 TraesCS2B01G440500 chr2D 83.852 1511 135 64 1565 2986 532606934 532605444 0.000000e+00 1338
4 TraesCS2B01G440500 chr2D 83.645 1498 163 39 876 2329 533030040 533028581 0.000000e+00 1334
5 TraesCS2B01G440500 chr2D 89.586 749 45 11 746 1470 532607735 532606996 0.000000e+00 920
6 TraesCS2B01G440500 chr2D 88.957 489 44 8 1 485 532608688 532608206 2.100000e-166 595
7 TraesCS2B01G440500 chr2A 85.452 2509 204 65 745 3165 677039668 677037233 0.000000e+00 2462
8 TraesCS2B01G440500 chr2A 84.839 1649 143 64 1564 3125 677172129 677170501 0.000000e+00 1561
9 TraesCS2B01G440500 chr2A 84.251 1435 143 34 767 2181 677368766 677367395 0.000000e+00 1321
10 TraesCS2B01G440500 chr2A 83.119 1244 124 55 1564 2738 677100855 677099629 0.000000e+00 1055
11 TraesCS2B01G440500 chr2A 81.510 1298 175 46 1037 2308 30567659 30568917 0.000000e+00 1007
12 TraesCS2B01G440500 chr2A 88.950 733 43 10 745 1445 677069723 677068997 0.000000e+00 870
13 TraesCS2B01G440500 chr2A 87.952 747 53 21 1 734 677040435 677039713 0.000000e+00 846
14 TraesCS2B01G440500 chr2A 84.394 833 88 29 1564 2368 677068914 677068096 0.000000e+00 780
15 TraesCS2B01G440500 chr2A 84.394 833 88 29 1564 2368 677156926 677156108 0.000000e+00 780
16 TraesCS2B01G440500 chr2A 87.611 678 71 9 1 674 677173989 677173321 0.000000e+00 774
17 TraesCS2B01G440500 chr2A 86.762 627 60 11 52 674 677070713 677070106 0.000000e+00 676
18 TraesCS2B01G440500 chr2A 86.603 627 61 11 52 674 677102654 677102047 0.000000e+00 671
19 TraesCS2B01G440500 chr2A 86.284 627 63 11 52 674 677158719 677158112 0.000000e+00 660
20 TraesCS2B01G440500 chrUn 83.234 1509 131 70 1565 2986 304976516 304977989 0.000000e+00 1273
21 TraesCS2B01G440500 chrUn 83.113 1510 132 68 1565 2986 183904968 183906442 0.000000e+00 1262
22 TraesCS2B01G440500 chrUn 82.980 1510 134 68 1565 2986 235134949 235133475 0.000000e+00 1251
23 TraesCS2B01G440500 chrUn 82.980 1510 134 65 1565 2986 279914872 279916346 0.000000e+00 1251
24 TraesCS2B01G440500 chrUn 82.914 1510 135 65 1565 2986 240849407 240850881 0.000000e+00 1245
25 TraesCS2B01G440500 chrUn 82.848 1510 136 65 1565 2986 260028820 260030294 0.000000e+00 1240
26 TraesCS2B01G440500 chrUn 87.246 1035 64 23 484 1470 362478981 362479995 0.000000e+00 1118
27 TraesCS2B01G440500 chrUn 86.769 1043 62 29 484 1470 260027736 260028758 0.000000e+00 1092
28 TraesCS2B01G440500 chrUn 86.494 1044 64 28 484 1470 240848322 240849345 0.000000e+00 1075
29 TraesCS2B01G440500 chrUn 89.062 768 49 13 728 1470 183904149 183904906 0.000000e+00 920
30 TraesCS2B01G440500 chrUn 89.319 749 47 11 746 1470 235135750 235135011 0.000000e+00 909
31 TraesCS2B01G440500 chrUn 89.319 749 47 11 746 1470 277810824 277810085 0.000000e+00 909
32 TraesCS2B01G440500 chrUn 89.319 749 47 11 746 1470 395778017 395777278 0.000000e+00 909
33 TraesCS2B01G440500 chrUn 85.963 805 43 23 484 1232 397613459 397614249 0.000000e+00 797
34 TraesCS2B01G440500 chrUn 85.238 630 38 27 2390 2986 403431226 403430619 5.840000e-167 597
35 TraesCS2B01G440500 chrUn 88.477 486 46 8 1 482 183903211 183903690 2.120000e-161 579
36 TraesCS2B01G440500 chrUn 88.344 489 47 8 1 485 235136704 235136222 2.120000e-161 579
37 TraesCS2B01G440500 chrUn 88.477 486 46 8 1 482 240847653 240848132 2.120000e-161 579
38 TraesCS2B01G440500 chrUn 88.477 486 46 8 1 482 260027067 260027546 2.120000e-161 579
39 TraesCS2B01G440500 chrUn 88.344 489 47 8 1 485 277811777 277811295 2.120000e-161 579
40 TraesCS2B01G440500 chrUn 88.477 486 46 8 1 482 362478312 362478791 2.120000e-161 579
41 TraesCS2B01G440500 chrUn 88.235 255 16 6 484 735 235136035 235135792 3.090000e-75 292
42 TraesCS2B01G440500 chrUn 85.866 283 25 7 484 762 183903880 183904151 1.440000e-73 287
43 TraesCS2B01G440500 chrUn 92.473 186 11 3 2803 2986 396550631 396550447 2.420000e-66 263
44 TraesCS2B01G440500 chr5D 82.916 1358 161 42 842 2160 268934628 268933303 0.000000e+00 1157
45 TraesCS2B01G440500 chr5B 82.455 1328 176 35 869 2160 304655604 304654298 0.000000e+00 1109
46 TraesCS2B01G440500 chr5A 82.034 1347 150 49 844 2160 356594717 356593433 0.000000e+00 1062
47 TraesCS2B01G440500 chr7D 83.394 277 27 14 2807 3074 51791178 51790912 4.080000e-59 239


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 TraesCS2B01G440500 chr2B 632511269 632514433 3164 True 5845.000000 5845 100.000000 1 3165 1 chr2B.!!$R1 3164
1 TraesCS2B01G440500 chr2B 632563001 632563812 811 True 900.000000 900 87.393000 1738 2518 1 chr2B.!!$R2 780
2 TraesCS2B01G440500 chr2D 532498124 532500866 2742 True 2817.000000 2817 85.724000 1 2713 1 chr2D.!!$R1 2712
3 TraesCS2B01G440500 chr2D 533028581 533030040 1459 True 1334.000000 1334 83.645000 876 2329 1 chr2D.!!$R2 1453
4 TraesCS2B01G440500 chr2D 532605444 532608688 3244 True 951.000000 1338 87.465000 1 2986 3 chr2D.!!$R3 2985
5 TraesCS2B01G440500 chr2A 677037233 677040435 3202 True 1654.000000 2462 86.702000 1 3165 2 chr2A.!!$R2 3164
6 TraesCS2B01G440500 chr2A 677367395 677368766 1371 True 1321.000000 1321 84.251000 767 2181 1 chr2A.!!$R1 1414
7 TraesCS2B01G440500 chr2A 677170501 677173989 3488 True 1167.500000 1561 86.225000 1 3125 2 chr2A.!!$R6 3124
8 TraesCS2B01G440500 chr2A 30567659 30568917 1258 False 1007.000000 1007 81.510000 1037 2308 1 chr2A.!!$F1 1271
9 TraesCS2B01G440500 chr2A 677099629 677102654 3025 True 863.000000 1055 84.861000 52 2738 2 chr2A.!!$R4 2686
10 TraesCS2B01G440500 chr2A 677068096 677070713 2617 True 775.333333 870 86.702000 52 2368 3 chr2A.!!$R3 2316
11 TraesCS2B01G440500 chr2A 677156108 677158719 2611 True 720.000000 780 85.339000 52 2368 2 chr2A.!!$R5 2316
12 TraesCS2B01G440500 chrUn 304976516 304977989 1473 False 1273.000000 1273 83.234000 1565 2986 1 chrUn.!!$F2 1421
13 TraesCS2B01G440500 chrUn 279914872 279916346 1474 False 1251.000000 1251 82.980000 1565 2986 1 chrUn.!!$F1 1421
14 TraesCS2B01G440500 chrUn 260027067 260030294 3227 False 970.333333 1240 86.031333 1 2986 3 chrUn.!!$F6 2985
15 TraesCS2B01G440500 chrUn 240847653 240850881 3228 False 966.333333 1245 85.961667 1 2986 3 chrUn.!!$F5 2985
16 TraesCS2B01G440500 chrUn 395777278 395778017 739 True 909.000000 909 89.319000 746 1470 1 chrUn.!!$R1 724
17 TraesCS2B01G440500 chrUn 362478312 362479995 1683 False 848.500000 1118 87.861500 1 1470 2 chrUn.!!$F7 1469
18 TraesCS2B01G440500 chrUn 397613459 397614249 790 False 797.000000 797 85.963000 484 1232 1 chrUn.!!$F3 748
19 TraesCS2B01G440500 chrUn 183903211 183906442 3231 False 762.000000 1262 86.629500 1 2986 4 chrUn.!!$F4 2985
20 TraesCS2B01G440500 chrUn 235133475 235136704 3229 True 757.750000 1251 87.219500 1 2986 4 chrUn.!!$R4 2985
21 TraesCS2B01G440500 chrUn 277810085 277811777 1692 True 744.000000 909 88.831500 1 1470 2 chrUn.!!$R5 1469
22 TraesCS2B01G440500 chrUn 403430619 403431226 607 True 597.000000 597 85.238000 2390 2986 1 chrUn.!!$R3 596
23 TraesCS2B01G440500 chr5D 268933303 268934628 1325 True 1157.000000 1157 82.916000 842 2160 1 chr5D.!!$R1 1318
24 TraesCS2B01G440500 chr5B 304654298 304655604 1306 True 1109.000000 1109 82.455000 869 2160 1 chr5B.!!$R1 1291
25 TraesCS2B01G440500 chr5A 356593433 356594717 1284 True 1062.000000 1062 82.034000 844 2160 1 chr5A.!!$R1 1316

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
353 372 0.601841 CGTCCTTGTGTTTAGCGGGT 60.602 55.0 0.00 0.0 0.00 5.28 F
1624 2301 0.179108 GGCTCGTAAAGATCGCCACT 60.179 55.0 1.17 0.0 39.32 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1856 2539 0.609957 TCCTGCAACTTGCCCTCATG 60.610 55.000 11.29 0.00 44.23 3.07 R
2465 3247 1.277739 CGACGATCCATGCATGTGC 59.722 57.895 24.58 12.36 42.50 4.57 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
83 96 6.850752 AAAGAAAAAGGAAACCAGACTGAA 57.149 33.333 3.32 0.00 0.00 3.02
100 113 4.147321 ACTGAAAGGATGCACAACAAGAT 58.853 39.130 0.00 0.00 39.30 2.40
148 162 0.886490 GTGAGCTGTCCCAGTTGGTG 60.886 60.000 0.00 0.00 33.43 4.17
201 215 5.122239 TGGAGTTTGAATTCTACTTCATGCG 59.878 40.000 14.56 0.00 35.20 4.73
251 268 8.812972 AGAAGATAAACACTACTCCATGTACAA 58.187 33.333 0.00 0.00 0.00 2.41
313 331 8.991783 ATGACCATCATTGTCTTTCTTATGAT 57.008 30.769 0.00 0.00 38.03 2.45
353 372 0.601841 CGTCCTTGTGTTTAGCGGGT 60.602 55.000 0.00 0.00 0.00 5.28
375 394 5.298276 GGTGTGTACCAAATCAGAAGTGAAA 59.702 40.000 0.00 0.00 46.71 2.69
408 427 7.176589 TGTTTGACATTTTTGGTACTTTCCT 57.823 32.000 0.00 0.00 0.00 3.36
413 432 6.039270 TGACATTTTTGGTACTTTCCTGTGAG 59.961 38.462 0.00 0.00 0.00 3.51
482 506 5.512788 CCGTGCACATTTTCTTGCTTTATAG 59.487 40.000 18.64 0.00 39.62 1.31
485 509 7.216317 CGTGCACATTTTCTTGCTTTATAGTAC 59.784 37.037 18.64 0.00 39.62 2.73
486 510 8.237267 GTGCACATTTTCTTGCTTTATAGTACT 58.763 33.333 13.17 0.00 39.62 2.73
559 774 8.830580 CATGTATTTTGTCGTTCTCCTATGAAT 58.169 33.333 0.00 0.00 0.00 2.57
568 783 9.244292 TGTCGTTCTCCTATGAATATATAAGCT 57.756 33.333 0.00 0.00 0.00 3.74
601 817 1.016627 CACCACATACATCGGCCAAG 58.983 55.000 2.24 0.00 0.00 3.61
605 821 1.867233 CACATACATCGGCCAAGCTAC 59.133 52.381 2.24 0.00 0.00 3.58
708 1201 0.679002 ATGCATGTGGACAGAGCACC 60.679 55.000 0.00 0.00 41.41 5.01
735 1228 1.253100 GCCATCGGGGAAACAAGAAA 58.747 50.000 0.00 0.00 40.01 2.52
737 1230 2.036604 GCCATCGGGGAAACAAGAAAAA 59.963 45.455 0.00 0.00 40.01 1.94
761 1304 7.707774 AAAACTCGAGAAGAAGAAGAAGAAG 57.292 36.000 21.68 0.00 0.00 2.85
765 1308 3.984633 CGAGAAGAAGAAGAAGAAGCGTT 59.015 43.478 0.00 0.00 0.00 4.84
798 1341 1.140452 CATCCATGGACTCCCAGTCAG 59.860 57.143 18.99 0.00 46.79 3.51
866 1409 3.454375 GAAAAGTATGGAATCCGCTCGA 58.546 45.455 0.00 0.00 0.00 4.04
938 1494 2.073056 CATGGTTGCTACGTGTGCTTA 58.927 47.619 14.67 2.88 0.00 3.09
963 1519 0.793861 TCGCTCGTAAACCATTGCAC 59.206 50.000 0.00 0.00 0.00 4.57
980 1537 1.335689 GCACTGCAAGAAGAAGCAAGG 60.336 52.381 0.00 0.00 40.73 3.61
1010 1575 1.832411 GCTAGCTTAATGGCGCCGAC 61.832 60.000 23.90 7.01 37.29 4.79
1276 1865 1.975407 TTCTCCGACCTCACCGACC 60.975 63.158 0.00 0.00 0.00 4.79
1379 1977 2.079925 GAACATGTCCAAGGCTCAGTC 58.920 52.381 0.00 0.00 0.00 3.51
1410 2008 1.666011 GGACAGCGTTGACTGGAGA 59.334 57.895 6.16 0.00 42.21 3.71
1471 2074 2.991250 ACTGCGGTAAGATTCTGCATT 58.009 42.857 0.00 0.00 44.52 3.56
1473 2076 3.127548 ACTGCGGTAAGATTCTGCATTTG 59.872 43.478 0.00 0.00 44.52 2.32
1509 2173 3.871594 AGAGCATATACCAAAGTTCGCAC 59.128 43.478 0.00 0.00 0.00 5.34
1526 2192 3.376859 TCGCACATGAATAAATGTCCACC 59.623 43.478 0.00 0.00 38.75 4.61
1527 2193 3.128415 CGCACATGAATAAATGTCCACCA 59.872 43.478 0.00 0.00 38.75 4.17
1528 2194 4.380339 CGCACATGAATAAATGTCCACCAA 60.380 41.667 0.00 0.00 38.75 3.67
1529 2195 4.864247 GCACATGAATAAATGTCCACCAAC 59.136 41.667 0.00 0.00 38.75 3.77
1531 2197 6.632909 CACATGAATAAATGTCCACCAACAT 58.367 36.000 0.00 0.00 38.75 2.71
1533 2199 7.276218 CACATGAATAAATGTCCACCAACATTC 59.724 37.037 0.00 0.00 46.49 2.67
1536 2202 7.377398 TGAATAAATGTCCACCAACATTCAAG 58.623 34.615 3.00 0.00 46.49 3.02
1541 2207 5.667539 TGTCCACCAACATTCAAGAAAAA 57.332 34.783 0.00 0.00 0.00 1.94
1624 2301 0.179108 GGCTCGTAAAGATCGCCACT 60.179 55.000 1.17 0.00 39.32 4.00
1657 2334 0.743701 CCATGTCAGAGCAGCAGGTC 60.744 60.000 0.00 0.00 42.53 3.85
1887 2570 4.704833 GCAGGAGCTCGTGGCCAA 62.705 66.667 31.40 0.00 43.05 4.52
1925 2608 1.675219 GTGGAGGCCACGGAGTTTA 59.325 57.895 5.01 0.00 44.95 2.01
1993 2676 1.598130 GCAGAACCTGAACCACGCT 60.598 57.895 0.00 0.00 32.44 5.07
1999 2682 1.961277 CCTGAACCACGCTGTGACC 60.961 63.158 9.75 0.98 35.23 4.02
2152 2835 0.262580 ACGCCTACTACCCCACCATA 59.737 55.000 0.00 0.00 0.00 2.74
2176 2859 4.632153 ACAGCTCTTAAACACCAGTACTG 58.368 43.478 16.34 16.34 0.00 2.74
2184 2876 1.267121 ACACCAGTACTGCTACCAGG 58.733 55.000 17.86 4.45 43.53 4.45
2276 3002 7.063426 GCAGCTGCAGACGTATATATGAATTTA 59.937 37.037 33.36 0.00 41.59 1.40
2572 3368 6.885952 TTTCCTAATTCAATGAAACGGACA 57.114 33.333 0.00 0.00 0.00 4.02
2598 3394 2.445145 TCAATGTTCTTCCCTTGTCCCA 59.555 45.455 0.00 0.00 0.00 4.37
2605 3401 0.938192 TTCCCTTGTCCCACCCTTTT 59.062 50.000 0.00 0.00 0.00 2.27
2671 3467 9.961265 CACAAATCTGCATCATCTATATTTGTT 57.039 29.630 0.00 0.00 41.56 2.83
2691 3492 6.446781 TGTTTCGTATTACCTCTACAGGAG 57.553 41.667 0.00 0.00 43.65 3.69
2694 3495 4.726583 TCGTATTACCTCTACAGGAGCAT 58.273 43.478 0.00 0.00 43.65 3.79
2695 3496 4.760715 TCGTATTACCTCTACAGGAGCATC 59.239 45.833 0.00 0.00 43.65 3.91
2713 3518 7.343833 AGGAGCATCTTTTCATCAAAATGGTAT 59.656 33.333 0.00 0.00 30.91 2.73
2773 3580 8.415553 TGAACATGTGACTGAATTCTCATTTTT 58.584 29.630 7.05 0.00 29.28 1.94
2829 3655 1.021202 TGCCGGTGACTTTCTTGTTG 58.979 50.000 1.90 0.00 0.00 3.33
2872 3698 4.454728 TGATGATCATGTTCACTCACGA 57.545 40.909 14.30 0.00 0.00 4.35
2889 3715 1.802960 ACGAGAGCTTTGCTGAATGTG 59.197 47.619 0.00 0.00 39.88 3.21
2904 3731 6.538021 TGCTGAATGTGTTTTTAGTTGCATTT 59.462 30.769 0.00 0.00 0.00 2.32
2905 3732 6.847289 GCTGAATGTGTTTTTAGTTGCATTTG 59.153 34.615 0.00 0.00 0.00 2.32
2906 3733 6.713520 TGAATGTGTTTTTAGTTGCATTTGC 58.286 32.000 0.00 0.00 42.50 3.68
2908 3735 6.923928 ATGTGTTTTTAGTTGCATTTGCTT 57.076 29.167 3.94 0.00 42.66 3.91
2909 3736 6.104439 TGTGTTTTTAGTTGCATTTGCTTG 57.896 33.333 3.94 0.00 42.66 4.01
2910 3737 5.871524 TGTGTTTTTAGTTGCATTTGCTTGA 59.128 32.000 3.94 0.00 42.66 3.02
2911 3738 6.538021 TGTGTTTTTAGTTGCATTTGCTTGAT 59.462 30.769 3.94 0.00 42.66 2.57
2967 3794 8.998377 GTCACATACATATGCCAATATACACAA 58.002 33.333 1.58 0.00 37.19 3.33
2990 3817 0.808755 AAGCCTCCGGTAATTTTGCG 59.191 50.000 0.00 0.00 0.00 4.85
3014 3855 9.520204 GCGTACTATTATGTTTTTAGTAGGTCA 57.480 33.333 0.00 0.00 36.98 4.02
3155 3996 1.514678 GGAGTGCATTGCGTGGTCAA 61.515 55.000 3.84 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 94 4.771590 TCATCTTGTTGTGCATCCTTTC 57.228 40.909 0.00 0.00 0.00 2.62
83 96 6.839124 TTATTCATCTTGTTGTGCATCCTT 57.161 33.333 0.00 0.00 0.00 3.36
148 162 2.041206 GATCCCTTCCACCCGCTACC 62.041 65.000 0.00 0.00 0.00 3.18
263 280 4.600012 TTATAAACTCTTTGCTCGCTGC 57.400 40.909 0.00 0.00 43.25 5.25
299 317 5.690097 GCCATACCCCATCATAAGAAAGACA 60.690 44.000 0.00 0.00 0.00 3.41
300 318 4.762251 GCCATACCCCATCATAAGAAAGAC 59.238 45.833 0.00 0.00 0.00 3.01
301 319 4.665009 AGCCATACCCCATCATAAGAAAGA 59.335 41.667 0.00 0.00 0.00 2.52
313 331 3.433031 CGACTCAAATTAGCCATACCCCA 60.433 47.826 0.00 0.00 0.00 4.96
315 333 3.805207 ACGACTCAAATTAGCCATACCC 58.195 45.455 0.00 0.00 0.00 3.69
353 372 7.581213 AATTTCACTTCTGATTTGGTACACA 57.419 32.000 0.00 0.00 39.29 3.72
391 410 5.010012 AGCTCACAGGAAAGTACCAAAAATG 59.990 40.000 0.00 0.00 0.00 2.32
398 417 7.916914 TTATAAAAGCTCACAGGAAAGTACC 57.083 36.000 0.00 0.00 0.00 3.34
456 480 0.597118 GCAAGAAAATGTGCACGGCA 60.597 50.000 13.13 0.00 40.58 5.69
482 506 8.627403 TGGTAGATACAGCAAATGTACTAGTAC 58.373 37.037 23.58 23.58 47.00 2.73
485 509 7.489160 TGTGGTAGATACAGCAAATGTACTAG 58.511 38.462 0.00 0.00 47.00 2.57
486 510 7.412853 TGTGGTAGATACAGCAAATGTACTA 57.587 36.000 0.00 0.00 47.00 1.82
530 745 4.935808 AGGAGAACGACAAAATACATGACC 59.064 41.667 0.00 0.00 0.00 4.02
559 774 9.991906 GGTGTGGATTACAAGTTAGCTTATATA 57.008 33.333 0.00 0.00 41.89 0.86
568 783 6.770542 TGTATGTGGTGTGGATTACAAGTTA 58.229 36.000 0.00 0.00 41.89 2.24
582 798 1.016627 CTTGGCCGATGTATGTGGTG 58.983 55.000 0.00 0.00 0.00 4.17
601 817 1.825474 TGCAGTACTCTCCCAAGTAGC 59.175 52.381 0.00 0.00 32.52 3.58
605 821 0.737715 GCGTGCAGTACTCTCCCAAG 60.738 60.000 0.00 0.00 0.00 3.61
737 1230 6.201997 GCTTCTTCTTCTTCTTCTCGAGTTTT 59.798 38.462 13.13 0.00 0.00 2.43
738 1231 5.694458 GCTTCTTCTTCTTCTTCTCGAGTTT 59.306 40.000 13.13 0.00 0.00 2.66
739 1232 5.227152 GCTTCTTCTTCTTCTTCTCGAGTT 58.773 41.667 13.13 0.00 0.00 3.01
740 1233 4.614993 CGCTTCTTCTTCTTCTTCTCGAGT 60.615 45.833 13.13 0.00 0.00 4.18
741 1234 3.851403 CGCTTCTTCTTCTTCTTCTCGAG 59.149 47.826 5.93 5.93 0.00 4.04
744 1237 4.747605 ACAACGCTTCTTCTTCTTCTTCTC 59.252 41.667 0.00 0.00 0.00 2.87
745 1238 4.698575 ACAACGCTTCTTCTTCTTCTTCT 58.301 39.130 0.00 0.00 0.00 2.85
748 1241 3.053455 CGACAACGCTTCTTCTTCTTCT 58.947 45.455 0.00 0.00 0.00 2.85
749 1242 2.155924 CCGACAACGCTTCTTCTTCTTC 59.844 50.000 0.00 0.00 38.29 2.87
755 1298 2.602878 TGTATCCGACAACGCTTCTTC 58.397 47.619 0.00 0.00 34.15 2.87
798 1341 1.847027 GCCGTAGTCGAACGTACGTAC 60.847 57.143 23.12 16.30 40.33 3.67
938 1494 1.171308 TGGTTTACGAGCGAGCTAGT 58.829 50.000 14.67 14.67 36.03 2.57
963 1519 3.317430 AGTTTCCTTGCTTCTTCTTGCAG 59.683 43.478 0.00 0.00 40.46 4.41
1276 1865 3.755404 CGTCTCCGCGAACTCTTG 58.245 61.111 8.23 0.00 0.00 3.02
1332 1921 1.374125 CATCGGCGTGTTGTCCTCA 60.374 57.895 6.85 0.00 0.00 3.86
1488 2091 3.621268 TGTGCGAACTTTGGTATATGCTC 59.379 43.478 0.00 0.00 0.00 4.26
1495 2115 6.561737 TTTATTCATGTGCGAACTTTGGTA 57.438 33.333 0.00 0.00 0.00 3.25
1496 2160 5.446143 TTTATTCATGTGCGAACTTTGGT 57.554 34.783 0.00 0.00 0.00 3.67
1541 2207 7.122650 CCCTGTAAGTGTGGTCATTTATTCATT 59.877 37.037 0.00 0.00 30.69 2.57
1542 2208 6.603201 CCCTGTAAGTGTGGTCATTTATTCAT 59.397 38.462 0.00 0.00 30.69 2.57
1543 2209 5.943416 CCCTGTAAGTGTGGTCATTTATTCA 59.057 40.000 0.00 0.00 30.69 2.57
1544 2210 6.177610 TCCCTGTAAGTGTGGTCATTTATTC 58.822 40.000 0.00 0.00 30.69 1.75
1545 2211 6.134535 TCCCTGTAAGTGTGGTCATTTATT 57.865 37.500 0.00 0.00 30.69 1.40
1546 2212 5.250774 ACTCCCTGTAAGTGTGGTCATTTAT 59.749 40.000 0.00 0.00 30.69 1.40
1547 2213 4.595781 ACTCCCTGTAAGTGTGGTCATTTA 59.404 41.667 0.00 0.00 0.00 1.40
1548 2214 3.394606 ACTCCCTGTAAGTGTGGTCATTT 59.605 43.478 0.00 0.00 0.00 2.32
1549 2215 2.979678 ACTCCCTGTAAGTGTGGTCATT 59.020 45.455 0.00 0.00 0.00 2.57
1550 2216 2.621070 ACTCCCTGTAAGTGTGGTCAT 58.379 47.619 0.00 0.00 0.00 3.06
1551 2217 2.097110 ACTCCCTGTAAGTGTGGTCA 57.903 50.000 0.00 0.00 0.00 4.02
1552 2218 2.767505 CAACTCCCTGTAAGTGTGGTC 58.232 52.381 0.00 0.00 0.00 4.02
1553 2219 1.202770 GCAACTCCCTGTAAGTGTGGT 60.203 52.381 0.00 0.00 0.00 4.16
1554 2220 1.072331 AGCAACTCCCTGTAAGTGTGG 59.928 52.381 0.00 0.00 0.00 4.17
1560 2237 1.378762 GCCCAGCAACTCCCTGTAA 59.621 57.895 0.00 0.00 0.00 2.41
1624 2301 2.506644 TGACATGGAGATGAGATTGCCA 59.493 45.455 0.00 0.00 33.36 4.92
1630 2307 2.694109 CTGCTCTGACATGGAGATGAGA 59.306 50.000 0.00 0.00 33.36 3.27
1697 2374 1.387084 GCTTAGAGCTTCGTTGACACG 59.613 52.381 0.00 0.00 42.33 4.49
1711 2388 1.008881 CGCGGCGATGTAGCTTAGA 60.009 57.895 19.16 0.00 37.29 2.10
1856 2539 0.609957 TCCTGCAACTTGCCCTCATG 60.610 55.000 11.29 0.00 44.23 3.07
1865 2548 1.302033 CCACGAGCTCCTGCAACTT 60.302 57.895 8.47 0.00 42.74 2.66
1866 2549 2.345244 CCACGAGCTCCTGCAACT 59.655 61.111 8.47 0.00 42.74 3.16
1921 2604 3.998341 TCATGTAGTGCCGGAAGTTAAAC 59.002 43.478 5.05 0.00 0.00 2.01
1925 2608 1.676014 GCTCATGTAGTGCCGGAAGTT 60.676 52.381 5.05 0.00 0.00 2.66
1993 2676 2.122945 TACCCCACCACGGTCACA 60.123 61.111 0.00 0.00 34.66 3.58
2152 2835 4.589374 AGTACTGGTGTTTAAGAGCTGTCT 59.411 41.667 7.05 3.37 32.81 3.41
2176 2859 2.695314 GCATGTACTGCCTGGTAGC 58.305 57.895 12.02 0.00 45.66 3.58
2184 2876 4.091075 CATACTCGATGATGCATGTACTGC 59.909 45.833 2.46 9.52 43.98 4.40
2276 3002 6.322201 ACGAGGATCCATGCTTTATTCAAAAT 59.678 34.615 15.82 0.00 0.00 1.82
2373 3112 1.929836 CTAGCCAACACTCGATGCTTC 59.070 52.381 0.00 0.00 33.63 3.86
2465 3247 1.277739 CGACGATCCATGCATGTGC 59.722 57.895 24.58 12.36 42.50 4.57
2572 3368 5.003096 ACAAGGGAAGAACATTGAGGAAT 57.997 39.130 0.00 0.00 0.00 3.01
2591 3387 2.838637 AAGACAAAAGGGTGGGACAA 57.161 45.000 0.00 0.00 44.16 3.18
2598 3394 2.893489 GGCATGAGAAAGACAAAAGGGT 59.107 45.455 0.00 0.00 0.00 4.34
2605 3401 1.347707 AGAACGGGCATGAGAAAGACA 59.652 47.619 0.00 0.00 0.00 3.41
2671 3467 4.529897 TGCTCCTGTAGAGGTAATACGAA 58.470 43.478 5.71 0.00 43.46 3.85
2691 3492 7.437267 CCTCATACCATTTTGATGAAAAGATGC 59.563 37.037 0.00 0.00 34.53 3.91
2694 3495 6.664816 AGCCTCATACCATTTTGATGAAAAGA 59.335 34.615 0.00 0.00 34.53 2.52
2695 3496 6.870769 AGCCTCATACCATTTTGATGAAAAG 58.129 36.000 0.00 0.00 34.53 2.27
2713 3518 1.890876 AATGTTGCAACGTAGCCTCA 58.109 45.000 24.02 4.62 0.00 3.86
2793 3602 3.930400 CATGCATGCACGCAATACT 57.070 47.368 25.37 0.38 46.87 2.12
2819 3645 5.842327 GCGATGCAAAAATTCAACAAGAAAG 59.158 36.000 0.00 0.00 40.22 2.62
2872 3698 4.660789 AAAACACATTCAGCAAAGCTCT 57.339 36.364 0.00 0.00 36.40 4.09
2908 3735 9.494271 GCACTCAAATAGTCCTATCAATTATCA 57.506 33.333 0.00 0.00 35.76 2.15
2909 3736 9.494271 TGCACTCAAATAGTCCTATCAATTATC 57.506 33.333 0.00 0.00 35.76 1.75
2911 3738 9.276590 CATGCACTCAAATAGTCCTATCAATTA 57.723 33.333 0.00 0.00 35.76 1.40
3134 3975 1.915614 GACCACGCAATGCACTCCAG 61.916 60.000 5.91 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.