Multiple sequence alignment - TraesCS5D01G045300

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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 TraesCS5D01G045300 chr5D 100.000 5843 0 0 1 5843 44574543 44568701 0.000000e+00 10791.0
1 TraesCS5D01G045300 chr5D 84.261 1671 242 13 3053 4715 6822556 6820899 0.000000e+00 1609.0
2 TraesCS5D01G045300 chr5D 96.226 53 2 0 1175 1227 6823648 6823596 2.900000e-13 87.9
3 TraesCS5D01G045300 chr5A 95.489 1840 78 3 2981 4819 34982840 34981005 0.000000e+00 2933.0
4 TraesCS5D01G045300 chr5A 90.018 1693 105 29 1006 2672 34986562 34984908 0.000000e+00 2132.0
5 TraesCS5D01G045300 chr5A 85.516 1588 225 3 3071 4657 3086900 3088483 0.000000e+00 1653.0
6 TraesCS5D01G045300 chr5A 81.568 1237 212 12 3057 4286 3132605 3133832 0.000000e+00 1007.0
7 TraesCS5D01G045300 chr5A 90.402 646 54 6 1 645 34987635 34986997 0.000000e+00 843.0
8 TraesCS5D01G045300 chr5A 88.477 243 13 7 2650 2886 34984862 34984629 4.460000e-71 279.0
9 TraesCS5D01G045300 chr5A 78.571 210 27 15 796 1001 34986789 34986594 7.950000e-24 122.0
10 TraesCS5D01G045300 chr5A 77.451 204 34 9 1033 1227 3085694 3085894 1.720000e-20 111.0
11 TraesCS5D01G045300 chr5A 96.774 62 1 1 2912 2972 34984645 34984584 1.040000e-17 102.0
12 TraesCS5D01G045300 chr5A 80.576 139 18 6 5026 5159 568038894 568039028 1.340000e-16 99.0
13 TraesCS5D01G045300 chr5B 94.981 1833 88 3 2981 4813 44140218 44142046 0.000000e+00 2872.0
14 TraesCS5D01G045300 chr5B 84.217 1603 246 5 3057 4657 862700 861103 0.000000e+00 1552.0
15 TraesCS5D01G045300 chr5B 89.902 1228 76 32 1781 2972 43959234 43958019 0.000000e+00 1537.0
16 TraesCS5D01G045300 chr5B 86.312 1410 106 36 4478 5843 43957976 43956610 0.000000e+00 1454.0
17 TraesCS5D01G045300 chr5B 89.891 1098 63 25 1005 2083 44137657 44138725 0.000000e+00 1369.0
18 TraesCS5D01G045300 chr5B 92.896 732 45 6 60 788 44135588 44136315 0.000000e+00 1057.0
19 TraesCS5D01G045300 chr5B 89.833 777 39 19 1005 1766 43968002 43967251 0.000000e+00 961.0
20 TraesCS5D01G045300 chr5B 94.422 502 16 5 2072 2570 44139142 44139634 0.000000e+00 761.0
21 TraesCS5D01G045300 chr5B 89.163 526 43 5 129 643 43969063 43968541 1.370000e-180 643.0
22 TraesCS5D01G045300 chr5B 89.163 526 43 5 129 643 44136596 44137118 1.370000e-180 643.0
23 TraesCS5D01G045300 chr5B 91.420 338 13 8 2648 2972 44139694 44140028 3.210000e-122 449.0
24 TraesCS5D01G045300 chr5B 82.564 390 24 11 651 1001 43968430 43968046 2.650000e-78 303.0
25 TraesCS5D01G045300 chr5B 82.564 390 24 11 651 1001 44137229 44137613 2.650000e-78 303.0
26 TraesCS5D01G045300 chr5B 98.571 70 1 0 1 70 44134091 44134160 2.210000e-24 124.0
27 TraesCS5D01G045300 chr5B 92.308 39 2 1 4872 4910 464603842 464603879 3.000000e-03 54.7
28 TraesCS5D01G045300 chr2D 81.691 1644 287 10 3067 4709 15991428 15989798 0.000000e+00 1356.0
29 TraesCS5D01G045300 chr2D 80.545 257 50 0 4401 4657 607839043 607838787 1.280000e-46 198.0
30 TraesCS5D01G045300 chr2D 78.571 154 26 6 4871 5018 621574589 621574437 1.730000e-15 95.3
31 TraesCS5D01G045300 chr2D 90.000 50 5 0 4871 4920 324259282 324259331 1.360000e-06 65.8
32 TraesCS5D01G045300 chr2A 81.092 1666 297 15 3045 4709 17870952 17869304 0.000000e+00 1315.0
33 TraesCS5D01G045300 chr2A 92.157 51 4 0 4871 4921 394400593 394400543 8.120000e-09 73.1
34 TraesCS5D01G045300 chr2B 80.860 1651 296 15 3072 4718 28175333 28173699 0.000000e+00 1280.0
35 TraesCS5D01G045300 chr7A 84.242 1155 172 6 3506 4657 47511682 47512829 0.000000e+00 1116.0
36 TraesCS5D01G045300 chr7A 87.209 86 5 5 1154 1233 47511500 47511585 6.230000e-15 93.5
37 TraesCS5D01G045300 chr7A 82.609 69 10 2 3926 3993 26057419 26057352 6.320000e-05 60.2
38 TraesCS5D01G045300 chrUn 89.833 777 39 19 1005 1766 369137393 369136642 0.000000e+00 961.0
39 TraesCS5D01G045300 chrUn 89.163 526 43 5 129 643 369138454 369137932 1.370000e-180 643.0
40 TraesCS5D01G045300 chrUn 82.564 390 24 11 651 1001 369137821 369137437 2.650000e-78 303.0
41 TraesCS5D01G045300 chr7D 86.548 394 53 0 3879 4272 45279325 45279718 8.990000e-118 435.0
42 TraesCS5D01G045300 chr7D 80.916 393 66 3 4311 4694 45279712 45280104 9.520000e-78 302.0
43 TraesCS5D01G045300 chr7D 85.366 82 10 2 5080 5159 395293411 395293492 3.750000e-12 84.2
44 TraesCS5D01G045300 chr7D 95.745 47 2 0 4869 4915 15074140 15074094 6.280000e-10 76.8
45 TraesCS5D01G045300 chr6B 76.758 327 41 25 4861 5166 434297538 434297226 3.650000e-32 150.0
46 TraesCS5D01G045300 chr6B 95.455 44 2 0 4872 4915 630483555 630483598 2.920000e-08 71.3
47 TraesCS5D01G045300 chr6A 80.690 145 26 2 5017 5159 4583845 4583989 1.720000e-20 111.0
48 TraesCS5D01G045300 chr1A 77.703 148 27 4 5017 5159 572220614 572220468 1.040000e-12 86.1
49 TraesCS5D01G045300 chr1B 77.273 154 21 11 4871 5018 44648420 44648565 1.750000e-10 78.7
50 TraesCS5D01G045300 chr1D 92.157 51 4 0 1177 1227 71339677 71339727 8.120000e-09 73.1
51 TraesCS5D01G045300 chr3B 84.507 71 9 2 2754 2822 766834145 766834075 1.050000e-07 69.4


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 TraesCS5D01G045300 chr5D 44568701 44574543 5842 True 10791.000000 10791 100.000000 1 5843 1 chr5D.!!$R1 5842
1 TraesCS5D01G045300 chr5D 6820899 6823648 2749 True 848.450000 1609 90.243500 1175 4715 2 chr5D.!!$R2 3540
2 TraesCS5D01G045300 chr5A 34981005 34987635 6630 True 1068.500000 2933 89.955167 1 4819 6 chr5A.!!$R1 4818
3 TraesCS5D01G045300 chr5A 3132605 3133832 1227 False 1007.000000 1007 81.568000 3057 4286 1 chr5A.!!$F1 1229
4 TraesCS5D01G045300 chr5A 3085694 3088483 2789 False 882.000000 1653 81.483500 1033 4657 2 chr5A.!!$F3 3624
5 TraesCS5D01G045300 chr5B 861103 862700 1597 True 1552.000000 1552 84.217000 3057 4657 1 chr5B.!!$R1 1600
6 TraesCS5D01G045300 chr5B 43956610 43959234 2624 True 1495.500000 1537 88.107000 1781 5843 2 chr5B.!!$R2 4062
7 TraesCS5D01G045300 chr5B 44134091 44142046 7955 False 947.250000 2872 91.738500 1 4813 8 chr5B.!!$F2 4812
8 TraesCS5D01G045300 chr5B 43967251 43969063 1812 True 635.666667 961 87.186667 129 1766 3 chr5B.!!$R3 1637
9 TraesCS5D01G045300 chr2D 15989798 15991428 1630 True 1356.000000 1356 81.691000 3067 4709 1 chr2D.!!$R1 1642
10 TraesCS5D01G045300 chr2A 17869304 17870952 1648 True 1315.000000 1315 81.092000 3045 4709 1 chr2A.!!$R1 1664
11 TraesCS5D01G045300 chr2B 28173699 28175333 1634 True 1280.000000 1280 80.860000 3072 4718 1 chr2B.!!$R1 1646
12 TraesCS5D01G045300 chr7A 47511500 47512829 1329 False 604.750000 1116 85.725500 1154 4657 2 chr7A.!!$F1 3503
13 TraesCS5D01G045300 chrUn 369136642 369138454 1812 True 635.666667 961 87.186667 129 1766 3 chrUn.!!$R1 1637
14 TraesCS5D01G045300 chr7D 45279325 45280104 779 False 368.500000 435 83.732000 3879 4694 2 chr7D.!!$F2 815

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
454 2846 0.655733 CCTACGCCCGCATACTTTTG 59.344 55.000 0.0 0.0 0.0 2.44 F
1561 4286 0.174845 CCACAAATCAGCAGCCCATG 59.825 55.000 0.0 0.0 0.0 3.66 F
1671 4439 1.203300 TCCTCCTCATTCCTGACCACA 60.203 52.381 0.0 0.0 0.0 4.17 F
2764 6134 1.301677 CTTTTCTCCAGCCCTCACGC 61.302 60.000 0.0 0.0 0.0 5.34 F
3732 8842 1.192146 TCACTAGCTTCGCCCAGGTT 61.192 55.000 0.0 0.0 0.0 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2217 5475 0.037734 AATCACCACCCCGGAAGAAC 59.962 55.000 0.73 0.00 38.63 3.01 R
3341 8451 0.955428 TTTGGATGAGCTGCACGTCC 60.955 55.000 25.51 25.51 42.02 4.79 R
3639 8749 2.517875 GCGCATGAGAGGCCCATT 60.518 61.111 0.30 0.00 0.00 3.16 R
3759 8871 3.123620 CCACGAGCTTGCAGGAGC 61.124 66.667 0.00 0.00 43.02 4.70 R
5568 10731 0.104934 ACCAACCACTCCCTCTGTCT 60.105 55.000 0.00 0.00 0.00 3.41 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
72 1511 9.083422 TCTTTTACACATATCACAATGGGAAAA 57.917 29.630 0.00 0.00 34.23 2.29
86 1525 3.772387 TGGGAAAATGTTGGTGATAGCA 58.228 40.909 0.00 0.00 0.00 3.49
88 1527 4.590647 TGGGAAAATGTTGGTGATAGCAAA 59.409 37.500 0.00 0.00 37.34 3.68
89 1528 5.070981 TGGGAAAATGTTGGTGATAGCAAAA 59.929 36.000 0.00 0.00 37.34 2.44
90 1529 6.172630 GGGAAAATGTTGGTGATAGCAAAAT 58.827 36.000 0.00 0.00 37.34 1.82
168 2549 3.702623 TCCAGTACCCCCTCCCCC 61.703 72.222 0.00 0.00 0.00 5.40
244 2636 9.599866 TCACACGTTCATGATTATCTAATTCTT 57.400 29.630 0.00 0.00 0.00 2.52
349 2741 8.400947 CACCTTAAATCTACATCCAAATCTGTG 58.599 37.037 0.00 0.00 0.00 3.66
357 2749 7.874940 TCTACATCCAAATCTGTGAACTTTTG 58.125 34.615 0.00 0.00 0.00 2.44
385 2777 4.251268 GGTGTACCGAAGCAAAACTCTAT 58.749 43.478 0.00 0.00 0.00 1.98
454 2846 0.655733 CCTACGCCCGCATACTTTTG 59.344 55.000 0.00 0.00 0.00 2.44
487 2879 9.177608 CTAATTTCCTTGATTGGACATTGAGTA 57.822 33.333 5.49 0.00 37.18 2.59
543 2935 4.021807 TCACTCAAATGCAGGTAGTACGAA 60.022 41.667 0.00 0.00 0.00 3.85
545 2937 5.178623 CACTCAAATGCAGGTAGTACGAAAA 59.821 40.000 0.00 0.00 0.00 2.29
548 2940 5.992829 TCAAATGCAGGTAGTACGAAAAAGA 59.007 36.000 0.00 0.00 0.00 2.52
558 2950 1.658994 ACGAAAAAGACGCTTCACCA 58.341 45.000 0.00 0.00 0.00 4.17
562 2954 4.148891 CGAAAAAGACGCTTCACCAATAC 58.851 43.478 0.00 0.00 0.00 1.89
576 2968 1.945394 CCAATACAGACATGGAGCTGC 59.055 52.381 0.00 0.00 36.27 5.25
601 2993 2.203351 GGCCCGGGCTCCTTTATG 60.203 66.667 42.70 3.74 41.60 1.90
603 2995 2.595095 CCCGGGCTCCTTTATGCA 59.405 61.111 8.08 0.00 0.00 3.96
611 3003 1.410153 GCTCCTTTATGCATGGTTGGG 59.590 52.381 10.16 4.69 0.00 4.12
614 3006 3.096092 TCCTTTATGCATGGTTGGGTTC 58.904 45.455 10.16 0.00 0.00 3.62
630 3022 6.347969 GGTTGGGTTCGTTTCAATTAGAGTAC 60.348 42.308 0.00 0.00 0.00 2.73
645 3037 8.976471 CAATTAGAGTACTAATCATCTGCACTG 58.024 37.037 0.00 0.00 45.19 3.66
647 3039 8.747538 TTAGAGTACTAATCATCTGCACTGTA 57.252 34.615 0.00 0.00 34.21 2.74
648 3040 7.033530 AGAGTACTAATCATCTGCACTGTAC 57.966 40.000 0.00 0.00 0.00 2.90
649 3041 5.822278 AGTACTAATCATCTGCACTGTACG 58.178 41.667 0.00 0.00 35.56 3.67
675 3172 2.964740 TGCTTCTCACTCACATGTAGC 58.035 47.619 0.00 1.58 0.00 3.58
726 3227 3.209410 AGAGAGCAAATAATTGAGGGCG 58.791 45.455 0.00 0.00 38.94 6.13
751 3252 1.176527 TTATTTGCCTCCAGCTGCAC 58.823 50.000 8.66 0.00 44.23 4.57
783 3284 4.333649 GGCTTCACAAATTCGATCAGATGA 59.666 41.667 0.00 0.00 0.00 2.92
839 3340 5.401033 GCTTTCTGCAGTACATCTGTATG 57.599 43.478 14.67 0.00 45.23 2.39
840 3341 4.872691 GCTTTCTGCAGTACATCTGTATGT 59.127 41.667 14.67 0.00 45.23 2.29
841 3342 6.042777 GCTTTCTGCAGTACATCTGTATGTA 58.957 40.000 14.67 0.00 45.23 2.29
842 3343 6.535150 GCTTTCTGCAGTACATCTGTATGTAA 59.465 38.462 14.67 0.00 44.09 2.41
972 3513 2.932569 TTATACGGCCGGCCTCTCCA 62.933 60.000 41.01 21.99 34.01 3.86
981 3522 2.730524 GGCCTCTCCACCTCTGCTC 61.731 68.421 0.00 0.00 34.01 4.26
1017 3598 3.036577 CTTGGTGTGTGCCAGCTG 58.963 61.111 6.78 6.78 42.19 4.24
1045 3629 2.289320 GCTTGCCTAGTGATCGATGGAT 60.289 50.000 0.54 0.00 34.96 3.41
1054 3638 3.758023 AGTGATCGATGGATGCAAACAAA 59.242 39.130 0.54 0.00 31.51 2.83
1081 3665 4.154347 CCGCAGCAGGAGGAGGAC 62.154 72.222 0.00 0.00 39.08 3.85
1241 3849 2.726821 GTGATTGTCACCACATCCCAT 58.273 47.619 0.00 0.00 41.37 4.00
1247 3855 1.492176 GTCACCACATCCCATCCATCT 59.508 52.381 0.00 0.00 0.00 2.90
1248 3856 2.705658 GTCACCACATCCCATCCATCTA 59.294 50.000 0.00 0.00 0.00 1.98
1249 3857 2.974794 TCACCACATCCCATCCATCTAG 59.025 50.000 0.00 0.00 0.00 2.43
1250 3858 1.701847 ACCACATCCCATCCATCTAGC 59.298 52.381 0.00 0.00 0.00 3.42
1253 3861 2.905085 CACATCCCATCCATCTAGCTCT 59.095 50.000 0.00 0.00 0.00 4.09
1256 3864 2.603021 TCCCATCCATCTAGCTCTGTC 58.397 52.381 0.00 0.00 0.00 3.51
1274 3893 1.547372 GTCTGTTTTCCCTGCATGCAT 59.453 47.619 22.97 0.00 0.00 3.96
1291 3910 6.370718 TGCATGCATATGTCACATCTTCTATC 59.629 38.462 18.46 0.00 36.65 2.08
1294 3913 4.867047 GCATATGTCACATCTTCTATCCGG 59.133 45.833 4.29 0.00 0.00 5.14
1343 4006 6.434028 TCCTATTGTTTTTCTTGACCTGGATG 59.566 38.462 0.00 0.00 0.00 3.51
1383 4070 3.120130 TGCCATCGTAAATGAACCGAAAC 60.120 43.478 0.00 0.00 33.89 2.78
1386 4073 3.799137 TCGTAAATGAACCGAAACAGC 57.201 42.857 0.00 0.00 0.00 4.40
1387 4074 3.132160 TCGTAAATGAACCGAAACAGCA 58.868 40.909 0.00 0.00 0.00 4.41
1388 4075 3.185594 TCGTAAATGAACCGAAACAGCAG 59.814 43.478 0.00 0.00 0.00 4.24
1389 4076 3.185594 CGTAAATGAACCGAAACAGCAGA 59.814 43.478 0.00 0.00 0.00 4.26
1390 4077 3.626028 AAATGAACCGAAACAGCAGAC 57.374 42.857 0.00 0.00 0.00 3.51
1391 4078 2.254546 ATGAACCGAAACAGCAGACA 57.745 45.000 0.00 0.00 0.00 3.41
1392 4079 1.581934 TGAACCGAAACAGCAGACAG 58.418 50.000 0.00 0.00 0.00 3.51
1393 4080 1.134521 TGAACCGAAACAGCAGACAGT 60.135 47.619 0.00 0.00 0.00 3.55
1394 4081 2.101750 TGAACCGAAACAGCAGACAGTA 59.898 45.455 0.00 0.00 0.00 2.74
1395 4082 2.902705 ACCGAAACAGCAGACAGTAA 57.097 45.000 0.00 0.00 0.00 2.24
1396 4083 3.188159 ACCGAAACAGCAGACAGTAAA 57.812 42.857 0.00 0.00 0.00 2.01
1397 4084 3.131396 ACCGAAACAGCAGACAGTAAAG 58.869 45.455 0.00 0.00 0.00 1.85
1398 4085 3.131396 CCGAAACAGCAGACAGTAAAGT 58.869 45.455 0.00 0.00 0.00 2.66
1399 4086 3.560068 CCGAAACAGCAGACAGTAAAGTT 59.440 43.478 0.00 0.00 0.00 2.66
1416 4103 2.047061 AGTTGTGCAGGACAAGTAGGA 58.953 47.619 13.17 0.00 44.93 2.94
1492 4211 4.501714 GTGCCGTGCCATGCCATG 62.502 66.667 0.00 0.00 0.00 3.66
1496 4221 1.943116 GCCGTGCCATGCCATGTTTA 61.943 55.000 3.63 0.00 0.00 2.01
1555 4280 0.524862 GAGTGCCCACAAATCAGCAG 59.475 55.000 0.82 0.00 35.56 4.24
1556 4281 1.080298 GTGCCCACAAATCAGCAGC 60.080 57.895 0.00 0.00 35.56 5.25
1557 4282 2.277591 TGCCCACAAATCAGCAGCC 61.278 57.895 0.00 0.00 0.00 4.85
1558 4283 3.010413 GCCCACAAATCAGCAGCCC 62.010 63.158 0.00 0.00 0.00 5.19
1559 4284 1.607178 CCCACAAATCAGCAGCCCA 60.607 57.895 0.00 0.00 0.00 5.36
1560 4285 0.974010 CCCACAAATCAGCAGCCCAT 60.974 55.000 0.00 0.00 0.00 4.00
1561 4286 0.174845 CCACAAATCAGCAGCCCATG 59.825 55.000 0.00 0.00 0.00 3.66
1671 4439 1.203300 TCCTCCTCATTCCTGACCACA 60.203 52.381 0.00 0.00 0.00 4.17
1700 4468 5.066117 GCAAAATACTGTAGCCCCTAGTTTC 59.934 44.000 0.00 0.00 0.00 2.78
1721 4492 9.120538 AGTTTCTCTAAGCAGTTCAAAACAATA 57.879 29.630 0.00 0.00 0.00 1.90
1749 4520 4.873768 AAACGCAACCAAAATCCAAAAG 57.126 36.364 0.00 0.00 0.00 2.27
1885 4671 6.776603 TGATATTATGGATCCACACATTTGCA 59.223 34.615 18.99 6.26 0.00 4.08
1901 4687 8.522830 ACACATTTGCATTTTACTGTAGCTTAT 58.477 29.630 0.00 0.00 0.00 1.73
1902 4688 8.800972 CACATTTGCATTTTACTGTAGCTTATG 58.199 33.333 0.00 0.00 0.00 1.90
1949 4767 3.829886 ACGCACATGTAGAAACCAATG 57.170 42.857 0.00 0.00 0.00 2.82
1952 4770 4.094887 ACGCACATGTAGAAACCAATGATC 59.905 41.667 0.00 0.00 0.00 2.92
1979 4799 3.888930 TGTGGGATGTTTTCAGAGTTTCC 59.111 43.478 0.00 0.00 0.00 3.13
2123 5374 4.803452 ACTTCCATTCCTTGTTTTCCTCA 58.197 39.130 0.00 0.00 0.00 3.86
2129 5380 6.953520 TCCATTCCTTGTTTTCCTCATACAAT 59.046 34.615 0.00 0.00 31.96 2.71
2132 5383 8.928733 CATTCCTTGTTTTCCTCATACAATTTG 58.071 33.333 0.00 0.00 31.96 2.32
2554 5816 6.027749 GTCAAAGTCGACAAAACAAAGTGAT 58.972 36.000 19.50 0.00 35.88 3.06
2598 5860 4.089239 TGTTGGCGCCGCATCCTA 62.089 61.111 23.90 0.00 0.00 2.94
2603 5865 3.272334 GCGCCGCATCCTAACAGG 61.272 66.667 3.15 0.00 36.46 4.00
2606 5868 2.911143 CCGCATCCTAACAGGGCT 59.089 61.111 0.00 0.00 35.59 5.19
2612 5874 2.092699 GCATCCTAACAGGGCTTCTTCT 60.093 50.000 0.00 0.00 35.59 2.85
2613 5875 3.623453 GCATCCTAACAGGGCTTCTTCTT 60.623 47.826 0.00 0.00 35.59 2.52
2614 5876 3.983044 TCCTAACAGGGCTTCTTCTTC 57.017 47.619 0.00 0.00 35.59 2.87
2679 6040 3.081061 AGAACACACACACACAACACAT 58.919 40.909 0.00 0.00 0.00 3.21
2708 6069 2.351738 GGAAGATCACAAACGGCTTTGG 60.352 50.000 12.03 0.00 41.12 3.28
2712 6073 4.331968 AGATCACAAACGGCTTTGGAATA 58.668 39.130 12.03 0.00 41.12 1.75
2764 6134 1.301677 CTTTTCTCCAGCCCTCACGC 61.302 60.000 0.00 0.00 0.00 5.34
2876 6251 2.132517 ATCACGTACGTGCACGACCA 62.133 55.000 42.94 24.77 44.69 4.02
2909 6284 6.385176 AGATCCTTGAAACACTCCATGATCTA 59.615 38.462 0.00 0.00 0.00 1.98
2972 6347 8.458843 CACCAATAATTAACTCCACTAACCAAG 58.541 37.037 0.00 0.00 0.00 3.61
2973 6348 7.122204 ACCAATAATTAACTCCACTAACCAAGC 59.878 37.037 0.00 0.00 0.00 4.01
2975 6350 4.650972 ATTAACTCCACTAACCAAGCCA 57.349 40.909 0.00 0.00 0.00 4.75
2977 6352 3.525800 AACTCCACTAACCAAGCCATT 57.474 42.857 0.00 0.00 0.00 3.16
2979 6354 1.474077 CTCCACTAACCAAGCCATTGC 59.526 52.381 0.00 0.00 34.91 3.56
3018 8128 7.626999 TTACCTACCAAGCCATTGTATAGAT 57.373 36.000 0.00 0.00 34.39 1.98
3019 8129 8.730093 TTACCTACCAAGCCATTGTATAGATA 57.270 34.615 0.00 0.00 34.39 1.98
3020 8130 7.005709 ACCTACCAAGCCATTGTATAGATAC 57.994 40.000 0.00 0.00 34.39 2.24
3021 8131 6.787957 ACCTACCAAGCCATTGTATAGATACT 59.212 38.462 1.60 0.00 34.39 2.12
3135 8245 3.200483 GTCGAACTTGTTGGTGTACCTT 58.800 45.455 2.32 0.00 36.82 3.50
3341 8451 3.077556 CCACTCCCTCCACCCTCG 61.078 72.222 0.00 0.00 0.00 4.63
3732 8842 1.192146 TCACTAGCTTCGCCCAGGTT 61.192 55.000 0.00 0.00 0.00 3.50
4266 9378 1.745653 CTCTCAGTGGTCACGATGCTA 59.254 52.381 0.00 0.00 36.20 3.49
4356 9468 4.408821 CAGTTGCTGGCGGGGCTA 62.409 66.667 0.00 0.00 0.00 3.93
4780 9907 5.347620 AGTATTACGTAACTGGGATGCAA 57.652 39.130 10.81 0.00 0.00 4.08
4781 9908 5.925509 AGTATTACGTAACTGGGATGCAAT 58.074 37.500 10.81 0.00 0.00 3.56
4803 9930 7.387948 GCAATCATAGATCGTTAGGTTAATGGT 59.612 37.037 0.00 0.00 0.00 3.55
4846 9973 6.834959 ATGTGTGTGTATGATCGATCTTTC 57.165 37.500 25.02 16.89 0.00 2.62
4856 9983 5.459536 TGATCGATCTTTCATCCTAGTGG 57.540 43.478 25.02 0.00 0.00 4.00
4858 9985 4.655762 TCGATCTTTCATCCTAGTGGTG 57.344 45.455 0.00 0.00 34.23 4.17
4859 9986 4.278310 TCGATCTTTCATCCTAGTGGTGA 58.722 43.478 0.00 0.00 34.23 4.02
4860 9987 4.895889 TCGATCTTTCATCCTAGTGGTGAT 59.104 41.667 0.00 0.00 34.23 3.06
4861 9988 5.363868 TCGATCTTTCATCCTAGTGGTGATT 59.636 40.000 0.00 0.00 34.23 2.57
4862 9989 6.549736 TCGATCTTTCATCCTAGTGGTGATTA 59.450 38.462 0.00 0.00 34.23 1.75
4863 9990 6.865726 CGATCTTTCATCCTAGTGGTGATTAG 59.134 42.308 0.00 0.00 34.23 1.73
4864 9991 7.470702 CGATCTTTCATCCTAGTGGTGATTAGT 60.471 40.741 0.00 0.00 34.23 2.24
4865 9992 8.783660 ATCTTTCATCCTAGTGGTGATTAGTA 57.216 34.615 0.00 0.00 34.23 1.82
4866 9993 8.239038 TCTTTCATCCTAGTGGTGATTAGTAG 57.761 38.462 0.00 0.00 34.23 2.57
4867 9994 7.839705 TCTTTCATCCTAGTGGTGATTAGTAGT 59.160 37.037 0.00 0.00 34.23 2.73
4868 9995 9.132923 CTTTCATCCTAGTGGTGATTAGTAGTA 57.867 37.037 0.00 0.00 34.23 1.82
4869 9996 8.461249 TTCATCCTAGTGGTGATTAGTAGTAC 57.539 38.462 0.00 0.00 34.23 2.73
4870 9997 7.813331 TCATCCTAGTGGTGATTAGTAGTACT 58.187 38.462 8.14 8.14 34.23 2.73
4871 9998 8.942033 TCATCCTAGTGGTGATTAGTAGTACTA 58.058 37.037 5.90 5.90 34.23 1.82
4872 9999 9.001542 CATCCTAGTGGTGATTAGTAGTACTAC 57.998 40.741 23.03 23.03 34.02 2.73
4873 10000 8.329346 TCCTAGTGGTGATTAGTAGTACTACT 57.671 38.462 32.39 32.39 40.76 2.57
4874 10001 9.439461 TCCTAGTGGTGATTAGTAGTACTACTA 57.561 37.037 30.50 30.50 39.58 1.82
4875 10002 9.709495 CCTAGTGGTGATTAGTAGTACTACTAG 57.291 40.741 31.49 21.71 45.92 2.57
4876 10003 9.709495 CTAGTGGTGATTAGTAGTACTACTAGG 57.291 40.741 31.49 15.06 45.92 3.02
4877 10004 8.329346 AGTGGTGATTAGTAGTACTACTAGGA 57.671 38.462 31.49 23.05 45.92 2.94
4878 10005 8.431222 AGTGGTGATTAGTAGTACTACTAGGAG 58.569 40.741 31.49 0.00 45.92 3.69
4879 10006 7.661027 GTGGTGATTAGTAGTACTACTAGGAGG 59.339 44.444 31.49 0.00 45.92 4.30
4886 10013 2.037901 GTACTACTAGGAGGGTTGGGC 58.962 57.143 6.98 0.00 0.00 5.36
4897 10024 2.355009 GTTGGGCGTGCTTTGCTG 60.355 61.111 0.00 0.00 0.00 4.41
4921 10048 1.135344 CGTTGGTGTCGTTGGGTTTTT 60.135 47.619 0.00 0.00 0.00 1.94
4924 10051 4.684877 GTTGGTGTCGTTGGGTTTTTATT 58.315 39.130 0.00 0.00 0.00 1.40
4926 10053 4.934515 TGGTGTCGTTGGGTTTTTATTTC 58.065 39.130 0.00 0.00 0.00 2.17
4980 10110 8.712285 AGATGCATTGGTTTTTAGAAATGATG 57.288 30.769 0.00 0.00 32.86 3.07
5094 10245 4.866921 TGCGCTCGATATTTTTAGCTCTA 58.133 39.130 9.73 0.00 32.73 2.43
5095 10246 5.286438 TGCGCTCGATATTTTTAGCTCTAA 58.714 37.500 9.73 0.00 32.73 2.10
5113 10264 7.360361 AGCTCTAAACTTGGTCAAAATTAACG 58.640 34.615 0.00 0.00 0.00 3.18
5174 10325 8.830201 TTAGAATTGAAATGAAACCAACCATG 57.170 30.769 0.00 0.00 0.00 3.66
5191 10342 3.199677 CCATGCATGCATAAAAGTTGGG 58.800 45.455 31.73 21.51 34.91 4.12
5192 10343 3.199677 CATGCATGCATAAAAGTTGGGG 58.800 45.455 31.73 12.42 34.91 4.96
5196 10347 0.540830 TGCATAAAAGTTGGGGCCGT 60.541 50.000 0.00 0.00 0.00 5.68
5206 10357 2.158813 AGTTGGGGCCGTTACATATCTG 60.159 50.000 0.00 0.00 0.00 2.90
5208 10359 2.680251 TGGGGCCGTTACATATCTGTA 58.320 47.619 0.00 0.00 36.79 2.74
5211 10362 4.839550 TGGGGCCGTTACATATCTGTATTA 59.160 41.667 0.00 0.00 37.68 0.98
5215 10366 7.392393 GGGGCCGTTACATATCTGTATTATTTT 59.608 37.037 0.00 0.00 37.68 1.82
5216 10367 8.448615 GGGCCGTTACATATCTGTATTATTTTC 58.551 37.037 0.00 0.00 37.68 2.29
5217 10368 9.216117 GGCCGTTACATATCTGTATTATTTTCT 57.784 33.333 0.00 0.00 37.68 2.52
5247 10405 2.159366 CGCACCTCATAGTCGACTTCTT 60.159 50.000 25.44 6.46 0.00 2.52
5260 10418 7.279470 AGTCGACTTCTTCTTAAAAATAGCG 57.721 36.000 13.58 0.00 0.00 4.26
5324 10483 3.117663 TGCCAGGTCTTGAACTTAAACCT 60.118 43.478 0.00 0.00 40.97 3.50
5331 10490 4.036380 GTCTTGAACTTAAACCTGTGTGGG 59.964 45.833 0.00 0.00 41.11 4.61
5365 10528 6.831868 ACCACAAGAAACATAACCAAGTTACT 59.168 34.615 0.00 0.00 30.49 2.24
5366 10529 7.138736 CCACAAGAAACATAACCAAGTTACTG 58.861 38.462 0.00 0.00 30.49 2.74
5382 10545 2.528797 CTGTAAGTTCGCGGTTGCT 58.471 52.632 6.13 0.00 39.65 3.91
5397 10560 6.869388 TCGCGGTTGCTTGTATATATTAATGA 59.131 34.615 6.13 0.00 39.65 2.57
5398 10561 7.385478 TCGCGGTTGCTTGTATATATTAATGAA 59.615 33.333 6.13 0.00 39.65 2.57
5399 10562 7.688167 CGCGGTTGCTTGTATATATTAATGAAG 59.312 37.037 0.00 0.00 39.65 3.02
5400 10563 8.504005 GCGGTTGCTTGTATATATTAATGAAGT 58.496 33.333 0.00 0.00 38.39 3.01
5444 10607 5.689383 ACATGTACCATTTAATCCATCGC 57.311 39.130 0.00 0.00 0.00 4.58
5494 10657 6.086785 ACTGCTTTAGAATATACTCCGTCC 57.913 41.667 0.00 0.00 0.00 4.79
5499 10662 6.514705 GCTTTAGAATATACTCCGTCCGTCTT 60.515 42.308 0.00 0.00 0.00 3.01
5507 10670 3.387397 ACTCCGTCCGTCTTAACAAAAG 58.613 45.455 0.00 0.00 0.00 2.27
5508 10671 2.137523 TCCGTCCGTCTTAACAAAAGC 58.862 47.619 0.00 0.00 0.00 3.51
5576 10739 7.678947 AATGACACTTATTTTGAGACAGAGG 57.321 36.000 0.00 0.00 0.00 3.69
5581 10744 5.641209 CACTTATTTTGAGACAGAGGGAGTG 59.359 44.000 0.00 0.00 0.00 3.51
5610 10773 7.657761 TGGTCAAACATTTTTACAACAACAAGT 59.342 29.630 0.00 0.00 0.00 3.16
5641 10804 9.855021 TCTATTTTGGCTAGTTTTAATTTCAGC 57.145 29.630 0.00 0.00 0.00 4.26
5669 10832 2.791383 TCCCACATTTTGCAAAGACG 57.209 45.000 12.41 7.42 0.00 4.18
5678 10841 3.955771 TTTGCAAAGACGTCCTAACAC 57.044 42.857 13.01 0.00 0.00 3.32
5683 10846 4.201871 TGCAAAGACGTCCTAACACTTTTG 60.202 41.667 13.01 14.08 32.86 2.44
5733 10896 9.047371 TGTATGTATACAACAAATACCCAATCG 57.953 33.333 10.14 0.00 42.70 3.34
5743 10906 4.572985 AATACCCAATCGATGCAACATG 57.427 40.909 0.00 0.00 0.00 3.21
5761 10924 7.625553 GCAACATGCAAAAACATACAAACTTA 58.374 30.769 0.00 0.00 44.26 2.24
5815 10978 5.291614 AGCAAACACAAATTCATCACAACAC 59.708 36.000 0.00 0.00 0.00 3.32
5819 10982 4.402155 ACACAAATTCATCACAACACACCT 59.598 37.500 0.00 0.00 0.00 4.00
5831 10994 8.768019 CATCACAACACACCTTCTATATATGTG 58.232 37.037 10.51 10.51 44.92 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.886542 CCCGCCCCTTAGATAATTTGC 59.113 52.381 0.00 0.00 0.00 3.68
72 1511 8.344098 CAACAAAAATTTTGCTATCACCAACAT 58.656 29.630 17.39 0.00 0.00 2.71
86 1525 9.157104 ACCATTTTAGACGACAACAAAAATTTT 57.843 25.926 0.00 0.00 29.66 1.82
88 1527 9.458374 CTACCATTTTAGACGACAACAAAAATT 57.542 29.630 0.00 0.00 29.66 1.82
89 1528 8.626526 ACTACCATTTTAGACGACAACAAAAAT 58.373 29.630 0.00 0.00 31.67 1.82
90 1529 7.987649 ACTACCATTTTAGACGACAACAAAAA 58.012 30.769 0.00 0.00 0.00 1.94
95 1535 8.248117 ACATAACTACCATTTTAGACGACAAC 57.752 34.615 0.00 0.00 0.00 3.32
168 2549 2.815503 CGTGTAAACTTTTAGGGGTGGG 59.184 50.000 0.00 0.00 0.00 4.61
215 2607 7.987268 TTAGATAATCATGAACGTGTGAGAC 57.013 36.000 0.00 0.00 0.00 3.36
329 2721 8.641498 AAGTTCACAGATTTGGATGTAGATTT 57.359 30.769 0.00 0.00 0.00 2.17
349 2741 3.415212 GGTACACCCCCTACAAAAGTTC 58.585 50.000 0.00 0.00 0.00 3.01
357 2749 1.259840 TGCTTCGGTACACCCCCTAC 61.260 60.000 0.00 0.00 0.00 3.18
432 2824 1.610554 AAGTATGCGGGCGTAGGTGT 61.611 55.000 0.00 0.00 0.00 4.16
454 2846 7.084486 GTCCAATCAAGGAAATTAGTCACAAC 58.916 38.462 0.00 0.00 39.92 3.32
487 2879 1.346722 GCCCCACTACTAGTGTTGTGT 59.653 52.381 14.00 0.00 44.50 3.72
505 2897 1.675641 GTGATCCACCCACTGTGCC 60.676 63.158 1.29 0.00 44.01 5.01
521 2913 3.845178 TCGTACTACCTGCATTTGAGTG 58.155 45.455 0.00 0.00 0.00 3.51
543 2935 4.213482 GTCTGTATTGGTGAAGCGTCTTTT 59.787 41.667 0.31 0.00 0.00 2.27
545 2937 3.244078 TGTCTGTATTGGTGAAGCGTCTT 60.244 43.478 0.31 0.00 0.00 3.01
548 2940 2.831685 TGTCTGTATTGGTGAAGCGT 57.168 45.000 0.00 0.00 0.00 5.07
558 2950 1.133976 GGGCAGCTCCATGTCTGTATT 60.134 52.381 0.00 0.00 36.21 1.89
562 2954 2.124403 GGGGCAGCTCCATGTCTG 60.124 66.667 6.37 0.00 36.21 3.51
583 2975 3.873812 ATAAAGGAGCCCGGGCCG 61.874 66.667 41.72 21.46 43.17 6.13
601 2993 0.671251 TGAAACGAACCCAACCATGC 59.329 50.000 0.00 0.00 0.00 4.06
603 2995 5.074115 TCTAATTGAAACGAACCCAACCAT 58.926 37.500 0.00 0.00 0.00 3.55
645 3037 1.204941 AGTGAGAAGCATCCCACGTAC 59.795 52.381 0.00 0.00 34.93 3.67
647 3039 0.247736 GAGTGAGAAGCATCCCACGT 59.752 55.000 0.00 0.00 34.93 4.49
648 3040 0.247460 TGAGTGAGAAGCATCCCACG 59.753 55.000 0.00 0.00 34.93 4.94
649 3041 1.002430 TGTGAGTGAGAAGCATCCCAC 59.998 52.381 0.00 0.00 0.00 4.61
720 3221 1.269257 GGCAAATAATTGAGCGCCCTC 60.269 52.381 2.29 0.00 38.94 4.30
723 3224 1.269257 GGAGGCAAATAATTGAGCGCC 60.269 52.381 2.29 0.00 38.94 6.53
726 3227 2.692041 AGCTGGAGGCAAATAATTGAGC 59.308 45.455 0.00 0.00 44.79 4.26
751 3252 1.173043 TTTGTGAAGCCGGCCATAAG 58.827 50.000 26.15 0.00 0.00 1.73
783 3284 2.420967 GGAGAGAGACGAGCTAGTCCTT 60.421 54.545 21.62 11.32 41.83 3.36
841 3342 9.930693 GAGGATTGAAATCTCTAACCGTATATT 57.069 33.333 3.21 0.00 35.73 1.28
842 3343 9.315363 AGAGGATTGAAATCTCTAACCGTATAT 57.685 33.333 3.21 0.00 35.73 0.86
857 3358 6.069440 AGAGAGAGAGAGAGAGAGGATTGAAA 60.069 42.308 0.00 0.00 0.00 2.69
858 3359 5.429762 AGAGAGAGAGAGAGAGAGGATTGAA 59.570 44.000 0.00 0.00 0.00 2.69
859 3360 4.971282 AGAGAGAGAGAGAGAGAGGATTGA 59.029 45.833 0.00 0.00 0.00 2.57
860 3361 5.071519 AGAGAGAGAGAGAGAGAGAGGATTG 59.928 48.000 0.00 0.00 0.00 2.67
861 3362 5.222870 AGAGAGAGAGAGAGAGAGAGGATT 58.777 45.833 0.00 0.00 0.00 3.01
863 3364 4.078922 AGAGAGAGAGAGAGAGAGAGAGGA 60.079 50.000 0.00 0.00 0.00 3.71
1001 3542 3.218470 GCAGCTGGCACACACCAA 61.218 61.111 17.12 0.00 43.97 3.67
1017 3598 0.606401 TCACTAGGCAAGCACCAAGC 60.606 55.000 0.00 0.00 46.19 4.01
1045 3629 1.732917 CCGCTGAGGTTTGTTTGCA 59.267 52.632 0.00 0.00 34.51 4.08
1081 3665 1.523258 CTCGCTCATGGGCTTCTGG 60.523 63.158 17.16 0.00 0.00 3.86
1241 3849 4.081420 GGAAAACAGACAGAGCTAGATGGA 60.081 45.833 0.00 0.00 0.00 3.41
1247 3855 2.289694 GCAGGGAAAACAGACAGAGCTA 60.290 50.000 0.00 0.00 0.00 3.32
1248 3856 1.544314 GCAGGGAAAACAGACAGAGCT 60.544 52.381 0.00 0.00 0.00 4.09
1249 3857 0.877743 GCAGGGAAAACAGACAGAGC 59.122 55.000 0.00 0.00 0.00 4.09
1250 3858 2.260844 TGCAGGGAAAACAGACAGAG 57.739 50.000 0.00 0.00 0.00 3.35
1253 3861 0.961019 GCATGCAGGGAAAACAGACA 59.039 50.000 14.21 0.00 0.00 3.41
1256 3864 3.131577 ACATATGCATGCAGGGAAAACAG 59.868 43.478 26.69 9.99 35.39 3.16
1274 3893 5.386060 AGACCGGATAGAAGATGTGACATA 58.614 41.667 9.46 0.00 0.00 2.29
1294 3913 1.064654 GCAATGAATTCAGCGGGAGAC 59.935 52.381 14.54 0.00 0.00 3.36
1383 4070 2.613595 TGCACAACTTTACTGTCTGCTG 59.386 45.455 0.00 0.00 0.00 4.41
1386 4073 3.248602 GTCCTGCACAACTTTACTGTCTG 59.751 47.826 0.00 0.00 0.00 3.51
1387 4074 3.118408 TGTCCTGCACAACTTTACTGTCT 60.118 43.478 0.00 0.00 29.30 3.41
1388 4075 3.202906 TGTCCTGCACAACTTTACTGTC 58.797 45.455 0.00 0.00 29.30 3.51
1389 4076 3.275617 TGTCCTGCACAACTTTACTGT 57.724 42.857 0.00 0.00 29.30 3.55
1390 4077 3.627577 ACTTGTCCTGCACAACTTTACTG 59.372 43.478 0.00 0.00 40.29 2.74
1391 4078 3.886123 ACTTGTCCTGCACAACTTTACT 58.114 40.909 0.00 0.00 40.29 2.24
1392 4079 4.213482 CCTACTTGTCCTGCACAACTTTAC 59.787 45.833 0.00 0.00 40.29 2.01
1393 4080 4.101898 TCCTACTTGTCCTGCACAACTTTA 59.898 41.667 0.00 0.00 40.29 1.85
1394 4081 3.118038 TCCTACTTGTCCTGCACAACTTT 60.118 43.478 0.00 0.00 40.29 2.66
1395 4082 2.438021 TCCTACTTGTCCTGCACAACTT 59.562 45.455 0.00 0.00 40.29 2.66
1396 4083 2.047061 TCCTACTTGTCCTGCACAACT 58.953 47.619 0.00 0.00 40.29 3.16
1397 4084 2.543777 TCCTACTTGTCCTGCACAAC 57.456 50.000 0.00 0.00 40.29 3.32
1398 4085 2.805295 CGTTCCTACTTGTCCTGCACAA 60.805 50.000 0.00 0.00 43.12 3.33
1399 4086 1.270094 CGTTCCTACTTGTCCTGCACA 60.270 52.381 0.00 0.00 0.00 4.57
1416 4103 5.253330 ACTGAATTATTGTCACCATCCGTT 58.747 37.500 0.00 0.00 0.00 4.44
1492 4211 6.291112 GCAACGCAAAGAGAAAGAAGTTAAAC 60.291 38.462 0.00 0.00 0.00 2.01
1493 4212 5.741982 GCAACGCAAAGAGAAAGAAGTTAAA 59.258 36.000 0.00 0.00 0.00 1.52
1496 4221 3.378427 AGCAACGCAAAGAGAAAGAAGTT 59.622 39.130 0.00 0.00 0.00 2.66
1556 4281 3.151710 CACATGGCCTGGCATGGG 61.152 66.667 29.74 25.19 33.41 4.00
1557 4282 2.363276 ACACATGGCCTGGCATGG 60.363 61.111 29.74 22.17 33.41 3.66
1558 4283 1.980232 ACACACATGGCCTGGCATG 60.980 57.895 26.40 26.40 35.13 4.06
1559 4284 1.980232 CACACACATGGCCTGGCAT 60.980 57.895 22.05 7.62 0.00 4.40
1560 4285 2.598099 CACACACATGGCCTGGCA 60.598 61.111 22.05 5.12 0.00 4.92
1561 4286 2.598394 ACACACACATGGCCTGGC 60.598 61.111 11.05 11.05 0.00 4.85
1671 4439 4.777366 AGGGGCTACAGTATTTTGCATTTT 59.223 37.500 0.00 0.00 0.00 1.82
1721 4492 7.321745 TGGATTTTGGTTGCGTTTTTAAATT 57.678 28.000 0.00 0.00 0.00 1.82
1794 4565 7.639850 ACGTAAAGCGATGTATTGATGATTTTG 59.360 33.333 0.00 0.00 44.77 2.44
1943 4761 4.166725 ACATCCCACATACAGATCATTGGT 59.833 41.667 0.00 0.00 0.00 3.67
1949 4767 6.115446 TCTGAAAACATCCCACATACAGATC 58.885 40.000 0.00 0.00 0.00 2.75
1952 4770 5.248640 ACTCTGAAAACATCCCACATACAG 58.751 41.667 0.00 0.00 0.00 2.74
2001 4823 4.207165 GAGCCCAGTGCCTTTGAAATATA 58.793 43.478 0.00 0.00 42.71 0.86
2008 4830 1.304713 ATGGAGCCCAGTGCCTTTG 60.305 57.895 0.41 0.00 42.71 2.77
2054 4878 7.148120 TGTCGTAGGAGAGTAGTATTTTGGAAG 60.148 40.741 0.00 0.00 0.00 3.46
2129 5380 4.978083 ATGTGCAATTTGCCAAAACAAA 57.022 31.818 18.27 0.00 44.23 2.83
2132 5383 4.918037 TGAAATGTGCAATTTGCCAAAAC 58.082 34.783 18.27 10.27 44.23 2.43
2217 5475 0.037734 AATCACCACCCCGGAAGAAC 59.962 55.000 0.73 0.00 38.63 3.01
2268 5526 5.104735 ACTGATACAATCCCTTTCTGAGTCC 60.105 44.000 0.00 0.00 0.00 3.85
2554 5816 9.029243 CAAGTTGCATCAAGTTACAAACAAATA 57.971 29.630 0.00 0.00 35.17 1.40
2598 5860 4.393834 GAAGAAGAAGAAGAAGCCCTGTT 58.606 43.478 0.00 0.00 0.00 3.16
2603 5865 4.222810 AGAGAGGAAGAAGAAGAAGAAGCC 59.777 45.833 0.00 0.00 0.00 4.35
2606 5868 6.553100 AGTTGAGAGAGGAAGAAGAAGAAGAA 59.447 38.462 0.00 0.00 0.00 2.52
2612 5874 7.410174 AGAGATAGTTGAGAGAGGAAGAAGAA 58.590 38.462 0.00 0.00 0.00 2.52
2613 5875 6.969043 AGAGATAGTTGAGAGAGGAAGAAGA 58.031 40.000 0.00 0.00 0.00 2.87
2614 5876 7.122650 ACAAGAGATAGTTGAGAGAGGAAGAAG 59.877 40.741 0.00 0.00 0.00 2.85
2679 6040 2.622942 GTTTGTGATCTTCCTTGGTGCA 59.377 45.455 0.00 0.00 0.00 4.57
2708 6069 1.751351 GCCAAGGAAGGTGCCTTATTC 59.249 52.381 3.11 0.00 46.29 1.75
2764 6134 5.906073 ACTTTGAGTCAATGAAAAAGTGGG 58.094 37.500 21.87 0.00 39.08 4.61
2793 6168 3.844211 AGGCAAACCTCCTCTGTGTATAA 59.156 43.478 0.00 0.00 46.34 0.98
2909 6284 1.067582 GCTGCTTAGCCGGTCGTAT 59.932 57.895 1.90 0.00 0.00 3.06
2975 6350 5.012975 AGGTAATTCAACAAACCCATGCAAT 59.987 36.000 0.00 0.00 32.10 3.56
2977 6352 3.900601 AGGTAATTCAACAAACCCATGCA 59.099 39.130 0.00 0.00 32.10 3.96
2979 6354 5.478679 TGGTAGGTAATTCAACAAACCCATG 59.521 40.000 0.00 0.00 32.10 3.66
3044 8154 7.523293 ACAGACAATCCATTTCATTGTTACA 57.477 32.000 0.00 0.00 43.16 2.41
3135 8245 1.337703 GGCATGTGGTATACCGTCGTA 59.662 52.381 17.13 2.03 39.43 3.43
3341 8451 0.955428 TTTGGATGAGCTGCACGTCC 60.955 55.000 25.51 25.51 42.02 4.79
3639 8749 2.517875 GCGCATGAGAGGCCCATT 60.518 61.111 0.30 0.00 0.00 3.16
3732 8842 4.680237 CGGGTGGCAGCAACGAGA 62.680 66.667 19.48 0.00 0.00 4.04
3759 8871 3.123620 CCACGAGCTTGCAGGAGC 61.124 66.667 0.00 0.00 43.02 4.70
4356 9468 4.814294 GCACCGAACGCCTCCGAT 62.814 66.667 0.00 0.00 38.29 4.18
4772 9899 4.872691 CCTAACGATCTATGATTGCATCCC 59.127 45.833 0.00 0.00 35.94 3.85
4781 9908 8.582437 CCTTACCATTAACCTAACGATCTATGA 58.418 37.037 0.00 0.00 0.00 2.15
4820 9947 9.626045 GAAAGATCGATCATACACACACATATA 57.374 33.333 26.47 0.00 0.00 0.86
4821 9948 8.143835 TGAAAGATCGATCATACACACACATAT 58.856 33.333 26.47 0.00 0.00 1.78
4822 9949 7.488322 TGAAAGATCGATCATACACACACATA 58.512 34.615 26.47 0.00 0.00 2.29
4823 9950 6.340522 TGAAAGATCGATCATACACACACAT 58.659 36.000 26.47 0.00 0.00 3.21
4824 9951 5.719173 TGAAAGATCGATCATACACACACA 58.281 37.500 26.47 10.28 0.00 3.72
4825 9952 6.074088 GGATGAAAGATCGATCATACACACAC 60.074 42.308 26.47 14.46 36.96 3.82
4826 9953 5.985530 GGATGAAAGATCGATCATACACACA 59.014 40.000 26.47 15.39 36.96 3.72
4827 9954 6.219473 AGGATGAAAGATCGATCATACACAC 58.781 40.000 26.47 16.49 39.02 3.82
4843 9970 7.973048 ACTACTAATCACCACTAGGATGAAA 57.027 36.000 0.00 0.00 38.69 2.69
4846 9973 9.001542 GTAGTACTACTAATCACCACTAGGATG 57.998 40.741 23.17 0.00 33.65 3.51
4856 9983 7.744733 ACCCTCCTAGTAGTACTACTAATCAC 58.255 42.308 32.34 11.90 45.03 3.06
4858 9985 7.665145 CCAACCCTCCTAGTAGTACTACTAATC 59.335 44.444 32.34 10.89 45.03 1.75
4859 9986 7.422325 CCCAACCCTCCTAGTAGTACTACTAAT 60.422 44.444 32.34 17.81 45.03 1.73
4860 9987 6.126361 CCCAACCCTCCTAGTAGTACTACTAA 60.126 46.154 32.34 22.32 45.03 2.24
4861 9988 5.370880 CCCAACCCTCCTAGTAGTACTACTA 59.629 48.000 31.39 31.39 43.98 1.82
4863 9990 4.468713 CCCAACCCTCCTAGTAGTACTAC 58.531 52.174 23.03 23.03 36.35 2.73
4864 9991 3.117360 GCCCAACCCTCCTAGTAGTACTA 60.117 52.174 9.66 9.66 0.00 1.82
4865 9992 2.359037 GCCCAACCCTCCTAGTAGTACT 60.359 54.545 8.14 8.14 0.00 2.73
4866 9993 2.037901 GCCCAACCCTCCTAGTAGTAC 58.962 57.143 0.00 0.00 0.00 2.73
4867 9994 1.410648 CGCCCAACCCTCCTAGTAGTA 60.411 57.143 0.00 0.00 0.00 1.82
4868 9995 0.686769 CGCCCAACCCTCCTAGTAGT 60.687 60.000 0.00 0.00 0.00 2.73
4869 9996 0.686769 ACGCCCAACCCTCCTAGTAG 60.687 60.000 0.00 0.00 0.00 2.57
4870 9997 0.974010 CACGCCCAACCCTCCTAGTA 60.974 60.000 0.00 0.00 0.00 1.82
4871 9998 2.122056 ACGCCCAACCCTCCTAGT 59.878 61.111 0.00 0.00 0.00 2.57
4872 9999 2.584608 CACGCCCAACCCTCCTAG 59.415 66.667 0.00 0.00 0.00 3.02
4873 10000 3.712907 GCACGCCCAACCCTCCTA 61.713 66.667 0.00 0.00 0.00 2.94
4875 10002 4.660938 AAGCACGCCCAACCCTCC 62.661 66.667 0.00 0.00 0.00 4.30
4876 10003 2.597510 AAAGCACGCCCAACCCTC 60.598 61.111 0.00 0.00 0.00 4.30
4877 10004 2.912025 CAAAGCACGCCCAACCCT 60.912 61.111 0.00 0.00 0.00 4.34
4878 10005 4.662961 GCAAAGCACGCCCAACCC 62.663 66.667 0.00 0.00 0.00 4.11
4879 10006 3.605664 AGCAAAGCACGCCCAACC 61.606 61.111 0.00 0.00 0.00 3.77
4897 10024 4.659874 CAACGACACCAACGGCGC 62.660 66.667 6.90 0.00 34.93 6.53
4901 10028 0.452585 AAAACCCAACGACACCAACG 59.547 50.000 0.00 0.00 0.00 4.10
4902 10029 2.658373 AAAAACCCAACGACACCAAC 57.342 45.000 0.00 0.00 0.00 3.77
4903 10030 5.127356 AGAAATAAAAACCCAACGACACCAA 59.873 36.000 0.00 0.00 0.00 3.67
4957 10087 8.938906 GTTCATCATTTCTAAAAACCAATGCAT 58.061 29.630 0.00 0.00 0.00 3.96
4958 10088 7.930325 TGTTCATCATTTCTAAAAACCAATGCA 59.070 29.630 0.00 0.00 0.00 3.96
4959 10089 8.309163 TGTTCATCATTTCTAAAAACCAATGC 57.691 30.769 0.00 0.00 0.00 3.56
4971 10101 9.415544 GCAACTTAAAAGATGTTCATCATTTCT 57.584 29.630 15.80 1.43 36.83 2.52
4972 10102 8.650714 GGCAACTTAAAAGATGTTCATCATTTC 58.349 33.333 15.80 4.93 36.83 2.17
4979 10109 7.768120 ACAAATTGGCAACTTAAAAGATGTTCA 59.232 29.630 0.00 0.00 32.10 3.18
4980 10110 8.141835 ACAAATTGGCAACTTAAAAGATGTTC 57.858 30.769 0.00 0.00 32.10 3.18
5057 10207 7.798486 ATCGAGCGCAATACTAAATAAGTAG 57.202 36.000 11.47 0.00 43.90 2.57
5076 10226 9.099454 ACCAAGTTTAGAGCTAAAAATATCGAG 57.901 33.333 4.39 0.00 36.86 4.04
5094 10245 8.608317 CAAATTCCGTTAATTTTGACCAAGTTT 58.392 29.630 3.65 0.00 43.75 2.66
5095 10246 7.982354 TCAAATTCCGTTAATTTTGACCAAGTT 59.018 29.630 3.65 0.00 43.75 2.66
5161 10312 1.046204 TGCATGCATGGTTGGTTTCA 58.954 45.000 27.34 11.60 0.00 2.69
5163 10314 3.977134 TTATGCATGCATGGTTGGTTT 57.023 38.095 37.43 15.82 37.82 3.27
5174 10325 1.655484 GCCCCAACTTTTATGCATGC 58.345 50.000 11.82 11.82 0.00 4.06
5191 10342 9.216117 AGAAAATAATACAGATATGTAACGGCC 57.784 33.333 3.97 0.00 0.00 6.13
5206 10357 7.491696 AGGTGCGTGTCTCTAAGAAAATAATAC 59.508 37.037 0.00 0.00 0.00 1.89
5208 10359 6.407202 AGGTGCGTGTCTCTAAGAAAATAAT 58.593 36.000 0.00 0.00 0.00 1.28
5211 10362 4.246458 GAGGTGCGTGTCTCTAAGAAAAT 58.754 43.478 0.00 0.00 0.00 1.82
5215 10366 1.905637 TGAGGTGCGTGTCTCTAAGA 58.094 50.000 0.00 0.00 0.00 2.10
5216 10367 2.949451 ATGAGGTGCGTGTCTCTAAG 57.051 50.000 0.00 0.00 0.00 2.18
5217 10368 3.353557 ACTATGAGGTGCGTGTCTCTAA 58.646 45.455 0.00 0.00 0.00 2.10
5218 10369 2.943690 GACTATGAGGTGCGTGTCTCTA 59.056 50.000 0.00 0.00 0.00 2.43
5220 10371 1.532090 CGACTATGAGGTGCGTGTCTC 60.532 57.143 0.00 0.00 0.00 3.36
5222 10373 0.450583 TCGACTATGAGGTGCGTGTC 59.549 55.000 0.00 0.00 0.00 3.67
5324 10483 0.759812 TGGTCGAACCTACCCACACA 60.760 55.000 0.00 0.00 39.58 3.72
5326 10485 2.051941 GTGGTCGAACCTACCCACA 58.948 57.895 13.99 0.00 45.34 4.17
5331 10490 3.460103 TGTTTCTTGTGGTCGAACCTAC 58.540 45.455 0.00 0.00 39.58 3.18
5365 10528 0.584396 CAAGCAACCGCGAACTTACA 59.416 50.000 8.23 0.00 45.49 2.41
5366 10529 0.584876 ACAAGCAACCGCGAACTTAC 59.415 50.000 8.23 0.00 45.49 2.34
5374 10537 8.504005 ACTTCATTAATATATACAAGCAACCGC 58.496 33.333 0.00 0.00 38.99 5.68
5397 10560 8.997323 GTATGTATGGTAGTACGATAGACACTT 58.003 37.037 5.35 0.00 36.56 3.16
5398 10561 8.152898 TGTATGTATGGTAGTACGATAGACACT 58.847 37.037 10.71 0.00 38.22 3.55
5399 10562 8.315391 TGTATGTATGGTAGTACGATAGACAC 57.685 38.462 5.35 4.91 41.38 3.67
5400 10563 8.943002 CATGTATGTATGGTAGTACGATAGACA 58.057 37.037 5.35 9.92 41.38 3.41
5491 10654 1.399343 GGCGCTTTTGTTAAGACGGAC 60.399 52.381 7.64 0.00 0.00 4.79
5494 10657 1.263217 AGTGGCGCTTTTGTTAAGACG 59.737 47.619 7.64 0.00 0.00 4.18
5499 10662 5.440234 TTAAATCAGTGGCGCTTTTGTTA 57.560 34.783 7.64 0.00 0.00 2.41
5507 10670 6.751888 AGAATTTTGTATTAAATCAGTGGCGC 59.248 34.615 0.00 0.00 0.00 6.53
5508 10671 9.221775 GTAGAATTTTGTATTAAATCAGTGGCG 57.778 33.333 0.00 0.00 0.00 5.69
5568 10731 0.104934 ACCAACCACTCCCTCTGTCT 60.105 55.000 0.00 0.00 0.00 3.41
5572 10735 1.143073 GTTTGACCAACCACTCCCTCT 59.857 52.381 0.00 0.00 0.00 3.69
5576 10739 4.400529 AAAATGTTTGACCAACCACTCC 57.599 40.909 0.00 0.00 33.97 3.85
5581 10744 6.969828 TGTTGTAAAAATGTTTGACCAACC 57.030 33.333 13.43 0.00 34.08 3.77
5615 10778 9.855021 GCTGAAATTAAAACTAGCCAAAATAGA 57.145 29.630 0.00 0.00 0.00 1.98
5616 10779 9.860898 AGCTGAAATTAAAACTAGCCAAAATAG 57.139 29.630 0.00 0.00 31.82 1.73
5623 10786 5.897377 TCCAGCTGAAATTAAAACTAGCC 57.103 39.130 17.39 0.00 31.82 3.93
5669 10832 9.503427 GCATTATATGTTCAAAAGTGTTAGGAC 57.497 33.333 0.00 0.00 0.00 3.85
5708 10871 9.263538 TCGATTGGGTATTTGTTGTATACATAC 57.736 33.333 6.36 5.77 36.44 2.39
5803 10966 9.546428 CATATATAGAAGGTGTGTTGTGATGAA 57.454 33.333 0.00 0.00 0.00 2.57
5815 10978 8.178313 TGGTACAGACACATATATAGAAGGTG 57.822 38.462 0.00 2.18 35.66 4.00


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

AutoCloner maintained by Alex Coulton.