Multiple sequence alignment - TraesCS1A01G114500

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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 TraesCS1A01G114500 chr1A 100.000 5618 0 0 2207 7824 118762690 118768307 0.000000e+00 10375.0
1 TraesCS1A01G114500 chr1A 100.000 1745 0 0 1 1745 118760484 118762228 0.000000e+00 3223.0
2 TraesCS1A01G114500 chr1A 90.251 718 63 6 7112 7824 577182586 577181871 0.000000e+00 931.0
3 TraesCS1A01G114500 chr1A 96.057 558 21 1 1 557 118753642 118754199 0.000000e+00 907.0
4 TraesCS1A01G114500 chr1A 96.050 557 21 1 1 556 302849746 302850302 0.000000e+00 905.0
5 TraesCS1A01G114500 chr1A 96.050 557 21 1 1 556 593520527 593519971 0.000000e+00 905.0
6 TraesCS1A01G114500 chr1A 99.231 130 1 0 7037 7166 118808428 118808557 1.310000e-57 235.0
7 TraesCS1A01G114500 chr1B 96.981 3246 80 8 2207 5444 171031056 171034291 0.000000e+00 5435.0
8 TraesCS1A01G114500 chr1B 94.408 912 37 5 840 1745 171030101 171031004 0.000000e+00 1389.0
9 TraesCS1A01G114500 chr1B 97.081 788 19 4 6251 7035 171035219 171036005 0.000000e+00 1325.0
10 TraesCS1A01G114500 chr1B 96.015 778 25 4 5443 6219 171034452 171035224 0.000000e+00 1260.0
11 TraesCS1A01G114500 chr1B 96.296 729 24 2 7098 7824 355090980 355090253 0.000000e+00 1194.0
12 TraesCS1A01G114500 chr1D 97.287 2285 57 5 4751 7035 111719288 111721567 0.000000e+00 3871.0
13 TraesCS1A01G114500 chr1D 95.411 937 25 3 2522 3457 111700005 111700924 0.000000e+00 1476.0
14 TraesCS1A01G114500 chr1D 94.073 928 30 12 840 1745 111694285 111695209 0.000000e+00 1386.0
15 TraesCS1A01G114500 chr1D 97.997 649 13 0 4111 4759 111712289 111712937 0.000000e+00 1127.0
16 TraesCS1A01G114500 chr1D 95.573 497 17 2 3531 4027 111711793 111712284 0.000000e+00 791.0
17 TraesCS1A01G114500 chr1D 95.625 320 11 2 2207 2526 111695253 111695569 1.950000e-140 510.0
18 TraesCS1A01G114500 chr1D 91.259 286 25 0 557 842 180246747 180247032 2.650000e-104 390.0
19 TraesCS1A01G114500 chr1D 91.259 286 25 0 557 842 377802249 377802534 2.650000e-104 390.0
20 TraesCS1A01G114500 chr1D 90.909 286 26 0 557 842 180172975 180173260 1.230000e-102 385.0
21 TraesCS1A01G114500 chr1D 97.674 43 0 1 4030 4072 107622180 107622221 1.090000e-08 73.1
22 TraesCS1A01G114500 chr5A 95.949 790 26 5 7037 7824 33900877 33900092 0.000000e+00 1277.0
23 TraesCS1A01G114500 chr5A 96.050 557 21 1 1 556 536022782 536023338 0.000000e+00 905.0
24 TraesCS1A01G114500 chr5A 95.886 559 21 2 1 557 698476247 698475689 0.000000e+00 904.0
25 TraesCS1A01G114500 chr3B 95.575 791 28 4 7037 7824 25498097 25498883 0.000000e+00 1260.0
26 TraesCS1A01G114500 chr3B 86.639 726 84 10 4085 4803 739133574 739132855 0.000000e+00 791.0
27 TraesCS1A01G114500 chr3B 84.114 598 82 9 4814 5405 739132770 739132180 4.100000e-157 566.0
28 TraesCS1A01G114500 chr3B 75.451 1108 186 45 2883 3944 739134755 739133688 1.990000e-125 460.0
29 TraesCS1A01G114500 chr3B 78.040 551 76 30 5693 6230 739131987 739131469 9.860000e-79 305.0
30 TraesCS1A01G114500 chr3A 95.785 783 27 5 7044 7824 8127575 8126797 0.000000e+00 1258.0
31 TraesCS1A01G114500 chr3A 96.237 558 20 1 1 557 364939281 364939838 0.000000e+00 913.0
32 TraesCS1A01G114500 chr3A 95.878 558 22 1 1 557 369442085 369441528 0.000000e+00 902.0
33 TraesCS1A01G114500 chr3A 83.153 647 94 13 4814 5452 693167108 693166469 1.890000e-160 577.0
34 TraesCS1A01G114500 chr3A 86.653 487 51 11 4324 4803 693167672 693167193 1.930000e-145 527.0
35 TraesCS1A01G114500 chr3A 85.902 305 42 1 4085 4389 693167980 693167677 2.720000e-84 324.0
36 TraesCS1A01G114500 chr3A 78.108 539 73 29 5693 6218 693166322 693165816 4.590000e-77 300.0
37 TraesCS1A01G114500 chr3A 100.000 32 0 0 6990 7021 581389367 581389398 8.480000e-05 60.2
38 TraesCS1A01G114500 chr5B 96.296 729 25 1 7098 7824 440229199 440229927 0.000000e+00 1195.0
39 TraesCS1A01G114500 chr5B 90.797 728 51 9 7111 7824 548055214 548054489 0.000000e+00 959.0
40 TraesCS1A01G114500 chr4A 91.794 719 53 5 7111 7824 612499459 612498742 0.000000e+00 996.0
41 TraesCS1A01G114500 chr4A 91.238 719 57 5 7111 7824 232104134 232104851 0.000000e+00 974.0
42 TraesCS1A01G114500 chr2A 96.237 558 20 1 1 557 393335431 393334874 0.000000e+00 913.0
43 TraesCS1A01G114500 chr2A 95.556 45 1 1 4030 4074 59062368 59062325 3.920000e-08 71.3
44 TraesCS1A01G114500 chr7A 95.878 558 22 1 1 557 487365038 487365595 0.000000e+00 902.0
45 TraesCS1A01G114500 chr7A 97.619 42 0 1 6988 7029 496960335 496960295 3.920000e-08 71.3
46 TraesCS1A01G114500 chr7A 93.617 47 2 1 4030 4076 696999101 696999056 1.410000e-07 69.4
47 TraesCS1A01G114500 chr3D 83.386 638 94 9 4814 5444 556150862 556150230 1.460000e-161 580.0
48 TraesCS1A01G114500 chr3D 86.420 486 50 11 4324 4803 556151422 556150947 1.160000e-142 518.0
49 TraesCS1A01G114500 chr3D 75.549 1092 193 46 2883 3932 556152945 556151886 3.310000e-128 470.0
50 TraesCS1A01G114500 chr3D 84.776 335 50 1 4085 4419 556151760 556151427 1.260000e-87 335.0
51 TraesCS1A01G114500 chr3D 77.495 551 77 30 5693 6230 556150077 556149561 3.570000e-73 287.0
52 TraesCS1A01G114500 chr6D 90.909 286 25 1 557 842 469799113 469799397 4.430000e-102 383.0
53 TraesCS1A01G114500 chr6D 97.500 40 1 0 6981 7020 115106368 115106407 1.410000e-07 69.4
54 TraesCS1A01G114500 chr4D 90.877 285 26 0 558 842 3274310 3274594 4.430000e-102 383.0
55 TraesCS1A01G114500 chr7D 90.592 287 26 1 557 842 185747765 185747479 5.730000e-101 379.0
56 TraesCS1A01G114500 chr7D 93.878 49 2 1 4030 4078 429482627 429482580 1.090000e-08 73.1
57 TraesCS1A01G114500 chr7D 93.617 47 2 1 4030 4076 615482057 615482012 1.410000e-07 69.4
58 TraesCS1A01G114500 chr6A 90.559 286 27 0 557 842 52313959 52314244 5.730000e-101 379.0
59 TraesCS1A01G114500 chr5D 90.559 286 27 0 557 842 432156024 432156309 5.730000e-101 379.0
60 TraesCS1A01G114500 chr2D 90.559 286 27 0 557 842 353285947 353286232 5.730000e-101 379.0
61 TraesCS1A01G114500 chr2D 89.655 58 3 3 4030 4087 601181601 601181655 3.920000e-08 71.3
62 TraesCS1A01G114500 chr2B 97.561 41 1 0 6990 7030 472252546 472252506 3.920000e-08 71.3
63 TraesCS1A01G114500 chr2B 89.091 55 2 4 4030 4082 185378320 185378268 1.820000e-06 65.8
64 TraesCS1A01G114500 chr6B 92.000 50 3 1 4030 4079 457875501 457875549 1.410000e-07 69.4


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 TraesCS1A01G114500 chr1A 118760484 118768307 7823 False 6799.00 10375 100.00000 1 7824 2 chr1A.!!$F4 7823
1 TraesCS1A01G114500 chr1A 577181871 577182586 715 True 931.00 931 90.25100 7112 7824 1 chr1A.!!$R1 712
2 TraesCS1A01G114500 chr1A 118753642 118754199 557 False 907.00 907 96.05700 1 557 1 chr1A.!!$F1 556
3 TraesCS1A01G114500 chr1A 302849746 302850302 556 False 905.00 905 96.05000 1 556 1 chr1A.!!$F3 555
4 TraesCS1A01G114500 chr1A 593519971 593520527 556 True 905.00 905 96.05000 1 556 1 chr1A.!!$R2 555
5 TraesCS1A01G114500 chr1B 171030101 171036005 5904 False 2352.25 5435 96.12125 840 7035 4 chr1B.!!$F1 6195
6 TraesCS1A01G114500 chr1B 355090253 355090980 727 True 1194.00 1194 96.29600 7098 7824 1 chr1B.!!$R1 726
7 TraesCS1A01G114500 chr1D 111719288 111721567 2279 False 3871.00 3871 97.28700 4751 7035 1 chr1D.!!$F3 2284
8 TraesCS1A01G114500 chr1D 111700005 111700924 919 False 1476.00 1476 95.41100 2522 3457 1 chr1D.!!$F2 935
9 TraesCS1A01G114500 chr1D 111711793 111712937 1144 False 959.00 1127 96.78500 3531 4759 2 chr1D.!!$F8 1228
10 TraesCS1A01G114500 chr1D 111694285 111695569 1284 False 948.00 1386 94.84900 840 2526 2 chr1D.!!$F7 1686
11 TraesCS1A01G114500 chr5A 33900092 33900877 785 True 1277.00 1277 95.94900 7037 7824 1 chr5A.!!$R1 787
12 TraesCS1A01G114500 chr5A 536022782 536023338 556 False 905.00 905 96.05000 1 556 1 chr5A.!!$F1 555
13 TraesCS1A01G114500 chr5A 698475689 698476247 558 True 904.00 904 95.88600 1 557 1 chr5A.!!$R2 556
14 TraesCS1A01G114500 chr3B 25498097 25498883 786 False 1260.00 1260 95.57500 7037 7824 1 chr3B.!!$F1 787
15 TraesCS1A01G114500 chr3B 739131469 739134755 3286 True 530.50 791 81.06100 2883 6230 4 chr3B.!!$R1 3347
16 TraesCS1A01G114500 chr3A 8126797 8127575 778 True 1258.00 1258 95.78500 7044 7824 1 chr3A.!!$R1 780
17 TraesCS1A01G114500 chr3A 364939281 364939838 557 False 913.00 913 96.23700 1 557 1 chr3A.!!$F1 556
18 TraesCS1A01G114500 chr3A 369441528 369442085 557 True 902.00 902 95.87800 1 557 1 chr3A.!!$R2 556
19 TraesCS1A01G114500 chr3A 693165816 693167980 2164 True 432.00 577 83.45400 4085 6218 4 chr3A.!!$R3 2133
20 TraesCS1A01G114500 chr5B 440229199 440229927 728 False 1195.00 1195 96.29600 7098 7824 1 chr5B.!!$F1 726
21 TraesCS1A01G114500 chr5B 548054489 548055214 725 True 959.00 959 90.79700 7111 7824 1 chr5B.!!$R1 713
22 TraesCS1A01G114500 chr4A 612498742 612499459 717 True 996.00 996 91.79400 7111 7824 1 chr4A.!!$R1 713
23 TraesCS1A01G114500 chr4A 232104134 232104851 717 False 974.00 974 91.23800 7111 7824 1 chr4A.!!$F1 713
24 TraesCS1A01G114500 chr2A 393334874 393335431 557 True 913.00 913 96.23700 1 557 1 chr2A.!!$R2 556
25 TraesCS1A01G114500 chr7A 487365038 487365595 557 False 902.00 902 95.87800 1 557 1 chr7A.!!$F1 556
26 TraesCS1A01G114500 chr3D 556149561 556152945 3384 True 438.00 580 81.52520 2883 6230 5 chr3D.!!$R1 3347

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
692 695 0.032403 GTGTTGGCCGGGGTAAAAAC 59.968 55.000 2.18 0.00 0.00 2.43 F
814 817 0.033228 GATCCTCAGATCTGGCGGTG 59.967 60.000 22.42 7.12 44.78 4.94 F
838 841 0.171903 CGTTCCGGTGTCGTATCCTT 59.828 55.000 0.00 0.00 33.95 3.36 F
1413 1434 0.533755 ACTTGAGGCTGTCTGTGTGC 60.534 55.000 0.00 0.00 0.00 4.57 F
1555 1576 0.671781 CCGAGGACCAGCTCTTGTTG 60.672 60.000 0.00 0.00 0.00 3.33 F
3340 3410 0.447801 GGTGTTTCAGCATAGCCACG 59.552 55.000 0.00 0.00 0.00 4.94 F
4510 4711 1.939934 GAAGCTGCGCCAATGTATACA 59.060 47.619 8.27 8.27 0.00 2.29 F
4998 5278 2.349886 GGAAGCTCGTACTGAAGCATTG 59.650 50.000 12.46 0.00 0.00 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1536 1557 0.671781 CAACAAGAGCTGGTCCTCGG 60.672 60.000 2.76 0.0 36.95 4.63 R
2457 2484 1.065031 CATTGAAAACCGGAAGCGCG 61.065 55.000 9.46 0.0 0.00 6.86 R
2580 2609 1.227089 GCATCGCATCGTGAGGAGT 60.227 57.895 0.00 0.0 0.00 3.85 R
3316 3386 3.694072 TGGCTATGCTGAAACACCATTAC 59.306 43.478 0.00 0.0 0.00 1.89 R
3657 3729 5.050499 GCAGAACTCATCATCTTATCCAACG 60.050 44.000 0.00 0.0 0.00 4.10 R
4657 4862 0.315251 CGGCGATCCTTCTATCAGCA 59.685 55.000 0.00 0.0 31.45 4.41 R
5717 6165 2.095059 CACACTGAATAACTGCTTGCCC 60.095 50.000 0.00 0.0 0.00 5.36 R
7067 7529 2.027314 CGGCGCATGAGAGAGAGG 59.973 66.667 10.83 0.0 0.00 3.69 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
154 155 5.013287 TGCACCTTTATAGTCACCCAGTTAA 59.987 40.000 0.00 0.00 0.00 2.01
197 198 5.303589 CCCAAAGTATTCCTACAGTATCCGA 59.696 44.000 0.00 0.00 0.00 4.55
218 219 3.755378 GAGAGTTGCACAATCTCATGGTT 59.245 43.478 16.26 0.00 39.42 3.67
292 294 2.620251 TGCGCTATGCTTAGGATTGT 57.380 45.000 9.73 0.00 46.63 2.71
302 304 2.673368 GCTTAGGATTGTGTCTTGTCCG 59.327 50.000 0.00 0.00 35.89 4.79
353 355 5.067674 CCCGTTATCAATGACATCCAATGTT 59.932 40.000 0.00 0.00 45.03 2.71
385 387 6.542370 CAGGAAACCGTAACCATCTATTGATT 59.458 38.462 0.00 0.00 0.00 2.57
557 560 7.445121 TGTCTCTATGGCATATTTCTAACAGG 58.555 38.462 7.81 0.00 0.00 4.00
558 561 6.370166 GTCTCTATGGCATATTTCTAACAGGC 59.630 42.308 7.81 0.00 0.00 4.85
559 562 5.237815 TCTATGGCATATTTCTAACAGGCG 58.762 41.667 7.81 0.00 0.00 5.52
560 563 2.571212 TGGCATATTTCTAACAGGCGG 58.429 47.619 0.00 0.00 0.00 6.13
561 564 2.092646 TGGCATATTTCTAACAGGCGGT 60.093 45.455 0.00 0.00 0.00 5.68
562 565 2.548480 GGCATATTTCTAACAGGCGGTC 59.452 50.000 0.00 0.00 0.00 4.79
563 566 2.548480 GCATATTTCTAACAGGCGGTCC 59.452 50.000 0.00 0.00 0.00 4.46
564 567 3.744530 GCATATTTCTAACAGGCGGTCCT 60.745 47.826 0.00 0.00 45.66 3.85
576 579 4.408821 GGTCCTGGTGGCGATGCA 62.409 66.667 0.00 0.00 0.00 3.96
577 580 3.127533 GTCCTGGTGGCGATGCAC 61.128 66.667 0.00 0.00 0.00 4.57
578 581 4.758251 TCCTGGTGGCGATGCACG 62.758 66.667 0.00 0.00 45.66 5.34
586 589 3.121030 GCGATGCACGGTGCTCTT 61.121 61.111 30.81 17.23 45.31 2.85
587 590 2.780643 CGATGCACGGTGCTCTTG 59.219 61.111 30.81 18.72 45.31 3.02
588 591 2.743752 CGATGCACGGTGCTCTTGG 61.744 63.158 30.81 14.76 45.31 3.61
589 592 2.360350 ATGCACGGTGCTCTTGGG 60.360 61.111 30.81 0.00 45.31 4.12
592 595 3.052082 CACGGTGCTCTTGGGCAG 61.052 66.667 0.00 0.00 43.25 4.85
593 596 3.241530 ACGGTGCTCTTGGGCAGA 61.242 61.111 0.00 0.00 43.25 4.26
605 608 2.743928 GGCAGAGCCCGTGTCTTG 60.744 66.667 0.00 0.00 44.06 3.02
606 609 2.743928 GCAGAGCCCGTGTCTTGG 60.744 66.667 0.00 0.00 0.00 3.61
614 617 3.782244 CGTGTCTTGGCGCTGCTC 61.782 66.667 7.64 0.00 0.00 4.26
615 618 3.782244 GTGTCTTGGCGCTGCTCG 61.782 66.667 7.64 0.00 42.12 5.03
624 627 3.190849 CGCTGCTCGGTGACCATG 61.191 66.667 1.11 0.00 33.78 3.66
625 628 2.821366 GCTGCTCGGTGACCATGG 60.821 66.667 11.19 11.19 0.00 3.66
626 629 2.821366 CTGCTCGGTGACCATGGC 60.821 66.667 13.04 5.35 0.00 4.40
627 630 4.408821 TGCTCGGTGACCATGGCC 62.409 66.667 13.04 0.00 0.00 5.36
629 632 4.082523 CTCGGTGACCATGGCCGT 62.083 66.667 23.41 0.00 45.11 5.68
630 633 4.386951 TCGGTGACCATGGCCGTG 62.387 66.667 23.41 18.73 45.11 4.94
631 634 4.697756 CGGTGACCATGGCCGTGT 62.698 66.667 23.39 11.63 40.53 4.49
632 635 2.282180 GGTGACCATGGCCGTGTT 60.282 61.111 23.39 9.91 0.00 3.32
633 636 2.625823 GGTGACCATGGCCGTGTTG 61.626 63.158 23.39 11.66 0.00 3.33
634 637 2.282110 TGACCATGGCCGTGTTGG 60.282 61.111 23.39 16.75 42.50 3.77
645 648 4.622456 GTGTTGGCGGCGTGGTTG 62.622 66.667 9.37 0.00 0.00 3.77
655 658 4.317444 CGTGGTTGCCGGGGTGTA 62.317 66.667 2.18 0.00 0.00 2.90
656 659 2.359478 GTGGTTGCCGGGGTGTAG 60.359 66.667 2.18 0.00 0.00 2.74
657 660 2.850130 TGGTTGCCGGGGTGTAGT 60.850 61.111 2.18 0.00 0.00 2.73
658 661 2.359478 GGTTGCCGGGGTGTAGTG 60.359 66.667 2.18 0.00 0.00 2.74
659 662 2.428622 GTTGCCGGGGTGTAGTGT 59.571 61.111 2.18 0.00 0.00 3.55
660 663 1.228033 GTTGCCGGGGTGTAGTGTT 60.228 57.895 2.18 0.00 0.00 3.32
661 664 1.071814 TTGCCGGGGTGTAGTGTTC 59.928 57.895 2.18 0.00 0.00 3.18
662 665 1.697082 TTGCCGGGGTGTAGTGTTCA 61.697 55.000 2.18 0.00 0.00 3.18
663 666 1.071814 GCCGGGGTGTAGTGTTCAA 59.928 57.895 2.18 0.00 0.00 2.69
664 667 0.322187 GCCGGGGTGTAGTGTTCAAT 60.322 55.000 2.18 0.00 0.00 2.57
665 668 1.448985 CCGGGGTGTAGTGTTCAATG 58.551 55.000 0.00 0.00 0.00 2.82
666 669 1.448985 CGGGGTGTAGTGTTCAATGG 58.551 55.000 0.00 0.00 0.00 3.16
667 670 1.173913 GGGGTGTAGTGTTCAATGGC 58.826 55.000 0.00 0.00 0.00 4.40
668 671 0.802494 GGGTGTAGTGTTCAATGGCG 59.198 55.000 0.00 0.00 0.00 5.69
669 672 0.802494 GGTGTAGTGTTCAATGGCGG 59.198 55.000 0.00 0.00 0.00 6.13
670 673 1.519408 GTGTAGTGTTCAATGGCGGT 58.481 50.000 0.00 0.00 0.00 5.68
671 674 1.196808 GTGTAGTGTTCAATGGCGGTG 59.803 52.381 0.00 0.00 0.00 4.94
672 675 1.070914 TGTAGTGTTCAATGGCGGTGA 59.929 47.619 0.00 0.00 0.00 4.02
673 676 1.732259 GTAGTGTTCAATGGCGGTGAG 59.268 52.381 0.00 0.00 0.00 3.51
674 677 0.108585 AGTGTTCAATGGCGGTGAGT 59.891 50.000 0.00 0.00 0.00 3.41
675 678 0.238289 GTGTTCAATGGCGGTGAGTG 59.762 55.000 0.00 0.00 0.00 3.51
676 679 0.179032 TGTTCAATGGCGGTGAGTGT 60.179 50.000 0.00 0.00 0.00 3.55
677 680 0.951558 GTTCAATGGCGGTGAGTGTT 59.048 50.000 0.00 0.00 0.00 3.32
678 681 0.950836 TTCAATGGCGGTGAGTGTTG 59.049 50.000 0.00 0.00 0.00 3.33
679 682 0.888736 TCAATGGCGGTGAGTGTTGG 60.889 55.000 0.00 0.00 0.00 3.77
680 683 2.268076 AATGGCGGTGAGTGTTGGC 61.268 57.895 0.00 0.00 0.00 4.52
681 684 4.947147 TGGCGGTGAGTGTTGGCC 62.947 66.667 0.00 0.00 44.00 5.36
686 689 4.265056 GTGAGTGTTGGCCGGGGT 62.265 66.667 2.18 0.00 0.00 4.95
687 690 2.527123 TGAGTGTTGGCCGGGGTA 60.527 61.111 2.18 0.00 0.00 3.69
688 691 2.148052 TGAGTGTTGGCCGGGGTAA 61.148 57.895 2.18 0.00 0.00 2.85
689 692 1.073548 GAGTGTTGGCCGGGGTAAA 59.926 57.895 2.18 0.00 0.00 2.01
690 693 0.537828 GAGTGTTGGCCGGGGTAAAA 60.538 55.000 2.18 0.00 0.00 1.52
691 694 0.106116 AGTGTTGGCCGGGGTAAAAA 60.106 50.000 2.18 0.00 0.00 1.94
692 695 0.032403 GTGTTGGCCGGGGTAAAAAC 59.968 55.000 2.18 0.00 0.00 2.43
693 696 1.114119 TGTTGGCCGGGGTAAAAACC 61.114 55.000 2.18 0.00 0.00 3.27
694 697 0.828762 GTTGGCCGGGGTAAAAACCT 60.829 55.000 2.18 0.00 0.00 3.50
695 698 0.828343 TTGGCCGGGGTAAAAACCTG 60.828 55.000 2.18 0.00 0.00 4.00
696 699 2.642254 GGCCGGGGTAAAAACCTGC 61.642 63.158 2.18 0.00 32.85 4.85
697 700 1.605451 GCCGGGGTAAAAACCTGCT 60.605 57.895 2.18 0.00 32.85 4.24
698 701 1.592400 GCCGGGGTAAAAACCTGCTC 61.592 60.000 2.18 0.00 32.85 4.26
699 702 0.037734 CCGGGGTAAAAACCTGCTCT 59.962 55.000 0.00 0.00 32.85 4.09
700 703 1.279846 CCGGGGTAAAAACCTGCTCTA 59.720 52.381 0.00 0.00 32.85 2.43
701 704 2.092592 CCGGGGTAAAAACCTGCTCTAT 60.093 50.000 0.00 0.00 32.85 1.98
702 705 3.203716 CGGGGTAAAAACCTGCTCTATC 58.796 50.000 0.00 0.00 0.00 2.08
703 706 3.118371 CGGGGTAAAAACCTGCTCTATCT 60.118 47.826 0.00 0.00 0.00 1.98
704 707 4.625564 CGGGGTAAAAACCTGCTCTATCTT 60.626 45.833 0.00 0.00 0.00 2.40
705 708 4.882427 GGGGTAAAAACCTGCTCTATCTTC 59.118 45.833 0.00 0.00 0.00 2.87
706 709 4.571176 GGGTAAAAACCTGCTCTATCTTCG 59.429 45.833 0.00 0.00 0.00 3.79
707 710 5.416947 GGTAAAAACCTGCTCTATCTTCGA 58.583 41.667 0.00 0.00 0.00 3.71
708 711 5.873164 GGTAAAAACCTGCTCTATCTTCGAA 59.127 40.000 0.00 0.00 0.00 3.71
709 712 5.864628 AAAAACCTGCTCTATCTTCGAAC 57.135 39.130 0.00 0.00 0.00 3.95
710 713 2.853731 ACCTGCTCTATCTTCGAACG 57.146 50.000 0.00 0.00 0.00 3.95
711 714 1.405821 ACCTGCTCTATCTTCGAACGG 59.594 52.381 0.00 0.00 0.00 4.44
712 715 1.676529 CCTGCTCTATCTTCGAACGGA 59.323 52.381 0.00 0.00 0.00 4.69
713 716 2.541999 CCTGCTCTATCTTCGAACGGAC 60.542 54.545 0.00 0.00 0.00 4.79
714 717 1.404391 TGCTCTATCTTCGAACGGACC 59.596 52.381 0.00 0.00 0.00 4.46
715 718 1.597445 GCTCTATCTTCGAACGGACCG 60.597 57.143 13.61 13.61 0.00 4.79
716 719 1.002684 CTCTATCTTCGAACGGACCGG 60.003 57.143 20.00 0.00 0.00 5.28
717 720 0.594284 CTATCTTCGAACGGACCGGC 60.594 60.000 20.00 8.92 0.00 6.13
718 721 1.314534 TATCTTCGAACGGACCGGCA 61.315 55.000 20.00 0.00 0.00 5.69
719 722 2.162338 ATCTTCGAACGGACCGGCAA 62.162 55.000 20.00 3.98 0.00 4.52
720 723 2.662527 TTCGAACGGACCGGCAAC 60.663 61.111 20.00 5.39 0.00 4.17
742 745 2.316119 CGAAGCTCGTTCCCTTTTTG 57.684 50.000 0.00 0.00 34.72 2.44
743 746 1.871039 CGAAGCTCGTTCCCTTTTTGA 59.129 47.619 0.00 0.00 34.72 2.69
744 747 2.289547 CGAAGCTCGTTCCCTTTTTGAA 59.710 45.455 0.00 0.00 34.72 2.69
745 748 3.607078 CGAAGCTCGTTCCCTTTTTGAAG 60.607 47.826 0.00 0.00 34.72 3.02
746 749 2.230660 AGCTCGTTCCCTTTTTGAAGG 58.769 47.619 0.00 0.00 39.68 3.46
747 750 1.335964 GCTCGTTCCCTTTTTGAAGGC 60.336 52.381 0.00 0.00 38.63 4.35
748 751 0.948678 TCGTTCCCTTTTTGAAGGCG 59.051 50.000 0.00 0.00 38.63 5.52
749 752 0.666374 CGTTCCCTTTTTGAAGGCGT 59.334 50.000 0.00 0.00 38.63 5.68
750 753 1.334689 CGTTCCCTTTTTGAAGGCGTC 60.335 52.381 0.00 0.00 38.63 5.19
751 754 0.948678 TTCCCTTTTTGAAGGCGTCG 59.051 50.000 0.00 0.00 38.63 5.12
752 755 0.179040 TCCCTTTTTGAAGGCGTCGT 60.179 50.000 0.00 0.00 38.63 4.34
753 756 0.237498 CCCTTTTTGAAGGCGTCGTC 59.763 55.000 0.00 0.00 38.63 4.20
754 757 0.110823 CCTTTTTGAAGGCGTCGTCG 60.111 55.000 0.00 0.00 40.37 5.12
773 776 4.899239 GGCTCTCACCGCCCATCG 62.899 72.222 0.00 0.00 41.73 3.84
774 777 4.148825 GCTCTCACCGCCCATCGT 62.149 66.667 0.00 0.00 36.19 3.73
775 778 2.202797 CTCTCACCGCCCATCGTG 60.203 66.667 0.00 0.00 36.19 4.35
776 779 4.451150 TCTCACCGCCCATCGTGC 62.451 66.667 0.00 0.00 36.19 5.34
784 787 4.812476 CCCATCGTGCGGCTTCGA 62.812 66.667 18.69 18.69 40.28 3.71
785 788 2.813474 CCATCGTGCGGCTTCGAA 60.813 61.111 19.78 0.00 39.45 3.71
786 789 2.697425 CATCGTGCGGCTTCGAAG 59.303 61.111 21.02 21.02 39.45 3.79
787 790 1.805539 CATCGTGCGGCTTCGAAGA 60.806 57.895 28.95 6.41 39.45 2.87
788 791 1.080093 ATCGTGCGGCTTCGAAGAA 60.080 52.632 28.95 7.71 45.90 2.52
789 792 0.669318 ATCGTGCGGCTTCGAAGAAA 60.669 50.000 28.95 7.35 45.90 2.52
790 793 0.876777 TCGTGCGGCTTCGAAGAAAA 60.877 50.000 28.95 7.70 45.90 2.29
791 794 0.721483 CGTGCGGCTTCGAAGAAAAC 60.721 55.000 28.95 17.48 45.90 2.43
792 795 0.586802 GTGCGGCTTCGAAGAAAACT 59.413 50.000 28.95 0.00 45.90 2.66
793 796 0.865769 TGCGGCTTCGAAGAAAACTC 59.134 50.000 28.95 9.40 45.90 3.01
794 797 1.149148 GCGGCTTCGAAGAAAACTCT 58.851 50.000 28.95 0.00 45.90 3.24
795 798 1.136224 GCGGCTTCGAAGAAAACTCTG 60.136 52.381 28.95 14.87 45.90 3.35
796 799 2.404215 CGGCTTCGAAGAAAACTCTGA 58.596 47.619 28.95 0.00 45.90 3.27
797 800 2.996621 CGGCTTCGAAGAAAACTCTGAT 59.003 45.455 28.95 0.00 45.90 2.90
798 801 3.061429 CGGCTTCGAAGAAAACTCTGATC 59.939 47.826 28.95 5.94 45.90 2.92
799 802 3.372514 GGCTTCGAAGAAAACTCTGATCC 59.627 47.826 28.95 11.38 45.90 3.36
800 803 4.249661 GCTTCGAAGAAAACTCTGATCCT 58.750 43.478 28.95 0.00 45.90 3.24
801 804 4.328712 GCTTCGAAGAAAACTCTGATCCTC 59.671 45.833 28.95 1.00 45.90 3.71
802 805 5.468540 TTCGAAGAAAACTCTGATCCTCA 57.531 39.130 0.00 0.00 45.90 3.86
803 806 5.065704 TCGAAGAAAACTCTGATCCTCAG 57.934 43.478 0.00 0.00 45.59 3.35
813 816 2.435418 GATCCTCAGATCTGGCGGT 58.565 57.895 22.42 9.04 44.78 5.68
814 817 0.033228 GATCCTCAGATCTGGCGGTG 59.967 60.000 22.42 7.12 44.78 4.94
815 818 1.406065 ATCCTCAGATCTGGCGGTGG 61.406 60.000 22.42 15.52 0.00 4.61
816 819 2.202987 CTCAGATCTGGCGGTGGC 60.203 66.667 22.42 0.00 38.90 5.01
817 820 3.002583 TCAGATCTGGCGGTGGCA 61.003 61.111 22.42 0.00 42.47 4.92
834 837 3.281240 AGCGTTCCGGTGTCGTAT 58.719 55.556 0.00 0.00 35.85 3.06
835 838 1.138247 AGCGTTCCGGTGTCGTATC 59.862 57.895 0.00 0.00 35.85 2.24
836 839 1.875364 GCGTTCCGGTGTCGTATCC 60.875 63.158 0.00 0.00 33.95 2.59
837 840 1.805254 CGTTCCGGTGTCGTATCCT 59.195 57.895 0.00 0.00 33.95 3.24
838 841 0.171903 CGTTCCGGTGTCGTATCCTT 59.828 55.000 0.00 0.00 33.95 3.36
843 846 2.158564 TCCGGTGTCGTATCCTTCCTAT 60.159 50.000 0.00 0.00 33.95 2.57
849 852 5.689068 GGTGTCGTATCCTTCCTATAAAACG 59.311 44.000 0.00 0.00 0.00 3.60
871 874 6.758149 ACGTAACTTTAAACATACGCAGATG 58.242 36.000 19.99 0.00 43.53 2.90
894 897 5.104900 TGTCTTCCCTGCCTATTTAAGTCTC 60.105 44.000 0.00 0.00 0.00 3.36
896 899 4.008916 TCCCTGCCTATTTAAGTCTCCT 57.991 45.455 0.00 0.00 0.00 3.69
1068 1071 1.736645 CACCAAGGAGCCGTACGTG 60.737 63.158 15.21 6.95 0.00 4.49
1209 1215 2.774439 TTTTTGTCTTCGCTTCTGCC 57.226 45.000 0.00 0.00 35.36 4.85
1218 1227 2.429739 GCTTCTGCCGCTGTTTGC 60.430 61.111 0.00 0.00 38.57 3.68
1413 1434 0.533755 ACTTGAGGCTGTCTGTGTGC 60.534 55.000 0.00 0.00 0.00 4.57
1536 1557 7.382488 CGTGGCATATATGGTATAGCTGTAATC 59.618 40.741 14.51 0.00 0.00 1.75
1555 1576 0.671781 CCGAGGACCAGCTCTTGTTG 60.672 60.000 0.00 0.00 0.00 3.33
1593 1614 8.459521 CAATATTTTGCAATAAAAGGTCGTCA 57.540 30.769 0.00 0.00 0.00 4.35
1599 1620 7.401484 TTGCAATAAAAGGTCGTCATTTTTC 57.599 32.000 10.03 0.46 38.30 2.29
1631 1652 3.699085 CGAAATGCTCGCGAGATTC 57.301 52.632 38.74 31.20 41.49 2.52
2333 2360 9.971922 AAAAGTCTTCCTTGTGAAATAAATGAG 57.028 29.630 0.00 0.00 32.32 2.90
2335 2362 6.151817 AGTCTTCCTTGTGAAATAAATGAGCC 59.848 38.462 0.00 0.00 31.06 4.70
2457 2484 3.487544 GCCATTTCGGTTACATCAAGCTC 60.488 47.826 0.00 0.00 36.97 4.09
2475 2502 1.209127 CGCGCTTCCGGTTTTCAAT 59.791 52.632 5.56 0.00 34.32 2.57
2495 2522 5.637810 TCAATGTCGGATTCTTCAACAGTAC 59.362 40.000 0.00 0.00 0.00 2.73
2580 2609 8.813951 TGTTTTAGTTTTTCCTTTCCTTAACCA 58.186 29.630 0.00 0.00 0.00 3.67
2652 2681 2.879026 GAGAAAGACCGCCAAGAGTTTT 59.121 45.455 0.00 0.00 0.00 2.43
2671 2700 6.788218 AGTTTTTGAAGAGGATGAGGAATCT 58.212 36.000 0.00 0.00 35.43 2.40
2698 2727 2.287915 CAGAAGTACTGCACAAAAGCGT 59.712 45.455 3.00 0.00 39.86 5.07
2790 2819 8.237267 GCAAGCTTACTTCTAATGCTTCTTTTA 58.763 33.333 0.00 0.00 41.31 1.52
2821 2850 8.579006 TCTTATGTTGCTCATCACTTGAAAAAT 58.421 29.630 0.00 0.00 37.91 1.82
2822 2851 9.844790 CTTATGTTGCTCATCACTTGAAAAATA 57.155 29.630 0.00 0.00 37.91 1.40
2823 2852 9.624697 TTATGTTGCTCATCACTTGAAAAATAC 57.375 29.630 0.00 0.00 37.91 1.89
2826 2855 8.506437 TGTTGCTCATCACTTGAAAAATACTAG 58.494 33.333 0.00 0.00 32.78 2.57
2852 2881 6.650120 ACATAGTAATAAACACCTGACCTGG 58.350 40.000 0.00 0.00 0.00 4.45
3105 3138 4.494484 TGAGGTAGATGTCGTTTGTCATG 58.506 43.478 0.00 0.00 0.00 3.07
3316 3386 8.792633 TGGTAATAAAATGAGGTTTGTTCTCTG 58.207 33.333 0.00 0.00 32.78 3.35
3340 3410 0.447801 GGTGTTTCAGCATAGCCACG 59.552 55.000 0.00 0.00 0.00 4.94
3582 3653 4.261197 GGCGACTTTTGTGTTCTCTGATTT 60.261 41.667 0.00 0.00 0.00 2.17
3657 3729 3.305608 CCAAGGCCAGAACTGATTGTTTC 60.306 47.826 5.01 0.00 39.30 2.78
3796 3869 9.168353 GTGCCAACAAAATTGAATATTTTGAAC 57.832 29.630 22.63 12.49 46.36 3.18
4022 4120 8.035394 TGATCATTTTCACTCTGGTAGTACTTC 58.965 37.037 0.00 0.00 35.76 3.01
4366 4566 2.902705 TGTCCATAGGTTACCGATGC 57.097 50.000 17.28 6.99 35.72 3.91
4368 4568 3.568443 TGTCCATAGGTTACCGATGCTA 58.432 45.455 17.28 6.37 35.72 3.49
4380 4580 7.012989 AGGTTACCGATGCTATTTATTTTCACC 59.987 37.037 0.00 0.00 0.00 4.02
4499 4700 3.384668 TCATAACATAGAGAAGCTGCGC 58.615 45.455 0.00 0.00 0.00 6.09
4510 4711 1.939934 GAAGCTGCGCCAATGTATACA 59.060 47.619 8.27 8.27 0.00 2.29
4657 4862 8.545472 TGGACTACATTTAGGCACTTAAAGTAT 58.455 33.333 0.00 0.00 41.75 2.12
4726 4931 4.035675 GTCGAAAGGCATTTAGAAGATGGG 59.964 45.833 8.22 0.00 32.73 4.00
4998 5278 2.349886 GGAAGCTCGTACTGAAGCATTG 59.650 50.000 12.46 0.00 0.00 2.82
5264 5544 6.072649 TCATATCTTGGTGATGCAATGGAAT 58.927 36.000 0.00 0.00 36.65 3.01
5435 5721 6.769822 AGTTAAGAGGAGATGCATGGTAAATG 59.230 38.462 2.46 0.00 0.00 2.32
5575 6023 9.809096 TTCTATGCATAACAAAAGACAACAAAA 57.191 25.926 8.00 0.00 0.00 2.44
5717 6165 1.667724 CAGCCTATTGAGCTTTGGACG 59.332 52.381 0.00 0.00 38.95 4.79
5726 6174 2.956987 CTTTGGACGGGCAAGCAG 59.043 61.111 0.00 0.00 0.00 4.24
5973 6427 9.150348 GCTTTGCTAAAAATGCCTTTAATAAGA 57.850 29.630 0.00 0.00 32.92 2.10
6175 6634 9.651913 ATTGTTTATTTGATGTTGGAATGGTAC 57.348 29.630 0.00 0.00 0.00 3.34
6188 6647 8.106462 TGTTGGAATGGTACTATTTCATCTTGA 58.894 33.333 13.22 0.00 0.00 3.02
6283 6742 4.816925 GTGCTCCACTTCTGTAGAAAGTTT 59.183 41.667 0.00 0.00 33.07 2.66
6646 7106 8.702438 CATCCATGTTTGTAAAAATCACTGTTC 58.298 33.333 0.00 0.00 0.00 3.18
6727 7187 7.765819 AGTTTTATTGGATTTTTATCTGCAGGC 59.234 33.333 15.13 0.00 0.00 4.85
6793 7253 0.107800 ATTCTCATGCTGCAGCGAGT 60.108 50.000 30.52 20.07 45.83 4.18
6917 7377 1.168407 GCTCCTGTGTGCTTGCTCAA 61.168 55.000 0.00 0.00 0.00 3.02
6944 7404 5.163216 GGAGAATGAGAATGGAAGGACATCT 60.163 44.000 0.00 0.00 0.00 2.90
6978 7438 6.317857 CCTTTTAGCATGTAAGCTTGTCTTC 58.682 40.000 9.86 0.00 43.70 2.87
7035 7497 0.106167 ATCCAAGGATGCATGCAGCT 60.106 50.000 32.57 15.01 45.94 4.24
7047 7509 2.800629 GCATGCAGCTTGTCAAACAACT 60.801 45.455 14.21 0.00 41.15 3.16
7066 7528 3.399330 ACTTATCAACCTGTCACGTTGG 58.601 45.455 12.82 2.46 40.80 3.77
7067 7529 1.803334 TATCAACCTGTCACGTTGGC 58.197 50.000 12.82 0.00 40.80 4.52
7068 7530 0.889186 ATCAACCTGTCACGTTGGCC 60.889 55.000 12.82 0.00 40.80 5.36
7548 8025 3.256960 GCCCAACCCTCTCCACCA 61.257 66.667 0.00 0.00 0.00 4.17
7606 8083 1.059584 TCCTCAGCACCCTCACCAAA 61.060 55.000 0.00 0.00 0.00 3.28
7668 8145 4.103103 CTGGACGACGCTCGCAGA 62.103 66.667 0.00 0.00 45.12 4.26
7768 8245 3.056328 GCCACCTTCTTCGCCCAC 61.056 66.667 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 5.337554 CACTCGGTAAGACATCATCGTAAA 58.662 41.667 0.00 0.00 0.00 2.01
154 155 1.202359 GGTGTGCCAAACGTCACAATT 60.202 47.619 9.13 0.00 43.78 2.32
197 198 3.430042 ACCATGAGATTGTGCAACTCT 57.570 42.857 0.00 0.00 38.04 3.24
292 294 3.006859 AGAATGATGTGACGGACAAGACA 59.993 43.478 0.00 0.00 38.36 3.41
353 355 2.289819 GGTTACGGTTTCCTGACCATGA 60.290 50.000 0.00 0.00 39.78 3.07
385 387 3.626670 GCCTCTAGTTGACTAGCTCGTTA 59.373 47.826 12.30 0.00 44.24 3.18
534 537 6.467677 GCCTGTTAGAAATATGCCATAGAGA 58.532 40.000 0.00 0.00 0.00 3.10
540 543 2.092646 ACCGCCTGTTAGAAATATGCCA 60.093 45.455 0.00 0.00 0.00 4.92
559 562 4.408821 TGCATCGCCACCAGGACC 62.409 66.667 0.00 0.00 36.89 4.46
560 563 3.127533 GTGCATCGCCACCAGGAC 61.128 66.667 0.00 0.00 36.89 3.85
561 564 4.758251 CGTGCATCGCCACCAGGA 62.758 66.667 0.00 0.00 36.89 3.86
575 578 3.052082 CTGCCCAAGAGCACCGTG 61.052 66.667 0.00 0.00 38.00 4.94
576 579 3.241530 TCTGCCCAAGAGCACCGT 61.242 61.111 0.00 0.00 38.00 4.83
577 580 2.435586 CTCTGCCCAAGAGCACCG 60.436 66.667 0.00 0.00 45.93 4.94
589 592 2.743928 CCAAGACACGGGCTCTGC 60.744 66.667 0.00 0.00 0.00 4.26
590 593 2.743928 GCCAAGACACGGGCTCTG 60.744 66.667 0.00 0.00 46.74 3.35
597 600 3.782244 GAGCAGCGCCAAGACACG 61.782 66.667 2.29 0.00 0.00 4.49
598 601 3.782244 CGAGCAGCGCCAAGACAC 61.782 66.667 2.29 0.00 0.00 3.67
607 610 3.190849 CATGGTCACCGAGCAGCG 61.191 66.667 2.11 0.00 43.30 5.18
608 611 2.821366 CCATGGTCACCGAGCAGC 60.821 66.667 2.57 0.00 43.30 5.25
609 612 2.821366 GCCATGGTCACCGAGCAG 60.821 66.667 14.67 0.00 43.30 4.24
610 613 4.408821 GGCCATGGTCACCGAGCA 62.409 66.667 12.68 0.00 44.17 4.26
615 618 2.282180 AACACGGCCATGGTCACC 60.282 61.111 18.31 7.00 0.00 4.02
616 619 2.625823 CCAACACGGCCATGGTCAC 61.626 63.158 18.31 5.15 0.00 3.67
617 620 2.282110 CCAACACGGCCATGGTCA 60.282 61.111 18.31 0.00 0.00 4.02
628 631 4.622456 CAACCACGCCGCCAACAC 62.622 66.667 0.00 0.00 0.00 3.32
638 641 4.317444 TACACCCCGGCAACCACG 62.317 66.667 0.00 0.00 0.00 4.94
639 642 2.359478 CTACACCCCGGCAACCAC 60.359 66.667 0.00 0.00 0.00 4.16
640 643 2.850130 ACTACACCCCGGCAACCA 60.850 61.111 0.00 0.00 0.00 3.67
641 644 2.359478 CACTACACCCCGGCAACC 60.359 66.667 0.00 0.00 0.00 3.77
642 645 1.228033 AACACTACACCCCGGCAAC 60.228 57.895 0.00 0.00 0.00 4.17
643 646 1.071814 GAACACTACACCCCGGCAA 59.928 57.895 0.00 0.00 0.00 4.52
644 647 1.697082 TTGAACACTACACCCCGGCA 61.697 55.000 0.00 0.00 0.00 5.69
645 648 0.322187 ATTGAACACTACACCCCGGC 60.322 55.000 0.00 0.00 0.00 6.13
646 649 1.448985 CATTGAACACTACACCCCGG 58.551 55.000 0.00 0.00 0.00 5.73
647 650 1.448985 CCATTGAACACTACACCCCG 58.551 55.000 0.00 0.00 0.00 5.73
648 651 1.173913 GCCATTGAACACTACACCCC 58.826 55.000 0.00 0.00 0.00 4.95
649 652 0.802494 CGCCATTGAACACTACACCC 59.198 55.000 0.00 0.00 0.00 4.61
650 653 0.802494 CCGCCATTGAACACTACACC 59.198 55.000 0.00 0.00 0.00 4.16
651 654 1.196808 CACCGCCATTGAACACTACAC 59.803 52.381 0.00 0.00 0.00 2.90
652 655 1.070914 TCACCGCCATTGAACACTACA 59.929 47.619 0.00 0.00 0.00 2.74
653 656 1.732259 CTCACCGCCATTGAACACTAC 59.268 52.381 0.00 0.00 0.00 2.73
654 657 1.346395 ACTCACCGCCATTGAACACTA 59.654 47.619 0.00 0.00 0.00 2.74
655 658 0.108585 ACTCACCGCCATTGAACACT 59.891 50.000 0.00 0.00 0.00 3.55
656 659 0.238289 CACTCACCGCCATTGAACAC 59.762 55.000 0.00 0.00 0.00 3.32
657 660 0.179032 ACACTCACCGCCATTGAACA 60.179 50.000 0.00 0.00 0.00 3.18
658 661 0.951558 AACACTCACCGCCATTGAAC 59.048 50.000 0.00 0.00 0.00 3.18
659 662 0.950836 CAACACTCACCGCCATTGAA 59.049 50.000 0.00 0.00 0.00 2.69
660 663 0.888736 CCAACACTCACCGCCATTGA 60.889 55.000 0.00 0.00 0.00 2.57
661 664 1.580942 CCAACACTCACCGCCATTG 59.419 57.895 0.00 0.00 0.00 2.82
662 665 2.268076 GCCAACACTCACCGCCATT 61.268 57.895 0.00 0.00 0.00 3.16
663 666 2.672996 GCCAACACTCACCGCCAT 60.673 61.111 0.00 0.00 0.00 4.40
664 667 4.947147 GGCCAACACTCACCGCCA 62.947 66.667 0.00 0.00 39.50 5.69
669 672 2.400269 TTACCCCGGCCAACACTCAC 62.400 60.000 2.24 0.00 0.00 3.51
670 673 1.706995 TTTACCCCGGCCAACACTCA 61.707 55.000 2.24 0.00 0.00 3.41
671 674 0.537828 TTTTACCCCGGCCAACACTC 60.538 55.000 2.24 0.00 0.00 3.51
672 675 0.106116 TTTTTACCCCGGCCAACACT 60.106 50.000 2.24 0.00 0.00 3.55
673 676 0.032403 GTTTTTACCCCGGCCAACAC 59.968 55.000 2.24 0.00 0.00 3.32
674 677 1.114119 GGTTTTTACCCCGGCCAACA 61.114 55.000 2.24 0.00 0.00 3.33
675 678 0.828762 AGGTTTTTACCCCGGCCAAC 60.829 55.000 2.24 0.00 0.00 3.77
676 679 0.828343 CAGGTTTTTACCCCGGCCAA 60.828 55.000 2.24 0.00 0.00 4.52
677 680 1.228613 CAGGTTTTTACCCCGGCCA 60.229 57.895 2.24 0.00 0.00 5.36
678 681 2.642254 GCAGGTTTTTACCCCGGCC 61.642 63.158 0.00 0.00 36.13 6.13
679 682 1.592400 GAGCAGGTTTTTACCCCGGC 61.592 60.000 0.00 0.00 41.53 6.13
680 683 0.037734 AGAGCAGGTTTTTACCCCGG 59.962 55.000 0.00 0.00 0.00 5.73
681 684 2.773993 TAGAGCAGGTTTTTACCCCG 57.226 50.000 0.00 0.00 0.00 5.73
682 685 4.505324 AGATAGAGCAGGTTTTTACCCC 57.495 45.455 0.00 0.00 0.00 4.95
683 686 4.571176 CGAAGATAGAGCAGGTTTTTACCC 59.429 45.833 0.00 0.00 0.00 3.69
684 687 5.416947 TCGAAGATAGAGCAGGTTTTTACC 58.583 41.667 0.00 0.00 0.00 2.85
685 688 6.453922 CGTTCGAAGATAGAGCAGGTTTTTAC 60.454 42.308 0.00 0.00 35.04 2.01
686 689 5.575606 CGTTCGAAGATAGAGCAGGTTTTTA 59.424 40.000 0.00 0.00 35.04 1.52
687 690 4.389077 CGTTCGAAGATAGAGCAGGTTTTT 59.611 41.667 0.00 0.00 35.04 1.94
688 691 3.927142 CGTTCGAAGATAGAGCAGGTTTT 59.073 43.478 0.00 0.00 35.04 2.43
689 692 3.512680 CGTTCGAAGATAGAGCAGGTTT 58.487 45.455 0.00 0.00 35.04 3.27
690 693 2.159226 CCGTTCGAAGATAGAGCAGGTT 60.159 50.000 0.00 0.00 35.04 3.50
691 694 1.405821 CCGTTCGAAGATAGAGCAGGT 59.594 52.381 0.00 0.00 35.04 4.00
692 695 1.676529 TCCGTTCGAAGATAGAGCAGG 59.323 52.381 0.00 0.00 35.04 4.85
693 696 2.541999 GGTCCGTTCGAAGATAGAGCAG 60.542 54.545 0.00 0.00 35.04 4.24
694 697 1.404391 GGTCCGTTCGAAGATAGAGCA 59.596 52.381 0.00 0.00 35.04 4.26
695 698 1.597445 CGGTCCGTTCGAAGATAGAGC 60.597 57.143 2.08 2.05 35.04 4.09
696 699 1.002684 CCGGTCCGTTCGAAGATAGAG 60.003 57.143 11.06 0.00 35.04 2.43
697 700 1.019673 CCGGTCCGTTCGAAGATAGA 58.980 55.000 11.06 0.00 35.04 1.98
698 701 0.594284 GCCGGTCCGTTCGAAGATAG 60.594 60.000 11.06 0.00 35.04 2.08
699 702 1.314534 TGCCGGTCCGTTCGAAGATA 61.315 55.000 11.06 0.00 35.04 1.98
700 703 2.162338 TTGCCGGTCCGTTCGAAGAT 62.162 55.000 11.06 0.00 35.04 2.40
701 704 2.858862 TTGCCGGTCCGTTCGAAGA 61.859 57.895 11.06 0.00 0.00 2.87
702 705 2.356553 TTGCCGGTCCGTTCGAAG 60.357 61.111 11.06 0.00 0.00 3.79
703 706 2.662527 GTTGCCGGTCCGTTCGAA 60.663 61.111 11.06 0.00 0.00 3.71
716 719 3.631049 GAACGAGCTTCGCCGTTGC 62.631 63.158 14.74 4.46 45.12 4.17
717 720 2.470286 GAACGAGCTTCGCCGTTG 59.530 61.111 14.74 0.00 45.12 4.10
718 721 2.737376 GGAACGAGCTTCGCCGTT 60.737 61.111 10.32 10.32 45.12 4.44
719 722 4.736896 GGGAACGAGCTTCGCCGT 62.737 66.667 5.63 0.00 45.12 5.68
720 723 3.934391 AAGGGAACGAGCTTCGCCG 62.934 63.158 5.63 0.00 45.12 6.46
721 724 1.235281 AAAAGGGAACGAGCTTCGCC 61.235 55.000 5.63 1.00 45.12 5.54
722 725 0.591659 AAAAAGGGAACGAGCTTCGC 59.408 50.000 5.63 0.00 45.12 4.70
723 726 1.871039 TCAAAAAGGGAACGAGCTTCG 59.129 47.619 0.00 0.00 46.93 3.79
724 727 3.890128 CTTCAAAAAGGGAACGAGCTTC 58.110 45.455 0.00 0.00 0.00 3.86
725 728 3.990318 CTTCAAAAAGGGAACGAGCTT 57.010 42.857 0.00 0.00 0.00 3.74
736 739 3.345087 CGACGACGCCTTCAAAAAG 57.655 52.632 0.00 0.00 0.00 2.27
757 760 4.148825 ACGATGGGCGGTGAGAGC 62.149 66.667 0.00 0.00 46.49 4.09
758 761 2.202797 CACGATGGGCGGTGAGAG 60.203 66.667 0.00 0.00 46.49 3.20
759 762 4.451150 GCACGATGGGCGGTGAGA 62.451 66.667 0.00 0.00 46.49 3.27
767 770 4.812476 TCGAAGCCGCACGATGGG 62.812 66.667 8.25 0.00 33.62 4.00
768 771 2.802667 CTTCGAAGCCGCACGATGG 61.803 63.158 13.09 6.39 38.30 3.51
769 772 1.351430 TTCTTCGAAGCCGCACGATG 61.351 55.000 20.56 13.56 38.30 3.84
770 773 0.669318 TTTCTTCGAAGCCGCACGAT 60.669 50.000 20.56 0.00 38.30 3.73
771 774 0.876777 TTTTCTTCGAAGCCGCACGA 60.877 50.000 20.56 8.25 36.75 4.35
772 775 0.721483 GTTTTCTTCGAAGCCGCACG 60.721 55.000 20.56 0.00 35.37 5.34
773 776 0.586802 AGTTTTCTTCGAAGCCGCAC 59.413 50.000 20.56 13.12 35.37 5.34
774 777 0.865769 GAGTTTTCTTCGAAGCCGCA 59.134 50.000 20.56 0.00 35.37 5.69
775 778 1.136224 CAGAGTTTTCTTCGAAGCCGC 60.136 52.381 20.56 9.97 35.37 6.53
776 779 2.404215 TCAGAGTTTTCTTCGAAGCCG 58.596 47.619 20.56 0.00 37.07 5.52
777 780 3.372514 GGATCAGAGTTTTCTTCGAAGCC 59.627 47.826 20.56 7.24 0.00 4.35
778 781 4.249661 AGGATCAGAGTTTTCTTCGAAGC 58.750 43.478 20.56 6.35 0.00 3.86
779 782 5.473931 TGAGGATCAGAGTTTTCTTCGAAG 58.526 41.667 19.35 19.35 42.56 3.79
780 783 5.468540 TGAGGATCAGAGTTTTCTTCGAA 57.531 39.130 0.00 0.00 42.56 3.71
795 798 0.033228 CACCGCCAGATCTGAGGATC 59.967 60.000 30.96 13.49 46.33 3.36
796 799 1.406065 CCACCGCCAGATCTGAGGAT 61.406 60.000 30.96 18.48 34.13 3.24
797 800 2.060383 CCACCGCCAGATCTGAGGA 61.060 63.158 30.96 0.00 34.13 3.71
798 801 2.503061 CCACCGCCAGATCTGAGG 59.497 66.667 24.62 25.36 35.40 3.86
799 802 2.202987 GCCACCGCCAGATCTGAG 60.203 66.667 24.62 16.37 0.00 3.35
800 803 3.002583 TGCCACCGCCAGATCTGA 61.003 61.111 24.62 0.00 0.00 3.27
801 804 2.513204 CTGCCACCGCCAGATCTG 60.513 66.667 16.24 16.24 0.00 2.90
802 805 4.479993 GCTGCCACCGCCAGATCT 62.480 66.667 0.00 0.00 0.00 2.75
820 823 1.470458 GGAAGGATACGACACCGGAAC 60.470 57.143 9.46 0.00 46.39 3.62
821 824 0.819582 GGAAGGATACGACACCGGAA 59.180 55.000 9.46 0.00 46.39 4.30
822 825 0.033796 AGGAAGGATACGACACCGGA 60.034 55.000 9.46 0.00 46.39 5.14
823 826 1.683943 TAGGAAGGATACGACACCGG 58.316 55.000 0.00 0.00 46.39 5.28
824 827 5.443185 TTTATAGGAAGGATACGACACCG 57.557 43.478 0.00 0.00 46.39 4.94
825 828 5.689068 CGTTTTATAGGAAGGATACGACACC 59.311 44.000 0.00 0.00 46.39 4.16
826 829 6.268566 ACGTTTTATAGGAAGGATACGACAC 58.731 40.000 0.00 0.00 46.39 3.67
827 830 6.455360 ACGTTTTATAGGAAGGATACGACA 57.545 37.500 0.00 0.00 46.39 4.35
828 831 8.131731 AGTTACGTTTTATAGGAAGGATACGAC 58.868 37.037 0.00 0.00 46.39 4.34
829 832 8.225603 AGTTACGTTTTATAGGAAGGATACGA 57.774 34.615 0.00 0.00 46.39 3.43
830 833 8.862550 AAGTTACGTTTTATAGGAAGGATACG 57.137 34.615 0.00 0.00 46.39 3.06
843 846 8.759641 TCTGCGTATGTTTAAAGTTACGTTTTA 58.240 29.630 21.55 0.00 39.56 1.52
849 852 7.960793 AGACATCTGCGTATGTTTAAAGTTAC 58.039 34.615 5.33 0.00 40.17 2.50
864 867 3.805267 GCAGGGAAGACATCTGCG 58.195 61.111 0.00 0.00 43.28 5.18
871 874 5.360649 AGACTTAAATAGGCAGGGAAGAC 57.639 43.478 0.00 0.00 32.58 3.01
1068 1071 1.805945 GTGAGTGCCGTCGTCATCC 60.806 63.158 0.00 0.00 0.00 3.51
1128 1134 2.249557 AAGCGAGCAATCAAGCAGCG 62.250 55.000 0.00 0.00 42.48 5.18
1195 1201 2.433318 AGCGGCAGAAGCGAAGAC 60.433 61.111 1.45 0.00 43.41 3.01
1196 1202 2.433145 CAGCGGCAGAAGCGAAGA 60.433 61.111 1.45 0.00 43.41 2.87
1218 1227 2.215907 AGAGACGCAAATCATCCGAG 57.784 50.000 0.00 0.00 0.00 4.63
1413 1434 4.610951 GCAACATAAATACACACACACACG 59.389 41.667 0.00 0.00 0.00 4.49
1498 1519 6.095860 CCATATATGCCACGGATTGATCAATT 59.904 38.462 21.57 3.84 0.00 2.32
1536 1557 0.671781 CAACAAGAGCTGGTCCTCGG 60.672 60.000 2.76 0.00 36.95 4.63
1555 1576 5.701029 CAAAATATTGCGTGAAATGTCCC 57.299 39.130 0.00 0.00 0.00 4.46
2331 2358 4.012374 TCACAGAAATCTTCCATTGGCTC 58.988 43.478 0.00 0.00 0.00 4.70
2333 2360 4.996788 ATCACAGAAATCTTCCATTGGC 57.003 40.909 0.00 0.00 0.00 4.52
2335 2362 9.212641 ACGATATATCACAGAAATCTTCCATTG 57.787 33.333 13.11 0.00 0.00 2.82
2457 2484 1.065031 CATTGAAAACCGGAAGCGCG 61.065 55.000 9.46 0.00 0.00 6.86
2475 2502 3.613193 CGGTACTGTTGAAGAATCCGACA 60.613 47.826 0.00 0.00 38.30 4.35
2495 2522 1.333308 TGCACTTCAACACATTGACGG 59.667 47.619 0.00 0.00 44.66 4.79
2580 2609 1.227089 GCATCGCATCGTGAGGAGT 60.227 57.895 0.00 0.00 0.00 3.85
2652 2681 5.275630 TCTCAGATTCCTCATCCTCTTCAA 58.724 41.667 0.00 0.00 31.20 2.69
2790 2819 7.609146 TCAAGTGATGAGCAACATAAGAAAGAT 59.391 33.333 0.00 0.00 39.56 2.40
2823 2852 9.962783 GGTCAGGTGTTTATTACTATGTACTAG 57.037 37.037 0.00 0.00 0.00 2.57
2826 2855 7.709613 CCAGGTCAGGTGTTTATTACTATGTAC 59.290 40.741 0.00 0.00 0.00 2.90
2852 2881 6.561737 AGAAGGTTAAGTTCTAAAAGCTGC 57.438 37.500 0.00 0.00 32.29 5.25
3105 3138 6.364435 CCGAAAGTAACAAGTACTCCTGTAAC 59.636 42.308 0.00 0.00 42.55 2.50
3316 3386 3.694072 TGGCTATGCTGAAACACCATTAC 59.306 43.478 0.00 0.00 0.00 1.89
3657 3729 5.050499 GCAGAACTCATCATCTTATCCAACG 60.050 44.000 0.00 0.00 0.00 4.10
3755 3827 8.810652 TTTGTTGGCACAGTTTATCTATTTTC 57.189 30.769 0.00 0.00 42.39 2.29
4022 4120 6.092259 CCTTTAGTCCCAAACAAGTCGAATAG 59.908 42.308 0.00 0.00 0.00 1.73
4027 4125 2.225727 GCCTTTAGTCCCAAACAAGTCG 59.774 50.000 0.00 0.00 0.00 4.18
4185 4286 0.622665 AAAGAGAGGGGGCATCACTG 59.377 55.000 0.00 0.00 0.00 3.66
4380 4580 9.826574 ATAATGACATGAAAAATCAATTGGAGG 57.173 29.630 5.42 0.00 0.00 4.30
4510 4711 6.296374 CCCTGGATGTTTATTTGGTCCATTTT 60.296 38.462 0.00 0.00 38.23 1.82
4657 4862 0.315251 CGGCGATCCTTCTATCAGCA 59.685 55.000 0.00 0.00 31.45 4.41
4998 5278 1.421646 AGTGCTACCCCCATAAGCATC 59.578 52.381 0.00 0.00 46.99 3.91
5101 5381 9.109393 GTACATAGATTATTCTGAACCTGCAAA 57.891 33.333 0.00 0.00 33.17 3.68
5264 5544 4.202461 GGCTGGTGTTGGGAGATCAATATA 60.202 45.833 0.00 0.00 0.00 0.86
5382 5667 5.450412 CCAGTAGAAGCACAAACAACACAAT 60.450 40.000 0.00 0.00 0.00 2.71
5466 5914 3.681034 CGAGCAAGGATGTCTCATTTCCT 60.681 47.826 0.00 0.00 41.68 3.36
5543 5991 8.637986 TGTCTTTTGTTATGCATAGAAAAAGGT 58.362 29.630 31.05 5.56 36.03 3.50
5627 6075 4.098914 AGAAGGCTAACATGGACAAACA 57.901 40.909 0.00 0.00 0.00 2.83
5717 6165 2.095059 CACACTGAATAACTGCTTGCCC 60.095 50.000 0.00 0.00 0.00 5.36
5726 6174 6.385033 AGGACGTACTAACACACTGAATAAC 58.615 40.000 0.00 0.00 0.00 1.89
6646 7106 5.844301 AAATTCAAAAATTAGCACAGGCG 57.156 34.783 0.00 0.00 38.47 5.52
6727 7187 2.051334 TGCCCTCGTTATTCCCATTG 57.949 50.000 0.00 0.00 0.00 2.82
6793 7253 5.446143 ACTTTGCCAAACGATTCATACAA 57.554 34.783 0.00 0.00 0.00 2.41
6917 7377 5.044624 TGTCCTTCCATTCTCATTCTCCAAT 60.045 40.000 0.00 0.00 0.00 3.16
6944 7404 8.466798 GCTTACATGCTAAAAGGGAATAAAGAA 58.533 33.333 0.00 0.00 0.00 2.52
6951 7411 5.076873 ACAAGCTTACATGCTAAAAGGGAA 58.923 37.500 0.00 0.00 43.24 3.97
7035 7497 6.375736 TGACAGGTTGATAAGTTGTTTGACAA 59.624 34.615 0.00 0.00 35.42 3.18
7047 7509 2.147958 GCCAACGTGACAGGTTGATAA 58.852 47.619 32.24 0.00 44.19 1.75
7066 7528 2.280052 GGCGCATGAGAGAGAGGC 60.280 66.667 10.83 0.00 0.00 4.70
7067 7529 2.027314 CGGCGCATGAGAGAGAGG 59.973 66.667 10.83 0.00 0.00 3.69
7068 7530 2.657944 GCGGCGCATGAGAGAGAG 60.658 66.667 29.21 0.00 0.00 3.20
7096 7558 2.447429 CCTATCTCCTGGTGGACTCCTA 59.553 54.545 0.00 0.00 37.46 2.94
7548 8025 2.283809 CCTCCCGGACCCAGAGAT 59.716 66.667 0.73 0.00 0.00 2.75
7668 8145 4.160439 TCAAAGACTGCGAGGAGAACATAT 59.840 41.667 0.00 0.00 0.00 1.78


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

AutoCloner maintained by Alex Coulton.