Multiple sequence alignment - TraesCS3A01G181200

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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 TraesCS3A01G181200 chr3A 100.000 6724 0 0 1 6724 209401060 209407783 0.000000e+00 12417
1 TraesCS3A01G181200 chr3A 87.402 127 16 0 1754 1880 209402778 209402904 5.430000e-31 147
2 TraesCS3A01G181200 chr3A 87.402 127 16 0 1719 1845 209402813 209402939 5.430000e-31 147
3 TraesCS3A01G181200 chr3D 93.159 4824 196 54 1700 6441 172020455 172025226 0.000000e+00 6957
4 TraesCS3A01G181200 chr3D 95.136 699 14 5 864 1550 172019567 172020257 0.000000e+00 1085
5 TraesCS3A01G181200 chr3D 91.834 698 39 9 186 878 172018863 172019547 0.000000e+00 957
6 TraesCS3A01G181200 chr3D 83.195 482 46 14 3 454 347730054 347730530 6.280000e-110 409
7 TraesCS3A01G181200 chr3D 90.110 273 23 3 187 457 307196884 307196614 1.070000e-92 351
8 TraesCS3A01G181200 chr3D 89.963 269 26 1 186 454 611905636 611905369 4.990000e-91 346
9 TraesCS3A01G181200 chr3D 94.382 178 8 1 6443 6620 172025269 172025444 8.590000e-69 272
10 TraesCS3A01G181200 chr3D 95.000 100 5 0 1602 1701 462197411 462197510 2.510000e-34 158
11 TraesCS3A01G181200 chr3D 88.189 127 15 0 1754 1880 172020474 172020600 1.170000e-32 152
12 TraesCS3A01G181200 chr3D 95.238 63 2 1 1548 1609 172020398 172020460 1.540000e-16 99
13 TraesCS3A01G181200 chr3B 94.692 2223 98 13 1719 3935 250462481 250464689 0.000000e+00 3434
14 TraesCS3A01G181200 chr3B 93.883 2027 61 20 3935 5927 250466491 250468488 0.000000e+00 2998
15 TraesCS3A01G181200 chr3B 92.301 1182 44 18 454 1609 250461237 250462397 0.000000e+00 1635
16 TraesCS3A01G181200 chr3B 85.907 518 36 11 5935 6422 250469334 250469844 1.000000e-142 518
17 TraesCS3A01G181200 chr3B 90.406 271 22 4 186 454 182637354 182637086 2.980000e-93 353
18 TraesCS3A01G181200 chr3B 87.709 179 22 0 1700 1878 250462392 250462570 6.830000e-50 209
19 TraesCS3A01G181200 chr3B 98.131 107 1 1 6615 6721 112435619 112435724 1.150000e-42 185
20 TraesCS3A01G181200 chr3B 98.980 98 1 0 1604 1701 224471743 224471646 6.930000e-40 176
21 TraesCS3A01G181200 chr3B 86.614 127 17 0 1754 1880 250462411 250462537 2.530000e-29 141
22 TraesCS3A01G181200 chr2D 84.407 481 46 13 1 454 480067661 480067183 4.780000e-121 446
23 TraesCS3A01G181200 chr2D 89.818 275 23 5 186 457 514872523 514872251 1.390000e-91 348
24 TraesCS3A01G181200 chr2D 89.455 275 25 4 186 458 465568585 465568313 1.800000e-90 344
25 TraesCS3A01G181200 chr2D 89.189 185 20 0 1 185 479316395 479316211 1.460000e-56 231
26 TraesCS3A01G181200 chr2D 94.059 101 6 0 1601 1701 613097111 613097011 3.250000e-33 154
27 TraesCS3A01G181200 chr2B 90.942 276 20 4 186 459 88357634 88357906 3.830000e-97 366
28 TraesCS3A01G181200 chr2B 99.057 106 1 0 6619 6724 679154991 679155096 2.480000e-44 191
29 TraesCS3A01G181200 chr2B 94.845 97 5 0 1605 1701 440223863 440223767 1.170000e-32 152
30 TraesCS3A01G181200 chr5A 90.370 270 23 2 186 454 532980539 532980806 1.070000e-92 351
31 TraesCS3A01G181200 chr5A 89.189 185 19 1 1 185 575870867 575870684 5.240000e-56 230
32 TraesCS3A01G181200 chr1D 90.370 270 22 3 187 454 483689374 483689641 1.070000e-92 351
33 TraesCS3A01G181200 chr1D 94.949 99 5 0 1603 1701 190767278 190767376 9.030000e-34 156
34 TraesCS3A01G181200 chr5D 90.074 272 23 4 186 454 480455957 480456227 3.860000e-92 350
35 TraesCS3A01G181200 chr5D 95.000 100 5 0 1603 1702 253168142 253168241 2.510000e-34 158
36 TraesCS3A01G181200 chr7A 88.393 224 23 3 1 222 15483369 15483591 4.000000e-67 267
37 TraesCS3A01G181200 chr7A 88.393 224 23 3 1 222 15486199 15486421 4.000000e-67 267
38 TraesCS3A01G181200 chr7A 87.838 222 24 3 3 222 15429677 15429897 2.410000e-64 257
39 TraesCS3A01G181200 chr6B 89.247 186 19 1 1 185 650807001 650807186 1.460000e-56 231
40 TraesCS3A01G181200 chr1B 89.247 186 18 2 1 185 305247133 305246949 1.460000e-56 231
41 TraesCS3A01G181200 chr7B 100.000 104 0 0 6621 6724 130269065 130268962 6.880000e-45 193
42 TraesCS3A01G181200 chr5B 100.000 104 0 0 6621 6724 703089698 703089801 6.880000e-45 193
43 TraesCS3A01G181200 chr4B 100.000 104 0 0 6621 6724 385954573 385954470 6.880000e-45 193
44 TraesCS3A01G181200 chr1A 100.000 104 0 0 6621 6724 60805118 60805015 6.880000e-45 193
45 TraesCS3A01G181200 chr1A 99.038 104 1 0 6621 6724 142903988 142903885 3.200000e-43 187
46 TraesCS3A01G181200 chr6A 97.222 108 3 0 6617 6724 237919285 237919392 4.140000e-42 183
47 TraesCS3A01G181200 chrUn 99.010 101 1 0 6621 6721 136640907 136641007 1.490000e-41 182
48 TraesCS3A01G181200 chr7D 94.175 103 6 0 1604 1706 60439595 60439697 2.510000e-34 158
49 TraesCS3A01G181200 chr7D 95.000 100 5 0 1603 1702 528060319 528060418 2.510000e-34 158
50 TraesCS3A01G181200 chr7D 94.949 99 5 0 1604 1702 83082494 83082396 9.030000e-34 156


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 TraesCS3A01G181200 chr3A 209401060 209407783 6723 False 12417.000000 12417 100.000000 1 6724 1 chr3A.!!$F1 6723
1 TraesCS3A01G181200 chr3D 172018863 172025226 6363 False 2274.500000 6957 93.841750 186 6441 4 chr3D.!!$F5 6255
2 TraesCS3A01G181200 chr3B 250461237 250469844 8607 False 1489.166667 3434 90.184333 454 6422 6 chr3B.!!$F2 5968
3 TraesCS3A01G181200 chr7A 15483369 15486421 3052 False 267.000000 267 88.393000 1 222 2 chr7A.!!$F2 221

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
270 309 0.387239 GCACGAGTTTGATGGTTGCC 60.387 55.000 0.00 0.0 0.00 4.52 F
880 2321 0.615331 CTGCTTAAGAGGCTGGGTGA 59.385 55.000 6.67 0.0 0.00 4.02 F
998 2459 0.739561 ACGTAGCCCAAAACGCAAAA 59.260 45.000 0.00 0.0 42.74 2.44 F
1922 3600 0.968901 TCCCTGTCGGATGCGTACTT 60.969 55.000 6.49 0.0 34.86 2.24 F
2360 4040 1.226746 GGCTGTCACGTTGTTTAGCT 58.773 50.000 0.00 0.0 0.00 3.32 F
2361 4041 2.224090 TGGCTGTCACGTTGTTTAGCTA 60.224 45.455 0.00 0.0 0.00 3.32 F
2362 4042 2.412089 GGCTGTCACGTTGTTTAGCTAG 59.588 50.000 0.00 0.0 0.00 3.42 F
4162 7669 3.255149 CGTTAGAATGGGAGGTAGCGTAT 59.745 47.826 0.00 0.0 0.00 3.06 F
4902 8409 0.763223 ACTGGTCAACTCCCGTCCTT 60.763 55.000 0.00 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1690 3298 0.382515 CGAAAGAGCTACTCCCTCCG 59.617 60.000 0.00 0.0 0.00 4.63 R
2336 4016 0.732571 AACAACGTGACAGCCAACAG 59.267 50.000 0.00 0.0 0.00 3.16 R
2340 4020 0.941542 GCTAAACAACGTGACAGCCA 59.058 50.000 0.00 0.0 0.00 4.75 R
3615 5318 2.353889 CCACACAGAGCTATCAATGTGC 59.646 50.000 10.15 0.0 45.41 4.57 R
4095 7602 3.201290 AGAATCAGCTCTTGCATAACCG 58.799 45.455 0.00 0.0 42.74 4.44 R
4227 7734 4.256110 TCAAAGCCTATGCCGATCATATG 58.744 43.478 0.00 0.0 37.07 1.78 R
4228 7735 4.558226 TCAAAGCCTATGCCGATCATAT 57.442 40.909 0.00 0.0 37.07 1.78 R
5355 8877 0.322975 TCACAGCTTCTGCCTTCCTC 59.677 55.000 0.00 0.0 40.80 3.71 R
6631 11439 0.601057 CCGAAAAGAACGGCCCATTT 59.399 50.000 0.00 0.0 43.74 2.32 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
44 45 5.906113 ATAAAAATATTGTGGGCACGTGA 57.094 34.783 22.23 0.00 0.00 4.35
117 118 7.992608 TGATGTCTGGTTATGCACTAAATATGT 59.007 33.333 0.00 0.00 0.00 2.29
142 143 9.736023 GTTAATAAAACAGGATTTATGAGCTGG 57.264 33.333 0.00 0.00 36.03 4.85
146 147 7.486407 AAAACAGGATTTATGAGCTGGAATT 57.514 32.000 0.00 0.00 0.00 2.17
160 161 4.593206 AGCTGGAATTAGTAATCCATCCGA 59.407 41.667 11.92 1.74 44.41 4.55
174 175 3.259625 TCCATCCGATTATGCCATCGTAA 59.740 43.478 8.66 0.00 43.86 3.18
208 210 2.921834 TAGCTACCAAGTGAGGAGGT 57.078 50.000 0.00 0.00 39.41 3.85
238 276 2.680352 GAGACAGAGGCGGACCCA 60.680 66.667 0.00 0.00 36.11 4.51
248 286 0.960861 GGCGGACCCAGAGGAAAAAG 60.961 60.000 0.00 0.00 36.73 2.27
260 299 2.879026 GAGGAAAAAGAGGCACGAGTTT 59.121 45.455 0.00 0.00 0.00 2.66
270 309 0.387239 GCACGAGTTTGATGGTTGCC 60.387 55.000 0.00 0.00 0.00 4.52
289 328 2.582436 CCACGCCGACTAACCCAT 59.418 61.111 0.00 0.00 0.00 4.00
324 363 3.274067 GGGACAAACATGACCCGC 58.726 61.111 0.00 0.00 34.42 6.13
343 382 1.270358 GCGAGAAGACCACAACTCCTT 60.270 52.381 0.00 0.00 0.00 3.36
347 386 4.709250 GAGAAGACCACAACTCCTTTCTT 58.291 43.478 0.00 0.00 0.00 2.52
369 408 1.106944 TCGCACCGCTATGGAGATCA 61.107 55.000 0.00 0.00 42.00 2.92
382 421 7.120285 CGCTATGGAGATCATTTTTATGGACAT 59.880 37.037 0.00 0.00 37.30 3.06
409 448 6.769822 TCAATTATCTCTTCCATTGCTTCTCC 59.230 38.462 0.00 0.00 0.00 3.71
429 468 4.037927 TCCCAAAGAAATATCTCTCCCGT 58.962 43.478 0.00 0.00 33.77 5.28
450 489 1.800032 CAACGCACGGGCATATGTT 59.200 52.632 11.77 1.88 41.24 2.71
466 542 9.422681 GGGCATATGTTCTAATAGTCTCCTATA 57.577 37.037 4.29 0.00 32.57 1.31
477 553 1.912043 GTCTCCTATATGGGCTGGCAT 59.088 52.381 0.00 0.00 36.20 4.40
506 582 4.501285 TCCCCGCCGTCTCGAGAT 62.501 66.667 19.90 0.00 0.00 2.75
533 609 6.915590 CTTCTAGAAGGTTGGTTTTTCCAGGA 60.916 42.308 22.67 0.00 39.84 3.86
585 1547 4.202111 TGTTTTTCTGCTAGGTTTTGCTCC 60.202 41.667 0.00 0.00 0.00 4.70
589 1551 0.685097 TGCTAGGTTTTGCTCCGTCT 59.315 50.000 0.00 0.00 0.00 4.18
786 2192 4.088762 CCGCATGTGTCACGTGGC 62.089 66.667 23.42 14.58 35.71 5.01
839 2246 9.406113 GAGTTTATCCCTTACTAGTAGTTGAGA 57.594 37.037 8.40 1.65 0.00 3.27
840 2247 9.765295 AGTTTATCCCTTACTAGTAGTTGAGAA 57.235 33.333 8.40 2.14 0.00 2.87
842 2249 6.718522 ATCCCTTACTAGTAGTTGAGAAGC 57.281 41.667 8.40 0.00 0.00 3.86
843 2250 4.639310 TCCCTTACTAGTAGTTGAGAAGCG 59.361 45.833 8.40 0.00 0.00 4.68
880 2321 0.615331 CTGCTTAAGAGGCTGGGTGA 59.385 55.000 6.67 0.00 0.00 4.02
907 2348 0.892063 TTATGGAAAAGCCGCCCAAC 59.108 50.000 0.00 0.00 40.66 3.77
998 2459 0.739561 ACGTAGCCCAAAACGCAAAA 59.260 45.000 0.00 0.00 42.74 2.44
1042 2503 1.648302 CCTCCAGCCCCATTGATCCA 61.648 60.000 0.00 0.00 0.00 3.41
1113 2576 4.914420 CTCGCGGCTACCTGCTCG 62.914 72.222 6.13 0.00 42.39 5.03
1381 2844 2.158769 CCCATCATTGGATTCGAGGTGA 60.159 50.000 0.00 0.00 46.92 4.02
1393 2856 2.032681 AGGTGAGTTCTTGCGCCC 59.967 61.111 4.18 0.00 35.28 6.13
1394 2857 2.032681 GGTGAGTTCTTGCGCCCT 59.967 61.111 4.18 0.00 0.00 5.19
1606 3214 4.501071 TCACGACTTTAGCTGGGAAATAC 58.499 43.478 0.00 0.00 0.00 1.89
1607 3215 4.222145 TCACGACTTTAGCTGGGAAATACT 59.778 41.667 0.00 0.00 0.00 2.12
1608 3216 4.567159 CACGACTTTAGCTGGGAAATACTC 59.433 45.833 0.00 0.00 0.00 2.59
1609 3217 4.120589 CGACTTTAGCTGGGAAATACTCC 58.879 47.826 0.00 0.00 44.54 3.85
1618 3226 2.616634 GGAAATACTCCCTCCGTTCC 57.383 55.000 0.00 0.00 38.44 3.62
1619 3227 1.835531 GGAAATACTCCCTCCGTTCCA 59.164 52.381 0.00 0.00 38.44 3.53
1620 3228 2.237893 GGAAATACTCCCTCCGTTCCAA 59.762 50.000 0.00 0.00 38.44 3.53
1621 3229 3.307904 GGAAATACTCCCTCCGTTCCAAA 60.308 47.826 0.00 0.00 38.44 3.28
1622 3230 4.329392 GAAATACTCCCTCCGTTCCAAAA 58.671 43.478 0.00 0.00 0.00 2.44
1623 3231 4.586306 AATACTCCCTCCGTTCCAAAAT 57.414 40.909 0.00 0.00 0.00 1.82
1624 3232 5.703730 AATACTCCCTCCGTTCCAAAATA 57.296 39.130 0.00 0.00 0.00 1.40
1625 3233 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
1626 3234 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
1627 3235 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
1628 3236 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
1629 3237 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
1630 3238 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
1631 3239 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
1632 3240 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
1633 3241 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
1634 3242 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
1635 3243 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
1636 3244 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
1637 3245 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
1638 3246 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
1639 3247 7.094549 CGTTCCAAAATAGATGACCCAACTTTA 60.095 37.037 0.00 0.00 0.00 1.85
1640 3248 8.749354 GTTCCAAAATAGATGACCCAACTTTAT 58.251 33.333 0.00 0.00 0.00 1.40
1641 3249 9.983024 TTCCAAAATAGATGACCCAACTTTATA 57.017 29.630 0.00 0.00 0.00 0.98
1642 3250 9.403583 TCCAAAATAGATGACCCAACTTTATAC 57.596 33.333 0.00 0.00 0.00 1.47
1643 3251 9.408648 CCAAAATAGATGACCCAACTTTATACT 57.591 33.333 0.00 0.00 0.00 2.12
1650 3258 9.838339 AGATGACCCAACTTTATACTAAGATTG 57.162 33.333 0.00 0.00 0.00 2.67
1651 3259 9.614792 GATGACCCAACTTTATACTAAGATTGT 57.385 33.333 0.00 0.00 0.00 2.71
1653 3261 9.880157 TGACCCAACTTTATACTAAGATTGTAC 57.120 33.333 0.00 0.00 0.00 2.90
1691 3299 9.107367 GAAAGTTGAGTCATCTATTTTGAAACG 57.893 33.333 4.14 0.00 0.00 3.60
1692 3300 7.133891 AGTTGAGTCATCTATTTTGAAACGG 57.866 36.000 1.70 0.00 0.00 4.44
1693 3301 6.934645 AGTTGAGTCATCTATTTTGAAACGGA 59.065 34.615 1.70 0.00 0.00 4.69
1694 3302 6.968131 TGAGTCATCTATTTTGAAACGGAG 57.032 37.500 0.00 0.00 0.00 4.63
1695 3303 5.874810 TGAGTCATCTATTTTGAAACGGAGG 59.125 40.000 0.00 0.00 0.00 4.30
1696 3304 5.186198 AGTCATCTATTTTGAAACGGAGGG 58.814 41.667 0.00 0.00 0.00 4.30
1697 3305 5.045869 AGTCATCTATTTTGAAACGGAGGGA 60.046 40.000 0.00 0.00 0.00 4.20
1698 3306 5.294552 GTCATCTATTTTGAAACGGAGGGAG 59.705 44.000 0.00 0.00 0.00 4.30
1699 3307 4.903045 TCTATTTTGAAACGGAGGGAGT 57.097 40.909 0.00 0.00 0.00 3.85
1700 3308 6.155565 TCATCTATTTTGAAACGGAGGGAGTA 59.844 38.462 0.00 0.00 0.00 2.59
1922 3600 0.968901 TCCCTGTCGGATGCGTACTT 60.969 55.000 6.49 0.00 34.86 2.24
1951 3629 6.100404 ACAACATTGCAGAATACCACATTT 57.900 33.333 0.00 0.00 0.00 2.32
2009 3687 8.426489 GGTTCAGTCTTATATGGTTGGTGTATA 58.574 37.037 0.00 0.00 0.00 1.47
2076 3754 7.069455 TCACTCTGTGCTATTGCTATAAACCTA 59.931 37.037 0.00 0.00 40.48 3.08
2257 3935 4.194640 ACAACACTATGAATGCTGCCTAG 58.805 43.478 0.00 0.00 0.00 3.02
2276 3954 8.263940 TGCCTAGTTCTAATTGATTTGTGTAC 57.736 34.615 0.00 0.00 0.00 2.90
2336 4016 3.119955 GCTGTTGAATTTTCGGACCCTAC 60.120 47.826 0.00 0.00 0.00 3.18
2340 4020 4.360951 TGAATTTTCGGACCCTACTGTT 57.639 40.909 0.00 0.00 0.00 3.16
2360 4040 1.226746 GGCTGTCACGTTGTTTAGCT 58.773 50.000 0.00 0.00 0.00 3.32
2361 4041 2.224090 TGGCTGTCACGTTGTTTAGCTA 60.224 45.455 0.00 0.00 0.00 3.32
2362 4042 2.412089 GGCTGTCACGTTGTTTAGCTAG 59.588 50.000 0.00 0.00 0.00 3.42
2496 4176 9.485206 ACATATTGTCCTCGGTGTTATATAAAC 57.515 33.333 0.00 0.00 0.00 2.01
2628 4311 8.893727 GCACCAAGATTAACACACTATTTAGAT 58.106 33.333 0.00 0.00 0.00 1.98
2848 4535 7.780271 ACCATGTTTTAGAAAGTTTCTCCTCTT 59.220 33.333 21.25 6.91 41.14 2.85
2860 4547 4.963318 TTCTCCTCTTTCAGTCATGTGT 57.037 40.909 0.00 0.00 0.00 3.72
2989 4676 6.814954 ACTACATCTATGTTGGACCTCATT 57.185 37.500 0.12 0.00 41.97 2.57
3026 4713 4.129380 TGTTTGGATGTGTCTCTGAACAG 58.871 43.478 0.00 0.00 0.00 3.16
3082 4776 9.853555 CTTCATTTGTTTGCAACACCTTATATA 57.146 29.630 0.00 0.00 41.97 0.86
3159 4853 3.598299 ACATGCCCAACATAAATTGCAC 58.402 40.909 0.00 0.00 36.64 4.57
3222 4916 7.377398 TGTAAATTTGTTGCACAATAGATGCT 58.623 30.769 0.00 0.00 43.77 3.79
3227 4921 3.989167 TGTTGCACAATAGATGCTTTTGC 59.011 39.130 0.00 0.00 43.77 3.68
3270 4971 8.070171 GTCAGCGTTTTTCTTGTATGCATATAT 58.930 33.333 10.16 0.00 0.00 0.86
3307 5008 6.205658 AGACCTACTTCTTGCTTGTTTTGATC 59.794 38.462 0.00 0.00 0.00 2.92
3595 5298 5.807909 TGAGGAATCATGTGTTCTGAATCA 58.192 37.500 11.46 0.00 0.00 2.57
3631 5334 4.127907 AGACATGCACATTGATAGCTCTG 58.872 43.478 0.00 0.00 0.00 3.35
3632 5335 3.875727 GACATGCACATTGATAGCTCTGT 59.124 43.478 0.00 0.00 0.00 3.41
3771 5476 6.270695 AGGACATTCATGAAACTTTTCCCATT 59.729 34.615 13.09 0.00 36.36 3.16
3825 5530 7.500227 CCCACATGATACTGAACTACAAATGAT 59.500 37.037 0.00 0.00 0.00 2.45
3956 7463 5.659440 ATACCAATGTTGTTCCATTCACC 57.341 39.130 0.00 0.00 32.81 4.02
3984 7491 3.933332 AGTCTGTAAGCTTTCAATACCGC 59.067 43.478 3.20 0.00 0.00 5.68
4009 7516 8.837389 GCGAAGAGTATAGGTTTCCAAATATTT 58.163 33.333 0.00 0.00 0.00 1.40
4162 7669 3.255149 CGTTAGAATGGGAGGTAGCGTAT 59.745 47.826 0.00 0.00 0.00 3.06
4219 7726 5.649782 AGACAATGCATTCTCCGATTTTT 57.350 34.783 9.53 0.00 0.00 1.94
4227 7734 9.736023 AATGCATTCTCCGATTTTTCTTTATAC 57.264 29.630 5.99 0.00 0.00 1.47
4228 7735 8.275015 TGCATTCTCCGATTTTTCTTTATACA 57.725 30.769 0.00 0.00 0.00 2.29
4454 7961 3.131709 TGGAAGCTCCAGAACAGAAAG 57.868 47.619 1.25 0.00 42.67 2.62
4682 8189 3.048600 AGCTTAGGCATCCACTGGATTA 58.951 45.455 7.95 0.00 40.98 1.75
4730 8237 8.631797 TGTCATGCATATGCTTTATTATTGTGT 58.368 29.630 27.13 0.00 42.66 3.72
4785 8292 9.877178 ATACTAGTTATAATGCTGGAAGTATGC 57.123 33.333 0.00 0.00 38.77 3.14
4792 8299 3.535280 TGCTGGAAGTATGCGATAACA 57.465 42.857 0.00 0.00 35.30 2.41
4887 8394 7.557719 AGGAAATTTCATCAGGTAACATACTGG 59.442 37.037 19.49 0.00 41.41 4.00
4902 8409 0.763223 ACTGGTCAACTCCCGTCCTT 60.763 55.000 0.00 0.00 0.00 3.36
4906 8413 2.027561 TGGTCAACTCCCGTCCTTAATG 60.028 50.000 0.00 0.00 0.00 1.90
5024 8531 5.505173 AGGAACTGTGTCAGAAAAACATG 57.495 39.130 3.70 0.00 37.18 3.21
5051 8558 2.302733 TCAAGCTGCCTGTGTTGATCTA 59.697 45.455 0.00 0.00 0.00 1.98
5106 8613 6.041523 AGCTAAAGAACAGTATGATCTCCCTC 59.958 42.308 0.00 0.00 45.88 4.30
5158 8680 5.769662 TCTCTTTATGAGTTGTGTGCCAAAT 59.230 36.000 0.00 0.00 43.13 2.32
5355 8877 5.366460 AGATGTTTCTGCAGATACAGATGG 58.634 41.667 33.34 1.35 45.75 3.51
5758 9659 3.443099 GGCTTGATTGATTGCCTTACC 57.557 47.619 0.00 0.00 41.92 2.85
5826 9727 1.202031 CGAAAACTTAGCATGGGACGC 60.202 52.381 0.00 0.00 0.00 5.19
5829 9730 0.328258 AACTTAGCATGGGACGCCTT 59.672 50.000 0.00 0.00 0.00 4.35
5830 9731 0.392998 ACTTAGCATGGGACGCCTTG 60.393 55.000 0.00 0.00 0.00 3.61
5832 9733 1.558167 TTAGCATGGGACGCCTTGGA 61.558 55.000 0.00 0.00 0.00 3.53
5833 9734 1.971505 TAGCATGGGACGCCTTGGAG 61.972 60.000 0.00 0.00 0.00 3.86
5846 9764 3.243724 GCCTTGGAGTAGATGATACCCT 58.756 50.000 0.00 0.00 0.00 4.34
5851 9769 5.397553 TGGAGTAGATGATACCCTGTGTA 57.602 43.478 0.00 0.00 0.00 2.90
5884 9802 9.284131 AGGGAATTCATAGTAATATGCAGGATA 57.716 33.333 7.93 0.00 0.00 2.59
6064 10846 3.855858 TGTGGTTTGTGCCTTCTTTTTC 58.144 40.909 0.00 0.00 0.00 2.29
6076 10858 6.420903 GTGCCTTCTTTTTCCAGTAAAATGAC 59.579 38.462 0.00 0.00 39.57 3.06
6105 10887 3.628032 TGTGTTCCGTTTCTTGTGCAATA 59.372 39.130 0.00 0.00 0.00 1.90
6167 10949 6.888632 AGTATTCTCAGCATTCCAATTTCACT 59.111 34.615 0.00 0.00 0.00 3.41
6190 10972 6.929606 ACTTGTGAACAACCATTAGTAGAGAC 59.070 38.462 0.00 0.00 0.00 3.36
6194 10976 7.094075 TGTGAACAACCATTAGTAGAGACGTAT 60.094 37.037 0.00 0.00 0.00 3.06
6195 10977 7.431668 GTGAACAACCATTAGTAGAGACGTATC 59.568 40.741 0.86 0.86 0.00 2.24
6196 10978 7.121611 TGAACAACCATTAGTAGAGACGTATCA 59.878 37.037 13.45 0.00 0.00 2.15
6197 10979 7.028926 ACAACCATTAGTAGAGACGTATCAG 57.971 40.000 13.45 0.00 0.00 2.90
6198 10980 6.039493 ACAACCATTAGTAGAGACGTATCAGG 59.961 42.308 13.45 4.97 0.00 3.86
6227 11009 5.007724 GTGCCTACTACTTATTGACATTGGC 59.992 44.000 0.00 0.00 36.38 4.52
6295 11080 1.212751 GCCTTGTTCATTCCCGTGC 59.787 57.895 0.00 0.00 0.00 5.34
6388 11190 6.114089 AGATGGATGAGACATTTCTTCAGTG 58.886 40.000 0.00 0.00 29.47 3.66
6442 11250 9.660180 AAATGGTGTTAAACAAATTTGTACTGT 57.340 25.926 23.53 11.96 41.31 3.55
6465 11273 8.378172 TGTATATAACAGAATAGGCAAGTTGC 57.622 34.615 19.87 19.87 36.72 4.17
6466 11274 8.210946 TGTATATAACAGAATAGGCAAGTTGCT 58.789 33.333 26.16 14.95 37.26 3.91
6467 11275 9.706691 GTATATAACAGAATAGGCAAGTTGCTA 57.293 33.333 26.16 16.50 44.28 3.49
6471 11279 9.799106 ATAACAGAATAGGCAAGTTGCTATATT 57.201 29.630 26.16 25.78 44.28 1.28
6474 11282 9.442047 ACAGAATAGGCAAGTTGCTATATTATC 57.558 33.333 26.16 17.69 44.28 1.75
6494 11302 7.953005 TTATCAAAACATAAAGCATGGAGGA 57.047 32.000 0.00 0.00 39.13 3.71
6495 11303 8.537728 TTATCAAAACATAAAGCATGGAGGAT 57.462 30.769 0.00 0.00 39.13 3.24
6496 11304 6.211587 TCAAAACATAAAGCATGGAGGATG 57.788 37.500 0.00 0.00 39.13 3.51
6498 11306 3.959495 ACATAAAGCATGGAGGATGGT 57.041 42.857 0.00 0.00 44.97 3.55
6499 11307 5.387113 AACATAAAGCATGGAGGATGGTA 57.613 39.130 0.00 0.00 42.13 3.25
6500 11308 4.978099 ACATAAAGCATGGAGGATGGTAG 58.022 43.478 0.00 0.00 42.13 3.18
6501 11309 4.413520 ACATAAAGCATGGAGGATGGTAGT 59.586 41.667 0.00 0.00 42.13 2.73
6503 11311 6.273260 ACATAAAGCATGGAGGATGGTAGTAT 59.727 38.462 0.00 0.00 42.13 2.12
6504 11312 4.630644 AAGCATGGAGGATGGTAGTATG 57.369 45.455 0.00 0.00 42.13 2.39
6506 11314 3.837146 AGCATGGAGGATGGTAGTATGAG 59.163 47.826 0.00 0.00 41.13 2.90
6507 11315 3.618507 GCATGGAGGATGGTAGTATGAGC 60.619 52.174 0.00 0.00 31.99 4.26
6508 11316 3.328535 TGGAGGATGGTAGTATGAGCA 57.671 47.619 0.00 0.00 0.00 4.26
6510 11318 3.388024 TGGAGGATGGTAGTATGAGCAAC 59.612 47.826 0.00 0.00 0.00 4.17
6512 11320 4.040952 GGAGGATGGTAGTATGAGCAACAT 59.959 45.833 2.31 2.31 42.39 2.71
6514 11322 6.070538 GGAGGATGGTAGTATGAGCAACATAT 60.071 42.308 6.84 1.32 42.42 1.78
6515 11323 6.940739 AGGATGGTAGTATGAGCAACATATC 58.059 40.000 6.84 1.95 42.42 1.63
6517 11325 7.016563 AGGATGGTAGTATGAGCAACATATCAA 59.983 37.037 6.84 0.00 42.42 2.57
6518 11326 7.826252 GGATGGTAGTATGAGCAACATATCAAT 59.174 37.037 6.84 2.21 42.42 2.57
6519 11327 7.967890 TGGTAGTATGAGCAACATATCAATG 57.032 36.000 6.84 0.00 42.42 2.82
6589 11397 9.597999 GAAAACAAATTCACATATCAAAAAGGC 57.402 29.630 0.00 0.00 0.00 4.35
6591 11399 8.851541 AACAAATTCACATATCAAAAAGGCAT 57.148 26.923 0.00 0.00 0.00 4.40
6612 11420 6.846350 GCATATGCCCTTTACATAGATTGAC 58.154 40.000 17.26 0.00 33.69 3.18
6613 11421 6.430925 GCATATGCCCTTTACATAGATTGACA 59.569 38.462 17.26 0.00 33.69 3.58
6614 11422 7.121759 GCATATGCCCTTTACATAGATTGACAT 59.878 37.037 17.26 0.00 33.69 3.06
6615 11423 6.889301 ATGCCCTTTACATAGATTGACATG 57.111 37.500 0.00 0.00 0.00 3.21
6616 11424 5.132502 TGCCCTTTACATAGATTGACATGG 58.867 41.667 0.00 0.00 0.00 3.66
6618 11426 5.827797 GCCCTTTACATAGATTGACATGGAA 59.172 40.000 0.00 0.00 0.00 3.53
6619 11427 6.491403 GCCCTTTACATAGATTGACATGGAAT 59.509 38.462 0.00 0.00 0.00 3.01
6620 11428 7.014615 GCCCTTTACATAGATTGACATGGAATT 59.985 37.037 0.00 0.00 0.00 2.17
6621 11429 9.573166 CCCTTTACATAGATTGACATGGAATTA 57.427 33.333 0.00 0.00 0.00 1.40
6627 11435 9.445878 ACATAGATTGACATGGAATTATAGCTG 57.554 33.333 0.00 0.00 0.00 4.24
6629 11437 5.709164 AGATTGACATGGAATTATAGCTGGC 59.291 40.000 0.00 0.00 0.00 4.85
6630 11438 3.754965 TGACATGGAATTATAGCTGGCC 58.245 45.455 0.00 0.00 0.00 5.36
6631 11439 3.138098 TGACATGGAATTATAGCTGGCCA 59.862 43.478 4.71 4.71 0.00 5.36
6632 11440 4.144297 GACATGGAATTATAGCTGGCCAA 58.856 43.478 7.01 0.00 0.00 4.52
6633 11441 4.545678 ACATGGAATTATAGCTGGCCAAA 58.454 39.130 7.01 0.00 0.00 3.28
6635 11443 5.011329 ACATGGAATTATAGCTGGCCAAATG 59.989 40.000 7.01 0.00 0.00 2.32
6637 11445 3.259123 GGAATTATAGCTGGCCAAATGGG 59.741 47.826 7.01 0.00 40.85 4.00
6648 11456 2.078849 CCAAATGGGCCGTTCTTTTC 57.921 50.000 12.25 0.00 0.00 2.29
6649 11457 1.668628 CCAAATGGGCCGTTCTTTTCG 60.669 52.381 12.25 0.00 0.00 3.46
6654 11462 4.097863 GCCGTTCTTTTCGGGCCG 62.098 66.667 22.51 22.51 46.90 6.13
6655 11463 3.428282 CCGTTCTTTTCGGGCCGG 61.428 66.667 27.98 10.15 43.68 6.13
6657 11465 3.744719 GTTCTTTTCGGGCCGGCC 61.745 66.667 38.57 38.57 0.00 6.13
6718 11526 4.825252 CGGTCTAAACGGGCCGGG 62.825 72.222 31.78 16.63 40.45 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 6.587990 TCACGTGCCCACAATATTTTTATTTG 59.412 34.615 11.67 0.00 0.00 2.32
29 30 1.739929 CGCTCACGTGCCCACAATA 60.740 57.895 11.67 0.00 33.53 1.90
117 118 9.693739 TCCAGCTCATAAATCCTGTTTTATTAA 57.306 29.630 0.00 0.00 31.08 1.40
122 123 7.486407 AATTCCAGCTCATAAATCCTGTTTT 57.514 32.000 0.00 0.00 0.00 2.43
137 138 4.593206 TCGGATGGATTACTAATTCCAGCT 59.407 41.667 7.10 0.00 38.56 4.24
160 161 6.169094 CCATTCTCTCTTACGATGGCATAAT 58.831 40.000 0.00 0.00 0.00 1.28
174 175 1.047002 AGCTATGCGCCATTCTCTCT 58.953 50.000 4.18 0.00 40.39 3.10
181 182 0.469917 ACTTGGTAGCTATGCGCCAT 59.530 50.000 4.18 0.63 37.98 4.40
199 201 2.290134 GGGGTTTTGTCTACCTCCTCAC 60.290 54.545 0.00 0.00 35.92 3.51
208 210 2.561419 CTCTGTCTCGGGGTTTTGTCTA 59.439 50.000 0.00 0.00 0.00 2.59
238 276 1.694696 ACTCGTGCCTCTTTTTCCTCT 59.305 47.619 0.00 0.00 0.00 3.69
248 286 1.197721 CAACCATCAAACTCGTGCCTC 59.802 52.381 0.00 0.00 0.00 4.70
289 328 3.632604 GTCCCGTGAGATCTTGATAGTGA 59.367 47.826 0.00 0.00 0.00 3.41
324 363 2.821991 AAGGAGTTGTGGTCTTCTCG 57.178 50.000 0.00 0.00 0.00 4.04
343 382 1.075542 CATAGCGGTGCGACAAAGAA 58.924 50.000 0.00 0.00 0.00 2.52
347 386 1.153647 CTCCATAGCGGTGCGACAA 60.154 57.895 0.00 0.00 35.57 3.18
382 421 9.499479 GAGAAGCAATGGAAGAGATAATTGATA 57.501 33.333 0.00 0.00 32.86 2.15
396 435 3.524095 TTCTTTGGGAGAAGCAATGGA 57.476 42.857 0.00 0.00 39.44 3.41
409 448 4.035675 GCAACGGGAGAGATATTTCTTTGG 59.964 45.833 0.00 0.00 30.30 3.28
429 468 2.043405 ATATGCCCGTGCGTTGCAA 61.043 52.632 0.00 0.00 41.47 4.08
439 478 5.186021 AGGAGACTATTAGAACATATGCCCG 59.814 44.000 1.58 0.00 40.61 6.13
466 542 2.050754 ATCTACCTATGCCAGCCCAT 57.949 50.000 0.00 0.00 0.00 4.00
477 553 1.139455 CGGCGGGGAAAAATCTACCTA 59.861 52.381 0.00 0.00 0.00 3.08
570 646 0.685097 AGACGGAGCAAAACCTAGCA 59.315 50.000 0.00 0.00 0.00 3.49
585 1547 5.583969 AAACACAAAAACCAAACAAGACG 57.416 34.783 0.00 0.00 0.00 4.18
693 2098 8.877808 AGAAAATTCTCGCAGAAAAAGAAATT 57.122 26.923 3.27 0.00 37.82 1.82
694 2099 8.877808 AAGAAAATTCTCGCAGAAAAAGAAAT 57.122 26.923 0.00 0.00 37.82 2.17
696 2101 8.702163 AAAAGAAAATTCTCGCAGAAAAAGAA 57.298 26.923 0.00 0.00 37.82 2.52
697 2102 9.796120 TTAAAAGAAAATTCTCGCAGAAAAAGA 57.204 25.926 0.00 0.00 37.82 2.52
764 2170 0.032952 ACGTGACACATGCGGTAAGT 59.967 50.000 6.37 0.00 0.00 2.24
771 2177 4.088762 CGGCCACGTGACACATGC 62.089 66.667 19.30 10.55 34.81 4.06
859 2266 1.300963 CCCAGCCTCTTAAGCAGCA 59.699 57.895 16.00 0.00 0.00 4.41
907 2348 1.500396 GCGTTTAAGGCCCAGTTCG 59.500 57.895 0.00 0.34 0.00 3.95
952 2393 7.025963 GGTCATTAAATGCTTTCAACAGAGAG 58.974 38.462 0.00 0.00 0.00 3.20
953 2394 6.716628 AGGTCATTAAATGCTTTCAACAGAGA 59.283 34.615 0.00 0.00 0.00 3.10
954 2395 6.917533 AGGTCATTAAATGCTTTCAACAGAG 58.082 36.000 0.00 0.00 0.00 3.35
955 2396 6.899393 AGGTCATTAAATGCTTTCAACAGA 57.101 33.333 0.00 0.00 0.00 3.41
956 2397 6.742718 CGTAGGTCATTAAATGCTTTCAACAG 59.257 38.462 0.00 0.00 0.00 3.16
1381 2844 1.490574 ATAGAGAGGGCGCAAGAACT 58.509 50.000 10.83 5.28 43.02 3.01
1393 2856 6.100004 TCAGCGTCCTAAAAACAATAGAGAG 58.900 40.000 0.00 0.00 0.00 3.20
1394 2857 6.032956 TCAGCGTCCTAAAAACAATAGAGA 57.967 37.500 0.00 0.00 0.00 3.10
1432 2897 2.708325 GGCCCTAATTGTCTCCTCAGAT 59.292 50.000 0.00 0.00 0.00 2.90
1561 3169 9.754382 GTGATGATGCAGGAATAATTTGTAAAT 57.246 29.630 0.00 0.00 0.00 1.40
1606 3214 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
1607 3215 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
1608 3216 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
1609 3217 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
1610 3218 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
1611 3219 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
1612 3220 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
1613 3221 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
1614 3222 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
1615 3223 8.893563 ATAAAGTTGGGTCATCTATTTTGGAA 57.106 30.769 0.00 0.00 0.00 3.53
1616 3224 9.403583 GTATAAAGTTGGGTCATCTATTTTGGA 57.596 33.333 0.00 0.00 0.00 3.53
1617 3225 9.408648 AGTATAAAGTTGGGTCATCTATTTTGG 57.591 33.333 0.00 0.00 0.00 3.28
1624 3232 9.838339 CAATCTTAGTATAAAGTTGGGTCATCT 57.162 33.333 0.00 0.00 0.00 2.90
1625 3233 9.614792 ACAATCTTAGTATAAAGTTGGGTCATC 57.385 33.333 0.00 0.00 0.00 2.92
1627 3235 9.880157 GTACAATCTTAGTATAAAGTTGGGTCA 57.120 33.333 0.00 0.00 0.00 4.02
1665 3273 9.107367 CGTTTCAAAATAGATGACTCAACTTTC 57.893 33.333 0.00 0.00 0.00 2.62
1666 3274 8.076178 CCGTTTCAAAATAGATGACTCAACTTT 58.924 33.333 0.00 0.00 0.00 2.66
1667 3275 7.444183 TCCGTTTCAAAATAGATGACTCAACTT 59.556 33.333 0.00 0.00 0.00 2.66
1668 3276 6.934645 TCCGTTTCAAAATAGATGACTCAACT 59.065 34.615 0.00 0.00 0.00 3.16
1669 3277 7.129109 TCCGTTTCAAAATAGATGACTCAAC 57.871 36.000 0.00 0.00 0.00 3.18
1670 3278 6.371548 CCTCCGTTTCAAAATAGATGACTCAA 59.628 38.462 0.00 0.00 0.00 3.02
1671 3279 5.874810 CCTCCGTTTCAAAATAGATGACTCA 59.125 40.000 0.00 0.00 0.00 3.41
1672 3280 5.294552 CCCTCCGTTTCAAAATAGATGACTC 59.705 44.000 0.00 0.00 0.00 3.36
1673 3281 5.045869 TCCCTCCGTTTCAAAATAGATGACT 60.046 40.000 0.00 0.00 0.00 3.41
1674 3282 5.183228 TCCCTCCGTTTCAAAATAGATGAC 58.817 41.667 0.00 0.00 0.00 3.06
1675 3283 5.045869 ACTCCCTCCGTTTCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
1676 3284 5.186198 ACTCCCTCCGTTTCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
1677 3285 5.437191 ACTCCCTCCGTTTCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
1678 3286 4.903045 ACTCCCTCCGTTTCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
1679 3287 4.571176 GCTACTCCCTCCGTTTCAAAATAG 59.429 45.833 0.00 0.00 0.00 1.73
1680 3288 4.224370 AGCTACTCCCTCCGTTTCAAAATA 59.776 41.667 0.00 0.00 0.00 1.40
1681 3289 3.009143 AGCTACTCCCTCCGTTTCAAAAT 59.991 43.478 0.00 0.00 0.00 1.82
1682 3290 2.370849 AGCTACTCCCTCCGTTTCAAAA 59.629 45.455 0.00 0.00 0.00 2.44
1683 3291 1.975680 AGCTACTCCCTCCGTTTCAAA 59.024 47.619 0.00 0.00 0.00 2.69
1684 3292 1.549170 GAGCTACTCCCTCCGTTTCAA 59.451 52.381 0.00 0.00 0.00 2.69
1685 3293 1.183549 GAGCTACTCCCTCCGTTTCA 58.816 55.000 0.00 0.00 0.00 2.69
1686 3294 1.476477 AGAGCTACTCCCTCCGTTTC 58.524 55.000 0.00 0.00 0.00 2.78
1687 3295 1.939980 AAGAGCTACTCCCTCCGTTT 58.060 50.000 0.00 0.00 0.00 3.60
1688 3296 1.826096 GAAAGAGCTACTCCCTCCGTT 59.174 52.381 0.00 0.00 0.00 4.44
1689 3297 1.476477 GAAAGAGCTACTCCCTCCGT 58.524 55.000 0.00 0.00 0.00 4.69
1690 3298 0.382515 CGAAAGAGCTACTCCCTCCG 59.617 60.000 0.00 0.00 0.00 4.63
1691 3299 1.765230 TCGAAAGAGCTACTCCCTCC 58.235 55.000 0.00 0.00 34.84 4.30
1750 3358 2.091720 ACAGCTCCCAATTGCATATGGA 60.092 45.455 17.48 0.00 39.12 3.41
1887 3565 6.021596 CGACAGGGAAAATTTATTTCAGACG 58.978 40.000 0.00 0.00 0.00 4.18
1922 3600 2.079170 TTCTGCAATGTTGTTCCCCA 57.921 45.000 0.00 0.00 0.00 4.96
1951 3629 5.399991 TGAGTCCTTTCTTCTGGGTAACTA 58.600 41.667 0.00 0.00 0.00 2.24
2172 3850 2.870175 TGGTTCAACGTTGATCCCATT 58.130 42.857 37.47 0.45 43.32 3.16
2231 3909 4.437930 GGCAGCATTCATAGTGTTGTTCTC 60.438 45.833 0.00 0.00 31.44 2.87
2293 3972 5.120674 CAGCGTCTTCATCAAACAATACAGA 59.879 40.000 0.00 0.00 0.00 3.41
2313 3992 1.401018 GGGTCCGAAAATTCAACAGCG 60.401 52.381 0.00 0.00 0.00 5.18
2336 4016 0.732571 AACAACGTGACAGCCAACAG 59.267 50.000 0.00 0.00 0.00 3.16
2340 4020 0.941542 GCTAAACAACGTGACAGCCA 59.058 50.000 0.00 0.00 0.00 4.75
2513 4193 3.696045 TGGTTGCACCTGCTTATACAAT 58.304 40.909 6.83 0.00 39.58 2.71
2514 4194 3.147553 TGGTTGCACCTGCTTATACAA 57.852 42.857 6.83 0.00 39.58 2.41
2515 4195 2.869101 TGGTTGCACCTGCTTATACA 57.131 45.000 6.83 0.00 39.58 2.29
2516 4196 4.638421 TGTAATGGTTGCACCTGCTTATAC 59.362 41.667 6.83 0.00 39.58 1.47
2517 4197 4.849518 TGTAATGGTTGCACCTGCTTATA 58.150 39.130 6.83 0.35 39.58 0.98
2518 4198 3.696045 TGTAATGGTTGCACCTGCTTAT 58.304 40.909 6.83 0.00 39.58 1.73
2523 4203 5.138125 AGATTTTGTAATGGTTGCACCTG 57.862 39.130 6.83 0.00 39.58 4.00
2628 4311 8.319057 ACCACCTCTAGTCATACAATTGAATA 57.681 34.615 13.59 0.00 0.00 1.75
2781 4465 2.418280 TGTGCATGGTGCTAATACAACG 59.582 45.455 3.41 0.00 45.31 4.10
2848 4535 3.638627 AGAGAGTGTGACACATGACTGAA 59.361 43.478 18.95 0.00 36.74 3.02
2860 4547 2.354103 GCACTGGCATTAGAGAGTGTGA 60.354 50.000 0.00 0.00 38.47 3.58
2989 4676 7.012610 CACATCCAAACATATCATAACTGCTCA 59.987 37.037 0.00 0.00 0.00 4.26
3026 4713 9.702494 AAACCTAACTACACACACTAATAGTTC 57.298 33.333 0.00 0.00 38.49 3.01
3159 4853 9.385902 CTTGTTTGTGTTAAGTAACATCAGATG 57.614 33.333 9.03 9.03 46.56 2.90
3222 4916 6.978659 TGACCATTTAAAACGTACATGCAAAA 59.021 30.769 0.00 0.00 0.00 2.44
3227 4921 4.786068 CGCTGACCATTTAAAACGTACATG 59.214 41.667 0.00 0.00 0.00 3.21
3270 4971 8.780249 GCAAGAAGTAGGTCTAATGTTTTACAA 58.220 33.333 0.00 0.00 0.00 2.41
3280 4981 7.051623 TCAAAACAAGCAAGAAGTAGGTCTAA 58.948 34.615 0.00 0.00 0.00 2.10
3335 5036 8.697846 AAAATGCTAAATGAGAACATGACATG 57.302 30.769 14.02 14.02 36.79 3.21
3595 5298 7.806409 TGTGCATGTCTATTATAGCAATGTT 57.194 32.000 12.33 0.00 33.37 2.71
3615 5318 2.353889 CCACACAGAGCTATCAATGTGC 59.646 50.000 10.15 0.00 45.41 4.57
3692 5395 9.290483 GGAGCTATTTTGCTTTAATACAACTTC 57.710 33.333 0.00 0.00 44.17 3.01
3825 5530 4.551702 TCTACTGCTTGAACTATGGCAA 57.448 40.909 0.00 0.00 34.21 4.52
3956 7463 8.753175 GGTATTGAAAGCTTACAGACTATAACG 58.247 37.037 0.00 0.00 0.00 3.18
4095 7602 3.201290 AGAATCAGCTCTTGCATAACCG 58.799 45.455 0.00 0.00 42.74 4.44
4096 7603 4.450053 AGAGAATCAGCTCTTGCATAACC 58.550 43.478 0.00 0.00 42.41 2.85
4162 7669 9.079833 GTTATTATTGTCTACAACTACGAGCAA 57.920 33.333 0.00 0.00 38.86 3.91
4219 7726 7.069950 AGCCTATGCCGATCATATGTATAAAGA 59.930 37.037 1.90 0.00 37.07 2.52
4227 7734 4.256110 TCAAAGCCTATGCCGATCATATG 58.744 43.478 0.00 0.00 37.07 1.78
4228 7735 4.558226 TCAAAGCCTATGCCGATCATAT 57.442 40.909 0.00 0.00 37.07 1.78
4454 7961 8.738645 ATTACCTAGACAAAACTGATTCCATC 57.261 34.615 0.00 0.00 0.00 3.51
4646 8153 4.878397 GCCTAAGCTACATGAACACTGATT 59.122 41.667 0.00 0.00 35.50 2.57
4682 8189 8.959548 TGACATGAATACATTTAAGTGCTTCAT 58.040 29.630 16.87 16.87 36.49 2.57
4785 8292 6.255020 GTGTCCTACAAAGTACCATGTTATCG 59.745 42.308 6.47 0.00 0.00 2.92
4902 8409 6.594744 AGTATGGTCATGCTGATTCACATTA 58.405 36.000 0.88 0.00 32.46 1.90
5051 8558 8.800332 AGTTTAAGCAGATCAATTTGATTCTGT 58.200 29.630 24.09 15.72 37.20 3.41
5106 8613 4.845307 GGGGAGGGAGGGGAAGGG 62.845 77.778 0.00 0.00 0.00 3.95
5158 8680 3.534357 TGGCATTCCCCTGTAAAGAAA 57.466 42.857 0.00 0.00 0.00 2.52
5188 8710 3.005791 GCTTGTGGGTTAGTTTCATTGCT 59.994 43.478 0.00 0.00 0.00 3.91
5355 8877 0.322975 TCACAGCTTCTGCCTTCCTC 59.677 55.000 0.00 0.00 40.80 3.71
5594 9382 4.841443 ATTTACACCCCGAAAAGTTGAC 57.159 40.909 0.00 0.00 0.00 3.18
5758 9659 0.738389 ACGAACCCAACAGCAACAAG 59.262 50.000 0.00 0.00 0.00 3.16
5826 9727 4.039730 CACAGGGTATCATCTACTCCAAGG 59.960 50.000 0.00 0.00 0.00 3.61
5829 9730 4.265856 ACACAGGGTATCATCTACTCCA 57.734 45.455 0.00 0.00 0.00 3.86
5830 9731 6.267928 ACAATACACAGGGTATCATCTACTCC 59.732 42.308 0.00 0.00 41.87 3.85
5832 9733 7.344612 TCAACAATACACAGGGTATCATCTACT 59.655 37.037 0.00 0.00 41.87 2.57
5833 9734 7.497595 TCAACAATACACAGGGTATCATCTAC 58.502 38.462 0.00 0.00 41.87 2.59
5846 9764 7.402054 ACTATGAATTCCCTCAACAATACACA 58.598 34.615 2.27 0.00 0.00 3.72
5998 10754 9.169468 CTTGCATGTTACTACTTGTTTTTACAG 57.831 33.333 0.00 0.00 33.28 2.74
6007 10763 8.598924 CATAGTTCTCTTGCATGTTACTACTTG 58.401 37.037 0.00 0.00 33.72 3.16
6008 10764 7.278868 GCATAGTTCTCTTGCATGTTACTACTT 59.721 37.037 0.00 0.00 36.40 2.24
6009 10765 6.758886 GCATAGTTCTCTTGCATGTTACTACT 59.241 38.462 0.00 0.00 36.40 2.57
6010 10766 6.535150 TGCATAGTTCTCTTGCATGTTACTAC 59.465 38.462 0.00 0.00 41.18 2.73
6011 10767 6.639563 TGCATAGTTCTCTTGCATGTTACTA 58.360 36.000 0.00 6.59 41.18 1.82
6012 10768 5.491070 TGCATAGTTCTCTTGCATGTTACT 58.509 37.500 0.00 4.81 41.18 2.24
6064 10846 3.623060 CACATCTCCGGTCATTTTACTGG 59.377 47.826 0.00 0.00 45.84 4.00
6105 10887 2.104967 CACATGCCCATCCAGTTGATT 58.895 47.619 0.00 0.00 0.00 2.57
6167 10949 5.924254 CGTCTCTACTAATGGTTGTTCACAA 59.076 40.000 0.00 0.00 0.00 3.33
6190 10972 1.067212 GTAGGCACCTGACCTGATACG 59.933 57.143 0.00 0.00 38.26 3.06
6194 10976 1.358103 AGTAGTAGGCACCTGACCTGA 59.642 52.381 0.00 0.00 38.26 3.86
6195 10977 1.853963 AGTAGTAGGCACCTGACCTG 58.146 55.000 0.00 0.00 38.26 4.00
6196 10978 2.625282 AAGTAGTAGGCACCTGACCT 57.375 50.000 0.00 0.00 41.57 3.85
6197 10979 4.404715 TCAATAAGTAGTAGGCACCTGACC 59.595 45.833 0.00 0.00 0.00 4.02
6198 10980 5.105473 TGTCAATAAGTAGTAGGCACCTGAC 60.105 44.000 0.00 0.00 0.00 3.51
6370 11172 4.823442 TGCAACACTGAAGAAATGTCTCAT 59.177 37.500 0.00 0.00 30.70 2.90
6388 11190 1.214589 CTGCCTGCCTGATTGCAAC 59.785 57.895 0.00 0.00 41.51 4.17
6441 11249 8.608844 AGCAACTTGCCTATTCTGTTATATAC 57.391 34.615 10.25 0.00 46.52 1.47
6449 11257 9.440773 TGATAATATAGCAACTTGCCTATTCTG 57.559 33.333 16.70 0.00 46.52 3.02
6469 11277 8.537728 TCCTCCATGCTTTATGTTTTGATAAT 57.462 30.769 0.00 0.00 34.87 1.28
6470 11278 7.953005 TCCTCCATGCTTTATGTTTTGATAA 57.047 32.000 0.00 0.00 34.87 1.75
6471 11279 7.014518 CCATCCTCCATGCTTTATGTTTTGATA 59.985 37.037 0.00 0.00 34.87 2.15
6474 11282 5.105228 ACCATCCTCCATGCTTTATGTTTTG 60.105 40.000 0.00 0.00 34.87 2.44
6479 11287 4.978099 ACTACCATCCTCCATGCTTTATG 58.022 43.478 0.00 0.00 36.50 1.90
6482 11290 4.660303 TCATACTACCATCCTCCATGCTTT 59.340 41.667 0.00 0.00 0.00 3.51
6483 11291 4.234550 TCATACTACCATCCTCCATGCTT 58.765 43.478 0.00 0.00 0.00 3.91
6484 11292 3.837146 CTCATACTACCATCCTCCATGCT 59.163 47.826 0.00 0.00 0.00 3.79
6486 11294 3.580022 TGCTCATACTACCATCCTCCATG 59.420 47.826 0.00 0.00 0.00 3.66
6487 11295 3.861846 TGCTCATACTACCATCCTCCAT 58.138 45.455 0.00 0.00 0.00 3.41
6488 11296 3.328535 TGCTCATACTACCATCCTCCA 57.671 47.619 0.00 0.00 0.00 3.86
6489 11297 3.388024 TGTTGCTCATACTACCATCCTCC 59.612 47.826 0.00 0.00 0.00 4.30
6490 11298 4.672587 TGTTGCTCATACTACCATCCTC 57.327 45.455 0.00 0.00 0.00 3.71
6491 11299 6.498303 TGATATGTTGCTCATACTACCATCCT 59.502 38.462 4.77 0.00 41.13 3.24
6492 11300 6.701340 TGATATGTTGCTCATACTACCATCC 58.299 40.000 4.77 0.00 41.13 3.51
6494 11302 8.159447 ACATTGATATGTTGCTCATACTACCAT 58.841 33.333 4.77 0.00 42.29 3.55
6495 11303 7.508687 ACATTGATATGTTGCTCATACTACCA 58.491 34.615 4.77 0.73 42.29 3.25
6496 11304 7.969536 ACATTGATATGTTGCTCATACTACC 57.030 36.000 4.77 0.00 42.29 3.18
6563 11371 9.597999 GCCTTTTTGATATGTGAATTTGTTTTC 57.402 29.630 0.00 0.00 0.00 2.29
6564 11372 9.118300 TGCCTTTTTGATATGTGAATTTGTTTT 57.882 25.926 0.00 0.00 0.00 2.43
6565 11373 8.674263 TGCCTTTTTGATATGTGAATTTGTTT 57.326 26.923 0.00 0.00 0.00 2.83
6566 11374 8.851541 ATGCCTTTTTGATATGTGAATTTGTT 57.148 26.923 0.00 0.00 0.00 2.83
6570 11378 8.597662 GCATATGCCTTTTTGATATGTGAATT 57.402 30.769 17.26 0.00 34.06 2.17
6588 11396 6.430925 TGTCAATCTATGTAAAGGGCATATGC 59.569 38.462 19.79 19.79 41.14 3.14
6589 11397 7.984422 TGTCAATCTATGTAAAGGGCATATG 57.016 36.000 0.00 0.00 0.00 1.78
6591 11399 6.942005 CCATGTCAATCTATGTAAAGGGCATA 59.058 38.462 0.00 0.00 0.00 3.14
6593 11401 5.104151 TCCATGTCAATCTATGTAAAGGGCA 60.104 40.000 0.00 0.00 0.00 5.36
6594 11402 5.376625 TCCATGTCAATCTATGTAAAGGGC 58.623 41.667 0.00 0.00 0.00 5.19
6601 11409 9.445878 CAGCTATAATTCCATGTCAATCTATGT 57.554 33.333 0.00 0.00 0.00 2.29
6603 11411 7.555554 GCCAGCTATAATTCCATGTCAATCTAT 59.444 37.037 0.00 0.00 0.00 1.98
6604 11412 6.881065 GCCAGCTATAATTCCATGTCAATCTA 59.119 38.462 0.00 0.00 0.00 1.98
6605 11413 5.709164 GCCAGCTATAATTCCATGTCAATCT 59.291 40.000 0.00 0.00 0.00 2.40
6606 11414 5.105997 GGCCAGCTATAATTCCATGTCAATC 60.106 44.000 0.00 0.00 0.00 2.67
6607 11415 4.768968 GGCCAGCTATAATTCCATGTCAAT 59.231 41.667 0.00 0.00 0.00 2.57
6608 11416 4.144297 GGCCAGCTATAATTCCATGTCAA 58.856 43.478 0.00 0.00 0.00 3.18
6609 11417 3.138098 TGGCCAGCTATAATTCCATGTCA 59.862 43.478 0.00 0.00 0.00 3.58
6610 11418 3.754965 TGGCCAGCTATAATTCCATGTC 58.245 45.455 0.00 0.00 0.00 3.06
6611 11419 3.882102 TGGCCAGCTATAATTCCATGT 57.118 42.857 0.00 0.00 0.00 3.21
6612 11420 5.475719 CATTTGGCCAGCTATAATTCCATG 58.524 41.667 5.11 0.00 0.00 3.66
6613 11421 4.529377 CCATTTGGCCAGCTATAATTCCAT 59.471 41.667 5.11 0.00 0.00 3.41
6614 11422 3.896888 CCATTTGGCCAGCTATAATTCCA 59.103 43.478 5.11 0.00 0.00 3.53
6615 11423 3.259123 CCCATTTGGCCAGCTATAATTCC 59.741 47.826 5.11 0.00 0.00 3.01
6616 11424 4.525912 CCCATTTGGCCAGCTATAATTC 57.474 45.455 5.11 0.00 0.00 2.17
6629 11437 1.668628 CGAAAAGAACGGCCCATTTGG 60.669 52.381 0.00 0.00 37.09 3.28
6630 11438 1.668628 CCGAAAAGAACGGCCCATTTG 60.669 52.381 0.00 0.00 43.74 2.32
6631 11439 0.601057 CCGAAAAGAACGGCCCATTT 59.399 50.000 0.00 0.00 43.74 2.32
6632 11440 2.263153 CCGAAAAGAACGGCCCATT 58.737 52.632 0.00 0.00 43.74 3.16
6633 11441 3.996614 CCGAAAAGAACGGCCCAT 58.003 55.556 0.00 0.00 43.74 4.00
6639 11447 4.097863 GCCGGCCCGAAAAGAACG 62.098 66.667 18.11 0.00 0.00 3.95
6640 11448 3.744719 GGCCGGCCCGAAAAGAAC 61.745 66.667 36.64 5.01 0.00 3.01
6690 11498 3.583276 TTAGACCGTGCCGTGCCTG 62.583 63.158 0.00 0.00 0.00 4.85
6691 11499 2.874664 TTTAGACCGTGCCGTGCCT 61.875 57.895 0.00 0.00 0.00 4.75
6692 11500 2.357760 TTTAGACCGTGCCGTGCC 60.358 61.111 0.00 0.00 0.00 5.01
6693 11501 2.858158 GTTTAGACCGTGCCGTGC 59.142 61.111 0.00 0.00 0.00 5.34
6694 11502 2.377310 CCGTTTAGACCGTGCCGTG 61.377 63.158 0.00 0.00 0.00 4.94
6695 11503 2.048877 CCGTTTAGACCGTGCCGT 60.049 61.111 0.00 0.00 0.00 5.68
6696 11504 2.812178 CCCGTTTAGACCGTGCCG 60.812 66.667 0.00 0.00 0.00 5.69
6697 11505 3.122971 GCCCGTTTAGACCGTGCC 61.123 66.667 0.00 0.00 0.00 5.01
6698 11506 3.122971 GGCCCGTTTAGACCGTGC 61.123 66.667 0.00 0.00 0.00 5.34
6699 11507 2.812178 CGGCCCGTTTAGACCGTG 60.812 66.667 0.00 0.00 40.77 4.94
6700 11508 4.073200 CCGGCCCGTTTAGACCGT 62.073 66.667 0.85 0.00 44.14 4.83
6701 11509 4.825252 CCCGGCCCGTTTAGACCG 62.825 72.222 0.85 0.00 45.21 4.79


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

AutoCloner maintained by Alex Coulton.