Multiple sequence alignment - TraesCS7B01G271200

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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 TraesCS7B01G271200 chr7B 100.000 7802 0 0 1 7802 498092364 498084563 0.000000e+00 14408.0
1 TraesCS7B01G271200 chr7B 82.549 659 104 8 6140 6797 106859047 106858399 3.160000e-158 569.0
2 TraesCS7B01G271200 chr7B 80.952 294 44 7 6515 6802 497966353 497966066 1.020000e-53 222.0
3 TraesCS7B01G271200 chr7A 88.725 3929 278 81 3226 7060 522020761 522024618 0.000000e+00 4649.0
4 TraesCS7B01G271200 chr7A 84.388 3081 233 114 1 2948 522017278 522020243 0.000000e+00 2796.0
5 TraesCS7B01G271200 chr7A 83.005 659 101 8 6140 6797 144170873 144170225 3.140000e-163 586.0
6 TraesCS7B01G271200 chr7A 80.719 306 47 8 6503 6802 522111324 522111025 2.190000e-55 228.0
7 TraesCS7B01G271200 chr7A 80.000 190 24 9 3966 4151 209401472 209401293 2.290000e-25 128.0
8 TraesCS7B01G271200 chr7D 90.676 2456 76 50 309 2661 474014607 474012202 0.000000e+00 3125.0
9 TraesCS7B01G271200 chr7D 93.659 1782 82 12 2648 4422 474010487 474008730 0.000000e+00 2636.0
10 TraesCS7B01G271200 chr7D 91.515 1320 73 13 4803 6083 474007418 474006099 0.000000e+00 1781.0
11 TraesCS7B01G271200 chr7D 95.869 1041 30 5 6123 7158 474006096 474005064 0.000000e+00 1672.0
12 TraesCS7B01G271200 chr7D 94.418 627 35 0 7176 7802 530742582 530743208 0.000000e+00 965.0
13 TraesCS7B01G271200 chr7D 83.005 659 101 8 6140 6797 141562150 141562798 3.140000e-163 586.0
14 TraesCS7B01G271200 chr7D 93.254 252 10 3 4540 4789 474008725 474008479 1.600000e-96 364.0
15 TraesCS7B01G271200 chr7D 89.212 241 24 1 3227 3467 79873921 79873683 4.580000e-77 300.0
16 TraesCS7B01G271200 chr7D 85.765 281 37 3 6134 6412 473649858 473649579 2.130000e-75 294.0
17 TraesCS7B01G271200 chr7D 80.456 307 46 9 6503 6802 473649530 473649231 1.020000e-53 222.0
18 TraesCS7B01G271200 chr7D 98.333 120 2 0 1 120 474014769 474014650 2.210000e-50 211.0
19 TraesCS7B01G271200 chr7D 100.000 37 0 0 218 254 474014657 474014621 1.400000e-07 69.4
20 TraesCS7B01G271200 chr1D 93.770 626 39 0 7177 7802 22099461 22100086 0.000000e+00 941.0
21 TraesCS7B01G271200 chr1D 90.164 244 22 1 3227 3470 465991034 465990793 4.540000e-82 316.0
22 TraesCS7B01G271200 chr1D 89.212 241 23 2 3227 3467 323916556 323916793 1.650000e-76 298.0
23 TraesCS7B01G271200 chr1D 80.749 187 29 5 83 262 379800326 379800140 1.060000e-28 139.0
24 TraesCS7B01G271200 chr1D 81.183 186 19 10 3966 4148 254487830 254488002 1.370000e-27 135.0
25 TraesCS7B01G271200 chr1D 79.570 186 19 11 3966 4148 244400306 244400475 1.780000e-21 115.0
26 TraesCS7B01G271200 chr1D 79.032 186 21 13 3966 4148 244422293 244422463 2.300000e-20 111.0
27 TraesCS7B01G271200 chr3B 88.197 610 55 5 7193 7802 29604962 29605554 0.000000e+00 712.0
28 TraesCS7B01G271200 chr1A 88.730 488 55 0 7178 7665 549508573 549509060 1.450000e-166 597.0
29 TraesCS7B01G271200 chr1A 77.041 196 38 4 56 244 480927877 480927682 1.070000e-18 106.0
30 TraesCS7B01G271200 chr2D 80.938 661 100 19 6147 6797 574656800 574657444 4.200000e-137 499.0
31 TraesCS7B01G271200 chr2D 81.183 186 21 8 3966 4148 628283804 628283978 3.800000e-28 137.0
32 TraesCS7B01G271200 chr2D 80.645 186 21 9 3966 4148 28725230 28725403 6.350000e-26 130.0
33 TraesCS7B01G271200 chr2B 80.488 656 106 16 6147 6794 690931109 690931750 4.230000e-132 483.0
34 TraesCS7B01G271200 chr2A 80.211 662 100 20 6147 6797 713016599 713017240 1.190000e-127 468.0
35 TraesCS7B01G271200 chr3A 91.026 234 21 0 7569 7802 737460000 737460233 4.540000e-82 316.0
36 TraesCS7B01G271200 chr6A 90.083 242 21 2 3227 3467 578513320 578513081 2.110000e-80 311.0
37 TraesCS7B01G271200 chr6A 88.755 249 26 1 3219 3467 514705120 514704874 3.540000e-78 303.0
38 TraesCS7B01G271200 chr4D 89.627 241 23 1 3227 3467 177493752 177493990 9.840000e-79 305.0
39 TraesCS7B01G271200 chr6B 87.023 262 27 5 3209 3468 22739938 22740194 9.910000e-74 289.0
40 TraesCS7B01G271200 chr1B 78.113 265 50 5 5 262 509895066 509894803 2.250000e-35 161.0
41 TraesCS7B01G271200 chr6D 80.645 186 22 8 3966 4148 431398157 431398331 1.770000e-26 132.0


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 TraesCS7B01G271200 chr7B 498084563 498092364 7801 True 14408.000000 14408 100.0000 1 7802 1 chr7B.!!$R3 7801
1 TraesCS7B01G271200 chr7B 106858399 106859047 648 True 569.000000 569 82.5490 6140 6797 1 chr7B.!!$R1 657
2 TraesCS7B01G271200 chr7A 522017278 522024618 7340 False 3722.500000 4649 86.5565 1 7060 2 chr7A.!!$F1 7059
3 TraesCS7B01G271200 chr7A 144170225 144170873 648 True 586.000000 586 83.0050 6140 6797 1 chr7A.!!$R1 657
4 TraesCS7B01G271200 chr7D 474005064 474014769 9705 True 1408.342857 3125 94.7580 1 7158 7 chr7D.!!$R3 7157
5 TraesCS7B01G271200 chr7D 530742582 530743208 626 False 965.000000 965 94.4180 7176 7802 1 chr7D.!!$F2 626
6 TraesCS7B01G271200 chr7D 141562150 141562798 648 False 586.000000 586 83.0050 6140 6797 1 chr7D.!!$F1 657
7 TraesCS7B01G271200 chr7D 473649231 473649858 627 True 258.000000 294 83.1105 6134 6802 2 chr7D.!!$R2 668
8 TraesCS7B01G271200 chr1D 22099461 22100086 625 False 941.000000 941 93.7700 7177 7802 1 chr1D.!!$F1 625
9 TraesCS7B01G271200 chr3B 29604962 29605554 592 False 712.000000 712 88.1970 7193 7802 1 chr3B.!!$F1 609
10 TraesCS7B01G271200 chr2D 574656800 574657444 644 False 499.000000 499 80.9380 6147 6797 1 chr2D.!!$F2 650
11 TraesCS7B01G271200 chr2B 690931109 690931750 641 False 483.000000 483 80.4880 6147 6794 1 chr2B.!!$F1 647
12 TraesCS7B01G271200 chr2A 713016599 713017240 641 False 468.000000 468 80.2110 6147 6797 1 chr2A.!!$F1 650

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
156 157 0.617935 GAGCTCAAGAAAGAGGGGCT 59.382 55.000 9.40 0.00 36.15 5.19 F
268 270 0.858961 GCAGATCAACGTGCGAATGC 60.859 55.000 10.86 10.86 43.20 3.56 F
1642 1705 1.446907 ACGTACGGTCACTAGTCCTG 58.553 55.000 21.06 0.00 0.00 3.86 F
2184 2315 0.172127 GCGCATCTCTGACTGACTGA 59.828 55.000 0.30 0.00 0.00 3.41 F
3091 5348 0.600255 CGTAGATCATGGGGCCGTTC 60.600 60.000 0.00 0.00 0.00 3.95 F
3575 5865 1.202818 GGTTCCCCTACATGCATCTCC 60.203 57.143 0.00 0.00 0.00 3.71 F
5309 8690 0.613853 TCACCTTCTACACCTCCGGG 60.614 60.000 0.00 0.00 38.88 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1979 2078 0.098376 GTGCATAGAAGCAGCAGCAC 59.902 55.0 3.17 0.0 46.69 4.40 R
1990 2101 0.608130 AGCTGTTCACCGTGCATAGA 59.392 50.0 0.00 0.0 0.00 1.98 R
2458 2630 0.243907 CCAGTATATCGCGTCAGGGG 59.756 60.0 5.77 0.0 0.00 4.79 R
3224 5487 0.700564 ACCAGGACGGAGGTAGTACA 59.299 55.0 2.06 0.0 36.07 2.90 R
4446 6749 0.537143 AAATTGTGCAGCCCTCGTCA 60.537 50.0 0.00 0.0 0.00 4.35 R
5557 8953 0.319083 TCGTGTACCCGATTGCAGTT 59.681 50.0 0.00 0.0 30.63 3.16 R
6982 10418 0.339859 ACATCTGGAGCCTGTAGGGA 59.660 55.0 0.00 0.0 37.23 4.20 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
23 24 6.705863 GCACAAAAAGAGAGGATGGATTAT 57.294 37.500 0.00 0.00 0.00 1.28
80 81 3.197927 AGGAGAGGATTGACTTGGAGT 57.802 47.619 0.00 0.00 0.00 3.85
143 144 4.515191 AGACTTTTGCGTTAATTGAGCTCA 59.485 37.500 13.74 13.74 0.00 4.26
152 153 5.672321 GCGTTAATTGAGCTCAAGAAAGAGG 60.672 44.000 31.14 20.15 39.47 3.69
154 155 2.867109 TTGAGCTCAAGAAAGAGGGG 57.133 50.000 25.16 0.00 36.15 4.79
156 157 0.617935 GAGCTCAAGAAAGAGGGGCT 59.382 55.000 9.40 0.00 36.15 5.19
162 163 1.787462 AAGAAAGAGGGGCTGCAGCT 61.787 55.000 35.82 18.89 41.70 4.24
208 209 4.388499 TTGGCCGACGCTTCCCTC 62.388 66.667 0.00 0.00 34.44 4.30
216 218 1.433534 GACGCTTCCCTCTTTGACTG 58.566 55.000 0.00 0.00 0.00 3.51
259 261 3.124297 GGTGAAGAAGAAGCAGATCAACG 59.876 47.826 0.00 0.00 0.00 4.10
260 262 3.743396 GTGAAGAAGAAGCAGATCAACGT 59.257 43.478 0.00 0.00 0.00 3.99
261 263 3.742882 TGAAGAAGAAGCAGATCAACGTG 59.257 43.478 0.00 0.00 0.00 4.49
268 270 0.858961 GCAGATCAACGTGCGAATGC 60.859 55.000 10.86 10.86 43.20 3.56
283 285 5.904872 GCGAATGCGAATGATTCATTATC 57.095 39.130 11.79 7.46 40.82 1.75
291 293 6.644592 TGCGAATGATTCATTATCGTATCACA 59.355 34.615 17.49 7.72 33.90 3.58
346 349 4.619973 TGTGGAATTGTTGAATTGTGCTC 58.380 39.130 0.00 0.00 31.58 4.26
457 460 2.630580 GAGGATAAATGAGGAGCCGTCT 59.369 50.000 0.00 0.00 0.00 4.18
531 534 6.153067 CGGATTAGGTTGTAGATGCTCTTAG 58.847 44.000 0.00 0.00 0.00 2.18
651 656 8.426569 TTGGTTGGTTGAAGTATACTACTACT 57.573 34.615 5.65 0.00 38.26 2.57
652 657 9.532494 TTGGTTGGTTGAAGTATACTACTACTA 57.468 33.333 5.65 0.00 38.26 1.82
653 658 9.182214 TGGTTGGTTGAAGTATACTACTACTAG 57.818 37.037 5.65 0.00 38.26 2.57
654 659 9.183368 GGTTGGTTGAAGTATACTACTACTAGT 57.817 37.037 5.65 0.00 38.26 2.57
828 837 2.465920 GATAGCATACGCGCGTGC 59.534 61.111 42.78 36.34 45.49 5.34
865 877 6.022107 TCACCGCCTGTATATATATAGGGT 57.978 41.667 27.61 18.77 40.72 4.34
1227 1259 2.614212 CACGCTTAATTATCACGTGCG 58.386 47.619 11.67 10.22 46.11 5.34
1228 1260 2.990774 CGCTTAATTATCACGTGCGT 57.009 45.000 11.67 4.49 37.62 5.24
1230 1262 2.028763 CGCTTAATTATCACGTGCGTGT 59.971 45.455 21.63 12.91 45.55 4.49
1231 1263 3.594312 GCTTAATTATCACGTGCGTGTC 58.406 45.455 21.63 1.54 45.55 3.67
1232 1264 3.543460 GCTTAATTATCACGTGCGTGTCC 60.543 47.826 21.63 0.00 45.55 4.02
1273 1305 2.973316 GCCAAAACACTACCGCCGG 61.973 63.158 0.00 0.00 0.00 6.13
1274 1306 2.559330 CAAAACACTACCGCCGGC 59.441 61.111 19.07 19.07 0.00 6.13
1275 1307 2.670592 AAAACACTACCGCCGGCC 60.671 61.111 23.46 2.84 0.00 6.13
1325 1361 3.049674 CTTGTGCCATCGCCACGT 61.050 61.111 0.00 0.00 0.00 4.49
1326 1362 2.593148 TTGTGCCATCGCCACGTT 60.593 55.556 0.00 0.00 0.00 3.99
1327 1363 2.784957 CTTGTGCCATCGCCACGTTG 62.785 60.000 0.00 0.00 0.00 4.10
1328 1364 4.101790 GTGCCATCGCCACGTTGG 62.102 66.667 11.72 11.72 45.92 3.77
1329 1365 4.321966 TGCCATCGCCACGTTGGA 62.322 61.111 18.54 3.94 46.01 3.53
1330 1366 3.799755 GCCATCGCCACGTTGGAC 61.800 66.667 18.54 8.06 46.01 4.02
1331 1367 3.124921 CCATCGCCACGTTGGACC 61.125 66.667 10.78 0.00 46.01 4.46
1333 1369 3.632080 ATCGCCACGTTGGACCCA 61.632 61.111 8.04 0.00 40.96 4.51
1334 1370 3.894547 ATCGCCACGTTGGACCCAC 62.895 63.158 8.04 0.00 40.96 4.61
1579 1633 3.001736 GGAAGAAACTATCATGCTCGCAC 59.998 47.826 0.00 0.00 0.00 5.34
1642 1705 1.446907 ACGTACGGTCACTAGTCCTG 58.553 55.000 21.06 0.00 0.00 3.86
1674 1737 3.141522 TTGGACGGTTGTCGCGTCT 62.142 57.895 5.77 0.00 46.49 4.18
1676 1739 2.254651 GACGGTTGTCGCGTCTCT 59.745 61.111 5.77 0.00 43.89 3.10
1706 1774 4.839668 TTTGGTTTCGTTCCAAATCGAT 57.160 36.364 13.87 0.00 45.99 3.59
1707 1775 4.413495 TTGGTTTCGTTCCAAATCGATC 57.587 40.909 0.00 0.00 41.25 3.69
1708 1776 2.413796 TGGTTTCGTTCCAAATCGATCG 59.586 45.455 9.36 9.36 36.01 3.69
1835 1911 9.613428 AGATTTGTCTCGATACCAATATTTTGA 57.387 29.630 0.96 0.00 34.60 2.69
1836 1912 9.869844 GATTTGTCTCGATACCAATATTTTGAG 57.130 33.333 0.96 0.00 34.60 3.02
1933 2028 1.976474 GCATTGGAGGGAAACGGCA 60.976 57.895 0.00 0.00 0.00 5.69
1961 2060 6.405842 CCTGTTCACTGTGCATGACTATACTA 60.406 42.308 2.12 0.00 0.00 1.82
2017 2128 2.633657 GTGAACAGCTGTGCACCG 59.366 61.111 38.23 9.51 46.51 4.94
2142 2273 2.279517 GGGTAGCGTGGATGCTCG 60.280 66.667 4.18 4.18 45.87 5.03
2143 2274 2.494918 GGTAGCGTGGATGCTCGT 59.505 61.111 10.35 0.64 45.87 4.18
2144 2275 1.878522 GGTAGCGTGGATGCTCGTG 60.879 63.158 10.35 0.00 45.87 4.35
2145 2276 1.878522 GTAGCGTGGATGCTCGTGG 60.879 63.158 10.35 0.00 45.87 4.94
2147 2278 2.279502 TAGCGTGGATGCTCGTGGTC 62.280 60.000 10.35 0.00 45.87 4.02
2148 2279 2.509336 CGTGGATGCTCGTGGTCC 60.509 66.667 0.09 0.00 0.00 4.46
2151 2282 0.464036 GTGGATGCTCGTGGTCCATA 59.536 55.000 0.00 0.00 43.38 2.74
2152 2283 1.070758 GTGGATGCTCGTGGTCCATAT 59.929 52.381 0.00 0.00 43.38 1.78
2153 2284 1.070601 TGGATGCTCGTGGTCCATATG 59.929 52.381 0.00 0.00 37.12 1.78
2182 2313 1.138459 CGCGCATCTCTGACTGACT 59.862 57.895 8.75 0.00 0.00 3.41
2183 2314 1.138636 CGCGCATCTCTGACTGACTG 61.139 60.000 8.75 0.00 0.00 3.51
2184 2315 0.172127 GCGCATCTCTGACTGACTGA 59.828 55.000 0.30 0.00 0.00 3.41
2185 2316 1.906757 CGCATCTCTGACTGACTGAC 58.093 55.000 0.00 0.00 0.00 3.51
2252 2386 3.821841 CACGTGTTGGAAGGAAATTAGC 58.178 45.455 7.58 0.00 0.00 3.09
2257 2391 4.462483 GTGTTGGAAGGAAATTAGCATCCA 59.538 41.667 0.00 0.00 38.23 3.41
2413 2566 3.368843 CCTGTCAATCTCACCAACTCGAT 60.369 47.826 0.00 0.00 0.00 3.59
2458 2630 2.093658 TCTTACCCGGCAGAATCTGTTC 60.094 50.000 12.29 4.13 33.43 3.18
2463 2635 0.745845 CGGCAGAATCTGTTCCCCTG 60.746 60.000 12.29 0.00 34.81 4.45
2509 2683 2.297597 GAGCCAAGCCGTATCAGTATCT 59.702 50.000 0.00 0.00 0.00 1.98
2535 2709 3.551846 GGTCAAGTTTCCCTTTCAGTCA 58.448 45.455 0.00 0.00 0.00 3.41
2555 2731 5.946377 AGTCAATTCCCTTGGACAATTCTAC 59.054 40.000 0.00 0.00 35.43 2.59
2628 2804 4.631813 ACACAGAGCCGATATGAACTTTTC 59.368 41.667 0.00 0.00 0.00 2.29
2630 2806 6.042777 CACAGAGCCGATATGAACTTTTCTA 58.957 40.000 0.00 0.00 0.00 2.10
2693 4597 2.112718 GGCCTAGGCATGGAGCTG 59.887 66.667 34.09 0.00 44.79 4.24
2733 4638 1.725641 CCTTCAACGCAGCAGATACA 58.274 50.000 0.00 0.00 0.00 2.29
2804 4721 3.329386 GGAAAAAGATGGCCTTGCTTTC 58.671 45.455 15.18 11.76 33.76 2.62
3006 5263 5.941146 AGTCAATATCCTCTCCTCCTAGT 57.059 43.478 0.00 0.00 0.00 2.57
3015 5272 4.016479 TCCTCTCCTCCTAGTTACCATGTT 60.016 45.833 0.00 0.00 0.00 2.71
3020 5277 4.030913 CCTCCTAGTTACCATGTTGAGGA 58.969 47.826 0.00 0.00 40.43 3.71
3074 5331 3.656045 CCGGCCGAAAGCAAACGT 61.656 61.111 30.73 0.00 46.50 3.99
3091 5348 0.600255 CGTAGATCATGGGGCCGTTC 60.600 60.000 0.00 0.00 0.00 3.95
3126 5383 2.821969 ACATTCATGAGGCCTTGTGTTC 59.178 45.455 6.77 0.00 0.00 3.18
3136 5393 3.123050 GGCCTTGTGTTCACATTTGTTC 58.877 45.455 6.47 0.00 0.00 3.18
3206 5469 5.646577 ATCGGTTCTATGTACTAGGATGC 57.353 43.478 0.00 0.00 0.00 3.91
3335 5598 9.095529 CATGTCATCAAAAATTATACATCGTCG 57.904 33.333 0.00 0.00 0.00 5.12
3437 5700 8.596380 GGTCAAAATTCAACACAAAATACGAAA 58.404 29.630 0.00 0.00 0.00 3.46
3439 5702 8.812329 TCAAAATTCAACACAAAATACGAAAGG 58.188 29.630 0.00 0.00 0.00 3.11
3453 5716 4.042271 ACGAAAGGGACCAATAAACCAT 57.958 40.909 0.00 0.00 0.00 3.55
3525 5815 7.591426 GCAAAGTACACACAATTTTTCTCTAGG 59.409 37.037 0.00 0.00 0.00 3.02
3526 5816 8.621286 CAAAGTACACACAATTTTTCTCTAGGT 58.379 33.333 0.00 0.00 0.00 3.08
3527 5817 9.841295 AAAGTACACACAATTTTTCTCTAGGTA 57.159 29.630 0.00 0.00 0.00 3.08
3528 5818 9.490379 AAGTACACACAATTTTTCTCTAGGTAG 57.510 33.333 0.00 0.00 0.00 3.18
3529 5819 8.648693 AGTACACACAATTTTTCTCTAGGTAGT 58.351 33.333 0.00 0.00 0.00 2.73
3530 5820 9.918630 GTACACACAATTTTTCTCTAGGTAGTA 57.081 33.333 0.00 0.00 0.00 1.82
3575 5865 1.202818 GGTTCCCCTACATGCATCTCC 60.203 57.143 0.00 0.00 0.00 3.71
3576 5866 1.490490 GTTCCCCTACATGCATCTCCA 59.510 52.381 0.00 0.00 0.00 3.86
3580 5870 3.205056 TCCCCTACATGCATCTCCAATTT 59.795 43.478 0.00 0.00 0.00 1.82
3766 6067 4.891627 TGTATGATACAAAATGGCACGG 57.108 40.909 2.20 0.00 35.38 4.94
3868 6170 5.644188 TCAAGGTCAGGATTTCCTTTTGAT 58.356 37.500 0.00 0.00 46.09 2.57
3916 6219 9.057089 AGTTAGACCTTTTGAAAATGTAGACAG 57.943 33.333 0.00 0.00 0.00 3.51
4080 6383 2.946990 TCTTCCGTTGAAGGGTTGTTTC 59.053 45.455 3.62 0.00 46.61 2.78
4098 6401 9.608617 GGTTGTTTCTATTTTTAGACTAGTTGC 57.391 33.333 0.00 0.00 0.00 4.17
4217 6520 9.419297 GAAATAGTATTCATACTTACCATGCGA 57.581 33.333 4.80 0.00 43.06 5.10
4394 6697 3.130633 TGTTCTCTGTTTGATCCACACG 58.869 45.455 0.00 0.00 0.00 4.49
4422 6725 2.163818 TGATTTTTCTGTCGAGGCGT 57.836 45.000 0.00 0.00 0.00 5.68
4425 6728 2.074547 TTTTTCTGTCGAGGCGTAGG 57.925 50.000 0.00 0.00 0.00 3.18
4466 6769 1.271108 TGACGAGGGCTGCACAATTTA 60.271 47.619 4.01 0.00 0.00 1.40
4565 6869 1.118838 AGTAGCCTCATGCCTGTCTC 58.881 55.000 0.00 0.00 42.71 3.36
4683 6988 9.308000 TCCCAAGATAATGTTTTGTTAGTGAAT 57.692 29.630 0.00 0.00 0.00 2.57
4754 7059 6.343226 TGCAAATTTCGGCTAAAATTATGC 57.657 33.333 20.58 20.58 37.75 3.14
4774 7080 1.539388 CCCATTTGTGCGCTGTTTAGA 59.461 47.619 9.73 0.00 0.00 2.10
4777 7083 3.670055 CCATTTGTGCGCTGTTTAGAAAG 59.330 43.478 9.73 0.00 0.00 2.62
4843 8196 7.698836 ATTTTCTTCATAAAGCACACACAAC 57.301 32.000 0.00 0.00 32.18 3.32
4877 8230 6.095432 TGGGTCAAAATTGTTAGGTTCATG 57.905 37.500 0.00 0.00 0.00 3.07
4996 8367 9.515020 TGCAAATCATCGTTATATTTTTCCTTC 57.485 29.630 0.00 0.00 0.00 3.46
4997 8368 9.736023 GCAAATCATCGTTATATTTTTCCTTCT 57.264 29.630 0.00 0.00 0.00 2.85
5019 8390 9.586435 CTTCTGAACTTTGGTAGATTTTTGTTT 57.414 29.630 0.00 0.00 0.00 2.83
5022 8393 8.696410 TGAACTTTGGTAGATTTTTGTTTGTC 57.304 30.769 0.00 0.00 0.00 3.18
5023 8394 7.486551 TGAACTTTGGTAGATTTTTGTTTGTCG 59.513 33.333 0.00 0.00 0.00 4.35
5026 8397 7.911727 ACTTTGGTAGATTTTTGTTTGTCGTAC 59.088 33.333 0.00 0.00 0.00 3.67
5042 8413 5.555552 TGTCGTACATGTTATCAAAATGCG 58.444 37.500 2.30 0.00 0.00 4.73
5087 8458 4.916983 AGTTTCAGCAGCAATTACAACA 57.083 36.364 0.00 0.00 0.00 3.33
5097 8468 2.724174 GCAATTACAACAACGGAACAGC 59.276 45.455 0.00 0.00 0.00 4.40
5109 8480 4.976224 ACGGAACAGCACTAAAACTTTT 57.024 36.364 0.00 0.00 0.00 2.27
5114 8485 5.232202 GGAACAGCACTAAAACTTTTCAAGC 59.768 40.000 0.00 0.00 0.00 4.01
5117 8488 4.207841 CAGCACTAAAACTTTTCAAGCTGC 59.792 41.667 15.74 0.00 40.16 5.25
5146 8527 3.812053 AGAACTGACTGACAATCTTGTGC 59.188 43.478 0.00 0.00 42.43 4.57
5147 8528 2.138320 ACTGACTGACAATCTTGTGCG 58.862 47.619 0.00 0.00 42.43 5.34
5151 8532 3.433274 TGACTGACAATCTTGTGCGATTC 59.567 43.478 0.00 0.00 42.43 2.52
5162 8543 2.390599 TGCGATTCGTTGAGCAGGC 61.391 57.895 8.03 0.00 34.39 4.85
5296 8677 1.446907 CTCTTCGCAGCAATCACCTT 58.553 50.000 0.00 0.00 0.00 3.50
5309 8690 0.613853 TCACCTTCTACACCTCCGGG 60.614 60.000 0.00 0.00 38.88 5.73
5413 8794 4.397481 TGAGTAAGTCTCATGCCTCATG 57.603 45.455 0.59 0.59 46.77 3.07
5557 8953 1.001048 CAGTACGTCAACTTGGTCGGA 60.001 52.381 0.00 1.79 0.00 4.55
5644 9042 7.355778 ACAAAGTTTTCAATGTCTCGAGATTC 58.644 34.615 19.90 7.29 0.00 2.52
5656 9054 3.070018 CTCGAGATTCTGTGTTTTGGCT 58.930 45.455 6.58 0.00 0.00 4.75
5658 9056 3.498397 TCGAGATTCTGTGTTTTGGCTTC 59.502 43.478 0.00 0.00 0.00 3.86
5789 9196 1.555533 GGGGTCGTCCAGATCTTCTTT 59.444 52.381 0.04 0.00 37.22 2.52
6020 9427 0.945813 CCTTCGCCTACTCCTACTCG 59.054 60.000 0.00 0.00 0.00 4.18
6050 9457 4.774124 TCATAGAAATCCAGGTGAGCAAG 58.226 43.478 0.00 0.00 0.00 4.01
6052 9459 1.353694 AGAAATCCAGGTGAGCAAGCT 59.646 47.619 0.00 0.00 36.97 3.74
6053 9460 2.165998 GAAATCCAGGTGAGCAAGCTT 58.834 47.619 0.00 0.00 33.14 3.74
6083 9493 0.106669 ATCCCCGAGTCTGACGATGA 60.107 55.000 1.52 0.00 0.00 2.92
6084 9494 0.323087 TCCCCGAGTCTGACGATGAA 60.323 55.000 1.52 0.00 0.00 2.57
6086 9496 0.526211 CCCGAGTCTGACGATGAACA 59.474 55.000 1.52 0.00 0.00 3.18
6087 9497 1.135139 CCCGAGTCTGACGATGAACAT 59.865 52.381 1.52 0.00 0.00 2.71
6088 9498 2.188524 CCGAGTCTGACGATGAACATG 58.811 52.381 1.52 0.00 0.00 3.21
6089 9499 2.159379 CCGAGTCTGACGATGAACATGA 60.159 50.000 0.00 0.00 0.00 3.07
6090 9500 3.501950 CGAGTCTGACGATGAACATGAA 58.498 45.455 0.00 0.00 0.00 2.57
6091 9501 3.920412 CGAGTCTGACGATGAACATGAAA 59.080 43.478 0.00 0.00 0.00 2.69
6092 9502 4.385748 CGAGTCTGACGATGAACATGAAAA 59.614 41.667 0.00 0.00 0.00 2.29
6093 9503 5.597813 AGTCTGACGATGAACATGAAAAC 57.402 39.130 0.00 0.00 0.00 2.43
6094 9504 4.150627 AGTCTGACGATGAACATGAAAACG 59.849 41.667 0.00 1.16 0.00 3.60
6096 9506 4.385748 TCTGACGATGAACATGAAAACGAG 59.614 41.667 0.00 0.00 0.00 4.18
6097 9507 4.055360 TGACGATGAACATGAAAACGAGT 58.945 39.130 0.00 0.00 0.00 4.18
6098 9508 4.149922 TGACGATGAACATGAAAACGAGTC 59.850 41.667 0.00 1.56 0.00 3.36
6099 9509 4.055360 ACGATGAACATGAAAACGAGTCA 58.945 39.130 0.00 0.00 0.00 3.41
6100 9510 4.084537 ACGATGAACATGAAAACGAGTCAC 60.085 41.667 0.00 0.00 0.00 3.67
6101 9511 4.150627 CGATGAACATGAAAACGAGTCACT 59.849 41.667 0.00 0.00 0.00 3.41
6102 9512 4.794248 TGAACATGAAAACGAGTCACTG 57.206 40.909 0.00 0.00 0.00 3.66
6103 9513 4.188462 TGAACATGAAAACGAGTCACTGT 58.812 39.130 0.00 0.00 0.00 3.55
6104 9514 4.634004 TGAACATGAAAACGAGTCACTGTT 59.366 37.500 0.00 2.96 33.43 3.16
6105 9515 4.536364 ACATGAAAACGAGTCACTGTTG 57.464 40.909 0.00 0.00 0.00 3.33
6106 9516 3.938963 ACATGAAAACGAGTCACTGTTGT 59.061 39.130 0.00 0.00 0.00 3.32
6107 9517 4.201812 ACATGAAAACGAGTCACTGTTGTG 60.202 41.667 0.00 0.00 45.07 3.33
6108 9518 3.331150 TGAAAACGAGTCACTGTTGTGT 58.669 40.909 0.00 0.00 44.14 3.72
6109 9519 3.369756 TGAAAACGAGTCACTGTTGTGTC 59.630 43.478 0.00 0.00 44.14 3.67
6110 9520 2.961526 AACGAGTCACTGTTGTGTCT 57.038 45.000 0.00 0.00 43.24 3.41
6111 9521 2.961526 ACGAGTCACTGTTGTGTCTT 57.038 45.000 0.00 0.00 41.30 3.01
6112 9522 2.810650 ACGAGTCACTGTTGTGTCTTC 58.189 47.619 0.00 0.00 41.30 2.87
6113 9523 2.165641 ACGAGTCACTGTTGTGTCTTCA 59.834 45.455 0.00 0.00 41.30 3.02
6114 9524 2.791560 CGAGTCACTGTTGTGTCTTCAG 59.208 50.000 0.00 0.00 41.30 3.02
6115 9525 3.735208 CGAGTCACTGTTGTGTCTTCAGT 60.735 47.826 0.00 0.00 41.30 3.41
6116 9526 4.497507 CGAGTCACTGTTGTGTCTTCAGTA 60.498 45.833 0.00 0.00 41.30 2.74
6117 9527 4.938080 AGTCACTGTTGTGTCTTCAGTAG 58.062 43.478 0.00 0.00 44.14 2.57
6118 9528 4.402793 AGTCACTGTTGTGTCTTCAGTAGT 59.597 41.667 0.00 0.00 44.14 2.73
6119 9529 4.504461 GTCACTGTTGTGTCTTCAGTAGTG 59.496 45.833 0.00 0.00 44.14 2.74
6120 9530 4.401202 TCACTGTTGTGTCTTCAGTAGTGA 59.599 41.667 0.00 0.00 44.14 3.41
6121 9531 4.742167 CACTGTTGTGTCTTCAGTAGTGAG 59.258 45.833 0.00 0.00 39.89 3.51
6729 10152 3.241530 TTCCTGGTGTCGCTGGCT 61.242 61.111 0.00 0.00 0.00 4.75
6783 10206 0.526662 CGCTCAAGAACTACGTCCCT 59.473 55.000 0.00 0.00 0.00 4.20
6869 10299 3.791789 GCTTGTTTGTGCGTGAGAAATCA 60.792 43.478 0.00 0.00 0.00 2.57
6870 10300 4.539870 CTTGTTTGTGCGTGAGAAATCAT 58.460 39.130 0.00 0.00 0.00 2.45
6871 10301 4.145876 TGTTTGTGCGTGAGAAATCATC 57.854 40.909 0.00 0.00 0.00 2.92
6872 10302 3.814842 TGTTTGTGCGTGAGAAATCATCT 59.185 39.130 0.00 0.00 42.61 2.90
6886 10316 1.373497 CATCTATCGTCGGCTGGGC 60.373 63.158 0.00 0.00 0.00 5.36
6934 10368 3.357079 CCCGGCTGTGTTGCTCAC 61.357 66.667 0.00 5.83 46.31 3.51
6975 10409 8.824783 CAAGGAAGGGAGAGATTTATAGATCAT 58.175 37.037 6.08 0.00 0.00 2.45
7029 10465 9.880157 GGTCCTGACTTTATGTACATAAACTTA 57.120 33.333 28.96 18.74 38.08 2.24
7072 10508 2.938838 TGTTTAACTTGAGTGGTGGGG 58.061 47.619 0.00 0.00 0.00 4.96
7074 10510 0.847373 TTAACTTGAGTGGTGGGGCA 59.153 50.000 0.00 0.00 0.00 5.36
7100 10536 4.280819 CTTCCTCATCTTCTCACTCTCCT 58.719 47.826 0.00 0.00 0.00 3.69
7101 10537 4.329638 TCCTCATCTTCTCACTCTCCTT 57.670 45.455 0.00 0.00 0.00 3.36
7125 10562 2.844946 TGAAATGTGTTCTTCGCCTCA 58.155 42.857 0.00 0.00 0.00 3.86
7137 10574 1.669115 CGCCTCACTCCACCACTTG 60.669 63.158 0.00 0.00 0.00 3.16
7143 10580 2.571653 CTCACTCCACCACTTGGGATAA 59.428 50.000 0.00 0.00 46.92 1.75
7150 10587 3.701040 CCACCACTTGGGATAATTGAAGG 59.299 47.826 0.00 0.00 42.54 3.46
7151 10588 4.569653 CCACCACTTGGGATAATTGAAGGA 60.570 45.833 0.00 0.00 42.54 3.36
7158 10595 6.209391 ACTTGGGATAATTGAAGGAAGTTGTG 59.791 38.462 0.00 0.00 0.00 3.33
7159 10596 5.640147 TGGGATAATTGAAGGAAGTTGTGT 58.360 37.500 0.00 0.00 0.00 3.72
7160 10597 6.074648 TGGGATAATTGAAGGAAGTTGTGTT 58.925 36.000 0.00 0.00 0.00 3.32
7161 10598 6.553100 TGGGATAATTGAAGGAAGTTGTGTTT 59.447 34.615 0.00 0.00 0.00 2.83
7162 10599 7.070571 TGGGATAATTGAAGGAAGTTGTGTTTT 59.929 33.333 0.00 0.00 0.00 2.43
7163 10600 7.931407 GGGATAATTGAAGGAAGTTGTGTTTTT 59.069 33.333 0.00 0.00 0.00 1.94
7340 10777 2.361104 GCCAATCTCCGCCAACCA 60.361 61.111 0.00 0.00 0.00 3.67
7417 10854 3.916544 CTAGGCTCGCCGGCATCA 61.917 66.667 28.98 8.56 41.95 3.07
7419 10856 2.721971 CTAGGCTCGCCGGCATCATT 62.722 60.000 28.98 11.16 41.95 2.57
7454 10891 1.195442 TCCCACGTCAAGCACCCATA 61.195 55.000 0.00 0.00 0.00 2.74
7495 10932 4.408821 GGACATGTGCCTCCGCCA 62.409 66.667 1.15 0.00 0.00 5.69
7505 10942 4.415150 CTCCGCCACCAGTGCCAT 62.415 66.667 0.00 0.00 0.00 4.40
7625 11062 1.610379 TGCTGCCTCACCTCTGCTA 60.610 57.895 0.00 0.00 0.00 3.49
7629 11066 0.826715 TGCCTCACCTCTGCTATGAC 59.173 55.000 0.00 0.00 0.00 3.06
7696 11133 0.874390 GCTGGCAACTCGTCAAATCA 59.126 50.000 0.00 0.00 37.61 2.57
7698 11135 0.865111 TGGCAACTCGTCAAATCACG 59.135 50.000 0.00 0.00 41.36 4.35
7722 11159 4.169696 CCCGCGCCACCCAGATTA 62.170 66.667 0.00 0.00 0.00 1.75
7783 11220 1.600485 CTTAAAGGCCGTTGTTGTCGT 59.400 47.619 14.75 0.00 0.00 4.34
7792 11229 1.453015 TTGTTGTCGTTGCCTGGCT 60.453 52.632 21.03 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.227249 TTGTTCACCCTTTCCCCTCA 58.773 50.000 0.00 0.00 0.00 3.86
80 81 2.106477 TTGACATACGGCTCATGCAA 57.894 45.000 0.00 0.00 41.91 4.08
143 144 1.303970 GCTGCAGCCCCTCTTTCTT 60.304 57.895 28.76 0.00 34.31 2.52
177 178 2.511600 CCAACACGATCCTCGCCC 60.512 66.667 0.00 0.00 45.12 6.13
208 209 3.004106 CACTTCTTGCCTTCCAGTCAAAG 59.996 47.826 0.00 0.00 0.00 2.77
216 218 0.600057 CAAGCCACTTCTTGCCTTCC 59.400 55.000 0.00 0.00 37.27 3.46
259 261 2.456942 TGAATCATTCGCATTCGCAC 57.543 45.000 0.00 0.00 38.40 5.34
260 262 3.696281 AATGAATCATTCGCATTCGCA 57.304 38.095 2.07 0.00 38.40 5.10
261 263 4.489842 CGATAATGAATCATTCGCATTCGC 59.510 41.667 12.23 0.00 35.54 4.70
531 534 5.289434 GCGGGTGAATCAAAATTTGAGATTC 59.711 40.000 25.27 25.27 43.98 2.52
602 607 3.220674 AGCAGATCCCCTTAATCAAGC 57.779 47.619 0.00 0.00 0.00 4.01
650 655 6.606395 AGATTGGGTTGGTGTAGTAGTACTAG 59.394 42.308 10.38 0.00 30.12 2.57
651 656 6.496743 AGATTGGGTTGGTGTAGTAGTACTA 58.503 40.000 5.90 5.90 0.00 1.82
652 657 5.339477 AGATTGGGTTGGTGTAGTAGTACT 58.661 41.667 8.14 8.14 0.00 2.73
653 658 5.672421 AGATTGGGTTGGTGTAGTAGTAC 57.328 43.478 0.37 0.37 0.00 2.73
654 659 7.795534 TTTAGATTGGGTTGGTGTAGTAGTA 57.204 36.000 0.00 0.00 0.00 1.82
655 660 6.691255 TTTAGATTGGGTTGGTGTAGTAGT 57.309 37.500 0.00 0.00 0.00 2.73
656 661 6.938030 TGTTTTAGATTGGGTTGGTGTAGTAG 59.062 38.462 0.00 0.00 0.00 2.57
657 662 6.711645 GTGTTTTAGATTGGGTTGGTGTAGTA 59.288 38.462 0.00 0.00 0.00 1.82
658 663 5.533528 GTGTTTTAGATTGGGTTGGTGTAGT 59.466 40.000 0.00 0.00 0.00 2.73
837 846 0.969894 ATATACAGGCGGTGAGGAGC 59.030 55.000 0.00 0.00 0.00 4.70
847 856 7.471890 AGAGCCTACCCTATATATATACAGGC 58.528 42.308 20.25 20.25 45.07 4.85
865 877 4.604156 TGACAATCAGAGAGAAGAGCCTA 58.396 43.478 0.00 0.00 0.00 3.93
1198 1230 1.256812 AATTAAGCGTGCAAGCCCTT 58.743 45.000 21.32 12.28 38.01 3.95
1604 1658 2.159934 CGTAAACACGTTTGACCGATCC 60.160 50.000 5.42 0.00 34.23 3.36
1674 1737 2.101917 ACGAAACCAAAGAGACCGAAGA 59.898 45.455 0.00 0.00 0.00 2.87
1676 1739 2.607631 ACGAAACCAAAGAGACCGAA 57.392 45.000 0.00 0.00 0.00 4.30
1705 1773 1.204941 GTGTAGTCACAAGCCTCCGAT 59.795 52.381 0.00 0.00 43.37 4.18
1706 1774 0.601558 GTGTAGTCACAAGCCTCCGA 59.398 55.000 0.00 0.00 43.37 4.55
1707 1775 0.389948 GGTGTAGTCACAAGCCTCCG 60.390 60.000 0.98 0.00 45.45 4.63
1708 1776 0.685097 TGGTGTAGTCACAAGCCTCC 59.315 55.000 0.98 0.00 45.45 4.30
1777 1848 2.101249 TGCACGTCAGATGATATGCTCA 59.899 45.455 17.13 1.91 38.10 4.26
1778 1849 2.474359 GTGCACGTCAGATGATATGCTC 59.526 50.000 17.13 12.25 38.10 4.26
1860 1942 0.681733 ACCATGTGAGCACTCGTCTT 59.318 50.000 1.99 0.00 0.00 3.01
1933 2028 1.134128 TCATGCACAGTGAACAGGTGT 60.134 47.619 4.15 0.00 35.05 4.16
1979 2078 0.098376 GTGCATAGAAGCAGCAGCAC 59.902 55.000 3.17 0.00 46.69 4.40
1990 2101 0.608130 AGCTGTTCACCGTGCATAGA 59.392 50.000 0.00 0.00 0.00 1.98
2103 2230 2.390599 CCGCCCACACGATGACAAG 61.391 63.158 0.00 0.00 34.06 3.16
2142 2273 3.821033 GCCTGTAATTCCATATGGACCAC 59.179 47.826 24.47 20.02 45.39 4.16
2143 2274 3.495983 CGCCTGTAATTCCATATGGACCA 60.496 47.826 24.47 16.04 45.39 4.02
2144 2275 3.074412 CGCCTGTAATTCCATATGGACC 58.926 50.000 24.47 12.50 45.39 4.46
2145 2276 2.484264 GCGCCTGTAATTCCATATGGAC 59.516 50.000 24.47 13.66 45.39 4.02
2147 2278 1.464608 CGCGCCTGTAATTCCATATGG 59.535 52.381 16.25 16.25 0.00 2.74
2148 2279 1.135972 GCGCGCCTGTAATTCCATATG 60.136 52.381 23.24 0.00 0.00 1.78
2151 2282 0.819259 ATGCGCGCCTGTAATTCCAT 60.819 50.000 30.77 8.15 0.00 3.41
2152 2283 1.436195 GATGCGCGCCTGTAATTCCA 61.436 55.000 30.77 5.62 0.00 3.53
2153 2284 1.160329 AGATGCGCGCCTGTAATTCC 61.160 55.000 30.77 4.63 0.00 3.01
2182 2313 2.813474 GCACGCGCATGTAGGTCA 60.813 61.111 5.73 0.00 38.36 4.02
2183 2314 3.913573 CGCACGCGCATGTAGGTC 61.914 66.667 5.73 0.00 38.40 3.85
2184 2315 2.822418 TAACGCACGCGCATGTAGGT 62.822 55.000 12.02 2.04 44.19 3.08
2185 2316 2.162120 TAACGCACGCGCATGTAGG 61.162 57.895 12.02 0.00 44.19 3.18
2208 2339 5.012664 TGCTGGTCAAGGAATCTGTAAAGTA 59.987 40.000 0.00 0.00 0.00 2.24
2252 2386 1.428869 AAGGCTAGCTAGGGTGGATG 58.571 55.000 22.10 0.00 0.00 3.51
2257 2391 2.642807 TGTCAAAAAGGCTAGCTAGGGT 59.357 45.455 22.10 0.00 0.00 4.34
2304 2449 4.632974 GGGCAGCGCTATCCTGGG 62.633 72.222 22.33 6.11 0.00 4.45
2413 2566 1.228124 CACCAACGAGGGGCTTTCA 60.228 57.895 0.00 0.00 43.89 2.69
2448 2620 0.250513 GCGTCAGGGGAACAGATTCT 59.749 55.000 0.00 0.00 34.98 2.40
2458 2630 0.243907 CCAGTATATCGCGTCAGGGG 59.756 60.000 5.77 0.00 0.00 4.79
2463 2635 2.087009 GCGCCCAGTATATCGCGTC 61.087 63.158 5.77 0.00 46.09 5.19
2535 2709 4.270008 CCGTAGAATTGTCCAAGGGAATT 58.730 43.478 0.00 0.00 31.38 2.17
2555 2731 7.807907 GTGCAAGTAATATTATTTCCATTCCCG 59.192 37.037 0.00 0.00 0.00 5.14
2679 4583 2.109517 ATCCGCAGCTCCATGCCTAG 62.110 60.000 0.00 0.00 43.49 3.02
2733 4638 1.879575 TGCTTGCCCATAGGAGTAGT 58.120 50.000 0.00 0.00 33.47 2.73
2804 4721 0.703466 GCTTCTCGAGTCAAACGACG 59.297 55.000 13.13 0.00 38.51 5.12
3074 5331 0.758734 CTGAACGGCCCCATGATCTA 59.241 55.000 0.00 0.00 0.00 1.98
3091 5348 3.354948 TGAATGTCCCTTGATGACCTG 57.645 47.619 0.00 0.00 31.60 4.00
3126 5383 5.458041 AAACCATGGAGAGAACAAATGTG 57.542 39.130 21.47 0.00 0.00 3.21
3136 5393 7.393234 TGAAATAAACCACTAAACCATGGAGAG 59.607 37.037 21.47 14.23 39.46 3.20
3224 5487 0.700564 ACCAGGACGGAGGTAGTACA 59.299 55.000 2.06 0.00 36.07 2.90
3328 5591 6.285790 TGTTCAAATATGAATCCGACGATG 57.714 37.500 0.00 0.00 46.67 3.84
3421 5684 4.036971 TGGTCCCTTTCGTATTTTGTGTTG 59.963 41.667 0.00 0.00 0.00 3.33
3437 5700 3.591527 TCTGTCATGGTTTATTGGTCCCT 59.408 43.478 0.00 0.00 0.00 4.20
3439 5702 5.010282 ACTTCTGTCATGGTTTATTGGTCC 58.990 41.667 0.00 0.00 0.00 4.46
3478 5767 5.784915 GCGCTATAATTTTACGCTTTTCC 57.215 39.130 0.00 0.00 45.71 3.13
3580 5870 8.726988 CAAGGATTACACTTCGAAATTCCTTTA 58.273 33.333 15.94 0.00 32.26 1.85
3739 6040 7.467947 CGTGCCATTTTGTATCATACATGGTTA 60.468 37.037 14.74 4.99 38.18 2.85
3761 6062 1.804151 TGTAGAATTGCAGTTCCGTGC 59.196 47.619 17.41 5.50 44.27 5.34
3916 6219 8.677148 ACATGTGTATATCTTTAACCCATGTC 57.323 34.615 0.00 0.00 36.57 3.06
4046 6349 4.058817 CAACGGAAGAGTACAGCTTCTTT 58.941 43.478 20.77 14.34 41.11 2.52
4047 6350 3.321111 TCAACGGAAGAGTACAGCTTCTT 59.679 43.478 20.77 10.52 41.11 2.52
4048 6351 2.891580 TCAACGGAAGAGTACAGCTTCT 59.108 45.455 20.77 3.13 41.11 2.85
4049 6352 3.299340 TCAACGGAAGAGTACAGCTTC 57.701 47.619 16.04 16.04 40.72 3.86
4050 6353 3.746045 TTCAACGGAAGAGTACAGCTT 57.254 42.857 0.00 0.00 0.00 3.74
4191 6494 9.419297 TCGCATGGTAAGTATGAATACTATTTC 57.581 33.333 3.46 0.00 42.47 2.17
4267 6570 2.357952 GACGGGCCTTTTGGATGAATAC 59.642 50.000 0.84 0.00 44.07 1.89
4355 6658 8.971073 CAGAGAACATAAATAAAGGGTCCAATT 58.029 33.333 0.00 0.00 0.00 2.32
4394 6697 5.451908 TCGACAGAAAAATCATTCACTTGC 58.548 37.500 0.00 0.00 0.00 4.01
4446 6749 0.537143 AAATTGTGCAGCCCTCGTCA 60.537 50.000 0.00 0.00 0.00 4.35
4448 6751 1.904287 TTAAATTGTGCAGCCCTCGT 58.096 45.000 0.00 0.00 0.00 4.18
4450 6753 3.381272 TGCTATTAAATTGTGCAGCCCTC 59.619 43.478 0.00 0.00 0.00 4.30
4487 6791 6.920210 TGCACAGATCTCTTAGAAATATCACG 59.080 38.462 0.00 0.00 0.00 4.35
4496 6800 9.842775 ATCAAATTTATGCACAGATCTCTTAGA 57.157 29.630 0.00 0.00 0.00 2.10
4553 6857 2.265739 GGCACGAGACAGGCATGA 59.734 61.111 4.84 0.00 0.00 3.07
4565 6869 0.880278 CCTATTGTGATCGGGGCACG 60.880 60.000 0.68 0.68 46.11 5.34
4683 6988 1.952990 TGCTCAACATTTTCTGGCGAA 59.047 42.857 0.00 0.00 0.00 4.70
4685 6990 1.689959 GTGCTCAACATTTTCTGGCG 58.310 50.000 0.00 0.00 0.00 5.69
4741 7046 4.273235 GCACAAATGGGCATAATTTTAGCC 59.727 41.667 2.06 6.88 45.57 3.93
4754 7059 1.539388 TCTAAACAGCGCACAAATGGG 59.461 47.619 11.47 0.00 41.65 4.00
4774 7080 3.566322 TGCAACCGTATGTAACTTGCTTT 59.434 39.130 0.00 0.00 39.07 3.51
4777 7083 3.546002 TTGCAACCGTATGTAACTTGC 57.454 42.857 0.00 0.00 38.88 4.01
4840 8193 1.411977 TGACCCAAATTGTGCCAGTTG 59.588 47.619 0.00 0.00 0.00 3.16
4843 8196 2.906691 TTTGACCCAAATTGTGCCAG 57.093 45.000 0.00 0.00 0.00 4.85
4908 8261 7.472334 AATGCAGTTAGAAGTCATGGAAAAT 57.528 32.000 0.00 0.00 0.00 1.82
4996 8367 8.702163 ACAAACAAAAATCTACCAAAGTTCAG 57.298 30.769 0.00 0.00 0.00 3.02
4997 8368 7.486551 CGACAAACAAAAATCTACCAAAGTTCA 59.513 33.333 0.00 0.00 0.00 3.18
5019 8390 5.446607 CCGCATTTTGATAACATGTACGACA 60.447 40.000 0.00 0.00 0.00 4.35
5022 8393 5.150342 TCCGCATTTTGATAACATGTACG 57.850 39.130 0.00 0.00 0.00 3.67
5023 8394 5.965334 CACTCCGCATTTTGATAACATGTAC 59.035 40.000 0.00 0.00 0.00 2.90
5026 8397 4.985413 ACACTCCGCATTTTGATAACATG 58.015 39.130 0.00 0.00 0.00 3.21
5042 8413 7.916977 ACTTTACGGTTTCAATTTAAACACTCC 59.083 33.333 15.25 0.00 40.42 3.85
5087 8458 4.976224 AAAGTTTTAGTGCTGTTCCGTT 57.024 36.364 0.00 0.00 0.00 4.44
5109 8480 2.620115 CAGTTCTTGGAAAGCAGCTTGA 59.380 45.455 8.88 0.00 45.70 3.02
5114 8485 3.249559 GTCAGTCAGTTCTTGGAAAGCAG 59.750 47.826 0.00 0.00 45.70 4.24
5146 8527 1.421485 GTGCCTGCTCAACGAATCG 59.579 57.895 0.00 0.00 0.00 3.34
5147 8528 1.421485 CGTGCCTGCTCAACGAATC 59.579 57.895 0.00 0.00 0.00 2.52
5151 8532 1.447838 ATACCGTGCCTGCTCAACG 60.448 57.895 0.00 0.00 0.00 4.10
5162 8543 1.878522 GCTCGCTGTCCATACCGTG 60.879 63.158 0.00 0.00 0.00 4.94
5285 8666 2.237392 GGAGGTGTAGAAGGTGATTGCT 59.763 50.000 0.00 0.00 0.00 3.91
5413 8794 0.393820 TCGGTGGTCAGTTGGGTTAC 59.606 55.000 0.00 0.00 0.00 2.50
5557 8953 0.319083 TCGTGTACCCGATTGCAGTT 59.681 50.000 0.00 0.00 30.63 3.16
5644 9042 2.033801 CCAGTCAGAAGCCAAAACACAG 59.966 50.000 0.00 0.00 0.00 3.66
5895 9302 0.035820 TTGCCGGTTGGACCTGATAC 60.036 55.000 1.90 0.00 35.66 2.24
6050 9457 0.820226 GGGGATTTCTCAGGCAAAGC 59.180 55.000 0.00 0.00 0.00 3.51
6052 9459 0.695924 TCGGGGATTTCTCAGGCAAA 59.304 50.000 0.00 0.00 0.00 3.68
6053 9460 0.253044 CTCGGGGATTTCTCAGGCAA 59.747 55.000 0.00 0.00 0.00 4.52
6083 9493 4.394920 ACAACAGTGACTCGTTTTCATGTT 59.605 37.500 0.00 0.00 31.03 2.71
6084 9494 3.938963 ACAACAGTGACTCGTTTTCATGT 59.061 39.130 0.00 0.00 0.00 3.21
6086 9496 3.938963 ACACAACAGTGACTCGTTTTCAT 59.061 39.130 0.00 0.00 37.04 2.57
6087 9497 3.331150 ACACAACAGTGACTCGTTTTCA 58.669 40.909 0.00 0.00 37.04 2.69
6088 9498 3.617263 AGACACAACAGTGACTCGTTTTC 59.383 43.478 0.00 0.00 34.05 2.29
6089 9499 3.596214 AGACACAACAGTGACTCGTTTT 58.404 40.909 0.00 0.00 34.05 2.43
6090 9500 3.247006 AGACACAACAGTGACTCGTTT 57.753 42.857 0.00 0.00 34.05 3.60
6091 9501 2.961526 AGACACAACAGTGACTCGTT 57.038 45.000 0.00 0.00 34.05 3.85
6092 9502 2.165641 TGAAGACACAACAGTGACTCGT 59.834 45.455 0.00 0.00 37.30 4.18
6093 9503 2.791560 CTGAAGACACAACAGTGACTCG 59.208 50.000 0.00 0.00 37.30 4.18
6094 9504 3.786635 ACTGAAGACACAACAGTGACTC 58.213 45.455 0.00 0.00 42.18 3.36
6096 9506 4.504461 CACTACTGAAGACACAACAGTGAC 59.496 45.833 0.00 0.00 43.33 3.67
6097 9507 4.401202 TCACTACTGAAGACACAACAGTGA 59.599 41.667 0.00 0.00 43.33 3.41
6098 9508 4.682787 TCACTACTGAAGACACAACAGTG 58.317 43.478 0.00 0.00 43.33 3.66
6099 9509 4.645136 TCTCACTACTGAAGACACAACAGT 59.355 41.667 0.00 0.00 45.06 3.55
6100 9510 5.188327 TCTCACTACTGAAGACACAACAG 57.812 43.478 0.00 0.00 37.62 3.16
6101 9511 4.645136 ACTCTCACTACTGAAGACACAACA 59.355 41.667 0.00 0.00 0.00 3.33
6102 9512 5.009210 AGACTCTCACTACTGAAGACACAAC 59.991 44.000 0.00 0.00 0.00 3.32
6103 9513 5.009110 CAGACTCTCACTACTGAAGACACAA 59.991 44.000 0.00 0.00 32.90 3.33
6104 9514 4.517075 CAGACTCTCACTACTGAAGACACA 59.483 45.833 0.00 0.00 32.90 3.72
6105 9515 4.757657 TCAGACTCTCACTACTGAAGACAC 59.242 45.833 0.00 0.00 36.63 3.67
6106 9516 4.757657 GTCAGACTCTCACTACTGAAGACA 59.242 45.833 0.00 0.00 40.30 3.41
6107 9517 4.757657 TGTCAGACTCTCACTACTGAAGAC 59.242 45.833 1.31 0.00 40.30 3.01
6108 9518 4.974399 TGTCAGACTCTCACTACTGAAGA 58.026 43.478 1.31 0.00 40.30 2.87
6109 9519 5.000591 TCTGTCAGACTCTCACTACTGAAG 58.999 45.833 0.00 0.00 40.30 3.02
6110 9520 4.974399 TCTGTCAGACTCTCACTACTGAA 58.026 43.478 0.00 0.00 40.30 3.02
6111 9521 4.625607 TCTGTCAGACTCTCACTACTGA 57.374 45.455 0.00 0.00 37.11 3.41
6112 9522 5.414144 TCATTCTGTCAGACTCTCACTACTG 59.586 44.000 0.78 0.00 0.00 2.74
6113 9523 5.565509 TCATTCTGTCAGACTCTCACTACT 58.434 41.667 0.78 0.00 0.00 2.57
6114 9524 5.888691 TCATTCTGTCAGACTCTCACTAC 57.111 43.478 0.78 0.00 0.00 2.73
6115 9525 5.770162 TGTTCATTCTGTCAGACTCTCACTA 59.230 40.000 0.78 0.00 0.00 2.74
6116 9526 4.586421 TGTTCATTCTGTCAGACTCTCACT 59.414 41.667 0.78 0.00 0.00 3.41
6117 9527 4.876125 TGTTCATTCTGTCAGACTCTCAC 58.124 43.478 0.78 0.00 0.00 3.51
6118 9528 5.011431 ACATGTTCATTCTGTCAGACTCTCA 59.989 40.000 0.78 0.00 0.00 3.27
6119 9529 5.477510 ACATGTTCATTCTGTCAGACTCTC 58.522 41.667 0.78 0.00 0.00 3.20
6120 9530 5.480642 ACATGTTCATTCTGTCAGACTCT 57.519 39.130 0.78 0.00 0.00 3.24
6121 9531 5.468072 ACAACATGTTCATTCTGTCAGACTC 59.532 40.000 8.48 0.00 0.00 3.36
6489 9912 1.349357 AGCCTGAAGAGGTTGAGGTTC 59.651 52.381 0.00 0.00 39.20 3.62
6783 10206 4.705110 TCCTCATGACTTGGTCTTGAAA 57.295 40.909 14.16 6.18 42.95 2.69
6869 10299 2.920645 CGCCCAGCCGACGATAGAT 61.921 63.158 0.00 0.00 41.38 1.98
6870 10300 3.592814 CGCCCAGCCGACGATAGA 61.593 66.667 0.00 0.00 41.38 1.98
6886 10316 2.567564 ATAAACCCCTCACCGACGCG 62.568 60.000 3.53 3.53 0.00 6.01
6934 10368 5.239525 CCCTTCCTTGAGTAAGTTGAGTTTG 59.760 44.000 0.00 0.00 31.80 2.93
6975 10409 4.357097 TCTGGAGCCTGTAGGGATATAAGA 59.643 45.833 0.00 0.00 37.23 2.10
6981 10417 1.061812 ACATCTGGAGCCTGTAGGGAT 60.062 52.381 0.00 0.00 37.23 3.85
6982 10418 0.339859 ACATCTGGAGCCTGTAGGGA 59.660 55.000 0.00 0.00 37.23 4.20
6983 10419 1.134280 CAACATCTGGAGCCTGTAGGG 60.134 57.143 0.00 0.00 35.18 3.53
7047 10483 5.301805 CCCACCACTCAAGTTAAACAATCTT 59.698 40.000 0.00 0.00 0.00 2.40
7072 10508 0.915364 AGAAGATGAGGAAGGGGTGC 59.085 55.000 0.00 0.00 0.00 5.01
7074 10510 2.192263 GTGAGAAGATGAGGAAGGGGT 58.808 52.381 0.00 0.00 0.00 4.95
7100 10536 4.109050 GGCGAAGAACACATTTCAACAAA 58.891 39.130 0.00 0.00 0.00 2.83
7101 10537 3.380004 AGGCGAAGAACACATTTCAACAA 59.620 39.130 0.00 0.00 0.00 2.83
7137 10574 6.590234 AACACAACTTCCTTCAATTATCCC 57.410 37.500 0.00 0.00 0.00 3.85
7163 10600 1.529438 GGTCGACGCTGATGTGAAAAA 59.471 47.619 9.92 0.00 0.00 1.94
7164 10601 1.144969 GGTCGACGCTGATGTGAAAA 58.855 50.000 9.92 0.00 0.00 2.29
7165 10602 1.006825 CGGTCGACGCTGATGTGAAA 61.007 55.000 9.92 0.00 34.82 2.69
7166 10603 1.443702 CGGTCGACGCTGATGTGAA 60.444 57.895 9.92 0.00 34.82 3.18
7167 10604 2.178273 CGGTCGACGCTGATGTGA 59.822 61.111 9.92 0.00 34.82 3.58
7315 10752 4.115199 GGAGATTGGCTGGCCGGT 62.115 66.667 14.55 0.00 39.42 5.28
7414 10851 1.153369 CGTGGACCGAGGCAATGAT 60.153 57.895 0.00 0.00 39.56 2.45
7426 10863 4.736896 GACGTGGGAGCCGTGGAC 62.737 72.222 0.00 0.00 38.92 4.02
7454 10891 1.076777 CCAGATTTGACCGGGGCAT 60.077 57.895 1.80 0.00 0.00 4.40
7495 10932 2.359107 CGCAGACATGGCACTGGT 60.359 61.111 0.00 0.00 35.05 4.00
7625 11062 4.479993 GAGCTGGCCGGCAGTCAT 62.480 66.667 37.26 17.68 34.17 3.06
7722 11159 3.884704 TTGAATGCTTGGGCGGCCT 62.885 57.895 29.87 7.33 42.25 5.19
7783 11220 2.853542 TGACCAGGAGCCAGGCAA 60.854 61.111 15.80 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.