Multiple sequence alignment - TraesCS5B01G358800

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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 TraesCS5B01G358800 chr5B 100.000 3510 0 0 1 3510 538716395 538719904 0.000000e+00 6482
1 TraesCS5B01G358800 chr5D 91.040 1462 70 23 802 2259 442496505 442497909 0.000000e+00 1917
2 TraesCS5B01G358800 chr5D 84.791 1006 72 31 2334 3303 442498002 442498962 0.000000e+00 935
3 TraesCS5B01G358800 chr5D 88.116 345 8 11 437 772 442496114 442496434 2.560000e-101 379
4 TraesCS5B01G358800 chr5D 84.980 253 8 10 165 408 442495885 442496116 2.730000e-56 230
5 TraesCS5B01G358800 chr5D 91.176 170 8 2 1 163 556017281 556017112 1.270000e-54 224
6 TraesCS5B01G358800 chr5A 93.299 1149 44 18 1118 2253 558683164 558684292 0.000000e+00 1664
7 TraesCS5B01G358800 chr5A 85.859 990 65 16 2564 3510 558684765 558685722 0.000000e+00 983
8 TraesCS5B01G358800 chr5A 93.392 227 9 2 2316 2536 558684372 558684598 7.260000e-87 331
9 TraesCS5B01G358800 chr5A 89.697 165 10 5 148 308 558682208 558682369 1.650000e-48 204
10 TraesCS5B01G358800 chr5A 80.588 170 10 11 348 505 558682382 558682540 3.700000e-20 110
11 TraesCS5B01G358800 chr7B 99.329 149 1 0 1 149 439251857 439251709 1.610000e-68 270
12 TraesCS5B01G358800 chr7B 98.658 149 2 0 1 149 499869873 499870021 7.470000e-67 265
13 TraesCS5B01G358800 chr3A 98.000 150 3 0 1 150 650049950 650049801 9.660000e-66 261
14 TraesCS5B01G358800 chr2A 97.987 149 3 0 1 149 46845361 46845509 3.480000e-65 259
15 TraesCS5B01G358800 chr6D 92.308 156 6 1 1 150 333346139 333345984 2.120000e-52 217
16 TraesCS5B01G358800 chr4D 91.667 156 6 4 1 149 276140728 276140883 3.550000e-50 209
17 TraesCS5B01G358800 chr4D 90.968 155 8 1 1 149 65848448 65848602 1.650000e-48 204
18 TraesCS5B01G358800 chr3D 88.710 124 8 1 1 118 388819172 388819295 2.820000e-31 147


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 TraesCS5B01G358800 chr5B 538716395 538719904 3509 False 6482.00 6482 100.00000 1 3510 1 chr5B.!!$F1 3509
1 TraesCS5B01G358800 chr5D 442495885 442498962 3077 False 865.25 1917 87.23175 165 3303 4 chr5D.!!$F1 3138
2 TraesCS5B01G358800 chr5A 558682208 558685722 3514 False 658.40 1664 88.56700 148 3510 5 chr5A.!!$F1 3362

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
409 426 0.107456 GCATCCATGATCCACGTCCT 59.893 55.0 0.0 0.0 0.00 3.85 F
1472 1612 0.103026 CGACATGCTGCCACTAGCTA 59.897 55.0 0.0 0.0 44.01 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2259 2411 0.315886 TGTCATGCGTAAGTGTCCGT 59.684 50.0 0.00 0.0 41.68 4.69 R
2734 3086 0.615850 GCCTGCAGATAGATACCCCC 59.384 60.0 17.39 0.0 0.00 5.40 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
23 24 5.671493 AGCATAGTTAATTAGTTCAGGCGT 58.329 37.500 0.00 0.00 0.00 5.68
24 25 5.523916 AGCATAGTTAATTAGTTCAGGCGTG 59.476 40.000 0.00 0.00 0.00 5.34
25 26 5.293569 GCATAGTTAATTAGTTCAGGCGTGT 59.706 40.000 6.26 0.00 0.00 4.49
26 27 6.705782 CATAGTTAATTAGTTCAGGCGTGTG 58.294 40.000 6.26 0.00 0.00 3.82
27 28 4.638304 AGTTAATTAGTTCAGGCGTGTGT 58.362 39.130 6.26 0.00 0.00 3.72
28 29 5.786311 AGTTAATTAGTTCAGGCGTGTGTA 58.214 37.500 6.26 0.00 0.00 2.90
29 30 5.636543 AGTTAATTAGTTCAGGCGTGTGTAC 59.363 40.000 6.26 3.96 0.00 2.90
30 31 3.671008 ATTAGTTCAGGCGTGTGTACA 57.329 42.857 6.26 0.00 0.00 2.90
31 32 3.671008 TTAGTTCAGGCGTGTGTACAT 57.329 42.857 6.26 0.00 0.00 2.29
32 33 2.080286 AGTTCAGGCGTGTGTACATC 57.920 50.000 6.26 0.00 0.00 3.06
33 34 1.618837 AGTTCAGGCGTGTGTACATCT 59.381 47.619 6.26 0.00 0.00 2.90
34 35 2.823747 AGTTCAGGCGTGTGTACATCTA 59.176 45.455 6.26 0.00 0.00 1.98
35 36 3.257375 AGTTCAGGCGTGTGTACATCTAA 59.743 43.478 6.26 0.00 0.00 2.10
36 37 3.226346 TCAGGCGTGTGTACATCTAAC 57.774 47.619 6.26 0.00 0.00 2.34
37 38 2.559231 TCAGGCGTGTGTACATCTAACA 59.441 45.455 6.26 0.00 0.00 2.41
38 39 2.923655 CAGGCGTGTGTACATCTAACAG 59.076 50.000 0.00 0.00 0.00 3.16
39 40 2.561419 AGGCGTGTGTACATCTAACAGT 59.439 45.455 0.00 0.00 0.00 3.55
40 41 3.006537 AGGCGTGTGTACATCTAACAGTT 59.993 43.478 0.00 0.00 0.00 3.16
41 42 3.122948 GGCGTGTGTACATCTAACAGTTG 59.877 47.826 0.00 0.00 0.00 3.16
42 43 3.122948 GCGTGTGTACATCTAACAGTTGG 59.877 47.826 0.00 0.00 0.00 3.77
43 44 3.122948 CGTGTGTACATCTAACAGTTGGC 59.877 47.826 0.00 0.00 0.00 4.52
44 45 4.315803 GTGTGTACATCTAACAGTTGGCT 58.684 43.478 0.00 0.00 0.00 4.75
46 47 4.039852 TGTGTACATCTAACAGTTGGCTGA 59.960 41.667 7.43 0.00 45.28 4.26
47 48 4.627467 GTGTACATCTAACAGTTGGCTGAG 59.373 45.833 7.43 0.00 45.28 3.35
48 49 2.704572 ACATCTAACAGTTGGCTGAGC 58.295 47.619 7.43 0.00 45.28 4.26
49 50 2.304180 ACATCTAACAGTTGGCTGAGCT 59.696 45.455 3.72 0.00 45.28 4.09
50 51 2.462456 TCTAACAGTTGGCTGAGCTG 57.538 50.000 3.72 0.00 45.28 4.24
51 52 1.970640 TCTAACAGTTGGCTGAGCTGA 59.029 47.619 3.72 0.00 45.28 4.26
52 53 2.568956 TCTAACAGTTGGCTGAGCTGAT 59.431 45.455 3.72 0.00 45.28 2.90
53 54 2.283145 AACAGTTGGCTGAGCTGATT 57.717 45.000 3.72 0.00 45.28 2.57
54 55 3.423539 AACAGTTGGCTGAGCTGATTA 57.576 42.857 3.72 0.00 45.28 1.75
55 56 2.983229 ACAGTTGGCTGAGCTGATTAG 58.017 47.619 3.72 0.00 45.28 1.73
56 57 2.304180 ACAGTTGGCTGAGCTGATTAGT 59.696 45.455 3.72 0.00 45.28 2.24
57 58 3.244700 ACAGTTGGCTGAGCTGATTAGTT 60.245 43.478 3.72 0.00 45.28 2.24
58 59 3.126514 CAGTTGGCTGAGCTGATTAGTTG 59.873 47.826 3.72 0.00 45.28 3.16
59 60 3.077359 GTTGGCTGAGCTGATTAGTTGT 58.923 45.455 3.72 0.00 0.00 3.32
60 61 3.423539 TGGCTGAGCTGATTAGTTGTT 57.576 42.857 3.72 0.00 0.00 2.83
61 62 4.551702 TGGCTGAGCTGATTAGTTGTTA 57.448 40.909 3.72 0.00 0.00 2.41
62 63 4.253685 TGGCTGAGCTGATTAGTTGTTAC 58.746 43.478 3.72 0.00 0.00 2.50
63 64 4.020218 TGGCTGAGCTGATTAGTTGTTACT 60.020 41.667 3.72 0.00 38.44 2.24
64 65 5.186992 TGGCTGAGCTGATTAGTTGTTACTA 59.813 40.000 3.72 0.00 35.78 1.82
66 67 6.594159 GGCTGAGCTGATTAGTTGTTACTAAA 59.406 38.462 3.72 0.00 46.80 1.85
67 68 7.281100 GGCTGAGCTGATTAGTTGTTACTAAAT 59.719 37.037 3.72 0.00 46.80 1.40
68 69 8.669243 GCTGAGCTGATTAGTTGTTACTAAATT 58.331 33.333 0.00 0.00 46.80 1.82
86 87 7.086376 ACTAAATTTCATATCAATGCATCCGC 58.914 34.615 0.00 0.00 39.24 5.54
87 88 3.541071 TTTCATATCAATGCATCCGCG 57.459 42.857 0.00 0.00 42.97 6.46
88 89 2.453983 TCATATCAATGCATCCGCGA 57.546 45.000 8.23 0.00 42.97 5.87
89 90 2.340337 TCATATCAATGCATCCGCGAG 58.660 47.619 8.23 0.00 42.97 5.03
90 91 1.081892 ATATCAATGCATCCGCGAGC 58.918 50.000 8.23 9.70 42.97 5.03
91 92 1.284297 TATCAATGCATCCGCGAGCG 61.284 55.000 8.23 10.86 42.97 5.03
92 93 3.566853 CAATGCATCCGCGAGCGT 61.567 61.111 8.23 7.43 42.97 5.07
93 94 3.264897 AATGCATCCGCGAGCGTC 61.265 61.111 8.23 3.46 42.97 5.19
97 98 3.315521 CATCCGCGAGCGTCGAAG 61.316 66.667 8.23 0.00 43.74 3.79
98 99 3.506096 ATCCGCGAGCGTCGAAGA 61.506 61.111 8.23 6.30 43.74 2.87
99 100 3.047718 ATCCGCGAGCGTCGAAGAA 62.048 57.895 8.23 0.00 43.74 2.52
100 101 2.921538 ATCCGCGAGCGTCGAAGAAG 62.922 60.000 8.23 0.00 43.74 2.85
101 102 3.241059 CGCGAGCGTCGAAGAAGG 61.241 66.667 0.00 0.00 43.74 3.46
102 103 3.546397 GCGAGCGTCGAAGAAGGC 61.546 66.667 1.37 0.00 43.74 4.35
103 104 2.126463 CGAGCGTCGAAGAAGGCA 60.126 61.111 1.37 0.00 43.74 4.75
104 105 2.437343 CGAGCGTCGAAGAAGGCAC 61.437 63.158 1.37 0.00 43.74 5.01
105 106 2.430921 AGCGTCGAAGAAGGCACG 60.431 61.111 1.37 0.00 40.15 5.34
106 107 3.479269 GCGTCGAAGAAGGCACGG 61.479 66.667 1.37 0.00 39.69 4.94
107 108 3.479269 CGTCGAAGAAGGCACGGC 61.479 66.667 0.00 0.00 39.69 5.68
108 109 2.357034 GTCGAAGAAGGCACGGCA 60.357 61.111 0.00 0.00 39.69 5.69
109 110 2.048222 TCGAAGAAGGCACGGCAG 60.048 61.111 0.00 0.00 0.00 4.85
110 111 2.048222 CGAAGAAGGCACGGCAGA 60.048 61.111 0.00 0.00 0.00 4.26
111 112 2.383527 CGAAGAAGGCACGGCAGAC 61.384 63.158 0.00 0.00 0.00 3.51
124 125 3.108289 CAGACGTGCCGTGCTCAG 61.108 66.667 4.94 0.00 41.37 3.35
125 126 4.363990 AGACGTGCCGTGCTCAGG 62.364 66.667 4.94 0.00 41.37 3.86
135 136 3.390521 TGCTCAGGGGCACGGTAG 61.391 66.667 0.00 0.00 37.29 3.18
136 137 3.075005 GCTCAGGGGCACGGTAGA 61.075 66.667 0.00 0.00 0.00 2.59
137 138 3.082579 GCTCAGGGGCACGGTAGAG 62.083 68.421 0.00 0.00 0.00 2.43
138 139 2.363795 TCAGGGGCACGGTAGAGG 60.364 66.667 0.00 0.00 0.00 3.69
139 140 2.363795 CAGGGGCACGGTAGAGGA 60.364 66.667 0.00 0.00 0.00 3.71
140 141 2.042843 AGGGGCACGGTAGAGGAG 60.043 66.667 0.00 0.00 0.00 3.69
141 142 3.851128 GGGGCACGGTAGAGGAGC 61.851 72.222 0.00 0.00 0.00 4.70
142 143 3.851128 GGGCACGGTAGAGGAGCC 61.851 72.222 0.00 0.00 44.48 4.70
286 299 1.534235 AGGTGCTCCTTGTCTCCGT 60.534 57.895 0.18 0.00 42.12 4.69
287 300 1.122019 AGGTGCTCCTTGTCTCCGTT 61.122 55.000 0.18 0.00 42.12 4.44
312 325 2.357517 CCACGTGTCTGTCAGCCC 60.358 66.667 15.65 0.00 0.00 5.19
409 426 0.107456 GCATCCATGATCCACGTCCT 59.893 55.000 0.00 0.00 0.00 3.85
412 429 1.592669 CCATGATCCACGTCCTCGC 60.593 63.158 0.00 0.00 41.18 5.03
428 445 4.697102 GCCTCTGGCTCTACCTCT 57.303 61.111 0.73 0.00 46.69 3.69
429 446 2.123409 GCCTCTGGCTCTACCTCTG 58.877 63.158 0.73 0.00 46.69 3.35
432 449 0.396974 CTCTGGCTCTACCTCTGGCT 60.397 60.000 0.00 0.00 40.22 4.75
433 450 0.396417 TCTGGCTCTACCTCTGGCTC 60.396 60.000 0.00 0.00 40.22 4.70
434 451 0.396974 CTGGCTCTACCTCTGGCTCT 60.397 60.000 0.00 0.00 40.22 4.09
435 452 0.685785 TGGCTCTACCTCTGGCTCTG 60.686 60.000 0.00 0.00 40.22 3.35
613 651 2.698797 GGAGGATTATTCCACTGGTCGA 59.301 50.000 6.44 0.00 45.30 4.20
615 653 4.561105 GAGGATTATTCCACTGGTCGATC 58.439 47.826 6.44 0.00 45.30 3.69
617 655 4.594920 AGGATTATTCCACTGGTCGATCAT 59.405 41.667 0.00 0.00 45.30 2.45
618 656 5.780282 AGGATTATTCCACTGGTCGATCATA 59.220 40.000 0.00 0.00 45.30 2.15
663 712 2.701163 GATCGTGTCGGCCCATCTCC 62.701 65.000 0.00 0.00 0.00 3.71
682 738 2.698763 GCCTGCCTCAAGCTTGCTC 61.699 63.158 21.99 12.62 44.23 4.26
688 744 1.730501 CCTCAAGCTTGCTCGATTGA 58.269 50.000 21.99 0.57 37.01 2.57
690 746 2.681848 CCTCAAGCTTGCTCGATTGATT 59.318 45.455 21.99 0.00 38.46 2.57
691 747 3.487042 CCTCAAGCTTGCTCGATTGATTG 60.487 47.826 21.99 0.00 38.46 2.67
692 748 3.076621 TCAAGCTTGCTCGATTGATTGT 58.923 40.909 21.99 0.00 34.70 2.71
693 749 3.503363 TCAAGCTTGCTCGATTGATTGTT 59.497 39.130 21.99 0.00 34.70 2.83
694 750 4.022935 TCAAGCTTGCTCGATTGATTGTTT 60.023 37.500 21.99 0.00 34.70 2.83
695 751 3.829948 AGCTTGCTCGATTGATTGTTTG 58.170 40.909 0.00 0.00 0.00 2.93
696 752 3.254166 AGCTTGCTCGATTGATTGTTTGT 59.746 39.130 0.00 0.00 0.00 2.83
772 828 2.046285 CCTGGCGTCCAATCCAACC 61.046 63.158 0.35 0.00 30.80 3.77
773 829 2.359354 TGGCGTCCAATCCAACCG 60.359 61.111 0.00 0.00 0.00 4.44
775 831 2.396157 GGCGTCCAATCCAACCGAC 61.396 63.158 0.00 0.00 0.00 4.79
776 832 1.669760 GCGTCCAATCCAACCGACA 60.670 57.895 0.00 0.00 0.00 4.35
780 836 2.474266 CAATCCAACCGACACGCG 59.526 61.111 3.53 3.53 40.47 6.01
814 918 1.959848 GCACTGGAGAAAAGTGGGC 59.040 57.895 5.78 0.00 44.29 5.36
909 1013 0.589708 GACGTTACAAAAAGGCCGCT 59.410 50.000 0.00 0.00 0.00 5.52
921 1025 3.712907 GCCGCTACCCAGGACCAA 61.713 66.667 0.00 0.00 0.00 3.67
930 1034 0.909610 CCCAGGACCAAGGAGTAGCA 60.910 60.000 4.63 0.00 0.00 3.49
964 1068 1.351707 CGCACACAACACAGTGACC 59.648 57.895 7.81 0.00 42.05 4.02
1371 1511 1.019805 GCAAGGAGTACGCCAAGACC 61.020 60.000 18.53 0.00 0.00 3.85
1405 1545 2.755876 AGCTCATGACGCCGGAGA 60.756 61.111 13.83 0.00 0.00 3.71
1407 1547 2.775856 GCTCATGACGCCGGAGAGA 61.776 63.158 13.83 3.27 0.00 3.10
1408 1548 1.064946 CTCATGACGCCGGAGAGAC 59.935 63.158 13.83 3.50 0.00 3.36
1438 1578 2.165167 TCTGGGCGATATACGGTAAGG 58.835 52.381 0.00 0.00 42.83 2.69
1442 1582 0.108472 GCGATATACGGTAAGGCCCC 60.108 60.000 0.00 0.00 42.83 5.80
1443 1583 0.533951 CGATATACGGTAAGGCCCCC 59.466 60.000 0.00 0.00 38.46 5.40
1472 1612 0.103026 CGACATGCTGCCACTAGCTA 59.897 55.000 0.00 0.00 44.01 3.32
1473 1613 1.471501 CGACATGCTGCCACTAGCTAA 60.472 52.381 0.00 0.00 44.01 3.09
1474 1614 1.936547 GACATGCTGCCACTAGCTAAC 59.063 52.381 0.00 0.00 44.01 2.34
1475 1615 1.556911 ACATGCTGCCACTAGCTAACT 59.443 47.619 0.00 0.00 44.01 2.24
1513 1661 2.320587 CGCAACAGCAGGAGGTCAC 61.321 63.158 0.00 0.00 0.00 3.67
1514 1662 1.227943 GCAACAGCAGGAGGTCACA 60.228 57.895 0.00 0.00 0.00 3.58
1541 1689 5.001232 GTGGTTACTAACTTCTTGGATGCA 58.999 41.667 0.00 0.00 0.00 3.96
1543 1691 5.647658 TGGTTACTAACTTCTTGGATGCATG 59.352 40.000 2.46 0.00 0.00 4.06
1674 1826 2.586079 CGGCCCTACGACATGCTG 60.586 66.667 0.00 0.00 35.47 4.41
1992 2144 9.680315 GTGTCAGTTCAGTTGTATATATACCTC 57.320 37.037 18.20 11.72 32.33 3.85
1995 2147 7.447545 TCAGTTCAGTTGTATATATACCTCGCT 59.552 37.037 18.20 9.22 32.33 4.93
2008 2160 2.427506 ACCTCGCTTTCTGAATTCACC 58.572 47.619 3.38 0.00 0.00 4.02
2009 2161 2.039084 ACCTCGCTTTCTGAATTCACCT 59.961 45.455 3.38 0.00 0.00 4.00
2020 2172 1.589716 AATTCACCTGCTCTTGCCGC 61.590 55.000 0.00 0.00 38.71 6.53
2088 2240 3.538614 GGATCTACCTGCCGCAGA 58.461 61.111 22.35 1.90 32.44 4.26
2171 2323 0.465278 GGAGGAGCTTCATGAAGGGC 60.465 60.000 31.41 21.43 38.80 5.19
2259 2411 2.185867 GATGGCCGGTAAGTGCGA 59.814 61.111 1.90 0.00 0.00 5.10
2260 2412 2.125269 ATGGCCGGTAAGTGCGAC 60.125 61.111 1.90 0.00 0.00 5.19
2261 2413 4.728102 TGGCCGGTAAGTGCGACG 62.728 66.667 1.90 0.00 0.00 5.12
2265 2417 2.256158 CGGTAAGTGCGACGGACA 59.744 61.111 21.84 0.00 0.00 4.02
2266 2418 2.084681 CGGTAAGTGCGACGGACAC 61.085 63.158 21.84 11.49 38.35 3.67
2270 2422 4.959446 AGTGCGACGGACACTTAC 57.041 55.556 21.84 0.00 46.01 2.34
2271 2423 1.081641 AGTGCGACGGACACTTACG 60.082 57.895 21.84 0.00 46.01 3.18
2273 2425 2.429571 GCGACGGACACTTACGCA 60.430 61.111 0.00 0.00 46.75 5.24
2274 2426 1.804326 GCGACGGACACTTACGCAT 60.804 57.895 0.00 0.00 46.75 4.73
2275 2427 1.988409 CGACGGACACTTACGCATG 59.012 57.895 0.00 0.00 0.00 4.06
2276 2428 0.455464 CGACGGACACTTACGCATGA 60.455 55.000 0.00 0.00 0.00 3.07
2277 2429 0.989890 GACGGACACTTACGCATGAC 59.010 55.000 0.00 0.00 0.00 3.06
2278 2430 0.315886 ACGGACACTTACGCATGACA 59.684 50.000 0.00 0.00 0.00 3.58
2279 2431 0.713883 CGGACACTTACGCATGACAC 59.286 55.000 0.00 0.00 0.00 3.67
2280 2432 1.668919 CGGACACTTACGCATGACACT 60.669 52.381 0.00 0.00 0.00 3.55
2281 2433 2.413837 GGACACTTACGCATGACACTT 58.586 47.619 0.00 0.00 0.00 3.16
2282 2434 2.806244 GGACACTTACGCATGACACTTT 59.194 45.455 0.00 0.00 0.00 2.66
2283 2435 3.120649 GGACACTTACGCATGACACTTTC 60.121 47.826 0.00 0.00 0.00 2.62
2284 2436 3.728845 ACACTTACGCATGACACTTTCT 58.271 40.909 0.00 0.00 0.00 2.52
2285 2437 4.127171 ACACTTACGCATGACACTTTCTT 58.873 39.130 0.00 0.00 0.00 2.52
2286 2438 4.211374 ACACTTACGCATGACACTTTCTTC 59.789 41.667 0.00 0.00 0.00 2.87
2287 2439 4.449068 CACTTACGCATGACACTTTCTTCT 59.551 41.667 0.00 0.00 0.00 2.85
2288 2440 5.050091 CACTTACGCATGACACTTTCTTCTT 60.050 40.000 0.00 0.00 0.00 2.52
2289 2441 5.177696 ACTTACGCATGACACTTTCTTCTTC 59.822 40.000 0.00 0.00 0.00 2.87
2290 2442 3.466836 ACGCATGACACTTTCTTCTTCA 58.533 40.909 0.00 0.00 0.00 3.02
2291 2443 3.876914 ACGCATGACACTTTCTTCTTCAA 59.123 39.130 0.00 0.00 0.00 2.69
2292 2444 4.516698 ACGCATGACACTTTCTTCTTCAAT 59.483 37.500 0.00 0.00 0.00 2.57
2293 2445 5.084722 CGCATGACACTTTCTTCTTCAATC 58.915 41.667 0.00 0.00 0.00 2.67
2294 2446 5.334337 CGCATGACACTTTCTTCTTCAATCA 60.334 40.000 0.00 0.00 0.00 2.57
2295 2447 5.855395 GCATGACACTTTCTTCTTCAATCAC 59.145 40.000 0.00 0.00 0.00 3.06
2296 2448 6.376978 CATGACACTTTCTTCTTCAATCACC 58.623 40.000 0.00 0.00 0.00 4.02
2297 2449 5.684704 TGACACTTTCTTCTTCAATCACCT 58.315 37.500 0.00 0.00 0.00 4.00
2298 2450 5.760253 TGACACTTTCTTCTTCAATCACCTC 59.240 40.000 0.00 0.00 0.00 3.85
2299 2451 4.752101 ACACTTTCTTCTTCAATCACCTCG 59.248 41.667 0.00 0.00 0.00 4.63
2305 2457 3.401033 TCTTCAATCACCTCGCAGAAA 57.599 42.857 0.00 0.00 34.09 2.52
2368 2578 1.134965 GCATCTCTGCTTCTGTACCGT 60.135 52.381 0.00 0.00 45.32 4.83
2473 2683 1.003580 CTGCCCAAAGCTTACCTCAGA 59.996 52.381 0.00 0.00 44.23 3.27
2485 2695 1.059006 ACCTCAGATCCCTCATGCCC 61.059 60.000 0.00 0.00 0.00 5.36
2499 2712 4.475135 GCCCCCTCCTTCGCAGAC 62.475 72.222 0.00 0.00 34.32 3.51
2516 2729 0.247145 GACGCGCCGTTAATCAGTTG 60.247 55.000 5.73 0.00 41.37 3.16
2524 2737 2.673368 CCGTTAATCAGTTGGCTCTGAC 59.327 50.000 13.22 3.56 45.40 3.51
2538 2751 3.068873 GGCTCTGACCCTCTAGTGTAATG 59.931 52.174 0.00 0.00 0.00 1.90
2539 2752 3.954904 GCTCTGACCCTCTAGTGTAATGA 59.045 47.826 0.00 0.00 0.00 2.57
2541 2754 5.508825 GCTCTGACCCTCTAGTGTAATGATG 60.509 48.000 0.00 0.00 0.00 3.07
2558 2780 2.830321 TGATGACACACAGAGAGCAGAT 59.170 45.455 0.00 0.00 0.00 2.90
2566 2788 3.194542 ACACAGAGAGCAGATCCTTGTAC 59.805 47.826 0.00 0.00 0.00 2.90
2568 2790 4.642437 CACAGAGAGCAGATCCTTGTACTA 59.358 45.833 0.00 0.00 0.00 1.82
2571 2793 4.887071 AGAGAGCAGATCCTTGTACTAGTG 59.113 45.833 5.39 0.00 0.00 2.74
2618 2969 8.035394 CAGATTTAAGCTAGACCTTGTGAGTAA 58.965 37.037 0.00 0.00 0.00 2.24
2619 2970 8.594550 AGATTTAAGCTAGACCTTGTGAGTAAA 58.405 33.333 0.00 0.00 0.00 2.01
2697 3049 6.566197 AATGATCTTGGTGAAAACAGAGAC 57.434 37.500 0.00 0.00 0.00 3.36
2703 3055 6.053005 TCTTGGTGAAAACAGAGACGTATTT 58.947 36.000 0.00 0.00 0.00 1.40
2705 3057 6.774354 TGGTGAAAACAGAGACGTATTTAC 57.226 37.500 0.00 0.00 0.00 2.01
2734 3086 0.325933 TCATCTTGGTGAGCTGGGTG 59.674 55.000 0.00 0.00 0.00 4.61
2826 3204 6.506147 TGGCAAGTGATTGTATATGAAATGC 58.494 36.000 0.00 0.00 0.00 3.56
2884 3273 2.912295 TCCATCCCTGAAGTCAACATGA 59.088 45.455 0.00 0.00 0.00 3.07
2928 3317 5.833082 AGTACAGATAGCATCGTTTGGTAG 58.167 41.667 0.00 0.00 41.36 3.18
2942 3331 5.935206 TCGTTTGGTAGTGCAAGAATCATAA 59.065 36.000 0.00 0.00 0.00 1.90
2945 3334 6.603237 TTGGTAGTGCAAGAATCATAATCG 57.397 37.500 0.00 0.00 0.00 3.34
2950 3339 4.745125 AGTGCAAGAATCATAATCGTACCG 59.255 41.667 0.00 0.00 0.00 4.02
2979 3368 3.188048 GCTCACCAAGATCTTGAGTTGTG 59.812 47.826 32.49 28.13 42.93 3.33
3031 3420 3.547746 ACTGTATTTTGGTCGTGTGGTT 58.452 40.909 0.00 0.00 0.00 3.67
3032 3421 3.314080 ACTGTATTTTGGTCGTGTGGTTG 59.686 43.478 0.00 0.00 0.00 3.77
3033 3422 3.542648 TGTATTTTGGTCGTGTGGTTGA 58.457 40.909 0.00 0.00 0.00 3.18
3034 3423 3.945921 TGTATTTTGGTCGTGTGGTTGAA 59.054 39.130 0.00 0.00 0.00 2.69
3035 3424 4.398358 TGTATTTTGGTCGTGTGGTTGAAA 59.602 37.500 0.00 0.00 0.00 2.69
3036 3425 2.923605 TTTGGTCGTGTGGTTGAAAC 57.076 45.000 0.00 0.00 0.00 2.78
3037 3426 2.116827 TTGGTCGTGTGGTTGAAACT 57.883 45.000 0.00 0.00 0.00 2.66
3038 3427 2.983907 TGGTCGTGTGGTTGAAACTA 57.016 45.000 0.00 0.00 0.00 2.24
3039 3428 2.828877 TGGTCGTGTGGTTGAAACTAG 58.171 47.619 0.00 0.00 0.00 2.57
3084 3473 2.100989 AGATACCCTCAACGACACCTC 58.899 52.381 0.00 0.00 0.00 3.85
3102 3491 5.175859 CACCTCGTCTAGCCTTATTTTTCA 58.824 41.667 0.00 0.00 0.00 2.69
3118 3507 3.114616 CAAGAGCCTCGGCACACG 61.115 66.667 11.02 0.00 44.88 4.49
3143 3532 3.006112 ACGAGCTCCATTCACTAGAGA 57.994 47.619 8.47 0.00 0.00 3.10
3163 3553 3.967715 GGTCTTGAAGTGACCGCC 58.032 61.111 0.00 0.00 43.55 6.13
3172 3562 1.474332 AAGTGACCGCCGAACCCTTA 61.474 55.000 0.00 0.00 0.00 2.69
3173 3563 1.739196 GTGACCGCCGAACCCTTAC 60.739 63.158 0.00 0.00 0.00 2.34
3174 3564 2.208619 TGACCGCCGAACCCTTACA 61.209 57.895 0.00 0.00 0.00 2.41
3175 3565 1.004679 GACCGCCGAACCCTTACAA 60.005 57.895 0.00 0.00 0.00 2.41
3176 3566 1.004200 ACCGCCGAACCCTTACAAG 60.004 57.895 0.00 0.00 0.00 3.16
3177 3567 2.396157 CCGCCGAACCCTTACAAGC 61.396 63.158 0.00 0.00 0.00 4.01
3178 3568 1.375523 CGCCGAACCCTTACAAGCT 60.376 57.895 0.00 0.00 0.00 3.74
3179 3569 0.953960 CGCCGAACCCTTACAAGCTT 60.954 55.000 0.00 0.00 0.00 3.74
3180 3570 0.803117 GCCGAACCCTTACAAGCTTC 59.197 55.000 0.00 0.00 0.00 3.86
3181 3571 1.610886 GCCGAACCCTTACAAGCTTCT 60.611 52.381 0.00 0.00 0.00 2.85
3182 3572 2.354403 GCCGAACCCTTACAAGCTTCTA 60.354 50.000 0.00 0.00 0.00 2.10
3183 3573 3.522553 CCGAACCCTTACAAGCTTCTAG 58.477 50.000 0.00 0.00 0.00 2.43
3184 3574 3.194968 CCGAACCCTTACAAGCTTCTAGA 59.805 47.826 0.00 0.00 0.00 2.43
3185 3575 4.322499 CCGAACCCTTACAAGCTTCTAGAA 60.322 45.833 4.81 4.81 0.00 2.10
3186 3576 4.626172 CGAACCCTTACAAGCTTCTAGAAC 59.374 45.833 0.00 0.00 0.00 3.01
3187 3577 5.548406 GAACCCTTACAAGCTTCTAGAACA 58.452 41.667 0.00 0.00 0.00 3.18
3188 3578 5.763876 ACCCTTACAAGCTTCTAGAACAT 57.236 39.130 0.00 0.00 0.00 2.71
3191 3581 6.655425 ACCCTTACAAGCTTCTAGAACATTTC 59.345 38.462 0.00 0.00 0.00 2.17
3212 3602 4.253685 TCAACCTAGAAGCTTCCGAAATG 58.746 43.478 22.81 15.95 0.00 2.32
3213 3603 3.268023 ACCTAGAAGCTTCCGAAATGG 57.732 47.619 22.81 16.48 40.09 3.16
3225 3615 0.804989 CGAAATGGCTCCAACAGTCC 59.195 55.000 0.00 0.00 0.00 3.85
3309 3701 2.932261 ACTTTCCCCACACAGAGTTTC 58.068 47.619 0.00 0.00 0.00 2.78
3318 3710 5.643777 CCCCACACAGAGTTTCTAACTTATG 59.356 44.000 0.00 0.00 43.03 1.90
3320 3712 6.464222 CCACACAGAGTTTCTAACTTATGGA 58.536 40.000 0.00 0.00 43.03 3.41
3323 3715 8.660373 CACACAGAGTTTCTAACTTATGGAATC 58.340 37.037 0.00 0.00 43.03 2.52
3357 3749 7.900782 TTAGGTCACTAATGTTGTTTAGCTC 57.099 36.000 0.00 0.00 34.35 4.09
3365 3757 7.752239 CACTAATGTTGTTTAGCTCAAATCCAG 59.248 37.037 0.00 0.00 33.34 3.86
3372 3764 9.129209 GTTGTTTAGCTCAAATCCAGAATTAAC 57.871 33.333 0.00 0.00 0.00 2.01
3379 3771 9.638176 AGCTCAAATCCAGAATTAACTATGAAT 57.362 29.630 0.00 0.00 0.00 2.57
3408 3800 5.334414 GGCAGATTAGATCGCAACCTAATTG 60.334 44.000 0.00 0.00 41.69 2.32
3468 3876 8.432805 CACTCCTTATGGGTTTGAGAATATACT 58.567 37.037 0.00 0.00 36.25 2.12
3472 3880 7.998964 CCTTATGGGTTTGAGAATATACTGGTT 59.001 37.037 0.00 0.00 0.00 3.67
3476 3884 5.066505 GGGTTTGAGAATATACTGGTTGCAG 59.933 44.000 0.00 0.00 0.00 4.41
3479 3887 5.675684 TGAGAATATACTGGTTGCAGACA 57.324 39.130 0.00 0.00 0.00 3.41
3481 3889 6.108687 TGAGAATATACTGGTTGCAGACAAG 58.891 40.000 0.00 2.88 36.16 3.16
3500 3908 4.835615 ACAAGTGGGGCATGTTGTAATTTA 59.164 37.500 0.00 0.00 31.37 1.40
3506 3914 3.727726 GGCATGTTGTAATTTATGGCCC 58.272 45.455 0.00 0.00 39.39 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.523916 CACGCCTGAACTAATTAACTATGCT 59.476 40.000 0.00 0.00 0.00 3.79
1 2 5.293569 ACACGCCTGAACTAATTAACTATGC 59.706 40.000 0.00 0.00 0.00 3.14
2 3 6.312918 ACACACGCCTGAACTAATTAACTATG 59.687 38.462 0.00 0.00 0.00 2.23
3 4 6.403878 ACACACGCCTGAACTAATTAACTAT 58.596 36.000 0.00 0.00 0.00 2.12
4 5 5.786311 ACACACGCCTGAACTAATTAACTA 58.214 37.500 0.00 0.00 0.00 2.24
6 7 5.406175 TGTACACACGCCTGAACTAATTAAC 59.594 40.000 0.00 0.00 0.00 2.01
7 8 5.539979 TGTACACACGCCTGAACTAATTAA 58.460 37.500 0.00 0.00 0.00 1.40
8 9 5.136816 TGTACACACGCCTGAACTAATTA 57.863 39.130 0.00 0.00 0.00 1.40
9 10 3.997762 TGTACACACGCCTGAACTAATT 58.002 40.909 0.00 0.00 0.00 1.40
10 11 3.671008 TGTACACACGCCTGAACTAAT 57.329 42.857 0.00 0.00 0.00 1.73
11 12 3.257375 AGATGTACACACGCCTGAACTAA 59.743 43.478 0.00 0.00 0.00 2.24
12 13 2.823747 AGATGTACACACGCCTGAACTA 59.176 45.455 0.00 0.00 0.00 2.24
13 14 1.618837 AGATGTACACACGCCTGAACT 59.381 47.619 0.00 0.00 0.00 3.01
14 15 2.080286 AGATGTACACACGCCTGAAC 57.920 50.000 0.00 0.00 0.00 3.18
15 16 3.006003 TGTTAGATGTACACACGCCTGAA 59.994 43.478 0.00 0.00 0.00 3.02
16 17 2.559231 TGTTAGATGTACACACGCCTGA 59.441 45.455 0.00 0.00 0.00 3.86
17 18 2.923655 CTGTTAGATGTACACACGCCTG 59.076 50.000 0.00 0.00 0.00 4.85
18 19 2.561419 ACTGTTAGATGTACACACGCCT 59.439 45.455 0.00 0.00 0.00 5.52
19 20 2.955614 ACTGTTAGATGTACACACGCC 58.044 47.619 0.00 0.00 0.00 5.68
20 21 3.122948 CCAACTGTTAGATGTACACACGC 59.877 47.826 0.00 0.00 0.00 5.34
21 22 3.122948 GCCAACTGTTAGATGTACACACG 59.877 47.826 0.00 0.00 0.00 4.49
22 23 4.152402 CAGCCAACTGTTAGATGTACACAC 59.848 45.833 0.00 0.00 39.22 3.82
23 24 4.039852 TCAGCCAACTGTTAGATGTACACA 59.960 41.667 0.00 0.00 44.77 3.72
24 25 4.566004 TCAGCCAACTGTTAGATGTACAC 58.434 43.478 0.00 0.00 44.77 2.90
25 26 4.820897 CTCAGCCAACTGTTAGATGTACA 58.179 43.478 0.00 0.00 44.77 2.90
26 27 3.619038 GCTCAGCCAACTGTTAGATGTAC 59.381 47.826 4.30 0.00 44.77 2.90
27 28 3.515502 AGCTCAGCCAACTGTTAGATGTA 59.484 43.478 4.30 0.00 44.77 2.29
28 29 2.304180 AGCTCAGCCAACTGTTAGATGT 59.696 45.455 4.30 0.00 44.77 3.06
29 30 2.676839 CAGCTCAGCCAACTGTTAGATG 59.323 50.000 0.00 0.00 44.77 2.90
30 31 2.568956 TCAGCTCAGCCAACTGTTAGAT 59.431 45.455 0.00 0.00 44.77 1.98
31 32 1.970640 TCAGCTCAGCCAACTGTTAGA 59.029 47.619 0.00 0.00 44.77 2.10
32 33 2.462456 TCAGCTCAGCCAACTGTTAG 57.538 50.000 0.00 0.00 44.77 2.34
33 34 3.423539 AATCAGCTCAGCCAACTGTTA 57.576 42.857 0.00 0.00 44.77 2.41
34 35 2.283145 AATCAGCTCAGCCAACTGTT 57.717 45.000 0.00 0.00 44.77 3.16
35 36 2.304180 ACTAATCAGCTCAGCCAACTGT 59.696 45.455 0.00 0.00 44.77 3.55
36 37 2.983229 ACTAATCAGCTCAGCCAACTG 58.017 47.619 0.00 0.00 45.95 3.16
37 38 3.244700 ACAACTAATCAGCTCAGCCAACT 60.245 43.478 0.00 0.00 0.00 3.16
38 39 3.077359 ACAACTAATCAGCTCAGCCAAC 58.923 45.455 0.00 0.00 0.00 3.77
39 40 3.423539 ACAACTAATCAGCTCAGCCAA 57.576 42.857 0.00 0.00 0.00 4.52
40 41 3.423539 AACAACTAATCAGCTCAGCCA 57.576 42.857 0.00 0.00 0.00 4.75
41 42 4.508662 AGTAACAACTAATCAGCTCAGCC 58.491 43.478 0.00 0.00 0.00 4.85
42 43 7.596749 TTTAGTAACAACTAATCAGCTCAGC 57.403 36.000 0.00 0.00 32.89 4.26
60 61 8.236586 GCGGATGCATTGATATGAAATTTAGTA 58.763 33.333 0.00 0.00 42.15 1.82
61 62 7.086376 GCGGATGCATTGATATGAAATTTAGT 58.914 34.615 0.00 0.00 42.15 2.24
62 63 6.249893 CGCGGATGCATTGATATGAAATTTAG 59.750 38.462 0.00 0.00 42.97 1.85
63 64 6.072783 TCGCGGATGCATTGATATGAAATTTA 60.073 34.615 6.13 0.00 42.97 1.40
64 65 4.919168 CGCGGATGCATTGATATGAAATTT 59.081 37.500 0.00 0.00 42.97 1.82
65 66 4.216042 TCGCGGATGCATTGATATGAAATT 59.784 37.500 6.13 0.00 42.97 1.82
66 67 3.752747 TCGCGGATGCATTGATATGAAAT 59.247 39.130 6.13 0.00 42.97 2.17
67 68 3.137533 TCGCGGATGCATTGATATGAAA 58.862 40.909 6.13 0.00 42.97 2.69
68 69 2.738314 CTCGCGGATGCATTGATATGAA 59.262 45.455 6.13 0.00 42.97 2.57
69 70 2.340337 CTCGCGGATGCATTGATATGA 58.660 47.619 6.13 0.00 42.97 2.15
70 71 1.201998 GCTCGCGGATGCATTGATATG 60.202 52.381 6.13 0.00 42.97 1.78
71 72 1.081892 GCTCGCGGATGCATTGATAT 58.918 50.000 6.13 0.00 42.97 1.63
72 73 1.284297 CGCTCGCGGATGCATTGATA 61.284 55.000 6.13 0.00 42.97 2.15
73 74 2.601398 CGCTCGCGGATGCATTGAT 61.601 57.895 6.13 0.00 42.97 2.57
74 75 3.264159 CGCTCGCGGATGCATTGA 61.264 61.111 6.13 0.00 42.97 2.57
75 76 3.497407 GACGCTCGCGGATGCATTG 62.497 63.158 16.18 0.00 44.69 2.82
76 77 3.264897 GACGCTCGCGGATGCATT 61.265 61.111 16.18 0.00 44.69 3.56
80 81 3.315521 CTTCGACGCTCGCGGATG 61.316 66.667 16.18 4.94 44.69 3.51
81 82 2.921538 CTTCTTCGACGCTCGCGGAT 62.922 60.000 16.18 0.00 44.69 4.18
82 83 3.662623 CTTCTTCGACGCTCGCGGA 62.663 63.158 16.18 1.19 44.69 5.54
83 84 3.241059 CTTCTTCGACGCTCGCGG 61.241 66.667 16.18 0.00 44.69 6.46
84 85 3.241059 CCTTCTTCGACGCTCGCG 61.241 66.667 10.06 10.06 40.21 5.87
85 86 3.546397 GCCTTCTTCGACGCTCGC 61.546 66.667 0.00 0.00 40.21 5.03
86 87 2.126463 TGCCTTCTTCGACGCTCG 60.126 61.111 0.00 1.67 42.10 5.03
87 88 2.437343 CGTGCCTTCTTCGACGCTC 61.437 63.158 0.00 0.00 0.00 5.03
88 89 2.430921 CGTGCCTTCTTCGACGCT 60.431 61.111 0.00 0.00 0.00 5.07
89 90 3.479269 CCGTGCCTTCTTCGACGC 61.479 66.667 0.00 0.00 0.00 5.19
90 91 3.479269 GCCGTGCCTTCTTCGACG 61.479 66.667 0.00 0.00 0.00 5.12
91 92 2.357034 TGCCGTGCCTTCTTCGAC 60.357 61.111 0.00 0.00 0.00 4.20
92 93 2.048222 CTGCCGTGCCTTCTTCGA 60.048 61.111 0.00 0.00 0.00 3.71
93 94 2.048222 TCTGCCGTGCCTTCTTCG 60.048 61.111 0.00 0.00 0.00 3.79
94 95 2.383527 CGTCTGCCGTGCCTTCTTC 61.384 63.158 0.00 0.00 0.00 2.87
95 96 2.357517 CGTCTGCCGTGCCTTCTT 60.358 61.111 0.00 0.00 0.00 2.52
118 119 3.390521 CTACCGTGCCCCTGAGCA 61.391 66.667 0.00 0.00 41.46 4.26
119 120 3.075005 TCTACCGTGCCCCTGAGC 61.075 66.667 0.00 0.00 0.00 4.26
120 121 2.427245 CCTCTACCGTGCCCCTGAG 61.427 68.421 0.00 0.00 0.00 3.35
121 122 2.363795 CCTCTACCGTGCCCCTGA 60.364 66.667 0.00 0.00 0.00 3.86
122 123 2.363795 TCCTCTACCGTGCCCCTG 60.364 66.667 0.00 0.00 0.00 4.45
123 124 2.042843 CTCCTCTACCGTGCCCCT 60.043 66.667 0.00 0.00 0.00 4.79
124 125 3.851128 GCTCCTCTACCGTGCCCC 61.851 72.222 0.00 0.00 0.00 5.80
125 126 3.851128 GGCTCCTCTACCGTGCCC 61.851 72.222 0.00 0.00 37.81 5.36
126 127 4.208686 CGGCTCCTCTACCGTGCC 62.209 72.222 0.00 0.00 44.46 5.01
199 209 1.668751 TCGTGGCTTGTTGTTGTCTTC 59.331 47.619 0.00 0.00 0.00 2.87
203 213 1.299541 CTCTCGTGGCTTGTTGTTGT 58.700 50.000 0.00 0.00 0.00 3.32
286 299 2.028484 GACACGTGGACGCTGGAA 59.972 61.111 21.57 0.00 44.43 3.53
287 300 2.910479 AGACACGTGGACGCTGGA 60.910 61.111 21.57 0.00 44.43 3.86
412 429 1.398958 GCCAGAGGTAGAGCCAGAGG 61.399 65.000 0.00 0.00 40.61 3.69
420 437 0.394488 CGACCAGAGCCAGAGGTAGA 60.394 60.000 0.00 0.00 35.36 2.59
423 440 2.681778 CCGACCAGAGCCAGAGGT 60.682 66.667 0.00 0.00 38.63 3.85
424 441 2.681778 ACCGACCAGAGCCAGAGG 60.682 66.667 0.00 0.00 0.00 3.69
425 442 2.575993 CACCGACCAGAGCCAGAG 59.424 66.667 0.00 0.00 0.00 3.35
426 443 2.997315 CCACCGACCAGAGCCAGA 60.997 66.667 0.00 0.00 0.00 3.86
427 444 3.314331 ACCACCGACCAGAGCCAG 61.314 66.667 0.00 0.00 0.00 4.85
428 445 3.625897 CACCACCGACCAGAGCCA 61.626 66.667 0.00 0.00 0.00 4.75
429 446 4.394712 CCACCACCGACCAGAGCC 62.395 72.222 0.00 0.00 0.00 4.70
432 449 2.200370 AGACCACCACCGACCAGA 59.800 61.111 0.00 0.00 0.00 3.86
433 450 2.343758 CAGACCACCACCGACCAG 59.656 66.667 0.00 0.00 0.00 4.00
434 451 3.238497 CCAGACCACCACCGACCA 61.238 66.667 0.00 0.00 0.00 4.02
435 452 3.236003 GACCAGACCACCACCGACC 62.236 68.421 0.00 0.00 0.00 4.79
613 651 7.311092 TGTAGGAATTTACCGACCATATGAT 57.689 36.000 3.65 0.00 35.27 2.45
615 653 6.594159 GGATGTAGGAATTTACCGACCATATG 59.406 42.308 0.00 0.00 35.27 1.78
617 655 5.603395 TGGATGTAGGAATTTACCGACCATA 59.397 40.000 0.00 0.00 35.27 2.74
618 656 4.410883 TGGATGTAGGAATTTACCGACCAT 59.589 41.667 0.00 0.00 35.27 3.55
663 712 4.112341 GCAAGCTTGAGGCAGGCG 62.112 66.667 30.39 0.00 41.40 5.52
682 738 3.801050 TGTTGCCAACAAACAATCAATCG 59.199 39.130 8.02 0.00 38.72 3.34
688 744 6.165577 GGATATTCTGTTGCCAACAAACAAT 58.834 36.000 11.99 11.75 41.61 2.71
690 746 4.320861 CGGATATTCTGTTGCCAACAAACA 60.321 41.667 11.99 0.00 41.61 2.83
691 747 4.165779 CGGATATTCTGTTGCCAACAAAC 58.834 43.478 11.99 0.00 41.61 2.93
692 748 3.823873 ACGGATATTCTGTTGCCAACAAA 59.176 39.130 11.99 9.23 41.61 2.83
693 749 3.417101 ACGGATATTCTGTTGCCAACAA 58.583 40.909 11.99 0.00 41.61 2.83
694 750 3.006940 GACGGATATTCTGTTGCCAACA 58.993 45.455 10.31 10.31 35.83 3.33
695 751 2.354821 GGACGGATATTCTGTTGCCAAC 59.645 50.000 0.00 0.00 35.83 3.77
696 752 2.026729 TGGACGGATATTCTGTTGCCAA 60.027 45.455 0.00 0.00 35.83 4.52
755 811 2.398554 CGGTTGGATTGGACGCCAG 61.399 63.158 0.00 0.00 35.23 4.85
772 828 3.103911 GAACTGACCCGCGTGTCG 61.104 66.667 16.80 13.37 38.11 4.35
773 829 3.103911 CGAACTGACCCGCGTGTC 61.104 66.667 15.16 15.16 35.77 3.67
890 994 0.589708 AGCGGCCTTTTTGTAACGTC 59.410 50.000 0.00 0.00 0.00 4.34
909 1013 1.621622 GCTACTCCTTGGTCCTGGGTA 60.622 57.143 0.00 0.00 0.00 3.69
919 1023 1.021390 CGGTGGCTTGCTACTCCTTG 61.021 60.000 8.87 0.00 0.00 3.61
921 1025 1.192146 TTCGGTGGCTTGCTACTCCT 61.192 55.000 8.87 0.00 0.00 3.69
1179 1319 0.107993 CGACACAGTCCATGCTCCAT 60.108 55.000 0.00 0.00 0.00 3.41
1371 1511 1.448540 CTGCGTGGCCAGGTAGAAG 60.449 63.158 32.25 18.05 31.97 2.85
1513 1661 6.464222 TCCAAGAAGTTAGTAACCACATCTG 58.536 40.000 9.46 0.97 0.00 2.90
1514 1662 6.681729 TCCAAGAAGTTAGTAACCACATCT 57.318 37.500 9.46 6.03 0.00 2.90
1990 2142 2.159599 GCAGGTGAATTCAGAAAGCGAG 60.160 50.000 8.80 0.00 0.00 5.03
1992 2144 1.808945 AGCAGGTGAATTCAGAAAGCG 59.191 47.619 8.80 0.00 0.00 4.68
1995 2147 3.254166 GCAAGAGCAGGTGAATTCAGAAA 59.746 43.478 8.80 0.00 41.58 2.52
2020 2172 1.227205 GTCAGAGATGAGCGGGCAG 60.227 63.158 0.00 0.00 0.00 4.85
2023 2175 2.279120 GCGTCAGAGATGAGCGGG 60.279 66.667 0.00 0.00 0.00 6.13
2025 2177 2.653448 CGGCGTCAGAGATGAGCG 60.653 66.667 0.00 0.00 0.00 5.03
2171 2323 4.598894 CTGGCCCTCGCGATCTGG 62.599 72.222 10.36 12.31 35.02 3.86
2255 2407 2.429571 GCGTAAGTGTCCGTCGCA 60.430 61.111 0.00 0.00 45.01 5.10
2259 2411 0.315886 TGTCATGCGTAAGTGTCCGT 59.684 50.000 0.00 0.00 41.68 4.69
2260 2412 0.713883 GTGTCATGCGTAAGTGTCCG 59.286 55.000 0.00 0.00 41.68 4.79
2261 2413 2.080286 AGTGTCATGCGTAAGTGTCC 57.920 50.000 0.00 0.00 41.68 4.02
2262 2414 3.741344 AGAAAGTGTCATGCGTAAGTGTC 59.259 43.478 0.00 0.00 41.68 3.67
2263 2415 3.728845 AGAAAGTGTCATGCGTAAGTGT 58.271 40.909 0.00 0.00 41.68 3.55
2264 2416 4.449068 AGAAGAAAGTGTCATGCGTAAGTG 59.551 41.667 0.00 0.00 41.68 3.16
2265 2417 4.632153 AGAAGAAAGTGTCATGCGTAAGT 58.368 39.130 0.00 0.00 41.68 2.24
2266 2418 5.177511 TGAAGAAGAAAGTGTCATGCGTAAG 59.822 40.000 0.00 0.00 43.44 2.34
2267 2419 5.053811 TGAAGAAGAAAGTGTCATGCGTAA 58.946 37.500 0.00 0.00 0.00 3.18
2268 2420 4.627058 TGAAGAAGAAAGTGTCATGCGTA 58.373 39.130 0.00 0.00 0.00 4.42
2269 2421 3.466836 TGAAGAAGAAAGTGTCATGCGT 58.533 40.909 0.00 0.00 0.00 5.24
2270 2422 4.472691 TTGAAGAAGAAAGTGTCATGCG 57.527 40.909 0.00 0.00 0.00 4.73
2271 2423 5.855395 GTGATTGAAGAAGAAAGTGTCATGC 59.145 40.000 0.00 0.00 0.00 4.06
2272 2424 6.206243 AGGTGATTGAAGAAGAAAGTGTCATG 59.794 38.462 0.00 0.00 0.00 3.07
2273 2425 6.302269 AGGTGATTGAAGAAGAAAGTGTCAT 58.698 36.000 0.00 0.00 0.00 3.06
2274 2426 5.684704 AGGTGATTGAAGAAGAAAGTGTCA 58.315 37.500 0.00 0.00 0.00 3.58
2275 2427 5.107298 CGAGGTGATTGAAGAAGAAAGTGTC 60.107 44.000 0.00 0.00 0.00 3.67
2276 2428 4.752101 CGAGGTGATTGAAGAAGAAAGTGT 59.248 41.667 0.00 0.00 0.00 3.55
2277 2429 4.377841 GCGAGGTGATTGAAGAAGAAAGTG 60.378 45.833 0.00 0.00 0.00 3.16
2278 2430 3.748568 GCGAGGTGATTGAAGAAGAAAGT 59.251 43.478 0.00 0.00 0.00 2.66
2279 2431 3.748048 TGCGAGGTGATTGAAGAAGAAAG 59.252 43.478 0.00 0.00 0.00 2.62
2280 2432 3.738982 TGCGAGGTGATTGAAGAAGAAA 58.261 40.909 0.00 0.00 0.00 2.52
2281 2433 3.006859 TCTGCGAGGTGATTGAAGAAGAA 59.993 43.478 0.00 0.00 0.00 2.52
2282 2434 2.562738 TCTGCGAGGTGATTGAAGAAGA 59.437 45.455 0.00 0.00 0.00 2.87
2283 2435 2.964740 TCTGCGAGGTGATTGAAGAAG 58.035 47.619 0.00 0.00 0.00 2.85
2284 2436 3.401033 TTCTGCGAGGTGATTGAAGAA 57.599 42.857 0.00 0.00 34.88 2.52
2285 2437 3.401033 TTTCTGCGAGGTGATTGAAGA 57.599 42.857 0.00 0.00 0.00 2.87
2286 2438 4.437930 GGAATTTCTGCGAGGTGATTGAAG 60.438 45.833 0.00 0.00 0.00 3.02
2287 2439 3.440173 GGAATTTCTGCGAGGTGATTGAA 59.560 43.478 0.00 0.00 0.00 2.69
2288 2440 3.009723 GGAATTTCTGCGAGGTGATTGA 58.990 45.455 0.00 0.00 0.00 2.57
2289 2441 2.749076 TGGAATTTCTGCGAGGTGATTG 59.251 45.455 0.00 0.00 0.00 2.67
2290 2442 3.071874 TGGAATTTCTGCGAGGTGATT 57.928 42.857 0.00 0.00 0.00 2.57
2291 2443 2.787473 TGGAATTTCTGCGAGGTGAT 57.213 45.000 0.00 0.00 0.00 3.06
2292 2444 2.027285 TGATGGAATTTCTGCGAGGTGA 60.027 45.455 0.00 0.00 0.00 4.02
2293 2445 2.358957 TGATGGAATTTCTGCGAGGTG 58.641 47.619 0.00 0.00 0.00 4.00
2294 2446 2.787473 TGATGGAATTTCTGCGAGGT 57.213 45.000 0.00 0.00 0.00 3.85
2295 2447 3.691118 TCTTTGATGGAATTTCTGCGAGG 59.309 43.478 0.00 0.00 0.00 4.63
2296 2448 4.952262 TCTTTGATGGAATTTCTGCGAG 57.048 40.909 0.00 0.00 0.00 5.03
2297 2449 5.902613 AATCTTTGATGGAATTTCTGCGA 57.097 34.783 0.00 0.00 0.00 5.10
2298 2450 7.028962 TGTTAATCTTTGATGGAATTTCTGCG 58.971 34.615 0.00 0.00 0.00 5.18
2299 2451 8.814235 CATGTTAATCTTTGATGGAATTTCTGC 58.186 33.333 0.00 0.00 0.00 4.26
2330 2537 2.201708 CCCACACCTGCATGCACAA 61.202 57.895 18.46 0.00 0.00 3.33
2331 2538 2.598099 CCCACACCTGCATGCACA 60.598 61.111 18.46 0.00 0.00 4.57
2368 2578 1.141053 TCGATCTCGTCCAGGATCTGA 59.859 52.381 0.00 0.00 40.80 3.27
2473 2683 2.451294 GGAGGGGGCATGAGGGAT 60.451 66.667 0.00 0.00 0.00 3.85
2499 2712 1.060308 CCAACTGATTAACGGCGCG 59.940 57.895 6.90 0.00 0.00 6.86
2508 2721 1.280421 GAGGGTCAGAGCCAACTGATT 59.720 52.381 21.01 0.00 46.36 2.57
2516 2729 2.438800 TACACTAGAGGGTCAGAGCC 57.561 55.000 11.04 11.04 35.59 4.70
2524 2737 5.105351 TGTGTGTCATCATTACACTAGAGGG 60.105 44.000 3.79 0.00 45.95 4.30
2538 2751 3.446799 GATCTGCTCTCTGTGTGTCATC 58.553 50.000 0.00 0.00 0.00 2.92
2539 2752 2.168106 GGATCTGCTCTCTGTGTGTCAT 59.832 50.000 0.00 0.00 0.00 3.06
2541 2754 1.824230 AGGATCTGCTCTCTGTGTGTC 59.176 52.381 0.00 0.00 0.00 3.67
2547 2769 4.887071 ACTAGTACAAGGATCTGCTCTCTG 59.113 45.833 0.00 0.00 0.00 3.35
2558 2780 6.420638 TCACTGCTATACACTAGTACAAGGA 58.579 40.000 0.00 0.00 31.96 3.36
2566 2788 7.265647 ACTGTACATCACTGCTATACACTAG 57.734 40.000 0.00 0.00 0.00 2.57
2568 2790 6.602009 TGTACTGTACATCACTGCTATACACT 59.398 38.462 16.26 0.00 32.89 3.55
2571 2793 7.260558 TCTGTACTGTACATCACTGCTATAC 57.739 40.000 19.99 0.00 38.15 1.47
2641 2993 8.482429 CAAGCACATAATTTTTCTTCAACACTC 58.518 33.333 0.00 0.00 0.00 3.51
2697 3049 5.601662 AGATGACCATCCACAGTAAATACG 58.398 41.667 6.40 0.00 38.58 3.06
2703 3055 3.055167 CACCAAGATGACCATCCACAGTA 60.055 47.826 6.40 0.00 38.58 2.74
2705 3057 2.026915 TCACCAAGATGACCATCCACAG 60.027 50.000 6.40 0.00 38.58 3.66
2734 3086 0.615850 GCCTGCAGATAGATACCCCC 59.384 60.000 17.39 0.00 0.00 5.40
2792 3144 6.594788 ACAATCACTTGCCATTTTCAGTAT 57.405 33.333 0.00 0.00 35.69 2.12
2826 3204 5.237127 TCAACAACTATGCTGACAAGAACAG 59.763 40.000 0.00 0.00 38.27 3.16
2914 3303 1.806542 CTTGCACTACCAAACGATGCT 59.193 47.619 0.00 0.00 37.20 3.79
2945 3334 1.521681 GGTGAGCTCATGCCGGTAC 60.522 63.158 21.47 3.76 40.80 3.34
2950 3339 1.134159 AGATCTTGGTGAGCTCATGCC 60.134 52.381 21.47 17.74 36.60 4.40
2979 3368 0.804989 CACTTGATGGTTCGGGAAGC 59.195 55.000 3.76 3.76 39.12 3.86
3031 3420 3.641436 TCCTCTCAGTTGCACTAGTTTCA 59.359 43.478 0.00 0.00 0.00 2.69
3032 3421 4.241681 CTCCTCTCAGTTGCACTAGTTTC 58.758 47.826 0.00 0.00 0.00 2.78
3033 3422 3.007398 CCTCCTCTCAGTTGCACTAGTTT 59.993 47.826 0.00 0.00 0.00 2.66
3034 3423 2.564947 CCTCCTCTCAGTTGCACTAGTT 59.435 50.000 0.00 0.00 0.00 2.24
3035 3424 2.175202 CCTCCTCTCAGTTGCACTAGT 58.825 52.381 0.00 0.00 0.00 2.57
3036 3425 2.451490 TCCTCCTCTCAGTTGCACTAG 58.549 52.381 0.00 0.00 0.00 2.57
3037 3426 2.604912 TCCTCCTCTCAGTTGCACTA 57.395 50.000 0.00 0.00 0.00 2.74
3038 3427 1.722034 TTCCTCCTCTCAGTTGCACT 58.278 50.000 0.00 0.00 0.00 4.40
3039 3428 2.147150 GTTTCCTCCTCTCAGTTGCAC 58.853 52.381 0.00 0.00 0.00 4.57
3047 3436 5.179533 GGTATCTTTGTGTTTCCTCCTCTC 58.820 45.833 0.00 0.00 0.00 3.20
3084 3473 5.220681 GGCTCTTGAAAAATAAGGCTAGACG 60.221 44.000 0.00 0.00 0.00 4.18
3102 3491 3.303135 TCGTGTGCCGAGGCTCTT 61.303 61.111 15.75 0.00 41.60 2.85
3118 3507 2.966050 AGTGAATGGAGCTCGTTCTTC 58.034 47.619 22.97 15.98 40.95 2.87
3163 3553 4.451629 TCTAGAAGCTTGTAAGGGTTCG 57.548 45.455 2.10 0.00 43.33 3.95
3172 3562 6.064717 AGGTTGAAATGTTCTAGAAGCTTGT 58.935 36.000 2.10 1.06 0.00 3.16
3173 3563 6.566197 AGGTTGAAATGTTCTAGAAGCTTG 57.434 37.500 2.10 0.00 0.00 4.01
3174 3564 7.680730 TCTAGGTTGAAATGTTCTAGAAGCTT 58.319 34.615 5.12 0.00 35.08 3.74
3175 3565 7.246171 TCTAGGTTGAAATGTTCTAGAAGCT 57.754 36.000 5.12 0.00 35.08 3.74
3176 3566 7.907214 TTCTAGGTTGAAATGTTCTAGAAGC 57.093 36.000 5.12 1.92 40.19 3.86
3178 3568 7.680730 AGCTTCTAGGTTGAAATGTTCTAGAA 58.319 34.615 0.00 0.00 41.73 2.10
3179 3569 7.246171 AGCTTCTAGGTTGAAATGTTCTAGA 57.754 36.000 0.00 0.00 35.88 2.43
3180 3570 7.065204 GGAAGCTTCTAGGTTGAAATGTTCTAG 59.935 40.741 25.05 0.00 35.86 2.43
3181 3571 6.879458 GGAAGCTTCTAGGTTGAAATGTTCTA 59.121 38.462 25.05 0.00 35.86 2.10
3182 3572 5.707764 GGAAGCTTCTAGGTTGAAATGTTCT 59.292 40.000 25.05 0.00 35.86 3.01
3183 3573 5.390991 CGGAAGCTTCTAGGTTGAAATGTTC 60.391 44.000 25.05 2.61 35.86 3.18
3184 3574 4.455877 CGGAAGCTTCTAGGTTGAAATGTT 59.544 41.667 25.05 0.00 35.86 2.71
3185 3575 4.003648 CGGAAGCTTCTAGGTTGAAATGT 58.996 43.478 25.05 0.00 35.86 2.71
3186 3576 4.253685 TCGGAAGCTTCTAGGTTGAAATG 58.746 43.478 25.05 2.66 35.86 2.32
3187 3577 4.553330 TCGGAAGCTTCTAGGTTGAAAT 57.447 40.909 25.05 0.00 35.86 2.17
3188 3578 4.345859 TTCGGAAGCTTCTAGGTTGAAA 57.654 40.909 25.05 7.67 35.86 2.69
3191 3581 3.375299 CCATTTCGGAAGCTTCTAGGTTG 59.625 47.826 25.05 16.46 35.86 3.77
3212 3602 1.298014 CTCCTGGACTGTTGGAGCC 59.702 63.158 10.80 0.00 40.52 4.70
3332 3724 7.934665 TGAGCTAAACAACATTAGTGACCTAAA 59.065 33.333 0.00 0.00 36.76 1.85
3372 3764 8.333908 GCGATCTAATCTGCCATTTATTCATAG 58.666 37.037 0.00 0.00 0.00 2.23
3378 3770 5.182001 GGTTGCGATCTAATCTGCCATTTAT 59.818 40.000 0.00 0.00 0.00 1.40
3379 3771 4.515191 GGTTGCGATCTAATCTGCCATTTA 59.485 41.667 0.00 0.00 0.00 1.40
3385 3777 5.334414 CCAATTAGGTTGCGATCTAATCTGC 60.334 44.000 18.06 0.00 35.76 4.26
3392 3784 3.197766 TGAGTCCAATTAGGTTGCGATCT 59.802 43.478 0.00 0.00 39.02 2.75
3408 3800 2.048444 ATGCCATGACATGTGAGTCC 57.952 50.000 14.26 0.00 37.73 3.85
3452 3860 4.947388 TGCAACCAGTATATTCTCAAACCC 59.053 41.667 0.00 0.00 0.00 4.11
3468 3876 1.152777 CCCCACTTGTCTGCAACCA 60.153 57.895 0.00 0.00 0.00 3.67
3472 3880 1.604308 CATGCCCCACTTGTCTGCA 60.604 57.895 0.00 0.00 36.23 4.41
3476 3884 1.904287 TACAACATGCCCCACTTGTC 58.096 50.000 0.85 0.00 35.71 3.18
3479 3887 5.104982 CCATAAATTACAACATGCCCCACTT 60.105 40.000 0.00 0.00 0.00 3.16
3481 3889 4.692228 CCATAAATTACAACATGCCCCAC 58.308 43.478 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.