Multiple sequence alignment - TraesCS7A01G431200

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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 TraesCS7A01G431200 chr7A 100.000 4989 0 0 1 4989 625605227 625600239 0.000000e+00 9214
1 TraesCS7A01G431200 chr7A 89.405 2539 264 4 1197 3732 625539856 625537320 0.000000e+00 3193
2 TraesCS7A01G431200 chr7A 88.510 2376 249 7 1197 3558 617738622 617736257 0.000000e+00 2854
3 TraesCS7A01G431200 chr7A 87.419 2472 302 6 1250 3714 625535274 625532805 0.000000e+00 2833
4 TraesCS7A01G431200 chr7A 88.074 2264 262 5 1448 3704 617705325 617703063 0.000000e+00 2678
5 TraesCS7A01G431200 chr7A 85.050 2582 342 32 1293 3857 625617204 625614650 0.000000e+00 2590
6 TraesCS7A01G431200 chr7A 94.071 253 15 0 1200 1452 617731241 617730989 7.830000e-103 385
7 TraesCS7A01G431200 chr7A 83.648 159 12 6 4566 4716 617733048 617732896 2.420000e-28 137
8 TraesCS7A01G431200 chr7D 97.178 2764 73 2 1197 3959 543627229 543624470 0.000000e+00 4667
9 TraesCS7A01G431200 chr7D 86.944 2520 306 13 1207 3714 543563712 543561204 0.000000e+00 2809
10 TraesCS7A01G431200 chr7D 86.655 2368 291 14 1409 3773 543610565 543608220 0.000000e+00 2599
11 TraesCS7A01G431200 chr7D 89.612 645 29 9 4078 4720 543624373 543623765 0.000000e+00 785
12 TraesCS7A01G431200 chr7D 92.446 278 12 5 4713 4989 543623097 543622828 6.060000e-104 388
13 TraesCS7A01G431200 chr7B 89.494 2532 258 5 1197 3725 586968920 586966394 0.000000e+00 3195
14 TraesCS7A01G431200 chr7B 92.911 1199 79 6 1 1196 637271500 637272695 0.000000e+00 1738
15 TraesCS7A01G431200 chr6B 98.830 1197 14 0 1 1197 705570356 705569160 0.000000e+00 2134
16 TraesCS7A01G431200 chr6B 82.358 2426 399 22 1271 3683 694667799 694665390 0.000000e+00 2082
17 TraesCS7A01G431200 chr3A 98.411 1196 19 0 1 1196 639155182 639156377 0.000000e+00 2104
18 TraesCS7A01G431200 chr5B 98.002 1201 22 2 1 1200 481061795 481062994 0.000000e+00 2084
19 TraesCS7A01G431200 chr5B 94.078 1199 66 5 1 1196 471120430 471121626 0.000000e+00 1816
20 TraesCS7A01G431200 chr2B 97.993 1196 24 0 1 1196 358913071 358914266 0.000000e+00 2076
21 TraesCS7A01G431200 chr1B 94.412 1199 64 3 1 1197 340455974 340457171 0.000000e+00 1840
22 TraesCS7A01G431200 chr1A 92.240 1134 82 5 5 1137 50617473 50616345 0.000000e+00 1602
23 TraesCS7A01G431200 chr1A 91.927 1152 77 6 5 1154 549307873 549306736 0.000000e+00 1598


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 TraesCS7A01G431200 chr7A 625600239 625605227 4988 True 9214.000000 9214 100.000000 1 4989 1 chr7A.!!$R2 4988
1 TraesCS7A01G431200 chr7A 625532805 625539856 7051 True 3013.000000 3193 88.412000 1197 3732 2 chr7A.!!$R5 2535
2 TraesCS7A01G431200 chr7A 617703063 617705325 2262 True 2678.000000 2678 88.074000 1448 3704 1 chr7A.!!$R1 2256
3 TraesCS7A01G431200 chr7A 625614650 625617204 2554 True 2590.000000 2590 85.050000 1293 3857 1 chr7A.!!$R3 2564
4 TraesCS7A01G431200 chr7A 617730989 617738622 7633 True 1125.333333 2854 88.743000 1197 4716 3 chr7A.!!$R4 3519
5 TraesCS7A01G431200 chr7D 543561204 543563712 2508 True 2809.000000 2809 86.944000 1207 3714 1 chr7D.!!$R1 2507
6 TraesCS7A01G431200 chr7D 543608220 543610565 2345 True 2599.000000 2599 86.655000 1409 3773 1 chr7D.!!$R2 2364
7 TraesCS7A01G431200 chr7D 543622828 543627229 4401 True 1946.666667 4667 93.078667 1197 4989 3 chr7D.!!$R3 3792
8 TraesCS7A01G431200 chr7B 586966394 586968920 2526 True 3195.000000 3195 89.494000 1197 3725 1 chr7B.!!$R1 2528
9 TraesCS7A01G431200 chr7B 637271500 637272695 1195 False 1738.000000 1738 92.911000 1 1196 1 chr7B.!!$F1 1195
10 TraesCS7A01G431200 chr6B 705569160 705570356 1196 True 2134.000000 2134 98.830000 1 1197 1 chr6B.!!$R2 1196
11 TraesCS7A01G431200 chr6B 694665390 694667799 2409 True 2082.000000 2082 82.358000 1271 3683 1 chr6B.!!$R1 2412
12 TraesCS7A01G431200 chr3A 639155182 639156377 1195 False 2104.000000 2104 98.411000 1 1196 1 chr3A.!!$F1 1195
13 TraesCS7A01G431200 chr5B 481061795 481062994 1199 False 2084.000000 2084 98.002000 1 1200 1 chr5B.!!$F2 1199
14 TraesCS7A01G431200 chr5B 471120430 471121626 1196 False 1816.000000 1816 94.078000 1 1196 1 chr5B.!!$F1 1195
15 TraesCS7A01G431200 chr2B 358913071 358914266 1195 False 2076.000000 2076 97.993000 1 1196 1 chr2B.!!$F1 1195
16 TraesCS7A01G431200 chr1B 340455974 340457171 1197 False 1840.000000 1840 94.412000 1 1197 1 chr1B.!!$F1 1196
17 TraesCS7A01G431200 chr1A 50616345 50617473 1128 True 1602.000000 1602 92.240000 5 1137 1 chr1A.!!$R1 1132
18 TraesCS7A01G431200 chr1A 549306736 549307873 1137 True 1598.000000 1598 91.927000 5 1154 1 chr1A.!!$R2 1149

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
912 916 2.046023 TTGTGCGATGGAGGGCTG 60.046 61.111 0.0 0.0 0.0 4.85 F
1465 1485 0.467290 GCAAACCCTCCCAAGACACA 60.467 55.000 0.0 0.0 0.0 3.72 F
2590 2617 0.948678 TTTACCTGCGTGTTTCTGCC 59.051 50.000 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2426 2453 0.592247 CAAACTTGTGCACACTCGCC 60.592 55.0 21.56 0.0 0.00 5.54 R
3432 3475 1.094785 ATGCACAGGGAAATACACGC 58.905 50.0 0.00 0.0 0.00 5.34 R
4042 5305 0.040942 TGGGGTGCCAATTACAGCAT 59.959 50.0 10.82 0.0 41.86 3.79 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
37 38 3.621805 TTGGAGGAGTTGCGGCGA 61.622 61.111 12.98 0.00 0.00 5.54
462 464 2.680913 GCATGTGCGCGAAGAAGGT 61.681 57.895 12.10 0.00 0.00 3.50
912 916 2.046023 TTGTGCGATGGAGGGCTG 60.046 61.111 0.00 0.00 0.00 4.85
963 968 5.425217 TCTGATTACCATGTGAGAAAGGCTA 59.575 40.000 0.00 0.00 0.00 3.93
1017 1022 1.134907 CGTGTTTATAGGCAGGGTCGT 60.135 52.381 0.00 0.00 0.00 4.34
1087 1093 8.052621 AGAACAAGGGATAGACTAGAGATAGT 57.947 38.462 0.00 0.00 0.00 2.12
1204 1211 5.448796 GTCACGTTGTTTAACACCTTTTACG 59.551 40.000 13.76 13.76 36.58 3.18
1226 1233 3.209410 GCTATGACCAGACAATTGAGGG 58.791 50.000 13.59 12.26 0.00 4.30
1279 1287 2.309755 TCAGGTTTGCCATCCTCTTCAT 59.690 45.455 0.00 0.00 37.19 2.57
1308 1316 7.017319 TCATGCATCTCCTCATAGATTTCAT 57.983 36.000 0.00 0.00 33.87 2.57
1465 1485 0.467290 GCAAACCCTCCCAAGACACA 60.467 55.000 0.00 0.00 0.00 3.72
1495 1515 4.020543 GGTACCTTGGCATATGGTTCAAA 58.979 43.478 4.06 0.00 37.87 2.69
1707 1727 4.527038 TGGAAATCTCGTCCTAACAGACTT 59.473 41.667 0.00 0.00 36.03 3.01
1923 1946 3.587061 ACACCATTGAACTCCTCCATACA 59.413 43.478 0.00 0.00 0.00 2.29
2374 2397 4.222886 CAGACAAGTTCTACTCTGTGTCG 58.777 47.826 0.00 0.00 40.19 4.35
2465 2492 1.392853 GTCTGAGTGATTGCTCTTGCG 59.607 52.381 0.00 0.00 43.34 4.85
2539 2566 6.329838 CTCAATATAAGAGCGCTAGAATGC 57.670 41.667 11.50 0.00 0.00 3.56
2578 2605 5.611374 TCAACTGGAGAAACTCTTTACCTG 58.389 41.667 0.00 0.00 0.00 4.00
2590 2617 0.948678 TTTACCTGCGTGTTTCTGCC 59.051 50.000 0.00 0.00 0.00 4.85
2602 2629 4.559300 CGTGTTTCTGCCAAAGATTTCCAT 60.559 41.667 0.00 0.00 33.93 3.41
2718 2749 6.849588 AATGATTTGGAGAAACAAAAGCAC 57.150 33.333 0.00 0.00 42.91 4.40
2856 2887 7.013846 CAGTTTTGGTTCTGTATTCAAGGGTTA 59.986 37.037 0.00 0.00 0.00 2.85
2948 2979 2.816087 GCTGAAGTGAGCTCAATTGGAA 59.184 45.455 32.03 16.62 34.01 3.53
3050 3081 3.928992 GTCAAATCGCTCTCTTGATGTCA 59.071 43.478 0.00 0.00 32.08 3.58
3133 3164 3.391626 GGGTTGCTAGAGGGTTAGCTTAT 59.608 47.826 0.00 0.00 44.99 1.73
3323 3363 2.945440 GCACCTGAATGGATTAGTGGCA 60.945 50.000 0.00 0.00 39.71 4.92
3432 3475 0.250901 ACTAGCAGTGGCAACCTTGG 60.251 55.000 0.00 0.00 44.61 3.61
3749 4848 6.426587 AGTTGCACCTGGAGATGTTATAATT 58.573 36.000 0.00 0.00 0.00 1.40
3750 4849 7.573710 AGTTGCACCTGGAGATGTTATAATTA 58.426 34.615 0.00 0.00 0.00 1.40
3751 4850 8.052748 AGTTGCACCTGGAGATGTTATAATTAA 58.947 33.333 0.00 0.00 0.00 1.40
3752 4851 7.801716 TGCACCTGGAGATGTTATAATTAAC 57.198 36.000 0.00 0.00 38.56 2.01
3959 5222 6.830838 GGGAAACTAGATGGATTTCATGTTCT 59.169 38.462 0.00 0.00 35.97 3.01
3960 5223 7.993183 GGGAAACTAGATGGATTTCATGTTCTA 59.007 37.037 0.00 0.00 35.97 2.10
3967 5230 8.405418 AGATGGATTTCATGTTCTATGATTGG 57.595 34.615 0.00 0.00 35.97 3.16
3968 5231 8.222637 AGATGGATTTCATGTTCTATGATTGGA 58.777 33.333 0.00 0.00 35.97 3.53
3969 5232 7.812690 TGGATTTCATGTTCTATGATTGGAG 57.187 36.000 0.00 0.00 0.00 3.86
3970 5233 7.576403 TGGATTTCATGTTCTATGATTGGAGA 58.424 34.615 0.00 0.00 0.00 3.71
3971 5234 8.222637 TGGATTTCATGTTCTATGATTGGAGAT 58.777 33.333 0.00 0.00 0.00 2.75
3972 5235 8.512956 GGATTTCATGTTCTATGATTGGAGATG 58.487 37.037 0.00 0.00 0.00 2.90
3974 5237 5.932455 TCATGTTCTATGATTGGAGATGCA 58.068 37.500 0.00 0.00 0.00 3.96
3975 5238 6.540083 TCATGTTCTATGATTGGAGATGCAT 58.460 36.000 0.00 0.00 0.00 3.96
3977 5240 6.628919 TGTTCTATGATTGGAGATGCATTG 57.371 37.500 0.00 0.00 0.00 2.82
3979 5242 7.281841 TGTTCTATGATTGGAGATGCATTGTA 58.718 34.615 0.00 0.00 0.00 2.41
3982 5245 8.557592 TCTATGATTGGAGATGCATTGTATTC 57.442 34.615 0.00 0.00 0.00 1.75
3987 5250 4.795469 TGGAGATGCATTGTATTCCATGT 58.205 39.130 0.00 0.00 30.21 3.21
3988 5251 5.939447 TGGAGATGCATTGTATTCCATGTA 58.061 37.500 0.00 0.00 30.21 2.29
3990 5253 7.005902 TGGAGATGCATTGTATTCCATGTAAT 58.994 34.615 0.00 0.00 30.21 1.89
3992 5255 9.013229 GGAGATGCATTGTATTCCATGTAATAA 57.987 33.333 0.00 0.00 0.00 1.40
3997 5260 9.800433 TGCATTGTATTCCATGTAATAAAGTTG 57.200 29.630 0.00 0.00 0.00 3.16
4025 5288 6.560253 AATGGTTTGAATGTACTCAGTGTC 57.440 37.500 0.00 0.00 0.00 3.67
4026 5289 4.055360 TGGTTTGAATGTACTCAGTGTCG 58.945 43.478 0.00 0.00 0.00 4.35
4027 5290 4.056050 GGTTTGAATGTACTCAGTGTCGT 58.944 43.478 0.00 0.00 0.00 4.34
4028 5291 4.150098 GGTTTGAATGTACTCAGTGTCGTC 59.850 45.833 0.00 0.00 0.00 4.20
4031 5294 3.004002 TGAATGTACTCAGTGTCGTCGTT 59.996 43.478 0.00 0.00 0.00 3.85
4032 5295 2.394545 TGTACTCAGTGTCGTCGTTG 57.605 50.000 0.00 0.00 0.00 4.10
4033 5296 1.672363 TGTACTCAGTGTCGTCGTTGT 59.328 47.619 0.00 0.00 0.00 3.32
4035 5298 1.022735 ACTCAGTGTCGTCGTTGTCT 58.977 50.000 0.00 0.00 0.00 3.41
4036 5299 1.002684 ACTCAGTGTCGTCGTTGTCTC 60.003 52.381 0.00 0.00 0.00 3.36
4037 5300 0.041576 TCAGTGTCGTCGTTGTCTCG 60.042 55.000 0.00 0.00 0.00 4.04
4039 5302 0.873054 AGTGTCGTCGTTGTCTCGAT 59.127 50.000 0.00 0.00 41.78 3.59
4040 5303 1.136029 AGTGTCGTCGTTGTCTCGATC 60.136 52.381 0.00 0.00 41.78 3.69
4041 5304 0.167470 TGTCGTCGTTGTCTCGATCC 59.833 55.000 0.00 0.00 41.78 3.36
4042 5305 0.167470 GTCGTCGTTGTCTCGATCCA 59.833 55.000 0.00 0.00 41.78 3.41
4047 5310 0.926155 CGTTGTCTCGATCCATGCTG 59.074 55.000 0.00 0.00 0.00 4.41
4049 5312 2.479560 CGTTGTCTCGATCCATGCTGTA 60.480 50.000 0.00 0.00 0.00 2.74
4050 5313 3.521560 GTTGTCTCGATCCATGCTGTAA 58.478 45.455 0.00 0.00 0.00 2.41
4051 5314 4.122776 GTTGTCTCGATCCATGCTGTAAT 58.877 43.478 0.00 0.00 0.00 1.89
4052 5315 4.406648 TGTCTCGATCCATGCTGTAATT 57.593 40.909 0.00 0.00 0.00 1.40
4053 5316 4.122046 TGTCTCGATCCATGCTGTAATTG 58.878 43.478 0.00 0.00 0.00 2.32
4054 5317 3.496130 GTCTCGATCCATGCTGTAATTGG 59.504 47.826 0.00 0.00 0.00 3.16
4055 5318 2.221169 TCGATCCATGCTGTAATTGGC 58.779 47.619 0.00 0.00 0.00 4.52
4056 5319 1.948834 CGATCCATGCTGTAATTGGCA 59.051 47.619 5.34 5.34 42.80 4.92
4058 5321 1.473258 TCCATGCTGTAATTGGCACC 58.527 50.000 5.05 0.00 41.39 5.01
4059 5322 0.461135 CCATGCTGTAATTGGCACCC 59.539 55.000 5.05 0.00 41.39 4.61
4060 5323 0.461135 CATGCTGTAATTGGCACCCC 59.539 55.000 5.05 0.00 41.39 4.95
4061 5324 0.040942 ATGCTGTAATTGGCACCCCA 59.959 50.000 5.05 0.00 41.39 4.96
4062 5325 0.611618 TGCTGTAATTGGCACCCCAG 60.612 55.000 0.00 0.00 43.37 4.45
4063 5326 0.323360 GCTGTAATTGGCACCCCAGA 60.323 55.000 6.78 0.00 43.37 3.86
4064 5327 1.686115 GCTGTAATTGGCACCCCAGAT 60.686 52.381 6.78 0.00 43.37 2.90
4065 5328 2.422803 GCTGTAATTGGCACCCCAGATA 60.423 50.000 6.78 0.00 43.37 1.98
4067 5330 4.473444 CTGTAATTGGCACCCCAGATATT 58.527 43.478 0.00 0.00 43.37 1.28
4068 5331 4.877773 TGTAATTGGCACCCCAGATATTT 58.122 39.130 0.00 0.00 43.37 1.40
4069 5332 4.892934 TGTAATTGGCACCCCAGATATTTC 59.107 41.667 0.00 0.00 43.37 2.17
4070 5333 3.979501 ATTGGCACCCCAGATATTTCT 57.020 42.857 0.00 0.00 43.37 2.52
4071 5334 3.756082 TTGGCACCCCAGATATTTCTT 57.244 42.857 0.00 0.00 43.37 2.52
4072 5335 3.756082 TGGCACCCCAGATATTTCTTT 57.244 42.857 0.00 0.00 35.79 2.52
4073 5336 4.059773 TGGCACCCCAGATATTTCTTTT 57.940 40.909 0.00 0.00 35.79 2.27
4074 5337 4.023291 TGGCACCCCAGATATTTCTTTTC 58.977 43.478 0.00 0.00 35.79 2.29
4075 5338 3.384789 GGCACCCCAGATATTTCTTTTCC 59.615 47.826 0.00 0.00 0.00 3.13
4076 5339 4.281657 GCACCCCAGATATTTCTTTTCCT 58.718 43.478 0.00 0.00 0.00 3.36
4114 5384 5.409214 GCTTACAACGGTAACACCAAATCTA 59.591 40.000 0.00 0.00 38.47 1.98
4237 5509 4.754667 GTGGGGAAGACGGCGACC 62.755 72.222 16.62 11.12 0.00 4.79
4281 5553 2.159057 GCTGCACAATTAAATGAGGGGG 60.159 50.000 0.00 0.00 0.00 5.40
4701 7660 2.206900 TCAGGGGAAGGCCTGACA 59.793 61.111 5.69 0.00 38.03 3.58
4778 8412 4.060900 ACAGTCAAACAGCAGTATCACAG 58.939 43.478 0.00 0.00 0.00 3.66
4806 8440 4.021104 GCTGAAGGCAATTAAAGGAAACCT 60.021 41.667 0.00 0.00 41.35 3.50
4853 10311 8.427774 GCATTTCTAGCAATTGTTTTTAGTCAC 58.572 33.333 7.40 0.00 0.00 3.67
4854 10312 9.683069 CATTTCTAGCAATTGTTTTTAGTCACT 57.317 29.630 7.40 0.00 0.00 3.41
4873 10386 8.410673 AGTCACTATATATACTTGGTGTCAGG 57.589 38.462 8.77 0.00 0.00 3.86
4930 10444 3.347216 GTGTATGGACTGCTGACCATTT 58.653 45.455 26.80 11.90 44.09 2.32
4939 10453 0.037975 GCTGACCATTTGGCCAACAG 60.038 55.000 20.35 21.72 39.32 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 1.001393 CACCAACAATAGGGGCGGT 60.001 57.895 0.00 0.00 0.00 5.68
462 464 1.595929 GGAAACCAGTCCGTTGCGA 60.596 57.895 0.00 0.00 0.00 5.10
912 916 1.627834 CTCTTCCATCCATCTAGCCCC 59.372 57.143 0.00 0.00 0.00 5.80
963 968 2.251642 GCAAAGGCACGACGTTCCT 61.252 57.895 13.73 13.73 40.72 3.36
1017 1022 1.064240 TGTACGCTATCAGGGAGGTCA 60.064 52.381 0.00 0.00 31.91 4.02
1204 1211 3.209410 CCTCAATTGTCTGGTCATAGCC 58.791 50.000 5.13 0.00 0.00 3.93
1226 1233 7.116090 CAGATACTGCAGATATAAGTGCTCAAC 59.884 40.741 23.35 0.00 40.54 3.18
1279 1287 6.429521 TCTATGAGGAGATGCATGATGAAA 57.570 37.500 2.46 0.00 0.00 2.69
1308 1316 0.322975 GCACAGGAAGAGGAGCAAGA 59.677 55.000 0.00 0.00 0.00 3.02
1403 1414 1.226295 GCGCGTACCTGCCATTTTC 60.226 57.895 8.43 0.00 0.00 2.29
1495 1515 4.280929 GCAGAAGTAAATTTGGGGACTGTT 59.719 41.667 0.00 0.00 0.00 3.16
1636 1656 6.151691 GCTATTTCTTGTGATGTTTGCTTGA 58.848 36.000 0.00 0.00 0.00 3.02
1923 1946 4.407621 TCCATACACCTGTCGACCAATATT 59.592 41.667 14.12 0.00 0.00 1.28
2374 2397 2.234300 TCTCCGGAAACTCAACACAC 57.766 50.000 5.23 0.00 0.00 3.82
2426 2453 0.592247 CAAACTTGTGCACACTCGCC 60.592 55.000 21.56 0.00 0.00 5.54
2465 2492 1.295792 TCGTTGAAGGAATATGCGGC 58.704 50.000 0.00 0.00 0.00 6.53
2539 2566 4.273480 CCAGTTGAACTTGAAGTACCACTG 59.727 45.833 17.34 17.34 0.00 3.66
2578 2605 2.422276 AATCTTTGGCAGAAACACGC 57.578 45.000 0.00 0.00 34.16 5.34
2590 2617 6.985645 TGTTTTTCACTCCATGGAAATCTTTG 59.014 34.615 17.00 4.55 35.61 2.77
2602 2629 4.159506 CCCTTTCTGTTGTTTTTCACTCCA 59.840 41.667 0.00 0.00 0.00 3.86
2718 2749 5.339177 CATTGAGTATATGGCTAGAGCTCG 58.661 45.833 8.37 0.00 41.70 5.03
2856 2887 7.667557 TGCTATAGCTACCGAGTCATTTAAAT 58.332 34.615 24.61 0.00 42.66 1.40
2948 2979 6.959639 AACTAAATTGATGTGTTGGACAGT 57.040 33.333 0.00 0.00 38.23 3.55
3133 3164 1.273327 TCTCGACAGCTCTCATGCAAA 59.727 47.619 0.00 0.00 34.99 3.68
3323 3363 5.543507 TCAACTTTTGGTGTAATGGCAAT 57.456 34.783 0.00 0.00 38.53 3.56
3432 3475 1.094785 ATGCACAGGGAAATACACGC 58.905 50.000 0.00 0.00 0.00 5.34
3725 4823 5.435686 TTATAACATCTCCAGGTGCAACT 57.564 39.130 0.00 0.00 36.74 3.16
3925 5188 0.756903 TCTAGTTTCCCTATGGCGCC 59.243 55.000 22.73 22.73 0.00 6.53
3959 5222 7.232910 TGGAATACAATGCATCTCCAATCATA 58.767 34.615 0.00 0.00 30.12 2.15
3960 5223 6.072649 TGGAATACAATGCATCTCCAATCAT 58.927 36.000 0.00 0.00 30.12 2.45
3962 5225 6.015688 ACATGGAATACAATGCATCTCCAATC 60.016 38.462 14.58 4.80 36.59 2.67
3963 5226 5.836898 ACATGGAATACAATGCATCTCCAAT 59.163 36.000 14.58 7.04 36.59 3.16
3964 5227 5.202765 ACATGGAATACAATGCATCTCCAA 58.797 37.500 14.58 3.89 36.59 3.53
3965 5228 4.795469 ACATGGAATACAATGCATCTCCA 58.205 39.130 0.00 8.16 37.37 3.86
3966 5229 6.882610 TTACATGGAATACAATGCATCTCC 57.117 37.500 0.00 2.34 0.00 3.71
3971 5234 9.800433 CAACTTTATTACATGGAATACAATGCA 57.200 29.630 10.04 0.00 0.00 3.96
3972 5235 9.801873 ACAACTTTATTACATGGAATACAATGC 57.198 29.630 10.04 0.00 0.00 3.56
3997 5260 9.988350 CACTGAGTACATTCAAACCATTATTAC 57.012 33.333 0.00 0.00 0.00 1.89
4002 5265 5.179368 CGACACTGAGTACATTCAAACCATT 59.821 40.000 0.00 0.00 0.00 3.16
4005 5268 4.056050 ACGACACTGAGTACATTCAAACC 58.944 43.478 0.00 0.00 0.00 3.27
4006 5269 4.143597 CGACGACACTGAGTACATTCAAAC 60.144 45.833 0.00 0.00 0.00 2.93
4007 5270 3.978855 CGACGACACTGAGTACATTCAAA 59.021 43.478 0.00 0.00 0.00 2.69
4009 5272 2.551032 ACGACGACACTGAGTACATTCA 59.449 45.455 0.00 0.00 0.00 2.57
4010 5273 3.198863 ACGACGACACTGAGTACATTC 57.801 47.619 0.00 0.00 0.00 2.67
4013 5276 1.672363 ACAACGACGACACTGAGTACA 59.328 47.619 0.00 0.00 0.00 2.90
4014 5277 2.032204 AGACAACGACGACACTGAGTAC 60.032 50.000 0.00 0.00 0.00 2.73
4021 5284 1.248721 GATCGAGACAACGACGACAC 58.751 55.000 0.00 0.00 44.84 3.67
4025 5288 1.191944 CATGGATCGAGACAACGACG 58.808 55.000 0.00 0.00 44.84 5.12
4026 5289 0.924090 GCATGGATCGAGACAACGAC 59.076 55.000 0.00 0.00 44.84 4.34
4027 5290 0.817654 AGCATGGATCGAGACAACGA 59.182 50.000 0.00 0.00 46.04 3.85
4028 5291 0.926155 CAGCATGGATCGAGACAACG 59.074 55.000 0.00 0.00 0.00 4.10
4031 5294 4.122046 CAATTACAGCATGGATCGAGACA 58.878 43.478 0.00 0.00 43.62 3.41
4032 5295 3.496130 CCAATTACAGCATGGATCGAGAC 59.504 47.826 0.00 0.00 43.62 3.36
4033 5296 3.732212 CCAATTACAGCATGGATCGAGA 58.268 45.455 0.00 0.00 43.62 4.04
4035 5298 2.221169 GCCAATTACAGCATGGATCGA 58.779 47.619 0.00 0.00 43.62 3.59
4036 5299 1.948834 TGCCAATTACAGCATGGATCG 59.051 47.619 0.00 0.00 43.62 3.69
4037 5300 2.035066 GGTGCCAATTACAGCATGGATC 59.965 50.000 0.00 0.00 43.62 3.36
4039 5302 1.473258 GGTGCCAATTACAGCATGGA 58.527 50.000 0.00 0.00 43.62 3.41
4040 5303 0.461135 GGGTGCCAATTACAGCATGG 59.539 55.000 10.82 0.00 43.62 3.66
4041 5304 0.461135 GGGGTGCCAATTACAGCATG 59.539 55.000 10.82 0.00 41.86 4.06
4042 5305 0.040942 TGGGGTGCCAATTACAGCAT 59.959 50.000 10.82 0.00 41.86 3.79
4047 5310 5.140454 AGAAATATCTGGGGTGCCAATTAC 58.860 41.667 0.00 0.00 33.59 1.89
4049 5312 4.270317 AGAAATATCTGGGGTGCCAATT 57.730 40.909 0.00 0.00 33.59 2.32
4050 5313 3.979501 AGAAATATCTGGGGTGCCAAT 57.020 42.857 0.00 0.00 33.59 3.16
4051 5314 3.756082 AAGAAATATCTGGGGTGCCAA 57.244 42.857 0.00 0.00 35.59 4.52
4052 5315 3.756082 AAAGAAATATCTGGGGTGCCA 57.244 42.857 0.00 0.00 35.59 4.92
4053 5316 3.384789 GGAAAAGAAATATCTGGGGTGCC 59.615 47.826 0.00 0.00 35.59 5.01
4054 5317 4.281657 AGGAAAAGAAATATCTGGGGTGC 58.718 43.478 0.00 0.00 35.59 5.01
4055 5318 5.951747 TGAAGGAAAAGAAATATCTGGGGTG 59.048 40.000 0.00 0.00 35.59 4.61
4056 5319 5.952347 GTGAAGGAAAAGAAATATCTGGGGT 59.048 40.000 0.00 0.00 35.59 4.95
4058 5321 7.651027 ATGTGAAGGAAAAGAAATATCTGGG 57.349 36.000 0.00 0.00 35.59 4.45
4059 5322 9.933723 AAAATGTGAAGGAAAAGAAATATCTGG 57.066 29.630 0.00 0.00 35.59 3.86
4064 5327 8.296713 CGGAGAAAATGTGAAGGAAAAGAAATA 58.703 33.333 0.00 0.00 0.00 1.40
4065 5328 7.147976 CGGAGAAAATGTGAAGGAAAAGAAAT 58.852 34.615 0.00 0.00 0.00 2.17
4067 5330 5.507315 GCGGAGAAAATGTGAAGGAAAAGAA 60.507 40.000 0.00 0.00 0.00 2.52
4068 5331 4.023193 GCGGAGAAAATGTGAAGGAAAAGA 60.023 41.667 0.00 0.00 0.00 2.52
4069 5332 4.022849 AGCGGAGAAAATGTGAAGGAAAAG 60.023 41.667 0.00 0.00 0.00 2.27
4070 5333 3.888930 AGCGGAGAAAATGTGAAGGAAAA 59.111 39.130 0.00 0.00 0.00 2.29
4071 5334 3.486383 AGCGGAGAAAATGTGAAGGAAA 58.514 40.909 0.00 0.00 0.00 3.13
4072 5335 3.140325 AGCGGAGAAAATGTGAAGGAA 57.860 42.857 0.00 0.00 0.00 3.36
4073 5336 2.859165 AGCGGAGAAAATGTGAAGGA 57.141 45.000 0.00 0.00 0.00 3.36
4074 5337 3.751175 TGTAAGCGGAGAAAATGTGAAGG 59.249 43.478 0.00 0.00 0.00 3.46
4075 5338 5.147162 GTTGTAAGCGGAGAAAATGTGAAG 58.853 41.667 0.00 0.00 0.00 3.02
4076 5339 4.319190 CGTTGTAAGCGGAGAAAATGTGAA 60.319 41.667 0.00 0.00 0.00 3.18
4114 5384 1.002087 CCGAGCAAGGGTGAAACTACT 59.998 52.381 0.00 0.00 36.74 2.57
4171 5443 1.956170 CGCGTGCTCAGGTGAGTTT 60.956 57.895 8.74 0.00 43.85 2.66
4237 5509 2.305853 CGCGCCGGAGATTGAGATG 61.306 63.158 10.31 0.00 0.00 2.90
4281 5553 5.106908 GCGCCATTGGACTCTATCTAATTTC 60.107 44.000 6.95 0.00 36.42 2.17
4292 5564 0.940126 CATAGTGCGCCATTGGACTC 59.060 55.000 6.95 0.00 39.96 3.36
4343 5616 0.976073 GGAGGTGAGGTTGGGATCGA 60.976 60.000 0.00 0.00 0.00 3.59
4548 7288 4.867599 CTTACTCCGGCCCGCGTC 62.868 72.222 4.92 0.00 0.00 5.19
4550 7290 4.867599 GTCTTACTCCGGCCCGCG 62.868 72.222 0.00 0.00 0.00 6.46
4551 7291 4.525949 GGTCTTACTCCGGCCCGC 62.526 72.222 0.00 0.00 0.00 6.13
4552 7292 4.203076 CGGTCTTACTCCGGCCCG 62.203 72.222 0.00 0.00 43.68 6.13
4553 7293 4.525949 GCGGTCTTACTCCGGCCC 62.526 72.222 0.00 0.00 46.90 5.80
4554 7294 4.867599 CGCGGTCTTACTCCGGCC 62.868 72.222 0.00 0.00 46.90 6.13
4555 7295 4.867599 CCGCGGTCTTACTCCGGC 62.868 72.222 19.50 0.00 46.90 6.13
4594 7545 4.006532 CGCGGCTTCTTATGCGTA 57.993 55.556 0.00 0.00 45.12 4.42
4676 7627 3.083997 CTTCCCCTGACCTCCGGG 61.084 72.222 0.00 0.00 41.19 5.73
4679 7638 3.412408 GGCCTTCCCCTGACCTCC 61.412 72.222 0.00 0.00 0.00 4.30
4731 8365 2.217620 CCGTTGAAACAAAATGCCGTTC 59.782 45.455 0.00 0.00 0.00 3.95
4778 8412 3.119352 CCTTTAATTGCCTTCAGCCTGAC 60.119 47.826 0.00 0.00 42.71 3.51
4855 10313 9.998106 GATAAACACCTGACACCAAGTATATAT 57.002 33.333 0.00 0.00 0.00 0.86
4856 10314 8.426489 GGATAAACACCTGACACCAAGTATATA 58.574 37.037 0.00 0.00 0.00 0.86
4857 10315 7.092623 TGGATAAACACCTGACACCAAGTATAT 60.093 37.037 0.00 0.00 0.00 0.86
4872 10385 2.041216 AGGGTCAGGTTGGATAAACACC 59.959 50.000 0.00 0.00 40.86 4.16
4873 10386 3.009143 AGAGGGTCAGGTTGGATAAACAC 59.991 47.826 0.00 0.00 40.86 3.32
4909 10422 2.698855 ATGGTCAGCAGTCCATACAC 57.301 50.000 6.09 0.00 41.06 2.90
4930 10444 1.719063 AAGGCTCCTTCTGTTGGCCA 61.719 55.000 0.00 0.00 44.60 5.36


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

AutoCloner maintained by Alex Coulton.