Multiple sequence alignment - TraesCS3A01G225400

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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 TraesCS3A01G225400 chr3A 100.000 2426 0 0 1 2426 422737070 422739495 0.000000e+00 4481.0
1 TraesCS3A01G225400 chr3A 89.066 1189 87 15 571 1757 288745730 288746877 0.000000e+00 1435.0
2 TraesCS3A01G225400 chr3A 90.435 690 59 7 1742 2426 451701381 451702068 0.000000e+00 902.0
3 TraesCS3A01G225400 chr3A 88.040 694 72 10 1731 2418 678282597 678281909 0.000000e+00 811.0
4 TraesCS3A01G225400 chr3A 87.064 688 78 10 1745 2426 678274708 678274026 0.000000e+00 767.0
5 TraesCS3A01G225400 chr3A 90.342 497 42 6 1 493 316611503 316611997 0.000000e+00 647.0
6 TraesCS3A01G225400 chr3A 90.342 497 40 8 1 493 316591868 316592360 0.000000e+00 645.0
7 TraesCS3A01G225400 chr3A 89.608 510 44 9 1 503 50143705 50143198 7.310000e-180 640.0
8 TraesCS3A01G225400 chr3A 89.538 411 39 4 1283 1691 400954697 400955105 3.580000e-143 518.0
9 TraesCS3A01G225400 chr3A 87.013 385 44 5 251 634 286485836 286486215 1.720000e-116 429.0
10 TraesCS3A01G225400 chr3A 86.047 387 38 12 251 631 286478210 286478586 3.760000e-108 401.0
11 TraesCS3A01G225400 chr3A 90.244 287 28 0 1441 1727 166611336 166611622 2.280000e-100 375.0
12 TraesCS3A01G225400 chr3A 89.895 287 29 0 1441 1727 166619265 166619551 1.060000e-98 370.0
13 TraesCS3A01G225400 chr3A 90.604 149 13 1 1543 1691 144421385 144421532 1.900000e-46 196.0
14 TraesCS3A01G225400 chr3A 96.552 58 2 0 1707 1764 353634804 353634747 1.990000e-16 97.1
15 TraesCS3A01G225400 chr3A 94.828 58 3 0 1707 1764 283417782 283417725 9.240000e-15 91.6
16 TraesCS3A01G225400 chr3A 90.000 70 5 2 1163 1231 251704064 251704132 3.320000e-14 89.8
17 TraesCS3A01G225400 chr3A 88.889 72 7 1 1132 1203 12070450 12070520 1.190000e-13 87.9
18 TraesCS3A01G225400 chr3A 96.226 53 2 0 1707 1759 245731512 245731564 1.190000e-13 87.9
19 TraesCS3A01G225400 chr3A 94.643 56 3 0 1707 1762 388844958 388844903 1.190000e-13 87.9
20 TraesCS3A01G225400 chr3A 97.561 41 1 0 700 740 331333231 331333191 1.200000e-08 71.3
21 TraesCS3A01G225400 chr4A 91.730 1185 81 12 522 1700 263897854 263896681 0.000000e+00 1629.0
22 TraesCS3A01G225400 chr4A 87.045 880 94 7 571 1448 391151137 391151998 0.000000e+00 976.0
23 TraesCS3A01G225400 chr4A 89.823 678 59 9 1746 2418 395908619 395909291 0.000000e+00 861.0
24 TraesCS3A01G225400 chr4A 91.903 494 33 7 1 488 395913544 395914036 0.000000e+00 684.0
25 TraesCS3A01G225400 chr4A 89.340 197 18 3 1210 1405 368325302 368325108 6.700000e-61 244.0
26 TraesCS3A01G225400 chr4A 86.747 83 10 1 1055 1137 356487067 356487148 9.240000e-15 91.6
27 TraesCS3A01G225400 chr4A 89.041 73 6 2 1135 1207 328904392 328904322 3.320000e-14 89.8
28 TraesCS3A01G225400 chr6A 94.313 721 39 2 1707 2426 259305195 259305914 0.000000e+00 1103.0
29 TraesCS3A01G225400 chr6A 92.788 721 50 2 1707 2426 259284820 259285539 0.000000e+00 1042.0
30 TraesCS3A01G225400 chr6A 91.840 576 43 4 875 1450 546379945 546379374 0.000000e+00 800.0
31 TraesCS3A01G225400 chr6A 90.468 577 50 5 875 1450 546388021 546387449 0.000000e+00 756.0
32 TraesCS3A01G225400 chr6A 86.880 686 72 15 1746 2425 539363534 539362861 0.000000e+00 752.0
33 TraesCS3A01G225400 chr6A 89.474 513 39 15 1 503 472186911 472187418 3.400000e-178 634.0
34 TraesCS3A01G225400 chr6A 90.391 281 26 1 1439 1719 369593076 369593355 3.810000e-98 368.0
35 TraesCS3A01G225400 chr6A 90.036 281 28 0 1439 1719 369600789 369601069 4.930000e-97 364.0
36 TraesCS3A01G225400 chr6A 86.364 286 32 4 1478 1757 254143394 254143678 3.030000e-79 305.0
37 TraesCS3A01G225400 chr6A 89.545 220 17 5 527 745 279080946 279081160 8.550000e-70 274.0
38 TraesCS3A01G225400 chr6A 91.011 178 16 0 866 1043 413230744 413230921 8.670000e-60 241.0
39 TraesCS3A01G225400 chr6A 91.772 158 13 0 980 1137 396400848 396400691 1.130000e-53 220.0
40 TraesCS3A01G225400 chr6A 89.820 167 12 4 1331 1494 335232423 335232259 2.440000e-50 209.0
41 TraesCS3A01G225400 chr6A 94.444 108 6 0 1030 1137 396450063 396449956 1.490000e-37 167.0
42 TraesCS3A01G225400 chr6A 80.864 162 16 11 522 677 87026887 87027039 1.970000e-21 113.0
43 TraesCS3A01G225400 chr6A 97.917 48 1 0 1163 1210 324804940 324804987 1.550000e-12 84.2
44 TraesCS3A01G225400 chr5A 89.201 676 65 8 1747 2418 162757263 162757934 0.000000e+00 837.0
45 TraesCS3A01G225400 chr5A 92.457 464 31 4 1 461 245960783 245961245 0.000000e+00 660.0
46 TraesCS3A01G225400 chr5A 82.203 236 24 12 530 763 219797037 219796818 1.150000e-43 187.0
47 TraesCS3A01G225400 chr5A 81.277 235 22 13 530 763 86366963 86366750 1.150000e-38 171.0
48 TraesCS3A01G225400 chr7A 89.015 619 50 15 875 1491 332757818 332758420 0.000000e+00 750.0
49 TraesCS3A01G225400 chr7A 90.486 494 40 7 1 488 457394745 457395237 0.000000e+00 645.0
50 TraesCS3A01G225400 chr7A 89.655 174 18 0 866 1039 400527476 400527649 3.140000e-54 222.0
51 TraesCS3A01G225400 chr7A 88.571 70 6 2 1163 1231 177664087 177664019 1.550000e-12 84.2
52 TraesCS3A01G225400 chr7A 97.561 41 1 0 700 740 600538793 600538753 1.200000e-08 71.3
53 TraesCS3A01G225400 chr1A 86.455 694 80 10 1742 2426 35654843 35655531 0.000000e+00 749.0
54 TraesCS3A01G225400 chr1A 89.412 510 45 8 1 503 224086465 224085958 3.400000e-178 634.0
55 TraesCS3A01G225400 chr1A 88.889 72 7 1 1132 1203 400241968 400242038 1.190000e-13 87.9
56 TraesCS3A01G225400 chr1A 97.619 42 0 1 693 733 407021404 407021445 1.200000e-08 71.3
57 TraesCS3A01G225400 chr2A 91.365 498 35 8 1 493 384871085 384871579 0.000000e+00 675.0
58 TraesCS3A01G225400 chr2A 82.353 391 33 26 375 758 288060719 288061080 8.430000e-80 307.0
59 TraesCS3A01G225400 chr2A 93.855 179 11 0 1438 1616 200630579 200630757 1.110000e-68 270.0
60 TraesCS3A01G225400 chr2A 88.500 200 20 3 1207 1405 177358141 177358338 3.120000e-59 239.0
61 TraesCS3A01G225400 chr2A 88.500 200 20 3 1207 1405 177370696 177370893 3.120000e-59 239.0
62 TraesCS3A01G225400 chr2A 97.561 41 1 0 700 740 176680139 176680179 1.200000e-08 71.3
63 TraesCS3A01G225400 chr7D 86.364 66 9 0 1662 1727 9200460 9200525 3.350000e-09 73.1


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 TraesCS3A01G225400 chr3A 422737070 422739495 2425 False 4481 4481 100.000 1 2426 1 chr3A.!!$F13 2425
1 TraesCS3A01G225400 chr3A 288745730 288746877 1147 False 1435 1435 89.066 571 1757 1 chr3A.!!$F9 1186
2 TraesCS3A01G225400 chr3A 451701381 451702068 687 False 902 902 90.435 1742 2426 1 chr3A.!!$F14 684
3 TraesCS3A01G225400 chr3A 678281909 678282597 688 True 811 811 88.040 1731 2418 1 chr3A.!!$R7 687
4 TraesCS3A01G225400 chr3A 678274026 678274708 682 True 767 767 87.064 1745 2426 1 chr3A.!!$R6 681
5 TraesCS3A01G225400 chr3A 50143198 50143705 507 True 640 640 89.608 1 503 1 chr3A.!!$R1 502
6 TraesCS3A01G225400 chr4A 263896681 263897854 1173 True 1629 1629 91.730 522 1700 1 chr4A.!!$R1 1178
7 TraesCS3A01G225400 chr4A 391151137 391151998 861 False 976 976 87.045 571 1448 1 chr4A.!!$F2 877
8 TraesCS3A01G225400 chr4A 395908619 395909291 672 False 861 861 89.823 1746 2418 1 chr4A.!!$F3 672
9 TraesCS3A01G225400 chr6A 259305195 259305914 719 False 1103 1103 94.313 1707 2426 1 chr6A.!!$F4 719
10 TraesCS3A01G225400 chr6A 259284820 259285539 719 False 1042 1042 92.788 1707 2426 1 chr6A.!!$F3 719
11 TraesCS3A01G225400 chr6A 546379374 546379945 571 True 800 800 91.840 875 1450 1 chr6A.!!$R5 575
12 TraesCS3A01G225400 chr6A 546387449 546388021 572 True 756 756 90.468 875 1450 1 chr6A.!!$R6 575
13 TraesCS3A01G225400 chr6A 539362861 539363534 673 True 752 752 86.880 1746 2425 1 chr6A.!!$R4 679
14 TraesCS3A01G225400 chr6A 472186911 472187418 507 False 634 634 89.474 1 503 1 chr6A.!!$F10 502
15 TraesCS3A01G225400 chr5A 162757263 162757934 671 False 837 837 89.201 1747 2418 1 chr5A.!!$F1 671
16 TraesCS3A01G225400 chr7A 332757818 332758420 602 False 750 750 89.015 875 1491 1 chr7A.!!$F1 616
17 TraesCS3A01G225400 chr1A 35654843 35655531 688 False 749 749 86.455 1742 2426 1 chr1A.!!$F1 684
18 TraesCS3A01G225400 chr1A 224085958 224086465 507 True 634 634 89.412 1 503 1 chr1A.!!$R1 502

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
410 412 0.033503 CGGGAAAATAGCCCCCTTGT 60.034 55.0 0.0 0.0 42.92 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1592 1605 0.46187 TTGACGGATCCAATGCCTCG 60.462 55.0 13.41 0.0 0.0 4.63 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
104 105 4.458989 CACCCATAACACAATTGCACTACT 59.541 41.667 5.05 0.00 0.00 2.57
131 132 2.176889 CTCTTCCCTTACCCGACTCAA 58.823 52.381 0.00 0.00 0.00 3.02
139 140 3.297736 CTTACCCGACTCAACCTCCTAT 58.702 50.000 0.00 0.00 0.00 2.57
234 236 7.698506 AATCTGCCCATAAATCACATCTATG 57.301 36.000 0.00 0.00 0.00 2.23
246 248 4.556697 TCACATCTATGGTGTAGGGTCAT 58.443 43.478 0.00 0.00 37.52 3.06
297 299 7.384932 AGTTCATTTGAATGGGTTTCGAAATTC 59.615 33.333 14.69 13.55 40.36 2.17
331 333 0.521291 AAATCCAACGCGTGTGGATG 59.479 50.000 35.19 22.74 41.18 3.51
334 336 0.033642 TCCAACGCGTGTGGATGTTA 59.966 50.000 27.88 13.71 0.00 2.41
349 351 8.793592 GTGTGGATGTTACTTCCTCTAAAAATT 58.206 33.333 16.54 0.00 34.17 1.82
398 400 4.021016 CACATTTTTATGGGTCCGGGAAAA 60.021 41.667 0.00 0.00 0.00 2.29
400 402 5.958987 ACATTTTTATGGGTCCGGGAAAATA 59.041 36.000 0.00 0.00 0.00 1.40
401 403 6.097696 ACATTTTTATGGGTCCGGGAAAATAG 59.902 38.462 0.00 0.00 0.00 1.73
402 404 2.943036 TATGGGTCCGGGAAAATAGC 57.057 50.000 0.00 0.00 0.00 2.97
405 407 1.152819 GGTCCGGGAAAATAGCCCC 60.153 63.158 0.00 0.00 42.92 5.80
407 409 1.308392 TCCGGGAAAATAGCCCCCT 60.308 57.895 0.00 0.00 42.92 4.79
409 411 0.755327 CCGGGAAAATAGCCCCCTTG 60.755 60.000 0.00 0.00 42.92 3.61
410 412 0.033503 CGGGAAAATAGCCCCCTTGT 60.034 55.000 0.00 0.00 42.92 3.16
411 413 1.213430 CGGGAAAATAGCCCCCTTGTA 59.787 52.381 0.00 0.00 42.92 2.41
417 419 5.163447 GGAAAATAGCCCCCTTGTACAAATC 60.163 44.000 10.03 0.00 0.00 2.17
430 432 4.925836 TGTACAAATCCTTTCCCTAACCC 58.074 43.478 0.00 0.00 0.00 4.11
449 453 5.654901 ACCCTCCTTTTCTTTTCTTCTCT 57.345 39.130 0.00 0.00 0.00 3.10
450 454 5.626142 ACCCTCCTTTTCTTTTCTTCTCTC 58.374 41.667 0.00 0.00 0.00 3.20
488 495 9.813826 TTTTAAAAAGAAAGATGAGGGAGAGAT 57.186 29.630 0.00 0.00 0.00 2.75
493 500 6.173427 AGAAAGATGAGGGAGAGATAAAGC 57.827 41.667 0.00 0.00 0.00 3.51
494 501 5.664908 AGAAAGATGAGGGAGAGATAAAGCA 59.335 40.000 0.00 0.00 0.00 3.91
495 502 5.549742 AAGATGAGGGAGAGATAAAGCAG 57.450 43.478 0.00 0.00 0.00 4.24
496 503 4.555689 AGATGAGGGAGAGATAAAGCAGT 58.444 43.478 0.00 0.00 0.00 4.40
517 524 3.801997 CCAGGCCGGCTCATCCTT 61.802 66.667 28.56 0.26 0.00 3.36
518 525 2.203126 CAGGCCGGCTCATCCTTC 60.203 66.667 28.56 6.68 0.00 3.46
519 526 3.483869 AGGCCGGCTCATCCTTCC 61.484 66.667 28.56 5.83 0.00 3.46
520 527 4.570874 GGCCGGCTCATCCTTCCC 62.571 72.222 28.56 0.41 0.00 3.97
521 528 4.570874 GCCGGCTCATCCTTCCCC 62.571 72.222 22.15 0.00 0.00 4.81
522 529 4.241555 CCGGCTCATCCTTCCCCG 62.242 72.222 0.00 0.00 38.71 5.73
523 530 4.918201 CGGCTCATCCTTCCCCGC 62.918 72.222 0.00 0.00 31.87 6.13
524 531 3.797353 GGCTCATCCTTCCCCGCA 61.797 66.667 0.00 0.00 0.00 5.69
525 532 2.203126 GCTCATCCTTCCCCGCAG 60.203 66.667 0.00 0.00 0.00 5.18
526 533 3.036429 GCTCATCCTTCCCCGCAGT 62.036 63.158 0.00 0.00 0.00 4.40
536 543 3.151022 CCCGCAGTCTCCCTCTCC 61.151 72.222 0.00 0.00 0.00 3.71
540 547 1.896694 GCAGTCTCCCTCTCCACTG 59.103 63.158 0.00 0.00 39.47 3.66
567 574 3.324108 GTTCCACCGGCCCACCTA 61.324 66.667 0.00 0.00 0.00 3.08
589 596 0.848735 TCTAACCCTAGCGCTCCCTA 59.151 55.000 16.34 0.00 0.00 3.53
590 597 1.202903 TCTAACCCTAGCGCTCCCTAG 60.203 57.143 16.34 5.33 35.62 3.02
605 612 3.161450 TAGCCCGATCCCCTGCAC 61.161 66.667 0.00 0.00 0.00 4.57
689 697 4.314440 GCGCTCCCACACACAGGA 62.314 66.667 0.00 0.00 0.00 3.86
775 783 4.862092 CGCCTCGAGCTGCGTCAT 62.862 66.667 22.78 0.00 45.43 3.06
829 837 1.371183 CCACTGCTCCTTTCCGTGA 59.629 57.895 0.00 0.00 0.00 4.35
850 858 1.635487 CATCCCCCTCTTCCTCAACAA 59.365 52.381 0.00 0.00 0.00 2.83
855 863 1.421646 CCCTCTTCCTCAACAACCAGT 59.578 52.381 0.00 0.00 0.00 4.00
909 918 2.898840 CTGCATCCATTCGCCGCT 60.899 61.111 0.00 0.00 0.00 5.52
969 978 4.351938 CCTCGCGTCGTTCCACCA 62.352 66.667 5.77 0.00 0.00 4.17
1079 1088 2.283894 TTCTCCTGCGAGCTCCCA 60.284 61.111 8.47 4.19 35.94 4.37
1218 1227 3.394836 GCTCCTTGGAGTCGCCCT 61.395 66.667 16.95 0.00 34.97 5.19
1343 1353 2.255316 GTGTTGTTTTGTGTTGGACGG 58.745 47.619 0.00 0.00 0.00 4.79
1433 1445 0.258194 AGTACTCGGTGACCCTAGGG 59.742 60.000 27.36 27.36 42.03 3.53
1434 1446 1.076485 TACTCGGTGACCCTAGGGC 60.076 63.158 28.88 20.22 39.32 5.19
1555 1567 2.437343 GCGAGACGAAGAACGCCAG 61.437 63.158 0.00 0.00 46.94 4.85
1592 1605 0.251073 AACATGTACCACTACGCCCC 59.749 55.000 0.00 0.00 0.00 5.80
1678 1691 5.828299 TTCGTCAAGTTCACCTTCAAAAT 57.172 34.783 0.00 0.00 0.00 1.82
1691 1704 6.497259 TCACCTTCAAAATGAGTACCTCTACT 59.503 38.462 0.00 0.00 35.77 2.57
1735 1748 1.067060 CCTCGCCATGACTATGAACGA 59.933 52.381 0.00 0.00 39.04 3.85
1782 1796 4.023450 CCGCCTGAACGTCTATAGAACATA 60.023 45.833 3.40 0.00 0.00 2.29
1841 1855 0.034380 TGTTTTGACCCCGAACACCA 60.034 50.000 0.00 0.00 0.00 4.17
1860 1874 3.260884 ACCAACGGAGTGTGAACATCTAT 59.739 43.478 0.00 0.00 45.00 1.98
1915 1929 1.069358 CGAGAATGCCTACTTCCCTCC 59.931 57.143 0.00 0.00 0.00 4.30
1934 1948 2.304470 TCCACGAACTTGATCCATTCCA 59.696 45.455 0.00 0.00 0.00 3.53
1970 1984 4.641541 TCGAAAGGTATAACCATCGAGACA 59.358 41.667 17.57 2.70 46.52 3.41
1976 1990 3.604875 ATAACCATCGAGACAACCGTT 57.395 42.857 0.00 0.00 0.00 4.44
2063 2084 3.058293 CGCTTGCATGTTTCTCCTTGTTA 60.058 43.478 1.14 0.00 0.00 2.41
2066 2087 3.153919 TGCATGTTTCTCCTTGTTACCC 58.846 45.455 0.00 0.00 0.00 3.69
2162 2185 2.481212 GCACCGGCATCTCAATCAA 58.519 52.632 0.00 0.00 40.72 2.57
2163 2186 0.379669 GCACCGGCATCTCAATCAAG 59.620 55.000 0.00 0.00 40.72 3.02
2174 2199 3.170717 TCTCAATCAAGTACCGGAACCT 58.829 45.455 9.46 0.00 0.00 3.50
2217 2242 1.275657 GTTGTCGTTGTCGTGGCAG 59.724 57.895 0.00 0.00 38.33 4.85
2259 2284 6.127925 ACGATGACAAATGCTTCATAACATGT 60.128 34.615 0.00 0.00 32.43 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 4.158394 AGTGCAATTGTGTTATGGGTGATC 59.842 41.667 7.40 0.00 0.00 2.92
104 105 2.565834 CGGGTAAGGGAAGAGTTGAAGA 59.434 50.000 0.00 0.00 0.00 2.87
131 132 3.451540 GTCGAAAAGGAAGGATAGGAGGT 59.548 47.826 0.00 0.00 0.00 3.85
139 140 5.687780 ACTTAAAAGGTCGAAAAGGAAGGA 58.312 37.500 0.00 0.00 0.00 3.36
234 236 6.936968 AATTATAGGAGATGACCCTACACC 57.063 41.667 0.00 0.00 38.94 4.16
246 248 7.647827 TCCAAATGGGTTGAAATTATAGGAGA 58.352 34.615 0.00 0.00 39.87 3.71
297 299 4.497473 TGGATTTAACTCGGCAAGTTTG 57.503 40.909 8.78 0.00 46.26 2.93
331 333 7.148222 GGCCTGAGAATTTTTAGAGGAAGTAAC 60.148 40.741 0.00 0.00 0.00 2.50
334 336 5.222130 TGGCCTGAGAATTTTTAGAGGAAGT 60.222 40.000 3.32 0.00 0.00 3.01
364 366 7.512992 ACCCATAAAAATGTGTGGAATTTGAA 58.487 30.769 0.00 0.00 33.53 2.69
374 376 2.041891 TCCCGGACCCATAAAAATGTGT 59.958 45.455 0.73 0.00 0.00 3.72
377 379 4.810191 TTTTCCCGGACCCATAAAAATG 57.190 40.909 0.73 0.00 0.00 2.32
384 386 0.185175 GGCTATTTTCCCGGACCCAT 59.815 55.000 0.73 0.00 0.00 4.00
385 387 1.610873 GGCTATTTTCCCGGACCCA 59.389 57.895 0.73 0.00 0.00 4.51
387 389 1.152819 GGGGCTATTTTCCCGGACC 60.153 63.158 0.73 0.00 44.86 4.46
398 400 3.131252 AGGATTTGTACAAGGGGGCTAT 58.869 45.455 8.56 0.00 0.00 2.97
400 402 1.382914 AGGATTTGTACAAGGGGGCT 58.617 50.000 8.56 0.00 0.00 5.19
401 403 2.231716 AAGGATTTGTACAAGGGGGC 57.768 50.000 8.56 0.00 0.00 5.80
402 404 3.096852 GGAAAGGATTTGTACAAGGGGG 58.903 50.000 8.56 0.00 39.27 5.40
405 407 5.417894 GGTTAGGGAAAGGATTTGTACAAGG 59.582 44.000 8.56 0.00 39.27 3.61
407 409 5.075344 AGGGTTAGGGAAAGGATTTGTACAA 59.925 40.000 3.59 3.59 39.27 2.41
409 411 5.188988 AGGGTTAGGGAAAGGATTTGTAC 57.811 43.478 0.00 0.00 39.27 2.90
410 412 4.228895 GGAGGGTTAGGGAAAGGATTTGTA 59.771 45.833 0.00 0.00 39.27 2.41
411 413 3.011369 GGAGGGTTAGGGAAAGGATTTGT 59.989 47.826 0.00 0.00 39.27 2.83
417 419 3.333980 AGAAAAGGAGGGTTAGGGAAAGG 59.666 47.826 0.00 0.00 0.00 3.11
461 466 9.813826 TCTCTCCCTCATCTTTCTTTTTAAAAT 57.186 29.630 0.55 0.00 0.00 1.82
471 476 5.923204 TGCTTTATCTCTCCCTCATCTTTC 58.077 41.667 0.00 0.00 0.00 2.62
474 479 4.555689 ACTGCTTTATCTCTCCCTCATCT 58.444 43.478 0.00 0.00 0.00 2.90
479 486 2.433970 GCTGACTGCTTTATCTCTCCCT 59.566 50.000 0.00 0.00 38.95 4.20
481 488 2.169352 TGGCTGACTGCTTTATCTCTCC 59.831 50.000 4.20 0.00 42.39 3.71
488 495 1.002134 GGCCTGGCTGACTGCTTTA 60.002 57.895 19.68 0.00 42.39 1.85
503 510 4.570874 GGGAAGGATGAGCCGGCC 62.571 72.222 26.15 15.80 43.43 6.13
504 511 4.570874 GGGGAAGGATGAGCCGGC 62.571 72.222 21.89 21.89 43.43 6.13
505 512 4.241555 CGGGGAAGGATGAGCCGG 62.242 72.222 0.00 0.00 43.43 6.13
506 513 4.918201 GCGGGGAAGGATGAGCCG 62.918 72.222 0.00 0.00 43.43 5.52
507 514 3.764160 CTGCGGGGAAGGATGAGCC 62.764 68.421 0.00 0.00 0.00 4.70
508 515 2.203126 CTGCGGGGAAGGATGAGC 60.203 66.667 0.00 0.00 0.00 4.26
509 516 1.144936 GACTGCGGGGAAGGATGAG 59.855 63.158 0.00 0.00 0.00 2.90
510 517 1.306141 AGACTGCGGGGAAGGATGA 60.306 57.895 0.00 0.00 0.00 2.92
511 518 1.144936 GAGACTGCGGGGAAGGATG 59.855 63.158 0.00 0.00 0.00 3.51
512 519 2.066999 GGAGACTGCGGGGAAGGAT 61.067 63.158 0.00 0.00 0.00 3.24
513 520 2.683933 GGAGACTGCGGGGAAGGA 60.684 66.667 0.00 0.00 0.00 3.36
514 521 3.787001 GGGAGACTGCGGGGAAGG 61.787 72.222 0.00 0.00 0.00 3.46
515 522 2.685380 AGGGAGACTGCGGGGAAG 60.685 66.667 0.00 0.00 0.00 3.46
516 523 2.683933 GAGGGAGACTGCGGGGAA 60.684 66.667 0.00 0.00 0.00 3.97
517 524 3.663815 GAGAGGGAGACTGCGGGGA 62.664 68.421 0.00 0.00 0.00 4.81
518 525 3.151022 GAGAGGGAGACTGCGGGG 61.151 72.222 0.00 0.00 0.00 5.73
519 526 3.151022 GGAGAGGGAGACTGCGGG 61.151 72.222 0.00 0.00 0.00 6.13
520 527 2.363018 TGGAGAGGGAGACTGCGG 60.363 66.667 0.00 0.00 0.00 5.69
521 528 1.680651 AGTGGAGAGGGAGACTGCG 60.681 63.158 0.00 0.00 0.00 5.18
522 529 1.612395 CCAGTGGAGAGGGAGACTGC 61.612 65.000 1.68 0.00 35.50 4.40
523 530 2.589494 CCAGTGGAGAGGGAGACTG 58.411 63.158 1.68 0.00 36.40 3.51
550 557 3.324108 TAGGTGGGCCGGTGGAAC 61.324 66.667 1.90 0.00 40.50 3.62
551 558 3.006728 CTAGGTGGGCCGGTGGAA 61.007 66.667 1.90 0.00 40.50 3.53
554 561 4.162690 GAGCTAGGTGGGCCGGTG 62.163 72.222 1.90 0.00 40.50 4.94
555 562 2.525284 TTAGAGCTAGGTGGGCCGGT 62.525 60.000 1.90 0.00 40.50 5.28
556 563 1.760875 TTAGAGCTAGGTGGGCCGG 60.761 63.158 0.00 0.00 40.50 6.13
558 565 1.697082 GGGTTAGAGCTAGGTGGGCC 61.697 65.000 0.00 0.00 0.00 5.80
559 566 0.691413 AGGGTTAGAGCTAGGTGGGC 60.691 60.000 0.00 0.00 0.00 5.36
560 567 2.599677 CTAGGGTTAGAGCTAGGTGGG 58.400 57.143 0.00 0.00 0.00 4.61
562 569 1.609555 CGCTAGGGTTAGAGCTAGGTG 59.390 57.143 0.00 0.00 36.50 4.00
563 570 1.984066 CGCTAGGGTTAGAGCTAGGT 58.016 55.000 0.00 0.00 36.50 3.08
569 576 0.468400 AGGGAGCGCTAGGGTTAGAG 60.468 60.000 11.50 0.00 0.00 2.43
605 612 0.178947 AGCGAATAGAGAGGAGGGGG 60.179 60.000 0.00 0.00 0.00 5.40
689 697 3.782443 GAGGGGAATCGGGCACGT 61.782 66.667 8.89 0.00 41.85 4.49
789 797 4.284550 GCAGGGGCAACACCTCCA 62.285 66.667 0.00 0.00 46.76 3.86
829 837 1.290134 GTTGAGGAAGAGGGGGATGT 58.710 55.000 0.00 0.00 0.00 3.06
963 972 2.867855 GCGTGACAGAGGTGGTGGA 61.868 63.158 0.00 0.00 0.00 4.02
969 978 3.991051 CACCGGCGTGACAGAGGT 61.991 66.667 6.01 0.00 43.14 3.85
1011 1020 3.325753 GTCCTGGCCTGGCAGAGT 61.326 66.667 23.46 0.00 0.00 3.24
1194 1203 2.438075 CTCCAAGGAGCAGCAGCC 60.438 66.667 2.68 0.00 43.56 4.85
1218 1227 1.153269 TCGTGCTGGTTGCTGACAA 60.153 52.632 0.00 0.00 43.37 3.18
1473 1485 4.454504 GTGGTACTTGTCGAAATCCACATT 59.545 41.667 14.20 0.00 42.04 2.71
1555 1567 2.288395 TGTTCGTTTTCGGAGAGGTACC 60.288 50.000 2.73 2.73 44.25 3.34
1592 1605 0.461870 TTGACGGATCCAATGCCTCG 60.462 55.000 13.41 0.00 0.00 4.63
1600 1613 0.530744 CTTCGGACTTGACGGATCCA 59.469 55.000 13.41 0.00 32.35 3.41
1841 1855 4.801330 TCATAGATGTTCACACTCCGTT 57.199 40.909 0.00 0.00 0.00 4.44
1860 1874 2.095364 GGAAGTAGTCGTTCTCGCTTCA 60.095 50.000 18.08 0.00 38.66 3.02
1915 1929 4.970662 ATTGGAATGGATCAAGTTCGTG 57.029 40.909 0.00 0.00 0.00 4.35
1934 1948 2.747446 ACCTTTCGAAGCGTGCATTATT 59.253 40.909 0.00 0.00 0.00 1.40
2063 2084 4.928140 ACGGGTGGACGACAGGGT 62.928 66.667 0.00 0.00 37.61 4.34
2160 2183 3.053831 ACATTCAGGTTCCGGTACTTG 57.946 47.619 15.96 15.96 0.00 3.16
2162 2185 2.874457 GCAACATTCAGGTTCCGGTACT 60.874 50.000 11.29 0.23 0.00 2.73
2163 2186 1.467342 GCAACATTCAGGTTCCGGTAC 59.533 52.381 0.00 0.55 0.00 3.34
2301 2328 5.172460 TGTTGTTATCATGATGCGAATGG 57.828 39.130 18.72 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.