Multiple sequence alignment - TraesCS4A01G362300

Loading Multiple Alignment...

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 TraesCS4A01G362300 chr4A 100.000 3966 0 0 1 3966 636086325 636082360 0.000000e+00 7324.0
1 TraesCS4A01G362300 chr4A 88.480 2066 168 34 1056 3095 636101702 636099681 0.000000e+00 2433.0
2 TraesCS4A01G362300 chr4A 95.741 1033 41 2 3 1034 636102577 636101547 0.000000e+00 1661.0
3 TraesCS4A01G362300 chr4A 85.941 818 103 8 2288 3102 636043265 636042457 0.000000e+00 863.0
4 TraesCS4A01G362300 chr4A 83.612 598 76 20 1656 2243 636043847 636043262 3.490000e-150 542.0
5 TraesCS4A01G362300 chr4A 88.841 233 24 2 804 1034 636077161 636076929 6.490000e-73 285.0
6 TraesCS4A01G362300 chr4A 85.824 261 28 8 1056 1310 636077085 636076828 6.530000e-68 268.0
7 TraesCS4A01G362300 chr4A 97.436 156 4 0 879 1034 636085270 636085115 2.350000e-67 267.0
8 TraesCS4A01G362300 chr4A 97.436 156 4 0 1056 1211 636085447 636085292 2.350000e-67 267.0
9 TraesCS4A01G362300 chr4A 82.249 338 32 14 3455 3766 636099494 636099159 2.350000e-67 267.0
10 TraesCS4A01G362300 chr4A 81.783 258 31 11 1056 1305 635961388 635961139 6.720000e-48 202.0
11 TraesCS4A01G362300 chr4A 80.992 242 40 4 1056 1293 636218486 636218247 1.880000e-43 187.0
12 TraesCS4A01G362300 chr4A 90.909 132 11 1 1344 1475 60654156 60654286 4.070000e-40 176.0
13 TraesCS4A01G362300 chr4A 82.412 199 31 4 838 1034 636218527 636218331 1.900000e-38 171.0
14 TraesCS4A01G362300 chr4A 81.373 204 34 4 833 1034 635961434 635961233 3.170000e-36 163.0
15 TraesCS4A01G362300 chr4A 100.000 28 0 0 472 499 636085774 636085747 7.000000e-03 52.8
16 TraesCS4A01G362300 chr4A 100.000 28 0 0 552 579 636085854 636085827 7.000000e-03 52.8
17 TraesCS4A01G362300 chr4A 100.000 28 0 0 472 499 636102028 636102001 7.000000e-03 52.8
18 TraesCS4A01G362300 chr5D 93.459 3990 157 43 3 3966 535815047 535818958 0.000000e+00 5827.0
19 TraesCS4A01G362300 chr5D 79.202 1303 200 35 1653 2935 535862628 535863879 0.000000e+00 839.0
20 TraesCS4A01G362300 chr5D 78.571 1106 201 23 1849 2934 535866938 535868027 0.000000e+00 697.0
21 TraesCS4A01G362300 chr5D 78.466 952 172 18 1671 2607 535549760 535550693 3.410000e-165 592.0
22 TraesCS4A01G362300 chr5D 88.841 233 24 2 804 1034 535822109 535822341 6.490000e-73 285.0
23 TraesCS4A01G362300 chr5D 98.077 156 3 0 1056 1211 535815923 535816078 5.050000e-69 272.0
24 TraesCS4A01G362300 chr5D 98.077 156 3 0 879 1034 535816100 535816255 5.050000e-69 272.0
25 TraesCS4A01G362300 chr5D 88.000 225 24 3 1056 1277 535822185 535822409 3.040000e-66 263.0
26 TraesCS4A01G362300 chr5D 81.505 319 56 3 2106 2422 535573535 535573852 3.930000e-65 259.0
27 TraesCS4A01G362300 chr5D 80.088 226 41 4 811 1034 535727719 535727942 8.820000e-37 165.0
28 TraesCS4A01G362300 chr5D 79.339 242 44 4 1056 1293 535727787 535728026 8.820000e-37 165.0
29 TraesCS4A01G362300 chr5D 100.000 28 0 0 552 579 535815515 535815542 7.000000e-03 52.8
30 TraesCS4A01G362300 chr5B 79.219 1357 227 34 1651 2982 676272408 676273734 0.000000e+00 893.0
31 TraesCS4A01G362300 chr5B 80.349 229 45 0 2751 2979 676252162 676252390 1.470000e-39 174.0
32 TraesCS4A01G362300 chr5B 90.654 107 10 0 1363 1469 532856169 532856063 4.130000e-30 143.0
33 TraesCS4A01G362300 chr3D 77.923 1300 228 45 1659 2930 75545090 75546358 0.000000e+00 756.0
34 TraesCS4A01G362300 chr3D 90.244 123 11 1 1357 1478 524713705 524713583 4.100000e-35 159.0
35 TraesCS4A01G362300 chr3D 89.744 117 12 0 1359 1475 47480162 47480278 2.470000e-32 150.0
36 TraesCS4A01G362300 chr3D 90.141 71 7 0 1582 1652 496099831 496099901 4.220000e-15 93.5
37 TraesCS4A01G362300 chr3B 77.334 1328 223 52 1651 2941 121642691 121643977 0.000000e+00 713.0
38 TraesCS4A01G362300 chr3B 85.366 123 15 3 1370 1490 449807528 449807407 1.500000e-24 124.0
39 TraesCS4A01G362300 chr3A 77.143 1330 238 49 1651 2948 89578779 89580074 0.000000e+00 712.0
40 TraesCS4A01G362300 chr3A 78.974 975 168 31 1651 2609 89666992 89667945 7.230000e-177 630.0
41 TraesCS4A01G362300 chr3A 83.920 199 30 2 2751 2948 89668090 89668287 5.230000e-44 189.0
42 TraesCS4A01G362300 chr3A 92.500 120 9 0 1359 1478 659015496 659015377 5.270000e-39 172.0
43 TraesCS4A01G362300 chr3A 89.041 73 8 0 1580 1652 635331538 635331610 1.520000e-14 91.6
44 TraesCS4A01G362300 chr3A 84.416 77 11 1 1577 1652 25876847 25876771 1.530000e-09 75.0
45 TraesCS4A01G362300 chr7D 89.706 136 14 0 1340 1475 469842392 469842527 1.470000e-39 174.0
46 TraesCS4A01G362300 chr7B 89.076 119 13 0 1357 1475 602092597 602092479 8.880000e-32 148.0
47 TraesCS4A01G362300 chr7B 87.023 131 15 2 1346 1475 568677136 568677007 3.190000e-31 147.0
48 TraesCS4A01G362300 chrUn 95.122 41 2 0 1580 1620 731647 731687 9.200000e-07 65.8
49 TraesCS4A01G362300 chr7A 92.857 42 3 0 1580 1621 474731885 474731844 1.190000e-05 62.1
50 TraesCS4A01G362300 chr7A 100.000 31 0 0 1591 1621 533576707 533576677 1.540000e-04 58.4
51 TraesCS4A01G362300 chr1A 92.857 42 3 0 1579 1620 486665401 486665360 1.190000e-05 62.1


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 TraesCS4A01G362300 chr4A 636082360 636086325 3965 True 1592.72 7324 98.97440 1 3966 5 chr4A.!!$R4 3965
1 TraesCS4A01G362300 chr4A 636099159 636102577 3418 True 1103.45 2433 91.61750 3 3766 4 chr4A.!!$R5 3763
2 TraesCS4A01G362300 chr4A 636042457 636043847 1390 True 702.50 863 84.77650 1656 3102 2 chr4A.!!$R2 1446
3 TraesCS4A01G362300 chr5D 535815047 535818958 3911 False 1605.95 5827 97.40325 3 3966 4 chr5D.!!$F4 3963
4 TraesCS4A01G362300 chr5D 535862628 535868027 5399 False 768.00 839 78.88650 1653 2935 2 chr5D.!!$F6 1282
5 TraesCS4A01G362300 chr5D 535549760 535550693 933 False 592.00 592 78.46600 1671 2607 1 chr5D.!!$F1 936
6 TraesCS4A01G362300 chr5B 676272408 676273734 1326 False 893.00 893 79.21900 1651 2982 1 chr5B.!!$F2 1331
7 TraesCS4A01G362300 chr3D 75545090 75546358 1268 False 756.00 756 77.92300 1659 2930 1 chr3D.!!$F2 1271
8 TraesCS4A01G362300 chr3B 121642691 121643977 1286 False 713.00 713 77.33400 1651 2941 1 chr3B.!!$F1 1290
9 TraesCS4A01G362300 chr3A 89578779 89580074 1295 False 712.00 712 77.14300 1651 2948 1 chr3A.!!$F1 1297
10 TraesCS4A01G362300 chr3A 89666992 89668287 1295 False 409.50 630 81.44700 1651 2948 2 chr3A.!!$F3 1297

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
107 108 0.768622 TGTTCGGGTGGAATTGGAGT 59.231 50.0 0.00 0.00 36.92 3.85 F
836 840 1.704641 TCCTCGATGATGGTGGGTAG 58.295 55.0 0.00 0.00 0.00 3.18 F
1973 2180 0.039764 TGAGGTCGAGGGTGTGATCT 59.960 55.0 0.00 0.00 0.00 2.75 F
2617 2832 0.994247 TCCCTTCTGGACATGCATGT 59.006 50.0 31.82 31.82 45.16 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1184 1365 0.904649 TGGGTGCGTCTGATCAGATT 59.095 50.0 27.51 0.00 39.97 2.40 R
2528 2743 0.322546 GGGCAGGGTCGATCAAAAGT 60.323 55.0 0.00 0.00 0.00 2.66 R
2873 3121 0.167908 TTGTCATCGGCAATGAACGC 59.832 50.0 2.87 0.00 45.88 4.84 R
3539 7957 0.179070 GGAAGGGCTCCGAGACATTC 60.179 60.0 18.55 18.55 42.91 2.67 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
62 63 4.353437 GGGCGTCGTCGGTGAGTT 62.353 66.667 3.90 0.00 37.56 3.01
107 108 0.768622 TGTTCGGGTGGAATTGGAGT 59.231 50.000 0.00 0.00 36.92 3.85
117 118 2.642311 TGGAATTGGAGTGCTACTTGGA 59.358 45.455 0.00 0.00 0.00 3.53
316 317 2.290071 CCGGTAGTTTCATCCAAGTGGT 60.290 50.000 0.00 0.00 36.34 4.16
353 354 1.745232 TATCGGCATTGGTTGTGACC 58.255 50.000 0.00 0.00 46.71 4.02
501 502 3.322541 TCCTCGACACCTTGTATTGTTCA 59.677 43.478 0.00 0.00 0.00 3.18
503 504 4.307432 CTCGACACCTTGTATTGTTCAGT 58.693 43.478 0.00 0.00 0.00 3.41
625 627 7.066766 AGCTAAATGGTTTTTGATTTTTGCACA 59.933 29.630 0.00 0.00 0.00 4.57
637 639 7.798596 TGATTTTTGCACATTGTTTAACCAT 57.201 28.000 0.00 0.00 0.00 3.55
638 640 8.218338 TGATTTTTGCACATTGTTTAACCATT 57.782 26.923 0.00 0.00 0.00 3.16
702 706 6.369890 CACACATAGAAGAACATAGTGTTGCT 59.630 38.462 0.00 0.00 41.28 3.91
712 716 9.502091 AAGAACATAGTGTTGCTAGTATTTCAA 57.498 29.630 0.00 0.00 41.28 2.69
809 813 4.220382 TGATCTTTGGTATTTTGCAGGTGG 59.780 41.667 0.00 0.00 0.00 4.61
836 840 1.704641 TCCTCGATGATGGTGGGTAG 58.295 55.000 0.00 0.00 0.00 3.18
855 859 5.407691 GGGTAGACCAGTTTTACGAGAAAAG 59.592 44.000 0.21 0.00 39.85 2.27
914 918 4.900684 AGTCCTTTCTTTCTGAAGGTAGC 58.099 43.478 0.00 0.00 35.89 3.58
1034 1215 2.852449 TCAGACGCACCCAACAATTAA 58.148 42.857 0.00 0.00 0.00 1.40
1035 1216 2.811431 TCAGACGCACCCAACAATTAAG 59.189 45.455 0.00 0.00 0.00 1.85
1036 1217 2.552315 CAGACGCACCCAACAATTAAGT 59.448 45.455 0.00 0.00 0.00 2.24
1037 1218 2.812011 AGACGCACCCAACAATTAAGTC 59.188 45.455 0.00 0.00 0.00 3.01
1038 1219 1.883926 ACGCACCCAACAATTAAGTCC 59.116 47.619 0.00 0.00 0.00 3.85
1039 1220 2.159382 CGCACCCAACAATTAAGTCCT 58.841 47.619 0.00 0.00 0.00 3.85
1040 1221 2.556622 CGCACCCAACAATTAAGTCCTT 59.443 45.455 0.00 0.00 0.00 3.36
1041 1222 3.005367 CGCACCCAACAATTAAGTCCTTT 59.995 43.478 0.00 0.00 0.00 3.11
1042 1223 4.556233 GCACCCAACAATTAAGTCCTTTC 58.444 43.478 0.00 0.00 0.00 2.62
1043 1224 4.280929 GCACCCAACAATTAAGTCCTTTCT 59.719 41.667 0.00 0.00 0.00 2.52
1044 1225 5.221441 GCACCCAACAATTAAGTCCTTTCTT 60.221 40.000 0.00 0.00 0.00 2.52
1045 1226 6.685368 GCACCCAACAATTAAGTCCTTTCTTT 60.685 38.462 0.00 0.00 0.00 2.52
1046 1227 6.923508 CACCCAACAATTAAGTCCTTTCTTTC 59.076 38.462 0.00 0.00 0.00 2.62
1047 1228 6.839134 ACCCAACAATTAAGTCCTTTCTTTCT 59.161 34.615 0.00 0.00 0.00 2.52
1048 1229 8.002459 ACCCAACAATTAAGTCCTTTCTTTCTA 58.998 33.333 0.00 0.00 0.00 2.10
1049 1230 8.856103 CCCAACAATTAAGTCCTTTCTTTCTAA 58.144 33.333 0.00 0.00 0.00 2.10
1062 1243 7.503521 CTTTCTTTCTAAAGGACTTCTTGCT 57.496 36.000 2.77 0.00 36.67 3.91
1063 1244 7.881775 TTTCTTTCTAAAGGACTTCTTGCTT 57.118 32.000 2.77 0.00 37.52 3.91
1064 1245 7.497925 TTCTTTCTAAAGGACTTCTTGCTTC 57.502 36.000 2.77 0.00 34.10 3.86
1065 1246 6.591935 TCTTTCTAAAGGACTTCTTGCTTCA 58.408 36.000 2.77 0.00 34.10 3.02
1066 1247 7.054124 TCTTTCTAAAGGACTTCTTGCTTCAA 58.946 34.615 2.77 0.00 34.10 2.69
1067 1248 6.867662 TTCTAAAGGACTTCTTGCTTCAAG 57.132 37.500 0.37 0.37 42.25 3.02
1068 1249 6.174720 TCTAAAGGACTTCTTGCTTCAAGA 57.825 37.500 5.25 5.25 46.93 3.02
1078 1259 5.041191 TCTTGCTTCAAGAAGTCCTTTCT 57.959 39.130 11.14 0.00 45.84 2.52
1101 1282 9.939802 TTCTTTCTAAAGGTAGTTCTGATAACC 57.060 33.333 2.77 0.00 36.67 2.85
1102 1283 9.322769 TCTTTCTAAAGGTAGTTCTGATAACCT 57.677 33.333 2.77 1.48 44.24 3.50
1103 1284 9.372369 CTTTCTAAAGGTAGTTCTGATAACCTG 57.628 37.037 6.81 0.00 41.51 4.00
1104 1285 6.875076 TCTAAAGGTAGTTCTGATAACCTGC 58.125 40.000 6.81 0.00 41.51 4.85
1105 1286 5.763876 AAAGGTAGTTCTGATAACCTGCT 57.236 39.130 6.81 0.00 41.51 4.24
1106 1287 4.744795 AGGTAGTTCTGATAACCTGCTG 57.255 45.455 5.58 0.00 40.83 4.41
1107 1288 4.097418 AGGTAGTTCTGATAACCTGCTGT 58.903 43.478 5.58 0.00 40.83 4.40
1108 1289 4.081420 AGGTAGTTCTGATAACCTGCTGTG 60.081 45.833 5.58 0.00 40.83 3.66
1109 1290 4.081642 GGTAGTTCTGATAACCTGCTGTGA 60.082 45.833 0.00 0.00 0.00 3.58
1110 1291 4.623932 AGTTCTGATAACCTGCTGTGAA 57.376 40.909 0.00 0.00 0.00 3.18
1111 1292 4.319177 AGTTCTGATAACCTGCTGTGAAC 58.681 43.478 0.00 0.00 34.55 3.18
1112 1293 4.040952 AGTTCTGATAACCTGCTGTGAACT 59.959 41.667 0.00 0.00 38.28 3.01
1113 1294 5.246203 AGTTCTGATAACCTGCTGTGAACTA 59.754 40.000 0.00 0.00 40.35 2.24
1114 1295 5.073311 TCTGATAACCTGCTGTGAACTAC 57.927 43.478 0.00 0.00 0.00 2.73
1115 1296 4.526650 TCTGATAACCTGCTGTGAACTACA 59.473 41.667 0.00 0.00 37.78 2.74
1116 1297 5.187772 TCTGATAACCTGCTGTGAACTACAT 59.812 40.000 0.00 0.00 38.92 2.29
1117 1298 5.804639 TGATAACCTGCTGTGAACTACATT 58.195 37.500 0.00 0.00 38.92 2.71
1118 1299 6.237901 TGATAACCTGCTGTGAACTACATTT 58.762 36.000 0.00 0.00 38.92 2.32
1119 1300 6.714810 TGATAACCTGCTGTGAACTACATTTT 59.285 34.615 0.00 0.00 38.92 1.82
1120 1301 5.852282 AACCTGCTGTGAACTACATTTTT 57.148 34.783 0.00 0.00 38.92 1.94
1142 1323 8.514330 TTTTTCTAGCCAGTTGAAGTTTCTAA 57.486 30.769 0.00 0.00 0.00 2.10
1143 1324 8.691661 TTTTCTAGCCAGTTGAAGTTTCTAAT 57.308 30.769 0.00 0.00 0.00 1.73
1144 1325 9.787435 TTTTCTAGCCAGTTGAAGTTTCTAATA 57.213 29.630 0.00 0.00 0.00 0.98
1145 1326 9.787435 TTTCTAGCCAGTTGAAGTTTCTAATAA 57.213 29.630 0.00 0.00 0.00 1.40
1146 1327 9.436957 TTCTAGCCAGTTGAAGTTTCTAATAAG 57.563 33.333 0.00 0.00 0.00 1.73
1147 1328 8.594550 TCTAGCCAGTTGAAGTTTCTAATAAGT 58.405 33.333 0.00 0.00 0.00 2.24
1148 1329 9.220767 CTAGCCAGTTGAAGTTTCTAATAAGTT 57.779 33.333 0.00 0.00 0.00 2.66
1149 1330 8.465273 AGCCAGTTGAAGTTTCTAATAAGTTT 57.535 30.769 0.00 0.00 0.00 2.66
1150 1331 8.568794 AGCCAGTTGAAGTTTCTAATAAGTTTC 58.431 33.333 0.00 0.00 0.00 2.78
1151 1332 8.349983 GCCAGTTGAAGTTTCTAATAAGTTTCA 58.650 33.333 0.00 0.00 0.00 2.69
1154 1335 9.899226 AGTTGAAGTTTCTAATAAGTTTCATGC 57.101 29.630 0.00 0.00 0.00 4.06
1155 1336 9.899226 GTTGAAGTTTCTAATAAGTTTCATGCT 57.101 29.630 0.00 0.00 0.00 3.79
1160 1341 9.507329 AGTTTCTAATAAGTTTCATGCTTCTCA 57.493 29.630 0.00 0.00 0.00 3.27
1161 1342 9.766277 GTTTCTAATAAGTTTCATGCTTCTCAG 57.234 33.333 0.00 0.00 0.00 3.35
1175 1356 4.483311 GCTTCTCAGCTTTTCTCAAATGG 58.517 43.478 0.00 0.00 43.51 3.16
1176 1357 4.483311 CTTCTCAGCTTTTCTCAAATGGC 58.517 43.478 0.00 0.00 0.00 4.40
1177 1358 3.489355 TCTCAGCTTTTCTCAAATGGCA 58.511 40.909 0.00 0.00 0.00 4.92
1178 1359 4.084287 TCTCAGCTTTTCTCAAATGGCAT 58.916 39.130 0.00 0.00 0.00 4.40
1179 1360 4.082408 TCTCAGCTTTTCTCAAATGGCATG 60.082 41.667 0.00 0.00 0.00 4.06
1180 1361 3.827876 TCAGCTTTTCTCAAATGGCATGA 59.172 39.130 0.00 0.00 0.00 3.07
1181 1362 4.281435 TCAGCTTTTCTCAAATGGCATGAA 59.719 37.500 0.00 0.00 0.00 2.57
1182 1363 4.992319 CAGCTTTTCTCAAATGGCATGAAA 59.008 37.500 0.00 3.57 0.00 2.69
1183 1364 5.120208 CAGCTTTTCTCAAATGGCATGAAAG 59.880 40.000 0.00 6.56 0.00 2.62
1184 1365 5.011329 AGCTTTTCTCAAATGGCATGAAAGA 59.989 36.000 0.00 1.10 0.00 2.52
1185 1366 5.697633 GCTTTTCTCAAATGGCATGAAAGAA 59.302 36.000 0.00 7.61 0.00 2.52
1186 1367 6.370718 GCTTTTCTCAAATGGCATGAAAGAAT 59.629 34.615 15.26 0.00 0.00 2.40
1187 1368 7.412672 GCTTTTCTCAAATGGCATGAAAGAATC 60.413 37.037 15.26 7.82 0.00 2.52
1188 1369 6.845758 TTCTCAAATGGCATGAAAGAATCT 57.154 33.333 0.00 0.00 0.00 2.40
1189 1370 6.203808 TCTCAAATGGCATGAAAGAATCTG 57.796 37.500 0.00 0.00 0.00 2.90
1190 1371 5.947566 TCTCAAATGGCATGAAAGAATCTGA 59.052 36.000 0.00 0.00 0.00 3.27
1191 1372 6.605995 TCTCAAATGGCATGAAAGAATCTGAT 59.394 34.615 0.00 0.00 0.00 2.90
1192 1373 6.802608 TCAAATGGCATGAAAGAATCTGATC 58.197 36.000 0.00 0.00 0.00 2.92
1193 1374 6.378848 TCAAATGGCATGAAAGAATCTGATCA 59.621 34.615 0.00 0.00 0.00 2.92
1194 1375 6.392625 AATGGCATGAAAGAATCTGATCAG 57.607 37.500 17.07 17.07 0.00 2.90
1195 1376 5.106876 TGGCATGAAAGAATCTGATCAGA 57.893 39.130 27.03 27.03 42.37 3.27
1196 1377 4.880120 TGGCATGAAAGAATCTGATCAGAC 59.120 41.667 27.37 15.69 40.75 3.51
1197 1378 4.025061 GGCATGAAAGAATCTGATCAGACG 60.025 45.833 27.37 0.17 40.75 4.18
1198 1379 4.552378 GCATGAAAGAATCTGATCAGACGC 60.552 45.833 27.37 20.55 40.75 5.19
1199 1380 4.192429 TGAAAGAATCTGATCAGACGCA 57.808 40.909 27.37 15.18 40.75 5.24
1200 1381 3.928992 TGAAAGAATCTGATCAGACGCAC 59.071 43.478 27.37 17.24 40.75 5.34
1201 1382 2.593346 AGAATCTGATCAGACGCACC 57.407 50.000 27.37 13.96 40.75 5.01
1202 1383 1.137872 AGAATCTGATCAGACGCACCC 59.862 52.381 27.37 12.36 40.75 4.61
1203 1384 0.904649 AATCTGATCAGACGCACCCA 59.095 50.000 27.37 3.10 40.75 4.51
1204 1385 0.904649 ATCTGATCAGACGCACCCAA 59.095 50.000 27.37 2.31 40.75 4.12
1205 1386 0.904649 TCTGATCAGACGCACCCAAT 59.095 50.000 21.67 0.00 31.41 3.16
1206 1387 2.107366 TCTGATCAGACGCACCCAATA 58.893 47.619 21.67 0.00 31.41 1.90
1207 1388 2.499693 TCTGATCAGACGCACCCAATAA 59.500 45.455 21.67 0.00 31.41 1.40
1208 1389 3.134623 TCTGATCAGACGCACCCAATAAT 59.865 43.478 21.67 0.00 31.41 1.28
1209 1390 3.879295 CTGATCAGACGCACCCAATAATT 59.121 43.478 18.34 0.00 0.00 1.40
1210 1391 5.029807 TGATCAGACGCACCCAATAATTA 57.970 39.130 0.00 0.00 0.00 1.40
1443 1625 6.982852 AGGTACATCCGTATCTAGACAAATG 58.017 40.000 0.00 0.00 37.29 2.32
1669 1859 4.162509 GGAGTAGGATACAAAAGGCTGTCT 59.837 45.833 0.00 0.00 46.26 3.41
1710 1911 9.520515 TCTTTATTAGCTCTTTCCTTGATGTTT 57.479 29.630 0.00 0.00 0.00 2.83
1714 1915 8.814038 ATTAGCTCTTTCCTTGATGTTTATGT 57.186 30.769 0.00 0.00 0.00 2.29
1715 1916 9.905713 ATTAGCTCTTTCCTTGATGTTTATGTA 57.094 29.630 0.00 0.00 0.00 2.29
1716 1917 9.905713 TTAGCTCTTTCCTTGATGTTTATGTAT 57.094 29.630 0.00 0.00 0.00 2.29
1717 1918 8.814038 AGCTCTTTCCTTGATGTTTATGTATT 57.186 30.769 0.00 0.00 0.00 1.89
1859 2066 4.023707 ACAAATTTGAGGTTCTCTCTTGCG 60.024 41.667 24.64 0.00 42.86 4.85
1973 2180 0.039764 TGAGGTCGAGGGTGTGATCT 59.960 55.000 0.00 0.00 0.00 2.75
2528 2743 7.122948 ACAAGTACAAACCTGTGAAATTGGTTA 59.877 33.333 0.00 0.00 42.53 2.85
2617 2832 0.994247 TCCCTTCTGGACATGCATGT 59.006 50.000 31.82 31.82 45.16 3.21
2749 2994 2.224079 CGGTTCCACAGATTTGACAGTG 59.776 50.000 0.00 0.00 0.00 3.66
2873 3121 1.519751 TTTTGGCGTTCCATGGTCGG 61.520 55.000 24.44 12.30 43.05 4.79
2984 7382 6.074409 CGCTTGATATGATTTCTCACTCACTC 60.074 42.308 0.00 0.00 33.22 3.51
3007 7405 8.478527 CTCGACAGAGTTATTATTAAGTCGTC 57.521 38.462 0.00 16.69 45.34 4.20
3029 7427 2.263077 GTTCGTCATCAGTCGCTTCAT 58.737 47.619 0.00 0.00 0.00 2.57
3043 7441 1.407979 GCTTCATTGGGATTCTGGCTG 59.592 52.381 0.00 0.00 0.00 4.85
3044 7442 2.731572 CTTCATTGGGATTCTGGCTGT 58.268 47.619 0.00 0.00 0.00 4.40
3045 7443 2.133281 TCATTGGGATTCTGGCTGTG 57.867 50.000 0.00 0.00 0.00 3.66
3046 7444 0.458669 CATTGGGATTCTGGCTGTGC 59.541 55.000 0.00 0.00 0.00 4.57
3051 7449 0.727398 GGATTCTGGCTGTGCGTAAC 59.273 55.000 0.00 0.00 0.00 2.50
3058 7456 0.602905 GGCTGTGCGTAACCTGAGTT 60.603 55.000 0.00 0.00 40.15 3.01
3106 7507 1.455383 AACACTTTGGCGCCTGAAGG 61.455 55.000 32.11 25.48 38.53 3.46
3116 7517 2.486796 GCCTGAAGGTGAAGGATGC 58.513 57.895 0.00 0.00 35.40 3.91
3124 7525 2.731572 AGGTGAAGGATGCAAGGAATG 58.268 47.619 0.00 0.00 0.00 2.67
3126 7527 2.621407 GGTGAAGGATGCAAGGAATGGA 60.621 50.000 0.00 0.00 0.00 3.41
3127 7528 2.424956 GTGAAGGATGCAAGGAATGGAC 59.575 50.000 0.00 0.00 29.34 4.02
3128 7529 2.027385 GAAGGATGCAAGGAATGGACC 58.973 52.381 0.00 0.00 29.34 4.46
3136 7537 0.909610 AAGGAATGGACCGAGGCTCA 60.910 55.000 15.95 0.00 34.73 4.26
3158 7559 8.408601 GCTCATGGCTTCTTAGAATGAAATTTA 58.591 33.333 0.00 0.00 35.47 1.40
3159 7560 9.727627 CTCATGGCTTCTTAGAATGAAATTTAC 57.272 33.333 0.00 0.00 36.07 2.01
3182 7583 6.187682 ACATTTCTTCAAGATTAATCGGGGT 58.812 36.000 9.78 0.00 0.00 4.95
3201 7602 2.838202 GGTGGTAGACCCTTTGATCTCA 59.162 50.000 0.00 0.00 39.10 3.27
3210 7611 6.842676 AGACCCTTTGATCTCACTTTACTTT 58.157 36.000 0.00 0.00 0.00 2.66
3212 7613 7.445707 AGACCCTTTGATCTCACTTTACTTTTC 59.554 37.037 0.00 0.00 0.00 2.29
3272 7673 2.552599 TACCGTCTTGTTTCATGCCA 57.447 45.000 0.00 0.00 0.00 4.92
3282 7690 4.787135 TGTTTCATGCCATATGGTAGGA 57.213 40.909 21.26 21.26 38.76 2.94
3283 7691 5.323382 TGTTTCATGCCATATGGTAGGAT 57.677 39.130 24.75 9.37 40.10 3.24
3305 7718 6.591834 GGATGATTCCTTATTACTCCATGTCG 59.408 42.308 0.00 0.00 39.14 4.35
3306 7719 5.297547 TGATTCCTTATTACTCCATGTCGC 58.702 41.667 0.00 0.00 0.00 5.19
3425 7842 2.742053 CACTTGTATCAAGTCGGGGTTG 59.258 50.000 11.47 0.00 0.00 3.77
3426 7843 2.635915 ACTTGTATCAAGTCGGGGTTGA 59.364 45.455 9.00 0.00 38.28 3.18
3427 7844 2.754946 TGTATCAAGTCGGGGTTGAC 57.245 50.000 0.00 0.00 36.76 3.18
3471 7888 2.268796 TCACCTGATCCTTGGATCCA 57.731 50.000 22.54 11.44 0.00 3.41
3539 7957 6.520272 AGTTTCTCAAAGATATCCTCGGATG 58.480 40.000 8.69 0.00 36.17 3.51
3584 8022 6.649436 TCGTCAAGATATCGAAATGATTTGC 58.351 36.000 0.00 0.00 38.57 3.68
3588 8026 8.435430 GTCAAGATATCGAAATGATTTGCGATA 58.565 33.333 22.17 22.17 45.91 2.92
3599 8042 8.984891 AAATGATTTGCGATAATTGTTCTTCA 57.015 26.923 0.00 0.00 0.00 3.02
3602 8045 7.592938 TGATTTGCGATAATTGTTCTTCAGTT 58.407 30.769 0.00 0.00 0.00 3.16
3609 8052 6.530534 CGATAATTGTTCTTCAGTTACTCCGT 59.469 38.462 0.00 0.00 32.56 4.69
3653 8096 1.468914 GTCGCCTTTGTTCAATCTCCC 59.531 52.381 0.00 0.00 0.00 4.30
3720 8163 1.604593 GCCCTCTTTCAAGCCTGCA 60.605 57.895 0.00 0.00 0.00 4.41
3723 8166 0.239347 CCTCTTTCAAGCCTGCAACG 59.761 55.000 0.00 0.00 0.00 4.10
3786 8235 7.762159 GTCTTCGAATGATTTCCTTACTCTTCT 59.238 37.037 0.00 0.00 0.00 2.85
3794 8243 3.176924 TCCTTACTCTTCTGAGGCAGT 57.823 47.619 0.00 0.00 44.29 4.40
3802 8251 2.105477 TCTTCTGAGGCAGTTGCTTTCT 59.895 45.455 3.88 0.00 41.70 2.52
3829 8278 8.078060 TCTCTTTTACATCCAGTGTGATGATA 57.922 34.615 21.37 11.30 43.94 2.15
3841 8290 6.594547 CCAGTGTGATGATAATCTCATGGATC 59.405 42.308 13.24 0.00 44.83 3.36
3852 8301 0.387239 TCATGGATCGAGCATACGCG 60.387 55.000 3.53 3.53 45.49 6.01
3854 8303 3.106407 GGATCGAGCATACGCGCC 61.106 66.667 5.73 0.00 45.49 6.53
3855 8304 2.049985 GATCGAGCATACGCGCCT 60.050 61.111 5.73 0.00 45.49 5.52
3887 8336 5.250200 TGAACACAACAGGAAAAGTACAGT 58.750 37.500 0.00 0.00 0.00 3.55
3910 8359 9.781834 CAGTGTTTACAATGTCTTCTTTTGTTA 57.218 29.630 2.38 0.00 37.20 2.41
3926 8375 8.990163 TCTTTTGTTACTAAAAAGTCCTCCAT 57.010 30.769 8.12 0.00 42.59 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.022287 CACAACGCTTCTGCCGTT 58.978 55.556 0.00 0.00 36.77 4.44
48 49 2.019951 CCCAAACTCACCGACGACG 61.020 63.158 0.00 0.00 39.43 5.12
107 108 1.771854 TCAAGGTTGGTCCAAGTAGCA 59.228 47.619 3.96 0.00 39.02 3.49
261 262 3.745240 CTCCAGCATGCTGCCGCTA 62.745 63.158 37.11 19.68 46.52 4.26
316 317 3.853103 CGATATCAAACCACGAACACGTA 59.147 43.478 3.12 0.00 38.51 3.57
353 354 4.410400 GAGGCCGGACCACCAAGG 62.410 72.222 1.76 0.00 43.14 3.61
503 504 6.020971 TGCTTTATAGAGAAAGTCACACGA 57.979 37.500 0.00 0.00 38.46 4.35
674 678 8.939929 CAACACTATGTTCTTCTATGTGTGATT 58.060 33.333 0.00 0.00 38.77 2.57
675 679 7.065085 GCAACACTATGTTCTTCTATGTGTGAT 59.935 37.037 0.00 0.00 38.77 3.06
680 684 7.841956 ACTAGCAACACTATGTTCTTCTATGT 58.158 34.615 0.00 0.00 38.77 2.29
809 813 2.428890 ACCATCATCGAGGAAGAGTCAC 59.571 50.000 2.91 0.00 0.00 3.67
836 840 4.812626 TGGTCTTTTCTCGTAAAACTGGTC 59.187 41.667 0.00 0.00 0.00 4.02
855 859 8.358148 AGAATTGCTGAATTGATATGAATGGTC 58.642 33.333 0.00 0.00 31.58 4.02
914 918 6.925211 TGTAGTTCACAGAAGGTTATCAGAG 58.075 40.000 0.00 0.00 31.89 3.35
1038 1219 7.503521 AGCAAGAAGTCCTTTAGAAAGAAAG 57.496 36.000 3.52 0.00 38.28 2.62
1039 1220 7.556275 TGAAGCAAGAAGTCCTTTAGAAAGAAA 59.444 33.333 3.52 0.00 38.28 2.52
1040 1221 7.054124 TGAAGCAAGAAGTCCTTTAGAAAGAA 58.946 34.615 3.52 0.00 38.28 2.52
1041 1222 6.591935 TGAAGCAAGAAGTCCTTTAGAAAGA 58.408 36.000 3.52 0.00 38.28 2.52
1042 1223 6.867662 TGAAGCAAGAAGTCCTTTAGAAAG 57.132 37.500 0.00 0.00 31.42 2.62
1043 1224 7.054124 TCTTGAAGCAAGAAGTCCTTTAGAAA 58.946 34.615 7.36 0.00 45.84 2.52
1044 1225 6.591935 TCTTGAAGCAAGAAGTCCTTTAGAA 58.408 36.000 7.36 0.00 45.84 2.10
1045 1226 6.174720 TCTTGAAGCAAGAAGTCCTTTAGA 57.825 37.500 7.36 0.00 45.84 2.10
1056 1237 5.041191 AGAAAGGACTTCTTGAAGCAAGA 57.959 39.130 9.98 5.81 46.93 3.02
1075 1256 9.939802 GGTTATCAGAACTACCTTTAGAAAGAA 57.060 33.333 3.52 0.00 38.28 2.52
1076 1257 9.322769 AGGTTATCAGAACTACCTTTAGAAAGA 57.677 33.333 3.52 0.00 37.75 2.52
1077 1258 9.372369 CAGGTTATCAGAACTACCTTTAGAAAG 57.628 37.037 0.00 0.00 38.93 2.62
1078 1259 7.822822 GCAGGTTATCAGAACTACCTTTAGAAA 59.177 37.037 0.00 0.00 38.93 2.52
1079 1260 7.180408 AGCAGGTTATCAGAACTACCTTTAGAA 59.820 37.037 0.00 0.00 38.93 2.10
1080 1261 6.668283 AGCAGGTTATCAGAACTACCTTTAGA 59.332 38.462 0.00 0.00 38.93 2.10
1081 1262 6.758886 CAGCAGGTTATCAGAACTACCTTTAG 59.241 42.308 0.00 0.00 38.93 1.85
1082 1263 6.212791 ACAGCAGGTTATCAGAACTACCTTTA 59.787 38.462 0.00 0.00 38.93 1.85
1083 1264 5.013183 ACAGCAGGTTATCAGAACTACCTTT 59.987 40.000 0.00 0.00 38.93 3.11
1084 1265 4.532521 ACAGCAGGTTATCAGAACTACCTT 59.467 41.667 0.00 0.00 38.93 3.50
1085 1266 4.081420 CACAGCAGGTTATCAGAACTACCT 60.081 45.833 0.00 0.00 41.58 3.08
1086 1267 4.081642 TCACAGCAGGTTATCAGAACTACC 60.082 45.833 0.00 0.00 0.00 3.18
1087 1268 5.073311 TCACAGCAGGTTATCAGAACTAC 57.927 43.478 0.00 0.00 0.00 2.73
1088 1269 5.246203 AGTTCACAGCAGGTTATCAGAACTA 59.754 40.000 0.00 0.00 41.64 2.24
1089 1270 4.040952 AGTTCACAGCAGGTTATCAGAACT 59.959 41.667 0.00 0.00 39.47 3.01
1090 1271 4.319177 AGTTCACAGCAGGTTATCAGAAC 58.681 43.478 0.00 0.00 35.58 3.01
1091 1272 4.623932 AGTTCACAGCAGGTTATCAGAA 57.376 40.909 0.00 0.00 0.00 3.02
1092 1273 4.526650 TGTAGTTCACAGCAGGTTATCAGA 59.473 41.667 0.00 0.00 31.89 3.27
1093 1274 4.820897 TGTAGTTCACAGCAGGTTATCAG 58.179 43.478 0.00 0.00 31.89 2.90
1094 1275 4.882842 TGTAGTTCACAGCAGGTTATCA 57.117 40.909 0.00 0.00 31.89 2.15
1095 1276 6.743575 AAATGTAGTTCACAGCAGGTTATC 57.256 37.500 0.00 0.00 41.51 1.75
1096 1277 7.524717 AAAAATGTAGTTCACAGCAGGTTAT 57.475 32.000 0.00 0.00 41.51 1.89
1097 1278 6.952773 AAAAATGTAGTTCACAGCAGGTTA 57.047 33.333 0.00 0.00 41.51 2.85
1098 1279 5.852282 AAAAATGTAGTTCACAGCAGGTT 57.148 34.783 0.00 0.00 41.51 3.50
1117 1298 8.514330 TTAGAAACTTCAACTGGCTAGAAAAA 57.486 30.769 3.17 0.00 0.00 1.94
1118 1299 8.691661 ATTAGAAACTTCAACTGGCTAGAAAA 57.308 30.769 3.17 0.00 0.00 2.29
1119 1300 9.787435 TTATTAGAAACTTCAACTGGCTAGAAA 57.213 29.630 3.17 0.00 0.00 2.52
1120 1301 9.436957 CTTATTAGAAACTTCAACTGGCTAGAA 57.563 33.333 3.17 0.00 0.00 2.10
1121 1302 8.594550 ACTTATTAGAAACTTCAACTGGCTAGA 58.405 33.333 3.17 0.00 0.00 2.43
1122 1303 8.779354 ACTTATTAGAAACTTCAACTGGCTAG 57.221 34.615 0.00 0.00 0.00 3.42
1123 1304 9.569122 AAACTTATTAGAAACTTCAACTGGCTA 57.431 29.630 0.00 0.00 0.00 3.93
1124 1305 8.465273 AAACTTATTAGAAACTTCAACTGGCT 57.535 30.769 0.00 0.00 0.00 4.75
1125 1306 8.349983 TGAAACTTATTAGAAACTTCAACTGGC 58.650 33.333 0.00 0.00 0.00 4.85
1128 1309 9.899226 GCATGAAACTTATTAGAAACTTCAACT 57.101 29.630 0.00 0.00 0.00 3.16
1129 1310 9.899226 AGCATGAAACTTATTAGAAACTTCAAC 57.101 29.630 0.00 0.00 0.00 3.18
1134 1315 9.507329 TGAGAAGCATGAAACTTATTAGAAACT 57.493 29.630 0.00 0.00 0.00 2.66
1135 1316 9.766277 CTGAGAAGCATGAAACTTATTAGAAAC 57.234 33.333 0.00 0.00 26.85 2.78
1136 1317 8.454106 GCTGAGAAGCATGAAACTTATTAGAAA 58.546 33.333 0.00 0.00 34.41 2.52
1137 1318 7.826252 AGCTGAGAAGCATGAAACTTATTAGAA 59.174 33.333 0.00 0.00 37.25 2.10
1138 1319 7.334090 AGCTGAGAAGCATGAAACTTATTAGA 58.666 34.615 0.00 0.00 37.25 2.10
1139 1320 7.551035 AGCTGAGAAGCATGAAACTTATTAG 57.449 36.000 0.00 0.00 37.25 1.73
1140 1321 7.928307 AAGCTGAGAAGCATGAAACTTATTA 57.072 32.000 0.00 0.00 37.25 0.98
1141 1322 6.830873 AAGCTGAGAAGCATGAAACTTATT 57.169 33.333 0.00 0.00 37.25 1.40
1142 1323 6.830873 AAAGCTGAGAAGCATGAAACTTAT 57.169 33.333 0.00 0.00 37.25 1.73
1143 1324 6.488006 AGAAAAGCTGAGAAGCATGAAACTTA 59.512 34.615 0.00 0.00 37.25 2.24
1144 1325 5.301298 AGAAAAGCTGAGAAGCATGAAACTT 59.699 36.000 0.00 0.00 37.25 2.66
1145 1326 4.826183 AGAAAAGCTGAGAAGCATGAAACT 59.174 37.500 0.00 0.00 37.25 2.66
1146 1327 5.118642 AGAAAAGCTGAGAAGCATGAAAC 57.881 39.130 0.00 0.00 37.25 2.78
1147 1328 4.823442 TGAGAAAAGCTGAGAAGCATGAAA 59.177 37.500 0.00 0.00 37.25 2.69
1148 1329 4.392047 TGAGAAAAGCTGAGAAGCATGAA 58.608 39.130 0.00 0.00 37.25 2.57
1149 1330 4.011966 TGAGAAAAGCTGAGAAGCATGA 57.988 40.909 0.00 0.00 37.25 3.07
1150 1331 4.761235 TTGAGAAAAGCTGAGAAGCATG 57.239 40.909 0.00 0.00 37.25 4.06
1151 1332 5.336531 CCATTTGAGAAAAGCTGAGAAGCAT 60.337 40.000 0.00 0.00 37.25 3.79
1152 1333 4.022589 CCATTTGAGAAAAGCTGAGAAGCA 60.023 41.667 0.00 0.00 37.25 3.91
1153 1334 4.483311 CCATTTGAGAAAAGCTGAGAAGC 58.517 43.478 0.00 0.00 0.00 3.86
1154 1335 4.022589 TGCCATTTGAGAAAAGCTGAGAAG 60.023 41.667 0.00 0.00 0.00 2.85
1155 1336 3.890756 TGCCATTTGAGAAAAGCTGAGAA 59.109 39.130 0.00 0.00 0.00 2.87
1156 1337 3.489355 TGCCATTTGAGAAAAGCTGAGA 58.511 40.909 0.00 0.00 0.00 3.27
1157 1338 3.928727 TGCCATTTGAGAAAAGCTGAG 57.071 42.857 0.00 0.00 0.00 3.35
1158 1339 3.827876 TCATGCCATTTGAGAAAAGCTGA 59.172 39.130 0.00 0.00 0.00 4.26
1159 1340 4.182693 TCATGCCATTTGAGAAAAGCTG 57.817 40.909 0.00 0.00 0.00 4.24
1160 1341 4.877378 TTCATGCCATTTGAGAAAAGCT 57.123 36.364 0.00 0.00 0.00 3.74
1161 1342 5.232463 TCTTTCATGCCATTTGAGAAAAGC 58.768 37.500 0.00 0.00 0.00 3.51
1162 1343 7.817962 AGATTCTTTCATGCCATTTGAGAAAAG 59.182 33.333 0.00 0.00 0.00 2.27
1163 1344 7.601130 CAGATTCTTTCATGCCATTTGAGAAAA 59.399 33.333 0.00 0.00 0.00 2.29
1164 1345 7.039574 TCAGATTCTTTCATGCCATTTGAGAAA 60.040 33.333 0.00 0.00 0.00 2.52
1165 1346 6.434965 TCAGATTCTTTCATGCCATTTGAGAA 59.565 34.615 0.00 0.00 0.00 2.87
1166 1347 5.947566 TCAGATTCTTTCATGCCATTTGAGA 59.052 36.000 0.00 0.00 0.00 3.27
1167 1348 6.203808 TCAGATTCTTTCATGCCATTTGAG 57.796 37.500 0.00 0.00 0.00 3.02
1168 1349 6.378848 TGATCAGATTCTTTCATGCCATTTGA 59.621 34.615 0.00 0.00 0.00 2.69
1169 1350 6.569780 TGATCAGATTCTTTCATGCCATTTG 58.430 36.000 0.00 0.00 0.00 2.32
1170 1351 6.605995 TCTGATCAGATTCTTTCATGCCATTT 59.394 34.615 21.67 0.00 31.41 2.32
1171 1352 6.039493 GTCTGATCAGATTCTTTCATGCCATT 59.961 38.462 27.51 0.00 39.97 3.16
1172 1353 5.531659 GTCTGATCAGATTCTTTCATGCCAT 59.468 40.000 27.51 0.00 39.97 4.40
1173 1354 4.880120 GTCTGATCAGATTCTTTCATGCCA 59.120 41.667 27.51 0.00 39.97 4.92
1174 1355 4.025061 CGTCTGATCAGATTCTTTCATGCC 60.025 45.833 27.51 9.69 39.97 4.40
1175 1356 4.552378 GCGTCTGATCAGATTCTTTCATGC 60.552 45.833 27.51 15.46 39.97 4.06
1176 1357 4.569564 TGCGTCTGATCAGATTCTTTCATG 59.430 41.667 27.51 9.77 39.97 3.07
1177 1358 4.569966 GTGCGTCTGATCAGATTCTTTCAT 59.430 41.667 27.51 0.00 39.97 2.57
1178 1359 3.928992 GTGCGTCTGATCAGATTCTTTCA 59.071 43.478 27.51 15.43 39.97 2.69
1179 1360 3.308323 GGTGCGTCTGATCAGATTCTTTC 59.692 47.826 27.51 12.94 39.97 2.62
1180 1361 3.265791 GGTGCGTCTGATCAGATTCTTT 58.734 45.455 27.51 0.00 39.97 2.52
1181 1362 2.419297 GGGTGCGTCTGATCAGATTCTT 60.419 50.000 27.51 0.00 39.97 2.52
1182 1363 1.137872 GGGTGCGTCTGATCAGATTCT 59.862 52.381 27.51 0.00 39.97 2.40
1183 1364 1.134699 TGGGTGCGTCTGATCAGATTC 60.135 52.381 27.51 20.85 39.97 2.52
1184 1365 0.904649 TGGGTGCGTCTGATCAGATT 59.095 50.000 27.51 0.00 39.97 2.40
1185 1366 0.904649 TTGGGTGCGTCTGATCAGAT 59.095 50.000 27.51 0.00 39.97 2.90
1186 1367 0.904649 ATTGGGTGCGTCTGATCAGA 59.095 50.000 21.67 21.67 34.56 3.27
1187 1368 2.602257 TATTGGGTGCGTCTGATCAG 57.398 50.000 17.07 17.07 0.00 2.90
1188 1369 3.558931 ATTATTGGGTGCGTCTGATCA 57.441 42.857 0.00 0.00 0.00 2.92
1189 1370 4.452455 CCTAATTATTGGGTGCGTCTGATC 59.548 45.833 0.00 0.00 0.00 2.92
1190 1371 4.102524 TCCTAATTATTGGGTGCGTCTGAT 59.897 41.667 7.22 0.00 32.34 2.90
1191 1372 3.452990 TCCTAATTATTGGGTGCGTCTGA 59.547 43.478 7.22 0.00 32.34 3.27
1192 1373 3.804036 TCCTAATTATTGGGTGCGTCTG 58.196 45.455 7.22 0.00 32.34 3.51
1193 1374 4.706842 ATCCTAATTATTGGGTGCGTCT 57.293 40.909 7.22 0.00 32.34 4.18
1194 1375 4.556699 GCAATCCTAATTATTGGGTGCGTC 60.557 45.833 7.22 0.00 35.34 5.19
1195 1376 3.317993 GCAATCCTAATTATTGGGTGCGT 59.682 43.478 7.22 0.00 35.34 5.24
1196 1377 3.569701 AGCAATCCTAATTATTGGGTGCG 59.430 43.478 14.04 3.81 38.71 5.34
1197 1378 4.584325 TCAGCAATCCTAATTATTGGGTGC 59.416 41.667 12.70 12.70 35.34 5.01
1198 1379 6.906157 ATCAGCAATCCTAATTATTGGGTG 57.094 37.500 7.22 0.98 35.34 4.61
1199 1380 7.068702 TGAATCAGCAATCCTAATTATTGGGT 58.931 34.615 7.22 0.00 35.34 4.51
1200 1381 7.309621 CCTGAATCAGCAATCCTAATTATTGGG 60.310 40.741 4.40 0.52 35.34 4.12
1201 1382 7.232127 ACCTGAATCAGCAATCCTAATTATTGG 59.768 37.037 4.40 0.00 35.34 3.16
1202 1383 8.174733 ACCTGAATCAGCAATCCTAATTATTG 57.825 34.615 4.40 0.00 37.39 1.90
1203 1384 9.866655 TTACCTGAATCAGCAATCCTAATTATT 57.133 29.630 4.40 0.00 0.00 1.40
1205 1386 9.288576 CATTACCTGAATCAGCAATCCTAATTA 57.711 33.333 4.40 0.00 0.00 1.40
1206 1387 7.781693 ACATTACCTGAATCAGCAATCCTAATT 59.218 33.333 4.40 0.00 0.00 1.40
1207 1388 7.230108 CACATTACCTGAATCAGCAATCCTAAT 59.770 37.037 4.40 0.00 0.00 1.73
1208 1389 6.543465 CACATTACCTGAATCAGCAATCCTAA 59.457 38.462 4.40 0.00 0.00 2.69
1209 1390 6.057533 CACATTACCTGAATCAGCAATCCTA 58.942 40.000 4.40 0.00 0.00 2.94
1210 1391 4.885907 CACATTACCTGAATCAGCAATCCT 59.114 41.667 4.40 0.00 0.00 3.24
1348 1530 6.708285 ACAACTAATTCGGGATGAAAGTAGT 58.292 36.000 0.00 0.00 40.49 2.73
1406 1588 5.928264 ACGGATGTACCTAACACTAAAACAC 59.072 40.000 0.00 0.00 42.09 3.32
1407 1589 6.100404 ACGGATGTACCTAACACTAAAACA 57.900 37.500 0.00 0.00 42.09 2.83
1443 1625 6.260271 CCTCCGTCCCAAATTATTTCTCTTAC 59.740 42.308 0.00 0.00 0.00 2.34
1736 1943 3.701040 TCCATAAAGGCATTTTCCTCTGC 59.299 43.478 0.00 0.00 34.82 4.26
1859 2066 2.998279 GCTGACTGCAATGCCCCAC 61.998 63.158 1.53 0.00 42.31 4.61
1973 2180 2.342650 GGAATTCCTTGGCTGCGCA 61.343 57.895 17.73 10.98 0.00 6.09
2023 2230 3.823304 GGCTCTATCAAATTGGGATCACC 59.177 47.826 0.00 0.00 40.81 4.02
2088 2296 6.491714 AGTACACCAAATAGATGATCTGCT 57.508 37.500 4.96 0.00 0.00 4.24
2528 2743 0.322546 GGGCAGGGTCGATCAAAAGT 60.323 55.000 0.00 0.00 0.00 2.66
2557 2772 2.460918 CGTGTTAGATCCAGGTAAGCG 58.539 52.381 0.00 0.00 0.00 4.68
2617 2832 1.522668 CAAGCCGGAAGTCATGTGAA 58.477 50.000 5.05 0.00 0.00 3.18
2749 2994 3.696051 TCCTTGCAGCAAACTCAATATCC 59.304 43.478 9.65 0.00 0.00 2.59
2873 3121 0.167908 TTGTCATCGGCAATGAACGC 59.832 50.000 2.87 0.00 45.88 4.84
2956 7353 5.664457 AGTGAGAAATCATATCAAGCGTGA 58.336 37.500 4.40 4.40 38.41 4.35
2999 7397 3.501062 ACTGATGACGAACAGACGACTTA 59.499 43.478 0.00 0.00 37.54 2.24
3000 7398 2.293677 ACTGATGACGAACAGACGACTT 59.706 45.455 0.00 0.00 37.54 3.01
3007 7405 1.651138 GAAGCGACTGATGACGAACAG 59.349 52.381 0.00 0.00 39.65 3.16
3029 7427 1.675310 CGCACAGCCAGAATCCCAA 60.675 57.895 0.00 0.00 0.00 4.12
3043 7441 5.077424 CGAAATTAAACTCAGGTTACGCAC 58.923 41.667 0.00 0.00 34.90 5.34
3044 7442 4.751098 ACGAAATTAAACTCAGGTTACGCA 59.249 37.500 0.00 0.00 34.90 5.24
3045 7443 5.273523 ACGAAATTAAACTCAGGTTACGC 57.726 39.130 0.00 0.00 34.90 4.42
3046 7444 9.815936 AAATAACGAAATTAAACTCAGGTTACG 57.184 29.630 0.00 0.00 34.90 3.18
3058 7456 9.393249 CAGCAGAGACAAAAATAACGAAATTAA 57.607 29.630 0.00 0.00 0.00 1.40
3077 7475 1.000938 GCCAAAGTGTTTCCAGCAGAG 60.001 52.381 0.00 0.00 0.00 3.35
3106 7507 2.424956 GTCCATTCCTTGCATCCTTCAC 59.575 50.000 0.00 0.00 0.00 3.18
3112 7513 1.303309 CTCGGTCCATTCCTTGCATC 58.697 55.000 0.00 0.00 0.00 3.91
3115 7516 2.115291 GCCTCGGTCCATTCCTTGC 61.115 63.158 0.00 0.00 0.00 4.01
3116 7517 0.462759 GAGCCTCGGTCCATTCCTTG 60.463 60.000 0.00 0.00 0.00 3.61
3124 7525 2.932130 GAAGCCATGAGCCTCGGTCC 62.932 65.000 0.00 0.00 45.47 4.46
3126 7527 1.557269 AAGAAGCCATGAGCCTCGGT 61.557 55.000 0.00 0.00 45.47 4.69
3127 7528 0.465705 TAAGAAGCCATGAGCCTCGG 59.534 55.000 0.00 0.00 45.47 4.63
3128 7529 1.410517 TCTAAGAAGCCATGAGCCTCG 59.589 52.381 0.00 0.00 45.47 4.63
3158 7559 6.095440 CACCCCGATTAATCTTGAAGAAATGT 59.905 38.462 13.45 0.00 0.00 2.71
3159 7560 6.460123 CCACCCCGATTAATCTTGAAGAAATG 60.460 42.308 13.45 0.61 0.00 2.32
3161 7562 4.947388 CCACCCCGATTAATCTTGAAGAAA 59.053 41.667 13.45 0.00 0.00 2.52
3162 7563 4.018779 ACCACCCCGATTAATCTTGAAGAA 60.019 41.667 13.45 0.00 0.00 2.52
3163 7564 3.521937 ACCACCCCGATTAATCTTGAAGA 59.478 43.478 13.45 0.00 0.00 2.87
3164 7565 3.886123 ACCACCCCGATTAATCTTGAAG 58.114 45.455 13.45 0.00 0.00 3.02
3165 7566 4.717778 TCTACCACCCCGATTAATCTTGAA 59.282 41.667 13.45 0.00 0.00 2.69
3166 7567 4.100498 GTCTACCACCCCGATTAATCTTGA 59.900 45.833 13.45 0.00 0.00 3.02
3167 7568 4.377897 GTCTACCACCCCGATTAATCTTG 58.622 47.826 13.45 4.64 0.00 3.02
3168 7569 3.390311 GGTCTACCACCCCGATTAATCTT 59.610 47.826 13.45 0.00 39.69 2.40
3169 7570 2.970640 GGTCTACCACCCCGATTAATCT 59.029 50.000 13.45 0.00 39.69 2.40
3170 7571 3.397849 GGTCTACCACCCCGATTAATC 57.602 52.381 5.30 5.30 39.69 1.75
3182 7583 3.791320 AGTGAGATCAAAGGGTCTACCA 58.209 45.455 0.81 0.00 43.89 3.25
3210 7611 9.483916 TTGACGACTACAATTAATCTTGAAGAA 57.516 29.630 0.00 0.00 0.00 2.52
3212 7613 8.926710 ACTTGACGACTACAATTAATCTTGAAG 58.073 33.333 0.00 0.00 0.00 3.02
3225 7626 6.092396 TGCTTAACAAAAACTTGACGACTACA 59.908 34.615 0.00 0.00 0.00 2.74
3282 7690 5.934625 GCGACATGGAGTAATAAGGAATCAT 59.065 40.000 0.00 0.00 0.00 2.45
3283 7691 5.297547 GCGACATGGAGTAATAAGGAATCA 58.702 41.667 0.00 0.00 0.00 2.57
3431 7848 7.046033 GGTGAATCCTAACTCTATCGGAAAAA 58.954 38.462 0.00 0.00 0.00 1.94
3432 7849 6.383147 AGGTGAATCCTAACTCTATCGGAAAA 59.617 38.462 0.00 0.00 46.10 2.29
3433 7850 5.897824 AGGTGAATCCTAACTCTATCGGAAA 59.102 40.000 0.00 0.00 46.10 3.13
3434 7851 5.302059 CAGGTGAATCCTAACTCTATCGGAA 59.698 44.000 0.00 0.00 46.24 4.30
3435 7852 4.827835 CAGGTGAATCCTAACTCTATCGGA 59.172 45.833 0.00 0.00 46.24 4.55
3436 7853 4.827835 TCAGGTGAATCCTAACTCTATCGG 59.172 45.833 0.00 0.00 46.24 4.18
3437 7854 6.349777 GGATCAGGTGAATCCTAACTCTATCG 60.350 46.154 0.00 0.00 46.24 2.92
3438 7855 6.723977 AGGATCAGGTGAATCCTAACTCTATC 59.276 42.308 2.84 0.00 46.24 2.08
3439 7856 6.629156 AGGATCAGGTGAATCCTAACTCTAT 58.371 40.000 2.84 0.00 46.24 1.98
3440 7857 6.031964 AGGATCAGGTGAATCCTAACTCTA 57.968 41.667 2.84 0.00 46.24 2.43
3441 7858 4.889780 AGGATCAGGTGAATCCTAACTCT 58.110 43.478 2.84 0.00 46.24 3.24
3442 7859 5.363939 CAAGGATCAGGTGAATCCTAACTC 58.636 45.833 5.15 0.00 46.24 3.01
3443 7860 4.164988 CCAAGGATCAGGTGAATCCTAACT 59.835 45.833 5.15 0.00 46.24 2.24
3444 7861 4.164221 TCCAAGGATCAGGTGAATCCTAAC 59.836 45.833 5.15 0.00 46.24 2.34
3445 7862 4.370776 TCCAAGGATCAGGTGAATCCTAA 58.629 43.478 5.15 0.00 46.24 2.69
3446 7863 4.007581 TCCAAGGATCAGGTGAATCCTA 57.992 45.455 5.15 0.00 46.24 2.94
3448 7865 3.872459 ATCCAAGGATCAGGTGAATCC 57.128 47.619 0.00 0.00 34.77 3.01
3525 7943 4.397730 CGAGACATTCATCCGAGGATATCT 59.602 45.833 4.05 3.59 32.93 1.98
3539 7957 0.179070 GGAAGGGCTCCGAGACATTC 60.179 60.000 18.55 18.55 42.91 2.67
3584 8022 6.530534 ACGGAGTAACTGAAGAACAATTATCG 59.469 38.462 0.00 0.00 41.94 2.92
3609 8052 2.447443 ACACCGAAGATCACTAGCTGA 58.553 47.619 0.00 0.00 0.00 4.26
3786 8235 3.517100 AGAGATAGAAAGCAACTGCCTCA 59.483 43.478 0.00 0.00 43.38 3.86
3794 8243 8.103305 ACTGGATGTAAAAGAGATAGAAAGCAA 58.897 33.333 0.00 0.00 0.00 3.91
3802 8251 8.078060 TCATCACACTGGATGTAAAAGAGATA 57.922 34.615 0.00 0.00 44.00 1.98
3829 8278 3.842820 CGTATGCTCGATCCATGAGATT 58.157 45.455 8.49 0.00 34.42 2.40
3841 8290 0.446616 TAGATAGGCGCGTATGCTCG 59.553 55.000 25.92 0.00 39.65 5.03
3852 8301 5.525378 CCTGTTGTGTTCATCTTAGATAGGC 59.475 44.000 0.00 0.00 0.00 3.93
3854 8303 8.777865 TTTCCTGTTGTGTTCATCTTAGATAG 57.222 34.615 0.00 0.00 0.00 2.08
3855 8304 9.219603 CTTTTCCTGTTGTGTTCATCTTAGATA 57.780 33.333 0.00 0.00 0.00 1.98
3898 8347 9.117183 GGAGGACTTTTTAGTAACAAAAGAAGA 57.883 33.333 12.10 0.00 41.81 2.87
3900 8349 8.810990 TGGAGGACTTTTTAGTAACAAAAGAA 57.189 30.769 12.10 0.00 41.81 2.52
3901 8350 8.846211 CATGGAGGACTTTTTAGTAACAAAAGA 58.154 33.333 12.10 0.00 41.81 2.52
3902 8351 8.082242 CCATGGAGGACTTTTTAGTAACAAAAG 58.918 37.037 5.56 5.79 43.89 2.27
3910 8359 4.724279 ACACCATGGAGGACTTTTTAGT 57.276 40.909 21.47 0.00 41.22 2.24
3921 8370 5.977129 GTCAAACTTTGTAAACACCATGGAG 59.023 40.000 21.47 14.24 0.00 3.86


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

AutoCloner maintained by Alex Coulton.