Multiple sequence alignment - TraesCS7D01G099200

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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 TraesCS7D01G099200 chr7D 100.000 5028 0 0 1 5028 59412722 59417749 0.000000e+00 9286.0
1 TraesCS7D01G099200 chr7D 80.307 1432 228 39 921 2334 14586666 14588061 0.000000e+00 1033.0
2 TraesCS7D01G099200 chr7D 81.448 1008 149 26 3082 4078 14588554 14589534 0.000000e+00 791.0
3 TraesCS7D01G099200 chr7D 86.345 249 32 2 2788 3034 14588146 14588394 2.310000e-68 270.0
4 TraesCS7D01G099200 chr7D 84.524 168 13 6 2359 2525 454079075 454079230 2.420000e-33 154.0
5 TraesCS7D01G099200 chr7A 96.769 1981 58 5 3049 5028 63778765 63780740 0.000000e+00 3299.0
6 TraesCS7D01G099200 chr7A 93.520 1034 39 10 812 1821 63776947 63777976 0.000000e+00 1513.0
7 TraesCS7D01G099200 chr7A 81.705 1044 169 22 3082 4109 13830303 13831340 0.000000e+00 850.0
8 TraesCS7D01G099200 chr7A 88.274 614 52 13 1 595 63775601 63776213 0.000000e+00 717.0
9 TraesCS7D01G099200 chr7A 79.205 981 180 21 3084 4051 13971654 13970685 0.000000e+00 660.0
10 TraesCS7D01G099200 chr7A 94.245 417 9 6 2618 3034 63778231 63778632 1.540000e-174 623.0
11 TraesCS7D01G099200 chr7A 94.737 228 11 1 2416 2642 63778000 63778227 2.230000e-93 353.0
12 TraesCS7D01G099200 chr7A 86.611 239 32 0 2796 3034 13829905 13830143 1.070000e-66 265.0
13 TraesCS7D01G099200 chr7A 91.391 151 8 4 561 709 63776251 63776398 8.540000e-48 202.0
14 TraesCS7D01G099200 chr7A 84.058 207 31 2 2154 2358 13972362 13972156 1.100000e-46 198.0
15 TraesCS7D01G099200 chr7A 97.143 35 1 0 561 595 63776215 63776249 5.440000e-05 60.2
16 TraesCS7D01G099200 chr4A 80.556 1044 181 21 3082 4109 722298060 722297023 0.000000e+00 784.0
17 TraesCS7D01G099200 chr4A 80.096 1045 187 19 3082 4109 722334178 722333138 0.000000e+00 758.0
18 TraesCS7D01G099200 chr4A 86.192 239 33 0 2796 3034 722298460 722298222 4.990000e-65 259.0
19 TraesCS7D01G099200 chr4A 85.537 242 32 2 2796 3034 722334581 722334340 3.010000e-62 250.0
20 TraesCS7D01G099200 chr4A 80.357 168 22 6 2360 2527 3450397 3450241 3.180000e-22 117.0
21 TraesCS7D01G099200 chrUn 80.478 1045 183 19 3082 4109 307994537 307993497 0.000000e+00 780.0
22 TraesCS7D01G099200 chrUn 87.387 222 24 4 2815 3034 273912518 273912737 8.360000e-63 252.0
23 TraesCS7D01G099200 chrUn 87.387 222 24 4 2815 3034 285593103 285592884 8.360000e-63 252.0
24 TraesCS7D01G099200 chrUn 87.578 161 18 2 2184 2343 15426189 15426030 8.600000e-43 185.0
25 TraesCS7D01G099200 chrUn 87.578 161 18 2 2184 2343 15583804 15583645 8.600000e-43 185.0
26 TraesCS7D01G099200 chrUn 87.578 161 18 2 2184 2343 274165440 274165281 8.600000e-43 185.0
27 TraesCS7D01G099200 chrUn 86.957 161 19 2 2184 2343 273912225 273912384 4.000000e-41 180.0
28 TraesCS7D01G099200 chrUn 86.957 161 19 2 2184 2343 285593396 285593237 4.000000e-41 180.0
29 TraesCS7D01G099200 chrUn 86.957 161 19 2 2184 2343 339565278 339565119 4.000000e-41 180.0
30 TraesCS7D01G099200 chrUn 86.957 161 19 2 2184 2343 374915488 374915647 4.000000e-41 180.0
31 TraesCS7D01G099200 chr3A 80.376 958 152 26 3106 4050 20897263 20898197 0.000000e+00 695.0
32 TraesCS7D01G099200 chr3A 75.660 341 74 6 1409 1740 20895994 20896334 1.450000e-35 161.0
33 TraesCS7D01G099200 chr3A 82.857 105 15 1 2361 2462 98825748 98825644 1.930000e-14 91.6
34 TraesCS7D01G099200 chr3A 76.023 171 24 7 2371 2537 530173407 530173564 6.980000e-09 73.1
35 TraesCS7D01G099200 chr2D 79.088 1009 175 19 3108 4109 2440728 2439749 0.000000e+00 662.0
36 TraesCS7D01G099200 chr2D 82.456 114 18 2 1087 1199 189676256 189676144 1.150000e-16 99.0
37 TraesCS7D01G099200 chr2D 76.923 117 25 2 1083 1198 189705120 189705005 1.170000e-06 65.8
38 TraesCS7D01G099200 chr3B 87.281 228 27 2 2810 3035 22473342 22473115 4.990000e-65 259.0
39 TraesCS7D01G099200 chr3D 86.842 228 28 2 2810 3035 15348903 15348676 2.320000e-63 254.0
40 TraesCS7D01G099200 chr3D 80.508 118 11 6 2409 2526 387307524 387307419 4.170000e-11 80.5
41 TraesCS7D01G099200 chr5B 78.338 337 63 5 1428 1756 704301754 704302088 5.100000e-50 209.0
42 TraesCS7D01G099200 chr5B 82.443 131 10 7 2395 2525 406538047 406537930 8.910000e-18 102.0
43 TraesCS7D01G099200 chr5B 100.000 28 0 0 2361 2388 652625338 652625311 9.000000e-03 52.8
44 TraesCS7D01G099200 chr5D 77.778 333 64 5 1428 1752 558348383 558348053 3.970000e-46 196.0
45 TraesCS7D01G099200 chr6A 84.483 174 27 0 2156 2329 528359188 528359361 6.690000e-39 172.0
46 TraesCS7D01G099200 chr6A 80.702 171 20 4 2358 2528 117350660 117350817 2.460000e-23 121.0
47 TraesCS7D01G099200 chr6A 86.916 107 13 1 431 536 297710317 297710423 8.840000e-23 119.0
48 TraesCS7D01G099200 chr6A 76.074 163 18 15 2361 2523 411083276 411083417 1.170000e-06 65.8
49 TraesCS7D01G099200 chr7B 85.124 121 16 2 431 551 420072796 420072678 6.840000e-24 122.0
50 TraesCS7D01G099200 chr6D 80.606 165 20 2 2358 2522 429020837 429020989 3.180000e-22 117.0
51 TraesCS7D01G099200 chr6D 85.849 106 15 0 431 536 218447224 218447329 4.110000e-21 113.0
52 TraesCS7D01G099200 chr6D 85.047 107 15 1 430 536 325600870 325600765 1.910000e-19 108.0
53 TraesCS7D01G099200 chr6B 80.117 171 21 4 2358 2528 183308243 183308400 1.140000e-21 115.0
54 TraesCS7D01G099200 chr6B 78.571 168 24 6 2358 2525 646254523 646254678 3.200000e-17 100.0
55 TraesCS7D01G099200 chr6B 92.982 57 3 1 2419 2475 673334053 673334108 1.160000e-11 82.4
56 TraesCS7D01G099200 chr4D 85.321 109 15 1 431 539 441486814 441486707 1.480000e-20 111.0
57 TraesCS7D01G099200 chr1D 83.761 117 17 2 420 536 110734814 110734928 5.320000e-20 110.0
58 TraesCS7D01G099200 chr1D 84.545 110 16 1 431 540 95869703 95869811 1.910000e-19 108.0
59 TraesCS7D01G099200 chr1B 82.927 123 19 2 431 553 88542088 88542208 5.320000e-20 110.0
60 TraesCS7D01G099200 chr1B 77.241 145 20 12 4805 4939 4200949 4201090 6.980000e-09 73.1
61 TraesCS7D01G099200 chr1A 87.234 94 9 3 2361 2453 518020789 518020698 2.480000e-18 104.0
62 TraesCS7D01G099200 chr2A 80.357 112 20 2 2361 2471 385979436 385979546 3.230000e-12 84.2
63 TraesCS7D01G099200 chr2A 77.778 117 24 2 1083 1198 203537288 203537173 2.510000e-08 71.3
64 TraesCS7D01G099200 chr2A 77.876 113 23 2 1087 1198 203461355 203461244 9.030000e-08 69.4
65 TraesCS7D01G099200 chr2A 85.965 57 5 2 1163 1219 203464940 203464887 1.960000e-04 58.4
66 TraesCS7D01G099200 chr2B 78.846 104 20 2 1096 1198 246004002 246003900 9.030000e-08 69.4
67 TraesCS7D01G099200 chr2B 97.059 34 1 0 2495 2528 513712589 513712556 1.960000e-04 58.4
68 TraesCS7D01G099200 chr2B 96.875 32 1 0 2361 2392 374682950 374682981 3.000000e-03 54.7
69 TraesCS7D01G099200 chr2B 100.000 28 0 0 2361 2388 556190226 556190199 9.000000e-03 52.8


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 TraesCS7D01G099200 chr7D 59412722 59417749 5027 False 9286.000000 9286 100.000000 1 5028 1 chr7D.!!$F1 5027
1 TraesCS7D01G099200 chr7D 14586666 14589534 2868 False 698.000000 1033 82.700000 921 4078 3 chr7D.!!$F3 3157
2 TraesCS7D01G099200 chr7A 63775601 63780740 5139 False 966.742857 3299 93.725571 1 5028 7 chr7A.!!$F2 5027
3 TraesCS7D01G099200 chr7A 13829905 13831340 1435 False 557.500000 850 84.158000 2796 4109 2 chr7A.!!$F1 1313
4 TraesCS7D01G099200 chr7A 13970685 13972362 1677 True 429.000000 660 81.631500 2154 4051 2 chr7A.!!$R1 1897
5 TraesCS7D01G099200 chr4A 722297023 722298460 1437 True 521.500000 784 83.374000 2796 4109 2 chr4A.!!$R2 1313
6 TraesCS7D01G099200 chr4A 722333138 722334581 1443 True 504.000000 758 82.816500 2796 4109 2 chr4A.!!$R3 1313
7 TraesCS7D01G099200 chrUn 307993497 307994537 1040 True 780.000000 780 80.478000 3082 4109 1 chrUn.!!$R4 1027
8 TraesCS7D01G099200 chrUn 273912225 273912737 512 False 216.000000 252 87.172000 2184 3034 2 chrUn.!!$F2 850
9 TraesCS7D01G099200 chrUn 285592884 285593396 512 True 216.000000 252 87.172000 2184 3034 2 chrUn.!!$R6 850
10 TraesCS7D01G099200 chr3A 20895994 20898197 2203 False 428.000000 695 78.018000 1409 4050 2 chr3A.!!$F2 2641
11 TraesCS7D01G099200 chr2D 2439749 2440728 979 True 662.000000 662 79.088000 3108 4109 1 chr2D.!!$R1 1001

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
944 1533 1.202639 TGCTGATAAGTATGCCACGGG 60.203 52.381 0.00 0.0 0.00 5.28 F
1307 1896 0.034337 GGAACCCGCTATTATGCCGA 59.966 55.000 0.00 0.0 0.00 5.54 F
1956 2570 0.524862 CGGCAGCAGCATTTCTCTTT 59.475 50.000 2.65 0.0 44.61 2.52 F
2211 2833 1.075536 AGAACTAGTTTGGCAAGGGGG 59.924 52.381 10.02 0.0 0.00 5.40 F
2741 3432 1.075601 AATGCTGACAGAAGGGGGAA 58.924 50.000 6.65 0.0 0.00 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2756 3447 0.394762 TGCTTCCATCCTGGTCATGC 60.395 55.000 0.00 0.00 39.03 4.06 R
2832 3525 1.546029 GTAAGCTTGCCCTGGGAAAAG 59.454 52.381 19.27 19.21 0.00 2.27 R
3515 4382 0.784778 CAAAGCTGAAGACGTCGGAC 59.215 55.000 10.46 6.34 34.07 4.79 R
3717 4645 1.255882 TAACTGCCATGCCTGTTTGG 58.744 50.000 4.27 0.00 39.35 3.28 R
4419 5351 0.324091 TCACGGGAGTAAGGGGAGAC 60.324 60.000 0.00 0.00 44.67 3.36 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
40 41 5.858581 GCACACCAGTCAATCTTACAATTTC 59.141 40.000 0.00 0.00 0.00 2.17
43 44 5.711976 CACCAGTCAATCTTACAATTTCCCT 59.288 40.000 0.00 0.00 0.00 4.20
45 46 7.393234 CACCAGTCAATCTTACAATTTCCCTAA 59.607 37.037 0.00 0.00 0.00 2.69
63 64 9.816787 TTTCCCTAACAATAAATCTACCTTTGT 57.183 29.630 0.00 0.00 32.19 2.83
82 83 2.367567 TGTCATATCTTAAGACCGCCCC 59.632 50.000 7.48 0.00 0.00 5.80
91 92 1.262640 AAGACCGCCCCAATCGTACT 61.263 55.000 0.00 0.00 0.00 2.73
93 94 2.279252 CCGCCCCAATCGTACTCG 60.279 66.667 0.00 0.00 38.55 4.18
107 108 4.348656 TCGTACTCGTGAGTAAATCATGC 58.651 43.478 11.11 0.00 44.62 4.06
125 126 9.988350 AAATCATGCTCAAAAGTAGTATTAACG 57.012 29.630 0.00 0.00 0.00 3.18
147 148 4.609947 GTTAAGTTTAACAAACCCCACCG 58.390 43.478 9.32 0.00 42.34 4.94
148 149 2.732844 AGTTTAACAAACCCCACCGA 57.267 45.000 0.00 0.00 42.34 4.69
185 186 4.870123 TGGTGACCAATTTGAATCCTTG 57.130 40.909 0.00 0.00 0.00 3.61
188 189 4.475944 GTGACCAATTTGAATCCTTGTCG 58.524 43.478 0.00 0.00 0.00 4.35
189 190 4.023193 GTGACCAATTTGAATCCTTGTCGT 60.023 41.667 0.00 0.00 0.00 4.34
190 191 4.215399 TGACCAATTTGAATCCTTGTCGTC 59.785 41.667 0.00 0.00 0.00 4.20
191 192 4.398319 ACCAATTTGAATCCTTGTCGTCT 58.602 39.130 0.00 0.00 0.00 4.18
192 193 4.827284 ACCAATTTGAATCCTTGTCGTCTT 59.173 37.500 0.00 0.00 0.00 3.01
193 194 5.301805 ACCAATTTGAATCCTTGTCGTCTTT 59.698 36.000 0.00 0.00 0.00 2.52
194 195 6.183360 ACCAATTTGAATCCTTGTCGTCTTTT 60.183 34.615 0.00 0.00 0.00 2.27
195 196 6.701400 CCAATTTGAATCCTTGTCGTCTTTTT 59.299 34.615 0.00 0.00 0.00 1.94
243 257 6.930667 AGAATCCTTCTCGTCTTAGTCTAC 57.069 41.667 0.00 0.00 34.07 2.59
249 263 5.415077 CCTTCTCGTCTTAGTCTACTGGAAA 59.585 44.000 0.00 0.00 0.00 3.13
319 333 1.471287 CAATGGTGCTGGAGACATGTG 59.529 52.381 1.15 0.00 41.51 3.21
323 341 2.093500 TGGTGCTGGAGACATGTGATAC 60.093 50.000 1.15 0.00 41.51 2.24
331 349 5.237815 TGGAGACATGTGATACAGACAAAC 58.762 41.667 1.15 0.00 33.40 2.93
342 360 2.550978 ACAGACAAACACTTGACTCGG 58.449 47.619 0.00 0.00 35.72 4.63
425 445 9.632638 ACATCAATACTTGCTCCTACATTTAAT 57.367 29.630 0.00 0.00 0.00 1.40
437 457 7.419172 GCTCCTACATTTAATTGAGTACTCCCT 60.419 40.741 20.11 7.02 0.00 4.20
479 499 8.465999 TGTCGCAGAAATGGATGTATTTTAAAT 58.534 29.630 0.00 0.00 39.69 1.40
518 538 8.078060 AGATAAATTCATTTCCCCGACAAATT 57.922 30.769 0.00 0.00 0.00 1.82
579 599 7.845037 ACATAGGATGATGACATGTATCGATT 58.155 34.615 1.71 0.00 36.82 3.34
595 615 8.221801 TGTATCGATTTCCAAAAATGAAAACG 57.778 30.769 1.71 8.49 44.36 3.60
597 617 4.985409 TCGATTTCCAAAAATGAAAACGGG 59.015 37.500 13.00 0.00 43.67 5.28
598 618 4.985409 CGATTTCCAAAAATGAAAACGGGA 59.015 37.500 7.30 0.00 41.42 5.14
601 621 5.799827 TTCCAAAAATGAAAACGGGAGAT 57.200 34.783 0.00 0.00 0.00 2.75
652 745 8.177663 CACGTATTGTTTGCATAAGAATCTCTT 58.822 33.333 7.09 0.00 40.35 2.85
653 746 8.730680 ACGTATTGTTTGCATAAGAATCTCTTT 58.269 29.630 7.09 0.00 37.89 2.52
679 772 7.510428 TTTTTGCGAGAAATGCATAAGAATC 57.490 32.000 0.00 0.00 42.84 2.52
694 787 6.546034 GCATAAGAATCCTTTGGTAGCCTTTA 59.454 38.462 0.00 0.00 33.94 1.85
695 788 7.231519 GCATAAGAATCCTTTGGTAGCCTTTAT 59.768 37.037 0.00 0.00 33.94 1.40
699 792 8.697507 AGAATCCTTTGGTAGCCTTTATTATG 57.302 34.615 0.00 0.00 0.00 1.90
700 793 8.282256 AGAATCCTTTGGTAGCCTTTATTATGT 58.718 33.333 0.00 0.00 0.00 2.29
701 794 9.569122 GAATCCTTTGGTAGCCTTTATTATGTA 57.431 33.333 0.00 0.00 0.00 2.29
702 795 8.919777 ATCCTTTGGTAGCCTTTATTATGTAC 57.080 34.615 0.00 0.00 0.00 2.90
744 982 6.070938 ACGGGCTAACTAAACTCTCTACAAAT 60.071 38.462 0.00 0.00 0.00 2.32
745 983 6.817140 CGGGCTAACTAAACTCTCTACAAATT 59.183 38.462 0.00 0.00 0.00 1.82
746 984 7.010275 CGGGCTAACTAAACTCTCTACAAATTC 59.990 40.741 0.00 0.00 0.00 2.17
747 985 7.280428 GGGCTAACTAAACTCTCTACAAATTCC 59.720 40.741 0.00 0.00 0.00 3.01
748 986 7.280428 GGCTAACTAAACTCTCTACAAATTCCC 59.720 40.741 0.00 0.00 0.00 3.97
749 987 7.280428 GCTAACTAAACTCTCTACAAATTCCCC 59.720 40.741 0.00 0.00 0.00 4.81
750 988 5.731591 ACTAAACTCTCTACAAATTCCCCG 58.268 41.667 0.00 0.00 0.00 5.73
751 989 2.693267 ACTCTCTACAAATTCCCCGC 57.307 50.000 0.00 0.00 0.00 6.13
752 990 1.906574 ACTCTCTACAAATTCCCCGCA 59.093 47.619 0.00 0.00 0.00 5.69
753 991 2.304761 ACTCTCTACAAATTCCCCGCAA 59.695 45.455 0.00 0.00 0.00 4.85
754 992 3.244770 ACTCTCTACAAATTCCCCGCAAA 60.245 43.478 0.00 0.00 0.00 3.68
755 993 3.756434 CTCTCTACAAATTCCCCGCAAAA 59.244 43.478 0.00 0.00 0.00 2.44
756 994 4.145807 TCTCTACAAATTCCCCGCAAAAA 58.854 39.130 0.00 0.00 0.00 1.94
797 1035 3.549070 GCAGCAACAACAAAAGAACTCTG 59.451 43.478 0.00 0.00 0.00 3.35
798 1036 4.737054 CAGCAACAACAAAAGAACTCTGT 58.263 39.130 0.00 0.00 0.00 3.41
800 1038 6.498304 CAGCAACAACAAAAGAACTCTGTAT 58.502 36.000 0.00 0.00 0.00 2.29
810 1054 9.136323 ACAAAAGAACTCTGTATGGAAGAAAAT 57.864 29.630 0.00 0.00 0.00 1.82
944 1533 1.202639 TGCTGATAAGTATGCCACGGG 60.203 52.381 0.00 0.00 0.00 5.28
945 1534 1.202651 GCTGATAAGTATGCCACGGGT 60.203 52.381 0.00 0.00 0.00 5.28
1141 1730 2.340809 CGGTACACTTCGCCACCA 59.659 61.111 0.00 0.00 0.00 4.17
1212 1801 2.102420 TGGTGACATTCTCAACGACACT 59.898 45.455 0.00 0.00 39.84 3.55
1219 1808 1.301244 CTCAACGACACTGCCTGCT 60.301 57.895 0.00 0.00 0.00 4.24
1285 1874 1.226974 CCGGACATGGAGTGCTACG 60.227 63.158 0.00 0.00 36.26 3.51
1289 1878 2.311688 GACATGGAGTGCTACGGGGG 62.312 65.000 0.00 0.00 0.00 5.40
1290 1879 2.063979 CATGGAGTGCTACGGGGGA 61.064 63.158 0.00 0.00 0.00 4.81
1291 1880 1.306654 ATGGAGTGCTACGGGGGAA 60.307 57.895 0.00 0.00 0.00 3.97
1307 1896 0.034337 GGAACCCGCTATTATGCCGA 59.966 55.000 0.00 0.00 0.00 5.54
1308 1897 1.429463 GAACCCGCTATTATGCCGAG 58.571 55.000 0.00 0.00 0.00 4.63
1309 1898 0.756903 AACCCGCTATTATGCCGAGT 59.243 50.000 0.00 0.00 0.00 4.18
1312 1901 3.359033 ACCCGCTATTATGCCGAGTATA 58.641 45.455 0.00 0.00 0.00 1.47
1353 1942 0.904865 ACGACATCCTTGCTCCCTCA 60.905 55.000 0.00 0.00 0.00 3.86
1542 2134 3.127533 GTCATGGACAGCGGCACC 61.128 66.667 1.45 3.28 32.09 5.01
1590 2188 4.228567 TGCACGCCGGACTTGTCA 62.229 61.111 5.05 0.88 0.00 3.58
1773 2383 0.878523 CGACTCCAGGCGAACACAAA 60.879 55.000 0.00 0.00 0.00 2.83
1787 2397 5.121142 GCGAACACAAAAGTAAGCCTATACA 59.879 40.000 0.00 0.00 0.00 2.29
1825 2439 9.733556 TTCTAGTTATGCCAAGAATTAAGAACA 57.266 29.630 0.00 0.00 0.00 3.18
1832 2446 7.615582 TGCCAAGAATTAAGAACATGTAGAG 57.384 36.000 0.00 0.00 0.00 2.43
1833 2447 6.599244 TGCCAAGAATTAAGAACATGTAGAGG 59.401 38.462 0.00 0.00 0.00 3.69
1844 2458 7.962995 AGAACATGTAGAGGACTAATTCAGA 57.037 36.000 0.00 0.00 0.00 3.27
1845 2459 8.006298 AGAACATGTAGAGGACTAATTCAGAG 57.994 38.462 0.00 0.00 0.00 3.35
1846 2460 6.155475 ACATGTAGAGGACTAATTCAGAGC 57.845 41.667 0.00 0.00 0.00 4.09
1848 2462 7.063593 ACATGTAGAGGACTAATTCAGAGCTA 58.936 38.462 0.00 0.00 0.00 3.32
1849 2463 7.561722 ACATGTAGAGGACTAATTCAGAGCTAA 59.438 37.037 0.00 0.00 0.00 3.09
1850 2464 7.336161 TGTAGAGGACTAATTCAGAGCTAAC 57.664 40.000 0.00 0.00 0.00 2.34
1851 2465 6.890268 TGTAGAGGACTAATTCAGAGCTAACA 59.110 38.462 0.00 0.00 0.00 2.41
1852 2466 7.561722 TGTAGAGGACTAATTCAGAGCTAACAT 59.438 37.037 0.00 0.00 0.00 2.71
1853 2467 6.815089 AGAGGACTAATTCAGAGCTAACATG 58.185 40.000 0.00 0.00 0.00 3.21
1854 2468 5.363939 AGGACTAATTCAGAGCTAACATGC 58.636 41.667 0.00 0.00 0.00 4.06
1856 2470 5.819901 GGACTAATTCAGAGCTAACATGCTT 59.180 40.000 0.00 0.00 44.17 3.91
1857 2471 6.238320 GGACTAATTCAGAGCTAACATGCTTG 60.238 42.308 0.00 0.00 44.17 4.01
1858 2472 4.978083 AATTCAGAGCTAACATGCTTGG 57.022 40.909 4.44 0.00 44.17 3.61
1859 2473 3.423539 TTCAGAGCTAACATGCTTGGT 57.576 42.857 4.44 0.00 44.17 3.67
1860 2474 3.423539 TCAGAGCTAACATGCTTGGTT 57.576 42.857 4.44 0.00 44.17 3.67
1861 2475 3.076621 TCAGAGCTAACATGCTTGGTTG 58.923 45.455 4.44 0.00 44.17 3.77
1862 2476 2.163010 CAGAGCTAACATGCTTGGTTGG 59.837 50.000 4.44 0.20 44.17 3.77
1863 2477 3.423848 GCTAACATGCTTGGTTGGC 57.576 52.632 4.44 6.45 43.69 4.52
1872 2486 1.105457 GCTTGGTTGGCATGCTATCA 58.895 50.000 18.92 9.87 0.00 2.15
1915 2529 4.607955 CATGAGCAAGCTGTGGATAATTG 58.392 43.478 0.00 0.00 0.00 2.32
1933 2547 8.784043 GGATAATTGCCATAGTTTTAGTACCTG 58.216 37.037 0.00 0.00 0.00 4.00
1938 2552 4.743644 GCCATAGTTTTAGTACCTGTAGCG 59.256 45.833 0.00 0.00 0.00 4.26
1956 2570 0.524862 CGGCAGCAGCATTTCTCTTT 59.475 50.000 2.65 0.00 44.61 2.52
1963 2577 4.863131 CAGCAGCATTTCTCTTTTTCATCC 59.137 41.667 0.00 0.00 0.00 3.51
1965 2579 5.948162 AGCAGCATTTCTCTTTTTCATCCTA 59.052 36.000 0.00 0.00 0.00 2.94
1970 2584 9.336171 AGCATTTCTCTTTTTCATCCTATACTC 57.664 33.333 0.00 0.00 0.00 2.59
1977 2591 6.318144 TCTTTTTCATCCTATACTCTCGTCGT 59.682 38.462 0.00 0.00 0.00 4.34
2046 2660 8.258007 AGTTCTGAAACGATGTTCCATTCTATA 58.742 33.333 0.00 0.00 40.48 1.31
2047 2661 8.879759 GTTCTGAAACGATGTTCCATTCTATAA 58.120 33.333 0.00 0.00 0.00 0.98
2055 2669 9.613428 ACGATGTTCCATTCTATAATTTCAAGA 57.387 29.630 0.00 0.00 0.00 3.02
2057 2671 9.890352 GATGTTCCATTCTATAATTTCAAGAGC 57.110 33.333 0.00 0.00 0.00 4.09
2078 2692 7.885297 AGAGCATTTTTACTTGCAGTTAATCA 58.115 30.769 0.00 0.00 41.35 2.57
2081 2695 9.793252 AGCATTTTTACTTGCAGTTAATCATAG 57.207 29.630 0.00 0.00 41.35 2.23
2082 2696 9.573133 GCATTTTTACTTGCAGTTAATCATAGT 57.427 29.630 0.00 0.00 38.72 2.12
2092 2706 8.797266 TGCAGTTAATCATAGTGTTAGATACG 57.203 34.615 0.00 0.00 0.00 3.06
2094 2708 8.903723 GCAGTTAATCATAGTGTTAGATACGAC 58.096 37.037 0.00 0.00 0.00 4.34
2100 2714 9.661187 AATCATAGTGTTAGATACGACTAAACG 57.339 33.333 0.00 0.00 34.74 3.60
2110 2732 3.672767 ACGACTAAACGTGAGGGATTT 57.327 42.857 0.00 0.00 44.84 2.17
2111 2733 3.582780 ACGACTAAACGTGAGGGATTTC 58.417 45.455 0.00 0.00 44.84 2.17
2112 2734 2.928116 CGACTAAACGTGAGGGATTTCC 59.072 50.000 0.00 0.00 0.00 3.13
2144 2766 9.929180 TCTCAATCATATATTTAGGTACACTGC 57.071 33.333 0.00 0.00 0.00 4.40
2149 2771 8.706322 TCATATATTTAGGTACACTGCTGAGA 57.294 34.615 0.00 0.00 0.00 3.27
2173 2795 4.336889 ACAAGGATCAAGACGTTCTCAA 57.663 40.909 0.00 0.00 0.00 3.02
2210 2832 2.586648 AGAACTAGTTTGGCAAGGGG 57.413 50.000 10.02 0.00 0.00 4.79
2211 2833 1.075536 AGAACTAGTTTGGCAAGGGGG 59.924 52.381 10.02 0.00 0.00 5.40
2236 2858 6.071728 GGAATTCAGAGTTCATGGTGTTTGAT 60.072 38.462 7.93 0.00 0.00 2.57
2329 2952 7.333323 GCCCTGTCTACAAGGTAAATTAGTAA 58.667 38.462 0.00 0.00 30.14 2.24
2363 3011 8.269317 TGATTTCCGTATTTATTGGGAACTACT 58.731 33.333 0.00 0.00 38.23 2.57
2365 3013 6.165700 TCCGTATTTATTGGGAACTACTCC 57.834 41.667 0.00 0.00 44.54 3.85
2376 3024 2.370849 GGAACTACTCCCTTGGTTCACA 59.629 50.000 0.00 0.00 39.55 3.58
2377 3025 3.181448 GGAACTACTCCCTTGGTTCACAA 60.181 47.826 0.00 0.00 39.55 3.33
2379 3027 4.724279 ACTACTCCCTTGGTTCACAAAT 57.276 40.909 0.00 0.00 38.91 2.32
2380 3028 5.836024 ACTACTCCCTTGGTTCACAAATA 57.164 39.130 0.00 0.00 38.91 1.40
2381 3029 6.388619 ACTACTCCCTTGGTTCACAAATAT 57.611 37.500 0.00 0.00 38.91 1.28
2382 3030 7.504926 ACTACTCCCTTGGTTCACAAATATA 57.495 36.000 0.00 0.00 38.91 0.86
2384 3032 8.047310 ACTACTCCCTTGGTTCACAAATATAAG 58.953 37.037 0.00 0.00 38.91 1.73
2385 3033 7.027874 ACTCCCTTGGTTCACAAATATAAGA 57.972 36.000 0.00 0.00 38.91 2.10
2386 3034 7.643123 ACTCCCTTGGTTCACAAATATAAGAT 58.357 34.615 0.00 0.00 38.91 2.40
2387 3035 7.557719 ACTCCCTTGGTTCACAAATATAAGATG 59.442 37.037 0.00 0.00 38.91 2.90
2390 3038 8.571336 CCCTTGGTTCACAAATATAAGATGATC 58.429 37.037 0.00 0.00 38.91 2.92
2391 3039 9.347240 CCTTGGTTCACAAATATAAGATGATCT 57.653 33.333 0.00 0.00 38.91 2.75
2430 3078 9.909644 AGTCGGATGTATATAGACATGTTTTAC 57.090 33.333 17.40 8.33 40.18 2.01
2455 3103 4.843728 TGTTTGTTCACTCCTTTCAGTCT 58.156 39.130 0.00 0.00 0.00 3.24
2456 3104 5.984725 TGTTTGTTCACTCCTTTCAGTCTA 58.015 37.500 0.00 0.00 0.00 2.59
2741 3432 1.075601 AATGCTGACAGAAGGGGGAA 58.924 50.000 6.65 0.00 0.00 3.97
2756 3447 2.820197 GGGGGAAAAACTAACAGCTCAG 59.180 50.000 0.00 0.00 0.00 3.35
2793 3484 6.126507 TGGAAGCATAATTTACATGAGGAGGA 60.127 38.462 0.00 0.00 0.00 3.71
2794 3485 6.944862 GGAAGCATAATTTACATGAGGAGGAT 59.055 38.462 0.00 0.00 0.00 3.24
2804 3495 4.265073 ACATGAGGAGGATTAGTGCAAAC 58.735 43.478 0.00 0.00 0.00 2.93
2812 3503 5.488341 GAGGATTAGTGCAAACTGGTAGAA 58.512 41.667 0.00 0.00 0.00 2.10
3044 3895 3.306019 CCAAACAAAAGCCCCATGAGTAC 60.306 47.826 0.00 0.00 0.00 2.73
3047 3903 1.474077 CAAAAGCCCCATGAGTACAGC 59.526 52.381 0.00 0.00 0.00 4.40
3176 4037 3.551846 ACTGGAATGGTCGAAACTTGTT 58.448 40.909 0.00 0.00 0.00 2.83
3515 4382 4.464244 TCACAGGGTGTCTTCTCTATCAAG 59.536 45.833 0.00 0.00 34.79 3.02
3626 4493 8.672823 TCAATCTTCTTGGATATGTGAGATTG 57.327 34.615 13.97 13.97 40.51 2.67
3717 4645 8.793592 AGAAGTTATAACACAACCTCCAATTTC 58.206 33.333 17.65 7.61 0.00 2.17
3733 4661 0.680618 TTTCCAAACAGGCATGGCAG 59.319 50.000 22.64 16.46 36.62 4.85
4211 5143 3.600388 GAAATGATTCTGACCACTCCGT 58.400 45.455 0.00 0.00 32.57 4.69
4316 5248 0.948623 CATCCACGCGTTTCTCCACA 60.949 55.000 10.22 0.00 0.00 4.17
4317 5249 0.949105 ATCCACGCGTTTCTCCACAC 60.949 55.000 10.22 0.00 0.00 3.82
4324 5256 1.502231 CGTTTCTCCACACCACTGAG 58.498 55.000 0.00 0.00 0.00 3.35
4346 5278 3.379688 GCCATCTTCTTCCTTGTGAATCC 59.620 47.826 0.00 0.00 31.06 3.01
4381 5313 6.899393 TTCACAATGAAGCAAACCTCTAAT 57.101 33.333 0.00 0.00 31.83 1.73
4382 5314 6.258230 TCACAATGAAGCAAACCTCTAATG 57.742 37.500 0.00 0.00 0.00 1.90
4390 5322 1.737793 CAAACCTCTAATGTGACGGGC 59.262 52.381 0.00 0.00 0.00 6.13
4419 5351 0.962855 TGTCAGTCTGAGCCTCTCGG 60.963 60.000 1.75 0.00 38.15 4.63
4468 5400 2.154389 CGGTGTTCTTGTACGTAGTTGC 59.846 50.000 0.00 0.00 37.78 4.17
4509 5441 3.805267 GCCTGGAGCGATGTGAAG 58.195 61.111 0.00 0.00 0.00 3.02
4523 5455 0.464916 GTGAAGGACGGTGGTTTGGT 60.465 55.000 0.00 0.00 0.00 3.67
4562 5494 3.837570 AAAGGGCGACGGGGTTCAC 62.838 63.158 0.00 0.00 0.00 3.18
4568 5500 2.879907 GACGGGGTTCACGATCGA 59.120 61.111 24.34 0.00 34.93 3.59
4629 5561 0.958091 CCACCAAACGAAGCAATCCA 59.042 50.000 0.00 0.00 0.00 3.41
4632 5564 2.811431 CACCAAACGAAGCAATCCACTA 59.189 45.455 0.00 0.00 0.00 2.74
4701 5633 2.267006 CGTCCATGGCTGCTGTCT 59.733 61.111 6.96 0.00 0.00 3.41
4709 5641 1.253593 TGGCTGCTGTCTCATCGAGT 61.254 55.000 0.00 0.00 0.00 4.18
4713 5645 2.528125 CTGCTGTCTCATCGAGTTCAG 58.472 52.381 0.00 11.51 36.61 3.02
4758 5690 4.796830 CAGCAATAGTTCATGCAACATGAC 59.203 41.667 9.69 6.04 44.95 3.06
4765 5697 9.836864 AATAGTTCATGCAACATGACTTCTATA 57.163 29.630 9.69 0.00 37.48 1.31
4799 5731 3.779759 TGACCTTTGTTGCAACACAATC 58.220 40.909 31.17 23.56 41.27 2.67
4804 5736 4.446385 CCTTTGTTGCAACACAATCTGATG 59.554 41.667 31.17 15.96 41.27 3.07
4885 5817 0.027455 CTGCAGACGTTTTTGCACGA 59.973 50.000 8.42 0.79 44.72 4.35
4898 5830 6.031417 CGTTTTTGCACGATCTCTATTTCAAC 59.969 38.462 0.00 0.00 43.15 3.18
4899 5831 6.552859 TTTTGCACGATCTCTATTTCAACA 57.447 33.333 0.00 0.00 0.00 3.33
4964 5896 5.772672 ACCTATGCCACAAATGTTTCTGTAA 59.227 36.000 0.00 0.00 0.00 2.41
4989 5921 6.016527 ACATTAGCTCTATTGCAATGGTGATG 60.017 38.462 23.81 22.12 36.61 3.07
4994 5926 0.457035 ATTGCAATGGTGATGGACGC 59.543 50.000 12.09 0.00 0.00 5.19
4997 5929 1.996786 GCAATGGTGATGGACGCTGG 61.997 60.000 0.00 0.00 0.00 4.85
5014 5946 0.739462 TGGTCAGCCGCTTGATAACG 60.739 55.000 0.00 0.00 37.67 3.18
5024 5956 4.795268 CCGCTTGATAACGCTAGATCTAA 58.205 43.478 3.57 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.901827 TGACTGGTGTGCGGATGTAT 59.098 50.000 0.00 0.00 0.00 2.29
11 12 0.729116 GATTGACTGGTGTGCGGATG 59.271 55.000 0.00 0.00 0.00 3.51
18 19 5.476945 GGGAAATTGTAAGATTGACTGGTGT 59.523 40.000 0.00 0.00 0.00 4.16
40 41 8.801882 TGACAAAGGTAGATTTATTGTTAGGG 57.198 34.615 0.00 0.00 34.59 3.53
63 64 2.684943 TGGGGCGGTCTTAAGATATGA 58.315 47.619 8.75 0.00 0.00 2.15
77 78 1.876714 CACGAGTACGATTGGGGCG 60.877 63.158 0.00 0.00 42.66 6.13
82 83 6.560433 GCATGATTTACTCACGAGTACGATTG 60.560 42.308 6.41 3.56 43.02 2.67
91 92 5.700832 ACTTTTGAGCATGATTTACTCACGA 59.299 36.000 0.00 0.00 40.03 4.35
93 94 8.034058 ACTACTTTTGAGCATGATTTACTCAC 57.966 34.615 0.00 0.00 40.03 3.51
118 119 9.125026 TGGGGTTTGTTAAACTTAACGTTAATA 57.875 29.630 20.39 8.29 44.52 0.98
125 126 4.337836 TCGGTGGGGTTTGTTAAACTTAAC 59.662 41.667 5.56 5.56 42.51 2.01
133 134 1.138568 TCCTTCGGTGGGGTTTGTTA 58.861 50.000 0.00 0.00 0.00 2.41
147 148 3.130516 TCACCATCAGTATCGTGTCCTTC 59.869 47.826 0.00 0.00 0.00 3.46
148 149 3.096852 TCACCATCAGTATCGTGTCCTT 58.903 45.455 0.00 0.00 0.00 3.36
223 224 5.104444 TCCAGTAGACTAAGACGAGAAGGAT 60.104 44.000 0.00 0.00 0.00 3.24
224 225 4.224594 TCCAGTAGACTAAGACGAGAAGGA 59.775 45.833 0.00 0.00 0.00 3.36
225 226 4.515361 TCCAGTAGACTAAGACGAGAAGG 58.485 47.826 0.00 0.00 0.00 3.46
227 228 6.657966 TGATTTCCAGTAGACTAAGACGAGAA 59.342 38.462 0.00 0.00 0.00 2.87
228 229 6.178324 TGATTTCCAGTAGACTAAGACGAGA 58.822 40.000 0.00 0.00 0.00 4.04
229 230 6.438259 TGATTTCCAGTAGACTAAGACGAG 57.562 41.667 0.00 0.00 0.00 4.18
230 231 6.438259 CTGATTTCCAGTAGACTAAGACGA 57.562 41.667 0.00 0.00 38.10 4.20
301 315 0.986527 TCACATGTCTCCAGCACCAT 59.013 50.000 0.00 0.00 0.00 3.55
316 330 5.670485 AGTCAAGTGTTTGTCTGTATCACA 58.330 37.500 0.00 0.00 32.60 3.58
319 333 4.386049 CCGAGTCAAGTGTTTGTCTGTATC 59.614 45.833 0.00 0.00 33.72 2.24
323 341 2.821546 TCCGAGTCAAGTGTTTGTCTG 58.178 47.619 0.00 0.00 33.72 3.51
331 349 2.915463 GTGACGTATTCCGAGTCAAGTG 59.085 50.000 0.00 0.00 45.04 3.16
342 360 4.579270 GGCACTTAACTGTGACGTATTC 57.421 45.455 0.00 0.00 40.12 1.75
425 445 1.684734 GGGCGGAGGGAGTACTCAA 60.685 63.158 23.91 0.00 39.27 3.02
437 457 0.108041 GACAAGTAATTCGGGGCGGA 60.108 55.000 0.00 0.00 0.00 5.54
492 512 8.760980 ATTTGTCGGGGAAATGAATTTATCTA 57.239 30.769 0.00 0.00 0.00 1.98
518 538 0.685131 TGCTCCCTCCGTCCGAAATA 60.685 55.000 0.00 0.00 0.00 1.40
579 599 5.799827 ATCTCCCGTTTTCATTTTTGGAA 57.200 34.783 0.00 0.00 0.00 3.53
595 615 5.359194 TTGTGAAGTCTCCATTATCTCCC 57.641 43.478 0.00 0.00 0.00 4.30
661 754 6.183360 ACCAAAGGATTCTTATGCATTTCTCG 60.183 38.462 3.54 0.00 32.01 4.04
695 788 9.251792 CGTGTTTGGCACTAATATAGTACATAA 57.748 33.333 0.00 0.00 45.57 1.90
697 790 6.704493 CCGTGTTTGGCACTAATATAGTACAT 59.296 38.462 0.00 0.00 45.57 2.29
698 791 6.044046 CCGTGTTTGGCACTAATATAGTACA 58.956 40.000 0.00 0.00 45.57 2.90
699 792 5.464389 CCCGTGTTTGGCACTAATATAGTAC 59.536 44.000 0.00 0.00 45.57 2.73
700 793 5.603596 CCCGTGTTTGGCACTAATATAGTA 58.396 41.667 0.00 0.00 45.57 1.82
701 794 4.448210 CCCGTGTTTGGCACTAATATAGT 58.552 43.478 0.00 0.00 45.57 2.12
721 959 7.280428 GGAATTTGTAGAGAGTTTAGTTAGCCC 59.720 40.741 0.00 0.00 0.00 5.19
756 994 5.048083 TGCTGCGGAATTTGTAGAGATTTTT 60.048 36.000 0.00 0.00 0.00 1.94
757 995 4.458989 TGCTGCGGAATTTGTAGAGATTTT 59.541 37.500 0.00 0.00 0.00 1.82
758 996 4.009675 TGCTGCGGAATTTGTAGAGATTT 58.990 39.130 0.00 0.00 0.00 2.17
759 997 3.609853 TGCTGCGGAATTTGTAGAGATT 58.390 40.909 0.00 0.00 0.00 2.40
760 998 3.266510 TGCTGCGGAATTTGTAGAGAT 57.733 42.857 0.00 0.00 0.00 2.75
761 999 2.742053 GTTGCTGCGGAATTTGTAGAGA 59.258 45.455 0.00 0.00 0.00 3.10
762 1000 2.483877 TGTTGCTGCGGAATTTGTAGAG 59.516 45.455 0.00 0.00 0.00 2.43
763 1001 2.499197 TGTTGCTGCGGAATTTGTAGA 58.501 42.857 0.00 0.00 0.00 2.59
764 1002 2.979813 GTTGTTGCTGCGGAATTTGTAG 59.020 45.455 0.00 0.00 0.00 2.74
765 1003 2.359214 TGTTGTTGCTGCGGAATTTGTA 59.641 40.909 0.00 0.00 0.00 2.41
766 1004 1.135915 TGTTGTTGCTGCGGAATTTGT 59.864 42.857 0.00 0.00 0.00 2.83
767 1005 1.850377 TGTTGTTGCTGCGGAATTTG 58.150 45.000 0.00 0.00 0.00 2.32
768 1006 2.593346 TTGTTGTTGCTGCGGAATTT 57.407 40.000 0.00 0.00 0.00 1.82
769 1007 2.593346 TTTGTTGTTGCTGCGGAATT 57.407 40.000 0.00 0.00 0.00 2.17
770 1008 2.100584 TCTTTTGTTGTTGCTGCGGAAT 59.899 40.909 0.00 0.00 0.00 3.01
771 1009 1.474478 TCTTTTGTTGTTGCTGCGGAA 59.526 42.857 0.00 0.00 0.00 4.30
778 1016 5.687285 CCATACAGAGTTCTTTTGTTGTTGC 59.313 40.000 0.00 0.00 0.00 4.17
810 1054 9.974980 GTCAAAACCTAACTTTGGAATCATAAA 57.025 29.630 0.00 0.00 35.03 1.40
816 1060 7.996644 TGACTAGTCAAAACCTAACTTTGGAAT 59.003 33.333 23.24 0.00 36.53 3.01
863 1429 2.391678 CTTATTTCTGGCCAGCCCATT 58.608 47.619 28.91 12.63 44.33 3.16
864 1430 2.031097 GCTTATTTCTGGCCAGCCCAT 61.031 52.381 28.91 19.93 44.33 4.00
899 1474 7.086685 AGTCACCTGGAAAAAGGAATAGTAA 57.913 36.000 0.00 0.00 40.02 2.24
916 1491 4.446371 GCATACTTATCAGCAAGTCACCT 58.554 43.478 0.00 0.00 39.45 4.00
1219 1808 4.373116 GTTGGCGACGCTCTGGGA 62.373 66.667 20.77 0.00 0.00 4.37
1273 1862 1.306654 TTCCCCCGTAGCACTCCAT 60.307 57.895 0.00 0.00 0.00 3.41
1289 1878 1.270147 ACTCGGCATAATAGCGGGTTC 60.270 52.381 0.00 0.00 35.76 3.62
1290 1879 0.756903 ACTCGGCATAATAGCGGGTT 59.243 50.000 0.00 0.00 35.76 4.11
1291 1880 1.624336 TACTCGGCATAATAGCGGGT 58.376 50.000 0.00 0.00 35.76 5.28
1294 1883 6.372185 GGATACTATACTCGGCATAATAGCG 58.628 44.000 0.00 0.00 34.64 4.26
1353 1942 7.672660 TCATCTCCCGTACTATTGGTGTATATT 59.327 37.037 0.00 0.00 0.00 1.28
1585 2183 2.112297 GCAGTCCCCGGTTGACAA 59.888 61.111 19.90 0.00 35.15 3.18
1762 2372 1.607148 AGGCTTACTTTTGTGTTCGCC 59.393 47.619 0.00 0.00 34.29 5.54
1763 2373 4.680171 ATAGGCTTACTTTTGTGTTCGC 57.320 40.909 0.00 0.00 0.00 4.70
1773 2383 8.322091 AGAATCAACAAGTGTATAGGCTTACTT 58.678 33.333 0.00 0.00 33.94 2.24
1787 2397 7.168219 TGGCATAACTAGAAGAATCAACAAGT 58.832 34.615 0.00 0.00 0.00 3.16
1825 2439 7.561722 TGTTAGCTCTGAATTAGTCCTCTACAT 59.438 37.037 0.00 0.00 0.00 2.29
1832 2446 5.363939 AGCATGTTAGCTCTGAATTAGTCC 58.636 41.667 0.00 0.00 42.18 3.85
1833 2447 6.238320 CCAAGCATGTTAGCTCTGAATTAGTC 60.238 42.308 0.00 0.00 45.89 2.59
1840 2454 3.076621 CAACCAAGCATGTTAGCTCTGA 58.923 45.455 0.00 0.00 45.89 3.27
1842 2456 2.440409 CCAACCAAGCATGTTAGCTCT 58.560 47.619 0.00 0.00 45.89 4.09
1843 2457 1.135286 GCCAACCAAGCATGTTAGCTC 60.135 52.381 0.00 0.00 45.89 4.09
1845 2459 0.602562 TGCCAACCAAGCATGTTAGC 59.397 50.000 0.00 0.00 34.69 3.09
1852 2466 1.105457 GATAGCATGCCAACCAAGCA 58.895 50.000 15.66 0.00 45.94 3.91
1853 2467 1.105457 TGATAGCATGCCAACCAAGC 58.895 50.000 15.66 0.00 38.39 4.01
1854 2468 3.364889 CATGATAGCATGCCAACCAAG 57.635 47.619 15.66 1.03 44.76 3.61
1864 2478 7.991460 CCCTGATATGAACATACATGATAGCAT 59.009 37.037 0.00 0.00 34.29 3.79
1867 2481 6.478016 CGCCCTGATATGAACATACATGATAG 59.522 42.308 0.00 0.00 0.00 2.08
1872 2486 3.244526 TGCGCCCTGATATGAACATACAT 60.245 43.478 4.18 0.00 0.00 2.29
1874 2488 2.766313 TGCGCCCTGATATGAACATAC 58.234 47.619 4.18 0.00 0.00 2.39
1877 2491 1.140652 TCATGCGCCCTGATATGAACA 59.859 47.619 4.18 0.00 0.00 3.18
1915 2529 4.743644 CGCTACAGGTACTAAAACTATGGC 59.256 45.833 0.00 0.00 36.02 4.40
1933 2547 1.063166 GAAATGCTGCTGCCGCTAC 59.937 57.895 16.81 2.83 38.71 3.58
1938 2552 2.738013 AAAAGAGAAATGCTGCTGCC 57.262 45.000 13.47 0.00 38.71 4.85
1970 2584 1.487482 TTGCTTTGTGAGACGACGAG 58.513 50.000 0.00 0.00 0.00 4.18
1977 2591 5.885912 AGTACCTTTTCTTTGCTTTGTGAGA 59.114 36.000 0.00 0.00 0.00 3.27
2046 2660 8.080083 CTGCAAGTAAAAATGCTCTTGAAATT 57.920 30.769 7.75 0.00 42.97 1.82
2047 2661 7.647907 CTGCAAGTAAAAATGCTCTTGAAAT 57.352 32.000 7.75 0.00 42.97 2.17
2068 2682 8.903723 GTCGTATCTAACACTATGATTAACTGC 58.096 37.037 0.00 0.00 0.00 4.40
2078 2692 8.201554 TCACGTTTAGTCGTATCTAACACTAT 57.798 34.615 0.00 0.00 42.27 2.12
2081 2695 5.736358 CCTCACGTTTAGTCGTATCTAACAC 59.264 44.000 0.00 0.00 42.27 3.32
2082 2696 5.163723 CCCTCACGTTTAGTCGTATCTAACA 60.164 44.000 0.00 0.00 42.27 2.41
2083 2697 5.065218 TCCCTCACGTTTAGTCGTATCTAAC 59.935 44.000 0.00 0.00 42.27 2.34
2084 2698 5.185454 TCCCTCACGTTTAGTCGTATCTAA 58.815 41.667 0.00 0.00 42.27 2.10
2085 2699 4.769688 TCCCTCACGTTTAGTCGTATCTA 58.230 43.478 0.00 0.00 42.27 1.98
2086 2700 3.614092 TCCCTCACGTTTAGTCGTATCT 58.386 45.455 0.00 0.00 42.27 1.98
2087 2701 4.564940 ATCCCTCACGTTTAGTCGTATC 57.435 45.455 0.00 0.00 42.27 2.24
2088 2702 4.996788 AATCCCTCACGTTTAGTCGTAT 57.003 40.909 0.00 0.00 42.27 3.06
2091 2705 2.928116 GGAAATCCCTCACGTTTAGTCG 59.072 50.000 0.00 0.00 0.00 4.18
2128 2750 8.924303 TGTAATCTCAGCAGTGTACCTAAATAT 58.076 33.333 0.00 0.00 0.00 1.28
2129 2751 8.301252 TGTAATCTCAGCAGTGTACCTAAATA 57.699 34.615 0.00 0.00 0.00 1.40
2130 2752 7.182817 TGTAATCTCAGCAGTGTACCTAAAT 57.817 36.000 0.00 0.00 0.00 1.40
2132 2754 6.351033 CCTTGTAATCTCAGCAGTGTACCTAA 60.351 42.308 0.00 0.00 0.00 2.69
2133 2755 5.127194 CCTTGTAATCTCAGCAGTGTACCTA 59.873 44.000 0.00 0.00 0.00 3.08
2138 2760 4.223700 TGATCCTTGTAATCTCAGCAGTGT 59.776 41.667 0.00 0.00 0.00 3.55
2139 2761 4.763073 TGATCCTTGTAATCTCAGCAGTG 58.237 43.478 0.00 0.00 0.00 3.66
2141 2763 5.523188 GTCTTGATCCTTGTAATCTCAGCAG 59.477 44.000 0.00 0.00 0.00 4.24
2144 2766 5.655488 ACGTCTTGATCCTTGTAATCTCAG 58.345 41.667 0.00 0.00 0.00 3.35
2149 2771 6.037786 TGAGAACGTCTTGATCCTTGTAAT 57.962 37.500 0.00 0.00 0.00 1.89
2173 2795 4.849235 AGTTCTTCCTCTCCTTCCAAATCT 59.151 41.667 0.00 0.00 0.00 2.40
2210 2832 3.690460 ACACCATGAACTCTGAATTCCC 58.310 45.455 2.27 0.00 0.00 3.97
2211 2833 5.241506 TCAAACACCATGAACTCTGAATTCC 59.758 40.000 2.27 0.00 0.00 3.01
2236 2858 3.326588 TGGCCTCTAGTAGCTGTTCAAAA 59.673 43.478 3.32 0.00 0.00 2.44
2306 2928 8.258708 AGCTTACTAATTTACCTTGTAGACAGG 58.741 37.037 0.00 0.00 0.00 4.00
2356 3004 3.764237 TGTGAACCAAGGGAGTAGTTC 57.236 47.619 0.00 0.00 39.22 3.01
2357 3005 4.513406 TTTGTGAACCAAGGGAGTAGTT 57.487 40.909 0.00 0.00 33.75 2.24
2359 3007 8.265055 TCTTATATTTGTGAACCAAGGGAGTAG 58.735 37.037 0.00 0.00 33.75 2.57
2361 3009 7.027874 TCTTATATTTGTGAACCAAGGGAGT 57.972 36.000 0.00 0.00 33.75 3.85
2363 3011 7.638444 TCATCTTATATTTGTGAACCAAGGGA 58.362 34.615 0.00 0.00 33.75 4.20
2365 3013 9.347240 AGATCATCTTATATTTGTGAACCAAGG 57.653 33.333 0.00 0.00 33.75 3.61
2398 3046 7.576861 TGTCTATATACATCCGACTCACAAA 57.423 36.000 0.00 0.00 0.00 2.83
2400 3048 6.715264 ACATGTCTATATACATCCGACTCACA 59.285 38.462 0.94 0.00 38.01 3.58
2401 3049 7.147143 ACATGTCTATATACATCCGACTCAC 57.853 40.000 0.94 0.00 38.01 3.51
2402 3050 7.761038 AACATGTCTATATACATCCGACTCA 57.239 36.000 0.00 0.00 38.01 3.41
2404 3052 9.909644 GTAAAACATGTCTATATACATCCGACT 57.090 33.333 0.00 0.00 38.01 4.18
2405 3053 9.909644 AGTAAAACATGTCTATATACATCCGAC 57.090 33.333 0.00 0.00 38.01 4.79
2419 3067 9.382244 GAGTGAACAAACATAGTAAAACATGTC 57.618 33.333 0.00 0.00 34.32 3.06
2420 3068 8.349983 GGAGTGAACAAACATAGTAAAACATGT 58.650 33.333 0.00 0.00 36.96 3.21
2430 3078 6.708054 AGACTGAAAGGAGTGAACAAACATAG 59.292 38.462 0.00 0.00 39.30 2.23
2432 3080 5.440610 AGACTGAAAGGAGTGAACAAACAT 58.559 37.500 0.00 0.00 39.30 2.71
2441 3089 8.687242 TGAACTACATATAGACTGAAAGGAGTG 58.313 37.037 0.00 0.00 32.32 3.51
2495 3143 6.712547 CCCTCCCTTCACAAATATAAGATGTC 59.287 42.308 0.00 0.00 0.00 3.06
2728 3419 4.466827 TGTTAGTTTTTCCCCCTTCTGTC 58.533 43.478 0.00 0.00 0.00 3.51
2741 3432 3.503748 GGTCATGCTGAGCTGTTAGTTTT 59.496 43.478 5.83 0.00 41.34 2.43
2756 3447 0.394762 TGCTTCCATCCTGGTCATGC 60.395 55.000 0.00 0.00 39.03 4.06
2793 3484 5.242795 AGGTTCTACCAGTTTGCACTAAT 57.757 39.130 0.00 0.00 41.95 1.73
2794 3485 4.699925 AGGTTCTACCAGTTTGCACTAA 57.300 40.909 0.00 0.00 41.95 2.24
2804 3495 8.842358 TGTATTCAAAAGTTAGGTTCTACCAG 57.158 34.615 0.00 0.00 41.95 4.00
2832 3525 1.546029 GTAAGCTTGCCCTGGGAAAAG 59.454 52.381 19.27 19.21 0.00 2.27
3044 3895 4.202264 CCAGTTACCTAGGGAATACAGCTG 60.202 50.000 10.41 13.48 0.00 4.24
3047 3903 3.071167 GGCCAGTTACCTAGGGAATACAG 59.929 52.174 10.41 0.68 0.00 2.74
3176 4037 3.987868 GTGCTATTCCTTCGATTATCGCA 59.012 43.478 10.02 0.00 40.21 5.10
3515 4382 0.784778 CAAAGCTGAAGACGTCGGAC 59.215 55.000 10.46 6.34 34.07 4.79
3626 4493 9.573133 AAAATGCATGCTTAAGTTTCTGTATAC 57.427 29.630 20.33 0.00 0.00 1.47
3717 4645 1.255882 TAACTGCCATGCCTGTTTGG 58.744 50.000 4.27 0.00 39.35 3.28
3733 4661 2.158608 CCACCTTCCCTCATCCCATAAC 60.159 54.545 0.00 0.00 0.00 1.89
4111 5043 5.368816 GGACTATACACCAATTAGGAAGGGT 59.631 44.000 1.54 0.00 41.22 4.34
4211 5143 1.379443 ACACCCGCACCTAGATCGA 60.379 57.895 0.00 0.00 0.00 3.59
4235 5167 3.054503 ACGTCGCGTGCTAGAGGT 61.055 61.111 5.77 0.00 39.18 3.85
4247 5179 3.478394 CACATGGGACGCACGTCG 61.478 66.667 16.19 5.78 45.41 5.12
4316 5248 1.280421 GGAAGAAGATGGCTCAGTGGT 59.720 52.381 0.00 0.00 0.00 4.16
4317 5249 1.558756 AGGAAGAAGATGGCTCAGTGG 59.441 52.381 0.00 0.00 0.00 4.00
4324 5256 3.379688 GGATTCACAAGGAAGAAGATGGC 59.620 47.826 0.00 0.00 39.30 4.40
4346 5278 6.152379 GCTTCATTGTGAAAGAACTTAAGGG 58.848 40.000 7.53 0.00 35.73 3.95
4381 5313 0.820074 AAACAAATCCGCCCGTCACA 60.820 50.000 0.00 0.00 0.00 3.58
4382 5314 0.386731 CAAACAAATCCGCCCGTCAC 60.387 55.000 0.00 0.00 0.00 3.67
4390 5322 3.364366 GCTCAGACTGACAAACAAATCCG 60.364 47.826 0.00 0.00 0.00 4.18
4419 5351 0.324091 TCACGGGAGTAAGGGGAGAC 60.324 60.000 0.00 0.00 44.67 3.36
4468 5400 4.083581 CCAAAATTAGTGCTTGGTCTCG 57.916 45.455 0.00 0.00 35.80 4.04
4507 5439 1.826487 GCACCAAACCACCGTCCTT 60.826 57.895 0.00 0.00 0.00 3.36
4509 5441 3.292159 GGCACCAAACCACCGTCC 61.292 66.667 0.00 0.00 0.00 4.79
4697 5629 1.067565 GTGGCTGAACTCGATGAGACA 60.068 52.381 0.00 0.47 33.32 3.41
4699 5631 1.256812 TGTGGCTGAACTCGATGAGA 58.743 50.000 0.00 0.00 33.32 3.27
4701 5633 1.608025 GGTTGTGGCTGAACTCGATGA 60.608 52.381 0.00 0.00 0.00 2.92
4709 5641 2.280524 CCGACGGTTGTGGCTGAA 60.281 61.111 5.48 0.00 0.00 3.02
4765 5697 0.037877 AAGGTCATGCTGCTTCTGCT 59.962 50.000 0.00 0.00 40.48 4.24
4775 5707 1.860326 GTGTTGCAACAAAGGTCATGC 59.140 47.619 32.61 13.92 41.21 4.06
4799 5731 5.800438 CAGAGATCATGTTGCAAAACATCAG 59.200 40.000 0.00 0.00 41.12 2.90
4832 5764 6.127394 TGCAACATGGTCATAGTGCATAATTT 60.127 34.615 13.37 0.00 35.88 1.82
4878 5810 6.741992 AATGTTGAAATAGAGATCGTGCAA 57.258 33.333 0.00 0.00 0.00 4.08
4905 5837 8.519526 AGAAACATTTGCAACGGAGATTATTTA 58.480 29.630 0.00 0.00 0.00 1.40
4907 5839 6.808212 CAGAAACATTTGCAACGGAGATTATT 59.192 34.615 0.00 0.00 0.00 1.40
4964 5896 5.439721 TCACCATTGCAATAGAGCTAATGT 58.560 37.500 12.53 0.00 34.33 2.71
4994 5926 1.009829 GTTATCAAGCGGCTGACCAG 58.990 55.000 1.81 0.00 34.57 4.00
4997 5929 1.084370 AGCGTTATCAAGCGGCTGAC 61.084 55.000 1.81 0.00 38.61 3.51


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

AutoCloner maintained by Alex Coulton.