Multiple sequence alignment - TraesCS6B01G378000

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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 TraesCS6B01G378000 chr6B 100.000 2642 0 0 1 2642 653014037 653016678 0.000000e+00 4879.0
1 TraesCS6B01G378000 chr6B 82.778 180 25 4 1875 2052 653099638 653099813 3.520000e-34 156.0
2 TraesCS6B01G378000 chr6B 94.000 50 2 1 1 49 189135832 189135783 1.010000e-09 75.0
3 TraesCS6B01G378000 chr6B 80.198 101 19 1 2051 2151 620530713 620530812 1.010000e-09 75.0
4 TraesCS6B01G378000 chr6A 90.888 1284 79 14 799 2055 578982893 578984165 0.000000e+00 1688.0
5 TraesCS6B01G378000 chr6A 85.253 651 41 25 46 664 578981983 578982610 1.040000e-173 619.0
6 TraesCS6B01G378000 chr6A 83.616 177 24 3 1876 2052 579007802 579007973 7.570000e-36 161.0
7 TraesCS6B01G378000 chr6D 88.016 1285 75 36 799 2053 432884318 432885553 0.000000e+00 1447.0
8 TraesCS6B01G378000 chr6D 82.588 626 61 12 2050 2642 464193916 464194526 2.350000e-140 508.0
9 TraesCS6B01G378000 chr6D 81.102 635 50 35 172 770 432883593 432884193 6.710000e-121 444.0
10 TraesCS6B01G378000 chr6D 87.755 98 4 3 47 144 432883513 432883602 1.000000e-19 108.0
11 TraesCS6B01G378000 chr6D 91.667 48 3 1 3 49 455666321 455666368 6.100000e-07 65.8
12 TraesCS6B01G378000 chrUn 84.158 606 69 9 2053 2642 134358081 134357487 1.780000e-156 562.0
13 TraesCS6B01G378000 chr4D 87.935 489 43 10 2165 2642 484672218 484672701 1.780000e-156 562.0
14 TraesCS6B01G378000 chr2B 86.427 501 42 12 2150 2638 401151968 401152454 2.330000e-145 525.0
15 TraesCS6B01G378000 chr2D 82.686 618 70 9 2053 2642 110626335 110626943 5.040000e-142 514.0
16 TraesCS6B01G378000 chr2D 88.180 423 40 6 2226 2642 566107831 566107413 1.830000e-136 496.0
17 TraesCS6B01G378000 chr2D 83.903 497 61 10 2144 2636 3001949 3002430 8.620000e-125 457.0
18 TraesCS6B01G378000 chr2D 86.139 101 14 0 2051 2151 495046798 495046698 2.780000e-20 110.0
19 TraesCS6B01G378000 chr5D 82.059 641 62 23 2051 2640 544154352 544153714 5.080000e-137 497.0
20 TraesCS6B01G378000 chr3B 82.540 504 63 11 2144 2641 477368363 477367879 1.130000e-113 420.0
21 TraesCS6B01G378000 chr3B 84.848 99 15 0 2052 2150 252342735 252342637 1.670000e-17 100.0
22 TraesCS6B01G378000 chr7A 84.211 399 55 5 2239 2637 652752284 652751894 5.340000e-102 381.0
23 TraesCS6B01G378000 chr7D 85.754 358 45 5 2288 2640 227564645 227564289 8.930000e-100 374.0
24 TraesCS6B01G378000 chr7D 82.258 310 32 6 2050 2343 8607734 8607432 2.030000e-61 246.0
25 TraesCS6B01G378000 chr7D 85.859 99 14 0 2053 2151 606802781 606802879 3.600000e-19 106.0
26 TraesCS6B01G378000 chr7B 89.153 295 22 6 909 1197 31433265 31433555 2.500000e-95 359.0
27 TraesCS6B01G378000 chr7B 94.000 50 2 1 1 49 328514501 328514452 1.010000e-09 75.0
28 TraesCS6B01G378000 chr5A 80.193 414 46 9 2055 2433 372589150 372589562 7.200000e-71 278.0
29 TraesCS6B01G378000 chr1D 84.585 253 21 7 2150 2388 42888716 42888468 4.400000e-58 235.0
30 TraesCS6B01G378000 chr1D 85.294 102 15 0 2050 2151 466932727 466932626 3.600000e-19 106.0
31 TraesCS6B01G378000 chr4A 86.598 97 13 0 2055 2151 689359490 689359586 1.000000e-19 108.0
32 TraesCS6B01G378000 chr1B 85.149 101 15 0 2051 2151 615427752 615427852 1.290000e-18 104.0
33 TraesCS6B01G378000 chr1B 84.158 101 16 0 2051 2151 615390416 615390516 6.020000e-17 99.0
34 TraesCS6B01G378000 chr3D 82.828 99 16 1 2053 2151 7503297 7503200 1.300000e-13 87.9
35 TraesCS6B01G378000 chr4B 94.000 50 2 1 1 49 634608011 634607962 1.010000e-09 75.0
36 TraesCS6B01G378000 chr1A 94.000 50 2 1 1 49 324838102 324838151 1.010000e-09 75.0


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 TraesCS6B01G378000 chr6B 653014037 653016678 2641 False 4879.000000 4879 100.000000 1 2642 1 chr6B.!!$F2 2641
1 TraesCS6B01G378000 chr6A 578981983 578984165 2182 False 1153.500000 1688 88.070500 46 2055 2 chr6A.!!$F2 2009
2 TraesCS6B01G378000 chr6D 432883513 432885553 2040 False 666.333333 1447 85.624333 47 2053 3 chr6D.!!$F3 2006
3 TraesCS6B01G378000 chr6D 464193916 464194526 610 False 508.000000 508 82.588000 2050 2642 1 chr6D.!!$F2 592
4 TraesCS6B01G378000 chrUn 134357487 134358081 594 True 562.000000 562 84.158000 2053 2642 1 chrUn.!!$R1 589
5 TraesCS6B01G378000 chr2D 110626335 110626943 608 False 514.000000 514 82.686000 2053 2642 1 chr2D.!!$F2 589
6 TraesCS6B01G378000 chr5D 544153714 544154352 638 True 497.000000 497 82.059000 2051 2640 1 chr5D.!!$R1 589

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
82 83 0.173255 GCATGCACCGCTACCATTTT 59.827 50.0 14.21 0.0 0.0 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1714 2073 0.035881 ACACTGCCATGACAGACAGG 59.964 55.0 16.61 4.85 40.25 4.0 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
32 33 5.864474 TCTGAAGAATTGTCTTTAGACGAGC 59.136 40.000 6.81 1.58 46.23 5.03
33 34 5.635280 CTGAAGAATTGTCTTTAGACGAGCA 59.365 40.000 6.05 0.00 45.83 4.26
34 35 6.183360 CTGAAGAATTGTCTTTAGACGAGCAG 60.183 42.308 6.05 4.89 45.83 4.24
35 36 9.449093 CTGAAGAATTGTCTTTAGACGAGCAGC 62.449 44.444 6.05 0.00 45.83 5.25
39 40 3.916405 GTCTTTAGACGAGCAGCAATC 57.084 47.619 0.00 0.00 35.12 2.67
40 41 3.254060 GTCTTTAGACGAGCAGCAATCA 58.746 45.455 0.00 0.00 35.12 2.57
41 42 3.868077 GTCTTTAGACGAGCAGCAATCAT 59.132 43.478 0.00 0.00 35.12 2.45
42 43 4.026145 GTCTTTAGACGAGCAGCAATCATC 60.026 45.833 0.00 0.00 35.12 2.92
43 44 3.808466 TTAGACGAGCAGCAATCATCT 57.192 42.857 0.00 0.00 0.00 2.90
44 45 2.687700 AGACGAGCAGCAATCATCTT 57.312 45.000 0.00 0.00 0.00 2.40
75 76 2.749839 GGTTGGCATGCACCGCTA 60.750 61.111 21.36 0.91 0.00 4.26
82 83 0.173255 GCATGCACCGCTACCATTTT 59.827 50.000 14.21 0.00 0.00 1.82
83 84 1.404047 GCATGCACCGCTACCATTTTT 60.404 47.619 14.21 0.00 0.00 1.94
117 118 4.838486 CGCTCGCGGTGGAGACTC 62.838 72.222 6.13 0.00 36.08 3.36
118 119 4.838486 GCTCGCGGTGGAGACTCG 62.838 72.222 6.13 0.00 36.08 4.18
119 120 4.180946 CTCGCGGTGGAGACTCGG 62.181 72.222 6.13 0.00 36.08 4.63
147 148 4.717629 CACAACCGAGCGAGCCGA 62.718 66.667 7.36 0.00 0.00 5.54
248 249 2.042831 GCAACGCCAAGCTCCTCAT 61.043 57.895 0.00 0.00 0.00 2.90
328 335 4.639824 CACACAGTGGTTGCATGC 57.360 55.556 11.82 11.82 0.00 4.06
463 487 2.817396 GTCAAGCTCGCTGCCTCC 60.817 66.667 0.00 0.00 44.23 4.30
475 500 1.839424 CTGCCTCCCTTGGTAAAAGG 58.161 55.000 0.00 0.00 37.17 3.11
490 515 5.751509 TGGTAAAAGGTATCGAATGTGATCG 59.248 40.000 0.00 0.00 44.04 3.69
553 608 2.080286 ACAGACGACATGGCAGTTAC 57.920 50.000 0.00 0.00 0.00 2.50
605 661 0.740868 CCCGTCGTACGTACCTCTGA 60.741 60.000 19.67 8.41 40.58 3.27
609 665 2.096268 CGTCGTACGTACCTCTGACAAA 60.096 50.000 22.71 0.00 36.74 2.83
634 690 2.094182 AGCGGTCAACACTGTACCATAG 60.094 50.000 2.68 0.00 32.55 2.23
666 745 2.353307 CGTGGGAATGTAGCAGTACACA 60.353 50.000 0.00 0.00 42.06 3.72
702 789 3.056107 ACACAACGACCTGCATACATACT 60.056 43.478 0.00 0.00 0.00 2.12
725 812 2.076863 GGAATGTTTCGTCCTGACAGG 58.923 52.381 15.99 15.99 36.46 4.00
761 848 0.824109 CCGCCTGATGGAGAACTACA 59.176 55.000 0.00 0.00 34.95 2.74
762 849 1.471676 CCGCCTGATGGAGAACTACAC 60.472 57.143 0.00 0.00 34.95 2.90
763 850 1.478510 CGCCTGATGGAGAACTACACT 59.521 52.381 0.00 0.00 34.95 3.55
764 851 2.093973 CGCCTGATGGAGAACTACACTT 60.094 50.000 0.00 0.00 34.95 3.16
765 852 3.130516 CGCCTGATGGAGAACTACACTTA 59.869 47.826 0.00 0.00 34.95 2.24
766 853 4.688021 GCCTGATGGAGAACTACACTTAG 58.312 47.826 0.00 0.00 34.57 2.18
767 854 4.442192 GCCTGATGGAGAACTACACTTAGG 60.442 50.000 8.01 8.01 34.57 2.69
768 855 4.712337 CCTGATGGAGAACTACACTTAGGT 59.288 45.833 0.00 0.00 34.57 3.08
769 856 5.892119 CCTGATGGAGAACTACACTTAGGTA 59.108 44.000 0.00 0.00 34.57 3.08
787 944 2.878117 GGTAGTAACCTGCATTGGCACA 60.878 50.000 0.00 0.00 46.35 4.57
810 1139 4.659115 ACCCAAGTTACCAGGTTGATAAC 58.341 43.478 0.00 0.00 0.00 1.89
909 1248 5.453567 TGTGAGCTCGCAGTACATATAAT 57.546 39.130 25.69 0.00 31.95 1.28
910 1249 6.569179 TGTGAGCTCGCAGTACATATAATA 57.431 37.500 25.69 0.00 31.95 0.98
911 1250 6.977213 TGTGAGCTCGCAGTACATATAATAA 58.023 36.000 25.69 0.00 31.95 1.40
931 1270 1.097232 TTTTGCATCGCTCCATCCAG 58.903 50.000 0.00 0.00 0.00 3.86
955 1294 0.399454 AGCTCTGCTCCACAACACAT 59.601 50.000 0.00 0.00 30.62 3.21
978 1320 3.154710 CACACTCCACTGACCACTACTA 58.845 50.000 0.00 0.00 0.00 1.82
979 1321 3.057456 CACACTCCACTGACCACTACTAC 60.057 52.174 0.00 0.00 0.00 2.73
980 1322 3.181431 ACACTCCACTGACCACTACTACT 60.181 47.826 0.00 0.00 0.00 2.57
981 1323 3.440872 CACTCCACTGACCACTACTACTC 59.559 52.174 0.00 0.00 0.00 2.59
982 1324 2.678836 CTCCACTGACCACTACTACTCG 59.321 54.545 0.00 0.00 0.00 4.18
997 1344 0.323908 ACTCGAGGGGGAGTGAGAAG 60.324 60.000 18.41 0.00 45.24 2.85
1404 1763 1.452108 GAACATCTTCTGGGGCGGG 60.452 63.158 0.00 0.00 0.00 6.13
1593 1952 2.434185 GGCGGCGTCTTCATGACA 60.434 61.111 9.37 0.00 45.60 3.58
1611 1970 0.814010 CATGCAACTACTACCCGCCC 60.814 60.000 0.00 0.00 0.00 6.13
1614 1973 3.464494 AACTACTACCCGCCCGGC 61.464 66.667 0.00 0.00 33.26 6.13
1690 2049 6.491394 GCGACATTCTAGGAGCATATACTAG 58.509 44.000 0.00 0.00 36.42 2.57
1746 2105 1.512926 GCAGTGTTGTTCCTGTCGAT 58.487 50.000 0.00 0.00 0.00 3.59
1755 2114 5.163447 TGTTGTTCCTGTCGATATTCTAGGG 60.163 44.000 0.00 0.00 0.00 3.53
1758 2117 1.202582 CCTGTCGATATTCTAGGGGCG 59.797 57.143 0.00 0.00 0.00 6.13
1784 2148 4.248859 TGTAAGCTGATTTGAGAGCAGAC 58.751 43.478 0.00 0.00 37.70 3.51
1791 2155 4.005650 TGATTTGAGAGCAGACCAATGAC 58.994 43.478 0.00 0.00 0.00 3.06
1796 2160 0.801251 GAGCAGACCAATGACAGTGC 59.199 55.000 0.00 0.00 0.00 4.40
1815 2179 1.508632 CCACCGTCGTGACTGAATTT 58.491 50.000 0.00 0.00 43.14 1.82
1819 2183 4.478699 CACCGTCGTGACTGAATTTAGTA 58.521 43.478 2.38 0.00 43.14 1.82
1822 2186 4.503007 CCGTCGTGACTGAATTTAGTATGG 59.497 45.833 2.38 0.00 0.00 2.74
1840 2204 6.845908 AGTATGGCAAATAGAGATGGATGTT 58.154 36.000 0.00 0.00 0.00 2.71
1918 2288 2.165641 TGGAAGTCGTCGTAATCTGCAT 59.834 45.455 0.00 0.00 0.00 3.96
1937 2307 2.533266 TGTGGCAGAAGAGAACTGAC 57.467 50.000 0.00 0.00 43.02 3.51
1947 2317 6.292596 GCAGAAGAGAACTGACTTAAACTGTG 60.293 42.308 0.00 0.00 37.54 3.66
1976 2348 6.403866 ACTGAACATTACAGAATGGCAAAA 57.596 33.333 0.00 0.00 45.83 2.44
2009 2381 3.748568 GGTAGAAGTTGAGTGAAGCAAGG 59.251 47.826 0.00 0.00 0.00 3.61
2011 2383 3.471680 AGAAGTTGAGTGAAGCAAGGAC 58.528 45.455 0.00 0.00 0.00 3.85
2028 2400 2.280628 GGACTGGCCTTGTAATCTTCG 58.719 52.381 3.32 0.00 0.00 3.79
2029 2401 1.666189 GACTGGCCTTGTAATCTTCGC 59.334 52.381 3.32 0.00 0.00 4.70
2031 2403 2.290323 ACTGGCCTTGTAATCTTCGCTT 60.290 45.455 3.32 0.00 0.00 4.68
2074 2446 1.676678 GCATCTCTAGCACACCCCGA 61.677 60.000 0.00 0.00 0.00 5.14
2078 2450 1.275291 TCTCTAGCACACCCCGAAAAG 59.725 52.381 0.00 0.00 0.00 2.27
2085 2458 2.856988 ACCCCGAAAAGAGCCCCA 60.857 61.111 0.00 0.00 0.00 4.96
2090 2463 1.074951 CGAAAAGAGCCCCAACCCT 59.925 57.895 0.00 0.00 0.00 4.34
2130 2503 2.818274 GTCGGCGCGGAAAATCCT 60.818 61.111 19.96 0.00 33.30 3.24
2133 2506 3.134127 GGCGCGGAAAATCCTGCT 61.134 61.111 8.83 0.00 36.30 4.24
2183 2572 1.511887 CGCGGCAAAATCTTGACCG 60.512 57.895 0.00 9.41 46.26 4.79
2272 2680 1.153539 TGGTGGGGAGGACATTTCAA 58.846 50.000 0.00 0.00 0.00 2.69
2275 2683 1.075536 GTGGGGAGGACATTTCAACCT 59.924 52.381 0.00 0.00 36.68 3.50
2286 2694 1.398692 TTTCAACCTGCGCTTTTCCT 58.601 45.000 9.73 0.00 0.00 3.36
2343 2764 1.153449 GTCCGTCGCCCATGATTCA 60.153 57.895 0.00 0.00 0.00 2.57
2354 2788 1.271762 CCATGATTCAGGCGGGATCAT 60.272 52.381 14.74 14.74 32.75 2.45
2476 2923 1.618343 CCAGATTTGGCTTTTCCGGTT 59.382 47.619 0.00 0.00 37.73 4.44
2477 2924 2.823154 CCAGATTTGGCTTTTCCGGTTA 59.177 45.455 0.00 0.00 37.73 2.85
2520 2967 3.625632 ATGGTCGGGGAGCACCTCT 62.626 63.158 0.00 0.00 42.86 3.69
2528 2975 2.659610 GAGCACCTCTCGCAACCT 59.340 61.111 0.00 0.00 31.20 3.50
2544 2991 1.348064 ACCTCGACAAAGTCCCATCA 58.652 50.000 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.521503 CGTCTAAAGACAATTCTTCAGATATCA 57.478 33.333 10.55 0.00 38.24 2.15
4 5 9.737427 TCGTCTAAAGACAATTCTTCAGATATC 57.263 33.333 10.55 0.00 38.24 1.63
5 6 9.743057 CTCGTCTAAAGACAATTCTTCAGATAT 57.257 33.333 10.55 0.00 38.24 1.63
6 7 7.702772 GCTCGTCTAAAGACAATTCTTCAGATA 59.297 37.037 10.55 0.00 38.24 1.98
7 8 6.533367 GCTCGTCTAAAGACAATTCTTCAGAT 59.467 38.462 10.55 0.00 38.24 2.90
8 9 5.864474 GCTCGTCTAAAGACAATTCTTCAGA 59.136 40.000 10.55 0.00 41.56 3.27
9 10 5.635280 TGCTCGTCTAAAGACAATTCTTCAG 59.365 40.000 10.55 0.00 41.56 3.02
10 11 5.538118 TGCTCGTCTAAAGACAATTCTTCA 58.462 37.500 10.55 0.00 41.56 3.02
11 12 5.445275 GCTGCTCGTCTAAAGACAATTCTTC 60.445 44.000 10.55 0.00 41.56 2.87
12 13 4.390297 GCTGCTCGTCTAAAGACAATTCTT 59.610 41.667 10.55 0.00 44.53 2.52
13 14 3.929610 GCTGCTCGTCTAAAGACAATTCT 59.070 43.478 10.55 0.00 44.99 2.40
14 15 3.679980 TGCTGCTCGTCTAAAGACAATTC 59.320 43.478 10.55 0.00 44.99 2.17
15 16 3.664107 TGCTGCTCGTCTAAAGACAATT 58.336 40.909 10.55 0.00 44.99 2.32
16 17 3.319137 TGCTGCTCGTCTAAAGACAAT 57.681 42.857 10.55 0.00 44.99 2.71
17 18 2.812358 TGCTGCTCGTCTAAAGACAA 57.188 45.000 10.55 0.00 44.99 3.18
18 19 2.812358 TTGCTGCTCGTCTAAAGACA 57.188 45.000 10.55 0.00 44.99 3.41
19 20 3.254060 TGATTGCTGCTCGTCTAAAGAC 58.746 45.455 0.00 0.00 41.47 3.01
20 21 3.592898 TGATTGCTGCTCGTCTAAAGA 57.407 42.857 0.00 0.00 0.00 2.52
21 22 4.118410 AGATGATTGCTGCTCGTCTAAAG 58.882 43.478 10.80 0.00 37.25 1.85
22 23 4.128925 AGATGATTGCTGCTCGTCTAAA 57.871 40.909 10.80 0.00 37.25 1.85
23 24 3.808466 AGATGATTGCTGCTCGTCTAA 57.192 42.857 10.80 0.00 37.25 2.10
24 25 3.808466 AAGATGATTGCTGCTCGTCTA 57.192 42.857 12.36 0.00 37.89 2.59
25 26 2.676839 CAAAGATGATTGCTGCTCGTCT 59.323 45.455 7.57 7.57 40.00 4.18
26 27 2.674852 TCAAAGATGATTGCTGCTCGTC 59.325 45.455 0.00 2.03 0.00 4.20
27 28 2.703416 TCAAAGATGATTGCTGCTCGT 58.297 42.857 0.00 0.00 0.00 4.18
28 29 3.423571 GTTCAAAGATGATTGCTGCTCG 58.576 45.455 0.00 0.00 34.96 5.03
29 30 3.125829 TCGTTCAAAGATGATTGCTGCTC 59.874 43.478 0.00 0.00 34.96 4.26
30 31 3.076621 TCGTTCAAAGATGATTGCTGCT 58.923 40.909 0.00 0.00 34.96 4.24
31 32 3.423571 CTCGTTCAAAGATGATTGCTGC 58.576 45.455 0.00 0.00 34.96 5.25
32 33 3.423571 GCTCGTTCAAAGATGATTGCTG 58.576 45.455 0.00 0.00 34.96 4.41
33 34 2.421424 GGCTCGTTCAAAGATGATTGCT 59.579 45.455 0.00 0.00 34.96 3.91
34 35 2.789092 CGGCTCGTTCAAAGATGATTGC 60.789 50.000 0.00 0.00 34.96 3.56
35 36 2.223112 CCGGCTCGTTCAAAGATGATTG 60.223 50.000 0.00 0.00 34.96 2.67
36 37 2.009774 CCGGCTCGTTCAAAGATGATT 58.990 47.619 0.00 0.00 34.96 2.57
37 38 1.656652 CCGGCTCGTTCAAAGATGAT 58.343 50.000 0.00 0.00 34.96 2.45
38 39 1.019278 GCCGGCTCGTTCAAAGATGA 61.019 55.000 22.15 0.00 0.00 2.92
39 40 1.425428 GCCGGCTCGTTCAAAGATG 59.575 57.895 22.15 0.00 0.00 2.90
40 41 2.100631 CGCCGGCTCGTTCAAAGAT 61.101 57.895 26.68 0.00 0.00 2.40
41 42 2.736995 CGCCGGCTCGTTCAAAGA 60.737 61.111 26.68 0.00 0.00 2.52
42 43 3.788766 CCGCCGGCTCGTTCAAAG 61.789 66.667 26.68 4.88 0.00 2.77
43 44 4.612412 ACCGCCGGCTCGTTCAAA 62.612 61.111 26.68 0.00 0.00 2.69
44 45 4.612412 AACCGCCGGCTCGTTCAA 62.612 61.111 26.68 0.00 0.00 2.69
75 76 2.706834 GGCCGCCGCTAAAAATGGT 61.707 57.895 0.00 0.00 34.44 3.55
113 114 1.973281 TGGTACGTGTCCCCGAGTC 60.973 63.158 0.00 0.00 0.00 3.36
114 115 2.115910 TGGTACGTGTCCCCGAGT 59.884 61.111 0.00 0.00 0.00 4.18
115 116 1.808531 TTGTGGTACGTGTCCCCGAG 61.809 60.000 0.00 0.00 0.00 4.63
116 117 1.831726 TTGTGGTACGTGTCCCCGA 60.832 57.895 0.00 0.00 0.00 5.14
117 118 1.665599 GTTGTGGTACGTGTCCCCG 60.666 63.158 0.00 0.00 0.00 5.73
118 119 1.301953 GGTTGTGGTACGTGTCCCC 60.302 63.158 0.00 0.00 0.00 4.81
119 120 1.665599 CGGTTGTGGTACGTGTCCC 60.666 63.158 0.00 0.00 0.00 4.46
120 121 0.665369 CTCGGTTGTGGTACGTGTCC 60.665 60.000 0.00 0.87 0.00 4.02
260 261 4.980805 GACCAACCGCTCCGTGCA 62.981 66.667 0.00 0.00 43.06 4.57
261 262 4.980805 TGACCAACCGCTCCGTGC 62.981 66.667 0.00 0.00 38.57 5.34
262 263 3.041940 GTGACCAACCGCTCCGTG 61.042 66.667 0.00 0.00 0.00 4.94
263 264 4.657824 CGTGACCAACCGCTCCGT 62.658 66.667 0.00 0.00 0.00 4.69
340 347 2.355599 CATCGCTAGCTGCTCGGG 60.356 66.667 13.93 8.87 40.11 5.14
341 348 3.034923 GCATCGCTAGCTGCTCGG 61.035 66.667 18.88 1.38 36.63 4.63
342 349 3.034923 GGCATCGCTAGCTGCTCG 61.035 66.667 23.47 4.69 39.29 5.03
343 350 3.034923 CGGCATCGCTAGCTGCTC 61.035 66.667 23.47 14.81 39.29 4.26
344 351 4.598894 CCGGCATCGCTAGCTGCT 62.599 66.667 23.47 7.57 39.29 4.24
463 487 5.878116 TCACATTCGATACCTTTTACCAAGG 59.122 40.000 0.00 0.00 43.05 3.61
475 500 5.517411 TGTTTGTACCGATCACATTCGATAC 59.483 40.000 0.00 0.00 41.62 2.24
490 515 0.738389 CCCCATGCGATGTTTGTACC 59.262 55.000 0.00 0.00 0.00 3.34
497 529 1.477700 CACATTTTCCCCATGCGATGT 59.522 47.619 0.00 0.00 0.00 3.06
498 530 1.477700 ACACATTTTCCCCATGCGATG 59.522 47.619 0.00 0.00 0.00 3.84
634 690 0.250513 ATTCCCACGGACAGAGCTTC 59.749 55.000 0.00 0.00 0.00 3.86
666 745 4.025480 GTCGTTGTGTAAATTTCCGTGACT 60.025 41.667 0.00 0.00 0.00 3.41
702 789 4.562757 CCTGTCAGGACGAAACATTCCTAA 60.563 45.833 14.26 0.00 40.52 2.69
737 824 4.899239 CTCCATCAGGCGGCGACC 62.899 72.222 10.28 11.10 33.74 4.79
746 833 5.923733 ACCTAAGTGTAGTTCTCCATCAG 57.076 43.478 0.00 0.00 0.00 2.90
766 853 2.122783 TGCCAATGCAGGTTACTACC 57.877 50.000 0.00 0.00 44.23 3.18
782 939 0.958822 CTGGTAACTTGGGTTGTGCC 59.041 55.000 0.00 0.00 36.92 5.01
787 944 3.895704 ATCAACCTGGTAACTTGGGTT 57.104 42.857 0.00 0.00 42.20 4.11
797 954 5.751243 GATAATTGCGTTATCAACCTGGT 57.249 39.130 13.71 0.00 45.28 4.00
858 1191 1.798813 GGCGATTCGTTTGTCTCTTGT 59.201 47.619 8.03 0.00 0.00 3.16
862 1195 1.429463 ACAGGCGATTCGTTTGTCTC 58.571 50.000 8.03 0.00 0.00 3.36
909 1248 3.286353 TGGATGGAGCGATGCAAAATTA 58.714 40.909 0.00 0.00 0.00 1.40
910 1249 2.100252 CTGGATGGAGCGATGCAAAATT 59.900 45.455 0.00 0.00 0.00 1.82
911 1250 1.679680 CTGGATGGAGCGATGCAAAAT 59.320 47.619 0.00 0.00 0.00 1.82
931 1270 2.116983 TTGTGGAGCAGAGCTGGGAC 62.117 60.000 0.00 0.00 39.88 4.46
955 1294 0.398522 AGTGGTCAGTGGAGTGTGGA 60.399 55.000 0.00 0.00 0.00 4.02
978 1320 0.323908 CTTCTCACTCCCCCTCGAGT 60.324 60.000 12.31 0.00 44.03 4.18
979 1321 1.671901 GCTTCTCACTCCCCCTCGAG 61.672 65.000 5.13 5.13 35.88 4.04
980 1322 1.682684 GCTTCTCACTCCCCCTCGA 60.683 63.158 0.00 0.00 0.00 4.04
981 1323 2.726351 GGCTTCTCACTCCCCCTCG 61.726 68.421 0.00 0.00 0.00 4.63
982 1324 0.985490 ATGGCTTCTCACTCCCCCTC 60.985 60.000 0.00 0.00 0.00 4.30
1102 1449 0.310543 ACCGTCGCGTTGTACTTGTA 59.689 50.000 5.77 0.00 0.00 2.41
1593 1952 1.525442 GGGCGGGTAGTAGTTGCAT 59.475 57.895 0.00 0.00 0.00 3.96
1662 2021 1.300233 CTCCTAGAATGTCGCGCCC 60.300 63.158 0.00 0.00 0.00 6.13
1714 2073 0.035881 ACACTGCCATGACAGACAGG 59.964 55.000 16.61 4.85 40.25 4.00
1746 2105 4.836736 AGCTTACAATACGCCCCTAGAATA 59.163 41.667 0.00 0.00 0.00 1.75
1755 2114 4.570772 TCTCAAATCAGCTTACAATACGCC 59.429 41.667 0.00 0.00 0.00 5.68
1758 2117 6.536582 TCTGCTCTCAAATCAGCTTACAATAC 59.463 38.462 0.00 0.00 36.53 1.89
1784 2148 1.600636 ACGGTGGCACTGTCATTGG 60.601 57.895 25.95 4.01 30.45 3.16
1796 2160 1.508632 AAATTCAGTCACGACGGTGG 58.491 50.000 0.00 0.00 44.50 4.61
1815 2179 7.559335 ACATCCATCTCTATTTGCCATACTA 57.441 36.000 0.00 0.00 0.00 1.82
1819 2183 6.131264 TGAAACATCCATCTCTATTTGCCAT 58.869 36.000 0.00 0.00 0.00 4.40
1822 2186 7.486647 ACATTGAAACATCCATCTCTATTTGC 58.513 34.615 0.00 0.00 0.00 3.68
1840 2204 2.287644 CAGTCACAGCAACGACATTGAA 59.712 45.455 0.00 0.00 41.23 2.69
1918 2288 2.042464 AGTCAGTTCTCTTCTGCCACA 58.958 47.619 0.00 0.00 33.48 4.17
1929 2299 4.150897 TGCCACAGTTTAAGTCAGTTCT 57.849 40.909 0.00 0.00 0.00 3.01
1937 2307 6.312399 TGTTCAGTTATGCCACAGTTTAAG 57.688 37.500 0.00 0.00 0.00 1.85
1947 2317 6.498304 CCATTCTGTAATGTTCAGTTATGCC 58.502 40.000 0.00 0.00 40.84 4.40
1987 2359 3.748568 CCTTGCTTCACTCAACTTCTACC 59.251 47.826 0.00 0.00 0.00 3.18
1988 2360 4.449405 GTCCTTGCTTCACTCAACTTCTAC 59.551 45.833 0.00 0.00 0.00 2.59
1989 2361 4.345257 AGTCCTTGCTTCACTCAACTTCTA 59.655 41.667 0.00 0.00 0.00 2.10
2009 2381 1.666189 GCGAAGATTACAAGGCCAGTC 59.334 52.381 5.01 0.00 0.00 3.51
2011 2383 2.029838 AGCGAAGATTACAAGGCCAG 57.970 50.000 5.01 0.00 0.00 4.85
2028 2400 6.852858 AACTTGAGAGTCTAAACAAGAAGC 57.147 37.500 20.99 0.00 41.16 3.86
2029 2401 9.405587 CTCTAACTTGAGAGTCTAAACAAGAAG 57.594 37.037 20.99 17.16 41.16 2.85
2031 2403 7.014326 TGCTCTAACTTGAGAGTCTAAACAAGA 59.986 37.037 20.99 8.43 44.21 3.02
2067 2439 2.361230 GGGGCTCTTTTCGGGGTG 60.361 66.667 0.00 0.00 0.00 4.61
2074 2446 3.338110 TTTAAGGGTTGGGGCTCTTTT 57.662 42.857 0.00 0.00 30.78 2.27
2078 2450 3.449737 GGTTATTTTAAGGGTTGGGGCTC 59.550 47.826 0.00 0.00 0.00 4.70
2085 2458 9.838975 CGTATTTTAACGGTTATTTTAAGGGTT 57.161 29.630 0.73 0.00 39.19 4.11
2130 2503 4.373116 GCGGGGTCTGTTCGAGCA 62.373 66.667 0.88 0.88 41.89 4.26
2133 2506 0.464013 TTTTTGCGGGGTCTGTTCGA 60.464 50.000 0.00 0.00 0.00 3.71
2272 2680 1.600916 GGTGAGGAAAAGCGCAGGT 60.601 57.895 11.47 0.00 44.60 4.00
2275 2683 0.321298 GGTAGGTGAGGAAAAGCGCA 60.321 55.000 11.47 0.00 0.00 6.09
2286 2694 1.153695 AGAGGGGAGGTGGTAGGTGA 61.154 60.000 0.00 0.00 0.00 4.02
2326 2734 1.143838 CTGAATCATGGGCGACGGA 59.856 57.895 0.00 0.00 0.00 4.69
2337 2745 0.535780 GCATGATCCCGCCTGAATCA 60.536 55.000 0.00 0.00 0.00 2.57
2343 2764 2.947938 CTTTCGGCATGATCCCGCCT 62.948 60.000 17.65 0.00 46.62 5.52
2458 2904 2.823747 GGTAACCGGAAAAGCCAAATCT 59.176 45.455 9.46 0.00 35.94 2.40
2520 2967 0.599204 GGACTTTGTCGAGGTTGCGA 60.599 55.000 0.00 0.00 38.07 5.10
2528 2975 0.037697 CGGTGATGGGACTTTGTCGA 60.038 55.000 0.00 0.00 32.65 4.20
2544 2991 4.467084 CCCGTACCTGCATGCGGT 62.467 66.667 28.46 28.46 45.39 5.68


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

AutoCloner maintained by Alex Coulton.