Multiple sequence alignment - TraesCS2A01G157600

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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 TraesCS2A01G157600 chr2A 100.000 3708 0 0 1 3708 104449076 104452783 0.000000e+00 6848.0
1 TraesCS2A01G157600 chr2A 97.619 504 12 0 1 504 144034203 144033700 0.000000e+00 865.0
2 TraesCS2A01G157600 chr2A 97.244 508 14 0 1 508 507964537 507964030 0.000000e+00 861.0
3 TraesCS2A01G157600 chr2A 97.222 504 14 0 1 504 687327901 687328404 0.000000e+00 854.0
4 TraesCS2A01G157600 chr2A 82.609 138 22 2 1547 1683 572487553 572487417 1.810000e-23 121.0
5 TraesCS2A01G157600 chr2D 91.740 3281 144 56 503 3708 108312263 108315491 0.000000e+00 4440.0
6 TraesCS2A01G157600 chr2D 82.734 139 22 2 1547 1684 417625369 417625506 5.030000e-24 122.0
7 TraesCS2A01G157600 chr2D 88.608 79 9 0 1679 1757 417626499 417626577 3.050000e-16 97.1
8 TraesCS2A01G157600 chr2B 92.412 2280 81 37 567 2809 158145616 158147840 0.000000e+00 3168.0
9 TraesCS2A01G157600 chr2B 84.161 423 53 7 2830 3246 158147934 158148348 7.460000e-107 398.0
10 TraesCS2A01G157600 chr2B 90.268 298 19 5 3249 3539 158148381 158148675 7.510000e-102 381.0
11 TraesCS2A01G157600 chr2B 88.506 174 16 4 3536 3708 158149599 158149769 1.350000e-49 207.0
12 TraesCS2A01G157600 chr2B 92.857 98 6 1 3611 3708 158149130 158149226 1.390000e-29 141.0
13 TraesCS2A01G157600 chr2B 82.609 138 22 2 1548 1684 489849194 489849330 1.810000e-23 121.0
14 TraesCS2A01G157600 chr5B 97.619 504 12 0 1 504 138779833 138779330 0.000000e+00 865.0
15 TraesCS2A01G157600 chr5B 93.662 142 8 1 1544 1684 402751423 402751282 1.040000e-50 211.0
16 TraesCS2A01G157600 chr5B 90.000 80 4 4 1680 1757 266501783 266501860 2.360000e-17 100.0
17 TraesCS2A01G157600 chr5B 88.608 79 9 0 1679 1757 704916514 704916592 3.050000e-16 97.1
18 TraesCS2A01G157600 chr4B 97.619 504 12 0 1 504 28957722 28957219 0.000000e+00 865.0
19 TraesCS2A01G157600 chr4B 91.150 113 10 0 1305 1417 168984879 168984991 1.780000e-33 154.0
20 TraesCS2A01G157600 chr4B 86.022 93 8 5 1680 1770 168985244 168985333 1.100000e-15 95.3
21 TraesCS2A01G157600 chr3D 97.421 504 13 0 1 504 609957347 609956844 0.000000e+00 859.0
22 TraesCS2A01G157600 chr5A 96.881 513 13 2 1 512 11949993 11950503 0.000000e+00 856.0
23 TraesCS2A01G157600 chr5A 94.203 138 8 0 1547 1684 443742557 443742420 1.040000e-50 211.0
24 TraesCS2A01G157600 chr5A 85.507 138 20 0 1301 1438 316085017 316085154 1.070000e-30 145.0
25 TraesCS2A01G157600 chr5A 88.608 79 9 0 1679 1757 316085399 316085477 3.050000e-16 97.1
26 TraesCS2A01G157600 chr4A 96.869 511 15 1 1 511 155831026 155830517 0.000000e+00 854.0
27 TraesCS2A01G157600 chr4A 91.150 113 10 0 1305 1417 468603250 468603362 1.780000e-33 154.0
28 TraesCS2A01G157600 chr3A 96.693 514 15 1 1 514 424767479 424766968 0.000000e+00 854.0
29 TraesCS2A01G157600 chr5D 93.478 138 9 0 1547 1684 342712890 342712753 4.850000e-49 206.0
30 TraesCS2A01G157600 chr5D 85.926 135 19 0 1304 1438 238557792 238557658 1.070000e-30 145.0
31 TraesCS2A01G157600 chr5D 90.909 77 3 4 1683 1757 238557411 238557337 2.360000e-17 100.0
32 TraesCS2A01G157600 chr5D 97.500 40 1 0 3209 3248 386648922 386648883 6.640000e-08 69.4
33 TraesCS2A01G157600 chr5D 95.349 43 2 0 3206 3248 526559562 526559604 6.640000e-08 69.4
34 TraesCS2A01G157600 chr4D 91.150 113 10 0 1305 1417 107710734 107710622 1.780000e-33 154.0
35 TraesCS2A01G157600 chr4D 86.667 90 7 5 1683 1770 107710356 107710270 1.100000e-15 95.3
36 TraesCS2A01G157600 chr7D 95.349 43 2 0 3206 3248 518683974 518684016 6.640000e-08 69.4
37 TraesCS2A01G157600 chr7A 95.349 43 2 0 3202 3244 325734256 325734298 6.640000e-08 69.4
38 TraesCS2A01G157600 chr6A 95.349 43 2 0 3206 3248 226275662 226275704 6.640000e-08 69.4
39 TraesCS2A01G157600 chr1D 91.667 48 3 1 3201 3248 462985153 462985107 8.600000e-07 65.8
40 TraesCS2A01G157600 chr6B 87.500 56 2 5 3193 3248 149447167 149447217 4.000000e-05 60.2


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 TraesCS2A01G157600 chr2A 104449076 104452783 3707 False 6848 6848 100.0000 1 3708 1 chr2A.!!$F1 3707
1 TraesCS2A01G157600 chr2A 144033700 144034203 503 True 865 865 97.6190 1 504 1 chr2A.!!$R1 503
2 TraesCS2A01G157600 chr2A 507964030 507964537 507 True 861 861 97.2440 1 508 1 chr2A.!!$R2 507
3 TraesCS2A01G157600 chr2A 687327901 687328404 503 False 854 854 97.2220 1 504 1 chr2A.!!$F2 503
4 TraesCS2A01G157600 chr2D 108312263 108315491 3228 False 4440 4440 91.7400 503 3708 1 chr2D.!!$F1 3205
5 TraesCS2A01G157600 chr2B 158145616 158149769 4153 False 859 3168 89.6408 567 3708 5 chr2B.!!$F2 3141
6 TraesCS2A01G157600 chr5B 138779330 138779833 503 True 865 865 97.6190 1 504 1 chr5B.!!$R1 503
7 TraesCS2A01G157600 chr4B 28957219 28957722 503 True 865 865 97.6190 1 504 1 chr4B.!!$R1 503
8 TraesCS2A01G157600 chr3D 609956844 609957347 503 True 859 859 97.4210 1 504 1 chr3D.!!$R1 503
9 TraesCS2A01G157600 chr5A 11949993 11950503 510 False 856 856 96.8810 1 512 1 chr5A.!!$F1 511
10 TraesCS2A01G157600 chr4A 155830517 155831026 509 True 854 854 96.8690 1 511 1 chr4A.!!$R1 510
11 TraesCS2A01G157600 chr3A 424766968 424767479 511 True 854 854 96.6930 1 514 1 chr3A.!!$R1 513

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
836 852 0.248702 GCTCGCAGGCTACAGTACTC 60.249 60.0 0.00 0.00 0.0 2.59 F
2415 2454 0.248949 GTTCCCCTAGCTCGCGTTAG 60.249 60.0 5.77 7.02 0.0 2.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2432 2471 0.035152 TTAGGTGGGCATGCAGTGAG 60.035 55.0 21.36 0.0 0.00 3.51 R
3577 4059 0.102120 TTTCAGTTGTGCTTTGGGCG 59.898 50.0 0.00 0.0 45.43 6.13 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
249 250 2.438075 GCAGGCCTCCAGAAGCTG 60.438 66.667 0.00 0.00 0.00 4.24
254 255 1.599047 GCCTCCAGAAGCTGCAGTA 59.401 57.895 16.64 0.00 0.00 2.74
337 338 4.087182 ACATGAGAGGAGTCCGTTAAGAA 58.913 43.478 2.76 0.00 0.00 2.52
386 387 0.563173 AGCTAGCTATGGACAGGGGA 59.437 55.000 17.69 0.00 0.00 4.81
404 405 2.619074 GGGAGTGTGGAAGCTTGCTATT 60.619 50.000 19.34 5.12 0.00 1.73
437 438 2.086869 CCATGAGTTGGTTGCGAGATT 58.913 47.619 0.00 0.00 40.99 2.40
457 458 7.272144 AGATTTTATGGGTTTCACCTCTAGT 57.728 36.000 0.00 0.00 38.64 2.57
464 465 3.566111 GGGTTTCACCTCTAGTCTACCCT 60.566 52.174 0.00 0.00 38.64 4.34
484 485 5.103813 ACCCTAACTTGTTTGGGACTAAAGT 60.104 40.000 29.81 10.70 42.11 2.66
541 542 2.995547 GGAGGTAACGGGCCATGT 59.004 61.111 4.39 0.00 46.39 3.21
565 566 2.030412 ACGCAGGTCGCAACATGA 59.970 55.556 0.00 0.00 39.53 3.07
715 716 2.027625 GACTTTGCCACGAGACCGG 61.028 63.158 0.00 0.00 40.78 5.28
736 745 1.073763 AGTAAATGCACACTCTGGCCA 59.926 47.619 4.71 4.71 0.00 5.36
754 763 1.539157 CACTTTCCCTTTCTCCCTGC 58.461 55.000 0.00 0.00 0.00 4.85
773 789 2.283604 TCTGCACGCACCTCCCTA 60.284 61.111 0.00 0.00 0.00 3.53
787 803 2.308866 CCTCCCTATCTCCCTCTCTCTC 59.691 59.091 0.00 0.00 0.00 3.20
788 804 3.260205 CTCCCTATCTCCCTCTCTCTCT 58.740 54.545 0.00 0.00 0.00 3.10
798 814 5.890985 TCTCCCTCTCTCTCTATTTTGACTG 59.109 44.000 0.00 0.00 0.00 3.51
834 850 1.227002 GGCTCGCAGGCTACAGTAC 60.227 63.158 0.00 0.00 37.85 2.73
836 852 0.248702 GCTCGCAGGCTACAGTACTC 60.249 60.000 0.00 0.00 0.00 2.59
841 857 1.682323 GCAGGCTACAGTACTCCTACC 59.318 57.143 0.73 0.00 0.00 3.18
843 859 2.688958 CAGGCTACAGTACTCCTACCAC 59.311 54.545 0.73 0.00 0.00 4.16
1044 1061 1.194781 TGCTTGTCCTCACCCTCCTC 61.195 60.000 0.00 0.00 0.00 3.71
1100 1121 0.780637 TCTCCACCTCACCTCAGTCT 59.219 55.000 0.00 0.00 0.00 3.24
1101 1122 1.993301 TCTCCACCTCACCTCAGTCTA 59.007 52.381 0.00 0.00 0.00 2.59
1102 1123 2.025793 TCTCCACCTCACCTCAGTCTAG 60.026 54.545 0.00 0.00 0.00 2.43
1103 1124 0.820871 CCACCTCACCTCAGTCTAGC 59.179 60.000 0.00 0.00 0.00 3.42
1104 1125 0.820871 CACCTCACCTCAGTCTAGCC 59.179 60.000 0.00 0.00 0.00 3.93
1105 1126 0.707616 ACCTCACCTCAGTCTAGCCT 59.292 55.000 0.00 0.00 0.00 4.58
1203 1229 4.974438 ACCTCTTGTCCCCGCCCA 62.974 66.667 0.00 0.00 0.00 5.36
1204 1230 3.411517 CCTCTTGTCCCCGCCCAT 61.412 66.667 0.00 0.00 0.00 4.00
1206 1232 2.285368 TCTTGTCCCCGCCCATCT 60.285 61.111 0.00 0.00 0.00 2.90
1249 1275 1.612739 ACCCCTCCGTCCCTTTCTC 60.613 63.158 0.00 0.00 0.00 2.87
1250 1276 2.368011 CCCCTCCGTCCCTTTCTCC 61.368 68.421 0.00 0.00 0.00 3.71
1253 1279 1.331399 CCTCCGTCCCTTTCTCCCTC 61.331 65.000 0.00 0.00 0.00 4.30
1259 1288 1.765904 GTCCCTTTCTCCCTCTCATCC 59.234 57.143 0.00 0.00 0.00 3.51
1270 1299 1.100510 CTCTCATCCCGTTCGGTGTA 58.899 55.000 10.36 0.00 0.00 2.90
1282 1311 3.612251 GGTGTAGCCGAGGTAGCA 58.388 61.111 0.00 0.00 0.00 3.49
1459 1493 1.212616 CGCATCCGTCCATCTTCTTC 58.787 55.000 0.00 0.00 0.00 2.87
1460 1494 1.202463 CGCATCCGTCCATCTTCTTCT 60.202 52.381 0.00 0.00 0.00 2.85
1461 1495 2.739932 CGCATCCGTCCATCTTCTTCTT 60.740 50.000 0.00 0.00 0.00 2.52
1462 1496 2.869192 GCATCCGTCCATCTTCTTCTTC 59.131 50.000 0.00 0.00 0.00 2.87
1463 1497 3.431486 GCATCCGTCCATCTTCTTCTTCT 60.431 47.826 0.00 0.00 0.00 2.85
1490 1524 3.208747 TCTTCTTCTTCTTGCCGGTTT 57.791 42.857 1.90 0.00 0.00 3.27
1494 1528 3.020984 TCTTCTTCTTGCCGGTTTTTGT 58.979 40.909 1.90 0.00 0.00 2.83
1504 1538 2.532723 GCCGGTTTTTGTCTTCGTTTTC 59.467 45.455 1.90 0.00 0.00 2.29
1513 1547 4.066646 TGTCTTCGTTTTCTGTGGATCA 57.933 40.909 0.00 0.00 0.00 2.92
1515 1549 3.057019 TCTTCGTTTTCTGTGGATCACG 58.943 45.455 0.00 0.00 37.14 4.35
1522 1556 1.044611 TCTGTGGATCACGTGGTTGA 58.955 50.000 17.00 0.00 37.14 3.18
1606 1643 4.388499 ACCAACTACCTGCGCCCG 62.388 66.667 4.18 0.00 0.00 6.13
1666 1703 2.039624 ATCGTCCACCTCCAGGCT 59.960 61.111 0.00 0.00 39.32 4.58
1914 1951 2.990735 GCTCGACGACATCAAGCG 59.009 61.111 0.00 0.00 0.00 4.68
2088 2125 3.771160 GATGCTCGACGGGTGGGT 61.771 66.667 0.00 0.00 0.00 4.51
2386 2423 1.369625 CTCCACCGTGCCAAGTTATC 58.630 55.000 0.00 0.00 0.00 1.75
2415 2454 0.248949 GTTCCCCTAGCTCGCGTTAG 60.249 60.000 5.77 7.02 0.00 2.34
2432 2471 2.996621 GTTAGTGATGTGAGGAGTGTGC 59.003 50.000 0.00 0.00 0.00 4.57
2522 2561 0.689623 AGCTTCCTTGGTCTCCTGTG 59.310 55.000 0.00 0.00 0.00 3.66
2581 2622 0.178301 GGGAGGTTGTGGTAGCTAGC 59.822 60.000 16.08 16.08 0.00 3.42
2640 2686 4.526650 ACTATGTTCATGGGTTTTGGGTTC 59.473 41.667 0.00 0.00 0.00 3.62
2662 2708 3.766151 TGTACTTTGAAGTAGATCCGCG 58.234 45.455 0.00 0.00 41.81 6.46
2700 2746 5.862924 AATGTGGACGAATAAAGTCAGTG 57.137 39.130 0.00 0.00 40.20 3.66
2727 2773 7.549134 TGTCAATTAGTACATGTCATGTCTTCC 59.451 37.037 21.65 8.83 43.67 3.46
2743 2792 7.552687 TCATGTCTTCCATCACTAATTAACCAC 59.447 37.037 0.00 0.00 0.00 4.16
2956 3093 9.771534 TTTAAGTGGGGAAATAGTTTCATTTTG 57.228 29.630 4.98 0.00 41.43 2.44
2976 3113 9.971922 CATTTTGTTTCTCTCTATTTCCTGTTT 57.028 29.630 0.00 0.00 0.00 2.83
2978 3115 9.801873 TTTTGTTTCTCTCTATTTCCTGTTTTG 57.198 29.630 0.00 0.00 0.00 2.44
3000 3137 3.412722 TTTTTGCTTCCTCGGAGCA 57.587 47.368 0.00 6.14 36.72 4.26
3019 3156 1.726791 CAGTCCACTACATGACAACGC 59.273 52.381 0.00 0.00 33.89 4.84
3040 3177 0.539986 TTGTCCCTCGGGTGATTAGC 59.460 55.000 1.18 0.00 36.47 3.09
3041 3178 0.325296 TGTCCCTCGGGTGATTAGCT 60.325 55.000 1.18 0.00 36.47 3.32
3048 3185 2.176045 TCGGGTGATTAGCTGAGTTGA 58.824 47.619 0.00 0.00 34.90 3.18
3061 3198 4.813161 AGCTGAGTTGATACCAATTGATCG 59.187 41.667 7.12 0.00 34.39 3.69
3064 3201 6.662414 TGAGTTGATACCAATTGATCGAAC 57.338 37.500 7.12 9.70 34.39 3.95
3067 3204 5.817816 AGTTGATACCAATTGATCGAACCTC 59.182 40.000 7.12 0.00 34.39 3.85
3084 3221 2.034558 ACCTCAAATTTGACTTGGTGCG 59.965 45.455 22.95 10.19 33.54 5.34
3106 3243 8.911662 GTGCGTGTATTTTTCTACAATTGATTT 58.088 29.630 13.59 0.00 33.59 2.17
3128 3265 2.413453 GGCGTCTAAAGCTGTTCAAGAG 59.587 50.000 0.00 0.00 34.52 2.85
3135 3272 5.919141 TCTAAAGCTGTTCAAGAGTTCGTAC 59.081 40.000 0.00 0.00 0.00 3.67
3166 3303 8.787852 AGAAAATCTGAGAACAAACACTATTCC 58.212 33.333 0.00 0.00 0.00 3.01
3167 3304 8.463930 AAAATCTGAGAACAAACACTATTCCA 57.536 30.769 0.00 0.00 0.00 3.53
3200 3341 7.394872 GTGAGAATAAACGCTAGATGAACAAG 58.605 38.462 0.00 0.00 0.00 3.16
3209 3350 8.581057 AACGCTAGATGAACAAGATATTACTG 57.419 34.615 0.00 0.00 0.00 2.74
3214 3355 7.372260 AGATGAACAAGATATTACTGCTCCT 57.628 36.000 0.00 0.00 0.00 3.69
3251 3424 9.499479 AATATAAGAGCATTTAGATCACTGTGG 57.501 33.333 8.11 0.00 34.30 4.17
3290 3464 5.407502 CATGAGCATGTTTGTGACATTGAT 58.592 37.500 2.34 0.00 46.80 2.57
3419 3601 8.801882 TGTAAAATCACCCGAATTAAATCTCT 57.198 30.769 0.00 0.00 0.00 3.10
3434 3616 2.099141 TCTCTGCCCATGAAGAAACG 57.901 50.000 0.00 0.00 0.00 3.60
3563 4045 7.455891 TCATAAAGCATCACACCATATCATCT 58.544 34.615 0.00 0.00 0.00 2.90
3601 4083 4.610945 CCCAAAGCACAACTGAAAACTAG 58.389 43.478 0.00 0.00 0.00 2.57
3662 4227 4.564782 TGCCCATGCATCCAAATAAAAA 57.435 36.364 0.00 0.00 44.23 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 0.389948 CTCCGCCACACCTAACTGTC 60.390 60.000 0.00 0.00 0.00 3.51
249 250 1.949631 GCCGTCCGCTATGTACTGC 60.950 63.158 0.00 0.00 0.00 4.40
337 338 5.422331 TCGATACTCCAATCCTTCAAGTCTT 59.578 40.000 0.00 0.00 0.00 3.01
386 387 3.423539 TGAATAGCAAGCTTCCACACT 57.576 42.857 0.00 0.00 0.00 3.55
404 405 0.107361 CTCATGGCTCTGGCACATGA 60.107 55.000 15.19 15.19 45.03 3.07
457 458 4.237018 AGTCCCAAACAAGTTAGGGTAGA 58.763 43.478 0.00 0.00 42.12 2.59
464 465 7.612633 ACAAAGACTTTAGTCCCAAACAAGTTA 59.387 33.333 6.28 0.00 45.85 2.24
484 485 4.230657 CGGAACAACAACAACAACAAAGA 58.769 39.130 0.00 0.00 0.00 2.52
565 566 1.748879 GTGGCGTGGCACCATATGT 60.749 57.895 14.99 0.00 39.95 2.29
715 716 1.740025 GGCCAGAGTGTGCATTTACTC 59.260 52.381 16.42 16.42 42.77 2.59
736 745 0.405973 GGCAGGGAGAAAGGGAAAGT 59.594 55.000 0.00 0.00 0.00 2.66
754 763 4.767255 GGGAGGTGCGTGCAGAGG 62.767 72.222 0.00 0.00 0.00 3.69
770 779 7.176690 GTCAAAATAGAGAGAGAGGGAGATAGG 59.823 44.444 0.00 0.00 0.00 2.57
773 789 6.550854 CAGTCAAAATAGAGAGAGAGGGAGAT 59.449 42.308 0.00 0.00 0.00 2.75
787 803 5.248640 TCCTTCCTTGAGCAGTCAAAATAG 58.751 41.667 0.00 0.00 42.27 1.73
788 804 5.241403 TCCTTCCTTGAGCAGTCAAAATA 57.759 39.130 0.00 0.00 42.27 1.40
834 850 1.403687 GCTAGCCAGGGTGGTAGGAG 61.404 65.000 2.29 0.00 40.46 3.69
836 852 1.383248 AGCTAGCCAGGGTGGTAGG 60.383 63.158 12.13 0.00 40.46 3.18
841 857 1.519719 GAGACAGCTAGCCAGGGTG 59.480 63.158 12.13 5.13 38.06 4.61
843 859 2.790791 CCGAGACAGCTAGCCAGGG 61.791 68.421 12.13 1.14 0.00 4.45
924 940 3.741476 GGCCCAGAGCAAAGCACG 61.741 66.667 0.00 0.00 46.50 5.34
981 998 4.778143 CAGGGGTGCGGTGTAGGC 62.778 72.222 0.00 0.00 0.00 3.93
1078 1099 1.599606 CTGAGGTGAGGTGGAGACGG 61.600 65.000 0.00 0.00 0.00 4.79
1100 1121 0.553819 GAGGTGAGGAGAGGAGGCTA 59.446 60.000 0.00 0.00 0.00 3.93
1101 1122 1.309688 GAGGTGAGGAGAGGAGGCT 59.690 63.158 0.00 0.00 0.00 4.58
1102 1123 1.000993 TGAGGTGAGGAGAGGAGGC 59.999 63.158 0.00 0.00 0.00 4.70
1103 1124 0.334676 AGTGAGGTGAGGAGAGGAGG 59.665 60.000 0.00 0.00 0.00 4.30
1104 1125 1.684869 GGAGTGAGGTGAGGAGAGGAG 60.685 61.905 0.00 0.00 0.00 3.69
1105 1126 0.333312 GGAGTGAGGTGAGGAGAGGA 59.667 60.000 0.00 0.00 0.00 3.71
1188 1214 2.190578 GATGGGCGGGGACAAGAG 59.809 66.667 0.00 0.00 0.00 2.85
1189 1215 2.285368 AGATGGGCGGGGACAAGA 60.285 61.111 0.00 0.00 0.00 3.02
1203 1229 0.953727 TTTTGCTGCAGTTGCGAGAT 59.046 45.000 16.64 0.00 45.83 2.75
1204 1230 0.308684 CTTTTGCTGCAGTTGCGAGA 59.691 50.000 16.64 0.00 45.83 4.04
1206 1232 1.359833 CCTTTTGCTGCAGTTGCGA 59.640 52.632 16.64 0.00 45.83 5.10
1210 1236 1.360192 GTCGCCTTTTGCTGCAGTT 59.640 52.632 16.64 0.00 38.05 3.16
1211 1237 2.555547 GGTCGCCTTTTGCTGCAGT 61.556 57.895 16.64 0.00 38.05 4.40
1249 1275 2.058595 ACCGAACGGGATGAGAGGG 61.059 63.158 17.44 0.00 39.97 4.30
1250 1276 1.141881 CACCGAACGGGATGAGAGG 59.858 63.158 17.44 0.00 39.97 3.69
1253 1279 0.527817 GCTACACCGAACGGGATGAG 60.528 60.000 17.44 9.57 39.97 2.90
1270 1299 4.148825 CCGCTTGCTACCTCGGCT 62.149 66.667 0.00 0.00 35.20 5.52
1298 1327 3.801997 CGGCCTCCCCATGCTCTT 61.802 66.667 0.00 0.00 0.00 2.85
1447 1481 7.386059 AGAAGAAGAAGAAGAAGAAGATGGAC 58.614 38.462 0.00 0.00 0.00 4.02
1459 1493 7.307930 GGCAAGAAGAAGAAGAAGAAGAAGAAG 60.308 40.741 0.00 0.00 0.00 2.85
1460 1494 6.484977 GGCAAGAAGAAGAAGAAGAAGAAGAA 59.515 38.462 0.00 0.00 0.00 2.52
1461 1495 5.994668 GGCAAGAAGAAGAAGAAGAAGAAGA 59.005 40.000 0.00 0.00 0.00 2.87
1462 1496 5.107143 CGGCAAGAAGAAGAAGAAGAAGAAG 60.107 44.000 0.00 0.00 0.00 2.85
1463 1497 4.752101 CGGCAAGAAGAAGAAGAAGAAGAA 59.248 41.667 0.00 0.00 0.00 2.52
1490 1524 4.878971 TGATCCACAGAAAACGAAGACAAA 59.121 37.500 0.00 0.00 0.00 2.83
1494 1528 3.057019 CGTGATCCACAGAAAACGAAGA 58.943 45.455 0.00 0.00 37.17 2.87
1504 1538 2.099141 ATCAACCACGTGATCCACAG 57.901 50.000 19.30 0.00 32.65 3.66
1513 1547 3.478857 TTAGTCCACAATCAACCACGT 57.521 42.857 0.00 0.00 0.00 4.49
1515 1549 5.310720 GGATTTAGTCCACAATCAACCAC 57.689 43.478 0.00 0.00 46.96 4.16
1541 1575 2.034532 CATCAGGCCTGCACACCA 59.965 61.111 28.91 10.24 0.00 4.17
1542 1576 3.446570 GCATCAGGCCTGCACACC 61.447 66.667 28.91 10.15 39.46 4.16
1543 1577 3.807538 CGCATCAGGCCTGCACAC 61.808 66.667 28.91 15.43 39.64 3.82
1666 1703 2.031012 CACCTGTTGCCGAGCAGA 59.969 61.111 0.00 0.00 40.61 4.26
1891 1928 1.868251 GATGTCGTCGAGCGTGGTC 60.868 63.158 0.00 0.00 42.13 4.02
2038 2075 2.646719 GTGGTGAGCACGTACGGA 59.353 61.111 21.06 0.00 0.00 4.69
2350 2387 3.319689 GTGGAGCTAGCTAGAAAGGGTAG 59.680 52.174 25.15 0.00 37.69 3.18
2386 2423 1.473434 GCTAGGGGAACATCGACCTTG 60.473 57.143 0.00 0.00 34.59 3.61
2415 2454 1.001293 TGAGCACACTCCTCACATCAC 59.999 52.381 0.00 0.00 42.74 3.06
2432 2471 0.035152 TTAGGTGGGCATGCAGTGAG 60.035 55.000 21.36 0.00 0.00 3.51
2522 2561 8.718102 TGAAAACTATGCAGATCCTAAGTAAC 57.282 34.615 0.00 0.00 0.00 2.50
2581 2622 3.262420 ACAGCAGTAAATAACAGGAGCG 58.738 45.455 0.00 0.00 0.00 5.03
2640 2686 3.791887 CGCGGATCTACTTCAAAGTACAG 59.208 47.826 0.00 0.00 40.37 2.74
2700 2746 7.834068 AGACATGACATGTACTAATTGACAC 57.166 36.000 20.85 4.44 45.03 3.67
2727 2773 7.566760 TTGGCATAGTGGTTAATTAGTGATG 57.433 36.000 0.00 0.00 0.00 3.07
2789 2849 9.739276 TGACATACTCCAAAGATTAATCAACTT 57.261 29.630 17.56 5.14 0.00 2.66
2936 3073 8.028652 AGAAACAAAATGAAACTATTTCCCCA 57.971 30.769 0.00 0.00 38.90 4.96
2956 3093 9.803315 AAAACAAAACAGGAAATAGAGAGAAAC 57.197 29.630 0.00 0.00 0.00 2.78
2983 3120 0.108585 ACTGCTCCGAGGAAGCAAAA 59.891 50.000 14.05 0.00 38.15 2.44
2999 3136 1.726791 GCGTTGTCATGTAGTGGACTG 59.273 52.381 0.00 0.00 35.11 3.51
3000 3137 1.618837 AGCGTTGTCATGTAGTGGACT 59.381 47.619 0.00 0.00 35.11 3.85
3019 3156 2.906354 CTAATCACCCGAGGGACAAAG 58.094 52.381 16.26 1.94 38.96 2.77
3040 3177 6.238211 GGTTCGATCAATTGGTATCAACTCAG 60.238 42.308 5.42 0.00 35.48 3.35
3041 3178 5.584649 GGTTCGATCAATTGGTATCAACTCA 59.415 40.000 5.42 0.00 35.48 3.41
3048 3185 7.645058 AATTTGAGGTTCGATCAATTGGTAT 57.355 32.000 5.42 0.00 36.60 2.73
3061 3198 4.051237 GCACCAAGTCAAATTTGAGGTTC 58.949 43.478 21.80 16.12 37.98 3.62
3064 3201 2.034558 ACGCACCAAGTCAAATTTGAGG 59.965 45.455 21.05 19.65 37.98 3.86
3067 3204 2.808244 ACACGCACCAAGTCAAATTTG 58.192 42.857 12.15 12.15 0.00 2.32
3084 3221 8.372521 CGCCAAATCAATTGTAGAAAAATACAC 58.627 33.333 5.13 0.00 35.44 2.90
3106 3243 2.143122 CTTGAACAGCTTTAGACGCCA 58.857 47.619 0.00 0.00 0.00 5.69
3128 3265 9.794653 GTTCTCAGATTTTCTAAAAGTACGAAC 57.205 33.333 0.00 0.00 0.00 3.95
3165 3302 3.670203 GTTTATTCTCACGCGTGAATGG 58.330 45.455 38.11 27.79 39.39 3.16
3166 3303 3.333723 CGTTTATTCTCACGCGTGAATG 58.666 45.455 38.11 28.48 39.39 2.67
3167 3304 3.634730 CGTTTATTCTCACGCGTGAAT 57.365 42.857 38.11 31.03 39.39 2.57
3200 3341 8.718102 TTGTTTACAGAAGGAGCAGTAATATC 57.282 34.615 0.00 0.00 0.00 1.63
3209 3350 8.338986 GCTCTTATATTTGTTTACAGAAGGAGC 58.661 37.037 0.00 0.00 0.00 4.70
3251 3424 3.768406 CTCATGCAGATCTAGATACGCC 58.232 50.000 18.49 2.88 0.00 5.68
3419 3601 1.202114 GCATTCGTTTCTTCATGGGCA 59.798 47.619 0.00 0.00 0.00 5.36
3526 3708 4.604843 TGCTTTATGAAATGTCTCGCTG 57.395 40.909 0.00 0.00 0.00 5.18
3563 4045 4.274950 GCTTTGGGCGCTTGTCTTTATATA 59.725 41.667 7.64 0.00 0.00 0.86
3577 4059 0.102120 TTTCAGTTGTGCTTTGGGCG 59.898 50.000 0.00 0.00 45.43 6.13
3601 4083 3.193479 CCCCAGCATTGTACCTTTCTTTC 59.807 47.826 0.00 0.00 0.00 2.62
3662 4227 4.135153 CCGCGAGCTAGCTGTGGT 62.135 66.667 24.99 0.00 34.40 4.16
3690 4255 4.505217 GGCACGTCGATTGCTGCG 62.505 66.667 18.27 5.72 40.07 5.18


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

AutoCloner maintained by Alex Coulton.