Multiple sequence alignment - TraesCS5D01G278700

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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 TraesCS5D01G278700 chr5D 100.000 5459 0 0 1 5459 381020733 381026191 0.000000e+00 10081.0
1 TraesCS5D01G278700 chr5D 80.612 392 37 19 593 958 380854097 380854475 3.240000e-67 267.0
2 TraesCS5D01G278700 chr5D 84.000 150 6 9 1 149 380852387 380852519 1.600000e-25 128.0
3 TraesCS5D01G278700 chr5B 89.368 3800 222 101 7 3722 457119790 457123491 0.000000e+00 4612.0
4 TraesCS5D01G278700 chr5B 89.399 1764 127 31 3708 5426 457123511 457125259 0.000000e+00 2167.0
5 TraesCS5D01G278700 chr5B 80.913 241 22 11 1 230 457018066 457018293 9.400000e-38 169.0
6 TraesCS5D01G278700 chr5B 86.014 143 8 5 427 562 457018659 457018796 5.700000e-30 143.0
7 TraesCS5D01G278700 chr5B 94.595 37 2 0 5423 5459 57017476 57017512 2.120000e-04 58.4
8 TraesCS5D01G278700 chr5A 94.655 2058 83 13 3383 5426 481891691 481893735 0.000000e+00 3166.0
9 TraesCS5D01G278700 chr5A 93.626 1459 77 15 1930 3380 481890080 481891530 0.000000e+00 2165.0
10 TraesCS5D01G278700 chr5A 81.980 1010 100 49 634 1621 481888858 481889807 0.000000e+00 782.0
11 TraesCS5D01G278700 chr5A 79.082 937 84 68 1 879 481888231 481889113 4.810000e-150 542.0
12 TraesCS5D01G278700 chr5A 93.333 195 13 0 1744 1938 481889859 481890053 6.920000e-74 289.0
13 TraesCS5D01G278700 chr1A 93.750 64 4 0 2925 2988 333536581 333536644 4.500000e-16 97.1
14 TraesCS5D01G278700 chr1D 100.000 37 0 0 5423 5459 207658418 207658382 9.810000e-08 69.4
15 TraesCS5D01G278700 chr6A 97.436 39 1 0 5421 5459 100668018 100668056 3.530000e-07 67.6
16 TraesCS5D01G278700 chr6A 97.297 37 1 0 5423 5459 119604382 119604346 4.570000e-06 63.9
17 TraesCS5D01G278700 chr7D 94.595 37 2 0 5423 5459 309508850 309508814 2.120000e-04 58.4


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 TraesCS5D01G278700 chr5D 381020733 381026191 5458 False 10081.0 10081 100.0000 1 5459 1 chr5D.!!$F1 5458
1 TraesCS5D01G278700 chr5B 457119790 457125259 5469 False 3389.5 4612 89.3835 7 5426 2 chr5B.!!$F3 5419
2 TraesCS5D01G278700 chr5A 481888231 481893735 5504 False 1388.8 3166 88.5352 1 5426 5 chr5A.!!$F1 5425

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
92 94 0.036732 GGAGCATCACCAGTTCACCA 59.963 55.0 0.0 0.0 36.25 4.17 F
1092 1200 0.034767 CCTCCTGCAATCTCCAGCAA 60.035 55.0 0.0 0.0 40.73 3.91 F
1806 1938 0.029300 CCTTGTGTGCCGTTTCAGTG 59.971 55.0 0.0 0.0 0.00 3.66 F
2153 2321 0.793104 CGCCGAATCGCAAGGTTTTC 60.793 55.0 0.0 0.0 43.78 2.29 F
4112 4495 0.114954 ATTGCCCACACCATTGTCCT 59.885 50.0 0.0 0.0 31.66 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1701 1824 0.108851 CCATGCCAAAACCCGCTAAC 60.109 55.0 0.00 0.0 0.00 2.34 R
2104 2271 0.171903 AATGTGCGAGGATTTGCAGC 59.828 50.0 0.00 0.0 44.28 5.25 R
2618 2792 1.032794 CGCATCTGTCTAGCACCCTA 58.967 55.0 0.00 0.0 0.00 3.53 R
4130 4513 0.523072 CTGCCACAGGGTGAATTTCG 59.477 55.0 0.00 0.0 35.23 3.46 R
5366 5793 0.097325 CGAGTCGTCTCTTTCCCGAG 59.903 60.0 3.82 0.0 38.45 4.63 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
58 60 1.343506 GTCGGATCACGCTACGTTTT 58.656 50.000 0.00 0.00 43.86 2.43
85 87 3.571401 AGAAAAACAAGGAGCATCACCAG 59.429 43.478 0.00 0.00 36.25 4.00
86 88 2.664402 AAACAAGGAGCATCACCAGT 57.336 45.000 0.00 0.00 36.25 4.00
87 89 2.664402 AACAAGGAGCATCACCAGTT 57.336 45.000 0.00 0.00 36.25 3.16
88 90 2.191128 ACAAGGAGCATCACCAGTTC 57.809 50.000 0.00 0.00 36.25 3.01
89 91 1.421268 ACAAGGAGCATCACCAGTTCA 59.579 47.619 0.00 0.00 36.25 3.18
90 92 1.808945 CAAGGAGCATCACCAGTTCAC 59.191 52.381 0.00 0.00 36.25 3.18
91 93 0.326264 AGGAGCATCACCAGTTCACC 59.674 55.000 0.00 0.00 36.25 4.02
92 94 0.036732 GGAGCATCACCAGTTCACCA 59.963 55.000 0.00 0.00 36.25 4.17
99 101 1.134521 TCACCAGTTCACCACACTCAC 60.135 52.381 0.00 0.00 0.00 3.51
111 113 2.344950 CACACTCACTCATTCAGCCTC 58.655 52.381 0.00 0.00 0.00 4.70
112 114 1.067283 ACACTCACTCATTCAGCCTCG 60.067 52.381 0.00 0.00 0.00 4.63
113 115 0.108424 ACTCACTCATTCAGCCTCGC 60.108 55.000 0.00 0.00 0.00 5.03
114 116 0.108472 CTCACTCATTCAGCCTCGCA 60.108 55.000 0.00 0.00 0.00 5.10
115 117 0.390340 TCACTCATTCAGCCTCGCAC 60.390 55.000 0.00 0.00 0.00 5.34
116 118 0.390866 CACTCATTCAGCCTCGCACT 60.391 55.000 0.00 0.00 0.00 4.40
117 119 0.108424 ACTCATTCAGCCTCGCACTC 60.108 55.000 0.00 0.00 0.00 3.51
118 120 0.108472 CTCATTCAGCCTCGCACTCA 60.108 55.000 0.00 0.00 0.00 3.41
137 139 2.930562 ACTCACCTGCCCTCCCAC 60.931 66.667 0.00 0.00 0.00 4.61
185 224 8.371699 AGAAGAAGCAGATAATAATACTCCACC 58.628 37.037 0.00 0.00 0.00 4.61
323 372 1.464734 TGCTTCCTCTCTACTCACCG 58.535 55.000 0.00 0.00 0.00 4.94
324 373 1.004394 TGCTTCCTCTCTACTCACCGA 59.996 52.381 0.00 0.00 0.00 4.69
325 374 1.673920 GCTTCCTCTCTACTCACCGAG 59.326 57.143 0.00 0.00 35.52 4.63
326 375 1.673920 CTTCCTCTCTACTCACCGAGC 59.326 57.143 0.00 0.00 32.04 5.03
327 376 0.462225 TCCTCTCTACTCACCGAGCG 60.462 60.000 0.00 0.00 32.04 5.03
389 438 1.614317 GCTTGCTTAGCCTTTCCCTCA 60.614 52.381 0.29 0.00 44.48 3.86
390 439 2.087646 CTTGCTTAGCCTTTCCCTCAC 58.912 52.381 0.29 0.00 0.00 3.51
397 446 1.282157 AGCCTTTCCCTCACGCTTTAT 59.718 47.619 0.00 0.00 0.00 1.40
464 513 1.562008 CCTTCCTTTCTCCTTCTCCCC 59.438 57.143 0.00 0.00 0.00 4.81
514 573 2.443016 ATTCCTCGCCTCGCCTCT 60.443 61.111 0.00 0.00 0.00 3.69
515 574 2.494530 ATTCCTCGCCTCGCCTCTC 61.495 63.158 0.00 0.00 0.00 3.20
518 577 3.591835 CTCGCCTCGCCTCTCCTC 61.592 72.222 0.00 0.00 0.00 3.71
581 640 2.609183 CTAGCCTGTACCGTCGGCAC 62.609 65.000 12.28 9.84 46.14 5.01
621 680 3.055530 AGTTGCTCATCTTCTCCGTGATT 60.056 43.478 0.00 0.00 0.00 2.57
643 732 0.466555 TAGCCGCCTTCTCTCTCTCC 60.467 60.000 0.00 0.00 0.00 3.71
656 745 0.397254 TCTCTCCCCGTCCTCCATTC 60.397 60.000 0.00 0.00 0.00 2.67
657 746 0.397816 CTCTCCCCGTCCTCCATTCT 60.398 60.000 0.00 0.00 0.00 2.40
685 774 4.735132 CGGCCGCGTCTTCTTCCA 62.735 66.667 14.67 0.00 0.00 3.53
701 790 2.100631 CCAGTCGCCGACATCCAAC 61.101 63.158 20.65 0.00 34.60 3.77
705 794 0.589223 GTCGCCGACATCCAACAAAA 59.411 50.000 13.23 0.00 32.09 2.44
713 802 1.001815 ACATCCAACAAAACTTCCGCG 60.002 47.619 0.00 0.00 0.00 6.46
714 803 0.596082 ATCCAACAAAACTTCCGCGG 59.404 50.000 22.12 22.12 0.00 6.46
715 804 0.464013 TCCAACAAAACTTCCGCGGA 60.464 50.000 27.28 27.28 0.00 5.54
716 805 0.317519 CCAACAAAACTTCCGCGGAC 60.318 55.000 31.19 0.00 0.00 4.79
717 806 0.378962 CAACAAAACTTCCGCGGACA 59.621 50.000 31.19 18.10 0.00 4.02
718 807 0.661020 AACAAAACTTCCGCGGACAG 59.339 50.000 31.19 27.74 0.00 3.51
834 932 4.154347 GCAGCTCGAGGTGAGGGG 62.154 72.222 40.57 19.76 45.66 4.79
856 954 3.085947 CCTGCCCTGCCTCTGCTA 61.086 66.667 0.00 0.00 38.71 3.49
857 955 2.505006 CTGCCCTGCCTCTGCTAG 59.495 66.667 0.00 0.00 38.71 3.42
858 956 2.039462 TGCCCTGCCTCTGCTAGA 59.961 61.111 0.00 0.00 38.71 2.43
859 957 1.383664 TGCCCTGCCTCTGCTAGAT 60.384 57.895 0.00 0.00 38.71 1.98
860 958 0.984961 TGCCCTGCCTCTGCTAGATT 60.985 55.000 0.00 0.00 38.71 2.40
871 973 1.287503 GCTAGATTCTCCCTCCGCG 59.712 63.158 0.00 0.00 0.00 6.46
886 988 1.081556 CCGCGTGGACGAATTCATCA 61.082 55.000 10.20 0.00 43.02 3.07
906 1008 3.198582 GCCGGAGCGAGAGTTACT 58.801 61.111 5.05 0.00 0.00 2.24
907 1009 1.226717 GCCGGAGCGAGAGTTACTG 60.227 63.158 5.05 0.00 0.00 2.74
908 1010 1.433879 CCGGAGCGAGAGTTACTGG 59.566 63.158 0.00 0.00 0.00 4.00
909 1011 1.030488 CCGGAGCGAGAGTTACTGGA 61.030 60.000 0.00 0.00 0.00 3.86
910 1012 0.378962 CGGAGCGAGAGTTACTGGAG 59.621 60.000 0.00 0.00 0.00 3.86
911 1013 1.465794 GGAGCGAGAGTTACTGGAGT 58.534 55.000 0.00 0.00 0.00 3.85
912 1014 1.819903 GGAGCGAGAGTTACTGGAGTT 59.180 52.381 0.00 0.00 0.00 3.01
1092 1200 0.034767 CCTCCTGCAATCTCCAGCAA 60.035 55.000 0.00 0.00 40.73 3.91
1095 1203 1.136147 CTGCAATCTCCAGCAACGC 59.864 57.895 0.00 0.00 40.73 4.84
1101 1209 2.842394 ATCTCCAGCAACGCCACTCG 62.842 60.000 0.00 0.00 45.38 4.18
1124 1232 2.125431 GTTAGCACCGCCCGCTTA 60.125 61.111 0.00 0.00 40.96 3.09
1125 1233 1.523032 GTTAGCACCGCCCGCTTAT 60.523 57.895 0.00 0.00 40.96 1.73
1126 1234 1.093496 GTTAGCACCGCCCGCTTATT 61.093 55.000 0.00 0.00 40.96 1.40
1127 1235 0.812412 TTAGCACCGCCCGCTTATTC 60.812 55.000 0.00 0.00 40.96 1.75
1128 1236 1.682451 TAGCACCGCCCGCTTATTCT 61.682 55.000 0.00 0.00 40.96 2.40
1129 1237 2.112815 GCACCGCCCGCTTATTCTT 61.113 57.895 0.00 0.00 0.00 2.52
1130 1238 2.014594 CACCGCCCGCTTATTCTTC 58.985 57.895 0.00 0.00 0.00 2.87
1131 1239 0.462047 CACCGCCCGCTTATTCTTCT 60.462 55.000 0.00 0.00 0.00 2.85
1132 1240 0.252197 ACCGCCCGCTTATTCTTCTT 59.748 50.000 0.00 0.00 0.00 2.52
1133 1241 0.938008 CCGCCCGCTTATTCTTCTTC 59.062 55.000 0.00 0.00 0.00 2.87
1134 1242 1.473434 CCGCCCGCTTATTCTTCTTCT 60.473 52.381 0.00 0.00 0.00 2.85
1135 1243 1.594862 CGCCCGCTTATTCTTCTTCTG 59.405 52.381 0.00 0.00 0.00 3.02
1178 1286 9.034800 TCCTCCAATACTTCAATTGCTATTTTT 57.965 29.630 0.00 0.00 35.85 1.94
1179 1287 9.305925 CCTCCAATACTTCAATTGCTATTTTTC 57.694 33.333 0.00 0.00 35.85 2.29
1180 1288 9.859427 CTCCAATACTTCAATTGCTATTTTTCA 57.141 29.630 0.00 0.00 35.85 2.69
1255 1366 7.713942 AGAATTAAGAATTATACACCGACCCAC 59.286 37.037 0.00 0.00 0.00 4.61
1289 1403 1.555075 TGTCCTGATTACCTGTGGAGC 59.445 52.381 0.00 0.00 0.00 4.70
1350 1465 4.650972 TGGCACCCAACTTAAACTCTAT 57.349 40.909 0.00 0.00 0.00 1.98
1374 1491 4.224370 ACTCCAATCCATAACCAAGTACGT 59.776 41.667 0.00 0.00 0.00 3.57
1375 1492 5.168647 TCCAATCCATAACCAAGTACGTT 57.831 39.130 0.00 0.00 0.00 3.99
1376 1493 5.180271 TCCAATCCATAACCAAGTACGTTC 58.820 41.667 0.00 0.00 0.00 3.95
1377 1494 4.938832 CCAATCCATAACCAAGTACGTTCA 59.061 41.667 0.00 0.00 0.00 3.18
1378 1495 5.064707 CCAATCCATAACCAAGTACGTTCAG 59.935 44.000 0.00 0.00 0.00 3.02
1379 1496 4.877378 TCCATAACCAAGTACGTTCAGT 57.123 40.909 0.00 0.00 0.00 3.41
1380 1497 5.217978 TCCATAACCAAGTACGTTCAGTT 57.782 39.130 0.00 0.00 0.00 3.16
1381 1498 5.613329 TCCATAACCAAGTACGTTCAGTTT 58.387 37.500 0.00 0.00 0.00 2.66
1382 1499 6.757237 TCCATAACCAAGTACGTTCAGTTTA 58.243 36.000 0.00 0.00 0.00 2.01
1383 1500 6.869913 TCCATAACCAAGTACGTTCAGTTTAG 59.130 38.462 0.00 0.00 0.00 1.85
1424 1545 8.194104 TGCATACAGAACACTTAACAATTTTGT 58.806 29.630 0.00 0.00 44.72 2.83
1514 1636 6.070021 ACATCTCATTCATCTCCTTTACACCA 60.070 38.462 0.00 0.00 0.00 4.17
1558 1680 2.100418 GGATGCTCAGCCTTCATTTTCC 59.900 50.000 0.00 0.00 33.23 3.13
1630 1753 2.040278 ACCACTTCACCTGCATGTATGT 59.960 45.455 0.00 0.00 0.00 2.29
1650 1773 5.565455 TGTATGGACTCCATGAATGCATA 57.435 39.130 19.49 0.00 44.84 3.14
1652 1775 5.999600 TGTATGGACTCCATGAATGCATAAG 59.000 40.000 19.49 0.00 44.84 1.73
1688 1811 9.941325 AAATACAGAATTGATTTATGGTGCAAA 57.059 25.926 0.00 0.00 0.00 3.68
1689 1812 9.941325 AATACAGAATTGATTTATGGTGCAAAA 57.059 25.926 0.00 0.00 0.00 2.44
1691 1814 8.259049 ACAGAATTGATTTATGGTGCAAAATG 57.741 30.769 0.00 0.00 0.00 2.32
1692 1815 7.148373 ACAGAATTGATTTATGGTGCAAAATGC 60.148 33.333 0.00 0.00 45.29 3.56
1696 1819 7.507733 TTGATTTATGGTGCAAAATGCTTTT 57.492 28.000 3.78 0.00 45.31 2.27
1741 1873 5.989477 TGGAATCTGATCAGACGGTAATTT 58.011 37.500 27.37 15.55 40.75 1.82
1802 1934 3.907894 TTATTCCTTGTGTGCCGTTTC 57.092 42.857 0.00 0.00 0.00 2.78
1806 1938 0.029300 CCTTGTGTGCCGTTTCAGTG 59.971 55.000 0.00 0.00 0.00 3.66
1862 1994 1.640428 CGCGATTCTCCTACTGCAAA 58.360 50.000 0.00 0.00 0.00 3.68
1911 2043 7.763172 TGCAAACTTTTCGACATTTTTACAT 57.237 28.000 0.00 0.00 0.00 2.29
1983 2150 5.762825 ATCACATATTGCAGACCATCAAC 57.237 39.130 0.00 0.00 0.00 3.18
2073 2240 3.211045 CTCCAGGAAAACAACGGAAAGA 58.789 45.455 0.00 0.00 0.00 2.52
2104 2271 3.373748 GGCAACTTCAAAGGTTTGGTTTG 59.626 43.478 2.69 5.33 38.66 2.93
2116 2283 2.802247 GTTTGGTTTGCTGCAAATCCTC 59.198 45.455 29.51 17.57 33.95 3.71
2153 2321 0.793104 CGCCGAATCGCAAGGTTTTC 60.793 55.000 0.00 0.00 43.78 2.29
2210 2378 9.605955 GATATGCGTGTCTTATATCTATGCTAG 57.394 37.037 0.00 0.00 33.24 3.42
2211 2379 6.819397 TGCGTGTCTTATATCTATGCTAGT 57.181 37.500 0.00 0.00 0.00 2.57
2212 2380 7.916914 TGCGTGTCTTATATCTATGCTAGTA 57.083 36.000 0.00 0.00 0.00 1.82
2232 2406 8.766151 GCTAGTATGTTTTTATTCTGGAGTAGC 58.234 37.037 0.00 0.00 0.00 3.58
2241 2415 8.918202 TTTTATTCTGGAGTAGCTTCTTTTCA 57.082 30.769 0.00 0.00 0.00 2.69
2242 2416 9.520515 TTTTATTCTGGAGTAGCTTCTTTTCAT 57.479 29.630 0.00 0.00 0.00 2.57
2272 2446 4.383948 GTCTAACTAAGGTAACACACACGC 59.616 45.833 0.00 0.00 41.41 5.34
2382 2556 1.605710 GGAAGGCATGGATGTTCATCG 59.394 52.381 6.70 0.00 0.00 3.84
2383 2557 2.292267 GAAGGCATGGATGTTCATCGT 58.708 47.619 6.70 0.00 0.00 3.73
2384 2558 3.466836 GAAGGCATGGATGTTCATCGTA 58.533 45.455 6.70 0.12 0.00 3.43
2385 2559 2.838736 AGGCATGGATGTTCATCGTAC 58.161 47.619 6.70 0.00 0.00 3.67
2387 2561 2.485479 GGCATGGATGTTCATCGTACCT 60.485 50.000 6.70 0.00 0.00 3.08
2390 2564 4.260784 GCATGGATGTTCATCGTACCTTTC 60.261 45.833 6.70 0.00 0.00 2.62
2391 2565 3.517602 TGGATGTTCATCGTACCTTTCG 58.482 45.455 6.70 0.00 0.00 3.46
2500 2674 2.777094 GCAGATTTAGCTGGGGAGATC 58.223 52.381 0.00 0.00 36.41 2.75
2575 2749 2.099263 CAGAAGGGCATTTGATCAGCAG 59.901 50.000 7.62 0.00 0.00 4.24
2611 2785 2.221055 CAGTTTTGTGAGCGAGGTACAC 59.779 50.000 0.00 0.00 35.45 2.90
2614 2788 2.605837 TTGTGAGCGAGGTACACAAA 57.394 45.000 0.00 0.00 46.56 2.83
2615 2789 1.860676 TGTGAGCGAGGTACACAAAC 58.139 50.000 0.00 0.00 40.72 2.93
2636 2810 2.224161 CCTTAGGGTGCTAGACAGATGC 60.224 54.545 0.00 0.00 0.00 3.91
2673 2850 6.372381 TCATGACAACAGTATGAAGTCCAATG 59.628 38.462 0.00 0.00 40.67 2.82
2674 2851 4.455533 TGACAACAGTATGAAGTCCAATGC 59.544 41.667 0.00 0.00 40.67 3.56
2718 2895 1.200948 GCAGGTGGATCAAGAAGCAAC 59.799 52.381 0.00 0.00 0.00 4.17
2880 3057 4.705023 ACCCAAGCAACATAATGTTCCTAC 59.295 41.667 0.00 0.00 38.77 3.18
2906 3083 5.774690 TGGAAATATGCCTCACTCAACTTTT 59.225 36.000 0.00 0.00 0.00 2.27
3124 3301 6.251655 AGTCATTCTGTTTCATCTTCAAGC 57.748 37.500 0.00 0.00 0.00 4.01
3207 3384 0.324368 AGCCCTCGCCGATATCCATA 60.324 55.000 0.00 0.00 34.57 2.74
3209 3386 0.460311 CCCTCGCCGATATCCATACC 59.540 60.000 0.00 0.00 0.00 2.73
3210 3387 1.182667 CCTCGCCGATATCCATACCA 58.817 55.000 0.00 0.00 0.00 3.25
3229 3406 7.201679 CCATACCAAAAAGAGAATAGTGAGCAG 60.202 40.741 0.00 0.00 0.00 4.24
3353 3530 7.654022 AACAAGAGGAACATTGGTTTTTCTA 57.346 32.000 0.00 0.00 37.36 2.10
3380 3557 8.697507 ACTGGAATTGAAGTTAAGAAAGATGT 57.302 30.769 0.00 0.00 0.00 3.06
3381 3558 9.136323 ACTGGAATTGAAGTTAAGAAAGATGTT 57.864 29.630 0.00 0.00 0.00 2.71
3382 3559 9.403110 CTGGAATTGAAGTTAAGAAAGATGTTG 57.597 33.333 0.00 0.00 0.00 3.33
3383 3560 7.867403 TGGAATTGAAGTTAAGAAAGATGTTGC 59.133 33.333 0.00 0.00 0.00 4.17
3384 3561 8.084684 GGAATTGAAGTTAAGAAAGATGTTGCT 58.915 33.333 0.00 0.00 0.00 3.91
3385 3562 9.468532 GAATTGAAGTTAAGAAAGATGTTGCTT 57.531 29.630 0.81 0.81 35.50 3.91
3386 3563 9.468532 AATTGAAGTTAAGAAAGATGTTGCTTC 57.531 29.630 0.00 0.00 33.17 3.86
3387 3564 6.658831 TGAAGTTAAGAAAGATGTTGCTTCG 58.341 36.000 0.00 0.00 33.17 3.79
3388 3565 5.613358 AGTTAAGAAAGATGTTGCTTCGG 57.387 39.130 0.00 0.00 33.17 4.30
3389 3566 5.063880 AGTTAAGAAAGATGTTGCTTCGGT 58.936 37.500 0.00 0.00 33.17 4.69
3404 3739 6.229936 TGCTTCGGTCACTAACCTATAAAT 57.770 37.500 0.00 0.00 46.87 1.40
3471 3806 3.745975 TCGATCCAACAAAGATGACACAC 59.254 43.478 0.00 0.00 0.00 3.82
3574 3924 4.420143 CGTGGATGGTTAGCCTCG 57.580 61.111 0.00 0.00 41.96 4.63
3580 3930 2.241176 TGGATGGTTAGCCTCGGAAATT 59.759 45.455 0.00 0.00 32.18 1.82
3616 3966 7.896811 TCTAACCTATATACTGCCTTGTGATG 58.103 38.462 0.00 0.00 0.00 3.07
3863 4245 3.520290 TTGGTATGACCTGCTTCTACG 57.480 47.619 0.00 0.00 39.58 3.51
3865 4247 2.426024 TGGTATGACCTGCTTCTACGAC 59.574 50.000 0.00 0.00 39.58 4.34
3868 4250 1.324383 TGACCTGCTTCTACGACACA 58.676 50.000 0.00 0.00 0.00 3.72
3911 4293 9.659830 CTATTAACAAGAACAAACACACTAACC 57.340 33.333 0.00 0.00 0.00 2.85
3938 4321 1.594293 CTTCACAGTGGGTTCGCGT 60.594 57.895 5.77 0.00 0.00 6.01
3948 4331 2.530497 GGTTCGCGTGCTGTTCACA 61.530 57.895 5.77 0.00 45.92 3.58
3964 4347 3.228188 TCACACCAGCAAAAAGATCCT 57.772 42.857 0.00 0.00 0.00 3.24
3993 4376 3.015145 ACGGCAAGGCACCCCTAT 61.015 61.111 0.00 0.00 41.90 2.57
3996 4379 2.276740 GCAAGGCACCCCTATGCT 59.723 61.111 0.00 0.00 45.38 3.79
4015 4398 1.218047 CTTCACCATTCCGAGCCGA 59.782 57.895 0.00 0.00 0.00 5.54
4041 4424 2.859273 ATTTCGCGCTCTCCACAGGG 62.859 60.000 5.56 0.00 0.00 4.45
4056 4439 1.780309 ACAGGGACATTTTCAGACCCA 59.220 47.619 0.00 0.00 42.41 4.51
4083 4466 2.399916 GCTCCTCAGCATCTCAAACT 57.600 50.000 0.00 0.00 46.06 2.66
4084 4467 2.709213 GCTCCTCAGCATCTCAAACTT 58.291 47.619 0.00 0.00 46.06 2.66
4097 4480 2.211806 TCAAACTTTTGCTGCCATTGC 58.788 42.857 0.00 0.00 38.05 3.56
4105 4488 2.601067 CTGCCATTGCCCACACCA 60.601 61.111 0.00 0.00 36.33 4.17
4107 4490 1.535930 TGCCATTGCCCACACCATT 60.536 52.632 0.00 0.00 36.33 3.16
4108 4491 1.078988 GCCATTGCCCACACCATTG 60.079 57.895 0.00 0.00 0.00 2.82
4109 4492 1.829523 GCCATTGCCCACACCATTGT 61.830 55.000 0.00 0.00 35.84 2.71
4111 4494 0.247185 CATTGCCCACACCATTGTCC 59.753 55.000 0.00 0.00 31.66 4.02
4112 4495 0.114954 ATTGCCCACACCATTGTCCT 59.885 50.000 0.00 0.00 31.66 3.85
4113 4496 0.539438 TTGCCCACACCATTGTCCTC 60.539 55.000 0.00 0.00 31.66 3.71
4114 4497 1.074775 GCCCACACCATTGTCCTCA 59.925 57.895 0.00 0.00 31.66 3.86
4130 4513 5.245531 TGTCCTCATGTAAAATCTCACCAC 58.754 41.667 0.00 0.00 0.00 4.16
4141 4524 2.178912 TCTCACCACGAAATTCACCC 57.821 50.000 0.00 0.00 0.00 4.61
4221 4604 0.107017 CCGAGTTCATCCAGGCCAAT 60.107 55.000 5.01 0.00 0.00 3.16
4356 4739 2.203126 CAGCGGAAGGAGATGGCC 60.203 66.667 0.00 0.00 0.00 5.36
4382 4765 2.347490 GCACCGGCTCAGGAGAAA 59.653 61.111 0.00 0.00 36.96 2.52
4410 4793 4.269523 TGTGTGGAGTGGCTGCCC 62.270 66.667 17.53 7.66 0.00 5.36
4630 5020 2.108168 GCTGGGTGTACTGGTGATCTA 58.892 52.381 0.00 0.00 0.00 1.98
4639 5029 6.313905 GGTGTACTGGTGATCTAAATTGTGAG 59.686 42.308 0.00 0.00 0.00 3.51
4968 5391 6.026947 AGTAACTGAGCTCTATTCAACGTT 57.973 37.500 16.19 0.00 0.00 3.99
5292 5719 1.457346 CCTGGAGCTTGGATGTGTTC 58.543 55.000 0.00 0.00 0.00 3.18
5337 5764 0.898320 GGTTACTGAGCCTGCAGAGA 59.102 55.000 17.39 0.00 39.20 3.10
5366 5793 4.483476 AGGTACGCATTTCAGTCAAAAC 57.517 40.909 0.00 0.00 0.00 2.43
5379 5806 3.495001 CAGTCAAAACTCGGGAAAGAGAC 59.505 47.826 0.00 0.00 40.57 3.36
5382 5809 2.435533 AAACTCGGGAAAGAGACGAC 57.564 50.000 0.00 0.00 40.57 4.34
5383 5810 1.618487 AACTCGGGAAAGAGACGACT 58.382 50.000 0.00 0.00 40.57 4.18
5426 5856 4.132336 TGCAGCAAGAGCAGATATTAAGG 58.868 43.478 0.00 0.00 45.49 2.69
5427 5857 3.058363 GCAGCAAGAGCAGATATTAAGGC 60.058 47.826 0.00 0.00 45.49 4.35
5428 5858 3.501445 CAGCAAGAGCAGATATTAAGGCC 59.499 47.826 0.00 0.00 45.49 5.19
5429 5859 2.816672 GCAAGAGCAGATATTAAGGCCC 59.183 50.000 0.00 0.00 41.58 5.80
5430 5860 3.497584 GCAAGAGCAGATATTAAGGCCCT 60.498 47.826 0.00 0.00 41.58 5.19
5431 5861 4.070716 CAAGAGCAGATATTAAGGCCCTG 58.929 47.826 0.00 0.00 0.00 4.45
5432 5862 3.321950 AGAGCAGATATTAAGGCCCTGT 58.678 45.455 0.00 0.00 0.00 4.00
5433 5863 3.718956 AGAGCAGATATTAAGGCCCTGTT 59.281 43.478 0.00 0.00 0.00 3.16
5434 5864 4.068599 GAGCAGATATTAAGGCCCTGTTC 58.931 47.826 0.00 1.15 0.00 3.18
5435 5865 2.808543 GCAGATATTAAGGCCCTGTTCG 59.191 50.000 0.00 0.00 0.00 3.95
5436 5866 3.403038 CAGATATTAAGGCCCTGTTCGG 58.597 50.000 0.00 0.00 0.00 4.30
5437 5867 3.071023 CAGATATTAAGGCCCTGTTCGGA 59.929 47.826 0.00 0.00 33.16 4.55
5438 5868 3.325135 AGATATTAAGGCCCTGTTCGGAG 59.675 47.826 0.00 0.00 33.16 4.63
5439 5869 0.546598 ATTAAGGCCCTGTTCGGAGG 59.453 55.000 0.00 0.00 33.16 4.30
5440 5870 0.545787 TTAAGGCCCTGTTCGGAGGA 60.546 55.000 0.00 0.00 34.69 3.71
5441 5871 1.262640 TAAGGCCCTGTTCGGAGGAC 61.263 60.000 0.00 0.00 34.69 3.85
5442 5872 4.097361 GGCCCTGTTCGGAGGACC 62.097 72.222 0.00 0.00 34.69 4.46
5443 5873 3.003763 GCCCTGTTCGGAGGACCT 61.004 66.667 0.00 0.00 34.69 3.85
5444 5874 3.020237 GCCCTGTTCGGAGGACCTC 62.020 68.421 13.60 13.60 34.69 3.85
5445 5875 2.359967 CCCTGTTCGGAGGACCTCC 61.360 68.421 28.50 28.50 46.44 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.953960 ACACCGCCTTTTCCATCGTC 60.954 55.000 0.00 0.00 0.00 4.20
58 60 4.644234 TGATGCTCCTTGTTTTTCTTGTGA 59.356 37.500 0.00 0.00 0.00 3.58
76 78 0.593128 GTGTGGTGAACTGGTGATGC 59.407 55.000 0.00 0.00 0.00 3.91
85 87 3.466836 TGAATGAGTGAGTGTGGTGAAC 58.533 45.455 0.00 0.00 0.00 3.18
86 88 3.732212 CTGAATGAGTGAGTGTGGTGAA 58.268 45.455 0.00 0.00 0.00 3.18
87 89 2.548707 GCTGAATGAGTGAGTGTGGTGA 60.549 50.000 0.00 0.00 0.00 4.02
88 90 1.802960 GCTGAATGAGTGAGTGTGGTG 59.197 52.381 0.00 0.00 0.00 4.17
89 91 1.271054 GGCTGAATGAGTGAGTGTGGT 60.271 52.381 0.00 0.00 0.00 4.16
90 92 1.002888 AGGCTGAATGAGTGAGTGTGG 59.997 52.381 0.00 0.00 0.00 4.17
91 93 2.344950 GAGGCTGAATGAGTGAGTGTG 58.655 52.381 0.00 0.00 0.00 3.82
92 94 1.067283 CGAGGCTGAATGAGTGAGTGT 60.067 52.381 0.00 0.00 0.00 3.55
99 101 0.108472 TGAGTGCGAGGCTGAATGAG 60.108 55.000 0.00 0.00 0.00 2.90
111 113 2.313172 GCAGGTGAGTGTGAGTGCG 61.313 63.158 0.00 0.00 0.00 5.34
112 114 1.963338 GGCAGGTGAGTGTGAGTGC 60.963 63.158 0.00 0.00 0.00 4.40
113 115 1.302033 GGGCAGGTGAGTGTGAGTG 60.302 63.158 0.00 0.00 0.00 3.51
114 116 1.460305 AGGGCAGGTGAGTGTGAGT 60.460 57.895 0.00 0.00 0.00 3.41
115 117 1.294780 GAGGGCAGGTGAGTGTGAG 59.705 63.158 0.00 0.00 0.00 3.51
116 118 2.217038 GGAGGGCAGGTGAGTGTGA 61.217 63.158 0.00 0.00 0.00 3.58
117 119 2.348998 GGAGGGCAGGTGAGTGTG 59.651 66.667 0.00 0.00 0.00 3.82
118 120 2.930562 GGGAGGGCAGGTGAGTGT 60.931 66.667 0.00 0.00 0.00 3.55
185 224 5.459536 TGATGGAGAAGATACGAGAATGG 57.540 43.478 0.00 0.00 0.00 3.16
226 265 8.235226 CACTGCGCTAGCTAATACTACTAAATA 58.765 37.037 13.93 0.00 45.42 1.40
227 266 7.040617 TCACTGCGCTAGCTAATACTACTAAAT 60.041 37.037 13.93 0.00 45.42 1.40
228 267 6.261603 TCACTGCGCTAGCTAATACTACTAAA 59.738 38.462 13.93 0.00 45.42 1.85
229 268 5.761726 TCACTGCGCTAGCTAATACTACTAA 59.238 40.000 13.93 0.00 45.42 2.24
230 269 5.303165 TCACTGCGCTAGCTAATACTACTA 58.697 41.667 13.93 0.00 45.42 1.82
231 270 4.135306 TCACTGCGCTAGCTAATACTACT 58.865 43.478 13.93 0.00 45.42 2.57
232 271 4.468643 CTCACTGCGCTAGCTAATACTAC 58.531 47.826 13.93 0.00 45.42 2.73
233 272 3.502595 CCTCACTGCGCTAGCTAATACTA 59.497 47.826 13.93 0.00 45.42 1.82
234 273 2.294791 CCTCACTGCGCTAGCTAATACT 59.705 50.000 13.93 0.00 45.42 2.12
235 274 2.608261 CCCTCACTGCGCTAGCTAATAC 60.608 54.545 13.93 0.00 45.42 1.89
243 282 1.754621 CTCCTCCCTCACTGCGCTA 60.755 63.158 9.73 0.00 0.00 4.26
371 420 1.610624 CGTGAGGGAAAGGCTAAGCAA 60.611 52.381 0.00 0.00 0.00 3.91
372 421 0.036388 CGTGAGGGAAAGGCTAAGCA 60.036 55.000 0.00 0.00 0.00 3.91
414 463 4.987408 TCGAACAATGGCATCAATCAAT 57.013 36.364 0.00 0.00 0.00 2.57
415 464 4.987408 ATCGAACAATGGCATCAATCAA 57.013 36.364 0.00 0.00 0.00 2.57
416 465 4.641541 AGAATCGAACAATGGCATCAATCA 59.358 37.500 0.00 0.00 0.00 2.57
417 466 5.008415 AGAGAATCGAACAATGGCATCAATC 59.992 40.000 0.00 0.00 42.67 2.67
418 467 4.885907 AGAGAATCGAACAATGGCATCAAT 59.114 37.500 0.00 0.00 42.67 2.57
530 589 2.652313 CGGAGCAGAGGAGATAGGG 58.348 63.158 0.00 0.00 0.00 3.53
581 640 4.321230 GCAACTAACCAAGTGATCCTTTGG 60.321 45.833 18.73 18.73 38.88 3.28
621 680 1.077644 AGAGAGAAGGCGGCTACGA 60.078 57.895 13.71 0.00 44.60 3.43
643 732 1.407437 CCAAGAAGAATGGAGGACGGG 60.407 57.143 0.00 0.00 40.56 5.28
672 761 3.755404 CGACTGGAAGAAGACGCG 58.245 61.111 3.53 3.53 37.43 6.01
685 774 0.250124 TTTGTTGGATGTCGGCGACT 60.250 50.000 36.17 23.51 33.15 4.18
701 790 1.082104 GCTGTCCGCGGAAGTTTTG 60.082 57.895 32.93 16.57 0.00 2.44
761 858 0.901124 AGCAATGAAGTCTCCGCTCT 59.099 50.000 0.00 0.00 0.00 4.09
770 867 1.843368 CATGGGTGGAGCAATGAAGT 58.157 50.000 0.00 0.00 0.00 3.01
813 911 1.153862 CTCACCTCGAGCTGCTGTC 60.154 63.158 7.01 0.00 34.18 3.51
834 932 3.883549 GAGGCAGGGCAGGGGATC 61.884 72.222 0.00 0.00 0.00 3.36
850 948 1.988293 CGGAGGGAGAATCTAGCAGA 58.012 55.000 0.00 0.00 33.73 4.26
856 954 2.427245 CCACGCGGAGGGAGAATCT 61.427 63.158 12.47 0.00 46.37 2.40
857 955 2.107141 CCACGCGGAGGGAGAATC 59.893 66.667 12.47 0.00 46.37 2.52
858 956 2.363795 TCCACGCGGAGGGAGAAT 60.364 61.111 12.47 0.00 46.37 2.40
859 957 3.379445 GTCCACGCGGAGGGAGAA 61.379 66.667 12.47 0.00 43.99 2.87
871 973 1.261619 GGCGATGATGAATTCGTCCAC 59.738 52.381 22.07 15.20 37.10 4.02
878 980 2.621763 GCTCCGGCGATGATGAATT 58.378 52.632 9.30 0.00 0.00 2.17
897 999 2.739379 GCAAGCAACTCCAGTAACTCTC 59.261 50.000 0.00 0.00 0.00 3.20
898 1000 2.104792 TGCAAGCAACTCCAGTAACTCT 59.895 45.455 0.00 0.00 0.00 3.24
899 1001 2.494059 TGCAAGCAACTCCAGTAACTC 58.506 47.619 0.00 0.00 0.00 3.01
900 1002 2.638480 TGCAAGCAACTCCAGTAACT 57.362 45.000 0.00 0.00 0.00 2.24
901 1003 3.253188 TCAATGCAAGCAACTCCAGTAAC 59.747 43.478 0.00 0.00 0.00 2.50
902 1004 3.485394 TCAATGCAAGCAACTCCAGTAA 58.515 40.909 0.00 0.00 0.00 2.24
903 1005 3.076621 CTCAATGCAAGCAACTCCAGTA 58.923 45.455 0.00 0.00 0.00 2.74
904 1006 1.884579 CTCAATGCAAGCAACTCCAGT 59.115 47.619 0.00 0.00 0.00 4.00
905 1007 2.156917 TCTCAATGCAAGCAACTCCAG 58.843 47.619 0.00 0.00 0.00 3.86
906 1008 2.275134 TCTCAATGCAAGCAACTCCA 57.725 45.000 0.00 0.00 0.00 3.86
907 1009 3.648339 TTTCTCAATGCAAGCAACTCC 57.352 42.857 0.00 0.00 0.00 3.85
908 1010 3.924686 CCATTTCTCAATGCAAGCAACTC 59.075 43.478 0.00 0.00 38.88 3.01
909 1011 3.306502 CCCATTTCTCAATGCAAGCAACT 60.307 43.478 0.00 0.00 38.88 3.16
910 1012 2.997986 CCCATTTCTCAATGCAAGCAAC 59.002 45.455 0.00 0.00 38.88 4.17
911 1013 2.898612 TCCCATTTCTCAATGCAAGCAA 59.101 40.909 0.00 0.00 38.88 3.91
912 1014 2.494471 CTCCCATTTCTCAATGCAAGCA 59.506 45.455 0.00 0.00 38.88 3.91
1010 1112 4.925861 GCGCCCCTGATCTCCAGC 62.926 72.222 0.00 0.00 41.57 4.85
1095 1203 0.737715 GTGCTAACCTCTGCGAGTGG 60.738 60.000 0.00 4.36 35.12 4.00
1101 1209 2.820037 GGCGGTGCTAACCTCTGC 60.820 66.667 0.00 0.00 45.17 4.26
1116 1224 2.906354 TCAGAAGAAGAATAAGCGGGC 58.094 47.619 0.00 0.00 0.00 6.13
1129 1237 7.015682 AGGAAACTCTGTCTGTAATTCAGAAGA 59.984 37.037 8.55 11.21 46.49 2.87
1130 1238 7.158021 AGGAAACTCTGTCTGTAATTCAGAAG 58.842 38.462 8.55 6.44 46.49 2.85
1131 1239 7.067496 AGGAAACTCTGTCTGTAATTCAGAA 57.933 36.000 8.55 0.00 46.49 3.02
1132 1240 6.672266 AGGAAACTCTGTCTGTAATTCAGA 57.328 37.500 4.18 4.18 44.06 3.27
1182 1290 8.990163 ACTCCTTTTGTTCCTTTATTTAGTGA 57.010 30.769 0.00 0.00 0.00 3.41
1186 1294 9.816787 ACCATACTCCTTTTGTTCCTTTATTTA 57.183 29.630 0.00 0.00 0.00 1.40
1187 1295 8.721133 ACCATACTCCTTTTGTTCCTTTATTT 57.279 30.769 0.00 0.00 0.00 1.40
1203 1312 5.476945 ACTGAAAATGACCAAACCATACTCC 59.523 40.000 0.00 0.00 0.00 3.85
1206 1315 8.106247 TCTTACTGAAAATGACCAAACCATAC 57.894 34.615 0.00 0.00 0.00 2.39
1247 1358 0.689745 TTCCCTCCTATGTGGGTCGG 60.690 60.000 5.22 0.00 44.29 4.79
1248 1359 1.200519 TTTCCCTCCTATGTGGGTCG 58.799 55.000 5.22 0.00 44.29 4.79
1270 1384 1.555075 TGCTCCACAGGTAATCAGGAC 59.445 52.381 0.00 0.00 0.00 3.85
1313 1427 3.243704 GGTGCCAATTTGCAGTGTTTCTA 60.244 43.478 4.12 0.00 43.02 2.10
1350 1465 5.422970 ACGTACTTGGTTATGGATTGGAGTA 59.577 40.000 0.00 0.00 0.00 2.59
1374 1491 0.675083 TGGGCGACGACTAAACTGAA 59.325 50.000 0.00 0.00 0.00 3.02
1375 1492 0.892755 ATGGGCGACGACTAAACTGA 59.107 50.000 0.00 0.00 0.00 3.41
1376 1493 2.572191 TATGGGCGACGACTAAACTG 57.428 50.000 0.00 0.00 0.00 3.16
1377 1494 4.806330 CATATATGGGCGACGACTAAACT 58.194 43.478 0.00 0.00 0.00 2.66
1378 1495 3.367025 GCATATATGGGCGACGACTAAAC 59.633 47.826 14.51 0.00 0.00 2.01
1379 1496 3.006003 TGCATATATGGGCGACGACTAAA 59.994 43.478 14.51 0.00 0.00 1.85
1380 1497 2.559231 TGCATATATGGGCGACGACTAA 59.441 45.455 14.51 0.00 0.00 2.24
1381 1498 2.164338 TGCATATATGGGCGACGACTA 58.836 47.619 14.51 0.00 0.00 2.59
1382 1499 0.966179 TGCATATATGGGCGACGACT 59.034 50.000 14.51 0.00 0.00 4.18
1383 1500 2.010145 ATGCATATATGGGCGACGAC 57.990 50.000 14.51 0.00 0.00 4.34
1452 1573 3.275020 CGCGTACAGTATACAGTACACG 58.725 50.000 27.85 26.29 38.32 4.49
1524 1646 2.036098 CATCCTTGCACAGGGGCA 59.964 61.111 12.99 0.00 44.12 5.36
1558 1680 2.223456 TGTGAGTCAACCATTTTGTGCG 60.223 45.455 0.00 0.00 0.00 5.34
1590 1712 2.092323 GTGGGTCTGCCATTAACTTCC 58.908 52.381 0.00 0.00 36.17 3.46
1594 1716 1.173913 GTGGTGGGTCTGCCATTAAC 58.826 55.000 0.00 0.00 37.09 2.01
1612 1735 4.164030 TCCATACATACATGCAGGTGAAGT 59.836 41.667 15.48 11.89 0.00 3.01
1613 1736 4.512944 GTCCATACATACATGCAGGTGAAG 59.487 45.833 15.48 6.20 0.00 3.02
1630 1753 5.999600 CACTTATGCATTCATGGAGTCCATA 59.000 40.000 24.40 10.76 43.15 2.74
1696 1819 2.891580 TGCCAAAACCCGCTAACATAAA 59.108 40.909 0.00 0.00 0.00 1.40
1699 1822 1.204467 CATGCCAAAACCCGCTAACAT 59.796 47.619 0.00 0.00 0.00 2.71
1701 1824 0.108851 CCATGCCAAAACCCGCTAAC 60.109 55.000 0.00 0.00 0.00 2.34
1705 1828 0.460109 GATTCCATGCCAAAACCCGC 60.460 55.000 0.00 0.00 0.00 6.13
1706 1829 1.135024 CAGATTCCATGCCAAAACCCG 60.135 52.381 0.00 0.00 0.00 5.28
1707 1830 2.178580 TCAGATTCCATGCCAAAACCC 58.821 47.619 0.00 0.00 0.00 4.11
1708 1831 3.448301 TGATCAGATTCCATGCCAAAACC 59.552 43.478 0.00 0.00 0.00 3.27
1709 1832 4.400251 TCTGATCAGATTCCATGCCAAAAC 59.600 41.667 21.67 0.00 31.41 2.43
1741 1873 7.867305 TTCCACGCCAAAATCAACTAATATA 57.133 32.000 0.00 0.00 0.00 0.86
1802 1934 1.068083 ACGTGTCCTCAGCACACTG 59.932 57.895 0.00 0.00 45.95 3.66
1806 1938 1.373497 CCTCACGTGTCCTCAGCAC 60.373 63.158 16.51 0.00 0.00 4.40
1862 1994 6.306987 AGACAAATCCAATTTACTCACAGGT 58.693 36.000 0.00 0.00 0.00 4.00
1911 2043 5.004448 TGCGTAATGGTGGAAGAAACATAA 58.996 37.500 0.00 0.00 0.00 1.90
2073 2240 3.633986 CCTTTGAAGTTGCCTTCTGAGTT 59.366 43.478 4.63 0.00 46.07 3.01
2104 2271 0.171903 AATGTGCGAGGATTTGCAGC 59.828 50.000 0.00 0.00 44.28 5.25
2116 2283 2.341168 GGCGTATTTGAAACAATGTGCG 59.659 45.455 0.00 0.00 0.00 5.34
2153 2321 5.508124 TTTTTCAGCTTCAACAAAACACG 57.492 34.783 0.00 0.00 0.00 4.49
2186 2354 8.507524 ACTAGCATAGATATAAGACACGCATA 57.492 34.615 0.00 0.00 42.77 3.14
2210 2378 9.384764 AGAAGCTACTCCAGAATAAAAACATAC 57.615 33.333 0.00 0.00 0.00 2.39
2211 2379 9.959721 AAGAAGCTACTCCAGAATAAAAACATA 57.040 29.630 0.00 0.00 0.00 2.29
2212 2380 8.870075 AAGAAGCTACTCCAGAATAAAAACAT 57.130 30.769 0.00 0.00 0.00 2.71
2241 2415 9.305555 TGTGTTACCTTAGTTAGACTACTCAAT 57.694 33.333 0.00 0.00 28.93 2.57
2242 2416 8.571336 GTGTGTTACCTTAGTTAGACTACTCAA 58.429 37.037 0.00 0.00 28.93 3.02
2288 2462 5.703978 TTTCATGGATTAGTGGTGTGTTG 57.296 39.130 0.00 0.00 0.00 3.33
2289 2463 5.774690 ACATTTCATGGATTAGTGGTGTGTT 59.225 36.000 0.00 0.00 33.60 3.32
2290 2464 5.324409 ACATTTCATGGATTAGTGGTGTGT 58.676 37.500 0.00 0.00 33.60 3.72
2575 2749 2.246719 AACTGCAGGAATCGGATAGC 57.753 50.000 19.93 0.00 0.00 2.97
2615 2789 2.224161 GCATCTGTCTAGCACCCTAAGG 60.224 54.545 0.00 0.00 40.04 2.69
2618 2792 1.032794 CGCATCTGTCTAGCACCCTA 58.967 55.000 0.00 0.00 0.00 3.53
2636 2810 5.234329 ACTGTTGTCATGACTGAAAAGTACG 59.766 40.000 25.55 6.63 29.01 3.67
2673 2850 4.488126 TTCATGGCATTAATCTTAGCGC 57.512 40.909 0.00 0.00 0.00 5.92
2674 2851 5.820131 TGTTTCATGGCATTAATCTTAGCG 58.180 37.500 0.00 0.00 0.00 4.26
2718 2895 3.059597 CGCGCCCTCATCAATACTTTTAG 60.060 47.826 0.00 0.00 0.00 1.85
2779 2956 4.090761 AGAATCTGAGACAGTTGGCAAA 57.909 40.909 0.00 0.00 32.61 3.68
2880 3057 3.565764 TGAGTGAGGCATATTTCCAGG 57.434 47.619 0.00 0.00 0.00 4.45
2895 3072 4.534168 CTGTGAGATGCAAAAGTTGAGTG 58.466 43.478 0.00 0.00 0.00 3.51
2906 3083 1.683385 CGATACCTCCTGTGAGATGCA 59.317 52.381 0.00 0.00 41.42 3.96
3031 3208 1.394917 CAGTAGACCGAAGCAATGCAC 59.605 52.381 8.35 0.00 0.00 4.57
3207 3384 5.869579 TCTGCTCACTATTCTCTTTTTGGT 58.130 37.500 0.00 0.00 0.00 3.67
3209 3386 7.194607 TGTTCTGCTCACTATTCTCTTTTTG 57.805 36.000 0.00 0.00 0.00 2.44
3210 3387 7.992754 ATGTTCTGCTCACTATTCTCTTTTT 57.007 32.000 0.00 0.00 0.00 1.94
3229 3406 5.300034 TGGAACAATGATCATGCCTATGTTC 59.700 40.000 27.36 27.36 42.56 3.18
3404 3739 4.141482 GGGACCTGGATGCAGTAGAAATAA 60.141 45.833 13.65 0.00 0.00 1.40
3448 3783 4.393062 GTGTGTCATCTTTGTTGGATCGAT 59.607 41.667 0.00 0.00 0.00 3.59
3450 3785 3.423515 CGTGTGTCATCTTTGTTGGATCG 60.424 47.826 0.00 0.00 0.00 3.69
3557 3907 1.227263 CCGAGGCTAACCATCCACG 60.227 63.158 0.00 0.00 39.06 4.94
3863 4245 3.494251 GGGCATTTCATGTTTTGTGTGTC 59.506 43.478 0.00 0.00 0.00 3.67
3865 4247 3.731089 AGGGCATTTCATGTTTTGTGTG 58.269 40.909 0.00 0.00 0.00 3.82
3868 4250 7.675062 TGTTAATAGGGCATTTCATGTTTTGT 58.325 30.769 0.00 0.00 0.00 2.83
3882 4264 5.918576 GTGTGTTTGTTCTTGTTAATAGGGC 59.081 40.000 0.00 0.00 0.00 5.19
3885 4267 9.659830 GGTTAGTGTGTTTGTTCTTGTTAATAG 57.340 33.333 0.00 0.00 0.00 1.73
3911 4293 2.086869 CCCACTGTGAAGGTAATGCTG 58.913 52.381 9.86 0.00 0.00 4.41
3948 4331 1.620323 GCCAAGGATCTTTTTGCTGGT 59.380 47.619 0.00 0.00 0.00 4.00
3981 4364 0.548510 GAAGAGCATAGGGGTGCCTT 59.451 55.000 0.00 0.00 46.19 4.35
3993 4376 3.840831 CTCGGAATGGTGAAGAGCA 57.159 52.632 0.00 0.00 0.00 4.26
3996 4379 1.218047 CGGCTCGGAATGGTGAAGA 59.782 57.895 0.00 0.00 0.00 2.87
4020 4403 1.005037 TGTGGAGAGCGCGAAATGT 60.005 52.632 12.10 0.00 0.00 2.71
4041 4424 1.165270 CGGGTGGGTCTGAAAATGTC 58.835 55.000 0.00 0.00 0.00 3.06
4056 4439 0.978146 ATGCTGAGGAGCTTACGGGT 60.978 55.000 0.00 0.00 46.39 5.28
4083 4466 1.071128 GTGGGCAATGGCAGCAAAA 59.929 52.632 9.51 0.00 43.71 2.44
4084 4467 2.138831 TGTGGGCAATGGCAGCAAA 61.139 52.632 9.51 0.00 43.71 3.68
4097 4480 1.272092 ACATGAGGACAATGGTGTGGG 60.272 52.381 0.00 0.00 38.41 4.61
4105 4488 6.375455 GTGGTGAGATTTTACATGAGGACAAT 59.625 38.462 0.00 0.00 0.00 2.71
4107 4490 5.245531 GTGGTGAGATTTTACATGAGGACA 58.754 41.667 0.00 0.00 0.00 4.02
4108 4491 4.330074 CGTGGTGAGATTTTACATGAGGAC 59.670 45.833 0.00 0.00 0.00 3.85
4109 4492 4.221924 TCGTGGTGAGATTTTACATGAGGA 59.778 41.667 0.00 0.00 0.00 3.71
4111 4494 6.480524 TTTCGTGGTGAGATTTTACATGAG 57.519 37.500 0.00 0.00 0.00 2.90
4112 4495 7.174080 TGAATTTCGTGGTGAGATTTTACATGA 59.826 33.333 0.00 0.00 31.95 3.07
4113 4496 7.271223 GTGAATTTCGTGGTGAGATTTTACATG 59.729 37.037 0.00 0.00 31.95 3.21
4114 4497 7.305474 GTGAATTTCGTGGTGAGATTTTACAT 58.695 34.615 0.00 0.00 31.95 2.29
4130 4513 0.523072 CTGCCACAGGGTGAATTTCG 59.477 55.000 0.00 0.00 35.23 3.46
4158 4541 1.626321 TGGATCTTCTTGGCCGTGTAA 59.374 47.619 0.00 0.00 0.00 2.41
4197 4580 1.605058 CCTGGATGAACTCGGTCCGT 61.605 60.000 11.88 0.00 34.72 4.69
4221 4604 1.664649 CTGCTTCTTCACCGCGACA 60.665 57.895 8.23 0.00 0.00 4.35
4371 4754 2.949451 TGTCGATCTTTCTCCTGAGC 57.051 50.000 0.00 0.00 0.00 4.26
4381 4764 2.365617 ACTCCACACACTTGTCGATCTT 59.634 45.455 0.00 0.00 31.66 2.40
4382 4765 1.964223 ACTCCACACACTTGTCGATCT 59.036 47.619 0.00 0.00 31.66 2.75
4410 4793 5.710984 ACGTATCTGAAGTTGGACTTGTAG 58.289 41.667 0.00 0.00 38.80 2.74
4492 4882 7.994334 ACTACTTACACCATAAGAACAAAACCA 59.006 33.333 0.81 0.00 0.00 3.67
4639 5029 4.240096 CACAATGGCAAAATGAGAAGGTC 58.760 43.478 0.00 0.00 0.00 3.85
4657 5047 2.700722 TTGAGCAGTACACACCACAA 57.299 45.000 0.00 0.00 0.00 3.33
4954 5375 7.378461 TGAAACATTTGAAACGTTGAATAGAGC 59.622 33.333 0.00 0.00 0.00 4.09
4965 5388 5.886715 TCAGCAATGAAACATTTGAAACG 57.113 34.783 0.00 0.00 0.00 3.60
4968 5391 8.610248 ATTCAATCAGCAATGAAACATTTGAA 57.390 26.923 0.00 0.00 38.88 2.69
5292 5719 0.654683 GAAAGCAGGCGTATCAGCTG 59.345 55.000 7.63 7.63 37.41 4.24
5337 5764 5.003804 ACTGAAATGCGTACCTTGAAATCT 58.996 37.500 0.00 0.00 0.00 2.40
5366 5793 0.097325 CGAGTCGTCTCTTTCCCGAG 59.903 60.000 3.82 0.00 38.45 4.63
5379 5806 9.199184 CAAACATACATATTTTTCTTCGAGTCG 57.801 33.333 6.09 6.09 0.00 4.18
5382 5809 8.894409 TGCAAACATACATATTTTTCTTCGAG 57.106 30.769 0.00 0.00 0.00 4.04
5383 5810 7.484641 GCTGCAAACATACATATTTTTCTTCGA 59.515 33.333 0.00 0.00 0.00 3.71
5426 5856 3.003763 AGGTCCTCCGAACAGGGC 61.004 66.667 0.00 0.00 41.52 5.19
5427 5857 2.359967 GGAGGTCCTCCGAACAGGG 61.360 68.421 22.53 0.00 41.08 4.45
5428 5858 3.300013 GGAGGTCCTCCGAACAGG 58.700 66.667 22.53 0.00 41.08 4.00


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

AutoCloner maintained by Alex Coulton.