Multiple sequence alignment - TraesCS3A01G010000

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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 TraesCS3A01G010000 chr3A 100.000 3882 0 0 1 3882 8862515 8866396 0.000000e+00 7169
1 TraesCS3A01G010000 chr3B 87.107 3436 268 92 1 3349 5956084 5952737 0.000000e+00 3729
2 TraesCS3A01G010000 chr3B 91.498 247 16 4 3637 3881 5952518 5952275 6.210000e-88 335
3 TraesCS3A01G010000 chr3B 76.680 253 22 16 3377 3615 5952740 5952511 5.300000e-19 106
4 TraesCS3A01G010000 chr3D 91.172 1971 133 22 1354 3312 776012 774071 0.000000e+00 2638
5 TraesCS3A01G010000 chr3D 87.752 1339 107 35 1 1293 777364 776037 0.000000e+00 1511
6 TraesCS3A01G010000 chr3D 75.794 504 49 33 1 444 778046 777556 1.840000e-43 187


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 TraesCS3A01G010000 chr3A 8862515 8866396 3881 False 7169.000000 7169 100.000 1 3882 1 chr3A.!!$F1 3881
1 TraesCS3A01G010000 chr3B 5952275 5956084 3809 True 1390.000000 3729 85.095 1 3881 3 chr3B.!!$R1 3880
2 TraesCS3A01G010000 chr3D 774071 778046 3975 True 1445.333333 2638 84.906 1 3312 3 chr3D.!!$R1 3311

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
684 1395 1.301087 CCGACGGCAAACCAGTACA 60.301 57.895 0.00 0.00 34.57 2.9 F
1528 2276 0.108615 ACAGTGGCGAGTGATAGCAC 60.109 55.000 10.85 2.01 45.49 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2604 3371 0.386476 CAACTGCAGGCAAGCAAGAA 59.614 50.0 19.93 0.0 45.13 2.52 R
3024 3804 0.106335 TTAACCACCGCAAACCTCGA 59.894 50.0 0.00 0.0 0.00 4.04 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
56 739 4.293648 CACGGTGTCGCTGTCCCA 62.294 66.667 0.00 0.00 40.63 4.37
57 740 4.295119 ACGGTGTCGCTGTCCCAC 62.295 66.667 0.00 0.00 40.63 4.61
69 752 3.950232 TCCCACGGGATCTGTAGC 58.050 61.111 0.00 0.00 39.76 3.58
101 785 4.987408 TTGGAATGTGGTGCATGATAAG 57.013 40.909 0.00 0.00 37.96 1.73
106 790 5.475909 GGAATGTGGTGCATGATAAGATGAT 59.524 40.000 0.00 0.00 37.96 2.45
109 793 4.818005 TGTGGTGCATGATAAGATGATCAC 59.182 41.667 0.00 0.00 38.64 3.06
198 882 1.812235 TGCATGCTTGAACTCGACAT 58.188 45.000 20.33 0.00 0.00 3.06
229 914 4.998400 TTGCGCCGGCTGTTGCTA 62.998 61.111 26.68 14.51 40.82 3.49
339 1040 6.620678 TGATTGCAAGCTTCCAAGTATTAAC 58.379 36.000 16.73 0.00 0.00 2.01
433 1141 4.061596 GTTCCAAGAGTCTCAAAGGACAG 58.938 47.826 1.94 0.00 38.57 3.51
452 1160 4.085733 ACAGTGCCCAATTGTAAATGCTA 58.914 39.130 4.43 0.00 0.00 3.49
454 1162 3.131046 AGTGCCCAATTGTAAATGCTAGC 59.869 43.478 8.10 8.10 0.00 3.42
456 1164 3.705579 TGCCCAATTGTAAATGCTAGCAT 59.294 39.130 24.67 24.67 38.46 3.79
549 1258 6.596106 GTCTTATCCTCTGGTTCTTTCCTTTC 59.404 42.308 0.00 0.00 0.00 2.62
558 1267 7.343357 TCTGGTTCTTTCCTTTCTTTAGTTCA 58.657 34.615 0.00 0.00 0.00 3.18
572 1281 4.896562 TTAGTTCAAATCAGCACGTACG 57.103 40.909 15.01 15.01 0.00 3.67
601 1310 3.974871 TTCTTTGCGTTACCTTTGTCC 57.025 42.857 0.00 0.00 0.00 4.02
674 1383 3.119065 TCAGTTTGATAATACCGACGGCA 60.119 43.478 15.39 0.00 0.00 5.69
677 1386 4.093850 AGTTTGATAATACCGACGGCAAAC 59.906 41.667 25.40 25.40 42.12 2.93
678 1387 2.553086 TGATAATACCGACGGCAAACC 58.447 47.619 15.39 0.00 0.00 3.27
684 1395 1.301087 CCGACGGCAAACCAGTACA 60.301 57.895 0.00 0.00 34.57 2.90
688 1399 2.737783 CGACGGCAAACCAGTACATAAA 59.262 45.455 0.00 0.00 34.57 1.40
784 1495 4.082125 ACTCCACACATCAATTCTTTCCC 58.918 43.478 0.00 0.00 0.00 3.97
894 1605 5.344884 GTTGTCGGTTTCAATTCTTCCAAA 58.655 37.500 0.00 0.00 0.00 3.28
908 1619 4.879197 CTTCCAAAGAAGGGAAAAGCAT 57.121 40.909 0.00 0.00 44.97 3.79
910 1621 6.535963 CTTCCAAAGAAGGGAAAAGCATAT 57.464 37.500 0.00 0.00 44.97 1.78
911 1622 6.933514 TTCCAAAGAAGGGAAAAGCATATT 57.066 33.333 0.00 0.00 41.30 1.28
914 1625 6.725834 TCCAAAGAAGGGAAAAGCATATTTCT 59.274 34.615 8.81 0.00 38.92 2.52
915 1626 7.235399 TCCAAAGAAGGGAAAAGCATATTTCTT 59.765 33.333 8.81 0.00 38.92 2.52
916 1627 7.879677 CCAAAGAAGGGAAAAGCATATTTCTTT 59.120 33.333 8.81 4.09 41.45 2.52
917 1628 9.276590 CAAAGAAGGGAAAAGCATATTTCTTTT 57.723 29.630 10.59 10.59 43.91 2.27
918 1629 9.851686 AAAGAAGGGAAAAGCATATTTCTTTTT 57.148 25.926 11.60 0.49 42.02 1.94
995 1742 7.501559 AGATGATTTATCTTGTGCAGCAATACT 59.498 33.333 0.00 0.00 43.68 2.12
996 1743 8.681486 ATGATTTATCTTGTGCAGCAATACTA 57.319 30.769 0.00 0.00 36.36 1.82
997 1744 8.681486 TGATTTATCTTGTGCAGCAATACTAT 57.319 30.769 0.00 0.00 36.36 2.12
998 1745 9.123902 TGATTTATCTTGTGCAGCAATACTATT 57.876 29.630 0.00 0.00 36.36 1.73
1007 1754 6.485313 TGTGCAGCAATACTATTTATGGGTAC 59.515 38.462 0.00 0.00 0.00 3.34
1051 1798 1.506025 AGAGGAGCTGGATTCTTCCC 58.494 55.000 0.00 0.00 41.83 3.97
1054 1801 3.041946 GAGGAGCTGGATTCTTCCCTTA 58.958 50.000 0.00 0.00 41.83 2.69
1062 1809 2.303311 GGATTCTTCCCTTATCCCTCCG 59.697 54.545 0.00 0.00 35.84 4.63
1065 1812 1.049402 CTTCCCTTATCCCTCCGTCC 58.951 60.000 0.00 0.00 0.00 4.79
1081 1828 1.453155 GTCCAGCGACAACATGGAAT 58.547 50.000 0.00 0.00 44.45 3.01
1102 1849 0.468226 GCCGGATGATAAGGGTGACA 59.532 55.000 5.05 0.00 0.00 3.58
1108 1855 5.470098 CCGGATGATAAGGGTGACAATTTAG 59.530 44.000 0.00 0.00 0.00 1.85
1110 1857 5.827797 GGATGATAAGGGTGACAATTTAGCA 59.172 40.000 0.00 0.00 0.00 3.49
1139 1886 1.340889 GGGCACTGTCAATGCTGAAAA 59.659 47.619 6.19 0.00 42.93 2.29
1155 1902 4.440880 CTGAAAATTCTTTGGGTGCACAA 58.559 39.130 20.43 1.81 0.00 3.33
1161 1908 2.507484 TCTTTGGGTGCACAATCTGAG 58.493 47.619 20.43 8.35 0.00 3.35
1168 1915 1.089112 TGCACAATCTGAGAATGGCG 58.911 50.000 2.21 0.00 0.00 5.69
1173 1920 1.857217 CAATCTGAGAATGGCGTCTCG 59.143 52.381 11.91 7.95 46.00 4.04
1185 1932 1.536284 GGCGTCTCGGAACCATTAGAG 60.536 57.143 0.00 0.00 0.00 2.43
1206 1953 2.615912 GGCTGCTGATGTAAATGGAGAC 59.384 50.000 0.00 0.00 0.00 3.36
1220 1967 1.208776 TGGAGACACTGAGCATGATGG 59.791 52.381 0.00 0.00 33.40 3.51
1250 1997 0.179045 ACTGGCCACACTGAACAGAC 60.179 55.000 0.00 0.00 33.57 3.51
1251 1998 0.886490 CTGGCCACACTGAACAGACC 60.886 60.000 0.00 3.08 0.00 3.85
1252 1999 1.148273 GGCCACACTGAACAGACCA 59.852 57.895 8.87 0.00 0.00 4.02
1257 2004 2.549754 CCACACTGAACAGACCAATGAC 59.450 50.000 8.87 0.00 0.00 3.06
1272 2019 3.749088 CCAATGACGGTAAGCTTGTTGTA 59.251 43.478 9.86 0.00 0.00 2.41
1276 2023 5.199024 TGACGGTAAGCTTGTTGTAGTTA 57.801 39.130 9.86 0.00 0.00 2.24
1279 2026 6.707161 TGACGGTAAGCTTGTTGTAGTTAATT 59.293 34.615 9.86 0.00 0.00 1.40
1330 2077 9.987272 TGTACTAAATATCTGATCAACTGGATG 57.013 33.333 0.00 0.00 36.00 3.51
1331 2078 9.429359 GTACTAAATATCTGATCAACTGGATGG 57.571 37.037 0.00 0.00 36.00 3.51
1332 2079 8.267620 ACTAAATATCTGATCAACTGGATGGA 57.732 34.615 0.00 0.00 36.00 3.41
1333 2080 8.888419 ACTAAATATCTGATCAACTGGATGGAT 58.112 33.333 0.00 0.00 36.00 3.41
1334 2081 9.381033 CTAAATATCTGATCAACTGGATGGATC 57.619 37.037 0.00 0.00 36.00 3.36
1335 2082 6.947376 ATATCTGATCAACTGGATGGATCA 57.053 37.500 0.00 0.00 43.63 2.92
1336 2083 5.844773 ATCTGATCAACTGGATGGATCAT 57.155 39.130 0.00 0.00 44.46 2.45
1337 2084 5.224821 TCTGATCAACTGGATGGATCATC 57.775 43.478 0.00 0.00 44.46 2.92
1338 2085 4.906060 TCTGATCAACTGGATGGATCATCT 59.094 41.667 0.00 0.00 44.46 2.90
1339 2086 5.368816 TCTGATCAACTGGATGGATCATCTT 59.631 40.000 0.00 0.00 44.46 2.40
1340 2087 5.374071 TGATCAACTGGATGGATCATCTTG 58.626 41.667 0.00 5.34 41.67 3.02
1341 2088 4.849813 TCAACTGGATGGATCATCTTGT 57.150 40.909 7.68 4.78 40.39 3.16
1342 2089 5.955961 TCAACTGGATGGATCATCTTGTA 57.044 39.130 7.68 0.00 40.39 2.41
1343 2090 5.674525 TCAACTGGATGGATCATCTTGTAC 58.325 41.667 7.68 0.00 40.39 2.90
1344 2091 5.426509 TCAACTGGATGGATCATCTTGTACT 59.573 40.000 7.68 0.00 40.39 2.73
1345 2092 6.611236 TCAACTGGATGGATCATCTTGTACTA 59.389 38.462 7.68 0.00 40.39 1.82
1346 2093 7.125659 TCAACTGGATGGATCATCTTGTACTAA 59.874 37.037 7.68 0.00 40.39 2.24
1347 2094 7.437713 ACTGGATGGATCATCTTGTACTAAA 57.562 36.000 7.68 0.00 40.39 1.85
1348 2095 8.038862 ACTGGATGGATCATCTTGTACTAAAT 57.961 34.615 7.68 0.00 40.39 1.40
1349 2096 7.935755 ACTGGATGGATCATCTTGTACTAAATG 59.064 37.037 7.68 0.00 40.39 2.32
1350 2097 7.805163 TGGATGGATCATCTTGTACTAAATGT 58.195 34.615 7.68 0.00 40.39 2.71
1351 2098 7.933577 TGGATGGATCATCTTGTACTAAATGTC 59.066 37.037 7.68 0.00 40.39 3.06
1368 2115 1.208052 TGTCTGGAGCAGCCTAATGAC 59.792 52.381 0.00 0.00 37.63 3.06
1382 2129 7.013274 GCAGCCTAATGACAATTAATGGTTCTA 59.987 37.037 0.00 0.00 0.00 2.10
1384 2131 9.071276 AGCCTAATGACAATTAATGGTTCTATG 57.929 33.333 0.00 0.00 0.00 2.23
1418 2166 0.831966 CTGCAGATGAAGCCTCTCCT 59.168 55.000 8.42 0.00 0.00 3.69
1419 2167 0.540454 TGCAGATGAAGCCTCTCCTG 59.460 55.000 0.00 0.00 0.00 3.86
1423 2171 1.830477 AGATGAAGCCTCTCCTGTCAC 59.170 52.381 0.00 0.00 0.00 3.67
1425 2173 1.216710 GAAGCCTCTCCTGTCACCG 59.783 63.158 0.00 0.00 0.00 4.94
1439 2187 1.135632 GTCACCGTCGAGAAAGGAGAG 60.136 57.143 0.00 0.00 0.00 3.20
1443 2191 0.882474 CGTCGAGAAAGGAGAGGTGT 59.118 55.000 0.00 0.00 0.00 4.16
1452 2200 1.901591 AGGAGAGGTGTTGCAACATG 58.098 50.000 33.16 0.00 41.59 3.21
1469 2217 5.789643 AACATGGTGTTGAAATTAGTGCT 57.210 34.783 0.00 0.00 39.45 4.40
1470 2218 5.789643 ACATGGTGTTGAAATTAGTGCTT 57.210 34.783 0.00 0.00 0.00 3.91
1472 2220 6.677913 ACATGGTGTTGAAATTAGTGCTTAC 58.322 36.000 0.00 0.00 0.00 2.34
1483 2231 6.952935 AATTAGTGCTTACGAACAAGAGAG 57.047 37.500 0.00 0.00 0.00 3.20
1490 2238 5.164954 GCTTACGAACAAGAGAGTCAAGAT 58.835 41.667 0.00 0.00 0.00 2.40
1513 2261 2.325583 TTTCCAGCGACAGAAACAGT 57.674 45.000 0.00 0.00 0.00 3.55
1526 2274 1.661112 GAAACAGTGGCGAGTGATAGC 59.339 52.381 10.85 0.00 0.00 2.97
1527 2275 0.608130 AACAGTGGCGAGTGATAGCA 59.392 50.000 10.85 0.00 34.54 3.49
1528 2276 0.108615 ACAGTGGCGAGTGATAGCAC 60.109 55.000 10.85 2.01 45.49 4.40
1532 2280 1.299468 GGCGAGTGATAGCACCTCG 60.299 63.158 20.91 20.91 46.32 4.63
1618 2366 1.095130 TACCCTCCAGACCTACCCAA 58.905 55.000 0.00 0.00 0.00 4.12
1619 2367 0.421904 ACCCTCCAGACCTACCCAAT 59.578 55.000 0.00 0.00 0.00 3.16
1626 2374 2.359900 CAGACCTACCCAATGACAAGC 58.640 52.381 0.00 0.00 0.00 4.01
1628 2376 2.084546 GACCTACCCAATGACAAGCAC 58.915 52.381 0.00 0.00 0.00 4.40
1630 2378 2.108250 ACCTACCCAATGACAAGCACTT 59.892 45.455 0.00 0.00 0.00 3.16
1631 2379 2.489329 CCTACCCAATGACAAGCACTTG 59.511 50.000 8.82 8.82 45.58 3.16
1637 2385 2.880268 CAATGACAAGCACTTGACTGGA 59.120 45.455 16.95 0.00 42.93 3.86
1638 2386 2.708216 TGACAAGCACTTGACTGGAA 57.292 45.000 16.95 0.00 42.93 3.53
1639 2387 2.997980 TGACAAGCACTTGACTGGAAA 58.002 42.857 16.95 0.00 42.93 3.13
1640 2388 3.554934 TGACAAGCACTTGACTGGAAAT 58.445 40.909 16.95 0.00 42.93 2.17
1641 2389 3.316029 TGACAAGCACTTGACTGGAAATG 59.684 43.478 16.95 0.00 42.93 2.32
1642 2390 2.624838 ACAAGCACTTGACTGGAAATGG 59.375 45.455 16.95 0.00 42.93 3.16
1643 2391 2.886523 CAAGCACTTGACTGGAAATGGA 59.113 45.455 4.31 0.00 42.93 3.41
1715 2463 7.123547 ACGAAGAAGATGAAGGTAATCTCTCTT 59.876 37.037 0.00 0.00 35.98 2.85
1718 2466 9.665719 AAGAAGATGAAGGTAATCTCTCTTTTC 57.334 33.333 0.00 0.00 33.07 2.29
1769 2520 8.912988 CAGTTCCTTGCCCATTATCTTTATAAA 58.087 33.333 0.00 0.00 31.44 1.40
1810 2564 8.263940 ACAACATGCGTAATTCTATACTTGTT 57.736 30.769 0.00 0.00 0.00 2.83
1831 2585 7.315247 TGTTATTTATGTATGTCCTGCACAC 57.685 36.000 0.00 0.00 38.04 3.82
1974 2728 4.340894 AAGCACACATGTTATACGCTTG 57.659 40.909 13.26 0.00 36.89 4.01
1982 2737 5.050363 CACATGTTATACGCTTGTATCACCC 60.050 44.000 0.00 0.00 39.49 4.61
1988 2743 0.527817 CGCTTGTATCACCCGTCTCC 60.528 60.000 0.00 0.00 0.00 3.71
2015 2770 7.867403 TCCAAAATGCTTAGTTCAACAATCTTC 59.133 33.333 0.00 0.00 0.00 2.87
2022 2777 4.170292 AGTTCAACAATCTTCTGCATGC 57.830 40.909 11.82 11.82 0.00 4.06
2160 2915 1.127567 CATGGCGAGGGATAGGGGAA 61.128 60.000 0.00 0.00 0.00 3.97
2277 3032 5.887754 TGGAAGCTAGGTTGAAGGTAATTT 58.112 37.500 12.82 0.00 0.00 1.82
2299 3056 5.534207 TGTCTTGTTTCAGCATTTTCCAT 57.466 34.783 0.00 0.00 0.00 3.41
2345 3106 7.015226 TGTGTACATGTTGAAGAGTTTTCAG 57.985 36.000 2.30 0.00 0.00 3.02
2354 3115 6.208599 TGTTGAAGAGTTTTCAGAACCAAACT 59.791 34.615 0.00 0.00 44.26 2.66
2395 3156 3.009363 TGTGAATGAATCTGCAGAGGGAA 59.991 43.478 22.96 8.04 0.00 3.97
2510 3271 6.042208 GGCTGAATACAAGAAGGTAGGTAGAT 59.958 42.308 0.00 0.00 0.00 1.98
2554 3321 6.231211 TCTAGTCCATTGGTCTTCAGAAAAC 58.769 40.000 7.77 0.00 0.00 2.43
2575 3342 6.573617 AACGCTTTGATCTTGAAAAGTTTG 57.426 33.333 0.00 0.00 46.34 2.93
2581 3348 9.899226 GCTTTGATCTTGAAAAGTTTGTAGTAT 57.101 29.630 0.00 0.00 46.34 2.12
2591 3358 9.793259 TGAAAAGTTTGTAGTATTGATTCCTCT 57.207 29.630 0.00 0.00 0.00 3.69
2596 3363 7.819900 AGTTTGTAGTATTGATTCCTCTCACAC 59.180 37.037 0.00 0.00 0.00 3.82
2604 3371 5.233083 TGATTCCTCTCACACAATGAACT 57.767 39.130 0.00 0.00 36.69 3.01
2802 3578 2.341101 GGCAGCAGCAGCAACATCT 61.341 57.895 12.41 0.00 45.49 2.90
2908 3684 2.093021 GCATCTGCTTCTTCTTCCTCCT 60.093 50.000 0.00 0.00 38.21 3.69
2919 3695 1.077169 TCTTCCTCCTGCAGTACCTGA 59.923 52.381 13.81 0.89 32.44 3.86
2924 3700 2.419297 CCTCCTGCAGTACCTGATTCAC 60.419 54.545 13.81 0.00 32.44 3.18
2933 3709 5.911752 CAGTACCTGATTCACTGCTAGATT 58.088 41.667 0.00 0.00 33.86 2.40
2937 3713 6.059787 ACCTGATTCACTGCTAGATTCTTT 57.940 37.500 0.00 0.00 0.00 2.52
2940 3716 6.183360 CCTGATTCACTGCTAGATTCTTTTGG 60.183 42.308 0.00 0.00 0.00 3.28
2949 3725 4.202090 GCTAGATTCTTTTGGCTTCATGGG 60.202 45.833 0.00 0.00 0.00 4.00
3022 3802 0.241213 TGAGAGTGACTTCGGCTTCG 59.759 55.000 0.00 0.00 0.00 3.79
3024 3804 1.133407 GAGAGTGACTTCGGCTTCGAT 59.867 52.381 0.00 0.00 42.93 3.59
3046 3829 1.951602 GAGGTTTGCGGTGGTTAAGTT 59.048 47.619 0.00 0.00 0.00 2.66
3047 3830 3.140623 GAGGTTTGCGGTGGTTAAGTTA 58.859 45.455 0.00 0.00 0.00 2.24
3080 3863 5.049680 GATAATAAGTTATGCACACGGGGTG 60.050 44.000 5.89 5.89 39.30 4.61
3081 3864 7.404565 GATAATAAGTTATGCACACGGGGTGT 61.405 42.308 12.67 0.00 38.91 4.16
3128 3912 4.994907 ACAAGGGTTTTTGTGTCCTAAC 57.005 40.909 0.00 0.00 39.68 2.34
3147 3931 6.535150 TCCTAACTATTTCATCTCACTTTGCG 59.465 38.462 0.00 0.00 0.00 4.85
3200 3984 4.931601 TGCTGTCTCTGTACAAATGATGTC 59.068 41.667 0.00 0.00 42.70 3.06
3263 4047 0.524862 CACTCATGCAAACAGAGGGC 59.475 55.000 11.75 0.00 33.76 5.19
3363 4147 7.936496 TTATGTTGCATTGATCTTAAGTGGA 57.064 32.000 1.63 0.00 0.00 4.02
3364 4148 5.885230 TGTTGCATTGATCTTAAGTGGAG 57.115 39.130 1.63 0.00 0.00 3.86
3365 4149 5.316167 TGTTGCATTGATCTTAAGTGGAGT 58.684 37.500 1.63 0.00 0.00 3.85
3366 4150 5.769662 TGTTGCATTGATCTTAAGTGGAGTT 59.230 36.000 1.63 0.00 0.00 3.01
3367 4151 6.265196 TGTTGCATTGATCTTAAGTGGAGTTT 59.735 34.615 1.63 0.00 0.00 2.66
3368 4152 6.258230 TGCATTGATCTTAAGTGGAGTTTG 57.742 37.500 1.63 0.00 0.00 2.93
3369 4153 5.183713 TGCATTGATCTTAAGTGGAGTTTGG 59.816 40.000 1.63 0.00 0.00 3.28
3370 4154 5.183904 GCATTGATCTTAAGTGGAGTTTGGT 59.816 40.000 1.63 0.00 0.00 3.67
3371 4155 6.374333 GCATTGATCTTAAGTGGAGTTTGGTA 59.626 38.462 1.63 0.00 0.00 3.25
3372 4156 7.414540 GCATTGATCTTAAGTGGAGTTTGGTAG 60.415 40.741 1.63 0.00 0.00 3.18
3373 4157 6.681729 TGATCTTAAGTGGAGTTTGGTAGT 57.318 37.500 1.63 0.00 0.00 2.73
3374 4158 7.074653 TGATCTTAAGTGGAGTTTGGTAGTT 57.925 36.000 1.63 0.00 0.00 2.24
3375 4159 7.159372 TGATCTTAAGTGGAGTTTGGTAGTTC 58.841 38.462 1.63 0.00 0.00 3.01
3376 4160 6.742559 TCTTAAGTGGAGTTTGGTAGTTCT 57.257 37.500 1.63 0.00 0.00 3.01
3377 4161 6.522054 TCTTAAGTGGAGTTTGGTAGTTCTG 58.478 40.000 1.63 0.00 0.00 3.02
3378 4162 3.127425 AGTGGAGTTTGGTAGTTCTGC 57.873 47.619 0.00 0.00 0.00 4.26
3379 4163 2.438021 AGTGGAGTTTGGTAGTTCTGCA 59.562 45.455 0.00 0.00 0.00 4.41
3380 4164 3.118038 AGTGGAGTTTGGTAGTTCTGCAA 60.118 43.478 0.00 0.00 30.92 4.08
3381 4165 3.821033 GTGGAGTTTGGTAGTTCTGCAAT 59.179 43.478 0.00 0.00 30.92 3.56
3388 4172 9.129209 GAGTTTGGTAGTTCTGCAATTTTTATC 57.871 33.333 0.00 0.00 0.00 1.75
3402 4186 9.311916 TGCAATTTTTATCTGGTTGTATAATGC 57.688 29.630 0.00 0.00 0.00 3.56
3403 4187 9.311916 GCAATTTTTATCTGGTTGTATAATGCA 57.688 29.630 0.00 0.00 0.00 3.96
3406 4190 5.666969 TTATCTGGTTGTATAATGCACGC 57.333 39.130 0.00 0.00 0.00 5.34
3407 4191 2.979240 TCTGGTTGTATAATGCACGCA 58.021 42.857 0.00 0.00 0.00 5.24
3413 4197 7.442666 TCTGGTTGTATAATGCACGCAATATTA 59.557 33.333 5.00 0.00 0.00 0.98
3428 4213 8.073167 CACGCAATATTATGTTTTATGTGGCTA 58.927 33.333 0.00 0.00 0.00 3.93
3435 4220 7.624360 TTATGTTTTATGTGGCTACTTCTGG 57.376 36.000 0.64 0.00 0.00 3.86
3436 4221 4.980573 TGTTTTATGTGGCTACTTCTGGT 58.019 39.130 0.64 0.00 0.00 4.00
3440 4225 2.543777 TGTGGCTACTTCTGGTGAAC 57.456 50.000 0.64 0.00 0.00 3.18
3458 4243 7.950512 TGGTGAACAGATTGAATACAAAATGT 58.049 30.769 0.00 0.00 39.04 2.71
3459 4244 8.420222 TGGTGAACAGATTGAATACAAAATGTT 58.580 29.630 12.42 12.42 44.02 2.71
3460 4245 8.702438 GGTGAACAGATTGAATACAAAATGTTG 58.298 33.333 15.41 0.00 42.78 3.33
3465 4250 8.308931 ACAGATTGAATACAAAATGTTGCAGAT 58.691 29.630 0.00 0.00 39.54 2.90
3469 4254 8.523523 TTGAATACAAAATGTTGCAGATGAAG 57.476 30.769 0.00 0.00 38.39 3.02
3485 4270 6.091713 GCAGATGAAGCATTTTTACTTGCAAT 59.908 34.615 0.00 0.00 41.35 3.56
3486 4271 7.672738 CAGATGAAGCATTTTTACTTGCAATC 58.327 34.615 0.00 0.00 41.35 2.67
3487 4272 7.544566 CAGATGAAGCATTTTTACTTGCAATCT 59.455 33.333 0.00 0.00 41.35 2.40
3488 4273 8.742777 AGATGAAGCATTTTTACTTGCAATCTA 58.257 29.630 0.00 0.00 41.35 1.98
3489 4274 9.525409 GATGAAGCATTTTTACTTGCAATCTAT 57.475 29.630 0.00 0.00 41.35 1.98
3490 4275 8.692110 TGAAGCATTTTTACTTGCAATCTATG 57.308 30.769 0.00 0.11 41.35 2.23
3491 4276 8.522003 TGAAGCATTTTTACTTGCAATCTATGA 58.478 29.630 0.00 0.00 41.35 2.15
3492 4277 8.693542 AAGCATTTTTACTTGCAATCTATGAC 57.306 30.769 0.00 0.00 41.35 3.06
3493 4278 8.059798 AGCATTTTTACTTGCAATCTATGACT 57.940 30.769 0.00 0.00 41.35 3.41
3494 4279 9.177608 AGCATTTTTACTTGCAATCTATGACTA 57.822 29.630 0.00 0.00 41.35 2.59
3495 4280 9.956720 GCATTTTTACTTGCAATCTATGACTAT 57.043 29.630 0.00 0.00 38.72 2.12
3558 4356 5.297527 CAGAGCATGTTGGAATAGCATGTTA 59.702 40.000 0.00 0.00 46.23 2.41
3607 4405 3.069443 TCCAAGGCAAACAAAATCCAGAC 59.931 43.478 0.00 0.00 0.00 3.51
3612 4410 4.832266 AGGCAAACAAAATCCAGACACATA 59.168 37.500 0.00 0.00 0.00 2.29
3615 4413 5.858581 GCAAACAAAATCCAGACACATAGAC 59.141 40.000 0.00 0.00 0.00 2.59
3617 4415 7.424803 CAAACAAAATCCAGACACATAGACAA 58.575 34.615 0.00 0.00 0.00 3.18
3618 4416 6.808008 ACAAAATCCAGACACATAGACAAG 57.192 37.500 0.00 0.00 0.00 3.16
3620 4418 6.428159 ACAAAATCCAGACACATAGACAAGAC 59.572 38.462 0.00 0.00 0.00 3.01
3621 4419 4.744795 ATCCAGACACATAGACAAGACC 57.255 45.455 0.00 0.00 0.00 3.85
3622 4420 3.779444 TCCAGACACATAGACAAGACCT 58.221 45.455 0.00 0.00 0.00 3.85
3623 4421 3.511540 TCCAGACACATAGACAAGACCTG 59.488 47.826 0.00 0.00 0.00 4.00
3624 4422 3.368843 CCAGACACATAGACAAGACCTGG 60.369 52.174 0.00 0.00 33.65 4.45
3625 4423 2.834549 AGACACATAGACAAGACCTGGG 59.165 50.000 0.00 0.00 0.00 4.45
3626 4424 2.832129 GACACATAGACAAGACCTGGGA 59.168 50.000 0.00 0.00 0.00 4.37
3627 4425 3.248024 ACACATAGACAAGACCTGGGAA 58.752 45.455 0.00 0.00 0.00 3.97
3628 4426 3.846588 ACACATAGACAAGACCTGGGAAT 59.153 43.478 0.00 0.00 0.00 3.01
3629 4427 5.030147 ACACATAGACAAGACCTGGGAATA 58.970 41.667 0.00 0.00 0.00 1.75
3630 4428 5.129485 ACACATAGACAAGACCTGGGAATAG 59.871 44.000 0.00 0.00 0.00 1.73
3631 4429 4.101741 ACATAGACAAGACCTGGGAATAGC 59.898 45.833 0.00 0.00 0.00 2.97
3632 4430 1.840635 AGACAAGACCTGGGAATAGCC 59.159 52.381 0.00 0.00 0.00 3.93
3633 4431 1.840635 GACAAGACCTGGGAATAGCCT 59.159 52.381 0.00 0.00 36.66 4.58
3634 4432 1.840635 ACAAGACCTGGGAATAGCCTC 59.159 52.381 0.00 0.00 36.66 4.70
3635 4433 2.122768 CAAGACCTGGGAATAGCCTCT 58.877 52.381 0.00 0.00 36.66 3.69
3636 4434 2.507471 CAAGACCTGGGAATAGCCTCTT 59.493 50.000 0.00 0.00 36.66 2.85
3637 4435 3.708236 AGACCTGGGAATAGCCTCTTA 57.292 47.619 0.00 0.00 36.66 2.10
3638 4436 3.310193 AGACCTGGGAATAGCCTCTTAC 58.690 50.000 0.00 0.00 36.66 2.34
3639 4437 3.039011 GACCTGGGAATAGCCTCTTACA 58.961 50.000 0.00 0.00 36.66 2.41
3640 4438 3.648545 GACCTGGGAATAGCCTCTTACAT 59.351 47.826 0.00 0.00 36.66 2.29
3641 4439 4.827789 ACCTGGGAATAGCCTCTTACATA 58.172 43.478 0.00 0.00 36.66 2.29
3642 4440 4.841246 ACCTGGGAATAGCCTCTTACATAG 59.159 45.833 0.00 0.00 36.66 2.23
3643 4441 4.841246 CCTGGGAATAGCCTCTTACATAGT 59.159 45.833 0.00 0.00 36.66 2.12
3644 4442 5.279708 CCTGGGAATAGCCTCTTACATAGTG 60.280 48.000 0.00 0.00 36.66 2.74
3645 4443 5.464069 TGGGAATAGCCTCTTACATAGTGA 58.536 41.667 0.00 0.00 36.66 3.41
3646 4444 6.084738 TGGGAATAGCCTCTTACATAGTGAT 58.915 40.000 0.00 0.00 36.66 3.06
3647 4445 7.246027 TGGGAATAGCCTCTTACATAGTGATA 58.754 38.462 0.00 0.00 36.66 2.15
3648 4446 7.397476 TGGGAATAGCCTCTTACATAGTGATAG 59.603 40.741 0.00 0.00 36.66 2.08
3662 4460 7.155328 ACATAGTGATAGTTATTGCTGCTACC 58.845 38.462 0.00 0.00 0.00 3.18
3666 4464 4.653801 TGATAGTTATTGCTGCTACCTGGA 59.346 41.667 0.00 0.00 0.00 3.86
3688 4486 6.122277 GGAGTATTTGGGACTGAATGATTCA 58.878 40.000 7.73 7.73 38.17 2.57
3690 4488 7.286316 GGAGTATTTGGGACTGAATGATTCAAT 59.714 37.037 9.39 0.00 39.58 2.57
3712 4510 8.599774 TCAATTTTCAAAGGAATTTCGTCAAAC 58.400 29.630 0.00 0.00 31.93 2.93
3721 4519 5.238650 AGGAATTTCGTCAAACCTGTACAAG 59.761 40.000 0.00 0.00 0.00 3.16
3731 4529 7.255001 CGTCAAACCTGTACAAGTAATTCCTTT 60.255 37.037 0.00 0.00 0.00 3.11
3767 4566 6.199937 ACATGAATCCTATGAAAACTGCAC 57.800 37.500 0.00 0.00 0.00 4.57
3771 4570 5.645067 TGAATCCTATGAAAACTGCACAGAG 59.355 40.000 4.31 0.00 0.00 3.35
3773 4572 5.426689 TCCTATGAAAACTGCACAGAGAT 57.573 39.130 4.31 0.00 0.00 2.75
3774 4573 6.544928 TCCTATGAAAACTGCACAGAGATA 57.455 37.500 4.31 0.00 0.00 1.98
3789 4588 3.750130 CAGAGATACACAAGCAAGCAGTT 59.250 43.478 0.00 0.00 0.00 3.16
3790 4589 3.750130 AGAGATACACAAGCAAGCAGTTG 59.250 43.478 0.00 0.00 36.67 3.16
3829 4628 5.483811 TCGAAATTCAGCACTTGTGGTATA 58.516 37.500 5.11 0.00 0.00 1.47
3844 4643 7.987458 ACTTGTGGTATAATAACTCCAGACATG 59.013 37.037 0.00 0.00 0.00 3.21
3849 4648 7.155328 GGTATAATAACTCCAGACATGACAGG 58.845 42.308 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 752 1.468520 CACATTCCAAACTAGCACGGG 59.531 52.381 0.00 0.00 0.00 5.28
73 756 1.885887 GCACCACATTCCAAACTAGCA 59.114 47.619 0.00 0.00 0.00 3.49
101 785 4.859629 GGTAGTTTTGACCGTGATCATC 57.140 45.455 0.00 0.00 0.00 2.92
198 882 2.042259 CGCAAGGCCAATCTGCTCA 61.042 57.895 5.01 0.00 0.00 4.26
339 1040 5.571784 TGACCCGTTAGTGACATAGTTAG 57.428 43.478 0.00 0.00 0.00 2.34
433 1141 3.119173 TGCTAGCATTTACAATTGGGCAC 60.119 43.478 14.93 0.00 0.00 5.01
549 1258 5.305812 CGTACGTGCTGATTTGAACTAAAG 58.694 41.667 7.22 0.00 0.00 1.85
558 1267 1.078708 CCCCCGTACGTGCTGATTT 60.079 57.895 15.21 0.00 0.00 2.17
572 1281 0.966179 AACGCAAAGAATTGACCCCC 59.034 50.000 0.00 0.00 38.94 5.40
601 1310 1.942776 AGCAAAAGGGGAATCAAGGG 58.057 50.000 0.00 0.00 0.00 3.95
648 1357 5.005394 CCGTCGGTATTATCAAACTGAGTTG 59.995 44.000 2.08 0.00 31.78 3.16
674 1383 7.410174 TCCTCCAATCATTTATGTACTGGTTT 58.590 34.615 0.00 0.00 0.00 3.27
677 1386 7.389884 CAGATCCTCCAATCATTTATGTACTGG 59.610 40.741 0.00 0.00 0.00 4.00
678 1387 7.389884 CCAGATCCTCCAATCATTTATGTACTG 59.610 40.741 0.00 0.00 0.00 2.74
684 1395 9.120658 TCTAATCCAGATCCTCCAATCATTTAT 57.879 33.333 0.00 0.00 0.00 1.40
688 1399 7.239143 TCATTCTAATCCAGATCCTCCAATCAT 59.761 37.037 0.00 0.00 31.77 2.45
784 1495 2.564062 AGGAAAATGACATGCAGGGTTG 59.436 45.455 2.31 0.00 0.00 3.77
813 1524 4.400567 ACGTGGACACTATAGTTCCTTACC 59.599 45.833 23.24 13.48 0.00 2.85
862 1573 1.843753 GAAACCGACAACGCAACAAAG 59.156 47.619 0.00 0.00 38.29 2.77
863 1574 1.199327 TGAAACCGACAACGCAACAAA 59.801 42.857 0.00 0.00 38.29 2.83
973 1718 9.956720 AAATAGTATTGCTGCACAAGATAAATC 57.043 29.630 0.00 0.00 42.87 2.17
991 1738 8.562949 ACAACCTCAGTACCCATAAATAGTAT 57.437 34.615 0.00 0.00 0.00 2.12
995 1742 7.070322 GGAGTACAACCTCAGTACCCATAAATA 59.930 40.741 0.00 0.00 42.09 1.40
996 1743 6.126854 GGAGTACAACCTCAGTACCCATAAAT 60.127 42.308 0.00 0.00 42.09 1.40
997 1744 5.188359 GGAGTACAACCTCAGTACCCATAAA 59.812 44.000 0.00 0.00 42.09 1.40
998 1745 4.713321 GGAGTACAACCTCAGTACCCATAA 59.287 45.833 0.00 0.00 42.09 1.90
1007 1754 4.020218 TGGAAGATTGGAGTACAACCTCAG 60.020 45.833 9.82 0.00 42.94 3.35
1051 1798 1.107538 TCGCTGGACGGAGGGATAAG 61.108 60.000 0.00 0.00 43.89 1.73
1054 1801 3.148279 GTCGCTGGACGGAGGGAT 61.148 66.667 0.00 0.00 43.89 3.85
1062 1809 1.398390 GATTCCATGTTGTCGCTGGAC 59.602 52.381 0.00 0.00 38.75 4.02
1065 1812 3.883779 CGATTCCATGTTGTCGCTG 57.116 52.632 0.00 0.00 0.00 5.18
1081 1828 0.757561 TCACCCTTATCATCCGGCGA 60.758 55.000 9.30 0.00 0.00 5.54
1102 1849 3.057526 GTGCCCGAAAGTTCTGCTAAATT 60.058 43.478 0.00 0.00 0.00 1.82
1108 1855 1.166531 ACAGTGCCCGAAAGTTCTGC 61.167 55.000 0.00 0.00 0.00 4.26
1110 1857 0.468226 TGACAGTGCCCGAAAGTTCT 59.532 50.000 0.00 0.00 0.00 3.01
1139 1886 3.499338 TCAGATTGTGCACCCAAAGAAT 58.501 40.909 15.69 5.93 0.00 2.40
1155 1902 0.387202 CCGAGACGCCATTCTCAGAT 59.613 55.000 2.20 0.00 42.03 2.90
1161 1908 0.462047 ATGGTTCCGAGACGCCATTC 60.462 55.000 0.00 0.00 38.45 2.67
1168 1915 1.757699 AGCCTCTAATGGTTCCGAGAC 59.242 52.381 0.00 0.00 0.00 3.36
1173 1920 1.210478 TCAGCAGCCTCTAATGGTTCC 59.790 52.381 0.00 0.00 0.00 3.62
1185 1932 2.615912 GTCTCCATTTACATCAGCAGCC 59.384 50.000 0.00 0.00 0.00 4.85
1206 1953 2.286872 GAGGAACCATCATGCTCAGTG 58.713 52.381 0.00 0.00 35.55 3.66
1240 1987 1.416401 ACCGTCATTGGTCTGTTCAGT 59.584 47.619 0.00 0.00 37.91 3.41
1250 1997 2.552315 ACAACAAGCTTACCGTCATTGG 59.448 45.455 0.00 0.00 0.00 3.16
1251 1998 3.896648 ACAACAAGCTTACCGTCATTG 57.103 42.857 0.00 0.00 0.00 2.82
1252 1999 4.638304 ACTACAACAAGCTTACCGTCATT 58.362 39.130 0.00 0.00 0.00 2.57
1257 2004 6.894828 ACAATTAACTACAACAAGCTTACCG 58.105 36.000 0.00 0.00 0.00 4.02
1304 2051 9.987272 CATCCAGTTGATCAGATATTTAGTACA 57.013 33.333 0.00 0.00 0.00 2.90
1305 2052 9.429359 CCATCCAGTTGATCAGATATTTAGTAC 57.571 37.037 0.00 0.00 0.00 2.73
1306 2053 9.379770 TCCATCCAGTTGATCAGATATTTAGTA 57.620 33.333 0.00 0.00 0.00 1.82
1307 2054 8.267620 TCCATCCAGTTGATCAGATATTTAGT 57.732 34.615 0.00 0.00 0.00 2.24
1308 2055 9.381033 GATCCATCCAGTTGATCAGATATTTAG 57.619 37.037 0.00 0.00 35.93 1.85
1312 2059 6.947376 TGATCCATCCAGTTGATCAGATAT 57.053 37.500 0.00 0.00 39.81 1.63
1314 2061 5.548446 AGATGATCCATCCAGTTGATCAGAT 59.452 40.000 7.40 0.00 45.67 2.90
1316 2063 5.230323 AGATGATCCATCCAGTTGATCAG 57.770 43.478 7.40 0.00 45.67 2.90
1329 2076 7.125659 TCCAGACATTTAGTACAAGATGATCCA 59.874 37.037 0.00 0.00 0.00 3.41
1330 2077 7.500992 TCCAGACATTTAGTACAAGATGATCC 58.499 38.462 0.00 0.00 0.00 3.36
1331 2078 7.170658 GCTCCAGACATTTAGTACAAGATGATC 59.829 40.741 0.00 0.00 0.00 2.92
1332 2079 6.989169 GCTCCAGACATTTAGTACAAGATGAT 59.011 38.462 0.00 0.00 0.00 2.45
1333 2080 6.070824 TGCTCCAGACATTTAGTACAAGATGA 60.071 38.462 0.00 0.00 0.00 2.92
1334 2081 6.108687 TGCTCCAGACATTTAGTACAAGATG 58.891 40.000 0.00 0.00 0.00 2.90
1335 2082 6.299805 TGCTCCAGACATTTAGTACAAGAT 57.700 37.500 0.00 0.00 0.00 2.40
1336 2083 5.724328 CTGCTCCAGACATTTAGTACAAGA 58.276 41.667 0.00 0.00 32.44 3.02
1337 2084 4.331168 GCTGCTCCAGACATTTAGTACAAG 59.669 45.833 0.00 0.00 32.44 3.16
1338 2085 4.253685 GCTGCTCCAGACATTTAGTACAA 58.746 43.478 0.00 0.00 32.44 2.41
1339 2086 3.369471 GGCTGCTCCAGACATTTAGTACA 60.369 47.826 0.00 0.00 39.71 2.90
1340 2087 3.118592 AGGCTGCTCCAGACATTTAGTAC 60.119 47.826 0.00 0.00 42.99 2.73
1341 2088 3.107601 AGGCTGCTCCAGACATTTAGTA 58.892 45.455 0.00 0.00 42.99 1.82
1342 2089 1.912043 AGGCTGCTCCAGACATTTAGT 59.088 47.619 0.00 0.00 42.99 2.24
1343 2090 2.706339 AGGCTGCTCCAGACATTTAG 57.294 50.000 0.00 0.00 42.99 1.85
1344 2091 4.164030 TCATTAGGCTGCTCCAGACATTTA 59.836 41.667 0.00 0.00 42.99 1.40
1345 2092 3.054139 TCATTAGGCTGCTCCAGACATTT 60.054 43.478 0.00 0.00 42.99 2.32
1346 2093 2.507058 TCATTAGGCTGCTCCAGACATT 59.493 45.455 0.00 0.00 42.99 2.71
1347 2094 2.121948 TCATTAGGCTGCTCCAGACAT 58.878 47.619 0.00 0.00 42.99 3.06
1348 2095 1.208052 GTCATTAGGCTGCTCCAGACA 59.792 52.381 0.00 0.00 42.99 3.41
1349 2096 1.208052 TGTCATTAGGCTGCTCCAGAC 59.792 52.381 0.00 3.03 40.37 3.51
1350 2097 1.571955 TGTCATTAGGCTGCTCCAGA 58.428 50.000 0.00 0.00 37.29 3.86
1351 2098 2.408271 TTGTCATTAGGCTGCTCCAG 57.592 50.000 0.00 0.00 37.29 3.86
1368 2115 8.437360 TCTGCAGTACATAGAACCATTAATTG 57.563 34.615 14.67 0.00 0.00 2.32
1399 2147 0.831966 AGGAGAGGCTTCATCTGCAG 59.168 55.000 7.63 7.63 37.58 4.41
1418 2166 0.596577 CTCCTTTCTCGACGGTGACA 59.403 55.000 0.00 0.00 0.00 3.58
1419 2167 0.879765 TCTCCTTTCTCGACGGTGAC 59.120 55.000 0.00 0.00 0.00 3.67
1423 2171 0.171455 CACCTCTCCTTTCTCGACGG 59.829 60.000 0.00 0.00 0.00 4.79
1425 2173 2.678324 CAACACCTCTCCTTTCTCGAC 58.322 52.381 0.00 0.00 0.00 4.20
1452 2200 5.600908 TCGTAAGCACTAATTTCAACACC 57.399 39.130 0.00 0.00 37.18 4.16
1469 2217 6.072838 ACGTATCTTGACTCTCTTGTTCGTAA 60.073 38.462 0.00 0.00 0.00 3.18
1470 2218 5.410746 ACGTATCTTGACTCTCTTGTTCGTA 59.589 40.000 0.00 0.00 0.00 3.43
1472 2220 4.724303 ACGTATCTTGACTCTCTTGTTCG 58.276 43.478 0.00 0.00 0.00 3.95
1483 2231 2.344741 GTCGCTGGAAACGTATCTTGAC 59.655 50.000 0.00 0.00 0.00 3.18
1490 2238 2.129607 GTTTCTGTCGCTGGAAACGTA 58.870 47.619 0.00 0.00 40.80 3.57
1513 2261 1.816537 GAGGTGCTATCACTCGCCA 59.183 57.895 0.00 0.00 42.72 5.69
1517 2265 1.103803 TGACCGAGGTGCTATCACTC 58.896 55.000 0.00 0.00 42.72 3.51
1526 2274 2.031870 TCCATAGATGTGACCGAGGTG 58.968 52.381 0.00 0.00 0.00 4.00
1527 2275 2.454336 TCCATAGATGTGACCGAGGT 57.546 50.000 0.00 0.00 0.00 3.85
1528 2276 2.959030 TCTTCCATAGATGTGACCGAGG 59.041 50.000 0.00 0.00 0.00 4.63
1607 2355 1.985159 TGCTTGTCATTGGGTAGGTCT 59.015 47.619 0.00 0.00 0.00 3.85
1610 2358 2.489329 CAAGTGCTTGTCATTGGGTAGG 59.511 50.000 3.91 0.00 35.92 3.18
1618 2366 2.936919 TCCAGTCAAGTGCTTGTCAT 57.063 45.000 11.17 0.00 41.16 3.06
1619 2367 2.708216 TTCCAGTCAAGTGCTTGTCA 57.292 45.000 11.17 0.00 41.16 3.58
1626 2374 4.523943 TCCATTTCCATTTCCAGTCAAGTG 59.476 41.667 0.00 0.00 0.00 3.16
1628 2376 5.726980 TTCCATTTCCATTTCCAGTCAAG 57.273 39.130 0.00 0.00 0.00 3.02
1630 2378 5.543405 ACATTTCCATTTCCATTTCCAGTCA 59.457 36.000 0.00 0.00 0.00 3.41
1631 2379 6.041423 ACATTTCCATTTCCATTTCCAGTC 57.959 37.500 0.00 0.00 0.00 3.51
1637 2385 8.827832 TCTCATAGACATTTCCATTTCCATTT 57.172 30.769 0.00 0.00 0.00 2.32
1638 2386 8.689972 GTTCTCATAGACATTTCCATTTCCATT 58.310 33.333 0.00 0.00 0.00 3.16
1639 2387 7.012704 CGTTCTCATAGACATTTCCATTTCCAT 59.987 37.037 0.00 0.00 0.00 3.41
1640 2388 6.316140 CGTTCTCATAGACATTTCCATTTCCA 59.684 38.462 0.00 0.00 0.00 3.53
1641 2389 6.719365 CGTTCTCATAGACATTTCCATTTCC 58.281 40.000 0.00 0.00 0.00 3.13
1642 2390 6.183360 TGCGTTCTCATAGACATTTCCATTTC 60.183 38.462 0.00 0.00 0.00 2.17
1643 2391 5.647658 TGCGTTCTCATAGACATTTCCATTT 59.352 36.000 0.00 0.00 0.00 2.32
1715 2463 5.105392 ACTCATGCAAAACAACAGGAAGAAA 60.105 36.000 0.00 0.00 0.00 2.52
1718 2466 4.037208 AGACTCATGCAAAACAACAGGAAG 59.963 41.667 0.00 0.00 0.00 3.46
1824 2578 5.616424 GCTTCTCTGTAAGAAATGTGTGCAG 60.616 44.000 0.00 0.00 46.34 4.41
1827 2581 4.667668 GCGCTTCTCTGTAAGAAATGTGTG 60.668 45.833 0.00 0.00 46.34 3.82
1831 2585 2.668457 ACGCGCTTCTCTGTAAGAAATG 59.332 45.455 5.73 0.00 46.34 2.32
1974 2728 1.481871 TTGGAGGAGACGGGTGATAC 58.518 55.000 0.00 0.00 0.00 2.24
1982 2737 3.600388 ACTAAGCATTTTGGAGGAGACG 58.400 45.455 0.00 0.00 0.00 4.18
1988 2743 7.373493 AGATTGTTGAACTAAGCATTTTGGAG 58.627 34.615 0.00 0.00 0.00 3.86
2015 2770 1.394572 TCGACGATTTTCTGCATGCAG 59.605 47.619 36.80 36.80 44.86 4.41
2022 2777 5.120830 AGTCTTTCCATTCGACGATTTTCTG 59.879 40.000 0.00 0.00 33.10 3.02
2025 2780 6.164176 AGTAGTCTTTCCATTCGACGATTTT 58.836 36.000 0.00 0.00 33.10 1.82
2184 2939 6.494893 TGAATAGTACTGCAACAAACCATC 57.505 37.500 5.39 0.00 0.00 3.51
2277 3032 4.998671 TGGAAAATGCTGAAACAAGACA 57.001 36.364 0.00 0.00 0.00 3.41
2299 3056 5.221441 ACAAAATAGGATCCGTCGATCATCA 60.221 40.000 5.98 0.00 45.89 3.07
2317 3074 9.301153 GAAAACTCTTCAACATGTACACAAAAT 57.699 29.630 0.00 0.00 0.00 1.82
2345 3106 9.383519 TGTAATAGATCAATGAGAGTTTGGTTC 57.616 33.333 0.00 0.00 0.00 3.62
2395 3156 1.001503 CCTGAGAGCCTCCTCCTGT 59.998 63.158 0.00 0.00 38.96 4.00
2530 3291 6.231211 GTTTTCTGAAGACCAATGGACTAGA 58.769 40.000 6.16 3.03 0.00 2.43
2535 3296 2.552315 GCGTTTTCTGAAGACCAATGGA 59.448 45.455 6.16 0.00 0.00 3.41
2554 3321 6.912591 ACTACAAACTTTTCAAGATCAAAGCG 59.087 34.615 0.00 0.00 33.92 4.68
2575 3342 7.981789 TCATTGTGTGAGAGGAATCAATACTAC 59.018 37.037 0.00 0.00 31.80 2.73
2581 3348 5.624159 AGTTCATTGTGTGAGAGGAATCAA 58.376 37.500 0.00 0.00 38.29 2.57
2591 3358 4.734402 GCAAGCAAGAAGTTCATTGTGTGA 60.734 41.667 5.50 0.00 34.25 3.58
2596 3363 3.314553 CAGGCAAGCAAGAAGTTCATTG 58.685 45.455 5.50 7.95 0.00 2.82
2604 3371 0.386476 CAACTGCAGGCAAGCAAGAA 59.614 50.000 19.93 0.00 45.13 2.52
2644 3411 3.689002 CTTCCTCCCCAGCTTCGGC 62.689 68.421 0.00 0.00 42.17 5.54
2802 3578 0.885879 CTTGGATGAGCTTGCTGCAA 59.114 50.000 15.16 15.16 45.94 4.08
2919 3695 5.259632 AGCCAAAAGAATCTAGCAGTGAAT 58.740 37.500 0.00 0.00 0.00 2.57
2924 3700 5.450137 CCATGAAGCCAAAAGAATCTAGCAG 60.450 44.000 0.00 0.00 0.00 4.24
2933 3709 2.673775 TGACCCATGAAGCCAAAAGA 57.326 45.000 0.00 0.00 0.00 2.52
2937 3713 0.409092 ACCATGACCCATGAAGCCAA 59.591 50.000 8.38 0.00 43.81 4.52
2940 3716 1.838112 TTCACCATGACCCATGAAGC 58.162 50.000 8.38 0.00 43.81 3.86
2949 3725 3.937706 CTGGACTCAGATTTCACCATGAC 59.062 47.826 0.00 0.00 43.49 3.06
2995 3774 5.361285 AGCCGAAGTCACTCTCATAACTTAT 59.639 40.000 0.00 0.00 32.34 1.73
3022 3802 0.953960 AACCACCGCAAACCTCGATC 60.954 55.000 0.00 0.00 0.00 3.69
3024 3804 0.106335 TTAACCACCGCAAACCTCGA 59.894 50.000 0.00 0.00 0.00 4.04
3080 3863 1.959899 CTCGCTCACGGCACATTCAC 61.960 60.000 0.00 0.00 41.91 3.18
3081 3864 1.737735 CTCGCTCACGGCACATTCA 60.738 57.895 0.00 0.00 41.91 2.57
3263 4047 2.671130 ACCACCAACAAGCAAACAAG 57.329 45.000 0.00 0.00 0.00 3.16
3341 4125 5.948162 ACTCCACTTAAGATCAATGCAACAT 59.052 36.000 10.09 0.00 0.00 2.71
3342 4126 5.316167 ACTCCACTTAAGATCAATGCAACA 58.684 37.500 10.09 0.00 0.00 3.33
3343 4127 5.886960 ACTCCACTTAAGATCAATGCAAC 57.113 39.130 10.09 0.00 0.00 4.17
3344 4128 6.294675 CCAAACTCCACTTAAGATCAATGCAA 60.295 38.462 10.09 0.00 0.00 4.08
3349 4133 7.074653 ACTACCAAACTCCACTTAAGATCAA 57.925 36.000 10.09 0.00 0.00 2.57
3350 4134 6.681729 ACTACCAAACTCCACTTAAGATCA 57.318 37.500 10.09 0.00 0.00 2.92
3351 4135 7.332182 CAGAACTACCAAACTCCACTTAAGATC 59.668 40.741 10.09 0.00 0.00 2.75
3352 4136 7.162082 CAGAACTACCAAACTCCACTTAAGAT 58.838 38.462 10.09 0.00 0.00 2.40
3353 4137 6.522054 CAGAACTACCAAACTCCACTTAAGA 58.478 40.000 10.09 0.00 0.00 2.10
3354 4138 5.179555 GCAGAACTACCAAACTCCACTTAAG 59.820 44.000 0.00 0.00 0.00 1.85
3355 4139 5.061179 GCAGAACTACCAAACTCCACTTAA 58.939 41.667 0.00 0.00 0.00 1.85
3356 4140 4.101898 TGCAGAACTACCAAACTCCACTTA 59.898 41.667 0.00 0.00 0.00 2.24
3357 4141 3.118038 TGCAGAACTACCAAACTCCACTT 60.118 43.478 0.00 0.00 0.00 3.16
3358 4142 2.438021 TGCAGAACTACCAAACTCCACT 59.562 45.455 0.00 0.00 0.00 4.00
3359 4143 2.846193 TGCAGAACTACCAAACTCCAC 58.154 47.619 0.00 0.00 0.00 4.02
3360 4144 3.569194 TTGCAGAACTACCAAACTCCA 57.431 42.857 0.00 0.00 0.00 3.86
3361 4145 5.453567 AAATTGCAGAACTACCAAACTCC 57.546 39.130 0.00 0.00 0.00 3.85
3362 4146 9.129209 GATAAAAATTGCAGAACTACCAAACTC 57.871 33.333 0.00 0.00 0.00 3.01
3363 4147 8.860088 AGATAAAAATTGCAGAACTACCAAACT 58.140 29.630 0.00 0.00 0.00 2.66
3364 4148 8.915654 CAGATAAAAATTGCAGAACTACCAAAC 58.084 33.333 0.00 0.00 0.00 2.93
3365 4149 8.087750 CCAGATAAAAATTGCAGAACTACCAAA 58.912 33.333 0.00 0.00 0.00 3.28
3366 4150 7.232534 ACCAGATAAAAATTGCAGAACTACCAA 59.767 33.333 0.00 0.00 0.00 3.67
3367 4151 6.719370 ACCAGATAAAAATTGCAGAACTACCA 59.281 34.615 0.00 0.00 0.00 3.25
3368 4152 7.158099 ACCAGATAAAAATTGCAGAACTACC 57.842 36.000 0.00 0.00 0.00 3.18
3369 4153 8.082242 ACAACCAGATAAAAATTGCAGAACTAC 58.918 33.333 0.00 0.00 0.00 2.73
3370 4154 8.177119 ACAACCAGATAAAAATTGCAGAACTA 57.823 30.769 0.00 0.00 0.00 2.24
3371 4155 7.054491 ACAACCAGATAAAAATTGCAGAACT 57.946 32.000 0.00 0.00 0.00 3.01
3372 4156 8.986477 ATACAACCAGATAAAAATTGCAGAAC 57.014 30.769 0.00 0.00 0.00 3.01
3376 4160 9.311916 GCATTATACAACCAGATAAAAATTGCA 57.688 29.630 0.00 0.00 0.00 4.08
3377 4161 9.311916 TGCATTATACAACCAGATAAAAATTGC 57.688 29.630 0.00 0.00 0.00 3.56
3379 4163 9.515020 CGTGCATTATACAACCAGATAAAAATT 57.485 29.630 0.00 0.00 0.00 1.82
3380 4164 7.647715 GCGTGCATTATACAACCAGATAAAAAT 59.352 33.333 0.00 0.00 0.00 1.82
3381 4165 6.970043 GCGTGCATTATACAACCAGATAAAAA 59.030 34.615 0.00 0.00 0.00 1.94
3388 4172 3.755965 TTGCGTGCATTATACAACCAG 57.244 42.857 0.00 0.00 0.00 4.00
3402 4186 6.917477 AGCCACATAAAACATAATATTGCGTG 59.083 34.615 0.00 0.00 0.00 5.34
3403 4187 7.038154 AGCCACATAAAACATAATATTGCGT 57.962 32.000 0.00 0.00 0.00 5.24
3404 4188 8.289618 AGTAGCCACATAAAACATAATATTGCG 58.710 33.333 0.00 0.00 0.00 4.85
3413 4197 5.415701 CACCAGAAGTAGCCACATAAAACAT 59.584 40.000 0.00 0.00 0.00 2.71
3435 4220 8.216453 GCAACATTTTGTATTCAATCTGTTCAC 58.784 33.333 8.73 3.70 36.91 3.18
3436 4221 7.924947 TGCAACATTTTGTATTCAATCTGTTCA 59.075 29.630 8.73 8.01 36.91 3.18
3440 4225 8.592155 CATCTGCAACATTTTGTATTCAATCTG 58.408 33.333 0.00 0.00 34.90 2.90
3450 4235 4.325028 TGCTTCATCTGCAACATTTTGT 57.675 36.364 0.00 0.00 37.51 2.83
3451 4236 5.856126 AATGCTTCATCTGCAACATTTTG 57.144 34.783 0.00 0.00 44.01 2.44
3452 4237 6.870971 AAAATGCTTCATCTGCAACATTTT 57.129 29.167 0.00 0.00 44.01 1.82
3453 4238 6.870971 AAAAATGCTTCATCTGCAACATTT 57.129 29.167 0.00 0.00 44.01 2.32
3454 4239 7.156673 AGTAAAAATGCTTCATCTGCAACATT 58.843 30.769 0.00 0.00 44.01 2.71
3455 4240 6.694447 AGTAAAAATGCTTCATCTGCAACAT 58.306 32.000 0.00 0.00 44.01 2.71
3456 4241 6.088016 AGTAAAAATGCTTCATCTGCAACA 57.912 33.333 0.00 0.00 44.01 3.33
3457 4242 6.617105 GCAAGTAAAAATGCTTCATCTGCAAC 60.617 38.462 0.00 0.00 44.01 4.17
3458 4243 5.406175 GCAAGTAAAAATGCTTCATCTGCAA 59.594 36.000 0.00 0.00 44.01 4.08
3459 4244 4.925054 GCAAGTAAAAATGCTTCATCTGCA 59.075 37.500 0.00 0.00 44.95 4.41
3460 4245 4.925054 TGCAAGTAAAAATGCTTCATCTGC 59.075 37.500 0.00 0.00 42.97 4.26
3465 4250 8.522003 TCATAGATTGCAAGTAAAAATGCTTCA 58.478 29.630 4.94 0.00 42.97 3.02
3469 4254 9.956720 ATAGTCATAGATTGCAAGTAAAAATGC 57.043 29.630 4.94 0.00 42.86 3.56
3485 4270 6.146140 AGGAGCACATAGGATAGTCATAGA 57.854 41.667 0.00 0.00 0.00 1.98
3486 4271 7.946381 TTAGGAGCACATAGGATAGTCATAG 57.054 40.000 0.00 0.00 0.00 2.23
3487 4272 8.753133 CAATTAGGAGCACATAGGATAGTCATA 58.247 37.037 0.00 0.00 0.00 2.15
3488 4273 7.619050 CAATTAGGAGCACATAGGATAGTCAT 58.381 38.462 0.00 0.00 0.00 3.06
3489 4274 6.519043 GCAATTAGGAGCACATAGGATAGTCA 60.519 42.308 0.00 0.00 0.00 3.41
3490 4275 5.872070 GCAATTAGGAGCACATAGGATAGTC 59.128 44.000 0.00 0.00 0.00 2.59
3491 4276 5.280215 GGCAATTAGGAGCACATAGGATAGT 60.280 44.000 0.00 0.00 0.00 2.12
3492 4277 5.046014 AGGCAATTAGGAGCACATAGGATAG 60.046 44.000 0.00 0.00 0.00 2.08
3493 4278 4.846367 AGGCAATTAGGAGCACATAGGATA 59.154 41.667 0.00 0.00 0.00 2.59
3494 4279 3.654806 AGGCAATTAGGAGCACATAGGAT 59.345 43.478 0.00 0.00 0.00 3.24
3495 4280 3.048600 AGGCAATTAGGAGCACATAGGA 58.951 45.455 0.00 0.00 0.00 2.94
3532 4317 1.336125 GCTATTCCAACATGCTCTGGC 59.664 52.381 0.00 0.00 39.26 4.85
3534 4319 3.630769 ACATGCTATTCCAACATGCTCTG 59.369 43.478 0.00 0.00 43.96 3.35
3535 4320 3.894759 ACATGCTATTCCAACATGCTCT 58.105 40.909 0.00 0.00 43.96 4.09
3536 4321 4.644103 AACATGCTATTCCAACATGCTC 57.356 40.909 0.00 0.00 43.96 4.26
3538 4323 5.756195 TCTAACATGCTATTCCAACATGC 57.244 39.130 0.00 0.00 43.96 4.06
3540 4325 9.807649 GAAAATTCTAACATGCTATTCCAACAT 57.192 29.630 0.00 0.00 0.00 2.71
3541 4326 9.023962 AGAAAATTCTAACATGCTATTCCAACA 57.976 29.630 0.00 0.00 35.34 3.33
3545 4330 9.617975 GCATAGAAAATTCTAACATGCTATTCC 57.382 33.333 16.59 0.00 42.55 3.01
3548 4333 7.725397 TGGGCATAGAAAATTCTAACATGCTAT 59.275 33.333 20.40 0.00 42.34 2.97
3558 4356 4.088634 TGCAACTGGGCATAGAAAATTCT 58.911 39.130 0.77 0.77 39.25 2.40
3587 4385 3.803778 GTGTCTGGATTTTGTTTGCCTTG 59.196 43.478 0.00 0.00 0.00 3.61
3607 4405 3.981071 TTCCCAGGTCTTGTCTATGTG 57.019 47.619 0.00 0.00 0.00 3.21
3612 4410 1.840635 GGCTATTCCCAGGTCTTGTCT 59.159 52.381 0.00 0.00 0.00 3.41
3615 4413 2.122768 AGAGGCTATTCCCAGGTCTTG 58.877 52.381 0.00 0.00 34.51 3.02
3617 4415 2.577772 AAGAGGCTATTCCCAGGTCT 57.422 50.000 0.00 0.00 34.51 3.85
3618 4416 3.039011 TGTAAGAGGCTATTCCCAGGTC 58.961 50.000 0.00 0.00 34.51 3.85
3620 4418 4.841246 ACTATGTAAGAGGCTATTCCCAGG 59.159 45.833 0.00 0.00 34.51 4.45
3621 4419 5.540337 TCACTATGTAAGAGGCTATTCCCAG 59.460 44.000 0.00 0.00 34.51 4.45
3622 4420 5.464069 TCACTATGTAAGAGGCTATTCCCA 58.536 41.667 0.00 0.00 34.51 4.37
3623 4421 6.613153 ATCACTATGTAAGAGGCTATTCCC 57.387 41.667 0.00 0.00 34.51 3.97
3624 4422 8.356000 ACTATCACTATGTAAGAGGCTATTCC 57.644 38.462 0.00 0.00 0.00 3.01
3629 4427 8.091449 GCAATAACTATCACTATGTAAGAGGCT 58.909 37.037 0.00 0.00 0.00 4.58
3630 4428 8.091449 AGCAATAACTATCACTATGTAAGAGGC 58.909 37.037 0.00 0.00 0.00 4.70
3631 4429 9.416794 CAGCAATAACTATCACTATGTAAGAGG 57.583 37.037 0.00 0.00 0.00 3.69
3632 4430 8.920665 GCAGCAATAACTATCACTATGTAAGAG 58.079 37.037 0.00 0.00 0.00 2.85
3633 4431 8.642432 AGCAGCAATAACTATCACTATGTAAGA 58.358 33.333 0.00 0.00 0.00 2.10
3634 4432 8.824159 AGCAGCAATAACTATCACTATGTAAG 57.176 34.615 0.00 0.00 0.00 2.34
3635 4433 9.692749 GTAGCAGCAATAACTATCACTATGTAA 57.307 33.333 0.00 0.00 0.00 2.41
3636 4434 8.304596 GGTAGCAGCAATAACTATCACTATGTA 58.695 37.037 0.00 0.00 0.00 2.29
3637 4435 7.015682 AGGTAGCAGCAATAACTATCACTATGT 59.984 37.037 0.00 0.00 0.00 2.29
3638 4436 7.330454 CAGGTAGCAGCAATAACTATCACTATG 59.670 40.741 0.00 0.00 0.00 2.23
3639 4437 7.382110 CAGGTAGCAGCAATAACTATCACTAT 58.618 38.462 0.00 0.00 0.00 2.12
3640 4438 6.239317 CCAGGTAGCAGCAATAACTATCACTA 60.239 42.308 0.00 0.00 0.00 2.74
3641 4439 5.453903 CCAGGTAGCAGCAATAACTATCACT 60.454 44.000 0.00 0.00 0.00 3.41
3642 4440 4.752101 CCAGGTAGCAGCAATAACTATCAC 59.248 45.833 0.00 0.00 0.00 3.06
3643 4441 4.653801 TCCAGGTAGCAGCAATAACTATCA 59.346 41.667 0.00 0.00 0.00 2.15
3644 4442 5.215252 TCCAGGTAGCAGCAATAACTATC 57.785 43.478 0.00 0.00 0.00 2.08
3645 4443 4.656112 ACTCCAGGTAGCAGCAATAACTAT 59.344 41.667 0.00 0.00 0.00 2.12
3646 4444 4.030913 ACTCCAGGTAGCAGCAATAACTA 58.969 43.478 0.00 0.00 0.00 2.24
3647 4445 2.840651 ACTCCAGGTAGCAGCAATAACT 59.159 45.455 0.00 0.00 0.00 2.24
3648 4446 3.268023 ACTCCAGGTAGCAGCAATAAC 57.732 47.619 0.00 0.00 0.00 1.89
3662 4460 5.102953 TCATTCAGTCCCAAATACTCCAG 57.897 43.478 0.00 0.00 0.00 3.86
3666 4464 8.599624 AATTGAATCATTCAGTCCCAAATACT 57.400 30.769 0.00 0.00 41.38 2.12
3688 4486 7.768582 AGGTTTGACGAAATTCCTTTGAAAATT 59.231 29.630 0.00 0.00 33.32 1.82
3690 4488 6.533367 CAGGTTTGACGAAATTCCTTTGAAAA 59.467 34.615 0.00 0.00 33.32 2.29
3712 4510 9.667107 TCTTATCAAAGGAATTACTTGTACAGG 57.333 33.333 2.96 2.98 33.22 4.00
3745 4544 6.094464 TCTGTGCAGTTTTCATAGGATTCATG 59.906 38.462 0.00 0.00 0.00 3.07
3767 4566 3.332919 ACTGCTTGCTTGTGTATCTCTG 58.667 45.455 0.00 0.00 0.00 3.35
3829 4628 4.532126 TGTCCTGTCATGTCTGGAGTTATT 59.468 41.667 16.67 0.00 36.41 1.40
3844 4643 2.531206 GAGCACGATTACTGTCCTGTC 58.469 52.381 0.00 0.00 0.00 3.51
3849 4648 0.179134 AGGCGAGCACGATTACTGTC 60.179 55.000 8.01 0.00 42.66 3.51


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

AutoCloner maintained by Alex Coulton.