Multiple sequence alignment - TraesCS1A01G123700

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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 TraesCS1A01G123700 chr1A 100.000 2294 0 0 1 2294 144551721 144554014 0.000000e+00 4237.0
1 TraesCS1A01G123700 chr1D 89.786 2056 143 32 4 2012 144678917 144676882 0.000000e+00 2571.0
2 TraesCS1A01G123700 chr1B 88.847 1596 124 26 6 1568 194358876 194357302 0.000000e+00 1912.0
3 TraesCS1A01G123700 chr1B 93.172 454 24 3 1565 2012 194357180 194356728 0.000000e+00 660.0
4 TraesCS1A01G123700 chr1B 92.171 281 22 0 2010 2290 466844452 466844732 4.590000e-107 398.0
5 TraesCS1A01G123700 chr6A 84.371 755 77 19 718 1445 98605857 98605117 0.000000e+00 702.0
6 TraesCS1A01G123700 chr6B 82.872 759 83 20 718 1445 156932746 156932004 2.490000e-179 638.0
7 TraesCS1A01G123700 chr6B 91.837 49 3 1 1660 1707 224867902 224867950 1.470000e-07 67.6
8 TraesCS1A01G123700 chr6D 81.722 755 93 28 718 1445 82092993 82092257 2.540000e-164 588.0
9 TraesCS1A01G123700 chr6D 93.617 47 3 0 1661 1707 345735800 345735846 1.140000e-08 71.3
10 TraesCS1A01G123700 chr6D 91.667 48 3 1 1661 1707 83933304 83933257 5.290000e-07 65.8
11 TraesCS1A01G123700 chr6D 91.667 48 3 1 1660 1706 126431441 126431488 5.290000e-07 65.8
12 TraesCS1A01G123700 chr3A 93.640 283 18 0 2010 2292 434834053 434833771 7.580000e-115 424.0
13 TraesCS1A01G123700 chr7A 93.357 286 18 1 2007 2292 126686741 126687025 2.720000e-114 422.0
14 TraesCS1A01G123700 chr5D 92.683 287 20 1 2006 2292 80893840 80894125 1.640000e-111 412.0
15 TraesCS1A01G123700 chr5D 81.443 97 18 0 546 642 529291964 529292060 1.890000e-11 80.5
16 TraesCS1A01G123700 chr4A 92.069 290 19 1 2007 2292 462046918 462047207 2.740000e-109 405.0
17 TraesCS1A01G123700 chr2A 92.580 283 20 1 2010 2292 748150633 748150914 2.740000e-109 405.0
18 TraesCS1A01G123700 chr2A 91.844 282 23 0 2009 2290 622757868 622757587 5.940000e-106 394.0
19 TraesCS1A01G123700 chr2B 92.553 282 20 1 2010 2290 603641226 603640945 9.870000e-109 403.0
20 TraesCS1A01G123700 chr2B 91.844 282 23 0 2009 2290 494273259 494272978 5.940000e-106 394.0
21 TraesCS1A01G123700 chr2D 82.540 126 19 3 518 642 95142103 95142226 8.670000e-20 108.0
22 TraesCS1A01G123700 chr2D 95.745 47 2 0 1661 1707 312629969 312630015 2.440000e-10 76.8
23 TraesCS1A01G123700 chr7D 81.746 126 20 3 518 642 43431505 43431382 4.030000e-18 102.0
24 TraesCS1A01G123700 chr3B 87.692 65 7 1 518 582 612109282 612109219 8.790000e-10 75.0
25 TraesCS1A01G123700 chr4D 93.750 48 2 1 1661 1707 254571635 254571682 1.140000e-08 71.3
26 TraesCS1A01G123700 chr4D 95.455 44 1 1 1661 1703 42500115 42500158 4.090000e-08 69.4


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 TraesCS1A01G123700 chr1A 144551721 144554014 2293 False 4237 4237 100.0000 1 2294 1 chr1A.!!$F1 2293
1 TraesCS1A01G123700 chr1D 144676882 144678917 2035 True 2571 2571 89.7860 4 2012 1 chr1D.!!$R1 2008
2 TraesCS1A01G123700 chr1B 194356728 194358876 2148 True 1286 1912 91.0095 6 2012 2 chr1B.!!$R1 2006
3 TraesCS1A01G123700 chr6A 98605117 98605857 740 True 702 702 84.3710 718 1445 1 chr6A.!!$R1 727
4 TraesCS1A01G123700 chr6B 156932004 156932746 742 True 638 638 82.8720 718 1445 1 chr6B.!!$R1 727
5 TraesCS1A01G123700 chr6D 82092257 82092993 736 True 588 588 81.7220 718 1445 1 chr6D.!!$R1 727

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
366 396 0.030705 TTCCCTCAGGCCTCAGCTAT 60.031 55.0 0.0 0.0 39.73 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1648 1858 0.035056 AATCGAAGGTGCCTCAAGGG 60.035 55.0 0.0 0.0 35.18 3.95 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
22 23 3.625897 CCCAGTGCACCACTCGGA 61.626 66.667 14.63 0.00 43.72 4.55
38 39 6.649557 ACCACTCGGAAAAGTGTAGATAAAAG 59.350 38.462 3.60 0.00 44.22 2.27
39 40 6.649557 CCACTCGGAAAAGTGTAGATAAAAGT 59.350 38.462 3.60 0.00 44.22 2.66
40 41 7.816031 CCACTCGGAAAAGTGTAGATAAAAGTA 59.184 37.037 3.60 0.00 44.22 2.24
89 90 9.607285 ACTAATAAAATGCTTTTGACAAGTACG 57.393 29.630 0.00 0.00 34.19 3.67
90 91 6.927933 ATAAAATGCTTTTGACAAGTACGC 57.072 33.333 0.00 0.00 34.19 4.42
129 130 8.907222 ATTGCAAACAGAGAAAATAAAATGGT 57.093 26.923 1.71 0.00 0.00 3.55
170 172 2.489971 CAACACCTACTCGGCAAAGAA 58.510 47.619 0.00 0.00 35.61 2.52
171 173 2.875933 CAACACCTACTCGGCAAAGAAA 59.124 45.455 0.00 0.00 35.61 2.52
172 174 3.202829 ACACCTACTCGGCAAAGAAAA 57.797 42.857 0.00 0.00 35.61 2.29
173 175 3.547746 ACACCTACTCGGCAAAGAAAAA 58.452 40.909 0.00 0.00 35.61 1.94
206 210 9.946165 AAAGTACAAAGAGGAGAAAATAAAACG 57.054 29.630 0.00 0.00 0.00 3.60
294 323 6.481954 ACGAAAGTAAAAGAGCACTATTGG 57.518 37.500 0.00 0.00 46.88 3.16
316 346 1.402852 GCAAAATCTTTGCGAGGACCC 60.403 52.381 8.24 0.00 35.58 4.46
331 361 2.443255 AGGACCCAACTCATCAAACACT 59.557 45.455 0.00 0.00 0.00 3.55
345 375 6.426633 TCATCAAACACTATGACAACGTCAAT 59.573 34.615 0.22 0.00 45.96 2.57
347 377 5.525745 TCAAACACTATGACAACGTCAATGT 59.474 36.000 0.22 3.99 45.96 2.71
350 380 4.451096 ACACTATGACAACGTCAATGTTCC 59.549 41.667 0.22 0.00 45.96 3.62
351 381 4.000988 ACTATGACAACGTCAATGTTCCC 58.999 43.478 0.22 0.00 45.96 3.97
352 382 2.631160 TGACAACGTCAATGTTCCCT 57.369 45.000 0.00 0.00 39.78 4.20
353 383 2.489971 TGACAACGTCAATGTTCCCTC 58.510 47.619 0.00 0.00 39.78 4.30
354 384 2.158885 TGACAACGTCAATGTTCCCTCA 60.159 45.455 0.00 0.00 39.78 3.86
355 385 2.480419 GACAACGTCAATGTTCCCTCAG 59.520 50.000 0.00 0.00 32.09 3.35
356 386 1.806542 CAACGTCAATGTTCCCTCAGG 59.193 52.381 0.00 0.00 0.00 3.86
365 395 0.978146 GTTCCCTCAGGCCTCAGCTA 60.978 60.000 0.00 0.00 39.73 3.32
366 396 0.030705 TTCCCTCAGGCCTCAGCTAT 60.031 55.000 0.00 0.00 39.73 2.97
367 397 0.470833 TCCCTCAGGCCTCAGCTATC 60.471 60.000 0.00 0.00 39.73 2.08
380 410 0.978146 AGCTATCGCCACTTGGGACT 60.978 55.000 0.00 0.00 38.94 3.85
404 434 0.960364 TCCAGCCATTTGCCGAGTTC 60.960 55.000 0.00 0.00 42.71 3.01
415 445 3.478857 TGCCGAGTTCTAGGTTTTTGA 57.521 42.857 1.40 0.00 0.00 2.69
416 446 3.135994 TGCCGAGTTCTAGGTTTTTGAC 58.864 45.455 1.40 0.00 0.00 3.18
462 492 2.748461 TTTTGCCGAGTTCTTTGTCG 57.252 45.000 0.00 0.00 35.91 4.35
512 543 7.396540 AATAGCATGGTATAGCAAAATAGCC 57.603 36.000 17.37 0.00 34.23 3.93
513 544 4.990526 AGCATGGTATAGCAAAATAGCCT 58.009 39.130 8.98 0.00 34.23 4.58
514 545 6.126863 AGCATGGTATAGCAAAATAGCCTA 57.873 37.500 8.98 0.00 34.23 3.93
516 547 5.940470 GCATGGTATAGCAAAATAGCCTAGT 59.060 40.000 8.98 0.00 34.23 2.57
537 569 7.543868 CCTAGTCTATTAGCAATGCTACATCAC 59.456 40.741 15.31 9.55 41.12 3.06
538 570 6.820335 AGTCTATTAGCAATGCTACATCACA 58.180 36.000 15.31 0.00 41.12 3.58
542 574 8.421002 TCTATTAGCAATGCTACATCACACTAA 58.579 33.333 15.31 0.00 41.12 2.24
544 576 7.680442 TTAGCAATGCTACATCACACTAAAA 57.320 32.000 15.31 0.00 41.12 1.52
555 587 7.661127 ACATCACACTAAAACGTGCTATTAA 57.339 32.000 0.00 0.00 38.45 1.40
573 605 6.750501 GCTATTAACGAGACATTGTACACTGA 59.249 38.462 19.02 0.00 0.00 3.41
603 635 5.343307 AAAGAGCCATTTTTCAACACACT 57.657 34.783 0.00 0.00 0.00 3.55
605 637 5.438761 AGAGCCATTTTTCAACACACTAC 57.561 39.130 0.00 0.00 0.00 2.73
607 639 5.359576 AGAGCCATTTTTCAACACACTACAA 59.640 36.000 0.00 0.00 0.00 2.41
609 641 4.206200 GCCATTTTTCAACACACTACAACG 59.794 41.667 0.00 0.00 0.00 4.10
612 645 5.608676 TTTTTCAACACACTACAACGTGA 57.391 34.783 0.00 0.00 38.27 4.35
617 650 7.485418 TTCAACACACTACAACGTGATATTT 57.515 32.000 0.00 0.00 38.27 1.40
621 654 3.181524 ACACTACAACGTGATATTTGCGC 60.182 43.478 0.00 0.00 38.27 6.09
623 656 1.160989 ACAACGTGATATTTGCGCCA 58.839 45.000 4.18 0.00 0.00 5.69
648 682 1.791662 CGCGCTATTTTTCCGGTGT 59.208 52.632 5.56 0.00 0.00 4.16
713 747 5.344933 GCCCGATAAAATGAACTTGACAAAC 59.655 40.000 0.00 0.00 0.00 2.93
778 812 6.144724 GTGATGTGTTCTCACTAAGTTGACTC 59.855 42.308 0.00 0.00 44.14 3.36
921 963 3.799281 CATATTTGCACCCATTCCGTT 57.201 42.857 0.00 0.00 0.00 4.44
922 964 3.705604 CATATTTGCACCCATTCCGTTC 58.294 45.455 0.00 0.00 0.00 3.95
923 965 0.894835 ATTTGCACCCATTCCGTTCC 59.105 50.000 0.00 0.00 0.00 3.62
924 966 0.178975 TTTGCACCCATTCCGTTCCT 60.179 50.000 0.00 0.00 0.00 3.36
1040 1105 6.476706 GCCATTATGATACTTTCCTTGTTTGC 59.523 38.462 0.00 0.00 0.00 3.68
1107 1172 0.251354 ATCAACCACAGATGCTCGCT 59.749 50.000 0.00 0.00 0.00 4.93
1130 1195 1.949847 AAGACGATCAGCCCACCTCG 61.950 60.000 0.00 0.00 37.17 4.63
1166 1231 4.276678 TCCAGATTTGCTTCAAGTGTTCAG 59.723 41.667 0.00 0.00 0.00 3.02
1200 1265 2.159382 CCAATCCCTGTTACGTTTGCT 58.841 47.619 0.00 0.00 0.00 3.91
1203 1268 0.250553 TCCCTGTTACGTTTGCTGGG 60.251 55.000 16.81 16.81 41.12 4.45
1209 1274 2.952978 TGTTACGTTTGCTGGGAACATT 59.047 40.909 0.00 0.00 41.51 2.71
1250 1315 4.436998 GCGTGCTAGCCAGGTCGT 62.437 66.667 13.29 0.00 0.00 4.34
1251 1316 2.202623 CGTGCTAGCCAGGTCGTC 60.203 66.667 13.29 0.00 0.00 4.20
1252 1317 2.202623 GTGCTAGCCAGGTCGTCG 60.203 66.667 13.29 0.00 0.00 5.12
1255 1320 0.961857 TGCTAGCCAGGTCGTCGTTA 60.962 55.000 13.29 0.00 0.00 3.18
1260 1325 1.447314 CCAGGTCGTCGTTAAGGGC 60.447 63.158 0.00 0.00 0.00 5.19
1263 1328 0.896940 AGGTCGTCGTTAAGGGCTCA 60.897 55.000 0.00 0.00 0.00 4.26
1298 1363 2.202623 CGGTCACCACTAGCTCGC 60.203 66.667 0.00 0.00 0.00 5.03
1311 1376 0.600557 AGCTCGCCGATCCTCTAATG 59.399 55.000 0.00 0.00 0.00 1.90
1353 1418 9.335891 CTCTACATTTCACACATATCGATCTAC 57.664 37.037 0.00 0.00 0.00 2.59
1362 1434 5.871524 ACACATATCGATCTACATGAATGGC 59.128 40.000 11.85 0.00 0.00 4.40
1459 1542 3.932545 ATGTAACCATGAAAAGCGCAA 57.067 38.095 11.47 0.00 0.00 4.85
1469 1552 1.717645 GAAAAGCGCAACATGCTCTTG 59.282 47.619 11.47 0.00 46.37 3.02
1531 1614 4.811024 TCGAGAATATGTCATGAAAGGCAC 59.189 41.667 0.00 0.00 0.00 5.01
1618 1826 3.213206 TCTCAACTTGGTTGCTGTCAT 57.787 42.857 5.63 0.00 42.55 3.06
1641 1849 7.868922 TCATTTTGGATTGTTTCATCACTTCTG 59.131 33.333 0.00 0.00 0.00 3.02
1663 1873 1.995376 TTTTCCCTTGAGGCACCTTC 58.005 50.000 0.00 0.00 34.51 3.46
1664 1874 0.250727 TTTCCCTTGAGGCACCTTCG 60.251 55.000 0.00 0.00 34.51 3.79
1669 1879 1.611673 CCTTGAGGCACCTTCGATTGT 60.612 52.381 0.00 0.00 0.00 2.71
1806 2016 8.221100 GCGCGAAGAAACATATCATAATTTAGA 58.779 33.333 12.10 0.00 0.00 2.10
1891 2106 2.555757 ACCTTGCTCAATTGCTGTCTTC 59.444 45.455 0.00 0.00 0.00 2.87
1899 2114 5.390885 GCTCAATTGCTGTCTTCGAATTACA 60.391 40.000 11.62 11.62 0.00 2.41
1912 2127 5.908916 TCGAATTACAATGTCGTGTTTCA 57.091 34.783 0.00 0.00 36.21 2.69
1924 2139 4.083855 TGTCGTGTTTCATGCATTTCTCTC 60.084 41.667 0.00 0.00 0.00 3.20
1952 2167 4.996758 CGCTGTGATTATGACCAATGGATA 59.003 41.667 6.16 0.00 0.00 2.59
2018 2238 8.753497 AAAATATCTGACAAAATACTCCCTCC 57.247 34.615 0.00 0.00 0.00 4.30
2019 2239 3.887621 TCTGACAAAATACTCCCTCCG 57.112 47.619 0.00 0.00 0.00 4.63
2020 2240 3.170717 TCTGACAAAATACTCCCTCCGT 58.829 45.455 0.00 0.00 0.00 4.69
2021 2241 3.194968 TCTGACAAAATACTCCCTCCGTC 59.805 47.826 0.00 0.00 0.00 4.79
2022 2242 2.235402 TGACAAAATACTCCCTCCGTCC 59.765 50.000 0.00 0.00 0.00 4.79
2023 2243 1.558294 ACAAAATACTCCCTCCGTCCC 59.442 52.381 0.00 0.00 0.00 4.46
2024 2244 0.828677 AAAATACTCCCTCCGTCCCG 59.171 55.000 0.00 0.00 0.00 5.14
2025 2245 0.032813 AAATACTCCCTCCGTCCCGA 60.033 55.000 0.00 0.00 0.00 5.14
2026 2246 0.032813 AATACTCCCTCCGTCCCGAA 60.033 55.000 0.00 0.00 0.00 4.30
2027 2247 0.032813 ATACTCCCTCCGTCCCGAAA 60.033 55.000 0.00 0.00 0.00 3.46
2028 2248 0.251742 TACTCCCTCCGTCCCGAAAA 60.252 55.000 0.00 0.00 0.00 2.29
2029 2249 1.123246 ACTCCCTCCGTCCCGAAAAA 61.123 55.000 0.00 0.00 0.00 1.94
2030 2250 0.672711 CTCCCTCCGTCCCGAAAAAC 60.673 60.000 0.00 0.00 0.00 2.43
2031 2251 1.071814 CCCTCCGTCCCGAAAAACA 59.928 57.895 0.00 0.00 0.00 2.83
2032 2252 0.322187 CCCTCCGTCCCGAAAAACAT 60.322 55.000 0.00 0.00 0.00 2.71
2033 2253 0.802494 CCTCCGTCCCGAAAAACATG 59.198 55.000 0.00 0.00 0.00 3.21
2034 2254 1.519408 CTCCGTCCCGAAAAACATGT 58.481 50.000 0.00 0.00 0.00 3.21
2035 2255 1.463444 CTCCGTCCCGAAAAACATGTC 59.537 52.381 0.00 0.00 0.00 3.06
2036 2256 0.165079 CCGTCCCGAAAAACATGTCG 59.835 55.000 0.00 0.00 37.01 4.35
2037 2257 0.452122 CGTCCCGAAAAACATGTCGC 60.452 55.000 0.00 0.00 35.93 5.19
2038 2258 0.452122 GTCCCGAAAAACATGTCGCG 60.452 55.000 0.00 0.00 35.93 5.87
2039 2259 1.154301 CCCGAAAAACATGTCGCGG 60.154 57.895 6.13 16.83 35.93 6.46
2040 2260 1.154301 CCGAAAAACATGTCGCGGG 60.154 57.895 6.13 0.00 35.93 6.13
2041 2261 1.795962 CGAAAAACATGTCGCGGGC 60.796 57.895 6.13 0.00 0.00 6.13
2042 2262 1.284408 GAAAAACATGTCGCGGGCA 59.716 52.632 6.13 6.50 0.00 5.36
2043 2263 0.109319 GAAAAACATGTCGCGGGCAT 60.109 50.000 6.13 8.86 0.00 4.40
2044 2264 1.131504 GAAAAACATGTCGCGGGCATA 59.868 47.619 6.13 0.00 0.00 3.14
2045 2265 0.732571 AAAACATGTCGCGGGCATAG 59.267 50.000 6.13 8.89 0.00 2.23
2046 2266 0.392461 AAACATGTCGCGGGCATAGT 60.392 50.000 6.13 9.46 0.00 2.12
2047 2267 0.392461 AACATGTCGCGGGCATAGTT 60.392 50.000 6.13 14.12 0.00 2.24
2048 2268 0.810031 ACATGTCGCGGGCATAGTTC 60.810 55.000 6.13 0.00 0.00 3.01
2049 2269 0.809636 CATGTCGCGGGCATAGTTCA 60.810 55.000 6.13 0.00 0.00 3.18
2050 2270 0.106708 ATGTCGCGGGCATAGTTCAT 59.893 50.000 6.13 0.00 0.00 2.57
2051 2271 0.107897 TGTCGCGGGCATAGTTCATT 60.108 50.000 6.13 0.00 0.00 2.57
2052 2272 0.304705 GTCGCGGGCATAGTTCATTG 59.695 55.000 6.13 0.00 0.00 2.82
2053 2273 0.813610 TCGCGGGCATAGTTCATTGG 60.814 55.000 6.13 0.00 0.00 3.16
2054 2274 1.095228 CGCGGGCATAGTTCATTGGT 61.095 55.000 0.00 0.00 0.00 3.67
2055 2275 1.808512 CGCGGGCATAGTTCATTGGTA 60.809 52.381 0.00 0.00 0.00 3.25
2056 2276 2.294074 GCGGGCATAGTTCATTGGTAA 58.706 47.619 0.00 0.00 0.00 2.85
2057 2277 2.884639 GCGGGCATAGTTCATTGGTAAT 59.115 45.455 0.00 0.00 0.00 1.89
2058 2278 3.317993 GCGGGCATAGTTCATTGGTAATT 59.682 43.478 0.00 0.00 0.00 1.40
2059 2279 4.202111 GCGGGCATAGTTCATTGGTAATTT 60.202 41.667 0.00 0.00 0.00 1.82
2060 2280 5.681179 GCGGGCATAGTTCATTGGTAATTTT 60.681 40.000 0.00 0.00 0.00 1.82
2061 2281 5.748152 CGGGCATAGTTCATTGGTAATTTTG 59.252 40.000 0.00 0.00 0.00 2.44
2062 2282 5.523552 GGGCATAGTTCATTGGTAATTTTGC 59.476 40.000 0.00 0.00 0.00 3.68
2063 2283 6.105333 GGCATAGTTCATTGGTAATTTTGCA 58.895 36.000 0.00 0.00 0.00 4.08
2064 2284 6.593382 GGCATAGTTCATTGGTAATTTTGCAA 59.407 34.615 0.00 0.00 0.00 4.08
2065 2285 7.118971 GGCATAGTTCATTGGTAATTTTGCAAA 59.881 33.333 8.05 8.05 0.00 3.68
2066 2286 8.502387 GCATAGTTCATTGGTAATTTTGCAAAA 58.498 29.630 25.76 25.76 0.00 2.44
2089 2309 1.757682 ACCTCGTGGTTTCAAAAGCA 58.242 45.000 2.61 3.39 46.05 3.91
2090 2310 2.306847 ACCTCGTGGTTTCAAAAGCAT 58.693 42.857 2.61 0.00 46.05 3.79
2091 2311 2.693074 ACCTCGTGGTTTCAAAAGCATT 59.307 40.909 2.61 0.00 46.05 3.56
2092 2312 3.132111 ACCTCGTGGTTTCAAAAGCATTT 59.868 39.130 2.61 0.00 46.05 2.32
2093 2313 3.735746 CCTCGTGGTTTCAAAAGCATTTC 59.264 43.478 10.23 0.00 46.52 2.17
2094 2314 4.358851 CTCGTGGTTTCAAAAGCATTTCA 58.641 39.130 10.23 0.00 46.52 2.69
2095 2315 4.748892 TCGTGGTTTCAAAAGCATTTCAA 58.251 34.783 10.23 0.00 46.52 2.69
2096 2316 5.171476 TCGTGGTTTCAAAAGCATTTCAAA 58.829 33.333 10.23 0.00 46.52 2.69
2097 2317 5.062809 TCGTGGTTTCAAAAGCATTTCAAAC 59.937 36.000 5.48 5.48 46.52 2.93
2098 2318 5.163913 CGTGGTTTCAAAAGCATTTCAAACA 60.164 36.000 14.37 3.48 46.52 2.83
2099 2319 6.606768 GTGGTTTCAAAAGCATTTCAAACAA 58.393 32.000 14.37 1.92 46.52 2.83
2100 2320 7.080724 GTGGTTTCAAAAGCATTTCAAACAAA 58.919 30.769 14.37 1.43 46.52 2.83
2101 2321 7.754475 GTGGTTTCAAAAGCATTTCAAACAAAT 59.246 29.630 14.37 0.00 46.52 2.32
2102 2322 7.967303 TGGTTTCAAAAGCATTTCAAACAAATC 59.033 29.630 14.37 0.09 40.12 2.17
2103 2323 7.431960 GGTTTCAAAAGCATTTCAAACAAATCC 59.568 33.333 14.37 0.00 40.12 3.01
2104 2324 6.616774 TCAAAAGCATTTCAAACAAATCCC 57.383 33.333 0.00 0.00 37.28 3.85
2105 2325 6.355747 TCAAAAGCATTTCAAACAAATCCCT 58.644 32.000 0.00 0.00 37.28 4.20
2106 2326 6.482973 TCAAAAGCATTTCAAACAAATCCCTC 59.517 34.615 0.00 0.00 37.28 4.30
2107 2327 4.541973 AGCATTTCAAACAAATCCCTCC 57.458 40.909 0.00 0.00 0.00 4.30
2108 2328 3.056607 AGCATTTCAAACAAATCCCTCCG 60.057 43.478 0.00 0.00 0.00 4.63
2109 2329 3.253230 CATTTCAAACAAATCCCTCCGC 58.747 45.455 0.00 0.00 0.00 5.54
2110 2330 1.253100 TTCAAACAAATCCCTCCGCC 58.747 50.000 0.00 0.00 0.00 6.13
2111 2331 0.610785 TCAAACAAATCCCTCCGCCC 60.611 55.000 0.00 0.00 0.00 6.13
2112 2332 1.304962 AAACAAATCCCTCCGCCCC 60.305 57.895 0.00 0.00 0.00 5.80
2113 2333 3.638592 AACAAATCCCTCCGCCCCG 62.639 63.158 0.00 0.00 0.00 5.73
2114 2334 4.109675 CAAATCCCTCCGCCCCGT 62.110 66.667 0.00 0.00 0.00 5.28
2115 2335 3.793888 AAATCCCTCCGCCCCGTC 61.794 66.667 0.00 0.00 0.00 4.79
2116 2336 4.798682 AATCCCTCCGCCCCGTCT 62.799 66.667 0.00 0.00 0.00 4.18
2117 2337 4.798682 ATCCCTCCGCCCCGTCTT 62.799 66.667 0.00 0.00 0.00 3.01
2120 2340 3.391382 CCTCCGCCCCGTCTTCTT 61.391 66.667 0.00 0.00 0.00 2.52
2121 2341 2.184579 CTCCGCCCCGTCTTCTTC 59.815 66.667 0.00 0.00 0.00 2.87
2122 2342 3.372554 CTCCGCCCCGTCTTCTTCC 62.373 68.421 0.00 0.00 0.00 3.46
2123 2343 3.391382 CCGCCCCGTCTTCTTCCT 61.391 66.667 0.00 0.00 0.00 3.36
2124 2344 2.184579 CGCCCCGTCTTCTTCCTC 59.815 66.667 0.00 0.00 0.00 3.71
2125 2345 2.585153 GCCCCGTCTTCTTCCTCC 59.415 66.667 0.00 0.00 0.00 4.30
2126 2346 2.893398 CCCCGTCTTCTTCCTCCG 59.107 66.667 0.00 0.00 0.00 4.63
2127 2347 1.982938 CCCCGTCTTCTTCCTCCGT 60.983 63.158 0.00 0.00 0.00 4.69
2128 2348 1.511768 CCCGTCTTCTTCCTCCGTC 59.488 63.158 0.00 0.00 0.00 4.79
2129 2349 1.511768 CCGTCTTCTTCCTCCGTCC 59.488 63.158 0.00 0.00 0.00 4.79
2130 2350 1.136984 CGTCTTCTTCCTCCGTCCG 59.863 63.158 0.00 0.00 0.00 4.79
2131 2351 1.584380 CGTCTTCTTCCTCCGTCCGT 61.584 60.000 0.00 0.00 0.00 4.69
2132 2352 0.170784 GTCTTCTTCCTCCGTCCGTC 59.829 60.000 0.00 0.00 0.00 4.79
2133 2353 1.136984 CTTCTTCCTCCGTCCGTCG 59.863 63.158 0.00 0.00 39.52 5.12
2134 2354 2.868999 CTTCTTCCTCCGTCCGTCGC 62.869 65.000 0.00 0.00 38.35 5.19
2135 2355 4.493747 CTTCCTCCGTCCGTCGCC 62.494 72.222 0.00 0.00 38.35 5.54
2157 2377 4.838152 CATCGCCAGGGGACGGTG 62.838 72.222 8.73 0.00 36.35 4.94
2177 2397 3.869272 GCCCAGCTGCGTGATTCG 61.869 66.667 8.66 0.00 43.12 3.34
2186 2406 2.280186 CGTGATTCGCTAGGGGCC 60.280 66.667 6.99 0.00 37.74 5.80
2187 2407 2.280186 GTGATTCGCTAGGGGCCG 60.280 66.667 6.99 0.00 37.74 6.13
2188 2408 3.546543 TGATTCGCTAGGGGCCGG 61.547 66.667 6.99 0.00 37.74 6.13
2189 2409 4.990553 GATTCGCTAGGGGCCGGC 62.991 72.222 21.18 21.18 37.74 6.13
2202 2422 4.899239 CCGGCGAGCCCAGCTAAG 62.899 72.222 9.30 0.00 39.88 2.18
2204 2424 4.168291 GGCGAGCCCAGCTAAGCT 62.168 66.667 9.31 9.31 39.88 3.74
2208 2428 3.640761 AGCCCAGCTAAGCTCCTC 58.359 61.111 3.87 0.00 36.40 3.71
2209 2429 2.069430 AGCCCAGCTAAGCTCCTCC 61.069 63.158 3.87 0.00 36.40 4.30
2210 2430 2.818132 CCCAGCTAAGCTCCTCCG 59.182 66.667 0.00 0.00 36.40 4.63
2211 2431 2.107953 CCAGCTAAGCTCCTCCGC 59.892 66.667 0.00 0.00 36.40 5.54
2212 2432 2.107953 CAGCTAAGCTCCTCCGCC 59.892 66.667 0.00 0.00 36.40 6.13
2213 2433 3.532155 AGCTAAGCTCCTCCGCCG 61.532 66.667 0.00 0.00 30.62 6.46
2214 2434 3.839432 GCTAAGCTCCTCCGCCGT 61.839 66.667 0.00 0.00 0.00 5.68
2215 2435 2.413765 CTAAGCTCCTCCGCCGTC 59.586 66.667 0.00 0.00 0.00 4.79
2216 2436 3.471244 CTAAGCTCCTCCGCCGTCG 62.471 68.421 0.00 0.00 0.00 5.12
2223 2443 4.124351 CTCCGCCGTCGCCAAGTA 62.124 66.667 0.00 0.00 0.00 2.24
2224 2444 4.424566 TCCGCCGTCGCCAAGTAC 62.425 66.667 0.00 0.00 0.00 2.73
2225 2445 4.728102 CCGCCGTCGCCAAGTACA 62.728 66.667 0.00 0.00 0.00 2.90
2226 2446 2.735478 CGCCGTCGCCAAGTACAA 60.735 61.111 0.00 0.00 0.00 2.41
2227 2447 2.726691 CGCCGTCGCCAAGTACAAG 61.727 63.158 0.00 0.00 0.00 3.16
2228 2448 3.023591 GCCGTCGCCAAGTACAAGC 62.024 63.158 0.00 0.00 0.00 4.01
2229 2449 1.374252 CCGTCGCCAAGTACAAGCT 60.374 57.895 0.00 0.00 0.00 3.74
2230 2450 1.352156 CCGTCGCCAAGTACAAGCTC 61.352 60.000 0.00 0.00 0.00 4.09
2231 2451 0.388649 CGTCGCCAAGTACAAGCTCT 60.389 55.000 0.00 0.00 0.00 4.09
2232 2452 1.351153 GTCGCCAAGTACAAGCTCTC 58.649 55.000 0.00 0.00 0.00 3.20
2233 2453 0.109272 TCGCCAAGTACAAGCTCTCG 60.109 55.000 0.00 0.00 0.00 4.04
2234 2454 1.687494 CGCCAAGTACAAGCTCTCGC 61.687 60.000 0.00 0.00 0.00 5.03
2235 2455 1.362406 GCCAAGTACAAGCTCTCGCC 61.362 60.000 0.00 0.00 36.60 5.54
2236 2456 1.078759 CCAAGTACAAGCTCTCGCCG 61.079 60.000 0.00 0.00 36.60 6.46
2237 2457 1.446272 AAGTACAAGCTCTCGCCGC 60.446 57.895 0.00 0.00 36.60 6.53
2238 2458 2.837371 AAGTACAAGCTCTCGCCGCC 62.837 60.000 0.00 0.00 36.60 6.13
2239 2459 3.378602 TACAAGCTCTCGCCGCCA 61.379 61.111 0.00 0.00 36.60 5.69
2240 2460 2.721167 TACAAGCTCTCGCCGCCAT 61.721 57.895 0.00 0.00 36.60 4.40
2241 2461 2.629050 TACAAGCTCTCGCCGCCATC 62.629 60.000 0.00 0.00 36.60 3.51
2242 2462 4.880537 AAGCTCTCGCCGCCATCG 62.881 66.667 0.00 0.00 36.60 3.84
2254 2474 4.857251 CCATCGGCAGTTACCTCC 57.143 61.111 0.00 0.00 0.00 4.30
2255 2475 2.212327 CCATCGGCAGTTACCTCCT 58.788 57.895 0.00 0.00 0.00 3.69
2256 2476 0.105039 CCATCGGCAGTTACCTCCTC 59.895 60.000 0.00 0.00 0.00 3.71
2257 2477 0.105039 CATCGGCAGTTACCTCCTCC 59.895 60.000 0.00 0.00 0.00 4.30
2258 2478 0.325296 ATCGGCAGTTACCTCCTCCA 60.325 55.000 0.00 0.00 0.00 3.86
2259 2479 1.218316 CGGCAGTTACCTCCTCCAC 59.782 63.158 0.00 0.00 0.00 4.02
2260 2480 1.258445 CGGCAGTTACCTCCTCCACT 61.258 60.000 0.00 0.00 0.00 4.00
2261 2481 0.250513 GGCAGTTACCTCCTCCACTG 59.749 60.000 0.00 0.00 39.79 3.66
2262 2482 3.842869 CAGTTACCTCCTCCACTGC 57.157 57.895 0.00 0.00 30.79 4.40
2263 2483 0.250513 CAGTTACCTCCTCCACTGCC 59.749 60.000 0.00 0.00 30.79 4.85
2264 2484 1.218316 GTTACCTCCTCCACTGCCG 59.782 63.158 0.00 0.00 0.00 5.69
2265 2485 2.656069 TTACCTCCTCCACTGCCGC 61.656 63.158 0.00 0.00 0.00 6.53
2266 2486 3.897681 TACCTCCTCCACTGCCGCA 62.898 63.158 0.00 0.00 0.00 5.69
2267 2487 4.463879 CCTCCTCCACTGCCGCAG 62.464 72.222 19.08 19.08 37.52 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.588252 CTTTTCCGAGTGGTGCACTG 59.412 55.000 17.98 1.87 45.44 3.66
74 75 1.602377 AGTGGCGTACTTGTCAAAAGC 59.398 47.619 0.00 0.00 35.67 3.51
105 106 9.823647 TTACCATTTTATTTTCTCTGTTTGCAA 57.176 25.926 0.00 0.00 0.00 4.08
150 152 2.163818 TCTTTGCCGAGTAGGTGTTG 57.836 50.000 0.00 0.00 43.70 3.33
151 153 2.922740 TTCTTTGCCGAGTAGGTGTT 57.077 45.000 0.00 0.00 43.70 3.32
170 172 8.257306 TCTCCTCTTTGTACTTTTTGCATTTTT 58.743 29.630 0.00 0.00 0.00 1.94
171 173 7.781056 TCTCCTCTTTGTACTTTTTGCATTTT 58.219 30.769 0.00 0.00 0.00 1.82
172 174 7.346751 TCTCCTCTTTGTACTTTTTGCATTT 57.653 32.000 0.00 0.00 0.00 2.32
173 175 6.959639 TCTCCTCTTTGTACTTTTTGCATT 57.040 33.333 0.00 0.00 0.00 3.56
174 176 6.959639 TTCTCCTCTTTGTACTTTTTGCAT 57.040 33.333 0.00 0.00 0.00 3.96
176 178 9.744468 TTATTTTCTCCTCTTTGTACTTTTTGC 57.256 29.630 0.00 0.00 0.00 3.68
264 292 6.967199 AGTGCTCTTTTACTTTCGTTCTTTTG 59.033 34.615 0.00 0.00 0.00 2.44
272 301 5.324697 GCCAATAGTGCTCTTTTACTTTCG 58.675 41.667 0.00 0.00 0.00 3.46
316 346 6.073369 CGTTGTCATAGTGTTTGATGAGTTG 58.927 40.000 0.00 0.00 32.81 3.16
331 361 4.250464 GAGGGAACATTGACGTTGTCATA 58.750 43.478 0.00 0.00 42.40 2.15
345 375 2.596851 GCTGAGGCCTGAGGGAACA 61.597 63.158 21.61 4.54 33.58 3.18
347 377 0.030705 ATAGCTGAGGCCTGAGGGAA 60.031 55.000 21.61 0.00 39.73 3.97
350 380 1.664873 CGATAGCTGAGGCCTGAGG 59.335 63.158 21.61 6.60 39.73 3.86
365 395 2.283529 ACGAGTCCCAAGTGGCGAT 61.284 57.895 0.00 0.00 0.00 4.58
366 396 2.915659 ACGAGTCCCAAGTGGCGA 60.916 61.111 0.00 0.00 0.00 5.54
367 397 2.738521 CACGAGTCCCAAGTGGCG 60.739 66.667 0.00 0.00 32.68 5.69
380 410 1.971167 GGCAAATGGCTGGACACGA 60.971 57.895 0.00 0.00 44.01 4.35
404 434 5.527582 AGTGCAACACTAGTCAAAAACCTAG 59.472 40.000 0.00 0.00 43.46 3.02
437 467 1.967319 AGAACTCGGCAAAAAGAGCA 58.033 45.000 0.00 0.00 37.99 4.26
438 468 3.045688 CAAAGAACTCGGCAAAAAGAGC 58.954 45.455 0.00 0.00 37.99 4.09
490 521 6.126863 AGGCTATTTTGCTATACCATGCTA 57.873 37.500 0.00 0.00 0.00 3.49
493 524 7.390027 AGACTAGGCTATTTTGCTATACCATG 58.610 38.462 0.00 0.00 0.00 3.66
494 525 7.560796 AGACTAGGCTATTTTGCTATACCAT 57.439 36.000 0.00 0.00 0.00 3.55
512 543 8.084684 TGTGATGTAGCATTGCTAATAGACTAG 58.915 37.037 19.55 0.00 43.07 2.57
513 544 7.867909 GTGTGATGTAGCATTGCTAATAGACTA 59.132 37.037 19.55 2.41 43.07 2.59
514 545 6.703607 GTGTGATGTAGCATTGCTAATAGACT 59.296 38.462 19.55 1.97 43.07 3.24
516 547 6.820335 AGTGTGATGTAGCATTGCTAATAGA 58.180 36.000 19.55 5.36 43.07 1.98
537 569 6.088483 TGTCTCGTTAATAGCACGTTTTAGTG 59.912 38.462 0.00 0.00 44.47 2.74
538 570 6.151691 TGTCTCGTTAATAGCACGTTTTAGT 58.848 36.000 0.00 0.00 38.81 2.24
542 574 5.407387 ACAATGTCTCGTTAATAGCACGTTT 59.593 36.000 0.00 0.00 38.81 3.60
544 576 4.491676 ACAATGTCTCGTTAATAGCACGT 58.508 39.130 0.00 0.00 38.81 4.49
555 587 8.547967 AAATAATTCAGTGTACAATGTCTCGT 57.452 30.769 21.56 7.79 0.00 4.18
582 614 5.359576 TGTAGTGTGTTGAAAAATGGCTCTT 59.640 36.000 0.00 0.00 0.00 2.85
583 615 4.887071 TGTAGTGTGTTGAAAAATGGCTCT 59.113 37.500 0.00 0.00 0.00 4.09
593 625 7.348956 CAAATATCACGTTGTAGTGTGTTGAA 58.651 34.615 0.00 0.00 42.40 2.69
597 629 4.143200 CGCAAATATCACGTTGTAGTGTGT 60.143 41.667 0.00 0.00 42.40 3.72
603 635 2.094575 GTGGCGCAAATATCACGTTGTA 59.905 45.455 10.83 0.00 0.00 2.41
605 637 1.130373 AGTGGCGCAAATATCACGTTG 59.870 47.619 10.83 0.00 35.50 4.10
607 639 2.303163 TAGTGGCGCAAATATCACGT 57.697 45.000 10.83 0.05 35.50 4.49
609 641 3.181530 CGCTATAGTGGCGCAAATATCAC 60.182 47.826 8.24 6.05 45.83 3.06
621 654 3.120649 GGAAAAATAGCGCGCTATAGTGG 60.121 47.826 43.81 0.00 38.20 4.00
623 656 2.729882 CGGAAAAATAGCGCGCTATAGT 59.270 45.455 43.81 33.47 38.20 2.12
713 747 5.006746 GGACCGACACAAATAATAGAGCTTG 59.993 44.000 0.00 0.00 0.00 4.01
723 757 5.504337 CGTTTTCTTTGGACCGACACAAATA 60.504 40.000 0.00 0.00 36.16 1.40
778 812 1.293924 GATGATGGAGTTCGTGGCTG 58.706 55.000 0.00 0.00 0.00 4.85
912 954 3.670625 TGTGTAAGAAGGAACGGAATGG 58.329 45.455 0.00 0.00 0.00 3.16
915 957 5.026038 TCTTTGTGTAAGAAGGAACGGAA 57.974 39.130 0.00 0.00 39.90 4.30
1107 1172 0.532573 GTGGGCTGATCGTCTTCTCA 59.467 55.000 0.00 0.00 0.00 3.27
1130 1195 4.683781 GCAAATCTGGAGATGACGAGTATC 59.316 45.833 0.00 0.00 34.49 2.24
1185 1250 0.250553 TCCCAGCAAACGTAACAGGG 60.251 55.000 6.54 6.54 36.15 4.45
1200 1265 1.065491 CCGGTGATCTCAATGTTCCCA 60.065 52.381 0.00 0.00 0.00 4.37
1203 1268 1.398390 GCACCGGTGATCTCAATGTTC 59.602 52.381 38.30 11.71 0.00 3.18
1209 1274 1.296392 CTTGGCACCGGTGATCTCA 59.704 57.895 38.30 24.14 0.00 3.27
1250 1315 0.245539 CGGAACTGAGCCCTTAACGA 59.754 55.000 0.00 0.00 0.00 3.85
1251 1316 0.245539 TCGGAACTGAGCCCTTAACG 59.754 55.000 0.00 0.00 0.00 3.18
1252 1317 2.011540 CTCGGAACTGAGCCCTTAAC 57.988 55.000 0.00 0.00 0.00 2.01
1278 1343 1.306642 CGAGCTAGTGGTGACCGACT 61.307 60.000 10.67 10.67 0.00 4.18
1284 1349 1.725557 GATCGGCGAGCTAGTGGTGA 61.726 60.000 19.09 0.00 0.00 4.02
1287 1352 2.136196 GAGGATCGGCGAGCTAGTGG 62.136 65.000 25.16 0.00 0.00 4.00
1362 1434 3.811722 ATATGTTGAACGGCATATGCG 57.188 42.857 21.04 17.65 43.26 4.73
1397 1471 5.294552 CCTAAGTAGCTAATCTTTGTGGCAC 59.705 44.000 11.55 11.55 0.00 5.01
1398 1472 5.045869 ACCTAAGTAGCTAATCTTTGTGGCA 60.046 40.000 0.00 0.00 0.00 4.92
1459 1542 2.932614 GCAGTACGATTCAAGAGCATGT 59.067 45.455 0.00 0.00 0.00 3.21
1469 1552 4.946784 ACAAATCAAGGCAGTACGATTC 57.053 40.909 0.00 0.00 0.00 2.52
1605 1813 4.141756 ACAATCCAAAATGACAGCAACCAA 60.142 37.500 0.00 0.00 0.00 3.67
1618 1826 7.111247 ACAGAAGTGATGAAACAATCCAAAA 57.889 32.000 0.00 0.00 0.00 2.44
1648 1858 0.035056 AATCGAAGGTGCCTCAAGGG 60.035 55.000 0.00 0.00 35.18 3.95
1649 1859 1.089920 CAATCGAAGGTGCCTCAAGG 58.910 55.000 0.00 0.00 38.53 3.61
1663 1873 7.867445 AAGCTACCAACAAAAATTACAATCG 57.133 32.000 0.00 0.00 0.00 3.34
1700 1910 3.889538 AGGTACCTCAAGAAAAACCAAGC 59.110 43.478 9.21 0.00 0.00 4.01
1806 2016 8.283699 TGTTTAGTTTGTAACCTGCTAAAGTT 57.716 30.769 0.00 0.00 33.87 2.66
1891 2106 5.002468 GCATGAAACACGACATTGTAATTCG 59.998 40.000 0.00 0.00 38.73 3.34
1899 2114 5.048504 AGAGAAATGCATGAAACACGACATT 60.049 36.000 0.00 0.00 0.00 2.71
1924 2139 3.123050 TGGTCATAATCACAGCGAATCG 58.877 45.455 0.00 0.00 0.00 3.34
2019 2239 3.378013 GCGACATGTTTTTCGGGAC 57.622 52.632 0.00 0.00 35.73 4.46
2021 2241 1.154301 CCGCGACATGTTTTTCGGG 60.154 57.895 8.23 14.67 45.06 5.14
2022 2242 1.154301 CCCGCGACATGTTTTTCGG 60.154 57.895 8.23 16.78 35.73 4.30
2023 2243 1.795962 GCCCGCGACATGTTTTTCG 60.796 57.895 8.23 0.00 38.31 3.46
2024 2244 0.109319 ATGCCCGCGACATGTTTTTC 60.109 50.000 8.23 0.00 0.00 2.29
2025 2245 1.132262 CTATGCCCGCGACATGTTTTT 59.868 47.619 20.47 1.41 0.00 1.94
2026 2246 0.732571 CTATGCCCGCGACATGTTTT 59.267 50.000 20.47 2.03 0.00 2.43
2027 2247 0.392461 ACTATGCCCGCGACATGTTT 60.392 50.000 20.47 5.75 0.00 2.83
2028 2248 0.392461 AACTATGCCCGCGACATGTT 60.392 50.000 20.47 18.02 0.00 2.71
2029 2249 0.810031 GAACTATGCCCGCGACATGT 60.810 55.000 20.47 0.00 0.00 3.21
2030 2250 0.809636 TGAACTATGCCCGCGACATG 60.810 55.000 20.47 13.95 0.00 3.21
2031 2251 0.106708 ATGAACTATGCCCGCGACAT 59.893 50.000 8.23 13.95 0.00 3.06
2032 2252 0.107897 AATGAACTATGCCCGCGACA 60.108 50.000 8.23 5.84 0.00 4.35
2033 2253 0.304705 CAATGAACTATGCCCGCGAC 59.695 55.000 8.23 0.00 0.00 5.19
2034 2254 0.813610 CCAATGAACTATGCCCGCGA 60.814 55.000 8.23 0.00 0.00 5.87
2035 2255 1.095228 ACCAATGAACTATGCCCGCG 61.095 55.000 0.00 0.00 0.00 6.46
2036 2256 1.961793 TACCAATGAACTATGCCCGC 58.038 50.000 0.00 0.00 0.00 6.13
2037 2257 5.514274 AAATTACCAATGAACTATGCCCG 57.486 39.130 0.00 0.00 0.00 6.13
2038 2258 5.523552 GCAAAATTACCAATGAACTATGCCC 59.476 40.000 0.00 0.00 0.00 5.36
2039 2259 6.105333 TGCAAAATTACCAATGAACTATGCC 58.895 36.000 0.00 0.00 0.00 4.40
2040 2260 7.593875 TTGCAAAATTACCAATGAACTATGC 57.406 32.000 0.00 0.00 0.00 3.14
2071 2291 3.369546 AATGCTTTTGAAACCACGAGG 57.630 42.857 0.00 0.00 42.21 4.63
2072 2292 4.358851 TGAAATGCTTTTGAAACCACGAG 58.641 39.130 1.76 0.00 0.00 4.18
2073 2293 4.377839 TGAAATGCTTTTGAAACCACGA 57.622 36.364 1.76 0.00 0.00 4.35
2074 2294 5.163913 TGTTTGAAATGCTTTTGAAACCACG 60.164 36.000 25.92 0.00 43.80 4.94
2075 2295 6.175712 TGTTTGAAATGCTTTTGAAACCAC 57.824 33.333 25.92 11.75 43.80 4.16
2076 2296 6.808008 TTGTTTGAAATGCTTTTGAAACCA 57.192 29.167 25.92 17.97 43.80 3.67
2077 2297 7.431960 GGATTTGTTTGAAATGCTTTTGAAACC 59.568 33.333 25.92 15.93 43.80 3.27
2078 2298 7.431960 GGGATTTGTTTGAAATGCTTTTGAAAC 59.568 33.333 23.80 23.80 44.33 2.78
2079 2299 7.338957 AGGGATTTGTTTGAAATGCTTTTGAAA 59.661 29.630 1.76 4.04 0.00 2.69
2080 2300 6.827762 AGGGATTTGTTTGAAATGCTTTTGAA 59.172 30.769 1.76 0.00 0.00 2.69
2081 2301 6.355747 AGGGATTTGTTTGAAATGCTTTTGA 58.644 32.000 1.76 0.00 0.00 2.69
2082 2302 6.293571 GGAGGGATTTGTTTGAAATGCTTTTG 60.294 38.462 1.76 0.00 0.00 2.44
2083 2303 5.764686 GGAGGGATTTGTTTGAAATGCTTTT 59.235 36.000 0.00 0.00 0.00 2.27
2084 2304 5.308014 GGAGGGATTTGTTTGAAATGCTTT 58.692 37.500 0.00 0.00 0.00 3.51
2085 2305 4.561326 CGGAGGGATTTGTTTGAAATGCTT 60.561 41.667 0.00 0.00 0.00 3.91
2086 2306 3.056607 CGGAGGGATTTGTTTGAAATGCT 60.057 43.478 0.00 0.00 0.00 3.79
2087 2307 3.253230 CGGAGGGATTTGTTTGAAATGC 58.747 45.455 0.00 0.00 0.00 3.56
2088 2308 3.253230 GCGGAGGGATTTGTTTGAAATG 58.747 45.455 0.00 0.00 0.00 2.32
2089 2309 2.233676 GGCGGAGGGATTTGTTTGAAAT 59.766 45.455 0.00 0.00 0.00 2.17
2090 2310 1.616374 GGCGGAGGGATTTGTTTGAAA 59.384 47.619 0.00 0.00 0.00 2.69
2091 2311 1.253100 GGCGGAGGGATTTGTTTGAA 58.747 50.000 0.00 0.00 0.00 2.69
2092 2312 0.610785 GGGCGGAGGGATTTGTTTGA 60.611 55.000 0.00 0.00 0.00 2.69
2093 2313 1.604147 GGGGCGGAGGGATTTGTTTG 61.604 60.000 0.00 0.00 0.00 2.93
2094 2314 1.304962 GGGGCGGAGGGATTTGTTT 60.305 57.895 0.00 0.00 0.00 2.83
2095 2315 2.359011 GGGGCGGAGGGATTTGTT 59.641 61.111 0.00 0.00 0.00 2.83
2096 2316 4.109675 CGGGGCGGAGGGATTTGT 62.110 66.667 0.00 0.00 0.00 2.83
2097 2317 4.109675 ACGGGGCGGAGGGATTTG 62.110 66.667 0.00 0.00 0.00 2.32
2098 2318 3.793888 GACGGGGCGGAGGGATTT 61.794 66.667 0.00 0.00 0.00 2.17
2099 2319 4.798682 AGACGGGGCGGAGGGATT 62.799 66.667 0.00 0.00 0.00 3.01
2100 2320 4.798682 AAGACGGGGCGGAGGGAT 62.799 66.667 0.00 0.00 0.00 3.85
2103 2323 3.372554 GAAGAAGACGGGGCGGAGG 62.373 68.421 0.00 0.00 0.00 4.30
2104 2324 2.184579 GAAGAAGACGGGGCGGAG 59.815 66.667 0.00 0.00 0.00 4.63
2105 2325 3.387947 GGAAGAAGACGGGGCGGA 61.388 66.667 0.00 0.00 0.00 5.54
2106 2326 3.372554 GAGGAAGAAGACGGGGCGG 62.373 68.421 0.00 0.00 0.00 6.13
2107 2327 2.184579 GAGGAAGAAGACGGGGCG 59.815 66.667 0.00 0.00 0.00 6.13
2108 2328 2.585153 GGAGGAAGAAGACGGGGC 59.415 66.667 0.00 0.00 0.00 5.80
2109 2329 1.946475 GACGGAGGAAGAAGACGGGG 61.946 65.000 0.00 0.00 0.00 5.73
2110 2330 1.511768 GACGGAGGAAGAAGACGGG 59.488 63.158 0.00 0.00 0.00 5.28
2111 2331 1.511768 GGACGGAGGAAGAAGACGG 59.488 63.158 0.00 0.00 0.00 4.79
2112 2332 1.136984 CGGACGGAGGAAGAAGACG 59.863 63.158 0.00 0.00 0.00 4.18
2113 2333 0.170784 GACGGACGGAGGAAGAAGAC 59.829 60.000 0.00 0.00 0.00 3.01
2114 2334 1.303799 CGACGGACGGAGGAAGAAGA 61.304 60.000 0.00 0.00 38.46 2.87
2115 2335 1.136984 CGACGGACGGAGGAAGAAG 59.863 63.158 0.00 0.00 38.46 2.85
2116 2336 2.986306 GCGACGGACGGAGGAAGAA 61.986 63.158 1.66 0.00 42.83 2.52
2117 2337 3.437795 GCGACGGACGGAGGAAGA 61.438 66.667 1.66 0.00 42.83 2.87
2118 2338 4.493747 GGCGACGGACGGAGGAAG 62.494 72.222 1.66 0.00 42.83 3.46
2140 2360 4.838152 CACCGTCCCCTGGCGATG 62.838 72.222 0.00 0.00 0.00 3.84
2160 2380 3.869272 CGAATCACGCAGCTGGGC 61.869 66.667 28.90 12.37 34.51 5.36
2169 2389 2.280186 GGCCCCTAGCGAATCACG 60.280 66.667 0.00 0.00 45.17 4.35
2170 2390 2.280186 CGGCCCCTAGCGAATCAC 60.280 66.667 0.00 0.00 45.17 3.06
2171 2391 3.546543 CCGGCCCCTAGCGAATCA 61.547 66.667 0.00 0.00 45.17 2.57
2172 2392 4.990553 GCCGGCCCCTAGCGAATC 62.991 72.222 18.11 0.00 45.17 2.52
2185 2405 4.899239 CTTAGCTGGGCTCGCCGG 62.899 72.222 0.00 0.00 40.44 6.13
2187 2407 4.168291 AGCTTAGCTGGGCTCGCC 62.168 66.667 5.70 0.00 40.44 5.54
2188 2408 2.587473 GAGCTTAGCTGGGCTCGC 60.587 66.667 13.01 6.41 44.01 5.03
2191 2411 2.069430 GGAGGAGCTTAGCTGGGCT 61.069 63.158 13.01 13.75 39.88 5.19
2192 2412 2.508436 GGAGGAGCTTAGCTGGGC 59.492 66.667 13.01 0.00 39.88 5.36
2193 2413 2.818132 CGGAGGAGCTTAGCTGGG 59.182 66.667 13.01 0.00 39.88 4.45
2194 2414 2.107953 GCGGAGGAGCTTAGCTGG 59.892 66.667 13.01 0.00 39.88 4.85
2195 2415 2.107953 GGCGGAGGAGCTTAGCTG 59.892 66.667 13.01 0.00 39.88 4.24
2196 2416 3.532155 CGGCGGAGGAGCTTAGCT 61.532 66.667 6.37 6.37 43.88 3.32
2197 2417 3.776659 GACGGCGGAGGAGCTTAGC 62.777 68.421 13.24 0.00 37.29 3.09
2198 2418 2.413765 GACGGCGGAGGAGCTTAG 59.586 66.667 13.24 0.00 37.29 2.18
2199 2419 3.515286 CGACGGCGGAGGAGCTTA 61.515 66.667 13.24 0.00 37.29 3.09
2206 2426 4.124351 TACTTGGCGACGGCGGAG 62.124 66.667 15.06 18.05 41.24 4.63
2207 2427 4.424566 GTACTTGGCGACGGCGGA 62.425 66.667 15.06 7.01 41.24 5.54
2208 2428 4.728102 TGTACTTGGCGACGGCGG 62.728 66.667 15.06 13.94 41.24 6.13
2209 2429 2.726691 CTTGTACTTGGCGACGGCG 61.727 63.158 17.16 6.12 41.24 6.46
2210 2430 3.023591 GCTTGTACTTGGCGACGGC 62.024 63.158 15.43 15.43 38.90 5.68
2211 2431 1.352156 GAGCTTGTACTTGGCGACGG 61.352 60.000 0.00 0.00 0.00 4.79
2212 2432 0.388649 AGAGCTTGTACTTGGCGACG 60.389 55.000 0.00 0.00 0.00 5.12
2213 2433 1.351153 GAGAGCTTGTACTTGGCGAC 58.649 55.000 0.00 0.00 0.00 5.19
2214 2434 0.109272 CGAGAGCTTGTACTTGGCGA 60.109 55.000 0.00 0.00 0.00 5.54
2215 2435 2.363807 CGAGAGCTTGTACTTGGCG 58.636 57.895 0.00 0.00 0.00 5.69
2246 2466 1.218316 CGGCAGTGGAGGAGGTAAC 59.782 63.158 0.00 0.00 0.00 2.50
2247 2467 2.656069 GCGGCAGTGGAGGAGGTAA 61.656 63.158 0.00 0.00 0.00 2.85
2248 2468 3.075005 GCGGCAGTGGAGGAGGTA 61.075 66.667 0.00 0.00 0.00 3.08
2250 2470 4.463879 CTGCGGCAGTGGAGGAGG 62.464 72.222 21.60 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.