Multiple sequence alignment - TraesCS1A01G307500

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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 TraesCS1A01G307500 chr1A 100.000 2970 0 0 1 2970 499174582 499177551 0.000000e+00 5485.0
1 TraesCS1A01G307500 chr1D 91.582 1188 85 12 1501 2678 403664032 403665214 0.000000e+00 1626.0
2 TraesCS1A01G307500 chr1D 91.366 1135 65 18 63 1181 403662885 403664002 0.000000e+00 1522.0
3 TraesCS1A01G307500 chr1D 92.910 268 17 1 2703 2970 403665406 403665671 3.590000e-104 388.0
4 TraesCS1A01G307500 chr1D 86.034 179 13 11 1329 1496 452848304 452848481 6.540000e-42 182.0
5 TraesCS1A01G307500 chr1D 84.916 179 15 7 1320 1490 238940191 238940365 1.420000e-38 171.0
6 TraesCS1A01G307500 chr1D 74.411 297 62 7 2089 2384 252853049 252852766 6.730000e-22 115.0
7 TraesCS1A01G307500 chr1D 80.451 133 18 5 53 184 60178445 60178570 8.760000e-16 95.3
8 TraesCS1A01G307500 chr1B 90.117 941 66 13 2 924 542956779 542957710 0.000000e+00 1197.0
9 TraesCS1A01G307500 chr1B 94.072 388 20 3 1501 1885 542958026 542958413 1.190000e-163 586.0
10 TraesCS1A01G307500 chr1B 92.138 318 20 3 866 1181 542957685 542957999 7.550000e-121 444.0
11 TraesCS1A01G307500 chr1B 79.455 477 66 19 1898 2370 542958399 542958847 2.880000e-80 309.0
12 TraesCS1A01G307500 chr1B 85.965 171 15 7 1339 1503 523211914 523211747 1.090000e-39 174.0
13 TraesCS1A01G307500 chr6B 81.250 704 95 21 1 684 205359131 205359817 4.360000e-148 534.0
14 TraesCS1A01G307500 chr6B 88.679 159 11 7 1348 1499 171210866 171210708 1.410000e-43 187.0
15 TraesCS1A01G307500 chr7D 79.579 617 76 25 1 606 595029429 595030006 2.150000e-106 396.0
16 TraesCS1A01G307500 chr5D 77.151 709 99 30 1 684 536156657 536157327 1.310000e-93 353.0
17 TraesCS1A01G307500 chr5D 80.932 236 41 4 2054 2287 548675147 548674914 1.820000e-42 183.0
18 TraesCS1A01G307500 chr5D 77.558 303 33 17 413 684 300950170 300949872 1.840000e-32 150.0
19 TraesCS1A01G307500 chr7A 77.722 597 86 26 122 677 66605343 66605933 3.690000e-84 322.0
20 TraesCS1A01G307500 chr2D 79.022 491 64 19 1 487 85865322 85864867 1.730000e-77 300.0
21 TraesCS1A01G307500 chr2D 98.438 64 1 0 1181 1244 116829781 116829718 2.420000e-21 113.0
22 TraesCS1A01G307500 chr2D 75.510 245 42 10 1632 1866 47006686 47006450 1.460000e-18 104.0
23 TraesCS1A01G307500 chr2D 96.721 61 2 0 1181 1241 617967286 617967346 5.240000e-18 102.0
24 TraesCS1A01G307500 chr3A 79.437 462 60 21 236 677 1060865 1060419 8.050000e-76 294.0
25 TraesCS1A01G307500 chr3A 80.534 262 36 9 345 593 509014723 509014982 1.410000e-43 187.0
26 TraesCS1A01G307500 chr3A 96.875 64 2 0 1181 1244 34980900 34980837 1.130000e-19 108.0
27 TraesCS1A01G307500 chr3D 78.742 461 61 22 236 677 3568291 3567849 1.050000e-69 274.0
28 TraesCS1A01G307500 chr3D 78.134 343 52 12 363 682 387558962 387558620 2.340000e-46 196.0
29 TraesCS1A01G307500 chr3D 76.302 384 80 10 1991 2370 14295901 14296277 8.400000e-46 195.0
30 TraesCS1A01G307500 chr3D 85.211 142 18 3 351 490 29410062 29410202 3.090000e-30 143.0
31 TraesCS1A01G307500 chr2B 80.702 342 37 15 392 710 138817036 138816701 3.830000e-59 239.0
32 TraesCS1A01G307500 chr2B 88.199 161 12 3 1346 1499 741379625 741379465 5.060000e-43 185.0
33 TraesCS1A01G307500 chr4A 79.751 321 55 6 1 317 634878158 634878472 1.070000e-54 224.0
34 TraesCS1A01G307500 chr4A 88.199 161 14 5 1341 1496 40438397 40438557 1.410000e-43 187.0
35 TraesCS1A01G307500 chr4A 88.199 161 14 5 1341 1496 40493395 40493555 1.410000e-43 187.0
36 TraesCS1A01G307500 chr4A 81.915 188 19 4 509 684 36159549 36159733 8.580000e-31 145.0
37 TraesCS1A01G307500 chr3B 78.916 332 63 7 1997 2326 631612299 631612625 4.980000e-53 219.0
38 TraesCS1A01G307500 chr3B 87.805 164 13 3 1347 1503 12102281 12102118 5.060000e-43 185.0
39 TraesCS1A01G307500 chr3B 79.654 231 29 14 458 677 773840505 773840728 1.840000e-32 150.0
40 TraesCS1A01G307500 chr3B 79.149 235 35 11 458 683 773872451 773872222 1.840000e-32 150.0
41 TraesCS1A01G307500 chr3B 83.562 146 18 4 346 490 50239665 50239805 6.680000e-27 132.0
42 TraesCS1A01G307500 chr6A 78.644 295 59 4 1992 2284 617751676 617751968 3.020000e-45 193.0
43 TraesCS1A01G307500 chr6A 94.937 79 4 0 1246 1324 603085808 603085730 1.120000e-24 124.0
44 TraesCS1A01G307500 chr6A 96.875 64 2 0 1181 1244 513334155 513334092 1.130000e-19 108.0
45 TraesCS1A01G307500 chr5B 76.944 360 69 11 2011 2369 464314883 464314537 3.020000e-45 193.0
46 TraesCS1A01G307500 chr5B 76.944 360 69 11 2011 2369 464318921 464318575 3.020000e-45 193.0
47 TraesCS1A01G307500 chr5B 76.944 360 69 11 2011 2369 464320268 464319922 3.020000e-45 193.0
48 TraesCS1A01G307500 chr5B 88.608 158 11 3 1340 1490 531298070 531298227 5.060000e-43 185.0
49 TraesCS1A01G307500 chr5B 80.000 220 14 13 412 601 10078073 10077854 5.160000e-28 135.0
50 TraesCS1A01G307500 chr5B 96.721 61 2 0 1181 1241 419522559 419522619 5.240000e-18 102.0
51 TraesCS1A01G307500 chr5B 96.721 61 2 0 1181 1241 491851043 491851103 5.240000e-18 102.0
52 TraesCS1A01G307500 chr5A 78.523 298 60 4 1992 2287 563420320 563420025 3.020000e-45 193.0
53 TraesCS1A01G307500 chr5A 96.875 64 2 0 1181 1244 138080194 138080131 1.130000e-19 108.0
54 TraesCS1A01G307500 chr5A 95.238 42 2 0 434 475 675534363 675534322 1.910000e-07 67.6
55 TraesCS1A01G307500 chrUn 78.030 264 30 12 444 684 216304303 216304045 1.110000e-29 141.0
56 TraesCS1A01G307500 chrUn 92.857 84 5 1 1246 1329 80139339 80139257 1.450000e-23 121.0
57 TraesCS1A01G307500 chrUn 92.857 84 5 1 1246 1329 223956760 223956842 1.450000e-23 121.0
58 TraesCS1A01G307500 chrUn 96.875 64 2 0 1181 1244 8839885 8839822 1.130000e-19 108.0
59 TraesCS1A01G307500 chr2A 86.154 130 17 1 171 299 141511850 141511721 3.990000e-29 139.0
60 TraesCS1A01G307500 chr2A 93.333 90 4 1 1246 1335 102679676 102679589 6.680000e-27 132.0
61 TraesCS1A01G307500 chr2A 96.154 78 3 0 1246 1323 394743575 394743498 8.640000e-26 128.0
62 TraesCS1A01G307500 chr4D 96.154 78 3 0 1246 1323 75795367 75795290 8.640000e-26 128.0
63 TraesCS1A01G307500 chr4D 94.872 78 4 0 1246 1323 51917225 51917302 4.020000e-24 122.0
64 TraesCS1A01G307500 chr4D 88.350 103 6 4 1226 1324 7914003 7914103 5.200000e-23 119.0
65 TraesCS1A01G307500 chr4B 94.048 84 4 1 1246 1328 465734075 465733992 3.110000e-25 126.0
66 TraesCS1A01G307500 chr6D 98.361 61 1 0 1181 1241 39090292 39090352 1.130000e-19 108.0
67 TraesCS1A01G307500 chr6D 80.159 126 20 3 59 184 368299540 368299660 4.080000e-14 89.8


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 TraesCS1A01G307500 chr1A 499174582 499177551 2969 False 5485.000000 5485 100.000000 1 2970 1 chr1A.!!$F1 2969
1 TraesCS1A01G307500 chr1D 403662885 403665671 2786 False 1178.666667 1626 91.952667 63 2970 3 chr1D.!!$F4 2907
2 TraesCS1A01G307500 chr1B 542956779 542958847 2068 False 634.000000 1197 88.945500 2 2370 4 chr1B.!!$F1 2368
3 TraesCS1A01G307500 chr6B 205359131 205359817 686 False 534.000000 534 81.250000 1 684 1 chr6B.!!$F1 683
4 TraesCS1A01G307500 chr7D 595029429 595030006 577 False 396.000000 396 79.579000 1 606 1 chr7D.!!$F1 605
5 TraesCS1A01G307500 chr5D 536156657 536157327 670 False 353.000000 353 77.151000 1 684 1 chr5D.!!$F1 683
6 TraesCS1A01G307500 chr7A 66605343 66605933 590 False 322.000000 322 77.722000 122 677 1 chr7A.!!$F1 555

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
196 214 0.179045 GCCTCCATGAACGCCTGTAT 60.179 55.000 0.0 0.0 0.00 2.29 F
339 360 1.078918 GTGTACGGCCTACCAACCC 60.079 63.158 0.0 0.0 34.57 4.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1182 1307 0.248215 CCCTCGCAAAATGACATCGC 60.248 55.0 0.0 0.0 0.0 4.58 R
2217 2351 0.032912 TCTGGTGCGGTGGTCCTATA 60.033 55.0 0.0 0.0 0.0 1.31 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
184 202 7.200434 AGAAATATAATATGACCGCCTCCAT 57.800 36.000 0.00 0.00 0.00 3.41
191 209 4.778143 ACCGCCTCCATGAACGCC 62.778 66.667 0.00 0.00 0.00 5.68
196 214 0.179045 GCCTCCATGAACGCCTGTAT 60.179 55.000 0.00 0.00 0.00 2.29
197 215 1.871080 CCTCCATGAACGCCTGTATC 58.129 55.000 0.00 0.00 0.00 2.24
198 216 1.541233 CCTCCATGAACGCCTGTATCC 60.541 57.143 0.00 0.00 0.00 2.59
300 320 3.492337 AGGTGAAGGCGAAAATAAACCA 58.508 40.909 0.00 0.00 0.00 3.67
339 360 1.078918 GTGTACGGCCTACCAACCC 60.079 63.158 0.00 0.00 34.57 4.11
340 361 2.292559 TGTACGGCCTACCAACCCC 61.293 63.158 0.00 0.00 34.57 4.95
341 362 2.688299 TACGGCCTACCAACCCCC 60.688 66.667 0.00 0.00 34.57 5.40
456 500 8.795786 TGTTGTATTAGAAAAGTTGTGATTGC 57.204 30.769 0.00 0.00 0.00 3.56
507 552 1.825090 TGGCAGCACATTAAGGAGTG 58.175 50.000 0.00 0.00 38.74 3.51
701 782 3.249189 GGGGTGTGAGGTGAGGCA 61.249 66.667 0.00 0.00 0.00 4.75
864 953 4.260866 GCGAGGAGAGTTAGTACATCACTC 60.261 50.000 9.87 9.87 38.80 3.51
865 954 4.876679 CGAGGAGAGTTAGTACATCACTCA 59.123 45.833 16.88 0.00 39.63 3.41
882 971 9.797642 ACATCACTCATCCTAAATTAATGCATA 57.202 29.630 0.00 0.00 0.00 3.14
975 1099 4.693566 GCGTACAATGGCCTATAAATAGCA 59.306 41.667 3.32 0.00 0.00 3.49
979 1103 4.832823 ACAATGGCCTATAAATAGCAACCC 59.167 41.667 3.32 0.00 0.00 4.11
1127 1251 1.867233 GCAATGGAGGTACGCATGTAG 59.133 52.381 0.00 0.00 0.00 2.74
1128 1252 2.741878 GCAATGGAGGTACGCATGTAGT 60.742 50.000 0.00 0.00 0.00 2.73
1129 1253 3.491964 GCAATGGAGGTACGCATGTAGTA 60.492 47.826 0.00 0.00 0.00 1.82
1168 1292 4.023279 GCACACAAATACCTGAACACATCA 60.023 41.667 0.00 0.00 36.38 3.07
1181 1306 6.389830 TGAACACATCACTACTTTGCATTT 57.610 33.333 0.00 0.00 31.50 2.32
1182 1307 6.207928 TGAACACATCACTACTTTGCATTTG 58.792 36.000 0.00 0.00 31.50 2.32
1183 1308 4.549458 ACACATCACTACTTTGCATTTGC 58.451 39.130 0.00 0.00 42.50 3.68
1184 1309 3.605056 CACATCACTACTTTGCATTTGCG 59.395 43.478 0.00 0.00 45.83 4.85
1185 1310 3.501828 ACATCACTACTTTGCATTTGCGA 59.498 39.130 0.00 0.00 45.83 5.10
1186 1311 4.156556 ACATCACTACTTTGCATTTGCGAT 59.843 37.500 0.00 0.00 45.83 4.58
1187 1312 4.082274 TCACTACTTTGCATTTGCGATG 57.918 40.909 0.00 1.41 45.83 3.84
1188 1313 3.501828 TCACTACTTTGCATTTGCGATGT 59.498 39.130 13.80 13.80 45.83 3.06
1189 1314 3.848019 CACTACTTTGCATTTGCGATGTC 59.152 43.478 12.96 0.00 45.83 3.06
1190 1315 3.501828 ACTACTTTGCATTTGCGATGTCA 59.498 39.130 12.96 2.84 45.83 3.58
1191 1316 3.581024 ACTTTGCATTTGCGATGTCAT 57.419 38.095 5.69 0.00 45.83 3.06
1192 1317 3.916761 ACTTTGCATTTGCGATGTCATT 58.083 36.364 5.69 0.00 45.83 2.57
1193 1318 4.309099 ACTTTGCATTTGCGATGTCATTT 58.691 34.783 5.69 0.00 45.83 2.32
1194 1319 4.751098 ACTTTGCATTTGCGATGTCATTTT 59.249 33.333 5.69 0.00 45.83 1.82
1195 1320 4.648917 TTGCATTTGCGATGTCATTTTG 57.351 36.364 0.00 0.00 45.83 2.44
1196 1321 2.412429 TGCATTTGCGATGTCATTTTGC 59.588 40.909 0.00 0.00 45.83 3.68
1197 1322 2.533365 GCATTTGCGATGTCATTTTGCG 60.533 45.455 0.00 0.00 0.00 4.85
1198 1323 2.695613 TTTGCGATGTCATTTTGCGA 57.304 40.000 0.00 0.00 0.00 5.10
1199 1324 2.245795 TTGCGATGTCATTTTGCGAG 57.754 45.000 0.00 0.00 0.00 5.03
1200 1325 0.447406 TGCGATGTCATTTTGCGAGG 59.553 50.000 0.00 0.00 0.00 4.63
1201 1326 0.248215 GCGATGTCATTTTGCGAGGG 60.248 55.000 0.00 0.00 0.00 4.30
1202 1327 1.086696 CGATGTCATTTTGCGAGGGT 58.913 50.000 0.00 0.00 0.00 4.34
1203 1328 1.468520 CGATGTCATTTTGCGAGGGTT 59.531 47.619 0.00 0.00 0.00 4.11
1204 1329 2.095263 CGATGTCATTTTGCGAGGGTTT 60.095 45.455 0.00 0.00 0.00 3.27
1205 1330 2.791383 TGTCATTTTGCGAGGGTTTG 57.209 45.000 0.00 0.00 0.00 2.93
1206 1331 2.028130 TGTCATTTTGCGAGGGTTTGT 58.972 42.857 0.00 0.00 0.00 2.83
1207 1332 2.223688 TGTCATTTTGCGAGGGTTTGTG 60.224 45.455 0.00 0.00 0.00 3.33
1208 1333 1.339610 TCATTTTGCGAGGGTTTGTGG 59.660 47.619 0.00 0.00 0.00 4.17
1209 1334 1.068434 CATTTTGCGAGGGTTTGTGGT 59.932 47.619 0.00 0.00 0.00 4.16
1210 1335 1.187087 TTTTGCGAGGGTTTGTGGTT 58.813 45.000 0.00 0.00 0.00 3.67
1211 1336 0.457851 TTTGCGAGGGTTTGTGGTTG 59.542 50.000 0.00 0.00 0.00 3.77
1212 1337 0.681564 TTGCGAGGGTTTGTGGTTGT 60.682 50.000 0.00 0.00 0.00 3.32
1213 1338 0.681564 TGCGAGGGTTTGTGGTTGTT 60.682 50.000 0.00 0.00 0.00 2.83
1214 1339 0.248866 GCGAGGGTTTGTGGTTGTTG 60.249 55.000 0.00 0.00 0.00 3.33
1215 1340 0.248866 CGAGGGTTTGTGGTTGTTGC 60.249 55.000 0.00 0.00 0.00 4.17
1216 1341 0.820871 GAGGGTTTGTGGTTGTTGCA 59.179 50.000 0.00 0.00 0.00 4.08
1217 1342 1.412343 GAGGGTTTGTGGTTGTTGCAT 59.588 47.619 0.00 0.00 0.00 3.96
1218 1343 1.138661 AGGGTTTGTGGTTGTTGCATG 59.861 47.619 0.00 0.00 0.00 4.06
1219 1344 1.134551 GGGTTTGTGGTTGTTGCATGT 60.135 47.619 0.00 0.00 0.00 3.21
1220 1345 2.626840 GGTTTGTGGTTGTTGCATGTT 58.373 42.857 0.00 0.00 0.00 2.71
1221 1346 3.430929 GGGTTTGTGGTTGTTGCATGTTA 60.431 43.478 0.00 0.00 0.00 2.41
1222 1347 4.376146 GGTTTGTGGTTGTTGCATGTTAT 58.624 39.130 0.00 0.00 0.00 1.89
1223 1348 4.210955 GGTTTGTGGTTGTTGCATGTTATG 59.789 41.667 0.00 0.00 0.00 1.90
1224 1349 4.662468 TTGTGGTTGTTGCATGTTATGT 57.338 36.364 0.00 0.00 0.00 2.29
1225 1350 5.774498 TTGTGGTTGTTGCATGTTATGTA 57.226 34.783 0.00 0.00 0.00 2.29
1226 1351 5.973899 TGTGGTTGTTGCATGTTATGTAT 57.026 34.783 0.00 0.00 0.00 2.29
1227 1352 5.707931 TGTGGTTGTTGCATGTTATGTATG 58.292 37.500 0.00 0.00 0.00 2.39
1228 1353 5.242615 TGTGGTTGTTGCATGTTATGTATGT 59.757 36.000 0.00 0.00 0.00 2.29
1229 1354 6.155827 GTGGTTGTTGCATGTTATGTATGTT 58.844 36.000 0.00 0.00 0.00 2.71
1230 1355 6.644592 GTGGTTGTTGCATGTTATGTATGTTT 59.355 34.615 0.00 0.00 0.00 2.83
1231 1356 6.644181 TGGTTGTTGCATGTTATGTATGTTTG 59.356 34.615 0.00 0.00 0.00 2.93
1232 1357 6.644592 GGTTGTTGCATGTTATGTATGTTTGT 59.355 34.615 0.00 0.00 0.00 2.83
1233 1358 7.170658 GGTTGTTGCATGTTATGTATGTTTGTT 59.829 33.333 0.00 0.00 0.00 2.83
1234 1359 7.634809 TGTTGCATGTTATGTATGTTTGTTG 57.365 32.000 0.00 0.00 0.00 3.33
1235 1360 6.644181 TGTTGCATGTTATGTATGTTTGTTGG 59.356 34.615 0.00 0.00 0.00 3.77
1236 1361 5.718146 TGCATGTTATGTATGTTTGTTGGG 58.282 37.500 0.00 0.00 0.00 4.12
1237 1362 5.244851 TGCATGTTATGTATGTTTGTTGGGT 59.755 36.000 0.00 0.00 0.00 4.51
1238 1363 6.162777 GCATGTTATGTATGTTTGTTGGGTT 58.837 36.000 0.00 0.00 0.00 4.11
1239 1364 6.090628 GCATGTTATGTATGTTTGTTGGGTTG 59.909 38.462 0.00 0.00 0.00 3.77
1240 1365 6.961360 TGTTATGTATGTTTGTTGGGTTGA 57.039 33.333 0.00 0.00 0.00 3.18
1241 1366 7.531857 TGTTATGTATGTTTGTTGGGTTGAT 57.468 32.000 0.00 0.00 0.00 2.57
1242 1367 7.598278 TGTTATGTATGTTTGTTGGGTTGATC 58.402 34.615 0.00 0.00 0.00 2.92
1243 1368 4.757799 TGTATGTTTGTTGGGTTGATCG 57.242 40.909 0.00 0.00 0.00 3.69
1244 1369 3.504134 TGTATGTTTGTTGGGTTGATCGG 59.496 43.478 0.00 0.00 0.00 4.18
1245 1370 2.060050 TGTTTGTTGGGTTGATCGGT 57.940 45.000 0.00 0.00 0.00 4.69
1246 1371 1.950909 TGTTTGTTGGGTTGATCGGTC 59.049 47.619 0.00 0.00 0.00 4.79
1247 1372 1.268625 GTTTGTTGGGTTGATCGGTCC 59.731 52.381 0.00 0.00 0.00 4.46
1248 1373 0.604243 TTGTTGGGTTGATCGGTCCG 60.604 55.000 4.39 4.39 0.00 4.79
1249 1374 1.004200 GTTGGGTTGATCGGTCCGT 60.004 57.895 11.88 0.00 0.00 4.69
1250 1375 0.604511 GTTGGGTTGATCGGTCCGTT 60.605 55.000 11.88 2.07 0.00 4.44
1251 1376 0.975135 TTGGGTTGATCGGTCCGTTA 59.025 50.000 11.88 0.00 0.00 3.18
1252 1377 0.975135 TGGGTTGATCGGTCCGTTAA 59.025 50.000 11.88 2.45 0.00 2.01
1253 1378 1.555992 TGGGTTGATCGGTCCGTTAAT 59.444 47.619 11.88 0.00 0.00 1.40
1254 1379 2.027007 TGGGTTGATCGGTCCGTTAATT 60.027 45.455 11.88 0.00 0.00 1.40
1255 1380 3.197333 TGGGTTGATCGGTCCGTTAATTA 59.803 43.478 11.88 0.00 0.00 1.40
1256 1381 4.190772 GGGTTGATCGGTCCGTTAATTAA 58.809 43.478 11.88 0.00 0.00 1.40
1257 1382 4.034394 GGGTTGATCGGTCCGTTAATTAAC 59.966 45.833 16.87 16.87 0.00 2.01
1258 1383 4.872124 GGTTGATCGGTCCGTTAATTAACT 59.128 41.667 22.57 5.43 34.12 2.24
1259 1384 5.220529 GGTTGATCGGTCCGTTAATTAACTG 60.221 44.000 22.57 17.46 34.12 3.16
1260 1385 4.435425 TGATCGGTCCGTTAATTAACTGG 58.565 43.478 22.57 22.56 34.12 4.00
1261 1386 3.249986 TCGGTCCGTTAATTAACTGGG 57.750 47.619 25.42 20.06 33.65 4.45
1262 1387 1.667212 CGGTCCGTTAATTAACTGGGC 59.333 52.381 25.42 24.62 35.37 5.36
1263 1388 2.713877 GGTCCGTTAATTAACTGGGCA 58.286 47.619 28.47 15.45 36.72 5.36
1264 1389 3.083293 GGTCCGTTAATTAACTGGGCAA 58.917 45.455 28.47 14.98 36.72 4.52
1265 1390 3.697542 GGTCCGTTAATTAACTGGGCAAT 59.302 43.478 28.47 0.00 36.72 3.56
1266 1391 4.158949 GGTCCGTTAATTAACTGGGCAATT 59.841 41.667 28.47 0.00 36.72 2.32
1267 1392 5.337554 GTCCGTTAATTAACTGGGCAATTC 58.662 41.667 25.45 13.37 35.81 2.17
1268 1393 5.124936 GTCCGTTAATTAACTGGGCAATTCT 59.875 40.000 25.45 0.00 35.81 2.40
1269 1394 5.355910 TCCGTTAATTAACTGGGCAATTCTC 59.644 40.000 25.42 2.87 33.65 2.87
1270 1395 5.357032 CCGTTAATTAACTGGGCAATTCTCT 59.643 40.000 22.57 0.00 34.12 3.10
1271 1396 6.127730 CCGTTAATTAACTGGGCAATTCTCTT 60.128 38.462 22.57 0.00 34.12 2.85
1272 1397 6.967199 CGTTAATTAACTGGGCAATTCTCTTC 59.033 38.462 22.57 0.00 34.12 2.87
1273 1398 7.148239 CGTTAATTAACTGGGCAATTCTCTTCT 60.148 37.037 22.57 0.00 34.12 2.85
1274 1399 8.523658 GTTAATTAACTGGGCAATTCTCTTCTT 58.476 33.333 19.07 0.00 33.52 2.52
1275 1400 6.765915 ATTAACTGGGCAATTCTCTTCTTC 57.234 37.500 0.00 0.00 0.00 2.87
1276 1401 4.379302 AACTGGGCAATTCTCTTCTTCT 57.621 40.909 0.00 0.00 0.00 2.85
1277 1402 4.379302 ACTGGGCAATTCTCTTCTTCTT 57.621 40.909 0.00 0.00 0.00 2.52
1278 1403 5.505181 ACTGGGCAATTCTCTTCTTCTTA 57.495 39.130 0.00 0.00 0.00 2.10
1279 1404 5.880901 ACTGGGCAATTCTCTTCTTCTTAA 58.119 37.500 0.00 0.00 0.00 1.85
1280 1405 6.488715 ACTGGGCAATTCTCTTCTTCTTAAT 58.511 36.000 0.00 0.00 0.00 1.40
1281 1406 6.950619 ACTGGGCAATTCTCTTCTTCTTAATT 59.049 34.615 0.00 0.00 0.00 1.40
1282 1407 8.109634 ACTGGGCAATTCTCTTCTTCTTAATTA 58.890 33.333 0.00 0.00 0.00 1.40
1283 1408 8.877864 TGGGCAATTCTCTTCTTCTTAATTAA 57.122 30.769 0.00 0.00 0.00 1.40
1284 1409 9.479549 TGGGCAATTCTCTTCTTCTTAATTAAT 57.520 29.630 0.00 0.00 0.00 1.40
1285 1410 9.958234 GGGCAATTCTCTTCTTCTTAATTAATC 57.042 33.333 0.00 0.00 0.00 1.75
1305 1430 9.822185 ATTAATCAATGAGGTAAATCTTTTGCC 57.178 29.630 0.00 0.00 0.00 4.52
1306 1431 7.486407 AATCAATGAGGTAAATCTTTTGCCT 57.514 32.000 9.04 9.04 0.00 4.75
1307 1432 6.916360 TCAATGAGGTAAATCTTTTGCCTT 57.084 33.333 10.36 0.00 0.00 4.35
1308 1433 6.924111 TCAATGAGGTAAATCTTTTGCCTTC 58.076 36.000 10.36 5.70 0.00 3.46
1309 1434 5.567138 ATGAGGTAAATCTTTTGCCTTCG 57.433 39.130 10.36 0.00 0.00 3.79
1310 1435 4.394729 TGAGGTAAATCTTTTGCCTTCGT 58.605 39.130 10.36 0.00 0.00 3.85
1311 1436 4.825085 TGAGGTAAATCTTTTGCCTTCGTT 59.175 37.500 10.36 0.00 0.00 3.85
1312 1437 5.300792 TGAGGTAAATCTTTTGCCTTCGTTT 59.699 36.000 10.36 0.00 0.00 3.60
1313 1438 6.156748 AGGTAAATCTTTTGCCTTCGTTTT 57.843 33.333 4.07 0.00 0.00 2.43
1314 1439 5.983118 AGGTAAATCTTTTGCCTTCGTTTTG 59.017 36.000 4.07 0.00 0.00 2.44
1315 1440 5.980715 GGTAAATCTTTTGCCTTCGTTTTGA 59.019 36.000 0.52 0.00 0.00 2.69
1316 1441 6.477360 GGTAAATCTTTTGCCTTCGTTTTGAA 59.523 34.615 0.52 0.00 34.74 2.69
1317 1442 6.976636 AAATCTTTTGCCTTCGTTTTGAAA 57.023 29.167 0.00 0.00 35.79 2.69
1318 1443 6.976636 AATCTTTTGCCTTCGTTTTGAAAA 57.023 29.167 0.00 0.00 35.79 2.29
1356 1484 7.125792 TCTCCATTTCATAAGTACTTCCTCC 57.874 40.000 12.39 0.00 0.00 4.30
1357 1485 5.914033 TCCATTTCATAAGTACTTCCTCCG 58.086 41.667 12.39 0.00 0.00 4.63
1358 1486 5.424252 TCCATTTCATAAGTACTTCCTCCGT 59.576 40.000 12.39 0.00 0.00 4.69
1359 1487 6.070424 TCCATTTCATAAGTACTTCCTCCGTT 60.070 38.462 12.39 0.00 0.00 4.44
1360 1488 6.598064 CCATTTCATAAGTACTTCCTCCGTTT 59.402 38.462 12.39 0.00 0.00 3.60
1361 1489 7.201617 CCATTTCATAAGTACTTCCTCCGTTTC 60.202 40.741 12.39 0.00 0.00 2.78
1362 1490 6.600882 TTCATAAGTACTTCCTCCGTTTCT 57.399 37.500 12.39 0.00 0.00 2.52
1363 1491 7.707624 TTCATAAGTACTTCCTCCGTTTCTA 57.292 36.000 12.39 0.00 0.00 2.10
1364 1492 7.707624 TCATAAGTACTTCCTCCGTTTCTAA 57.292 36.000 12.39 0.00 0.00 2.10
1365 1493 8.125978 TCATAAGTACTTCCTCCGTTTCTAAA 57.874 34.615 12.39 0.00 0.00 1.85
1366 1494 8.755977 TCATAAGTACTTCCTCCGTTTCTAAAT 58.244 33.333 12.39 0.00 0.00 1.40
1370 1498 9.955102 AAGTACTTCCTCCGTTTCTAAATATTT 57.045 29.630 1.12 5.89 0.00 1.40
1371 1499 9.955102 AGTACTTCCTCCGTTTCTAAATATTTT 57.045 29.630 5.91 0.00 0.00 1.82
1374 1502 9.516546 ACTTCCTCCGTTTCTAAATATTTTTCT 57.483 29.630 5.91 0.00 0.00 2.52
1453 1581 9.912634 AATGTAGATTCATTCATTTCGTTTTGT 57.087 25.926 0.00 0.00 33.43 2.83
1465 1593 9.952188 TTCATTTCGTTTTGTATGTATTGTTGA 57.048 25.926 0.00 0.00 0.00 3.18
1466 1594 9.952188 TCATTTCGTTTTGTATGTATTGTTGAA 57.048 25.926 0.00 0.00 0.00 2.69
1471 1599 9.820229 TCGTTTTGTATGTATTGTTGAAATCTC 57.180 29.630 0.00 0.00 0.00 2.75
1472 1600 9.825972 CGTTTTGTATGTATTGTTGAAATCTCT 57.174 29.630 0.00 0.00 0.00 3.10
1481 1609 9.996554 TGTATTGTTGAAATCTCTAGAAAGACA 57.003 29.630 0.00 0.00 0.00 3.41
1515 1643 3.057019 CGAAGAAAGATCACGAACACCA 58.943 45.455 0.00 0.00 32.27 4.17
1524 1652 4.223032 AGATCACGAACACCAGGAACTAAT 59.777 41.667 0.00 0.00 36.02 1.73
1525 1654 3.659786 TCACGAACACCAGGAACTAATG 58.340 45.455 0.00 0.00 36.02 1.90
1527 1656 3.432252 CACGAACACCAGGAACTAATGAC 59.568 47.826 0.00 0.00 36.02 3.06
1529 1658 3.556213 CGAACACCAGGAACTAATGACCA 60.556 47.826 0.00 0.00 36.02 4.02
1544 1673 1.911357 TGACCAGACAATGCAGGAGAT 59.089 47.619 0.00 0.00 0.00 2.75
1707 1836 0.586748 CGACTCCTCAATCGACGTCG 60.587 60.000 31.30 31.30 40.86 5.12
1716 1845 1.874345 AATCGACGTCGTCCCTGCTT 61.874 55.000 34.40 15.71 40.80 3.91
1889 2018 8.034804 GCACCATAATGTTTAAGGACTCATTTT 58.965 33.333 0.00 0.00 33.48 1.82
1941 2073 5.190925 ACCATGGAAAAGTATACAGCTGGTA 59.809 40.000 21.47 7.85 36.16 3.25
1959 2091 1.126296 GTAGTGGAAAGAACGAAGCGC 59.874 52.381 0.00 0.00 0.00 5.92
1975 2107 3.004752 AGCGCAGGAAATAAATGGAGT 57.995 42.857 11.47 0.00 0.00 3.85
1976 2108 4.150897 AGCGCAGGAAATAAATGGAGTA 57.849 40.909 11.47 0.00 0.00 2.59
2048 2180 9.826574 TTTATTCATCAACGGTTAAGCTAGTAT 57.173 29.630 2.76 0.00 0.00 2.12
2121 2255 1.372683 GAGGACAAGCACTGGAGCA 59.627 57.895 0.00 0.00 36.85 4.26
2158 2292 1.678627 CCGTCATCGTCTCTTCCTCAT 59.321 52.381 0.00 0.00 35.01 2.90
2159 2293 2.099921 CCGTCATCGTCTCTTCCTCATT 59.900 50.000 0.00 0.00 35.01 2.57
2205 2339 1.038280 AGACAACCGGAAAGTCGTCT 58.962 50.000 9.46 7.39 37.36 4.18
2208 2342 1.134610 ACAACCGGAAAGTCGTCTTGT 60.135 47.619 9.46 1.16 33.79 3.16
2210 2344 1.578583 ACCGGAAAGTCGTCTTGTTG 58.421 50.000 9.46 0.00 33.79 3.33
2217 2351 0.759346 AGTCGTCTTGTTGAGGCCTT 59.241 50.000 6.77 0.00 0.00 4.35
2260 2394 7.393234 AGAAAATTAACCATCACCGATGAAGAA 59.607 33.333 5.54 0.00 42.09 2.52
2316 2452 2.964768 GCAAACATGAACGAACGAAGAC 59.035 45.455 0.00 0.00 0.00 3.01
2325 2461 1.067776 ACGAACGAAGACTGGATCCAC 60.068 52.381 11.44 1.59 0.00 4.02
2348 2484 4.214119 CACAGATCCATTGAAGACAAACGT 59.786 41.667 0.00 0.00 39.54 3.99
2350 2486 4.452114 CAGATCCATTGAAGACAAACGTCA 59.548 41.667 0.00 0.00 39.54 4.35
2361 2497 2.288458 GACAAACGTCAACCGAATCCAA 59.712 45.455 0.00 0.00 40.70 3.53
2370 2506 1.191535 ACCGAATCCAACGAGATCCA 58.808 50.000 0.00 0.00 0.00 3.41
2393 2529 2.932614 CAGTAACAAATCTCTGCCTCCG 59.067 50.000 0.00 0.00 0.00 4.63
2432 2568 2.209315 GGGCCATGTTGTTGCTGGT 61.209 57.895 4.39 0.00 32.42 4.00
2448 2584 3.643978 GTGCGCGCATCTCATCCC 61.644 66.667 38.62 18.06 0.00 3.85
2456 2592 1.204231 CGCATCTCATCCCTGATCGAT 59.796 52.381 0.00 0.00 0.00 3.59
2590 2727 3.593442 ACTTTCCAGTCCCATTGTTGA 57.407 42.857 0.00 0.00 0.00 3.18
2591 2728 3.222603 ACTTTCCAGTCCCATTGTTGAC 58.777 45.455 0.00 0.00 0.00 3.18
2595 2732 0.960364 CAGTCCCATTGTTGACCCCG 60.960 60.000 0.00 0.00 31.76 5.73
2597 2734 2.157452 TCCCATTGTTGACCCCGGT 61.157 57.895 0.00 0.00 0.00 5.28
2601 2738 0.250727 CATTGTTGACCCCGGTGAGT 60.251 55.000 0.00 0.00 0.00 3.41
2617 2754 1.006571 AGTACCGGTGTTGCGTCAG 60.007 57.895 19.93 0.00 0.00 3.51
2635 2772 3.248171 GCGCTAGGCTCGACAACG 61.248 66.667 0.00 0.00 39.11 4.10
2640 2777 1.380785 TAGGCTCGACAACGGGGAT 60.381 57.895 0.00 0.00 40.74 3.85
2644 2781 2.047655 TCGACAACGGGGATGTGC 60.048 61.111 0.00 0.00 40.21 4.57
2679 2817 3.791973 TTTTTCACCAAGCGACACATT 57.208 38.095 0.00 0.00 0.00 2.71
2680 2818 4.902443 TTTTTCACCAAGCGACACATTA 57.098 36.364 0.00 0.00 0.00 1.90
2682 2820 2.831685 TCACCAAGCGACACATTAGT 57.168 45.000 0.00 0.00 0.00 2.24
2684 2822 2.805671 TCACCAAGCGACACATTAGTTG 59.194 45.455 0.00 0.00 0.00 3.16
2695 2851 0.676466 CATTAGTTGGCTGGCACGGA 60.676 55.000 2.29 0.00 36.31 4.69
2701 2857 2.877691 GGCTGGCACGGACATTTC 59.122 61.111 0.00 0.00 46.51 2.17
2710 3015 3.305064 GGCACGGACATTTCTTTTTGCTA 60.305 43.478 0.00 0.00 0.00 3.49
2763 3068 1.979855 TTTTTGCAGGCACTAGCAGA 58.020 45.000 0.00 0.00 41.67 4.26
2869 3174 3.243367 CCGCCATCTTCAGTTTTTGTTGA 60.243 43.478 0.00 0.00 0.00 3.18
2882 3187 1.115467 TTGTTGAAACCAACGCCCAT 58.885 45.000 0.00 0.00 45.10 4.00
2897 3202 2.477863 CGCCCATTTTTGCTACTACTGC 60.478 50.000 0.00 0.00 0.00 4.40
2919 3224 0.685785 TGCTGGCTTTTGGTGGAACA 60.686 50.000 0.00 0.00 39.98 3.18
2936 3241 5.542176 TGGAACAAAAAGGTGCCATAGCAT 61.542 41.667 0.00 0.00 45.10 3.79
2965 3270 1.975680 ACCGACACCCTGTTATCTTGT 59.024 47.619 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 6.183360 GCAGAAATGAATCCACTTAAGAGGTC 60.183 42.308 17.25 9.99 0.00 3.85
23 24 5.649831 GCAGAAATGAATCCACTTAAGAGGT 59.350 40.000 17.25 0.54 0.00 3.85
184 202 2.185867 GCCGGATACAGGCGTTCA 59.814 61.111 5.05 0.00 44.09 3.18
645 722 7.666063 AATCAAATCTCATTAAAGGGGAAGG 57.334 36.000 0.00 0.00 0.00 3.46
685 766 1.768684 TTCTGCCTCACCTCACACCC 61.769 60.000 0.00 0.00 0.00 4.61
711 792 2.990514 GCTTCTCCTCACTTTTCGTCTC 59.009 50.000 0.00 0.00 0.00 3.36
715 796 4.748892 TGATAGCTTCTCCTCACTTTTCG 58.251 43.478 0.00 0.00 0.00 3.46
887 976 9.639563 TGCATTAATTTAGGATTAGACATGGAA 57.360 29.630 0.00 0.00 0.00 3.53
975 1099 7.460910 TGAATCACATATACTGCATATGGGTT 58.539 34.615 9.39 4.56 46.93 4.11
1031 1155 2.385013 ATCACTAAGATGTGCGCACA 57.615 45.000 41.97 41.97 46.44 4.57
1127 1251 5.286797 TGTGTGCGAAAACGATACTGTATAC 59.713 40.000 0.00 0.00 0.00 1.47
1128 1252 5.400703 TGTGTGCGAAAACGATACTGTATA 58.599 37.500 0.00 0.00 0.00 1.47
1129 1253 4.239304 TGTGTGCGAAAACGATACTGTAT 58.761 39.130 0.00 0.00 0.00 2.29
1168 1292 3.501828 TGACATCGCAAATGCAAAGTAGT 59.498 39.130 6.18 0.00 42.21 2.73
1181 1306 0.447406 CCTCGCAAAATGACATCGCA 59.553 50.000 0.00 0.00 0.00 5.10
1182 1307 0.248215 CCCTCGCAAAATGACATCGC 60.248 55.000 0.00 0.00 0.00 4.58
1183 1308 1.086696 ACCCTCGCAAAATGACATCG 58.913 50.000 0.00 0.00 0.00 3.84
1184 1309 3.244976 CAAACCCTCGCAAAATGACATC 58.755 45.455 0.00 0.00 0.00 3.06
1185 1310 2.627699 ACAAACCCTCGCAAAATGACAT 59.372 40.909 0.00 0.00 0.00 3.06
1186 1311 2.028130 ACAAACCCTCGCAAAATGACA 58.972 42.857 0.00 0.00 0.00 3.58
1187 1312 2.393764 CACAAACCCTCGCAAAATGAC 58.606 47.619 0.00 0.00 0.00 3.06
1188 1313 1.339610 CCACAAACCCTCGCAAAATGA 59.660 47.619 0.00 0.00 0.00 2.57
1189 1314 1.068434 ACCACAAACCCTCGCAAAATG 59.932 47.619 0.00 0.00 0.00 2.32
1190 1315 1.408969 ACCACAAACCCTCGCAAAAT 58.591 45.000 0.00 0.00 0.00 1.82
1191 1316 1.134965 CAACCACAAACCCTCGCAAAA 60.135 47.619 0.00 0.00 0.00 2.44
1192 1317 0.457851 CAACCACAAACCCTCGCAAA 59.542 50.000 0.00 0.00 0.00 3.68
1193 1318 0.681564 ACAACCACAAACCCTCGCAA 60.682 50.000 0.00 0.00 0.00 4.85
1194 1319 0.681564 AACAACCACAAACCCTCGCA 60.682 50.000 0.00 0.00 0.00 5.10
1195 1320 0.248866 CAACAACCACAAACCCTCGC 60.249 55.000 0.00 0.00 0.00 5.03
1196 1321 0.248866 GCAACAACCACAAACCCTCG 60.249 55.000 0.00 0.00 0.00 4.63
1197 1322 0.820871 TGCAACAACCACAAACCCTC 59.179 50.000 0.00 0.00 0.00 4.30
1198 1323 1.138661 CATGCAACAACCACAAACCCT 59.861 47.619 0.00 0.00 0.00 4.34
1199 1324 1.134551 ACATGCAACAACCACAAACCC 60.135 47.619 0.00 0.00 0.00 4.11
1200 1325 2.307934 ACATGCAACAACCACAAACC 57.692 45.000 0.00 0.00 0.00 3.27
1201 1326 4.808364 ACATAACATGCAACAACCACAAAC 59.192 37.500 0.00 0.00 0.00 2.93
1202 1327 5.016051 ACATAACATGCAACAACCACAAA 57.984 34.783 0.00 0.00 0.00 2.83
1203 1328 4.662468 ACATAACATGCAACAACCACAA 57.338 36.364 0.00 0.00 0.00 3.33
1204 1329 5.242615 ACATACATAACATGCAACAACCACA 59.757 36.000 0.00 0.00 0.00 4.17
1205 1330 5.708948 ACATACATAACATGCAACAACCAC 58.291 37.500 0.00 0.00 0.00 4.16
1206 1331 5.973899 ACATACATAACATGCAACAACCA 57.026 34.783 0.00 0.00 0.00 3.67
1207 1332 6.644592 ACAAACATACATAACATGCAACAACC 59.355 34.615 0.00 0.00 0.00 3.77
1208 1333 7.636259 ACAAACATACATAACATGCAACAAC 57.364 32.000 0.00 0.00 0.00 3.32
1209 1334 7.170489 CCAACAAACATACATAACATGCAACAA 59.830 33.333 0.00 0.00 0.00 2.83
1210 1335 6.644181 CCAACAAACATACATAACATGCAACA 59.356 34.615 0.00 0.00 0.00 3.33
1211 1336 6.090628 CCCAACAAACATACATAACATGCAAC 59.909 38.462 0.00 0.00 0.00 4.17
1212 1337 6.162079 CCCAACAAACATACATAACATGCAA 58.838 36.000 0.00 0.00 0.00 4.08
1213 1338 5.244851 ACCCAACAAACATACATAACATGCA 59.755 36.000 0.00 0.00 0.00 3.96
1214 1339 5.719173 ACCCAACAAACATACATAACATGC 58.281 37.500 0.00 0.00 0.00 4.06
1215 1340 7.374272 TCAACCCAACAAACATACATAACATG 58.626 34.615 0.00 0.00 0.00 3.21
1216 1341 7.531857 TCAACCCAACAAACATACATAACAT 57.468 32.000 0.00 0.00 0.00 2.71
1217 1342 6.961360 TCAACCCAACAAACATACATAACA 57.039 33.333 0.00 0.00 0.00 2.41
1218 1343 6.745450 CGATCAACCCAACAAACATACATAAC 59.255 38.462 0.00 0.00 0.00 1.89
1219 1344 6.127869 CCGATCAACCCAACAAACATACATAA 60.128 38.462 0.00 0.00 0.00 1.90
1220 1345 5.355630 CCGATCAACCCAACAAACATACATA 59.644 40.000 0.00 0.00 0.00 2.29
1221 1346 4.157656 CCGATCAACCCAACAAACATACAT 59.842 41.667 0.00 0.00 0.00 2.29
1222 1347 3.504134 CCGATCAACCCAACAAACATACA 59.496 43.478 0.00 0.00 0.00 2.29
1223 1348 3.504520 ACCGATCAACCCAACAAACATAC 59.495 43.478 0.00 0.00 0.00 2.39
1224 1349 3.754323 GACCGATCAACCCAACAAACATA 59.246 43.478 0.00 0.00 0.00 2.29
1225 1350 2.556622 GACCGATCAACCCAACAAACAT 59.443 45.455 0.00 0.00 0.00 2.71
1226 1351 1.950909 GACCGATCAACCCAACAAACA 59.049 47.619 0.00 0.00 0.00 2.83
1227 1352 1.268625 GGACCGATCAACCCAACAAAC 59.731 52.381 0.00 0.00 0.00 2.93
1228 1353 1.611519 GGACCGATCAACCCAACAAA 58.388 50.000 0.00 0.00 0.00 2.83
1229 1354 0.604243 CGGACCGATCAACCCAACAA 60.604 55.000 8.64 0.00 0.00 2.83
1230 1355 1.004320 CGGACCGATCAACCCAACA 60.004 57.895 8.64 0.00 0.00 3.33
1231 1356 0.604511 AACGGACCGATCAACCCAAC 60.605 55.000 23.38 0.00 0.00 3.77
1232 1357 0.975135 TAACGGACCGATCAACCCAA 59.025 50.000 23.38 0.00 0.00 4.12
1233 1358 0.975135 TTAACGGACCGATCAACCCA 59.025 50.000 23.38 0.00 0.00 4.51
1234 1359 2.320745 ATTAACGGACCGATCAACCC 57.679 50.000 23.38 0.00 0.00 4.11
1235 1360 4.872124 AGTTAATTAACGGACCGATCAACC 59.128 41.667 23.38 1.09 40.96 3.77
1236 1361 5.220529 CCAGTTAATTAACGGACCGATCAAC 60.221 44.000 24.48 14.15 40.96 3.18
1237 1362 4.871557 CCAGTTAATTAACGGACCGATCAA 59.128 41.667 24.48 11.26 40.96 2.57
1238 1363 4.435425 CCAGTTAATTAACGGACCGATCA 58.565 43.478 24.48 0.00 40.96 2.92
1239 1364 3.805971 CCCAGTTAATTAACGGACCGATC 59.194 47.826 26.78 0.00 40.96 3.69
1240 1365 3.800531 CCCAGTTAATTAACGGACCGAT 58.199 45.455 26.78 12.20 40.96 4.18
1241 1366 2.677613 GCCCAGTTAATTAACGGACCGA 60.678 50.000 26.78 0.00 40.96 4.69
1242 1367 1.667212 GCCCAGTTAATTAACGGACCG 59.333 52.381 26.78 13.61 40.96 4.79
1243 1368 2.713877 TGCCCAGTTAATTAACGGACC 58.286 47.619 26.78 20.34 40.96 4.46
1244 1369 4.976224 ATTGCCCAGTTAATTAACGGAC 57.024 40.909 26.78 20.66 40.96 4.79
1245 1370 5.258051 AGAATTGCCCAGTTAATTAACGGA 58.742 37.500 26.78 13.37 40.96 4.69
1246 1371 5.357032 AGAGAATTGCCCAGTTAATTAACGG 59.643 40.000 19.92 21.15 40.96 4.44
1247 1372 6.436843 AGAGAATTGCCCAGTTAATTAACG 57.563 37.500 19.92 15.03 40.96 3.18
1248 1373 8.056407 AGAAGAGAATTGCCCAGTTAATTAAC 57.944 34.615 18.77 18.77 36.46 2.01
1249 1374 8.650143 AAGAAGAGAATTGCCCAGTTAATTAA 57.350 30.769 0.00 0.00 0.00 1.40
1250 1375 8.109634 AGAAGAAGAGAATTGCCCAGTTAATTA 58.890 33.333 0.00 0.00 0.00 1.40
1251 1376 6.950619 AGAAGAAGAGAATTGCCCAGTTAATT 59.049 34.615 0.00 0.00 0.00 1.40
1252 1377 6.488715 AGAAGAAGAGAATTGCCCAGTTAAT 58.511 36.000 0.00 0.00 0.00 1.40
1253 1378 5.880901 AGAAGAAGAGAATTGCCCAGTTAA 58.119 37.500 0.00 0.00 0.00 2.01
1254 1379 5.505181 AGAAGAAGAGAATTGCCCAGTTA 57.495 39.130 0.00 0.00 0.00 2.24
1255 1380 4.379302 AGAAGAAGAGAATTGCCCAGTT 57.621 40.909 0.00 0.00 0.00 3.16
1256 1381 4.379302 AAGAAGAAGAGAATTGCCCAGT 57.621 40.909 0.00 0.00 0.00 4.00
1257 1382 7.401955 AATTAAGAAGAAGAGAATTGCCCAG 57.598 36.000 0.00 0.00 0.00 4.45
1258 1383 8.877864 TTAATTAAGAAGAAGAGAATTGCCCA 57.122 30.769 0.00 0.00 0.00 5.36
1259 1384 9.958234 GATTAATTAAGAAGAAGAGAATTGCCC 57.042 33.333 3.94 0.00 0.00 5.36
1279 1404 9.822185 GGCAAAAGATTTACCTCATTGATTAAT 57.178 29.630 0.00 0.00 0.00 1.40
1280 1405 9.034800 AGGCAAAAGATTTACCTCATTGATTAA 57.965 29.630 0.00 0.00 0.00 1.40
1281 1406 8.593945 AGGCAAAAGATTTACCTCATTGATTA 57.406 30.769 0.00 0.00 0.00 1.75
1282 1407 7.486407 AGGCAAAAGATTTACCTCATTGATT 57.514 32.000 0.00 0.00 0.00 2.57
1283 1408 7.486407 AAGGCAAAAGATTTACCTCATTGAT 57.514 32.000 0.00 0.00 0.00 2.57
1284 1409 6.349280 CGAAGGCAAAAGATTTACCTCATTGA 60.349 38.462 0.00 0.00 0.00 2.57
1285 1410 5.801947 CGAAGGCAAAAGATTTACCTCATTG 59.198 40.000 0.00 0.00 0.00 2.82
1286 1411 5.476945 ACGAAGGCAAAAGATTTACCTCATT 59.523 36.000 0.00 0.00 0.00 2.57
1287 1412 5.010282 ACGAAGGCAAAAGATTTACCTCAT 58.990 37.500 0.00 0.00 0.00 2.90
1288 1413 4.394729 ACGAAGGCAAAAGATTTACCTCA 58.605 39.130 0.00 0.00 0.00 3.86
1289 1414 5.372547 AACGAAGGCAAAAGATTTACCTC 57.627 39.130 0.00 0.00 0.00 3.85
1290 1415 5.784578 AAACGAAGGCAAAAGATTTACCT 57.215 34.783 0.00 0.00 0.00 3.08
1291 1416 5.980715 TCAAAACGAAGGCAAAAGATTTACC 59.019 36.000 0.00 0.00 0.00 2.85
1292 1417 7.458038 TTCAAAACGAAGGCAAAAGATTTAC 57.542 32.000 0.00 0.00 0.00 2.01
1293 1418 8.480643 TTTTCAAAACGAAGGCAAAAGATTTA 57.519 26.923 0.00 0.00 34.32 1.40
1294 1419 6.976636 TTTCAAAACGAAGGCAAAAGATTT 57.023 29.167 0.00 0.00 34.32 2.17
1295 1420 6.976636 TTTTCAAAACGAAGGCAAAAGATT 57.023 29.167 0.00 0.00 34.32 2.40
1296 1421 6.976636 TTTTTCAAAACGAAGGCAAAAGAT 57.023 29.167 0.00 0.00 34.32 2.40
1427 1555 9.912634 ACAAAACGAAATGAATGAATCTACATT 57.087 25.926 0.00 0.00 42.19 2.71
1439 1567 9.952188 TCAACAATACATACAAAACGAAATGAA 57.048 25.926 0.00 0.00 0.00 2.57
1440 1568 9.952188 TTCAACAATACATACAAAACGAAATGA 57.048 25.926 0.00 0.00 0.00 2.57
1445 1573 9.820229 GAGATTTCAACAATACATACAAAACGA 57.180 29.630 0.00 0.00 0.00 3.85
1446 1574 9.825972 AGAGATTTCAACAATACATACAAAACG 57.174 29.630 0.00 0.00 0.00 3.60
1455 1583 9.996554 TGTCTTTCTAGAGATTTCAACAATACA 57.003 29.630 0.00 0.00 0.00 2.29
1485 1613 9.166126 GTTCGTGATCTTTCTTCGTTTTTAAAT 57.834 29.630 0.00 0.00 0.00 1.40
1486 1614 8.176365 TGTTCGTGATCTTTCTTCGTTTTTAAA 58.824 29.630 0.00 0.00 0.00 1.52
1487 1615 7.637132 GTGTTCGTGATCTTTCTTCGTTTTTAA 59.363 33.333 0.00 0.00 0.00 1.52
1488 1616 7.121272 GTGTTCGTGATCTTTCTTCGTTTTTA 58.879 34.615 0.00 0.00 0.00 1.52
1489 1617 5.963586 GTGTTCGTGATCTTTCTTCGTTTTT 59.036 36.000 0.00 0.00 0.00 1.94
1490 1618 5.499047 GTGTTCGTGATCTTTCTTCGTTTT 58.501 37.500 0.00 0.00 0.00 2.43
1491 1619 4.025145 GGTGTTCGTGATCTTTCTTCGTTT 60.025 41.667 0.00 0.00 0.00 3.60
1492 1620 3.493503 GGTGTTCGTGATCTTTCTTCGTT 59.506 43.478 0.00 0.00 0.00 3.85
1493 1621 3.057734 GGTGTTCGTGATCTTTCTTCGT 58.942 45.455 0.00 0.00 0.00 3.85
1494 1622 3.057019 TGGTGTTCGTGATCTTTCTTCG 58.943 45.455 0.00 0.00 0.00 3.79
1495 1623 3.433615 CCTGGTGTTCGTGATCTTTCTTC 59.566 47.826 0.00 0.00 0.00 2.87
1496 1624 3.071023 TCCTGGTGTTCGTGATCTTTCTT 59.929 43.478 0.00 0.00 0.00 2.52
1497 1625 2.632996 TCCTGGTGTTCGTGATCTTTCT 59.367 45.455 0.00 0.00 0.00 2.52
1498 1626 3.040147 TCCTGGTGTTCGTGATCTTTC 57.960 47.619 0.00 0.00 0.00 2.62
1499 1627 3.139077 GTTCCTGGTGTTCGTGATCTTT 58.861 45.455 0.00 0.00 0.00 2.52
1500 1628 2.368875 AGTTCCTGGTGTTCGTGATCTT 59.631 45.455 0.00 0.00 0.00 2.40
1501 1629 1.971357 AGTTCCTGGTGTTCGTGATCT 59.029 47.619 0.00 0.00 0.00 2.75
1502 1630 2.457366 AGTTCCTGGTGTTCGTGATC 57.543 50.000 0.00 0.00 0.00 2.92
1503 1631 4.020573 TCATTAGTTCCTGGTGTTCGTGAT 60.021 41.667 0.00 0.00 0.00 3.06
1504 1632 3.322541 TCATTAGTTCCTGGTGTTCGTGA 59.677 43.478 0.00 0.00 0.00 4.35
1509 1637 3.650942 TCTGGTCATTAGTTCCTGGTGTT 59.349 43.478 0.00 0.00 0.00 3.32
1515 1643 4.263462 TGCATTGTCTGGTCATTAGTTCCT 60.263 41.667 0.00 0.00 0.00 3.36
1524 1652 1.351076 TCTCCTGCATTGTCTGGTCA 58.649 50.000 0.00 0.00 0.00 4.02
1525 1654 2.286872 CATCTCCTGCATTGTCTGGTC 58.713 52.381 0.00 0.00 0.00 4.02
1649 1778 1.165284 TCACGTTGAGCTGCATGCAA 61.165 50.000 22.88 3.32 45.94 4.08
1707 1836 1.641577 GTGATCGTGTAAGCAGGGAC 58.358 55.000 0.00 0.00 0.00 4.46
1716 1845 2.486504 GTCCGGCGTGATCGTGTA 59.513 61.111 6.01 0.00 39.49 2.90
1861 1990 5.647658 TGAGTCCTTAAACATTATGGTGCTG 59.352 40.000 0.00 0.00 0.00 4.41
1941 2073 0.531974 TGCGCTTCGTTCTTTCCACT 60.532 50.000 9.73 0.00 0.00 4.00
1959 2091 7.307989 CGGCAAGTATACTCCATTTATTTCCTG 60.308 40.741 5.70 0.00 0.00 3.86
2020 2152 7.822822 ACTAGCTTAACCGTTGATGAATAAACT 59.177 33.333 0.00 0.00 0.00 2.66
2158 2292 2.943036 AAAGGTTTGTCCGGCTCTAA 57.057 45.000 0.00 0.00 41.99 2.10
2159 2293 2.943036 AAAAGGTTTGTCCGGCTCTA 57.057 45.000 0.00 0.00 41.99 2.43
2205 2339 3.054655 GTGGTCCTATAAGGCCTCAACAA 60.055 47.826 5.23 0.00 34.61 2.83
2208 2342 2.124411 GGTGGTCCTATAAGGCCTCAA 58.876 52.381 5.23 0.00 34.61 3.02
2210 2344 0.680061 CGGTGGTCCTATAAGGCCTC 59.320 60.000 5.23 0.00 34.61 4.70
2217 2351 0.032912 TCTGGTGCGGTGGTCCTATA 60.033 55.000 0.00 0.00 0.00 1.31
2227 2361 3.192422 TGATGGTTAATTTTCTGGTGCGG 59.808 43.478 0.00 0.00 0.00 5.69
2287 2423 5.275326 CGTTCGTTCATGTTTGCGTTTTTAA 60.275 36.000 0.00 0.00 0.00 1.52
2290 2426 2.528287 CGTTCGTTCATGTTTGCGTTTT 59.472 40.909 0.00 0.00 0.00 2.43
2295 2431 2.964768 GTCTTCGTTCGTTCATGTTTGC 59.035 45.455 0.00 0.00 0.00 3.68
2325 2461 4.214119 ACGTTTGTCTTCAATGGATCTGTG 59.786 41.667 0.00 0.00 33.32 3.66
2335 2471 2.619147 TCGGTTGACGTTTGTCTTCAA 58.381 42.857 0.00 0.00 45.70 2.69
2348 2484 2.418197 GGATCTCGTTGGATTCGGTTGA 60.418 50.000 0.00 0.00 0.00 3.18
2350 2486 1.553248 TGGATCTCGTTGGATTCGGTT 59.447 47.619 0.00 0.00 0.00 4.44
2361 2497 4.223032 AGATTTGTTACTGGTGGATCTCGT 59.777 41.667 0.00 0.00 0.00 4.18
2370 2506 3.307762 GGAGGCAGAGATTTGTTACTGGT 60.308 47.826 0.00 0.00 0.00 4.00
2432 2568 3.853487 AGGGATGAGATGCGCGCA 61.853 61.111 38.27 38.27 0.00 6.09
2448 2584 1.371022 CGACCTCGCCATCGATCAG 60.371 63.158 0.00 0.00 44.56 2.90
2467 2603 4.451150 GGAGGTGCGTGATGCCGA 62.451 66.667 0.00 0.00 45.60 5.54
2507 2643 0.957395 ATGCTCTTGTTCGCCACAGG 60.957 55.000 0.00 0.00 36.48 4.00
2509 2645 1.291184 CGATGCTCTTGTTCGCCACA 61.291 55.000 0.00 0.00 0.00 4.17
2510 2646 1.014044 TCGATGCTCTTGTTCGCCAC 61.014 55.000 0.00 0.00 33.08 5.01
2550 2687 1.961277 CCAACACCCTCTGACGCAC 60.961 63.158 0.00 0.00 0.00 5.34
2595 2732 2.025418 CGCAACACCGGTACTCACC 61.025 63.158 6.87 0.00 41.93 4.02
2597 2734 1.007038 GACGCAACACCGGTACTCA 60.007 57.895 6.87 0.00 0.00 3.41
2601 2738 2.340809 CCTGACGCAACACCGGTA 59.659 61.111 6.87 0.00 0.00 4.02
2617 2754 2.886124 GTTGTCGAGCCTAGCGCC 60.886 66.667 2.29 0.00 38.78 6.53
2623 2760 2.683933 ATCCCCGTTGTCGAGCCT 60.684 61.111 0.00 0.00 39.71 4.58
2628 2765 2.047274 AGCACATCCCCGTTGTCG 60.047 61.111 0.00 0.00 0.00 4.35
2631 2768 2.751436 CCCAGCACATCCCCGTTG 60.751 66.667 0.00 0.00 0.00 4.10
2635 2772 2.649129 GCAAACCCAGCACATCCCC 61.649 63.158 0.00 0.00 0.00 4.81
2678 2816 1.302192 GTCCGTGCCAGCCAACTAA 60.302 57.895 0.00 0.00 0.00 2.24
2679 2817 1.836999 ATGTCCGTGCCAGCCAACTA 61.837 55.000 0.00 0.00 0.00 2.24
2680 2818 2.697147 AATGTCCGTGCCAGCCAACT 62.697 55.000 0.00 0.00 0.00 3.16
2682 2820 1.523154 GAAATGTCCGTGCCAGCCAA 61.523 55.000 0.00 0.00 0.00 4.52
2684 2822 1.244019 AAGAAATGTCCGTGCCAGCC 61.244 55.000 0.00 0.00 0.00 4.85
2695 2851 3.058501 CCGGACGTAGCAAAAAGAAATGT 60.059 43.478 0.00 0.00 0.00 2.71
2697 2853 2.095415 GCCGGACGTAGCAAAAAGAAAT 60.095 45.455 5.05 0.00 0.00 2.17
2698 2854 1.264826 GCCGGACGTAGCAAAAAGAAA 59.735 47.619 5.05 0.00 0.00 2.52
2699 2855 0.869730 GCCGGACGTAGCAAAAAGAA 59.130 50.000 5.05 0.00 0.00 2.52
2700 2856 1.286354 CGCCGGACGTAGCAAAAAGA 61.286 55.000 5.05 0.00 36.87 2.52
2701 2857 1.131826 CGCCGGACGTAGCAAAAAG 59.868 57.895 5.05 0.00 36.87 2.27
2710 3015 1.003851 CAAATAATGTCGCCGGACGT 58.996 50.000 5.05 0.00 46.49 4.34
2805 3110 3.387699 CCAACAAGAAACACCCCAATTCT 59.612 43.478 0.00 0.00 35.00 2.40
2811 3116 1.411246 GGTTCCAACAAGAAACACCCC 59.589 52.381 0.00 0.00 33.45 4.95
2869 3174 1.134250 AGCAAAAATGGGCGTTGGTTT 60.134 42.857 0.00 0.00 34.54 3.27
2882 3187 3.253188 CAGCAAGGCAGTAGTAGCAAAAA 59.747 43.478 0.00 0.00 0.00 1.94
2897 3202 1.114722 TCCACCAAAAGCCAGCAAGG 61.115 55.000 0.00 0.00 41.84 3.61
2912 3217 2.908688 ATGGCACCTTTTTGTTCCAC 57.091 45.000 0.00 0.00 0.00 4.02
2936 3241 2.110213 GGTGTCGGTGCACTTGGA 59.890 61.111 17.98 9.16 39.21 3.53


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

AutoCloner maintained by Alex Coulton.