Multiple sequence alignment - TraesCS3A01G377200

Loading Multiple Alignment...

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 TraesCS3A01G377200 chr3A 100.000 3696 0 0 2795 6490 626669899 626666204 0.000000e+00 6826.0
1 TraesCS3A01G377200 chr3A 100.000 2425 0 0 1 2425 626672693 626670269 0.000000e+00 4479.0
2 TraesCS3A01G377200 chr3A 88.235 561 58 8 2 558 626680034 626680590 0.000000e+00 664.0
3 TraesCS3A01G377200 chr3A 86.335 161 21 1 1304 1463 453527088 453526928 2.410000e-39 174.0
4 TraesCS3A01G377200 chr3B 95.762 3256 115 13 3255 6490 646708994 646705742 0.000000e+00 5227.0
5 TraesCS3A01G377200 chr3B 95.887 705 27 2 597 1300 646711460 646710757 0.000000e+00 1140.0
6 TraesCS3A01G377200 chr3B 93.636 550 24 5 2 542 646712009 646711462 0.000000e+00 811.0
7 TraesCS3A01G377200 chr3B 91.124 507 40 5 30 532 646718271 646718776 0.000000e+00 682.0
8 TraesCS3A01G377200 chr3B 94.393 321 16 1 2942 3262 646709349 646709031 5.850000e-135 492.0
9 TraesCS3A01G377200 chr3B 93.910 312 6 7 1461 1761 646710758 646710449 5.930000e-125 459.0
10 TraesCS3A01G377200 chr3B 86.170 282 17 6 2012 2293 646710192 646709933 1.070000e-72 285.0
11 TraesCS3A01G377200 chr3B 95.055 182 6 2 1834 2012 646710434 646710253 3.830000e-72 283.0
12 TraesCS3A01G377200 chr3B 87.500 192 20 3 2102 2293 151201199 151201012 1.100000e-52 219.0
13 TraesCS3A01G377200 chr3B 94.595 37 2 0 198 234 793179386 793179350 2.530000e-04 58.4
14 TraesCS3A01G377200 chr3D 94.943 2274 74 12 3255 5501 484095303 484093044 0.000000e+00 3524.0
15 TraesCS3A01G377200 chr3D 94.919 1043 44 5 5450 6490 484093054 484092019 0.000000e+00 1624.0
16 TraesCS3A01G377200 chr3D 96.738 705 22 1 597 1300 484119134 484118430 0.000000e+00 1173.0
17 TraesCS3A01G377200 chr3D 94.421 466 26 0 2795 3260 484095807 484095342 0.000000e+00 717.0
18 TraesCS3A01G377200 chr3D 89.520 563 31 9 23 580 484119657 484119118 0.000000e+00 688.0
19 TraesCS3A01G377200 chr3D 91.751 497 36 5 65 558 484121786 484122280 0.000000e+00 686.0
20 TraesCS3A01G377200 chr3D 94.974 378 7 4 1461 1834 484118431 484118062 3.370000e-162 582.0
21 TraesCS3A01G377200 chr3D 93.143 175 11 1 2012 2185 484096444 484096270 8.350000e-64 255.0
22 TraesCS3A01G377200 chr3D 97.849 93 2 0 1832 1924 484115423 484115331 1.870000e-35 161.0
23 TraesCS3A01G377200 chr3D 96.970 33 1 0 194 226 442144984 442145016 1.000000e-03 56.5
24 TraesCS3A01G377200 chr7A 81.624 702 116 9 4767 5461 127903398 127904093 2.630000e-158 569.0
25 TraesCS3A01G377200 chr7A 100.000 29 0 0 2137 2165 386944232 386944204 3.000000e-03 54.7
26 TraesCS3A01G377200 chr7B 80.435 690 119 13 4770 5449 88870345 88871028 4.490000e-141 512.0
27 TraesCS3A01G377200 chr7B 83.832 167 26 1 1297 1462 693343356 693343190 2.420000e-34 158.0
28 TraesCS3A01G377200 chr7B 87.903 124 15 0 646 769 493525846 493525969 5.240000e-31 147.0
29 TraesCS3A01G377200 chr7B 87.597 129 13 3 649 775 682239450 682239577 5.240000e-31 147.0
30 TraesCS3A01G377200 chr7B 85.714 70 9 1 6120 6188 13309074 13309143 9.030000e-09 73.1
31 TraesCS3A01G377200 chr7B 85.714 70 9 1 6120 6188 16155934 16155865 9.030000e-09 73.1
32 TraesCS3A01G377200 chr5D 88.601 193 21 1 2101 2293 255699336 255699145 3.910000e-57 233.0
33 TraesCS3A01G377200 chr5D 89.362 141 14 1 1304 1443 16895922 16896062 6.690000e-40 176.0
34 TraesCS3A01G377200 chr5B 83.770 191 25 4 2102 2290 211147646 211147832 6.690000e-40 176.0
35 TraesCS3A01G377200 chr5B 88.194 144 16 1 1304 1446 56695048 56695191 3.110000e-38 171.0
36 TraesCS3A01G377200 chr5B 85.897 156 21 1 1293 1447 587469519 587469674 1.450000e-36 165.0
37 TraesCS3A01G377200 chr7D 85.802 162 19 4 1304 1463 407620253 407620094 1.120000e-37 169.0
38 TraesCS3A01G377200 chr7D 88.462 130 15 0 646 775 469842392 469842521 2.420000e-34 158.0
39 TraesCS3A01G377200 chr6D 87.500 144 17 1 1304 1446 414453598 414453741 1.450000e-36 165.0
40 TraesCS3A01G377200 chr1B 84.848 165 24 1 1304 1467 273653429 273653593 1.450000e-36 165.0
41 TraesCS3A01G377200 chr1B 83.077 65 8 2 2103 2165 327219617 327219680 1.000000e-03 56.5
42 TraesCS3A01G377200 chr6A 86.577 149 18 2 1304 1451 616663248 616663395 5.210000e-36 163.0
43 TraesCS3A01G377200 chr6A 87.097 124 16 0 652 775 352665669 352665792 2.440000e-29 141.0
44 TraesCS3A01G377200 chr2B 86.260 131 18 0 653 783 572791182 572791052 6.780000e-30 143.0
45 TraesCS3A01G377200 chr2D 86.992 123 16 0 653 775 489409547 489409425 8.770000e-29 139.0
46 TraesCS3A01G377200 chr2D 100.000 29 0 0 206 234 58840221 58840249 3.000000e-03 54.7
47 TraesCS3A01G377200 chr2A 85.496 131 19 0 653 783 632952429 632952299 3.160000e-28 137.0
48 TraesCS3A01G377200 chr4A 76.103 272 51 10 6217 6480 732843665 732843930 5.280000e-26 130.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G377200 chr3A 626666204 626672693 6489 True 5652.500000 6826 100.000000 1 6490 2 chr3A.!!$R2 6489
1 TraesCS3A01G377200 chr3A 626680034 626680590 556 False 664.000000 664 88.235000 2 558 1 chr3A.!!$F1 556
2 TraesCS3A01G377200 chr3B 646705742 646712009 6267 True 1242.428571 5227 93.544714 2 6490 7 chr3B.!!$R3 6488
3 TraesCS3A01G377200 chr3B 646718271 646718776 505 False 682.000000 682 91.124000 30 532 1 chr3B.!!$F1 502
4 TraesCS3A01G377200 chr3D 484092019 484096444 4425 True 1530.000000 3524 94.356500 2012 6490 4 chr3D.!!$R1 4478
5 TraesCS3A01G377200 chr3D 484115331 484119657 4326 True 651.000000 1173 94.770250 23 1924 4 chr3D.!!$R2 1901
6 TraesCS3A01G377200 chr7A 127903398 127904093 695 False 569.000000 569 81.624000 4767 5461 1 chr7A.!!$F1 694
7 TraesCS3A01G377200 chr7B 88870345 88871028 683 False 512.000000 512 80.435000 4770 5449 1 chr7B.!!$F2 679

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
49 61 0.606944 TTGTCGGGTTTTCATCGGGG 60.607 55.000 0.00 0.0 0.00 5.73 F
410 428 0.768622 ATTCGTCAAGGGTCCCAACA 59.231 50.000 11.55 0.0 0.00 3.33 F
920 947 1.224592 CCAGCCACCACCTACCATC 59.775 63.158 0.00 0.0 0.00 3.51 F
2316 5184 0.108138 CGATCCCGAGAAAAGCCACT 60.108 55.000 0.00 0.0 38.22 4.00 F
2833 5704 1.068250 GGCAGCGGTGTAGAGGATC 59.932 63.158 17.07 0.0 0.00 3.36 F
4304 7246 1.196808 GGCATGTCAACGTTCGATGTT 59.803 47.619 0.00 0.0 0.00 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1116 1143 0.605319 TTGCACCGACTTGGGATGAC 60.605 55.000 0.00 0.0 44.64 3.06 R
2207 4951 1.061131 CTTTGGATAAGCTCGTGCGTG 59.939 52.381 8.17 0.0 45.42 5.34 R
2818 5689 1.478510 CAACAGATCCTCTACACCGCT 59.521 52.381 0.00 0.0 0.00 5.52 R
4268 7210 1.334160 TGCCACCGAAGAGTACAGAA 58.666 50.000 0.00 0.0 0.00 3.02 R
4360 7302 4.430441 ACTACTGAAGTCCTTCCCTTGAT 58.570 43.478 4.67 0.0 38.77 2.57 R
5744 8738 0.894835 CGAGGGGAAACAAAATGGGG 59.105 55.000 0.00 0.0 0.00 4.96 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
49 61 0.606944 TTGTCGGGTTTTCATCGGGG 60.607 55.000 0.00 0.00 0.00 5.73
138 151 8.203485 ACAAATACATGAACACCTTCACATTTT 58.797 29.630 0.00 0.00 39.28 1.82
180 194 7.810766 TGAACTTTTTGAAATCTGTGAACAC 57.189 32.000 0.00 0.00 0.00 3.32
410 428 0.768622 ATTCGTCAAGGGTCCCAACA 59.231 50.000 11.55 0.00 0.00 3.33
463 488 3.748048 GTGAGCAGTCAAAATGTCTAGCA 59.252 43.478 0.00 0.00 33.27 3.49
481 507 1.656095 GCAAGTCTCGACCGATTGAAG 59.344 52.381 8.01 0.00 0.00 3.02
495 521 4.354587 CGATTGAAGTCAGTGATCGATCA 58.645 43.478 23.99 23.99 41.37 2.92
542 568 1.813513 CCTTAATAGATGCGGCCCAG 58.186 55.000 0.00 0.00 0.00 4.45
576 602 2.354259 GGCTCATCTCTTGGACAACAG 58.646 52.381 0.00 0.00 0.00 3.16
577 603 2.027745 GGCTCATCTCTTGGACAACAGA 60.028 50.000 0.00 0.00 0.00 3.41
578 604 3.370315 GGCTCATCTCTTGGACAACAGAT 60.370 47.826 0.00 0.00 0.00 2.90
579 605 4.260170 GCTCATCTCTTGGACAACAGATT 58.740 43.478 0.83 0.00 0.00 2.40
580 606 4.094590 GCTCATCTCTTGGACAACAGATTG 59.905 45.833 0.83 0.11 41.98 2.67
581 607 4.005650 TCATCTCTTGGACAACAGATTGC 58.994 43.478 0.83 0.00 39.66 3.56
582 608 3.777106 TCTCTTGGACAACAGATTGCT 57.223 42.857 0.00 0.00 39.66 3.91
583 609 3.668447 TCTCTTGGACAACAGATTGCTC 58.332 45.455 0.00 0.00 39.66 4.26
584 610 3.071457 TCTCTTGGACAACAGATTGCTCA 59.929 43.478 0.00 0.00 39.66 4.26
585 611 3.817084 CTCTTGGACAACAGATTGCTCAA 59.183 43.478 0.00 0.00 39.66 3.02
586 612 4.206375 TCTTGGACAACAGATTGCTCAAA 58.794 39.130 0.00 0.00 39.66 2.69
587 613 4.644234 TCTTGGACAACAGATTGCTCAAAA 59.356 37.500 0.00 0.00 39.66 2.44
588 614 4.998671 TGGACAACAGATTGCTCAAAAA 57.001 36.364 0.00 0.00 39.66 1.94
678 704 5.192522 ACTCCCTCCATCATGAATTAGTTGT 59.807 40.000 0.00 0.00 0.00 3.32
735 761 5.858049 CACGTTTTAGTGTTCGGTACATCTA 59.142 40.000 0.00 0.00 39.39 1.98
770 796 7.520451 AATTTTAGACAACTACTTTGGGACC 57.480 36.000 0.00 0.00 39.84 4.46
800 826 9.209175 GGAGTATATGCCAACTGTAAATCTAAG 57.791 37.037 0.00 0.00 0.00 2.18
920 947 1.224592 CCAGCCACCACCTACCATC 59.775 63.158 0.00 0.00 0.00 3.51
1116 1143 8.977505 CAGTTTATGGTATTCTTGTTTGTTTGG 58.022 33.333 0.00 0.00 0.00 3.28
1297 1324 5.432885 TGCTAGATTTGATGCATCACATG 57.567 39.130 28.40 17.07 39.84 3.21
1298 1325 4.885325 TGCTAGATTTGATGCATCACATGT 59.115 37.500 28.40 25.99 39.84 3.21
1299 1326 6.056884 TGCTAGATTTGATGCATCACATGTA 58.943 36.000 28.40 25.75 39.84 2.29
1300 1327 6.713450 TGCTAGATTTGATGCATCACATGTAT 59.287 34.615 28.40 17.49 39.84 2.29
1301 1328 7.229907 TGCTAGATTTGATGCATCACATGTATT 59.770 33.333 28.40 15.15 39.84 1.89
1302 1329 8.080417 GCTAGATTTGATGCATCACATGTATTT 58.920 33.333 28.40 14.71 39.84 1.40
1303 1330 9.608617 CTAGATTTGATGCATCACATGTATTTC 57.391 33.333 28.40 15.96 39.84 2.17
1304 1331 7.431249 AGATTTGATGCATCACATGTATTTCC 58.569 34.615 28.40 14.44 39.84 3.13
1305 1332 6.778834 TTTGATGCATCACATGTATTTCCT 57.221 33.333 28.72 0.00 39.84 3.36
1306 1333 6.381481 TTGATGCATCACATGTATTTCCTC 57.619 37.500 28.72 0.00 39.84 3.71
1307 1334 4.823442 TGATGCATCACATGTATTTCCTCC 59.177 41.667 25.42 0.00 39.84 4.30
1308 1335 3.205338 TGCATCACATGTATTTCCTCCG 58.795 45.455 0.00 0.00 0.00 4.63
1309 1336 3.206150 GCATCACATGTATTTCCTCCGT 58.794 45.455 0.00 0.00 0.00 4.69
1310 1337 3.627577 GCATCACATGTATTTCCTCCGTT 59.372 43.478 0.00 0.00 0.00 4.44
1311 1338 4.496341 GCATCACATGTATTTCCTCCGTTG 60.496 45.833 0.00 0.00 0.00 4.10
1312 1339 3.006940 TCACATGTATTTCCTCCGTTGC 58.993 45.455 0.00 0.00 0.00 4.17
1313 1340 3.009723 CACATGTATTTCCTCCGTTGCT 58.990 45.455 0.00 0.00 0.00 3.91
1314 1341 4.081365 TCACATGTATTTCCTCCGTTGCTA 60.081 41.667 0.00 0.00 0.00 3.49
1315 1342 4.634004 CACATGTATTTCCTCCGTTGCTAA 59.366 41.667 0.00 0.00 0.00 3.09
1316 1343 5.123186 CACATGTATTTCCTCCGTTGCTAAA 59.877 40.000 0.00 0.00 0.00 1.85
1317 1344 5.885912 ACATGTATTTCCTCCGTTGCTAAAT 59.114 36.000 0.00 0.00 0.00 1.40
1318 1345 7.011950 CACATGTATTTCCTCCGTTGCTAAATA 59.988 37.037 0.00 0.00 0.00 1.40
1319 1346 7.719633 ACATGTATTTCCTCCGTTGCTAAATAT 59.280 33.333 0.00 0.00 0.00 1.28
1320 1347 9.214957 CATGTATTTCCTCCGTTGCTAAATATA 57.785 33.333 0.00 0.00 0.00 0.86
1321 1348 9.787435 ATGTATTTCCTCCGTTGCTAAATATAA 57.213 29.630 0.00 0.00 0.00 0.98
1322 1349 9.268268 TGTATTTCCTCCGTTGCTAAATATAAG 57.732 33.333 0.00 0.00 0.00 1.73
1323 1350 9.269453 GTATTTCCTCCGTTGCTAAATATAAGT 57.731 33.333 0.00 0.00 0.00 2.24
1324 1351 8.747538 ATTTCCTCCGTTGCTAAATATAAGTT 57.252 30.769 0.00 0.00 0.00 2.66
1325 1352 8.570068 TTTCCTCCGTTGCTAAATATAAGTTT 57.430 30.769 0.00 0.00 0.00 2.66
1326 1353 8.570068 TTCCTCCGTTGCTAAATATAAGTTTT 57.430 30.769 0.00 0.00 0.00 2.43
1327 1354 8.570068 TCCTCCGTTGCTAAATATAAGTTTTT 57.430 30.769 0.00 0.00 0.00 1.94
1353 1380 9.809096 TTTAGACATTTTAAATGAACTGCAACA 57.191 25.926 22.53 5.27 0.00 3.33
1354 1381 9.979578 TTAGACATTTTAAATGAACTGCAACAT 57.020 25.926 22.53 0.00 0.00 2.71
1356 1383 9.410556 AGACATTTTAAATGAACTGCAACATAC 57.589 29.630 22.53 0.84 0.00 2.39
1357 1384 9.190858 GACATTTTAAATGAACTGCAACATACA 57.809 29.630 22.53 0.00 0.00 2.29
1358 1385 9.195411 ACATTTTAAATGAACTGCAACATACAG 57.805 29.630 22.53 0.00 41.08 2.74
1359 1386 9.409312 CATTTTAAATGAACTGCAACATACAGA 57.591 29.630 11.89 0.00 38.55 3.41
1361 1388 8.969121 TTTAAATGAACTGCAACATACAGATG 57.031 30.769 0.00 0.00 38.55 2.90
1363 1390 7.686438 AAATGAACTGCAACATACAGATGTA 57.314 32.000 0.00 0.00 45.93 2.29
1364 1391 7.870509 AATGAACTGCAACATACAGATGTAT 57.129 32.000 0.00 0.00 45.93 2.29
1400 1427 7.843490 TTAAGTGTAGGTTCACTCATATTGC 57.157 36.000 0.00 0.00 46.25 3.56
1401 1428 5.683876 AGTGTAGGTTCACTCATATTGCT 57.316 39.130 0.00 0.00 44.07 3.91
1402 1429 5.665459 AGTGTAGGTTCACTCATATTGCTC 58.335 41.667 0.00 0.00 44.07 4.26
1403 1430 4.811557 GTGTAGGTTCACTCATATTGCTCC 59.188 45.833 0.00 0.00 35.68 4.70
1404 1431 3.185246 AGGTTCACTCATATTGCTCCG 57.815 47.619 0.00 0.00 0.00 4.63
1405 1432 2.501723 AGGTTCACTCATATTGCTCCGT 59.498 45.455 0.00 0.00 0.00 4.69
1406 1433 3.704566 AGGTTCACTCATATTGCTCCGTA 59.295 43.478 0.00 0.00 0.00 4.02
1407 1434 4.345257 AGGTTCACTCATATTGCTCCGTAT 59.655 41.667 0.00 0.00 0.00 3.06
1408 1435 4.449068 GGTTCACTCATATTGCTCCGTATG 59.551 45.833 0.00 0.00 0.00 2.39
1409 1436 4.937201 TCACTCATATTGCTCCGTATGT 57.063 40.909 0.00 0.00 31.75 2.29
1410 1437 6.213677 GTTCACTCATATTGCTCCGTATGTA 58.786 40.000 0.00 0.00 31.75 2.29
1411 1438 6.013842 TCACTCATATTGCTCCGTATGTAG 57.986 41.667 0.00 0.00 31.75 2.74
1412 1439 5.535030 TCACTCATATTGCTCCGTATGTAGT 59.465 40.000 0.00 0.00 31.75 2.73
1413 1440 5.859114 CACTCATATTGCTCCGTATGTAGTC 59.141 44.000 0.00 0.00 31.75 2.59
1414 1441 5.535030 ACTCATATTGCTCCGTATGTAGTCA 59.465 40.000 0.00 0.00 31.75 3.41
1415 1442 6.209589 ACTCATATTGCTCCGTATGTAGTCAT 59.790 38.462 0.00 0.00 38.00 3.06
1416 1443 6.621613 TCATATTGCTCCGTATGTAGTCATC 58.378 40.000 0.00 0.00 35.70 2.92
1417 1444 6.434340 TCATATTGCTCCGTATGTAGTCATCT 59.566 38.462 0.00 0.00 35.70 2.90
1418 1445 3.990318 TGCTCCGTATGTAGTCATCTG 57.010 47.619 0.00 0.00 35.70 2.90
1419 1446 3.288092 TGCTCCGTATGTAGTCATCTGT 58.712 45.455 0.00 0.00 35.70 3.41
1420 1447 3.699538 TGCTCCGTATGTAGTCATCTGTT 59.300 43.478 0.00 0.00 35.70 3.16
1421 1448 4.885325 TGCTCCGTATGTAGTCATCTGTTA 59.115 41.667 0.00 0.00 35.70 2.41
1422 1449 5.008712 TGCTCCGTATGTAGTCATCTGTTAG 59.991 44.000 0.00 0.00 35.70 2.34
1423 1450 5.238868 GCTCCGTATGTAGTCATCTGTTAGA 59.761 44.000 0.00 0.00 35.70 2.10
1424 1451 6.238676 GCTCCGTATGTAGTCATCTGTTAGAA 60.239 42.308 0.00 0.00 35.70 2.10
1425 1452 7.522399 GCTCCGTATGTAGTCATCTGTTAGAAT 60.522 40.741 0.00 0.00 35.70 2.40
1426 1453 8.913487 TCCGTATGTAGTCATCTGTTAGAATA 57.087 34.615 0.00 0.00 35.70 1.75
1427 1454 9.516546 TCCGTATGTAGTCATCTGTTAGAATAT 57.483 33.333 0.00 0.00 35.70 1.28
1428 1455 9.776158 CCGTATGTAGTCATCTGTTAGAATATC 57.224 37.037 0.00 0.00 35.70 1.63
1456 1483 8.043710 AGAAAGACTTATATTTGTGGACAGAGG 58.956 37.037 0.00 0.00 0.00 3.69
1457 1484 7.496346 AAGACTTATATTTGTGGACAGAGGA 57.504 36.000 0.00 0.00 0.00 3.71
1458 1485 7.496346 AGACTTATATTTGTGGACAGAGGAA 57.504 36.000 0.00 0.00 0.00 3.36
1459 1486 7.560368 AGACTTATATTTGTGGACAGAGGAAG 58.440 38.462 0.00 0.00 0.00 3.46
1603 1631 8.500753 TTATTTGTTTTGGTCGTATAGCTGAT 57.499 30.769 0.00 0.00 0.00 2.90
1609 1637 8.609176 TGTTTTGGTCGTATAGCTGATATTTTC 58.391 33.333 0.00 0.00 0.00 2.29
1763 1801 3.808728 CCCGATTCCAGAACACATGTAT 58.191 45.455 0.00 0.00 0.00 2.29
1764 1802 3.561310 CCCGATTCCAGAACACATGTATG 59.439 47.826 0.00 0.00 0.00 2.39
1765 1803 3.002656 CCGATTCCAGAACACATGTATGC 59.997 47.826 0.00 0.00 0.00 3.14
1766 1804 3.622612 CGATTCCAGAACACATGTATGCA 59.377 43.478 0.00 0.00 0.00 3.96
1767 1805 4.274214 CGATTCCAGAACACATGTATGCAT 59.726 41.667 3.79 3.79 35.32 3.96
1883 4562 8.365647 AGCAGAAAATGATTCTCAAATTTCACT 58.634 29.630 15.27 11.28 38.06 3.41
1890 4569 6.845302 TGATTCTCAAATTTCACTGGATTCG 58.155 36.000 0.00 0.00 0.00 3.34
1955 4635 7.614124 AAGATGCAACACAAAATTCAAAACT 57.386 28.000 0.00 0.00 0.00 2.66
2125 4869 4.703899 TTCTTTCAAGAGTACGCGAAAC 57.296 40.909 15.93 11.03 36.22 2.78
2156 4900 7.201857 GCCATGTTTTTATAGAAGGCAGAAGAT 60.202 37.037 0.00 0.00 40.50 2.40
2182 4926 3.654414 ACAAAAGACTACTTCTCGCTGG 58.346 45.455 0.00 0.00 35.05 4.85
2200 4944 3.149196 CTGGGAACAACAAGTGTAGCAT 58.851 45.455 0.00 0.00 40.60 3.79
2207 4951 3.815401 ACAACAAGTGTAGCATGAACTCC 59.185 43.478 0.00 0.00 39.29 3.85
2210 4954 2.370281 AGTGTAGCATGAACTCCACG 57.630 50.000 0.00 0.00 32.23 4.94
2211 4955 0.721718 GTGTAGCATGAACTCCACGC 59.278 55.000 0.00 0.00 33.49 5.34
2212 4956 0.320050 TGTAGCATGAACTCCACGCA 59.680 50.000 0.00 0.00 36.24 5.24
2263 5007 3.773860 TGCTACAACCACAACACAAAG 57.226 42.857 0.00 0.00 0.00 2.77
2264 5008 2.425312 TGCTACAACCACAACACAAAGG 59.575 45.455 0.00 0.00 0.00 3.11
2316 5184 0.108138 CGATCCCGAGAAAAGCCACT 60.108 55.000 0.00 0.00 38.22 4.00
2411 5282 1.679680 TCTCAGGACTTTCGTGAACGT 59.320 47.619 2.37 0.00 40.25 3.99
2833 5704 1.068250 GGCAGCGGTGTAGAGGATC 59.932 63.158 17.07 0.00 0.00 3.36
2882 5753 2.190578 CTGGATTGCGGGGGAGAC 59.809 66.667 0.00 0.00 0.00 3.36
2895 5766 2.043248 GAGACGGGTGGGGAGCTA 60.043 66.667 0.00 0.00 0.00 3.32
2972 5843 1.465188 ATTGGTGGGTGTGGGAGGA 60.465 57.895 0.00 0.00 0.00 3.71
3073 5944 4.323028 CGACCATCTATTACCTGATGCCAT 60.323 45.833 0.00 0.00 38.84 4.40
3119 5990 2.125832 GCCAACGTGGTAGCGCTA 60.126 61.111 14.45 14.45 40.46 4.26
3352 6268 7.859598 TGACAAATTCCAAAACAATTGTATGC 58.140 30.769 12.39 0.50 0.00 3.14
3612 6544 6.571537 CGTTTAACTAACAATGGCCAAATCCT 60.572 38.462 10.96 0.00 36.50 3.24
3668 6600 3.303938 TCCCATGGAAAGCTTGTTTTCA 58.696 40.909 15.22 0.00 38.51 2.69
3725 6657 6.183360 TCATCTTTTTATGAAGCAATGGCGAT 60.183 34.615 0.00 0.00 36.66 4.58
3772 6705 9.790389 TTAAGCGTTTTCTTGTTTTTCTTGATA 57.210 25.926 0.00 0.00 0.00 2.15
3874 6813 4.922206 TCAAATACAGATCCAACCAGCTT 58.078 39.130 0.00 0.00 0.00 3.74
3992 6934 2.038387 ATGTCTGTTGGGCCGTATTC 57.962 50.000 0.00 0.00 0.00 1.75
4005 6947 1.418367 GTATTCGTTCGCGCTTGCA 59.582 52.632 5.56 0.00 41.05 4.08
4015 6957 1.968540 GCGCTTGCAAGTTCCTCCT 60.969 57.895 26.55 0.00 38.92 3.69
4045 6987 4.838423 TGTTTCTGTTCACTAGAGGATCCA 59.162 41.667 15.82 0.00 33.66 3.41
4261 7203 9.286170 CCTACAGTATGCTCTAATTGAGTACTA 57.714 37.037 0.00 0.00 44.41 1.82
4268 7210 7.646548 TGCTCTAATTGAGTACTACACAGAT 57.353 36.000 0.00 0.00 44.41 2.90
4304 7246 1.196808 GGCATGTCAACGTTCGATGTT 59.803 47.619 0.00 0.00 0.00 2.71
4473 7415 5.490159 TGGAATGCATGGATTTTCTTTTCC 58.510 37.500 14.12 9.88 0.00 3.13
4539 7482 6.877322 TGCGAAAACTTTATAGCTACTTCCTT 59.123 34.615 0.00 0.00 0.00 3.36
4809 7752 0.813184 GCATGACAGGTTGATGGGTG 59.187 55.000 0.00 0.00 0.00 4.61
4884 7827 1.395826 GCGCCTATCACTCCAGGAGT 61.396 60.000 17.31 17.31 44.44 3.85
4888 7831 1.678627 CCTATCACTCCAGGAGTCACG 59.321 57.143 20.30 9.11 41.37 4.35
4954 7897 4.794334 TCAAGGTAAGCAGTTAAAACCCA 58.206 39.130 0.00 0.00 0.00 4.51
5598 8592 4.508662 GGCTCTCCTTGTATGCCATATAC 58.491 47.826 0.00 0.00 42.79 1.47
5703 8697 4.284234 ACAGCAATCAAAATATATGCCCCC 59.716 41.667 0.00 0.00 37.73 5.40
5744 8738 4.390297 CGTTTCTCTTTCACCATTCTCTCC 59.610 45.833 0.00 0.00 0.00 3.71
5769 8763 4.461081 CCATTTTGTTTCCCCTCGACAATA 59.539 41.667 0.00 0.00 33.73 1.90
5770 8764 5.127031 CCATTTTGTTTCCCCTCGACAATAT 59.873 40.000 0.00 0.00 33.73 1.28
5773 8767 2.841266 TGTTTCCCCTCGACAATATCCA 59.159 45.455 0.00 0.00 0.00 3.41
5781 8775 5.368145 CCCTCGACAATATCCATTTCTTCA 58.632 41.667 0.00 0.00 0.00 3.02
5800 8794 1.408453 ATAGCCGTACCTCCCTTGCC 61.408 60.000 0.00 0.00 0.00 4.52
5805 8799 0.541863 CGTACCTCCCTTGCCAGAAT 59.458 55.000 0.00 0.00 0.00 2.40
5826 8820 2.877043 GATGGCATGTGGTTTCCATC 57.123 50.000 3.81 10.74 45.39 3.51
5831 8825 3.299503 GGCATGTGGTTTCCATCCTTAT 58.700 45.455 0.00 0.00 35.28 1.73
6252 9246 7.487484 TGATCATGAAAACAAACTACTGCAAA 58.513 30.769 0.00 0.00 0.00 3.68
6350 9344 7.716799 AAATAAATTCCATGTGAGCCAAGTA 57.283 32.000 0.00 0.00 0.00 2.24
6364 9358 5.068591 TGAGCCAAGTAATAATGCGACTCTA 59.931 40.000 0.00 0.00 0.00 2.43
6370 9366 9.309516 CCAAGTAATAATGCGACTCTAGTAAAA 57.690 33.333 0.00 0.00 0.00 1.52
6410 9406 0.461961 GGGAACTGCATCTAGCTCGT 59.538 55.000 0.00 0.00 45.94 4.18
6436 9432 2.616969 GTCATGTGACGCAACACCT 58.383 52.632 7.60 0.00 39.69 4.00
6466 9462 2.730404 CTCATCGATAGTGCATGTGAGC 59.270 50.000 0.00 0.00 37.40 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 6.566942 CGATGAAAACCCGACAAACAAATAGA 60.567 38.462 0.00 0.00 0.00 1.98
22 23 5.567534 CGATGAAAACCCGACAAACAAATAG 59.432 40.000 0.00 0.00 0.00 1.73
23 24 5.453648 CGATGAAAACCCGACAAACAAATA 58.546 37.500 0.00 0.00 0.00 1.40
24 25 4.295051 CGATGAAAACCCGACAAACAAAT 58.705 39.130 0.00 0.00 0.00 2.32
28 39 1.068816 CCCGATGAAAACCCGACAAAC 60.069 52.381 0.00 0.00 0.00 2.93
49 61 7.909267 AGAAAGCAGCAAACAGAAAATAAAAC 58.091 30.769 0.00 0.00 0.00 2.43
463 488 2.557056 TGACTTCAATCGGTCGAGACTT 59.443 45.455 3.09 0.00 35.45 3.01
481 507 5.342806 TGTTTTGTTGATCGATCACTGAC 57.657 39.130 27.28 21.92 36.36 3.51
495 521 1.134175 CTTCGGTGCACCTGTTTTGTT 59.866 47.619 32.28 0.00 0.00 2.83
542 568 1.811679 GAGCCGCTAGCCAACTGAC 60.812 63.158 9.66 0.00 45.47 3.51
594 620 9.975218 AGGTTATAAATATGTTGTCCAAGAGTT 57.025 29.630 0.00 0.00 0.00 3.01
595 621 9.975218 AAGGTTATAAATATGTTGTCCAAGAGT 57.025 29.630 0.00 0.00 0.00 3.24
597 623 8.682710 GCAAGGTTATAAATATGTTGTCCAAGA 58.317 33.333 0.00 0.00 0.00 3.02
598 624 8.686334 AGCAAGGTTATAAATATGTTGTCCAAG 58.314 33.333 0.00 0.00 0.00 3.61
599 625 8.588290 AGCAAGGTTATAAATATGTTGTCCAA 57.412 30.769 0.00 0.00 0.00 3.53
600 626 9.860650 ATAGCAAGGTTATAAATATGTTGTCCA 57.139 29.630 0.00 0.00 0.00 4.02
649 675 8.820831 ACTAATTCATGATGGAGGGAGTATTAG 58.179 37.037 11.97 11.97 0.00 1.73
770 796 2.365617 ACAGTTGGCATATACTCCCTCG 59.634 50.000 0.00 0.00 0.00 4.63
892 919 1.626686 TGGTGGCTGGTAACCATTTG 58.373 50.000 0.00 0.00 41.56 2.32
1116 1143 0.605319 TTGCACCGACTTGGGATGAC 60.605 55.000 0.00 0.00 44.64 3.06
1158 1185 6.203530 GCCTCATTTGATTCGTATTCTCATCA 59.796 38.462 0.00 0.00 0.00 3.07
1297 1324 9.269453 ACTTATATTTAGCAACGGAGGAAATAC 57.731 33.333 0.00 0.00 0.00 1.89
1298 1325 9.841295 AACTTATATTTAGCAACGGAGGAAATA 57.159 29.630 0.00 0.00 0.00 1.40
1299 1326 8.747538 AACTTATATTTAGCAACGGAGGAAAT 57.252 30.769 0.00 0.00 0.00 2.17
1300 1327 8.570068 AAACTTATATTTAGCAACGGAGGAAA 57.430 30.769 0.00 0.00 0.00 3.13
1301 1328 8.570068 AAAACTTATATTTAGCAACGGAGGAA 57.430 30.769 0.00 0.00 0.00 3.36
1302 1329 8.570068 AAAAACTTATATTTAGCAACGGAGGA 57.430 30.769 0.00 0.00 0.00 3.71
1327 1354 9.809096 TGTTGCAGTTCATTTAAAATGTCTAAA 57.191 25.926 0.00 0.00 0.00 1.85
1328 1355 9.979578 ATGTTGCAGTTCATTTAAAATGTCTAA 57.020 25.926 0.00 0.00 0.00 2.10
1330 1357 9.410556 GTATGTTGCAGTTCATTTAAAATGTCT 57.589 29.630 6.46 0.00 0.00 3.41
1331 1358 9.190858 TGTATGTTGCAGTTCATTTAAAATGTC 57.809 29.630 6.46 0.00 0.00 3.06
1332 1359 9.195411 CTGTATGTTGCAGTTCATTTAAAATGT 57.805 29.630 6.46 0.00 0.00 2.71
1333 1360 9.409312 TCTGTATGTTGCAGTTCATTTAAAATG 57.591 29.630 6.46 0.00 35.60 2.32
1335 1362 9.409312 CATCTGTATGTTGCAGTTCATTTAAAA 57.591 29.630 6.46 0.00 35.60 1.52
1336 1363 8.575589 ACATCTGTATGTTGCAGTTCATTTAAA 58.424 29.630 6.46 0.00 44.07 1.52
1337 1364 8.109705 ACATCTGTATGTTGCAGTTCATTTAA 57.890 30.769 6.46 0.00 44.07 1.52
1338 1365 7.686438 ACATCTGTATGTTGCAGTTCATTTA 57.314 32.000 6.46 0.00 44.07 1.40
1339 1366 6.579666 ACATCTGTATGTTGCAGTTCATTT 57.420 33.333 6.46 0.00 44.07 2.32
1340 1367 7.870509 ATACATCTGTATGTTGCAGTTCATT 57.129 32.000 2.10 0.00 44.07 2.57
1380 1407 4.811557 GGAGCAATATGAGTGAACCTACAC 59.188 45.833 0.00 0.00 40.60 2.90
1381 1408 4.441495 CGGAGCAATATGAGTGAACCTACA 60.441 45.833 0.00 0.00 0.00 2.74
1382 1409 4.051922 CGGAGCAATATGAGTGAACCTAC 58.948 47.826 0.00 0.00 0.00 3.18
1383 1410 3.704566 ACGGAGCAATATGAGTGAACCTA 59.295 43.478 0.00 0.00 0.00 3.08
1384 1411 2.501723 ACGGAGCAATATGAGTGAACCT 59.498 45.455 0.00 0.00 0.00 3.50
1385 1412 2.906354 ACGGAGCAATATGAGTGAACC 58.094 47.619 0.00 0.00 0.00 3.62
1386 1413 5.050490 ACATACGGAGCAATATGAGTGAAC 58.950 41.667 0.00 0.00 33.73 3.18
1387 1414 5.276461 ACATACGGAGCAATATGAGTGAA 57.724 39.130 0.00 0.00 33.73 3.18
1388 1415 4.937201 ACATACGGAGCAATATGAGTGA 57.063 40.909 0.00 0.00 33.73 3.41
1389 1416 5.773575 ACTACATACGGAGCAATATGAGTG 58.226 41.667 0.00 0.00 33.73 3.51
1390 1417 5.535030 TGACTACATACGGAGCAATATGAGT 59.465 40.000 0.00 0.00 33.73 3.41
1391 1418 6.013842 TGACTACATACGGAGCAATATGAG 57.986 41.667 0.00 0.00 33.73 2.90
1392 1419 6.434340 AGATGACTACATACGGAGCAATATGA 59.566 38.462 0.00 0.00 36.82 2.15
1393 1420 6.529477 CAGATGACTACATACGGAGCAATATG 59.471 42.308 0.00 0.00 36.82 1.78
1394 1421 6.209589 ACAGATGACTACATACGGAGCAATAT 59.790 38.462 0.00 0.00 36.82 1.28
1395 1422 5.535030 ACAGATGACTACATACGGAGCAATA 59.465 40.000 0.00 0.00 36.82 1.90
1396 1423 4.342378 ACAGATGACTACATACGGAGCAAT 59.658 41.667 0.00 0.00 36.82 3.56
1397 1424 3.699538 ACAGATGACTACATACGGAGCAA 59.300 43.478 0.00 0.00 36.82 3.91
1398 1425 3.288092 ACAGATGACTACATACGGAGCA 58.712 45.455 0.00 0.00 36.82 4.26
1399 1426 3.992260 ACAGATGACTACATACGGAGC 57.008 47.619 0.00 0.00 36.82 4.70
1400 1427 6.862711 TCTAACAGATGACTACATACGGAG 57.137 41.667 0.00 0.00 36.82 4.63
1401 1428 7.818997 ATTCTAACAGATGACTACATACGGA 57.181 36.000 0.00 0.00 36.82 4.69
1402 1429 9.776158 GATATTCTAACAGATGACTACATACGG 57.224 37.037 0.00 0.00 36.82 4.02
1430 1457 8.043710 CCTCTGTCCACAAATATAAGTCTTTCT 58.956 37.037 0.00 0.00 0.00 2.52
1431 1458 8.041323 TCCTCTGTCCACAAATATAAGTCTTTC 58.959 37.037 0.00 0.00 0.00 2.62
1432 1459 7.918076 TCCTCTGTCCACAAATATAAGTCTTT 58.082 34.615 0.00 0.00 0.00 2.52
1433 1460 7.496346 TCCTCTGTCCACAAATATAAGTCTT 57.504 36.000 0.00 0.00 0.00 3.01
1434 1461 7.181125 ACTTCCTCTGTCCACAAATATAAGTCT 59.819 37.037 0.00 0.00 0.00 3.24
1435 1462 7.331791 ACTTCCTCTGTCCACAAATATAAGTC 58.668 38.462 0.00 0.00 0.00 3.01
1436 1463 7.259088 ACTTCCTCTGTCCACAAATATAAGT 57.741 36.000 0.00 0.00 0.00 2.24
1437 1464 8.258007 TGTACTTCCTCTGTCCACAAATATAAG 58.742 37.037 0.00 0.00 0.00 1.73
1438 1465 8.141298 TGTACTTCCTCTGTCCACAAATATAA 57.859 34.615 0.00 0.00 0.00 0.98
1439 1466 7.727578 TGTACTTCCTCTGTCCACAAATATA 57.272 36.000 0.00 0.00 0.00 0.86
1440 1467 6.620877 TGTACTTCCTCTGTCCACAAATAT 57.379 37.500 0.00 0.00 0.00 1.28
1441 1468 6.013725 ACATGTACTTCCTCTGTCCACAAATA 60.014 38.462 0.00 0.00 0.00 1.40
1442 1469 4.974645 TGTACTTCCTCTGTCCACAAAT 57.025 40.909 0.00 0.00 0.00 2.32
1443 1470 4.102524 ACATGTACTTCCTCTGTCCACAAA 59.897 41.667 0.00 0.00 0.00 2.83
1444 1471 3.646162 ACATGTACTTCCTCTGTCCACAA 59.354 43.478 0.00 0.00 0.00 3.33
1445 1472 3.006859 CACATGTACTTCCTCTGTCCACA 59.993 47.826 0.00 0.00 0.00 4.17
1446 1473 3.258372 TCACATGTACTTCCTCTGTCCAC 59.742 47.826 0.00 0.00 0.00 4.02
1447 1474 3.258372 GTCACATGTACTTCCTCTGTCCA 59.742 47.826 0.00 0.00 0.00 4.02
1448 1475 3.368531 GGTCACATGTACTTCCTCTGTCC 60.369 52.174 0.00 0.00 0.00 4.02
1449 1476 3.368531 GGGTCACATGTACTTCCTCTGTC 60.369 52.174 0.00 0.00 0.00 3.51
1450 1477 2.567615 GGGTCACATGTACTTCCTCTGT 59.432 50.000 0.00 0.00 0.00 3.41
1451 1478 2.567169 TGGGTCACATGTACTTCCTCTG 59.433 50.000 0.00 0.00 0.00 3.35
1452 1479 2.902608 TGGGTCACATGTACTTCCTCT 58.097 47.619 0.00 0.00 0.00 3.69
1453 1480 3.695830 TTGGGTCACATGTACTTCCTC 57.304 47.619 0.00 0.00 0.00 3.71
1454 1481 4.657814 AATTGGGTCACATGTACTTCCT 57.342 40.909 0.00 0.00 0.00 3.36
1455 1482 5.497474 AGTAATTGGGTCACATGTACTTCC 58.503 41.667 0.00 0.00 29.47 3.46
1456 1483 8.732746 ATAAGTAATTGGGTCACATGTACTTC 57.267 34.615 12.09 0.00 38.70 3.01
1457 1484 8.325787 TGATAAGTAATTGGGTCACATGTACTT 58.674 33.333 12.93 12.93 39.92 2.24
1458 1485 7.769044 GTGATAAGTAATTGGGTCACATGTACT 59.231 37.037 0.00 0.00 36.78 2.73
1459 1486 7.551262 TGTGATAAGTAATTGGGTCACATGTAC 59.449 37.037 13.11 0.00 40.47 2.90
1556 1584 1.519408 TTACGCAAAGACCAGCTTCC 58.481 50.000 0.00 0.00 35.24 3.46
1763 1801 6.348950 GGTTATGTGTAAAACTAGTGCATGCA 60.349 38.462 18.46 18.46 0.00 3.96
1764 1802 6.027749 GGTTATGTGTAAAACTAGTGCATGC 58.972 40.000 11.82 11.82 0.00 4.06
1765 1803 7.021196 GTGGTTATGTGTAAAACTAGTGCATG 58.979 38.462 0.00 0.00 0.00 4.06
1766 1804 6.128391 CGTGGTTATGTGTAAAACTAGTGCAT 60.128 38.462 0.00 0.00 0.00 3.96
1767 1805 5.177881 CGTGGTTATGTGTAAAACTAGTGCA 59.822 40.000 0.00 0.00 0.00 4.57
1768 1806 5.178067 ACGTGGTTATGTGTAAAACTAGTGC 59.822 40.000 0.00 0.00 0.00 4.40
1769 1807 6.643770 AGACGTGGTTATGTGTAAAACTAGTG 59.356 38.462 0.00 0.00 0.00 2.74
1770 1808 6.643770 CAGACGTGGTTATGTGTAAAACTAGT 59.356 38.462 0.00 0.00 0.00 2.57
1883 4562 3.958147 TCTAGATGTACCTTGCGAATCCA 59.042 43.478 0.00 0.00 0.00 3.41
1890 4569 5.465056 GCTTCTCATTCTAGATGTACCTTGC 59.535 44.000 0.00 0.00 0.00 4.01
1955 4635 3.073062 GGGCAGCCATCTCTTATTTCCTA 59.927 47.826 15.19 0.00 0.00 2.94
2125 4869 3.666883 TCTATAAAAACATGGCACGCG 57.333 42.857 3.53 3.53 0.00 6.01
2156 4900 7.544566 CCAGCGAGAAGTAGTCTTTTGTAATTA 59.455 37.037 0.00 0.00 36.41 1.40
2182 4926 4.275936 AGTTCATGCTACACTTGTTGTTCC 59.724 41.667 0.00 0.00 39.91 3.62
2200 4944 2.355837 GCTCGTGCGTGGAGTTCA 60.356 61.111 0.00 0.00 34.00 3.18
2207 4951 1.061131 CTTTGGATAAGCTCGTGCGTG 59.939 52.381 8.17 0.00 45.42 5.34
2210 4954 2.346803 TGTCTTTGGATAAGCTCGTGC 58.653 47.619 0.07 0.07 40.05 5.34
2211 4955 4.590400 CTTGTCTTTGGATAAGCTCGTG 57.410 45.455 0.00 0.00 34.78 4.35
2234 4978 4.359434 TGTGGTTGTAGCATTTGAGGTA 57.641 40.909 0.00 0.00 0.00 3.08
2263 5007 3.219281 TGTTCTGTTTAGGGCAAGTTCC 58.781 45.455 0.00 0.00 0.00 3.62
2264 5008 4.338400 AGTTGTTCTGTTTAGGGCAAGTTC 59.662 41.667 0.00 0.00 0.00 3.01
2270 5014 3.190744 GGCTTAGTTGTTCTGTTTAGGGC 59.809 47.826 0.00 0.00 0.00 5.19
2316 5184 7.450014 TGAGTTAATTTATTTGAGTCCAAGGCA 59.550 33.333 0.00 0.00 33.23 4.75
2381 5250 5.174395 CGAAAGTCCTGAGAATCTGATGTT 58.826 41.667 0.00 0.00 35.94 2.71
2818 5689 1.478510 CAACAGATCCTCTACACCGCT 59.521 52.381 0.00 0.00 0.00 5.52
2892 5763 2.415426 GAGCTCCTCTGCGGTAGC 59.585 66.667 0.87 8.60 45.41 3.58
2895 5766 3.386237 GTGGAGCTCCTCTGCGGT 61.386 66.667 32.28 0.00 35.70 5.68
2956 5827 2.529136 CTCCTCCCACACCCACCA 60.529 66.667 0.00 0.00 0.00 4.17
2972 5843 2.989055 CTTCGTCCACGCAACCACCT 62.989 60.000 0.00 0.00 39.60 4.00
3455 6386 9.323985 GCTCATAAAATAAAATTGCCATGGTTA 57.676 29.630 14.67 3.81 0.00 2.85
3531 6463 5.176407 TCCAACAAAAGTTACCATGTTCG 57.824 39.130 0.00 0.00 33.97 3.95
3846 6785 6.009589 TGGTTGGATCTGTATTTGAACACAT 58.990 36.000 0.00 0.00 0.00 3.21
3992 6934 2.052237 AACTTGCAAGCGCGAACG 60.052 55.556 26.27 1.10 42.97 3.95
4005 6947 3.983044 AACATTCGCTAGGAGGAACTT 57.017 42.857 0.00 0.00 41.55 2.66
4015 6957 6.020971 TCTAGTGAACAGAAACATTCGCTA 57.979 37.500 6.97 6.97 42.42 4.26
4092 7034 4.613437 AGGACCCTTATACTAAACCGACA 58.387 43.478 0.00 0.00 0.00 4.35
4139 7081 8.463930 TTTCTAAATCAAATCGGGAGCATTAT 57.536 30.769 0.00 0.00 0.00 1.28
4261 7203 3.827302 ACCGAAGAGTACAGAATCTGTGT 59.173 43.478 24.74 12.46 45.01 3.72
4262 7204 4.169508 CACCGAAGAGTACAGAATCTGTG 58.830 47.826 24.74 8.64 45.01 3.66
4268 7210 1.334160 TGCCACCGAAGAGTACAGAA 58.666 50.000 0.00 0.00 0.00 3.02
4304 7246 9.029368 TGGTGATTGACATTTTTCATACCATAA 57.971 29.630 0.00 0.00 33.19 1.90
4326 7268 5.106038 ACATGTGTGATGAGCTTATTTGGTG 60.106 40.000 0.00 0.00 0.00 4.17
4356 7298 6.394345 ACTGAAGTCCTTCCCTTGATTAAT 57.606 37.500 4.67 0.00 38.77 1.40
4358 7300 6.023603 ACTACTGAAGTCCTTCCCTTGATTA 58.976 40.000 4.67 0.00 38.77 1.75
4359 7301 4.846940 ACTACTGAAGTCCTTCCCTTGATT 59.153 41.667 4.67 0.00 38.77 2.57
4360 7302 4.430441 ACTACTGAAGTCCTTCCCTTGAT 58.570 43.478 4.67 0.00 38.77 2.57
4738 7681 6.926630 TGCTAAGAAAATGTTAACCCCAAT 57.073 33.333 2.48 0.00 0.00 3.16
4809 7752 5.665459 AGTCATAGCATCCAGTTGACTTAC 58.335 41.667 0.00 0.00 43.24 2.34
4884 7827 1.862201 CGTTTTTGTGGTCTAGCGTGA 59.138 47.619 0.00 0.00 0.00 4.35
4888 7831 3.974871 TTTCCGTTTTTGTGGTCTAGC 57.025 42.857 0.00 0.00 0.00 3.42
5258 8208 3.041946 AGCACTCCCGGAATTAGAGAAT 58.958 45.455 0.73 0.00 0.00 2.40
5536 8530 9.866936 TGTCGAAATAACTTGTAAACACATTAC 57.133 29.630 0.00 0.00 43.52 1.89
5744 8738 0.894835 CGAGGGGAAACAAAATGGGG 59.105 55.000 0.00 0.00 0.00 4.96
5769 8763 4.348168 AGGTACGGCTATGAAGAAATGGAT 59.652 41.667 0.00 0.00 0.00 3.41
5770 8764 3.709653 AGGTACGGCTATGAAGAAATGGA 59.290 43.478 0.00 0.00 0.00 3.41
5773 8767 3.071167 GGGAGGTACGGCTATGAAGAAAT 59.929 47.826 0.00 0.00 0.00 2.17
5781 8775 1.408453 GGCAAGGGAGGTACGGCTAT 61.408 60.000 0.00 0.00 0.00 2.97
5800 8794 3.880047 AACCACATGCCATCAATTCTG 57.120 42.857 0.00 0.00 0.00 3.02
5805 8799 2.006805 TGGAAACCACATGCCATCAA 57.993 45.000 0.00 0.00 0.00 2.57
6370 9366 3.519107 CCCCCTTCCATTATGCTTGTTTT 59.481 43.478 0.00 0.00 0.00 2.43
6393 9389 3.701532 AGTACGAGCTAGATGCAGTTC 57.298 47.619 0.00 0.00 45.94 3.01
6410 9406 3.859411 TGCGTCACATGACACATAGTA 57.141 42.857 12.32 0.00 44.99 1.82
6430 9426 2.810400 CGATGAGTGGGTTGAAGGTGTT 60.810 50.000 0.00 0.00 0.00 3.32
6436 9432 3.678806 GCACTATCGATGAGTGGGTTGAA 60.679 47.826 24.03 0.00 43.78 2.69
6466 9462 2.035704 CGATGGTGAGAGGAAGAGATGG 59.964 54.545 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.