Multiple sequence alignment - TraesCS5D01G252400

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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 TraesCS5D01G252400 chr5D 100.000 5992 0 0 1 5992 358016909 358010918 0.000000e+00 11066.0
1 TraesCS5D01G252400 chr5A 92.813 4021 203 47 1486 5475 458971968 458968003 0.000000e+00 5746.0
2 TraesCS5D01G252400 chr5A 82.244 1132 58 39 309 1365 458973472 458972409 0.000000e+00 845.0
3 TraesCS5D01G252400 chr5A 94.273 454 22 4 5542 5992 458967908 458967456 0.000000e+00 691.0
4 TraesCS5D01G252400 chr5A 81.722 755 36 40 732 1435 458973012 458972309 2.460000e-148 536.0
5 TraesCS5D01G252400 chr5A 86.667 150 10 5 6 151 458975747 458975604 2.240000e-34 158.0
6 TraesCS5D01G252400 chr5B 92.330 2764 182 16 3247 5992 423228680 423225929 0.000000e+00 3903.0
7 TraesCS5D01G252400 chr5B 87.304 1528 135 32 1592 3105 423230160 423228678 0.000000e+00 1692.0
8 TraesCS5D01G252400 chr5B 86.571 1601 83 48 94 1593 423231806 423230237 0.000000e+00 1644.0
9 TraesCS5D01G252400 chr5B 93.750 96 2 3 6 97 423232200 423232105 2.250000e-29 141.0
10 TraesCS5D01G252400 chr2D 86.167 347 25 9 2242 2588 422564118 422564441 2.660000e-93 353.0
11 TraesCS5D01G252400 chr2D 82.816 419 30 10 1827 2244 422563579 422563956 2.680000e-88 337.0
12 TraesCS5D01G252400 chr2B 100.000 28 0 0 3101 3128 620619284 620619311 1.100000e-02 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 TraesCS5D01G252400 chr5D 358010918 358016909 5991 True 11066.0 11066 100.00000 1 5992 1 chr5D.!!$R1 5991
1 TraesCS5D01G252400 chr5A 458967456 458975747 8291 True 1595.2 5746 87.54380 6 5992 5 chr5A.!!$R1 5986
2 TraesCS5D01G252400 chr5B 423225929 423232200 6271 True 1845.0 3903 89.98875 6 5992 4 chr5B.!!$R1 5986
3 TraesCS5D01G252400 chr2D 422563579 422564441 862 False 345.0 353 84.49150 1827 2588 2 chr2D.!!$F1 761

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
604 2921 0.034896 GAGAAGCGTTCCTGAACCCA 59.965 55.000 4.54 0.0 38.03 4.51 F
1175 3550 0.179048 GCCGTGTGGGATGATGATCA 60.179 55.000 0.00 0.0 38.47 2.92 F
1537 4256 0.540365 CCAGTGGACACAGCCCAATT 60.540 55.000 1.68 0.0 35.12 2.32 F
2434 5415 1.077140 TGCTGTGTTTCTGGGTGCA 60.077 52.632 0.00 0.0 0.00 4.57 F
3212 6207 0.035439 CCAACCAATCACTAGCCGGT 60.035 55.000 1.90 0.0 0.00 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2275 5252 0.107703 TAATTCTGCGGTCTGGCCAG 60.108 55.000 27.87 27.87 36.97 4.85 R
2335 5316 0.108233 CCAGACAGAGAGCCAAGAGC 60.108 60.000 0.00 0.00 44.25 4.09 R
3199 6194 1.128200 TGGCATACCGGCTAGTGATT 58.872 50.000 0.00 0.00 41.89 2.57 R
4097 7094 2.158534 ACCAACACATTAGGCACCTGAA 60.159 45.455 0.00 0.00 0.00 3.02 R
5176 8182 0.759959 TTGTCCCGGCAGTTTACAGA 59.240 50.000 0.00 0.00 0.00 3.41 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
100 403 4.456280 TCAGTCGACAGCATTCTTGTAT 57.544 40.909 19.50 0.00 0.00 2.29
217 552 1.001378 CGTTTTTCCCCACTGAGCAAG 60.001 52.381 0.00 0.00 0.00 4.01
248 584 1.994507 ATAGCACTCGCGCTCTCGTT 61.995 55.000 5.56 0.00 42.62 3.85
263 599 1.805945 CGTTACGTGGCCAGCTCTC 60.806 63.158 5.11 0.00 0.00 3.20
545 2841 3.053896 CGTCCCCGTTTGCCTTCC 61.054 66.667 0.00 0.00 0.00 3.46
581 2898 3.136123 CCCTCACAGGCAATGGCG 61.136 66.667 0.00 0.00 42.47 5.69
598 2915 1.355066 GCGAAGGAGAAGCGTTCCTG 61.355 60.000 7.35 0.00 44.24 3.86
599 2916 0.243907 CGAAGGAGAAGCGTTCCTGA 59.756 55.000 7.35 0.00 44.24 3.86
600 2917 1.336887 CGAAGGAGAAGCGTTCCTGAA 60.337 52.381 7.35 0.00 44.24 3.02
601 2918 2.070028 GAAGGAGAAGCGTTCCTGAAC 58.930 52.381 7.35 0.00 44.24 3.18
602 2919 0.321996 AGGAGAAGCGTTCCTGAACC 59.678 55.000 5.99 0.00 43.38 3.62
603 2920 0.673956 GGAGAAGCGTTCCTGAACCC 60.674 60.000 4.54 0.00 38.03 4.11
604 2921 0.034896 GAGAAGCGTTCCTGAACCCA 59.965 55.000 4.54 0.00 38.03 4.51
605 2922 0.250338 AGAAGCGTTCCTGAACCCAC 60.250 55.000 4.54 0.00 38.03 4.61
718 3035 3.118482 ACGTGACTCGGAGTTCCTATCTA 60.118 47.826 12.67 0.00 44.69 1.98
719 3036 4.066490 CGTGACTCGGAGTTCCTATCTAT 58.934 47.826 12.67 0.00 35.71 1.98
720 3037 4.152759 CGTGACTCGGAGTTCCTATCTATC 59.847 50.000 12.67 0.00 35.71 2.08
721 3038 5.310451 GTGACTCGGAGTTCCTATCTATCT 58.690 45.833 12.67 0.00 0.00 1.98
723 3040 4.076394 ACTCGGAGTTCCTATCTATCTGC 58.924 47.826 4.45 0.00 0.00 4.26
724 3041 4.075682 CTCGGAGTTCCTATCTATCTGCA 58.924 47.826 0.00 0.00 0.00 4.41
726 3043 3.365465 CGGAGTTCCTATCTATCTGCACG 60.365 52.174 0.00 0.00 0.00 5.34
727 3044 3.057174 GGAGTTCCTATCTATCTGCACGG 60.057 52.174 0.00 0.00 0.00 4.94
728 3045 3.821600 GAGTTCCTATCTATCTGCACGGA 59.178 47.826 0.00 0.00 0.00 4.69
729 3046 3.570550 AGTTCCTATCTATCTGCACGGAC 59.429 47.826 0.00 0.00 0.00 4.79
927 3286 3.357079 GCACCACTCGTTGCTGGG 61.357 66.667 0.00 0.00 0.00 4.45
932 3291 0.744281 CCACTCGTTGCTGGGTTTTT 59.256 50.000 0.00 0.00 0.00 1.94
933 3292 1.269051 CCACTCGTTGCTGGGTTTTTC 60.269 52.381 0.00 0.00 0.00 2.29
934 3293 1.676006 CACTCGTTGCTGGGTTTTTCT 59.324 47.619 0.00 0.00 0.00 2.52
935 3294 2.875933 CACTCGTTGCTGGGTTTTTCTA 59.124 45.455 0.00 0.00 0.00 2.10
936 3295 2.876550 ACTCGTTGCTGGGTTTTTCTAC 59.123 45.455 0.00 0.00 0.00 2.59
1003 3363 3.617531 CGGAACCTGCTGAAGTTCTATGT 60.618 47.826 4.17 0.00 41.69 2.29
1090 3450 3.390521 TGGCGGCTCGATCACCTT 61.391 61.111 11.43 0.00 0.00 3.50
1136 3502 1.974265 CCTGCTGTCGAGGATAGAGA 58.026 55.000 0.00 0.00 31.48 3.10
1137 3503 1.879380 CCTGCTGTCGAGGATAGAGAG 59.121 57.143 0.00 0.00 34.25 3.20
1175 3550 0.179048 GCCGTGTGGGATGATGATCA 60.179 55.000 0.00 0.00 38.47 2.92
1208 3583 0.989890 CGGTGAGCGTGCTAACTAAC 59.010 55.000 9.17 0.00 0.00 2.34
1217 3592 3.606153 GCGTGCTAACTAACCTTGTGTTG 60.606 47.826 0.00 0.00 37.83 3.33
1242 3617 7.140705 GTGATCAAGAAATGTTGTCATGTTCA 58.859 34.615 0.00 0.00 34.19 3.18
1252 3630 3.126001 TGTCATGTTCAGTTCAGGGAC 57.874 47.619 0.00 0.00 0.00 4.46
1254 3632 3.072915 TGTCATGTTCAGTTCAGGGACAT 59.927 43.478 0.00 0.00 32.37 3.06
1259 3637 5.560722 TGTTCAGTTCAGGGACATTTCTA 57.439 39.130 0.00 0.00 0.00 2.10
1314 3702 3.455469 GACTGCCCAATGCCCAGC 61.455 66.667 0.00 0.00 40.16 4.85
1332 3724 1.514443 CTCGTTCCCTTCTCGACGC 60.514 63.158 0.00 0.00 35.63 5.19
1431 3859 1.661341 GACCGCTAACTACTCCGAGA 58.339 55.000 1.33 0.00 0.00 4.04
1456 3896 5.941948 ACAACATTAACAGGCAGTAAGTC 57.058 39.130 0.00 0.00 0.00 3.01
1483 4175 6.679392 GCACAAACCAACATTAACACACTACT 60.679 38.462 0.00 0.00 0.00 2.57
1484 4176 7.467539 GCACAAACCAACATTAACACACTACTA 60.468 37.037 0.00 0.00 0.00 1.82
1537 4256 0.540365 CCAGTGGACACAGCCCAATT 60.540 55.000 1.68 0.00 35.12 2.32
1549 4268 7.054491 ACACAGCCCAATTATTCATTATTCC 57.946 36.000 0.00 0.00 0.00 3.01
1556 4275 7.653311 GCCCAATTATTCATTATTCCACTGTTC 59.347 37.037 0.00 0.00 0.00 3.18
1568 4287 1.733041 ACTGTTCATGACGCGTCGG 60.733 57.895 31.88 25.96 0.00 4.79
1612 4409 2.124570 CGTGGGCCCAGGAATCAG 60.125 66.667 36.29 13.07 34.13 2.90
1621 4419 1.272648 CCCAGGAATCAGAAAAGGCCA 60.273 52.381 5.01 0.00 0.00 5.36
1623 4421 1.821136 CAGGAATCAGAAAAGGCCACC 59.179 52.381 5.01 0.00 0.00 4.61
1669 4471 3.864686 CTGCGGAATCCAACGGCG 61.865 66.667 4.80 4.80 36.60 6.46
1721 4523 4.308458 CGCCCAAGACGTCACCCA 62.308 66.667 19.50 0.00 0.00 4.51
1748 4550 2.085320 CACTCGTACAGCTGTACTCCT 58.915 52.381 39.83 25.26 46.43 3.69
1749 4551 2.488545 CACTCGTACAGCTGTACTCCTT 59.511 50.000 39.83 25.14 46.43 3.36
1750 4552 2.748532 ACTCGTACAGCTGTACTCCTTC 59.251 50.000 39.83 22.42 46.43 3.46
1751 4553 2.089980 TCGTACAGCTGTACTCCTTCC 58.910 52.381 39.83 21.82 46.43 3.46
1752 4554 2.093106 CGTACAGCTGTACTCCTTCCT 58.907 52.381 39.83 12.50 46.43 3.36
1825 4627 3.887110 CCCAACGACCCTAATTTATTCCC 59.113 47.826 0.00 0.00 0.00 3.97
2098 4901 2.200370 TGAGTGTGACTCCCCCGT 59.800 61.111 1.36 0.00 44.44 5.28
2179 4992 1.209275 CGGCAGATCGGTGATTCGAC 61.209 60.000 0.00 0.00 42.21 4.20
2273 5250 6.398234 TTTGTAGCTTTGTTGCTTTGGATA 57.602 33.333 0.00 0.00 43.74 2.59
2275 5252 5.768317 TGTAGCTTTGTTGCTTTGGATAAC 58.232 37.500 0.00 0.00 43.74 1.89
2335 5316 8.867112 ATTTCTGCTATGATATGTTTTTGCTG 57.133 30.769 0.00 0.00 0.00 4.41
2362 5343 1.566211 CTCTCTGTCTGGGTGGTGAT 58.434 55.000 0.00 0.00 0.00 3.06
2401 5382 9.745880 TTAGAAGTTTTTAGAGTAGTGTCTGTG 57.254 33.333 0.00 0.00 0.00 3.66
2434 5415 1.077140 TGCTGTGTTTCTGGGTGCA 60.077 52.632 0.00 0.00 0.00 4.57
2489 5470 3.117851 GGGTTAATTTAGCTGGCCTCTCT 60.118 47.826 3.32 0.23 0.00 3.10
2490 5471 4.527944 GGTTAATTTAGCTGGCCTCTCTT 58.472 43.478 3.32 0.00 0.00 2.85
2497 5478 1.686052 AGCTGGCCTCTCTTATTCTCG 59.314 52.381 3.32 0.00 0.00 4.04
2512 5493 7.759465 TCTTATTCTCGGTGTCACTAGTTTAG 58.241 38.462 2.35 0.00 0.00 1.85
2533 5514 3.133691 GTGTGCATGTCTCTGTTCTTCA 58.866 45.455 0.00 0.00 0.00 3.02
2534 5515 3.750130 GTGTGCATGTCTCTGTTCTTCAT 59.250 43.478 0.00 0.00 0.00 2.57
2535 5516 4.931601 GTGTGCATGTCTCTGTTCTTCATA 59.068 41.667 0.00 0.00 0.00 2.15
2605 5586 5.182001 GGAATAATAAATCTCGGCATGTGCT 59.818 40.000 4.84 0.00 41.70 4.40
2713 5695 4.085357 TGTAGTGATGCACTGTTTTCCT 57.915 40.909 10.15 0.00 45.01 3.36
2804 5786 8.366359 AGCATTTTAAATTACATCTTGGGACT 57.634 30.769 0.00 0.00 0.00 3.85
2821 5810 3.199946 GGGACTGTTAGTCATGGATTCCA 59.800 47.826 8.08 8.08 46.79 3.53
2863 5852 7.463431 TGATTAGTTCCAGTTTAGCCCTTTAA 58.537 34.615 0.00 0.00 0.00 1.52
2865 5854 5.320488 AGTTCCAGTTTAGCCCTTTAAGT 57.680 39.130 0.00 0.00 0.00 2.24
2869 5858 6.190346 TCCAGTTTAGCCCTTTAAGTTGTA 57.810 37.500 0.00 0.00 0.00 2.41
2870 5859 5.999600 TCCAGTTTAGCCCTTTAAGTTGTAC 59.000 40.000 0.00 0.00 0.00 2.90
2871 5860 6.002082 CCAGTTTAGCCCTTTAAGTTGTACT 58.998 40.000 0.00 0.00 0.00 2.73
2873 5866 7.118825 CCAGTTTAGCCCTTTAAGTTGTACTAC 59.881 40.741 0.00 0.00 0.00 2.73
2927 5920 2.038820 AGAATTGGGGCACACATTTTGG 59.961 45.455 0.00 0.00 0.00 3.28
2943 5936 7.920682 ACACATTTTGGTTTGTTGAGTATTCTC 59.079 33.333 0.00 0.00 40.79 2.87
2952 5945 3.512329 TGTTGAGTATTCTCGGCTGGTTA 59.488 43.478 0.00 0.00 43.09 2.85
2953 5946 4.113354 GTTGAGTATTCTCGGCTGGTTAG 58.887 47.826 0.00 0.00 43.09 2.34
2992 5985 5.960113 ACTGTGTAGTGCTATCTCTGAAAG 58.040 41.667 0.00 0.00 35.34 2.62
3013 6006 8.190122 TGAAAGCGAAATGAAATGCTAACATAT 58.810 29.630 0.00 0.00 36.49 1.78
3041 6034 2.040278 TGCAGTAGGCCTGAAATGAACT 59.960 45.455 17.99 5.78 44.49 3.01
3048 6041 4.948847 AGGCCTGAAATGAACTTTTTGTC 58.051 39.130 3.11 0.00 0.00 3.18
3059 6052 7.734538 ATGAACTTTTTGTCAACTTAACGTG 57.265 32.000 0.00 0.00 0.00 4.49
3083 6076 6.183360 TGGTGCTGGAAAACACTGAATTTTAT 60.183 34.615 0.00 0.00 36.99 1.40
3127 6120 4.768448 AGAGCATGATTGGTTTGATGTCAA 59.232 37.500 0.00 0.00 32.62 3.18
3187 6182 5.591877 ACTTGTGAGATCAGCAAGAAAAGTT 59.408 36.000 22.16 4.69 37.86 2.66
3212 6207 0.035439 CCAACCAATCACTAGCCGGT 60.035 55.000 1.90 0.00 0.00 5.28
3220 6215 0.177141 TCACTAGCCGGTATGCCAAC 59.823 55.000 1.90 0.00 34.09 3.77
3343 6339 1.329906 GCAGGAGCGATTTCTCATGTG 59.670 52.381 7.17 0.00 44.18 3.21
3359 6355 1.055849 TGTGCTACAAAGGCCTCAGA 58.944 50.000 5.23 0.00 0.00 3.27
3420 6416 6.729187 TCAACATGATACTGTAGATGAGACG 58.271 40.000 13.64 0.00 0.00 4.18
3557 6553 9.817809 AAGTTAGATGAATATCTTTGTCGCTTA 57.182 29.630 0.00 0.00 40.79 3.09
3562 6558 6.327177 TGAATATCTTTGTCGCTTAACGTC 57.673 37.500 0.00 0.00 44.19 4.34
3641 6638 2.092914 AGCAAACACCAGAGGTATAGCC 60.093 50.000 0.00 0.00 32.11 3.93
3684 6681 8.603242 AATCTTCGTAATTTTCACTGTACTGT 57.397 30.769 0.00 0.00 0.00 3.55
3747 6744 1.372004 CATGGTGGTTGCTTGTGCG 60.372 57.895 0.00 0.00 43.34 5.34
3894 6891 9.903185 TTTTATTAAACTTTTAAAGCAACGCAC 57.097 25.926 4.42 0.00 36.35 5.34
4104 7101 4.654091 ATTGTGTTCCTTTGTTCAGGTG 57.346 40.909 0.00 0.00 35.15 4.00
4161 7158 0.950116 GCATCCAGGCACTAATGAGC 59.050 55.000 0.00 0.00 36.02 4.26
4221 7218 7.470192 ACAATTCTCTTCCCATTTCTCCTTTA 58.530 34.615 0.00 0.00 0.00 1.85
4444 7441 6.511929 GCAAGAAGTAGGAACTGTCTGAAAAC 60.512 42.308 0.00 0.00 41.52 2.43
4449 7446 6.357367 AGTAGGAACTGTCTGAAAACATTGT 58.643 36.000 0.00 0.00 41.52 2.71
4615 7615 9.463443 GTTTTGTAGCTCTACATGTCAAAATTT 57.537 29.630 17.23 0.00 44.54 1.82
4678 7678 4.634004 TGATCAATGTACGGTTCCATGAAC 59.366 41.667 0.00 0.00 41.32 3.18
4987 7993 6.261118 GTCTTGATCAATGAACAGGCATTAC 58.739 40.000 8.96 0.00 36.39 1.89
5056 8062 0.601558 ACTCTGCCATTTTGCTGCTG 59.398 50.000 0.00 0.00 0.00 4.41
5058 8064 1.000506 CTCTGCCATTTTGCTGCTGTT 59.999 47.619 0.00 0.00 0.00 3.16
5062 8068 2.211806 GCCATTTTGCTGCTGTTTTCA 58.788 42.857 0.00 0.00 0.00 2.69
5081 8087 0.963962 ATTGCAACTTGCTCCAGGTG 59.036 50.000 14.78 0.00 45.31 4.00
5089 8095 2.578021 ACTTGCTCCAGGTGGTATTGAT 59.422 45.455 0.00 0.00 36.34 2.57
5092 8098 5.103940 ACTTGCTCCAGGTGGTATTGATATT 60.104 40.000 0.00 0.00 36.34 1.28
5166 8172 6.701937 ACACAGCGAACAATACATTATTACG 58.298 36.000 0.00 0.00 0.00 3.18
5244 8250 6.517597 CGTTTTCTGTCTAGAATCGTGAAAG 58.482 40.000 0.00 0.00 42.25 2.62
5278 8284 6.902224 AAAACTGCAAAACCATAGTCAAAC 57.098 33.333 0.00 0.00 0.00 2.93
5284 8290 4.145756 GCAAAACCATAGTCAAACGAAACG 59.854 41.667 0.00 0.00 0.00 3.60
5289 8296 4.151689 ACCATAGTCAAACGAAACGATGTG 59.848 41.667 0.00 0.00 29.62 3.21
5469 8478 6.654582 TGCTATTTTGAATCTGTACTGCTTCA 59.345 34.615 13.12 13.12 0.00 3.02
5510 8563 7.880195 ACATCCCAAATATTGTAGTAGCTCATC 59.120 37.037 0.00 0.00 0.00 2.92
5530 8583 9.507329 GCTCATCTCCATTCCTATTTATTTGTA 57.493 33.333 0.00 0.00 0.00 2.41
5572 8625 2.473816 TGAGAGCGATATTTCTTGCCG 58.526 47.619 0.00 0.00 0.00 5.69
5766 8822 3.944055 TCTCTCAGTGCCTGTACTTTC 57.056 47.619 0.00 0.00 32.61 2.62
5797 8856 5.491070 CATTACAGAACCTGAAGGACATGA 58.509 41.667 2.62 0.00 38.94 3.07
5902 8964 3.067106 AGGTTGATACACGCTTGTGAAG 58.933 45.455 6.03 0.00 46.91 3.02
5916 8978 0.664166 GTGAAGCAAACATGGTGGCG 60.664 55.000 3.97 0.00 0.00 5.69
5973 9035 2.202797 GATGAGCGCCGAGAAGCA 60.203 61.111 2.29 0.00 35.48 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.709141 ACAACTTGTTTGGTGCCCTAATT 59.291 39.130 0.00 0.00 39.84 1.40
16 17 3.069443 CACAACTTGTTTGGTGCCCTAAT 59.931 43.478 0.00 0.00 39.84 1.73
188 523 1.285950 GGGAAAAACGCTGTCTGGC 59.714 57.895 0.00 0.00 0.00 4.85
217 552 0.965439 AGTGCTATCCGAGATGCTCC 59.035 55.000 0.00 0.00 0.00 4.70
248 584 3.449227 CCGAGAGCTGGCCACGTA 61.449 66.667 0.00 0.00 0.00 3.57
307 643 0.778815 GCGTCTCTGTCTGTGTTTCG 59.221 55.000 0.00 0.00 0.00 3.46
452 2748 4.230002 TGCCTATGCCGCCGGTAC 62.230 66.667 4.45 0.00 36.33 3.34
552 2848 2.038813 TGAGGGGATCGGTGCTCA 59.961 61.111 0.00 0.00 0.00 4.26
554 2850 2.284625 TGTGAGGGGATCGGTGCT 60.285 61.111 0.00 0.00 0.00 4.40
581 2898 2.070028 GTTCAGGAACGCTTCTCCTTC 58.930 52.381 0.00 0.00 41.61 3.46
598 2915 3.998672 TCGTGGGCTCGTGGGTTC 61.999 66.667 3.18 0.00 0.00 3.62
599 2916 4.309950 GTCGTGGGCTCGTGGGTT 62.310 66.667 3.18 0.00 0.00 4.11
602 2919 4.742201 CTGGTCGTGGGCTCGTGG 62.742 72.222 3.18 0.00 0.00 4.94
603 2920 4.742201 CCTGGTCGTGGGCTCGTG 62.742 72.222 3.18 0.00 0.00 4.35
604 2921 4.988716 TCCTGGTCGTGGGCTCGT 62.989 66.667 0.00 0.00 0.00 4.18
605 2922 3.649277 CTTCCTGGTCGTGGGCTCG 62.649 68.421 0.00 0.00 0.00 5.03
660 2977 0.179200 CTTTTGCATACACGGCCGTC 60.179 55.000 31.80 18.05 0.00 4.79
724 3041 1.710013 GTGATGATTGACACGTCCGT 58.290 50.000 0.00 0.00 0.00 4.69
981 3341 2.743636 TAGAACTTCAGCAGGTTCCG 57.256 50.000 0.00 0.00 41.69 4.30
1003 3363 2.515996 GATCGCAAGGACCACGGGAA 62.516 60.000 0.00 0.00 38.47 3.97
1208 3583 5.835257 ACATTTCTTGATCACAACACAAGG 58.165 37.500 0.00 0.00 40.60 3.61
1217 3592 7.140705 TGAACATGACAACATTTCTTGATCAC 58.859 34.615 0.00 0.00 34.15 3.06
1242 3617 4.472833 AGCAGATAGAAATGTCCCTGAACT 59.527 41.667 0.00 0.00 0.00 3.01
1280 3658 1.014564 GTCGGTAGCCAGACAAGCAC 61.015 60.000 0.00 0.00 37.34 4.40
1314 3702 1.514443 GCGTCGAGAAGGGAACGAG 60.514 63.158 0.00 0.00 36.74 4.18
1332 3724 2.481903 TCGATCAATCAGCACGAGAG 57.518 50.000 0.00 0.00 0.00 3.20
1343 3735 3.514706 AGATGGATGCTAGCTCGATCAAT 59.485 43.478 25.67 17.15 32.22 2.57
1431 3859 7.883311 AGACTTACTGCCTGTTAATGTTGTTAT 59.117 33.333 0.00 0.00 0.00 1.89
1456 3896 4.267452 GTGTGTTAATGTTGGTTTGTGCAG 59.733 41.667 0.00 0.00 0.00 4.41
1459 3899 6.791303 AGTAGTGTGTTAATGTTGGTTTGTG 58.209 36.000 0.00 0.00 0.00 3.33
1483 4175 4.098349 ACTGTCTTGTCAACCTACGTGTTA 59.902 41.667 0.00 0.00 0.00 2.41
1484 4176 3.118884 ACTGTCTTGTCAACCTACGTGTT 60.119 43.478 0.00 0.00 0.00 3.32
1537 4256 7.254761 GCGTCATGAACAGTGGAATAATGAATA 60.255 37.037 0.00 0.00 0.00 1.75
1549 4268 1.412226 CGACGCGTCATGAACAGTG 59.588 57.895 35.71 14.63 0.00 3.66
1568 4287 0.654683 CTTATCGAGTTGCTGCCTGC 59.345 55.000 0.00 0.00 43.25 4.85
1573 4292 1.600957 CCATGGCTTATCGAGTTGCTG 59.399 52.381 0.00 0.00 0.00 4.41
1574 4293 1.959042 CCATGGCTTATCGAGTTGCT 58.041 50.000 0.00 0.00 0.00 3.91
1669 4471 0.316841 GCTCTGATGGGACGATCCTC 59.683 60.000 0.00 0.00 36.57 3.71
1721 4523 1.006102 GCTGTACGAGTGTGCTGGT 60.006 57.895 0.00 0.00 37.44 4.00
2087 4890 4.393778 GGGGAGACGGGGGAGTCA 62.394 72.222 0.00 0.00 43.24 3.41
2187 5000 4.832608 CGCCCTCAGGGTAACGCC 62.833 72.222 12.83 0.00 46.51 5.68
2273 5250 2.129555 ATTCTGCGGTCTGGCCAGTT 62.130 55.000 31.58 4.63 36.97 3.16
2275 5252 0.107703 TAATTCTGCGGTCTGGCCAG 60.108 55.000 27.87 27.87 36.97 4.85
2335 5316 0.108233 CCAGACAGAGAGCCAAGAGC 60.108 60.000 0.00 0.00 44.25 4.09
2362 5343 2.226330 ACTTCTAATTTGTGCACGGCA 58.774 42.857 13.13 0.00 35.60 5.69
2401 5382 2.095567 CACAGCAGCTCCACATAAACAC 60.096 50.000 0.00 0.00 0.00 3.32
2489 5470 7.458409 ACTAAACTAGTGACACCGAGAATAA 57.542 36.000 11.16 0.00 37.69 1.40
2512 5493 3.133691 TGAAGAACAGAGACATGCACAC 58.866 45.455 0.00 0.00 0.00 3.82
2521 5502 8.051901 TGACGAAATAGTATGAAGAACAGAGA 57.948 34.615 0.00 0.00 0.00 3.10
2533 5514 8.692710 TCTTCCATAACACTGACGAAATAGTAT 58.307 33.333 0.00 0.00 0.00 2.12
2534 5515 8.058667 TCTTCCATAACACTGACGAAATAGTA 57.941 34.615 0.00 0.00 0.00 1.82
2535 5516 6.931838 TCTTCCATAACACTGACGAAATAGT 58.068 36.000 0.00 0.00 0.00 2.12
2695 5677 3.144506 CAGAGGAAAACAGTGCATCACT 58.855 45.455 0.00 0.00 46.51 3.41
2724 5706 9.569122 GAACTATGCCCACCTAATTTATCTTAA 57.431 33.333 0.00 0.00 0.00 1.85
2727 5709 6.998673 GTGAACTATGCCCACCTAATTTATCT 59.001 38.462 0.00 0.00 0.00 1.98
2735 5717 3.704566 CAGTAGTGAACTATGCCCACCTA 59.295 47.826 0.00 0.00 35.76 3.08
2736 5718 2.501723 CAGTAGTGAACTATGCCCACCT 59.498 50.000 0.00 0.00 35.76 4.00
2737 5719 2.906354 CAGTAGTGAACTATGCCCACC 58.094 52.381 0.00 0.00 35.76 4.61
2738 5720 2.280628 GCAGTAGTGAACTATGCCCAC 58.719 52.381 0.42 0.00 35.76 4.61
2804 5786 6.244654 TGACAATTGGAATCCATGACTAACA 58.755 36.000 10.83 0.10 31.53 2.41
2809 5798 6.643770 GCATATTGACAATTGGAATCCATGAC 59.356 38.462 10.83 4.43 31.53 3.06
2869 5858 9.646427 GAGTGAAAGAGAGATAACATTTGTAGT 57.354 33.333 0.00 0.00 0.00 2.73
2870 5859 9.645059 TGAGTGAAAGAGAGATAACATTTGTAG 57.355 33.333 0.00 0.00 0.00 2.74
2871 5860 9.996554 TTGAGTGAAAGAGAGATAACATTTGTA 57.003 29.630 0.00 0.00 0.00 2.41
2873 5866 9.604626 GTTTGAGTGAAAGAGAGATAACATTTG 57.395 33.333 0.00 0.00 0.00 2.32
2927 5920 3.125316 CCAGCCGAGAATACTCAACAAAC 59.875 47.826 0.00 0.00 42.72 2.93
2943 5936 1.792949 GCATAATCGACTAACCAGCCG 59.207 52.381 0.00 0.00 0.00 5.52
2952 5945 4.193826 ACAGTTGTGAGCATAATCGACT 57.806 40.909 0.00 0.00 0.00 4.18
2992 5985 7.591057 TGCTTATATGTTAGCATTTCATTTCGC 59.409 33.333 0.00 0.00 42.12 4.70
3013 6006 2.042686 CAGGCCTACTGCATTGCTTA 57.957 50.000 3.98 0.60 43.89 3.09
3041 6034 4.082679 AGCACCACGTTAAGTTGACAAAAA 60.083 37.500 0.00 0.00 0.00 1.94
3048 6041 1.588674 TCCAGCACCACGTTAAGTTG 58.411 50.000 0.00 0.00 0.00 3.16
3059 6052 3.733443 AATTCAGTGTTTTCCAGCACC 57.267 42.857 0.00 0.00 36.35 5.01
3083 6076 6.039717 GCTCTTAATATCAAGTGGGCAAATCA 59.960 38.462 0.00 0.00 0.00 2.57
3127 6120 5.049828 GCAACTTTTGATTTTGCCTACTGT 58.950 37.500 0.00 0.00 39.82 3.55
3166 6159 4.261322 GCAACTTTTCTTGCTGATCTCACA 60.261 41.667 0.00 0.00 42.84 3.58
3167 6160 4.225208 GCAACTTTTCTTGCTGATCTCAC 58.775 43.478 0.00 0.00 42.84 3.51
3187 6182 3.343617 GCTAGTGATTGGTTGGTTAGCA 58.656 45.455 0.00 0.00 33.92 3.49
3189 6184 2.936498 CGGCTAGTGATTGGTTGGTTAG 59.064 50.000 0.00 0.00 0.00 2.34
3199 6194 1.128200 TGGCATACCGGCTAGTGATT 58.872 50.000 0.00 0.00 41.89 2.57
3234 6229 6.798315 ATCAAAGATTTAGAGCATGATCGG 57.202 37.500 5.12 0.00 0.00 4.18
3343 6339 2.770164 TCTTCTGAGGCCTTTGTAGC 57.230 50.000 6.77 0.00 0.00 3.58
3359 6355 2.681976 CGGGTCAAGCCAGAATGATCTT 60.682 50.000 0.00 0.00 39.69 2.40
3553 6549 3.717350 ACAAATACAGCGACGTTAAGC 57.283 42.857 0.00 0.00 0.00 3.09
3557 6553 3.052036 ACGTTACAAATACAGCGACGTT 58.948 40.909 0.00 0.00 38.91 3.99
3562 6558 2.732500 TGACCACGTTACAAATACAGCG 59.267 45.455 0.00 0.00 0.00 5.18
3641 6638 8.023128 ACGAAGATTTGGAATTAACATGACAAG 58.977 33.333 0.00 0.00 0.00 3.16
3872 6869 7.764695 AAGTGCGTTGCTTTAAAAGTTTAAT 57.235 28.000 0.00 0.00 33.12 1.40
3890 6887 4.452455 AGAACTTCCACAATAGAAAGTGCG 59.548 41.667 0.00 0.00 34.48 5.34
4097 7094 2.158534 ACCAACACATTAGGCACCTGAA 60.159 45.455 0.00 0.00 0.00 3.02
4104 7101 2.290705 ACCTACCACCAACACATTAGGC 60.291 50.000 0.00 0.00 30.94 3.93
4161 7158 7.278211 TCGATCGTCTTTCTTACTTTTCATG 57.722 36.000 15.94 0.00 0.00 3.07
4235 7232 5.476599 AGGCTTGCATCATGTAAAAGTACAA 59.523 36.000 0.00 0.00 43.41 2.41
4444 7441 5.396484 CAATGCACTACTCTGGAAACAATG 58.604 41.667 0.00 0.00 42.06 2.82
4449 7446 4.574674 ATCCAATGCACTACTCTGGAAA 57.425 40.909 0.00 0.00 39.54 3.13
4522 7519 7.342026 ACCAAGAAAGTAACCTTGAGTGAAAAT 59.658 33.333 0.00 0.00 41.56 1.82
4524 7521 6.184789 ACCAAGAAAGTAACCTTGAGTGAAA 58.815 36.000 0.00 0.00 41.56 2.69
4526 7523 5.367945 ACCAAGAAAGTAACCTTGAGTGA 57.632 39.130 0.00 0.00 41.56 3.41
4615 7615 1.532523 TTTGGCATGCATGTCGAGAA 58.467 45.000 25.23 16.72 34.48 2.87
4678 7678 4.676546 TCAACTATCTCACATGCTCGAAG 58.323 43.478 0.00 0.00 0.00 3.79
4737 7737 6.968904 ACAATTTATTCAATGTCAGACGATGC 59.031 34.615 0.00 0.00 0.00 3.91
4876 7882 4.217118 GTCCACTTCTCAAATGTGCAATCT 59.783 41.667 0.00 0.00 0.00 2.40
4987 7993 7.489757 GCAGAGTGAACTTTACCAGAGTATAAG 59.510 40.741 0.00 0.00 0.00 1.73
5062 8068 5.656206 TACCACCTGGAGCAAGTTGCAAT 62.656 47.826 28.65 10.08 41.81 3.56
5166 8172 5.333875 CCGGCAGTTTACAGACTTTACTTTC 60.334 44.000 0.00 0.00 0.00 2.62
5176 8182 0.759959 TTGTCCCGGCAGTTTACAGA 59.240 50.000 0.00 0.00 0.00 3.41
5244 8250 0.675522 TGCAGTTTTACTAGCCGCCC 60.676 55.000 0.00 0.00 0.00 6.13
5278 8284 2.430956 GCAGCATTACACATCGTTTCG 58.569 47.619 0.00 0.00 0.00 3.46
5311 8318 5.880054 ATACAGATGTTACAACACAAGGC 57.120 39.130 0.00 0.00 42.51 4.35
5407 8416 3.120234 TGCTTATTTGAGTCACACATGCG 60.120 43.478 0.00 0.00 0.00 4.73
5489 8498 7.445121 TGGAGATGAGCTACTACAATATTTGG 58.555 38.462 0.00 0.00 34.12 3.28
5530 8583 5.839063 TCAGATAACAGAAACCTCCCGATAT 59.161 40.000 0.00 0.00 0.00 1.63
5572 8625 3.126000 GCAGTACAGAGTCATGAAAAGGC 59.874 47.826 0.00 0.00 0.00 4.35
5766 8822 2.485426 CAGGTTCTGTAATGGCAGTGTG 59.515 50.000 0.00 0.00 37.70 3.82
5797 8856 2.353406 GCTGGCTTTGCAATCACTGAAT 60.353 45.455 0.00 0.00 0.00 2.57
5859 8921 8.653036 ACCTGTAGGATTAGTAGGCTTATAAG 57.347 38.462 8.20 8.20 38.94 1.73
5860 8922 8.867097 CAACCTGTAGGATTAGTAGGCTTATAA 58.133 37.037 4.64 0.00 38.94 0.98
5861 8923 8.229605 TCAACCTGTAGGATTAGTAGGCTTATA 58.770 37.037 4.64 0.00 38.94 0.98
5863 8925 6.437755 TCAACCTGTAGGATTAGTAGGCTTA 58.562 40.000 4.64 0.00 38.94 3.09
5902 8964 2.431260 CTGCGCCACCATGTTTGC 60.431 61.111 4.18 0.00 0.00 3.68
5903 8965 1.210931 CTCTGCGCCACCATGTTTG 59.789 57.895 4.18 0.00 0.00 2.93
5911 8973 2.879070 CGATGATGCTCTGCGCCAC 61.879 63.158 4.18 0.00 38.05 5.01
5916 8978 0.649475 GTGACACGATGATGCTCTGC 59.351 55.000 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.