Multiple sequence alignment - TraesCS5A01G230300

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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 TraesCS5A01G230300 chr5A 100.000 2510 0 0 1 2510 445249104 445251613 0.000000e+00 4636.0
1 TraesCS5A01G230300 chr5A 87.225 681 48 15 1517 2192 698130683 698130037 0.000000e+00 739.0
2 TraesCS5A01G230300 chr5B 91.538 839 45 8 678 1509 405700296 405701115 0.000000e+00 1133.0
3 TraesCS5A01G230300 chr5B 88.955 335 36 1 139 473 405699695 405700028 1.800000e-111 412.0
4 TraesCS5A01G230300 chr5B 93.000 100 5 2 591 689 405700182 405700280 7.240000e-31 145.0
5 TraesCS5A01G230300 chr5B 93.333 90 5 1 2403 2492 530707476 530707388 5.630000e-27 132.0
6 TraesCS5A01G230300 chr5B 93.976 83 5 0 500 582 405700028 405700110 2.620000e-25 126.0
7 TraesCS5A01G230300 chr5B 90.217 92 7 2 2403 2493 375800819 375800909 4.390000e-23 119.0
8 TraesCS5A01G230300 chr5D 90.156 833 40 7 678 1508 345943819 345943027 0.000000e+00 1046.0
9 TraesCS5A01G230300 chr5D 91.093 247 13 5 449 689 345944078 345943835 2.410000e-85 326.0
10 TraesCS5A01G230300 chr5D 81.677 322 36 6 45 362 345944553 345944251 1.930000e-61 246.0
11 TraesCS5A01G230300 chr5D 97.727 44 1 0 2203 2246 345943025 345942982 2.680000e-10 76.8
12 TraesCS5A01G230300 chr6A 91.533 685 48 10 1517 2193 562592319 562593001 0.000000e+00 935.0
13 TraesCS5A01G230300 chr6A 89.322 693 43 18 1510 2192 108949425 108950096 0.000000e+00 841.0
14 TraesCS5A01G230300 chr4A 90.803 685 53 9 1517 2192 683126010 683126693 0.000000e+00 907.0
15 TraesCS5A01G230300 chr4A 90.525 686 53 11 1517 2192 335509829 335510512 0.000000e+00 896.0
16 TraesCS5A01G230300 chr7A 90.671 686 51 10 1517 2192 507860079 507860761 0.000000e+00 900.0
17 TraesCS5A01G230300 chr7A 89.725 691 56 10 1517 2192 38136174 38135484 0.000000e+00 869.0
18 TraesCS5A01G230300 chr7A 85.517 290 36 2 1210 1493 634379396 634379685 5.250000e-77 298.0
19 TraesCS5A01G230300 chr7A 86.528 193 25 1 1517 1708 448482521 448482713 7.030000e-51 211.0
20 TraesCS5A01G230300 chr2A 89.327 684 61 12 1517 2192 634768361 634767682 0.000000e+00 848.0
21 TraesCS5A01G230300 chr1A 88.921 695 47 17 1518 2202 567981694 567982368 0.000000e+00 830.0
22 TraesCS5A01G230300 chr3A 88.092 697 59 17 1518 2192 714091160 714090466 0.000000e+00 806.0
23 TraesCS5A01G230300 chr3A 91.209 91 7 1 2403 2493 44352203 44352114 3.390000e-24 122.0
24 TraesCS5A01G230300 chr7B 85.666 293 34 4 1209 1493 592503134 592503426 4.060000e-78 302.0
25 TraesCS5A01G230300 chr7B 90.323 93 7 2 2403 2494 720027337 720027428 1.220000e-23 121.0
26 TraesCS5A01G230300 chr7D 78.137 526 76 23 998 1493 548885463 548885979 5.250000e-77 298.0
27 TraesCS5A01G230300 chr4B 92.473 93 5 2 2403 2494 602379432 602379523 5.630000e-27 132.0
28 TraesCS5A01G230300 chr1D 92.308 91 6 1 2403 2493 486753431 486753342 7.290000e-26 128.0
29 TraesCS5A01G230300 chr1D 95.000 40 2 0 74 113 24142568 24142529 2.080000e-06 63.9
30 TraesCS5A01G230300 chrUn 91.954 87 5 2 2409 2494 241070294 241070209 1.220000e-23 121.0
31 TraesCS5A01G230300 chr6D 90.217 92 7 2 2403 2493 397351160 397351250 4.390000e-23 119.0
32 TraesCS5A01G230300 chr2B 88.000 100 8 4 2403 2499 87745394 87745296 5.670000e-22 115.0
33 TraesCS5A01G230300 chr1B 97.059 34 0 1 251 283 597457352 597457385 3.490000e-04 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 TraesCS5A01G230300 chr5A 445249104 445251613 2509 False 4636.0 4636 100.00000 1 2510 1 chr5A.!!$F1 2509
1 TraesCS5A01G230300 chr5A 698130037 698130683 646 True 739.0 739 87.22500 1517 2192 1 chr5A.!!$R1 675
2 TraesCS5A01G230300 chr5B 405699695 405701115 1420 False 454.0 1133 91.86725 139 1509 4 chr5B.!!$F2 1370
3 TraesCS5A01G230300 chr5D 345942982 345944553 1571 True 423.7 1046 90.16325 45 2246 4 chr5D.!!$R1 2201
4 TraesCS5A01G230300 chr6A 562592319 562593001 682 False 935.0 935 91.53300 1517 2193 1 chr6A.!!$F2 676
5 TraesCS5A01G230300 chr6A 108949425 108950096 671 False 841.0 841 89.32200 1510 2192 1 chr6A.!!$F1 682
6 TraesCS5A01G230300 chr4A 683126010 683126693 683 False 907.0 907 90.80300 1517 2192 1 chr4A.!!$F2 675
7 TraesCS5A01G230300 chr4A 335509829 335510512 683 False 896.0 896 90.52500 1517 2192 1 chr4A.!!$F1 675
8 TraesCS5A01G230300 chr7A 507860079 507860761 682 False 900.0 900 90.67100 1517 2192 1 chr7A.!!$F2 675
9 TraesCS5A01G230300 chr7A 38135484 38136174 690 True 869.0 869 89.72500 1517 2192 1 chr7A.!!$R1 675
10 TraesCS5A01G230300 chr2A 634767682 634768361 679 True 848.0 848 89.32700 1517 2192 1 chr2A.!!$R1 675
11 TraesCS5A01G230300 chr1A 567981694 567982368 674 False 830.0 830 88.92100 1518 2202 1 chr1A.!!$F1 684
12 TraesCS5A01G230300 chr3A 714090466 714091160 694 True 806.0 806 88.09200 1518 2192 1 chr3A.!!$R2 674
13 TraesCS5A01G230300 chr7D 548885463 548885979 516 False 298.0 298 78.13700 998 1493 1 chr7D.!!$F1 495

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
223 224 0.32586 ACCCCTCATACCGGCACTAA 60.326 55.0 0.0 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2066 2339 0.728843 ATTCAACCCTCCCCTCCCTA 59.271 55.0 0.0 0.0 0.0 3.53 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
31 32 3.982241 GCAGCAAAAGGCCGCACT 61.982 61.111 0.00 0.00 45.43 4.40
32 33 2.049802 CAGCAAAAGGCCGCACTG 60.050 61.111 0.00 0.00 46.50 3.66
33 34 2.519302 AGCAAAAGGCCGCACTGT 60.519 55.556 0.00 0.00 46.50 3.55
34 35 2.127232 AGCAAAAGGCCGCACTGTT 61.127 52.632 0.00 0.00 46.50 3.16
35 36 1.227234 GCAAAAGGCCGCACTGTTT 60.227 52.632 0.00 0.00 36.11 2.83
36 37 1.489881 GCAAAAGGCCGCACTGTTTG 61.490 55.000 0.00 4.07 36.11 2.93
95 96 6.712095 TCCTCAATACTCCATTTCATATGCAC 59.288 38.462 0.00 0.00 0.00 4.57
99 100 9.002600 TCAATACTCCATTTCATATGCACATAC 57.997 33.333 0.00 0.00 0.00 2.39
101 102 6.624352 ACTCCATTTCATATGCACATACAC 57.376 37.500 0.00 0.00 0.00 2.90
116 117 7.083858 TGCACATACACAAAATCTTTTAGAGC 58.916 34.615 0.00 0.00 0.00 4.09
167 168 1.884075 TATGTCTGTGCGGACGGCTT 61.884 55.000 11.58 7.36 44.05 4.35
169 170 4.680237 TCTGTGCGGACGGCTTGG 62.680 66.667 11.58 0.00 44.05 3.61
173 174 4.243008 TGCGGACGGCTTGGTCAA 62.243 61.111 6.55 0.00 44.05 3.18
175 176 2.332654 GCGGACGGCTTGGTCAATT 61.333 57.895 0.00 0.00 38.70 2.32
182 183 2.014128 CGGCTTGGTCAATTATCGGTT 58.986 47.619 0.00 0.00 0.00 4.44
223 224 0.325860 ACCCCTCATACCGGCACTAA 60.326 55.000 0.00 0.00 0.00 2.24
235 236 1.135527 CGGCACTAAACATCCGGACTA 59.864 52.381 6.12 0.00 38.35 2.59
237 238 2.934553 GGCACTAAACATCCGGACTAAC 59.065 50.000 6.12 0.00 0.00 2.34
239 240 3.618019 GCACTAAACATCCGGACTAACCA 60.618 47.826 6.12 0.00 38.90 3.67
248 253 0.399075 CGGACTAACCAACACCCCTT 59.601 55.000 0.00 0.00 38.90 3.95
362 367 3.353836 CGTGGAAACCCAGCGGTG 61.354 66.667 7.86 7.86 43.71 4.94
439 530 3.717400 TTAACTGTGCGGCAAAAATCA 57.283 38.095 3.23 0.00 0.00 2.57
464 555 6.844606 GAAACGTCACCGGCATGACATTTT 62.845 45.833 21.26 18.37 43.07 1.82
465 556 2.723124 GTCACCGGCATGACATTTTT 57.277 45.000 17.83 0.00 46.89 1.94
584 675 8.925161 TTGCCAAAAATATGCAAAGTATACTC 57.075 30.769 5.70 0.00 41.63 2.59
598 752 7.573096 GCAAAGTATACTCAGCTAAGCACAAAA 60.573 37.037 17.59 0.00 0.00 2.44
664 823 0.968405 CCACCCAAACATTCCAGGTG 59.032 55.000 0.00 0.00 46.14 4.00
688 875 4.226761 CAAAATAGTCGCTCCCAACAAAC 58.773 43.478 0.00 0.00 0.00 2.93
704 891 6.153067 CCAACAAACGATAAATAACCAAGCA 58.847 36.000 0.00 0.00 0.00 3.91
784 973 0.889186 ACAGCCGTCCAATTCACACC 60.889 55.000 0.00 0.00 0.00 4.16
815 1004 1.524621 CGACACCATGAGCCCCATC 60.525 63.158 0.00 0.00 31.94 3.51
816 1005 1.152881 GACACCATGAGCCCCATCC 60.153 63.158 0.00 0.00 31.94 3.51
817 1006 2.196776 CACCATGAGCCCCATCCC 59.803 66.667 0.00 0.00 31.94 3.85
818 1007 3.105928 ACCATGAGCCCCATCCCC 61.106 66.667 0.00 0.00 31.94 4.81
819 1008 2.780040 CCATGAGCCCCATCCCCT 60.780 66.667 0.00 0.00 31.94 4.79
862 1052 3.330720 AGCTTCCCCACCCTTCCG 61.331 66.667 0.00 0.00 0.00 4.30
884 1074 4.742201 CTCCACACGACCCGGCAG 62.742 72.222 0.00 0.00 0.00 4.85
911 1101 1.526575 AAAAGCGCCATGGACCAGTG 61.527 55.000 18.40 0.00 0.00 3.66
930 1120 3.423162 CTCTTCCTGAGCGAGCCCG 62.423 68.421 0.00 0.00 35.84 6.13
1033 1223 3.003173 CTTCAGCCCCCTCGTCCA 61.003 66.667 0.00 0.00 0.00 4.02
1133 1332 4.883354 CCTCCCATCCAAGCCGCC 62.883 72.222 0.00 0.00 0.00 6.13
1219 1427 2.896801 GCTCACAGCAACCACCACG 61.897 63.158 0.00 0.00 41.89 4.94
1220 1428 2.203139 TCACAGCAACCACCACGG 60.203 61.111 0.00 0.00 42.50 4.94
1221 1429 3.286751 CACAGCAACCACCACGGG 61.287 66.667 0.00 0.00 40.22 5.28
1447 1685 3.569049 CTCAACTCCGTCGGGCGTT 62.569 63.158 12.29 12.27 41.85 4.84
1501 1739 0.535335 TGTCGGGGTAATGCACTCTC 59.465 55.000 0.00 0.00 0.00 3.20
1509 1747 2.170607 GGTAATGCACTCTCCCAGCTAA 59.829 50.000 0.00 0.00 0.00 3.09
1510 1748 3.181450 GGTAATGCACTCTCCCAGCTAAT 60.181 47.826 0.00 0.00 0.00 1.73
1511 1749 3.659183 AATGCACTCTCCCAGCTAATT 57.341 42.857 0.00 0.00 0.00 1.40
1512 1750 3.659183 ATGCACTCTCCCAGCTAATTT 57.341 42.857 0.00 0.00 0.00 1.82
1513 1751 2.715046 TGCACTCTCCCAGCTAATTTG 58.285 47.619 0.00 0.00 0.00 2.32
1514 1752 2.040278 TGCACTCTCCCAGCTAATTTGT 59.960 45.455 0.00 0.00 0.00 2.83
1515 1753 2.680339 GCACTCTCCCAGCTAATTTGTC 59.320 50.000 0.00 0.00 0.00 3.18
1537 1775 7.108194 TGTCAGAGAGAAGTGCATATTTCAAT 58.892 34.615 10.07 0.47 0.00 2.57
1538 1776 7.609146 TGTCAGAGAGAAGTGCATATTTCAATT 59.391 33.333 10.07 0.00 0.00 2.32
1600 1839 6.549433 TCAATACCGTCTAAATTACACCCT 57.451 37.500 0.00 0.00 0.00 4.34
1628 1867 1.550072 CAAAACCGGCCAGGATTCAAT 59.450 47.619 18.74 0.00 45.00 2.57
1630 1869 0.331278 AACCGGCCAGGATTCAATCA 59.669 50.000 18.74 0.00 45.00 2.57
1648 1887 3.874383 TCATCCCTTCTTTGTTGACCA 57.126 42.857 0.00 0.00 0.00 4.02
1654 1893 4.775253 TCCCTTCTTTGTTGACCAGTTTTT 59.225 37.500 0.00 0.00 0.00 1.94
1699 1938 1.002430 TCAACAGGTCCAGTCAGCATC 59.998 52.381 0.00 0.00 0.00 3.91
1762 2002 6.940298 ACCTGTAAAATCGAAGAAAATCCAGA 59.060 34.615 0.00 0.00 43.58 3.86
2090 2363 2.050918 GAGGGGAGGGTTGAATCCTAG 58.949 57.143 0.00 0.00 35.80 3.02
2092 2365 1.512735 GGGAGGGTTGAATCCTAGCT 58.487 55.000 0.00 0.00 35.80 3.32
2099 2372 4.291249 AGGGTTGAATCCTAGCTGGTTTTA 59.709 41.667 0.00 0.00 37.07 1.52
2108 2381 4.595781 TCCTAGCTGGTTTTAAGACTTGGA 59.404 41.667 0.00 0.00 37.07 3.53
2178 2451 3.951680 GGACAAGAGTTCAGGGTTGAAAA 59.048 43.478 0.00 0.00 44.49 2.29
2195 2468 4.380531 TGAAAAATGCACTTCTCTCGTCT 58.619 39.130 0.00 0.00 0.00 4.18
2196 2469 4.449068 TGAAAAATGCACTTCTCTCGTCTC 59.551 41.667 0.00 0.00 0.00 3.36
2198 2471 3.667497 AATGCACTTCTCTCGTCTCAA 57.333 42.857 0.00 0.00 0.00 3.02
2201 2474 3.995199 TGCACTTCTCTCGTCTCAATTT 58.005 40.909 0.00 0.00 0.00 1.82
2214 2487 6.053005 TCGTCTCAATTTGTTACTCCAGTTT 58.947 36.000 0.00 0.00 0.00 2.66
2246 2519 8.932791 TCGAGAATACCTGTTAGTTTTGATTTC 58.067 33.333 0.00 0.00 0.00 2.17
2247 2520 8.936864 CGAGAATACCTGTTAGTTTTGATTTCT 58.063 33.333 0.00 0.00 0.00 2.52
2253 2526 8.974060 ACCTGTTAGTTTTGATTTCTACAGAA 57.026 30.769 0.00 0.00 0.00 3.02
2254 2527 9.403583 ACCTGTTAGTTTTGATTTCTACAGAAA 57.596 29.630 6.85 6.85 46.60 2.52
2261 2534 8.414003 AGTTTTGATTTCTACAGAAAAACCTCC 58.586 33.333 8.39 0.00 45.81 4.30
2262 2535 8.414003 GTTTTGATTTCTACAGAAAAACCTCCT 58.586 33.333 8.39 0.00 45.81 3.69
2263 2536 7.745620 TTGATTTCTACAGAAAAACCTCCTC 57.254 36.000 8.39 1.43 45.81 3.71
2264 2537 7.079451 TGATTTCTACAGAAAAACCTCCTCT 57.921 36.000 8.39 0.00 45.81 3.69
2265 2538 7.162082 TGATTTCTACAGAAAAACCTCCTCTC 58.838 38.462 8.39 0.19 45.81 3.20
2266 2539 5.485209 TTCTACAGAAAAACCTCCTCTCC 57.515 43.478 0.00 0.00 0.00 3.71
2267 2540 4.753186 TCTACAGAAAAACCTCCTCTCCT 58.247 43.478 0.00 0.00 0.00 3.69
2268 2541 4.773149 TCTACAGAAAAACCTCCTCTCCTC 59.227 45.833 0.00 0.00 0.00 3.71
2269 2542 3.592865 ACAGAAAAACCTCCTCTCCTCT 58.407 45.455 0.00 0.00 0.00 3.69
2270 2543 3.326297 ACAGAAAAACCTCCTCTCCTCTG 59.674 47.826 0.00 0.00 36.09 3.35
2271 2544 3.326297 CAGAAAAACCTCCTCTCCTCTGT 59.674 47.826 0.00 0.00 0.00 3.41
2272 2545 4.528596 CAGAAAAACCTCCTCTCCTCTGTA 59.471 45.833 0.00 0.00 0.00 2.74
2273 2546 5.012148 CAGAAAAACCTCCTCTCCTCTGTAA 59.988 44.000 0.00 0.00 0.00 2.41
2274 2547 5.607171 AGAAAAACCTCCTCTCCTCTGTAAA 59.393 40.000 0.00 0.00 0.00 2.01
2275 2548 5.491323 AAAACCTCCTCTCCTCTGTAAAG 57.509 43.478 0.00 0.00 0.00 1.85
2276 2549 4.405756 AACCTCCTCTCCTCTGTAAAGA 57.594 45.455 0.00 0.00 0.00 2.52
2277 2550 4.405756 ACCTCCTCTCCTCTGTAAAGAA 57.594 45.455 0.00 0.00 0.00 2.52
2278 2551 4.753186 ACCTCCTCTCCTCTGTAAAGAAA 58.247 43.478 0.00 0.00 0.00 2.52
2279 2552 5.346270 ACCTCCTCTCCTCTGTAAAGAAAT 58.654 41.667 0.00 0.00 0.00 2.17
2280 2553 6.503944 ACCTCCTCTCCTCTGTAAAGAAATA 58.496 40.000 0.00 0.00 0.00 1.40
2281 2554 7.136203 ACCTCCTCTCCTCTGTAAAGAAATAT 58.864 38.462 0.00 0.00 0.00 1.28
2282 2555 8.290277 ACCTCCTCTCCTCTGTAAAGAAATATA 58.710 37.037 0.00 0.00 0.00 0.86
2283 2556 9.148879 CCTCCTCTCCTCTGTAAAGAAATATAA 57.851 37.037 0.00 0.00 0.00 0.98
2285 2558 9.937876 TCCTCTCCTCTGTAAAGAAATATAAGA 57.062 33.333 0.00 0.00 0.00 2.10
2288 2561 8.643324 TCTCCTCTGTAAAGAAATATAAGAGGC 58.357 37.037 10.33 0.00 39.95 4.70
2289 2562 8.319057 TCCTCTGTAAAGAAATATAAGAGGCA 57.681 34.615 10.33 0.00 39.95 4.75
2290 2563 8.424918 TCCTCTGTAAAGAAATATAAGAGGCAG 58.575 37.037 10.33 0.00 39.95 4.85
2291 2564 7.172361 CCTCTGTAAAGAAATATAAGAGGCAGC 59.828 40.741 3.07 0.00 34.80 5.25
2292 2565 7.796054 TCTGTAAAGAAATATAAGAGGCAGCT 58.204 34.615 0.00 0.00 0.00 4.24
2293 2566 8.267894 TCTGTAAAGAAATATAAGAGGCAGCTT 58.732 33.333 0.00 0.00 0.00 3.74
2294 2567 8.213518 TGTAAAGAAATATAAGAGGCAGCTTG 57.786 34.615 0.00 0.00 0.00 4.01
2295 2568 8.046708 TGTAAAGAAATATAAGAGGCAGCTTGA 58.953 33.333 0.00 0.00 0.00 3.02
2296 2569 9.061435 GTAAAGAAATATAAGAGGCAGCTTGAT 57.939 33.333 0.00 0.00 0.00 2.57
2297 2570 7.507733 AAGAAATATAAGAGGCAGCTTGATG 57.492 36.000 0.00 0.00 0.00 3.07
2298 2571 6.835174 AGAAATATAAGAGGCAGCTTGATGA 58.165 36.000 0.00 0.00 0.00 2.92
2299 2572 6.709846 AGAAATATAAGAGGCAGCTTGATGAC 59.290 38.462 0.00 0.00 0.00 3.06
2300 2573 5.822132 ATATAAGAGGCAGCTTGATGACT 57.178 39.130 0.00 0.00 42.89 3.41
2301 2574 2.110901 AAGAGGCAGCTTGATGACTG 57.889 50.000 0.00 0.00 39.20 3.51
2302 2575 1.273759 AGAGGCAGCTTGATGACTGA 58.726 50.000 0.00 0.00 39.20 3.41
2303 2576 1.627329 AGAGGCAGCTTGATGACTGAA 59.373 47.619 0.00 0.00 39.20 3.02
2304 2577 2.039480 AGAGGCAGCTTGATGACTGAAA 59.961 45.455 0.00 0.00 39.20 2.69
2305 2578 2.816087 GAGGCAGCTTGATGACTGAAAA 59.184 45.455 0.00 0.00 39.20 2.29
2306 2579 2.818432 AGGCAGCTTGATGACTGAAAAG 59.182 45.455 0.00 0.00 37.09 2.27
2307 2580 2.555757 GGCAGCTTGATGACTGAAAAGT 59.444 45.455 0.00 0.00 35.90 2.66
2308 2581 3.005155 GGCAGCTTGATGACTGAAAAGTT 59.995 43.478 0.00 0.00 35.90 2.66
2309 2582 4.225208 GCAGCTTGATGACTGAAAAGTTC 58.775 43.478 0.00 0.00 35.90 3.01
2310 2583 4.023365 GCAGCTTGATGACTGAAAAGTTCT 60.023 41.667 0.00 0.00 35.90 3.01
2311 2584 5.180117 GCAGCTTGATGACTGAAAAGTTCTA 59.820 40.000 0.00 0.00 35.90 2.10
2312 2585 6.597614 CAGCTTGATGACTGAAAAGTTCTAC 58.402 40.000 0.00 0.00 35.90 2.59
2313 2586 6.426328 CAGCTTGATGACTGAAAAGTTCTACT 59.574 38.462 0.00 0.00 35.90 2.57
2314 2587 6.648725 AGCTTGATGACTGAAAAGTTCTACTC 59.351 38.462 0.00 0.00 0.00 2.59
2315 2588 6.128418 GCTTGATGACTGAAAAGTTCTACTCC 60.128 42.308 0.00 0.00 0.00 3.85
2316 2589 6.672266 TGATGACTGAAAAGTTCTACTCCT 57.328 37.500 0.00 0.00 0.00 3.69
2317 2590 7.067496 TGATGACTGAAAAGTTCTACTCCTT 57.933 36.000 0.00 0.00 0.00 3.36
2318 2591 7.155328 TGATGACTGAAAAGTTCTACTCCTTC 58.845 38.462 0.00 0.00 0.00 3.46
2319 2592 5.855045 TGACTGAAAAGTTCTACTCCTTCC 58.145 41.667 0.00 0.00 0.00 3.46
2320 2593 5.365605 TGACTGAAAAGTTCTACTCCTTCCA 59.634 40.000 0.00 0.00 0.00 3.53
2321 2594 6.043243 TGACTGAAAAGTTCTACTCCTTCCAT 59.957 38.462 0.00 0.00 0.00 3.41
2322 2595 6.842676 ACTGAAAAGTTCTACTCCTTCCATT 58.157 36.000 0.00 0.00 0.00 3.16
2323 2596 7.290813 ACTGAAAAGTTCTACTCCTTCCATTT 58.709 34.615 0.00 0.00 0.00 2.32
2324 2597 8.437575 ACTGAAAAGTTCTACTCCTTCCATTTA 58.562 33.333 0.00 0.00 0.00 1.40
2325 2598 8.617290 TGAAAAGTTCTACTCCTTCCATTTAC 57.383 34.615 0.00 0.00 0.00 2.01
2326 2599 7.386848 TGAAAAGTTCTACTCCTTCCATTTACG 59.613 37.037 0.00 0.00 0.00 3.18
2327 2600 4.756502 AGTTCTACTCCTTCCATTTACGC 58.243 43.478 0.00 0.00 0.00 4.42
2328 2601 3.814005 TCTACTCCTTCCATTTACGCC 57.186 47.619 0.00 0.00 0.00 5.68
2329 2602 3.371965 TCTACTCCTTCCATTTACGCCT 58.628 45.455 0.00 0.00 0.00 5.52
2330 2603 2.693267 ACTCCTTCCATTTACGCCTC 57.307 50.000 0.00 0.00 0.00 4.70
2331 2604 2.188817 ACTCCTTCCATTTACGCCTCT 58.811 47.619 0.00 0.00 0.00 3.69
2332 2605 2.168728 ACTCCTTCCATTTACGCCTCTC 59.831 50.000 0.00 0.00 0.00 3.20
2333 2606 1.485066 TCCTTCCATTTACGCCTCTCC 59.515 52.381 0.00 0.00 0.00 3.71
2334 2607 1.486726 CCTTCCATTTACGCCTCTCCT 59.513 52.381 0.00 0.00 0.00 3.69
2335 2608 2.483889 CCTTCCATTTACGCCTCTCCTC 60.484 54.545 0.00 0.00 0.00 3.71
2336 2609 2.160721 TCCATTTACGCCTCTCCTCT 57.839 50.000 0.00 0.00 0.00 3.69
2337 2610 2.032620 TCCATTTACGCCTCTCCTCTC 58.967 52.381 0.00 0.00 0.00 3.20
2338 2611 1.269309 CCATTTACGCCTCTCCTCTCG 60.269 57.143 0.00 0.00 0.00 4.04
2339 2612 0.386113 ATTTACGCCTCTCCTCTCGC 59.614 55.000 0.00 0.00 0.00 5.03
2343 2616 3.894947 GCCTCTCCTCTCGCGACC 61.895 72.222 3.71 0.00 0.00 4.79
2344 2617 3.578272 CCTCTCCTCTCGCGACCG 61.578 72.222 3.71 0.00 0.00 4.79
2345 2618 4.244802 CTCTCCTCTCGCGACCGC 62.245 72.222 3.71 4.06 37.85 5.68
2384 2657 4.477975 CCGTGCGACGACCTCCTC 62.478 72.222 0.00 0.00 46.05 3.71
2385 2658 4.477975 CGTGCGACGACCTCCTCC 62.478 72.222 0.00 0.00 46.05 4.30
2386 2659 3.063084 GTGCGACGACCTCCTCCT 61.063 66.667 0.00 0.00 0.00 3.69
2387 2660 2.750637 TGCGACGACCTCCTCCTC 60.751 66.667 0.00 0.00 0.00 3.71
2388 2661 3.519930 GCGACGACCTCCTCCTCC 61.520 72.222 0.00 0.00 0.00 4.30
2389 2662 2.272797 CGACGACCTCCTCCTCCT 59.727 66.667 0.00 0.00 0.00 3.69
2390 2663 1.820481 CGACGACCTCCTCCTCCTC 60.820 68.421 0.00 0.00 0.00 3.71
2391 2664 1.610873 GACGACCTCCTCCTCCTCT 59.389 63.158 0.00 0.00 0.00 3.69
2392 2665 0.838608 GACGACCTCCTCCTCCTCTA 59.161 60.000 0.00 0.00 0.00 2.43
2393 2666 0.547553 ACGACCTCCTCCTCCTCTAC 59.452 60.000 0.00 0.00 0.00 2.59
2394 2667 0.179012 CGACCTCCTCCTCCTCTACC 60.179 65.000 0.00 0.00 0.00 3.18
2395 2668 0.186630 GACCTCCTCCTCCTCTACCC 59.813 65.000 0.00 0.00 0.00 3.69
2396 2669 1.298157 ACCTCCTCCTCCTCTACCCC 61.298 65.000 0.00 0.00 0.00 4.95
2397 2670 1.002242 CCTCCTCCTCCTCTACCCCT 61.002 65.000 0.00 0.00 0.00 4.79
2398 2671 0.938192 CTCCTCCTCCTCTACCCCTT 59.062 60.000 0.00 0.00 0.00 3.95
2399 2672 0.935194 TCCTCCTCCTCTACCCCTTC 59.065 60.000 0.00 0.00 0.00 3.46
2400 2673 0.105401 CCTCCTCCTCTACCCCTTCC 60.105 65.000 0.00 0.00 0.00 3.46
2401 2674 0.938192 CTCCTCCTCTACCCCTTCCT 59.062 60.000 0.00 0.00 0.00 3.36
2402 2675 0.935194 TCCTCCTCTACCCCTTCCTC 59.065 60.000 0.00 0.00 0.00 3.71
2403 2676 0.105401 CCTCCTCTACCCCTTCCTCC 60.105 65.000 0.00 0.00 0.00 4.30
2404 2677 0.468400 CTCCTCTACCCCTTCCTCCG 60.468 65.000 0.00 0.00 0.00 4.63
2405 2678 1.457831 CCTCTACCCCTTCCTCCGG 60.458 68.421 0.00 0.00 0.00 5.14
2406 2679 2.042230 TCTACCCCTTCCTCCGGC 60.042 66.667 0.00 0.00 0.00 6.13
2407 2680 2.041819 CTACCCCTTCCTCCGGCT 60.042 66.667 0.00 0.00 0.00 5.52
2408 2681 1.689582 CTACCCCTTCCTCCGGCTT 60.690 63.158 0.00 0.00 0.00 4.35
2409 2682 1.972660 CTACCCCTTCCTCCGGCTTG 61.973 65.000 0.00 0.00 0.00 4.01
2410 2683 4.115199 CCCCTTCCTCCGGCTTGG 62.115 72.222 0.00 0.00 40.09 3.61
2411 2684 4.803908 CCCTTCCTCCGGCTTGGC 62.804 72.222 0.00 0.00 37.80 4.52
2412 2685 4.803908 CCTTCCTCCGGCTTGGCC 62.804 72.222 0.00 0.00 46.75 5.36
2421 2694 4.883354 GGCTTGGCCTCGGGGATG 62.883 72.222 4.80 0.00 46.69 3.51
2423 2696 3.801997 CTTGGCCTCGGGGATGCT 61.802 66.667 4.80 0.00 33.58 3.79
2424 2697 4.113815 TTGGCCTCGGGGATGCTG 62.114 66.667 4.80 0.00 33.58 4.41
2427 2700 4.864334 GCCTCGGGGATGCTGGTG 62.864 72.222 4.80 0.00 33.58 4.17
2428 2701 4.181010 CCTCGGGGATGCTGGTGG 62.181 72.222 0.00 0.00 33.58 4.61
2429 2702 4.864334 CTCGGGGATGCTGGTGGC 62.864 72.222 0.00 0.00 42.22 5.01
2446 2719 4.785453 CAGCGCCCCCTGACCTTC 62.785 72.222 2.29 0.00 34.77 3.46
2451 2724 2.692741 CCCCCTGACCTTCCCCTC 60.693 72.222 0.00 0.00 0.00 4.30
2452 2725 2.692741 CCCCTGACCTTCCCCTCC 60.693 72.222 0.00 0.00 0.00 4.30
2453 2726 2.456840 CCCTGACCTTCCCCTCCT 59.543 66.667 0.00 0.00 0.00 3.69
2454 2727 1.997874 CCCTGACCTTCCCCTCCTG 60.998 68.421 0.00 0.00 0.00 3.86
2455 2728 1.997874 CCTGACCTTCCCCTCCTGG 60.998 68.421 0.00 0.00 0.00 4.45
2456 2729 1.229658 CTGACCTTCCCCTCCTGGT 60.230 63.158 0.00 0.00 35.23 4.00
2457 2730 1.538876 TGACCTTCCCCTCCTGGTG 60.539 63.158 0.00 0.00 32.30 4.17
2458 2731 2.204151 ACCTTCCCCTCCTGGTGG 60.204 66.667 7.84 7.84 0.00 4.61
2459 2732 3.732849 CCTTCCCCTCCTGGTGGC 61.733 72.222 9.33 0.00 0.00 5.01
2460 2733 2.612115 CTTCCCCTCCTGGTGGCT 60.612 66.667 9.33 0.00 0.00 4.75
2461 2734 2.610859 TTCCCCTCCTGGTGGCTC 60.611 66.667 9.33 0.00 0.00 4.70
2462 2735 3.194025 TTCCCCTCCTGGTGGCTCT 62.194 63.158 9.33 0.00 0.00 4.09
2463 2736 3.086600 CCCCTCCTGGTGGCTCTC 61.087 72.222 9.33 0.00 0.00 3.20
2464 2737 3.086600 CCCTCCTGGTGGCTCTCC 61.087 72.222 9.33 0.00 0.00 3.71
2465 2738 3.465403 CCTCCTGGTGGCTCTCCG 61.465 72.222 1.18 0.00 34.14 4.63
2466 2739 3.465403 CTCCTGGTGGCTCTCCGG 61.465 72.222 0.00 0.00 34.14 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.799281 TTGCTGCCAGGCATAATTTAC 57.201 42.857 16.64 0.00 42.09 2.01
2 3 3.602483 CTTTTGCTGCCAGGCATAATTT 58.398 40.909 16.64 0.00 42.09 1.82
3 4 2.093341 CCTTTTGCTGCCAGGCATAATT 60.093 45.455 16.64 0.00 42.09 1.40
4 5 1.483415 CCTTTTGCTGCCAGGCATAAT 59.517 47.619 16.64 0.00 42.09 1.28
6 7 2.582272 CCTTTTGCTGCCAGGCATA 58.418 52.632 16.64 4.25 42.09 3.14
7 8 3.384348 CCTTTTGCTGCCAGGCAT 58.616 55.556 16.64 0.00 42.09 4.40
16 17 1.675720 AAACAGTGCGGCCTTTTGCT 61.676 50.000 0.00 0.00 40.92 3.91
17 18 1.227234 AAACAGTGCGGCCTTTTGC 60.227 52.632 0.00 0.00 40.16 3.68
18 19 1.489881 GCAAACAGTGCGGCCTTTTG 61.490 55.000 0.00 8.86 45.10 2.44
19 20 1.227234 GCAAACAGTGCGGCCTTTT 60.227 52.632 0.00 0.00 45.10 2.27
20 21 2.417097 GCAAACAGTGCGGCCTTT 59.583 55.556 0.00 0.00 45.10 3.11
31 32 7.600960 TGCAATGATTTATTAGACTGCAAACA 58.399 30.769 0.00 0.00 0.00 2.83
32 33 8.638685 ATGCAATGATTTATTAGACTGCAAAC 57.361 30.769 0.00 0.00 29.86 2.93
33 34 8.468399 TGATGCAATGATTTATTAGACTGCAAA 58.532 29.630 0.00 0.00 29.86 3.68
34 35 7.916977 GTGATGCAATGATTTATTAGACTGCAA 59.083 33.333 0.00 0.00 29.86 4.08
35 36 7.067251 TGTGATGCAATGATTTATTAGACTGCA 59.933 33.333 0.00 0.00 30.39 4.41
36 37 7.420002 TGTGATGCAATGATTTATTAGACTGC 58.580 34.615 0.00 0.00 0.00 4.40
52 53 7.878547 TTGAGGATATTTGTATGTGATGCAA 57.121 32.000 0.00 0.00 32.98 4.08
99 100 9.334693 GTTGTAGATGCTCTAAAAGATTTTGTG 57.665 33.333 0.82 0.00 27.41 3.33
101 102 7.693951 CGGTTGTAGATGCTCTAAAAGATTTTG 59.306 37.037 0.82 0.00 27.41 2.44
113 114 1.653151 GAACCCGGTTGTAGATGCTC 58.347 55.000 7.78 0.00 0.00 4.26
115 116 0.252197 AGGAACCCGGTTGTAGATGC 59.748 55.000 7.78 0.00 0.00 3.91
116 117 1.553248 TGAGGAACCCGGTTGTAGATG 59.447 52.381 7.78 0.00 0.00 2.90
122 123 1.946267 CGTTTGAGGAACCCGGTTG 59.054 57.895 7.78 0.00 34.67 3.77
124 125 2.281276 GCGTTTGAGGAACCCGGT 60.281 61.111 0.00 0.00 34.67 5.28
125 126 3.053896 GGCGTTTGAGGAACCCGG 61.054 66.667 0.00 0.00 34.67 5.73
130 131 3.709653 ACATATAGAGGGCGTTTGAGGAA 59.290 43.478 0.00 0.00 0.00 3.36
167 168 7.201574 CGAGATTTTGTAACCGATAATTGACCA 60.202 37.037 0.00 0.00 0.00 4.02
169 170 7.844653 GTCGAGATTTTGTAACCGATAATTGAC 59.155 37.037 0.00 0.00 0.00 3.18
173 174 5.756833 GGGTCGAGATTTTGTAACCGATAAT 59.243 40.000 0.00 0.00 0.00 1.28
175 176 4.160065 TGGGTCGAGATTTTGTAACCGATA 59.840 41.667 0.00 0.00 0.00 2.92
182 183 1.404986 CGGCTGGGTCGAGATTTTGTA 60.405 52.381 0.00 0.00 29.41 2.41
223 224 2.551504 GGTGTTGGTTAGTCCGGATGTT 60.552 50.000 7.81 0.00 39.52 2.71
235 236 3.372675 GCTGGATATAAGGGGTGTTGGTT 60.373 47.826 0.00 0.00 0.00 3.67
237 238 2.443255 AGCTGGATATAAGGGGTGTTGG 59.557 50.000 0.00 0.00 0.00 3.77
239 240 3.393687 TGAGCTGGATATAAGGGGTGTT 58.606 45.455 0.00 0.00 0.00 3.32
248 253 5.825151 CCGTCTCAGATATGAGCTGGATATA 59.175 44.000 17.79 0.00 35.97 0.86
294 299 4.451150 GTGGCGGACGCATCCAGA 62.451 66.667 18.95 0.00 46.67 3.86
327 332 1.149854 GGTTTTCCGTGTGGGTCCT 59.850 57.895 0.00 0.00 37.00 3.85
365 370 2.811317 CCTGAGCGGCGTTCTCAC 60.811 66.667 23.75 0.00 35.81 3.51
584 675 3.347958 TTTCCGTTTTGTGCTTAGCTG 57.652 42.857 5.60 0.00 0.00 4.24
598 752 5.585820 AAGTAATTGGTGTTGTTTTCCGT 57.414 34.783 0.00 0.00 0.00 4.69
664 823 3.071479 TGTTGGGAGCGACTATTTTGTC 58.929 45.455 0.00 0.00 0.00 3.18
688 875 5.940192 TGGCTATGCTTGGTTATTTATCG 57.060 39.130 0.00 0.00 0.00 2.92
784 973 2.213483 GTGTCGTCACCGTGTTGAG 58.787 57.895 0.96 0.00 38.51 3.02
816 1005 3.958860 GATCATGGCCGGGGAGGG 61.959 72.222 2.18 0.00 41.48 4.30
817 1006 2.475371 GATGATCATGGCCGGGGAGG 62.475 65.000 14.30 0.00 44.97 4.30
818 1007 1.002868 GATGATCATGGCCGGGGAG 60.003 63.158 14.30 0.00 0.00 4.30
819 1008 1.462043 AGATGATCATGGCCGGGGA 60.462 57.895 14.30 0.00 0.00 4.81
828 1017 1.072678 CTGCGGGCCAGATGATCAT 59.927 57.895 8.25 8.25 44.64 2.45
862 1052 2.048127 GGGTCGTGTGGAGAGTGC 60.048 66.667 0.00 0.00 0.00 4.40
889 1079 1.080569 GGTCCATGGCGCTTTTGTG 60.081 57.895 6.96 0.00 0.00 3.33
890 1080 1.526575 CTGGTCCATGGCGCTTTTGT 61.527 55.000 6.96 0.00 0.00 2.83
1203 1402 2.203139 CCGTGGTGGTTGCTGTGA 60.203 61.111 0.00 0.00 0.00 3.58
1269 1507 2.124570 CCCCCATGCAGGTTCGAG 60.125 66.667 0.00 0.00 34.66 4.04
1270 1508 2.609299 TCCCCCATGCAGGTTCGA 60.609 61.111 0.00 0.00 34.66 3.71
1375 1613 2.725008 GAGACCGAGGGAGATGCG 59.275 66.667 0.00 0.00 0.00 4.73
1501 1739 4.478206 TCTCTCTGACAAATTAGCTGGG 57.522 45.455 0.00 0.00 0.00 4.45
1509 1747 7.609146 TGAAATATGCACTTCTCTCTGACAAAT 59.391 33.333 0.00 0.00 0.00 2.32
1510 1748 6.936335 TGAAATATGCACTTCTCTCTGACAAA 59.064 34.615 0.00 0.00 0.00 2.83
1511 1749 6.466812 TGAAATATGCACTTCTCTCTGACAA 58.533 36.000 0.00 0.00 0.00 3.18
1512 1750 6.041423 TGAAATATGCACTTCTCTCTGACA 57.959 37.500 0.00 0.00 0.00 3.58
1513 1751 6.974932 TTGAAATATGCACTTCTCTCTGAC 57.025 37.500 0.00 0.00 0.00 3.51
1514 1752 8.045507 AGAATTGAAATATGCACTTCTCTCTGA 58.954 33.333 0.00 0.00 32.03 3.27
1515 1753 8.123575 CAGAATTGAAATATGCACTTCTCTCTG 58.876 37.037 0.00 3.47 34.35 3.35
1537 1775 4.706842 AGACTAGGGCAAAAGTTCAGAA 57.293 40.909 0.00 0.00 0.00 3.02
1538 1776 5.818678 TTAGACTAGGGCAAAAGTTCAGA 57.181 39.130 0.00 0.00 0.00 3.27
1600 1839 2.500229 CTGGCCGGTTTTGAGAGTTAA 58.500 47.619 2.29 0.00 0.00 2.01
1628 1867 3.138283 ACTGGTCAACAAAGAAGGGATGA 59.862 43.478 0.00 0.00 0.00 2.92
1630 1869 3.884037 ACTGGTCAACAAAGAAGGGAT 57.116 42.857 0.00 0.00 0.00 3.85
1648 1887 4.094830 ACCGATCAACCAGGTAAAAACT 57.905 40.909 0.00 0.00 36.34 2.66
1654 1893 3.404899 GTCAAAACCGATCAACCAGGTA 58.595 45.455 0.00 0.00 37.26 3.08
1728 1967 8.665643 TCTTCGATTTTACAGGTTGTTTTCTA 57.334 30.769 0.00 0.00 0.00 2.10
1731 1970 8.989653 TTTTCTTCGATTTTACAGGTTGTTTT 57.010 26.923 0.00 0.00 0.00 2.43
1762 2002 8.956533 TTCGGAAATTGGATTTCTTTCTTTTT 57.043 26.923 11.79 0.00 46.03 1.94
1993 2264 1.089920 AGCATGCCACGTCAGAATTC 58.910 50.000 15.66 0.00 0.00 2.17
2066 2339 0.728843 ATTCAACCCTCCCCTCCCTA 59.271 55.000 0.00 0.00 0.00 3.53
2090 2363 3.487372 ACCTCCAAGTCTTAAAACCAGC 58.513 45.455 0.00 0.00 0.00 4.85
2092 2365 4.862371 ACAACCTCCAAGTCTTAAAACCA 58.138 39.130 0.00 0.00 0.00 3.67
2099 2372 7.611855 CCATCTAAATTACAACCTCCAAGTCTT 59.388 37.037 0.00 0.00 0.00 3.01
2123 2396 4.370094 ACAACCCCGAACTTTAATACCA 57.630 40.909 0.00 0.00 0.00 3.25
2178 2451 3.667497 TTGAGACGAGAGAAGTGCATT 57.333 42.857 0.00 0.00 0.00 3.56
2195 2468 8.519799 AGAGAAAAACTGGAGTAACAAATTGA 57.480 30.769 0.00 0.00 0.00 2.57
2196 2469 7.587757 CGAGAGAAAAACTGGAGTAACAAATTG 59.412 37.037 0.00 0.00 0.00 2.32
2198 2471 6.990349 TCGAGAGAAAAACTGGAGTAACAAAT 59.010 34.615 0.00 0.00 37.03 2.32
2201 2474 5.301045 TCTCGAGAGAAAAACTGGAGTAACA 59.699 40.000 12.08 0.00 39.80 2.41
2246 2519 4.775253 AGAGGAGAGGAGGTTTTTCTGTAG 59.225 45.833 0.00 0.00 0.00 2.74
2247 2520 4.528596 CAGAGGAGAGGAGGTTTTTCTGTA 59.471 45.833 0.00 0.00 0.00 2.74
2248 2521 3.326297 CAGAGGAGAGGAGGTTTTTCTGT 59.674 47.826 0.00 0.00 0.00 3.41
2249 2522 3.326297 ACAGAGGAGAGGAGGTTTTTCTG 59.674 47.826 0.00 0.00 37.43 3.02
2250 2523 3.592865 ACAGAGGAGAGGAGGTTTTTCT 58.407 45.455 0.00 0.00 0.00 2.52
2251 2524 5.485209 TTACAGAGGAGAGGAGGTTTTTC 57.515 43.478 0.00 0.00 0.00 2.29
2252 2525 5.607171 TCTTTACAGAGGAGAGGAGGTTTTT 59.393 40.000 0.00 0.00 0.00 1.94
2253 2526 5.155905 TCTTTACAGAGGAGAGGAGGTTTT 58.844 41.667 0.00 0.00 0.00 2.43
2254 2527 4.753186 TCTTTACAGAGGAGAGGAGGTTT 58.247 43.478 0.00 0.00 0.00 3.27
2255 2528 4.405756 TCTTTACAGAGGAGAGGAGGTT 57.594 45.455 0.00 0.00 0.00 3.50
2256 2529 4.405756 TTCTTTACAGAGGAGAGGAGGT 57.594 45.455 0.00 0.00 0.00 3.85
2257 2530 5.948742 ATTTCTTTACAGAGGAGAGGAGG 57.051 43.478 0.00 0.00 0.00 4.30
2259 2532 9.937876 TCTTATATTTCTTTACAGAGGAGAGGA 57.062 33.333 0.00 0.00 0.00 3.71
2262 2535 8.643324 GCCTCTTATATTTCTTTACAGAGGAGA 58.357 37.037 15.11 0.00 46.15 3.71
2263 2536 8.424918 TGCCTCTTATATTTCTTTACAGAGGAG 58.575 37.037 15.11 0.00 46.15 3.69
2264 2537 8.319057 TGCCTCTTATATTTCTTTACAGAGGA 57.681 34.615 15.11 0.00 46.15 3.71
2265 2538 7.172361 GCTGCCTCTTATATTTCTTTACAGAGG 59.828 40.741 7.80 7.80 46.04 3.69
2266 2539 7.930865 AGCTGCCTCTTATATTTCTTTACAGAG 59.069 37.037 0.00 0.00 0.00 3.35
2267 2540 7.796054 AGCTGCCTCTTATATTTCTTTACAGA 58.204 34.615 0.00 0.00 0.00 3.41
2268 2541 8.341173 CAAGCTGCCTCTTATATTTCTTTACAG 58.659 37.037 0.00 0.00 0.00 2.74
2269 2542 8.046708 TCAAGCTGCCTCTTATATTTCTTTACA 58.953 33.333 0.00 0.00 0.00 2.41
2270 2543 8.438676 TCAAGCTGCCTCTTATATTTCTTTAC 57.561 34.615 0.00 0.00 0.00 2.01
2271 2544 9.060347 CATCAAGCTGCCTCTTATATTTCTTTA 57.940 33.333 0.00 0.00 0.00 1.85
2272 2545 7.776969 TCATCAAGCTGCCTCTTATATTTCTTT 59.223 33.333 0.00 0.00 0.00 2.52
2273 2546 7.228308 GTCATCAAGCTGCCTCTTATATTTCTT 59.772 37.037 0.00 0.00 0.00 2.52
2274 2547 6.709846 GTCATCAAGCTGCCTCTTATATTTCT 59.290 38.462 0.00 0.00 0.00 2.52
2275 2548 6.709846 AGTCATCAAGCTGCCTCTTATATTTC 59.290 38.462 0.00 0.00 0.00 2.17
2276 2549 6.485984 CAGTCATCAAGCTGCCTCTTATATTT 59.514 38.462 0.00 0.00 0.00 1.40
2277 2550 5.996513 CAGTCATCAAGCTGCCTCTTATATT 59.003 40.000 0.00 0.00 0.00 1.28
2278 2551 5.306419 TCAGTCATCAAGCTGCCTCTTATAT 59.694 40.000 0.00 0.00 33.09 0.86
2279 2552 4.651045 TCAGTCATCAAGCTGCCTCTTATA 59.349 41.667 0.00 0.00 33.09 0.98
2280 2553 3.453717 TCAGTCATCAAGCTGCCTCTTAT 59.546 43.478 0.00 0.00 33.09 1.73
2281 2554 2.833943 TCAGTCATCAAGCTGCCTCTTA 59.166 45.455 0.00 0.00 33.09 2.10
2282 2555 1.627329 TCAGTCATCAAGCTGCCTCTT 59.373 47.619 0.00 0.00 33.09 2.85
2283 2556 1.273759 TCAGTCATCAAGCTGCCTCT 58.726 50.000 0.00 0.00 33.09 3.69
2284 2557 2.105006 TTCAGTCATCAAGCTGCCTC 57.895 50.000 0.00 0.00 33.09 4.70
2285 2558 2.574006 TTTCAGTCATCAAGCTGCCT 57.426 45.000 0.00 0.00 33.09 4.75
2286 2559 2.555757 ACTTTTCAGTCATCAAGCTGCC 59.444 45.455 0.00 0.00 33.09 4.85
2287 2560 3.911661 ACTTTTCAGTCATCAAGCTGC 57.088 42.857 0.00 0.00 33.09 5.25
2288 2561 5.686159 AGAACTTTTCAGTCATCAAGCTG 57.314 39.130 0.00 0.00 30.45 4.24
2289 2562 6.529220 AGTAGAACTTTTCAGTCATCAAGCT 58.471 36.000 0.00 0.00 30.45 3.74
2290 2563 6.128418 GGAGTAGAACTTTTCAGTCATCAAGC 60.128 42.308 0.00 0.00 30.45 4.01
2291 2564 7.158021 AGGAGTAGAACTTTTCAGTCATCAAG 58.842 38.462 0.00 0.00 30.45 3.02
2292 2565 7.067496 AGGAGTAGAACTTTTCAGTCATCAA 57.933 36.000 0.00 0.00 30.45 2.57
2293 2566 6.672266 AGGAGTAGAACTTTTCAGTCATCA 57.328 37.500 0.00 0.00 30.45 3.07
2294 2567 6.592220 GGAAGGAGTAGAACTTTTCAGTCATC 59.408 42.308 7.24 0.00 30.45 2.92
2295 2568 6.043243 TGGAAGGAGTAGAACTTTTCAGTCAT 59.957 38.462 7.24 0.00 30.45 3.06
2296 2569 5.365605 TGGAAGGAGTAGAACTTTTCAGTCA 59.634 40.000 7.24 0.00 30.45 3.41
2297 2570 5.855045 TGGAAGGAGTAGAACTTTTCAGTC 58.145 41.667 7.24 0.00 30.45 3.51
2298 2571 5.888982 TGGAAGGAGTAGAACTTTTCAGT 57.111 39.130 7.24 0.00 33.11 3.41
2299 2572 7.751768 AAATGGAAGGAGTAGAACTTTTCAG 57.248 36.000 7.24 0.00 0.00 3.02
2300 2573 7.386848 CGTAAATGGAAGGAGTAGAACTTTTCA 59.613 37.037 7.24 0.00 0.00 2.69
2301 2574 7.623715 GCGTAAATGGAAGGAGTAGAACTTTTC 60.624 40.741 0.00 0.00 0.00 2.29
2302 2575 6.148976 GCGTAAATGGAAGGAGTAGAACTTTT 59.851 38.462 0.00 0.00 0.00 2.27
2303 2576 5.642491 GCGTAAATGGAAGGAGTAGAACTTT 59.358 40.000 0.00 0.00 0.00 2.66
2304 2577 5.176592 GCGTAAATGGAAGGAGTAGAACTT 58.823 41.667 0.00 0.00 0.00 2.66
2305 2578 4.382793 GGCGTAAATGGAAGGAGTAGAACT 60.383 45.833 0.00 0.00 0.00 3.01
2306 2579 3.869832 GGCGTAAATGGAAGGAGTAGAAC 59.130 47.826 0.00 0.00 0.00 3.01
2307 2580 3.773119 AGGCGTAAATGGAAGGAGTAGAA 59.227 43.478 0.00 0.00 0.00 2.10
2308 2581 3.371965 AGGCGTAAATGGAAGGAGTAGA 58.628 45.455 0.00 0.00 0.00 2.59
2309 2582 3.385111 AGAGGCGTAAATGGAAGGAGTAG 59.615 47.826 0.00 0.00 0.00 2.57
2310 2583 3.371965 AGAGGCGTAAATGGAAGGAGTA 58.628 45.455 0.00 0.00 0.00 2.59
2311 2584 2.168728 GAGAGGCGTAAATGGAAGGAGT 59.831 50.000 0.00 0.00 0.00 3.85
2312 2585 2.483889 GGAGAGGCGTAAATGGAAGGAG 60.484 54.545 0.00 0.00 0.00 3.69
2313 2586 1.485066 GGAGAGGCGTAAATGGAAGGA 59.515 52.381 0.00 0.00 0.00 3.36
2314 2587 1.486726 AGGAGAGGCGTAAATGGAAGG 59.513 52.381 0.00 0.00 0.00 3.46
2315 2588 2.432510 AGAGGAGAGGCGTAAATGGAAG 59.567 50.000 0.00 0.00 0.00 3.46
2316 2589 2.431057 GAGAGGAGAGGCGTAAATGGAA 59.569 50.000 0.00 0.00 0.00 3.53
2317 2590 2.032620 GAGAGGAGAGGCGTAAATGGA 58.967 52.381 0.00 0.00 0.00 3.41
2318 2591 1.269309 CGAGAGGAGAGGCGTAAATGG 60.269 57.143 0.00 0.00 0.00 3.16
2319 2592 1.866063 GCGAGAGGAGAGGCGTAAATG 60.866 57.143 0.00 0.00 0.00 2.32
2320 2593 0.386113 GCGAGAGGAGAGGCGTAAAT 59.614 55.000 0.00 0.00 0.00 1.40
2321 2594 1.807886 GCGAGAGGAGAGGCGTAAA 59.192 57.895 0.00 0.00 0.00 2.01
2322 2595 2.470362 CGCGAGAGGAGAGGCGTAA 61.470 63.158 0.00 0.00 43.36 3.18
2323 2596 2.895865 CGCGAGAGGAGAGGCGTA 60.896 66.667 0.00 0.00 43.36 4.42
2326 2599 3.894947 GGTCGCGAGAGGAGAGGC 61.895 72.222 10.24 0.00 43.49 4.70
2327 2600 3.578272 CGGTCGCGAGAGGAGAGG 61.578 72.222 10.24 0.00 43.49 3.69
2328 2601 4.244802 GCGGTCGCGAGAGGAGAG 62.245 72.222 10.24 0.00 43.49 3.20
2367 2640 4.477975 GAGGAGGTCGTCGCACGG 62.478 72.222 8.46 0.00 42.81 4.94
2368 2641 4.477975 GGAGGAGGTCGTCGCACG 62.478 72.222 2.79 2.79 44.19 5.34
2369 2642 3.053849 GAGGAGGAGGTCGTCGCAC 62.054 68.421 0.00 0.00 30.65 5.34
2370 2643 2.750637 GAGGAGGAGGTCGTCGCA 60.751 66.667 0.00 0.00 30.65 5.10
2371 2644 3.519930 GGAGGAGGAGGTCGTCGC 61.520 72.222 0.00 0.00 40.43 5.19
2372 2645 1.820481 GAGGAGGAGGAGGTCGTCG 60.820 68.421 0.00 0.00 40.43 5.12
2373 2646 0.838608 TAGAGGAGGAGGAGGTCGTC 59.161 60.000 0.00 0.00 39.05 4.20
2374 2647 0.547553 GTAGAGGAGGAGGAGGTCGT 59.452 60.000 0.00 0.00 0.00 4.34
2375 2648 0.179012 GGTAGAGGAGGAGGAGGTCG 60.179 65.000 0.00 0.00 0.00 4.79
2376 2649 0.186630 GGGTAGAGGAGGAGGAGGTC 59.813 65.000 0.00 0.00 0.00 3.85
2377 2650 1.298157 GGGGTAGAGGAGGAGGAGGT 61.298 65.000 0.00 0.00 0.00 3.85
2378 2651 1.002242 AGGGGTAGAGGAGGAGGAGG 61.002 65.000 0.00 0.00 0.00 4.30
2379 2652 0.938192 AAGGGGTAGAGGAGGAGGAG 59.062 60.000 0.00 0.00 0.00 3.69
2380 2653 0.935194 GAAGGGGTAGAGGAGGAGGA 59.065 60.000 0.00 0.00 0.00 3.71
2381 2654 0.105401 GGAAGGGGTAGAGGAGGAGG 60.105 65.000 0.00 0.00 0.00 4.30
2382 2655 0.938192 AGGAAGGGGTAGAGGAGGAG 59.062 60.000 0.00 0.00 0.00 3.69
2383 2656 0.935194 GAGGAAGGGGTAGAGGAGGA 59.065 60.000 0.00 0.00 0.00 3.71
2384 2657 0.105401 GGAGGAAGGGGTAGAGGAGG 60.105 65.000 0.00 0.00 0.00 4.30
2385 2658 0.468400 CGGAGGAAGGGGTAGAGGAG 60.468 65.000 0.00 0.00 0.00 3.69
2386 2659 1.619143 CGGAGGAAGGGGTAGAGGA 59.381 63.158 0.00 0.00 0.00 3.71
2387 2660 4.279326 CGGAGGAAGGGGTAGAGG 57.721 66.667 0.00 0.00 0.00 3.69
2406 2679 3.801997 AGCATCCCCGAGGCCAAG 61.802 66.667 5.01 0.00 40.43 3.61
2407 2680 4.113815 CAGCATCCCCGAGGCCAA 62.114 66.667 5.01 0.00 40.43 4.52
2410 2683 4.864334 CACCAGCATCCCCGAGGC 62.864 72.222 0.00 0.00 39.81 4.70
2411 2684 4.181010 CCACCAGCATCCCCGAGG 62.181 72.222 0.00 0.00 0.00 4.63
2412 2685 4.864334 GCCACCAGCATCCCCGAG 62.864 72.222 0.00 0.00 42.97 4.63
2429 2702 4.785453 GAAGGTCAGGGGGCGCTG 62.785 72.222 7.64 0.00 0.00 5.18
2434 2707 2.692741 GAGGGGAAGGTCAGGGGG 60.693 72.222 0.00 0.00 0.00 5.40
2435 2708 2.692741 GGAGGGGAAGGTCAGGGG 60.693 72.222 0.00 0.00 0.00 4.79
2436 2709 1.997874 CAGGAGGGGAAGGTCAGGG 60.998 68.421 0.00 0.00 0.00 4.45
2437 2710 1.997874 CCAGGAGGGGAAGGTCAGG 60.998 68.421 0.00 0.00 0.00 3.86
2438 2711 1.229658 ACCAGGAGGGGAAGGTCAG 60.230 63.158 0.00 0.00 42.91 3.51
2439 2712 1.538876 CACCAGGAGGGGAAGGTCA 60.539 63.158 0.00 0.00 42.79 4.02
2440 2713 2.301738 CCACCAGGAGGGGAAGGTC 61.302 68.421 0.00 0.00 42.79 3.85
2441 2714 2.204151 CCACCAGGAGGGGAAGGT 60.204 66.667 0.00 0.00 42.79 3.50
2442 2715 3.732849 GCCACCAGGAGGGGAAGG 61.733 72.222 4.89 0.00 42.79 3.46
2443 2716 2.612115 AGCCACCAGGAGGGGAAG 60.612 66.667 4.89 0.00 42.79 3.46
2444 2717 2.610859 GAGCCACCAGGAGGGGAA 60.611 66.667 4.89 0.00 42.79 3.97
2445 2718 3.615811 AGAGCCACCAGGAGGGGA 61.616 66.667 4.89 0.00 42.79 4.81
2446 2719 3.086600 GAGAGCCACCAGGAGGGG 61.087 72.222 4.89 0.00 42.91 4.79
2447 2720 3.086600 GGAGAGCCACCAGGAGGG 61.087 72.222 4.89 1.19 44.81 4.30
2448 2721 3.465403 CGGAGAGCCACCAGGAGG 61.465 72.222 0.00 0.00 42.21 4.30
2449 2722 3.465403 CCGGAGAGCCACCAGGAG 61.465 72.222 0.00 0.00 36.89 3.69


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

AutoCloner maintained by Alex Coulton.