Multiple sequence alignment - TraesCS3A01G017800

Loading Multiple Alignment...

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 TraesCS3A01G017800 chr3A 100.000 4333 0 0 1 4333 11348647 11352979 0.000000e+00 8002.0
1 TraesCS3A01G017800 chr3A 86.207 1160 108 26 2511 3638 11389297 11388158 0.000000e+00 1208.0
2 TraesCS3A01G017800 chr3A 95.833 744 31 0 1 744 55556095 55556838 0.000000e+00 1203.0
3 TraesCS3A01G017800 chr3A 95.833 744 31 0 1 744 55598089 55598832 0.000000e+00 1203.0
4 TraesCS3A01G017800 chr3A 95.699 744 32 0 1 744 747532310 747533053 0.000000e+00 1197.0
5 TraesCS3A01G017800 chr3A 95.556 90 4 0 1158 1247 11349747 11349836 1.260000e-30 145.0
6 TraesCS3A01G017800 chr3A 95.556 90 4 0 1101 1190 11349804 11349893 1.260000e-30 145.0
7 TraesCS3A01G017800 chr3A 100.000 37 0 0 1994 2030 686534609 686534573 7.780000e-08 69.4
8 TraesCS3A01G017800 chrUn 91.258 2425 142 27 1101 3470 225573142 225570733 0.000000e+00 3240.0
9 TraesCS3A01G017800 chrUn 91.259 2391 139 27 1135 3470 237451262 237453637 0.000000e+00 3193.0
10 TraesCS3A01G017800 chrUn 89.963 2411 173 30 1366 3720 34663030 34660633 0.000000e+00 3048.0
11 TraesCS3A01G017800 chrUn 89.864 2052 139 31 1471 3470 36337227 36335193 0.000000e+00 2573.0
12 TraesCS3A01G017800 chrUn 89.864 2052 139 31 1471 3470 345668503 345666469 0.000000e+00 2573.0
13 TraesCS3A01G017800 chrUn 85.944 2049 219 33 1920 3926 35323405 35321384 0.000000e+00 2124.0
14 TraesCS3A01G017800 chrUn 89.180 305 24 5 943 1247 225573519 225573224 5.290000e-99 372.0
15 TraesCS3A01G017800 chrUn 84.029 407 39 12 3946 4330 35319469 35319067 6.850000e-98 368.0
16 TraesCS3A01G017800 chrUn 88.435 294 28 2 747 1034 225576740 225576447 2.480000e-92 350.0
17 TraesCS3A01G017800 chrUn 88.435 294 28 2 747 1034 297547311 297547604 2.480000e-92 350.0
18 TraesCS3A01G017800 chrUn 91.373 255 18 3 3469 3720 32295443 32295190 3.210000e-91 346.0
19 TraesCS3A01G017800 chrUn 88.800 250 21 4 747 995 35324537 35324294 2.530000e-77 300.0
20 TraesCS3A01G017800 chrUn 88.538 253 18 6 3469 3720 225570619 225570377 3.280000e-76 296.0
21 TraesCS3A01G017800 chrUn 88.538 253 18 6 3469 3720 237453751 237453993 3.280000e-76 296.0
22 TraesCS3A01G017800 chrUn 92.398 171 7 1 1204 1368 34663171 34663001 5.600000e-59 239.0
23 TraesCS3A01G017800 chrUn 89.000 200 13 5 943 1142 297550532 297550722 5.600000e-59 239.0
24 TraesCS3A01G017800 chrUn 94.558 147 8 0 1101 1247 225573256 225573110 1.210000e-55 228.0
25 TraesCS3A01G017800 chrUn 93.878 147 9 0 1101 1247 225573313 225573167 5.640000e-54 222.0
26 TraesCS3A01G017800 chrUn 92.517 147 11 0 1101 1247 225573199 225573053 1.220000e-50 211.0
27 TraesCS3A01G017800 chrUn 80.399 301 30 16 3946 4244 35320825 35320552 7.350000e-48 202.0
28 TraesCS3A01G017800 chrUn 94.444 90 5 0 1101 1190 225573085 225572996 5.840000e-29 139.0
29 TraesCS3A01G017800 chrUn 79.703 202 24 8 943 1133 34663323 34663128 3.520000e-26 130.0
30 TraesCS3A01G017800 chrUn 85.586 111 6 7 3942 4043 32294929 32294820 1.650000e-19 108.0
31 TraesCS3A01G017800 chrUn 87.324 71 9 0 1180 1250 35324174 35324104 9.990000e-12 82.4
32 TraesCS3A01G017800 chrUn 92.857 56 4 0 1192 1247 237451262 237451317 9.990000e-12 82.4
33 TraesCS3A01G017800 chr7A 95.968 744 30 0 1 744 677781589 677780846 0.000000e+00 1208.0
34 TraesCS3A01G017800 chr7A 95.833 744 30 1 1 744 718236496 718237238 0.000000e+00 1201.0
35 TraesCS3A01G017800 chr5A 95.833 744 31 0 1 744 2527833 2528576 0.000000e+00 1203.0
36 TraesCS3A01G017800 chr5A 95.833 744 31 0 1 744 587239265 587238522 0.000000e+00 1203.0
37 TraesCS3A01G017800 chr5A 95.699 744 31 1 1 744 28811733 28812475 0.000000e+00 1195.0
38 TraesCS3A01G017800 chr6A 95.251 758 34 2 1 756 3110204 3110961 0.000000e+00 1199.0
39 TraesCS3A01G017800 chr5B 83.381 349 35 13 3352 3682 586820576 586820233 7.040000e-78 302.0
40 TraesCS3A01G017800 chr6B 100.000 28 0 0 1997 2024 57453363 57453390 8.000000e-03 52.8


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 TraesCS3A01G017800 chr3A 11348647 11352979 4332 False 2764.000000 8002 97.037333 1 4333 3 chr3A.!!$F4 4332
1 TraesCS3A01G017800 chr3A 11388158 11389297 1139 True 1208.000000 1208 86.207000 2511 3638 1 chr3A.!!$R1 1127
2 TraesCS3A01G017800 chr3A 55556095 55556838 743 False 1203.000000 1203 95.833000 1 744 1 chr3A.!!$F1 743
3 TraesCS3A01G017800 chr3A 55598089 55598832 743 False 1203.000000 1203 95.833000 1 744 1 chr3A.!!$F2 743
4 TraesCS3A01G017800 chr3A 747532310 747533053 743 False 1197.000000 1197 95.699000 1 744 1 chr3A.!!$F3 743
5 TraesCS3A01G017800 chrUn 36335193 36337227 2034 True 2573.000000 2573 89.864000 1471 3470 1 chrUn.!!$R1 1999
6 TraesCS3A01G017800 chrUn 345666469 345668503 2034 True 2573.000000 2573 89.864000 1471 3470 1 chrUn.!!$R2 1999
7 TraesCS3A01G017800 chrUn 237451262 237453993 2731 False 1190.466667 3193 90.884667 1135 3720 3 chrUn.!!$F1 2585
8 TraesCS3A01G017800 chrUn 34660633 34663323 2690 True 1139.000000 3048 87.354667 943 3720 3 chrUn.!!$R4 2777
9 TraesCS3A01G017800 chrUn 225570377 225576740 6363 True 632.250000 3240 91.601000 747 3720 8 chrUn.!!$R6 2973
10 TraesCS3A01G017800 chrUn 35319067 35324537 5470 True 615.280000 2124 85.299200 747 4330 5 chrUn.!!$R5 3583
11 TraesCS3A01G017800 chrUn 297547311 297550722 3411 False 294.500000 350 88.717500 747 1142 2 chrUn.!!$F2 395
12 TraesCS3A01G017800 chrUn 32294820 32295443 623 True 227.000000 346 88.479500 3469 4043 2 chrUn.!!$R3 574
13 TraesCS3A01G017800 chr7A 677780846 677781589 743 True 1208.000000 1208 95.968000 1 744 1 chr7A.!!$R1 743
14 TraesCS3A01G017800 chr7A 718236496 718237238 742 False 1201.000000 1201 95.833000 1 744 1 chr7A.!!$F1 743
15 TraesCS3A01G017800 chr5A 2527833 2528576 743 False 1203.000000 1203 95.833000 1 744 1 chr5A.!!$F1 743
16 TraesCS3A01G017800 chr5A 587238522 587239265 743 True 1203.000000 1203 95.833000 1 744 1 chr5A.!!$R1 743
17 TraesCS3A01G017800 chr5A 28811733 28812475 742 False 1195.000000 1195 95.699000 1 744 1 chr5A.!!$F2 743
18 TraesCS3A01G017800 chr6A 3110204 3110961 757 False 1199.000000 1199 95.251000 1 756 1 chr6A.!!$F1 755

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
301 302 0.250338 GTTTGGAGGTCGAGCTTGGT 60.250 55.0 19.66 0.0 0.00 3.67 F
1714 5045 0.249398 CCCTTTCCGGACGAGTTCAT 59.751 55.0 1.83 0.0 33.16 2.57 F
2662 6029 0.105964 GTTGGCACTTTGAAACCCCC 59.894 55.0 0.00 0.0 0.00 5.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1808 5145 1.081242 GCACCTGGACAACAATGCG 60.081 57.895 0.0 0.0 33.24 4.73 R
3278 6680 0.543410 TCACCGTGTCCCTGTATGGT 60.543 55.000 0.0 0.0 36.65 3.55 R
4103 9569 0.243636 GGCCCACAGAAAATCAACCG 59.756 55.000 0.0 0.0 0.00 4.44 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
43 44 2.280404 TAGACAGGACGAGGGCCGAT 62.280 60.000 0.00 0.00 41.76 4.18
273 274 8.426489 ACCGCTAAACCTAGACAAATATTATGA 58.574 33.333 0.00 0.00 0.00 2.15
301 302 0.250338 GTTTGGAGGTCGAGCTTGGT 60.250 55.000 19.66 0.00 0.00 3.67
302 303 1.001633 GTTTGGAGGTCGAGCTTGGTA 59.998 52.381 19.66 2.89 0.00 3.25
359 360 2.839975 TCGAACACCTTGTGTGCATAA 58.160 42.857 6.19 0.00 46.79 1.90
360 361 3.206964 TCGAACACCTTGTGTGCATAAA 58.793 40.909 6.19 0.00 46.79 1.40
376 377 4.133078 GCATAAAAGGTGAGCTAGAGCAT 58.867 43.478 4.01 0.00 45.16 3.79
682 683 2.719376 CAATGCCCCTATTGGTCCG 58.281 57.895 0.00 0.00 35.03 4.79
696 697 4.113617 TCCGGGTTCTGGACTGAG 57.886 61.111 0.00 0.00 0.00 3.35
744 745 3.181423 TGGACCAAAGCCCTGTTTTCTAT 60.181 43.478 0.00 0.00 0.00 1.98
745 746 3.193479 GGACCAAAGCCCTGTTTTCTATG 59.807 47.826 0.00 0.00 0.00 2.23
753 754 3.622455 GCCCTGTTTTCTATGTGGCTACT 60.622 47.826 0.64 0.00 34.61 2.57
754 755 4.192317 CCCTGTTTTCTATGTGGCTACTC 58.808 47.826 0.64 0.00 0.00 2.59
766 767 8.198109 TCTATGTGGCTACTCTAAATTCAGTTC 58.802 37.037 0.64 0.00 0.00 3.01
803 804 7.588488 ACATTCGGTTTAAATTCAGTTTACACG 59.412 33.333 0.00 0.00 35.01 4.49
834 835 2.768253 TCCTTTGCGTGATCATCTGT 57.232 45.000 0.00 0.00 0.00 3.41
874 875 5.009610 AGTGCAACAACGAGTTTAAATCCAT 59.990 36.000 0.00 0.00 41.43 3.41
880 881 8.414173 CAACAACGAGTTTAAATCCATTTTACG 58.586 33.333 0.00 0.00 38.74 3.18
886 887 6.977213 AGTTTAAATCCATTTTACGCAGTGT 58.023 32.000 0.00 0.00 45.73 3.55
888 889 8.736244 AGTTTAAATCCATTTTACGCAGTGTAT 58.264 29.630 0.00 0.00 45.73 2.29
899 900 7.892778 TTTACGCAGTGTATCATTCAGTTTA 57.107 32.000 0.00 0.00 45.73 2.01
929 930 3.680786 GGCTTTTGACCGGGCCAC 61.681 66.667 3.83 0.00 43.59 5.01
930 931 4.038080 GCTTTTGACCGGGCCACG 62.038 66.667 3.83 5.77 43.80 4.94
1006 1022 2.235898 CTGAGAGAAACCCTAAGCAGCT 59.764 50.000 0.00 0.00 0.00 4.24
1015 4041 1.147153 CTAAGCAGCTAGGCACCCC 59.853 63.158 0.00 0.00 35.83 4.95
1714 5045 0.249398 CCCTTTCCGGACGAGTTCAT 59.751 55.000 1.83 0.00 33.16 2.57
1731 5068 5.072741 AGTTCATGAAATGCAACTACCACT 58.927 37.500 10.35 0.00 46.21 4.00
1808 5145 0.250513 ACGAGAGCCCATTCAAGGTC 59.749 55.000 0.00 0.00 0.00 3.85
1825 5162 0.238289 GTCGCATTGTTGTCCAGGTG 59.762 55.000 0.00 0.00 0.00 4.00
1827 5164 1.081242 GCATTGTTGTCCAGGTGCG 60.081 57.895 0.00 0.00 30.31 5.34
1828 5165 1.514678 GCATTGTTGTCCAGGTGCGA 61.515 55.000 0.00 0.00 30.31 5.10
1837 5180 2.888414 TGTCCAGGTGCGATAATCGATA 59.112 45.455 0.00 0.00 43.74 2.92
1887 5230 2.744823 CGCACATGGGCAGACCTTATAA 60.745 50.000 22.05 0.00 41.11 0.98
1892 5235 5.009010 CACATGGGCAGACCTTATAACAATC 59.991 44.000 0.00 0.00 41.11 2.67
2147 5496 6.386927 TCCTAGAAATATGGCTGAGGAAGAAA 59.613 38.462 0.00 0.00 0.00 2.52
2249 5604 0.831711 AGCGGTGGCCAAAAATCCTT 60.832 50.000 7.24 0.00 41.24 3.36
2362 5717 6.507958 TGATGAAAGCCGTTTGATGAAATA 57.492 33.333 0.00 0.00 0.00 1.40
2366 5721 3.764885 AGCCGTTTGATGAAATACTGC 57.235 42.857 0.00 0.00 0.00 4.40
2660 6027 1.754226 TCAGTTGGCACTTTGAAACCC 59.246 47.619 0.00 0.00 0.00 4.11
2662 6029 0.105964 GTTGGCACTTTGAAACCCCC 59.894 55.000 0.00 0.00 0.00 5.40
2939 6306 5.901853 ACATGATGAGGGATGAGTTTAGAGA 59.098 40.000 0.00 0.00 0.00 3.10
2943 6310 6.385176 TGATGAGGGATGAGTTTAGAGAACAT 59.615 38.462 0.00 0.00 0.00 2.71
3011 6379 7.321717 TCTCCATCCTTAATATTCCTTCCAG 57.678 40.000 0.00 0.00 0.00 3.86
3112 6482 4.117685 ACGGAAGCGAGTTATATTTGTCC 58.882 43.478 0.00 0.00 0.00 4.02
3268 6648 8.247562 GGACACAAGGATACAGATACAGATATC 58.752 40.741 0.00 0.00 38.00 1.63
3278 6680 7.437713 ACAGATACAGATATCCCAGAAACAA 57.562 36.000 0.00 0.00 38.43 2.83
3285 6687 6.069673 ACAGATATCCCAGAAACAACCATACA 60.070 38.462 0.00 0.00 0.00 2.29
3386 6791 2.423538 GCGATCAAAGTACTGCCCATTT 59.576 45.455 0.00 0.00 0.00 2.32
3455 6860 1.640428 GCTGATGCTGCAAGTACGTA 58.360 50.000 6.36 0.00 35.30 3.57
3458 6863 3.990469 GCTGATGCTGCAAGTACGTATAT 59.010 43.478 6.36 0.00 35.30 0.86
3463 6868 6.640907 TGATGCTGCAAGTACGTATATGTAAG 59.359 38.462 6.36 2.02 35.30 2.34
3466 6871 7.136772 TGCTGCAAGTACGTATATGTAAGTAG 58.863 38.462 6.37 9.36 35.30 2.57
3467 6872 7.012610 TGCTGCAAGTACGTATATGTAAGTAGA 59.987 37.037 6.37 0.00 35.30 2.59
3539 7059 9.736414 AATTATATTTGTGAGATCTGGGATCAG 57.264 33.333 0.00 0.00 42.21 2.90
3540 7060 6.760440 ATATTTGTGAGATCTGGGATCAGT 57.240 37.500 0.00 0.00 41.59 3.41
3620 7140 5.524284 TGGTTTCATTTCCACGTTTGTATG 58.476 37.500 0.00 0.00 0.00 2.39
3630 7150 3.558006 CCACGTTTGTATGTGACTGAACA 59.442 43.478 0.00 0.00 42.72 3.18
3631 7151 4.213270 CCACGTTTGTATGTGACTGAACAT 59.787 41.667 0.00 6.13 42.72 2.71
3653 7175 3.737559 ATGCAACTGAAACAGGGGATA 57.262 42.857 0.00 0.00 35.51 2.59
3731 7253 6.942976 TCAGGTCGGATTTAGTTGTATCTTT 58.057 36.000 0.00 0.00 0.00 2.52
3783 7305 5.175491 CCTGTCCATGTTTTTCACATTTTCG 59.825 40.000 0.00 0.00 44.40 3.46
3802 7334 5.801350 TTCGTCTAATGCTTTGATTGGAG 57.199 39.130 0.00 0.00 0.00 3.86
3817 7379 4.096833 TGATTGGAGGAATTTGCATTCTCG 59.903 41.667 0.36 0.00 39.17 4.04
3849 7411 4.899502 CCTATGAGGTTACTTGCCATAGG 58.100 47.826 11.01 11.01 45.71 2.57
3854 7416 2.772515 AGGTTACTTGCCATAGGAGGAC 59.227 50.000 0.00 0.00 0.00 3.85
3855 7417 2.158798 GGTTACTTGCCATAGGAGGACC 60.159 54.545 0.00 0.00 0.00 4.46
3893 7455 5.107298 GCAAGACACTGCTAGAAACTTACTG 60.107 44.000 0.00 0.00 39.34 2.74
3921 7889 8.597167 TCATGTTCTGAATTCTAAGAGGAAAGA 58.403 33.333 7.05 0.00 0.00 2.52
3933 7901 1.734465 GAGGAAAGACAAGTGCGATGG 59.266 52.381 0.00 0.00 0.00 3.51
3936 7904 0.537143 AAAGACAAGTGCGATGGCCA 60.537 50.000 8.56 8.56 38.85 5.36
3968 8067 1.402968 CTGCCGCATTCAAGCACTATT 59.597 47.619 0.00 0.00 32.06 1.73
4038 9504 1.575419 ATGCACCAATCAAGGCCAAT 58.425 45.000 5.01 0.00 0.00 3.16
4043 9509 2.093869 CACCAATCAAGGCCAATTCCTG 60.094 50.000 5.01 0.00 36.38 3.86
4053 9519 1.425428 CAATTCCTGTTCGGCGCTC 59.575 57.895 7.64 0.00 0.00 5.03
4078 9544 1.787155 CGCCAGTTATAGCGCTTGTAG 59.213 52.381 18.68 0.78 46.50 2.74
4090 9556 2.583868 TTGTAGGTATGCGGCGCG 60.584 61.111 28.09 0.00 0.00 6.86
4114 9580 2.351738 CCACCTGCTTCGGTTGATTTTC 60.352 50.000 0.00 0.00 34.29 2.29
4117 9583 2.554032 CCTGCTTCGGTTGATTTTCTGT 59.446 45.455 0.00 0.00 0.00 3.41
4136 9602 2.282462 GGCCGGCCCATCAATAGG 60.282 66.667 36.64 0.00 0.00 2.57
4139 9605 0.605589 GCCGGCCCATCAATAGGTAC 60.606 60.000 18.11 0.00 0.00 3.34
4209 9675 2.105649 TCCCTTTTGGTTTTTGGATGGC 59.894 45.455 0.00 0.00 38.10 4.40
4219 9685 5.767168 TGGTTTTTGGATGGCTTTTATTTGG 59.233 36.000 0.00 0.00 0.00 3.28
4220 9686 5.182950 GGTTTTTGGATGGCTTTTATTTGGG 59.817 40.000 0.00 0.00 0.00 4.12
4226 9692 6.000840 TGGATGGCTTTTATTTGGGTTTTTC 58.999 36.000 0.00 0.00 0.00 2.29
4230 9717 7.946381 TGGCTTTTATTTGGGTTTTTCTTTT 57.054 28.000 0.00 0.00 0.00 2.27
4295 9782 6.525578 AATTCTAAATTTCCCTTCGAACCC 57.474 37.500 0.00 0.00 0.00 4.11
4296 9783 3.602483 TCTAAATTTCCCTTCGAACCCG 58.398 45.455 0.00 0.00 37.07 5.28
4309 9796 5.409214 CCTTCGAACCCGTGAAACTATTTTA 59.591 40.000 0.00 0.00 37.05 1.52
4313 9800 8.721019 TCGAACCCGTGAAACTATTTTATTAT 57.279 30.769 0.00 0.00 37.05 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.959030 CCCTCGTCCTGTCTATGATTCA 59.041 50.000 0.00 0.00 0.00 2.57
43 44 2.041686 GTTTTGGTATCCGCGCCCA 61.042 57.895 0.00 0.00 0.00 5.36
47 48 0.303493 CGATGGTTTTGGTATCCGCG 59.697 55.000 0.00 0.00 0.00 6.46
273 274 3.821033 CTCGACCTCCAAACTCCATTTTT 59.179 43.478 0.00 0.00 0.00 1.94
283 284 1.344065 TACCAAGCTCGACCTCCAAA 58.656 50.000 0.00 0.00 0.00 3.28
301 302 6.932960 GCCACACTACTTAAGTTTTCTCCTTA 59.067 38.462 14.49 0.00 35.76 2.69
302 303 5.763698 GCCACACTACTTAAGTTTTCTCCTT 59.236 40.000 14.49 0.00 35.76 3.36
359 360 3.258971 GTGATGCTCTAGCTCACCTTT 57.741 47.619 16.90 0.00 40.23 3.11
360 361 2.977772 GTGATGCTCTAGCTCACCTT 57.022 50.000 16.90 0.00 40.23 3.50
376 377 2.610859 GGGGAGAGGGCTTGGTGA 60.611 66.667 0.00 0.00 0.00 4.02
421 422 1.658686 CCCTCGCGTAAGAGCAGAGT 61.659 60.000 5.77 0.00 43.02 3.24
673 674 0.906775 GTCCAGAACCCGGACCAATA 59.093 55.000 0.73 0.00 46.12 1.90
682 683 2.266055 CGGCTCAGTCCAGAACCC 59.734 66.667 0.00 0.00 0.00 4.11
696 697 2.203209 CAGCCCATTAGTCCCGGC 60.203 66.667 0.00 0.00 41.96 6.13
720 721 0.555769 AAACAGGGCTTTGGTCCAGA 59.444 50.000 0.00 0.00 40.27 3.86
744 745 5.932303 GTGAACTGAATTTAGAGTAGCCACA 59.068 40.000 3.94 0.00 0.00 4.17
745 746 5.932303 TGTGAACTGAATTTAGAGTAGCCAC 59.068 40.000 3.94 5.66 0.00 5.01
753 754 3.496884 GCACGGTGTGAACTGAATTTAGA 59.503 43.478 10.24 0.00 35.23 2.10
754 755 3.364964 GGCACGGTGTGAACTGAATTTAG 60.365 47.826 10.24 0.00 35.23 1.85
766 767 2.555782 CGAATGTGGCACGGTGTG 59.444 61.111 13.77 0.00 36.51 3.82
860 861 6.248420 CACTGCGTAAAATGGATTTAAACTCG 59.752 38.462 0.00 0.00 35.33 4.18
874 875 6.795098 AACTGAATGATACACTGCGTAAAA 57.205 33.333 0.00 0.00 32.59 1.52
899 900 4.261867 GGTCAAAAGCCCACGAGTTTAATT 60.262 41.667 0.00 0.00 0.00 1.40
986 987 2.260822 AGCTGCTTAGGGTTTCTCTCA 58.739 47.619 0.00 0.00 0.00 3.27
1090 4116 3.564027 CCGTCGCCTTGGATTCGC 61.564 66.667 0.00 0.00 0.00 4.70
1441 4749 1.812571 CGGTGCTGGCTCATAAAGTTT 59.187 47.619 0.00 0.00 0.00 2.66
1642 4970 2.051345 CAACAAGACGCGCCAACC 60.051 61.111 5.73 0.00 0.00 3.77
1714 5045 3.331150 CCGTAGTGGTAGTTGCATTTCA 58.669 45.455 0.00 0.00 0.00 2.69
1731 5068 2.603473 ACAGAGCACAGCCCCGTA 60.603 61.111 0.00 0.00 0.00 4.02
1808 5145 1.081242 GCACCTGGACAACAATGCG 60.081 57.895 0.00 0.00 33.24 4.73
1825 5162 6.730175 ACAGAGGTGATATATCGATTATCGC 58.270 40.000 20.81 20.81 40.21 4.58
1837 5180 7.904558 TCTGATGAGTAAACAGAGGTGATAT 57.095 36.000 0.00 0.00 36.04 1.63
1876 5219 5.463724 GGAGCTTCGATTGTTATAAGGTCTG 59.536 44.000 11.49 0.00 42.93 3.51
1877 5220 5.128827 TGGAGCTTCGATTGTTATAAGGTCT 59.871 40.000 11.49 0.00 42.93 3.85
1887 5230 6.381801 CAACTTTAAATGGAGCTTCGATTGT 58.618 36.000 0.00 0.00 0.00 2.71
1892 5235 4.154918 AGAGCAACTTTAAATGGAGCTTCG 59.845 41.667 0.00 0.00 0.00 3.79
2147 5496 1.336755 GTGGCAAGACCGTGACATTTT 59.663 47.619 0.00 0.00 39.22 1.82
2150 5499 1.667830 CGTGGCAAGACCGTGACAT 60.668 57.895 0.00 0.00 39.22 3.06
2249 5604 1.634960 TGTTGTCCTCGTCATACCCA 58.365 50.000 0.00 0.00 0.00 4.51
2362 5717 1.075482 CTGGTGAATGGGTGGCAGT 59.925 57.895 0.00 0.00 0.00 4.40
2366 5721 2.292828 AGAAACTGGTGAATGGGTGG 57.707 50.000 0.00 0.00 0.00 4.61
2660 6027 6.486657 TGGATAAAGAATAGAATTCGCTTGGG 59.513 38.462 0.00 0.00 0.00 4.12
2969 6337 4.832266 TGGAGAATTTAGCTGGCAAAAAGA 59.168 37.500 0.00 0.00 0.00 2.52
3092 6462 3.059800 GCGGACAAATATAACTCGCTTCC 60.060 47.826 0.00 0.00 38.82 3.46
3112 6482 3.740832 TGAGACAGTTAGAAACATGTGCG 59.259 43.478 0.00 0.00 0.00 5.34
3268 6648 2.041081 TCCCTGTATGGTTGTTTCTGGG 59.959 50.000 0.00 0.00 38.20 4.45
3278 6680 0.543410 TCACCGTGTCCCTGTATGGT 60.543 55.000 0.00 0.00 36.65 3.55
3285 6687 4.174704 TGTATATACTCACCGTGTCCCT 57.825 45.455 13.89 0.00 0.00 4.20
3386 6791 3.149196 GGAGATGAAGGCAGAAAACACA 58.851 45.455 0.00 0.00 0.00 3.72
3539 7059 7.119699 TCCACATTACATGACAGAATCAAGAAC 59.880 37.037 0.00 0.00 41.93 3.01
3540 7060 7.119699 GTCCACATTACATGACAGAATCAAGAA 59.880 37.037 0.00 0.00 41.93 2.52
3583 7103 6.694877 AATGAAACCAGATGATCTCACATG 57.305 37.500 0.00 0.00 0.00 3.21
3596 7116 4.040445 ACAAACGTGGAAATGAAACCAG 57.960 40.909 0.00 0.00 36.82 4.00
3620 7140 5.611796 TCAGTTGCATTATGTTCAGTCAC 57.388 39.130 0.00 0.00 0.00 3.67
3630 7150 4.046286 TCCCCTGTTTCAGTTGCATTAT 57.954 40.909 0.00 0.00 0.00 1.28
3631 7151 3.517296 TCCCCTGTTTCAGTTGCATTA 57.483 42.857 0.00 0.00 0.00 1.90
3653 7175 2.766263 TGTCTGTCTTTCCAGTCACACT 59.234 45.455 0.00 0.00 34.02 3.55
3747 7269 6.994421 AACATGGACAGGTTCCTTAAATTT 57.006 33.333 0.00 0.00 46.10 1.82
3750 7272 6.381420 TGAAAAACATGGACAGGTTCCTTAAA 59.619 34.615 2.65 0.00 46.10 1.52
3753 7275 4.099419 GTGAAAAACATGGACAGGTTCCTT 59.901 41.667 2.65 0.61 46.10 3.36
3755 7277 3.383185 TGTGAAAAACATGGACAGGTTCC 59.617 43.478 2.65 0.00 38.30 3.62
3769 7291 8.538856 CAAAGCATTAGACGAAAATGTGAAAAA 58.461 29.630 0.00 0.00 36.82 1.94
3783 7305 6.705863 ATTCCTCCAATCAAAGCATTAGAC 57.294 37.500 0.00 0.00 0.00 2.59
3802 7334 4.370364 TTTAGCCGAGAATGCAAATTCC 57.630 40.909 0.00 0.00 0.00 3.01
3817 7379 7.468768 GCAAGTAACCTCATAGGAATTTTAGCC 60.469 40.741 0.00 0.00 37.67 3.93
3849 7411 3.194719 CCGTGTAGTCCGGTCCTC 58.805 66.667 0.00 0.00 40.59 3.71
3855 7417 2.048597 TTGCAGCCGTGTAGTCCG 60.049 61.111 0.00 0.00 0.00 4.79
3879 7441 7.385205 TCAGAACATGAACAGTAAGTTTCTAGC 59.615 37.037 0.00 0.00 41.51 3.42
3921 7889 2.672996 GGTGGCCATCGCACTTGT 60.673 61.111 9.72 0.00 36.38 3.16
4038 9504 2.537792 CTACGAGCGCCGAACAGGAA 62.538 60.000 22.10 1.56 45.00 3.36
4053 9519 2.421131 CGCTATAACTGGCGCTACG 58.579 57.895 7.64 0.00 45.46 3.51
4061 9527 4.386049 GCATACCTACAAGCGCTATAACTG 59.614 45.833 12.05 7.56 0.00 3.16
4093 9559 1.247567 AAATCAACCGAAGCAGGTGG 58.752 50.000 0.00 0.00 45.21 4.61
4103 9569 0.243636 GGCCCACAGAAAATCAACCG 59.756 55.000 0.00 0.00 0.00 4.44
4130 9596 1.065701 ACTGCGCTCGAGTACCTATTG 59.934 52.381 15.13 0.00 0.00 1.90
4136 9602 1.403972 CCGAAACTGCGCTCGAGTAC 61.404 60.000 17.17 7.09 37.23 2.73
4139 9605 3.843240 GCCGAAACTGCGCTCGAG 61.843 66.667 17.17 8.45 37.23 4.04
4181 9647 5.707764 TCCAAAAACCAAAAGGGAAAAACAG 59.292 36.000 0.00 0.00 41.15 3.16
4182 9648 5.631119 TCCAAAAACCAAAAGGGAAAAACA 58.369 33.333 0.00 0.00 41.15 2.83
4219 9685 8.561738 AGAAAAGGAAAAGGAAAAGAAAAACC 57.438 30.769 0.00 0.00 0.00 3.27
4269 9756 8.692710 GGGTTCGAAGGGAAATTTAGAATTTAT 58.307 33.333 0.00 0.00 36.14 1.40
4270 9757 7.148205 CGGGTTCGAAGGGAAATTTAGAATTTA 60.148 37.037 0.00 0.00 36.14 1.40
4277 9764 3.075884 CACGGGTTCGAAGGGAAATTTA 58.924 45.455 0.00 0.00 40.11 1.40
4284 9771 0.250166 AGTTTCACGGGTTCGAAGGG 60.250 55.000 0.00 0.00 40.11 3.95


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

AutoCloner maintained by Alex Coulton.