Multiple sequence alignment - TraesCS2B01G475900

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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 TraesCS2B01G475900 chr2B 100.000 2972 0 0 1 2972 672826858 672823887 0.000000e+00 5489
1 TraesCS2B01G475900 chr2B 94.183 1358 61 11 1614 2961 585753308 585754657 0.000000e+00 2054
2 TraesCS2B01G475900 chr2B 92.624 583 43 0 1 583 733998318 733998900 0.000000e+00 839
3 TraesCS2B01G475900 chr2B 89.614 674 37 14 962 1618 672636445 672637102 0.000000e+00 826
4 TraesCS2B01G475900 chr2B 84.749 459 46 14 962 1420 672776280 672775846 3.520000e-119 438
5 TraesCS2B01G475900 chr2B 84.120 466 48 10 954 1418 672668536 672668976 7.610000e-116 427
6 TraesCS2B01G475900 chr2B 82.268 485 59 17 949 1422 673050776 673051244 7.720000e-106 394
7 TraesCS2B01G475900 chr2B 89.385 179 17 2 581 759 672627366 672627542 1.070000e-54 224
8 TraesCS2B01G475900 chr2B 90.152 132 12 1 1427 1557 672796570 672796439 1.420000e-38 171
9 TraesCS2B01G475900 chr1B 96.302 1352 44 5 1612 2961 454925014 454926361 0.000000e+00 2215
10 TraesCS2B01G475900 chr1B 94.244 1355 65 8 1619 2966 115452787 115454135 0.000000e+00 2058
11 TraesCS2B01G475900 chr7B 95.932 1352 47 6 1617 2967 84110546 84109202 0.000000e+00 2185
12 TraesCS2B01G475900 chr7B 95.800 1357 46 8 1617 2972 92810703 92809357 0.000000e+00 2180
13 TraesCS2B01G475900 chr6B 95.378 1363 53 7 1617 2972 60086239 60084880 0.000000e+00 2159
14 TraesCS2B01G475900 chr6B 95.662 1337 49 7 1614 2948 144027414 144028743 0.000000e+00 2139
15 TraesCS2B01G475900 chr6B 92.796 583 42 0 1 583 719727740 719727158 0.000000e+00 845
16 TraesCS2B01G475900 chr6B 92.624 583 43 0 1 583 705177612 705177030 0.000000e+00 839
17 TraesCS2B01G475900 chr4A 94.436 1366 62 8 1613 2972 739511199 739509842 0.000000e+00 2089
18 TraesCS2B01G475900 chr4A 92.624 583 43 0 1 583 668795872 668795290 0.000000e+00 839
19 TraesCS2B01G475900 chr3B 93.654 1371 67 9 1614 2972 337214489 337215851 0.000000e+00 2032
20 TraesCS2B01G475900 chr5B 92.808 584 41 1 1 584 403154339 403154921 0.000000e+00 845
21 TraesCS2B01G475900 chr5B 92.796 583 42 0 1 583 614364337 614364919 0.000000e+00 845
22 TraesCS2B01G475900 chr5B 92.624 583 42 1 1 583 699242326 699242907 0.000000e+00 837
23 TraesCS2B01G475900 chr7A 92.624 583 43 0 1 583 540869009 540868427 0.000000e+00 839
24 TraesCS2B01G475900 chrUn 92.453 583 44 0 1 583 2576852 2576270 0.000000e+00 833
25 TraesCS2B01G475900 chr2D 86.948 498 36 8 949 1427 562587764 562588251 1.570000e-147 532
26 TraesCS2B01G475900 chr2D 86.681 473 46 9 943 1412 562839508 562839966 2.640000e-140 508
27 TraesCS2B01G475900 chr2D 85.281 462 51 10 968 1423 562807767 562808217 7.510000e-126 460
28 TraesCS2B01G475900 chr2D 84.375 480 53 11 949 1427 562845213 562845671 4.520000e-123 451
29 TraesCS2B01G475900 chr2D 84.797 467 48 10 954 1417 562753951 562754397 5.840000e-122 448
30 TraesCS2B01G475900 chr2D 86.877 381 36 6 1042 1422 562735047 562735413 5.930000e-112 414
31 TraesCS2B01G475900 chr2D 85.496 131 16 3 1427 1555 562754462 562754591 1.860000e-27 134
32 TraesCS2B01G475900 chr2D 92.308 78 6 0 682 759 562587502 562587579 8.710000e-21 111
33 TraesCS2B01G475900 chr2D 81.884 138 15 5 1427 1555 562685399 562685535 1.130000e-19 108
34 TraesCS2B01G475900 chr2A 80.873 779 62 37 648 1420 703122745 703123442 1.570000e-147 532
35 TraesCS2B01G475900 chr2A 84.134 479 52 12 949 1427 703345836 703346290 2.720000e-120 442
36 TraesCS2B01G475900 chr2A 82.171 129 15 1 1427 1555 703208590 703208710 1.460000e-18 104


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 TraesCS2B01G475900 chr2B 672823887 672826858 2971 True 5489.0 5489 100.0000 1 2972 1 chr2B.!!$R3 2971
1 TraesCS2B01G475900 chr2B 585753308 585754657 1349 False 2054.0 2054 94.1830 1614 2961 1 chr2B.!!$F1 1347
2 TraesCS2B01G475900 chr2B 733998318 733998900 582 False 839.0 839 92.6240 1 583 1 chr2B.!!$F6 582
3 TraesCS2B01G475900 chr2B 672636445 672637102 657 False 826.0 826 89.6140 962 1618 1 chr2B.!!$F3 656
4 TraesCS2B01G475900 chr1B 454925014 454926361 1347 False 2215.0 2215 96.3020 1612 2961 1 chr1B.!!$F2 1349
5 TraesCS2B01G475900 chr1B 115452787 115454135 1348 False 2058.0 2058 94.2440 1619 2966 1 chr1B.!!$F1 1347
6 TraesCS2B01G475900 chr7B 84109202 84110546 1344 True 2185.0 2185 95.9320 1617 2967 1 chr7B.!!$R1 1350
7 TraesCS2B01G475900 chr7B 92809357 92810703 1346 True 2180.0 2180 95.8000 1617 2972 1 chr7B.!!$R2 1355
8 TraesCS2B01G475900 chr6B 60084880 60086239 1359 True 2159.0 2159 95.3780 1617 2972 1 chr6B.!!$R1 1355
9 TraesCS2B01G475900 chr6B 144027414 144028743 1329 False 2139.0 2139 95.6620 1614 2948 1 chr6B.!!$F1 1334
10 TraesCS2B01G475900 chr6B 719727158 719727740 582 True 845.0 845 92.7960 1 583 1 chr6B.!!$R3 582
11 TraesCS2B01G475900 chr6B 705177030 705177612 582 True 839.0 839 92.6240 1 583 1 chr6B.!!$R2 582
12 TraesCS2B01G475900 chr4A 739509842 739511199 1357 True 2089.0 2089 94.4360 1613 2972 1 chr4A.!!$R2 1359
13 TraesCS2B01G475900 chr4A 668795290 668795872 582 True 839.0 839 92.6240 1 583 1 chr4A.!!$R1 582
14 TraesCS2B01G475900 chr3B 337214489 337215851 1362 False 2032.0 2032 93.6540 1614 2972 1 chr3B.!!$F1 1358
15 TraesCS2B01G475900 chr5B 403154339 403154921 582 False 845.0 845 92.8080 1 584 1 chr5B.!!$F1 583
16 TraesCS2B01G475900 chr5B 614364337 614364919 582 False 845.0 845 92.7960 1 583 1 chr5B.!!$F2 582
17 TraesCS2B01G475900 chr5B 699242326 699242907 581 False 837.0 837 92.6240 1 583 1 chr5B.!!$F3 582
18 TraesCS2B01G475900 chr7A 540868427 540869009 582 True 839.0 839 92.6240 1 583 1 chr7A.!!$R1 582
19 TraesCS2B01G475900 chrUn 2576270 2576852 582 True 833.0 833 92.4530 1 583 1 chrUn.!!$R1 582
20 TraesCS2B01G475900 chr2D 562587502 562588251 749 False 321.5 532 89.6280 682 1427 2 chr2D.!!$F6 745
21 TraesCS2B01G475900 chr2D 562753951 562754591 640 False 291.0 448 85.1465 954 1555 2 chr2D.!!$F7 601
22 TraesCS2B01G475900 chr2A 703122745 703123442 697 False 532.0 532 80.8730 648 1420 1 chr2A.!!$F1 772

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
366 367 0.46546 TTGAAGGTCCGCAAAGCTGT 60.465 50.0 0.0 0.0 0.0 4.40 F
1034 1095 0.17895 TCCCATCATCCTCCCTCTCG 60.179 60.0 0.0 0.0 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1460 1596 0.541863 CCGGTCCAGGTTAGAGCATT 59.458 55.0 0.00 0.00 0.0 3.56 R
2581 2736 0.792640 CAAGTCAGCTAGCACCGTTG 59.207 55.0 18.83 11.07 0.0 4.10 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
29 30 4.712122 TTTGGAAACCAGTCTGTTCAAC 57.288 40.909 0.00 0.00 33.81 3.18
107 108 3.578272 TTGCGACGGCGTTTGCTT 61.578 55.556 29.28 2.47 44.10 3.91
182 183 1.067213 TGCATCGACGACATCTGGAAA 60.067 47.619 0.00 0.00 0.00 3.13
224 225 0.743345 GGTTCGTGGATGGCAGGTAC 60.743 60.000 0.00 0.00 0.00 3.34
240 241 1.405121 GGTACGGTTTCCTTCTGCGAT 60.405 52.381 0.00 0.00 0.00 4.58
283 284 3.119291 CAGATCTGGATTTCGAAGACGG 58.881 50.000 15.38 0.00 40.21 4.79
336 337 4.578928 TCAACAGTAAGGGCTTCACTTTTC 59.421 41.667 0.00 0.00 0.00 2.29
350 351 2.354510 CACTTTTCGTGAGCCACTTTGA 59.645 45.455 4.21 0.00 46.81 2.69
366 367 0.465460 TTGAAGGTCCGCAAAGCTGT 60.465 50.000 0.00 0.00 0.00 4.40
410 411 0.755686 GCTCGGATGAGGAGGTGATT 59.244 55.000 0.00 0.00 42.79 2.57
415 416 2.632028 CGGATGAGGAGGTGATTCATCT 59.368 50.000 0.00 0.00 44.12 2.90
426 427 7.727634 AGGAGGTGATTCATCTTTCTTTTCTTT 59.272 33.333 0.00 0.00 0.00 2.52
465 466 2.285969 AGAGGCAGGTGATGGGCT 60.286 61.111 0.00 0.00 43.26 5.19
476 477 1.686052 GTGATGGGCTTTGGTGTCAAA 59.314 47.619 0.00 0.00 40.23 2.69
477 478 2.299867 GTGATGGGCTTTGGTGTCAAAT 59.700 45.455 0.00 0.00 41.45 2.32
491 492 6.768483 TGGTGTCAAATTCAGAGATGTTCTA 58.232 36.000 0.00 0.00 33.83 2.10
542 543 8.028938 GGTCCTTACGTGACTTGTACTTTAATA 58.971 37.037 0.00 0.00 33.22 0.98
602 603 6.793492 AAAATCGGCTATAGAATGAAGAGC 57.207 37.500 3.21 0.00 0.00 4.09
603 604 5.736951 AATCGGCTATAGAATGAAGAGCT 57.263 39.130 3.21 0.00 33.57 4.09
604 605 4.511617 TCGGCTATAGAATGAAGAGCTG 57.488 45.455 3.21 0.00 40.24 4.24
605 606 3.891977 TCGGCTATAGAATGAAGAGCTGT 59.108 43.478 3.21 0.00 39.91 4.40
606 607 5.070685 TCGGCTATAGAATGAAGAGCTGTA 58.929 41.667 3.21 0.00 39.91 2.74
607 608 5.712446 TCGGCTATAGAATGAAGAGCTGTAT 59.288 40.000 3.21 0.00 39.91 2.29
608 609 6.884836 TCGGCTATAGAATGAAGAGCTGTATA 59.115 38.462 3.21 0.00 39.91 1.47
609 610 7.066404 TCGGCTATAGAATGAAGAGCTGTATAG 59.934 40.741 3.21 0.00 39.91 1.31
610 611 7.066404 CGGCTATAGAATGAAGAGCTGTATAGA 59.934 40.741 3.21 0.00 35.27 1.98
611 612 8.188139 GGCTATAGAATGAAGAGCTGTATAGAC 58.812 40.741 3.21 0.00 33.57 2.59
612 613 8.956426 GCTATAGAATGAAGAGCTGTATAGACT 58.044 37.037 3.21 0.00 0.00 3.24
640 641 6.463995 TTTTTAAACTGAGTTGCATGACCT 57.536 33.333 0.00 0.00 0.00 3.85
641 642 7.575414 TTTTTAAACTGAGTTGCATGACCTA 57.425 32.000 0.00 0.00 0.00 3.08
642 643 7.759489 TTTTAAACTGAGTTGCATGACCTAT 57.241 32.000 0.00 0.00 0.00 2.57
643 644 7.759489 TTTAAACTGAGTTGCATGACCTATT 57.241 32.000 0.00 0.00 0.00 1.73
644 645 7.759489 TTAAACTGAGTTGCATGACCTATTT 57.241 32.000 0.00 0.00 0.00 1.40
645 646 6.655078 AAACTGAGTTGCATGACCTATTTT 57.345 33.333 0.00 0.00 0.00 1.82
646 647 6.655078 AACTGAGTTGCATGACCTATTTTT 57.345 33.333 0.00 0.00 0.00 1.94
675 676 8.237267 ACAATACAAAAAGCTCCTCGAATTTAG 58.763 33.333 0.00 0.00 0.00 1.85
684 685 7.365840 AGCTCCTCGAATTTAGTAACTTTTG 57.634 36.000 0.00 0.00 0.00 2.44
728 732 8.031864 TGTATTTTTGAGAGTTTTCAAGCACAA 58.968 29.630 0.00 0.00 38.25 3.33
763 767 7.195839 ACTCTTCAGAAAATAGCACAACTTC 57.804 36.000 0.00 0.00 0.00 3.01
764 768 6.767902 ACTCTTCAGAAAATAGCACAACTTCA 59.232 34.615 0.00 0.00 0.00 3.02
765 769 7.446625 ACTCTTCAGAAAATAGCACAACTTCAT 59.553 33.333 0.00 0.00 0.00 2.57
766 770 7.810658 TCTTCAGAAAATAGCACAACTTCATC 58.189 34.615 0.00 0.00 0.00 2.92
767 771 6.500684 TCAGAAAATAGCACAACTTCATCC 57.499 37.500 0.00 0.00 0.00 3.51
768 772 6.003326 TCAGAAAATAGCACAACTTCATCCA 58.997 36.000 0.00 0.00 0.00 3.41
769 773 6.072508 TCAGAAAATAGCACAACTTCATCCAC 60.073 38.462 0.00 0.00 0.00 4.02
770 774 5.769662 AGAAAATAGCACAACTTCATCCACA 59.230 36.000 0.00 0.00 0.00 4.17
771 775 6.265196 AGAAAATAGCACAACTTCATCCACAA 59.735 34.615 0.00 0.00 0.00 3.33
772 776 6.403866 AAATAGCACAACTTCATCCACAAA 57.596 33.333 0.00 0.00 0.00 2.83
773 777 6.403866 AATAGCACAACTTCATCCACAAAA 57.596 33.333 0.00 0.00 0.00 2.44
813 817 4.691860 ATAGCTCAACTTGCATCAACAC 57.308 40.909 0.00 0.00 0.00 3.32
815 819 2.954318 AGCTCAACTTGCATCAACACTT 59.046 40.909 0.00 0.00 0.00 3.16
816 820 3.004106 AGCTCAACTTGCATCAACACTTC 59.996 43.478 0.00 0.00 0.00 3.01
817 821 3.243168 GCTCAACTTGCATCAACACTTCA 60.243 43.478 0.00 0.00 0.00 3.02
818 822 4.734402 GCTCAACTTGCATCAACACTTCAA 60.734 41.667 0.00 0.00 0.00 2.69
819 823 4.671377 TCAACTTGCATCAACACTTCAAC 58.329 39.130 0.00 0.00 0.00 3.18
820 824 4.157472 TCAACTTGCATCAACACTTCAACA 59.843 37.500 0.00 0.00 0.00 3.33
825 829 2.880890 GCATCAACACTTCAACAGGACT 59.119 45.455 0.00 0.00 0.00 3.85
835 839 3.845781 TCAACAGGACTTTCAAGAGCT 57.154 42.857 0.00 0.00 0.00 4.09
892 900 2.092882 CCGGTCGTTTTCCTCTCGC 61.093 63.158 0.00 0.00 0.00 5.03
941 959 0.847670 CGTCCAACGCGCGATATTTA 59.152 50.000 39.36 13.49 33.65 1.40
948 966 1.611592 CGCGCGATATTTACCCGACC 61.612 60.000 28.94 0.00 0.00 4.79
951 969 1.287041 GCGATATTTACCCGACCCGC 61.287 60.000 0.00 0.00 34.71 6.13
1034 1095 0.178950 TCCCATCATCCTCCCTCTCG 60.179 60.000 0.00 0.00 0.00 4.04
1106 1184 2.167219 CGATAGCCACCTGCACACG 61.167 63.158 0.00 0.00 44.83 4.49
1116 1194 1.736282 CTGCACACGCGTACCATGA 60.736 57.895 13.44 0.00 42.97 3.07
1157 1235 1.870016 CTTCTTCGACGCCGAGCTC 60.870 63.158 2.73 2.73 46.39 4.09
1253 1331 2.623418 TCATGTACAGAGGGGACACT 57.377 50.000 0.33 0.00 0.00 3.55
1302 1380 3.706563 GAGATGCAGCTCGACGCCA 62.707 63.158 17.38 0.00 40.39 5.69
1304 1382 2.124983 ATGCAGCTCGACGCCATT 60.125 55.556 0.00 0.00 40.39 3.16
1379 1457 2.566529 CGTAGGCAGCGACAGTCA 59.433 61.111 0.41 0.00 0.00 3.41
1380 1458 1.080772 CGTAGGCAGCGACAGTCAA 60.081 57.895 0.41 0.00 0.00 3.18
1381 1459 1.073216 CGTAGGCAGCGACAGTCAAG 61.073 60.000 0.41 0.00 0.00 3.02
1382 1460 0.737715 GTAGGCAGCGACAGTCAAGG 60.738 60.000 0.41 0.00 0.00 3.61
1383 1461 1.185618 TAGGCAGCGACAGTCAAGGT 61.186 55.000 0.41 0.00 0.00 3.50
1384 1462 2.029844 GGCAGCGACAGTCAAGGTC 61.030 63.158 0.41 0.00 0.00 3.85
1385 1463 1.005630 GCAGCGACAGTCAAGGTCT 60.006 57.895 0.41 0.00 33.11 3.85
1386 1464 1.011451 GCAGCGACAGTCAAGGTCTC 61.011 60.000 0.41 0.00 33.11 3.36
1423 1504 3.330720 AGCTAACTGGCCGGCCTT 61.331 61.111 43.34 32.40 36.94 4.35
1449 1585 0.747255 AGAACCATCGATGTCTCCGG 59.253 55.000 23.27 9.97 0.00 5.14
1567 1704 3.313526 ACGAAGCATGGCAAGCTAATTAG 59.686 43.478 18.48 8.20 42.53 1.73
1630 1767 7.546250 TTTGAAATAGTAGGAAAATTGCCCA 57.454 32.000 0.00 0.00 0.00 5.36
1641 1778 3.058218 TTGCCCATGCGTTGCAAT 58.942 50.000 0.59 0.00 43.62 3.56
1645 1782 1.590665 CCCATGCGTTGCAATGGAA 59.409 52.632 17.22 0.00 43.62 3.53
1671 1808 7.139896 ACGTGCTATTAAAACATTGTCATGA 57.860 32.000 0.00 0.00 34.11 3.07
1689 1830 6.807720 TGTCATGATGTGAAAACATGCATAAC 59.192 34.615 0.00 0.00 40.47 1.89
1698 1841 8.886719 TGTGAAAACATGCATAACAAATGAAAA 58.113 25.926 0.00 0.00 0.00 2.29
1985 2131 3.861113 TCGAATAAAGTTGTTCGCGCTAT 59.139 39.130 15.49 0.00 46.74 2.97
1986 2132 4.327898 TCGAATAAAGTTGTTCGCGCTATT 59.672 37.500 15.49 0.00 46.74 1.73
1990 2136 7.372396 CGAATAAAGTTGTTCGCGCTATTATTT 59.628 33.333 5.56 1.21 42.95 1.40
2204 2350 8.682936 AATAGATCAGACCACCATCAATTAAC 57.317 34.615 0.00 0.00 0.00 2.01
2205 2351 6.065976 AGATCAGACCACCATCAATTAACA 57.934 37.500 0.00 0.00 0.00 2.41
2656 2816 6.980593 TGCTTGCTTGTTTGATTAACTACAT 58.019 32.000 0.00 0.00 37.64 2.29
2735 2901 3.960102 ACCACCTTTTGTGTTCATCATGT 59.040 39.130 0.00 0.00 43.85 3.21
2739 2905 6.429692 CCACCTTTTGTGTTCATCATGTACTA 59.570 38.462 0.00 0.00 43.85 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 2.588877 CCGCCACGCCATCCTTAG 60.589 66.667 0.00 0.00 0.00 2.18
48 49 1.077501 CCACCATGAGGATGCCGTT 60.078 57.895 0.00 0.00 38.69 4.44
88 89 4.307908 GCAAACGCCGTCGCAACT 62.308 61.111 6.72 0.00 39.84 3.16
182 183 0.467290 AACCCAGCACATGTTCCGTT 60.467 50.000 0.00 0.00 0.00 4.44
224 225 0.721718 GACATCGCAGAAGGAAACCG 59.278 55.000 0.00 0.00 43.58 4.44
240 241 2.642254 CCCCACCGCGACTAAGACA 61.642 63.158 8.23 0.00 0.00 3.41
272 273 2.652530 CCGGACCCGTCTTCGAAA 59.347 61.111 0.00 0.00 39.71 3.46
278 279 4.948080 AACACCCCGGACCCGTCT 62.948 66.667 0.73 0.00 37.81 4.18
336 337 0.868406 GACCTTCAAAGTGGCTCACG 59.132 55.000 0.49 0.00 39.64 4.35
346 347 0.667993 CAGCTTTGCGGACCTTCAAA 59.332 50.000 8.06 8.06 0.00 2.69
350 351 3.118408 TGATATACAGCTTTGCGGACCTT 60.118 43.478 0.00 0.00 0.00 3.50
410 411 4.895297 AGCCACCAAAGAAAAGAAAGATGA 59.105 37.500 0.00 0.00 0.00 2.92
415 416 2.765699 AGCAGCCACCAAAGAAAAGAAA 59.234 40.909 0.00 0.00 0.00 2.52
426 427 4.624364 CCACGACAGCAGCCACCA 62.624 66.667 0.00 0.00 0.00 4.17
447 448 1.919600 AAGCCCATCACCTGCCTCTC 61.920 60.000 0.00 0.00 0.00 3.20
448 449 1.504275 AAAGCCCATCACCTGCCTCT 61.504 55.000 0.00 0.00 0.00 3.69
465 466 6.547141 AGAACATCTCTGAATTTGACACCAAA 59.453 34.615 0.00 0.00 38.63 3.28
496 497 7.616313 AGGACCAACATAACAAAACTGAAAAA 58.384 30.769 0.00 0.00 0.00 1.94
510 511 4.039488 ACAAGTCACGTAAGGACCAACATA 59.961 41.667 0.00 0.00 46.39 2.29
515 516 3.225104 AGTACAAGTCACGTAAGGACCA 58.775 45.455 0.00 0.00 46.39 4.02
584 585 4.250116 ACAGCTCTTCATTCTATAGCCG 57.750 45.455 0.00 0.00 33.63 5.52
585 586 8.188139 GTCTATACAGCTCTTCATTCTATAGCC 58.812 40.741 0.00 0.00 33.63 3.93
586 587 8.956426 AGTCTATACAGCTCTTCATTCTATAGC 58.044 37.037 0.00 0.00 0.00 2.97
617 618 6.463995 AGGTCATGCAACTCAGTTTAAAAA 57.536 33.333 0.00 0.00 0.00 1.94
618 619 7.759489 ATAGGTCATGCAACTCAGTTTAAAA 57.241 32.000 0.00 0.00 0.00 1.52
619 620 7.759489 AATAGGTCATGCAACTCAGTTTAAA 57.241 32.000 0.00 0.00 0.00 1.52
620 621 7.759489 AAATAGGTCATGCAACTCAGTTTAA 57.241 32.000 0.00 0.00 0.00 1.52
621 622 7.759489 AAAATAGGTCATGCAACTCAGTTTA 57.241 32.000 0.00 0.00 0.00 2.01
622 623 6.655078 AAAATAGGTCATGCAACTCAGTTT 57.345 33.333 0.00 0.00 0.00 2.66
623 624 6.655078 AAAAATAGGTCATGCAACTCAGTT 57.345 33.333 0.00 0.00 0.00 3.16
643 644 6.695278 CGAGGAGCTTTTTGTATTGTGAAAAA 59.305 34.615 0.00 0.00 31.81 1.94
644 645 6.038825 TCGAGGAGCTTTTTGTATTGTGAAAA 59.961 34.615 0.00 0.00 0.00 2.29
645 646 5.529430 TCGAGGAGCTTTTTGTATTGTGAAA 59.471 36.000 0.00 0.00 0.00 2.69
646 647 5.060506 TCGAGGAGCTTTTTGTATTGTGAA 58.939 37.500 0.00 0.00 0.00 3.18
647 648 4.637276 TCGAGGAGCTTTTTGTATTGTGA 58.363 39.130 0.00 0.00 0.00 3.58
648 649 5.356882 TTCGAGGAGCTTTTTGTATTGTG 57.643 39.130 0.00 0.00 0.00 3.33
649 650 6.575162 AATTCGAGGAGCTTTTTGTATTGT 57.425 33.333 0.00 0.00 0.00 2.71
650 651 8.237267 ACTAAATTCGAGGAGCTTTTTGTATTG 58.763 33.333 0.00 0.00 0.00 1.90
651 652 8.336801 ACTAAATTCGAGGAGCTTTTTGTATT 57.663 30.769 0.00 0.00 0.00 1.89
652 653 7.923414 ACTAAATTCGAGGAGCTTTTTGTAT 57.077 32.000 0.00 0.00 0.00 2.29
660 661 6.935208 ACAAAAGTTACTAAATTCGAGGAGCT 59.065 34.615 0.00 0.00 0.00 4.09
661 662 7.130303 ACAAAAGTTACTAAATTCGAGGAGC 57.870 36.000 0.00 0.00 0.00 4.70
724 728 8.818141 TTCTGAAGAGTAGAAATGTAGTTGTG 57.182 34.615 0.00 0.00 31.62 3.33
783 787 9.709495 TGATGCAAGTTGAGCTATTTTTATTTT 57.291 25.926 7.16 0.00 0.00 1.82
784 788 9.709495 TTGATGCAAGTTGAGCTATTTTTATTT 57.291 25.926 7.16 0.00 0.00 1.40
785 789 9.143631 GTTGATGCAAGTTGAGCTATTTTTATT 57.856 29.630 7.16 0.00 0.00 1.40
786 790 8.306038 TGTTGATGCAAGTTGAGCTATTTTTAT 58.694 29.630 7.16 0.00 0.00 1.40
787 791 7.594758 GTGTTGATGCAAGTTGAGCTATTTTTA 59.405 33.333 7.16 0.00 0.00 1.52
788 792 6.421801 GTGTTGATGCAAGTTGAGCTATTTTT 59.578 34.615 7.16 0.00 0.00 1.94
797 801 4.157472 TGTTGAAGTGTTGATGCAAGTTGA 59.843 37.500 7.16 0.00 0.00 3.18
813 817 4.133078 AGCTCTTGAAAGTCCTGTTGAAG 58.867 43.478 0.00 0.00 0.00 3.02
815 819 3.845781 AGCTCTTGAAAGTCCTGTTGA 57.154 42.857 0.00 0.00 0.00 3.18
816 820 4.999950 ACATAGCTCTTGAAAGTCCTGTTG 59.000 41.667 0.00 0.00 0.00 3.33
817 821 5.012561 AGACATAGCTCTTGAAAGTCCTGTT 59.987 40.000 0.00 0.00 0.00 3.16
818 822 4.530161 AGACATAGCTCTTGAAAGTCCTGT 59.470 41.667 0.00 0.00 0.00 4.00
819 823 5.083533 AGACATAGCTCTTGAAAGTCCTG 57.916 43.478 0.00 0.00 0.00 3.86
820 824 4.161377 GGAGACATAGCTCTTGAAAGTCCT 59.839 45.833 0.00 0.00 35.26 3.85
825 829 3.840666 ACCAGGAGACATAGCTCTTGAAA 59.159 43.478 0.00 0.00 42.63 2.69
835 839 0.750546 CGGGTCGACCAGGAGACATA 60.751 60.000 34.40 0.00 40.22 2.29
876 884 1.014564 CCAGCGAGAGGAAAACGACC 61.015 60.000 0.00 0.00 0.00 4.79
892 900 2.125106 GGTGGTAAGCGGCTCCAG 60.125 66.667 10.42 0.00 31.54 3.86
927 943 0.248990 TCGGGTAAATATCGCGCGTT 60.249 50.000 30.98 24.41 40.19 4.84
1106 1184 1.490693 CTGATGCCGTCATGGTACGC 61.491 60.000 1.57 0.00 41.51 4.42
1253 1331 1.754621 CTCCTCGCTGCAGTAGGGA 60.755 63.158 27.13 22.47 45.08 4.20
1365 1443 2.345244 CCTTGACTGTCGCTGCCT 59.655 61.111 2.98 0.00 0.00 4.75
1379 1457 1.353091 GACACCTTCCTGGAGACCTT 58.647 55.000 0.00 0.00 39.71 3.50
1380 1458 0.900647 CGACACCTTCCTGGAGACCT 60.901 60.000 0.00 0.00 39.71 3.85
1381 1459 1.592223 CGACACCTTCCTGGAGACC 59.408 63.158 0.00 0.00 39.71 3.85
1382 1460 1.186267 ACCGACACCTTCCTGGAGAC 61.186 60.000 0.00 0.00 39.71 3.36
1383 1461 0.898789 GACCGACACCTTCCTGGAGA 60.899 60.000 0.00 0.00 39.71 3.71
1384 1462 1.592223 GACCGACACCTTCCTGGAG 59.408 63.158 0.00 0.00 39.71 3.86
1385 1463 2.273179 CGACCGACACCTTCCTGGA 61.273 63.158 0.00 0.00 39.71 3.86
1386 1464 2.261671 CGACCGACACCTTCCTGG 59.738 66.667 0.00 0.00 42.93 4.45
1423 1504 1.278985 ACATCGATGGTTCTTCAGGCA 59.721 47.619 28.09 0.00 0.00 4.75
1449 1585 2.032860 TAGAGCATTGGCCGGAGAGC 62.033 60.000 5.05 0.30 42.56 4.09
1460 1596 0.541863 CCGGTCCAGGTTAGAGCATT 59.458 55.000 0.00 0.00 0.00 3.56
1489 1625 3.349006 CGACGCCAAGCTGCACTT 61.349 61.111 1.02 0.00 40.05 3.16
1522 1659 2.045242 CTGATGCTGCTGCCCTGT 60.045 61.111 13.47 0.00 38.71 4.00
1615 1752 1.476488 ACGCATGGGCAATTTTCCTAC 59.524 47.619 10.10 0.00 41.24 3.18
1630 1767 1.269517 ACGTTTTCCATTGCAACGCAT 60.270 42.857 0.00 0.00 45.70 4.73
1641 1778 7.203910 ACAATGTTTTAATAGCACGTTTTCCA 58.796 30.769 0.00 0.00 0.00 3.53
1645 1782 8.079203 TCATGACAATGTTTTAATAGCACGTTT 58.921 29.630 0.00 0.00 35.15 3.60
1649 1786 8.800972 CACATCATGACAATGTTTTAATAGCAC 58.199 33.333 0.00 0.00 35.19 4.40
1671 1808 8.604640 TTCATTTGTTATGCATGTTTTCACAT 57.395 26.923 10.16 0.00 45.18 3.21
1689 1830 7.499232 ACGGAGGGAGTATAATCTTTTCATTTG 59.501 37.037 0.00 0.00 0.00 2.32
1698 1841 4.194678 TGGAACGGAGGGAGTATAATCT 57.805 45.455 0.00 0.00 0.00 2.40
2204 2350 6.968335 CACAATTCCATATATGTGTGTGTGTG 59.032 38.462 19.00 15.82 38.62 3.82
2205 2351 6.404623 GCACAATTCCATATATGTGTGTGTGT 60.405 38.462 24.08 13.37 43.82 3.72
2363 2516 8.103305 AGAAACATATAGCAGTCTTTCTTCCAA 58.897 33.333 0.00 0.00 0.00 3.53
2573 2728 1.539827 GCTAGCACCGTTGTGGAATTT 59.460 47.619 10.63 0.00 42.99 1.82
2581 2736 0.792640 CAAGTCAGCTAGCACCGTTG 59.207 55.000 18.83 11.07 0.00 4.10
2656 2816 2.955660 AGTGAAATCGAAAAACTGGCCA 59.044 40.909 4.71 4.71 0.00 5.36


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

AutoCloner maintained by Alex Coulton.