Multiple sequence alignment - TraesCS3D01G226000

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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 TraesCS3D01G226000 chr3D 100.000 4187 0 0 1 4187 307838883 307834697 0.000000e+00 7733.0
1 TraesCS3D01G226000 chr3B 96.985 1791 38 3 1593 3367 413958851 413960641 0.000000e+00 2994.0
2 TraesCS3D01G226000 chr3B 92.665 1227 67 14 220 1437 413957507 413958719 0.000000e+00 1746.0
3 TraesCS3D01G226000 chr3B 87.417 151 7 2 2 152 413957362 413957500 3.350000e-36 163.0
4 TraesCS3D01G226000 chr3B 90.566 106 5 3 3756 3861 434067195 434067095 7.300000e-28 135.0
5 TraesCS3D01G226000 chr3B 86.585 82 6 2 3370 3451 413963558 413963634 7.460000e-13 86.1
6 TraesCS3D01G226000 chr3A 94.712 1891 58 17 1593 3447 427103286 427101402 0.000000e+00 2900.0
7 TraesCS3D01G226000 chr3A 93.289 909 38 7 552 1437 427104324 427103416 0.000000e+00 1319.0
8 TraesCS3D01G226000 chr3A 88.788 553 50 4 2 554 427104967 427104427 0.000000e+00 667.0
9 TraesCS3D01G226000 chr3A 94.241 191 10 1 3865 4054 596487380 596487190 1.470000e-74 291.0
10 TraesCS3D01G226000 chr3A 91.892 148 10 1 3603 3748 427099894 427099747 5.490000e-49 206.0
11 TraesCS3D01G226000 chr3A 96.262 107 3 1 3756 3861 596487952 596487846 1.550000e-39 174.0
12 TraesCS3D01G226000 chr3A 89.381 113 7 2 4075 4187 427099257 427099150 2.030000e-28 137.0
13 TraesCS3D01G226000 chr1B 78.540 918 151 27 2308 3188 160486672 160487580 2.830000e-156 562.0
14 TraesCS3D01G226000 chr1B 91.463 164 12 2 3897 4059 368139280 368139118 1.510000e-54 224.0
15 TraesCS3D01G226000 chr1B 78.846 208 36 5 16 221 171181409 171181208 2.630000e-27 134.0
16 TraesCS3D01G226000 chr1B 86.607 112 14 1 2 113 15136119 15136009 5.680000e-24 122.0
17 TraesCS3D01G226000 chr1D 78.357 901 157 25 2317 3188 106371986 106371095 2.200000e-152 549.0
18 TraesCS3D01G226000 chr1D 74.664 596 114 23 1620 2196 106373968 106373391 3.260000e-56 230.0
19 TraesCS3D01G226000 chr2D 95.960 198 6 2 3862 4059 633881068 633881263 1.880000e-83 320.0
20 TraesCS3D01G226000 chr2D 85.342 307 40 5 28 333 472846106 472845804 3.140000e-81 313.0
21 TraesCS3D01G226000 chr2D 91.150 113 3 2 3754 3861 633880486 633880596 3.370000e-31 147.0
22 TraesCS3D01G226000 chr2D 87.500 112 13 1 2 113 589669486 589669376 1.220000e-25 128.0
23 TraesCS3D01G226000 chr2B 83.434 332 54 1 2 333 240302523 240302853 1.460000e-79 307.0
24 TraesCS3D01G226000 chrUn 94.180 189 9 2 3865 4052 22854966 22854779 1.900000e-73 287.0
25 TraesCS3D01G226000 chrUn 92.453 106 5 2 3756 3861 22855532 22855430 9.380000e-32 148.0
26 TraesCS3D01G226000 chr6A 92.929 198 8 5 3865 4059 12220339 12220145 2.460000e-72 283.0
27 TraesCS3D01G226000 chr6A 94.505 91 5 0 3760 3850 12220760 12220670 1.570000e-29 141.0
28 TraesCS3D01G226000 chr7D 92.821 195 12 2 3865 4059 89214785 89214593 8.860000e-72 281.0
29 TraesCS3D01G226000 chr7D 93.458 107 5 2 3756 3861 89215393 89215288 1.560000e-34 158.0
30 TraesCS3D01G226000 chr6D 91.282 195 15 2 3865 4059 67396557 67396365 8.930000e-67 265.0
31 TraesCS3D01G226000 chr6D 85.714 112 15 1 2 113 176484567 176484677 2.640000e-22 117.0
32 TraesCS3D01G226000 chr2A 90.955 199 13 3 3862 4059 383337906 383338100 3.210000e-66 263.0
33 TraesCS3D01G226000 chr2A 92.537 67 5 0 4080 4146 82133813 82133747 3.450000e-16 97.1
34 TraesCS3D01G226000 chr4D 93.125 160 10 1 3862 4021 124532586 124532428 2.520000e-57 233.0
35 TraesCS3D01G226000 chr4D 95.283 106 3 2 3756 3861 124533158 124533055 2.590000e-37 167.0
36 TraesCS3D01G226000 chr5B 83.871 217 31 3 2 217 286882424 286882211 1.970000e-48 204.0
37 TraesCS3D01G226000 chr5B 94.340 106 2 1 3756 3861 312140517 312140416 4.330000e-35 159.0
38 TraesCS3D01G226000 chr5B 91.509 106 3 4 3756 3861 664649992 664649893 1.570000e-29 141.0
39 TraesCS3D01G226000 chr7B 79.275 193 33 4 30 221 723944796 723944610 1.220000e-25 128.0
40 TraesCS3D01G226000 chr1A 86.726 113 12 3 2 113 362870314 362870204 5.680000e-24 122.0


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 TraesCS3D01G226000 chr3D 307834697 307838883 4186 True 7733.000 7733 100.0000 1 4187 1 chr3D.!!$R1 4186
1 TraesCS3D01G226000 chr3B 413957362 413963634 6272 False 1247.275 2994 90.9130 2 3451 4 chr3B.!!$F1 3449
2 TraesCS3D01G226000 chr3A 427099150 427104967 5817 True 1045.800 2900 91.6124 2 4187 5 chr3A.!!$R1 4185
3 TraesCS3D01G226000 chr3A 596487190 596487952 762 True 232.500 291 95.2515 3756 4054 2 chr3A.!!$R2 298
4 TraesCS3D01G226000 chr1B 160486672 160487580 908 False 562.000 562 78.5400 2308 3188 1 chr1B.!!$F1 880
5 TraesCS3D01G226000 chr1D 106371095 106373968 2873 True 389.500 549 76.5105 1620 3188 2 chr1D.!!$R1 1568
6 TraesCS3D01G226000 chr2D 633880486 633881263 777 False 233.500 320 93.5550 3754 4059 2 chr2D.!!$F1 305
7 TraesCS3D01G226000 chrUn 22854779 22855532 753 True 217.500 287 93.3165 3756 4052 2 chrUn.!!$R1 296
8 TraesCS3D01G226000 chr6A 12220145 12220760 615 True 212.000 283 93.7170 3760 4059 2 chr6A.!!$R1 299
9 TraesCS3D01G226000 chr7D 89214593 89215393 800 True 219.500 281 93.1395 3756 4059 2 chr7D.!!$R1 303

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
980 1107 0.306533 GTACCGCACCACACAGTTTG 59.693 55.0 0.0 0.0 0.00 2.93 F
1332 1459 1.321474 TCGTCAAGGAACACGGTAGT 58.679 50.0 0.0 0.0 36.64 2.73 F
1808 1977 1.359459 GACGGTGAGAAATGGGCGAC 61.359 60.0 0.0 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2474 3937 0.033228 CGGTGCTCATCCTCATCCTC 59.967 60.000 0.00 0.0 0.0 3.71 R
3132 4629 1.065926 TGAGGATGCAGTGTGATGACC 60.066 52.381 0.00 0.0 0.0 4.02 R
3584 9392 0.040425 GCACAGGCGACGTCATTTTT 60.040 50.000 17.16 0.0 0.0 1.94 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 1.737008 GGAACGACACCGAAGAGCC 60.737 63.158 0.00 0.00 39.50 4.70
73 74 3.149196 GAGCAAGTTTTCACCCAGATCA 58.851 45.455 0.00 0.00 0.00 2.92
75 76 2.352127 GCAAGTTTTCACCCAGATCAGC 60.352 50.000 0.00 0.00 0.00 4.26
78 79 1.734465 GTTTTCACCCAGATCAGCTCG 59.266 52.381 0.00 0.00 0.00 5.03
114 115 1.738099 GTCTTGTGCACGGATCGCT 60.738 57.895 13.13 0.00 0.00 4.93
115 116 0.457853 GTCTTGTGCACGGATCGCTA 60.458 55.000 13.13 0.00 0.00 4.26
152 153 2.711547 ACTAGACAAAAAGGGTCCAGCT 59.288 45.455 0.00 0.00 35.89 4.24
240 241 0.754217 TAGCCCATCGCCGTAGAACT 60.754 55.000 0.00 0.00 38.78 3.01
292 293 2.577059 GCGAGATCCGTGAACCCA 59.423 61.111 5.66 0.00 41.15 4.51
295 296 1.901085 GAGATCCGTGAACCCAGCT 59.099 57.895 0.00 0.00 0.00 4.24
349 350 2.838736 CCGCTTATTGCCATGTAGAGT 58.161 47.619 0.00 0.00 38.78 3.24
352 353 3.871006 CGCTTATTGCCATGTAGAGTTCA 59.129 43.478 0.00 0.00 38.78 3.18
358 359 3.169908 TGCCATGTAGAGTTCAGGTGTA 58.830 45.455 0.00 0.00 0.00 2.90
369 370 5.187772 AGAGTTCAGGTGTATGCTCATTGTA 59.812 40.000 0.00 0.00 0.00 2.41
565 673 3.671008 ACAACCACTTACGTATCTGCA 57.329 42.857 0.00 0.00 0.00 4.41
722 838 1.452145 TTGGGTTTCTTGCCACGCTC 61.452 55.000 0.00 0.00 0.00 5.03
764 881 4.400529 AAAAACGAATCCAGCCTTTTGT 57.599 36.364 0.00 0.00 0.00 2.83
832 949 1.580439 CGCGAAAATGTTGTGACGAG 58.420 50.000 0.00 0.00 0.00 4.18
842 959 5.914085 ATGTTGTGACGAGAAAGAAGAAG 57.086 39.130 0.00 0.00 0.00 2.85
844 961 3.452755 TGTGACGAGAAAGAAGAAGCA 57.547 42.857 0.00 0.00 0.00 3.91
901 1018 1.153429 GCACCCACCCTCGTATCAC 60.153 63.158 0.00 0.00 0.00 3.06
973 1094 1.271379 CTCTAGTTGTACCGCACCACA 59.729 52.381 0.00 0.00 0.00 4.17
980 1107 0.306533 GTACCGCACCACACAGTTTG 59.693 55.000 0.00 0.00 0.00 2.93
984 1111 1.876799 CCGCACCACACAGTTTGATTA 59.123 47.619 0.00 0.00 0.00 1.75
988 1115 3.315191 GCACCACACAGTTTGATTACAGT 59.685 43.478 0.00 0.00 0.00 3.55
989 1116 4.513692 GCACCACACAGTTTGATTACAGTA 59.486 41.667 0.00 0.00 0.00 2.74
1010 1137 6.421202 CAGTATAAGAAACTAATGGAGGTCGC 59.579 42.308 0.00 0.00 0.00 5.19
1023 1150 3.488090 GTCGCCGTAGCAGCAACC 61.488 66.667 0.00 0.00 39.83 3.77
1044 1171 1.674980 ACTCGGAGTCGGAGGTGAC 60.675 63.158 26.10 0.00 39.21 3.67
1332 1459 1.321474 TCGTCAAGGAACACGGTAGT 58.679 50.000 0.00 0.00 36.64 2.73
1390 1517 8.110860 TCTGGTCCAATATGTCTTTCTTTTTC 57.889 34.615 0.00 0.00 0.00 2.29
1391 1518 6.908825 TGGTCCAATATGTCTTTCTTTTTCG 58.091 36.000 0.00 0.00 0.00 3.46
1396 1523 9.810545 TCCAATATGTCTTTCTTTTTCGTTTTT 57.189 25.926 0.00 0.00 0.00 1.94
1414 1547 7.585867 TCGTTTTTCCGACATGAAAATTGATA 58.414 30.769 0.00 0.00 42.16 2.15
1449 1582 8.526667 ACTGAAGTATCTACTATTGCTCTTCA 57.473 34.615 0.00 0.00 38.01 3.02
1451 1584 8.526667 TGAAGTATCTACTATTGCTCTTCAGT 57.473 34.615 0.00 0.00 36.31 3.41
1452 1585 9.628500 TGAAGTATCTACTATTGCTCTTCAGTA 57.372 33.333 0.00 0.00 36.31 2.74
1529 1662 3.531538 TCTTTTACGGGCATCTGATGAC 58.468 45.455 21.30 18.39 37.65 3.06
1561 1694 6.254281 GCTCAAGGTAGCATTAAAACAAGA 57.746 37.500 0.00 0.00 42.30 3.02
1616 1782 4.749099 CCAAAAATTTCTGACGGCAATCAA 59.251 37.500 0.00 0.00 0.00 2.57
1808 1977 1.359459 GACGGTGAGAAATGGGCGAC 61.359 60.000 0.00 0.00 0.00 5.19
1909 2078 1.371183 CCGATCAGGGTGTGTGTGT 59.629 57.895 0.00 0.00 35.97 3.72
2137 2316 3.036783 GCTTCAGGCAGAGCAAGCG 62.037 63.158 2.50 0.00 41.35 4.68
2469 3932 2.125512 CGAACAAGGAGAGCGGGG 60.126 66.667 0.00 0.00 0.00 5.73
2666 4132 2.048127 AACTTCGACGGCCTCAGC 60.048 61.111 0.00 0.00 38.76 4.26
2791 4285 4.711846 TGATACTGTATGAAGTGCTCAGGT 59.288 41.667 4.79 0.00 37.52 4.00
3003 4500 2.592993 CCAGCCGGTCTTCTTCCCA 61.593 63.158 1.90 0.00 0.00 4.37
3379 7811 5.772521 CAAAGTTGGTTCATACAGGGAAAG 58.227 41.667 0.00 0.00 0.00 2.62
3440 7888 1.003118 AGCAGGCACCGATACAGAAAA 59.997 47.619 0.00 0.00 0.00 2.29
3467 9259 2.620627 GGGACGGGATCTGACCATTTTT 60.621 50.000 8.59 0.00 0.00 1.94
3470 9262 3.347216 ACGGGATCTGACCATTTTTCTG 58.653 45.455 0.00 0.00 0.00 3.02
3471 9263 2.098117 CGGGATCTGACCATTTTTCTGC 59.902 50.000 0.00 0.00 0.00 4.26
3473 9265 3.091545 GGATCTGACCATTTTTCTGCCA 58.908 45.455 0.00 0.00 0.00 4.92
3486 9278 1.153745 CTGCCACCGTAGTCTCTGC 60.154 63.158 0.00 0.00 0.00 4.26
3488 9280 2.490217 CCACCGTAGTCTCTGCCG 59.510 66.667 0.00 0.00 0.00 5.69
3489 9281 2.490217 CACCGTAGTCTCTGCCGG 59.510 66.667 0.00 0.00 45.72 6.13
3492 9284 2.023318 CCGTAGTCTCTGCCGGTAG 58.977 63.158 14.20 14.20 35.78 3.18
3494 9286 0.463295 CGTAGTCTCTGCCGGTAGGA 60.463 60.000 20.19 12.68 41.02 2.94
3500 9292 2.029623 TCTCTGCCGGTAGGATAACAC 58.970 52.381 20.19 0.00 41.02 3.32
3510 9302 1.861982 AGGATAACACTGCCTACCGT 58.138 50.000 0.00 0.00 0.00 4.83
3513 9305 2.102588 GGATAACACTGCCTACCGTCAT 59.897 50.000 0.00 0.00 0.00 3.06
3514 9306 2.665649 TAACACTGCCTACCGTCATG 57.334 50.000 0.00 0.00 0.00 3.07
3515 9307 0.036388 AACACTGCCTACCGTCATGG 60.036 55.000 0.00 0.00 46.41 3.66
3529 9321 2.417379 CGTCATGGTCTTGGTCTTCGAT 60.417 50.000 0.00 0.00 0.00 3.59
3566 9374 7.447374 TTGTGTCATGAAAAATACCCTACTG 57.553 36.000 0.00 0.00 0.00 2.74
3568 9376 4.947388 TGTCATGAAAAATACCCTACTGCC 59.053 41.667 0.00 0.00 0.00 4.85
3571 9379 6.096846 GTCATGAAAAATACCCTACTGCCAAT 59.903 38.462 0.00 0.00 0.00 3.16
3572 9380 7.284489 GTCATGAAAAATACCCTACTGCCAATA 59.716 37.037 0.00 0.00 0.00 1.90
3573 9381 8.004215 TCATGAAAAATACCCTACTGCCAATAT 58.996 33.333 0.00 0.00 0.00 1.28
3577 9385 8.465273 AAAAATACCCTACTGCCAATATCTTC 57.535 34.615 0.00 0.00 0.00 2.87
3578 9386 5.763876 ATACCCTACTGCCAATATCTTCC 57.236 43.478 0.00 0.00 0.00 3.46
3579 9387 3.669949 ACCCTACTGCCAATATCTTCCT 58.330 45.455 0.00 0.00 0.00 3.36
3580 9388 4.047883 ACCCTACTGCCAATATCTTCCTT 58.952 43.478 0.00 0.00 0.00 3.36
3581 9389 4.478686 ACCCTACTGCCAATATCTTCCTTT 59.521 41.667 0.00 0.00 0.00 3.11
3583 9391 5.893824 CCCTACTGCCAATATCTTCCTTTTT 59.106 40.000 0.00 0.00 0.00 1.94
3584 9392 7.060421 CCCTACTGCCAATATCTTCCTTTTTA 58.940 38.462 0.00 0.00 0.00 1.52
3586 9394 8.966868 CCTACTGCCAATATCTTCCTTTTTAAA 58.033 33.333 0.00 0.00 0.00 1.52
3596 9404 9.769093 ATATCTTCCTTTTTAAAAATGACGTCG 57.231 29.630 15.55 3.31 0.00 5.12
3597 9405 5.910723 TCTTCCTTTTTAAAAATGACGTCGC 59.089 36.000 15.55 0.00 0.00 5.19
3598 9406 4.538917 TCCTTTTTAAAAATGACGTCGCC 58.461 39.130 13.55 0.00 0.00 5.54
3599 9407 4.276431 TCCTTTTTAAAAATGACGTCGCCT 59.724 37.500 13.55 0.00 0.00 5.52
3600 9408 4.381566 CCTTTTTAAAAATGACGTCGCCTG 59.618 41.667 13.55 0.00 0.00 4.85
3601 9409 4.555348 TTTTAAAAATGACGTCGCCTGT 57.445 36.364 11.62 0.00 0.00 4.00
3637 9445 2.718731 CTGGACCGCGTTTTGCAA 59.281 55.556 4.92 0.00 46.97 4.08
3677 9487 4.765449 TGCCTGCGCTGCCTACTG 62.765 66.667 17.68 1.37 35.36 2.74
3690 9500 0.965439 CCTACTGCCTGCCTAGCTAG 59.035 60.000 14.20 14.20 0.00 3.42
3696 9506 1.822114 GCCTGCCTAGCTAGCTACCC 61.822 65.000 20.67 13.95 0.00 3.69
3716 9526 2.094078 CCGTGCATCCCATCAATTGTTT 60.094 45.455 5.13 0.00 0.00 2.83
3726 9536 7.353414 TCCCATCAATTGTTTAAGTTTGTGA 57.647 32.000 5.13 0.00 0.00 3.58
3900 10505 0.460284 GCTACGTACCAGCAGCACAT 60.460 55.000 3.93 0.00 38.93 3.21
4067 10676 3.631046 GCCTAGGGCCCAGATCCG 61.631 72.222 27.56 5.71 44.06 4.18
4068 10677 3.631046 CCTAGGGCCCAGATCCGC 61.631 72.222 27.56 0.00 0.00 5.54
4069 10678 3.631046 CTAGGGCCCAGATCCGCC 61.631 72.222 27.56 7.40 44.92 6.13
4073 10682 4.962836 GGCCCAGATCCGCCCATG 62.963 72.222 5.00 0.00 39.39 3.66
4084 10693 4.532490 GCCCATGCGTGCTAGTAA 57.468 55.556 0.00 0.00 0.00 2.24
4116 10725 4.404394 GTGGGTGGAAAGAGAAAGGAAAAA 59.596 41.667 0.00 0.00 0.00 1.94
4136 10745 2.425143 ATGGATGCGAGTGGATGTTT 57.575 45.000 0.00 0.00 0.00 2.83
4163 10772 1.275505 CTATGCAGTGCGTCACAGAG 58.724 55.000 14.43 0.93 36.74 3.35
4165 10774 0.668706 ATGCAGTGCGTCACAGAGAC 60.669 55.000 11.20 0.00 44.02 3.36
4171 10780 0.950555 TGCGTCACAGAGACCAATGC 60.951 55.000 0.00 0.00 44.66 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.109226 CTCTTCGGTGTCGTTCCCTC 60.109 60.000 0.00 0.00 37.69 4.30
73 74 1.561643 TGATGGAGGTTCTTCGAGCT 58.438 50.000 0.00 0.00 0.00 4.09
75 76 2.275318 GCTTGATGGAGGTTCTTCGAG 58.725 52.381 0.00 0.00 0.00 4.04
78 79 2.003301 GACGCTTGATGGAGGTTCTTC 58.997 52.381 0.00 0.00 0.00 2.87
114 115 0.702902 AGTCCCCGTCAGAGAAGGTA 59.297 55.000 0.00 0.00 29.35 3.08
115 116 0.702902 TAGTCCCCGTCAGAGAAGGT 59.297 55.000 0.00 0.00 29.35 3.50
185 186 3.127533 CACCGGCTGCTTAGGCAC 61.128 66.667 0.00 0.00 44.28 5.01
212 213 2.203070 GATGGGCTAGCACGGTGG 60.203 66.667 18.24 0.00 0.00 4.61
217 218 3.146726 TACGGCGATGGGCTAGCAC 62.147 63.158 16.62 14.86 42.94 4.40
218 219 2.835895 TACGGCGATGGGCTAGCA 60.836 61.111 16.62 0.00 42.94 3.49
292 293 2.433446 CTCCTGTGGTGGCAAGCT 59.567 61.111 0.00 0.00 0.00 3.74
340 341 5.016051 AGCATACACCTGAACTCTACATG 57.984 43.478 0.00 0.00 0.00 3.21
349 350 7.992608 ACATAATACAATGAGCATACACCTGAA 59.007 33.333 0.00 0.00 0.00 3.02
369 370 8.627208 AATGGAGCATCGAGAAAATACATAAT 57.373 30.769 0.00 0.00 34.37 1.28
405 406 7.169158 TCATTATTGACAAAGGGTGGATTTC 57.831 36.000 0.00 0.00 0.00 2.17
413 414 6.906157 ATGGCTATCATTATTGACAAAGGG 57.094 37.500 0.00 0.00 33.85 3.95
516 518 7.491696 GGATACAGCTCAGTTTCTATAAAACGT 59.508 37.037 0.00 0.00 35.42 3.99
722 838 1.336440 TGTTGTTGTTTCCATCGGCAG 59.664 47.619 0.00 0.00 0.00 4.85
745 861 4.119136 CAAACAAAAGGCTGGATTCGTTT 58.881 39.130 0.00 0.00 0.00 3.60
764 881 0.323816 TGCCACACACCAAGGACAAA 60.324 50.000 0.00 0.00 0.00 2.83
842 959 8.857216 CATCACATGTTTTTCTTATCTTCTTGC 58.143 33.333 0.00 0.00 0.00 4.01
844 961 8.031277 GGCATCACATGTTTTTCTTATCTTCTT 58.969 33.333 0.00 0.00 0.00 2.52
901 1018 0.436150 CACAGCAAGTGTCGTCGATG 59.564 55.000 0.00 0.00 43.40 3.84
930 1047 1.017387 GTGCGGTGGAAGATGGAATC 58.983 55.000 0.00 0.00 46.04 2.52
984 1111 7.490000 CGACCTCCATTAGTTTCTTATACTGT 58.510 38.462 0.00 0.00 0.00 3.55
988 1115 5.508489 CGGCGACCTCCATTAGTTTCTTATA 60.508 44.000 0.00 0.00 0.00 0.98
989 1116 4.704965 GGCGACCTCCATTAGTTTCTTAT 58.295 43.478 0.00 0.00 0.00 1.73
1010 1137 1.291877 GAGTGTGGTTGCTGCTACGG 61.292 60.000 8.06 0.00 0.00 4.02
1023 1150 1.972223 ACCTCCGACTCCGAGTGTG 60.972 63.158 5.57 0.00 38.22 3.82
1044 1171 1.135257 AGCGATGAAGGAGAAGACACG 60.135 52.381 0.00 0.00 0.00 4.49
1332 1459 7.542890 TCAACTTGAGCAACAACAAAATTCTA 58.457 30.769 0.00 0.00 34.56 2.10
1390 1517 6.689178 ATCAATTTTCATGTCGGAAAAACG 57.311 33.333 5.33 1.11 46.39 3.60
1396 1523 8.731275 ACTGTAATATCAATTTTCATGTCGGA 57.269 30.769 0.00 0.00 0.00 4.55
1485 1618 9.890629 AAGAAGAGCAATAGTAACATATTGTGA 57.109 29.630 7.94 0.00 42.59 3.58
1491 1624 9.309516 CCGTAAAAGAAGAGCAATAGTAACATA 57.690 33.333 0.00 0.00 0.00 2.29
1492 1625 7.280205 CCCGTAAAAGAAGAGCAATAGTAACAT 59.720 37.037 0.00 0.00 0.00 2.71
1512 1645 1.496060 AGGTCATCAGATGCCCGTAA 58.504 50.000 16.15 0.00 0.00 3.18
1557 1690 9.755804 TGAAGTAGAGACAGCAATAATATCTTG 57.244 33.333 0.00 0.00 0.00 3.02
1589 1726 3.118592 TGCCGTCAGAAATTTTTGGGTTT 60.119 39.130 8.70 0.00 0.00 3.27
1590 1727 2.432510 TGCCGTCAGAAATTTTTGGGTT 59.567 40.909 8.70 0.00 0.00 4.11
1591 1728 2.035632 TGCCGTCAGAAATTTTTGGGT 58.964 42.857 8.70 0.00 0.00 4.51
1616 1782 4.559153 GTTGCCTACATGCAGTTCAAAAT 58.441 39.130 0.00 0.00 43.21 1.82
1808 1977 1.363744 GTTCAAGATCCTCCTGTGCG 58.636 55.000 0.00 0.00 0.00 5.34
2137 2316 2.262423 AGGCCTTGATAATTCGCTCC 57.738 50.000 0.00 0.00 0.00 4.70
2439 3902 1.532437 CTTGTTCGACTGCAGCATCAA 59.468 47.619 15.27 11.21 0.00 2.57
2469 3932 0.039617 CTCATCCTCATCCTCGACGC 60.040 60.000 0.00 0.00 0.00 5.19
2474 3937 0.033228 CGGTGCTCATCCTCATCCTC 59.967 60.000 0.00 0.00 0.00 3.71
2791 4285 4.006357 GACCGCCGGTGGGTACAA 62.006 66.667 36.25 0.00 38.07 2.41
3132 4629 1.065926 TGAGGATGCAGTGTGATGACC 60.066 52.381 0.00 0.00 0.00 4.02
3223 4720 3.007182 TCTTCCACTTACCAAGTTACCCG 59.993 47.826 0.00 0.00 40.46 5.28
3367 4885 0.625849 AGGCACCCTTTCCCTGTATG 59.374 55.000 0.00 0.00 0.00 2.39
3396 7828 2.755952 ACAGGCACCTTTCCTTTTCT 57.244 45.000 0.00 0.00 0.00 2.52
3404 7852 0.183492 TGCTCTGAACAGGCACCTTT 59.817 50.000 11.67 0.00 32.41 3.11
3405 7853 0.250640 CTGCTCTGAACAGGCACCTT 60.251 55.000 11.67 0.00 33.35 3.50
3406 7854 1.374190 CTGCTCTGAACAGGCACCT 59.626 57.895 11.67 0.00 33.35 4.00
3407 7855 3.978272 CTGCTCTGAACAGGCACC 58.022 61.111 11.67 0.00 33.35 5.01
3440 7888 4.144727 AGATCCCGTCCCGCCTCT 62.145 66.667 0.00 0.00 0.00 3.69
3451 7899 2.428530 GGCAGAAAAATGGTCAGATCCC 59.571 50.000 0.00 0.00 0.00 3.85
3461 9253 3.074412 AGACTACGGTGGCAGAAAAATG 58.926 45.455 0.00 0.00 0.00 2.32
3462 9254 3.008049 AGAGACTACGGTGGCAGAAAAAT 59.992 43.478 0.00 0.00 0.00 1.82
3467 9259 1.595993 GCAGAGACTACGGTGGCAGA 61.596 60.000 0.00 0.00 0.00 4.26
3470 9262 2.184579 GGCAGAGACTACGGTGGC 59.815 66.667 0.00 0.00 0.00 5.01
3471 9263 2.490217 CGGCAGAGACTACGGTGG 59.510 66.667 0.00 0.00 0.00 4.61
3486 9278 1.120530 AGGCAGTGTTATCCTACCGG 58.879 55.000 0.00 0.00 0.00 5.28
3490 9282 2.954318 GACGGTAGGCAGTGTTATCCTA 59.046 50.000 0.00 0.00 0.00 2.94
3492 9284 1.479323 TGACGGTAGGCAGTGTTATCC 59.521 52.381 0.00 0.00 0.00 2.59
3494 9286 2.158957 CCATGACGGTAGGCAGTGTTAT 60.159 50.000 0.00 0.00 39.80 1.89
3507 9299 1.726853 GAAGACCAAGACCATGACGG 58.273 55.000 0.00 0.00 42.50 4.79
3510 9302 2.831526 TCATCGAAGACCAAGACCATGA 59.168 45.455 0.00 0.00 42.51 3.07
3513 9305 4.278310 TCTATCATCGAAGACCAAGACCA 58.722 43.478 0.00 0.00 42.51 4.02
3514 9306 4.920640 TCTATCATCGAAGACCAAGACC 57.079 45.455 0.00 0.00 42.51 3.85
3515 9307 7.778470 AAATTCTATCATCGAAGACCAAGAC 57.222 36.000 0.00 0.00 42.51 3.01
3519 9311 9.613428 ACAATTAAATTCTATCATCGAAGACCA 57.387 29.630 0.00 0.00 42.51 4.02
3542 9334 6.072175 GCAGTAGGGTATTTTTCATGACACAA 60.072 38.462 0.00 0.00 0.00 3.33
3544 9336 5.163652 GGCAGTAGGGTATTTTTCATGACAC 60.164 44.000 0.00 0.00 0.00 3.67
3571 9379 7.747357 GCGACGTCATTTTTAAAAAGGAAGATA 59.253 33.333 32.67 12.09 39.93 1.98
3572 9380 6.581166 GCGACGTCATTTTTAAAAAGGAAGAT 59.419 34.615 32.67 22.20 39.93 2.40
3573 9381 5.910723 GCGACGTCATTTTTAAAAAGGAAGA 59.089 36.000 32.67 19.31 39.93 2.87
3577 9385 4.381566 CAGGCGACGTCATTTTTAAAAAGG 59.618 41.667 17.08 17.08 0.00 3.11
3578 9386 4.973663 ACAGGCGACGTCATTTTTAAAAAG 59.026 37.500 17.16 10.50 0.00 2.27
3579 9387 4.735822 CACAGGCGACGTCATTTTTAAAAA 59.264 37.500 17.16 15.38 0.00 1.94
3580 9388 4.283678 CACAGGCGACGTCATTTTTAAAA 58.716 39.130 17.16 0.00 0.00 1.52
3581 9389 3.850374 GCACAGGCGACGTCATTTTTAAA 60.850 43.478 17.16 0.00 0.00 1.52
3583 9391 1.195900 GCACAGGCGACGTCATTTTTA 59.804 47.619 17.16 0.00 0.00 1.52
3584 9392 0.040425 GCACAGGCGACGTCATTTTT 60.040 50.000 17.16 0.00 0.00 1.94
3586 9394 0.955428 ATGCACAGGCGACGTCATTT 60.955 50.000 17.16 0.00 45.35 2.32
3587 9395 1.375908 ATGCACAGGCGACGTCATT 60.376 52.632 17.16 0.00 45.35 2.57
3590 9398 4.152625 GCATGCACAGGCGACGTC 62.153 66.667 14.21 5.18 45.35 4.34
3592 9400 3.502455 ATGCATGCACAGGCGACG 61.502 61.111 25.37 0.00 45.35 5.12
3593 9401 2.101575 CATGCATGCACAGGCGAC 59.898 61.111 25.37 0.00 45.35 5.19
3626 9434 1.321148 CAGCCATAATTGCAAAACGCG 59.679 47.619 3.53 3.53 46.97 6.01
3677 9487 1.668867 GGTAGCTAGCTAGGCAGGC 59.331 63.158 24.78 11.56 0.00 4.85
3679 9489 0.824182 ACGGGTAGCTAGCTAGGCAG 60.824 60.000 24.78 17.31 0.00 4.85
3690 9500 1.598130 GATGGGATGCACGGGTAGC 60.598 63.158 0.00 0.00 0.00 3.58
3696 9506 2.945447 AACAATTGATGGGATGCACG 57.055 45.000 13.59 0.00 0.00 5.34
3716 9526 4.460263 AGCTTGGACATGTCACAAACTTA 58.540 39.130 26.47 6.79 0.00 2.24
3748 9558 2.510238 CTCCGCCACTGCTAGCAC 60.510 66.667 14.93 2.78 34.43 4.40
3749 9559 4.457496 GCTCCGCCACTGCTAGCA 62.457 66.667 18.22 18.22 41.32 3.49
3819 9858 2.580783 TGTATTTTTCAGGGAGGGGGAG 59.419 50.000 0.00 0.00 0.00 4.30
3820 9859 2.580783 CTGTATTTTTCAGGGAGGGGGA 59.419 50.000 0.00 0.00 0.00 4.81
3900 10505 2.435372 ACAACAAAGACAGAAGGGCA 57.565 45.000 0.00 0.00 0.00 5.36
4067 10676 0.588252 CATTACTAGCACGCATGGGC 59.412 55.000 10.10 0.00 0.00 5.36
4068 10677 2.238942 TCATTACTAGCACGCATGGG 57.761 50.000 8.44 8.44 0.00 4.00
4069 10678 2.096069 GCATCATTACTAGCACGCATGG 60.096 50.000 0.00 0.00 0.00 3.66
4070 10679 2.545106 TGCATCATTACTAGCACGCATG 59.455 45.455 0.00 0.00 31.05 4.06
4071 10680 2.837498 TGCATCATTACTAGCACGCAT 58.163 42.857 0.00 0.00 31.05 4.73
4072 10681 2.307934 TGCATCATTACTAGCACGCA 57.692 45.000 0.00 0.00 31.05 5.24
4073 10682 2.545526 ACATGCATCATTACTAGCACGC 59.454 45.455 0.00 0.00 40.14 5.34
4084 10693 2.104967 CTTTCCACCCACATGCATCAT 58.895 47.619 0.00 0.00 0.00 2.45
4116 10725 2.424601 CAAACATCCACTCGCATCCATT 59.575 45.455 0.00 0.00 0.00 3.16
4125 10734 6.052840 CATAGTATGCACAAACATCCACTC 57.947 41.667 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.