Multiple sequence alignment - TraesCS4A01G332300

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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 TraesCS4A01G332300 chr4A 100.000 3470 0 0 1 3470 616619711 616616242 0.000000e+00 6408.0
1 TraesCS4A01G332300 chr4A 78.053 1818 325 45 1012 2797 624452634 624450859 0.000000e+00 1079.0
2 TraesCS4A01G332300 chr4A 77.371 1613 263 56 1339 2932 616791367 616789838 0.000000e+00 863.0
3 TraesCS4A01G332300 chr4A 79.258 1321 203 42 1005 2280 616238391 616237097 0.000000e+00 856.0
4 TraesCS4A01G332300 chr4A 80.714 420 47 17 3039 3457 625544942 625545328 2.620000e-76 296.0
5 TraesCS4A01G332300 chr5D 92.617 1517 64 14 858 2371 551611329 551612800 0.000000e+00 2137.0
6 TraesCS4A01G332300 chr5D 97.736 1104 21 2 2369 3470 551612893 551613994 0.000000e+00 1897.0
7 TraesCS4A01G332300 chr5D 77.637 1811 318 57 980 2746 551119823 551121590 0.000000e+00 1020.0
8 TraesCS4A01G332300 chr5D 76.831 1174 235 29 1009 2162 552422792 552421636 8.180000e-176 627.0
9 TraesCS4A01G332300 chr5D 79.632 869 134 25 1833 2683 552394903 552394060 4.990000e-163 584.0
10 TraesCS4A01G332300 chr5D 73.969 1625 320 69 1012 2592 551447709 551449274 2.340000e-156 562.0
11 TraesCS4A01G332300 chr5D 75.084 1184 209 60 1006 2164 543503711 543502589 1.130000e-129 473.0
12 TraesCS4A01G332300 chr5D 80.619 485 61 17 2914 3380 543463948 543463479 9.220000e-91 344.0
13 TraesCS4A01G332300 chr5D 80.094 427 43 24 3039 3457 543462611 543462219 2.640000e-71 279.0
14 TraesCS4A01G332300 chr5D 89.571 163 12 4 564 724 432310707 432310548 5.870000e-48 202.0
15 TraesCS4A01G332300 chr5D 89.571 163 12 4 564 724 444306811 444306652 5.870000e-48 202.0
16 TraesCS4A01G332300 chr5D 88.957 163 13 4 564 724 6241632 6241473 2.730000e-46 196.0
17 TraesCS4A01G332300 chr5D 88.957 163 13 4 564 724 503325162 503325321 2.730000e-46 196.0
18 TraesCS4A01G332300 chr5D 100.000 34 0 0 1 34 551610553 551610586 2.890000e-06 63.9
19 TraesCS4A01G332300 chr5B 93.092 1158 74 5 1301 2456 699998168 699999321 0.000000e+00 1690.0
20 TraesCS4A01G332300 chr5B 95.306 980 39 5 2494 3469 699999312 700000288 0.000000e+00 1548.0
21 TraesCS4A01G332300 chr5B 81.227 1598 247 28 1006 2581 677812041 677813607 0.000000e+00 1240.0
22 TraesCS4A01G332300 chr5B 78.487 1864 307 56 980 2797 699415078 699416893 0.000000e+00 1134.0
23 TraesCS4A01G332300 chr5B 78.483 1859 310 56 980 2792 703529333 703531147 0.000000e+00 1134.0
24 TraesCS4A01G332300 chr5B 80.293 1365 228 27 1025 2375 703634128 703635465 0.000000e+00 992.0
25 TraesCS4A01G332300 chr5B 79.814 1288 222 27 1005 2280 699260091 699261352 0.000000e+00 904.0
26 TraesCS4A01G332300 chr5B 82.359 1026 140 20 1555 2566 699437466 699438464 0.000000e+00 854.0
27 TraesCS4A01G332300 chr5B 80.697 1005 143 23 2279 3251 699274550 699275535 0.000000e+00 734.0
28 TraesCS4A01G332300 chr5B 74.549 1497 329 35 1030 2506 685499501 685500965 1.070000e-169 606.0
29 TraesCS4A01G332300 chr5B 82.803 692 61 17 2564 3229 699438514 699439173 1.810000e-157 566.0
30 TraesCS4A01G332300 chr5B 75.639 1174 240 33 1014 2164 698256563 698257713 3.050000e-150 542.0
31 TraesCS4A01G332300 chr5B 77.778 576 80 24 2914 3470 685255437 685254891 9.350000e-81 311.0
32 TraesCS4A01G332300 chr5B 79.765 425 47 20 3039 3457 685254092 685253701 4.410000e-69 272.0
33 TraesCS4A01G332300 chr5B 83.333 102 12 5 911 1009 699277626 699277725 4.770000e-14 89.8
34 TraesCS4A01G332300 chr1A 78.712 916 171 18 1007 1910 569698627 569699530 1.070000e-164 590.0
35 TraesCS4A01G332300 chr1A 78.097 904 173 18 1020 1910 569656851 569657742 1.820000e-152 549.0
36 TraesCS4A01G332300 chr4B 89.506 162 12 4 565 724 22277277 22277435 2.110000e-47 200.0
37 TraesCS4A01G332300 chr2A 90.323 155 10 4 572 724 359079088 359079239 7.600000e-47 198.0
38 TraesCS4A01G332300 chr2A 88.957 163 12 5 564 724 588086344 588086502 2.730000e-46 196.0
39 TraesCS4A01G332300 chr7A 88.820 161 17 1 564 724 537844957 537845116 2.730000e-46 196.0
40 TraesCS4A01G332300 chr2D 88.957 163 13 4 564 724 643862245 643862086 2.730000e-46 196.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G332300 chr4A 616616242 616619711 3469 True 6408.000000 6408 100.000000 1 3470 1 chr4A.!!$R2 3469
1 TraesCS4A01G332300 chr4A 624450859 624452634 1775 True 1079.000000 1079 78.053000 1012 2797 1 chr4A.!!$R4 1785
2 TraesCS4A01G332300 chr4A 616789838 616791367 1529 True 863.000000 863 77.371000 1339 2932 1 chr4A.!!$R3 1593
3 TraesCS4A01G332300 chr4A 616237097 616238391 1294 True 856.000000 856 79.258000 1005 2280 1 chr4A.!!$R1 1275
4 TraesCS4A01G332300 chr5D 551610553 551613994 3441 False 1365.966667 2137 96.784333 1 3470 3 chr5D.!!$F4 3469
5 TraesCS4A01G332300 chr5D 551119823 551121590 1767 False 1020.000000 1020 77.637000 980 2746 1 chr5D.!!$F2 1766
6 TraesCS4A01G332300 chr5D 552421636 552422792 1156 True 627.000000 627 76.831000 1009 2162 1 chr5D.!!$R6 1153
7 TraesCS4A01G332300 chr5D 552394060 552394903 843 True 584.000000 584 79.632000 1833 2683 1 chr5D.!!$R5 850
8 TraesCS4A01G332300 chr5D 551447709 551449274 1565 False 562.000000 562 73.969000 1012 2592 1 chr5D.!!$F3 1580
9 TraesCS4A01G332300 chr5D 543502589 543503711 1122 True 473.000000 473 75.084000 1006 2164 1 chr5D.!!$R4 1158
10 TraesCS4A01G332300 chr5D 543462219 543463948 1729 True 311.500000 344 80.356500 2914 3457 2 chr5D.!!$R7 543
11 TraesCS4A01G332300 chr5B 699998168 700000288 2120 False 1619.000000 1690 94.199000 1301 3469 2 chr5B.!!$F10 2168
12 TraesCS4A01G332300 chr5B 677812041 677813607 1566 False 1240.000000 1240 81.227000 1006 2581 1 chr5B.!!$F1 1575
13 TraesCS4A01G332300 chr5B 699415078 699416893 1815 False 1134.000000 1134 78.487000 980 2797 1 chr5B.!!$F5 1817
14 TraesCS4A01G332300 chr5B 703529333 703531147 1814 False 1134.000000 1134 78.483000 980 2792 1 chr5B.!!$F6 1812
15 TraesCS4A01G332300 chr5B 703634128 703635465 1337 False 992.000000 992 80.293000 1025 2375 1 chr5B.!!$F7 1350
16 TraesCS4A01G332300 chr5B 699260091 699261352 1261 False 904.000000 904 79.814000 1005 2280 1 chr5B.!!$F4 1275
17 TraesCS4A01G332300 chr5B 699437466 699439173 1707 False 710.000000 854 82.581000 1555 3229 2 chr5B.!!$F9 1674
18 TraesCS4A01G332300 chr5B 685499501 685500965 1464 False 606.000000 606 74.549000 1030 2506 1 chr5B.!!$F2 1476
19 TraesCS4A01G332300 chr5B 698256563 698257713 1150 False 542.000000 542 75.639000 1014 2164 1 chr5B.!!$F3 1150
20 TraesCS4A01G332300 chr5B 699274550 699277725 3175 False 411.900000 734 82.015000 911 3251 2 chr5B.!!$F8 2340
21 TraesCS4A01G332300 chr5B 685253701 685255437 1736 True 291.500000 311 78.771500 2914 3470 2 chr5B.!!$R1 556
22 TraesCS4A01G332300 chr1A 569698627 569699530 903 False 590.000000 590 78.712000 1007 1910 1 chr1A.!!$F2 903
23 TraesCS4A01G332300 chr1A 569656851 569657742 891 False 549.000000 549 78.097000 1020 1910 1 chr1A.!!$F1 890

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
36 37 0.028770 CTCAGCTAGACGCCTCTTCG 59.971 60.0 0.0 0.0 40.39 3.79 F
49 50 0.035458 CTCTTCGGGGCTGTGTTCTT 59.965 55.0 0.0 0.0 0.00 2.52 F
206 207 0.103208 CCATGTCCTCTAGTCCGCAC 59.897 60.0 0.0 0.0 0.00 5.34 F
735 739 0.112606 TCATACCCACCCCGCAAAAA 59.887 50.0 0.0 0.0 0.00 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1519 1736 0.181587 TTCAGGCCGACAAAGACCAA 59.818 50.000 0.00 0.00 0.0 3.67 R
1639 1906 0.976641 AGATGAAGACCAAGGCACGA 59.023 50.000 0.00 0.00 0.0 4.35 R
2084 2361 0.179034 CCATAGCCTCTTCCACTGCC 60.179 60.000 0.00 0.00 0.0 4.85 R
2509 2929 2.281761 ACCGCCTCCAAGCTTGTG 60.282 61.111 24.35 15.73 0.0 3.33 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
34 35 1.203523 CAACTCAGCTAGACGCCTCTT 59.796 52.381 0.00 0.00 40.39 2.85
35 36 1.099689 ACTCAGCTAGACGCCTCTTC 58.900 55.000 0.00 0.00 40.39 2.87
36 37 0.028770 CTCAGCTAGACGCCTCTTCG 59.971 60.000 0.00 0.00 40.39 3.79
37 38 1.064946 CAGCTAGACGCCTCTTCGG 59.935 63.158 0.00 0.00 40.39 4.30
38 39 2.122167 AGCTAGACGCCTCTTCGGG 61.122 63.158 0.00 0.00 40.39 5.14
45 46 4.021925 GCCTCTTCGGGGCTGTGT 62.022 66.667 0.00 0.00 45.57 3.72
46 47 2.750350 CCTCTTCGGGGCTGTGTT 59.250 61.111 0.00 0.00 0.00 3.32
47 48 1.376037 CCTCTTCGGGGCTGTGTTC 60.376 63.158 0.00 0.00 0.00 3.18
48 49 1.674057 CTCTTCGGGGCTGTGTTCT 59.326 57.895 0.00 0.00 0.00 3.01
49 50 0.035458 CTCTTCGGGGCTGTGTTCTT 59.965 55.000 0.00 0.00 0.00 2.52
50 51 0.250295 TCTTCGGGGCTGTGTTCTTG 60.250 55.000 0.00 0.00 0.00 3.02
51 52 0.535102 CTTCGGGGCTGTGTTCTTGT 60.535 55.000 0.00 0.00 0.00 3.16
52 53 0.106918 TTCGGGGCTGTGTTCTTGTT 60.107 50.000 0.00 0.00 0.00 2.83
53 54 0.534203 TCGGGGCTGTGTTCTTGTTC 60.534 55.000 0.00 0.00 0.00 3.18
54 55 0.817634 CGGGGCTGTGTTCTTGTTCA 60.818 55.000 0.00 0.00 0.00 3.18
55 56 1.620822 GGGGCTGTGTTCTTGTTCAT 58.379 50.000 0.00 0.00 0.00 2.57
56 57 1.270550 GGGGCTGTGTTCTTGTTCATG 59.729 52.381 0.00 0.00 0.00 3.07
57 58 1.270550 GGGCTGTGTTCTTGTTCATGG 59.729 52.381 0.00 0.00 0.00 3.66
58 59 1.270550 GGCTGTGTTCTTGTTCATGGG 59.729 52.381 0.00 0.00 0.00 4.00
59 60 1.956477 GCTGTGTTCTTGTTCATGGGT 59.044 47.619 0.00 0.00 0.00 4.51
60 61 2.362077 GCTGTGTTCTTGTTCATGGGTT 59.638 45.455 0.00 0.00 0.00 4.11
61 62 3.181476 GCTGTGTTCTTGTTCATGGGTTT 60.181 43.478 0.00 0.00 0.00 3.27
62 63 4.362279 CTGTGTTCTTGTTCATGGGTTTG 58.638 43.478 0.00 0.00 0.00 2.93
63 64 3.766591 TGTGTTCTTGTTCATGGGTTTGT 59.233 39.130 0.00 0.00 0.00 2.83
64 65 4.142271 TGTGTTCTTGTTCATGGGTTTGTC 60.142 41.667 0.00 0.00 0.00 3.18
65 66 3.383185 TGTTCTTGTTCATGGGTTTGTCC 59.617 43.478 0.00 0.00 0.00 4.02
66 67 3.593442 TCTTGTTCATGGGTTTGTCCT 57.407 42.857 0.00 0.00 36.25 3.85
67 68 3.909732 TCTTGTTCATGGGTTTGTCCTT 58.090 40.909 0.00 0.00 36.25 3.36
68 69 3.888930 TCTTGTTCATGGGTTTGTCCTTC 59.111 43.478 0.00 0.00 36.25 3.46
69 70 3.304911 TGTTCATGGGTTTGTCCTTCA 57.695 42.857 0.00 0.00 36.25 3.02
70 71 3.636679 TGTTCATGGGTTTGTCCTTCAA 58.363 40.909 0.00 0.00 36.25 2.69
71 72 3.383185 TGTTCATGGGTTTGTCCTTCAAC 59.617 43.478 0.00 0.00 35.61 3.18
72 73 3.593442 TCATGGGTTTGTCCTTCAACT 57.407 42.857 0.00 0.00 35.61 3.16
73 74 3.486383 TCATGGGTTTGTCCTTCAACTC 58.514 45.455 0.00 0.00 35.61 3.01
74 75 3.117701 TCATGGGTTTGTCCTTCAACTCA 60.118 43.478 0.00 0.00 35.61 3.41
75 76 2.930950 TGGGTTTGTCCTTCAACTCAG 58.069 47.619 0.00 0.00 35.61 3.35
76 77 1.609072 GGGTTTGTCCTTCAACTCAGC 59.391 52.381 0.00 0.00 35.61 4.26
77 78 2.576615 GGTTTGTCCTTCAACTCAGCT 58.423 47.619 0.00 0.00 35.61 4.24
78 79 3.496160 GGGTTTGTCCTTCAACTCAGCTA 60.496 47.826 0.00 0.00 35.61 3.32
79 80 3.748568 GGTTTGTCCTTCAACTCAGCTAG 59.251 47.826 0.00 0.00 35.61 3.42
80 81 4.503296 GGTTTGTCCTTCAACTCAGCTAGA 60.503 45.833 0.00 0.00 35.61 2.43
81 82 3.944055 TGTCCTTCAACTCAGCTAGAC 57.056 47.619 0.00 0.00 0.00 2.59
82 83 2.229062 TGTCCTTCAACTCAGCTAGACG 59.771 50.000 0.00 0.00 0.00 4.18
83 84 1.202582 TCCTTCAACTCAGCTAGACGC 59.797 52.381 0.00 0.00 39.57 5.19
84 85 1.634702 CTTCAACTCAGCTAGACGCC 58.365 55.000 0.00 0.00 40.39 5.68
85 86 1.203523 CTTCAACTCAGCTAGACGCCT 59.796 52.381 0.00 0.00 40.39 5.52
86 87 0.811915 TCAACTCAGCTAGACGCCTC 59.188 55.000 0.00 0.00 40.39 4.70
87 88 0.814457 CAACTCAGCTAGACGCCTCT 59.186 55.000 0.00 0.00 40.39 3.69
88 89 1.203523 CAACTCAGCTAGACGCCTCTT 59.796 52.381 0.00 0.00 40.39 2.85
100 101 2.888863 CCTCTTCTCTTCGGCGCT 59.111 61.111 7.64 0.00 0.00 5.92
157 158 2.370445 CCCCTCCCATGCGTCTTCT 61.370 63.158 0.00 0.00 0.00 2.85
171 172 3.082548 CGTCTTCTCCTCTAGGTGAACA 58.917 50.000 8.99 0.00 41.25 3.18
178 179 1.486726 CCTCTAGGTGAACACATCCCC 59.513 57.143 7.25 0.00 0.00 4.81
180 181 2.432510 CTCTAGGTGAACACATCCCCTC 59.567 54.545 7.25 0.00 0.00 4.30
203 204 3.522553 GAAAACCATGTCCTCTAGTCCG 58.477 50.000 0.00 0.00 0.00 4.79
204 205 0.824759 AACCATGTCCTCTAGTCCGC 59.175 55.000 0.00 0.00 0.00 5.54
205 206 0.324368 ACCATGTCCTCTAGTCCGCA 60.324 55.000 0.00 0.00 0.00 5.69
206 207 0.103208 CCATGTCCTCTAGTCCGCAC 59.897 60.000 0.00 0.00 0.00 5.34
207 208 0.817654 CATGTCCTCTAGTCCGCACA 59.182 55.000 0.00 0.00 0.00 4.57
208 209 1.410517 CATGTCCTCTAGTCCGCACAT 59.589 52.381 0.00 0.00 0.00 3.21
209 210 2.430248 TGTCCTCTAGTCCGCACATA 57.570 50.000 0.00 0.00 0.00 2.29
210 211 2.298610 TGTCCTCTAGTCCGCACATAG 58.701 52.381 0.00 0.00 0.00 2.23
211 212 2.092592 TGTCCTCTAGTCCGCACATAGA 60.093 50.000 0.00 0.00 0.00 1.98
212 213 2.950309 GTCCTCTAGTCCGCACATAGAA 59.050 50.000 0.00 0.00 0.00 2.10
213 214 3.380637 GTCCTCTAGTCCGCACATAGAAA 59.619 47.826 0.00 0.00 0.00 2.52
214 215 3.632604 TCCTCTAGTCCGCACATAGAAAG 59.367 47.826 0.00 0.00 0.00 2.62
215 216 3.632604 CCTCTAGTCCGCACATAGAAAGA 59.367 47.826 0.00 0.00 0.00 2.52
222 223 2.679837 CCGCACATAGAAAGAGCATTGT 59.320 45.455 0.00 0.00 0.00 2.71
247 248 1.283029 AGCTTCCACCATACATGTGCT 59.717 47.619 9.11 1.82 0.00 4.40
248 249 2.505407 AGCTTCCACCATACATGTGCTA 59.495 45.455 9.11 0.00 0.00 3.49
262 263 2.694065 TGCTATGGACGAGCATTGC 58.306 52.632 0.00 0.00 44.89 3.56
266 267 1.004610 CTATGGACGAGCATTGCAACG 60.005 52.381 20.51 20.51 36.89 4.10
271 272 0.235665 ACGAGCATTGCAACGACTTG 59.764 50.000 25.98 11.36 35.52 3.16
278 279 3.610114 GCATTGCAACGACTTGTCTCATT 60.610 43.478 0.00 0.00 0.00 2.57
284 285 4.447724 GCAACGACTTGTCTCATTTGAGTA 59.552 41.667 7.42 0.00 42.60 2.59
287 288 5.597806 ACGACTTGTCTCATTTGAGTACAA 58.402 37.500 17.05 17.05 42.60 2.41
293 294 6.951256 TGTCTCATTTGAGTACAAGAATCG 57.049 37.500 7.42 0.00 42.60 3.34
294 295 5.869344 TGTCTCATTTGAGTACAAGAATCGG 59.131 40.000 7.42 0.00 42.60 4.18
295 296 5.292101 GTCTCATTTGAGTACAAGAATCGGG 59.708 44.000 7.42 0.00 42.60 5.14
310 311 0.387929 TCGGGGATCGTTGATGTAGC 59.612 55.000 0.00 0.00 40.32 3.58
313 314 1.603172 GGGGATCGTTGATGTAGCTCG 60.603 57.143 0.00 0.00 0.00 5.03
329 330 1.469251 GCTCGCGAAGATAGTTCCACA 60.469 52.381 11.33 0.00 0.00 4.17
341 342 6.215845 AGATAGTTCCACAACAAATGTTTGC 58.784 36.000 5.44 0.00 41.46 3.68
355 356 4.804868 ATGTTTGCCTTATTGCATCACA 57.195 36.364 0.00 0.00 41.70 3.58
399 402 1.431243 ACCCTCCCAGCTAGATCTAGG 59.569 57.143 27.21 13.98 33.87 3.02
404 407 1.555967 CCAGCTAGATCTAGGCTCCC 58.444 60.000 27.21 12.76 33.87 4.30
421 424 2.911636 CTCCCCATAGAAGCTCATGGAT 59.088 50.000 18.80 0.00 43.80 3.41
437 440 1.774254 TGGATCACCAGTTCACCACTT 59.226 47.619 0.00 0.00 41.77 3.16
438 441 2.154462 GGATCACCAGTTCACCACTTG 58.846 52.381 0.00 0.00 30.92 3.16
439 442 2.154462 GATCACCAGTTCACCACTTGG 58.846 52.381 0.00 0.00 42.17 3.61
440 443 5.643560 GGATCACCAGTTCACCACTTGGT 62.644 52.174 0.00 0.00 42.06 3.67
475 478 9.525826 AGACAATTACATCCAAGAAATTCTTCT 57.474 29.630 5.09 0.00 44.11 2.85
488 491 5.415701 AGAAATTCTTCTTTGCGCCATCTAA 59.584 36.000 4.18 0.00 38.89 2.10
498 501 8.896320 TCTTTGCGCCATCTAATTTTATACTA 57.104 30.769 4.18 0.00 0.00 1.82
499 502 8.770828 TCTTTGCGCCATCTAATTTTATACTAC 58.229 33.333 4.18 0.00 0.00 2.73
501 504 8.615878 TTGCGCCATCTAATTTTATACTACAT 57.384 30.769 4.18 0.00 0.00 2.29
528 532 9.855021 ATGCTTTATTTATTTTAAGAACACGCT 57.145 25.926 0.00 0.00 0.00 5.07
567 571 6.715344 TTTAGTATTAGCACAACAGTTCCG 57.285 37.500 0.00 0.00 0.00 4.30
568 572 3.000727 AGTATTAGCACAACAGTTCCGC 58.999 45.455 0.00 0.00 0.00 5.54
569 573 0.796312 ATTAGCACAACAGTTCCGCG 59.204 50.000 0.00 0.00 0.00 6.46
570 574 0.531090 TTAGCACAACAGTTCCGCGT 60.531 50.000 4.92 0.00 0.00 6.01
571 575 0.314618 TAGCACAACAGTTCCGCGTA 59.685 50.000 4.92 0.00 0.00 4.42
572 576 0.944311 AGCACAACAGTTCCGCGTAG 60.944 55.000 4.92 0.00 0.00 3.51
592 596 6.487103 CGTAGCTCAAAATTGTATCCTTTCC 58.513 40.000 0.00 0.00 0.00 3.13
593 597 5.921962 AGCTCAAAATTGTATCCTTTCCC 57.078 39.130 0.00 0.00 0.00 3.97
595 599 6.019108 AGCTCAAAATTGTATCCTTTCCCTT 58.981 36.000 0.00 0.00 0.00 3.95
596 600 6.153510 AGCTCAAAATTGTATCCTTTCCCTTC 59.846 38.462 0.00 0.00 0.00 3.46
598 602 7.466746 TCAAAATTGTATCCTTTCCCTTCTG 57.533 36.000 0.00 0.00 0.00 3.02
599 603 5.921962 AAATTGTATCCTTTCCCTTCTGC 57.078 39.130 0.00 0.00 0.00 4.26
603 607 2.521547 ATCCTTTCCCTTCTGCTTGG 57.478 50.000 0.00 0.00 0.00 3.61
604 608 1.444933 TCCTTTCCCTTCTGCTTGGA 58.555 50.000 0.00 0.00 0.00 3.53
605 609 1.073923 TCCTTTCCCTTCTGCTTGGAC 59.926 52.381 0.00 0.00 0.00 4.02
607 611 1.882623 CTTTCCCTTCTGCTTGGACAC 59.117 52.381 0.00 0.00 0.00 3.67
608 612 0.250295 TTCCCTTCTGCTTGGACACG 60.250 55.000 0.00 0.00 0.00 4.49
611 615 1.151668 CCTTCTGCTTGGACACGAAG 58.848 55.000 0.00 0.00 0.00 3.79
612 616 1.270305 CCTTCTGCTTGGACACGAAGA 60.270 52.381 0.00 0.00 34.50 2.87
613 617 2.064762 CTTCTGCTTGGACACGAAGAG 58.935 52.381 0.00 0.00 34.50 2.85
615 619 1.895798 TCTGCTTGGACACGAAGAGAT 59.104 47.619 0.00 0.00 0.00 2.75
617 621 3.119459 TCTGCTTGGACACGAAGAGATAC 60.119 47.826 0.00 0.00 0.00 2.24
618 622 2.560981 TGCTTGGACACGAAGAGATACA 59.439 45.455 0.00 0.00 0.00 2.29
619 623 3.195610 TGCTTGGACACGAAGAGATACAT 59.804 43.478 0.00 0.00 0.00 2.29
620 624 4.401202 TGCTTGGACACGAAGAGATACATA 59.599 41.667 0.00 0.00 0.00 2.29
621 625 5.105513 TGCTTGGACACGAAGAGATACATAA 60.106 40.000 0.00 0.00 0.00 1.90
622 626 5.986135 GCTTGGACACGAAGAGATACATAAT 59.014 40.000 0.00 0.00 0.00 1.28
623 627 7.145985 GCTTGGACACGAAGAGATACATAATA 58.854 38.462 0.00 0.00 0.00 0.98
624 628 7.115095 GCTTGGACACGAAGAGATACATAATAC 59.885 40.741 0.00 0.00 0.00 1.89
625 629 7.818997 TGGACACGAAGAGATACATAATACT 57.181 36.000 0.00 0.00 0.00 2.12
626 630 8.234136 TGGACACGAAGAGATACATAATACTT 57.766 34.615 0.00 0.00 0.00 2.24
627 631 8.135529 TGGACACGAAGAGATACATAATACTTG 58.864 37.037 0.00 0.00 0.00 3.16
628 632 8.350722 GGACACGAAGAGATACATAATACTTGA 58.649 37.037 0.00 0.00 0.00 3.02
629 633 9.171701 GACACGAAGAGATACATAATACTTGAC 57.828 37.037 0.00 0.00 0.00 3.18
630 634 8.904834 ACACGAAGAGATACATAATACTTGACT 58.095 33.333 0.00 0.00 0.00 3.41
646 650 9.533831 AATACTTGACTAAAACTGGATTCCATT 57.466 29.630 5.70 0.00 30.82 3.16
647 651 7.454260 ACTTGACTAAAACTGGATTCCATTC 57.546 36.000 5.70 0.00 30.82 2.67
648 652 7.234355 ACTTGACTAAAACTGGATTCCATTCT 58.766 34.615 5.70 0.00 30.82 2.40
649 653 8.383175 ACTTGACTAAAACTGGATTCCATTCTA 58.617 33.333 5.70 0.00 30.82 2.10
650 654 8.561738 TTGACTAAAACTGGATTCCATTCTAC 57.438 34.615 5.70 0.00 30.82 2.59
651 655 7.918076 TGACTAAAACTGGATTCCATTCTACT 58.082 34.615 5.70 0.00 30.82 2.57
652 656 8.383175 TGACTAAAACTGGATTCCATTCTACTT 58.617 33.333 5.70 0.00 30.82 2.24
653 657 9.232473 GACTAAAACTGGATTCCATTCTACTTT 57.768 33.333 5.70 1.30 30.82 2.66
654 658 9.232473 ACTAAAACTGGATTCCATTCTACTTTC 57.768 33.333 5.70 0.00 30.82 2.62
655 659 7.468141 AAAACTGGATTCCATTCTACTTTCC 57.532 36.000 5.70 0.00 30.82 3.13
656 660 6.394345 AACTGGATTCCATTCTACTTTCCT 57.606 37.500 5.70 0.00 30.82 3.36
657 661 7.510675 AACTGGATTCCATTCTACTTTCCTA 57.489 36.000 5.70 0.00 30.82 2.94
658 662 6.890293 ACTGGATTCCATTCTACTTTCCTAC 58.110 40.000 5.70 0.00 30.82 3.18
659 663 6.674419 ACTGGATTCCATTCTACTTTCCTACT 59.326 38.462 5.70 0.00 30.82 2.57
660 664 7.182930 ACTGGATTCCATTCTACTTTCCTACTT 59.817 37.037 5.70 0.00 30.82 2.24
661 665 7.565680 TGGATTCCATTCTACTTTCCTACTTC 58.434 38.462 0.00 0.00 0.00 3.01
662 666 7.403231 TGGATTCCATTCTACTTTCCTACTTCT 59.597 37.037 0.00 0.00 0.00 2.85
663 667 7.713073 GGATTCCATTCTACTTTCCTACTTCTG 59.287 40.741 0.00 0.00 0.00 3.02
664 668 7.792364 TTCCATTCTACTTTCCTACTTCTGA 57.208 36.000 0.00 0.00 0.00 3.27
665 669 7.792364 TCCATTCTACTTTCCTACTTCTGAA 57.208 36.000 0.00 0.00 0.00 3.02
666 670 7.612677 TCCATTCTACTTTCCTACTTCTGAAC 58.387 38.462 0.00 0.00 0.00 3.18
667 671 7.234782 TCCATTCTACTTTCCTACTTCTGAACA 59.765 37.037 0.00 0.00 0.00 3.18
668 672 7.878127 CCATTCTACTTTCCTACTTCTGAACAA 59.122 37.037 0.00 0.00 0.00 2.83
669 673 8.713271 CATTCTACTTTCCTACTTCTGAACAAC 58.287 37.037 0.00 0.00 0.00 3.32
670 674 7.356089 TCTACTTTCCTACTTCTGAACAACA 57.644 36.000 0.00 0.00 0.00 3.33
671 675 7.788026 TCTACTTTCCTACTTCTGAACAACAA 58.212 34.615 0.00 0.00 0.00 2.83
672 676 6.679327 ACTTTCCTACTTCTGAACAACAAC 57.321 37.500 0.00 0.00 0.00 3.32
673 677 6.415573 ACTTTCCTACTTCTGAACAACAACT 58.584 36.000 0.00 0.00 0.00 3.16
674 678 6.884836 ACTTTCCTACTTCTGAACAACAACTT 59.115 34.615 0.00 0.00 0.00 2.66
675 679 8.044908 ACTTTCCTACTTCTGAACAACAACTTA 58.955 33.333 0.00 0.00 0.00 2.24
676 680 8.974060 TTTCCTACTTCTGAACAACAACTTAT 57.026 30.769 0.00 0.00 0.00 1.73
677 681 7.962964 TCCTACTTCTGAACAACAACTTATG 57.037 36.000 0.00 0.00 0.00 1.90
678 682 7.506114 TCCTACTTCTGAACAACAACTTATGT 58.494 34.615 0.00 0.00 46.82 2.29
714 718 9.606631 TTTGGTTTTAGCAAAGTTATCAATTGT 57.393 25.926 5.13 0.00 40.22 2.71
715 719 8.810652 TGGTTTTAGCAAAGTTATCAATTGTC 57.189 30.769 5.13 0.00 0.00 3.18
716 720 8.637986 TGGTTTTAGCAAAGTTATCAATTGTCT 58.362 29.630 5.13 0.00 0.00 3.41
717 721 9.129209 GGTTTTAGCAAAGTTATCAATTGTCTC 57.871 33.333 5.13 0.00 0.00 3.36
718 722 9.677567 GTTTTAGCAAAGTTATCAATTGTCTCA 57.322 29.630 5.13 0.00 0.00 3.27
722 726 7.989826 AGCAAAGTTATCAATTGTCTCATACC 58.010 34.615 5.13 0.00 0.00 2.73
723 727 7.067494 AGCAAAGTTATCAATTGTCTCATACCC 59.933 37.037 5.13 0.00 0.00 3.69
724 728 7.148086 GCAAAGTTATCAATTGTCTCATACCCA 60.148 37.037 5.13 0.00 0.00 4.51
725 729 7.865706 AAGTTATCAATTGTCTCATACCCAC 57.134 36.000 5.13 0.00 0.00 4.61
726 730 6.357367 AGTTATCAATTGTCTCATACCCACC 58.643 40.000 5.13 0.00 0.00 4.61
727 731 3.644966 TCAATTGTCTCATACCCACCC 57.355 47.619 5.13 0.00 0.00 4.61
728 732 2.241176 TCAATTGTCTCATACCCACCCC 59.759 50.000 5.13 0.00 0.00 4.95
729 733 0.837272 ATTGTCTCATACCCACCCCG 59.163 55.000 0.00 0.00 0.00 5.73
730 734 1.906105 TTGTCTCATACCCACCCCGC 61.906 60.000 0.00 0.00 0.00 6.13
731 735 2.039787 TCTCATACCCACCCCGCA 59.960 61.111 0.00 0.00 0.00 5.69
732 736 1.613928 TCTCATACCCACCCCGCAA 60.614 57.895 0.00 0.00 0.00 4.85
733 737 1.202099 TCTCATACCCACCCCGCAAA 61.202 55.000 0.00 0.00 0.00 3.68
734 738 0.322997 CTCATACCCACCCCGCAAAA 60.323 55.000 0.00 0.00 0.00 2.44
735 739 0.112606 TCATACCCACCCCGCAAAAA 59.887 50.000 0.00 0.00 0.00 1.94
765 769 9.753674 AATTTGTCTCATACCCTATTTTCTTGA 57.246 29.630 0.00 0.00 0.00 3.02
766 770 9.927081 ATTTGTCTCATACCCTATTTTCTTGAT 57.073 29.630 0.00 0.00 0.00 2.57
767 771 9.753674 TTTGTCTCATACCCTATTTTCTTGATT 57.246 29.630 0.00 0.00 0.00 2.57
768 772 9.753674 TTGTCTCATACCCTATTTTCTTGATTT 57.246 29.630 0.00 0.00 0.00 2.17
831 835 5.186198 AGTACAAGAAATCGGAATCCCAAG 58.814 41.667 0.00 0.00 0.00 3.61
833 837 4.010349 ACAAGAAATCGGAATCCCAAGTC 58.990 43.478 0.00 0.00 0.00 3.01
836 840 1.295020 AATCGGAATCCCAAGTCCCA 58.705 50.000 0.00 0.00 36.24 4.37
837 841 1.295020 ATCGGAATCCCAAGTCCCAA 58.705 50.000 0.00 0.00 36.24 4.12
838 842 0.326927 TCGGAATCCCAAGTCCCAAC 59.673 55.000 0.00 0.00 36.24 3.77
839 843 0.328258 CGGAATCCCAAGTCCCAACT 59.672 55.000 0.00 0.00 36.24 3.16
841 845 2.679930 CGGAATCCCAAGTCCCAACTAC 60.680 54.545 0.00 0.00 36.24 2.73
842 846 2.356844 GGAATCCCAAGTCCCAACTACC 60.357 54.545 0.00 0.00 33.40 3.18
843 847 1.296002 ATCCCAAGTCCCAACTACCC 58.704 55.000 0.00 0.00 33.48 3.69
844 848 0.843343 TCCCAAGTCCCAACTACCCC 60.843 60.000 0.00 0.00 33.48 4.95
845 849 0.845102 CCCAAGTCCCAACTACCCCT 60.845 60.000 0.00 0.00 33.48 4.79
879 1058 2.892425 GAATCCCGTGAGCAGCCG 60.892 66.667 0.00 0.00 0.00 5.52
899 1078 3.699894 CCCACTCTCGCTGCCAGT 61.700 66.667 0.00 0.00 0.00 4.00
900 1079 2.125753 CCACTCTCGCTGCCAGTC 60.126 66.667 0.00 0.00 0.00 3.51
901 1080 2.125753 CACTCTCGCTGCCAGTCC 60.126 66.667 0.00 0.00 0.00 3.85
902 1081 3.386237 ACTCTCGCTGCCAGTCCC 61.386 66.667 0.00 0.00 0.00 4.46
903 1082 4.504916 CTCTCGCTGCCAGTCCCG 62.505 72.222 0.00 0.00 0.00 5.14
920 1099 2.908015 GCTCCGGCCCACATAAGA 59.092 61.111 0.00 0.00 0.00 2.10
928 1107 1.408822 GGCCCACATAAGACAGGGAAG 60.409 57.143 0.00 0.00 44.30 3.46
944 1123 1.536662 AAGGAAGGCCACGTCTCCT 60.537 57.895 5.01 4.96 36.29 3.69
950 1129 2.126031 GCCACGTCTCCTTCGTCC 60.126 66.667 0.00 0.00 39.55 4.79
958 1137 2.757099 TCCTTCGTCCCCGCCTAC 60.757 66.667 0.00 0.00 0.00 3.18
974 1153 2.032290 GCCTACGCGTCAAACTTTTCTT 60.032 45.455 18.63 0.00 0.00 2.52
1258 1455 2.237965 CCCATCCCCCACTTCACCA 61.238 63.158 0.00 0.00 0.00 4.17
1319 1531 1.370064 GGGTGCACCTGAACTACGT 59.630 57.895 33.91 0.00 35.85 3.57
1639 1906 0.620556 ATTTGATCAGTGGGGCGAGT 59.379 50.000 0.00 0.00 0.00 4.18
2084 2361 3.986128 ACGAAATTAATGTCAAGTCGCG 58.014 40.909 0.00 0.00 0.00 5.87
2108 2385 3.198635 CAGTGGAAGAGGCTATGGAAGAA 59.801 47.826 0.00 0.00 0.00 2.52
2423 2834 7.701924 CACCGACAAATATATGTTTGCAGAAAT 59.298 33.333 20.96 4.44 41.61 2.17
2509 2929 5.163774 GCCACTCTCATCAACAAGAAAGATC 60.164 44.000 0.00 0.00 0.00 2.75
2857 3371 6.382869 ACCTTTGAACTTTCATGAGTTGAG 57.617 37.500 5.16 1.39 39.84 3.02
2944 3462 3.391506 TCATGTTGTCTCACTCACTGG 57.608 47.619 0.00 0.00 0.00 4.00
3006 3528 3.407424 AGCAGAGCAATGTTACTGACA 57.593 42.857 0.00 0.00 43.71 3.58
3171 3711 6.782082 TTTTTGGCCTACAATGCATATACA 57.218 33.333 3.32 0.00 39.21 2.29
3290 3830 3.569250 AATTCCCGGTTTGATTTCACG 57.431 42.857 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 0.534203 GAACAAGAACACAGCCCCGA 60.534 55.000 0.00 0.00 0.00 5.14
35 36 0.817634 TGAACAAGAACACAGCCCCG 60.818 55.000 0.00 0.00 0.00 5.73
36 37 1.270550 CATGAACAAGAACACAGCCCC 59.729 52.381 0.00 0.00 0.00 5.80
37 38 1.270550 CCATGAACAAGAACACAGCCC 59.729 52.381 0.00 0.00 0.00 5.19
38 39 1.270550 CCCATGAACAAGAACACAGCC 59.729 52.381 0.00 0.00 0.00 4.85
39 40 1.956477 ACCCATGAACAAGAACACAGC 59.044 47.619 0.00 0.00 0.00 4.40
40 41 4.142182 ACAAACCCATGAACAAGAACACAG 60.142 41.667 0.00 0.00 0.00 3.66
41 42 3.766591 ACAAACCCATGAACAAGAACACA 59.233 39.130 0.00 0.00 0.00 3.72
42 43 4.359706 GACAAACCCATGAACAAGAACAC 58.640 43.478 0.00 0.00 0.00 3.32
43 44 3.383185 GGACAAACCCATGAACAAGAACA 59.617 43.478 0.00 0.00 0.00 3.18
44 45 3.636764 AGGACAAACCCATGAACAAGAAC 59.363 43.478 0.00 0.00 40.05 3.01
45 46 3.909732 AGGACAAACCCATGAACAAGAA 58.090 40.909 0.00 0.00 40.05 2.52
46 47 3.593442 AGGACAAACCCATGAACAAGA 57.407 42.857 0.00 0.00 40.05 3.02
47 48 3.636300 TGAAGGACAAACCCATGAACAAG 59.364 43.478 0.00 0.00 40.05 3.16
48 49 3.636679 TGAAGGACAAACCCATGAACAA 58.363 40.909 0.00 0.00 40.05 2.83
49 50 3.304911 TGAAGGACAAACCCATGAACA 57.695 42.857 0.00 0.00 40.05 3.18
50 51 3.636764 AGTTGAAGGACAAACCCATGAAC 59.363 43.478 0.00 0.00 40.36 3.18
51 52 3.888930 GAGTTGAAGGACAAACCCATGAA 59.111 43.478 0.00 0.00 40.36 2.57
52 53 3.117701 TGAGTTGAAGGACAAACCCATGA 60.118 43.478 0.00 0.00 40.36 3.07
53 54 3.221771 TGAGTTGAAGGACAAACCCATG 58.778 45.455 0.00 0.00 40.36 3.66
54 55 3.490348 CTGAGTTGAAGGACAAACCCAT 58.510 45.455 0.00 0.00 40.36 4.00
55 56 2.930950 CTGAGTTGAAGGACAAACCCA 58.069 47.619 0.00 0.00 40.36 4.51
56 57 1.609072 GCTGAGTTGAAGGACAAACCC 59.391 52.381 0.00 0.00 40.36 4.11
57 58 2.576615 AGCTGAGTTGAAGGACAAACC 58.423 47.619 0.00 0.00 40.36 3.27
58 59 4.449405 GTCTAGCTGAGTTGAAGGACAAAC 59.551 45.833 0.00 0.00 40.36 2.93
59 60 4.632153 GTCTAGCTGAGTTGAAGGACAAA 58.368 43.478 0.00 0.00 40.36 2.83
60 61 3.305403 CGTCTAGCTGAGTTGAAGGACAA 60.305 47.826 0.00 0.00 36.02 3.18
61 62 2.229062 CGTCTAGCTGAGTTGAAGGACA 59.771 50.000 0.00 0.00 0.00 4.02
62 63 2.869897 CGTCTAGCTGAGTTGAAGGAC 58.130 52.381 0.00 0.00 0.00 3.85
63 64 1.202582 GCGTCTAGCTGAGTTGAAGGA 59.797 52.381 0.00 0.00 44.04 3.36
64 65 1.634702 GCGTCTAGCTGAGTTGAAGG 58.365 55.000 0.00 0.00 44.04 3.46
76 77 1.332375 CCGAAGAGAAGAGGCGTCTAG 59.668 57.143 9.76 0.00 30.45 2.43
77 78 1.380524 CCGAAGAGAAGAGGCGTCTA 58.619 55.000 9.76 0.00 30.45 2.59
78 79 1.939769 GCCGAAGAGAAGAGGCGTCT 61.940 60.000 2.32 2.32 40.17 4.18
79 80 1.517475 GCCGAAGAGAAGAGGCGTC 60.517 63.158 0.00 0.00 40.17 5.19
80 81 2.574399 GCCGAAGAGAAGAGGCGT 59.426 61.111 0.00 0.00 40.17 5.68
82 83 2.844072 AAGCGCCGAAGAGAAGAGGC 62.844 60.000 2.29 0.00 45.67 4.70
83 84 0.804156 GAAGCGCCGAAGAGAAGAGG 60.804 60.000 2.29 0.00 0.00 3.69
84 85 0.804156 GGAAGCGCCGAAGAGAAGAG 60.804 60.000 2.29 0.00 0.00 2.85
85 86 1.215647 GGAAGCGCCGAAGAGAAGA 59.784 57.895 2.29 0.00 0.00 2.87
86 87 1.811679 GGGAAGCGCCGAAGAGAAG 60.812 63.158 2.29 0.00 37.63 2.85
87 88 2.107041 TTGGGAAGCGCCGAAGAGAA 62.107 55.000 2.29 0.00 37.63 2.87
88 89 2.579657 TTGGGAAGCGCCGAAGAGA 61.580 57.895 2.29 0.00 37.63 3.10
100 101 3.961414 GCCCTCCACCGTTGGGAA 61.961 66.667 0.00 0.00 44.11 3.97
137 138 2.595009 GAAGACGCATGGGAGGGGAC 62.595 65.000 17.76 0.00 0.00 4.46
139 140 2.190578 GAAGACGCATGGGAGGGG 59.809 66.667 17.76 0.00 0.00 4.79
157 158 2.467880 GGGATGTGTTCACCTAGAGGA 58.532 52.381 1.60 0.00 38.94 3.71
171 172 0.999712 ATGGTTTTCCGAGGGGATGT 59.000 50.000 0.00 0.00 43.41 3.06
178 179 2.770164 AGAGGACATGGTTTTCCGAG 57.230 50.000 0.00 0.00 44.36 4.63
180 181 3.522553 GACTAGAGGACATGGTTTTCCG 58.477 50.000 0.00 0.00 44.36 4.30
203 204 3.691118 TCCACAATGCTCTTTCTATGTGC 59.309 43.478 0.00 0.00 37.44 4.57
204 205 5.885230 TTCCACAATGCTCTTTCTATGTG 57.115 39.130 0.00 0.00 38.25 3.21
205 206 5.105997 GCTTTCCACAATGCTCTTTCTATGT 60.106 40.000 0.00 0.00 31.39 2.29
206 207 5.125097 AGCTTTCCACAATGCTCTTTCTATG 59.875 40.000 0.00 0.00 38.34 2.23
207 208 5.259632 AGCTTTCCACAATGCTCTTTCTAT 58.740 37.500 0.00 0.00 38.34 1.98
208 209 4.655963 AGCTTTCCACAATGCTCTTTCTA 58.344 39.130 0.00 0.00 38.34 2.10
209 210 3.494332 AGCTTTCCACAATGCTCTTTCT 58.506 40.909 0.00 0.00 38.34 2.52
210 211 3.930634 AGCTTTCCACAATGCTCTTTC 57.069 42.857 0.00 0.00 38.34 2.62
211 212 4.248691 GAAGCTTTCCACAATGCTCTTT 57.751 40.909 0.00 0.00 41.09 2.52
212 213 3.930634 GAAGCTTTCCACAATGCTCTT 57.069 42.857 0.00 0.00 41.09 2.85
240 241 3.367678 TGCTCGTCCATAGCACATG 57.632 52.632 0.00 0.00 44.78 3.21
247 248 1.006086 CGTTGCAATGCTCGTCCATA 58.994 50.000 6.82 0.00 0.00 2.74
248 249 0.673333 TCGTTGCAATGCTCGTCCAT 60.673 50.000 14.04 0.00 0.00 3.41
262 263 5.462068 TGTACTCAAATGAGACAAGTCGTTG 59.538 40.000 16.93 0.00 44.74 4.10
266 267 7.715265 TTCTTGTACTCAAATGAGACAAGTC 57.285 36.000 29.44 13.89 46.19 3.01
271 272 5.292101 CCCGATTCTTGTACTCAAATGAGAC 59.708 44.000 16.93 10.66 44.74 3.36
278 279 3.181479 CGATCCCCGATTCTTGTACTCAA 60.181 47.826 0.00 0.00 41.76 3.02
284 285 1.553248 TCAACGATCCCCGATTCTTGT 59.447 47.619 0.00 0.00 41.76 3.16
287 288 1.762957 ACATCAACGATCCCCGATTCT 59.237 47.619 0.00 0.00 41.76 2.40
288 289 2.240493 ACATCAACGATCCCCGATTC 57.760 50.000 0.00 0.00 41.76 2.52
290 291 1.000955 GCTACATCAACGATCCCCGAT 59.999 52.381 0.00 0.00 41.76 4.18
291 292 0.387929 GCTACATCAACGATCCCCGA 59.612 55.000 0.00 0.00 41.76 5.14
292 293 0.389391 AGCTACATCAACGATCCCCG 59.611 55.000 0.00 0.00 45.44 5.73
293 294 1.603172 CGAGCTACATCAACGATCCCC 60.603 57.143 0.00 0.00 0.00 4.81
294 295 1.772182 CGAGCTACATCAACGATCCC 58.228 55.000 0.00 0.00 0.00 3.85
295 296 1.132588 GCGAGCTACATCAACGATCC 58.867 55.000 0.00 0.00 0.00 3.36
310 311 2.561733 TGTGGAACTATCTTCGCGAG 57.438 50.000 9.59 3.89 38.04 5.03
313 314 4.742438 TTTGTTGTGGAACTATCTTCGC 57.258 40.909 0.00 0.00 38.04 4.70
369 372 4.184649 AGCTGGGAGGGTAAATATTTGG 57.815 45.455 11.05 0.00 0.00 3.28
375 378 4.220861 AGATCTAGCTGGGAGGGTAAAT 57.779 45.455 0.00 0.00 0.00 1.40
399 402 1.271271 CCATGAGCTTCTATGGGGAGC 60.271 57.143 14.50 0.00 40.11 4.70
404 407 3.072038 TGGTGATCCATGAGCTTCTATGG 59.928 47.826 15.63 15.63 44.15 2.74
421 424 3.798794 CCAAGTGGTGAACTGGTGA 57.201 52.632 0.00 0.00 39.81 4.02
432 435 2.036733 TGTCTAGGAACGAACCAAGTGG 59.963 50.000 0.00 0.00 42.17 4.00
434 437 4.618920 ATTGTCTAGGAACGAACCAAGT 57.381 40.909 0.00 0.00 0.00 3.16
437 440 5.471556 TGTAATTGTCTAGGAACGAACCA 57.528 39.130 0.00 0.00 0.00 3.67
438 441 5.522824 GGATGTAATTGTCTAGGAACGAACC 59.477 44.000 0.00 0.00 0.00 3.62
439 442 6.103997 TGGATGTAATTGTCTAGGAACGAAC 58.896 40.000 0.00 0.00 0.00 3.95
440 443 6.288941 TGGATGTAATTGTCTAGGAACGAA 57.711 37.500 0.00 0.00 0.00 3.85
441 444 5.925506 TGGATGTAATTGTCTAGGAACGA 57.074 39.130 0.00 0.00 0.00 3.85
442 445 6.338146 TCTTGGATGTAATTGTCTAGGAACG 58.662 40.000 0.00 0.00 0.00 3.95
443 446 8.561738 TTTCTTGGATGTAATTGTCTAGGAAC 57.438 34.615 0.00 0.00 0.00 3.62
444 447 9.753674 AATTTCTTGGATGTAATTGTCTAGGAA 57.246 29.630 0.00 0.00 0.00 3.36
445 448 9.396022 GAATTTCTTGGATGTAATTGTCTAGGA 57.604 33.333 0.00 0.00 0.00 2.94
446 449 9.401058 AGAATTTCTTGGATGTAATTGTCTAGG 57.599 33.333 0.00 0.00 0.00 3.02
449 452 9.525826 AGAAGAATTTCTTGGATGTAATTGTCT 57.474 29.630 16.17 0.12 40.79 3.41
475 478 8.439993 TGTAGTATAAAATTAGATGGCGCAAA 57.560 30.769 10.83 0.00 0.00 3.68
546 550 4.178540 GCGGAACTGTTGTGCTAATACTA 58.821 43.478 0.00 0.00 0.00 1.82
564 568 1.803334 ACAATTTTGAGCTACGCGGA 58.197 45.000 12.47 0.00 0.00 5.54
565 569 3.303132 GGATACAATTTTGAGCTACGCGG 60.303 47.826 12.47 0.00 0.00 6.46
566 570 3.555956 AGGATACAATTTTGAGCTACGCG 59.444 43.478 3.53 3.53 41.41 6.01
567 571 5.485662 AAGGATACAATTTTGAGCTACGC 57.514 39.130 0.00 0.00 41.41 4.42
568 572 6.458342 GGGAAAGGATACAATTTTGAGCTACG 60.458 42.308 0.00 0.00 41.41 3.51
569 573 6.603599 AGGGAAAGGATACAATTTTGAGCTAC 59.396 38.462 0.00 0.00 41.41 3.58
570 574 6.731467 AGGGAAAGGATACAATTTTGAGCTA 58.269 36.000 0.00 0.00 41.41 3.32
571 575 5.583932 AGGGAAAGGATACAATTTTGAGCT 58.416 37.500 0.00 0.00 41.41 4.09
572 576 5.921962 AGGGAAAGGATACAATTTTGAGC 57.078 39.130 0.00 0.00 41.41 4.26
573 577 7.542025 CAGAAGGGAAAGGATACAATTTTGAG 58.458 38.462 0.00 0.00 41.41 3.02
575 579 6.071165 AGCAGAAGGGAAAGGATACAATTTTG 60.071 38.462 0.00 0.00 41.41 2.44
577 581 5.583932 AGCAGAAGGGAAAGGATACAATTT 58.416 37.500 0.00 0.00 41.41 1.82
578 582 5.198602 AGCAGAAGGGAAAGGATACAATT 57.801 39.130 0.00 0.00 41.41 2.32
579 583 4.870021 AGCAGAAGGGAAAGGATACAAT 57.130 40.909 0.00 0.00 41.41 2.71
580 584 4.335416 CAAGCAGAAGGGAAAGGATACAA 58.665 43.478 0.00 0.00 41.41 2.41
581 585 3.308402 CCAAGCAGAAGGGAAAGGATACA 60.308 47.826 0.00 0.00 41.41 2.29
582 586 3.054361 TCCAAGCAGAAGGGAAAGGATAC 60.054 47.826 0.00 0.00 0.00 2.24
583 587 3.054361 GTCCAAGCAGAAGGGAAAGGATA 60.054 47.826 0.00 0.00 31.32 2.59
585 589 1.073923 GTCCAAGCAGAAGGGAAAGGA 59.926 52.381 0.00 0.00 31.32 3.36
586 590 1.202927 TGTCCAAGCAGAAGGGAAAGG 60.203 52.381 0.00 0.00 31.32 3.11
587 591 1.882623 GTGTCCAAGCAGAAGGGAAAG 59.117 52.381 0.00 0.00 31.32 2.62
589 593 0.250295 CGTGTCCAAGCAGAAGGGAA 60.250 55.000 0.00 0.00 31.32 3.97
590 594 1.118965 TCGTGTCCAAGCAGAAGGGA 61.119 55.000 0.00 0.00 0.00 4.20
591 595 0.250295 TTCGTGTCCAAGCAGAAGGG 60.250 55.000 0.00 0.00 0.00 3.95
592 596 1.151668 CTTCGTGTCCAAGCAGAAGG 58.848 55.000 0.00 0.00 35.84 3.46
593 597 2.064762 CTCTTCGTGTCCAAGCAGAAG 58.935 52.381 0.00 0.00 39.52 2.85
595 599 1.328279 TCTCTTCGTGTCCAAGCAGA 58.672 50.000 0.00 0.00 0.00 4.26
596 600 2.376808 ATCTCTTCGTGTCCAAGCAG 57.623 50.000 0.00 0.00 0.00 4.24
598 602 3.232213 TGTATCTCTTCGTGTCCAAGC 57.768 47.619 0.00 0.00 0.00 4.01
599 603 8.353684 AGTATTATGTATCTCTTCGTGTCCAAG 58.646 37.037 0.00 0.00 0.00 3.61
603 607 9.171701 GTCAAGTATTATGTATCTCTTCGTGTC 57.828 37.037 0.00 0.00 0.00 3.67
604 608 8.904834 AGTCAAGTATTATGTATCTCTTCGTGT 58.095 33.333 0.00 0.00 0.00 4.49
620 624 9.533831 AATGGAATCCAGTTTTAGTCAAGTATT 57.466 29.630 8.40 0.00 36.75 1.89
621 625 9.178758 GAATGGAATCCAGTTTTAGTCAAGTAT 57.821 33.333 8.40 0.00 36.75 2.12
622 626 8.383175 AGAATGGAATCCAGTTTTAGTCAAGTA 58.617 33.333 8.40 0.00 36.75 2.24
623 627 7.234355 AGAATGGAATCCAGTTTTAGTCAAGT 58.766 34.615 8.40 0.00 36.75 3.16
624 628 7.693969 AGAATGGAATCCAGTTTTAGTCAAG 57.306 36.000 8.40 0.00 36.75 3.02
625 629 8.383175 AGTAGAATGGAATCCAGTTTTAGTCAA 58.617 33.333 8.40 0.00 36.75 3.18
626 630 7.918076 AGTAGAATGGAATCCAGTTTTAGTCA 58.082 34.615 8.40 0.00 36.75 3.41
627 631 8.794335 AAGTAGAATGGAATCCAGTTTTAGTC 57.206 34.615 8.40 0.00 36.75 2.59
628 632 9.232473 GAAAGTAGAATGGAATCCAGTTTTAGT 57.768 33.333 8.40 2.77 36.75 2.24
629 633 8.678199 GGAAAGTAGAATGGAATCCAGTTTTAG 58.322 37.037 8.40 0.00 36.75 1.85
630 634 8.390921 AGGAAAGTAGAATGGAATCCAGTTTTA 58.609 33.333 8.40 0.00 36.75 1.52
631 635 7.241628 AGGAAAGTAGAATGGAATCCAGTTTT 58.758 34.615 8.40 2.36 36.75 2.43
632 636 6.794534 AGGAAAGTAGAATGGAATCCAGTTT 58.205 36.000 8.40 2.63 36.75 2.66
633 637 6.394345 AGGAAAGTAGAATGGAATCCAGTT 57.606 37.500 8.40 2.43 36.75 3.16
634 638 6.674419 AGTAGGAAAGTAGAATGGAATCCAGT 59.326 38.462 8.40 4.62 36.75 4.00
635 639 7.130681 AGTAGGAAAGTAGAATGGAATCCAG 57.869 40.000 8.40 0.00 36.75 3.86
636 640 7.403231 AGAAGTAGGAAAGTAGAATGGAATCCA 59.597 37.037 3.67 3.67 38.19 3.41
637 641 7.713073 CAGAAGTAGGAAAGTAGAATGGAATCC 59.287 40.741 0.00 0.00 0.00 3.01
638 642 8.478877 TCAGAAGTAGGAAAGTAGAATGGAATC 58.521 37.037 0.00 0.00 0.00 2.52
639 643 8.380742 TCAGAAGTAGGAAAGTAGAATGGAAT 57.619 34.615 0.00 0.00 0.00 3.01
640 644 7.792364 TCAGAAGTAGGAAAGTAGAATGGAA 57.208 36.000 0.00 0.00 0.00 3.53
641 645 7.234782 TGTTCAGAAGTAGGAAAGTAGAATGGA 59.765 37.037 0.00 0.00 0.00 3.41
642 646 7.386851 TGTTCAGAAGTAGGAAAGTAGAATGG 58.613 38.462 0.00 0.00 0.00 3.16
643 647 8.713271 GTTGTTCAGAAGTAGGAAAGTAGAATG 58.287 37.037 0.00 0.00 0.00 2.67
644 648 8.429641 TGTTGTTCAGAAGTAGGAAAGTAGAAT 58.570 33.333 0.00 0.00 0.00 2.40
645 649 7.788026 TGTTGTTCAGAAGTAGGAAAGTAGAA 58.212 34.615 0.00 0.00 0.00 2.10
646 650 7.356089 TGTTGTTCAGAAGTAGGAAAGTAGA 57.644 36.000 0.00 0.00 0.00 2.59
647 651 7.711339 AGTTGTTGTTCAGAAGTAGGAAAGTAG 59.289 37.037 0.00 0.00 0.00 2.57
648 652 7.562135 AGTTGTTGTTCAGAAGTAGGAAAGTA 58.438 34.615 0.00 0.00 0.00 2.24
649 653 6.415573 AGTTGTTGTTCAGAAGTAGGAAAGT 58.584 36.000 0.00 0.00 0.00 2.66
650 654 6.927294 AGTTGTTGTTCAGAAGTAGGAAAG 57.073 37.500 0.00 0.00 0.00 2.62
651 655 8.836413 CATAAGTTGTTGTTCAGAAGTAGGAAA 58.164 33.333 0.00 0.00 0.00 3.13
652 656 7.990886 ACATAAGTTGTTGTTCAGAAGTAGGAA 59.009 33.333 0.00 0.00 33.74 3.36
653 657 7.506114 ACATAAGTTGTTGTTCAGAAGTAGGA 58.494 34.615 0.00 0.00 33.74 2.94
654 658 7.730364 ACATAAGTTGTTGTTCAGAAGTAGG 57.270 36.000 0.00 0.00 33.74 3.18
688 692 9.606631 ACAATTGATAACTTTGCTAAAACCAAA 57.393 25.926 13.59 0.00 0.00 3.28
689 693 9.255304 GACAATTGATAACTTTGCTAAAACCAA 57.745 29.630 13.59 0.00 0.00 3.67
690 694 8.637986 AGACAATTGATAACTTTGCTAAAACCA 58.362 29.630 13.59 0.00 0.00 3.67
691 695 9.129209 GAGACAATTGATAACTTTGCTAAAACC 57.871 33.333 13.59 0.00 0.00 3.27
692 696 9.677567 TGAGACAATTGATAACTTTGCTAAAAC 57.322 29.630 13.59 0.00 0.00 2.43
696 700 9.109393 GGTATGAGACAATTGATAACTTTGCTA 57.891 33.333 13.59 0.00 0.00 3.49
697 701 7.067494 GGGTATGAGACAATTGATAACTTTGCT 59.933 37.037 13.59 0.00 0.00 3.91
698 702 7.148086 TGGGTATGAGACAATTGATAACTTTGC 60.148 37.037 13.59 2.60 0.00 3.68
699 703 8.184192 GTGGGTATGAGACAATTGATAACTTTG 58.816 37.037 13.59 0.00 0.00 2.77
700 704 7.339466 GGTGGGTATGAGACAATTGATAACTTT 59.661 37.037 13.59 0.00 0.00 2.66
701 705 6.828785 GGTGGGTATGAGACAATTGATAACTT 59.171 38.462 13.59 2.17 0.00 2.66
702 706 6.357367 GGTGGGTATGAGACAATTGATAACT 58.643 40.000 13.59 5.75 0.00 2.24
703 707 5.531287 GGGTGGGTATGAGACAATTGATAAC 59.469 44.000 13.59 1.87 0.00 1.89
704 708 5.398581 GGGGTGGGTATGAGACAATTGATAA 60.399 44.000 13.59 0.00 0.00 1.75
705 709 4.104102 GGGGTGGGTATGAGACAATTGATA 59.896 45.833 13.59 0.00 0.00 2.15
706 710 3.117512 GGGGTGGGTATGAGACAATTGAT 60.118 47.826 13.59 0.00 0.00 2.57
707 711 2.241176 GGGGTGGGTATGAGACAATTGA 59.759 50.000 13.59 0.00 0.00 2.57
708 712 2.654863 GGGGTGGGTATGAGACAATTG 58.345 52.381 3.24 3.24 0.00 2.32
709 713 1.211949 CGGGGTGGGTATGAGACAATT 59.788 52.381 0.00 0.00 0.00 2.32
710 714 0.837272 CGGGGTGGGTATGAGACAAT 59.163 55.000 0.00 0.00 0.00 2.71
711 715 1.906105 GCGGGGTGGGTATGAGACAA 61.906 60.000 0.00 0.00 0.00 3.18
712 716 2.363975 GCGGGGTGGGTATGAGACA 61.364 63.158 0.00 0.00 0.00 3.41
713 717 1.906105 TTGCGGGGTGGGTATGAGAC 61.906 60.000 0.00 0.00 0.00 3.36
714 718 1.202099 TTTGCGGGGTGGGTATGAGA 61.202 55.000 0.00 0.00 0.00 3.27
715 719 0.322997 TTTTGCGGGGTGGGTATGAG 60.323 55.000 0.00 0.00 0.00 2.90
716 720 0.112606 TTTTTGCGGGGTGGGTATGA 59.887 50.000 0.00 0.00 0.00 2.15
717 721 2.659800 TTTTTGCGGGGTGGGTATG 58.340 52.632 0.00 0.00 0.00 2.39
739 743 9.753674 TCAAGAAAATAGGGTATGAGACAAATT 57.246 29.630 0.00 0.00 0.00 1.82
740 744 9.927081 ATCAAGAAAATAGGGTATGAGACAAAT 57.073 29.630 0.00 0.00 0.00 2.32
741 745 9.753674 AATCAAGAAAATAGGGTATGAGACAAA 57.246 29.630 0.00 0.00 0.00 2.83
742 746 9.753674 AAATCAAGAAAATAGGGTATGAGACAA 57.246 29.630 0.00 0.00 0.00 3.18
797 801 9.412460 TCCGATTTCTTGTACTTCCTATACTAA 57.588 33.333 0.00 0.00 0.00 2.24
807 811 5.174037 TGGGATTCCGATTTCTTGTACTT 57.826 39.130 0.00 0.00 35.24 2.24
815 819 2.298610 GGGACTTGGGATTCCGATTTC 58.701 52.381 0.00 0.00 35.24 2.17
831 835 2.963599 TTTTGAGGGGTAGTTGGGAC 57.036 50.000 0.00 0.00 0.00 4.46
879 1058 4.828925 GGCAGCGAGAGTGGGCTC 62.829 72.222 0.00 0.00 41.94 4.70
885 1064 3.386237 GGGACTGGCAGCGAGAGT 61.386 66.667 15.89 0.37 0.00 3.24
902 1081 2.588877 CTTATGTGGGCCGGAGCG 60.589 66.667 5.05 0.00 41.24 5.03
903 1082 1.523938 GTCTTATGTGGGCCGGAGC 60.524 63.158 5.05 0.00 38.76 4.70
904 1083 0.179073 CTGTCTTATGTGGGCCGGAG 60.179 60.000 5.05 0.00 0.00 4.63
916 1095 1.286248 GGCCTTCCTTCCCTGTCTTA 58.714 55.000 0.00 0.00 0.00 2.10
920 1099 2.895424 CGTGGCCTTCCTTCCCTGT 61.895 63.158 3.32 0.00 0.00 4.00
928 1107 3.069778 AAGGAGACGTGGCCTTCC 58.930 61.111 11.68 3.48 40.37 3.46
958 1137 3.059634 TGGAAAGAAAAGTTTGACGCG 57.940 42.857 3.53 3.53 0.00 6.01
961 1140 6.170506 AGGGTTTTGGAAAGAAAAGTTTGAC 58.829 36.000 0.00 0.00 0.00 3.18
974 1153 1.074248 GGAGGCGAGGGTTTTGGAA 59.926 57.895 0.00 0.00 0.00 3.53
1229 1426 2.358258 GGGGGATGGGATATTTCTCCA 58.642 52.381 0.00 0.00 37.01 3.86
1258 1455 1.852067 GCAGCGAATTTCGTGGTGGT 61.852 55.000 19.10 0.00 42.81 4.16
1480 1697 4.969196 CGCACGGTGGTCACAGCT 62.969 66.667 10.60 0.00 42.79 4.24
1519 1736 0.181587 TTCAGGCCGACAAAGACCAA 59.818 50.000 0.00 0.00 0.00 3.67
1639 1906 0.976641 AGATGAAGACCAAGGCACGA 59.023 50.000 0.00 0.00 0.00 4.35
1836 2110 1.202615 CCATCTGACATCGCCATGAGT 60.203 52.381 0.00 0.00 33.72 3.41
2084 2361 0.179034 CCATAGCCTCTTCCACTGCC 60.179 60.000 0.00 0.00 0.00 4.85
2108 2385 5.691754 GGAATCAAAGCACAAAATTTCTCGT 59.308 36.000 0.00 0.00 0.00 4.18
2423 2834 2.766313 CCGTTTGACTGAGAATCACCA 58.234 47.619 0.00 0.00 42.56 4.17
2509 2929 2.281761 ACCGCCTCCAAGCTTGTG 60.282 61.111 24.35 15.73 0.00 3.33
2857 3371 4.005487 AGCTCTAGGCATGTCATCAATC 57.995 45.455 0.00 0.00 44.79 2.67
3030 3553 7.224362 GCAATAGAGCACCATATCTTATAGCTG 59.776 40.741 0.00 0.00 0.00 4.24
3086 3625 6.679392 GCAGTTTTGTGGAGTTACTAAAGCAA 60.679 38.462 0.00 0.00 0.00 3.91
3087 3626 5.220970 GCAGTTTTGTGGAGTTACTAAAGCA 60.221 40.000 0.00 0.00 0.00 3.91
3171 3711 2.037251 ACACGGACATTGCAGTCTACTT 59.963 45.455 6.11 0.00 38.57 2.24
3331 3872 9.705290 AAAAATAAACAGGGATAAATGTGTGTC 57.295 29.630 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.