Multiple sequence alignment - TraesCS4A01G014600

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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 TraesCS4A01G014600 chr4A 100.000 4504 0 0 1 4504 9395879 9400382 0.000000e+00 8318.0
1 TraesCS4A01G014600 chr4A 97.959 49 1 0 3072 3120 9398914 9398962 8.030000e-13 86.1
2 TraesCS4A01G014600 chr4A 97.959 49 1 0 3036 3084 9398950 9398998 8.030000e-13 86.1
3 TraesCS4A01G014600 chr4B 92.300 1052 47 10 1701 2718 574176180 574175129 0.000000e+00 1463.0
4 TraesCS4A01G014600 chr4B 93.929 593 27 5 1081 1672 574176855 574176271 0.000000e+00 887.0
5 TraesCS4A01G014600 chr4B 87.913 786 39 29 2730 3508 574175074 574174338 0.000000e+00 874.0
6 TraesCS4A01G014600 chr4B 94.015 518 28 1 3986 4503 574171492 574170978 0.000000e+00 782.0
7 TraesCS4A01G014600 chr4B 79.758 909 112 41 137 1036 574177696 574176851 1.080000e-165 593.0
8 TraesCS4A01G014600 chr4B 92.233 103 7 1 3620 3721 574173242 574173140 1.310000e-30 145.0
9 TraesCS4A01G014600 chr4D 82.817 1583 132 41 126 1672 459424401 459422923 0.000000e+00 1288.0
10 TraesCS4A01G014600 chr4D 91.337 658 38 6 3860 4504 459385582 459384931 0.000000e+00 881.0
11 TraesCS4A01G014600 chr4D 90.583 669 39 14 1761 2408 459422795 459422130 0.000000e+00 865.0
12 TraesCS4A01G014600 chr4D 89.740 692 45 11 2408 3084 459390380 459389700 0.000000e+00 861.0
13 TraesCS4A01G014600 chr4D 92.906 437 23 4 3079 3508 459389741 459389306 2.960000e-176 628.0
14 TraesCS4A01G014600 chr2D 84.925 670 58 21 2448 3084 335118523 335117864 4.910000e-179 638.0
15 TraesCS4A01G014600 chr2D 90.351 456 39 3 3079 3529 335117906 335117451 1.080000e-165 593.0
16 TraesCS4A01G014600 chr2D 95.283 212 10 0 1457 1668 335121802 335121591 2.010000e-88 337.0
17 TraesCS4A01G014600 chr2D 80.000 220 34 8 539 755 175933380 175933168 2.170000e-33 154.0
18 TraesCS4A01G014600 chr2B 84.776 670 59 19 2448 3084 403086258 403085599 2.290000e-177 632.0
19 TraesCS4A01G014600 chr2B 91.228 399 29 4 3131 3526 403085427 403085032 5.130000e-149 538.0
20 TraesCS4A01G014600 chr2B 94.811 212 11 0 1457 1668 403092053 403091842 9.340000e-87 331.0
21 TraesCS4A01G014600 chr2A 84.627 670 60 19 2448 3084 445712541 445711882 1.060000e-175 627.0
22 TraesCS4A01G014600 chr2A 90.508 453 38 3 3079 3526 445711924 445711472 1.080000e-165 593.0
23 TraesCS4A01G014600 chr2A 94.340 212 12 0 1457 1668 445715758 445715547 4.340000e-85 326.0
24 TraesCS4A01G014600 chr7A 92.093 430 31 2 4075 4504 121846435 121846009 1.790000e-168 603.0
25 TraesCS4A01G014600 chr7A 81.364 220 35 6 539 755 287243839 287244055 1.670000e-39 174.0
26 TraesCS4A01G014600 chr7A 83.871 124 16 4 539 660 712826432 712826311 1.020000e-21 115.0
27 TraesCS4A01G014600 chr7D 92.075 429 31 2 4076 4504 117465287 117464862 6.450000e-168 601.0
28 TraesCS4A01G014600 chr1B 73.361 732 137 39 164 869 189688684 189689383 7.590000e-53 219.0
29 TraesCS4A01G014600 chr6D 81.092 238 35 8 499 733 40979304 40979074 9.950000e-42 182.0
30 TraesCS4A01G014600 chr5B 79.452 219 40 5 539 755 377087962 377088177 2.810000e-32 150.0
31 TraesCS4A01G014600 chr3D 77.515 169 29 9 498 661 546821853 546821689 4.800000e-15 93.5
32 TraesCS4A01G014600 chr5A 76.871 147 26 8 498 640 523928331 523928189 4.830000e-10 76.8


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 TraesCS4A01G014600 chr4A 9395879 9400382 4503 False 2830.066667 8318 98.639333 1 4504 3 chr4A.!!$F1 4503
1 TraesCS4A01G014600 chr4B 574170978 574177696 6718 True 790.666667 1463 90.024667 137 4503 6 chr4B.!!$R1 4366
2 TraesCS4A01G014600 chr4D 459422130 459424401 2271 True 1076.500000 1288 86.700000 126 2408 2 chr4D.!!$R2 2282
3 TraesCS4A01G014600 chr4D 459384931 459390380 5449 True 790.000000 881 91.327667 2408 4504 3 chr4D.!!$R1 2096
4 TraesCS4A01G014600 chr2D 335117451 335121802 4351 True 522.666667 638 90.186333 1457 3529 3 chr2D.!!$R2 2072
5 TraesCS4A01G014600 chr2B 403085032 403086258 1226 True 585.000000 632 88.002000 2448 3526 2 chr2B.!!$R2 1078
6 TraesCS4A01G014600 chr2A 445711472 445715758 4286 True 515.333333 627 89.825000 1457 3526 3 chr2A.!!$R1 2069
7 TraesCS4A01G014600 chr1B 189688684 189689383 699 False 219.000000 219 73.361000 164 869 1 chr1B.!!$F1 705

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
119 120 0.032017 ATACTCCTGCGGTCCTTCCT 60.032 55.0 0.00 0.0 0.0 3.36 F
1001 1069 0.172803 GACCGCACGACCTAACTGAT 59.827 55.0 0.00 0.0 0.0 2.90 F
1144 1222 0.323178 GGTCTCTACACAGTCCCGGA 60.323 60.0 0.73 0.0 0.0 5.14 F
3082 7538 0.379316 GCCCGTTCGACTTTGTTGTT 59.621 50.0 0.00 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1261 1339 0.034756 ACACTGTGACGCTATTGGCA 59.965 50.000 15.86 0.00 41.91 4.92 R
1834 2009 3.311871 CACCTAGATGTCAAATCAGCAGC 59.688 47.826 0.00 0.00 0.00 5.25 R
3084 7540 0.988063 TGGGCTACATACAGGTGCAA 59.012 50.000 0.00 0.00 0.00 4.08 R
4022 12881 0.304401 GATGTATCGCGCATGTGCAA 59.696 50.000 29.19 13.84 42.21 4.08 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
20 21 3.827008 AAAGTGAGAGTGACTTCTGCA 57.173 42.857 0.00 0.00 32.33 4.41
21 22 3.827008 AAGTGAGAGTGACTTCTGCAA 57.173 42.857 0.00 0.00 0.00 4.08
22 23 3.383620 AGTGAGAGTGACTTCTGCAAG 57.616 47.619 0.00 0.00 35.50 4.01
23 24 2.036992 AGTGAGAGTGACTTCTGCAAGG 59.963 50.000 0.00 0.00 33.37 3.61
24 25 1.345741 TGAGAGTGACTTCTGCAAGGG 59.654 52.381 0.00 0.00 33.37 3.95
25 26 1.620819 GAGAGTGACTTCTGCAAGGGA 59.379 52.381 0.00 0.00 33.37 4.20
26 27 2.235898 GAGAGTGACTTCTGCAAGGGAT 59.764 50.000 0.00 0.00 33.37 3.85
27 28 3.445008 AGAGTGACTTCTGCAAGGGATA 58.555 45.455 0.00 0.00 33.37 2.59
28 29 3.196685 AGAGTGACTTCTGCAAGGGATAC 59.803 47.826 0.00 0.00 33.37 2.24
47 48 7.803279 GGATACCCCTTAGTTAGTGATTTTG 57.197 40.000 0.00 0.00 0.00 2.44
48 49 6.771267 GGATACCCCTTAGTTAGTGATTTTGG 59.229 42.308 0.00 0.00 0.00 3.28
49 50 5.594199 ACCCCTTAGTTAGTGATTTTGGT 57.406 39.130 0.00 0.00 0.00 3.67
50 51 5.960704 ACCCCTTAGTTAGTGATTTTGGTT 58.039 37.500 0.00 0.00 0.00 3.67
51 52 6.378745 ACCCCTTAGTTAGTGATTTTGGTTT 58.621 36.000 0.00 0.00 0.00 3.27
52 53 6.842280 ACCCCTTAGTTAGTGATTTTGGTTTT 59.158 34.615 0.00 0.00 0.00 2.43
53 54 7.346175 ACCCCTTAGTTAGTGATTTTGGTTTTT 59.654 33.333 0.00 0.00 0.00 1.94
91 92 8.782137 AAAACACATAGGATTTTATATGGGCT 57.218 30.769 0.00 0.00 36.45 5.19
92 93 8.409358 AAACACATAGGATTTTATATGGGCTC 57.591 34.615 0.00 0.00 36.45 4.70
93 94 7.090319 ACACATAGGATTTTATATGGGCTCA 57.910 36.000 0.00 0.00 36.45 4.26
94 95 7.526041 ACACATAGGATTTTATATGGGCTCAA 58.474 34.615 0.00 0.00 36.45 3.02
95 96 7.667219 ACACATAGGATTTTATATGGGCTCAAG 59.333 37.037 0.00 0.00 36.45 3.02
96 97 7.884877 CACATAGGATTTTATATGGGCTCAAGA 59.115 37.037 0.00 0.00 34.36 3.02
97 98 8.618385 ACATAGGATTTTATATGGGCTCAAGAT 58.382 33.333 0.00 0.00 34.36 2.40
98 99 9.471702 CATAGGATTTTATATGGGCTCAAGATT 57.528 33.333 0.00 0.00 0.00 2.40
99 100 9.692325 ATAGGATTTTATATGGGCTCAAGATTC 57.308 33.333 0.00 0.00 0.00 2.52
100 101 7.529555 AGGATTTTATATGGGCTCAAGATTCA 58.470 34.615 0.00 0.00 0.00 2.57
101 102 8.175431 AGGATTTTATATGGGCTCAAGATTCAT 58.825 33.333 0.00 0.00 0.00 2.57
102 103 9.466497 GGATTTTATATGGGCTCAAGATTCATA 57.534 33.333 0.00 0.00 0.00 2.15
105 106 9.507329 TTTTATATGGGCTCAAGATTCATACTC 57.493 33.333 0.00 0.00 0.00 2.59
106 107 3.845781 TGGGCTCAAGATTCATACTCC 57.154 47.619 0.00 0.00 0.00 3.85
107 108 3.387962 TGGGCTCAAGATTCATACTCCT 58.612 45.455 0.00 0.00 0.00 3.69
108 109 3.135348 TGGGCTCAAGATTCATACTCCTG 59.865 47.826 0.00 0.00 0.00 3.86
109 110 3.137533 GGCTCAAGATTCATACTCCTGC 58.862 50.000 0.00 0.00 0.00 4.85
110 111 2.799412 GCTCAAGATTCATACTCCTGCG 59.201 50.000 0.00 0.00 0.00 5.18
111 112 3.388308 CTCAAGATTCATACTCCTGCGG 58.612 50.000 0.00 0.00 0.00 5.69
112 113 2.766263 TCAAGATTCATACTCCTGCGGT 59.234 45.455 0.00 0.00 0.00 5.68
113 114 3.126831 CAAGATTCATACTCCTGCGGTC 58.873 50.000 0.00 0.00 0.00 4.79
114 115 1.689273 AGATTCATACTCCTGCGGTCC 59.311 52.381 0.00 0.00 0.00 4.46
115 116 1.689273 GATTCATACTCCTGCGGTCCT 59.311 52.381 0.00 0.00 0.00 3.85
116 117 1.568504 TTCATACTCCTGCGGTCCTT 58.431 50.000 0.00 0.00 0.00 3.36
117 118 1.112113 TCATACTCCTGCGGTCCTTC 58.888 55.000 0.00 0.00 0.00 3.46
118 119 0.105039 CATACTCCTGCGGTCCTTCC 59.895 60.000 0.00 0.00 0.00 3.46
119 120 0.032017 ATACTCCTGCGGTCCTTCCT 60.032 55.000 0.00 0.00 0.00 3.36
120 121 0.970937 TACTCCTGCGGTCCTTCCTG 60.971 60.000 0.00 0.00 0.00 3.86
121 122 1.984570 CTCCTGCGGTCCTTCCTGA 60.985 63.158 0.00 0.00 0.00 3.86
122 123 1.306141 TCCTGCGGTCCTTCCTGAT 60.306 57.895 0.00 0.00 0.00 2.90
123 124 1.153289 CCTGCGGTCCTTCCTGATG 60.153 63.158 0.00 0.00 0.00 3.07
124 125 1.617018 CCTGCGGTCCTTCCTGATGA 61.617 60.000 0.00 0.00 0.00 2.92
135 136 0.937441 TCCTGATGAGAGCCCCTAGT 59.063 55.000 0.00 0.00 0.00 2.57
193 194 4.382831 CGTGTTGTGCGACTACTAAAATG 58.617 43.478 0.00 0.00 0.00 2.32
204 207 5.935789 CGACTACTAAAATGTCCCCAAAAGA 59.064 40.000 0.00 0.00 0.00 2.52
206 209 7.120726 CGACTACTAAAATGTCCCCAAAAGAAT 59.879 37.037 0.00 0.00 0.00 2.40
207 210 8.721133 ACTACTAAAATGTCCCCAAAAGAATT 57.279 30.769 0.00 0.00 0.00 2.17
239 242 1.128692 GAGGAATCAAACTCGCAACCG 59.871 52.381 0.00 0.00 0.00 4.44
285 291 1.224075 CACTTGAGCTGGTGAGTGTG 58.776 55.000 0.00 1.16 35.84 3.82
331 339 5.711976 ACTAATAAGAACAAATGCAGTGGCT 59.288 36.000 5.27 0.00 41.91 4.75
389 397 7.455641 TCTTGGAAAACTGTGAACAAGTTTA 57.544 32.000 2.26 0.00 37.27 2.01
390 398 7.887381 TCTTGGAAAACTGTGAACAAGTTTAA 58.113 30.769 2.26 0.00 37.27 1.52
391 399 8.361139 TCTTGGAAAACTGTGAACAAGTTTAAA 58.639 29.630 2.26 0.00 37.27 1.52
518 538 9.392021 ACACAATTTTTGAAAATGTGAACAAAC 57.608 25.926 23.49 0.00 38.53 2.93
537 557 5.754890 ACAAACTTCAAATTCTGGACAATGC 59.245 36.000 0.00 0.00 0.00 3.56
539 559 5.382618 ACTTCAAATTCTGGACAATGCTC 57.617 39.130 0.00 0.00 0.00 4.26
556 577 7.043565 ACAATGCTCTTGAACTGTGAAAATTT 58.956 30.769 6.59 0.00 0.00 1.82
557 578 7.550196 ACAATGCTCTTGAACTGTGAAAATTTT 59.450 29.630 2.28 2.28 0.00 1.82
559 580 8.807667 ATGCTCTTGAACTGTGAAAATTTTAG 57.192 30.769 2.75 0.46 0.00 1.85
746 774 8.789881 CATTTTTCAATGTACGGTGAACTTTA 57.210 30.769 9.81 0.00 35.86 1.85
753 805 8.071368 TCAATGTACGGTGAACTTTATTTTGAC 58.929 33.333 0.00 0.00 0.00 3.18
756 808 7.759465 TGTACGGTGAACTTTATTTTGACAAA 58.241 30.769 0.00 0.00 0.00 2.83
758 810 5.740099 ACGGTGAACTTTATTTTGACAAACG 59.260 36.000 0.00 0.00 0.00 3.60
759 811 5.740099 CGGTGAACTTTATTTTGACAAACGT 59.260 36.000 0.00 0.00 0.00 3.99
760 812 6.290851 CGGTGAACTTTATTTTGACAAACGTG 60.291 38.462 0.00 0.00 0.00 4.49
763 815 6.748198 TGAACTTTATTTTGACAAACGTGACC 59.252 34.615 0.00 0.00 0.00 4.02
769 821 9.582431 TTTATTTTGACAAACGTGACCAATTTA 57.418 25.926 0.00 0.00 0.00 1.40
770 822 9.751542 TTATTTTGACAAACGTGACCAATTTAT 57.248 25.926 0.00 0.00 0.00 1.40
771 823 7.456684 TTTTGACAAACGTGACCAATTTATG 57.543 32.000 0.00 0.00 0.00 1.90
790 842 9.928236 AATTTATGAAAACGTGAACAAATTTGG 57.072 25.926 21.74 6.49 0.00 3.28
815 867 7.279758 GGAAAATGTGACCAATTTCTGAAAACA 59.720 33.333 6.95 6.26 39.43 2.83
823 875 7.492020 TGACCAATTTCTGAAAACATGAACAAG 59.508 33.333 6.95 0.00 0.00 3.16
829 881 6.279513 TCTGAAAACATGAACAAGTTTGGT 57.720 33.333 0.00 0.00 37.94 3.67
830 882 6.098679 TCTGAAAACATGAACAAGTTTGGTG 58.901 36.000 0.00 3.60 37.94 4.17
962 1030 6.401955 AAACAAAATAATCCATTTTCGGCG 57.598 33.333 0.00 0.00 43.51 6.46
979 1047 1.202698 GGCGAATAGGATCTGCCAACT 60.203 52.381 0.00 0.00 45.06 3.16
983 1051 3.004419 CGAATAGGATCTGCCAACTACGA 59.996 47.826 0.00 0.00 40.02 3.43
985 1053 0.824759 AGGATCTGCCAACTACGACC 59.175 55.000 0.00 0.00 40.02 4.79
998 1066 0.955428 TACGACCGCACGACCTAACT 60.955 55.000 6.49 0.00 37.03 2.24
1001 1069 0.172803 GACCGCACGACCTAACTGAT 59.827 55.000 0.00 0.00 0.00 2.90
1140 1218 1.474879 GCTGAGGTCTCTACACAGTCC 59.525 57.143 0.00 0.00 35.45 3.85
1142 1220 1.096416 GAGGTCTCTACACAGTCCCG 58.904 60.000 0.00 0.00 0.00 5.14
1144 1222 0.323178 GGTCTCTACACAGTCCCGGA 60.323 60.000 0.73 0.00 0.00 5.14
1145 1223 1.685491 GGTCTCTACACAGTCCCGGAT 60.685 57.143 0.73 0.00 0.00 4.18
1219 1297 3.885521 GTCGCCGTCCTACTCCCG 61.886 72.222 0.00 0.00 0.00 5.14
1255 1333 6.670233 TGCACTCGGTAATTTTATCGTTTTT 58.330 32.000 3.19 0.00 38.37 1.94
1347 1425 5.244402 TGTTGATGGAACTCAATTTGATGCT 59.756 36.000 0.00 0.00 37.47 3.79
1407 1485 3.245016 TGAGGAATATGGGTGATGATGGC 60.245 47.826 0.00 0.00 0.00 4.40
1568 1646 4.393371 GCTCTTGTCAAAGTGGTAGATTCC 59.607 45.833 0.00 0.00 34.78 3.01
1657 1735 3.118038 ACATACACGCCATCCAAGGTAAT 60.118 43.478 0.00 0.00 0.00 1.89
1668 1746 5.545723 CCATCCAAGGTAATATCTGTCTCCT 59.454 44.000 0.00 0.00 0.00 3.69
1688 1838 9.638239 GTCTCCTTATGTTATCAAAATTGCAAA 57.362 29.630 1.71 0.00 0.00 3.68
1690 1840 8.770438 TCCTTATGTTATCAAAATTGCAAACC 57.230 30.769 1.71 0.00 0.00 3.27
1691 1841 7.821846 TCCTTATGTTATCAAAATTGCAAACCC 59.178 33.333 1.71 0.00 0.00 4.11
1692 1842 7.605691 CCTTATGTTATCAAAATTGCAAACCCA 59.394 33.333 1.71 0.00 0.00 4.51
1693 1843 9.165035 CTTATGTTATCAAAATTGCAAACCCAT 57.835 29.630 1.71 0.00 0.00 4.00
1695 1845 8.721019 ATGTTATCAAAATTGCAAACCCATAG 57.279 30.769 1.71 0.00 0.00 2.23
1696 1846 7.675062 TGTTATCAAAATTGCAAACCCATAGT 58.325 30.769 1.71 0.00 0.00 2.12
1699 1849 5.923204 TCAAAATTGCAAACCCATAGTGTT 58.077 33.333 1.71 0.00 0.00 3.32
1704 1854 5.957842 TTGCAAACCCATAGTGTTCTTAG 57.042 39.130 0.00 0.00 0.00 2.18
1725 1875 4.240323 AGTAGGAAAGAAGGGGAAGTCAA 58.760 43.478 0.00 0.00 0.00 3.18
1737 1911 5.793817 AGGGGAAGTCAAATAATGTTTTGC 58.206 37.500 0.00 0.00 36.69 3.68
1738 1912 5.306678 AGGGGAAGTCAAATAATGTTTTGCA 59.693 36.000 0.00 0.00 36.69 4.08
1739 1913 5.994668 GGGGAAGTCAAATAATGTTTTGCAA 59.005 36.000 0.00 0.00 36.69 4.08
1740 1914 6.654582 GGGGAAGTCAAATAATGTTTTGCAAT 59.345 34.615 0.00 0.00 36.69 3.56
1741 1915 7.148423 GGGGAAGTCAAATAATGTTTTGCAATC 60.148 37.037 0.00 0.00 36.69 2.67
1742 1916 7.603784 GGGAAGTCAAATAATGTTTTGCAATCT 59.396 33.333 0.00 0.00 36.69 2.40
1743 1917 8.650714 GGAAGTCAAATAATGTTTTGCAATCTC 58.349 33.333 0.00 0.00 36.69 2.75
1744 1918 7.801547 AGTCAAATAATGTTTTGCAATCTCG 57.198 32.000 0.00 0.00 36.69 4.04
1745 1919 7.370383 AGTCAAATAATGTTTTGCAATCTCGT 58.630 30.769 0.00 0.00 36.69 4.18
1746 1920 7.538678 AGTCAAATAATGTTTTGCAATCTCGTC 59.461 33.333 0.00 0.00 36.69 4.20
1747 1921 7.325821 GTCAAATAATGTTTTGCAATCTCGTCA 59.674 33.333 0.00 0.00 36.69 4.35
1748 1922 7.538334 TCAAATAATGTTTTGCAATCTCGTCAG 59.462 33.333 0.00 0.00 36.69 3.51
1749 1923 3.837213 ATGTTTTGCAATCTCGTCAGG 57.163 42.857 0.00 0.00 0.00 3.86
1750 1924 2.571212 TGTTTTGCAATCTCGTCAGGT 58.429 42.857 0.00 0.00 0.00 4.00
1751 1925 2.948979 TGTTTTGCAATCTCGTCAGGTT 59.051 40.909 0.00 0.00 0.00 3.50
1752 1926 3.380004 TGTTTTGCAATCTCGTCAGGTTT 59.620 39.130 0.00 0.00 0.00 3.27
1753 1927 4.576873 TGTTTTGCAATCTCGTCAGGTTTA 59.423 37.500 0.00 0.00 0.00 2.01
1754 1928 4.742438 TTTGCAATCTCGTCAGGTTTAC 57.258 40.909 0.00 0.00 0.00 2.01
1755 1929 3.678056 TGCAATCTCGTCAGGTTTACT 57.322 42.857 0.00 0.00 0.00 2.24
1756 1930 4.794278 TGCAATCTCGTCAGGTTTACTA 57.206 40.909 0.00 0.00 0.00 1.82
1757 1931 4.491676 TGCAATCTCGTCAGGTTTACTAC 58.508 43.478 0.00 0.00 0.00 2.73
1758 1932 4.219944 TGCAATCTCGTCAGGTTTACTACT 59.780 41.667 0.00 0.00 0.00 2.57
1759 1933 5.169295 GCAATCTCGTCAGGTTTACTACTT 58.831 41.667 0.00 0.00 0.00 2.24
1784 1958 7.781056 TCAAGGAGTAATGGATTTTTAATGGC 58.219 34.615 0.00 0.00 0.00 4.40
1795 1969 6.922957 TGGATTTTTAATGGCGCTTATCAATC 59.077 34.615 7.64 9.31 0.00 2.67
1873 2048 3.356290 AGGTGGTAGATTGTTCATTGCC 58.644 45.455 0.00 0.00 0.00 4.52
1985 2167 9.586435 TCTTTTGATGCATATACCATACTATCG 57.414 33.333 0.00 0.00 0.00 2.92
2101 2302 0.957395 ATTGTCCGCACTTCAGGCAG 60.957 55.000 0.00 0.00 0.00 4.85
2175 2537 4.628074 GCGAACTGGTGCCTTCTATATAA 58.372 43.478 0.00 0.00 0.00 0.98
2248 2625 5.438698 TTATAAGGTGGAAATGAACCGGA 57.561 39.130 9.46 0.00 41.61 5.14
2249 2626 1.905637 AAGGTGGAAATGAACCGGAC 58.094 50.000 9.46 1.77 41.61 4.79
2252 2634 2.167662 GGTGGAAATGAACCGGACAAT 58.832 47.619 9.46 0.00 0.00 2.71
2457 6836 9.762933 AAGTCCTAGTTCTTACGTACTATCTAG 57.237 37.037 0.00 6.02 0.00 2.43
2513 6892 7.376336 CGATTGTGGTTTGTGTTTAACGATTAA 59.624 33.333 0.00 0.00 0.00 1.40
2533 6925 7.752239 CGATTAATAGCATGGATTTAGCCTTTG 59.248 37.037 0.00 0.00 0.00 2.77
2553 6945 3.995199 TGCTTCTTGAATATAGGCCTCG 58.005 45.455 9.68 0.00 0.00 4.63
2556 6948 2.257207 TCTTGAATATAGGCCTCGGGG 58.743 52.381 9.68 0.00 0.00 5.73
2701 7093 9.658799 TTTCTTGAGAGAACTATAATGGAACAG 57.341 33.333 0.00 0.00 41.51 3.16
2748 7183 4.520492 GGTGAATCCTTTGGCCTATGTATG 59.480 45.833 3.32 0.00 0.00 2.39
2873 7308 8.642935 TCCTGTCATTGTTTATGGATTTGTAA 57.357 30.769 0.00 0.00 34.85 2.41
2922 7364 9.043079 GGCAATAAGGAAATAAGTACTACAGAC 57.957 37.037 0.00 0.00 0.00 3.51
2923 7365 9.819267 GCAATAAGGAAATAAGTACTACAGACT 57.181 33.333 0.00 0.00 0.00 3.24
2979 7434 5.452777 GTCAGTTCCTGTGAATTTTGTAGC 58.547 41.667 0.00 0.00 31.98 3.58
3015 7471 0.647410 CTGCTGAATTGGCGTAGTCG 59.353 55.000 0.00 0.00 40.37 4.18
3038 7494 5.452496 CGTTACTGATCATGGAATCAGGACT 60.452 44.000 21.93 9.17 42.25 3.85
3039 7495 6.352516 GTTACTGATCATGGAATCAGGACTT 58.647 40.000 21.93 8.91 42.25 3.01
3040 7496 5.447778 ACTGATCATGGAATCAGGACTTT 57.552 39.130 21.93 4.68 42.25 2.66
3041 7497 5.191426 ACTGATCATGGAATCAGGACTTTG 58.809 41.667 21.93 3.74 42.25 2.77
3046 7502 5.139727 TCATGGAATCAGGACTTTGTTGTT 58.860 37.500 0.00 0.00 0.00 2.83
3070 7526 1.935933 CACCTGTATGTAGCCCGTTC 58.064 55.000 0.00 0.00 0.00 3.95
3071 7527 0.458669 ACCTGTATGTAGCCCGTTCG 59.541 55.000 0.00 0.00 0.00 3.95
3072 7528 0.742505 CCTGTATGTAGCCCGTTCGA 59.257 55.000 0.00 0.00 0.00 3.71
3073 7529 1.535437 CCTGTATGTAGCCCGTTCGAC 60.535 57.143 0.00 0.00 0.00 4.20
3074 7530 1.404391 CTGTATGTAGCCCGTTCGACT 59.596 52.381 0.00 0.00 0.00 4.18
3075 7531 1.820519 TGTATGTAGCCCGTTCGACTT 59.179 47.619 0.00 0.00 0.00 3.01
3076 7532 2.231964 TGTATGTAGCCCGTTCGACTTT 59.768 45.455 0.00 0.00 0.00 2.66
3077 7533 1.722011 ATGTAGCCCGTTCGACTTTG 58.278 50.000 0.00 0.00 0.00 2.77
3078 7534 0.390124 TGTAGCCCGTTCGACTTTGT 59.610 50.000 0.00 0.00 0.00 2.83
3079 7535 1.202557 TGTAGCCCGTTCGACTTTGTT 60.203 47.619 0.00 0.00 0.00 2.83
3080 7536 1.193874 GTAGCCCGTTCGACTTTGTTG 59.806 52.381 0.00 0.00 0.00 3.33
3081 7537 0.463116 AGCCCGTTCGACTTTGTTGT 60.463 50.000 0.00 0.00 0.00 3.32
3082 7538 0.379316 GCCCGTTCGACTTTGTTGTT 59.621 50.000 0.00 0.00 0.00 2.83
3083 7539 1.858399 GCCCGTTCGACTTTGTTGTTG 60.858 52.381 0.00 0.00 0.00 3.33
3084 7540 1.399089 CCCGTTCGACTTTGTTGTTGT 59.601 47.619 0.00 0.00 0.00 3.32
3085 7541 2.159490 CCCGTTCGACTTTGTTGTTGTT 60.159 45.455 0.00 0.00 0.00 2.83
3086 7542 2.843643 CCGTTCGACTTTGTTGTTGTTG 59.156 45.455 0.00 0.00 0.00 3.33
3087 7543 2.275253 CGTTCGACTTTGTTGTTGTTGC 59.725 45.455 0.00 0.00 0.00 4.17
3088 7544 3.238441 GTTCGACTTTGTTGTTGTTGCA 58.762 40.909 0.00 0.00 0.00 4.08
3089 7545 2.857618 TCGACTTTGTTGTTGTTGCAC 58.142 42.857 0.00 0.00 0.00 4.57
3090 7546 1.917303 CGACTTTGTTGTTGTTGCACC 59.083 47.619 0.00 0.00 0.00 5.01
3091 7547 2.415357 CGACTTTGTTGTTGTTGCACCT 60.415 45.455 0.00 0.00 0.00 4.00
3092 7548 2.923020 GACTTTGTTGTTGTTGCACCTG 59.077 45.455 0.00 0.00 0.00 4.00
3093 7549 2.298729 ACTTTGTTGTTGTTGCACCTGT 59.701 40.909 0.00 0.00 0.00 4.00
3094 7550 3.508012 ACTTTGTTGTTGTTGCACCTGTA 59.492 39.130 0.00 0.00 0.00 2.74
3095 7551 4.159506 ACTTTGTTGTTGTTGCACCTGTAT 59.840 37.500 0.00 0.00 0.00 2.29
3096 7552 3.706802 TGTTGTTGTTGCACCTGTATG 57.293 42.857 0.00 0.00 0.00 2.39
3097 7553 3.020274 TGTTGTTGTTGCACCTGTATGT 58.980 40.909 0.00 0.00 0.00 2.29
3098 7554 4.200092 TGTTGTTGTTGCACCTGTATGTA 58.800 39.130 0.00 0.00 0.00 2.29
3099 7555 4.274705 TGTTGTTGTTGCACCTGTATGTAG 59.725 41.667 0.00 0.00 0.00 2.74
3100 7556 2.811431 TGTTGTTGCACCTGTATGTAGC 59.189 45.455 0.00 0.00 0.00 3.58
3101 7557 2.107950 TGTTGCACCTGTATGTAGCC 57.892 50.000 0.00 0.00 0.00 3.93
3102 7558 1.339631 TGTTGCACCTGTATGTAGCCC 60.340 52.381 0.00 0.00 0.00 5.19
3103 7559 0.988063 TTGCACCTGTATGTAGCCCA 59.012 50.000 0.00 0.00 0.00 5.36
3104 7560 1.212375 TGCACCTGTATGTAGCCCAT 58.788 50.000 0.00 0.00 37.58 4.00
3105 7561 1.563879 TGCACCTGTATGTAGCCCATT 59.436 47.619 0.00 0.00 34.86 3.16
3106 7562 2.222027 GCACCTGTATGTAGCCCATTC 58.778 52.381 0.00 0.00 34.86 2.67
3276 7909 1.528586 GCATATTTGAGACGCTGCGAT 59.471 47.619 30.47 16.64 0.00 4.58
3386 8019 1.411977 CTTTTGTGTGCCCATCCACAA 59.588 47.619 1.37 1.37 46.28 3.33
3401 8034 0.941463 CACAAACGCTGCGAGAGACT 60.941 55.000 30.47 1.03 0.00 3.24
3477 8110 1.267806 CAGTTGTGGCACTGATCAACC 59.732 52.381 19.83 0.00 46.29 3.77
3532 8221 6.455647 ACACGTTTTCTCTTCATGTAGATGA 58.544 36.000 2.17 0.00 36.78 2.92
3570 8259 9.167311 ACACTGAAATGAAGTTATTACAGATCC 57.833 33.333 0.00 0.00 0.00 3.36
3589 8278 7.044181 CAGATCCAAAGTGCAGAGTTTAGATA 58.956 38.462 0.00 0.00 27.01 1.98
3595 8284 7.360438 CCAAAGTGCAGAGTTTAGATACTTCAC 60.360 40.741 0.00 0.00 0.00 3.18
3618 10372 4.402474 CCCTGTTTGGAACTGAAAGACTTT 59.598 41.667 0.00 0.00 38.35 2.66
3650 10406 3.364889 TGTTGGTCTAACTCACTGTCG 57.635 47.619 0.46 0.00 40.05 4.35
3664 10421 1.086696 CTGTCGTTAGCATTGTGGGG 58.913 55.000 0.00 0.00 0.00 4.96
3727 10484 5.298276 TGTGCCTATTTGATTTATCCCGAAC 59.702 40.000 0.00 0.00 0.00 3.95
3728 10485 5.531287 GTGCCTATTTGATTTATCCCGAACT 59.469 40.000 0.00 0.00 0.00 3.01
3737 10494 9.467258 TTTGATTTATCCCGAACTATAGTAACG 57.533 33.333 18.98 18.98 0.00 3.18
3739 10496 3.930634 ATCCCGAACTATAGTAACGGC 57.069 47.619 29.80 10.78 42.39 5.68
3752 10509 1.063027 GTAACGGCGTAAAGGATTGGC 59.937 52.381 15.20 0.00 0.00 4.52
3755 10512 2.478033 GGCGTAAAGGATTGGCCCG 61.478 63.158 0.00 0.00 37.37 6.13
3756 10513 2.478033 GCGTAAAGGATTGGCCCGG 61.478 63.158 0.00 0.00 37.37 5.73
3779 10536 9.991906 CCGGTAATAATACAAATAAGGAGAGAA 57.008 33.333 0.00 0.00 33.45 2.87
3797 10554 6.293462 GGAGAGAACCACGAAATTATAATGGC 60.293 42.308 0.00 0.00 33.46 4.40
3798 10555 6.357367 AGAGAACCACGAAATTATAATGGCT 58.643 36.000 0.00 0.00 33.46 4.75
3799 10556 7.506114 AGAGAACCACGAAATTATAATGGCTA 58.494 34.615 0.00 0.00 33.46 3.93
3800 10557 7.990886 AGAGAACCACGAAATTATAATGGCTAA 59.009 33.333 0.00 0.00 33.46 3.09
3801 10558 8.691661 AGAACCACGAAATTATAATGGCTAAT 57.308 30.769 0.00 0.00 33.46 1.73
3802 10559 9.131791 AGAACCACGAAATTATAATGGCTAATT 57.868 29.630 0.00 0.00 33.46 1.40
3803 10560 9.744468 GAACCACGAAATTATAATGGCTAATTT 57.256 29.630 0.00 2.84 39.99 1.82
3818 10575 9.474313 AATGGCTAATTTACACTTGATCCTAAA 57.526 29.630 0.00 0.00 0.00 1.85
3819 10576 8.871629 TGGCTAATTTACACTTGATCCTAAAA 57.128 30.769 0.00 0.00 0.00 1.52
3843 10600 8.691661 AAAAAGAGAGGCTAATTTACACTTGA 57.308 30.769 0.00 0.00 0.00 3.02
3908 12525 4.410883 CCCCATACAGACATACCAAACCTA 59.589 45.833 0.00 0.00 0.00 3.08
3909 12526 5.454755 CCCCATACAGACATACCAAACCTAG 60.455 48.000 0.00 0.00 0.00 3.02
3910 12527 5.454755 CCCATACAGACATACCAAACCTAGG 60.455 48.000 7.41 7.41 0.00 3.02
3911 12528 5.365605 CCATACAGACATACCAAACCTAGGA 59.634 44.000 17.98 0.00 0.00 2.94
3913 12530 5.359194 ACAGACATACCAAACCTAGGATG 57.641 43.478 17.98 13.72 0.00 3.51
3914 12531 4.783227 ACAGACATACCAAACCTAGGATGT 59.217 41.667 17.98 13.49 32.99 3.06
3937 12554 8.722480 TGTGGATGTACATTCTCTTTTCATAG 57.278 34.615 15.27 0.00 0.00 2.23
3950 12580 6.422701 TCTCTTTTCATAGTTAACACACACGG 59.577 38.462 8.61 0.00 0.00 4.94
3964 12594 3.430895 CACACACGGTGTAGGTTTATGAC 59.569 47.826 14.30 0.00 45.65 3.06
3967 12597 7.523439 ACACACGGTGTAGGTTTATGACCTC 62.523 48.000 14.30 0.92 46.75 3.85
3989 12619 5.592054 TCCAATGCATTCTACTCTTACTCG 58.408 41.667 9.53 0.00 0.00 4.18
3991 12621 5.233050 CCAATGCATTCTACTCTTACTCGTG 59.767 44.000 9.53 0.00 0.00 4.35
4014 12873 0.329596 AGAGAACAAGTGGGCATCCC 59.670 55.000 0.00 0.00 45.71 3.85
4034 12893 3.600437 GCGAATTGCACATGCGCG 61.600 61.111 15.32 0.00 45.83 6.86
4051 12910 2.666069 GCGCGATACATCTAGACCAGTC 60.666 54.545 12.10 0.00 0.00 3.51
4118 12977 2.746277 GACGGACATGGTGCCACC 60.746 66.667 7.01 7.01 39.22 4.61
4153 13012 3.052620 ATGGACGAGAGCACGGACG 62.053 63.158 0.00 0.00 37.61 4.79
4154 13013 3.429141 GGACGAGAGCACGGACGA 61.429 66.667 0.00 0.00 37.61 4.20
4155 13014 2.202324 GACGAGAGCACGGACGAC 60.202 66.667 0.00 0.00 37.61 4.34
4226 13085 4.803426 CAGCACCTCCTCGCCGTC 62.803 72.222 0.00 0.00 0.00 4.79
4406 13265 4.699522 GACCCACCGCACCAGGAC 62.700 72.222 0.00 0.00 34.73 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.827008 TGCAGAAGTCACTCTCACTTT 57.173 42.857 0.00 0.00 34.10 2.66
1 2 3.494048 CCTTGCAGAAGTCACTCTCACTT 60.494 47.826 0.00 0.00 36.77 3.16
2 3 2.036992 CCTTGCAGAAGTCACTCTCACT 59.963 50.000 0.00 0.00 0.00 3.41
3 4 2.411904 CCTTGCAGAAGTCACTCTCAC 58.588 52.381 0.00 0.00 0.00 3.51
4 5 1.345741 CCCTTGCAGAAGTCACTCTCA 59.654 52.381 0.00 0.00 0.00 3.27
5 6 1.620819 TCCCTTGCAGAAGTCACTCTC 59.379 52.381 0.00 0.00 0.00 3.20
6 7 1.722034 TCCCTTGCAGAAGTCACTCT 58.278 50.000 0.00 0.00 0.00 3.24
7 8 2.777832 ATCCCTTGCAGAAGTCACTC 57.222 50.000 0.00 0.00 0.00 3.51
8 9 2.237392 GGTATCCCTTGCAGAAGTCACT 59.763 50.000 0.00 0.00 0.00 3.41
9 10 2.633488 GGTATCCCTTGCAGAAGTCAC 58.367 52.381 0.00 0.00 0.00 3.67
10 11 1.559682 GGGTATCCCTTGCAGAAGTCA 59.440 52.381 0.00 0.00 41.34 3.41
11 12 2.333688 GGGTATCCCTTGCAGAAGTC 57.666 55.000 0.00 0.00 41.34 3.01
23 24 6.771267 CCAAAATCACTAACTAAGGGGTATCC 59.229 42.308 0.00 0.00 0.00 2.59
24 25 7.344134 ACCAAAATCACTAACTAAGGGGTATC 58.656 38.462 0.00 0.00 0.00 2.24
25 26 7.280044 ACCAAAATCACTAACTAAGGGGTAT 57.720 36.000 0.00 0.00 0.00 2.73
26 27 6.707273 ACCAAAATCACTAACTAAGGGGTA 57.293 37.500 0.00 0.00 0.00 3.69
27 28 5.594199 ACCAAAATCACTAACTAAGGGGT 57.406 39.130 0.00 0.00 0.00 4.95
28 29 6.911250 AAACCAAAATCACTAACTAAGGGG 57.089 37.500 0.00 0.00 0.00 4.79
65 66 9.212593 AGCCCATATAAAATCCTATGTGTTTTT 57.787 29.630 0.00 0.00 0.00 1.94
66 67 8.782137 AGCCCATATAAAATCCTATGTGTTTT 57.218 30.769 0.00 0.00 0.00 2.43
67 68 8.004215 TGAGCCCATATAAAATCCTATGTGTTT 58.996 33.333 0.00 0.00 0.00 2.83
68 69 7.526041 TGAGCCCATATAAAATCCTATGTGTT 58.474 34.615 0.00 0.00 0.00 3.32
69 70 7.090319 TGAGCCCATATAAAATCCTATGTGT 57.910 36.000 0.00 0.00 0.00 3.72
70 71 7.884877 TCTTGAGCCCATATAAAATCCTATGTG 59.115 37.037 0.00 0.00 0.00 3.21
71 72 7.988937 TCTTGAGCCCATATAAAATCCTATGT 58.011 34.615 0.00 0.00 0.00 2.29
72 73 9.471702 AATCTTGAGCCCATATAAAATCCTATG 57.528 33.333 0.00 0.00 0.00 2.23
73 74 9.692325 GAATCTTGAGCCCATATAAAATCCTAT 57.308 33.333 0.00 0.00 0.00 2.57
74 75 8.668653 TGAATCTTGAGCCCATATAAAATCCTA 58.331 33.333 0.00 0.00 0.00 2.94
75 76 7.529555 TGAATCTTGAGCCCATATAAAATCCT 58.470 34.615 0.00 0.00 0.00 3.24
76 77 7.765695 TGAATCTTGAGCCCATATAAAATCC 57.234 36.000 0.00 0.00 0.00 3.01
79 80 9.507329 GAGTATGAATCTTGAGCCCATATAAAA 57.493 33.333 0.00 0.00 0.00 1.52
80 81 8.103305 GGAGTATGAATCTTGAGCCCATATAAA 58.897 37.037 0.00 0.00 0.00 1.40
81 82 7.459125 AGGAGTATGAATCTTGAGCCCATATAA 59.541 37.037 0.00 0.00 0.00 0.98
82 83 6.962311 AGGAGTATGAATCTTGAGCCCATATA 59.038 38.462 0.00 0.00 0.00 0.86
83 84 5.789575 AGGAGTATGAATCTTGAGCCCATAT 59.210 40.000 0.00 0.00 0.00 1.78
84 85 5.012458 CAGGAGTATGAATCTTGAGCCCATA 59.988 44.000 0.00 0.00 0.00 2.74
85 86 3.979347 AGGAGTATGAATCTTGAGCCCAT 59.021 43.478 0.00 0.00 0.00 4.00
86 87 3.135348 CAGGAGTATGAATCTTGAGCCCA 59.865 47.826 0.00 0.00 0.00 5.36
87 88 3.737850 CAGGAGTATGAATCTTGAGCCC 58.262 50.000 0.00 0.00 0.00 5.19
88 89 3.137533 GCAGGAGTATGAATCTTGAGCC 58.862 50.000 0.00 0.00 0.00 4.70
89 90 2.799412 CGCAGGAGTATGAATCTTGAGC 59.201 50.000 0.00 0.00 0.00 4.26
106 107 0.179089 CTCATCAGGAAGGACCGCAG 60.179 60.000 0.00 0.00 44.74 5.18
107 108 0.614697 TCTCATCAGGAAGGACCGCA 60.615 55.000 0.00 0.00 44.74 5.69
108 109 0.103937 CTCTCATCAGGAAGGACCGC 59.896 60.000 0.00 0.00 44.74 5.68
109 110 0.103937 GCTCTCATCAGGAAGGACCG 59.896 60.000 0.00 0.00 44.74 4.79
110 111 0.467804 GGCTCTCATCAGGAAGGACC 59.532 60.000 0.00 0.00 39.35 4.46
111 112 0.467804 GGGCTCTCATCAGGAAGGAC 59.532 60.000 0.00 0.00 0.00 3.85
112 113 0.692419 GGGGCTCTCATCAGGAAGGA 60.692 60.000 0.00 0.00 0.00 3.36
113 114 0.693767 AGGGGCTCTCATCAGGAAGG 60.694 60.000 0.00 0.00 0.00 3.46
114 115 1.969923 CTAGGGGCTCTCATCAGGAAG 59.030 57.143 0.00 0.00 0.00 3.46
115 116 1.292242 ACTAGGGGCTCTCATCAGGAA 59.708 52.381 0.00 0.00 0.00 3.36
116 117 0.937441 ACTAGGGGCTCTCATCAGGA 59.063 55.000 0.00 0.00 0.00 3.86
117 118 1.415659 CAACTAGGGGCTCTCATCAGG 59.584 57.143 0.00 0.00 0.00 3.86
118 119 2.102252 GTCAACTAGGGGCTCTCATCAG 59.898 54.545 0.00 0.00 0.00 2.90
119 120 2.111384 GTCAACTAGGGGCTCTCATCA 58.889 52.381 0.00 0.00 0.00 3.07
120 121 1.067821 CGTCAACTAGGGGCTCTCATC 59.932 57.143 0.00 0.00 0.00 2.92
121 122 1.115467 CGTCAACTAGGGGCTCTCAT 58.885 55.000 0.00 0.00 0.00 2.90
122 123 1.605058 GCGTCAACTAGGGGCTCTCA 61.605 60.000 0.00 0.00 0.00 3.27
123 124 1.142097 GCGTCAACTAGGGGCTCTC 59.858 63.158 0.00 0.00 0.00 3.20
124 125 1.305381 AGCGTCAACTAGGGGCTCT 60.305 57.895 0.00 0.00 0.00 4.09
204 207 0.037326 TCCTCGACAGAGCGCAAATT 60.037 50.000 11.47 0.00 43.05 1.82
206 209 0.037326 ATTCCTCGACAGAGCGCAAA 60.037 50.000 11.47 0.00 43.05 3.68
207 210 0.458543 GATTCCTCGACAGAGCGCAA 60.459 55.000 11.47 0.00 43.05 4.85
239 242 0.607489 ACACCTGCTCTCCAATGTGC 60.607 55.000 0.00 0.00 32.39 4.57
285 291 1.070577 CGCGCTGCCTATTAATCACAC 60.071 52.381 5.56 0.00 0.00 3.82
458 478 9.837525 CATTTTTGAATTTTTGTCCACTTTTCA 57.162 25.926 0.00 0.00 0.00 2.69
459 479 9.838975 ACATTTTTGAATTTTTGTCCACTTTTC 57.161 25.926 0.00 0.00 0.00 2.29
518 538 5.640189 AGAGCATTGTCCAGAATTTGAAG 57.360 39.130 0.00 0.00 0.00 3.02
665 687 6.695292 AGAAAAATTGTTCGACATGCATTC 57.305 33.333 0.00 0.00 32.50 2.67
746 774 7.923344 TCATAAATTGGTCACGTTTGTCAAAAT 59.077 29.630 0.00 0.00 0.00 1.82
753 805 6.197468 ACGTTTTCATAAATTGGTCACGTTTG 59.803 34.615 0.00 0.00 33.47 2.93
756 808 5.007823 TCACGTTTTCATAAATTGGTCACGT 59.992 36.000 0.00 0.00 35.89 4.49
758 810 6.693545 TGTTCACGTTTTCATAAATTGGTCAC 59.306 34.615 0.00 0.00 0.00 3.67
759 811 6.796426 TGTTCACGTTTTCATAAATTGGTCA 58.204 32.000 0.00 0.00 0.00 4.02
760 812 7.687005 TTGTTCACGTTTTCATAAATTGGTC 57.313 32.000 0.00 0.00 0.00 4.02
769 821 7.602517 TTTCCAAATTTGTTCACGTTTTCAT 57.397 28.000 16.73 0.00 0.00 2.57
770 822 7.421530 TTTTCCAAATTTGTTCACGTTTTCA 57.578 28.000 16.73 0.00 0.00 2.69
771 823 7.960195 ACATTTTCCAAATTTGTTCACGTTTTC 59.040 29.630 16.73 0.00 0.00 2.29
790 842 8.195617 TGTTTTCAGAAATTGGTCACATTTTC 57.804 30.769 0.00 6.88 42.76 2.29
815 867 4.974368 TCGAAACACCAAACTTGTTCAT 57.026 36.364 0.00 0.00 36.13 2.57
823 875 6.205784 TCAGAAAATGATCGAAACACCAAAC 58.794 36.000 0.00 0.00 31.12 2.93
957 1025 1.112916 TGGCAGATCCTATTCGCCGA 61.113 55.000 0.00 0.00 46.02 5.54
962 1030 4.299978 GTCGTAGTTGGCAGATCCTATTC 58.700 47.826 0.00 0.00 35.26 1.75
979 1047 0.955428 AGTTAGGTCGTGCGGTCGTA 60.955 55.000 0.00 0.00 0.00 3.43
983 1051 0.108804 CATCAGTTAGGTCGTGCGGT 60.109 55.000 0.00 0.00 0.00 5.68
985 1053 1.550065 CTCATCAGTTAGGTCGTGCG 58.450 55.000 0.00 0.00 0.00 5.34
998 1066 1.903294 GGACTGCAGGAGCTCATCA 59.097 57.895 19.93 8.71 42.74 3.07
1001 1069 4.074526 GCGGACTGCAGGAGCTCA 62.075 66.667 19.93 0.00 45.45 4.26
1117 1195 0.114364 TGTGTAGAGACCTCAGCCCA 59.886 55.000 0.00 0.00 0.00 5.36
1255 1333 2.881513 TGTGACGCTATTGGCAGAAAAA 59.118 40.909 0.00 0.00 41.91 1.94
1258 1336 1.001974 ACTGTGACGCTATTGGCAGAA 59.998 47.619 0.00 0.00 41.91 3.02
1259 1337 0.608130 ACTGTGACGCTATTGGCAGA 59.392 50.000 0.00 0.00 41.91 4.26
1260 1338 0.723414 CACTGTGACGCTATTGGCAG 59.277 55.000 0.32 0.00 41.91 4.85
1261 1339 0.034756 ACACTGTGACGCTATTGGCA 59.965 50.000 15.86 0.00 41.91 4.92
1262 1340 0.443869 CACACTGTGACGCTATTGGC 59.556 55.000 15.86 0.00 35.23 4.52
1364 1442 8.701895 TCCTCAACTCACTTTTCTACTTCTTTA 58.298 33.333 0.00 0.00 0.00 1.85
1365 1443 7.565680 TCCTCAACTCACTTTTCTACTTCTTT 58.434 34.615 0.00 0.00 0.00 2.52
1379 1457 4.487714 TCACCCATATTCCTCAACTCAC 57.512 45.455 0.00 0.00 0.00 3.51
1568 1646 2.213499 AGTGCTTGTTTGACTTCCTCG 58.787 47.619 0.00 0.00 0.00 4.63
1614 1692 0.106519 CCTCGGCCCATTTGAATCCT 60.107 55.000 0.00 0.00 0.00 3.24
1683 1833 4.980573 ACTAAGAACACTATGGGTTTGCA 58.019 39.130 0.00 0.00 0.00 4.08
1688 1838 6.958192 TCTTTCCTACTAAGAACACTATGGGT 59.042 38.462 0.00 0.00 0.00 4.51
1690 1840 7.982354 CCTTCTTTCCTACTAAGAACACTATGG 59.018 40.741 0.00 0.00 36.86 2.74
1691 1841 7.982354 CCCTTCTTTCCTACTAAGAACACTATG 59.018 40.741 0.00 0.00 36.86 2.23
1692 1842 7.125963 CCCCTTCTTTCCTACTAAGAACACTAT 59.874 40.741 0.00 0.00 36.86 2.12
1693 1843 6.439692 CCCCTTCTTTCCTACTAAGAACACTA 59.560 42.308 0.00 0.00 36.86 2.74
1694 1844 5.248705 CCCCTTCTTTCCTACTAAGAACACT 59.751 44.000 0.00 0.00 36.86 3.55
1695 1845 5.247792 TCCCCTTCTTTCCTACTAAGAACAC 59.752 44.000 0.00 0.00 36.86 3.32
1696 1846 5.408824 TCCCCTTCTTTCCTACTAAGAACA 58.591 41.667 0.00 0.00 36.86 3.18
1699 1849 5.662597 ACTTCCCCTTCTTTCCTACTAAGA 58.337 41.667 0.00 0.00 0.00 2.10
1704 1854 4.635699 TTGACTTCCCCTTCTTTCCTAC 57.364 45.455 0.00 0.00 0.00 3.18
1725 1875 6.071952 ACCTGACGAGATTGCAAAACATTATT 60.072 34.615 1.71 0.00 0.00 1.40
1737 1911 6.387465 TGAAGTAGTAAACCTGACGAGATTG 58.613 40.000 0.00 0.00 0.00 2.67
1738 1912 6.585695 TGAAGTAGTAAACCTGACGAGATT 57.414 37.500 0.00 0.00 0.00 2.40
1739 1913 6.350277 CCTTGAAGTAGTAAACCTGACGAGAT 60.350 42.308 0.00 0.00 0.00 2.75
1740 1914 5.048224 CCTTGAAGTAGTAAACCTGACGAGA 60.048 44.000 0.00 0.00 0.00 4.04
1741 1915 5.048224 TCCTTGAAGTAGTAAACCTGACGAG 60.048 44.000 0.00 0.00 0.00 4.18
1742 1916 4.828939 TCCTTGAAGTAGTAAACCTGACGA 59.171 41.667 0.00 0.00 0.00 4.20
1743 1917 5.130292 TCCTTGAAGTAGTAAACCTGACG 57.870 43.478 0.00 0.00 0.00 4.35
1744 1918 6.099159 ACTCCTTGAAGTAGTAAACCTGAC 57.901 41.667 0.00 0.00 0.00 3.51
1745 1919 7.844493 TTACTCCTTGAAGTAGTAAACCTGA 57.156 36.000 7.77 0.00 33.84 3.86
1746 1920 7.549488 CCATTACTCCTTGAAGTAGTAAACCTG 59.451 40.741 13.23 8.14 38.72 4.00
1747 1921 7.456902 TCCATTACTCCTTGAAGTAGTAAACCT 59.543 37.037 13.23 0.00 38.72 3.50
1748 1922 7.618137 TCCATTACTCCTTGAAGTAGTAAACC 58.382 38.462 13.23 0.00 38.72 3.27
1749 1923 9.668497 AATCCATTACTCCTTGAAGTAGTAAAC 57.332 33.333 13.23 0.00 38.72 2.01
1757 1931 9.807649 CCATTAAAAATCCATTACTCCTTGAAG 57.192 33.333 0.00 0.00 0.00 3.02
1758 1932 8.257306 GCCATTAAAAATCCATTACTCCTTGAA 58.743 33.333 0.00 0.00 0.00 2.69
1759 1933 7.416213 CGCCATTAAAAATCCATTACTCCTTGA 60.416 37.037 0.00 0.00 0.00 3.02
1784 1958 4.576053 TGTCCATTTCAGGATTGATAAGCG 59.424 41.667 0.00 0.00 40.42 4.68
1795 1969 7.674120 TGATCAGATACTATGTCCATTTCAGG 58.326 38.462 0.00 0.00 0.00 3.86
1834 2009 3.311871 CACCTAGATGTCAAATCAGCAGC 59.688 47.826 0.00 0.00 0.00 5.25
1873 2048 5.775686 TCTTCATGCAATTTCTTTCCACAG 58.224 37.500 0.00 0.00 0.00 3.66
2014 2197 8.432805 CACCTATCCTGTTTGACTTTATCCTAT 58.567 37.037 0.00 0.00 0.00 2.57
2026 2209 4.599047 TTTTTGCCACCTATCCTGTTTG 57.401 40.909 0.00 0.00 0.00 2.93
2175 2537 6.681729 TCTGGATTTCGGCCTATAATACTT 57.318 37.500 0.00 0.00 0.00 2.24
2248 2625 5.129815 CCCCATTTTTCCATCAGATCATTGT 59.870 40.000 0.00 0.00 0.00 2.71
2249 2626 5.364446 TCCCCATTTTTCCATCAGATCATTG 59.636 40.000 0.00 0.00 0.00 2.82
2252 2634 4.606476 TCCCCATTTTTCCATCAGATCA 57.394 40.909 0.00 0.00 0.00 2.92
2313 6630 5.104374 GTGGTGCAATATGGAAATGAAGTG 58.896 41.667 0.00 0.00 0.00 3.16
2457 6836 5.073311 TGGTACAGTGAAGCAGAAGATAC 57.927 43.478 0.00 0.00 0.00 2.24
2513 6892 4.861102 GCAAAGGCTAAATCCATGCTAT 57.139 40.909 0.00 0.00 37.86 2.97
2533 6925 3.330267 CCGAGGCCTATATTCAAGAAGC 58.670 50.000 4.42 0.00 0.00 3.86
2553 6945 6.345096 TCAACTTGAAGATTTGAATTCCCC 57.655 37.500 0.00 0.00 0.00 4.81
2556 6948 8.530269 AATGCTCAACTTGAAGATTTGAATTC 57.470 30.769 0.00 0.00 0.00 2.17
2722 7114 4.167892 ACATAGGCCAAAGGATTCACCATA 59.832 41.667 5.01 0.00 42.04 2.74
2832 7267 8.396390 CAATGACAGGAGAATCAAAATCTGTAG 58.604 37.037 0.00 0.00 33.71 2.74
2889 7324 9.923143 GTACTTATTTCCTTATTGCCAAAAAGT 57.077 29.630 0.00 0.00 0.00 2.66
2922 7364 7.664082 ATGGACATATTTCGAAATGCTAGAG 57.336 36.000 29.20 15.69 0.00 2.43
2923 7365 8.988934 GTAATGGACATATTTCGAAATGCTAGA 58.011 33.333 29.20 12.50 0.00 2.43
3038 7494 4.081972 ACATACAGGTGCAACAACAACAAA 60.082 37.500 3.64 0.00 39.98 2.83
3039 7495 3.445450 ACATACAGGTGCAACAACAACAA 59.555 39.130 3.64 0.00 39.98 2.83
3040 7496 3.020274 ACATACAGGTGCAACAACAACA 58.980 40.909 3.64 0.00 39.98 3.33
3041 7497 3.708563 ACATACAGGTGCAACAACAAC 57.291 42.857 3.64 0.00 39.98 3.32
3046 7502 1.339631 GGGCTACATACAGGTGCAACA 60.340 52.381 3.64 0.00 39.98 3.33
3070 7526 1.917303 GGTGCAACAACAACAAAGTCG 59.083 47.619 0.00 0.00 39.98 4.18
3071 7527 2.923020 CAGGTGCAACAACAACAAAGTC 59.077 45.455 3.64 0.00 39.98 3.01
3072 7528 2.298729 ACAGGTGCAACAACAACAAAGT 59.701 40.909 3.64 0.00 39.98 2.66
3073 7529 2.958213 ACAGGTGCAACAACAACAAAG 58.042 42.857 3.64 0.00 39.98 2.77
3074 7530 4.081972 ACATACAGGTGCAACAACAACAAA 60.082 37.500 3.64 0.00 39.98 2.83
3075 7531 3.445450 ACATACAGGTGCAACAACAACAA 59.555 39.130 3.64 0.00 39.98 2.83
3076 7532 3.020274 ACATACAGGTGCAACAACAACA 58.980 40.909 3.64 0.00 39.98 3.33
3077 7533 3.708563 ACATACAGGTGCAACAACAAC 57.291 42.857 3.64 0.00 39.98 3.32
3078 7534 3.252215 GCTACATACAGGTGCAACAACAA 59.748 43.478 3.64 0.00 39.98 2.83
3079 7535 2.811431 GCTACATACAGGTGCAACAACA 59.189 45.455 3.64 0.00 39.98 3.33
3080 7536 2.161609 GGCTACATACAGGTGCAACAAC 59.838 50.000 3.64 0.00 39.98 3.32
3081 7537 2.432444 GGCTACATACAGGTGCAACAA 58.568 47.619 3.64 0.00 39.98 2.83
3082 7538 1.339631 GGGCTACATACAGGTGCAACA 60.340 52.381 3.64 0.00 39.98 3.33
3083 7539 1.339631 TGGGCTACATACAGGTGCAAC 60.340 52.381 0.00 0.00 0.00 4.17
3084 7540 0.988063 TGGGCTACATACAGGTGCAA 59.012 50.000 0.00 0.00 0.00 4.08
3085 7541 1.212375 ATGGGCTACATACAGGTGCA 58.788 50.000 0.00 0.00 38.26 4.57
3086 7542 2.222027 GAATGGGCTACATACAGGTGC 58.778 52.381 0.00 0.00 39.40 5.01
3087 7543 2.102420 TCGAATGGGCTACATACAGGTG 59.898 50.000 0.00 0.00 39.40 4.00
3088 7544 2.102588 GTCGAATGGGCTACATACAGGT 59.897 50.000 0.00 0.00 39.40 4.00
3089 7545 2.365617 AGTCGAATGGGCTACATACAGG 59.634 50.000 0.00 0.00 39.40 4.00
3090 7546 3.735237 AGTCGAATGGGCTACATACAG 57.265 47.619 0.00 0.00 39.40 2.74
3091 7547 4.188462 CAAAGTCGAATGGGCTACATACA 58.812 43.478 0.00 0.00 39.40 2.29
3092 7548 4.189231 ACAAAGTCGAATGGGCTACATAC 58.811 43.478 0.00 0.00 39.40 2.39
3093 7549 4.481368 ACAAAGTCGAATGGGCTACATA 57.519 40.909 0.00 0.00 39.40 2.29
3094 7550 3.350219 ACAAAGTCGAATGGGCTACAT 57.650 42.857 0.00 0.00 43.07 2.29
3095 7551 2.811431 CAACAAAGTCGAATGGGCTACA 59.189 45.455 0.00 0.00 0.00 2.74
3096 7552 2.812011 ACAACAAAGTCGAATGGGCTAC 59.188 45.455 0.00 0.00 0.00 3.58
3097 7553 3.134574 ACAACAAAGTCGAATGGGCTA 57.865 42.857 0.00 0.00 0.00 3.93
3098 7554 1.981256 ACAACAAAGTCGAATGGGCT 58.019 45.000 0.00 0.00 0.00 5.19
3099 7555 2.393764 CAACAACAAAGTCGAATGGGC 58.606 47.619 0.00 0.00 0.00 5.36
3100 7556 2.621055 TCCAACAACAAAGTCGAATGGG 59.379 45.455 0.00 0.00 0.00 4.00
3101 7557 3.563808 TCTCCAACAACAAAGTCGAATGG 59.436 43.478 0.00 0.00 0.00 3.16
3102 7558 4.811555 TCTCCAACAACAAAGTCGAATG 57.188 40.909 0.00 0.00 0.00 2.67
3103 7559 4.881850 AGTTCTCCAACAACAAAGTCGAAT 59.118 37.500 0.00 0.00 34.60 3.34
3104 7560 4.258543 AGTTCTCCAACAACAAAGTCGAA 58.741 39.130 0.00 0.00 34.60 3.71
3105 7561 3.869065 AGTTCTCCAACAACAAAGTCGA 58.131 40.909 0.00 0.00 34.60 4.20
3106 7562 4.342772 CAAGTTCTCCAACAACAAAGTCG 58.657 43.478 0.00 0.00 34.60 4.18
3217 7844 8.247562 TCAGCAATAAGTTAAACAAACAACAGT 58.752 29.630 0.00 0.00 40.83 3.55
3220 7847 8.401046 TGTCAGCAATAAGTTAAACAAACAAC 57.599 30.769 0.00 0.00 40.83 3.32
3276 7909 0.618458 ACGATAAGAGGCTTGCCCAA 59.382 50.000 8.17 0.00 35.39 4.12
3386 8019 1.081108 GACAGTCTCTCGCAGCGTT 60.081 57.895 15.93 0.00 0.00 4.84
3401 8034 0.751643 TCAGATCCATCGCCTCGACA 60.752 55.000 0.00 0.00 39.18 4.35
3532 8221 9.705290 ACTTCATTTCAGTGTTTTGTTAAACTT 57.295 25.926 0.00 0.00 43.25 2.66
3545 8234 9.166173 TGGATCTGTAATAACTTCATTTCAGTG 57.834 33.333 0.00 0.00 35.77 3.66
3561 8250 4.623932 ACTCTGCACTTTGGATCTGTAA 57.376 40.909 0.00 0.00 0.00 2.41
3569 8258 6.650807 TGAAGTATCTAAACTCTGCACTTTGG 59.349 38.462 0.00 0.00 0.00 3.28
3570 8259 7.360438 GGTGAAGTATCTAAACTCTGCACTTTG 60.360 40.741 0.00 0.00 31.77 2.77
3589 8278 2.241176 TCAGTTCCAAACAGGGTGAAGT 59.759 45.455 0.00 0.00 38.24 3.01
3595 8284 3.555966 AGTCTTTCAGTTCCAAACAGGG 58.444 45.455 0.00 0.00 38.24 4.45
3622 10376 5.708230 AGTGAGTTAGACCAACAACAACAAA 59.292 36.000 0.00 0.00 39.81 2.83
3650 10406 4.736126 AATTTAGCCCCACAATGCTAAC 57.264 40.909 3.62 0.00 46.56 2.34
3664 10421 6.215845 ACATGACAAGTGGTGAAAATTTAGC 58.784 36.000 0.00 0.00 0.00 3.09
3727 10484 5.632347 CCAATCCTTTACGCCGTTACTATAG 59.368 44.000 0.00 0.00 0.00 1.31
3728 10485 5.531634 CCAATCCTTTACGCCGTTACTATA 58.468 41.667 0.00 0.00 0.00 1.31
3736 10493 2.478033 GGGCCAATCCTTTACGCCG 61.478 63.158 4.39 0.00 40.67 6.46
3737 10494 2.478033 CGGGCCAATCCTTTACGCC 61.478 63.158 4.39 0.00 38.96 5.68
3739 10496 0.178533 TACCGGGCCAATCCTTTACG 59.821 55.000 6.32 0.00 34.39 3.18
3752 10509 8.591072 TCTCTCCTTATTTGTATTATTACCGGG 58.409 37.037 6.32 0.00 0.00 5.73
3818 10575 8.691661 TCAAGTGTAAATTAGCCTCTCTTTTT 57.308 30.769 0.00 0.00 0.00 1.94
3819 10576 8.157476 TCTCAAGTGTAAATTAGCCTCTCTTTT 58.843 33.333 0.00 0.00 0.00 2.27
3821 10578 7.246171 TCTCAAGTGTAAATTAGCCTCTCTT 57.754 36.000 0.00 0.00 0.00 2.85
3822 10579 6.127196 CCTCTCAAGTGTAAATTAGCCTCTCT 60.127 42.308 0.00 0.00 0.00 3.10
3824 10581 5.104735 CCCTCTCAAGTGTAAATTAGCCTCT 60.105 44.000 0.00 0.00 0.00 3.69
3825 10582 5.119694 CCCTCTCAAGTGTAAATTAGCCTC 58.880 45.833 0.00 0.00 0.00 4.70
3826 10583 4.536489 ACCCTCTCAAGTGTAAATTAGCCT 59.464 41.667 0.00 0.00 0.00 4.58
3827 10584 4.844884 ACCCTCTCAAGTGTAAATTAGCC 58.155 43.478 0.00 0.00 0.00 3.93
3828 10585 6.819397 AAACCCTCTCAAGTGTAAATTAGC 57.181 37.500 0.00 0.00 0.00 3.09
3843 10600 8.695456 CATAGGCAATATTTTACAAAACCCTCT 58.305 33.333 0.00 0.00 0.00 3.69
3874 12491 1.376466 GTATGGGGCGATGGCTGAT 59.624 57.895 0.00 0.00 39.81 2.90
3908 12525 5.965033 AAGAGAATGTACATCCACATCCT 57.035 39.130 9.23 0.11 38.19 3.24
3909 12526 6.599244 TGAAAAGAGAATGTACATCCACATCC 59.401 38.462 9.23 0.00 38.19 3.51
3910 12527 7.615582 TGAAAAGAGAATGTACATCCACATC 57.384 36.000 9.23 2.48 38.19 3.06
3911 12528 9.334947 CTATGAAAAGAGAATGTACATCCACAT 57.665 33.333 9.23 8.93 40.90 3.21
3913 12530 8.723942 ACTATGAAAAGAGAATGTACATCCAC 57.276 34.615 9.23 4.34 0.00 4.02
3964 12594 5.923204 AGTAAGAGTAGAATGCATTGGAGG 58.077 41.667 18.59 0.00 0.00 4.30
3967 12597 5.233050 CACGAGTAAGAGTAGAATGCATTGG 59.767 44.000 18.59 0.00 0.00 3.16
3989 12619 0.947244 CCCACTTGTTCTCTGTGCAC 59.053 55.000 10.75 10.75 0.00 4.57
3991 12621 0.819259 TGCCCACTTGTTCTCTGTGC 60.819 55.000 0.00 0.00 0.00 4.57
4014 12873 1.870458 CGCATGTGCAATTCGCCAG 60.870 57.895 5.77 0.00 42.21 4.85
4022 12881 0.304401 GATGTATCGCGCATGTGCAA 59.696 50.000 29.19 13.84 42.21 4.08
4034 12893 7.285858 AGGTTAACTGACTGGTCTAGATGTATC 59.714 40.741 5.42 0.00 0.00 2.24
4051 12910 3.429960 GCGGGGTACTAGAAGGTTAACTG 60.430 52.174 5.42 0.00 0.00 3.16
4104 12963 3.976701 CTCCGGTGGCACCATGTCC 62.977 68.421 34.11 8.53 38.47 4.02
4118 12977 1.381872 ATGACCTGGTCCTCCTCCG 60.382 63.158 23.42 0.00 34.23 4.63
4162 13021 2.320339 GATCCCGACTCGTCCGTGAC 62.320 65.000 0.00 0.00 0.00 3.67
4163 13022 2.045634 ATCCCGACTCGTCCGTGA 60.046 61.111 0.00 0.00 0.00 4.35
4226 13085 2.832931 CAGGTCTGCCAGTTTCTCG 58.167 57.895 0.00 0.00 37.19 4.04


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

AutoCloner maintained by Alex Coulton.