Multiple sequence alignment - TraesCS3A01G243500

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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 TraesCS3A01G243500 chr3A 100.000 4244 0 0 1 4244 456805664 456809907 0.000000e+00 7838
1 TraesCS3A01G243500 chr3A 96.029 554 20 2 1487 2038 733263348 733262795 0.000000e+00 900
2 TraesCS3A01G243500 chr3A 82.456 171 23 5 3312 3482 175363565 175363402 4.420000e-30 143
3 TraesCS3A01G243500 chr3D 96.426 1231 32 3 2077 3307 338581624 338582842 0.000000e+00 2019
4 TraesCS3A01G243500 chr3D 90.537 856 22 16 654 1488 338580788 338581605 0.000000e+00 1077
5 TraesCS3A01G243500 chr3D 88.099 563 55 10 3688 4241 381772757 381773316 0.000000e+00 658
6 TraesCS3A01G243500 chr3D 88.288 555 58 5 3692 4240 455345924 455346477 0.000000e+00 658
7 TraesCS3A01G243500 chr3D 80.124 161 23 7 3304 3463 299693224 299693072 1.250000e-20 111
8 TraesCS3A01G243500 chr3B 92.599 1243 68 7 2077 3307 436837723 436838953 0.000000e+00 1764
9 TraesCS3A01G243500 chr3B 95.356 323 13 2 3 324 683517448 683517769 2.930000e-141 512
10 TraesCS3A01G243500 chr3B 88.115 244 18 4 700 940 436821491 436821726 3.230000e-71 279
11 TraesCS3A01G243500 chr3B 92.228 193 15 0 1242 1434 436837475 436837667 1.500000e-69 274
12 TraesCS3A01G243500 chr3B 84.354 294 20 7 981 1250 436791028 436791319 9.050000e-67 265
13 TraesCS3A01G243500 chr3B 84.354 294 20 7 981 1250 436821723 436822014 9.050000e-67 265
14 TraesCS3A01G243500 chr6A 97.554 654 16 0 1 654 486383343 486383996 0.000000e+00 1120
15 TraesCS3A01G243500 chr6A 92.638 652 46 2 1 652 29170564 29169915 0.000000e+00 937
16 TraesCS3A01G243500 chr5D 95.719 654 26 2 1 653 440926505 440925853 0.000000e+00 1051
17 TraesCS3A01G243500 chr5D 86.877 602 64 10 3653 4241 329804790 329805389 0.000000e+00 660
18 TraesCS3A01G243500 chr4A 94.385 659 26 8 1 650 632313825 632314481 0.000000e+00 1002
19 TraesCS3A01G243500 chr4A 91.091 651 56 2 3 652 552270966 552271615 0.000000e+00 880
20 TraesCS3A01G243500 chr4A 90.519 559 49 3 1484 2039 615045121 615045678 0.000000e+00 736
21 TraesCS3A01G243500 chr4A 90.433 554 50 3 1488 2039 615083241 615083793 0.000000e+00 726
22 TraesCS3A01G243500 chr4A 86.726 113 13 1 3544 3656 697990035 697990145 1.600000e-24 124
23 TraesCS3A01G243500 chr6B 99.456 551 2 1 1488 2037 654186773 654186223 0.000000e+00 1000
24 TraesCS3A01G243500 chr6B 87.805 656 76 4 1 653 133347879 133348533 0.000000e+00 765
25 TraesCS3A01G243500 chr6B 73.615 1137 224 57 2083 3171 615092147 615091039 6.700000e-98 368
26 TraesCS3A01G243500 chr6B 85.833 120 12 4 3536 3654 508161585 508161470 5.760000e-24 122
27 TraesCS3A01G243500 chr7B 93.109 653 43 2 1 652 493222918 493223569 0.000000e+00 955
28 TraesCS3A01G243500 chr7B 89.408 557 52 5 3691 4240 226051466 226050910 0.000000e+00 695
29 TraesCS3A01G243500 chr5B 92.824 655 45 2 1 654 94083069 94083722 0.000000e+00 948
30 TraesCS3A01G243500 chr5B 88.406 552 55 9 1491 2037 470441007 470441554 0.000000e+00 656
31 TraesCS3A01G243500 chr5B 87.500 112 12 1 3543 3654 67031507 67031398 1.240000e-25 128
32 TraesCS3A01G243500 chr1B 93.146 642 42 2 1 641 477490200 477490840 0.000000e+00 941
33 TraesCS3A01G243500 chr1B 88.770 561 50 8 3692 4241 401436331 401436889 0.000000e+00 675
34 TraesCS3A01G243500 chr1B 86.154 130 15 2 3536 3664 58755124 58754997 2.060000e-28 137
35 TraesCS3A01G243500 chr1B 86.555 119 13 3 3536 3654 550923158 550923043 1.240000e-25 128
36 TraesCS3A01G243500 chr7D 89.606 558 50 5 3692 4244 171648137 171648691 0.000000e+00 702
37 TraesCS3A01G243500 chr7D 86.891 595 63 11 3661 4241 285031334 285031927 0.000000e+00 652
38 TraesCS3A01G243500 chr7D 85.831 614 64 16 3650 4244 494398089 494398698 7.740000e-177 630
39 TraesCS3A01G243500 chr7D 87.207 555 57 9 1491 2040 92281421 92280876 1.680000e-173 619
40 TraesCS3A01G243500 chr7D 82.321 560 80 18 1491 2038 52517619 52517067 6.430000e-128 468
41 TraesCS3A01G243500 chr7D 86.555 119 14 1 3536 3654 126503818 126503702 3.440000e-26 130
42 TraesCS3A01G243500 chr2D 88.455 563 58 6 3688 4244 198728541 198727980 0.000000e+00 673
43 TraesCS3A01G243500 chr2D 88.235 119 12 1 3536 3654 430224997 430224881 1.590000e-29 141
44 TraesCS3A01G243500 chr4B 87.978 549 59 7 1493 2037 345646814 345646269 3.580000e-180 641
45 TraesCS3A01G243500 chr4B 85.587 562 56 12 1491 2040 661261792 661262340 2.210000e-157 566
46 TraesCS3A01G243500 chr6D 73.707 1141 249 35 2104 3214 409481109 409479990 8.550000e-107 398
47 TraesCS3A01G243500 chr2B 73.983 1057 211 43 2136 3147 549248834 549247797 1.860000e-98 370
48 TraesCS3A01G243500 chrUn 84.354 294 20 7 981 1250 461319947 461319656 9.050000e-67 265
49 TraesCS3A01G243500 chr4D 86.555 119 14 2 3536 3654 35348756 35348640 3.440000e-26 130
50 TraesCS3A01G243500 chr7A 94.048 84 5 0 3571 3654 735449151 735449068 1.240000e-25 128
51 TraesCS3A01G243500 chr1A 81.176 170 22 7 3312 3481 313267080 313266921 1.240000e-25 128
52 TraesCS3A01G243500 chr1A 79.268 164 32 2 3312 3475 448903371 448903210 3.470000e-21 113


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 TraesCS3A01G243500 chr3A 456805664 456809907 4243 False 7838 7838 100.0000 1 4244 1 chr3A.!!$F1 4243
1 TraesCS3A01G243500 chr3A 733262795 733263348 553 True 900 900 96.0290 1487 2038 1 chr3A.!!$R2 551
2 TraesCS3A01G243500 chr3D 338580788 338582842 2054 False 1548 2019 93.4815 654 3307 2 chr3D.!!$F3 2653
3 TraesCS3A01G243500 chr3D 381772757 381773316 559 False 658 658 88.0990 3688 4241 1 chr3D.!!$F1 553
4 TraesCS3A01G243500 chr3D 455345924 455346477 553 False 658 658 88.2880 3692 4240 1 chr3D.!!$F2 548
5 TraesCS3A01G243500 chr3B 436837475 436838953 1478 False 1019 1764 92.4135 1242 3307 2 chr3B.!!$F4 2065
6 TraesCS3A01G243500 chr3B 436821491 436822014 523 False 272 279 86.2345 700 1250 2 chr3B.!!$F3 550
7 TraesCS3A01G243500 chr6A 486383343 486383996 653 False 1120 1120 97.5540 1 654 1 chr6A.!!$F1 653
8 TraesCS3A01G243500 chr6A 29169915 29170564 649 True 937 937 92.6380 1 652 1 chr6A.!!$R1 651
9 TraesCS3A01G243500 chr5D 440925853 440926505 652 True 1051 1051 95.7190 1 653 1 chr5D.!!$R1 652
10 TraesCS3A01G243500 chr5D 329804790 329805389 599 False 660 660 86.8770 3653 4241 1 chr5D.!!$F1 588
11 TraesCS3A01G243500 chr4A 632313825 632314481 656 False 1002 1002 94.3850 1 650 1 chr4A.!!$F4 649
12 TraesCS3A01G243500 chr4A 552270966 552271615 649 False 880 880 91.0910 3 652 1 chr4A.!!$F1 649
13 TraesCS3A01G243500 chr4A 615045121 615045678 557 False 736 736 90.5190 1484 2039 1 chr4A.!!$F2 555
14 TraesCS3A01G243500 chr4A 615083241 615083793 552 False 726 726 90.4330 1488 2039 1 chr4A.!!$F3 551
15 TraesCS3A01G243500 chr6B 654186223 654186773 550 True 1000 1000 99.4560 1488 2037 1 chr6B.!!$R3 549
16 TraesCS3A01G243500 chr6B 133347879 133348533 654 False 765 765 87.8050 1 653 1 chr6B.!!$F1 652
17 TraesCS3A01G243500 chr6B 615091039 615092147 1108 True 368 368 73.6150 2083 3171 1 chr6B.!!$R2 1088
18 TraesCS3A01G243500 chr7B 493222918 493223569 651 False 955 955 93.1090 1 652 1 chr7B.!!$F1 651
19 TraesCS3A01G243500 chr7B 226050910 226051466 556 True 695 695 89.4080 3691 4240 1 chr7B.!!$R1 549
20 TraesCS3A01G243500 chr5B 94083069 94083722 653 False 948 948 92.8240 1 654 1 chr5B.!!$F1 653
21 TraesCS3A01G243500 chr5B 470441007 470441554 547 False 656 656 88.4060 1491 2037 1 chr5B.!!$F2 546
22 TraesCS3A01G243500 chr1B 477490200 477490840 640 False 941 941 93.1460 1 641 1 chr1B.!!$F2 640
23 TraesCS3A01G243500 chr1B 401436331 401436889 558 False 675 675 88.7700 3692 4241 1 chr1B.!!$F1 549
24 TraesCS3A01G243500 chr7D 171648137 171648691 554 False 702 702 89.6060 3692 4244 1 chr7D.!!$F1 552
25 TraesCS3A01G243500 chr7D 285031334 285031927 593 False 652 652 86.8910 3661 4241 1 chr7D.!!$F2 580
26 TraesCS3A01G243500 chr7D 494398089 494398698 609 False 630 630 85.8310 3650 4244 1 chr7D.!!$F3 594
27 TraesCS3A01G243500 chr7D 92280876 92281421 545 True 619 619 87.2070 1491 2040 1 chr7D.!!$R2 549
28 TraesCS3A01G243500 chr7D 52517067 52517619 552 True 468 468 82.3210 1491 2038 1 chr7D.!!$R1 547
29 TraesCS3A01G243500 chr2D 198727980 198728541 561 True 673 673 88.4550 3688 4244 1 chr2D.!!$R1 556
30 TraesCS3A01G243500 chr4B 345646269 345646814 545 True 641 641 87.9780 1493 2037 1 chr4B.!!$R1 544
31 TraesCS3A01G243500 chr4B 661261792 661262340 548 False 566 566 85.5870 1491 2040 1 chr4B.!!$F1 549
32 TraesCS3A01G243500 chr6D 409479990 409481109 1119 True 398 398 73.7070 2104 3214 1 chr6D.!!$R1 1110
33 TraesCS3A01G243500 chr2B 549247797 549248834 1037 True 370 370 73.9830 2136 3147 1 chr2B.!!$R1 1011

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
973 994 0.038343 TGTTCCCAAGGCGTACGTAC 60.038 55.000 17.90 15.9 0.00 3.67 F
1338 1383 1.065928 GAGGGTCGGCGACATACTG 59.934 63.158 37.13 0.0 33.68 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2049 2110 0.387929 CGGCGTCCAAGAGGCTATTA 59.612 55.0 0.00 0.0 42.20 0.98 R
3321 3454 0.031178 GCATATGCTCCCAAAAGCCG 59.969 55.0 20.64 0.0 41.77 5.52 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
49 50 3.828921 AGGAAAGTTCAAACCCAGTACC 58.171 45.455 0.00 0.00 0.00 3.34
50 51 3.203487 AGGAAAGTTCAAACCCAGTACCA 59.797 43.478 0.00 0.00 0.00 3.25
68 69 9.293404 CCAGTACCATTTATGAGAATGATCAAT 57.707 33.333 0.00 0.00 38.93 2.57
242 251 1.202639 TCTTCGACTGCCTTTCTTGCA 60.203 47.619 0.00 0.00 37.17 4.08
364 375 3.446161 CGAGTGGTTATGGAGGTTGACTA 59.554 47.826 0.00 0.00 0.00 2.59
432 443 1.202371 CGGTAGCGCCAGTTCTATTGA 60.202 52.381 2.29 0.00 36.97 2.57
571 583 1.023719 TGGATGGACTCCCCTCCTAA 58.976 55.000 12.76 0.00 44.72 2.69
759 771 1.651138 CTCAGATCGAAACACACTCGC 59.349 52.381 0.00 0.00 36.25 5.03
844 856 3.972950 CAGCTACGTATAGTCTGCTGT 57.027 47.619 18.87 0.00 46.17 4.40
845 857 3.622828 CAGCTACGTATAGTCTGCTGTG 58.377 50.000 18.87 1.94 46.17 3.66
846 858 2.033550 AGCTACGTATAGTCTGCTGTGC 59.966 50.000 4.17 0.00 39.89 4.57
847 859 2.033550 GCTACGTATAGTCTGCTGTGCT 59.966 50.000 0.00 0.00 32.28 4.40
848 860 2.568696 ACGTATAGTCTGCTGTGCTG 57.431 50.000 0.00 0.00 0.00 4.41
874 886 3.181487 GCCGTAAAGTAGTCAACCGGATA 60.181 47.826 9.46 0.00 36.12 2.59
924 945 4.988598 AGTTGACACCTGCGCCGG 62.989 66.667 17.13 17.13 0.00 6.13
941 962 2.483876 CCGGCATCGATCATTGTACTT 58.516 47.619 0.00 0.00 39.00 2.24
942 963 2.221749 CCGGCATCGATCATTGTACTTG 59.778 50.000 0.00 0.00 39.00 3.16
943 964 2.866156 CGGCATCGATCATTGTACTTGT 59.134 45.455 0.00 0.00 39.00 3.16
959 980 0.651551 TTGTACGTGCGTGTTGTTCC 59.348 50.000 7.55 0.00 0.00 3.62
960 981 1.152989 TGTACGTGCGTGTTGTTCCC 61.153 55.000 7.55 0.00 0.00 3.97
970 991 0.881159 TGTTGTTCCCAAGGCGTACG 60.881 55.000 11.84 11.84 0.00 3.67
971 992 0.881600 GTTGTTCCCAAGGCGTACGT 60.882 55.000 17.90 0.00 0.00 3.57
972 993 0.678395 TTGTTCCCAAGGCGTACGTA 59.322 50.000 17.90 0.00 0.00 3.57
973 994 0.038343 TGTTCCCAAGGCGTACGTAC 60.038 55.000 17.90 15.90 0.00 3.67
1068 1098 1.516603 GCCAACGCGTCTACTCTCC 60.517 63.158 14.44 0.00 0.00 3.71
1100 1130 1.139734 CACCCACATCCTCTCGACG 59.860 63.158 0.00 0.00 0.00 5.12
1209 1254 3.157217 GATCAGCGCCCTCCACGAT 62.157 63.158 2.29 0.00 0.00 3.73
1338 1383 1.065928 GAGGGTCGGCGACATACTG 59.934 63.158 37.13 0.00 33.68 2.74
1375 1420 3.403558 GGGTCCTCCTCCACAGCC 61.404 72.222 0.00 0.00 0.00 4.85
2049 2110 1.064825 AACCTTGGTCCAGATCCGTT 58.935 50.000 0.00 0.00 0.00 4.44
2055 2116 3.746045 TGGTCCAGATCCGTTAATAGC 57.254 47.619 0.00 0.00 0.00 2.97
2068 2129 0.387929 TAATAGCCTCTTGGACGCCG 59.612 55.000 0.00 0.00 34.57 6.46
2069 2130 1.327690 AATAGCCTCTTGGACGCCGA 61.328 55.000 0.00 0.00 34.57 5.54
2070 2131 2.017559 ATAGCCTCTTGGACGCCGAC 62.018 60.000 0.00 0.00 34.57 4.79
2072 2133 3.744719 CCTCTTGGACGCCGACGA 61.745 66.667 0.00 0.00 44.16 4.20
2073 2134 2.504244 CTCTTGGACGCCGACGAC 60.504 66.667 0.00 0.00 43.93 4.34
2074 2135 3.263503 CTCTTGGACGCCGACGACA 62.264 63.158 0.00 0.00 43.93 4.35
2075 2136 2.805353 CTTGGACGCCGACGACAG 60.805 66.667 0.00 0.00 43.93 3.51
2128 2189 1.646189 GCTCGAGTTCTTCATCACCC 58.354 55.000 15.13 0.00 0.00 4.61
2129 2190 1.066858 GCTCGAGTTCTTCATCACCCA 60.067 52.381 15.13 0.00 0.00 4.51
2130 2191 2.611518 CTCGAGTTCTTCATCACCCAC 58.388 52.381 3.62 0.00 0.00 4.61
2131 2192 1.967779 TCGAGTTCTTCATCACCCACA 59.032 47.619 0.00 0.00 0.00 4.17
2132 2193 2.367241 TCGAGTTCTTCATCACCCACAA 59.633 45.455 0.00 0.00 0.00 3.33
2133 2194 2.738846 CGAGTTCTTCATCACCCACAAG 59.261 50.000 0.00 0.00 0.00 3.16
2134 2195 3.077359 GAGTTCTTCATCACCCACAAGG 58.923 50.000 0.00 0.00 43.78 3.61
2323 2387 3.551496 TTGGAGGTTGCCTGCTCCG 62.551 63.158 8.11 0.00 42.66 4.63
2430 2497 4.771356 TCGTGCACGCGGCTACTC 62.771 66.667 33.63 0.00 45.15 2.59
2443 2510 1.153745 CTACTCGTGCTGCACCTCC 60.154 63.158 25.61 2.43 0.00 4.30
2481 2551 1.597027 GGACAAGGTCGTGGTGGTG 60.597 63.158 0.00 0.00 32.65 4.17
2482 2552 1.597027 GACAAGGTCGTGGTGGTGG 60.597 63.158 0.00 0.00 0.00 4.61
2483 2553 2.319890 GACAAGGTCGTGGTGGTGGT 62.320 60.000 0.00 0.00 0.00 4.16
2506 2576 3.136750 CCCCCAGCTCAGAGATCG 58.863 66.667 0.00 0.00 0.00 3.69
2690 2784 2.944049 GCGCCAATACTTTGCGCG 60.944 61.111 12.42 0.00 46.27 6.86
3144 3277 1.448540 CTGGGAGATGGTGACGCAC 60.449 63.158 1.92 1.92 0.00 5.34
3231 3364 3.134458 CTCCACAACTCCTGTTCAACTC 58.866 50.000 0.00 0.00 35.47 3.01
3292 3425 1.185315 GCCCCTTGCATACACAATGT 58.815 50.000 0.00 0.00 40.77 2.71
3295 3428 3.181487 GCCCCTTGCATACACAATGTTAG 60.181 47.826 0.00 0.00 40.77 2.34
3308 3441 5.640732 CACAATGTTAGCTGTGTAAATCCC 58.359 41.667 0.00 0.00 38.49 3.85
3309 3442 4.394920 ACAATGTTAGCTGTGTAAATCCCG 59.605 41.667 0.00 0.00 0.00 5.14
3310 3443 3.965379 TGTTAGCTGTGTAAATCCCGA 57.035 42.857 0.00 0.00 0.00 5.14
3311 3444 4.274602 TGTTAGCTGTGTAAATCCCGAA 57.725 40.909 0.00 0.00 0.00 4.30
3312 3445 4.643463 TGTTAGCTGTGTAAATCCCGAAA 58.357 39.130 0.00 0.00 0.00 3.46
3313 3446 5.064558 TGTTAGCTGTGTAAATCCCGAAAA 58.935 37.500 0.00 0.00 0.00 2.29
3314 3447 5.708230 TGTTAGCTGTGTAAATCCCGAAAAT 59.292 36.000 0.00 0.00 0.00 1.82
3315 3448 4.965119 AGCTGTGTAAATCCCGAAAATC 57.035 40.909 0.00 0.00 0.00 2.17
3316 3449 3.694566 AGCTGTGTAAATCCCGAAAATCC 59.305 43.478 0.00 0.00 0.00 3.01
3317 3450 3.442273 GCTGTGTAAATCCCGAAAATCCA 59.558 43.478 0.00 0.00 0.00 3.41
3318 3451 4.082463 GCTGTGTAAATCCCGAAAATCCAA 60.082 41.667 0.00 0.00 0.00 3.53
3319 3452 5.394115 GCTGTGTAAATCCCGAAAATCCAAT 60.394 40.000 0.00 0.00 0.00 3.16
3320 3453 6.597832 TGTGTAAATCCCGAAAATCCAATT 57.402 33.333 0.00 0.00 0.00 2.32
3321 3454 6.626302 TGTGTAAATCCCGAAAATCCAATTC 58.374 36.000 0.00 0.00 0.00 2.17
3322 3455 5.741982 GTGTAAATCCCGAAAATCCAATTCG 59.258 40.000 1.93 1.93 46.86 3.34
3329 3462 4.566659 CGAAAATCCAATTCGGCTTTTG 57.433 40.909 10.95 4.81 41.96 2.44
3330 3463 3.367630 CGAAAATCCAATTCGGCTTTTGG 59.632 43.478 10.95 7.75 41.96 3.28
3331 3464 3.333029 AAATCCAATTCGGCTTTTGGG 57.667 42.857 9.24 0.00 42.21 4.12
3332 3465 2.230130 ATCCAATTCGGCTTTTGGGA 57.770 45.000 9.24 0.00 42.21 4.37
3333 3466 1.544724 TCCAATTCGGCTTTTGGGAG 58.455 50.000 9.24 0.00 42.21 4.30
3334 3467 0.108662 CCAATTCGGCTTTTGGGAGC 60.109 55.000 2.95 0.00 38.98 4.70
3335 3468 0.602562 CAATTCGGCTTTTGGGAGCA 59.397 50.000 0.00 0.00 44.49 4.26
3336 3469 1.205417 CAATTCGGCTTTTGGGAGCAT 59.795 47.619 0.00 0.00 44.49 3.79
3337 3470 2.426738 CAATTCGGCTTTTGGGAGCATA 59.573 45.455 0.00 0.00 44.49 3.14
3338 3471 2.435372 TTCGGCTTTTGGGAGCATAT 57.565 45.000 0.00 0.00 44.49 1.78
3339 3472 1.679139 TCGGCTTTTGGGAGCATATG 58.321 50.000 0.00 0.00 44.49 1.78
3340 3473 0.031178 CGGCTTTTGGGAGCATATGC 59.969 55.000 20.36 20.36 44.49 3.14
3355 3488 4.077844 TGCTCCTGCGCATGAAAA 57.922 50.000 12.24 1.24 43.34 2.29
3356 3489 2.339403 TGCTCCTGCGCATGAAAAA 58.661 47.368 12.24 0.00 43.34 1.94
3357 3490 0.889994 TGCTCCTGCGCATGAAAAAT 59.110 45.000 12.24 0.00 43.34 1.82
3358 3491 1.274596 GCTCCTGCGCATGAAAAATG 58.725 50.000 12.24 2.20 0.00 2.32
3359 3492 1.403249 GCTCCTGCGCATGAAAAATGT 60.403 47.619 12.24 0.00 0.00 2.71
3360 3493 2.927871 GCTCCTGCGCATGAAAAATGTT 60.928 45.455 12.24 0.00 0.00 2.71
3361 3494 3.319755 CTCCTGCGCATGAAAAATGTTT 58.680 40.909 12.24 0.00 0.00 2.83
3362 3495 3.726607 TCCTGCGCATGAAAAATGTTTT 58.273 36.364 12.24 0.00 0.00 2.43
3363 3496 4.125703 TCCTGCGCATGAAAAATGTTTTT 58.874 34.783 12.24 3.30 42.60 1.94
3410 3543 9.768662 AAAAAGAAAAATAGATGTGCTCATTGT 57.231 25.926 2.26 0.00 34.06 2.71
3411 3544 8.976986 AAAGAAAAATAGATGTGCTCATTGTC 57.023 30.769 2.26 0.00 34.06 3.18
3412 3545 7.692460 AGAAAAATAGATGTGCTCATTGTCA 57.308 32.000 2.26 0.00 34.06 3.58
3413 3546 7.533426 AGAAAAATAGATGTGCTCATTGTCAC 58.467 34.615 2.26 5.34 34.06 3.67
3414 3547 6.822667 AAAATAGATGTGCTCATTGTCACA 57.177 33.333 13.69 13.69 45.81 3.58
3415 3548 5.808042 AATAGATGTGCTCATTGTCACAC 57.192 39.130 13.63 7.67 44.74 3.82
3416 3549 2.430465 AGATGTGCTCATTGTCACACC 58.570 47.619 13.63 7.16 44.74 4.16
3417 3550 2.153645 GATGTGCTCATTGTCACACCA 58.846 47.619 13.63 1.39 44.74 4.17
3418 3551 2.049888 TGTGCTCATTGTCACACCAA 57.950 45.000 9.33 0.00 38.18 3.67
3419 3552 2.373224 TGTGCTCATTGTCACACCAAA 58.627 42.857 9.33 0.00 38.18 3.28
3420 3553 2.757314 TGTGCTCATTGTCACACCAAAA 59.243 40.909 9.33 0.00 38.18 2.44
3421 3554 3.115554 GTGCTCATTGTCACACCAAAAC 58.884 45.455 6.84 0.00 33.63 2.43
3422 3555 2.223456 TGCTCATTGTCACACCAAAACG 60.223 45.455 0.00 0.00 0.00 3.60
3423 3556 2.384382 CTCATTGTCACACCAAAACGC 58.616 47.619 0.00 0.00 0.00 4.84
3424 3557 2.020720 TCATTGTCACACCAAAACGCT 58.979 42.857 0.00 0.00 0.00 5.07
3425 3558 3.206964 TCATTGTCACACCAAAACGCTA 58.793 40.909 0.00 0.00 0.00 4.26
3426 3559 3.628032 TCATTGTCACACCAAAACGCTAA 59.372 39.130 0.00 0.00 0.00 3.09
3427 3560 3.408288 TTGTCACACCAAAACGCTAAC 57.592 42.857 0.00 0.00 0.00 2.34
3428 3561 2.634600 TGTCACACCAAAACGCTAACT 58.365 42.857 0.00 0.00 0.00 2.24
3429 3562 2.353269 TGTCACACCAAAACGCTAACTG 59.647 45.455 0.00 0.00 0.00 3.16
3430 3563 1.332375 TCACACCAAAACGCTAACTGC 59.668 47.619 0.00 0.00 38.57 4.40
3431 3564 1.064803 CACACCAAAACGCTAACTGCA 59.935 47.619 0.00 0.00 43.06 4.41
3432 3565 1.746220 ACACCAAAACGCTAACTGCAA 59.254 42.857 0.00 0.00 43.06 4.08
3433 3566 2.164624 ACACCAAAACGCTAACTGCAAA 59.835 40.909 0.00 0.00 43.06 3.68
3434 3567 3.181480 ACACCAAAACGCTAACTGCAAAT 60.181 39.130 0.00 0.00 43.06 2.32
3435 3568 3.801594 CACCAAAACGCTAACTGCAAATT 59.198 39.130 0.00 0.00 43.06 1.82
3436 3569 4.048504 ACCAAAACGCTAACTGCAAATTC 58.951 39.130 0.00 0.00 43.06 2.17
3437 3570 4.202111 ACCAAAACGCTAACTGCAAATTCT 60.202 37.500 0.00 0.00 43.06 2.40
3438 3571 4.744631 CCAAAACGCTAACTGCAAATTCTT 59.255 37.500 0.00 0.00 43.06 2.52
3439 3572 5.918011 CCAAAACGCTAACTGCAAATTCTTA 59.082 36.000 0.00 0.00 43.06 2.10
3440 3573 6.088085 CCAAAACGCTAACTGCAAATTCTTAG 59.912 38.462 0.00 0.00 43.06 2.18
3441 3574 4.946784 ACGCTAACTGCAAATTCTTAGG 57.053 40.909 0.00 0.00 43.06 2.69
3442 3575 4.575885 ACGCTAACTGCAAATTCTTAGGA 58.424 39.130 0.00 0.00 43.06 2.94
3443 3576 4.631813 ACGCTAACTGCAAATTCTTAGGAG 59.368 41.667 0.00 0.00 43.06 3.69
3444 3577 4.034510 CGCTAACTGCAAATTCTTAGGAGG 59.965 45.833 0.00 0.00 43.06 4.30
3445 3578 5.186198 GCTAACTGCAAATTCTTAGGAGGA 58.814 41.667 0.00 0.00 42.31 3.71
3446 3579 5.648092 GCTAACTGCAAATTCTTAGGAGGAA 59.352 40.000 0.00 0.00 42.31 3.36
3447 3580 6.151144 GCTAACTGCAAATTCTTAGGAGGAAA 59.849 38.462 0.00 0.00 42.31 3.13
3448 3581 6.581171 AACTGCAAATTCTTAGGAGGAAAG 57.419 37.500 0.00 0.00 0.00 2.62
3449 3582 4.460731 ACTGCAAATTCTTAGGAGGAAAGC 59.539 41.667 0.00 0.00 0.00 3.51
3450 3583 4.666512 TGCAAATTCTTAGGAGGAAAGCT 58.333 39.130 0.00 0.00 0.00 3.74
3451 3584 5.079643 TGCAAATTCTTAGGAGGAAAGCTT 58.920 37.500 0.00 0.00 0.00 3.74
3452 3585 6.245408 TGCAAATTCTTAGGAGGAAAGCTTA 58.755 36.000 0.00 0.00 0.00 3.09
3453 3586 6.719370 TGCAAATTCTTAGGAGGAAAGCTTAA 59.281 34.615 0.00 0.00 0.00 1.85
3454 3587 7.094205 TGCAAATTCTTAGGAGGAAAGCTTAAG 60.094 37.037 0.00 0.00 0.00 1.85
3455 3588 7.094162 GCAAATTCTTAGGAGGAAAGCTTAAGT 60.094 37.037 0.00 0.00 0.00 2.24
3456 3589 9.449719 CAAATTCTTAGGAGGAAAGCTTAAGTA 57.550 33.333 0.00 0.00 0.00 2.24
3460 3593 9.668497 TTCTTAGGAGGAAAGCTTAAGTATTTC 57.332 33.333 19.13 19.13 33.20 2.17
3461 3594 7.980099 TCTTAGGAGGAAAGCTTAAGTATTTCG 59.020 37.037 19.93 10.64 34.47 3.46
3462 3595 6.295719 AGGAGGAAAGCTTAAGTATTTCGA 57.704 37.500 19.93 0.00 34.47 3.71
3463 3596 6.890293 AGGAGGAAAGCTTAAGTATTTCGAT 58.110 36.000 19.93 14.66 34.47 3.59
3464 3597 6.987404 AGGAGGAAAGCTTAAGTATTTCGATC 59.013 38.462 19.93 19.10 34.47 3.69
3465 3598 6.987404 GGAGGAAAGCTTAAGTATTTCGATCT 59.013 38.462 19.93 14.82 34.47 2.75
3466 3599 8.142551 GGAGGAAAGCTTAAGTATTTCGATCTA 58.857 37.037 19.93 0.00 34.47 1.98
3467 3600 9.530633 GAGGAAAGCTTAAGTATTTCGATCTAA 57.469 33.333 19.93 0.00 34.47 2.10
3468 3601 9.535878 AGGAAAGCTTAAGTATTTCGATCTAAG 57.464 33.333 19.93 0.00 34.47 2.18
3469 3602 8.277018 GGAAAGCTTAAGTATTTCGATCTAAGC 58.723 37.037 19.93 9.79 38.98 3.09
3470 3603 8.718102 AAAGCTTAAGTATTTCGATCTAAGCA 57.282 30.769 16.68 0.00 40.54 3.91
3471 3604 8.718102 AAGCTTAAGTATTTCGATCTAAGCAA 57.282 30.769 16.68 0.00 40.54 3.91
3472 3605 8.718102 AGCTTAAGTATTTCGATCTAAGCAAA 57.282 30.769 16.68 0.00 40.54 3.68
3473 3606 9.162764 AGCTTAAGTATTTCGATCTAAGCAAAA 57.837 29.630 16.68 0.00 40.54 2.44
3474 3607 9.769093 GCTTAAGTATTTCGATCTAAGCAAAAA 57.231 29.630 11.92 0.00 38.66 1.94
3535 3668 4.012554 CGAATCATCGTCACCCCG 57.987 61.111 0.00 0.00 44.06 5.73
3536 3669 1.141019 CGAATCATCGTCACCCCGT 59.859 57.895 0.00 0.00 44.06 5.28
3537 3670 0.459585 CGAATCATCGTCACCCCGTT 60.460 55.000 0.00 0.00 44.06 4.44
3538 3671 1.734163 GAATCATCGTCACCCCGTTT 58.266 50.000 0.00 0.00 0.00 3.60
3539 3672 1.664151 GAATCATCGTCACCCCGTTTC 59.336 52.381 0.00 0.00 0.00 2.78
3540 3673 0.611200 ATCATCGTCACCCCGTTTCA 59.389 50.000 0.00 0.00 0.00 2.69
3541 3674 0.393448 TCATCGTCACCCCGTTTCAA 59.607 50.000 0.00 0.00 0.00 2.69
3542 3675 1.002659 TCATCGTCACCCCGTTTCAAT 59.997 47.619 0.00 0.00 0.00 2.57
3543 3676 2.234168 TCATCGTCACCCCGTTTCAATA 59.766 45.455 0.00 0.00 0.00 1.90
3544 3677 2.835580 TCGTCACCCCGTTTCAATAA 57.164 45.000 0.00 0.00 0.00 1.40
3545 3678 2.415776 TCGTCACCCCGTTTCAATAAC 58.584 47.619 0.00 0.00 0.00 1.89
3546 3679 2.144730 CGTCACCCCGTTTCAATAACA 58.855 47.619 0.00 0.00 0.00 2.41
3547 3680 2.548904 CGTCACCCCGTTTCAATAACAA 59.451 45.455 0.00 0.00 0.00 2.83
3548 3681 3.364565 CGTCACCCCGTTTCAATAACAAG 60.365 47.826 0.00 0.00 0.00 3.16
3549 3682 3.816523 GTCACCCCGTTTCAATAACAAGA 59.183 43.478 0.00 0.00 0.00 3.02
3550 3683 4.276431 GTCACCCCGTTTCAATAACAAGAA 59.724 41.667 0.00 0.00 0.00 2.52
3551 3684 4.276431 TCACCCCGTTTCAATAACAAGAAC 59.724 41.667 0.00 0.00 0.00 3.01
3552 3685 4.036971 CACCCCGTTTCAATAACAAGAACA 59.963 41.667 0.00 0.00 0.00 3.18
3553 3686 4.830600 ACCCCGTTTCAATAACAAGAACAT 59.169 37.500 0.00 0.00 0.00 2.71
3554 3687 5.048294 ACCCCGTTTCAATAACAAGAACATC 60.048 40.000 0.00 0.00 0.00 3.06
3555 3688 5.183140 CCCCGTTTCAATAACAAGAACATCT 59.817 40.000 0.00 0.00 0.00 2.90
3556 3689 6.373216 CCCCGTTTCAATAACAAGAACATCTA 59.627 38.462 0.00 0.00 0.00 1.98
3557 3690 7.241376 CCCGTTTCAATAACAAGAACATCTAC 58.759 38.462 0.00 0.00 0.00 2.59
3558 3691 6.953743 CCGTTTCAATAACAAGAACATCTACG 59.046 38.462 0.00 0.00 0.00 3.51
3559 3692 7.148705 CCGTTTCAATAACAAGAACATCTACGA 60.149 37.037 0.00 0.00 29.39 3.43
3560 3693 8.218441 CGTTTCAATAACAAGAACATCTACGAA 58.782 33.333 0.00 0.00 29.39 3.85
3624 3757 7.391148 TTGAATTTACTGTTCATTAGGGAGC 57.609 36.000 0.00 0.00 35.68 4.70
3625 3758 6.480763 TGAATTTACTGTTCATTAGGGAGCA 58.519 36.000 0.00 0.00 31.07 4.26
3626 3759 7.118723 TGAATTTACTGTTCATTAGGGAGCAT 58.881 34.615 0.00 0.00 31.07 3.79
3627 3760 8.271458 TGAATTTACTGTTCATTAGGGAGCATA 58.729 33.333 0.00 0.00 31.07 3.14
3628 3761 9.289782 GAATTTACTGTTCATTAGGGAGCATAT 57.710 33.333 0.00 0.00 0.00 1.78
3629 3762 8.627208 ATTTACTGTTCATTAGGGAGCATATG 57.373 34.615 0.00 0.00 0.00 1.78
3630 3763 4.392940 ACTGTTCATTAGGGAGCATATGC 58.607 43.478 20.36 20.36 42.49 3.14
3649 3782 2.800881 CTCCCAAGAGCCAAAACAAC 57.199 50.000 0.00 0.00 32.13 3.32
3650 3783 1.341209 CTCCCAAGAGCCAAAACAACC 59.659 52.381 0.00 0.00 32.13 3.77
3651 3784 0.392706 CCCAAGAGCCAAAACAACCC 59.607 55.000 0.00 0.00 0.00 4.11
3656 3789 2.587522 AGAGCCAAAACAACCCTCTTC 58.412 47.619 0.00 0.00 29.04 2.87
3658 3791 2.554462 GAGCCAAAACAACCCTCTTCTC 59.446 50.000 0.00 0.00 0.00 2.87
3660 3793 2.554462 GCCAAAACAACCCTCTTCTCTC 59.446 50.000 0.00 0.00 0.00 3.20
3685 3818 2.323968 TTTTTGTTGGGCTCTTTGGC 57.676 45.000 0.00 0.00 40.96 4.52
3882 4035 5.994054 AGCCACAAATACTATGTCAGCTATG 59.006 40.000 0.00 0.00 36.30 2.23
3896 4050 4.334759 GTCAGCTATGTGATCATGCAAAGT 59.665 41.667 0.00 0.00 35.70 2.66
3967 4127 7.063934 TGCATGGCAATATATTTTGGAATGA 57.936 32.000 7.83 0.00 34.76 2.57
3997 4157 7.717875 TGAAAACACCATAATAGGTAGGTATGC 59.282 37.037 0.00 0.00 40.77 3.14
3998 4158 6.757173 AACACCATAATAGGTAGGTATGCA 57.243 37.500 0.00 0.00 40.77 3.96
3999 4159 6.952605 ACACCATAATAGGTAGGTATGCAT 57.047 37.500 3.79 3.79 40.77 3.96
4011 4171 5.997746 GGTAGGTATGCATGCTATTTTGAGA 59.002 40.000 20.33 0.00 0.00 3.27
4036 4196 7.380423 AAGATATAAGGAGGCTTATGTGTGT 57.620 36.000 0.00 0.00 32.44 3.72
4039 4199 8.934697 AGATATAAGGAGGCTTATGTGTGTTAA 58.065 33.333 0.00 0.00 32.44 2.01
4152 4312 2.755103 GGAAATTGCGGAAAGGTGAGAT 59.245 45.455 0.00 0.00 0.00 2.75
4160 4320 3.063997 GCGGAAAGGTGAGATTGTGTATG 59.936 47.826 0.00 0.00 0.00 2.39
4168 4328 5.367644 AGGTGAGATTGTGTATGATCCATGA 59.632 40.000 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 9.914131 AAGCATCATTGATCATTCTCATAAATG 57.086 29.630 0.00 0.00 37.87 2.32
68 69 1.002746 TAGCACCGCCAAAGCATCA 60.003 52.632 0.00 0.00 39.83 3.07
364 375 3.261897 CCACAGATCAACTACCTCCTTGT 59.738 47.826 0.00 0.00 0.00 3.16
492 504 2.036256 GTGGGCTGGAGCATTGGT 59.964 61.111 0.20 0.00 44.36 3.67
571 583 5.237344 GCCATAACGCTAGTCATGAGAAAAT 59.763 40.000 0.00 0.00 0.00 1.82
681 693 3.069443 CCTATTCTGCCTGGTTCTCTCTC 59.931 52.174 0.00 0.00 0.00 3.20
682 694 3.037549 CCTATTCTGCCTGGTTCTCTCT 58.962 50.000 0.00 0.00 0.00 3.10
683 695 2.769095 ACCTATTCTGCCTGGTTCTCTC 59.231 50.000 0.00 0.00 0.00 3.20
717 729 1.120530 ATTACAGGGGAGCCACGTAG 58.879 55.000 0.00 0.00 0.00 3.51
718 730 2.431782 GTTATTACAGGGGAGCCACGTA 59.568 50.000 0.00 0.00 0.00 3.57
759 771 0.718220 GCAACGAAAACTCTCGCACG 60.718 55.000 0.00 0.00 42.69 5.34
844 856 0.108992 CTACTTTACGGCCGTCAGCA 60.109 55.000 38.01 21.14 46.50 4.41
845 857 0.108945 ACTACTTTACGGCCGTCAGC 60.109 55.000 38.01 0.00 42.60 4.26
846 858 1.200716 TGACTACTTTACGGCCGTCAG 59.799 52.381 38.01 31.73 0.00 3.51
847 859 1.246649 TGACTACTTTACGGCCGTCA 58.753 50.000 38.01 23.63 0.00 4.35
848 860 1.988467 GTTGACTACTTTACGGCCGTC 59.012 52.381 38.01 18.63 0.00 4.79
874 886 1.138459 CGATGAGACGCAGCTCACT 59.862 57.895 7.58 0.00 46.72 3.41
924 945 4.503007 ACGTACAAGTACAATGATCGATGC 59.497 41.667 0.54 0.00 35.87 3.91
941 962 1.152989 GGGAACAACACGCACGTACA 61.153 55.000 0.00 0.00 0.00 2.90
942 963 1.152989 TGGGAACAACACGCACGTAC 61.153 55.000 0.00 0.00 37.44 3.67
943 964 1.143401 TGGGAACAACACGCACGTA 59.857 52.632 0.00 0.00 37.44 3.57
970 991 2.751806 ACTGGCTTGTACTCCTACGTAC 59.248 50.000 0.00 0.00 40.06 3.67
971 992 3.077484 ACTGGCTTGTACTCCTACGTA 57.923 47.619 0.00 0.00 0.00 3.57
972 993 1.920610 ACTGGCTTGTACTCCTACGT 58.079 50.000 0.00 0.00 0.00 3.57
973 994 2.607187 CAACTGGCTTGTACTCCTACG 58.393 52.381 0.00 0.00 0.00 3.51
974 995 2.347731 GCAACTGGCTTGTACTCCTAC 58.652 52.381 0.00 0.00 40.25 3.18
975 996 2.762535 GCAACTGGCTTGTACTCCTA 57.237 50.000 0.00 0.00 40.25 2.94
976 997 3.633361 GCAACTGGCTTGTACTCCT 57.367 52.632 0.00 0.00 40.25 3.69
1068 1098 1.898574 GGGTGCTGTTGGTCCTGTG 60.899 63.158 0.00 0.00 0.00 3.66
1205 1250 1.327303 GAGGAGGAGCAGATCATCGT 58.673 55.000 0.00 0.00 39.69 3.73
1209 1254 0.753479 GGACGAGGAGGAGCAGATCA 60.753 60.000 0.00 0.00 0.00 2.92
1403 1448 0.654160 TATGCCGTCGAGTCTGTACG 59.346 55.000 0.00 3.39 36.42 3.67
1785 1841 0.603975 GAGTTTGACTCCTGCGGCTT 60.604 55.000 0.00 0.00 39.28 4.35
2040 2101 4.039245 TCCAAGAGGCTATTAACGGATCTG 59.961 45.833 0.00 0.00 33.74 2.90
2041 2102 4.039366 GTCCAAGAGGCTATTAACGGATCT 59.961 45.833 3.16 0.00 33.74 2.75
2049 2110 0.387929 CGGCGTCCAAGAGGCTATTA 59.612 55.000 0.00 0.00 42.20 0.98
2055 2116 3.744719 TCGTCGGCGTCCAAGAGG 61.745 66.667 10.18 0.00 39.49 3.69
2078 2139 3.127533 CTTTCCGGCGAGCTTGGG 61.128 66.667 9.30 0.00 0.00 4.12
2079 2140 1.966451 AACTTTCCGGCGAGCTTGG 60.966 57.895 9.30 0.00 0.00 3.61
2091 2152 3.202097 GAGCCTCAGCCTATCAACTTTC 58.798 50.000 0.00 0.00 41.25 2.62
2128 2189 1.066257 GCTGTGTTGTGGCCTTGTG 59.934 57.895 3.32 0.00 0.00 3.33
2129 2190 2.127232 GGCTGTGTTGTGGCCTTGT 61.127 57.895 3.32 0.00 42.31 3.16
2130 2191 2.730094 GGCTGTGTTGTGGCCTTG 59.270 61.111 3.32 0.00 42.31 3.61
2133 2194 3.982241 GCAGGCTGTGTTGTGGCC 61.982 66.667 17.16 0.00 45.57 5.36
2134 2195 2.567497 ATGCAGGCTGTGTTGTGGC 61.567 57.895 17.16 0.00 0.00 5.01
2400 2467 1.078848 GCACGAGGTGAAGATGCCT 60.079 57.895 0.00 0.00 35.23 4.75
2430 2497 2.740055 GAGTGGAGGTGCAGCACG 60.740 66.667 19.42 0.00 34.83 5.34
2481 2551 4.512914 GAGCTGGGGGCATCCACC 62.513 72.222 0.00 0.00 44.79 4.61
2482 2552 3.711059 CTGAGCTGGGGGCATCCAC 62.711 68.421 0.00 0.00 44.79 4.02
2483 2553 3.414193 CTGAGCTGGGGGCATCCA 61.414 66.667 0.00 0.00 44.79 3.41
2506 2576 2.486042 GTGGACGACGAGCTCTCC 59.514 66.667 12.85 12.27 0.00 3.71
2690 2784 3.073274 ACAAATCCAGTTCTAGGTGCC 57.927 47.619 0.00 0.00 0.00 5.01
3144 3277 2.507484 TCTTCAGTCCATGTGCTTTGG 58.493 47.619 0.00 0.00 35.45 3.28
3231 3364 0.445436 GAGTGCATCAGCCGAAGTTG 59.555 55.000 0.00 0.00 41.13 3.16
3292 3425 5.355910 GGATTTTCGGGATTTACACAGCTAA 59.644 40.000 0.00 0.00 0.00 3.09
3295 3428 3.442273 TGGATTTTCGGGATTTACACAGC 59.558 43.478 0.00 0.00 0.00 4.40
3315 3448 0.108662 GCTCCCAAAAGCCGAATTGG 60.109 55.000 0.00 0.00 44.61 3.16
3316 3449 0.602562 TGCTCCCAAAAGCCGAATTG 59.397 50.000 0.00 0.00 41.77 2.32
3317 3450 1.560505 ATGCTCCCAAAAGCCGAATT 58.439 45.000 0.00 0.00 41.77 2.17
3318 3451 2.435372 TATGCTCCCAAAAGCCGAAT 57.565 45.000 0.00 0.00 41.77 3.34
3319 3452 2.023673 CATATGCTCCCAAAAGCCGAA 58.976 47.619 0.00 0.00 41.77 4.30
3320 3453 1.679139 CATATGCTCCCAAAAGCCGA 58.321 50.000 0.00 0.00 41.77 5.54
3321 3454 0.031178 GCATATGCTCCCAAAAGCCG 59.969 55.000 20.64 0.00 41.77 5.52
3322 3455 3.974222 GCATATGCTCCCAAAAGCC 57.026 52.632 20.64 0.00 41.77 4.35
3339 3472 1.274596 CATTTTTCATGCGCAGGAGC 58.725 50.000 24.84 0.00 37.71 4.70
3340 3473 2.642139 ACATTTTTCATGCGCAGGAG 57.358 45.000 24.84 15.23 0.00 3.69
3341 3474 3.383620 AAACATTTTTCATGCGCAGGA 57.616 38.095 22.47 22.47 0.00 3.86
3342 3475 4.471157 AAAAACATTTTTCATGCGCAGG 57.529 36.364 17.42 17.42 35.61 4.85
3384 3517 9.768662 ACAATGAGCACATCTATTTTTCTTTTT 57.231 25.926 0.00 0.00 35.50 1.94
3385 3518 9.415544 GACAATGAGCACATCTATTTTTCTTTT 57.584 29.630 0.00 0.00 35.50 2.27
3386 3519 8.579006 TGACAATGAGCACATCTATTTTTCTTT 58.421 29.630 0.00 0.00 35.50 2.52
3387 3520 8.025445 GTGACAATGAGCACATCTATTTTTCTT 58.975 33.333 0.00 0.00 35.50 2.52
3388 3521 7.175467 TGTGACAATGAGCACATCTATTTTTCT 59.825 33.333 8.94 0.00 39.86 2.52
3389 3522 7.272084 GTGTGACAATGAGCACATCTATTTTTC 59.728 37.037 14.22 0.00 45.59 2.29
3390 3523 7.086376 GTGTGACAATGAGCACATCTATTTTT 58.914 34.615 14.22 0.00 45.59 1.94
3391 3524 6.349611 GGTGTGACAATGAGCACATCTATTTT 60.350 38.462 14.22 0.00 45.59 1.82
3392 3525 5.124457 GGTGTGACAATGAGCACATCTATTT 59.876 40.000 14.22 0.00 45.59 1.40
3393 3526 4.637534 GGTGTGACAATGAGCACATCTATT 59.362 41.667 14.22 0.00 45.59 1.73
3394 3527 4.194640 GGTGTGACAATGAGCACATCTAT 58.805 43.478 14.22 0.00 45.59 1.98
3395 3528 3.007831 TGGTGTGACAATGAGCACATCTA 59.992 43.478 18.82 9.12 45.59 1.98
3396 3529 2.224597 TGGTGTGACAATGAGCACATCT 60.225 45.455 18.82 0.00 45.59 2.90
3397 3530 2.153645 TGGTGTGACAATGAGCACATC 58.846 47.619 14.22 14.11 45.59 3.06
3398 3531 2.275134 TGGTGTGACAATGAGCACAT 57.725 45.000 14.22 0.00 45.59 3.21
3399 3532 2.049888 TTGGTGTGACAATGAGCACA 57.950 45.000 8.94 8.94 42.25 4.57
3400 3533 3.115554 GTTTTGGTGTGACAATGAGCAC 58.884 45.455 0.00 4.58 35.63 4.40
3401 3534 2.223456 CGTTTTGGTGTGACAATGAGCA 60.223 45.455 0.00 0.00 0.00 4.26
3402 3535 2.384382 CGTTTTGGTGTGACAATGAGC 58.616 47.619 0.00 0.00 0.00 4.26
3403 3536 2.033299 AGCGTTTTGGTGTGACAATGAG 59.967 45.455 0.00 0.00 0.00 2.90
3404 3537 2.020720 AGCGTTTTGGTGTGACAATGA 58.979 42.857 0.00 0.00 0.00 2.57
3405 3538 2.490328 AGCGTTTTGGTGTGACAATG 57.510 45.000 0.00 0.00 0.00 2.82
3406 3539 3.630312 AGTTAGCGTTTTGGTGTGACAAT 59.370 39.130 0.00 0.00 0.00 2.71
3407 3540 3.011119 AGTTAGCGTTTTGGTGTGACAA 58.989 40.909 0.00 0.00 0.00 3.18
3408 3541 2.353269 CAGTTAGCGTTTTGGTGTGACA 59.647 45.455 0.00 0.00 0.00 3.58
3409 3542 2.853281 GCAGTTAGCGTTTTGGTGTGAC 60.853 50.000 0.00 0.00 0.00 3.67
3410 3543 1.332375 GCAGTTAGCGTTTTGGTGTGA 59.668 47.619 0.00 0.00 0.00 3.58
3411 3544 1.753956 GCAGTTAGCGTTTTGGTGTG 58.246 50.000 0.00 0.00 0.00 3.82
3422 3555 5.186198 TCCTCCTAAGAATTTGCAGTTAGC 58.814 41.667 0.00 0.00 45.96 3.09
3423 3556 7.627300 GCTTTCCTCCTAAGAATTTGCAGTTAG 60.627 40.741 0.00 0.00 0.00 2.34
3424 3557 6.151144 GCTTTCCTCCTAAGAATTTGCAGTTA 59.849 38.462 0.00 0.00 0.00 2.24
3425 3558 5.047731 GCTTTCCTCCTAAGAATTTGCAGTT 60.048 40.000 0.00 0.00 0.00 3.16
3426 3559 4.460731 GCTTTCCTCCTAAGAATTTGCAGT 59.539 41.667 0.00 0.00 0.00 4.40
3427 3560 4.704057 AGCTTTCCTCCTAAGAATTTGCAG 59.296 41.667 0.00 0.00 0.00 4.41
3428 3561 4.666512 AGCTTTCCTCCTAAGAATTTGCA 58.333 39.130 0.00 0.00 0.00 4.08
3429 3562 5.651387 AAGCTTTCCTCCTAAGAATTTGC 57.349 39.130 0.00 0.00 0.00 3.68
3430 3563 8.341892 ACTTAAGCTTTCCTCCTAAGAATTTG 57.658 34.615 3.20 0.00 0.00 2.32
3434 3567 9.668497 GAAATACTTAAGCTTTCCTCCTAAGAA 57.332 33.333 3.20 0.00 0.00 2.52
3435 3568 7.980099 CGAAATACTTAAGCTTTCCTCCTAAGA 59.020 37.037 18.39 0.00 0.00 2.10
3436 3569 7.980099 TCGAAATACTTAAGCTTTCCTCCTAAG 59.020 37.037 18.39 2.51 0.00 2.18
3437 3570 7.844009 TCGAAATACTTAAGCTTTCCTCCTAA 58.156 34.615 18.39 0.00 0.00 2.69
3438 3571 7.414222 TCGAAATACTTAAGCTTTCCTCCTA 57.586 36.000 18.39 0.00 0.00 2.94
3439 3572 6.295719 TCGAAATACTTAAGCTTTCCTCCT 57.704 37.500 18.39 0.00 0.00 3.69
3440 3573 6.987404 AGATCGAAATACTTAAGCTTTCCTCC 59.013 38.462 18.39 11.14 0.00 4.30
3441 3574 9.530633 TTAGATCGAAATACTTAAGCTTTCCTC 57.469 33.333 18.39 15.84 0.00 3.71
3442 3575 9.535878 CTTAGATCGAAATACTTAAGCTTTCCT 57.464 33.333 18.39 14.16 0.00 3.36
3443 3576 8.277018 GCTTAGATCGAAATACTTAAGCTTTCC 58.723 37.037 18.39 9.73 36.65 3.13
3444 3577 8.818057 TGCTTAGATCGAAATACTTAAGCTTTC 58.182 33.333 3.20 15.96 39.30 2.62
3445 3578 8.718102 TGCTTAGATCGAAATACTTAAGCTTT 57.282 30.769 3.20 2.86 39.30 3.51
3446 3579 8.718102 TTGCTTAGATCGAAATACTTAAGCTT 57.282 30.769 15.76 3.48 39.30 3.74
3447 3580 8.718102 TTTGCTTAGATCGAAATACTTAAGCT 57.282 30.769 15.76 0.00 39.30 3.74
3448 3581 9.769093 TTTTTGCTTAGATCGAAATACTTAAGC 57.231 29.630 1.29 10.54 39.10 3.09
3519 3652 1.664151 GAAACGGGGTGACGATGATTC 59.336 52.381 0.00 0.00 37.61 2.52
3520 3653 1.002659 TGAAACGGGGTGACGATGATT 59.997 47.619 0.00 0.00 37.61 2.57
3521 3654 0.611200 TGAAACGGGGTGACGATGAT 59.389 50.000 0.00 0.00 37.61 2.45
3522 3655 0.393448 TTGAAACGGGGTGACGATGA 59.607 50.000 0.00 0.00 37.61 2.92
3523 3656 1.448985 ATTGAAACGGGGTGACGATG 58.551 50.000 0.00 0.00 37.61 3.84
3524 3657 3.004862 GTTATTGAAACGGGGTGACGAT 58.995 45.455 0.00 0.00 37.61 3.73
3525 3658 2.224233 TGTTATTGAAACGGGGTGACGA 60.224 45.455 0.00 0.00 37.61 4.20
3526 3659 2.144730 TGTTATTGAAACGGGGTGACG 58.855 47.619 0.00 0.00 40.31 4.35
3527 3660 3.816523 TCTTGTTATTGAAACGGGGTGAC 59.183 43.478 0.00 0.00 0.00 3.67
3528 3661 4.088056 TCTTGTTATTGAAACGGGGTGA 57.912 40.909 0.00 0.00 0.00 4.02
3529 3662 4.036971 TGTTCTTGTTATTGAAACGGGGTG 59.963 41.667 0.00 0.00 0.00 4.61
3530 3663 4.208746 TGTTCTTGTTATTGAAACGGGGT 58.791 39.130 0.00 0.00 0.00 4.95
3531 3664 4.839668 TGTTCTTGTTATTGAAACGGGG 57.160 40.909 0.00 0.00 0.00 5.73
3532 3665 6.254281 AGATGTTCTTGTTATTGAAACGGG 57.746 37.500 0.00 0.00 0.00 5.28
3533 3666 6.953743 CGTAGATGTTCTTGTTATTGAAACGG 59.046 38.462 0.00 0.00 0.00 4.44
3534 3667 7.726079 TCGTAGATGTTCTTGTTATTGAAACG 58.274 34.615 0.00 0.00 0.00 3.60
3598 3731 8.303876 GCTCCCTAATGAACAGTAAATTCAAAA 58.696 33.333 0.00 0.00 39.43 2.44
3599 3732 7.450014 TGCTCCCTAATGAACAGTAAATTCAAA 59.550 33.333 0.00 0.00 39.43 2.69
3600 3733 6.945435 TGCTCCCTAATGAACAGTAAATTCAA 59.055 34.615 0.00 0.00 39.43 2.69
3601 3734 6.480763 TGCTCCCTAATGAACAGTAAATTCA 58.519 36.000 0.00 0.00 40.25 2.57
3602 3735 7.573968 ATGCTCCCTAATGAACAGTAAATTC 57.426 36.000 0.00 0.00 0.00 2.17
3603 3736 9.071276 CATATGCTCCCTAATGAACAGTAAATT 57.929 33.333 0.00 0.00 0.00 1.82
3604 3737 7.175641 GCATATGCTCCCTAATGAACAGTAAAT 59.824 37.037 20.64 0.00 38.21 1.40
3605 3738 6.486657 GCATATGCTCCCTAATGAACAGTAAA 59.513 38.462 20.64 0.00 38.21 2.01
3606 3739 5.997746 GCATATGCTCCCTAATGAACAGTAA 59.002 40.000 20.64 0.00 38.21 2.24
3607 3740 5.551233 GCATATGCTCCCTAATGAACAGTA 58.449 41.667 20.64 0.00 38.21 2.74
3608 3741 4.392940 GCATATGCTCCCTAATGAACAGT 58.607 43.478 20.64 0.00 38.21 3.55
3630 3763 1.341209 GGTTGTTTTGGCTCTTGGGAG 59.659 52.381 0.00 0.00 42.18 4.30
3631 3764 1.408969 GGTTGTTTTGGCTCTTGGGA 58.591 50.000 0.00 0.00 0.00 4.37
3632 3765 0.392706 GGGTTGTTTTGGCTCTTGGG 59.607 55.000 0.00 0.00 0.00 4.12
3633 3766 1.341209 GAGGGTTGTTTTGGCTCTTGG 59.659 52.381 0.00 0.00 0.00 3.61
3634 3767 2.310538 AGAGGGTTGTTTTGGCTCTTG 58.689 47.619 0.00 0.00 0.00 3.02
3635 3768 2.755952 AGAGGGTTGTTTTGGCTCTT 57.244 45.000 0.00 0.00 0.00 2.85
3636 3769 2.175715 AGAAGAGGGTTGTTTTGGCTCT 59.824 45.455 0.00 0.00 0.00 4.09
3637 3770 2.554462 GAGAAGAGGGTTGTTTTGGCTC 59.446 50.000 0.00 0.00 0.00 4.70
3638 3771 2.175715 AGAGAAGAGGGTTGTTTTGGCT 59.824 45.455 0.00 0.00 0.00 4.75
3639 3772 2.554462 GAGAGAAGAGGGTTGTTTTGGC 59.446 50.000 0.00 0.00 0.00 4.52
3640 3773 4.068599 GAGAGAGAAGAGGGTTGTTTTGG 58.931 47.826 0.00 0.00 0.00 3.28
3641 3774 4.967036 AGAGAGAGAAGAGGGTTGTTTTG 58.033 43.478 0.00 0.00 0.00 2.44
3642 3775 5.638530 AAGAGAGAGAAGAGGGTTGTTTT 57.361 39.130 0.00 0.00 0.00 2.43
3643 3776 5.638530 AAAGAGAGAGAAGAGGGTTGTTT 57.361 39.130 0.00 0.00 0.00 2.83
3644 3777 5.638530 AAAAGAGAGAGAAGAGGGTTGTT 57.361 39.130 0.00 0.00 0.00 2.83
3645 3778 5.638530 AAAAAGAGAGAGAAGAGGGTTGT 57.361 39.130 0.00 0.00 0.00 3.32
3770 3922 8.412456 CCAGAGGCATACATATAGAGTCTTATG 58.588 40.741 0.00 9.01 33.08 1.90
3804 3956 3.135167 TGCTAGATCATTGCACATCCTGA 59.865 43.478 0.00 0.00 34.60 3.86
3840 3992 5.100344 TGGCTCAACCACCGTTATTATTA 57.900 39.130 0.00 0.00 46.36 0.98
3882 4035 9.177304 CATTGTCATATTACTTTGCATGATCAC 57.823 33.333 0.00 0.00 30.63 3.06
3914 4068 6.322456 TCCACTGTTCCATTTTTATGACACAA 59.678 34.615 0.00 0.00 0.00 3.33
3958 4118 6.968263 TGGTGTTTTCATAGTCATTCCAAA 57.032 33.333 0.00 0.00 0.00 3.28
3967 4127 8.999895 ACCTACCTATTATGGTGTTTTCATAGT 58.000 33.333 0.00 0.00 41.05 2.12
3977 4137 5.586243 GCATGCATACCTACCTATTATGGTG 59.414 44.000 14.21 0.00 41.05 4.17
3999 4159 9.784531 CCTCCTTATATCTTTCTCAAAATAGCA 57.215 33.333 0.00 0.00 0.00 3.49
4011 4171 7.806180 ACACACATAAGCCTCCTTATATCTTT 58.194 34.615 0.00 0.00 41.23 2.52
4036 4196 6.121776 ACCCCGTGATATGATATGCTTTAA 57.878 37.500 0.00 0.00 0.00 1.52
4039 4199 4.640771 AACCCCGTGATATGATATGCTT 57.359 40.909 0.00 0.00 0.00 3.91
4152 4312 5.803552 TGTGAGTTCATGGATCATACACAA 58.196 37.500 0.00 0.00 33.82 3.33
4160 4320 8.893219 TTATGACTAATGTGAGTTCATGGATC 57.107 34.615 0.00 0.00 0.00 3.36
4168 4328 9.209175 GTGAGTTCTTTATGACTAATGTGAGTT 57.791 33.333 0.00 0.00 0.00 3.01
4216 4376 7.754475 GTGTAGTAGTACTTTACTTTGAGGCTC 59.246 40.741 8.40 7.79 40.14 4.70


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

AutoCloner maintained by Alex Coulton.