Multiple sequence alignment - TraesCS5A01G262700

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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 TraesCS5A01G262700 chr5A 100.000 2841 0 0 821 3661 475749394 475752234 0.000000e+00 5247.0
1 TraesCS5A01G262700 chr5A 100.000 395 0 0 1 395 475748574 475748968 0.000000e+00 730.0
2 TraesCS5A01G262700 chr5B 89.039 1405 66 26 1496 2850 445594243 445595609 0.000000e+00 1661.0
3 TraesCS5A01G262700 chr5B 83.212 548 53 24 823 1333 445593674 445594219 1.990000e-127 466.0
4 TraesCS5A01G262700 chr5B 88.614 404 15 22 1 393 445593289 445593672 2.580000e-126 462.0
5 TraesCS5A01G262700 chr5B 92.647 68 4 1 1262 1329 691773526 691773460 3.010000e-16 97.1
6 TraesCS5A01G262700 chr5B 89.189 74 7 1 1262 1335 691798227 691798155 1.400000e-14 91.6
7 TraesCS5A01G262700 chr5D 90.923 1267 57 30 1598 2832 373951701 373952941 0.000000e+00 1650.0
8 TraesCS5A01G262700 chr5D 84.217 849 98 20 2845 3661 349856597 349857441 0.000000e+00 793.0
9 TraesCS5A01G262700 chr5D 84.116 831 108 20 2848 3661 3748079 3748902 0.000000e+00 782.0
10 TraesCS5A01G262700 chr5D 85.101 792 85 16 2862 3623 464701916 464702704 0.000000e+00 778.0
11 TraesCS5A01G262700 chr5D 81.115 789 84 37 826 1577 373950947 373951707 4.100000e-159 571.0
12 TraesCS5A01G262700 chr5D 92.099 405 20 9 1 395 373950546 373950948 8.880000e-156 560.0
13 TraesCS5A01G262700 chr5D 89.333 75 8 0 1261 1335 547840962 547840888 1.080000e-15 95.3
14 TraesCS5A01G262700 chr5D 89.333 75 8 0 1261 1335 547892605 547892531 1.080000e-15 95.3
15 TraesCS5A01G262700 chr5D 88.462 78 7 2 1261 1337 547926062 547925986 3.890000e-15 93.5
16 TraesCS5A01G262700 chr5D 87.838 74 8 1 1262 1335 547883861 547883789 6.510000e-13 86.1
17 TraesCS5A01G262700 chr6B 85.190 844 88 21 2850 3661 26218588 26217750 0.000000e+00 832.0
18 TraesCS5A01G262700 chr7D 85.089 845 90 16 2849 3661 611665650 611664810 0.000000e+00 830.0
19 TraesCS5A01G262700 chr7D 84.005 844 99 17 2849 3661 321046308 321045470 0.000000e+00 778.0
20 TraesCS5A01G262700 chr2B 85.024 848 91 21 2847 3661 522824289 522825133 0.000000e+00 830.0
21 TraesCS5A01G262700 chr2B 84.558 803 91 15 2890 3661 711322197 711322997 0.000000e+00 765.0
22 TraesCS5A01G262700 chr4A 84.788 848 93 19 2846 3661 740743971 740743128 0.000000e+00 819.0
23 TraesCS5A01G262700 chr4A 84.979 719 77 13 2972 3661 728115019 728114303 0.000000e+00 701.0
24 TraesCS5A01G262700 chr4A 90.667 75 7 0 1261 1335 618418798 618418724 2.330000e-17 100.0
25 TraesCS5A01G262700 chr4A 89.333 75 8 0 1261 1335 618464284 618464210 1.080000e-15 95.3
26 TraesCS5A01G262700 chr4A 88.732 71 8 0 1261 1331 618529550 618529480 1.810000e-13 87.9
27 TraesCS5A01G262700 chr3B 84.716 844 92 17 2848 3661 708391916 708392752 0.000000e+00 809.0
28 TraesCS5A01G262700 chr1B 84.652 847 90 22 2848 3661 643025801 643024962 0.000000e+00 808.0
29 TraesCS5A01G262700 chrUn 84.279 846 96 16 2848 3661 263186145 263185305 0.000000e+00 791.0
30 TraesCS5A01G262700 chrUn 84.161 846 97 16 2848 3661 50437486 50438326 0.000000e+00 785.0
31 TraesCS5A01G262700 chr4D 84.161 846 96 18 2847 3661 17070115 17069277 0.000000e+00 785.0
32 TraesCS5A01G262700 chr4D 85.079 697 75 11 2994 3661 37603440 37604136 0.000000e+00 684.0
33 TraesCS5A01G262700 chr4D 83.665 251 16 10 3436 3661 503349612 503349362 2.860000e-51 213.0
34 TraesCS5A01G262700 chr1D 83.840 823 101 13 2868 3661 486401998 486402817 0.000000e+00 754.0


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 TraesCS5A01G262700 chr5A 475748574 475752234 3660 False 2988.5 5247 100.000000 1 3661 2 chr5A.!!$F1 3660
1 TraesCS5A01G262700 chr5B 445593289 445595609 2320 False 863.0 1661 86.955000 1 2850 3 chr5B.!!$F1 2849
2 TraesCS5A01G262700 chr5D 373950546 373952941 2395 False 927.0 1650 88.045667 1 2832 3 chr5D.!!$F4 2831
3 TraesCS5A01G262700 chr5D 349856597 349857441 844 False 793.0 793 84.217000 2845 3661 1 chr5D.!!$F2 816
4 TraesCS5A01G262700 chr5D 3748079 3748902 823 False 782.0 782 84.116000 2848 3661 1 chr5D.!!$F1 813
5 TraesCS5A01G262700 chr5D 464701916 464702704 788 False 778.0 778 85.101000 2862 3623 1 chr5D.!!$F3 761
6 TraesCS5A01G262700 chr6B 26217750 26218588 838 True 832.0 832 85.190000 2850 3661 1 chr6B.!!$R1 811
7 TraesCS5A01G262700 chr7D 611664810 611665650 840 True 830.0 830 85.089000 2849 3661 1 chr7D.!!$R2 812
8 TraesCS5A01G262700 chr7D 321045470 321046308 838 True 778.0 778 84.005000 2849 3661 1 chr7D.!!$R1 812
9 TraesCS5A01G262700 chr2B 522824289 522825133 844 False 830.0 830 85.024000 2847 3661 1 chr2B.!!$F1 814
10 TraesCS5A01G262700 chr2B 711322197 711322997 800 False 765.0 765 84.558000 2890 3661 1 chr2B.!!$F2 771
11 TraesCS5A01G262700 chr4A 740743128 740743971 843 True 819.0 819 84.788000 2846 3661 1 chr4A.!!$R5 815
12 TraesCS5A01G262700 chr4A 728114303 728115019 716 True 701.0 701 84.979000 2972 3661 1 chr4A.!!$R4 689
13 TraesCS5A01G262700 chr3B 708391916 708392752 836 False 809.0 809 84.716000 2848 3661 1 chr3B.!!$F1 813
14 TraesCS5A01G262700 chr1B 643024962 643025801 839 True 808.0 808 84.652000 2848 3661 1 chr1B.!!$R1 813
15 TraesCS5A01G262700 chrUn 263185305 263186145 840 True 791.0 791 84.279000 2848 3661 1 chrUn.!!$R1 813
16 TraesCS5A01G262700 chrUn 50437486 50438326 840 False 785.0 785 84.161000 2848 3661 1 chrUn.!!$F1 813
17 TraesCS5A01G262700 chr4D 17069277 17070115 838 True 785.0 785 84.161000 2847 3661 1 chr4D.!!$R1 814
18 TraesCS5A01G262700 chr4D 37603440 37604136 696 False 684.0 684 85.079000 2994 3661 1 chr4D.!!$F1 667
19 TraesCS5A01G262700 chr1D 486401998 486402817 819 False 754.0 754 83.840000 2868 3661 1 chr1D.!!$F1 793

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
952 980 1.531912 CGAAGCCGTCGTAGTACTTG 58.468 55.0 0.00 0.0 45.09 3.16 F
1506 1577 0.037697 TTGCGCAGAGATGTAACGGT 60.038 50.0 11.31 0.0 0.00 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2362 2469 0.034476 CTGCTGCTTCTGGTCTGTCA 59.966 55.0 0.0 0.0 0.0 3.58 R
2840 2959 0.320697 ACGAGAGAAAAACGGAGGGG 59.679 55.0 0.0 0.0 0.0 4.79 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
83 86 4.336993 TCACGTCAAGGCAACATTTTAACT 59.663 37.500 0.00 0.00 41.41 2.24
115 118 2.235402 CCGGTAACTTCAGAGGCCTTAA 59.765 50.000 6.77 0.78 0.00 1.85
132 135 3.617263 CCTTAATAACAGCGAGGTGACAC 59.383 47.826 9.41 0.00 0.00 3.67
144 147 3.502920 GAGGTGACACGACAGTTATCAG 58.497 50.000 0.00 0.00 0.00 2.90
305 312 2.071688 GAGCTGTCGAACACATGACT 57.928 50.000 0.00 0.00 36.10 3.41
354 369 3.751698 GGCGGGCTTTGTATTAAGATAGG 59.248 47.826 0.00 0.00 0.00 2.57
897 912 2.623889 AGGAGATGAGGTAACGGAATCG 59.376 50.000 0.00 0.00 46.39 3.34
900 915 2.034812 AGATGAGGTAACGGAATCGAGC 59.965 50.000 0.00 0.00 46.39 5.03
907 922 2.885644 CGGAATCGAGCCGTGGTG 60.886 66.667 18.34 0.00 43.66 4.17
908 923 3.195698 GGAATCGAGCCGTGGTGC 61.196 66.667 0.00 0.00 0.00 5.01
909 924 2.125512 GAATCGAGCCGTGGTGCT 60.126 61.111 0.00 0.00 46.37 4.40
912 927 1.605058 AATCGAGCCGTGGTGCTACT 61.605 55.000 0.00 0.00 42.95 2.57
952 980 1.531912 CGAAGCCGTCGTAGTACTTG 58.468 55.000 0.00 0.00 45.09 3.16
963 991 4.738740 GTCGTAGTACTTGCATATCCACAC 59.261 45.833 0.00 0.00 0.00 3.82
964 992 3.729217 CGTAGTACTTGCATATCCACACG 59.271 47.826 0.00 0.00 0.00 4.49
965 993 2.550978 AGTACTTGCATATCCACACGC 58.449 47.619 0.00 0.00 0.00 5.34
968 1020 3.192541 ACTTGCATATCCACACGCATA 57.807 42.857 0.00 0.00 33.71 3.14
974 1026 3.574614 CATATCCACACGCATACATCGA 58.425 45.455 0.00 0.00 0.00 3.59
994 1046 3.830192 CATTCGCCTGCCTTGCCC 61.830 66.667 0.00 0.00 0.00 5.36
1000 1052 4.028490 CCTGCCTTGCCCGGTGTA 62.028 66.667 0.00 0.00 0.00 2.90
1001 1053 2.272146 CTGCCTTGCCCGGTGTAT 59.728 61.111 0.00 0.00 0.00 2.29
1002 1054 2.045438 TGCCTTGCCCGGTGTATG 60.045 61.111 0.00 0.00 0.00 2.39
1003 1055 2.045340 GCCTTGCCCGGTGTATGT 60.045 61.111 0.00 0.00 0.00 2.29
1004 1056 1.222387 GCCTTGCCCGGTGTATGTA 59.778 57.895 0.00 0.00 0.00 2.29
1024 1079 2.979814 TATGTCGACAATGGAGGTGG 57.020 50.000 24.13 0.00 0.00 4.61
1125 1180 0.461961 GCAGGTTCGAGCTGAGGTAT 59.538 55.000 15.22 0.00 45.98 2.73
1131 1186 3.491104 GGTTCGAGCTGAGGTATTTCGAT 60.491 47.826 0.00 0.00 39.65 3.59
1162 1217 0.528470 CCTGGACGAGTTCTCAGGTC 59.472 60.000 0.00 1.03 37.66 3.85
1165 1220 0.109039 GGACGAGTTCTCAGGTCAGC 60.109 60.000 0.00 0.00 0.00 4.26
1166 1221 0.109039 GACGAGTTCTCAGGTCAGCC 60.109 60.000 0.00 0.00 0.00 4.85
1167 1222 1.216710 CGAGTTCTCAGGTCAGCCC 59.783 63.158 0.79 0.00 34.57 5.19
1168 1223 1.599576 GAGTTCTCAGGTCAGCCCC 59.400 63.158 0.00 0.00 34.57 5.80
1192 1247 2.131067 CGCTTCCTCCTCCTCCCTC 61.131 68.421 0.00 0.00 0.00 4.30
1193 1248 2.131067 GCTTCCTCCTCCTCCCTCG 61.131 68.421 0.00 0.00 0.00 4.63
1197 1252 1.758906 CCTCCTCCTCCCTCGGTTC 60.759 68.421 0.00 0.00 0.00 3.62
1199 1254 2.362632 CCTCCTCCCTCGGTTCGT 60.363 66.667 0.00 0.00 0.00 3.85
1205 1260 3.116531 CCCTCGGTTCGTTTCGGC 61.117 66.667 0.00 0.00 0.00 5.54
1206 1261 3.475774 CCTCGGTTCGTTTCGGCG 61.476 66.667 0.00 0.00 0.00 6.46
1209 1275 2.009625 CTCGGTTCGTTTCGGCGATG 62.010 60.000 11.76 3.97 40.76 3.84
1219 1285 1.563111 TTCGGCGATGGTCGTTAATC 58.437 50.000 11.76 0.00 43.10 1.75
1325 1391 1.022735 ACCTACATGCTCGAGGTACG 58.977 55.000 15.58 4.91 41.91 3.67
1326 1392 0.317938 CCTACATGCTCGAGGTACGC 60.318 60.000 15.58 0.00 42.26 4.42
1327 1393 0.380733 CTACATGCTCGAGGTACGCA 59.619 55.000 15.58 6.66 42.26 5.24
1328 1394 0.099968 TACATGCTCGAGGTACGCAC 59.900 55.000 15.58 0.00 42.26 5.34
1346 1412 0.388907 ACGCATGCATTTCTGTTGCC 60.389 50.000 19.57 0.00 39.39 4.52
1409 1476 4.232221 CACTGCTAGAAAACTGCCAAATG 58.768 43.478 0.00 0.00 0.00 2.32
1418 1485 2.584835 ACTGCCAAATGAACCTAGCA 57.415 45.000 0.00 0.00 0.00 3.49
1420 1487 2.440409 CTGCCAAATGAACCTAGCAGT 58.560 47.619 0.00 0.00 42.09 4.40
1421 1488 3.609853 CTGCCAAATGAACCTAGCAGTA 58.390 45.455 0.00 0.00 42.09 2.74
1422 1489 4.202441 CTGCCAAATGAACCTAGCAGTAT 58.798 43.478 0.00 0.00 42.09 2.12
1424 1491 4.199310 GCCAAATGAACCTAGCAGTATGA 58.801 43.478 0.00 0.00 39.69 2.15
1426 1493 5.449177 GCCAAATGAACCTAGCAGTATGAAC 60.449 44.000 0.00 0.00 39.69 3.18
1427 1494 5.647658 CCAAATGAACCTAGCAGTATGAACA 59.352 40.000 0.00 0.00 39.69 3.18
1428 1495 6.319658 CCAAATGAACCTAGCAGTATGAACAT 59.680 38.462 0.00 0.00 39.69 2.71
1429 1496 7.412853 CAAATGAACCTAGCAGTATGAACATC 58.587 38.462 0.00 0.00 39.69 3.06
1430 1497 5.023533 TGAACCTAGCAGTATGAACATCC 57.976 43.478 0.00 0.00 39.69 3.51
1432 1499 2.224066 ACCTAGCAGTATGAACATCCGC 60.224 50.000 0.00 0.00 39.69 5.54
1433 1500 2.224042 CCTAGCAGTATGAACATCCGCA 60.224 50.000 0.00 0.00 39.69 5.69
1434 1501 1.945387 AGCAGTATGAACATCCGCAG 58.055 50.000 0.00 0.00 39.69 5.18
1437 1504 1.863454 CAGTATGAACATCCGCAGAGC 59.137 52.381 0.00 0.00 39.69 4.09
1446 1517 2.793160 ATCCGCAGAGCACACACCAG 62.793 60.000 0.00 0.00 0.00 4.00
1456 1527 2.489329 AGCACACACCAGAATACATTGC 59.511 45.455 0.00 0.00 0.00 3.56
1459 1530 3.444742 CACACACCAGAATACATTGCCAT 59.555 43.478 0.00 0.00 0.00 4.40
1460 1531 3.696051 ACACACCAGAATACATTGCCATC 59.304 43.478 0.00 0.00 0.00 3.51
1461 1532 3.067180 CACACCAGAATACATTGCCATCC 59.933 47.826 0.00 0.00 0.00 3.51
1462 1533 3.053395 ACACCAGAATACATTGCCATCCT 60.053 43.478 0.00 0.00 0.00 3.24
1463 1534 3.317149 CACCAGAATACATTGCCATCCTG 59.683 47.826 0.00 0.00 0.00 3.86
1464 1535 3.202818 ACCAGAATACATTGCCATCCTGA 59.797 43.478 0.00 0.00 0.00 3.86
1465 1536 4.209538 CCAGAATACATTGCCATCCTGAA 58.790 43.478 0.00 0.00 0.00 3.02
1467 1538 4.037208 CAGAATACATTGCCATCCTGAACC 59.963 45.833 0.00 0.00 0.00 3.62
1468 1539 2.435372 TACATTGCCATCCTGAACCC 57.565 50.000 0.00 0.00 0.00 4.11
1469 1540 0.706433 ACATTGCCATCCTGAACCCT 59.294 50.000 0.00 0.00 0.00 4.34
1470 1541 1.077663 ACATTGCCATCCTGAACCCTT 59.922 47.619 0.00 0.00 0.00 3.95
1471 1542 2.181975 CATTGCCATCCTGAACCCTTT 58.818 47.619 0.00 0.00 0.00 3.11
1476 1547 3.017442 GCCATCCTGAACCCTTTCTTAC 58.983 50.000 0.00 0.00 32.36 2.34
1481 1552 6.599638 CCATCCTGAACCCTTTCTTACTTAAG 59.400 42.308 0.00 0.00 32.36 1.85
1484 1555 5.938710 CCTGAACCCTTTCTTACTTAAGTCC 59.061 44.000 12.39 0.00 34.93 3.85
1489 1560 6.246163 ACCCTTTCTTACTTAAGTCCCATTG 58.754 40.000 12.39 0.36 34.93 2.82
1490 1561 5.125578 CCCTTTCTTACTTAAGTCCCATTGC 59.874 44.000 12.39 0.00 34.93 3.56
1491 1562 5.163754 CCTTTCTTACTTAAGTCCCATTGCG 60.164 44.000 12.39 0.00 34.93 4.85
1492 1563 3.267483 TCTTACTTAAGTCCCATTGCGC 58.733 45.455 12.39 0.00 34.93 6.09
1493 1564 2.772077 TACTTAAGTCCCATTGCGCA 57.228 45.000 12.39 5.66 0.00 6.09
1497 1568 0.901827 TAAGTCCCATTGCGCAGAGA 59.098 50.000 11.31 3.20 0.00 3.10
1506 1577 0.037697 TTGCGCAGAGATGTAACGGT 60.038 50.000 11.31 0.00 0.00 4.83
1522 1593 1.289109 CGGTAGTGGCACCTTTGACG 61.289 60.000 15.27 7.16 36.35 4.35
1570 1641 3.479590 GCGTTCCGTTTGTCAAACTTAAC 59.520 43.478 22.69 21.91 39.23 2.01
1577 1648 4.264380 CGTTTGTCAAACTTAACTGCAACC 59.736 41.667 22.69 0.00 39.23 3.77
1579 1650 4.630894 TGTCAAACTTAACTGCAACCTG 57.369 40.909 0.00 0.00 0.00 4.00
1580 1651 3.380004 TGTCAAACTTAACTGCAACCTGG 59.620 43.478 0.00 0.00 0.00 4.45
1581 1652 3.630312 GTCAAACTTAACTGCAACCTGGA 59.370 43.478 0.00 0.00 0.00 3.86
1582 1653 4.097286 GTCAAACTTAACTGCAACCTGGAA 59.903 41.667 0.00 0.00 0.00 3.53
1583 1654 4.097286 TCAAACTTAACTGCAACCTGGAAC 59.903 41.667 0.00 0.00 0.00 3.62
1585 1656 2.174854 ACTTAACTGCAACCTGGAACCT 59.825 45.455 0.00 0.00 0.00 3.50
1586 1657 3.222603 CTTAACTGCAACCTGGAACCTT 58.777 45.455 0.00 0.00 0.00 3.50
1587 1658 2.159179 AACTGCAACCTGGAACCTTT 57.841 45.000 0.00 0.00 0.00 3.11
1588 1659 2.159179 ACTGCAACCTGGAACCTTTT 57.841 45.000 0.00 0.00 0.00 2.27
1589 1660 2.466846 ACTGCAACCTGGAACCTTTTT 58.533 42.857 0.00 0.00 0.00 1.94
1622 1694 3.297134 ACTTTTCTTGCCCTTCACTCA 57.703 42.857 0.00 0.00 0.00 3.41
1625 1697 4.142160 ACTTTTCTTGCCCTTCACTCAAAC 60.142 41.667 0.00 0.00 0.00 2.93
1631 1703 0.961753 CCCTTCACTCAAACAAGCCC 59.038 55.000 0.00 0.00 0.00 5.19
1653 1725 2.203294 AACGCGGGTCCTGCTTTT 60.203 55.556 20.58 10.49 0.00 2.27
1791 1881 2.808958 AACGATGGCGCGCATACAC 61.809 57.895 34.42 15.80 42.48 2.90
1808 1898 5.584649 GCATACACTAGTAGATTTGTTGGCA 59.415 40.000 3.59 0.00 32.86 4.92
1959 2049 2.887568 GTGCACTCCGAGATGCCG 60.888 66.667 10.32 0.00 41.33 5.69
2025 2115 2.407090 GCCTCCAAGAACAAAATGTGC 58.593 47.619 0.00 0.00 0.00 4.57
2029 2119 1.522258 CCAAGAACAAAATGTGCGCAC 59.478 47.619 33.11 33.11 28.94 5.34
2031 2121 2.405892 AGAACAAAATGTGCGCACTC 57.594 45.000 37.59 25.34 28.94 3.51
2036 2126 3.825308 ACAAAATGTGCGCACTCTATTG 58.175 40.909 37.59 32.62 0.00 1.90
2038 2128 4.156556 ACAAAATGTGCGCACTCTATTGAT 59.843 37.500 37.59 20.30 0.00 2.57
2047 2137 4.728882 GCGCACTCTATTGATTTCACCTTG 60.729 45.833 0.30 0.00 0.00 3.61
2065 2172 1.679305 GCTCTCTCCCGTCTGACCA 60.679 63.158 1.55 0.00 0.00 4.02
2071 2178 2.049433 CCCGTCTGACCACGTCAC 60.049 66.667 1.55 0.00 37.67 3.67
2100 2207 1.513178 CGATGACTAACACGTGCGATC 59.487 52.381 17.22 9.03 0.00 3.69
2101 2208 1.513178 GATGACTAACACGTGCGATCG 59.487 52.381 17.22 11.69 0.00 3.69
2102 2209 0.518195 TGACTAACACGTGCGATCGA 59.482 50.000 21.57 0.59 34.70 3.59
2365 2472 3.186047 CGTGTTCGGGCCGATGAC 61.186 66.667 31.59 25.56 35.23 3.06
2366 2473 2.047655 GTGTTCGGGCCGATGACA 60.048 61.111 31.59 27.96 35.23 3.58
2367 2474 2.100631 GTGTTCGGGCCGATGACAG 61.101 63.158 31.59 0.00 35.23 3.51
2368 2475 2.279810 TGTTCGGGCCGATGACAGA 61.280 57.895 31.59 11.10 35.23 3.41
2369 2476 1.810030 GTTCGGGCCGATGACAGAC 60.810 63.158 31.59 19.86 35.23 3.51
2370 2477 3.014085 TTCGGGCCGATGACAGACC 62.014 63.158 31.59 0.00 35.23 3.85
2371 2478 3.770040 CGGGCCGATGACAGACCA 61.770 66.667 24.41 0.00 0.00 4.02
2372 2479 2.187946 GGGCCGATGACAGACCAG 59.812 66.667 0.00 0.00 0.00 4.00
2373 2480 2.359169 GGGCCGATGACAGACCAGA 61.359 63.158 0.00 0.00 0.00 3.86
2374 2481 1.596934 GGCCGATGACAGACCAGAA 59.403 57.895 0.00 0.00 0.00 3.02
2375 2482 0.460987 GGCCGATGACAGACCAGAAG 60.461 60.000 0.00 0.00 0.00 2.85
2376 2483 1.086634 GCCGATGACAGACCAGAAGC 61.087 60.000 0.00 0.00 0.00 3.86
2377 2484 0.247460 CCGATGACAGACCAGAAGCA 59.753 55.000 0.00 0.00 0.00 3.91
2378 2485 1.638133 CGATGACAGACCAGAAGCAG 58.362 55.000 0.00 0.00 0.00 4.24
2379 2486 1.367659 GATGACAGACCAGAAGCAGC 58.632 55.000 0.00 0.00 0.00 5.25
2380 2487 0.689055 ATGACAGACCAGAAGCAGCA 59.311 50.000 0.00 0.00 0.00 4.41
2381 2488 0.034476 TGACAGACCAGAAGCAGCAG 59.966 55.000 0.00 0.00 0.00 4.24
2382 2489 0.673022 GACAGACCAGAAGCAGCAGG 60.673 60.000 0.00 0.00 0.00 4.85
2418 2525 2.901840 CGCACCACCTGCTGTTGT 60.902 61.111 0.00 0.00 44.64 3.32
2420 2527 1.066257 GCACCACCTGCTGTTGTTG 59.934 57.895 0.00 0.00 43.33 3.33
2428 2535 2.203480 GCTGTTGTTGGGGCAGGA 60.203 61.111 0.00 0.00 0.00 3.86
2648 2755 1.594331 TGATCGCGCTAGAGCTAGAA 58.406 50.000 16.69 0.00 39.32 2.10
2662 2769 4.822896 AGAGCTAGAATACGTAGGGTGAAG 59.177 45.833 0.08 0.00 0.00 3.02
2755 2874 3.912496 TTCATCCCGACATCAGTGATT 57.088 42.857 1.86 0.00 0.00 2.57
2841 2960 9.978336 ATACTGAATTATACTCCTACTACTCCC 57.022 37.037 0.00 0.00 0.00 4.30
2842 2961 7.240167 ACTGAATTATACTCCTACTACTCCCC 58.760 42.308 0.00 0.00 0.00 4.81
2843 2962 6.559429 TGAATTATACTCCTACTACTCCCCC 58.441 44.000 0.00 0.00 0.00 5.40
2844 2963 6.337472 TGAATTATACTCCTACTACTCCCCCT 59.663 42.308 0.00 0.00 0.00 4.79
2860 2979 1.270678 CCCCTCCGTTTTTCTCTCGTT 60.271 52.381 0.00 0.00 0.00 3.85
2876 2997 3.646715 TTCCTGGGGCTGGAACCG 61.647 66.667 0.00 0.00 36.73 4.44
2878 2999 4.722700 CCTGGGGCTGGAACCGTG 62.723 72.222 0.00 0.00 0.00 4.94
2934 3057 2.365635 CCGGTGACTCCCCTCCAT 60.366 66.667 0.00 0.00 0.00 3.41
2946 3069 3.209812 CTCCATCGGCGACCTCGA 61.210 66.667 13.76 4.22 43.02 4.04
2948 3071 2.076622 CTCCATCGGCGACCTCGATT 62.077 60.000 13.76 0.00 43.75 3.34
3050 3177 0.817634 TGTCTTGGCTTTGGTGACGG 60.818 55.000 0.00 0.00 0.00 4.79
3103 3230 2.093128 TCCTTTCCTAACGAGGCCATTC 60.093 50.000 5.01 0.00 43.40 2.67
3104 3231 2.092914 CCTTTCCTAACGAGGCCATTCT 60.093 50.000 5.01 0.00 43.40 2.40
3118 3245 2.682563 GCCATTCTTCGTATGGTTGGGA 60.683 50.000 0.00 0.00 43.65 4.37
3133 3261 3.326297 GGTTGGGAATGGATTTGGAAACA 59.674 43.478 0.00 0.00 39.83 2.83
3196 3327 2.836154 GACCTGTGTCCTTGGGCA 59.164 61.111 0.00 0.00 35.34 5.36
3295 3426 0.924090 GCATCGACGACATCTGGAAC 59.076 55.000 0.00 0.00 0.00 3.62
3322 3453 1.039856 GTGTGCTGGGTTCATGGTTT 58.960 50.000 0.00 0.00 0.00 3.27
3337 3468 1.173913 GGTTTGTGGATGGCAGGTAC 58.826 55.000 0.00 0.00 0.00 3.34
3429 3561 2.290260 TGCCTCGGTCTGATTGTTCAAT 60.290 45.455 0.00 0.00 0.00 2.57
3431 3563 2.096496 CCTCGGTCTGATTGTTCAATGC 59.904 50.000 2.63 0.00 0.00 3.56
3571 3728 0.871057 GTTGGTGTCAAGCTCAGAGC 59.129 55.000 15.25 15.25 42.84 4.09
3601 3758 6.151691 TGCTATCTTTTCAGTTTTGTCATGC 58.848 36.000 0.00 0.00 0.00 4.06
3632 3789 5.713822 ACGTGACTTGTACTTTGTTCTTC 57.286 39.130 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 104 3.557595 CGCTGTTATTAAGGCCTCTGAAG 59.442 47.826 5.23 0.00 0.00 3.02
103 106 2.764010 TCGCTGTTATTAAGGCCTCTGA 59.236 45.455 5.23 0.00 0.00 3.27
106 109 2.158943 ACCTCGCTGTTATTAAGGCCTC 60.159 50.000 5.23 0.00 0.00 4.70
115 118 0.885879 TCGTGTCACCTCGCTGTTAT 59.114 50.000 0.00 0.00 0.00 1.89
132 135 4.332819 GGGTTTTGATCCTGATAACTGTCG 59.667 45.833 0.00 0.00 0.00 4.35
144 147 2.746803 CCGTCGCGGGTTTTGATCC 61.747 63.158 6.13 0.00 44.15 3.36
333 340 4.638304 TCCTATCTTAATACAAAGCCCGC 58.362 43.478 0.00 0.00 0.00 6.13
354 369 3.753797 CCCAGCTAGTTTCTTGACCTTTC 59.246 47.826 0.00 0.00 0.00 2.62
820 835 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
833 848 1.004277 AGCGACAGTTCCTCTCTCTCT 59.996 52.381 0.00 0.00 0.00 3.10
834 849 1.400494 GAGCGACAGTTCCTCTCTCTC 59.600 57.143 0.00 0.00 0.00 3.20
835 850 1.004277 AGAGCGACAGTTCCTCTCTCT 59.996 52.381 0.00 0.00 30.46 3.10
839 854 0.039035 AGGAGAGCGACAGTTCCTCT 59.961 55.000 4.13 4.13 35.11 3.69
880 895 2.395654 GCTCGATTCCGTTACCTCATC 58.604 52.381 0.00 0.00 37.05 2.92
881 896 1.068741 GGCTCGATTCCGTTACCTCAT 59.931 52.381 0.00 0.00 37.05 2.90
882 897 0.458669 GGCTCGATTCCGTTACCTCA 59.541 55.000 0.00 0.00 37.05 3.86
883 898 0.594284 CGGCTCGATTCCGTTACCTC 60.594 60.000 15.58 0.00 41.85 3.85
884 899 1.436336 CGGCTCGATTCCGTTACCT 59.564 57.895 15.58 0.00 41.85 3.08
897 912 1.035932 TAGGAGTAGCACCACGGCTC 61.036 60.000 0.00 0.00 44.54 4.70
900 915 5.008331 TCTTATATAGGAGTAGCACCACGG 58.992 45.833 0.00 0.00 0.00 4.94
903 918 6.246919 GGTCTCTTATATAGGAGTAGCACCA 58.753 44.000 18.44 0.00 31.97 4.17
904 919 5.653330 GGGTCTCTTATATAGGAGTAGCACC 59.347 48.000 18.44 17.28 31.97 5.01
905 920 5.354792 CGGGTCTCTTATATAGGAGTAGCAC 59.645 48.000 18.44 10.87 31.97 4.40
907 922 4.336153 GCGGGTCTCTTATATAGGAGTAGC 59.664 50.000 18.44 15.34 31.97 3.58
908 923 4.571580 CGCGGGTCTCTTATATAGGAGTAG 59.428 50.000 18.44 10.98 31.97 2.57
909 924 4.223700 TCGCGGGTCTCTTATATAGGAGTA 59.776 45.833 18.44 6.02 31.97 2.59
912 927 3.341823 GTCGCGGGTCTCTTATATAGGA 58.658 50.000 6.13 0.00 0.00 2.94
952 980 2.092681 CGATGTATGCGTGTGGATATGC 59.907 50.000 0.00 0.00 30.62 3.14
974 1026 2.123428 GCAAGGCAGGCGAATGGAT 61.123 57.895 0.00 0.00 0.00 3.41
994 1046 5.344933 CCATTGTCGACATATACATACACCG 59.655 44.000 20.80 0.00 0.00 4.94
1000 1052 5.511373 CCACCTCCATTGTCGACATATACAT 60.511 44.000 20.80 6.46 0.00 2.29
1001 1053 4.202212 CCACCTCCATTGTCGACATATACA 60.202 45.833 20.80 3.86 0.00 2.29
1002 1054 4.307432 CCACCTCCATTGTCGACATATAC 58.693 47.826 20.80 0.00 0.00 1.47
1003 1055 3.244078 GCCACCTCCATTGTCGACATATA 60.244 47.826 20.80 4.74 0.00 0.86
1004 1056 2.485479 GCCACCTCCATTGTCGACATAT 60.485 50.000 20.80 12.68 0.00 1.78
1177 1232 1.812113 AACCGAGGGAGGAGGAGGAA 61.812 60.000 0.00 0.00 34.73 3.36
1178 1233 2.226149 GAACCGAGGGAGGAGGAGGA 62.226 65.000 0.00 0.00 34.73 3.71
1179 1234 1.758906 GAACCGAGGGAGGAGGAGG 60.759 68.421 0.00 0.00 34.73 4.30
1180 1235 2.122167 CGAACCGAGGGAGGAGGAG 61.122 68.421 0.00 0.00 34.73 3.69
1182 1237 1.542187 AAACGAACCGAGGGAGGAGG 61.542 60.000 0.00 0.00 34.73 4.30
1186 1241 1.445582 CCGAAACGAACCGAGGGAG 60.446 63.158 0.00 0.00 0.00 4.30
1192 1247 2.394136 CATCGCCGAAACGAACCG 59.606 61.111 0.00 0.00 46.59 4.44
1193 1248 1.963190 GACCATCGCCGAAACGAACC 61.963 60.000 0.00 0.00 46.59 3.62
1197 1252 1.072116 TAACGACCATCGCCGAAACG 61.072 55.000 0.00 0.00 45.12 3.60
1199 1254 1.928503 GATTAACGACCATCGCCGAAA 59.071 47.619 0.00 0.00 45.12 3.46
1219 1285 0.454600 TTCGGACGAGGAAGGAATCG 59.545 55.000 0.00 0.00 44.36 3.34
1225 1291 1.394917 CAGCAAATTCGGACGAGGAAG 59.605 52.381 0.00 0.00 0.00 3.46
1231 1297 1.135699 GCATGCAGCAAATTCGGACG 61.136 55.000 14.21 0.00 44.79 4.79
1326 1392 0.711670 GCAACAGAAATGCATGCGTG 59.288 50.000 14.40 7.66 43.29 5.34
1327 1393 0.388907 GGCAACAGAAATGCATGCGT 60.389 50.000 14.09 10.53 45.60 5.24
1328 1394 1.407721 CGGCAACAGAAATGCATGCG 61.408 55.000 14.09 0.00 45.60 4.73
1391 1458 4.021981 AGGTTCATTTGGCAGTTTTCTAGC 60.022 41.667 0.00 0.00 0.00 3.42
1392 1459 5.712152 AGGTTCATTTGGCAGTTTTCTAG 57.288 39.130 0.00 0.00 0.00 2.43
1393 1460 5.183140 GCTAGGTTCATTTGGCAGTTTTCTA 59.817 40.000 0.00 0.00 0.00 2.10
1409 1476 4.051922 CGGATGTTCATACTGCTAGGTTC 58.948 47.826 0.00 0.00 0.00 3.62
1418 1485 1.482182 TGCTCTGCGGATGTTCATACT 59.518 47.619 0.00 0.00 0.00 2.12
1419 1486 1.594862 GTGCTCTGCGGATGTTCATAC 59.405 52.381 0.00 0.00 0.00 2.39
1420 1487 1.206849 TGTGCTCTGCGGATGTTCATA 59.793 47.619 0.00 0.00 0.00 2.15
1421 1488 0.036105 TGTGCTCTGCGGATGTTCAT 60.036 50.000 0.00 0.00 0.00 2.57
1422 1489 0.950555 GTGTGCTCTGCGGATGTTCA 60.951 55.000 0.00 0.00 0.00 3.18
1424 1491 1.071299 TGTGTGCTCTGCGGATGTT 59.929 52.632 0.00 0.00 0.00 2.71
1426 1493 2.393768 GGTGTGTGCTCTGCGGATG 61.394 63.158 0.00 0.00 0.00 3.51
1427 1494 2.046892 GGTGTGTGCTCTGCGGAT 60.047 61.111 0.00 0.00 0.00 4.18
1428 1495 3.519973 CTGGTGTGTGCTCTGCGGA 62.520 63.158 0.00 0.00 0.00 5.54
1429 1496 2.994387 TTCTGGTGTGTGCTCTGCGG 62.994 60.000 0.00 0.00 0.00 5.69
1430 1497 0.952497 ATTCTGGTGTGTGCTCTGCG 60.952 55.000 0.00 0.00 0.00 5.18
1432 1499 3.044235 TGTATTCTGGTGTGTGCTCTG 57.956 47.619 0.00 0.00 0.00 3.35
1433 1500 3.988976 ATGTATTCTGGTGTGTGCTCT 57.011 42.857 0.00 0.00 0.00 4.09
1434 1501 3.426695 GCAATGTATTCTGGTGTGTGCTC 60.427 47.826 0.00 0.00 0.00 4.26
1437 1504 2.819019 TGGCAATGTATTCTGGTGTGTG 59.181 45.455 0.00 0.00 0.00 3.82
1446 1517 3.319122 GGGTTCAGGATGGCAATGTATTC 59.681 47.826 0.00 0.00 36.16 1.75
1456 1527 4.576330 AGTAAGAAAGGGTTCAGGATGG 57.424 45.455 0.00 0.00 36.09 3.51
1459 1530 6.239800 GGACTTAAGTAAGAAAGGGTTCAGGA 60.240 42.308 8.42 0.00 36.09 3.86
1460 1531 5.938710 GGACTTAAGTAAGAAAGGGTTCAGG 59.061 44.000 8.42 0.00 36.09 3.86
1461 1532 5.938710 GGGACTTAAGTAAGAAAGGGTTCAG 59.061 44.000 8.42 0.00 36.09 3.02
1462 1533 5.370289 TGGGACTTAAGTAAGAAAGGGTTCA 59.630 40.000 8.42 0.00 36.09 3.18
1463 1534 5.872963 TGGGACTTAAGTAAGAAAGGGTTC 58.127 41.667 8.42 0.00 37.08 3.62
1464 1535 5.917545 TGGGACTTAAGTAAGAAAGGGTT 57.082 39.130 8.42 0.00 37.08 4.11
1465 1536 6.246163 CAATGGGACTTAAGTAAGAAAGGGT 58.754 40.000 8.42 0.00 37.08 4.34
1467 1538 5.163754 CGCAATGGGACTTAAGTAAGAAAGG 60.164 44.000 8.42 0.00 37.08 3.11
1468 1539 5.673818 GCGCAATGGGACTTAAGTAAGAAAG 60.674 44.000 8.42 0.00 37.08 2.62
1469 1540 4.155280 GCGCAATGGGACTTAAGTAAGAAA 59.845 41.667 8.42 0.00 37.08 2.52
1470 1541 3.687698 GCGCAATGGGACTTAAGTAAGAA 59.312 43.478 8.42 0.00 37.08 2.52
1471 1542 3.267483 GCGCAATGGGACTTAAGTAAGA 58.733 45.455 8.42 0.00 37.08 2.10
1476 1547 1.667724 CTCTGCGCAATGGGACTTAAG 59.332 52.381 13.05 0.00 0.00 1.85
1481 1552 0.745845 ACATCTCTGCGCAATGGGAC 60.746 55.000 21.19 0.00 0.00 4.46
1484 1555 1.004610 CGTTACATCTCTGCGCAATGG 60.005 52.381 21.19 10.70 0.00 3.16
1489 1560 1.202268 ACTACCGTTACATCTCTGCGC 60.202 52.381 0.00 0.00 0.00 6.09
1490 1561 2.451132 CACTACCGTTACATCTCTGCG 58.549 52.381 0.00 0.00 0.00 5.18
1491 1562 2.810650 CCACTACCGTTACATCTCTGC 58.189 52.381 0.00 0.00 0.00 4.26
1492 1563 2.165641 TGCCACTACCGTTACATCTCTG 59.834 50.000 0.00 0.00 0.00 3.35
1493 1564 2.165845 GTGCCACTACCGTTACATCTCT 59.834 50.000 0.00 0.00 0.00 3.10
1497 1568 1.272807 AGGTGCCACTACCGTTACAT 58.727 50.000 0.00 0.00 45.56 2.29
1506 1577 0.034337 GGTCGTCAAAGGTGCCACTA 59.966 55.000 0.00 0.00 0.00 2.74
1522 1593 1.175983 TCCCCGTTGCATGTTTGGTC 61.176 55.000 0.00 0.00 0.00 4.02
1587 1658 6.567511 GCAAGAAAAGTTCCAAGTTGCAAAAA 60.568 34.615 0.00 0.00 37.19 1.94
1588 1659 5.106752 GCAAGAAAAGTTCCAAGTTGCAAAA 60.107 36.000 0.00 0.00 37.19 2.44
1589 1660 4.391523 GCAAGAAAAGTTCCAAGTTGCAAA 59.608 37.500 0.00 0.00 37.19 3.68
1590 1661 3.932089 GCAAGAAAAGTTCCAAGTTGCAA 59.068 39.130 0.00 0.00 37.19 4.08
1591 1662 3.520569 GCAAGAAAAGTTCCAAGTTGCA 58.479 40.909 0.00 0.00 37.19 4.08
1592 1663 2.866156 GGCAAGAAAAGTTCCAAGTTGC 59.134 45.455 0.00 0.00 36.78 4.17
1593 1664 3.132824 AGGGCAAGAAAAGTTCCAAGTTG 59.867 43.478 0.00 0.00 0.00 3.16
1594 1665 3.374764 AGGGCAAGAAAAGTTCCAAGTT 58.625 40.909 0.00 0.00 0.00 2.66
1595 1666 3.032265 AGGGCAAGAAAAGTTCCAAGT 57.968 42.857 0.00 0.00 0.00 3.16
1596 1667 3.384467 TGAAGGGCAAGAAAAGTTCCAAG 59.616 43.478 0.00 0.00 0.00 3.61
1597 1668 3.132111 GTGAAGGGCAAGAAAAGTTCCAA 59.868 43.478 0.00 0.00 0.00 3.53
1599 1670 2.959030 AGTGAAGGGCAAGAAAAGTTCC 59.041 45.455 0.00 0.00 0.00 3.62
1622 1694 1.507141 CGCGTTCAGAGGGCTTGTTT 61.507 55.000 0.00 0.00 0.00 2.83
1625 1697 3.121030 CCGCGTTCAGAGGGCTTG 61.121 66.667 4.92 0.00 36.04 4.01
1631 1703 2.125912 CAGGACCCGCGTTCAGAG 60.126 66.667 4.92 0.00 0.00 3.35
1653 1725 0.760567 AGATCGATGCCAGGCTACCA 60.761 55.000 14.15 0.00 0.00 3.25
1722 1794 4.609691 TTTCACACGGTTTTCAGAAGAC 57.390 40.909 0.00 0.00 0.00 3.01
1791 1881 4.671766 GCGGTTTGCCAACAAATCTACTAG 60.672 45.833 2.78 0.00 46.93 2.57
1808 1898 2.430367 GTCAGGTCAGGGCGGTTT 59.570 61.111 0.00 0.00 0.00 3.27
2025 2115 4.728882 GCAAGGTGAAATCAATAGAGTGCG 60.729 45.833 0.00 0.00 0.00 5.34
2029 2119 6.347696 AGAGAGCAAGGTGAAATCAATAGAG 58.652 40.000 0.00 0.00 0.00 2.43
2031 2121 5.526846 GGAGAGAGCAAGGTGAAATCAATAG 59.473 44.000 0.00 0.00 0.00 1.73
2036 2126 2.637947 GGGAGAGAGCAAGGTGAAATC 58.362 52.381 0.00 0.00 0.00 2.17
2038 2128 0.321671 CGGGAGAGAGCAAGGTGAAA 59.678 55.000 0.00 0.00 0.00 2.69
2047 2137 1.679305 TGGTCAGACGGGAGAGAGC 60.679 63.158 0.00 0.00 0.00 4.09
2077 2184 1.465187 CGCACGTGTTAGTCATCGAGA 60.465 52.381 18.38 0.00 0.00 4.04
2101 2208 2.413765 GCTCGACCCTGGATCGTC 59.586 66.667 10.85 0.79 40.50 4.20
2102 2209 3.148279 GGCTCGACCCTGGATCGT 61.148 66.667 10.85 0.00 40.50 3.73
2120 2227 0.613853 TCTGGAACTCCTGGTACCCG 60.614 60.000 10.07 2.14 35.87 5.28
2321 2428 0.793478 CCTCGAGCACGTACACGAAG 60.793 60.000 6.99 0.01 43.02 3.79
2362 2469 0.034476 CTGCTGCTTCTGGTCTGTCA 59.966 55.000 0.00 0.00 0.00 3.58
2364 2471 1.374190 CCTGCTGCTTCTGGTCTGT 59.626 57.895 0.00 0.00 0.00 3.41
2365 2472 2.039405 GCCTGCTGCTTCTGGTCTG 61.039 63.158 0.00 0.00 36.87 3.51
2366 2473 2.350514 GCCTGCTGCTTCTGGTCT 59.649 61.111 0.00 0.00 36.87 3.85
2367 2474 3.123620 CGCCTGCTGCTTCTGGTC 61.124 66.667 0.00 0.00 38.05 4.02
2368 2475 4.711949 CCGCCTGCTGCTTCTGGT 62.712 66.667 0.00 0.00 38.05 4.00
2415 2522 4.966787 GCCGTCCTGCCCCAACAA 62.967 66.667 0.00 0.00 0.00 2.83
2648 2755 5.396436 CCATTCTTTCCTTCACCCTACGTAT 60.396 44.000 0.00 0.00 0.00 3.06
2662 2769 3.507622 CAGTTTGTCCTCCCATTCTTTCC 59.492 47.826 0.00 0.00 0.00 3.13
2755 2874 8.744568 TGTTATGGAATATGTACATGAAAGCA 57.255 30.769 18.81 0.00 0.00 3.91
2832 2951 2.629017 AAAACGGAGGGGGAGTAGTA 57.371 50.000 0.00 0.00 0.00 1.82
2833 2952 1.627329 GAAAAACGGAGGGGGAGTAGT 59.373 52.381 0.00 0.00 0.00 2.73
2834 2953 1.907255 AGAAAAACGGAGGGGGAGTAG 59.093 52.381 0.00 0.00 0.00 2.57
2835 2954 1.904537 GAGAAAAACGGAGGGGGAGTA 59.095 52.381 0.00 0.00 0.00 2.59
2836 2955 0.691332 GAGAAAAACGGAGGGGGAGT 59.309 55.000 0.00 0.00 0.00 3.85
2837 2956 0.984995 AGAGAAAAACGGAGGGGGAG 59.015 55.000 0.00 0.00 0.00 4.30
2838 2957 0.981943 GAGAGAAAAACGGAGGGGGA 59.018 55.000 0.00 0.00 0.00 4.81
2839 2958 0.391263 CGAGAGAAAAACGGAGGGGG 60.391 60.000 0.00 0.00 0.00 5.40
2840 2959 0.320697 ACGAGAGAAAAACGGAGGGG 59.679 55.000 0.00 0.00 0.00 4.79
2841 2960 2.067013 GAACGAGAGAAAAACGGAGGG 58.933 52.381 0.00 0.00 0.00 4.30
2842 2961 2.067013 GGAACGAGAGAAAAACGGAGG 58.933 52.381 0.00 0.00 0.00 4.30
2843 2962 2.731976 CAGGAACGAGAGAAAAACGGAG 59.268 50.000 0.00 0.00 0.00 4.63
2844 2963 2.547218 CCAGGAACGAGAGAAAAACGGA 60.547 50.000 0.00 0.00 0.00 4.69
2860 2979 4.974438 ACGGTTCCAGCCCCAGGA 62.974 66.667 0.00 0.00 0.00 3.86
2886 3007 1.207791 GGAAGATTGGCCTCTCCTGA 58.792 55.000 3.32 0.00 35.26 3.86
2921 3044 2.764128 GCCGATGGAGGGGAGTCA 60.764 66.667 0.00 0.00 0.00 3.41
2923 3046 4.458829 TCGCCGATGGAGGGGAGT 62.459 66.667 0.00 0.00 46.44 3.85
2934 3057 2.488355 GACAATCGAGGTCGCCGA 59.512 61.111 4.49 0.00 40.53 5.54
2946 3069 2.602676 CCCCCTCACCACCGACAAT 61.603 63.158 0.00 0.00 0.00 2.71
2982 3106 2.390938 GAAAGTAAAAAGCGGTGCACC 58.609 47.619 26.78 26.78 0.00 5.01
2986 3110 1.605232 ACGGGAAAGTAAAAAGCGGTG 59.395 47.619 0.00 0.00 0.00 4.94
2988 3112 4.393990 AGATTACGGGAAAGTAAAAAGCGG 59.606 41.667 0.00 0.00 39.65 5.52
2992 3116 8.922931 AAACCTAGATTACGGGAAAGTAAAAA 57.077 30.769 0.00 0.00 39.65 1.94
3031 3158 0.817634 CCGTCACCAAAGCCAAGACA 60.818 55.000 0.00 0.00 0.00 3.41
3103 3230 3.275617 TCCATTCCCAACCATACGAAG 57.724 47.619 0.00 0.00 0.00 3.79
3104 3231 3.943671 ATCCATTCCCAACCATACGAA 57.056 42.857 0.00 0.00 0.00 3.85
3133 3261 4.892934 TGCCATCCTTACTTGAACAAACTT 59.107 37.500 0.00 0.00 0.00 2.66
3201 3332 1.199789 GGAGCAAATGTCATCGCAACA 59.800 47.619 9.23 0.00 0.00 3.33
3233 3364 0.413832 TGGACTACCTCCCAAGCTCT 59.586 55.000 0.00 0.00 38.49 4.09
3256 3387 6.371271 CGATGCATACCACAATATGTATCCAA 59.629 38.462 0.00 0.00 45.00 3.53
3257 3388 5.874261 CGATGCATACCACAATATGTATCCA 59.126 40.000 0.00 0.00 45.00 3.41
3322 3453 0.908910 AATCGTACCTGCCATCCACA 59.091 50.000 0.00 0.00 0.00 4.17
3431 3563 1.341080 ACCAAATGTGAAGCCCTTGG 58.659 50.000 0.00 0.00 41.91 3.61
3461 3593 2.669569 GCAGCTTTGCGGACCTCA 60.670 61.111 0.00 0.00 0.00 3.86
3539 3671 2.355363 CCAACGCTCGTCACCGAA 60.355 61.111 0.00 0.00 43.69 4.30
3540 3672 3.598715 ACCAACGCTCGTCACCGA 61.599 61.111 0.00 0.00 41.73 4.69
3571 3728 7.420800 ACAAAACTGAAAAGATAGCAGAACAG 58.579 34.615 0.00 0.00 33.94 3.16
3601 3758 0.316204 ACAAGTCACGTAAGGACCGG 59.684 55.000 0.00 0.00 46.39 5.28
3632 3789 8.864024 GGTAATACGTGTCTCATTCATATCATG 58.136 37.037 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.