Multiple sequence alignment - TraesCS2A01G069900

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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 TraesCS2A01G069900 chr2A 100.000 1897 0 0 2080 3976 30765490 30767386 0.000000e+00 3504.0
1 TraesCS2A01G069900 chr2A 100.000 1732 0 0 1 1732 30763411 30765142 0.000000e+00 3199.0
2 TraesCS2A01G069900 chr2A 91.266 790 54 9 3192 3976 11662299 11661520 0.000000e+00 1062.0
3 TraesCS2A01G069900 chr2A 85.000 920 114 13 2080 2989 30858035 30858940 0.000000e+00 913.0
4 TraesCS2A01G069900 chr2A 87.500 400 34 9 844 1236 30857128 30857518 7.840000e-122 448.0
5 TraesCS2A01G069900 chr2A 91.803 244 10 1 3192 3435 30793292 30793525 8.240000e-87 331.0
6 TraesCS2A01G069900 chr2A 91.803 244 10 1 3192 3435 30813622 30813855 8.240000e-87 331.0
7 TraesCS2A01G069900 chr2A 86.611 239 24 7 1301 1536 30857611 30857844 1.420000e-64 257.0
8 TraesCS2A01G069900 chr2A 97.778 45 1 0 3129 3173 30793634 30793590 1.180000e-10 78.7
9 TraesCS2A01G069900 chr2A 97.778 45 1 0 3129 3173 30813964 30813920 1.180000e-10 78.7
10 TraesCS2A01G069900 chr2B 90.524 1203 77 17 550 1732 46503909 46505094 0.000000e+00 1555.0
11 TraesCS2A01G069900 chr2B 88.444 1125 106 13 2080 3191 46505152 46506265 0.000000e+00 1336.0
12 TraesCS2A01G069900 chr2B 84.674 920 116 12 2080 2990 46672619 46673522 0.000000e+00 894.0
13 TraesCS2A01G069900 chr2B 93.134 568 24 10 1 556 46502412 46502976 0.000000e+00 819.0
14 TraesCS2A01G069900 chr2B 89.628 511 42 7 2663 3173 46323552 46324051 1.200000e-179 640.0
15 TraesCS2A01G069900 chr2B 85.433 508 40 14 733 1231 46669088 46669570 7.670000e-137 497.0
16 TraesCS2A01G069900 chr2B 85.957 235 26 6 1305 1536 46671999 46672229 1.100000e-60 244.0
17 TraesCS2A01G069900 chr2D 91.015 857 67 4 2320 3173 28828615 28829464 0.000000e+00 1147.0
18 TraesCS2A01G069900 chr2D 86.489 977 92 29 777 1732 28827393 28828350 0.000000e+00 1037.0
19 TraesCS2A01G069900 chr2D 85.185 918 116 10 2080 2989 28895774 28896679 0.000000e+00 924.0
20 TraesCS2A01G069900 chr2D 85.490 510 43 15 733 1235 28894770 28895255 1.650000e-138 503.0
21 TraesCS2A01G069900 chr2D 98.030 203 4 0 2080 2282 28828411 28828613 1.760000e-93 353.0
22 TraesCS2A01G069900 chr2D 85.259 251 30 5 1289 1536 28895338 28895584 6.600000e-63 252.0
23 TraesCS2A01G069900 chrUn 93.298 761 45 5 3187 3943 132225682 132226440 0.000000e+00 1118.0
24 TraesCS2A01G069900 chrUn 84.500 800 97 14 2200 2989 359864169 359864951 0.000000e+00 765.0
25 TraesCS2A01G069900 chrUn 83.724 768 98 16 2083 2840 423412780 423412030 0.000000e+00 701.0
26 TraesCS2A01G069900 chrUn 81.420 845 84 39 733 1536 17182844 17183656 1.210000e-174 623.0
27 TraesCS2A01G069900 chrUn 90.079 252 21 3 3192 3439 132250878 132251129 1.380000e-84 324.0
28 TraesCS2A01G069900 chr1A 91.593 797 54 10 3192 3976 58330183 58329388 0.000000e+00 1088.0
29 TraesCS2A01G069900 chr6B 91.508 789 63 3 3191 3976 387233082 387232295 0.000000e+00 1083.0
30 TraesCS2A01G069900 chr6B 87.698 252 27 4 3192 3440 387228116 387227866 1.400000e-74 291.0
31 TraesCS2A01G069900 chr7A 90.783 792 58 10 3190 3976 711658750 711659531 0.000000e+00 1044.0
32 TraesCS2A01G069900 chr7A 89.388 801 60 15 3189 3976 115641779 115640991 0.000000e+00 985.0
33 TraesCS2A01G069900 chr1B 90.446 785 66 5 3192 3976 550029178 550028403 0.000000e+00 1026.0
34 TraesCS2A01G069900 chr4B 86.634 808 74 20 3192 3976 222614587 222613791 0.000000e+00 863.0
35 TraesCS2A01G069900 chr4B 86.776 794 73 22 3192 3976 651749289 651748519 0.000000e+00 856.0
36 TraesCS2A01G069900 chr5B 81.470 626 93 13 2382 2991 488015888 488016506 3.570000e-135 492.0
37 TraesCS2A01G069900 chr5B 81.090 624 99 13 2382 2991 488112656 488113274 7.730000e-132 481.0
38 TraesCS2A01G069900 chr5B 90.086 232 20 2 1003 1231 488014617 488014848 8.350000e-77 298.0
39 TraesCS2A01G069900 chr5B 86.076 158 22 0 2080 2237 129335186 129335029 1.900000e-38 171.0
40 TraesCS2A01G069900 chr5A 80.929 624 100 10 2382 2991 512459701 512460319 3.600000e-130 475.0
41 TraesCS2A01G069900 chr5A 85.039 254 31 4 989 1236 512599980 512600232 6.600000e-63 252.0
42 TraesCS2A01G069900 chr5A 86.076 158 22 0 2080 2237 126639473 126639630 1.900000e-38 171.0
43 TraesCS2A01G069900 chr5D 90.086 232 20 2 1003 1231 407108630 407108399 8.350000e-77 298.0
44 TraesCS2A01G069900 chr5D 88.745 231 24 1 2080 2308 407107373 407107143 8.410000e-72 281.0
45 TraesCS2A01G069900 chr3D 89.069 247 17 1 3192 3438 577863794 577863558 8.350000e-77 298.0
46 TraesCS2A01G069900 chr7B 88.000 250 16 7 3192 3438 14863719 14863957 2.340000e-72 283.0


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 TraesCS2A01G069900 chr2A 30763411 30767386 3975 False 3351.500000 3504 100.000000 1 3976 2 chr2A.!!$F3 3975
1 TraesCS2A01G069900 chr2A 11661520 11662299 779 True 1062.000000 1062 91.266000 3192 3976 1 chr2A.!!$R1 784
2 TraesCS2A01G069900 chr2A 30857128 30858940 1812 False 539.333333 913 86.370333 844 2989 3 chr2A.!!$F4 2145
3 TraesCS2A01G069900 chr2B 46502412 46506265 3853 False 1236.666667 1555 90.700667 1 3191 3 chr2B.!!$F2 3190
4 TraesCS2A01G069900 chr2B 46669088 46673522 4434 False 545.000000 894 85.354667 733 2990 3 chr2B.!!$F3 2257
5 TraesCS2A01G069900 chr2D 28827393 28829464 2071 False 845.666667 1147 91.844667 777 3173 3 chr2D.!!$F1 2396
6 TraesCS2A01G069900 chr2D 28894770 28896679 1909 False 559.666667 924 85.311333 733 2989 3 chr2D.!!$F2 2256
7 TraesCS2A01G069900 chrUn 132225682 132226440 758 False 1118.000000 1118 93.298000 3187 3943 1 chrUn.!!$F2 756
8 TraesCS2A01G069900 chrUn 359864169 359864951 782 False 765.000000 765 84.500000 2200 2989 1 chrUn.!!$F4 789
9 TraesCS2A01G069900 chrUn 423412030 423412780 750 True 701.000000 701 83.724000 2083 2840 1 chrUn.!!$R1 757
10 TraesCS2A01G069900 chrUn 17182844 17183656 812 False 623.000000 623 81.420000 733 1536 1 chrUn.!!$F1 803
11 TraesCS2A01G069900 chr1A 58329388 58330183 795 True 1088.000000 1088 91.593000 3192 3976 1 chr1A.!!$R1 784
12 TraesCS2A01G069900 chr6B 387232295 387233082 787 True 1083.000000 1083 91.508000 3191 3976 1 chr6B.!!$R2 785
13 TraesCS2A01G069900 chr7A 711658750 711659531 781 False 1044.000000 1044 90.783000 3190 3976 1 chr7A.!!$F1 786
14 TraesCS2A01G069900 chr7A 115640991 115641779 788 True 985.000000 985 89.388000 3189 3976 1 chr7A.!!$R1 787
15 TraesCS2A01G069900 chr1B 550028403 550029178 775 True 1026.000000 1026 90.446000 3192 3976 1 chr1B.!!$R1 784
16 TraesCS2A01G069900 chr4B 222613791 222614587 796 True 863.000000 863 86.634000 3192 3976 1 chr4B.!!$R1 784
17 TraesCS2A01G069900 chr4B 651748519 651749289 770 True 856.000000 856 86.776000 3192 3976 1 chr4B.!!$R2 784
18 TraesCS2A01G069900 chr5B 488112656 488113274 618 False 481.000000 481 81.090000 2382 2991 1 chr5B.!!$F1 609
19 TraesCS2A01G069900 chr5B 488014617 488016506 1889 False 395.000000 492 85.778000 1003 2991 2 chr5B.!!$F2 1988
20 TraesCS2A01G069900 chr5A 512459701 512460319 618 False 475.000000 475 80.929000 2382 2991 1 chr5A.!!$F2 609
21 TraesCS2A01G069900 chr5D 407107143 407108630 1487 True 289.500000 298 89.415500 1003 2308 2 chr5D.!!$R1 1305

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
195 205 0.107456 CGTCATGAGCCTAGCCCAAT 59.893 55.0 0.0 0.0 0.00 3.16 F
1007 2008 0.991920 AGAAAGGAAGGAATGGCGGA 59.008 50.0 0.0 0.0 0.00 5.54 F
1296 4985 0.109723 CCCGAGTCTTGTTTCCCCAA 59.890 55.0 0.0 0.0 0.00 4.12 F
2480 6546 0.036952 AGGAGCATGACCTCAACACG 60.037 55.0 0.0 0.0 33.47 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1206 2210 0.618458 CCCCAAGGACGAATTCTGGA 59.382 55.000 11.29 0.00 33.47 3.86 R
2323 6383 1.328680 CGTGGATCGCTGAGAAATTGG 59.671 52.381 0.00 0.00 0.00 3.16 R
2657 6739 1.905215 AGCCTCATGTTGAGTAGTGCT 59.095 47.619 4.00 2.73 42.80 4.40 R
3763 7907 2.104792 AGCACAGAGGCAGAGTACAAAA 59.895 45.455 0.00 0.00 35.83 2.44 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
44 45 3.433615 GCTGCACTATTAGAATTAGCCGG 59.566 47.826 0.00 0.00 0.00 6.13
56 57 1.580059 TTAGCCGGTCTTCCTTCCAT 58.420 50.000 1.90 0.00 0.00 3.41
75 76 1.089978 TCCAGTCCACCCTTCTCCTA 58.910 55.000 0.00 0.00 0.00 2.94
89 90 5.762218 CCCTTCTCCTATTTGTATCAGCAAG 59.238 44.000 0.00 0.00 0.00 4.01
98 99 3.902261 TGTATCAGCAAGCAGTTTGTG 57.098 42.857 0.00 0.00 39.08 3.33
119 120 2.410262 GCGTTGATCGAACAGTGAACTG 60.410 50.000 8.91 8.91 44.91 3.16
131 132 2.291741 CAGTGAACTGCCCACTTTTCTC 59.708 50.000 0.00 0.00 42.44 2.87
142 143 2.811431 CCACTTTTCTCGTAATGCCACA 59.189 45.455 0.00 0.00 0.00 4.17
163 164 1.464997 CCCACTTTTCTTGTAGCGAGC 59.535 52.381 0.00 0.00 0.00 5.03
195 205 0.107456 CGTCATGAGCCTAGCCCAAT 59.893 55.000 0.00 0.00 0.00 3.16
232 242 1.907936 AGAGACAGAAGCTCATGCCTT 59.092 47.619 0.00 0.00 40.80 4.35
424 437 4.822026 ACAAAATTTGTTCGTGGGTTTGA 58.178 34.783 5.41 0.00 42.22 2.69
539 552 7.694388 TGAAAATGTGTAGCTATGTATCGTC 57.306 36.000 0.00 0.00 0.00 4.20
543 556 5.989551 TGTGTAGCTATGTATCGTCGTTA 57.010 39.130 0.00 0.00 0.00 3.18
558 1510 2.892373 CGTTACAACGCATGGTCAAT 57.108 45.000 1.04 0.00 46.06 2.57
598 1550 1.966845 AAAGCTTAGCCTCACCCCTA 58.033 50.000 0.00 0.00 0.00 3.53
626 1582 1.068588 TCAGTGTCGGAGAACCTTGTG 59.931 52.381 0.00 0.00 39.69 3.33
641 1597 8.301252 AGAACCTTGTGTTTACCTTTTACATT 57.699 30.769 0.00 0.00 37.29 2.71
665 1621 1.667212 CGTGTGCATGCATGTCACTAT 59.333 47.619 33.68 1.67 36.48 2.12
666 1622 2.865551 CGTGTGCATGCATGTCACTATA 59.134 45.455 33.68 21.85 36.48 1.31
703 1659 5.477984 TCTTGTTAGAAATCAGCTTGCCAAT 59.522 36.000 0.00 0.00 0.00 3.16
722 1678 9.716556 TTGCCAATTATTAGTTTATTTCCCCTA 57.283 29.630 0.00 0.00 0.00 3.53
851 1820 4.392138 GGAGAAGACGAACCCAGTTTTATG 59.608 45.833 0.00 0.00 0.00 1.90
953 1938 6.470235 CGTTTGATATCTGAAAAATCACCAGC 59.530 38.462 3.98 0.00 29.64 4.85
955 1940 6.932356 TGATATCTGAAAAATCACCAGCTC 57.068 37.500 3.98 0.00 0.00 4.09
956 1941 6.417258 TGATATCTGAAAAATCACCAGCTCA 58.583 36.000 3.98 0.00 0.00 4.26
957 1942 7.058525 TGATATCTGAAAAATCACCAGCTCAT 58.941 34.615 3.98 0.00 0.00 2.90
958 1943 5.831702 ATCTGAAAAATCACCAGCTCATC 57.168 39.130 0.00 0.00 0.00 2.92
959 1944 3.686241 TCTGAAAAATCACCAGCTCATCG 59.314 43.478 0.00 0.00 0.00 3.84
998 1990 2.224548 ACGTCCAGGAAAGAAAGGAAGG 60.225 50.000 0.00 0.00 34.54 3.46
1007 2008 0.991920 AGAAAGGAAGGAATGGCGGA 59.008 50.000 0.00 0.00 0.00 5.54
1206 2210 2.750657 GCACCAGGAGCCCAGCTAT 61.751 63.158 0.00 0.00 39.88 2.97
1209 2213 1.767672 CCAGGAGCCCAGCTATCCA 60.768 63.158 8.62 0.00 39.88 3.41
1221 2225 3.181461 CCAGCTATCCAGAATTCGTCCTT 60.181 47.826 0.00 0.00 0.00 3.36
1231 2235 1.497161 ATTCGTCCTTGGGGAGGTAG 58.503 55.000 4.95 0.00 46.39 3.18
1296 4985 0.109723 CCCGAGTCTTGTTTCCCCAA 59.890 55.000 0.00 0.00 0.00 4.12
1337 5027 1.069358 GCCTCCGTGAATCCTTCCTAG 59.931 57.143 0.00 0.00 0.00 3.02
1459 5149 2.012673 CACCTTGATCACTAAGCCTGC 58.987 52.381 0.00 0.00 0.00 4.85
1499 5189 2.158900 CCATCCTGAATTACCGCTGTCT 60.159 50.000 0.00 0.00 0.00 3.41
1506 5196 4.665212 TGAATTACCGCTGTCTTACTACG 58.335 43.478 0.00 0.00 0.00 3.51
1525 5215 0.667792 GCAGGTGTTCTCGGTGAGTC 60.668 60.000 0.00 0.00 0.00 3.36
1542 5233 1.990563 AGTCCACTTTTATTCGTCGCG 59.009 47.619 0.00 0.00 0.00 5.87
1588 5290 4.340950 ACATTTTCATGTTCTGGAAACGGT 59.659 37.500 0.00 0.00 41.16 4.83
1621 5325 3.589495 ACTTTCTTGGTAGACCGTAGC 57.411 47.619 0.00 0.00 39.43 3.58
1641 5345 3.192422 AGCCTGCTACTCTGCTATAATCG 59.808 47.826 0.00 0.00 30.97 3.34
1647 5351 5.025190 GCTACTCTGCTATAATCGATCACG 58.975 45.833 0.00 0.00 41.26 4.35
1657 5361 8.301720 TGCTATAATCGATCACGTAATTAAGGT 58.698 33.333 0.00 0.00 40.69 3.50
1658 5362 9.778993 GCTATAATCGATCACGTAATTAAGGTA 57.221 33.333 0.00 0.00 40.69 3.08
1663 5367 7.194607 TCGATCACGTAATTAAGGTACTAGG 57.805 40.000 3.43 0.00 38.25 3.02
1714 5770 2.476619 CACTCGTGTCTGCTACTTTTGG 59.523 50.000 0.00 0.00 0.00 3.28
2107 6163 5.562696 GCATTTTCTGGATTCTTCAACGTGA 60.563 40.000 0.00 0.00 0.00 4.35
2248 6304 2.673368 GAGAAGGTTTGTACATGCTCGG 59.327 50.000 0.00 0.00 31.52 4.63
2252 6308 2.552315 AGGTTTGTACATGCTCGGTTTG 59.448 45.455 0.00 0.00 0.00 2.93
2282 6338 2.639327 GGTTGTGCACATCCCCAGC 61.639 63.158 29.31 16.96 31.18 4.85
2323 6383 1.986575 GATTCTGTCGCTGCCCTTGC 61.987 60.000 0.00 0.00 38.26 4.01
2334 6394 1.203994 CTGCCCTTGCCAATTTCTCAG 59.796 52.381 0.00 0.00 36.33 3.35
2341 6403 1.339920 TGCCAATTTCTCAGCGATCCA 60.340 47.619 0.00 0.00 0.00 3.41
2478 6544 1.980765 AGAAGGAGCATGACCTCAACA 59.019 47.619 11.36 0.00 36.67 3.33
2480 6546 0.036952 AGGAGCATGACCTCAACACG 60.037 55.000 0.00 0.00 33.47 4.49
2522 6588 0.324275 GCCCCTTTCCTTGCCATACA 60.324 55.000 0.00 0.00 0.00 2.29
2572 6654 7.007723 TGGTCCAATTAACCAGAAGTAATTGT 58.992 34.615 7.60 0.00 41.84 2.71
2644 6726 0.470341 TTCGACAATGTGGGTGGTGA 59.530 50.000 0.00 0.00 0.00 4.02
2735 6818 1.371183 CAACCTGGAGCGTCCTGAA 59.629 57.895 0.00 0.00 37.65 3.02
2995 7082 2.811410 ACATCACATGCCAGGATGTTT 58.189 42.857 13.81 0.00 46.93 2.83
3054 7141 8.689251 TCGCTGAAATATATATGTAGTTCTGC 57.311 34.615 26.60 26.60 43.66 4.26
3055 7142 8.303876 TCGCTGAAATATATATGTAGTTCTGCA 58.696 33.333 30.89 22.16 45.49 4.41
3056 7143 9.091784 CGCTGAAATATATATGTAGTTCTGCAT 57.908 33.333 30.89 8.29 45.49 3.96
3074 7161 5.998454 TGCATTATTAGCAGAGAAAGCTC 57.002 39.130 0.00 0.00 42.32 4.09
3173 7260 6.071984 TCTAGGGTGCAAACTTTCCAAAATA 58.928 36.000 0.00 0.00 0.00 1.40
3174 7261 5.823861 AGGGTGCAAACTTTCCAAAATAT 57.176 34.783 0.00 0.00 0.00 1.28
3175 7262 6.186420 AGGGTGCAAACTTTCCAAAATATT 57.814 33.333 0.00 0.00 0.00 1.28
3176 7263 6.230472 AGGGTGCAAACTTTCCAAAATATTC 58.770 36.000 0.00 0.00 0.00 1.75
3178 7265 6.368791 GGGTGCAAACTTTCCAAAATATTCTC 59.631 38.462 0.00 0.00 0.00 2.87
3179 7266 6.368791 GGTGCAAACTTTCCAAAATATTCTCC 59.631 38.462 0.00 0.00 0.00 3.71
3180 7267 6.928492 GTGCAAACTTTCCAAAATATTCTCCA 59.072 34.615 0.00 0.00 0.00 3.86
3196 7287 4.486125 TCTCCATGCTAGTATTTGTGCA 57.514 40.909 0.00 0.00 39.83 4.57
3288 7380 2.273557 ACGCGTACAAGAGTTTGTTGT 58.726 42.857 11.67 0.00 45.01 3.32
3347 7454 6.854778 AGCTAGCTAGTAGTTACAACAGAAC 58.145 40.000 17.69 0.00 0.00 3.01
3525 7668 4.679662 CAATGCCTTTGTGAATCCATCTC 58.320 43.478 0.00 0.00 0.00 2.75
3565 7708 3.119316 TGCACAAACCGAATGTCAAGTTT 60.119 39.130 0.00 0.00 32.84 2.66
3638 7782 3.942829 TGTTCTAGCATGAAAGACTGGG 58.057 45.455 0.00 0.00 0.00 4.45
3730 7874 7.721399 ACCAAGTTCTTTCAACATAGACTGAAT 59.279 33.333 0.00 0.00 31.85 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 5.574830 CGGCTAATTCTAATAGTGCAGCTAG 59.425 44.000 0.00 0.00 32.45 3.42
44 45 1.909302 TGGACTGGATGGAAGGAAGAC 59.091 52.381 0.00 0.00 0.00 3.01
56 57 1.089978 TAGGAGAAGGGTGGACTGGA 58.910 55.000 0.00 0.00 0.00 3.86
75 76 5.224888 CACAAACTGCTTGCTGATACAAAT 58.775 37.500 6.50 0.00 38.75 2.32
89 90 0.234625 TCGATCAACGCACAAACTGC 59.765 50.000 0.00 0.00 43.21 4.40
98 99 1.792949 AGTTCACTGTTCGATCAACGC 59.207 47.619 0.00 0.00 42.26 4.84
101 102 2.143122 GGCAGTTCACTGTTCGATCAA 58.857 47.619 8.72 0.00 45.45 2.57
112 113 1.264288 CGAGAAAAGTGGGCAGTTCAC 59.736 52.381 0.00 0.00 35.51 3.18
119 120 1.132453 GGCATTACGAGAAAAGTGGGC 59.868 52.381 0.00 0.00 0.00 5.36
131 132 1.243902 AAAGTGGGTGTGGCATTACG 58.756 50.000 0.00 0.00 0.00 3.18
142 143 2.767505 CTCGCTACAAGAAAAGTGGGT 58.232 47.619 0.00 0.00 0.00 4.51
171 181 1.948138 CTAGGCTCATGACGCGCAG 60.948 63.158 5.73 2.42 0.00 5.18
195 205 2.090760 CTCTAGCTCTGACTGTGCTCA 58.909 52.381 11.54 1.28 43.48 4.26
543 556 4.320608 AGAAAAATTGACCATGCGTTGT 57.679 36.364 0.00 0.00 0.00 3.32
603 1555 3.181454 ACAAGGTTCTCCGACACTGATTT 60.181 43.478 0.00 0.00 39.05 2.17
607 1559 1.202533 ACACAAGGTTCTCCGACACTG 60.203 52.381 0.00 0.00 39.05 3.66
626 1582 6.357766 GCACACGTACAATGTAAAAGGTAAAC 59.642 38.462 0.00 0.00 0.00 2.01
641 1597 0.795698 GACATGCATGCACACGTACA 59.204 50.000 25.37 0.00 0.00 2.90
687 1643 8.707938 AAACTAATAATTGGCAAGCTGATTTC 57.292 30.769 5.96 0.00 0.00 2.17
806 1775 0.673985 CAGGACAGACCAACTCGTCA 59.326 55.000 0.00 0.00 42.04 4.35
953 1938 0.802222 AACGCACCGATGACGATGAG 60.802 55.000 0.55 0.00 38.72 2.90
955 1940 1.344837 CAACGCACCGATGACGATG 59.655 57.895 0.55 0.00 42.66 3.84
956 1941 2.452813 GCAACGCACCGATGACGAT 61.453 57.895 0.55 0.00 42.66 3.73
957 1942 3.109547 GCAACGCACCGATGACGA 61.110 61.111 0.55 0.00 42.66 4.20
958 1943 4.483683 CGCAACGCACCGATGACG 62.484 66.667 0.00 0.00 31.46 4.35
959 1944 2.089936 TACGCAACGCACCGATGAC 61.090 57.895 0.00 0.00 31.46 3.06
998 1990 4.918201 CCTCCGCCTCCGCCATTC 62.918 72.222 0.00 0.00 0.00 2.67
1007 2008 2.738213 CTTGTTGCTCACCTCCGCCT 62.738 60.000 0.00 0.00 0.00 5.52
1206 2210 0.618458 CCCCAAGGACGAATTCTGGA 59.382 55.000 11.29 0.00 33.47 3.86
1296 4985 5.128663 AGGCACAAAAATGTAAGTGTTCCTT 59.871 36.000 0.00 0.00 34.51 3.36
1337 5027 4.393990 ACGCCAAAAGTAGTTATAACCTGC 59.606 41.667 12.05 3.16 0.00 4.85
1459 5149 4.661993 TGGTTGATCTTGAAAATCGACG 57.338 40.909 0.00 0.00 38.09 5.12
1499 5189 1.200716 CCGAGAACACCTGCGTAGTAA 59.799 52.381 0.00 0.00 0.00 2.24
1506 5196 0.667792 GACTCACCGAGAACACCTGC 60.668 60.000 0.00 0.00 33.32 4.85
1525 5215 1.266891 GCTCGCGACGAATAAAAGTGG 60.267 52.381 3.71 0.00 34.74 4.00
1568 5259 4.993029 AACCGTTTCCAGAACATGAAAA 57.007 36.364 0.00 0.00 32.68 2.29
1575 5277 5.180680 AGCAATAACTAACCGTTTCCAGAAC 59.819 40.000 0.00 0.00 37.05 3.01
1581 5283 8.501580 AGAAAGTAAGCAATAACTAACCGTTTC 58.498 33.333 0.00 0.00 37.05 2.78
1584 5286 7.094933 CCAAGAAAGTAAGCAATAACTAACCGT 60.095 37.037 0.00 0.00 0.00 4.83
1621 5325 5.124617 TGATCGATTATAGCAGAGTAGCAGG 59.875 44.000 0.00 0.00 36.85 4.85
1641 5345 6.979465 AGCCTAGTACCTTAATTACGTGATC 58.021 40.000 0.00 0.00 0.00 2.92
1663 5367 2.232696 GCTTCTAGGATGGGCTAGTAGC 59.767 54.545 14.09 14.09 38.62 3.58
2323 6383 1.328680 CGTGGATCGCTGAGAAATTGG 59.671 52.381 0.00 0.00 0.00 3.16
2334 6394 3.100817 CACATTCAATTTCGTGGATCGC 58.899 45.455 0.00 0.00 39.67 4.58
2478 6544 3.439129 GCAATTAACCTCTTTAGTGCCGT 59.561 43.478 0.00 0.00 31.10 5.68
2480 6546 5.385509 TTGCAATTAACCTCTTTAGTGCC 57.614 39.130 0.00 0.00 34.11 5.01
2550 6632 8.472007 ACAACAATTACTTCTGGTTAATTGGA 57.528 30.769 15.10 0.00 41.57 3.53
2572 6654 8.308931 ACCTACGAGAACAAAGTATTATGACAA 58.691 33.333 0.00 0.00 0.00 3.18
2657 6739 1.905215 AGCCTCATGTTGAGTAGTGCT 59.095 47.619 4.00 2.73 42.80 4.40
2995 7082 3.071892 AGGACACAGTTTTCACCCGAATA 59.928 43.478 0.00 0.00 0.00 1.75
3054 7141 7.408123 CAACTGAGCTTTCTCTGCTAATAATG 58.592 38.462 0.00 0.00 41.30 1.90
3055 7142 6.541641 CCAACTGAGCTTTCTCTGCTAATAAT 59.458 38.462 0.00 0.00 41.30 1.28
3056 7143 5.877012 CCAACTGAGCTTTCTCTGCTAATAA 59.123 40.000 0.00 0.00 41.30 1.40
3067 7154 9.476202 AAATTAACATTTACCAACTGAGCTTTC 57.524 29.630 0.00 0.00 30.22 2.62
3074 7161 7.213678 ACACCCAAATTAACATTTACCAACTG 58.786 34.615 0.00 0.00 30.90 3.16
3173 7260 5.439721 TGCACAAATACTAGCATGGAGAAT 58.560 37.500 0.00 0.00 31.05 2.40
3174 7261 4.842574 TGCACAAATACTAGCATGGAGAA 58.157 39.130 0.00 0.00 31.05 2.87
3175 7262 4.486125 TGCACAAATACTAGCATGGAGA 57.514 40.909 0.00 0.00 31.05 3.71
3176 7263 5.506815 CCAATGCACAAATACTAGCATGGAG 60.507 44.000 0.00 0.00 46.10 3.86
3178 7265 4.613944 CCAATGCACAAATACTAGCATGG 58.386 43.478 0.00 0.00 46.10 3.66
3179 7266 4.046462 GCCAATGCACAAATACTAGCATG 58.954 43.478 0.00 0.00 46.10 4.06
3196 7287 2.433436 GGGTAAGACGTTTCTGCCAAT 58.567 47.619 0.00 0.00 32.15 3.16
3202 7293 3.631227 CCTAGATCGGGTAAGACGTTTCT 59.369 47.826 0.00 0.00 0.00 2.52
3288 7380 7.735917 TCTTTCTTCTTCCTCAAGTTGTATCA 58.264 34.615 2.11 0.00 0.00 2.15
3347 7454 4.319139 AGATAGCTAGGCGCATATGATG 57.681 45.455 10.83 0.00 42.61 3.07
3525 7668 2.289882 TGCACTCCAGAGATCAAGTTGG 60.290 50.000 2.34 0.00 0.00 3.77
3565 7708 2.975489 AGAGAAAGGGTTGCTCAGAAGA 59.025 45.455 0.00 0.00 0.00 2.87
3638 7782 2.284190 GCCACCTATCTCTCTGCAAAC 58.716 52.381 0.00 0.00 0.00 2.93
3763 7907 2.104792 AGCACAGAGGCAGAGTACAAAA 59.895 45.455 0.00 0.00 35.83 2.44


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

AutoCloner maintained by Alex Coulton.