Multiple sequence alignment - TraesCS3D01G423200

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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 TraesCS3D01G423200 chr3D 100.000 3956 0 0 1 3956 535777791 535773836 0.000000e+00 7306.0
1 TraesCS3D01G423200 chr3B 92.150 2102 140 17 108 2199 707418963 707416877 0.000000e+00 2944.0
2 TraesCS3D01G423200 chr3B 94.162 1593 64 11 2194 3772 707416837 707415260 0.000000e+00 2399.0
3 TraesCS3D01G423200 chr3B 93.119 218 12 3 340 555 92328743 92328959 2.290000e-82 316.0
4 TraesCS3D01G423200 chr3B 95.783 166 5 1 3787 3952 707415275 707415112 2.340000e-67 267.0
5 TraesCS3D01G423200 chr3A 95.765 1275 39 4 2194 3458 671020936 671019667 0.000000e+00 2041.0
6 TraesCS3D01G423200 chr3A 88.600 1693 135 31 107 1755 671023228 671021550 0.000000e+00 2004.0
7 TraesCS3D01G423200 chr3A 90.909 473 14 7 1756 2199 671021448 671020976 3.380000e-170 608.0
8 TraesCS3D01G423200 chr3A 92.760 221 13 3 340 558 694364670 694364451 2.290000e-82 316.0
9 TraesCS3D01G423200 chr3A 95.906 171 6 1 3787 3956 671019265 671019095 3.890000e-70 276.0
10 TraesCS3D01G423200 chr3A 89.333 75 7 1 2 75 671023301 671023227 4.210000e-15 93.5
11 TraesCS3D01G423200 chrUn 93.119 218 12 3 340 555 86451476 86451692 2.290000e-82 316.0
12 TraesCS3D01G423200 chrUn 93.119 218 12 3 340 555 86457475 86457691 2.290000e-82 316.0
13 TraesCS3D01G423200 chr4D 93.119 218 12 3 340 555 123434628 123434844 2.290000e-82 316.0
14 TraesCS3D01G423200 chr2D 93.119 218 12 3 340 555 322913531 322913747 2.290000e-82 316.0
15 TraesCS3D01G423200 chr1A 93.119 218 12 3 340 555 238123767 238123983 2.290000e-82 316.0
16 TraesCS3D01G423200 chr5D 76.727 275 41 12 28 299 334241299 334241553 8.920000e-27 132.0
17 TraesCS3D01G423200 chr7B 74.216 287 62 10 19 298 628450874 628450593 4.180000e-20 110.0
18 TraesCS3D01G423200 chr7B 75.100 249 46 12 61 299 711164416 711164174 6.990000e-18 102.0


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 TraesCS3D01G423200 chr3D 535773836 535777791 3955 True 7306.0 7306 100.000000 1 3956 1 chr3D.!!$R1 3955
1 TraesCS3D01G423200 chr3B 707415112 707418963 3851 True 1870.0 2944 94.031667 108 3952 3 chr3B.!!$R1 3844
2 TraesCS3D01G423200 chr3A 671019095 671023301 4206 True 1004.5 2041 92.102600 2 3956 5 chr3A.!!$R2 3954

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
83 85 0.036388 GTCTCCGGTGGATCTTGCAA 60.036 55.0 0.0 0.0 0.00 4.08 F
1078 1121 0.036765 ATGCAATCGTACCCGTGTGT 60.037 50.0 0.0 0.0 35.01 3.72 F
1325 1368 0.960861 CCGGCTGTCCTTCCTTTTCC 60.961 60.0 0.0 0.0 0.00 3.13 F
2353 2575 0.322816 GCCTGGACTCAAGATGCCAA 60.323 55.0 0.0 0.0 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1334 1380 0.249741 CGCCAGTAACCCTAATCCCG 60.250 60.0 0.00 0.00 0.00 5.14 R
2158 2334 0.532862 AGTTGAAGTGGTCCTGTGCG 60.533 55.0 0.00 0.00 0.00 5.34 R
2861 3094 0.877743 GGCTGTTTCAGAAGCAGGAC 59.122 55.0 23.93 11.29 41.36 3.85 R
3814 4175 0.027979 CGCGTTAACTGCCCATGATG 59.972 55.0 14.03 0.00 0.00 3.07 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
22 24 3.141488 CCTCGCCTAGCACCGTCT 61.141 66.667 0.00 0.00 0.00 4.18
74 76 1.183030 TGTAGGTGTGTCTCCGGTGG 61.183 60.000 0.00 0.00 0.00 4.61
75 77 0.896940 GTAGGTGTGTCTCCGGTGGA 60.897 60.000 0.00 0.00 0.00 4.02
76 78 0.040646 TAGGTGTGTCTCCGGTGGAT 59.959 55.000 0.00 0.00 0.00 3.41
77 79 1.218316 GGTGTGTCTCCGGTGGATC 59.782 63.158 0.00 0.63 0.00 3.36
78 80 1.258445 GGTGTGTCTCCGGTGGATCT 61.258 60.000 0.00 0.00 0.00 2.75
79 81 0.608640 GTGTGTCTCCGGTGGATCTT 59.391 55.000 0.00 0.00 0.00 2.40
80 82 0.608130 TGTGTCTCCGGTGGATCTTG 59.392 55.000 0.00 0.00 0.00 3.02
81 83 0.741221 GTGTCTCCGGTGGATCTTGC 60.741 60.000 0.00 0.00 0.00 4.01
82 84 1.191489 TGTCTCCGGTGGATCTTGCA 61.191 55.000 0.00 0.00 0.00 4.08
83 85 0.036388 GTCTCCGGTGGATCTTGCAA 60.036 55.000 0.00 0.00 0.00 4.08
84 86 0.250234 TCTCCGGTGGATCTTGCAAG 59.750 55.000 20.81 20.81 0.00 4.01
85 87 0.250234 CTCCGGTGGATCTTGCAAGA 59.750 55.000 30.23 30.23 39.78 3.02
87 89 1.281867 TCCGGTGGATCTTGCAAGATT 59.718 47.619 35.91 22.79 45.39 2.40
88 90 1.672881 CCGGTGGATCTTGCAAGATTC 59.327 52.381 35.91 34.26 45.39 2.52
89 91 2.358957 CGGTGGATCTTGCAAGATTCA 58.641 47.619 36.40 36.40 46.28 2.57
94 96 3.760151 TGGATCTTGCAAGATTCAGTTGG 59.240 43.478 36.40 7.43 44.21 3.77
95 97 3.428589 GGATCTTGCAAGATTCAGTTGGC 60.429 47.826 35.91 22.61 45.39 4.52
96 98 1.536766 TCTTGCAAGATTCAGTTGGCG 59.463 47.619 25.16 0.00 0.00 5.69
97 99 0.597568 TTGCAAGATTCAGTTGGCGG 59.402 50.000 0.00 0.00 0.00 6.13
98 100 0.537143 TGCAAGATTCAGTTGGCGGT 60.537 50.000 0.00 0.00 0.00 5.68
99 101 0.598065 GCAAGATTCAGTTGGCGGTT 59.402 50.000 0.00 0.00 0.00 4.44
100 102 1.666888 GCAAGATTCAGTTGGCGGTTG 60.667 52.381 0.00 0.00 0.00 3.77
101 103 1.608590 CAAGATTCAGTTGGCGGTTGT 59.391 47.619 0.00 0.00 0.00 3.32
102 104 1.523758 AGATTCAGTTGGCGGTTGTC 58.476 50.000 0.00 0.00 0.00 3.18
103 105 0.165944 GATTCAGTTGGCGGTTGTCG 59.834 55.000 0.00 0.00 42.76 4.35
104 106 0.534203 ATTCAGTTGGCGGTTGTCGT 60.534 50.000 0.00 0.00 41.72 4.34
105 107 1.155424 TTCAGTTGGCGGTTGTCGTC 61.155 55.000 0.00 0.00 44.94 4.20
115 117 0.813184 GGTTGTCGTCGGTGGATCTA 59.187 55.000 0.00 0.00 0.00 1.98
132 134 3.095912 TCTAGTTGGATCCGGTCTTGA 57.904 47.619 7.39 8.65 0.00 3.02
138 140 3.433306 TGGATCCGGTCTTGATTTGTT 57.567 42.857 7.39 0.00 0.00 2.83
141 143 3.506067 GGATCCGGTCTTGATTTGTTTGT 59.494 43.478 0.00 0.00 0.00 2.83
145 147 4.158764 TCCGGTCTTGATTTGTTTGTGTTT 59.841 37.500 0.00 0.00 0.00 2.83
157 159 2.490115 GTTTGTGTTTGTGTGTCCTCCA 59.510 45.455 0.00 0.00 0.00 3.86
169 171 5.192927 GTGTGTCCTCCAATTGGATCATTA 58.807 41.667 27.20 15.40 44.46 1.90
170 172 5.829924 GTGTGTCCTCCAATTGGATCATTAT 59.170 40.000 27.20 0.00 44.46 1.28
246 248 1.202382 GGCCTTAGCACGACGACTTAT 60.202 52.381 0.00 0.00 42.56 1.73
250 252 6.833400 GCCTTAGCACGACGACTTATCGAT 62.833 50.000 0.00 2.16 44.91 3.59
267 271 3.585862 TCGATTGTCTGCTAACAAGGTC 58.414 45.455 9.71 3.94 42.09 3.85
271 275 1.270839 TGTCTGCTAACAAGGTCTGCC 60.271 52.381 0.00 0.00 0.00 4.85
273 277 0.037326 CTGCTAACAAGGTCTGCCGA 60.037 55.000 0.00 0.00 40.50 5.54
280 284 1.072331 ACAAGGTCTGCCGACTTCAAT 59.928 47.619 8.25 0.00 40.10 2.57
287 291 0.250234 TGCCGACTTCAATGAGGGAG 59.750 55.000 0.00 0.00 0.00 4.30
302 307 2.498941 GGAGGGGCGATGACGATGA 61.499 63.158 0.00 0.00 42.66 2.92
303 308 1.441729 GAGGGGCGATGACGATGAA 59.558 57.895 0.00 0.00 42.66 2.57
319 324 0.036388 TGAAGCGCCTTAGGTTCCAG 60.036 55.000 2.29 0.00 45.11 3.86
350 355 1.202651 CCTCGTTGCCCCGAAGAATAT 60.203 52.381 0.00 0.00 36.24 1.28
365 370 6.418226 CCGAAGAATATAGACGAAAGGAAGTG 59.582 42.308 0.00 0.00 0.00 3.16
366 371 6.074782 CGAAGAATATAGACGAAAGGAAGTGC 60.075 42.308 0.00 0.00 0.00 4.40
393 399 7.521509 AAGAAGAAATAAAGTACGTGGATCG 57.478 36.000 0.00 0.00 46.00 3.69
458 464 1.075374 TGGAAACCAAGAGGGACATGG 59.925 52.381 0.00 0.00 41.15 3.66
461 467 2.586648 AACCAAGAGGGACATGGAAC 57.413 50.000 0.00 0.00 41.15 3.62
536 544 3.409026 AAGGAAAGAGATCACAAGCGT 57.591 42.857 0.00 0.00 0.00 5.07
542 550 5.220491 GGAAAGAGATCACAAGCGTTATCAC 60.220 44.000 0.00 0.00 29.58 3.06
544 552 5.078411 AGAGATCACAAGCGTTATCACTT 57.922 39.130 0.00 0.00 26.44 3.16
552 560 2.607187 AGCGTTATCACTTTCCAGACG 58.393 47.619 0.00 0.00 0.00 4.18
555 563 2.345641 CGTTATCACTTTCCAGACGCAG 59.654 50.000 0.00 0.00 0.00 5.18
556 564 2.010145 TATCACTTTCCAGACGCAGC 57.990 50.000 0.00 0.00 0.00 5.25
577 585 6.318900 GCAGCTTTGGTTTAATAGTACATCCT 59.681 38.462 0.00 0.00 0.00 3.24
641 681 9.865321 CTAACCTTGATGTTTGATGAATTGATT 57.135 29.630 0.00 0.00 0.00 2.57
655 695 5.702865 TGAATTGATTGGAAGCTTTTCTCG 58.297 37.500 0.00 0.00 0.00 4.04
656 697 3.559238 TTGATTGGAAGCTTTTCTCGC 57.441 42.857 0.00 0.00 0.00 5.03
657 698 1.464608 TGATTGGAAGCTTTTCTCGCG 59.535 47.619 0.00 0.00 0.00 5.87
746 787 0.251341 GCTCCCAGAGAAAAGCCCAA 60.251 55.000 0.00 0.00 0.00 4.12
748 789 1.352352 CTCCCAGAGAAAAGCCCAAGA 59.648 52.381 0.00 0.00 0.00 3.02
750 791 1.202927 CCCAGAGAAAAGCCCAAGACA 60.203 52.381 0.00 0.00 0.00 3.41
759 800 0.179018 AGCCCAAGACAGTGTCCAAC 60.179 55.000 19.71 5.56 32.18 3.77
793 834 1.269051 CGGGCCAACACTTTTCTCAAC 60.269 52.381 4.39 0.00 0.00 3.18
796 837 3.186909 GGCCAACACTTTTCTCAACAAC 58.813 45.455 0.00 0.00 0.00 3.32
801 844 6.293135 GCCAACACTTTTCTCAACAACAAAAA 60.293 34.615 0.00 0.00 0.00 1.94
802 845 7.290118 CCAACACTTTTCTCAACAACAAAAAG 58.710 34.615 5.21 5.21 41.96 2.27
846 889 3.435186 GAAGCGGCCCAGCAACTC 61.435 66.667 5.37 0.00 40.15 3.01
1067 1110 2.349817 GCGATTAACCCTCATGCAATCG 60.350 50.000 9.88 9.88 46.54 3.34
1073 1116 0.880278 CCCTCATGCAATCGTACCCG 60.880 60.000 0.00 0.00 0.00 5.28
1078 1121 0.036765 ATGCAATCGTACCCGTGTGT 60.037 50.000 0.00 0.00 35.01 3.72
1098 1141 3.605749 ATCCAGTCCGGCGGTGTTG 62.606 63.158 27.32 20.63 33.14 3.33
1114 1157 5.563842 CGGTGTTGCTATTTCTCAAGAATC 58.436 41.667 0.00 0.00 33.54 2.52
1325 1368 0.960861 CCGGCTGTCCTTCCTTTTCC 60.961 60.000 0.00 0.00 0.00 3.13
1334 1380 4.284746 TGTCCTTCCTTTTCCTTCTCTCTC 59.715 45.833 0.00 0.00 0.00 3.20
1360 1406 1.784358 AGGGTTACTGGCGTGCTATA 58.216 50.000 0.00 0.00 0.00 1.31
1363 1409 2.159000 GGGTTACTGGCGTGCTATAAGT 60.159 50.000 0.00 0.00 0.00 2.24
1371 1417 3.255725 GGCGTGCTATAAGTGTGTGTTA 58.744 45.455 0.00 0.00 0.00 2.41
1412 1458 1.310216 GCCATACGGGTGGGTGAAAC 61.310 60.000 9.94 0.00 39.73 2.78
1420 1466 1.810755 GGGTGGGTGAAACTTTCGATC 59.189 52.381 0.00 0.00 36.74 3.69
1500 1546 4.587262 GGATGGTCTTAGGGTTGTGTTTTT 59.413 41.667 0.00 0.00 0.00 1.94
1553 1600 3.028130 TGAGGTGGGTTTTTGGTTTCTC 58.972 45.455 0.00 0.00 0.00 2.87
1787 1935 5.883661 CAATCAGTTAACATTGCTGTAGGG 58.116 41.667 8.61 0.00 33.36 3.53
1801 1949 5.116180 TGCTGTAGGGTTTCATTCGAATAG 58.884 41.667 10.97 5.83 0.00 1.73
1811 1959 5.560966 TTCATTCGAATAGAAAACCTGCC 57.439 39.130 10.97 0.00 42.91 4.85
2010 2178 7.797038 AGGTGTTTACTACAGTTTAAACCAG 57.203 36.000 14.72 11.67 37.45 4.00
2026 2194 9.363763 GTTTAAACCAGTACCAGTCTCTATAAC 57.636 37.037 7.12 0.00 0.00 1.89
2085 2261 7.817418 AAAATTCCAGAGCTACAAGTAACAA 57.183 32.000 0.00 0.00 0.00 2.83
2311 2533 9.932207 TGTCATATTTGAGCATTCTGAAATTTT 57.068 25.926 0.00 0.00 37.35 1.82
2335 2557 3.574284 TGTATTGCACACTCCATTTGC 57.426 42.857 0.00 0.00 36.76 3.68
2353 2575 0.322816 GCCTGGACTCAAGATGCCAA 60.323 55.000 0.00 0.00 0.00 4.52
2354 2576 1.684248 GCCTGGACTCAAGATGCCAAT 60.684 52.381 0.00 0.00 0.00 3.16
2356 2578 2.022195 CTGGACTCAAGATGCCAATGG 58.978 52.381 0.00 0.00 0.00 3.16
2357 2579 1.355381 TGGACTCAAGATGCCAATGGT 59.645 47.619 0.00 0.00 0.00 3.55
2373 2596 5.745770 GCCAATGGTTTTTCCCTTGAGAATT 60.746 40.000 0.00 0.00 42.03 2.17
2400 2623 2.927014 GCTATCATTCCCCGTCGTCATC 60.927 54.545 0.00 0.00 0.00 2.92
2604 2827 6.986817 AGATACGAGTTGGAAGGATTGTTATG 59.013 38.462 0.00 0.00 0.00 1.90
2643 2866 5.104151 TGGCTTGTATATGTCCATCTTTCCA 60.104 40.000 0.00 0.00 0.00 3.53
2788 3011 3.911868 TGTTTGCCATAGATTTGTGCAC 58.088 40.909 10.75 10.75 0.00 4.57
2861 3094 7.410728 GGTTCTTGTTGCACGATTATCATTTTG 60.411 37.037 0.00 0.00 0.00 2.44
3019 3252 3.503827 AGCATCGATCTTGAACGTGTA 57.496 42.857 0.00 0.00 0.00 2.90
3116 3349 0.764369 TGGCCCTGTTCTCTGACTGT 60.764 55.000 0.00 0.00 0.00 3.55
3213 3446 2.349590 TCAGAATCAATGCGTCTGGTG 58.650 47.619 11.35 0.00 39.42 4.17
3218 3451 0.973632 TCAATGCGTCTGGTGGTACT 59.026 50.000 0.00 0.00 0.00 2.73
3219 3452 2.172679 TCAATGCGTCTGGTGGTACTA 58.827 47.619 0.00 0.00 0.00 1.82
3220 3453 2.094390 TCAATGCGTCTGGTGGTACTAC 60.094 50.000 0.00 0.00 0.00 2.73
3366 3602 9.236691 CTTTATTGATTGTTACATGTATGTGCC 57.763 33.333 6.36 0.00 41.89 5.01
3398 3634 4.214545 TGATTTTGTTTGCCGACGATAAGT 59.785 37.500 0.00 0.00 0.00 2.24
3693 4054 3.244044 GGTTTGTGTTGCTCTCTCTCTCT 60.244 47.826 0.00 0.00 0.00 3.10
3694 4055 3.932545 TTGTGTTGCTCTCTCTCTCTC 57.067 47.619 0.00 0.00 0.00 3.20
3695 4056 3.153369 TGTGTTGCTCTCTCTCTCTCT 57.847 47.619 0.00 0.00 0.00 3.10
3696 4057 3.081061 TGTGTTGCTCTCTCTCTCTCTC 58.919 50.000 0.00 0.00 0.00 3.20
3697 4058 3.081061 GTGTTGCTCTCTCTCTCTCTCA 58.919 50.000 0.00 0.00 0.00 3.27
3698 4059 3.081061 TGTTGCTCTCTCTCTCTCTCAC 58.919 50.000 0.00 0.00 0.00 3.51
3699 4060 3.081061 GTTGCTCTCTCTCTCTCTCACA 58.919 50.000 0.00 0.00 0.00 3.58
3700 4061 2.710377 TGCTCTCTCTCTCTCTCACAC 58.290 52.381 0.00 0.00 0.00 3.82
3701 4062 2.039613 TGCTCTCTCTCTCTCTCACACA 59.960 50.000 0.00 0.00 0.00 3.72
3702 4063 2.420022 GCTCTCTCTCTCTCTCACACAC 59.580 54.545 0.00 0.00 0.00 3.82
3742 4103 6.456449 GGTTTGCATATAAGACCAACGTACTG 60.456 42.308 0.00 0.00 0.00 2.74
3758 4119 3.188254 CGTACTGTTCCATGCACATCAAA 59.812 43.478 0.00 0.00 0.00 2.69
3759 4120 4.320129 CGTACTGTTCCATGCACATCAAAA 60.320 41.667 0.00 0.00 0.00 2.44
3760 4121 4.247267 ACTGTTCCATGCACATCAAAAG 57.753 40.909 0.00 0.00 0.00 2.27
3761 4122 3.006110 ACTGTTCCATGCACATCAAAAGG 59.994 43.478 0.00 0.00 0.00 3.11
3762 4123 2.288948 TGTTCCATGCACATCAAAAGGC 60.289 45.455 0.00 0.00 0.00 4.35
3763 4124 1.630223 TCCATGCACATCAAAAGGCA 58.370 45.000 0.00 0.00 41.00 4.75
3764 4125 1.546923 TCCATGCACATCAAAAGGCAG 59.453 47.619 0.00 0.00 39.95 4.85
3765 4126 1.274167 CCATGCACATCAAAAGGCAGT 59.726 47.619 0.00 0.00 39.95 4.40
3766 4127 2.333926 CATGCACATCAAAAGGCAGTG 58.666 47.619 0.00 0.00 39.95 3.66
3767 4128 0.675083 TGCACATCAAAAGGCAGTGG 59.325 50.000 0.00 0.00 0.00 4.00
3768 4129 0.675633 GCACATCAAAAGGCAGTGGT 59.324 50.000 0.00 0.00 0.00 4.16
3769 4130 1.603678 GCACATCAAAAGGCAGTGGTG 60.604 52.381 0.00 0.00 31.88 4.17
3782 4143 3.847621 TGGTGCACCATCGCAAAA 58.152 50.000 34.74 9.57 45.14 2.44
3783 4144 2.119009 TGGTGCACCATCGCAAAAA 58.881 47.368 34.74 8.74 45.14 1.94
3814 4175 0.608856 TGGTGCATGATGACCCACAC 60.609 55.000 0.00 0.00 0.00 3.82
3920 4281 2.661866 GGATTCCGCCGTGATCCG 60.662 66.667 1.01 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.739338 CGGTGCTAGGCGAGGAGAAT 61.739 60.000 0.00 0.00 0.00 2.40
33 35 2.348888 ACCCTCCAACGACGCTAGG 61.349 63.158 0.00 0.00 0.00 3.02
41 43 0.320421 CCTACACACACCCTCCAACG 60.320 60.000 0.00 0.00 0.00 4.10
44 46 0.399376 ACACCTACACACACCCTCCA 60.399 55.000 0.00 0.00 0.00 3.86
74 76 3.730061 CGCCAACTGAATCTTGCAAGATC 60.730 47.826 35.67 27.81 44.67 2.75
76 78 1.536766 CGCCAACTGAATCTTGCAAGA 59.463 47.619 30.23 30.23 39.78 3.02
77 79 1.401931 CCGCCAACTGAATCTTGCAAG 60.402 52.381 20.81 20.81 0.00 4.01
78 80 0.597568 CCGCCAACTGAATCTTGCAA 59.402 50.000 0.00 0.00 0.00 4.08
79 81 0.537143 ACCGCCAACTGAATCTTGCA 60.537 50.000 0.00 0.00 0.00 4.08
80 82 0.598065 AACCGCCAACTGAATCTTGC 59.402 50.000 0.00 0.00 0.00 4.01
81 83 1.608590 ACAACCGCCAACTGAATCTTG 59.391 47.619 0.00 0.00 0.00 3.02
82 84 1.880027 GACAACCGCCAACTGAATCTT 59.120 47.619 0.00 0.00 0.00 2.40
83 85 1.523758 GACAACCGCCAACTGAATCT 58.476 50.000 0.00 0.00 0.00 2.40
84 86 0.165944 CGACAACCGCCAACTGAATC 59.834 55.000 0.00 0.00 0.00 2.52
85 87 0.534203 ACGACAACCGCCAACTGAAT 60.534 50.000 0.00 0.00 43.32 2.57
86 88 1.153329 ACGACAACCGCCAACTGAA 60.153 52.632 0.00 0.00 43.32 3.02
87 89 1.593209 GACGACAACCGCCAACTGA 60.593 57.895 0.00 0.00 43.32 3.41
88 90 2.935955 GACGACAACCGCCAACTG 59.064 61.111 0.00 0.00 43.32 3.16
89 91 2.660552 CGACGACAACCGCCAACT 60.661 61.111 0.00 0.00 43.32 3.16
90 92 3.708734 CCGACGACAACCGCCAAC 61.709 66.667 0.00 0.00 43.32 3.77
91 93 4.224274 ACCGACGACAACCGCCAA 62.224 61.111 0.00 0.00 43.32 4.52
92 94 4.953868 CACCGACGACAACCGCCA 62.954 66.667 0.00 0.00 43.32 5.69
94 96 3.927163 ATCCACCGACGACAACCGC 62.927 63.158 0.00 0.00 43.32 5.68
95 97 1.804326 GATCCACCGACGACAACCG 60.804 63.158 0.00 0.00 45.44 4.44
96 98 0.813184 TAGATCCACCGACGACAACC 59.187 55.000 0.00 0.00 0.00 3.77
97 99 1.471684 ACTAGATCCACCGACGACAAC 59.528 52.381 0.00 0.00 0.00 3.32
98 100 1.830279 ACTAGATCCACCGACGACAA 58.170 50.000 0.00 0.00 0.00 3.18
99 101 1.471287 CAACTAGATCCACCGACGACA 59.529 52.381 0.00 0.00 0.00 4.35
100 102 1.202268 CCAACTAGATCCACCGACGAC 60.202 57.143 0.00 0.00 0.00 4.34
101 103 1.100510 CCAACTAGATCCACCGACGA 58.899 55.000 0.00 0.00 0.00 4.20
102 104 1.100510 TCCAACTAGATCCACCGACG 58.899 55.000 0.00 0.00 0.00 5.12
103 105 3.372660 GATCCAACTAGATCCACCGAC 57.627 52.381 0.00 0.00 37.31 4.79
115 117 3.244911 ACAAATCAAGACCGGATCCAACT 60.245 43.478 9.46 4.53 0.00 3.16
130 132 4.926238 GGACACACAAACACAAACAAATCA 59.074 37.500 0.00 0.00 0.00 2.57
132 134 5.146010 AGGACACACAAACACAAACAAAT 57.854 34.783 0.00 0.00 0.00 2.32
138 140 2.498644 TGGAGGACACACAAACACAA 57.501 45.000 0.00 0.00 0.00 3.33
141 143 2.692557 CCAATTGGAGGACACACAAACA 59.307 45.455 20.50 0.00 37.39 2.83
169 171 4.261405 CCGACGAAGAGAAGCTTAGATCAT 60.261 45.833 0.00 0.00 36.83 2.45
170 172 3.065510 CCGACGAAGAGAAGCTTAGATCA 59.934 47.826 0.00 0.00 36.83 2.92
177 179 0.241481 GTCACCGACGAAGAGAAGCT 59.759 55.000 0.00 0.00 0.00 3.74
246 248 3.258372 AGACCTTGTTAGCAGACAATCGA 59.742 43.478 5.52 0.00 38.71 3.59
250 252 2.494059 GCAGACCTTGTTAGCAGACAA 58.506 47.619 5.05 5.05 37.87 3.18
256 258 2.457080 GTCGGCAGACCTTGTTAGC 58.543 57.895 5.60 0.00 41.41 3.09
267 271 0.250234 TCCCTCATTGAAGTCGGCAG 59.750 55.000 0.00 0.00 0.00 4.85
271 275 0.179000 CCCCTCCCTCATTGAAGTCG 59.821 60.000 0.00 0.00 0.00 4.18
273 277 1.915078 CGCCCCTCCCTCATTGAAGT 61.915 60.000 0.00 0.00 0.00 3.01
280 284 2.764128 GTCATCGCCCCTCCCTCA 60.764 66.667 0.00 0.00 0.00 3.86
287 291 2.247437 GCTTCATCGTCATCGCCCC 61.247 63.158 0.00 0.00 36.96 5.80
302 307 1.066358 GTACTGGAACCTAAGGCGCTT 60.066 52.381 7.64 0.00 0.00 4.68
303 308 0.535797 GTACTGGAACCTAAGGCGCT 59.464 55.000 7.64 0.00 0.00 5.92
319 324 3.243670 GGGGCAACGAGGACTATAAGTAC 60.244 52.174 0.00 0.00 37.60 2.73
350 355 3.005050 TCTTTCGCACTTCCTTTCGTCTA 59.995 43.478 0.00 0.00 0.00 2.59
365 370 6.013689 CCACGTACTTTATTTCTTCTTTCGC 58.986 40.000 0.00 0.00 0.00 4.70
366 371 7.342318 TCCACGTACTTTATTTCTTCTTTCG 57.658 36.000 0.00 0.00 0.00 3.46
442 448 1.075536 GGTTCCATGTCCCTCTTGGTT 59.924 52.381 0.00 0.00 40.77 3.67
444 450 0.034089 GGGTTCCATGTCCCTCTTGG 60.034 60.000 9.67 0.00 40.48 3.61
458 464 4.202305 ACTGATAGAGCTGCTAATGGGTTC 60.202 45.833 0.15 0.00 31.66 3.62
461 467 4.348863 AACTGATAGAGCTGCTAATGGG 57.651 45.455 0.15 0.00 31.66 4.00
536 544 2.028112 AGCTGCGTCTGGAAAGTGATAA 60.028 45.455 0.00 0.00 0.00 1.75
542 550 0.239347 CCAAAGCTGCGTCTGGAAAG 59.761 55.000 10.91 0.00 0.00 2.62
544 552 0.465460 AACCAAAGCTGCGTCTGGAA 60.465 50.000 19.87 0.00 32.97 3.53
552 560 6.318900 AGGATGTACTATTAAACCAAAGCTGC 59.681 38.462 0.00 0.00 0.00 5.25
577 585 4.839121 ACAAGCATGGTCGTCCTTTATTA 58.161 39.130 0.00 0.00 34.23 0.98
594 602 8.129211 GGTTAGAAATTACATCCATGTACAAGC 58.871 37.037 0.00 0.00 42.48 4.01
633 641 4.560427 GCGAGAAAAGCTTCCAATCAATTC 59.440 41.667 0.00 0.00 31.28 2.17
637 677 1.464608 CGCGAGAAAAGCTTCCAATCA 59.535 47.619 0.00 0.00 31.28 2.57
675 716 6.106003 TCTTTGCAGTTAGAAGCATATTCGA 58.894 36.000 0.00 0.00 40.94 3.71
707 748 2.233676 GCAAACAAGGGGAAAATCCGAT 59.766 45.455 0.00 0.00 37.43 4.18
708 749 1.616374 GCAAACAAGGGGAAAATCCGA 59.384 47.619 0.00 0.00 37.43 4.55
709 750 1.618343 AGCAAACAAGGGGAAAATCCG 59.382 47.619 0.00 0.00 37.43 4.18
711 752 2.028112 GGGAGCAAACAAGGGGAAAATC 60.028 50.000 0.00 0.00 0.00 2.17
712 753 1.977854 GGGAGCAAACAAGGGGAAAAT 59.022 47.619 0.00 0.00 0.00 1.82
746 787 0.249489 GACGCTGTTGGACACTGTCT 60.249 55.000 9.08 0.00 32.47 3.41
748 789 0.530650 CAGACGCTGTTGGACACTGT 60.531 55.000 0.00 0.00 0.00 3.55
750 791 1.595382 GCAGACGCTGTTGGACACT 60.595 57.895 8.32 0.00 33.43 3.55
793 834 4.653555 GCCCGAGCCTTTTTGTTG 57.346 55.556 0.00 0.00 0.00 3.33
812 855 1.392853 CTTCTTGCGATGCAGAGTGTC 59.607 52.381 0.00 0.00 40.61 3.67
860 903 2.145397 TGCTCTGTTCCTATCGGAGT 57.855 50.000 0.00 0.00 41.25 3.85
902 945 4.813526 CGTCGTCTGACCGGCTCG 62.814 72.222 0.00 0.00 42.37 5.03
903 946 3.664223 GACGTCGTCTGACCGGCTC 62.664 68.421 18.09 0.00 42.37 4.70
1028 1071 1.741401 CAGGATGCGCGGAAGAACA 60.741 57.895 3.18 0.00 0.00 3.18
1067 1110 0.606604 ACTGGATGACACACGGGTAC 59.393 55.000 0.00 0.00 0.00 3.34
1073 1116 1.741770 GCCGGACTGGATGACACAC 60.742 63.158 5.05 0.00 42.00 3.82
1078 1121 3.770040 CACCGCCGGACTGGATGA 61.770 66.667 11.71 0.00 42.00 2.92
1098 1141 5.293079 AGAACGCAGATTCTTGAGAAATAGC 59.707 40.000 0.00 1.94 35.29 2.97
1133 1176 1.541310 ATCGACGACCTCCTGCCAAA 61.541 55.000 0.00 0.00 0.00 3.28
1180 1223 1.152839 CTCCTCCTCCTCGTCCTCC 60.153 68.421 0.00 0.00 0.00 4.30
1183 1226 1.671901 CTTGCTCCTCCTCCTCGTCC 61.672 65.000 0.00 0.00 0.00 4.79
1305 1348 0.250770 GAAAAGGAAGGACAGCCGGT 60.251 55.000 1.90 0.00 39.96 5.28
1325 1368 2.952116 ACCCTAATCCCGAGAGAGAAG 58.048 52.381 0.00 0.00 0.00 2.85
1334 1380 0.249741 CGCCAGTAACCCTAATCCCG 60.250 60.000 0.00 0.00 0.00 5.14
1360 1406 1.673920 CGGCAAACCTAACACACACTT 59.326 47.619 0.00 0.00 0.00 3.16
1363 1409 1.448922 GCCGGCAAACCTAACACACA 61.449 55.000 24.80 0.00 0.00 3.72
1412 1458 3.560068 CCCTAACCAAATCGGATCGAAAG 59.440 47.826 0.00 0.00 39.99 2.62
1420 1466 4.578928 CCTATCAAACCCTAACCAAATCGG 59.421 45.833 0.00 0.00 42.50 4.18
1500 1546 4.892934 ACACCCAATGAAAGTAGAAGCAAA 59.107 37.500 0.00 0.00 0.00 3.68
1553 1600 2.328099 GCCGCTCTCCACCAACTTG 61.328 63.158 0.00 0.00 0.00 3.16
1787 1935 5.800438 GGCAGGTTTTCTATTCGAATGAAAC 59.200 40.000 20.87 22.76 37.71 2.78
1811 1959 5.400066 AACATGTTTATTTTCGAAGGGGG 57.600 39.130 4.92 0.00 0.00 5.40
1828 1976 7.682824 TGCATTGTTGTGAGTTTAAAAACATG 58.317 30.769 8.21 0.00 41.30 3.21
1905 2073 7.521529 TGCTTTACGAGAAATCAAGAGAAATG 58.478 34.615 0.00 0.00 0.00 2.32
2010 2178 7.843490 TTGCAAATGTTATAGAGACTGGTAC 57.157 36.000 0.00 0.00 0.00 3.34
2026 2194 9.719279 AACAAAACATTTAACTCATTGCAAATG 57.281 25.926 1.71 2.33 41.79 2.32
2158 2334 0.532862 AGTTGAAGTGGTCCTGTGCG 60.533 55.000 0.00 0.00 0.00 5.34
2311 2533 5.288015 CAAATGGAGTGTGCAATACAACAA 58.712 37.500 5.30 0.00 41.89 2.83
2335 2557 2.022195 CATTGGCATCTTGAGTCCAGG 58.978 52.381 0.00 0.00 0.00 4.45
2353 2575 9.559732 CTTTTAAATTCTCAAGGGAAAAACCAT 57.440 29.630 0.00 0.00 41.20 3.55
2354 2576 7.497579 GCTTTTAAATTCTCAAGGGAAAAACCA 59.502 33.333 0.00 0.00 41.20 3.67
2356 2578 8.662781 AGCTTTTAAATTCTCAAGGGAAAAAC 57.337 30.769 0.00 0.00 0.00 2.43
2373 2596 4.124238 CGACGGGGAATGATAGCTTTTAA 58.876 43.478 0.00 0.00 0.00 1.52
2626 2849 8.933653 TGACACTTATGGAAAGATGGACATATA 58.066 33.333 0.00 0.00 0.00 0.86
2643 2866 5.509670 GCTTTTTCCCTTGCTTGACACTTAT 60.510 40.000 0.00 0.00 0.00 1.73
2687 2910 5.012664 TCCTGTTACAGTAAGGAAGCAATCA 59.987 40.000 11.68 0.00 37.16 2.57
2788 3011 5.863935 GCTTAGGGCTGTTATTGACAAAAAG 59.136 40.000 0.00 0.00 37.93 2.27
2861 3094 0.877743 GGCTGTTTCAGAAGCAGGAC 59.122 55.000 23.93 11.29 41.36 3.85
3019 3252 2.627515 TGCTGCTTCTCTGAAGTGTT 57.372 45.000 0.00 0.00 0.00 3.32
3116 3349 5.235850 ACAAATACAGTGTGGTGATGGTA 57.764 39.130 5.88 0.00 0.00 3.25
3220 3453 1.125021 GTTTGACATGAGACACGCGAG 59.875 52.381 15.93 7.88 0.00 5.03
3398 3634 1.585297 GTTCGAAAGGACCGGACAAA 58.415 50.000 9.46 0.00 35.69 2.83
3465 3701 2.301902 GAATCGACAGCCAAGCAGCG 62.302 60.000 0.00 0.00 38.01 5.18
3498 3735 4.331168 GCCAAACAGCACAACAAACAAATA 59.669 37.500 0.00 0.00 0.00 1.40
3508 3745 1.180907 TCAACAGCCAAACAGCACAA 58.819 45.000 0.00 0.00 34.23 3.33
3693 4054 1.957177 GACCAGAGAGTGTGTGTGAGA 59.043 52.381 0.00 0.00 0.00 3.27
3694 4055 1.683385 TGACCAGAGAGTGTGTGTGAG 59.317 52.381 0.00 0.00 0.00 3.51
3695 4056 1.683385 CTGACCAGAGAGTGTGTGTGA 59.317 52.381 0.00 0.00 0.00 3.58
3696 4057 1.683385 TCTGACCAGAGAGTGTGTGTG 59.317 52.381 0.00 0.00 32.82 3.82
3697 4058 2.073252 TCTGACCAGAGAGTGTGTGT 57.927 50.000 0.00 0.00 32.82 3.72
3742 4103 2.288948 TGCCTTTTGATGTGCATGGAAC 60.289 45.455 0.00 0.00 0.00 3.62
3785 4146 1.412079 TCATGCACCACTGCCTTTTT 58.588 45.000 0.00 0.00 43.51 1.94
3786 4147 1.274167 CATCATGCACCACTGCCTTTT 59.726 47.619 0.00 0.00 43.51 2.27
3787 4148 0.892755 CATCATGCACCACTGCCTTT 59.107 50.000 0.00 0.00 43.51 3.11
3814 4175 0.027979 CGCGTTAACTGCCCATGATG 59.972 55.000 14.03 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.