Multiple sequence alignment - TraesCS5B01G431600

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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 TraesCS5B01G431600 chr5B 100.000 3593 0 0 1 3593 606300171 606303763 0.000000e+00 6636
1 TraesCS5B01G431600 chr5B 78.857 1050 199 18 1455 2485 45393549 45394594 0.000000e+00 688
2 TraesCS5B01G431600 chr5B 79.720 286 55 2 1066 1348 45392370 45392655 1.690000e-48 204
3 TraesCS5B01G431600 chr5D 94.558 2848 101 30 350 3175 491526657 491529472 0.000000e+00 4351
4 TraesCS5B01G431600 chr5D 93.950 281 10 4 3315 3593 491529624 491529899 5.550000e-113 418
5 TraesCS5B01G431600 chr5D 80.000 285 54 2 1066 1347 45380087 45379803 1.310000e-49 207
6 TraesCS5B01G431600 chr5D 79.758 331 22 17 21 351 491526333 491526618 7.870000e-47 198
7 TraesCS5B01G431600 chr5A 89.836 3286 156 77 124 3305 613699326 613702537 0.000000e+00 4054
8 TraesCS5B01G431600 chr5A 78.857 1050 196 21 1455 2485 36330854 36331896 0.000000e+00 686
9 TraesCS5B01G431600 chr5A 94.326 282 8 4 3315 3593 613702678 613702954 3.320000e-115 425
10 TraesCS5B01G431600 chr2B 92.732 798 45 3 1650 2447 298515211 298514427 0.000000e+00 1140
11 TraesCS5B01G431600 chr2B 91.685 457 38 0 1987 2443 105742910 105743366 5.060000e-178 634
12 TraesCS5B01G431600 chr4A 78.833 1063 204 14 1455 2505 597014699 597015752 0.000000e+00 697
13 TraesCS5B01G431600 chr4D 78.998 1038 193 18 1455 2478 6424425 6425451 0.000000e+00 686
14 TraesCS5B01G431600 chr4B 78.491 1060 213 11 1455 2505 11657229 11656176 0.000000e+00 680
15 TraesCS5B01G431600 chr3B 92.140 458 36 0 1987 2444 130115237 130115694 0.000000e+00 647
16 TraesCS5B01G431600 chr3B 76.200 1000 199 30 1456 2431 795839880 795840864 3.220000e-135 492
17 TraesCS5B01G431600 chr3A 77.342 918 166 34 1496 2389 724515644 724516543 4.140000e-139 505
18 TraesCS5B01G431600 chr3D 76.875 960 177 35 1496 2428 593236177 593237118 5.360000e-138 501
19 TraesCS5B01G431600 chr6A 74.673 995 197 33 1460 2428 609157824 609158789 1.210000e-104 390
20 TraesCS5B01G431600 chr6B 74.400 1000 191 43 1460 2428 704852631 704851666 5.670000e-98 368


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 TraesCS5B01G431600 chr5B 606300171 606303763 3592 False 6636.000000 6636 100.0000 1 3593 1 chr5B.!!$F1 3592
1 TraesCS5B01G431600 chr5B 45392370 45394594 2224 False 446.000000 688 79.2885 1066 2485 2 chr5B.!!$F2 1419
2 TraesCS5B01G431600 chr5D 491526333 491529899 3566 False 1655.666667 4351 89.4220 21 3593 3 chr5D.!!$F1 3572
3 TraesCS5B01G431600 chr5A 613699326 613702954 3628 False 2239.500000 4054 92.0810 124 3593 2 chr5A.!!$F2 3469
4 TraesCS5B01G431600 chr5A 36330854 36331896 1042 False 686.000000 686 78.8570 1455 2485 1 chr5A.!!$F1 1030
5 TraesCS5B01G431600 chr2B 298514427 298515211 784 True 1140.000000 1140 92.7320 1650 2447 1 chr2B.!!$R1 797
6 TraesCS5B01G431600 chr4A 597014699 597015752 1053 False 697.000000 697 78.8330 1455 2505 1 chr4A.!!$F1 1050
7 TraesCS5B01G431600 chr4D 6424425 6425451 1026 False 686.000000 686 78.9980 1455 2478 1 chr4D.!!$F1 1023
8 TraesCS5B01G431600 chr4B 11656176 11657229 1053 True 680.000000 680 78.4910 1455 2505 1 chr4B.!!$R1 1050
9 TraesCS5B01G431600 chr3B 795839880 795840864 984 False 492.000000 492 76.2000 1456 2431 1 chr3B.!!$F2 975
10 TraesCS5B01G431600 chr3A 724515644 724516543 899 False 505.000000 505 77.3420 1496 2389 1 chr3A.!!$F1 893
11 TraesCS5B01G431600 chr3D 593236177 593237118 941 False 501.000000 501 76.8750 1496 2428 1 chr3D.!!$F1 932
12 TraesCS5B01G431600 chr6A 609157824 609158789 965 False 390.000000 390 74.6730 1460 2428 1 chr6A.!!$F1 968
13 TraesCS5B01G431600 chr6B 704851666 704852631 965 True 368.000000 368 74.4000 1460 2428 1 chr6B.!!$R1 968

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
92 93 0.033504 TTTCTTTCTCCAGCGTCGCT 59.966 50.0 15.47 15.47 40.77 4.93 F
655 731 0.037326 TTCACATGTGAGTCTCGCCC 60.037 55.0 26.48 0.00 41.13 6.13 F
909 1005 0.940126 CGGATCGGCAAATCTTGAGG 59.060 55.0 0.00 0.00 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1213 1309 0.683179 ACCATGACCTCGATGTCGGA 60.683 55.000 17.35 3.26 38.11 4.55 R
1491 2397 0.736325 CGAAGGTGCCGTTGTAGGAG 60.736 60.000 0.00 0.00 0.00 3.69 R
2682 3616 2.415090 CCAGTACAAAGACTCGTACCGG 60.415 54.545 0.00 0.00 39.03 5.28 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
18 19 3.259832 GTGCGCGAAAAAGGGAAAA 57.740 47.368 12.10 0.00 0.00 2.29
19 20 1.562017 GTGCGCGAAAAAGGGAAAAA 58.438 45.000 12.10 0.00 0.00 1.94
47 48 1.942585 CTTCTTCTTCGCACGCAAAG 58.057 50.000 0.00 0.00 0.00 2.77
61 62 2.167487 ACGCAAAGCCTTTTCTTTTCCA 59.833 40.909 0.00 0.00 34.31 3.53
64 65 4.441792 GCAAAGCCTTTTCTTTTCCAAGA 58.558 39.130 0.00 0.00 37.24 3.02
88 89 4.983671 AAAAACTTTCTTTCTCCAGCGT 57.016 36.364 0.00 0.00 0.00 5.07
89 90 4.553756 AAAACTTTCTTTCTCCAGCGTC 57.446 40.909 0.00 0.00 0.00 5.19
90 91 1.784525 ACTTTCTTTCTCCAGCGTCG 58.215 50.000 0.00 0.00 0.00 5.12
91 92 0.440371 CTTTCTTTCTCCAGCGTCGC 59.560 55.000 9.80 9.80 0.00 5.19
92 93 0.033504 TTTCTTTCTCCAGCGTCGCT 59.966 50.000 15.47 15.47 40.77 4.93
93 94 0.885879 TTCTTTCTCCAGCGTCGCTA 59.114 50.000 21.25 4.21 36.40 4.26
94 95 0.885879 TCTTTCTCCAGCGTCGCTAA 59.114 50.000 21.25 7.82 36.40 3.09
95 96 1.271379 TCTTTCTCCAGCGTCGCTAAA 59.729 47.619 21.25 15.32 36.40 1.85
96 97 2.066262 CTTTCTCCAGCGTCGCTAAAA 58.934 47.619 21.25 15.72 36.40 1.52
97 98 1.425412 TTCTCCAGCGTCGCTAAAAC 58.575 50.000 21.25 0.00 36.40 2.43
98 99 0.731514 TCTCCAGCGTCGCTAAAACG 60.732 55.000 21.25 6.99 42.87 3.60
99 100 1.683790 CTCCAGCGTCGCTAAAACGG 61.684 60.000 21.25 16.50 40.41 4.44
100 101 1.735198 CCAGCGTCGCTAAAACGGA 60.735 57.895 21.25 0.00 40.41 4.69
101 102 1.414897 CAGCGTCGCTAAAACGGAC 59.585 57.895 21.25 0.00 40.41 4.79
102 103 1.007038 AGCGTCGCTAAAACGGACA 60.007 52.632 20.25 0.00 40.41 4.02
103 104 1.007336 AGCGTCGCTAAAACGGACAG 61.007 55.000 20.25 0.00 40.41 3.51
104 105 1.005294 GCGTCGCTAAAACGGACAGA 61.005 55.000 10.68 0.00 40.41 3.41
105 106 1.411394 CGTCGCTAAAACGGACAGAA 58.589 50.000 0.00 0.00 36.51 3.02
106 107 1.385743 CGTCGCTAAAACGGACAGAAG 59.614 52.381 0.00 0.00 36.51 2.85
107 108 1.126296 GTCGCTAAAACGGACAGAAGC 59.874 52.381 0.00 0.00 0.00 3.86
108 109 0.442699 CGCTAAAACGGACAGAAGCC 59.557 55.000 0.00 0.00 0.00 4.35
115 116 3.491652 GGACAGAAGCCGAAGCGC 61.492 66.667 0.00 0.00 46.67 5.92
116 117 3.843240 GACAGAAGCCGAAGCGCG 61.843 66.667 0.00 0.00 46.67 6.86
333 352 3.326578 CACCCCACCCCACGATCA 61.327 66.667 0.00 0.00 0.00 2.92
334 353 3.327404 ACCCCACCCCACGATCAC 61.327 66.667 0.00 0.00 0.00 3.06
351 370 0.246635 CACTCATCCGTTCCGTTCCT 59.753 55.000 0.00 0.00 0.00 3.36
385 444 5.893824 ACCATCAACCCCTCATAAATTCTTC 59.106 40.000 0.00 0.00 0.00 2.87
479 538 3.264845 TGCCCCCTTTCTGACCCC 61.265 66.667 0.00 0.00 0.00 4.95
585 661 0.529992 CCTCGACGCTTTCCATACCC 60.530 60.000 0.00 0.00 0.00 3.69
612 688 5.099575 TCTGTTTCGTTTCTTGCCTTTTTC 58.900 37.500 0.00 0.00 0.00 2.29
655 731 0.037326 TTCACATGTGAGTCTCGCCC 60.037 55.000 26.48 0.00 41.13 6.13
656 732 1.448540 CACATGTGAGTCTCGCCCC 60.449 63.158 21.64 0.00 0.00 5.80
657 733 1.610673 ACATGTGAGTCTCGCCCCT 60.611 57.895 10.87 0.00 0.00 4.79
658 734 1.153489 CATGTGAGTCTCGCCCCTG 60.153 63.158 10.87 2.71 0.00 4.45
679 755 1.128188 CCCTATCCCTTTCTCCCCCG 61.128 65.000 0.00 0.00 0.00 5.73
723 799 2.708325 GGATCAGATAGGAAAGCCCAGT 59.292 50.000 0.00 0.00 37.41 4.00
741 817 1.061485 GTCTCAGAAGAAACCGCGTC 58.939 55.000 4.92 0.00 31.93 5.19
909 1005 0.940126 CGGATCGGCAAATCTTGAGG 59.060 55.000 0.00 0.00 0.00 3.86
942 1038 1.673009 GGATTCCCAAACCGTCGCA 60.673 57.895 0.00 0.00 0.00 5.10
945 1041 1.366111 ATTCCCAAACCGTCGCATCG 61.366 55.000 0.00 0.00 0.00 3.84
970 1066 3.449377 AGATCTTCTCCCTTCTTTCGTCC 59.551 47.826 0.00 0.00 0.00 4.79
996 1092 1.685421 GGAGAGCAGAGAGGCCTGT 60.685 63.158 12.00 5.74 36.57 4.00
997 1093 1.264045 GGAGAGCAGAGAGGCCTGTT 61.264 60.000 12.00 0.00 36.57 3.16
1371 1470 1.539869 AGCCCCTCTTCCTCTTGCA 60.540 57.895 0.00 0.00 0.00 4.08
1435 1536 7.495901 AGTTCATGGACTACTTACTGATGATG 58.504 38.462 4.30 0.00 0.00 3.07
1436 1537 7.124901 AGTTCATGGACTACTTACTGATGATGT 59.875 37.037 4.30 0.00 0.00 3.06
1438 1539 6.607198 TCATGGACTACTTACTGATGATGTGA 59.393 38.462 0.00 0.00 0.00 3.58
1439 1540 7.288621 TCATGGACTACTTACTGATGATGTGAT 59.711 37.037 0.00 0.00 0.00 3.06
1440 1541 6.809869 TGGACTACTTACTGATGATGTGATG 58.190 40.000 0.00 0.00 0.00 3.07
1441 1542 6.381133 TGGACTACTTACTGATGATGTGATGT 59.619 38.462 0.00 0.00 0.00 3.06
1442 1543 7.093333 TGGACTACTTACTGATGATGTGATGTT 60.093 37.037 0.00 0.00 0.00 2.71
1443 1544 7.436673 GGACTACTTACTGATGATGTGATGTTC 59.563 40.741 0.00 0.00 0.00 3.18
1453 2359 5.929697 TGATGTGATGTTCTGTTCTGTTC 57.070 39.130 0.00 0.00 0.00 3.18
1827 2739 2.354305 GTCGACGGCGTCAACACT 60.354 61.111 35.62 1.56 38.98 3.55
2598 3531 5.107530 GCTCTTGATGTCGCATTAGAGAATC 60.108 44.000 22.12 11.04 32.79 2.52
2682 3616 7.028926 TCAGCAGTAGTTACTAGCAGTAATC 57.971 40.000 10.56 6.40 42.06 1.75
2717 3651 5.654603 TTGTACTGGAGGCATATATACCG 57.345 43.478 0.00 0.00 0.00 4.02
2815 3749 5.133153 TCATTCAGAATCCCAGATCCAATGA 59.867 40.000 0.00 0.00 0.00 2.57
2816 3750 4.428294 TCAGAATCCCAGATCCAATGAC 57.572 45.455 0.00 0.00 0.00 3.06
2948 3918 6.183360 TGGAGTATATACAAAGTGAGCAGGAC 60.183 42.308 15.18 0.00 0.00 3.85
3175 4150 7.477945 TTTTCAGTTTTTAACCACCTACCAA 57.522 32.000 0.00 0.00 0.00 3.67
3176 4151 6.702716 TTCAGTTTTTAACCACCTACCAAG 57.297 37.500 0.00 0.00 0.00 3.61
3200 4175 5.415221 GCAGAGCCTACAGATGATTATACC 58.585 45.833 0.00 0.00 0.00 2.73
3201 4176 5.047021 GCAGAGCCTACAGATGATTATACCA 60.047 44.000 0.00 0.00 0.00 3.25
3205 4180 5.482175 AGCCTACAGATGATTATACCACTCC 59.518 44.000 0.00 0.00 0.00 3.85
3207 4182 5.477291 CCTACAGATGATTATACCACTCCGT 59.523 44.000 0.00 0.00 0.00 4.69
3222 4197 4.093408 CCACTCCGTTGTTGATCAATACTG 59.907 45.833 12.12 9.55 38.38 2.74
3223 4198 4.690748 CACTCCGTTGTTGATCAATACTGT 59.309 41.667 12.12 8.94 38.38 3.55
3224 4199 5.867174 CACTCCGTTGTTGATCAATACTGTA 59.133 40.000 12.12 0.00 38.38 2.74
3225 4200 5.867716 ACTCCGTTGTTGATCAATACTGTAC 59.132 40.000 12.12 3.20 38.38 2.90
3227 4202 6.460781 TCCGTTGTTGATCAATACTGTACTT 58.539 36.000 12.12 0.00 38.38 2.24
3229 4204 7.543172 TCCGTTGTTGATCAATACTGTACTTAC 59.457 37.037 12.12 0.69 38.38 2.34
3230 4205 7.544566 CCGTTGTTGATCAATACTGTACTTACT 59.455 37.037 12.12 0.00 38.38 2.24
3231 4206 9.563898 CGTTGTTGATCAATACTGTACTTACTA 57.436 33.333 12.12 0.00 38.38 1.82
3272 4253 7.849804 ATCATTGTACTCATCAACAAGTACC 57.150 36.000 9.48 0.00 44.66 3.34
3280 4261 7.476540 ACTCATCAACAAGTACCACTATGTA 57.523 36.000 0.00 0.00 0.00 2.29
3286 4267 7.903145 TCAACAAGTACCACTATGTAATCTGT 58.097 34.615 0.00 0.00 0.00 3.41
3287 4268 8.033038 TCAACAAGTACCACTATGTAATCTGTC 58.967 37.037 0.00 0.00 0.00 3.51
3292 4273 7.833786 AGTACCACTATGTAATCTGTCGAAAA 58.166 34.615 0.00 0.00 0.00 2.29
3294 4275 9.095065 GTACCACTATGTAATCTGTCGAAAAAT 57.905 33.333 0.00 0.00 0.00 1.82
3309 4290 8.555166 TGTCGAAAAATAAACAAATCAGACAC 57.445 30.769 0.00 0.00 0.00 3.67
3310 4291 8.402472 TGTCGAAAAATAAACAAATCAGACACT 58.598 29.630 0.00 0.00 0.00 3.55
3312 4293 8.836413 TCGAAAAATAAACAAATCAGACACTCT 58.164 29.630 0.00 0.00 0.00 3.24
3313 4294 8.895845 CGAAAAATAAACAAATCAGACACTCTG 58.104 33.333 0.00 0.00 45.59 3.35
3353 4465 4.806330 TCTGTGCAGCAAACTACTACTAC 58.194 43.478 0.00 0.00 0.00 2.73
3355 4467 4.556233 TGTGCAGCAAACTACTACTACTG 58.444 43.478 0.00 0.00 0.00 2.74
3356 4468 3.927142 GTGCAGCAAACTACTACTACTGG 59.073 47.826 0.00 0.00 0.00 4.00
3357 4469 3.576982 TGCAGCAAACTACTACTACTGGT 59.423 43.478 0.00 0.00 0.00 4.00
3358 4470 3.927142 GCAGCAAACTACTACTACTGGTG 59.073 47.826 0.00 0.00 35.84 4.17
3373 4485 6.465084 ACTACTGGTGGATCTTTTCTACAAC 58.535 40.000 0.00 0.00 37.55 3.32
3405 4517 8.264347 TCTCCAACTCATAGTATAAAATGCACA 58.736 33.333 0.00 0.00 0.00 4.57
3407 4519 8.892723 TCCAACTCATAGTATAAAATGCACAAG 58.107 33.333 0.00 0.00 0.00 3.16
3408 4520 8.677300 CCAACTCATAGTATAAAATGCACAAGT 58.323 33.333 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.562017 TTTTTCCCTTTTTCGCGCAC 58.438 45.000 8.75 0.00 0.00 5.34
18 19 2.095212 GCGAAGAAGAAGCGGGATTTTT 60.095 45.455 0.00 0.00 0.00 1.94
19 20 1.468914 GCGAAGAAGAAGCGGGATTTT 59.531 47.619 0.00 0.00 0.00 1.82
31 32 1.441016 GGCTTTGCGTGCGAAGAAG 60.441 57.895 22.83 8.81 39.23 2.85
80 81 1.683790 CCGTTTTAGCGACGCTGGAG 61.684 60.000 31.69 16.99 40.10 3.86
82 83 1.735198 TCCGTTTTAGCGACGCTGG 60.735 57.895 31.69 22.80 40.10 4.85
86 87 1.385743 CTTCTGTCCGTTTTAGCGACG 59.614 52.381 0.00 0.00 40.05 5.12
87 88 1.126296 GCTTCTGTCCGTTTTAGCGAC 59.874 52.381 0.00 0.00 0.00 5.19
88 89 1.425412 GCTTCTGTCCGTTTTAGCGA 58.575 50.000 0.00 0.00 0.00 4.93
89 90 0.442699 GGCTTCTGTCCGTTTTAGCG 59.557 55.000 0.00 0.00 0.00 4.26
90 91 0.442699 CGGCTTCTGTCCGTTTTAGC 59.557 55.000 0.00 0.00 41.85 3.09
91 92 2.074547 TCGGCTTCTGTCCGTTTTAG 57.925 50.000 1.22 0.00 46.49 1.85
92 93 2.409975 CTTCGGCTTCTGTCCGTTTTA 58.590 47.619 1.22 0.00 46.49 1.52
93 94 1.226746 CTTCGGCTTCTGTCCGTTTT 58.773 50.000 1.22 0.00 46.49 2.43
94 95 1.228657 GCTTCGGCTTCTGTCCGTTT 61.229 55.000 1.22 0.00 46.49 3.60
95 96 1.668151 GCTTCGGCTTCTGTCCGTT 60.668 57.895 1.22 0.00 46.49 4.44
96 97 2.048127 GCTTCGGCTTCTGTCCGT 60.048 61.111 1.22 0.00 46.49 4.69
98 99 3.491652 GCGCTTCGGCTTCTGTCC 61.492 66.667 0.00 0.00 39.13 4.02
99 100 3.843240 CGCGCTTCGGCTTCTGTC 61.843 66.667 5.56 0.00 39.13 3.51
289 303 1.229051 TCAGTGGTGGATGGACGGA 60.229 57.895 0.00 0.00 0.00 4.69
290 304 1.079127 GTCAGTGGTGGATGGACGG 60.079 63.158 0.00 0.00 0.00 4.79
291 305 1.079127 GGTCAGTGGTGGATGGACG 60.079 63.158 0.00 0.00 0.00 4.79
292 306 0.036010 CTGGTCAGTGGTGGATGGAC 60.036 60.000 0.00 0.00 0.00 4.02
293 307 0.473694 ACTGGTCAGTGGTGGATGGA 60.474 55.000 2.46 0.00 40.75 3.41
294 308 0.036010 GACTGGTCAGTGGTGGATGG 60.036 60.000 8.49 0.00 42.66 3.51
295 309 0.036010 GGACTGGTCAGTGGTGGATG 60.036 60.000 8.49 0.00 42.66 3.51
296 310 0.473694 TGGACTGGTCAGTGGTGGAT 60.474 55.000 8.49 0.00 42.66 3.41
351 370 0.615331 GGTTGATGGTGAGCAGAGGA 59.385 55.000 0.00 0.00 0.00 3.71
385 444 1.610886 GGGACAAGGAACCGAGAAAGG 60.611 57.143 0.00 0.00 37.30 3.11
479 538 0.820871 CGAGGTTGAGAGGGAAGGAG 59.179 60.000 0.00 0.00 0.00 3.69
526 585 1.623359 CGGCGAAGAAAGAGAGAGTG 58.377 55.000 0.00 0.00 0.00 3.51
585 661 1.266989 GCAAGAAACGAAACAGAGGGG 59.733 52.381 0.00 0.00 0.00 4.79
612 688 2.394604 GAAATTCCTTCCCGGAGCG 58.605 57.895 0.73 0.00 44.28 5.03
632 708 2.614779 CGAGACTCACATGTGAATGCT 58.385 47.619 27.63 22.76 39.39 3.79
655 731 0.767998 GAGAAAGGGATAGGGGCAGG 59.232 60.000 0.00 0.00 0.00 4.85
656 732 0.767998 GGAGAAAGGGATAGGGGCAG 59.232 60.000 0.00 0.00 0.00 4.85
657 733 0.697854 GGGAGAAAGGGATAGGGGCA 60.698 60.000 0.00 0.00 0.00 5.36
658 734 1.427895 GGGGAGAAAGGGATAGGGGC 61.428 65.000 0.00 0.00 0.00 5.80
723 799 0.959553 AGACGCGGTTTCTTCTGAGA 59.040 50.000 12.47 0.00 0.00 3.27
741 817 1.154225 GATTGCGCACGGAAACCAG 60.154 57.895 11.12 0.00 0.00 4.00
843 925 2.094700 CGAGATTCAGTCGAACAGGGAA 60.095 50.000 0.00 0.00 39.92 3.97
909 1005 0.332972 AATCCAGGAACAGGGGAAGC 59.667 55.000 0.00 0.00 34.89 3.86
970 1066 4.116328 TCTGCTCTCCGGCGAACG 62.116 66.667 9.30 0.00 43.80 3.95
982 1078 0.990374 ATTGAACAGGCCTCTCTGCT 59.010 50.000 0.00 0.00 38.26 4.24
996 1092 1.653094 GATTCACCGCCGCCATTGAA 61.653 55.000 0.00 0.00 32.71 2.69
997 1093 2.045438 ATTCACCGCCGCCATTGA 60.045 55.556 0.00 0.00 0.00 2.57
1213 1309 0.683179 ACCATGACCTCGATGTCGGA 60.683 55.000 17.35 3.26 38.11 4.55
1435 1536 2.543848 TGCGAACAGAACAGAACATCAC 59.456 45.455 0.00 0.00 0.00 3.06
1436 1537 2.832563 TGCGAACAGAACAGAACATCA 58.167 42.857 0.00 0.00 0.00 3.07
1491 2397 0.736325 CGAAGGTGCCGTTGTAGGAG 60.736 60.000 0.00 0.00 0.00 3.69
2314 3247 2.914289 GTAGCAGCTGGAGCCCAT 59.086 61.111 17.12 0.00 43.38 4.00
2316 3249 4.537433 CCGTAGCAGCTGGAGCCC 62.537 72.222 17.12 0.00 43.38 5.19
2394 3327 3.986006 TCGCACGCCTCGTCCTTT 61.986 61.111 0.00 0.00 38.32 3.11
2598 3531 7.541783 TCAACTGATGAAAAACAAGTCTGTTTG 59.458 33.333 4.13 0.00 43.32 2.93
2682 3616 2.415090 CCAGTACAAAGACTCGTACCGG 60.415 54.545 0.00 0.00 39.03 5.28
2717 3651 5.426689 TGCCATCTGAACATATATCCTCC 57.573 43.478 0.00 0.00 0.00 4.30
2846 3780 6.262944 TCAGCAAGTACAACACATCAAGATTT 59.737 34.615 0.00 0.00 0.00 2.17
2882 3824 6.194967 TCTGGGACTCTGAATCAACTGTATA 58.805 40.000 0.00 0.00 0.00 1.47
2883 3825 5.026121 TCTGGGACTCTGAATCAACTGTAT 58.974 41.667 0.00 0.00 0.00 2.29
2948 3918 4.881273 TGCAGTACTATATTGCCAACCAAG 59.119 41.667 0.00 0.00 40.27 3.61
3054 4029 0.533491 TGCCTGCATTGGAAGCATTC 59.467 50.000 0.00 0.00 46.67 2.67
3177 4152 5.047021 TGGTATAATCATCTGTAGGCTCTGC 60.047 44.000 0.00 0.00 0.00 4.26
3178 4153 6.210385 AGTGGTATAATCATCTGTAGGCTCTG 59.790 42.308 0.00 0.00 0.00 3.35
3179 4154 6.318913 AGTGGTATAATCATCTGTAGGCTCT 58.681 40.000 0.00 0.00 0.00 4.09
3180 4155 6.350612 GGAGTGGTATAATCATCTGTAGGCTC 60.351 46.154 0.00 0.00 0.00 4.70
3181 4156 5.482175 GGAGTGGTATAATCATCTGTAGGCT 59.518 44.000 0.00 0.00 0.00 4.58
3182 4157 5.622460 CGGAGTGGTATAATCATCTGTAGGC 60.622 48.000 0.00 0.00 0.00 3.93
3183 4158 5.477291 ACGGAGTGGTATAATCATCTGTAGG 59.523 44.000 0.00 0.00 42.51 3.18
3184 4159 6.576662 ACGGAGTGGTATAATCATCTGTAG 57.423 41.667 0.00 0.00 42.51 2.74
3185 4160 6.322969 ACAACGGAGTGGTATAATCATCTGTA 59.677 38.462 0.00 0.00 46.84 2.74
3186 4161 5.128827 ACAACGGAGTGGTATAATCATCTGT 59.871 40.000 0.00 0.00 46.84 3.41
3187 4162 5.601662 ACAACGGAGTGGTATAATCATCTG 58.398 41.667 0.00 0.00 46.84 2.90
3188 4163 5.871396 ACAACGGAGTGGTATAATCATCT 57.129 39.130 0.00 0.00 46.84 2.90
3200 4175 4.690748 ACAGTATTGATCAACAACGGAGTG 59.309 41.667 21.65 14.48 45.00 3.51
3205 4180 8.462143 AGTAAGTACAGTATTGATCAACAACG 57.538 34.615 11.07 10.58 41.52 4.10
3257 4238 8.948631 ATTACATAGTGGTACTTGTTGATGAG 57.051 34.615 0.00 0.00 0.00 2.90
3259 4240 8.820933 CAGATTACATAGTGGTACTTGTTGATG 58.179 37.037 0.00 0.00 0.00 3.07
3267 4248 7.400599 TTTCGACAGATTACATAGTGGTACT 57.599 36.000 0.00 0.00 0.00 2.73
3286 4267 8.836413 AGAGTGTCTGATTTGTTTATTTTTCGA 58.164 29.630 0.00 0.00 0.00 3.71
3294 4275 8.956426 AGAAAAACAGAGTGTCTGATTTGTTTA 58.044 29.630 10.89 0.00 44.95 2.01
3297 4278 6.825721 AGAGAAAAACAGAGTGTCTGATTTGT 59.174 34.615 10.89 9.31 44.95 2.83
3298 4279 7.011763 TCAGAGAAAAACAGAGTGTCTGATTTG 59.988 37.037 10.89 1.13 44.95 2.32
3305 4286 5.006165 CACTGTCAGAGAAAAACAGAGTGTC 59.994 44.000 6.91 0.00 42.37 3.67
3306 4287 4.872691 CACTGTCAGAGAAAAACAGAGTGT 59.127 41.667 6.91 0.00 42.37 3.55
3309 4290 6.145858 CAGATCACTGTCAGAGAAAAACAGAG 59.854 42.308 6.91 1.28 42.37 3.35
3310 4291 5.987953 CAGATCACTGTCAGAGAAAAACAGA 59.012 40.000 6.91 0.00 42.37 3.41
3353 4465 5.355350 GGATGTTGTAGAAAAGATCCACCAG 59.645 44.000 7.92 0.00 45.16 4.00
3355 4467 4.640647 GGGATGTTGTAGAAAAGATCCACC 59.359 45.833 13.25 0.00 46.77 4.61
3356 4468 5.501156 AGGGATGTTGTAGAAAAGATCCAC 58.499 41.667 13.25 5.07 46.77 4.02
3357 4469 5.488919 AGAGGGATGTTGTAGAAAAGATCCA 59.511 40.000 13.25 0.00 46.77 3.41
3358 4470 5.995446 AGAGGGATGTTGTAGAAAAGATCC 58.005 41.667 4.88 4.88 45.12 3.36
3373 4485 7.782897 TTATACTATGAGTTGGAGAGGGATG 57.217 40.000 0.00 0.00 0.00 3.51
3405 4517 8.575589 TGTTATGTGTTCAAATCAGCAATACTT 58.424 29.630 0.00 0.00 0.00 2.24
3407 4519 7.807433 TGTGTTATGTGTTCAAATCAGCAATAC 59.193 33.333 0.00 0.00 0.00 1.89
3408 4520 7.807433 GTGTGTTATGTGTTCAAATCAGCAATA 59.193 33.333 0.00 0.00 0.00 1.90
3409 4521 6.642131 GTGTGTTATGTGTTCAAATCAGCAAT 59.358 34.615 0.00 0.00 0.00 3.56
3559 4675 9.899661 AGGTGCACTTCTGTTTATTTACATATA 57.100 29.630 17.98 0.00 0.00 0.86


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

AutoCloner maintained by Alex Coulton.