Multiple sequence alignment - TraesCS4D01G277400

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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 TraesCS4D01G277400 chr4D 100.000 5959 0 0 1 5959 449724393 449730351 0.000000e+00 11005
1 TraesCS4D01G277400 chr4D 94.231 104 5 1 1512 1615 230489641 230489539 2.220000e-34 158
2 TraesCS4D01G277400 chr4A 92.458 4296 182 63 1611 5870 17267323 17263134 0.000000e+00 6008
3 TraesCS4D01G277400 chr4A 94.933 967 29 8 547 1502 17268308 17267351 0.000000e+00 1496
4 TraesCS4D01G277400 chr4A 92.012 338 24 3 1 338 17287729 17287395 6.990000e-129 472
5 TraesCS4D01G277400 chr4A 90.000 120 10 2 433 550 17287391 17287272 2.880000e-33 154
6 TraesCS4D01G277400 chr4B 96.217 2961 90 12 1611 4560 562349534 562352483 0.000000e+00 4828
7 TraesCS4D01G277400 chr4B 91.254 1395 73 21 4577 5959 562352665 562354022 0.000000e+00 1855
8 TraesCS4D01G277400 chr4B 94.889 763 23 5 741 1495 562348745 562349499 0.000000e+00 1179
9 TraesCS4D01G277400 chr4B 92.388 762 39 12 1 750 562343017 562343771 0.000000e+00 1068
10 TraesCS4D01G277400 chr2B 94.495 109 6 0 1511 1619 208229174 208229066 1.030000e-37 169
11 TraesCS4D01G277400 chr2B 91.892 111 9 0 1510 1620 690805806 690805916 8.000000e-34 156
12 TraesCS4D01G277400 chr7B 92.241 116 8 1 1501 1616 159510712 159510598 4.780000e-36 163
13 TraesCS4D01G277400 chr7B 93.458 107 6 1 1512 1618 413721639 413721534 2.220000e-34 158
14 TraesCS4D01G277400 chr5D 95.098 102 5 0 1512 1613 462455214 462455315 1.720000e-35 161
15 TraesCS4D01G277400 chr5D 90.435 115 10 1 1506 1620 513514556 513514669 3.720000e-32 150
16 TraesCS4D01G277400 chr7D 94.286 105 5 1 1508 1612 407716637 407716534 6.180000e-35 159
17 TraesCS4D01G277400 chr6B 93.519 108 5 2 1512 1619 38619594 38619699 6.180000e-35 159


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 TraesCS4D01G277400 chr4D 449724393 449730351 5958 False 11005.000000 11005 100.0000 1 5959 1 chr4D.!!$F1 5958
1 TraesCS4D01G277400 chr4A 17263134 17268308 5174 True 3752.000000 6008 93.6955 547 5870 2 chr4A.!!$R1 5323
2 TraesCS4D01G277400 chr4B 562348745 562354022 5277 False 2620.666667 4828 94.1200 741 5959 3 chr4B.!!$F2 5218
3 TraesCS4D01G277400 chr4B 562343017 562343771 754 False 1068.000000 1068 92.3880 1 750 1 chr4B.!!$F1 749

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
57 59 0.106149 ACACCCCACTTCTGAACGTC 59.894 55.000 0.00 0.0 0.00 4.34 F
1518 1563 0.108615 CGCTGCACTGGTTAGCTACT 60.109 55.000 0.00 0.0 35.36 2.57 F
1531 1576 0.252103 AGCTACTCCCTCCGTTCCAA 60.252 55.000 0.00 0.0 0.00 3.53 F
1532 1577 0.611714 GCTACTCCCTCCGTTCCAAA 59.388 55.000 0.00 0.0 0.00 3.28 F
2891 2942 0.835276 ATGCTGCACTAGATCTGCCA 59.165 50.000 3.57 0.0 33.36 4.92 F
3518 3573 4.148128 GTCACCATGACATCTGGATTCT 57.852 45.455 1.99 0.0 46.22 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1597 1642 0.105039 CAATCTACTCCCTCCGTGCC 59.895 60.000 0.0 0.00 0.00 5.01 R
2502 2553 4.058124 TGCTTTGGATCAGTATCATACGC 58.942 43.478 0.0 0.00 33.41 4.42 R
3349 3400 4.908736 AGGATGAACGAATGCATAAAACG 58.091 39.130 0.0 6.79 0.00 3.60 R
3358 3409 6.749139 TGTTAGGATCTAGGATGAACGAATG 58.251 40.000 0.0 0.00 0.00 2.67 R
3960 4025 2.962421 CCCTAAGGGTCAAAAACTTGCA 59.038 45.455 0.0 0.00 38.25 4.08 R
5350 5592 1.089920 CAGATTTCTCAGGCAACGGG 58.910 55.000 0.0 0.00 46.39 5.28 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
40 41 7.836479 TGAATGAATGGCCAATTATATGACA 57.164 32.000 10.96 0.00 0.00 3.58
43 44 4.832266 TGAATGGCCAATTATATGACACCC 59.168 41.667 10.96 0.00 0.00 4.61
57 59 0.106149 ACACCCCACTTCTGAACGTC 59.894 55.000 0.00 0.00 0.00 4.34
66 68 3.247648 CACTTCTGAACGTCGGTGATTTT 59.752 43.478 0.00 0.00 0.00 1.82
67 69 3.247648 ACTTCTGAACGTCGGTGATTTTG 59.752 43.478 0.00 0.00 0.00 2.44
68 70 1.529438 TCTGAACGTCGGTGATTTTGC 59.471 47.619 0.00 0.00 0.00 3.68
70 72 1.944024 TGAACGTCGGTGATTTTGCTT 59.056 42.857 0.00 0.00 0.00 3.91
71 73 2.286713 TGAACGTCGGTGATTTTGCTTG 60.287 45.455 0.00 0.00 0.00 4.01
72 74 1.305201 ACGTCGGTGATTTTGCTTGT 58.695 45.000 0.00 0.00 0.00 3.16
73 75 1.673920 ACGTCGGTGATTTTGCTTGTT 59.326 42.857 0.00 0.00 0.00 2.83
117 119 8.778059 TGATACCTTGAACTAATGGAAGGTTAT 58.222 33.333 7.54 0.96 44.75 1.89
126 128 7.645058 ACTAATGGAAGGTTATTGTTGATGG 57.355 36.000 0.00 0.00 0.00 3.51
157 159 2.359214 TGTGTTGTAGCCGCATGAAAAA 59.641 40.909 0.00 0.00 0.00 1.94
164 166 0.737367 GCCGCATGAAAAAGCCTTCC 60.737 55.000 0.00 0.00 0.00 3.46
230 232 0.605319 TCAACCTTGCACCATCGGAC 60.605 55.000 0.00 0.00 0.00 4.79
238 240 1.005512 CACCATCGGACGACCACAA 60.006 57.895 4.48 0.00 35.59 3.33
303 305 1.878953 TGAGAACCGGCTTCTTTGTC 58.121 50.000 16.93 6.39 39.53 3.18
308 310 3.169198 CGGCTTCTTTGTCGGAGC 58.831 61.111 0.00 0.00 0.00 4.70
341 343 4.001618 TTGTCGATGACAACCATCTGAA 57.998 40.909 8.21 0.00 45.88 3.02
379 381 2.356553 TTGGCACGCACCTACGAC 60.357 61.111 0.00 0.00 36.70 4.34
398 400 3.736720 GACGAGAAACCCTAACCTTGTT 58.263 45.455 0.00 0.00 0.00 2.83
399 401 3.473625 ACGAGAAACCCTAACCTTGTTG 58.526 45.455 0.00 0.00 0.00 3.33
400 402 3.118149 ACGAGAAACCCTAACCTTGTTGT 60.118 43.478 0.00 0.00 0.00 3.32
425 427 1.063567 AGGAGACGGCAGGAATCTACT 60.064 52.381 0.00 0.00 0.00 2.57
429 431 1.338655 GACGGCAGGAATCTACTCTCC 59.661 57.143 0.00 0.00 0.00 3.71
430 432 1.342076 ACGGCAGGAATCTACTCTCCA 60.342 52.381 0.00 0.00 33.83 3.86
441 443 2.093075 TCTACTCTCCATCGACTCCGTT 60.093 50.000 0.00 0.00 37.05 4.44
457 459 2.159476 TCCGTTCTAATGGACGAACTCG 60.159 50.000 0.00 0.00 39.13 4.18
470 472 1.296727 GAACTCGGATTAAAGCCCGG 58.703 55.000 12.37 0.00 45.36 5.73
516 518 2.034879 CATCCGCTGAAACGCCACT 61.035 57.895 0.00 0.00 0.00 4.00
708 720 1.102809 TGGCCTTCTGTGCTGTTGTG 61.103 55.000 3.32 0.00 0.00 3.33
755 767 1.643868 CCGCCTTAGAACATTGCGCA 61.644 55.000 5.66 5.66 43.59 6.09
761 773 0.320858 TAGAACATTGCGCACGGGAA 60.321 50.000 11.12 0.00 0.00 3.97
766 778 2.690778 ATTGCGCACGGGAAGCTTC 61.691 57.895 18.54 18.54 0.00 3.86
782 794 1.202076 GCTTCATCGTGCACTTTAGCC 60.202 52.381 16.19 0.00 0.00 3.93
1425 1453 0.895559 CAGGAAGGTTTGGTCAGGCC 60.896 60.000 0.00 0.00 37.90 5.19
1426 1454 1.971695 GGAAGGTTTGGTCAGGCCG 60.972 63.158 0.00 0.00 41.21 6.13
1517 1562 1.696832 GCGCTGCACTGGTTAGCTAC 61.697 60.000 0.00 0.00 35.36 3.58
1518 1563 0.108615 CGCTGCACTGGTTAGCTACT 60.109 55.000 0.00 0.00 35.36 2.57
1519 1564 1.646189 GCTGCACTGGTTAGCTACTC 58.354 55.000 0.00 0.00 34.70 2.59
1520 1565 1.740718 GCTGCACTGGTTAGCTACTCC 60.741 57.143 0.00 0.00 34.70 3.85
1521 1566 0.902531 TGCACTGGTTAGCTACTCCC 59.097 55.000 10.51 4.49 0.00 4.30
1522 1567 1.196012 GCACTGGTTAGCTACTCCCT 58.804 55.000 10.51 0.00 0.00 4.20
1523 1568 1.137282 GCACTGGTTAGCTACTCCCTC 59.863 57.143 10.51 0.00 0.00 4.30
1524 1569 1.757699 CACTGGTTAGCTACTCCCTCC 59.242 57.143 10.51 1.17 0.00 4.30
1525 1570 1.033574 CTGGTTAGCTACTCCCTCCG 58.966 60.000 10.51 0.00 0.00 4.63
1526 1571 0.333993 TGGTTAGCTACTCCCTCCGT 59.666 55.000 10.51 0.00 0.00 4.69
1527 1572 1.272872 TGGTTAGCTACTCCCTCCGTT 60.273 52.381 10.51 0.00 0.00 4.44
1528 1573 1.408340 GGTTAGCTACTCCCTCCGTTC 59.592 57.143 0.00 0.00 0.00 3.95
1529 1574 1.408340 GTTAGCTACTCCCTCCGTTCC 59.592 57.143 0.00 0.00 0.00 3.62
1530 1575 0.627451 TAGCTACTCCCTCCGTTCCA 59.373 55.000 0.00 0.00 0.00 3.53
1531 1576 0.252103 AGCTACTCCCTCCGTTCCAA 60.252 55.000 0.00 0.00 0.00 3.53
1532 1577 0.611714 GCTACTCCCTCCGTTCCAAA 59.388 55.000 0.00 0.00 0.00 3.28
1533 1578 1.002773 GCTACTCCCTCCGTTCCAAAA 59.997 52.381 0.00 0.00 0.00 2.44
1534 1579 2.355818 GCTACTCCCTCCGTTCCAAAAT 60.356 50.000 0.00 0.00 0.00 1.82
1535 1580 3.118519 GCTACTCCCTCCGTTCCAAAATA 60.119 47.826 0.00 0.00 0.00 1.40
1536 1581 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
1537 1582 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
1538 1583 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
1539 1584 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
1540 1585 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
1541 1586 4.226394 TCCCTCCGTTCCAAAATAGATGAA 59.774 41.667 0.00 0.00 0.00 2.57
1542 1587 4.335594 CCCTCCGTTCCAAAATAGATGAAC 59.664 45.833 0.00 0.00 35.03 3.18
1543 1588 4.335594 CCTCCGTTCCAAAATAGATGAACC 59.664 45.833 0.00 0.00 34.93 3.62
1544 1589 4.912586 TCCGTTCCAAAATAGATGAACCA 58.087 39.130 0.00 0.00 34.93 3.67
1545 1590 5.317808 TCCGTTCCAAAATAGATGAACCAA 58.682 37.500 0.00 0.00 34.93 3.67
1546 1591 5.182380 TCCGTTCCAAAATAGATGAACCAAC 59.818 40.000 0.00 0.00 34.93 3.77
1547 1592 5.183140 CCGTTCCAAAATAGATGAACCAACT 59.817 40.000 0.00 0.00 34.93 3.16
1548 1593 6.294508 CCGTTCCAAAATAGATGAACCAACTT 60.295 38.462 0.00 0.00 34.93 2.66
1549 1594 7.145323 CGTTCCAAAATAGATGAACCAACTTT 58.855 34.615 0.00 0.00 34.93 2.66
1550 1595 7.114811 CGTTCCAAAATAGATGAACCAACTTTG 59.885 37.037 0.00 0.00 34.93 2.77
1551 1596 7.595819 TCCAAAATAGATGAACCAACTTTGT 57.404 32.000 0.00 0.00 0.00 2.83
1552 1597 8.698973 TCCAAAATAGATGAACCAACTTTGTA 57.301 30.769 0.00 0.00 0.00 2.41
1553 1598 8.573035 TCCAAAATAGATGAACCAACTTTGTAC 58.427 33.333 0.00 0.00 0.00 2.90
1554 1599 8.576442 CCAAAATAGATGAACCAACTTTGTACT 58.424 33.333 0.00 0.00 0.00 2.73
1560 1605 8.747538 AGATGAACCAACTTTGTACTAACTTT 57.252 30.769 0.00 0.00 0.00 2.66
1561 1606 8.621286 AGATGAACCAACTTTGTACTAACTTTG 58.379 33.333 0.00 0.00 0.00 2.77
1562 1607 7.690952 TGAACCAACTTTGTACTAACTTTGT 57.309 32.000 0.00 0.00 0.00 2.83
1563 1608 8.789825 TGAACCAACTTTGTACTAACTTTGTA 57.210 30.769 0.00 0.00 0.00 2.41
1564 1609 8.667463 TGAACCAACTTTGTACTAACTTTGTAC 58.333 33.333 6.58 6.58 40.27 2.90
1565 1610 8.797350 AACCAACTTTGTACTAACTTTGTACT 57.203 30.769 12.73 0.00 40.44 2.73
1566 1611 9.889128 AACCAACTTTGTACTAACTTTGTACTA 57.111 29.630 12.73 4.86 40.44 1.82
1567 1612 9.889128 ACCAACTTTGTACTAACTTTGTACTAA 57.111 29.630 12.73 10.75 40.44 2.24
1598 1643 9.823647 AGTACATAGTTGACTCATCTATTTTGG 57.176 33.333 6.84 0.97 27.74 3.28
1599 1644 7.559590 ACATAGTTGACTCATCTATTTTGGC 57.440 36.000 6.84 0.00 27.74 4.52
1600 1645 7.112122 ACATAGTTGACTCATCTATTTTGGCA 58.888 34.615 6.84 0.00 27.74 4.92
1601 1646 5.886960 AGTTGACTCATCTATTTTGGCAC 57.113 39.130 0.00 0.00 0.00 5.01
1602 1647 4.393062 AGTTGACTCATCTATTTTGGCACG 59.607 41.667 0.00 0.00 0.00 5.34
1603 1648 3.270027 TGACTCATCTATTTTGGCACGG 58.730 45.455 0.00 0.00 0.00 4.94
1604 1649 3.055458 TGACTCATCTATTTTGGCACGGA 60.055 43.478 0.00 0.00 0.00 4.69
1605 1650 3.535561 ACTCATCTATTTTGGCACGGAG 58.464 45.455 0.00 0.00 0.00 4.63
1606 1651 2.874701 CTCATCTATTTTGGCACGGAGG 59.125 50.000 0.00 0.00 0.00 4.30
1607 1652 1.949525 CATCTATTTTGGCACGGAGGG 59.050 52.381 0.00 0.00 0.00 4.30
1608 1653 1.281419 TCTATTTTGGCACGGAGGGA 58.719 50.000 0.00 0.00 0.00 4.20
1609 1654 1.209504 TCTATTTTGGCACGGAGGGAG 59.790 52.381 0.00 0.00 0.00 4.30
1610 1655 0.988832 TATTTTGGCACGGAGGGAGT 59.011 50.000 0.00 0.00 0.00 3.85
1611 1656 0.988832 ATTTTGGCACGGAGGGAGTA 59.011 50.000 0.00 0.00 0.00 2.59
1632 1677 1.279271 GATTGCTACCACCACCTCACT 59.721 52.381 0.00 0.00 0.00 3.41
1694 1739 6.856757 AGATCCCTAATATGCCATTCAGTTT 58.143 36.000 0.00 0.00 0.00 2.66
1708 1753 3.454042 TCAGTTTTCATCACATTCGCG 57.546 42.857 0.00 0.00 0.00 5.87
1793 1838 7.517320 TGGTGCATGAGTGGTCTTATTATATT 58.483 34.615 0.00 0.00 0.00 1.28
1867 1913 9.866655 AAGATAATGTTTATATGTGGACCATGT 57.133 29.630 0.00 0.00 34.86 3.21
1868 1914 9.288576 AGATAATGTTTATATGTGGACCATGTG 57.711 33.333 0.00 0.00 34.86 3.21
1869 1915 6.713762 AATGTTTATATGTGGACCATGTGG 57.286 37.500 0.00 0.00 42.17 4.17
1881 1927 1.446907 CCATGTGGTTCAGACAGCTC 58.553 55.000 0.00 0.00 0.00 4.09
1894 1940 3.059325 CAGACAGCTCTCCGAAGTTTTTG 60.059 47.826 0.00 0.00 0.00 2.44
1969 2016 2.615447 ACTATTTCATGCTGCACCATCG 59.385 45.455 3.57 0.00 0.00 3.84
2200 2248 7.984391 TCTTGCATTTTTCTCGCAATATCTTA 58.016 30.769 0.00 0.00 44.09 2.10
2277 2325 9.476202 CACATCAATATTTACGATTGAGGACTA 57.524 33.333 14.74 0.00 44.11 2.59
2287 2335 6.710597 ACGATTGAGGACTATTTAGCACTA 57.289 37.500 0.00 0.00 0.00 2.74
2331 2379 5.636543 GCCTTCATAATTTGCATATCCTTGC 59.363 40.000 0.00 0.00 43.07 4.01
2435 2486 2.280524 CTTCGTGGGTGCGTTCCA 60.281 61.111 1.03 0.00 0.00 3.53
2502 2553 1.064166 AGTCTCATGGCTTTGGATGGG 60.064 52.381 0.00 0.00 0.00 4.00
2504 2555 1.731433 CTCATGGCTTTGGATGGGCG 61.731 60.000 0.00 0.00 0.00 6.13
2662 2713 4.021544 TGGGCAATGTTTGTAAATCAGGTC 60.022 41.667 0.00 0.00 0.00 3.85
2891 2942 0.835276 ATGCTGCACTAGATCTGCCA 59.165 50.000 3.57 0.00 33.36 4.92
3160 3211 5.277857 ACAGATGTCTTTAAGGGGTATCG 57.722 43.478 0.00 0.00 0.00 2.92
3195 3246 7.343316 ACTGAACATAGTCCTCAAGCTATAACT 59.657 37.037 0.00 0.00 0.00 2.24
3326 3377 7.875971 AGTACCATCTGAGACATTTTGTTTTC 58.124 34.615 0.00 0.00 0.00 2.29
3349 3400 9.778993 TTTCGCTTAGTTATATCGTATATCACC 57.221 33.333 0.00 0.00 0.00 4.02
3518 3573 4.148128 GTCACCATGACATCTGGATTCT 57.852 45.455 1.99 0.00 46.22 2.40
3545 3600 9.914834 TTGTTATATATTTGTCCTTGCTAGGTT 57.085 29.630 14.12 0.00 42.60 3.50
3886 3950 8.981647 CCTTTCAGAAAGTATTGTGGATTTTTG 58.018 33.333 19.58 0.00 36.77 2.44
3902 3967 8.860088 GTGGATTTTTGAATTATGGTAGCCTAT 58.140 33.333 0.00 0.00 0.00 2.57
3915 3980 4.663120 TGGTAGCCTATATGGTCAATTGGT 59.337 41.667 5.42 0.00 38.35 3.67
3918 3983 6.013639 GGTAGCCTATATGGTCAATTGGTAGT 60.014 42.308 5.42 0.00 38.35 2.73
3960 4025 2.718609 CCCATTCCCCAGTTCTATGGAT 59.281 50.000 0.00 0.00 43.57 3.41
3969 4034 4.463891 CCCAGTTCTATGGATGCAAGTTTT 59.536 41.667 0.00 0.00 43.57 2.43
4001 4066 0.118346 TGCCCTCTAACCCTCCTCAA 59.882 55.000 0.00 0.00 0.00 3.02
4094 4159 7.775053 TTAATATTTTTCTGCTTCACCCAGT 57.225 32.000 0.00 0.00 0.00 4.00
4137 4202 9.793252 ACTGAATTTGTACTGAAATGCATAATC 57.207 29.630 0.00 2.21 31.62 1.75
4192 4258 6.485648 TCATTTGAGACTGGATATCATTGCTG 59.514 38.462 4.83 0.00 0.00 4.41
4218 4284 9.962759 GTATTGAATGCTTTTTCATTGTGAATC 57.037 29.630 0.00 0.00 36.11 2.52
4347 4413 1.064758 TGTTGCACACAAAGGAGGTCT 60.065 47.619 0.00 0.00 37.58 3.85
4348 4414 2.024414 GTTGCACACAAAGGAGGTCTT 58.976 47.619 0.00 0.00 37.58 3.01
4591 4822 3.715628 TGTTGCTTCTTTCAAGGCTTC 57.284 42.857 0.00 0.00 0.00 3.86
4608 4839 4.452455 AGGCTTCTTTGTCATGTTTCTACG 59.548 41.667 0.00 0.00 0.00 3.51
4644 4875 4.154015 GGAATTGCAATTGGTGTTAAAGCC 59.846 41.667 28.67 15.08 0.00 4.35
4837 5070 9.283768 AGTGAGAGACTATATGTGTTCTATCAG 57.716 37.037 0.00 0.00 30.86 2.90
4947 5180 2.288458 GAGTCTAAGGATGAGGTCGTCG 59.712 54.545 0.00 0.00 32.78 5.12
4992 5225 6.343716 TGACCGTTGTACATAGAAGGTAAA 57.656 37.500 3.96 0.00 0.00 2.01
4999 5232 7.117236 CGTTGTACATAGAAGGTAAACATGTGT 59.883 37.037 0.00 0.00 32.39 3.72
5045 5280 5.360591 CCATCCTTTCTTCTTAGCACGTAT 58.639 41.667 0.00 0.00 0.00 3.06
5138 5373 3.826729 GCAAACCCCATCTTTGACTAGTT 59.173 43.478 0.00 0.00 31.32 2.24
5161 5396 9.628500 AGTTTGAGTTTTCTTATAAGGTGTCTT 57.372 29.630 12.54 0.00 37.03 3.01
5178 5413 9.442047 AAGGTGTCTTATCTTTTTGAGTCTATG 57.558 33.333 0.00 0.00 0.00 2.23
5212 5447 8.299570 ACACTTTCCTATTCTAATTTGCACTTG 58.700 33.333 0.00 0.00 0.00 3.16
5286 5521 6.204882 CCTCTGGTTCTTACTTAGTTTGTTGG 59.795 42.308 0.00 0.00 0.00 3.77
5310 5550 2.045524 AGTCATTCTCGAGGATGCCAT 58.954 47.619 26.34 12.91 0.00 4.40
5344 5584 5.352569 CCTGACTGGAAATACACAGCTAAAG 59.647 44.000 0.00 0.00 38.25 1.85
5350 5592 4.095036 GGAAATACACAGCTAAAGAGTGCC 59.905 45.833 1.28 0.00 36.76 5.01
5359 5601 1.774894 TAAAGAGTGCCCCGTTGCCT 61.775 55.000 0.00 0.00 0.00 4.75
5371 5613 1.466167 CCGTTGCCTGAGAAATCTGTG 59.534 52.381 0.00 0.00 0.00 3.66
5374 5616 3.141398 GTTGCCTGAGAAATCTGTGACA 58.859 45.455 0.00 0.00 0.00 3.58
5410 5652 7.255569 TGAAGATGTACGATAACGATGAGTTT 58.744 34.615 0.00 0.00 43.86 2.66
5441 5683 1.825281 TTTTGCCCCTCCCATTTGCG 61.825 55.000 0.00 0.00 0.00 4.85
5444 5686 2.442643 CCCCTCCCATTTGCGCAT 60.443 61.111 12.75 0.00 0.00 4.73
5475 5717 0.887836 CTGCTTGAGGCTTGAGCACA 60.888 55.000 18.15 2.04 41.15 4.57
5476 5718 1.168407 TGCTTGAGGCTTGAGCACAC 61.168 55.000 18.15 0.00 41.15 3.82
5477 5719 0.888285 GCTTGAGGCTTGAGCACACT 60.888 55.000 15.49 0.00 44.36 3.55
5478 5720 0.873054 CTTGAGGCTTGAGCACACTG 59.127 55.000 5.24 0.00 44.36 3.66
5479 5721 0.535780 TTGAGGCTTGAGCACACTGG 60.536 55.000 5.24 0.00 44.36 4.00
5480 5722 1.072159 GAGGCTTGAGCACACTGGT 59.928 57.895 5.24 0.00 44.36 4.00
5559 5805 2.241941 TGGCTGTGTGGGTATCATCAAT 59.758 45.455 0.00 0.00 0.00 2.57
5574 5820 8.562892 GGTATCATCAATCTTGAAACATCGATT 58.437 33.333 0.00 0.00 41.13 3.34
5576 5822 6.708676 TCATCAATCTTGAAACATCGATTCG 58.291 36.000 0.00 0.00 41.13 3.34
5577 5823 6.534793 TCATCAATCTTGAAACATCGATTCGA 59.465 34.615 11.73 11.73 41.13 3.71
5579 5825 6.765089 TCAATCTTGAAACATCGATTCGAAG 58.235 36.000 13.47 11.36 35.11 3.79
5583 5829 6.387465 TCTTGAAACATCGATTCGAAGTACT 58.613 36.000 16.28 7.79 36.81 2.73
5585 5831 7.696872 TCTTGAAACATCGATTCGAAGTACTAG 59.303 37.037 16.28 16.87 36.81 2.57
5674 5921 8.536407 GTGTGTATGTTTTGTGTGTTATTTTCC 58.464 33.333 0.00 0.00 0.00 3.13
5677 5924 9.877178 TGTATGTTTTGTGTGTTATTTTCCTTT 57.123 25.926 0.00 0.00 0.00 3.11
5681 5928 9.273016 TGTTTTGTGTGTTATTTTCCTTTTTGA 57.727 25.926 0.00 0.00 0.00 2.69
5693 5940 5.447624 TTCCTTTTTGATTCGAGGGAAAC 57.552 39.130 0.00 0.00 35.40 2.78
5722 5972 0.879090 GCTTTGTTACTCAACGGGGG 59.121 55.000 0.00 0.00 37.48 5.40
5751 6001 0.866906 CGGCCAATACAAATGCAGCG 60.867 55.000 2.24 0.00 0.00 5.18
5771 6021 2.806382 CGGTACATGCAGGCACATCATA 60.806 50.000 3.85 0.00 0.00 2.15
5781 6031 1.071385 GGCACATCATACTCCCAGAGG 59.929 57.143 0.00 0.00 33.35 3.69
5810 6060 4.583871 CAAAGCTCCTTGATCCTTGTAGT 58.416 43.478 0.00 0.00 0.00 2.73
5814 6064 4.965532 AGCTCCTTGATCCTTGTAGTACAT 59.034 41.667 3.28 0.00 0.00 2.29
5858 6108 4.860907 GCAAGTTGATGAGCAGGTTTATTG 59.139 41.667 7.16 0.00 0.00 1.90
5870 6120 4.101119 GCAGGTTTATTGAGCTCCCTAGTA 59.899 45.833 12.15 0.00 0.00 1.82
5871 6121 5.740513 GCAGGTTTATTGAGCTCCCTAGTAG 60.741 48.000 12.15 0.00 0.00 2.57
5872 6122 5.364157 CAGGTTTATTGAGCTCCCTAGTAGT 59.636 44.000 12.15 0.00 0.00 2.73
5890 6140 1.555533 AGTACTAGGGCAGGCAAGAAC 59.444 52.381 0.00 0.00 0.00 3.01
5923 6173 9.712305 CAATCTTGGATAAATTAGTACGGAGAT 57.288 33.333 0.00 0.00 0.00 2.75
5924 6174 9.712305 AATCTTGGATAAATTAGTACGGAGATG 57.288 33.333 0.00 0.00 0.00 2.90
5925 6175 8.246430 TCTTGGATAAATTAGTACGGAGATGT 57.754 34.615 0.00 0.00 0.00 3.06
5937 6187 3.297391 GAGATGTTCCTCCATCGCC 57.703 57.895 0.00 0.00 44.76 5.54
5940 6190 4.812476 TGTTCCTCCATCGCCGCG 62.812 66.667 6.39 6.39 0.00 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.665212 CCATTCATTCATTCGTTCACCAG 58.335 43.478 0.00 0.00 0.00 4.00
8 9 3.087781 TGGCCATTCATTCATTCGTTCA 58.912 40.909 0.00 0.00 0.00 3.18
40 41 1.366366 CGACGTTCAGAAGTGGGGT 59.634 57.895 0.00 0.00 0.00 4.95
43 44 0.031585 TCACCGACGTTCAGAAGTGG 59.968 55.000 0.00 0.00 0.00 4.00
57 59 3.980775 CCAGTAAACAAGCAAAATCACCG 59.019 43.478 0.00 0.00 0.00 4.94
66 68 4.022935 CAGCAAGATTCCAGTAAACAAGCA 60.023 41.667 0.00 0.00 0.00 3.91
67 69 4.216257 TCAGCAAGATTCCAGTAAACAAGC 59.784 41.667 0.00 0.00 0.00 4.01
68 70 5.947228 TCAGCAAGATTCCAGTAAACAAG 57.053 39.130 0.00 0.00 0.00 3.16
70 72 5.559770 TCATCAGCAAGATTCCAGTAAACA 58.440 37.500 0.00 0.00 33.72 2.83
71 73 6.690194 ATCATCAGCAAGATTCCAGTAAAC 57.310 37.500 0.00 0.00 33.72 2.01
72 74 6.767902 GGTATCATCAGCAAGATTCCAGTAAA 59.232 38.462 0.00 0.00 33.72 2.01
73 75 6.100279 AGGTATCATCAGCAAGATTCCAGTAA 59.900 38.462 0.00 0.00 35.04 2.24
117 119 3.631686 CACAACTCAACTCCCATCAACAA 59.368 43.478 0.00 0.00 0.00 2.83
126 128 2.548480 GGCTACAACACAACTCAACTCC 59.452 50.000 0.00 0.00 0.00 3.85
157 159 2.632987 ACAAAACAGTACGGAAGGCT 57.367 45.000 0.00 0.00 0.00 4.58
215 217 2.100631 GTCGTCCGATGGTGCAAGG 61.101 63.158 0.00 0.00 0.00 3.61
217 219 2.047655 GGTCGTCCGATGGTGCAA 60.048 61.111 0.00 0.00 0.00 4.08
230 232 2.274437 CAGAGATGATGGTTGTGGTCG 58.726 52.381 0.00 0.00 0.00 4.79
238 240 4.298103 ACAAAGAAGCAGAGATGATGGT 57.702 40.909 0.00 0.00 0.00 3.55
303 305 1.270550 ACAAAATCAAAGCCAGCTCCG 59.729 47.619 0.00 0.00 0.00 4.63
308 310 4.161333 GTCATCGACAAAATCAAAGCCAG 58.839 43.478 0.00 0.00 32.09 4.85
332 334 3.646162 TGGTGTCAAGTACTTCAGATGGT 59.354 43.478 4.77 0.00 0.00 3.55
337 339 6.260936 ACAAGATTTGGTGTCAAGTACTTCAG 59.739 38.462 4.77 0.00 33.98 3.02
341 343 5.299279 CCAACAAGATTTGGTGTCAAGTACT 59.701 40.000 6.15 0.00 46.85 2.73
369 371 0.735287 GGGTTTCTCGTCGTAGGTGC 60.735 60.000 0.00 0.00 0.00 5.01
379 381 3.473625 ACAACAAGGTTAGGGTTTCTCG 58.526 45.455 0.00 0.00 0.00 4.04
408 410 2.303175 GAGAGTAGATTCCTGCCGTCT 58.697 52.381 0.00 0.00 0.00 4.18
425 427 2.704464 TAGAACGGAGTCGATGGAGA 57.296 50.000 0.00 0.00 45.00 3.71
429 431 3.372954 GTCCATTAGAACGGAGTCGATG 58.627 50.000 0.00 0.00 45.00 3.84
430 432 2.033049 CGTCCATTAGAACGGAGTCGAT 59.967 50.000 0.00 0.00 45.00 3.59
441 443 5.840243 TTAATCCGAGTTCGTCCATTAGA 57.160 39.130 0.48 0.00 37.74 2.10
457 459 2.711978 AGTCTTCCGGGCTTTAATCC 57.288 50.000 0.00 0.00 0.00 3.01
470 472 4.267452 CGCTTCATCTTCAAGCTAGTCTTC 59.733 45.833 3.14 0.00 43.57 2.87
532 534 8.571336 GCTTCGGTTAGTAGTTAGGTTATGATA 58.429 37.037 0.00 0.00 0.00 2.15
708 720 1.230635 ACGCCTTCATGTGACAGCAC 61.231 55.000 0.00 0.00 45.35 4.40
755 767 1.741770 GCACGATGAAGCTTCCCGT 60.742 57.895 27.46 27.46 36.43 5.28
761 773 1.734465 GCTAAAGTGCACGATGAAGCT 59.266 47.619 12.01 0.00 0.00 3.74
766 778 0.447801 GGTGGCTAAAGTGCACGATG 59.552 55.000 12.01 4.57 34.04 3.84
782 794 0.958822 AGCTTTTACGCAAAGGGGTG 59.041 50.000 9.17 0.00 42.18 4.61
863 877 8.842358 AAGAGTACGAATTTGTTTAGATTCCA 57.158 30.769 3.03 0.00 0.00 3.53
1426 1454 4.147322 ATACGCTGCAACGCACGC 62.147 61.111 9.87 0.00 36.88 5.34
1517 1562 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
1518 1563 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
1519 1564 4.150897 TCATCTATTTTGGAACGGAGGG 57.849 45.455 0.00 0.00 0.00 4.30
1520 1565 4.335594 GGTTCATCTATTTTGGAACGGAGG 59.664 45.833 0.00 0.00 40.30 4.30
1521 1566 4.941263 TGGTTCATCTATTTTGGAACGGAG 59.059 41.667 0.00 0.00 40.30 4.63
1522 1567 4.912586 TGGTTCATCTATTTTGGAACGGA 58.087 39.130 0.00 0.00 40.30 4.69
1523 1568 5.183140 AGTTGGTTCATCTATTTTGGAACGG 59.817 40.000 0.00 0.00 40.30 4.44
1524 1569 6.254281 AGTTGGTTCATCTATTTTGGAACG 57.746 37.500 0.00 0.00 40.30 3.95
1525 1570 7.926018 ACAAAGTTGGTTCATCTATTTTGGAAC 59.074 33.333 0.00 0.00 39.04 3.62
1526 1571 8.017418 ACAAAGTTGGTTCATCTATTTTGGAA 57.983 30.769 0.00 0.00 0.00 3.53
1527 1572 7.595819 ACAAAGTTGGTTCATCTATTTTGGA 57.404 32.000 0.00 0.00 0.00 3.53
1528 1573 8.576442 AGTACAAAGTTGGTTCATCTATTTTGG 58.424 33.333 0.00 0.00 0.00 3.28
1534 1579 9.841295 AAAGTTAGTACAAAGTTGGTTCATCTA 57.159 29.630 0.00 0.00 0.00 1.98
1535 1580 8.621286 CAAAGTTAGTACAAAGTTGGTTCATCT 58.379 33.333 0.00 0.00 0.00 2.90
1536 1581 8.403236 ACAAAGTTAGTACAAAGTTGGTTCATC 58.597 33.333 0.00 0.00 0.00 2.92
1537 1582 8.288689 ACAAAGTTAGTACAAAGTTGGTTCAT 57.711 30.769 0.00 0.00 0.00 2.57
1538 1583 7.690952 ACAAAGTTAGTACAAAGTTGGTTCA 57.309 32.000 0.00 0.00 0.00 3.18
1539 1584 8.886719 AGTACAAAGTTAGTACAAAGTTGGTTC 58.113 33.333 6.30 0.00 43.24 3.62
1540 1585 8.797350 AGTACAAAGTTAGTACAAAGTTGGTT 57.203 30.769 6.30 0.00 43.24 3.67
1541 1586 9.889128 TTAGTACAAAGTTAGTACAAAGTTGGT 57.111 29.630 6.30 0.00 43.24 3.67
1572 1617 9.823647 CCAAAATAGATGAGTCAACTATGTACT 57.176 33.333 20.11 5.38 31.50 2.73
1573 1618 8.552034 GCCAAAATAGATGAGTCAACTATGTAC 58.448 37.037 20.11 7.67 31.50 2.90
1574 1619 8.264347 TGCCAAAATAGATGAGTCAACTATGTA 58.736 33.333 20.11 7.61 31.50 2.29
1575 1620 7.066284 GTGCCAAAATAGATGAGTCAACTATGT 59.934 37.037 20.11 13.87 31.50 2.29
1576 1621 7.412853 GTGCCAAAATAGATGAGTCAACTATG 58.587 38.462 20.11 11.54 31.50 2.23
1577 1622 6.258727 CGTGCCAAAATAGATGAGTCAACTAT 59.741 38.462 15.24 15.24 32.22 2.12
1578 1623 5.580691 CGTGCCAAAATAGATGAGTCAACTA 59.419 40.000 12.03 12.03 0.00 2.24
1579 1624 4.393062 CGTGCCAAAATAGATGAGTCAACT 59.607 41.667 8.12 8.12 0.00 3.16
1580 1625 4.437390 CCGTGCCAAAATAGATGAGTCAAC 60.437 45.833 0.00 0.00 0.00 3.18
1581 1626 3.689161 CCGTGCCAAAATAGATGAGTCAA 59.311 43.478 0.00 0.00 0.00 3.18
1582 1627 3.055458 TCCGTGCCAAAATAGATGAGTCA 60.055 43.478 0.00 0.00 0.00 3.41
1583 1628 3.531538 TCCGTGCCAAAATAGATGAGTC 58.468 45.455 0.00 0.00 0.00 3.36
1584 1629 3.535561 CTCCGTGCCAAAATAGATGAGT 58.464 45.455 0.00 0.00 0.00 3.41
1585 1630 2.874701 CCTCCGTGCCAAAATAGATGAG 59.125 50.000 0.00 0.00 0.00 2.90
1586 1631 2.421388 CCCTCCGTGCCAAAATAGATGA 60.421 50.000 0.00 0.00 0.00 2.92
1587 1632 1.949525 CCCTCCGTGCCAAAATAGATG 59.050 52.381 0.00 0.00 0.00 2.90
1588 1633 1.843851 TCCCTCCGTGCCAAAATAGAT 59.156 47.619 0.00 0.00 0.00 1.98
1589 1634 1.209504 CTCCCTCCGTGCCAAAATAGA 59.790 52.381 0.00 0.00 0.00 1.98
1590 1635 1.065418 ACTCCCTCCGTGCCAAAATAG 60.065 52.381 0.00 0.00 0.00 1.73
1591 1636 0.988832 ACTCCCTCCGTGCCAAAATA 59.011 50.000 0.00 0.00 0.00 1.40
1592 1637 0.988832 TACTCCCTCCGTGCCAAAAT 59.011 50.000 0.00 0.00 0.00 1.82
1593 1638 0.323629 CTACTCCCTCCGTGCCAAAA 59.676 55.000 0.00 0.00 0.00 2.44
1594 1639 0.543410 TCTACTCCCTCCGTGCCAAA 60.543 55.000 0.00 0.00 0.00 3.28
1595 1640 0.325296 ATCTACTCCCTCCGTGCCAA 60.325 55.000 0.00 0.00 0.00 4.52
1596 1641 0.325296 AATCTACTCCCTCCGTGCCA 60.325 55.000 0.00 0.00 0.00 4.92
1597 1642 0.105039 CAATCTACTCCCTCCGTGCC 59.895 60.000 0.00 0.00 0.00 5.01
1598 1643 0.530870 GCAATCTACTCCCTCCGTGC 60.531 60.000 0.00 0.00 0.00 5.34
1599 1644 1.115467 AGCAATCTACTCCCTCCGTG 58.885 55.000 0.00 0.00 0.00 4.94
1600 1645 2.308690 GTAGCAATCTACTCCCTCCGT 58.691 52.381 0.00 0.00 41.47 4.69
1601 1646 1.614413 GGTAGCAATCTACTCCCTCCG 59.386 57.143 2.95 0.00 43.61 4.63
1602 1647 2.365941 GTGGTAGCAATCTACTCCCTCC 59.634 54.545 0.00 0.00 43.61 4.30
1603 1648 2.365941 GGTGGTAGCAATCTACTCCCTC 59.634 54.545 0.00 0.00 43.61 4.30
1604 1649 2.292918 TGGTGGTAGCAATCTACTCCCT 60.293 50.000 0.00 0.00 43.61 4.20
1605 1650 2.116238 TGGTGGTAGCAATCTACTCCC 58.884 52.381 0.00 0.00 43.61 4.30
1606 1651 2.158943 GGTGGTGGTAGCAATCTACTCC 60.159 54.545 0.00 0.00 43.61 3.85
1607 1652 2.766828 AGGTGGTGGTAGCAATCTACTC 59.233 50.000 0.00 0.00 43.61 2.59
1608 1653 2.766828 GAGGTGGTGGTAGCAATCTACT 59.233 50.000 0.00 0.00 43.61 2.57
1609 1654 2.500098 TGAGGTGGTGGTAGCAATCTAC 59.500 50.000 0.00 0.00 43.43 2.59
1610 1655 2.500098 GTGAGGTGGTGGTAGCAATCTA 59.500 50.000 0.00 0.00 0.00 1.98
1611 1656 1.279271 GTGAGGTGGTGGTAGCAATCT 59.721 52.381 0.00 0.00 0.00 2.40
1632 1677 0.606096 TCAGCAAGCTAAGGCGTACA 59.394 50.000 0.00 0.00 44.37 2.90
1694 1739 0.952984 TGGCACGCGAATGTGATGAA 60.953 50.000 15.93 0.00 42.55 2.57
1708 1753 2.688446 GCCTCTAACCCTTAAATGGCAC 59.312 50.000 0.00 0.00 38.99 5.01
1793 1838 7.223971 GCAAGGATAACTGTACATGTCGAAATA 59.776 37.037 0.00 0.00 0.00 1.40
1803 1848 7.759489 AATTCAAAGCAAGGATAACTGTACA 57.241 32.000 0.00 0.00 0.00 2.90
1861 1907 5.436247 GAGAGCTGTCTGAACCACATGGT 62.436 52.174 3.06 0.00 41.47 3.55
1862 1908 1.002888 AGAGCTGTCTGAACCACATGG 59.997 52.381 0.00 0.00 42.17 3.66
1863 1909 2.344950 GAGAGCTGTCTGAACCACATG 58.655 52.381 3.06 0.00 30.97 3.21
1864 1910 1.277557 GGAGAGCTGTCTGAACCACAT 59.722 52.381 11.11 0.00 30.97 3.21
1865 1911 0.681733 GGAGAGCTGTCTGAACCACA 59.318 55.000 11.11 0.00 30.97 4.17
1866 1912 0.389166 CGGAGAGCTGTCTGAACCAC 60.389 60.000 14.46 0.00 30.97 4.16
1867 1913 0.539669 TCGGAGAGCTGTCTGAACCA 60.540 55.000 19.49 0.00 30.97 3.67
1868 1914 0.603569 TTCGGAGAGCTGTCTGAACC 59.396 55.000 26.66 3.34 36.99 3.62
1869 1915 1.271102 ACTTCGGAGAGCTGTCTGAAC 59.729 52.381 26.66 3.13 36.99 3.18
1881 1927 5.761165 TTAGAAACCCAAAAACTTCGGAG 57.239 39.130 0.00 0.00 0.00 4.63
1915 1962 5.105310 TGCCTACAGTCAAATTCCTCTACTC 60.105 44.000 0.00 0.00 0.00 2.59
1947 1994 3.065786 CGATGGTGCAGCATGAAATAGTT 59.934 43.478 34.35 9.46 39.69 2.24
1951 1998 1.466856 ACGATGGTGCAGCATGAAAT 58.533 45.000 34.35 12.70 39.69 2.17
1969 2016 7.438459 CCACAATACTGAAATAGGCTACAGTAC 59.562 40.741 19.71 3.38 44.65 2.73
2101 2148 4.338879 CACCTCTTGATTCCAGTGGAAAT 58.661 43.478 27.93 16.19 45.41 2.17
2102 2149 3.754965 CACCTCTTGATTCCAGTGGAAA 58.245 45.455 27.93 10.51 45.41 3.13
2294 2342 5.957842 TTATGAAGGCCAAAACTGTACTG 57.042 39.130 5.01 0.00 0.00 2.74
2435 2486 6.714810 TGGATGCATACACTAACAGTTTCTTT 59.285 34.615 7.78 0.00 0.00 2.52
2502 2553 4.058124 TGCTTTGGATCAGTATCATACGC 58.942 43.478 0.00 0.00 33.41 4.42
2504 2555 6.933521 AGTCATGCTTTGGATCAGTATCATAC 59.066 38.462 0.00 0.00 33.41 2.39
2662 2713 5.923204 AGCAGTCTATCTATCCCAACTTTG 58.077 41.667 0.00 0.00 0.00 2.77
2891 2942 8.370182 ACTATTGCAATTTTCTCAGGTTTTGAT 58.630 29.630 18.75 0.00 34.68 2.57
3326 3377 7.404985 ACGGTGATATACGATATAACTAAGCG 58.595 38.462 0.00 0.00 0.00 4.68
3349 3400 4.908736 AGGATGAACGAATGCATAAAACG 58.091 39.130 0.00 6.79 0.00 3.60
3358 3409 6.749139 TGTTAGGATCTAGGATGAACGAATG 58.251 40.000 0.00 0.00 0.00 2.67
3545 3600 4.950475 ACTGAGGTTCGAGAATACTCATCA 59.050 41.667 17.29 6.19 42.72 3.07
3674 3729 4.820894 ATACCTGTACTCTGGTTTGGTC 57.179 45.455 10.15 0.00 43.78 4.02
3744 3799 5.183713 TCATTTCTAGAACAACCATTGCCTG 59.816 40.000 4.18 0.00 0.00 4.85
3798 3861 7.040062 CCTGTAAACTATCATCAGGAGAGGTAG 60.040 44.444 3.76 0.00 45.76 3.18
3886 3950 9.686683 AATTGACCATATAGGCTACCATAATTC 57.313 33.333 0.00 0.00 43.14 2.17
3915 3980 7.666804 GGGGGACAAACTTGAAATTTACTACTA 59.333 37.037 0.00 0.00 0.00 1.82
3918 3983 6.374588 TGGGGGACAAACTTGAAATTTACTA 58.625 36.000 0.00 0.00 0.00 1.82
3924 3989 3.582647 GGAATGGGGGACAAACTTGAAAT 59.417 43.478 0.00 0.00 0.00 2.17
3960 4025 2.962421 CCCTAAGGGTCAAAAACTTGCA 59.038 45.455 0.00 0.00 38.25 4.08
4094 4159 5.551305 TTCAGTTTCAGGAGATTGTCAGA 57.449 39.130 0.00 0.00 0.00 3.27
4168 4234 6.262496 ACAGCAATGATATCCAGTCTCAAATG 59.738 38.462 0.00 0.00 0.00 2.32
4192 4258 9.962759 GATTCACAATGAAAAAGCATTCAATAC 57.037 29.630 4.10 0.00 42.22 1.89
4591 4822 7.328493 TCACATAGTCGTAGAAACATGACAAAG 59.672 37.037 0.00 0.00 39.69 2.77
4608 4839 3.609853 TGCAATTCCCTGTCACATAGTC 58.390 45.455 0.00 0.00 0.00 2.59
4644 4875 3.824414 AAATCTTGCTTCGTTAACCCG 57.176 42.857 0.00 0.00 0.00 5.28
4947 5180 3.983741 ACGGCATTATCTACTTCTGAGC 58.016 45.455 0.00 0.00 0.00 4.26
4992 5225 6.017109 GTGACAGGTCAAAAGAATACACATGT 60.017 38.462 3.28 0.00 41.85 3.21
4999 5232 5.880332 GGCATAGTGACAGGTCAAAAGAATA 59.120 40.000 3.28 0.00 41.85 1.75
5212 5447 3.942130 ATTTCCTTGCTAACAACCAGC 57.058 42.857 0.00 0.00 39.56 4.85
5286 5521 2.200067 CATCCTCGAGAATGACTGCAC 58.800 52.381 15.71 0.00 0.00 4.57
5310 5550 2.342279 CAGTCAGGTTTCGGCCGA 59.658 61.111 27.28 27.28 0.00 5.54
5344 5584 4.329545 TCAGGCAACGGGGCACTC 62.330 66.667 5.74 0.00 46.44 3.51
5350 5592 1.089920 CAGATTTCTCAGGCAACGGG 58.910 55.000 0.00 0.00 46.39 5.28
5359 5601 4.761739 GGGTTCATTGTCACAGATTTCTCA 59.238 41.667 0.00 0.00 0.00 3.27
5371 5613 4.583871 ACATCTTCAGAGGGTTCATTGTC 58.416 43.478 0.00 0.00 0.00 3.18
5374 5616 4.466370 TCGTACATCTTCAGAGGGTTCATT 59.534 41.667 0.00 0.00 0.00 2.57
5427 5669 1.616091 AAATGCGCAAATGGGAGGGG 61.616 55.000 17.11 0.00 0.00 4.79
5441 5683 3.256631 TCAAGCAGGAAGGAAAGAAATGC 59.743 43.478 0.00 0.00 0.00 3.56
5475 5717 1.120530 AACTCAACGACCAGACCAGT 58.879 50.000 0.00 0.00 0.00 4.00
5476 5718 2.135933 GAAACTCAACGACCAGACCAG 58.864 52.381 0.00 0.00 0.00 4.00
5477 5719 1.760613 AGAAACTCAACGACCAGACCA 59.239 47.619 0.00 0.00 0.00 4.02
5478 5720 2.528041 AGAAACTCAACGACCAGACC 57.472 50.000 0.00 0.00 0.00 3.85
5479 5721 4.260661 GGAAAAGAAACTCAACGACCAGAC 60.261 45.833 0.00 0.00 0.00 3.51
5480 5722 3.875134 GGAAAAGAAACTCAACGACCAGA 59.125 43.478 0.00 0.00 0.00 3.86
5559 5805 6.387465 AGTACTTCGAATCGATGTTTCAAGA 58.613 36.000 25.09 7.35 40.39 3.02
5574 5820 4.280174 ACTGGTTTTCTGCTAGTACTTCGA 59.720 41.667 0.00 0.00 0.00 3.71
5576 5822 5.298347 ACACTGGTTTTCTGCTAGTACTTC 58.702 41.667 0.00 0.00 0.00 3.01
5577 5823 5.291905 ACACTGGTTTTCTGCTAGTACTT 57.708 39.130 0.00 0.00 0.00 2.24
5579 5825 7.769220 TCTATACACTGGTTTTCTGCTAGTAC 58.231 38.462 0.00 0.00 0.00 2.73
5583 5829 6.852420 ACTCTATACACTGGTTTTCTGCTA 57.148 37.500 0.00 0.00 0.00 3.49
5585 5831 6.803154 AAACTCTATACACTGGTTTTCTGC 57.197 37.500 0.00 0.00 0.00 4.26
5636 5882 7.229106 ACAAAACATACACACGGGTAATTAACT 59.771 33.333 0.00 0.00 0.00 2.24
5674 5921 3.234386 GCGTTTCCCTCGAATCAAAAAG 58.766 45.455 0.00 0.00 0.00 2.27
5677 5924 1.885560 TGCGTTTCCCTCGAATCAAA 58.114 45.000 0.00 0.00 0.00 2.69
5679 5926 2.107950 ATTGCGTTTCCCTCGAATCA 57.892 45.000 0.00 0.00 0.00 2.57
5681 5928 3.261981 ACTATTGCGTTTCCCTCGAAT 57.738 42.857 0.00 0.00 0.00 3.34
5684 5931 1.859080 GCTACTATTGCGTTTCCCTCG 59.141 52.381 0.00 0.00 0.00 4.63
5693 5940 6.241385 GTTGAGTAACAAAGCTACTATTGCG 58.759 40.000 0.00 0.00 40.36 4.85
5751 6001 1.683943 ATGATGTGCCTGCATGTACC 58.316 50.000 7.67 0.00 0.00 3.34
5771 6021 2.686835 GCTCTGGCCTCTGGGAGT 60.687 66.667 3.32 0.00 33.58 3.85
5795 6045 9.265901 CTATTTCATGTACTACAAGGATCAAGG 57.734 37.037 0.00 0.00 0.00 3.61
5810 6060 3.244422 GGATGGGGACGCTATTTCATGTA 60.244 47.826 0.00 0.00 0.00 2.29
5814 6064 0.472471 GGGATGGGGACGCTATTTCA 59.528 55.000 0.00 0.00 0.00 2.69
5870 6120 1.555533 GTTCTTGCCTGCCCTAGTACT 59.444 52.381 0.00 0.00 0.00 2.73
5871 6121 1.407025 GGTTCTTGCCTGCCCTAGTAC 60.407 57.143 0.00 0.00 0.00 2.73
5872 6122 0.909623 GGTTCTTGCCTGCCCTAGTA 59.090 55.000 0.00 0.00 0.00 1.82
5923 6173 4.812476 CGCGGCGATGGAGGAACA 62.812 66.667 19.16 0.00 0.00 3.18
5937 6187 3.880846 GATTCAAGCCTGGCCGCG 61.881 66.667 16.57 0.00 0.00 6.46
5940 6190 3.196040 TGATGATTCAAGCCTGGCC 57.804 52.632 16.57 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.