Multiple sequence alignment - TraesCS5D01G224100

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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 TraesCS5D01G224100 chr5D 100.000 7389 0 0 1 7389 332033283 332040671 0.000000e+00 13646.0
1 TraesCS5D01G224100 chr5D 97.872 47 1 0 6944 6990 332040177 332040223 1.710000e-11 82.4
2 TraesCS5D01G224100 chr5D 97.872 47 1 0 6895 6941 332040226 332040272 1.710000e-11 82.4
3 TraesCS5D01G224100 chr5B 95.414 7479 202 57 1 7389 387733163 387740590 0.000000e+00 11780.0
4 TraesCS5D01G224100 chr5B 97.872 47 1 0 6944 6990 387740094 387740140 1.710000e-11 82.4
5 TraesCS5D01G224100 chr5A 95.385 4117 122 23 3193 7281 432439446 432443522 0.000000e+00 6488.0
6 TraesCS5D01G224100 chr5A 93.280 1741 52 20 1 1690 432436197 432437923 0.000000e+00 2507.0
7 TraesCS5D01G224100 chr5A 95.611 1481 33 12 1685 3158 432437992 432439447 0.000000e+00 2346.0
8 TraesCS5D01G224100 chr5A 90.909 121 1 4 7279 7389 432443681 432443801 3.570000e-33 154.0
9 TraesCS5D01G224100 chr5A 100.000 47 0 0 6895 6941 432443190 432443236 3.670000e-13 87.9
10 TraesCS5D01G224100 chr5A 97.872 47 1 0 6944 6990 432443141 432443187 1.710000e-11 82.4
11 TraesCS5D01G224100 chrUn 86.017 472 49 10 6184 6642 83995135 83994668 2.400000e-134 490.0
12 TraesCS5D01G224100 chrUn 86.017 472 49 10 6184 6642 232033414 232032947 2.400000e-134 490.0
13 TraesCS5D01G224100 chrUn 86.017 472 49 10 6184 6642 232041621 232041154 2.400000e-134 490.0
14 TraesCS5D01G224100 chr7B 86.017 472 49 10 6184 6642 2315673 2315206 2.400000e-134 490.0
15 TraesCS5D01G224100 chr7B 97.826 46 1 0 1613 1658 686818554 686818509 6.150000e-11 80.5
16 TraesCS5D01G224100 chr7B 95.652 46 2 0 1613 1658 246008162 246008117 2.860000e-09 75.0
17 TraesCS5D01G224100 chr4A 85.714 469 53 9 6184 6642 731999351 731998887 4.010000e-132 483.0
18 TraesCS5D01G224100 chr7D 98.214 56 1 0 1613 1668 265703392 265703337 1.700000e-16 99.0
19 TraesCS5D01G224100 chr7A 98.214 56 1 0 1613 1668 290922172 290922117 1.700000e-16 99.0
20 TraesCS5D01G224100 chr7A 94.340 53 3 0 3538 3590 117981072 117981020 1.710000e-11 82.4


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 TraesCS5D01G224100 chr5D 332033283 332040671 7388 False 4603.600000 13646 98.581333 1 7389 3 chr5D.!!$F1 7388
1 TraesCS5D01G224100 chr5B 387733163 387740590 7427 False 5931.200000 11780 96.643000 1 7389 2 chr5B.!!$F1 7388
2 TraesCS5D01G224100 chr5A 432436197 432443801 7604 False 1944.216667 6488 95.509500 1 7389 6 chr5A.!!$F1 7388

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
636 702 0.037882 TTTGCGCTGTGAGAGAGAGG 60.038 55.0 9.73 0.00 0.00 3.69 F
912 988 0.259938 GGGGATTTGTGGCCTGATCT 59.740 55.0 3.32 0.00 0.00 2.75 F
1904 2062 0.665835 TTAACACTGCGGCTTGGTTG 59.334 50.0 0.00 0.00 0.00 3.77 F
2242 2400 1.062258 GCAATGCATTGTTGTCGGTG 58.938 50.0 33.67 12.34 39.88 4.94 F
3704 3907 0.859760 ATGAGAGAGAGGGAGGGGAG 59.140 60.0 0.00 0.00 0.00 4.30 F
5143 5355 1.279496 TGCCTATCCAAGTGTGCTCT 58.721 50.0 0.00 0.00 0.00 4.09 F
5152 5364 2.027745 CCAAGTGTGCTCTGAGGTATGT 60.028 50.0 6.83 0.00 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1700 1858 1.133976 GTGGCATGGGCAGTCTTAGAT 60.134 52.381 0.00 0.0 43.71 1.98 R
2242 2400 2.092323 GGATGGCAGTACCTTTGAACC 58.908 52.381 0.00 0.0 40.22 3.62 R
3689 3892 0.634465 ACTTCTCCCCTCCCTCTCTC 59.366 60.000 0.00 0.0 0.00 3.20 R
3891 4101 2.573462 ACTGCCACATATGAGAACACCT 59.427 45.455 10.38 0.0 0.00 4.00 R
5547 5761 0.591170 CGGTGTGGTTTCGCATCTTT 59.409 50.000 0.00 0.0 35.69 2.52 R
6271 6497 0.181350 GGGGGCAGATGTACTCCAAG 59.819 60.000 0.00 0.0 0.00 3.61 R
7121 7359 0.250513 GGCGAGGACAAGATCAAGGT 59.749 55.000 0.00 0.0 0.00 3.50 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
69 76 3.445518 TAATGAGGAGGCAGCGGCG 62.446 63.158 0.51 0.51 42.47 6.46
109 119 3.671971 CGCCAAGAGAACAACAACAACAA 60.672 43.478 0.00 0.00 0.00 2.83
110 120 3.612423 GCCAAGAGAACAACAACAACAAC 59.388 43.478 0.00 0.00 0.00 3.32
111 121 4.804108 CCAAGAGAACAACAACAACAACA 58.196 39.130 0.00 0.00 0.00 3.33
158 168 3.449227 ATCGACGGAGGAAGCGCA 61.449 61.111 11.47 0.00 0.00 6.09
159 169 3.001902 ATCGACGGAGGAAGCGCAA 62.002 57.895 11.47 0.00 0.00 4.85
161 171 2.261671 GACGGAGGAAGCGCAAGA 59.738 61.111 11.47 0.00 43.02 3.02
186 200 1.839407 CGCGAGCAAAGCACAAAAC 59.161 52.632 0.00 0.00 34.19 2.43
243 279 4.660938 AAAGTCCCCACTGCCCGC 62.661 66.667 0.00 0.00 31.06 6.13
359 395 5.654497 GATAATTATTATTGGCAGGCAGGC 58.346 41.667 0.00 0.00 44.50 4.85
360 396 2.754012 TTATTATTGGCAGGCAGGCT 57.246 45.000 4.85 0.00 44.55 4.58
361 397 2.276732 TATTATTGGCAGGCAGGCTC 57.723 50.000 4.85 0.00 44.55 4.70
362 398 0.554792 ATTATTGGCAGGCAGGCTCT 59.445 50.000 4.85 0.00 44.55 4.09
391 432 0.680921 TGGTTGCTGCTAATCAGGCC 60.681 55.000 0.00 0.00 43.06 5.19
575 635 0.968405 CAATTCCCCACCACCACAAG 59.032 55.000 0.00 0.00 0.00 3.16
635 701 1.348276 CTTTGCGCTGTGAGAGAGAG 58.652 55.000 9.73 0.00 0.00 3.20
636 702 0.037882 TTTGCGCTGTGAGAGAGAGG 60.038 55.000 9.73 0.00 0.00 3.69
905 981 0.682292 TTTTTCGGGGGATTTGTGGC 59.318 50.000 0.00 0.00 0.00 5.01
912 988 0.259938 GGGGATTTGTGGCCTGATCT 59.740 55.000 3.32 0.00 0.00 2.75
1183 1263 4.087907 GAGGTTGGAGGTCAGTTAGTAGT 58.912 47.826 0.00 0.00 0.00 2.73
1192 1272 2.094130 GTCAGTTAGTAGTGCCCTCACC 60.094 54.545 0.00 0.00 44.16 4.02
1339 1419 4.993705 ACCCAACTTCTTCTACATCCAA 57.006 40.909 0.00 0.00 0.00 3.53
1679 1763 5.666969 TGTTGTTGTTGATTCTAGTTCCG 57.333 39.130 0.00 0.00 0.00 4.30
1904 2062 0.665835 TTAACACTGCGGCTTGGTTG 59.334 50.000 0.00 0.00 0.00 3.77
1936 2094 4.706842 TTATCTGGAGGTTCCTATTGGC 57.293 45.455 0.00 0.00 37.46 4.52
1992 2150 9.884465 GGTAGACACATTAATCTTTGCAATATC 57.116 33.333 0.00 0.00 0.00 1.63
2066 2224 5.483685 AGGTTGCACACAGAAGTATCTAA 57.516 39.130 0.00 0.00 33.50 2.10
2072 2230 6.346096 TGCACACAGAAGTATCTAATAACCC 58.654 40.000 0.00 0.00 33.50 4.11
2242 2400 1.062258 GCAATGCATTGTTGTCGGTG 58.938 50.000 33.67 12.34 39.88 4.94
3013 3178 8.492673 TGGATGTTATCACATTTACACTCTTC 57.507 34.615 0.00 0.00 44.22 2.87
3033 3198 9.507329 ACTCTTCTTCAAAACATTTATGCTCTA 57.493 29.630 0.00 0.00 0.00 2.43
3081 3246 3.248024 TCCTCACTGGACAATGGTTACT 58.752 45.455 0.00 0.00 40.56 2.24
3097 3262 6.461110 TGGTTACTAGCAAGGACTACATAC 57.539 41.667 0.00 0.00 0.00 2.39
3158 3359 8.277270 TGCACGTAAATGAAATACTAGATACG 57.723 34.615 0.00 0.00 40.31 3.06
3159 3360 7.096353 TGCACGTAAATGAAATACTAGATACGC 60.096 37.037 0.00 0.00 38.64 4.42
3160 3361 7.096353 GCACGTAAATGAAATACTAGATACGCA 60.096 37.037 0.00 0.00 38.64 5.24
3161 3362 8.417928 CACGTAAATGAAATACTAGATACGCAG 58.582 37.037 0.00 0.00 38.64 5.18
3162 3363 7.114529 ACGTAAATGAAATACTAGATACGCAGC 59.885 37.037 0.00 0.00 38.64 5.25
3163 3364 7.326305 CGTAAATGAAATACTAGATACGCAGCT 59.674 37.037 0.00 0.00 0.00 4.24
3164 3365 8.979574 GTAAATGAAATACTAGATACGCAGCTT 58.020 33.333 0.00 0.00 0.00 3.74
3165 3366 7.413475 AATGAAATACTAGATACGCAGCTTG 57.587 36.000 0.00 0.00 0.00 4.01
3166 3367 6.144078 TGAAATACTAGATACGCAGCTTGA 57.856 37.500 0.00 0.00 0.00 3.02
3167 3368 6.209361 TGAAATACTAGATACGCAGCTTGAG 58.791 40.000 0.00 0.00 0.00 3.02
3168 3369 5.776173 AATACTAGATACGCAGCTTGAGT 57.224 39.130 0.00 0.00 34.10 3.41
3169 3370 5.776173 ATACTAGATACGCAGCTTGAGTT 57.224 39.130 0.00 0.00 31.51 3.01
3170 3371 4.035278 ACTAGATACGCAGCTTGAGTTC 57.965 45.455 0.00 0.00 31.51 3.01
3171 3372 3.444034 ACTAGATACGCAGCTTGAGTTCA 59.556 43.478 0.00 0.00 31.51 3.18
3172 3373 3.533606 AGATACGCAGCTTGAGTTCAT 57.466 42.857 0.00 0.00 31.51 2.57
3173 3374 3.866651 AGATACGCAGCTTGAGTTCATT 58.133 40.909 0.00 0.00 31.51 2.57
3174 3375 3.868077 AGATACGCAGCTTGAGTTCATTC 59.132 43.478 0.00 0.00 31.51 2.67
3175 3376 1.882912 ACGCAGCTTGAGTTCATTCA 58.117 45.000 0.00 0.00 0.00 2.57
3176 3377 1.802960 ACGCAGCTTGAGTTCATTCAG 59.197 47.619 0.00 0.00 0.00 3.02
3177 3378 1.802960 CGCAGCTTGAGTTCATTCAGT 59.197 47.619 0.00 0.00 0.00 3.41
3178 3379 2.225019 CGCAGCTTGAGTTCATTCAGTT 59.775 45.455 0.00 0.00 0.00 3.16
3179 3380 3.304257 CGCAGCTTGAGTTCATTCAGTTT 60.304 43.478 0.00 0.00 0.00 2.66
3180 3381 3.979495 GCAGCTTGAGTTCATTCAGTTTG 59.021 43.478 0.00 0.00 0.00 2.93
3181 3382 4.498682 GCAGCTTGAGTTCATTCAGTTTGT 60.499 41.667 0.00 0.00 0.00 2.83
3182 3383 5.277974 GCAGCTTGAGTTCATTCAGTTTGTA 60.278 40.000 0.00 0.00 0.00 2.41
3183 3384 6.138761 CAGCTTGAGTTCATTCAGTTTGTAC 58.861 40.000 0.00 0.00 0.00 2.90
3184 3385 5.822519 AGCTTGAGTTCATTCAGTTTGTACA 59.177 36.000 0.00 0.00 0.00 2.90
3185 3386 5.909610 GCTTGAGTTCATTCAGTTTGTACAC 59.090 40.000 0.00 0.00 0.00 2.90
3186 3387 6.458206 GCTTGAGTTCATTCAGTTTGTACACA 60.458 38.462 0.00 0.00 0.00 3.72
3187 3388 6.993786 TGAGTTCATTCAGTTTGTACACAA 57.006 33.333 0.00 0.00 0.00 3.33
3188 3389 7.384439 TGAGTTCATTCAGTTTGTACACAAA 57.616 32.000 3.44 3.44 42.90 2.83
3189 3390 7.821652 TGAGTTCATTCAGTTTGTACACAAAA 58.178 30.769 9.01 0.00 46.08 2.44
3190 3391 7.753132 TGAGTTCATTCAGTTTGTACACAAAAC 59.247 33.333 9.01 0.00 46.08 2.43
3191 3392 7.598278 AGTTCATTCAGTTTGTACACAAAACA 58.402 30.769 9.01 0.00 46.08 2.83
3192 3393 8.085296 AGTTCATTCAGTTTGTACACAAAACAA 58.915 29.630 9.01 3.65 46.08 2.83
3193 3394 7.804614 TCATTCAGTTTGTACACAAAACAAC 57.195 32.000 9.01 5.01 46.08 3.32
3376 3578 6.367695 GGGACCAAATAAAACAAATGTGCTAC 59.632 38.462 0.00 0.00 0.00 3.58
3454 3657 6.632834 CCACTTCTGTAATTCTGTTTGTTTCG 59.367 38.462 0.00 0.00 0.00 3.46
3704 3907 0.859760 ATGAGAGAGAGGGAGGGGAG 59.140 60.000 0.00 0.00 0.00 4.30
3830 4033 4.225208 GCAAGAAGTCTTTTCATCTGCAC 58.775 43.478 0.00 0.00 33.11 4.57
3891 4101 4.072131 GTGGGTAAAGCAGAAACTGATCA 58.928 43.478 0.00 0.00 32.44 2.92
3972 4182 2.258755 GGAATGGTTACAATGCGTTGC 58.741 47.619 18.61 2.91 38.96 4.17
4084 4294 6.234177 CCATACTTGAGACCTTTCTTGACTT 58.766 40.000 0.00 0.00 29.47 3.01
4112 4322 4.700213 ACACAAACTCATATGGTGCTTACC 59.300 41.667 2.13 0.00 32.89 2.85
4337 4547 5.860641 GCAACAGATATGCAACAAATTTGG 58.139 37.500 21.74 6.60 43.29 3.28
4346 4556 4.970711 TGCAACAAATTTGGATTCCATGT 58.029 34.783 21.74 5.02 31.53 3.21
4349 4559 5.335035 GCAACAAATTTGGATTCCATGTTGG 60.335 40.000 31.67 21.39 44.36 3.77
4444 4654 7.099764 TGCTACTTCTAATGCTCCTATTATGC 58.900 38.462 0.00 0.00 0.00 3.14
4448 4658 5.939764 TCTAATGCTCCTATTATGCGGAT 57.060 39.130 0.00 0.00 0.00 4.18
4453 4663 3.055819 TGCTCCTATTATGCGGATTCCTC 60.056 47.826 0.00 0.00 0.00 3.71
4996 5208 2.203480 TTGCCAGTTGCTCCACCC 60.203 61.111 0.00 0.00 42.00 4.61
5143 5355 1.279496 TGCCTATCCAAGTGTGCTCT 58.721 50.000 0.00 0.00 0.00 4.09
5152 5364 2.027745 CCAAGTGTGCTCTGAGGTATGT 60.028 50.000 6.83 0.00 0.00 2.29
5174 5386 4.356405 TTCTTTGAGCTTGATGAGGACA 57.644 40.909 0.00 0.00 0.00 4.02
5191 5403 9.906660 GATGAGGACAAAATGTCTCTATACTAG 57.093 37.037 10.06 0.00 46.19 2.57
5192 5404 9.647918 ATGAGGACAAAATGTCTCTATACTAGA 57.352 33.333 10.06 0.00 46.19 2.43
5193 5405 8.904834 TGAGGACAAAATGTCTCTATACTAGAC 58.095 37.037 10.06 0.00 46.19 2.59
5194 5406 9.127277 GAGGACAAAATGTCTCTATACTAGACT 57.873 37.037 10.06 0.00 46.19 3.24
5547 5761 3.202151 ACTGGAAGGGTCAAGTCTTTTCA 59.798 43.478 0.00 0.00 31.89 2.69
5610 5824 5.352284 AGTATCCACTATTCACTTCGCTTG 58.648 41.667 0.00 0.00 31.45 4.01
5672 5891 3.565307 TGCTGAAGAACAAGGGAACAAT 58.435 40.909 0.00 0.00 0.00 2.71
5676 5895 4.144297 TGAAGAACAAGGGAACAATCTGG 58.856 43.478 0.00 0.00 0.00 3.86
5745 5964 7.573843 GCATGTGCTTACTTAGTTTTGATCTGT 60.574 37.037 0.00 0.00 38.21 3.41
5810 6029 8.248253 TCTGAAATTTCATGATCACTTCCATTG 58.752 33.333 20.76 4.26 36.46 2.82
6227 6450 3.254657 CCCTCTCCATGATAACTCGTCTC 59.745 52.174 0.00 0.00 0.00 3.36
6256 6482 4.684485 CGGTCTTCTTCCTTGCAGGATTAT 60.684 45.833 0.00 0.00 45.34 1.28
6271 6497 2.481952 GGATTATGCGAAGACAGATGGC 59.518 50.000 0.00 0.00 0.00 4.40
6277 6503 1.649664 CGAAGACAGATGGCTTGGAG 58.350 55.000 5.46 0.00 44.93 3.86
6289 6515 0.464554 GCTTGGAGTACATCTGCCCC 60.465 60.000 0.00 0.00 33.42 5.80
6304 6530 2.371841 CTGCCCCCATTGTAGTATAGCA 59.628 50.000 0.00 0.00 0.00 3.49
6444 6671 0.979187 CTGCCCTAGGTTTCGGGGTA 60.979 60.000 8.29 0.00 42.01 3.69
6687 6916 0.884704 TGTTGTCCTTTGCTCGCTCC 60.885 55.000 0.00 0.00 0.00 4.70
6810 7048 2.941064 CAATGAGACAGGCAGGTACATG 59.059 50.000 2.43 2.43 0.00 3.21
6849 7087 4.588899 TGCAGAGCCAAAGTGTATTACAT 58.411 39.130 0.00 0.00 0.00 2.29
6887 7125 0.602905 CAGGGAAGGACGAACACACC 60.603 60.000 0.00 0.00 0.00 4.16
6995 7233 5.131642 GGCTTAATTTACAGGGTAGGGTAGT 59.868 44.000 0.00 0.00 0.00 2.73
6996 7234 6.053650 GCTTAATTTACAGGGTAGGGTAGTG 58.946 44.000 0.00 0.00 0.00 2.74
6997 7235 6.126968 GCTTAATTTACAGGGTAGGGTAGTGA 60.127 42.308 0.00 0.00 0.00 3.41
6998 7236 7.582048 GCTTAATTTACAGGGTAGGGTAGTGAA 60.582 40.741 0.00 0.00 0.00 3.18
6999 7237 5.952347 ATTTACAGGGTAGGGTAGTGAAG 57.048 43.478 0.00 0.00 0.00 3.02
7069 7307 2.815211 GCGCATCAGCTTCGGTCA 60.815 61.111 0.30 0.00 39.10 4.02
7120 7358 1.524621 CTTGAGGCGCGGGATCATT 60.525 57.895 8.83 0.00 0.00 2.57
7121 7359 0.249868 CTTGAGGCGCGGGATCATTA 60.250 55.000 8.83 0.00 0.00 1.90
7186 7424 2.203437 GTCCCGGTGGCCTTGTTT 60.203 61.111 3.32 0.00 0.00 2.83
7225 7463 1.790755 CGTCCATGGAAGTCGTTTGA 58.209 50.000 18.20 0.00 0.00 2.69
7318 7717 5.211174 ACTTCAAGTACTAGACAACACCC 57.789 43.478 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 76 1.596841 CGCTTTTCGTTTTCGCTGCC 61.597 55.000 0.00 0.00 43.73 4.85
71 78 1.596841 GGCGCTTTTCGTTTTCGCTG 61.597 55.000 7.64 0.00 44.51 5.18
72 79 1.370051 GGCGCTTTTCGTTTTCGCT 60.370 52.632 7.64 0.00 44.51 4.93
73 80 1.203600 TTGGCGCTTTTCGTTTTCGC 61.204 50.000 7.64 0.00 44.39 4.70
74 81 0.770008 CTTGGCGCTTTTCGTTTTCG 59.230 50.000 7.64 0.00 45.64 3.46
243 279 0.958382 TTGGATTTTGACGGCTCGGG 60.958 55.000 0.00 0.00 0.00 5.14
244 280 1.064060 GATTGGATTTTGACGGCTCGG 59.936 52.381 0.00 0.00 0.00 4.63
245 281 2.009774 AGATTGGATTTTGACGGCTCG 58.990 47.619 0.00 0.00 0.00 5.03
246 282 4.082787 TCAAAGATTGGATTTTGACGGCTC 60.083 41.667 0.00 0.00 38.12 4.70
289 325 1.196012 GGGGAGAACAGTAGGGTGAG 58.804 60.000 0.00 0.00 0.00 3.51
290 326 0.790993 AGGGGAGAACAGTAGGGTGA 59.209 55.000 0.00 0.00 0.00 4.02
291 327 1.196012 GAGGGGAGAACAGTAGGGTG 58.804 60.000 0.00 0.00 0.00 4.61
292 328 0.042881 GGAGGGGAGAACAGTAGGGT 59.957 60.000 0.00 0.00 0.00 4.34
359 395 0.890996 GCAACCACCAACCAGGAGAG 60.891 60.000 0.00 0.00 41.22 3.20
360 396 1.150536 GCAACCACCAACCAGGAGA 59.849 57.895 0.00 0.00 41.22 3.71
361 397 1.151450 AGCAACCACCAACCAGGAG 59.849 57.895 0.00 0.00 41.22 3.69
362 398 1.152777 CAGCAACCACCAACCAGGA 60.153 57.895 0.00 0.00 41.22 3.86
635 701 2.113243 ATCGCGGAAATAGCTCCCCC 62.113 60.000 6.13 0.00 31.03 5.40
636 702 0.250338 AATCGCGGAAATAGCTCCCC 60.250 55.000 6.13 0.00 31.03 4.81
676 742 0.452585 GGGGAGAAGACGAAGACGAG 59.547 60.000 0.00 0.00 42.66 4.18
680 746 1.248785 CGTGGGGGAGAAGACGAAGA 61.249 60.000 0.00 0.00 33.64 2.87
905 981 1.734465 GCGAAACACAAGGAGATCAGG 59.266 52.381 0.00 0.00 0.00 3.86
912 988 2.018544 CAACCGCGAAACACAAGGA 58.981 52.632 8.23 0.00 0.00 3.36
1183 1263 1.827789 GCACAACAAGGTGAGGGCA 60.828 57.895 0.00 0.00 41.32 5.36
1192 1272 1.252904 CCATCCCCAGGCACAACAAG 61.253 60.000 0.00 0.00 0.00 3.16
1641 1722 3.324993 ACAACAACAACAACAAAGCCTG 58.675 40.909 0.00 0.00 0.00 4.85
1700 1858 1.133976 GTGGCATGGGCAGTCTTAGAT 60.134 52.381 0.00 0.00 43.71 1.98
1904 2062 5.161943 ACCTCCAGATAAACCTGTGTTAC 57.838 43.478 0.00 0.00 33.30 2.50
1936 2094 3.657956 TGCTTGGGCAAGTTTTTCG 57.342 47.368 0.00 0.00 46.36 3.46
2066 2224 7.499895 TCTTTTGTGAAACTTAAGACGGGTTAT 59.500 33.333 10.09 0.00 38.04 1.89
2072 2230 9.284594 TGATTTTCTTTTGTGAAACTTAAGACG 57.715 29.630 10.09 0.00 36.93 4.18
2242 2400 2.092323 GGATGGCAGTACCTTTGAACC 58.908 52.381 0.00 0.00 40.22 3.62
2525 2683 9.872684 ATCATCATATATTTTTATAGCTGGGGG 57.127 33.333 0.00 0.00 0.00 5.40
2970 3135 7.765695 ACATCCATGTAATTGAGAAAACAGT 57.234 32.000 0.00 0.00 39.68 3.55
3013 3178 9.897744 TGAAACTAGAGCATAAATGTTTTGAAG 57.102 29.630 0.00 0.00 0.00 3.02
3033 3198 3.145286 GCTTCTTCTGGCTCTTGAAACT 58.855 45.455 0.00 0.00 0.00 2.66
3097 3262 6.144886 CCGCACATCATGATGGATTTTATTTG 59.855 38.462 33.31 21.59 42.91 2.32
3158 3359 3.911661 AACTGAATGAACTCAAGCTGC 57.088 42.857 0.00 0.00 0.00 5.25
3159 3360 5.179045 ACAAACTGAATGAACTCAAGCTG 57.821 39.130 0.00 0.00 0.00 4.24
3160 3361 5.822519 TGTACAAACTGAATGAACTCAAGCT 59.177 36.000 0.00 0.00 0.00 3.74
3161 3362 5.909610 GTGTACAAACTGAATGAACTCAAGC 59.090 40.000 0.00 0.00 0.00 4.01
3162 3363 7.015226 TGTGTACAAACTGAATGAACTCAAG 57.985 36.000 0.00 0.00 0.00 3.02
3163 3364 6.993786 TGTGTACAAACTGAATGAACTCAA 57.006 33.333 0.00 0.00 0.00 3.02
3164 3365 6.993786 TTGTGTACAAACTGAATGAACTCA 57.006 33.333 0.00 0.00 32.11 3.41
3165 3366 7.753132 TGTTTTGTGTACAAACTGAATGAACTC 59.247 33.333 9.52 0.00 44.56 3.01
3166 3367 7.598278 TGTTTTGTGTACAAACTGAATGAACT 58.402 30.769 9.52 0.00 44.56 3.01
3167 3368 7.804614 TGTTTTGTGTACAAACTGAATGAAC 57.195 32.000 9.52 4.25 44.56 3.18
3168 3369 7.867909 TGTTGTTTTGTGTACAAACTGAATGAA 59.132 29.630 9.52 0.00 44.56 2.57
3169 3370 7.371159 TGTTGTTTTGTGTACAAACTGAATGA 58.629 30.769 9.52 0.00 44.56 2.57
3170 3371 7.573916 TGTTGTTTTGTGTACAAACTGAATG 57.426 32.000 9.52 0.00 44.56 2.67
3171 3372 8.085296 TCTTGTTGTTTTGTGTACAAACTGAAT 58.915 29.630 9.52 0.00 44.56 2.57
3172 3373 7.380065 GTCTTGTTGTTTTGTGTACAAACTGAA 59.620 33.333 9.52 1.46 44.56 3.02
3173 3374 6.858993 GTCTTGTTGTTTTGTGTACAAACTGA 59.141 34.615 9.52 0.00 44.56 3.41
3174 3375 6.861055 AGTCTTGTTGTTTTGTGTACAAACTG 59.139 34.615 9.52 0.00 44.56 3.16
3175 3376 6.977213 AGTCTTGTTGTTTTGTGTACAAACT 58.023 32.000 9.52 0.00 44.56 2.66
3176 3377 8.019094 ACTAGTCTTGTTGTTTTGTGTACAAAC 58.981 33.333 9.52 0.00 44.56 2.93
3177 3378 8.101654 ACTAGTCTTGTTGTTTTGTGTACAAA 57.898 30.769 6.11 6.11 43.36 2.83
3178 3379 7.675962 ACTAGTCTTGTTGTTTTGTGTACAA 57.324 32.000 0.00 0.00 33.37 2.41
3179 3380 8.774890 TTACTAGTCTTGTTGTTTTGTGTACA 57.225 30.769 0.00 0.00 0.00 2.90
3180 3381 9.090692 TCTTACTAGTCTTGTTGTTTTGTGTAC 57.909 33.333 0.00 0.00 0.00 2.90
3181 3382 9.656040 TTCTTACTAGTCTTGTTGTTTTGTGTA 57.344 29.630 0.00 0.00 0.00 2.90
3182 3383 8.556213 TTCTTACTAGTCTTGTTGTTTTGTGT 57.444 30.769 0.00 0.00 0.00 3.72
3183 3384 8.879759 TCTTCTTACTAGTCTTGTTGTTTTGTG 58.120 33.333 0.00 0.00 0.00 3.33
3184 3385 9.614792 ATCTTCTTACTAGTCTTGTTGTTTTGT 57.385 29.630 0.00 0.00 0.00 2.83
3185 3386 9.869844 CATCTTCTTACTAGTCTTGTTGTTTTG 57.130 33.333 0.00 0.00 0.00 2.44
3186 3387 8.560374 GCATCTTCTTACTAGTCTTGTTGTTTT 58.440 33.333 0.00 0.00 0.00 2.43
3187 3388 7.715249 TGCATCTTCTTACTAGTCTTGTTGTTT 59.285 33.333 0.00 0.00 0.00 2.83
3188 3389 7.217200 TGCATCTTCTTACTAGTCTTGTTGTT 58.783 34.615 0.00 0.00 0.00 2.83
3189 3390 6.759272 TGCATCTTCTTACTAGTCTTGTTGT 58.241 36.000 0.00 0.00 0.00 3.32
3190 3391 7.010923 GGATGCATCTTCTTACTAGTCTTGTTG 59.989 40.741 25.28 0.00 0.00 3.33
3191 3392 7.044798 GGATGCATCTTCTTACTAGTCTTGTT 58.955 38.462 25.28 0.00 0.00 2.83
3192 3393 6.382570 AGGATGCATCTTCTTACTAGTCTTGT 59.617 38.462 25.28 0.00 0.00 3.16
3193 3394 6.815089 AGGATGCATCTTCTTACTAGTCTTG 58.185 40.000 25.28 0.00 0.00 3.02
3327 3529 9.184523 CCCTTGTTTTATTTGTGTATCCATCTA 57.815 33.333 0.00 0.00 0.00 1.98
3376 3578 5.033589 ACAAATCCTGGAGCATCTAAGAG 57.966 43.478 1.52 0.00 33.73 2.85
3689 3892 0.634465 ACTTCTCCCCTCCCTCTCTC 59.366 60.000 0.00 0.00 0.00 3.20
3841 4044 3.198068 TCTTTGACGAAGATATGGCAGC 58.802 45.455 0.59 0.00 39.44 5.25
3891 4101 2.573462 ACTGCCACATATGAGAACACCT 59.427 45.455 10.38 0.00 0.00 4.00
4084 4294 4.071423 CACCATATGAGTTTGTGTGGTCA 58.929 43.478 3.65 0.00 37.84 4.02
4112 4322 3.063725 GCTTTCTAGAAGCTGCAGACATG 59.936 47.826 20.43 1.64 40.01 3.21
4246 4456 5.780282 TCATCCAGACTTCAAAGGTAGAAGA 59.220 40.000 9.65 0.00 44.00 2.87
4337 4547 2.100252 CACATCAGCCCAACATGGAATC 59.900 50.000 0.00 0.00 40.96 2.52
4346 4556 2.212812 TAATGCACACATCAGCCCAA 57.787 45.000 0.00 0.00 34.62 4.12
4349 4559 2.947652 ACAGATAATGCACACATCAGCC 59.052 45.455 0.00 0.00 34.62 4.85
4516 4727 7.307493 TCCAGAAAATAATGTTCAGTCATCG 57.693 36.000 0.00 0.00 0.00 3.84
4573 4785 2.432146 TGCAACTAGGCTCCTGTATGAG 59.568 50.000 0.00 0.00 35.40 2.90
4874 5086 2.557920 ATAGGCCTCATAGTTGCAGC 57.442 50.000 9.68 0.00 0.00 5.25
4996 5208 5.008019 AGGTGCTGAATTATGATGCTTAACG 59.992 40.000 0.00 0.00 0.00 3.18
5143 5355 5.620206 TCAAGCTCAAAGAAACATACCTCA 58.380 37.500 0.00 0.00 0.00 3.86
5152 5364 4.717877 TGTCCTCATCAAGCTCAAAGAAA 58.282 39.130 0.00 0.00 0.00 2.52
5191 5403 7.868415 CCATTATTCTAGCTTGGTGTAGTAGTC 59.132 40.741 0.00 0.00 0.00 2.59
5192 5404 7.202011 CCCATTATTCTAGCTTGGTGTAGTAGT 60.202 40.741 0.00 0.00 0.00 2.73
5193 5405 7.155328 CCCATTATTCTAGCTTGGTGTAGTAG 58.845 42.308 0.00 0.00 0.00 2.57
5194 5406 6.614087 ACCCATTATTCTAGCTTGGTGTAGTA 59.386 38.462 0.00 0.00 0.00 1.82
5236 5449 1.674221 CCTTCAGAAAGTCCTCCTGCG 60.674 57.143 0.00 0.00 0.00 5.18
5547 5761 0.591170 CGGTGTGGTTTCGCATCTTT 59.409 50.000 0.00 0.00 35.69 2.52
5634 5851 8.151141 TCTTCAGCATTGATAGCTAAAAGATG 57.849 34.615 0.00 1.72 41.14 2.90
5672 5891 1.002624 GAAATGGCCGACACCCAGA 60.003 57.895 0.00 0.00 35.48 3.86
5676 5895 2.280628 CTTCTAGAAATGGCCGACACC 58.719 52.381 6.63 0.00 0.00 4.16
5719 5938 6.744537 CAGATCAAAACTAAGTAAGCACATGC 59.255 38.462 0.00 0.00 42.49 4.06
5779 5998 9.557338 GAAGTGATCATGAAATTTCAGAGAAAG 57.443 33.333 24.17 10.82 41.08 2.62
5810 6029 2.426842 AACTTGCTATGAAGGGAGCC 57.573 50.000 0.00 0.00 37.94 4.70
6227 6450 2.263077 CAAGGAAGAAGACCGATCGTG 58.737 52.381 15.09 8.18 0.00 4.35
6256 6482 0.674581 CCAAGCCATCTGTCTTCGCA 60.675 55.000 0.00 0.00 0.00 5.10
6271 6497 0.181350 GGGGGCAGATGTACTCCAAG 59.819 60.000 0.00 0.00 0.00 3.61
6277 6503 2.172717 ACTACAATGGGGGCAGATGTAC 59.827 50.000 0.00 0.00 0.00 2.90
6304 6530 5.257262 GGAGGAGGCTTCTTCTTGTAATTT 58.743 41.667 7.88 0.00 30.61 1.82
6336 6562 1.873863 GCAAACCCGTTGGCTACTC 59.126 57.895 0.00 0.00 36.60 2.59
6444 6671 0.971959 TACCCTACCACCGACGCATT 60.972 55.000 0.00 0.00 0.00 3.56
6687 6916 0.450583 TCCGAATTCCGAGACGACTG 59.549 55.000 0.00 0.00 41.76 3.51
6718 6947 3.366679 GCACCTCAATTCACAACATCCAG 60.367 47.826 0.00 0.00 0.00 3.86
6810 7048 2.134201 GCAAAGTGCAAACCTGGTAC 57.866 50.000 0.00 0.00 44.26 3.34
6849 7087 4.764823 CCCTGTAAATTAAGCCTGTGTTGA 59.235 41.667 0.00 0.00 0.00 3.18
6887 7125 5.167845 ACCAATAAATAAACTTTGGCAGCG 58.832 37.500 0.62 0.00 41.89 5.18
6995 7233 0.389817 CGAAGGCGGTGTGATCTTCA 60.390 55.000 0.00 0.00 36.39 3.02
6996 7234 2.373938 CGAAGGCGGTGTGATCTTC 58.626 57.895 0.00 0.00 34.09 2.87
6997 7235 4.598257 CGAAGGCGGTGTGATCTT 57.402 55.556 0.00 0.00 0.00 2.40
7120 7358 1.480954 GGCGAGGACAAGATCAAGGTA 59.519 52.381 0.00 0.00 0.00 3.08
7121 7359 0.250513 GGCGAGGACAAGATCAAGGT 59.749 55.000 0.00 0.00 0.00 3.50
7186 7424 0.817634 CAACAAAGGTGTCTGGGCGA 60.818 55.000 0.00 0.00 36.80 5.54
7225 7463 2.365293 GTGGTGGCCTTTGATCTTGTTT 59.635 45.455 3.32 0.00 0.00 2.83
7271 7509 6.562518 TGTTTCCATGCACATGTATATGTTG 58.437 36.000 16.05 0.00 45.01 3.33


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

AutoCloner maintained by Alex Coulton.