Multiple sequence alignment - TraesCS4B01G121200

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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 TraesCS4B01G121200 chr4B 100.000 6128 0 0 1 6128 142912799 142918926 0.000000e+00 11317.0
1 TraesCS4B01G121200 chr4B 92.857 140 9 1 2083 2221 535246100 535246239 1.040000e-47 202.0
2 TraesCS4B01G121200 chr4B 91.156 147 11 2 2083 2227 148644550 148644404 1.350000e-46 198.0
3 TraesCS4B01G121200 chr4A 92.784 3326 148 38 2842 6128 475917232 475913960 0.000000e+00 4728.0
4 TraesCS4B01G121200 chr4A 89.887 1414 91 30 133 1523 475919987 475918603 0.000000e+00 1772.0
5 TraesCS4B01G121200 chr4A 93.693 983 59 3 1717 2697 475918531 475917550 0.000000e+00 1469.0
6 TraesCS4B01G121200 chr4A 98.630 146 2 0 2698 2843 475917471 475917326 6.090000e-65 259.0
7 TraesCS4B01G121200 chr4D 93.465 1622 69 17 1 1601 100561118 100562723 0.000000e+00 2374.0
8 TraesCS4B01G121200 chr4D 94.810 1368 48 11 4774 6128 100565986 100567343 0.000000e+00 2111.0
9 TraesCS4B01G121200 chr4D 91.316 1497 83 21 2700 4176 100563840 100565309 0.000000e+00 2001.0
10 TraesCS4B01G121200 chr4D 94.135 1023 44 8 1684 2700 100562722 100563734 0.000000e+00 1543.0
11 TraesCS4B01G121200 chr4D 95.786 617 24 2 4158 4772 100565321 100565937 0.000000e+00 994.0
12 TraesCS4B01G121200 chr4D 98.837 86 1 0 1600 1685 379169332 379169417 2.960000e-33 154.0
13 TraesCS4B01G121200 chr5D 81.766 351 36 18 406 737 478288457 478288116 1.010000e-67 268.0
14 TraesCS4B01G121200 chr5D 97.778 90 2 0 1599 1688 276292519 276292430 8.220000e-34 156.0
15 TraesCS4B01G121200 chr5D 97.727 88 2 0 1600 1687 496216342 496216255 1.060000e-32 152.0
16 TraesCS4B01G121200 chr5B 88.018 217 22 3 2587 2800 118626392 118626607 2.840000e-63 254.0
17 TraesCS4B01G121200 chr5B 78.551 345 50 17 407 735 680682326 680682662 8.050000e-49 206.0
18 TraesCS4B01G121200 chr5B 79.333 300 55 7 2491 2786 256953225 256952929 2.900000e-48 204.0
19 TraesCS4B01G121200 chr5B 91.156 147 11 2 2083 2227 381856626 381856480 1.350000e-46 198.0
20 TraesCS4B01G121200 chr7B 79.765 341 54 11 406 736 561282752 561282417 3.690000e-57 233.0
21 TraesCS4B01G121200 chr7B 79.063 363 48 15 2470 2806 438988837 438989197 2.220000e-54 224.0
22 TraesCS4B01G121200 chr7B 82.381 210 20 10 2597 2802 505470059 505470255 3.800000e-37 167.0
23 TraesCS4B01G121200 chr7B 75.595 336 56 13 405 735 291570036 291570350 6.400000e-30 143.0
24 TraesCS4B01G121200 chr7B 88.571 70 7 1 2738 2806 65824563 65824632 3.940000e-12 84.2
25 TraesCS4B01G121200 chr7B 100.000 28 0 0 430 457 521589254 521589227 1.100000e-02 52.8
26 TraesCS4B01G121200 chr5A 83.462 260 30 11 2552 2806 10916105 10916356 4.780000e-56 230.0
27 TraesCS4B01G121200 chr5A 79.310 348 50 11 2476 2802 311987087 311986741 2.220000e-54 224.0
28 TraesCS4B01G121200 chr5A 98.864 88 1 0 1600 1687 309680177 309680264 2.290000e-34 158.0
29 TraesCS4B01G121200 chr5A 97.727 88 2 0 1599 1686 328723624 328723711 1.060000e-32 152.0
30 TraesCS4B01G121200 chr7D 79.213 356 47 15 406 739 37101591 37101941 7.990000e-54 222.0
31 TraesCS4B01G121200 chr2D 79.217 332 56 7 2477 2797 361393344 361393673 1.030000e-52 219.0
32 TraesCS4B01G121200 chr6D 97.581 124 3 0 2083 2206 267532934 267532811 4.810000e-51 213.0
33 TraesCS4B01G121200 chr6A 97.581 124 3 0 2083 2206 381088827 381088704 4.810000e-51 213.0
34 TraesCS4B01G121200 chr6A 90.066 151 11 3 2086 2233 100319299 100319150 6.270000e-45 193.0
35 TraesCS4B01G121200 chr6A 78.551 345 35 14 408 736 615138701 615138380 2.250000e-44 191.0
36 TraesCS4B01G121200 chr2A 93.431 137 9 0 2083 2219 5637493 5637357 2.900000e-48 204.0
37 TraesCS4B01G121200 chrUn 79.430 316 42 16 399 700 49987484 49987790 1.040000e-47 202.0
38 TraesCS4B01G121200 chrUn 78.539 219 28 11 406 611 87945861 87946073 6.450000e-25 126.0
39 TraesCS4B01G121200 chr3D 82.609 230 37 3 2529 2756 123282806 123283034 3.750000e-47 200.0
40 TraesCS4B01G121200 chr3D 83.673 147 18 6 592 735 374687035 374687178 3.850000e-27 134.0
41 TraesCS4B01G121200 chr3D 86.486 111 10 5 592 700 374397452 374397559 3.880000e-22 117.0
42 TraesCS4B01G121200 chr1B 98.901 91 1 0 1599 1689 133188942 133188852 4.910000e-36 163.0
43 TraesCS4B01G121200 chr1B 97.727 88 2 0 1600 1687 608052565 608052478 1.060000e-32 152.0
44 TraesCS4B01G121200 chr3A 82.632 190 17 9 406 587 497296186 497296367 2.960000e-33 154.0
45 TraesCS4B01G121200 chr3A 83.333 150 14 11 592 735 497208174 497208318 1.790000e-25 128.0
46 TraesCS4B01G121200 chr2B 97.753 89 2 0 1600 1688 799148771 799148683 2.960000e-33 154.0
47 TraesCS4B01G121200 chr2B 94.845 97 5 0 1592 1688 79295747 79295651 1.060000e-32 152.0
48 TraesCS4B01G121200 chr2B 77.509 289 30 15 2536 2806 603433538 603433267 2.300000e-29 141.0
49 TraesCS4B01G121200 chr3B 87.705 122 12 2 580 700 809044569 809044450 8.280000e-29 139.0


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 TraesCS4B01G121200 chr4B 142912799 142918926 6127 False 11317.0 11317 100.0000 1 6128 1 chr4B.!!$F1 6127
1 TraesCS4B01G121200 chr4A 475913960 475919987 6027 True 2057.0 4728 93.7485 133 6128 4 chr4A.!!$R1 5995
2 TraesCS4B01G121200 chr4D 100561118 100567343 6225 False 1804.6 2374 93.9024 1 6128 5 chr4D.!!$F2 6127

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
683 713 0.033504 ACGGACATCACACACTCCAC 59.966 55.0 0.0 0.0 0.0 4.02 F
1844 1884 0.036732 TTCTGGAGCATGTGTCACCC 59.963 55.0 0.0 0.0 0.0 4.61 F
2517 2558 1.337118 TGCTTTGGGGATTGGTTGAC 58.663 50.0 0.0 0.0 0.0 3.18 F
4041 4312 0.178990 GGGTATCTTCATGGGTGGGC 60.179 60.0 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2251 2292 0.251297 CTGTTGTTGCATGGAGGGGA 60.251 55.000 0.00 0.0 0.00 4.81 R
2863 3111 1.463056 TGTGTAACTACAATGCGCTGC 59.537 47.619 9.73 0.0 38.04 5.25 R
4306 4607 0.036858 AGCGGCTCTCTTCAAAGGAC 60.037 55.000 0.00 0.0 0.00 3.85 R
5730 6122 0.032403 ACGCTGCTGTTAACCGTGTA 59.968 50.000 2.48 0.0 0.00 2.90 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
43 44 2.183679 CTTGCTGGTAGGAGAAGAGGT 58.816 52.381 0.00 0.00 0.00 3.85
48 49 1.338890 GGTAGGAGAAGAGGTGGGGC 61.339 65.000 0.00 0.00 0.00 5.80
97 101 2.067091 GACGTGGCGATATGGGACGA 62.067 60.000 0.00 0.00 34.22 4.20
128 137 2.811514 ATGGCGAGATGGTGGCGAT 61.812 57.895 0.00 0.00 0.00 4.58
138 147 4.759096 GTGGCGATGCAACGTGGC 62.759 66.667 17.99 8.35 35.59 5.01
225 235 1.405821 CTACCCGCTCGTCATCTTCTT 59.594 52.381 0.00 0.00 0.00 2.52
233 243 3.482112 GCTCGTCATCTTCTTGTAAACGC 60.482 47.826 0.00 0.00 0.00 4.84
263 273 2.158066 AGGGGTGATTATACGGGATCCA 60.158 50.000 15.23 0.00 0.00 3.41
295 307 6.515035 AAAATCGGTTTTACAAGAGCTCTTGG 60.515 38.462 43.74 31.07 42.05 3.61
309 321 3.092301 GCTCTTGGAGGGCTATTTTTGT 58.908 45.455 0.00 0.00 0.00 2.83
424 437 5.304101 AGAGACGAATATCCAATTCTGAGCT 59.696 40.000 0.00 0.00 0.00 4.09
462 477 4.979815 CCCCGTGAACAGTAAATTCAAAAC 59.020 41.667 0.00 0.00 37.80 2.43
465 480 6.198216 CCCGTGAACAGTAAATTCAAAACAAG 59.802 38.462 0.00 0.00 37.80 3.16
519 534 7.465916 GCATGAAAGATATTTTAGTGCGTGAGA 60.466 37.037 0.00 0.00 0.00 3.27
562 577 5.452496 GCATTTGGACATCTGAGTAGCTCTA 60.452 44.000 0.00 0.00 0.00 2.43
563 578 5.843673 TTTGGACATCTGAGTAGCTCTAG 57.156 43.478 0.00 0.00 0.00 2.43
564 579 3.218453 TGGACATCTGAGTAGCTCTAGC 58.782 50.000 0.00 0.00 42.49 3.42
565 580 3.218453 GGACATCTGAGTAGCTCTAGCA 58.782 50.000 4.54 0.00 45.16 3.49
617 646 5.853572 TTACAGACCCCAAATTAGTCCTT 57.146 39.130 0.00 0.00 0.00 3.36
618 647 4.741928 ACAGACCCCAAATTAGTCCTTT 57.258 40.909 0.00 0.00 0.00 3.11
619 648 5.074746 ACAGACCCCAAATTAGTCCTTTT 57.925 39.130 0.00 0.00 0.00 2.27
650 680 4.225942 AGAGCTACCCAGACATTCAAATGA 59.774 41.667 9.62 0.00 39.67 2.57
681 711 1.291877 GCACGGACATCACACACTCC 61.292 60.000 0.00 0.00 0.00 3.85
683 713 0.033504 ACGGACATCACACACTCCAC 59.966 55.000 0.00 0.00 0.00 4.02
701 731 4.803452 TCCACCATCTTTCTCCAAAAACT 58.197 39.130 0.00 0.00 0.00 2.66
772 803 1.296392 CGGCTCATGTGAACCAGGA 59.704 57.895 0.00 0.00 30.83 3.86
953 984 4.406972 CCTCTTCCTTATCACCATCACTCA 59.593 45.833 0.00 0.00 0.00 3.41
1008 1039 1.006688 AACGAAAACAATGGCCGCC 60.007 52.632 1.04 1.04 0.00 6.13
1191 1222 4.283722 TCTCCTCGACCTAAGCTTTCTTTT 59.716 41.667 3.20 0.00 33.85 2.27
1192 1223 4.969484 TCCTCGACCTAAGCTTTCTTTTT 58.031 39.130 3.20 0.00 33.85 1.94
1193 1224 6.014840 TCTCCTCGACCTAAGCTTTCTTTTTA 60.015 38.462 3.20 0.00 33.85 1.52
1194 1225 6.164176 TCCTCGACCTAAGCTTTCTTTTTAG 58.836 40.000 3.20 0.00 33.85 1.85
1504 1537 0.178953 AGCAGGGTCAATTTGGCACT 60.179 50.000 0.00 0.00 35.09 4.40
1529 1562 6.693466 TCGACATATTCCTGTGTTTGTCTTA 58.307 36.000 0.00 0.00 33.14 2.10
1603 1641 8.603242 TCTGTGGAAGTTCTTGTTTTATACTC 57.397 34.615 2.25 0.00 0.00 2.59
1604 1642 7.660208 TCTGTGGAAGTTCTTGTTTTATACTCC 59.340 37.037 2.25 0.00 0.00 3.85
1605 1643 6.713450 TGTGGAAGTTCTTGTTTTATACTCCC 59.287 38.462 2.25 0.00 0.00 4.30
1606 1644 6.940867 GTGGAAGTTCTTGTTTTATACTCCCT 59.059 38.462 2.25 0.00 0.00 4.20
1607 1645 7.119407 GTGGAAGTTCTTGTTTTATACTCCCTC 59.881 40.741 2.25 0.00 0.00 4.30
1608 1646 6.598457 GGAAGTTCTTGTTTTATACTCCCTCC 59.402 42.308 2.25 0.00 0.00 4.30
1609 1647 5.731591 AGTTCTTGTTTTATACTCCCTCCG 58.268 41.667 0.00 0.00 0.00 4.63
1610 1648 5.247792 AGTTCTTGTTTTATACTCCCTCCGT 59.752 40.000 0.00 0.00 0.00 4.69
1611 1649 5.750352 TCTTGTTTTATACTCCCTCCGTT 57.250 39.130 0.00 0.00 0.00 4.44
1612 1650 5.727434 TCTTGTTTTATACTCCCTCCGTTC 58.273 41.667 0.00 0.00 0.00 3.95
1613 1651 4.476628 TGTTTTATACTCCCTCCGTTCC 57.523 45.455 0.00 0.00 0.00 3.62
1614 1652 3.839490 TGTTTTATACTCCCTCCGTTCCA 59.161 43.478 0.00 0.00 0.00 3.53
1615 1653 4.472108 TGTTTTATACTCCCTCCGTTCCAT 59.528 41.667 0.00 0.00 0.00 3.41
1616 1654 5.662208 TGTTTTATACTCCCTCCGTTCCATA 59.338 40.000 0.00 0.00 0.00 2.74
1617 1655 6.328148 TGTTTTATACTCCCTCCGTTCCATAT 59.672 38.462 0.00 0.00 0.00 1.78
1618 1656 7.147444 TGTTTTATACTCCCTCCGTTCCATATT 60.147 37.037 0.00 0.00 0.00 1.28
1619 1657 4.891992 ATACTCCCTCCGTTCCATATTG 57.108 45.455 0.00 0.00 0.00 1.90
1620 1658 1.141053 ACTCCCTCCGTTCCATATTGC 59.859 52.381 0.00 0.00 0.00 3.56
1621 1659 1.417890 CTCCCTCCGTTCCATATTGCT 59.582 52.381 0.00 0.00 0.00 3.91
1622 1660 1.416401 TCCCTCCGTTCCATATTGCTC 59.584 52.381 0.00 0.00 0.00 4.26
1623 1661 1.502231 CCTCCGTTCCATATTGCTCG 58.498 55.000 0.00 0.00 0.00 5.03
1624 1662 1.202533 CCTCCGTTCCATATTGCTCGT 60.203 52.381 0.00 0.00 0.00 4.18
1625 1663 2.128035 CTCCGTTCCATATTGCTCGTC 58.872 52.381 0.00 0.00 0.00 4.20
1626 1664 0.852777 CCGTTCCATATTGCTCGTCG 59.147 55.000 0.00 0.00 0.00 5.12
1627 1665 0.229753 CGTTCCATATTGCTCGTCGC 59.770 55.000 0.00 0.00 39.77 5.19
1628 1666 1.571919 GTTCCATATTGCTCGTCGCT 58.428 50.000 0.00 0.00 40.11 4.93
1629 1667 1.258982 GTTCCATATTGCTCGTCGCTG 59.741 52.381 0.00 0.00 40.11 5.18
1630 1668 0.744281 TCCATATTGCTCGTCGCTGA 59.256 50.000 0.00 0.00 40.11 4.26
1631 1669 1.341209 TCCATATTGCTCGTCGCTGAT 59.659 47.619 0.00 0.00 40.11 2.90
1632 1670 2.138320 CCATATTGCTCGTCGCTGATT 58.862 47.619 0.00 0.00 40.11 2.57
1633 1671 2.545526 CCATATTGCTCGTCGCTGATTT 59.454 45.455 0.00 0.00 40.11 2.17
1634 1672 3.740832 CCATATTGCTCGTCGCTGATTTA 59.259 43.478 0.00 0.00 40.11 1.40
1635 1673 4.143242 CCATATTGCTCGTCGCTGATTTAG 60.143 45.833 0.00 0.00 40.11 1.85
1636 1674 2.363788 TTGCTCGTCGCTGATTTAGT 57.636 45.000 0.00 0.00 40.11 2.24
1637 1675 3.497297 TTGCTCGTCGCTGATTTAGTA 57.503 42.857 0.00 0.00 40.11 1.82
1638 1676 2.793933 TGCTCGTCGCTGATTTAGTAC 58.206 47.619 0.00 0.00 40.11 2.73
1639 1677 2.162809 TGCTCGTCGCTGATTTAGTACA 59.837 45.455 0.00 0.00 40.11 2.90
1640 1678 3.176708 GCTCGTCGCTGATTTAGTACAA 58.823 45.455 0.00 0.00 35.14 2.41
1641 1679 3.000971 GCTCGTCGCTGATTTAGTACAAC 60.001 47.826 0.00 0.00 35.14 3.32
1642 1680 4.413087 CTCGTCGCTGATTTAGTACAACT 58.587 43.478 0.00 0.00 0.00 3.16
1643 1681 4.801891 TCGTCGCTGATTTAGTACAACTT 58.198 39.130 0.00 0.00 0.00 2.66
1644 1682 5.224888 TCGTCGCTGATTTAGTACAACTTT 58.775 37.500 0.00 0.00 0.00 2.66
1645 1683 5.118050 TCGTCGCTGATTTAGTACAACTTTG 59.882 40.000 0.00 0.00 0.00 2.77
1646 1684 5.107607 CGTCGCTGATTTAGTACAACTTTGT 60.108 40.000 0.00 0.00 44.86 2.83
1647 1685 6.088483 CGTCGCTGATTTAGTACAACTTTGTA 59.912 38.462 0.00 0.00 42.35 2.41
1660 1698 6.224420 ACAACTTTGTACTAAATCAGCGAC 57.776 37.500 0.00 0.00 40.16 5.19
1661 1699 5.756347 ACAACTTTGTACTAAATCAGCGACA 59.244 36.000 0.00 0.00 40.16 4.35
1662 1700 6.259167 ACAACTTTGTACTAAATCAGCGACAA 59.741 34.615 0.00 0.00 40.16 3.18
1663 1701 6.467723 ACTTTGTACTAAATCAGCGACAAG 57.532 37.500 0.00 0.00 35.77 3.16
1664 1702 5.989777 ACTTTGTACTAAATCAGCGACAAGT 59.010 36.000 0.00 0.00 35.77 3.16
1665 1703 7.149973 ACTTTGTACTAAATCAGCGACAAGTA 58.850 34.615 0.00 0.00 35.77 2.24
1666 1704 7.654520 ACTTTGTACTAAATCAGCGACAAGTAA 59.345 33.333 0.00 0.00 35.77 2.24
1667 1705 8.542497 TTTGTACTAAATCAGCGACAAGTAAT 57.458 30.769 0.00 0.00 35.77 1.89
1668 1706 9.642327 TTTGTACTAAATCAGCGACAAGTAATA 57.358 29.630 0.00 0.00 35.77 0.98
1669 1707 9.811995 TTGTACTAAATCAGCGACAAGTAATAT 57.188 29.630 0.00 0.00 31.65 1.28
1670 1708 9.244799 TGTACTAAATCAGCGACAAGTAATATG 57.755 33.333 0.00 0.00 0.00 1.78
1671 1709 7.715265 ACTAAATCAGCGACAAGTAATATGG 57.285 36.000 0.00 0.00 0.00 2.74
1672 1710 7.497595 ACTAAATCAGCGACAAGTAATATGGA 58.502 34.615 0.00 0.00 0.00 3.41
1673 1711 7.985184 ACTAAATCAGCGACAAGTAATATGGAA 59.015 33.333 0.00 0.00 0.00 3.53
1674 1712 6.604735 AATCAGCGACAAGTAATATGGAAC 57.395 37.500 0.00 0.00 0.00 3.62
1675 1713 4.109766 TCAGCGACAAGTAATATGGAACG 58.890 43.478 0.00 0.00 0.00 3.95
1676 1714 3.245284 CAGCGACAAGTAATATGGAACGG 59.755 47.826 0.00 0.00 0.00 4.44
1677 1715 3.131577 AGCGACAAGTAATATGGAACGGA 59.868 43.478 0.00 0.00 0.00 4.69
1678 1716 3.489785 GCGACAAGTAATATGGAACGGAG 59.510 47.826 0.00 0.00 0.00 4.63
1679 1717 4.049186 CGACAAGTAATATGGAACGGAGG 58.951 47.826 0.00 0.00 0.00 4.30
1680 1718 4.377897 GACAAGTAATATGGAACGGAGGG 58.622 47.826 0.00 0.00 0.00 4.30
1681 1719 4.035112 ACAAGTAATATGGAACGGAGGGA 58.965 43.478 0.00 0.00 0.00 4.20
1682 1720 4.101119 ACAAGTAATATGGAACGGAGGGAG 59.899 45.833 0.00 0.00 0.00 4.30
1683 1721 3.924922 AGTAATATGGAACGGAGGGAGT 58.075 45.455 0.00 0.00 0.00 3.85
1684 1722 5.070823 AGTAATATGGAACGGAGGGAGTA 57.929 43.478 0.00 0.00 0.00 2.59
1731 1769 1.405121 GGTATGACCGCCTTTTCGAGT 60.405 52.381 0.00 0.00 0.00 4.18
1833 1873 3.948473 GTCCTTATTTTCCCTTCTGGAGC 59.052 47.826 0.00 0.00 46.24 4.70
1844 1884 0.036732 TTCTGGAGCATGTGTCACCC 59.963 55.000 0.00 0.00 0.00 4.61
1899 1939 7.279758 AGCTATGTTTCTTCAAATCTCTGTAGC 59.720 37.037 0.00 0.00 0.00 3.58
1946 1987 6.693113 CCTTGTGAACTGAGCTTTAAAGTTTC 59.307 38.462 16.38 14.02 34.37 2.78
1987 2028 8.644374 TCAAGCAAAATTATAACTACAAGGGT 57.356 30.769 0.00 0.00 0.00 4.34
2004 2045 6.122964 ACAAGGGTCCAGCTAAAGATAATTC 58.877 40.000 0.00 0.00 0.00 2.17
2010 2051 6.864165 GGTCCAGCTAAAGATAATTCTCTACG 59.136 42.308 0.00 0.00 0.00 3.51
2049 2090 1.917872 AAGGCCGTCCATTTAGCAAA 58.082 45.000 0.00 0.00 33.74 3.68
2251 2292 9.453572 TGTGAGAAGCATCTATATGAACTTTTT 57.546 29.630 0.00 0.00 35.54 1.94
2493 2534 2.901249 TCAAACTAGATGCTAACCCGC 58.099 47.619 0.00 0.00 0.00 6.13
2502 2543 3.419759 CTAACCCGCGCGTTGCTT 61.420 61.111 29.95 15.41 43.27 3.91
2503 2544 2.961669 CTAACCCGCGCGTTGCTTT 61.962 57.895 29.95 15.36 43.27 3.51
2517 2558 1.337118 TGCTTTGGGGATTGGTTGAC 58.663 50.000 0.00 0.00 0.00 3.18
2527 2569 7.416964 TGGGGATTGGTTGACATATTTTTAG 57.583 36.000 0.00 0.00 0.00 1.85
2626 2670 7.631822 CATTTCTCATGCATGTTAAGAGAGAG 58.368 38.462 25.43 12.50 36.77 3.20
2627 2671 5.273674 TCTCATGCATGTTAAGAGAGAGG 57.726 43.478 25.43 0.00 32.11 3.69
2631 2675 6.053650 TCATGCATGTTAAGAGAGAGGATTG 58.946 40.000 25.43 0.00 0.00 2.67
2880 3128 0.996462 TCGCAGCGCATTGTAGTTAC 59.004 50.000 10.87 0.00 0.00 2.50
2884 3132 2.095853 GCAGCGCATTGTAGTTACACAT 59.904 45.455 11.47 0.00 35.64 3.21
2989 3237 5.920273 CAGTTTGTGTTCATGGATTTGGTAC 59.080 40.000 0.00 0.00 0.00 3.34
3027 3277 9.628746 TGACTCAAATATGTCATGACAATTTTG 57.371 29.630 34.19 34.19 45.41 2.44
3049 3301 7.504922 TTGTTTCTCGATTCTGTTTGTTTTG 57.495 32.000 0.00 0.00 0.00 2.44
3177 3431 2.706555 GCACTGGCTGGTACTTTTTC 57.293 50.000 0.00 0.00 36.96 2.29
3194 3448 3.006728 CTTCTACCGGGGTGGCCA 61.007 66.667 0.00 0.00 43.94 5.36
3209 3463 3.383505 GGTGGCCAAAAGAACAAGTAACT 59.616 43.478 7.24 0.00 0.00 2.24
3215 3469 5.529800 GCCAAAAGAACAAGTAACTGGTCTA 59.470 40.000 0.00 0.00 42.70 2.59
3255 3509 3.486383 GGAATTCAGAACCTTGGTCACA 58.514 45.455 7.93 0.00 0.00 3.58
3277 3531 0.611896 ACAATTACCTGCCACCTGCC 60.612 55.000 0.00 0.00 40.16 4.85
3325 3579 2.353889 GCACATGCTGTAAGTGATGAGG 59.646 50.000 5.31 0.00 38.21 3.86
3332 3586 6.985188 TGCTGTAAGTGATGAGGTAATTTC 57.015 37.500 0.00 0.00 35.30 2.17
3382 3636 6.351371 CCAGTCACTACAGGAGTTTATGTGAT 60.351 42.308 0.00 0.00 35.64 3.06
3607 3861 6.542370 GTCTAAGGATGGCAGTTTTAAGCATA 59.458 38.462 0.00 0.00 0.00 3.14
3748 4006 5.629020 CGCCCATCCGATTAACATTTTAATG 59.371 40.000 1.59 1.03 37.92 1.90
3846 4117 5.070001 CCCCCGTCATCATAATATGTTGTT 58.930 41.667 10.15 0.00 33.00 2.83
3848 4119 5.048782 CCCCGTCATCATAATATGTTGTTGG 60.049 44.000 10.15 11.75 33.00 3.77
3901 4172 8.572828 TTGCTATGTTTGAGTTGTTATTTGTG 57.427 30.769 0.00 0.00 0.00 3.33
3918 4189 0.807496 GTGCATGCTGAGAAGAACCC 59.193 55.000 20.33 0.00 0.00 4.11
4015 4286 1.377202 AAGCACTACCGTGGGCATG 60.377 57.895 0.00 0.00 41.51 4.06
4041 4312 0.178990 GGGTATCTTCATGGGTGGGC 60.179 60.000 0.00 0.00 0.00 5.36
4042 4313 0.846693 GGTATCTTCATGGGTGGGCT 59.153 55.000 0.00 0.00 0.00 5.19
4065 4336 3.559069 TCCATTGCCATCATTCTCCTTC 58.441 45.455 0.00 0.00 0.00 3.46
4066 4337 2.626743 CCATTGCCATCATTCTCCTTCC 59.373 50.000 0.00 0.00 0.00 3.46
4110 4381 1.004745 GAAGTGGAGCCTGAAATCCCA 59.995 52.381 0.00 0.00 34.47 4.37
4119 4390 1.001974 CCTGAAATCCCACTCGTCACA 59.998 52.381 0.00 0.00 0.00 3.58
4306 4607 7.710907 TCTCATCATAATTTACCTTTCCAGACG 59.289 37.037 0.00 0.00 0.00 4.18
4318 4619 3.386768 TTCCAGACGTCCTTTGAAGAG 57.613 47.619 13.01 0.00 0.00 2.85
4436 4737 7.827701 TCCTATTATGTGCTATTACCTTCTCG 58.172 38.462 0.00 0.00 0.00 4.04
4437 4738 7.036220 CCTATTATGTGCTATTACCTTCTCGG 58.964 42.308 0.00 0.00 39.35 4.63
4461 4762 6.810182 GGTCTTTTCGATACTGTGCTAGTTAA 59.190 38.462 0.00 0.00 40.89 2.01
4693 5006 6.315144 TCATACAACGACAAGTAATCCCATTG 59.685 38.462 0.00 0.00 0.00 2.82
4726 5039 1.785041 TTTTGCACTCAGGCGAGCAC 61.785 55.000 6.32 0.87 43.66 4.40
4739 5052 1.268234 GCGAGCACATCATTTGGTAGC 60.268 52.381 0.00 0.00 36.24 3.58
4772 5085 6.902948 TGTCTAAACATTGACGTTTCTTTTCG 59.097 34.615 0.00 0.00 39.70 3.46
4782 5142 5.522460 TGACGTTTCTTTTCGAGTGAAGAAT 59.478 36.000 16.38 6.82 40.44 2.40
4817 5180 9.646427 GCCTTTTATGTTCATGTTATTGGTTAA 57.354 29.630 0.00 0.00 0.00 2.01
4861 5224 5.208294 TCTCTCCTAGTATGGTTTCCTGT 57.792 43.478 0.00 0.00 0.00 4.00
4935 5308 3.573538 GAGCTTGCATCCTCTCTCAGATA 59.426 47.826 6.83 0.00 0.00 1.98
4949 5322 4.540715 TCTCAGATACTGGCTTGATCAGA 58.459 43.478 0.00 0.00 36.22 3.27
4989 5363 6.823689 AGCTGGTTAACGTCATCTGAATTATT 59.176 34.615 0.00 0.00 0.00 1.40
4991 5365 7.640240 GCTGGTTAACGTCATCTGAATTATTTC 59.360 37.037 0.00 0.00 0.00 2.17
5186 5563 2.039879 GAGCTAGTTTTCTTGTCCCCCA 59.960 50.000 0.00 0.00 0.00 4.96
5272 5655 2.363975 GGACCATCTACACCGGGCA 61.364 63.158 6.32 0.00 0.00 5.36
5316 5700 1.304617 CTGGGCCCCTTTCTCCTTC 59.695 63.158 22.27 0.00 0.00 3.46
5394 5783 3.708563 AACAAACGGTGAATGTGGAAG 57.291 42.857 0.00 0.00 0.00 3.46
5724 6116 3.120979 CTCCGTCGCGACCTGCATA 62.121 63.158 31.84 11.01 46.97 3.14
5728 6120 0.317519 CGTCGCGACCTGCATACATA 60.318 55.000 31.84 0.00 46.97 2.29
5729 6121 1.409412 GTCGCGACCTGCATACATAG 58.591 55.000 28.61 0.00 46.97 2.23
5730 6122 1.029681 TCGCGACCTGCATACATAGT 58.970 50.000 3.71 0.00 46.97 2.12
5748 6140 0.437295 GTACACGGTTAACAGCAGCG 59.563 55.000 8.10 3.84 40.95 5.18
5752 6144 2.019951 CGGTTAACAGCAGCGTCGT 61.020 57.895 8.10 0.00 0.00 4.34
6009 6402 1.734477 CTTCGTGACCGTCAGCTGG 60.734 63.158 15.13 0.00 35.01 4.85
6087 6484 5.334105 CGACACAAGAGGATTTACTTGGTTG 60.334 44.000 0.00 0.00 45.03 3.77
6088 6485 4.827284 ACACAAGAGGATTTACTTGGTTGG 59.173 41.667 0.00 0.00 45.03 3.77
6089 6486 4.827284 CACAAGAGGATTTACTTGGTTGGT 59.173 41.667 0.00 0.00 45.03 3.67
6090 6487 5.301805 CACAAGAGGATTTACTTGGTTGGTT 59.698 40.000 0.00 0.00 45.03 3.67
6115 6512 6.884295 TCACCATTGGAGAACTTATTTACAGG 59.116 38.462 10.37 0.00 0.00 4.00
6121 6518 4.876679 GGAGAACTTATTTACAGGACCTGC 59.123 45.833 21.95 0.84 34.37 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 81 1.660575 GTCCCATATCGCCACGTCG 60.661 63.158 0.00 0.00 0.00 5.12
114 118 1.815003 TTGCATCGCCACCATCTCG 60.815 57.895 0.00 0.00 0.00 4.04
225 235 1.175983 CCTTGCCCCTTGCGTTTACA 61.176 55.000 0.00 0.00 45.60 2.41
233 243 0.334676 TAATCACCCCTTGCCCCTTG 59.665 55.000 0.00 0.00 0.00 3.61
295 307 5.707764 AGAAGTTGAGACAAAAATAGCCCTC 59.292 40.000 0.00 0.00 0.00 4.30
309 321 5.023533 ACTACTGTTTGCAGAAGTTGAGA 57.976 39.130 11.72 0.00 45.28 3.27
495 510 8.554528 CATCTCACGCACTAAAATATCTTTCAT 58.445 33.333 0.00 0.00 0.00 2.57
519 534 1.799994 GCTTTGAAATTTGGCACGCAT 59.200 42.857 0.00 0.00 0.00 4.73
571 586 4.360951 AAGTTTACTGTTTGGATCCCGA 57.639 40.909 9.90 0.00 0.00 5.14
572 587 5.447624 AAAAGTTTACTGTTTGGATCCCG 57.552 39.130 9.90 0.00 0.00 5.14
596 625 5.853572 AAAGGACTAATTTGGGGTCTGTA 57.146 39.130 0.00 0.00 0.00 2.74
618 647 2.371841 TCTGGGTAGCTCTCAGCAAAAA 59.628 45.455 7.86 0.00 45.56 1.94
619 648 1.977854 TCTGGGTAGCTCTCAGCAAAA 59.022 47.619 7.86 0.00 45.56 2.44
635 665 8.869897 CAAATTTCAGATCATTTGAATGTCTGG 58.130 33.333 21.92 12.40 41.18 3.86
650 680 2.513753 TGTCCGTGCCAAATTTCAGAT 58.486 42.857 0.00 0.00 0.00 2.90
681 711 7.848223 AAAAAGTTTTTGGAGAAAGATGGTG 57.152 32.000 12.74 0.00 0.00 4.17
743 774 1.004745 ACATGAGCCGGGAGTGAAATT 59.995 47.619 2.18 0.00 0.00 1.82
745 776 0.321564 CACATGAGCCGGGAGTGAAA 60.322 55.000 2.18 0.00 32.14 2.69
746 777 1.191489 TCACATGAGCCGGGAGTGAA 61.191 55.000 2.18 0.00 36.39 3.18
747 778 1.191489 TTCACATGAGCCGGGAGTGA 61.191 55.000 2.18 0.38 37.43 3.41
772 803 4.035102 GAGAGGGGCGTTTGGGCT 62.035 66.667 0.00 0.00 41.87 5.19
773 804 2.595009 CTAGAGAGGGGCGTTTGGGC 62.595 65.000 0.00 0.00 41.35 5.36
774 805 1.265454 ACTAGAGAGGGGCGTTTGGG 61.265 60.000 0.00 0.00 0.00 4.12
993 1024 1.215382 GAGGGCGGCCATTGTTTTC 59.785 57.895 31.59 13.26 0.00 2.29
1191 1222 9.298250 GGAACACACTATGATATCTCCTACTAA 57.702 37.037 3.98 0.00 0.00 2.24
1192 1223 7.606839 CGGAACACACTATGATATCTCCTACTA 59.393 40.741 3.98 0.00 0.00 1.82
1193 1224 6.431543 CGGAACACACTATGATATCTCCTACT 59.568 42.308 3.98 0.00 0.00 2.57
1194 1225 6.613233 CGGAACACACTATGATATCTCCTAC 58.387 44.000 3.98 0.00 0.00 3.18
1309 1340 7.040201 CCATATGTAGAGGAATGTGATTTTGGG 60.040 40.741 1.24 0.00 0.00 4.12
1319 1350 6.484643 CAGAACCAACCATATGTAGAGGAATG 59.515 42.308 1.24 0.00 0.00 2.67
1369 1400 3.496870 GGCCTTCAGGTGAAAGAAGAGAA 60.497 47.826 0.00 0.00 42.95 2.87
1421 1452 1.737363 GCTGAGCAAAGAGGAGGTACG 60.737 57.143 0.00 0.00 0.00 3.67
1504 1537 5.547465 AGACAAACACAGGAATATGTCGAA 58.453 37.500 0.00 0.00 41.43 3.71
1601 1639 1.417890 AGCAATATGGAACGGAGGGAG 59.582 52.381 0.00 0.00 0.00 4.30
1602 1640 1.416401 GAGCAATATGGAACGGAGGGA 59.584 52.381 0.00 0.00 0.00 4.20
1603 1641 1.873903 CGAGCAATATGGAACGGAGGG 60.874 57.143 0.00 0.00 0.00 4.30
1604 1642 1.202533 ACGAGCAATATGGAACGGAGG 60.203 52.381 0.00 0.00 0.00 4.30
1605 1643 2.128035 GACGAGCAATATGGAACGGAG 58.872 52.381 0.00 0.00 0.00 4.63
1606 1644 1.535226 CGACGAGCAATATGGAACGGA 60.535 52.381 0.00 0.00 0.00 4.69
1607 1645 0.852777 CGACGAGCAATATGGAACGG 59.147 55.000 0.00 0.00 0.00 4.44
1620 1658 4.413087 AGTTGTACTAAATCAGCGACGAG 58.587 43.478 0.00 0.00 0.00 4.18
1621 1659 4.430137 AGTTGTACTAAATCAGCGACGA 57.570 40.909 0.00 0.00 0.00 4.20
1622 1660 5.107607 ACAAAGTTGTACTAAATCAGCGACG 60.108 40.000 0.00 0.00 40.16 5.12
1623 1661 6.224420 ACAAAGTTGTACTAAATCAGCGAC 57.776 37.500 0.00 0.00 40.16 5.19
1636 1674 6.924612 TGTCGCTGATTTAGTACAAAGTTGTA 59.075 34.615 0.00 0.00 42.35 2.41
1637 1675 5.756347 TGTCGCTGATTTAGTACAAAGTTGT 59.244 36.000 1.75 1.75 44.86 3.32
1638 1676 6.223138 TGTCGCTGATTTAGTACAAAGTTG 57.777 37.500 0.00 0.00 0.00 3.16
1639 1677 6.482308 ACTTGTCGCTGATTTAGTACAAAGTT 59.518 34.615 0.00 0.00 35.46 2.66
1640 1678 5.989777 ACTTGTCGCTGATTTAGTACAAAGT 59.010 36.000 0.00 0.00 35.46 2.66
1641 1679 6.467723 ACTTGTCGCTGATTTAGTACAAAG 57.532 37.500 0.00 0.00 35.46 2.77
1642 1680 7.949903 TTACTTGTCGCTGATTTAGTACAAA 57.050 32.000 0.00 0.00 35.46 2.83
1643 1681 9.811995 ATATTACTTGTCGCTGATTTAGTACAA 57.188 29.630 0.00 0.00 34.99 2.41
1644 1682 9.244799 CATATTACTTGTCGCTGATTTAGTACA 57.755 33.333 0.00 0.00 0.00 2.90
1645 1683 8.700644 CCATATTACTTGTCGCTGATTTAGTAC 58.299 37.037 0.00 0.00 0.00 2.73
1646 1684 8.635328 TCCATATTACTTGTCGCTGATTTAGTA 58.365 33.333 0.00 0.00 0.00 1.82
1647 1685 7.497595 TCCATATTACTTGTCGCTGATTTAGT 58.502 34.615 0.00 0.00 0.00 2.24
1648 1686 7.946655 TCCATATTACTTGTCGCTGATTTAG 57.053 36.000 0.00 0.00 0.00 1.85
1649 1687 7.042992 CGTTCCATATTACTTGTCGCTGATTTA 60.043 37.037 0.00 0.00 0.00 1.40
1650 1688 6.238103 CGTTCCATATTACTTGTCGCTGATTT 60.238 38.462 0.00 0.00 0.00 2.17
1651 1689 5.234329 CGTTCCATATTACTTGTCGCTGATT 59.766 40.000 0.00 0.00 0.00 2.57
1652 1690 4.745125 CGTTCCATATTACTTGTCGCTGAT 59.255 41.667 0.00 0.00 0.00 2.90
1653 1691 4.109766 CGTTCCATATTACTTGTCGCTGA 58.890 43.478 0.00 0.00 0.00 4.26
1654 1692 3.245284 CCGTTCCATATTACTTGTCGCTG 59.755 47.826 0.00 0.00 0.00 5.18
1655 1693 3.131577 TCCGTTCCATATTACTTGTCGCT 59.868 43.478 0.00 0.00 0.00 4.93
1656 1694 3.450578 TCCGTTCCATATTACTTGTCGC 58.549 45.455 0.00 0.00 0.00 5.19
1657 1695 4.049186 CCTCCGTTCCATATTACTTGTCG 58.951 47.826 0.00 0.00 0.00 4.35
1658 1696 4.100498 TCCCTCCGTTCCATATTACTTGTC 59.900 45.833 0.00 0.00 0.00 3.18
1659 1697 4.035112 TCCCTCCGTTCCATATTACTTGT 58.965 43.478 0.00 0.00 0.00 3.16
1660 1698 4.101119 ACTCCCTCCGTTCCATATTACTTG 59.899 45.833 0.00 0.00 0.00 3.16
1661 1699 4.296056 ACTCCCTCCGTTCCATATTACTT 58.704 43.478 0.00 0.00 0.00 2.24
1662 1700 3.924922 ACTCCCTCCGTTCCATATTACT 58.075 45.455 0.00 0.00 0.00 2.24
1663 1701 4.831710 ACTACTCCCTCCGTTCCATATTAC 59.168 45.833 0.00 0.00 0.00 1.89
1664 1702 5.070823 ACTACTCCCTCCGTTCCATATTA 57.929 43.478 0.00 0.00 0.00 0.98
1665 1703 3.924922 ACTACTCCCTCCGTTCCATATT 58.075 45.455 0.00 0.00 0.00 1.28
1666 1704 3.614568 ACTACTCCCTCCGTTCCATAT 57.385 47.619 0.00 0.00 0.00 1.78
1667 1705 3.393426 AACTACTCCCTCCGTTCCATA 57.607 47.619 0.00 0.00 0.00 2.74
1668 1706 2.249309 AACTACTCCCTCCGTTCCAT 57.751 50.000 0.00 0.00 0.00 3.41
1669 1707 2.019807 AAACTACTCCCTCCGTTCCA 57.980 50.000 0.00 0.00 0.00 3.53
1670 1708 4.502016 CTTAAAACTACTCCCTCCGTTCC 58.498 47.826 0.00 0.00 0.00 3.62
1671 1709 4.502016 CCTTAAAACTACTCCCTCCGTTC 58.498 47.826 0.00 0.00 0.00 3.95
1672 1710 3.262660 CCCTTAAAACTACTCCCTCCGTT 59.737 47.826 0.00 0.00 0.00 4.44
1673 1711 2.836372 CCCTTAAAACTACTCCCTCCGT 59.164 50.000 0.00 0.00 0.00 4.69
1674 1712 2.419713 GCCCTTAAAACTACTCCCTCCG 60.420 54.545 0.00 0.00 0.00 4.63
1675 1713 2.092538 GGCCCTTAAAACTACTCCCTCC 60.093 54.545 0.00 0.00 0.00 4.30
1676 1714 2.574824 TGGCCCTTAAAACTACTCCCTC 59.425 50.000 0.00 0.00 0.00 4.30
1677 1715 2.639487 TGGCCCTTAAAACTACTCCCT 58.361 47.619 0.00 0.00 0.00 4.20
1678 1716 3.288092 CATGGCCCTTAAAACTACTCCC 58.712 50.000 0.00 0.00 0.00 4.30
1679 1717 2.688446 GCATGGCCCTTAAAACTACTCC 59.312 50.000 0.00 0.00 0.00 3.85
1680 1718 3.352648 TGCATGGCCCTTAAAACTACTC 58.647 45.455 0.00 0.00 0.00 2.59
1681 1719 3.010138 TCTGCATGGCCCTTAAAACTACT 59.990 43.478 0.00 0.00 0.00 2.57
1682 1720 3.352648 TCTGCATGGCCCTTAAAACTAC 58.647 45.455 0.00 0.00 0.00 2.73
1683 1721 3.620488 CTCTGCATGGCCCTTAAAACTA 58.380 45.455 0.00 0.00 0.00 2.24
1684 1722 2.450476 CTCTGCATGGCCCTTAAAACT 58.550 47.619 0.00 0.00 0.00 2.66
1708 1746 0.750546 GAAAAGGCGGTCATACCCCC 60.751 60.000 0.00 0.00 36.44 5.40
1741 1781 9.715121 ATAAGTGAATACGTTCTCCTAAAAACA 57.285 29.630 0.00 0.00 35.33 2.83
1789 1829 7.224753 AGGACATGTAGCAGTGAATTATTTACG 59.775 37.037 0.00 0.00 0.00 3.18
1844 1884 1.446907 GGTGCATTGAGAGGTGAGTG 58.553 55.000 0.00 0.00 0.00 3.51
1899 1939 5.968387 GGTTCAGTATCTGTACCATTTCG 57.032 43.478 16.66 0.00 46.51 3.46
1911 1951 4.894784 TCAGTTCACAAGGGTTCAGTATC 58.105 43.478 0.00 0.00 0.00 2.24
1912 1952 4.804261 GCTCAGTTCACAAGGGTTCAGTAT 60.804 45.833 0.00 0.00 0.00 2.12
1913 1953 3.494398 GCTCAGTTCACAAGGGTTCAGTA 60.494 47.826 0.00 0.00 0.00 2.74
1961 2002 8.739972 ACCCTTGTAGTTATAATTTTGCTTGAG 58.260 33.333 0.00 0.00 0.00 3.02
1987 2028 6.040504 TGCGTAGAGAATTATCTTTAGCTGGA 59.959 38.462 8.09 0.00 35.54 3.86
2004 2045 2.096496 CCTTTGCTTTCCATGCGTAGAG 59.904 50.000 0.00 0.00 0.00 2.43
2031 2072 1.173913 GTTTGCTAAATGGACGGCCT 58.826 50.000 9.82 0.00 34.31 5.19
2078 2119 2.798148 CTTCCACGCACCCCTGGTAC 62.798 65.000 0.00 0.00 32.11 3.34
2251 2292 0.251297 CTGTTGTTGCATGGAGGGGA 60.251 55.000 0.00 0.00 0.00 4.81
2493 2534 1.444212 CAATCCCCAAAGCAACGCG 60.444 57.895 3.53 3.53 0.00 6.01
2502 2543 6.694445 AAAAATATGTCAACCAATCCCCAA 57.306 33.333 0.00 0.00 0.00 4.12
2503 2544 6.957020 ACTAAAAATATGTCAACCAATCCCCA 59.043 34.615 0.00 0.00 0.00 4.96
2626 2670 4.339247 CCACCTCATCAATTACACCAATCC 59.661 45.833 0.00 0.00 0.00 3.01
2627 2671 4.202050 GCCACCTCATCAATTACACCAATC 60.202 45.833 0.00 0.00 0.00 2.67
2631 2675 2.722094 TGCCACCTCATCAATTACACC 58.278 47.619 0.00 0.00 0.00 4.16
2846 3094 5.163963 TGCGCTGCGATATAAATGATAAGTG 60.164 40.000 28.07 0.00 0.00 3.16
2851 3099 4.154737 ACAATGCGCTGCGATATAAATGAT 59.845 37.500 28.07 0.09 0.00 2.45
2863 3111 1.463056 TGTGTAACTACAATGCGCTGC 59.537 47.619 9.73 0.00 38.04 5.25
2880 3128 8.402472 TGAAAGTGTAAGAAAGTGGTAAATGTG 58.598 33.333 0.00 0.00 0.00 3.21
2884 3132 8.974060 ATCTGAAAGTGTAAGAAAGTGGTAAA 57.026 30.769 0.00 0.00 33.76 2.01
3027 3277 6.076092 CGTCAAAACAAACAGAATCGAGAAAC 60.076 38.462 0.00 0.00 0.00 2.78
3177 3431 2.132089 TTTGGCCACCCCGGTAGAAG 62.132 60.000 3.88 0.00 36.97 2.85
3209 3463 6.373216 CGGTTGGAATTTCTGTTAATAGACCA 59.627 38.462 0.77 3.56 0.00 4.02
3240 3494 2.364632 TGTGTTGTGACCAAGGTTCTG 58.635 47.619 0.00 0.00 0.00 3.02
3255 3509 2.238521 CAGGTGGCAGGTAATTGTGTT 58.761 47.619 0.00 0.00 0.00 3.32
3325 3579 5.176592 AGCTTCCTAACTGTCCGAAATTAC 58.823 41.667 0.00 0.00 0.00 1.89
3332 3586 3.018149 ACTCTAGCTTCCTAACTGTCCG 58.982 50.000 0.00 0.00 0.00 4.79
3382 3636 8.141909 GCATAACTCAGTACATAGTTATCCACA 58.858 37.037 21.13 5.71 43.63 4.17
3545 3799 5.611796 TGGATCGAAACATCTGTGAAAAG 57.388 39.130 0.00 0.00 0.00 2.27
3607 3861 5.839063 TCTCAGATACCGGATATCAAAACCT 59.161 40.000 9.46 0.00 42.11 3.50
3655 3909 6.243216 TGGGTTACCTATGGACAAAGATAC 57.757 41.667 0.00 0.00 37.76 2.24
3659 3913 5.505780 TGATTGGGTTACCTATGGACAAAG 58.494 41.667 0.00 0.00 37.76 2.77
3669 3923 2.573463 ACCTCCATGATTGGGTTACCT 58.427 47.619 0.00 0.00 43.81 3.08
3846 4117 8.482943 AGCTCAACAACTATGTATACAATACCA 58.517 33.333 10.14 0.00 39.40 3.25
3862 4133 7.594758 TCAAACATAGCAAATAAGCTCAACAAC 59.405 33.333 0.00 0.00 45.26 3.32
3901 4172 0.674895 ACGGGTTCTTCTCAGCATGC 60.675 55.000 10.51 10.51 34.76 4.06
3980 4251 0.680921 CTTGTCACCCGCCCATGAAT 60.681 55.000 0.00 0.00 0.00 2.57
4015 4286 1.355720 CCATGAAGATACCCATCCCCC 59.644 57.143 0.00 0.00 0.00 5.40
4041 4312 4.919793 AGGAGAATGATGGCAATGGATAG 58.080 43.478 0.00 0.00 0.00 2.08
4042 4313 5.319453 GAAGGAGAATGATGGCAATGGATA 58.681 41.667 0.00 0.00 0.00 2.59
4110 4381 4.579454 TTTTAGCTAGTGTGTGACGAGT 57.421 40.909 0.00 0.00 30.27 4.18
4306 4607 0.036858 AGCGGCTCTCTTCAAAGGAC 60.037 55.000 0.00 0.00 0.00 3.85
4318 4619 0.992802 CTGACTCGTTTAAGCGGCTC 59.007 55.000 11.93 7.14 0.00 4.70
4436 4737 4.745649 ACTAGCACAGTATCGAAAAGACC 58.254 43.478 0.00 0.00 34.98 3.85
4437 4738 7.807687 TTAACTAGCACAGTATCGAAAAGAC 57.192 36.000 0.00 0.00 36.04 3.01
4461 4762 6.346096 AGTGTGCACGGATATACAGTAAAAT 58.654 36.000 13.13 0.00 36.20 1.82
4540 4846 1.555075 GTCAGCCTAACAGTGATGGGA 59.445 52.381 7.00 0.00 0.00 4.37
4670 4983 6.093495 CACAATGGGATTACTTGTCGTTGTAT 59.907 38.462 0.00 0.00 30.99 2.29
4726 5039 1.648720 CGGCCGCTACCAAATGATG 59.351 57.895 14.67 0.00 0.00 3.07
4739 5052 0.802494 AATGTTTAGACAAGCGGCCG 59.198 50.000 24.05 24.05 39.66 6.13
4772 5085 4.322567 AGGCTGTTGAGAATTCTTCACTC 58.677 43.478 9.87 6.00 0.00 3.51
4782 5142 6.265196 ACATGAACATAAAAGGCTGTTGAGAA 59.735 34.615 0.00 0.00 35.80 2.87
4789 5149 7.322664 ACCAATAACATGAACATAAAAGGCTG 58.677 34.615 0.00 0.00 0.00 4.85
4935 5308 4.498894 TCATCAATCTGATCAAGCCAGT 57.501 40.909 0.00 0.00 34.28 4.00
4949 5322 3.596101 ACCAGCTCTAGGGATCATCAAT 58.404 45.455 0.00 0.00 0.00 2.57
4989 5363 2.105134 TCCTGCGAAACAAGGTAAGGAA 59.895 45.455 0.00 0.00 29.56 3.36
4991 5365 2.076863 CTCCTGCGAAACAAGGTAAGG 58.923 52.381 0.00 0.00 0.00 2.69
5209 5586 7.816945 AAAGAGACAATGTTGTGAACTTTTG 57.183 32.000 2.65 0.00 42.43 2.44
5239 5616 5.564550 AGATGGTCCCAGTATGATAAATGC 58.435 41.667 0.00 0.00 39.69 3.56
5316 5700 5.696270 TGTTAAGACTACACATTGTCAGCTG 59.304 40.000 7.63 7.63 35.81 4.24
5394 5783 4.356289 ACATTTTCCAACGTGTACTTTGC 58.644 39.130 0.00 0.00 0.00 3.68
5592 5984 0.896226 ACCCTACAGAGTTCTTCCGC 59.104 55.000 0.00 0.00 0.00 5.54
5724 6116 4.491676 CTGCTGTTAACCGTGTACTATGT 58.508 43.478 2.48 0.00 0.00 2.29
5728 6120 1.792006 GCTGCTGTTAACCGTGTACT 58.208 50.000 2.48 0.00 0.00 2.73
5729 6121 0.437295 CGCTGCTGTTAACCGTGTAC 59.563 55.000 2.48 0.00 0.00 2.90
5730 6122 0.032403 ACGCTGCTGTTAACCGTGTA 59.968 50.000 2.48 0.00 0.00 2.90
5748 6140 2.380084 TGGACCAGAGCATTTACGAC 57.620 50.000 0.00 0.00 0.00 4.34
5752 6144 2.565391 TCGACTTGGACCAGAGCATTTA 59.435 45.455 0.00 0.00 0.00 1.40
5851 6243 3.775654 GGGCCTCACTCGGTCAGG 61.776 72.222 0.84 0.00 0.00 3.86
5852 6244 2.681778 AGGGCCTCACTCGGTCAG 60.682 66.667 0.00 0.00 0.00 3.51
6009 6402 2.613506 CCCGTTCTTCAACCGCCAC 61.614 63.158 0.00 0.00 0.00 5.01
6089 6486 7.393234 CCTGTAAATAAGTTCTCCAATGGTGAA 59.607 37.037 12.24 12.24 33.56 3.18
6090 6487 6.884295 CCTGTAAATAAGTTCTCCAATGGTGA 59.116 38.462 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.