Multiple sequence alignment - TraesCS3A01G538200

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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 TraesCS3A01G538200 chr3A 100.000 6899 0 0 1 6899 749401236 749408134 0.000000e+00 12741.0
1 TraesCS3A01G538200 chr3A 81.901 989 156 18 4372 5347 749405553 749406531 0.000000e+00 813.0
2 TraesCS3A01G538200 chr3A 81.901 989 156 18 4318 5296 749405607 749406582 0.000000e+00 813.0
3 TraesCS3A01G538200 chr3A 81.889 773 108 20 2029 2773 749403087 749403855 2.110000e-174 623.0
4 TraesCS3A01G538200 chr3A 81.889 773 108 21 1852 2620 749403264 749404008 2.110000e-174 623.0
5 TraesCS3A01G538200 chr3A 92.035 113 4 4 6281 6391 65839646 65839537 3.330000e-33 154.0
6 TraesCS3A01G538200 chr3A 100.000 28 0 0 6121 6148 253925923 253925896 1.300000e-02 52.8
7 TraesCS3A01G538200 chr3D 94.626 4336 156 14 1625 5956 613733563 613737825 0.000000e+00 6645.0
8 TraesCS3A01G538200 chr3D 89.711 1662 73 20 3 1625 613732057 613733659 0.000000e+00 2032.0
9 TraesCS3A01G538200 chr3D 79.495 990 154 26 4318 5296 613736292 613737243 0.000000e+00 658.0
10 TraesCS3A01G538200 chr3D 80.234 855 128 29 2029 2849 613733784 613734631 7.650000e-169 604.0
11 TraesCS3A01G538200 chr3D 82.225 737 94 26 1852 2580 613733961 613734668 9.900000e-168 601.0
12 TraesCS3A01G538200 chr3D 77.647 935 155 26 4318 5240 613736346 613737238 2.850000e-143 520.0
13 TraesCS3A01G538200 chr3D 82.308 650 23 39 6128 6719 613738076 613738691 4.840000e-131 479.0
14 TraesCS3A01G538200 chr3D 85.532 470 27 16 6406 6844 5568876 5568417 2.930000e-123 453.0
15 TraesCS3A01G538200 chr3D 85.093 483 25 18 6391 6844 558905609 558906073 3.800000e-122 449.0
16 TraesCS3A01G538200 chr3D 84.664 476 22 17 6398 6844 215740638 215740185 1.780000e-115 427.0
17 TraesCS3A01G538200 chr3D 83.871 496 29 23 6392 6844 584374787 584375274 6.400000e-115 425.0
18 TraesCS3A01G538200 chr3D 85.829 374 14 11 6499 6844 344157046 344157408 1.830000e-95 361.0
19 TraesCS3A01G538200 chr3D 80.556 468 81 7 4879 5341 613736724 613737186 1.100000e-92 351.0
20 TraesCS3A01G538200 chr3D 93.571 140 2 2 5953 6091 613737865 613737998 1.170000e-47 202.0
21 TraesCS3A01G538200 chr3D 92.035 113 4 3 6281 6391 504820948 504821057 3.330000e-33 154.0
22 TraesCS3A01G538200 chr3D 92.035 113 4 3 6281 6391 584374637 584374746 3.330000e-33 154.0
23 TraesCS3A01G538200 chr3B 94.770 2677 107 9 2701 5347 822969937 822972610 0.000000e+00 4137.0
24 TraesCS3A01G538200 chr3B 88.982 1670 87 25 3 1625 822967389 822969008 0.000000e+00 1975.0
25 TraesCS3A01G538200 chr3B 93.127 1033 66 3 1625 2653 822968909 822969940 0.000000e+00 1509.0
26 TraesCS3A01G538200 chr3B 83.094 1674 228 36 4318 5956 822971680 822973333 0.000000e+00 1472.0
27 TraesCS3A01G538200 chr3B 82.498 1057 159 19 4318 5357 822971626 822972673 0.000000e+00 904.0
28 TraesCS3A01G538200 chr3B 80.749 774 115 26 2029 2773 822969139 822969907 2.160000e-159 573.0
29 TraesCS3A01G538200 chr3B 83.131 658 82 19 1852 2507 822969316 822969946 2.160000e-159 573.0
30 TraesCS3A01G538200 chr3B 77.434 904 161 27 4473 5347 822971568 822972457 3.720000e-137 499.0
31 TraesCS3A01G538200 chr3B 77.096 847 158 25 4529 5351 822971573 822972407 2.270000e-124 457.0
32 TraesCS3A01G538200 chr3B 78.732 757 54 60 6128 6849 822973606 822974290 2.320000e-109 407.0
33 TraesCS3A01G538200 chr3B 75.985 533 98 17 4318 4834 822972046 822972564 1.490000e-61 248.0
34 TraesCS3A01G538200 chr3B 93.077 130 6 1 5962 6091 822973382 822973508 3.290000e-43 187.0
35 TraesCS3A01G538200 chr3B 78.073 301 55 8 4325 4624 822972422 822972712 5.500000e-41 180.0
36 TraesCS3A01G538200 chr3B 80.952 126 15 5 2547 2669 822969936 822970055 2.650000e-14 91.6
37 TraesCS3A01G538200 chr4D 85.954 477 26 15 6391 6844 381523038 381522580 8.100000e-129 472.0
38 TraesCS3A01G538200 chr4D 83.817 482 31 21 6392 6844 279519039 279519502 1.380000e-111 414.0
39 TraesCS3A01G538200 chr4D 91.150 113 5 3 6281 6391 381523185 381523076 1.550000e-31 148.0
40 TraesCS3A01G538200 chrUn 85.532 470 27 16 6406 6844 287762008 287761549 2.930000e-123 453.0
41 TraesCS3A01G538200 chrUn 84.855 482 26 15 6392 6844 30177011 30177474 6.350000e-120 442.0
42 TraesCS3A01G538200 chrUn 92.035 113 4 3 6281 6391 150825645 150825754 3.330000e-33 154.0
43 TraesCS3A01G538200 chrUn 100.000 28 0 0 6121 6148 220534281 220534254 1.300000e-02 52.8
44 TraesCS3A01G538200 chrUn 100.000 28 0 0 6121 6148 374994099 374994126 1.300000e-02 52.8
45 TraesCS3A01G538200 chr2D 84.221 488 30 21 6391 6844 151644266 151643792 1.370000e-116 431.0
46 TraesCS3A01G538200 chr2D 91.150 113 5 3 6281 6391 151644413 151644304 1.550000e-31 148.0
47 TraesCS3A01G538200 chr5D 84.265 483 29 16 6391 6844 487766415 487766879 1.780000e-115 427.0
48 TraesCS3A01G538200 chr7D 82.988 482 26 20 6392 6844 539400280 539400734 1.090000e-102 385.0
49 TraesCS3A01G538200 chr7D 91.525 118 4 4 6275 6391 539400128 539400240 2.580000e-34 158.0
50 TraesCS3A01G538200 chr7D 98.333 60 1 0 6032 6091 158431245 158431186 9.460000e-19 106.0
51 TraesCS3A01G538200 chr7D 98.333 60 1 0 6032 6091 366417619 366417560 9.460000e-19 106.0
52 TraesCS3A01G538200 chr1A 90.688 247 12 5 6602 6844 357337741 357337502 1.120000e-82 318.0
53 TraesCS3A01G538200 chr2A 92.035 113 4 3 6281 6391 24233680 24233789 3.330000e-33 154.0
54 TraesCS3A01G538200 chr2A 98.333 60 1 0 6032 6091 214138024 214137965 9.460000e-19 106.0
55 TraesCS3A01G538200 chr7A 98.333 60 1 0 6032 6091 81941608 81941549 9.460000e-19 106.0
56 TraesCS3A01G538200 chr7A 98.333 60 1 0 6032 6091 668633979 668633920 9.460000e-19 106.0
57 TraesCS3A01G538200 chr7A 100.000 28 0 0 6121 6148 171730180 171730207 1.300000e-02 52.8
58 TraesCS3A01G538200 chr7A 100.000 28 0 0 6121 6148 171844695 171844722 1.300000e-02 52.8
59 TraesCS3A01G538200 chr5A 98.333 60 1 0 6032 6091 696287235 696287176 9.460000e-19 106.0
60 TraesCS3A01G538200 chr4A 98.333 60 1 0 6032 6091 531838262 531838203 9.460000e-19 106.0


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 TraesCS3A01G538200 chr3A 749401236 749408134 6898 False 12741.000000 12741 100.000000 1 6899 1 chr3A.!!$F1 6898
1 TraesCS3A01G538200 chr3A 749403087 749406582 3495 False 718.000000 813 81.895000 1852 5347 4 chr3A.!!$F2 3495
2 TraesCS3A01G538200 chr3D 613732057 613737825 5768 False 4338.500000 6645 92.168500 3 5956 2 chr3D.!!$F5 5953
3 TraesCS3A01G538200 chr3D 613733784 613738691 4907 False 487.857143 658 82.290857 1852 6719 7 chr3D.!!$F6 4867
4 TraesCS3A01G538200 chr3D 584374637 584375274 637 False 289.500000 425 87.953000 6281 6844 2 chr3D.!!$F4 563
5 TraesCS3A01G538200 chr3B 822967389 822974290 6901 False 943.757143 4137 83.407143 3 6849 14 chr3B.!!$F1 6846
6 TraesCS3A01G538200 chr4D 381522580 381523185 605 True 310.000000 472 88.552000 6281 6844 2 chr4D.!!$R1 563
7 TraesCS3A01G538200 chr2D 151643792 151644413 621 True 289.500000 431 87.685500 6281 6844 2 chr2D.!!$R1 563
8 TraesCS3A01G538200 chr7D 539400128 539400734 606 False 271.500000 385 87.256500 6275 6844 2 chr7D.!!$F1 569

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
328 339 0.111639 GTGGCCCCTTTGTCCTAACA 59.888 55.0 0.00 0.0 0.00 2.41 F
1639 1707 0.178767 TGATGATGCTCCGACCAAGG 59.821 55.0 0.00 0.0 0.00 3.61 F
1691 1759 0.029967 TCATCGCGTGAGAGAGATGC 59.970 55.0 5.77 0.0 44.90 3.91 F
1692 1760 0.030504 CATCGCGTGAGAGAGATGCT 59.969 55.0 5.77 0.0 44.90 3.79 F
1693 1761 0.030504 ATCGCGTGAGAGAGATGCTG 59.969 55.0 5.77 0.0 44.90 4.41 F
1780 1848 0.741221 GGACACCTCCGAAGATGCAC 60.741 60.0 0.00 0.0 0.00 4.57 F
5556 5813 0.990374 ACAAGGCAGAGGCAGAGAAT 59.010 50.0 0.00 0.0 43.71 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1672 1740 0.029967 GCATCTCTCTCACGCGATGA 59.970 55.000 15.93 12.26 36.29 2.92 R
5384 5614 8.307483 ACCAGTAATCGTCCTTCATATTATCAG 58.693 37.037 0.00 0.00 0.00 2.90 R
5425 5655 2.432628 CAGCGGTTCCTCCACGTC 60.433 66.667 0.00 0.00 35.57 4.34 R
5711 5968 3.063084 GCTGGTCCGTCTCCGTCT 61.063 66.667 0.00 0.00 0.00 4.18 R
5818 6075 3.764466 CCGGAAGCTGTCGAGGCT 61.764 66.667 0.00 6.96 42.31 4.58 R
5835 6092 2.126031 GACGGGAAGTCGGTGAGC 60.126 66.667 0.00 0.00 40.43 4.26 R
6860 7381 1.113788 AGATCAGACTGAGCTCCAGC 58.886 55.000 17.44 0.00 39.11 4.85 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
95 102 1.996898 CCTTAATTATATCGCGCCGCA 59.003 47.619 10.75 0.00 0.00 5.69
107 114 1.272715 CGCCGCACACACGAATATC 59.727 57.895 0.00 0.00 34.06 1.63
114 121 4.508971 CGCACACACGAATATCTCATTTC 58.491 43.478 0.00 0.00 34.06 2.17
181 192 7.459795 AAGAAAAAGGAAGAGATTCCATCAC 57.540 36.000 9.55 0.00 43.54 3.06
187 198 1.588239 AGAGATTCCATCACCAGGCA 58.412 50.000 0.00 0.00 0.00 4.75
190 201 0.548031 GATTCCATCACCAGGCAGGA 59.452 55.000 1.67 0.00 41.22 3.86
235 246 5.523438 GTGTGATTGAACACCCCTTTTTA 57.477 39.130 0.00 0.00 43.84 1.52
276 287 3.437741 GGAGGCCAAATTGCAAAATGAAG 59.562 43.478 5.01 0.00 0.00 3.02
286 297 1.542915 GCAAAATGAAGCAGAGGCAGA 59.457 47.619 0.00 0.00 44.61 4.26
287 298 2.415625 GCAAAATGAAGCAGAGGCAGAG 60.416 50.000 0.00 0.00 44.61 3.35
288 299 1.461559 AAATGAAGCAGAGGCAGAGC 58.538 50.000 0.00 0.00 44.61 4.09
319 330 3.837399 TTATTTACCAGTGGCCCCTTT 57.163 42.857 9.78 0.00 0.00 3.11
328 339 0.111639 GTGGCCCCTTTGTCCTAACA 59.888 55.000 0.00 0.00 0.00 2.41
329 340 0.404040 TGGCCCCTTTGTCCTAACAG 59.596 55.000 0.00 0.00 36.57 3.16
350 361 2.179427 GAATTCCCCAAACCCTCCAAG 58.821 52.381 0.00 0.00 0.00 3.61
408 419 1.352622 TTCCCATCCATTCTCCCCCG 61.353 60.000 0.00 0.00 0.00 5.73
409 420 1.770110 CCCATCCATTCTCCCCCGA 60.770 63.158 0.00 0.00 0.00 5.14
410 421 1.136329 CCCATCCATTCTCCCCCGAT 61.136 60.000 0.00 0.00 0.00 4.18
411 422 0.773644 CCATCCATTCTCCCCCGATT 59.226 55.000 0.00 0.00 0.00 3.34
516 540 4.387343 TCCCCGACGGTAAGCCCT 62.387 66.667 13.94 0.00 0.00 5.19
527 551 0.621082 GTAAGCCCTTTGCCTCTCCT 59.379 55.000 0.00 0.00 42.71 3.69
528 552 0.912486 TAAGCCCTTTGCCTCTCCTC 59.088 55.000 0.00 0.00 42.71 3.71
529 553 1.857638 AAGCCCTTTGCCTCTCCTCC 61.858 60.000 0.00 0.00 42.71 4.30
530 554 3.002371 CCCTTTGCCTCTCCTCCC 58.998 66.667 0.00 0.00 0.00 4.30
531 555 1.617839 CCCTTTGCCTCTCCTCCCT 60.618 63.158 0.00 0.00 0.00 4.20
532 556 1.631071 CCCTTTGCCTCTCCTCCCTC 61.631 65.000 0.00 0.00 0.00 4.30
533 557 1.631071 CCTTTGCCTCTCCTCCCTCC 61.631 65.000 0.00 0.00 0.00 4.30
534 558 1.616628 TTTGCCTCTCCTCCCTCCC 60.617 63.158 0.00 0.00 0.00 4.30
535 559 2.125066 TTTGCCTCTCCTCCCTCCCT 62.125 60.000 0.00 0.00 0.00 4.20
629 653 3.006728 TGCCCTAACCCCTGTCCG 61.007 66.667 0.00 0.00 0.00 4.79
631 655 3.027675 GCCCTAACCCCTGTCCGTC 62.028 68.421 0.00 0.00 0.00 4.79
1083 1142 2.045242 TCCAGCTACGTCGCCTCT 60.045 61.111 8.64 0.00 0.00 3.69
1185 1244 2.556144 AGCAGCAGATTCACAACTCA 57.444 45.000 0.00 0.00 0.00 3.41
1377 1436 1.067295 TGAGGTGTCCAATGGAGCTT 58.933 50.000 0.27 0.00 29.39 3.74
1394 1453 4.322567 GAGCTTCCTGAGTTTGTCATCTT 58.677 43.478 0.00 0.00 33.51 2.40
1410 1469 2.594536 TCTTCCAGGGGATTGAGGAT 57.405 50.000 0.00 0.00 0.00 3.24
1440 1499 1.220206 CGTTGCTCCTGAGGCTGAT 59.780 57.895 0.00 0.00 0.00 2.90
1441 1500 1.088340 CGTTGCTCCTGAGGCTGATG 61.088 60.000 0.00 0.00 0.00 3.07
1442 1501 1.077930 TTGCTCCTGAGGCTGATGC 60.078 57.895 0.00 0.00 38.76 3.91
1443 1502 1.559965 TTGCTCCTGAGGCTGATGCT 61.560 55.000 0.00 0.00 39.59 3.79
1444 1503 1.524165 GCTCCTGAGGCTGATGCTG 60.524 63.158 0.00 0.00 39.59 4.41
1445 1504 1.969200 GCTCCTGAGGCTGATGCTGA 61.969 60.000 0.00 0.00 39.59 4.26
1446 1505 0.759959 CTCCTGAGGCTGATGCTGAT 59.240 55.000 0.00 0.00 39.59 2.90
1447 1506 0.468648 TCCTGAGGCTGATGCTGATG 59.531 55.000 0.00 0.00 39.59 3.07
1448 1507 1.167155 CCTGAGGCTGATGCTGATGC 61.167 60.000 0.00 0.00 39.59 3.91
1449 1508 0.179043 CTGAGGCTGATGCTGATGCT 60.179 55.000 0.00 0.00 40.48 3.79
1450 1509 0.463833 TGAGGCTGATGCTGATGCTG 60.464 55.000 0.00 0.00 40.48 4.41
1451 1510 0.179054 GAGGCTGATGCTGATGCTGA 60.179 55.000 0.00 0.00 40.48 4.26
1452 1511 0.474614 AGGCTGATGCTGATGCTGAT 59.525 50.000 0.00 0.00 40.48 2.90
1458 1517 2.155279 GATGCTGATGCTGATGCTGAT 58.845 47.619 0.00 0.00 40.48 2.90
1563 1628 1.398692 AGGAGAAGAGATCGAGGCAC 58.601 55.000 0.00 0.00 0.00 5.01
1586 1654 0.803768 GAGAGCTCATCGCGCAAGAA 60.804 55.000 17.77 0.00 45.59 2.52
1612 1680 2.847327 TCCTGCAGAGGAACAAGAAG 57.153 50.000 17.39 0.00 46.19 2.85
1613 1681 2.329267 TCCTGCAGAGGAACAAGAAGA 58.671 47.619 17.39 0.00 46.19 2.87
1614 1682 2.301296 TCCTGCAGAGGAACAAGAAGAG 59.699 50.000 17.39 0.00 46.19 2.85
1615 1683 2.614987 CCTGCAGAGGAACAAGAAGAGG 60.615 54.545 17.39 0.00 42.93 3.69
1616 1684 1.271054 TGCAGAGGAACAAGAAGAGGC 60.271 52.381 0.00 0.00 0.00 4.70
1617 1685 1.948144 GCAGAGGAACAAGAAGAGGCC 60.948 57.143 0.00 0.00 0.00 5.19
1618 1686 1.349026 CAGAGGAACAAGAAGAGGCCA 59.651 52.381 5.01 0.00 0.00 5.36
1619 1687 2.026449 CAGAGGAACAAGAAGAGGCCAT 60.026 50.000 5.01 0.00 0.00 4.40
1620 1688 2.646798 AGAGGAACAAGAAGAGGCCATT 59.353 45.455 5.01 0.00 0.00 3.16
1621 1689 2.751806 GAGGAACAAGAAGAGGCCATTG 59.248 50.000 5.01 4.29 0.00 2.82
1622 1690 2.376518 AGGAACAAGAAGAGGCCATTGA 59.623 45.455 5.01 0.00 0.00 2.57
1623 1691 3.011032 AGGAACAAGAAGAGGCCATTGAT 59.989 43.478 5.01 0.00 0.00 2.57
1624 1692 3.129988 GGAACAAGAAGAGGCCATTGATG 59.870 47.826 5.01 3.34 0.00 3.07
1625 1693 3.726557 ACAAGAAGAGGCCATTGATGA 57.273 42.857 5.01 0.00 0.00 2.92
1626 1694 4.246712 ACAAGAAGAGGCCATTGATGAT 57.753 40.909 5.01 0.00 0.00 2.45
1627 1695 3.952323 ACAAGAAGAGGCCATTGATGATG 59.048 43.478 5.01 0.00 35.42 3.07
1628 1696 2.584236 AGAAGAGGCCATTGATGATGC 58.416 47.619 5.01 0.00 34.25 3.91
1629 1697 2.175069 AGAAGAGGCCATTGATGATGCT 59.825 45.455 5.01 0.00 34.25 3.79
1630 1698 2.273538 AGAGGCCATTGATGATGCTC 57.726 50.000 5.01 0.00 34.25 4.26
1631 1699 1.202903 AGAGGCCATTGATGATGCTCC 60.203 52.381 5.01 0.00 34.25 4.70
1632 1700 0.536687 AGGCCATTGATGATGCTCCG 60.537 55.000 5.01 0.00 34.19 4.63
1633 1701 0.535780 GGCCATTGATGATGCTCCGA 60.536 55.000 0.00 0.00 34.25 4.55
1634 1702 0.590195 GCCATTGATGATGCTCCGAC 59.410 55.000 0.00 0.00 34.25 4.79
1635 1703 1.233019 CCATTGATGATGCTCCGACC 58.767 55.000 0.00 0.00 34.25 4.79
1636 1704 1.475571 CCATTGATGATGCTCCGACCA 60.476 52.381 0.00 0.00 34.25 4.02
1637 1705 2.291365 CATTGATGATGCTCCGACCAA 58.709 47.619 0.00 0.00 0.00 3.67
1638 1706 2.028420 TTGATGATGCTCCGACCAAG 57.972 50.000 0.00 0.00 0.00 3.61
1639 1707 0.178767 TGATGATGCTCCGACCAAGG 59.821 55.000 0.00 0.00 0.00 3.61
1640 1708 0.465705 GATGATGCTCCGACCAAGGA 59.534 55.000 0.00 0.00 38.80 3.36
1647 1715 2.977578 TCCGACCAAGGAGGAGAAG 58.022 57.895 0.00 0.00 41.22 2.85
1648 1716 0.408309 TCCGACCAAGGAGGAGAAGA 59.592 55.000 0.00 0.00 41.22 2.87
1649 1717 1.203137 TCCGACCAAGGAGGAGAAGAA 60.203 52.381 0.00 0.00 41.22 2.52
1650 1718 1.623811 CCGACCAAGGAGGAGAAGAAA 59.376 52.381 0.00 0.00 41.22 2.52
1651 1719 2.237392 CCGACCAAGGAGGAGAAGAAAT 59.763 50.000 0.00 0.00 41.22 2.17
1652 1720 3.526534 CGACCAAGGAGGAGAAGAAATC 58.473 50.000 0.00 0.00 41.22 2.17
1653 1721 3.055819 CGACCAAGGAGGAGAAGAAATCA 60.056 47.826 0.00 0.00 41.22 2.57
1654 1722 4.563580 CGACCAAGGAGGAGAAGAAATCAA 60.564 45.833 0.00 0.00 41.22 2.57
1655 1723 4.916183 ACCAAGGAGGAGAAGAAATCAAG 58.084 43.478 0.00 0.00 41.22 3.02
1656 1724 4.263683 ACCAAGGAGGAGAAGAAATCAAGG 60.264 45.833 0.00 0.00 41.22 3.61
1657 1725 4.018960 CCAAGGAGGAGAAGAAATCAAGGA 60.019 45.833 0.00 0.00 41.22 3.36
1658 1726 5.184711 CAAGGAGGAGAAGAAATCAAGGAG 58.815 45.833 0.00 0.00 0.00 3.69
1659 1727 3.779738 AGGAGGAGAAGAAATCAAGGAGG 59.220 47.826 0.00 0.00 0.00 4.30
1660 1728 3.540617 GAGGAGAAGAAATCAAGGAGGC 58.459 50.000 0.00 0.00 0.00 4.70
1661 1729 2.093235 AGGAGAAGAAATCAAGGAGGCG 60.093 50.000 0.00 0.00 0.00 5.52
1662 1730 2.355209 GGAGAAGAAATCAAGGAGGCGT 60.355 50.000 0.00 0.00 0.00 5.68
1663 1731 2.675348 GAGAAGAAATCAAGGAGGCGTG 59.325 50.000 0.00 0.00 0.00 5.34
1664 1732 1.740025 GAAGAAATCAAGGAGGCGTGG 59.260 52.381 0.00 0.00 0.00 4.94
1665 1733 0.678048 AGAAATCAAGGAGGCGTGGC 60.678 55.000 0.00 0.00 0.00 5.01
1666 1734 1.982073 GAAATCAAGGAGGCGTGGCG 61.982 60.000 0.00 0.00 0.00 5.69
1667 1735 2.463589 AAATCAAGGAGGCGTGGCGA 62.464 55.000 0.00 0.00 0.00 5.54
1668 1736 2.859273 AATCAAGGAGGCGTGGCGAG 62.859 60.000 0.00 0.00 0.00 5.03
1669 1737 4.069232 CAAGGAGGCGTGGCGAGA 62.069 66.667 0.00 0.00 0.00 4.04
1670 1738 3.764466 AAGGAGGCGTGGCGAGAG 61.764 66.667 0.00 0.00 0.00 3.20
1682 1750 2.405191 CGAGAGCTCATCGCGTGA 59.595 61.111 17.77 0.00 45.00 4.35
1691 1759 0.029967 TCATCGCGTGAGAGAGATGC 59.970 55.000 5.77 0.00 44.90 3.91
1692 1760 0.030504 CATCGCGTGAGAGAGATGCT 59.969 55.000 5.77 0.00 44.90 3.79
1693 1761 0.030504 ATCGCGTGAGAGAGATGCTG 59.969 55.000 5.77 0.00 44.90 4.41
1694 1762 2.229589 CGCGTGAGAGAGATGCTGC 61.230 63.158 0.00 0.00 0.00 5.25
1695 1763 1.141449 GCGTGAGAGAGATGCTGCT 59.859 57.895 0.00 0.00 0.00 4.24
1696 1764 1.146957 GCGTGAGAGAGATGCTGCTG 61.147 60.000 0.00 0.00 0.00 4.41
1697 1765 1.146957 CGTGAGAGAGATGCTGCTGC 61.147 60.000 8.89 8.89 40.20 5.25
1780 1848 0.741221 GGACACCTCCGAAGATGCAC 60.741 60.000 0.00 0.00 0.00 4.57
1815 1883 1.670967 GCTCCTGCAAACAAAGATGCC 60.671 52.381 0.00 0.00 41.87 4.40
5425 5655 6.860539 CGATTACTGGTCTGACATTCTCATAG 59.139 42.308 10.38 0.00 0.00 2.23
5493 5723 4.157289 GGCAAGATGAGATCAAGCAAGAAA 59.843 41.667 0.00 0.00 34.38 2.52
5556 5813 0.990374 ACAAGGCAGAGGCAGAGAAT 59.010 50.000 0.00 0.00 43.71 2.40
5615 5872 4.194720 GGAGGACGCGTCGCTGAT 62.195 66.667 30.99 15.17 0.00 2.90
5643 5900 3.754068 CTGCACTTCAGCAAGCCA 58.246 55.556 0.00 0.00 45.13 4.75
5835 6092 3.764466 AGCCTCGACAGCTTCCGG 61.764 66.667 0.00 0.00 37.24 5.14
5852 6109 2.126031 GCTCACCGACTTCCCGTC 60.126 66.667 0.00 0.00 39.33 4.79
6021 6334 3.192422 TGTGTTGTTGGTTTCAGGTGAAG 59.808 43.478 0.00 0.00 35.21 3.02
6065 6378 5.708230 TGTTATTTAGGTGGTGGTAGCTTTG 59.292 40.000 0.00 0.00 0.00 2.77
6120 6452 3.447742 CTTTGTGGTGTCTTTTTGGAGC 58.552 45.455 0.00 0.00 0.00 4.70
6122 6454 2.297701 TGTGGTGTCTTTTTGGAGCTC 58.702 47.619 4.71 4.71 0.00 4.09
6123 6455 1.609072 GTGGTGTCTTTTTGGAGCTCC 59.391 52.381 26.78 26.78 0.00 4.70
6124 6456 1.248486 GGTGTCTTTTTGGAGCTCCC 58.752 55.000 29.95 12.91 34.29 4.30
6125 6457 1.202940 GGTGTCTTTTTGGAGCTCCCT 60.203 52.381 29.95 0.00 35.38 4.20
6161 6537 7.602644 TGCTGAGAGGTGTTTGTTATTAAGTAG 59.397 37.037 0.00 0.00 0.00 2.57
6217 6601 2.812836 TGTGAGGATTGGATGCATGT 57.187 45.000 2.46 0.00 0.00 3.21
6218 6602 2.371306 TGTGAGGATTGGATGCATGTG 58.629 47.619 2.46 0.00 0.00 3.21
6219 6603 2.026075 TGTGAGGATTGGATGCATGTGA 60.026 45.455 2.46 0.00 0.00 3.58
6220 6604 2.617308 GTGAGGATTGGATGCATGTGAG 59.383 50.000 2.46 0.00 0.00 3.51
6221 6605 2.228059 GAGGATTGGATGCATGTGAGG 58.772 52.381 2.46 0.00 0.00 3.86
6222 6606 1.848388 AGGATTGGATGCATGTGAGGA 59.152 47.619 2.46 0.00 0.00 3.71
6256 6640 2.227194 CTGGTGACTTTGTTGGTACCC 58.773 52.381 10.07 0.00 0.00 3.69
6276 6660 3.056465 CCCTACCTGAAAGTCTGTCTGTC 60.056 52.174 0.00 0.00 0.00 3.51
6278 6662 4.282195 CCTACCTGAAAGTCTGTCTGTCTT 59.718 45.833 0.00 0.00 31.90 3.01
6279 6663 4.065321 ACCTGAAAGTCTGTCTGTCTTG 57.935 45.455 0.00 0.00 31.90 3.02
6280 6664 3.452627 ACCTGAAAGTCTGTCTGTCTTGT 59.547 43.478 0.00 0.00 31.90 3.16
6281 6665 3.806521 CCTGAAAGTCTGTCTGTCTTGTG 59.193 47.826 0.00 0.00 31.90 3.33
6282 6666 4.437239 CTGAAAGTCTGTCTGTCTTGTGT 58.563 43.478 0.00 0.00 31.90 3.72
6283 6667 4.832248 TGAAAGTCTGTCTGTCTTGTGTT 58.168 39.130 0.00 0.00 31.90 3.32
6284 6668 4.631377 TGAAAGTCTGTCTGTCTTGTGTTG 59.369 41.667 0.00 0.00 31.90 3.33
6285 6669 3.895232 AGTCTGTCTGTCTTGTGTTGT 57.105 42.857 0.00 0.00 0.00 3.32
6286 6670 3.525537 AGTCTGTCTGTCTTGTGTTGTG 58.474 45.455 0.00 0.00 0.00 3.33
6316 6700 5.455392 GTTGAATTGTGTGGTGAATGAGAG 58.545 41.667 0.00 0.00 0.00 3.20
6330 6714 2.787473 TGAGAGTGCTATTGGTTGGG 57.213 50.000 0.00 0.00 0.00 4.12
6352 6749 4.457949 GGGGTCACTAGTTGTTATTGTTGG 59.542 45.833 0.00 0.00 0.00 3.77
6353 6750 5.067954 GGGTCACTAGTTGTTATTGTTGGT 58.932 41.667 0.00 0.00 0.00 3.67
6354 6751 5.048991 GGGTCACTAGTTGTTATTGTTGGTG 60.049 44.000 0.00 0.00 0.00 4.17
6362 6759 4.640789 TGTTATTGTTGGTGTTGTGGTC 57.359 40.909 0.00 0.00 0.00 4.02
6391 6788 2.676748 AGCAGCAGAGGAGTAATAGCT 58.323 47.619 0.00 0.00 0.00 3.32
6392 6789 3.037549 AGCAGCAGAGGAGTAATAGCTT 58.962 45.455 0.00 0.00 0.00 3.74
6393 6790 3.454082 AGCAGCAGAGGAGTAATAGCTTT 59.546 43.478 0.00 0.00 0.00 3.51
6394 6791 4.080638 AGCAGCAGAGGAGTAATAGCTTTT 60.081 41.667 0.00 0.00 0.00 2.27
6395 6792 5.129485 AGCAGCAGAGGAGTAATAGCTTTTA 59.871 40.000 0.00 0.00 0.00 1.52
6396 6793 5.235401 GCAGCAGAGGAGTAATAGCTTTTAC 59.765 44.000 16.59 16.59 33.20 2.01
6397 6794 6.578023 CAGCAGAGGAGTAATAGCTTTTACT 58.422 40.000 24.18 24.18 43.39 2.24
6399 6796 8.364142 CAGCAGAGGAGTAATAGCTTTTACTAT 58.636 37.037 24.04 17.44 41.36 2.12
6400 6797 9.589461 AGCAGAGGAGTAATAGCTTTTACTATA 57.411 33.333 24.04 0.00 41.36 1.31
6452 6901 8.942338 TTGGCATGACTAGTAATTACTAACTG 57.058 34.615 22.47 17.37 38.24 3.16
6476 6926 6.183360 TGGTAACTGATAGTGTGATACCCATG 60.183 42.308 0.00 0.00 30.48 3.66
6478 6928 5.798125 ACTGATAGTGTGATACCCATGAG 57.202 43.478 0.00 0.00 0.00 2.90
6482 6932 1.487976 AGTGTGATACCCATGAGGCAG 59.512 52.381 0.00 0.00 40.58 4.85
6483 6933 0.839277 TGTGATACCCATGAGGCAGG 59.161 55.000 0.00 0.00 40.58 4.85
6484 6934 0.536006 GTGATACCCATGAGGCAGGC 60.536 60.000 0.00 0.00 40.58 4.85
6485 6935 0.987613 TGATACCCATGAGGCAGGCA 60.988 55.000 0.00 0.00 40.58 4.75
6511 6961 2.618379 GCTTTAGGCAGGCTTGGTAGC 61.618 57.143 0.00 2.80 42.89 3.58
6588 7050 2.710724 AAGCAGCAAAGGCAAGCAGC 62.711 55.000 0.00 5.36 43.22 5.25
6661 7145 6.913170 TCTTTTAAACTGAACATGCTCATCC 58.087 36.000 0.00 0.00 0.00 3.51
6669 7189 4.903054 TGAACATGCTCATCCATCTATCC 58.097 43.478 0.00 0.00 0.00 2.59
6678 7198 6.324254 TGCTCATCCATCTATCCATCTATCTG 59.676 42.308 0.00 0.00 0.00 2.90
6800 7320 4.314121 GAAGACAGATGCTTCAGTCAGTT 58.686 43.478 21.84 11.71 39.99 3.16
6805 7325 4.202295 ACAGATGCTTCAGTCAGTTTCAGA 60.202 41.667 2.07 0.00 0.00 3.27
6848 7369 2.745698 CTGACTGGCTGGCAGTGA 59.254 61.111 37.03 28.99 46.57 3.41
6849 7370 1.670406 CTGACTGGCTGGCAGTGAC 60.670 63.158 37.03 24.71 46.57 3.67
6850 7371 2.109517 CTGACTGGCTGGCAGTGACT 62.110 60.000 37.03 16.17 46.57 3.41
6851 7372 1.670406 GACTGGCTGGCAGTGACTG 60.670 63.158 37.03 8.52 32.33 3.51
6860 7381 4.280676 CAGTGACTGCAGCTGGAG 57.719 61.111 31.17 31.17 39.57 3.86
6861 7382 2.033755 CAGTGACTGCAGCTGGAGC 61.034 63.158 32.47 24.47 36.94 4.70
6878 7399 3.665544 GCTGGAGCTCAGTCTGATC 57.334 57.895 17.19 0.00 45.08 2.92
6879 7400 1.113788 GCTGGAGCTCAGTCTGATCT 58.886 55.000 17.19 5.90 45.08 2.75
6880 7401 1.067516 GCTGGAGCTCAGTCTGATCTC 59.932 57.143 20.78 20.78 45.08 2.75
6881 7402 2.377073 CTGGAGCTCAGTCTGATCTCA 58.623 52.381 26.92 16.03 40.38 3.27
6882 7403 2.960384 CTGGAGCTCAGTCTGATCTCAT 59.040 50.000 26.92 4.57 40.38 2.90
6883 7404 2.957680 TGGAGCTCAGTCTGATCTCATC 59.042 50.000 26.92 15.62 40.38 2.92
6884 7405 3.225104 GGAGCTCAGTCTGATCTCATCT 58.775 50.000 26.92 9.30 40.38 2.90
6885 7406 3.005050 GGAGCTCAGTCTGATCTCATCTG 59.995 52.174 26.92 6.58 40.38 2.90
6886 7407 3.884693 GAGCTCAGTCTGATCTCATCTGA 59.115 47.826 22.99 11.77 38.94 3.27
6887 7408 4.476297 AGCTCAGTCTGATCTCATCTGAT 58.524 43.478 2.22 0.00 39.06 2.90
6888 7409 4.279922 AGCTCAGTCTGATCTCATCTGATG 59.720 45.833 11.42 11.42 39.06 3.07
6889 7410 4.559906 GCTCAGTCTGATCTCATCTGATGG 60.560 50.000 17.06 8.49 39.06 3.51
6890 7411 4.801164 TCAGTCTGATCTCATCTGATGGA 58.199 43.478 17.06 13.12 39.06 3.41
6891 7412 4.828387 TCAGTCTGATCTCATCTGATGGAG 59.172 45.833 17.06 12.67 39.06 3.86
6892 7413 4.828387 CAGTCTGATCTCATCTGATGGAGA 59.172 45.833 17.06 16.77 43.71 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.036958 ATTTGTCCGATGCCGATGAA 57.963 45.000 0.00 0.00 38.22 2.57
6 7 2.780993 CAACGTAATTTGTCCGATGCC 58.219 47.619 0.00 0.00 0.00 4.40
8 9 3.463533 TGCAACGTAATTTGTCCGATG 57.536 42.857 0.00 0.00 0.00 3.84
12 13 6.119144 ACAGATATGCAACGTAATTTGTCC 57.881 37.500 0.00 0.00 0.00 4.02
77 84 2.156117 GTGTGCGGCGCGATATAATTAA 59.844 45.455 28.09 1.60 0.00 1.40
95 102 4.119862 CCCGAAATGAGATATTCGTGTGT 58.880 43.478 7.08 0.00 45.12 3.72
166 177 2.092753 TGCCTGGTGATGGAATCTCTTC 60.093 50.000 0.00 0.00 45.81 2.87
171 182 0.548031 TCCTGCCTGGTGATGGAATC 59.452 55.000 0.00 0.00 38.12 2.52
175 186 1.202855 CCTATTCCTGCCTGGTGATGG 60.203 57.143 0.00 0.00 37.07 3.51
181 192 2.061790 GCCTCCCTATTCCTGCCTGG 62.062 65.000 0.00 0.00 37.10 4.45
187 198 2.711174 ACATGATGCCTCCCTATTCCT 58.289 47.619 0.00 0.00 0.00 3.36
190 201 4.406649 CCAAAAACATGATGCCTCCCTATT 59.593 41.667 0.00 0.00 0.00 1.73
235 246 5.712446 GCCTCCTTCTTTCTCCTGTATTTTT 59.288 40.000 0.00 0.00 0.00 1.94
256 267 2.815503 GCTTCATTTTGCAATTTGGCCT 59.184 40.909 3.32 0.00 0.00 5.19
286 297 2.177016 GGTAAATAATCCCACCCTGGCT 59.823 50.000 0.00 0.00 35.79 4.75
287 298 2.091555 TGGTAAATAATCCCACCCTGGC 60.092 50.000 0.00 0.00 35.79 4.85
288 299 3.204382 ACTGGTAAATAATCCCACCCTGG 59.796 47.826 0.00 0.00 37.25 4.45
289 300 4.207165 CACTGGTAAATAATCCCACCCTG 58.793 47.826 0.00 0.00 0.00 4.45
297 308 3.595190 AGGGGCCACTGGTAAATAATC 57.405 47.619 6.78 0.00 0.00 1.75
319 330 2.638325 TGGGGAATTCCTGTTAGGACA 58.362 47.619 23.63 7.74 45.78 4.02
328 339 0.710588 GGAGGGTTTGGGGAATTCCT 59.289 55.000 23.63 1.06 35.95 3.36
329 340 0.411848 TGGAGGGTTTGGGGAATTCC 59.588 55.000 16.74 16.74 0.00 3.01
350 361 2.162408 GGAGGAACAGCAACAGCAATAC 59.838 50.000 0.00 0.00 0.00 1.89
355 366 0.036022 AGAGGAGGAACAGCAACAGC 59.964 55.000 0.00 0.00 0.00 4.40
360 371 3.838565 CCTATAGAGAGGAGGAACAGCA 58.161 50.000 0.00 0.00 39.15 4.41
361 372 2.560981 GCCTATAGAGAGGAGGAACAGC 59.439 54.545 0.00 0.00 39.15 4.40
362 373 4.079253 GAGCCTATAGAGAGGAGGAACAG 58.921 52.174 0.00 0.00 39.15 3.16
363 374 3.724738 AGAGCCTATAGAGAGGAGGAACA 59.275 47.826 0.00 0.00 39.15 3.18
364 375 4.079253 CAGAGCCTATAGAGAGGAGGAAC 58.921 52.174 0.00 0.00 39.15 3.62
365 376 3.724738 ACAGAGCCTATAGAGAGGAGGAA 59.275 47.826 0.00 0.00 39.15 3.36
408 419 1.966354 GGCTGGAATGGGGAATCAATC 59.034 52.381 0.00 0.00 0.00 2.67
409 420 1.291637 TGGCTGGAATGGGGAATCAAT 59.708 47.619 0.00 0.00 0.00 2.57
410 421 0.709397 TGGCTGGAATGGGGAATCAA 59.291 50.000 0.00 0.00 0.00 2.57
411 422 0.259647 CTGGCTGGAATGGGGAATCA 59.740 55.000 0.00 0.00 0.00 2.57
516 540 1.616628 GGGAGGGAGGAGAGGCAAA 60.617 63.158 0.00 0.00 0.00 3.68
527 551 3.036959 GAGGGAGGGAGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
528 552 4.179599 GGAGGGAGGGAGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
529 553 3.039526 AGGAGGGAGGGAGGGAGG 61.040 72.222 0.00 0.00 0.00 4.30
530 554 2.612251 GAGGAGGGAGGGAGGGAG 59.388 72.222 0.00 0.00 0.00 4.30
531 555 3.430497 CGAGGAGGGAGGGAGGGA 61.430 72.222 0.00 0.00 0.00 4.20
532 556 4.548513 CCGAGGAGGGAGGGAGGG 62.549 77.778 0.00 0.00 35.97 4.30
533 557 2.319410 ATTCCGAGGAGGGAGGGAGG 62.319 65.000 0.00 0.00 41.52 4.30
534 558 1.118356 CATTCCGAGGAGGGAGGGAG 61.118 65.000 0.00 0.00 41.52 4.30
535 559 1.075226 CATTCCGAGGAGGGAGGGA 60.075 63.158 0.00 0.00 41.52 4.20
629 653 0.041312 TGCGCGAAAAGAAGCAAGAC 60.041 50.000 12.10 0.00 36.60 3.01
631 655 1.332882 GCTGCGCGAAAAGAAGCAAG 61.333 55.000 12.10 0.00 39.26 4.01
1185 1244 2.368878 GCCCCTTCCCTGATCCCT 60.369 66.667 0.00 0.00 0.00 4.20
1377 1436 3.008375 CCTGGAAGATGACAAACTCAGGA 59.992 47.826 11.74 0.00 42.06 3.86
1394 1453 1.565759 CAACATCCTCAATCCCCTGGA 59.434 52.381 0.00 0.00 35.55 3.86
1410 1469 4.268939 GCAACGGCAGCAGCAACA 62.269 61.111 2.65 0.00 44.61 3.33
1440 1499 1.308998 CATCAGCATCAGCATCAGCA 58.691 50.000 0.00 0.00 45.49 4.41
1441 1500 0.039978 GCATCAGCATCAGCATCAGC 60.040 55.000 0.00 0.00 45.49 4.26
1442 1501 1.265365 CAGCATCAGCATCAGCATCAG 59.735 52.381 0.00 0.00 45.49 2.90
1443 1502 1.134220 TCAGCATCAGCATCAGCATCA 60.134 47.619 0.00 0.00 45.49 3.07
1444 1503 1.594331 TCAGCATCAGCATCAGCATC 58.406 50.000 0.00 0.00 45.49 3.91
1445 1504 1.882623 CATCAGCATCAGCATCAGCAT 59.117 47.619 0.00 0.00 45.49 3.79
1446 1505 1.308998 CATCAGCATCAGCATCAGCA 58.691 50.000 0.00 0.00 45.49 4.41
1447 1506 0.039978 GCATCAGCATCAGCATCAGC 60.040 55.000 0.00 0.00 45.49 4.26
1448 1507 1.265365 CAGCATCAGCATCAGCATCAG 59.735 52.381 0.00 0.00 45.49 2.90
1449 1508 1.134220 TCAGCATCAGCATCAGCATCA 60.134 47.619 0.00 0.00 45.49 3.07
1450 1509 1.594331 TCAGCATCAGCATCAGCATC 58.406 50.000 0.00 0.00 45.49 3.91
1451 1510 1.882623 CATCAGCATCAGCATCAGCAT 59.117 47.619 0.00 0.00 45.49 3.79
1452 1511 1.308998 CATCAGCATCAGCATCAGCA 58.691 50.000 0.00 0.00 45.49 4.41
1458 1517 1.001887 TGCCACATCAGCATCAGCA 60.002 52.632 0.00 0.00 45.49 4.41
1531 1593 2.273449 CTCCTTGGCCGGAGCATT 59.727 61.111 13.13 0.00 43.69 3.56
1600 1668 2.751806 CAATGGCCTCTTCTTGTTCCTC 59.248 50.000 3.32 0.00 0.00 3.71
1601 1669 2.376518 TCAATGGCCTCTTCTTGTTCCT 59.623 45.455 3.32 0.00 0.00 3.36
1602 1670 2.795329 TCAATGGCCTCTTCTTGTTCC 58.205 47.619 3.32 0.00 0.00 3.62
1603 1671 4.012374 TCATCAATGGCCTCTTCTTGTTC 58.988 43.478 3.32 0.00 0.00 3.18
1604 1672 4.038271 TCATCAATGGCCTCTTCTTGTT 57.962 40.909 3.32 0.00 0.00 2.83
1605 1673 3.726557 TCATCAATGGCCTCTTCTTGT 57.273 42.857 3.32 0.00 0.00 3.16
1606 1674 3.243434 GCATCATCAATGGCCTCTTCTTG 60.243 47.826 3.32 0.26 35.77 3.02
1607 1675 2.957006 GCATCATCAATGGCCTCTTCTT 59.043 45.455 3.32 0.00 35.77 2.52
1608 1676 2.175069 AGCATCATCAATGGCCTCTTCT 59.825 45.455 3.32 0.00 35.77 2.85
1609 1677 2.553172 GAGCATCATCAATGGCCTCTTC 59.447 50.000 3.32 0.00 35.77 2.87
1610 1678 2.584236 GAGCATCATCAATGGCCTCTT 58.416 47.619 3.32 0.00 35.77 2.85
1611 1679 1.202903 GGAGCATCATCAATGGCCTCT 60.203 52.381 3.32 0.00 36.25 3.69
1612 1680 1.245732 GGAGCATCATCAATGGCCTC 58.754 55.000 3.32 0.00 36.25 4.70
1613 1681 0.536687 CGGAGCATCATCAATGGCCT 60.537 55.000 3.32 0.00 36.25 5.19
1614 1682 0.535780 TCGGAGCATCATCAATGGCC 60.536 55.000 0.00 0.00 36.25 5.36
1615 1683 0.590195 GTCGGAGCATCATCAATGGC 59.410 55.000 0.00 0.00 36.25 4.40
1616 1684 1.233019 GGTCGGAGCATCATCAATGG 58.767 55.000 1.64 0.00 36.25 3.16
1617 1685 1.957668 TGGTCGGAGCATCATCAATG 58.042 50.000 5.66 0.00 36.25 2.82
1618 1686 2.569059 CTTGGTCGGAGCATCATCAAT 58.431 47.619 11.09 0.00 36.25 2.57
1619 1687 1.407299 CCTTGGTCGGAGCATCATCAA 60.407 52.381 11.09 0.00 36.25 2.57
1620 1688 0.178767 CCTTGGTCGGAGCATCATCA 59.821 55.000 11.09 0.00 36.25 3.07
1621 1689 0.465705 TCCTTGGTCGGAGCATCATC 59.534 55.000 11.09 0.00 36.25 2.92
1622 1690 0.467384 CTCCTTGGTCGGAGCATCAT 59.533 55.000 11.09 0.00 43.69 2.45
1623 1691 1.900351 CTCCTTGGTCGGAGCATCA 59.100 57.895 11.09 0.00 43.69 3.07
1624 1692 4.844420 CTCCTTGGTCGGAGCATC 57.156 61.111 11.09 0.00 43.69 3.91
1629 1697 0.408309 TCTTCTCCTCCTTGGTCGGA 59.592 55.000 0.00 0.00 37.07 4.55
1630 1698 1.267121 TTCTTCTCCTCCTTGGTCGG 58.733 55.000 0.00 0.00 37.07 4.79
1631 1699 3.055819 TGATTTCTTCTCCTCCTTGGTCG 60.056 47.826 0.00 0.00 37.07 4.79
1632 1700 4.559862 TGATTTCTTCTCCTCCTTGGTC 57.440 45.455 0.00 0.00 37.07 4.02
1633 1701 4.263683 CCTTGATTTCTTCTCCTCCTTGGT 60.264 45.833 0.00 0.00 37.07 3.67
1634 1702 4.018960 TCCTTGATTTCTTCTCCTCCTTGG 60.019 45.833 0.00 0.00 37.10 3.61
1635 1703 5.171339 TCCTTGATTTCTTCTCCTCCTTG 57.829 43.478 0.00 0.00 0.00 3.61
1636 1704 4.227073 CCTCCTTGATTTCTTCTCCTCCTT 59.773 45.833 0.00 0.00 0.00 3.36
1637 1705 3.779738 CCTCCTTGATTTCTTCTCCTCCT 59.220 47.826 0.00 0.00 0.00 3.69
1638 1706 3.684130 GCCTCCTTGATTTCTTCTCCTCC 60.684 52.174 0.00 0.00 0.00 4.30
1639 1707 3.540617 GCCTCCTTGATTTCTTCTCCTC 58.459 50.000 0.00 0.00 0.00 3.71
1640 1708 2.093235 CGCCTCCTTGATTTCTTCTCCT 60.093 50.000 0.00 0.00 0.00 3.69
1641 1709 2.284190 CGCCTCCTTGATTTCTTCTCC 58.716 52.381 0.00 0.00 0.00 3.71
1642 1710 2.675348 CACGCCTCCTTGATTTCTTCTC 59.325 50.000 0.00 0.00 0.00 2.87
1643 1711 2.616510 CCACGCCTCCTTGATTTCTTCT 60.617 50.000 0.00 0.00 0.00 2.85
1644 1712 1.740025 CCACGCCTCCTTGATTTCTTC 59.260 52.381 0.00 0.00 0.00 2.87
1645 1713 1.826385 CCACGCCTCCTTGATTTCTT 58.174 50.000 0.00 0.00 0.00 2.52
1646 1714 0.678048 GCCACGCCTCCTTGATTTCT 60.678 55.000 0.00 0.00 0.00 2.52
1647 1715 1.803289 GCCACGCCTCCTTGATTTC 59.197 57.895 0.00 0.00 0.00 2.17
1648 1716 2.040544 CGCCACGCCTCCTTGATTT 61.041 57.895 0.00 0.00 0.00 2.17
1649 1717 2.436646 CGCCACGCCTCCTTGATT 60.437 61.111 0.00 0.00 0.00 2.57
1650 1718 3.376935 CTCGCCACGCCTCCTTGAT 62.377 63.158 0.00 0.00 0.00 2.57
1651 1719 4.069232 CTCGCCACGCCTCCTTGA 62.069 66.667 0.00 0.00 0.00 3.02
1652 1720 3.997064 CTCTCGCCACGCCTCCTTG 62.997 68.421 0.00 0.00 0.00 3.61
1653 1721 3.764466 CTCTCGCCACGCCTCCTT 61.764 66.667 0.00 0.00 0.00 3.36
1656 1724 4.863925 GAGCTCTCGCCACGCCTC 62.864 72.222 6.43 0.00 36.60 4.70
1658 1726 4.521062 ATGAGCTCTCGCCACGCC 62.521 66.667 16.19 0.00 36.60 5.68
1659 1727 2.959071 GATGAGCTCTCGCCACGC 60.959 66.667 16.19 0.00 36.60 5.34
1660 1728 2.653448 CGATGAGCTCTCGCCACG 60.653 66.667 16.19 7.67 36.60 4.94
1665 1733 2.405191 TCACGCGATGAGCTCTCG 59.595 61.111 22.99 22.99 45.59 4.04
1672 1740 0.029967 GCATCTCTCTCACGCGATGA 59.970 55.000 15.93 12.26 36.29 2.92
1673 1741 0.030504 AGCATCTCTCTCACGCGATG 59.969 55.000 15.93 7.85 37.05 3.84
1674 1742 0.030504 CAGCATCTCTCTCACGCGAT 59.969 55.000 15.93 0.00 0.00 4.58
1675 1743 1.431036 CAGCATCTCTCTCACGCGA 59.569 57.895 15.93 0.00 0.00 5.87
1676 1744 2.229589 GCAGCATCTCTCTCACGCG 61.230 63.158 3.53 3.53 0.00 6.01
1677 1745 1.141449 AGCAGCATCTCTCTCACGC 59.859 57.895 0.00 0.00 0.00 5.34
1678 1746 1.146957 GCAGCAGCATCTCTCTCACG 61.147 60.000 0.00 0.00 41.58 4.35
1679 1747 2.680429 GCAGCAGCATCTCTCTCAC 58.320 57.895 0.00 0.00 41.58 3.51
1690 1758 1.174712 TCTGGTTCCTTTGCAGCAGC 61.175 55.000 0.00 0.00 38.23 5.25
1691 1759 1.268899 CTTCTGGTTCCTTTGCAGCAG 59.731 52.381 0.00 0.00 39.44 4.24
1692 1760 1.321474 CTTCTGGTTCCTTTGCAGCA 58.679 50.000 0.00 0.00 0.00 4.41
1693 1761 1.000938 CACTTCTGGTTCCTTTGCAGC 60.001 52.381 0.00 0.00 0.00 5.25
1694 1762 1.610522 CCACTTCTGGTTCCTTTGCAG 59.389 52.381 0.00 0.00 32.03 4.41
1695 1763 1.691196 CCACTTCTGGTTCCTTTGCA 58.309 50.000 0.00 0.00 32.03 4.08
1696 1764 0.315251 GCCACTTCTGGTTCCTTTGC 59.685 55.000 0.00 0.00 40.17 3.68
1697 1765 0.961753 GGCCACTTCTGGTTCCTTTG 59.038 55.000 0.00 0.00 40.17 2.77
1698 1766 0.555769 TGGCCACTTCTGGTTCCTTT 59.444 50.000 0.00 0.00 40.17 3.11
1780 1848 0.682292 GGAGCTTCTCCCTTATCCGG 59.318 60.000 0.00 0.00 44.36 5.14
1815 1883 2.040544 GGTGTCCTCAACCATGGCG 61.041 63.158 13.04 3.06 0.00 5.69
5384 5614 8.307483 ACCAGTAATCGTCCTTCATATTATCAG 58.693 37.037 0.00 0.00 0.00 2.90
5389 5619 6.323996 TCAGACCAGTAATCGTCCTTCATATT 59.676 38.462 0.00 0.00 0.00 1.28
5425 5655 2.432628 CAGCGGTTCCTCCACGTC 60.433 66.667 0.00 0.00 35.57 4.34
5711 5968 3.063084 GCTGGTCCGTCTCCGTCT 61.063 66.667 0.00 0.00 0.00 4.18
5818 6075 3.764466 CCGGAAGCTGTCGAGGCT 61.764 66.667 0.00 6.96 42.31 4.58
5835 6092 2.126031 GACGGGAAGTCGGTGAGC 60.126 66.667 0.00 0.00 40.43 4.26
6021 6334 0.041982 AACACCTCCTCCTCTCCTCC 59.958 60.000 0.00 0.00 0.00 4.30
6065 6378 4.204799 ACTCCTCCTTTTAACACAACCAC 58.795 43.478 0.00 0.00 0.00 4.16
6102 6434 2.297701 GAGCTCCAAAAAGACACCACA 58.702 47.619 0.87 0.00 0.00 4.17
6120 6452 0.535328 CAGCATCAGCATCCAGGGAG 60.535 60.000 0.00 0.00 45.49 4.30
6122 6454 0.535328 CTCAGCATCAGCATCCAGGG 60.535 60.000 0.00 0.00 45.49 4.45
6123 6455 0.468648 TCTCAGCATCAGCATCCAGG 59.531 55.000 0.00 0.00 45.49 4.45
6124 6456 1.541452 CCTCTCAGCATCAGCATCCAG 60.541 57.143 0.00 0.00 45.49 3.86
6125 6457 0.468648 CCTCTCAGCATCAGCATCCA 59.531 55.000 0.00 0.00 45.49 3.41
6166 6542 9.071276 CCATGCCATAGTCTTTTTACATCTTAT 57.929 33.333 0.00 0.00 0.00 1.73
6217 6601 4.148838 CCAGGTTTTTACACCAATCCTCA 58.851 43.478 0.00 0.00 39.62 3.86
6218 6602 4.022329 CACCAGGTTTTTACACCAATCCTC 60.022 45.833 0.00 0.00 39.62 3.71
6219 6603 3.895041 CACCAGGTTTTTACACCAATCCT 59.105 43.478 0.00 0.00 39.62 3.24
6220 6604 3.892588 TCACCAGGTTTTTACACCAATCC 59.107 43.478 0.00 0.00 39.62 3.01
6221 6605 4.583073 AGTCACCAGGTTTTTACACCAATC 59.417 41.667 0.00 0.00 39.62 2.67
6222 6606 4.542697 AGTCACCAGGTTTTTACACCAAT 58.457 39.130 0.00 0.00 39.62 3.16
6256 6640 5.221342 ACAAGACAGACAGACTTTCAGGTAG 60.221 44.000 0.00 0.00 29.73 3.18
6276 6660 2.746904 TCAACCAGACACACAACACAAG 59.253 45.455 0.00 0.00 0.00 3.16
6278 6662 2.481289 TCAACCAGACACACAACACA 57.519 45.000 0.00 0.00 0.00 3.72
6279 6663 4.104776 CAATTCAACCAGACACACAACAC 58.895 43.478 0.00 0.00 0.00 3.32
6280 6664 3.761218 ACAATTCAACCAGACACACAACA 59.239 39.130 0.00 0.00 0.00 3.33
6281 6665 4.104776 CACAATTCAACCAGACACACAAC 58.895 43.478 0.00 0.00 0.00 3.32
6282 6666 3.761218 ACACAATTCAACCAGACACACAA 59.239 39.130 0.00 0.00 0.00 3.33
6283 6667 3.128415 CACACAATTCAACCAGACACACA 59.872 43.478 0.00 0.00 0.00 3.72
6284 6668 3.489059 CCACACAATTCAACCAGACACAC 60.489 47.826 0.00 0.00 0.00 3.82
6285 6669 2.687425 CCACACAATTCAACCAGACACA 59.313 45.455 0.00 0.00 0.00 3.72
6286 6670 2.687935 ACCACACAATTCAACCAGACAC 59.312 45.455 0.00 0.00 0.00 3.67
6316 6700 0.039035 TGACCCCCAACCAATAGCAC 59.961 55.000 0.00 0.00 0.00 4.40
6330 6714 5.048991 CACCAACAATAACAACTAGTGACCC 60.049 44.000 0.00 0.00 30.03 4.46
6352 6749 3.066064 TGCTACAAACATGACCACAACAC 59.934 43.478 0.00 0.00 0.00 3.32
6353 6750 3.282885 TGCTACAAACATGACCACAACA 58.717 40.909 0.00 0.00 0.00 3.33
6354 6751 3.853307 GCTGCTACAAACATGACCACAAC 60.853 47.826 0.00 0.00 0.00 3.32
6362 6759 2.676839 CTCCTCTGCTGCTACAAACATG 59.323 50.000 0.00 0.00 0.00 3.21
6393 6790 9.706529 ACTCCAGCTCATCATATCATATAGTAA 57.293 33.333 0.00 0.00 0.00 2.24
6395 6792 9.880254 ATACTCCAGCTCATCATATCATATAGT 57.120 33.333 0.00 0.00 0.00 2.12
6399 6796 8.835550 AAGATACTCCAGCTCATCATATCATA 57.164 34.615 0.00 0.00 0.00 2.15
6400 6797 7.736881 AAGATACTCCAGCTCATCATATCAT 57.263 36.000 0.00 0.00 0.00 2.45
6401 6798 8.835550 ATAAGATACTCCAGCTCATCATATCA 57.164 34.615 0.00 0.00 0.00 2.15
6413 6857 6.294473 AGTCATGCCAAATAAGATACTCCAG 58.706 40.000 0.00 0.00 0.00 3.86
6414 6858 6.252599 AGTCATGCCAAATAAGATACTCCA 57.747 37.500 0.00 0.00 0.00 3.86
6445 6894 7.719871 ATCACACTATCAGTTACCAGTTAGT 57.280 36.000 0.00 0.00 0.00 2.24
6447 6896 7.069085 GGGTATCACACTATCAGTTACCAGTTA 59.931 40.741 7.06 0.00 32.24 2.24
6448 6897 6.127140 GGGTATCACACTATCAGTTACCAGTT 60.127 42.308 7.06 0.00 32.24 3.16
6449 6898 5.363005 GGGTATCACACTATCAGTTACCAGT 59.637 44.000 7.06 0.00 32.24 4.00
6450 6899 5.362717 TGGGTATCACACTATCAGTTACCAG 59.637 44.000 7.06 0.00 32.24 4.00
6451 6900 5.274015 TGGGTATCACACTATCAGTTACCA 58.726 41.667 7.06 0.00 32.24 3.25
6452 6901 5.864418 TGGGTATCACACTATCAGTTACC 57.136 43.478 0.00 0.00 30.65 2.85
6521 6971 3.925630 ATCCCACGGCAGCACAAGG 62.926 63.158 0.00 0.00 0.00 3.61
6588 7050 5.001237 TGCATATCAAAAGTTGGCATCTG 57.999 39.130 0.00 0.00 0.00 2.90
6661 7145 6.778834 AGCAGACAGATAGATGGATAGATG 57.221 41.667 0.00 0.00 0.00 2.90
6729 7249 9.810545 CTTTCACATTACCTTTACTTTTCCAAA 57.189 29.630 0.00 0.00 0.00 3.28
6732 7252 8.173542 TCCTTTCACATTACCTTTACTTTTCC 57.826 34.615 0.00 0.00 0.00 3.13
6734 7254 9.416284 TCTTCCTTTCACATTACCTTTACTTTT 57.584 29.630 0.00 0.00 0.00 2.27
6800 7320 5.470098 GTCACTCAAATTAAGCTGGTCTGAA 59.530 40.000 0.00 0.00 0.00 3.02
6805 7325 5.769662 TGATTGTCACTCAAATTAAGCTGGT 59.230 36.000 0.00 0.00 39.62 4.00
6860 7381 1.113788 AGATCAGACTGAGCTCCAGC 58.886 55.000 17.44 0.00 39.11 4.85
6866 7387 4.552355 CATCAGATGAGATCAGACTGAGC 58.448 47.826 12.88 12.88 42.07 4.26
6867 7388 4.828387 TCCATCAGATGAGATCAGACTGAG 59.172 45.833 12.41 14.12 42.07 3.35
6868 7389 4.801164 TCCATCAGATGAGATCAGACTGA 58.199 43.478 12.41 7.80 42.53 3.41
6869 7390 4.828387 TCTCCATCAGATGAGATCAGACTG 59.172 45.833 12.41 0.00 36.37 3.51
6870 7391 5.064314 TCTCCATCAGATGAGATCAGACT 57.936 43.478 12.41 0.00 0.00 3.24
6871 7392 5.988310 ATCTCCATCAGATGAGATCAGAC 57.012 43.478 12.41 0.00 40.71 3.51


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

AutoCloner maintained by Alex Coulton.