Multiple sequence alignment - TraesCS3A01G336800

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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 TraesCS3A01G336800 chr3A 100.000 2882 0 0 1 2882 583747193 583750074 0.000000e+00 5323.0
1 TraesCS3A01G336800 chr3A 86.632 1339 95 35 932 2256 434799150 434800418 0.000000e+00 1404.0
2 TraesCS3A01G336800 chr3A 81.443 97 15 3 2535 2629 448326160 448326065 3.080000e-10 76.8
3 TraesCS3A01G336800 chr3B 88.294 1905 112 49 435 2256 580062075 580063951 0.000000e+00 2180.0
4 TraesCS3A01G336800 chr3B 92.381 630 42 4 2257 2882 580063986 580064613 0.000000e+00 893.0
5 TraesCS3A01G336800 chr3B 83.945 218 17 12 177 388 580061754 580061959 2.930000e-45 193.0
6 TraesCS3A01G336800 chr3B 100.000 38 0 0 17 54 580061560 580061597 1.430000e-08 71.3
7 TraesCS3A01G336800 chr3D 92.701 1370 64 11 906 2256 442511362 442512714 0.000000e+00 1943.0
8 TraesCS3A01G336800 chr3D 92.031 640 36 6 2257 2882 442512749 442513387 0.000000e+00 885.0
9 TraesCS3A01G336800 chr3D 88.473 347 23 7 420 759 442510824 442511160 1.240000e-108 403.0
10 TraesCS3A01G336800 chr3D 84.375 256 16 14 151 388 442510453 442510702 2.230000e-56 230.0
11 TraesCS3A01G336800 chr3D 81.529 157 11 10 1 149 442510259 442510405 2.350000e-21 113.0
12 TraesCS3A01G336800 chr2D 89.222 1234 87 18 932 2150 568757274 568758476 0.000000e+00 1500.0
13 TraesCS3A01G336800 chr5B 88.943 1239 87 20 932 2150 524221797 524220589 0.000000e+00 1483.0
14 TraesCS3A01G336800 chr1B 88.673 1236 93 19 932 2150 443488938 443487733 0.000000e+00 1463.0
15 TraesCS3A01G336800 chr1B 85.437 103 5 4 2706 2802 310311835 310311933 6.570000e-17 99.0
16 TraesCS3A01G336800 chr7A 88.483 1233 83 17 932 2150 48766855 48765668 0.000000e+00 1435.0
17 TraesCS3A01G336800 chr4D 87.916 1233 83 27 932 2150 30394034 30395214 0.000000e+00 1391.0
18 TraesCS3A01G336800 chr7D 89.454 1081 74 12 1083 2150 207789238 207788185 0.000000e+00 1328.0
19 TraesCS3A01G336800 chr1A 87.343 798 58 22 1474 2256 512465714 512466483 0.000000e+00 874.0
20 TraesCS3A01G336800 chr6A 90.476 462 28 8 1703 2150 535421583 535421124 1.910000e-166 595.0
21 TraesCS3A01G336800 chr6A 83.733 375 27 16 932 1300 535421936 535421590 9.960000e-85 324.0
22 TraesCS3A01G336800 chr7B 85.417 96 6 2 2711 2802 3130714 3130623 3.060000e-15 93.5


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 TraesCS3A01G336800 chr3A 583747193 583750074 2881 False 5323.000 5323 100.0000 1 2882 1 chr3A.!!$F2 2881
1 TraesCS3A01G336800 chr3A 434799150 434800418 1268 False 1404.000 1404 86.6320 932 2256 1 chr3A.!!$F1 1324
2 TraesCS3A01G336800 chr3B 580061560 580064613 3053 False 834.325 2180 91.1550 17 2882 4 chr3B.!!$F1 2865
3 TraesCS3A01G336800 chr3D 442510259 442513387 3128 False 714.800 1943 87.8218 1 2882 5 chr3D.!!$F1 2881
4 TraesCS3A01G336800 chr2D 568757274 568758476 1202 False 1500.000 1500 89.2220 932 2150 1 chr2D.!!$F1 1218
5 TraesCS3A01G336800 chr5B 524220589 524221797 1208 True 1483.000 1483 88.9430 932 2150 1 chr5B.!!$R1 1218
6 TraesCS3A01G336800 chr1B 443487733 443488938 1205 True 1463.000 1463 88.6730 932 2150 1 chr1B.!!$R1 1218
7 TraesCS3A01G336800 chr7A 48765668 48766855 1187 True 1435.000 1435 88.4830 932 2150 1 chr7A.!!$R1 1218
8 TraesCS3A01G336800 chr4D 30394034 30395214 1180 False 1391.000 1391 87.9160 932 2150 1 chr4D.!!$F1 1218
9 TraesCS3A01G336800 chr7D 207788185 207789238 1053 True 1328.000 1328 89.4540 1083 2150 1 chr7D.!!$R1 1067
10 TraesCS3A01G336800 chr1A 512465714 512466483 769 False 874.000 874 87.3430 1474 2256 1 chr1A.!!$F1 782
11 TraesCS3A01G336800 chr6A 535421124 535421936 812 True 459.500 595 87.1045 932 2150 2 chr6A.!!$R1 1218


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
414 608 0.034198 TCTGGTCGCCGTGAAAATCA 59.966 50.0 0.00 0.0 0.00 2.57 F
894 1238 0.320334 GGCCCGGTTTGTTTGGAATG 60.320 55.0 0.00 0.0 0.00 2.67 F
1117 1504 0.321671 CTTCCACTTCGAGAAGCCCA 59.678 55.0 12.32 0.0 41.99 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1301 1711 0.312416 GGAGAGGACGATGATGACGG 59.688 60.0 0.0 0.0 34.93 4.79 R
1866 2281 0.390472 GGCGTCAGTTCCTCCAGAAG 60.390 60.0 0.0 0.0 34.29 2.85 R
2142 2579 0.746204 TCCGTCAGCAGCAACACAAA 60.746 50.0 0.0 0.0 0.00 2.83 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
60 110 1.851304 TGGGCATGGACCAAGAATTC 58.149 50.000 0.00 0.00 38.06 2.17
61 111 0.740737 GGGCATGGACCAAGAATTCG 59.259 55.000 0.00 0.00 0.00 3.34
62 112 1.463674 GGCATGGACCAAGAATTCGT 58.536 50.000 0.00 0.00 0.00 3.85
63 113 1.401905 GGCATGGACCAAGAATTCGTC 59.598 52.381 0.00 1.74 0.00 4.20
64 114 2.083774 GCATGGACCAAGAATTCGTCA 58.916 47.619 0.00 0.00 0.00 4.35
65 115 2.684881 GCATGGACCAAGAATTCGTCAT 59.315 45.455 0.00 2.05 0.00 3.06
66 116 3.242870 GCATGGACCAAGAATTCGTCATC 60.243 47.826 0.00 4.27 0.00 2.92
67 117 2.616960 TGGACCAAGAATTCGTCATCG 58.383 47.619 12.24 0.00 38.55 3.84
68 118 2.028476 TGGACCAAGAATTCGTCATCGT 60.028 45.455 12.24 0.41 38.33 3.73
69 119 3.193903 TGGACCAAGAATTCGTCATCGTA 59.806 43.478 12.24 0.00 38.33 3.43
70 120 3.550678 GGACCAAGAATTCGTCATCGTAC 59.449 47.826 12.24 0.00 38.33 3.67
71 121 4.421948 GACCAAGAATTCGTCATCGTACT 58.578 43.478 0.00 0.00 38.33 2.73
72 122 4.421948 ACCAAGAATTCGTCATCGTACTC 58.578 43.478 0.00 0.00 38.33 2.59
73 123 4.158025 ACCAAGAATTCGTCATCGTACTCT 59.842 41.667 0.00 0.00 38.33 3.24
74 124 5.356190 ACCAAGAATTCGTCATCGTACTCTA 59.644 40.000 0.00 0.00 38.33 2.43
75 125 5.910166 CCAAGAATTCGTCATCGTACTCTAG 59.090 44.000 0.00 0.00 38.33 2.43
76 126 5.676532 AGAATTCGTCATCGTACTCTAGG 57.323 43.478 0.00 0.00 38.33 3.02
77 127 5.366460 AGAATTCGTCATCGTACTCTAGGA 58.634 41.667 0.00 0.00 38.33 2.94
78 128 5.467399 AGAATTCGTCATCGTACTCTAGGAG 59.533 44.000 0.00 0.00 38.33 3.69
79 129 2.481854 TCGTCATCGTACTCTAGGAGC 58.518 52.381 0.00 0.00 38.33 4.70
80 130 1.532007 CGTCATCGTACTCTAGGAGCC 59.468 57.143 0.00 0.00 32.04 4.70
81 131 2.807472 CGTCATCGTACTCTAGGAGCCT 60.807 54.545 0.00 0.00 32.04 4.58
82 132 2.809696 GTCATCGTACTCTAGGAGCCTC 59.190 54.545 0.00 0.00 32.04 4.70
83 133 2.156098 CATCGTACTCTAGGAGCCTCC 58.844 57.143 1.26 1.26 36.58 4.30
96 146 2.818132 CCTCCTGAGGCGTCCATC 59.182 66.667 3.56 0.00 42.44 3.51
97 147 2.801631 CCTCCTGAGGCGTCCATCC 61.802 68.421 3.56 0.00 42.44 3.51
98 148 2.038813 TCCTGAGGCGTCCATCCA 59.961 61.111 3.56 0.00 0.00 3.41
99 149 2.025767 CTCCTGAGGCGTCCATCCAG 62.026 65.000 3.56 0.00 0.00 3.86
100 150 2.202987 CTGAGGCGTCCATCCAGC 60.203 66.667 3.56 0.00 0.00 4.85
142 192 4.209703 GGATACTCCGTCGATCGATCTATC 59.790 50.000 22.50 18.18 42.86 2.08
145 195 2.074576 TCCGTCGATCGATCTATCCAC 58.925 52.381 22.50 5.14 42.86 4.02
146 196 2.077627 CCGTCGATCGATCTATCCACT 58.922 52.381 22.50 0.00 42.86 4.00
147 197 2.159639 CCGTCGATCGATCTATCCACTG 60.160 54.545 22.50 5.20 42.86 3.66
148 198 2.726373 CGTCGATCGATCTATCCACTGC 60.726 54.545 22.50 2.42 42.86 4.40
149 199 2.226674 GTCGATCGATCTATCCACTGCA 59.773 50.000 22.50 0.00 0.00 4.41
150 200 3.084786 TCGATCGATCTATCCACTGCAT 58.915 45.455 22.43 0.00 0.00 3.96
152 202 4.333926 TCGATCGATCTATCCACTGCATAG 59.666 45.833 22.43 2.68 0.00 2.23
153 203 3.857549 TCGATCTATCCACTGCATAGC 57.142 47.619 0.00 0.00 0.00 2.97
154 204 3.157087 TCGATCTATCCACTGCATAGCA 58.843 45.455 0.00 0.00 36.92 3.49
156 206 3.056962 CGATCTATCCACTGCATAGCACT 60.057 47.826 0.00 0.00 33.79 4.40
157 207 4.156739 CGATCTATCCACTGCATAGCACTA 59.843 45.833 0.00 0.00 33.79 2.74
158 208 5.649557 GATCTATCCACTGCATAGCACTAG 58.350 45.833 0.00 0.00 33.79 2.57
165 261 3.634448 CACTGCATAGCACTAGTAGGAGT 59.366 47.826 1.45 0.00 33.79 3.85
170 266 5.996513 TGCATAGCACTAGTAGGAGTACTAC 59.003 44.000 4.13 4.13 42.26 2.73
223 378 0.602638 CGTGTTGGACCAAGCTGCTA 60.603 55.000 7.31 0.00 0.00 3.49
226 381 1.168714 GTTGGACCAAGCTGCTAAGG 58.831 55.000 7.31 16.74 0.00 2.69
289 462 4.749310 CGCGCCTCTGCTGGTTCT 62.749 66.667 0.00 0.00 34.43 3.01
291 464 2.507992 CGCCTCTGCTGGTTCTCG 60.508 66.667 0.00 0.00 34.43 4.04
294 467 2.125350 CTCTGCTGGTTCTCGCCC 60.125 66.667 0.00 0.00 0.00 6.13
309 482 4.404098 CCCCTACCCGTGTGCACC 62.404 72.222 15.69 4.74 0.00 5.01
310 483 3.632080 CCCTACCCGTGTGCACCA 61.632 66.667 15.69 0.00 0.00 4.17
401 595 2.125350 CGCCTTCCTGCTCTGGTC 60.125 66.667 0.00 0.00 0.00 4.02
411 605 1.959226 GCTCTGGTCGCCGTGAAAA 60.959 57.895 0.00 0.00 0.00 2.29
413 607 0.721718 CTCTGGTCGCCGTGAAAATC 59.278 55.000 0.00 0.00 0.00 2.17
414 608 0.034198 TCTGGTCGCCGTGAAAATCA 59.966 50.000 0.00 0.00 0.00 2.57
415 609 1.086696 CTGGTCGCCGTGAAAATCAT 58.913 50.000 0.00 0.00 0.00 2.45
416 610 2.093921 TCTGGTCGCCGTGAAAATCATA 60.094 45.455 0.00 0.00 0.00 2.15
417 611 2.004017 TGGTCGCCGTGAAAATCATAC 58.996 47.619 0.00 0.00 0.00 2.39
418 612 2.277084 GGTCGCCGTGAAAATCATACT 58.723 47.619 0.00 0.00 0.00 2.12
419 613 2.284417 GGTCGCCGTGAAAATCATACTC 59.716 50.000 0.00 0.00 0.00 2.59
420 614 2.034842 GTCGCCGTGAAAATCATACTCG 60.035 50.000 0.00 0.00 0.00 4.18
421 615 1.257936 CGCCGTGAAAATCATACTCGG 59.742 52.381 0.00 0.00 41.50 4.63
422 616 1.597663 GCCGTGAAAATCATACTCGGG 59.402 52.381 0.00 0.00 39.81 5.14
424 618 2.550978 CGTGAAAATCATACTCGGGCT 58.449 47.619 0.00 0.00 0.00 5.19
466 737 2.944349 GTCCCCTCGAACTACTCTACTG 59.056 54.545 0.00 0.00 0.00 2.74
468 739 3.458857 TCCCCTCGAACTACTCTACTGAT 59.541 47.826 0.00 0.00 0.00 2.90
492 767 1.890979 GCCGATGGATCCAGCTGTG 60.891 63.158 26.56 15.90 0.00 3.66
551 826 3.446570 GCATCGCTTGCCTTGCCT 61.447 61.111 0.00 0.00 46.15 4.75
574 854 2.045926 GCGGTGCAGTCCAGGATT 60.046 61.111 0.00 0.00 0.00 3.01
597 877 1.783071 TTCACACCTTTGTTTCCCCC 58.217 50.000 0.00 0.00 31.66 5.40
622 902 5.400066 AATCAAAACCTTCCATAAACCCG 57.600 39.130 0.00 0.00 0.00 5.28
652 939 3.411351 CCACGCGGTTTCCAGTCG 61.411 66.667 12.47 0.00 0.00 4.18
656 943 2.087009 CGCGGTTTCCAGTCGAGTC 61.087 63.158 0.00 0.00 0.00 3.36
657 944 1.737008 GCGGTTTCCAGTCGAGTCC 60.737 63.158 0.00 0.00 0.00 3.85
658 945 1.663739 CGGTTTCCAGTCGAGTCCA 59.336 57.895 0.00 0.00 0.00 4.02
659 946 0.388649 CGGTTTCCAGTCGAGTCCAG 60.389 60.000 0.00 0.00 0.00 3.86
660 947 0.680061 GGTTTCCAGTCGAGTCCAGT 59.320 55.000 0.00 0.00 0.00 4.00
731 1018 2.159366 CCGCCCTCTGCTCTATATAACG 60.159 54.545 0.00 0.00 38.05 3.18
741 1028 0.892755 CTATATAACGCCCTCCGCCA 59.107 55.000 0.00 0.00 41.76 5.69
759 1046 4.517934 CCGACCCTCCCCGCTCTA 62.518 72.222 0.00 0.00 0.00 2.43
762 1049 1.909287 GACCCTCCCCGCTCTATCC 60.909 68.421 0.00 0.00 0.00 2.59
763 1050 2.374781 GACCCTCCCCGCTCTATCCT 62.375 65.000 0.00 0.00 0.00 3.24
764 1051 1.152226 CCCTCCCCGCTCTATCCTT 60.152 63.158 0.00 0.00 0.00 3.36
766 1053 1.188871 CCTCCCCGCTCTATCCTTCC 61.189 65.000 0.00 0.00 0.00 3.46
772 1107 0.682292 CGCTCTATCCTTCCCCTTCC 59.318 60.000 0.00 0.00 0.00 3.46
775 1110 2.427150 GCTCTATCCTTCCCCTTCCTCT 60.427 54.545 0.00 0.00 0.00 3.69
776 1111 3.238597 CTCTATCCTTCCCCTTCCTCTG 58.761 54.545 0.00 0.00 0.00 3.35
784 1119 1.676967 CCCTTCCTCTGCCACAAGC 60.677 63.158 0.00 0.00 44.14 4.01
809 1144 0.962855 GAGAGAAACCCCAAGCCAGC 60.963 60.000 0.00 0.00 0.00 4.85
890 1234 3.984749 CCGGCCCGGTTTGTTTGG 61.985 66.667 15.86 0.00 42.73 3.28
891 1235 2.907917 CGGCCCGGTTTGTTTGGA 60.908 61.111 0.00 0.00 0.00 3.53
893 1237 1.811645 CGGCCCGGTTTGTTTGGAAT 61.812 55.000 0.00 0.00 0.00 3.01
894 1238 0.320334 GGCCCGGTTTGTTTGGAATG 60.320 55.000 0.00 0.00 0.00 2.67
896 1240 1.614413 GCCCGGTTTGTTTGGAATGTA 59.386 47.619 0.00 0.00 0.00 2.29
897 1241 2.608506 GCCCGGTTTGTTTGGAATGTAC 60.609 50.000 0.00 0.00 0.00 2.90
912 1293 4.275936 GGAATGTACTACCAATGTGCATCC 59.724 45.833 0.00 0.00 39.22 3.51
917 1298 6.600388 TGTACTACCAATGTGCATCCATTAT 58.400 36.000 2.51 0.00 33.37 1.28
927 1308 4.576053 TGTGCATCCATTATAACTGACAGC 59.424 41.667 1.25 0.00 0.00 4.40
930 1311 4.084328 GCATCCATTATAACTGACAGCGTC 60.084 45.833 1.25 2.32 0.00 5.19
945 1326 2.547798 GTCGCACGGACGGTTTTC 59.452 61.111 0.00 0.00 35.61 2.29
947 1328 1.301087 TCGCACGGACGGTTTTCAT 60.301 52.632 0.00 0.00 0.00 2.57
948 1329 1.154488 CGCACGGACGGTTTTCATG 60.154 57.895 0.00 0.00 0.00 3.07
949 1330 1.209127 GCACGGACGGTTTTCATGG 59.791 57.895 0.00 0.00 0.00 3.66
1004 1385 2.356793 GGAGCGGCCGATGATGAG 60.357 66.667 33.48 0.00 0.00 2.90
1117 1504 0.321671 CTTCCACTTCGAGAAGCCCA 59.678 55.000 12.32 0.00 41.99 5.36
1248 1647 0.737715 GCCTCTTCCAGCACTACACG 60.738 60.000 0.00 0.00 0.00 4.49
1306 1716 3.449227 CCTGCCTCTACGCCGTCA 61.449 66.667 0.00 0.00 0.00 4.35
1309 1719 2.004808 CTGCCTCTACGCCGTCATCA 62.005 60.000 0.00 0.00 0.00 3.07
1310 1720 1.364171 GCCTCTACGCCGTCATCAT 59.636 57.895 0.00 0.00 0.00 2.45
1866 2281 2.027625 CGTCAAGGTGCCGTTCCTC 61.028 63.158 0.00 0.00 33.76 3.71
1911 2326 3.658757 TGCAAGACAAAAATGGCTACC 57.341 42.857 0.00 0.00 0.00 3.18
1928 2343 2.049985 CGGCCGATTAGGAGAGCG 60.050 66.667 24.07 0.00 45.00 5.03
1941 2356 1.294659 GAGAGCGGTTCTTGCAGGTG 61.295 60.000 0.00 0.00 35.87 4.00
2045 2478 2.561733 TTGTCCGTCGAGATCATGTC 57.438 50.000 0.00 0.00 0.00 3.06
2133 2570 4.141756 TGAAAGAAAATGGTGTTGGTGCAT 60.142 37.500 0.00 0.00 0.00 3.96
2295 2781 7.882179 ACTCCACTTTACAATTGGTCATTTAC 58.118 34.615 10.83 0.00 0.00 2.01
2349 2835 2.951642 ACACACAAGTCCCATGACAAAG 59.048 45.455 0.00 0.00 44.33 2.77
2375 2861 0.675633 ATTCAGCACCAAGGCAACAC 59.324 50.000 0.00 0.00 41.41 3.32
2392 2878 2.201732 ACACGCATGCTTATTAGTCCG 58.798 47.619 17.13 0.00 0.00 4.79
2450 2936 0.459063 CTCAGCTCGTGCATGCACTA 60.459 55.000 39.46 31.25 44.16 2.74
2496 2992 6.106003 TGAACAAATCAGCTCGTACATATGT 58.894 36.000 13.93 13.93 33.04 2.29
2518 3014 4.397481 TCAGACTTGCAGGTCAGATATG 57.603 45.455 28.25 17.88 38.57 1.78
2565 3061 3.370978 TCGTTCAGATCCATTTCGAAAGC 59.629 43.478 16.80 0.00 0.00 3.51
2566 3062 3.125146 CGTTCAGATCCATTTCGAAAGCA 59.875 43.478 16.80 2.82 0.00 3.91
2623 3120 2.300433 TCAGCACTTCAGCACAACAAT 58.700 42.857 0.00 0.00 36.85 2.71
2636 3133 7.085746 TCAGCACAACAATCTTTGACAATATG 58.914 34.615 0.00 0.00 0.00 1.78
2747 3244 0.806492 GCGGCTAAGTGTAGTGCCTC 60.806 60.000 0.00 0.00 42.90 4.70
2769 3266 3.423154 GTCTTGGCCGGCTGAACG 61.423 66.667 28.56 10.32 0.00 3.95
2863 3360 2.735663 CTCAAGACAGTTAGTGCAGCTG 59.264 50.000 10.11 10.11 41.05 4.24
2876 3373 2.427232 GCAGCTGCATGAACTTTGAA 57.573 45.000 33.36 0.00 41.59 2.69
2877 3374 2.056577 GCAGCTGCATGAACTTTGAAC 58.943 47.619 33.36 0.00 41.59 3.18
2878 3375 2.288030 GCAGCTGCATGAACTTTGAACT 60.288 45.455 33.36 0.00 41.59 3.01
2880 3377 4.557296 GCAGCTGCATGAACTTTGAACTAA 60.557 41.667 33.36 0.00 41.59 2.24
2881 3378 5.706916 CAGCTGCATGAACTTTGAACTAAT 58.293 37.500 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 104 5.366460 TCCTAGAGTACGATGACGAATTCT 58.634 41.667 3.52 0.00 42.66 2.40
55 105 5.670149 TCCTAGAGTACGATGACGAATTC 57.330 43.478 0.00 0.00 42.66 2.17
56 106 4.023878 GCTCCTAGAGTACGATGACGAATT 60.024 45.833 0.00 0.00 36.31 2.17
57 107 3.499157 GCTCCTAGAGTACGATGACGAAT 59.501 47.826 0.00 0.00 36.31 3.34
58 108 2.871022 GCTCCTAGAGTACGATGACGAA 59.129 50.000 0.00 0.00 36.31 3.85
59 109 2.481854 GCTCCTAGAGTACGATGACGA 58.518 52.381 0.00 0.00 36.31 4.20
60 110 1.532007 GGCTCCTAGAGTACGATGACG 59.468 57.143 0.00 0.00 37.49 4.35
61 111 2.809696 GAGGCTCCTAGAGTACGATGAC 59.190 54.545 2.15 0.00 31.39 3.06
62 112 2.224572 GGAGGCTCCTAGAGTACGATGA 60.225 54.545 26.44 0.00 32.53 2.92
63 113 2.156098 GGAGGCTCCTAGAGTACGATG 58.844 57.143 26.44 0.00 32.53 3.84
64 114 2.572209 GGAGGCTCCTAGAGTACGAT 57.428 55.000 26.44 0.00 32.53 3.73
80 130 2.025767 CTGGATGGACGCCTCAGGAG 62.026 65.000 0.00 0.00 0.00 3.69
81 131 2.038813 TGGATGGACGCCTCAGGA 59.961 61.111 0.00 0.00 0.00 3.86
82 132 2.503061 CTGGATGGACGCCTCAGG 59.497 66.667 0.00 0.00 0.00 3.86
83 133 2.202987 GCTGGATGGACGCCTCAG 60.203 66.667 0.00 0.00 0.00 3.35
84 134 2.685017 AGCTGGATGGACGCCTCA 60.685 61.111 0.00 0.00 0.00 3.86
85 135 2.107953 GAGCTGGATGGACGCCTC 59.892 66.667 0.00 0.00 0.00 4.70
86 136 3.474570 GGAGCTGGATGGACGCCT 61.475 66.667 0.00 0.00 0.00 5.52
87 137 3.746949 CTGGAGCTGGATGGACGCC 62.747 68.421 0.00 0.00 0.00 5.68
88 138 2.202987 CTGGAGCTGGATGGACGC 60.203 66.667 0.00 0.00 0.00 5.19
89 139 2.202987 GCTGGAGCTGGATGGACG 60.203 66.667 0.00 0.00 38.21 4.79
127 177 2.726373 GCAGTGGATAGATCGATCGACG 60.726 54.545 22.06 16.38 38.98 5.12
142 192 2.959030 TCCTACTAGTGCTATGCAGTGG 59.041 50.000 5.39 9.28 42.60 4.00
145 195 5.067273 AGTACTCCTACTAGTGCTATGCAG 58.933 45.833 5.39 0.00 40.17 4.41
146 196 5.050126 AGTACTCCTACTAGTGCTATGCA 57.950 43.478 5.39 0.00 40.17 3.96
147 197 6.484818 GTAGTACTCCTACTAGTGCTATGC 57.515 45.833 5.39 0.00 43.56 3.14
158 208 7.255555 GGAGCCAAAGAATAGTAGTACTCCTAC 60.256 44.444 5.96 0.00 45.47 3.18
165 261 7.113658 CTCTTGGAGCCAAAGAATAGTAGTA 57.886 40.000 3.24 0.00 35.33 1.82
223 378 1.449601 CGTATTGGTGCTCCGCCTT 60.450 57.895 0.00 0.00 34.70 4.35
226 381 2.461110 CCACGTATTGGTGCTCCGC 61.461 63.158 0.00 0.00 41.10 5.54
237 392 2.812178 GCAACGCGACCCACGTAT 60.812 61.111 15.93 0.00 44.30 3.06
276 442 2.125350 GGCGAGAACCAGCAGAGG 60.125 66.667 0.00 0.00 34.54 3.69
283 449 2.686106 GGGTAGGGGCGAGAACCA 60.686 66.667 0.00 0.00 33.46 3.67
286 452 3.072468 CACGGGTAGGGGCGAGAA 61.072 66.667 0.00 0.00 0.00 2.87
294 467 2.047274 CTGGTGCACACGGGTAGG 60.047 66.667 20.43 0.00 0.00 3.18
388 566 4.069232 CGGCGACCAGAGCAGGAA 62.069 66.667 0.00 0.00 36.08 3.36
401 595 1.257936 CCGAGTATGATTTTCACGGCG 59.742 52.381 4.80 4.80 28.15 6.46
411 605 0.674534 GAACCGAGCCCGAGTATGAT 59.325 55.000 0.00 0.00 38.22 2.45
413 607 0.527817 GTGAACCGAGCCCGAGTATG 60.528 60.000 0.00 0.00 38.22 2.39
414 608 1.673808 GGTGAACCGAGCCCGAGTAT 61.674 60.000 0.00 0.00 38.22 2.12
415 609 2.345760 GGTGAACCGAGCCCGAGTA 61.346 63.158 0.00 0.00 38.22 2.59
416 610 3.692406 GGTGAACCGAGCCCGAGT 61.692 66.667 0.00 0.00 38.22 4.18
417 611 3.019003 ATGGTGAACCGAGCCCGAG 62.019 63.158 0.00 0.00 39.43 4.63
418 612 3.000819 ATGGTGAACCGAGCCCGA 61.001 61.111 0.00 0.00 39.43 5.14
419 613 2.819595 CATGGTGAACCGAGCCCG 60.820 66.667 0.00 0.00 39.43 6.13
420 614 3.134127 GCATGGTGAACCGAGCCC 61.134 66.667 0.00 0.00 39.43 5.19
421 615 3.499737 CGCATGGTGAACCGAGCC 61.500 66.667 9.52 0.00 39.43 4.70
422 616 1.815421 ATCGCATGGTGAACCGAGC 60.815 57.895 0.00 6.03 39.43 5.03
424 618 2.106074 GCATCGCATGGTGAACCGA 61.106 57.895 0.00 0.00 39.43 4.69
492 767 2.541762 GGATCTCTGCTCGTTAATGCAC 59.458 50.000 0.00 0.00 35.20 4.57
574 854 3.386402 GGGGAAACAAAGGTGTGAAATCA 59.614 43.478 0.00 0.00 38.27 2.57
597 877 7.033185 CGGGTTTATGGAAGGTTTTGATTAAG 58.967 38.462 0.00 0.00 0.00 1.85
652 939 0.978667 GAAGGAGGGGGACTGGACTC 60.979 65.000 0.00 0.00 0.00 3.36
656 943 2.038975 TCGAAGGAGGGGGACTGG 59.961 66.667 0.00 0.00 0.00 4.00
657 944 1.608717 CTGTCGAAGGAGGGGGACTG 61.609 65.000 0.00 0.00 0.00 3.51
658 945 1.305381 CTGTCGAAGGAGGGGGACT 60.305 63.158 0.00 0.00 0.00 3.85
659 946 3.020237 GCTGTCGAAGGAGGGGGAC 62.020 68.421 0.00 0.00 0.00 4.46
660 947 2.683933 GCTGTCGAAGGAGGGGGA 60.684 66.667 0.00 0.00 0.00 4.81
712 999 2.417515 GGCGTTATATAGAGCAGAGGGC 60.418 54.545 11.82 0.00 45.30 5.19
713 1000 2.166664 GGGCGTTATATAGAGCAGAGGG 59.833 54.545 11.82 0.00 0.00 4.30
714 1001 3.093057 AGGGCGTTATATAGAGCAGAGG 58.907 50.000 11.82 0.00 0.00 3.69
715 1002 3.129638 GGAGGGCGTTATATAGAGCAGAG 59.870 52.174 11.82 0.00 0.00 3.35
716 1003 3.090037 GGAGGGCGTTATATAGAGCAGA 58.910 50.000 11.82 0.00 0.00 4.26
717 1004 2.159366 CGGAGGGCGTTATATAGAGCAG 60.159 54.545 11.82 0.00 0.00 4.24
718 1005 1.816835 CGGAGGGCGTTATATAGAGCA 59.183 52.381 11.82 0.00 0.00 4.26
759 1046 0.990818 GGCAGAGGAAGGGGAAGGAT 60.991 60.000 0.00 0.00 0.00 3.24
762 1049 1.301293 GTGGCAGAGGAAGGGGAAG 59.699 63.158 0.00 0.00 0.00 3.46
763 1050 1.065410 TTGTGGCAGAGGAAGGGGAA 61.065 55.000 0.00 0.00 0.00 3.97
764 1051 1.463214 TTGTGGCAGAGGAAGGGGA 60.463 57.895 0.00 0.00 0.00 4.81
766 1053 1.676967 GCTTGTGGCAGAGGAAGGG 60.677 63.158 0.00 0.00 41.35 3.95
776 1111 0.604780 TCTCTCTGCTTGCTTGTGGC 60.605 55.000 0.00 0.00 42.22 5.01
784 1119 2.157738 CTTGGGGTTTCTCTCTGCTTG 58.842 52.381 0.00 0.00 0.00 4.01
785 1120 1.546548 GCTTGGGGTTTCTCTCTGCTT 60.547 52.381 0.00 0.00 0.00 3.91
786 1121 0.037447 GCTTGGGGTTTCTCTCTGCT 59.963 55.000 0.00 0.00 0.00 4.24
787 1122 0.962855 GGCTTGGGGTTTCTCTCTGC 60.963 60.000 0.00 0.00 0.00 4.26
788 1123 0.401738 TGGCTTGGGGTTTCTCTCTG 59.598 55.000 0.00 0.00 0.00 3.35
789 1124 0.695347 CTGGCTTGGGGTTTCTCTCT 59.305 55.000 0.00 0.00 0.00 3.10
790 1125 0.962855 GCTGGCTTGGGGTTTCTCTC 60.963 60.000 0.00 0.00 0.00 3.20
791 1126 1.075659 GCTGGCTTGGGGTTTCTCT 59.924 57.895 0.00 0.00 0.00 3.10
809 1144 2.325082 CCGGCGTTGTTTCTCCCTG 61.325 63.158 6.01 0.00 0.00 4.45
836 1171 2.667318 CGCACCTTGTACGGCTGTG 61.667 63.158 8.92 0.00 0.00 3.66
879 1214 4.515944 TGGTAGTACATTCCAAACAAACCG 59.484 41.667 2.06 0.00 0.00 4.44
881 1225 7.381139 CACATTGGTAGTACATTCCAAACAAAC 59.619 37.037 16.26 0.00 43.11 2.93
890 1234 4.881273 TGGATGCACATTGGTAGTACATTC 59.119 41.667 2.06 0.00 0.00 2.67
891 1235 4.854173 TGGATGCACATTGGTAGTACATT 58.146 39.130 2.06 0.00 0.00 2.71
893 1237 3.990959 TGGATGCACATTGGTAGTACA 57.009 42.857 2.06 0.00 0.00 2.90
894 1238 8.504005 GTTATAATGGATGCACATTGGTAGTAC 58.496 37.037 11.69 0.00 40.97 2.73
896 1240 7.229306 CAGTTATAATGGATGCACATTGGTAGT 59.771 37.037 11.69 0.00 40.97 2.73
897 1241 7.445096 TCAGTTATAATGGATGCACATTGGTAG 59.555 37.037 11.69 0.11 40.97 3.18
912 1293 2.857748 TGCGACGCTGTCAGTTATAATG 59.142 45.455 22.08 0.00 32.09 1.90
917 1298 1.728074 CGTGCGACGCTGTCAGTTA 60.728 57.895 22.08 0.00 33.65 2.24
930 1311 1.154488 CATGAAAACCGTCCGTGCG 60.154 57.895 0.00 0.00 0.00 5.34
945 1326 2.286008 CGAATCAATCTGCGACACCATG 60.286 50.000 0.00 0.00 0.00 3.66
947 1328 1.358877 CGAATCAATCTGCGACACCA 58.641 50.000 0.00 0.00 0.00 4.17
948 1329 0.026803 GCGAATCAATCTGCGACACC 59.973 55.000 0.00 0.00 0.00 4.16
949 1330 0.721154 TGCGAATCAATCTGCGACAC 59.279 50.000 0.00 0.00 32.55 3.67
1128 1515 4.750695 TTCTGGGGATGCGGGGGA 62.751 66.667 0.00 0.00 0.00 4.81
1300 1710 0.318275 GAGAGGACGATGATGACGGC 60.318 60.000 0.00 0.00 38.12 5.68
1301 1711 0.312416 GGAGAGGACGATGATGACGG 59.688 60.000 0.00 0.00 34.93 4.79
1304 1714 1.815795 CGAGGGAGAGGACGATGATGA 60.816 57.143 0.00 0.00 0.00 2.92
1306 1716 1.175983 GCGAGGGAGAGGACGATGAT 61.176 60.000 0.00 0.00 0.00 2.45
1309 1719 2.519780 GGCGAGGGAGAGGACGAT 60.520 66.667 0.00 0.00 0.00 3.73
1344 1754 4.371417 AGGTAGACGGCCCCGACA 62.371 66.667 14.44 0.00 42.83 4.35
1502 1912 3.583276 TAGTGCACGCCGACCTTGG 62.583 63.158 12.01 0.00 0.00 3.61
1699 2109 4.651008 GTCGAACGGCACCGACCA 62.651 66.667 17.40 0.00 46.54 4.02
1866 2281 0.390472 GGCGTCAGTTCCTCCAGAAG 60.390 60.000 0.00 0.00 34.29 2.85
1911 2326 2.049985 CGCTCTCCTAATCGGCCG 60.050 66.667 22.12 22.12 0.00 6.13
1928 2343 3.365265 CCGCCACCTGCAAGAACC 61.365 66.667 0.00 0.00 41.33 3.62
1941 2356 2.485122 CACGAATCCTTTGCCGCC 59.515 61.111 0.00 0.00 0.00 6.13
1981 2401 7.967908 TCAAACCAACATACAAATTAATGGGT 58.032 30.769 0.00 0.00 0.00 4.51
2045 2478 2.504681 GCACAATTTCGCGGCAGG 60.505 61.111 6.13 0.00 0.00 4.85
2066 2499 2.415512 GCACCTCGTGAACATCTTAACC 59.584 50.000 0.00 0.00 35.23 2.85
2133 2570 2.159170 GCAGCAACACAAAAGGTACCAA 60.159 45.455 15.94 0.00 0.00 3.67
2142 2579 0.746204 TCCGTCAGCAGCAACACAAA 60.746 50.000 0.00 0.00 0.00 2.83
2236 2685 4.674475 TGCGAACGATATGTAGTTGCTAA 58.326 39.130 0.00 0.00 0.00 3.09
2276 2762 7.867445 AAAGCGTAAATGACCAATTGTAAAG 57.133 32.000 4.43 0.00 0.00 1.85
2283 2769 4.250116 TGCAAAAGCGTAAATGACCAAT 57.750 36.364 0.00 0.00 0.00 3.16
2285 2771 3.717400 TTGCAAAAGCGTAAATGACCA 57.283 38.095 0.00 0.00 0.00 4.02
2295 2781 3.670055 AGTTCGAATTGATTGCAAAAGCG 59.330 39.130 1.71 3.08 37.59 4.68
2312 2798 2.668457 GTGTGTGAGCCTTCATAGTTCG 59.332 50.000 0.00 0.00 35.39 3.95
2349 2835 2.863704 GCCTTGGTGCTGAATGTTCAAC 60.864 50.000 0.00 0.00 36.64 3.18
2375 2861 1.148310 CCCGGACTAATAAGCATGCG 58.852 55.000 13.01 0.00 0.00 4.73
2392 2878 5.048013 CACAGAATTTTGAGTTACTTCCCCC 60.048 44.000 2.48 0.00 0.00 5.40
2450 2936 4.750098 CAGTCGGTGTTAGTCTGAACATTT 59.250 41.667 0.00 0.00 41.21 2.32
2496 2992 4.223700 ACATATCTGACCTGCAAGTCTGAA 59.776 41.667 23.61 15.30 44.59 3.02
2623 3120 6.697455 GTCATCGAGCTACATATTGTCAAAGA 59.303 38.462 0.00 0.00 0.00 2.52
2731 3228 2.732597 CGTGAGAGGCACTACACTTAGC 60.733 54.545 10.71 0.00 45.49 3.09
2747 3244 4.379243 AGCCGGCCAAGACGTGAG 62.379 66.667 26.15 0.00 28.54 3.51
2769 3266 8.514594 TGACAATTTCTCTGATATGGTTTTCAC 58.485 33.333 0.00 0.00 0.00 3.18



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

AutoCloner maintained by Alex Coulton.