Multiple sequence alignment - TraesCS7D01G039000

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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 TraesCS7D01G039000 chr7D 100.000 3671 0 0 611 4281 19924826 19928496 0.000000e+00 6780.0
1 TraesCS7D01G039000 chr7D 95.614 1368 59 1 611 1978 19861602 19862968 0.000000e+00 2193.0
2 TraesCS7D01G039000 chr7D 94.905 1374 69 1 611 1984 19815426 19816798 0.000000e+00 2148.0
3 TraesCS7D01G039000 chr7D 92.077 1199 84 7 791 1984 19742632 19743824 0.000000e+00 1677.0
4 TraesCS7D01G039000 chr7D 91.189 1203 86 11 795 1984 19774355 19775550 0.000000e+00 1616.0
5 TraesCS7D01G039000 chr7D 90.405 1209 100 10 791 1984 19835837 19837044 0.000000e+00 1576.0
6 TraesCS7D01G039000 chr7D 90.389 1207 102 9 791 1984 19907814 19909019 0.000000e+00 1574.0
7 TraesCS7D01G039000 chr7D 92.475 1010 74 2 977 1984 19817009 19818018 0.000000e+00 1443.0
8 TraesCS7D01G039000 chr7D 92.087 1011 77 3 977 1984 19863185 19864195 0.000000e+00 1421.0
9 TraesCS7D01G039000 chr7D 100.000 325 0 0 1 325 19924216 19924540 6.130000e-168 601.0
10 TraesCS7D01G039000 chr7D 98.462 325 5 0 1 325 19861192 19861516 1.340000e-159 573.0
11 TraesCS7D01G039000 chr7D 92.878 337 9 4 1 324 19814962 19815296 3.870000e-130 475.0
12 TraesCS7D01G039000 chr7D 93.989 183 10 1 614 795 19742422 19742604 4.220000e-70 276.0
13 TraesCS7D01G039000 chr7D 83.750 320 21 13 30 324 19907159 19907472 1.520000e-69 274.0
14 TraesCS7D01G039000 chr7D 83.660 306 32 13 30 324 19773713 19774011 5.450000e-69 272.0
15 TraesCS7D01G039000 chr7D 93.443 183 11 1 611 792 19907601 19907783 1.960000e-68 270.0
16 TraesCS7D01G039000 chr7D 83.819 309 23 11 35 320 19835187 19835491 7.060000e-68 268.0
17 TraesCS7D01G039000 chr7D 92.857 182 12 1 612 792 19835625 19835806 3.280000e-66 263.0
18 TraesCS7D01G039000 chr7D 92.350 183 13 1 611 792 19774138 19774320 4.250000e-65 259.0
19 TraesCS7D01G039000 chr7D 83.240 179 9 7 159 324 19742123 19742293 1.240000e-30 145.0
20 TraesCS7D01G039000 chr7D 90.196 51 1 4 4 51 545608400 545608351 3.570000e-06 63.9
21 TraesCS7D01G039000 chr7D 85.246 61 6 3 1 59 80504183 80504242 4.620000e-05 60.2
22 TraesCS7D01G039000 chrUn 87.359 1946 205 17 2356 4281 50642469 50640545 0.000000e+00 2193.0
23 TraesCS7D01G039000 chrUn 91.869 1070 86 1 960 2028 50646689 50645620 0.000000e+00 1493.0
24 TraesCS7D01G039000 chrUn 78.049 1558 293 34 2745 4279 96156347 96154816 0.000000e+00 937.0
25 TraesCS7D01G039000 chrUn 78.384 1522 270 34 2729 4234 95709639 95711117 0.000000e+00 933.0
26 TraesCS7D01G039000 chrUn 77.778 1575 296 37 2718 4279 95985483 95987016 0.000000e+00 920.0
27 TraesCS7D01G039000 chrUn 76.452 1584 332 29 2715 4279 96230221 96228660 0.000000e+00 821.0
28 TraesCS7D01G039000 chrUn 74.905 1582 327 40 2743 4279 96287045 96285489 0.000000e+00 658.0
29 TraesCS7D01G039000 chrUn 94.086 186 10 1 611 795 50647021 50646836 9.060000e-72 281.0
30 TraesCS7D01G039000 chrUn 83.495 309 26 12 31 324 50647452 50647154 9.130000e-67 265.0
31 TraesCS7D01G039000 chrUn 97.333 75 2 0 795 869 50646804 50646730 1.250000e-25 128.0
32 TraesCS7D01G039000 chrUn 90.196 51 1 4 1 51 469493022 469492976 3.570000e-06 63.9
33 TraesCS7D01G039000 chr7A 90.719 1530 101 11 681 2178 20025060 20026580 0.000000e+00 2001.0
34 TraesCS7D01G039000 chr7A 89.917 724 73 0 3558 4281 20033585 20034308 0.000000e+00 933.0
35 TraesCS7D01G039000 chr7A 91.633 490 40 1 2681 3170 20027102 20027590 0.000000e+00 676.0
36 TraesCS7D01G039000 chr7A 93.564 404 26 0 3159 3562 20027905 20028308 1.700000e-168 603.0
37 TraesCS7D01G039000 chr7A 85.670 321 18 14 30 324 20022479 20022797 3.210000e-81 313.0
38 TraesCS7D01G039000 chr7A 80.588 170 21 6 2493 2650 20026935 20027104 2.090000e-23 121.0
39 TraesCS7D01G039000 chr7A 94.286 70 4 0 612 681 20022928 20022997 1.630000e-19 108.0
40 TraesCS7D01G039000 chr7A 88.889 54 3 3 4 55 705216421 705216369 3.570000e-06 63.9
41 TraesCS7D01G039000 chr6A 79.310 1537 271 34 2765 4279 26962884 26964395 0.000000e+00 1033.0
42 TraesCS7D01G039000 chr6A 78.047 1526 290 29 2715 4219 614961931 614963432 0.000000e+00 920.0
43 TraesCS7D01G039000 chr6B 77.965 1543 305 20 2753 4279 46926449 46924926 0.000000e+00 933.0
44 TraesCS7D01G039000 chr6B 76.046 1578 320 41 2724 4279 46961512 46959971 0.000000e+00 767.0
45 TraesCS7D01G039000 chr6D 78.071 1514 287 30 2739 4231 470296496 470295007 0.000000e+00 915.0
46 TraesCS7D01G039000 chr6D 77.249 1534 277 39 2715 4226 470098311 470099794 0.000000e+00 833.0
47 TraesCS7D01G039000 chr7B 72.338 1005 225 39 2821 3803 744271369 744272342 2.540000e-67 267.0
48 TraesCS7D01G039000 chr7B 96.970 33 1 0 1 33 479780550 479780582 5.980000e-04 56.5
49 TraesCS7D01G039000 chr1B 91.667 48 3 1 4 51 503352932 503352886 9.940000e-07 65.8
50 TraesCS7D01G039000 chr1B 84.127 63 6 4 4 63 376618346 376618285 1.660000e-04 58.4


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 TraesCS7D01G039000 chr7D 19924216 19928496 4280 False 3690.500000 6780 100.000000 1 4281 2 chr7D.!!$F8 4280
1 TraesCS7D01G039000 chr7D 19861192 19864195 3003 False 1395.666667 2193 95.387667 1 1984 3 chr7D.!!$F6 1983
2 TraesCS7D01G039000 chr7D 19814962 19818018 3056 False 1355.333333 2148 93.419333 1 1984 3 chr7D.!!$F4 1983
3 TraesCS7D01G039000 chr7D 19773713 19775550 1837 False 715.666667 1616 89.066333 30 1984 3 chr7D.!!$F3 1954
4 TraesCS7D01G039000 chr7D 19907159 19909019 1860 False 706.000000 1574 89.194000 30 1984 3 chr7D.!!$F7 1954
5 TraesCS7D01G039000 chr7D 19835187 19837044 1857 False 702.333333 1576 89.027000 35 1984 3 chr7D.!!$F5 1949
6 TraesCS7D01G039000 chr7D 19742123 19743824 1701 False 699.333333 1677 89.768667 159 1984 3 chr7D.!!$F2 1825
7 TraesCS7D01G039000 chrUn 96154816 96156347 1531 True 937.000000 937 78.049000 2745 4279 1 chrUn.!!$R1 1534
8 TraesCS7D01G039000 chrUn 95709639 95711117 1478 False 933.000000 933 78.384000 2729 4234 1 chrUn.!!$F1 1505
9 TraesCS7D01G039000 chrUn 95985483 95987016 1533 False 920.000000 920 77.778000 2718 4279 1 chrUn.!!$F2 1561
10 TraesCS7D01G039000 chrUn 50640545 50647452 6907 True 872.000000 2193 90.828400 31 4281 5 chrUn.!!$R5 4250
11 TraesCS7D01G039000 chrUn 96228660 96230221 1561 True 821.000000 821 76.452000 2715 4279 1 chrUn.!!$R2 1564
12 TraesCS7D01G039000 chrUn 96285489 96287045 1556 True 658.000000 658 74.905000 2743 4279 1 chrUn.!!$R3 1536
13 TraesCS7D01G039000 chr7A 20033585 20034308 723 False 933.000000 933 89.917000 3558 4281 1 chr7A.!!$F1 723
14 TraesCS7D01G039000 chr7A 20022479 20028308 5829 False 637.000000 2001 89.410000 30 3562 6 chr7A.!!$F2 3532
15 TraesCS7D01G039000 chr6A 26962884 26964395 1511 False 1033.000000 1033 79.310000 2765 4279 1 chr6A.!!$F1 1514
16 TraesCS7D01G039000 chr6A 614961931 614963432 1501 False 920.000000 920 78.047000 2715 4219 1 chr6A.!!$F2 1504
17 TraesCS7D01G039000 chr6B 46924926 46926449 1523 True 933.000000 933 77.965000 2753 4279 1 chr6B.!!$R1 1526
18 TraesCS7D01G039000 chr6B 46959971 46961512 1541 True 767.000000 767 76.046000 2724 4279 1 chr6B.!!$R2 1555
19 TraesCS7D01G039000 chr6D 470295007 470296496 1489 True 915.000000 915 78.071000 2739 4231 1 chr6D.!!$R1 1492
20 TraesCS7D01G039000 chr6D 470098311 470099794 1483 False 833.000000 833 77.249000 2715 4226 1 chr6D.!!$F1 1511
21 TraesCS7D01G039000 chr7B 744271369 744272342 973 False 267.000000 267 72.338000 2821 3803 1 chr7B.!!$F2 982

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
671 704 1.078426 CGCGGAAAGGGATCAACCT 60.078 57.895 0.0 0.0 44.56 3.50 F
1879 6464 0.034670 ACTCAATGCTCCCTTCAGCC 60.035 55.000 0.0 0.0 38.80 4.85 F
2347 9845 0.035056 GGTTCTACCAGCCTGCATGT 60.035 55.000 0.0 0.0 38.42 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2328 9826 0.035056 ACATGCAGGCTGGTAGAACC 60.035 55.0 17.64 0.0 39.22 3.62 R
3210 11207 0.814410 TACTGCCTCGTCTCTAGCCG 60.814 60.0 0.00 0.0 0.00 5.52 R
4119 12159 0.107017 AGCAGGAAGTTGTGTGCAGT 60.107 50.0 0.00 0.0 38.44 4.40 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
320 353 1.224592 CAGCTTTCTACGGGGGCAT 59.775 57.895 0.00 0.00 0.00 4.40
671 704 1.078426 CGCGGAAAGGGATCAACCT 60.078 57.895 0.00 0.00 44.56 3.50
690 2786 2.304180 CCTTTGTCAGGTCTCAGGTCAT 59.696 50.000 0.00 0.00 37.99 3.06
1387 3530 1.954362 GAGGCTGGACGACATCTGCT 61.954 60.000 0.00 0.00 0.00 4.24
1388 3531 1.078848 GGCTGGACGACATCTGCTT 60.079 57.895 0.00 0.00 0.00 3.91
1497 3640 2.665185 GTGTTGGAACGCTCGGCT 60.665 61.111 0.00 0.00 36.52 5.52
1667 3812 9.489393 GGAAATTCAACACAAATTTGAAAAGAC 57.511 29.630 24.64 5.54 44.14 3.01
1701 3846 2.408050 GTCACACAAGACTTCAGCGAT 58.592 47.619 0.00 0.00 35.65 4.58
1803 5167 1.192534 CTTCTCAACGCCGTCAGAAAC 59.807 52.381 11.42 0.00 0.00 2.78
1809 5173 0.179067 ACGCCGTCAGAAACCAGAAA 60.179 50.000 0.00 0.00 0.00 2.52
1879 6464 0.034670 ACTCAATGCTCCCTTCAGCC 60.035 55.000 0.00 0.00 38.80 4.85
1923 6508 3.588955 TGTCATCACCACGAGAAATGAG 58.411 45.455 0.00 0.00 0.00 2.90
1934 6519 0.322546 AGAAATGAGACGGTTGCCCC 60.323 55.000 0.00 0.00 0.00 5.80
1971 6556 1.152963 GCCCTACCACCGCATTGAT 60.153 57.895 0.00 0.00 0.00 2.57
2019 6604 2.970974 GCTCAGGAAACAGGTGCGC 61.971 63.158 0.00 0.00 0.00 6.09
2022 6607 1.008538 CAGGAAACAGGTGCGCAAC 60.009 57.895 20.21 20.21 0.00 4.17
2041 9116 5.867716 CGCAACTAATTAACTGGTAGTGACT 59.132 40.000 0.00 0.00 0.00 3.41
2129 9213 9.996554 TTTAGTTGATCTTAGAAGTTGATGACA 57.003 29.630 0.00 0.00 0.00 3.58
2134 9218 8.908786 TGATCTTAGAAGTTGATGACAAAACT 57.091 30.769 0.00 1.96 38.25 2.66
2149 9233 9.160496 GATGACAAAACTAGAATCAGAGATGTT 57.840 33.333 0.00 0.00 0.00 2.71
2161 9245 8.890718 AGAATCAGAGATGTTATGTCAATGTTG 58.109 33.333 0.00 0.00 0.00 3.33
2167 9251 4.926140 TGTTATGTCAATGTTGTTGGCA 57.074 36.364 0.00 0.00 38.49 4.92
2175 9259 3.446873 TCAATGTTGTTGGCAGTTTGTCT 59.553 39.130 0.00 0.00 0.00 3.41
2176 9260 2.937469 TGTTGTTGGCAGTTTGTCTG 57.063 45.000 0.00 0.00 46.12 3.51
2177 9261 2.441410 TGTTGTTGGCAGTTTGTCTGA 58.559 42.857 0.00 0.00 46.27 3.27
2183 9267 2.384899 GGCAGTTTGTCTGACGAAAC 57.615 50.000 11.91 16.44 46.27 2.78
2187 9271 4.024387 GGCAGTTTGTCTGACGAAACATTA 60.024 41.667 24.22 1.28 46.27 1.90
2194 9278 9.478019 GTTTGTCTGACGAAACATTATGATTAG 57.522 33.333 20.67 0.00 33.16 1.73
2195 9279 8.771920 TTGTCTGACGAAACATTATGATTAGT 57.228 30.769 0.00 0.00 0.00 2.24
2196 9280 8.771920 TGTCTGACGAAACATTATGATTAGTT 57.228 30.769 0.00 0.00 0.00 2.24
2214 9712 0.688487 TTACTTCCTGTTCGGGTGGG 59.312 55.000 0.00 0.00 0.00 4.61
2217 9715 3.485346 TTCCTGTTCGGGTGGGCAC 62.485 63.158 0.00 0.00 0.00 5.01
2237 9735 2.040178 CCTAGTAGGTAGCCTGGTTGG 58.960 57.143 8.17 0.00 34.61 3.77
2247 9745 2.980541 CCTGGTTGGCATTGATGGT 58.019 52.632 0.00 0.00 0.00 3.55
2248 9746 0.533491 CCTGGTTGGCATTGATGGTG 59.467 55.000 0.00 0.00 0.00 4.17
2249 9747 1.259609 CTGGTTGGCATTGATGGTGT 58.740 50.000 0.00 0.00 0.00 4.16
2250 9748 1.203052 CTGGTTGGCATTGATGGTGTC 59.797 52.381 0.00 0.00 0.00 3.67
2251 9749 1.255882 GGTTGGCATTGATGGTGTCA 58.744 50.000 0.00 0.00 34.25 3.58
2252 9750 1.067635 GGTTGGCATTGATGGTGTCAC 60.068 52.381 0.00 0.00 36.32 3.67
2253 9751 1.067635 GTTGGCATTGATGGTGTCACC 60.068 52.381 15.64 15.64 36.32 4.02
2254 9752 0.959867 TGGCATTGATGGTGTCACCG 60.960 55.000 17.27 2.86 42.58 4.94
2255 9753 0.676466 GGCATTGATGGTGTCACCGA 60.676 55.000 17.27 7.03 42.58 4.69
2256 9754 1.382522 GCATTGATGGTGTCACCGAT 58.617 50.000 17.27 11.41 42.58 4.18
2257 9755 1.064505 GCATTGATGGTGTCACCGATG 59.935 52.381 17.27 17.01 42.58 3.84
2258 9756 1.672363 CATTGATGGTGTCACCGATGG 59.328 52.381 17.27 1.10 42.58 3.51
2259 9757 0.676466 TTGATGGTGTCACCGATGGC 60.676 55.000 17.27 5.18 42.58 4.40
2260 9758 1.819632 GATGGTGTCACCGATGGCC 60.820 63.158 17.27 0.00 42.58 5.36
2261 9759 3.344137 ATGGTGTCACCGATGGCCC 62.344 63.158 17.27 0.00 42.58 5.80
2262 9760 3.717294 GGTGTCACCGATGGCCCT 61.717 66.667 6.18 0.00 0.00 5.19
2265 9763 4.408821 GTCACCGATGGCCCTGCA 62.409 66.667 0.00 0.00 0.00 4.41
2270 9768 0.751643 ACCGATGGCCCTGCATTAAC 60.752 55.000 0.00 0.00 0.00 2.01
2272 9770 0.947244 CGATGGCCCTGCATTAACTC 59.053 55.000 0.00 0.00 0.00 3.01
2285 9783 3.411446 CATTAACTCTGTGACCAGCCAA 58.589 45.455 0.00 0.00 38.66 4.52
2296 9794 4.771577 TGTGACCAGCCAATTGATTTATGT 59.228 37.500 7.12 0.00 0.00 2.29
2298 9796 5.577945 GTGACCAGCCAATTGATTTATGTTG 59.422 40.000 7.12 0.00 0.00 3.33
2299 9797 5.245751 TGACCAGCCAATTGATTTATGTTGT 59.754 36.000 7.12 0.00 0.00 3.32
2300 9798 6.112927 ACCAGCCAATTGATTTATGTTGTT 57.887 33.333 7.12 0.00 0.00 2.83
2301 9799 6.532826 ACCAGCCAATTGATTTATGTTGTTT 58.467 32.000 7.12 0.00 0.00 2.83
2302 9800 6.650390 ACCAGCCAATTGATTTATGTTGTTTC 59.350 34.615 7.12 0.00 0.00 2.78
2303 9801 6.649973 CCAGCCAATTGATTTATGTTGTTTCA 59.350 34.615 7.12 0.00 0.00 2.69
2304 9802 7.172875 CCAGCCAATTGATTTATGTTGTTTCAA 59.827 33.333 7.12 0.00 0.00 2.69
2305 9803 8.557864 CAGCCAATTGATTTATGTTGTTTCAAA 58.442 29.630 7.12 0.00 30.81 2.69
2306 9804 9.118300 AGCCAATTGATTTATGTTGTTTCAAAA 57.882 25.926 7.12 0.00 30.81 2.44
2307 9805 9.727627 GCCAATTGATTTATGTTGTTTCAAAAA 57.272 25.926 7.12 0.00 30.81 1.94
2328 9826 8.603181 CAAAAAGTCCAAGTAAAGTCAATTTGG 58.397 33.333 0.00 0.00 39.66 3.28
2329 9827 6.405278 AAGTCCAAGTAAAGTCAATTTGGG 57.595 37.500 0.00 0.00 38.98 4.12
2332 9830 6.040504 AGTCCAAGTAAAGTCAATTTGGGTTC 59.959 38.462 0.00 0.00 38.98 3.62
2336 9834 7.368059 CAAGTAAAGTCAATTTGGGTTCTACC 58.632 38.462 0.00 0.00 32.92 3.18
2337 9835 6.607019 AGTAAAGTCAATTTGGGTTCTACCA 58.393 36.000 0.00 0.00 39.17 3.25
2338 9836 6.715264 AGTAAAGTCAATTTGGGTTCTACCAG 59.285 38.462 0.00 0.00 42.47 4.00
2339 9837 3.421844 AGTCAATTTGGGTTCTACCAGC 58.578 45.455 0.00 0.00 42.47 4.85
2340 9838 2.492088 GTCAATTTGGGTTCTACCAGCC 59.508 50.000 0.00 0.00 42.47 4.85
2342 9840 2.493278 CAATTTGGGTTCTACCAGCCTG 59.507 50.000 0.00 0.00 42.47 4.85
2344 9842 1.422977 TTGGGTTCTACCAGCCTGCA 61.423 55.000 0.00 0.00 42.47 4.41
2346 9844 0.749454 GGGTTCTACCAGCCTGCATG 60.749 60.000 0.00 0.00 41.02 4.06
2347 9845 0.035056 GGTTCTACCAGCCTGCATGT 60.035 55.000 0.00 0.00 38.42 3.21
2349 9847 0.983467 TTCTACCAGCCTGCATGTGA 59.017 50.000 0.00 0.00 0.00 3.58
2350 9848 0.250234 TCTACCAGCCTGCATGTGAC 59.750 55.000 0.00 0.00 0.00 3.67
2351 9849 0.036105 CTACCAGCCTGCATGTGACA 60.036 55.000 0.00 0.00 0.00 3.58
2353 9851 0.892358 ACCAGCCTGCATGTGACAAG 60.892 55.000 0.00 0.00 0.00 3.16
2354 9852 1.211969 CAGCCTGCATGTGACAAGC 59.788 57.895 5.76 5.76 0.00 4.01
2361 9859 3.030209 CATGTGACAAGCTGCATGC 57.970 52.632 11.82 11.82 43.29 4.06
2376 9874 1.003476 ATGCACTCATGGTCACGCA 60.003 52.632 0.00 0.00 0.00 5.24
2377 9875 1.022982 ATGCACTCATGGTCACGCAG 61.023 55.000 0.00 0.00 29.96 5.18
2378 9876 1.374631 GCACTCATGGTCACGCAGA 60.375 57.895 0.00 0.00 0.00 4.26
2379 9877 1.357258 GCACTCATGGTCACGCAGAG 61.357 60.000 0.00 0.00 0.00 3.35
2381 9879 1.188219 ACTCATGGTCACGCAGAGGT 61.188 55.000 0.00 0.00 0.00 3.85
2382 9880 0.817654 CTCATGGTCACGCAGAGGTA 59.182 55.000 0.00 0.00 0.00 3.08
2383 9881 1.410517 CTCATGGTCACGCAGAGGTAT 59.589 52.381 0.00 0.00 0.00 2.73
2384 9882 1.136891 TCATGGTCACGCAGAGGTATG 59.863 52.381 0.00 0.00 0.00 2.39
2385 9883 1.134699 CATGGTCACGCAGAGGTATGT 60.135 52.381 0.00 0.00 0.00 2.29
2386 9884 1.842052 TGGTCACGCAGAGGTATGTA 58.158 50.000 0.00 0.00 0.00 2.29
2387 9885 2.172679 TGGTCACGCAGAGGTATGTAA 58.827 47.619 0.00 0.00 0.00 2.41
2388 9886 2.563620 TGGTCACGCAGAGGTATGTAAA 59.436 45.455 0.00 0.00 0.00 2.01
2419 9917 6.834168 AAAACATTGTCGGTATCATTCCTT 57.166 33.333 0.00 0.00 0.00 3.36
2422 9920 6.920569 ACATTGTCGGTATCATTCCTTTAC 57.079 37.500 0.00 0.00 0.00 2.01
2427 9925 5.815222 TGTCGGTATCATTCCTTTACACATG 59.185 40.000 0.00 0.00 0.00 3.21
2441 9939 2.341318 CACATGCTGGTGTCATTGTG 57.659 50.000 0.00 0.00 34.09 3.33
2442 9940 1.610038 CACATGCTGGTGTCATTGTGT 59.390 47.619 0.00 0.00 34.09 3.72
2443 9941 2.813172 CACATGCTGGTGTCATTGTGTA 59.187 45.455 0.00 0.00 34.09 2.90
2444 9942 3.441222 CACATGCTGGTGTCATTGTGTAT 59.559 43.478 0.00 0.00 34.09 2.29
2445 9943 4.081406 ACATGCTGGTGTCATTGTGTATT 58.919 39.130 0.00 0.00 0.00 1.89
2447 9945 5.010922 ACATGCTGGTGTCATTGTGTATTTT 59.989 36.000 0.00 0.00 0.00 1.82
2449 9947 6.641169 TGCTGGTGTCATTGTGTATTTTAA 57.359 33.333 0.00 0.00 0.00 1.52
2489 9987 9.717942 TCAAAATGGGATTAGTAAAAACCAATG 57.282 29.630 7.41 7.49 30.94 2.82
2491 9989 7.806680 AATGGGATTAGTAAAAACCAATGGT 57.193 32.000 0.00 0.00 37.65 3.55
2511 10123 5.870706 TGGTTCATTTGACACCACATACTA 58.129 37.500 9.23 0.00 33.49 1.82
2512 10124 5.703592 TGGTTCATTTGACACCACATACTAC 59.296 40.000 9.23 0.00 33.49 2.73
2513 10125 5.703592 GGTTCATTTGACACCACATACTACA 59.296 40.000 6.90 0.00 0.00 2.74
2522 10138 4.099573 ACACCACATACTACATAGCTCCAC 59.900 45.833 0.00 0.00 0.00 4.02
2525 10141 3.641436 CACATACTACATAGCTCCACCCA 59.359 47.826 0.00 0.00 0.00 4.51
2528 10144 1.051812 CTACATAGCTCCACCCAGGG 58.948 60.000 2.85 2.85 38.24 4.45
2532 10148 0.983378 ATAGCTCCACCCAGGGTCAC 60.983 60.000 8.79 0.00 38.24 3.67
2538 10154 1.553690 CCACCCAGGGTCACGAGAAT 61.554 60.000 8.79 0.00 31.02 2.40
2539 10155 0.324943 CACCCAGGGTCACGAGAATT 59.675 55.000 8.79 0.00 31.02 2.17
2574 10190 7.010923 GGGTCGATTATCTAATCTGCATGATTC 59.989 40.741 12.69 0.49 43.69 2.52
2582 10198 6.189859 TCTAATCTGCATGATTCCACCTTTT 58.810 36.000 12.69 0.00 43.69 2.27
2619 10242 3.255642 ACGCAATTCTAAATGGCACTTGT 59.744 39.130 0.00 0.00 0.00 3.16
2658 10324 3.876274 AGTATGCTGACTGACAACGAT 57.124 42.857 0.00 0.00 0.00 3.73
2659 10325 3.775202 AGTATGCTGACTGACAACGATC 58.225 45.455 0.00 0.00 0.00 3.69
2660 10326 3.445450 AGTATGCTGACTGACAACGATCT 59.555 43.478 0.00 0.00 0.00 2.75
2661 10327 4.640647 AGTATGCTGACTGACAACGATCTA 59.359 41.667 0.00 0.00 0.00 1.98
2662 10328 4.662468 ATGCTGACTGACAACGATCTAT 57.338 40.909 0.00 0.00 0.00 1.98
2663 10329 4.456280 TGCTGACTGACAACGATCTATT 57.544 40.909 0.00 0.00 0.00 1.73
2664 10330 4.424626 TGCTGACTGACAACGATCTATTC 58.575 43.478 0.00 0.00 0.00 1.75
2665 10331 3.799420 GCTGACTGACAACGATCTATTCC 59.201 47.826 0.00 0.00 0.00 3.01
2666 10332 4.440802 GCTGACTGACAACGATCTATTCCT 60.441 45.833 0.00 0.00 0.00 3.36
2667 10333 5.655488 CTGACTGACAACGATCTATTCCTT 58.345 41.667 0.00 0.00 0.00 3.36
2668 10334 6.037786 TGACTGACAACGATCTATTCCTTT 57.962 37.500 0.00 0.00 0.00 3.11
2669 10335 6.464222 TGACTGACAACGATCTATTCCTTTT 58.536 36.000 0.00 0.00 0.00 2.27
2670 10336 6.934645 TGACTGACAACGATCTATTCCTTTTT 59.065 34.615 0.00 0.00 0.00 1.94
2695 10361 3.763360 CCCAGTCACTTGCCAATTCATTA 59.237 43.478 0.00 0.00 0.00 1.90
2702 10368 6.532657 GTCACTTGCCAATTCATTAAATCTGG 59.467 38.462 0.00 0.00 32.82 3.86
2706 10372 6.211587 TGCCAATTCATTAAATCTGGTCTG 57.788 37.500 0.00 0.00 32.52 3.51
2709 10375 7.124599 TGCCAATTCATTAAATCTGGTCTGAAT 59.875 33.333 0.00 0.00 35.47 2.57
2710 10376 7.650903 GCCAATTCATTAAATCTGGTCTGAATC 59.349 37.037 0.00 0.00 33.48 2.52
2713 10379 7.870509 TTCATTAAATCTGGTCTGAATCCTG 57.129 36.000 0.00 0.00 0.00 3.86
2727 10393 3.131577 TGAATCCTGAATTGATTGCAGGC 59.868 43.478 0.00 0.00 46.82 4.85
2737 10403 0.251354 GATTGCAGGCAGTCTCAGGA 59.749 55.000 9.24 0.00 31.22 3.86
2751 10417 0.337773 TCAGGAGAGGCAGATGGACT 59.662 55.000 0.00 0.00 37.85 3.85
2762 10428 4.285517 AGGCAGATGGACTTGATATCGATT 59.714 41.667 1.71 0.00 0.00 3.34
2767 10433 5.699915 AGATGGACTTGATATCGATTTGCTG 59.300 40.000 1.71 0.00 0.00 4.41
2833 10499 3.420893 TCTTGCTGTCAAAGTAATGGGG 58.579 45.455 0.00 0.00 29.37 4.96
3145 10816 2.562296 AGGAACCTTATTGAGCCAGGA 58.438 47.619 0.00 0.00 0.00 3.86
3170 11167 9.209175 GAATACAGTATATTGATGACCCAGTTC 57.791 37.037 1.74 0.00 0.00 3.01
3210 11207 2.598589 TCGCTCATTTGCTCAATTTGC 58.401 42.857 0.00 0.00 0.00 3.68
3296 11296 8.032952 TGCACAATAGTTTCTTCACTTATCTG 57.967 34.615 0.00 0.00 0.00 2.90
3391 11391 4.893424 AATATGTGTCGGCCATGTAAAC 57.107 40.909 2.24 0.00 0.00 2.01
3528 11562 5.657745 TGAGGTACTTGTCCATACGGAATTA 59.342 40.000 0.00 0.00 41.58 1.40
3587 11621 5.868257 TGAAATTCTTGCAGTACATTAGCG 58.132 37.500 0.00 0.00 0.00 4.26
3592 11626 1.732941 TGCAGTACATTAGCGTTGGG 58.267 50.000 0.00 0.00 0.00 4.12
3595 11629 1.065709 CAGTACATTAGCGTTGGGGGT 60.066 52.381 0.00 0.00 0.00 4.95
3664 11698 4.348486 AGCTATGGTCTCTTGACTTCAGA 58.652 43.478 0.00 0.00 42.54 3.27
3673 11707 5.708230 GTCTCTTGACTTCAGAGGAACTAGA 59.292 44.000 0.00 0.00 38.54 2.43
3781 11815 1.155155 TTTGGAAGAGTTGGGCCCC 59.845 57.895 22.27 4.15 0.00 5.80
3782 11816 2.706952 TTTGGAAGAGTTGGGCCCCG 62.707 60.000 22.27 0.00 0.00 5.73
3905 11939 7.290842 CAACTTGTATTTACAGTGCAGTAGTG 58.709 38.462 0.00 0.00 37.52 2.74
4099 12139 1.622811 CTCAGGTGCTTGAGGACTCTT 59.377 52.381 3.72 0.00 40.69 2.85
4115 12155 4.163078 GGACTCTTTGGATGGAAGATCTGA 59.837 45.833 0.00 0.00 33.05 3.27
4119 12159 6.441924 ACTCTTTGGATGGAAGATCTGACTTA 59.558 38.462 0.00 0.00 33.05 2.24
4148 12188 0.106519 ACTTCCTGCTGGCTTGTGTT 60.107 50.000 4.42 0.00 0.00 3.32
4208 12248 3.955145 TCCATCAAGCGTGTTGGAT 57.045 47.368 23.40 0.00 45.01 3.41
4228 12268 2.845659 TCAGAATTCCTCCAGCCCTAA 58.154 47.619 0.65 0.00 0.00 2.69
4234 12274 2.196742 TCCTCCAGCCCTAACATCAT 57.803 50.000 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
260 293 3.818787 GCTACGAAGACGGCGGGA 61.819 66.667 13.24 0.00 44.46 5.14
671 704 4.162320 GGATATGACCTGAGACCTGACAAA 59.838 45.833 0.00 0.00 0.00 2.83
690 2786 0.629058 GGGGTGGCAAGAAAGGGATA 59.371 55.000 0.00 0.00 0.00 2.59
774 2872 0.537143 ACGGTGCCTTGCTTGAATCA 60.537 50.000 0.00 0.00 0.00 2.57
1497 3640 4.838423 TCTTCAATCTTCTCACCTACCACA 59.162 41.667 0.00 0.00 0.00 4.17
1667 3812 2.125952 TGACGCTCAGCCACATCG 60.126 61.111 0.00 0.00 0.00 3.84
1701 3846 1.896220 CCAACCTTAGCAGCTCAACA 58.104 50.000 0.00 0.00 0.00 3.33
1803 5167 8.796475 TCATCCAAAACTAGAAGAAATTTCTGG 58.204 33.333 21.15 14.64 37.65 3.86
1971 6556 1.073284 GCATCCTCGGGCCCTAATTTA 59.927 52.381 22.43 0.00 0.00 1.40
1996 6581 2.233271 CACCTGTTTCCTGAGCAATGT 58.767 47.619 0.00 0.00 0.00 2.71
2122 9206 8.316946 ACATCTCTGATTCTAGTTTTGTCATCA 58.683 33.333 0.00 0.00 0.00 3.07
2149 9233 5.163468 ACAAACTGCCAACAACATTGACATA 60.163 36.000 0.00 0.00 0.00 2.29
2151 9235 3.056250 ACAAACTGCCAACAACATTGACA 60.056 39.130 0.00 0.00 0.00 3.58
2152 9236 3.520569 ACAAACTGCCAACAACATTGAC 58.479 40.909 0.00 0.00 0.00 3.18
2156 9240 3.023119 TCAGACAAACTGCCAACAACAT 58.977 40.909 0.00 0.00 45.38 2.71
2160 9244 1.013596 CGTCAGACAAACTGCCAACA 58.986 50.000 0.41 0.00 45.38 3.33
2161 9245 1.295792 TCGTCAGACAAACTGCCAAC 58.704 50.000 0.41 0.00 45.38 3.77
2167 9251 7.672983 ATCATAATGTTTCGTCAGACAAACT 57.327 32.000 20.15 10.33 34.22 2.66
2177 9261 9.886132 AGGAAGTAACTAATCATAATGTTTCGT 57.114 29.630 0.00 0.00 0.00 3.85
2183 9267 8.765219 CCGAACAGGAAGTAACTAATCATAATG 58.235 37.037 0.00 0.00 45.00 1.90
2187 9271 5.189145 ACCCGAACAGGAAGTAACTAATCAT 59.811 40.000 0.00 0.00 45.00 2.45
2194 9278 1.609841 CCCACCCGAACAGGAAGTAAC 60.610 57.143 0.00 0.00 45.00 2.50
2195 9279 0.688487 CCCACCCGAACAGGAAGTAA 59.312 55.000 0.00 0.00 45.00 2.24
2196 9280 1.833787 GCCCACCCGAACAGGAAGTA 61.834 60.000 0.00 0.00 45.00 2.24
2200 9284 3.948719 GTGCCCACCCGAACAGGA 61.949 66.667 0.00 0.00 45.00 3.86
2217 9715 2.040178 CCAACCAGGCTACCTACTAGG 58.960 57.143 0.00 0.00 42.49 3.02
2229 9727 0.533491 CACCATCAATGCCAACCAGG 59.467 55.000 0.00 0.00 41.84 4.45
2230 9728 1.203052 GACACCATCAATGCCAACCAG 59.797 52.381 0.00 0.00 0.00 4.00
2231 9729 1.255882 GACACCATCAATGCCAACCA 58.744 50.000 0.00 0.00 0.00 3.67
2235 9733 0.959867 CGGTGACACCATCAATGCCA 60.960 55.000 24.18 0.00 39.72 4.92
2236 9734 0.676466 TCGGTGACACCATCAATGCC 60.676 55.000 24.18 0.00 39.72 4.40
2237 9735 1.064505 CATCGGTGACACCATCAATGC 59.935 52.381 24.18 0.00 39.72 3.56
2238 9736 1.672363 CCATCGGTGACACCATCAATG 59.328 52.381 24.18 18.57 39.72 2.82
2239 9737 2.018644 GCCATCGGTGACACCATCAAT 61.019 52.381 24.18 8.89 39.72 2.57
2240 9738 0.676466 GCCATCGGTGACACCATCAA 60.676 55.000 24.18 6.92 39.72 2.57
2241 9739 1.078497 GCCATCGGTGACACCATCA 60.078 57.895 24.18 7.85 38.47 3.07
2242 9740 1.819632 GGCCATCGGTGACACCATC 60.820 63.158 24.18 7.58 38.47 3.51
2243 9741 2.272146 GGCCATCGGTGACACCAT 59.728 61.111 24.18 13.45 38.47 3.55
2244 9742 4.028490 GGGCCATCGGTGACACCA 62.028 66.667 24.18 11.77 38.47 4.17
2245 9743 3.717294 AGGGCCATCGGTGACACC 61.717 66.667 15.13 15.13 34.05 4.16
2246 9744 2.436646 CAGGGCCATCGGTGACAC 60.437 66.667 6.18 0.00 0.00 3.67
2247 9745 4.408821 GCAGGGCCATCGGTGACA 62.409 66.667 6.18 0.00 0.00 3.58
2248 9746 3.704231 ATGCAGGGCCATCGGTGAC 62.704 63.158 6.18 0.00 0.00 3.67
2249 9747 1.631071 TAATGCAGGGCCATCGGTGA 61.631 55.000 6.18 0.00 0.00 4.02
2250 9748 0.751277 TTAATGCAGGGCCATCGGTG 60.751 55.000 6.18 0.00 0.00 4.94
2251 9749 0.751643 GTTAATGCAGGGCCATCGGT 60.752 55.000 6.18 0.00 0.00 4.69
2252 9750 0.466189 AGTTAATGCAGGGCCATCGG 60.466 55.000 6.18 0.00 0.00 4.18
2253 9751 0.947244 GAGTTAATGCAGGGCCATCG 59.053 55.000 6.18 0.00 0.00 3.84
2254 9752 1.952296 CAGAGTTAATGCAGGGCCATC 59.048 52.381 6.18 0.00 0.00 3.51
2255 9753 1.285962 ACAGAGTTAATGCAGGGCCAT 59.714 47.619 6.18 0.00 0.00 4.40
2256 9754 0.698238 ACAGAGTTAATGCAGGGCCA 59.302 50.000 6.18 0.00 0.00 5.36
2257 9755 1.098050 CACAGAGTTAATGCAGGGCC 58.902 55.000 0.00 0.00 0.00 5.80
2258 9756 1.740025 GTCACAGAGTTAATGCAGGGC 59.260 52.381 0.00 0.00 0.00 5.19
2259 9757 2.290260 TGGTCACAGAGTTAATGCAGGG 60.290 50.000 0.00 0.00 0.00 4.45
2260 9758 3.057969 TGGTCACAGAGTTAATGCAGG 57.942 47.619 0.00 0.00 0.00 4.85
2296 9794 8.361139 TGACTTTACTTGGACTTTTTGAAACAA 58.639 29.630 0.00 0.00 0.00 2.83
2298 9796 8.751302 TTGACTTTACTTGGACTTTTTGAAAC 57.249 30.769 0.00 0.00 0.00 2.78
2299 9797 9.936759 AATTGACTTTACTTGGACTTTTTGAAA 57.063 25.926 0.00 0.00 0.00 2.69
2300 9798 9.936759 AAATTGACTTTACTTGGACTTTTTGAA 57.063 25.926 0.00 0.00 0.00 2.69
2301 9799 9.364989 CAAATTGACTTTACTTGGACTTTTTGA 57.635 29.630 0.00 0.00 0.00 2.69
2302 9800 8.603181 CCAAATTGACTTTACTTGGACTTTTTG 58.397 33.333 0.00 0.00 39.12 2.44
2303 9801 7.768582 CCCAAATTGACTTTACTTGGACTTTTT 59.231 33.333 0.00 0.00 39.12 1.94
2304 9802 7.093068 ACCCAAATTGACTTTACTTGGACTTTT 60.093 33.333 0.00 0.00 39.12 2.27
2305 9803 6.382859 ACCCAAATTGACTTTACTTGGACTTT 59.617 34.615 0.00 0.00 39.12 2.66
2306 9804 5.897250 ACCCAAATTGACTTTACTTGGACTT 59.103 36.000 0.00 0.00 39.12 3.01
2307 9805 5.454966 ACCCAAATTGACTTTACTTGGACT 58.545 37.500 0.00 0.00 39.12 3.85
2308 9806 5.784578 ACCCAAATTGACTTTACTTGGAC 57.215 39.130 0.00 0.00 39.12 4.02
2314 9812 6.569801 GCTGGTAGAACCCAAATTGACTTTAC 60.570 42.308 0.00 0.00 37.50 2.01
2316 9814 4.280929 GCTGGTAGAACCCAAATTGACTTT 59.719 41.667 0.00 0.00 37.50 2.66
2328 9826 0.035056 ACATGCAGGCTGGTAGAACC 60.035 55.000 17.64 0.00 39.22 3.62
2329 9827 1.089920 CACATGCAGGCTGGTAGAAC 58.910 55.000 17.64 0.00 0.00 3.01
2332 9830 0.036105 TGTCACATGCAGGCTGGTAG 60.036 55.000 17.64 1.76 0.00 3.18
2336 9834 1.211969 GCTTGTCACATGCAGGCTG 59.788 57.895 10.94 10.94 36.26 4.85
2337 9835 1.074423 AGCTTGTCACATGCAGGCT 59.926 52.632 17.34 3.15 43.05 4.58
2338 9836 1.211969 CAGCTTGTCACATGCAGGC 59.788 57.895 17.34 0.00 37.06 4.85
2339 9837 1.211969 GCAGCTTGTCACATGCAGG 59.788 57.895 17.34 10.07 37.06 4.85
2340 9838 1.953772 TGCAGCTTGTCACATGCAG 59.046 52.632 17.34 10.71 43.34 4.41
2342 9840 3.030209 CATGCAGCTTGTCACATGC 57.970 52.632 7.59 7.59 39.14 4.06
2344 9842 0.242825 GTGCATGCAGCTTGTCACAT 59.757 50.000 23.41 0.00 45.94 3.21
2346 9844 0.109873 GAGTGCATGCAGCTTGTCAC 60.110 55.000 23.41 19.36 45.94 3.67
2347 9845 0.535553 TGAGTGCATGCAGCTTGTCA 60.536 50.000 23.41 15.52 45.94 3.58
2349 9847 0.526211 CATGAGTGCATGCAGCTTGT 59.474 50.000 23.41 10.74 44.76 3.16
2350 9848 3.329114 CATGAGTGCATGCAGCTTG 57.671 52.632 23.41 19.11 44.76 4.01
2361 9859 0.738762 CCTCTGCGTGACCATGAGTG 60.739 60.000 0.00 0.00 0.00 3.51
2374 9872 3.543680 TCTGGCTTTACATACCTCTGC 57.456 47.619 0.00 0.00 0.00 4.26
2422 9920 1.610038 ACACAATGACACCAGCATGTG 59.390 47.619 4.28 4.28 42.05 3.21
2427 9925 6.072175 TCCTTAAAATACACAATGACACCAGC 60.072 38.462 0.00 0.00 0.00 4.85
2469 9967 6.782988 TGAACCATTGGTTTTTACTAATCCCA 59.217 34.615 21.66 8.08 46.95 4.37
2470 9968 7.234661 TGAACCATTGGTTTTTACTAATCCC 57.765 36.000 21.66 5.66 46.95 3.85
2484 9982 3.069300 TGTGGTGTCAAATGAACCATTGG 59.931 43.478 15.56 0.00 45.35 3.16
2485 9983 4.319139 TGTGGTGTCAAATGAACCATTG 57.681 40.909 15.56 0.00 45.35 2.82
2486 9984 5.774690 AGTATGTGGTGTCAAATGAACCATT 59.225 36.000 15.56 11.18 45.35 3.16
2488 9986 4.724399 AGTATGTGGTGTCAAATGAACCA 58.276 39.130 11.11 11.11 41.66 3.67
2489 9987 5.703592 TGTAGTATGTGGTGTCAAATGAACC 59.296 40.000 7.43 7.43 34.38 3.62
2491 9989 7.279981 GCTATGTAGTATGTGGTGTCAAATGAA 59.720 37.037 0.00 0.00 0.00 2.57
2511 10123 0.983378 GACCCTGGGTGGAGCTATGT 60.983 60.000 26.16 0.00 35.25 2.29
2512 10124 0.982852 TGACCCTGGGTGGAGCTATG 60.983 60.000 26.16 0.00 35.25 2.23
2513 10125 0.983378 GTGACCCTGGGTGGAGCTAT 60.983 60.000 26.16 0.00 35.25 2.97
2522 10138 3.343941 TTTAATTCTCGTGACCCTGGG 57.656 47.619 12.28 12.28 0.00 4.45
2550 10166 7.547019 TGGAATCATGCAGATTAGATAATCGAC 59.453 37.037 10.22 4.59 46.76 4.20
2558 10174 5.378230 AAGGTGGAATCATGCAGATTAGA 57.622 39.130 10.22 0.00 46.76 2.10
2593 10209 6.935741 AGTGCCATTTAGAATTGCGTATTA 57.064 33.333 0.00 0.00 0.00 0.98
2598 10214 3.836949 ACAAGTGCCATTTAGAATTGCG 58.163 40.909 0.00 0.00 0.00 4.85
2611 10234 7.009540 GCATACTAAAATGAATTGACAAGTGCC 59.990 37.037 0.00 0.00 0.00 5.01
2612 10235 7.541783 TGCATACTAAAATGAATTGACAAGTGC 59.458 33.333 0.00 0.00 0.00 4.40
2668 10334 2.151502 TGGCAAGTGACTGGGAAAAA 57.848 45.000 0.00 0.00 0.00 1.94
2669 10335 2.151502 TTGGCAAGTGACTGGGAAAA 57.848 45.000 0.00 0.00 0.00 2.29
2670 10336 2.380064 ATTGGCAAGTGACTGGGAAA 57.620 45.000 5.96 0.00 0.00 3.13
2671 10337 2.238521 GAATTGGCAAGTGACTGGGAA 58.761 47.619 4.31 0.00 0.00 3.97
2672 10338 1.144708 TGAATTGGCAAGTGACTGGGA 59.855 47.619 4.31 0.00 0.00 4.37
2673 10339 1.619654 TGAATTGGCAAGTGACTGGG 58.380 50.000 4.31 0.00 0.00 4.45
2674 10340 3.947910 AATGAATTGGCAAGTGACTGG 57.052 42.857 4.31 0.00 0.00 4.00
2675 10341 7.274904 CAGATTTAATGAATTGGCAAGTGACTG 59.725 37.037 4.31 0.00 0.00 3.51
2676 10342 7.318141 CAGATTTAATGAATTGGCAAGTGACT 58.682 34.615 4.31 0.00 0.00 3.41
2677 10343 6.532657 CCAGATTTAATGAATTGGCAAGTGAC 59.467 38.462 4.31 0.00 0.00 3.67
2678 10344 6.211184 ACCAGATTTAATGAATTGGCAAGTGA 59.789 34.615 4.31 0.00 33.15 3.41
2679 10345 6.400568 ACCAGATTTAATGAATTGGCAAGTG 58.599 36.000 4.31 0.00 33.15 3.16
2680 10346 6.438425 AGACCAGATTTAATGAATTGGCAAGT 59.562 34.615 5.96 1.86 33.15 3.16
2681 10347 6.755141 CAGACCAGATTTAATGAATTGGCAAG 59.245 38.462 5.96 0.00 33.15 4.01
2695 10361 6.487828 TCAATTCAGGATTCAGACCAGATTT 58.512 36.000 0.00 0.00 0.00 2.17
2702 10368 5.571784 TGCAATCAATTCAGGATTCAGAC 57.428 39.130 0.00 0.00 32.86 3.51
2713 10379 2.751259 TGAGACTGCCTGCAATCAATTC 59.249 45.455 3.25 0.00 0.00 2.17
2727 10393 1.409790 CATCTGCCTCTCCTGAGACTG 59.590 57.143 0.00 0.00 42.73 3.51
2737 10403 3.257873 CGATATCAAGTCCATCTGCCTCT 59.742 47.826 3.12 0.00 0.00 3.69
2751 10417 8.724229 CAATATCCTTCAGCAAATCGATATCAA 58.276 33.333 0.00 0.00 0.00 2.57
2762 10428 4.279982 TGCAATCCAATATCCTTCAGCAA 58.720 39.130 0.00 0.00 0.00 3.91
2767 10433 4.646492 ACCACTTGCAATCCAATATCCTTC 59.354 41.667 0.00 0.00 31.91 3.46
2797 10463 1.336240 GCAAGAGGCAAACCATCACAC 60.336 52.381 0.00 0.00 43.97 3.82
2833 10499 1.266989 CCTTTCTGACGCAAAAGTCCC 59.733 52.381 0.00 0.00 40.26 4.46
2989 10657 4.299485 CACCTTTAGGGAGAAGGGAGTAT 58.701 47.826 7.70 0.00 46.37 2.12
3145 10816 8.938883 AGAACTGGGTCATCAATATACTGTATT 58.061 33.333 5.52 0.00 0.00 1.89
3170 11167 4.673761 GCGAACAACATCATGCATATTGAG 59.326 41.667 13.39 8.56 0.00 3.02
3210 11207 0.814410 TACTGCCTCGTCTCTAGCCG 60.814 60.000 0.00 0.00 0.00 5.52
3278 11278 9.640963 GCTTTCTACAGATAAGTGAAGAAACTA 57.359 33.333 0.00 0.00 31.61 2.24
3296 11296 7.865707 TCTGATTCTGAAACTTTGCTTTCTAC 58.134 34.615 0.00 0.00 32.25 2.59
3391 11391 3.181497 CCAACGAATCACCAGGCTTTATG 60.181 47.826 0.00 0.00 0.00 1.90
3464 11498 6.995686 TGTAAAGATTCAACCAGTAGAGCAAA 59.004 34.615 0.00 0.00 0.00 3.68
3528 11562 7.015974 TGTTCTCTGGCAGACAAGATATATCAT 59.984 37.037 14.43 0.00 0.00 2.45
3592 11626 1.139853 TCCACAAATTGTTGGCAACCC 59.860 47.619 26.31 4.32 39.22 4.11
3595 11629 3.902881 AGTTCCACAAATTGTTGGCAA 57.097 38.095 0.00 0.00 39.22 4.52
3781 11815 3.335356 ATCCCTGAGCTGGCCAACG 62.335 63.158 7.01 0.00 0.00 4.10
3782 11816 1.452833 GATCCCTGAGCTGGCCAAC 60.453 63.158 7.01 0.92 0.00 3.77
3825 11859 1.068281 AGGCAGACGATGTAGCAGATG 59.932 52.381 0.00 0.00 0.00 2.90
3870 11904 7.067532 TGTAAATACAAGTTGGTAAGATGCG 57.932 36.000 7.96 0.00 32.40 4.73
3905 11939 1.818674 CAGCCCATCAACCCAAAGTAC 59.181 52.381 0.00 0.00 0.00 2.73
4099 12139 5.627735 GCAGTAAGTCAGATCTTCCATCCAA 60.628 44.000 0.00 0.00 0.00 3.53
4115 12155 3.206150 CAGGAAGTTGTGTGCAGTAAGT 58.794 45.455 0.00 0.00 0.00 2.24
4119 12159 0.107017 AGCAGGAAGTTGTGTGCAGT 60.107 50.000 0.00 0.00 38.44 4.40
4208 12248 2.505819 GTTAGGGCTGGAGGAATTCTGA 59.494 50.000 5.23 0.00 0.00 3.27
4228 12268 1.520494 GATGAGCGCCATGATGATGT 58.480 50.000 14.84 0.00 35.17 3.06
4234 12274 0.464373 GGAAAGGATGAGCGCCATGA 60.464 55.000 14.84 0.00 35.17 3.07


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

AutoCloner maintained by Alex Coulton.