Multiple sequence alignment - TraesCS7A01G434100

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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 TraesCS7A01G434100 chr7A 100.000 5571 0 0 1 5571 627239219 627233649 0.000000e+00 10288.0
1 TraesCS7A01G434100 chr7A 93.264 861 57 1 3700 4559 627015210 627014350 0.000000e+00 1267.0
2 TraesCS7A01G434100 chr7A 93.148 861 58 1 3700 4559 627052886 627052026 0.000000e+00 1262.0
3 TraesCS7A01G434100 chr7A 93.162 585 32 6 4260 4843 628386923 628386346 0.000000e+00 852.0
4 TraesCS7A01G434100 chr7A 76.039 722 153 15 2677 3391 627010059 627009351 1.910000e-94 357.0
5 TraesCS7A01G434100 chr7A 91.020 245 22 0 825 1069 627165613 627165369 1.160000e-86 331.0
6 TraesCS7A01G434100 chr7A 90.283 247 21 2 825 1068 627011344 627011098 2.500000e-83 320.0
7 TraesCS7A01G434100 chr7A 90.283 247 21 2 825 1068 627049113 627048867 2.500000e-83 320.0
8 TraesCS7A01G434100 chr7A 91.102 236 21 0 833 1068 628363561 628363326 2.500000e-83 320.0
9 TraesCS7A01G434100 chr7A 88.000 225 24 3 624 847 627165853 627165631 4.280000e-66 263.0
10 TraesCS7A01G434100 chr7A 97.727 132 3 0 2276 2407 310454802 310454933 1.560000e-55 228.0
11 TraesCS7A01G434100 chr7A 100.000 28 0 0 5157 5184 580504521 580504494 1.000000e-02 52.8
12 TraesCS7A01G434100 chr1B 91.734 2589 152 34 2404 4951 133127342 133124775 0.000000e+00 3539.0
13 TraesCS7A01G434100 chr1B 92.183 1484 70 13 825 2276 133128808 133127339 0.000000e+00 2056.0
14 TraesCS7A01G434100 chr1B 81.484 1307 192 35 2742 4029 133113911 133112636 0.000000e+00 1027.0
15 TraesCS7A01G434100 chr1B 80.493 1338 216 29 2696 4021 426499555 426498251 0.000000e+00 983.0
16 TraesCS7A01G434100 chr1B 93.425 365 18 3 485 847 133129186 133128826 2.280000e-148 536.0
17 TraesCS7A01G434100 chr1B 99.083 218 2 0 5354 5571 368674658 368674441 5.230000e-105 392.0
18 TraesCS7A01G434100 chr1B 98.624 218 3 0 5354 5571 485306335 485306552 2.430000e-103 387.0
19 TraesCS7A01G434100 chr1B 88.254 315 24 5 5207 5514 368674847 368674539 1.140000e-96 364.0
20 TraesCS7A01G434100 chr1B 88.387 310 24 6 5208 5514 485306154 485306454 4.100000e-96 363.0
21 TraesCS7A01G434100 chr1B 89.767 215 21 1 633 847 426502603 426502390 1.980000e-69 274.0
22 TraesCS7A01G434100 chr1B 96.970 99 2 1 4992 5089 133124615 133124517 1.240000e-36 165.0
23 TraesCS7A01G434100 chr7B 94.510 1603 80 7 2404 4003 588881271 588879674 0.000000e+00 2466.0
24 TraesCS7A01G434100 chr7B 87.584 1490 68 28 830 2276 588882683 588881268 0.000000e+00 1618.0
25 TraesCS7A01G434100 chr7B 89.048 767 44 18 4216 4951 588879553 588878796 0.000000e+00 915.0
26 TraesCS7A01G434100 chr7B 95.775 355 10 3 485 837 588883066 588882715 8.100000e-158 568.0
27 TraesCS7A01G434100 chr7B 92.913 254 18 0 825 1078 588869176 588868923 2.450000e-98 370.0
28 TraesCS7A01G434100 chr7B 91.262 206 17 1 642 847 588502363 588502159 4.250000e-71 279.0
29 TraesCS7A01G434100 chr7B 89.583 192 13 6 4657 4846 589919306 589919492 2.590000e-58 237.0
30 TraesCS7A01G434100 chr7B 96.970 99 2 1 4992 5089 588878638 588878540 1.240000e-36 165.0
31 TraesCS7A01G434100 chr7B 96.591 88 2 1 5003 5089 589919489 589919576 1.620000e-30 145.0
32 TraesCS7A01G434100 chr7B 97.222 36 1 0 5064 5099 588878514 588878479 1.680000e-05 62.1
33 TraesCS7A01G434100 chr7B 100.000 28 0 0 5157 5184 498300115 498300088 1.000000e-02 52.8
34 TraesCS7A01G434100 chr7B 100.000 28 0 0 5157 5184 537825692 537825665 1.000000e-02 52.8
35 TraesCS7A01G434100 chr2B 90.699 1602 127 17 3123 4712 127792235 127790644 0.000000e+00 2113.0
36 TraesCS7A01G434100 chr2B 89.519 1164 92 19 3744 4897 135511153 135512296 0.000000e+00 1447.0
37 TraesCS7A01G434100 chr2B 95.110 593 27 2 3224 3816 135510219 135510809 0.000000e+00 933.0
38 TraesCS7A01G434100 chr2B 94.198 293 14 1 545 837 182147906 182147617 1.420000e-120 444.0
39 TraesCS7A01G434100 chr2B 78.843 605 114 9 2675 3277 182141119 182140527 4.040000e-106 396.0
40 TraesCS7A01G434100 chr2B 98.165 218 4 0 5354 5571 652613483 652613700 1.130000e-101 381.0
41 TraesCS7A01G434100 chr2B 88.852 305 24 4 5213 5514 652613305 652613602 3.170000e-97 366.0
42 TraesCS7A01G434100 chr2B 93.939 99 2 3 4992 5089 135512381 135512476 4.500000e-31 147.0
43 TraesCS7A01G434100 chr2B 100.000 28 0 0 5157 5184 127790192 127790165 1.000000e-02 52.8
44 TraesCS7A01G434100 chr5D 90.166 1505 90 17 825 2276 289500938 289499439 0.000000e+00 1906.0
45 TraesCS7A01G434100 chr5D 89.611 1492 124 26 3318 4790 289498308 289496829 0.000000e+00 1868.0
46 TraesCS7A01G434100 chr5D 95.047 848 30 6 1 847 289501792 289500956 0.000000e+00 1323.0
47 TraesCS7A01G434100 chr5D 97.203 572 14 2 2404 2973 289499442 289498871 0.000000e+00 966.0
48 TraesCS7A01G434100 chr5D 80.029 1367 221 34 2677 4029 289423452 289422124 0.000000e+00 965.0
49 TraesCS7A01G434100 chr5D 91.916 668 39 9 4184 4851 289356720 289356068 0.000000e+00 920.0
50 TraesCS7A01G434100 chr5D 90.531 697 55 6 3320 4008 289357504 289356811 0.000000e+00 911.0
51 TraesCS7A01G434100 chr5D 94.667 300 16 0 3001 3300 289498874 289498575 3.040000e-127 466.0
52 TraesCS7A01G434100 chr5D 92.929 99 3 3 4992 5089 289355773 289355678 2.090000e-29 141.0
53 TraesCS7A01G434100 chr5D 97.222 36 1 0 5064 5099 289355652 289355617 1.680000e-05 62.1
54 TraesCS7A01G434100 chr5D 100.000 28 0 0 5157 5184 29876495 29876468 1.000000e-02 52.8
55 TraesCS7A01G434100 chr6A 88.831 573 49 5 4218 4790 107263265 107263822 0.000000e+00 689.0
56 TraesCS7A01G434100 chr6A 100.000 28 0 0 5157 5184 107264368 107264395 1.000000e-02 52.8
57 TraesCS7A01G434100 chr7D 92.055 365 12 9 485 847 545270707 545270358 1.080000e-136 497.0
58 TraesCS7A01G434100 chr7D 91.903 247 17 2 825 1068 545270340 545270094 5.340000e-90 342.0
59 TraesCS7A01G434100 chr7D 92.237 219 14 3 5354 5571 148237302 148237086 1.950000e-79 307.0
60 TraesCS7A01G434100 chr3A 99.083 218 2 0 5354 5571 79393892 79394109 5.230000e-105 392.0
61 TraesCS7A01G434100 chr3A 98.165 218 4 0 5354 5571 297927416 297927199 1.130000e-101 381.0
62 TraesCS7A01G434100 chr3A 98.174 219 3 1 5354 5571 646853718 646853500 1.130000e-101 381.0
63 TraesCS7A01G434100 chr3A 89.068 311 22 6 5208 5514 646853900 646853598 5.270000e-100 375.0
64 TraesCS7A01G434100 chr3A 88.852 305 24 4 5213 5514 297927594 297927297 3.170000e-97 366.0
65 TraesCS7A01G434100 chr3A 98.462 130 2 0 2279 2408 547195988 547196117 4.340000e-56 230.0
66 TraesCS7A01G434100 chr5B 93.421 228 7 8 5213 5438 661283739 661283518 1.160000e-86 331.0
67 TraesCS7A01G434100 chr5B 92.576 229 11 5 5210 5438 61657954 61658176 1.940000e-84 324.0
68 TraesCS7A01G434100 chr5B 91.667 228 9 8 5213 5438 661280246 661280027 1.950000e-79 307.0
69 TraesCS7A01G434100 chr5B 97.744 133 2 1 2276 2407 621230366 621230234 1.560000e-55 228.0
70 TraesCS7A01G434100 chr5B 96.350 137 4 1 2269 2405 82212165 82212300 2.020000e-54 224.0
71 TraesCS7A01G434100 chr3B 93.607 219 4 9 5213 5430 631050095 631050304 9.010000e-83 318.0
72 TraesCS7A01G434100 chr3B 91.518 224 10 4 5354 5571 28799780 28799560 3.260000e-77 300.0
73 TraesCS7A01G434100 chr3B 99.219 128 1 0 2279 2406 545071888 545072015 1.210000e-56 231.0
74 TraesCS7A01G434100 chrUn 92.793 222 9 2 5357 5571 36427484 36427705 1.170000e-81 315.0
75 TraesCS7A01G434100 chrUn 89.302 215 22 1 633 847 383291375 383291588 9.200000e-68 268.0
76 TraesCS7A01G434100 chr2A 98.485 132 2 0 2276 2407 517026918 517026787 3.360000e-57 233.0
77 TraesCS7A01G434100 chr1A 98.485 132 2 0 2276 2407 487800125 487799994 3.360000e-57 233.0
78 TraesCS7A01G434100 chr1A 97.727 132 3 0 2276 2407 415124955 415125086 1.560000e-55 228.0
79 TraesCS7A01G434100 chr4B 95.139 144 4 3 2271 2413 294107567 294107708 2.020000e-54 224.0
80 TraesCS7A01G434100 chr5A 100.000 28 0 0 5157 5184 30651876 30651849 1.000000e-02 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 TraesCS7A01G434100 chr7A 627233649 627239219 5570 True 10288.000000 10288 100.000000 1 5571 1 chr7A.!!$R2 5570
1 TraesCS7A01G434100 chr7A 628386346 628386923 577 True 852.000000 852 93.162000 4260 4843 1 chr7A.!!$R4 583
2 TraesCS7A01G434100 chr7A 627048867 627052886 4019 True 791.000000 1262 91.715500 825 4559 2 chr7A.!!$R6 3734
3 TraesCS7A01G434100 chr7A 627009351 627015210 5859 True 648.000000 1267 86.528667 825 4559 3 chr7A.!!$R5 3734
4 TraesCS7A01G434100 chr1B 133124517 133129186 4669 True 1574.000000 3539 93.578000 485 5089 4 chr1B.!!$R2 4604
5 TraesCS7A01G434100 chr1B 133112636 133113911 1275 True 1027.000000 1027 81.484000 2742 4029 1 chr1B.!!$R1 1287
6 TraesCS7A01G434100 chr1B 426498251 426502603 4352 True 628.500000 983 85.130000 633 4021 2 chr1B.!!$R4 3388
7 TraesCS7A01G434100 chr7B 588878479 588883066 4587 True 965.683333 2466 93.518167 485 5099 6 chr7B.!!$R5 4614
8 TraesCS7A01G434100 chr2B 127790165 127792235 2070 True 1082.900000 2113 95.349500 3123 5184 2 chr2B.!!$R3 2061
9 TraesCS7A01G434100 chr2B 135510219 135512476 2257 False 842.333333 1447 92.856000 3224 5089 3 chr2B.!!$F1 1865
10 TraesCS7A01G434100 chr2B 182140527 182141119 592 True 396.000000 396 78.843000 2675 3277 1 chr2B.!!$R1 602
11 TraesCS7A01G434100 chr5D 289496829 289501792 4963 True 1305.800000 1906 93.338800 1 4790 5 chr5D.!!$R4 4789
12 TraesCS7A01G434100 chr5D 289422124 289423452 1328 True 965.000000 965 80.029000 2677 4029 1 chr5D.!!$R2 1352
13 TraesCS7A01G434100 chr5D 289355617 289357504 1887 True 508.525000 920 93.149500 3320 5099 4 chr5D.!!$R3 1779
14 TraesCS7A01G434100 chr6A 107263265 107264395 1130 False 370.900000 689 94.415500 4218 5184 2 chr6A.!!$F1 966
15 TraesCS7A01G434100 chr7D 545270094 545270707 613 True 419.500000 497 91.979000 485 1068 2 chr7D.!!$R2 583
16 TraesCS7A01G434100 chr5B 661280027 661283739 3712 True 319.000000 331 92.544000 5213 5438 2 chr5B.!!$R2 225

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
251 252 1.135257 TGGTTTTCACGCACCTTGTTG 60.135 47.619 0.00 0.00 33.76 3.33 F
477 479 3.157087 AGGCCATGTGTGTCCTTAAAAG 58.843 45.455 5.01 0.00 0.00 2.27 F
1105 1148 0.094730 CGCCGCTTAGTAGTTGCAAC 59.905 55.000 22.17 22.17 0.00 4.17 F
1646 1731 1.544246 GCCACCGCTTGGTTTAGATTT 59.456 47.619 3.38 0.00 46.51 2.17 F
2200 2312 0.674581 TATGTCTGTGTGCTGCTGCC 60.675 55.000 13.47 5.20 38.71 4.85 F
3139 3256 0.806868 ACTTGATGAGCATGCAACCG 59.193 50.000 21.98 3.72 0.00 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1100 1143 1.313772 TAAGCGCCAAGAAAGTTGCA 58.686 45.0 2.29 0.0 0.00 4.08 R
2186 2298 1.651240 GGTATGGCAGCAGCACACAG 61.651 60.0 2.65 0.0 44.61 3.66 R
2200 2312 2.048444 AACATGAGCTGCAGGGTATG 57.952 50.0 17.12 8.8 31.20 2.39 R
3194 3311 0.107654 GCACCACCCTAGCAACCTAG 60.108 60.0 0.00 0.0 40.64 3.02 R
3730 4105 0.618458 GCTGATACCTGGTTCCCACA 59.382 55.0 3.84 0.0 0.00 4.17 R
4870 5859 0.802494 AATGTGCCGGCTAAGTTTCG 59.198 50.0 29.70 0.0 0.00 3.46 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
19 20 1.141881 ACTTAGCGGTGGCATCTCG 59.858 57.895 0.00 0.00 43.41 4.04
41 42 5.803461 TCGATGTAAATAACGTCAACTCCAG 59.197 40.000 0.00 0.00 43.27 3.86
42 43 5.575606 CGATGTAAATAACGTCAACTCCAGT 59.424 40.000 0.00 0.00 43.27 4.00
43 44 6.090358 CGATGTAAATAACGTCAACTCCAGTT 59.910 38.462 0.00 0.00 43.27 3.16
44 45 7.359765 CGATGTAAATAACGTCAACTCCAGTTT 60.360 37.037 0.00 0.00 43.27 2.66
45 46 7.556733 TGTAAATAACGTCAACTCCAGTTTT 57.443 32.000 0.00 0.00 35.83 2.43
46 47 7.632721 TGTAAATAACGTCAACTCCAGTTTTC 58.367 34.615 0.00 0.00 35.83 2.29
47 48 5.684550 AATAACGTCAACTCCAGTTTTCC 57.315 39.130 0.00 0.00 35.83 3.13
74 75 1.303236 TGGATCACCCAAACTGCCG 60.303 57.895 0.00 0.00 43.29 5.69
87 88 3.615536 CTGCCGCTCCGCCTTTTTG 62.616 63.158 0.00 0.00 0.00 2.44
138 139 1.682257 GCTTCTTGGAGCTGGACCT 59.318 57.895 0.00 0.00 39.57 3.85
154 155 2.751837 CTTTCGGGCCAGCTTCCC 60.752 66.667 4.39 10.22 40.43 3.97
156 157 2.771328 CTTTCGGGCCAGCTTCCCTT 62.771 60.000 16.56 0.00 41.69 3.95
168 169 4.517285 CAGCTTCCCTTGTAGATTTGCTA 58.483 43.478 0.00 0.00 0.00 3.49
234 235 8.868522 TGAATTTTGACAATCTTAGATCTGGT 57.131 30.769 5.18 0.00 0.00 4.00
235 236 9.300681 TGAATTTTGACAATCTTAGATCTGGTT 57.699 29.630 5.18 0.00 0.00 3.67
251 252 1.135257 TGGTTTTCACGCACCTTGTTG 60.135 47.619 0.00 0.00 33.76 3.33
377 378 8.327429 GTCAACAACAATGGTAAAGTTGATTTG 58.673 33.333 14.99 6.55 43.93 2.32
388 389 8.240682 TGGTAAAGTTGATTTGTGGATTATTCG 58.759 33.333 0.00 0.00 32.01 3.34
398 399 5.029807 TGTGGATTATTCGCCATGTCTTA 57.970 39.130 0.00 0.00 36.41 2.10
399 400 5.620206 TGTGGATTATTCGCCATGTCTTAT 58.380 37.500 0.00 0.00 36.41 1.73
477 479 3.157087 AGGCCATGTGTGTCCTTAAAAG 58.843 45.455 5.01 0.00 0.00 2.27
589 593 4.024302 CACAGACACGCCGATAGATACTAA 60.024 45.833 0.00 0.00 39.76 2.24
1100 1143 1.992170 CTTGTCGCCGCTTAGTAGTT 58.008 50.000 0.00 0.00 0.00 2.24
1105 1148 0.094730 CGCCGCTTAGTAGTTGCAAC 59.905 55.000 22.17 22.17 0.00 4.17
1135 1178 3.302480 GCGCTTATGTGGAAGTTCGTATG 60.302 47.826 0.00 0.00 0.00 2.39
1329 1396 8.742777 AGCAATTCTGATTTTGTTTATAGAGCA 58.257 29.630 0.00 0.00 0.00 4.26
1349 1416 3.808618 GCACCTCAATCACAGAACCTCTT 60.809 47.826 0.00 0.00 0.00 2.85
1474 1541 7.819900 AGTAGTCACATCAGGTCAGTTAATTTC 59.180 37.037 0.00 0.00 0.00 2.17
1535 1620 4.111916 CAAAGTTTTGTGGCGTCTTTGAT 58.888 39.130 9.42 0.00 44.04 2.57
1542 1627 2.290367 TGTGGCGTCTTTGATCAAACAG 59.710 45.455 16.91 8.71 0.00 3.16
1591 1676 3.126858 TCTGACAAAGTGACAAGTGCAAC 59.873 43.478 0.00 0.00 0.00 4.17
1607 1692 2.224843 TGCAACCCAGATGACTGTTGAT 60.225 45.455 5.49 0.00 42.05 2.57
1646 1731 1.544246 GCCACCGCTTGGTTTAGATTT 59.456 47.619 3.38 0.00 46.51 2.17
1652 1737 5.292101 CACCGCTTGGTTTAGATTTCTAGAG 59.708 44.000 0.00 0.00 46.51 2.43
1842 1931 8.579850 TTGTCATTAAGCATCCTTCTTATGTT 57.420 30.769 0.00 0.00 32.47 2.71
1853 1943 7.339466 GCATCCTTCTTATGTTCCTTTTTAGGA 59.661 37.037 0.00 0.00 35.93 2.94
1881 1973 7.896383 TTTTCCCTTATATTGAATCCCTGTG 57.104 36.000 0.00 0.00 0.00 3.66
1882 1974 6.840090 TTCCCTTATATTGAATCCCTGTGA 57.160 37.500 0.00 0.00 0.00 3.58
1883 1975 6.840090 TCCCTTATATTGAATCCCTGTGAA 57.160 37.500 0.00 0.00 0.00 3.18
2013 2116 6.180472 AGAGCTTTGGAATTCTCCGAAATAA 58.820 36.000 5.23 0.00 43.43 1.40
2047 2150 4.580167 AGCTACTGAACTTTGCATTGTTGA 59.420 37.500 9.17 1.31 0.00 3.18
2118 2221 6.719365 CACTTAAGCATGAACTTAGGTATGC 58.281 40.000 1.29 4.91 39.59 3.14
2186 2298 8.538409 AGGATTTTGAATTGCTTTGTTATGTC 57.462 30.769 0.00 0.00 0.00 3.06
2200 2312 0.674581 TATGTCTGTGTGCTGCTGCC 60.675 55.000 13.47 5.20 38.71 4.85
2210 2322 2.273123 CTGCTGCCATACCCTGCA 59.727 61.111 0.00 0.00 36.09 4.41
2243 2355 9.241317 GTTTTTGGATATATTGCAACAGAGATG 57.759 33.333 0.00 0.00 35.14 2.90
2245 2357 8.929260 TTTGGATATATTGCAACAGAGATGAT 57.071 30.769 0.00 0.00 35.14 2.45
2293 2405 6.956202 AATATATATACTCCCTCCGTTCCG 57.044 41.667 0.00 0.00 0.00 4.30
2294 2406 2.965671 ATATACTCCCTCCGTTCCGA 57.034 50.000 0.00 0.00 0.00 4.55
2295 2407 2.734755 TATACTCCCTCCGTTCCGAA 57.265 50.000 0.00 0.00 0.00 4.30
2296 2408 2.083628 ATACTCCCTCCGTTCCGAAT 57.916 50.000 0.00 0.00 0.00 3.34
2297 2409 1.856629 TACTCCCTCCGTTCCGAATT 58.143 50.000 0.00 0.00 0.00 2.17
2298 2410 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
2299 2411 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
2300 2412 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
2301 2413 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
2302 2414 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2303 2415 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2304 2416 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2305 2417 3.368116 CCTCCGTTCCGAATTACTTGTCT 60.368 47.826 0.00 0.00 0.00 3.41
2306 2418 4.243270 CTCCGTTCCGAATTACTTGTCTT 58.757 43.478 0.00 0.00 0.00 3.01
2307 2419 5.389859 TCCGTTCCGAATTACTTGTCTTA 57.610 39.130 0.00 0.00 0.00 2.10
2308 2420 5.404946 TCCGTTCCGAATTACTTGTCTTAG 58.595 41.667 0.00 0.00 0.00 2.18
2309 2421 5.183713 TCCGTTCCGAATTACTTGTCTTAGA 59.816 40.000 0.00 0.00 0.00 2.10
2310 2422 6.040878 CCGTTCCGAATTACTTGTCTTAGAT 58.959 40.000 0.00 0.00 0.00 1.98
2311 2423 6.534079 CCGTTCCGAATTACTTGTCTTAGATT 59.466 38.462 0.00 0.00 0.00 2.40
2312 2424 7.064253 CCGTTCCGAATTACTTGTCTTAGATTT 59.936 37.037 0.00 0.00 0.00 2.17
2313 2425 7.898309 CGTTCCGAATTACTTGTCTTAGATTTG 59.102 37.037 0.00 0.00 0.00 2.32
2314 2426 8.718734 GTTCCGAATTACTTGTCTTAGATTTGT 58.281 33.333 0.00 0.00 0.00 2.83
2315 2427 8.475331 TCCGAATTACTTGTCTTAGATTTGTC 57.525 34.615 0.00 0.00 0.00 3.18
2316 2428 8.311836 TCCGAATTACTTGTCTTAGATTTGTCT 58.688 33.333 0.00 0.00 0.00 3.41
2317 2429 9.582431 CCGAATTACTTGTCTTAGATTTGTCTA 57.418 33.333 0.00 0.00 0.00 2.59
2324 2436 8.407064 ACTTGTCTTAGATTTGTCTAGATACGG 58.593 37.037 0.00 0.00 0.00 4.02
2325 2437 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
2326 2438 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
2327 2439 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
2328 2440 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
2329 2441 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
2346 2458 8.873215 ACGGATGTATCTAACACTAAAATGAG 57.127 34.615 0.00 0.00 42.09 2.90
2347 2459 8.475639 ACGGATGTATCTAACACTAAAATGAGT 58.524 33.333 0.00 0.00 42.09 3.41
2348 2460 8.969267 CGGATGTATCTAACACTAAAATGAGTC 58.031 37.037 0.00 0.00 42.09 3.36
2360 2472 8.353684 ACACTAAAATGAGTCTAGATACATCCG 58.646 37.037 12.66 6.68 0.00 4.18
2361 2473 8.353684 CACTAAAATGAGTCTAGATACATCCGT 58.646 37.037 12.66 7.10 0.00 4.69
2362 2474 9.570468 ACTAAAATGAGTCTAGATACATCCGTA 57.430 33.333 12.66 6.93 0.00 4.02
2376 2488 7.776618 ATACATCCGTATCTAGACAAATCCA 57.223 36.000 0.00 0.00 32.66 3.41
2377 2489 6.479972 ACATCCGTATCTAGACAAATCCAA 57.520 37.500 0.00 0.00 0.00 3.53
2378 2490 6.516718 ACATCCGTATCTAGACAAATCCAAG 58.483 40.000 0.00 0.00 0.00 3.61
2379 2491 6.323996 ACATCCGTATCTAGACAAATCCAAGA 59.676 38.462 0.00 0.00 0.00 3.02
2380 2492 6.145338 TCCGTATCTAGACAAATCCAAGAC 57.855 41.667 0.00 0.00 0.00 3.01
2381 2493 5.655090 TCCGTATCTAGACAAATCCAAGACA 59.345 40.000 0.00 0.00 0.00 3.41
2382 2494 6.153851 TCCGTATCTAGACAAATCCAAGACAA 59.846 38.462 0.00 0.00 0.00 3.18
2383 2495 6.477033 CCGTATCTAGACAAATCCAAGACAAG 59.523 42.308 0.00 0.00 0.00 3.16
2384 2496 7.036220 CGTATCTAGACAAATCCAAGACAAGT 58.964 38.462 0.00 0.00 0.00 3.16
2385 2497 8.188799 CGTATCTAGACAAATCCAAGACAAGTA 58.811 37.037 0.00 0.00 0.00 2.24
2386 2498 9.871238 GTATCTAGACAAATCCAAGACAAGTAA 57.129 33.333 0.00 0.00 0.00 2.24
2388 2500 9.965902 ATCTAGACAAATCCAAGACAAGTAATT 57.034 29.630 0.00 0.00 0.00 1.40
2389 2501 9.793259 TCTAGACAAATCCAAGACAAGTAATTT 57.207 29.630 0.00 0.00 0.00 1.82
2392 2504 9.793259 AGACAAATCCAAGACAAGTAATTTAGA 57.207 29.630 0.00 0.00 0.00 2.10
2395 2507 9.329913 CAAATCCAAGACAAGTAATTTAGAACG 57.670 33.333 0.00 0.00 0.00 3.95
2396 2508 7.611213 ATCCAAGACAAGTAATTTAGAACGG 57.389 36.000 0.00 0.00 0.00 4.44
2397 2509 6.761312 TCCAAGACAAGTAATTTAGAACGGA 58.239 36.000 0.00 0.00 0.00 4.69
2398 2510 6.872020 TCCAAGACAAGTAATTTAGAACGGAG 59.128 38.462 0.00 0.00 0.00 4.63
2399 2511 6.092259 CCAAGACAAGTAATTTAGAACGGAGG 59.908 42.308 0.00 0.00 0.00 4.30
2400 2512 5.731591 AGACAAGTAATTTAGAACGGAGGG 58.268 41.667 0.00 0.00 0.00 4.30
2401 2513 5.482878 AGACAAGTAATTTAGAACGGAGGGA 59.517 40.000 0.00 0.00 0.00 4.20
2402 2514 5.731591 ACAAGTAATTTAGAACGGAGGGAG 58.268 41.667 0.00 0.00 0.00 4.30
2403 2515 5.247792 ACAAGTAATTTAGAACGGAGGGAGT 59.752 40.000 0.00 0.00 0.00 3.85
2404 2516 6.438425 ACAAGTAATTTAGAACGGAGGGAGTA 59.562 38.462 0.00 0.00 0.00 2.59
2405 2517 7.125356 ACAAGTAATTTAGAACGGAGGGAGTAT 59.875 37.037 0.00 0.00 0.00 2.12
2409 2521 9.822185 GTAATTTAGAACGGAGGGAGTATAAAA 57.178 33.333 0.00 0.00 0.00 1.52
2417 2529 9.939802 GAACGGAGGGAGTATAAAATTATACAT 57.060 33.333 19.96 9.28 44.96 2.29
2493 2605 3.244665 ACTGTGTCACATGTCATGGTGAT 60.245 43.478 17.08 1.50 44.94 3.06
2789 2902 9.527157 TTATCCATGAATCAGGAAAAGTTAACA 57.473 29.630 8.61 0.00 37.48 2.41
2933 3046 3.034635 TCAGAGAGGAGAATACTTGGGC 58.965 50.000 0.00 0.00 0.00 5.36
3025 3140 2.290323 CGTCCTCCTTGTCTTCCCAATT 60.290 50.000 0.00 0.00 0.00 2.32
3138 3255 2.089980 AGACTTGATGAGCATGCAACC 58.910 47.619 21.98 9.11 0.00 3.77
3139 3256 0.806868 ACTTGATGAGCATGCAACCG 59.193 50.000 21.98 3.72 0.00 4.44
3153 3270 4.955925 TGCAACCGTATTTGATTTCGAT 57.044 36.364 0.00 0.00 0.00 3.59
3171 3288 5.065096 TCGATAGTGAATTGCAGCTTGCG 62.065 47.826 0.00 0.00 41.90 4.85
3194 3311 1.202268 GCTTCAGCATGCCAATCTGAC 60.202 52.381 15.66 0.00 41.59 3.51
3204 3321 2.837591 TGCCAATCTGACTAGGTTGCTA 59.162 45.455 0.00 0.00 42.50 3.49
3282 3399 5.192722 TGGTTCCTTGGACCATTACATATCA 59.807 40.000 0.00 0.00 42.06 2.15
3286 3403 5.065914 CCTTGGACCATTACATATCAGGTG 58.934 45.833 0.00 0.00 31.57 4.00
3294 3411 6.835488 ACCATTACATATCAGGTGCATTTTCT 59.165 34.615 0.00 0.00 0.00 2.52
3505 3878 8.497554 GTTGCAATTTGATTATCTTTTGCAGAA 58.502 29.630 20.08 10.95 46.80 3.02
3521 3894 4.997565 TGCAGAAAGAACAAAAGGACAAG 58.002 39.130 0.00 0.00 0.00 3.16
3526 3899 4.376340 AAGAACAAAAGGACAAGTGCTG 57.624 40.909 0.00 0.00 0.00 4.41
3730 4105 1.533469 AAGAGCGCACGAGTAGGGTT 61.533 55.000 11.47 0.00 0.00 4.11
3773 4148 7.173907 AGCTGCCTACAATATCAATAATCACAC 59.826 37.037 0.00 0.00 0.00 3.82
3869 4663 2.675583 AGCTCCAGAGTATGCATCTCA 58.324 47.619 20.87 6.68 34.73 3.27
3881 4675 6.951971 AGTATGCATCTCAAGGAGTTTACTT 58.048 36.000 0.19 0.00 0.00 2.24
4102 4902 8.828751 AGTGGTGAGTTTTAACCTATACCATTA 58.171 33.333 0.00 0.00 38.97 1.90
4170 4974 7.881775 AGCAAGACTTATTTTAATACCTGGG 57.118 36.000 0.00 0.00 0.00 4.45
4481 5323 1.136110 ACACGGCATCGACATACATGA 59.864 47.619 0.00 0.00 40.11 3.07
4490 5332 3.721035 TCGACATACATGAGCCAATCAG 58.279 45.455 0.00 0.00 42.53 2.90
4651 5566 3.052944 TGGGCTTTTTATGGCTCAGGTAT 60.053 43.478 0.00 0.00 33.66 2.73
4719 5641 1.737236 ACATGTGTGTGTGTGTGTGTC 59.263 47.619 0.00 0.00 37.14 3.67
4870 5859 3.500299 ACAACTGTTTGCAAACCAAAACC 59.500 39.130 33.33 12.49 44.48 3.27
4927 5941 7.922278 TGAGAAAATCATCAAACTTCAAGTTGG 59.078 33.333 2.78 0.00 33.72 3.77
4938 5952 6.658974 AACTTCAAGTTGGCAAGCAGCAAA 62.659 41.667 0.68 0.00 39.14 3.68
4953 5971 2.175878 GCAAAGAGCTCAGAGTTCCA 57.824 50.000 17.77 0.00 41.15 3.53
4954 5972 1.803555 GCAAAGAGCTCAGAGTTCCAC 59.196 52.381 17.77 0.00 41.15 4.02
4979 6330 7.667219 ACACACATCAGGATCTCAAAATAAGTT 59.333 33.333 0.00 0.00 0.00 2.66
4982 6333 6.096001 ACATCAGGATCTCAAAATAAGTTGGC 59.904 38.462 0.00 0.00 0.00 4.52
4983 6334 5.569355 TCAGGATCTCAAAATAAGTTGGCA 58.431 37.500 0.00 0.00 0.00 4.92
4984 6335 6.009589 TCAGGATCTCAAAATAAGTTGGCAA 58.990 36.000 0.00 0.00 0.00 4.52
4985 6336 6.151648 TCAGGATCTCAAAATAAGTTGGCAAG 59.848 38.462 0.00 0.00 0.00 4.01
4988 6339 8.055181 AGGATCTCAAAATAAGTTGGCAAGATA 58.945 33.333 0.00 0.00 0.00 1.98
4990 6341 9.508567 GATCTCAAAATAAGTTGGCAAGATAAC 57.491 33.333 0.00 0.00 0.00 1.89
5095 6467 0.990374 AGGCATTCTTCTGCAGGTCT 59.010 50.000 15.13 0.00 44.12 3.85
5096 6468 1.353694 AGGCATTCTTCTGCAGGTCTT 59.646 47.619 15.13 0.00 44.12 3.01
5097 6469 2.165998 GGCATTCTTCTGCAGGTCTTT 58.834 47.619 15.13 0.00 44.12 2.52
5098 6470 2.560105 GGCATTCTTCTGCAGGTCTTTT 59.440 45.455 15.13 0.00 44.12 2.27
5099 6471 3.006217 GGCATTCTTCTGCAGGTCTTTTT 59.994 43.478 15.13 0.00 44.12 1.94
5133 6843 4.171754 GCATTCTTCTGCAGGTCATTTTC 58.828 43.478 15.13 0.00 41.87 2.29
5134 6844 4.082354 GCATTCTTCTGCAGGTCATTTTCT 60.082 41.667 15.13 0.00 41.87 2.52
5136 6846 4.356405 TCTTCTGCAGGTCATTTTCTGA 57.644 40.909 15.13 0.00 33.11 3.27
5137 6847 4.914983 TCTTCTGCAGGTCATTTTCTGAT 58.085 39.130 15.13 0.00 35.97 2.90
5138 6848 4.698780 TCTTCTGCAGGTCATTTTCTGATG 59.301 41.667 15.13 0.00 35.97 3.07
5139 6849 4.290711 TCTGCAGGTCATTTTCTGATGA 57.709 40.909 15.13 0.00 35.97 2.92
5140 6850 4.851843 TCTGCAGGTCATTTTCTGATGAT 58.148 39.130 15.13 0.00 38.25 2.45
5141 6851 4.638865 TCTGCAGGTCATTTTCTGATGATG 59.361 41.667 15.13 0.00 38.25 3.07
5142 6852 3.129813 TGCAGGTCATTTTCTGATGATGC 59.870 43.478 6.53 6.53 40.18 3.91
5146 6856 5.124936 CAGGTCATTTTCTGATGATGCAAGA 59.875 40.000 0.00 0.00 38.25 3.02
5147 6857 5.713389 AGGTCATTTTCTGATGATGCAAGAA 59.287 36.000 0.00 0.00 38.25 2.52
5148 6858 6.034591 GGTCATTTTCTGATGATGCAAGAAG 58.965 40.000 0.00 0.00 38.25 2.85
5149 6859 6.349944 GGTCATTTTCTGATGATGCAAGAAGT 60.350 38.462 0.00 0.00 38.25 3.01
5151 6861 6.431852 TCATTTTCTGATGATGCAAGAAGTCA 59.568 34.615 0.00 0.00 31.35 3.41
5153 6863 6.829229 TTTCTGATGATGCAAGAAGTCATT 57.171 33.333 1.48 0.00 33.03 2.57
5154 6864 6.829229 TTCTGATGATGCAAGAAGTCATTT 57.171 33.333 1.48 0.00 33.03 2.32
5184 6906 3.310303 CGACTCGGATTCAAATTGCTC 57.690 47.619 0.00 0.00 0.00 4.26
5185 6907 2.932614 CGACTCGGATTCAAATTGCTCT 59.067 45.455 0.00 0.00 0.00 4.09
5186 6908 3.372206 CGACTCGGATTCAAATTGCTCTT 59.628 43.478 0.00 0.00 0.00 2.85
5187 6909 4.493220 CGACTCGGATTCAAATTGCTCTTC 60.493 45.833 0.00 0.00 0.00 2.87
5188 6910 4.583871 ACTCGGATTCAAATTGCTCTTCT 58.416 39.130 0.00 0.00 0.00 2.85
5189 6911 4.394300 ACTCGGATTCAAATTGCTCTTCTG 59.606 41.667 0.00 0.00 0.00 3.02
5190 6912 3.691118 TCGGATTCAAATTGCTCTTCTGG 59.309 43.478 0.00 0.00 0.00 3.86
5191 6913 3.181493 CGGATTCAAATTGCTCTTCTGGG 60.181 47.826 0.00 0.00 0.00 4.45
5192 6914 3.429960 GGATTCAAATTGCTCTTCTGGGC 60.430 47.826 0.00 0.00 0.00 5.36
5193 6915 2.592102 TCAAATTGCTCTTCTGGGCT 57.408 45.000 0.00 0.00 0.00 5.19
5194 6916 2.165167 TCAAATTGCTCTTCTGGGCTG 58.835 47.619 0.00 0.00 0.00 4.85
5195 6917 1.891150 CAAATTGCTCTTCTGGGCTGT 59.109 47.619 0.00 0.00 0.00 4.40
5196 6918 3.084039 CAAATTGCTCTTCTGGGCTGTA 58.916 45.455 0.00 0.00 0.00 2.74
5197 6919 3.439857 AATTGCTCTTCTGGGCTGTAA 57.560 42.857 0.00 0.00 0.00 2.41
5198 6920 2.949177 TTGCTCTTCTGGGCTGTAAA 57.051 45.000 0.00 0.00 0.00 2.01
5199 6921 2.185004 TGCTCTTCTGGGCTGTAAAC 57.815 50.000 0.00 0.00 0.00 2.01
5200 6922 1.079503 GCTCTTCTGGGCTGTAAACG 58.920 55.000 0.00 0.00 0.00 3.60
5201 6923 1.608283 GCTCTTCTGGGCTGTAAACGT 60.608 52.381 0.00 0.00 0.00 3.99
5202 6924 2.767505 CTCTTCTGGGCTGTAAACGTT 58.232 47.619 0.00 0.00 0.00 3.99
5203 6925 3.139077 CTCTTCTGGGCTGTAAACGTTT 58.861 45.455 18.90 18.90 0.00 3.60
5204 6926 3.135994 TCTTCTGGGCTGTAAACGTTTC 58.864 45.455 18.42 9.90 0.00 2.78
5205 6927 1.886886 TCTGGGCTGTAAACGTTTCC 58.113 50.000 18.42 12.25 0.00 3.13
5206 6928 0.879090 CTGGGCTGTAAACGTTTCCC 59.121 55.000 22.54 22.54 0.00 3.97
5207 6929 0.475044 TGGGCTGTAAACGTTTCCCT 59.525 50.000 26.85 6.30 34.89 4.20
5208 6930 1.133730 TGGGCTGTAAACGTTTCCCTT 60.134 47.619 26.85 5.96 34.89 3.95
5209 6931 1.958579 GGGCTGTAAACGTTTCCCTTT 59.041 47.619 22.21 1.17 0.00 3.11
5210 6932 2.287970 GGGCTGTAAACGTTTCCCTTTG 60.288 50.000 22.21 9.18 0.00 2.77
5211 6933 2.359848 GGCTGTAAACGTTTCCCTTTGT 59.640 45.455 18.42 0.00 0.00 2.83
5305 7028 2.514824 GCGGTTGGATCTGGAGCC 60.515 66.667 0.00 0.00 37.40 4.70
5376 7100 3.822035 TCTCCGGCGAGATCCCCT 61.822 66.667 9.30 0.00 40.34 4.79
5434 7158 2.187946 GGCACATCTCCGGTGAGG 59.812 66.667 16.03 16.03 39.23 3.86
5439 7163 2.765807 ATCTCCGGTGAGGCCCAG 60.766 66.667 12.42 0.00 39.23 4.45
5445 7169 4.106925 GGTGAGGCCCAGCTCCAG 62.107 72.222 14.04 0.00 40.01 3.86
5542 14193 4.778415 CGGAGCCTCACGTCACCG 62.778 72.222 0.00 0.00 40.83 4.94
5543 14194 4.436998 GGAGCCTCACGTCACCGG 62.437 72.222 0.00 0.00 38.78 5.28
5561 14212 3.118454 CCGCAGCACCCGTTGTAG 61.118 66.667 0.00 0.00 0.00 2.74
5565 14216 1.293498 CAGCACCCGTTGTAGAGCT 59.707 57.895 0.00 0.00 0.00 4.09
5566 14217 0.737715 CAGCACCCGTTGTAGAGCTC 60.738 60.000 5.27 5.27 0.00 4.09
5567 14218 1.805945 GCACCCGTTGTAGAGCTCG 60.806 63.158 8.37 0.00 0.00 5.03
5568 14219 1.585006 CACCCGTTGTAGAGCTCGT 59.415 57.895 8.37 0.00 0.00 4.18
5570 14221 1.177256 ACCCGTTGTAGAGCTCGTGT 61.177 55.000 8.37 0.00 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 7.306051 GGAGTTGACGTTATTTACATCGAGATG 60.306 40.741 11.19 11.19 44.15 2.90
19 20 6.963049 ACTGGAGTTGACGTTATTTACATC 57.037 37.500 0.00 0.00 0.00 3.06
41 42 4.207955 GTGATCCAGGAATAGGGGAAAAC 58.792 47.826 0.00 0.00 33.73 2.43
42 43 3.204382 GGTGATCCAGGAATAGGGGAAAA 59.796 47.826 0.00 0.00 33.73 2.29
43 44 2.783510 GGTGATCCAGGAATAGGGGAAA 59.216 50.000 0.00 0.00 33.73 3.13
44 45 2.418669 GGTGATCCAGGAATAGGGGAA 58.581 52.381 0.00 0.00 33.73 3.97
45 46 1.416013 GGGTGATCCAGGAATAGGGGA 60.416 57.143 0.00 0.00 35.00 4.81
46 47 1.068121 GGGTGATCCAGGAATAGGGG 58.932 60.000 0.00 0.00 35.00 4.79
47 48 1.819753 TGGGTGATCCAGGAATAGGG 58.180 55.000 0.00 0.00 41.46 3.53
87 88 3.485877 GGATTGAAGCTGCGTTCATGTAC 60.486 47.826 12.85 0.00 36.34 2.90
154 155 6.018343 GCTCCTAGCTTTAGCAAATCTACAAG 60.018 42.308 4.33 0.00 45.16 3.16
156 157 5.360591 GCTCCTAGCTTTAGCAAATCTACA 58.639 41.667 4.33 0.00 45.16 2.74
190 191 3.757270 TCAAAAATTAGGGCCTGTTCGA 58.243 40.909 18.53 6.27 0.00 3.71
230 231 0.738389 ACAAGGTGCGTGAAAACCAG 59.262 50.000 0.00 0.00 39.05 4.00
234 235 2.159310 CCTTCAACAAGGTGCGTGAAAA 60.159 45.455 0.00 0.00 44.11 2.29
235 236 1.403679 CCTTCAACAAGGTGCGTGAAA 59.596 47.619 0.00 0.00 44.11 2.69
251 252 3.949842 AAGCTCAAGGAAAATGCCTTC 57.050 42.857 0.00 0.00 44.89 3.46
264 265 5.407407 AAAGAAGGACTCGATAAGCTCAA 57.593 39.130 0.00 0.00 0.00 3.02
265 266 5.186021 AGAAAAGAAGGACTCGATAAGCTCA 59.814 40.000 0.00 0.00 0.00 4.26
377 378 6.204688 TGAATAAGACATGGCGAATAATCCAC 59.795 38.462 0.00 0.00 34.81 4.02
388 389 3.809832 AGTACGCATGAATAAGACATGGC 59.190 43.478 0.00 0.00 43.39 4.40
519 523 1.463444 GGTATGTGTGTGGACTTTCGC 59.537 52.381 0.00 0.00 0.00 4.70
589 593 2.616330 CGTTGCCGCCATTGACACT 61.616 57.895 0.00 0.00 0.00 3.55
985 1028 2.422127 TGAACATGTCGATCTCGTGCTA 59.578 45.455 0.00 0.00 40.80 3.49
1091 1134 5.452777 GCCAAGAAAGTTGCAACTACTAAG 58.547 41.667 31.31 23.79 38.57 2.18
1100 1143 1.313772 TAAGCGCCAAGAAAGTTGCA 58.686 45.000 2.29 0.00 0.00 4.08
1105 1148 2.083774 TCCACATAAGCGCCAAGAAAG 58.916 47.619 2.29 0.00 0.00 2.62
1135 1178 7.759433 CACATACTACCATGGGTTTCAATTTTC 59.241 37.037 18.09 0.00 37.09 2.29
1193 1259 7.009179 AGGATCACTTGAACAGATCAGTTTA 57.991 36.000 4.86 0.00 39.77 2.01
1245 1311 5.543507 ATTTGCAGTTACACCCAATTCAA 57.456 34.783 0.00 0.00 0.00 2.69
1326 1393 1.701847 AGGTTCTGTGATTGAGGTGCT 59.298 47.619 0.00 0.00 0.00 4.40
1329 1396 3.906846 AGAAGAGGTTCTGTGATTGAGGT 59.093 43.478 0.00 0.00 41.78 3.85
1474 1541 8.442605 AAAAACGATGATAAAATACACAACGG 57.557 30.769 0.00 0.00 34.04 4.44
1535 1620 1.764134 ACCTCCCACGTTACTGTTTGA 59.236 47.619 0.00 0.00 0.00 2.69
1542 1627 2.416747 GTGGTTAACCTCCCACGTTAC 58.583 52.381 24.78 8.08 41.55 2.50
1591 1676 6.877855 CCTAATATGATCAACAGTCATCTGGG 59.122 42.308 0.00 0.00 45.14 4.45
1607 1692 5.163343 GGTGGCACTAGTCAACCTAATATGA 60.163 44.000 18.45 0.00 28.25 2.15
1646 1731 6.665680 AGCTCTGAACCAGATTTTACTCTAGA 59.334 38.462 0.00 0.00 39.92 2.43
1652 1737 6.457528 GCATGTAGCTCTGAACCAGATTTTAC 60.458 42.308 0.00 2.63 39.92 2.01
1723 1808 5.106277 ACAAAGTCATTGATCTGATGCACAG 60.106 40.000 9.27 9.27 43.39 3.66
1877 1969 6.258727 ACATAACTTGACTTCACAGTTCACAG 59.741 38.462 8.93 3.85 33.07 3.66
1878 1970 6.112734 ACATAACTTGACTTCACAGTTCACA 58.887 36.000 8.93 0.00 33.07 3.58
1879 1971 6.604735 ACATAACTTGACTTCACAGTTCAC 57.395 37.500 8.93 0.00 33.07 3.18
1880 1972 6.423905 GCTACATAACTTGACTTCACAGTTCA 59.576 38.462 8.93 0.00 33.07 3.18
1881 1973 6.647067 AGCTACATAACTTGACTTCACAGTTC 59.353 38.462 8.93 0.00 33.07 3.01
1882 1974 6.425114 CAGCTACATAACTTGACTTCACAGTT 59.575 38.462 0.00 9.96 34.30 3.16
1883 1975 5.928839 CAGCTACATAACTTGACTTCACAGT 59.071 40.000 0.00 0.00 35.17 3.55
1943 2046 3.888930 TCCTAAAAGGTGGCAAGTTTCAG 59.111 43.478 0.00 0.00 36.53 3.02
1949 2052 2.554032 CACACTCCTAAAAGGTGGCAAG 59.446 50.000 0.00 0.00 36.53 4.01
2013 2116 4.009370 GTTCAGTAGCTCCTTGAACCTT 57.991 45.455 19.44 0.00 42.91 3.50
2095 2198 6.414732 TGCATACCTAAGTTCATGCTTAAGT 58.585 36.000 4.02 0.00 43.30 2.24
2118 2221 7.119699 TGGCATGAAACTTCACTCTACTAATTG 59.880 37.037 0.00 0.00 40.49 2.32
2186 2298 1.651240 GGTATGGCAGCAGCACACAG 61.651 60.000 2.65 0.00 44.61 3.66
2200 2312 2.048444 AACATGAGCTGCAGGGTATG 57.952 50.000 17.12 8.80 31.20 2.39
2210 2322 7.350744 TGCAATATATCCAAAAACATGAGCT 57.649 32.000 0.00 0.00 0.00 4.09
2288 2400 8.718734 ACAAATCTAAGACAAGTAATTCGGAAC 58.281 33.333 0.00 0.00 0.00 3.62
2289 2401 8.842358 ACAAATCTAAGACAAGTAATTCGGAA 57.158 30.769 0.00 0.00 0.00 4.30
2290 2402 8.311836 AGACAAATCTAAGACAAGTAATTCGGA 58.688 33.333 0.00 0.00 31.46 4.55
2291 2403 8.480643 AGACAAATCTAAGACAAGTAATTCGG 57.519 34.615 0.00 0.00 31.46 4.30
2298 2410 8.407064 CCGTATCTAGACAAATCTAAGACAAGT 58.593 37.037 0.00 0.00 36.98 3.16
2299 2411 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
2300 2412 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
2301 2413 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
2302 2414 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
2303 2415 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
2320 2432 9.961265 CTCATTTTAGTGTTAGATACATCCGTA 57.039 33.333 0.00 0.00 39.39 4.02
2321 2433 8.475639 ACTCATTTTAGTGTTAGATACATCCGT 58.524 33.333 0.00 0.00 39.39 4.69
2322 2434 8.873215 ACTCATTTTAGTGTTAGATACATCCG 57.127 34.615 0.00 0.00 39.39 4.18
2334 2446 8.353684 CGGATGTATCTAGACTCATTTTAGTGT 58.646 37.037 11.25 0.00 0.00 3.55
2335 2447 8.353684 ACGGATGTATCTAGACTCATTTTAGTG 58.646 37.037 11.25 3.85 0.00 2.74
2336 2448 8.466617 ACGGATGTATCTAGACTCATTTTAGT 57.533 34.615 11.25 7.70 0.00 2.24
2352 2464 7.776618 TGGATTTGTCTAGATACGGATGTAT 57.223 36.000 0.00 0.00 43.97 2.29
2353 2465 7.504574 TCTTGGATTTGTCTAGATACGGATGTA 59.495 37.037 0.00 0.00 34.45 2.29
2354 2466 6.323996 TCTTGGATTTGTCTAGATACGGATGT 59.676 38.462 0.00 0.00 0.00 3.06
2355 2467 6.642950 GTCTTGGATTTGTCTAGATACGGATG 59.357 42.308 0.00 0.00 0.00 3.51
2356 2468 6.323996 TGTCTTGGATTTGTCTAGATACGGAT 59.676 38.462 0.00 0.00 0.00 4.18
2357 2469 5.655090 TGTCTTGGATTTGTCTAGATACGGA 59.345 40.000 0.00 0.00 0.00 4.69
2358 2470 5.902681 TGTCTTGGATTTGTCTAGATACGG 58.097 41.667 0.00 0.00 0.00 4.02
2359 2471 7.036220 ACTTGTCTTGGATTTGTCTAGATACG 58.964 38.462 0.00 0.00 0.00 3.06
2360 2472 9.871238 TTACTTGTCTTGGATTTGTCTAGATAC 57.129 33.333 0.00 0.00 0.00 2.24
2362 2474 9.965902 AATTACTTGTCTTGGATTTGTCTAGAT 57.034 29.630 0.00 0.00 0.00 1.98
2363 2475 9.793259 AAATTACTTGTCTTGGATTTGTCTAGA 57.207 29.630 0.00 0.00 0.00 2.43
2366 2478 9.793259 TCTAAATTACTTGTCTTGGATTTGTCT 57.207 29.630 0.00 0.00 0.00 3.41
2369 2481 9.329913 CGTTCTAAATTACTTGTCTTGGATTTG 57.670 33.333 0.00 0.00 0.00 2.32
2370 2482 8.512138 CCGTTCTAAATTACTTGTCTTGGATTT 58.488 33.333 0.00 0.00 0.00 2.17
2371 2483 7.881232 TCCGTTCTAAATTACTTGTCTTGGATT 59.119 33.333 0.00 0.00 0.00 3.01
2372 2484 7.391620 TCCGTTCTAAATTACTTGTCTTGGAT 58.608 34.615 0.00 0.00 0.00 3.41
2373 2485 6.761312 TCCGTTCTAAATTACTTGTCTTGGA 58.239 36.000 0.00 0.00 0.00 3.53
2374 2486 6.092259 CCTCCGTTCTAAATTACTTGTCTTGG 59.908 42.308 0.00 0.00 0.00 3.61
2375 2487 6.092259 CCCTCCGTTCTAAATTACTTGTCTTG 59.908 42.308 0.00 0.00 0.00 3.02
2376 2488 6.013984 TCCCTCCGTTCTAAATTACTTGTCTT 60.014 38.462 0.00 0.00 0.00 3.01
2377 2489 5.482878 TCCCTCCGTTCTAAATTACTTGTCT 59.517 40.000 0.00 0.00 0.00 3.41
2378 2490 5.727434 TCCCTCCGTTCTAAATTACTTGTC 58.273 41.667 0.00 0.00 0.00 3.18
2379 2491 5.247792 ACTCCCTCCGTTCTAAATTACTTGT 59.752 40.000 0.00 0.00 0.00 3.16
2380 2492 5.731591 ACTCCCTCCGTTCTAAATTACTTG 58.268 41.667 0.00 0.00 0.00 3.16
2381 2493 7.672122 ATACTCCCTCCGTTCTAAATTACTT 57.328 36.000 0.00 0.00 0.00 2.24
2382 2494 8.773033 TTATACTCCCTCCGTTCTAAATTACT 57.227 34.615 0.00 0.00 0.00 2.24
2383 2495 9.822185 TTTTATACTCCCTCCGTTCTAAATTAC 57.178 33.333 0.00 0.00 0.00 1.89
2385 2497 9.916360 AATTTTATACTCCCTCCGTTCTAAATT 57.084 29.630 0.00 0.00 0.00 1.82
2390 2502 9.151177 TGTATAATTTTATACTCCCTCCGTTCT 57.849 33.333 17.11 0.00 43.63 3.01
2391 2503 9.939802 ATGTATAATTTTATACTCCCTCCGTTC 57.060 33.333 17.11 0.00 43.63 3.95
2392 2504 9.720769 CATGTATAATTTTATACTCCCTCCGTT 57.279 33.333 17.11 0.00 43.63 4.44
2393 2505 8.877195 ACATGTATAATTTTATACTCCCTCCGT 58.123 33.333 17.11 5.65 43.63 4.69
2394 2506 9.151471 CACATGTATAATTTTATACTCCCTCCG 57.849 37.037 17.11 5.23 43.63 4.63
2395 2507 8.947115 GCACATGTATAATTTTATACTCCCTCC 58.053 37.037 17.11 3.57 43.63 4.30
2396 2508 9.502091 TGCACATGTATAATTTTATACTCCCTC 57.498 33.333 17.11 8.00 43.63 4.30
2417 2529 6.567959 TGTTTGTCATGAAAAAGTATGCACA 58.432 32.000 11.46 2.35 0.00 4.57
2786 2899 6.808829 TGAAGATTTTCTGTTCTTGCATGTT 58.191 32.000 0.00 0.00 32.46 2.71
2789 2902 6.808829 TGTTGAAGATTTTCTGTTCTTGCAT 58.191 32.000 0.00 0.00 32.46 3.96
2825 2938 4.275810 TCTATACGGGTACAAAGCTCAGT 58.724 43.478 0.00 0.00 0.00 3.41
2933 3046 2.762535 ACTGTACCGAATCCACCAAG 57.237 50.000 0.00 0.00 0.00 3.61
3025 3140 9.605275 CATTCTATCAACAGAAATCAGGTCTTA 57.395 33.333 0.00 0.00 38.03 2.10
3138 3255 7.850492 TGCAATTCACTATCGAAATCAAATACG 59.150 33.333 0.00 0.00 0.00 3.06
3139 3256 9.162793 CTGCAATTCACTATCGAAATCAAATAC 57.837 33.333 0.00 0.00 0.00 1.89
3153 3270 1.807139 TCGCAAGCTGCAATTCACTA 58.193 45.000 1.02 0.00 45.36 2.74
3171 3288 1.749634 AGATTGGCATGCTGAAGCTTC 59.250 47.619 19.89 19.89 42.66 3.86
3194 3311 0.107654 GCACCACCCTAGCAACCTAG 60.108 60.000 0.00 0.00 40.64 3.02
3204 3321 1.000739 CCCATGAATGCACCACCCT 59.999 57.895 0.00 0.00 0.00 4.34
3282 3399 7.568349 TCTCTGATAATACAGAAAATGCACCT 58.432 34.615 0.00 0.00 44.62 4.00
3379 3747 6.379386 GTGAAAACTAGATTTGTTGTAGCCC 58.621 40.000 2.29 0.00 0.00 5.19
3505 3878 3.131046 CCAGCACTTGTCCTTTTGTTCTT 59.869 43.478 0.00 0.00 0.00 2.52
3521 3894 0.737715 CGCTTAGACCAGTCCAGCAC 60.738 60.000 16.00 0.00 36.64 4.40
3526 3899 2.961526 TGAATCGCTTAGACCAGTCC 57.038 50.000 0.00 0.00 0.00 3.85
3730 4105 0.618458 GCTGATACCTGGTTCCCACA 59.382 55.000 3.84 0.00 0.00 4.17
3773 4148 7.101054 ACATCTGAAAACAAATGATGGGAATG 58.899 34.615 0.00 0.00 38.88 2.67
3869 4663 5.036117 TGTCTTCAGCAAGTAAACTCCTT 57.964 39.130 0.00 0.00 0.00 3.36
3881 4675 3.396560 CTGAACACATCTGTCTTCAGCA 58.603 45.455 13.12 0.00 41.61 4.41
4029 4828 9.959749 GTCTATTTTCTAATACTGAGAGTGGAG 57.040 37.037 0.00 0.00 0.00 3.86
4058 4857 6.544197 TCACCACTTTAGTAAAAACATGCAGA 59.456 34.615 0.00 0.00 0.00 4.26
4061 4860 6.735130 ACTCACCACTTTAGTAAAAACATGC 58.265 36.000 0.00 0.00 0.00 4.06
4102 4902 4.160252 AGTTCACAACTTTTGATGCCAAGT 59.840 37.500 0.00 0.00 39.04 3.16
4170 4974 6.395629 AGAGATGCAATGCAATTTATATGGC 58.604 36.000 13.45 0.00 43.62 4.40
4466 5308 1.869774 TGGCTCATGTATGTCGATGC 58.130 50.000 0.00 0.00 0.00 3.91
4490 5332 4.150897 TGGTTATGTCTATTGTCCTGCC 57.849 45.455 0.00 0.00 0.00 4.85
4576 5480 9.809096 ATTATATATGCTACTGAATGTTCTCCG 57.191 33.333 0.00 0.00 0.00 4.63
4682 5599 8.637986 ACACACATGTTTATTTTTACTCCACAT 58.362 29.630 0.00 0.00 34.46 3.21
4691 5608 6.870965 ACACACACACACACATGTTTATTTTT 59.129 30.769 0.00 0.00 36.72 1.94
4705 5623 0.925466 GGTACGACACACACACACAC 59.075 55.000 0.00 0.00 0.00 3.82
4719 5641 1.460504 TCAGTCTGGTAGCTGGTACG 58.539 55.000 10.55 0.00 33.81 3.67
4870 5859 0.802494 AATGTGCCGGCTAAGTTTCG 59.198 50.000 29.70 0.00 0.00 3.46
4902 5891 7.095899 GCCAACTTGAAGTTTGATGATTTTCTC 60.096 37.037 12.69 0.00 36.03 2.87
4923 5937 0.942884 GCTCTTTGCTGCTTGCCAAC 60.943 55.000 0.00 0.00 42.00 3.77
4938 5952 1.342819 GTGTGTGGAACTCTGAGCTCT 59.657 52.381 16.19 0.00 38.04 4.09
4951 5969 3.339253 TTGAGATCCTGATGTGTGTGG 57.661 47.619 0.00 0.00 0.00 4.17
4953 5971 7.170965 ACTTATTTTGAGATCCTGATGTGTGT 58.829 34.615 0.00 0.00 0.00 3.72
4954 5972 7.621428 ACTTATTTTGAGATCCTGATGTGTG 57.379 36.000 0.00 0.00 0.00 3.82
4979 6330 2.523245 TGGTGCATTGTTATCTTGCCA 58.477 42.857 0.00 0.00 35.51 4.92
5026 6398 4.537015 CTTTGTTAACTTTCAGGCCTTCG 58.463 43.478 0.00 0.00 0.00 3.79
5133 6843 5.340803 CCAAATGACTTCTTGCATCATCAG 58.659 41.667 0.40 0.00 31.84 2.90
5134 6844 4.381185 GCCAAATGACTTCTTGCATCATCA 60.381 41.667 0.40 0.00 31.84 3.07
5136 6846 3.118884 GGCCAAATGACTTCTTGCATCAT 60.119 43.478 0.00 0.00 34.52 2.45
5137 6847 2.231964 GGCCAAATGACTTCTTGCATCA 59.768 45.455 0.00 0.00 0.00 3.07
5138 6848 2.494870 AGGCCAAATGACTTCTTGCATC 59.505 45.455 5.01 0.00 0.00 3.91
5139 6849 2.232941 CAGGCCAAATGACTTCTTGCAT 59.767 45.455 5.01 0.00 0.00 3.96
5140 6850 1.614903 CAGGCCAAATGACTTCTTGCA 59.385 47.619 5.01 0.00 0.00 4.08
5141 6851 1.067354 CCAGGCCAAATGACTTCTTGC 60.067 52.381 5.01 0.00 0.00 4.01
5142 6852 1.547372 CCCAGGCCAAATGACTTCTTG 59.453 52.381 5.01 0.00 0.00 3.02
5146 6856 4.118584 GCCCAGGCCAAATGACTT 57.881 55.556 5.01 0.00 34.56 3.01
5184 6906 2.225727 GGAAACGTTTACAGCCCAGAAG 59.774 50.000 18.49 0.00 0.00 2.85
5185 6907 2.223745 GGAAACGTTTACAGCCCAGAA 58.776 47.619 18.49 0.00 0.00 3.02
5186 6908 1.543871 GGGAAACGTTTACAGCCCAGA 60.544 52.381 24.13 0.00 35.63 3.86
5187 6909 0.879090 GGGAAACGTTTACAGCCCAG 59.121 55.000 24.13 0.00 35.63 4.45
5188 6910 0.475044 AGGGAAACGTTTACAGCCCA 59.525 50.000 27.93 0.00 38.04 5.36
5189 6911 1.612676 AAGGGAAACGTTTACAGCCC 58.387 50.000 24.13 22.98 34.05 5.19
5190 6912 2.359848 ACAAAGGGAAACGTTTACAGCC 59.640 45.455 24.13 15.58 45.93 4.85
5191 6913 3.368495 CACAAAGGGAAACGTTTACAGC 58.632 45.455 24.13 8.40 45.93 4.40
5192 6914 3.959943 CCACAAAGGGAAACGTTTACAG 58.040 45.455 24.13 12.91 45.93 2.74
5317 7040 1.546029 GAAGAAGCTGGGGCGATTTTT 59.454 47.619 0.00 0.00 44.37 1.94
5323 7046 1.746991 GGAAGAAGAAGCTGGGGCG 60.747 63.158 0.00 0.00 44.37 6.13
5420 7144 3.083997 GGGCCTCACCGGAGATGT 61.084 66.667 9.46 0.00 44.26 3.06
5545 14196 2.048597 TCTACAACGGGTGCTGCG 60.049 61.111 0.00 0.00 0.00 5.18
5546 14197 2.391389 GCTCTACAACGGGTGCTGC 61.391 63.158 0.00 0.00 0.00 5.25
5547 14198 0.737715 GAGCTCTACAACGGGTGCTG 60.738 60.000 6.43 0.00 33.35 4.41
5548 14199 1.592223 GAGCTCTACAACGGGTGCT 59.408 57.895 6.43 0.00 35.43 4.40
5549 14200 1.805945 CGAGCTCTACAACGGGTGC 60.806 63.158 12.85 0.00 0.00 5.01
5551 14202 1.177256 ACACGAGCTCTACAACGGGT 61.177 55.000 12.85 1.67 37.56 5.28


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

AutoCloner maintained by Alex Coulton.