Multiple sequence alignment - TraesCS7A01G278600

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 TraesCS7A01G278600 chr7A 100.000 4902 0 0 1 4902 294414605 294409704 0.000000e+00 9053.0
1 TraesCS7A01G278600 chr7A 93.548 62 1 2 463 522 678972827 678972887 6.760000e-14 89.8
2 TraesCS7A01G278600 chr7A 93.548 62 1 2 463 522 678987036 678987096 6.760000e-14 89.8
3 TraesCS7A01G278600 chr7D 94.890 3307 82 27 1636 4902 268554368 268551109 0.000000e+00 5090.0
4 TraesCS7A01G278600 chr7D 83.705 1706 133 78 3 1597 268556045 268554374 0.000000e+00 1476.0
5 TraesCS7A01G278600 chr7D 93.548 62 4 0 461 522 610533503 610533442 5.220000e-15 93.5
6 TraesCS7A01G278600 chr7D 89.552 67 4 3 457 522 21093729 21093665 1.130000e-11 82.4
7 TraesCS7A01G278600 chr7B 94.029 3316 96 34 1636 4902 248548626 248545364 0.000000e+00 4933.0
8 TraesCS7A01G278600 chr7B 87.374 895 61 28 588 1449 248549745 248548870 0.000000e+00 979.0
9 TraesCS7A01G278600 chr6A 94.828 58 3 0 465 522 611177947 611178004 1.880000e-14 91.6
10 TraesCS7A01G278600 chr6A 94.737 57 1 2 469 525 444676711 444676657 2.430000e-13 87.9
11 TraesCS7A01G278600 chr2D 91.803 61 5 0 462 522 349931226 349931286 8.740000e-13 86.1
12 TraesCS7A01G278600 chr2A 89.706 68 4 3 468 532 453795648 453795715 3.140000e-12 84.2


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 TraesCS7A01G278600 chr7A 294409704 294414605 4901 True 9053 9053 100.0000 1 4902 1 chr7A.!!$R1 4901
1 TraesCS7A01G278600 chr7D 268551109 268556045 4936 True 3283 5090 89.2975 3 4902 2 chr7D.!!$R3 4899
2 TraesCS7A01G278600 chr7B 248545364 248549745 4381 True 2956 4933 90.7015 588 4902 2 chr7B.!!$R1 4314

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
84 86 0.107508 GTGGCTTGATCTAGCTGGCA 60.108 55.000 24.93 14.06 40.99 4.92 F
934 994 0.176680 TCTGCTCGCATCTTCCTTCC 59.823 55.000 0.00 0.00 0.00 3.46 F
935 995 0.177604 CTGCTCGCATCTTCCTTCCT 59.822 55.000 0.00 0.00 0.00 3.36 F
1602 1806 0.470766 TGGTTGGCAAACGTAGAGGT 59.529 50.000 11.20 0.00 37.15 3.85 F
1603 1807 1.134037 TGGTTGGCAAACGTAGAGGTT 60.134 47.619 11.20 0.00 37.15 3.50 F
2880 3096 2.100197 GTTAGGCCATCAAAAGGGACC 58.900 52.381 5.01 0.00 33.58 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1136 1200 0.105709 AACAACAGGTGGGAAAGGGG 60.106 55.000 0.00 0.00 0.00 4.79 R
2880 3096 0.314935 ACCTTGCTTGCAAATGACGG 59.685 50.000 9.39 8.84 0.00 4.79 R
2912 3128 2.281761 AAAGCTCCACCCAGCACG 60.282 61.111 0.00 0.00 42.40 5.34 R
3193 3420 5.543020 GCTAGTAGTTAACCCCCATACTCAT 59.457 44.000 0.88 0.00 0.00 2.90 R
3303 3530 6.108687 CCAATCTCTGTAGAACTTGCACATA 58.891 40.000 0.00 0.00 34.73 2.29 R
4236 4480 1.207329 AGATCAGGTTTAGCCCGACAC 59.793 52.381 0.00 0.00 38.26 3.67 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
36 37 4.265056 GAAGGTGGCGTGGTGGGT 62.265 66.667 0.00 0.00 0.00 4.51
80 82 1.211457 CCTTGGTGGCTTGATCTAGCT 59.789 52.381 24.93 0.00 40.99 3.32
82 84 0.543277 TGGTGGCTTGATCTAGCTGG 59.457 55.000 24.93 0.00 40.99 4.85
83 85 0.817229 GGTGGCTTGATCTAGCTGGC 60.817 60.000 24.93 15.89 40.99 4.85
84 86 0.107508 GTGGCTTGATCTAGCTGGCA 60.108 55.000 24.93 14.06 40.99 4.92
85 87 0.179702 TGGCTTGATCTAGCTGGCAG 59.820 55.000 24.93 10.94 40.99 4.85
86 88 0.179936 GGCTTGATCTAGCTGGCAGT 59.820 55.000 24.93 5.61 40.99 4.40
120 137 2.047560 GGTTCCCTTCCACGACGG 60.048 66.667 0.00 0.00 0.00 4.79
132 149 1.134640 CCACGACGGTTATGGATCCAA 60.135 52.381 20.67 5.49 35.33 3.53
168 185 0.915364 GATGGCAACCTCCCTTCTCT 59.085 55.000 0.00 0.00 0.00 3.10
172 189 0.322906 GCAACCTCCCTTCTCTTGGG 60.323 60.000 0.00 0.00 45.90 4.12
212 229 5.528043 TGCTACCAATTCTCTCATCTCTC 57.472 43.478 0.00 0.00 0.00 3.20
216 233 6.424509 GCTACCAATTCTCTCATCTCTCATTG 59.575 42.308 0.00 0.00 0.00 2.82
227 244 8.703378 TCTCATCTCTCATTGAATAGCTTAGA 57.297 34.615 0.00 0.00 0.00 2.10
232 249 7.711846 TCTCTCATTGAATAGCTTAGACACTC 58.288 38.462 0.00 0.00 0.00 3.51
234 251 7.261325 TCTCATTGAATAGCTTAGACACTCAC 58.739 38.462 0.00 0.00 0.00 3.51
300 319 8.830201 ATGAATATTTTAGCAACAAAAGCACA 57.170 26.923 0.00 0.00 31.29 4.57
330 349 6.276091 TGATCCATAATTCTTGTCGTGAGAG 58.724 40.000 0.00 0.00 43.49 3.20
349 368 7.009631 CGTGAGAGAAGAACGACATTATTTCAT 59.990 37.037 0.00 0.00 39.64 2.57
350 369 8.113062 GTGAGAGAAGAACGACATTATTTCATG 58.887 37.037 0.00 0.00 0.00 3.07
369 388 2.040544 CCAATTGCGACGGAGGCTT 61.041 57.895 0.00 0.00 0.00 4.35
375 394 2.391389 GCGACGGAGGCTTTTCTGG 61.391 63.158 0.00 0.00 0.00 3.86
377 396 1.003233 GACGGAGGCTTTTCTGGCT 60.003 57.895 0.00 0.00 45.80 4.75
386 405 1.528129 CTTTTCTGGCTGACACCTCC 58.472 55.000 0.00 0.00 0.00 4.30
404 423 0.669318 CCAGAAGGCGCGACACTAAA 60.669 55.000 17.71 0.00 0.00 1.85
419 438 6.128227 GCGACACTAAAATTACCCACATGTAA 60.128 38.462 0.00 0.00 35.33 2.41
420 439 7.238571 CGACACTAAAATTACCCACATGTAAC 58.761 38.462 0.00 0.00 33.78 2.50
425 444 6.716934 AAAATTACCCACATGTAACACACA 57.283 33.333 0.00 0.00 42.69 3.72
431 450 3.629855 CCCACATGTAACACACACAAAGA 59.370 43.478 0.00 0.00 40.86 2.52
436 455 7.277539 CCACATGTAACACACACAAAGAAAAAT 59.722 33.333 0.00 0.00 40.86 1.82
437 456 8.320295 CACATGTAACACACACAAAGAAAAATC 58.680 33.333 0.00 0.00 40.86 2.17
438 457 8.031864 ACATGTAACACACACAAAGAAAAATCA 58.968 29.630 0.00 0.00 40.86 2.57
439 458 7.804614 TGTAACACACACAAAGAAAAATCAC 57.195 32.000 0.00 0.00 30.04 3.06
440 459 7.371159 TGTAACACACACAAAGAAAAATCACA 58.629 30.769 0.00 0.00 30.04 3.58
449 469 8.031864 ACACAAAGAAAAATCACACACATGTAA 58.968 29.630 0.00 0.00 36.72 2.41
479 499 6.978080 GTCAAATCAAACAAAAAGCTACTCCA 59.022 34.615 0.00 0.00 0.00 3.86
485 505 3.751518 ACAAAAAGCTACTCCATCCGTT 58.248 40.909 0.00 0.00 0.00 4.44
486 506 4.142038 ACAAAAAGCTACTCCATCCGTTT 58.858 39.130 0.00 0.00 0.00 3.60
487 507 4.215613 ACAAAAAGCTACTCCATCCGTTTC 59.784 41.667 0.00 0.00 0.00 2.78
491 511 4.222124 AGCTACTCCATCCGTTTCAAAT 57.778 40.909 0.00 0.00 0.00 2.32
496 516 6.238130 GCTACTCCATCCGTTTCAAATTACTC 60.238 42.308 0.00 0.00 0.00 2.59
500 520 4.491924 CCATCCGTTTCAAATTACTCGTCG 60.492 45.833 0.00 0.00 0.00 5.12
501 521 2.409378 TCCGTTTCAAATTACTCGTCGC 59.591 45.455 0.00 0.00 0.00 5.19
512 532 1.645034 ACTCGTCGCAGAAATGGATG 58.355 50.000 0.00 0.00 39.69 3.51
521 541 6.216569 GTCGCAGAAATGGATGTATCTAGAA 58.783 40.000 0.00 0.00 39.69 2.10
522 542 6.870965 GTCGCAGAAATGGATGTATCTAGAAT 59.129 38.462 0.00 0.00 39.69 2.40
523 543 8.029522 GTCGCAGAAATGGATGTATCTAGAATA 58.970 37.037 0.00 0.00 39.69 1.75
527 576 9.347934 CAGAAATGGATGTATCTAGAATACGAC 57.652 37.037 0.00 0.00 0.00 4.34
552 601 1.203112 TGTGGGGATGCCTTTGCTTTA 60.203 47.619 2.19 0.00 38.71 1.85
565 614 5.276270 CCTTTGCTTTATGGACATGATTCG 58.724 41.667 0.00 0.00 0.00 3.34
571 620 6.806249 TGCTTTATGGACATGATTCGTTTTTC 59.194 34.615 0.00 0.00 0.00 2.29
574 623 9.410556 CTTTATGGACATGATTCGTTTTTCTTT 57.589 29.630 0.00 0.00 0.00 2.52
575 624 9.757227 TTTATGGACATGATTCGTTTTTCTTTT 57.243 25.926 0.00 0.00 0.00 2.27
577 626 7.462109 TGGACATGATTCGTTTTTCTTTTTG 57.538 32.000 0.00 0.00 0.00 2.44
578 627 6.478344 TGGACATGATTCGTTTTTCTTTTTGG 59.522 34.615 0.00 0.00 0.00 3.28
579 628 6.478673 GGACATGATTCGTTTTTCTTTTTGGT 59.521 34.615 0.00 0.00 0.00 3.67
580 629 7.232945 ACATGATTCGTTTTTCTTTTTGGTG 57.767 32.000 0.00 0.00 0.00 4.17
581 630 7.038659 ACATGATTCGTTTTTCTTTTTGGTGA 58.961 30.769 0.00 0.00 0.00 4.02
583 632 6.039616 TGATTCGTTTTTCTTTTTGGTGAGG 58.960 36.000 0.00 0.00 0.00 3.86
584 633 5.646577 TTCGTTTTTCTTTTTGGTGAGGA 57.353 34.783 0.00 0.00 0.00 3.71
586 635 6.026947 TCGTTTTTCTTTTTGGTGAGGAAA 57.973 33.333 0.00 0.00 0.00 3.13
588 637 5.290885 CGTTTTTCTTTTTGGTGAGGAAAGG 59.709 40.000 0.00 0.00 32.62 3.11
589 638 6.403049 GTTTTTCTTTTTGGTGAGGAAAGGA 58.597 36.000 0.00 0.00 32.62 3.36
590 639 5.592104 TTTCTTTTTGGTGAGGAAAGGAC 57.408 39.130 0.00 0.00 32.62 3.85
591 640 4.243793 TCTTTTTGGTGAGGAAAGGACA 57.756 40.909 0.00 0.00 32.62 4.02
592 641 4.803452 TCTTTTTGGTGAGGAAAGGACAT 58.197 39.130 0.00 0.00 32.62 3.06
593 642 4.584325 TCTTTTTGGTGAGGAAAGGACATG 59.416 41.667 0.00 0.00 32.62 3.21
739 788 5.503927 CAAGATCTCATCTTCCTTTTCCCA 58.496 41.667 0.00 0.00 46.17 4.37
742 791 7.457380 AGATCTCATCTTCCTTTTCCCATTA 57.543 36.000 0.00 0.00 35.76 1.90
743 792 7.876371 AGATCTCATCTTCCTTTTCCCATTAA 58.124 34.615 0.00 0.00 35.76 1.40
813 867 1.770749 TACCCCCAACCTTCCGTGTG 61.771 60.000 0.00 0.00 0.00 3.82
859 914 0.951040 AGCGAGGCTCGTTGGAAAAG 60.951 55.000 34.41 7.30 42.81 2.27
863 918 0.250770 AGGCTCGTTGGAAAAGGGAC 60.251 55.000 0.00 0.00 32.04 4.46
864 919 0.536460 GGCTCGTTGGAAAAGGGACA 60.536 55.000 0.00 0.00 32.27 4.02
865 920 0.875059 GCTCGTTGGAAAAGGGACAG 59.125 55.000 0.00 0.00 0.00 3.51
866 921 1.814248 GCTCGTTGGAAAAGGGACAGT 60.814 52.381 0.00 0.00 0.00 3.55
867 922 2.143925 CTCGTTGGAAAAGGGACAGTC 58.856 52.381 0.00 0.00 0.00 3.51
868 923 1.766496 TCGTTGGAAAAGGGACAGTCT 59.234 47.619 0.00 0.00 0.00 3.24
897 956 2.668550 AAAGGGCGAGGTTGCGTC 60.669 61.111 0.00 0.00 35.06 5.19
933 993 1.569708 CTCTGCTCGCATCTTCCTTC 58.430 55.000 0.00 0.00 0.00 3.46
934 994 0.176680 TCTGCTCGCATCTTCCTTCC 59.823 55.000 0.00 0.00 0.00 3.46
935 995 0.177604 CTGCTCGCATCTTCCTTCCT 59.822 55.000 0.00 0.00 0.00 3.36
936 996 0.615331 TGCTCGCATCTTCCTTCCTT 59.385 50.000 0.00 0.00 0.00 3.36
1110 1174 4.224818 CCCTTCTCCATTGTTTCTCTCTCT 59.775 45.833 0.00 0.00 0.00 3.10
1111 1175 5.418676 CCTTCTCCATTGTTTCTCTCTCTC 58.581 45.833 0.00 0.00 0.00 3.20
1112 1176 5.187576 CCTTCTCCATTGTTTCTCTCTCTCT 59.812 44.000 0.00 0.00 0.00 3.10
1113 1177 5.913137 TCTCCATTGTTTCTCTCTCTCTC 57.087 43.478 0.00 0.00 0.00 3.20
1124 1188 2.872245 CTCTCTCTCTCGCTTCGATTCT 59.128 50.000 0.00 0.00 34.61 2.40
1128 1192 1.064803 TCTCTCGCTTCGATTCTCTGC 59.935 52.381 0.00 0.00 34.61 4.26
1131 1195 2.289274 TCTCGCTTCGATTCTCTGCTAG 59.711 50.000 0.00 0.00 34.61 3.42
1135 1199 3.120041 GCTTCGATTCTCTGCTAGTTCC 58.880 50.000 0.00 0.00 0.00 3.62
1136 1200 3.712187 CTTCGATTCTCTGCTAGTTCCC 58.288 50.000 0.00 0.00 0.00 3.97
1138 1202 1.069358 CGATTCTCTGCTAGTTCCCCC 59.931 57.143 0.00 0.00 0.00 5.40
1154 1224 1.541672 CCCCTTTCCCACCTGTTGT 59.458 57.895 0.00 0.00 0.00 3.32
1166 1236 4.321899 CCCACCTGTTGTTGACATTAATGG 60.322 45.833 19.37 0.33 37.69 3.16
1172 1242 6.097270 CCTGTTGTTGACATTAATGGATGGAT 59.903 38.462 19.37 0.00 37.69 3.41
1173 1243 6.865411 TGTTGTTGACATTAATGGATGGATG 58.135 36.000 19.37 0.00 32.00 3.51
1175 1245 5.764432 TGTTGACATTAATGGATGGATGGA 58.236 37.500 19.37 0.00 0.00 3.41
1176 1246 5.829391 TGTTGACATTAATGGATGGATGGAG 59.171 40.000 19.37 0.00 0.00 3.86
1177 1247 5.910355 TGACATTAATGGATGGATGGAGA 57.090 39.130 19.37 0.00 0.00 3.71
1182 1252 2.811322 ATGGATGGATGGAGAGGAGT 57.189 50.000 0.00 0.00 0.00 3.85
1183 1253 1.798626 TGGATGGATGGAGAGGAGTG 58.201 55.000 0.00 0.00 0.00 3.51
1184 1254 1.008815 TGGATGGATGGAGAGGAGTGT 59.991 52.381 0.00 0.00 0.00 3.55
1185 1255 1.415659 GGATGGATGGAGAGGAGTGTG 59.584 57.143 0.00 0.00 0.00 3.82
1186 1256 0.835941 ATGGATGGAGAGGAGTGTGC 59.164 55.000 0.00 0.00 0.00 4.57
1188 1258 0.908198 GGATGGAGAGGAGTGTGCTT 59.092 55.000 0.00 0.00 0.00 3.91
1206 1284 2.539750 GCTTGCTAGGCAGAAATTACGC 60.540 50.000 0.00 0.00 40.61 4.42
1229 1307 7.060748 ACGCTTCGTTATCATATTCTAACATCG 59.939 37.037 5.48 0.00 36.35 3.84
1247 1328 1.373748 GCGTACCACGAAAGCTCCA 60.374 57.895 2.35 0.00 46.05 3.86
1248 1329 1.623973 GCGTACCACGAAAGCTCCAC 61.624 60.000 2.35 0.00 46.05 4.02
1265 1346 4.320275 GCTCCACTTTGCTGTTACTTTACC 60.320 45.833 0.00 0.00 0.00 2.85
1266 1347 4.783055 TCCACTTTGCTGTTACTTTACCA 58.217 39.130 0.00 0.00 0.00 3.25
1289 1375 2.590575 CTCGCACGTGGTTGGGTT 60.591 61.111 18.88 0.00 0.00 4.11
1290 1376 1.301087 CTCGCACGTGGTTGGGTTA 60.301 57.895 18.88 0.00 0.00 2.85
1291 1377 0.672401 CTCGCACGTGGTTGGGTTAT 60.672 55.000 18.88 0.00 0.00 1.89
1292 1378 0.951525 TCGCACGTGGTTGGGTTATG 60.952 55.000 18.88 0.00 0.00 1.90
1301 1387 2.291024 TGGTTGGGTTATGTATGGCGTT 60.291 45.455 0.00 0.00 0.00 4.84
1354 1443 2.890474 GCCGTGCCACCATCTACG 60.890 66.667 0.00 0.00 36.39 3.51
1362 1451 1.355971 CCACCATCTACGACGGTTTG 58.644 55.000 0.00 0.00 0.00 2.93
1394 1488 1.889829 CCTTCTTCAGTGGAGTCGAGT 59.110 52.381 0.00 0.00 0.00 4.18
1397 1491 2.085320 TCTTCAGTGGAGTCGAGTAGC 58.915 52.381 0.00 0.00 0.00 3.58
1402 1496 3.069016 TCAGTGGAGTCGAGTAGCAAAAA 59.931 43.478 0.00 0.00 0.00 1.94
1403 1497 3.184581 CAGTGGAGTCGAGTAGCAAAAAC 59.815 47.826 0.00 0.00 0.00 2.43
1443 1539 4.816925 AGTTTTCTTCTGCAAGTGGAGTAC 59.183 41.667 0.00 0.00 34.87 2.73
1446 1542 5.392767 TTCTTCTGCAAGTGGAGTACTAG 57.607 43.478 0.00 0.00 39.18 2.57
1449 1545 5.415077 TCTTCTGCAAGTGGAGTACTAGTAC 59.585 44.000 23.03 23.03 39.18 2.73
1450 1546 4.919793 TCTGCAAGTGGAGTACTAGTACT 58.080 43.478 31.10 31.10 41.50 2.73
1466 1648 9.657121 GTACTAGTACTTACTTAATTAGCACCG 57.343 37.037 23.17 0.00 37.73 4.94
1472 1654 5.350640 ACTTACTTAATTAGCACCGAACTGC 59.649 40.000 0.00 0.00 37.44 4.40
1475 1657 0.796312 AATTAGCACCGAACTGCACG 59.204 50.000 3.07 0.00 39.86 5.34
1480 1662 2.126071 ACCGAACTGCACGATCCG 60.126 61.111 0.00 0.00 0.00 4.18
1497 1700 1.736249 CCGTTCGCTAGTTTACGGCG 61.736 60.000 4.80 4.80 45.75 6.46
1510 1713 2.052237 CGGCGCCGTAATTGATGC 60.052 61.111 39.71 0.53 34.35 3.91
1511 1714 2.534019 CGGCGCCGTAATTGATGCT 61.534 57.895 39.71 0.00 34.35 3.79
1512 1715 1.218875 CGGCGCCGTAATTGATGCTA 61.219 55.000 39.71 0.00 34.35 3.49
1514 1717 1.217882 GCGCCGTAATTGATGCTAGT 58.782 50.000 0.00 0.00 0.00 2.57
1515 1718 2.400399 GCGCCGTAATTGATGCTAGTA 58.600 47.619 0.00 0.00 0.00 1.82
1516 1719 2.993899 GCGCCGTAATTGATGCTAGTAT 59.006 45.455 0.00 0.00 0.00 2.12
1517 1720 3.181530 GCGCCGTAATTGATGCTAGTATG 60.182 47.826 0.00 0.00 0.00 2.39
1532 1736 8.704849 ATGCTAGTATGAGAGTTGTATCTTCT 57.295 34.615 0.00 0.00 0.00 2.85
1534 1738 7.041712 TGCTAGTATGAGAGTTGTATCTTCTCG 60.042 40.741 0.00 0.00 33.96 4.04
1554 1758 2.789339 CGCGAACATAGTGACATCGATT 59.211 45.455 0.00 0.00 35.65 3.34
1594 1798 6.367695 GGATACAACTTTTATGGTTGGCAAAC 59.632 38.462 8.70 8.70 45.61 2.93
1597 1801 5.163540 ACAACTTTTATGGTTGGCAAACGTA 60.164 36.000 13.06 13.06 45.61 3.57
1598 1802 5.116069 ACTTTTATGGTTGGCAAACGTAG 57.884 39.130 16.14 10.21 37.15 3.51
1600 1804 5.048991 ACTTTTATGGTTGGCAAACGTAGAG 60.049 40.000 16.14 18.33 37.15 2.43
1602 1806 0.470766 TGGTTGGCAAACGTAGAGGT 59.529 50.000 11.20 0.00 37.15 3.85
1603 1807 1.134037 TGGTTGGCAAACGTAGAGGTT 60.134 47.619 11.20 0.00 37.15 3.50
1612 1816 5.418310 CAAACGTAGAGGTTGTGTCAATT 57.582 39.130 0.00 0.00 42.44 2.32
1613 1817 6.533819 CAAACGTAGAGGTTGTGTCAATTA 57.466 37.500 0.00 0.00 42.44 1.40
1614 1818 7.129109 CAAACGTAGAGGTTGTGTCAATTAT 57.871 36.000 0.00 0.00 42.44 1.28
1615 1819 8.246908 CAAACGTAGAGGTTGTGTCAATTATA 57.753 34.615 0.00 0.00 42.44 0.98
1616 1820 8.714179 CAAACGTAGAGGTTGTGTCAATTATAA 58.286 33.333 0.00 0.00 42.44 0.98
1617 1821 9.444600 AAACGTAGAGGTTGTGTCAATTATAAT 57.555 29.630 0.00 0.00 0.00 1.28
1618 1822 9.444600 AACGTAGAGGTTGTGTCAATTATAATT 57.555 29.630 4.81 4.81 0.00 1.40
1619 1823 9.095065 ACGTAGAGGTTGTGTCAATTATAATTC 57.905 33.333 7.76 0.00 0.00 2.17
1620 1824 8.266682 CGTAGAGGTTGTGTCAATTATAATTCG 58.733 37.037 7.76 4.86 0.00 3.34
1621 1825 7.553881 AGAGGTTGTGTCAATTATAATTCGG 57.446 36.000 7.76 0.00 0.00 4.30
1622 1826 7.335627 AGAGGTTGTGTCAATTATAATTCGGA 58.664 34.615 7.76 1.33 0.00 4.55
1623 1827 7.993183 AGAGGTTGTGTCAATTATAATTCGGAT 59.007 33.333 7.76 0.00 0.00 4.18
1624 1828 8.519799 AGGTTGTGTCAATTATAATTCGGATT 57.480 30.769 7.76 0.00 0.00 3.01
1625 1829 8.405531 AGGTTGTGTCAATTATAATTCGGATTG 58.594 33.333 7.76 0.00 0.00 2.67
1626 1830 7.647715 GGTTGTGTCAATTATAATTCGGATTGG 59.352 37.037 7.76 0.00 31.97 3.16
1627 1831 8.402472 GTTGTGTCAATTATAATTCGGATTGGA 58.598 33.333 7.76 0.00 31.97 3.53
1628 1832 8.153479 TGTGTCAATTATAATTCGGATTGGAG 57.847 34.615 7.76 0.00 31.97 3.86
1629 1833 7.228507 TGTGTCAATTATAATTCGGATTGGAGG 59.771 37.037 7.76 0.00 31.97 4.30
1630 1834 6.714810 TGTCAATTATAATTCGGATTGGAGGG 59.285 38.462 7.76 0.00 31.97 4.30
1631 1835 6.940298 GTCAATTATAATTCGGATTGGAGGGA 59.060 38.462 7.76 0.00 31.97 4.20
1632 1836 7.119846 GTCAATTATAATTCGGATTGGAGGGAG 59.880 40.741 7.76 0.00 31.97 4.30
1633 1837 6.704056 ATTATAATTCGGATTGGAGGGAGT 57.296 37.500 0.00 0.00 0.00 3.85
1634 1838 7.808279 ATTATAATTCGGATTGGAGGGAGTA 57.192 36.000 0.00 0.00 0.00 2.59
1650 1854 9.166222 TGGAGGGAGTATTATTTATGCTTCTTA 57.834 33.333 0.00 0.00 28.37 2.10
1755 1959 5.179452 AGGATGCTGGTGTACATACTTTT 57.821 39.130 0.00 0.00 33.51 2.27
1821 2025 3.846754 GCATGCGCAACTCAAACC 58.153 55.556 17.11 0.00 38.36 3.27
1861 2065 6.828788 ACTACTACACGATATCTCCTTCTCA 58.171 40.000 0.34 0.00 0.00 3.27
1870 2074 6.310711 ACGATATCTCCTTCTCAAAACGAAAC 59.689 38.462 0.34 0.00 0.00 2.78
1875 2079 6.319399 TCTCCTTCTCAAAACGAAACAAAAC 58.681 36.000 0.00 0.00 0.00 2.43
1877 2081 6.448006 TCCTTCTCAAAACGAAACAAAACAA 58.552 32.000 0.00 0.00 0.00 2.83
1878 2082 6.924060 TCCTTCTCAAAACGAAACAAAACAAA 59.076 30.769 0.00 0.00 0.00 2.83
1879 2083 7.438459 TCCTTCTCAAAACGAAACAAAACAAAA 59.562 29.630 0.00 0.00 0.00 2.44
1880 2084 7.529185 CCTTCTCAAAACGAAACAAAACAAAAC 59.471 33.333 0.00 0.00 0.00 2.43
1881 2085 7.464830 TCTCAAAACGAAACAAAACAAAACA 57.535 28.000 0.00 0.00 0.00 2.83
1882 2086 7.906160 TCTCAAAACGAAACAAAACAAAACAA 58.094 26.923 0.00 0.00 0.00 2.83
1883 2087 8.388103 TCTCAAAACGAAACAAAACAAAACAAA 58.612 25.926 0.00 0.00 0.00 2.83
1884 2088 8.889849 TCAAAACGAAACAAAACAAAACAAAA 57.110 23.077 0.00 0.00 0.00 2.44
1885 2089 9.337091 TCAAAACGAAACAAAACAAAACAAAAA 57.663 22.222 0.00 0.00 0.00 1.94
1886 2090 9.385798 CAAAACGAAACAAAACAAAACAAAAAC 57.614 25.926 0.00 0.00 0.00 2.43
1898 2102 5.105513 ACAAAACAAAAACCCTCACCTGTAG 60.106 40.000 0.00 0.00 0.00 2.74
2020 2224 4.352009 TCATTGGGCTGACAACCATATTT 58.648 39.130 0.00 0.00 36.48 1.40
2026 2230 3.253230 GCTGACAACCATATTTGGCAAC 58.747 45.455 0.00 0.00 44.08 4.17
2035 2239 3.064820 CCATATTTGGCAACGTCACTACC 59.935 47.826 0.00 0.00 35.85 3.18
2100 2304 4.354587 CACTGTTGAGTTTTGCTTCTTCC 58.645 43.478 0.00 0.00 0.00 3.46
2332 2548 5.426833 ACTCTTGAGTGCCTACTGGATTATT 59.573 40.000 2.11 0.00 37.25 1.40
2565 2781 4.035441 TGTTAAACTACAGTTTCGGTTGGC 59.965 41.667 10.51 0.00 44.15 4.52
2649 2865 2.169769 TGGATCCGATGGTCTTGGTAAC 59.830 50.000 7.39 0.00 0.00 2.50
2821 3037 4.376340 AAAGCTATTTACCATGCTGTGC 57.624 40.909 0.00 0.00 35.79 4.57
2824 3040 7.522725 ATAAAGCTATTTACCATGCTGTGCATC 60.523 37.037 1.70 0.00 39.23 3.91
2880 3096 2.100197 GTTAGGCCATCAAAAGGGACC 58.900 52.381 5.01 0.00 33.58 4.46
3033 3249 2.879826 AGCAGAAACAACAACACAAGC 58.120 42.857 0.00 0.00 0.00 4.01
3173 3398 3.861276 TTACAGGTGATACCAGTGTCG 57.139 47.619 6.33 0.00 41.95 4.35
3193 3420 5.048294 TGTCGTCTTCATAGCTCAACTTGTA 60.048 40.000 0.00 0.00 0.00 2.41
3410 3637 0.798776 AAGTTGCCGCTGAATCTTCG 59.201 50.000 0.00 0.00 0.00 3.79
3585 3812 8.635328 CATACTTTGATGGATCATGGATTGAAA 58.365 33.333 0.00 0.00 38.03 2.69
3724 3951 6.238648 CAGTCCACTGGGTTAAATTCTAACT 58.761 40.000 0.00 0.00 40.20 2.24
3779 4006 5.160699 GCAAGATATTGATTGCTCGTTCA 57.839 39.130 3.77 0.00 46.49 3.18
3980 4207 2.901839 ACTCTCATGGCCAAAGCATTTT 59.098 40.909 10.96 0.00 42.56 1.82
4157 4392 0.179043 TACTCGTTGCTTTGTGCCCA 60.179 50.000 0.00 0.00 42.00 5.36
4161 4396 0.314935 CGTTGCTTTGTGCCCATCTT 59.685 50.000 0.00 0.00 42.00 2.40
4162 4397 1.787012 GTTGCTTTGTGCCCATCTTG 58.213 50.000 0.00 0.00 42.00 3.02
4193 4437 2.133281 AGCAGGCATATCTTTGCACA 57.867 45.000 0.00 0.00 44.59 4.57
4236 4480 2.423185 TCTATTTGCTCATGTTTGGCCG 59.577 45.455 0.00 0.00 0.00 6.13
4284 4528 3.511540 TGAGAGGTCGAACTGAACATGAT 59.488 43.478 8.28 0.00 36.45 2.45
4307 4551 8.421784 TGATTTGGCACTACTTCCTACTTATAG 58.578 37.037 0.00 0.00 0.00 1.31
4377 4621 1.469595 CGAACCGATTGCCATGCATTT 60.470 47.619 0.00 0.00 38.76 2.32
4422 4666 8.905850 TGCTTCAAACATGACATGAATACATAT 58.094 29.630 22.19 0.00 35.09 1.78
4773 5038 6.267242 TCTTGGGATCAAAATTGAACATGTCA 59.733 34.615 0.00 0.00 41.13 3.58
4893 5162 2.167662 TGAGACGTGAAGGACATGCTA 58.832 47.619 0.00 0.00 38.94 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.841663 CGCCACCTTCAGGAACAACG 61.842 60.000 0.00 0.00 38.94 4.10
12 13 1.227823 CACGCCACCTTCAGGAACA 60.228 57.895 0.00 0.00 38.94 3.18
63 65 0.543277 CCAGCTAGATCAAGCCACCA 59.457 55.000 0.00 0.00 43.86 4.17
105 122 1.066716 CATAACCGTCGTGGAAGGGAA 60.067 52.381 3.47 0.00 42.00 3.97
116 133 2.213499 CAGCTTGGATCCATAACCGTC 58.787 52.381 17.06 0.08 0.00 4.79
145 162 1.201429 AAGGGAGGTTGCCATCGACT 61.201 55.000 0.00 0.00 0.00 4.18
150 167 1.005215 CAAGAGAAGGGAGGTTGCCAT 59.995 52.381 0.00 0.00 0.00 4.40
182 199 2.024414 AGAATTGGTAGCAATTCCGCC 58.976 47.619 38.04 24.20 46.94 6.13
183 200 2.945668 AGAGAATTGGTAGCAATTCCGC 59.054 45.455 38.04 32.18 46.94 5.54
193 210 7.666063 TCAATGAGAGATGAGAGAATTGGTA 57.334 36.000 0.00 0.00 0.00 3.25
205 222 8.143193 AGTGTCTAAGCTATTCAATGAGAGATG 58.857 37.037 0.00 0.00 0.00 2.90
207 224 7.340487 TGAGTGTCTAAGCTATTCAATGAGAGA 59.660 37.037 0.00 0.00 0.00 3.10
212 229 8.194104 AGTAGTGAGTGTCTAAGCTATTCAATG 58.806 37.037 0.00 0.00 0.00 2.82
296 314 9.224267 ACAAGAATTATGGATCATAGTATGTGC 57.776 33.333 9.94 4.13 0.00 4.57
300 319 9.645059 CACGACAAGAATTATGGATCATAGTAT 57.355 33.333 0.00 0.00 0.00 2.12
305 324 6.820335 TCTCACGACAAGAATTATGGATCAT 58.180 36.000 0.00 0.00 0.00 2.45
330 349 5.879237 TGGCATGAAATAATGTCGTTCTTC 58.121 37.500 0.00 0.00 34.80 2.87
333 352 6.508404 GCAATTGGCATGAAATAATGTCGTTC 60.508 38.462 7.72 0.00 43.97 3.95
337 356 5.042593 TCGCAATTGGCATGAAATAATGTC 58.957 37.500 7.72 0.00 45.17 3.06
349 368 2.745884 CCTCCGTCGCAATTGGCA 60.746 61.111 7.72 0.00 45.17 4.92
350 369 4.179579 GCCTCCGTCGCAATTGGC 62.180 66.667 7.72 0.00 39.90 4.52
369 388 2.538790 TGGAGGTGTCAGCCAGAAA 58.461 52.632 0.00 0.00 0.00 2.52
386 405 1.144969 TTTTAGTGTCGCGCCTTCTG 58.855 50.000 0.00 0.00 0.00 3.02
394 413 4.155280 ACATGTGGGTAATTTTAGTGTCGC 59.845 41.667 0.00 0.00 0.00 5.19
396 415 8.019094 GTGTTACATGTGGGTAATTTTAGTGTC 58.981 37.037 9.11 0.00 35.83 3.67
397 416 7.502895 TGTGTTACATGTGGGTAATTTTAGTGT 59.497 33.333 9.11 0.00 35.83 3.55
398 417 7.806014 GTGTGTTACATGTGGGTAATTTTAGTG 59.194 37.037 9.11 0.00 35.83 2.74
404 423 5.133941 TGTGTGTGTTACATGTGGGTAATT 58.866 37.500 9.11 0.00 42.24 1.40
419 438 5.633182 GTGTGTGATTTTTCTTTGTGTGTGT 59.367 36.000 0.00 0.00 0.00 3.72
420 439 5.632764 TGTGTGTGATTTTTCTTTGTGTGTG 59.367 36.000 0.00 0.00 0.00 3.82
425 444 7.491048 GGTTACATGTGTGTGATTTTTCTTTGT 59.509 33.333 9.11 0.00 39.39 2.83
431 450 4.261825 CGGGGTTACATGTGTGTGATTTTT 60.262 41.667 9.11 0.00 39.39 1.94
436 455 0.759959 ACGGGGTTACATGTGTGTGA 59.240 50.000 9.11 0.00 39.39 3.58
437 456 1.153353 GACGGGGTTACATGTGTGTG 58.847 55.000 9.11 0.00 39.39 3.82
438 457 0.759959 TGACGGGGTTACATGTGTGT 59.240 50.000 9.11 0.00 42.39 3.72
439 458 1.885560 TTGACGGGGTTACATGTGTG 58.114 50.000 9.11 0.00 0.00 3.82
440 459 2.642154 TTTGACGGGGTTACATGTGT 57.358 45.000 9.11 0.00 0.00 3.72
449 469 4.438148 CTTTTTGTTTGATTTGACGGGGT 58.562 39.130 0.00 0.00 0.00 4.95
479 499 3.061697 GCGACGAGTAATTTGAAACGGAT 59.938 43.478 0.00 0.00 0.00 4.18
485 505 5.390461 CCATTTCTGCGACGAGTAATTTGAA 60.390 40.000 0.00 0.00 0.00 2.69
486 506 4.092821 CCATTTCTGCGACGAGTAATTTGA 59.907 41.667 0.00 0.00 0.00 2.69
487 507 4.092821 TCCATTTCTGCGACGAGTAATTTG 59.907 41.667 0.00 0.00 0.00 2.32
491 511 3.186909 CATCCATTTCTGCGACGAGTAA 58.813 45.455 0.00 0.00 0.00 2.24
496 516 3.384668 AGATACATCCATTTCTGCGACG 58.615 45.455 0.00 0.00 0.00 5.12
500 520 8.029522 TCGTATTCTAGATACATCCATTTCTGC 58.970 37.037 0.00 0.00 0.00 4.26
501 521 9.347934 GTCGTATTCTAGATACATCCATTTCTG 57.652 37.037 0.00 0.00 0.00 3.02
512 532 5.333952 CCACACTCCGTCGTATTCTAGATAC 60.334 48.000 0.00 0.00 0.00 2.24
521 541 0.396695 ATCCCCACACTCCGTCGTAT 60.397 55.000 0.00 0.00 0.00 3.06
522 542 1.000521 ATCCCCACACTCCGTCGTA 60.001 57.895 0.00 0.00 0.00 3.43
523 543 2.283676 ATCCCCACACTCCGTCGT 60.284 61.111 0.00 0.00 0.00 4.34
527 576 2.484287 AAAGGCATCCCCACACTCCG 62.484 60.000 0.00 0.00 35.39 4.63
552 601 7.171337 CCAAAAAGAAAAACGAATCATGTCCAT 59.829 33.333 0.00 0.00 0.00 3.41
565 614 6.312918 GTCCTTTCCTCACCAAAAAGAAAAAC 59.687 38.462 0.00 0.00 32.89 2.43
571 620 4.584325 TCATGTCCTTTCCTCACCAAAAAG 59.416 41.667 0.00 0.00 0.00 2.27
574 623 3.874383 TCATGTCCTTTCCTCACCAAA 57.126 42.857 0.00 0.00 0.00 3.28
575 624 4.335416 GAATCATGTCCTTTCCTCACCAA 58.665 43.478 0.00 0.00 0.00 3.67
577 626 2.939103 CGAATCATGTCCTTTCCTCACC 59.061 50.000 0.00 0.00 0.00 4.02
578 627 3.600388 ACGAATCATGTCCTTTCCTCAC 58.400 45.455 0.00 0.00 0.00 3.51
579 628 3.981071 ACGAATCATGTCCTTTCCTCA 57.019 42.857 0.00 0.00 0.00 3.86
580 629 6.927294 AATAACGAATCATGTCCTTTCCTC 57.073 37.500 0.00 0.00 0.00 3.71
581 630 8.840321 CAATAATAACGAATCATGTCCTTTCCT 58.160 33.333 0.00 0.00 0.00 3.36
583 632 7.591426 GGCAATAATAACGAATCATGTCCTTTC 59.409 37.037 0.00 0.00 0.00 2.62
584 633 7.425606 GGCAATAATAACGAATCATGTCCTTT 58.574 34.615 0.00 0.00 0.00 3.11
586 635 5.473504 GGGCAATAATAACGAATCATGTCCT 59.526 40.000 0.00 0.00 0.00 3.85
588 637 5.335661 GGGGGCAATAATAACGAATCATGTC 60.336 44.000 0.00 0.00 0.00 3.06
589 638 4.522789 GGGGGCAATAATAACGAATCATGT 59.477 41.667 0.00 0.00 0.00 3.21
590 639 5.059404 GGGGGCAATAATAACGAATCATG 57.941 43.478 0.00 0.00 0.00 3.07
687 736 3.822192 CCCGTCGGATCAGCGTGA 61.822 66.667 14.39 0.00 0.00 4.35
739 788 1.307647 CTGCTGGGGCTGGGTTAAT 59.692 57.895 0.00 0.00 39.59 1.40
813 867 4.025979 CCGGACTTTTATAGACGATGCAAC 60.026 45.833 0.00 0.00 32.37 4.17
868 923 0.324943 CGCCCTTTCCTTCTCCAGAA 59.675 55.000 0.00 0.00 0.00 3.02
878 937 3.431725 CGCAACCTCGCCCTTTCC 61.432 66.667 0.00 0.00 0.00 3.13
897 956 2.825836 GCCAAGTGGATGAGCGGG 60.826 66.667 0.18 0.00 37.39 6.13
1071 1135 0.636932 AGGGAGGGAGGGAGGGATTA 60.637 60.000 0.00 0.00 0.00 1.75
1110 1174 1.098869 AGCAGAGAATCGAAGCGAGA 58.901 50.000 0.00 0.00 42.67 4.04
1111 1175 2.032799 ACTAGCAGAGAATCGAAGCGAG 59.967 50.000 0.00 0.00 42.67 5.03
1112 1176 2.017782 ACTAGCAGAGAATCGAAGCGA 58.982 47.619 0.00 0.00 42.67 4.93
1113 1177 2.483583 ACTAGCAGAGAATCGAAGCG 57.516 50.000 0.00 0.00 42.67 4.68
1135 1199 1.228862 CAACAGGTGGGAAAGGGGG 60.229 63.158 0.00 0.00 0.00 5.40
1136 1200 0.105709 AACAACAGGTGGGAAAGGGG 60.106 55.000 0.00 0.00 0.00 4.79
1138 1202 1.681264 GTCAACAACAGGTGGGAAAGG 59.319 52.381 0.00 0.00 0.00 3.11
1154 1224 6.264771 TCTCCATCCATCCATTAATGTCAA 57.735 37.500 14.25 0.27 0.00 3.18
1166 1236 1.202627 GCACACTCCTCTCCATCCATC 60.203 57.143 0.00 0.00 0.00 3.51
1172 1242 1.123861 AGCAAGCACACTCCTCTCCA 61.124 55.000 0.00 0.00 0.00 3.86
1173 1243 0.898320 TAGCAAGCACACTCCTCTCC 59.102 55.000 0.00 0.00 0.00 3.71
1175 1245 0.901124 CCTAGCAAGCACACTCCTCT 59.099 55.000 0.00 0.00 0.00 3.69
1176 1246 0.742635 GCCTAGCAAGCACACTCCTC 60.743 60.000 0.00 0.00 0.00 3.71
1177 1247 1.298014 GCCTAGCAAGCACACTCCT 59.702 57.895 0.00 0.00 0.00 3.69
1182 1252 2.205022 ATTTCTGCCTAGCAAGCACA 57.795 45.000 0.00 0.00 38.41 4.57
1183 1253 3.485877 CGTAATTTCTGCCTAGCAAGCAC 60.486 47.826 0.00 0.00 38.41 4.40
1184 1254 2.677836 CGTAATTTCTGCCTAGCAAGCA 59.322 45.455 0.00 0.00 38.41 3.91
1185 1255 2.539750 GCGTAATTTCTGCCTAGCAAGC 60.540 50.000 0.00 0.00 38.41 4.01
1186 1256 2.939103 AGCGTAATTTCTGCCTAGCAAG 59.061 45.455 0.00 0.00 38.41 4.01
1188 1258 2.691409 AGCGTAATTTCTGCCTAGCA 57.309 45.000 0.00 0.00 36.92 3.49
1206 1284 7.060748 ACGCGATGTTAGAATATGATAACGAAG 59.939 37.037 15.93 0.00 35.16 3.79
1229 1307 1.373748 TGGAGCTTTCGTGGTACGC 60.374 57.895 0.00 0.00 42.21 4.42
1247 1328 5.527582 CAGAGTGGTAAAGTAACAGCAAAGT 59.472 40.000 0.00 0.00 0.00 2.66
1248 1329 5.560953 GCAGAGTGGTAAAGTAACAGCAAAG 60.561 44.000 0.00 0.00 0.00 2.77
1255 1336 2.666994 GCGAGCAGAGTGGTAAAGTAAC 59.333 50.000 0.00 0.00 0.00 2.50
1265 1346 3.108289 CCACGTGCGAGCAGAGTG 61.108 66.667 10.91 19.77 36.32 3.51
1266 1347 3.151958 AACCACGTGCGAGCAGAGT 62.152 57.895 10.91 0.00 0.00 3.24
1287 1373 3.440872 TGGGTTGAAACGCCATACATAAC 59.559 43.478 7.66 0.00 40.74 1.89
1289 1375 3.275143 CTGGGTTGAAACGCCATACATA 58.725 45.455 7.66 0.00 40.74 2.29
1290 1376 2.091541 CTGGGTTGAAACGCCATACAT 58.908 47.619 7.66 0.00 40.74 2.29
1291 1377 1.529226 CTGGGTTGAAACGCCATACA 58.471 50.000 7.66 0.00 40.74 2.29
1292 1378 0.170339 GCTGGGTTGAAACGCCATAC 59.830 55.000 7.66 0.08 40.74 2.39
1301 1387 3.565214 TCGGCAGGCTGGGTTGAA 61.565 61.111 17.64 0.00 0.00 2.69
1340 1426 4.088421 CGTCGTAGATGGTGGCAC 57.912 61.111 9.70 9.70 40.43 5.01
1362 1451 1.829222 TGAAGAAGGGGGTATGACGAC 59.171 52.381 0.00 0.00 0.00 4.34
1403 1497 5.524646 AGAAAACTGAACCACAATTGCATTG 59.475 36.000 5.05 7.16 45.59 2.82
1443 1539 9.230932 GTTCGGTGCTAATTAAGTAAGTACTAG 57.769 37.037 0.00 0.00 34.99 2.57
1446 1542 7.463780 GCAGTTCGGTGCTAATTAAGTAAGTAC 60.464 40.741 0.00 0.00 40.54 2.73
1449 1545 5.350365 TGCAGTTCGGTGCTAATTAAGTAAG 59.650 40.000 6.83 0.00 44.32 2.34
1450 1546 5.121142 GTGCAGTTCGGTGCTAATTAAGTAA 59.879 40.000 0.00 0.00 44.32 2.24
1466 1648 1.702299 CGAACGGATCGTGCAGTTC 59.298 57.895 0.00 11.04 46.52 3.01
1497 1700 5.470368 TCTCATACTAGCATCAATTACGGC 58.530 41.667 0.00 0.00 0.00 5.68
1509 1712 7.295201 CGAGAAGATACAACTCTCATACTAGC 58.705 42.308 0.00 0.00 0.00 3.42
1510 1713 7.295201 GCGAGAAGATACAACTCTCATACTAG 58.705 42.308 0.00 0.00 0.00 2.57
1511 1714 6.073711 CGCGAGAAGATACAACTCTCATACTA 60.074 42.308 0.00 0.00 0.00 1.82
1512 1715 5.277586 CGCGAGAAGATACAACTCTCATACT 60.278 44.000 0.00 0.00 0.00 2.12
1514 1717 4.814771 TCGCGAGAAGATACAACTCTCATA 59.185 41.667 3.71 0.00 37.03 2.15
1515 1718 3.628032 TCGCGAGAAGATACAACTCTCAT 59.372 43.478 3.71 0.00 37.03 2.90
1516 1719 3.007635 TCGCGAGAAGATACAACTCTCA 58.992 45.455 3.71 0.00 37.03 3.27
1517 1720 3.677190 TCGCGAGAAGATACAACTCTC 57.323 47.619 3.71 0.00 37.03 3.20
1532 1736 1.399089 TCGATGTCACTATGTTCGCGA 59.601 47.619 3.71 3.71 0.00 5.87
1534 1738 4.267690 TGAAATCGATGTCACTATGTTCGC 59.732 41.667 14.47 0.00 0.00 4.70
1554 1758 3.206964 TGTATCCAACAACGTTGCTGAA 58.793 40.909 28.46 13.10 34.29 3.02
1581 1785 2.303600 ACCTCTACGTTTGCCAACCATA 59.696 45.455 0.00 0.00 0.00 2.74
1585 1789 1.944709 ACAACCTCTACGTTTGCCAAC 59.055 47.619 0.00 0.00 0.00 3.77
1586 1790 1.944024 CACAACCTCTACGTTTGCCAA 59.056 47.619 0.00 0.00 0.00 4.52
1594 1798 8.266682 CGAATTATAATTGACACAACCTCTACG 58.733 37.037 15.39 4.03 0.00 3.51
1597 1801 7.335627 TCCGAATTATAATTGACACAACCTCT 58.664 34.615 15.39 0.00 0.00 3.69
1598 1802 7.548196 TCCGAATTATAATTGACACAACCTC 57.452 36.000 15.39 0.00 0.00 3.85
1600 1804 7.647715 CCAATCCGAATTATAATTGACACAACC 59.352 37.037 15.39 0.00 32.14 3.77
1602 1806 8.512966 TCCAATCCGAATTATAATTGACACAA 57.487 30.769 15.39 0.00 32.14 3.33
1603 1807 7.228507 CCTCCAATCCGAATTATAATTGACACA 59.771 37.037 15.39 0.00 32.14 3.72
1604 1808 7.308589 CCCTCCAATCCGAATTATAATTGACAC 60.309 40.741 15.39 0.47 32.14 3.67
1605 1809 6.714810 CCCTCCAATCCGAATTATAATTGACA 59.285 38.462 15.39 0.00 32.14 3.58
1606 1810 6.940298 TCCCTCCAATCCGAATTATAATTGAC 59.060 38.462 15.39 1.51 32.14 3.18
1607 1811 7.085476 TCCCTCCAATCCGAATTATAATTGA 57.915 36.000 15.39 7.90 32.14 2.57
1608 1812 6.942576 ACTCCCTCCAATCCGAATTATAATTG 59.057 38.462 15.39 7.79 0.00 2.32
1609 1813 7.091533 ACTCCCTCCAATCCGAATTATAATT 57.908 36.000 10.51 10.51 0.00 1.40
1610 1814 6.704056 ACTCCCTCCAATCCGAATTATAAT 57.296 37.500 0.00 0.00 0.00 1.28
1611 1815 7.808279 ATACTCCCTCCAATCCGAATTATAA 57.192 36.000 0.00 0.00 0.00 0.98
1612 1816 7.808279 AATACTCCCTCCAATCCGAATTATA 57.192 36.000 0.00 0.00 0.00 0.98
1613 1817 6.704056 AATACTCCCTCCAATCCGAATTAT 57.296 37.500 0.00 0.00 0.00 1.28
1614 1818 7.808279 ATAATACTCCCTCCAATCCGAATTA 57.192 36.000 0.00 0.00 0.00 1.40
1615 1819 6.704056 ATAATACTCCCTCCAATCCGAATT 57.296 37.500 0.00 0.00 0.00 2.17
1616 1820 6.704056 AATAATACTCCCTCCAATCCGAAT 57.296 37.500 0.00 0.00 0.00 3.34
1617 1821 6.509523 AAATAATACTCCCTCCAATCCGAA 57.490 37.500 0.00 0.00 0.00 4.30
1618 1822 7.620880 CATAAATAATACTCCCTCCAATCCGA 58.379 38.462 0.00 0.00 0.00 4.55
1619 1823 6.316390 GCATAAATAATACTCCCTCCAATCCG 59.684 42.308 0.00 0.00 0.00 4.18
1620 1824 7.406104 AGCATAAATAATACTCCCTCCAATCC 58.594 38.462 0.00 0.00 0.00 3.01
1621 1825 8.870075 AAGCATAAATAATACTCCCTCCAATC 57.130 34.615 0.00 0.00 0.00 2.67
1622 1826 8.673251 AGAAGCATAAATAATACTCCCTCCAAT 58.327 33.333 0.00 0.00 0.00 3.16
1623 1827 8.045720 AGAAGCATAAATAATACTCCCTCCAA 57.954 34.615 0.00 0.00 0.00 3.53
1624 1828 7.633018 AGAAGCATAAATAATACTCCCTCCA 57.367 36.000 0.00 0.00 0.00 3.86
1625 1829 9.438228 GTAAGAAGCATAAATAATACTCCCTCC 57.562 37.037 0.00 0.00 0.00 4.30
1626 1830 9.438228 GGTAAGAAGCATAAATAATACTCCCTC 57.562 37.037 0.00 0.00 0.00 4.30
1627 1831 8.945193 TGGTAAGAAGCATAAATAATACTCCCT 58.055 33.333 0.00 0.00 0.00 4.20
1628 1832 9.569122 TTGGTAAGAAGCATAAATAATACTCCC 57.431 33.333 0.00 0.00 32.06 4.30
1634 1838 9.474313 TGGAACTTGGTAAGAAGCATAAATAAT 57.526 29.630 0.00 0.00 32.06 1.28
1650 1854 2.365293 GTTTGGATTGCTGGAACTTGGT 59.635 45.455 0.00 0.00 0.00 3.67
1755 1959 5.843673 TTGAAAGCCAGTGTAACATTTGA 57.156 34.783 0.00 0.00 41.43 2.69
1861 2065 8.584600 GGTTTTTGTTTTGTTTTGTTTCGTTTT 58.415 25.926 0.00 0.00 0.00 2.43
1870 2074 5.471797 AGGTGAGGGTTTTTGTTTTGTTTTG 59.528 36.000 0.00 0.00 0.00 2.44
1875 2079 4.200838 ACAGGTGAGGGTTTTTGTTTTG 57.799 40.909 0.00 0.00 0.00 2.44
1877 2081 4.862371 TCTACAGGTGAGGGTTTTTGTTT 58.138 39.130 0.00 0.00 0.00 2.83
1878 2082 4.513406 TCTACAGGTGAGGGTTTTTGTT 57.487 40.909 0.00 0.00 0.00 2.83
1879 2083 4.513406 TTCTACAGGTGAGGGTTTTTGT 57.487 40.909 0.00 0.00 0.00 2.83
1880 2084 4.261614 GCTTTCTACAGGTGAGGGTTTTTG 60.262 45.833 0.00 0.00 0.00 2.44
1881 2085 3.889538 GCTTTCTACAGGTGAGGGTTTTT 59.110 43.478 0.00 0.00 0.00 1.94
1882 2086 3.138468 AGCTTTCTACAGGTGAGGGTTTT 59.862 43.478 0.00 0.00 0.00 2.43
1883 2087 2.711547 AGCTTTCTACAGGTGAGGGTTT 59.288 45.455 0.00 0.00 0.00 3.27
1884 2088 2.339769 AGCTTTCTACAGGTGAGGGTT 58.660 47.619 0.00 0.00 0.00 4.11
1885 2089 2.031495 AGCTTTCTACAGGTGAGGGT 57.969 50.000 0.00 0.00 0.00 4.34
1886 2090 4.762289 AATAGCTTTCTACAGGTGAGGG 57.238 45.455 0.00 0.00 0.00 4.30
2020 2224 1.287815 CTCGGTAGTGACGTTGCCA 59.712 57.895 0.00 0.00 0.00 4.92
2026 2230 2.610833 TGTAGCATACTCGGTAGTGACG 59.389 50.000 0.00 0.00 43.54 4.35
2100 2304 3.163594 CGGTTAGCAAAAGCAAGAATCG 58.836 45.455 2.56 0.00 0.00 3.34
2367 2583 4.699735 ACGAAATGGCATCTTGTACAATCA 59.300 37.500 9.13 0.00 0.00 2.57
2565 2781 4.022589 ACAAAAGTCATGTCATTCAGCTGG 60.023 41.667 15.13 0.00 0.00 4.85
2649 2865 2.564947 AGTAGGTGCAGGAAGAGACAAG 59.435 50.000 0.00 0.00 0.00 3.16
2880 3096 0.314935 ACCTTGCTTGCAAATGACGG 59.685 50.000 9.39 8.84 0.00 4.79
2912 3128 2.281761 AAAGCTCCACCCAGCACG 60.282 61.111 0.00 0.00 42.40 5.34
2992 3208 6.695429 TGCTTGTTCATAAATAATGCACCAA 58.305 32.000 0.00 0.00 31.44 3.67
3033 3249 7.165812 GCACAGTTGTACACTCAAAGTTTAATG 59.834 37.037 0.00 0.00 30.92 1.90
3173 3398 7.038659 ACTCATACAAGTTGAGCTATGAAGAC 58.961 38.462 10.54 0.00 43.57 3.01
3193 3420 5.543020 GCTAGTAGTTAACCCCCATACTCAT 59.457 44.000 0.88 0.00 0.00 2.90
3303 3530 6.108687 CCAATCTCTGTAGAACTTGCACATA 58.891 40.000 0.00 0.00 34.73 2.29
3610 3837 8.364142 GGTAGAGCTAATGTGATTTACTCAGAT 58.636 37.037 0.00 0.00 39.44 2.90
3619 3846 7.343316 ACTTGAGTAGGTAGAGCTAATGTGATT 59.657 37.037 0.00 0.00 0.00 2.57
3620 3847 6.836527 ACTTGAGTAGGTAGAGCTAATGTGAT 59.163 38.462 0.00 0.00 0.00 3.06
3671 3898 4.154195 GTGCGACACTTAAATCACCAGATT 59.846 41.667 3.20 0.00 46.20 2.40
3779 4006 2.949177 TTCCACCTGCAATGTAGTGT 57.051 45.000 0.00 0.00 0.00 3.55
4157 4392 4.022849 GCCTGCTAAACAAAGACACAAGAT 60.023 41.667 0.00 0.00 0.00 2.40
4161 4396 2.649190 TGCCTGCTAAACAAAGACACA 58.351 42.857 0.00 0.00 0.00 3.72
4162 4397 3.923017 ATGCCTGCTAAACAAAGACAC 57.077 42.857 0.00 0.00 0.00 3.67
4236 4480 1.207329 AGATCAGGTTTAGCCCGACAC 59.793 52.381 0.00 0.00 38.26 3.67
4284 4528 7.729124 ACTATAAGTAGGAAGTAGTGCCAAA 57.271 36.000 0.00 0.00 31.96 3.28
4335 4579 1.562008 TCCCACACAGAAACAGTTCCA 59.438 47.619 0.00 0.00 33.92 3.53
4377 4621 5.083533 AGCACAGGAATTTCACACAAAAA 57.916 34.783 0.00 0.00 0.00 1.94
4422 4666 8.765488 TTGAAATGAGCTGGGATGATAAAATA 57.235 30.769 0.00 0.00 0.00 1.40
4508 4763 6.912591 GGACATCATTGATCGGTGATAAAAAC 59.087 38.462 11.07 3.92 33.52 2.43
4519 4784 4.063998 TGGAGAAGGACATCATTGATCG 57.936 45.455 0.00 0.00 0.00 3.69
4675 4940 6.058833 TCAAGTATGTGCTCAAGTAAAACCA 58.941 36.000 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.