Multiple sequence alignment - TraesCS2D01G349200

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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 TraesCS2D01G349200 chr2D 100.000 3670 0 0 1 3670 446860427 446856758 0.000000e+00 6778.0
1 TraesCS2D01G349200 chr2D 76.813 1186 231 28 1503 2670 446942045 446943204 8.650000e-176 627.0
2 TraesCS2D01G349200 chr2D 81.743 482 76 8 1506 1984 447149093 447149565 3.440000e-105 392.0
3 TraesCS2D01G349200 chr2D 89.455 275 23 6 29 300 315859250 315858979 3.510000e-90 342.0
4 TraesCS2D01G349200 chr2D 89.773 264 24 3 30 290 380694289 380694552 5.870000e-88 335.0
5 TraesCS2D01G349200 chr2D 89.394 264 24 4 30 290 558801620 558801358 2.730000e-86 329.0
6 TraesCS2D01G349200 chr2D 73.951 572 111 28 2101 2665 447149698 447150238 2.890000e-46 196.0
7 TraesCS2D01G349200 chr2B 95.784 1423 46 10 1375 2789 526763237 526764653 0.000000e+00 2283.0
8 TraesCS2D01G349200 chr2B 85.402 1144 76 35 291 1382 526761958 526763062 0.000000e+00 1103.0
9 TraesCS2D01G349200 chr2B 76.471 1190 234 33 1503 2670 526776245 526777410 4.050000e-169 604.0
10 TraesCS2D01G349200 chr2B 93.750 288 16 2 3385 3670 526765789 526766076 7.280000e-117 431.0
11 TraesCS2D01G349200 chr2B 81.496 254 24 6 3138 3390 526765526 526765757 1.740000e-43 187.0
12 TraesCS2D01G349200 chr2B 72.902 572 115 30 2102 2665 526841635 526842174 1.050000e-35 161.0
13 TraesCS2D01G349200 chr2A 95.203 1355 41 7 1459 2806 591264482 591265819 0.000000e+00 2121.0
14 TraesCS2D01G349200 chr2A 86.198 1210 75 42 291 1456 591261503 591262664 0.000000e+00 1225.0
15 TraesCS2D01G349200 chr2A 77.295 1198 228 27 1490 2670 591278005 591279175 0.000000e+00 665.0
16 TraesCS2D01G349200 chr2A 89.686 446 29 12 3232 3670 591267116 591267551 1.490000e-153 553.0
17 TraesCS2D01G349200 chr2A 73.333 570 116 27 2102 2665 591605517 591606056 1.050000e-40 178.0
18 TraesCS2D01G349200 chr5D 78.083 1200 203 38 1491 2670 463087456 463088615 0.000000e+00 704.0
19 TraesCS2D01G349200 chr5D 91.667 264 18 4 30 290 279292870 279293132 2.690000e-96 363.0
20 TraesCS2D01G349200 chr5D 87.273 110 4 4 3561 3670 267818672 267818771 2.320000e-22 117.0
21 TraesCS2D01G349200 chr5A 77.982 1199 207 36 1491 2670 582980949 582982109 0.000000e+00 699.0
22 TraesCS2D01G349200 chr5A 87.273 110 4 4 3561 3670 355156687 355156786 2.320000e-22 117.0
23 TraesCS2D01G349200 chr5B 77.898 1199 198 41 1491 2670 569825554 569826704 0.000000e+00 684.0
24 TraesCS2D01G349200 chr5B 87.037 108 4 4 3563 3670 302838455 302838552 3.000000e-21 113.0
25 TraesCS2D01G349200 chr1B 92.969 256 15 2 31 284 442201897 442201643 1.610000e-98 370.0
26 TraesCS2D01G349200 chr6B 90.566 265 19 6 30 290 214870345 214870607 2.710000e-91 346.0
27 TraesCS2D01G349200 chr6B 90.661 257 20 3 30 284 536831433 536831179 4.540000e-89 339.0
28 TraesCS2D01G349200 chr3A 90.661 257 21 2 30 284 169225127 169225382 4.540000e-89 339.0
29 TraesCS2D01G349200 chr3A 87.013 77 8 2 2946 3021 728017057 728016982 6.530000e-13 86.1
30 TraesCS2D01G349200 chr3A 87.013 77 8 2 2946 3021 728032148 728032073 6.530000e-13 86.1
31 TraesCS2D01G349200 chr3A 85.542 83 10 2 2940 3021 729692203 729692284 6.530000e-13 86.1
32 TraesCS2D01G349200 chr3B 89.179 268 26 3 19 284 64603385 64603119 7.600000e-87 331.0
33 TraesCS2D01G349200 chr3B 92.453 53 2 2 3043 3095 732883655 732883705 1.410000e-09 75.0
34 TraesCS2D01G349200 chr7A 88.406 69 5 3 3043 3110 708631719 708631785 3.040000e-11 80.5
35 TraesCS2D01G349200 chr4A 91.525 59 4 1 3053 3110 597850979 597850921 3.040000e-11 80.5


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 TraesCS2D01G349200 chr2D 446856758 446860427 3669 True 6778.000000 6778 100.000000 1 3670 1 chr2D.!!$R2 3669
1 TraesCS2D01G349200 chr2D 446942045 446943204 1159 False 627.000000 627 76.813000 1503 2670 1 chr2D.!!$F2 1167
2 TraesCS2D01G349200 chr2D 447149093 447150238 1145 False 294.000000 392 77.847000 1506 2665 2 chr2D.!!$F3 1159
3 TraesCS2D01G349200 chr2B 526761958 526766076 4118 False 1001.000000 2283 89.108000 291 3670 4 chr2B.!!$F3 3379
4 TraesCS2D01G349200 chr2B 526776245 526777410 1165 False 604.000000 604 76.471000 1503 2670 1 chr2B.!!$F1 1167
5 TraesCS2D01G349200 chr2A 591261503 591267551 6048 False 1299.666667 2121 90.362333 291 3670 3 chr2A.!!$F3 3379
6 TraesCS2D01G349200 chr2A 591278005 591279175 1170 False 665.000000 665 77.295000 1490 2670 1 chr2A.!!$F1 1180
7 TraesCS2D01G349200 chr5D 463087456 463088615 1159 False 704.000000 704 78.083000 1491 2670 1 chr5D.!!$F3 1179
8 TraesCS2D01G349200 chr5A 582980949 582982109 1160 False 699.000000 699 77.982000 1491 2670 1 chr5A.!!$F2 1179
9 TraesCS2D01G349200 chr5B 569825554 569826704 1150 False 684.000000 684 77.898000 1491 2670 1 chr5B.!!$F2 1179

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
441 444 0.734309 TAAATGATGCCACTGCTGCG 59.266 50.000 0.00 0.0 38.71 5.18 F
720 730 1.021390 CGAATCAGTGACCAGGTGGC 61.021 60.000 0.00 0.0 39.32 5.01 F
985 1024 1.068194 CATTAGCCGATCGAGGAGGTC 60.068 57.143 18.66 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1421 1714 0.593128 ACAGTCAACGCCAGCATTTC 59.407 50.0 0.0 0.0 0.00 2.17 R
2050 4191 0.690762 GTCAGGTAAAGGGCTGGTCA 59.309 55.0 0.0 0.0 0.00 4.02 R
2797 4966 0.373716 CAAGTCCGCATAAAGCCGTC 59.626 55.0 0.0 0.0 41.38 4.79 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 7.849322 ATGGTCCTTGTTTTTAAATGGTACT 57.151 32.000 0.00 0.00 0.00 2.73
34 35 7.279750 TGGTCCTTGTTTTTAAATGGTACTC 57.720 36.000 0.00 0.00 0.00 2.59
35 36 6.265876 TGGTCCTTGTTTTTAAATGGTACTCC 59.734 38.462 0.00 0.00 0.00 3.85
36 37 6.294899 GGTCCTTGTTTTTAAATGGTACTCCC 60.295 42.308 0.00 0.00 0.00 4.30
37 38 6.492429 GTCCTTGTTTTTAAATGGTACTCCCT 59.508 38.462 0.00 0.00 0.00 4.20
38 39 6.717997 TCCTTGTTTTTAAATGGTACTCCCTC 59.282 38.462 0.00 0.00 0.00 4.30
39 40 6.071560 CCTTGTTTTTAAATGGTACTCCCTCC 60.072 42.308 0.00 0.00 0.00 4.30
40 41 5.005094 TGTTTTTAAATGGTACTCCCTCCG 58.995 41.667 0.00 0.00 0.00 4.63
41 42 4.914177 TTTTAAATGGTACTCCCTCCGT 57.086 40.909 0.00 0.00 0.00 4.69
42 43 4.914177 TTTAAATGGTACTCCCTCCGTT 57.086 40.909 0.00 0.00 34.83 4.44
43 44 4.914177 TTAAATGGTACTCCCTCCGTTT 57.086 40.909 0.00 0.00 42.94 3.60
44 45 3.801307 AAATGGTACTCCCTCCGTTTT 57.199 42.857 0.00 0.00 39.10 2.43
45 46 3.801307 AATGGTACTCCCTCCGTTTTT 57.199 42.857 0.00 0.00 29.82 1.94
46 47 4.914177 AATGGTACTCCCTCCGTTTTTA 57.086 40.909 0.00 0.00 29.82 1.52
47 48 5.446260 AATGGTACTCCCTCCGTTTTTAT 57.554 39.130 0.00 0.00 29.82 1.40
48 49 4.914177 TGGTACTCCCTCCGTTTTTATT 57.086 40.909 0.00 0.00 0.00 1.40
49 50 5.245584 TGGTACTCCCTCCGTTTTTATTT 57.754 39.130 0.00 0.00 0.00 1.40
50 51 6.371595 TGGTACTCCCTCCGTTTTTATTTA 57.628 37.500 0.00 0.00 0.00 1.40
51 52 6.408869 TGGTACTCCCTCCGTTTTTATTTAG 58.591 40.000 0.00 0.00 0.00 1.85
52 53 6.013466 TGGTACTCCCTCCGTTTTTATTTAGT 60.013 38.462 0.00 0.00 0.00 2.24
53 54 6.536582 GGTACTCCCTCCGTTTTTATTTAGTC 59.463 42.308 0.00 0.00 0.00 2.59
54 55 5.494724 ACTCCCTCCGTTTTTATTTAGTCC 58.505 41.667 0.00 0.00 0.00 3.85
55 56 5.013391 ACTCCCTCCGTTTTTATTTAGTCCA 59.987 40.000 0.00 0.00 0.00 4.02
56 57 6.069705 TCCCTCCGTTTTTATTTAGTCCAT 57.930 37.500 0.00 0.00 0.00 3.41
57 58 5.883673 TCCCTCCGTTTTTATTTAGTCCATG 59.116 40.000 0.00 0.00 0.00 3.66
58 59 5.650703 CCCTCCGTTTTTATTTAGTCCATGT 59.349 40.000 0.00 0.00 0.00 3.21
59 60 6.824704 CCCTCCGTTTTTATTTAGTCCATGTA 59.175 38.462 0.00 0.00 0.00 2.29
60 61 7.501225 CCCTCCGTTTTTATTTAGTCCATGTAT 59.499 37.037 0.00 0.00 0.00 2.29
61 62 8.899771 CCTCCGTTTTTATTTAGTCCATGTATT 58.100 33.333 0.00 0.00 0.00 1.89
64 65 9.659830 CCGTTTTTATTTAGTCCATGTATTAGC 57.340 33.333 0.00 0.00 0.00 3.09
75 76 8.723942 AGTCCATGTATTAGCTTTAGTCAAAG 57.276 34.615 0.00 0.00 43.46 2.77
76 77 8.322091 AGTCCATGTATTAGCTTTAGTCAAAGT 58.678 33.333 0.00 0.00 42.71 2.66
77 78 8.947115 GTCCATGTATTAGCTTTAGTCAAAGTT 58.053 33.333 0.00 0.00 42.71 2.66
80 81 9.901724 CATGTATTAGCTTTAGTCAAAGTTACG 57.098 33.333 0.00 0.00 42.71 3.18
81 82 7.956558 TGTATTAGCTTTAGTCAAAGTTACGC 58.043 34.615 0.00 0.00 42.71 4.42
82 83 7.816031 TGTATTAGCTTTAGTCAAAGTTACGCT 59.184 33.333 0.00 0.00 42.71 5.07
83 84 7.668525 ATTAGCTTTAGTCAAAGTTACGCTT 57.331 32.000 0.00 0.00 42.71 4.68
96 97 7.730067 AAAGTTACGCTTTGTAAACTTTGAC 57.270 32.000 10.33 0.00 45.00 3.18
97 98 6.425577 AGTTACGCTTTGTAAACTTTGACA 57.574 33.333 0.00 0.00 44.36 3.58
98 99 6.844254 AGTTACGCTTTGTAAACTTTGACAA 58.156 32.000 0.00 0.00 44.36 3.18
99 100 7.306953 AGTTACGCTTTGTAAACTTTGACAAA 58.693 30.769 0.00 0.00 44.36 2.83
252 253 7.548196 ACTTTACGAAGTTTGATTTCAGTCA 57.452 32.000 0.00 0.00 43.48 3.41
253 254 7.981142 ACTTTACGAAGTTTGATTTCAGTCAA 58.019 30.769 0.00 0.00 43.48 3.18
254 255 7.908601 ACTTTACGAAGTTTGATTTCAGTCAAC 59.091 33.333 0.00 0.00 43.48 3.18
255 256 7.548196 TTACGAAGTTTGATTTCAGTCAACT 57.452 32.000 0.00 0.00 37.78 3.16
256 257 6.436843 ACGAAGTTTGATTTCAGTCAACTT 57.563 33.333 8.04 8.04 37.78 2.66
257 258 6.852664 ACGAAGTTTGATTTCAGTCAACTTT 58.147 32.000 9.18 0.00 37.78 2.66
258 259 7.981142 ACGAAGTTTGATTTCAGTCAACTTTA 58.019 30.769 9.18 0.00 37.78 1.85
259 260 8.455682 ACGAAGTTTGATTTCAGTCAACTTTAA 58.544 29.630 9.18 0.00 37.78 1.52
260 261 9.450807 CGAAGTTTGATTTCAGTCAACTTTAAT 57.549 29.630 9.18 0.00 37.80 1.40
266 267 9.844790 TTGATTTCAGTCAACTTTAATATGCTG 57.155 29.630 0.00 0.00 33.41 4.41
267 268 9.230122 TGATTTCAGTCAACTTTAATATGCTGA 57.770 29.630 0.00 0.00 0.00 4.26
268 269 9.713740 GATTTCAGTCAACTTTAATATGCTGAG 57.286 33.333 0.00 0.00 32.75 3.35
269 270 8.621532 TTTCAGTCAACTTTAATATGCTGAGT 57.378 30.769 0.00 0.00 32.75 3.41
270 271 9.719355 TTTCAGTCAACTTTAATATGCTGAGTA 57.281 29.630 0.00 0.00 32.75 2.59
271 272 9.719355 TTCAGTCAACTTTAATATGCTGAGTAA 57.281 29.630 0.00 0.00 32.75 2.24
272 273 9.719355 TCAGTCAACTTTAATATGCTGAGTAAA 57.281 29.630 0.00 0.00 0.00 2.01
284 285 8.958119 ATATGCTGAGTAAATAAAAACGGAGA 57.042 30.769 0.00 0.00 0.00 3.71
285 286 7.681939 ATGCTGAGTAAATAAAAACGGAGAA 57.318 32.000 0.00 0.00 0.00 2.87
286 287 7.129109 TGCTGAGTAAATAAAAACGGAGAAG 57.871 36.000 0.00 0.00 0.00 2.85
287 288 6.708949 TGCTGAGTAAATAAAAACGGAGAAGT 59.291 34.615 0.00 0.00 0.00 3.01
288 289 7.874016 TGCTGAGTAAATAAAAACGGAGAAGTA 59.126 33.333 0.00 0.00 0.00 2.24
289 290 8.167345 GCTGAGTAAATAAAAACGGAGAAGTAC 58.833 37.037 0.00 0.00 0.00 2.73
441 444 0.734309 TAAATGATGCCACTGCTGCG 59.266 50.000 0.00 0.00 38.71 5.18
465 468 7.475015 CGAATCAAAATCCACATGAACACTAT 58.525 34.615 0.00 0.00 0.00 2.12
506 509 1.572085 GCCCAGCCAATCGATCGATG 61.572 60.000 29.99 21.84 34.70 3.84
567 574 2.310233 CCGCACAAGTCCACGTGAG 61.310 63.158 19.30 7.45 35.02 3.51
697 704 2.576893 CGCATCCAACGGATCGACG 61.577 63.158 0.00 0.00 40.98 5.12
720 730 1.021390 CGAATCAGTGACCAGGTGGC 61.021 60.000 0.00 0.00 39.32 5.01
833 843 3.686045 GGCCTCCGATCCTAGCCG 61.686 72.222 0.00 0.00 33.18 5.52
834 844 2.597805 GCCTCCGATCCTAGCCGA 60.598 66.667 0.00 0.00 0.00 5.54
835 845 1.979693 GCCTCCGATCCTAGCCGAT 60.980 63.158 0.00 0.00 0.00 4.18
836 846 1.939769 GCCTCCGATCCTAGCCGATC 61.940 65.000 0.23 0.23 36.16 3.69
837 847 1.316706 CCTCCGATCCTAGCCGATCC 61.317 65.000 4.09 0.00 36.13 3.36
838 848 1.649390 CTCCGATCCTAGCCGATCCG 61.649 65.000 4.09 0.00 36.13 4.18
839 849 1.972223 CCGATCCTAGCCGATCCGT 60.972 63.158 4.09 0.00 36.13 4.69
911 950 5.697473 CAGATAAGCTCTGTCCTCGATAA 57.303 43.478 0.00 0.00 45.42 1.75
977 1016 2.034179 TGTGAGGTACATTAGCCGATCG 59.966 50.000 8.51 8.51 33.42 3.69
985 1024 1.068194 CATTAGCCGATCGAGGAGGTC 60.068 57.143 18.66 0.00 0.00 3.85
989 1028 1.736586 CCGATCGAGGAGGTCAAGG 59.263 63.158 18.66 0.00 0.00 3.61
1098 1149 4.342092 AGCCACAAATCAAAGTTGCTTACT 59.658 37.500 0.00 0.00 33.51 2.24
1131 1197 3.215151 TGCTTGGTTCGTAATTTGGTGA 58.785 40.909 0.00 0.00 0.00 4.02
1135 1201 5.735070 GCTTGGTTCGTAATTTGGTGAAGTT 60.735 40.000 0.00 0.00 0.00 2.66
1145 1214 7.094975 CGTAATTTGGTGAAGTTGAATGGACTA 60.095 37.037 0.00 0.00 0.00 2.59
1184 1254 8.398665 GGGAGACTAATTTGCTAACTTGTTATG 58.601 37.037 0.00 0.00 0.00 1.90
1188 1258 9.556030 GACTAATTTGCTAACTTGTTATGGTTC 57.444 33.333 0.00 0.00 0.00 3.62
1210 1280 4.333095 TCTCGTCTTCTCGATGTTCTTAGG 59.667 45.833 0.00 0.00 39.12 2.69
1213 1283 4.036971 CGTCTTCTCGATGTTCTTAGGGAT 59.963 45.833 0.00 0.00 0.00 3.85
1236 1321 1.472376 GCCTGCTAGCTAGGTTGTCAG 60.472 57.143 24.84 17.94 37.64 3.51
1285 1377 8.148999 ACTCCCTGTAAGAAAGTTTACTGTTAG 58.851 37.037 0.00 0.00 34.07 2.34
1315 1419 3.825308 CGATTGCACAGCATAGTTTGTT 58.175 40.909 0.00 0.00 38.76 2.83
1316 1420 4.671508 GCGATTGCACAGCATAGTTTGTTA 60.672 41.667 0.00 0.00 38.76 2.41
1317 1421 4.788100 CGATTGCACAGCATAGTTTGTTAC 59.212 41.667 0.00 0.00 38.76 2.50
1334 1444 9.034544 AGTTTGTTACTACGTAAAAACCTGTAG 57.965 33.333 14.01 0.00 40.05 2.74
1351 1461 5.300792 ACCTGTAGTAGCTCAGCTTAGATTC 59.699 44.000 3.31 0.00 40.44 2.52
1361 1472 3.389329 TCAGCTTAGATTCAAGGGGCTAG 59.611 47.826 0.00 0.00 0.00 3.42
1421 1714 2.097038 CAGAGCGTTGCTTCTCCCG 61.097 63.158 0.00 0.00 39.88 5.14
1474 3583 2.694628 AGTTTCCTTCATGCAGCACAAA 59.305 40.909 0.00 0.00 0.00 2.83
1476 3585 3.581024 TTCCTTCATGCAGCACAAATC 57.419 42.857 0.00 0.00 0.00 2.17
2005 4128 4.475444 TCTACCCTCCCCAGGCCG 62.475 72.222 0.00 0.00 38.72 6.13
2050 4191 3.243336 GCATGAACTTTCGAGTACGTCT 58.757 45.455 0.00 0.00 40.69 4.18
2053 4194 3.881795 TGAACTTTCGAGTACGTCTGAC 58.118 45.455 0.00 0.00 40.69 3.51
2085 4247 2.094286 CCTGACTCTCTCTGTGCGATTT 60.094 50.000 0.00 0.00 0.00 2.17
2089 4251 2.071540 CTCTCTCTGTGCGATTTTGCA 58.928 47.619 0.00 0.00 43.95 4.08
2263 4426 0.885879 ATCAAGTACGTGGACTCGCA 59.114 50.000 8.98 0.00 0.00 5.10
2522 4685 2.258591 GCCTCGCTCGAGTTCACA 59.741 61.111 15.13 0.00 40.44 3.58
2708 4873 2.317609 CCGAAGTTGACGGCTGGTG 61.318 63.158 0.00 0.00 43.74 4.17
2736 4905 1.066430 TCTGAAACACAGGGTATCCGC 60.066 52.381 0.00 0.00 45.76 5.54
2775 4944 6.183360 TGGCAATTGTACCACTACACATTTTT 60.183 34.615 7.40 0.00 32.28 1.94
2816 5696 0.373716 GACGGCTTTATGCGGACTTG 59.626 55.000 4.80 0.00 43.58 3.16
2818 5763 1.369091 CGGCTTTATGCGGACTTGCT 61.369 55.000 0.00 0.00 43.58 3.91
2821 5766 2.422127 GGCTTTATGCGGACTTGCTAAA 59.578 45.455 0.00 0.00 44.05 1.85
2849 5794 5.636123 TGGCACCTGAACTTTATTTAGGAA 58.364 37.500 4.62 0.00 32.86 3.36
2898 5843 2.403252 CCGTTGAGGCTACTGGAAAT 57.597 50.000 0.00 0.00 0.00 2.17
2901 5846 3.535561 CGTTGAGGCTACTGGAAATGAT 58.464 45.455 0.00 0.00 0.00 2.45
2902 5847 3.557595 CGTTGAGGCTACTGGAAATGATC 59.442 47.826 0.00 0.00 0.00 2.92
2921 6663 7.814264 ATGATCCTCTGTTTAATCATGGAAC 57.186 36.000 10.51 9.21 37.44 3.62
2923 6665 5.160607 TCCTCTGTTTAATCATGGAACGT 57.839 39.130 0.00 0.00 0.00 3.99
2928 6670 7.124347 TCTGTTTAATCATGGAACGTTGTAC 57.876 36.000 5.00 0.00 0.00 2.90
2929 6671 6.148150 TCTGTTTAATCATGGAACGTTGTACC 59.852 38.462 5.00 0.57 0.00 3.34
3005 6758 9.541143 TCGCATATCTAAGTTTTATGTCATTGA 57.459 29.630 0.00 0.00 0.00 2.57
3015 6768 8.771920 AGTTTTATGTCATTGATCTTACGTGA 57.228 30.769 0.00 0.00 0.00 4.35
3016 6769 8.873830 AGTTTTATGTCATTGATCTTACGTGAG 58.126 33.333 0.00 0.00 0.00 3.51
3018 6771 9.863845 TTTTATGTCATTGATCTTACGTGAGTA 57.136 29.630 7.27 0.00 46.88 2.59
3048 6801 9.932207 TTTTTATGGTCGATTAAGTCACTTAGA 57.068 29.630 0.00 0.00 0.00 2.10
3050 6803 9.529325 TTTATGGTCGATTAAGTCACTTAGATG 57.471 33.333 0.00 0.00 0.00 2.90
3051 6804 5.902681 TGGTCGATTAAGTCACTTAGATGG 58.097 41.667 0.00 0.00 0.00 3.51
3052 6805 5.163447 TGGTCGATTAAGTCACTTAGATGGG 60.163 44.000 0.00 0.00 0.00 4.00
3053 6806 4.745620 GTCGATTAAGTCACTTAGATGGGC 59.254 45.833 0.00 0.00 0.00 5.36
3054 6807 4.649674 TCGATTAAGTCACTTAGATGGGCT 59.350 41.667 0.00 0.00 0.00 5.19
3055 6808 5.128827 TCGATTAAGTCACTTAGATGGGCTT 59.871 40.000 0.00 0.00 0.00 4.35
3056 6809 5.817816 CGATTAAGTCACTTAGATGGGCTTT 59.182 40.000 0.00 0.00 0.00 3.51
3057 6810 6.238211 CGATTAAGTCACTTAGATGGGCTTTG 60.238 42.308 0.00 0.00 0.00 2.77
3058 6811 3.356529 AGTCACTTAGATGGGCTTTGG 57.643 47.619 0.00 0.00 0.00 3.28
3059 6812 2.912956 AGTCACTTAGATGGGCTTTGGA 59.087 45.455 0.00 0.00 0.00 3.53
3060 6813 3.525199 AGTCACTTAGATGGGCTTTGGAT 59.475 43.478 0.00 0.00 0.00 3.41
3061 6814 3.879892 GTCACTTAGATGGGCTTTGGATC 59.120 47.826 0.00 0.00 0.00 3.36
3062 6815 3.523157 TCACTTAGATGGGCTTTGGATCA 59.477 43.478 0.00 0.00 0.00 2.92
3063 6816 4.166725 TCACTTAGATGGGCTTTGGATCAT 59.833 41.667 0.00 0.00 0.00 2.45
3064 6817 4.518211 CACTTAGATGGGCTTTGGATCATC 59.482 45.833 0.00 0.00 37.02 2.92
3065 6818 4.414846 ACTTAGATGGGCTTTGGATCATCT 59.585 41.667 9.23 9.23 45.48 2.90
3066 6819 3.967467 AGATGGGCTTTGGATCATCTT 57.033 42.857 0.00 0.00 42.30 2.40
3067 6820 3.563223 AGATGGGCTTTGGATCATCTTG 58.437 45.455 0.00 0.00 42.30 3.02
3068 6821 3.203710 AGATGGGCTTTGGATCATCTTGA 59.796 43.478 0.00 0.00 42.30 3.02
3069 6822 3.675348 TGGGCTTTGGATCATCTTGAT 57.325 42.857 0.00 0.00 40.34 2.57
3083 6836 8.632906 GATCATCTTGATCCACCTTGATTAAT 57.367 34.615 6.27 0.00 45.66 1.40
3084 6837 7.812690 TCATCTTGATCCACCTTGATTAATG 57.187 36.000 0.00 0.00 0.00 1.90
3085 6838 7.576403 TCATCTTGATCCACCTTGATTAATGA 58.424 34.615 0.00 0.00 0.00 2.57
3086 6839 8.054572 TCATCTTGATCCACCTTGATTAATGAA 58.945 33.333 0.00 0.00 0.00 2.57
3087 6840 8.689061 CATCTTGATCCACCTTGATTAATGAAA 58.311 33.333 0.00 0.00 0.00 2.69
3088 6841 8.284945 TCTTGATCCACCTTGATTAATGAAAG 57.715 34.615 0.00 0.00 0.00 2.62
3089 6842 6.455360 TGATCCACCTTGATTAATGAAAGC 57.545 37.500 0.00 0.00 0.00 3.51
3090 6843 6.189859 TGATCCACCTTGATTAATGAAAGCT 58.810 36.000 0.00 0.00 0.00 3.74
3091 6844 7.345691 TGATCCACCTTGATTAATGAAAGCTA 58.654 34.615 0.00 0.00 0.00 3.32
3092 6845 8.000709 TGATCCACCTTGATTAATGAAAGCTAT 58.999 33.333 0.00 0.00 0.00 2.97
3093 6846 8.773033 ATCCACCTTGATTAATGAAAGCTATT 57.227 30.769 0.00 0.00 0.00 1.73
3094 6847 8.593945 TCCACCTTGATTAATGAAAGCTATTT 57.406 30.769 0.00 0.00 0.00 1.40
3095 6848 9.034800 TCCACCTTGATTAATGAAAGCTATTTT 57.965 29.630 0.00 0.00 0.00 1.82
3096 6849 9.305925 CCACCTTGATTAATGAAAGCTATTTTC 57.694 33.333 0.00 0.00 44.45 2.29
3130 6883 8.587952 AAAAGTCACTTAAATGTGCCATAAAC 57.412 30.769 0.00 0.00 37.81 2.01
3131 6884 6.892658 AGTCACTTAAATGTGCCATAAACA 57.107 33.333 0.00 0.00 37.81 2.83
3132 6885 6.913170 AGTCACTTAAATGTGCCATAAACAG 58.087 36.000 0.00 0.00 37.81 3.16
3133 6886 6.714810 AGTCACTTAAATGTGCCATAAACAGA 59.285 34.615 0.00 0.00 37.81 3.41
3134 6887 6.801862 GTCACTTAAATGTGCCATAAACAGAC 59.198 38.462 0.00 0.00 37.81 3.51
3135 6888 6.072175 TCACTTAAATGTGCCATAAACAGACC 60.072 38.462 0.00 0.00 37.81 3.85
3136 6889 5.185056 ACTTAAATGTGCCATAAACAGACCC 59.815 40.000 0.00 0.00 0.00 4.46
3137 6890 2.897271 ATGTGCCATAAACAGACCCA 57.103 45.000 0.00 0.00 0.00 4.51
3138 6891 2.666272 TGTGCCATAAACAGACCCAA 57.334 45.000 0.00 0.00 0.00 4.12
3139 6892 2.235016 TGTGCCATAAACAGACCCAAC 58.765 47.619 0.00 0.00 0.00 3.77
3140 6893 2.235016 GTGCCATAAACAGACCCAACA 58.765 47.619 0.00 0.00 0.00 3.33
3141 6894 2.625790 GTGCCATAAACAGACCCAACAA 59.374 45.455 0.00 0.00 0.00 2.83
3142 6895 2.625790 TGCCATAAACAGACCCAACAAC 59.374 45.455 0.00 0.00 0.00 3.32
3143 6896 2.351350 GCCATAAACAGACCCAACAACG 60.351 50.000 0.00 0.00 0.00 4.10
3144 6897 2.882137 CCATAAACAGACCCAACAACGT 59.118 45.455 0.00 0.00 0.00 3.99
3145 6898 3.316868 CCATAAACAGACCCAACAACGTT 59.683 43.478 0.00 0.00 0.00 3.99
3146 6899 4.202070 CCATAAACAGACCCAACAACGTTT 60.202 41.667 0.00 0.00 0.00 3.60
3153 6906 4.095185 CAGACCCAACAACGTTTTTCTACA 59.905 41.667 0.00 0.00 0.00 2.74
3158 6912 5.336744 CCAACAACGTTTTTCTACACATGT 58.663 37.500 0.00 0.00 0.00 3.21
3162 6916 6.255215 ACAACGTTTTTCTACACATGTCTTG 58.745 36.000 0.00 0.00 0.00 3.02
3163 6917 4.844267 ACGTTTTTCTACACATGTCTTGC 58.156 39.130 0.00 0.00 0.00 4.01
3192 6948 6.067217 AGCTGGATAGGACATTTTTAGTGT 57.933 37.500 0.00 0.00 0.00 3.55
3193 6949 7.195374 AGCTGGATAGGACATTTTTAGTGTA 57.805 36.000 0.00 0.00 0.00 2.90
3215 6971 7.493971 GTGTATGTGAAGAGAATAGAATGCACT 59.506 37.037 0.00 0.00 0.00 4.40
3216 6972 8.043113 TGTATGTGAAGAGAATAGAATGCACTT 58.957 33.333 0.00 0.00 0.00 3.16
3217 6973 9.534565 GTATGTGAAGAGAATAGAATGCACTTA 57.465 33.333 0.00 0.00 0.00 2.24
3219 6975 8.846943 TGTGAAGAGAATAGAATGCACTTAAA 57.153 30.769 0.00 0.00 0.00 1.52
3220 6976 9.283768 TGTGAAGAGAATAGAATGCACTTAAAA 57.716 29.630 0.00 0.00 0.00 1.52
3255 7011 9.852091 AAGAAAAGAATAGAATGCAAAGTGATC 57.148 29.630 0.00 0.00 0.00 2.92
3256 7012 8.180267 AGAAAAGAATAGAATGCAAAGTGATCG 58.820 33.333 0.00 0.00 0.00 3.69
3278 7034 3.538634 AGATTCGGCTGTAACTAACCC 57.461 47.619 0.00 0.00 0.00 4.11
3283 7039 2.081462 CGGCTGTAACTAACCCAAAGG 58.919 52.381 0.00 0.00 40.04 3.11
3288 7044 5.245301 GGCTGTAACTAACCCAAAGGAAATT 59.755 40.000 0.00 0.00 36.73 1.82
3390 7146 2.022129 CACGCCTCAGACGAACCAC 61.022 63.158 0.00 0.00 0.00 4.16
3393 7186 2.432628 CCTCAGACGAACCACGCC 60.433 66.667 0.00 0.00 46.94 5.68
3533 7329 1.910580 GAATTCCTCCAGCCCACCGA 61.911 60.000 0.00 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 9.369672 AGTACCATTTAAAAACAAGGACCATAA 57.630 29.630 0.00 0.00 0.00 1.90
8 9 8.943594 AGTACCATTTAAAAACAAGGACCATA 57.056 30.769 0.00 0.00 0.00 2.74
9 10 7.039293 GGAGTACCATTTAAAAACAAGGACCAT 60.039 37.037 0.00 0.00 35.97 3.55
10 11 6.265876 GGAGTACCATTTAAAAACAAGGACCA 59.734 38.462 0.00 0.00 35.97 4.02
11 12 6.294899 GGGAGTACCATTTAAAAACAAGGACC 60.295 42.308 0.00 0.00 39.85 4.46
12 13 6.492429 AGGGAGTACCATTTAAAAACAAGGAC 59.508 38.462 0.00 0.00 43.89 3.85
13 14 6.616577 AGGGAGTACCATTTAAAAACAAGGA 58.383 36.000 0.00 0.00 43.89 3.36
14 15 6.071560 GGAGGGAGTACCATTTAAAAACAAGG 60.072 42.308 0.00 0.00 43.89 3.61
15 16 6.349033 CGGAGGGAGTACCATTTAAAAACAAG 60.349 42.308 0.00 0.00 43.89 3.16
16 17 5.474189 CGGAGGGAGTACCATTTAAAAACAA 59.526 40.000 0.00 0.00 43.89 2.83
17 18 5.005094 CGGAGGGAGTACCATTTAAAAACA 58.995 41.667 0.00 0.00 43.89 2.83
18 19 5.005740 ACGGAGGGAGTACCATTTAAAAAC 58.994 41.667 0.00 0.00 43.89 2.43
19 20 5.245584 ACGGAGGGAGTACCATTTAAAAA 57.754 39.130 0.00 0.00 43.89 1.94
20 21 4.914177 ACGGAGGGAGTACCATTTAAAA 57.086 40.909 0.00 0.00 43.89 1.52
21 22 4.914177 AACGGAGGGAGTACCATTTAAA 57.086 40.909 0.00 0.00 43.89 1.52
22 23 4.914177 AAACGGAGGGAGTACCATTTAA 57.086 40.909 0.00 0.00 43.89 1.52
23 24 4.914177 AAAACGGAGGGAGTACCATTTA 57.086 40.909 0.00 0.00 43.89 1.40
24 25 3.801307 AAAACGGAGGGAGTACCATTT 57.199 42.857 0.00 0.00 43.89 2.32
25 26 3.801307 AAAAACGGAGGGAGTACCATT 57.199 42.857 0.00 0.00 43.89 3.16
26 27 5.446260 AATAAAAACGGAGGGAGTACCAT 57.554 39.130 0.00 0.00 43.89 3.55
27 28 4.914177 AATAAAAACGGAGGGAGTACCA 57.086 40.909 0.00 0.00 43.89 3.25
28 29 6.409704 ACTAAATAAAAACGGAGGGAGTACC 58.590 40.000 0.00 0.00 40.67 3.34
29 30 6.536582 GGACTAAATAAAAACGGAGGGAGTAC 59.463 42.308 0.00 0.00 0.00 2.73
30 31 6.213195 TGGACTAAATAAAAACGGAGGGAGTA 59.787 38.462 0.00 0.00 0.00 2.59
31 32 5.013391 TGGACTAAATAAAAACGGAGGGAGT 59.987 40.000 0.00 0.00 0.00 3.85
32 33 5.493809 TGGACTAAATAAAAACGGAGGGAG 58.506 41.667 0.00 0.00 0.00 4.30
33 34 5.502089 TGGACTAAATAAAAACGGAGGGA 57.498 39.130 0.00 0.00 0.00 4.20
34 35 5.650703 ACATGGACTAAATAAAAACGGAGGG 59.349 40.000 0.00 0.00 0.00 4.30
35 36 6.753107 ACATGGACTAAATAAAAACGGAGG 57.247 37.500 0.00 0.00 0.00 4.30
38 39 9.659830 GCTAATACATGGACTAAATAAAAACGG 57.340 33.333 0.00 0.00 0.00 4.44
49 50 9.817809 CTTTGACTAAAGCTAATACATGGACTA 57.182 33.333 0.00 0.00 37.12 2.59
50 51 8.322091 ACTTTGACTAAAGCTAATACATGGACT 58.678 33.333 0.00 0.00 45.72 3.85
51 52 8.494016 ACTTTGACTAAAGCTAATACATGGAC 57.506 34.615 0.00 0.00 45.72 4.02
54 55 9.901724 CGTAACTTTGACTAAAGCTAATACATG 57.098 33.333 0.00 0.00 45.72 3.21
55 56 8.601476 GCGTAACTTTGACTAAAGCTAATACAT 58.399 33.333 0.00 0.00 45.72 2.29
56 57 7.816031 AGCGTAACTTTGACTAAAGCTAATACA 59.184 33.333 0.00 0.00 45.72 2.29
57 58 8.182658 AGCGTAACTTTGACTAAAGCTAATAC 57.817 34.615 0.00 0.00 45.72 1.89
58 59 8.767478 AAGCGTAACTTTGACTAAAGCTAATA 57.233 30.769 0.00 0.00 45.72 0.98
59 60 7.668525 AAGCGTAACTTTGACTAAAGCTAAT 57.331 32.000 0.00 0.00 45.72 1.73
60 61 7.486802 AAAGCGTAACTTTGACTAAAGCTAA 57.513 32.000 0.00 0.00 47.00 3.09
73 74 6.844254 TGTCAAAGTTTACAAAGCGTAACTT 58.156 32.000 0.00 0.00 39.84 2.66
74 75 6.425577 TGTCAAAGTTTACAAAGCGTAACT 57.574 33.333 0.00 0.00 39.84 2.24
75 76 7.495339 TTTGTCAAAGTTTACAAAGCGTAAC 57.505 32.000 14.22 0.00 39.88 2.50
229 230 8.122952 AGTTGACTGAAATCAAACTTCGTAAAG 58.877 33.333 0.00 0.00 40.22 1.85
230 231 7.981142 AGTTGACTGAAATCAAACTTCGTAAA 58.019 30.769 0.00 0.00 40.22 2.01
231 232 7.548196 AGTTGACTGAAATCAAACTTCGTAA 57.452 32.000 0.00 0.00 40.22 3.18
232 233 7.548196 AAGTTGACTGAAATCAAACTTCGTA 57.452 32.000 6.08 0.00 40.22 3.43
233 234 6.436843 AAGTTGACTGAAATCAAACTTCGT 57.563 33.333 6.08 0.00 40.22 3.85
234 235 8.835467 TTAAAGTTGACTGAAATCAAACTTCG 57.165 30.769 10.51 0.00 40.22 3.79
240 241 9.844790 CAGCATATTAAAGTTGACTGAAATCAA 57.155 29.630 0.00 0.00 36.23 2.57
241 242 9.230122 TCAGCATATTAAAGTTGACTGAAATCA 57.770 29.630 0.00 0.00 30.46 2.57
242 243 9.713740 CTCAGCATATTAAAGTTGACTGAAATC 57.286 33.333 0.00 0.00 32.94 2.17
243 244 9.236006 ACTCAGCATATTAAAGTTGACTGAAAT 57.764 29.630 0.00 0.00 32.94 2.17
244 245 8.621532 ACTCAGCATATTAAAGTTGACTGAAA 57.378 30.769 0.00 0.00 32.94 2.69
245 246 9.719355 TTACTCAGCATATTAAAGTTGACTGAA 57.281 29.630 0.00 0.00 32.94 3.02
246 247 9.719355 TTTACTCAGCATATTAAAGTTGACTGA 57.281 29.630 0.00 0.00 0.00 3.41
258 259 9.391006 TCTCCGTTTTTATTTACTCAGCATATT 57.609 29.630 0.00 0.00 0.00 1.28
259 260 8.958119 TCTCCGTTTTTATTTACTCAGCATAT 57.042 30.769 0.00 0.00 0.00 1.78
260 261 8.780846 TTCTCCGTTTTTATTTACTCAGCATA 57.219 30.769 0.00 0.00 0.00 3.14
261 262 7.390718 ACTTCTCCGTTTTTATTTACTCAGCAT 59.609 33.333 0.00 0.00 0.00 3.79
262 263 6.708949 ACTTCTCCGTTTTTATTTACTCAGCA 59.291 34.615 0.00 0.00 0.00 4.41
263 264 7.130303 ACTTCTCCGTTTTTATTTACTCAGC 57.870 36.000 0.00 0.00 0.00 4.26
264 265 8.371053 CGTACTTCTCCGTTTTTATTTACTCAG 58.629 37.037 0.00 0.00 0.00 3.35
265 266 8.081633 TCGTACTTCTCCGTTTTTATTTACTCA 58.918 33.333 0.00 0.00 0.00 3.41
266 267 8.452989 TCGTACTTCTCCGTTTTTATTTACTC 57.547 34.615 0.00 0.00 0.00 2.59
267 268 8.992835 ATCGTACTTCTCCGTTTTTATTTACT 57.007 30.769 0.00 0.00 0.00 2.24
270 271 8.992835 AGTATCGTACTTCTCCGTTTTTATTT 57.007 30.769 0.00 0.00 34.86 1.40
271 272 9.727627 CTAGTATCGTACTTCTCCGTTTTTATT 57.272 33.333 3.56 0.00 40.14 1.40
272 273 8.897752 ACTAGTATCGTACTTCTCCGTTTTTAT 58.102 33.333 0.00 0.00 40.14 1.40
273 274 8.177663 CACTAGTATCGTACTTCTCCGTTTTTA 58.822 37.037 0.00 0.00 40.14 1.52
274 275 7.025963 CACTAGTATCGTACTTCTCCGTTTTT 58.974 38.462 0.00 0.00 40.14 1.94
275 276 6.404074 CCACTAGTATCGTACTTCTCCGTTTT 60.404 42.308 0.00 0.00 40.14 2.43
276 277 5.065731 CCACTAGTATCGTACTTCTCCGTTT 59.934 44.000 0.00 0.00 40.14 3.60
277 278 4.574013 CCACTAGTATCGTACTTCTCCGTT 59.426 45.833 0.00 0.00 40.14 4.44
278 279 4.125703 CCACTAGTATCGTACTTCTCCGT 58.874 47.826 0.00 0.00 40.14 4.69
279 280 4.210955 GTCCACTAGTATCGTACTTCTCCG 59.789 50.000 0.00 0.00 40.14 4.63
280 281 4.514816 GGTCCACTAGTATCGTACTTCTCC 59.485 50.000 0.00 0.00 40.14 3.71
281 282 5.121811 TGGTCCACTAGTATCGTACTTCTC 58.878 45.833 0.00 0.00 40.14 2.87
282 283 5.108187 TGGTCCACTAGTATCGTACTTCT 57.892 43.478 0.00 0.00 40.14 2.85
283 284 5.530171 TGATGGTCCACTAGTATCGTACTTC 59.470 44.000 0.00 0.00 40.14 3.01
284 285 5.443283 TGATGGTCCACTAGTATCGTACTT 58.557 41.667 0.00 0.00 40.14 2.24
285 286 5.045012 TGATGGTCCACTAGTATCGTACT 57.955 43.478 0.00 3.71 42.68 2.73
286 287 4.820716 ACTGATGGTCCACTAGTATCGTAC 59.179 45.833 7.85 0.00 0.00 3.67
287 288 4.820173 CACTGATGGTCCACTAGTATCGTA 59.180 45.833 9.01 0.00 0.00 3.43
288 289 3.632604 CACTGATGGTCCACTAGTATCGT 59.367 47.826 9.01 0.00 0.00 3.73
289 290 3.551046 GCACTGATGGTCCACTAGTATCG 60.551 52.174 9.01 0.88 0.00 2.92
441 444 8.246180 ACATAGTGTTCATGTGGATTTTGATTC 58.754 33.333 0.00 0.00 35.33 2.52
465 468 1.119684 CAGGTATCCGGGTGATCACA 58.880 55.000 26.47 7.13 34.76 3.58
506 509 1.045911 AGGATTCCGCTGTCTCCTCC 61.046 60.000 0.00 0.00 32.62 4.30
577 584 3.121030 GTGTGGTAGCAGGCGCAG 61.121 66.667 10.83 1.27 42.27 5.18
637 644 2.152699 GTCGTGCGTGGACTCGATG 61.153 63.158 0.00 0.00 34.93 3.84
697 704 1.482593 ACCTGGTCACTGATTCGATCC 59.517 52.381 0.00 0.00 0.00 3.36
817 827 1.939769 GATCGGCTAGGATCGGAGGC 61.940 65.000 8.52 8.52 34.07 4.70
823 833 1.502640 CGACGGATCGGCTAGGATC 59.497 63.158 0.00 0.00 44.99 3.36
824 834 3.669686 CGACGGATCGGCTAGGAT 58.330 61.111 0.00 0.00 44.99 3.24
905 940 4.946445 TCTCTCGAGCTTCTACTTATCGA 58.054 43.478 7.81 0.00 39.85 3.59
911 950 5.093849 AGTAGTTCTCTCGAGCTTCTACT 57.906 43.478 21.63 21.63 34.56 2.57
977 1016 3.787001 CCCGCCCTTGACCTCCTC 61.787 72.222 0.00 0.00 0.00 3.71
985 1024 1.153086 CCATCTTCTCCCGCCCTTG 60.153 63.158 0.00 0.00 0.00 3.61
989 1028 0.250081 GATCACCATCTTCTCCCGCC 60.250 60.000 0.00 0.00 0.00 6.13
1084 1123 3.550820 TGCAAGGAGTAAGCAACTTTGA 58.449 40.909 7.47 0.00 39.07 2.69
1085 1124 3.988379 TGCAAGGAGTAAGCAACTTTG 57.012 42.857 0.00 0.00 39.07 2.77
1135 1201 7.458806 TCCCATATGAATCTGATAGTCCATTCA 59.541 37.037 3.65 0.00 39.09 2.57
1145 1214 9.736414 CAAATTAGTCTCCCATATGAATCTGAT 57.264 33.333 3.65 0.00 0.00 2.90
1184 1254 2.923605 ACATCGAGAAGACGAGAACC 57.076 50.000 0.00 0.00 45.22 3.62
1188 1258 4.496673 CCCTAAGAACATCGAGAAGACGAG 60.497 50.000 0.00 0.00 45.22 4.18
1210 1280 0.607620 CCTAGCTAGCAGGCTGATCC 59.392 60.000 20.86 6.98 43.01 3.36
1213 1283 0.826715 CAACCTAGCTAGCAGGCTGA 59.173 55.000 24.56 0.00 43.01 4.26
1236 1321 8.828688 AGTTAATAACCAGACACTAGTTTCAC 57.171 34.615 11.48 0.00 0.00 3.18
1250 1335 7.981142 ACTTTCTTACAGGGAGTTAATAACCA 58.019 34.615 0.00 0.00 0.00 3.67
1260 1345 8.148999 ACTAACAGTAAACTTTCTTACAGGGAG 58.851 37.037 0.00 0.00 34.75 4.30
1279 1371 3.120234 TGCAATCGCATGACAACTAACAG 60.120 43.478 0.00 0.00 45.36 3.16
1315 1419 7.390440 TGAGCTACTACAGGTTTTTACGTAGTA 59.610 37.037 0.00 0.00 42.01 1.82
1316 1420 6.207417 TGAGCTACTACAGGTTTTTACGTAGT 59.793 38.462 0.00 0.00 44.93 2.73
1317 1421 6.615088 TGAGCTACTACAGGTTTTTACGTAG 58.385 40.000 0.00 0.00 37.84 3.51
1334 1444 4.376146 CCCTTGAATCTAAGCTGAGCTAC 58.624 47.826 7.68 0.00 38.25 3.58
1351 1461 3.321111 TCGCTAATCTTACTAGCCCCTTG 59.679 47.826 0.00 0.00 38.88 3.61
1361 1472 9.211556 GATGCTTAAAAAGTTCGCTAATCTTAC 57.788 33.333 0.00 0.00 0.00 2.34
1421 1714 0.593128 ACAGTCAACGCCAGCATTTC 59.407 50.000 0.00 0.00 0.00 2.17
1474 3583 4.774726 ACATGACAGTGTTAGAGACAGGAT 59.225 41.667 0.00 0.00 39.39 3.24
1476 3585 4.021981 TCACATGACAGTGTTAGAGACAGG 60.022 45.833 0.00 0.00 39.39 4.00
2005 4128 3.711541 ATCGTGTCTTACCGCCGGC 62.712 63.158 19.07 19.07 0.00 6.13
2050 4191 0.690762 GTCAGGTAAAGGGCTGGTCA 59.309 55.000 0.00 0.00 0.00 4.02
2053 4194 1.208293 GAGAGTCAGGTAAAGGGCTGG 59.792 57.143 0.00 0.00 0.00 4.85
2085 4247 1.601903 GTCTGGACAAACACGATGCAA 59.398 47.619 0.00 0.00 0.00 4.08
2123 4286 4.821589 GGCCCCTGCTCGAAGTCG 62.822 72.222 0.00 0.00 41.45 4.18
2522 4685 2.574955 GGTCCGGCTATGGATCGCT 61.575 63.158 0.00 0.00 40.91 4.93
2708 4873 3.843632 TGTGTTTCAGACGCAATGC 57.156 47.368 0.00 0.00 45.27 3.56
2797 4966 0.373716 CAAGTCCGCATAAAGCCGTC 59.626 55.000 0.00 0.00 41.38 4.79
2816 5696 3.507622 AGTTCAGGTGCCAGAAATTTAGC 59.492 43.478 0.00 0.00 0.00 3.09
2818 5763 7.775053 ATAAAGTTCAGGTGCCAGAAATTTA 57.225 32.000 21.87 21.87 41.93 1.40
2821 5766 6.670695 AAATAAAGTTCAGGTGCCAGAAAT 57.329 33.333 0.00 0.00 0.00 2.17
2849 5794 1.977594 GACGGCGGCGATGTTCAAAT 61.978 55.000 38.93 12.27 0.00 2.32
2898 5843 5.817296 CGTTCCATGATTAAACAGAGGATCA 59.183 40.000 9.53 0.00 37.82 2.92
2901 5846 5.160607 ACGTTCCATGATTAAACAGAGGA 57.839 39.130 0.00 5.82 0.00 3.71
2902 5847 5.181245 ACAACGTTCCATGATTAAACAGAGG 59.819 40.000 0.00 1.83 0.00 3.69
2905 5850 6.072948 TGGTACAACGTTCCATGATTAAACAG 60.073 38.462 0.00 0.00 31.92 3.16
2906 5851 5.763698 TGGTACAACGTTCCATGATTAAACA 59.236 36.000 0.00 0.00 31.92 2.83
2979 6732 9.541143 TCAATGACATAAAACTTAGATATGCGA 57.459 29.630 0.00 0.00 31.66 5.10
2989 6742 9.214957 TCACGTAAGATCAATGACATAAAACTT 57.785 29.630 0.00 0.00 43.62 2.66
2990 6743 8.771920 TCACGTAAGATCAATGACATAAAACT 57.228 30.769 0.00 0.00 43.62 2.66
2991 6744 8.656849 ACTCACGTAAGATCAATGACATAAAAC 58.343 33.333 0.00 0.00 43.62 2.43
2992 6745 8.771920 ACTCACGTAAGATCAATGACATAAAA 57.228 30.769 0.00 0.00 43.62 1.52
2996 6749 8.948631 AAATACTCACGTAAGATCAATGACAT 57.051 30.769 0.00 0.00 43.62 3.06
2997 6750 8.771920 AAAATACTCACGTAAGATCAATGACA 57.228 30.769 0.00 0.00 43.62 3.58
3022 6775 9.932207 TCTAAGTGACTTAATCGACCATAAAAA 57.068 29.630 6.51 0.00 0.00 1.94
3024 6777 9.529325 CATCTAAGTGACTTAATCGACCATAAA 57.471 33.333 6.51 0.00 0.00 1.40
3025 6778 8.141909 CCATCTAAGTGACTTAATCGACCATAA 58.858 37.037 6.51 0.00 0.00 1.90
3026 6779 7.255836 CCCATCTAAGTGACTTAATCGACCATA 60.256 40.741 6.51 0.00 0.00 2.74
3027 6780 6.463049 CCCATCTAAGTGACTTAATCGACCAT 60.463 42.308 6.51 0.00 0.00 3.55
3028 6781 5.163447 CCCATCTAAGTGACTTAATCGACCA 60.163 44.000 6.51 0.00 0.00 4.02
3029 6782 5.290386 CCCATCTAAGTGACTTAATCGACC 58.710 45.833 6.51 0.00 0.00 4.79
3030 6783 4.745620 GCCCATCTAAGTGACTTAATCGAC 59.254 45.833 6.51 0.00 0.00 4.20
3031 6784 4.649674 AGCCCATCTAAGTGACTTAATCGA 59.350 41.667 6.51 1.18 0.00 3.59
3032 6785 4.950050 AGCCCATCTAAGTGACTTAATCG 58.050 43.478 6.51 0.00 0.00 3.34
3033 6786 6.038714 CCAAAGCCCATCTAAGTGACTTAATC 59.961 42.308 6.51 0.00 0.00 1.75
3034 6787 5.888161 CCAAAGCCCATCTAAGTGACTTAAT 59.112 40.000 6.51 1.18 0.00 1.40
3035 6788 5.013704 TCCAAAGCCCATCTAAGTGACTTAA 59.986 40.000 6.51 0.00 0.00 1.85
3036 6789 4.534500 TCCAAAGCCCATCTAAGTGACTTA 59.466 41.667 4.81 4.81 0.00 2.24
3037 6790 3.330701 TCCAAAGCCCATCTAAGTGACTT 59.669 43.478 2.37 2.37 0.00 3.01
3038 6791 2.912956 TCCAAAGCCCATCTAAGTGACT 59.087 45.455 0.00 0.00 0.00 3.41
3039 6792 3.350219 TCCAAAGCCCATCTAAGTGAC 57.650 47.619 0.00 0.00 0.00 3.67
3040 6793 3.523157 TGATCCAAAGCCCATCTAAGTGA 59.477 43.478 0.00 0.00 0.00 3.41
3041 6794 3.889815 TGATCCAAAGCCCATCTAAGTG 58.110 45.455 0.00 0.00 0.00 3.16
3042 6795 4.414846 AGATGATCCAAAGCCCATCTAAGT 59.585 41.667 0.00 0.00 42.57 2.24
3043 6796 4.983053 AGATGATCCAAAGCCCATCTAAG 58.017 43.478 0.00 0.00 42.57 2.18
3044 6797 5.103982 TCAAGATGATCCAAAGCCCATCTAA 60.104 40.000 0.00 0.00 43.29 2.10
3045 6798 4.413189 TCAAGATGATCCAAAGCCCATCTA 59.587 41.667 0.00 0.00 43.29 1.98
3046 6799 3.203710 TCAAGATGATCCAAAGCCCATCT 59.796 43.478 0.00 0.00 45.25 2.90
3047 6800 3.559069 TCAAGATGATCCAAAGCCCATC 58.441 45.455 0.00 0.00 36.56 3.51
3048 6801 3.675348 TCAAGATGATCCAAAGCCCAT 57.325 42.857 0.00 0.00 0.00 4.00
3049 6802 3.559069 GATCAAGATGATCCAAAGCCCA 58.441 45.455 8.79 0.00 45.66 5.36
3059 6812 8.222637 TCATTAATCAAGGTGGATCAAGATGAT 58.777 33.333 0.00 0.00 40.34 2.45
3060 6813 7.576403 TCATTAATCAAGGTGGATCAAGATGA 58.424 34.615 0.00 0.00 0.00 2.92
3061 6814 7.812690 TCATTAATCAAGGTGGATCAAGATG 57.187 36.000 0.00 0.00 0.00 2.90
3062 6815 8.827832 TTTCATTAATCAAGGTGGATCAAGAT 57.172 30.769 0.00 0.00 0.00 2.40
3063 6816 7.148018 GCTTTCATTAATCAAGGTGGATCAAGA 60.148 37.037 0.00 0.00 0.00 3.02
3064 6817 6.976925 GCTTTCATTAATCAAGGTGGATCAAG 59.023 38.462 0.00 0.00 0.00 3.02
3065 6818 6.664816 AGCTTTCATTAATCAAGGTGGATCAA 59.335 34.615 7.51 0.00 0.00 2.57
3066 6819 6.189859 AGCTTTCATTAATCAAGGTGGATCA 58.810 36.000 7.51 0.00 0.00 2.92
3067 6820 6.705863 AGCTTTCATTAATCAAGGTGGATC 57.294 37.500 7.51 0.00 0.00 3.36
3068 6821 8.773033 AATAGCTTTCATTAATCAAGGTGGAT 57.227 30.769 14.76 3.63 30.99 3.41
3069 6822 8.593945 AAATAGCTTTCATTAATCAAGGTGGA 57.406 30.769 14.76 1.92 30.99 4.02
3070 6823 9.305925 GAAAATAGCTTTCATTAATCAAGGTGG 57.694 33.333 14.76 0.00 42.68 4.61
3071 6824 9.859427 TGAAAATAGCTTTCATTAATCAAGGTG 57.141 29.630 14.76 0.00 46.80 4.00
3120 6873 2.235016 TGTTGGGTCTGTTTATGGCAC 58.765 47.619 0.00 0.00 0.00 5.01
3121 6874 2.625790 GTTGTTGGGTCTGTTTATGGCA 59.374 45.455 0.00 0.00 0.00 4.92
3122 6875 2.351350 CGTTGTTGGGTCTGTTTATGGC 60.351 50.000 0.00 0.00 0.00 4.40
3123 6876 2.882137 ACGTTGTTGGGTCTGTTTATGG 59.118 45.455 0.00 0.00 0.00 2.74
3124 6877 4.561735 AACGTTGTTGGGTCTGTTTATG 57.438 40.909 0.00 0.00 0.00 1.90
3125 6878 5.585820 AAAACGTTGTTGGGTCTGTTTAT 57.414 34.783 0.00 0.00 0.00 1.40
3126 6879 5.183522 AGAAAAACGTTGTTGGGTCTGTTTA 59.816 36.000 8.82 0.00 0.00 2.01
3127 6880 3.945981 AAAACGTTGTTGGGTCTGTTT 57.054 38.095 0.00 0.00 0.00 2.83
3128 6881 3.508402 AGAAAAACGTTGTTGGGTCTGTT 59.492 39.130 8.82 0.00 0.00 3.16
3129 6882 3.086282 AGAAAAACGTTGTTGGGTCTGT 58.914 40.909 8.82 0.00 0.00 3.41
3130 6883 3.775661 AGAAAAACGTTGTTGGGTCTG 57.224 42.857 8.82 0.00 0.00 3.51
3131 6884 4.095334 GTGTAGAAAAACGTTGTTGGGTCT 59.905 41.667 8.82 1.89 0.00 3.85
3132 6885 4.142643 TGTGTAGAAAAACGTTGTTGGGTC 60.143 41.667 8.82 0.00 0.00 4.46
3133 6886 3.757493 TGTGTAGAAAAACGTTGTTGGGT 59.243 39.130 8.82 0.00 0.00 4.51
3134 6887 4.358494 TGTGTAGAAAAACGTTGTTGGG 57.642 40.909 8.82 0.00 0.00 4.12
3135 6888 5.336744 ACATGTGTAGAAAAACGTTGTTGG 58.663 37.500 8.82 0.00 0.00 3.77
3136 6889 6.255215 AGACATGTGTAGAAAAACGTTGTTG 58.745 36.000 8.82 0.00 0.00 3.33
3137 6890 6.431198 AGACATGTGTAGAAAAACGTTGTT 57.569 33.333 1.15 2.60 0.00 2.83
3138 6891 6.255215 CAAGACATGTGTAGAAAAACGTTGT 58.745 36.000 1.15 0.00 0.00 3.32
3139 6892 5.171337 GCAAGACATGTGTAGAAAAACGTTG 59.829 40.000 1.15 0.00 0.00 4.10
3140 6893 5.065988 AGCAAGACATGTGTAGAAAAACGTT 59.934 36.000 1.15 0.00 0.00 3.99
3141 6894 4.574828 AGCAAGACATGTGTAGAAAAACGT 59.425 37.500 1.15 0.00 0.00 3.99
3142 6895 5.095691 AGCAAGACATGTGTAGAAAAACG 57.904 39.130 1.15 0.00 0.00 3.60
3143 6896 5.452777 GGAGCAAGACATGTGTAGAAAAAC 58.547 41.667 1.15 0.00 0.00 2.43
3144 6897 4.213270 CGGAGCAAGACATGTGTAGAAAAA 59.787 41.667 1.15 0.00 0.00 1.94
3145 6898 3.745975 CGGAGCAAGACATGTGTAGAAAA 59.254 43.478 1.15 0.00 0.00 2.29
3146 6899 3.244078 ACGGAGCAAGACATGTGTAGAAA 60.244 43.478 1.15 0.00 0.00 2.52
3163 6917 1.982660 TGTCCTATCCAGCTACGGAG 58.017 55.000 0.00 0.00 38.83 4.63
3193 6949 9.453572 TTTAAGTGCATTCTATTCTCTTCACAT 57.546 29.630 0.00 0.00 0.00 3.21
3220 6976 9.481340 GCATTCTATTCTTTTCTTTTCCTGTTT 57.519 29.630 0.00 0.00 0.00 2.83
3221 6977 8.641541 TGCATTCTATTCTTTTCTTTTCCTGTT 58.358 29.630 0.00 0.00 0.00 3.16
3222 6978 8.181904 TGCATTCTATTCTTTTCTTTTCCTGT 57.818 30.769 0.00 0.00 0.00 4.00
3223 6979 9.480053 TTTGCATTCTATTCTTTTCTTTTCCTG 57.520 29.630 0.00 0.00 0.00 3.86
3224 6980 9.702494 CTTTGCATTCTATTCTTTTCTTTTCCT 57.298 29.630 0.00 0.00 0.00 3.36
3225 6981 9.481340 ACTTTGCATTCTATTCTTTTCTTTTCC 57.519 29.630 0.00 0.00 0.00 3.13
3231 6987 8.177663 TCGATCACTTTGCATTCTATTCTTTTC 58.822 33.333 0.00 0.00 0.00 2.29
3234 6990 7.550551 TCTTCGATCACTTTGCATTCTATTCTT 59.449 33.333 0.00 0.00 0.00 2.52
3239 6995 7.239166 GAATCTTCGATCACTTTGCATTCTA 57.761 36.000 0.00 0.00 0.00 2.10
3256 7012 3.869832 GGGTTAGTTACAGCCGAATCTTC 59.130 47.826 0.00 0.00 0.00 2.87
3301 7057 8.395633 CCGATTCTATTCCGTTTTATTCAGTTT 58.604 33.333 0.00 0.00 0.00 2.66
3302 7058 7.767198 TCCGATTCTATTCCGTTTTATTCAGTT 59.233 33.333 0.00 0.00 0.00 3.16
3303 7059 7.270047 TCCGATTCTATTCCGTTTTATTCAGT 58.730 34.615 0.00 0.00 0.00 3.41
3383 7139 1.203313 GACGAAAAGGCGTGGTTCG 59.797 57.895 18.52 18.52 45.72 3.95
3390 7146 1.868498 TGTAAACTGGACGAAAAGGCG 59.132 47.619 0.00 0.00 37.29 5.52
3393 7186 5.941948 AATCCTGTAAACTGGACGAAAAG 57.058 39.130 10.51 0.00 44.92 2.27
3492 7286 6.075762 TCGTTTATTTATAGTGGCGAGCTA 57.924 37.500 0.00 0.00 0.00 3.32
3533 7329 4.283722 GGTCAGAATAGTATCGGTGGGATT 59.716 45.833 0.00 0.00 36.55 3.01


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

AutoCloner maintained by Alex Coulton.