Multiple sequence alignment - TraesCS7A01G388800

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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 TraesCS7A01G388800 chr7A 100.000 3416 0 0 1 3416 564348157 564344742 0.000000e+00 6309
1 TraesCS7A01G388800 chr7B 92.461 2865 106 46 3 2814 526885445 526882638 0.000000e+00 3993
2 TraesCS7A01G388800 chr7B 88.254 613 56 13 2816 3416 526882607 526881999 0.000000e+00 719
3 TraesCS7A01G388800 chr7D 94.098 2389 61 32 344 2691 498529494 498527145 0.000000e+00 3557
4 TraesCS7A01G388800 chr7D 88.842 475 49 3 2943 3416 498501676 498501205 6.350000e-162 580
5 TraesCS7A01G388800 chr7D 83.333 234 24 8 108 338 498529755 498529534 5.780000e-48 202
6 TraesCS7A01G388800 chr7D 93.893 131 3 1 2678 2803 498526471 498526341 3.480000e-45 193
7 TraesCS7A01G388800 chr7D 92.771 83 4 2 2796 2877 498510545 498510464 5.990000e-23 119
8 TraesCS7A01G388800 chr6A 84.483 232 29 6 1265 1493 183766951 183766724 4.440000e-54 222
9 TraesCS7A01G388800 chr6A 87.059 170 20 2 1892 2060 183766397 183766229 1.250000e-44 191
10 TraesCS7A01G388800 chr6D 87.647 170 19 2 1892 2060 140038278 140038446 2.690000e-46 196
11 TraesCS7A01G388800 chr6B 87.059 170 20 2 1892 2060 239913788 239913956 1.250000e-44 191


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 TraesCS7A01G388800 chr7A 564344742 564348157 3415 True 6309.000000 6309 100.000000 1 3416 1 chr7A.!!$R1 3415
1 TraesCS7A01G388800 chr7B 526881999 526885445 3446 True 2356.000000 3993 90.357500 3 3416 2 chr7B.!!$R1 3413
2 TraesCS7A01G388800 chr7D 498526341 498529755 3414 True 1317.333333 3557 90.441333 108 2803 3 chr7D.!!$R3 2695
3 TraesCS7A01G388800 chr6A 183766229 183766951 722 True 206.500000 222 85.771000 1265 2060 2 chr6A.!!$R1 795

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
617 668 0.030101 GAGAGCACGCACTAGCTAGG 59.970 60.0 24.35 14.1 42.04 3.02 F
960 1051 0.037303 CTGCTGGGATGAGGTGTTGT 59.963 55.0 0.00 0.0 0.00 3.32 F
1490 1581 0.762418 AACATTGTCCAGGTCCGTCA 59.238 50.0 0.00 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1545 1651 0.169672 GATATGCATGCATGGCGGAC 59.830 55.000 37.43 19.6 37.82 4.79 R
2156 2332 1.069204 GCGGCCTCAGATTCTGACATA 59.931 52.381 12.38 0.0 35.39 2.29 R
3139 4042 0.384230 CCATGTTGTGTTGTCGTCGC 60.384 55.000 0.00 0.0 0.00 5.19 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
34 35 2.699954 CCACTGTTAGGCGAGATTGTT 58.300 47.619 0.00 0.00 0.00 2.83
90 91 2.282391 GCCCTGCCATCACACACA 60.282 61.111 0.00 0.00 0.00 3.72
91 92 2.629656 GCCCTGCCATCACACACAC 61.630 63.158 0.00 0.00 0.00 3.82
92 93 1.973281 CCCTGCCATCACACACACC 60.973 63.158 0.00 0.00 0.00 4.16
93 94 1.973281 CCTGCCATCACACACACCC 60.973 63.158 0.00 0.00 0.00 4.61
94 95 1.228215 CTGCCATCACACACACCCA 60.228 57.895 0.00 0.00 0.00 4.51
95 96 1.228215 TGCCATCACACACACCCAG 60.228 57.895 0.00 0.00 0.00 4.45
96 97 1.228245 GCCATCACACACACCCAGT 60.228 57.895 0.00 0.00 0.00 4.00
206 207 1.959042 CAGCTGGTGATGTCATACCC 58.041 55.000 5.57 2.41 36.10 3.69
265 270 3.106242 TCATACACACACACACACTCC 57.894 47.619 0.00 0.00 0.00 3.85
323 334 1.299926 GTACGTAGCCCCTGATGCG 60.300 63.158 0.00 0.00 41.89 4.73
324 335 2.495409 TACGTAGCCCCTGATGCGG 61.495 63.158 0.00 0.00 40.42 5.69
404 449 1.581934 TACAGATATTGCAGGTGCGC 58.418 50.000 0.00 0.00 45.83 6.09
464 515 1.382695 TGGCCTAGCTACCACTCCC 60.383 63.158 3.32 0.00 0.00 4.30
535 586 3.451178 TGAGCGCCTTTAATTAGTCTCCT 59.549 43.478 2.29 0.00 0.00 3.69
551 602 2.494918 CTCCGTCCGTCCATCCAC 59.505 66.667 0.00 0.00 0.00 4.02
565 616 0.394565 ATCCACGGCTTATCTCCAGC 59.605 55.000 0.00 0.00 36.45 4.85
566 617 0.975556 TCCACGGCTTATCTCCAGCA 60.976 55.000 0.00 0.00 39.21 4.41
567 618 0.107456 CCACGGCTTATCTCCAGCAT 59.893 55.000 0.00 0.00 39.21 3.79
617 668 0.030101 GAGAGCACGCACTAGCTAGG 59.970 60.000 24.35 14.10 42.04 3.02
618 669 1.590259 GAGCACGCACTAGCTAGGC 60.590 63.158 24.35 21.20 42.04 3.93
705 773 0.593518 TTTGCCATTTGTGTCGTGCG 60.594 50.000 0.00 0.00 0.00 5.34
707 775 1.154413 GCCATTTGTGTCGTGCGAG 60.154 57.895 0.00 0.00 0.00 5.03
741 818 0.179145 CTCGGTGTAGGTTAGGTGCG 60.179 60.000 0.00 0.00 0.00 5.34
764 841 5.084722 GTCATTCGGATAAGGTATCGTACG 58.915 45.833 9.53 9.53 36.03 3.67
766 843 2.426522 TCGGATAAGGTATCGTACGGG 58.573 52.381 16.52 0.00 36.03 5.28
767 844 1.470098 CGGATAAGGTATCGTACGGGG 59.530 57.143 16.52 0.00 36.03 5.73
806 894 0.605319 TTTCACTCATGGGCACGGAC 60.605 55.000 0.00 0.00 0.00 4.79
808 896 2.034879 CACTCATGGGCACGGACAC 61.035 63.158 0.00 0.00 0.00 3.67
810 898 4.386951 TCATGGGCACGGACACGG 62.387 66.667 0.00 0.00 46.48 4.94
948 1039 2.739996 CCTAGTCCCTGCTGCTGGG 61.740 68.421 32.12 32.12 42.93 4.45
955 1046 2.677289 CCTGCTGCTGGGATGAGGT 61.677 63.158 16.96 0.00 0.00 3.85
957 1048 2.194388 CTGCTGCTGGGATGAGGTGT 62.194 60.000 0.00 0.00 0.00 4.16
958 1049 1.001641 GCTGCTGGGATGAGGTGTT 60.002 57.895 0.00 0.00 0.00 3.32
959 1050 1.310933 GCTGCTGGGATGAGGTGTTG 61.311 60.000 0.00 0.00 0.00 3.33
960 1051 0.037303 CTGCTGGGATGAGGTGTTGT 59.963 55.000 0.00 0.00 0.00 3.32
1203 1294 2.103042 GTCGTGGTCCATGCTGCTC 61.103 63.158 6.17 0.00 0.00 4.26
1487 1578 0.960364 CCCAACATTGTCCAGGTCCG 60.960 60.000 0.00 0.00 0.00 4.79
1490 1581 0.762418 AACATTGTCCAGGTCCGTCA 59.238 50.000 0.00 0.00 0.00 4.35
1506 1597 2.422127 CCGTCACCTCTCTTTCTCTCTC 59.578 54.545 0.00 0.00 0.00 3.20
1507 1598 2.095213 CGTCACCTCTCTTTCTCTCTCG 59.905 54.545 0.00 0.00 0.00 4.04
1540 1646 3.746045 TTCCTCTTGTACACACTGACC 57.254 47.619 0.00 0.00 0.00 4.02
1545 1651 2.029380 TCTTGTACACACTGACCGATGG 60.029 50.000 0.00 0.00 0.00 3.51
1582 1700 8.105097 TGCATATCTTACACTGACTAGAGATC 57.895 38.462 0.00 0.00 0.00 2.75
1587 1705 7.575414 TCTTACACTGACTAGAGATCAATCC 57.425 40.000 0.00 0.00 0.00 3.01
1598 1716 8.375608 ACTAGAGATCAATCCGATTTGATTTG 57.624 34.615 12.22 3.70 44.35 2.32
2092 2258 2.675423 CACCCCGTCCGTCTCTCA 60.675 66.667 0.00 0.00 0.00 3.27
2142 2318 2.100916 ACGTACTTGTCTCTGCTTGTGT 59.899 45.455 0.00 0.00 0.00 3.72
2143 2319 2.726760 CGTACTTGTCTCTGCTTGTGTC 59.273 50.000 0.00 0.00 0.00 3.67
2144 2320 3.551046 CGTACTTGTCTCTGCTTGTGTCT 60.551 47.826 0.00 0.00 0.00 3.41
2145 2321 2.831333 ACTTGTCTCTGCTTGTGTCTG 58.169 47.619 0.00 0.00 0.00 3.51
2146 2322 2.169352 ACTTGTCTCTGCTTGTGTCTGT 59.831 45.455 0.00 0.00 0.00 3.41
2147 2323 2.229675 TGTCTCTGCTTGTGTCTGTG 57.770 50.000 0.00 0.00 0.00 3.66
2155 2331 1.662629 GCTTGTGTCTGTGATGATCGG 59.337 52.381 0.00 0.00 0.00 4.18
2156 2332 2.932622 GCTTGTGTCTGTGATGATCGGT 60.933 50.000 0.00 0.00 0.00 4.69
2268 2444 0.750850 GGCCGGAGTTCAGCTACATA 59.249 55.000 5.05 0.00 0.00 2.29
2419 2595 1.742761 ACCGGTGCATTCTTGATCAG 58.257 50.000 6.12 0.00 0.00 2.90
2420 2596 1.003580 ACCGGTGCATTCTTGATCAGT 59.996 47.619 6.12 0.00 0.00 3.41
2421 2597 1.667724 CCGGTGCATTCTTGATCAGTC 59.332 52.381 0.00 0.00 0.00 3.51
2428 2604 2.542020 TTCTTGATCAGTCGTTGCCA 57.458 45.000 0.00 0.00 0.00 4.92
2429 2605 1.795768 TCTTGATCAGTCGTTGCCAC 58.204 50.000 0.00 0.00 0.00 5.01
2431 2607 0.107643 TTGATCAGTCGTTGCCACCA 59.892 50.000 0.00 0.00 0.00 4.17
2433 2609 1.234821 GATCAGTCGTTGCCACCAAA 58.765 50.000 0.00 0.00 31.68 3.28
2443 2619 4.219507 TCGTTGCCACCAAAATTGATACAT 59.780 37.500 0.00 0.00 31.68 2.29
2446 2622 6.253298 CGTTGCCACCAAAATTGATACATAAG 59.747 38.462 0.00 0.00 31.68 1.73
2447 2623 6.219417 TGCCACCAAAATTGATACATAAGG 57.781 37.500 0.00 0.00 0.00 2.69
2448 2624 5.954752 TGCCACCAAAATTGATACATAAGGA 59.045 36.000 0.00 0.00 0.00 3.36
2449 2625 6.096705 TGCCACCAAAATTGATACATAAGGAG 59.903 38.462 0.00 0.00 0.00 3.69
2511 2691 3.703286 TGTAACTATGCGCTCGTATGT 57.297 42.857 9.73 0.00 0.00 2.29
2512 2692 4.816786 TGTAACTATGCGCTCGTATGTA 57.183 40.909 9.73 0.00 0.00 2.29
2513 2693 5.172460 TGTAACTATGCGCTCGTATGTAA 57.828 39.130 9.73 0.00 0.00 2.41
2600 2780 8.187913 TGGTTTAATTTCACATGGAGATCAAA 57.812 30.769 0.00 0.00 0.00 2.69
2668 2848 1.834188 ACCAAAGAATCGGCGGATTT 58.166 45.000 19.20 8.05 42.86 2.17
2669 2849 2.167662 ACCAAAGAATCGGCGGATTTT 58.832 42.857 19.20 11.95 42.86 1.82
2683 3550 5.060446 CGGCGGATTTTTCATTTGAAACTAC 59.940 40.000 5.26 0.00 43.01 2.73
2710 3577 8.882736 TGGAATTGATGTCGAATATATATGTGC 58.117 33.333 0.00 0.00 0.00 4.57
2731 3603 2.763448 CAGAGGGCTACAGCTAGACTTT 59.237 50.000 0.54 0.00 41.70 2.66
2814 3686 7.466746 AGGCAAAAATAAACTAGATGAAGCA 57.533 32.000 0.00 0.00 0.00 3.91
2841 3742 5.440234 ACTAGGCTATACACAAGATCACG 57.560 43.478 0.00 0.00 0.00 4.35
2860 3762 1.872197 GAGGGGAGGATCTCGATGCG 61.872 65.000 0.00 0.00 35.32 4.73
2869 3771 2.913054 ATCTCGATGCGTGTGGGCTG 62.913 60.000 0.00 0.00 0.00 4.85
2889 3792 4.922026 GCGAACCCACCGTGGTGT 62.922 66.667 16.55 10.80 44.02 4.16
2894 3797 0.035739 AACCCACCGTGGTGTGATAC 59.964 55.000 16.55 0.00 44.02 2.24
2897 3800 0.895530 CCACCGTGGTGTGATACTCT 59.104 55.000 17.31 0.00 44.02 3.24
2921 3824 3.879295 AGATACATTTGATGGCCTTGACG 59.121 43.478 3.32 0.00 33.60 4.35
2971 3874 3.769189 TTACTACATGGGGAGGAGTGA 57.231 47.619 0.00 0.00 0.00 3.41
3020 3923 4.624024 TGTTGATCGATGAACCTCGTTAAC 59.376 41.667 22.42 1.99 39.62 2.01
3028 3931 6.529125 TCGATGAACCTCGTTAACAAATACTC 59.471 38.462 6.39 0.00 39.62 2.59
3029 3932 6.530534 CGATGAACCTCGTTAACAAATACTCT 59.469 38.462 6.39 0.00 34.00 3.24
3031 3934 8.617290 ATGAACCTCGTTAACAAATACTCTTT 57.383 30.769 6.39 0.00 0.00 2.52
3051 3954 5.249393 TCTTTTCTGGGTCTAAATCTCTGCT 59.751 40.000 0.00 0.00 0.00 4.24
3078 3981 7.592938 TGATGCAACTGGTAAATTCTAACAAG 58.407 34.615 0.00 0.00 0.00 3.16
3085 3988 8.788325 ACTGGTAAATTCTAACAAGTGGTATC 57.212 34.615 0.00 0.00 28.51 2.24
3115 4018 3.306919 GGTTGCAAATTGGATCATGGTGT 60.307 43.478 0.00 0.00 0.00 4.16
3126 4029 6.303903 TGGATCATGGTGTGGATGATATAG 57.696 41.667 0.00 0.00 40.03 1.31
3129 4032 6.070596 GGATCATGGTGTGGATGATATAGACA 60.071 42.308 0.00 0.00 40.03 3.41
3137 4040 8.099537 GGTGTGGATGATATAGACAAAGATGAT 58.900 37.037 0.00 0.00 0.00 2.45
3176 4081 6.757897 ACATGGTGATGTATGTTGTAAAGG 57.242 37.500 0.00 0.00 41.27 3.11
3184 4089 8.564574 GTGATGTATGTTGTAAAGGAAAGACAA 58.435 33.333 0.00 0.00 0.00 3.18
3186 4091 8.691661 ATGTATGTTGTAAAGGAAAGACAAGT 57.308 30.769 0.00 0.00 33.91 3.16
3191 4096 7.535139 TGTTGTAAAGGAAAGACAAGTTTCTG 58.465 34.615 0.00 0.00 36.76 3.02
3211 4116 0.963856 TAGGAGCGAGTGGAGCGAAA 60.964 55.000 0.00 0.00 40.04 3.46
3218 4123 0.537188 GAGTGGAGCGAAATGGAGGA 59.463 55.000 0.00 0.00 0.00 3.71
3219 4124 1.139853 GAGTGGAGCGAAATGGAGGAT 59.860 52.381 0.00 0.00 0.00 3.24
3240 4145 1.821216 AAACGATTGAAGTCGCCCAT 58.179 45.000 0.00 0.00 45.12 4.00
3244 4149 1.202177 CGATTGAAGTCGCCCATTTGG 60.202 52.381 0.00 0.00 34.56 3.28
3256 4161 2.780065 CCATTTGGGCATACACGATG 57.220 50.000 0.00 0.00 38.73 3.84
3281 4194 3.650950 GCTGAAGGGGTGCCAGGA 61.651 66.667 0.00 0.00 0.00 3.86
3285 4198 2.936032 AAGGGGTGCCAGGAGGTC 60.936 66.667 0.00 0.00 37.19 3.85
3297 4210 3.633986 GCCAGGAGGTCATAAATGGAAAG 59.366 47.826 0.00 0.00 37.19 2.62
3314 4227 3.248363 GGAAAGCAAAGGAAACACAATGC 59.752 43.478 0.00 0.00 0.00 3.56
3331 4244 1.592064 TGCATCAAAGAGCACACGAA 58.408 45.000 0.00 0.00 35.51 3.85
3356 4269 4.263462 TGCCTAGCCCAAAATATCGATCAT 60.263 41.667 0.00 0.00 0.00 2.45
3359 4272 6.118170 CCTAGCCCAAAATATCGATCATGAT 58.882 40.000 8.25 8.25 0.00 2.45
3374 4287 7.252708 TCGATCATGATTTTCTGAAACAATGG 58.747 34.615 10.14 0.00 0.00 3.16
3377 4290 7.484993 TCATGATTTTCTGAAACAATGGGAT 57.515 32.000 1.58 0.00 0.00 3.85
3381 4294 6.494491 TGATTTTCTGAAACAATGGGATGAGT 59.506 34.615 1.58 0.00 0.00 3.41
3392 4305 4.970860 ATGGGATGAGTATGGAGAACAG 57.029 45.455 0.00 0.00 0.00 3.16
3396 4309 5.724370 TGGGATGAGTATGGAGAACAGTTTA 59.276 40.000 0.00 0.00 0.00 2.01
3398 4311 7.567250 TGGGATGAGTATGGAGAACAGTTTATA 59.433 37.037 0.00 0.00 0.00 0.98
3399 4312 8.598041 GGGATGAGTATGGAGAACAGTTTATAT 58.402 37.037 0.00 0.00 0.00 0.86
3400 4313 9.646427 GGATGAGTATGGAGAACAGTTTATATC 57.354 37.037 0.00 0.00 0.00 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.047179 GTGGCCCAGTTCCGAGAC 60.047 66.667 0.00 0.00 0.00 3.36
1 2 2.203788 AGTGGCCCAGTTCCGAGA 60.204 61.111 0.00 0.00 0.00 4.04
26 27 3.428045 CCGGAAAATCTGCCAACAATCTC 60.428 47.826 0.00 0.00 0.00 2.75
34 35 2.362375 GGGCCGGAAAATCTGCCA 60.362 61.111 5.05 0.00 45.83 4.92
85 86 1.525995 GTGGGTGACTGGGTGTGTG 60.526 63.158 0.00 0.00 0.00 3.82
86 87 1.692749 AGTGGGTGACTGGGTGTGT 60.693 57.895 0.00 0.00 31.75 3.72
87 88 3.240491 AGTGGGTGACTGGGTGTG 58.760 61.111 0.00 0.00 31.75 3.82
206 207 2.742372 GCCGGTGTGTGCTGGTAG 60.742 66.667 1.90 0.00 37.24 3.18
236 237 1.796459 GTGTGTGTATGAACGGGTGAC 59.204 52.381 0.00 0.00 0.00 3.67
265 270 1.966451 GGGGAGCGTTTCTGTGGTG 60.966 63.158 0.00 0.00 0.00 4.17
323 334 2.162408 GACATGCCTGAAAGTTACAGCC 59.838 50.000 0.00 0.00 34.47 4.85
324 335 2.813754 TGACATGCCTGAAAGTTACAGC 59.186 45.455 0.00 0.00 34.47 4.40
326 337 3.814842 CAGTGACATGCCTGAAAGTTACA 59.185 43.478 0.00 0.00 0.00 2.41
404 449 3.610669 CGAGGGAGGGATGAGGCG 61.611 72.222 0.00 0.00 0.00 5.52
535 586 3.445687 CGTGGATGGACGGACGGA 61.446 66.667 0.00 0.00 35.65 4.69
551 602 1.793258 CTGATGCTGGAGATAAGCCG 58.207 55.000 0.00 0.00 40.06 5.52
617 668 1.359459 CCGTCCTTGTTCTTAGGCGC 61.359 60.000 0.00 0.00 33.74 6.53
618 669 0.245539 TCCGTCCTTGTTCTTAGGCG 59.754 55.000 0.00 0.00 34.38 5.52
741 818 5.084722 CGTACGATACCTTATCCGAATGAC 58.915 45.833 10.44 0.00 31.43 3.06
784 872 1.586154 CGTGCCCATGAGTGAAACCC 61.586 60.000 0.00 0.00 37.80 4.11
786 874 0.605319 TCCGTGCCCATGAGTGAAAC 60.605 55.000 0.00 0.00 0.00 2.78
806 894 2.753966 CCGAGGCAAAGCATCCGTG 61.754 63.158 0.00 0.00 35.86 4.94
808 896 1.502163 GATCCGAGGCAAAGCATCCG 61.502 60.000 0.00 0.00 35.86 4.18
809 897 1.502163 CGATCCGAGGCAAAGCATCC 61.502 60.000 0.00 0.00 35.86 3.51
810 898 0.811616 ACGATCCGAGGCAAAGCATC 60.812 55.000 0.00 0.00 35.92 3.91
890 981 4.996434 ACACCACGCCAGAGCAGC 62.996 66.667 0.00 0.00 39.83 5.25
891 982 2.740055 GACACCACGCCAGAGCAG 60.740 66.667 0.00 0.00 39.83 4.24
892 983 4.662961 CGACACCACGCCAGAGCA 62.663 66.667 0.00 0.00 39.83 4.26
948 1039 1.537202 GACCAGCAACAACACCTCATC 59.463 52.381 0.00 0.00 0.00 2.92
955 1046 2.530497 GCGACGACCAGCAACAACA 61.530 57.895 0.00 0.00 0.00 3.33
957 1048 2.970324 GGCGACGACCAGCAACAA 60.970 61.111 0.00 0.00 34.54 2.83
1487 1578 2.159435 GCGAGAGAGAAAGAGAGGTGAC 60.159 54.545 0.00 0.00 0.00 3.67
1490 1581 2.026262 AGAGCGAGAGAGAAAGAGAGGT 60.026 50.000 0.00 0.00 0.00 3.85
1506 1597 0.592754 GAGGAAACCGATCGAGAGCG 60.593 60.000 18.66 3.56 40.29 5.03
1507 1598 0.741915 AGAGGAAACCGATCGAGAGC 59.258 55.000 18.66 3.02 0.00 4.09
1545 1651 0.169672 GATATGCATGCATGGCGGAC 59.830 55.000 37.43 19.60 37.82 4.79
1547 1653 0.885879 AAGATATGCATGCATGGCGG 59.114 50.000 37.43 2.89 37.82 6.13
1582 1700 4.487948 ACTGCACAAATCAAATCGGATTG 58.512 39.130 3.59 0.00 37.55 2.67
1587 1705 4.261349 CGATGAACTGCACAAATCAAATCG 59.739 41.667 0.00 0.00 0.00 3.34
1598 1716 4.505217 CGCCGCGATGAACTGCAC 62.505 66.667 8.23 0.00 0.00 4.57
1753 1871 1.878522 CGCGTGCAGGTACTCCATC 60.879 63.158 8.40 0.00 34.60 3.51
2072 2238 4.736896 GAGACGGACGGGGTGTGC 62.737 72.222 0.00 0.00 35.21 4.57
2092 2258 7.172875 CAGATTCATTTCAGAGTGACAAGAACT 59.827 37.037 0.00 0.00 0.00 3.01
2142 2318 4.207165 TCTGACATACCGATCATCACAGA 58.793 43.478 0.00 0.00 0.00 3.41
2143 2319 4.574599 TCTGACATACCGATCATCACAG 57.425 45.455 0.00 0.00 0.00 3.66
2144 2320 5.302823 AGATTCTGACATACCGATCATCACA 59.697 40.000 0.00 0.00 0.00 3.58
2145 2321 5.632764 CAGATTCTGACATACCGATCATCAC 59.367 44.000 8.00 0.00 32.44 3.06
2146 2322 5.536161 TCAGATTCTGACATACCGATCATCA 59.464 40.000 12.38 0.00 35.39 3.07
2147 2323 6.018589 TCAGATTCTGACATACCGATCATC 57.981 41.667 12.38 0.00 35.39 2.92
2155 2331 2.748605 CGGCCTCAGATTCTGACATAC 58.251 52.381 12.38 2.73 35.39 2.39
2156 2332 1.069204 GCGGCCTCAGATTCTGACATA 59.931 52.381 12.38 0.00 35.39 2.29
2268 2444 1.069765 CTTGTCCAGCACCGACACT 59.930 57.895 0.54 0.00 39.89 3.55
2419 2595 2.500509 TCAATTTTGGTGGCAACGAC 57.499 45.000 0.00 0.00 42.51 4.34
2420 2596 3.570125 TGTATCAATTTTGGTGGCAACGA 59.430 39.130 0.00 0.00 42.51 3.85
2421 2597 3.906998 TGTATCAATTTTGGTGGCAACG 58.093 40.909 0.00 0.00 42.51 4.10
2428 2604 9.396022 CTGTACTCCTTATGTATCAATTTTGGT 57.604 33.333 0.00 0.00 0.00 3.67
2429 2605 9.613428 TCTGTACTCCTTATGTATCAATTTTGG 57.387 33.333 0.00 0.00 0.00 3.28
2431 2607 9.314321 CGTCTGTACTCCTTATGTATCAATTTT 57.686 33.333 0.00 0.00 0.00 1.82
2433 2609 6.924060 GCGTCTGTACTCCTTATGTATCAATT 59.076 38.462 0.00 0.00 0.00 2.32
2466 2642 5.494724 AGCAATATCTTTGTCTGAAGCTGA 58.505 37.500 0.00 0.00 0.00 4.26
2467 2643 5.814764 AGCAATATCTTTGTCTGAAGCTG 57.185 39.130 0.00 0.00 0.00 4.24
2468 2644 6.618811 CAAAGCAATATCTTTGTCTGAAGCT 58.381 36.000 8.17 0.00 44.69 3.74
2499 2675 4.109766 GGCATATATTACATACGAGCGCA 58.890 43.478 11.47 0.00 0.00 6.09
2511 2691 3.776969 AGCTAGCAGCAGGGCATATATTA 59.223 43.478 18.83 0.00 45.56 0.98
2512 2692 2.575279 AGCTAGCAGCAGGGCATATATT 59.425 45.455 18.83 0.00 45.56 1.28
2513 2693 2.093075 CAGCTAGCAGCAGGGCATATAT 60.093 50.000 18.83 0.00 45.56 0.86
2600 2780 5.763204 CAGACTTGTATTACACTGTTGGGTT 59.237 40.000 0.00 0.00 0.00 4.11
2668 2848 9.695526 CATCAATTCCAGTAGTTTCAAATGAAA 57.304 29.630 4.52 4.52 41.29 2.69
2669 2849 8.859090 ACATCAATTCCAGTAGTTTCAAATGAA 58.141 29.630 0.00 0.00 0.00 2.57
2710 3577 2.065899 AGTCTAGCTGTAGCCCTCTG 57.934 55.000 0.00 0.00 43.38 3.35
2731 3603 3.130280 ACGCATCCATCTGCATATTCA 57.870 42.857 0.00 0.00 42.40 2.57
2808 3680 5.068723 GTGTATAGCCTAGTTACCTGCTTCA 59.931 44.000 0.00 0.00 35.34 3.02
2814 3686 7.014422 GTGATCTTGTGTATAGCCTAGTTACCT 59.986 40.741 0.00 0.00 0.00 3.08
2822 3723 3.319405 CCTCGTGATCTTGTGTATAGCCT 59.681 47.826 0.00 0.00 0.00 4.58
2841 3742 1.872197 CGCATCGAGATCCTCCCCTC 61.872 65.000 0.00 0.00 0.00 4.30
2855 3757 3.434319 CCACAGCCCACACGCATC 61.434 66.667 0.00 0.00 0.00 3.91
2860 3762 3.660111 GTTCGCCACAGCCCACAC 61.660 66.667 0.00 0.00 34.57 3.82
2889 3792 7.157347 GCCATCAAATGTATCTCAGAGTATCA 58.843 38.462 0.00 0.00 37.82 2.15
2894 3797 4.970711 AGGCCATCAAATGTATCTCAGAG 58.029 43.478 5.01 0.00 0.00 3.35
2897 3800 4.883585 GTCAAGGCCATCAAATGTATCTCA 59.116 41.667 5.01 0.00 0.00 3.27
2921 3824 7.306225 GGCATAGTATAACGAACTACGAAAACC 60.306 40.741 0.00 0.00 45.77 3.27
2930 3833 7.655490 AGTAAATCGGCATAGTATAACGAACT 58.345 34.615 11.02 8.28 37.11 3.01
2934 3837 8.795341 CATGTAGTAAATCGGCATAGTATAACG 58.205 37.037 0.00 0.55 0.00 3.18
2971 3874 1.575419 TCTTGGGGGCATAACTACGT 58.425 50.000 0.00 0.00 0.00 3.57
2978 3881 1.774254 CACCTACATCTTGGGGGCATA 59.226 52.381 0.00 0.00 0.00 3.14
2986 3889 5.351458 TCATCGATCAACACCTACATCTTG 58.649 41.667 0.00 0.00 0.00 3.02
2988 3891 5.352284 GTTCATCGATCAACACCTACATCT 58.648 41.667 7.35 0.00 0.00 2.90
3020 3923 9.454859 AGATTTAGACCCAGAAAAGAGTATTTG 57.545 33.333 0.00 0.00 0.00 2.32
3028 3931 5.495640 AGCAGAGATTTAGACCCAGAAAAG 58.504 41.667 0.00 0.00 0.00 2.27
3029 3932 5.505181 AGCAGAGATTTAGACCCAGAAAA 57.495 39.130 0.00 0.00 0.00 2.29
3031 3934 5.899547 TCATAGCAGAGATTTAGACCCAGAA 59.100 40.000 0.00 0.00 0.00 3.02
3051 3954 8.800370 TGTTAGAATTTACCAGTTGCATCATA 57.200 30.769 0.00 0.00 0.00 2.15
3078 3981 3.674997 TGCAACCTTTCTCAGATACCAC 58.325 45.455 0.00 0.00 0.00 4.16
3085 3988 4.589216 TCCAATTTGCAACCTTTCTCAG 57.411 40.909 0.00 0.00 0.00 3.35
3115 4018 8.193438 CGCTATCATCTTTGTCTATATCATCCA 58.807 37.037 0.00 0.00 0.00 3.41
3126 4029 3.435566 TGTCGTCGCTATCATCTTTGTC 58.564 45.455 0.00 0.00 0.00 3.18
3129 4032 3.612860 GTGTTGTCGTCGCTATCATCTTT 59.387 43.478 0.00 0.00 0.00 2.52
3137 4040 1.790043 CATGTTGTGTTGTCGTCGCTA 59.210 47.619 0.00 0.00 0.00 4.26
3138 4041 0.581529 CATGTTGTGTTGTCGTCGCT 59.418 50.000 0.00 0.00 0.00 4.93
3139 4042 0.384230 CCATGTTGTGTTGTCGTCGC 60.384 55.000 0.00 0.00 0.00 5.19
3170 4075 7.713942 TCCTACAGAAACTTGTCTTTCCTTTAC 59.286 37.037 0.00 0.00 31.44 2.01
3175 4080 4.452795 GCTCCTACAGAAACTTGTCTTTCC 59.547 45.833 0.00 0.00 31.44 3.13
3176 4081 4.150804 CGCTCCTACAGAAACTTGTCTTTC 59.849 45.833 0.00 0.00 32.56 2.62
3184 4089 1.546476 CCACTCGCTCCTACAGAAACT 59.454 52.381 0.00 0.00 0.00 2.66
3186 4091 1.819288 CTCCACTCGCTCCTACAGAAA 59.181 52.381 0.00 0.00 0.00 2.52
3191 4096 1.654954 TTCGCTCCACTCGCTCCTAC 61.655 60.000 0.00 0.00 0.00 3.18
3211 4116 5.523916 CGACTTCAATCGTTTTATCCTCCAT 59.476 40.000 0.00 0.00 37.33 3.41
3218 4123 3.340034 TGGGCGACTTCAATCGTTTTAT 58.660 40.909 0.00 0.00 44.13 1.40
3219 4124 2.768698 TGGGCGACTTCAATCGTTTTA 58.231 42.857 0.00 0.00 44.13 1.52
3240 4145 1.364721 CGTCATCGTGTATGCCCAAA 58.635 50.000 0.00 0.00 35.38 3.28
3252 4157 1.354337 CCTTCAGCCACACGTCATCG 61.354 60.000 0.00 0.00 43.34 3.84
3253 4158 1.021390 CCCTTCAGCCACACGTCATC 61.021 60.000 0.00 0.00 0.00 2.92
3254 4159 1.003355 CCCTTCAGCCACACGTCAT 60.003 57.895 0.00 0.00 0.00 3.06
3255 4160 2.425592 CCCTTCAGCCACACGTCA 59.574 61.111 0.00 0.00 0.00 4.35
3256 4161 2.358737 CCCCTTCAGCCACACGTC 60.359 66.667 0.00 0.00 0.00 4.34
3265 4178 2.673523 CTCCTGGCACCCCTTCAG 59.326 66.667 0.00 0.00 0.00 3.02
3281 4194 5.332743 TCCTTTGCTTTCCATTTATGACCT 58.667 37.500 0.00 0.00 0.00 3.85
3285 4198 6.705381 TGTGTTTCCTTTGCTTTCCATTTATG 59.295 34.615 0.00 0.00 0.00 1.90
3297 4210 3.391965 TGATGCATTGTGTTTCCTTTGC 58.608 40.909 0.00 0.00 0.00 3.68
3314 4227 2.912967 GCAATTCGTGTGCTCTTTGATG 59.087 45.455 1.38 0.00 39.00 3.07
3331 4244 4.098914 TCGATATTTTGGGCTAGGCAAT 57.901 40.909 19.14 11.60 0.00 3.56
3356 4269 6.494491 ACTCATCCCATTGTTTCAGAAAATCA 59.506 34.615 0.00 0.00 0.00 2.57
3359 4272 7.093814 CCATACTCATCCCATTGTTTCAGAAAA 60.094 37.037 0.00 0.00 0.00 2.29
3372 4285 3.724478 ACTGTTCTCCATACTCATCCCA 58.276 45.455 0.00 0.00 0.00 4.37
3374 4287 9.646427 GATATAAACTGTTCTCCATACTCATCC 57.354 37.037 0.00 0.00 0.00 3.51
3377 4290 8.459911 TCGATATAAACTGTTCTCCATACTCA 57.540 34.615 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.