Multiple sequence alignment - TraesCS2B01G322600

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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 TraesCS2B01G322600 chr2B 100.000 4501 0 0 1 4501 461126276 461130776 0.000000e+00 8312.0
1 TraesCS2B01G322600 chr2B 86.486 629 78 6 3781 4407 120561394 120562017 0.000000e+00 684.0
2 TraesCS2B01G322600 chr2B 86.465 628 78 6 3781 4406 95792360 95792982 0.000000e+00 682.0
3 TraesCS2B01G322600 chr2B 85.737 638 86 5 3781 4415 67211660 67211025 0.000000e+00 669.0
4 TraesCS2B01G322600 chr2B 76.548 840 111 46 1188 1996 717363235 717364019 9.140000e-102 381.0
5 TraesCS2B01G322600 chr2D 94.467 1934 63 17 1849 3762 389289611 389291520 0.000000e+00 2939.0
6 TraesCS2B01G322600 chr2D 92.685 998 48 10 885 1868 389287153 389288139 0.000000e+00 1415.0
7 TraesCS2B01G322600 chr2D 95.886 316 10 3 526 841 389286848 389287160 4.020000e-140 508.0
8 TraesCS2B01G322600 chr2D 86.982 169 13 5 236 401 389286543 389286705 9.950000e-42 182.0
9 TraesCS2B01G322600 chr2A 92.708 1728 66 18 1853 3531 526098639 526100355 0.000000e+00 2438.0
10 TraesCS2B01G322600 chr2A 91.716 1340 63 29 371 1676 526097190 526098515 0.000000e+00 1816.0
11 TraesCS2B01G322600 chr2A 89.114 395 31 5 3639 4022 526100409 526100802 8.760000e-132 481.0
12 TraesCS2B01G322600 chr2A 82.687 387 34 18 2 385 526096530 526096886 3.380000e-81 313.0
13 TraesCS2B01G322600 chr2A 79.055 487 69 15 4024 4501 526113963 526114425 2.030000e-78 303.0
14 TraesCS2B01G322600 chr2A 78.850 487 70 15 4024 4501 526102457 526102919 9.470000e-77 298.0
15 TraesCS2B01G322600 chr4D 87.479 607 73 3 3781 4385 504283308 504283913 0.000000e+00 697.0
16 TraesCS2B01G322600 chr1B 86.624 628 77 6 3781 4406 57805046 57805668 0.000000e+00 688.0
17 TraesCS2B01G322600 chr1B 86.146 628 80 6 3781 4406 599317171 599317793 0.000000e+00 671.0
18 TraesCS2B01G322600 chr4A 86.538 624 80 4 3781 4402 726419936 726420557 0.000000e+00 684.0
19 TraesCS2B01G322600 chr4A 86.508 630 74 10 3781 4406 661815246 661815868 0.000000e+00 682.0
20 TraesCS2B01G322600 chr7A 86.328 629 78 7 3781 4406 433744874 433744251 0.000000e+00 678.0
21 TraesCS2B01G322600 chr7A 82.310 407 51 9 1225 1631 329013065 329013450 2.590000e-87 333.0
22 TraesCS2B01G322600 chr7B 78.761 791 115 31 1225 1996 361790411 361791167 8.760000e-132 481.0
23 TraesCS2B01G322600 chr7B 77.251 822 113 43 1206 1996 226614510 226613732 9.010000e-112 414.0
24 TraesCS2B01G322600 chr5A 78.084 835 116 41 1188 1996 288907055 288907848 2.450000e-127 466.0
25 TraesCS2B01G322600 chr5A 82.213 253 31 10 1754 1996 701899237 701898989 5.900000e-49 206.0
26 TraesCS2B01G322600 chr5B 78.644 693 98 30 1328 1996 24648882 24648216 9.010000e-112 414.0
27 TraesCS2B01G322600 chr6D 78.930 598 76 29 1206 1786 472449561 472448997 1.190000e-95 361.0
28 TraesCS2B01G322600 chr6A 75.908 826 109 49 1207 1996 617538376 617539147 1.550000e-89 340.0
29 TraesCS2B01G322600 chr7D 88.557 201 22 1 1431 1631 290559899 290560098 4.500000e-60 243.0
30 TraesCS2B01G322600 chr3A 75.735 136 31 2 1487 1621 396019501 396019635 2.910000e-07 67.6


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 TraesCS2B01G322600 chr2B 461126276 461130776 4500 False 8312.0 8312 100.000 1 4501 1 chr2B.!!$F3 4500
1 TraesCS2B01G322600 chr2B 120561394 120562017 623 False 684.0 684 86.486 3781 4407 1 chr2B.!!$F2 626
2 TraesCS2B01G322600 chr2B 95792360 95792982 622 False 682.0 682 86.465 3781 4406 1 chr2B.!!$F1 625
3 TraesCS2B01G322600 chr2B 67211025 67211660 635 True 669.0 669 85.737 3781 4415 1 chr2B.!!$R1 634
4 TraesCS2B01G322600 chr2B 717363235 717364019 784 False 381.0 381 76.548 1188 1996 1 chr2B.!!$F4 808
5 TraesCS2B01G322600 chr2D 389286543 389291520 4977 False 1261.0 2939 92.505 236 3762 4 chr2D.!!$F1 3526
6 TraesCS2B01G322600 chr2A 526096530 526102919 6389 False 1069.2 2438 87.015 2 4501 5 chr2A.!!$F2 4499
7 TraesCS2B01G322600 chr4D 504283308 504283913 605 False 697.0 697 87.479 3781 4385 1 chr4D.!!$F1 604
8 TraesCS2B01G322600 chr1B 57805046 57805668 622 False 688.0 688 86.624 3781 4406 1 chr1B.!!$F1 625
9 TraesCS2B01G322600 chr1B 599317171 599317793 622 False 671.0 671 86.146 3781 4406 1 chr1B.!!$F2 625
10 TraesCS2B01G322600 chr4A 726419936 726420557 621 False 684.0 684 86.538 3781 4402 1 chr4A.!!$F2 621
11 TraesCS2B01G322600 chr4A 661815246 661815868 622 False 682.0 682 86.508 3781 4406 1 chr4A.!!$F1 625
12 TraesCS2B01G322600 chr7A 433744251 433744874 623 True 678.0 678 86.328 3781 4406 1 chr7A.!!$R1 625
13 TraesCS2B01G322600 chr7B 361790411 361791167 756 False 481.0 481 78.761 1225 1996 1 chr7B.!!$F1 771
14 TraesCS2B01G322600 chr7B 226613732 226614510 778 True 414.0 414 77.251 1206 1996 1 chr7B.!!$R1 790
15 TraesCS2B01G322600 chr5A 288907055 288907848 793 False 466.0 466 78.084 1188 1996 1 chr5A.!!$F1 808
16 TraesCS2B01G322600 chr5B 24648216 24648882 666 True 414.0 414 78.644 1328 1996 1 chr5B.!!$R1 668
17 TraesCS2B01G322600 chr6D 472448997 472449561 564 True 361.0 361 78.930 1206 1786 1 chr6D.!!$R1 580
18 TraesCS2B01G322600 chr6A 617538376 617539147 771 False 340.0 340 75.908 1207 1996 1 chr6A.!!$F1 789

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
954 1315 0.179000 CTGGTCAAATCGAGGAGGGG 59.821 60.0 0.0 0.0 0.0 4.79 F
1911 3839 0.235926 GACGTGCTCTGCTTTCAACC 59.764 55.0 0.0 0.0 0.0 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2108 4073 0.595095 GCAGGCAGGTTTCAGACTTG 59.405 55.0 0.0 0.0 38.32 3.16 R
3599 5587 0.180406 ACACACACCAAGTCTCCACC 59.820 55.0 0.0 0.0 0.00 4.61 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
21 22 3.268103 AAGCCGCCGGAAGATGGTT 62.268 57.895 7.68 0.00 0.00 3.67
22 23 3.202706 GCCGCCGGAAGATGGTTC 61.203 66.667 7.68 0.00 0.00 3.62
23 24 2.890474 CCGCCGGAAGATGGTTCG 60.890 66.667 5.05 0.00 0.00 3.95
42 44 1.804326 CGTCAAACCCTAGTCGCCG 60.804 63.158 0.00 0.00 0.00 6.46
71 73 3.305064 CCACCACATGTTTTAGGGTTTCG 60.305 47.826 0.00 0.00 0.00 3.46
74 76 2.230266 CACATGTTTTAGGGTTTCGGGG 59.770 50.000 0.00 0.00 0.00 5.73
81 83 4.875561 TTTAGGGTTTCGGGGAAAAATG 57.124 40.909 0.00 0.00 33.14 2.32
82 84 2.391926 AGGGTTTCGGGGAAAAATGT 57.608 45.000 0.00 0.00 33.14 2.71
84 86 2.631062 AGGGTTTCGGGGAAAAATGTTC 59.369 45.455 0.00 0.00 33.14 3.18
85 87 2.365941 GGGTTTCGGGGAAAAATGTTCA 59.634 45.455 0.00 0.00 33.14 3.18
86 88 3.007506 GGGTTTCGGGGAAAAATGTTCAT 59.992 43.478 0.00 0.00 33.14 2.57
87 89 3.993736 GGTTTCGGGGAAAAATGTTCATG 59.006 43.478 0.00 0.00 33.14 3.07
88 90 4.262249 GGTTTCGGGGAAAAATGTTCATGA 60.262 41.667 0.00 0.00 33.14 3.07
89 91 5.478407 GTTTCGGGGAAAAATGTTCATGAT 58.522 37.500 0.00 0.00 33.14 2.45
101 104 9.726232 AAAAATGTTCATGATTGATGATACGAG 57.274 29.630 0.00 0.00 40.92 4.18
104 107 4.605640 TCATGATTGATGATACGAGCCA 57.394 40.909 0.00 0.00 36.06 4.75
118 121 6.542005 TGATACGAGCCATTGATTTGTTATGT 59.458 34.615 0.00 0.00 0.00 2.29
135 138 8.759481 TTGTTATGTTCCAATGGCTAATATCA 57.241 30.769 0.00 0.00 0.00 2.15
137 140 7.230510 TGTTATGTTCCAATGGCTAATATCACC 59.769 37.037 0.00 0.00 0.00 4.02
138 141 5.122707 TGTTCCAATGGCTAATATCACCA 57.877 39.130 0.00 0.00 37.99 4.17
147 150 4.598807 TGGCTAATATCACCATCACCTCAT 59.401 41.667 0.00 0.00 0.00 2.90
149 152 5.645497 GGCTAATATCACCATCACCTCATTC 59.355 44.000 0.00 0.00 0.00 2.67
152 155 6.949352 AATATCACCATCACCTCATTCAAC 57.051 37.500 0.00 0.00 0.00 3.18
155 158 0.734889 CCATCACCTCATTCAACCGC 59.265 55.000 0.00 0.00 0.00 5.68
170 173 2.662309 CCGCGTGGGGGTAGTATAT 58.338 57.895 7.26 0.00 0.00 0.86
175 178 3.256631 CGCGTGGGGGTAGTATATACTTT 59.743 47.826 20.21 0.30 37.73 2.66
179 182 6.071165 GCGTGGGGGTAGTATATACTTTACAT 60.071 42.308 20.21 0.00 37.73 2.29
210 213 8.357402 GCAGACAAAGACCTAAAAAGGAAAATA 58.643 33.333 0.00 0.00 0.00 1.40
263 266 9.884465 AATATAGCGACATTAAAGCAGAAAATC 57.116 29.630 0.00 0.00 0.00 2.17
390 714 4.864916 ATAATTGCTAGCACTTGACACG 57.135 40.909 25.69 0.00 0.00 4.49
434 758 2.645838 ATGGAGTGAAATATGCGCCT 57.354 45.000 4.18 0.00 0.00 5.52
458 782 8.336806 CCTTTTGTTAGAAATACACGTACAACA 58.663 33.333 0.00 0.00 0.00 3.33
494 818 5.363939 TGTTTTAAGAGCAAAACCCCATTG 58.636 37.500 8.51 0.00 44.28 2.82
527 851 9.120538 TCTTTTTGCAGTTAACTTAGAGACAAT 57.879 29.630 5.07 0.00 0.00 2.71
532 856 8.032952 TGCAGTTAACTTAGAGACAATCAATG 57.967 34.615 5.07 0.00 0.00 2.82
559 883 0.737019 GGTGCACATGCCATTTTCCG 60.737 55.000 20.43 0.00 41.18 4.30
570 894 4.580868 TGCCATTTTCCGAGTATACACAA 58.419 39.130 5.50 0.00 0.00 3.33
615 945 0.745468 ACTCCGAGAATCCCGTTAGC 59.255 55.000 1.33 0.00 0.00 3.09
853 1200 1.359848 CGCCGCAAAGCCTATATAGG 58.640 55.000 22.63 22.63 46.42 2.57
886 1237 4.101077 CCCTCCCTCCCTGCTCCT 62.101 72.222 0.00 0.00 0.00 3.69
902 1253 3.470888 CTCCGCACCCTTCCCGAT 61.471 66.667 0.00 0.00 0.00 4.18
954 1315 0.179000 CTGGTCAAATCGAGGAGGGG 59.821 60.000 0.00 0.00 0.00 4.79
955 1316 1.153147 GGTCAAATCGAGGAGGGGC 60.153 63.158 0.00 0.00 0.00 5.80
1090 1451 2.224378 CGGAGGGAGATGGTACGTACTA 60.224 54.545 24.07 19.58 0.00 1.82
1127 1489 6.187682 TCATTTCTTCCATTTTCTCTACCCC 58.812 40.000 0.00 0.00 0.00 4.95
1285 1650 2.559330 GGTAAAACTGTGGCGGCG 59.441 61.111 0.51 0.51 0.00 6.46
1286 1651 2.559330 GTAAAACTGTGGCGGCGG 59.441 61.111 9.78 0.00 0.00 6.13
1287 1652 3.358707 TAAAACTGTGGCGGCGGC 61.359 61.111 27.76 27.76 38.90 6.53
1324 1689 4.189188 CGTCCGTGCCGTAGAGGG 62.189 72.222 0.00 0.00 41.48 4.30
1631 2000 1.740296 CCTTCCCCGTAAGCACACG 60.740 63.158 3.35 3.35 41.59 4.49
1661 2035 1.304381 GGAACTTCCCTGCATGCCA 60.304 57.895 16.68 2.21 0.00 4.92
1692 2089 3.441572 AGATTCAAGGATTTTGGTGCTCG 59.558 43.478 0.00 0.00 0.00 5.03
1794 2215 0.969149 TGACTCTCGAGTGGCATTGT 59.031 50.000 18.82 4.72 42.66 2.71
1861 2285 6.984474 CGTATGACTTGTGTTATATTCAGGGT 59.016 38.462 0.00 0.00 29.41 4.34
1907 3835 1.495069 GCTGACGTGCTCTGCTTTC 59.505 57.895 0.00 0.00 40.01 2.62
1911 3839 0.235926 GACGTGCTCTGCTTTCAACC 59.764 55.000 0.00 0.00 0.00 3.77
2087 4052 9.309516 GTATGCTCATTCAATTTGATTTCATGT 57.690 29.630 0.00 0.00 0.00 3.21
2093 4058 9.434420 TCATTCAATTTGATTTCATGTTAACCC 57.566 29.630 2.48 0.00 0.00 4.11
2096 4061 6.209589 TCAATTTGATTTCATGTTAACCCGGA 59.790 34.615 0.73 0.00 0.00 5.14
2098 4063 6.406692 TTTGATTTCATGTTAACCCGGAAA 57.593 33.333 0.73 14.69 32.66 3.13
2108 4073 4.396790 TGTTAACCCGGAAATCATAACTGC 59.603 41.667 0.73 0.00 0.00 4.40
2178 4143 6.349300 TGCTTGAACCAGATAGTAAATCTCC 58.651 40.000 0.00 0.00 0.00 3.71
2183 4148 6.897966 TGAACCAGATAGTAAATCTCCTGTCT 59.102 38.462 0.00 0.00 30.31 3.41
2185 4150 5.069781 ACCAGATAGTAAATCTCCTGTCTGC 59.930 44.000 7.61 0.00 42.35 4.26
2204 4169 2.098934 TGCTGTGTCAATTTTGCGTCTT 59.901 40.909 0.00 0.00 0.00 3.01
2281 4246 3.223589 GGCACCAACAAAGGCGGT 61.224 61.111 0.00 0.00 0.00 5.68
2323 4288 2.353803 GCTGTTCCTCGTCATGTACCTT 60.354 50.000 0.00 0.00 0.00 3.50
2428 4393 2.307686 GGTCCTCCCAAGTTGTCCATAA 59.692 50.000 1.45 0.00 0.00 1.90
2432 4397 6.184789 GTCCTCCCAAGTTGTCCATAAAATA 58.815 40.000 1.45 0.00 0.00 1.40
2433 4398 6.318900 GTCCTCCCAAGTTGTCCATAAAATAG 59.681 42.308 1.45 0.00 0.00 1.73
2439 4404 7.147846 CCCAAGTTGTCCATAAAATAGAATGCT 60.148 37.037 1.45 0.00 0.00 3.79
2576 4545 1.479994 GTCGTACGTGTTCACGCAC 59.520 57.895 22.35 18.93 38.05 5.34
2825 4794 0.682209 TCAGCTACCTGTACGACCCC 60.682 60.000 0.00 0.00 40.09 4.95
2826 4795 0.968901 CAGCTACCTGTACGACCCCA 60.969 60.000 0.00 0.00 34.31 4.96
2837 4806 2.863346 CGACCCCACCAACGAGACA 61.863 63.158 0.00 0.00 0.00 3.41
3320 5289 1.294780 CTGCTCCGTCTTCCTGCTT 59.705 57.895 0.00 0.00 0.00 3.91
3335 5304 2.666812 CTTCCCACCGTGTACCCC 59.333 66.667 0.00 0.00 0.00 4.95
3392 5361 3.047877 GGCGTCGTCCTGGGTTTG 61.048 66.667 0.00 0.00 0.00 2.93
3513 5491 0.176910 GGTCTGAGAGCCAAGTAGCC 59.823 60.000 0.00 0.00 0.00 3.93
3547 5535 4.394729 AGTCATTCTTTTTCGTTGGGCTA 58.605 39.130 0.00 0.00 0.00 3.93
3565 5553 0.940833 TATGCGTGTGTGTGTGTTGG 59.059 50.000 0.00 0.00 0.00 3.77
3567 5555 1.237954 TGCGTGTGTGTGTGTTGGTT 61.238 50.000 0.00 0.00 0.00 3.67
3577 5565 3.183775 GTGTGTGTTGGTTGTATCGTCTC 59.816 47.826 0.00 0.00 0.00 3.36
3598 5586 4.553323 TCGTCAGTGAACTTAGTTTAGGC 58.447 43.478 0.00 0.00 0.00 3.93
3599 5587 3.364023 CGTCAGTGAACTTAGTTTAGGCG 59.636 47.826 0.00 0.00 0.00 5.52
3608 5596 2.226962 TAGTTTAGGCGGTGGAGACT 57.773 50.000 0.00 0.00 0.00 3.24
3612 5600 0.834687 TTAGGCGGTGGAGACTTGGT 60.835 55.000 0.00 0.00 0.00 3.67
3613 5601 1.541310 TAGGCGGTGGAGACTTGGTG 61.541 60.000 0.00 0.00 0.00 4.17
3620 5608 0.104120 TGGAGACTTGGTGTGTGTCG 59.896 55.000 0.00 0.00 36.01 4.35
3624 5612 1.752498 AGACTTGGTGTGTGTCGTACA 59.248 47.619 0.00 0.00 36.01 2.90
3733 5721 2.377310 CCGATCGAAAACGCCGTGT 61.377 57.895 18.66 0.00 0.00 4.49
3737 5725 1.897398 ATCGAAAACGCCGTGTGCTC 61.897 55.000 0.00 0.00 38.05 4.26
3752 5740 5.106555 CCGTGTGCTCAAATGAATAGAAAGT 60.107 40.000 0.00 0.00 0.00 2.66
3816 5814 7.992008 TCTATCATGACAGTACAACGAACATA 58.008 34.615 0.00 0.00 0.00 2.29
3818 5816 7.899178 ATCATGACAGTACAACGAACATAAA 57.101 32.000 0.00 0.00 0.00 1.40
3851 5850 8.258007 TGAAAATTACATCCAGATTCGTAGACT 58.742 33.333 0.00 0.00 34.32 3.24
3870 5869 3.338249 ACTACCTAGCGACGACTACAAA 58.662 45.455 0.00 0.00 0.00 2.83
3927 5926 3.677284 CTCCCTCGTCGGAGTCGGA 62.677 68.421 11.10 0.00 43.94 4.55
3932 5931 2.176055 CGTCGGAGTCGGACACAG 59.824 66.667 25.17 5.13 35.06 3.66
4066 7718 0.236711 AGACACACGAACGTAGACGG 59.763 55.000 7.04 5.94 44.95 4.79
4084 7736 2.178912 GGACAACAACCAGATCCGAA 57.821 50.000 0.00 0.00 0.00 4.30
4129 7781 1.740285 GAGACACACCTCCACACGT 59.260 57.895 0.00 0.00 0.00 4.49
4137 7789 1.147376 CCTCCACACGTCCACCAAA 59.853 57.895 0.00 0.00 0.00 3.28
4198 7850 6.653989 GGAGACCTTTATTTCATCTTCAGGA 58.346 40.000 0.00 0.00 0.00 3.86
4203 7855 5.890419 CCTTTATTTCATCTTCAGGAAGCCT 59.110 40.000 4.15 0.00 38.28 4.58
4241 7893 1.985159 TGAGCAGGACACAAACCCTAT 59.015 47.619 0.00 0.00 0.00 2.57
4297 7949 2.291043 ACCGGCCCTCGTCAAGATT 61.291 57.895 0.00 0.00 37.11 2.40
4299 7951 1.878522 CGGCCCTCGTCAAGATTCG 60.879 63.158 0.00 0.00 0.00 3.34
4320 7973 2.445845 CGCCCCATGACCCTAGGA 60.446 66.667 11.48 0.00 0.00 2.94
4331 7984 4.348020 TGACCCTAGGACCACTAAAGAT 57.652 45.455 11.48 0.00 0.00 2.40
4341 7994 3.162666 ACCACTAAAGATGAGACGGACA 58.837 45.455 0.00 0.00 0.00 4.02
4367 8020 2.887568 CATCCACGAGAGGCACGC 60.888 66.667 0.00 0.00 0.00 5.34
4374 8027 1.320344 ACGAGAGGCACGCATCCTAA 61.320 55.000 0.00 0.00 33.24 2.69
4376 8029 0.175760 GAGAGGCACGCATCCTAACA 59.824 55.000 0.00 0.00 33.24 2.41
4418 8077 1.872679 GCGGCTGCGTAGTACTGTC 60.873 63.158 5.39 0.00 0.00 3.51
4466 8134 3.322191 ACCCCTCTCATCTCCTTCTAC 57.678 52.381 0.00 0.00 0.00 2.59
4496 8164 2.751806 CTGGAGAGCCAAAGAATTGACC 59.248 50.000 0.00 0.00 45.41 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.399181 ATCTTCCGGCGGCTTCCA 61.399 61.111 23.83 0.00 0.00 3.53
4 5 3.682292 GAACCATCTTCCGGCGGCT 62.682 63.158 23.83 2.28 0.00 5.52
6 7 2.890474 CGAACCATCTTCCGGCGG 60.890 66.667 22.51 22.51 0.00 6.13
9 10 2.125673 ACGCGAACCATCTTCCGG 60.126 61.111 15.93 0.00 0.00 5.14
12 13 1.136057 GGTTTGACGCGAACCATCTTC 60.136 52.381 19.93 2.98 44.87 2.87
21 22 1.210931 CGACTAGGGTTTGACGCGA 59.789 57.895 15.93 0.00 36.04 5.87
22 23 2.442188 GCGACTAGGGTTTGACGCG 61.442 63.158 3.53 3.53 37.56 6.01
23 24 2.098831 GGCGACTAGGGTTTGACGC 61.099 63.158 0.00 0.00 43.86 5.19
42 44 1.241315 AAACATGTGGTGGCGCCTAC 61.241 55.000 29.70 22.61 38.35 3.18
46 48 0.109319 CCTAAAACATGTGGTGGCGC 60.109 55.000 0.00 0.00 0.00 6.53
51 53 2.888414 CCGAAACCCTAAAACATGTGGT 59.112 45.455 0.00 0.00 0.00 4.16
71 73 6.642430 TCATCAATCATGAACATTTTTCCCC 58.358 36.000 0.00 0.00 38.68 4.81
74 76 9.720667 TCGTATCATCAATCATGAACATTTTTC 57.279 29.630 0.00 0.00 45.06 2.29
81 83 4.751600 TGGCTCGTATCATCAATCATGAAC 59.248 41.667 0.00 0.00 45.06 3.18
82 84 4.959723 TGGCTCGTATCATCAATCATGAA 58.040 39.130 0.00 0.00 45.06 2.57
84 86 5.410439 TCAATGGCTCGTATCATCAATCATG 59.590 40.000 0.00 0.00 0.00 3.07
85 87 5.554070 TCAATGGCTCGTATCATCAATCAT 58.446 37.500 0.00 0.00 0.00 2.45
86 88 4.959723 TCAATGGCTCGTATCATCAATCA 58.040 39.130 0.00 0.00 0.00 2.57
87 89 6.492007 AATCAATGGCTCGTATCATCAATC 57.508 37.500 0.00 0.00 0.00 2.67
88 90 6.263842 ACAAATCAATGGCTCGTATCATCAAT 59.736 34.615 0.00 0.00 0.00 2.57
89 91 5.589855 ACAAATCAATGGCTCGTATCATCAA 59.410 36.000 0.00 0.00 0.00 2.57
101 104 6.037391 CCATTGGAACATAACAAATCAATGGC 59.963 38.462 16.00 0.00 46.90 4.40
104 107 6.949715 AGCCATTGGAACATAACAAATCAAT 58.050 32.000 6.95 0.00 39.30 2.57
118 121 5.769662 GTGATGGTGATATTAGCCATTGGAA 59.230 40.000 6.95 0.00 42.48 3.53
135 138 1.950484 GCGGTTGAATGAGGTGATGGT 60.950 52.381 0.00 0.00 0.00 3.55
137 140 0.374758 CGCGGTTGAATGAGGTGATG 59.625 55.000 0.00 0.00 0.00 3.07
138 141 0.036388 ACGCGGTTGAATGAGGTGAT 60.036 50.000 12.47 0.00 0.00 3.06
147 150 3.240011 TACCCCCACGCGGTTGAA 61.240 61.111 12.47 0.00 34.66 2.69
149 152 1.963464 ATACTACCCCCACGCGGTTG 61.963 60.000 12.47 0.00 34.66 3.77
152 155 1.474077 GTATATACTACCCCCACGCGG 59.526 57.143 12.47 0.00 0.00 6.46
155 158 6.899393 TGTAAAGTATATACTACCCCCACG 57.101 41.667 15.74 0.00 34.99 4.94
170 173 6.868864 GTCTTTGTCTGCAGAGATGTAAAGTA 59.131 38.462 18.89 9.81 38.01 2.24
175 178 3.834813 AGGTCTTTGTCTGCAGAGATGTA 59.165 43.478 18.89 0.00 38.01 2.29
179 182 4.955811 TTTAGGTCTTTGTCTGCAGAGA 57.044 40.909 18.89 14.32 34.04 3.10
223 226 7.332557 TGTCGCTATATTTACCTCAGGAAAAA 58.667 34.615 0.00 0.00 0.00 1.94
224 227 6.880484 TGTCGCTATATTTACCTCAGGAAAA 58.120 36.000 0.00 0.00 0.00 2.29
225 228 6.474140 TGTCGCTATATTTACCTCAGGAAA 57.526 37.500 0.00 0.00 0.00 3.13
226 229 6.665992 ATGTCGCTATATTTACCTCAGGAA 57.334 37.500 0.00 0.00 0.00 3.36
227 230 6.665992 AATGTCGCTATATTTACCTCAGGA 57.334 37.500 0.00 0.00 0.00 3.86
228 231 8.827177 TTTAATGTCGCTATATTTACCTCAGG 57.173 34.615 0.00 0.00 0.00 3.86
229 232 8.436200 GCTTTAATGTCGCTATATTTACCTCAG 58.564 37.037 0.00 0.00 0.00 3.35
230 233 7.929245 TGCTTTAATGTCGCTATATTTACCTCA 59.071 33.333 0.00 0.00 0.00 3.86
231 234 8.306680 TGCTTTAATGTCGCTATATTTACCTC 57.693 34.615 0.00 0.00 0.00 3.85
232 235 8.148351 TCTGCTTTAATGTCGCTATATTTACCT 58.852 33.333 0.00 0.00 0.00 3.08
233 236 8.306680 TCTGCTTTAATGTCGCTATATTTACC 57.693 34.615 0.00 0.00 0.00 2.85
500 824 8.500753 TGTCTCTAAGTTAACTGCAAAAAGAA 57.499 30.769 9.34 0.00 0.00 2.52
501 825 8.500753 TTGTCTCTAAGTTAACTGCAAAAAGA 57.499 30.769 9.34 4.39 0.00 2.52
502 826 9.387123 GATTGTCTCTAAGTTAACTGCAAAAAG 57.613 33.333 9.34 2.13 0.00 2.27
513 837 6.595326 CACTGGCATTGATTGTCTCTAAGTTA 59.405 38.462 0.00 0.00 0.00 2.24
527 851 1.152798 TGCACCACACTGGCATTGA 60.153 52.632 12.15 0.00 42.67 2.57
559 883 4.825085 CCTCTCTCCCTCTTGTGTATACTC 59.175 50.000 4.17 0.83 0.00 2.59
570 894 1.203050 GCAGCTATCCTCTCTCCCTCT 60.203 57.143 0.00 0.00 0.00 3.69
856 1203 3.787001 GAGGGGGTGAAGGGAGCG 61.787 72.222 0.00 0.00 0.00 5.03
886 1237 2.042741 TATCGGGAAGGGTGCGGA 60.043 61.111 0.00 0.00 0.00 5.54
910 1261 3.785859 TGATGCCTGCCTCGGGAC 61.786 66.667 0.00 0.00 29.82 4.46
931 1282 2.479730 CCTCCTCGATTTGACCAGTACG 60.480 54.545 0.00 0.00 0.00 3.67
933 1284 2.108168 CCCTCCTCGATTTGACCAGTA 58.892 52.381 0.00 0.00 0.00 2.74
954 1315 0.960861 CTTCTCCAAGGTTTCCCGGC 60.961 60.000 0.00 0.00 35.12 6.13
955 1316 0.322546 CCTTCTCCAAGGTTTCCCGG 60.323 60.000 0.00 0.00 44.11 5.73
984 1345 0.104304 CCATGGCGAGTACCTACCAC 59.896 60.000 0.00 0.00 34.36 4.16
985 1346 1.682451 GCCATGGCGAGTACCTACCA 61.682 60.000 23.48 1.24 36.43 3.25
1090 1451 2.057922 AGAAATGATGAGGGGCCGTAT 58.942 47.619 0.00 0.00 0.00 3.06
1285 1650 0.800683 GAAAATTAGCCAACGCCGCC 60.801 55.000 0.00 0.00 34.57 6.13
1286 1651 0.170339 AGAAAATTAGCCAACGCCGC 59.830 50.000 0.00 0.00 34.57 6.53
1287 1652 2.515912 GAAGAAAATTAGCCAACGCCG 58.484 47.619 0.00 0.00 34.57 6.46
1324 1689 1.667212 TCATGCAAGATCACATCACGC 59.333 47.619 0.00 0.00 0.00 5.34
1631 2000 1.338484 GGAAGTTCCGGGAAGGTGTAC 60.338 57.143 10.35 0.00 41.99 2.90
1661 2035 1.358152 TCCTTGAATCTGGGAACGGT 58.642 50.000 0.00 0.00 38.16 4.83
1692 2089 6.094048 TGAATTCTACAAGCAGAGCATAAACC 59.906 38.462 7.05 0.00 0.00 3.27
1794 2215 2.951457 TCAAGATACGGTCATTGCGA 57.049 45.000 0.00 0.00 0.00 5.10
1806 2227 9.330063 CAGCTACAGGAAAATACATTCAAGATA 57.670 33.333 0.00 0.00 0.00 1.98
1924 3864 5.327091 CAGTTGTCTGTTGTCAAACAAGAG 58.673 41.667 9.92 9.92 46.98 2.85
2087 4052 4.590918 TGCAGTTATGATTTCCGGGTTAA 58.409 39.130 0.00 0.00 0.00 2.01
2092 4057 3.941483 AGACTTGCAGTTATGATTTCCGG 59.059 43.478 0.00 0.00 0.00 5.14
2093 4058 4.631377 TCAGACTTGCAGTTATGATTTCCG 59.369 41.667 0.00 0.00 0.00 4.30
2096 4061 6.491403 AGGTTTCAGACTTGCAGTTATGATTT 59.509 34.615 0.00 0.00 28.68 2.17
2098 4063 5.413833 CAGGTTTCAGACTTGCAGTTATGAT 59.586 40.000 0.00 0.00 28.68 2.45
2108 4073 0.595095 GCAGGCAGGTTTCAGACTTG 59.405 55.000 0.00 0.00 38.32 3.16
2123 4088 3.134458 AGAAAGAACAAGAACGAGCAGG 58.866 45.455 0.00 0.00 0.00 4.85
2178 4143 3.047796 GCAAAATTGACACAGCAGACAG 58.952 45.455 0.00 0.00 0.00 3.51
2183 4148 1.675483 AGACGCAAAATTGACACAGCA 59.325 42.857 0.00 0.00 0.00 4.41
2185 4150 3.951306 TGAAGACGCAAAATTGACACAG 58.049 40.909 0.00 0.00 0.00 3.66
2204 4169 1.105457 GCATAGGCCTGCAACAATGA 58.895 50.000 17.99 0.00 41.87 2.57
2323 4288 1.005450 GCCCAGATGAAGGTTAACCCA 59.995 52.381 21.30 13.19 36.42 4.51
2439 4404 3.551454 CGGTGTACCTCTTTCAGTCGAAA 60.551 47.826 0.00 0.00 38.83 3.46
2576 4545 3.720106 CTCCGGCGTCGTCTCGAAG 62.720 68.421 9.28 1.28 37.72 3.79
2825 4794 2.738521 CCGGCTGTCTCGTTGGTG 60.739 66.667 0.00 0.00 0.00 4.17
2826 4795 4.681978 GCCGGCTGTCTCGTTGGT 62.682 66.667 22.15 0.00 0.00 3.67
3233 5202 3.537874 CGGAGGTAGAAGGGGCCG 61.538 72.222 0.00 0.00 0.00 6.13
3320 5289 1.991167 GATGGGGTACACGGTGGGA 60.991 63.158 13.48 0.00 0.00 4.37
3335 5304 4.330250 AGTTGAAGGTGTCCATCTTGATG 58.670 43.478 0.00 3.77 30.64 3.07
3389 5358 1.355381 ACCCACCAGAGCATGATCAAA 59.645 47.619 14.38 0.00 0.00 2.69
3390 5359 0.994247 ACCCACCAGAGCATGATCAA 59.006 50.000 14.38 0.00 0.00 2.57
3392 5361 0.531532 CGACCCACCAGAGCATGATC 60.532 60.000 1.78 1.78 0.00 2.92
3513 5491 5.481200 AAAGAATGACTTGATCGAGCATG 57.519 39.130 14.27 14.27 38.98 4.06
3547 5535 1.029408 ACCAACACACACACACGCAT 61.029 50.000 0.00 0.00 0.00 4.73
3565 5553 3.466712 TCACTGACGAGACGATACAAC 57.533 47.619 0.00 0.00 0.00 3.32
3567 5555 3.072211 AGTTCACTGACGAGACGATACA 58.928 45.455 0.00 0.00 0.00 2.29
3577 5565 3.364023 CGCCTAAACTAAGTTCACTGACG 59.636 47.826 0.00 0.00 0.00 4.35
3598 5586 0.880278 CACACACCAAGTCTCCACCG 60.880 60.000 0.00 0.00 0.00 4.94
3599 5587 0.180406 ACACACACCAAGTCTCCACC 59.820 55.000 0.00 0.00 0.00 4.61
3620 5608 8.521176 TCAACCTATCTCTAGTTTCTTGTGTAC 58.479 37.037 0.00 0.00 0.00 2.90
3624 5612 7.878644 GGTTTCAACCTATCTCTAGTTTCTTGT 59.121 37.037 1.08 0.00 45.75 3.16
3625 5613 8.257830 GGTTTCAACCTATCTCTAGTTTCTTG 57.742 38.462 1.08 0.00 45.75 3.02
3733 5721 6.094048 GGCACTACTTTCTATTCATTTGAGCA 59.906 38.462 0.00 0.00 0.00 4.26
3737 5725 8.514594 TCTTTGGCACTACTTTCTATTCATTTG 58.485 33.333 0.00 0.00 0.00 2.32
3772 5760 8.684386 TGATAGAAGATGAATAGAGTTCTCGT 57.316 34.615 0.00 0.00 0.00 4.18
3773 5761 9.558648 CATGATAGAAGATGAATAGAGTTCTCG 57.441 37.037 0.00 0.00 0.00 4.04
3778 5766 9.365906 ACTGTCATGATAGAAGATGAATAGAGT 57.634 33.333 24.50 0.00 30.45 3.24
3826 5825 8.649973 AGTCTACGAATCTGGATGTAATTTTC 57.350 34.615 0.00 0.00 0.00 2.29
3851 5850 4.216257 AGTTTTTGTAGTCGTCGCTAGGTA 59.784 41.667 0.00 0.00 0.00 3.08
3870 5869 0.951040 CCTTCGGCTCGCTTCAGTTT 60.951 55.000 0.00 0.00 0.00 2.66
3892 5891 3.845259 GGGGCGATGACGGTAGCA 61.845 66.667 0.00 0.00 40.15 3.49
3927 5926 4.099573 ACTGTCTACTACAACAAGCTGTGT 59.900 41.667 0.00 0.00 44.64 3.72
3932 5931 7.652507 ACTTTCTAACTGTCTACTACAACAAGC 59.347 37.037 0.00 0.00 37.74 4.01
4041 7693 2.019951 CGTTCGTGTGTCTTCGGGG 61.020 63.158 0.00 0.00 0.00 5.73
4066 7718 2.489971 TGTTCGGATCTGGTTGTTGTC 58.510 47.619 0.62 0.00 0.00 3.18
4129 7781 1.559682 GGGTCTAGCATCTTTGGTGGA 59.440 52.381 0.00 0.00 38.35 4.02
4137 7789 1.043816 CGGTGATGGGTCTAGCATCT 58.956 55.000 9.39 0.00 0.00 2.90
4203 7855 0.319555 CAGGAAGTTGAGACGGCGAA 60.320 55.000 16.62 0.00 0.00 4.70
4257 7909 2.027837 GGAAGGGCTCCGTTGTTAGTTA 60.028 50.000 0.00 0.00 33.37 2.24
4288 7940 2.395690 GCGTGGCGAATCTTGACG 59.604 61.111 0.00 0.00 0.00 4.35
4290 7942 2.435938 GGGCGTGGCGAATCTTGA 60.436 61.111 0.00 0.00 0.00 3.02
4320 7973 3.162666 TGTCCGTCTCATCTTTAGTGGT 58.837 45.455 0.00 0.00 0.00 4.16
4352 8005 3.356639 GATGCGTGCCTCTCGTGGA 62.357 63.158 0.00 0.00 0.00 4.02
4354 8007 2.004808 TAGGATGCGTGCCTCTCGTG 62.005 60.000 0.00 0.00 36.96 4.35
4407 8066 1.986698 CCCAAACGGACAGTACTACG 58.013 55.000 10.96 10.96 0.00 3.51
4418 8077 6.485313 TGTTAGATATAATCTTGCCCAAACGG 59.515 38.462 0.00 0.00 40.76 4.44
4437 8105 5.103043 AGGAGATGAGAGGGGTTATGTTAGA 60.103 44.000 0.00 0.00 0.00 2.10
4466 8134 2.438075 GCTCTCCAGCAAGGCAGG 60.438 66.667 0.00 0.00 46.06 4.85
4481 8149 0.539438 TGCCGGTCAATTCTTTGGCT 60.539 50.000 1.90 0.00 42.87 4.75


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

AutoCloner maintained by Alex Coulton.