Multiple sequence alignment - TraesCS7D01G457800

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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 TraesCS7D01G457800 chr7D 100.000 8083 0 0 1 8083 575872583 575864501 0.000000e+00 14927.0
1 TraesCS7D01G457800 chr7D 96.226 53 2 0 1193 1245 241737172 241737120 4.020000e-13 87.9
2 TraesCS7D01G457800 chr7A 91.320 6728 313 92 1251 7803 666613374 666606743 0.000000e+00 8938.0
3 TraesCS7D01G457800 chr7A 89.651 802 47 12 188 962 666614687 666613895 0.000000e+00 989.0
4 TraesCS7D01G457800 chr7A 95.548 292 9 1 7796 8083 666606716 666606425 1.590000e-126 464.0
5 TraesCS7D01G457800 chr7A 97.328 262 5 2 992 1252 666613664 666613404 2.070000e-120 444.0
6 TraesCS7D01G457800 chr7A 91.463 164 11 2 10 171 666614896 666614734 1.060000e-53 222.0
7 TraesCS7D01G457800 chr7B 93.234 2424 124 26 1789 4189 638076102 638073696 0.000000e+00 3531.0
8 TraesCS7D01G457800 chr7B 88.374 2546 163 70 5614 8083 638072239 638069751 0.000000e+00 2939.0
9 TraesCS7D01G457800 chr7B 84.335 1315 135 40 4191 5466 638073626 638072344 0.000000e+00 1221.0
10 TraesCS7D01G457800 chr7B 88.250 800 38 26 447 1195 638077551 638076757 0.000000e+00 905.0
11 TraesCS7D01G457800 chr7B 92.192 333 23 1 1346 1675 638076436 638076104 1.230000e-127 468.0
12 TraesCS7D01G457800 chr7B 97.917 48 1 0 1260 1307 638076743 638076696 5.200000e-12 84.2
13 TraesCS7D01G457800 chr6D 83.588 524 66 11 5064 5585 157316477 157315972 2.640000e-129 473.0
14 TraesCS7D01G457800 chr1D 82.927 328 49 5 5566 5893 460262131 460261811 1.030000e-73 289.0
15 TraesCS7D01G457800 chr4D 88.889 99 11 0 12 110 49773177 49773275 1.100000e-23 122.0
16 TraesCS7D01G457800 chr3B 98.039 51 1 0 1195 1245 70582219 70582169 1.120000e-13 89.8
17 TraesCS7D01G457800 chr3B 97.778 45 1 0 1201 1245 773046142 773046098 2.420000e-10 78.7
18 TraesCS7D01G457800 chr3A 98.039 51 1 0 1195 1245 114429557 114429507 1.120000e-13 89.8
19 TraesCS7D01G457800 chr5A 91.935 62 5 0 1202 1263 450883240 450883179 4.020000e-13 87.9
20 TraesCS7D01G457800 chr2D 93.103 58 4 0 1188 1245 68867481 68867424 1.450000e-12 86.1
21 TraesCS7D01G457800 chr6A 91.803 61 3 2 1185 1245 21747913 21747855 5.200000e-12 84.2
22 TraesCS7D01G457800 chr2B 90.476 63 4 2 1185 1245 796342623 796342685 1.870000e-11 82.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G457800 chr7D 575864501 575872583 8082 True 14927.0 14927 100.000 1 8083 1 chr7D.!!$R2 8082
1 TraesCS7D01G457800 chr7A 666606425 666614896 8471 True 2211.4 8938 93.062 10 8083 5 chr7A.!!$R1 8073
2 TraesCS7D01G457800 chr7B 638069751 638077551 7800 True 1524.7 3531 90.717 447 8083 6 chr7B.!!$R1 7636
3 TraesCS7D01G457800 chr6D 157315972 157316477 505 True 473.0 473 83.588 5064 5585 1 chr6D.!!$R1 521

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
738 801 0.029834 AGCCATTACGTACGTAGCCG 59.970 55.000 25.56 17.80 40.83 5.52 F
1339 1653 0.035820 GTGCGTGGGGGAAGTTCATA 60.036 55.000 5.01 0.00 0.00 2.15 F
1625 2160 0.668401 CCGTGACCGACCAAGTTACC 60.668 60.000 0.00 0.00 35.63 2.85 F
2562 3116 0.966920 GAGGTGGAGACGTCCTTTCA 59.033 55.000 13.01 0.00 44.30 2.69 F
2870 3436 3.371591 CCAATTGTTGTACCATGCAATGC 59.628 43.478 4.43 0.00 44.97 3.56 F
4010 4619 2.715005 CCGCCATTGCACGGTATG 59.285 61.111 5.36 0.00 44.46 2.39 F
5219 5935 0.472044 TTAGTGTGCAGAGTTGGCCA 59.528 50.000 0.00 0.00 0.00 5.36 F
5510 6265 0.038343 TTGAAGCAAATTGAGGGCGC 60.038 50.000 0.00 0.00 0.00 6.53 F
5515 6270 0.458370 GCAAATTGAGGGCGCGATTT 60.458 50.000 12.10 2.27 33.24 2.17 F
6892 7675 0.038159 CCGTCGAGAAAAGGTGAGCT 60.038 55.000 0.00 0.00 0.00 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1609 2144 1.005867 GCGGTAACTTGGTCGGTCA 60.006 57.895 0.00 0.0 0.00 4.02 R
3325 3908 1.037493 CATCCATTGACCCCTGCATG 58.963 55.000 0.00 0.0 0.00 4.06 R
3507 4091 5.532406 TGGATAGCCAAATATCTGCAAGTTC 59.468 40.000 0.00 0.0 42.49 3.01 R
3977 4586 1.269831 GGCGGAGGTAGTTAGCATCTG 60.270 57.143 0.00 0.0 0.00 2.90 R
4254 4933 4.278419 GGCAAGTGTCAACCATTTTCTACT 59.722 41.667 0.00 0.0 0.00 2.57 R
5496 6251 0.458370 AAATCGCGCCCTCAATTTGC 60.458 50.000 0.00 0.0 0.00 3.68 R
6713 7496 0.179078 ACGTTTGGTGAACAGGCGTA 60.179 50.000 0.00 0.0 38.71 4.42 R
6876 7659 0.320771 GGCAGCTCACCTTTTCTCGA 60.321 55.000 0.00 0.0 0.00 4.04 R
7012 7796 0.448593 GACGGTCTCTTCTCCACTCG 59.551 60.000 0.00 0.0 0.00 4.18 R
8014 8932 1.123077 TTGTCGGATGAGCAGCCTAT 58.877 50.000 3.05 0.0 33.99 2.57 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
25 26 5.929697 TTATCCATTCTTGATCACGATGC 57.070 39.130 2.32 0.00 0.00 3.91
26 27 3.548745 TCCATTCTTGATCACGATGCT 57.451 42.857 2.32 0.00 0.00 3.79
27 28 3.461061 TCCATTCTTGATCACGATGCTC 58.539 45.455 2.32 0.00 0.00 4.26
28 29 3.133542 TCCATTCTTGATCACGATGCTCT 59.866 43.478 2.32 0.00 0.00 4.09
29 30 4.342092 TCCATTCTTGATCACGATGCTCTA 59.658 41.667 2.32 0.00 0.00 2.43
30 31 4.447054 CCATTCTTGATCACGATGCTCTAC 59.553 45.833 2.32 0.00 0.00 2.59
72 73 4.158384 GTCATGTACAAAAATCTGGCACG 58.842 43.478 0.00 0.00 0.00 5.34
82 83 1.003839 TCTGGCACGGATCACAACC 60.004 57.895 0.00 0.00 39.80 3.77
105 106 4.734398 AAAAACAGTCTGGACATTTGCA 57.266 36.364 4.53 0.00 0.00 4.08
155 156 5.545063 TCTTCTCCGTGGCATCAATATTA 57.455 39.130 0.00 0.00 0.00 0.98
177 178 5.613358 AGCAAGACAAAATTCTTACTCCG 57.387 39.130 0.00 0.00 33.89 4.63
179 180 5.049405 AGCAAGACAAAATTCTTACTCCGTG 60.049 40.000 0.00 0.00 33.89 4.94
180 181 5.689819 CAAGACAAAATTCTTACTCCGTGG 58.310 41.667 0.00 0.00 33.89 4.94
181 182 5.223449 AGACAAAATTCTTACTCCGTGGA 57.777 39.130 0.00 0.00 0.00 4.02
182 183 4.995487 AGACAAAATTCTTACTCCGTGGAC 59.005 41.667 0.00 0.00 0.00 4.02
184 185 5.313712 ACAAAATTCTTACTCCGTGGACAT 58.686 37.500 0.00 0.00 0.00 3.06
185 186 5.411669 ACAAAATTCTTACTCCGTGGACATC 59.588 40.000 0.00 0.00 0.00 3.06
186 187 3.821421 ATTCTTACTCCGTGGACATCC 57.179 47.619 0.00 0.00 0.00 3.51
195 226 4.451150 TGGACATCCGCCACTCGC 62.451 66.667 0.00 0.00 39.43 5.03
219 250 1.013755 CGCGCGAACTTGATTACCG 60.014 57.895 28.94 0.00 0.00 4.02
223 254 2.153247 GCGCGAACTTGATTACCGATAG 59.847 50.000 12.10 0.00 0.00 2.08
225 256 3.179795 CGCGAACTTGATTACCGATAGTG 59.820 47.826 0.00 0.00 0.00 2.74
230 261 7.556433 CGAACTTGATTACCGATAGTGATTTC 58.444 38.462 0.00 0.00 0.00 2.17
233 264 5.777850 TGATTACCGATAGTGATTTCCGA 57.222 39.130 0.00 0.00 0.00 4.55
238 269 2.544267 CCGATAGTGATTTCCGAAAGCC 59.456 50.000 6.66 0.00 0.00 4.35
263 294 1.600107 GATGGACGTACTTGGGCCA 59.400 57.895 0.00 0.00 0.00 5.36
267 298 1.079336 GACGTACTTGGGCCAGGAC 60.079 63.158 23.86 14.74 0.00 3.85
284 315 2.284798 GACGATCCTCTGGAAGCGCA 62.285 60.000 11.47 0.00 37.17 6.09
300 331 0.521867 CGCATGCCGTCAAATCACAG 60.522 55.000 13.15 0.00 0.00 3.66
308 339 2.600420 CCGTCAAATCACAGAGTCATCG 59.400 50.000 0.00 0.00 0.00 3.84
341 372 7.012327 TGTGAATGAAAAGTCCTAACTTCACAG 59.988 37.037 9.89 0.00 45.07 3.66
342 373 7.226720 GTGAATGAAAAGTCCTAACTTCACAGA 59.773 37.037 0.00 0.00 45.07 3.41
344 375 5.047847 TGAAAAGTCCTAACTTCACAGACG 58.952 41.667 0.00 0.00 45.07 4.18
364 396 2.601266 CGACCAACCAACAAAAGCTACG 60.601 50.000 0.00 0.00 0.00 3.51
368 400 3.004315 CCAACCAACAAAAGCTACGTGAT 59.996 43.478 0.00 0.00 0.00 3.06
406 438 3.735237 TCAGATCTGAATAACCGGCTC 57.265 47.619 23.17 0.00 36.53 4.70
427 459 4.015872 CCGAAGGCTATAAATTAGGCCA 57.984 45.455 17.48 0.00 46.14 5.36
442 474 2.716217 AGGCCAGAGACAACATTTAGC 58.284 47.619 5.01 0.00 0.00 3.09
586 627 1.596260 CCACATCATCACTGCTTAGCG 59.404 52.381 0.00 0.00 0.00 4.26
681 729 3.743017 GAGGGCAGCCAATGGGGA 61.743 66.667 15.19 0.00 40.01 4.81
684 732 3.464494 GGCAGCCAATGGGGAAGC 61.464 66.667 6.55 0.00 40.01 3.86
689 737 0.257039 AGCCAATGGGGAAGCACTAG 59.743 55.000 0.00 0.00 40.01 2.57
690 738 0.753111 GCCAATGGGGAAGCACTAGG 60.753 60.000 0.00 0.00 40.01 3.02
691 739 0.918983 CCAATGGGGAAGCACTAGGA 59.081 55.000 0.00 0.00 40.01 2.94
692 740 1.133976 CCAATGGGGAAGCACTAGGAG 60.134 57.143 0.00 0.00 40.01 3.69
693 741 0.548510 AATGGGGAAGCACTAGGAGC 59.451 55.000 0.00 0.00 0.00 4.70
694 742 1.348775 ATGGGGAAGCACTAGGAGCC 61.349 60.000 5.89 0.00 0.00 4.70
695 743 1.995626 GGGGAAGCACTAGGAGCCA 60.996 63.158 5.89 0.00 0.00 4.75
696 744 1.348775 GGGGAAGCACTAGGAGCCAT 61.349 60.000 5.89 0.00 0.00 4.40
697 745 1.424638 GGGAAGCACTAGGAGCCATA 58.575 55.000 5.89 0.00 0.00 2.74
738 801 0.029834 AGCCATTACGTACGTAGCCG 59.970 55.000 25.56 17.80 40.83 5.52
924 1000 0.389948 ACTCTCGCCACCGAATCAAC 60.390 55.000 0.00 0.00 43.87 3.18
962 1039 2.443203 TCCAGCTAATCCGGCCGA 60.443 61.111 30.73 13.82 0.00 5.54
963 1040 2.029666 CCAGCTAATCCGGCCGAG 59.970 66.667 30.73 17.72 0.00 4.63
964 1041 2.029666 CAGCTAATCCGGCCGAGG 59.970 66.667 30.73 11.63 0.00 4.63
965 1042 3.234730 AGCTAATCCGGCCGAGGG 61.235 66.667 30.73 10.73 0.00 4.30
966 1043 4.315941 GCTAATCCGGCCGAGGGG 62.316 72.222 30.73 10.28 0.00 4.79
967 1044 2.523412 CTAATCCGGCCGAGGGGA 60.523 66.667 30.73 16.38 36.61 4.81
969 1046 2.772622 AATCCGGCCGAGGGGATT 60.773 61.111 30.73 23.07 45.78 3.01
1088 1366 4.129737 CGTCGACCAGATGCGGGT 62.130 66.667 10.58 0.00 42.61 5.28
1129 1408 2.477880 GGTGCTAACCCATTCACGG 58.522 57.895 0.00 0.00 41.04 4.94
1130 1409 1.654023 GGTGCTAACCCATTCACGGC 61.654 60.000 0.00 0.00 41.04 5.68
1318 1632 4.919168 CAGTTAAATCAATGTGCTGGTGTG 59.081 41.667 0.00 0.00 0.00 3.82
1319 1633 4.584325 AGTTAAATCAATGTGCTGGTGTGT 59.416 37.500 0.00 0.00 0.00 3.72
1320 1634 3.374220 AAATCAATGTGCTGGTGTGTG 57.626 42.857 0.00 0.00 0.00 3.82
1321 1635 1.985473 ATCAATGTGCTGGTGTGTGT 58.015 45.000 0.00 0.00 0.00 3.72
1322 1636 1.023502 TCAATGTGCTGGTGTGTGTG 58.976 50.000 0.00 0.00 0.00 3.82
1323 1637 0.595567 CAATGTGCTGGTGTGTGTGC 60.596 55.000 0.00 0.00 0.00 4.57
1325 1639 3.202001 GTGCTGGTGTGTGTGCGT 61.202 61.111 0.00 0.00 0.00 5.24
1328 1642 3.279116 CTGGTGTGTGTGCGTGGG 61.279 66.667 0.00 0.00 0.00 4.61
1329 1643 4.866224 TGGTGTGTGTGCGTGGGG 62.866 66.667 0.00 0.00 0.00 4.96
1331 1645 4.555709 GTGTGTGTGCGTGGGGGA 62.556 66.667 0.00 0.00 0.00 4.81
1332 1646 3.798511 TGTGTGTGCGTGGGGGAA 61.799 61.111 0.00 0.00 0.00 3.97
1333 1647 2.978010 GTGTGTGCGTGGGGGAAG 60.978 66.667 0.00 0.00 0.00 3.46
1334 1648 3.484806 TGTGTGCGTGGGGGAAGT 61.485 61.111 0.00 0.00 0.00 3.01
1335 1649 2.203294 GTGTGCGTGGGGGAAGTT 60.203 61.111 0.00 0.00 0.00 2.66
1336 1650 2.112297 TGTGCGTGGGGGAAGTTC 59.888 61.111 0.00 0.00 0.00 3.01
1337 1651 2.112297 GTGCGTGGGGGAAGTTCA 59.888 61.111 5.01 0.00 0.00 3.18
1338 1652 1.303317 GTGCGTGGGGGAAGTTCAT 60.303 57.895 5.01 0.00 0.00 2.57
1339 1653 0.035820 GTGCGTGGGGGAAGTTCATA 60.036 55.000 5.01 0.00 0.00 2.15
1366 1901 5.361135 AGCATTTAATTTTGTGCTTTGCC 57.639 34.783 5.60 0.00 44.92 4.52
1428 1963 4.129737 GGCGCTGTACTCGGAGCA 62.130 66.667 7.64 0.00 45.28 4.26
1441 1976 2.894387 GAGCAGCAGATGGCCGAC 60.894 66.667 0.00 0.00 46.50 4.79
1444 1979 2.434884 CAGCAGATGGCCGACGTT 60.435 61.111 0.00 0.00 46.50 3.99
1497 2032 1.437573 CTCGTATCCTTGGCTCGCA 59.562 57.895 0.00 0.00 0.00 5.10
1500 2035 1.684450 TCGTATCCTTGGCTCGCATTA 59.316 47.619 0.00 0.00 0.00 1.90
1503 2038 2.936919 ATCCTTGGCTCGCATTATCA 57.063 45.000 0.00 0.00 0.00 2.15
1609 2144 3.381983 TGACTCGAGCATGGCCGT 61.382 61.111 13.61 0.00 0.00 5.68
1625 2160 0.668401 CCGTGACCGACCAAGTTACC 60.668 60.000 0.00 0.00 35.63 2.85
1631 2166 1.666553 CGACCAAGTTACCGCTGCA 60.667 57.895 0.00 0.00 0.00 4.41
1661 2199 3.844211 AGGTACCTTTCTGGCTTGTATCA 59.156 43.478 9.21 0.00 40.22 2.15
1672 2210 3.327757 TGGCTTGTATCAAGTCAGTCCTT 59.672 43.478 11.87 0.00 0.00 3.36
1685 2223 8.762645 TCAAGTCAGTCCTTTCTACATAATCAT 58.237 33.333 0.00 0.00 0.00 2.45
1686 2224 9.388506 CAAGTCAGTCCTTTCTACATAATCATT 57.611 33.333 0.00 0.00 0.00 2.57
1709 2247 7.644986 TTGGCAATAAACATTTTTAAGACCG 57.355 32.000 0.00 0.00 30.86 4.79
1713 2251 7.382759 GGCAATAAACATTTTTAAGACCGAACA 59.617 33.333 0.00 0.00 30.86 3.18
1761 2299 1.080298 GCCAATGCTGGACACTTGC 60.080 57.895 0.00 0.00 46.92 4.01
1762 2300 1.588082 CCAATGCTGGACACTTGCC 59.412 57.895 0.00 0.00 46.92 4.52
1763 2301 1.210931 CAATGCTGGACACTTGCCG 59.789 57.895 0.00 0.00 0.00 5.69
1778 2316 1.388547 TGCCGATGAGGTTATTTGCC 58.611 50.000 0.00 0.00 43.70 4.52
1779 2317 1.340502 TGCCGATGAGGTTATTTGCCA 60.341 47.619 0.00 0.00 43.70 4.92
1782 2320 3.189287 GCCGATGAGGTTATTTGCCATAG 59.811 47.826 0.00 0.00 43.70 2.23
1811 2349 7.559335 TCCATTCATGTCCTAATGTAGCTAT 57.441 36.000 0.00 0.00 32.34 2.97
1832 2370 6.469595 GCTATTAGTGTCTGTCTCAACTTACG 59.530 42.308 0.00 0.00 0.00 3.18
1865 2403 7.442364 TCAGAAATGCTCAAACTACATATAGCC 59.558 37.037 0.00 0.00 30.75 3.93
1943 2481 4.517285 AGATACTGTGATTTGCCGACATT 58.483 39.130 0.00 0.00 0.00 2.71
1955 2493 2.351418 TGCCGACATTTTGCTCTATTCG 59.649 45.455 0.00 0.00 0.00 3.34
1975 2513 5.295431 TCGATGCATTTGAGTAAGTTTGG 57.705 39.130 0.00 0.00 0.00 3.28
2071 2613 7.281774 CCAAGAGACTACAAATGCATATTCACT 59.718 37.037 0.00 0.00 0.00 3.41
2203 2745 8.541234 AGAGAGTATCCTTCCGTTAAAATTCTT 58.459 33.333 0.00 0.00 33.66 2.52
2373 2927 7.805071 CCATAAAGTTGAGAAGTTCATGTTGAC 59.195 37.037 5.50 0.00 35.27 3.18
2553 3107 3.493767 AACCAAAGAAGAGGTGGAGAC 57.506 47.619 0.00 0.00 38.37 3.36
2562 3116 0.966920 GAGGTGGAGACGTCCTTTCA 59.033 55.000 13.01 0.00 44.30 2.69
2728 3284 8.992835 AATTTGATTGACTTGCTTTATCTTCC 57.007 30.769 0.00 0.00 0.00 3.46
2737 3293 8.950210 TGACTTGCTTTATCTTCCTTAGATTTG 58.050 33.333 0.00 0.00 40.84 2.32
2870 3436 3.371591 CCAATTGTTGTACCATGCAATGC 59.628 43.478 4.43 0.00 44.97 3.56
2882 3448 5.358922 ACCATGCAATGCACATAAATAACC 58.641 37.500 11.23 0.00 44.97 2.85
2905 3472 5.282510 CCGAATATCTAACTGCGAAGTTCT 58.717 41.667 13.39 1.52 33.59 3.01
2919 3486 6.046593 TGCGAAGTTCTTTCTTCAAACTCTA 58.953 36.000 0.56 0.00 42.53 2.43
3007 3578 5.121221 AGCCAAATTTAAAGTTCCACTCG 57.879 39.130 0.00 0.00 0.00 4.18
3787 4391 6.778559 AGGTTTTGTGTTGCCCTACTTAATTA 59.221 34.615 0.00 0.00 0.00 1.40
3957 4566 5.807520 CGTTCTTAAGCATAGCTTCTCTTCA 59.192 40.000 7.62 0.00 46.77 3.02
3977 4586 9.727627 CTCTTCAGCATGGTTTTAAGATAATTC 57.272 33.333 12.16 0.00 36.16 2.17
4010 4619 2.715005 CCGCCATTGCACGGTATG 59.285 61.111 5.36 0.00 44.46 2.39
4094 4703 3.118629 TCTCTTGTAGGCACACATCATCC 60.119 47.826 0.00 0.00 33.30 3.51
4118 4727 6.314896 CCCTTGCTACTTATGTGAGAAAGAAG 59.685 42.308 0.00 0.00 0.00 2.85
4125 4734 6.471146 ACTTATGTGAGAAAGAAGATGCTGT 58.529 36.000 0.00 0.00 0.00 4.40
4254 4933 7.523293 TGCTATTTTTCTGTTTCTTCCATCA 57.477 32.000 0.00 0.00 0.00 3.07
4266 4945 7.004086 TGTTTCTTCCATCAGTAGAAAATGGT 58.996 34.615 0.00 0.00 39.01 3.55
4365 5070 2.957402 AGGTGGCAGATTTGAAGACA 57.043 45.000 0.00 0.00 0.00 3.41
4531 5245 1.272425 CCCATGTTGGTTCCTTGGCTA 60.272 52.381 0.00 0.00 35.17 3.93
4922 5636 9.713740 GAGTTATCACTTATCAGCAATCTTTTG 57.286 33.333 0.00 0.00 31.22 2.44
4960 5676 5.525378 TCTGAAGTTTCTGCAGTCTTCTTTC 59.475 40.000 29.06 20.43 38.27 2.62
5219 5935 0.472044 TTAGTGTGCAGAGTTGGCCA 59.528 50.000 0.00 0.00 0.00 5.36
5251 5967 6.186420 TGGTGGTATGTGTGCATTCTATAT 57.814 37.500 0.00 0.00 36.58 0.86
5324 6040 7.434013 GGCCATAAACTGACATTTTATAAACCG 59.566 37.037 9.67 0.00 29.75 4.44
5433 6149 5.640189 AACTGAATCATTCCTGCTTTCTG 57.360 39.130 0.00 0.00 0.00 3.02
5509 6264 2.437200 TTTGAAGCAAATTGAGGGCG 57.563 45.000 0.00 0.00 0.00 6.13
5510 6265 0.038343 TTGAAGCAAATTGAGGGCGC 60.038 50.000 0.00 0.00 0.00 6.53
5511 6266 1.514873 GAAGCAAATTGAGGGCGCG 60.515 57.895 0.00 0.00 0.00 6.86
5512 6267 1.922135 GAAGCAAATTGAGGGCGCGA 61.922 55.000 12.10 0.00 0.00 5.87
5513 6268 1.315257 AAGCAAATTGAGGGCGCGAT 61.315 50.000 12.10 0.00 0.00 4.58
5514 6269 1.139520 GCAAATTGAGGGCGCGATT 59.860 52.632 12.10 0.00 0.00 3.34
5515 6270 0.458370 GCAAATTGAGGGCGCGATTT 60.458 50.000 12.10 2.27 33.24 2.17
5516 6271 1.270971 CAAATTGAGGGCGCGATTTG 58.729 50.000 12.10 12.30 40.99 2.32
5520 6275 1.524848 TTGAGGGCGCGATTTGTAAA 58.475 45.000 12.10 0.00 0.00 2.01
5550 6309 9.743057 CCACTACTTTGTTCATTTTGTTATTGA 57.257 29.630 0.00 0.00 0.00 2.57
5597 6356 8.575649 AAACAAATAGTATGGTTACAGAAGGG 57.424 34.615 1.99 0.00 0.00 3.95
5721 6481 5.390991 CCTGTCAGGATTTCTTTTTAGCGTC 60.391 44.000 14.26 0.00 37.67 5.19
5800 6560 2.431454 CTGGAACTTGGGAAGCTCTTC 58.569 52.381 1.12 1.12 38.80 2.87
5996 6756 4.217767 GCCTTTTTATTTGGAGACGGTCTT 59.782 41.667 12.67 0.00 0.00 3.01
6009 6771 3.255149 AGACGGTCTTGAGTTTCACGTAT 59.745 43.478 4.45 0.00 27.89 3.06
6012 6774 3.852536 CGGTCTTGAGTTTCACGTATCTC 59.147 47.826 0.00 0.00 0.00 2.75
6072 6834 8.012957 ACGAGGTAGAAAGTTATGATGAGAAT 57.987 34.615 0.00 0.00 0.00 2.40
6141 6903 4.717877 TGAGATGTTCAAGCTCCAAGAAA 58.282 39.130 0.00 0.00 40.82 2.52
6145 6907 4.900635 TGTTCAAGCTCCAAGAAAAGTC 57.099 40.909 0.00 0.00 0.00 3.01
6163 6925 0.826715 TCTCTGCACATCTACTGGCC 59.173 55.000 0.00 0.00 0.00 5.36
6305 7067 2.759839 TTTTCTTTCCCCGTTCCCTT 57.240 45.000 0.00 0.00 0.00 3.95
6322 7084 5.309323 TCCCTTCTTATTGCAAAATGACG 57.691 39.130 1.71 0.00 0.00 4.35
6345 7107 6.030228 CGAAAAAGGGCTCTAATTGTTCATC 58.970 40.000 0.00 0.00 0.00 2.92
6355 7117 7.917505 GGCTCTAATTGTTCATCGAAATCATTT 59.082 33.333 0.00 0.00 0.00 2.32
6387 7149 5.419788 TGCAATTTTGACTGCCTCAGATAAT 59.580 36.000 0.29 0.00 37.79 1.28
6388 7150 5.747197 GCAATTTTGACTGCCTCAGATAATG 59.253 40.000 0.29 0.00 35.18 1.90
6494 7256 3.761657 TGTTGATGCAATGAGATTTCGC 58.238 40.909 0.00 0.00 0.00 4.70
6598 7360 7.321745 CTGTAAGTGTTCTTTTCCTTTCAGT 57.678 36.000 0.00 0.00 35.36 3.41
6663 7425 7.873505 ACTTCCTTGTTATAACTTCAGAGTGAC 59.126 37.037 16.33 0.00 35.91 3.67
6666 7449 7.038302 TCCTTGTTATAACTTCAGAGTGACCAT 60.038 37.037 16.33 0.00 35.91 3.55
6668 7451 7.004555 TGTTATAACTTCAGAGTGACCATGT 57.995 36.000 16.33 0.00 35.91 3.21
6671 7454 4.422073 AACTTCAGAGTGACCATGTTCA 57.578 40.909 0.00 0.00 35.91 3.18
6674 7457 4.999950 ACTTCAGAGTGACCATGTTCATTC 59.000 41.667 7.56 7.56 33.99 2.67
6675 7458 4.897509 TCAGAGTGACCATGTTCATTCT 57.102 40.909 11.77 11.77 41.81 2.40
6705 7488 6.665248 ACAAAATCCTGAAGGCTAGCTATTTT 59.335 34.615 15.72 11.61 34.44 1.82
6713 7496 7.446625 CCTGAAGGCTAGCTATTTTGACATATT 59.553 37.037 15.72 0.00 0.00 1.28
6716 7499 7.891183 AGGCTAGCTATTTTGACATATTACG 57.109 36.000 15.72 0.00 0.00 3.18
6730 7513 4.155280 ACATATTACGCCTGTTCACCAAAC 59.845 41.667 0.00 0.00 38.43 2.93
6740 7523 2.182014 GTTCACCAAACGTTGCTGAAC 58.818 47.619 21.00 21.00 44.31 3.18
6756 7539 0.591659 GAACCACTCCTTCCGTTTGC 59.408 55.000 0.00 0.00 0.00 3.68
6861 7644 1.295423 GAAGGAACCGCTGGCTACA 59.705 57.895 0.00 0.00 0.00 2.74
6876 7659 1.120530 CTACATTGGCCTCCTACCGT 58.879 55.000 3.32 0.00 0.00 4.83
6892 7675 0.038159 CCGTCGAGAAAAGGTGAGCT 60.038 55.000 0.00 0.00 0.00 4.09
6893 7676 1.063806 CGTCGAGAAAAGGTGAGCTG 58.936 55.000 0.00 0.00 0.00 4.24
6894 7677 0.793250 GTCGAGAAAAGGTGAGCTGC 59.207 55.000 0.00 0.00 0.00 5.25
6895 7678 0.320771 TCGAGAAAAGGTGAGCTGCC 60.321 55.000 0.00 0.00 0.00 4.85
6896 7679 0.321122 CGAGAAAAGGTGAGCTGCCT 60.321 55.000 0.00 0.00 38.11 4.75
7001 7785 3.942748 TGTTTGGTGTCCTGTTGAACTAC 59.057 43.478 0.00 0.00 0.00 2.73
7012 7796 3.374745 TGTTGAACTACGAAGACGGTTC 58.625 45.455 0.00 0.00 44.46 3.62
7016 7800 1.517242 ACTACGAAGACGGTTCGAGT 58.483 50.000 23.81 18.80 43.97 4.18
7091 7878 2.661594 TCGACAGAGTGATTTCGTGTG 58.338 47.619 0.00 0.00 33.20 3.82
7115 7902 1.200760 TACAGAGCCAGCACCCACAT 61.201 55.000 0.00 0.00 0.00 3.21
7159 7951 1.961793 TGCTTAGGACAACACACACC 58.038 50.000 0.00 0.00 0.00 4.16
7180 7972 4.338682 ACCCAGTGCGTGTAACAATTTTTA 59.661 37.500 0.00 0.00 35.74 1.52
7183 7975 6.422400 CCCAGTGCGTGTAACAATTTTTAAAT 59.578 34.615 0.00 0.00 35.74 1.40
7184 7976 7.280055 CCAGTGCGTGTAACAATTTTTAAATG 58.720 34.615 0.00 0.00 35.74 2.32
7185 7977 6.785164 CAGTGCGTGTAACAATTTTTAAATGC 59.215 34.615 10.57 10.57 35.74 3.56
7186 7978 6.699642 AGTGCGTGTAACAATTTTTAAATGCT 59.300 30.769 16.16 0.00 33.78 3.79
7187 7979 7.223777 AGTGCGTGTAACAATTTTTAAATGCTT 59.776 29.630 16.16 5.76 33.78 3.91
7188 7980 7.317736 GTGCGTGTAACAATTTTTAAATGCTTG 59.682 33.333 16.16 0.00 33.78 4.01
7244 8053 9.934190 AAATAACTTGAAACATGTGAAAAATGC 57.066 25.926 0.00 0.00 33.78 3.56
7270 8079 3.066291 TGTAAACGGTTCAGATGCCAT 57.934 42.857 0.00 0.00 0.00 4.40
7317 8126 8.676401 CCTATGAACATGACATTTGTATGACAA 58.324 33.333 0.00 0.00 39.29 3.18
7340 8149 7.930865 ACAACATGCCAGTTTTGTATTTGTAAT 59.069 29.630 0.00 0.00 30.39 1.89
7355 8164 1.084289 GTAATCACGGAACACAGCCC 58.916 55.000 0.00 0.00 0.00 5.19
7375 8184 3.584834 CCAGCATTTTTAAAACCGAGGG 58.415 45.455 0.00 0.00 0.00 4.30
7382 8191 6.630071 CATTTTTAAAACCGAGGGACATGAT 58.370 36.000 0.00 0.00 0.00 2.45
7410 8247 4.338379 TGAGCTCATGATGATTCCAGAG 57.662 45.455 13.74 0.00 0.00 3.35
7559 8397 1.006922 CGTCAGCTCACTCACTGCA 60.007 57.895 0.00 0.00 33.80 4.41
7588 8456 4.235079 TGCAGCAGAAAGGGTATTACAT 57.765 40.909 0.00 0.00 0.00 2.29
7784 8660 1.098869 TCAGGCACGCAGTTTCAAAA 58.901 45.000 0.00 0.00 41.61 2.44
7810 8721 8.270744 AGTTGAGGACTGATTATATTCAGCTTT 58.729 33.333 19.77 8.90 45.75 3.51
8014 8932 1.005394 GGAACAAACCTCGGAGCGA 60.005 57.895 0.00 0.00 0.00 4.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.800408 GCATCGTGATCAAGAATGGATAAATG 59.200 38.462 15.39 7.02 0.00 2.32
1 2 6.713903 AGCATCGTGATCAAGAATGGATAAAT 59.286 34.615 15.39 0.00 0.00 1.40
3 4 5.614308 AGCATCGTGATCAAGAATGGATAA 58.386 37.500 15.39 0.00 0.00 1.75
5 6 4.063689 GAGCATCGTGATCAAGAATGGAT 58.936 43.478 15.39 7.06 32.15 3.41
6 7 3.133542 AGAGCATCGTGATCAAGAATGGA 59.866 43.478 15.39 0.00 42.67 3.41
7 8 3.464907 AGAGCATCGTGATCAAGAATGG 58.535 45.455 15.39 9.20 42.67 3.16
10 11 4.991153 AGTAGAGCATCGTGATCAAGAA 57.009 40.909 15.39 0.00 42.67 2.52
11 12 4.991153 AAGTAGAGCATCGTGATCAAGA 57.009 40.909 13.84 13.84 42.67 3.02
14 15 4.207955 AGGTAAGTAGAGCATCGTGATCA 58.792 43.478 0.00 0.00 42.67 2.92
15 16 4.839668 AGGTAAGTAGAGCATCGTGATC 57.160 45.455 0.00 0.00 42.67 2.92
16 17 4.737946 GCAAGGTAAGTAGAGCATCGTGAT 60.738 45.833 0.00 0.00 42.67 3.06
17 18 3.428999 GCAAGGTAAGTAGAGCATCGTGA 60.429 47.826 0.00 0.00 42.67 4.35
18 19 2.860735 GCAAGGTAAGTAGAGCATCGTG 59.139 50.000 0.00 0.00 42.67 4.35
21 22 3.198872 GGTGCAAGGTAAGTAGAGCATC 58.801 50.000 0.00 0.00 34.24 3.91
22 23 2.571653 TGGTGCAAGGTAAGTAGAGCAT 59.428 45.455 0.00 0.00 34.24 3.79
23 24 1.974957 TGGTGCAAGGTAAGTAGAGCA 59.025 47.619 0.00 0.00 0.00 4.26
24 25 2.762535 TGGTGCAAGGTAAGTAGAGC 57.237 50.000 0.00 0.00 0.00 4.09
25 26 3.751698 GGTTTGGTGCAAGGTAAGTAGAG 59.248 47.826 0.00 0.00 0.00 2.43
26 27 3.136809 TGGTTTGGTGCAAGGTAAGTAGA 59.863 43.478 0.00 0.00 0.00 2.59
27 28 3.482436 TGGTTTGGTGCAAGGTAAGTAG 58.518 45.455 0.00 0.00 0.00 2.57
28 29 3.579534 TGGTTTGGTGCAAGGTAAGTA 57.420 42.857 0.00 0.00 0.00 2.24
29 30 2.445682 TGGTTTGGTGCAAGGTAAGT 57.554 45.000 0.00 0.00 0.00 2.24
30 31 2.627699 ACATGGTTTGGTGCAAGGTAAG 59.372 45.455 0.00 0.00 0.00 2.34
126 127 4.101585 TGATGCCACGGAGAAGATATTTCT 59.898 41.667 0.00 1.33 0.00 2.52
131 132 5.745312 ATATTGATGCCACGGAGAAGATA 57.255 39.130 0.00 0.00 0.00 1.98
171 172 2.420568 GGCGGATGTCCACGGAGTA 61.421 63.158 0.00 0.00 41.61 2.59
195 226 3.777925 CAAGTTCGCGCGGGTGAG 61.778 66.667 31.69 13.87 33.51 3.51
201 232 1.013755 CGGTAATCAAGTTCGCGCG 60.014 57.895 26.76 26.76 0.00 6.86
202 233 0.928229 ATCGGTAATCAAGTTCGCGC 59.072 50.000 0.00 0.00 0.00 6.86
204 235 4.357142 TCACTATCGGTAATCAAGTTCGC 58.643 43.478 0.00 0.00 0.00 4.70
206 237 7.306632 CGGAAATCACTATCGGTAATCAAGTTC 60.307 40.741 0.00 0.00 0.00 3.01
219 250 4.816385 TCATGGCTTTCGGAAATCACTATC 59.184 41.667 3.24 0.00 0.00 2.08
223 254 2.478539 GCTCATGGCTTTCGGAAATCAC 60.479 50.000 3.24 0.00 38.06 3.06
225 256 1.268234 CGCTCATGGCTTTCGGAAATC 60.268 52.381 3.24 0.00 39.13 2.17
230 261 1.645455 CATCGCTCATGGCTTTCGG 59.355 57.895 0.00 0.00 39.13 4.30
238 269 1.854743 CAAGTACGTCCATCGCTCATG 59.145 52.381 0.00 0.00 44.19 3.07
248 279 2.267961 CCTGGCCCAAGTACGTCC 59.732 66.667 0.00 0.00 0.00 4.79
267 298 1.068753 ATGCGCTTCCAGAGGATCG 59.931 57.895 9.73 0.00 42.67 3.69
273 304 4.393155 ACGGCATGCGCTTCCAGA 62.393 61.111 12.44 0.00 38.60 3.86
284 315 2.289631 TGACTCTGTGATTTGACGGCAT 60.290 45.455 0.00 0.00 0.00 4.40
300 331 0.038251 TCACACTGTGGCGATGACTC 60.038 55.000 13.09 0.00 33.87 3.36
308 339 3.550842 GGACTTTTCATTCACACTGTGGC 60.551 47.826 13.09 0.00 33.87 5.01
341 372 1.404035 AGCTTTTGTTGGTTGGTCGTC 59.596 47.619 0.00 0.00 0.00 4.20
342 373 1.470051 AGCTTTTGTTGGTTGGTCGT 58.530 45.000 0.00 0.00 0.00 4.34
344 375 2.356695 ACGTAGCTTTTGTTGGTTGGTC 59.643 45.455 0.00 0.00 0.00 4.02
364 396 9.481340 TCTGATGAGCTTATGTTAATGTATCAC 57.519 33.333 0.00 0.00 0.00 3.06
368 400 9.702494 CAGATCTGATGAGCTTATGTTAATGTA 57.298 33.333 18.34 0.00 36.73 2.29
381 413 3.993081 CCGGTTATTCAGATCTGATGAGC 59.007 47.826 25.64 20.06 39.64 4.26
406 438 4.003648 CTGGCCTAATTTATAGCCTTCGG 58.996 47.826 3.32 0.00 45.94 4.30
418 450 5.358160 GCTAAATGTTGTCTCTGGCCTAATT 59.642 40.000 3.32 0.00 0.00 1.40
442 474 2.754472 TGTCTGTCTCGTGGAACATTG 58.246 47.619 0.00 0.00 44.52 2.82
542 583 1.376553 GTCCAGGCCAGCTCACTTC 60.377 63.158 5.01 0.00 0.00 3.01
603 646 2.234661 TCAATGGCGTCACATTCTCTCT 59.765 45.455 0.00 0.00 38.94 3.10
681 729 2.324541 CTCCTATGGCTCCTAGTGCTT 58.675 52.381 5.20 0.00 0.00 3.91
684 732 1.638529 CCCTCCTATGGCTCCTAGTG 58.361 60.000 0.00 0.00 0.00 2.74
689 737 0.694444 TTGACCCCTCCTATGGCTCC 60.694 60.000 0.00 0.00 0.00 4.70
690 738 1.349357 GATTGACCCCTCCTATGGCTC 59.651 57.143 0.00 0.00 0.00 4.70
691 739 1.439543 GATTGACCCCTCCTATGGCT 58.560 55.000 0.00 0.00 0.00 4.75
692 740 0.402121 GGATTGACCCCTCCTATGGC 59.598 60.000 0.00 0.00 0.00 4.40
693 741 0.687354 CGGATTGACCCCTCCTATGG 59.313 60.000 0.00 0.00 34.64 2.74
694 742 1.070758 CACGGATTGACCCCTCCTATG 59.929 57.143 0.00 0.00 34.64 2.23
695 743 1.424638 CACGGATTGACCCCTCCTAT 58.575 55.000 0.00 0.00 34.64 2.57
696 744 1.335132 GCACGGATTGACCCCTCCTA 61.335 60.000 0.00 0.00 34.64 2.94
697 745 2.670148 GCACGGATTGACCCCTCCT 61.670 63.158 0.00 0.00 34.64 3.69
830 894 1.219393 GAGTGGAGAAAGGGAGCCG 59.781 63.158 0.00 0.00 0.00 5.52
964 1041 3.930012 CTCGCTCCCCCGAATCCC 61.930 72.222 0.00 0.00 36.72 3.85
965 1042 3.930012 CCTCGCTCCCCCGAATCC 61.930 72.222 0.00 0.00 36.72 3.01
966 1043 3.930012 CCCTCGCTCCCCCGAATC 61.930 72.222 0.00 0.00 36.72 2.52
1318 1632 2.203294 AACTTCCCCCACGCACAC 60.203 61.111 0.00 0.00 0.00 3.82
1319 1633 2.063015 ATGAACTTCCCCCACGCACA 62.063 55.000 0.00 0.00 0.00 4.57
1320 1634 0.035820 TATGAACTTCCCCCACGCAC 60.036 55.000 0.00 0.00 0.00 5.34
1321 1635 0.916086 ATATGAACTTCCCCCACGCA 59.084 50.000 0.00 0.00 0.00 5.24
1322 1636 1.134220 TGATATGAACTTCCCCCACGC 60.134 52.381 0.00 0.00 0.00 5.34
1323 1637 3.492102 ATGATATGAACTTCCCCCACG 57.508 47.619 0.00 0.00 0.00 4.94
1325 1639 3.980022 TGCTATGATATGAACTTCCCCCA 59.020 43.478 0.00 0.00 0.00 4.96
1355 1890 0.175302 CACAACCAGGCAAAGCACAA 59.825 50.000 0.00 0.00 0.00 3.33
1360 1895 1.152567 TCCCCACAACCAGGCAAAG 60.153 57.895 0.00 0.00 0.00 2.77
1366 1901 2.034687 CCTGCTCCCCACAACCAG 59.965 66.667 0.00 0.00 0.00 4.00
1428 1963 2.434884 CAACGTCGGCCATCTGCT 60.435 61.111 2.24 0.00 40.92 4.24
1441 1976 0.393077 AGGTGAGGTCCTTGACAACG 59.607 55.000 0.00 0.00 33.52 4.10
1444 1979 0.105194 TGGAGGTGAGGTCCTTGACA 60.105 55.000 0.00 0.00 38.02 3.58
1500 2035 9.082313 ACAGGAAATAAAACAATGTCTCTTGAT 57.918 29.630 0.00 0.00 0.00 2.57
1609 2144 1.005867 GCGGTAACTTGGTCGGTCA 60.006 57.895 0.00 0.00 0.00 4.02
1631 2166 1.066143 CAGAAAGGTACCTGATGGCGT 60.066 52.381 17.14 0.00 36.63 5.68
1661 2199 9.388506 CAATGATTATGTAGAAAGGACTGACTT 57.611 33.333 0.00 0.00 0.00 3.01
1685 2223 7.434492 TCGGTCTTAAAAATGTTTATTGCCAA 58.566 30.769 0.00 0.00 0.00 4.52
1686 2224 6.982852 TCGGTCTTAAAAATGTTTATTGCCA 58.017 32.000 0.00 0.00 0.00 4.92
1701 2239 3.965379 TGCTATGGTGTTCGGTCTTAA 57.035 42.857 0.00 0.00 0.00 1.85
1709 2247 4.697352 ACAGAAACTGATGCTATGGTGTTC 59.303 41.667 5.76 0.00 35.18 3.18
1713 2251 4.292186 ACACAGAAACTGATGCTATGGT 57.708 40.909 5.76 0.00 35.18 3.55
1753 2291 2.380084 TAACCTCATCGGCAAGTGTC 57.620 50.000 0.00 0.00 35.61 3.67
1754 2292 3.350219 AATAACCTCATCGGCAAGTGT 57.650 42.857 0.00 0.00 35.61 3.55
1755 2293 3.731867 GCAAATAACCTCATCGGCAAGTG 60.732 47.826 0.00 0.00 35.61 3.16
1756 2294 2.423538 GCAAATAACCTCATCGGCAAGT 59.576 45.455 0.00 0.00 35.61 3.16
1757 2295 2.223572 GGCAAATAACCTCATCGGCAAG 60.224 50.000 0.00 0.00 35.61 4.01
1758 2296 1.748493 GGCAAATAACCTCATCGGCAA 59.252 47.619 0.00 0.00 35.61 4.52
1759 2297 1.340502 TGGCAAATAACCTCATCGGCA 60.341 47.619 0.00 0.00 35.61 5.69
1760 2298 1.388547 TGGCAAATAACCTCATCGGC 58.611 50.000 0.00 0.00 35.61 5.54
1761 2299 4.641396 TCTATGGCAAATAACCTCATCGG 58.359 43.478 0.00 0.00 39.35 4.18
1762 2300 8.498054 AATATCTATGGCAAATAACCTCATCG 57.502 34.615 0.00 0.00 0.00 3.84
1763 2301 8.897752 GGAATATCTATGGCAAATAACCTCATC 58.102 37.037 0.00 0.00 0.00 2.92
1782 2320 8.887717 GCTACATTAGGACATGAATGGAATATC 58.112 37.037 0.00 0.00 37.37 1.63
1811 2349 4.581824 ACCGTAAGTTGAGACAGACACTAA 59.418 41.667 0.00 0.00 0.00 2.24
1832 2370 6.319141 AGTTTGAGCATTTCTGAACTTACC 57.681 37.500 0.00 0.00 32.62 2.85
1840 2378 7.227314 TGGCTATATGTAGTTTGAGCATTTCTG 59.773 37.037 0.00 0.00 0.00 3.02
1943 2481 5.355071 ACTCAAATGCATCGAATAGAGCAAA 59.645 36.000 0.00 0.00 36.87 3.68
1955 2493 6.072508 TGACTCCAAACTTACTCAAATGCATC 60.073 38.462 0.00 0.00 0.00 3.91
2203 2745 7.348080 CCAGTAAGGTTGTGATCTGATACTA 57.652 40.000 0.00 0.00 0.00 1.82
2220 2762 2.839486 TCAACAGCCAGACCAGTAAG 57.161 50.000 0.00 0.00 0.00 2.34
2252 2795 1.894881 TGCAGCTTGTATGTCAGCAA 58.105 45.000 0.00 0.00 0.00 3.91
2347 2890 7.805071 GTCAACATGAACTTCTCAACTTTATGG 59.195 37.037 0.00 0.00 37.67 2.74
2373 2927 4.876107 ACAAATTCTACAAGATACCCTGCG 59.124 41.667 0.00 0.00 0.00 5.18
2487 3041 2.816411 TCGGAACTAGGACTTCCATGT 58.184 47.619 10.34 0.00 37.62 3.21
2553 3107 4.058124 TCTGACAATTCTGTGAAAGGACG 58.942 43.478 0.00 0.00 35.30 4.79
2562 3116 3.760684 GGCTTCCATTCTGACAATTCTGT 59.239 43.478 0.00 0.00 38.98 3.41
2623 3177 7.165460 TCTTGATAGTATGTGAAGAACGGAA 57.835 36.000 0.00 0.00 0.00 4.30
2707 3263 8.321353 TCTAAGGAAGATAAAGCAAGTCAATCA 58.679 33.333 0.00 0.00 0.00 2.57
2837 3395 4.686191 ACAACAATTGGGCTTGAAATGA 57.314 36.364 10.83 0.00 34.12 2.57
2882 3448 5.282510 AGAACTTCGCAGTTAGATATTCGG 58.717 41.667 0.00 0.00 43.79 4.30
2919 3486 9.883142 TTTTTCTTGTTCCACATAATCACTTTT 57.117 25.926 0.00 0.00 0.00 2.27
2964 3531 9.679661 TTGGCTTTCATTCTATATGTAACTCAA 57.320 29.630 0.00 0.00 0.00 3.02
2979 3546 8.153479 GTGGAACTTTAAATTTGGCTTTCATT 57.847 30.769 0.00 0.00 0.00 2.57
3078 3658 7.984050 TGCAAACAGATTCCAATTGTTTTCTAA 59.016 29.630 4.43 0.00 41.60 2.10
3304 3887 9.660180 TGCATGTTGTGTAATTAGTAAGTATGA 57.340 29.630 0.00 0.00 0.00 2.15
3325 3908 1.037493 CATCCATTGACCCCTGCATG 58.963 55.000 0.00 0.00 0.00 4.06
3507 4091 5.532406 TGGATAGCCAAATATCTGCAAGTTC 59.468 40.000 0.00 0.00 42.49 3.01
3957 4566 8.139989 GCATCTGAATTATCTTAAAACCATGCT 58.860 33.333 0.00 0.00 0.00 3.79
3977 4586 1.269831 GGCGGAGGTAGTTAGCATCTG 60.270 57.143 0.00 0.00 0.00 2.90
4094 4703 7.099764 TCTTCTTTCTCACATAAGTAGCAAGG 58.900 38.462 0.00 0.00 0.00 3.61
4254 4933 4.278419 GGCAAGTGTCAACCATTTTCTACT 59.722 41.667 0.00 0.00 0.00 2.57
4266 4945 5.565509 TCTTATATTGGTGGCAAGTGTCAA 58.434 37.500 0.00 0.00 0.00 3.18
4365 5070 6.211184 TCAAATTGAATGTGATTGTAGGGCTT 59.789 34.615 0.00 0.00 0.00 4.35
4531 5245 4.410099 TGCAAGACAGATGAGGGAAAATT 58.590 39.130 0.00 0.00 0.00 1.82
4865 5579 7.574607 AGAGGATCCAAGTAACGGAAATATTT 58.425 34.615 15.82 0.00 35.77 1.40
4868 5582 5.897824 AGAGAGGATCCAAGTAACGGAAATA 59.102 40.000 15.82 0.00 35.77 1.40
4922 5636 9.670719 CAGAAACTTCAGAAATTCCTAGAAAAC 57.329 33.333 0.00 0.00 0.00 2.43
4960 5676 4.188462 TGGATGCTATTGGTTTAGACACG 58.812 43.478 0.00 0.00 0.00 4.49
5061 5777 5.009911 GCATGCCAACAGATATACAATCCAA 59.990 40.000 6.36 0.00 0.00 3.53
5219 5935 3.009115 ATACCACCAGCGGCCAGT 61.009 61.111 2.24 0.00 0.00 4.00
5251 5967 9.412460 AGATACAAATGAAAGAATAAGCCATGA 57.588 29.630 0.00 0.00 0.00 3.07
5324 6040 6.862711 AAGCCTAAGTAAAGAAGACAACAC 57.137 37.500 0.00 0.00 0.00 3.32
5363 6079 2.290577 ACCTGATCCTTGAAGAAGCCAC 60.291 50.000 0.00 0.00 0.00 5.01
5419 6135 3.316029 TGAACACACAGAAAGCAGGAATG 59.684 43.478 0.00 0.00 0.00 2.67
5433 6149 6.349033 GGTGTTATCCATAAGGTTGAACACAC 60.349 42.308 21.53 13.34 44.81 3.82
5494 6249 1.315257 ATCGCGCCCTCAATTTGCTT 61.315 50.000 0.00 0.00 0.00 3.91
5495 6250 1.315257 AATCGCGCCCTCAATTTGCT 61.315 50.000 0.00 0.00 0.00 3.91
5496 6251 0.458370 AAATCGCGCCCTCAATTTGC 60.458 50.000 0.00 0.00 0.00 3.68
5497 6252 1.270971 CAAATCGCGCCCTCAATTTG 58.729 50.000 12.40 12.40 34.05 2.32
5498 6253 0.887933 ACAAATCGCGCCCTCAATTT 59.112 45.000 0.00 0.00 0.00 1.82
5499 6254 1.745232 TACAAATCGCGCCCTCAATT 58.255 45.000 0.00 0.00 0.00 2.32
5500 6255 1.745232 TTACAAATCGCGCCCTCAAT 58.255 45.000 0.00 0.00 0.00 2.57
5501 6256 1.524848 TTTACAAATCGCGCCCTCAA 58.475 45.000 0.00 0.00 0.00 3.02
5502 6257 1.745232 ATTTACAAATCGCGCCCTCA 58.255 45.000 0.00 0.00 0.00 3.86
5503 6258 2.032290 GGTATTTACAAATCGCGCCCTC 60.032 50.000 0.00 0.00 0.00 4.30
5504 6259 1.944709 GGTATTTACAAATCGCGCCCT 59.055 47.619 0.00 0.00 0.00 5.19
5505 6260 1.002142 GGGTATTTACAAATCGCGCCC 60.002 52.381 0.00 0.00 0.00 6.13
5506 6261 1.671845 TGGGTATTTACAAATCGCGCC 59.328 47.619 0.00 0.00 0.00 6.53
5507 6262 2.353579 AGTGGGTATTTACAAATCGCGC 59.646 45.455 0.00 0.00 0.00 6.86
5508 6263 4.807304 AGTAGTGGGTATTTACAAATCGCG 59.193 41.667 0.00 0.00 0.00 5.87
5509 6264 6.673154 AAGTAGTGGGTATTTACAAATCGC 57.327 37.500 0.00 0.00 0.00 4.58
5510 6265 8.036273 ACAAAGTAGTGGGTATTTACAAATCG 57.964 34.615 0.00 0.00 0.00 3.34
5511 6266 9.836076 GAACAAAGTAGTGGGTATTTACAAATC 57.164 33.333 0.00 0.00 0.00 2.17
5512 6267 9.357161 TGAACAAAGTAGTGGGTATTTACAAAT 57.643 29.630 0.00 0.00 0.00 2.32
5513 6268 8.749026 TGAACAAAGTAGTGGGTATTTACAAA 57.251 30.769 0.00 0.00 0.00 2.83
5514 6269 8.927675 ATGAACAAAGTAGTGGGTATTTACAA 57.072 30.769 0.00 0.00 0.00 2.41
5515 6270 8.927675 AATGAACAAAGTAGTGGGTATTTACA 57.072 30.769 0.00 0.00 0.00 2.41
5520 6275 7.833285 ACAAAATGAACAAAGTAGTGGGTAT 57.167 32.000 0.00 0.00 0.00 2.73
5550 6309 6.365970 TTTACTGGAGAGCTCAAGAAATCT 57.634 37.500 17.77 0.00 34.26 2.40
5597 6356 4.070716 CTGGGATGCATAATCTGTCTTCC 58.929 47.826 0.00 0.00 35.43 3.46
5677 6436 1.197036 GCAGGTTCGCCAACTAACTTC 59.803 52.381 0.00 0.00 40.60 3.01
5721 6481 6.176183 ACCTGAAGAATATGGAACTCAACTG 58.824 40.000 0.00 0.00 0.00 3.16
5800 6560 4.083110 TCCTTTCGTTTAGGTGACTCTACG 60.083 45.833 0.00 0.00 44.20 3.51
5996 6756 4.079970 AGTCTGGAGATACGTGAAACTCA 58.920 43.478 0.00 0.00 31.75 3.41
6009 6771 6.683537 TCCAGGATTATTCTAAGTCTGGAGA 58.316 40.000 0.00 0.00 42.74 3.71
6012 6774 8.844244 CAAATTCCAGGATTATTCTAAGTCTGG 58.156 37.037 0.00 0.00 40.99 3.86
6072 6834 2.839975 TCGCTGAACCATGTGTTTACA 58.160 42.857 0.00 0.00 41.89 2.41
6141 6903 2.093764 GCCAGTAGATGTGCAGAGACTT 60.094 50.000 0.00 0.00 0.00 3.01
6145 6907 0.538584 TGGCCAGTAGATGTGCAGAG 59.461 55.000 0.00 0.00 0.00 3.35
6163 6925 1.550065 CTGCATAGACGACCGTTCTG 58.450 55.000 0.00 0.00 0.00 3.02
6305 7067 6.644592 CCCTTTTTCGTCATTTTGCAATAAGA 59.355 34.615 0.00 0.00 0.00 2.10
6322 7084 6.030228 CGATGAACAATTAGAGCCCTTTTTC 58.970 40.000 0.00 0.00 0.00 2.29
6355 7117 5.480073 AGGCAGTCAAAATTGCAGGTTATTA 59.520 36.000 0.00 0.00 39.73 0.98
6362 7124 2.555325 TCTGAGGCAGTCAAAATTGCAG 59.445 45.455 0.00 0.00 39.73 4.41
6363 7125 2.585330 TCTGAGGCAGTCAAAATTGCA 58.415 42.857 0.00 0.00 39.73 4.08
6387 7149 7.864108 AATGCTGTGCAAATAAGACTATACA 57.136 32.000 0.00 0.00 43.62 2.29
6388 7150 9.226345 GAAAATGCTGTGCAAATAAGACTATAC 57.774 33.333 0.00 0.00 43.62 1.47
6494 7256 3.290710 CCCAGAGATAACAATGTTGGGG 58.709 50.000 9.15 6.21 40.04 4.96
6598 7360 2.088104 AGCCCTTCTGTCGATGGATA 57.912 50.000 0.00 0.00 36.77 2.59
6622 7384 3.023119 AGGAAGTTCAATTGTGTGCACA 58.977 40.909 17.42 17.42 39.98 4.57
6663 7425 9.492973 AGGATTTTGTTAAAAGAATGAACATGG 57.507 29.630 0.00 0.00 33.33 3.66
6668 7451 9.762933 CCTTCAGGATTTTGTTAAAAGAATGAA 57.237 29.630 0.00 0.00 37.39 2.57
6671 7454 7.966812 AGCCTTCAGGATTTTGTTAAAAGAAT 58.033 30.769 0.00 0.00 37.39 2.40
6674 7457 6.808704 GCTAGCCTTCAGGATTTTGTTAAAAG 59.191 38.462 2.29 0.00 37.39 2.27
6675 7458 6.493458 AGCTAGCCTTCAGGATTTTGTTAAAA 59.507 34.615 12.13 0.00 37.39 1.52
6691 7474 7.095187 GCGTAATATGTCAAAATAGCTAGCCTT 60.095 37.037 12.13 2.33 0.00 4.35
6705 7488 3.055747 TGGTGAACAGGCGTAATATGTCA 60.056 43.478 0.00 0.00 0.00 3.58
6713 7496 0.179078 ACGTTTGGTGAACAGGCGTA 60.179 50.000 0.00 0.00 38.71 4.42
6716 7499 0.869880 GCAACGTTTGGTGAACAGGC 60.870 55.000 0.00 0.00 38.18 4.85
6730 7513 0.868406 GAAGGAGTGGTTCAGCAACG 59.132 55.000 0.00 0.00 32.68 4.10
6740 7523 2.325082 CGGCAAACGGAAGGAGTGG 61.325 63.158 0.00 0.00 39.42 4.00
6756 7539 2.279851 TGCACACGAACAGTCCGG 60.280 61.111 0.00 0.00 0.00 5.14
6766 7549 1.742880 CTCCCATGGACTGCACACG 60.743 63.158 15.22 0.00 0.00 4.49
6861 7644 1.380785 TCGACGGTAGGAGGCCAAT 60.381 57.895 5.01 0.00 0.00 3.16
6876 7659 0.320771 GGCAGCTCACCTTTTCTCGA 60.321 55.000 0.00 0.00 0.00 4.04
6893 7676 3.060615 CTCAACAGGCAGGCAGGC 61.061 66.667 0.00 0.00 44.61 4.85
6894 7677 3.060615 GCTCAACAGGCAGGCAGG 61.061 66.667 0.00 0.00 0.00 4.85
6895 7678 3.429141 CGCTCAACAGGCAGGCAG 61.429 66.667 0.00 0.00 0.00 4.85
6896 7679 3.889134 CTCGCTCAACAGGCAGGCA 62.889 63.158 0.00 0.00 0.00 4.75
6936 7719 9.840427 ACATATGAACAGCATAAAAAGTTACAC 57.160 29.630 10.38 0.00 42.45 2.90
6942 7726 8.984891 TGGAAACATATGAACAGCATAAAAAG 57.015 30.769 10.38 0.00 42.45 2.27
7001 7785 0.454620 CTCCACTCGAACCGTCTTCG 60.455 60.000 6.21 6.21 42.74 3.79
7012 7796 0.448593 GACGGTCTCTTCTCCACTCG 59.551 60.000 0.00 0.00 0.00 4.18
7016 7800 1.587043 CTGCGACGGTCTCTTCTCCA 61.587 60.000 6.57 0.00 0.00 3.86
7068 7855 3.243434 ACACGAAATCACTCTGTCGAAGT 60.243 43.478 0.00 0.00 36.98 3.01
7091 7878 0.813210 GGTGCTGGCTCTGTATCTGC 60.813 60.000 0.00 0.00 0.00 4.26
7115 7902 1.774110 TTGCCAAGCACCTTTTCTGA 58.226 45.000 0.00 0.00 38.71 3.27
7142 7930 2.158813 ACTGGGTGTGTGTTGTCCTAAG 60.159 50.000 0.00 0.00 0.00 2.18
7159 7951 6.814076 TTTAAAAATTGTTACACGCACTGG 57.186 33.333 0.00 0.00 0.00 4.00
7165 7957 8.324567 ACACAAGCATTTAAAAATTGTTACACG 58.675 29.630 11.27 5.44 0.00 4.49
7221 8030 8.659925 ATGCATTTTTCACATGTTTCAAGTTA 57.340 26.923 0.00 0.00 0.00 2.24
7224 8033 8.301730 ACTATGCATTTTTCACATGTTTCAAG 57.698 30.769 3.54 0.00 0.00 3.02
7244 8053 5.447279 GGCATCTGAACCGTTTACAACTATG 60.447 44.000 0.00 0.00 0.00 2.23
7313 8122 5.752955 ACAAATACAAAACTGGCATGTTGTC 59.247 36.000 12.19 0.00 35.82 3.18
7317 8126 7.598493 GTGATTACAAATACAAAACTGGCATGT 59.402 33.333 0.00 0.00 0.00 3.21
7340 8149 2.425592 CTGGGCTGTGTTCCGTGA 59.574 61.111 0.00 0.00 0.00 4.35
7355 8164 4.234574 GTCCCTCGGTTTTAAAAATGCTG 58.765 43.478 1.31 0.00 0.00 4.41
7392 8201 2.809119 CAGCTCTGGAATCATCATGAGC 59.191 50.000 0.09 0.00 45.06 4.26
7410 8247 6.426937 TCTCAGTAGTTGTTACCAAATTCAGC 59.573 38.462 0.00 0.00 32.37 4.26
7465 8302 5.761234 TGTCCTGAACAGTTGTTATACCAAC 59.239 40.000 5.06 5.06 44.00 3.77
7559 8397 2.430465 CCTTTCTGCTGCATACACAGT 58.570 47.619 1.31 0.00 39.96 3.55
7588 8456 5.074804 TGTTACTTAGCTGTCCTGTCTGTA 58.925 41.667 0.00 0.00 0.00 2.74
7641 8509 6.531923 ACTGCTGCTATGAATATCATCAACT 58.468 36.000 0.00 0.00 38.26 3.16
7651 8519 6.042552 AGAGGTGTTATACTGCTGCTATGAAT 59.957 38.462 0.00 0.00 0.00 2.57
7771 8647 3.013921 TCCTCAACTTTTGAAACTGCGT 58.986 40.909 0.00 0.00 39.58 5.24
7784 8660 7.372260 AGCTGAATATAATCAGTCCTCAACT 57.628 36.000 17.19 3.57 46.85 3.16
7966 8882 2.147436 TGAACGCAATTTTGGCCTTC 57.853 45.000 3.32 0.00 0.00 3.46
8014 8932 1.123077 TTGTCGGATGAGCAGCCTAT 58.877 50.000 3.05 0.00 33.99 2.57


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

AutoCloner maintained by Alex Coulton.