Multiple sequence alignment - TraesCS1B01G359900

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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 TraesCS1B01G359900 chr1B 100.000 4225 0 0 2117 6341 588645648 588649872 0.000000e+00 7803.0
1 TraesCS1B01G359900 chr1B 100.000 1761 0 0 1 1761 588643532 588645292 0.000000e+00 3253.0
2 TraesCS1B01G359900 chr1B 81.162 1343 192 33 3352 4657 588320099 588318781 0.000000e+00 1022.0
3 TraesCS1B01G359900 chr1B 85.517 435 59 4 423 855 588321840 588321408 9.690000e-123 451.0
4 TraesCS1B01G359900 chr1B 79.708 616 103 11 4676 5285 588318790 588318191 5.880000e-115 425.0
5 TraesCS1B01G359900 chr1B 83.120 391 63 3 467 856 588489861 588489473 2.810000e-93 353.0
6 TraesCS1B01G359900 chr1B 74.738 764 130 36 3925 4654 588487368 588486634 3.740000e-72 283.0
7 TraesCS1B01G359900 chr1B 83.553 152 23 1 4481 4630 588483503 588483654 2.380000e-29 141.0
8 TraesCS1B01G359900 chr1A 89.935 2166 138 36 4219 6341 532911449 532913577 0.000000e+00 2719.0
9 TraesCS1B01G359900 chr1A 91.929 1462 86 12 2251 3704 532891422 532892859 0.000000e+00 2017.0
10 TraesCS1B01G359900 chr1A 81.696 1344 183 36 3352 4657 532616960 532615642 0.000000e+00 1061.0
11 TraesCS1B01G359900 chr1A 94.015 518 31 0 3705 4222 532892922 532893439 0.000000e+00 785.0
12 TraesCS1B01G359900 chr1A 93.169 366 21 3 15 377 532830278 532830642 9.360000e-148 534.0
13 TraesCS1B01G359900 chr1A 85.977 435 57 4 423 855 532618698 532618266 4.480000e-126 462.0
14 TraesCS1B01G359900 chr1A 80.163 615 102 11 4676 5285 532615651 532615052 5.830000e-120 442.0
15 TraesCS1B01G359900 chr1A 96.186 236 9 0 647 882 532832428 532832663 2.770000e-103 387.0
16 TraesCS1B01G359900 chr1A 86.648 352 36 9 1419 1761 532868091 532868440 4.640000e-101 379.0
17 TraesCS1B01G359900 chr1A 75.521 768 142 32 3904 4654 532765453 532764715 1.020000e-87 335.0
18 TraesCS1B01G359900 chr1A 77.640 483 85 22 4688 5157 532742695 532742223 8.100000e-69 272.0
19 TraesCS1B01G359900 chr1A 84.286 280 38 6 4874 5149 532764491 532764214 1.050000e-67 268.0
20 TraesCS1B01G359900 chr1A 90.594 202 12 4 951 1145 532832650 532832851 1.750000e-65 261.0
21 TraesCS1B01G359900 chr1A 77.320 291 64 2 2739 3028 532766663 532766374 3.040000e-38 171.0
22 TraesCS1B01G359900 chr1A 79.268 246 46 5 866 1109 532766998 532766756 3.930000e-37 167.0
23 TraesCS1B01G359900 chr1A 84.568 162 25 0 4493 4654 532742862 532742701 1.830000e-35 161.0
24 TraesCS1B01G359900 chr1A 91.071 112 2 4 2399 2507 112777395 112777289 1.840000e-30 145.0
25 TraesCS1B01G359900 chr1A 97.826 46 1 0 1164 1209 532866814 532866859 5.270000e-11 80.5
26 TraesCS1B01G359900 chr1D 88.752 1787 124 30 2124 3867 435344908 435346660 0.000000e+00 2115.0
27 TraesCS1B01G359900 chr1D 88.239 1420 108 28 3883 5280 435346703 435348085 0.000000e+00 1642.0
28 TraesCS1B01G359900 chr1D 93.203 868 41 7 447 1304 435343671 435344530 0.000000e+00 1260.0
29 TraesCS1B01G359900 chr1D 92.201 359 20 6 25 378 435340335 435340690 9.490000e-138 501.0
30 TraesCS1B01G359900 chr1D 87.812 361 34 9 1411 1761 435344529 435344889 1.270000e-111 414.0
31 TraesCS1B01G359900 chr1D 82.955 440 64 9 424 856 435154004 435153569 2.770000e-103 387.0
32 TraesCS1B01G359900 chr1D 78.541 466 80 20 4688 5141 435151067 435150610 8.040000e-74 289.0
33 TraesCS1B01G359900 chr1D 79.141 326 56 8 510 826 424453296 424453618 1.380000e-51 215.0
34 TraesCS1B01G359900 chr1D 74.938 403 82 14 4236 4630 435147217 435147608 3.930000e-37 167.0
35 TraesCS1B01G359900 chr1D 91.071 112 2 4 2399 2507 19956673 19956779 1.840000e-30 145.0
36 TraesCS1B01G359900 chr6D 80.806 422 70 8 506 923 84685428 84685014 2.850000e-83 320.0
37 TraesCS1B01G359900 chr6D 83.881 335 49 4 506 836 85505051 85505384 1.330000e-81 315.0
38 TraesCS1B01G359900 chr6D 83.951 81 12 1 1345 1424 27672235 27672315 6.820000e-10 76.8
39 TraesCS1B01G359900 chr6B 80.095 422 73 7 506 923 161352972 161352558 2.870000e-78 303.0
40 TraesCS1B01G359900 chrUn 91.071 112 2 4 2399 2507 331682529 331682635 1.840000e-30 145.0
41 TraesCS1B01G359900 chrUn 91.071 112 2 4 2399 2507 440189918 440190024 1.840000e-30 145.0
42 TraesCS1B01G359900 chr7D 91.071 112 2 4 2399 2507 484627484 484627590 1.840000e-30 145.0
43 TraesCS1B01G359900 chr7B 91.071 112 2 4 2399 2507 485864572 485864466 1.840000e-30 145.0
44 TraesCS1B01G359900 chr7B 91.304 69 6 0 1345 1413 747594355 747594287 1.880000e-15 95.3
45 TraesCS1B01G359900 chr5D 91.071 112 2 4 2399 2507 240136344 240136450 1.840000e-30 145.0
46 TraesCS1B01G359900 chr3D 91.071 112 2 4 2399 2507 21903264 21903370 1.840000e-30 145.0
47 TraesCS1B01G359900 chr3D 92.647 68 5 0 1345 1412 483523949 483523882 1.450000e-16 99.0
48 TraesCS1B01G359900 chr5B 73.793 290 63 9 1454 1733 120574965 120574679 1.120000e-17 102.0
49 TraesCS1B01G359900 chr4B 91.549 71 6 0 1345 1415 585726666 585726736 1.450000e-16 99.0
50 TraesCS1B01G359900 chr4B 91.304 69 6 0 1345 1413 87686895 87686963 1.880000e-15 95.3
51 TraesCS1B01G359900 chr6A 90.278 72 7 0 1345 1416 1139593 1139522 1.880000e-15 95.3
52 TraesCS1B01G359900 chr5A 90.769 65 6 0 1345 1409 684315411 684315347 3.150000e-13 87.9
53 TraesCS1B01G359900 chr5A 88.571 70 6 2 1345 1412 611030136 611030067 4.070000e-12 84.2
54 TraesCS1B01G359900 chr2A 89.855 69 6 1 1345 1413 55949915 55949982 3.150000e-13 87.9
55 TraesCS1B01G359900 chr3B 94.444 36 1 1 2333 2367 555154492 555154457 3.000000e-03 54.7


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 TraesCS1B01G359900 chr1B 588643532 588649872 6340 False 5528.000000 7803 100.000000 1 6341 2 chr1B.!!$F2 6340
1 TraesCS1B01G359900 chr1B 588318191 588321840 3649 True 632.666667 1022 82.129000 423 5285 3 chr1B.!!$R1 4862
2 TraesCS1B01G359900 chr1B 588486634 588489861 3227 True 318.000000 353 78.929000 467 4654 2 chr1B.!!$R2 4187
3 TraesCS1B01G359900 chr1A 532911449 532913577 2128 False 2719.000000 2719 89.935000 4219 6341 1 chr1A.!!$F1 2122
4 TraesCS1B01G359900 chr1A 532891422 532893439 2017 False 1401.000000 2017 92.972000 2251 4222 2 chr1A.!!$F4 1971
5 TraesCS1B01G359900 chr1A 532615052 532618698 3646 True 655.000000 1061 82.612000 423 5285 3 chr1A.!!$R2 4862
6 TraesCS1B01G359900 chr1A 532830278 532832851 2573 False 394.000000 534 93.316333 15 1145 3 chr1A.!!$F2 1130
7 TraesCS1B01G359900 chr1A 532764214 532766998 2784 True 235.250000 335 79.098750 866 5149 4 chr1A.!!$R4 4283
8 TraesCS1B01G359900 chr1A 532866814 532868440 1626 False 229.750000 379 92.237000 1164 1761 2 chr1A.!!$F3 597
9 TraesCS1B01G359900 chr1A 532742223 532742862 639 True 216.500000 272 81.104000 4493 5157 2 chr1A.!!$R3 664
10 TraesCS1B01G359900 chr1D 435340335 435348085 7750 False 1186.400000 2115 90.041400 25 5280 5 chr1D.!!$F4 5255
11 TraesCS1B01G359900 chr1D 435150610 435154004 3394 True 338.000000 387 80.748000 424 5141 2 chr1D.!!$R1 4717

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
453 921 0.467474 TCTCGGCCGAGTACATGGAT 60.467 55.000 44.61 0.0 42.49 3.41 F
1039 5476 0.670854 GAGCAACGACTCCAGGAACC 60.671 60.000 0.00 0.0 0.00 3.62 F
2434 8202 0.671251 GTCGCTCCATCTCGAGGAAT 59.329 55.000 13.56 0.0 35.21 3.01 F
2615 8392 2.815503 CTGAATGCCTGTCACACAATCA 59.184 45.455 0.00 0.0 0.00 2.57 F
3997 10155 1.630369 AGACCAACTCTATGCTTGCCA 59.370 47.619 0.00 0.0 0.00 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2405 8173 0.620556 ATGGAGCGACTTGGGTTGAT 59.379 50.000 0.0 0.0 0.00 2.57 R
2928 8705 0.319555 GCAGTGTCGAGTTGGCAGTA 60.320 55.000 0.0 0.0 0.00 2.74 R
3440 9473 1.399440 CTCAAACCGCCAGATGACATG 59.601 52.381 0.0 0.0 0.00 3.21 R
4330 10492 1.678101 GTACCATCATGCAAGAAGCCC 59.322 52.381 0.0 0.0 44.83 5.19 R
5432 11695 0.030638 ATTGTTGGACGTTGTGCTGC 59.969 50.000 0.0 0.0 0.00 5.25 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
58 59 6.331369 TGGAAGAAGTAGCAAAGGAATTTG 57.669 37.500 0.00 0.00 35.15 2.32
106 107 5.452777 GCTAGGTGCTCAAAAGTTAAACTG 58.547 41.667 0.00 0.00 38.95 3.16
109 110 5.130350 AGGTGCTCAAAAGTTAAACTGCTA 58.870 37.500 0.00 0.00 0.00 3.49
154 155 2.913617 AGGGGGTTCTTTGAGGAGTTAG 59.086 50.000 0.00 0.00 0.00 2.34
453 921 0.467474 TCTCGGCCGAGTACATGGAT 60.467 55.000 44.61 0.00 42.49 3.41
463 931 1.960763 TACATGGATCCGCGCATGC 60.961 57.895 19.92 7.91 32.02 4.06
501 3436 4.680237 CGCAGCTTCCCGGACACA 62.680 66.667 0.73 0.00 0.00 3.72
718 4816 3.628280 GACGACTCGGTGCAGGTCC 62.628 68.421 2.98 0.00 0.00 4.46
901 5338 2.203015 CATACGACCGGGCTTGGG 60.203 66.667 5.33 0.00 0.00 4.12
1039 5476 0.670854 GAGCAACGACTCCAGGAACC 60.671 60.000 0.00 0.00 0.00 3.62
1063 5500 1.350193 CATTGACTTCTCGTGGGACG 58.650 55.000 0.00 0.00 44.19 4.79
1135 5577 3.186702 TGTCCACTTCACAACATCGAA 57.813 42.857 0.00 0.00 0.00 3.71
1257 6992 5.491982 CCACTTACCTCTTTTAGAGCACAT 58.508 41.667 0.00 0.00 40.98 3.21
1258 6993 5.352569 CCACTTACCTCTTTTAGAGCACATG 59.647 44.000 0.00 0.00 40.98 3.21
1259 6994 4.938226 ACTTACCTCTTTTAGAGCACATGC 59.062 41.667 0.00 0.00 40.98 4.06
1260 6995 3.423539 ACCTCTTTTAGAGCACATGCA 57.576 42.857 6.64 0.00 40.98 3.96
1261 6996 3.754965 ACCTCTTTTAGAGCACATGCAA 58.245 40.909 6.64 0.00 40.98 4.08
1288 7023 3.317149 GCTATGCACCATTGTCACATCAT 59.683 43.478 0.00 0.00 0.00 2.45
1311 7046 9.268282 TCATCCCAATTATATAGTACTTCCTCC 57.732 37.037 0.00 0.00 0.00 4.30
1314 7049 7.395489 TCCCAATTATATAGTACTTCCTCCGTC 59.605 40.741 0.00 0.00 0.00 4.79
1315 7050 7.363617 CCCAATTATATAGTACTTCCTCCGTCC 60.364 44.444 0.00 0.00 0.00 4.79
1316 7051 7.363617 CCAATTATATAGTACTTCCTCCGTCCC 60.364 44.444 0.00 0.00 0.00 4.46
1320 7055 3.684408 AGTACTTCCTCCGTCCCTAAT 57.316 47.619 0.00 0.00 0.00 1.73
1321 7056 3.991683 AGTACTTCCTCCGTCCCTAATT 58.008 45.455 0.00 0.00 0.00 1.40
1325 7060 5.354842 ACTTCCTCCGTCCCTAATTTAAG 57.645 43.478 0.00 0.00 0.00 1.85
1329 7064 4.966805 TCCTCCGTCCCTAATTTAAGACAT 59.033 41.667 6.92 0.00 0.00 3.06
1330 7065 5.427481 TCCTCCGTCCCTAATTTAAGACATT 59.573 40.000 6.92 0.00 0.00 2.71
1331 7066 6.069847 TCCTCCGTCCCTAATTTAAGACATTT 60.070 38.462 6.92 0.00 0.00 2.32
1332 7067 6.602009 CCTCCGTCCCTAATTTAAGACATTTT 59.398 38.462 6.92 0.00 0.00 1.82
1333 7068 7.122204 CCTCCGTCCCTAATTTAAGACATTTTT 59.878 37.037 6.92 0.00 0.00 1.94
1356 7091 7.504924 TTTTTCCAGATGAATGTAAGACGTT 57.495 32.000 0.00 0.00 31.67 3.99
1357 7092 7.504924 TTTTCCAGATGAATGTAAGACGTTT 57.495 32.000 0.00 0.00 31.67 3.60
1358 7093 7.504924 TTTCCAGATGAATGTAAGACGTTTT 57.495 32.000 0.00 0.00 31.67 2.43
1359 7094 7.504924 TTCCAGATGAATGTAAGACGTTTTT 57.495 32.000 0.00 0.00 0.00 1.94
1409 7144 4.717778 TCTTACATTATGGAACGGAGGGAA 59.282 41.667 0.00 0.00 0.00 3.97
1436 7171 8.504812 AGTTGCCAACAATTCAATAAAAACTT 57.495 26.923 10.69 0.00 38.27 2.66
1440 7175 7.921214 TGCCAACAATTCAATAAAAACTTCGTA 59.079 29.630 0.00 0.00 0.00 3.43
1509 7247 4.388577 AAGAGGGTGAGGTTTTATTGCT 57.611 40.909 0.00 0.00 0.00 3.91
1513 7251 5.044846 AGAGGGTGAGGTTTTATTGCTATGT 60.045 40.000 0.00 0.00 0.00 2.29
1529 7267 6.258230 TGCTATGTGAAATTCCAAGTTGAG 57.742 37.500 3.87 0.00 0.00 3.02
1532 7270 6.072508 GCTATGTGAAATTCCAAGTTGAGACA 60.073 38.462 3.87 0.00 0.00 3.41
1590 7334 5.865552 GCAATGAATAGTGATGTTGCTGTTT 59.134 36.000 0.00 0.00 38.97 2.83
1604 7348 4.870123 TGCTGTTTGGCACTATTCAATT 57.130 36.364 0.00 0.00 37.29 2.32
1658 7402 9.829507 TCATGTAATTTGAACTTGGAATTTTGT 57.170 25.926 0.00 0.00 0.00 2.83
1699 7443 9.627123 CCACCCTCTTAACATCATTTAATTCTA 57.373 33.333 0.00 0.00 0.00 2.10
1740 7484 6.650390 ACTTCAAAACATATTTTCCATGTGGC 59.350 34.615 0.00 0.00 35.79 5.01
1747 7491 5.650266 ACATATTTTCCATGTGGCTTCGTTA 59.350 36.000 0.00 0.00 35.33 3.18
1748 7492 3.907894 TTTTCCATGTGGCTTCGTTAC 57.092 42.857 0.00 0.00 34.44 2.50
1749 7493 2.552599 TTCCATGTGGCTTCGTTACA 57.447 45.000 0.00 0.00 34.44 2.41
1750 7494 2.779755 TCCATGTGGCTTCGTTACAT 57.220 45.000 0.00 0.00 35.56 2.29
2137 7882 1.745653 ACTTACGTAAGGAGGCCGTAC 59.254 52.381 32.63 0.00 46.39 3.67
2165 7910 2.715763 AGGTGTAGTTCCCTTCTCCA 57.284 50.000 0.00 0.00 0.00 3.86
2216 7982 7.284919 TCGCTATGAAGTGGTGAATTAGATA 57.715 36.000 0.00 0.00 33.82 1.98
2261 8027 3.935828 GCTGTTTGATCTACCTTGAGACC 59.064 47.826 0.00 0.00 0.00 3.85
2263 8029 5.105310 GCTGTTTGATCTACCTTGAGACCTA 60.105 44.000 0.00 0.00 0.00 3.08
2284 8050 8.637196 ACCTATAATATGACTCGTGATCTTGA 57.363 34.615 0.00 0.00 0.00 3.02
2405 8173 6.590656 AATTTGTGATGAGGGGGTATAAGA 57.409 37.500 0.00 0.00 0.00 2.10
2421 8189 2.100605 AAGATCAACCCAAGTCGCTC 57.899 50.000 0.00 0.00 0.00 5.03
2428 8196 1.227089 CCCAAGTCGCTCCATCTCG 60.227 63.158 0.00 0.00 0.00 4.04
2434 8202 0.671251 GTCGCTCCATCTCGAGGAAT 59.329 55.000 13.56 0.00 35.21 3.01
2615 8392 2.815503 CTGAATGCCTGTCACACAATCA 59.184 45.455 0.00 0.00 0.00 2.57
2617 8394 3.441222 TGAATGCCTGTCACACAATCATC 59.559 43.478 0.00 0.00 0.00 2.92
2624 8401 5.391310 GCCTGTCACACAATCATCTACTTTG 60.391 44.000 0.00 0.00 0.00 2.77
2928 8705 4.672587 ATACAACTACACCATGATCGCT 57.327 40.909 0.00 0.00 0.00 4.93
3050 8907 4.355543 TGGAAGCTTATTTTCGCACATC 57.644 40.909 0.00 0.00 0.00 3.06
3051 8908 3.181511 TGGAAGCTTATTTTCGCACATCG 60.182 43.478 0.00 0.00 40.15 3.84
3052 8909 3.063452 GGAAGCTTATTTTCGCACATCGA 59.937 43.478 0.00 0.00 46.88 3.59
3340 9354 6.320164 TGCCTTTTTGAAAAGAACTACAGCTA 59.680 34.615 15.79 1.01 46.39 3.32
3343 9357 8.352942 CCTTTTTGAAAAGAACTACAGCTATGT 58.647 33.333 15.79 0.00 46.39 2.29
3345 9359 9.730420 TTTTTGAAAAGAACTACAGCTATGTTC 57.270 29.630 14.15 14.15 41.01 3.18
3351 9365 6.842437 AGAACTACAGCTATGTTCTGAAGA 57.158 37.500 20.26 0.00 45.67 2.87
3419 9447 6.576185 AGAACAATGCTGTTTCAACTGAAAT 58.424 32.000 8.07 0.00 45.98 2.17
3465 9498 2.410322 ATCTGGCGGTTTGAGTGGCA 62.410 55.000 0.00 0.00 36.67 4.92
3644 9686 7.830099 GGATCAATTCCTAATGTCCTTTCAT 57.170 36.000 0.00 0.00 41.78 2.57
3699 9741 5.491070 TCCGCATTATGATATCTTTGAGGG 58.509 41.667 3.98 0.55 0.00 4.30
3701 9743 4.940046 CGCATTATGATATCTTTGAGGGCT 59.060 41.667 3.98 0.00 0.00 5.19
3702 9744 6.108687 CGCATTATGATATCTTTGAGGGCTA 58.891 40.000 3.98 0.00 0.00 3.93
3703 9745 6.036517 CGCATTATGATATCTTTGAGGGCTAC 59.963 42.308 3.98 0.00 0.00 3.58
3704 9746 6.036517 GCATTATGATATCTTTGAGGGCTACG 59.963 42.308 3.98 0.00 0.00 3.51
3772 9897 2.168521 TCCCCTTAGAGATTTGACTGCG 59.831 50.000 0.00 0.00 0.00 5.18
3852 9977 7.954620 CCCCCTAGTTATTAGGTTAGTACATCT 59.045 40.741 0.00 0.00 46.55 2.90
3966 10124 2.840296 GCAATAGTTCTTGCCAGCTC 57.160 50.000 0.00 0.00 44.56 4.09
3997 10155 1.630369 AGACCAACTCTATGCTTGCCA 59.370 47.619 0.00 0.00 0.00 4.92
4052 10210 4.790123 GCTGATAGGAGCACTTGTAGTACG 60.790 50.000 0.00 0.00 38.95 3.67
4093 10251 3.851458 AAAGGAAAGGTAACACTCCGT 57.149 42.857 0.00 0.00 42.75 4.69
4235 10397 2.559698 TGGACATGGACAACACGAAT 57.440 45.000 0.00 0.00 0.00 3.34
4330 10492 1.737793 GGGTTCGGCACTGTTTATGAG 59.262 52.381 0.00 0.00 0.00 2.90
4716 10909 9.070179 TCTATGTCAAGTTACACACTACTAACA 57.930 33.333 0.00 0.00 32.94 2.41
4726 10919 9.467258 GTTACACACTACTAACATTAGTCACAA 57.533 33.333 7.56 0.00 42.66 3.33
5010 11241 6.690194 AACATCCTACTGAATGCAAATCTC 57.310 37.500 0.00 0.00 0.00 2.75
5227 11464 5.789521 TGTATGTATGCAGGTACGCAATAT 58.210 37.500 0.00 0.00 46.87 1.28
5242 11479 5.057149 ACGCAATATCCCTACAACTGAATC 58.943 41.667 0.00 0.00 0.00 2.52
5285 11522 2.366590 TCGGCATCGTACTACTAGAGGA 59.633 50.000 0.00 0.00 37.69 3.71
5286 11523 3.136763 CGGCATCGTACTACTAGAGGAA 58.863 50.000 0.00 0.00 0.00 3.36
5287 11524 3.186817 CGGCATCGTACTACTAGAGGAAG 59.813 52.174 0.00 0.00 0.00 3.46
5288 11525 3.502979 GGCATCGTACTACTAGAGGAAGG 59.497 52.174 0.00 0.00 0.00 3.46
5290 11527 3.205784 TCGTACTACTAGAGGAAGGCC 57.794 52.381 0.00 0.00 0.00 5.19
5291 11528 2.507058 TCGTACTACTAGAGGAAGGCCA 59.493 50.000 5.01 0.00 36.29 5.36
5292 11529 3.137913 TCGTACTACTAGAGGAAGGCCAT 59.862 47.826 5.01 0.00 36.29 4.40
5293 11530 3.502979 CGTACTACTAGAGGAAGGCCATC 59.497 52.174 5.01 0.92 36.29 3.51
5294 11531 2.965562 ACTACTAGAGGAAGGCCATCC 58.034 52.381 19.73 19.73 39.96 3.51
5295 11532 2.247635 ACTACTAGAGGAAGGCCATCCA 59.752 50.000 28.12 7.56 42.27 3.41
5297 11534 1.273838 ACTAGAGGAAGGCCATCCACA 60.274 52.381 28.12 11.78 42.27 4.17
5305 11568 0.477204 AGGCCATCCACATCATCCAG 59.523 55.000 5.01 0.00 33.74 3.86
5327 11590 2.035449 TGGACACGACTACACCTCAAAG 59.965 50.000 0.00 0.00 0.00 2.77
5328 11591 2.609737 GGACACGACTACACCTCAAAGG 60.610 54.545 0.00 0.00 42.49 3.11
5329 11592 2.295349 GACACGACTACACCTCAAAGGA 59.705 50.000 0.00 0.00 37.67 3.36
5330 11593 2.296471 ACACGACTACACCTCAAAGGAG 59.704 50.000 0.00 0.00 37.67 3.69
5350 11613 1.270550 GGCAACATTGAGGAAGTGGTG 59.729 52.381 0.00 0.00 33.78 4.17
5354 11617 1.270839 ACATTGAGGAAGTGGTGGACG 60.271 52.381 0.00 0.00 0.00 4.79
5383 11646 3.001838 TGCAACGTGACTACAACATCAAC 59.998 43.478 0.00 0.00 0.00 3.18
5384 11647 3.001838 GCAACGTGACTACAACATCAACA 59.998 43.478 0.00 0.00 0.00 3.33
5403 11666 3.579302 TGTGTGGAAGGCCCTGGG 61.579 66.667 8.86 8.86 35.38 4.45
5432 11695 1.968017 AAGTGCACCGACCATGCTG 60.968 57.895 14.63 0.00 43.77 4.41
5435 11698 3.807538 GCACCGACCATGCTGCAG 61.808 66.667 10.11 10.11 40.08 4.41
5464 11727 3.505680 GTCCAACAATGACTAATGTGGCA 59.494 43.478 0.00 0.00 0.00 4.92
5470 11733 0.403655 TGACTAATGTGGCAGCCCAA 59.596 50.000 9.64 0.00 44.33 4.12
5513 11776 2.745515 GGGTGAAGACCACACTAGAC 57.254 55.000 0.00 0.00 45.64 2.59
5554 11817 2.443887 ACATGACAGCCAATTGCAAC 57.556 45.000 0.00 0.00 44.83 4.17
5607 11870 1.555967 AATGTAACCCATGGCACCAC 58.444 50.000 6.09 1.58 32.82 4.16
5648 11911 8.313292 TCAACATTAATTCATTTTTGGAGGGAG 58.687 33.333 0.00 0.00 0.00 4.30
5745 12008 2.100631 CGCCATTGAGACGGACCAC 61.101 63.158 0.00 0.00 0.00 4.16
5776 12039 9.979578 TCATTTTAACACAGAAAGTATGCAAAT 57.020 25.926 0.00 0.00 0.00 2.32
5778 12041 9.762933 ATTTTAACACAGAAAGTATGCAAATGT 57.237 25.926 0.00 0.00 0.00 2.71
5823 12086 7.715249 TCCCATTAGACATGTTCTAGTTATTGC 59.285 37.037 0.00 0.00 38.12 3.56
5824 12087 7.041098 CCCATTAGACATGTTCTAGTTATTGCC 60.041 40.741 0.00 0.00 38.12 4.52
5826 12089 8.768955 CATTAGACATGTTCTAGTTATTGCCTC 58.231 37.037 0.00 0.00 38.12 4.70
5830 12093 4.826274 TGTTCTAGTTATTGCCTCTGCT 57.174 40.909 0.00 0.00 38.71 4.24
5865 12128 0.909610 AGTCAGAATCCTTCCCGGCA 60.910 55.000 0.00 0.00 0.00 5.69
5866 12129 0.462759 GTCAGAATCCTTCCCGGCAG 60.463 60.000 0.00 0.00 0.00 4.85
5927 12190 7.864686 TCTGTATAGAATGCATATGTTTGTGC 58.135 34.615 0.00 0.00 40.14 4.57
5941 12204 8.964150 CATATGTTTGTGCATATGTCATTTCAG 58.036 33.333 14.46 0.00 46.63 3.02
6045 12309 2.552315 ACGACATACCCTTGCAAAACTG 59.448 45.455 0.00 0.00 0.00 3.16
6049 12313 2.065899 TACCCTTGCAAAACTGTGCT 57.934 45.000 0.00 0.00 45.17 4.40
6054 12318 0.459489 TTGCAAAACTGTGCTCCACC 59.541 50.000 0.00 0.00 45.17 4.61
6055 12319 1.363807 GCAAAACTGTGCTCCACCC 59.636 57.895 0.00 0.00 41.51 4.61
6058 12322 0.032615 AAAACTGTGCTCCACCCCAA 60.033 50.000 0.00 0.00 32.73 4.12
6067 12331 1.825641 GCTCCACCCCAAAGGCTTAAA 60.826 52.381 0.00 0.00 40.58 1.52
6091 12355 4.387598 GCATTGTTGCTCCTCTAGATGAT 58.612 43.478 0.00 0.00 45.77 2.45
6124 12388 4.797604 GCGGCTACACTACATTGATCATCT 60.798 45.833 0.00 0.00 0.00 2.90
6132 12396 4.815308 ACTACATTGATCATCTTGAGCTGC 59.185 41.667 0.00 0.00 33.24 5.25
6164 12428 5.806654 AGTTTGCATGGTTCATTTTAGGT 57.193 34.783 0.00 0.00 0.00 3.08
6167 12431 2.896044 TGCATGGTTCATTTTAGGTGCA 59.104 40.909 0.00 0.00 38.83 4.57
6177 12441 4.096231 TCATTTTAGGTGCAACATCATCGG 59.904 41.667 3.64 0.00 39.98 4.18
6196 12460 1.860078 CCTTCCGCACGTTCTTGAC 59.140 57.895 0.00 0.00 0.00 3.18
6210 12474 7.485913 GCACGTTCTTGACATCATTTTATCATT 59.514 33.333 0.00 0.00 0.00 2.57
6229 12493 2.872557 CATGCGCAAGTCCACCAG 59.127 61.111 17.11 0.00 41.68 4.00
6232 12496 3.050275 GCGCAAGTCCACCAGGTC 61.050 66.667 0.30 0.00 41.68 3.85
6242 12506 2.554032 GTCCACCAGGTCTTTGATGTTG 59.446 50.000 0.00 0.00 35.89 3.33
6251 12515 2.028748 GTCTTTGATGTTGCCAAGCCAT 60.029 45.455 0.00 0.00 0.00 4.40
6269 12533 3.004734 GCCATTGGAGATCCCATTAAACG 59.995 47.826 6.95 0.00 46.10 3.60
6278 12542 6.715264 GGAGATCCCATTAAACGATATTGGTT 59.285 38.462 0.00 0.00 34.14 3.67
6281 12545 7.559897 AGATCCCATTAAACGATATTGGTTGTT 59.440 33.333 3.27 0.00 0.00 2.83
6284 12548 6.127591 CCCATTAAACGATATTGGTTGTTCCA 60.128 38.462 3.27 0.00 45.60 3.53
6328 12593 2.434336 CCTCGTTATCACCTCCAATGGA 59.566 50.000 0.48 0.48 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.225734 TGCATACACTATATTTGCACAACGTAT 59.774 33.333 0.00 0.00 38.32 3.06
4 5 6.535508 TGCATACACTATATTTGCACAACGTA 59.464 34.615 0.00 0.00 38.32 3.57
5 6 5.352846 TGCATACACTATATTTGCACAACGT 59.647 36.000 0.00 0.00 38.32 3.99
6 7 5.805229 TGCATACACTATATTTGCACAACG 58.195 37.500 0.00 0.00 38.32 4.10
9 10 7.994194 TCATTTGCATACACTATATTTGCACA 58.006 30.769 0.00 0.00 42.51 4.57
10 11 8.908678 CATCATTTGCATACACTATATTTGCAC 58.091 33.333 0.00 0.00 42.51 4.57
11 12 8.083462 CCATCATTTGCATACACTATATTTGCA 58.917 33.333 0.00 0.00 41.22 4.08
12 13 8.298854 TCCATCATTTGCATACACTATATTTGC 58.701 33.333 0.00 0.00 0.00 3.68
15 16 9.797642 TCTTCCATCATTTGCATACACTATATT 57.202 29.630 0.00 0.00 0.00 1.28
16 17 9.797642 TTCTTCCATCATTTGCATACACTATAT 57.202 29.630 0.00 0.00 0.00 0.86
17 18 9.276590 CTTCTTCCATCATTTGCATACACTATA 57.723 33.333 0.00 0.00 0.00 1.31
18 19 7.776969 ACTTCTTCCATCATTTGCATACACTAT 59.223 33.333 0.00 0.00 0.00 2.12
19 20 7.112122 ACTTCTTCCATCATTTGCATACACTA 58.888 34.615 0.00 0.00 0.00 2.74
20 21 5.948162 ACTTCTTCCATCATTTGCATACACT 59.052 36.000 0.00 0.00 0.00 3.55
21 22 6.199937 ACTTCTTCCATCATTTGCATACAC 57.800 37.500 0.00 0.00 0.00 2.90
32 33 4.908601 TCCTTTGCTACTTCTTCCATCA 57.091 40.909 0.00 0.00 0.00 3.07
58 59 7.273712 CCCTTCTTCATAACTTAACTCCCTAC 58.726 42.308 0.00 0.00 0.00 3.18
117 118 5.295454 ACCCCCTAGAACTTTAACTCCTA 57.705 43.478 0.00 0.00 0.00 2.94
126 127 3.330998 CCTCAAAGAACCCCCTAGAACTT 59.669 47.826 0.00 0.00 0.00 2.66
154 155 4.890581 TCTCTAGGCTTCTCCTGTAATGTC 59.109 45.833 0.00 0.00 46.98 3.06
249 252 6.260936 TGAGAGTTCATTTGTCAACTTTCTCC 59.739 38.462 0.00 0.00 35.66 3.71
254 257 7.572523 TTGATGAGAGTTCATTTGTCAACTT 57.427 32.000 0.00 0.00 44.01 2.66
463 931 1.302511 CGTTGAGGTGGGTTCTGGG 60.303 63.158 0.00 0.00 0.00 4.45
1021 5458 1.371558 GGTTCCTGGAGTCGTTGCT 59.628 57.895 0.00 0.00 0.00 3.91
1039 5476 2.341257 CCACGAGAAGTCAATGGTCTG 58.659 52.381 0.00 0.00 0.00 3.51
1063 5500 2.775032 TAGGCGTGGTTTGGCTCGAC 62.775 60.000 0.00 0.00 42.80 4.20
1177 5623 9.379791 GTTCTTGGTGTAAATGTACTAGCTAAT 57.620 33.333 0.00 0.00 0.00 1.73
1288 7023 7.243824 ACGGAGGAAGTACTATATAATTGGGA 58.756 38.462 0.00 0.00 0.00 4.37
1304 7039 5.105064 TGTCTTAAATTAGGGACGGAGGAAG 60.105 44.000 0.00 0.00 0.00 3.46
1308 7043 7.625828 AAAATGTCTTAAATTAGGGACGGAG 57.374 36.000 0.00 0.00 0.00 4.63
1332 7067 7.504924 AACGTCTTACATTCATCTGGAAAAA 57.495 32.000 0.00 0.00 39.39 1.94
1333 7068 7.504924 AAACGTCTTACATTCATCTGGAAAA 57.495 32.000 0.00 0.00 39.39 2.29
1334 7069 7.504924 AAAACGTCTTACATTCATCTGGAAA 57.495 32.000 0.00 0.00 39.39 3.13
1335 7070 7.504924 AAAAACGTCTTACATTCATCTGGAA 57.495 32.000 0.00 0.00 40.46 3.53
1379 7114 6.943718 TCCGTTCCATAATGTAAGACCTTTTT 59.056 34.615 0.00 0.00 0.00 1.94
1380 7115 6.478129 TCCGTTCCATAATGTAAGACCTTTT 58.522 36.000 0.00 0.00 0.00 2.27
1381 7116 6.057321 TCCGTTCCATAATGTAAGACCTTT 57.943 37.500 0.00 0.00 0.00 3.11
1382 7117 5.396436 CCTCCGTTCCATAATGTAAGACCTT 60.396 44.000 0.00 0.00 0.00 3.50
1383 7118 4.101119 CCTCCGTTCCATAATGTAAGACCT 59.899 45.833 0.00 0.00 0.00 3.85
1384 7119 4.377897 CCTCCGTTCCATAATGTAAGACC 58.622 47.826 0.00 0.00 0.00 3.85
1385 7120 4.100498 TCCCTCCGTTCCATAATGTAAGAC 59.900 45.833 0.00 0.00 0.00 3.01
1391 7126 5.228945 ACTATTCCCTCCGTTCCATAATG 57.771 43.478 0.00 0.00 0.00 1.90
1395 7130 2.421529 GCAACTATTCCCTCCGTTCCAT 60.422 50.000 0.00 0.00 0.00 3.41
1401 7136 1.339631 TGTTGGCAACTATTCCCTCCG 60.340 52.381 28.71 0.00 37.61 4.63
1402 7137 2.507407 TGTTGGCAACTATTCCCTCC 57.493 50.000 28.71 1.15 37.61 4.30
1409 7144 9.777297 AGTTTTTATTGAATTGTTGGCAACTAT 57.223 25.926 28.71 23.94 37.44 2.12
1479 7217 2.196595 CCTCACCCTCTTAACATCCCA 58.803 52.381 0.00 0.00 0.00 4.37
1509 7247 6.770303 TGTGTCTCAACTTGGAATTTCACATA 59.230 34.615 0.00 0.00 0.00 2.29
1513 7251 6.713762 AATGTGTCTCAACTTGGAATTTCA 57.286 33.333 0.00 0.00 0.00 2.69
2118 7863 1.268234 CGTACGGCCTCCTTACGTAAG 60.268 57.143 25.33 25.33 43.55 2.34
2119 7864 0.732571 CGTACGGCCTCCTTACGTAA 59.267 55.000 7.57 7.94 43.55 3.18
2120 7865 2.393557 CGTACGGCCTCCTTACGTA 58.606 57.895 7.57 0.00 43.55 3.57
2121 7866 3.190878 CGTACGGCCTCCTTACGT 58.809 61.111 7.57 0.00 43.55 3.57
2134 7879 5.098211 GGAACTACACCTATGTGAACGTAC 58.902 45.833 5.05 0.00 45.76 3.67
2137 7882 3.194968 AGGGAACTACACCTATGTGAACG 59.805 47.826 5.05 0.00 45.65 3.95
2187 7932 6.851222 ATTCACCACTTCATAGCGAATTAG 57.149 37.500 0.00 0.00 31.69 1.73
2189 7934 7.047891 TCTAATTCACCACTTCATAGCGAATT 58.952 34.615 0.00 0.00 36.09 2.17
2190 7935 6.582636 TCTAATTCACCACTTCATAGCGAAT 58.417 36.000 0.00 0.00 31.69 3.34
2191 7936 5.972935 TCTAATTCACCACTTCATAGCGAA 58.027 37.500 0.00 0.00 0.00 4.70
2192 7937 5.592104 TCTAATTCACCACTTCATAGCGA 57.408 39.130 0.00 0.00 0.00 4.93
2193 7938 7.946655 TTATCTAATTCACCACTTCATAGCG 57.053 36.000 0.00 0.00 0.00 4.26
2216 7982 7.335422 CAGCTGTGAGACTCCTAAATACAAATT 59.665 37.037 5.25 0.00 0.00 1.82
2233 7999 4.199432 AGGTAGATCAAACAGCTGTGAG 57.801 45.455 22.49 16.07 0.00 3.51
2263 8029 8.135529 TCGTTTCAAGATCACGAGTCATATTAT 58.864 33.333 1.46 0.00 38.00 1.28
2321 8087 6.984474 CGGAGGTTGTACAATGTTATGTATCT 59.016 38.462 12.26 0.00 38.03 1.98
2388 8156 4.597507 GGTTGATCTTATACCCCCTCATCA 59.402 45.833 0.00 0.00 0.00 3.07
2391 8159 3.323775 GGGTTGATCTTATACCCCCTCA 58.676 50.000 12.25 0.00 44.75 3.86
2397 8165 3.808174 GCGACTTGGGTTGATCTTATACC 59.192 47.826 0.00 0.00 0.00 2.73
2405 8173 0.620556 ATGGAGCGACTTGGGTTGAT 59.379 50.000 0.00 0.00 0.00 2.57
2421 8189 1.617322 TACCGGATTCCTCGAGATGG 58.383 55.000 15.71 8.36 0.00 3.51
2428 8196 4.750021 AAAGTACCTTACCGGATTCCTC 57.250 45.455 9.46 0.00 36.31 3.71
2434 8202 3.390639 TGTTCCAAAAGTACCTTACCGGA 59.609 43.478 9.46 0.00 36.31 5.14
2520 8291 7.073854 TCTTTAGCCCAGATGTTATAGTACCT 58.926 38.462 0.00 0.00 0.00 3.08
2615 8392 5.621193 AGTTGTAAGCCACACAAAGTAGAT 58.379 37.500 0.00 0.00 37.62 1.98
2617 8394 5.751243 AAGTTGTAAGCCACACAAAGTAG 57.249 39.130 0.00 0.00 37.62 2.57
2624 8401 5.298527 AGGAAGTAAAAGTTGTAAGCCACAC 59.701 40.000 0.00 0.00 36.69 3.82
2726 8503 6.826741 ACCAATGCACCTACGATTAGTTAAAT 59.173 34.615 0.00 0.00 0.00 1.40
2928 8705 0.319555 GCAGTGTCGAGTTGGCAGTA 60.320 55.000 0.00 0.00 0.00 2.74
3006 8783 6.263168 CCATATGTTTACCATCCTGACTTTCC 59.737 42.308 1.24 0.00 34.86 3.13
3009 8786 6.575244 TCCATATGTTTACCATCCTGACTT 57.425 37.500 1.24 0.00 34.86 3.01
3078 8944 8.457261 AGCTCTGTTTTATGAAAAGCTTATCAG 58.543 33.333 0.00 0.00 27.69 2.90
3184 9149 5.939883 TCCAATTCTTCTTCACATGGTACTG 59.060 40.000 0.00 0.00 0.00 2.74
3343 9357 7.481483 CGCGATGACAAATTAAATTCTTCAGAA 59.519 33.333 0.00 0.00 38.56 3.02
3345 9359 6.290748 GCGCGATGACAAATTAAATTCTTCAG 60.291 38.462 12.10 0.00 0.00 3.02
3351 9365 4.480541 TGTGCGCGATGACAAATTAAATT 58.519 34.783 12.10 0.00 0.00 1.82
3425 9454 5.475909 AGATGACATGTTTCTTGCAGAACAT 59.524 36.000 15.30 15.30 33.26 2.71
3440 9473 1.399440 CTCAAACCGCCAGATGACATG 59.601 52.381 0.00 0.00 0.00 3.21
3549 9590 6.700352 ACAAAATATGTGAACCATTTCCCTG 58.300 36.000 0.00 0.00 41.93 4.45
3678 9720 4.940046 AGCCCTCAAAGATATCATAATGCG 59.060 41.667 5.32 0.00 0.00 4.73
3772 9897 5.491635 GAATTGATCCACTAAGCTGGTTC 57.508 43.478 0.00 0.00 32.54 3.62
3898 10056 7.436376 GCCATATCTGCCAATAAGAAGAAAAAC 59.564 37.037 0.00 0.00 0.00 2.43
3935 10093 3.691609 AGAACTATTGCTGCTACAAAGGC 59.308 43.478 0.00 0.00 32.27 4.35
3997 10155 7.114095 ACAAATACGGGAACAACAATATAGGT 58.886 34.615 0.00 0.00 0.00 3.08
4052 10210 8.037758 TCCTTTTTCTCACTATGAAGATCAGTC 58.962 37.037 0.00 0.00 0.00 3.51
4330 10492 1.678101 GTACCATCATGCAAGAAGCCC 59.322 52.381 0.00 0.00 44.83 5.19
4672 10864 9.579932 TGACATAGAGATTTCTAATGCTCTCTA 57.420 33.333 9.78 9.78 46.08 2.43
4716 10909 3.950397 TCCCTGCGAAATTGTGACTAAT 58.050 40.909 0.00 0.00 0.00 1.73
4726 10919 1.168714 GCTGTCTTTCCCTGCGAAAT 58.831 50.000 0.00 0.00 39.73 2.17
4730 10923 0.169672 CATTGCTGTCTTTCCCTGCG 59.830 55.000 0.00 0.00 0.00 5.18
5010 11241 0.886490 AGTCAGCAACTTTGGCCTCG 60.886 55.000 3.32 0.00 33.03 4.63
5204 11441 3.528597 TTGCGTACCTGCATACATACA 57.471 42.857 0.00 0.00 45.78 2.29
5285 11522 0.928505 TGGATGATGTGGATGGCCTT 59.071 50.000 3.32 0.00 34.31 4.35
5286 11523 0.477204 CTGGATGATGTGGATGGCCT 59.523 55.000 3.32 0.00 34.31 5.19
5287 11524 0.184451 ACTGGATGATGTGGATGGCC 59.816 55.000 0.00 0.00 0.00 5.36
5288 11525 1.315690 CACTGGATGATGTGGATGGC 58.684 55.000 0.00 0.00 0.00 4.40
5294 11531 1.066929 TCGTGTCCACTGGATGATGTG 60.067 52.381 0.00 0.00 32.73 3.21
5295 11532 1.066858 GTCGTGTCCACTGGATGATGT 60.067 52.381 0.00 0.00 32.73 3.06
5297 11534 1.561643 AGTCGTGTCCACTGGATGAT 58.438 50.000 0.00 0.00 32.73 2.45
5305 11568 0.956633 TGAGGTGTAGTCGTGTCCAC 59.043 55.000 0.00 0.00 0.00 4.02
5327 11590 1.815003 CACTTCCTCAATGTTGCCTCC 59.185 52.381 0.00 0.00 0.00 4.30
5328 11591 1.815003 CCACTTCCTCAATGTTGCCTC 59.185 52.381 0.00 0.00 0.00 4.70
5329 11592 1.145738 ACCACTTCCTCAATGTTGCCT 59.854 47.619 0.00 0.00 0.00 4.75
5330 11593 1.270550 CACCACTTCCTCAATGTTGCC 59.729 52.381 0.00 0.00 0.00 4.52
5331 11594 1.270550 CCACCACTTCCTCAATGTTGC 59.729 52.381 0.00 0.00 0.00 4.17
5332 11595 2.554032 GTCCACCACTTCCTCAATGTTG 59.446 50.000 0.00 0.00 0.00 3.33
5333 11596 2.810400 CGTCCACCACTTCCTCAATGTT 60.810 50.000 0.00 0.00 0.00 2.71
5334 11597 1.270839 CGTCCACCACTTCCTCAATGT 60.271 52.381 0.00 0.00 0.00 2.71
5366 11629 3.802139 ACACTGTTGATGTTGTAGTCACG 59.198 43.478 0.00 0.00 0.00 4.35
5383 11646 1.601759 CAGGGCCTTCCACACACTG 60.602 63.158 1.32 0.00 38.24 3.66
5384 11647 2.833913 CCAGGGCCTTCCACACACT 61.834 63.158 1.32 0.00 38.24 3.55
5432 11695 0.030638 ATTGTTGGACGTTGTGCTGC 59.969 50.000 0.00 0.00 0.00 5.25
5435 11698 1.333619 AGTCATTGTTGGACGTTGTGC 59.666 47.619 0.00 0.00 40.20 4.57
5437 11700 4.819630 ACATTAGTCATTGTTGGACGTTGT 59.180 37.500 0.00 0.00 40.20 3.32
5440 11703 3.751175 CCACATTAGTCATTGTTGGACGT 59.249 43.478 0.00 0.00 40.20 4.34
5464 11727 3.569701 CGAGGCAATATTGTAATTGGGCT 59.430 43.478 16.61 6.41 37.34 5.19
5470 11733 7.551585 CCTCTAGATCGAGGCAATATTGTAAT 58.448 38.462 16.61 3.39 43.69 1.89
5573 11836 7.446625 ATGGGTTACATTAGTAGTAGACTACGG 59.553 40.741 12.91 7.81 44.26 4.02
5574 11837 8.288208 CATGGGTTACATTAGTAGTAGACTACG 58.712 40.741 12.91 3.32 44.54 3.51
5575 11838 8.574737 CCATGGGTTACATTAGTAGTAGACTAC 58.425 40.741 2.85 11.20 42.41 2.73
5576 11839 7.232127 GCCATGGGTTACATTAGTAGTAGACTA 59.768 40.741 15.13 0.00 37.36 2.59
5577 11840 6.041751 GCCATGGGTTACATTAGTAGTAGACT 59.958 42.308 15.13 0.00 38.96 3.24
5578 11841 6.183360 TGCCATGGGTTACATTAGTAGTAGAC 60.183 42.308 15.13 0.00 37.84 2.59
5579 11842 5.900699 TGCCATGGGTTACATTAGTAGTAGA 59.099 40.000 15.13 0.00 37.84 2.59
5580 11843 5.989777 GTGCCATGGGTTACATTAGTAGTAG 59.010 44.000 15.13 0.00 37.84 2.57
5581 11844 5.163280 GGTGCCATGGGTTACATTAGTAGTA 60.163 44.000 15.13 0.00 37.84 1.82
5582 11845 4.384868 GGTGCCATGGGTTACATTAGTAGT 60.385 45.833 15.13 0.00 37.84 2.73
5583 11846 4.134563 GGTGCCATGGGTTACATTAGTAG 58.865 47.826 15.13 0.00 37.84 2.57
5584 11847 3.523972 TGGTGCCATGGGTTACATTAGTA 59.476 43.478 15.13 0.00 37.84 1.82
5585 11848 2.310349 TGGTGCCATGGGTTACATTAGT 59.690 45.455 15.13 0.00 37.84 2.24
5634 11897 1.276138 GGTTGGCTCCCTCCAAAAATG 59.724 52.381 0.00 0.00 46.63 2.32
5712 11975 9.209175 GTCTCAATGGCGAAAAATATCTAGTAT 57.791 33.333 0.00 0.00 0.00 2.12
5798 12061 7.041098 GGCAATAACTAGAACATGTCTAATGGG 60.041 40.741 0.00 0.00 38.41 4.00
5823 12086 5.695851 AATGTTTTGACTAACAGCAGAGG 57.304 39.130 0.00 0.00 40.99 3.69
5824 12087 7.171508 TGACTAATGTTTTGACTAACAGCAGAG 59.828 37.037 0.00 0.00 40.99 3.35
5826 12089 7.171508 TCTGACTAATGTTTTGACTAACAGCAG 59.828 37.037 0.00 0.00 40.99 4.24
5830 12093 8.999431 GGATTCTGACTAATGTTTTGACTAACA 58.001 33.333 0.00 0.00 41.81 2.41
5890 12153 7.119699 TGCATTCTATACAGAAAACAACTCCAG 59.880 37.037 0.00 0.00 43.89 3.86
5920 12183 6.151691 ACACTGAAATGACATATGCACAAAC 58.848 36.000 1.58 1.54 0.00 2.93
5927 12190 8.724229 TCTTCTTTGACACTGAAATGACATATG 58.276 33.333 0.00 0.00 0.00 1.78
6011 12275 4.394920 GGGTATGTCGTGTGATGAAAATGT 59.605 41.667 0.00 0.00 0.00 2.71
6045 12309 2.991540 GCCTTTGGGGTGGAGCAC 60.992 66.667 0.00 0.00 37.43 4.40
6049 12313 2.534990 CATTTAAGCCTTTGGGGTGGA 58.465 47.619 0.00 0.00 43.29 4.02
6054 12318 3.941573 ACAATGCATTTAAGCCTTTGGG 58.058 40.909 9.83 0.00 33.49 4.12
6055 12319 5.285798 CAACAATGCATTTAAGCCTTTGG 57.714 39.130 9.83 0.00 33.49 3.28
6091 12355 0.319555 GTGTAGCCGCAAGACTGTCA 60.320 55.000 10.88 0.00 43.02 3.58
6139 12403 7.012232 CACCTAAAATGAACCATGCAAACTTTT 59.988 33.333 0.00 0.00 0.00 2.27
6162 12426 1.315257 AAGGCCGATGATGTTGCACC 61.315 55.000 0.00 0.00 0.00 5.01
6164 12428 1.031571 GGAAGGCCGATGATGTTGCA 61.032 55.000 0.00 0.00 0.00 4.08
6177 12441 1.959226 TCAAGAACGTGCGGAAGGC 60.959 57.895 0.00 0.00 43.96 4.35
6184 12448 6.314018 TGATAAAATGATGTCAAGAACGTGC 58.686 36.000 0.00 0.00 0.00 5.34
6187 12451 7.485595 TGCAATGATAAAATGATGTCAAGAACG 59.514 33.333 0.00 0.00 0.00 3.95
6255 12519 7.060421 ACAACCAATATCGTTTAATGGGATCT 58.940 34.615 0.00 0.00 35.44 2.75
6257 12521 7.201875 GGAACAACCAATATCGTTTAATGGGAT 60.202 37.037 7.02 0.00 38.79 3.85
6278 12542 4.297768 TCCATCCTATGATGTCTGGAACA 58.702 43.478 7.16 0.00 45.78 3.18
6281 12545 4.202398 GCTTTCCATCCTATGATGTCTGGA 60.202 45.833 7.16 0.00 45.78 3.86
6284 12548 5.619220 GAAGCTTTCCATCCTATGATGTCT 58.381 41.667 0.00 0.00 45.78 3.41
6306 12571 2.434336 CCATTGGAGGTGATAACGAGGA 59.566 50.000 0.00 0.00 0.00 3.71
6309 12574 3.262151 TGTTCCATTGGAGGTGATAACGA 59.738 43.478 5.36 0.00 31.21 3.85
6311 12576 4.396166 CACTGTTCCATTGGAGGTGATAAC 59.604 45.833 20.89 10.58 33.72 1.89


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

AutoCloner maintained by Alex Coulton.