Multiple sequence alignment - TraesCS7A01G566500

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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 TraesCS7A01G566500 chr7A 100.000 5735 0 0 1 5735 735786950 735781216 0.000000e+00 10591.0
1 TraesCS7A01G566500 chr7A 91.191 2066 165 14 2390 4448 735962518 735964573 0.000000e+00 2791.0
2 TraesCS7A01G566500 chr7A 89.196 2064 211 11 2390 4448 735844230 735842174 0.000000e+00 2566.0
3 TraesCS7A01G566500 chr7A 88.840 2061 224 5 2390 4448 736006525 736004469 0.000000e+00 2527.0
4 TraesCS7A01G566500 chr7A 91.532 1488 90 18 696 2178 735960313 735961769 0.000000e+00 2017.0
5 TraesCS7A01G566500 chr7A 88.820 1297 119 9 2248 3525 736001662 736000373 0.000000e+00 1568.0
6 TraesCS7A01G566500 chr7A 87.024 1156 127 14 905 2056 736096560 736095424 0.000000e+00 1282.0
7 TraesCS7A01G566500 chr7A 81.885 1369 216 22 779 2136 736329700 736328353 0.000000e+00 1125.0
8 TraesCS7A01G566500 chr7A 92.284 648 31 7 5095 5734 735946228 735946864 0.000000e+00 902.0
9 TraesCS7A01G566500 chr7A 91.654 647 52 1 4448 5094 736004440 736003796 0.000000e+00 894.0
10 TraesCS7A01G566500 chr7A 86.462 650 68 7 4446 5094 735930019 735930649 0.000000e+00 695.0
11 TraesCS7A01G566500 chr7A 81.363 499 84 7 5244 5735 736067397 736066901 1.160000e-106 398.0
12 TraesCS7A01G566500 chr7A 80.876 502 81 12 5244 5735 735999006 735998510 1.170000e-101 381.0
13 TraesCS7A01G566500 chr7A 78.535 587 115 8 5113 5694 736324287 736323707 5.430000e-100 375.0
14 TraesCS7A01G566500 chr7A 80.728 467 80 6 5250 5710 736003583 736003121 7.070000e-94 355.0
15 TraesCS7A01G566500 chr7A 78.522 433 48 27 42 454 735959757 735960164 5.740000e-60 243.0
16 TraesCS7A01G566500 chr7A 82.432 296 21 15 525 794 736096979 736096689 4.470000e-56 230.0
17 TraesCS7A01G566500 chr7A 91.667 72 5 1 384 455 193933148 193933218 1.320000e-16 99.0
18 TraesCS7A01G566500 chr7A 91.549 71 1 3 157 227 193932805 193932870 6.120000e-15 93.5
19 TraesCS7A01G566500 chr7A 94.545 55 0 2 173 227 736097873 736097822 1.320000e-11 82.4
20 TraesCS7A01G566500 chr7A 97.727 44 1 0 397 440 736097044 736097001 6.160000e-10 76.8
21 TraesCS7A01G566500 chr7A 87.692 65 4 4 2125 2189 736002294 736002234 7.970000e-09 73.1
22 TraesCS7A01G566500 chr7A 84.000 75 11 1 696 769 736329742 736329668 2.870000e-08 71.3
23 TraesCS7A01G566500 chr7A 100.000 33 0 0 451 483 680021873 680021905 1.730000e-05 62.1
24 TraesCS7A01G566500 chr7B 89.407 2209 210 13 2248 4448 744293397 744291205 0.000000e+00 2761.0
25 TraesCS7A01G566500 chr7B 88.840 2061 224 5 2390 4448 744249839 744251895 0.000000e+00 2527.0
26 TraesCS7A01G566500 chr7B 88.283 2091 238 6 2358 4445 743652525 743654611 0.000000e+00 2497.0
27 TraesCS7A01G566500 chr7B 94.444 1296 55 10 905 2193 745230065 745231350 0.000000e+00 1978.0
28 TraesCS7A01G566500 chr7B 88.986 1371 117 12 696 2060 743650320 743651662 0.000000e+00 1664.0
29 TraesCS7A01G566500 chr7B 91.501 1106 88 4 1079 2181 743999177 743998075 0.000000e+00 1517.0
30 TraesCS7A01G566500 chr7B 89.118 1213 117 9 990 2193 744239551 744240757 0.000000e+00 1495.0
31 TraesCS7A01G566500 chr7B 87.627 1180 127 10 999 2174 744248065 744249229 0.000000e+00 1352.0
32 TraesCS7A01G566500 chr7B 91.909 964 63 5 1098 2060 744143224 744144173 0.000000e+00 1334.0
33 TraesCS7A01G566500 chr7B 92.616 623 35 6 5103 5716 743993992 743993372 0.000000e+00 885.0
34 TraesCS7A01G566500 chr7B 89.008 655 64 6 4446 5094 744273370 744274022 0.000000e+00 804.0
35 TraesCS7A01G566500 chr7B 88.754 658 57 11 4446 5094 744067842 744068491 0.000000e+00 789.0
36 TraesCS7A01G566500 chr7B 86.350 652 80 7 4446 5094 744251922 744252567 0.000000e+00 702.0
37 TraesCS7A01G566500 chr7B 85.692 650 89 4 4446 5094 744190036 744190682 0.000000e+00 682.0
38 TraesCS7A01G566500 chr7B 92.086 417 31 1 4680 5094 743994495 743994079 2.300000e-163 586.0
39 TraesCS7A01G566500 chr7B 88.315 445 48 4 4652 5094 745243039 745243481 1.090000e-146 531.0
40 TraesCS7A01G566500 chr7B 78.608 589 111 10 5112 5693 743655320 743655900 5.430000e-100 375.0
41 TraesCS7A01G566500 chr7B 90.047 211 15 4 4446 4656 745234231 745234435 9.470000e-68 268.0
42 TraesCS7A01G566500 chr7B 80.000 425 29 16 1 384 743649600 743650009 4.410000e-66 263.0
43 TraesCS7A01G566500 chr7B 98.876 89 1 0 12 100 745229217 745229305 5.950000e-35 159.0
44 TraesCS7A01G566500 chr7B 90.278 72 4 3 384 454 745229673 745229742 2.200000e-14 91.6
45 TraesCS7A01G566500 chr7B 97.674 43 1 0 398 440 745202426 745202384 2.220000e-09 75.0
46 TraesCS7A01G566500 chr7B 77.895 95 19 2 236 328 745229408 745229502 2.230000e-04 58.4
47 TraesCS7A01G566500 chr7D 90.204 2062 194 7 2390 4448 632143099 632145155 0.000000e+00 2682.0
48 TraesCS7A01G566500 chr7D 89.122 2096 217 10 2358 4448 632098396 632100485 0.000000e+00 2597.0
49 TraesCS7A01G566500 chr7D 88.981 2060 223 3 2390 4448 632081161 632083217 0.000000e+00 2543.0
50 TraesCS7A01G566500 chr7D 87.153 1658 170 15 3468 5094 632046385 632048030 0.000000e+00 1842.0
51 TraesCS7A01G566500 chr7D 89.519 1288 111 14 905 2187 632141124 632142392 0.000000e+00 1609.0
52 TraesCS7A01G566500 chr7D 87.577 652 72 6 4446 5094 632100512 632101157 0.000000e+00 747.0
53 TraesCS7A01G566500 chr7D 83.729 590 87 7 5112 5694 621264147 621264734 3.020000e-152 549.0
54 TraesCS7A01G566500 chr7D 78.401 588 116 8 5112 5694 632145861 632146442 7.020000e-99 372.0
55 TraesCS7A01G566500 chr7D 84.746 236 22 7 1 226 632139801 632140032 2.080000e-54 224.0
56 TraesCS7A01G566500 chr7D 90.411 73 6 1 384 456 632140719 632140790 1.700000e-15 95.3
57 TraesCS7A01G566500 chr1B 81.608 1343 212 25 860 2190 577928925 577927606 0.000000e+00 1079.0
58 TraesCS7A01G566500 chr1B 73.684 608 115 36 5111 5690 577922945 577922355 1.630000e-45 195.0
59 TraesCS7A01G566500 chr5A 93.056 72 4 1 384 455 574016139 574016069 2.830000e-18 104.0
60 TraesCS7A01G566500 chr5A 90.667 75 2 3 153 227 574016480 574016411 1.700000e-15 95.3
61 TraesCS7A01G566500 chr3A 90.667 75 1 3 153 227 642605636 642605704 1.700000e-15 95.3
62 TraesCS7A01G566500 chr3A 100.000 34 0 0 449 482 194655921 194655954 4.800000e-06 63.9
63 TraesCS7A01G566500 chr1A 90.667 75 1 3 153 227 582060699 582060631 1.700000e-15 95.3
64 TraesCS7A01G566500 chr1A 90.278 72 6 1 384 455 582060354 582060284 6.120000e-15 93.5
65 TraesCS7A01G566500 chr6A 95.238 42 1 1 153 194 15397260 15397300 1.330000e-06 65.8
66 TraesCS7A01G566500 chr6A 90.698 43 1 2 525 564 15414943 15414985 3.000000e-03 54.7
67 TraesCS7A01G566500 chr5B 95.000 40 2 0 451 490 638303065 638303026 4.800000e-06 63.9
68 TraesCS7A01G566500 chr5B 100.000 33 0 0 450 482 219083585 219083617 1.730000e-05 62.1
69 TraesCS7A01G566500 chr6D 97.222 36 1 0 447 482 83011811 83011846 1.730000e-05 62.1
70 TraesCS7A01G566500 chr2B 97.143 35 1 0 448 482 486633770 486633736 6.210000e-05 60.2
71 TraesCS7A01G566500 chr2A 97.143 35 1 0 448 482 125020433 125020399 6.210000e-05 60.2
72 TraesCS7A01G566500 chr6B 90.909 44 2 2 441 482 415731729 415731772 2.230000e-04 58.4
73 TraesCS7A01G566500 chr1D 90.909 44 1 2 435 477 58567557 58567598 8.030000e-04 56.5


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 TraesCS7A01G566500 chr7A 735781216 735786950 5734 True 10591.000000 10591 100.000000 1 5735 1 chr7A.!!$R1 5734
1 TraesCS7A01G566500 chr7A 735842174 735844230 2056 True 2566.000000 2566 89.196000 2390 4448 1 chr7A.!!$R2 2058
2 TraesCS7A01G566500 chr7A 735959757 735964573 4816 False 1683.666667 2791 87.081667 42 4448 3 chr7A.!!$F5 4406
3 TraesCS7A01G566500 chr7A 735998510 736006525 8015 True 966.350000 2527 86.435000 2125 5735 6 chr7A.!!$R5 3610
4 TraesCS7A01G566500 chr7A 735946228 735946864 636 False 902.000000 902 92.284000 5095 5734 1 chr7A.!!$F3 639
5 TraesCS7A01G566500 chr7A 735930019 735930649 630 False 695.000000 695 86.462000 4446 5094 1 chr7A.!!$F2 648
6 TraesCS7A01G566500 chr7A 736328353 736329742 1389 True 598.150000 1125 82.942500 696 2136 2 chr7A.!!$R7 1440
7 TraesCS7A01G566500 chr7A 736095424 736097873 2449 True 417.800000 1282 90.432000 173 2056 4 chr7A.!!$R6 1883
8 TraesCS7A01G566500 chr7A 736323707 736324287 580 True 375.000000 375 78.535000 5113 5694 1 chr7A.!!$R4 581
9 TraesCS7A01G566500 chr7B 744291205 744293397 2192 True 2761.000000 2761 89.407000 2248 4448 1 chr7B.!!$R1 2200
10 TraesCS7A01G566500 chr7B 744248065 744252567 4502 False 1527.000000 2527 87.605667 999 5094 3 chr7B.!!$F8 4095
11 TraesCS7A01G566500 chr7B 744239551 744240757 1206 False 1495.000000 1495 89.118000 990 2193 1 chr7B.!!$F4 1203
12 TraesCS7A01G566500 chr7B 744143224 744144173 949 False 1334.000000 1334 91.909000 1098 2060 1 chr7B.!!$F2 962
13 TraesCS7A01G566500 chr7B 743649600 743655900 6300 False 1199.750000 2497 83.969250 1 5693 4 chr7B.!!$F7 5692
14 TraesCS7A01G566500 chr7B 743993372 743999177 5805 True 996.000000 1517 92.067667 1079 5716 3 chr7B.!!$R3 4637
15 TraesCS7A01G566500 chr7B 744273370 744274022 652 False 804.000000 804 89.008000 4446 5094 1 chr7B.!!$F5 648
16 TraesCS7A01G566500 chr7B 744067842 744068491 649 False 789.000000 789 88.754000 4446 5094 1 chr7B.!!$F1 648
17 TraesCS7A01G566500 chr7B 744190036 744190682 646 False 682.000000 682 85.692000 4446 5094 1 chr7B.!!$F3 648
18 TraesCS7A01G566500 chr7B 745229217 745234435 5218 False 511.000000 1978 90.308000 12 4656 5 chr7B.!!$F9 4644
19 TraesCS7A01G566500 chr7D 632081161 632083217 2056 False 2543.000000 2543 88.981000 2390 4448 1 chr7D.!!$F3 2058
20 TraesCS7A01G566500 chr7D 632046385 632048030 1645 False 1842.000000 1842 87.153000 3468 5094 1 chr7D.!!$F2 1626
21 TraesCS7A01G566500 chr7D 632098396 632101157 2761 False 1672.000000 2597 88.349500 2358 5094 2 chr7D.!!$F4 2736
22 TraesCS7A01G566500 chr7D 632139801 632146442 6641 False 996.460000 2682 86.656200 1 5694 5 chr7D.!!$F5 5693
23 TraesCS7A01G566500 chr7D 621264147 621264734 587 False 549.000000 549 83.729000 5112 5694 1 chr7D.!!$F1 582
24 TraesCS7A01G566500 chr1B 577927606 577928925 1319 True 1079.000000 1079 81.608000 860 2190 1 chr1B.!!$R2 1330

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
650 1796 0.034283 TATTGGTGCCTGCATGCTGA 60.034 50.0 24.53 4.02 0.00 4.26 F
2041 3298 0.035317 AGATGCTTGGTCGTTGCTCA 59.965 50.0 0.00 0.00 0.00 4.26 F
2044 3301 0.179059 TGCTTGGTCGTTGCTCAAGA 60.179 50.0 6.49 0.00 39.97 3.02 F
3736 7168 0.258484 CCACATCAATGGTGCCCCTA 59.742 55.0 0.00 0.00 34.77 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2502 5443 0.035056 CCCCCTCTTTCACGCAAGAT 60.035 55.0 0.0 0.00 43.62 2.40 R
3400 6346 0.039256 CCAAACTGCACCAATCACCG 60.039 55.0 0.0 0.00 0.00 4.94 R
3971 7403 0.109532 TTCTCCAAACGGCACATGGA 59.890 50.0 0.0 2.65 0.00 3.41 R
5264 8837 0.107508 CCGACATCCAAGCCATCTGT 60.108 55.0 0.0 0.00 0.00 3.41 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
91 100 2.459934 CGTCCAACTCAAAAGGTTTGC 58.540 47.619 0.00 0.00 0.00 3.68
134 143 6.200878 TGTTCCTCCTTCCTTGAGTAATTT 57.799 37.500 0.00 0.00 0.00 1.82
360 1346 6.639632 ACTGAAAATTGAACTGCTGTGTAT 57.360 33.333 0.00 0.00 0.00 2.29
442 1561 3.160777 GCATCCAGCCATCTCAAAAAG 57.839 47.619 0.00 0.00 37.23 2.27
455 1580 8.135529 GCCATCTCAAAAAGTTAGTTTTGTACT 58.864 33.333 9.50 0.00 44.97 2.73
456 1581 9.665264 CCATCTCAAAAAGTTAGTTTTGTACTC 57.335 33.333 9.50 0.00 44.97 2.59
459 1584 8.050930 TCTCAAAAAGTTAGTTTTGTACTCCCT 58.949 33.333 9.50 0.00 44.97 4.20
460 1585 8.217131 TCAAAAAGTTAGTTTTGTACTCCCTC 57.783 34.615 9.50 0.00 44.97 4.30
461 1586 7.283807 TCAAAAAGTTAGTTTTGTACTCCCTCC 59.716 37.037 9.50 0.00 44.97 4.30
462 1587 4.532314 AGTTAGTTTTGTACTCCCTCCG 57.468 45.455 0.00 0.00 38.33 4.63
464 1589 1.725803 AGTTTTGTACTCCCTCCGGT 58.274 50.000 0.00 0.00 28.23 5.28
466 1591 0.978907 TTTTGTACTCCCTCCGGTCC 59.021 55.000 0.00 0.00 0.00 4.46
468 1593 1.002069 TTGTACTCCCTCCGGTCCTA 58.998 55.000 0.00 0.00 0.00 2.94
469 1594 1.002069 TGTACTCCCTCCGGTCCTAA 58.998 55.000 0.00 0.00 0.00 2.69
470 1595 1.358787 TGTACTCCCTCCGGTCCTAAA 59.641 52.381 0.00 0.00 0.00 1.85
471 1596 2.023695 TGTACTCCCTCCGGTCCTAAAT 60.024 50.000 0.00 0.00 0.00 1.40
473 1598 3.632420 ACTCCCTCCGGTCCTAAATAT 57.368 47.619 0.00 0.00 0.00 1.28
476 1601 5.085219 ACTCCCTCCGGTCCTAAATATAAG 58.915 45.833 0.00 0.00 0.00 1.73
477 1602 5.083953 TCCCTCCGGTCCTAAATATAAGT 57.916 43.478 0.00 0.00 0.00 2.24
478 1603 5.082425 TCCCTCCGGTCCTAAATATAAGTC 58.918 45.833 0.00 0.00 0.00 3.01
480 1605 5.543020 CCCTCCGGTCCTAAATATAAGTCTT 59.457 44.000 0.00 0.00 0.00 3.01
482 1607 7.153315 CCTCCGGTCCTAAATATAAGTCTTTC 58.847 42.308 0.00 0.00 0.00 2.62
484 1609 6.612456 TCCGGTCCTAAATATAAGTCTTTCCA 59.388 38.462 0.00 0.00 0.00 3.53
485 1610 7.126115 TCCGGTCCTAAATATAAGTCTTTCCAA 59.874 37.037 0.00 0.00 0.00 3.53
487 1612 9.338622 CGGTCCTAAATATAAGTCTTTCCAAAT 57.661 33.333 0.00 0.00 0.00 2.32
614 1758 5.784578 TTATTGACCGCTAGCTGATTCTA 57.215 39.130 13.57 0.00 0.00 2.10
617 1761 4.672587 TGACCGCTAGCTGATTCTATTT 57.327 40.909 13.57 0.00 0.00 1.40
618 1762 4.371786 TGACCGCTAGCTGATTCTATTTG 58.628 43.478 13.57 0.00 0.00 2.32
624 1768 6.292381 CCGCTAGCTGATTCTATTTGTTGTAC 60.292 42.308 13.93 0.00 0.00 2.90
640 1786 4.998672 TGTTGTACTACTGTTATTGGTGCC 59.001 41.667 8.88 0.00 0.00 5.01
641 1787 5.221762 TGTTGTACTACTGTTATTGGTGCCT 60.222 40.000 8.88 0.00 0.00 4.75
642 1788 4.827692 TGTACTACTGTTATTGGTGCCTG 58.172 43.478 0.00 0.00 0.00 4.85
643 1789 2.711542 ACTACTGTTATTGGTGCCTGC 58.288 47.619 0.00 0.00 0.00 4.85
644 1790 2.039746 ACTACTGTTATTGGTGCCTGCA 59.960 45.455 0.00 0.00 0.00 4.41
645 1791 2.220653 ACTGTTATTGGTGCCTGCAT 57.779 45.000 0.00 0.00 0.00 3.96
646 1792 1.820519 ACTGTTATTGGTGCCTGCATG 59.179 47.619 0.00 0.00 0.00 4.06
647 1793 0.531657 TGTTATTGGTGCCTGCATGC 59.468 50.000 11.82 11.82 0.00 4.06
649 1795 0.818938 TTATTGGTGCCTGCATGCTG 59.181 50.000 20.33 18.55 0.00 4.41
650 1796 0.034283 TATTGGTGCCTGCATGCTGA 60.034 50.000 24.53 4.02 0.00 4.26
653 1799 0.901114 TGGTGCCTGCATGCTGAAAT 60.901 50.000 24.53 0.00 0.00 2.17
654 1800 0.248289 GGTGCCTGCATGCTGAAATT 59.752 50.000 24.53 0.00 0.00 1.82
655 1801 1.355971 GTGCCTGCATGCTGAAATTG 58.644 50.000 24.53 9.42 0.00 2.32
656 1802 0.248012 TGCCTGCATGCTGAAATTGG 59.752 50.000 24.53 12.60 0.00 3.16
688 1847 6.716628 ACCTGTTTCTTCATCTCATTGCTTAA 59.283 34.615 0.00 0.00 0.00 1.85
691 1850 6.432162 TGTTTCTTCATCTCATTGCTTAAGCT 59.568 34.615 26.90 6.19 42.66 3.74
717 1882 1.267121 ATGCAGACTTGTAGACGGGT 58.733 50.000 0.00 0.00 0.00 5.28
759 1967 2.622064 AAAGCGTGAGGTCTGTCTTT 57.378 45.000 0.00 0.00 43.76 2.52
794 2009 1.821216 ACCATTAAAGCGTCAGGGTG 58.179 50.000 0.00 0.00 0.00 4.61
806 2021 2.028476 CGTCAGGGTGAAGTGTCCAATA 60.028 50.000 0.00 0.00 0.00 1.90
1208 2459 4.666253 GGTGGGGCAGCTCAAGCA 62.666 66.667 4.59 0.00 45.16 3.91
1348 2602 1.697982 CCTCCCATGCTCATGAGATCA 59.302 52.381 27.04 15.64 41.20 2.92
1355 2609 0.179702 GCTCATGAGATCAGCACCCA 59.820 55.000 27.04 0.00 0.00 4.51
1581 2838 1.667724 CAGATCATGCAGACGGGAAAC 59.332 52.381 0.00 0.00 0.00 2.78
1671 2928 3.369892 CCCAGAAGGTCTTCAATGACGAT 60.370 47.826 12.54 0.00 41.84 3.73
1810 3067 1.165907 TGCAAAGACCAGCCTTCACG 61.166 55.000 0.00 0.00 0.00 4.35
1811 3068 0.884704 GCAAAGACCAGCCTTCACGA 60.885 55.000 0.00 0.00 0.00 4.35
1822 3079 1.542547 GCCTTCACGAAACCCTCAAGA 60.543 52.381 0.00 0.00 0.00 3.02
1824 3081 2.548480 CCTTCACGAAACCCTCAAGAAC 59.452 50.000 0.00 0.00 0.00 3.01
1832 3089 4.216257 CGAAACCCTCAAGAACACATTGAT 59.784 41.667 0.00 0.00 36.16 2.57
1833 3090 5.278463 CGAAACCCTCAAGAACACATTGATT 60.278 40.000 0.00 0.00 36.16 2.57
1845 3102 3.569701 ACACATTGATTGACCACAAGACC 59.430 43.478 0.00 0.00 39.46 3.85
1848 3105 4.895297 ACATTGATTGACCACAAGACCTTT 59.105 37.500 0.00 0.00 39.46 3.11
1870 3127 3.779738 TCTGGTAATGGATGATGTGTGGA 59.220 43.478 0.00 0.00 0.00 4.02
1873 3130 3.632145 GGTAATGGATGATGTGTGGAACC 59.368 47.826 0.00 0.00 34.36 3.62
1876 3133 4.794311 ATGGATGATGTGTGGAACCATA 57.206 40.909 0.00 0.00 35.34 2.74
1881 3138 2.571202 TGATGTGTGGAACCATAGAGCA 59.429 45.455 2.09 2.09 34.36 4.26
1896 3153 3.104766 GCATGGGATGACGTGCTG 58.895 61.111 0.00 0.00 47.00 4.41
1910 3167 4.251268 GACGTGCTGAAAATACCCTTAGT 58.749 43.478 0.00 0.00 0.00 2.24
1944 3201 2.202987 GGCAGCCGAGTCCTCATG 60.203 66.667 0.00 0.00 0.00 3.07
1968 3225 1.701847 ACCAGAGATGAAGGTGTTGCT 59.298 47.619 0.00 0.00 33.57 3.91
1970 3227 1.998315 CAGAGATGAAGGTGTTGCTCG 59.002 52.381 0.00 0.00 0.00 5.03
1979 3236 1.070786 GTGTTGCTCGAGGGGTGAA 59.929 57.895 15.58 0.00 0.00 3.18
1986 3243 1.539280 GCTCGAGGGGTGAAAGCTATC 60.539 57.143 15.58 0.00 0.00 2.08
1987 3244 1.757118 CTCGAGGGGTGAAAGCTATCA 59.243 52.381 3.91 0.00 0.00 2.15
1990 3247 0.548510 AGGGGTGAAAGCTATCAGGC 59.451 55.000 0.00 0.00 0.00 4.85
1991 3248 0.466372 GGGGTGAAAGCTATCAGGCC 60.466 60.000 0.00 0.00 0.00 5.19
1993 3250 0.107654 GGTGAAAGCTATCAGGCCGT 60.108 55.000 0.00 0.00 0.00 5.68
1995 3252 2.202566 GTGAAAGCTATCAGGCCGTAC 58.797 52.381 0.00 0.00 0.00 3.67
1996 3253 1.138266 TGAAAGCTATCAGGCCGTACC 59.862 52.381 0.00 0.00 39.61 3.34
1997 3254 1.138266 GAAAGCTATCAGGCCGTACCA 59.862 52.381 0.00 0.00 43.14 3.25
1998 3255 0.464452 AAGCTATCAGGCCGTACCAC 59.536 55.000 0.00 0.00 43.14 4.16
1999 3256 1.069258 GCTATCAGGCCGTACCACC 59.931 63.158 0.00 0.00 43.14 4.61
2001 3258 1.048601 CTATCAGGCCGTACCACCAT 58.951 55.000 0.00 0.00 43.14 3.55
2003 3260 1.271840 ATCAGGCCGTACCACCATGT 61.272 55.000 0.00 0.00 43.14 3.21
2004 3261 1.745115 CAGGCCGTACCACCATGTG 60.745 63.158 0.00 0.00 43.14 3.21
2018 3275 4.294523 TGTGGACACATTAGCGCC 57.705 55.556 2.29 0.00 36.21 6.53
2019 3276 1.676968 TGTGGACACATTAGCGCCT 59.323 52.632 2.29 0.00 36.21 5.52
2020 3277 0.673333 TGTGGACACATTAGCGCCTG 60.673 55.000 2.29 1.55 36.21 4.85
2021 3278 0.391130 GTGGACACATTAGCGCCTGA 60.391 55.000 2.29 0.00 0.00 3.86
2022 3279 0.323302 TGGACACATTAGCGCCTGAA 59.677 50.000 2.29 0.00 0.00 3.02
2023 3280 1.009829 GGACACATTAGCGCCTGAAG 58.990 55.000 2.29 1.14 0.00 3.02
2024 3281 1.405526 GGACACATTAGCGCCTGAAGA 60.406 52.381 2.29 0.00 0.00 2.87
2025 3282 2.555199 GACACATTAGCGCCTGAAGAT 58.445 47.619 2.29 0.00 0.00 2.40
2026 3283 2.283298 ACACATTAGCGCCTGAAGATG 58.717 47.619 2.29 2.22 0.00 2.90
2027 3284 1.003116 CACATTAGCGCCTGAAGATGC 60.003 52.381 2.29 0.00 0.00 3.91
2029 3286 1.945394 CATTAGCGCCTGAAGATGCTT 59.055 47.619 2.29 0.00 38.82 3.91
2030 3287 1.372582 TTAGCGCCTGAAGATGCTTG 58.627 50.000 2.29 0.00 38.82 4.01
2031 3288 0.462581 TAGCGCCTGAAGATGCTTGG 60.463 55.000 2.29 0.00 38.82 3.61
2033 3290 1.986575 GCGCCTGAAGATGCTTGGTC 61.987 60.000 0.00 0.00 0.00 4.02
2035 3292 0.674895 GCCTGAAGATGCTTGGTCGT 60.675 55.000 0.00 0.00 0.00 4.34
2036 3293 1.813513 CCTGAAGATGCTTGGTCGTT 58.186 50.000 0.00 0.00 0.00 3.85
2037 3294 1.466167 CCTGAAGATGCTTGGTCGTTG 59.534 52.381 0.00 0.00 0.00 4.10
2038 3295 0.874390 TGAAGATGCTTGGTCGTTGC 59.126 50.000 0.00 0.00 0.00 4.17
2039 3296 1.160137 GAAGATGCTTGGTCGTTGCT 58.840 50.000 0.00 0.00 0.00 3.91
2040 3297 1.129437 GAAGATGCTTGGTCGTTGCTC 59.871 52.381 0.00 0.00 0.00 4.26
2041 3298 0.035317 AGATGCTTGGTCGTTGCTCA 59.965 50.000 0.00 0.00 0.00 4.26
2043 3300 0.877071 ATGCTTGGTCGTTGCTCAAG 59.123 50.000 0.00 0.00 40.38 3.02
2044 3301 0.179059 TGCTTGGTCGTTGCTCAAGA 60.179 50.000 6.49 0.00 39.97 3.02
2045 3302 0.944386 GCTTGGTCGTTGCTCAAGAA 59.056 50.000 6.49 0.00 39.97 2.52
2046 3303 1.069636 GCTTGGTCGTTGCTCAAGAAG 60.070 52.381 6.49 0.00 39.97 2.85
2058 3315 3.951775 CTCAAGAAGCAGGTCTGTACT 57.048 47.619 0.00 0.00 0.00 2.73
2059 3316 4.264460 CTCAAGAAGCAGGTCTGTACTT 57.736 45.455 0.00 0.00 0.00 2.24
2060 3317 4.636249 CTCAAGAAGCAGGTCTGTACTTT 58.364 43.478 0.00 0.00 0.00 2.66
2061 3318 5.784177 CTCAAGAAGCAGGTCTGTACTTTA 58.216 41.667 0.00 0.00 0.00 1.85
2062 3319 6.360370 TCAAGAAGCAGGTCTGTACTTTAT 57.640 37.500 0.00 0.00 0.00 1.40
2063 3320 6.769512 TCAAGAAGCAGGTCTGTACTTTATT 58.230 36.000 0.00 0.00 0.00 1.40
2064 3321 7.903145 TCAAGAAGCAGGTCTGTACTTTATTA 58.097 34.615 0.00 0.00 0.00 0.98
2065 3322 8.372459 TCAAGAAGCAGGTCTGTACTTTATTAA 58.628 33.333 0.00 0.00 0.00 1.40
2066 3323 8.999431 CAAGAAGCAGGTCTGTACTTTATTAAA 58.001 33.333 0.00 0.00 0.00 1.52
2067 3324 9.740710 AAGAAGCAGGTCTGTACTTTATTAAAT 57.259 29.630 0.00 0.00 0.00 1.40
2261 4941 7.730364 AAACGAATAAAACAGTGATGAGAGT 57.270 32.000 0.00 0.00 0.00 3.24
2262 4942 8.827177 AAACGAATAAAACAGTGATGAGAGTA 57.173 30.769 0.00 0.00 0.00 2.59
2263 4943 8.467402 AACGAATAAAACAGTGATGAGAGTAG 57.533 34.615 0.00 0.00 0.00 2.57
2265 4950 8.088981 ACGAATAAAACAGTGATGAGAGTAGTT 58.911 33.333 0.00 0.00 0.00 2.24
2292 4977 3.863142 ATTCTTCTTGCAGCATGTTCC 57.137 42.857 8.09 0.00 39.31 3.62
2293 4978 2.275134 TCTTCTTGCAGCATGTTCCA 57.725 45.000 8.09 0.00 39.31 3.53
2294 4979 2.799017 TCTTCTTGCAGCATGTTCCAT 58.201 42.857 8.09 0.00 39.31 3.41
2295 4980 2.751259 TCTTCTTGCAGCATGTTCCATC 59.249 45.455 8.09 0.00 39.31 3.51
2502 5443 5.055265 TGTTGTTAAAGTGATGGGAGGAA 57.945 39.130 0.00 0.00 0.00 3.36
2557 5499 2.613691 GCAGCAGGTTTTGGATGATTG 58.386 47.619 0.00 0.00 0.00 2.67
2558 5500 2.613691 CAGCAGGTTTTGGATGATTGC 58.386 47.619 0.00 0.00 0.00 3.56
2598 5540 1.154205 GCCCGATGATCTCAACCACG 61.154 60.000 0.00 0.00 0.00 4.94
2603 5545 2.350522 GATGATCTCAACCACGCAGTT 58.649 47.619 0.00 0.00 41.61 3.16
2605 5547 1.872952 TGATCTCAACCACGCAGTTTG 59.127 47.619 0.00 0.00 41.61 2.93
2689 5632 9.720769 TCTTCCTAAAAGAAGACGTTTCATATT 57.279 29.630 11.33 6.82 45.67 1.28
2728 5671 7.301054 CAATGTGGATAAGCGAAGGATTTATC 58.699 38.462 0.00 0.00 34.55 1.75
2794 5737 7.133483 ACTACAAGGAGTTGGTATCTAGGAAT 58.867 38.462 0.00 0.00 38.07 3.01
2827 5770 8.046294 AGCCAGATAAATCGTATACTACTCTG 57.954 38.462 0.56 4.96 0.00 3.35
2857 5800 1.133598 AGCATGCATGATGTTGTTCGG 59.866 47.619 30.64 0.00 34.14 4.30
2866 5809 2.241722 GATGTTGTTCGGTCATTTGCG 58.758 47.619 0.00 0.00 0.00 4.85
2981 5924 6.035758 GTCCATAGAAACTAACCGATCACAAC 59.964 42.308 0.00 0.00 0.00 3.32
2995 5938 2.639065 TCACAACCAGGTGAACTTGAC 58.361 47.619 0.00 0.00 44.34 3.18
3063 6006 7.795047 TCAACTATCCAGATTAAGATGAAGCA 58.205 34.615 0.00 0.00 0.00 3.91
3098 6041 4.276431 TGGTTACTTTTTCTAGTTTGCGGG 59.724 41.667 0.00 0.00 0.00 6.13
3103 6046 2.561478 TTTCTAGTTTGCGGGCTCTT 57.439 45.000 0.00 0.00 0.00 2.85
3128 6071 7.724287 TCATATAGAATCTGCAGATATGGCTC 58.276 38.462 28.92 21.07 33.29 4.70
3136 6082 4.001652 CTGCAGATATGGCTCTATTGGTG 58.998 47.826 8.42 0.00 0.00 4.17
3142 6088 5.789575 AGATATGGCTCTATTGGTGGAATCT 59.210 40.000 0.00 0.00 0.00 2.40
3183 6129 7.468906 GCACCTGAGGTATCTAACACTAGTAAG 60.469 44.444 2.59 0.00 32.11 2.34
3215 6161 9.936329 ATATATTTGTACTTCCAGGGAACATTT 57.064 29.630 0.00 0.00 0.00 2.32
3262 6208 4.271696 TGACCTCTGTGGATGTACAAAG 57.728 45.455 0.00 0.00 39.71 2.77
3281 6227 3.045601 AGTTGGTGAATCTTCCTGACG 57.954 47.619 0.00 0.00 0.00 4.35
3360 6306 5.269505 CCTAGATGGTTTAGTGGTCTGAG 57.730 47.826 0.00 0.00 0.00 3.35
3400 6346 0.605319 TGTTTCGAGCCCACATGGAC 60.605 55.000 0.00 0.00 37.39 4.02
3425 6371 0.961019 TTGGTGCAGTTTGGATGAGC 59.039 50.000 0.00 0.00 0.00 4.26
3447 6393 1.611965 GGCCTCTTTCCCAGCTCAT 59.388 57.895 0.00 0.00 0.00 2.90
3457 6403 2.783135 TCCCAGCTCATGTTTCTTGAC 58.217 47.619 0.00 0.00 0.00 3.18
3510 6456 1.392589 TTTGCTGCTAATGCTAGGCC 58.607 50.000 0.00 0.00 40.48 5.19
3545 6491 6.748333 TGCATCTTATCAGGCTATTATTGC 57.252 37.500 0.00 0.00 0.00 3.56
3592 6538 2.716424 TGGGTTGGTCAAAGAGAAGGAT 59.284 45.455 0.00 0.00 0.00 3.24
3656 6602 0.547712 TAAGCTCTGCCCTCCACCTT 60.548 55.000 0.00 0.00 0.00 3.50
3671 6617 6.326583 CCCTCCACCTTGTGTAGAATATCTTA 59.673 42.308 0.00 0.00 0.00 2.10
3676 6622 9.396022 CCACCTTGTGTAGAATATCTTACAATT 57.604 33.333 9.05 0.00 34.33 2.32
3736 7168 0.258484 CCACATCAATGGTGCCCCTA 59.742 55.000 0.00 0.00 34.77 3.53
3780 7212 2.089201 TGATGATCTGGCTTGTTGCAG 58.911 47.619 0.00 0.00 45.15 4.41
3867 7299 2.927871 GCATCAAACATGTTGGGACTGC 60.928 50.000 12.82 17.53 0.00 4.40
3892 7324 2.187685 CAGGCGGCAGTAGCATCA 59.812 61.111 13.08 0.00 44.61 3.07
3951 7383 1.619363 TGGAATGGGAGGAGTGGGG 60.619 63.158 0.00 0.00 0.00 4.96
3971 7403 1.282157 GGTGGGAGGAGCAAGTACAAT 59.718 52.381 0.00 0.00 0.00 2.71
4087 7519 4.277515 AGTTCTAGAGCATGTCAAGCAA 57.722 40.909 9.43 0.00 0.00 3.91
4244 7676 2.039818 TATCGCTTCACTCGAGAGGT 57.960 50.000 21.68 0.00 39.47 3.85
4249 7681 1.606737 GCTTCACTCGAGAGGTTGCTT 60.607 52.381 21.68 0.00 0.00 3.91
4302 7734 5.464722 CAGAATACATGCGAGACATAAAGCT 59.535 40.000 0.00 0.00 36.64 3.74
4304 7736 6.642950 AGAATACATGCGAGACATAAAGCTAC 59.357 38.462 0.00 0.00 36.64 3.58
4306 7738 4.503910 ACATGCGAGACATAAAGCTACAA 58.496 39.130 0.00 0.00 36.64 2.41
4307 7739 4.935205 ACATGCGAGACATAAAGCTACAAA 59.065 37.500 0.00 0.00 36.64 2.83
4378 7810 1.064906 CAATCTGGCACTGAGTGGGAT 60.065 52.381 15.24 0.00 45.93 3.85
4390 7822 2.846206 TGAGTGGGATAAGTTCAGCCAT 59.154 45.455 0.00 0.00 0.00 4.40
4540 8006 7.112148 GTCTTAATTTGTTTGAGCACTCTTTCG 59.888 37.037 0.00 0.00 0.00 3.46
4552 8021 3.309954 GCACTCTTTCGGCCAGTTTATAG 59.690 47.826 2.24 0.00 0.00 1.31
4602 8072 7.926674 TTTGTCCATATATACTGCATGATGG 57.073 36.000 0.00 0.00 34.75 3.51
4617 8087 5.107133 GCATGATGGCCAGATATATTTTGC 58.893 41.667 13.05 6.29 0.00 3.68
4621 8091 2.884012 TGGCCAGATATATTTTGCACCG 59.116 45.455 0.00 0.00 0.00 4.94
4650 8122 5.473162 AGTGCATGTTGCTAAGTATTTGTCA 59.527 36.000 0.00 0.00 45.31 3.58
4736 8210 5.229423 TGTATTTTTCTTGCCATGCAGAAC 58.771 37.500 0.00 0.00 40.61 3.01
4761 8235 2.979814 TCATCTTGTATGGTGGACCG 57.020 50.000 0.00 0.00 39.43 4.79
4785 8259 5.788450 ACAAGGATTTGAGTCTCTGTACAG 58.212 41.667 17.17 17.17 37.73 2.74
4874 8348 1.360393 AAGGGAGCCCACCTTTGTCA 61.360 55.000 8.53 0.00 45.81 3.58
4977 8451 0.545309 TCCTCTCTTGGTGTGGAGGG 60.545 60.000 7.82 0.00 43.81 4.30
4983 8457 0.250901 CTTGGTGTGGAGGGGTCAAG 60.251 60.000 0.00 0.00 0.00 3.02
5100 8655 1.135859 GCGCAAGTTTGACATGGAGAG 60.136 52.381 0.30 0.00 41.68 3.20
5248 8821 2.530460 ATGGTGCTTGGCTTAATGGA 57.470 45.000 0.00 0.00 0.00 3.41
5255 8828 4.640201 GTGCTTGGCTTAATGGAAGTATGA 59.360 41.667 0.00 0.00 37.49 2.15
5264 8837 7.719633 GGCTTAATGGAAGTATGATGAGGTTAA 59.280 37.037 0.00 0.00 37.49 2.01
5295 8868 4.617253 TGGATGTCGGGGAATACATAAG 57.383 45.455 0.00 0.00 36.48 1.73
5322 8895 2.447443 TGCTGGATACACTCTTCGTCT 58.553 47.619 0.00 0.00 46.17 4.18
5471 9048 0.551131 AATGCCTCCAGGGAGAAGGT 60.551 55.000 16.89 0.00 44.53 3.50
5503 9080 7.228108 TCCAAATAATCAATCTGAGATGCACTC 59.772 37.037 0.00 8.75 45.11 3.51
5560 9137 2.182088 TGATAGACATGGAGGGGGATCA 59.818 50.000 0.00 0.00 0.00 2.92
5568 9145 0.104197 GGAGGGGGATCAGGAGGAAT 60.104 60.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 100 9.645059 AGGAACAAGAAAGAAAGAAAGAAAAAG 57.355 29.630 0.00 0.00 0.00 2.27
134 143 5.620738 ATCAGCTAGCAGACTTTCCAATA 57.379 39.130 18.83 0.00 0.00 1.90
228 262 2.024414 GAGACAAACAAACAGGCACCT 58.976 47.619 0.00 0.00 0.00 4.00
230 264 3.502191 TTGAGACAAACAAACAGGCAC 57.498 42.857 0.00 0.00 0.00 5.01
283 704 4.150098 CCCTGACGCGCTAAACTTATTATC 59.850 45.833 5.73 0.00 0.00 1.75
284 705 4.056050 CCCTGACGCGCTAAACTTATTAT 58.944 43.478 5.73 0.00 0.00 1.28
286 707 2.277084 CCCTGACGCGCTAAACTTATT 58.723 47.619 5.73 0.00 0.00 1.40
287 708 1.206371 ACCCTGACGCGCTAAACTTAT 59.794 47.619 5.73 0.00 0.00 1.73
288 709 0.604578 ACCCTGACGCGCTAAACTTA 59.395 50.000 5.73 0.00 0.00 2.24
289 710 0.604578 TACCCTGACGCGCTAAACTT 59.395 50.000 5.73 0.00 0.00 2.66
291 712 0.997196 CTTACCCTGACGCGCTAAAC 59.003 55.000 5.73 0.00 0.00 2.01
360 1346 2.951642 CTGCCTCACCAACTGAAGAAAA 59.048 45.455 0.00 0.00 0.00 2.29
440 1559 4.891260 CGGAGGGAGTACAAAACTAACTT 58.109 43.478 0.00 0.00 39.07 2.66
459 1584 6.612456 TGGAAAGACTTATATTTAGGACCGGA 59.388 38.462 9.46 0.00 0.00 5.14
460 1585 6.823497 TGGAAAGACTTATATTTAGGACCGG 58.177 40.000 0.00 0.00 0.00 5.28
461 1586 8.726870 TTTGGAAAGACTTATATTTAGGACCG 57.273 34.615 0.00 0.00 0.00 4.79
501 1626 8.557029 GCTATAAGTCTTTGTAGAGAGTCTCTC 58.443 40.741 25.94 20.50 43.70 3.20
502 1627 8.272173 AGCTATAAGTCTTTGTAGAGAGTCTCT 58.728 37.037 25.51 25.51 43.83 3.10
504 1629 9.908747 TTAGCTATAAGTCTTTGTAGAGAGTCT 57.091 33.333 0.00 0.00 31.67 3.24
600 1744 5.725110 ACAACAAATAGAATCAGCTAGCG 57.275 39.130 9.55 4.60 0.00 4.26
614 1758 7.308951 GGCACCAATAACAGTAGTACAACAAAT 60.309 37.037 2.52 0.00 0.00 2.32
617 1761 4.998672 GGCACCAATAACAGTAGTACAACA 59.001 41.667 2.52 0.00 0.00 3.33
618 1762 5.121768 CAGGCACCAATAACAGTAGTACAAC 59.878 44.000 2.52 0.00 0.00 3.32
624 1768 2.710377 TGCAGGCACCAATAACAGTAG 58.290 47.619 0.00 0.00 0.00 2.57
640 1786 2.876091 CTGACCAATTTCAGCATGCAG 58.124 47.619 21.98 12.90 36.83 4.41
656 1802 3.817647 AGATGAAGAAACAGGTTGCTGAC 59.182 43.478 0.00 0.00 0.00 3.51
661 1820 5.048224 AGCAATGAGATGAAGAAACAGGTTG 60.048 40.000 0.00 0.00 0.00 3.77
688 1847 8.616942 CGTCTACAAGTCTGCATATATATAGCT 58.383 37.037 14.28 0.00 0.00 3.32
691 1850 7.832685 ACCCGTCTACAAGTCTGCATATATATA 59.167 37.037 0.00 0.00 0.00 0.86
717 1882 5.367945 AATCTTAACGCTCCCCTGAATTA 57.632 39.130 0.00 0.00 0.00 1.40
759 1967 9.181061 GCTTTAATGGTTTAACCTTATCTACCA 57.819 33.333 15.68 0.00 39.58 3.25
1208 2459 2.368548 TCGGTAGCTTCATACATGGCAT 59.631 45.455 0.00 0.00 0.00 4.40
1348 2602 1.604593 GTGCCTTGATGTGGGTGCT 60.605 57.895 0.00 0.00 0.00 4.40
1355 2609 3.213206 TCTTGTTGAGTGCCTTGATGT 57.787 42.857 0.00 0.00 0.00 3.06
1581 2838 3.368495 CATGATGCCATTGTTGACATCG 58.632 45.455 0.00 0.00 41.43 3.84
1671 2928 2.231964 GCTGAATTCACCTTGGATTGCA 59.768 45.455 3.38 0.00 0.00 4.08
1810 3067 5.712152 ATCAATGTGTTCTTGAGGGTTTC 57.288 39.130 0.00 0.00 36.16 2.78
1811 3068 5.598005 TCAATCAATGTGTTCTTGAGGGTTT 59.402 36.000 0.00 0.00 36.16 3.27
1822 3079 4.037923 GGTCTTGTGGTCAATCAATGTGTT 59.962 41.667 0.00 0.00 32.82 3.32
1824 3081 3.822735 AGGTCTTGTGGTCAATCAATGTG 59.177 43.478 0.00 0.00 32.82 3.21
1832 3089 2.930950 CCAGAAAGGTCTTGTGGTCAA 58.069 47.619 4.88 0.00 28.78 3.18
1833 3090 2.638480 CCAGAAAGGTCTTGTGGTCA 57.362 50.000 4.88 0.00 28.78 4.02
1845 3102 5.066893 CCACACATCATCCATTACCAGAAAG 59.933 44.000 0.00 0.00 0.00 2.62
1848 3105 3.779738 TCCACACATCATCCATTACCAGA 59.220 43.478 0.00 0.00 0.00 3.86
1873 3130 2.410939 CACGTCATCCCATGCTCTATG 58.589 52.381 0.00 0.00 36.50 2.23
1876 3133 1.153289 GCACGTCATCCCATGCTCT 60.153 57.895 0.00 0.00 35.16 4.09
1881 3138 2.198827 TTTTCAGCACGTCATCCCAT 57.801 45.000 0.00 0.00 0.00 4.00
1889 3146 4.251268 GACTAAGGGTATTTTCAGCACGT 58.749 43.478 0.00 0.00 0.00 4.49
1890 3147 4.250464 TGACTAAGGGTATTTTCAGCACG 58.750 43.478 0.00 0.00 0.00 5.34
1896 3153 5.358160 AGCAGCATTGACTAAGGGTATTTTC 59.642 40.000 0.00 0.00 0.00 2.29
1910 3167 1.592400 GCCTGAAGCAGCAGCATTGA 61.592 55.000 3.17 0.00 45.49 2.57
1944 3201 4.499183 CAACACCTTCATCTCTGGTAGTC 58.501 47.826 0.00 0.00 32.13 2.59
1947 3204 2.906389 AGCAACACCTTCATCTCTGGTA 59.094 45.455 0.00 0.00 32.13 3.25
1950 3207 1.998315 CGAGCAACACCTTCATCTCTG 59.002 52.381 0.00 0.00 0.00 3.35
1968 3225 1.757118 CTGATAGCTTTCACCCCTCGA 59.243 52.381 2.39 0.00 0.00 4.04
1970 3227 1.475930 GCCTGATAGCTTTCACCCCTC 60.476 57.143 2.39 0.00 0.00 4.30
1979 3236 0.464452 GTGGTACGGCCTGATAGCTT 59.536 55.000 0.00 0.00 38.35 3.74
1986 3243 1.745115 CACATGGTGGTACGGCCTG 60.745 63.158 0.00 0.00 38.35 4.85
1987 3244 2.668632 CACATGGTGGTACGGCCT 59.331 61.111 0.00 0.00 38.35 5.19
2001 3258 0.673333 CAGGCGCTAATGTGTCCACA 60.673 55.000 7.64 2.09 46.44 4.17
2003 3260 0.323302 TTCAGGCGCTAATGTGTCCA 59.677 50.000 7.64 0.00 0.00 4.02
2004 3261 1.009829 CTTCAGGCGCTAATGTGTCC 58.990 55.000 7.64 0.00 0.00 4.02
2005 3262 2.010145 TCTTCAGGCGCTAATGTGTC 57.990 50.000 7.64 0.00 0.00 3.67
2006 3263 2.283298 CATCTTCAGGCGCTAATGTGT 58.717 47.619 7.64 0.00 0.00 3.72
2008 3265 1.134280 AGCATCTTCAGGCGCTAATGT 60.134 47.619 7.64 0.00 31.60 2.71
2009 3266 1.590932 AGCATCTTCAGGCGCTAATG 58.409 50.000 7.64 4.24 31.60 1.90
2011 3268 1.372582 CAAGCATCTTCAGGCGCTAA 58.627 50.000 7.64 0.00 33.45 3.09
2012 3269 0.462581 CCAAGCATCTTCAGGCGCTA 60.463 55.000 7.64 0.00 33.45 4.26
2014 3271 1.986575 GACCAAGCATCTTCAGGCGC 61.987 60.000 0.00 0.00 34.54 6.53
2015 3272 1.699656 CGACCAAGCATCTTCAGGCG 61.700 60.000 0.00 0.00 34.54 5.52
2016 3273 0.674895 ACGACCAAGCATCTTCAGGC 60.675 55.000 0.00 0.00 0.00 4.85
2017 3274 1.466167 CAACGACCAAGCATCTTCAGG 59.534 52.381 0.00 0.00 0.00 3.86
2018 3275 1.135859 GCAACGACCAAGCATCTTCAG 60.136 52.381 0.00 0.00 0.00 3.02
2019 3276 0.874390 GCAACGACCAAGCATCTTCA 59.126 50.000 0.00 0.00 0.00 3.02
2020 3277 1.129437 GAGCAACGACCAAGCATCTTC 59.871 52.381 0.00 0.00 0.00 2.87
2021 3278 1.160137 GAGCAACGACCAAGCATCTT 58.840 50.000 0.00 0.00 0.00 2.40
2022 3279 0.035317 TGAGCAACGACCAAGCATCT 59.965 50.000 0.00 0.00 0.00 2.90
2023 3280 0.874390 TTGAGCAACGACCAAGCATC 59.126 50.000 0.00 0.00 0.00 3.91
2024 3281 0.877071 CTTGAGCAACGACCAAGCAT 59.123 50.000 0.00 0.00 32.16 3.79
2025 3282 0.179059 TCTTGAGCAACGACCAAGCA 60.179 50.000 0.00 0.00 37.71 3.91
2026 3283 0.944386 TTCTTGAGCAACGACCAAGC 59.056 50.000 0.00 0.00 37.71 4.01
2027 3284 2.957576 CTTCTTGAGCAACGACCAAG 57.042 50.000 0.00 0.00 38.79 3.61
2038 3295 3.951775 AGTACAGACCTGCTTCTTGAG 57.048 47.619 0.00 0.00 0.00 3.02
2039 3296 4.689612 AAAGTACAGACCTGCTTCTTGA 57.310 40.909 0.00 0.00 0.00 3.02
2040 3297 8.547967 TTAATAAAGTACAGACCTGCTTCTTG 57.452 34.615 0.00 0.00 0.00 3.02
2041 3298 9.740710 ATTTAATAAAGTACAGACCTGCTTCTT 57.259 29.630 0.00 0.00 0.00 2.52
2079 3336 8.932610 AGATGGACATAGATTATTCACTTCACT 58.067 33.333 0.00 0.00 0.00 3.41
2233 4870 8.783093 TCTCATCACTGTTTTATTCGTTTTCAT 58.217 29.630 0.00 0.00 0.00 2.57
2234 4871 8.148807 TCTCATCACTGTTTTATTCGTTTTCA 57.851 30.769 0.00 0.00 0.00 2.69
2235 4872 8.283291 ACTCTCATCACTGTTTTATTCGTTTTC 58.717 33.333 0.00 0.00 0.00 2.29
2239 4876 7.603651 ACTACTCTCATCACTGTTTTATTCGT 58.396 34.615 0.00 0.00 0.00 3.85
2240 4877 8.467402 AACTACTCTCATCACTGTTTTATTCG 57.533 34.615 0.00 0.00 0.00 3.34
2263 4943 9.956720 ACATGCTGCAAGAAGAATATAATTAAC 57.043 29.630 12.28 0.00 34.07 2.01
2291 4976 7.039082 TCCTTTTCTTTTTACAAGATGGGATGG 60.039 37.037 0.00 0.00 0.00 3.51
2292 4977 7.895759 TCCTTTTCTTTTTACAAGATGGGATG 58.104 34.615 0.00 0.00 0.00 3.51
2293 4978 8.491045 TTCCTTTTCTTTTTACAAGATGGGAT 57.509 30.769 0.00 0.00 0.00 3.85
2294 4979 7.906199 TTCCTTTTCTTTTTACAAGATGGGA 57.094 32.000 0.00 0.00 0.00 4.37
2295 4980 8.421002 TCTTTCCTTTTCTTTTTACAAGATGGG 58.579 33.333 0.00 0.00 0.00 4.00
2502 5443 0.035056 CCCCCTCTTTCACGCAAGAT 60.035 55.000 0.00 0.00 43.62 2.40
2557 5499 5.334028 GGCATTTTAGTTGTTGACCATTTGC 60.334 40.000 0.00 0.00 0.00 3.68
2558 5500 5.179182 GGGCATTTTAGTTGTTGACCATTTG 59.821 40.000 0.00 0.00 37.22 2.32
2598 5540 9.552114 CATATATTCATAGCTTAAGCAAACTGC 57.448 33.333 28.39 1.07 45.46 4.40
2603 5545 8.868522 AAGGCATATATTCATAGCTTAAGCAA 57.131 30.769 28.39 14.61 45.16 3.91
2605 5547 8.729805 AGAAGGCATATATTCATAGCTTAAGC 57.270 34.615 20.09 20.09 42.49 3.09
2675 5617 6.590292 ACGACTTGATCAATATGAAACGTCTT 59.410 34.615 8.96 1.36 0.00 3.01
2684 5626 4.880886 TTGCCACGACTTGATCAATATG 57.119 40.909 8.96 4.13 0.00 1.78
2689 5632 1.805943 CACATTGCCACGACTTGATCA 59.194 47.619 0.00 0.00 0.00 2.92
2728 5671 5.500234 TCCAAATCACTAGAGTTTCCATGG 58.500 41.667 4.97 4.97 27.92 3.66
2819 5762 1.543429 GCTGCAAACCCACAGAGTAGT 60.543 52.381 0.00 0.00 35.90 2.73
2823 5766 0.242825 CATGCTGCAAACCCACAGAG 59.757 55.000 6.36 0.00 35.90 3.35
2857 5800 6.525121 TTAGTCATATACTGCGCAAATGAC 57.475 37.500 29.11 29.11 44.28 3.06
2866 5809 7.655328 AGTGCTTCATCTTTAGTCATATACTGC 59.345 37.037 0.00 0.00 39.39 4.40
2981 5924 2.638480 TTCCAGTCAAGTTCACCTGG 57.362 50.000 0.00 0.00 44.74 4.45
2995 5938 4.756642 TGTTGTGCTTGTAGAGATTTCCAG 59.243 41.667 0.00 0.00 0.00 3.86
3063 6006 6.777580 AGAAAAAGTAACCAGTGAATCACCAT 59.222 34.615 10.12 0.00 34.49 3.55
3098 6041 9.251792 CATATCTGCAGATTCTATATGAAGAGC 57.748 37.037 32.94 0.00 39.39 4.09
3103 6046 7.564292 AGAGCCATATCTGCAGATTCTATATGA 59.436 37.037 32.94 13.90 34.06 2.15
3128 6071 5.840243 TGATGCAAAGATTCCACCAATAG 57.160 39.130 0.00 0.00 0.00 1.73
3136 6082 4.171754 GCTTGAGTTGATGCAAAGATTCC 58.828 43.478 0.00 0.00 0.00 3.01
3142 6088 2.034939 CAGGTGCTTGAGTTGATGCAAA 59.965 45.455 0.00 0.00 37.17 3.68
3183 6129 6.428159 CCCTGGAAGTACAAATATATCAGCAC 59.572 42.308 0.00 0.00 0.00 4.40
3195 6141 3.572255 GCAAATGTTCCCTGGAAGTACAA 59.428 43.478 0.00 0.00 34.49 2.41
3239 6185 4.698201 TTGTACATCCACAGAGGTCAAA 57.302 40.909 0.00 0.00 38.21 2.69
3262 6208 2.076863 CCGTCAGGAAGATTCACCAAC 58.923 52.381 0.00 0.00 41.02 3.77
3281 6227 1.079612 GGCCAAGCTTCACAATGCC 60.080 57.895 0.00 0.00 0.00 4.40
3344 6290 7.252612 TCATATTTCTCAGACCACTAAACCA 57.747 36.000 0.00 0.00 0.00 3.67
3400 6346 0.039256 CCAAACTGCACCAATCACCG 60.039 55.000 0.00 0.00 0.00 4.94
3447 6393 9.130661 TCTCCAATTGAATTAAGTCAAGAAACA 57.869 29.630 21.37 0.17 40.72 2.83
3457 6403 9.674824 GCAGATACATTCTCCAATTGAATTAAG 57.325 33.333 7.12 0.00 32.47 1.85
3510 6456 5.608449 TGATAAGATGCATCTTCTCACTGG 58.392 41.667 35.57 0.00 43.27 4.00
3592 6538 1.251527 GCTCTTCCTCGGAGACACCA 61.252 60.000 6.58 0.00 38.90 4.17
3671 6617 3.445805 CGGCCAAAATACCCACTAATTGT 59.554 43.478 2.24 0.00 0.00 2.71
3676 6622 0.394625 GCCGGCCAAAATACCCACTA 60.395 55.000 18.11 0.00 0.00 2.74
3678 6624 1.536943 TTGCCGGCCAAAATACCCAC 61.537 55.000 26.77 0.00 0.00 4.61
3885 7317 7.415095 CGTTTAACCTTGGAAATGATGATGCTA 60.415 37.037 0.00 0.00 0.00 3.49
3886 7318 6.625740 CGTTTAACCTTGGAAATGATGATGCT 60.626 38.462 0.00 0.00 0.00 3.79
3887 7319 5.516339 CGTTTAACCTTGGAAATGATGATGC 59.484 40.000 0.00 0.00 0.00 3.91
3890 7322 7.931578 ATACGTTTAACCTTGGAAATGATGA 57.068 32.000 0.00 0.00 0.00 2.92
3892 7324 8.343168 TCAATACGTTTAACCTTGGAAATGAT 57.657 30.769 0.00 0.00 0.00 2.45
3951 7383 0.690762 TTGTACTTGCTCCTCCCACC 59.309 55.000 0.00 0.00 0.00 4.61
3971 7403 0.109532 TTCTCCAAACGGCACATGGA 59.890 50.000 0.00 2.65 0.00 3.41
4001 7433 0.250234 TGCCTCAGTCTGCATGTACC 59.750 55.000 0.00 0.00 31.31 3.34
4005 7437 2.812591 GGAATATGCCTCAGTCTGCATG 59.187 50.000 7.20 0.00 46.99 4.06
4045 7477 7.965107 AGAACTAATATTTTCAAAGAGCTTGCG 59.035 33.333 0.00 0.00 34.76 4.85
4075 7507 0.879765 AGCTGAGTTGCTTGACATGC 59.120 50.000 6.38 6.38 40.93 4.06
4244 7676 4.365514 TGTTGTAATCCTCCAGAAGCAA 57.634 40.909 0.00 0.00 0.00 3.91
4249 7681 5.512942 TTTCCATGTTGTAATCCTCCAGA 57.487 39.130 0.00 0.00 0.00 3.86
4345 7777 2.058595 AGATTGTCCCGCGGCTACT 61.059 57.895 22.85 9.56 0.00 2.57
4378 7810 1.350684 TGCTCCACATGGCTGAACTTA 59.649 47.619 0.00 0.00 34.44 2.24
4390 7822 0.038599 ATGCCTTGACATGCTCCACA 59.961 50.000 0.00 0.00 0.00 4.17
4432 7864 7.747155 TTTGAATCCAACGTACCATTTTCTA 57.253 32.000 0.00 0.00 30.88 2.10
4540 8006 6.715347 ATCAAATGAACCTATAAACTGGCC 57.285 37.500 0.00 0.00 0.00 5.36
4552 8021 7.105241 AGCAGGAGATAAAATCAAATGAACC 57.895 36.000 0.00 0.00 0.00 3.62
4602 8072 3.058224 GGACGGTGCAAAATATATCTGGC 60.058 47.826 0.00 0.00 0.00 4.85
4617 8087 1.078709 CAACATGCACTAGGACGGTG 58.921 55.000 0.00 0.00 37.70 4.94
4736 8210 5.308825 GTCCACCATACAAGATGATAAGGG 58.691 45.833 0.00 0.00 0.00 3.95
4761 8235 5.784177 TGTACAGAGACTCAAATCCTTGTC 58.216 41.667 5.02 0.00 33.94 3.18
4785 8259 4.322567 ACTGAAGGTGCTTCTTCTCATTC 58.677 43.478 16.45 0.00 42.54 2.67
4874 8348 5.304686 TGTAAAGACAACACTCTCCCATT 57.695 39.130 0.00 0.00 30.68 3.16
4908 8382 4.039004 AGTTCAGCATTCTCAGAGCGATAT 59.961 41.667 0.00 0.00 0.00 1.63
4977 8451 2.543777 TACCAGCAAGACACTTGACC 57.456 50.000 14.44 0.00 0.00 4.02
4983 8457 2.224305 ACCTGAGTTACCAGCAAGACAC 60.224 50.000 0.00 0.00 32.97 3.67
5100 8655 2.675348 GCTTGGATTAGCTCACTGTCAC 59.325 50.000 0.00 0.00 38.15 3.67
5248 8821 6.058183 GCCATCTGTTAACCTCATCATACTT 58.942 40.000 2.48 0.00 0.00 2.24
5255 8828 3.266772 TCCAAGCCATCTGTTAACCTCAT 59.733 43.478 2.48 0.00 0.00 2.90
5264 8837 0.107508 CCGACATCCAAGCCATCTGT 60.108 55.000 0.00 0.00 0.00 3.41
5295 8868 2.169352 AGAGTGTATCCAGCATCACCAC 59.831 50.000 0.00 0.00 0.00 4.16
5322 8895 0.685097 GTAAGGTGTCAGGAGCCACA 59.315 55.000 0.00 0.00 33.19 4.17
5471 9048 6.834969 TCTCAGATTGATTATTTGGATGCCAA 59.165 34.615 0.00 0.00 42.29 4.52
5503 9080 0.516877 ACAACATGTGCCGATTGTCG 59.483 50.000 0.00 0.00 40.07 4.35
5560 9137 2.022625 TCCTGATCCTCACATTCCTCCT 60.023 50.000 0.00 0.00 0.00 3.69
5568 9145 1.643286 ACTCTCCTCCTGATCCTCACA 59.357 52.381 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.