Multiple sequence alignment - TraesCS2A01G281700

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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 TraesCS2A01G281700 chr2A 100.000 7044 0 0 1 7044 470652836 470645793 0.000000e+00 13008.0
1 TraesCS2A01G281700 chr2A 89.404 151 15 1 2063 2213 79316158 79316009 9.330000e-44 189.0
2 TraesCS2A01G281700 chr2A 90.210 143 14 0 2063 2205 141506317 141506459 3.350000e-43 187.0
3 TraesCS2A01G281700 chr2D 93.637 4275 162 57 2502 6697 352766491 352762248 0.000000e+00 6287.0
4 TraesCS2A01G281700 chr2D 88.821 1789 88 31 316 2040 352768513 352766773 0.000000e+00 2093.0
5 TraesCS2A01G281700 chr2D 98.545 275 4 0 2214 2488 352766749 352766475 2.950000e-133 486.0
6 TraesCS2A01G281700 chr2D 83.974 312 18 5 6707 7018 352711576 352711297 3.240000e-68 270.0
7 TraesCS2A01G281700 chr2D 82.807 285 20 14 47 316 352768921 352768651 1.980000e-55 228.0
8 TraesCS2A01G281700 chr2D 89.474 152 16 0 2063 2214 79056320 79056169 7.210000e-45 193.0
9 TraesCS2A01G281700 chr2D 87.421 159 18 2 2058 2214 471216258 471216416 1.560000e-41 182.0
10 TraesCS2A01G281700 chr2B 87.579 2206 135 64 47 2184 418965781 418963647 0.000000e+00 2427.0
11 TraesCS2A01G281700 chr2B 92.262 1344 63 21 5690 7018 418956132 418954815 0.000000e+00 1868.0
12 TraesCS2A01G281700 chr2B 92.349 1307 75 14 4396 5688 418957468 418956173 0.000000e+00 1836.0
13 TraesCS2A01G281700 chr2B 92.725 701 40 7 3610 4300 418958309 418957610 0.000000e+00 1002.0
14 TraesCS2A01G281700 chr2B 93.431 274 17 1 2215 2488 418963161 418962889 8.510000e-109 405.0
15 TraesCS2A01G281700 chr2B 80.457 481 37 25 2502 2976 418962905 418962476 1.470000e-81 315.0
16 TraesCS2A01G281700 chr2B 82.022 178 20 8 3026 3201 418961000 418960833 2.650000e-29 141.0
17 TraesCS2A01G281700 chr3D 88.889 162 16 2 2055 2214 315480588 315480427 1.550000e-46 198.0
18 TraesCS2A01G281700 chr3D 97.368 38 0 1 7007 7044 6058248 6058212 5.900000e-06 63.9
19 TraesCS2A01G281700 chr7B 86.905 168 18 4 2064 2227 44939706 44939539 1.210000e-42 185.0
20 TraesCS2A01G281700 chr4D 87.821 156 17 2 2061 2214 74079508 74079353 1.560000e-41 182.0
21 TraesCS2A01G281700 chr3B 88.312 154 15 1 2055 2205 404830308 404830461 1.560000e-41 182.0
22 TraesCS2A01G281700 chr3B 93.023 43 1 2 7003 7044 809026646 809026687 2.120000e-05 62.1
23 TraesCS2A01G281700 chr3B 85.714 56 6 2 6989 7044 784100097 784100044 2.740000e-04 58.4
24 TraesCS2A01G281700 chr1B 95.349 43 0 2 7003 7044 668089468 668089427 4.560000e-07 67.6
25 TraesCS2A01G281700 chr7D 97.368 38 0 1 7007 7044 610780773 610780809 5.900000e-06 63.9
26 TraesCS2A01G281700 chr5B 95.122 41 1 1 7005 7044 299321534 299321574 5.900000e-06 63.9
27 TraesCS2A01G281700 chr4A 95.000 40 2 0 7005 7044 714331647 714331608 5.900000e-06 63.9
28 TraesCS2A01G281700 chr5A 95.000 40 1 1 7005 7044 386163002 386163040 2.120000e-05 62.1
29 TraesCS2A01G281700 chr1D 87.755 49 4 2 6998 7044 483867797 483867749 1.000000e-03 56.5


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 TraesCS2A01G281700 chr2A 470645793 470652836 7043 True 13008.0 13008 100.000000 1 7044 1 chr2A.!!$R2 7043
1 TraesCS2A01G281700 chr2D 352762248 352768921 6673 True 2273.5 6287 90.952500 47 6697 4 chr2D.!!$R3 6650
2 TraesCS2A01G281700 chr2B 418954815 418965781 10966 True 1142.0 2427 88.689286 47 7018 7 chr2B.!!$R1 6971

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
882 1074 0.031857 CAAGAGGAGAGATCGCGCAT 59.968 55.0 8.75 0.00 0.00 4.73 F
958 1150 0.251634 CAAGAAGGGGGAGACAGAGC 59.748 60.0 0.00 0.00 0.00 4.09 F
1611 1846 0.392461 TGGCCATTCTAGTGAACGCC 60.392 55.0 0.00 10.15 44.72 5.68 F
2981 3716 0.392461 GTTAGCGCCAGGGTGATGAA 60.392 55.0 2.29 0.00 0.00 2.57 F
3247 5393 0.884704 GTCAGTTGAGAAGCCGGCAA 60.885 55.0 31.54 11.17 0.00 4.52 F
4715 9268 0.250901 GCAGTTGGATCACCTGTGGT 60.251 55.0 0.00 0.00 35.62 4.16 F
5076 9634 0.985490 ACAGGATGAAGAGCCTCCCC 60.985 60.0 0.00 0.00 34.99 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2495 3203 0.179001 ACAGAACCCTTGTTTCCCCG 60.179 55.000 0.00 0.0 33.97 5.73 R
2667 3375 1.635487 AGAAAGAAGCCCCTATGTGCA 59.365 47.619 0.00 0.0 0.00 4.57 R
3075 5214 0.106015 ACCCTAACCCCGCGTATAGT 60.106 55.000 4.92 0.0 0.00 2.12 R
4428 8979 2.567169 AGGTGATTGACTCGATGGACAA 59.433 45.455 0.00 0.0 0.00 3.18 R
5161 9719 1.216678 TCCCCAGCTTTCAAACCAAGA 59.783 47.619 0.00 0.0 0.00 3.02 R
5725 10334 0.038599 TGTGAATGCATCCAGCCAGT 59.961 50.000 0.00 0.0 44.83 4.00 R
6124 10737 0.107263 TCTCCACAGCAACAGCAACA 60.107 50.000 0.00 0.0 0.00 3.33 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
17 18 3.998156 CCGTCCAAGTCTCCTCGA 58.002 61.111 0.00 0.00 0.00 4.04
18 19 1.803943 CCGTCCAAGTCTCCTCGAG 59.196 63.158 5.13 5.13 0.00 4.04
19 20 1.137825 CGTCCAAGTCTCCTCGAGC 59.862 63.158 6.99 0.00 0.00 5.03
20 21 1.309499 CGTCCAAGTCTCCTCGAGCT 61.309 60.000 6.99 0.00 0.00 4.09
21 22 0.454196 GTCCAAGTCTCCTCGAGCTC 59.546 60.000 6.99 2.73 0.00 4.09
22 23 1.027255 TCCAAGTCTCCTCGAGCTCG 61.027 60.000 30.03 30.03 41.45 5.03
23 24 1.309499 CCAAGTCTCCTCGAGCTCGT 61.309 60.000 33.33 11.70 40.80 4.18
24 25 1.370609 CAAGTCTCCTCGAGCTCGTA 58.629 55.000 33.33 19.74 40.80 3.43
25 26 1.329292 CAAGTCTCCTCGAGCTCGTAG 59.671 57.143 33.33 26.45 40.80 3.51
26 27 0.812412 AGTCTCCTCGAGCTCGTAGC 60.812 60.000 33.33 21.91 42.84 3.58
27 28 1.524165 TCTCCTCGAGCTCGTAGCC 60.524 63.158 33.33 0.00 43.77 3.93
28 29 2.887889 CTCCTCGAGCTCGTAGCCG 61.888 68.421 33.33 17.60 43.77 5.52
29 30 2.895865 CCTCGAGCTCGTAGCCGA 60.896 66.667 33.33 14.05 43.77 5.54
30 31 2.325166 CTCGAGCTCGTAGCCGAC 59.675 66.667 33.33 0.00 43.77 4.79
31 32 2.435410 TCGAGCTCGTAGCCGACA 60.435 61.111 33.33 10.92 43.77 4.35
32 33 2.277373 CGAGCTCGTAGCCGACAC 60.277 66.667 27.79 0.00 43.77 3.67
33 34 2.102553 GAGCTCGTAGCCGACACC 59.897 66.667 0.00 0.00 43.77 4.16
34 35 3.736482 GAGCTCGTAGCCGACACCG 62.736 68.421 0.00 0.00 43.77 4.94
35 36 3.807538 GCTCGTAGCCGACACCGA 61.808 66.667 0.00 0.00 38.40 4.69
36 37 2.403987 CTCGTAGCCGACACCGAG 59.596 66.667 0.00 0.00 38.40 4.63
37 38 2.359107 TCGTAGCCGACACCGAGT 60.359 61.111 0.00 0.00 38.40 4.18
38 39 2.202440 CGTAGCCGACACCGAGTG 60.202 66.667 2.92 2.92 39.75 3.51
39 40 2.506438 GTAGCCGACACCGAGTGC 60.506 66.667 4.23 0.00 36.98 4.40
40 41 4.111016 TAGCCGACACCGAGTGCG 62.111 66.667 4.23 8.28 36.98 5.34
72 73 1.617947 GCCGGATCTGACTTCCCACT 61.618 60.000 5.05 0.00 0.00 4.00
76 77 1.623834 GGATCTGACTTCCCACTCCCT 60.624 57.143 0.00 0.00 0.00 4.20
194 200 2.975536 CGACCGGCTAGGGTTTCA 59.024 61.111 0.00 0.00 46.96 2.69
199 205 0.254747 CCGGCTAGGGTTTCATCCAA 59.745 55.000 0.00 0.00 35.97 3.53
202 219 1.285078 GGCTAGGGTTTCATCCAAGGT 59.715 52.381 0.00 0.00 0.00 3.50
233 250 1.075600 GAGAGGGGGAGAGGACCTG 60.076 68.421 0.00 0.00 34.02 4.00
235 252 4.423209 AGGGGGAGAGGACCTGGC 62.423 72.222 0.00 0.00 32.26 4.85
246 263 3.163467 GAGGACCTGGCCGTAGTTATAT 58.837 50.000 0.00 0.00 0.00 0.86
250 267 4.157472 GGACCTGGCCGTAGTTATATACTC 59.843 50.000 0.00 0.00 38.33 2.59
366 521 3.799963 TGTAGTTATAAATCGTGCGCCTG 59.200 43.478 4.18 0.00 0.00 4.85
389 544 0.953960 GTAGCACACCCCGAACCTTG 60.954 60.000 0.00 0.00 0.00 3.61
404 564 6.071840 CCCGAACCTTGTGGATTACATAAAAA 60.072 38.462 0.00 0.00 39.48 1.94
422 582 4.976224 AAAAATAGTATTGACGTGGGCC 57.024 40.909 0.00 0.00 0.00 5.80
424 584 1.802553 ATAGTATTGACGTGGGCCCT 58.197 50.000 25.70 1.15 0.00 5.19
425 585 2.457813 TAGTATTGACGTGGGCCCTA 57.542 50.000 25.70 6.58 0.00 3.53
451 624 4.837972 CTGAAAGAGGGTAAGAAGGAAGG 58.162 47.826 0.00 0.00 34.07 3.46
476 649 1.591863 GCTAATCTCGCCACGTCCC 60.592 63.158 0.00 0.00 0.00 4.46
478 651 2.365095 CTAATCTCGCCACGTCCCCC 62.365 65.000 0.00 0.00 0.00 5.40
523 696 3.952811 AGCGGTTTTGCTCGTCTC 58.047 55.556 0.00 0.00 42.95 3.36
539 712 0.241213 TCTCGTCGCCAGAAACAGAG 59.759 55.000 0.00 0.00 0.00 3.35
541 714 0.318699 TCGTCGCCAGAAACAGAGTG 60.319 55.000 0.00 0.00 0.00 3.51
543 716 0.033504 GTCGCCAGAAACAGAGTGGA 59.966 55.000 0.00 0.00 32.60 4.02
544 717 0.318441 TCGCCAGAAACAGAGTGGAG 59.682 55.000 0.00 0.00 32.60 3.86
545 718 1.294659 CGCCAGAAACAGAGTGGAGC 61.295 60.000 0.00 0.00 32.60 4.70
568 743 2.625973 AAGCTCGATCTCCAGCAGCG 62.626 60.000 9.94 0.00 38.18 5.18
601 776 2.164422 TGGTCTCTCTATGTTGTGCTCG 59.836 50.000 0.00 0.00 0.00 5.03
692 871 2.637383 GCCCTTGTCGTCGTCTCCT 61.637 63.158 0.00 0.00 0.00 3.69
716 895 2.033675 TCGCGTTGACAGTTTAGACTCA 59.966 45.455 5.77 0.00 32.54 3.41
736 915 6.686630 ACTCACAGAGATAAGAACAAGACAG 58.313 40.000 0.31 0.00 33.32 3.51
815 994 2.504681 CGACGCAGCAATTTGGCC 60.505 61.111 0.00 0.00 0.00 5.36
816 995 2.964978 GACGCAGCAATTTGGCCT 59.035 55.556 3.32 0.00 0.00 5.19
817 996 1.643868 CGACGCAGCAATTTGGCCTA 61.644 55.000 3.32 0.00 0.00 3.93
818 997 0.099436 GACGCAGCAATTTGGCCTAG 59.901 55.000 3.32 0.00 0.00 3.02
819 998 0.322456 ACGCAGCAATTTGGCCTAGA 60.322 50.000 3.32 0.00 0.00 2.43
820 999 0.099436 CGCAGCAATTTGGCCTAGAC 59.901 55.000 3.32 0.00 0.00 2.59
882 1074 0.031857 CAAGAGGAGAGATCGCGCAT 59.968 55.000 8.75 0.00 0.00 4.73
958 1150 0.251634 CAAGAAGGGGGAGACAGAGC 59.748 60.000 0.00 0.00 0.00 4.09
967 1159 3.663815 GAGACAGAGCGGGGGAGGA 62.664 68.421 0.00 0.00 0.00 3.71
968 1160 3.462678 GACAGAGCGGGGGAGGAC 61.463 72.222 0.00 0.00 0.00 3.85
992 1184 4.388499 GCGCCGAGTTTGGGGAGA 62.388 66.667 0.00 0.00 44.30 3.71
993 1185 2.125512 CGCCGAGTTTGGGGAGAG 60.126 66.667 0.00 0.00 44.30 3.20
1167 1359 0.988832 ACCCCTCGCAAGGTAATCAA 59.011 50.000 0.00 0.00 41.59 2.57
1178 1370 4.501571 GCAAGGTAATCAATCCTCTCGCTA 60.502 45.833 0.00 0.00 33.09 4.26
1218 1411 6.091437 GCGCTCTTGTTTCTACTACTTTCTA 58.909 40.000 0.00 0.00 0.00 2.10
1332 1547 2.224205 GAAAAACTCGCGTCGCTCCC 62.224 60.000 16.36 0.00 0.00 4.30
1386 1603 0.535780 TGGATGCCGATTCCATCTGC 60.536 55.000 0.00 0.00 38.35 4.26
1408 1628 1.545136 TCGTTTGTGCGGATACTGGTA 59.455 47.619 0.00 0.00 0.00 3.25
1433 1660 1.336440 CCAGATGCTCGATCGTCTCTT 59.664 52.381 15.94 3.84 36.04 2.85
1434 1661 2.604373 CCAGATGCTCGATCGTCTCTTC 60.604 54.545 15.94 11.99 36.04 2.87
1435 1662 2.290367 CAGATGCTCGATCGTCTCTTCT 59.710 50.000 15.94 13.78 36.04 2.85
1436 1663 2.548057 AGATGCTCGATCGTCTCTTCTC 59.452 50.000 15.94 4.60 36.04 2.87
1437 1664 2.031258 TGCTCGATCGTCTCTTCTCT 57.969 50.000 15.94 0.00 0.00 3.10
1438 1665 1.937223 TGCTCGATCGTCTCTTCTCTC 59.063 52.381 15.94 0.00 0.00 3.20
1439 1666 2.210116 GCTCGATCGTCTCTTCTCTCT 58.790 52.381 15.94 0.00 0.00 3.10
1518 1753 1.768077 GTCCCTATCCTGCCTGCCT 60.768 63.158 0.00 0.00 0.00 4.75
1519 1754 1.767672 TCCCTATCCTGCCTGCCTG 60.768 63.158 0.00 0.00 0.00 4.85
1520 1755 2.112718 CCTATCCTGCCTGCCTGC 59.887 66.667 0.00 0.00 0.00 4.85
1521 1756 2.112718 CTATCCTGCCTGCCTGCC 59.887 66.667 0.00 0.00 0.00 4.85
1522 1757 2.367377 TATCCTGCCTGCCTGCCT 60.367 61.111 0.00 0.00 0.00 4.75
1523 1758 2.677765 CTATCCTGCCTGCCTGCCTG 62.678 65.000 0.00 0.00 0.00 4.85
1540 1775 0.740868 CTGCCATTCATGTCGACCGT 60.741 55.000 14.12 0.00 0.00 4.83
1541 1776 1.018752 TGCCATTCATGTCGACCGTG 61.019 55.000 14.12 12.16 0.00 4.94
1611 1846 0.392461 TGGCCATTCTAGTGAACGCC 60.392 55.000 0.00 10.15 44.72 5.68
1654 1889 6.519382 TGATTCTTGATATCAGTAGGCAGTG 58.481 40.000 5.39 0.00 0.00 3.66
1671 1906 4.320608 CAGTGGCACTGTTTTGGTTTAT 57.679 40.909 34.00 0.15 41.19 1.40
1712 1947 4.517075 AGGTTTGAAAGCTTCTAGCAAGTC 59.483 41.667 3.44 0.00 45.56 3.01
1744 1984 1.798813 CAGTACGTTCAACCCTTCAGC 59.201 52.381 0.00 0.00 0.00 4.26
1745 1985 0.788391 GTACGTTCAACCCTTCAGCG 59.212 55.000 0.00 0.00 0.00 5.18
1834 2074 2.885861 CCGTCCGGGACTCTCTTG 59.114 66.667 23.86 7.94 38.47 3.02
2045 2298 8.998989 GCTTTTGTTTTGTAAAAGAAGATTTGC 58.001 29.630 12.79 0.00 44.10 3.68
2073 2326 3.008157 TGCGTTAAATTGTACTCCCTCCA 59.992 43.478 0.00 0.00 0.00 3.86
2121 2374 8.818057 GGATATTTCAATATGGACTACATACGC 58.182 37.037 0.00 0.00 44.41 4.42
2124 2377 4.878439 TCAATATGGACTACATACGCACC 58.122 43.478 0.00 0.00 44.41 5.01
2125 2378 3.570926 ATATGGACTACATACGCACCG 57.429 47.619 0.00 0.00 44.41 4.94
2130 2383 2.538449 GGACTACATACGCACCGAAATG 59.462 50.000 0.00 0.00 33.06 2.32
2131 2384 3.441163 GACTACATACGCACCGAAATGA 58.559 45.455 10.10 0.00 31.99 2.57
2132 2385 3.184541 ACTACATACGCACCGAAATGAC 58.815 45.455 10.10 0.00 31.99 3.06
2144 2397 3.692101 ACCGAAATGACTGAACAAACACA 59.308 39.130 0.00 0.00 0.00 3.72
2145 2398 4.035017 CCGAAATGACTGAACAAACACAC 58.965 43.478 0.00 0.00 0.00 3.82
2146 2399 4.201910 CCGAAATGACTGAACAAACACACT 60.202 41.667 0.00 0.00 0.00 3.55
2150 2403 6.377327 AATGACTGAACAAACACACTAAGG 57.623 37.500 0.00 0.00 0.00 2.69
2151 2404 3.625764 TGACTGAACAAACACACTAAGGC 59.374 43.478 0.00 0.00 0.00 4.35
2152 2405 3.616219 ACTGAACAAACACACTAAGGCA 58.384 40.909 0.00 0.00 0.00 4.75
2156 2409 4.036262 TGAACAAACACACTAAGGCATGTC 59.964 41.667 0.00 0.00 0.00 3.06
2299 3007 4.664150 TCAACTTTTTGCCTAACTTGGG 57.336 40.909 0.00 0.00 32.17 4.12
2472 3180 5.336929 CCAATTCCATGCTGAATGTTCTCAA 60.337 40.000 0.00 0.00 35.21 3.02
2473 3181 4.771590 TTCCATGCTGAATGTTCTCAAC 57.228 40.909 0.00 0.00 34.11 3.18
2474 3182 3.753815 TCCATGCTGAATGTTCTCAACA 58.246 40.909 0.00 0.00 46.94 3.33
2475 3183 4.143543 TCCATGCTGAATGTTCTCAACAA 58.856 39.130 0.00 0.00 45.86 2.83
2476 3184 4.216902 TCCATGCTGAATGTTCTCAACAAG 59.783 41.667 0.00 0.00 45.86 3.16
2477 3185 4.482386 CATGCTGAATGTTCTCAACAAGG 58.518 43.478 0.00 0.00 45.86 3.61
2478 3186 3.819368 TGCTGAATGTTCTCAACAAGGA 58.181 40.909 0.00 0.00 45.86 3.36
2479 3187 4.401022 TGCTGAATGTTCTCAACAAGGAT 58.599 39.130 0.00 0.00 45.86 3.24
2480 3188 4.828939 TGCTGAATGTTCTCAACAAGGATT 59.171 37.500 0.00 0.00 45.86 3.01
2481 3189 5.048504 TGCTGAATGTTCTCAACAAGGATTC 60.049 40.000 0.00 0.00 45.86 2.52
2482 3190 5.182760 GCTGAATGTTCTCAACAAGGATTCT 59.817 40.000 0.00 0.00 45.86 2.40
2483 3191 6.564709 TGAATGTTCTCAACAAGGATTCTG 57.435 37.500 0.00 0.00 45.86 3.02
2484 3192 6.064060 TGAATGTTCTCAACAAGGATTCTGT 58.936 36.000 0.00 0.00 45.86 3.41
2485 3193 6.547141 TGAATGTTCTCAACAAGGATTCTGTT 59.453 34.615 0.00 0.00 45.86 3.16
2486 3194 6.566197 ATGTTCTCAACAAGGATTCTGTTC 57.434 37.500 0.00 0.00 45.86 3.18
2487 3195 5.684704 TGTTCTCAACAAGGATTCTGTTCT 58.315 37.500 0.00 0.00 38.72 3.01
2488 3196 6.122277 TGTTCTCAACAAGGATTCTGTTCTT 58.878 36.000 0.00 0.00 38.72 2.52
2489 3197 6.603201 TGTTCTCAACAAGGATTCTGTTCTTT 59.397 34.615 0.00 0.00 38.72 2.52
2490 3198 7.122650 TGTTCTCAACAAGGATTCTGTTCTTTT 59.877 33.333 0.00 0.00 38.72 2.27
2491 3199 7.264373 TCTCAACAAGGATTCTGTTCTTTTC 57.736 36.000 0.00 0.00 0.00 2.29
2492 3200 7.056635 TCTCAACAAGGATTCTGTTCTTTTCT 58.943 34.615 0.00 0.00 0.00 2.52
2493 3201 7.557719 TCTCAACAAGGATTCTGTTCTTTTCTT 59.442 33.333 0.00 0.00 0.00 2.52
2494 3202 7.483307 TCAACAAGGATTCTGTTCTTTTCTTG 58.517 34.615 0.00 0.00 37.12 3.02
2495 3203 5.836347 ACAAGGATTCTGTTCTTTTCTTGC 58.164 37.500 0.00 0.00 35.22 4.01
2496 3204 4.756084 AGGATTCTGTTCTTTTCTTGCG 57.244 40.909 0.00 0.00 0.00 4.85
2497 3205 3.503748 AGGATTCTGTTCTTTTCTTGCGG 59.496 43.478 0.00 0.00 0.00 5.69
2498 3206 3.366374 GGATTCTGTTCTTTTCTTGCGGG 60.366 47.826 0.00 0.00 0.00 6.13
2499 3207 1.604604 TCTGTTCTTTTCTTGCGGGG 58.395 50.000 0.00 0.00 0.00 5.73
2500 3208 1.142060 TCTGTTCTTTTCTTGCGGGGA 59.858 47.619 0.00 0.00 0.00 4.81
2501 3209 1.953686 CTGTTCTTTTCTTGCGGGGAA 59.046 47.619 0.00 0.00 0.00 3.97
2649 3357 1.341080 CAGAGCCCCCAAAACACAAT 58.659 50.000 0.00 0.00 0.00 2.71
2662 3370 7.305474 CCCAAAACACAATCACTTGTATCTAC 58.695 38.462 0.00 0.00 43.76 2.59
2663 3371 7.174946 CCCAAAACACAATCACTTGTATCTACT 59.825 37.037 0.00 0.00 43.76 2.57
2664 3372 9.214957 CCAAAACACAATCACTTGTATCTACTA 57.785 33.333 0.00 0.00 43.76 1.82
2795 3508 4.221482 GCATTTCCCACCTGAGAAGAAATT 59.779 41.667 0.00 0.00 35.53 1.82
2805 3518 6.038714 CACCTGAGAAGAAATTATTAGCACCC 59.961 42.308 0.00 0.00 0.00 4.61
2932 3645 7.041098 CCAAGTTAGCATGGATTAGGACATAAC 60.041 40.741 0.00 0.00 39.12 1.89
2981 3716 0.392461 GTTAGCGCCAGGGTGATGAA 60.392 55.000 2.29 0.00 0.00 2.57
3075 5214 9.267084 GTATTTTTGCACTTCCCTAAAATTTGA 57.733 29.630 7.97 0.00 32.65 2.69
3081 5220 8.276252 TGCACTTCCCTAAAATTTGACTATAC 57.724 34.615 0.00 0.00 0.00 1.47
3089 5228 2.994186 ATTTGACTATACGCGGGGTT 57.006 45.000 12.47 0.00 0.00 4.11
3134 5280 1.396543 GACTTGCACGACTAGCGACG 61.397 60.000 12.46 8.02 44.57 5.12
3228 5374 6.466308 TTCATGAACTCGTGATAACAACAG 57.534 37.500 3.38 0.00 41.09 3.16
3232 5378 4.982295 TGAACTCGTGATAACAACAGTCAG 59.018 41.667 0.00 0.00 0.00 3.51
3247 5393 0.884704 GTCAGTTGAGAAGCCGGCAA 60.885 55.000 31.54 11.17 0.00 4.52
3325 5471 6.147164 CGGTAATGTTTGTACAATCTGTGTCT 59.853 38.462 9.56 0.00 41.98 3.41
3337 5483 4.552166 ATCTGTGTCTTTGGTTTTCACG 57.448 40.909 0.00 0.00 32.55 4.35
3343 5489 4.911610 GTGTCTTTGGTTTTCACGATCATG 59.088 41.667 0.00 0.00 0.00 3.07
3488 5634 8.947940 CGATTCAGTCAAACAAGTTTTAAGAAG 58.052 33.333 0.00 0.00 0.00 2.85
3512 5658 6.070824 AGTGCCAATGTAATTCCTTTTTAGGG 60.071 38.462 0.00 0.00 31.22 3.53
3549 5852 9.886132 GGTAACTAGATAATCAAACCTTTCTGA 57.114 33.333 0.00 0.00 0.00 3.27
3558 5884 6.824305 ATCAAACCTTTCTGATACTGTTGG 57.176 37.500 0.00 0.00 30.43 3.77
3652 8148 9.898152 TTACATCATCATATAGGTTCAACACAA 57.102 29.630 0.00 0.00 0.00 3.33
3733 8230 7.880160 AATAGCTGATACCATGCTTTGTAAA 57.120 32.000 0.00 0.00 38.15 2.01
3903 8401 5.163784 CCTTGCTGATACTGTTGAGACATTG 60.164 44.000 0.00 0.00 34.72 2.82
4428 8979 4.442707 ACCTAGGCCTGATATCATTGGAT 58.557 43.478 17.99 5.20 37.55 3.41
4467 9018 6.627087 TCACCTTTCTAGGATCTTGTCAAT 57.373 37.500 0.00 0.00 45.05 2.57
4493 9044 4.083431 GCATCTTCACATCACTGATATGCC 60.083 45.833 9.64 0.00 35.67 4.40
4511 9062 4.932268 TGCCGACCTTTAAGTAAATTCG 57.068 40.909 7.50 7.50 33.70 3.34
4617 9170 4.083003 TGTGGAACTGATTATTTTCACGCC 60.083 41.667 0.00 0.00 38.04 5.68
4619 9172 3.442273 GGAACTGATTATTTTCACGCCCA 59.558 43.478 0.00 0.00 0.00 5.36
4715 9268 0.250901 GCAGTTGGATCACCTGTGGT 60.251 55.000 0.00 0.00 35.62 4.16
4907 9465 1.859427 CTGCAGTGACATGGCCACAC 61.859 60.000 8.16 12.86 37.01 3.82
4908 9466 1.601759 GCAGTGACATGGCCACACT 60.602 57.895 19.09 19.09 44.15 3.55
4909 9467 1.174712 GCAGTGACATGGCCACACTT 61.175 55.000 21.53 7.65 41.93 3.16
5034 9592 3.837146 AGACATCTGACACATTCCTCACT 59.163 43.478 0.00 0.00 0.00 3.41
5076 9634 0.985490 ACAGGATGAAGAGCCTCCCC 60.985 60.000 0.00 0.00 34.99 4.81
5160 9718 2.806745 GCTTGCAGAGTGTGTTGGACTA 60.807 50.000 0.00 0.00 0.00 2.59
5161 9719 3.668447 CTTGCAGAGTGTGTTGGACTAT 58.332 45.455 0.00 0.00 0.00 2.12
5184 9742 1.063266 TGGTTTGAAAGCTGGGGAACT 60.063 47.619 8.67 0.00 0.00 3.01
5195 9753 3.008485 AGCTGGGGAACTAAGAAACTCTG 59.992 47.826 0.00 0.00 0.00 3.35
5205 9763 3.933861 AAGAAACTCTGTGAACTGGGT 57.066 42.857 0.00 0.00 0.00 4.51
5265 9823 5.426509 ACCTCCTGAATGTGTAATCTCATCA 59.573 40.000 0.00 0.00 0.00 3.07
5266 9824 6.100859 ACCTCCTGAATGTGTAATCTCATCAT 59.899 38.462 0.00 0.00 0.00 2.45
5267 9825 6.649973 CCTCCTGAATGTGTAATCTCATCATC 59.350 42.308 0.00 0.00 0.00 2.92
5302 9860 8.620416 TGTTTGGCACATTGATCTGTATATAAC 58.380 33.333 0.00 0.00 39.30 1.89
5321 9879 8.716674 ATATAACGAGGAGGACAAGGTTTATA 57.283 34.615 0.00 0.00 0.00 0.98
5358 9916 7.253422 GCTCAACAGCTATACAATTGAACATT 58.747 34.615 13.59 0.00 43.09 2.71
5398 9956 4.394920 TGCAACTGAAGAACGAAAAACTCT 59.605 37.500 0.00 0.00 0.00 3.24
5423 9981 3.608474 CGTAAACTGTTTTACCTGCAGCC 60.608 47.826 11.48 0.00 42.90 4.85
5434 9995 1.331214 CCTGCAGCCAAAGAAAGGAA 58.669 50.000 8.66 0.00 0.00 3.36
5442 10003 5.045872 CAGCCAAAGAAAGGAAAACTCAAG 58.954 41.667 0.00 0.00 0.00 3.02
5506 10069 4.263331 CCAGTCCTAAAAGCCTTCCAACTA 60.263 45.833 0.00 0.00 0.00 2.24
5602 10165 6.935771 GCATCAGAGATGTCCAATATCTTCTT 59.064 38.462 8.60 0.00 35.14 2.52
5661 10229 8.100791 TGTAACTCTGGTTTATACTTGCTGATT 58.899 33.333 0.00 0.00 36.92 2.57
5688 10256 4.701956 ACTTATCTTTGCAAATCCGGTG 57.298 40.909 13.23 0.00 0.00 4.94
5694 10301 5.461032 TCTTTGCAAATCCGGTGTAATTT 57.539 34.783 13.23 0.00 0.00 1.82
5695 10302 5.226396 TCTTTGCAAATCCGGTGTAATTTG 58.774 37.500 13.23 17.68 42.88 2.32
5703 10310 4.209307 TCCGGTGTAATTTGCACTCATA 57.791 40.909 15.73 0.00 37.07 2.15
5725 10334 2.906389 AGAAGTGCCCTCTTGTATGACA 59.094 45.455 0.00 0.00 0.00 3.58
5800 10409 1.153208 GCACCATCTCCAGGAGCAG 60.153 63.158 12.26 6.31 41.59 4.24
5926 10535 2.356780 GGTCGACGACAAGGGGGAT 61.357 63.158 27.77 0.00 33.68 3.85
6055 10664 5.118664 CAGTACCGTATGACAAAACTCTGTG 59.881 44.000 0.00 0.00 0.00 3.66
6056 10665 4.330944 ACCGTATGACAAAACTCTGTGA 57.669 40.909 0.00 0.00 0.00 3.58
6059 10668 6.100004 ACCGTATGACAAAACTCTGTGATAG 58.900 40.000 0.00 0.00 27.84 2.08
6099 10712 6.225981 ACATTATCTTTTTGCTCATTCCCC 57.774 37.500 0.00 0.00 0.00 4.81
6110 10723 3.267812 TGCTCATTCCCCATCTTCTTCTT 59.732 43.478 0.00 0.00 0.00 2.52
6117 10730 5.843019 TCCCCATCTTCTTCTTAAGTTGT 57.157 39.130 1.63 0.00 0.00 3.32
6124 10737 5.437060 TCTTCTTCTTAAGTTGTGGTTGCT 58.563 37.500 1.63 0.00 0.00 3.91
6167 10780 2.752030 CTCTGTGGGGAGGACTAATGA 58.248 52.381 0.00 0.00 0.00 2.57
6168 10781 3.107601 CTCTGTGGGGAGGACTAATGAA 58.892 50.000 0.00 0.00 0.00 2.57
6247 10860 2.812591 GCGATGAGAATGATGATGCCTT 59.187 45.455 0.00 0.00 0.00 4.35
6342 10955 3.817647 GCTCTGGAACACTGTCATCTTTT 59.182 43.478 0.00 0.00 0.00 2.27
6359 10972 5.250235 TCTTTTGCCGTTATGTTTGACAA 57.750 34.783 0.00 0.00 0.00 3.18
6443 11056 0.036875 GGCTAGACCAAGGTGCAAGT 59.963 55.000 0.00 0.00 38.86 3.16
6478 11091 2.969950 CCCCCTCGTCCATCTATACAAA 59.030 50.000 0.00 0.00 0.00 2.83
6561 11193 7.481275 TGGATTTTGCATTTGAAAGAAGTTC 57.519 32.000 0.00 0.00 36.70 3.01
6569 11201 5.759763 GCATTTGAAAGAAGTTCCAAATGGT 59.240 36.000 28.34 8.78 40.48 3.55
6690 11343 1.142936 CAGATGGGTGGATGGATGGA 58.857 55.000 0.00 0.00 0.00 3.41
6713 11366 1.673665 GGGAGGCAGCAACAGTGAG 60.674 63.158 0.00 0.00 0.00 3.51
6756 11416 1.289160 AGATGCCAGTGCCCTTCTTA 58.711 50.000 0.00 0.00 36.33 2.10
6832 11492 5.508224 GCAGATGCACAACTTTTACGTTATC 59.492 40.000 0.00 0.00 41.59 1.75
6834 11494 6.519761 CAGATGCACAACTTTTACGTTATCAC 59.480 38.462 0.00 0.00 0.00 3.06
6836 11496 5.981174 TGCACAACTTTTACGTTATCACTC 58.019 37.500 0.00 0.00 0.00 3.51
6837 11497 5.756347 TGCACAACTTTTACGTTATCACTCT 59.244 36.000 0.00 0.00 0.00 3.24
6838 11498 6.924612 TGCACAACTTTTACGTTATCACTCTA 59.075 34.615 0.00 0.00 0.00 2.43
6839 11499 7.438757 TGCACAACTTTTACGTTATCACTCTAA 59.561 33.333 0.00 0.00 0.00 2.10
6840 11500 8.277713 GCACAACTTTTACGTTATCACTCTAAA 58.722 33.333 0.00 0.00 0.00 1.85
6889 11550 2.289565 GCTCATTAGGTGGTTACAGCC 58.710 52.381 0.00 0.00 46.03 4.85
6896 11557 6.384595 TCATTAGGTGGTTACAGCCTTACATA 59.615 38.462 2.63 0.00 46.03 2.29
6902 11563 4.196193 GGTTACAGCCTTACATACATGCA 58.804 43.478 0.00 0.00 0.00 3.96
6903 11564 4.273480 GGTTACAGCCTTACATACATGCAG 59.727 45.833 0.00 0.00 0.00 4.41
6904 11565 2.292267 ACAGCCTTACATACATGCAGC 58.708 47.619 0.00 0.00 0.00 5.25
6905 11566 2.092753 ACAGCCTTACATACATGCAGCT 60.093 45.455 0.00 0.00 0.00 4.24
6906 11567 3.134623 ACAGCCTTACATACATGCAGCTA 59.865 43.478 0.00 0.00 0.00 3.32
6907 11568 3.744942 CAGCCTTACATACATGCAGCTAG 59.255 47.826 0.00 0.00 0.00 3.42
6908 11569 2.481952 GCCTTACATACATGCAGCTAGC 59.518 50.000 6.62 6.62 45.96 3.42
6951 11612 3.999001 GGTACAAGTGCTACCCTACAAAC 59.001 47.826 0.00 0.00 0.00 2.93
6954 11615 4.134563 ACAAGTGCTACCCTACAAACTTG 58.865 43.478 10.84 10.84 46.22 3.16
6964 11625 1.986378 CTACAAACTTGCGAGTCTCCG 59.014 52.381 7.17 0.00 34.21 4.63
6969 11630 1.248785 ACTTGCGAGTCTCCGGCTAA 61.249 55.000 0.00 0.00 0.00 3.09
7007 11668 0.254178 GGTGGACACAGCATGGAGAT 59.746 55.000 4.69 0.00 44.32 2.75
7009 11670 2.092968 GGTGGACACAGCATGGAGATAA 60.093 50.000 4.69 0.00 44.32 1.75
7010 11671 3.434167 GGTGGACACAGCATGGAGATAAT 60.434 47.826 4.69 0.00 44.32 1.28
7012 11673 5.368145 GTGGACACAGCATGGAGATAATAA 58.632 41.667 0.00 0.00 43.62 1.40
7013 11674 6.000219 GTGGACACAGCATGGAGATAATAAT 59.000 40.000 0.00 0.00 43.62 1.28
7017 11678 6.715280 ACACAGCATGGAGATAATAATAGGG 58.285 40.000 0.00 0.00 43.62 3.53
7018 11679 6.501805 ACACAGCATGGAGATAATAATAGGGA 59.498 38.462 0.00 0.00 43.62 4.20
7019 11680 7.046652 CACAGCATGGAGATAATAATAGGGAG 58.953 42.308 0.00 0.00 43.62 4.30
7020 11681 6.732862 ACAGCATGGAGATAATAATAGGGAGT 59.267 38.462 0.00 0.00 43.62 3.85
7021 11682 7.901322 ACAGCATGGAGATAATAATAGGGAGTA 59.099 37.037 0.00 0.00 43.62 2.59
7022 11683 8.200792 CAGCATGGAGATAATAATAGGGAGTAC 58.799 40.741 0.00 0.00 0.00 2.73
7023 11684 7.345914 AGCATGGAGATAATAATAGGGAGTACC 59.654 40.741 0.00 0.00 40.67 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.803943 CTCGAGGAGACTTGGACGG 59.196 63.158 3.91 0.00 44.43 4.79
1 2 1.137825 GCTCGAGGAGACTTGGACG 59.862 63.158 15.58 0.00 44.43 4.79
2 3 0.454196 GAGCTCGAGGAGACTTGGAC 59.546 60.000 15.58 0.00 44.43 4.02
3 4 1.027255 CGAGCTCGAGGAGACTTGGA 61.027 60.000 32.06 0.00 44.43 3.53
4 5 1.309499 ACGAGCTCGAGGAGACTTGG 61.309 60.000 40.58 9.20 44.43 3.61
5 6 1.329292 CTACGAGCTCGAGGAGACTTG 59.671 57.143 40.58 14.71 44.43 3.16
6 7 1.658994 CTACGAGCTCGAGGAGACTT 58.341 55.000 40.58 19.13 44.43 3.01
7 8 0.812412 GCTACGAGCTCGAGGAGACT 60.812 60.000 40.58 19.88 40.67 3.24
8 9 1.644913 GCTACGAGCTCGAGGAGAC 59.355 63.158 40.58 22.89 43.02 3.36
9 10 1.524165 GGCTACGAGCTCGAGGAGA 60.524 63.158 40.58 18.70 41.99 3.71
10 11 2.887889 CGGCTACGAGCTCGAGGAG 61.888 68.421 40.58 30.61 44.60 3.69
11 12 2.895865 CGGCTACGAGCTCGAGGA 60.896 66.667 40.58 23.40 44.60 3.71
12 13 2.895865 TCGGCTACGAGCTCGAGG 60.896 66.667 40.58 29.66 45.59 4.63
21 22 2.202440 CACTCGGTGTCGGCTACG 60.202 66.667 0.00 0.00 42.74 3.51
22 23 2.506438 GCACTCGGTGTCGGCTAC 60.506 66.667 6.02 0.00 35.75 3.58
23 24 4.111016 CGCACTCGGTGTCGGCTA 62.111 66.667 6.02 0.00 35.75 3.93
76 77 3.390521 ACTTCCTCGCATCGGCCA 61.391 61.111 2.24 0.00 36.38 5.36
194 200 4.096003 CCCGTGGCGACCTTGGAT 62.096 66.667 0.00 0.00 0.00 3.41
233 250 3.753272 TGACCGAGTATATAACTACGGCC 59.247 47.826 0.00 0.00 45.24 6.13
235 252 6.963796 AGTTTGACCGAGTATATAACTACGG 58.036 40.000 0.00 0.00 46.03 4.02
353 508 2.495366 TACGTCCAGGCGCACGATTT 62.495 55.000 22.58 5.12 39.38 2.17
354 509 2.884087 CTACGTCCAGGCGCACGATT 62.884 60.000 22.58 5.78 39.38 3.34
366 521 2.934570 TTCGGGGTGTGCTACGTCC 61.935 63.158 0.00 0.00 0.00 4.79
404 564 2.124411 AGGGCCCACGTCAATACTATT 58.876 47.619 27.56 0.00 0.00 1.73
408 568 0.538118 TGTAGGGCCCACGTCAATAC 59.462 55.000 27.56 16.18 0.00 1.89
411 571 3.065306 CTGTAGGGCCCACGTCAA 58.935 61.111 27.56 1.61 0.00 3.18
412 572 3.702048 GCTGTAGGGCCCACGTCA 61.702 66.667 27.56 15.62 0.00 4.35
413 573 3.391382 AGCTGTAGGGCCCACGTC 61.391 66.667 27.56 14.58 0.00 4.34
414 574 3.706373 CAGCTGTAGGGCCCACGT 61.706 66.667 27.56 5.74 0.00 4.49
415 575 2.463589 TTTCAGCTGTAGGGCCCACG 62.464 60.000 27.56 16.05 0.00 4.94
417 577 0.840288 TCTTTCAGCTGTAGGGCCCA 60.840 55.000 27.56 7.27 0.00 5.36
418 578 0.107459 CTCTTTCAGCTGTAGGGCCC 60.107 60.000 16.46 16.46 0.00 5.80
419 579 0.107459 CCTCTTTCAGCTGTAGGGCC 60.107 60.000 14.67 0.00 0.00 5.80
420 580 0.107459 CCCTCTTTCAGCTGTAGGGC 60.107 60.000 23.59 0.00 40.51 5.19
422 582 3.769844 TCTTACCCTCTTTCAGCTGTAGG 59.230 47.826 14.67 15.29 0.00 3.18
424 584 4.223032 CCTTCTTACCCTCTTTCAGCTGTA 59.777 45.833 14.67 0.00 0.00 2.74
425 585 3.008485 CCTTCTTACCCTCTTTCAGCTGT 59.992 47.826 14.67 0.00 0.00 4.40
451 624 1.666189 GTGGCGAGATTAGCTGGTTTC 59.334 52.381 0.00 0.00 34.52 2.78
476 649 2.911143 CTCATGGAGAACCCGGGG 59.089 66.667 27.92 12.73 37.93 5.73
478 651 2.190578 GGCTCATGGAGAACCCGG 59.809 66.667 0.00 0.00 37.93 5.73
483 656 2.903357 GAGGCGGCTCATGGAGAA 59.097 61.111 31.94 0.00 0.00 2.87
523 696 1.284982 CCACTCTGTTTCTGGCGACG 61.285 60.000 0.00 0.00 0.00 5.12
544 717 1.005340 CTGGAGATCGAGCTTTGTGC 58.995 55.000 3.92 0.00 43.29 4.57
545 718 1.005340 GCTGGAGATCGAGCTTTGTG 58.995 55.000 3.92 0.00 43.18 3.33
585 760 0.894835 TGGCGAGCACAACATAGAGA 59.105 50.000 0.00 0.00 0.00 3.10
601 776 4.996434 AGCACGCTGACAGGTGGC 62.996 66.667 19.37 13.77 34.76 5.01
685 860 1.066114 GTCAACGCGAGAAGGAGACG 61.066 60.000 15.93 0.00 0.00 4.18
692 871 3.047796 GTCTAAACTGTCAACGCGAGAA 58.952 45.455 15.93 0.00 0.00 2.87
716 895 5.011533 AGTGCTGTCTTGTTCTTATCTCTGT 59.988 40.000 0.00 0.00 0.00 3.41
736 915 0.734253 CTCCGCAGTCAGTGTAGTGC 60.734 60.000 10.58 10.58 41.50 4.40
882 1074 6.121776 TCTCCCAACAGCTCTGTAAATAAA 57.878 37.500 2.62 0.00 44.13 1.40
975 1167 4.388499 TCTCCCCAAACTCGGCGC 62.388 66.667 0.00 0.00 0.00 6.53
991 1183 0.183971 TCCGTCTCCATCTCCTCCTC 59.816 60.000 0.00 0.00 0.00 3.71
992 1184 0.106419 GTCCGTCTCCATCTCCTCCT 60.106 60.000 0.00 0.00 0.00 3.69
993 1185 0.395862 TGTCCGTCTCCATCTCCTCC 60.396 60.000 0.00 0.00 0.00 4.30
1178 1370 2.641559 GCAAGCAAGCAAGCGAGT 59.358 55.556 0.00 0.00 40.15 4.18
1218 1411 5.683876 AGACAGGAGCAAACATATACTGT 57.316 39.130 0.00 0.00 40.84 3.55
1337 1552 2.993471 GCCGGTGGTTCCAATGCTG 61.993 63.158 1.90 0.00 35.57 4.41
1386 1603 1.327460 CCAGTATCCGCACAAACGATG 59.673 52.381 0.00 0.00 34.06 3.84
1408 1628 0.383590 CGATCGAGCATCTGGTCTGT 59.616 55.000 10.26 0.00 40.17 3.41
1415 1635 2.548057 GAGAAGAGACGATCGAGCATCT 59.452 50.000 24.34 14.13 0.00 2.90
1518 1753 1.026182 GTCGACATGAATGGCAGGCA 61.026 55.000 11.55 0.00 34.77 4.75
1519 1754 1.718757 GGTCGACATGAATGGCAGGC 61.719 60.000 18.91 0.00 34.77 4.85
1520 1755 1.431488 CGGTCGACATGAATGGCAGG 61.431 60.000 18.91 0.00 34.77 4.85
1521 1756 0.740868 ACGGTCGACATGAATGGCAG 60.741 55.000 18.91 0.00 34.77 4.85
1522 1757 1.018752 CACGGTCGACATGAATGGCA 61.019 55.000 18.91 0.00 34.77 4.92
1523 1758 1.705337 CCACGGTCGACATGAATGGC 61.705 60.000 18.91 0.00 0.00 4.40
1524 1759 1.089481 CCCACGGTCGACATGAATGG 61.089 60.000 18.91 15.33 0.00 3.16
1525 1760 1.089481 CCCCACGGTCGACATGAATG 61.089 60.000 18.91 7.27 0.00 2.67
1584 1819 0.176680 CTAGAATGGCCACGACAGCT 59.823 55.000 8.16 1.51 0.00 4.24
1611 1846 0.625849 AACCTGGAAGTGGGCTATGG 59.374 55.000 0.00 0.00 0.00 2.74
1654 1889 4.037446 TCACTCATAAACCAAAACAGTGCC 59.963 41.667 0.00 0.00 31.69 5.01
1671 1906 2.158623 ACCTCCACTGCATTTTCACTCA 60.159 45.455 0.00 0.00 0.00 3.41
1712 1947 4.069304 TGAACGTACTGGGATTTTGGAAG 58.931 43.478 0.00 0.00 0.00 3.46
1744 1984 2.355756 CACAATTGATGCCTCCCTTACG 59.644 50.000 13.59 0.00 0.00 3.18
1745 1985 2.099756 GCACAATTGATGCCTCCCTTAC 59.900 50.000 13.59 0.00 37.08 2.34
1785 2025 4.124238 CGGTGGTCTAACAAGTGAAAAGA 58.876 43.478 0.00 0.00 0.00 2.52
1909 2149 8.179509 TGGGAGAGTTTAGTATAAGCTGATAC 57.820 38.462 12.81 12.81 33.23 2.24
2045 2298 4.493545 GGAGTACAATTTAACGCATCCACG 60.494 45.833 0.00 0.00 39.50 4.94
2104 2357 3.570975 TCGGTGCGTATGTAGTCCATATT 59.429 43.478 0.00 0.00 38.29 1.28
2116 2369 2.665649 TCAGTCATTTCGGTGCGTAT 57.334 45.000 0.00 0.00 0.00 3.06
2121 2374 4.035017 GTGTTTGTTCAGTCATTTCGGTG 58.965 43.478 0.00 0.00 0.00 4.94
2124 2377 4.908736 AGTGTGTTTGTTCAGTCATTTCG 58.091 39.130 0.00 0.00 0.00 3.46
2125 2378 6.912591 CCTTAGTGTGTTTGTTCAGTCATTTC 59.087 38.462 0.00 0.00 0.00 2.17
2130 2383 3.625764 TGCCTTAGTGTGTTTGTTCAGTC 59.374 43.478 0.00 0.00 0.00 3.51
2131 2384 3.616219 TGCCTTAGTGTGTTTGTTCAGT 58.384 40.909 0.00 0.00 0.00 3.41
2132 2385 4.036734 ACATGCCTTAGTGTGTTTGTTCAG 59.963 41.667 0.00 0.00 0.00 3.02
2144 2397 6.890268 TCGGATGTATATAGACATGCCTTAGT 59.110 38.462 21.65 0.00 43.19 2.24
2145 2398 7.334844 TCGGATGTATATAGACATGCCTTAG 57.665 40.000 21.65 10.93 43.19 2.18
2146 2399 7.712204 TTCGGATGTATATAGACATGCCTTA 57.288 36.000 21.65 8.68 43.19 2.69
2150 2403 7.484140 TCTGATTCGGATGTATATAGACATGC 58.516 38.462 17.40 18.18 42.82 4.06
2151 2404 9.860898 TTTCTGATTCGGATGTATATAGACATG 57.139 33.333 17.40 4.78 40.18 3.21
2193 2446 9.159254 ACTGGTCTCCATCAGTTCATAAATATA 57.841 33.333 0.00 0.00 40.91 0.86
2194 2447 8.038862 ACTGGTCTCCATCAGTTCATAAATAT 57.961 34.615 0.00 0.00 40.91 1.28
2195 2448 7.437713 ACTGGTCTCCATCAGTTCATAAATA 57.562 36.000 0.00 0.00 40.91 1.40
2196 2449 6.319048 ACTGGTCTCCATCAGTTCATAAAT 57.681 37.500 0.00 0.00 40.91 1.40
2197 2450 5.762179 ACTGGTCTCCATCAGTTCATAAA 57.238 39.130 0.00 0.00 40.91 1.40
2198 2451 6.384015 ACATACTGGTCTCCATCAGTTCATAA 59.616 38.462 1.24 0.00 43.19 1.90
2199 2452 5.899547 ACATACTGGTCTCCATCAGTTCATA 59.100 40.000 1.24 0.00 43.19 2.15
2200 2453 4.718774 ACATACTGGTCTCCATCAGTTCAT 59.281 41.667 1.24 0.00 43.19 2.57
2201 2454 4.096681 ACATACTGGTCTCCATCAGTTCA 58.903 43.478 1.24 0.00 43.19 3.18
2202 2455 4.744795 ACATACTGGTCTCCATCAGTTC 57.255 45.455 1.24 0.00 43.19 3.01
2204 2457 5.458595 TCATACATACTGGTCTCCATCAGT 58.541 41.667 0.00 0.00 45.10 3.41
2205 2458 6.602410 ATCATACATACTGGTCTCCATCAG 57.398 41.667 0.00 0.00 37.07 2.90
2206 2459 7.379059 AAATCATACATACTGGTCTCCATCA 57.621 36.000 0.00 0.00 30.82 3.07
2207 2460 9.429359 CTAAAATCATACATACTGGTCTCCATC 57.571 37.037 0.00 0.00 30.82 3.51
2208 2461 8.938883 ACTAAAATCATACATACTGGTCTCCAT 58.061 33.333 0.00 0.00 30.82 3.41
2209 2462 8.319057 ACTAAAATCATACATACTGGTCTCCA 57.681 34.615 0.00 0.00 0.00 3.86
2210 2463 7.873505 GGACTAAAATCATACATACTGGTCTCC 59.126 40.741 0.00 0.00 0.00 3.71
2212 2465 7.471539 CGGGACTAAAATCATACATACTGGTCT 60.472 40.741 0.00 0.00 0.00 3.85
2299 3007 4.211374 AGTTCAACACAGAAATAGACGTGC 59.789 41.667 0.00 0.00 32.53 5.34
2472 3180 5.506317 CGCAAGAAAAGAACAGAATCCTTGT 60.506 40.000 0.00 0.00 43.02 3.16
2473 3181 4.913924 CGCAAGAAAAGAACAGAATCCTTG 59.086 41.667 0.00 0.00 43.02 3.61
2474 3182 4.022849 CCGCAAGAAAAGAACAGAATCCTT 60.023 41.667 0.00 0.00 43.02 3.36
2475 3183 3.503748 CCGCAAGAAAAGAACAGAATCCT 59.496 43.478 0.00 0.00 43.02 3.24
2476 3184 3.366374 CCCGCAAGAAAAGAACAGAATCC 60.366 47.826 0.00 0.00 43.02 3.01
2477 3185 3.366374 CCCCGCAAGAAAAGAACAGAATC 60.366 47.826 0.00 0.00 43.02 2.52
2478 3186 2.558359 CCCCGCAAGAAAAGAACAGAAT 59.442 45.455 0.00 0.00 43.02 2.40
2479 3187 1.953686 CCCCGCAAGAAAAGAACAGAA 59.046 47.619 0.00 0.00 43.02 3.02
2480 3188 1.142060 TCCCCGCAAGAAAAGAACAGA 59.858 47.619 0.00 0.00 43.02 3.41
2481 3189 1.604604 TCCCCGCAAGAAAAGAACAG 58.395 50.000 0.00 0.00 43.02 3.16
2482 3190 2.060050 TTCCCCGCAAGAAAAGAACA 57.940 45.000 0.00 0.00 43.02 3.18
2483 3191 2.100087 TGTTTCCCCGCAAGAAAAGAAC 59.900 45.455 0.00 0.00 43.02 3.01
2484 3192 2.379972 TGTTTCCCCGCAAGAAAAGAA 58.620 42.857 0.00 0.00 43.02 2.52
2485 3193 2.060050 TGTTTCCCCGCAAGAAAAGA 57.940 45.000 0.00 0.00 43.02 2.52
2486 3194 2.545742 CCTTGTTTCCCCGCAAGAAAAG 60.546 50.000 5.93 0.00 43.29 2.27
2487 3195 1.410882 CCTTGTTTCCCCGCAAGAAAA 59.589 47.619 5.93 0.00 43.29 2.29
2488 3196 1.036707 CCTTGTTTCCCCGCAAGAAA 58.963 50.000 5.93 0.00 43.29 2.52
2489 3197 0.825840 CCCTTGTTTCCCCGCAAGAA 60.826 55.000 5.93 0.00 43.29 2.52
2490 3198 1.228429 CCCTTGTTTCCCCGCAAGA 60.228 57.895 5.93 0.00 43.29 3.02
2491 3199 1.112916 AACCCTTGTTTCCCCGCAAG 61.113 55.000 0.00 0.00 41.08 4.01
2492 3200 1.075896 AACCCTTGTTTCCCCGCAA 60.076 52.632 0.00 0.00 0.00 4.85
2493 3201 1.529713 GAACCCTTGTTTCCCCGCA 60.530 57.895 0.00 0.00 33.97 5.69
2494 3202 1.228459 AGAACCCTTGTTTCCCCGC 60.228 57.895 0.00 0.00 33.97 6.13
2495 3203 0.179001 ACAGAACCCTTGTTTCCCCG 60.179 55.000 0.00 0.00 33.97 5.73
2496 3204 1.961394 GAACAGAACCCTTGTTTCCCC 59.039 52.381 0.00 0.00 33.97 4.81
2497 3205 2.945456 AGAACAGAACCCTTGTTTCCC 58.055 47.619 0.00 0.00 33.97 3.97
2498 3206 3.502595 GCTAGAACAGAACCCTTGTTTCC 59.497 47.826 0.00 0.00 33.97 3.13
2499 3207 4.390264 AGCTAGAACAGAACCCTTGTTTC 58.610 43.478 0.00 0.00 33.97 2.78
2500 3208 4.103311 AGAGCTAGAACAGAACCCTTGTTT 59.897 41.667 0.00 0.00 33.97 2.83
2501 3209 3.648545 AGAGCTAGAACAGAACCCTTGTT 59.351 43.478 0.00 0.00 37.42 2.83
2649 3357 9.750125 CTATGTGCAAATAGTAGATACAAGTGA 57.250 33.333 14.89 0.00 0.00 3.41
2662 3370 3.825328 AGAAGCCCCTATGTGCAAATAG 58.175 45.455 16.00 16.00 0.00 1.73
2663 3371 3.951563 AGAAGCCCCTATGTGCAAATA 57.048 42.857 0.00 0.00 0.00 1.40
2664 3372 2.834638 AGAAGCCCCTATGTGCAAAT 57.165 45.000 0.00 0.00 0.00 2.32
2665 3373 2.603075 AAGAAGCCCCTATGTGCAAA 57.397 45.000 0.00 0.00 0.00 3.68
2666 3374 2.041620 AGAAAGAAGCCCCTATGTGCAA 59.958 45.455 0.00 0.00 0.00 4.08
2667 3375 1.635487 AGAAAGAAGCCCCTATGTGCA 59.365 47.619 0.00 0.00 0.00 4.57
2668 3376 2.426842 AGAAAGAAGCCCCTATGTGC 57.573 50.000 0.00 0.00 0.00 4.57
2795 3508 8.792633 GTTAATCAATGCTAATGGGTGCTAATA 58.207 33.333 0.00 0.00 0.00 0.98
2932 3645 7.568267 TTTATTCGAGAAGCGCTAATCATAG 57.432 36.000 12.05 1.18 40.61 2.23
2981 3716 0.771127 TAAACAGAGCTTGGGGCACT 59.229 50.000 0.00 0.00 44.79 4.40
3018 3753 0.694444 GAAGCCCTATCCCACCTCCA 60.694 60.000 0.00 0.00 0.00 3.86
3075 5214 0.106015 ACCCTAACCCCGCGTATAGT 60.106 55.000 4.92 0.00 0.00 2.12
3089 5228 4.485530 CCCCTACGGCCCACCCTA 62.486 72.222 0.00 0.00 0.00 3.53
3134 5280 6.494893 TGTATTCTCCATGCAACAACTAAC 57.505 37.500 0.00 0.00 0.00 2.34
3228 5374 0.884704 TTGCCGGCTTCTCAACTGAC 60.885 55.000 29.70 0.00 0.00 3.51
3232 5378 1.153958 GCATTGCCGGCTTCTCAAC 60.154 57.895 29.70 6.79 0.00 3.18
3325 5471 5.046529 CCAAACATGATCGTGAAAACCAAA 58.953 37.500 21.75 0.00 0.00 3.28
3337 5483 6.389091 TGCAGATAAAACACCAAACATGATC 58.611 36.000 0.00 0.00 0.00 2.92
3428 5574 2.182825 CTGAACACCGTATGTAGCGAC 58.817 52.381 0.00 0.00 42.31 5.19
3488 5634 6.071051 TCCCTAAAAAGGAATTACATTGGCAC 60.071 38.462 0.00 0.00 0.00 5.01
3512 5658 6.973229 TTATCTAGTTACCTTGGCGTTTTC 57.027 37.500 0.00 0.00 0.00 2.29
3801 8299 7.594351 TTAGAATGCAGAGTGACTATGAGAT 57.406 36.000 11.95 0.00 0.00 2.75
3903 8401 7.095649 GGTGCACTCAAAATTTTATTCTTGGAC 60.096 37.037 17.98 7.88 0.00 4.02
4239 8740 8.410912 GTTACCCTCTAGACAAACAAACAAAAT 58.589 33.333 0.00 0.00 0.00 1.82
4244 8745 5.618236 AGGTTACCCTCTAGACAAACAAAC 58.382 41.667 0.00 0.00 35.62 2.93
4266 8772 8.728337 TCAGAACTGAAATCATATCTTCCAAG 57.272 34.615 1.79 0.00 36.53 3.61
4428 8979 2.567169 AGGTGATTGACTCGATGGACAA 59.433 45.455 0.00 0.00 0.00 3.18
4467 9018 6.370718 GCATATCAGTGATGTGAAGATGCATA 59.629 38.462 28.20 0.32 43.17 3.14
4493 9044 7.298507 TCATTCCGAATTTACTTAAAGGTCG 57.701 36.000 9.21 9.21 36.87 4.79
4557 9110 8.375465 CAAATAAAGCTTATAACTTGCTGCAAC 58.625 33.333 11.69 0.00 37.11 4.17
4617 9170 7.860918 AGCAATTATAGTCAGATATGCATGG 57.139 36.000 10.16 0.00 35.11 3.66
4619 9172 9.736414 AAGAAGCAATTATAGTCAGATATGCAT 57.264 29.630 3.79 3.79 35.11 3.96
4715 9268 5.398236 AGCCTAACCTAGATGCTAGATTGA 58.602 41.667 0.00 0.00 0.00 2.57
4897 9454 5.829924 AGGAGAATATAAAAGTGTGGCCATG 59.170 40.000 9.72 0.00 0.00 3.66
4907 9465 9.699703 GGTGCTAACTAGAGGAGAATATAAAAG 57.300 37.037 0.00 0.00 0.00 2.27
4908 9466 8.648693 GGGTGCTAACTAGAGGAGAATATAAAA 58.351 37.037 0.00 0.00 0.00 1.52
4909 9467 7.787904 TGGGTGCTAACTAGAGGAGAATATAAA 59.212 37.037 0.00 0.00 0.00 1.40
5034 9592 5.620738 ACTTGGATAGAAGAAGCAGCATA 57.379 39.130 0.00 0.00 0.00 3.14
5160 9718 2.158325 TCCCCAGCTTTCAAACCAAGAT 60.158 45.455 0.00 0.00 0.00 2.40
5161 9719 1.216678 TCCCCAGCTTTCAAACCAAGA 59.783 47.619 0.00 0.00 0.00 3.02
5184 9742 4.654262 AGACCCAGTTCACAGAGTTTCTTA 59.346 41.667 0.00 0.00 0.00 2.10
5195 9753 1.971357 TCAGAGGAAGACCCAGTTCAC 59.029 52.381 0.00 0.00 37.41 3.18
5205 9763 4.033009 TGTATGGCTTCATCAGAGGAAGA 58.967 43.478 25.64 8.61 43.46 2.87
5289 9847 7.362229 CCTTGTCCTCCTCGTTATATACAGATC 60.362 44.444 0.00 0.00 0.00 2.75
5302 9860 5.593679 TCTTATAAACCTTGTCCTCCTCG 57.406 43.478 0.00 0.00 0.00 4.63
5358 9916 6.544197 TCAGTTGCAGATAAACCAGTTTACAA 59.456 34.615 5.16 3.28 37.80 2.41
5398 9956 4.378774 TGCAGGTAAAACAGTTTACGCTA 58.621 39.130 0.00 0.00 46.84 4.26
5423 9981 5.291858 GCAACCTTGAGTTTTCCTTTCTTTG 59.708 40.000 0.00 0.00 36.18 2.77
5442 10003 2.421314 GGCAACACCAAGGCAACC 59.579 61.111 0.00 0.00 38.86 3.77
5506 10069 1.203300 CCAACCCCCTTTTCCCTCATT 60.203 52.381 0.00 0.00 0.00 2.57
5602 10165 4.475381 TGTTTGTATATCTTGGGGGCACTA 59.525 41.667 0.00 0.00 0.00 2.74
5661 10229 6.260050 CCGGATTTGCAAAGATAAGTAAGCTA 59.740 38.462 18.19 0.00 0.00 3.32
5667 10235 4.079253 ACACCGGATTTGCAAAGATAAGT 58.921 39.130 18.19 8.23 0.00 2.24
5696 10303 3.902881 AGAGGGCACTTCTTATGAGTG 57.097 47.619 0.00 0.10 36.70 3.51
5703 10310 3.327757 TGTCATACAAGAGGGCACTTCTT 59.672 43.478 0.00 0.00 0.00 2.52
5725 10334 0.038599 TGTGAATGCATCCAGCCAGT 59.961 50.000 0.00 0.00 44.83 4.00
5926 10535 1.755395 CGTGATCACCCCCTCGGTA 60.755 63.158 20.03 0.00 46.14 4.02
6016 10625 0.899720 TACTGTTTGCGGGTAGGGAG 59.100 55.000 0.00 0.00 0.00 4.30
6017 10626 0.609662 GTACTGTTTGCGGGTAGGGA 59.390 55.000 0.00 0.00 0.00 4.20
6099 10712 6.016777 AGCAACCACAACTTAAGAAGAAGATG 60.017 38.462 10.09 2.24 35.83 2.90
6110 10723 2.098934 CAGCAACAGCAACCACAACTTA 59.901 45.455 0.00 0.00 0.00 2.24
6117 10730 1.141449 GCAACAGCAACAGCAACCA 59.859 52.632 0.00 0.00 0.00 3.67
6124 10737 0.107263 TCTCCACAGCAACAGCAACA 60.107 50.000 0.00 0.00 0.00 3.33
6247 10860 4.438200 GCAACCGTCAACAAGAAAGAAGAA 60.438 41.667 0.00 0.00 0.00 2.52
6342 10955 6.320494 AGTAAATTGTCAAACATAACGGCA 57.680 33.333 0.00 0.00 0.00 5.69
6371 10984 5.136105 AGAATGTTTCTCCACAAGAGCTTT 58.864 37.500 0.00 0.00 42.90 3.51
6384 10997 2.893489 GCCCAAGACCAAGAATGTTTCT 59.107 45.455 0.00 0.00 43.15 2.52
6387 11000 1.202879 TCGCCCAAGACCAAGAATGTT 60.203 47.619 0.00 0.00 0.00 2.71
6438 11051 3.532542 GGGAGTACCATCTACAACTTGC 58.467 50.000 0.00 0.00 39.85 4.01
6443 11056 2.688817 CGAGGGGGAGTACCATCTACAA 60.689 54.545 0.00 0.00 42.91 2.41
6478 11091 6.921307 CGAAGTTAAACCAAATTAAAGTGGCT 59.079 34.615 7.52 0.00 38.58 4.75
6515 11128 7.353525 TCCATTTGAGACATATTATGTTGGGT 58.646 34.615 17.10 3.58 45.03 4.51
6516 11129 7.822161 TCCATTTGAGACATATTATGTTGGG 57.178 36.000 17.10 9.67 45.03 4.12
6690 11343 3.334054 GTTGCTGCCTCCCTCCCT 61.334 66.667 0.00 0.00 0.00 4.20
6704 11357 6.293081 CCAAACTCACTATGTTCTCACTGTTG 60.293 42.308 0.00 0.00 0.00 3.33
6770 11430 6.901081 AGCTGGGATTTTATATGCTTTACC 57.099 37.500 0.00 0.00 0.00 2.85
6776 11436 6.003950 TCTGGTAAGCTGGGATTTTATATGC 58.996 40.000 0.00 0.00 0.00 3.14
6839 11499 1.856920 TCTGGTCCCCTTCCTGTTTTT 59.143 47.619 0.00 0.00 0.00 1.94
6840 11500 1.145119 GTCTGGTCCCCTTCCTGTTTT 59.855 52.381 0.00 0.00 0.00 2.43
6844 11504 1.133809 TTGGTCTGGTCCCCTTCCTG 61.134 60.000 0.00 0.00 0.00 3.86
6845 11505 0.178831 ATTGGTCTGGTCCCCTTCCT 60.179 55.000 0.00 0.00 0.00 3.36
6846 11506 0.704664 AATTGGTCTGGTCCCCTTCC 59.295 55.000 0.00 0.00 0.00 3.46
6848 11508 0.704664 GGAATTGGTCTGGTCCCCTT 59.295 55.000 0.00 0.00 0.00 3.95
6849 11509 1.562672 CGGAATTGGTCTGGTCCCCT 61.563 60.000 0.00 0.00 0.00 4.79
6889 11550 2.156504 GCGCTAGCTGCATGTATGTAAG 59.843 50.000 21.32 0.29 43.06 2.34
6903 11564 1.149148 GTTATTGGCCTAGCGCTAGC 58.851 55.000 34.26 27.80 45.58 3.42
6904 11565 1.070134 TGGTTATTGGCCTAGCGCTAG 59.930 52.381 33.03 33.03 37.74 3.42
6905 11566 1.124780 TGGTTATTGGCCTAGCGCTA 58.875 50.000 17.75 17.75 37.74 4.26
6906 11567 0.463833 GTGGTTATTGGCCTAGCGCT 60.464 55.000 17.26 17.26 37.74 5.92
6907 11568 1.444917 GGTGGTTATTGGCCTAGCGC 61.445 60.000 3.32 0.00 0.00 5.92
6908 11569 0.818040 GGGTGGTTATTGGCCTAGCG 60.818 60.000 3.32 0.00 0.00 4.26
6909 11570 0.467474 GGGGTGGTTATTGGCCTAGC 60.467 60.000 3.32 0.00 0.00 3.42
6910 11571 0.179029 CGGGGTGGTTATTGGCCTAG 60.179 60.000 3.32 0.00 0.00 3.02
6936 11597 1.463444 CGCAAGTTTGTAGGGTAGCAC 59.537 52.381 0.00 0.00 0.00 4.40
6951 11612 0.108804 TTTAGCCGGAGACTCGCAAG 60.109 55.000 5.05 0.00 0.00 4.01
6954 11615 2.726832 ATATTTAGCCGGAGACTCGC 57.273 50.000 5.05 0.00 0.00 5.03
7009 11670 8.907050 AGATGAGTTCTAGGTACTCCCTATTAT 58.093 37.037 17.72 7.97 45.00 1.28
7010 11671 8.290463 AGATGAGTTCTAGGTACTCCCTATTA 57.710 38.462 17.72 4.58 45.00 0.98
7012 11673 6.790177 AGATGAGTTCTAGGTACTCCCTAT 57.210 41.667 17.72 8.99 45.00 2.57


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

AutoCloner maintained by Alex Coulton.