Multiple sequence alignment - TraesCS2D01G592600

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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 TraesCS2D01G592600 chr2D 100.000 2998 0 0 1 2998 647663875 647666872 0.000000e+00 5537.0
1 TraesCS2D01G592600 chr2A 99.039 1145 10 1 1 1144 772750014 772748870 0.000000e+00 2052.0
2 TraesCS2D01G592600 chr2A 97.985 794 15 1 1 793 498039659 498038866 0.000000e+00 1376.0
3 TraesCS2D01G592600 chr2A 87.631 574 55 6 1979 2537 8050664 8050092 0.000000e+00 652.0
4 TraesCS2D01G592600 chr2A 88.060 335 32 5 1983 2310 596429764 596430097 1.010000e-104 390.0
5 TraesCS2D01G592600 chr2A 94.472 199 8 1 2336 2531 596430326 596430524 1.350000e-78 303.0
6 TraesCS2D01G592600 chr2A 85.390 308 16 9 2694 2998 596430908 596431189 2.920000e-75 292.0
7 TraesCS2D01G592600 chr2A 82.865 356 30 17 262 589 308100113 308100465 1.050000e-74 291.0
8 TraesCS2D01G592600 chr2A 81.818 308 18 12 2694 2998 8049707 8049435 1.080000e-54 224.0
9 TraesCS2D01G592600 chr2A 91.250 80 3 1 2623 2702 8049895 8049820 4.090000e-19 106.0
10 TraesCS2D01G592600 chr2A 90.244 82 4 3 2621 2702 596430718 596430795 1.470000e-18 104.0
11 TraesCS2D01G592600 chr2A 86.957 69 2 2 2555 2623 596430523 596430584 1.490000e-08 71.3
12 TraesCS2D01G592600 chr2A 84.058 69 4 2 2555 2623 8050099 8050038 3.230000e-05 60.2
13 TraesCS2D01G592600 chr1A 97.951 1025 17 2 1978 2998 235845581 235844557 0.000000e+00 1773.0
14 TraesCS2D01G592600 chr1A 82.301 226 34 4 1982 2201 235843878 235844103 1.100000e-44 191.0
15 TraesCS2D01G592600 chr3A 97.481 794 19 1 1 793 727222773 727223566 0.000000e+00 1354.0
16 TraesCS2D01G592600 chr3A 91.155 814 43 9 3 793 58877717 58876910 0.000000e+00 1077.0
17 TraesCS2D01G592600 chr3A 89.813 481 28 10 1 478 547196355 547196817 5.530000e-167 597.0
18 TraesCS2D01G592600 chr3A 90.213 235 21 2 1 234 719773639 719773406 3.750000e-79 305.0
19 TraesCS2D01G592600 chr3A 89.163 203 20 2 601 801 719773065 719772863 4.960000e-63 252.0
20 TraesCS2D01G592600 chr5A 94.200 431 17 3 152 581 708742445 708742022 0.000000e+00 651.0
21 TraesCS2D01G592600 chr5A 94.301 193 9 2 1 191 708742658 708742466 8.130000e-76 294.0
22 TraesCS2D01G592600 chr1B 91.145 463 21 7 354 801 531195629 531195172 7.110000e-171 610.0
23 TraesCS2D01G592600 chr6D 86.606 545 47 19 262 801 143489481 143488958 2.000000e-161 579.0
24 TraesCS2D01G592600 chr6D 91.146 384 18 4 2626 2998 121298576 121298954 9.590000e-140 507.0
25 TraesCS2D01G592600 chr6A 80.312 706 127 9 1228 1930 11497297 11497993 9.520000e-145 523.0
26 TraesCS2D01G592600 chr2B 85.986 421 22 10 2206 2623 549261034 549260648 1.660000e-112 416.0
27 TraesCS2D01G592600 chr2B 88.854 314 20 4 2695 2998 549260321 549260013 3.650000e-99 372.0
28 TraesCS2D01G592600 chr2B 87.960 299 13 7 354 642 708205142 708204857 6.190000e-87 331.0
29 TraesCS2D01G592600 chr2B 89.062 256 25 3 1 255 707569624 707569877 6.240000e-82 315.0
30 TraesCS2D01G592600 chr2B 89.388 245 19 3 1983 2220 549261294 549261050 4.860000e-78 302.0
31 TraesCS2D01G592600 chr2B 91.667 192 14 2 601 790 707570318 707570509 6.370000e-67 265.0
32 TraesCS2D01G592600 chr2B 83.673 196 21 5 876 1061 788163030 788162836 1.100000e-39 174.0
33 TraesCS2D01G592600 chrUn 89.057 265 10 11 308 559 79208568 79208310 8.070000e-81 311.0
34 TraesCS2D01G592600 chr5B 89.706 204 20 1 600 802 403525993 403525790 2.960000e-65 259.0
35 TraesCS2D01G592600 chr5B 85.714 105 9 1 1 99 493935252 493935356 4.090000e-19 106.0
36 TraesCS2D01G592600 chr5D 82.738 168 22 6 1 166 221130976 221130814 3.120000e-30 143.0
37 TraesCS2D01G592600 chr6B 94.286 70 1 1 552 618 670215133 670215064 1.470000e-18 104.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G592600 chr2D 647663875 647666872 2997 False 5537.000000 5537 100.00000 1 2998 1 chr2D.!!$F1 2997
1 TraesCS2D01G592600 chr2A 772748870 772750014 1144 True 2052.000000 2052 99.03900 1 1144 1 chr2A.!!$R2 1143
2 TraesCS2D01G592600 chr2A 498038866 498039659 793 True 1376.000000 1376 97.98500 1 793 1 chr2A.!!$R1 792
3 TraesCS2D01G592600 chr2A 8049435 8050664 1229 True 260.550000 652 86.18925 1979 2998 4 chr2A.!!$R3 1019
4 TraesCS2D01G592600 chr2A 596429764 596431189 1425 False 232.060000 390 89.02460 1983 2998 5 chr2A.!!$F2 1015
5 TraesCS2D01G592600 chr1A 235844557 235845581 1024 True 1773.000000 1773 97.95100 1978 2998 1 chr1A.!!$R1 1020
6 TraesCS2D01G592600 chr3A 727222773 727223566 793 False 1354.000000 1354 97.48100 1 793 1 chr3A.!!$F2 792
7 TraesCS2D01G592600 chr3A 58876910 58877717 807 True 1077.000000 1077 91.15500 3 793 1 chr3A.!!$R1 790
8 TraesCS2D01G592600 chr3A 719772863 719773639 776 True 278.500000 305 89.68800 1 801 2 chr3A.!!$R2 800
9 TraesCS2D01G592600 chr5A 708742022 708742658 636 True 472.500000 651 94.25050 1 581 2 chr5A.!!$R1 580
10 TraesCS2D01G592600 chr6D 143488958 143489481 523 True 579.000000 579 86.60600 262 801 1 chr6D.!!$R1 539
11 TraesCS2D01G592600 chr6A 11497297 11497993 696 False 523.000000 523 80.31200 1228 1930 1 chr6A.!!$F1 702
12 TraesCS2D01G592600 chr2B 549260013 549261294 1281 True 363.333333 416 88.07600 1983 2998 3 chr2B.!!$R3 1015
13 TraesCS2D01G592600 chr2B 707569624 707570509 885 False 290.000000 315 90.36450 1 790 2 chr2B.!!$F1 789

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
154 165 4.379243 CTTGCACGAGGGAGCCGT 62.379 66.667 0.0 0.0 41.36 5.68 F
1669 2053 0.108424 AGCAGCGAGGAGATTGACAC 60.108 55.000 0.0 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1915 2299 0.108804 CCGCTCCAACATGTACGAGT 60.109 55.000 18.43 0.0 0.00 4.18 R
2871 3774 2.764010 TGTCGTGCCTGTTGATATAGGT 59.236 45.455 0.00 0.0 35.23 3.08 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
154 165 4.379243 CTTGCACGAGGGAGCCGT 62.379 66.667 0.00 0.00 41.36 5.68
973 1354 7.278424 CCCAAAATGAAATAAATGTAGTGGCTG 59.722 37.037 0.00 0.00 0.00 4.85
1149 1530 2.515641 CAGCACTTAACTGCATCACG 57.484 50.000 9.37 0.00 39.86 4.35
1150 1531 1.800586 CAGCACTTAACTGCATCACGT 59.199 47.619 9.37 0.00 39.86 4.49
1151 1532 2.993220 CAGCACTTAACTGCATCACGTA 59.007 45.455 9.37 0.00 39.86 3.57
1152 1533 2.993899 AGCACTTAACTGCATCACGTAC 59.006 45.455 9.37 0.00 39.86 3.67
1153 1534 2.093783 GCACTTAACTGCATCACGTACC 59.906 50.000 2.60 0.00 37.11 3.34
1154 1535 3.585862 CACTTAACTGCATCACGTACCT 58.414 45.455 0.00 0.00 0.00 3.08
1155 1536 4.740268 CACTTAACTGCATCACGTACCTA 58.260 43.478 0.00 0.00 0.00 3.08
1156 1537 5.348986 CACTTAACTGCATCACGTACCTAT 58.651 41.667 0.00 0.00 0.00 2.57
1157 1538 5.810587 CACTTAACTGCATCACGTACCTATT 59.189 40.000 0.00 0.00 0.00 1.73
1158 1539 5.810587 ACTTAACTGCATCACGTACCTATTG 59.189 40.000 0.00 0.00 0.00 1.90
1159 1540 3.887621 ACTGCATCACGTACCTATTGT 57.112 42.857 0.00 0.00 0.00 2.71
1160 1541 4.994907 ACTGCATCACGTACCTATTGTA 57.005 40.909 0.00 0.00 0.00 2.41
1161 1542 5.531122 ACTGCATCACGTACCTATTGTAT 57.469 39.130 0.00 0.00 0.00 2.29
1162 1543 5.529791 ACTGCATCACGTACCTATTGTATC 58.470 41.667 0.00 0.00 0.00 2.24
1163 1544 5.068591 ACTGCATCACGTACCTATTGTATCA 59.931 40.000 0.00 0.00 0.00 2.15
1164 1545 6.096673 TGCATCACGTACCTATTGTATCAT 57.903 37.500 0.00 0.00 0.00 2.45
1165 1546 6.521162 TGCATCACGTACCTATTGTATCATT 58.479 36.000 0.00 0.00 0.00 2.57
1166 1547 7.662897 TGCATCACGTACCTATTGTATCATTA 58.337 34.615 0.00 0.00 0.00 1.90
1167 1548 7.812669 TGCATCACGTACCTATTGTATCATTAG 59.187 37.037 0.00 0.00 0.00 1.73
1168 1549 7.813148 GCATCACGTACCTATTGTATCATTAGT 59.187 37.037 0.00 0.00 0.00 2.24
1169 1550 9.692749 CATCACGTACCTATTGTATCATTAGTT 57.307 33.333 0.00 0.00 0.00 2.24
1170 1551 9.692749 ATCACGTACCTATTGTATCATTAGTTG 57.307 33.333 0.00 0.00 0.00 3.16
1171 1552 8.905850 TCACGTACCTATTGTATCATTAGTTGA 58.094 33.333 0.00 0.00 39.12 3.18
1172 1553 9.692749 CACGTACCTATTGTATCATTAGTTGAT 57.307 33.333 0.00 0.00 46.86 2.57
1183 1564 9.516314 TGTATCATTAGTTGATTCACTAGTTCG 57.484 33.333 0.00 0.00 42.62 3.95
1184 1565 9.731819 GTATCATTAGTTGATTCACTAGTTCGA 57.268 33.333 0.00 0.00 42.62 3.71
1186 1567 8.462143 TCATTAGTTGATTCACTAGTTCGAAC 57.538 34.615 20.71 20.71 30.77 3.95
1187 1568 8.304596 TCATTAGTTGATTCACTAGTTCGAACT 58.695 33.333 31.70 31.70 42.91 3.01
1188 1569 9.569167 CATTAGTTGATTCACTAGTTCGAACTA 57.431 33.333 30.65 30.65 40.37 2.24
1191 1572 8.467402 AGTTGATTCACTAGTTCGAACTAATG 57.533 34.615 31.10 31.10 40.70 1.90
1192 1573 8.304596 AGTTGATTCACTAGTTCGAACTAATGA 58.695 33.333 33.83 33.83 43.51 2.57
1193 1574 9.088512 GTTGATTCACTAGTTCGAACTAATGAT 57.911 33.333 36.15 27.99 44.26 2.45
1194 1575 8.858003 TGATTCACTAGTTCGAACTAATGATC 57.142 34.615 36.15 31.71 44.26 2.92
1195 1576 8.466798 TGATTCACTAGTTCGAACTAATGATCA 58.533 33.333 36.15 33.09 44.26 2.92
1196 1577 8.635877 ATTCACTAGTTCGAACTAATGATCAC 57.364 34.615 36.15 9.06 44.26 3.06
1197 1578 6.561614 TCACTAGTTCGAACTAATGATCACC 58.438 40.000 33.83 5.74 41.26 4.02
1198 1579 6.377429 TCACTAGTTCGAACTAATGATCACCT 59.623 38.462 33.83 12.92 41.26 4.00
1199 1580 7.036220 CACTAGTTCGAACTAATGATCACCTT 58.964 38.462 32.57 11.14 40.20 3.50
1200 1581 8.188799 CACTAGTTCGAACTAATGATCACCTTA 58.811 37.037 32.57 13.19 40.20 2.69
1201 1582 8.915036 ACTAGTTCGAACTAATGATCACCTTAT 58.085 33.333 31.72 9.57 40.70 1.73
1202 1583 9.400638 CTAGTTCGAACTAATGATCACCTTATC 57.599 37.037 31.72 1.00 40.70 1.75
1203 1584 6.918569 AGTTCGAACTAATGATCACCTTATCG 59.081 38.462 28.80 6.63 37.52 2.92
1204 1585 5.220381 TCGAACTAATGATCACCTTATCGC 58.780 41.667 13.94 0.00 0.00 4.58
1205 1586 5.009710 TCGAACTAATGATCACCTTATCGCT 59.990 40.000 13.94 0.00 0.00 4.93
1206 1587 6.206048 TCGAACTAATGATCACCTTATCGCTA 59.794 38.462 13.94 0.50 0.00 4.26
1207 1588 6.305877 CGAACTAATGATCACCTTATCGCTAC 59.694 42.308 0.00 0.00 0.00 3.58
1208 1589 6.650427 ACTAATGATCACCTTATCGCTACA 57.350 37.500 0.00 0.00 0.00 2.74
1209 1590 7.233389 ACTAATGATCACCTTATCGCTACAT 57.767 36.000 0.00 0.00 0.00 2.29
1210 1591 7.093354 ACTAATGATCACCTTATCGCTACATG 58.907 38.462 0.00 0.00 0.00 3.21
1211 1592 4.937201 TGATCACCTTATCGCTACATGT 57.063 40.909 2.69 2.69 0.00 3.21
1212 1593 4.620982 TGATCACCTTATCGCTACATGTG 58.379 43.478 9.11 0.00 0.00 3.21
1213 1594 4.099419 TGATCACCTTATCGCTACATGTGT 59.901 41.667 9.11 0.00 0.00 3.72
1214 1595 3.780902 TCACCTTATCGCTACATGTGTG 58.219 45.455 9.11 4.72 0.00 3.82
1215 1596 2.285220 CACCTTATCGCTACATGTGTGC 59.715 50.000 9.11 11.82 0.00 4.57
1216 1597 1.522676 CCTTATCGCTACATGTGTGCG 59.477 52.381 29.50 29.50 42.46 5.34
1217 1598 0.927537 TTATCGCTACATGTGTGCGC 59.072 50.000 30.11 17.55 41.61 6.09
1218 1599 0.179124 TATCGCTACATGTGTGCGCA 60.179 50.000 30.11 22.52 41.61 6.09
1219 1600 0.811219 ATCGCTACATGTGTGCGCAT 60.811 50.000 30.11 23.31 41.61 4.73
1225 1606 2.715758 CATGTGTGCGCATGTTCAC 58.284 52.632 15.91 17.77 40.81 3.18
1226 1607 0.239082 CATGTGTGCGCATGTTCACT 59.761 50.000 23.89 11.06 40.81 3.41
1235 1616 3.194861 GCGCATGTTCACTCAGGTTATA 58.805 45.455 0.30 0.00 0.00 0.98
1241 1622 4.250464 TGTTCACTCAGGTTATAAAGGCG 58.750 43.478 0.00 0.00 0.00 5.52
1255 1636 1.315257 AAGGCGGACACCATTGATGC 61.315 55.000 0.00 0.00 0.00 3.91
1256 1637 2.045708 GGCGGACACCATTGATGCA 61.046 57.895 0.00 0.00 0.00 3.96
1259 1640 1.028330 CGGACACCATTGATGCAGCT 61.028 55.000 2.53 0.00 0.00 4.24
1261 1642 0.179145 GACACCATTGATGCAGCTGC 60.179 55.000 31.89 31.89 42.50 5.25
1266 1647 1.469251 CCATTGATGCAGCTGCTGAAC 60.469 52.381 36.61 24.00 42.66 3.18
1274 1655 1.198637 GCAGCTGCTGAACGAATTCTT 59.801 47.619 32.30 0.00 38.21 2.52
1275 1656 2.847901 CAGCTGCTGAACGAATTCTTG 58.152 47.619 24.88 0.00 35.69 3.02
1286 1667 7.258022 TGAACGAATTCTTGATGAACTCAAA 57.742 32.000 3.52 0.00 43.20 2.69
1289 1670 7.914537 ACGAATTCTTGATGAACTCAAAAAC 57.085 32.000 3.52 0.00 43.20 2.43
1291 1672 7.432252 ACGAATTCTTGATGAACTCAAAAACAC 59.568 33.333 3.52 0.00 43.20 3.32
1296 1677 8.731275 TCTTGATGAACTCAAAAACACTAGAA 57.269 30.769 0.00 0.00 43.20 2.10
1297 1678 8.830580 TCTTGATGAACTCAAAAACACTAGAAG 58.169 33.333 0.00 0.00 43.20 2.85
1298 1679 6.959361 TGATGAACTCAAAAACACTAGAAGC 58.041 36.000 0.00 0.00 0.00 3.86
1300 1681 6.363577 TGAACTCAAAAACACTAGAAGCAG 57.636 37.500 0.00 0.00 0.00 4.24
1301 1682 6.112734 TGAACTCAAAAACACTAGAAGCAGA 58.887 36.000 0.00 0.00 0.00 4.26
1302 1683 6.258727 TGAACTCAAAAACACTAGAAGCAGAG 59.741 38.462 0.00 0.00 0.00 3.35
1303 1684 5.918608 ACTCAAAAACACTAGAAGCAGAGA 58.081 37.500 0.00 0.00 0.00 3.10
1304 1685 5.988561 ACTCAAAAACACTAGAAGCAGAGAG 59.011 40.000 0.00 0.00 0.00 3.20
1305 1686 6.161855 TCAAAAACACTAGAAGCAGAGAGA 57.838 37.500 0.00 0.00 0.00 3.10
1306 1687 6.582636 TCAAAAACACTAGAAGCAGAGAGAA 58.417 36.000 0.00 0.00 0.00 2.87
1307 1688 7.220030 TCAAAAACACTAGAAGCAGAGAGAAT 58.780 34.615 0.00 0.00 0.00 2.40
1308 1689 7.172190 TCAAAAACACTAGAAGCAGAGAGAATG 59.828 37.037 0.00 0.00 0.00 2.67
1309 1690 4.122143 ACACTAGAAGCAGAGAGAATGC 57.878 45.455 0.00 0.00 44.18 3.56
1331 1712 4.263243 GCTATCTACTTTGATGGCTGGGAT 60.263 45.833 5.76 0.00 44.20 3.85
1334 1715 0.685458 ACTTTGATGGCTGGGATGGC 60.685 55.000 0.00 0.00 0.00 4.40
1360 1741 4.521062 ATCTGCCGTCCTGCGAGC 62.521 66.667 0.00 0.00 44.77 5.03
1390 1771 1.832167 GGCTGGCACCAAAGGAACA 60.832 57.895 0.00 0.00 0.00 3.18
1391 1772 1.398958 GGCTGGCACCAAAGGAACAA 61.399 55.000 0.00 0.00 0.00 2.83
1394 1775 1.480137 CTGGCACCAAAGGAACAAACA 59.520 47.619 0.00 0.00 0.00 2.83
1400 1781 1.202639 CCAAAGGAACAAACAAGGCCC 60.203 52.381 0.00 0.00 0.00 5.80
1403 1784 1.458588 GGAACAAACAAGGCCCCCA 60.459 57.895 0.00 0.00 0.00 4.96
1433 1814 4.147321 AGTTTGAGCAAGTCATCCACATT 58.853 39.130 0.00 0.00 34.17 2.71
1456 1837 0.979665 TCCTCAAAGTGGGAGAGCAG 59.020 55.000 0.00 0.00 34.24 4.24
1463 1844 1.153667 GTGGGAGAGCAGAAGAGCG 60.154 63.158 0.00 0.00 40.15 5.03
1464 1845 2.354401 TGGGAGAGCAGAAGAGCGG 61.354 63.158 0.00 0.00 40.15 5.52
1466 1847 1.153667 GGAGAGCAGAAGAGCGGTG 60.154 63.158 0.00 0.00 40.15 4.94
1472 1853 1.447489 CAGAAGAGCGGTGCAGAGG 60.447 63.158 0.00 0.00 0.00 3.69
1479 1860 1.078143 GCGGTGCAGAGGGAAATCT 60.078 57.895 0.00 0.00 0.00 2.40
1529 1910 4.036734 GTGAGGAAGATGTTTGACAAGCAA 59.963 41.667 8.88 0.00 33.88 3.91
1538 1919 4.401022 TGTTTGACAAGCAAGATGAGGAT 58.599 39.130 1.81 0.00 37.87 3.24
1549 1930 5.765677 AGCAAGATGAGGATGATGATTTCAG 59.234 40.000 0.00 0.00 37.89 3.02
1550 1931 5.563085 GCAAGATGAGGATGATGATTTCAGC 60.563 44.000 0.00 0.00 40.11 4.26
1553 1934 2.171237 TGAGGATGATGATTTCAGCGGT 59.829 45.455 0.00 0.00 41.80 5.68
1555 1936 4.040829 TGAGGATGATGATTTCAGCGGTAT 59.959 41.667 0.00 0.00 41.80 2.73
1556 1937 4.321718 AGGATGATGATTTCAGCGGTATG 58.678 43.478 0.00 0.00 41.80 2.39
1589 1973 2.098280 TCGCACTGAGATAGCAGAAGTC 59.902 50.000 0.00 0.00 39.20 3.01
1590 1974 2.159324 CGCACTGAGATAGCAGAAGTCA 60.159 50.000 0.00 0.00 39.20 3.41
1595 1979 1.407258 GAGATAGCAGAAGTCACGGCT 59.593 52.381 0.00 0.00 42.96 5.52
1604 1988 1.137872 GAAGTCACGGCTGAGATCCAT 59.862 52.381 0.00 0.00 0.00 3.41
1617 2001 2.566279 GAGATCCATAGGAGCATGCAGA 59.434 50.000 21.98 4.92 41.08 4.26
1646 2030 4.640647 AGGTTTCTTCTGGTTCTTCACAAC 59.359 41.667 0.00 0.00 0.00 3.32
1654 2038 1.264288 GGTTCTTCACAACGGAAGCAG 59.736 52.381 0.00 0.00 43.14 4.24
1655 2039 0.944386 TTCTTCACAACGGAAGCAGC 59.056 50.000 0.00 0.00 43.14 5.25
1669 2053 0.108424 AGCAGCGAGGAGATTGACAC 60.108 55.000 0.00 0.00 0.00 3.67
1672 2056 2.625737 CAGCGAGGAGATTGACACATT 58.374 47.619 0.00 0.00 0.00 2.71
1673 2057 3.005554 CAGCGAGGAGATTGACACATTT 58.994 45.455 0.00 0.00 0.00 2.32
1675 2059 4.631377 CAGCGAGGAGATTGACACATTTAA 59.369 41.667 0.00 0.00 0.00 1.52
1676 2060 4.631813 AGCGAGGAGATTGACACATTTAAC 59.368 41.667 0.00 0.00 0.00 2.01
1677 2061 4.201822 GCGAGGAGATTGACACATTTAACC 60.202 45.833 0.00 0.00 0.00 2.85
1679 2063 5.292101 CGAGGAGATTGACACATTTAACCTC 59.708 44.000 0.00 0.00 37.43 3.85
1688 2072 4.070009 ACACATTTAACCTCGGTCTTTCC 58.930 43.478 0.00 0.00 0.00 3.13
1689 2073 3.439129 CACATTTAACCTCGGTCTTTCCC 59.561 47.826 0.00 0.00 0.00 3.97
1694 2078 7.072076 ACATTTAACCTCGGTCTTTCCCTATAT 59.928 37.037 0.00 0.00 0.00 0.86
1695 2079 4.957684 AACCTCGGTCTTTCCCTATATG 57.042 45.455 0.00 0.00 0.00 1.78
1696 2080 3.240302 ACCTCGGTCTTTCCCTATATGG 58.760 50.000 0.00 0.00 0.00 2.74
1697 2081 3.116862 ACCTCGGTCTTTCCCTATATGGA 60.117 47.826 0.00 0.00 38.35 3.41
1700 2084 5.127356 CCTCGGTCTTTCCCTATATGGATAC 59.873 48.000 0.00 0.00 38.35 2.24
1705 2089 7.577807 CGGTCTTTCCCTATATGGATACTTGAG 60.578 44.444 0.00 0.00 38.35 3.02
1706 2090 7.235812 GGTCTTTCCCTATATGGATACTTGAGT 59.764 40.741 0.00 0.00 38.35 3.41
1708 2092 9.535170 TCTTTCCCTATATGGATACTTGAGTAG 57.465 37.037 0.00 0.00 38.35 2.57
1713 2097 7.397476 CCCTATATGGATACTTGAGTAGCAAGA 59.603 40.741 11.78 0.00 46.94 3.02
1743 2127 0.960861 CTTCCAAGGGAGGTTTCGGC 60.961 60.000 0.00 0.00 31.21 5.54
1745 2129 1.377333 CCAAGGGAGGTTTCGGCTC 60.377 63.158 0.00 0.00 0.00 4.70
1755 2139 3.894547 TTTCGGCTCGACCCCAAGC 62.895 63.158 0.00 0.00 34.89 4.01
1769 2153 0.886490 CCAAGCTGCGAGACAAGGTT 60.886 55.000 0.00 0.00 0.00 3.50
1770 2154 0.236711 CAAGCTGCGAGACAAGGTTG 59.763 55.000 0.00 0.80 32.57 3.77
1773 2157 1.845809 GCTGCGAGACAAGGTTGTGG 61.846 60.000 0.00 0.00 42.43 4.17
1774 2158 1.845809 CTGCGAGACAAGGTTGTGGC 61.846 60.000 0.00 2.10 42.43 5.01
1775 2159 1.891919 GCGAGACAAGGTTGTGGCA 60.892 57.895 0.00 0.00 42.43 4.92
1808 2192 3.842820 TGATGTTCTTCTCTCAGCTTCG 58.157 45.455 0.00 0.00 0.00 3.79
1809 2193 2.071688 TGTTCTTCTCTCAGCTTCGC 57.928 50.000 0.00 0.00 0.00 4.70
1827 2211 4.816990 GCTCTAAGCGAGACCCAC 57.183 61.111 0.00 0.00 42.62 4.61
1832 2216 2.428890 CTCTAAGCGAGACCCACAAGAT 59.571 50.000 0.00 0.00 42.62 2.40
1850 2234 6.549364 CACAAGATCTCTGGTCCTATCTACTT 59.451 42.308 0.00 0.00 0.00 2.24
1852 2236 6.780198 AGATCTCTGGTCCTATCTACTTCT 57.220 41.667 0.00 0.00 0.00 2.85
1854 2238 7.004086 AGATCTCTGGTCCTATCTACTTCTTG 58.996 42.308 0.00 0.00 0.00 3.02
1859 2243 7.182760 TCTGGTCCTATCTACTTCTTGAAGAA 58.817 38.462 16.21 7.49 32.50 2.52
1871 2255 4.175787 TCTTGAAGAAGCTAAGGACGTC 57.824 45.455 7.13 7.13 0.00 4.34
1872 2256 3.827302 TCTTGAAGAAGCTAAGGACGTCT 59.173 43.478 16.46 0.00 0.00 4.18
1874 2258 2.492484 TGAAGAAGCTAAGGACGTCTCC 59.508 50.000 16.46 0.00 36.71 3.71
1885 2269 1.364626 GACGTCTCCTGCAAGCATGG 61.365 60.000 8.70 0.00 0.00 3.66
1887 2271 2.044650 TCTCCTGCAAGCATGGCC 60.045 61.111 0.00 0.00 29.78 5.36
1889 2273 2.361992 TCCTGCAAGCATGGCCTG 60.362 61.111 3.32 0.34 29.78 4.85
1890 2274 3.458163 CCTGCAAGCATGGCCTGG 61.458 66.667 3.32 0.00 29.78 4.45
1891 2275 2.361992 CTGCAAGCATGGCCTGGA 60.362 61.111 3.32 0.00 29.78 3.86
1900 2284 1.076485 ATGGCCTGGATCCTGCAAC 60.076 57.895 22.82 11.91 0.00 4.17
1901 2285 1.578215 ATGGCCTGGATCCTGCAACT 61.578 55.000 22.82 8.49 0.00 3.16
1918 2302 2.447244 ACTGTTGCTGAGTGCTACTC 57.553 50.000 8.75 8.75 45.30 2.59
1930 2314 2.823747 AGTGCTACTCGTACATGTTGGA 59.176 45.455 2.30 0.55 0.00 3.53
1931 2315 3.119459 AGTGCTACTCGTACATGTTGGAG 60.119 47.826 18.87 18.87 0.00 3.86
1932 2316 2.194271 GCTACTCGTACATGTTGGAGC 58.806 52.381 19.88 14.33 0.00 4.70
1933 2317 2.451132 CTACTCGTACATGTTGGAGCG 58.549 52.381 19.88 11.12 0.00 5.03
1934 2318 0.108804 ACTCGTACATGTTGGAGCGG 60.109 55.000 19.88 4.62 0.00 5.52
1935 2319 0.172578 CTCGTACATGTTGGAGCGGA 59.827 55.000 2.30 0.00 0.00 5.54
1936 2320 0.172578 TCGTACATGTTGGAGCGGAG 59.827 55.000 2.30 0.00 0.00 4.63
1937 2321 0.108804 CGTACATGTTGGAGCGGAGT 60.109 55.000 2.30 0.00 0.00 3.85
1938 2322 1.671850 CGTACATGTTGGAGCGGAGTT 60.672 52.381 2.30 0.00 0.00 3.01
1939 2323 2.416296 CGTACATGTTGGAGCGGAGTTA 60.416 50.000 2.30 0.00 0.00 2.24
1940 2324 2.094762 ACATGTTGGAGCGGAGTTAC 57.905 50.000 0.00 0.00 0.00 2.50
1941 2325 1.346395 ACATGTTGGAGCGGAGTTACA 59.654 47.619 0.00 0.00 0.00 2.41
1942 2326 2.027192 ACATGTTGGAGCGGAGTTACAT 60.027 45.455 0.00 0.00 0.00 2.29
1943 2327 2.093306 TGTTGGAGCGGAGTTACATG 57.907 50.000 0.00 0.00 0.00 3.21
1944 2328 1.621317 TGTTGGAGCGGAGTTACATGA 59.379 47.619 0.00 0.00 0.00 3.07
1945 2329 2.271800 GTTGGAGCGGAGTTACATGAG 58.728 52.381 0.00 0.00 0.00 2.90
1946 2330 0.175760 TGGAGCGGAGTTACATGAGC 59.824 55.000 0.00 0.00 0.00 4.26
1947 2331 0.530870 GGAGCGGAGTTACATGAGCC 60.531 60.000 0.00 0.00 0.00 4.70
1948 2332 0.175760 GAGCGGAGTTACATGAGCCA 59.824 55.000 0.00 0.00 0.00 4.75
1949 2333 0.613260 AGCGGAGTTACATGAGCCAA 59.387 50.000 0.00 0.00 0.00 4.52
1950 2334 1.003118 AGCGGAGTTACATGAGCCAAA 59.997 47.619 0.00 0.00 0.00 3.28
1951 2335 1.810151 GCGGAGTTACATGAGCCAAAA 59.190 47.619 0.00 0.00 0.00 2.44
1952 2336 2.423538 GCGGAGTTACATGAGCCAAAAT 59.576 45.455 0.00 0.00 0.00 1.82
1953 2337 3.625764 GCGGAGTTACATGAGCCAAAATA 59.374 43.478 0.00 0.00 0.00 1.40
1954 2338 4.275936 GCGGAGTTACATGAGCCAAAATAT 59.724 41.667 0.00 0.00 0.00 1.28
1955 2339 5.560953 GCGGAGTTACATGAGCCAAAATATC 60.561 44.000 0.00 0.00 0.00 1.63
1956 2340 5.527214 CGGAGTTACATGAGCCAAAATATCA 59.473 40.000 0.00 0.00 0.00 2.15
1957 2341 6.205464 CGGAGTTACATGAGCCAAAATATCAT 59.795 38.462 0.00 0.00 34.02 2.45
1958 2342 7.255242 CGGAGTTACATGAGCCAAAATATCATT 60.255 37.037 0.00 0.00 31.38 2.57
1959 2343 7.864379 GGAGTTACATGAGCCAAAATATCATTG 59.136 37.037 0.00 0.00 31.38 2.82
1960 2344 8.523915 AGTTACATGAGCCAAAATATCATTGA 57.476 30.769 0.00 0.00 31.38 2.57
1961 2345 8.408601 AGTTACATGAGCCAAAATATCATTGAC 58.591 33.333 0.00 0.00 31.38 3.18
1962 2346 8.408601 GTTACATGAGCCAAAATATCATTGACT 58.591 33.333 0.00 0.00 31.38 3.41
1963 2347 9.625747 TTACATGAGCCAAAATATCATTGACTA 57.374 29.630 0.00 0.00 31.38 2.59
1964 2348 8.701908 ACATGAGCCAAAATATCATTGACTAT 57.298 30.769 0.00 0.00 31.38 2.12
1965 2349 8.573885 ACATGAGCCAAAATATCATTGACTATG 58.426 33.333 0.00 0.00 31.38 2.23
1966 2350 8.789762 CATGAGCCAAAATATCATTGACTATGA 58.210 33.333 2.00 2.00 46.86 2.15
1967 2351 8.387190 TGAGCCAAAATATCATTGACTATGAG 57.613 34.615 5.81 0.00 46.06 2.90
1968 2352 7.994911 TGAGCCAAAATATCATTGACTATGAGT 59.005 33.333 5.81 0.00 46.06 3.41
1969 2353 8.162878 AGCCAAAATATCATTGACTATGAGTG 57.837 34.615 5.81 0.10 46.06 3.51
1970 2354 7.230108 AGCCAAAATATCATTGACTATGAGTGG 59.770 37.037 5.81 8.19 46.06 4.00
1971 2355 7.229306 GCCAAAATATCATTGACTATGAGTGGA 59.771 37.037 14.53 1.01 46.06 4.02
1972 2356 8.562892 CCAAAATATCATTGACTATGAGTGGAC 58.437 37.037 5.81 0.00 46.06 4.02
1973 2357 9.334947 CAAAATATCATTGACTATGAGTGGACT 57.665 33.333 5.81 0.00 46.06 3.85
1974 2358 9.553064 AAAATATCATTGACTATGAGTGGACTC 57.447 33.333 5.81 0.00 46.06 3.36
1975 2359 8.489676 AATATCATTGACTATGAGTGGACTCT 57.510 34.615 8.24 0.00 46.06 3.24
1976 2360 5.843673 TCATTGACTATGAGTGGACTCTC 57.156 43.478 8.24 0.00 43.25 3.20
2232 2653 4.643387 GCCACGTTCTGGTGCCCT 62.643 66.667 0.00 0.00 42.99 5.19
2871 3774 1.619332 TCACATACACGTACAAGGGCA 59.381 47.619 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 107 4.217550 TGCGAATAAAACAAAAGAGAGGGG 59.782 41.667 0.00 0.00 0.00 4.79
1144 1525 9.692749 CAACTAATGATACAATAGGTACGTGAT 57.307 33.333 0.00 0.00 34.07 3.06
1145 1526 8.905850 TCAACTAATGATACAATAGGTACGTGA 58.094 33.333 0.00 0.00 34.07 4.35
1161 1542 8.304596 AGTTCGAACTAGTGAATCAACTAATGA 58.695 33.333 28.80 0.00 39.00 2.57
1162 1543 8.467402 AGTTCGAACTAGTGAATCAACTAATG 57.533 34.615 28.80 0.00 37.52 1.90
1165 1546 9.569167 CATTAGTTCGAACTAGTGAATCAACTA 57.431 33.333 37.87 21.60 46.23 2.24
1166 1547 8.467402 CATTAGTTCGAACTAGTGAATCAACT 57.533 34.615 37.87 16.28 46.23 3.16
1174 1555 6.565234 AGGTGATCATTAGTTCGAACTAGTG 58.435 40.000 36.41 36.41 45.31 2.74
1175 1556 6.777213 AGGTGATCATTAGTTCGAACTAGT 57.223 37.500 30.76 27.06 42.04 2.57
1176 1557 9.400638 GATAAGGTGATCATTAGTTCGAACTAG 57.599 37.037 30.76 22.76 42.04 2.57
1177 1558 8.074370 CGATAAGGTGATCATTAGTTCGAACTA 58.926 37.037 29.57 29.57 40.37 2.24
1178 1559 6.918569 CGATAAGGTGATCATTAGTTCGAACT 59.081 38.462 31.70 31.70 42.91 3.01
1179 1560 6.345882 GCGATAAGGTGATCATTAGTTCGAAC 60.346 42.308 20.71 20.71 29.64 3.95
1180 1561 5.690409 GCGATAAGGTGATCATTAGTTCGAA 59.310 40.000 18.43 0.00 29.64 3.71
1181 1562 5.009710 AGCGATAAGGTGATCATTAGTTCGA 59.990 40.000 18.43 0.00 29.64 3.71
1182 1563 5.223382 AGCGATAAGGTGATCATTAGTTCG 58.777 41.667 0.00 7.27 30.65 3.95
1183 1564 7.145985 TGTAGCGATAAGGTGATCATTAGTTC 58.854 38.462 0.00 0.00 0.00 3.01
1184 1565 7.050970 TGTAGCGATAAGGTGATCATTAGTT 57.949 36.000 0.00 0.00 0.00 2.24
1185 1566 6.650427 TGTAGCGATAAGGTGATCATTAGT 57.350 37.500 0.00 0.00 0.00 2.24
1186 1567 7.062722 CACATGTAGCGATAAGGTGATCATTAG 59.937 40.741 0.00 0.00 0.00 1.73
1187 1568 6.868339 CACATGTAGCGATAAGGTGATCATTA 59.132 38.462 0.00 0.00 0.00 1.90
1188 1569 5.698089 CACATGTAGCGATAAGGTGATCATT 59.302 40.000 0.00 0.00 0.00 2.57
1189 1570 5.221521 ACACATGTAGCGATAAGGTGATCAT 60.222 40.000 12.66 0.00 0.00 2.45
1190 1571 4.099419 ACACATGTAGCGATAAGGTGATCA 59.901 41.667 12.66 0.00 0.00 2.92
1191 1572 4.445718 CACACATGTAGCGATAAGGTGATC 59.554 45.833 12.66 0.00 0.00 2.92
1192 1573 4.371786 CACACATGTAGCGATAAGGTGAT 58.628 43.478 12.66 0.00 0.00 3.06
1193 1574 3.780902 CACACATGTAGCGATAAGGTGA 58.219 45.455 12.66 0.00 0.00 4.02
1194 1575 2.285220 GCACACATGTAGCGATAAGGTG 59.715 50.000 0.00 0.03 0.00 4.00
1195 1576 2.550978 GCACACATGTAGCGATAAGGT 58.449 47.619 0.00 0.00 0.00 3.50
1203 1584 4.676444 CATGCGCACACATGTAGC 57.324 55.556 14.90 11.36 42.05 3.58
1208 1589 0.518636 GAGTGAACATGCGCACACAT 59.481 50.000 25.04 13.53 37.48 3.21
1209 1590 0.813210 TGAGTGAACATGCGCACACA 60.813 50.000 25.04 15.16 37.48 3.72
1210 1591 0.110509 CTGAGTGAACATGCGCACAC 60.111 55.000 14.90 17.03 37.48 3.82
1211 1592 1.229975 CCTGAGTGAACATGCGCACA 61.230 55.000 14.90 2.35 37.48 4.57
1212 1593 1.230635 ACCTGAGTGAACATGCGCAC 61.231 55.000 14.90 0.00 35.30 5.34
1213 1594 0.534877 AACCTGAGTGAACATGCGCA 60.535 50.000 14.96 14.96 0.00 6.09
1214 1595 1.438651 TAACCTGAGTGAACATGCGC 58.561 50.000 0.00 0.00 0.00 6.09
1215 1596 5.220662 CCTTTATAACCTGAGTGAACATGCG 60.221 44.000 0.00 0.00 0.00 4.73
1216 1597 5.449177 GCCTTTATAACCTGAGTGAACATGC 60.449 44.000 0.00 0.00 0.00 4.06
1217 1598 5.220662 CGCCTTTATAACCTGAGTGAACATG 60.221 44.000 0.00 0.00 0.00 3.21
1218 1599 4.876107 CGCCTTTATAACCTGAGTGAACAT 59.124 41.667 0.00 0.00 0.00 2.71
1219 1600 4.250464 CGCCTTTATAACCTGAGTGAACA 58.750 43.478 0.00 0.00 0.00 3.18
1220 1601 3.621715 CCGCCTTTATAACCTGAGTGAAC 59.378 47.826 0.00 0.00 0.00 3.18
1221 1602 3.516300 TCCGCCTTTATAACCTGAGTGAA 59.484 43.478 0.00 0.00 0.00 3.18
1222 1603 3.101437 TCCGCCTTTATAACCTGAGTGA 58.899 45.455 0.00 0.00 0.00 3.41
1223 1604 3.195661 GTCCGCCTTTATAACCTGAGTG 58.804 50.000 0.00 0.00 0.00 3.51
1224 1605 2.835764 TGTCCGCCTTTATAACCTGAGT 59.164 45.455 0.00 0.00 0.00 3.41
1225 1606 3.195661 GTGTCCGCCTTTATAACCTGAG 58.804 50.000 0.00 0.00 0.00 3.35
1226 1607 2.093341 GGTGTCCGCCTTTATAACCTGA 60.093 50.000 0.00 0.00 0.00 3.86
1235 1616 1.176527 CATCAATGGTGTCCGCCTTT 58.823 50.000 0.00 0.00 0.00 3.11
1241 1622 0.454600 CAGCTGCATCAATGGTGTCC 59.545 55.000 0.00 0.00 0.00 4.02
1255 1636 2.481568 TCAAGAATTCGTTCAGCAGCTG 59.518 45.455 17.10 17.10 0.00 4.24
1256 1637 2.771089 TCAAGAATTCGTTCAGCAGCT 58.229 42.857 0.00 0.00 0.00 4.24
1259 1640 4.756642 AGTTCATCAAGAATTCGTTCAGCA 59.243 37.500 0.00 0.00 38.76 4.41
1261 1642 6.471976 TGAGTTCATCAAGAATTCGTTCAG 57.528 37.500 0.00 0.00 43.66 3.02
1274 1655 6.542005 TGCTTCTAGTGTTTTTGAGTTCATCA 59.458 34.615 0.00 0.00 35.62 3.07
1275 1656 6.959361 TGCTTCTAGTGTTTTTGAGTTCATC 58.041 36.000 0.00 0.00 0.00 2.92
1286 1667 4.934602 GCATTCTCTCTGCTTCTAGTGTTT 59.065 41.667 0.00 0.00 36.68 2.83
1297 1678 6.511416 TCAAAGTAGATAGCATTCTCTCTGC 58.489 40.000 0.00 0.00 39.97 4.26
1298 1679 7.599621 CCATCAAAGTAGATAGCATTCTCTCTG 59.400 40.741 0.00 0.00 29.82 3.35
1300 1681 6.368516 GCCATCAAAGTAGATAGCATTCTCTC 59.631 42.308 0.00 0.00 33.63 3.20
1301 1682 6.043012 AGCCATCAAAGTAGATAGCATTCTCT 59.957 38.462 0.00 0.00 35.49 3.10
1302 1683 6.147492 CAGCCATCAAAGTAGATAGCATTCTC 59.853 42.308 0.00 0.00 35.49 2.87
1303 1684 5.996513 CAGCCATCAAAGTAGATAGCATTCT 59.003 40.000 0.00 0.00 35.49 2.40
1304 1685 5.180868 CCAGCCATCAAAGTAGATAGCATTC 59.819 44.000 0.00 0.00 35.49 2.67
1305 1686 5.068636 CCAGCCATCAAAGTAGATAGCATT 58.931 41.667 0.00 0.00 35.49 3.56
1306 1687 4.506271 CCCAGCCATCAAAGTAGATAGCAT 60.506 45.833 0.00 0.00 35.49 3.79
1307 1688 3.181451 CCCAGCCATCAAAGTAGATAGCA 60.181 47.826 0.00 0.00 35.49 3.49
1308 1689 3.071602 TCCCAGCCATCAAAGTAGATAGC 59.928 47.826 0.00 0.00 33.61 2.97
1309 1690 4.963318 TCCCAGCCATCAAAGTAGATAG 57.037 45.455 0.00 0.00 0.00 2.08
1310 1691 4.042062 CCATCCCAGCCATCAAAGTAGATA 59.958 45.833 0.00 0.00 0.00 1.98
1373 1754 0.463620 TTTGTTCCTTTGGTGCCAGC 59.536 50.000 0.00 0.00 0.00 4.85
1374 1755 1.480137 TGTTTGTTCCTTTGGTGCCAG 59.520 47.619 0.00 0.00 0.00 4.85
1378 1759 2.549926 GCCTTGTTTGTTCCTTTGGTG 58.450 47.619 0.00 0.00 0.00 4.17
1380 1761 1.202639 GGGCCTTGTTTGTTCCTTTGG 60.203 52.381 0.84 0.00 0.00 3.28
1381 1762 1.202639 GGGGCCTTGTTTGTTCCTTTG 60.203 52.381 0.84 0.00 0.00 2.77
1390 1771 2.091283 AGTCCTGGGGGCCTTGTTT 61.091 57.895 0.84 0.00 0.00 2.83
1391 1772 2.452491 AGTCCTGGGGGCCTTGTT 60.452 61.111 0.84 0.00 0.00 2.83
1403 1784 1.771255 ACTTGCTCAAACTCCAGTCCT 59.229 47.619 0.00 0.00 0.00 3.85
1412 1793 4.022935 TCAATGTGGATGACTTGCTCAAAC 60.023 41.667 0.00 0.00 30.60 2.93
1438 1819 0.979665 TCTGCTCTCCCACTTTGAGG 59.020 55.000 0.00 0.00 0.00 3.86
1456 1837 2.125350 CCCTCTGCACCGCTCTTC 60.125 66.667 0.00 0.00 0.00 2.87
1463 1844 1.556911 TCTGAGATTTCCCTCTGCACC 59.443 52.381 0.00 0.00 34.38 5.01
1464 1845 2.903798 CTCTGAGATTTCCCTCTGCAC 58.096 52.381 0.00 0.00 34.38 4.57
1466 1847 1.209019 TGCTCTGAGATTTCCCTCTGC 59.791 52.381 9.28 0.00 34.38 4.26
1472 1853 2.687700 TCAGCTGCTCTGAGATTTCC 57.312 50.000 9.47 0.00 46.34 3.13
1500 1881 2.558359 CAAACATCTTCCTCACCCAACC 59.442 50.000 0.00 0.00 0.00 3.77
1501 1882 3.253432 GTCAAACATCTTCCTCACCCAAC 59.747 47.826 0.00 0.00 0.00 3.77
1510 1891 4.836125 TCTTGCTTGTCAAACATCTTCC 57.164 40.909 0.00 0.00 33.65 3.46
1529 1910 4.316645 CGCTGAAATCATCATCCTCATCT 58.683 43.478 0.00 0.00 37.44 2.90
1538 1919 3.836365 TCCATACCGCTGAAATCATCA 57.164 42.857 0.00 0.00 36.38 3.07
1549 1930 0.394565 AGAGCCTTGATCCATACCGC 59.605 55.000 0.00 0.00 0.00 5.68
1550 1931 1.336332 CGAGAGCCTTGATCCATACCG 60.336 57.143 0.00 0.00 0.00 4.02
1586 1970 1.959985 CTATGGATCTCAGCCGTGACT 59.040 52.381 0.00 0.00 0.00 3.41
1589 1973 1.271934 CTCCTATGGATCTCAGCCGTG 59.728 57.143 0.00 0.00 0.00 4.94
1590 1974 1.626686 CTCCTATGGATCTCAGCCGT 58.373 55.000 0.00 0.00 0.00 5.68
1595 1979 2.302157 CTGCATGCTCCTATGGATCTCA 59.698 50.000 20.33 0.00 0.00 3.27
1604 1988 2.817424 CGGCTCTGCATGCTCCTA 59.183 61.111 20.33 0.00 0.00 2.94
1617 2001 1.302832 CCAGAAGAAACCTGCGGCT 60.303 57.895 0.00 0.00 0.00 5.52
1629 2013 2.833794 TCCGTTGTGAAGAACCAGAAG 58.166 47.619 0.00 0.00 0.00 2.85
1631 2015 2.833794 CTTCCGTTGTGAAGAACCAGA 58.166 47.619 0.00 0.00 43.60 3.86
1632 2016 1.264288 GCTTCCGTTGTGAAGAACCAG 59.736 52.381 5.03 0.00 43.60 4.00
1638 2022 1.205064 CGCTGCTTCCGTTGTGAAG 59.795 57.895 0.00 0.00 43.71 3.02
1646 2030 1.142748 AATCTCCTCGCTGCTTCCG 59.857 57.895 0.00 0.00 0.00 4.30
1654 2038 4.201822 GGTTAAATGTGTCAATCTCCTCGC 60.202 45.833 0.00 0.00 0.00 5.03
1655 2039 5.178797 AGGTTAAATGTGTCAATCTCCTCG 58.821 41.667 0.00 0.00 0.00 4.63
1669 2053 3.951663 AGGGAAAGACCGAGGTTAAATG 58.048 45.455 0.00 0.00 40.11 2.32
1672 2056 5.306160 CCATATAGGGAAAGACCGAGGTTAA 59.694 44.000 0.00 0.00 40.11 2.01
1673 2057 4.836736 CCATATAGGGAAAGACCGAGGTTA 59.163 45.833 0.00 0.00 40.11 2.85
1675 2059 3.116862 TCCATATAGGGAAAGACCGAGGT 60.117 47.826 2.99 0.00 40.11 3.85
1676 2060 3.507411 TCCATATAGGGAAAGACCGAGG 58.493 50.000 2.99 0.00 40.11 4.63
1677 2061 5.952947 AGTATCCATATAGGGAAAGACCGAG 59.047 44.000 10.70 0.00 41.12 4.63
1679 2063 6.210784 TCAAGTATCCATATAGGGAAAGACCG 59.789 42.308 10.70 4.24 41.12 4.79
1705 2089 5.929538 GGAAGGTCCAAAGCATCTTGCTAC 61.930 50.000 1.88 0.00 44.69 3.58
1706 2090 3.873801 GGAAGGTCCAAAGCATCTTGCTA 60.874 47.826 1.88 0.00 44.69 3.49
1708 2092 1.203287 GGAAGGTCCAAAGCATCTTGC 59.797 52.381 0.00 0.00 39.15 4.01
1743 2127 3.997064 CTCGCAGCTTGGGGTCGAG 62.997 68.421 0.00 0.00 40.22 4.04
1745 2129 4.069232 TCTCGCAGCTTGGGGTCG 62.069 66.667 0.00 0.00 0.00 4.79
1755 2139 1.845809 GCCACAACCTTGTCTCGCAG 61.846 60.000 0.00 0.00 39.91 5.18
1758 2142 1.002468 CTTTGCCACAACCTTGTCTCG 60.002 52.381 0.00 0.00 39.91 4.04
1759 2143 2.297701 TCTTTGCCACAACCTTGTCTC 58.702 47.619 0.00 0.00 39.91 3.36
1769 2153 2.441410 TCAGTTGTGTTCTTTGCCACA 58.559 42.857 0.00 0.00 39.68 4.17
1770 2154 3.181487 ACATCAGTTGTGTTCTTTGCCAC 60.181 43.478 0.00 0.00 37.11 5.01
1787 2171 3.842820 CGAAGCTGAGAGAAGAACATCA 58.157 45.455 0.00 0.00 0.00 3.07
1813 2197 2.428890 AGATCTTGTGGGTCTCGCTTAG 59.571 50.000 0.00 0.00 0.00 2.18
1818 2202 1.135915 CCAGAGATCTTGTGGGTCTCG 59.864 57.143 14.65 0.00 42.40 4.04
1819 2203 2.167487 GACCAGAGATCTTGTGGGTCTC 59.833 54.545 22.66 11.85 41.17 3.36
1823 2207 1.577736 AGGACCAGAGATCTTGTGGG 58.422 55.000 22.66 13.26 35.48 4.61
1825 2209 6.068010 AGTAGATAGGACCAGAGATCTTGTG 58.932 44.000 0.00 0.00 31.25 3.33
1827 2211 7.004086 AGAAGTAGATAGGACCAGAGATCTTG 58.996 42.308 0.00 0.00 31.25 3.02
1832 2216 6.328782 TCAAGAAGTAGATAGGACCAGAGA 57.671 41.667 0.00 0.00 0.00 3.10
1850 2234 3.827302 AGACGTCCTTAGCTTCTTCAAGA 59.173 43.478 13.01 0.00 0.00 3.02
1852 2236 3.056749 GGAGACGTCCTTAGCTTCTTCAA 60.057 47.826 13.01 0.00 40.17 2.69
1854 2238 3.153676 GGAGACGTCCTTAGCTTCTTC 57.846 52.381 13.01 0.00 40.17 2.87
1865 2249 1.078848 ATGCTTGCAGGAGACGTCC 60.079 57.895 13.01 3.55 44.33 4.79
1866 2250 1.364626 CCATGCTTGCAGGAGACGTC 61.365 60.000 7.70 7.70 0.00 4.34
1868 2252 2.758089 GCCATGCTTGCAGGAGACG 61.758 63.158 8.91 0.00 0.00 4.18
1871 2255 2.044252 AGGCCATGCTTGCAGGAG 60.044 61.111 5.01 0.00 0.00 3.69
1872 2256 2.361992 CAGGCCATGCTTGCAGGA 60.362 61.111 5.01 0.00 0.00 3.86
1874 2258 1.735376 GATCCAGGCCATGCTTGCAG 61.735 60.000 5.01 0.00 34.24 4.41
1885 2269 0.610232 AACAGTTGCAGGATCCAGGC 60.610 55.000 15.82 17.47 0.00 4.85
1900 2284 1.336332 ACGAGTAGCACTCAGCAACAG 60.336 52.381 14.09 2.16 45.30 3.16
1901 2285 0.673985 ACGAGTAGCACTCAGCAACA 59.326 50.000 14.09 0.00 45.30 3.33
1906 2290 3.766676 ACATGTACGAGTAGCACTCAG 57.233 47.619 0.00 10.04 45.30 3.35
1907 2291 3.366985 CCAACATGTACGAGTAGCACTCA 60.367 47.826 0.00 0.00 45.30 3.41
1913 2297 2.451132 CGCTCCAACATGTACGAGTAG 58.549 52.381 18.43 11.83 0.00 2.57
1915 2299 0.108804 CCGCTCCAACATGTACGAGT 60.109 55.000 18.43 0.00 0.00 4.18
1918 2302 0.108804 ACTCCGCTCCAACATGTACG 60.109 55.000 0.00 0.00 0.00 3.67
1922 2306 2.093306 TGTAACTCCGCTCCAACATG 57.907 50.000 0.00 0.00 0.00 3.21
1923 2307 2.236146 TCATGTAACTCCGCTCCAACAT 59.764 45.455 0.00 0.00 0.00 2.71
1930 2314 0.613260 TTGGCTCATGTAACTCCGCT 59.387 50.000 0.00 0.00 0.00 5.52
1931 2315 1.448985 TTTGGCTCATGTAACTCCGC 58.551 50.000 0.00 0.00 0.00 5.54
1932 2316 5.527214 TGATATTTTGGCTCATGTAACTCCG 59.473 40.000 0.00 0.00 0.00 4.63
1933 2317 6.942532 TGATATTTTGGCTCATGTAACTCC 57.057 37.500 0.00 0.00 0.00 3.85
1934 2318 8.623903 TCAATGATATTTTGGCTCATGTAACTC 58.376 33.333 0.00 0.00 30.31 3.01
1935 2319 8.408601 GTCAATGATATTTTGGCTCATGTAACT 58.591 33.333 0.00 0.00 30.31 2.24
1936 2320 8.408601 AGTCAATGATATTTTGGCTCATGTAAC 58.591 33.333 0.00 0.00 33.97 2.50
1937 2321 8.523915 AGTCAATGATATTTTGGCTCATGTAA 57.476 30.769 0.00 0.00 33.97 2.41
1938 2322 9.797642 ATAGTCAATGATATTTTGGCTCATGTA 57.202 29.630 9.07 0.00 39.58 2.29
1939 2323 8.573885 CATAGTCAATGATATTTTGGCTCATGT 58.426 33.333 9.07 0.00 39.58 3.21
1940 2324 8.789762 TCATAGTCAATGATATTTTGGCTCATG 58.210 33.333 9.07 10.70 39.77 3.07
1941 2325 8.929260 TCATAGTCAATGATATTTTGGCTCAT 57.071 30.769 9.07 2.10 39.77 2.90
1942 2326 7.994911 ACTCATAGTCAATGATATTTTGGCTCA 59.005 33.333 9.07 0.34 43.70 4.26
1943 2327 8.288208 CACTCATAGTCAATGATATTTTGGCTC 58.712 37.037 9.07 0.00 43.70 4.70
1944 2328 7.230108 CCACTCATAGTCAATGATATTTTGGCT 59.770 37.037 10.25 10.25 43.70 4.75
1945 2329 7.229306 TCCACTCATAGTCAATGATATTTTGGC 59.771 37.037 0.00 0.00 43.70 4.52
1946 2330 8.562892 GTCCACTCATAGTCAATGATATTTTGG 58.437 37.037 0.00 0.00 43.70 3.28
1947 2331 9.334947 AGTCCACTCATAGTCAATGATATTTTG 57.665 33.333 0.00 0.00 43.70 2.44
1948 2332 9.553064 GAGTCCACTCATAGTCAATGATATTTT 57.447 33.333 1.61 0.00 43.70 1.82
1949 2333 8.932610 AGAGTCCACTCATAGTCAATGATATTT 58.067 33.333 9.39 0.00 43.70 1.40
1950 2334 8.489676 AGAGTCCACTCATAGTCAATGATATT 57.510 34.615 9.39 0.00 43.70 1.28
1951 2335 7.178274 GGAGAGTCCACTCATAGTCAATGATAT 59.822 40.741 9.39 0.00 45.21 1.63
1952 2336 6.491745 GGAGAGTCCACTCATAGTCAATGATA 59.508 42.308 9.39 0.00 45.21 2.15
1953 2337 5.304101 GGAGAGTCCACTCATAGTCAATGAT 59.696 44.000 9.39 0.00 45.21 2.45
1954 2338 4.646945 GGAGAGTCCACTCATAGTCAATGA 59.353 45.833 9.39 0.00 45.21 2.57
1955 2339 4.403752 TGGAGAGTCCACTCATAGTCAATG 59.596 45.833 9.39 0.00 42.67 2.82
1956 2340 4.614475 TGGAGAGTCCACTCATAGTCAAT 58.386 43.478 9.39 0.00 42.67 2.57
1957 2341 4.047627 TGGAGAGTCCACTCATAGTCAA 57.952 45.455 9.39 0.00 42.67 3.18
1958 2342 3.739401 TGGAGAGTCCACTCATAGTCA 57.261 47.619 9.39 0.00 42.67 3.41
1969 2353 2.961526 TTTACTCGCATGGAGAGTCC 57.038 50.000 15.51 0.00 44.87 3.85
1970 2354 3.126831 CCATTTACTCGCATGGAGAGTC 58.873 50.000 15.51 0.00 44.87 3.36
1972 2356 1.869767 GCCATTTACTCGCATGGAGAG 59.130 52.381 15.51 6.35 46.23 3.20
1973 2357 1.209261 TGCCATTTACTCGCATGGAGA 59.791 47.619 15.51 0.00 46.23 3.71
1975 2359 1.065491 AGTGCCATTTACTCGCATGGA 60.065 47.619 2.78 0.00 42.49 3.41
1976 2360 1.064505 CAGTGCCATTTACTCGCATGG 59.935 52.381 0.00 0.00 42.73 3.66
1981 2365 2.668457 GACTGTCAGTGCCATTTACTCG 59.332 50.000 11.04 0.00 0.00 4.18
2871 3774 2.764010 TGTCGTGCCTGTTGATATAGGT 59.236 45.455 0.00 0.00 35.23 3.08


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

AutoCloner maintained by Alex Coulton.