Multiple sequence alignment - TraesCS6A01G021200

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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 TraesCS6A01G021200 chr6A 100.000 3743 0 0 1 3743 10487234 10490976 0.000000e+00 6913.0
1 TraesCS6A01G021200 chr6A 89.216 204 4 3 2813 2998 558998542 558998339 4.830000e-59 239.0
2 TraesCS6A01G021200 chr6D 89.779 1810 109 38 799 2578 9462777 9464540 0.000000e+00 2248.0
3 TraesCS6A01G021200 chr6D 91.588 951 53 7 2577 3512 9464676 9465614 0.000000e+00 1288.0
4 TraesCS6A01G021200 chr6D 89.643 589 37 11 159 745 9406775 9407341 0.000000e+00 728.0
5 TraesCS6A01G021200 chr6D 93.827 162 9 1 1 161 9406533 9406694 3.740000e-60 243.0
6 TraesCS6A01G021200 chr6D 86.957 138 16 2 3543 3680 9465607 9465742 1.800000e-33 154.0
7 TraesCS6A01G021200 chr6B 85.037 1076 92 44 844 1868 17414273 17415330 0.000000e+00 1031.0
8 TraesCS6A01G021200 chr6B 85.618 744 54 19 2577 3288 17416303 17417025 0.000000e+00 732.0
9 TraesCS6A01G021200 chr6B 85.020 247 22 4 2328 2572 32918908 32919141 1.740000e-58 237.0
10 TraesCS6A01G021200 chr6B 88.835 206 5 4 2813 3000 32919486 32919691 1.740000e-58 237.0
11 TraesCS6A01G021200 chr6B 85.020 247 22 4 2328 2572 377941755 377941988 1.740000e-58 237.0
12 TraesCS6A01G021200 chr6B 88.835 206 5 3 2813 3000 377942333 377942538 1.740000e-58 237.0
13 TraesCS6A01G021200 chrUn 85.375 253 22 4 2328 2578 380890080 380889841 8.030000e-62 248.0
14 TraesCS6A01G021200 chrUn 84.980 253 23 4 2328 2578 39517686 39517447 3.740000e-60 243.0
15 TraesCS6A01G021200 chrUn 88.517 209 6 4 2813 3003 463662904 463662696 1.740000e-58 237.0
16 TraesCS6A01G021200 chrUn 87.923 207 6 4 2813 3000 214483164 214483370 3.760000e-55 226.0
17 TraesCS6A01G021200 chrUn 83.806 247 25 4 2328 2572 214482586 214482819 1.750000e-53 220.0
18 TraesCS6A01G021200 chrUn 87.310 197 16 6 2577 2765 214482962 214483157 2.260000e-52 217.0
19 TraesCS6A01G021200 chrUn 84.375 224 21 3 2328 2550 478105280 478105490 1.360000e-49 207.0
20 TraesCS6A01G021200 chrUn 88.764 178 2 3 2813 2972 380889502 380889325 6.340000e-48 202.0
21 TraesCS6A01G021200 chr4A 88.995 209 5 3 2813 3003 687558421 687558213 3.740000e-60 243.0
22 TraesCS6A01G021200 chr4B 87.923 207 6 4 2813 3000 367930703 367930909 3.760000e-55 226.0
23 TraesCS6A01G021200 chr4B 87.143 210 8 4 2813 3003 274678205 274677996 1.750000e-53 220.0
24 TraesCS6A01G021200 chr4B 83.399 253 27 4 2328 2578 274678783 274678544 1.750000e-53 220.0
25 TraesCS6A01G021200 chr4B 83.401 247 26 4 2328 2572 367930125 367930358 8.140000e-52 215.0
26 TraesCS6A01G021200 chr4B 86.802 197 17 6 2577 2765 367930501 367930696 1.050000e-50 211.0
27 TraesCS6A01G021200 chr2D 87.209 86 6 3 1590 1671 12880815 12880899 3.980000e-15 93.5


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G021200 chr6A 10487234 10490976 3742 False 6913.000000 6913 100.000000 1 3743 1 chr6A.!!$F1 3742
1 TraesCS6A01G021200 chr6D 9462777 9465742 2965 False 1230.000000 2248 89.441333 799 3680 3 chr6D.!!$F2 2881
2 TraesCS6A01G021200 chr6D 9406533 9407341 808 False 485.500000 728 91.735000 1 745 2 chr6D.!!$F1 744
3 TraesCS6A01G021200 chr6B 17414273 17417025 2752 False 881.500000 1031 85.327500 844 3288 2 chr6B.!!$F1 2444
4 TraesCS6A01G021200 chr6B 32918908 32919691 783 False 237.000000 237 86.927500 2328 3000 2 chr6B.!!$F2 672
5 TraesCS6A01G021200 chr6B 377941755 377942538 783 False 237.000000 237 86.927500 2328 3000 2 chr6B.!!$F3 672
6 TraesCS6A01G021200 chrUn 380889325 380890080 755 True 225.000000 248 87.069500 2328 2972 2 chrUn.!!$R3 644
7 TraesCS6A01G021200 chrUn 214482586 214483370 784 False 221.000000 226 86.346333 2328 3000 3 chrUn.!!$F2 672
8 TraesCS6A01G021200 chr4B 274677996 274678783 787 True 220.000000 220 85.271000 2328 3003 2 chr4B.!!$R1 675
9 TraesCS6A01G021200 chr4B 367930125 367930909 784 False 217.333333 226 86.042000 2328 3000 3 chr4B.!!$F1 672

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
888 984 0.033228 CTCTGTCTCATCGGCCCATC 59.967 60.0 0.0 0.0 0.0 3.51 F
1183 1320 0.254747 CCTCCCTCTCTCTCTGACGT 59.745 60.0 0.0 0.0 0.0 4.34 F
1443 1580 0.311165 CGTCGTGGTGAGTTGAGAGT 59.689 55.0 0.0 0.0 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2155 2469 1.267806 GCACTCAATCACCCAACTGTG 59.732 52.381 0.0 0.0 37.59 3.66 R
2612 3088 1.548582 GGATGGCCCCCAATACTCATG 60.549 57.143 0.0 0.0 36.95 3.07 R
3293 3802 0.169009 GGCAAAGGAATCTGACACGC 59.831 55.000 0.0 0.0 0.00 5.34 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
181 266 5.376854 ACATGGTGAGCAGTTTTCAATAC 57.623 39.130 0.00 0.00 0.00 1.89
189 274 3.684788 AGCAGTTTTCAATACGCGAAGAT 59.315 39.130 15.93 0.00 0.00 2.40
271 356 4.125703 TCAAATTTTGCGCATGGAGTTTT 58.874 34.783 12.75 3.20 0.00 2.43
402 489 1.043816 ACAGTGCGCTAGGAGCATAT 58.956 50.000 9.73 0.00 46.96 1.78
408 495 2.064762 GCGCTAGGAGCATATGAACAG 58.935 52.381 6.97 0.00 42.58 3.16
452 539 6.811954 TGACCTGGTTCTTAAACAATTTTCC 58.188 36.000 0.00 0.00 37.10 3.13
484 571 9.659135 TTATCCCAAATTCCATCTTTCATGTAT 57.341 29.630 0.00 0.00 0.00 2.29
486 573 8.463930 TCCCAAATTCCATCTTTCATGTATAC 57.536 34.615 0.00 0.00 0.00 1.47
487 574 7.228507 TCCCAAATTCCATCTTTCATGTATACG 59.771 37.037 0.00 0.00 0.00 3.06
503 590 3.720949 ATACGCCGTAGCAGTCATAAA 57.279 42.857 2.44 0.00 39.83 1.40
508 595 1.924524 CCGTAGCAGTCATAAACCGTG 59.075 52.381 0.00 0.00 0.00 4.94
509 596 1.924524 CGTAGCAGTCATAAACCGTGG 59.075 52.381 0.00 0.00 0.00 4.94
523 610 1.661821 CGTGGCCTAGATAGTGCGC 60.662 63.158 3.32 0.00 0.00 6.09
525 612 0.876342 GTGGCCTAGATAGTGCGCAC 60.876 60.000 32.79 32.79 0.00 5.34
526 613 1.661821 GGCCTAGATAGTGCGCACG 60.662 63.158 32.94 18.72 36.20 5.34
527 614 1.359117 GCCTAGATAGTGCGCACGA 59.641 57.895 32.94 29.29 36.20 4.35
528 615 0.039074 GCCTAGATAGTGCGCACGAT 60.039 55.000 32.12 32.12 36.20 3.73
529 616 1.970447 CCTAGATAGTGCGCACGATC 58.030 55.000 39.89 39.89 41.71 3.69
530 617 1.401670 CCTAGATAGTGCGCACGATCC 60.402 57.143 41.46 29.68 42.15 3.36
532 619 2.016704 GATAGTGCGCACGATCCGG 61.017 63.158 38.22 0.00 37.44 5.14
533 620 3.499929 ATAGTGCGCACGATCCGGG 62.500 63.158 32.94 0.00 36.20 5.73
538 625 4.907034 CGCACGATCCGGGAGACG 62.907 72.222 19.64 19.64 43.80 4.18
539 626 3.823330 GCACGATCCGGGAGACGT 61.823 66.667 20.70 20.70 42.24 4.34
540 627 2.475466 GCACGATCCGGGAGACGTA 61.475 63.158 24.03 0.00 42.24 3.57
541 628 1.647629 CACGATCCGGGAGACGTAG 59.352 63.158 24.03 16.95 42.24 3.51
542 629 0.812811 CACGATCCGGGAGACGTAGA 60.813 60.000 24.03 0.00 42.24 2.59
624 711 8.266392 AGCACAATTGTTTTTCAAATTCTGAA 57.734 26.923 8.77 0.00 42.48 3.02
627 714 8.449397 CACAATTGTTTTTCAAATTCTGAACCA 58.551 29.630 8.77 0.53 43.90 3.67
628 715 9.176460 ACAATTGTTTTTCAAATTCTGAACCAT 57.824 25.926 4.92 0.00 43.90 3.55
668 755 1.060698 GCCGAACAGTGCTACGAAATC 59.939 52.381 0.00 0.00 0.00 2.17
687 774 2.261345 TCGCAAACCGTTATTAGACCG 58.739 47.619 0.00 0.00 38.35 4.79
696 783 7.671495 AACCGTTATTAGACCGTAAACAATT 57.329 32.000 0.00 0.00 0.00 2.32
709 796 5.278071 CCGTAAACAATTCCTTTGCACACTA 60.278 40.000 0.00 0.00 39.03 2.74
710 797 6.378582 CGTAAACAATTCCTTTGCACACTAT 58.621 36.000 0.00 0.00 39.03 2.12
711 798 7.361371 CCGTAAACAATTCCTTTGCACACTATA 60.361 37.037 0.00 0.00 39.03 1.31
819 906 4.636648 TGTTTCTCCTAGAGAGCTAGAACG 59.363 45.833 0.00 0.00 45.71 3.95
848 935 1.769026 TCGAGACAATCCTGGAGAGG 58.231 55.000 1.52 0.00 41.39 3.69
851 938 0.908198 AGACAATCCTGGAGAGGCAC 59.092 55.000 1.52 0.00 39.57 5.01
873 969 5.062683 CACAACTTGTCCATATCGTTCTCTG 59.937 44.000 0.00 0.00 0.00 3.35
874 970 5.171476 CAACTTGTCCATATCGTTCTCTGT 58.829 41.667 0.00 0.00 0.00 3.41
876 972 4.707448 ACTTGTCCATATCGTTCTCTGTCT 59.293 41.667 0.00 0.00 0.00 3.41
888 984 0.033228 CTCTGTCTCATCGGCCCATC 59.967 60.000 0.00 0.00 0.00 3.51
1079 1189 2.202756 CTCCGTCGGCCTGCTAAC 60.203 66.667 6.34 0.00 0.00 2.34
1150 1268 3.823330 CCTTCGTACGCGCCCTCT 61.823 66.667 11.24 0.00 38.14 3.69
1151 1269 2.278013 CTTCGTACGCGCCCTCTC 60.278 66.667 11.24 0.00 38.14 3.20
1163 1281 3.039526 CCTCTCCCTCCCCCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
1168 1286 4.179599 CCCTCCCCCTCCTCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
1179 1316 1.143684 CTCCTCCTCCCTCTCTCTCTG 59.856 61.905 0.00 0.00 0.00 3.35
1180 1317 1.221635 CCTCCTCCCTCTCTCTCTGA 58.778 60.000 0.00 0.00 0.00 3.27
1182 1319 0.544223 TCCTCCCTCTCTCTCTGACG 59.456 60.000 0.00 0.00 0.00 4.35
1183 1320 0.254747 CCTCCCTCTCTCTCTGACGT 59.745 60.000 0.00 0.00 0.00 4.34
1184 1321 1.378531 CTCCCTCTCTCTCTGACGTG 58.621 60.000 0.00 0.00 0.00 4.49
1191 1328 1.130373 CTCTCTCTGACGTGCTCTCAC 59.870 57.143 0.00 0.00 39.78 3.51
1197 1334 1.374758 GACGTGCTCTCACCCTTGG 60.375 63.158 0.00 0.00 40.04 3.61
1198 1335 2.743928 CGTGCTCTCACCCTTGGC 60.744 66.667 0.00 0.00 40.04 4.52
1200 1337 3.241530 TGCTCTCACCCTTGGCGT 61.242 61.111 0.00 0.00 0.00 5.68
1201 1338 2.032681 GCTCTCACCCTTGGCGTT 59.967 61.111 0.00 0.00 0.00 4.84
1440 1577 4.245054 CCGTCGTGGTGAGTTGAG 57.755 61.111 0.00 0.00 0.00 3.02
1441 1578 1.658114 CCGTCGTGGTGAGTTGAGA 59.342 57.895 0.00 0.00 0.00 3.27
1442 1579 0.387367 CCGTCGTGGTGAGTTGAGAG 60.387 60.000 0.00 0.00 0.00 3.20
1443 1580 0.311165 CGTCGTGGTGAGTTGAGAGT 59.689 55.000 0.00 0.00 0.00 3.24
1444 1581 1.534163 CGTCGTGGTGAGTTGAGAGTA 59.466 52.381 0.00 0.00 0.00 2.59
1446 1583 1.884579 TCGTGGTGAGTTGAGAGTACC 59.115 52.381 0.00 0.00 0.00 3.34
1448 1585 1.067776 GTGGTGAGTTGAGAGTACCGG 60.068 57.143 0.00 0.00 34.16 5.28
1450 1587 2.100989 GGTGAGTTGAGAGTACCGGAT 58.899 52.381 9.46 0.00 0.00 4.18
1451 1588 2.496470 GGTGAGTTGAGAGTACCGGATT 59.504 50.000 9.46 0.00 0.00 3.01
1452 1589 3.512680 GTGAGTTGAGAGTACCGGATTG 58.487 50.000 9.46 0.00 0.00 2.67
1453 1590 3.192844 GTGAGTTGAGAGTACCGGATTGA 59.807 47.826 9.46 0.00 0.00 2.57
1457 1594 5.178797 AGTTGAGAGTACCGGATTGAATTG 58.821 41.667 9.46 0.00 0.00 2.32
1458 1595 4.137116 TGAGAGTACCGGATTGAATTGG 57.863 45.455 9.46 0.00 0.00 3.16
1459 1596 3.772572 TGAGAGTACCGGATTGAATTGGA 59.227 43.478 9.46 0.00 0.00 3.53
1467 1604 5.203528 ACCGGATTGAATTGGATTTCAGAT 58.796 37.500 9.46 0.00 36.97 2.90
1468 1605 5.658190 ACCGGATTGAATTGGATTTCAGATT 59.342 36.000 9.46 0.00 36.97 2.40
1469 1606 6.155049 ACCGGATTGAATTGGATTTCAGATTT 59.845 34.615 9.46 0.00 36.97 2.17
1470 1607 6.698766 CCGGATTGAATTGGATTTCAGATTTC 59.301 38.462 0.00 0.00 36.97 2.17
1474 1611 6.534475 TGAATTGGATTTCAGATTTCCAGG 57.466 37.500 2.87 0.00 40.48 4.45
1475 1612 5.105228 TGAATTGGATTTCAGATTTCCAGGC 60.105 40.000 2.87 0.00 40.48 4.85
1476 1613 3.744940 TGGATTTCAGATTTCCAGGCT 57.255 42.857 0.00 0.00 34.65 4.58
1477 1614 4.051661 TGGATTTCAGATTTCCAGGCTT 57.948 40.909 0.00 0.00 34.65 4.35
1478 1615 3.765511 TGGATTTCAGATTTCCAGGCTTG 59.234 43.478 0.00 0.00 34.65 4.01
1479 1616 3.766051 GGATTTCAGATTTCCAGGCTTGT 59.234 43.478 0.00 0.00 0.00 3.16
1480 1617 4.381292 GGATTTCAGATTTCCAGGCTTGTG 60.381 45.833 0.00 0.00 0.00 3.33
1481 1618 2.957402 TCAGATTTCCAGGCTTGTGT 57.043 45.000 0.00 0.00 0.00 3.72
1482 1619 2.783135 TCAGATTTCCAGGCTTGTGTC 58.217 47.619 0.00 0.00 0.00 3.67
1502 1639 6.126623 TGTGTCCTCTAGATATGACAGACTCT 60.127 42.308 16.03 0.00 38.32 3.24
1504 1641 7.284489 GTGTCCTCTAGATATGACAGACTCTTT 59.716 40.741 16.03 0.00 38.32 2.52
1531 1677 8.821686 TTTCAGATTTCCTAGATTTATGGCAA 57.178 30.769 0.00 0.00 0.00 4.52
1564 1720 2.380084 TCAGTATCAGAAACGGTGCC 57.620 50.000 0.00 0.00 0.00 5.01
1587 1743 4.079253 ACCGAGTTGCTGATGGTATTTTT 58.921 39.130 0.00 0.00 0.00 1.94
1601 1757 5.022122 TGGTATTTTTGGATGCCTGATGAA 58.978 37.500 0.00 0.00 33.46 2.57
1603 1759 6.156602 TGGTATTTTTGGATGCCTGATGAATT 59.843 34.615 0.00 0.00 33.46 2.17
1604 1760 6.480981 GGTATTTTTGGATGCCTGATGAATTG 59.519 38.462 0.00 0.00 0.00 2.32
1605 1761 5.486735 TTTTTGGATGCCTGATGAATTGT 57.513 34.783 0.00 0.00 0.00 2.71
1606 1762 4.459390 TTTGGATGCCTGATGAATTGTG 57.541 40.909 0.00 0.00 0.00 3.33
1645 1803 1.341976 GGTCATATTTGGGTGCAGGGT 60.342 52.381 0.00 0.00 0.00 4.34
1687 1845 3.685214 CTCGAGGCAGTTCGGACCG 62.685 68.421 7.84 7.84 40.83 4.79
1890 2199 8.149973 TGTAACTAGTGATGGTTTTGAACTTC 57.850 34.615 0.00 0.00 0.00 3.01
1921 2235 6.236017 TGAGTAACCGATTTTAAACTGCAG 57.764 37.500 13.48 13.48 0.00 4.41
1944 2258 8.944029 GCAGCTGTCATGTTATATCTTCATTAT 58.056 33.333 16.64 0.00 0.00 1.28
2008 2322 3.799281 TTGGCCAAAACAGAGTTTCAG 57.201 42.857 17.98 0.00 0.00 3.02
2030 2344 5.120830 CAGGTGCTTCAGTGTCTTTGTATAC 59.879 44.000 0.00 0.00 0.00 1.47
2034 2348 5.633601 TGCTTCAGTGTCTTTGTATACTTCG 59.366 40.000 4.17 0.00 0.00 3.79
2053 2367 9.978044 ATACTTCGAGGTTTAATTACTATGGTC 57.022 33.333 5.17 0.00 0.00 4.02
2054 2368 8.075761 ACTTCGAGGTTTAATTACTATGGTCT 57.924 34.615 0.00 0.00 0.00 3.85
2055 2369 7.980099 ACTTCGAGGTTTAATTACTATGGTCTG 59.020 37.037 0.00 0.00 0.00 3.51
2056 2370 6.278363 TCGAGGTTTAATTACTATGGTCTGC 58.722 40.000 0.00 0.00 0.00 4.26
2113 2427 1.516161 GCAGACATGTGCTGACTCAA 58.484 50.000 21.90 0.00 40.54 3.02
2155 2469 1.882623 GCTCTAGGCCCAACATAATGC 59.117 52.381 0.00 0.00 34.27 3.56
2235 2551 3.520862 CTAGTTACGCGCGGGGGA 61.521 66.667 35.22 13.50 0.00 4.81
2271 2587 9.716507 CCTTAATAATATCACAACCGTTCTTTG 57.283 33.333 0.00 0.00 0.00 2.77
2420 2752 8.463930 TCAGAGATTAAATGAGTGTTGGTTTT 57.536 30.769 0.00 0.00 0.00 2.43
2426 2758 9.959749 GATTAAATGAGTGTTGGTTTTAACTGA 57.040 29.630 0.00 0.00 0.00 3.41
2427 2759 9.965824 ATTAAATGAGTGTTGGTTTTAACTGAG 57.034 29.630 0.00 0.00 0.00 3.35
2433 2765 8.527810 TGAGTGTTGGTTTTAACTGAGAAATTT 58.472 29.630 0.00 0.00 0.00 1.82
2435 2767 9.150348 AGTGTTGGTTTTAACTGAGAAATTTTG 57.850 29.630 0.00 0.00 0.00 2.44
2489 2821 4.395854 TGCATTGTCTTGCTGATAATCGTT 59.604 37.500 0.00 0.00 43.18 3.85
2500 2832 5.107104 TGCTGATAATCGTTTTCACACACTC 60.107 40.000 0.00 0.00 0.00 3.51
2502 2834 4.986034 TGATAATCGTTTTCACACACTCGT 59.014 37.500 0.00 0.00 0.00 4.18
2509 2841 5.291371 TCGTTTTCACACACTCGTTATCAAA 59.709 36.000 0.00 0.00 0.00 2.69
2543 2876 7.902917 TGTAAATTCATTTGAATCTCGTAAGCG 59.097 33.333 6.27 0.00 43.41 4.68
2552 2885 9.651718 ATTTGAATCTCGTAAGCGATAAAATTC 57.348 29.630 0.00 0.00 46.80 2.17
2564 2898 8.738199 AAGCGATAAAATTCATTATGCATCAG 57.262 30.769 0.19 0.00 0.00 2.90
2736 3220 5.867330 AGGATTGGTGCAATTGATTCAAAA 58.133 33.333 10.34 0.00 33.90 2.44
2810 3294 2.579873 CCGATCATCCCTTTTCTGCAT 58.420 47.619 0.00 0.00 0.00 3.96
2980 3484 6.492007 GAATCTATGGCATGATTCGATTGT 57.508 37.500 23.84 7.06 39.08 2.71
3004 3510 6.020971 TGTGTCTCATGTCGTAACTTATGT 57.979 37.500 0.00 0.00 0.00 2.29
3064 3570 2.124151 GTTCCGGGCATGGCTGAT 60.124 61.111 28.56 0.00 0.00 2.90
3065 3571 2.124193 TTCCGGGCATGGCTGATG 60.124 61.111 28.56 13.37 34.84 3.07
3122 3631 1.089920 CATTCTCCTGGACCAAAGCG 58.910 55.000 0.00 0.00 0.00 4.68
3127 3636 0.036388 TCCTGGACCAAAGCGTGATC 60.036 55.000 0.00 0.00 0.00 2.92
3155 3664 7.348808 TGTGCATTGTAACATTTGCTTATTG 57.651 32.000 0.00 0.00 36.10 1.90
3172 3681 6.016108 TGCTTATTGTTAAGGCCGTTTTAAGT 60.016 34.615 0.00 0.00 36.18 2.24
3174 3683 7.507733 TTATTGTTAAGGCCGTTTTAAGTGA 57.492 32.000 0.00 0.00 0.00 3.41
3234 3743 8.031277 AGTGATTATTCAAGTTCAAGCCATTTC 58.969 33.333 0.00 0.00 32.48 2.17
3238 3747 2.030893 TCAAGTTCAAGCCATTTCAGCG 60.031 45.455 0.00 0.00 34.64 5.18
3239 3748 1.609208 AGTTCAAGCCATTTCAGCGT 58.391 45.000 0.00 0.00 34.64 5.07
3249 3758 4.154195 AGCCATTTCAGCGTAACTAAGTTG 59.846 41.667 0.00 0.00 34.64 3.16
3288 3797 0.322816 AGTGGGCAAGCTGTGTATGG 60.323 55.000 0.00 0.00 0.00 2.74
3291 3800 2.764314 GGCAAGCTGTGTATGGCGG 61.764 63.158 0.00 0.00 0.00 6.13
3292 3801 2.040544 GCAAGCTGTGTATGGCGGT 61.041 57.895 0.00 0.00 0.00 5.68
3293 3802 1.796151 CAAGCTGTGTATGGCGGTG 59.204 57.895 0.00 0.00 0.00 4.94
3294 3803 2.040544 AAGCTGTGTATGGCGGTGC 61.041 57.895 0.00 0.00 0.00 5.01
3300 3809 2.433491 GTATGGCGGTGCGTGTCA 60.433 61.111 0.00 0.00 0.00 3.58
3343 3852 5.767816 ATAGCGGAACATGGTAAAATTCC 57.232 39.130 0.00 0.00 37.79 3.01
3351 3860 5.906113 ACATGGTAAAATTCCGTATTGCA 57.094 34.783 0.00 0.00 0.00 4.08
3356 3865 8.663911 CATGGTAAAATTCCGTATTGCATTTTT 58.336 29.630 0.00 0.00 32.42 1.94
3377 3886 0.250467 AGGCTGTGTGAAGCATCGTT 60.250 50.000 0.00 0.00 45.43 3.85
3378 3887 0.593128 GGCTGTGTGAAGCATCGTTT 59.407 50.000 0.00 0.00 45.43 3.60
3379 3888 1.664016 GGCTGTGTGAAGCATCGTTTG 60.664 52.381 0.00 0.00 45.43 2.93
3380 3889 1.002468 GCTGTGTGAAGCATCGTTTGT 60.002 47.619 0.00 0.00 43.01 2.83
3381 3890 2.541588 GCTGTGTGAAGCATCGTTTGTT 60.542 45.455 0.00 0.00 43.01 2.83
3450 3959 7.184067 ACTTAATCACTCCTTGGTAACCTAG 57.816 40.000 0.00 0.00 0.00 3.02
3459 3968 6.380560 ACTCCTTGGTAACCTAGTGAGATTAC 59.619 42.308 2.00 0.00 32.73 1.89
3462 3971 3.956199 TGGTAACCTAGTGAGATTACGGG 59.044 47.826 0.00 0.00 0.00 5.28
3485 3994 2.345880 GATTGCGCCATTGCTCTGGG 62.346 60.000 4.18 0.00 36.75 4.45
3492 4001 1.137675 GCCATTGCTCTGGGAATTTCC 59.862 52.381 6.91 6.91 36.75 3.13
3512 4021 3.918258 CGAATTCATTTTCGGCGTAGA 57.082 42.857 6.85 0.00 43.59 2.59
3513 4022 3.594312 CGAATTCATTTTCGGCGTAGAC 58.406 45.455 6.85 0.00 43.59 2.59
3514 4023 3.306166 CGAATTCATTTTCGGCGTAGACT 59.694 43.478 6.85 0.00 43.59 3.24
3515 4024 4.578601 GAATTCATTTTCGGCGTAGACTG 58.421 43.478 6.85 0.00 0.00 3.51
3516 4025 2.004583 TCATTTTCGGCGTAGACTGG 57.995 50.000 6.85 0.00 0.00 4.00
3517 4026 1.274167 TCATTTTCGGCGTAGACTGGT 59.726 47.619 6.85 0.00 0.00 4.00
3518 4027 2.492881 TCATTTTCGGCGTAGACTGGTA 59.507 45.455 6.85 0.00 0.00 3.25
3519 4028 2.642139 TTTTCGGCGTAGACTGGTAG 57.358 50.000 6.85 0.00 0.00 3.18
3520 4029 0.813184 TTTCGGCGTAGACTGGTAGG 59.187 55.000 6.85 0.00 0.00 3.18
3521 4030 0.322816 TTCGGCGTAGACTGGTAGGT 60.323 55.000 6.85 0.00 0.00 3.08
3522 4031 1.028330 TCGGCGTAGACTGGTAGGTG 61.028 60.000 6.85 0.00 0.00 4.00
3523 4032 1.814527 GGCGTAGACTGGTAGGTGG 59.185 63.158 0.00 0.00 0.00 4.61
3524 4033 0.969409 GGCGTAGACTGGTAGGTGGT 60.969 60.000 0.00 0.00 0.00 4.16
3525 4034 0.893447 GCGTAGACTGGTAGGTGGTT 59.107 55.000 0.00 0.00 0.00 3.67
3526 4035 1.274447 GCGTAGACTGGTAGGTGGTTT 59.726 52.381 0.00 0.00 0.00 3.27
3527 4036 2.493278 GCGTAGACTGGTAGGTGGTTTA 59.507 50.000 0.00 0.00 0.00 2.01
3528 4037 3.674410 GCGTAGACTGGTAGGTGGTTTAC 60.674 52.174 0.00 0.00 0.00 2.01
3529 4038 3.760684 CGTAGACTGGTAGGTGGTTTACT 59.239 47.826 0.00 0.00 0.00 2.24
3530 4039 4.219288 CGTAGACTGGTAGGTGGTTTACTT 59.781 45.833 0.00 0.00 0.00 2.24
3531 4040 4.618920 AGACTGGTAGGTGGTTTACTTG 57.381 45.455 0.00 0.00 0.00 3.16
3532 4041 4.228824 AGACTGGTAGGTGGTTTACTTGA 58.771 43.478 0.00 0.00 0.00 3.02
3533 4042 4.844655 AGACTGGTAGGTGGTTTACTTGAT 59.155 41.667 0.00 0.00 0.00 2.57
3534 4043 5.046520 AGACTGGTAGGTGGTTTACTTGATC 60.047 44.000 0.00 0.00 0.00 2.92
3535 4044 4.595781 ACTGGTAGGTGGTTTACTTGATCA 59.404 41.667 0.00 0.00 0.00 2.92
3536 4045 5.072600 ACTGGTAGGTGGTTTACTTGATCAA 59.927 40.000 8.12 8.12 0.00 2.57
3537 4046 6.134535 TGGTAGGTGGTTTACTTGATCAAT 57.865 37.500 8.96 2.32 0.00 2.57
3538 4047 5.943416 TGGTAGGTGGTTTACTTGATCAATG 59.057 40.000 8.96 6.02 0.00 2.82
3539 4048 5.357032 GGTAGGTGGTTTACTTGATCAATGG 59.643 44.000 8.96 0.48 0.00 3.16
3540 4049 4.344104 AGGTGGTTTACTTGATCAATGGG 58.656 43.478 8.96 0.00 0.00 4.00
3541 4050 4.044065 AGGTGGTTTACTTGATCAATGGGA 59.956 41.667 8.96 0.00 0.00 4.37
3546 4055 0.327924 ACTTGATCAATGGGACGGCA 59.672 50.000 8.96 0.00 0.00 5.69
3559 4068 1.064060 GGACGGCATAGTTGTTGATGC 59.936 52.381 0.00 0.00 46.31 3.91
3575 4084 8.430063 GTTGTTGATGCTCAGAATGTTAATTTG 58.570 33.333 0.00 0.00 37.40 2.32
3604 4113 4.836825 TCACCTGAGCCTTTGATAAGAAG 58.163 43.478 0.00 0.00 32.92 2.85
3605 4114 3.376546 CACCTGAGCCTTTGATAAGAAGC 59.623 47.826 0.00 0.00 32.92 3.86
3606 4115 3.265479 ACCTGAGCCTTTGATAAGAAGCT 59.735 43.478 0.00 0.00 33.36 3.74
3607 4116 4.263683 ACCTGAGCCTTTGATAAGAAGCTT 60.264 41.667 0.00 0.00 31.61 3.74
3610 4119 5.503927 TGAGCCTTTGATAAGAAGCTTGAT 58.496 37.500 2.10 0.00 31.61 2.57
3613 4122 7.039504 TGAGCCTTTGATAAGAAGCTTGATTTT 60.040 33.333 2.10 0.00 31.61 1.82
3614 4123 7.095270 AGCCTTTGATAAGAAGCTTGATTTTG 58.905 34.615 2.10 0.00 32.92 2.44
3674 4183 2.508526 GCTGGGGCTAACAAGATATGG 58.491 52.381 0.00 0.00 35.22 2.74
3677 4186 4.792068 CTGGGGCTAACAAGATATGGAAA 58.208 43.478 0.00 0.00 0.00 3.13
3678 4187 4.792068 TGGGGCTAACAAGATATGGAAAG 58.208 43.478 0.00 0.00 0.00 2.62
3679 4188 4.476846 TGGGGCTAACAAGATATGGAAAGA 59.523 41.667 0.00 0.00 0.00 2.52
3680 4189 5.134339 TGGGGCTAACAAGATATGGAAAGAT 59.866 40.000 0.00 0.00 0.00 2.40
3681 4190 6.071320 GGGGCTAACAAGATATGGAAAGATT 58.929 40.000 0.00 0.00 0.00 2.40
3682 4191 6.551227 GGGGCTAACAAGATATGGAAAGATTT 59.449 38.462 0.00 0.00 0.00 2.17
3683 4192 7.069950 GGGGCTAACAAGATATGGAAAGATTTT 59.930 37.037 0.00 0.00 0.00 1.82
3684 4193 8.138074 GGGCTAACAAGATATGGAAAGATTTTC 58.862 37.037 0.00 0.00 0.00 2.29
3685 4194 8.686334 GGCTAACAAGATATGGAAAGATTTTCA 58.314 33.333 4.19 0.00 0.00 2.69
3689 4198 9.865321 AACAAGATATGGAAAGATTTTCATGTG 57.135 29.630 8.99 5.15 37.01 3.21
3690 4199 8.472413 ACAAGATATGGAAAGATTTTCATGTGG 58.528 33.333 8.99 0.00 37.01 4.17
3691 4200 7.047460 AGATATGGAAAGATTTTCATGTGGC 57.953 36.000 8.99 0.00 37.01 5.01
3692 4201 6.608405 AGATATGGAAAGATTTTCATGTGGCA 59.392 34.615 8.99 0.00 37.01 4.92
3693 4202 4.524316 TGGAAAGATTTTCATGTGGCAG 57.476 40.909 4.19 0.00 0.00 4.85
3694 4203 3.896888 TGGAAAGATTTTCATGTGGCAGT 59.103 39.130 4.19 0.00 0.00 4.40
3695 4204 4.344679 TGGAAAGATTTTCATGTGGCAGTT 59.655 37.500 4.19 0.00 0.00 3.16
3696 4205 4.687483 GGAAAGATTTTCATGTGGCAGTTG 59.313 41.667 4.19 0.00 0.00 3.16
3697 4206 4.942761 AAGATTTTCATGTGGCAGTTGT 57.057 36.364 0.00 0.00 0.00 3.32
3698 4207 4.247267 AGATTTTCATGTGGCAGTTGTG 57.753 40.909 0.00 0.00 0.00 3.33
3699 4208 3.638160 AGATTTTCATGTGGCAGTTGTGT 59.362 39.130 0.00 0.00 0.00 3.72
3700 4209 3.435105 TTTTCATGTGGCAGTTGTGTC 57.565 42.857 0.00 0.00 0.00 3.67
3701 4210 0.943673 TTCATGTGGCAGTTGTGTCG 59.056 50.000 0.00 0.00 0.00 4.35
3702 4211 0.179059 TCATGTGGCAGTTGTGTCGT 60.179 50.000 0.00 0.00 0.00 4.34
3703 4212 1.069358 TCATGTGGCAGTTGTGTCGTA 59.931 47.619 0.00 0.00 0.00 3.43
3704 4213 1.870402 CATGTGGCAGTTGTGTCGTAA 59.130 47.619 0.00 0.00 0.00 3.18
3705 4214 2.248280 TGTGGCAGTTGTGTCGTAAT 57.752 45.000 0.00 0.00 0.00 1.89
3706 4215 2.566913 TGTGGCAGTTGTGTCGTAATT 58.433 42.857 0.00 0.00 0.00 1.40
3707 4216 2.546368 TGTGGCAGTTGTGTCGTAATTC 59.454 45.455 0.00 0.00 0.00 2.17
3708 4217 1.795872 TGGCAGTTGTGTCGTAATTCG 59.204 47.619 0.00 0.00 41.41 3.34
3709 4218 2.063266 GGCAGTTGTGTCGTAATTCGA 58.937 47.619 0.00 0.00 46.83 3.71
3740 4249 8.305046 ACTAGAGATAATCTGAGAAAACAGCT 57.695 34.615 0.00 0.00 39.20 4.24
3741 4250 9.415008 ACTAGAGATAATCTGAGAAAACAGCTA 57.585 33.333 0.00 0.00 39.20 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 84 8.272545 TCATGGACACTTTCTGAAATTCATAG 57.727 34.615 2.88 0.00 0.00 2.23
162 247 2.225491 GCGTATTGAAAACTGCTCACCA 59.775 45.455 0.00 0.00 0.00 4.17
245 330 4.024977 ACTCCATGCGCAAAATTTGAAAAC 60.025 37.500 17.11 0.00 0.00 2.43
292 377 8.642908 AAAAGAGTTCCTTTATTTTTGGTTCG 57.357 30.769 0.00 0.00 43.90 3.95
336 423 8.083462 GAAACTGGTTTTGTGAGTTTCTTTTT 57.917 30.769 13.90 0.00 46.38 1.94
337 424 7.652300 GAAACTGGTTTTGTGAGTTTCTTTT 57.348 32.000 13.90 0.00 46.38 2.27
358 445 1.961394 ACACTCCACAGCTCGTAGAAA 59.039 47.619 0.00 0.00 34.09 2.52
402 489 6.389830 AAAGTAATGTTGCACATCTGTTCA 57.610 33.333 0.00 0.00 37.97 3.18
449 536 8.681584 AGATGGAATTTGGGATAATCATAGGAA 58.318 33.333 0.00 0.00 0.00 3.36
462 549 7.362662 CGTATACATGAAAGATGGAATTTGGG 58.637 38.462 0.00 0.00 0.00 4.12
484 571 2.480073 GGTTTATGACTGCTACGGCGTA 60.480 50.000 19.80 19.80 42.25 4.42
486 573 0.928229 GGTTTATGACTGCTACGGCG 59.072 55.000 4.80 4.80 42.25 6.46
487 574 0.928229 CGGTTTATGACTGCTACGGC 59.072 55.000 0.00 0.00 39.26 5.68
503 590 1.735376 CGCACTATCTAGGCCACGGT 61.735 60.000 5.01 0.00 0.00 4.83
508 595 1.661821 CGTGCGCACTATCTAGGCC 60.662 63.158 35.27 8.11 0.00 5.19
509 596 0.039074 ATCGTGCGCACTATCTAGGC 60.039 55.000 35.27 8.89 0.00 3.93
523 610 0.812811 TCTACGTCTCCCGGATCGTG 60.813 60.000 20.75 13.67 42.24 4.35
525 612 1.019673 TTTCTACGTCTCCCGGATCG 58.980 55.000 0.73 4.40 42.24 3.69
526 613 3.515330 TTTTTCTACGTCTCCCGGATC 57.485 47.619 0.73 0.00 42.24 3.36
558 645 2.185004 ATTTGTAGCTTCGCCACTGT 57.815 45.000 0.00 0.00 0.00 3.55
567 654 5.167845 CGCCCAACATTTTATTTGTAGCTT 58.832 37.500 0.00 0.00 0.00 3.74
599 686 7.846644 TCAGAATTTGAAAAACAATTGTGCT 57.153 28.000 12.82 0.00 38.36 4.40
644 731 0.095245 CGTAGCACTGTTCGGCATTG 59.905 55.000 0.00 0.00 0.00 2.82
648 735 1.060698 GATTTCGTAGCACTGTTCGGC 59.939 52.381 0.00 0.00 0.00 5.54
651 738 1.724623 TGCGATTTCGTAGCACTGTTC 59.275 47.619 1.55 0.00 42.22 3.18
668 755 1.994779 ACGGTCTAATAACGGTTTGCG 59.005 47.619 0.00 0.00 29.40 4.85
687 774 9.855021 ATTATAGTGTGCAAAGGAATTGTTTAC 57.145 29.630 0.00 0.00 41.32 2.01
792 879 7.540474 TCTAGCTCTCTAGGAGAAACAAAAA 57.460 36.000 11.19 0.00 44.45 1.94
793 880 7.379750 GTTCTAGCTCTCTAGGAGAAACAAAA 58.620 38.462 11.19 0.00 44.45 2.44
794 881 6.349445 CGTTCTAGCTCTCTAGGAGAAACAAA 60.349 42.308 11.19 0.00 44.45 2.83
795 882 5.124138 CGTTCTAGCTCTCTAGGAGAAACAA 59.876 44.000 11.19 0.00 44.45 2.83
796 883 4.636648 CGTTCTAGCTCTCTAGGAGAAACA 59.363 45.833 11.19 0.00 44.45 2.83
797 884 4.637091 ACGTTCTAGCTCTCTAGGAGAAAC 59.363 45.833 11.19 8.30 44.45 2.78
828 915 2.103373 CCTCTCCAGGATTGTCTCGAA 58.897 52.381 0.00 0.00 43.65 3.71
829 916 1.769026 CCTCTCCAGGATTGTCTCGA 58.231 55.000 0.00 0.00 43.65 4.04
830 917 0.103937 GCCTCTCCAGGATTGTCTCG 59.896 60.000 0.00 0.00 43.65 4.04
848 935 3.684788 AGAACGATATGGACAAGTTGTGC 59.315 43.478 19.61 19.61 39.30 4.57
851 938 5.171476 ACAGAGAACGATATGGACAAGTTG 58.829 41.667 0.00 0.00 0.00 3.16
873 969 0.033228 CTCAGATGGGCCGATGAGAC 59.967 60.000 21.47 0.00 41.35 3.36
874 970 1.752358 GCTCAGATGGGCCGATGAGA 61.752 60.000 27.11 9.81 41.35 3.27
876 972 1.340399 AAGCTCAGATGGGCCGATGA 61.340 55.000 4.37 0.00 0.00 2.92
907 1003 2.330216 AGGGTAATCTTCGGATCCCTG 58.670 52.381 6.06 0.00 43.28 4.45
955 1060 0.262876 GGGGGCTCTGATTGGGATTT 59.737 55.000 0.00 0.00 0.00 2.17
1148 1266 3.036959 GGAGGAGGGGGAGGGAGA 61.037 72.222 0.00 0.00 0.00 3.71
1149 1267 3.039526 AGGAGGAGGGGGAGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
1150 1268 3.036959 GAGGAGGAGGGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
1151 1269 4.179599 GGAGGAGGAGGGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
1163 1281 0.544223 CGTCAGAGAGAGAGGGAGGA 59.456 60.000 0.00 0.00 0.00 3.71
1168 1286 0.732571 GAGCACGTCAGAGAGAGAGG 59.267 60.000 0.00 0.00 0.00 3.69
1179 1316 1.374758 CCAAGGGTGAGAGCACGTC 60.375 63.158 0.00 0.00 46.09 4.34
1180 1317 2.743718 CCAAGGGTGAGAGCACGT 59.256 61.111 0.00 0.00 46.09 4.49
1182 1319 2.743928 CGCCAAGGGTGAGAGCAC 60.744 66.667 0.00 0.00 44.39 4.40
1183 1320 2.818169 AACGCCAAGGGTGAGAGCA 61.818 57.895 2.32 0.00 36.58 4.26
1184 1321 2.032681 AACGCCAAGGGTGAGAGC 59.967 61.111 2.32 0.00 36.58 4.09
1235 1372 4.715523 ACGTCCCCCGCCATGTTG 62.716 66.667 0.00 0.00 41.42 3.33
1412 1549 3.542676 ACGACGGTCTTGGTGGCA 61.543 61.111 6.57 0.00 0.00 4.92
1436 1573 4.224147 TCCAATTCAATCCGGTACTCTCAA 59.776 41.667 0.00 0.00 0.00 3.02
1437 1574 3.772572 TCCAATTCAATCCGGTACTCTCA 59.227 43.478 0.00 0.00 0.00 3.27
1438 1575 4.402056 TCCAATTCAATCCGGTACTCTC 57.598 45.455 0.00 0.00 0.00 3.20
1439 1576 5.373812 AATCCAATTCAATCCGGTACTCT 57.626 39.130 0.00 0.00 0.00 3.24
1440 1577 5.588648 TGAAATCCAATTCAATCCGGTACTC 59.411 40.000 0.00 0.00 36.42 2.59
1441 1578 5.505780 TGAAATCCAATTCAATCCGGTACT 58.494 37.500 0.00 0.00 36.42 2.73
1442 1579 5.588648 TCTGAAATCCAATTCAATCCGGTAC 59.411 40.000 0.00 0.00 38.75 3.34
1443 1580 5.750524 TCTGAAATCCAATTCAATCCGGTA 58.249 37.500 0.00 0.00 38.75 4.02
1444 1581 4.599041 TCTGAAATCCAATTCAATCCGGT 58.401 39.130 0.00 0.00 38.75 5.28
1446 1583 6.698766 GGAAATCTGAAATCCAATTCAATCCG 59.301 38.462 7.10 0.00 38.75 4.18
1448 1585 7.709613 CCTGGAAATCTGAAATCCAATTCAATC 59.290 37.037 13.64 0.00 42.41 2.67
1450 1587 6.574859 GCCTGGAAATCTGAAATCCAATTCAA 60.575 38.462 13.64 0.00 42.41 2.69
1451 1588 5.105228 GCCTGGAAATCTGAAATCCAATTCA 60.105 40.000 13.64 0.00 42.41 2.57
1452 1589 5.128335 AGCCTGGAAATCTGAAATCCAATTC 59.872 40.000 13.64 7.54 42.41 2.17
1453 1590 5.028131 AGCCTGGAAATCTGAAATCCAATT 58.972 37.500 13.64 3.05 42.41 2.32
1457 1594 3.766051 ACAAGCCTGGAAATCTGAAATCC 59.234 43.478 0.00 5.42 0.00 3.01
1458 1595 4.219288 ACACAAGCCTGGAAATCTGAAATC 59.781 41.667 0.00 0.00 0.00 2.17
1459 1596 4.154942 ACACAAGCCTGGAAATCTGAAAT 58.845 39.130 0.00 0.00 0.00 2.17
1467 1604 1.140312 AGAGGACACAAGCCTGGAAA 58.860 50.000 0.00 0.00 35.44 3.13
1468 1605 1.902508 CTAGAGGACACAAGCCTGGAA 59.097 52.381 0.00 0.00 35.44 3.53
1469 1606 1.077169 TCTAGAGGACACAAGCCTGGA 59.923 52.381 0.00 0.00 35.44 3.86
1470 1607 1.561643 TCTAGAGGACACAAGCCTGG 58.438 55.000 0.00 0.00 35.44 4.45
1474 1611 5.300539 TCTGTCATATCTAGAGGACACAAGC 59.699 44.000 16.39 0.00 35.51 4.01
1475 1612 6.545666 AGTCTGTCATATCTAGAGGACACAAG 59.454 42.308 16.39 10.14 35.51 3.16
1476 1613 6.427441 AGTCTGTCATATCTAGAGGACACAA 58.573 40.000 16.39 8.46 35.51 3.33
1477 1614 6.007485 AGTCTGTCATATCTAGAGGACACA 57.993 41.667 16.39 7.77 35.51 3.72
1478 1615 6.296026 AGAGTCTGTCATATCTAGAGGACAC 58.704 44.000 16.39 10.52 35.51 3.67
1479 1616 6.508030 AGAGTCTGTCATATCTAGAGGACA 57.492 41.667 18.24 18.24 37.89 4.02
1480 1617 7.817418 AAAGAGTCTGTCATATCTAGAGGAC 57.183 40.000 12.60 12.60 0.00 3.85
1561 1717 1.672030 CATCAGCAACTCGGTGGCA 60.672 57.895 6.24 0.00 43.59 4.92
1564 1720 2.315925 ATACCATCAGCAACTCGGTG 57.684 50.000 0.00 0.00 44.83 4.94
1572 1728 3.132646 GGCATCCAAAAATACCATCAGCA 59.867 43.478 0.00 0.00 0.00 4.41
1573 1729 3.385755 AGGCATCCAAAAATACCATCAGC 59.614 43.478 0.00 0.00 0.00 4.26
1575 1731 4.608269 TCAGGCATCCAAAAATACCATCA 58.392 39.130 0.00 0.00 0.00 3.07
1587 1743 3.090210 ACACAATTCATCAGGCATCCA 57.910 42.857 0.00 0.00 0.00 3.41
1601 1757 7.726738 ACCTTGTGGTACCTAAAATTACACAAT 59.273 33.333 14.36 0.00 46.43 2.71
1603 1759 6.603224 ACCTTGTGGTACCTAAAATTACACA 58.397 36.000 14.36 2.47 46.43 3.72
1843 2003 5.234329 ACATATTTAGACAGACGCCAAATCG 59.766 40.000 0.00 0.00 0.00 3.34
1900 2209 4.760204 AGCTGCAGTTTAAAATCGGTTACT 59.240 37.500 16.64 0.00 0.00 2.24
2008 2322 5.238583 AGTATACAAAGACACTGAAGCACC 58.761 41.667 5.50 0.00 0.00 5.01
2030 2344 7.042658 GCAGACCATAGTAATTAAACCTCGAAG 60.043 40.741 0.00 0.00 0.00 3.79
2034 2348 7.859325 TTGCAGACCATAGTAATTAAACCTC 57.141 36.000 0.00 0.00 0.00 3.85
2048 2362 6.549433 AATTTGGTGAATATTGCAGACCAT 57.451 33.333 0.00 0.00 36.59 3.55
2049 2363 5.999205 AATTTGGTGAATATTGCAGACCA 57.001 34.783 0.00 0.00 34.85 4.02
2050 2364 6.311200 GTCAAATTTGGTGAATATTGCAGACC 59.689 38.462 17.90 0.00 0.00 3.85
2051 2365 7.092716 AGTCAAATTTGGTGAATATTGCAGAC 58.907 34.615 17.90 3.89 0.00 3.51
2052 2366 7.230849 AGTCAAATTTGGTGAATATTGCAGA 57.769 32.000 17.90 0.00 0.00 4.26
2053 2367 8.984891 TTAGTCAAATTTGGTGAATATTGCAG 57.015 30.769 17.90 0.00 0.00 4.41
2054 2368 9.368674 CATTAGTCAAATTTGGTGAATATTGCA 57.631 29.630 17.90 0.00 0.00 4.08
2055 2369 9.585099 TCATTAGTCAAATTTGGTGAATATTGC 57.415 29.630 17.90 0.00 31.76 3.56
2155 2469 1.267806 GCACTCAATCACCCAACTGTG 59.732 52.381 0.00 0.00 37.59 3.66
2235 2551 9.860650 TTGTGATATTATTAAGGGCAATACTGT 57.139 29.630 0.00 0.00 0.00 3.55
2449 2781 9.613428 AGACAATGCAGTAGCTAAATAACATTA 57.387 29.630 0.00 0.00 42.74 1.90
2543 2876 8.086522 ACCAGCTGATGCATAATGAATTTTATC 58.913 33.333 17.39 0.00 42.74 1.75
2552 2885 4.023450 CCAACTACCAGCTGATGCATAATG 60.023 45.833 17.39 3.69 42.74 1.90
2556 2890 1.561076 TCCAACTACCAGCTGATGCAT 59.439 47.619 17.39 0.00 42.74 3.96
2564 2898 4.440112 GGTTAATGCATTCCAACTACCAGC 60.440 45.833 16.86 0.00 0.00 4.85
2612 3088 1.548582 GGATGGCCCCCAATACTCATG 60.549 57.143 0.00 0.00 36.95 3.07
2722 3206 6.803807 GTGTCCTACTCTTTTGAATCAATTGC 59.196 38.462 0.00 0.00 0.00 3.56
2724 3208 7.175641 CCTGTGTCCTACTCTTTTGAATCAATT 59.824 37.037 0.00 0.00 0.00 2.32
2736 3220 6.681729 TTCAATTTACCTGTGTCCTACTCT 57.318 37.500 0.00 0.00 0.00 3.24
2777 3261 5.483583 AGGGATGATCGGGAATTTTGAAAAA 59.516 36.000 0.00 0.00 0.00 1.94
2810 3294 8.841300 GGAAAAATGGCAAAAGGTAAATTAACA 58.159 29.630 0.00 0.00 0.00 2.41
2980 3484 6.452242 ACATAAGTTACGACATGAGACACAA 58.548 36.000 0.00 0.00 0.00 3.33
3004 3510 5.822519 AGTTCACTTTACAAGCATCACAGAA 59.177 36.000 0.00 0.00 0.00 3.02
3033 3539 3.670625 CCCGGAACTTGTAGTTTCATCA 58.329 45.455 0.73 0.00 38.80 3.07
3122 3631 5.107109 TGTTACAATGCACAACTGATCAC 57.893 39.130 0.00 0.00 0.00 3.06
3127 3636 4.746115 AGCAAATGTTACAATGCACAACTG 59.254 37.500 22.18 0.00 41.18 3.16
3155 3664 5.008911 TCCTTTCACTTAAAACGGCCTTAAC 59.991 40.000 0.00 0.00 0.00 2.01
3172 3681 5.309638 TCACCGATAACACAATTCCTTTCA 58.690 37.500 0.00 0.00 0.00 2.69
3174 3683 5.181245 CACTCACCGATAACACAATTCCTTT 59.819 40.000 0.00 0.00 0.00 3.11
3234 3743 3.496884 TCCAAAGCAACTTAGTTACGCTG 59.503 43.478 10.08 2.67 32.14 5.18
3238 3747 8.920509 TTTTTCTTCCAAAGCAACTTAGTTAC 57.079 30.769 0.00 0.00 0.00 2.50
3288 3797 2.740714 GGAATCTGACACGCACCGC 61.741 63.158 0.00 0.00 0.00 5.68
3291 3800 1.400242 GCAAAGGAATCTGACACGCAC 60.400 52.381 0.00 0.00 0.00 5.34
3292 3801 0.874390 GCAAAGGAATCTGACACGCA 59.126 50.000 0.00 0.00 0.00 5.24
3293 3802 0.169009 GGCAAAGGAATCTGACACGC 59.831 55.000 0.00 0.00 0.00 5.34
3294 3803 1.813513 AGGCAAAGGAATCTGACACG 58.186 50.000 0.00 0.00 0.00 4.49
3328 3837 6.274157 TGCAATACGGAATTTTACCATGTT 57.726 33.333 0.00 0.00 0.00 2.71
3329 3838 5.906113 TGCAATACGGAATTTTACCATGT 57.094 34.783 0.00 0.00 0.00 3.21
3330 3839 7.769272 AAATGCAATACGGAATTTTACCATG 57.231 32.000 0.00 0.00 0.00 3.66
3331 3840 8.785329 AAAAATGCAATACGGAATTTTACCAT 57.215 26.923 0.00 0.00 33.16 3.55
3332 3841 7.872993 TGAAAAATGCAATACGGAATTTTACCA 59.127 29.630 0.00 0.00 33.16 3.25
3343 3852 3.609373 CACAGCCTGAAAAATGCAATACG 59.391 43.478 0.00 0.00 0.00 3.06
3345 3854 4.280425 TCACACAGCCTGAAAAATGCAATA 59.720 37.500 0.00 0.00 0.00 1.90
3351 3860 2.694628 TGCTTCACACAGCCTGAAAAAT 59.305 40.909 0.00 0.00 39.25 1.82
3356 3865 0.671472 CGATGCTTCACACAGCCTGA 60.671 55.000 0.00 0.00 39.25 3.86
3432 3941 4.087182 CTCACTAGGTTACCAAGGAGTGA 58.913 47.826 19.71 19.71 40.62 3.41
3450 3959 3.951979 CAATCTTGCCCGTAATCTCAC 57.048 47.619 0.00 0.00 0.00 3.51
3472 3981 1.137675 GGAAATTCCCAGAGCAATGGC 59.862 52.381 0.00 0.00 39.17 4.40
3504 4013 1.432251 CACCTACCAGTCTACGCCG 59.568 63.158 0.00 0.00 0.00 6.46
3505 4014 0.969409 ACCACCTACCAGTCTACGCC 60.969 60.000 0.00 0.00 0.00 5.68
3506 4015 0.893447 AACCACCTACCAGTCTACGC 59.107 55.000 0.00 0.00 0.00 4.42
3507 4016 3.760684 AGTAAACCACCTACCAGTCTACG 59.239 47.826 0.00 0.00 0.00 3.51
3508 4017 5.244626 TCAAGTAAACCACCTACCAGTCTAC 59.755 44.000 0.00 0.00 0.00 2.59
3509 4018 5.396485 TCAAGTAAACCACCTACCAGTCTA 58.604 41.667 0.00 0.00 0.00 2.59
3510 4019 4.228824 TCAAGTAAACCACCTACCAGTCT 58.771 43.478 0.00 0.00 0.00 3.24
3511 4020 4.612264 TCAAGTAAACCACCTACCAGTC 57.388 45.455 0.00 0.00 0.00 3.51
3512 4021 4.595781 TGATCAAGTAAACCACCTACCAGT 59.404 41.667 0.00 0.00 0.00 4.00
3513 4022 5.160607 TGATCAAGTAAACCACCTACCAG 57.839 43.478 0.00 0.00 0.00 4.00
3514 4023 5.570205 TTGATCAAGTAAACCACCTACCA 57.430 39.130 3.38 0.00 0.00 3.25
3515 4024 5.357032 CCATTGATCAAGTAAACCACCTACC 59.643 44.000 14.54 0.00 0.00 3.18
3516 4025 5.357032 CCCATTGATCAAGTAAACCACCTAC 59.643 44.000 14.54 0.00 0.00 3.18
3517 4026 5.251932 TCCCATTGATCAAGTAAACCACCTA 59.748 40.000 14.54 0.00 0.00 3.08
3518 4027 4.044065 TCCCATTGATCAAGTAAACCACCT 59.956 41.667 14.54 0.00 0.00 4.00
3519 4028 4.157840 GTCCCATTGATCAAGTAAACCACC 59.842 45.833 14.54 0.00 0.00 4.61
3520 4029 4.142687 CGTCCCATTGATCAAGTAAACCAC 60.143 45.833 14.54 3.47 0.00 4.16
3521 4030 4.006989 CGTCCCATTGATCAAGTAAACCA 58.993 43.478 14.54 0.00 0.00 3.67
3522 4031 3.377172 CCGTCCCATTGATCAAGTAAACC 59.623 47.826 14.54 0.00 0.00 3.27
3523 4032 3.181500 GCCGTCCCATTGATCAAGTAAAC 60.181 47.826 14.54 8.65 0.00 2.01
3524 4033 3.013921 GCCGTCCCATTGATCAAGTAAA 58.986 45.455 14.54 0.00 0.00 2.01
3525 4034 2.026729 TGCCGTCCCATTGATCAAGTAA 60.027 45.455 14.54 0.00 0.00 2.24
3526 4035 1.557371 TGCCGTCCCATTGATCAAGTA 59.443 47.619 14.54 0.00 0.00 2.24
3527 4036 0.327924 TGCCGTCCCATTGATCAAGT 59.672 50.000 14.54 0.00 0.00 3.16
3528 4037 1.683943 ATGCCGTCCCATTGATCAAG 58.316 50.000 14.54 6.16 0.00 3.02
3529 4038 2.172505 ACTATGCCGTCCCATTGATCAA 59.827 45.455 11.26 11.26 0.00 2.57
3530 4039 1.768275 ACTATGCCGTCCCATTGATCA 59.232 47.619 0.00 0.00 0.00 2.92
3531 4040 2.549754 CAACTATGCCGTCCCATTGATC 59.450 50.000 0.00 0.00 0.00 2.92
3532 4041 2.092429 ACAACTATGCCGTCCCATTGAT 60.092 45.455 0.00 0.00 0.00 2.57
3533 4042 1.280710 ACAACTATGCCGTCCCATTGA 59.719 47.619 0.00 0.00 0.00 2.57
3534 4043 1.750193 ACAACTATGCCGTCCCATTG 58.250 50.000 0.00 0.00 0.00 2.82
3535 4044 2.091541 CAACAACTATGCCGTCCCATT 58.908 47.619 0.00 0.00 0.00 3.16
3536 4045 1.280710 TCAACAACTATGCCGTCCCAT 59.719 47.619 0.00 0.00 0.00 4.00
3537 4046 0.687920 TCAACAACTATGCCGTCCCA 59.312 50.000 0.00 0.00 0.00 4.37
3538 4047 1.670811 CATCAACAACTATGCCGTCCC 59.329 52.381 0.00 0.00 0.00 4.46
3539 4048 1.064060 GCATCAACAACTATGCCGTCC 59.936 52.381 0.00 0.00 42.13 4.79
3540 4049 2.458592 GCATCAACAACTATGCCGTC 57.541 50.000 0.00 0.00 42.13 4.79
3541 4050 2.615240 TGAGCATCAACAACTATGCCGT 60.615 45.455 3.80 0.00 45.97 5.68
3559 4068 8.233190 GTGAGGAGTTCAAATTAACATTCTGAG 58.767 37.037 0.00 0.00 37.61 3.35
3575 4084 0.980423 AAGGCTCAGGTGAGGAGTTC 59.020 55.000 9.03 0.00 42.29 3.01
3604 4113 8.915871 TTACAGATTTCATAGCAAAATCAAGC 57.084 30.769 10.27 0.00 42.81 4.01
3613 4122 7.775093 ACCAGCTATTTTACAGATTTCATAGCA 59.225 33.333 10.69 0.00 40.99 3.49
3614 4123 8.159344 ACCAGCTATTTTACAGATTTCATAGC 57.841 34.615 0.00 0.00 39.52 2.97
3631 4140 3.788227 TGTCTGTTTCCAACCAGCTAT 57.212 42.857 0.00 0.00 0.00 2.97
3634 4143 2.162408 GCTATGTCTGTTTCCAACCAGC 59.838 50.000 0.00 0.00 0.00 4.85
3672 4181 3.896888 ACTGCCACATGAAAATCTTTCCA 59.103 39.130 0.00 0.00 0.00 3.53
3674 4183 5.176223 CACAACTGCCACATGAAAATCTTTC 59.824 40.000 0.00 0.00 0.00 2.62
3677 4186 3.638160 ACACAACTGCCACATGAAAATCT 59.362 39.130 0.00 0.00 0.00 2.40
3678 4187 3.981211 ACACAACTGCCACATGAAAATC 58.019 40.909 0.00 0.00 0.00 2.17
3679 4188 3.550639 CGACACAACTGCCACATGAAAAT 60.551 43.478 0.00 0.00 0.00 1.82
3680 4189 2.223456 CGACACAACTGCCACATGAAAA 60.223 45.455 0.00 0.00 0.00 2.29
3681 4190 1.333308 CGACACAACTGCCACATGAAA 59.667 47.619 0.00 0.00 0.00 2.69
3682 4191 0.943673 CGACACAACTGCCACATGAA 59.056 50.000 0.00 0.00 0.00 2.57
3683 4192 0.179059 ACGACACAACTGCCACATGA 60.179 50.000 0.00 0.00 0.00 3.07
3684 4193 1.507562 TACGACACAACTGCCACATG 58.492 50.000 0.00 0.00 0.00 3.21
3685 4194 2.248280 TTACGACACAACTGCCACAT 57.752 45.000 0.00 0.00 0.00 3.21
3686 4195 2.248280 ATTACGACACAACTGCCACA 57.752 45.000 0.00 0.00 0.00 4.17
3687 4196 2.411031 CGAATTACGACACAACTGCCAC 60.411 50.000 0.00 0.00 45.77 5.01
3688 4197 1.795872 CGAATTACGACACAACTGCCA 59.204 47.619 0.00 0.00 45.77 4.92
3689 4198 2.063266 TCGAATTACGACACAACTGCC 58.937 47.619 0.00 0.00 46.45 4.85
3714 4223 9.415008 AGCTGTTTTCTCAGATTATCTCTAGTA 57.585 33.333 0.00 0.00 37.61 1.82
3715 4224 8.305046 AGCTGTTTTCTCAGATTATCTCTAGT 57.695 34.615 0.00 0.00 37.61 2.57


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

AutoCloner maintained by Alex Coulton.