Multiple sequence alignment - TraesCS5A01G141300

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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 TraesCS5A01G141300 chr5A 100.000 4262 0 0 1 4262 313319958 313315697 0.000000e+00 7871
1 TraesCS5A01G141300 chr5A 81.349 252 32 7 2 250 264409493 264409732 1.560000e-44 191
2 TraesCS5A01G141300 chr5D 92.852 2882 138 34 481 3339 240497404 240500240 0.000000e+00 4119
3 TraesCS5A01G141300 chr5D 92.092 961 47 15 3317 4262 240500253 240501199 0.000000e+00 1327
4 TraesCS5A01G141300 chr5D 83.612 299 47 2 405 702 533861782 533861485 3.250000e-71 279
5 TraesCS5A01G141300 chr5D 82.700 237 28 5 16 250 205982690 205982915 9.350000e-47 198
6 TraesCS5A01G141300 chr5B 97.802 1956 40 3 1386 3339 263229454 263227500 0.000000e+00 3371
7 TraesCS5A01G141300 chr5B 92.929 594 32 3 797 1388 263230296 263229711 0.000000e+00 856
8 TraesCS5A01G141300 chr5B 92.762 525 34 4 3317 3839 263227487 263226965 0.000000e+00 756
9 TraesCS5A01G141300 chr5B 87.273 440 30 13 3838 4262 263226733 263226305 2.980000e-131 479
10 TraesCS5A01G141300 chr5B 79.066 621 89 25 2 585 526275781 526276397 5.170000e-104 388
11 TraesCS5A01G141300 chr2B 79.207 731 107 32 12 702 201461392 201460667 2.320000e-127 466
12 TraesCS5A01G141300 chr4D 78.849 695 98 36 2 657 421211128 421211812 1.420000e-114 424
13 TraesCS5A01G141300 chr7A 82.609 460 75 5 245 702 218206875 218207331 6.640000e-108 401
14 TraesCS5A01G141300 chr3A 82.495 457 72 6 248 702 371290774 371291224 1.110000e-105 394
15 TraesCS5A01G141300 chr6D 83.610 421 60 8 287 702 163338798 163339214 1.860000e-103 387
16 TraesCS5A01G141300 chr6D 83.929 224 33 3 2 222 223834850 223835073 1.200000e-50 211
17 TraesCS5A01G141300 chr6D 85.096 208 26 5 20 223 223926905 223927111 1.550000e-49 207
18 TraesCS5A01G141300 chr2A 80.435 460 81 7 246 702 718131667 718131214 4.080000e-90 342
19 TraesCS5A01G141300 chr2A 85.259 251 26 7 2 250 718131936 718131695 9.150000e-62 248
20 TraesCS5A01G141300 chr3D 83.333 354 57 2 246 598 14120374 14120022 4.110000e-85 326
21 TraesCS5A01G141300 chr4A 85.771 253 32 4 1 250 627780352 627780101 9.090000e-67 265
22 TraesCS5A01G141300 chr7B 84.298 242 30 8 14 250 196393182 196392944 3.310000e-56 230
23 TraesCS5A01G141300 chr6B 86.700 203 25 2 23 223 382985152 382984950 1.540000e-54 224


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 TraesCS5A01G141300 chr5A 313315697 313319958 4261 True 7871.0 7871 100.0000 1 4262 1 chr5A.!!$R1 4261
1 TraesCS5A01G141300 chr5D 240497404 240501199 3795 False 2723.0 4119 92.4720 481 4262 2 chr5D.!!$F2 3781
2 TraesCS5A01G141300 chr5B 263226305 263230296 3991 True 1365.5 3371 92.6915 797 4262 4 chr5B.!!$R1 3465
3 TraesCS5A01G141300 chr5B 526275781 526276397 616 False 388.0 388 79.0660 2 585 1 chr5B.!!$F1 583
4 TraesCS5A01G141300 chr2B 201460667 201461392 725 True 466.0 466 79.2070 12 702 1 chr2B.!!$R1 690
5 TraesCS5A01G141300 chr4D 421211128 421211812 684 False 424.0 424 78.8490 2 657 1 chr4D.!!$F1 655
6 TraesCS5A01G141300 chr2A 718131214 718131936 722 True 295.0 342 82.8470 2 702 2 chr2A.!!$R1 700

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
613 652 0.249398 AGAGAAGGCCGCATAAACGT 59.751 50.000 0.00 0.0 0.00 3.99 F
1234 1287 0.183492 ATGTAATGCGCCACCAGGAT 59.817 50.000 4.18 0.0 36.89 3.24 F
1304 1357 0.934496 CAAGCGTCCGTTTGACTTCA 59.066 50.000 10.22 0.0 42.13 3.02 F
2837 3154 2.627699 GGCATCAACTTGTTCCAAGGAA 59.372 45.455 8.68 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2347 2664 1.896220 TACAAAGCAGGCCACAGAAG 58.104 50.000 5.01 0.0 0.00 2.85 R
2961 3278 0.107703 TCGAGGCCTAAATGTGCAGG 60.108 55.000 4.42 0.0 34.85 4.85 R
3036 3353 1.209383 CTCGTTCGCTTCCTCGTCA 59.791 57.895 0.00 0.0 0.00 4.35 R
4065 4665 0.251354 TGCCTCTCCAGAGCAATGTC 59.749 55.000 0.00 0.0 40.75 3.06 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
48 50 1.271325 ACCCGTGCATCAAGTCAATCA 60.271 47.619 0.00 0.00 0.00 2.57
91 94 5.350914 TCAACAAGAATGCAACAAGTTTTGG 59.649 36.000 0.00 0.00 34.12 3.28
120 124 1.965754 GAGAGCGTTGATGCCCTCCT 61.966 60.000 0.00 0.00 34.00 3.69
135 139 1.133009 CCTCCTATGAGTGGCCTAGGT 60.133 57.143 11.31 0.00 36.86 3.08
140 144 0.252696 ATGAGTGGCCTAGGTGTGGA 60.253 55.000 11.31 0.00 0.00 4.02
210 215 2.929641 TGTTGCATCTTGTGTCCTTCA 58.070 42.857 0.00 0.00 0.00 3.02
230 235 5.895636 TCACTATTACATTTGTGGCCTTG 57.104 39.130 3.32 0.00 0.00 3.61
258 295 7.517614 TTGATTGTGTAGGCATAAGAACAAA 57.482 32.000 6.63 0.00 31.90 2.83
259 296 7.517614 TGATTGTGTAGGCATAAGAACAAAA 57.482 32.000 6.63 0.00 31.90 2.44
270 307 6.071616 GGCATAAGAACAAAACATTCACCCTA 60.072 38.462 0.00 0.00 0.00 3.53
278 315 5.368230 ACAAAACATTCACCCTAACCCATTT 59.632 36.000 0.00 0.00 0.00 2.32
282 319 5.646215 ACATTCACCCTAACCCATTTGTTA 58.354 37.500 0.00 0.00 0.00 2.41
285 322 5.789574 TCACCCTAACCCATTTGTTAGAT 57.210 39.130 11.46 0.00 46.91 1.98
292 329 5.587388 AACCCATTTGTTAGATGCTCATG 57.413 39.130 0.00 0.00 0.00 3.07
304 341 5.481200 AGATGCTCATGAAAGATTGTTCG 57.519 39.130 0.00 0.00 0.00 3.95
332 370 8.589338 AGTCAAAGATCAATATACCGCTCTAAT 58.411 33.333 0.00 0.00 0.00 1.73
333 371 9.856488 GTCAAAGATCAATATACCGCTCTAATA 57.144 33.333 0.00 0.00 0.00 0.98
350 388 5.028131 TCTAATAAAGAAAGGAGGGTCGGT 58.972 41.667 0.00 0.00 0.00 4.69
374 412 1.004626 TGGCTGGGGATGGAGATGA 59.995 57.895 0.00 0.00 0.00 2.92
386 424 1.273495 TGGAGATGAGGTGAAGAGGCT 60.273 52.381 0.00 0.00 0.00 4.58
389 427 2.699846 GAGATGAGGTGAAGAGGCTGAT 59.300 50.000 0.00 0.00 0.00 2.90
452 490 3.547613 GCATCTATCGCCTTGCAAGAAAG 60.548 47.826 28.05 17.05 35.22 2.62
472 510 1.068333 GTTTGCGTGGCATGATGACTT 60.068 47.619 11.71 0.00 38.76 3.01
477 515 3.254411 TGCGTGGCATGATGACTTAAAAA 59.746 39.130 11.71 0.00 31.71 1.94
511 549 1.903183 AGAGGAAGCGCTAAGGAAAGT 59.097 47.619 12.05 0.00 0.00 2.66
512 550 2.303311 AGAGGAAGCGCTAAGGAAAGTT 59.697 45.455 12.05 0.00 0.00 2.66
548 587 8.688747 AAGATATATTTGGAGCTTCAAAGGAG 57.311 34.615 24.02 0.00 39.59 3.69
585 624 1.893801 GAGGTCGTCAAGAGGAGGAAA 59.106 52.381 0.00 0.00 41.68 3.13
607 646 3.580458 ACTCAATATAGAGAAGGCCGCAT 59.420 43.478 0.00 0.00 38.98 4.73
613 652 0.249398 AGAGAAGGCCGCATAAACGT 59.751 50.000 0.00 0.00 0.00 3.99
614 653 0.373716 GAGAAGGCCGCATAAACGTG 59.626 55.000 0.00 0.00 0.00 4.49
658 697 3.951775 ATGCCGATACCAAAGCAAAAA 57.048 38.095 0.00 0.00 38.99 1.94
680 719 7.849804 AAAAGTGACGTCTAGCAATTATGAT 57.150 32.000 17.92 0.00 0.00 2.45
684 723 6.017357 AGTGACGTCTAGCAATTATGATCGTA 60.017 38.462 17.92 0.00 0.00 3.43
734 783 8.511604 AAAAACCATGGACTTGAGTGATATAG 57.488 34.615 21.47 0.00 0.00 1.31
735 784 7.437713 AAACCATGGACTTGAGTGATATAGA 57.562 36.000 21.47 0.00 0.00 1.98
736 785 7.623999 AACCATGGACTTGAGTGATATAGAT 57.376 36.000 21.47 0.00 0.00 1.98
738 787 8.359875 ACCATGGACTTGAGTGATATAGATAG 57.640 38.462 21.47 0.00 0.00 2.08
740 789 9.199645 CCATGGACTTGAGTGATATAGATAGAT 57.800 37.037 5.56 0.00 0.00 1.98
763 812 9.984190 AGATAAAATTTAGATAGAACGGAGGTC 57.016 33.333 0.00 0.00 0.00 3.85
765 814 9.765795 ATAAAATTTAGATAGAACGGAGGTCTG 57.234 33.333 0.00 0.00 0.00 3.51
766 815 6.793505 AATTTAGATAGAACGGAGGTCTGT 57.206 37.500 0.00 0.00 36.96 3.41
768 817 6.600882 TTTAGATAGAACGGAGGTCTGTTT 57.399 37.500 5.67 0.07 44.81 2.83
770 819 5.838531 AGATAGAACGGAGGTCTGTTTAG 57.161 43.478 5.67 0.00 44.81 1.85
771 820 4.645588 AGATAGAACGGAGGTCTGTTTAGG 59.354 45.833 5.67 0.00 44.81 2.69
773 822 0.981943 AACGGAGGTCTGTTTAGGGG 59.018 55.000 0.00 0.00 42.39 4.79
775 824 0.535797 CGGAGGTCTGTTTAGGGGTC 59.464 60.000 0.00 0.00 0.00 4.46
777 826 2.197465 GGAGGTCTGTTTAGGGGTCAT 58.803 52.381 0.00 0.00 0.00 3.06
778 827 2.092914 GGAGGTCTGTTTAGGGGTCATG 60.093 54.545 0.00 0.00 0.00 3.07
779 828 1.916181 AGGTCTGTTTAGGGGTCATGG 59.084 52.381 0.00 0.00 0.00 3.66
781 830 2.092914 GGTCTGTTTAGGGGTCATGGAG 60.093 54.545 0.00 0.00 0.00 3.86
782 831 2.572104 GTCTGTTTAGGGGTCATGGAGT 59.428 50.000 0.00 0.00 0.00 3.85
783 832 3.009143 GTCTGTTTAGGGGTCATGGAGTT 59.991 47.826 0.00 0.00 0.00 3.01
784 833 3.009033 TCTGTTTAGGGGTCATGGAGTTG 59.991 47.826 0.00 0.00 0.00 3.16
827 880 1.004927 CGAAACATTTCCCGCGATCTC 60.005 52.381 8.23 0.00 33.68 2.75
880 933 2.874664 CGTTCCGTTCCCCACCTCA 61.875 63.158 0.00 0.00 0.00 3.86
928 981 1.825474 TCAAGCTAGGGTTTCTCCTCG 59.175 52.381 0.00 0.00 38.30 4.63
930 983 1.144276 GCTAGGGTTTCTCCTCGCC 59.856 63.158 0.00 0.00 39.03 5.54
931 984 1.823976 CTAGGGTTTCTCCTCGCCC 59.176 63.158 0.00 0.00 41.36 6.13
932 985 1.687297 CTAGGGTTTCTCCTCGCCCC 61.687 65.000 0.00 0.00 41.99 5.80
933 986 4.468689 GGGTTTCTCCTCGCCCCG 62.469 72.222 0.00 0.00 35.18 5.73
1183 1236 3.036091 CCTTCGATTAGTTCCACCCCTA 58.964 50.000 0.00 0.00 0.00 3.53
1186 1239 5.306160 CCTTCGATTAGTTCCACCCCTATTA 59.694 44.000 0.00 0.00 0.00 0.98
1230 1283 0.391793 TTCGATGTAATGCGCCACCA 60.392 50.000 4.18 0.00 0.00 4.17
1234 1287 0.183492 ATGTAATGCGCCACCAGGAT 59.817 50.000 4.18 0.00 36.89 3.24
1266 1319 2.682352 CCCATGTGTTCGATGTAATGCA 59.318 45.455 0.00 0.00 0.00 3.96
1270 1323 2.080693 GTGTTCGATGTAATGCACCCA 58.919 47.619 0.00 0.00 0.00 4.51
1283 1336 1.342819 TGCACCCATGGCAACTTTTAC 59.657 47.619 6.09 0.00 38.54 2.01
1297 1350 3.200483 ACTTTTACTCAAGCGTCCGTTT 58.800 40.909 0.00 0.00 0.00 3.60
1298 1351 3.001939 ACTTTTACTCAAGCGTCCGTTTG 59.998 43.478 9.58 9.58 37.61 2.93
1304 1357 0.934496 CAAGCGTCCGTTTGACTTCA 59.066 50.000 10.22 0.00 42.13 3.02
1369 1424 6.046593 CCAAAACCTTTCCTTTCCAGTAAAC 58.953 40.000 0.00 0.00 0.00 2.01
1388 1443 8.007716 CAGTAAACGAGTTTATGTTTGGTGTAG 58.992 37.037 11.04 0.00 38.64 2.74
1470 1786 7.697691 TCTTCTGATTGTCTCAAAAACAGAAC 58.302 34.615 16.84 0.00 37.77 3.01
1685 2002 2.744202 CCACTCACCAGCAACTATTCAC 59.256 50.000 0.00 0.00 0.00 3.18
2206 2523 8.383947 AGATATCCTGAATGTGTGATCATGATT 58.616 33.333 10.14 0.00 34.29 2.57
2315 2632 9.793252 GTAGCTTCATTCAATTGTGATTTACAT 57.207 29.630 5.13 0.00 39.48 2.29
2347 2664 4.307443 TGGACGAGTCATGATGTGTATC 57.693 45.455 0.00 0.00 0.00 2.24
2529 2846 9.278978 GTTCTCTCAAAAGGAAAAGACTCTTAT 57.721 33.333 0.00 0.00 0.00 1.73
2727 3044 3.496870 CCCTTGTTCTTGCCACTTACTCT 60.497 47.826 0.00 0.00 0.00 3.24
2747 3064 9.976511 TTACTCTGTACCATATATTGTACAAGC 57.023 33.333 22.98 4.17 44.72 4.01
2771 3088 9.654663 AGCGTTTTTGTAGAATCTCTATAAACT 57.345 29.630 5.43 0.00 38.96 2.66
2837 3154 2.627699 GGCATCAACTTGTTCCAAGGAA 59.372 45.455 8.68 0.00 0.00 3.36
2961 3278 5.708948 TGCCATCATTGTTTGCTAACTTAC 58.291 37.500 12.20 0.00 35.24 2.34
3036 3353 3.069318 GAAGGCGAGGACGAGGGT 61.069 66.667 0.00 0.00 42.66 4.34
3271 3588 5.651576 AGAAGGAAGAAATGATGGCTCTTTC 59.348 40.000 0.00 0.00 29.59 2.62
3275 3592 6.069731 AGGAAGAAATGATGGCTCTTTCTAGT 60.070 38.462 0.00 0.00 38.05 2.57
3281 3598 9.336171 GAAATGATGGCTCTTTCTAGTAAGATT 57.664 33.333 11.71 2.00 33.89 2.40
3435 3786 2.359975 CAAGGACAAGGACGGCCC 60.360 66.667 1.76 0.00 33.31 5.80
3451 3802 3.264947 CGGCCCCTGTTAGTTTAAGTAC 58.735 50.000 0.00 0.00 0.00 2.73
3452 3803 3.055602 CGGCCCCTGTTAGTTTAAGTACT 60.056 47.826 0.00 0.00 0.00 2.73
3454 3805 5.163374 CGGCCCCTGTTAGTTTAAGTACTAT 60.163 44.000 0.00 0.00 31.09 2.12
3455 3806 6.040842 CGGCCCCTGTTAGTTTAAGTACTATA 59.959 42.308 0.00 0.00 31.09 1.31
3457 3808 8.435187 GGCCCCTGTTAGTTTAAGTACTATAAT 58.565 37.037 0.00 0.00 31.09 1.28
3491 3842 1.202989 TGCCCTTCAGGTGTTGCATTA 60.203 47.619 0.00 0.00 38.26 1.90
3583 3934 4.814294 GCCGTCGGATCGTGCCTT 62.814 66.667 17.49 0.00 0.00 4.35
3585 3936 2.885644 CGTCGGATCGTGCCTTGG 60.886 66.667 0.00 0.00 0.00 3.61
3595 3946 1.002624 GTGCCTTGGGATCCGTGAA 60.003 57.895 5.45 0.00 0.00 3.18
3625 3981 4.716977 AGGGGTGGAGGTCGTCCC 62.717 72.222 9.08 0.95 46.31 4.46
3627 3983 3.391382 GGGTGGAGGTCGTCCCTG 61.391 72.222 9.08 0.00 46.51 4.45
3696 4052 4.888326 TGCCCGGTTTAAGTTAGACTAA 57.112 40.909 0.00 0.00 0.00 2.24
3904 4495 2.737783 CCGCATGAAAGGTAACACGTTA 59.262 45.455 0.00 0.00 41.41 3.18
3905 4496 3.181524 CCGCATGAAAGGTAACACGTTAG 60.182 47.826 0.00 0.00 41.41 2.34
4025 4620 3.830679 CTTCAGAGCACAGGAGGAC 57.169 57.895 0.00 0.00 0.00 3.85
4031 4626 2.262774 GAGCACAGGAGGACCATGGG 62.263 65.000 18.09 0.00 38.94 4.00
4065 4665 3.228749 CACTATGCTTTGTCGTGCTTTG 58.771 45.455 0.00 0.00 0.00 2.77
4067 4667 2.405892 ATGCTTTGTCGTGCTTTGAC 57.594 45.000 0.00 0.00 36.88 3.18
4079 4679 2.095364 GTGCTTTGACATTGCTCTGGAG 60.095 50.000 2.62 0.00 0.00 3.86
4081 4681 2.419324 GCTTTGACATTGCTCTGGAGAG 59.581 50.000 1.35 0.00 44.75 3.20
4082 4682 2.775911 TTGACATTGCTCTGGAGAGG 57.224 50.000 5.82 0.00 42.29 3.69
4171 4771 2.031508 ACAAACGCCGTTATGACCAAAG 60.032 45.455 1.51 0.00 0.00 2.77
4257 4864 5.220739 CCTCGCTTGTAGAATGATTTTCCTG 60.221 44.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.506288 GCAAATTTGTAGGACGCAAACTTT 59.494 37.500 19.03 0.00 38.44 2.66
53 55 5.246981 TCTTGTTGAGTGAATCCCATCTT 57.753 39.130 0.00 0.00 0.00 2.40
66 69 6.455913 CCAAAACTTGTTGCATTCTTGTTGAG 60.456 38.462 0.00 0.00 0.00 3.02
120 124 1.007842 TCCACACCTAGGCCACTCATA 59.992 52.381 9.30 0.00 0.00 2.15
135 139 1.274167 GGTCATACCAAGTCGTCCACA 59.726 52.381 0.00 0.00 38.42 4.17
140 144 2.496470 GGAAGAGGTCATACCAAGTCGT 59.504 50.000 0.00 0.00 41.95 4.34
210 215 5.570320 AGACAAGGCCACAAATGTAATAGT 58.430 37.500 5.01 0.00 0.00 2.12
230 235 6.985188 TCTTATGCCTACACAATCAAAGAC 57.015 37.500 0.00 0.00 0.00 3.01
258 295 4.488770 ACAAATGGGTTAGGGTGAATGTT 58.511 39.130 0.00 0.00 0.00 2.71
259 296 4.126520 ACAAATGGGTTAGGGTGAATGT 57.873 40.909 0.00 0.00 0.00 2.71
270 307 5.263599 TCATGAGCATCTAACAAATGGGTT 58.736 37.500 0.00 0.00 34.92 4.11
278 315 7.413328 CGAACAATCTTTCATGAGCATCTAACA 60.413 37.037 0.00 0.00 34.92 2.41
282 319 5.181009 TCGAACAATCTTTCATGAGCATCT 58.819 37.500 0.00 0.00 34.92 2.90
285 322 4.756642 ACTTCGAACAATCTTTCATGAGCA 59.243 37.500 0.00 0.00 0.00 4.26
292 329 7.576236 TGATCTTTGACTTCGAACAATCTTTC 58.424 34.615 0.00 0.00 0.00 2.62
304 341 6.926272 AGAGCGGTATATTGATCTTTGACTTC 59.074 38.462 0.00 0.00 0.00 3.01
322 360 4.141688 CCCTCCTTTCTTTATTAGAGCGGT 60.142 45.833 0.00 0.00 33.51 5.68
332 370 1.626825 CCACCGACCCTCCTTTCTTTA 59.373 52.381 0.00 0.00 0.00 1.85
333 371 0.400594 CCACCGACCCTCCTTTCTTT 59.599 55.000 0.00 0.00 0.00 2.52
374 412 1.919600 GCCCATCAGCCTCTTCACCT 61.920 60.000 0.00 0.00 0.00 4.00
386 424 0.321564 CGAGTTGGTCTTGCCCATCA 60.322 55.000 0.00 0.00 33.60 3.07
389 427 0.250295 CTTCGAGTTGGTCTTGCCCA 60.250 55.000 0.00 0.00 36.04 5.36
452 490 0.523072 AGTCATCATGCCACGCAAAC 59.477 50.000 0.00 0.00 43.62 2.93
477 515 3.804063 GCTTCCTCTCGTTCCTCACTTTT 60.804 47.826 0.00 0.00 0.00 2.27
478 516 2.289133 GCTTCCTCTCGTTCCTCACTTT 60.289 50.000 0.00 0.00 0.00 2.66
487 525 0.173708 CCTTAGCGCTTCCTCTCGTT 59.826 55.000 18.68 0.00 0.00 3.85
511 549 8.765488 TCCAAATATATCTTCATTTGCTCCAA 57.235 30.769 3.94 0.00 39.65 3.53
512 550 7.040201 GCTCCAAATATATCTTCATTTGCTCCA 60.040 37.037 3.94 0.00 39.65 3.86
545 584 2.026822 TCCTTCATGTCAAGCTTCCTCC 60.027 50.000 0.00 0.00 0.00 4.30
548 587 2.290577 ACCTCCTTCATGTCAAGCTTCC 60.291 50.000 0.00 0.00 0.00 3.46
585 624 2.965831 TGCGGCCTTCTCTATATTGAGT 59.034 45.455 12.92 0.00 35.68 3.41
589 628 4.929808 CGTTTATGCGGCCTTCTCTATATT 59.070 41.667 0.00 0.00 0.00 1.28
591 630 3.319972 ACGTTTATGCGGCCTTCTCTATA 59.680 43.478 0.00 0.00 35.98 1.31
594 633 0.249398 ACGTTTATGCGGCCTTCTCT 59.751 50.000 0.00 0.00 35.98 3.10
607 646 2.159894 CGATCGCAAGCTTTCACGTTTA 60.160 45.455 0.26 0.00 37.18 2.01
613 652 1.361668 GCCTCGATCGCAAGCTTTCA 61.362 55.000 11.09 0.00 37.18 2.69
614 653 1.349973 GCCTCGATCGCAAGCTTTC 59.650 57.895 11.09 0.00 37.18 2.62
658 697 5.687730 CGATCATAATTGCTAGACGTCACTT 59.312 40.000 19.50 0.00 0.00 3.16
661 700 5.183014 ACGATCATAATTGCTAGACGTCA 57.817 39.130 19.50 2.84 0.00 4.35
662 701 6.520447 GTCTACGATCATAATTGCTAGACGTC 59.480 42.308 7.70 7.70 29.81 4.34
663 702 6.205076 AGTCTACGATCATAATTGCTAGACGT 59.795 38.462 0.00 0.00 36.40 4.34
664 703 6.604012 AGTCTACGATCATAATTGCTAGACG 58.396 40.000 0.00 0.00 36.40 4.18
665 704 8.076781 TCAAGTCTACGATCATAATTGCTAGAC 58.923 37.037 0.00 0.00 34.36 2.59
666 705 8.076781 GTCAAGTCTACGATCATAATTGCTAGA 58.923 37.037 0.00 0.00 0.00 2.43
680 719 3.818387 GACATGTTCGTCAAGTCTACGA 58.182 45.455 0.00 0.00 46.82 3.43
712 761 7.623999 ATCTATATCACTCAAGTCCATGGTT 57.376 36.000 12.58 0.00 0.00 3.67
738 787 9.984190 AGACCTCCGTTCTATCTAAATTTTATC 57.016 33.333 0.00 0.00 0.00 1.75
740 789 8.755977 ACAGACCTCCGTTCTATCTAAATTTTA 58.244 33.333 0.00 0.00 0.00 1.52
743 792 6.793505 ACAGACCTCCGTTCTATCTAAATT 57.206 37.500 0.00 0.00 0.00 1.82
744 793 6.793505 AACAGACCTCCGTTCTATCTAAAT 57.206 37.500 0.00 0.00 0.00 1.40
745 794 6.600882 AAACAGACCTCCGTTCTATCTAAA 57.399 37.500 0.00 0.00 0.00 1.85
746 795 6.320672 CCTAAACAGACCTCCGTTCTATCTAA 59.679 42.308 0.00 0.00 0.00 2.10
747 796 5.826737 CCTAAACAGACCTCCGTTCTATCTA 59.173 44.000 0.00 0.00 0.00 1.98
749 798 4.202131 CCCTAAACAGACCTCCGTTCTATC 60.202 50.000 0.00 0.00 0.00 2.08
751 800 3.094572 CCCTAAACAGACCTCCGTTCTA 58.905 50.000 0.00 0.00 0.00 2.10
753 802 1.066358 CCCCTAAACAGACCTCCGTTC 60.066 57.143 0.00 0.00 0.00 3.95
754 803 0.981943 CCCCTAAACAGACCTCCGTT 59.018 55.000 0.00 0.00 0.00 4.44
755 804 0.178912 ACCCCTAAACAGACCTCCGT 60.179 55.000 0.00 0.00 0.00 4.69
756 805 0.535797 GACCCCTAAACAGACCTCCG 59.464 60.000 0.00 0.00 0.00 4.63
757 806 1.652947 TGACCCCTAAACAGACCTCC 58.347 55.000 0.00 0.00 0.00 4.30
758 807 2.092914 CCATGACCCCTAAACAGACCTC 60.093 54.545 0.00 0.00 0.00 3.85
759 808 1.916181 CCATGACCCCTAAACAGACCT 59.084 52.381 0.00 0.00 0.00 3.85
761 810 2.572104 ACTCCATGACCCCTAAACAGAC 59.428 50.000 0.00 0.00 0.00 3.51
762 811 2.915869 ACTCCATGACCCCTAAACAGA 58.084 47.619 0.00 0.00 0.00 3.41
763 812 3.347216 CAACTCCATGACCCCTAAACAG 58.653 50.000 0.00 0.00 0.00 3.16
765 814 2.041216 ACCAACTCCATGACCCCTAAAC 59.959 50.000 0.00 0.00 0.00 2.01
766 815 2.041081 CACCAACTCCATGACCCCTAAA 59.959 50.000 0.00 0.00 0.00 1.85
767 816 1.633432 CACCAACTCCATGACCCCTAA 59.367 52.381 0.00 0.00 0.00 2.69
768 817 1.203376 TCACCAACTCCATGACCCCTA 60.203 52.381 0.00 0.00 0.00 3.53
770 819 0.625849 ATCACCAACTCCATGACCCC 59.374 55.000 0.00 0.00 0.00 4.95
771 820 2.493278 CAAATCACCAACTCCATGACCC 59.507 50.000 0.00 0.00 0.00 4.46
773 822 2.493278 CCCAAATCACCAACTCCATGAC 59.507 50.000 0.00 0.00 0.00 3.06
775 824 1.205417 GCCCAAATCACCAACTCCATG 59.795 52.381 0.00 0.00 0.00 3.66
777 826 0.541764 GGCCCAAATCACCAACTCCA 60.542 55.000 0.00 0.00 0.00 3.86
778 827 0.541764 TGGCCCAAATCACCAACTCC 60.542 55.000 0.00 0.00 0.00 3.85
779 828 0.603065 GTGGCCCAAATCACCAACTC 59.397 55.000 0.00 0.00 34.63 3.01
800 853 1.443702 GGAAATGTTTCGCGGTGGC 60.444 57.895 6.13 0.00 38.06 5.01
880 933 4.171103 GGGTGGGATTACGCGGCT 62.171 66.667 12.47 0.00 0.00 5.52
936 989 4.035102 GATCTATGGGGGCGGGCC 62.035 72.222 13.01 13.01 0.00 5.80
937 990 4.035102 GGATCTATGGGGGCGGGC 62.035 72.222 0.00 0.00 0.00 6.13
1183 1236 2.351157 GGCGGCTACGAGTAACGATAAT 60.351 50.000 0.00 0.00 45.77 1.28
1186 1239 1.099879 AGGCGGCTACGAGTAACGAT 61.100 55.000 11.03 0.00 45.77 3.73
1230 1283 4.000928 ACATGGGTGACTAGAAGATCCT 57.999 45.455 0.00 0.00 0.00 3.24
1266 1319 3.237268 TGAGTAAAAGTTGCCATGGGT 57.763 42.857 15.13 0.00 0.00 4.51
1270 1323 2.884639 ACGCTTGAGTAAAAGTTGCCAT 59.115 40.909 0.00 0.00 0.00 4.40
1361 1416 6.140110 CACCAAACATAAACTCGTTTACTGG 58.860 40.000 4.52 10.59 37.80 4.00
1369 1424 5.607119 AAGCTACACCAAACATAAACTCG 57.393 39.130 0.00 0.00 0.00 4.18
1388 1443 9.468532 GATCCTCCATTGAACAATTATTAAAGC 57.531 33.333 0.00 0.00 0.00 3.51
1470 1786 3.242608 ACACACAAAACGAACCAAGATCG 60.243 43.478 0.00 0.00 45.47 3.69
1723 2040 4.034858 ACATGCTCGCAGATCAAATTGTAG 59.965 41.667 0.00 0.00 35.82 2.74
1830 2147 5.159273 TGTAGAATGCAATCTGTGGTACA 57.841 39.130 14.73 7.34 0.00 2.90
2206 2523 3.980022 TGGATGGGGTAGATGATGCTTTA 59.020 43.478 0.00 0.00 0.00 1.85
2315 2632 5.596772 TCATGACTCGTCCATCCTAATTGTA 59.403 40.000 0.00 0.00 0.00 2.41
2319 2636 4.590647 ACATCATGACTCGTCCATCCTAAT 59.409 41.667 0.00 0.00 0.00 1.73
2347 2664 1.896220 TACAAAGCAGGCCACAGAAG 58.104 50.000 5.01 0.00 0.00 2.85
2529 2846 4.391830 GCCAACGATCTTGTATCAGTTCAA 59.608 41.667 0.00 0.00 0.00 2.69
2727 3044 8.495361 AAAACGCTTGTACAATATATGGTACA 57.505 30.769 23.70 23.70 45.79 2.90
2771 3088 2.224499 TGCTGGTATCAGAGCACACAAA 60.224 45.455 7.33 0.00 43.49 2.83
2837 3154 3.657398 TGGATTCTCACATTGCATCCT 57.343 42.857 0.00 0.00 35.37 3.24
2961 3278 0.107703 TCGAGGCCTAAATGTGCAGG 60.108 55.000 4.42 0.00 34.85 4.85
3036 3353 1.209383 CTCGTTCGCTTCCTCGTCA 59.791 57.895 0.00 0.00 0.00 4.35
3271 3588 4.980434 GCATTGCATTGCCAATCTTACTAG 59.020 41.667 20.34 0.00 36.60 2.57
3275 3592 3.787785 CAGCATTGCATTGCCAATCTTA 58.212 40.909 25.62 0.00 43.83 2.10
3491 3842 2.025887 CAGGAGAAAAGTAGGGGCATGT 60.026 50.000 0.00 0.00 0.00 3.21
3496 3847 3.838903 ACTACACAGGAGAAAAGTAGGGG 59.161 47.826 0.00 0.00 37.17 4.79
3566 3917 4.814294 AAGGCACGATCCGACGGC 62.814 66.667 9.66 0.00 37.61 5.68
3595 3946 1.229529 ACCCCTCTGGATCGTGGTT 60.230 57.895 0.00 0.00 38.00 3.67
3639 3995 3.885297 CACTTCAGATTGTGTCTTTGGGT 59.115 43.478 0.00 0.00 34.00 4.51
3696 4052 2.695666 ACGTAGCTATCACCTGCTGAAT 59.304 45.455 0.00 0.00 40.08 2.57
3726 4082 2.654749 TCTATCACCACTTGTCGCAG 57.345 50.000 0.00 0.00 0.00 5.18
3904 4495 5.294552 CCGCTTCCTCGATCTTAATTTTTCT 59.705 40.000 0.00 0.00 0.00 2.52
3905 4496 5.293569 TCCGCTTCCTCGATCTTAATTTTTC 59.706 40.000 0.00 0.00 0.00 2.29
3972 4566 6.294286 CCCGTTGCTTCCTAAATGTTTCTTTA 60.294 38.462 0.00 0.00 0.00 1.85
3973 4567 5.508994 CCCGTTGCTTCCTAAATGTTTCTTT 60.509 40.000 0.00 0.00 0.00 2.52
3976 4570 3.504520 TCCCGTTGCTTCCTAAATGTTTC 59.495 43.478 0.00 0.00 0.00 2.78
3977 4571 3.254903 GTCCCGTTGCTTCCTAAATGTTT 59.745 43.478 0.00 0.00 0.00 2.83
3980 4574 2.432444 TGTCCCGTTGCTTCCTAAATG 58.568 47.619 0.00 0.00 0.00 2.32
3981 4575 2.871096 TGTCCCGTTGCTTCCTAAAT 57.129 45.000 0.00 0.00 0.00 1.40
3984 4579 1.543871 GGTTTGTCCCGTTGCTTCCTA 60.544 52.381 0.00 0.00 0.00 2.94
3989 4584 2.193536 GCTGGTTTGTCCCGTTGCT 61.194 57.895 0.00 0.00 34.77 3.91
4031 4626 3.781770 ATAGTGCTCGAGCGGCTGC 62.782 63.158 31.52 20.22 45.83 5.25
4053 4653 1.675483 AGCAATGTCAAAGCACGACAA 59.325 42.857 6.91 0.00 45.91 3.18
4058 4658 1.881973 TCCAGAGCAATGTCAAAGCAC 59.118 47.619 3.15 0.00 0.00 4.40
4065 4665 0.251354 TGCCTCTCCAGAGCAATGTC 59.749 55.000 0.00 0.00 40.75 3.06
4067 4667 1.830279 TTTGCCTCTCCAGAGCAATG 58.170 50.000 11.69 0.00 40.75 2.82
4079 4679 4.725790 AATGCTAGTTTCCATTTGCCTC 57.274 40.909 0.00 0.00 0.00 4.70
4171 4771 3.481453 ACTTTTGACAAGGCCTCTCTTC 58.519 45.455 5.23 0.21 0.00 2.87
4232 4839 4.496507 GGAAAATCATTCTACAAGCGAGGC 60.497 45.833 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.