Multiple sequence alignment - TraesCS4A01G209800

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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 TraesCS4A01G209800 chr4A 100.000 3425 0 0 1 3425 503618851 503615427 0.000000e+00 6325.0
1 TraesCS4A01G209800 chr4A 90.728 151 14 0 3274 3424 83353127 83352977 5.800000e-48 202.0
2 TraesCS4A01G209800 chr4D 95.561 2568 89 9 2 2560 91225858 91223307 0.000000e+00 4087.0
3 TraesCS4A01G209800 chr4D 96.600 647 18 3 2634 3276 91223313 91222667 0.000000e+00 1070.0
4 TraesCS4A01G209800 chr4D 96.026 151 6 0 3274 3424 97908319 97908469 2.640000e-61 246.0
5 TraesCS4A01G209800 chr4B 95.087 2585 101 8 1 2570 128027369 128024796 0.000000e+00 4047.0
6 TraesCS4A01G209800 chr4B 94.856 661 24 1 2616 3276 128024716 128024066 0.000000e+00 1024.0
7 TraesCS4A01G209800 chr4B 96.026 151 6 0 3274 3424 137737650 137737800 2.640000e-61 246.0
8 TraesCS4A01G209800 chr7B 98.026 152 3 0 3274 3425 450796148 450795997 7.290000e-67 265.0
9 TraesCS4A01G209800 chr7A 98.026 152 3 0 3274 3425 714591401 714591250 7.290000e-67 265.0
10 TraesCS4A01G209800 chr6B 98.000 150 3 0 3274 3423 623718200 623718349 9.430000e-66 261.0
11 TraesCS4A01G209800 chr5A 97.368 152 4 0 3274 3425 427317573 427317724 3.390000e-65 259.0
12 TraesCS4A01G209800 chr6D 84.706 85 12 1 2552 2635 13767623 13767539 2.190000e-12 84.2
13 TraesCS4A01G209800 chr2A 82.222 90 15 1 2547 2635 327213101 327213012 3.670000e-10 76.8
14 TraesCS4A01G209800 chr2A 81.319 91 14 3 2547 2635 327415056 327415145 1.710000e-08 71.3
15 TraesCS4A01G209800 chr2B 82.278 79 14 0 2557 2635 617734409 617734331 6.130000e-08 69.4
16 TraesCS4A01G209800 chr3B 81.707 82 9 6 2557 2635 173372777 173372855 2.850000e-06 63.9
17 TraesCS4A01G209800 chr2D 100.000 34 0 0 2603 2636 568755156 568755189 2.850000e-06 63.9
18 TraesCS4A01G209800 chr1A 88.889 45 4 1 2599 2643 96473382 96473425 2.000000e-03 54.7
19 TraesCS4A01G209800 chr6A 100.000 28 0 0 2557 2584 428427228 428427255 6.000000e-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 TraesCS4A01G209800 chr4A 503615427 503618851 3424 True 6325.0 6325 100.0000 1 3425 1 chr4A.!!$R2 3424
1 TraesCS4A01G209800 chr4D 91222667 91225858 3191 True 2578.5 4087 96.0805 2 3276 2 chr4D.!!$R1 3274
2 TraesCS4A01G209800 chr4B 128024066 128027369 3303 True 2535.5 4047 94.9715 1 3276 2 chr4B.!!$R1 3275

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
539 556 0.167908 CGCATTTTGTTGCCGCTCTA 59.832 50.0 0.00 0.00 39.52 2.43 F
1638 1661 0.442310 GCGATACACATGTGCACGTT 59.558 50.0 25.68 8.44 0.00 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1704 1727 0.392863 TGAGGTGGAATGACATGCCG 60.393 55.0 8.01 0.0 0.0 5.69 R
3300 3362 0.677731 CGAAGGAAAGGAGCATGCCA 60.678 55.0 15.66 0.0 0.0 4.92 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 49 4.313020 AGGCAGGAGAAACATTCAGATT 57.687 40.909 0.00 0.00 0.00 2.40
49 50 4.268359 AGGCAGGAGAAACATTCAGATTC 58.732 43.478 0.00 0.00 0.00 2.52
196 197 9.853555 CTATTGTCTACATCTCATAACTCCATC 57.146 37.037 0.00 0.00 0.00 3.51
276 291 8.664669 ATTGGTACCAAATAAAGAATCCAGTT 57.335 30.769 30.31 5.93 39.55 3.16
283 298 6.437162 CCAAATAAAGAATCCAGTTTGGGAGA 59.563 38.462 6.76 0.00 40.98 3.71
293 308 2.031870 AGTTTGGGAGAAAGTTGGTGC 58.968 47.619 0.00 0.00 0.00 5.01
434 449 4.401202 TGTATCAGACTGAATGAAGCGGTA 59.599 41.667 9.70 0.00 0.00 4.02
539 556 0.167908 CGCATTTTGTTGCCGCTCTA 59.832 50.000 0.00 0.00 39.52 2.43
574 591 1.810755 CATATGTGCAGGCCATAGCAG 59.189 52.381 16.51 2.85 42.14 4.24
688 705 3.190118 CAGTCCCTTCTGTTTCATTCTGC 59.810 47.826 0.00 0.00 0.00 4.26
724 741 1.879380 ACACATTGCACACGTATGCTT 59.121 42.857 20.95 4.61 46.28 3.91
860 877 5.178096 TCCAAGATCAGGACAATTTAGCA 57.822 39.130 3.01 0.00 0.00 3.49
867 884 4.271661 TCAGGACAATTTAGCATGCATCA 58.728 39.130 21.98 2.42 0.00 3.07
907 930 4.214971 CCACACATTCTCTTTTCTCCACTG 59.785 45.833 0.00 0.00 0.00 3.66
940 963 1.026718 CCTCCGCCATGTGGTTTCTC 61.027 60.000 0.35 0.00 37.57 2.87
951 974 5.520288 CCATGTGGTTTCTCTATAAGACACG 59.480 44.000 0.00 0.00 35.84 4.49
954 977 4.863131 GTGGTTTCTCTATAAGACACGGTG 59.137 45.833 6.58 6.58 35.84 4.94
961 984 1.267121 ATAAGACACGGTGTGAGGCT 58.733 50.000 20.06 6.44 36.96 4.58
1059 1082 0.615331 TCCCCACACATGAAGAGAGC 59.385 55.000 0.00 0.00 0.00 4.09
1061 1084 1.678123 CCCCACACATGAAGAGAGCAG 60.678 57.143 0.00 0.00 0.00 4.24
1560 1583 5.354767 CAGCAGATTATACAAGAGCTGTCA 58.645 41.667 0.00 0.00 42.08 3.58
1638 1661 0.442310 GCGATACACATGTGCACGTT 59.558 50.000 25.68 8.44 0.00 3.99
1678 1701 2.124570 GCATCCAGTGGCCATCGT 60.125 61.111 9.72 0.00 0.00 3.73
1729 1752 2.264480 CATTCCACCTCACGGCGA 59.736 61.111 16.62 0.00 0.00 5.54
1797 1820 3.816524 CGGCTCTCGGAGTTCGCT 61.817 66.667 4.69 0.00 39.05 4.93
1815 1838 0.247736 CTGACTCCTTGAACCTCCCG 59.752 60.000 0.00 0.00 0.00 5.14
1829 1852 0.108615 CTCCCGTTCCAGTACAGCTG 60.109 60.000 13.48 13.48 44.63 4.24
1842 1865 5.473931 CAGTACAGCTGTCTCTGTTTACAT 58.526 41.667 28.66 9.59 44.26 2.29
1884 1907 6.601332 TGAATTCTCCAAGAACTGTAAAGGT 58.399 36.000 7.05 0.00 37.00 3.50
1993 2016 4.214545 TGTTACAGCCAAAGTTAATGGTCG 59.785 41.667 0.00 0.00 40.23 4.79
2030 2053 3.178865 TGGTTAGAATCGGAAAGGAGGT 58.821 45.455 0.00 0.00 0.00 3.85
2109 2132 1.668151 GGTGTTCGAGTCACTGGCC 60.668 63.158 17.71 0.00 36.25 5.36
2184 2207 1.143329 TGGTGGGGCCAAGGATACAA 61.143 55.000 4.39 0.00 45.94 2.41
2209 2232 0.043485 TGTGGGGCAGTATGGGTCTA 59.957 55.000 0.00 0.00 35.86 2.59
2250 2273 2.156917 CCTCGGGTTTTGGAAAGGTAC 58.843 52.381 0.00 0.00 0.00 3.34
2468 2491 3.273919 AGCGTTGCAGTGAAGAATTTC 57.726 42.857 0.00 0.00 0.00 2.17
2522 2545 6.261826 CCTTATTTGGTTTCTATCTCAGCCTG 59.738 42.308 0.00 0.00 0.00 4.85
2555 2578 6.098266 TGCTCTTGTTGGCTTCTCATATACTA 59.902 38.462 0.00 0.00 0.00 1.82
2557 2580 7.661536 TCTTGTTGGCTTCTCATATACTACT 57.338 36.000 0.00 0.00 0.00 2.57
2558 2581 7.717568 TCTTGTTGGCTTCTCATATACTACTC 58.282 38.462 0.00 0.00 0.00 2.59
2560 2583 5.009710 TGTTGGCTTCTCATATACTACTCCG 59.990 44.000 0.00 0.00 0.00 4.63
2561 2584 4.726583 TGGCTTCTCATATACTACTCCGT 58.273 43.478 0.00 0.00 0.00 4.69
2562 2585 4.760715 TGGCTTCTCATATACTACTCCGTC 59.239 45.833 0.00 0.00 0.00 4.79
2563 2586 5.005094 GGCTTCTCATATACTACTCCGTCT 58.995 45.833 0.00 0.00 0.00 4.18
2565 2588 5.701750 GCTTCTCATATACTACTCCGTCTCA 59.298 44.000 0.00 0.00 0.00 3.27
2566 2589 6.373216 GCTTCTCATATACTACTCCGTCTCAT 59.627 42.308 0.00 0.00 0.00 2.90
2569 2592 9.961264 TTCTCATATACTACTCCGTCTCATAAT 57.039 33.333 0.00 0.00 0.00 1.28
2570 2593 9.384764 TCTCATATACTACTCCGTCTCATAATG 57.615 37.037 0.00 0.00 0.00 1.90
2577 2600 7.877003 ACTACTCCGTCTCATAATGTAAGATG 58.123 38.462 0.00 0.00 0.00 2.90
2578 2601 5.533482 ACTCCGTCTCATAATGTAAGATGC 58.467 41.667 0.00 0.00 0.00 3.91
2580 2603 6.161855 TCCGTCTCATAATGTAAGATGCTT 57.838 37.500 0.00 0.00 0.00 3.91
2581 2604 6.582636 TCCGTCTCATAATGTAAGATGCTTT 58.417 36.000 0.00 0.00 0.00 3.51
2582 2605 7.047891 TCCGTCTCATAATGTAAGATGCTTTT 58.952 34.615 0.00 0.00 0.00 2.27
2584 2607 7.852945 CCGTCTCATAATGTAAGATGCTTTTTC 59.147 37.037 0.00 0.00 0.00 2.29
2585 2608 8.390354 CGTCTCATAATGTAAGATGCTTTTTCA 58.610 33.333 0.00 0.00 0.00 2.69
2684 2742 4.689612 AGTCTCAAGTAGCAAGTGGAAA 57.310 40.909 0.00 0.00 0.00 3.13
2854 2913 4.244862 CCAAGTTGTATTGAAACCATGCC 58.755 43.478 1.45 0.00 31.55 4.40
2869 2928 0.034477 ATGCCTTTTAGGTCACCCCG 60.034 55.000 0.00 0.00 37.80 5.73
3024 3084 1.710816 TTTGGTCCATTTGTGGGGTC 58.289 50.000 0.00 0.00 0.00 4.46
3036 3096 0.984230 GTGGGGTCAGGACTGATTGA 59.016 55.000 5.19 0.00 42.18 2.57
3042 3102 3.769844 GGGTCAGGACTGATTGAAGACTA 59.230 47.826 5.19 0.00 42.18 2.59
3043 3103 4.142049 GGGTCAGGACTGATTGAAGACTAG 60.142 50.000 5.19 0.00 42.18 2.57
3140 3202 7.665559 AGAGACATTTTGTATTTTGTAGGAGCA 59.334 33.333 0.00 0.00 0.00 4.26
3176 3238 3.340928 CTGCTTTCAGTCACCATCATGA 58.659 45.455 0.00 0.00 35.61 3.07
3276 3338 3.634448 ACTCCCATCTGATCACTTACTCG 59.366 47.826 0.00 0.00 0.00 4.18
3277 3339 3.632333 TCCCATCTGATCACTTACTCGT 58.368 45.455 0.00 0.00 0.00 4.18
3278 3340 3.632604 TCCCATCTGATCACTTACTCGTC 59.367 47.826 0.00 0.00 0.00 4.20
3279 3341 3.243569 CCCATCTGATCACTTACTCGTCC 60.244 52.174 0.00 0.00 0.00 4.79
3280 3342 3.634448 CCATCTGATCACTTACTCGTCCT 59.366 47.826 0.00 0.00 0.00 3.85
3281 3343 4.098654 CCATCTGATCACTTACTCGTCCTT 59.901 45.833 0.00 0.00 0.00 3.36
3282 3344 4.966965 TCTGATCACTTACTCGTCCTTC 57.033 45.455 0.00 0.00 0.00 3.46
3283 3345 4.590918 TCTGATCACTTACTCGTCCTTCT 58.409 43.478 0.00 0.00 0.00 2.85
3284 3346 4.636648 TCTGATCACTTACTCGTCCTTCTC 59.363 45.833 0.00 0.00 0.00 2.87
3285 3347 4.332828 TGATCACTTACTCGTCCTTCTCA 58.667 43.478 0.00 0.00 0.00 3.27
3286 3348 4.396478 TGATCACTTACTCGTCCTTCTCAG 59.604 45.833 0.00 0.00 0.00 3.35
3287 3349 3.082548 TCACTTACTCGTCCTTCTCAGG 58.917 50.000 0.00 0.00 42.50 3.86
3288 3350 2.820787 CACTTACTCGTCCTTCTCAGGT 59.179 50.000 0.00 0.00 41.69 4.00
3289 3351 2.820787 ACTTACTCGTCCTTCTCAGGTG 59.179 50.000 0.00 0.00 41.69 4.00
3290 3352 1.174783 TACTCGTCCTTCTCAGGTGC 58.825 55.000 0.00 0.00 41.69 5.01
3291 3353 1.153939 CTCGTCCTTCTCAGGTGCG 60.154 63.158 0.00 0.00 41.69 5.34
3292 3354 1.867919 CTCGTCCTTCTCAGGTGCGT 61.868 60.000 7.48 0.00 41.69 5.24
3293 3355 1.444553 CGTCCTTCTCAGGTGCGTC 60.445 63.158 0.00 0.00 41.69 5.19
3294 3356 1.444553 GTCCTTCTCAGGTGCGTCG 60.445 63.158 0.00 0.00 41.69 5.12
3295 3357 2.125912 CCTTCTCAGGTGCGTCGG 60.126 66.667 0.00 0.00 35.06 4.79
3296 3358 2.125912 CTTCTCAGGTGCGTCGGG 60.126 66.667 0.00 0.00 0.00 5.14
3297 3359 3.649277 CTTCTCAGGTGCGTCGGGG 62.649 68.421 0.00 0.00 0.00 5.73
3313 3375 2.363406 GGGCTGGCATGCTCCTTT 60.363 61.111 18.92 0.00 0.00 3.11
3314 3376 2.421399 GGGCTGGCATGCTCCTTTC 61.421 63.158 18.92 0.00 0.00 2.62
3315 3377 2.421399 GGCTGGCATGCTCCTTTCC 61.421 63.158 18.92 6.90 0.00 3.13
3316 3378 1.379576 GCTGGCATGCTCCTTTCCT 60.380 57.895 18.92 0.00 0.00 3.36
3317 3379 0.969409 GCTGGCATGCTCCTTTCCTT 60.969 55.000 18.92 0.00 0.00 3.36
3318 3380 1.101331 CTGGCATGCTCCTTTCCTTC 58.899 55.000 18.92 0.00 0.00 3.46
3319 3381 0.677731 TGGCATGCTCCTTTCCTTCG 60.678 55.000 18.92 0.00 0.00 3.79
3320 3382 1.379642 GGCATGCTCCTTTCCTTCGG 61.380 60.000 18.92 0.00 0.00 4.30
3321 3383 1.997928 GCATGCTCCTTTCCTTCGGC 61.998 60.000 11.37 0.00 0.00 5.54
3322 3384 1.450312 ATGCTCCTTTCCTTCGGCG 60.450 57.895 0.00 0.00 0.00 6.46
3323 3385 3.500642 GCTCCTTTCCTTCGGCGC 61.501 66.667 0.00 0.00 0.00 6.53
3324 3386 2.266055 CTCCTTTCCTTCGGCGCT 59.734 61.111 7.64 0.00 0.00 5.92
3325 3387 2.047274 TCCTTTCCTTCGGCGCTG 60.047 61.111 10.86 10.86 0.00 5.18
3326 3388 2.358737 CCTTTCCTTCGGCGCTGT 60.359 61.111 17.37 0.00 0.00 4.40
3327 3389 2.391389 CCTTTCCTTCGGCGCTGTC 61.391 63.158 17.37 0.00 0.00 3.51
3328 3390 1.374758 CTTTCCTTCGGCGCTGTCT 60.375 57.895 17.37 0.00 0.00 3.41
3329 3391 1.355066 CTTTCCTTCGGCGCTGTCTC 61.355 60.000 17.37 0.00 0.00 3.36
3330 3392 3.626680 TTCCTTCGGCGCTGTCTCG 62.627 63.158 17.37 6.37 0.00 4.04
3331 3393 4.116328 CCTTCGGCGCTGTCTCGA 62.116 66.667 17.37 9.03 0.00 4.04
3332 3394 2.103143 CTTCGGCGCTGTCTCGAT 59.897 61.111 17.37 0.00 32.80 3.59
3333 3395 1.941734 CTTCGGCGCTGTCTCGATC 60.942 63.158 17.37 0.00 32.80 3.69
3334 3396 3.411418 TTCGGCGCTGTCTCGATCC 62.411 63.158 17.37 0.00 32.80 3.36
3336 3398 4.933064 GGCGCTGTCTCGATCCGG 62.933 72.222 7.64 0.00 0.00 5.14
3338 3400 3.893763 CGCTGTCTCGATCCGGCT 61.894 66.667 0.00 0.00 0.00 5.52
3339 3401 2.496817 GCTGTCTCGATCCGGCTT 59.503 61.111 0.00 0.00 0.00 4.35
3340 3402 1.880340 GCTGTCTCGATCCGGCTTG 60.880 63.158 0.00 0.00 0.00 4.01
3341 3403 1.880340 CTGTCTCGATCCGGCTTGC 60.880 63.158 0.00 0.00 0.00 4.01
3342 3404 2.586357 GTCTCGATCCGGCTTGCC 60.586 66.667 0.00 0.75 0.00 4.52
3343 3405 2.759973 TCTCGATCCGGCTTGCCT 60.760 61.111 10.12 0.00 0.00 4.75
3344 3406 2.279784 CTCGATCCGGCTTGCCTC 60.280 66.667 10.12 0.00 0.00 4.70
3345 3407 2.759973 TCGATCCGGCTTGCCTCT 60.760 61.111 10.12 0.00 0.00 3.69
3346 3408 2.587194 CGATCCGGCTTGCCTCTG 60.587 66.667 10.12 0.00 0.00 3.35
3347 3409 2.586792 GATCCGGCTTGCCTCTGT 59.413 61.111 10.12 0.00 0.00 3.41
3348 3410 1.817099 GATCCGGCTTGCCTCTGTG 60.817 63.158 10.12 0.00 0.00 3.66
3349 3411 3.984193 ATCCGGCTTGCCTCTGTGC 62.984 63.158 10.12 0.00 0.00 4.57
3394 3456 3.816524 CTTCTCCGGCGAGCGACT 61.817 66.667 9.30 0.00 35.94 4.18
3395 3457 4.116328 TTCTCCGGCGAGCGACTG 62.116 66.667 9.30 0.00 35.94 3.51
3397 3459 4.421479 CTCCGGCGAGCGACTGTT 62.421 66.667 9.30 0.00 0.00 3.16
3398 3460 4.415332 TCCGGCGAGCGACTGTTC 62.415 66.667 9.30 0.00 0.00 3.18
3400 3462 4.717629 CGGCGAGCGACTGTTCCA 62.718 66.667 0.00 0.00 0.00 3.53
3401 3463 2.811317 GGCGAGCGACTGTTCCAG 60.811 66.667 0.00 0.00 37.52 3.86
3402 3464 3.482783 GCGAGCGACTGTTCCAGC 61.483 66.667 0.00 0.00 34.37 4.85
3403 3465 2.259818 CGAGCGACTGTTCCAGCT 59.740 61.111 0.00 1.76 43.33 4.24
3405 3467 1.803519 GAGCGACTGTTCCAGCTCG 60.804 63.158 10.84 10.02 45.08 5.03
3406 3468 2.811317 GCGACTGTTCCAGCTCGG 60.811 66.667 13.79 0.00 36.41 4.63
3407 3469 2.125912 CGACTGTTCCAGCTCGGG 60.126 66.667 2.86 0.00 34.25 5.14
3408 3470 2.266055 GACTGTTCCAGCTCGGGG 59.734 66.667 2.86 0.00 34.37 5.73
3409 3471 2.203788 ACTGTTCCAGCTCGGGGA 60.204 61.111 2.86 0.00 34.37 4.81
3410 3472 2.232298 GACTGTTCCAGCTCGGGGAG 62.232 65.000 2.86 0.00 35.46 4.30
3411 3473 3.003173 TGTTCCAGCTCGGGGAGG 61.003 66.667 2.86 0.00 35.46 4.30
3412 3474 4.475135 GTTCCAGCTCGGGGAGGC 62.475 72.222 2.86 0.00 35.46 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 1.984570 AGGCTGCCTCTTGCTACGA 60.985 57.895 17.22 0.00 42.00 3.43
49 50 1.812922 CAGGCTGCCTCTTGCTACG 60.813 63.158 20.49 0.41 42.00 3.51
196 197 7.864379 GGTGATACAAATTATTGGCAGATTCTG 59.136 37.037 9.40 9.40 41.01 3.02
257 272 6.081356 TCCCAAACTGGATTCTTTATTTGGT 58.919 36.000 11.47 0.00 42.91 3.67
258 273 6.437162 TCTCCCAAACTGGATTCTTTATTTGG 59.563 38.462 6.58 6.58 40.96 3.28
276 291 0.260230 TGGCACCAACTTTCTCCCAA 59.740 50.000 0.00 0.00 0.00 4.12
283 298 7.602265 GTGTAATAAATTCATGGCACCAACTTT 59.398 33.333 0.00 0.00 0.00 2.66
323 338 9.619316 GTTAATTTTGTCATGCTAATGTGTGTA 57.381 29.630 0.00 0.00 35.15 2.90
339 354 5.122519 CAGCCCAAACCAAGTTAATTTTGT 58.877 37.500 0.00 0.00 0.00 2.83
574 591 2.033299 TGTGCTGTTGCTACTTCAAAGC 59.967 45.455 0.00 0.41 40.48 3.51
688 705 0.037975 GTGTCATTTTGCTGGCCTGG 60.038 55.000 12.06 1.66 0.00 4.45
860 877 1.399714 CACCTTCATGGCTGATGCAT 58.600 50.000 0.00 0.00 41.91 3.96
867 884 2.616458 GGACCCCACCTTCATGGCT 61.616 63.158 0.00 0.00 38.55 4.75
907 930 0.250081 CGGAGGGGCAAGAGATTAGC 60.250 60.000 0.00 0.00 0.00 3.09
940 963 2.427453 AGCCTCACACCGTGTCTTATAG 59.573 50.000 0.00 0.00 34.79 1.31
954 977 1.339055 TGCCTTGATGTGTAGCCTCAC 60.339 52.381 2.46 2.46 38.63 3.51
961 984 6.112734 ACGATAAGAATTGCCTTGATGTGTA 58.887 36.000 0.00 0.00 0.00 2.90
1059 1082 3.152341 AGGAGACCACATGAAAAAGCTG 58.848 45.455 0.00 0.00 0.00 4.24
1061 1084 3.149196 TGAGGAGACCACATGAAAAAGC 58.851 45.455 0.00 0.00 0.00 3.51
1524 1547 3.092192 CTGCTGCGCCGACATTCTG 62.092 63.158 4.18 0.00 0.00 3.02
1535 1558 3.183976 CAGCTCTTGTATAATCTGCTGCG 59.816 47.826 0.00 0.00 39.60 5.18
1539 1562 4.509600 GGTGACAGCTCTTGTATAATCTGC 59.490 45.833 0.00 0.00 41.05 4.26
1560 1583 1.226831 CGCAAACTTGGCAAACGGT 60.227 52.632 0.00 0.00 0.00 4.83
1638 1661 0.948623 CGCCAATGTTCAGGTCGACA 60.949 55.000 18.91 0.00 0.00 4.35
1678 1701 1.278985 ACGGGCAAGATCTGACATGAA 59.721 47.619 0.00 0.00 32.90 2.57
1704 1727 0.392863 TGAGGTGGAATGACATGCCG 60.393 55.000 8.01 0.00 0.00 5.69
1797 1820 0.471211 ACGGGAGGTTCAAGGAGTCA 60.471 55.000 0.00 0.00 0.00 3.41
1829 1852 7.489757 GGTCTTCATCACTATGTAAACAGAGAC 59.510 40.741 11.47 0.00 37.37 3.36
1842 1865 4.824479 TTCATGCAGGTCTTCATCACTA 57.176 40.909 0.00 0.00 0.00 2.74
1884 1907 1.476488 TCGCATGAGAAGATCACCGAA 59.524 47.619 0.00 0.00 41.91 4.30
1993 2016 1.465794 ACCAGCTCCTCTTCTACGAC 58.534 55.000 0.00 0.00 0.00 4.34
2030 2053 3.689872 AGGAGGCCTTACATAGAGACA 57.310 47.619 6.77 0.00 0.00 3.41
2109 2132 0.602638 TACCACCAACGAAGCAGCTG 60.603 55.000 10.11 10.11 0.00 4.24
2184 2207 1.004745 CCATACTGCCCCACAAAGTCT 59.995 52.381 0.00 0.00 0.00 3.24
2209 2232 1.696336 AGCAGTGACCTCAACTGTCAT 59.304 47.619 0.00 0.00 43.98 3.06
2234 2257 1.250328 CCCGTACCTTTCCAAAACCC 58.750 55.000 0.00 0.00 0.00 4.11
2250 2273 2.046892 CTCAGGTCACAAGCCCCG 60.047 66.667 0.00 0.00 0.00 5.73
2374 2397 2.421388 CCCAAACAGACACAGAGGTCAA 60.421 50.000 0.00 0.00 40.29 3.18
2468 2491 5.406175 TCACTAACCAAATACGTTTTCCTCG 59.594 40.000 0.00 0.00 0.00 4.63
2522 2545 1.803555 GCCAACAAGAGCAAGAGAGAC 59.196 52.381 0.00 0.00 0.00 3.36
2557 2580 5.791336 AGCATCTTACATTATGAGACGGA 57.209 39.130 0.00 0.00 0.00 4.69
2558 2581 6.851222 AAAGCATCTTACATTATGAGACGG 57.149 37.500 0.00 0.00 0.00 4.79
2562 2585 9.017669 GCTTGAAAAAGCATCTTACATTATGAG 57.982 33.333 0.00 0.00 44.85 2.90
2563 2586 8.915871 GCTTGAAAAAGCATCTTACATTATGA 57.084 30.769 0.00 0.00 44.85 2.15
2603 2626 4.155280 CCGTCCCATAATGAAAGACGTTTT 59.845 41.667 9.63 0.00 46.62 2.43
2604 2627 3.687698 CCGTCCCATAATGAAAGACGTTT 59.312 43.478 9.63 0.00 46.62 3.60
2605 2628 3.055675 TCCGTCCCATAATGAAAGACGTT 60.056 43.478 9.63 0.00 46.62 3.99
2608 2631 3.467803 CCTCCGTCCCATAATGAAAGAC 58.532 50.000 0.00 0.00 0.00 3.01
2610 2633 2.438021 TCCCTCCGTCCCATAATGAAAG 59.562 50.000 0.00 0.00 0.00 2.62
2611 2634 2.438021 CTCCCTCCGTCCCATAATGAAA 59.562 50.000 0.00 0.00 0.00 2.69
2612 2635 2.047061 CTCCCTCCGTCCCATAATGAA 58.953 52.381 0.00 0.00 0.00 2.57
2614 2637 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
2618 2676 0.861155 AGATACTCCCTCCGTCCCAT 59.139 55.000 0.00 0.00 0.00 4.00
2746 2804 6.634805 TGGTTCATAAGAGCAAAACAAACAA 58.365 32.000 0.00 0.00 0.00 2.83
2783 2841 1.342819 CTCCCTCCCTCTCTATTTGCG 59.657 57.143 0.00 0.00 0.00 4.85
2927 2987 7.362662 TGATGTTTTCTCTATTTTGTGCAGAC 58.637 34.615 0.00 0.00 0.00 3.51
3024 3084 4.159321 TGAGCTAGTCTTCAATCAGTCCTG 59.841 45.833 0.00 0.00 0.00 3.86
3036 3096 9.177608 TGTGCATTTTAAATATGAGCTAGTCTT 57.822 29.630 11.94 0.00 0.00 3.01
3042 3102 8.036575 ACATTGTGTGCATTTTAAATATGAGCT 58.963 29.630 11.94 0.00 0.00 4.09
3043 3103 8.188531 ACATTGTGTGCATTTTAAATATGAGC 57.811 30.769 11.94 0.00 0.00 4.26
3140 3202 2.645838 AGCAGTTCACACAGTTGGAT 57.354 45.000 0.00 0.00 0.00 3.41
3276 3338 1.444553 CGACGCACCTGAGAAGGAC 60.445 63.158 0.00 0.00 0.00 3.85
3277 3339 2.636412 CCGACGCACCTGAGAAGGA 61.636 63.158 0.00 0.00 0.00 3.36
3278 3340 2.125912 CCGACGCACCTGAGAAGG 60.126 66.667 0.00 0.00 0.00 3.46
3279 3341 2.125912 CCCGACGCACCTGAGAAG 60.126 66.667 0.00 0.00 0.00 2.85
3280 3342 3.691342 CCCCGACGCACCTGAGAA 61.691 66.667 0.00 0.00 0.00 2.87
3295 3357 3.970746 AAAGGAGCATGCCAGCCCC 62.971 63.158 15.66 8.25 34.23 5.80
3296 3358 2.363406 AAAGGAGCATGCCAGCCC 60.363 61.111 15.66 10.85 34.23 5.19
3297 3359 2.421399 GGAAAGGAGCATGCCAGCC 61.421 63.158 15.66 13.81 34.23 4.85
3298 3360 0.969409 AAGGAAAGGAGCATGCCAGC 60.969 55.000 15.66 3.98 0.00 4.85
3299 3361 1.101331 GAAGGAAAGGAGCATGCCAG 58.899 55.000 15.66 0.00 0.00 4.85
3300 3362 0.677731 CGAAGGAAAGGAGCATGCCA 60.678 55.000 15.66 0.00 0.00 4.92
3301 3363 2.101700 CGAAGGAAAGGAGCATGCC 58.898 57.895 15.66 5.80 0.00 4.40
3315 3377 1.941734 GATCGAGACAGCGCCGAAG 60.942 63.158 2.29 0.00 35.87 3.79
3316 3378 2.102357 GATCGAGACAGCGCCGAA 59.898 61.111 2.29 0.00 35.87 4.30
3317 3379 3.889044 GGATCGAGACAGCGCCGA 61.889 66.667 2.29 5.86 36.72 5.54
3319 3381 4.933064 CCGGATCGAGACAGCGCC 62.933 72.222 2.29 0.00 0.00 6.53
3321 3383 3.417275 AAGCCGGATCGAGACAGCG 62.417 63.158 5.05 0.00 0.00 5.18
3322 3384 1.880340 CAAGCCGGATCGAGACAGC 60.880 63.158 5.05 0.00 0.00 4.40
3323 3385 1.880340 GCAAGCCGGATCGAGACAG 60.880 63.158 5.05 0.00 0.00 3.51
3324 3386 2.184322 GCAAGCCGGATCGAGACA 59.816 61.111 5.05 0.00 0.00 3.41
3325 3387 2.586357 GGCAAGCCGGATCGAGAC 60.586 66.667 5.05 0.00 0.00 3.36
3326 3388 2.759973 AGGCAAGCCGGATCGAGA 60.760 61.111 5.05 0.00 41.95 4.04
3327 3389 2.279784 GAGGCAAGCCGGATCGAG 60.280 66.667 5.05 0.00 41.95 4.04
3328 3390 2.759973 AGAGGCAAGCCGGATCGA 60.760 61.111 5.05 0.00 41.95 3.59
3329 3391 2.587194 CAGAGGCAAGCCGGATCG 60.587 66.667 5.05 0.00 41.95 3.69
3330 3392 1.817099 CACAGAGGCAAGCCGGATC 60.817 63.158 5.05 0.00 41.95 3.36
3331 3393 2.270205 CACAGAGGCAAGCCGGAT 59.730 61.111 5.05 0.00 41.95 4.18
3332 3394 4.704833 GCACAGAGGCAAGCCGGA 62.705 66.667 5.05 0.00 41.95 5.14
3346 3408 4.824166 CAAGATGCAGCGGCGCAC 62.824 66.667 35.02 25.21 46.56 5.34
3377 3439 3.816524 AGTCGCTCGCCGGAGAAG 61.817 66.667 9.83 6.67 43.27 2.85
3378 3440 4.116328 CAGTCGCTCGCCGGAGAA 62.116 66.667 9.83 0.00 43.27 2.87
3380 3442 4.421479 AACAGTCGCTCGCCGGAG 62.421 66.667 5.05 0.00 43.46 4.63
3381 3443 4.415332 GAACAGTCGCTCGCCGGA 62.415 66.667 5.05 0.00 37.59 5.14
3383 3445 4.717629 TGGAACAGTCGCTCGCCG 62.718 66.667 0.00 0.00 38.61 6.46
3394 3456 3.003173 CCTCCCCGAGCTGGAACA 61.003 66.667 0.00 0.00 42.00 3.18
3395 3457 4.475135 GCCTCCCCGAGCTGGAAC 62.475 72.222 0.00 0.00 42.00 3.62


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

AutoCloner maintained by Alex Coulton.