Multiple sequence alignment - TraesCS3D01G283300

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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 TraesCS3D01G283300 chr3D 100.000 3979 0 0 1 3979 391601522 391597544 0.000000e+00 7348
1 TraesCS3D01G283300 chr3D 89.080 174 19 0 1078 1251 378036174 378036001 2.410000e-52 217
2 TraesCS3D01G283300 chr3D 81.857 237 38 5 2278 2512 378035092 378034859 1.130000e-45 195
3 TraesCS3D01G283300 chr3D 88.983 118 12 1 1660 1776 126294825 126294942 1.150000e-30 145
4 TraesCS3D01G283300 chr3D 81.212 165 21 7 1084 1240 44822921 44823083 1.500000e-24 124
5 TraesCS3D01G283300 chr3D 85.047 107 11 5 2351 2454 44823298 44823402 1.960000e-18 104
6 TraesCS3D01G283300 chr3A 90.537 2050 85 59 1970 3936 511754893 511752870 0.000000e+00 2610
7 TraesCS3D01G283300 chr3A 88.645 1048 47 30 649 1663 511756005 511754997 0.000000e+00 1210
8 TraesCS3D01G283300 chr3A 86.364 330 18 11 259 580 511756523 511756213 6.370000e-88 335
9 TraesCS3D01G283300 chr3A 88.571 175 20 0 1077 1251 502167845 502167671 3.110000e-51 213
10 TraesCS3D01G283300 chr3A 84.343 198 31 0 2278 2475 502166722 502166525 1.130000e-45 195
11 TraesCS3D01G283300 chr3A 90.511 137 8 5 85 220 511756650 511756518 4.090000e-40 176
12 TraesCS3D01G283300 chr3B 95.251 1074 33 11 1929 2985 508710067 508708995 0.000000e+00 1685
13 TraesCS3D01G283300 chr3B 89.701 1204 39 22 490 1663 508711322 508710174 0.000000e+00 1458
14 TraesCS3D01G283300 chr3B 91.826 991 46 19 2994 3970 508708954 508707985 0.000000e+00 1349
15 TraesCS3D01G283300 chr3B 91.729 399 11 9 98 493 508713420 508713041 5.850000e-148 534
16 TraesCS3D01G283300 chr3B 89.080 174 19 0 1078 1251 492613158 492612985 2.410000e-52 217
17 TraesCS3D01G283300 chr3B 82.456 228 35 5 2278 2503 492612055 492611831 1.130000e-45 195
18 TraesCS3D01G283300 chr3B 94.495 109 5 1 1772 1880 508710179 508710072 2.460000e-37 167
19 TraesCS3D01G283300 chr3B 86.992 123 12 3 1656 1776 621152245 621152125 6.940000e-28 135
20 TraesCS3D01G283300 chr1B 77.837 943 172 32 2050 2970 582544257 582545184 2.090000e-152 549
21 TraesCS3D01G283300 chr1B 86.528 193 24 2 1060 1251 582543980 582544171 1.120000e-50 211
22 TraesCS3D01G283300 chr1A 78.270 925 151 38 2050 2933 529664649 529665564 2.090000e-152 549
23 TraesCS3D01G283300 chr1A 86.977 215 21 7 1039 1251 529664303 529664512 6.650000e-58 235
24 TraesCS3D01G283300 chr1D 78.674 694 128 18 2252 2933 431426552 431427237 1.010000e-120 444
25 TraesCS3D01G283300 chr1D 89.349 169 18 0 1083 1251 431426032 431426200 3.110000e-51 213
26 TraesCS3D01G283300 chr1D 86.667 135 14 4 2050 2182 431426320 431426452 3.200000e-31 147
27 TraesCS3D01G283300 chr4D 95.041 121 5 1 1656 1775 31718937 31718817 5.250000e-44 189
28 TraesCS3D01G283300 chrUn 89.344 122 12 1 1656 1776 22143587 22143708 6.890000e-33 152
29 TraesCS3D01G283300 chr2D 89.655 116 12 0 1660 1775 550250225 550250110 8.910000e-32 148
30 TraesCS3D01G283300 chr2D 86.154 130 16 2 1653 1781 189521484 189521612 5.360000e-29 139
31 TraesCS3D01G283300 chr6A 87.903 124 13 2 1653 1775 9468758 9468880 1.150000e-30 145
32 TraesCS3D01G283300 chr2B 88.235 119 13 1 1660 1777 6740052 6740170 1.490000e-29 141
33 TraesCS3D01G283300 chr2A 87.805 123 12 3 1655 1775 687561841 687561962 1.490000e-29 141


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 TraesCS3D01G283300 chr3D 391597544 391601522 3978 True 7348.00 7348 100.000000 1 3979 1 chr3D.!!$R1 3978
1 TraesCS3D01G283300 chr3D 378034859 378036174 1315 True 206.00 217 85.468500 1078 2512 2 chr3D.!!$R2 1434
2 TraesCS3D01G283300 chr3A 511752870 511756650 3780 True 1082.75 2610 89.014250 85 3936 4 chr3A.!!$R2 3851
3 TraesCS3D01G283300 chr3A 502166525 502167845 1320 True 204.00 213 86.457000 1077 2475 2 chr3A.!!$R1 1398
4 TraesCS3D01G283300 chr3B 508707985 508713420 5435 True 1038.60 1685 92.600400 98 3970 5 chr3B.!!$R3 3872
5 TraesCS3D01G283300 chr3B 492611831 492613158 1327 True 206.00 217 85.768000 1078 2503 2 chr3B.!!$R2 1425
6 TraesCS3D01G283300 chr1B 582543980 582545184 1204 False 380.00 549 82.182500 1060 2970 2 chr1B.!!$F1 1910
7 TraesCS3D01G283300 chr1A 529664303 529665564 1261 False 392.00 549 82.623500 1039 2933 2 chr1A.!!$F1 1894
8 TraesCS3D01G283300 chr1D 431426032 431427237 1205 False 268.00 444 84.896667 1083 2933 3 chr1D.!!$F1 1850

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
184 185 0.101759 GAACTTGCCATGCATGCGAT 59.898 50.000 21.69 4.99 38.76 4.58 F
553 2294 0.178533 TACCTGTATTTTCGGCCGGG 59.821 55.000 27.83 18.25 0.00 5.73 F
837 2730 0.248134 GCGTGACTCGTGCTACCTAG 60.248 60.000 0.00 0.00 42.13 3.02 F
1230 3136 1.227823 CTTCACCAACGGCCTCACA 60.228 57.895 0.00 0.00 0.00 3.58 F
1773 3990 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1754 3971 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40 R
1755 3972 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17 R
1762 3979 0.173708 CTGCAAGTACTCCCTCCGTC 59.826 60.000 0.00 0.00 0.00 4.79 R
2657 5060 1.199327 GTGTTCATCTGGTCGACGAGA 59.801 52.381 28.89 28.89 35.23 4.04 R
3540 6018 0.034616 CCCTCCTTCCTGATGCGATC 59.965 60.000 0.00 0.00 0.00 3.69 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
26 27 4.659111 AAAAGGGTAAAAACCGACTTGG 57.341 40.909 0.00 0.00 46.41 3.61
27 28 2.281539 AGGGTAAAAACCGACTTGGG 57.718 50.000 0.00 0.00 44.64 4.12
28 29 1.496001 AGGGTAAAAACCGACTTGGGT 59.504 47.619 0.00 0.00 42.41 4.51
29 30 2.710471 AGGGTAAAAACCGACTTGGGTA 59.290 45.455 0.00 0.00 35.58 3.69
30 31 3.076621 GGGTAAAAACCGACTTGGGTAG 58.923 50.000 0.00 0.00 35.58 3.18
31 32 3.076621 GGTAAAAACCGACTTGGGTAGG 58.923 50.000 0.00 0.00 35.58 3.18
32 33 3.244526 GGTAAAAACCGACTTGGGTAGGA 60.245 47.826 2.56 0.00 35.58 2.94
33 34 3.801307 AAAAACCGACTTGGGTAGGAT 57.199 42.857 2.56 0.00 35.58 3.24
34 35 4.914177 AAAAACCGACTTGGGTAGGATA 57.086 40.909 2.56 0.00 35.58 2.59
35 36 3.900966 AAACCGACTTGGGTAGGATAC 57.099 47.619 2.56 0.00 35.58 2.24
36 37 2.537633 ACCGACTTGGGTAGGATACA 57.462 50.000 2.56 0.00 45.43 2.29
37 38 2.823959 ACCGACTTGGGTAGGATACAA 58.176 47.619 2.56 0.00 45.43 2.41
38 39 3.175594 ACCGACTTGGGTAGGATACAAA 58.824 45.455 2.56 0.00 45.43 2.83
39 40 3.583966 ACCGACTTGGGTAGGATACAAAA 59.416 43.478 2.56 0.00 45.43 2.44
40 41 3.937079 CCGACTTGGGTAGGATACAAAAC 59.063 47.826 0.00 0.00 45.43 2.43
41 42 4.323257 CCGACTTGGGTAGGATACAAAACT 60.323 45.833 0.00 0.00 45.43 2.66
42 43 4.630069 CGACTTGGGTAGGATACAAAACTG 59.370 45.833 0.00 0.00 45.43 3.16
43 44 5.568023 CGACTTGGGTAGGATACAAAACTGA 60.568 44.000 0.00 0.00 45.43 3.41
44 45 5.557866 ACTTGGGTAGGATACAAAACTGAC 58.442 41.667 0.00 0.00 45.43 3.51
45 46 5.309806 ACTTGGGTAGGATACAAAACTGACT 59.690 40.000 0.00 0.00 45.43 3.41
46 47 5.836024 TGGGTAGGATACAAAACTGACTT 57.164 39.130 0.00 0.00 45.43 3.01
47 48 5.556915 TGGGTAGGATACAAAACTGACTTG 58.443 41.667 0.00 0.00 45.43 3.16
48 49 4.941873 GGGTAGGATACAAAACTGACTTGG 59.058 45.833 0.00 0.00 45.43 3.61
49 50 5.280317 GGGTAGGATACAAAACTGACTTGGA 60.280 44.000 0.00 0.00 45.43 3.53
50 51 5.642491 GGTAGGATACAAAACTGACTTGGAC 59.358 44.000 0.00 0.00 45.43 4.02
51 52 5.568620 AGGATACAAAACTGACTTGGACT 57.431 39.130 0.00 0.00 41.41 3.85
52 53 6.681729 AGGATACAAAACTGACTTGGACTA 57.318 37.500 0.00 0.00 41.41 2.59
53 54 6.702329 AGGATACAAAACTGACTTGGACTAG 58.298 40.000 0.00 0.00 41.41 2.57
54 55 6.270231 AGGATACAAAACTGACTTGGACTAGT 59.730 38.462 0.00 0.00 41.41 2.57
55 56 7.453752 AGGATACAAAACTGACTTGGACTAGTA 59.546 37.037 0.00 0.00 41.41 1.82
56 57 7.760340 GGATACAAAACTGACTTGGACTAGTAG 59.240 40.741 0.00 0.00 0.00 2.57
57 58 6.481434 ACAAAACTGACTTGGACTAGTAGT 57.519 37.500 1.37 1.37 0.00 2.73
58 59 6.514063 ACAAAACTGACTTGGACTAGTAGTC 58.486 40.000 20.24 20.24 44.32 2.59
59 60 5.373981 AAACTGACTTGGACTAGTAGTCG 57.626 43.478 21.29 11.96 45.96 4.18
60 61 4.018484 ACTGACTTGGACTAGTAGTCGT 57.982 45.455 21.29 14.75 45.96 4.34
61 62 5.157940 ACTGACTTGGACTAGTAGTCGTA 57.842 43.478 21.29 11.87 45.96 3.43
62 63 5.743117 ACTGACTTGGACTAGTAGTCGTAT 58.257 41.667 21.29 8.96 45.96 3.06
63 64 6.882656 ACTGACTTGGACTAGTAGTCGTATA 58.117 40.000 21.29 7.46 45.96 1.47
64 65 6.760770 ACTGACTTGGACTAGTAGTCGTATAC 59.239 42.308 21.29 13.70 45.96 1.47
65 66 6.882656 TGACTTGGACTAGTAGTCGTATACT 58.117 40.000 21.29 4.35 45.96 2.12
66 67 8.011844 TGACTTGGACTAGTAGTCGTATACTA 57.988 38.462 21.29 6.01 45.96 1.82
67 68 8.646004 TGACTTGGACTAGTAGTCGTATACTAT 58.354 37.037 21.29 4.28 45.96 2.12
181 182 0.245539 ACAGAACTTGCCATGCATGC 59.754 50.000 21.69 11.82 38.76 4.06
182 183 0.800683 CAGAACTTGCCATGCATGCG 60.801 55.000 21.69 15.04 38.76 4.73
183 184 0.961857 AGAACTTGCCATGCATGCGA 60.962 50.000 21.69 14.63 38.76 5.10
184 185 0.101759 GAACTTGCCATGCATGCGAT 59.898 50.000 21.69 4.99 38.76 4.58
185 186 0.179121 AACTTGCCATGCATGCGATG 60.179 50.000 21.69 16.45 38.76 3.84
297 298 3.630289 CCCCGTTGGTAGCTAGCT 58.370 61.111 23.12 23.12 0.00 3.32
298 299 2.816746 CCCCGTTGGTAGCTAGCTA 58.183 57.895 20.67 20.67 0.00 3.32
299 300 0.674534 CCCCGTTGGTAGCTAGCTAG 59.325 60.000 24.78 16.84 0.00 3.42
364 365 2.770802 ACAGATCCATCTAAGCTGCAGT 59.229 45.455 16.64 0.00 34.85 4.40
380 381 0.317603 CAGTCTGCACTGCAAGCAAC 60.318 55.000 13.69 13.46 43.77 4.17
393 394 2.095059 GCAAGCAACCCAGTAATCACAG 60.095 50.000 0.00 0.00 0.00 3.66
397 398 2.870435 GCAACCCAGTAATCACAGTCGT 60.870 50.000 0.00 0.00 0.00 4.34
529 2270 0.868406 GTTCTGAAAGCCGTGTGGAG 59.132 55.000 0.00 0.00 37.49 3.86
553 2294 0.178533 TACCTGTATTTTCGGCCGGG 59.821 55.000 27.83 18.25 0.00 5.73
593 2447 8.255206 TCACTAACTTAAGTCACTCAAAACTCA 58.745 33.333 8.95 0.00 0.00 3.41
594 2448 8.328864 CACTAACTTAAGTCACTCAAAACTCAC 58.671 37.037 8.95 0.00 0.00 3.51
602 2456 3.252458 TCACTCAAAACTCACTCGATCGA 59.748 43.478 18.32 18.32 0.00 3.59
603 2457 4.082733 TCACTCAAAACTCACTCGATCGAT 60.083 41.667 19.78 0.00 0.00 3.59
604 2458 4.264145 CACTCAAAACTCACTCGATCGATC 59.736 45.833 19.78 15.68 0.00 3.69
605 2459 4.082733 ACTCAAAACTCACTCGATCGATCA 60.083 41.667 24.40 11.08 0.00 2.92
606 2460 4.415735 TCAAAACTCACTCGATCGATCAG 58.584 43.478 24.40 20.58 0.00 2.90
608 2462 5.123344 TCAAAACTCACTCGATCGATCAGTA 59.877 40.000 24.40 8.81 0.00 2.74
609 2463 4.539509 AACTCACTCGATCGATCAGTAC 57.460 45.455 24.40 0.00 0.00 2.73
610 2464 3.799366 ACTCACTCGATCGATCAGTACT 58.201 45.455 24.40 9.65 0.00 2.73
614 2468 6.483974 ACTCACTCGATCGATCAGTACTTAAT 59.516 38.462 24.40 7.86 0.00 1.40
619 2473 6.609533 TCGATCGATCAGTACTTAATTAGCC 58.390 40.000 24.40 0.00 0.00 3.93
745 2638 2.284331 TGCAGCCTCCTTCCGGTA 60.284 61.111 0.00 0.00 0.00 4.02
760 2653 2.962253 GTACCGCTCCATCGCTGC 60.962 66.667 0.00 0.00 0.00 5.25
761 2654 4.221422 TACCGCTCCATCGCTGCC 62.221 66.667 0.00 0.00 0.00 4.85
833 2726 1.945776 GCAAGCGTGACTCGTGCTAC 61.946 60.000 2.99 0.00 38.17 3.58
834 2727 1.080705 AAGCGTGACTCGTGCTACC 60.081 57.895 0.00 0.00 38.17 3.18
835 2728 1.524863 AAGCGTGACTCGTGCTACCT 61.525 55.000 0.00 0.00 38.17 3.08
836 2729 0.675837 AGCGTGACTCGTGCTACCTA 60.676 55.000 0.00 0.00 42.13 3.08
837 2730 0.248134 GCGTGACTCGTGCTACCTAG 60.248 60.000 0.00 0.00 42.13 3.02
859 2752 1.679305 GCTCCTCCTCTGGTCGACA 60.679 63.158 18.91 2.63 0.00 4.35
865 2758 1.753078 CCTCTGGTCGACATCCCGA 60.753 63.158 18.91 1.06 36.06 5.14
1230 3136 1.227823 CTTCACCAACGGCCTCACA 60.228 57.895 0.00 0.00 0.00 3.58
1269 3175 8.657074 TCGGTAATTATATAAGCATGCATACC 57.343 34.615 21.98 14.63 0.00 2.73
1270 3176 7.713507 TCGGTAATTATATAAGCATGCATACCC 59.286 37.037 21.98 5.29 0.00 3.69
1392 3369 4.021894 AGCTGAAGTGAATTGTCGTCTACT 60.022 41.667 0.00 0.00 0.00 2.57
1395 3372 6.570672 TGAAGTGAATTGTCGTCTACTACT 57.429 37.500 0.00 0.00 0.00 2.57
1503 3490 4.403752 GGGTAGGTGATAGAAAACGGTACT 59.596 45.833 0.00 0.00 0.00 2.73
1504 3491 5.451103 GGGTAGGTGATAGAAAACGGTACTC 60.451 48.000 0.00 0.00 0.00 2.59
1505 3492 4.732672 AGGTGATAGAAAACGGTACTCC 57.267 45.455 0.00 0.00 0.00 3.85
1506 3493 4.351127 AGGTGATAGAAAACGGTACTCCT 58.649 43.478 0.00 0.00 0.00 3.69
1507 3494 5.513233 AGGTGATAGAAAACGGTACTCCTA 58.487 41.667 0.00 0.00 0.00 2.94
1508 3495 5.593502 AGGTGATAGAAAACGGTACTCCTAG 59.406 44.000 0.00 0.00 0.00 3.02
1509 3496 5.280164 GTGATAGAAAACGGTACTCCTAGC 58.720 45.833 0.00 0.00 0.00 3.42
1510 3497 5.067544 GTGATAGAAAACGGTACTCCTAGCT 59.932 44.000 0.00 0.00 0.00 3.32
1511 3498 3.870633 AGAAAACGGTACTCCTAGCTG 57.129 47.619 0.00 0.00 0.00 4.24
1664 3781 1.817447 AGCCCGCCGATATAGTACTTC 59.183 52.381 0.00 0.00 0.00 3.01
1666 3783 2.444421 CCCGCCGATATAGTACTTCCT 58.556 52.381 0.00 0.00 0.00 3.36
1667 3784 2.422832 CCCGCCGATATAGTACTTCCTC 59.577 54.545 0.00 0.00 0.00 3.71
1668 3785 2.422832 CCGCCGATATAGTACTTCCTCC 59.577 54.545 0.00 0.00 0.00 4.30
1670 3787 3.080319 GCCGATATAGTACTTCCTCCGT 58.920 50.000 0.00 0.00 0.00 4.69
1671 3788 3.126686 GCCGATATAGTACTTCCTCCGTC 59.873 52.174 0.00 0.00 0.00 4.79
1672 3789 3.688673 CCGATATAGTACTTCCTCCGTCC 59.311 52.174 0.00 0.00 0.00 4.79
1673 3790 4.321718 CGATATAGTACTTCCTCCGTCCA 58.678 47.826 0.00 0.00 0.00 4.02
1674 3791 4.392445 CGATATAGTACTTCCTCCGTCCAG 59.608 50.000 0.00 0.00 0.00 3.86
1675 3792 3.947612 ATAGTACTTCCTCCGTCCAGA 57.052 47.619 0.00 0.00 0.00 3.86
1677 3794 2.885616 AGTACTTCCTCCGTCCAGAAA 58.114 47.619 0.00 0.00 0.00 2.52
1678 3795 3.442076 AGTACTTCCTCCGTCCAGAAAT 58.558 45.455 0.00 0.00 0.00 2.17
1679 3796 4.607239 AGTACTTCCTCCGTCCAGAAATA 58.393 43.478 0.00 0.00 0.00 1.40
1680 3797 3.889520 ACTTCCTCCGTCCAGAAATAC 57.110 47.619 0.00 0.00 0.00 1.89
1682 3799 3.447944 ACTTCCTCCGTCCAGAAATACTC 59.552 47.826 0.00 0.00 0.00 2.59
1683 3800 2.022195 TCCTCCGTCCAGAAATACTCG 58.978 52.381 0.00 0.00 0.00 4.18
1684 3801 1.749634 CCTCCGTCCAGAAATACTCGT 59.250 52.381 0.00 0.00 0.00 4.18
1685 3802 2.223525 CCTCCGTCCAGAAATACTCGTC 60.224 54.545 0.00 0.00 0.00 4.20
1686 3803 1.399440 TCCGTCCAGAAATACTCGTCG 59.601 52.381 0.00 0.00 0.00 5.12
1687 3804 1.533338 CCGTCCAGAAATACTCGTCGG 60.533 57.143 0.00 0.00 0.00 4.79
1688 3805 1.399440 CGTCCAGAAATACTCGTCGGA 59.601 52.381 0.00 0.00 0.00 4.55
1690 3807 2.681848 GTCCAGAAATACTCGTCGGAGA 59.318 50.000 0.00 0.00 43.27 3.71
1691 3808 3.128242 GTCCAGAAATACTCGTCGGAGAA 59.872 47.826 0.00 0.00 43.27 2.87
1692 3809 3.760151 TCCAGAAATACTCGTCGGAGAAA 59.240 43.478 0.00 0.00 43.27 2.52
1693 3810 4.401519 TCCAGAAATACTCGTCGGAGAAAT 59.598 41.667 0.00 0.00 43.27 2.17
1694 3811 5.591472 TCCAGAAATACTCGTCGGAGAAATA 59.409 40.000 0.00 0.00 43.27 1.40
1695 3812 5.915758 CCAGAAATACTCGTCGGAGAAATAG 59.084 44.000 0.00 0.00 43.27 1.73
1696 3813 5.915758 CAGAAATACTCGTCGGAGAAATAGG 59.084 44.000 0.00 0.00 43.27 2.57
1698 3815 6.769822 AGAAATACTCGTCGGAGAAATAGGTA 59.230 38.462 0.00 0.00 43.27 3.08
1699 3816 6.949352 AATACTCGTCGGAGAAATAGGTAA 57.051 37.500 0.00 0.00 43.27 2.85
1700 3817 6.949352 ATACTCGTCGGAGAAATAGGTAAA 57.051 37.500 0.00 0.00 43.27 2.01
1701 3818 5.649782 ACTCGTCGGAGAAATAGGTAAAA 57.350 39.130 0.00 0.00 43.27 1.52
1702 3819 6.029346 ACTCGTCGGAGAAATAGGTAAAAA 57.971 37.500 0.00 0.00 43.27 1.94
1704 3821 6.534079 ACTCGTCGGAGAAATAGGTAAAAATG 59.466 38.462 0.00 0.00 43.27 2.32
1705 3822 5.813672 TCGTCGGAGAAATAGGTAAAAATGG 59.186 40.000 0.00 0.00 39.69 3.16
1707 3824 6.482308 CGTCGGAGAAATAGGTAAAAATGGAT 59.518 38.462 0.00 0.00 39.69 3.41
1708 3825 7.518370 CGTCGGAGAAATAGGTAAAAATGGATG 60.518 40.741 0.00 0.00 39.69 3.51
1710 3827 6.039270 CGGAGAAATAGGTAAAAATGGATGCA 59.961 38.462 0.00 0.00 0.00 3.96
1711 3828 7.255590 CGGAGAAATAGGTAAAAATGGATGCAT 60.256 37.037 0.00 0.00 0.00 3.96
1712 3829 8.084684 GGAGAAATAGGTAAAAATGGATGCATC 58.915 37.037 18.81 18.81 0.00 3.91
1717 3834 9.866655 AATAGGTAAAAATGGATGCATCTAGAA 57.133 29.630 25.28 10.04 0.00 2.10
1720 3837 8.494433 AGGTAAAAATGGATGCATCTAGAACTA 58.506 33.333 25.28 8.32 0.00 2.24
1721 3838 9.120538 GGTAAAAATGGATGCATCTAGAACTAA 57.879 33.333 25.28 3.50 0.00 2.24
1731 3947 9.549509 GATGCATCTAGAACTAAATACGTCTAG 57.450 37.037 19.70 0.00 0.00 2.43
1732 3948 8.672823 TGCATCTAGAACTAAATACGTCTAGA 57.327 34.615 10.71 10.71 39.93 2.43
1748 3965 7.916128 ACGTCTAGATACATTCATTTCTTCG 57.084 36.000 0.00 0.00 0.00 3.79
1749 3966 7.704271 ACGTCTAGATACATTCATTTCTTCGA 58.296 34.615 0.00 0.00 0.00 3.71
1750 3967 7.644551 ACGTCTAGATACATTCATTTCTTCGAC 59.355 37.037 0.00 0.00 0.00 4.20
1751 3968 7.644157 CGTCTAGATACATTCATTTCTTCGACA 59.356 37.037 0.00 0.00 0.00 4.35
1752 3969 9.469807 GTCTAGATACATTCATTTCTTCGACAT 57.530 33.333 0.00 0.00 0.00 3.06
1753 3970 9.468532 TCTAGATACATTCATTTCTTCGACATG 57.531 33.333 0.00 0.00 0.00 3.21
1754 3971 9.254133 CTAGATACATTCATTTCTTCGACATGT 57.746 33.333 0.00 0.00 0.00 3.21
1756 3973 9.770097 AGATACATTCATTTCTTCGACATGTAT 57.230 29.630 0.00 0.00 38.47 2.29
1760 3977 8.184192 ACATTCATTTCTTCGACATGTATTTCC 58.816 33.333 0.00 0.00 0.00 3.13
1761 3978 6.344572 TCATTTCTTCGACATGTATTTCCG 57.655 37.500 0.00 0.00 0.00 4.30
1762 3979 5.293324 TCATTTCTTCGACATGTATTTCCGG 59.707 40.000 0.00 0.00 0.00 5.14
1763 3980 4.459390 TTCTTCGACATGTATTTCCGGA 57.541 40.909 0.00 0.00 0.00 5.14
1764 3981 3.777478 TCTTCGACATGTATTTCCGGAC 58.223 45.455 1.83 0.00 0.00 4.79
1765 3982 2.197792 TCGACATGTATTTCCGGACG 57.802 50.000 1.83 0.27 0.00 4.79
1766 3983 1.202325 TCGACATGTATTTCCGGACGG 60.202 52.381 1.83 3.96 0.00 4.79
1767 3984 1.202325 CGACATGTATTTCCGGACGGA 60.202 52.381 1.83 9.76 43.52 4.69
1768 3985 2.470821 GACATGTATTTCCGGACGGAG 58.529 52.381 13.64 3.15 46.06 4.63
1769 3986 1.138266 ACATGTATTTCCGGACGGAGG 59.862 52.381 13.64 0.00 46.06 4.30
1770 3987 0.756903 ATGTATTTCCGGACGGAGGG 59.243 55.000 13.64 0.00 46.06 4.30
1771 3988 0.324552 TGTATTTCCGGACGGAGGGA 60.325 55.000 13.64 4.95 46.06 4.20
1772 3989 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
1773 3990 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
1774 3991 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
1775 3992 0.967380 TTTCCGGACGGAGGGAGTAC 60.967 60.000 13.64 0.00 46.06 2.73
1776 3993 1.856539 TTCCGGACGGAGGGAGTACT 61.857 60.000 13.64 0.00 46.06 2.73
1777 3994 1.379576 CCGGACGGAGGGAGTACTT 60.380 63.158 4.40 0.00 37.50 2.24
1778 3995 1.664321 CCGGACGGAGGGAGTACTTG 61.664 65.000 4.40 0.00 37.50 3.16
1800 4017 1.098712 GTGTTCGGTGAGGGTTGCAA 61.099 55.000 0.00 0.00 0.00 4.08
1851 4068 0.770499 TCATCAAGAACCCACTGCCA 59.230 50.000 0.00 0.00 0.00 4.92
1867 4084 0.652592 GCCAAGATCCATCGTCGTTG 59.347 55.000 0.00 0.00 0.00 4.10
1965 4182 3.185246 ACATAGTGCTCCTACATGTGC 57.815 47.619 9.11 3.50 0.00 4.57
1995 4212 1.001378 GGTGGTTACGTACGTGTGTCT 60.001 52.381 30.25 5.02 0.00 3.41
2022 4245 6.754209 TGTCACGACTTAAAACGTTAACCTTA 59.246 34.615 0.00 0.00 40.76 2.69
2023 4246 7.437862 TGTCACGACTTAAAACGTTAACCTTAT 59.562 33.333 0.00 0.00 40.76 1.73
2025 4248 8.274939 TCACGACTTAAAACGTTAACCTTATTG 58.725 33.333 0.00 0.00 40.76 1.90
2026 4249 8.063630 CACGACTTAAAACGTTAACCTTATTGT 58.936 33.333 0.00 0.00 40.76 2.71
2027 4250 8.063630 ACGACTTAAAACGTTAACCTTATTGTG 58.936 33.333 0.00 0.00 39.75 3.33
2028 4251 8.274939 CGACTTAAAACGTTAACCTTATTGTGA 58.725 33.333 0.00 0.00 0.00 3.58
2079 4398 3.222603 ACTTCTGGGCTTCGACAATTTT 58.777 40.909 0.00 0.00 0.00 1.82
2208 4600 5.946298 ACGAAGTATACAGATCACAACGAA 58.054 37.500 5.50 0.00 41.94 3.85
2214 4606 2.771089 ACAGATCACAACGAACATGCT 58.229 42.857 0.00 0.00 0.00 3.79
2985 5391 2.038952 CTCGCATCCCTTTGATCCCATA 59.961 50.000 0.00 0.00 0.00 2.74
2986 5392 2.644299 TCGCATCCCTTTGATCCCATAT 59.356 45.455 0.00 0.00 0.00 1.78
2987 5393 2.751259 CGCATCCCTTTGATCCCATATG 59.249 50.000 0.00 0.00 0.00 1.78
2988 5394 2.494870 GCATCCCTTTGATCCCATATGC 59.505 50.000 0.00 0.00 32.62 3.14
2989 5395 3.770046 CATCCCTTTGATCCCATATGCA 58.230 45.455 0.00 0.00 0.00 3.96
2990 5396 3.969466 TCCCTTTGATCCCATATGCAA 57.031 42.857 0.00 0.00 0.00 4.08
2992 5398 4.217510 TCCCTTTGATCCCATATGCAAAG 58.782 43.478 18.96 18.96 44.05 2.77
3013 5451 6.636454 AAGATGTACAAGTCCCATTTCCTA 57.364 37.500 0.00 0.00 0.00 2.94
3058 5500 6.670077 AGGATTTCTTTTCGATCTGTAAGC 57.330 37.500 0.00 0.00 0.00 3.09
3061 5503 1.917955 TCTTTTCGATCTGTAAGCGCG 59.082 47.619 0.00 0.00 0.00 6.86
3062 5504 0.368907 TTTTCGATCTGTAAGCGCGC 59.631 50.000 26.66 26.66 31.81 6.86
3063 5505 1.739093 TTTCGATCTGTAAGCGCGCG 61.739 55.000 28.44 28.44 31.81 6.86
3064 5506 2.860690 TTCGATCTGTAAGCGCGCGT 62.861 55.000 32.35 26.23 31.81 6.01
3065 5507 1.653232 CGATCTGTAAGCGCGCGTA 60.653 57.895 32.35 24.95 0.00 4.42
3066 5508 0.997226 CGATCTGTAAGCGCGCGTAT 60.997 55.000 32.35 22.14 0.00 3.06
3072 5514 3.058708 TCTGTAAGCGCGCGTATATTAGT 60.059 43.478 32.35 3.67 0.00 2.24
3081 5523 4.143803 CGCGCGTATATTAGTCTGTTCTTG 60.144 45.833 24.19 0.00 0.00 3.02
3117 5559 2.632228 CGATGAATACGCATGCAGTTG 58.368 47.619 19.57 3.36 0.00 3.16
3222 5693 8.704668 AGGACAGTTAAATTCTGGTTTTCATTT 58.295 29.630 0.00 0.00 37.25 2.32
3264 5735 1.873591 GTGCTCCATTTCGTGTTGAGT 59.126 47.619 0.00 0.00 0.00 3.41
3361 5838 4.281688 CCAAGTCCAACCAACAGATCAAAT 59.718 41.667 0.00 0.00 0.00 2.32
3365 5842 6.068010 AGTCCAACCAACAGATCAAATACAA 58.932 36.000 0.00 0.00 0.00 2.41
3366 5843 6.549364 AGTCCAACCAACAGATCAAATACAAA 59.451 34.615 0.00 0.00 0.00 2.83
3427 5904 2.339712 GCACACGGCAGCCATTTT 59.660 55.556 13.30 0.00 43.97 1.82
3488 5965 1.116536 TCCACCTCACCACACGCTAA 61.117 55.000 0.00 0.00 0.00 3.09
3540 6018 0.386352 CCTGCATGCACAAGTCAACG 60.386 55.000 18.46 3.31 0.00 4.10
3559 6037 0.034616 GATCGCATCAGGAAGGAGGG 59.965 60.000 0.00 0.00 0.00 4.30
3596 6077 7.322664 TGAACATTCAGAAAAACAAAAGAGCT 58.677 30.769 0.00 0.00 32.50 4.09
3625 6106 4.626042 CAGATAGTGTATGGAGCAAGGAC 58.374 47.826 0.00 0.00 0.00 3.85
3626 6107 3.319405 AGATAGTGTATGGAGCAAGGACG 59.681 47.826 0.00 0.00 0.00 4.79
3627 6108 1.557099 AGTGTATGGAGCAAGGACGA 58.443 50.000 0.00 0.00 0.00 4.20
3894 6375 1.482593 AGAGGGAGCCTGAAACATACG 59.517 52.381 0.00 0.00 31.76 3.06
3903 6384 7.321153 GGAGCCTGAAACATACGTACATATAT 58.679 38.462 0.00 0.00 0.00 0.86
3928 6409 1.012841 GGCAGAGCGAAATCTTGAGG 58.987 55.000 0.00 0.00 0.00 3.86
3957 6438 1.395954 GCCCGAGGAACGAACAATAAC 59.604 52.381 0.00 0.00 45.77 1.89
3958 6439 2.933928 GCCCGAGGAACGAACAATAACT 60.934 50.000 0.00 0.00 45.77 2.24
3959 6440 2.671396 CCCGAGGAACGAACAATAACTG 59.329 50.000 0.00 0.00 45.77 3.16
3960 6441 3.581755 CCGAGGAACGAACAATAACTGA 58.418 45.455 0.00 0.00 45.77 3.41
3961 6442 3.991773 CCGAGGAACGAACAATAACTGAA 59.008 43.478 0.00 0.00 45.77 3.02
3962 6443 4.143179 CCGAGGAACGAACAATAACTGAAC 60.143 45.833 0.00 0.00 45.77 3.18
3963 6444 4.684703 CGAGGAACGAACAATAACTGAACT 59.315 41.667 0.00 0.00 45.77 3.01
3964 6445 5.860182 CGAGGAACGAACAATAACTGAACTA 59.140 40.000 0.00 0.00 45.77 2.24
3965 6446 6.364165 CGAGGAACGAACAATAACTGAACTAA 59.636 38.462 0.00 0.00 45.77 2.24
3966 6447 7.063074 CGAGGAACGAACAATAACTGAACTAAT 59.937 37.037 0.00 0.00 45.77 1.73
3967 6448 8.252964 AGGAACGAACAATAACTGAACTAATC 57.747 34.615 0.00 0.00 0.00 1.75
3968 6449 7.876068 AGGAACGAACAATAACTGAACTAATCA 59.124 33.333 0.00 0.00 36.38 2.57
3969 6450 8.500773 GGAACGAACAATAACTGAACTAATCAA 58.499 33.333 0.00 0.00 37.67 2.57
3970 6451 9.530129 GAACGAACAATAACTGAACTAATCAAG 57.470 33.333 0.00 0.00 37.67 3.02
3971 6452 7.519002 ACGAACAATAACTGAACTAATCAAGC 58.481 34.615 0.00 0.00 37.67 4.01
3972 6453 7.172532 ACGAACAATAACTGAACTAATCAAGCA 59.827 33.333 0.00 0.00 37.67 3.91
3973 6454 7.689812 CGAACAATAACTGAACTAATCAAGCAG 59.310 37.037 0.00 0.00 37.67 4.24
3974 6455 7.383102 ACAATAACTGAACTAATCAAGCAGG 57.617 36.000 0.00 0.00 37.67 4.85
3975 6456 6.375455 ACAATAACTGAACTAATCAAGCAGGG 59.625 38.462 0.00 0.00 37.67 4.45
3976 6457 3.356529 ACTGAACTAATCAAGCAGGGG 57.643 47.619 0.00 0.00 37.67 4.79
3977 6458 2.912956 ACTGAACTAATCAAGCAGGGGA 59.087 45.455 0.00 0.00 37.67 4.81
3978 6459 3.054802 ACTGAACTAATCAAGCAGGGGAG 60.055 47.826 0.00 0.00 37.67 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.176460 CCAAGTCGGTTTTTACCCTTTTATATA 57.824 33.333 0.00 0.00 0.00 0.86
1 2 7.123098 CCCAAGTCGGTTTTTACCCTTTTATAT 59.877 37.037 0.00 0.00 0.00 0.86
2 3 6.433716 CCCAAGTCGGTTTTTACCCTTTTATA 59.566 38.462 0.00 0.00 0.00 0.98
3 4 5.244402 CCCAAGTCGGTTTTTACCCTTTTAT 59.756 40.000 0.00 0.00 0.00 1.40
4 5 4.583907 CCCAAGTCGGTTTTTACCCTTTTA 59.416 41.667 0.00 0.00 0.00 1.52
5 6 3.385433 CCCAAGTCGGTTTTTACCCTTTT 59.615 43.478 0.00 0.00 0.00 2.27
6 7 2.960384 CCCAAGTCGGTTTTTACCCTTT 59.040 45.455 0.00 0.00 0.00 3.11
7 8 2.091720 ACCCAAGTCGGTTTTTACCCTT 60.092 45.455 0.00 0.00 29.19 3.95
8 9 1.496001 ACCCAAGTCGGTTTTTACCCT 59.504 47.619 0.00 0.00 29.19 4.34
9 10 1.985473 ACCCAAGTCGGTTTTTACCC 58.015 50.000 0.00 0.00 29.19 3.69
10 11 3.076621 CCTACCCAAGTCGGTTTTTACC 58.923 50.000 0.00 0.00 37.34 2.85
11 12 4.006780 TCCTACCCAAGTCGGTTTTTAC 57.993 45.455 0.00 0.00 37.34 2.01
12 13 4.914177 ATCCTACCCAAGTCGGTTTTTA 57.086 40.909 0.00 0.00 37.34 1.52
13 14 3.801307 ATCCTACCCAAGTCGGTTTTT 57.199 42.857 0.00 0.00 37.34 1.94
14 15 3.583966 TGTATCCTACCCAAGTCGGTTTT 59.416 43.478 0.00 0.00 37.34 2.43
15 16 3.175594 TGTATCCTACCCAAGTCGGTTT 58.824 45.455 0.00 0.00 37.34 3.27
16 17 2.823959 TGTATCCTACCCAAGTCGGTT 58.176 47.619 0.00 0.00 37.34 4.44
17 18 2.537633 TGTATCCTACCCAAGTCGGT 57.462 50.000 0.00 0.00 40.13 4.69
18 19 3.899052 TTTGTATCCTACCCAAGTCGG 57.101 47.619 0.00 0.00 0.00 4.79
19 20 4.630069 CAGTTTTGTATCCTACCCAAGTCG 59.370 45.833 0.00 0.00 0.00 4.18
20 21 5.642491 GTCAGTTTTGTATCCTACCCAAGTC 59.358 44.000 0.00 0.00 0.00 3.01
21 22 5.309806 AGTCAGTTTTGTATCCTACCCAAGT 59.690 40.000 0.00 0.00 0.00 3.16
22 23 5.805728 AGTCAGTTTTGTATCCTACCCAAG 58.194 41.667 0.00 0.00 0.00 3.61
23 24 5.836024 AGTCAGTTTTGTATCCTACCCAA 57.164 39.130 0.00 0.00 0.00 4.12
24 25 5.514136 CCAAGTCAGTTTTGTATCCTACCCA 60.514 44.000 0.00 0.00 0.00 4.51
25 26 4.941873 CCAAGTCAGTTTTGTATCCTACCC 59.058 45.833 0.00 0.00 0.00 3.69
26 27 5.642491 GTCCAAGTCAGTTTTGTATCCTACC 59.358 44.000 0.00 0.00 0.00 3.18
27 28 6.465084 AGTCCAAGTCAGTTTTGTATCCTAC 58.535 40.000 0.00 0.00 0.00 3.18
28 29 6.681729 AGTCCAAGTCAGTTTTGTATCCTA 57.318 37.500 0.00 0.00 0.00 2.94
29 30 5.568620 AGTCCAAGTCAGTTTTGTATCCT 57.431 39.130 0.00 0.00 0.00 3.24
30 31 6.465084 ACTAGTCCAAGTCAGTTTTGTATCC 58.535 40.000 0.00 0.00 0.00 2.59
31 32 8.305317 ACTACTAGTCCAAGTCAGTTTTGTATC 58.695 37.037 0.00 0.00 0.00 2.24
32 33 8.191534 ACTACTAGTCCAAGTCAGTTTTGTAT 57.808 34.615 0.00 0.00 0.00 2.29
33 34 7.521099 CGACTACTAGTCCAAGTCAGTTTTGTA 60.521 40.741 19.48 0.00 42.12 2.41
34 35 6.481434 ACTACTAGTCCAAGTCAGTTTTGT 57.519 37.500 0.00 0.00 0.00 2.83
35 36 5.629849 CGACTACTAGTCCAAGTCAGTTTTG 59.370 44.000 19.48 3.71 42.12 2.44
36 37 5.301298 ACGACTACTAGTCCAAGTCAGTTTT 59.699 40.000 19.48 1.39 42.12 2.43
37 38 4.826183 ACGACTACTAGTCCAAGTCAGTTT 59.174 41.667 19.48 3.28 42.12 2.66
38 39 4.396522 ACGACTACTAGTCCAAGTCAGTT 58.603 43.478 19.48 5.19 42.12 3.16
39 40 4.018484 ACGACTACTAGTCCAAGTCAGT 57.982 45.455 19.48 15.54 42.12 3.41
40 41 6.985645 AGTATACGACTACTAGTCCAAGTCAG 59.014 42.308 19.48 15.08 42.12 3.51
41 42 6.882656 AGTATACGACTACTAGTCCAAGTCA 58.117 40.000 19.48 6.10 42.12 3.41
65 66 8.773645 GCAGCATGTGTTACAGTAATCATTATA 58.226 33.333 0.00 0.00 39.31 0.98
66 67 7.255242 GGCAGCATGTGTTACAGTAATCATTAT 60.255 37.037 0.00 0.00 39.31 1.28
67 68 6.038161 GGCAGCATGTGTTACAGTAATCATTA 59.962 38.462 0.00 0.00 39.31 1.90
68 69 5.163622 GGCAGCATGTGTTACAGTAATCATT 60.164 40.000 0.00 0.00 39.31 2.57
69 70 4.336433 GGCAGCATGTGTTACAGTAATCAT 59.664 41.667 0.00 2.75 39.31 2.45
70 71 3.689161 GGCAGCATGTGTTACAGTAATCA 59.311 43.478 0.00 0.47 39.31 2.57
71 72 3.689161 TGGCAGCATGTGTTACAGTAATC 59.311 43.478 0.00 0.00 39.31 1.75
72 73 3.440173 GTGGCAGCATGTGTTACAGTAAT 59.560 43.478 0.00 0.00 39.31 1.89
73 74 2.811431 GTGGCAGCATGTGTTACAGTAA 59.189 45.455 0.00 0.00 39.31 2.24
74 75 2.422597 GTGGCAGCATGTGTTACAGTA 58.577 47.619 0.00 0.00 39.31 2.74
75 76 1.238439 GTGGCAGCATGTGTTACAGT 58.762 50.000 0.00 0.00 39.31 3.55
76 77 0.166597 CGTGGCAGCATGTGTTACAG 59.833 55.000 0.00 0.00 39.31 2.74
77 78 1.233950 CCGTGGCAGCATGTGTTACA 61.234 55.000 0.00 0.00 39.31 2.41
78 79 1.501741 CCGTGGCAGCATGTGTTAC 59.498 57.895 0.00 0.00 39.31 2.50
79 80 1.673993 CCCGTGGCAGCATGTGTTA 60.674 57.895 0.00 0.00 39.31 2.41
80 81 2.985282 CCCGTGGCAGCATGTGTT 60.985 61.111 0.00 0.00 39.31 3.32
181 182 1.517694 GGGTGCTTGCATTGCATCG 60.518 57.895 12.95 8.04 42.02 3.84
182 183 1.105457 TAGGGTGCTTGCATTGCATC 58.895 50.000 12.95 15.42 42.69 3.91
183 184 0.819582 GTAGGGTGCTTGCATTGCAT 59.180 50.000 12.95 0.00 42.69 3.96
184 185 0.539207 TGTAGGGTGCTTGCATTGCA 60.539 50.000 7.38 7.38 38.19 4.08
185 186 0.171903 CTGTAGGGTGCTTGCATTGC 59.828 55.000 0.46 0.46 0.00 3.56
296 297 4.040461 TCATTTAATTCTCCGGGCTCCTAG 59.960 45.833 0.00 0.00 0.00 3.02
297 298 3.971305 TCATTTAATTCTCCGGGCTCCTA 59.029 43.478 0.00 0.00 0.00 2.94
298 299 2.777692 TCATTTAATTCTCCGGGCTCCT 59.222 45.455 0.00 0.00 0.00 3.69
299 300 3.208747 TCATTTAATTCTCCGGGCTCC 57.791 47.619 0.00 0.00 0.00 4.70
342 343 3.132160 CTGCAGCTTAGATGGATCTGTG 58.868 50.000 0.00 0.00 37.76 3.66
364 365 2.195567 GGGTTGCTTGCAGTGCAGA 61.196 57.895 18.81 8.70 40.61 4.26
380 381 2.163010 ACGTACGACTGTGATTACTGGG 59.837 50.000 24.41 0.00 0.00 4.45
393 394 3.259207 AGTGTGTGTCTAACGTACGAC 57.741 47.619 24.41 10.20 0.00 4.34
397 398 4.603985 CTGTCAAGTGTGTGTCTAACGTA 58.396 43.478 0.00 0.00 0.00 3.57
488 507 0.248054 CCGTGCATCACCGCATTAAC 60.248 55.000 0.00 0.00 45.26 2.01
509 2250 0.534203 TCCACACGGCTTTCAGAACC 60.534 55.000 0.00 0.00 0.00 3.62
510 2251 0.868406 CTCCACACGGCTTTCAGAAC 59.132 55.000 0.00 0.00 0.00 3.01
529 2270 3.553105 CGGCCGAAAATACAGGTAGTAAC 59.447 47.826 24.07 0.00 36.05 2.50
553 2294 1.276622 TAGTGAACTGGGAAGAGGGC 58.723 55.000 0.00 0.00 0.00 5.19
593 2447 7.299586 GCTAATTAAGTACTGATCGATCGAGT 58.700 38.462 23.84 24.17 0.00 4.18
594 2448 6.743627 GGCTAATTAAGTACTGATCGATCGAG 59.256 42.308 23.84 18.71 0.00 4.04
602 2456 5.823045 GGCACTTGGCTAATTAAGTACTGAT 59.177 40.000 0.00 0.00 44.01 2.90
603 2457 5.183228 GGCACTTGGCTAATTAAGTACTGA 58.817 41.667 0.00 0.00 44.01 3.41
604 2458 4.941263 TGGCACTTGGCTAATTAAGTACTG 59.059 41.667 0.00 0.00 44.01 2.74
605 2459 5.174037 TGGCACTTGGCTAATTAAGTACT 57.826 39.130 4.25 0.00 44.01 2.73
606 2460 4.941873 ACTGGCACTTGGCTAATTAAGTAC 59.058 41.667 4.25 0.00 44.01 2.73
608 2462 4.034285 ACTGGCACTTGGCTAATTAAGT 57.966 40.909 4.25 0.00 44.01 2.24
609 2463 5.065218 CAGTACTGGCACTTGGCTAATTAAG 59.935 44.000 15.49 0.00 44.01 1.85
610 2464 4.941263 CAGTACTGGCACTTGGCTAATTAA 59.059 41.667 15.49 0.00 44.01 1.40
614 2468 1.697432 ACAGTACTGGCACTTGGCTAA 59.303 47.619 26.12 0.00 44.01 3.09
833 2726 1.114722 CAGAGGAGGAGCTGGCTAGG 61.115 65.000 0.00 0.00 0.00 3.02
834 2727 1.114722 CCAGAGGAGGAGCTGGCTAG 61.115 65.000 0.00 0.00 44.53 3.42
835 2728 1.075674 CCAGAGGAGGAGCTGGCTA 60.076 63.158 0.00 0.00 44.53 3.93
836 2729 2.365370 CCAGAGGAGGAGCTGGCT 60.365 66.667 0.00 0.00 44.53 4.75
839 2732 1.379176 TCGACCAGAGGAGGAGCTG 60.379 63.158 0.00 0.00 0.00 4.24
840 2733 1.379309 GTCGACCAGAGGAGGAGCT 60.379 63.158 3.51 0.00 0.00 4.09
841 2734 1.040339 ATGTCGACCAGAGGAGGAGC 61.040 60.000 14.12 0.00 0.00 4.70
842 2735 1.028905 GATGTCGACCAGAGGAGGAG 58.971 60.000 14.12 0.00 0.00 3.69
843 2736 0.395862 GGATGTCGACCAGAGGAGGA 60.396 60.000 14.12 0.00 0.00 3.71
844 2737 1.395826 GGGATGTCGACCAGAGGAGG 61.396 65.000 14.12 0.00 0.00 4.30
859 2752 2.123812 GGACGGAGAGGTCGGGAT 60.124 66.667 0.00 0.00 37.82 3.85
865 2758 1.705873 GTGGATATGGACGGAGAGGT 58.294 55.000 0.00 0.00 0.00 3.85
952 2851 1.953686 GCTAGCTTCCGATGAGAGACT 59.046 52.381 7.70 0.00 0.00 3.24
1286 3199 3.131400 GCCAGGTTAGTTTGGTTTTGACA 59.869 43.478 0.00 0.00 36.81 3.58
1299 3212 0.811616 GCTGATGACGGCCAGGTTAG 60.812 60.000 2.24 0.00 42.05 2.34
1503 3490 1.987807 GAATGCCAGGCCAGCTAGGA 61.988 60.000 17.61 0.00 41.22 2.94
1504 3491 1.527844 GAATGCCAGGCCAGCTAGG 60.528 63.158 17.61 6.59 41.84 3.02
1505 3492 1.527844 GGAATGCCAGGCCAGCTAG 60.528 63.158 17.61 0.00 0.00 3.42
1506 3493 2.597340 GGAATGCCAGGCCAGCTA 59.403 61.111 17.61 5.98 0.00 3.32
1507 3494 4.809496 CGGAATGCCAGGCCAGCT 62.809 66.667 17.61 0.00 0.00 4.24
1508 3495 4.802051 TCGGAATGCCAGGCCAGC 62.802 66.667 9.64 8.44 0.00 4.85
1509 3496 1.895707 GATCGGAATGCCAGGCCAG 60.896 63.158 9.64 0.00 0.00 4.85
1510 3497 2.192979 GATCGGAATGCCAGGCCA 59.807 61.111 9.64 0.00 0.00 5.36
1511 3498 2.595754 GGATCGGAATGCCAGGCC 60.596 66.667 9.64 0.00 0.00 5.19
1664 3781 1.749634 ACGAGTATTTCTGGACGGAGG 59.250 52.381 0.00 0.00 0.00 4.30
1666 3783 1.399440 CGACGAGTATTTCTGGACGGA 59.601 52.381 0.00 0.00 36.75 4.69
1667 3784 1.823828 CGACGAGTATTTCTGGACGG 58.176 55.000 0.00 0.00 36.75 4.79
1668 3785 1.399440 TCCGACGAGTATTTCTGGACG 59.601 52.381 0.00 0.00 38.91 4.79
1670 3787 2.995283 TCTCCGACGAGTATTTCTGGA 58.005 47.619 0.00 0.00 37.40 3.86
1671 3788 3.777465 TTCTCCGACGAGTATTTCTGG 57.223 47.619 0.00 0.00 37.40 3.86
1672 3789 5.915758 CCTATTTCTCCGACGAGTATTTCTG 59.084 44.000 0.00 0.00 37.40 3.02
1673 3790 5.593502 ACCTATTTCTCCGACGAGTATTTCT 59.406 40.000 0.00 0.00 37.40 2.52
1674 3791 5.829829 ACCTATTTCTCCGACGAGTATTTC 58.170 41.667 0.00 0.00 37.40 2.17
1675 3792 5.848833 ACCTATTTCTCCGACGAGTATTT 57.151 39.130 0.00 0.00 37.40 1.40
1677 3794 6.949352 TTTACCTATTTCTCCGACGAGTAT 57.051 37.500 0.00 0.00 37.40 2.12
1678 3795 6.757897 TTTTACCTATTTCTCCGACGAGTA 57.242 37.500 0.00 0.00 37.40 2.59
1679 3796 5.649782 TTTTACCTATTTCTCCGACGAGT 57.350 39.130 0.00 0.00 37.40 4.18
1680 3797 6.018994 CCATTTTTACCTATTTCTCCGACGAG 60.019 42.308 0.00 0.00 37.48 4.18
1682 3799 5.813672 TCCATTTTTACCTATTTCTCCGACG 59.186 40.000 0.00 0.00 0.00 5.12
1683 3800 7.639945 CATCCATTTTTACCTATTTCTCCGAC 58.360 38.462 0.00 0.00 0.00 4.79
1684 3801 6.262273 GCATCCATTTTTACCTATTTCTCCGA 59.738 38.462 0.00 0.00 0.00 4.55
1685 3802 6.039270 TGCATCCATTTTTACCTATTTCTCCG 59.961 38.462 0.00 0.00 0.00 4.63
1686 3803 7.346751 TGCATCCATTTTTACCTATTTCTCC 57.653 36.000 0.00 0.00 0.00 3.71
1687 3804 8.854117 AGATGCATCCATTTTTACCTATTTCTC 58.146 33.333 23.06 0.00 0.00 2.87
1688 3805 8.773033 AGATGCATCCATTTTTACCTATTTCT 57.227 30.769 23.06 0.00 0.00 2.52
1690 3807 9.866655 TCTAGATGCATCCATTTTTACCTATTT 57.133 29.630 23.06 1.25 0.00 1.40
1691 3808 9.866655 TTCTAGATGCATCCATTTTTACCTATT 57.133 29.630 23.06 1.91 0.00 1.73
1692 3809 9.289782 GTTCTAGATGCATCCATTTTTACCTAT 57.710 33.333 23.06 2.35 0.00 2.57
1693 3810 8.494433 AGTTCTAGATGCATCCATTTTTACCTA 58.506 33.333 23.06 4.13 0.00 3.08
1694 3811 7.349598 AGTTCTAGATGCATCCATTTTTACCT 58.650 34.615 23.06 3.09 0.00 3.08
1695 3812 7.573968 AGTTCTAGATGCATCCATTTTTACC 57.426 36.000 23.06 3.05 0.00 2.85
1700 3817 8.993121 CGTATTTAGTTCTAGATGCATCCATTT 58.007 33.333 23.06 7.24 0.00 2.32
1701 3818 8.150945 ACGTATTTAGTTCTAGATGCATCCATT 58.849 33.333 23.06 7.62 0.00 3.16
1702 3819 7.671302 ACGTATTTAGTTCTAGATGCATCCAT 58.329 34.615 23.06 8.39 0.00 3.41
1704 3821 7.371936 AGACGTATTTAGTTCTAGATGCATCC 58.628 38.462 23.06 7.42 0.00 3.51
1705 3822 9.549509 CTAGACGTATTTAGTTCTAGATGCATC 57.450 37.037 19.37 19.37 31.53 3.91
1707 3824 8.672823 TCTAGACGTATTTAGTTCTAGATGCA 57.327 34.615 0.00 0.00 33.50 3.96
1722 3839 9.613957 CGAAGAAATGAATGTATCTAGACGTAT 57.386 33.333 0.00 0.00 0.00 3.06
1725 3941 7.644157 TGTCGAAGAAATGAATGTATCTAGACG 59.356 37.037 0.00 0.00 39.69 4.18
1742 3959 4.178540 GTCCGGAAATACATGTCGAAGAA 58.821 43.478 5.23 0.00 39.69 2.52
1743 3960 3.732774 CGTCCGGAAATACATGTCGAAGA 60.733 47.826 5.23 0.00 0.00 2.87
1744 3961 2.534349 CGTCCGGAAATACATGTCGAAG 59.466 50.000 5.23 0.00 0.00 3.79
1745 3962 2.532235 CGTCCGGAAATACATGTCGAA 58.468 47.619 5.23 0.00 0.00 3.71
1746 3963 1.202325 CCGTCCGGAAATACATGTCGA 60.202 52.381 5.23 0.00 37.50 4.20
1747 3964 1.202325 TCCGTCCGGAAATACATGTCG 60.202 52.381 5.23 1.25 42.05 4.35
1748 3965 2.470821 CTCCGTCCGGAAATACATGTC 58.529 52.381 5.23 0.00 44.66 3.06
1749 3966 1.138266 CCTCCGTCCGGAAATACATGT 59.862 52.381 5.23 2.69 44.66 3.21
1750 3967 1.540363 CCCTCCGTCCGGAAATACATG 60.540 57.143 5.23 0.00 44.66 3.21
1751 3968 0.756903 CCCTCCGTCCGGAAATACAT 59.243 55.000 5.23 0.00 44.66 2.29
1752 3969 0.324552 TCCCTCCGTCCGGAAATACA 60.325 55.000 5.23 0.00 44.66 2.29
1753 3970 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
1754 3971 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
1755 3972 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
1756 3973 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
1757 3974 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
1758 3975 1.856539 AAGTACTCCCTCCGTCCGGA 61.857 60.000 0.00 0.00 42.90 5.14
1759 3976 1.379576 AAGTACTCCCTCCGTCCGG 60.380 63.158 0.00 0.00 0.00 5.14
1760 3977 1.807886 CAAGTACTCCCTCCGTCCG 59.192 63.158 0.00 0.00 0.00 4.79
1761 3978 1.255667 TGCAAGTACTCCCTCCGTCC 61.256 60.000 0.00 0.00 0.00 4.79
1762 3979 0.173708 CTGCAAGTACTCCCTCCGTC 59.826 60.000 0.00 0.00 0.00 4.79
1763 3980 2.277858 CTGCAAGTACTCCCTCCGT 58.722 57.895 0.00 0.00 0.00 4.69
1775 3992 1.230635 CCCTCACCGAACACTGCAAG 61.231 60.000 0.00 0.00 42.29 4.01
1776 3993 1.227823 CCCTCACCGAACACTGCAA 60.228 57.895 0.00 0.00 0.00 4.08
1777 3994 1.978455 AACCCTCACCGAACACTGCA 61.978 55.000 0.00 0.00 0.00 4.41
1778 3995 1.227853 AACCCTCACCGAACACTGC 60.228 57.895 0.00 0.00 0.00 4.40
1800 4017 1.484653 GCCCCGGCAAATTTAATTCCT 59.515 47.619 0.00 0.00 41.49 3.36
1851 4068 1.204704 TCTGCAACGACGATGGATCTT 59.795 47.619 0.00 0.00 0.00 2.40
1880 4097 9.242477 CTTTTTAGAACTAGTATTAGGTACGCC 57.758 37.037 0.00 0.00 38.38 5.68
1895 4112 9.754382 TGTGTACGTAGAAATCTTTTTAGAACT 57.246 29.630 0.00 0.00 0.00 3.01
1928 4145 6.979238 GCACTATGTACGTAGAGATCCTTTTT 59.021 38.462 25.55 0.00 0.00 1.94
1929 4146 6.321690 AGCACTATGTACGTAGAGATCCTTTT 59.678 38.462 25.55 0.32 0.00 2.27
1930 4147 5.828859 AGCACTATGTACGTAGAGATCCTTT 59.171 40.000 25.55 0.99 0.00 3.11
1931 4148 5.378332 AGCACTATGTACGTAGAGATCCTT 58.622 41.667 25.55 1.68 0.00 3.36
1932 4149 4.975631 AGCACTATGTACGTAGAGATCCT 58.024 43.478 25.55 9.86 0.00 3.24
1933 4150 4.154556 GGAGCACTATGTACGTAGAGATCC 59.845 50.000 29.05 29.05 39.45 3.36
1934 4151 4.998672 AGGAGCACTATGTACGTAGAGATC 59.001 45.833 25.55 23.69 30.29 2.75
1935 4152 4.975631 AGGAGCACTATGTACGTAGAGAT 58.024 43.478 25.55 17.82 0.00 2.75
1936 4153 4.418973 AGGAGCACTATGTACGTAGAGA 57.581 45.455 25.55 0.00 0.00 3.10
1937 4154 5.055144 TGTAGGAGCACTATGTACGTAGAG 58.945 45.833 25.55 19.34 33.43 2.43
1938 4155 5.027293 TGTAGGAGCACTATGTACGTAGA 57.973 43.478 25.55 0.00 33.43 2.59
1939 4156 5.238868 ACATGTAGGAGCACTATGTACGTAG 59.761 44.000 18.69 18.69 33.43 3.51
1940 4157 5.008316 CACATGTAGGAGCACTATGTACGTA 59.992 44.000 0.00 0.00 33.43 3.57
1941 4158 3.952323 ACATGTAGGAGCACTATGTACGT 59.048 43.478 0.00 0.00 33.43 3.57
1942 4159 4.290969 CACATGTAGGAGCACTATGTACG 58.709 47.826 0.00 0.00 33.43 3.67
1943 4160 4.051922 GCACATGTAGGAGCACTATGTAC 58.948 47.826 0.00 0.00 33.43 2.90
1944 4161 3.704061 TGCACATGTAGGAGCACTATGTA 59.296 43.478 0.00 0.00 33.43 2.29
1945 4162 2.501316 TGCACATGTAGGAGCACTATGT 59.499 45.455 0.00 0.00 33.43 2.29
1946 4163 3.129109 CTGCACATGTAGGAGCACTATG 58.871 50.000 0.00 0.00 33.43 2.23
1947 4164 3.465742 CTGCACATGTAGGAGCACTAT 57.534 47.619 0.00 0.00 33.43 2.12
1948 4165 2.967599 CTGCACATGTAGGAGCACTA 57.032 50.000 0.00 0.00 32.87 2.74
1949 4166 3.849002 CTGCACATGTAGGAGCACT 57.151 52.632 0.00 0.00 32.87 4.40
1965 4182 2.083774 ACGTAACCACCATTGATGCTG 58.916 47.619 0.00 0.00 0.00 4.41
1995 4212 6.922957 AGGTTAACGTTTTAAGTCGTGACATA 59.077 34.615 5.91 0.00 40.19 2.29
2022 4245 5.863397 CGCATGTTGGTAAAAAGATCACAAT 59.137 36.000 0.00 0.00 0.00 2.71
2023 4246 5.218885 CGCATGTTGGTAAAAAGATCACAA 58.781 37.500 0.00 0.00 0.00 3.33
2025 4248 3.608073 GCGCATGTTGGTAAAAAGATCAC 59.392 43.478 0.30 0.00 0.00 3.06
2026 4249 3.254411 TGCGCATGTTGGTAAAAAGATCA 59.746 39.130 5.66 0.00 0.00 2.92
2027 4250 3.832276 TGCGCATGTTGGTAAAAAGATC 58.168 40.909 5.66 0.00 0.00 2.75
2028 4251 3.932545 TGCGCATGTTGGTAAAAAGAT 57.067 38.095 5.66 0.00 0.00 2.40
2029 4252 3.573598 CATGCGCATGTTGGTAAAAAGA 58.426 40.909 36.45 0.00 34.23 2.52
2030 4253 2.092524 GCATGCGCATGTTGGTAAAAAG 59.907 45.455 41.40 19.45 40.80 2.27
2079 4398 2.599578 GCCGCGTAGGGAGGGATA 60.600 66.667 4.92 0.00 46.37 2.59
2191 4510 5.660460 AGCATGTTCGTTGTGATCTGTATA 58.340 37.500 0.00 0.00 0.00 1.47
2193 4512 3.925379 AGCATGTTCGTTGTGATCTGTA 58.075 40.909 0.00 0.00 0.00 2.74
2194 4513 2.771089 AGCATGTTCGTTGTGATCTGT 58.229 42.857 0.00 0.00 0.00 3.41
2214 4606 3.519107 TGAGATCCATGTTTGGCTCTGTA 59.481 43.478 3.26 0.00 46.16 2.74
2657 5060 1.199327 GTGTTCATCTGGTCGACGAGA 59.801 52.381 28.89 28.89 35.23 4.04
2985 5391 4.032960 TGGGACTTGTACATCTTTGCAT 57.967 40.909 0.00 0.00 0.00 3.96
2986 5392 3.500448 TGGGACTTGTACATCTTTGCA 57.500 42.857 0.00 0.00 0.00 4.08
2987 5393 5.391312 AAATGGGACTTGTACATCTTTGC 57.609 39.130 0.00 0.00 0.00 3.68
2988 5394 5.711976 AGGAAATGGGACTTGTACATCTTTG 59.288 40.000 0.00 0.00 0.00 2.77
2989 5395 5.892348 AGGAAATGGGACTTGTACATCTTT 58.108 37.500 0.00 0.00 0.00 2.52
2990 5396 5.520748 AGGAAATGGGACTTGTACATCTT 57.479 39.130 0.00 0.00 0.00 2.40
2992 5398 5.696724 CGATAGGAAATGGGACTTGTACATC 59.303 44.000 0.00 0.00 0.00 3.06
3057 5499 1.682982 ACAGACTAATATACGCGCGC 58.317 50.000 32.58 23.91 0.00 6.86
3058 5500 3.552541 AGAACAGACTAATATACGCGCG 58.447 45.455 30.96 30.96 0.00 6.86
3108 5550 6.036083 GTCTATACCTGTTACACAACTGCATG 59.964 42.308 0.00 0.00 35.56 4.06
3109 5551 6.106673 GTCTATACCTGTTACACAACTGCAT 58.893 40.000 0.00 0.00 35.56 3.96
3110 5552 5.011227 TGTCTATACCTGTTACACAACTGCA 59.989 40.000 0.00 0.00 35.56 4.41
3111 5553 5.475719 TGTCTATACCTGTTACACAACTGC 58.524 41.667 0.00 0.00 35.56 4.40
3116 5558 9.607988 CCAATTATTGTCTATACCTGTTACACA 57.392 33.333 4.15 0.00 0.00 3.72
3117 5559 9.609346 ACCAATTATTGTCTATACCTGTTACAC 57.391 33.333 4.15 0.00 0.00 2.90
3222 5693 5.008331 ACGACCACAACTAGTCTCTGAATA 58.992 41.667 0.00 0.00 0.00 1.75
3264 5735 8.735692 ATACATGTGAAATGTGATGTGATGTA 57.264 30.769 9.11 0.00 33.76 2.29
3343 5820 6.322456 TGTTTGTATTTGATCTGTTGGTTGGA 59.678 34.615 0.00 0.00 0.00 3.53
3361 5838 1.018148 CCTTGTGCCGTGTGTTTGTA 58.982 50.000 0.00 0.00 0.00 2.41
3365 5842 1.877443 GTTATCCTTGTGCCGTGTGTT 59.123 47.619 0.00 0.00 0.00 3.32
3366 5843 1.202710 TGTTATCCTTGTGCCGTGTGT 60.203 47.619 0.00 0.00 0.00 3.72
3427 5904 5.215252 AGAAGAGAAACGAGTGGAAATGA 57.785 39.130 0.00 0.00 0.00 2.57
3488 5965 3.783082 AGCCAAGAGAGCCTAGGTTTATT 59.217 43.478 11.31 0.00 0.00 1.40
3540 6018 0.034616 CCCTCCTTCCTGATGCGATC 59.965 60.000 0.00 0.00 0.00 3.69
3569 6050 8.060090 GCTCTTTTGTTTTTCTGAATGTTCATG 58.940 33.333 0.00 0.00 36.46 3.07
3584 6065 9.401058 ACTATCTGCATATAAGCTCTTTTGTTT 57.599 29.630 1.16 0.00 34.99 2.83
3596 6077 7.480760 TGCTCCATACACTATCTGCATATAA 57.519 36.000 0.00 0.00 0.00 0.98
3614 6095 1.863662 GAGTCGTCGTCCTTGCTCCA 61.864 60.000 0.00 0.00 0.00 3.86
3625 6106 2.543687 ATCCAAGCCGTGAGTCGTCG 62.544 60.000 1.37 1.37 37.94 5.12
3626 6107 1.078759 CATCCAAGCCGTGAGTCGTC 61.079 60.000 0.00 0.00 37.94 4.20
3627 6108 1.079819 CATCCAAGCCGTGAGTCGT 60.080 57.895 0.00 0.00 37.94 4.34
3666 6147 2.506217 TTCATCGAGACGCACGGC 60.506 61.111 0.00 0.00 0.00 5.68
3894 6375 7.260558 TCGCTCTGCCTATGTATATATGTAC 57.739 40.000 2.82 2.82 0.00 2.90
3903 6384 4.099419 TCAAGATTTCGCTCTGCCTATGTA 59.901 41.667 0.00 0.00 0.00 2.29
3928 6409 1.087501 GTTCCTCGGGCACTGAATTC 58.912 55.000 0.00 0.00 46.55 2.17
3957 6438 3.539604 CTCCCCTGCTTGATTAGTTCAG 58.460 50.000 0.00 0.00 35.27 3.02
3958 6439 3.634397 CTCCCCTGCTTGATTAGTTCA 57.366 47.619 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.