Multiple sequence alignment - TraesCS7A01G008700

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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 TraesCS7A01G008700 chr7A 100.000 2909 0 0 1 2909 3850860 3853768 0.000000e+00 5373
1 TraesCS7A01G008700 chr7D 89.619 2177 156 39 433 2578 4017967 4020104 0.000000e+00 2704
2 TraesCS7A01G008700 chr7D 96.364 330 11 1 2581 2909 4020212 4020541 2.550000e-150 542
3 TraesCS7A01G008700 chr7D 79.151 259 28 21 3 255 4017544 4017782 3.880000e-34 156
4 TraesCS7A01G008700 chr4A 92.247 1638 108 14 951 2579 739594832 739593205 0.000000e+00 2303
5 TraesCS7A01G008700 chr4A 95.152 330 13 3 2581 2909 739593139 739592812 4.300000e-143 518
6 TraesCS7A01G008700 chr4A 86.236 356 26 6 1 342 739595695 739595349 5.920000e-97 364
7 TraesCS7A01G008700 chr4A 83.410 217 22 8 203 418 688787092 688787295 3.830000e-44 189
8 TraesCS7A01G008700 chr4B 85.000 220 20 6 427 642 584073962 584073752 8.170000e-51 211
9 TraesCS7A01G008700 chr4D 87.200 125 11 4 2095 2214 1201753 1201629 1.410000e-28 137
10 TraesCS7A01G008700 chr6A 82.734 139 14 7 2773 2909 93264555 93264425 6.590000e-22 115


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 TraesCS7A01G008700 chr7A 3850860 3853768 2908 False 5373.000000 5373 100.000000 1 2909 1 chr7A.!!$F1 2908
1 TraesCS7A01G008700 chr7D 4017544 4020541 2997 False 1134.000000 2704 88.378000 3 2909 3 chr7D.!!$F1 2906
2 TraesCS7A01G008700 chr4A 739592812 739595695 2883 True 1061.666667 2303 91.211667 1 2909 3 chr4A.!!$R1 2908

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
157 169 0.036858 GAAGGCCACAGAGAGGTCAC 60.037 60.0 5.01 0.00 31.65 3.67 F
972 1092 0.098376 CATTTCCTCTTCGCTGCAGC 59.902 55.0 29.12 29.12 37.78 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1353 1474 0.107897 CGTCATCCCGGTTTCCATCA 60.108 55.0 0.0 0.0 0.00 3.07 R
2045 2168 0.886563 ATTGCTCAGAAACAGCCAGC 59.113 50.0 0.0 0.0 35.89 4.85 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
86 87 3.322466 CACGTGGGGCTCCTCCTT 61.322 66.667 7.95 0.00 34.39 3.36
135 147 4.853142 TAGCCCATCGGACCCGCT 62.853 66.667 3.13 0.00 39.59 5.52
155 167 1.599576 GGAAGGCCACAGAGAGGTC 59.400 63.158 5.01 0.00 0.00 3.85
156 168 1.194781 GGAAGGCCACAGAGAGGTCA 61.195 60.000 5.01 0.00 31.65 4.02
157 169 0.036858 GAAGGCCACAGAGAGGTCAC 60.037 60.000 5.01 0.00 31.65 3.67
158 170 0.764369 AAGGCCACAGAGAGGTCACA 60.764 55.000 5.01 0.00 31.65 3.58
159 171 1.190833 AGGCCACAGAGAGGTCACAG 61.191 60.000 5.01 0.00 31.65 3.66
160 172 1.375268 GCCACAGAGAGGTCACAGC 60.375 63.158 0.00 0.00 0.00 4.40
271 299 2.812499 CCGCCACGGTATGCTACT 59.188 61.111 0.00 0.00 42.73 2.57
273 301 1.299926 CGCCACGGTATGCTACTCC 60.300 63.158 0.00 0.00 0.00 3.85
277 305 1.831286 ACGGTATGCTACTCCCCCG 60.831 63.158 0.00 0.00 41.09 5.73
279 307 1.837499 GGTATGCTACTCCCCCGCT 60.837 63.158 0.00 0.00 0.00 5.52
299 381 1.492133 TTTCTCCCCACCTCAGCCAG 61.492 60.000 0.00 0.00 0.00 4.85
342 425 2.430921 CAGGCGTCGCTTTCGTCT 60.431 61.111 18.11 0.95 44.07 4.18
343 426 2.126424 AGGCGTCGCTTTCGTCTC 60.126 61.111 18.11 0.00 38.98 3.36
345 428 3.533691 GCGTCGCTTTCGTCTCCG 61.534 66.667 10.68 0.00 36.96 4.63
347 430 3.179939 GTCGCTTTCGTCTCCGGC 61.180 66.667 0.00 0.00 36.96 6.13
348 431 4.771356 TCGCTTTCGTCTCCGGCG 62.771 66.667 0.00 0.00 41.51 6.46
388 471 4.176752 GCTCCCCTACTTGCCCCG 62.177 72.222 0.00 0.00 0.00 5.73
412 495 4.501714 TCGCCGCCGTATGTGGTC 62.502 66.667 0.00 0.00 46.96 4.02
415 498 4.508128 CCGCCGTATGTGGTCGCT 62.508 66.667 0.00 0.00 39.95 4.93
417 500 2.890474 GCCGTATGTGGTCGCTGG 60.890 66.667 0.00 0.00 0.00 4.85
418 501 2.890474 CCGTATGTGGTCGCTGGC 60.890 66.667 0.00 0.00 0.00 4.85
419 502 2.125713 CGTATGTGGTCGCTGGCA 60.126 61.111 0.00 0.00 0.00 4.92
421 504 2.106683 GTATGTGGTCGCTGGCACC 61.107 63.158 7.06 7.06 0.00 5.01
422 505 2.290287 TATGTGGTCGCTGGCACCT 61.290 57.895 12.62 0.00 34.66 4.00
423 506 0.973496 TATGTGGTCGCTGGCACCTA 60.973 55.000 12.62 5.56 34.66 3.08
424 507 2.125512 GTGGTCGCTGGCACCTAG 60.126 66.667 12.62 0.00 34.66 3.02
433 521 0.459237 CTGGCACCTAGAAGAGCACG 60.459 60.000 0.00 0.00 0.00 5.34
490 578 2.360801 CTGTACCTTAGCTCCTCTGCTC 59.639 54.545 0.00 0.00 42.97 4.26
498 586 0.597118 GCTCCTCTGCTCGTGCTATG 60.597 60.000 11.19 1.64 40.48 2.23
507 595 1.071239 GCTCGTGCTATGTGTATTGCG 60.071 52.381 1.41 0.00 37.78 4.85
521 609 4.685447 TGCGTTACTGCAACCGAT 57.315 50.000 0.03 0.00 43.02 4.18
538 626 3.871594 ACCGATTGCTATTTGCTAGTGAC 59.128 43.478 0.00 0.00 43.37 3.67
542 630 5.748630 CGATTGCTATTTGCTAGTGACTACA 59.251 40.000 0.00 0.00 43.37 2.74
576 667 5.982890 AATTGGTCCATTTCTGTTACTGG 57.017 39.130 0.00 0.00 0.00 4.00
577 668 4.447138 TTGGTCCATTTCTGTTACTGGT 57.553 40.909 0.00 0.00 0.00 4.00
578 669 3.750371 TGGTCCATTTCTGTTACTGGTG 58.250 45.455 0.00 0.00 0.00 4.17
608 699 2.537625 CGCTAGCTGCTAACTCACATTC 59.462 50.000 13.93 0.00 40.11 2.67
620 718 3.117745 ACTCACATTCCCATCTCCATGA 58.882 45.455 0.00 0.00 30.57 3.07
622 720 3.881688 CTCACATTCCCATCTCCATGAAC 59.118 47.826 0.00 0.00 30.57 3.18
666 765 0.819259 TGCAAGTTCCAGTCCAGTGC 60.819 55.000 0.00 0.00 0.00 4.40
675 774 1.675116 CCAGTCCAGTGCACATCTCTG 60.675 57.143 21.04 19.36 36.37 3.35
680 779 3.755378 GTCCAGTGCACATCTCTGATTTT 59.245 43.478 21.04 0.00 38.27 1.82
682 781 3.119602 CCAGTGCACATCTCTGATTTTGG 60.120 47.826 21.04 9.26 38.27 3.28
684 783 4.022589 CAGTGCACATCTCTGATTTTGGTT 60.023 41.667 21.04 0.00 38.27 3.67
685 784 4.022589 AGTGCACATCTCTGATTTTGGTTG 60.023 41.667 21.04 0.00 0.00 3.77
686 785 3.248266 GCACATCTCTGATTTTGGTTGC 58.752 45.455 0.00 0.00 0.00 4.17
687 786 3.495193 CACATCTCTGATTTTGGTTGCG 58.505 45.455 0.00 0.00 0.00 4.85
688 787 3.189080 CACATCTCTGATTTTGGTTGCGA 59.811 43.478 0.00 0.00 0.00 5.10
704 807 1.065491 TGCGATGTGGGCTAACTGAAT 60.065 47.619 0.00 0.00 0.00 2.57
735 838 7.268199 TCATCAGGATCTCAAATGCAAATAC 57.732 36.000 0.00 0.00 0.00 1.89
739 842 4.036027 AGGATCTCAAATGCAAATACAGCG 59.964 41.667 0.00 0.00 33.85 5.18
778 882 3.056678 TCCACTGCGCAATTTTCATTCAT 60.057 39.130 13.05 0.00 0.00 2.57
808 920 6.522054 CACTACATATTACCCTGTTAGGTGG 58.478 44.000 0.00 0.00 41.42 4.61
815 927 5.881923 TTACCCTGTTAGGTGGATCATAC 57.118 43.478 0.00 0.00 41.42 2.39
816 928 4.008916 ACCCTGTTAGGTGGATCATACT 57.991 45.455 0.00 0.00 39.24 2.12
851 963 7.054124 AGACTGTTAGGTGAAAAACAATCAGA 58.946 34.615 0.00 0.00 35.02 3.27
852 964 7.721399 AGACTGTTAGGTGAAAAACAATCAGAT 59.279 33.333 0.00 0.00 35.02 2.90
854 966 8.352942 ACTGTTAGGTGAAAAACAATCAGATTC 58.647 33.333 0.00 0.00 35.32 2.52
856 968 9.567776 TGTTAGGTGAAAAACAATCAGATTCTA 57.432 29.630 0.00 0.00 32.86 2.10
859 971 7.542025 AGGTGAAAAACAATCAGATTCTATGC 58.458 34.615 0.00 0.00 0.00 3.14
860 972 7.395489 AGGTGAAAAACAATCAGATTCTATGCT 59.605 33.333 0.00 0.00 0.00 3.79
861 973 8.031277 GGTGAAAAACAATCAGATTCTATGCTT 58.969 33.333 0.00 0.00 0.00 3.91
885 997 2.034558 TGCTTTGCTTGCCAGTTTACTC 59.965 45.455 0.00 0.00 0.00 2.59
901 1013 0.178932 ACTCTGCCAGTACCTGTCCA 60.179 55.000 0.00 0.00 31.37 4.02
928 1040 2.158914 TCCATCCACCGATCTTGTCATG 60.159 50.000 0.00 0.00 0.00 3.07
931 1043 0.729116 CCACCGATCTTGTCATGCAC 59.271 55.000 0.00 0.00 0.00 4.57
939 1057 3.405823 TCTTGTCATGCACACATCTGA 57.594 42.857 1.24 0.00 33.41 3.27
948 1068 6.313658 GTCATGCACACATCTGACTTAATACA 59.686 38.462 8.31 0.00 32.87 2.29
949 1069 6.878389 TCATGCACACATCTGACTTAATACAA 59.122 34.615 0.00 0.00 32.87 2.41
972 1092 0.098376 CATTTCCTCTTCGCTGCAGC 59.902 55.000 29.12 29.12 37.78 5.25
985 1106 1.324736 GCTGCAGCGTCTTATACACAC 59.675 52.381 25.23 0.00 0.00 3.82
1005 1126 1.554160 CCTGAAGCAGACCTCATGAGT 59.446 52.381 21.11 9.51 32.44 3.41
1006 1127 2.619147 CTGAAGCAGACCTCATGAGTG 58.381 52.381 21.11 13.81 32.44 3.51
1107 1228 1.687146 CCTCTGCCTGCTCCACCTA 60.687 63.158 0.00 0.00 0.00 3.08
1110 1231 1.992277 CTGCCTGCTCCACCTACCT 60.992 63.158 0.00 0.00 0.00 3.08
1141 1262 3.178540 AAGGCCGCGTTCACCTTCT 62.179 57.895 4.92 0.00 39.65 2.85
1293 1414 3.816524 CTCGCGCTCTCCTCGGTT 61.817 66.667 5.56 0.00 0.00 4.44
1356 1477 2.289945 GCTGGAGGCGAGGATAAATGAT 60.290 50.000 0.00 0.00 0.00 2.45
1359 1480 2.303022 GGAGGCGAGGATAAATGATGGA 59.697 50.000 0.00 0.00 0.00 3.41
1368 1489 4.106341 AGGATAAATGATGGAAACCGGGAT 59.894 41.667 6.32 0.00 0.00 3.85
1371 1492 2.348411 ATGATGGAAACCGGGATGAC 57.652 50.000 6.32 0.00 0.00 3.06
1380 1501 2.202878 CGGGATGACGACGCCATT 60.203 61.111 0.00 0.00 35.47 3.16
1389 1510 0.537188 ACGACGCCATTCCTGAGAAT 59.463 50.000 0.00 0.00 43.74 2.40
1390 1511 1.754803 ACGACGCCATTCCTGAGAATA 59.245 47.619 0.00 0.00 40.89 1.75
1392 1513 3.181465 ACGACGCCATTCCTGAGAATATT 60.181 43.478 0.00 0.00 40.89 1.28
1455 1576 1.448540 GTACATGACGCTGCAGGCT 60.449 57.895 17.12 0.00 39.13 4.58
1458 1579 4.025858 ATGACGCTGCAGGCTGGT 62.026 61.111 17.12 5.12 39.13 4.00
1488 1609 1.064240 TCCACCATTGCTGATCATGCT 60.064 47.619 15.20 0.00 0.00 3.79
1491 1612 0.317854 CCATTGCTGATCATGCTGCG 60.318 55.000 15.20 6.20 35.75 5.18
1551 1672 3.503363 GCGCTGCCTCACCATGTC 61.503 66.667 0.00 0.00 0.00 3.06
1602 1723 2.524394 AGTGTGGCCGAGGAGTGT 60.524 61.111 0.00 0.00 0.00 3.55
1888 2009 1.528129 GCTGAAGCTAAACTGGCACT 58.472 50.000 0.00 0.00 38.21 4.40
1911 2034 3.664276 CGTGGCGAAACAAGTACTGAATG 60.664 47.826 0.00 0.00 0.00 2.67
1915 2038 4.094294 GGCGAAACAAGTACTGAATGCATA 59.906 41.667 0.00 0.00 0.00 3.14
1919 2042 7.465379 GCGAAACAAGTACTGAATGCATACATA 60.465 37.037 0.00 0.00 34.62 2.29
1921 2044 8.560355 AAACAAGTACTGAATGCATACATACA 57.440 30.769 0.00 0.00 34.62 2.29
1922 2045 8.737168 AACAAGTACTGAATGCATACATACAT 57.263 30.769 0.00 0.00 34.62 2.29
1924 2047 9.177608 ACAAGTACTGAATGCATACATACATTT 57.822 29.630 0.00 0.00 36.65 2.32
1931 2054 7.545489 TGAATGCATACATACATTTTGAAGCA 58.455 30.769 0.00 0.00 36.65 3.91
1948 2071 1.202394 AGCATGTTTGTTGAAAGCGCA 60.202 42.857 11.47 0.00 0.00 6.09
1950 2073 1.788308 CATGTTTGTTGAAAGCGCAGG 59.212 47.619 11.47 0.00 0.00 4.85
1986 2109 3.957288 CCAGACTAAACCTGGGGTG 57.043 57.895 0.00 0.00 45.66 4.61
1996 2119 1.755200 ACCTGGGGTGTCCATTTACT 58.245 50.000 0.00 0.00 46.01 2.24
1998 2121 1.633432 CCTGGGGTGTCCATTTACTGA 59.367 52.381 0.00 0.00 46.01 3.41
2042 2165 0.035630 AAAGGCTCTGCTACCTGCTG 60.036 55.000 0.00 0.00 43.37 4.41
2087 2210 8.490355 CAATTTTGATGTAGCTTCCTTTTTCAC 58.510 33.333 0.00 0.00 0.00 3.18
2092 2215 4.389374 TGTAGCTTCCTTTTTCACTGGAG 58.611 43.478 0.00 0.00 0.00 3.86
2161 2285 5.528690 CGACATGAGGTGGATGAATGTTATT 59.471 40.000 0.00 0.00 31.82 1.40
2214 2338 4.599041 CCCAGATTGTTCCAATACAAGGA 58.401 43.478 0.00 0.00 40.99 3.36
2219 2343 4.463050 TTGTTCCAATACAAGGAGGGTT 57.537 40.909 0.00 0.00 36.33 4.11
2234 2358 1.010046 AGGGTTGATGGATCCTCTGGA 59.990 52.381 14.23 0.00 35.55 3.86
2235 2359 1.141858 GGGTTGATGGATCCTCTGGAC 59.858 57.143 14.23 5.41 32.98 4.02
2263 2388 1.401761 TGACTTGTTGCACTGCCATT 58.598 45.000 0.00 0.00 0.00 3.16
2264 2389 2.580962 TGACTTGTTGCACTGCCATTA 58.419 42.857 0.00 0.00 0.00 1.90
2265 2390 3.156293 TGACTTGTTGCACTGCCATTAT 58.844 40.909 0.00 0.00 0.00 1.28
2266 2391 3.573538 TGACTTGTTGCACTGCCATTATT 59.426 39.130 0.00 0.00 0.00 1.40
2272 2397 4.142708 TGTTGCACTGCCATTATTAGTTCG 60.143 41.667 0.00 0.00 0.00 3.95
2290 2415 6.471233 AGTTCGATATTCAATGACCTCTGA 57.529 37.500 0.00 0.00 0.00 3.27
2292 2417 8.183104 AGTTCGATATTCAATGACCTCTGATA 57.817 34.615 0.00 0.00 0.00 2.15
2332 2459 1.560146 AGAAAGGGTTAGGCAGCTACC 59.440 52.381 0.00 0.00 0.00 3.18
2335 2462 3.235628 GGGTTAGGCAGCTACCCTA 57.764 57.895 13.58 10.68 46.55 3.53
2398 2526 1.242076 GGTGCAAGCTTCAGATGTGT 58.758 50.000 0.00 0.00 0.00 3.72
2471 2600 6.204301 CGATCTCAGATTTTCAGGTAATGCAT 59.796 38.462 0.00 0.00 0.00 3.96
2683 2921 2.406559 AGTGCCTATCTCAGCCTCATT 58.593 47.619 0.00 0.00 0.00 2.57
2750 2988 4.035324 AGTTAGGTACGACATCACATCTCG 59.965 45.833 0.00 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.505655 CGTTCCGTTCGGTTCTGTTC 59.494 55.000 11.04 0.00 0.00 3.18
86 87 2.364186 TCTGCGAGGCCCATCAGA 60.364 61.111 12.71 12.71 33.64 3.27
118 119 4.853142 AGCGGGTCCGATGGGCTA 62.853 66.667 14.15 0.00 42.83 3.93
135 147 1.984570 CCTCTCTGTGGCCTTCCGA 60.985 63.158 3.32 0.00 34.14 4.55
138 150 0.036858 GTGACCTCTCTGTGGCCTTC 60.037 60.000 3.32 0.00 0.00 3.46
155 167 1.448540 GGACTGGATCGTGGCTGTG 60.449 63.158 0.00 0.00 0.00 3.66
156 168 1.267574 ATGGACTGGATCGTGGCTGT 61.268 55.000 0.00 0.00 0.00 4.40
157 169 0.531532 GATGGACTGGATCGTGGCTG 60.532 60.000 0.00 0.00 0.00 4.85
158 170 1.826024 GATGGACTGGATCGTGGCT 59.174 57.895 0.00 0.00 0.00 4.75
159 171 1.592669 CGATGGACTGGATCGTGGC 60.593 63.158 0.00 0.00 38.31 5.01
160 172 4.738198 CGATGGACTGGATCGTGG 57.262 61.111 0.00 0.00 38.31 4.94
269 297 2.603652 GGGAGAAAAGCGGGGGAGT 61.604 63.158 0.00 0.00 0.00 3.85
271 299 3.335729 GGGGAGAAAAGCGGGGGA 61.336 66.667 0.00 0.00 0.00 4.81
273 301 2.361230 GTGGGGAGAAAAGCGGGG 60.361 66.667 0.00 0.00 0.00 5.73
277 305 0.962855 GCTGAGGTGGGGAGAAAAGC 60.963 60.000 0.00 0.00 0.00 3.51
279 307 1.065410 TGGCTGAGGTGGGGAGAAAA 61.065 55.000 0.00 0.00 0.00 2.29
326 409 2.126424 GAGACGAAAGCGACGCCT 60.126 61.111 17.79 4.81 41.64 5.52
405 488 2.244117 CTAGGTGCCAGCGACCACAT 62.244 60.000 11.93 2.03 35.76 3.21
407 490 2.125512 CTAGGTGCCAGCGACCAC 60.126 66.667 11.93 0.00 35.76 4.16
408 491 1.888436 CTTCTAGGTGCCAGCGACCA 61.888 60.000 11.93 1.14 35.76 4.02
412 495 1.520342 GCTCTTCTAGGTGCCAGCG 60.520 63.158 0.00 0.00 0.00 5.18
415 498 1.591703 CGTGCTCTTCTAGGTGCCA 59.408 57.895 0.00 0.00 0.00 4.92
417 500 1.153549 CCCGTGCTCTTCTAGGTGC 60.154 63.158 0.00 0.00 0.00 5.01
418 501 1.517832 CCCCGTGCTCTTCTAGGTG 59.482 63.158 0.00 0.00 0.00 4.00
419 502 2.359967 GCCCCGTGCTCTTCTAGGT 61.360 63.158 0.00 0.00 36.87 3.08
421 504 2.501610 GGCCCCGTGCTCTTCTAG 59.498 66.667 0.00 0.00 40.92 2.43
422 505 3.081409 GGGCCCCGTGCTCTTCTA 61.081 66.667 12.23 0.00 37.53 2.10
452 540 1.048724 CAGATCCAGTCCGGGCCTTA 61.049 60.000 0.08 0.00 34.36 2.69
490 578 3.550275 AGTAACGCAATACACATAGCACG 59.450 43.478 0.00 0.00 0.00 5.34
527 615 4.940463 ACTCGTTTGTAGTCACTAGCAAA 58.060 39.130 7.91 7.91 0.00 3.68
576 667 0.179150 CAGCTAGCGAGGTGTCTCAC 60.179 60.000 16.77 0.00 44.61 3.51
577 668 2.184323 CAGCTAGCGAGGTGTCTCA 58.816 57.895 16.77 0.00 44.61 3.27
591 682 1.630369 TGGGAATGTGAGTTAGCAGCT 59.370 47.619 0.00 0.00 0.00 4.24
608 699 1.656652 GTGTCGTTCATGGAGATGGG 58.343 55.000 0.00 0.00 0.00 4.00
620 718 1.274167 TCTAGAATTGGCGGTGTCGTT 59.726 47.619 0.00 0.00 38.89 3.85
622 720 1.659098 GTTCTAGAATTGGCGGTGTCG 59.341 52.381 8.75 0.00 39.81 4.35
659 758 3.708403 AAATCAGAGATGTGCACTGGA 57.292 42.857 19.41 6.75 36.09 3.86
666 765 3.189080 TCGCAACCAAAATCAGAGATGTG 59.811 43.478 0.00 0.00 0.00 3.21
675 774 1.994916 CCCACATCGCAACCAAAATC 58.005 50.000 0.00 0.00 0.00 2.17
680 779 0.958382 GTTAGCCCACATCGCAACCA 60.958 55.000 0.00 0.00 0.00 3.67
682 781 0.447801 CAGTTAGCCCACATCGCAAC 59.552 55.000 0.00 0.00 0.00 4.17
684 783 0.323302 TTCAGTTAGCCCACATCGCA 59.677 50.000 0.00 0.00 0.00 5.10
685 784 1.599542 GATTCAGTTAGCCCACATCGC 59.400 52.381 0.00 0.00 0.00 4.58
686 785 2.213499 GGATTCAGTTAGCCCACATCG 58.787 52.381 0.00 0.00 0.00 3.84
687 786 3.209410 CTGGATTCAGTTAGCCCACATC 58.791 50.000 0.00 0.00 36.30 3.06
688 787 3.287867 CTGGATTCAGTTAGCCCACAT 57.712 47.619 0.00 0.00 36.30 3.21
704 807 5.503634 TTTGAGATCCTGATGAAACTGGA 57.496 39.130 0.00 0.00 40.92 3.86
735 838 1.267806 ACTTGTGAAAATGAGGCGCTG 59.732 47.619 7.64 0.00 0.00 5.18
739 842 3.642705 GTGGAACTTGTGAAAATGAGGC 58.357 45.455 0.00 0.00 0.00 4.70
778 882 4.899457 ACAGGGTAATATGTAGTGCTAGCA 59.101 41.667 14.93 14.93 0.00 3.49
821 933 8.795842 TTGTTTTTCACCTAACAGTCTTAAGA 57.204 30.769 0.00 0.00 35.83 2.10
822 934 9.665264 GATTGTTTTTCACCTAACAGTCTTAAG 57.335 33.333 0.00 0.00 37.75 1.85
824 936 8.740123 TGATTGTTTTTCACCTAACAGTCTTA 57.260 30.769 0.00 0.00 39.96 2.10
825 937 7.556275 TCTGATTGTTTTTCACCTAACAGTCTT 59.444 33.333 0.00 0.00 39.96 3.01
858 970 1.997606 CTGGCAAGCAAAGCATTAAGC 59.002 47.619 0.00 0.00 46.19 3.09
859 971 3.308438 ACTGGCAAGCAAAGCATTAAG 57.692 42.857 0.00 0.00 0.00 1.85
860 972 3.749665 AACTGGCAAGCAAAGCATTAA 57.250 38.095 0.00 0.00 0.00 1.40
861 973 3.749665 AAACTGGCAAGCAAAGCATTA 57.250 38.095 0.00 0.00 0.00 1.90
862 974 2.625695 AAACTGGCAAGCAAAGCATT 57.374 40.000 0.00 0.00 0.00 3.56
921 1033 3.130280 AGTCAGATGTGTGCATGACAA 57.870 42.857 16.03 0.00 35.91 3.18
928 1040 6.537566 CAGTTGTATTAAGTCAGATGTGTGC 58.462 40.000 0.00 0.00 0.00 4.57
931 1043 6.726258 TGCAGTTGTATTAAGTCAGATGTG 57.274 37.500 0.00 0.00 0.00 3.21
939 1057 7.148407 CGAAGAGGAAATGCAGTTGTATTAAGT 60.148 37.037 3.09 0.00 30.21 2.24
948 1068 1.808945 CAGCGAAGAGGAAATGCAGTT 59.191 47.619 0.00 0.00 0.00 3.16
949 1069 1.446907 CAGCGAAGAGGAAATGCAGT 58.553 50.000 0.00 0.00 0.00 4.40
972 1092 3.845178 TGCTTCAGGTGTGTATAAGACG 58.155 45.455 0.00 0.00 0.00 4.18
973 1093 4.865365 GTCTGCTTCAGGTGTGTATAAGAC 59.135 45.833 0.00 0.00 31.51 3.01
985 1106 1.554160 ACTCATGAGGTCTGCTTCAGG 59.446 52.381 26.08 0.00 34.15 3.86
1141 1262 2.204461 TCTCGACGTTGAAGGCCCA 61.204 57.895 6.99 0.00 0.00 5.36
1344 1465 3.821033 CCCGGTTTCCATCATTTATCCTC 59.179 47.826 0.00 0.00 0.00 3.71
1350 1471 3.023832 GTCATCCCGGTTTCCATCATTT 58.976 45.455 0.00 0.00 0.00 2.32
1353 1474 0.107897 CGTCATCCCGGTTTCCATCA 60.108 55.000 0.00 0.00 0.00 3.07
1356 1477 1.294138 GTCGTCATCCCGGTTTCCA 59.706 57.895 0.00 0.00 0.00 3.53
1359 1480 2.433664 GCGTCGTCATCCCGGTTT 60.434 61.111 0.00 0.00 0.00 3.27
1368 1489 1.215382 CTCAGGAATGGCGTCGTCA 59.785 57.895 0.14 0.14 0.00 4.35
1371 1492 2.509052 TATTCTCAGGAATGGCGTCG 57.491 50.000 2.01 0.00 41.66 5.12
1380 1501 2.630098 CAGCTCCGGAATATTCTCAGGA 59.370 50.000 14.95 17.59 0.00 3.86
1389 1510 0.261991 ACCTCTCCAGCTCCGGAATA 59.738 55.000 5.23 0.00 33.65 1.75
1390 1511 0.261991 TACCTCTCCAGCTCCGGAAT 59.738 55.000 5.23 0.00 33.65 3.01
1392 1513 1.076923 GTACCTCTCCAGCTCCGGA 60.077 63.158 2.93 2.93 0.00 5.14
1473 1594 0.380733 ACGCAGCATGATCAGCAATG 59.619 50.000 16.20 5.06 39.69 2.82
1474 1595 0.661552 GACGCAGCATGATCAGCAAT 59.338 50.000 16.20 0.37 39.69 3.56
1488 1609 2.202810 TTGCCGATATGCGACGCA 60.203 55.556 26.68 26.68 44.57 5.24
1491 1612 2.939022 GCCTTGCCGATATGCGAC 59.061 61.111 0.00 0.00 44.57 5.19
1497 1618 2.499205 CCACTCGCCTTGCCGATA 59.501 61.111 0.00 0.00 36.54 2.92
1551 1672 2.019984 GGTATCTTCCCTTGCTTGCTG 58.980 52.381 0.00 0.00 0.00 4.41
1620 1741 4.640690 ACCTCTGTCCGGCCACCT 62.641 66.667 2.24 0.00 0.00 4.00
1888 2009 1.067364 TCAGTACTTGTTTCGCCACGA 59.933 47.619 0.00 0.00 0.00 4.35
1911 2034 7.760131 AACATGCTTCAAAATGTATGTATGC 57.240 32.000 0.00 0.00 38.26 3.14
1915 2038 7.710044 TCAACAAACATGCTTCAAAATGTATGT 59.290 29.630 0.00 0.00 40.27 2.29
1919 2042 6.981762 TTCAACAAACATGCTTCAAAATGT 57.018 29.167 0.00 0.00 38.66 2.71
1921 2044 6.488817 GCTTTCAACAAACATGCTTCAAAAT 58.511 32.000 0.00 0.00 0.00 1.82
1922 2045 5.445673 CGCTTTCAACAAACATGCTTCAAAA 60.446 36.000 0.00 0.00 0.00 2.44
1924 2047 3.551082 CGCTTTCAACAAACATGCTTCAA 59.449 39.130 0.00 0.00 0.00 2.69
1931 2054 1.408702 ACCTGCGCTTTCAACAAACAT 59.591 42.857 9.73 0.00 0.00 2.71
1948 2071 1.566018 GCTAAAACGCACGCTGACCT 61.566 55.000 0.00 0.00 0.00 3.85
1950 2073 1.154469 GGCTAAAACGCACGCTGAC 60.154 57.895 0.00 0.00 0.00 3.51
1956 2079 2.088950 TAGTCTGGGCTAAAACGCAC 57.911 50.000 0.00 0.00 0.00 5.34
2019 2142 2.354259 CAGGTAGCAGAGCCTTTCTTG 58.646 52.381 0.00 0.00 32.41 3.02
2045 2168 0.886563 ATTGCTCAGAAACAGCCAGC 59.113 50.000 0.00 0.00 35.89 4.85
2087 2210 1.542915 CCCAACAAAGCATGTCTCCAG 59.457 52.381 0.00 0.00 42.99 3.86
2092 2215 1.047801 AACCCCCAACAAAGCATGTC 58.952 50.000 0.00 0.00 42.99 3.06
2161 2285 3.620488 ACTGAAAGGACAAGCTCAACAA 58.380 40.909 0.00 0.00 39.30 2.83
2214 2338 1.010046 TCCAGAGGATCCATCAACCCT 59.990 52.381 15.82 0.00 33.66 4.34
2219 2343 1.114627 CACGTCCAGAGGATCCATCA 58.885 55.000 15.82 0.00 32.73 3.07
2234 2358 1.101049 CAACAAGTCAAGCCCCACGT 61.101 55.000 0.00 0.00 0.00 4.49
2235 2359 1.654220 CAACAAGTCAAGCCCCACG 59.346 57.895 0.00 0.00 0.00 4.94
2263 2388 9.914131 CAGAGGTCATTGAATATCGAACTAATA 57.086 33.333 0.00 0.00 0.00 0.98
2264 2389 8.642432 TCAGAGGTCATTGAATATCGAACTAAT 58.358 33.333 0.00 0.00 0.00 1.73
2265 2390 8.007405 TCAGAGGTCATTGAATATCGAACTAA 57.993 34.615 0.00 0.00 0.00 2.24
2266 2391 7.582667 TCAGAGGTCATTGAATATCGAACTA 57.417 36.000 0.00 0.00 0.00 2.24
2272 2397 7.901029 TCCTGTATCAGAGGTCATTGAATATC 58.099 38.462 0.00 0.00 32.44 1.63
2290 2415 6.975949 TCTCTCTTAGGTTCTCTTCCTGTAT 58.024 40.000 0.00 0.00 36.60 2.29
2292 2417 5.263872 TCTCTCTTAGGTTCTCTTCCTGT 57.736 43.478 0.00 0.00 36.60 4.00
2332 2459 7.730084 TCATATCCTTGTCAAGTCATCTTAGG 58.270 38.462 11.61 0.00 32.07 2.69
2335 2462 6.825721 GGTTCATATCCTTGTCAAGTCATCTT 59.174 38.462 11.61 0.00 0.00 2.40
2398 2526 2.589540 CCTTCATAGTGGGCGCCA 59.410 61.111 30.85 12.04 0.00 5.69
2471 2600 9.601810 ATGAGTAGATCCTTAACCACACATATA 57.398 33.333 0.00 0.00 0.00 0.86
2750 2988 9.548208 GTAAACAGAAACATCATAGAGAAAAGC 57.452 33.333 0.00 0.00 0.00 3.51
2801 3039 4.158764 CACCGGCCAACCTCATTTTATTTA 59.841 41.667 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.