Multiple sequence alignment - TraesCS4A01G214400

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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 TraesCS4A01G214400 chr4A 100.000 7350 0 0 1 7350 512546282 512538933 0.000000e+00 13573.0
1 TraesCS4A01G214400 chr4A 82.609 92 9 2 2090 2181 528736136 528736052 2.840000e-09 75.0
2 TraesCS4A01G214400 chr4B 94.846 6732 235 54 692 7350 107450911 107457603 0.000000e+00 10406.0
3 TraesCS4A01G214400 chr4B 90.852 317 29 0 2783 3099 282886666 282886350 6.820000e-115 425.0
4 TraesCS4A01G214400 chr4D 95.918 4777 136 32 542 5284 75044031 75048782 0.000000e+00 7686.0
5 TraesCS4A01G214400 chr4D 94.747 2094 62 26 5299 7350 75049799 75051886 0.000000e+00 3214.0
6 TraesCS4A01G214400 chr4D 90.031 321 32 0 2779 3099 211388337 211388017 4.100000e-112 416.0
7 TraesCS4A01G214400 chr7A 94.118 544 30 1 1 542 282342280 282341737 0.000000e+00 826.0
8 TraesCS4A01G214400 chr7A 93.934 544 29 4 1 541 185415146 185415688 0.000000e+00 819.0
9 TraesCS4A01G214400 chr7A 93.773 546 30 4 1 542 295301913 295302458 0.000000e+00 817.0
10 TraesCS4A01G214400 chr7A 93.601 547 33 1 1 545 276589556 276589010 0.000000e+00 815.0
11 TraesCS4A01G214400 chr3A 93.934 544 31 1 1 542 310566240 310565697 0.000000e+00 821.0
12 TraesCS4A01G214400 chr3A 88.994 318 27 5 2783 3100 164407962 164407653 3.220000e-103 387.0
13 TraesCS4A01G214400 chr3A 91.071 56 5 0 578 633 11124400 11124345 7.910000e-10 76.8
14 TraesCS4A01G214400 chr5A 93.761 545 30 4 1 541 294824629 294824085 0.000000e+00 815.0
15 TraesCS4A01G214400 chr2A 93.923 543 28 5 1 541 181877959 181878498 0.000000e+00 815.0
16 TraesCS4A01G214400 chr1A 93.190 558 31 7 1 552 268435486 268434930 0.000000e+00 813.0
17 TraesCS4A01G214400 chr1A 90.062 322 28 3 2783 3104 412467081 412466764 1.480000e-111 414.0
18 TraesCS4A01G214400 chr6A 93.394 545 32 4 1 541 312340422 312340966 0.000000e+00 804.0
19 TraesCS4A01G214400 chr7D 88.110 328 36 2 2779 3106 104883720 104883396 3.220000e-103 387.0
20 TraesCS4A01G214400 chr1D 88.509 322 30 6 2783 3104 326292315 326292001 4.160000e-102 383.0
21 TraesCS4A01G214400 chr1B 88.073 327 33 5 2779 3104 589068396 589068075 4.160000e-102 383.0
22 TraesCS4A01G214400 chrUn 91.071 56 5 0 578 633 299356034 299355979 7.910000e-10 76.8
23 TraesCS4A01G214400 chrUn 91.071 56 5 0 578 633 460676215 460676160 7.910000e-10 76.8


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 TraesCS4A01G214400 chr4A 512538933 512546282 7349 True 13573 13573 100.0000 1 7350 1 chr4A.!!$R1 7349
1 TraesCS4A01G214400 chr4B 107450911 107457603 6692 False 10406 10406 94.8460 692 7350 1 chr4B.!!$F1 6658
2 TraesCS4A01G214400 chr4D 75044031 75051886 7855 False 5450 7686 95.3325 542 7350 2 chr4D.!!$F1 6808
3 TraesCS4A01G214400 chr7A 282341737 282342280 543 True 826 826 94.1180 1 542 1 chr7A.!!$R2 541
4 TraesCS4A01G214400 chr7A 185415146 185415688 542 False 819 819 93.9340 1 541 1 chr7A.!!$F1 540
5 TraesCS4A01G214400 chr7A 295301913 295302458 545 False 817 817 93.7730 1 542 1 chr7A.!!$F2 541
6 TraesCS4A01G214400 chr7A 276589010 276589556 546 True 815 815 93.6010 1 545 1 chr7A.!!$R1 544
7 TraesCS4A01G214400 chr3A 310565697 310566240 543 True 821 821 93.9340 1 542 1 chr3A.!!$R3 541
8 TraesCS4A01G214400 chr5A 294824085 294824629 544 True 815 815 93.7610 1 541 1 chr5A.!!$R1 540
9 TraesCS4A01G214400 chr2A 181877959 181878498 539 False 815 815 93.9230 1 541 1 chr2A.!!$F1 540
10 TraesCS4A01G214400 chr1A 268434930 268435486 556 True 813 813 93.1900 1 552 1 chr1A.!!$R1 551
11 TraesCS4A01G214400 chr6A 312340422 312340966 544 False 804 804 93.3940 1 541 1 chr6A.!!$F1 540


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
180 186 0.322816 AACAGATGCAGGTGCCGATT 60.323 50.0 0.00 0.00 41.18 3.34 F
1462 1506 0.165944 GCACCACATGTTCGTACTGC 59.834 55.0 0.00 0.00 0.00 4.40 F
1659 1703 0.390998 GAGAAGGTCTCAGGTGCAGC 60.391 60.0 8.11 8.11 42.90 5.25 F
2243 2294 1.691196 TGGCGGAATTTGATCCCATC 58.309 50.0 0.00 0.00 36.00 3.51 F
4044 4102 0.734309 TGCTATGCCGCAACATGAAG 59.266 50.0 0.00 0.00 36.89 3.02 F
4481 4541 0.814457 TCAACACACACTGGTTTGCC 59.186 50.0 0.00 0.00 0.00 4.52 F
5349 6418 0.170561 CAGCTGTCTGATTTGCTGCC 59.829 55.0 5.25 0.00 44.72 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1651 1695 0.820891 CAGTGTTTCCAGCTGCACCT 60.821 55.000 8.66 1.78 32.75 4.00 R
3269 3325 2.042464 AGTTGAGCAGTGGAGTTCAGA 58.958 47.619 0.00 0.00 30.36 3.27 R
3447 3503 4.202202 CCCCTTAACAAAAGCACATGTCAA 60.202 41.667 0.00 0.00 0.00 3.18 R
4193 4251 3.430651 CCATACACCAATGAAACCCATGC 60.431 47.826 0.00 0.00 35.24 4.06 R
4863 4927 1.195115 ATATGGTGTCGCTGACTGGT 58.805 50.000 9.49 0.00 33.15 4.00 R
6007 7093 1.280421 AGAACCTTCAGGGACATCTGC 59.720 52.381 0.00 0.00 40.27 4.26 R
6647 7739 0.036010 CCGGCTCAAGGAGTTCATGT 60.036 55.000 0.00 0.00 31.39 3.21 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
60 61 3.124128 CACCATATATGCTAGTGCTTGCG 59.876 47.826 7.24 0.00 40.48 4.85
131 134 1.021390 CGTGAGGGTGTGAGATTGCC 61.021 60.000 0.00 0.00 0.00 4.52
180 186 0.322816 AACAGATGCAGGTGCCGATT 60.323 50.000 0.00 0.00 41.18 3.34
181 187 0.322816 ACAGATGCAGGTGCCGATTT 60.323 50.000 0.00 0.00 41.18 2.17
225 231 1.410004 ACTCAAGTGGGAGTTCGACA 58.590 50.000 0.00 0.00 45.59 4.35
283 289 1.203187 TCAGTAGAGGAGCCCAGTTGT 60.203 52.381 0.00 0.00 0.00 3.32
339 348 7.716123 TCTTTCTTTATTTGGTTCCGTAGTCAA 59.284 33.333 0.00 0.00 0.00 3.18
357 366 7.330946 CGTAGTCAAACCTTGATTGTATTCTGA 59.669 37.037 0.00 0.00 42.47 3.27
532 541 1.472878 GGAGATATAGCCGCATCGTGA 59.527 52.381 0.00 0.00 0.00 4.35
737 755 9.956720 TCAATCATCAAAGAAAAAGAAGAAGAC 57.043 29.630 0.00 0.00 0.00 3.01
763 781 9.638239 CCACATTATTTGATAAAAATATCCCCG 57.362 33.333 0.00 0.00 0.00 5.73
796 830 0.689080 ATGTCGGCTCCCATCTCACT 60.689 55.000 0.00 0.00 0.00 3.41
808 842 2.534298 CATCTCACTAACCTCGCAGTG 58.466 52.381 0.00 0.00 42.88 3.66
887 925 1.995626 CTCCCTCCAACCATCCCGT 60.996 63.158 0.00 0.00 0.00 5.28
1316 1355 1.412710 TCTTGTTGCTTCGACAGGAGT 59.587 47.619 0.00 0.00 30.56 3.85
1317 1356 2.626266 TCTTGTTGCTTCGACAGGAGTA 59.374 45.455 0.00 0.00 30.56 2.59
1318 1357 2.724977 TGTTGCTTCGACAGGAGTAG 57.275 50.000 0.00 0.00 0.00 2.57
1319 1358 1.961394 TGTTGCTTCGACAGGAGTAGT 59.039 47.619 0.00 0.00 0.00 2.73
1334 1378 3.467803 GAGTAGTGAGAGAGGAGAGAGC 58.532 54.545 0.00 0.00 0.00 4.09
1462 1506 0.165944 GCACCACATGTTCGTACTGC 59.834 55.000 0.00 0.00 0.00 4.40
1489 1533 0.478942 AGATCGGAGAGGATTCGGGA 59.521 55.000 0.00 0.00 43.63 5.14
1651 1695 2.438411 GACGAGAAGGAGAAGGTCTCA 58.562 52.381 7.52 0.00 45.12 3.27
1659 1703 0.390998 GAGAAGGTCTCAGGTGCAGC 60.391 60.000 8.11 8.11 42.90 5.25
1749 1793 2.891191 GGGTTGACCTTGGATACCAA 57.109 50.000 3.21 3.21 41.69 3.67
1927 1971 4.382386 TGATGATGGCATTGATGATCCT 57.618 40.909 0.00 0.00 34.11 3.24
2027 2077 2.746362 GCCTTGGAGAGACACATGAAAG 59.254 50.000 0.00 0.00 0.00 2.62
2054 2104 4.080919 CAGGTGGAAGGATTAGTGATGACA 60.081 45.833 0.00 0.00 0.00 3.58
2133 2183 2.693074 GGTCCAAGAAGAAACCAAAGCA 59.307 45.455 0.00 0.00 0.00 3.91
2227 2277 2.632512 TGGTTTTCTTCCCTGAATTGGC 59.367 45.455 0.00 0.00 0.00 4.52
2241 2292 2.157640 ATTGGCGGAATTTGATCCCA 57.842 45.000 0.00 0.00 36.00 4.37
2243 2294 1.691196 TGGCGGAATTTGATCCCATC 58.309 50.000 0.00 0.00 36.00 3.51
2436 2487 9.961265 TTAGCATGTATAAGATGTGTACTGTAC 57.039 33.333 10.98 10.98 0.00 2.90
2449 2500 7.065216 TGTGTACTGTACGTAGTGACTATTC 57.935 40.000 12.87 0.00 45.73 1.75
2512 2563 5.048846 ACCCAGTGGCTACCTAAATATTG 57.951 43.478 2.61 0.00 33.59 1.90
2622 2673 5.957842 TTGCTGTTGGATTTAAGAATCGT 57.042 34.783 0.00 0.00 42.12 3.73
2687 2738 7.060633 GGTGAATTAACTGAAAATGTTAGCACG 59.939 37.037 0.00 0.00 33.86 5.34
2750 2806 7.118971 AGTCAAAATCAGTATCTGTGAGCTTTC 59.881 37.037 0.00 0.00 32.61 2.62
2756 2812 8.885494 ATCAGTATCTGTGAGCTTTCTTATTC 57.115 34.615 0.00 0.00 32.61 1.75
2781 2837 7.450634 TCGGTCTATCAGTACCTTTGCTATATT 59.549 37.037 0.00 0.00 33.34 1.28
3178 3234 7.169645 GCAATCAAGCTTGTTTCATGTCTTTAA 59.830 33.333 25.19 1.76 0.00 1.52
3227 3283 7.611855 CCTCTGTTCTTGATGGTTACCTAATTT 59.388 37.037 2.07 0.00 0.00 1.82
3237 3293 6.394025 TGGTTACCTAATTTGTTGGAACAC 57.606 37.500 2.07 0.00 39.29 3.32
3447 3503 6.422100 GTCATACGTAGCTCATGATCAACAAT 59.578 38.462 0.00 0.00 31.74 2.71
3605 3661 4.021192 ACTCCATTTGGCAAAACAGTATGG 60.021 41.667 17.70 17.75 35.96 2.74
3778 3834 6.461110 TTAGCCTCGCTTTACTGTTATAGT 57.539 37.500 0.00 0.00 40.44 2.12
3813 3869 9.516314 ACTTGTCAAAGTTAAAGCAGTATTTTC 57.484 29.630 0.00 0.00 44.47 2.29
3930 3987 6.963049 TCTTTCGCTAAGTCCTTTAATGTC 57.037 37.500 0.00 0.00 35.28 3.06
3995 4053 7.016153 TCTAAAATCACCATAACCACACTCT 57.984 36.000 0.00 0.00 0.00 3.24
4004 4062 7.876068 TCACCATAACCACACTCTAAACTTAAG 59.124 37.037 0.00 0.00 0.00 1.85
4032 4090 4.218417 TCCTGACCTTTTCTTTTGCTATGC 59.782 41.667 0.00 0.00 0.00 3.14
4044 4102 0.734309 TGCTATGCCGCAACATGAAG 59.266 50.000 0.00 0.00 36.89 3.02
4062 4120 8.497910 ACATGAAGTATCCTGTAGTATCCATT 57.502 34.615 0.00 0.00 33.33 3.16
4063 4121 8.589338 ACATGAAGTATCCTGTAGTATCCATTC 58.411 37.037 0.00 0.00 33.33 2.67
4064 4122 8.588472 CATGAAGTATCCTGTAGTATCCATTCA 58.412 37.037 0.00 0.00 0.00 2.57
4065 4123 8.727100 TGAAGTATCCTGTAGTATCCATTCAT 57.273 34.615 0.00 0.00 0.00 2.57
4066 4124 8.807118 TGAAGTATCCTGTAGTATCCATTCATC 58.193 37.037 0.00 0.00 0.00 2.92
4067 4125 7.726033 AGTATCCTGTAGTATCCATTCATCC 57.274 40.000 0.00 0.00 0.00 3.51
4068 4126 7.248976 AGTATCCTGTAGTATCCATTCATCCA 58.751 38.462 0.00 0.00 0.00 3.41
4069 4127 7.903481 AGTATCCTGTAGTATCCATTCATCCAT 59.097 37.037 0.00 0.00 0.00 3.41
4070 4128 7.579940 ATCCTGTAGTATCCATTCATCCATT 57.420 36.000 0.00 0.00 0.00 3.16
4071 4129 7.392766 TCCTGTAGTATCCATTCATCCATTT 57.607 36.000 0.00 0.00 0.00 2.32
4404 4463 8.391075 ACTGTAGTTTTAAGTGTTATGCATGT 57.609 30.769 10.16 0.00 0.00 3.21
4418 4477 6.382282 TGTTATGCATGTAATTTCCCCATTGA 59.618 34.615 10.16 0.00 0.00 2.57
4480 4540 1.798813 GCTCAACACACACTGGTTTGC 60.799 52.381 0.00 0.00 0.00 3.68
4481 4541 0.814457 TCAACACACACTGGTTTGCC 59.186 50.000 0.00 0.00 0.00 4.52
4496 4556 4.154918 TGGTTTGCCATGTGTTTGTTTTTC 59.845 37.500 0.00 0.00 40.46 2.29
4530 4592 1.111277 GTTGTTTTGCACCAGGGAGT 58.889 50.000 0.00 0.00 0.00 3.85
4683 4745 6.017687 TCAGTATGCTAGCATAAAACTGCATG 60.018 38.462 34.50 22.25 38.98 4.06
4727 4789 3.778954 TGATGTTGTCACCATGTACCA 57.221 42.857 0.00 0.00 0.00 3.25
4879 4943 1.069090 GAACCAGTCAGCGACACCA 59.931 57.895 10.52 0.00 34.60 4.17
4880 4944 0.320771 GAACCAGTCAGCGACACCAT 60.321 55.000 10.52 0.00 34.60 3.55
4930 4994 0.778083 GAACCCTTTTCCACTCCCCT 59.222 55.000 0.00 0.00 0.00 4.79
4971 5036 4.705023 GGTATTTGTTCCAGGCAATACTGT 59.295 41.667 0.00 0.00 36.75 3.55
4976 5042 3.244875 TGTTCCAGGCAATACTGTCACAT 60.245 43.478 0.00 0.00 36.75 3.21
5012 5078 1.064758 TCCCCATCTGTATTGTGTGCC 60.065 52.381 0.00 0.00 0.00 5.01
5167 5233 1.284657 CTGTCCAATAGCAGTGCGAG 58.715 55.000 10.00 0.78 0.00 5.03
5224 5290 3.070018 CTCTCCATTGACACTGGAACAC 58.930 50.000 14.80 0.00 42.12 3.32
5338 6407 1.557099 TGGAATCGTACCAGCTGTCT 58.443 50.000 13.81 0.00 33.22 3.41
5349 6418 0.170561 CAGCTGTCTGATTTGCTGCC 59.829 55.000 5.25 0.00 44.72 4.85
5438 6514 1.160137 GCCGATCAGCACTTCAGTTT 58.840 50.000 0.00 0.00 0.00 2.66
5646 6729 5.263599 TGAACCATCCTGTTCTGCAATATT 58.736 37.500 5.61 0.00 43.96 1.28
5661 6744 8.389779 TCTGCAATATTGTTTGTCTAAGAACA 57.610 30.769 16.61 1.14 34.22 3.18
5954 7037 5.020795 TGTATGTTCTCTTACCTGCTGGTA 58.979 41.667 17.78 17.78 46.43 3.25
5989 7075 7.604164 AGTGTATGAATTGTGTTGACCTAAGAG 59.396 37.037 0.00 0.00 0.00 2.85
5990 7076 7.602644 GTGTATGAATTGTGTTGACCTAAGAGA 59.397 37.037 0.00 0.00 0.00 3.10
6007 7093 7.663493 ACCTAAGAGATCTTTTTCCTCTTGTTG 59.337 37.037 3.52 5.18 44.30 3.33
6280 7367 8.844244 CCTATAAATTTTCAGGATTGTGAGAGG 58.156 37.037 10.77 0.00 0.00 3.69
6356 7443 7.119846 GTGGACAGCTAACAAGATAACAAAGAT 59.880 37.037 0.00 0.00 0.00 2.40
6454 7546 3.849911 ACCACTGTCAACATCTATGTCG 58.150 45.455 0.00 0.00 40.80 4.35
6628 7720 6.037062 GTGAAGTTTTGTTCATTCTTTTGGGG 59.963 38.462 0.00 0.00 38.68 4.96
6647 7739 0.884704 GAAGAAACGGTCTGGCTGCA 60.885 55.000 0.50 0.00 36.40 4.41
6659 7751 0.111061 TGGCTGCACATGAACTCCTT 59.889 50.000 0.00 0.00 0.00 3.36
6778 7870 6.780031 TCTGTAATTCTCTCCAGGATAGGAAG 59.220 42.308 2.04 0.00 37.20 3.46
6815 7907 5.302568 TGCATGAACTTTTGGAATCTTCAGT 59.697 36.000 0.00 0.00 0.00 3.41
6822 7914 7.830099 ACTTTTGGAATCTTCAGTCTTGATT 57.170 32.000 0.00 0.00 32.27 2.57
6824 7916 8.699130 ACTTTTGGAATCTTCAGTCTTGATTTT 58.301 29.630 0.00 0.00 32.27 1.82
6875 7981 8.470002 ACCTAAATTTGTCTGATATTTCCAAGC 58.530 33.333 0.00 0.00 0.00 4.01
6877 7983 9.294030 CTAAATTTGTCTGATATTTCCAAGCAC 57.706 33.333 0.00 0.00 0.00 4.40
6878 7984 6.839124 ATTTGTCTGATATTTCCAAGCACA 57.161 33.333 0.00 0.00 0.00 4.57
6879 7985 6.839124 TTTGTCTGATATTTCCAAGCACAT 57.161 33.333 0.00 0.00 0.00 3.21
6880 7986 6.839124 TTGTCTGATATTTCCAAGCACATT 57.161 33.333 0.00 0.00 0.00 2.71
6882 7988 7.320443 TGTCTGATATTTCCAAGCACATTAC 57.680 36.000 0.00 0.00 0.00 1.89
6896 8005 6.147864 AGCACATTACTTTGTGTTGAATGT 57.852 33.333 6.46 0.00 46.93 2.71
6920 8029 7.116090 TGTGCAATAAACAATATGTTGCTTCAC 59.884 33.333 1.57 2.33 40.14 3.18
7152 8273 6.073385 TCAGCTGATCGATGAATTAGCAATTC 60.073 38.462 13.74 12.10 45.86 2.17
7241 8365 6.658188 TTAAAATTCACCCCGATTCAGTTT 57.342 33.333 0.00 0.00 0.00 2.66
7308 8432 3.539604 CCTGATCACCTCATCAAAGACC 58.460 50.000 0.00 0.00 32.24 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.153475 GTGGCTAACTTACGCAAATGAGAA 59.847 41.667 0.00 0.00 0.00 2.87
60 61 0.466124 GGTAGTGAGGTGGATCTGCC 59.534 60.000 0.00 0.00 37.10 4.85
225 231 3.703052 ACATAGTAACGTCCCGAATCCTT 59.297 43.478 0.00 0.00 0.00 3.36
283 289 2.276116 GCTAGATCCCCGATCGCCA 61.276 63.158 10.32 0.00 43.17 5.69
339 348 8.585471 ACATCATTCAGAATACAATCAAGGTT 57.415 30.769 0.00 0.00 0.00 3.50
379 388 5.643379 ACAATCGCCACTTCAAACAATAT 57.357 34.783 0.00 0.00 0.00 1.28
386 395 1.810151 GGCTTACAATCGCCACTTCAA 59.190 47.619 0.00 0.00 45.59 2.69
438 447 6.995091 GCAAGAGGGATAATCTTTACACATCT 59.005 38.462 0.00 0.00 34.80 2.90
592 601 1.166129 GCCGAAGTCTTTTTCCTCCC 58.834 55.000 0.00 0.00 0.00 4.30
597 606 1.000607 GGGGTTGCCGAAGTCTTTTTC 60.001 52.381 0.00 0.00 0.00 2.29
598 607 1.037493 GGGGTTGCCGAAGTCTTTTT 58.963 50.000 0.00 0.00 0.00 1.94
664 673 3.308438 AGCACAAATGACAATCCTTGC 57.692 42.857 0.00 0.00 0.00 4.01
665 674 5.633830 ACTAGCACAAATGACAATCCTTG 57.366 39.130 0.00 0.00 0.00 3.61
666 675 7.759489 TTAACTAGCACAAATGACAATCCTT 57.241 32.000 0.00 0.00 0.00 3.36
668 677 8.673711 TGTATTAACTAGCACAAATGACAATCC 58.326 33.333 0.00 0.00 0.00 3.01
737 755 9.638239 CGGGGATATTTTTATCAAATAATGTGG 57.362 33.333 0.00 0.00 0.00 4.17
762 780 1.255342 CGACATGTTAGGCATCGAACG 59.745 52.381 0.00 0.00 35.19 3.95
763 781 1.593006 CCGACATGTTAGGCATCGAAC 59.407 52.381 0.00 0.00 35.19 3.95
764 782 1.934589 CCGACATGTTAGGCATCGAA 58.065 50.000 0.00 0.00 35.19 3.71
808 842 3.394606 AGAGGTATCTCTCTCTCCCTCAC 59.605 52.174 0.00 0.00 46.79 3.51
887 925 4.526650 GGAGGGGCTTTTCTGTAATTTGAA 59.473 41.667 0.00 0.00 0.00 2.69
1265 1304 4.856801 CGCCTCAACCCATCCCCG 62.857 72.222 0.00 0.00 0.00 5.73
1294 1333 2.872245 CTCCTGTCGAAGCAACAAGAAA 59.128 45.455 0.00 0.00 0.00 2.52
1316 1355 4.308526 TTTGCTCTCTCCTCTCTCACTA 57.691 45.455 0.00 0.00 0.00 2.74
1317 1356 2.897271 TTGCTCTCTCCTCTCTCACT 57.103 50.000 0.00 0.00 0.00 3.41
1318 1357 3.430651 CCATTTGCTCTCTCCTCTCTCAC 60.431 52.174 0.00 0.00 0.00 3.51
1319 1358 2.765135 CCATTTGCTCTCTCCTCTCTCA 59.235 50.000 0.00 0.00 0.00 3.27
1334 1378 2.163010 AGAGCGTCAAAGATGCCATTTG 59.837 45.455 7.54 0.31 44.75 2.32
1462 1506 1.753649 TCCTCTCCGATCTCTGCAAAG 59.246 52.381 0.00 0.00 0.00 2.77
1651 1695 0.820891 CAGTGTTTCCAGCTGCACCT 60.821 55.000 8.66 1.78 32.75 4.00
1659 1703 1.199327 CAGCATCAGCAGTGTTTCCAG 59.801 52.381 0.00 0.00 45.49 3.86
1749 1793 1.645710 CTCCTTGTCAGTACCACCCT 58.354 55.000 0.00 0.00 0.00 4.34
1757 1801 1.974236 CTCTGGAACCTCCTTGTCAGT 59.026 52.381 0.00 0.00 37.46 3.41
1873 1917 2.131023 GGATCAACCTCCCTCATTCCT 58.869 52.381 0.00 0.00 35.41 3.36
1876 1920 2.850833 TCTGGATCAACCTCCCTCATT 58.149 47.619 0.00 0.00 39.86 2.57
2027 2077 1.065126 ACTAATCCTTCCACCTGCTGC 60.065 52.381 0.00 0.00 0.00 5.25
2054 2104 4.314961 TGATTCGTGTTAACAGCATCACT 58.685 39.130 8.98 0.00 0.00 3.41
2133 2183 5.501156 AGAACAACTCACCAGACTTTTTCT 58.499 37.500 0.00 0.00 33.33 2.52
2227 2277 2.936202 AGTGGATGGGATCAAATTCCG 58.064 47.619 0.00 0.00 36.58 4.30
2436 2487 6.150318 ACTCAACACTTGAATAGTCACTACG 58.850 40.000 0.00 0.00 39.58 3.51
2538 2589 6.091849 CAGTCTAACATGTTCAAGACATCCAG 59.908 42.308 29.87 14.74 45.88 3.86
2622 2673 7.397476 GGTCATCCAAGATCAGTACCATATCTA 59.603 40.741 0.00 0.00 29.89 1.98
2634 2685 4.387026 AAAACCTGGTCATCCAAGATCA 57.613 40.909 0.00 0.00 43.81 2.92
2638 2689 2.289010 GGCAAAAACCTGGTCATCCAAG 60.289 50.000 0.00 0.00 43.81 3.61
2750 2806 6.421202 GCAAAGGTACTGATAGACCGAATAAG 59.579 42.308 0.00 0.00 40.86 1.73
2756 2812 3.802948 AGCAAAGGTACTGATAGACCG 57.197 47.619 0.00 0.00 40.86 4.79
2781 2837 7.464589 TGGGGATGACTCTCTTAGGTATATAGA 59.535 40.741 0.00 0.00 0.00 1.98
3227 3283 3.904717 ACCTGGTTAATGTGTTCCAACA 58.095 40.909 0.00 0.00 36.38 3.33
3237 3293 5.766150 TCACAAGTTGAACCTGGTTAATG 57.234 39.130 12.96 9.53 0.00 1.90
3269 3325 2.042464 AGTTGAGCAGTGGAGTTCAGA 58.958 47.619 0.00 0.00 30.36 3.27
3447 3503 4.202202 CCCCTTAACAAAAGCACATGTCAA 60.202 41.667 0.00 0.00 0.00 3.18
3605 3661 4.708726 AGAGTTATGTGCCAAGAAATGC 57.291 40.909 0.00 0.00 0.00 3.56
3647 3703 8.742125 ACTTATACAGGATGGAGGAATCATAA 57.258 34.615 0.00 0.00 43.62 1.90
3778 3834 7.871463 GCTTTAACTTTGACAAGTACCTAGAGA 59.129 37.037 0.00 0.00 42.89 3.10
3813 3869 6.591448 TCTGTATGTGAAACTAATCAGCAGTG 59.409 38.462 0.00 0.00 38.04 3.66
3858 3915 7.512130 AGATGTGATTGCATTTCATAGACCTA 58.488 34.615 3.47 0.00 0.00 3.08
3930 3987 9.855361 GAGTTTTCAATCTTGTATCACATATCG 57.145 33.333 0.00 0.00 0.00 2.92
3995 4053 7.833285 AAAGGTCAGGAATTGCTTAAGTTTA 57.167 32.000 4.02 0.00 0.00 2.01
4004 4062 4.212004 GCAAAAGAAAAGGTCAGGAATTGC 59.788 41.667 0.00 0.00 33.62 3.56
4044 4102 7.482169 TGGATGAATGGATACTACAGGATAC 57.518 40.000 0.00 0.00 37.61 2.24
4193 4251 3.430651 CCATACACCAATGAAACCCATGC 60.431 47.826 0.00 0.00 35.24 4.06
4404 4463 8.482128 GGTTATGATTTGTCAATGGGGAAATTA 58.518 33.333 0.00 0.00 0.00 1.40
4418 4477 5.888161 GGGAGATCACAAGGTTATGATTTGT 59.112 40.000 0.00 0.00 35.67 2.83
4496 4556 7.639461 GTGCAAAACAACCTTGATTAAATTGTG 59.361 33.333 0.00 0.00 33.88 3.33
4530 4592 2.496070 CGATAAGGACTGGGACAACTGA 59.504 50.000 0.00 0.00 38.70 3.41
4623 4685 6.271488 TCTGAATCAAAACAGCAAATAGGG 57.729 37.500 0.00 0.00 34.57 3.53
4683 4745 9.838339 TCATCCTTTTCTCATAAACCTCTAATC 57.162 33.333 0.00 0.00 0.00 1.75
4770 4832 2.930040 CAACCACAGATAAGTAGCCACG 59.070 50.000 0.00 0.00 0.00 4.94
4863 4927 1.195115 ATATGGTGTCGCTGACTGGT 58.805 50.000 9.49 0.00 33.15 4.00
4879 4943 9.656323 TCTGTATTGAAACTACTGGACCTATAT 57.344 33.333 0.00 0.00 0.00 0.86
4880 4944 9.483489 TTCTGTATTGAAACTACTGGACCTATA 57.517 33.333 0.00 0.00 0.00 1.31
4930 4994 2.858644 ACCCAAGTCCCAGGATATGAA 58.141 47.619 0.00 0.00 0.00 2.57
4971 5036 2.516448 GGATGAGTCCCCGATGTGA 58.484 57.895 0.00 0.00 38.69 3.58
5012 5078 6.279123 TCTGAGCAAAGATATAAGCAGACAG 58.721 40.000 0.00 0.00 0.00 3.51
5338 6407 2.892215 TGATCAAGTTGGCAGCAAATCA 59.108 40.909 3.63 6.66 0.00 2.57
5468 6545 8.656849 ACAACTTATGCTACAGATTAAAAGACG 58.343 33.333 0.00 0.00 0.00 4.18
5543 6626 7.023575 GCACATTTACCTTTTCATACTGTGAG 58.976 38.462 0.00 0.00 38.29 3.51
5867 6950 3.074412 CAGTCCGTCAGCTTGGTAAAAT 58.926 45.455 0.00 0.00 0.00 1.82
5989 7075 5.695851 TCTGCAACAAGAGGAAAAAGATC 57.304 39.130 0.00 0.00 0.00 2.75
5990 7076 5.537674 ACATCTGCAACAAGAGGAAAAAGAT 59.462 36.000 0.00 0.00 32.39 2.40
6007 7093 1.280421 AGAACCTTCAGGGACATCTGC 59.720 52.381 0.00 0.00 40.27 4.26
6049 7135 6.037786 ACAAGAGAATAAGTTGGACATCGA 57.962 37.500 0.00 0.00 0.00 3.59
6230 7316 8.823818 AGGATAACGATTAAACTTAAACGGATG 58.176 33.333 13.97 0.00 41.36 3.51
6280 7367 5.101628 TGAAATAGTTTTGCCATTGATCGC 58.898 37.500 0.00 0.00 0.00 4.58
6356 7443 6.854578 TCTCTAAACCCACCCTTTGAAAATA 58.145 36.000 0.00 0.00 0.00 1.40
6454 7546 4.554036 GCATCGACTCCCTGGCCC 62.554 72.222 0.00 0.00 0.00 5.80
6628 7720 0.884704 TGCAGCCAGACCGTTTCTTC 60.885 55.000 0.00 0.00 28.96 2.87
6647 7739 0.036010 CCGGCTCAAGGAGTTCATGT 60.036 55.000 0.00 0.00 31.39 3.21
6791 7883 5.302568 ACTGAAGATTCCAAAAGTTCATGCA 59.697 36.000 0.00 0.00 0.00 3.96
6794 7886 7.503566 TCAAGACTGAAGATTCCAAAAGTTCAT 59.496 33.333 0.00 0.00 0.00 2.57
6846 7938 9.699410 TGGAAATATCAGACAAATTTAGGTCAT 57.301 29.630 10.33 0.99 36.50 3.06
6855 7961 6.839124 TGTGCTTGGAAATATCAGACAAAT 57.161 33.333 0.00 0.00 0.00 2.32
6877 7983 6.825284 TTGCACATTCAACACAAAGTAATG 57.175 33.333 0.00 0.00 34.04 1.90
6878 7984 9.539825 TTTATTGCACATTCAACACAAAGTAAT 57.460 25.926 0.00 0.00 0.00 1.89
6879 7985 8.812329 GTTTATTGCACATTCAACACAAAGTAA 58.188 29.630 0.00 0.00 0.00 2.24
6880 7986 7.976175 TGTTTATTGCACATTCAACACAAAGTA 59.024 29.630 0.00 0.00 0.00 2.24
6882 7988 7.231705 TGTTTATTGCACATTCAACACAAAG 57.768 32.000 0.00 0.00 0.00 2.77
6896 8005 7.150640 TGTGAAGCAACATATTGTTTATTGCA 58.849 30.769 9.65 0.00 46.38 4.08
6935 8047 1.239968 CCTGAACCAGCAAGAGCACC 61.240 60.000 0.00 0.00 45.49 5.01
7050 8164 5.350091 GTGTGGTTTTATGTGTTTGCACTTT 59.650 36.000 0.00 0.00 45.44 2.66
7053 8167 3.241784 CGTGTGGTTTTATGTGTTTGCAC 59.758 43.478 0.00 0.00 45.44 4.57
7119 8233 5.729974 TCATCGATCAGCTGAAATTTCTG 57.270 39.130 22.50 18.29 0.00 3.02
7152 8273 9.520204 GTTTGTAATGTTGGATTTGATATCCTG 57.480 33.333 0.00 0.00 38.95 3.86
7241 8365 2.677914 TCAGAGACAAGGTCCTCACAA 58.322 47.619 0.00 0.00 32.18 3.33
7308 8432 4.051237 TGTTCGACTGTGTTCTTGATCAG 58.949 43.478 0.00 0.00 0.00 2.90



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

AutoCloner maintained by Alex Coulton.