Multiple sequence alignment - TraesCS7D01G114300

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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 TraesCS7D01G114300 chr7D 100.000 7624 0 0 1 7624 69943549 69935926 0.000000e+00 14079.0
1 TraesCS7D01G114300 chr7D 95.418 4365 185 11 181 4536 70747038 70751396 0.000000e+00 6938.0
2 TraesCS7D01G114300 chr7D 93.566 4383 218 27 178 4536 70230292 70234634 0.000000e+00 6473.0
3 TraesCS7D01G114300 chr7D 86.346 3574 392 43 303 3826 71217762 71214235 0.000000e+00 3808.0
4 TraesCS7D01G114300 chr7D 92.645 2393 90 21 4534 6856 70751461 70753837 0.000000e+00 3365.0
5 TraesCS7D01G114300 chr7D 89.564 2338 206 21 181 2493 70832802 70830478 0.000000e+00 2931.0
6 TraesCS7D01G114300 chr7D 83.251 806 76 26 5850 6630 70827647 70826876 0.000000e+00 686.0
7 TraesCS7D01G114300 chr7D 89.817 383 37 2 3446 3826 71547135 71546753 2.470000e-134 490.0
8 TraesCS7D01G114300 chr7D 96.139 259 8 2 4534 4792 70234699 70234955 9.150000e-114 422.0
9 TraesCS7D01G114300 chr7D 80.617 454 34 23 6855 7282 70753916 70754341 1.240000e-77 302.0
10 TraesCS7D01G114300 chr7D 95.531 179 1 1 1 179 393026599 393026428 5.830000e-71 279.0
11 TraesCS7D01G114300 chr7D 95.531 179 1 1 1 179 420762919 420762748 5.830000e-71 279.0
12 TraesCS7D01G114300 chr7D 95.480 177 1 1 1 177 78617587 78617756 7.540000e-70 276.0
13 TraesCS7D01G114300 chr7D 94.413 179 3 1 1 179 78600071 78600242 1.260000e-67 268.0
14 TraesCS7D01G114300 chr7D 93.296 179 5 1 1 179 24325667 24325496 2.730000e-64 257.0
15 TraesCS7D01G114300 chr7D 92.105 152 12 0 6484 6635 71211364 71211213 1.670000e-51 215.0
16 TraesCS7D01G114300 chr7D 91.447 152 13 0 6484 6635 71313742 71313591 7.750000e-50 209.0
17 TraesCS7D01G114300 chr7D 94.340 53 3 0 7399 7451 70754457 70754509 1.760000e-11 82.4
18 TraesCS7D01G114300 chr7B 95.667 4362 167 14 181 4536 12538995 12534650 0.000000e+00 6988.0
19 TraesCS7D01G114300 chr7B 92.565 4223 225 40 178 4368 12805974 12810139 0.000000e+00 5976.0
20 TraesCS7D01G114300 chr7B 87.397 3150 326 33 303 3402 13881231 13878103 0.000000e+00 3552.0
21 TraesCS7D01G114300 chr7B 94.065 2359 94 9 4534 6858 12534585 12532239 0.000000e+00 3539.0
22 TraesCS7D01G114300 chr7B 89.778 2299 204 16 185 2463 13118847 13116560 0.000000e+00 2915.0
23 TraesCS7D01G114300 chr7B 95.814 1075 41 3 4534 5608 12810556 12811626 0.000000e+00 1733.0
24 TraesCS7D01G114300 chr7B 89.641 946 76 7 2510 3435 13116478 13115535 0.000000e+00 1184.0
25 TraesCS7D01G114300 chr7B 90.762 617 39 10 6912 7515 12531945 12531334 0.000000e+00 808.0
26 TraesCS7D01G114300 chr7B 90.078 383 37 1 3445 3826 13115422 13115040 5.310000e-136 496.0
27 TraesCS7D01G114300 chr7B 93.023 344 14 3 5849 6191 12819124 12819458 1.910000e-135 494.0
28 TraesCS7D01G114300 chr7B 87.316 339 33 7 6128 6463 13112736 13112405 5.580000e-101 379.0
29 TraesCS7D01G114300 chr7B 88.492 252 16 3 5591 5831 12812795 12813044 7.480000e-75 292.0
30 TraesCS7D01G114300 chr7B 86.617 269 30 3 5849 6113 13113058 13112792 7.480000e-75 292.0
31 TraesCS7D01G114300 chr7B 97.143 140 4 0 7356 7495 12531936 12532075 3.560000e-58 237.0
32 TraesCS7D01G114300 chr7A 94.453 4363 226 8 181 4536 76517580 76513227 0.000000e+00 6702.0
33 TraesCS7D01G114300 chr7A 88.113 3710 345 45 185 3816 76944237 76940546 0.000000e+00 4320.0
34 TraesCS7D01G114300 chr7A 92.964 2274 152 4 2260 4533 76828367 76830632 0.000000e+00 3306.0
35 TraesCS7D01G114300 chr7A 91.925 2390 100 18 4535 6856 76513161 76510797 0.000000e+00 3258.0
36 TraesCS7D01G114300 chr7A 93.706 1128 48 9 4534 5660 76830699 76831804 0.000000e+00 1668.0
37 TraesCS7D01G114300 chr7A 89.024 1148 64 27 5721 6821 76832359 76833491 0.000000e+00 1365.0
38 TraesCS7D01G114300 chr7A 84.955 997 116 15 4647 5629 76982568 76981592 0.000000e+00 979.0
39 TraesCS7D01G114300 chr7A 84.074 810 84 18 5853 6630 76939117 76938321 0.000000e+00 739.0
40 TraesCS7D01G114300 chr7A 81.779 461 27 25 6855 7288 76510718 76510288 4.410000e-87 333.0
41 TraesCS7D01G114300 chr7A 92.105 152 12 0 6484 6635 76980662 76980511 1.670000e-51 215.0
42 TraesCS7D01G114300 chr7A 94.340 53 3 0 7399 7451 76510169 76510117 1.760000e-11 82.4
43 TraesCS7D01G114300 chr7A 97.368 38 1 0 7478 7515 76510111 76510074 1.780000e-06 65.8
44 TraesCS7D01G114300 chr7A 96.970 33 1 0 5683 5715 47495528 47495496 1.000000e-03 56.5
45 TraesCS7D01G114300 chrUn 86.979 3141 326 35 303 3392 84239871 84236763 0.000000e+00 3458.0
46 TraesCS7D01G114300 chrUn 87.829 1594 132 26 1888 3434 84249170 84247592 0.000000e+00 1812.0
47 TraesCS7D01G114300 chrUn 87.649 1595 139 20 1884 3434 82528720 82527140 0.000000e+00 1801.0
48 TraesCS7D01G114300 chrUn 83.077 1235 167 26 4630 5834 82516139 82514917 0.000000e+00 1085.0
49 TraesCS7D01G114300 chrUn 82.011 1223 149 27 4648 5820 84284370 84283169 0.000000e+00 974.0
50 TraesCS7D01G114300 chrUn 82.011 1223 149 27 4648 5820 226937695 226936494 0.000000e+00 974.0
51 TraesCS7D01G114300 chrUn 84.293 573 78 9 5153 5721 329447367 329447931 4.020000e-152 549.0
52 TraesCS7D01G114300 chrUn 82.965 634 68 25 5849 6457 82514797 82514179 3.130000e-148 536.0
53 TraesCS7D01G114300 chrUn 86.197 355 38 6 6126 6476 82524990 82524643 2.600000e-99 374.0
54 TraesCS7D01G114300 chrUn 87.313 268 28 4 5849 6112 84245798 84245533 1.240000e-77 302.0
55 TraesCS7D01G114300 chrUn 86.716 271 28 6 5847 6112 82525355 82525088 2.080000e-75 294.0
56 TraesCS7D01G114300 chrUn 92.105 152 12 0 6484 6635 84282363 84282212 1.670000e-51 215.0
57 TraesCS7D01G114300 chrUn 92.105 152 12 0 6484 6635 226935688 226935537 1.670000e-51 215.0
58 TraesCS7D01G114300 chrUn 93.805 113 7 0 7512 7624 337838714 337838826 3.660000e-38 171.0
59 TraesCS7D01G114300 chr1A 83.016 1154 145 28 2330 3435 21775072 21773922 0.000000e+00 998.0
60 TraesCS7D01G114300 chr1A 82.038 991 139 20 4865 5831 21772865 21771890 0.000000e+00 808.0
61 TraesCS7D01G114300 chr1A 93.296 179 5 1 1 179 472529118 472529289 2.730000e-64 257.0
62 TraesCS7D01G114300 chr6D 95.531 179 7 1 1 179 469778602 469778425 1.250000e-72 285.0
63 TraesCS7D01G114300 chr6D 94.413 179 3 1 1 179 32857973 32857802 1.260000e-67 268.0
64 TraesCS7D01G114300 chr6D 90.000 110 8 1 7515 7624 346076658 346076764 1.030000e-28 139.0
65 TraesCS7D01G114300 chr5D 96.089 179 0 2 1 179 57116322 57116151 1.250000e-72 285.0
66 TraesCS7D01G114300 chr5D 95.531 179 1 1 1 179 57004580 57004751 5.830000e-71 279.0
67 TraesCS7D01G114300 chr5D 95.531 179 1 1 1 179 544198146 544198317 5.830000e-71 279.0
68 TraesCS7D01G114300 chr4D 96.089 179 0 2 1 179 20243216 20243387 1.250000e-72 285.0
69 TraesCS7D01G114300 chr4D 91.228 114 9 1 7512 7624 433399408 433399295 3.680000e-33 154.0
70 TraesCS7D01G114300 chr3D 95.531 179 1 1 1 179 44905347 44905518 5.830000e-71 279.0
71 TraesCS7D01G114300 chr1D 95.531 179 1 1 1 179 10564458 10564629 5.830000e-71 279.0
72 TraesCS7D01G114300 chr1D 95.055 182 1 2 1 181 47936580 47936406 5.830000e-71 279.0
73 TraesCS7D01G114300 chr1D 94.413 179 3 1 1 179 59535635 59535806 1.260000e-67 268.0
74 TraesCS7D01G114300 chr1D 88.182 110 13 0 7515 7624 415498452 415498561 1.730000e-26 132.0
75 TraesCS7D01G114300 chr4A 78.205 312 61 6 4035 4344 533200927 533200621 7.810000e-45 193.0
76 TraesCS7D01G114300 chr4A 86.486 111 14 1 7515 7624 483438103 483438213 3.740000e-23 121.0
77 TraesCS7D01G114300 chr4A 96.970 33 1 0 5683 5715 655448796 655448828 1.000000e-03 56.5
78 TraesCS7D01G114300 chr5B 76.582 316 66 7 4036 4346 535148588 535148276 4.730000e-37 167.0
79 TraesCS7D01G114300 chr4B 75.385 325 73 5 4036 4357 135146107 135146427 4.770000e-32 150.0
80 TraesCS7D01G114300 chr5A 88.696 115 12 1 7511 7624 554308314 554308428 1.030000e-28 139.0
81 TraesCS7D01G114300 chr1B 88.182 110 12 1 7516 7624 37265403 37265512 6.210000e-26 130.0
82 TraesCS7D01G114300 chr2D 87.387 111 13 1 7514 7624 13844420 13844311 8.030000e-25 126.0
83 TraesCS7D01G114300 chr6A 87.156 109 13 1 7516 7624 322532477 322532584 1.040000e-23 122.0


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 TraesCS7D01G114300 chr7D 69935926 69943549 7623 True 14079.000000 14079 100.000000 1 7624 1 chr7D.!!$R2 7623
1 TraesCS7D01G114300 chr7D 70230292 70234955 4663 False 3447.500000 6473 94.852500 178 4792 2 chr7D.!!$F3 4614
2 TraesCS7D01G114300 chr7D 70747038 70754509 7471 False 2671.850000 6938 90.755000 181 7451 4 chr7D.!!$F4 7270
3 TraesCS7D01G114300 chr7D 71211213 71217762 6549 True 2011.500000 3808 89.225500 303 6635 2 chr7D.!!$R8 6332
4 TraesCS7D01G114300 chr7D 70826876 70832802 5926 True 1808.500000 2931 86.407500 181 6630 2 chr7D.!!$R7 6449
5 TraesCS7D01G114300 chr7B 12531334 12538995 7661 True 3778.333333 6988 93.498000 181 7515 3 chr7B.!!$R2 7334
6 TraesCS7D01G114300 chr7B 13878103 13881231 3128 True 3552.000000 3552 87.397000 303 3402 1 chr7B.!!$R1 3099
7 TraesCS7D01G114300 chr7B 12805974 12813044 7070 False 2667.000000 5976 92.290333 178 5831 3 chr7B.!!$F3 5653
8 TraesCS7D01G114300 chr7B 13112405 13118847 6442 True 1053.200000 2915 88.686000 185 6463 5 chr7B.!!$R3 6278
9 TraesCS7D01G114300 chr7A 76938321 76944237 5916 True 2529.500000 4320 86.093500 185 6630 2 chr7A.!!$R3 6445
10 TraesCS7D01G114300 chr7A 76828367 76833491 5124 False 2113.000000 3306 91.898000 2260 6821 3 chr7A.!!$F1 4561
11 TraesCS7D01G114300 chr7A 76510074 76517580 7506 True 2088.240000 6702 91.973000 181 7515 5 chr7A.!!$R2 7334
12 TraesCS7D01G114300 chr7A 76980511 76982568 2057 True 597.000000 979 88.530000 4647 6635 2 chr7A.!!$R4 1988
13 TraesCS7D01G114300 chrUn 84236763 84239871 3108 True 3458.000000 3458 86.979000 303 3392 1 chrUn.!!$R1 3089
14 TraesCS7D01G114300 chrUn 84245533 84249170 3637 True 1057.000000 1812 87.571000 1888 6112 2 chrUn.!!$R4 4224
15 TraesCS7D01G114300 chrUn 82524643 82528720 4077 True 823.000000 1801 86.854000 1884 6476 3 chrUn.!!$R3 4592
16 TraesCS7D01G114300 chrUn 82514179 82516139 1960 True 810.500000 1085 83.021000 4630 6457 2 chrUn.!!$R2 1827
17 TraesCS7D01G114300 chrUn 84282212 84284370 2158 True 594.500000 974 87.058000 4648 6635 2 chrUn.!!$R5 1987
18 TraesCS7D01G114300 chrUn 226935537 226937695 2158 True 594.500000 974 87.058000 4648 6635 2 chrUn.!!$R6 1987
19 TraesCS7D01G114300 chrUn 329447367 329447931 564 False 549.000000 549 84.293000 5153 5721 1 chrUn.!!$F1 568
20 TraesCS7D01G114300 chr1A 21771890 21775072 3182 True 903.000000 998 82.527000 2330 5831 2 chr1A.!!$R1 3501

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
61 62 0.494551 TGGTCCCCACCTCCTCTTTA 59.505 55.000 0.00 0.0 44.17 1.85 F
208 209 0.835971 TCTGTCCCTACCAGCTGCAA 60.836 55.000 8.66 0.0 0.00 4.08 F
541 545 1.073025 TCACAGGCCACACCATCAC 59.927 57.895 5.01 0.0 43.14 3.06 F
2155 2205 0.476338 TTAGTGGTGGCCAGAAGCAA 59.524 50.000 5.11 0.0 46.50 3.91 F
3075 3315 1.107114 TTGTTCCGTGCACCAATGTT 58.893 45.000 12.15 0.0 0.00 2.71 F
4148 5287 0.528017 CTACAAGCACTGGAGCGAGA 59.472 55.000 0.00 0.0 40.15 4.04 F
4555 5947 0.178873 TGGGAGTAGCTTCTTGGGGT 60.179 55.000 0.00 0.0 0.00 4.95 F
4998 6444 0.611062 TCTCGATGGAACGGGTGAGT 60.611 55.000 0.00 0.0 35.11 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2046 2096 0.529773 GCACCTCACGAGTGTGTTGA 60.530 55.000 6.95 0.00 46.49 3.18 R
2146 2196 2.664851 TGGACGCGTTGCTTCTGG 60.665 61.111 15.53 0.00 0.00 3.86 R
2525 2746 3.432326 GCAGACCGAATAACCTCTCCATT 60.432 47.826 0.00 0.00 0.00 3.16 R
4148 5287 0.034574 TGACAGTGGTGCACCTTTGT 60.035 50.000 32.21 32.21 36.49 2.83 R
4158 5297 0.251341 GGAAGGGCAATGACAGTGGT 60.251 55.000 4.88 0.00 0.00 4.16 R
5215 6672 0.320697 AGTACAAGGGGTGCGTCTTC 59.679 55.000 0.00 0.00 37.18 2.87 R
6123 10105 1.739466 ACCAAACATCATGCTAGCACG 59.261 47.619 22.07 13.17 0.00 5.34 R
6740 10797 0.696501 TACTGGGGCAAGGAAACCTC 59.303 55.000 0.00 0.00 30.89 3.85 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
30 31 3.903783 CGAACCTCGTACCCCGTA 58.096 61.111 0.00 0.00 37.94 4.02
31 32 1.429423 CGAACCTCGTACCCCGTAC 59.571 63.158 0.00 0.00 37.94 3.67
32 33 1.809869 GAACCTCGTACCCCGTACC 59.190 63.158 0.00 0.00 35.81 3.34
33 34 1.667154 GAACCTCGTACCCCGTACCC 61.667 65.000 0.00 0.00 35.81 3.69
34 35 2.834968 CCTCGTACCCCGTACCCC 60.835 72.222 0.00 0.00 35.81 4.95
35 36 3.211963 CTCGTACCCCGTACCCCG 61.212 72.222 0.00 0.00 35.81 5.73
36 37 3.995506 CTCGTACCCCGTACCCCGT 62.996 68.421 0.00 0.00 35.81 5.28
37 38 3.825611 CGTACCCCGTACCCCGTG 61.826 72.222 0.00 0.00 35.81 4.94
38 39 4.147449 GTACCCCGTACCCCGTGC 62.147 72.222 0.00 0.00 33.38 5.34
56 57 4.354943 CCCTGGTCCCCACCTCCT 62.355 72.222 0.00 0.00 44.17 3.69
57 58 2.689034 CCTGGTCCCCACCTCCTC 60.689 72.222 0.00 0.00 44.17 3.71
58 59 2.452114 CTGGTCCCCACCTCCTCT 59.548 66.667 0.00 0.00 44.17 3.69
59 60 1.229658 CTGGTCCCCACCTCCTCTT 60.230 63.158 0.00 0.00 44.17 2.85
60 61 0.842467 CTGGTCCCCACCTCCTCTTT 60.842 60.000 0.00 0.00 44.17 2.52
61 62 0.494551 TGGTCCCCACCTCCTCTTTA 59.505 55.000 0.00 0.00 44.17 1.85
62 63 1.082194 TGGTCCCCACCTCCTCTTTAT 59.918 52.381 0.00 0.00 44.17 1.40
63 64 2.319747 TGGTCCCCACCTCCTCTTTATA 59.680 50.000 0.00 0.00 44.17 0.98
64 65 2.973406 GGTCCCCACCTCCTCTTTATAG 59.027 54.545 0.00 0.00 40.00 1.31
65 66 2.369203 GTCCCCACCTCCTCTTTATAGC 59.631 54.545 0.00 0.00 0.00 2.97
66 67 2.022428 TCCCCACCTCCTCTTTATAGCA 60.022 50.000 0.00 0.00 0.00 3.49
67 68 2.104963 CCCCACCTCCTCTTTATAGCAC 59.895 54.545 0.00 0.00 0.00 4.40
68 69 3.041946 CCCACCTCCTCTTTATAGCACT 58.958 50.000 0.00 0.00 0.00 4.40
69 70 3.181461 CCCACCTCCTCTTTATAGCACTG 60.181 52.174 0.00 0.00 0.00 3.66
70 71 3.462021 CACCTCCTCTTTATAGCACTGC 58.538 50.000 0.00 0.00 0.00 4.40
71 72 2.101582 ACCTCCTCTTTATAGCACTGCG 59.898 50.000 0.00 0.00 0.00 5.18
72 73 2.131183 CTCCTCTTTATAGCACTGCGC 58.869 52.381 0.00 0.00 42.91 6.09
97 98 3.688159 GCCCACCAGCCTTGCTTG 61.688 66.667 0.00 0.00 36.40 4.01
98 99 2.993264 CCCACCAGCCTTGCTTGG 60.993 66.667 0.72 0.72 36.40 3.61
99 100 2.993264 CCACCAGCCTTGCTTGGG 60.993 66.667 8.65 1.44 36.40 4.12
105 106 3.376918 GCCTTGCTTGGGCTGGAC 61.377 66.667 7.67 0.00 45.57 4.02
106 107 3.058160 CCTTGCTTGGGCTGGACG 61.058 66.667 0.00 0.00 39.59 4.79
107 108 3.741476 CTTGCTTGGGCTGGACGC 61.741 66.667 0.00 0.00 39.59 5.19
117 118 4.227134 CTGGACGCCCCCGATCAG 62.227 72.222 0.00 0.00 38.29 2.90
127 128 4.530857 CCGATCAGGGCGTGGGTC 62.531 72.222 7.42 5.53 35.97 4.46
128 129 3.770040 CGATCAGGGCGTGGGTCA 61.770 66.667 7.42 0.00 0.00 4.02
129 130 2.668632 GATCAGGGCGTGGGTCAA 59.331 61.111 7.42 0.00 0.00 3.18
130 131 1.450312 GATCAGGGCGTGGGTCAAG 60.450 63.158 7.42 0.00 0.00 3.02
131 132 2.876368 GATCAGGGCGTGGGTCAAGG 62.876 65.000 7.42 0.00 0.00 3.61
132 133 4.722700 CAGGGCGTGGGTCAAGGG 62.723 72.222 0.00 0.00 0.00 3.95
140 141 2.770130 GGGTCAAGGGCCCAATGA 59.230 61.111 27.56 24.65 45.40 2.57
141 142 1.380380 GGGTCAAGGGCCCAATGAG 60.380 63.158 27.56 8.67 45.40 2.90
142 143 2.054453 GGTCAAGGGCCCAATGAGC 61.054 63.158 31.53 31.53 34.85 4.26
148 149 3.451894 GGCCCAATGAGCCGTTGG 61.452 66.667 15.50 15.50 46.70 3.77
159 160 3.381136 CCGTTGGGCCCATTGGTG 61.381 66.667 29.23 13.60 0.00 4.17
160 161 3.381136 CGTTGGGCCCATTGGTGG 61.381 66.667 29.23 7.60 45.61 4.61
175 176 6.857777 CATTGGTGGAGAGATCAATCTAAC 57.142 41.667 0.00 0.00 37.25 2.34
176 177 6.351711 CATTGGTGGAGAGATCAATCTAACA 58.648 40.000 0.00 0.00 37.25 2.41
179 180 7.675161 TGGTGGAGAGATCAATCTAACATTA 57.325 36.000 0.00 0.00 37.25 1.90
203 204 1.834263 AGATGTTCTGTCCCTACCAGC 59.166 52.381 0.00 0.00 0.00 4.85
208 209 0.835971 TCTGTCCCTACCAGCTGCAA 60.836 55.000 8.66 0.00 0.00 4.08
266 267 6.387192 TGATGAAGAGGGTTATGGAGAAAA 57.613 37.500 0.00 0.00 0.00 2.29
291 292 1.923356 ATGGTTTGTACAAGCCCCTG 58.077 50.000 31.28 0.00 40.46 4.45
495 499 2.544694 CCAGTACTCGATGCTCATGGAC 60.545 54.545 0.00 0.00 0.00 4.02
541 545 1.073025 TCACAGGCCACACCATCAC 59.927 57.895 5.01 0.00 43.14 3.06
551 555 2.238144 CCACACCATCACTCTTCTGGAT 59.762 50.000 0.00 0.00 34.08 3.41
598 602 1.962807 TCGTGGTCTCGGGTTTCTTTA 59.037 47.619 0.00 0.00 0.00 1.85
990 994 3.563808 TGGCAATTCTATACAATGCGGTC 59.436 43.478 0.00 0.00 0.00 4.79
1545 1560 3.487574 CGATGAATTCGTGTAGCTTCTCC 59.512 47.826 4.51 0.00 43.01 3.71
2014 2064 5.413833 AGGAACTGTGCAAGACAATATTCTG 59.586 40.000 0.00 0.00 37.18 3.02
2046 2096 2.158900 CGATGGACAGGCAAAGATACCT 60.159 50.000 0.00 0.00 36.45 3.08
2146 2196 4.162509 AGAGGAGTAAATCTTAGTGGTGGC 59.837 45.833 0.00 0.00 0.00 5.01
2155 2205 0.476338 TTAGTGGTGGCCAGAAGCAA 59.524 50.000 5.11 0.00 46.50 3.91
2630 2851 5.801531 AGATACTATGGGTGTTTCGCATA 57.198 39.130 0.00 0.00 45.67 3.14
2767 3006 9.500785 CTAATCAAGAAAGAGGAAAGAGAAACT 57.499 33.333 0.00 0.00 0.00 2.66
2966 3206 4.684242 TGTACATTATTATCGGAGCTTGCG 59.316 41.667 0.00 0.00 0.00 4.85
3075 3315 1.107114 TTGTTCCGTGCACCAATGTT 58.893 45.000 12.15 0.00 0.00 2.71
3159 3420 5.046591 TGGTGATACAAGAAGTTACAGGGAG 60.047 44.000 0.00 0.00 0.00 4.30
3182 3443 7.020827 AGTTTCTCATGAGGGATTAACTTGA 57.979 36.000 22.42 0.00 0.00 3.02
3402 3664 9.983804 GTATGACTTTGTTACTTTATGGCTAAC 57.016 33.333 0.00 0.00 0.00 2.34
3746 4115 3.123790 GCGCTGTAGTTCTTTCTTCTTCC 59.876 47.826 0.00 0.00 0.00 3.46
3886 4824 8.774586 CCATTCTGGAATAGATAACGTTTTAGG 58.225 37.037 5.91 0.00 40.96 2.69
4073 5212 6.149129 TCATCATCTGTCATGGTAGTACAC 57.851 41.667 2.06 0.00 0.00 2.90
4108 5247 9.411189 AGAAGTAACAAAAATTACAACCAGGTA 57.589 29.630 0.00 0.00 37.49 3.08
4124 5263 2.037772 CAGGTATGTGGATCACCTAGCC 59.962 54.545 1.57 0.00 40.77 3.93
4148 5287 0.528017 CTACAAGCACTGGAGCGAGA 59.472 55.000 0.00 0.00 40.15 4.04
4150 5289 1.005748 CAAGCACTGGAGCGAGACA 60.006 57.895 0.00 0.00 40.15 3.41
4158 5297 1.301716 GGAGCGAGACAAAGGTGCA 60.302 57.895 0.00 0.00 0.00 4.57
4161 5300 1.891919 GCGAGACAAAGGTGCACCA 60.892 57.895 36.39 0.00 38.89 4.17
4189 5329 3.003173 CCTTCCTCACCGGAGCCA 61.003 66.667 9.46 0.00 44.28 4.75
4211 5351 2.556806 GCAAACGTTGTTGTAGTAGCG 58.443 47.619 0.00 0.00 0.00 4.26
4215 5355 1.337703 ACGTTGTTGTAGTAGCGGTCA 59.662 47.619 0.00 0.00 0.00 4.02
4253 5393 2.031012 TCCACAAGACCAGCGCAG 59.969 61.111 11.47 0.00 0.00 5.18
4267 5407 3.620615 CGCAGCAGAACAACAAACA 57.379 47.368 0.00 0.00 0.00 2.83
4273 5413 2.098934 AGCAGAACAACAAACATCGCAA 59.901 40.909 0.00 0.00 0.00 4.85
4287 5427 2.806288 TCGCAAATAAAGAGAAGCGC 57.194 45.000 0.00 0.00 44.27 5.92
4319 5459 5.263968 AGATCAAACCTATAGACACACGG 57.736 43.478 0.00 0.00 0.00 4.94
4368 5508 3.000819 ATCCACGTGCCCTCCGAA 61.001 61.111 10.91 0.00 0.00 4.30
4406 5731 2.505407 TCAAGATGGGGATCGAACATGT 59.495 45.455 0.00 0.00 0.00 3.21
4504 5829 2.692368 GGATCCCTCCCACTGGCA 60.692 66.667 0.00 0.00 35.28 4.92
4555 5947 0.178873 TGGGAGTAGCTTCTTGGGGT 60.179 55.000 0.00 0.00 0.00 4.95
4634 6034 4.142315 TGTTACACTCCGAGGTAGTAATGC 60.142 45.833 11.22 4.00 0.00 3.56
4645 6045 6.649141 CCGAGGTAGTAATGCTTATTATTGCA 59.351 38.462 0.00 0.00 43.67 4.08
4726 6151 0.961019 TTTCTCAAGCCACCACATGC 59.039 50.000 0.00 0.00 0.00 4.06
4984 6430 6.001449 ACCTTGGGAATCAAATAATCTCGA 57.999 37.500 0.00 0.00 34.56 4.04
4998 6444 0.611062 TCTCGATGGAACGGGTGAGT 60.611 55.000 0.00 0.00 35.11 3.41
5036 6482 1.876322 AGTGAAGCAGCAGAAGTCAC 58.124 50.000 0.00 0.25 39.09 3.67
5211 6668 8.956426 TGGATTTTCATTTGACAGATTAGGTAC 58.044 33.333 0.00 0.00 0.00 3.34
5215 6672 5.989477 TCATTTGACAGATTAGGTACAGGG 58.011 41.667 0.00 0.00 0.00 4.45
5220 6677 4.710375 TGACAGATTAGGTACAGGGAAGAC 59.290 45.833 0.00 0.00 0.00 3.01
5223 6680 1.927487 TTAGGTACAGGGAAGACGCA 58.073 50.000 0.00 0.00 0.00 5.24
5434 6893 3.644966 TGGGTATCATTCCACAAGACC 57.355 47.619 0.00 0.00 0.00 3.85
5435 6894 2.241176 TGGGTATCATTCCACAAGACCC 59.759 50.000 0.00 0.00 44.52 4.46
5608 8264 1.202758 ACACCGAAAGAACCTGATGCA 60.203 47.619 0.00 0.00 0.00 3.96
5724 8976 3.751479 AACAAAATGGGGTGAAAGAGC 57.249 42.857 0.00 0.00 0.00 4.09
5737 8989 5.126707 GGGTGAAAGAGCAATCTCAAATGAT 59.873 40.000 0.00 0.00 41.81 2.45
5756 9013 8.341173 CAAATGATAAGTTGCCTCTCTCATAAC 58.659 37.037 0.00 0.00 0.00 1.89
5787 9046 2.688958 CCCTAGGAGGAACTAGACAACG 59.311 54.545 11.48 0.00 41.55 4.10
5788 9047 3.354467 CCTAGGAGGAACTAGACAACGT 58.646 50.000 1.05 0.00 41.55 3.99
5825 9084 4.536765 AGAAATAGGCACCCGAATTTGAT 58.463 39.130 0.00 0.00 29.01 2.57
6123 10105 8.610896 AGTCGTATGCGTATTAGTTATATCCTC 58.389 37.037 2.37 0.00 39.49 3.71
6146 10128 4.749598 CGTGCTAGCATGATGTTTGGTATA 59.250 41.667 29.43 0.00 35.09 1.47
6154 10136 8.332996 AGCATGATGTTTGGTATAATCTCATC 57.667 34.615 0.00 0.00 0.00 2.92
6155 10137 7.392673 AGCATGATGTTTGGTATAATCTCATCC 59.607 37.037 0.00 0.00 32.17 3.51
6156 10138 7.175467 GCATGATGTTTGGTATAATCTCATCCA 59.825 37.037 0.00 0.00 32.17 3.41
6157 10139 9.239551 CATGATGTTTGGTATAATCTCATCCAT 57.760 33.333 0.00 0.00 32.17 3.41
6159 10141 9.948964 TGATGTTTGGTATAATCTCATCCATAG 57.051 33.333 0.00 0.00 32.17 2.23
6344 10329 0.530744 TTCAGAAGACCATCCGGACG 59.469 55.000 6.12 0.00 35.59 4.79
6401 10386 4.022589 CACCGTATACCGACAGTTATGGAT 60.023 45.833 0.00 0.00 39.56 3.41
6457 10442 5.163663 TGTTTCTCTTGCCGGCAAATTATAG 60.164 40.000 38.96 27.41 35.33 1.31
6740 10797 5.941555 AGGTAAACAGAGTAGATTCCTGG 57.058 43.478 0.00 0.00 32.52 4.45
6743 10800 5.163395 GGTAAACAGAGTAGATTCCTGGAGG 60.163 48.000 0.00 0.00 32.52 4.30
6763 10820 2.594131 GTTTCCTTGCCCCAGTAAACT 58.406 47.619 0.00 0.00 0.00 2.66
6797 10854 2.332654 GCAACCCTGCCAACCGTAG 61.333 63.158 0.00 0.00 43.26 3.51
6973 11319 7.719193 TGTTAAGAGCTGCCTATTTATATTGCA 59.281 33.333 0.00 0.00 0.00 4.08
7055 11404 8.291888 CGCAGCTCCTGTATAATGATATAATC 57.708 38.462 0.00 0.00 33.43 1.75
7056 11405 8.140628 CGCAGCTCCTGTATAATGATATAATCT 58.859 37.037 0.00 0.00 33.43 2.40
7094 11443 4.102524 TGAAACACTACCTCACTTCATGGT 59.897 41.667 0.00 0.00 37.83 3.55
7112 11480 2.208431 GGTCTTTCATCAGCCGATCAG 58.792 52.381 0.00 0.00 0.00 2.90
7125 11493 2.534298 CCGATCAGTTGCAGTCACTAG 58.466 52.381 0.00 0.00 0.00 2.57
7150 11524 4.695396 TGTTGTTTAGTAGTTCTTCCGCA 58.305 39.130 0.00 0.00 0.00 5.69
7154 11528 4.986659 TGTTTAGTAGTTCTTCCGCAGTTC 59.013 41.667 0.00 0.00 0.00 3.01
7167 11541 1.534175 CGCAGTTCGAGGTGGTATCTC 60.534 57.143 0.00 0.00 41.67 2.75
7189 11563 3.305131 CGTACTGTACCTGCAGAGACAAA 60.305 47.826 17.39 6.89 39.62 2.83
7215 11589 0.972134 TCCAGCAGTCTGAACAGAGG 59.028 55.000 3.32 3.17 42.95 3.69
7234 11608 3.288092 AGGTGTTTGAAAGAGAACCACC 58.712 45.455 5.32 5.32 32.24 4.61
7292 11666 2.135933 GAGCAATTAGATTAGCGCCGT 58.864 47.619 2.29 0.00 0.00 5.68
7298 11672 2.658373 TAGATTAGCGCCGTGAAACA 57.342 45.000 2.29 0.00 35.74 2.83
7327 11706 2.623878 TAACACGGCTCAAAACCTCA 57.376 45.000 0.00 0.00 0.00 3.86
7350 11729 7.509546 TCAAGAGGGATTCATCTATTTGGTAC 58.490 38.462 0.00 0.00 32.26 3.34
7472 11942 1.213926 ACTTCAGATCTGCAATCCCCC 59.786 52.381 18.36 0.00 0.00 5.40
7515 11985 5.479306 ACTGCCTATTTATATCGCGATGTT 58.521 37.500 31.05 19.87 0.00 2.71
7516 11986 5.932303 ACTGCCTATTTATATCGCGATGTTT 59.068 36.000 31.05 17.43 0.00 2.83
7517 11987 6.426937 ACTGCCTATTTATATCGCGATGTTTT 59.573 34.615 31.05 15.04 0.00 2.43
7518 11988 7.041372 ACTGCCTATTTATATCGCGATGTTTTT 60.041 33.333 31.05 15.04 0.00 1.94
7537 12007 0.887933 TTTTGGAAATGGAGGCGAGC 59.112 50.000 0.00 0.00 0.00 5.03
7538 12008 0.965363 TTTGGAAATGGAGGCGAGCC 60.965 55.000 5.89 5.89 0.00 4.70
7539 12009 2.517166 GGAAATGGAGGCGAGCCC 60.517 66.667 10.95 2.31 36.58 5.19
7540 12010 2.517166 GAAATGGAGGCGAGCCCC 60.517 66.667 10.95 12.01 36.58 5.80
7541 12011 4.129148 AAATGGAGGCGAGCCCCC 62.129 66.667 10.95 9.35 36.58 5.40
7555 12025 3.882326 CCCCGGCCTCTGCATCAT 61.882 66.667 0.00 0.00 40.13 2.45
7556 12026 2.593725 CCCGGCCTCTGCATCATG 60.594 66.667 0.00 0.00 40.13 3.07
7557 12027 2.507452 CCGGCCTCTGCATCATGA 59.493 61.111 0.00 0.00 40.13 3.07
7558 12028 1.153107 CCGGCCTCTGCATCATGAA 60.153 57.895 0.00 0.00 40.13 2.57
7559 12029 1.164662 CCGGCCTCTGCATCATGAAG 61.165 60.000 0.00 0.00 40.13 3.02
7560 12030 0.179065 CGGCCTCTGCATCATGAAGA 60.179 55.000 0.00 0.00 40.13 2.87
7561 12031 1.542767 CGGCCTCTGCATCATGAAGAT 60.543 52.381 0.00 0.00 40.13 2.40
7572 12042 5.761165 CATCATGAAGATGCATACAACCA 57.239 39.130 0.00 0.00 46.90 3.67
7573 12043 6.327279 CATCATGAAGATGCATACAACCAT 57.673 37.500 0.00 0.00 46.90 3.55
7574 12044 6.745116 CATCATGAAGATGCATACAACCATT 58.255 36.000 0.00 0.00 46.90 3.16
7575 12045 6.778834 TCATGAAGATGCATACAACCATTT 57.221 33.333 0.00 0.00 0.00 2.32
7576 12046 7.172868 TCATGAAGATGCATACAACCATTTT 57.827 32.000 0.00 0.00 0.00 1.82
7577 12047 8.291191 TCATGAAGATGCATACAACCATTTTA 57.709 30.769 0.00 0.00 0.00 1.52
7578 12048 8.916062 TCATGAAGATGCATACAACCATTTTAT 58.084 29.630 0.00 0.00 0.00 1.40
7579 12049 9.537192 CATGAAGATGCATACAACCATTTTATT 57.463 29.630 0.00 0.00 0.00 1.40
7592 12062 9.308000 ACAACCATTTTATTAGAAATCCAGTCA 57.692 29.630 0.00 0.00 0.00 3.41
7593 12063 9.793252 CAACCATTTTATTAGAAATCCAGTCAG 57.207 33.333 0.00 0.00 0.00 3.51
7594 12064 9.533831 AACCATTTTATTAGAAATCCAGTCAGT 57.466 29.630 0.00 0.00 0.00 3.41
7600 12070 9.745880 TTTATTAGAAATCCAGTCAGTATCGAC 57.254 33.333 0.00 0.00 36.08 4.20
7601 12071 6.769134 TTAGAAATCCAGTCAGTATCGACA 57.231 37.500 0.00 0.00 38.43 4.35
7602 12072 5.661056 AGAAATCCAGTCAGTATCGACAA 57.339 39.130 0.00 0.00 38.43 3.18
7603 12073 6.037786 AGAAATCCAGTCAGTATCGACAAA 57.962 37.500 0.00 0.00 38.43 2.83
7604 12074 6.464222 AGAAATCCAGTCAGTATCGACAAAA 58.536 36.000 0.00 0.00 38.43 2.44
7605 12075 6.934645 AGAAATCCAGTCAGTATCGACAAAAA 59.065 34.615 0.00 0.00 38.43 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.279918 GTTCGTCACCGCCACTGT 60.280 61.111 0.00 0.00 0.00 3.55
1 2 3.041940 GGTTCGTCACCGCCACTG 61.042 66.667 0.00 0.00 35.12 3.66
44 45 2.369203 GCTATAAAGAGGAGGTGGGGAC 59.631 54.545 0.00 0.00 0.00 4.46
45 46 2.022428 TGCTATAAAGAGGAGGTGGGGA 60.022 50.000 0.00 0.00 0.00 4.81
46 47 2.104963 GTGCTATAAAGAGGAGGTGGGG 59.895 54.545 0.00 0.00 0.00 4.96
47 48 3.041946 AGTGCTATAAAGAGGAGGTGGG 58.958 50.000 0.00 0.00 0.00 4.61
48 49 3.742640 GCAGTGCTATAAAGAGGAGGTGG 60.743 52.174 8.18 0.00 0.00 4.61
49 50 3.462021 GCAGTGCTATAAAGAGGAGGTG 58.538 50.000 8.18 0.00 0.00 4.00
50 51 2.101582 CGCAGTGCTATAAAGAGGAGGT 59.898 50.000 14.33 0.00 0.00 3.85
51 52 2.748605 CGCAGTGCTATAAAGAGGAGG 58.251 52.381 14.33 0.00 0.00 4.30
52 53 2.131183 GCGCAGTGCTATAAAGAGGAG 58.869 52.381 14.33 0.00 41.73 3.69
53 54 1.536072 CGCGCAGTGCTATAAAGAGGA 60.536 52.381 14.33 0.00 43.27 3.71
54 55 0.855349 CGCGCAGTGCTATAAAGAGG 59.145 55.000 14.33 0.00 43.27 3.69
55 56 1.518929 GTCGCGCAGTGCTATAAAGAG 59.481 52.381 14.33 0.00 43.27 2.85
56 57 1.135228 TGTCGCGCAGTGCTATAAAGA 60.135 47.619 14.33 0.54 43.27 2.52
57 58 1.256376 CTGTCGCGCAGTGCTATAAAG 59.744 52.381 14.33 1.65 43.27 1.85
58 59 1.277326 CTGTCGCGCAGTGCTATAAA 58.723 50.000 14.33 0.00 43.27 1.40
59 60 0.527600 CCTGTCGCGCAGTGCTATAA 60.528 55.000 22.70 0.00 43.55 0.98
60 61 1.065764 CCTGTCGCGCAGTGCTATA 59.934 57.895 22.70 0.00 43.55 1.31
61 62 2.202797 CCTGTCGCGCAGTGCTAT 60.203 61.111 22.70 0.00 43.55 2.97
62 63 4.435436 CCCTGTCGCGCAGTGCTA 62.435 66.667 22.70 0.00 43.55 3.49
80 81 3.688159 CAAGCAAGGCTGGTGGGC 61.688 66.667 0.00 0.00 39.62 5.36
81 82 2.993264 CCAAGCAAGGCTGGTGGG 60.993 66.667 1.78 0.00 39.62 4.61
82 83 2.993264 CCCAAGCAAGGCTGGTGG 60.993 66.667 2.62 2.62 39.62 4.61
89 90 3.058160 CGTCCAGCCCAAGCAAGG 61.058 66.667 0.00 0.00 43.56 3.61
90 91 3.741476 GCGTCCAGCCCAAGCAAG 61.741 66.667 0.00 0.00 43.56 4.01
100 101 4.227134 CTGATCGGGGGCGTCCAG 62.227 72.222 9.07 0.19 37.22 3.86
110 111 4.530857 GACCCACGCCCTGATCGG 62.531 72.222 0.00 0.00 0.00 4.18
111 112 3.309436 TTGACCCACGCCCTGATCG 62.309 63.158 0.00 0.00 0.00 3.69
112 113 1.450312 CTTGACCCACGCCCTGATC 60.450 63.158 0.00 0.00 0.00 2.92
113 114 2.671070 CTTGACCCACGCCCTGAT 59.329 61.111 0.00 0.00 0.00 2.90
114 115 3.636231 CCTTGACCCACGCCCTGA 61.636 66.667 0.00 0.00 0.00 3.86
115 116 4.722700 CCCTTGACCCACGCCCTG 62.723 72.222 0.00 0.00 0.00 4.45
124 125 2.054453 GCTCATTGGGCCCTTGACC 61.054 63.158 25.70 13.52 0.00 4.02
125 126 2.054453 GGCTCATTGGGCCCTTGAC 61.054 63.158 25.70 17.95 43.49 3.18
126 127 2.360191 GGCTCATTGGGCCCTTGA 59.640 61.111 25.70 23.46 43.49 3.02
127 128 3.142838 CGGCTCATTGGGCCCTTG 61.143 66.667 25.70 20.47 46.24 3.61
128 129 3.224007 AACGGCTCATTGGGCCCTT 62.224 57.895 25.70 13.67 46.24 3.95
129 130 3.661648 AACGGCTCATTGGGCCCT 61.662 61.111 25.70 7.66 46.24 5.19
130 131 3.451894 CAACGGCTCATTGGGCCC 61.452 66.667 21.89 17.59 46.24 5.80
131 132 3.451894 CCAACGGCTCATTGGGCC 61.452 66.667 18.15 18.15 42.57 5.80
142 143 3.381136 CACCAATGGGCCCAACGG 61.381 66.667 31.94 31.94 37.90 4.44
143 144 3.381136 CCACCAATGGGCCCAACG 61.381 66.667 32.58 22.68 43.04 4.10
149 150 6.518241 AGATTGATCTCTCCACCAATGGGC 62.518 50.000 3.55 0.00 38.57 5.36
150 151 3.137913 AGATTGATCTCTCCACCAATGGG 59.862 47.826 3.55 0.00 38.57 4.00
151 152 4.434545 AGATTGATCTCTCCACCAATGG 57.565 45.455 0.00 0.00 39.13 3.16
152 153 6.351711 TGTTAGATTGATCTCTCCACCAATG 58.648 40.000 0.00 0.00 38.32 2.82
153 154 6.566079 TGTTAGATTGATCTCTCCACCAAT 57.434 37.500 0.00 0.00 38.32 3.16
154 155 6.566079 ATGTTAGATTGATCTCTCCACCAA 57.434 37.500 0.00 0.00 38.32 3.67
155 156 6.566079 AATGTTAGATTGATCTCTCCACCA 57.434 37.500 0.00 0.00 38.32 4.17
156 157 9.566432 AAATAATGTTAGATTGATCTCTCCACC 57.434 33.333 0.00 0.00 38.32 4.61
170 171 9.832445 GGGACAGAACATCTAAATAATGTTAGA 57.168 33.333 1.76 0.00 45.02 2.10
171 172 9.838339 AGGGACAGAACATCTAAATAATGTTAG 57.162 33.333 1.76 1.68 45.02 2.34
174 175 8.211629 GGTAGGGACAGAACATCTAAATAATGT 58.788 37.037 0.00 0.00 38.98 2.71
175 176 8.210946 TGGTAGGGACAGAACATCTAAATAATG 58.789 37.037 0.00 0.00 0.00 1.90
176 177 8.331931 TGGTAGGGACAGAACATCTAAATAAT 57.668 34.615 0.00 0.00 0.00 1.28
179 180 5.396884 GCTGGTAGGGACAGAACATCTAAAT 60.397 44.000 0.00 0.00 38.20 1.40
203 204 3.362870 AAAGGAGGAGGAGAATTGCAG 57.637 47.619 0.00 0.00 0.00 4.41
208 209 1.763545 GCCGTAAAGGAGGAGGAGAAT 59.236 52.381 0.00 0.00 45.00 2.40
266 267 3.260632 GGGCTTGTACAAACCATTTCCAT 59.739 43.478 25.42 0.00 0.00 3.41
291 292 1.337071 TCACCGTCTGTCTCTGTGTTC 59.663 52.381 0.00 0.00 0.00 3.18
541 545 8.233190 GTGACAAGAAACAATAATCCAGAAGAG 58.767 37.037 0.00 0.00 0.00 2.85
551 555 5.270083 CACGCTTGTGACAAGAAACAATAA 58.730 37.500 27.97 0.00 46.91 1.40
598 602 2.173569 AGGTGAGAACCTTGAGCAAAGT 59.826 45.455 0.00 0.00 36.56 2.66
990 994 2.456989 GATGAAATCATTGCAGCACCG 58.543 47.619 0.00 0.00 44.70 4.94
1545 1560 5.887598 TGGTTTTGATGTATTCTCATCCCAG 59.112 40.000 4.59 0.00 42.24 4.45
1588 1603 0.694771 TCTCCAGCTTTGACTGCCAT 59.305 50.000 0.00 0.00 36.29 4.40
1728 1752 6.931281 TCTGAGTATGGCAGCTATTTCATTAC 59.069 38.462 0.00 0.00 33.45 1.89
1920 1969 7.555554 AGACTTGGATCTGAAATGTTTATCCAG 59.444 37.037 0.00 0.00 45.04 3.86
2014 2064 1.927174 CTGTCCATCGACGATCCAAAC 59.073 52.381 7.54 4.64 42.37 2.93
2046 2096 0.529773 GCACCTCACGAGTGTGTTGA 60.530 55.000 6.95 0.00 46.49 3.18
2146 2196 2.664851 TGGACGCGTTGCTTCTGG 60.665 61.111 15.53 0.00 0.00 3.86
2525 2746 3.432326 GCAGACCGAATAACCTCTCCATT 60.432 47.826 0.00 0.00 0.00 3.16
2630 2851 5.387113 TGATGGGGTATGTTATTCTTGCT 57.613 39.130 0.00 0.00 0.00 3.91
2767 3006 2.158475 AGACTTGAAAACTGCATCCCCA 60.158 45.455 0.00 0.00 0.00 4.96
3008 3248 4.385643 GGATCTTGATGACTGGATCCCAAA 60.386 45.833 9.90 0.00 44.87 3.28
3159 3420 7.012799 GGATCAAGTTAATCCCTCATGAGAAAC 59.987 40.741 24.62 17.20 37.33 2.78
3182 3443 5.583932 ACCTGCATTAGAAGAAAAAGGGAT 58.416 37.500 0.00 0.00 0.00 3.85
3361 3623 5.179452 AGTCATACCAATTACCTGCAACT 57.821 39.130 0.00 0.00 0.00 3.16
3886 4824 1.098050 GTTGGAGACCCATGTCATGC 58.902 55.000 7.35 0.00 44.33 4.06
4030 5169 7.413446 TGATGAATAGATTGAAAGTTTCCCCT 58.587 34.615 13.01 9.31 0.00 4.79
4033 5172 9.947669 CAGATGATGAATAGATTGAAAGTTTCC 57.052 33.333 13.01 0.00 0.00 3.13
4124 5263 1.702886 CTCCAGTGCTTGTAGTCGTG 58.297 55.000 0.00 0.00 0.00 4.35
4148 5287 0.034574 TGACAGTGGTGCACCTTTGT 60.035 50.000 32.21 32.21 36.49 2.83
4150 5289 1.682854 CAATGACAGTGGTGCACCTTT 59.317 47.619 34.75 20.69 34.49 3.11
4158 5297 0.251341 GGAAGGGCAATGACAGTGGT 60.251 55.000 4.88 0.00 0.00 4.16
4161 5300 1.067295 TGAGGAAGGGCAATGACAGT 58.933 50.000 0.00 0.00 0.00 3.55
4189 5329 2.546789 GCTACTACAACAACGTTTGCCT 59.453 45.455 0.00 0.00 0.00 4.75
4211 5351 4.430908 CTTAATACCACGACTTCCTGACC 58.569 47.826 0.00 0.00 0.00 4.02
4215 5355 3.105283 AGCCTTAATACCACGACTTCCT 58.895 45.455 0.00 0.00 0.00 3.36
4253 5393 2.118228 TGCGATGTTTGTTGTTCTGC 57.882 45.000 0.00 0.00 0.00 4.26
4267 5407 2.285834 CGCGCTTCTCTTTATTTGCGAT 60.286 45.455 5.56 0.00 46.52 4.58
4273 5413 2.128035 CGATCCGCGCTTCTCTTTATT 58.872 47.619 5.56 0.00 0.00 1.40
4287 5427 2.906354 AGGTTTGATCTTTCCGATCCG 58.094 47.619 0.00 0.00 46.52 4.18
4319 5459 1.329906 CAATCTTCGCATGTCTCTGGC 59.670 52.381 0.00 0.00 0.00 4.85
4368 5508 0.885879 TGATGTTGCGTCTACCGTCT 59.114 50.000 0.00 0.00 39.32 4.18
4406 5731 8.008104 TGTCCCCTAGTAGGAATAATATCTCA 57.992 38.462 18.43 0.15 37.67 3.27
4452 5777 0.675083 TTGGTTCAGCGTCTCGGTTA 59.325 50.000 0.00 0.00 34.62 2.85
4504 5829 2.058595 CAGAGAATCCCGACCCCGT 61.059 63.158 0.00 0.00 33.66 5.28
4555 5947 1.995542 AGGCATCTTTCCTTTCCTCCA 59.004 47.619 0.00 0.00 0.00 3.86
4645 6045 7.645402 CGAGGGCGGTAAATATAATTTTCTTT 58.355 34.615 0.00 0.00 0.00 2.52
4848 6294 7.663905 TGAAAGCAAGGAACTAATTAGTGCTAA 59.336 33.333 21.27 11.68 38.49 3.09
4984 6430 1.549170 GTACTGACTCACCCGTTCCAT 59.451 52.381 0.00 0.00 0.00 3.41
5036 6482 4.503910 TGGTAATGGTCGATTGTCTTCAG 58.496 43.478 0.00 0.00 0.00 3.02
5215 6672 0.320697 AGTACAAGGGGTGCGTCTTC 59.679 55.000 0.00 0.00 37.18 2.87
5220 6677 1.651987 CATGTAGTACAAGGGGTGCG 58.348 55.000 7.16 0.00 37.18 5.34
5223 6680 4.080526 GTGATTCCATGTAGTACAAGGGGT 60.081 45.833 21.35 12.04 37.54 4.95
5369 6826 6.747414 AGCCTATTGTACTGATATCCACAA 57.253 37.500 13.73 13.73 35.53 3.33
5434 6893 2.938838 TGTACCCTGGAAAAGTGTTGG 58.061 47.619 0.00 0.00 0.00 3.77
5435 6894 6.488683 TCTTATTGTACCCTGGAAAAGTGTTG 59.511 38.462 0.00 0.00 0.00 3.33
5681 8676 4.214980 ACGTGCTGAACTTTCTGAAATG 57.785 40.909 2.88 1.26 0.00 2.32
5756 9013 5.212745 AGTTCCTCCTAGGGAATCTAGTTG 58.787 45.833 9.46 0.00 45.62 3.16
5787 9046 8.303876 TGCCTATTTCTTCCATAAGTGAAAAAC 58.696 33.333 0.00 0.00 33.09 2.43
5788 9047 8.303876 GTGCCTATTTCTTCCATAAGTGAAAAA 58.696 33.333 0.00 0.00 33.09 1.94
5861 9729 4.953667 TGCAAGCACAATAACAAATGGAA 58.046 34.783 0.00 0.00 0.00 3.53
6123 10105 1.739466 ACCAAACATCATGCTAGCACG 59.261 47.619 22.07 13.17 0.00 5.34
6146 10128 8.173412 TCAGTACTATGGTCTATGGATGAGATT 58.827 37.037 0.00 0.00 0.00 2.40
6154 10136 7.767250 TCTTGATCAGTACTATGGTCTATGG 57.233 40.000 0.00 0.00 31.25 2.74
6155 10137 8.465999 GGATCTTGATCAGTACTATGGTCTATG 58.534 40.741 12.02 0.00 31.25 2.23
6156 10138 8.397957 AGGATCTTGATCAGTACTATGGTCTAT 58.602 37.037 12.02 0.00 31.25 1.98
6157 10139 7.667635 CAGGATCTTGATCAGTACTATGGTCTA 59.332 40.741 12.02 0.00 31.25 2.59
6158 10140 6.493115 CAGGATCTTGATCAGTACTATGGTCT 59.507 42.308 12.02 0.00 31.25 3.85
6159 10141 6.266558 ACAGGATCTTGATCAGTACTATGGTC 59.733 42.308 12.40 0.00 0.00 4.02
6160 10142 6.139671 ACAGGATCTTGATCAGTACTATGGT 58.860 40.000 12.40 0.00 0.00 3.55
6296 10281 8.043113 AGAACATCTGTTGCATTGTCTATAGAA 58.957 33.333 3.40 0.00 38.56 2.10
6401 10386 5.066375 GCTCATTGCAAGTACCATATCACAA 59.934 40.000 4.94 0.00 42.31 3.33
6457 10442 6.146021 CCTCACAAAGAAAACATTACATTGCC 59.854 38.462 0.00 0.00 0.00 4.52
6647 10704 4.826274 TTGTTGTAGCAAGAGATAGCCT 57.174 40.909 0.00 0.00 0.00 4.58
6740 10797 0.696501 TACTGGGGCAAGGAAACCTC 59.303 55.000 0.00 0.00 30.89 3.85
6763 10820 2.026262 GGTTGCAGATTTAGTCCCTCCA 60.026 50.000 0.00 0.00 0.00 3.86
6797 10854 6.806751 TGATACTATGAGCCTTACAGTTCAC 58.193 40.000 0.00 0.00 0.00 3.18
6973 11319 7.270757 TGCTGAAATGTTTGTACTGTACATT 57.729 32.000 20.31 11.70 42.55 2.71
7044 11393 9.654663 GTAAGGAAGCGGTTAGATTATATCATT 57.345 33.333 0.00 0.00 0.00 2.57
7046 11395 8.304596 CAGTAAGGAAGCGGTTAGATTATATCA 58.695 37.037 0.00 0.00 0.00 2.15
7047 11396 8.521176 TCAGTAAGGAAGCGGTTAGATTATATC 58.479 37.037 0.00 0.00 0.00 1.63
7048 11397 8.418597 TCAGTAAGGAAGCGGTTAGATTATAT 57.581 34.615 0.00 0.00 0.00 0.86
7049 11398 7.828508 TCAGTAAGGAAGCGGTTAGATTATA 57.171 36.000 0.00 0.00 0.00 0.98
7050 11399 6.726490 TCAGTAAGGAAGCGGTTAGATTAT 57.274 37.500 0.00 0.00 0.00 1.28
7051 11400 6.534475 TTCAGTAAGGAAGCGGTTAGATTA 57.466 37.500 0.00 0.00 0.00 1.75
7053 11402 5.176592 GTTTCAGTAAGGAAGCGGTTAGAT 58.823 41.667 0.00 0.00 0.00 1.98
7054 11403 4.039488 TGTTTCAGTAAGGAAGCGGTTAGA 59.961 41.667 0.00 0.00 31.49 2.10
7055 11404 4.151867 GTGTTTCAGTAAGGAAGCGGTTAG 59.848 45.833 0.00 0.00 31.49 2.34
7056 11405 4.060205 GTGTTTCAGTAAGGAAGCGGTTA 58.940 43.478 0.00 0.00 31.49 2.85
7057 11406 2.876550 GTGTTTCAGTAAGGAAGCGGTT 59.123 45.455 0.00 0.00 31.49 4.44
7058 11407 2.104281 AGTGTTTCAGTAAGGAAGCGGT 59.896 45.455 0.00 0.00 31.49 5.68
7059 11408 2.767505 AGTGTTTCAGTAAGGAAGCGG 58.232 47.619 0.00 0.00 31.49 5.52
7094 11443 3.264947 CAACTGATCGGCTGATGAAAGA 58.735 45.455 14.17 0.00 34.09 2.52
7112 11480 2.549754 ACAACATGCTAGTGACTGCAAC 59.450 45.455 12.31 0.00 42.74 4.17
7125 11493 5.618561 CGGAAGAACTACTAAACAACATGC 58.381 41.667 0.00 0.00 0.00 4.06
7167 11541 1.810755 TGTCTCTGCAGGTACAGTACG 59.189 52.381 15.13 0.00 38.84 3.67
7215 11589 2.940410 TCGGTGGTTCTCTTTCAAACAC 59.060 45.455 0.00 0.00 0.00 3.32
7292 11666 5.517054 GCCGTGTTAATTTTCAACTGTTTCA 59.483 36.000 0.00 0.00 0.00 2.69
7298 11672 5.508200 TTGAGCCGTGTTAATTTTCAACT 57.492 34.783 0.00 0.00 0.00 3.16
7327 11706 6.842676 GGTACCAAATAGATGAATCCCTCTT 58.157 40.000 7.15 0.00 0.00 2.85
7350 11729 2.383855 TGGTGTTGTCTTTCCTTTGGG 58.616 47.619 0.00 0.00 0.00 4.12
7358 11737 3.864789 AGGACAGATGGTGTTGTCTTT 57.135 42.857 4.82 0.00 40.56 2.52
7517 11987 1.272212 GCTCGCCTCCATTTCCAAAAA 59.728 47.619 0.00 0.00 0.00 1.94
7518 11988 0.887933 GCTCGCCTCCATTTCCAAAA 59.112 50.000 0.00 0.00 0.00 2.44
7519 11989 0.965363 GGCTCGCCTCCATTTCCAAA 60.965 55.000 0.00 0.00 0.00 3.28
7520 11990 1.378514 GGCTCGCCTCCATTTCCAA 60.379 57.895 0.00 0.00 0.00 3.53
7521 11991 2.272146 GGCTCGCCTCCATTTCCA 59.728 61.111 0.00 0.00 0.00 3.53
7522 11992 2.517166 GGGCTCGCCTCCATTTCC 60.517 66.667 8.00 0.00 36.10 3.13
7523 11993 2.517166 GGGGCTCGCCTCCATTTC 60.517 66.667 8.00 0.00 36.10 2.17
7538 12008 3.882326 ATGATGCAGAGGCCGGGG 61.882 66.667 2.18 0.00 40.13 5.73
7539 12009 2.593725 CATGATGCAGAGGCCGGG 60.594 66.667 2.18 0.00 40.13 5.73
7540 12010 1.153107 TTCATGATGCAGAGGCCGG 60.153 57.895 0.00 0.00 40.13 6.13
7541 12011 0.179065 TCTTCATGATGCAGAGGCCG 60.179 55.000 0.00 0.00 40.13 6.13
7542 12012 1.880675 CATCTTCATGATGCAGAGGCC 59.119 52.381 0.78 0.00 44.96 5.19
7551 12021 6.971726 AATGGTTGTATGCATCTTCATGAT 57.028 33.333 0.19 0.00 35.40 2.45
7552 12022 6.778834 AAATGGTTGTATGCATCTTCATGA 57.221 33.333 0.19 0.00 30.57 3.07
7553 12023 9.537192 AATAAAATGGTTGTATGCATCTTCATG 57.463 29.630 0.19 0.00 0.00 3.07
7566 12036 9.308000 TGACTGGATTTCTAATAAAATGGTTGT 57.692 29.630 0.00 0.00 0.00 3.32
7567 12037 9.793252 CTGACTGGATTTCTAATAAAATGGTTG 57.207 33.333 0.00 0.00 0.00 3.77
7568 12038 9.533831 ACTGACTGGATTTCTAATAAAATGGTT 57.466 29.630 0.00 0.00 0.00 3.67
7574 12044 9.745880 GTCGATACTGACTGGATTTCTAATAAA 57.254 33.333 0.00 0.00 35.95 1.40
7575 12045 8.909923 TGTCGATACTGACTGGATTTCTAATAA 58.090 33.333 0.00 0.00 39.64 1.40
7576 12046 8.459911 TGTCGATACTGACTGGATTTCTAATA 57.540 34.615 0.00 0.00 39.64 0.98
7577 12047 7.348080 TGTCGATACTGACTGGATTTCTAAT 57.652 36.000 0.00 0.00 39.64 1.73
7578 12048 6.769134 TGTCGATACTGACTGGATTTCTAA 57.231 37.500 0.00 0.00 39.64 2.10
7579 12049 6.769134 TTGTCGATACTGACTGGATTTCTA 57.231 37.500 0.00 0.00 39.64 2.10
7580 12050 5.661056 TTGTCGATACTGACTGGATTTCT 57.339 39.130 0.00 0.00 39.64 2.52
7581 12051 6.721571 TTTTGTCGATACTGACTGGATTTC 57.278 37.500 0.00 0.00 39.64 2.17


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

AutoCloner maintained by Alex Coulton.