Multiple sequence alignment - TraesCS4D01G175200

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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 TraesCS4D01G175200 chr4D 100.000 6594 0 0 1 6594 303523917 303517324 0.000000e+00 12177.0
1 TraesCS4D01G175200 chr4A 93.960 6060 215 61 629 6594 175852262 175858264 0.000000e+00 9023.0
2 TraesCS4D01G175200 chr4A 93.344 646 23 6 2 635 175851601 175852238 0.000000e+00 937.0
3 TraesCS4D01G175200 chr4A 83.871 93 13 2 5078 5169 668094170 668094079 3.280000e-13 87.9
4 TraesCS4D01G175200 chr4A 82.432 74 10 3 5078 5150 625488056 625488127 1.990000e-05 62.1
5 TraesCS4D01G175200 chr4B 93.231 2349 105 23 1138 3469 377942725 377940414 0.000000e+00 3408.0
6 TraesCS4D01G175200 chr4B 94.195 1912 58 16 4704 6592 377939008 377937127 0.000000e+00 2867.0
7 TraesCS4D01G175200 chr4B 93.180 1217 24 16 3493 4674 377940257 377939065 0.000000e+00 1733.0
8 TraesCS4D01G175200 chr4B 94.509 601 26 2 36 633 377943889 377943293 0.000000e+00 920.0
9 TraesCS4D01G175200 chr4B 96.832 505 14 1 629 1133 377943266 377942764 0.000000e+00 843.0
10 TraesCS4D01G175200 chr3D 74.788 353 77 12 5077 5423 445638660 445639006 1.480000e-31 148.0
11 TraesCS4D01G175200 chr3B 74.504 353 78 12 5077 5423 584551248 584551594 6.890000e-30 143.0
12 TraesCS4D01G175200 chr3B 83.571 140 23 0 5075 5214 76433115 76432976 1.490000e-26 132.0
13 TraesCS4D01G175200 chr3A 73.938 353 80 12 5077 5423 587408089 587408435 1.490000e-26 132.0
14 TraesCS4D01G175200 chr1D 80.000 90 14 4 4846 4933 48885950 48886037 5.520000e-06 63.9
15 TraesCS4D01G175200 chr5D 82.432 74 10 3 5078 5150 543609489 543609418 1.990000e-05 62.1
16 TraesCS4D01G175200 chr1A 81.013 79 11 4 4857 4933 48785635 48785711 7.140000e-05 60.2


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 TraesCS4D01G175200 chr4D 303517324 303523917 6593 True 12177.0 12177 100.0000 1 6594 1 chr4D.!!$R1 6593
1 TraesCS4D01G175200 chr4A 175851601 175858264 6663 False 4980.0 9023 93.6520 2 6594 2 chr4A.!!$F2 6592
2 TraesCS4D01G175200 chr4B 377937127 377943889 6762 True 1954.2 3408 94.3894 36 6592 5 chr4B.!!$R1 6556

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
512 524 0.312102 GACTTTCCAAGCAGCACCAC 59.688 55.000 0.00 0.0 0.00 4.16 F
963 1013 1.016130 ATCGGCTCACTTCTTGCGTG 61.016 55.000 0.00 0.0 0.00 5.34 F
1872 1980 1.055040 ACATCCCTGATGAGCTAGGC 58.945 55.000 10.84 0.0 42.09 3.93 F
2930 3043 0.036164 TGGTCTAATTGCACCGCAGT 59.964 50.000 0.00 0.0 40.61 4.40 F
3238 3357 1.194772 GTGTTCTTTAGAGTGCCGTGC 59.805 52.381 0.00 0.0 0.00 5.34 F
5003 5350 0.107654 GGAACGCTGGTAAGGCTCAT 60.108 55.000 0.00 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1940 2048 0.042188 CAGAGGAACAAACGTGCACG 60.042 55.000 35.99 35.99 46.33 5.34 R
2452 2565 4.296265 GGGATGTCACCGGTGAAC 57.704 61.111 37.75 28.83 41.85 3.18 R
2978 3091 0.250640 AGAGCTGTGGCAACTTCCAG 60.251 55.000 0.00 0.00 41.70 3.86 R
3914 4175 1.298667 GAACTCCTTGGGCGGCTTA 59.701 57.895 9.56 0.00 0.00 3.09 R
5057 5412 1.000938 CTGCAGGCCAAGAACAGAAAC 60.001 52.381 5.01 0.00 0.00 2.78 R
6004 6385 0.179150 TGTGCCGCAACAGTGTTTTC 60.179 50.000 5.57 0.28 0.00 2.29 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
134 136 6.258230 TCATGGAAAAACATGTGAGATCAC 57.742 37.500 0.00 6.01 46.39 3.06
153 155 4.495422 TCACGCTCAGTTTATCTTCCTTC 58.505 43.478 0.00 0.00 0.00 3.46
165 167 8.166726 AGTTTATCTTCCTTCTTTTGTGAGGAT 58.833 33.333 0.00 0.00 0.00 3.24
174 176 6.660949 CCTTCTTTTGTGAGGATATTCAACCT 59.339 38.462 0.00 0.00 39.41 3.50
267 269 4.038162 AGACACGGTCCTATTATCTCTTGC 59.962 45.833 1.06 0.00 32.18 4.01
287 289 3.143728 GCGAAGACCTTTTCCTTAACCA 58.856 45.455 0.00 0.00 0.00 3.67
499 511 5.276461 ACCCCAATGAAAAACAGACTTTC 57.724 39.130 0.00 0.00 34.09 2.62
500 512 4.100963 ACCCCAATGAAAAACAGACTTTCC 59.899 41.667 0.00 0.00 32.79 3.13
512 524 0.312102 GACTTTCCAAGCAGCACCAC 59.688 55.000 0.00 0.00 0.00 4.16
541 553 3.668447 ACATGAAAGACCAGCACACTAG 58.332 45.455 0.00 0.00 0.00 2.57
542 554 3.071602 ACATGAAAGACCAGCACACTAGT 59.928 43.478 0.00 0.00 0.00 2.57
543 555 3.386768 TGAAAGACCAGCACACTAGTC 57.613 47.619 0.00 0.00 35.06 2.59
544 556 2.698274 TGAAAGACCAGCACACTAGTCA 59.302 45.455 0.00 0.00 37.05 3.41
545 557 2.821991 AAGACCAGCACACTAGTCAC 57.178 50.000 0.00 0.00 37.05 3.67
546 558 2.002505 AGACCAGCACACTAGTCACT 57.997 50.000 0.00 0.00 37.05 3.41
547 559 3.156288 AGACCAGCACACTAGTCACTA 57.844 47.619 0.00 0.00 37.05 2.74
697 747 3.897681 TACAGCCAGCCACCGAGGA 62.898 63.158 0.00 0.00 41.22 3.71
752 802 3.266636 TGCTTTCAAGTCAAGTCGTTGA 58.733 40.909 0.00 0.00 40.55 3.18
753 803 3.876914 TGCTTTCAAGTCAAGTCGTTGAT 59.123 39.130 0.00 0.00 44.58 2.57
766 816 2.747446 GTCGTTGATATTTGGCACCACT 59.253 45.455 0.00 0.00 0.00 4.00
823 873 5.182760 CAGGATCCTATCATTTTAGCTTGGC 59.817 44.000 15.67 0.00 0.00 4.52
893 943 3.741476 GGTTGCCTTGCGCTCCAG 61.741 66.667 9.73 1.45 38.78 3.86
963 1013 1.016130 ATCGGCTCACTTCTTGCGTG 61.016 55.000 0.00 0.00 0.00 5.34
967 1017 1.202568 CTCACTTCTTGCGTGCGTG 59.797 57.895 0.00 0.00 32.54 5.34
1133 1199 6.844696 TCTTGCTTAGTTTCACAAGTACTG 57.155 37.500 0.00 0.00 40.29 2.74
1174 1274 6.236409 TGATGAGACAAGAATTTTGAGCTCT 58.764 36.000 16.19 0.00 0.00 4.09
1222 1323 7.387119 AGTATAACTCACGTGTGATAACTCA 57.613 36.000 23.32 0.00 39.13 3.41
1223 1324 7.997482 AGTATAACTCACGTGTGATAACTCAT 58.003 34.615 23.32 5.20 39.13 2.90
1224 1325 9.117183 AGTATAACTCACGTGTGATAACTCATA 57.883 33.333 23.32 4.30 39.13 2.15
1241 1342 5.202004 ACTCATACTACCTTGGAGTCGATT 58.798 41.667 0.00 0.00 33.84 3.34
1243 1344 4.954202 TCATACTACCTTGGAGTCGATTGT 59.046 41.667 0.00 0.00 0.00 2.71
1356 1457 1.499056 GGAGTGACATGCAGCAACG 59.501 57.895 0.00 0.00 0.00 4.10
1381 1482 3.198635 AGGGTGATCTCCATGTAAGTGTG 59.801 47.826 15.46 0.00 0.00 3.82
1410 1512 3.732721 GCTCAACAAGAATTTCACTGCAC 59.267 43.478 0.00 0.00 0.00 4.57
1411 1513 4.734402 GCTCAACAAGAATTTCACTGCACA 60.734 41.667 0.00 0.00 0.00 4.57
1419 1521 4.662961 TCACTGCACACTCCGCCG 62.663 66.667 0.00 0.00 0.00 6.46
1437 1540 1.608590 CCGAGTGCCAAGTCAACAAAT 59.391 47.619 0.00 0.00 0.00 2.32
1487 1590 2.958355 CAGAAAAGTGTCAACCATGGGT 59.042 45.455 18.09 6.57 37.65 4.51
1743 1849 2.350484 GCTTGCGACCTTGTAAGTTTCC 60.350 50.000 0.00 0.00 34.50 3.13
1754 1860 3.537580 TGTAAGTTTCCAAACGTGCTCT 58.462 40.909 7.48 0.00 43.51 4.09
1780 1887 6.541278 GCCTCTTGTTTTCGGTTAGGTTATAT 59.459 38.462 0.00 0.00 0.00 0.86
1797 1904 7.157347 AGGTTATATGTCACTATGCTCATGTG 58.843 38.462 0.00 0.00 0.00 3.21
1872 1980 1.055040 ACATCCCTGATGAGCTAGGC 58.945 55.000 10.84 0.00 42.09 3.93
1890 1998 3.956744 AGGCAGTCTTCCAAAACTATCC 58.043 45.455 0.00 0.00 0.00 2.59
1904 2012 8.475639 TCCAAAACTATCCTACATGTAAGAGAC 58.524 37.037 9.90 0.00 0.00 3.36
1915 2023 1.743958 TGTAAGAGACTACTCGCTGGC 59.256 52.381 0.00 0.00 46.64 4.85
1953 2061 2.096268 CAGATGATCGTGCACGTTTGTT 60.096 45.455 35.74 19.32 40.80 2.83
1982 2090 4.571984 GTGCTTCAGTTTTTGCAGGAAAAT 59.428 37.500 0.02 0.00 36.03 1.82
1988 2096 8.592105 TTCAGTTTTTGCAGGAAAATAATGAG 57.408 30.769 0.02 0.00 33.46 2.90
2100 2208 1.802069 TTGATGTCGCCGACAATCAA 58.198 45.000 25.07 25.90 45.96 2.57
2280 2393 3.003480 GGTGATCTGTAGCCACTTCAAC 58.997 50.000 0.00 0.00 0.00 3.18
2377 2490 4.465886 TGAAGCCCTCTCTGTCTATAGAC 58.534 47.826 23.53 23.53 44.97 2.59
2405 2518 3.266510 TCTCCTGCTTCGCAACATATT 57.733 42.857 0.00 0.00 38.41 1.28
2452 2565 4.142403 TGCAGGCTTTTCGATGGAAATAAG 60.142 41.667 3.57 1.10 41.54 1.73
2491 2604 3.075148 GGACTCTCTTGGGTTTGTTAGC 58.925 50.000 0.00 0.00 0.00 3.09
2720 2833 6.541111 AAGTAAGTGCAAGTACAAAGCTAC 57.459 37.500 9.93 0.00 0.00 3.58
2839 2952 9.371136 CTTCTCAATTATGTGTAAGCACTAAGA 57.629 33.333 0.00 0.00 45.44 2.10
2847 2960 4.994852 TGTGTAAGCACTAAGAAATTCGCT 59.005 37.500 0.00 0.00 45.44 4.93
2930 3043 0.036164 TGGTCTAATTGCACCGCAGT 59.964 50.000 0.00 0.00 40.61 4.40
3042 3155 7.913297 TGAAATAACTTTGCAACTTCACAGTAC 59.087 33.333 0.00 0.00 30.68 2.73
3057 3171 3.005791 CACAGTACATATGCTCGGATGGA 59.994 47.826 1.58 0.00 0.00 3.41
3224 3343 5.675684 AAAAATGGTGAAACTGGTGTTCT 57.324 34.783 0.00 0.00 34.96 3.01
3227 3346 6.783708 AAATGGTGAAACTGGTGTTCTTTA 57.216 33.333 0.00 0.00 34.96 1.85
3228 3347 6.391227 AATGGTGAAACTGGTGTTCTTTAG 57.609 37.500 0.00 0.00 34.96 1.85
3229 3348 5.105567 TGGTGAAACTGGTGTTCTTTAGA 57.894 39.130 0.00 0.00 34.96 2.10
3230 3349 5.123227 TGGTGAAACTGGTGTTCTTTAGAG 58.877 41.667 0.00 0.00 34.96 2.43
3231 3350 5.123936 GGTGAAACTGGTGTTCTTTAGAGT 58.876 41.667 0.00 0.00 34.96 3.24
3232 3351 5.007724 GGTGAAACTGGTGTTCTTTAGAGTG 59.992 44.000 0.00 0.00 34.96 3.51
3233 3352 4.574828 TGAAACTGGTGTTCTTTAGAGTGC 59.425 41.667 0.00 0.00 34.96 4.40
3234 3353 3.127425 ACTGGTGTTCTTTAGAGTGCC 57.873 47.619 0.00 0.00 0.00 5.01
3235 3354 2.069273 CTGGTGTTCTTTAGAGTGCCG 58.931 52.381 0.00 0.00 0.00 5.69
3236 3355 1.414919 TGGTGTTCTTTAGAGTGCCGT 59.585 47.619 0.00 0.00 0.00 5.68
3237 3356 1.798813 GGTGTTCTTTAGAGTGCCGTG 59.201 52.381 0.00 0.00 0.00 4.94
3238 3357 1.194772 GTGTTCTTTAGAGTGCCGTGC 59.805 52.381 0.00 0.00 0.00 5.34
3320 3439 2.370445 CGACCTGGGGAGGAGCATT 61.370 63.158 0.00 0.00 0.00 3.56
3572 3833 4.609018 ACACAGCACGCGCCTTCT 62.609 61.111 5.73 0.00 39.83 2.85
3914 4175 0.846693 ACCTCAGCAACCAGACCTTT 59.153 50.000 0.00 0.00 0.00 3.11
4170 4464 2.126463 TGCTGTCTACGCGCTCAC 60.126 61.111 5.73 0.00 0.00 3.51
4651 4952 3.696676 TACATGTCCGCCGGCACA 61.697 61.111 28.98 24.38 0.00 4.57
4674 4975 3.077519 GCGACAGCCTCACCGGTAT 62.078 63.158 6.87 0.00 37.42 2.73
4677 4978 2.238847 GACAGCCTCACCGGTATGCA 62.239 60.000 20.26 0.00 34.25 3.96
4678 4979 1.522355 CAGCCTCACCGGTATGCAG 60.522 63.158 20.26 11.29 34.25 4.41
4679 4980 1.685765 AGCCTCACCGGTATGCAGA 60.686 57.895 20.26 7.97 34.25 4.26
4680 4981 1.227380 GCCTCACCGGTATGCAGAG 60.227 63.158 6.87 9.57 34.25 3.35
4682 4983 1.517361 CTCACCGGTATGCAGAGCA 59.483 57.895 6.87 0.00 44.86 4.26
4700 5001 1.982395 ATGGCTTCGTCCCGTCTCA 60.982 57.895 0.00 0.00 0.00 3.27
4701 5002 1.541310 ATGGCTTCGTCCCGTCTCAA 61.541 55.000 0.00 0.00 0.00 3.02
4702 5003 1.218316 GGCTTCGTCCCGTCTCAAT 59.782 57.895 0.00 0.00 0.00 2.57
4703 5004 0.458669 GGCTTCGTCCCGTCTCAATA 59.541 55.000 0.00 0.00 0.00 1.90
4704 5005 1.134907 GGCTTCGTCCCGTCTCAATAA 60.135 52.381 0.00 0.00 0.00 1.40
4705 5006 2.483188 GGCTTCGTCCCGTCTCAATAAT 60.483 50.000 0.00 0.00 0.00 1.28
4707 5008 4.365723 GCTTCGTCCCGTCTCAATAATAA 58.634 43.478 0.00 0.00 0.00 1.40
4708 5009 4.989168 GCTTCGTCCCGTCTCAATAATAAT 59.011 41.667 0.00 0.00 0.00 1.28
4709 5010 5.118817 GCTTCGTCCCGTCTCAATAATAATC 59.881 44.000 0.00 0.00 0.00 1.75
4710 5011 4.790878 TCGTCCCGTCTCAATAATAATCG 58.209 43.478 0.00 0.00 0.00 3.34
4965 5300 2.045926 GACAGCGACAAGGGCCAT 60.046 61.111 6.18 0.00 0.00 4.40
5003 5350 0.107654 GGAACGCTGGTAAGGCTCAT 60.108 55.000 0.00 0.00 0.00 2.90
5057 5412 2.291465 CAGTGAATGTGACTTGGTGTGG 59.709 50.000 0.00 0.00 0.00 4.17
5061 5416 3.380004 TGAATGTGACTTGGTGTGGTTTC 59.620 43.478 0.00 0.00 0.00 2.78
5443 5798 3.838271 GCCTCGACATCCGCCTCA 61.838 66.667 0.00 0.00 38.37 3.86
5470 5825 3.424300 ACGGACTTCGACGTCACA 58.576 55.556 21.85 0.00 39.40 3.58
5530 5885 4.392940 CAAAGAAGGACAAGGACATGAGT 58.607 43.478 0.00 0.00 0.00 3.41
5551 5906 6.621316 AGTACAGACTCATTCGACGATTAT 57.379 37.500 0.00 0.00 0.00 1.28
5818 6186 7.122055 ACCAAACAAACAGTTCTGAATGAGTAA 59.878 33.333 6.83 0.00 40.26 2.24
5868 6239 8.625651 CCTATTTATGATACTAGATCGGTCCTG 58.374 40.741 0.00 0.00 0.00 3.86
5884 6255 1.140052 TCCTGACTTTTGCCAGACGAA 59.860 47.619 0.00 0.00 31.11 3.85
5930 6310 5.233225 TCACACACAAAAATGTTTTCAGCA 58.767 33.333 0.00 0.00 0.00 4.41
6096 6477 4.748277 TTACCAATCCTAAGTTCTCCCG 57.252 45.455 0.00 0.00 0.00 5.14
6141 6522 3.736252 CACTGACTCGACAAGTAACAAGG 59.264 47.826 0.00 0.00 38.74 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.158598 GCAGACAGATTTTTGAAGGCAATAA 58.841 36.000 0.00 0.00 33.25 1.40
11 12 5.234466 ACTCTAGGTGCAGACAGATTTTT 57.766 39.130 0.00 0.00 0.00 1.94
17 18 4.103365 CACTTACTCTAGGTGCAGACAG 57.897 50.000 0.00 0.00 0.00 3.51
134 136 6.073003 ACAAAAGAAGGAAGATAAACTGAGCG 60.073 38.462 0.00 0.00 0.00 5.03
153 155 6.095377 GCAAGGTTGAATATCCTCACAAAAG 58.905 40.000 0.00 0.00 33.09 2.27
165 167 2.584835 AGGCAGTGCAAGGTTGAATA 57.415 45.000 18.61 0.00 0.00 1.75
241 243 5.636123 AGAGATAATAGGACCGTGTCTCAT 58.364 41.667 16.40 5.05 34.55 2.90
267 269 4.379499 GCATGGTTAAGGAAAAGGTCTTCG 60.379 45.833 0.00 0.00 0.00 3.79
287 289 4.109877 AGGCATGCCTTAATTAGAGCAT 57.890 40.909 34.07 15.05 45.70 3.79
499 511 3.730761 GCTCGTGGTGCTGCTTGG 61.731 66.667 0.00 0.00 0.00 3.61
500 512 2.330372 ATGCTCGTGGTGCTGCTTG 61.330 57.895 0.00 0.00 0.00 4.01
512 524 2.349590 TGGTCTTTCATGTCATGCTCG 58.650 47.619 8.03 0.00 0.00 5.03
541 553 2.259505 GGTACGAGTGCACTAGTGAC 57.740 55.000 34.31 26.49 33.83 3.67
752 802 2.683742 CGGGAGAAGTGGTGCCAAATAT 60.684 50.000 0.00 0.00 0.00 1.28
753 803 1.339631 CGGGAGAAGTGGTGCCAAATA 60.340 52.381 0.00 0.00 0.00 1.40
766 816 2.431057 GAGAAAGATACAGGCGGGAGAA 59.569 50.000 0.00 0.00 0.00 2.87
823 873 0.305617 CATGATGGGACGTGCATTCG 59.694 55.000 9.96 0.00 0.00 3.34
893 943 1.813513 TAGGTGCTCAGCAAAAGCTC 58.186 50.000 0.00 0.00 41.47 4.09
933 983 4.263209 AGCCGATCGAGCTCGCAG 62.263 66.667 30.97 21.86 34.91 5.18
934 984 4.257510 GAGCCGATCGAGCTCGCA 62.258 66.667 30.97 19.58 46.58 5.10
1133 1199 7.862873 TGTCTCATCATCGATGAATTGTACTAC 59.137 37.037 30.41 19.03 46.51 2.73
1174 1274 6.262056 ACTTGGGTAAAGAAAGAGGAGAAA 57.738 37.500 0.00 0.00 39.38 2.52
1222 1323 5.009811 GCTACAATCGACTCCAAGGTAGTAT 59.990 44.000 0.00 0.00 31.73 2.12
1223 1324 4.337555 GCTACAATCGACTCCAAGGTAGTA 59.662 45.833 0.00 0.00 31.73 1.82
1224 1325 3.130693 GCTACAATCGACTCCAAGGTAGT 59.869 47.826 0.00 0.00 31.73 2.73
1241 1342 1.202582 GCTCGGAGAACAGAAGCTACA 59.797 52.381 9.69 0.00 34.09 2.74
1243 1344 0.452184 CGCTCGGAGAACAGAAGCTA 59.548 55.000 9.69 0.00 34.09 3.32
1292 1393 0.462375 CATCGGATTGTCCCCACGTA 59.538 55.000 0.00 0.00 31.13 3.57
1356 1457 3.452627 ACTTACATGGAGATCACCCTGTC 59.547 47.826 20.20 0.00 39.02 3.51
1381 1482 3.391506 AATTCTTGTTGAGCTTTGCCC 57.608 42.857 0.00 0.00 0.00 5.36
1419 1521 4.574599 AAGATTTGTTGACTTGGCACTC 57.425 40.909 0.00 0.00 0.00 3.51
1437 1540 8.698210 AGACACGGTTGTATAATAATGGTAAGA 58.302 33.333 0.00 0.00 35.47 2.10
1487 1590 4.711846 TCAGCAGCTAGAAGTCCTTTGATA 59.288 41.667 0.00 0.00 0.00 2.15
1618 1724 3.881688 GCTCATGTCATGGCTCAGTAATT 59.118 43.478 12.90 0.00 0.00 1.40
1728 1834 4.594136 CACGTTTGGAAACTTACAAGGTC 58.406 43.478 1.04 0.00 36.77 3.85
1743 1849 0.236711 CAAGAGGCAGAGCACGTTTG 59.763 55.000 0.00 0.00 0.00 2.93
1754 1860 2.158726 ACCTAACCGAAAACAAGAGGCA 60.159 45.455 0.00 0.00 0.00 4.75
1780 1887 4.006780 ACAACACATGAGCATAGTGACA 57.993 40.909 0.00 0.00 37.05 3.58
1797 1904 1.574428 CAGGCGGCACAAGTACAAC 59.426 57.895 13.08 0.00 0.00 3.32
1872 1980 7.106239 ACATGTAGGATAGTTTTGGAAGACTG 58.894 38.462 0.00 0.00 0.00 3.51
1890 1998 5.277586 CCAGCGAGTAGTCTCTTACATGTAG 60.278 48.000 5.56 0.00 38.45 2.74
1915 2023 1.769098 CTGTGCGGATGATTCCTGCG 61.769 60.000 0.00 0.00 41.48 5.18
1940 2048 0.042188 CAGAGGAACAAACGTGCACG 60.042 55.000 35.99 35.99 46.33 5.34
1982 2090 9.948964 TGAAAGAGAGTTTGATCAATCTCATTA 57.051 29.630 32.92 19.22 40.53 1.90
1988 2096 5.163673 GCCCTGAAAGAGAGTTTGATCAATC 60.164 44.000 9.40 8.74 34.07 2.67
2405 2518 5.116180 CCGAATATCTTAAGGTGTCAGCAA 58.884 41.667 4.59 0.00 0.00 3.91
2452 2565 4.296265 GGGATGTCACCGGTGAAC 57.704 61.111 37.75 28.83 41.85 3.18
2720 2833 5.762825 AGATAATGTGCTTACAATGGCTG 57.237 39.130 0.00 0.00 0.00 4.85
2930 3043 4.579753 TCAAATGTGTTGTTGCTCAGATCA 59.420 37.500 0.00 0.00 0.00 2.92
2978 3091 0.250640 AGAGCTGTGGCAACTTCCAG 60.251 55.000 0.00 0.00 41.70 3.86
3042 3155 6.257411 GTCAGATTTATCCATCCGAGCATATG 59.743 42.308 0.00 0.00 0.00 1.78
3057 3171 6.093219 GCATCACAAGACAGTGTCAGATTTAT 59.907 38.462 24.73 8.34 40.37 1.40
3221 3340 1.070134 ACAGCACGGCACTCTAAAGAA 59.930 47.619 0.00 0.00 0.00 2.52
3222 3341 0.679505 ACAGCACGGCACTCTAAAGA 59.320 50.000 0.00 0.00 0.00 2.52
3223 3342 0.792640 CACAGCACGGCACTCTAAAG 59.207 55.000 0.00 0.00 0.00 1.85
3224 3343 0.602638 CCACAGCACGGCACTCTAAA 60.603 55.000 0.00 0.00 0.00 1.85
3237 3356 1.068055 CCTTGTCAGATTTGCCACAGC 60.068 52.381 0.00 0.00 40.48 4.40
3238 3357 1.068055 GCCTTGTCAGATTTGCCACAG 60.068 52.381 0.00 0.00 0.00 3.66
3245 3364 2.560105 GCAAAGAGGCCTTGTCAGATTT 59.440 45.455 6.77 0.00 31.91 2.17
3572 3833 2.256158 CTTGTCGTGTACGCCCGA 59.744 61.111 0.00 0.00 39.60 5.14
3574 3835 3.116531 GGCTTGTCGTGTACGCCC 61.117 66.667 0.00 0.00 39.60 6.13
3914 4175 1.298667 GAACTCCTTGGGCGGCTTA 59.701 57.895 9.56 0.00 0.00 3.09
4074 4368 3.565961 TTGCTCTTGGATGCCGGCA 62.566 57.895 34.80 34.80 0.00 5.69
4081 4375 2.439156 GCGCCCTTGCTCTTGGAT 60.439 61.111 0.00 0.00 34.43 3.41
4133 4427 3.471244 CTCCGACGAGGGCGATGAC 62.471 68.421 0.00 0.00 41.52 3.06
4141 4435 3.691744 GACAGCAGCTCCGACGAGG 62.692 68.421 0.00 0.00 42.97 4.63
4186 4480 1.674057 CTCTTCCGTGGCCTTCTGT 59.326 57.895 3.32 0.00 0.00 3.41
4245 4540 7.616935 TGAAGAAAATGCTTTCAATCCTCCTAT 59.383 33.333 1.77 0.00 42.99 2.57
4247 4542 5.776716 TGAAGAAAATGCTTTCAATCCTCCT 59.223 36.000 1.77 0.00 42.99 3.69
4248 4543 5.866092 GTGAAGAAAATGCTTTCAATCCTCC 59.134 40.000 1.77 0.00 42.99 4.30
4252 4547 4.622740 CCGGTGAAGAAAATGCTTTCAATC 59.377 41.667 0.00 0.90 42.99 2.67
4254 4549 3.798548 GCCGGTGAAGAAAATGCTTTCAA 60.799 43.478 1.90 0.00 42.99 2.69
4282 4577 2.431057 ACCAGTTTCACTTCACTCGTCT 59.569 45.455 0.00 0.00 0.00 4.18
4674 4975 1.742880 GACGAAGCCATGCTCTGCA 60.743 57.895 0.00 0.00 44.86 4.41
4677 4978 2.586792 GGGACGAAGCCATGCTCT 59.413 61.111 0.00 0.00 38.25 4.09
4703 5004 9.871238 ACTTGTACTTGACTTGATACGATTATT 57.129 29.630 0.00 0.00 0.00 1.40
4704 5005 9.517609 GACTTGTACTTGACTTGATACGATTAT 57.482 33.333 0.00 0.00 0.00 1.28
4705 5006 7.972277 GGACTTGTACTTGACTTGATACGATTA 59.028 37.037 0.00 0.00 0.00 1.75
4707 5008 6.071560 TGGACTTGTACTTGACTTGATACGAT 60.072 38.462 0.00 0.00 0.00 3.73
4708 5009 5.242171 TGGACTTGTACTTGACTTGATACGA 59.758 40.000 0.00 0.00 0.00 3.43
4709 5010 5.466819 TGGACTTGTACTTGACTTGATACG 58.533 41.667 0.00 0.00 0.00 3.06
4710 5011 5.348997 GCTGGACTTGTACTTGACTTGATAC 59.651 44.000 0.00 0.00 0.00 2.24
4965 5300 1.679139 CTTTGACTTGGGTGCTGACA 58.321 50.000 0.00 0.00 0.00 3.58
5025 5372 4.154918 GTCACATTCACTGGAAGGAACATC 59.845 45.833 0.00 0.00 36.97 3.06
5057 5412 1.000938 CTGCAGGCCAAGAACAGAAAC 60.001 52.381 5.01 0.00 0.00 2.78
5061 5416 1.975407 CCCTGCAGGCCAAGAACAG 60.975 63.158 28.39 6.34 0.00 3.16
5530 5885 6.600350 GCTATAATCGTCGAATGAGTCTGTA 58.400 40.000 0.00 0.00 0.00 2.74
5548 5903 6.497259 ACTGGAAAGAATATCCTCCGCTATAA 59.503 38.462 0.00 0.00 37.85 0.98
5551 5906 4.223953 ACTGGAAAGAATATCCTCCGCTA 58.776 43.478 0.00 0.00 37.85 4.26
5785 6153 1.306141 TGTTTGTTTGGTGGCCCCA 60.306 52.632 8.74 8.74 43.27 4.96
5786 6154 1.334384 ACTGTTTGTTTGGTGGCCCC 61.334 55.000 0.00 0.85 0.00 5.80
5852 6223 5.452077 GCAAAAGTCAGGACCGATCTAGTAT 60.452 44.000 0.00 0.00 0.00 2.12
5868 6239 3.896648 TGAATTCGTCTGGCAAAAGTC 57.103 42.857 0.04 0.00 0.00 3.01
5884 6255 4.747810 GGAAATTCTTCCGTGCAATGAAT 58.252 39.130 0.00 0.00 41.89 2.57
5906 6286 5.348179 TGCTGAAAACATTTTTGTGTGTGAG 59.652 36.000 0.00 0.00 31.49 3.51
5930 6310 6.336566 TGTTTTCATGCAACAAATGTAGTGT 58.663 32.000 7.60 0.00 31.05 3.55
5999 6379 2.031157 GCCGCAACAGTGTTTTCTGTAT 60.031 45.455 5.57 0.00 46.25 2.29
6004 6385 0.179150 TGTGCCGCAACAGTGTTTTC 60.179 50.000 5.57 0.28 0.00 2.29
6096 6477 3.181501 TGCCTGTTTAATTGCACTATCGC 60.182 43.478 0.00 0.00 0.00 4.58
6141 6522 9.149225 CTCAGGAAATACAACATAGATAGATGC 57.851 37.037 0.00 0.00 0.00 3.91
6297 6678 2.478134 GCATGTGGAGCAGATACGAATC 59.522 50.000 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.