Multiple sequence alignment - TraesCS1B01G137300

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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 TraesCS1B01G137300 chr1B 100.000 7649 0 0 1 7649 175422481 175414833 0.000000e+00 14126.0
1 TraesCS1B01G137300 chr1B 94.964 139 5 2 3899 4037 649332727 649332863 4.650000e-52 217.0
2 TraesCS1B01G137300 chr1B 96.850 127 4 0 3903 4029 56893236 56893362 6.010000e-51 213.0
3 TraesCS1B01G137300 chr1B 87.963 108 13 0 6914 7021 543023057 543023164 2.240000e-25 128.0
4 TraesCS1B01G137300 chr1B 100.000 28 0 0 6116 6143 423847024 423847051 1.400000e-02 52.8
5 TraesCS1B01G137300 chr1A 97.749 2887 57 7 4026 6908 124888931 124886049 0.000000e+00 4964.0
6 TraesCS1B01G137300 chr1A 98.075 1818 33 2 2091 3907 124890767 124888951 0.000000e+00 3162.0
7 TraesCS1B01G137300 chr1A 89.947 2069 90 36 1 2018 124892765 124890764 0.000000e+00 2560.0
8 TraesCS1B01G137300 chr1A 86.480 392 32 8 7127 7502 124885917 124885531 1.990000e-110 411.0
9 TraesCS1B01G137300 chr1A 94.444 72 2 2 7053 7124 124886015 124885946 8.120000e-20 110.0
10 TraesCS1B01G137300 chr1D 97.875 2870 47 11 4026 6888 114357103 114354241 0.000000e+00 4950.0
11 TraesCS1B01G137300 chr1D 97.319 2499 57 9 1414 3907 114359616 114357123 0.000000e+00 4235.0
12 TraesCS1B01G137300 chr1D 89.961 1295 50 24 1 1278 114360922 114359691 0.000000e+00 1598.0
13 TraesCS1B01G137300 chr1D 85.323 402 27 12 7132 7505 114353785 114353388 3.350000e-103 387.0
14 TraesCS1B01G137300 chr1D 92.466 146 10 1 7502 7647 114353105 114352961 2.800000e-49 207.0
15 TraesCS1B01G137300 chr1D 90.678 118 7 4 7011 7127 114353986 114353872 3.700000e-33 154.0
16 TraesCS1B01G137300 chr1D 91.262 103 9 0 6917 7019 361353563 361353665 2.880000e-29 141.0
17 TraesCS1B01G137300 chr3B 83.740 492 64 16 4124 4610 133769607 133770087 1.170000e-122 451.0
18 TraesCS1B01G137300 chr3B 95.000 140 5 2 3896 4034 794286401 794286263 1.290000e-52 219.0
19 TraesCS1B01G137300 chr3B 91.000 100 9 0 6917 7016 255233969 255233870 1.340000e-27 135.0
20 TraesCS1B01G137300 chr6B 98.462 130 2 0 3900 4029 716890473 716890344 5.970000e-56 230.0
21 TraesCS1B01G137300 chr6B 100.000 28 0 0 6116 6143 637906006 637906033 1.400000e-02 52.8
22 TraesCS1B01G137300 chr4B 98.450 129 2 0 3902 4030 339479045 339478917 2.150000e-55 228.0
23 TraesCS1B01G137300 chr4B 100.000 28 0 0 6116 6143 429865363 429865390 1.400000e-02 52.8
24 TraesCS1B01G137300 chr2B 96.377 138 3 2 3893 4029 740744126 740744262 7.720000e-55 226.0
25 TraesCS1B01G137300 chr2B 90.741 108 10 0 6917 7024 314998852 314998745 2.220000e-30 145.0
26 TraesCS1B01G137300 chr2B 100.000 28 0 0 6116 6143 137198370 137198343 1.400000e-02 52.8
27 TraesCS1B01G137300 chr5B 97.692 130 2 1 3903 4032 24110981 24111109 9.990000e-54 222.0
28 TraesCS1B01G137300 chr5B 89.423 104 10 1 6911 7013 180913306 180913409 6.230000e-26 130.0
29 TraesCS1B01G137300 chr5B 100.000 28 0 0 6116 6143 193978999 193978972 1.400000e-02 52.8
30 TraesCS1B01G137300 chr5B 100.000 28 0 0 6116 6143 255223671 255223698 1.400000e-02 52.8
31 TraesCS1B01G137300 chr5B 100.000 28 0 0 6116 6143 262665222 262665249 1.400000e-02 52.8
32 TraesCS1B01G137300 chr2D 96.324 136 4 1 3902 4037 348846420 348846554 9.990000e-54 222.0
33 TraesCS1B01G137300 chr2D 87.850 107 13 0 6917 7023 7661703 7661597 8.060000e-25 126.0
34 TraesCS1B01G137300 chr4A 92.568 148 11 0 3903 4050 724728290 724728143 6.010000e-51 213.0
35 TraesCS1B01G137300 chrUn 92.157 102 8 0 6915 7016 314370671 314370570 2.220000e-30 145.0
36 TraesCS1B01G137300 chr7D 91.919 99 8 0 6917 7015 398878056 398877958 1.030000e-28 139.0
37 TraesCS1B01G137300 chr5D 88.679 106 12 0 6913 7018 558970535 558970430 6.230000e-26 130.0


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 TraesCS1B01G137300 chr1B 175414833 175422481 7648 True 14126.000000 14126 100.000000 1 7649 1 chr1B.!!$R1 7648
1 TraesCS1B01G137300 chr1A 124885531 124892765 7234 True 2241.400000 4964 93.339000 1 7502 5 chr1A.!!$R1 7501
2 TraesCS1B01G137300 chr1D 114352961 114360922 7961 True 1921.833333 4950 92.270333 1 7647 6 chr1D.!!$R1 7646

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
952 996 0.266152 ATCTTCTCTCCCCCGATGGT 59.734 55.000 0.00 0.00 0.00 3.55 F
1737 1803 0.027979 CGGTGTGTGAAGCTTGTGTG 59.972 55.000 2.10 0.00 0.00 3.82 F
1787 1853 0.453390 GTTAAGCAGAGCATGGCCAC 59.547 55.000 8.16 0.00 0.00 5.01 F
2382 2451 1.480137 TGGCTTTGTTTGTGTGGGAAG 59.520 47.619 0.00 0.00 0.00 3.46 F
3822 3892 1.340889 GTCAGAGCCAGAGAGCCATAG 59.659 57.143 0.00 0.00 0.00 2.23 F
4024 4095 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30 F
5803 5875 0.247736 AGTTCTGGGAGCGCTTACAG 59.752 55.000 26.86 26.86 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1901 1967 0.946221 GCAAGCATCCTATCGACCGG 60.946 60.000 0.00 0.0 0.00 5.28 R
2682 2752 1.470098 GCAAAGGCATGGTGTACAGAG 59.530 52.381 0.00 0.0 40.72 3.35 R
2902 2972 4.016444 ACACAGTCAACACAACTGGAAAT 58.984 39.130 8.03 0.0 46.73 2.17 R
4006 4077 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.0 44.66 2.12 R
5104 5176 0.664166 GCCACAAATCAACACCTGCG 60.664 55.000 0.00 0.0 0.00 5.18 R
5991 6063 0.976641 ACTCCAAGAAGGACGCATGA 59.023 50.000 0.00 0.0 43.07 3.07 R
7429 7767 0.167470 CATGACAACCTCGCAGCAAG 59.833 55.000 0.00 0.0 0.00 4.01 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
50 55 0.469144 TGTGAGGTTTTCCCCAAGGC 60.469 55.000 0.00 0.00 41.86 4.35
84 97 1.284313 TGTGTCCATGTGGCTCCATA 58.716 50.000 0.00 0.00 34.44 2.74
135 148 2.503775 CCAACTTGTGGTGCCAACT 58.496 52.632 0.00 0.00 43.20 3.16
136 149 0.823460 CCAACTTGTGGTGCCAACTT 59.177 50.000 0.00 0.00 43.20 2.66
137 150 1.471327 CCAACTTGTGGTGCCAACTTG 60.471 52.381 0.00 0.00 43.20 3.16
138 151 1.476085 CAACTTGTGGTGCCAACTTGA 59.524 47.619 0.00 0.00 0.00 3.02
139 152 2.071778 ACTTGTGGTGCCAACTTGAT 57.928 45.000 0.00 0.00 0.00 2.57
140 153 2.387757 ACTTGTGGTGCCAACTTGATT 58.612 42.857 0.00 0.00 0.00 2.57
141 154 2.765699 ACTTGTGGTGCCAACTTGATTT 59.234 40.909 0.00 0.00 0.00 2.17
142 155 3.197549 ACTTGTGGTGCCAACTTGATTTT 59.802 39.130 0.00 0.00 0.00 1.82
143 156 3.902881 TGTGGTGCCAACTTGATTTTT 57.097 38.095 0.00 0.00 0.00 1.94
239 252 6.874664 TGATTGCTATTGTTACGGTACTGAAA 59.125 34.615 9.17 0.00 0.00 2.69
243 256 7.045416 TGCTATTGTTACGGTACTGAAATCAT 58.955 34.615 9.17 0.00 0.00 2.45
244 257 7.551262 TGCTATTGTTACGGTACTGAAATCATT 59.449 33.333 9.17 1.74 0.00 2.57
254 267 6.349300 GGTACTGAAATCATTCTCAGGCTAA 58.651 40.000 11.78 0.00 42.83 3.09
307 324 5.537188 TCGATGTTAGCATGCATGTATGTA 58.463 37.500 26.79 12.17 35.07 2.29
308 325 5.405269 TCGATGTTAGCATGCATGTATGTAC 59.595 40.000 26.79 17.77 35.07 2.90
309 326 5.406477 CGATGTTAGCATGCATGTATGTACT 59.594 40.000 26.79 16.36 35.07 2.73
310 327 5.989551 TGTTAGCATGCATGTATGTACTG 57.010 39.130 26.79 0.85 0.00 2.74
311 328 5.427378 TGTTAGCATGCATGTATGTACTGT 58.573 37.500 26.79 7.54 0.00 3.55
312 329 6.578023 TGTTAGCATGCATGTATGTACTGTA 58.422 36.000 26.79 5.64 0.00 2.74
313 330 7.216494 TGTTAGCATGCATGTATGTACTGTAT 58.784 34.615 26.79 5.70 0.00 2.29
434 458 2.406401 CACCCCGTACGCTCGTAG 59.594 66.667 10.49 0.00 0.00 3.51
472 503 2.814913 AATCGCCCCGTTTCCCTGAC 62.815 60.000 0.00 0.00 0.00 3.51
486 524 0.459237 CCTGACTGCCATGTCTCGAC 60.459 60.000 0.00 0.00 37.79 4.20
616 655 2.186644 CACGGCATCATCGGGTCA 59.813 61.111 0.00 0.00 0.00 4.02
617 656 2.173669 CACGGCATCATCGGGTCAC 61.174 63.158 0.00 0.00 0.00 3.67
618 657 2.588877 CGGCATCATCGGGTCACC 60.589 66.667 0.00 0.00 0.00 4.02
619 658 2.203209 GGCATCATCGGGTCACCC 60.203 66.667 1.06 1.06 41.09 4.61
620 659 2.589540 GCATCATCGGGTCACCCA 59.410 61.111 15.17 0.00 45.83 4.51
621 660 1.524621 GCATCATCGGGTCACCCAG 60.525 63.158 15.17 5.98 45.83 4.45
771 813 4.864334 CTGGCCCCACGCAGATCC 62.864 72.222 0.00 0.00 40.31 3.36
792 834 2.180769 CATCGGCTCGAACGGACA 59.819 61.111 8.99 0.00 39.99 4.02
887 931 4.034742 CCACGTTTACTATTTTCATCGGGG 59.965 45.833 0.00 0.00 34.47 5.73
952 996 0.266152 ATCTTCTCTCCCCCGATGGT 59.734 55.000 0.00 0.00 0.00 3.55
955 999 0.981277 TTCTCTCCCCCGATGGTTCC 60.981 60.000 0.00 0.00 0.00 3.62
1234 1283 1.988982 GCCTCAATCCCCTCACCTCC 61.989 65.000 0.00 0.00 0.00 4.30
1238 1287 1.354368 TCAATCCCCTCACCTCCAAAC 59.646 52.381 0.00 0.00 0.00 2.93
1254 1303 0.822121 AAACTTCCTCCACGGGTTGC 60.822 55.000 0.00 0.00 0.00 4.17
1258 1307 2.672996 CCTCCACGGGTTGCTTGG 60.673 66.667 0.00 0.00 0.00 3.61
1259 1308 2.672996 CTCCACGGGTTGCTTGGG 60.673 66.667 0.00 0.00 0.00 4.12
1261 1310 2.520741 CCACGGGTTGCTTGGGTT 60.521 61.111 0.00 0.00 0.00 4.11
1283 1333 2.749441 GCTGGGTGCAGCTCCTTC 60.749 66.667 16.65 0.00 44.31 3.46
1284 1334 2.435586 CTGGGTGCAGCTCCTTCG 60.436 66.667 16.65 0.00 0.00 3.79
1285 1335 4.704833 TGGGTGCAGCTCCTTCGC 62.705 66.667 16.65 0.00 0.00 4.70
1286 1336 4.400961 GGGTGCAGCTCCTTCGCT 62.401 66.667 16.65 0.00 41.90 4.93
1302 1352 3.842126 CTGCATGCGGACGTGTCG 61.842 66.667 22.55 0.00 35.09 4.35
1307 1357 0.247262 CATGCGGACGTGTCGAATTG 60.247 55.000 11.42 2.61 0.00 2.32
1308 1358 0.389296 ATGCGGACGTGTCGAATTGA 60.389 50.000 11.42 0.00 0.00 2.57
1316 1366 4.590487 GTCGAATTGACGCCTCCA 57.410 55.556 0.00 0.00 37.96 3.86
1343 1400 6.691754 TTTGTCTGTTGCTCTTGTTGATTA 57.308 33.333 0.00 0.00 0.00 1.75
1354 1411 5.484715 CTCTTGTTGATTAAACTCGGGGTA 58.515 41.667 0.00 0.00 39.70 3.69
1358 1415 6.746745 TGTTGATTAAACTCGGGGTAATTC 57.253 37.500 0.00 0.00 39.70 2.17
1360 1417 7.622713 TGTTGATTAAACTCGGGGTAATTCTA 58.377 34.615 0.00 0.00 39.70 2.10
1366 1423 1.000955 CTCGGGGTAATTCTATGCGCT 59.999 52.381 9.73 0.00 0.00 5.92
1379 1436 4.765273 TCTATGCGCTTGAAGGAAATGTA 58.235 39.130 9.73 0.00 0.00 2.29
1380 1437 4.811024 TCTATGCGCTTGAAGGAAATGTAG 59.189 41.667 9.73 0.00 0.00 2.74
1382 1439 1.740025 GCGCTTGAAGGAAATGTAGCT 59.260 47.619 0.00 0.00 0.00 3.32
1383 1440 2.223135 GCGCTTGAAGGAAATGTAGCTC 60.223 50.000 0.00 0.00 0.00 4.09
1385 1442 3.686726 CGCTTGAAGGAAATGTAGCTCTT 59.313 43.478 0.00 0.00 0.00 2.85
1388 1454 6.128282 CGCTTGAAGGAAATGTAGCTCTTAAA 60.128 38.462 0.00 0.00 0.00 1.52
1401 1467 5.725110 AGCTCTTAAATTGATGCTGTACG 57.275 39.130 0.00 0.00 0.00 3.67
1406 1472 7.412563 GCTCTTAAATTGATGCTGTACGTGTTA 60.413 37.037 0.00 0.00 0.00 2.41
1407 1473 7.735500 TCTTAAATTGATGCTGTACGTGTTAC 58.264 34.615 0.00 0.00 0.00 2.50
1408 1474 7.601130 TCTTAAATTGATGCTGTACGTGTTACT 59.399 33.333 0.00 0.00 0.00 2.24
1409 1475 8.760103 TTAAATTGATGCTGTACGTGTTACTA 57.240 30.769 0.00 0.00 0.00 1.82
1410 1476 7.843490 AAATTGATGCTGTACGTGTTACTAT 57.157 32.000 0.00 0.00 0.00 2.12
1411 1477 7.843490 AATTGATGCTGTACGTGTTACTATT 57.157 32.000 0.00 0.00 0.00 1.73
1412 1478 7.843490 ATTGATGCTGTACGTGTTACTATTT 57.157 32.000 0.00 0.00 0.00 1.40
1413 1479 7.661127 TTGATGCTGTACGTGTTACTATTTT 57.339 32.000 0.00 0.00 0.00 1.82
1414 1480 7.661127 TGATGCTGTACGTGTTACTATTTTT 57.339 32.000 0.00 0.00 0.00 1.94
1450 1516 3.508744 ATGCGATTCTTCGGCAATTTT 57.491 38.095 0.00 0.00 45.59 1.82
1506 1572 8.482128 AGGGTGAATTTTTCTCTATCTCTGTAG 58.518 37.037 0.00 0.00 0.00 2.74
1527 1593 3.194968 AGCATTTCTTTGGCCATCTTCTG 59.805 43.478 6.09 1.52 0.00 3.02
1567 1633 5.088739 CGTTCTAATTACTTGCAGCTTTGG 58.911 41.667 0.00 0.00 0.00 3.28
1609 1675 0.458370 CCCCTGCAAAATTGTAGCGC 60.458 55.000 0.00 0.00 39.23 5.92
1613 1679 2.187707 CTGCAAAATTGTAGCGCCATC 58.812 47.619 2.29 0.00 34.26 3.51
1624 1690 2.015736 AGCGCCATCTCACTACTTTG 57.984 50.000 2.29 0.00 0.00 2.77
1723 1789 0.317160 TCTCTTCACGATTGCGGTGT 59.683 50.000 0.00 0.00 43.17 4.16
1734 1800 1.029408 TTGCGGTGTGTGAAGCTTGT 61.029 50.000 2.10 0.00 0.00 3.16
1737 1803 0.027979 CGGTGTGTGAAGCTTGTGTG 59.972 55.000 2.10 0.00 0.00 3.82
1787 1853 0.453390 GTTAAGCAGAGCATGGCCAC 59.547 55.000 8.16 0.00 0.00 5.01
1868 1934 7.943079 TGGCCTATTATCACATCATATTTGG 57.057 36.000 3.32 0.00 0.00 3.28
1901 1967 2.164422 GGGGCTAGTTTCAAATGTCTGC 59.836 50.000 0.00 0.00 0.00 4.26
2040 2108 6.378280 TCTCAGCTGTCAAGATAGTCATACAA 59.622 38.462 14.67 0.00 0.00 2.41
2064 2133 1.710013 ATGTGCTCTTACCGTGTTCG 58.290 50.000 0.00 0.00 0.00 3.95
2241 2310 4.889409 CCTTGCTATTTCCTTTGGCTGATA 59.111 41.667 0.00 0.00 0.00 2.15
2317 2386 5.046014 AGCAACATTTTATGGGGTAATGCAA 60.046 36.000 0.00 0.00 33.61 4.08
2382 2451 1.480137 TGGCTTTGTTTGTGTGGGAAG 59.520 47.619 0.00 0.00 0.00 3.46
2530 2600 8.999431 TGAACAAGTAGTTTCAAATATGACTCC 58.001 33.333 0.00 0.00 41.51 3.85
2570 2640 3.340034 TCCGCCAAACCTAAGTATTGTG 58.660 45.455 0.00 0.00 0.00 3.33
2603 2673 2.916934 TGGTATAGCCACACCTTTTCCT 59.083 45.455 0.00 0.00 43.61 3.36
2651 2721 9.620259 GAATTAGAAATCTGTGGAGGTCTTATT 57.380 33.333 0.00 0.00 0.00 1.40
2682 2752 6.865834 AGACAGGGAATATATGACTCATCC 57.134 41.667 0.00 0.00 0.00 3.51
2871 2941 1.946768 TGCTGCACCTAACAAGTCAAC 59.053 47.619 0.00 0.00 0.00 3.18
2891 2961 7.758528 AGTCAACGCTTATTTAAATCTACGACT 59.241 33.333 18.05 12.75 0.00 4.18
3822 3892 1.340889 GTCAGAGCCAGAGAGCCATAG 59.659 57.143 0.00 0.00 0.00 2.23
3904 3975 5.452777 CAGCTGCTTTTACCTCAAAACTAC 58.547 41.667 0.00 0.00 32.65 2.73
3907 3978 5.334957 GCTGCTTTTACCTCAAAACTACTCC 60.335 44.000 0.00 0.00 32.65 3.85
3908 3979 5.067954 TGCTTTTACCTCAAAACTACTCCC 58.932 41.667 0.00 0.00 32.65 4.30
3909 3980 5.163131 TGCTTTTACCTCAAAACTACTCCCT 60.163 40.000 0.00 0.00 32.65 4.20
3910 3981 5.411977 GCTTTTACCTCAAAACTACTCCCTC 59.588 44.000 0.00 0.00 32.65 4.30
3911 3982 5.494390 TTTACCTCAAAACTACTCCCTCC 57.506 43.478 0.00 0.00 0.00 4.30
3912 3983 1.900486 ACCTCAAAACTACTCCCTCCG 59.100 52.381 0.00 0.00 0.00 4.63
3913 3984 1.900486 CCTCAAAACTACTCCCTCCGT 59.100 52.381 0.00 0.00 0.00 4.69
3914 3985 2.094130 CCTCAAAACTACTCCCTCCGTC 60.094 54.545 0.00 0.00 0.00 4.79
3915 3986 1.897802 TCAAAACTACTCCCTCCGTCC 59.102 52.381 0.00 0.00 0.00 4.79
3917 3988 2.019807 AAACTACTCCCTCCGTCCAA 57.980 50.000 0.00 0.00 0.00 3.53
3919 3990 2.019807 ACTACTCCCTCCGTCCAAAA 57.980 50.000 0.00 0.00 0.00 2.44
3920 3991 2.332117 ACTACTCCCTCCGTCCAAAAA 58.668 47.619 0.00 0.00 0.00 1.94
3921 3992 2.910977 ACTACTCCCTCCGTCCAAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
3923 3994 3.345508 ACTCCCTCCGTCCAAAAATAC 57.654 47.619 0.00 0.00 0.00 1.89
3924 3995 2.910977 ACTCCCTCCGTCCAAAAATACT 59.089 45.455 0.00 0.00 0.00 2.12
3926 3997 3.681593 TCCCTCCGTCCAAAAATACTTG 58.318 45.455 0.00 0.00 0.00 3.16
3927 3998 3.073356 TCCCTCCGTCCAAAAATACTTGT 59.927 43.478 0.00 0.00 0.00 3.16
3928 3999 3.439129 CCCTCCGTCCAAAAATACTTGTC 59.561 47.826 0.00 0.00 0.00 3.18
3929 4000 4.069304 CCTCCGTCCAAAAATACTTGTCA 58.931 43.478 0.00 0.00 0.00 3.58
3930 4001 4.700213 CCTCCGTCCAAAAATACTTGTCAT 59.300 41.667 0.00 0.00 0.00 3.06
3931 4002 5.163754 CCTCCGTCCAAAAATACTTGTCATC 60.164 44.000 0.00 0.00 0.00 2.92
3932 4003 5.309638 TCCGTCCAAAAATACTTGTCATCA 58.690 37.500 0.00 0.00 0.00 3.07
3933 4004 5.765677 TCCGTCCAAAAATACTTGTCATCAA 59.234 36.000 0.00 0.00 0.00 2.57
3934 4005 6.263392 TCCGTCCAAAAATACTTGTCATCAAA 59.737 34.615 0.00 0.00 32.87 2.69
3935 4006 6.920758 CCGTCCAAAAATACTTGTCATCAAAA 59.079 34.615 0.00 0.00 32.87 2.44
3936 4007 7.598493 CCGTCCAAAAATACTTGTCATCAAAAT 59.402 33.333 0.00 0.00 32.87 1.82
3937 4008 8.427012 CGTCCAAAAATACTTGTCATCAAAATG 58.573 33.333 0.00 0.00 32.87 2.32
3938 4009 8.711457 GTCCAAAAATACTTGTCATCAAAATGG 58.289 33.333 0.00 0.00 33.42 3.16
3939 4010 8.646004 TCCAAAAATACTTGTCATCAAAATGGA 58.354 29.630 0.00 0.00 33.42 3.41
3940 4011 8.711457 CCAAAAATACTTGTCATCAAAATGGAC 58.289 33.333 0.00 0.00 33.42 4.02
3941 4012 9.258826 CAAAAATACTTGTCATCAAAATGGACA 57.741 29.630 0.00 0.00 33.42 4.02
3942 4013 9.829507 AAAAATACTTGTCATCAAAATGGACAA 57.170 25.926 0.00 0.00 34.59 3.18
3943 4014 9.829507 AAAATACTTGTCATCAAAATGGACAAA 57.170 25.926 7.70 0.00 34.98 2.83
3944 4015 9.829507 AAATACTTGTCATCAAAATGGACAAAA 57.170 25.926 7.70 0.84 34.98 2.44
3945 4016 9.829507 AATACTTGTCATCAAAATGGACAAAAA 57.170 25.926 7.70 0.55 34.98 1.94
3947 4018 8.145316 ACTTGTCATCAAAATGGACAAAAATG 57.855 30.769 7.70 0.11 34.98 2.32
3948 4019 7.986320 ACTTGTCATCAAAATGGACAAAAATGA 59.014 29.630 7.70 0.00 34.98 2.57
3949 4020 8.728337 TTGTCATCAAAATGGACAAAAATGAA 57.272 26.923 4.15 0.00 33.71 2.57
3950 4021 8.905660 TGTCATCAAAATGGACAAAAATGAAT 57.094 26.923 0.00 0.00 33.42 2.57
3951 4022 8.775527 TGTCATCAAAATGGACAAAAATGAATG 58.224 29.630 0.00 0.00 33.42 2.67
3952 4023 8.776470 GTCATCAAAATGGACAAAAATGAATGT 58.224 29.630 0.00 0.00 33.42 2.71
3953 4024 9.993454 TCATCAAAATGGACAAAAATGAATGTA 57.007 25.926 0.00 0.00 33.42 2.29
3962 4033 9.739276 TGGACAAAAATGAATGTATCTAGAACT 57.261 29.630 0.00 0.00 0.00 3.01
3986 4057 9.845214 ACTAAAATACATCTAGATACATCCCCT 57.155 33.333 4.54 0.00 0.00 4.79
3994 4065 9.170890 ACATCTAGATACATCCCCTTTTATTCA 57.829 33.333 4.54 0.00 0.00 2.57
4000 4071 9.713684 AGATACATCCCCTTTTATTCATTTTGA 57.286 29.630 0.00 0.00 0.00 2.69
4003 4074 8.378115 ACATCCCCTTTTATTCATTTTGATGA 57.622 30.769 0.00 0.00 32.39 2.92
4004 4075 8.260114 ACATCCCCTTTTATTCATTTTGATGAC 58.740 33.333 0.00 0.00 32.39 3.06
4005 4076 7.789202 TCCCCTTTTATTCATTTTGATGACA 57.211 32.000 0.00 0.00 0.00 3.58
4006 4077 8.200024 TCCCCTTTTATTCATTTTGATGACAA 57.800 30.769 0.00 0.00 0.00 3.18
4007 4078 8.313292 TCCCCTTTTATTCATTTTGATGACAAG 58.687 33.333 0.00 0.00 37.32 3.16
4008 4079 8.096414 CCCCTTTTATTCATTTTGATGACAAGT 58.904 33.333 0.00 0.00 37.32 3.16
4015 4086 8.915871 ATTCATTTTGATGACAAGTATTTCCG 57.084 30.769 0.00 0.00 37.32 4.30
4016 4087 6.851609 TCATTTTGATGACAAGTATTTCCGG 58.148 36.000 0.00 0.00 37.32 5.14
4017 4088 6.657117 TCATTTTGATGACAAGTATTTCCGGA 59.343 34.615 0.00 0.00 37.32 5.14
4018 4089 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
4019 4090 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
4020 4091 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
4021 4092 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
4022 4093 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
4023 4094 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
4024 4095 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
4047 4118 9.656323 AGGGAGTATGATTGTATCTGTTACTTA 57.344 33.333 0.00 0.00 0.00 2.24
4239 4311 3.090037 AGACGCTTACTCACTACATGGT 58.910 45.455 0.00 0.00 0.00 3.55
4563 4635 4.101114 ACTTATGGTGATACTGTGGACCA 58.899 43.478 9.08 9.08 42.60 4.02
4678 4750 5.520376 TGGACGGTAGCTAAGGTAATAAC 57.480 43.478 0.00 0.00 0.00 1.89
5104 5176 7.217200 TGTTCTCATGGTATAGAAATGCTACC 58.783 38.462 0.00 0.00 33.70 3.18
5236 5308 2.951642 TGTGGTCTTCTTGGCTTTTCAG 59.048 45.455 0.00 0.00 0.00 3.02
5537 5609 2.813754 CTCAAGGAATTGAAAGACGCCA 59.186 45.455 0.00 0.00 0.00 5.69
5552 5624 0.758734 CGCCATTATCACAGAGGGGA 59.241 55.000 0.00 0.00 34.56 4.81
5803 5875 0.247736 AGTTCTGGGAGCGCTTACAG 59.752 55.000 26.86 26.86 0.00 2.74
5816 5888 3.257393 CGCTTACAGCTTCTGTTCATCT 58.743 45.455 4.70 0.00 42.59 2.90
5881 5953 5.049474 TGTGTCTGTTCATTTCTTTCCATCG 60.049 40.000 0.00 0.00 0.00 3.84
5941 6013 2.907696 TCATTCAGGAAAACCGGGAGTA 59.092 45.455 6.32 0.00 0.00 2.59
5991 6063 1.302832 CAGGGTTCTTGAAGGCGCT 60.303 57.895 7.64 0.00 0.00 5.92
6069 6141 6.688637 TTCCAGCTGATTTATCTGTTGATG 57.311 37.500 17.39 0.00 38.56 3.07
6133 6205 1.821753 CGCTCCTCTTCTTCTTCCTCA 59.178 52.381 0.00 0.00 0.00 3.86
6151 6223 3.244946 CCTCATCATCATCAGGGAGCATT 60.245 47.826 0.00 0.00 0.00 3.56
6273 6345 1.003718 GGTTTCTGTCACTCCCGGG 60.004 63.158 16.85 16.85 0.00 5.73
6300 6375 8.407457 TGCATTTACTACATCTTTTAGTCTCG 57.593 34.615 0.00 0.00 31.99 4.04
6384 6459 1.869767 GAATCCATCACACGAGGCATC 59.130 52.381 0.00 0.00 0.00 3.91
6520 6595 4.715523 CCCCCATCCACGCGTTGT 62.716 66.667 10.22 0.00 0.00 3.32
6544 6621 5.632244 TTTTCGCCCTGTAAAATAACCTC 57.368 39.130 0.00 0.00 0.00 3.85
6653 6731 0.968901 CCTACACGGCCCTGACTACA 60.969 60.000 8.88 0.00 0.00 2.74
6654 6732 0.456221 CTACACGGCCCTGACTACAG 59.544 60.000 8.88 0.00 43.12 2.74
6678 6756 5.053978 AGGAGATTGTTCAACAAAGACCT 57.946 39.130 7.14 12.38 41.96 3.85
6798 6877 2.962827 CTGTGCAGAGCAAGTGCCG 61.963 63.158 0.00 0.00 41.47 5.69
6908 6989 1.006805 CGGCGAGGGAGCAATCTAG 60.007 63.158 0.00 0.00 39.27 2.43
6910 6991 1.329256 GGCGAGGGAGCAATCTAGTA 58.671 55.000 0.00 0.00 39.27 1.82
6911 6992 1.687123 GGCGAGGGAGCAATCTAGTAA 59.313 52.381 0.00 0.00 39.27 2.24
6912 6993 2.288518 GGCGAGGGAGCAATCTAGTAAG 60.289 54.545 0.00 0.00 39.27 2.34
6918 6999 6.073112 CGAGGGAGCAATCTAGTAAGTAGTAC 60.073 46.154 0.00 0.00 0.00 2.73
6919 7000 6.913545 AGGGAGCAATCTAGTAAGTAGTACT 58.086 40.000 0.00 0.00 45.42 2.73
6920 7001 6.999871 AGGGAGCAATCTAGTAAGTAGTACTC 59.000 42.308 2.58 0.00 42.37 2.59
6921 7002 6.207221 GGGAGCAATCTAGTAAGTAGTACTCC 59.793 46.154 2.58 0.00 42.37 3.85
6922 7003 6.207221 GGAGCAATCTAGTAAGTAGTACTCCC 59.793 46.154 2.58 0.00 42.37 4.30
6923 7004 6.913545 AGCAATCTAGTAAGTAGTACTCCCT 58.086 40.000 2.58 5.22 42.37 4.20
6925 7006 6.207221 GCAATCTAGTAAGTAGTACTCCCTCC 59.793 46.154 2.58 0.00 42.37 4.30
6926 7007 5.543507 TCTAGTAAGTAGTACTCCCTCCG 57.456 47.826 2.58 0.00 42.37 4.63
6928 7009 4.149511 AGTAAGTAGTACTCCCTCCGTC 57.850 50.000 2.58 0.00 38.84 4.79
6929 7010 3.779738 AGTAAGTAGTACTCCCTCCGTCT 59.220 47.826 2.58 0.00 38.84 4.18
6930 7011 3.280197 AAGTAGTACTCCCTCCGTCTC 57.720 52.381 2.58 0.00 0.00 3.36
6932 7013 2.575279 AGTAGTACTCCCTCCGTCTCAA 59.425 50.000 0.00 0.00 0.00 3.02
6934 7015 2.885616 AGTACTCCCTCCGTCTCAAAA 58.114 47.619 0.00 0.00 0.00 2.44
6935 7016 3.442076 AGTACTCCCTCCGTCTCAAAAT 58.558 45.455 0.00 0.00 0.00 1.82
6936 7017 4.607239 AGTACTCCCTCCGTCTCAAAATA 58.393 43.478 0.00 0.00 0.00 1.40
6937 7018 5.021458 AGTACTCCCTCCGTCTCAAAATAA 58.979 41.667 0.00 0.00 0.00 1.40
6938 7019 4.473477 ACTCCCTCCGTCTCAAAATAAG 57.527 45.455 0.00 0.00 0.00 1.73
6939 7020 3.838903 ACTCCCTCCGTCTCAAAATAAGT 59.161 43.478 0.00 0.00 0.00 2.24
6940 7021 4.184629 CTCCCTCCGTCTCAAAATAAGTG 58.815 47.826 0.00 0.00 0.00 3.16
6941 7022 3.581332 TCCCTCCGTCTCAAAATAAGTGT 59.419 43.478 0.00 0.00 0.00 3.55
6942 7023 3.933332 CCCTCCGTCTCAAAATAAGTGTC 59.067 47.826 0.00 0.00 0.00 3.67
6943 7024 4.322801 CCCTCCGTCTCAAAATAAGTGTCT 60.323 45.833 0.00 0.00 0.00 3.41
6944 7025 4.865365 CCTCCGTCTCAAAATAAGTGTCTC 59.135 45.833 0.00 0.00 0.00 3.36
6945 7026 5.462530 TCCGTCTCAAAATAAGTGTCTCA 57.537 39.130 0.00 0.00 0.00 3.27
6946 7027 5.849510 TCCGTCTCAAAATAAGTGTCTCAA 58.150 37.500 0.00 0.00 0.00 3.02
6947 7028 5.926542 TCCGTCTCAAAATAAGTGTCTCAAG 59.073 40.000 0.00 0.00 0.00 3.02
6948 7029 5.389935 CCGTCTCAAAATAAGTGTCTCAAGC 60.390 44.000 0.00 0.00 0.00 4.01
6949 7030 5.406780 CGTCTCAAAATAAGTGTCTCAAGCT 59.593 40.000 0.00 0.00 0.00 3.74
6950 7031 6.073548 CGTCTCAAAATAAGTGTCTCAAGCTT 60.074 38.462 0.00 0.00 0.00 3.74
6951 7032 7.116376 CGTCTCAAAATAAGTGTCTCAAGCTTA 59.884 37.037 0.00 0.00 0.00 3.09
6952 7033 8.439286 GTCTCAAAATAAGTGTCTCAAGCTTAG 58.561 37.037 0.00 0.00 0.00 2.18
6955 7036 9.507329 TCAAAATAAGTGTCTCAAGCTTAGAAT 57.493 29.630 0.00 0.00 0.00 2.40
6999 7080 9.581099 AGTACAAAGTTGAAACACTTATTTTGG 57.419 29.630 0.00 0.00 35.87 3.28
7000 7081 7.841915 ACAAAGTTGAAACACTTATTTTGGG 57.158 32.000 0.00 0.00 35.87 4.12
7001 7082 7.616313 ACAAAGTTGAAACACTTATTTTGGGA 58.384 30.769 0.00 0.00 35.87 4.37
7002 7083 7.547722 ACAAAGTTGAAACACTTATTTTGGGAC 59.452 33.333 0.00 0.00 35.87 4.46
7003 7084 6.783708 AGTTGAAACACTTATTTTGGGACA 57.216 33.333 0.00 0.00 0.00 4.02
7004 7085 6.805713 AGTTGAAACACTTATTTTGGGACAG 58.194 36.000 0.00 0.00 42.39 3.51
7008 7089 4.034285 ACACTTATTTTGGGACAGAGGG 57.966 45.455 0.00 0.00 42.39 4.30
7057 7286 0.693622 TTAACTGGAATGGGGACGCA 59.306 50.000 0.00 0.00 0.00 5.24
7079 7309 4.813697 CAGCTCCTCTAGTTTTATGGAAGC 59.186 45.833 0.00 0.00 0.00 3.86
7163 7419 2.955660 CCTCTCCTATCTCTTTCACGCT 59.044 50.000 0.00 0.00 0.00 5.07
7244 7566 0.323957 ACACCCGCTAAACCTCTTCC 59.676 55.000 0.00 0.00 0.00 3.46
7336 7658 1.223417 GCCACATGTGTTGCAAAGGC 61.223 55.000 23.79 13.82 36.77 4.35
7340 7662 1.530419 ATGTGTTGCAAAGGCCCGA 60.530 52.632 0.00 0.00 40.13 5.14
7367 7689 1.270839 GCAGGTCCAAGTACTTCTGCA 60.271 52.381 28.66 5.50 44.68 4.41
7374 7696 1.873591 CAAGTACTTCTGCAAAGCGGT 59.126 47.619 4.77 0.00 36.18 5.68
7386 7708 2.257286 AAAGCGGTGTGATGATGCGC 62.257 55.000 0.00 0.00 0.00 6.09
7429 7767 2.275318 GTGCTTCTGCTATGGTCAGTC 58.725 52.381 0.00 0.00 40.48 3.51
7473 7811 2.110213 AAAGTTGCACCCGCGAGA 59.890 55.556 8.23 0.00 42.97 4.04
7540 8163 2.126618 CGCGTGCTAGAACCGACA 60.127 61.111 0.00 0.00 0.00 4.35
7551 8174 1.732259 AGAACCGACATTGACGAATGC 59.268 47.619 10.04 0.00 42.54 3.56
7558 8181 0.734889 CATTGACGAATGCTGGGACC 59.265 55.000 0.00 0.00 32.83 4.46
7560 8183 0.605319 TTGACGAATGCTGGGACCAC 60.605 55.000 0.00 0.00 0.00 4.16
7561 8184 1.003839 GACGAATGCTGGGACCACA 60.004 57.895 0.00 0.00 0.00 4.17
7600 8223 0.872881 GGCATTGATGGATGTTGCGC 60.873 55.000 0.00 0.00 34.17 6.09
7639 8262 4.623886 GCTGGAACTGACATAGGTGAATGA 60.624 45.833 0.00 0.00 0.00 2.57
7647 8270 4.719273 TGACATAGGTGAATGATGGTACCA 59.281 41.667 18.99 18.99 35.66 3.25
7648 8271 5.369404 TGACATAGGTGAATGATGGTACCAT 59.631 40.000 27.70 27.70 39.69 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.091541 CCTCACAACCAACAACACTGT 58.908 47.619 0.00 0.00 37.39 3.55
28 33 1.686587 CTTGGGGAAAACCTCACAACC 59.313 52.381 0.00 0.00 40.03 3.77
50 55 4.494484 TGGACACAAATCTGACTACATCG 58.506 43.478 0.00 0.00 0.00 3.84
84 97 3.006537 AGCTACCAGTAAACATCACGTGT 59.993 43.478 16.51 0.00 44.84 4.49
144 157 9.030452 AGTATAATATCAAGTTGGCACCAAAAA 57.970 29.630 3.10 0.00 37.70 1.94
145 158 8.465999 CAGTATAATATCAAGTTGGCACCAAAA 58.534 33.333 3.10 0.00 37.70 2.44
146 159 7.831690 TCAGTATAATATCAAGTTGGCACCAAA 59.168 33.333 3.10 0.00 37.70 3.28
147 160 7.342581 TCAGTATAATATCAAGTTGGCACCAA 58.657 34.615 2.34 0.00 0.00 3.67
148 161 6.894682 TCAGTATAATATCAAGTTGGCACCA 58.105 36.000 2.34 0.00 0.00 4.17
149 162 7.801716 TTCAGTATAATATCAAGTTGGCACC 57.198 36.000 2.34 0.00 0.00 5.01
150 163 9.056005 TGATTCAGTATAATATCAAGTTGGCAC 57.944 33.333 2.34 0.00 0.00 5.01
151 164 9.625747 TTGATTCAGTATAATATCAAGTTGGCA 57.374 29.630 2.34 0.00 33.41 4.92
239 252 6.296317 CCTCATACCATTAGCCTGAGAATGAT 60.296 42.308 0.00 0.00 36.32 2.45
243 256 4.298626 ACCTCATACCATTAGCCTGAGAA 58.701 43.478 0.00 0.00 36.32 2.87
244 257 3.928754 ACCTCATACCATTAGCCTGAGA 58.071 45.455 0.00 0.00 36.32 3.27
254 267 3.370103 CCCGTTGTGTAACCTCATACCAT 60.370 47.826 0.00 0.00 34.36 3.55
307 324 6.099701 TGGAATGAGGTGCAACTATATACAGT 59.900 38.462 2.94 0.00 36.74 3.55
308 325 6.425114 GTGGAATGAGGTGCAACTATATACAG 59.575 42.308 2.94 0.00 36.74 2.74
309 326 6.126911 TGTGGAATGAGGTGCAACTATATACA 60.127 38.462 2.94 0.00 36.74 2.29
310 327 6.202954 GTGTGGAATGAGGTGCAACTATATAC 59.797 42.308 2.94 0.01 36.74 1.47
311 328 6.288294 GTGTGGAATGAGGTGCAACTATATA 58.712 40.000 2.94 0.00 36.74 0.86
312 329 5.126067 GTGTGGAATGAGGTGCAACTATAT 58.874 41.667 2.94 0.00 36.74 0.86
313 330 4.513442 GTGTGGAATGAGGTGCAACTATA 58.487 43.478 2.94 0.00 36.74 1.31
462 493 1.168714 GACATGGCAGTCAGGGAAAC 58.831 55.000 0.00 0.00 38.40 2.78
472 503 1.812922 GCCTGTCGAGACATGGCAG 60.813 63.158 26.54 10.48 45.91 4.85
598 637 2.588877 GACCCGATGATGCCGTGG 60.589 66.667 0.00 0.00 0.00 4.94
677 716 4.527583 CTCGCCTGCTCTGAGCCC 62.528 72.222 25.61 13.36 41.51 5.19
771 813 1.299165 CCGTTCGAGCCGATGGTAG 60.299 63.158 7.99 0.00 35.23 3.18
887 931 1.816863 TTCCCTCTCTGTCACGTGGC 61.817 60.000 14.58 14.58 0.00 5.01
922 966 0.605083 AGAGAAGATCAGTGTGCGCA 59.395 50.000 5.66 5.66 0.00 6.09
1234 1283 0.951558 CAACCCGTGGAGGAAGTTTG 59.048 55.000 0.00 0.00 45.00 2.93
1238 1287 1.073199 AAGCAACCCGTGGAGGAAG 59.927 57.895 0.00 0.00 45.00 3.46
1254 1303 0.104671 CACCCAGCAAACAACCCAAG 59.895 55.000 0.00 0.00 0.00 3.61
1284 1334 4.152625 GACACGTCCGCATGCAGC 62.153 66.667 19.57 5.79 40.87 5.25
1285 1335 3.842126 CGACACGTCCGCATGCAG 61.842 66.667 19.57 6.53 0.00 4.41
1286 1336 3.850095 TTCGACACGTCCGCATGCA 62.850 57.895 19.57 0.00 0.00 3.96
1287 1337 1.966493 AATTCGACACGTCCGCATGC 61.966 55.000 7.91 7.91 0.00 4.06
1296 1346 1.683790 GGAGGCGTCAATTCGACACG 61.684 60.000 8.91 0.00 45.70 4.49
1297 1347 0.669318 TGGAGGCGTCAATTCGACAC 60.669 55.000 8.91 0.00 45.70 3.67
1343 1400 3.463944 CGCATAGAATTACCCCGAGTTT 58.536 45.455 0.00 0.00 0.00 2.66
1354 1411 5.126061 ACATTTCCTTCAAGCGCATAGAATT 59.874 36.000 11.47 0.00 0.00 2.17
1358 1415 4.553547 GCTACATTTCCTTCAAGCGCATAG 60.554 45.833 11.47 0.00 0.00 2.23
1360 1417 2.098117 GCTACATTTCCTTCAAGCGCAT 59.902 45.455 11.47 0.00 0.00 4.73
1366 1423 9.295825 TCAATTTAAGAGCTACATTTCCTTCAA 57.704 29.630 0.00 0.00 0.00 2.69
1379 1436 5.063944 CACGTACAGCATCAATTTAAGAGCT 59.936 40.000 0.00 0.00 0.00 4.09
1380 1437 5.163854 ACACGTACAGCATCAATTTAAGAGC 60.164 40.000 0.00 0.00 0.00 4.09
1382 1439 6.795098 AACACGTACAGCATCAATTTAAGA 57.205 33.333 0.00 0.00 0.00 2.10
1383 1440 7.739295 AGTAACACGTACAGCATCAATTTAAG 58.261 34.615 0.00 0.00 34.88 1.85
1385 1442 8.936070 ATAGTAACACGTACAGCATCAATTTA 57.064 30.769 0.00 0.00 34.88 1.40
1388 1454 7.843490 AAATAGTAACACGTACAGCATCAAT 57.157 32.000 0.00 0.00 34.88 2.57
1411 1477 5.639506 TCGCATTCTTCCAAACAAACAAAAA 59.360 32.000 0.00 0.00 0.00 1.94
1412 1478 5.171476 TCGCATTCTTCCAAACAAACAAAA 58.829 33.333 0.00 0.00 0.00 2.44
1413 1479 4.748892 TCGCATTCTTCCAAACAAACAAA 58.251 34.783 0.00 0.00 0.00 2.83
1414 1480 4.377839 TCGCATTCTTCCAAACAAACAA 57.622 36.364 0.00 0.00 0.00 2.83
1415 1481 4.582701 ATCGCATTCTTCCAAACAAACA 57.417 36.364 0.00 0.00 0.00 2.83
1416 1482 5.500740 GAATCGCATTCTTCCAAACAAAC 57.499 39.130 2.73 0.00 36.37 2.93
1491 1557 7.984050 CCAAAGAAATGCTACAGAGATAGAGAA 59.016 37.037 0.00 0.00 0.00 2.87
1506 1572 3.518590 CAGAAGATGGCCAAAGAAATGC 58.481 45.455 10.96 0.00 0.00 3.56
1609 1675 4.021102 ACAACCCAAAGTAGTGAGATGG 57.979 45.455 0.00 0.00 0.00 3.51
1613 1679 8.385898 TGTTAATAACAACCCAAAGTAGTGAG 57.614 34.615 2.97 0.00 38.72 3.51
1624 1690 2.432874 GGGGCCATGTTAATAACAACCC 59.567 50.000 23.27 23.27 45.86 4.11
1723 1789 1.302366 CTCTGCACACAAGCTTCACA 58.698 50.000 0.00 0.00 34.99 3.58
1901 1967 0.946221 GCAAGCATCCTATCGACCGG 60.946 60.000 0.00 0.00 0.00 5.28
2241 2310 1.743958 ACGATAGCTAGCACGTGAAGT 59.256 47.619 25.11 5.14 42.67 3.01
2317 2386 3.244665 TGCATGAAGACAATGGACAGAGT 60.245 43.478 0.00 0.00 0.00 3.24
2382 2451 8.807667 AAAAATCAACTGAAGATGTCATGTTC 57.192 30.769 14.31 14.31 35.07 3.18
2409 2478 5.048782 GCCACATCAAGTAAAACACATCTCA 60.049 40.000 0.00 0.00 0.00 3.27
2682 2752 1.470098 GCAAAGGCATGGTGTACAGAG 59.530 52.381 0.00 0.00 40.72 3.35
2871 2941 8.689069 GGTAAGAGTCGTAGATTTAAATAAGCG 58.311 37.037 0.00 6.12 40.67 4.68
2891 2961 7.176589 ACACAACTGGAAATTTTTGGTAAGA 57.823 32.000 5.56 0.00 0.00 2.10
2902 2972 4.016444 ACACAGTCAACACAACTGGAAAT 58.984 39.130 8.03 0.00 46.73 2.17
3822 3892 1.957877 AGTAGCTGATCCTAGTTCGGC 59.042 52.381 13.34 13.34 44.24 5.54
3904 3975 3.629142 AGTATTTTTGGACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
3907 3978 4.069304 TGACAAGTATTTTTGGACGGAGG 58.931 43.478 0.00 0.00 32.32 4.30
3908 3979 5.411361 TGATGACAAGTATTTTTGGACGGAG 59.589 40.000 0.00 0.00 32.32 4.63
3909 3980 5.309638 TGATGACAAGTATTTTTGGACGGA 58.690 37.500 0.00 0.00 32.32 4.69
3910 3981 5.621197 TGATGACAAGTATTTTTGGACGG 57.379 39.130 0.00 0.00 32.32 4.79
3911 3982 7.922505 TTTTGATGACAAGTATTTTTGGACG 57.077 32.000 0.00 0.00 37.32 4.79
3912 3983 8.711457 CCATTTTGATGACAAGTATTTTTGGAC 58.289 33.333 0.00 0.00 37.32 4.02
3913 3984 8.646004 TCCATTTTGATGACAAGTATTTTTGGA 58.354 29.630 0.00 0.00 37.32 3.53
3914 3985 8.711457 GTCCATTTTGATGACAAGTATTTTTGG 58.289 33.333 0.00 0.00 37.32 3.28
3915 3986 9.258826 TGTCCATTTTGATGACAAGTATTTTTG 57.741 29.630 0.00 0.00 37.32 2.44
3917 3988 9.829507 TTTGTCCATTTTGATGACAAGTATTTT 57.170 25.926 0.00 0.00 37.13 1.82
3919 3990 9.829507 TTTTTGTCCATTTTGATGACAAGTATT 57.170 25.926 0.00 0.00 37.13 1.89
3921 3992 9.258826 CATTTTTGTCCATTTTGATGACAAGTA 57.741 29.630 0.00 0.00 37.13 2.24
3923 3994 8.367943 TCATTTTTGTCCATTTTGATGACAAG 57.632 30.769 0.00 0.00 37.13 3.16
3924 3995 8.728337 TTCATTTTTGTCCATTTTGATGACAA 57.272 26.923 0.00 0.00 34.47 3.18
3926 3997 8.776470 ACATTCATTTTTGTCCATTTTGATGAC 58.224 29.630 0.00 0.00 0.00 3.06
3927 3998 8.905660 ACATTCATTTTTGTCCATTTTGATGA 57.094 26.923 0.00 0.00 0.00 2.92
3936 4007 9.739276 AGTTCTAGATACATTCATTTTTGTCCA 57.261 29.630 0.00 0.00 0.00 4.02
3960 4031 9.845214 AGGGGATGTATCTAGATGTATTTTAGT 57.155 33.333 15.79 0.00 0.00 2.24
3968 4039 9.170890 TGAATAAAAGGGGATGTATCTAGATGT 57.829 33.333 15.79 1.25 0.00 3.06
3974 4045 9.713684 TCAAAATGAATAAAAGGGGATGTATCT 57.286 29.630 0.00 0.00 0.00 1.98
3977 4048 9.486123 TCATCAAAATGAATAAAAGGGGATGTA 57.514 29.630 0.00 0.00 38.97 2.29
3978 4049 8.260114 GTCATCAAAATGAATAAAAGGGGATGT 58.740 33.333 0.00 0.00 43.42 3.06
3979 4050 8.259411 TGTCATCAAAATGAATAAAAGGGGATG 58.741 33.333 0.00 0.00 43.42 3.51
3980 4051 8.378115 TGTCATCAAAATGAATAAAAGGGGAT 57.622 30.769 0.00 0.00 43.42 3.85
3981 4052 7.789202 TGTCATCAAAATGAATAAAAGGGGA 57.211 32.000 0.00 0.00 43.42 4.81
3982 4053 8.096414 ACTTGTCATCAAAATGAATAAAAGGGG 58.904 33.333 0.00 0.00 43.42 4.79
3990 4061 7.975616 CCGGAAATACTTGTCATCAAAATGAAT 59.024 33.333 0.00 0.00 43.42 2.57
3991 4062 7.175816 TCCGGAAATACTTGTCATCAAAATGAA 59.824 33.333 0.00 0.00 43.42 2.57
3992 4063 6.657117 TCCGGAAATACTTGTCATCAAAATGA 59.343 34.615 0.00 0.00 39.63 2.57
3993 4064 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
3994 4065 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
3995 4066 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
3996 4067 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
3997 4068 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
3998 4069 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
3999 4070 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
4000 4071 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
4001 4072 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
4002 4073 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
4003 4074 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
4004 4075 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
4005 4076 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
4006 4077 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
4007 4078 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
4008 4079 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
4009 4080 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
4010 4081 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
4011 4082 0.754217 CATACTCCCTCCGTCCGGAA 60.754 60.000 5.23 0.00 44.66 4.30
4012 4083 1.152819 CATACTCCCTCCGTCCGGA 60.153 63.158 0.00 0.00 42.90 5.14
4013 4084 0.539901 ATCATACTCCCTCCGTCCGG 60.540 60.000 0.00 0.00 0.00 5.14
4014 4085 1.000163 CAATCATACTCCCTCCGTCCG 60.000 57.143 0.00 0.00 0.00 4.79
4015 4086 2.040178 ACAATCATACTCCCTCCGTCC 58.960 52.381 0.00 0.00 0.00 4.79
4016 4087 4.767928 AGATACAATCATACTCCCTCCGTC 59.232 45.833 0.00 0.00 0.00 4.79
4017 4088 4.524714 CAGATACAATCATACTCCCTCCGT 59.475 45.833 0.00 0.00 0.00 4.69
4018 4089 4.524714 ACAGATACAATCATACTCCCTCCG 59.475 45.833 0.00 0.00 0.00 4.63
4019 4090 6.426646 AACAGATACAATCATACTCCCTCC 57.573 41.667 0.00 0.00 0.00 4.30
4020 4091 8.184304 AGTAACAGATACAATCATACTCCCTC 57.816 38.462 0.00 0.00 36.94 4.30
4021 4092 8.554490 AAGTAACAGATACAATCATACTCCCT 57.446 34.615 0.00 0.00 36.94 4.20
4563 4635 1.735571 GGGCAACGAATATGACAACGT 59.264 47.619 0.00 0.00 40.64 3.99
4678 4750 3.278574 TCCTGGATCCAAGTAAAATGCG 58.721 45.455 17.00 0.00 0.00 4.73
5104 5176 0.664166 GCCACAAATCAACACCTGCG 60.664 55.000 0.00 0.00 0.00 5.18
5236 5308 4.378874 GCAAGGTGAAACTGAATAGCTCAC 60.379 45.833 0.00 0.00 38.45 3.51
5373 5445 7.708051 TGTCGTCCATTTTAATGAAAACTTCA 58.292 30.769 4.07 0.00 45.01 3.02
5803 5875 1.472376 CGAGGGGAGATGAACAGAAGC 60.472 57.143 0.00 0.00 0.00 3.86
5881 5953 2.099592 TGCATAAGGCTGCTTTGCATAC 59.900 45.455 7.32 0.00 45.15 2.39
5941 6013 5.983333 AGAACAGATGAATATTCACCCCT 57.017 39.130 20.19 14.04 40.49 4.79
5991 6063 0.976641 ACTCCAAGAAGGACGCATGA 59.023 50.000 0.00 0.00 43.07 3.07
6069 6141 0.988145 TCCATGTCATCCCCCAGACC 60.988 60.000 0.00 0.00 33.89 3.85
6133 6205 2.891580 GCAAATGCTCCCTGATGATGAT 59.108 45.455 0.00 0.00 38.21 2.45
6151 6223 3.004315 GTGTCAAAGAATTTCGGGAGCAA 59.996 43.478 0.00 0.00 35.03 3.91
6273 6345 9.974750 GAGACTAAAAGATGTAGTAAATGCAAC 57.025 33.333 0.00 0.00 31.88 4.17
6300 6375 0.871722 TGACATGCTAAACCGCACAC 59.128 50.000 0.00 0.00 43.61 3.82
6319 6394 3.698040 CCAAATGAAATCCTAGCAGCAGT 59.302 43.478 0.00 0.00 0.00 4.40
6384 6459 5.406649 GCAGTATATTCAGAGGGATCTTCG 58.593 45.833 0.00 0.00 0.00 3.79
6653 6731 5.532779 GGTCTTTGTTGAACAATCTCCTTCT 59.467 40.000 11.97 0.00 38.00 2.85
6654 6732 5.532779 AGGTCTTTGTTGAACAATCTCCTTC 59.467 40.000 11.97 0.00 38.00 3.46
6727 6805 3.188254 TCATCCGTACGTTCACTTACGAA 59.812 43.478 15.21 0.00 43.80 3.85
6798 6877 2.543067 ATTTCTCCCCTGCAGCGACC 62.543 60.000 8.66 0.00 0.00 4.79
6908 6989 4.126437 GAGACGGAGGGAGTACTACTTAC 58.874 52.174 4.77 0.00 0.00 2.34
6910 6991 2.575279 TGAGACGGAGGGAGTACTACTT 59.425 50.000 4.77 0.00 0.00 2.24
6911 6992 2.194859 TGAGACGGAGGGAGTACTACT 58.805 52.381 4.77 1.85 0.00 2.57
6912 6993 2.706339 TGAGACGGAGGGAGTACTAC 57.294 55.000 0.00 0.00 0.00 2.73
6918 6999 4.184629 CACTTATTTTGAGACGGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
6919 7000 3.581332 ACACTTATTTTGAGACGGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
6920 7001 3.933332 GACACTTATTTTGAGACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
6921 7002 4.822026 AGACACTTATTTTGAGACGGAGG 58.178 43.478 0.00 0.00 0.00 4.30
6922 7003 5.470368 TGAGACACTTATTTTGAGACGGAG 58.530 41.667 0.00 0.00 0.00 4.63
6923 7004 5.462530 TGAGACACTTATTTTGAGACGGA 57.537 39.130 0.00 0.00 0.00 4.69
6925 7006 5.406780 AGCTTGAGACACTTATTTTGAGACG 59.593 40.000 0.00 0.00 0.00 4.18
6926 7007 6.793492 AGCTTGAGACACTTATTTTGAGAC 57.207 37.500 0.00 0.00 0.00 3.36
6928 7009 8.539770 TCTAAGCTTGAGACACTTATTTTGAG 57.460 34.615 9.86 0.00 0.00 3.02
6929 7010 8.902540 TTCTAAGCTTGAGACACTTATTTTGA 57.097 30.769 9.86 0.00 0.00 2.69
6937 7018 9.732130 AGAAATTTATTCTAAGCTTGAGACACT 57.268 29.630 9.86 0.00 0.00 3.55
6973 7054 9.581099 CCAAAATAAGTGTTTCAACTTTGTACT 57.419 29.630 0.00 0.00 40.77 2.73
6974 7055 8.813282 CCCAAAATAAGTGTTTCAACTTTGTAC 58.187 33.333 0.00 0.00 40.77 2.90
6975 7056 8.750298 TCCCAAAATAAGTGTTTCAACTTTGTA 58.250 29.630 0.00 0.00 40.77 2.41
6977 7058 7.547370 TGTCCCAAAATAAGTGTTTCAACTTTG 59.453 33.333 0.00 0.00 40.77 2.77
6978 7059 7.616313 TGTCCCAAAATAAGTGTTTCAACTTT 58.384 30.769 0.00 0.00 40.77 2.66
6980 7061 6.605594 TCTGTCCCAAAATAAGTGTTTCAACT 59.394 34.615 0.00 0.00 0.00 3.16
6981 7062 6.801575 TCTGTCCCAAAATAAGTGTTTCAAC 58.198 36.000 0.00 0.00 0.00 3.18
6983 7064 5.534654 CCTCTGTCCCAAAATAAGTGTTTCA 59.465 40.000 0.00 0.00 0.00 2.69
6984 7065 5.048013 CCCTCTGTCCCAAAATAAGTGTTTC 60.048 44.000 0.00 0.00 0.00 2.78
6985 7066 4.832823 CCCTCTGTCCCAAAATAAGTGTTT 59.167 41.667 0.00 0.00 0.00 2.83
6986 7067 4.105697 TCCCTCTGTCCCAAAATAAGTGTT 59.894 41.667 0.00 0.00 0.00 3.32
6987 7068 3.655777 TCCCTCTGTCCCAAAATAAGTGT 59.344 43.478 0.00 0.00 0.00 3.55
6989 7070 3.916989 ACTCCCTCTGTCCCAAAATAAGT 59.083 43.478 0.00 0.00 0.00 2.24
6990 7071 4.576330 ACTCCCTCTGTCCCAAAATAAG 57.424 45.455 0.00 0.00 0.00 1.73
6991 7072 6.652205 AATACTCCCTCTGTCCCAAAATAA 57.348 37.500 0.00 0.00 0.00 1.40
6992 7073 7.349859 ACATAATACTCCCTCTGTCCCAAAATA 59.650 37.037 0.00 0.00 0.00 1.40
6993 7074 6.160459 ACATAATACTCCCTCTGTCCCAAAAT 59.840 38.462 0.00 0.00 0.00 1.82
6994 7075 5.491078 ACATAATACTCCCTCTGTCCCAAAA 59.509 40.000 0.00 0.00 0.00 2.44
6996 7077 4.631234 ACATAATACTCCCTCTGTCCCAA 58.369 43.478 0.00 0.00 0.00 4.12
6997 7078 4.280789 ACATAATACTCCCTCTGTCCCA 57.719 45.455 0.00 0.00 0.00 4.37
6998 7079 5.104485 ACAAACATAATACTCCCTCTGTCCC 60.104 44.000 0.00 0.00 0.00 4.46
6999 7080 5.990668 ACAAACATAATACTCCCTCTGTCC 58.009 41.667 0.00 0.00 0.00 4.02
7000 7081 7.783042 ACTACAAACATAATACTCCCTCTGTC 58.217 38.462 0.00 0.00 0.00 3.51
7001 7082 7.735326 ACTACAAACATAATACTCCCTCTGT 57.265 36.000 0.00 0.00 0.00 3.41
7002 7083 8.692710 TGTACTACAAACATAATACTCCCTCTG 58.307 37.037 0.00 0.00 0.00 3.35
7003 7084 8.693625 GTGTACTACAAACATAATACTCCCTCT 58.306 37.037 0.00 0.00 0.00 3.69
7004 7085 7.924947 GGTGTACTACAAACATAATACTCCCTC 59.075 40.741 0.00 0.00 0.00 4.30
7008 7089 8.589629 CAACGGTGTACTACAAACATAATACTC 58.410 37.037 0.00 0.00 0.00 2.59
7057 7286 4.442192 CGCTTCCATAAAACTAGAGGAGCT 60.442 45.833 0.00 0.00 0.00 4.09
7079 7309 2.746803 GGTCGGCCGGTTTGAATCG 61.747 63.158 27.83 0.00 0.00 3.34
7367 7689 1.796151 CGCATCATCACACCGCTTT 59.204 52.632 0.00 0.00 0.00 3.51
7374 7696 1.888638 CCGATGGCGCATCATCACA 60.889 57.895 21.46 5.24 42.58 3.58
7429 7767 0.167470 CATGACAACCTCGCAGCAAG 59.833 55.000 0.00 0.00 0.00 4.01
7473 7811 1.280710 TGGTTCCAGCAATATGGTCGT 59.719 47.619 0.00 0.00 41.43 4.34
7524 8147 0.370273 CAATGTCGGTTCTAGCACGC 59.630 55.000 0.00 0.00 0.00 5.34
7525 8148 1.654105 GTCAATGTCGGTTCTAGCACG 59.346 52.381 0.00 0.00 0.00 5.34
7540 8163 0.327924 TGGTCCCAGCATTCGTCAAT 59.672 50.000 0.00 0.00 0.00 2.57
7551 8174 1.071471 GTGGTGACTGTGGTCCCAG 59.929 63.158 5.97 5.97 40.66 4.45
7558 8181 1.244816 TCTAGGACGTGGTGACTGTG 58.755 55.000 0.00 0.00 0.00 3.66
7560 8183 1.067776 GGTTCTAGGACGTGGTGACTG 60.068 57.143 0.00 0.00 0.00 3.51
7561 8184 1.254954 GGTTCTAGGACGTGGTGACT 58.745 55.000 0.00 0.00 0.00 3.41
7613 8236 1.977854 ACCTATGTCAGTTCCAGCACA 59.022 47.619 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.