Multiple sequence alignment - TraesCS5A01G200700

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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 TraesCS5A01G200700 chr5A 100.000 4852 0 0 1 4852 406538393 406533542 0.000000e+00 8961.0
1 TraesCS5A01G200700 chr5A 86.965 491 34 7 116 589 668587267 668586790 4.300000e-145 525.0
2 TraesCS5A01G200700 chr5A 83.333 252 36 4 4207 4452 661212788 661212537 1.360000e-55 228.0
3 TraesCS5A01G200700 chr5A 79.365 252 46 4 4207 4452 237553747 237553496 6.460000e-39 172.0
4 TraesCS5A01G200700 chr5D 89.737 2699 147 55 88 2712 312453736 312451094 0.000000e+00 3330.0
5 TraesCS5A01G200700 chr5D 88.158 1064 88 18 3397 4452 312450544 312449511 0.000000e+00 1232.0
6 TraesCS5A01G200700 chr5D 92.958 497 33 2 2762 3256 312451093 312450597 0.000000e+00 723.0
7 TraesCS5A01G200700 chr5D 87.184 593 44 21 1 589 26617478 26618042 0.000000e+00 645.0
8 TraesCS5A01G200700 chr5D 83.984 487 58 15 116 591 25160982 25160505 2.660000e-122 449.0
9 TraesCS5A01G200700 chr5D 90.878 296 13 4 4558 4852 312448642 312448360 7.620000e-103 385.0
10 TraesCS5A01G200700 chr5D 77.500 280 46 16 337 606 311067305 311067033 8.410000e-33 152.0
11 TraesCS5A01G200700 chr5D 78.453 181 33 4 609 789 287789539 287789365 3.970000e-21 113.0
12 TraesCS5A01G200700 chr5D 73.750 240 53 9 4207 4438 301627274 301627037 8.650000e-13 86.1
13 TraesCS5A01G200700 chr5D 87.273 55 6 1 4013 4067 456063609 456063662 1.460000e-05 62.1
14 TraesCS5A01G200700 chr5B 90.739 1447 111 15 609 2052 358894526 358893100 0.000000e+00 1908.0
15 TraesCS5A01G200700 chr5B 93.365 1281 66 10 2058 3330 358893131 358891862 0.000000e+00 1877.0
16 TraesCS5A01G200700 chr5B 94.328 670 27 6 3420 4087 358891822 358891162 0.000000e+00 1016.0
17 TraesCS5A01G200700 chr5B 86.318 402 36 8 116 498 137362597 137362998 2.090000e-113 420.0
18 TraesCS5A01G200700 chr5B 90.909 286 9 8 4573 4852 358890524 358890250 7.670000e-98 368.0
19 TraesCS5A01G200700 chr5B 83.399 253 35 6 4207 4452 547536408 547536156 1.360000e-55 228.0
20 TraesCS5A01G200700 chr5B 88.971 136 10 5 4206 4336 598979912 598979777 3.890000e-36 163.0
21 TraesCS5A01G200700 chr5B 94.203 69 4 0 3330 3398 539472945 539472877 6.640000e-19 106.0
22 TraesCS5A01G200700 chr5B 100.000 32 0 0 4505 4536 358890527 358890496 5.240000e-05 60.2
23 TraesCS5A01G200700 chr4D 85.065 616 55 22 1 606 44138617 44139205 1.160000e-165 593.0
24 TraesCS5A01G200700 chr4D 88.415 492 39 8 116 589 480327754 480328245 1.170000e-160 577.0
25 TraesCS5A01G200700 chr4D 83.794 253 34 6 4207 4452 414061870 414061618 2.920000e-57 233.0
26 TraesCS5A01G200700 chr4D 96.947 131 4 0 1 131 62090375 62090505 2.270000e-53 220.0
27 TraesCS5A01G200700 chr4D 88.462 52 6 0 4018 4069 20114854 20114905 4.050000e-06 63.9
28 TraesCS5A01G200700 chr2D 89.206 491 29 7 116 589 99499568 99500051 4.180000e-165 592.0
29 TraesCS5A01G200700 chr2D 82.540 252 38 5 4207 4452 106637173 106636922 2.940000e-52 217.0
30 TraesCS5A01G200700 chr2D 87.273 55 6 1 4013 4067 74975905 74975958 1.460000e-05 62.1
31 TraesCS5A01G200700 chr6D 88.595 491 36 9 116 589 380247592 380248079 3.260000e-161 579.0
32 TraesCS5A01G200700 chr6D 78.417 278 43 15 337 607 182633485 182633218 1.080000e-36 165.0
33 TraesCS5A01G200700 chr3A 87.891 512 37 9 116 606 314549303 314549810 3.260000e-161 579.0
34 TraesCS5A01G200700 chr3A 93.960 149 6 3 1 149 191926376 191926231 6.320000e-54 222.0
35 TraesCS5A01G200700 chr3A 91.549 71 5 1 3328 3398 12421945 12422014 4.000000e-16 97.1
36 TraesCS5A01G200700 chr3A 89.474 76 5 2 3327 3402 586407162 586407234 5.170000e-15 93.5
37 TraesCS5A01G200700 chr7D 88.525 488 37 9 121 589 612858989 612858502 1.510000e-159 573.0
38 TraesCS5A01G200700 chr7D 78.623 276 42 15 343 608 315252390 315252122 3.000000e-37 167.0
39 TraesCS5A01G200700 chr7D 94.366 71 2 1 3330 3398 126050231 126050301 1.850000e-19 108.0
40 TraesCS5A01G200700 chr7D 92.105 76 5 1 3327 3402 526526721 526526795 6.640000e-19 106.0
41 TraesCS5A01G200700 chr7D 89.474 76 7 1 3328 3402 188809774 188809849 1.440000e-15 95.3
42 TraesCS5A01G200700 chr7D 77.857 140 25 4 639 777 484322828 484322694 1.120000e-11 82.4
43 TraesCS5A01G200700 chr7D 90.385 52 2 3 4018 4067 190083218 190083268 1.130000e-06 65.8
44 TraesCS5A01G200700 chr3D 88.057 494 39 10 116 589 564728089 564727596 7.050000e-158 568.0
45 TraesCS5A01G200700 chr6A 88.032 493 39 9 116 589 55605676 55605185 2.530000e-157 566.0
46 TraesCS5A01G200700 chr6B 87.084 511 44 9 116 606 675681747 675682255 4.240000e-155 558.0
47 TraesCS5A01G200700 chr6B 92.737 179 6 2 1 172 581281210 581281388 8.060000e-63 252.0
48 TraesCS5A01G200700 chr6B 97.710 131 3 0 1 131 157682149 157682019 4.890000e-55 226.0
49 TraesCS5A01G200700 chr1D 84.602 591 47 22 1 589 389788592 389789140 9.180000e-152 547.0
50 TraesCS5A01G200700 chr4A 86.240 516 43 14 116 606 217676351 217675839 7.150000e-148 534.0
51 TraesCS5A01G200700 chr4A 84.244 476 50 10 116 569 665817840 665817368 1.600000e-119 440.0
52 TraesCS5A01G200700 chr4A 90.000 50 5 0 4018 4067 662286503 662286454 1.130000e-06 65.8
53 TraesCS5A01G200700 chr1A 86.263 495 49 9 130 606 66608274 66607781 2.000000e-143 520.0
54 TraesCS5A01G200700 chr1A 85.484 496 53 9 130 606 66653344 66652849 2.610000e-137 499.0
55 TraesCS5A01G200700 chr1A 83.203 256 37 5 4203 4452 31256173 31256428 3.780000e-56 230.0
56 TraesCS5A01G200700 chr1A 83.333 66 8 2 4018 4081 80190745 80190809 1.890000e-04 58.4
57 TraesCS5A01G200700 chr7A 83.891 329 23 20 1 327 503459289 503458989 2.210000e-73 287.0
58 TraesCS5A01G200700 chr7A 97.710 131 3 0 1 131 613506268 613506398 4.890000e-55 226.0
59 TraesCS5A01G200700 chr7A 93.421 76 4 1 3327 3402 606635694 606635768 1.430000e-20 111.0
60 TraesCS5A01G200700 chr7A 81.707 82 11 4 697 776 83548249 83548170 1.130000e-06 65.8
61 TraesCS5A01G200700 chr3B 84.190 253 33 6 4207 4452 519435691 519435943 6.280000e-59 239.0
62 TraesCS5A01G200700 chr3B 83.794 253 34 6 4207 4452 607486379 607486631 2.920000e-57 233.0
63 TraesCS5A01G200700 chr4B 84.127 252 32 7 4207 4452 670050297 670050048 2.260000e-58 237.0
64 TraesCS5A01G200700 chr1B 84.167 240 32 5 4207 4440 567111686 567111925 1.360000e-55 228.0
65 TraesCS5A01G200700 chr1B 77.509 289 49 15 337 617 2850589 2850869 5.030000e-35 159.0
66 TraesCS5A01G200700 chr1B 89.744 78 4 2 3328 3401 10201048 10200971 4.000000e-16 97.1
67 TraesCS5A01G200700 chr1B 83.333 66 8 2 4018 4081 138037400 138037464 1.890000e-04 58.4
68 TraesCS5A01G200700 chr2B 86.979 192 7 7 117 291 630045073 630045263 2.960000e-47 200.0
69 TraesCS5A01G200700 chr7B 90.789 76 6 1 3327 3402 563658980 563659054 3.090000e-17 100.0
70 TraesCS5A01G200700 chr2A 84.404 109 9 6 4207 4308 492601830 492601723 3.090000e-17 100.0


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 TraesCS5A01G200700 chr5A 406533542 406538393 4851 True 8961.00 8961 100.00000 1 4852 1 chr5A.!!$R2 4851
1 TraesCS5A01G200700 chr5D 312448360 312453736 5376 True 1417.50 3330 90.43275 88 4852 4 chr5D.!!$R5 4764
2 TraesCS5A01G200700 chr5D 26617478 26618042 564 False 645.00 645 87.18400 1 589 1 chr5D.!!$F1 588
3 TraesCS5A01G200700 chr5B 358890250 358894526 4276 True 1045.84 1908 93.86820 609 4852 5 chr5B.!!$R4 4243
4 TraesCS5A01G200700 chr4D 44138617 44139205 588 False 593.00 593 85.06500 1 606 1 chr4D.!!$F2 605
5 TraesCS5A01G200700 chr3A 314549303 314549810 507 False 579.00 579 87.89100 116 606 1 chr3A.!!$F2 490
6 TraesCS5A01G200700 chr6B 675681747 675682255 508 False 558.00 558 87.08400 116 606 1 chr6B.!!$F2 490
7 TraesCS5A01G200700 chr1D 389788592 389789140 548 False 547.00 547 84.60200 1 589 1 chr1D.!!$F1 588
8 TraesCS5A01G200700 chr4A 217675839 217676351 512 True 534.00 534 86.24000 116 606 1 chr4A.!!$R1 490

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
217 223 2.167693 AGGAACGCGGATTAGATTCACA 59.832 45.455 12.47 0.0 0.0 3.58 F
1328 1410 0.246086 CCTGCAGTTCTCTTCTCGCT 59.754 55.000 13.81 0.0 0.0 4.93 F
1564 1646 0.179234 TTGGCGTCAAGTTCAGGTGA 59.821 50.000 0.00 0.0 0.0 4.02 F
3343 3450 1.064832 ACGTACTACTCCCTCTGTCCC 60.065 57.143 0.00 0.0 0.0 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1455 1537 0.036732 AACATCTCGCCAGCTCCAAA 59.963 50.0 0.0 0.0 0.00 3.28 R
2730 2833 0.179043 TAAACAGGCGGAACAGTGCA 60.179 50.0 0.0 0.0 0.00 4.57 R
3378 3485 0.042131 TACTCCCTCCGTCCCACAAT 59.958 55.0 0.0 0.0 0.00 2.71 R
4476 4773 0.106708 AGAAACTTGTGCTCCAGCGA 59.893 50.0 0.0 0.0 45.83 4.93 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
38 39 9.814899 ATGACTATGATGATTATTAGCTAGTGC 57.185 33.333 0.00 0.00 40.05 4.40
216 222 2.822764 AGGAACGCGGATTAGATTCAC 58.177 47.619 12.47 0.00 0.00 3.18
217 223 2.167693 AGGAACGCGGATTAGATTCACA 59.832 45.455 12.47 0.00 0.00 3.58
222 228 2.476619 CGCGGATTAGATTCACATGGAC 59.523 50.000 0.00 0.00 0.00 4.02
223 229 3.466836 GCGGATTAGATTCACATGGACA 58.533 45.455 0.00 0.00 0.00 4.02
224 230 3.248602 GCGGATTAGATTCACATGGACAC 59.751 47.826 0.00 0.00 0.00 3.67
226 232 4.875536 CGGATTAGATTCACATGGACACAA 59.124 41.667 0.00 0.00 0.00 3.33
227 233 5.528690 CGGATTAGATTCACATGGACACAAT 59.471 40.000 0.00 0.00 0.00 2.71
228 234 6.038603 CGGATTAGATTCACATGGACACAATT 59.961 38.462 0.00 0.00 0.00 2.32
270 294 8.236586 CGTCCTAATTCAACTTTTGATTCATCA 58.763 33.333 0.00 0.00 39.84 3.07
479 524 5.902681 AGATTAGTAGCAACGCTTGTATGA 58.097 37.500 0.00 0.00 40.44 2.15
554 599 3.251571 GCTAAGTGTTAGTTGTAGCGCT 58.748 45.455 17.26 17.26 35.66 5.92
629 705 6.758886 TGTATTGGGTTTAAACAAGTTTGCTG 59.241 34.615 19.57 0.00 34.23 4.41
678 754 2.168947 AGCTTTGCTCACATCGCAG 58.831 52.632 0.00 0.00 38.80 5.18
770 846 6.182507 TGTAAGGATGTGTTTGTAAGGACT 57.817 37.500 0.00 0.00 0.00 3.85
843 920 5.536497 AATCCCTGAACCAACCTAGAATT 57.464 39.130 0.00 0.00 0.00 2.17
973 1054 3.973206 TCGCAAGGAGGAGTTTCATTA 57.027 42.857 0.00 0.00 38.47 1.90
987 1068 9.971922 AGGAGTTTCATTATTTCTTTGTTCAAG 57.028 29.630 0.00 0.00 0.00 3.02
1016 1098 1.076332 CGAGGAAAAACTGCGGTAGG 58.924 55.000 0.00 0.00 0.00 3.18
1111 1193 1.045911 GGCCCGTCTCCAATCTCTCT 61.046 60.000 0.00 0.00 0.00 3.10
1164 1246 4.862823 CCCCCGTCTCTCTCCCCC 62.863 77.778 0.00 0.00 0.00 5.40
1323 1405 0.251634 CCTCCCCTGCAGTTCTCTTC 59.748 60.000 13.81 0.00 0.00 2.87
1328 1410 0.246086 CCTGCAGTTCTCTTCTCGCT 59.754 55.000 13.81 0.00 0.00 4.93
1368 1450 6.210078 CGAGATTGTATGAGGTTACTCTTCC 58.790 44.000 0.00 0.00 44.29 3.46
1369 1451 6.487299 AGATTGTATGAGGTTACTCTTCCC 57.513 41.667 0.00 0.00 44.29 3.97
1372 1454 0.831307 ATGAGGTTACTCTTCCCCGC 59.169 55.000 0.00 0.00 44.29 6.13
1373 1455 1.262640 TGAGGTTACTCTTCCCCGCC 61.263 60.000 0.00 0.00 44.29 6.13
1420 1502 2.167861 GCGGCTGTCGTTCTGATCC 61.168 63.158 2.76 0.00 41.72 3.36
1425 1507 2.202623 GTCGTTCTGATCCGCGCT 60.203 61.111 5.56 0.00 0.00 5.92
1427 1509 2.202610 CGTTCTGATCCGCGCTCA 60.203 61.111 5.56 4.87 0.00 4.26
1455 1537 4.442403 CGAAACACATCGATTCGATCTGAT 59.558 41.667 24.86 14.22 45.19 2.90
1461 1543 4.987285 ACATCGATTCGATCTGATTTGGAG 59.013 41.667 18.28 6.40 45.19 3.86
1466 1548 0.942962 CGATCTGATTTGGAGCTGGC 59.057 55.000 0.00 0.00 0.00 4.85
1564 1646 0.179234 TTGGCGTCAAGTTCAGGTGA 59.821 50.000 0.00 0.00 0.00 4.02
1633 1715 6.062095 GGTGGTACTTAATGATGGTGCTTAT 58.938 40.000 0.00 0.00 0.00 1.73
1634 1716 6.017109 GGTGGTACTTAATGATGGTGCTTATG 60.017 42.308 0.00 0.00 0.00 1.90
1636 1718 6.992123 TGGTACTTAATGATGGTGCTTATGAG 59.008 38.462 0.00 0.00 0.00 2.90
1638 1720 6.006275 ACTTAATGATGGTGCTTATGAGGT 57.994 37.500 0.00 0.00 0.00 3.85
1640 1722 7.573710 ACTTAATGATGGTGCTTATGAGGTTA 58.426 34.615 0.00 0.00 0.00 2.85
1641 1723 8.220559 ACTTAATGATGGTGCTTATGAGGTTAT 58.779 33.333 0.00 0.00 0.00 1.89
1642 1724 8.621532 TTAATGATGGTGCTTATGAGGTTATC 57.378 34.615 0.00 0.00 0.00 1.75
1643 1725 5.628797 TGATGGTGCTTATGAGGTTATCA 57.371 39.130 0.00 0.00 43.70 2.15
1644 1726 5.614308 TGATGGTGCTTATGAGGTTATCAG 58.386 41.667 0.00 0.00 42.53 2.90
1645 1727 3.808728 TGGTGCTTATGAGGTTATCAGC 58.191 45.455 0.00 0.00 42.53 4.26
1646 1728 3.142174 GGTGCTTATGAGGTTATCAGCC 58.858 50.000 0.00 0.00 42.53 4.85
1680 1762 4.329801 TCTGCAACTGACGTTTATGCATAG 59.670 41.667 16.08 8.67 31.71 2.23
1693 1775 2.470983 TGCATAGTAGCTGCACAACA 57.529 45.000 4.12 0.00 44.30 3.33
1786 1868 6.143206 TCTTGTCCTATCATATCCTTGTCCA 58.857 40.000 0.00 0.00 0.00 4.02
1823 1905 7.036996 TCATATATCCTCAGAATCGATCAGC 57.963 40.000 0.00 0.00 0.00 4.26
1848 1930 1.680735 TGCCGTTGTTTGCTGATCTTT 59.319 42.857 0.00 0.00 0.00 2.52
1853 1935 3.119849 CGTTGTTTGCTGATCTTTAGGGG 60.120 47.826 0.00 0.00 0.00 4.79
1870 1952 1.423845 GGTTTGTATCGCTGCCACG 59.576 57.895 0.00 0.00 0.00 4.94
1881 1963 1.999071 GCTGCCACGGTGTTTTGTGA 61.999 55.000 7.45 0.00 38.36 3.58
1909 1991 7.332678 ACTGTAGTTTAGTGTTTCTGACGTTTT 59.667 33.333 0.00 0.00 0.00 2.43
1910 1992 8.700722 TGTAGTTTAGTGTTTCTGACGTTTTA 57.299 30.769 0.00 0.00 0.00 1.52
1969 2051 2.096811 GTGCATTTTGGTGATTGCGTTG 60.097 45.455 0.00 0.00 37.92 4.10
1974 2056 4.849111 TTTTGGTGATTGCGTTGTTTTC 57.151 36.364 0.00 0.00 0.00 2.29
1997 2080 8.575649 TTCCTTAACAGAATAATCACCTTTCC 57.424 34.615 0.00 0.00 0.00 3.13
2069 2154 9.781834 TGCAGAAACGGTATTTTTATATTCTTG 57.218 29.630 0.00 0.00 0.00 3.02
2070 2155 9.233232 GCAGAAACGGTATTTTTATATTCTTGG 57.767 33.333 0.00 0.00 0.00 3.61
2076 2161 9.457436 ACGGTATTTTTATATTCTTGGTTGTCT 57.543 29.630 0.00 0.00 0.00 3.41
2077 2162 9.931210 CGGTATTTTTATATTCTTGGTTGTCTC 57.069 33.333 0.00 0.00 0.00 3.36
2082 2167 9.691362 TTTTTATATTCTTGGTTGTCTCTTTGC 57.309 29.630 0.00 0.00 0.00 3.68
2084 2169 4.843220 ATTCTTGGTTGTCTCTTTGCAG 57.157 40.909 0.00 0.00 0.00 4.41
2085 2170 3.558931 TCTTGGTTGTCTCTTTGCAGA 57.441 42.857 0.00 0.00 0.00 4.26
2086 2171 3.884895 TCTTGGTTGTCTCTTTGCAGAA 58.115 40.909 0.00 0.00 0.00 3.02
2088 2173 4.096382 TCTTGGTTGTCTCTTTGCAGAAAC 59.904 41.667 0.00 0.00 0.00 2.78
2199 2287 4.532521 AGGCTAGTTGTACAATCAGGACTT 59.467 41.667 12.26 0.00 0.00 3.01
2226 2314 7.751047 TGCAGTTACTGTTATTAGATTCGAC 57.249 36.000 14.23 0.00 33.43 4.20
2232 2320 8.941923 GTTACTGTTATTAGATTCGACACTACG 58.058 37.037 0.00 0.00 0.00 3.51
2440 2540 5.560148 GTTGTCTTTGCTGGTATGTTATCG 58.440 41.667 0.00 0.00 0.00 2.92
2446 2546 7.703621 GTCTTTGCTGGTATGTTATCGTACTTA 59.296 37.037 3.74 0.00 36.58 2.24
2557 2657 3.431673 TGGATGTTGACCACTTGCATA 57.568 42.857 0.00 0.00 32.03 3.14
2637 2737 3.639672 TGACGTGGGTAGTATCTCTCA 57.360 47.619 0.00 0.00 0.00 3.27
2639 2739 4.338012 TGACGTGGGTAGTATCTCTCAAA 58.662 43.478 0.00 0.00 0.00 2.69
2698 2801 3.139077 GGGGAAATGGTAGTATGCTTCG 58.861 50.000 0.00 0.00 0.00 3.79
2699 2802 3.181458 GGGGAAATGGTAGTATGCTTCGA 60.181 47.826 0.00 0.00 0.00 3.71
2730 2833 6.549364 AGTTTCTAGCAGCACAGATATAGTCT 59.451 38.462 0.00 0.00 37.80 3.24
2741 2844 4.576216 AGATATAGTCTGCACTGTTCCG 57.424 45.455 0.00 0.00 35.31 4.30
2759 2863 3.078837 TCCGCCTGTTTAATCTTGTTCC 58.921 45.455 0.00 0.00 0.00 3.62
2775 2879 8.691661 ATCTTGTTCCAGTGTAGTAAATTTGT 57.308 30.769 0.00 0.00 0.00 2.83
2786 2890 9.216117 AGTGTAGTAAATTTGTCAACTCCATAC 57.784 33.333 0.00 0.00 0.00 2.39
2799 2903 6.200475 GTCAACTCCATACGGTAGCTATTTTC 59.800 42.308 0.00 0.00 0.00 2.29
2895 3000 9.601810 TTCTACTGACCATGGAGTGTATTATAT 57.398 33.333 21.47 0.00 0.00 0.86
2939 3046 6.446318 TGAGTTGCCATTTGAAATAACTCAC 58.554 36.000 21.68 7.02 45.09 3.51
3075 3182 5.381757 TGGTTCTTGGTATTGCTGTTAGTT 58.618 37.500 0.00 0.00 0.00 2.24
3101 3208 1.762957 AGCATGGCCGTAGTAACTGAT 59.237 47.619 0.00 0.00 0.00 2.90
3146 3253 9.471702 ACTTATTCATCTCATCAATTTTCAGGT 57.528 29.630 0.00 0.00 0.00 4.00
3208 3315 6.925165 CAGTTGTCTTTTTCATACTGGCAAAT 59.075 34.615 0.00 0.00 31.69 2.32
3242 3349 7.873719 TCCTTGAAGTTTAGAAACATGTTCA 57.126 32.000 12.39 0.00 41.30 3.18
3260 3367 4.253685 GTTCAGCATTTCAGTAGGCAGTA 58.746 43.478 0.00 0.00 0.00 2.74
3261 3368 4.128925 TCAGCATTTCAGTAGGCAGTAG 57.871 45.455 0.00 0.00 0.00 2.57
3262 3369 3.118629 TCAGCATTTCAGTAGGCAGTAGG 60.119 47.826 0.00 0.00 0.00 3.18
3263 3370 2.840651 AGCATTTCAGTAGGCAGTAGGT 59.159 45.455 0.00 0.00 0.00 3.08
3264 3371 4.030913 AGCATTTCAGTAGGCAGTAGGTA 58.969 43.478 0.00 0.00 0.00 3.08
3292 3399 5.924475 TCGAACTGAATTTCTCAACTTCC 57.076 39.130 0.00 0.00 32.17 3.46
3297 3404 4.757149 ACTGAATTTCTCAACTTCCGAAGG 59.243 41.667 12.77 0.00 41.59 3.46
3336 3443 3.884091 CAGAATGCTACGTACTACTCCCT 59.116 47.826 0.00 0.00 0.00 4.20
3337 3444 4.023878 CAGAATGCTACGTACTACTCCCTC 60.024 50.000 0.00 0.00 0.00 4.30
3338 3445 3.860968 ATGCTACGTACTACTCCCTCT 57.139 47.619 0.00 0.00 0.00 3.69
3339 3446 2.915349 TGCTACGTACTACTCCCTCTG 58.085 52.381 0.00 0.00 0.00 3.35
3340 3447 2.238144 TGCTACGTACTACTCCCTCTGT 59.762 50.000 0.00 0.00 0.00 3.41
3341 3448 2.871633 GCTACGTACTACTCCCTCTGTC 59.128 54.545 0.00 0.00 0.00 3.51
3342 3449 2.416680 ACGTACTACTCCCTCTGTCC 57.583 55.000 0.00 0.00 0.00 4.02
3343 3450 1.064832 ACGTACTACTCCCTCTGTCCC 60.065 57.143 0.00 0.00 0.00 4.46
3347 3454 4.688045 CGTACTACTCCCTCTGTCCCATAA 60.688 50.000 0.00 0.00 0.00 1.90
3348 3455 4.561254 ACTACTCCCTCTGTCCCATAAT 57.439 45.455 0.00 0.00 0.00 1.28
3349 3456 4.227197 ACTACTCCCTCTGTCCCATAATG 58.773 47.826 0.00 0.00 0.00 1.90
3350 3457 3.136641 ACTCCCTCTGTCCCATAATGT 57.863 47.619 0.00 0.00 0.00 2.71
3352 3459 4.631234 ACTCCCTCTGTCCCATAATGTAA 58.369 43.478 0.00 0.00 0.00 2.41
3353 3460 4.656112 ACTCCCTCTGTCCCATAATGTAAG 59.344 45.833 0.00 0.00 0.00 2.34
3354 3461 4.890988 TCCCTCTGTCCCATAATGTAAGA 58.109 43.478 0.00 0.00 0.00 2.10
3355 3462 4.654262 TCCCTCTGTCCCATAATGTAAGAC 59.346 45.833 0.00 0.00 0.00 3.01
3356 3463 4.501571 CCCTCTGTCCCATAATGTAAGACG 60.502 50.000 0.00 0.00 0.00 4.18
3358 3465 5.395324 CCTCTGTCCCATAATGTAAGACGTT 60.395 44.000 0.00 0.00 0.00 3.99
3359 3466 6.045072 TCTGTCCCATAATGTAAGACGTTT 57.955 37.500 0.00 0.00 0.00 3.60
3360 3467 6.469410 TCTGTCCCATAATGTAAGACGTTTT 58.531 36.000 0.00 0.00 0.00 2.43
3362 3469 6.904498 TGTCCCATAATGTAAGACGTTTTTG 58.096 36.000 0.00 0.00 0.00 2.44
3363 3470 5.798434 GTCCCATAATGTAAGACGTTTTTGC 59.202 40.000 0.00 0.00 0.00 3.68
3364 3471 5.473846 TCCCATAATGTAAGACGTTTTTGCA 59.526 36.000 0.00 1.87 0.00 4.08
3366 3473 6.307800 CCCATAATGTAAGACGTTTTTGCAAG 59.692 38.462 0.00 0.00 0.00 4.01
3367 3474 6.183359 CCATAATGTAAGACGTTTTTGCAAGC 60.183 38.462 0.00 0.00 0.00 4.01
3368 3475 4.568152 ATGTAAGACGTTTTTGCAAGCT 57.432 36.364 0.00 0.00 0.00 3.74
3369 3476 5.682943 ATGTAAGACGTTTTTGCAAGCTA 57.317 34.783 0.00 0.00 0.00 3.32
3370 3477 4.839796 TGTAAGACGTTTTTGCAAGCTAC 58.160 39.130 0.00 0.00 0.00 3.58
3371 3478 2.663279 AGACGTTTTTGCAAGCTACG 57.337 45.000 20.98 20.98 38.14 3.51
3372 3479 1.937899 AGACGTTTTTGCAAGCTACGT 59.062 42.857 25.44 25.44 46.73 3.57
3373 3480 2.378507 ACGTTTTTGCAAGCTACGTC 57.621 45.000 21.96 3.09 41.04 4.34
3374 3481 1.937899 ACGTTTTTGCAAGCTACGTCT 59.062 42.857 21.96 8.01 41.04 4.18
3375 3482 2.353579 ACGTTTTTGCAAGCTACGTCTT 59.646 40.909 21.96 7.48 41.04 3.01
3376 3483 3.556775 ACGTTTTTGCAAGCTACGTCTTA 59.443 39.130 21.96 0.00 41.04 2.10
3377 3484 3.898361 CGTTTTTGCAAGCTACGTCTTAC 59.102 43.478 16.87 0.00 0.00 2.34
3378 3485 4.551217 CGTTTTTGCAAGCTACGTCTTACA 60.551 41.667 16.87 0.00 0.00 2.41
3379 3486 5.449304 GTTTTTGCAAGCTACGTCTTACAT 58.551 37.500 0.00 0.00 0.00 2.29
3380 3487 5.682943 TTTTGCAAGCTACGTCTTACATT 57.317 34.783 0.00 0.00 0.00 2.71
3381 3488 4.661993 TTGCAAGCTACGTCTTACATTG 57.338 40.909 0.00 0.00 0.00 2.82
3382 3489 3.659786 TGCAAGCTACGTCTTACATTGT 58.340 40.909 0.00 0.00 0.00 2.71
3383 3490 3.431912 TGCAAGCTACGTCTTACATTGTG 59.568 43.478 0.00 0.00 0.00 3.33
3384 3491 3.181520 GCAAGCTACGTCTTACATTGTGG 60.182 47.826 0.00 0.00 0.00 4.17
3385 3492 3.247006 AGCTACGTCTTACATTGTGGG 57.753 47.619 0.00 0.00 0.00 4.61
3386 3493 2.829720 AGCTACGTCTTACATTGTGGGA 59.170 45.455 0.00 0.00 0.00 4.37
3387 3494 2.928116 GCTACGTCTTACATTGTGGGAC 59.072 50.000 0.00 6.72 0.00 4.46
3389 3496 1.355971 CGTCTTACATTGTGGGACGG 58.644 55.000 24.96 14.26 43.69 4.79
3390 3497 1.067425 CGTCTTACATTGTGGGACGGA 60.067 52.381 24.96 5.37 43.69 4.69
3391 3498 2.618053 GTCTTACATTGTGGGACGGAG 58.382 52.381 0.00 0.00 0.00 4.63
3392 3499 1.553248 TCTTACATTGTGGGACGGAGG 59.447 52.381 0.00 0.00 0.00 4.30
3393 3500 0.616371 TTACATTGTGGGACGGAGGG 59.384 55.000 0.00 0.00 0.00 4.30
3394 3501 0.252330 TACATTGTGGGACGGAGGGA 60.252 55.000 0.00 0.00 0.00 4.20
3395 3502 1.221840 CATTGTGGGACGGAGGGAG 59.778 63.158 0.00 0.00 0.00 4.30
3407 3514 4.202451 GGACGGAGGGAGTACTTAGTAGAT 60.202 50.000 0.00 0.00 0.00 1.98
3415 3522 7.420029 AGGGAGTACTTAGTAGATCTTTTCCA 58.580 38.462 0.00 0.00 0.00 3.53
3455 3562 1.080298 TGTGTGCTTTGTTTCGTCGT 58.920 45.000 0.00 0.00 0.00 4.34
3496 3603 4.726416 CACCTGTTGTTGCATCTGATTAC 58.274 43.478 0.00 0.00 0.00 1.89
3519 3626 2.415512 GGTGATTCACTTCGCAGTTACC 59.584 50.000 16.02 0.00 34.40 2.85
3620 3727 1.672356 GTGCAATCGGTGTGAGCCT 60.672 57.895 0.00 0.00 0.00 4.58
3820 3929 3.797039 TCTGCTATTGGAGGATGTTTCG 58.203 45.455 0.00 0.00 32.15 3.46
3826 3935 6.998074 TGCTATTGGAGGATGTTTCGATAAAT 59.002 34.615 0.00 0.00 0.00 1.40
3931 4042 2.697654 GTCTGAGCAGCAATGAGAGTT 58.302 47.619 0.00 0.00 0.00 3.01
3936 4047 5.764686 TCTGAGCAGCAATGAGAGTTAAAAA 59.235 36.000 0.00 0.00 0.00 1.94
3938 4049 5.048504 TGAGCAGCAATGAGAGTTAAAAAGG 60.049 40.000 0.00 0.00 0.00 3.11
3939 4050 3.922850 GCAGCAATGAGAGTTAAAAAGGC 59.077 43.478 0.00 0.00 0.00 4.35
3940 4051 4.321527 GCAGCAATGAGAGTTAAAAAGGCT 60.322 41.667 0.00 0.00 0.00 4.58
3941 4052 5.397326 CAGCAATGAGAGTTAAAAAGGCTC 58.603 41.667 0.00 0.00 0.00 4.70
3942 4053 5.182760 CAGCAATGAGAGTTAAAAAGGCTCT 59.817 40.000 0.00 0.00 41.72 4.09
3943 4054 6.372659 CAGCAATGAGAGTTAAAAAGGCTCTA 59.627 38.462 0.00 0.00 39.43 2.43
3944 4055 6.597280 AGCAATGAGAGTTAAAAAGGCTCTAG 59.403 38.462 0.00 0.00 39.43 2.43
3988 4099 8.777413 CACTGAGAGACATTTTTCAATAGAACA 58.223 33.333 0.00 0.00 32.39 3.18
4063 4174 5.949233 AGACGTTTTTGCAGTTCAATTTC 57.051 34.783 0.00 0.00 34.12 2.17
4073 4184 4.202040 TGCAGTTCAATTTCAACAGAGGTG 60.202 41.667 0.00 0.00 0.00 4.00
4076 4187 4.580580 AGTTCAATTTCAACAGAGGTGGTC 59.419 41.667 0.92 0.00 0.00 4.02
4107 4386 6.902224 AAGTGAATTGTAAGTTTTGTTGGC 57.098 33.333 0.00 0.00 0.00 4.52
4203 4486 9.057089 ACTGGTAAAGATTAAACTTGAGTTCAG 57.943 33.333 0.00 6.07 37.25 3.02
4204 4487 8.974060 TGGTAAAGATTAAACTTGAGTTCAGT 57.026 30.769 0.00 0.00 37.25 3.41
4205 4488 9.052759 TGGTAAAGATTAAACTTGAGTTCAGTC 57.947 33.333 0.00 0.00 37.25 3.51
4221 4508 2.714250 TCAGTCTTTTTAGGGAAGGCCA 59.286 45.455 5.01 0.00 35.15 5.36
4242 4529 4.569966 CCATCATGGCTAGCTTTATCGATC 59.430 45.833 15.72 0.00 0.00 3.69
4243 4530 3.838120 TCATGGCTAGCTTTATCGATCG 58.162 45.455 15.72 9.36 0.00 3.69
4256 4544 7.327275 AGCTTTATCGATCGAACTTGATACATC 59.673 37.037 23.50 0.00 0.00 3.06
4257 4545 7.114953 GCTTTATCGATCGAACTTGATACATCA 59.885 37.037 23.50 0.00 34.44 3.07
4262 4550 5.866092 CGATCGAACTTGATACATCATCCAT 59.134 40.000 10.26 0.00 36.56 3.41
4421 4710 9.123902 CAAAGATAAAGATATCCACACATTCCA 57.876 33.333 0.00 0.00 39.02 3.53
4454 4751 4.113815 CCGAGCCCCATCAAGCCA 62.114 66.667 0.00 0.00 0.00 4.75
4467 4764 2.585330 TCAAGCCAGAGCAACATTTGA 58.415 42.857 0.00 0.00 43.56 2.69
4470 4767 1.202976 AGCCAGAGCAACATTTGACCT 60.203 47.619 0.00 0.00 43.56 3.85
4471 4768 1.615392 GCCAGAGCAACATTTGACCTT 59.385 47.619 0.00 0.00 39.53 3.50
4475 4772 2.808543 AGAGCAACATTTGACCTTCGAC 59.191 45.455 0.00 0.00 0.00 4.20
4476 4773 2.808543 GAGCAACATTTGACCTTCGACT 59.191 45.455 0.00 0.00 0.00 4.18
4477 4774 2.808543 AGCAACATTTGACCTTCGACTC 59.191 45.455 0.00 0.00 0.00 3.36
4478 4775 2.411547 GCAACATTTGACCTTCGACTCG 60.412 50.000 0.00 0.00 0.00 4.18
4481 4778 1.391485 CATTTGACCTTCGACTCGCTG 59.609 52.381 0.00 0.00 0.00 5.18
4482 4779 0.319555 TTTGACCTTCGACTCGCTGG 60.320 55.000 7.66 7.66 0.00 4.85
4485 4782 2.202676 CCTTCGACTCGCTGGAGC 60.203 66.667 0.00 0.00 44.48 4.70
4486 4783 2.568612 CTTCGACTCGCTGGAGCA 59.431 61.111 0.00 0.00 44.48 4.26
4488 4785 2.477972 CTTCGACTCGCTGGAGCACA 62.478 60.000 0.00 0.00 44.48 4.57
4489 4786 2.049156 CGACTCGCTGGAGCACAA 60.049 61.111 0.00 0.00 44.48 3.33
4490 4787 2.091112 CGACTCGCTGGAGCACAAG 61.091 63.158 0.00 0.00 44.48 3.16
4493 4790 0.179045 ACTCGCTGGAGCACAAGTTT 60.179 50.000 0.00 0.00 44.48 2.66
4526 4851 8.815141 CAAGGATTGTGAAATTTGTTATGTGA 57.185 30.769 0.00 0.00 42.34 3.58
4536 4861 9.979578 TGAAATTTGTTATGTGAATTGTTAGCT 57.020 25.926 0.00 0.00 0.00 3.32
4540 4865 7.517614 TTGTTATGTGAATTGTTAGCTGGAA 57.482 32.000 0.00 0.00 0.00 3.53
4541 4866 7.144722 TGTTATGTGAATTGTTAGCTGGAAG 57.855 36.000 0.00 0.00 0.00 3.46
4553 4878 3.419793 CTGGAAGCCTGGAACACAA 57.580 52.632 0.00 0.00 0.00 3.33
4555 4880 0.550914 TGGAAGCCTGGAACACAACT 59.449 50.000 0.00 0.00 0.00 3.16
4567 5619 6.349777 CCTGGAACACAACTTTCTTAAACACA 60.350 38.462 0.00 0.00 0.00 3.72
4589 5641 5.757808 ACAAGGGTTGTGAAATTTGTTATGC 59.242 36.000 0.00 0.00 43.48 3.14
4641 5693 2.509964 TCCCTCCAAAATCCTAGCCTTC 59.490 50.000 0.00 0.00 0.00 3.46
4659 5711 2.511600 CCTGTTGGATCGGACGGC 60.512 66.667 0.00 0.00 34.57 5.68
4700 5752 4.383010 CCCACACAAAGAAAAGAAAAGGCT 60.383 41.667 0.00 0.00 0.00 4.58
4701 5753 4.805719 CCACACAAAGAAAAGAAAAGGCTC 59.194 41.667 0.00 0.00 0.00 4.70
4702 5754 4.805719 CACACAAAGAAAAGAAAAGGCTCC 59.194 41.667 0.00 0.00 0.00 4.70
4745 5801 6.183360 CCTGAATAGTCTTGAACCGATAAGGA 60.183 42.308 0.00 0.00 45.00 3.36
4776 5832 0.175073 CGTAAAACCCCGGAGAGGAG 59.825 60.000 0.73 0.00 45.00 3.69
4777 5833 0.107800 GTAAAACCCCGGAGAGGAGC 60.108 60.000 0.73 0.00 45.00 4.70
4778 5834 1.610554 TAAAACCCCGGAGAGGAGCG 61.611 60.000 0.73 0.00 45.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 5.529800 TCTTGCATCATATCATCACCAACAG 59.470 40.000 0.00 0.00 0.00 3.16
216 222 8.712363 CGATCCTACTAATTAATTGTGTCCATG 58.288 37.037 11.05 0.00 0.00 3.66
217 223 8.429641 ACGATCCTACTAATTAATTGTGTCCAT 58.570 33.333 11.05 3.55 0.00 3.41
222 228 7.114529 GGACGACGATCCTACTAATTAATTGTG 59.885 40.741 11.05 6.27 35.68 3.33
223 229 7.144000 GGACGACGATCCTACTAATTAATTGT 58.856 38.462 11.05 9.18 35.68 2.71
224 230 7.564044 GGACGACGATCCTACTAATTAATTG 57.436 40.000 11.05 3.88 35.68 2.32
414 458 1.170290 GCCCCGCGCTACCATTATTT 61.170 55.000 5.56 0.00 0.00 1.40
463 508 4.612712 GCACTTTTCATACAAGCGTTGCTA 60.613 41.667 0.00 0.00 38.25 3.49
554 599 2.086869 GGGTACCGCGCTACTGATATA 58.913 52.381 11.14 0.00 40.86 0.86
629 705 0.029567 CTAGGCATCCGTCTCGACAC 59.970 60.000 0.00 0.00 0.00 3.67
673 749 4.812476 CATTCCCCGACGCTGCGA 62.812 66.667 30.47 4.12 0.00 5.10
678 754 2.435938 TTCTGCATTCCCCGACGC 60.436 61.111 0.00 0.00 0.00 5.19
710 786 2.173519 CATCCAAATTCCTGGCAGTGT 58.826 47.619 14.43 0.00 36.32 3.55
715 791 3.214328 ACGATACATCCAAATTCCTGGC 58.786 45.455 0.00 0.00 36.32 4.85
803 879 9.135189 TCAGGGATTTATTTATGGAAATGTCTG 57.865 33.333 0.00 0.00 35.96 3.51
843 920 8.802267 GGTAGCTTTATCATAATTTGGGCAATA 58.198 33.333 0.00 0.00 0.00 1.90
973 1054 4.218417 CGATCACCCCTTGAACAAAGAAAT 59.782 41.667 0.00 0.00 37.92 2.17
987 1068 0.675522 TTTTTCCTCGCGATCACCCC 60.676 55.000 10.36 0.00 0.00 4.95
1087 1169 3.246687 TTGGAGACGGGCCAAAGT 58.753 55.556 4.39 0.06 42.13 2.66
1111 1193 1.005394 GAGAACGGCGAAGGTGGAA 60.005 57.895 16.62 0.00 0.00 3.53
1290 1372 2.043852 GAGGAGAGGGCTGACCGA 60.044 66.667 0.00 0.00 46.96 4.69
1323 1405 0.723129 GATCGAATCGACGGAGCGAG 60.723 60.000 7.77 0.00 44.26 5.03
1345 1427 6.463190 GGGGAAGAGTAACCTCATACAATCTC 60.463 46.154 0.00 0.00 40.40 2.75
1357 1439 2.186125 CGGCGGGGAAGAGTAACC 59.814 66.667 0.00 0.00 0.00 2.85
1358 1440 2.510918 GCGGCGGGGAAGAGTAAC 60.511 66.667 9.78 0.00 0.00 2.50
1404 1486 2.167861 GCGGATCAGAACGACAGCC 61.168 63.158 0.00 0.00 0.00 4.85
1405 1487 2.508891 CGCGGATCAGAACGACAGC 61.509 63.158 0.00 0.00 0.00 4.40
1410 1492 1.805539 TTGAGCGCGGATCAGAACG 60.806 57.895 8.83 0.00 0.00 3.95
1420 1502 2.307309 TGTTTCGAGGTTGAGCGCG 61.307 57.895 0.00 0.00 0.00 6.86
1425 1507 2.804697 TCGATGTGTTTCGAGGTTGA 57.195 45.000 0.00 0.00 42.81 3.18
1455 1537 0.036732 AACATCTCGCCAGCTCCAAA 59.963 50.000 0.00 0.00 0.00 3.28
1461 1543 1.089920 AATCACAACATCTCGCCAGC 58.910 50.000 0.00 0.00 0.00 4.85
1466 1548 5.402568 CCTAATCGGTAATCACAACATCTCG 59.597 44.000 0.00 0.00 0.00 4.04
1564 1646 0.476771 AAAATCCAGTCCCCACACGT 59.523 50.000 0.00 0.00 0.00 4.49
1633 1715 5.458595 TCTCTTATCAGGCTGATAACCTCA 58.541 41.667 34.86 20.93 42.52 3.86
1634 1716 6.437162 AGATCTCTTATCAGGCTGATAACCTC 59.563 42.308 34.86 27.16 42.52 3.85
1636 1718 6.397272 CAGATCTCTTATCAGGCTGATAACC 58.603 44.000 34.86 23.28 42.52 2.85
1638 1720 5.541484 TGCAGATCTCTTATCAGGCTGATAA 59.459 40.000 35.40 35.40 44.45 1.75
1640 1722 3.902467 TGCAGATCTCTTATCAGGCTGAT 59.098 43.478 30.89 30.89 40.72 2.90
1641 1723 3.303049 TGCAGATCTCTTATCAGGCTGA 58.697 45.455 21.19 21.19 0.00 4.26
1642 1724 3.747854 TGCAGATCTCTTATCAGGCTG 57.252 47.619 8.58 8.58 0.00 4.85
1643 1725 3.710677 AGTTGCAGATCTCTTATCAGGCT 59.289 43.478 0.00 0.00 0.00 4.58
1644 1726 3.808726 CAGTTGCAGATCTCTTATCAGGC 59.191 47.826 0.00 0.00 0.00 4.85
1645 1727 5.049167 GTCAGTTGCAGATCTCTTATCAGG 58.951 45.833 0.00 0.00 0.00 3.86
1646 1728 4.739228 CGTCAGTTGCAGATCTCTTATCAG 59.261 45.833 0.00 0.00 0.00 2.90
1692 1774 1.870402 TCCTGTGCATTACAACACGTG 59.130 47.619 15.48 15.48 39.20 4.49
1693 1775 2.248280 TCCTGTGCATTACAACACGT 57.752 45.000 0.00 0.00 39.20 4.49
1739 1821 4.318332 TGACTTCTGCACCATTCAACTAG 58.682 43.478 0.00 0.00 0.00 2.57
1786 1868 4.842948 AGGATATATGATGCACCTCTGTGT 59.157 41.667 0.00 0.00 44.65 3.72
1799 1881 6.238593 CGCTGATCGATTCTGAGGATATATGA 60.239 42.308 0.00 0.00 41.67 2.15
1823 1905 1.069568 TCAGCAAACAACGGCATTACG 60.070 47.619 0.00 0.00 40.31 3.18
1848 1930 0.179468 GGCAGCGATACAAACCCCTA 59.821 55.000 0.00 0.00 0.00 3.53
1853 1935 1.296056 ACCGTGGCAGCGATACAAAC 61.296 55.000 10.33 0.00 0.00 2.93
1935 2017 5.484998 ACCAAAATGCACCATCCTAGAATTT 59.515 36.000 0.00 0.00 0.00 1.82
1974 2056 6.458342 GCGGAAAGGTGATTATTCTGTTAAGG 60.458 42.308 0.00 0.00 33.08 2.69
2029 2114 4.084328 CGTTTCTGCAAAGAGACTACCAAG 60.084 45.833 0.00 0.00 0.00 3.61
2065 2150 3.558931 TCTGCAAAGAGACAACCAAGA 57.441 42.857 0.00 0.00 0.00 3.02
2066 2151 4.354587 GTTTCTGCAAAGAGACAACCAAG 58.645 43.478 0.00 0.00 0.00 3.61
2067 2152 3.130340 GGTTTCTGCAAAGAGACAACCAA 59.870 43.478 0.00 0.00 35.45 3.67
2068 2153 2.687935 GGTTTCTGCAAAGAGACAACCA 59.312 45.455 0.00 0.00 35.45 3.67
2069 2154 2.952310 AGGTTTCTGCAAAGAGACAACC 59.048 45.455 0.00 0.00 35.51 3.77
2070 2155 4.639135 AAGGTTTCTGCAAAGAGACAAC 57.361 40.909 0.00 0.00 0.00 3.32
2071 2156 6.321181 ACATAAAGGTTTCTGCAAAGAGACAA 59.679 34.615 0.00 0.00 0.00 3.18
2074 2159 5.278463 GCACATAAAGGTTTCTGCAAAGAGA 60.278 40.000 0.00 0.00 0.00 3.10
2076 2161 4.584325 AGCACATAAAGGTTTCTGCAAAGA 59.416 37.500 0.00 0.00 0.00 2.52
2077 2162 4.874970 AGCACATAAAGGTTTCTGCAAAG 58.125 39.130 0.00 0.00 0.00 2.77
2078 2163 4.935352 AGCACATAAAGGTTTCTGCAAA 57.065 36.364 0.00 0.00 0.00 3.68
2079 2164 4.935352 AAGCACATAAAGGTTTCTGCAA 57.065 36.364 0.00 0.00 0.00 4.08
2080 2165 4.935352 AAAGCACATAAAGGTTTCTGCA 57.065 36.364 0.00 0.00 31.69 4.41
2199 2287 8.194769 TCGAATCTAATAACAGTAACTGCATGA 58.805 33.333 0.00 0.00 34.37 3.07
2226 2314 2.743938 AGTTGCTGTTGACTCGTAGTG 58.256 47.619 0.00 0.00 0.00 2.74
2232 2320 2.849880 TTGCAAGTTGCTGTTGACTC 57.150 45.000 27.17 0.00 45.31 3.36
2270 2370 7.996385 ACAAGAAACTAGCACAATGTAAAAGT 58.004 30.769 0.00 0.00 0.00 2.66
2440 2540 9.315525 GAAGTGGTCTTAAAGATCCATAAGTAC 57.684 37.037 12.41 10.66 33.64 2.73
2557 2657 7.938140 AACATAACAACAGGCATATAACAGT 57.062 32.000 0.00 0.00 0.00 3.55
2639 2739 9.636789 ACCCAACTACAAACTTAGTTTAGAAAT 57.363 29.630 10.21 0.00 39.77 2.17
2698 2801 4.253685 TGTGCTGCTAGAAACTAACCATC 58.746 43.478 0.00 0.00 0.00 3.51
2699 2802 4.020218 TCTGTGCTGCTAGAAACTAACCAT 60.020 41.667 0.00 0.00 0.00 3.55
2730 2833 0.179043 TAAACAGGCGGAACAGTGCA 60.179 50.000 0.00 0.00 0.00 4.57
2731 2834 0.948678 TTAAACAGGCGGAACAGTGC 59.051 50.000 0.00 0.00 0.00 4.40
2732 2835 3.074412 AGATTAAACAGGCGGAACAGTG 58.926 45.455 0.00 0.00 0.00 3.66
2741 2844 4.278419 ACACTGGAACAAGATTAAACAGGC 59.722 41.667 0.00 0.00 38.70 4.85
2759 2863 7.490962 TGGAGTTGACAAATTTACTACACTG 57.509 36.000 0.40 0.00 0.00 3.66
2771 2875 3.259876 AGCTACCGTATGGAGTTGACAAA 59.740 43.478 8.33 0.00 39.21 2.83
2775 2879 5.864418 AAATAGCTACCGTATGGAGTTGA 57.136 39.130 8.33 0.00 39.21 3.18
2786 2890 7.607991 AGAATTCATATGGGAAAATAGCTACCG 59.392 37.037 8.44 0.00 0.00 4.02
2799 2903 2.629617 GGGTTGCCAGAATTCATATGGG 59.370 50.000 8.44 2.32 34.52 4.00
2895 3000 6.409704 ACTCAGCACTCAAGAAATAATGCTA 58.590 36.000 0.00 0.00 41.32 3.49
2939 3046 9.065871 CAACTGAAACAAAGAGACTAAAAGTTG 57.934 33.333 0.00 0.00 35.28 3.16
3019 3126 9.581099 CAAGGTAAATGTGTCTTTAAAAACACT 57.419 29.630 21.96 7.99 44.78 3.55
3040 3147 3.395941 ACCAAGAACCAGAGATTCAAGGT 59.604 43.478 0.00 0.00 33.32 3.50
3134 3241 5.302568 AGACAAAGCATGACCTGAAAATTGA 59.697 36.000 0.00 0.00 0.00 2.57
3146 3253 2.031769 CACGCTTCAAGACAAAGCATGA 60.032 45.455 0.00 0.00 43.58 3.07
3208 3315 7.994425 TCTAAACTTCAAGGATTATGTGCAA 57.006 32.000 0.00 0.00 0.00 4.08
3242 3349 2.840651 ACCTACTGCCTACTGAAATGCT 59.159 45.455 0.00 0.00 0.00 3.79
3260 3367 6.296803 AGAAATTCAGTTCGAAACCTTACCT 58.703 36.000 0.00 0.00 37.12 3.08
3261 3368 6.204108 TGAGAAATTCAGTTCGAAACCTTACC 59.796 38.462 0.00 0.00 37.12 2.85
3262 3369 7.186021 TGAGAAATTCAGTTCGAAACCTTAC 57.814 36.000 0.00 0.00 37.12 2.34
3263 3370 7.497909 AGTTGAGAAATTCAGTTCGAAACCTTA 59.502 33.333 0.00 0.00 37.12 2.69
3264 3371 6.318900 AGTTGAGAAATTCAGTTCGAAACCTT 59.681 34.615 0.00 0.00 37.12 3.50
3292 3399 3.125316 GTGCTACACAAGATTTCCCTTCG 59.875 47.826 0.00 0.00 34.08 3.79
3297 3404 5.634896 CATTCTGTGCTACACAAGATTTCC 58.365 41.667 1.64 0.00 44.08 3.13
3339 3446 5.798434 GCAAAAACGTCTTACATTATGGGAC 59.202 40.000 0.00 1.75 0.00 4.46
3340 3447 5.473846 TGCAAAAACGTCTTACATTATGGGA 59.526 36.000 0.00 0.00 0.00 4.37
3341 3448 5.704888 TGCAAAAACGTCTTACATTATGGG 58.295 37.500 0.00 0.00 0.00 4.00
3342 3449 6.183359 GCTTGCAAAAACGTCTTACATTATGG 60.183 38.462 0.00 0.00 0.00 2.74
3343 3450 6.582295 AGCTTGCAAAAACGTCTTACATTATG 59.418 34.615 0.00 0.00 0.00 1.90
3347 3454 4.568152 AGCTTGCAAAAACGTCTTACAT 57.432 36.364 0.00 0.00 0.00 2.29
3348 3455 4.551217 CGTAGCTTGCAAAAACGTCTTACA 60.551 41.667 15.79 0.00 0.00 2.41
3349 3456 3.898361 CGTAGCTTGCAAAAACGTCTTAC 59.102 43.478 15.79 4.09 0.00 2.34
3350 3457 3.556775 ACGTAGCTTGCAAAAACGTCTTA 59.443 39.130 21.11 0.00 42.62 2.10
3352 3459 1.937899 ACGTAGCTTGCAAAAACGTCT 59.062 42.857 21.11 6.48 42.62 4.18
3353 3460 2.378507 ACGTAGCTTGCAAAAACGTC 57.621 45.000 21.11 2.93 42.62 4.34
3355 3462 2.663279 AGACGTAGCTTGCAAAAACG 57.337 45.000 20.10 20.10 39.37 3.60
3356 3463 4.839796 TGTAAGACGTAGCTTGCAAAAAC 58.160 39.130 0.00 0.00 37.51 2.43
3358 3465 5.008217 ACAATGTAAGACGTAGCTTGCAAAA 59.992 36.000 10.88 0.00 42.34 2.44
3359 3466 4.513692 ACAATGTAAGACGTAGCTTGCAAA 59.486 37.500 10.88 0.00 42.34 3.68
3360 3467 4.062293 ACAATGTAAGACGTAGCTTGCAA 58.938 39.130 10.88 0.00 42.34 4.08
3362 3469 3.181520 CCACAATGTAAGACGTAGCTTGC 60.182 47.826 0.00 0.00 0.00 4.01
3363 3470 3.370978 CCCACAATGTAAGACGTAGCTTG 59.629 47.826 0.00 0.00 0.00 4.01
3364 3471 3.259876 TCCCACAATGTAAGACGTAGCTT 59.740 43.478 0.00 0.00 0.00 3.74
3366 3473 2.928116 GTCCCACAATGTAAGACGTAGC 59.072 50.000 0.00 0.00 0.00 3.58
3367 3474 3.176708 CGTCCCACAATGTAAGACGTAG 58.823 50.000 21.67 2.94 43.89 3.51
3368 3475 2.094597 CCGTCCCACAATGTAAGACGTA 60.095 50.000 25.28 0.00 46.62 3.57
3369 3476 1.337447 CCGTCCCACAATGTAAGACGT 60.337 52.381 25.28 0.00 46.62 4.34
3371 3478 2.618053 CTCCGTCCCACAATGTAAGAC 58.382 52.381 5.24 5.24 0.00 3.01
3372 3479 1.553248 CCTCCGTCCCACAATGTAAGA 59.447 52.381 0.00 0.00 0.00 2.10
3373 3480 1.406887 CCCTCCGTCCCACAATGTAAG 60.407 57.143 0.00 0.00 0.00 2.34
3374 3481 0.616371 CCCTCCGTCCCACAATGTAA 59.384 55.000 0.00 0.00 0.00 2.41
3375 3482 0.252330 TCCCTCCGTCCCACAATGTA 60.252 55.000 0.00 0.00 0.00 2.29
3376 3483 1.537889 TCCCTCCGTCCCACAATGT 60.538 57.895 0.00 0.00 0.00 2.71
3377 3484 1.221840 CTCCCTCCGTCCCACAATG 59.778 63.158 0.00 0.00 0.00 2.82
3378 3485 0.042131 TACTCCCTCCGTCCCACAAT 59.958 55.000 0.00 0.00 0.00 2.71
3379 3486 0.901580 GTACTCCCTCCGTCCCACAA 60.902 60.000 0.00 0.00 0.00 3.33
3380 3487 1.304713 GTACTCCCTCCGTCCCACA 60.305 63.158 0.00 0.00 0.00 4.17
3381 3488 0.614134 AAGTACTCCCTCCGTCCCAC 60.614 60.000 0.00 0.00 0.00 4.61
3382 3489 1.002069 TAAGTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
3383 3490 1.064091 ACTAAGTACTCCCTCCGTCCC 60.064 57.143 0.00 0.00 0.00 4.46
3384 3491 2.433662 ACTAAGTACTCCCTCCGTCC 57.566 55.000 0.00 0.00 0.00 4.79
3385 3492 4.414337 TCTACTAAGTACTCCCTCCGTC 57.586 50.000 0.00 0.00 0.00 4.79
3386 3493 4.659835 AGATCTACTAAGTACTCCCTCCGT 59.340 45.833 0.00 0.00 0.00 4.69
3387 3494 5.231702 AGATCTACTAAGTACTCCCTCCG 57.768 47.826 0.00 0.00 0.00 4.63
3388 3495 7.014518 GGAAAAGATCTACTAAGTACTCCCTCC 59.985 44.444 0.00 0.00 0.00 4.30
3389 3496 7.560626 TGGAAAAGATCTACTAAGTACTCCCTC 59.439 40.741 0.00 0.00 0.00 4.30
3390 3497 7.420029 TGGAAAAGATCTACTAAGTACTCCCT 58.580 38.462 0.00 0.00 0.00 4.20
3391 3498 7.657023 TGGAAAAGATCTACTAAGTACTCCC 57.343 40.000 0.00 0.00 0.00 4.30
3392 3499 7.147880 TGCTGGAAAAGATCTACTAAGTACTCC 60.148 40.741 0.00 0.00 0.00 3.85
3393 3500 7.773149 TGCTGGAAAAGATCTACTAAGTACTC 58.227 38.462 0.00 0.00 0.00 2.59
3394 3501 7.719871 TGCTGGAAAAGATCTACTAAGTACT 57.280 36.000 0.00 0.00 0.00 2.73
3395 3502 9.685828 CTATGCTGGAAAAGATCTACTAAGTAC 57.314 37.037 0.00 0.00 0.00 2.73
3407 3514 6.203530 CGATATTTGCTCTATGCTGGAAAAGA 59.796 38.462 0.00 0.00 43.37 2.52
3415 3522 4.758674 ACATTGCGATATTTGCTCTATGCT 59.241 37.500 0.00 0.00 43.37 3.79
3433 3540 2.463653 CGACGAAACAAAGCACACATTG 59.536 45.455 0.00 0.00 0.00 2.82
3455 3562 2.038033 GTGCTACCACAACCTACAAGGA 59.962 50.000 0.00 0.00 41.67 3.36
3496 3603 0.670546 ACTGCGAAGTGAATCACCCG 60.671 55.000 17.37 17.37 34.49 5.28
3620 3727 8.138928 TGAATCACTTTCTGGAAGATCTAAGA 57.861 34.615 1.91 3.68 46.36 2.10
3820 3929 6.927294 AAGATCCGAGGTCAACAATTTATC 57.073 37.500 0.00 0.00 0.00 1.75
3826 3935 3.762407 TCAAAGATCCGAGGTCAACAA 57.238 42.857 0.00 0.00 0.00 2.83
3922 4033 7.760340 CGTACTAGAGCCTTTTTAACTCTCATT 59.240 37.037 0.00 0.00 41.03 2.57
3931 4042 4.796038 AGCACGTACTAGAGCCTTTTTA 57.204 40.909 0.00 0.00 0.00 1.52
3936 4047 3.003482 CGAATTAGCACGTACTAGAGCCT 59.997 47.826 0.00 0.00 0.00 4.58
3938 4049 4.206698 TCGAATTAGCACGTACTAGAGC 57.793 45.455 0.00 0.00 0.00 4.09
3939 4050 6.357503 GTGAATCGAATTAGCACGTACTAGAG 59.642 42.308 0.00 0.00 0.00 2.43
3940 4051 6.037940 AGTGAATCGAATTAGCACGTACTAGA 59.962 38.462 0.00 0.00 34.82 2.43
3941 4052 6.140895 CAGTGAATCGAATTAGCACGTACTAG 59.859 42.308 0.00 0.00 34.82 2.57
3942 4053 5.969435 CAGTGAATCGAATTAGCACGTACTA 59.031 40.000 0.00 0.00 34.82 1.82
3943 4054 4.798907 CAGTGAATCGAATTAGCACGTACT 59.201 41.667 0.00 0.00 34.82 2.73
3944 4055 4.796830 TCAGTGAATCGAATTAGCACGTAC 59.203 41.667 0.00 0.00 34.82 3.67
4063 4174 8.204160 TCACTTTATATATGACCACCTCTGTTG 58.796 37.037 0.00 0.00 0.00 3.33
4107 4386 8.991026 TGTGATCCAAGCTGAATTTTTATTTTG 58.009 29.630 0.00 0.00 0.00 2.44
4170 4453 9.810545 CAAGTTTAATCTTTACCAGTTGGAAAA 57.189 29.630 4.92 0.00 38.94 2.29
4173 4456 7.996644 ACTCAAGTTTAATCTTTACCAGTTGGA 59.003 33.333 4.92 0.00 38.94 3.53
4176 4459 9.403583 TGAACTCAAGTTTAATCTTTACCAGTT 57.596 29.630 0.00 3.68 38.56 3.16
4177 4460 8.974060 TGAACTCAAGTTTAATCTTTACCAGT 57.026 30.769 0.00 0.00 38.56 4.00
4192 4475 6.248569 TCCCTAAAAAGACTGAACTCAAGT 57.751 37.500 0.00 0.00 0.00 3.16
4203 4486 3.697166 TGATGGCCTTCCCTAAAAAGAC 58.303 45.455 15.62 0.00 0.00 3.01
4204 4487 4.280819 CATGATGGCCTTCCCTAAAAAGA 58.719 43.478 15.62 0.00 0.00 2.52
4205 4488 3.385755 CCATGATGGCCTTCCCTAAAAAG 59.614 47.826 15.62 0.00 0.00 2.27
4221 4508 4.158579 TCGATCGATAAAGCTAGCCATGAT 59.841 41.667 15.15 6.65 0.00 2.45
4238 4525 5.222631 TGGATGATGTATCAAGTTCGATCG 58.777 41.667 9.36 9.36 40.69 3.69
4242 4529 5.107182 GCTCATGGATGATGTATCAAGTTCG 60.107 44.000 0.00 0.00 40.69 3.95
4243 4530 5.996513 AGCTCATGGATGATGTATCAAGTTC 59.003 40.000 0.00 0.00 40.69 3.01
4280 4568 1.118965 TGGACTGACGAGCCTCCAAA 61.119 55.000 0.00 0.00 29.50 3.28
4282 4570 1.533033 TTGGACTGACGAGCCTCCA 60.533 57.895 0.00 0.00 0.00 3.86
4283 4571 1.079750 GTTGGACTGACGAGCCTCC 60.080 63.158 0.00 0.00 0.00 4.30
4344 4633 3.276857 AGATCTGCAAATCAAGCGACAT 58.723 40.909 2.24 0.00 33.85 3.06
4347 4636 5.181056 TGTTTTAGATCTGCAAATCAAGCGA 59.819 36.000 5.18 0.00 33.85 4.93
4395 4684 9.123902 TGGAATGTGTGGATATCTTTATCTTTG 57.876 33.333 2.05 0.00 35.51 2.77
4396 4685 9.125026 GTGGAATGTGTGGATATCTTTATCTTT 57.875 33.333 2.05 0.00 35.51 2.52
4400 4689 8.821686 TTTGTGGAATGTGTGGATATCTTTAT 57.178 30.769 2.05 0.00 0.00 1.40
4403 4692 7.537596 TTTTTGTGGAATGTGTGGATATCTT 57.462 32.000 2.05 0.00 0.00 2.40
4447 4736 2.294233 GTCAAATGTTGCTCTGGCTTGA 59.706 45.455 0.00 0.00 39.59 3.02
4454 4751 2.808543 GTCGAAGGTCAAATGTTGCTCT 59.191 45.455 0.00 0.00 0.00 4.09
4467 4764 2.995872 GCTCCAGCGAGTCGAAGGT 61.996 63.158 18.61 0.00 38.49 3.50
4470 4767 2.082629 TTGTGCTCCAGCGAGTCGAA 62.083 55.000 18.61 0.00 45.83 3.71
4471 4768 2.477972 CTTGTGCTCCAGCGAGTCGA 62.478 60.000 18.61 0.00 45.83 4.20
4475 4772 0.514691 GAAACTTGTGCTCCAGCGAG 59.485 55.000 0.00 0.00 45.83 5.03
4476 4773 0.106708 AGAAACTTGTGCTCCAGCGA 59.893 50.000 0.00 0.00 45.83 4.93
4477 4774 1.795768 TAGAAACTTGTGCTCCAGCG 58.204 50.000 0.00 0.00 45.83 5.18
4478 4775 3.315191 TGTTTAGAAACTTGTGCTCCAGC 59.685 43.478 6.69 0.00 39.59 4.85
4481 4778 4.893424 TGTGTTTAGAAACTTGTGCTCC 57.107 40.909 6.69 0.00 39.59 4.70
4482 4779 5.065988 TCCTTGTGTTTAGAAACTTGTGCTC 59.934 40.000 6.69 0.00 39.59 4.26
4485 4782 7.257722 ACAATCCTTGTGTTTAGAAACTTGTG 58.742 34.615 6.69 0.00 43.48 3.33
4486 4783 7.404671 ACAATCCTTGTGTTTAGAAACTTGT 57.595 32.000 6.69 4.36 43.48 3.16
4514 4839 8.121305 TCCAGCTAACAATTCACATAACAAAT 57.879 30.769 0.00 0.00 0.00 2.32
4521 4846 3.445096 GGCTTCCAGCTAACAATTCACAT 59.555 43.478 0.00 0.00 41.99 3.21
4522 4847 2.819608 GGCTTCCAGCTAACAATTCACA 59.180 45.455 0.00 0.00 41.99 3.58
4525 4850 2.424956 CCAGGCTTCCAGCTAACAATTC 59.575 50.000 0.00 0.00 41.99 2.17
4526 4851 2.041620 TCCAGGCTTCCAGCTAACAATT 59.958 45.455 0.00 0.00 41.99 2.32
4528 4853 1.064003 TCCAGGCTTCCAGCTAACAA 58.936 50.000 0.00 0.00 41.99 2.83
4530 4855 1.271379 TGTTCCAGGCTTCCAGCTAAC 60.271 52.381 0.00 0.00 41.99 2.34
4533 4858 1.073897 GTGTTCCAGGCTTCCAGCT 59.926 57.895 0.00 0.00 41.99 4.24
4535 4860 0.954452 GTTGTGTTCCAGGCTTCCAG 59.046 55.000 0.00 0.00 0.00 3.86
4536 4861 0.550914 AGTTGTGTTCCAGGCTTCCA 59.449 50.000 0.00 0.00 0.00 3.53
4540 4865 2.736670 AGAAAGTTGTGTTCCAGGCT 57.263 45.000 0.00 0.00 0.00 4.58
4541 4866 4.911514 TTAAGAAAGTTGTGTTCCAGGC 57.088 40.909 0.00 0.00 0.00 4.85
4542 4867 6.033966 GTGTTTAAGAAAGTTGTGTTCCAGG 58.966 40.000 0.00 0.00 0.00 4.45
4543 4868 6.616947 TGTGTTTAAGAAAGTTGTGTTCCAG 58.383 36.000 0.00 0.00 0.00 3.86
4544 4869 6.576662 TGTGTTTAAGAAAGTTGTGTTCCA 57.423 33.333 0.00 0.00 0.00 3.53
4545 4870 6.530181 CCTTGTGTTTAAGAAAGTTGTGTTCC 59.470 38.462 0.00 0.00 0.00 3.62
4546 4871 6.530181 CCCTTGTGTTTAAGAAAGTTGTGTTC 59.470 38.462 0.00 0.00 0.00 3.18
4547 4872 6.014925 ACCCTTGTGTTTAAGAAAGTTGTGTT 60.015 34.615 0.00 0.00 0.00 3.32
4549 4874 5.961272 ACCCTTGTGTTTAAGAAAGTTGTG 58.039 37.500 0.00 0.00 0.00 3.33
4550 4875 6.014925 ACAACCCTTGTGTTTAAGAAAGTTGT 60.015 34.615 0.00 0.00 43.48 3.32
4551 4876 6.394809 ACAACCCTTGTGTTTAAGAAAGTTG 58.605 36.000 0.00 0.00 43.48 3.16
4552 4877 6.599356 ACAACCCTTGTGTTTAAGAAAGTT 57.401 33.333 0.00 0.00 43.48 2.66
4567 5619 4.987912 CGCATAACAAATTTCACAACCCTT 59.012 37.500 0.00 0.00 0.00 3.95
4589 5641 6.839301 GTGACACATATAACGCTAACAATTCG 59.161 38.462 0.00 0.00 0.00 3.34
4641 5693 2.186903 CCGTCCGATCCAACAGGG 59.813 66.667 0.00 0.00 38.37 4.45
4745 5801 1.543358 GGTTTTACGGTCGTCTCCTCT 59.457 52.381 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.