Multiple sequence alignment - TraesCS7B01G479200

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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 TraesCS7B01G479200 chr7B 100.000 6113 0 0 1 6113 733810146 733816258 0.000000e+00 11289.0
1 TraesCS7B01G479200 chr7B 76.103 3356 694 69 987 4282 733797603 733800910 0.000000e+00 1655.0
2 TraesCS7B01G479200 chr7B 78.187 2416 452 50 997 3376 733860340 733862716 0.000000e+00 1472.0
3 TraesCS7B01G479200 chr7B 78.865 1973 353 47 991 2928 733759172 733761115 0.000000e+00 1275.0
4 TraesCS7B01G479200 chr7B 80.157 1653 281 33 1749 3376 733885724 733887354 0.000000e+00 1192.0
5 TraesCS7B01G479200 chr7B 73.967 1283 285 39 3010 4275 733761254 733762504 1.990000e-129 473.0
6 TraesCS7B01G479200 chr7B 75.645 891 179 29 1076 1949 733594450 733595319 5.700000e-110 409.0
7 TraesCS7B01G479200 chr7B 77.941 204 37 6 392 587 192018586 192018789 2.990000e-23 121.0
8 TraesCS7B01G479200 chr7B 82.759 145 15 6 5367 5507 735301852 735301714 2.990000e-23 121.0
9 TraesCS7B01G479200 chr7D 96.156 5125 183 7 77 5192 631423425 631428544 0.000000e+00 8360.0
10 TraesCS7B01G479200 chr7D 75.730 3321 691 82 1008 4282 638670912 638667661 0.000000e+00 1561.0
11 TraesCS7B01G479200 chr7D 75.205 3053 600 103 1282 4282 631393643 631396590 0.000000e+00 1299.0
12 TraesCS7B01G479200 chr7D 95.718 397 16 1 5717 6113 631428565 631428960 6.680000e-179 638.0
13 TraesCS7B01G479200 chr7D 93.258 178 11 1 5187 5364 480637873 480637697 1.690000e-65 261.0
14 TraesCS7B01G479200 chr7D 90.789 76 6 1 2 77 140229636 140229710 3.900000e-17 100.0
15 TraesCS7B01G479200 chr7D 90.196 51 5 0 4535 4585 631401801 631401851 3.950000e-07 67.6
16 TraesCS7B01G479200 chrUn 96.137 1165 45 0 4028 5192 283734458 283735622 0.000000e+00 1903.0
17 TraesCS7B01G479200 chrUn 95.708 1165 50 0 4028 5192 277754657 277755821 0.000000e+00 1875.0
18 TraesCS7B01G479200 chrUn 95.551 1079 48 0 4114 5192 304658686 304659764 0.000000e+00 1727.0
19 TraesCS7B01G479200 chrUn 96.000 1000 40 0 4193 5192 422907670 422906671 0.000000e+00 1626.0
20 TraesCS7B01G479200 chrUn 95.277 847 40 0 4346 5192 442902078 442901232 0.000000e+00 1343.0
21 TraesCS7B01G479200 chrUn 94.778 766 24 5 5354 6113 336755459 336756214 0.000000e+00 1179.0
22 TraesCS7B01G479200 chrUn 94.517 766 26 5 5354 6113 277755820 277756575 0.000000e+00 1168.0
23 TraesCS7B01G479200 chrUn 94.517 766 26 5 5354 6113 304659763 304660518 0.000000e+00 1168.0
24 TraesCS7B01G479200 chrUn 94.256 766 28 5 5354 6113 277751787 277752542 0.000000e+00 1157.0
25 TraesCS7B01G479200 chrUn 93.750 560 35 0 4633 5192 277751229 277751788 0.000000e+00 841.0
26 TraesCS7B01G479200 chrUn 93.750 560 35 0 4633 5192 336754901 336755460 0.000000e+00 841.0
27 TraesCS7B01G479200 chrUn 98.267 404 7 0 4028 4431 277754255 277754658 0.000000e+00 708.0
28 TraesCS7B01G479200 chrUn 97.929 338 7 0 4094 4431 277757952 277758289 2.450000e-163 586.0
29 TraesCS7B01G479200 chrUn 97.633 338 8 0 4094 4431 277753919 277754256 1.140000e-161 580.0
30 TraesCS7B01G479200 chrUn 98.288 292 5 0 3595 3886 88643877 88644168 4.230000e-141 512.0
31 TraesCS7B01G479200 chrUn 98.288 292 5 0 3595 3886 283733968 283734259 4.230000e-141 512.0
32 TraesCS7B01G479200 chrUn 96.581 234 5 1 5354 5587 283735621 283735851 9.610000e-103 385.0
33 TraesCS7B01G479200 chrUn 96.970 231 4 1 5357 5587 422906669 422906442 9.610000e-103 385.0
34 TraesCS7B01G479200 chrUn 96.970 231 4 1 5357 5587 442901230 442901003 9.610000e-103 385.0
35 TraesCS7B01G479200 chrUn 98.058 206 3 1 4227 4431 88644163 88644368 2.100000e-94 357.0
36 TraesCS7B01G479200 chrUn 97.326 187 5 0 4028 4214 88644367 88644553 9.890000e-83 318.0
37 TraesCS7B01G479200 chrUn 97.326 187 5 0 4028 4214 277758288 277758474 9.890000e-83 318.0
38 TraesCS7B01G479200 chrUn 92.391 184 10 3 5183 5365 74544598 74544778 6.080000e-65 259.0
39 TraesCS7B01G479200 chrUn 79.085 306 43 11 5701 5996 334295075 334294781 2.250000e-44 191.0
40 TraesCS7B01G479200 chrUn 78.758 306 44 11 5701 5996 239734673 239734379 1.050000e-42 185.0
41 TraesCS7B01G479200 chrUn 78.758 306 44 11 5701 5996 319122844 319122550 1.050000e-42 185.0
42 TraesCS7B01G479200 chr7A 76.394 3317 662 87 1029 4282 726686199 726682941 0.000000e+00 1676.0
43 TraesCS7B01G479200 chr7A 77.934 2420 463 49 997 3376 727228717 727231105 0.000000e+00 1445.0
44 TraesCS7B01G479200 chr7A 77.636 2039 387 46 1748 3757 726814168 726812170 0.000000e+00 1175.0
45 TraesCS7B01G479200 chr7A 75.780 1218 236 38 1013 2199 727215334 727214145 1.490000e-155 560.0
46 TraesCS7B01G479200 chr7A 79.439 642 103 21 992 1614 726816232 726815601 1.570000e-115 427.0
47 TraesCS7B01G479200 chr7A 79.259 405 80 3 999 1401 726770308 726769906 4.670000e-71 279.0
48 TraesCS7B01G479200 chr6D 72.843 2839 641 92 994 3758 468910533 468913315 0.000000e+00 852.0
49 TraesCS7B01G479200 chr6D 92.818 181 11 1 5186 5366 145466480 145466658 1.690000e-65 261.0
50 TraesCS7B01G479200 chr4D 94.767 172 8 1 5189 5360 477898793 477898963 3.630000e-67 267.0
51 TraesCS7B01G479200 chr3D 93.820 178 9 2 5189 5364 272098432 272098609 3.630000e-67 267.0
52 TraesCS7B01G479200 chr3D 90.256 195 16 3 5163 5355 360695799 360695992 1.020000e-62 252.0
53 TraesCS7B01G479200 chr3D 77.162 451 55 22 146 587 595279954 595279543 1.030000e-52 219.0
54 TraesCS7B01G479200 chr1B 94.767 172 8 1 5190 5360 15441049 15441220 3.630000e-67 267.0
55 TraesCS7B01G479200 chr1B 73.523 457 90 21 4430 4872 17567589 17568028 1.780000e-30 145.0
56 TraesCS7B01G479200 chr1B 80.000 165 18 6 298 461 444672281 444672431 2.330000e-19 108.0
57 TraesCS7B01G479200 chr3A 93.750 176 11 0 5181 5356 641872773 641872948 1.310000e-66 265.0
58 TraesCS7B01G479200 chr1D 94.253 174 8 2 5190 5362 36612132 36612304 1.310000e-66 265.0
59 TraesCS7B01G479200 chr1D 89.333 75 7 1 7 81 1572311 1572238 6.520000e-15 93.5
60 TraesCS7B01G479200 chr2B 91.045 67 6 0 11 77 583800620 583800554 2.350000e-14 91.6


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 TraesCS7B01G479200 chr7B 733810146 733816258 6112 False 11289.000000 11289 100.000000 1 6113 1 chr7B.!!$F4 6112
1 TraesCS7B01G479200 chr7B 733797603 733800910 3307 False 1655.000000 1655 76.103000 987 4282 1 chr7B.!!$F3 3295
2 TraesCS7B01G479200 chr7B 733860340 733862716 2376 False 1472.000000 1472 78.187000 997 3376 1 chr7B.!!$F5 2379
3 TraesCS7B01G479200 chr7B 733885724 733887354 1630 False 1192.000000 1192 80.157000 1749 3376 1 chr7B.!!$F6 1627
4 TraesCS7B01G479200 chr7B 733759172 733762504 3332 False 874.000000 1275 76.416000 991 4275 2 chr7B.!!$F7 3284
5 TraesCS7B01G479200 chr7B 733594450 733595319 869 False 409.000000 409 75.645000 1076 1949 1 chr7B.!!$F2 873
6 TraesCS7B01G479200 chr7D 631423425 631428960 5535 False 4499.000000 8360 95.937000 77 6113 2 chr7D.!!$F4 6036
7 TraesCS7B01G479200 chr7D 638667661 638670912 3251 True 1561.000000 1561 75.730000 1008 4282 1 chr7D.!!$R2 3274
8 TraesCS7B01G479200 chr7D 631393643 631396590 2947 False 1299.000000 1299 75.205000 1282 4282 1 chr7D.!!$F2 3000
9 TraesCS7B01G479200 chrUn 304658686 304660518 1832 False 1447.500000 1727 95.034000 4114 6113 2 chrUn.!!$F5 1999
10 TraesCS7B01G479200 chrUn 336754901 336756214 1313 False 1010.000000 1179 94.264000 4633 6113 2 chrUn.!!$F6 1480
11 TraesCS7B01G479200 chrUn 422906442 422907670 1228 True 1005.500000 1626 96.485000 4193 5587 2 chrUn.!!$R4 1394
12 TraesCS7B01G479200 chrUn 283733968 283735851 1883 False 933.333333 1903 97.002000 3595 5587 3 chrUn.!!$F4 1992
13 TraesCS7B01G479200 chrUn 277751229 277758474 7245 False 904.125000 1875 96.173250 4028 6113 8 chrUn.!!$F3 2085
14 TraesCS7B01G479200 chrUn 442901003 442902078 1075 True 864.000000 1343 96.123500 4346 5587 2 chrUn.!!$R5 1241
15 TraesCS7B01G479200 chrUn 88643877 88644553 676 False 395.666667 512 97.890667 3595 4431 3 chrUn.!!$F2 836
16 TraesCS7B01G479200 chr7A 726682941 726686199 3258 True 1676.000000 1676 76.394000 1029 4282 1 chr7A.!!$R1 3253
17 TraesCS7B01G479200 chr7A 727228717 727231105 2388 False 1445.000000 1445 77.934000 997 3376 1 chr7A.!!$F1 2379
18 TraesCS7B01G479200 chr7A 726812170 726816232 4062 True 801.000000 1175 78.537500 992 3757 2 chr7A.!!$R4 2765
19 TraesCS7B01G479200 chr7A 727214145 727215334 1189 True 560.000000 560 75.780000 1013 2199 1 chr7A.!!$R3 1186
20 TraesCS7B01G479200 chr6D 468910533 468913315 2782 False 852.000000 852 72.843000 994 3758 1 chr6D.!!$F2 2764

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
58 59 0.320073 CCTTTAGTGCCGGTTCGTGA 60.320 55.000 1.90 0.00 0.00 4.35 F
98 99 0.404426 GGTCCCCACCTTTTAGTGCT 59.596 55.000 0.00 0.00 40.00 4.40 F
1614 1656 0.249120 TCGGCATAACTCCACACCAG 59.751 55.000 0.00 0.00 0.00 4.00 F
1689 1731 2.320805 CGCAGCATACATTGTATGGC 57.679 50.000 29.04 24.12 33.60 4.40 F
2252 3640 3.182152 AGTACCAAGGTGACCTAGCAAT 58.818 45.455 3.68 0.00 31.13 3.56 F
2382 3771 5.062809 TCTCGAAAACAACAAATGGCAAAAC 59.937 36.000 0.00 0.00 0.00 2.43 F
3190 4651 6.420903 GGTTGGAAAGATGAAGTGTTTAAAGC 59.579 38.462 0.00 0.00 0.00 3.51 F
4420 5943 2.439156 GGCCCATCGAAGCAGCTT 60.439 61.111 7.60 7.60 0.00 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1597 1639 0.394352 CCCTGGTGTGGAGTTATGCC 60.394 60.000 0.00 0.0 0.00 4.40 R
1689 1731 1.089920 CCTCGAAAATGTCTGCCCTG 58.910 55.000 0.00 0.0 0.00 4.45 R
3281 4742 5.917541 TGTCACCTTTTCAAGATTACGTC 57.082 39.130 0.00 0.0 0.00 4.34 R
3616 5079 3.126831 GGCGGATCTCACTAACTTCATG 58.873 50.000 0.00 0.0 0.00 3.07 R
4165 5688 2.494870 GCCATGGAAAGAAGTTGATGCT 59.505 45.455 18.40 0.0 0.00 3.79 R
4169 5692 4.016444 GGTATGCCATGGAAAGAAGTTGA 58.984 43.478 18.40 0.0 34.09 3.18 R
4862 6385 2.496899 ACTGATGAAACGGAGGCATT 57.503 45.000 0.00 0.0 0.00 3.56 R
5732 7255 0.531974 TCGGCCATAATCGTTCTGCC 60.532 55.000 2.24 0.0 35.55 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
46 47 1.937191 CCATTTGGTGGGCCTTTAGT 58.063 50.000 4.53 0.00 44.79 2.24
47 48 1.550072 CCATTTGGTGGGCCTTTAGTG 59.450 52.381 4.53 0.00 44.79 2.74
54 55 3.587095 GGCCTTTAGTGCCGGTTC 58.413 61.111 1.90 0.00 39.48 3.62
55 56 2.396157 GGCCTTTAGTGCCGGTTCG 61.396 63.158 1.90 0.00 39.48 3.95
57 58 1.908066 GCCTTTAGTGCCGGTTCGTG 61.908 60.000 1.90 0.00 0.00 4.35
58 59 0.320073 CCTTTAGTGCCGGTTCGTGA 60.320 55.000 1.90 0.00 0.00 4.35
61 62 1.794151 TTAGTGCCGGTTCGTGACGA 61.794 55.000 2.39 2.39 0.00 4.20
62 63 1.794151 TAGTGCCGGTTCGTGACGAA 61.794 55.000 17.28 17.28 43.75 3.85
75 76 2.004583 TGACGAATCGGCACTAAAGG 57.995 50.000 7.28 0.00 41.22 3.11
79 80 1.379527 GAATCGGCACTAAAGGGTGG 58.620 55.000 0.00 0.00 37.65 4.61
98 99 0.404426 GGTCCCCACCTTTTAGTGCT 59.596 55.000 0.00 0.00 40.00 4.40
104 105 1.000274 CCACCTTTTAGTGCTGGTTGC 60.000 52.381 0.00 0.00 43.25 4.17
127 128 1.539712 CCTTACGAACCGGGAATAGCC 60.540 57.143 6.32 0.00 0.00 3.93
147 148 2.534298 CCGATTCTGCACTAGTGTCTG 58.466 52.381 23.44 17.85 0.00 3.51
186 187 1.451504 TGGTGACAACAGGCCTCTG 59.548 57.895 0.00 5.97 40.57 3.35
230 231 1.160329 GCGTGCTTCTGTGTTGACCT 61.160 55.000 0.00 0.00 0.00 3.85
287 288 2.125633 GGCCGGGAGAAGACGAAC 60.126 66.667 2.18 0.00 0.00 3.95
297 298 4.758165 GGGAGAAGACGAACCAATGTTTTA 59.242 41.667 0.00 0.00 33.97 1.52
390 391 3.491581 CGTCCTAGCAAACGTCACT 57.508 52.632 0.00 0.00 34.30 3.41
411 412 7.385205 GTCACTGTTACATGTGAGATGTTAAGT 59.615 37.037 9.11 0.14 42.84 2.24
419 420 2.484264 GTGAGATGTTAAGTGGTGCCAC 59.516 50.000 13.13 13.13 46.50 5.01
440 441 2.205462 AGTCTGACTGGTGGGCCT 59.795 61.111 10.00 0.00 35.27 5.19
444 445 1.222936 CTGACTGGTGGGCCTCATC 59.777 63.158 4.53 0.00 35.27 2.92
446 447 1.222936 GACTGGTGGGCCTCATCTG 59.777 63.158 4.53 6.27 35.27 2.90
467 468 9.258826 CATCTGTCATAATCTCTCTTAACCAAG 57.741 37.037 0.00 0.00 0.00 3.61
468 469 8.595362 TCTGTCATAATCTCTCTTAACCAAGA 57.405 34.615 0.00 0.00 38.49 3.02
470 471 9.474920 CTGTCATAATCTCTCTTAACCAAGATC 57.525 37.037 0.00 0.00 40.03 2.75
471 472 8.424918 TGTCATAATCTCTCTTAACCAAGATCC 58.575 37.037 0.00 0.00 40.03 3.36
473 474 8.424918 TCATAATCTCTCTTAACCAAGATCCAC 58.575 37.037 0.00 0.00 40.03 4.02
477 478 5.960811 TCTCTCTTAACCAAGATCCACTGAT 59.039 40.000 0.00 0.00 40.03 2.90
478 479 5.982356 TCTCTTAACCAAGATCCACTGATG 58.018 41.667 0.00 0.00 40.03 3.07
508 517 5.579119 TGCAAATCGATTACACAAGACGTAT 59.421 36.000 11.83 0.00 0.00 3.06
538 547 5.049474 TCTGCAACAAAAGTGTAGCATAGTG 60.049 40.000 0.00 0.00 36.80 2.74
543 552 7.010091 GCAACAAAAGTGTAGCATAGTGTTTTT 59.990 33.333 0.00 0.00 36.80 1.94
573 582 3.525268 AGCCTTCAAAGTGGTTGTTTG 57.475 42.857 0.00 0.00 38.47 2.93
574 583 2.168313 AGCCTTCAAAGTGGTTGTTTGG 59.832 45.455 0.00 0.00 38.47 3.28
701 710 3.505680 TGCGATGCAATAATTGATACCCC 59.494 43.478 0.00 0.00 34.76 4.95
721 730 4.644234 CCCCACATGTAAATGTAGCAATGA 59.356 41.667 0.00 0.00 32.74 2.57
731 740 5.524971 AATGTAGCAATGACAATGGATGG 57.475 39.130 0.00 0.00 0.00 3.51
745 754 2.123589 TGGATGGACGGGATACACAAT 58.876 47.619 0.00 0.00 39.74 2.71
750 759 6.043358 TGGATGGACGGGATACACAATAATTA 59.957 38.462 0.00 0.00 39.74 1.40
753 762 6.292923 TGGACGGGATACACAATAATTAAGG 58.707 40.000 0.00 0.00 39.74 2.69
755 764 5.067954 ACGGGATACACAATAATTAAGGGC 58.932 41.667 0.00 0.00 39.74 5.19
764 773 1.686355 TAATTAAGGGCGCACATGGG 58.314 50.000 14.57 0.00 0.00 4.00
865 874 4.103365 ACGAGAGTCTTTATCAGCAGTG 57.897 45.455 0.00 0.00 44.19 3.66
919 928 2.917897 ATTCGCTTCCCAGCCCCAA 61.918 57.895 0.00 0.00 44.06 4.12
974 983 2.310538 CCCAATAATTGACCCCTGCTC 58.689 52.381 0.00 0.00 0.00 4.26
1095 1104 3.672447 TACGTCGCCAGCACCGAA 61.672 61.111 0.00 0.00 36.36 4.30
1597 1639 0.307760 GCCCGTATCCAATTTGCTCG 59.692 55.000 0.00 0.00 0.00 5.03
1614 1656 0.249120 TCGGCATAACTCCACACCAG 59.751 55.000 0.00 0.00 0.00 4.00
1689 1731 2.320805 CGCAGCATACATTGTATGGC 57.679 50.000 29.04 24.12 33.60 4.40
1822 3170 4.757019 TTCGCCCAACACCTGTATAATA 57.243 40.909 0.00 0.00 0.00 0.98
1991 3373 7.309012 CCAAATATCCATCGCAGAGAAAATCAT 60.309 37.037 0.00 0.00 43.63 2.45
1995 3377 3.302935 CCATCGCAGAGAAAATCATGTCG 60.303 47.826 0.00 0.00 43.63 4.35
2005 3387 7.324616 CAGAGAAAATCATGTCGAAAAGGTTTC 59.675 37.037 0.00 0.00 0.00 2.78
2252 3640 3.182152 AGTACCAAGGTGACCTAGCAAT 58.818 45.455 3.68 0.00 31.13 3.56
2382 3771 5.062809 TCTCGAAAACAACAAATGGCAAAAC 59.937 36.000 0.00 0.00 0.00 2.43
2453 3842 7.826252 TGATTACCTTCCTTCTCATCTGAAAAG 59.174 37.037 0.00 0.00 0.00 2.27
2462 3851 6.432162 CCTTCTCATCTGAAAAGATGTTTCCA 59.568 38.462 13.80 0.00 44.33 3.53
2783 4184 8.988934 TGAAGACAACTATGATGTGACTTTTAC 58.011 33.333 0.00 0.00 0.00 2.01
3190 4651 6.420903 GGTTGGAAAGATGAAGTGTTTAAAGC 59.579 38.462 0.00 0.00 0.00 3.51
3276 4737 6.954684 AGTTAACAGATCTTGGAGGAGAACTA 59.045 38.462 8.61 0.00 28.96 2.24
3281 4742 6.549364 ACAGATCTTGGAGGAGAACTATGTAG 59.451 42.308 0.00 0.00 28.96 2.74
4027 5502 6.590292 CCTGCGAAAAGTAGAGAAAATGAGTA 59.410 38.462 0.00 0.00 34.21 2.59
4028 5503 7.278868 CCTGCGAAAAGTAGAGAAAATGAGTAT 59.721 37.037 0.00 0.00 34.21 2.12
4030 5505 9.647797 TGCGAAAAGTAGAGAAAATGAGTATAA 57.352 29.630 0.00 0.00 0.00 0.98
4031 5506 9.903185 GCGAAAAGTAGAGAAAATGAGTATAAC 57.097 33.333 0.00 0.00 0.00 1.89
4165 5688 8.148351 GCCTCCAATATCTTACAGTATACAACA 58.852 37.037 5.50 0.00 0.00 3.33
4167 5690 9.197694 CTCCAATATCTTACAGTATACAACAGC 57.802 37.037 5.50 0.00 0.00 4.40
4168 5691 8.700973 TCCAATATCTTACAGTATACAACAGCA 58.299 33.333 5.50 0.00 0.00 4.41
4169 5692 9.494271 CCAATATCTTACAGTATACAACAGCAT 57.506 33.333 5.50 0.00 0.00 3.79
4420 5943 2.439156 GGCCCATCGAAGCAGCTT 60.439 61.111 7.60 7.60 0.00 3.74
4660 6183 4.574892 TGTATCAGCGGATTTGTTCTCAA 58.425 39.130 4.22 0.00 34.89 3.02
4700 6223 4.718961 ACTAACCTAATATTGCCTGCAGG 58.281 43.478 29.34 29.34 38.53 4.85
4862 6385 1.986413 GGGCTCTTCAGCTCCTCAA 59.014 57.895 0.00 0.00 46.03 3.02
4865 6388 2.015587 GGCTCTTCAGCTCCTCAAATG 58.984 52.381 0.00 0.00 46.03 2.32
4984 6507 4.672587 TGTCCTAAAATCCGATCTCTGG 57.327 45.455 0.00 0.00 0.00 3.86
5173 6696 2.561478 TTCCAACGAAGAAAGGGAGG 57.439 50.000 0.00 0.00 0.00 4.30
5195 6718 3.512680 CGATCCCGCAATTATCTACTCC 58.487 50.000 0.00 0.00 0.00 3.85
5196 6719 3.676324 CGATCCCGCAATTATCTACTCCC 60.676 52.174 0.00 0.00 0.00 4.30
5197 6720 2.972348 TCCCGCAATTATCTACTCCCT 58.028 47.619 0.00 0.00 0.00 4.20
5198 6721 3.314693 TCCCGCAATTATCTACTCCCTT 58.685 45.455 0.00 0.00 0.00 3.95
5199 6722 3.323979 TCCCGCAATTATCTACTCCCTTC 59.676 47.826 0.00 0.00 0.00 3.46
5200 6723 3.318017 CCGCAATTATCTACTCCCTTCG 58.682 50.000 0.00 0.00 0.00 3.79
5201 6724 3.243771 CCGCAATTATCTACTCCCTTCGT 60.244 47.826 0.00 0.00 0.00 3.85
5202 6725 4.369182 CGCAATTATCTACTCCCTTCGTT 58.631 43.478 0.00 0.00 0.00 3.85
5203 6726 4.444720 CGCAATTATCTACTCCCTTCGTTC 59.555 45.833 0.00 0.00 0.00 3.95
5204 6727 4.750598 GCAATTATCTACTCCCTTCGTTCC 59.249 45.833 0.00 0.00 0.00 3.62
5205 6728 5.453480 GCAATTATCTACTCCCTTCGTTCCT 60.453 44.000 0.00 0.00 0.00 3.36
5206 6729 6.239232 GCAATTATCTACTCCCTTCGTTCCTA 60.239 42.308 0.00 0.00 0.00 2.94
5207 6730 7.686127 GCAATTATCTACTCCCTTCGTTCCTAA 60.686 40.741 0.00 0.00 0.00 2.69
5208 6731 7.909485 ATTATCTACTCCCTTCGTTCCTAAA 57.091 36.000 0.00 0.00 0.00 1.85
5209 6732 7.909485 TTATCTACTCCCTTCGTTCCTAAAT 57.091 36.000 0.00 0.00 0.00 1.40
5210 6733 9.597681 ATTATCTACTCCCTTCGTTCCTAAATA 57.402 33.333 0.00 0.00 0.00 1.40
5211 6734 9.597681 TTATCTACTCCCTTCGTTCCTAAATAT 57.402 33.333 0.00 0.00 0.00 1.28
5212 6735 7.909485 TCTACTCCCTTCGTTCCTAAATATT 57.091 36.000 0.00 0.00 0.00 1.28
5213 6736 8.315220 TCTACTCCCTTCGTTCCTAAATATTT 57.685 34.615 5.89 5.89 0.00 1.40
5214 6737 8.202137 TCTACTCCCTTCGTTCCTAAATATTTG 58.798 37.037 11.05 1.40 0.00 2.32
5215 6738 6.718294 ACTCCCTTCGTTCCTAAATATTTGT 58.282 36.000 11.05 0.00 0.00 2.83
5216 6739 6.822170 ACTCCCTTCGTTCCTAAATATTTGTC 59.178 38.462 11.05 0.00 0.00 3.18
5217 6740 6.954232 TCCCTTCGTTCCTAAATATTTGTCT 58.046 36.000 11.05 0.00 0.00 3.41
5218 6741 7.399634 TCCCTTCGTTCCTAAATATTTGTCTT 58.600 34.615 11.05 0.00 0.00 3.01
5219 6742 7.886446 TCCCTTCGTTCCTAAATATTTGTCTTT 59.114 33.333 11.05 0.00 0.00 2.52
5220 6743 8.182227 CCCTTCGTTCCTAAATATTTGTCTTTC 58.818 37.037 11.05 0.00 0.00 2.62
5221 6744 8.947115 CCTTCGTTCCTAAATATTTGTCTTTCT 58.053 33.333 11.05 0.00 0.00 2.52
5248 6771 9.737427 AGAGATTTCAATAAGTGACTACATACG 57.263 33.333 0.00 0.00 35.39 3.06
5249 6772 8.873215 AGATTTCAATAAGTGACTACATACGG 57.127 34.615 0.00 0.00 35.39 4.02
5250 6773 8.692710 AGATTTCAATAAGTGACTACATACGGA 58.307 33.333 0.00 0.00 35.39 4.69
5251 6774 8.873215 ATTTCAATAAGTGACTACATACGGAG 57.127 34.615 0.00 0.00 35.39 4.63
5252 6775 5.828747 TCAATAAGTGACTACATACGGAGC 58.171 41.667 0.00 0.00 0.00 4.70
5253 6776 5.358725 TCAATAAGTGACTACATACGGAGCA 59.641 40.000 0.00 0.00 0.00 4.26
5254 6777 5.847111 ATAAGTGACTACATACGGAGCAA 57.153 39.130 0.00 0.00 0.00 3.91
5255 6778 4.530710 AAGTGACTACATACGGAGCAAA 57.469 40.909 0.00 0.00 0.00 3.68
5256 6779 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
5257 6780 4.495422 AGTGACTACATACGGAGCAAAAG 58.505 43.478 0.00 0.00 0.00 2.27
5258 6781 3.617263 GTGACTACATACGGAGCAAAAGG 59.383 47.826 0.00 0.00 0.00 3.11
5259 6782 3.512329 TGACTACATACGGAGCAAAAGGA 59.488 43.478 0.00 0.00 0.00 3.36
5260 6783 4.020928 TGACTACATACGGAGCAAAAGGAA 60.021 41.667 0.00 0.00 0.00 3.36
5261 6784 5.099042 ACTACATACGGAGCAAAAGGAAT 57.901 39.130 0.00 0.00 0.00 3.01
5262 6785 4.876107 ACTACATACGGAGCAAAAGGAATG 59.124 41.667 0.00 0.00 0.00 2.67
5263 6786 3.950397 ACATACGGAGCAAAAGGAATGA 58.050 40.909 0.00 0.00 0.00 2.57
5264 6787 4.331968 ACATACGGAGCAAAAGGAATGAA 58.668 39.130 0.00 0.00 0.00 2.57
5265 6788 4.949856 ACATACGGAGCAAAAGGAATGAAT 59.050 37.500 0.00 0.00 0.00 2.57
5266 6789 5.066505 ACATACGGAGCAAAAGGAATGAATC 59.933 40.000 0.00 0.00 0.00 2.52
5267 6790 3.690460 ACGGAGCAAAAGGAATGAATCT 58.310 40.909 0.00 0.00 0.00 2.40
5268 6791 3.441572 ACGGAGCAAAAGGAATGAATCTG 59.558 43.478 0.00 0.00 0.00 2.90
5269 6792 3.733077 CGGAGCAAAAGGAATGAATCTGC 60.733 47.826 0.00 0.00 0.00 4.26
5270 6793 3.194116 GGAGCAAAAGGAATGAATCTGCA 59.806 43.478 0.00 0.00 30.16 4.41
5271 6794 4.171754 GAGCAAAAGGAATGAATCTGCAC 58.828 43.478 0.00 0.00 30.16 4.57
5272 6795 3.830755 AGCAAAAGGAATGAATCTGCACT 59.169 39.130 0.00 0.00 30.16 4.40
5273 6796 4.082354 AGCAAAAGGAATGAATCTGCACTC 60.082 41.667 0.00 0.00 30.16 3.51
5274 6797 4.082354 GCAAAAGGAATGAATCTGCACTCT 60.082 41.667 0.00 0.00 0.00 3.24
5275 6798 5.124457 GCAAAAGGAATGAATCTGCACTCTA 59.876 40.000 0.00 0.00 0.00 2.43
5276 6799 6.349611 GCAAAAGGAATGAATCTGCACTCTAA 60.350 38.462 0.00 0.00 0.00 2.10
5277 6800 7.596494 CAAAAGGAATGAATCTGCACTCTAAA 58.404 34.615 0.00 0.00 0.00 1.85
5278 6801 7.765695 AAAGGAATGAATCTGCACTCTAAAA 57.234 32.000 0.00 0.00 0.00 1.52
5279 6802 7.951347 AAGGAATGAATCTGCACTCTAAAAT 57.049 32.000 0.00 0.00 0.00 1.82
5280 6803 9.466497 AAAGGAATGAATCTGCACTCTAAAATA 57.534 29.630 0.00 0.00 0.00 1.40
5281 6804 9.638176 AAGGAATGAATCTGCACTCTAAAATAT 57.362 29.630 0.00 0.00 0.00 1.28
5282 6805 9.064706 AGGAATGAATCTGCACTCTAAAATATG 57.935 33.333 0.00 0.00 0.00 1.78
5283 6806 8.844244 GGAATGAATCTGCACTCTAAAATATGT 58.156 33.333 0.00 0.00 0.00 2.29
5284 6807 9.875675 GAATGAATCTGCACTCTAAAATATGTC 57.124 33.333 0.00 0.00 0.00 3.06
5285 6808 9.624373 AATGAATCTGCACTCTAAAATATGTCT 57.376 29.630 0.00 0.00 0.00 3.41
5307 6830 9.990868 TGTCTATATACATCCATATGTGGTAGT 57.009 33.333 8.51 10.44 45.99 2.73
5314 6837 7.572523 ACATCCATATGTGGTAGTTCATTTG 57.427 36.000 8.51 0.00 44.79 2.32
5315 6838 7.345691 ACATCCATATGTGGTAGTTCATTTGA 58.654 34.615 8.51 0.00 44.79 2.69
5316 6839 7.833682 ACATCCATATGTGGTAGTTCATTTGAA 59.166 33.333 8.51 0.00 44.79 2.69
5317 6840 8.685427 CATCCATATGTGGTAGTTCATTTGAAA 58.315 33.333 8.51 0.00 46.16 2.69
5318 6841 8.821686 TCCATATGTGGTAGTTCATTTGAAAT 57.178 30.769 8.51 0.00 46.16 2.17
5319 6842 8.902806 TCCATATGTGGTAGTTCATTTGAAATC 58.097 33.333 8.51 0.00 46.16 2.17
5320 6843 8.906867 CCATATGTGGTAGTTCATTTGAAATCT 58.093 33.333 0.00 0.00 40.83 2.40
5321 6844 9.941664 CATATGTGGTAGTTCATTTGAAATCTC 57.058 33.333 0.00 0.00 35.58 2.75
5322 6845 9.911788 ATATGTGGTAGTTCATTTGAAATCTCT 57.088 29.630 0.00 0.00 35.58 3.10
5324 6847 9.739276 ATGTGGTAGTTCATTTGAAATCTCTAA 57.261 29.630 0.00 0.00 35.58 2.10
5325 6848 9.567776 TGTGGTAGTTCATTTGAAATCTCTAAA 57.432 29.630 0.00 0.00 35.58 1.85
5350 6873 8.581253 AAAGACAAATATTTAGGAACAGAGGG 57.419 34.615 0.00 0.00 0.00 4.30
5351 6874 7.510675 AGACAAATATTTAGGAACAGAGGGA 57.489 36.000 0.00 0.00 0.00 4.20
5352 6875 7.569240 AGACAAATATTTAGGAACAGAGGGAG 58.431 38.462 0.00 0.00 0.00 4.30
5355 6878 8.265764 ACAAATATTTAGGAACAGAGGGAGTAC 58.734 37.037 0.00 0.00 0.00 2.73
5371 6894 7.177041 AGAGGGAGTACTGTTTTGAAGTAGTAG 59.823 40.741 0.00 0.00 34.61 2.57
5467 6990 8.973182 TGTACATACTACATAGTCATGAAACCA 58.027 33.333 0.00 0.00 37.73 3.67
5548 7071 6.017357 TGTCTCGTATTATAGCACACAGGTAG 60.017 42.308 0.00 0.00 32.98 3.18
5549 7072 6.017275 GTCTCGTATTATAGCACACAGGTAGT 60.017 42.308 0.00 0.00 32.98 2.73
5550 7073 7.172190 GTCTCGTATTATAGCACACAGGTAGTA 59.828 40.741 0.00 0.00 32.98 1.82
5576 7099 6.717540 GCTAGTATTTGAGATGGAGAGGAGTA 59.282 42.308 0.00 0.00 0.00 2.59
5605 7128 3.443099 TGCACTCTATCGATGAACCTG 57.557 47.619 8.54 0.00 0.00 4.00
5606 7129 2.131183 GCACTCTATCGATGAACCTGC 58.869 52.381 8.54 4.78 0.00 4.85
5607 7130 2.748605 CACTCTATCGATGAACCTGCC 58.251 52.381 8.54 0.00 0.00 4.85
5608 7131 2.363680 CACTCTATCGATGAACCTGCCT 59.636 50.000 8.54 0.00 0.00 4.75
5618 7141 1.623811 TGAACCTGCCTAGAGGTGAAC 59.376 52.381 3.96 1.26 46.29 3.18
5715 7238 0.794473 GCCCGTTTTCTGACCTTACG 59.206 55.000 0.00 0.00 0.00 3.18
5732 7255 5.632347 ACCTTACGTTCATTACTCTGTTTCG 59.368 40.000 0.00 0.00 0.00 3.46
5745 7268 3.857052 TCTGTTTCGGCAGAACGATTAT 58.143 40.909 0.00 0.00 41.93 1.28
5764 7287 1.303317 GGCCGACAGTGGGATTTGT 60.303 57.895 5.63 0.00 0.00 2.83
5777 7300 6.884295 CAGTGGGATTTGTTATTCAGGACTTA 59.116 38.462 0.00 0.00 0.00 2.24
5797 7320 5.306678 ACTTAATTGGTTGCTCCATCCAAAA 59.693 36.000 10.70 3.20 43.52 2.44
5862 7385 2.035066 GCAGCTATACCAAGGCCATTTG 59.965 50.000 5.01 0.63 0.00 2.32
5896 7419 5.635280 TCGATCACTCTGTCACTTTCATTTC 59.365 40.000 0.00 0.00 0.00 2.17
5975 7498 1.621814 TGCTAGTTACCCTCCACACAC 59.378 52.381 0.00 0.00 0.00 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.118454 AAATGGCACGAGTCCGCG 61.118 61.111 0.00 0.00 39.95 6.46
17 18 1.671054 ACCAAATGGCACGAGTCCG 60.671 57.895 0.00 0.00 39.32 4.79
18 19 1.586154 CCACCAAATGGCACGAGTCC 61.586 60.000 0.00 0.00 43.24 3.85
19 20 1.875963 CCACCAAATGGCACGAGTC 59.124 57.895 0.00 0.00 43.24 3.36
20 21 4.079446 CCACCAAATGGCACGAGT 57.921 55.556 0.00 0.00 43.24 4.18
28 29 1.066929 GCACTAAAGGCCCACCAAATG 60.067 52.381 0.00 0.00 39.06 2.32
30 31 0.830023 GGCACTAAAGGCCCACCAAA 60.830 55.000 0.00 0.00 45.87 3.28
38 39 1.670083 ACGAACCGGCACTAAAGGC 60.670 57.895 0.00 0.00 0.00 4.35
39 40 0.320073 TCACGAACCGGCACTAAAGG 60.320 55.000 0.00 0.00 0.00 3.11
40 41 0.788391 GTCACGAACCGGCACTAAAG 59.212 55.000 0.00 0.00 0.00 1.85
41 42 0.940519 CGTCACGAACCGGCACTAAA 60.941 55.000 0.00 0.00 0.00 1.85
42 43 1.372004 CGTCACGAACCGGCACTAA 60.372 57.895 0.00 0.00 0.00 2.24
43 44 1.794151 TTCGTCACGAACCGGCACTA 61.794 55.000 9.01 0.00 41.05 2.74
44 45 3.141522 TTCGTCACGAACCGGCACT 62.142 57.895 9.01 0.00 41.05 4.40
54 55 1.320555 CTTTAGTGCCGATTCGTCACG 59.679 52.381 13.78 0.00 35.97 4.35
55 56 1.659098 CCTTTAGTGCCGATTCGTCAC 59.341 52.381 11.99 11.99 0.00 3.67
57 58 1.287425 CCCTTTAGTGCCGATTCGTC 58.713 55.000 5.20 0.00 0.00 4.20
58 59 0.611714 ACCCTTTAGTGCCGATTCGT 59.388 50.000 5.20 0.00 0.00 3.85
61 62 0.034477 CCCACCCTTTAGTGCCGATT 60.034 55.000 0.00 0.00 36.38 3.34
62 63 1.205460 ACCCACCCTTTAGTGCCGAT 61.205 55.000 0.00 0.00 36.38 4.18
64 65 1.376812 GACCCACCCTTTAGTGCCG 60.377 63.158 0.00 0.00 36.38 5.69
65 66 1.001269 GGACCCACCCTTTAGTGCC 60.001 63.158 0.00 0.00 36.38 5.01
66 67 4.736739 GGACCCACCCTTTAGTGC 57.263 61.111 0.00 0.00 36.38 4.40
98 99 0.887387 GGTTCGTAAGGCTGCAACCA 60.887 55.000 9.23 0.00 37.13 3.67
104 105 0.107848 ATTCCCGGTTCGTAAGGCTG 60.108 55.000 0.00 0.00 38.47 4.85
127 128 2.534298 CAGACACTAGTGCAGAATCGG 58.466 52.381 22.90 9.21 0.00 4.18
147 148 2.202987 CTGCACCGAGGATGAGGC 60.203 66.667 0.00 0.00 0.00 4.70
214 215 0.179020 CCCAGGTCAACACAGAAGCA 60.179 55.000 0.00 0.00 0.00 3.91
230 231 4.980805 GTCGTCGTTGCTGCCCCA 62.981 66.667 0.00 0.00 0.00 4.96
268 269 4.728110 TCGTCTTCTCCCGGCCGA 62.728 66.667 30.73 6.52 0.00 5.54
344 345 5.289675 GGTAGCGTTATATCATCATGTGAGC 59.710 44.000 0.00 0.00 40.92 4.26
388 389 6.650807 CCACTTAACATCTCACATGTAACAGT 59.349 38.462 0.00 0.00 0.00 3.55
390 391 6.426633 CACCACTTAACATCTCACATGTAACA 59.573 38.462 0.00 0.00 0.00 2.41
411 412 2.131067 TCAGACTGACGTGGCACCA 61.131 57.895 12.86 4.12 0.00 4.17
440 441 8.539117 TGGTTAAGAGAGATTATGACAGATGA 57.461 34.615 0.00 0.00 0.00 2.92
444 445 9.474920 GATCTTGGTTAAGAGAGATTATGACAG 57.525 37.037 0.00 0.00 45.53 3.51
446 447 8.424918 TGGATCTTGGTTAAGAGAGATTATGAC 58.575 37.037 0.00 0.00 45.53 3.06
467 468 6.020121 CGATTTGCAAAAATCATCAGTGGATC 60.020 38.462 17.19 2.89 38.70 3.36
468 469 5.808540 CGATTTGCAAAAATCATCAGTGGAT 59.191 36.000 17.19 0.00 38.70 3.41
470 471 5.162794 TCGATTTGCAAAAATCATCAGTGG 58.837 37.500 17.19 0.00 38.70 4.00
471 472 6.880822 ATCGATTTGCAAAAATCATCAGTG 57.119 33.333 17.19 0.00 38.70 3.66
473 474 8.316046 GTGTAATCGATTTGCAAAAATCATCAG 58.684 33.333 17.19 5.75 38.70 2.90
477 478 7.864882 TCTTGTGTAATCGATTTGCAAAAATCA 59.135 29.630 17.19 7.14 38.70 2.57
478 479 8.155923 GTCTTGTGTAATCGATTTGCAAAAATC 58.844 33.333 17.19 9.32 36.17 2.17
508 517 6.942886 CTACACTTTTGTTGCAGAAAACAA 57.057 33.333 0.00 0.00 45.77 2.83
543 552 5.222048 ACCACTTTGAAGGCTAGGTCAATAA 60.222 40.000 1.23 0.00 33.90 1.40
551 560 4.499696 CCAAACAACCACTTTGAAGGCTAG 60.500 45.833 0.00 0.00 38.73 3.42
573 582 5.006358 ACGAATATGACGAGTAAATTGCACC 59.994 40.000 9.07 0.00 34.70 5.01
574 583 6.032722 ACGAATATGACGAGTAAATTGCAC 57.967 37.500 9.07 0.00 34.70 4.57
610 619 0.538977 TGAGAGAACCGGTCGTCCTT 60.539 55.000 8.04 0.00 0.00 3.36
615 624 1.064296 CGGATGAGAGAACCGGTCG 59.936 63.158 8.04 0.00 42.48 4.79
701 710 7.221259 CCATTGTCATTGCTACATTTACATGTG 59.779 37.037 9.11 0.00 43.92 3.21
721 730 2.123589 TGTATCCCGTCCATCCATTGT 58.876 47.619 0.00 0.00 0.00 2.71
731 740 5.180680 GCCCTTAATTATTGTGTATCCCGTC 59.819 44.000 0.00 0.00 0.00 4.79
745 754 1.686355 CCCATGTGCGCCCTTAATTA 58.314 50.000 4.18 0.00 0.00 1.40
865 874 2.124151 ATGGAATGGCAGCGGACC 60.124 61.111 0.00 0.00 0.00 4.46
926 935 2.078665 CAGGTGGGATTCGGGGGAT 61.079 63.158 0.00 0.00 0.00 3.85
927 936 2.690881 CAGGTGGGATTCGGGGGA 60.691 66.667 0.00 0.00 0.00 4.81
928 937 4.506255 GCAGGTGGGATTCGGGGG 62.506 72.222 0.00 0.00 0.00 5.40
932 941 1.597742 CTTATGGCAGGTGGGATTCG 58.402 55.000 0.00 0.00 0.00 3.34
933 942 1.322442 GCTTATGGCAGGTGGGATTC 58.678 55.000 0.00 0.00 41.35 2.52
1597 1639 0.394352 CCCTGGTGTGGAGTTATGCC 60.394 60.000 0.00 0.00 0.00 4.40
1689 1731 1.089920 CCTCGAAAATGTCTGCCCTG 58.910 55.000 0.00 0.00 0.00 4.45
1822 3170 7.315890 GCAAAGTGCTCTTGTATCCTTTTATT 58.684 34.615 1.02 0.00 40.96 1.40
1991 3373 6.687081 ACACAATTAGAAACCTTTTCGACA 57.313 33.333 0.00 0.00 0.00 4.35
1995 3377 9.528018 TCATCAAACACAATTAGAAACCTTTTC 57.472 29.630 0.00 0.00 0.00 2.29
2252 3640 0.969917 AGCAATGGCCCGTGCAATAA 60.970 50.000 24.98 0.00 43.42 1.40
2382 3771 7.384115 GTCATAATGCCATCATCATTTTCTTGG 59.616 37.037 0.00 0.00 35.87 3.61
2453 3842 9.045223 GGAATAAGGCAAAATATTGGAAACATC 57.955 33.333 0.00 0.00 42.32 3.06
2462 3851 8.788238 ATCTTCAGGGAATAAGGCAAAATATT 57.212 30.769 0.00 0.00 0.00 1.28
2510 3899 8.621532 TCCTATTGCAATCCAGAAATATGTAC 57.378 34.615 16.86 0.00 0.00 2.90
2783 4184 8.509690 TGCTCTTCAACTTAATCATTTCTTCAG 58.490 33.333 0.00 0.00 0.00 3.02
2830 4231 7.968014 ATCTTCTAAAAATCATCAAAGCCCT 57.032 32.000 0.00 0.00 0.00 5.19
2883 4284 5.964477 ACCCTCTACATCCTTGAAAGTATCA 59.036 40.000 0.00 0.00 35.85 2.15
3190 4651 7.092137 TCATGACATGGAATTCTTTAAGCTG 57.908 36.000 15.37 0.00 0.00 4.24
3276 4737 7.331193 GTCACCTTTTCAAGATTACGTCTACAT 59.669 37.037 0.00 0.00 35.67 2.29
3281 4742 5.917541 TGTCACCTTTTCAAGATTACGTC 57.082 39.130 0.00 0.00 0.00 4.34
3616 5079 3.126831 GGCGGATCTCACTAACTTCATG 58.873 50.000 0.00 0.00 0.00 3.07
4165 5688 2.494870 GCCATGGAAAGAAGTTGATGCT 59.505 45.455 18.40 0.00 0.00 3.79
4167 5690 4.730949 ATGCCATGGAAAGAAGTTGATG 57.269 40.909 18.40 0.00 0.00 3.07
4168 5691 4.646492 GGTATGCCATGGAAAGAAGTTGAT 59.354 41.667 18.40 0.00 34.09 2.57
4169 5692 4.016444 GGTATGCCATGGAAAGAAGTTGA 58.984 43.478 18.40 0.00 34.09 3.18
4420 5943 3.953612 GGCAAAGGATTGATGATGGTGTA 59.046 43.478 0.00 0.00 38.94 2.90
4660 6183 3.525800 AGTCCTTGCTACCACCAATTT 57.474 42.857 0.00 0.00 0.00 1.82
4700 6223 2.511145 CTCGCAGCTGGAAGGAGC 60.511 66.667 17.12 0.00 39.46 4.70
4862 6385 2.496899 ACTGATGAAACGGAGGCATT 57.503 45.000 0.00 0.00 0.00 3.56
4865 6388 4.438744 CCATAAAACTGATGAAACGGAGGC 60.439 45.833 0.00 0.00 0.00 4.70
5192 6715 7.048512 AGACAAATATTTAGGAACGAAGGGAG 58.951 38.462 0.00 0.00 0.00 4.30
5193 6716 6.954232 AGACAAATATTTAGGAACGAAGGGA 58.046 36.000 0.00 0.00 0.00 4.20
5194 6717 7.625828 AAGACAAATATTTAGGAACGAAGGG 57.374 36.000 0.00 0.00 0.00 3.95
5195 6718 8.947115 AGAAAGACAAATATTTAGGAACGAAGG 58.053 33.333 0.00 0.00 0.00 3.46
5222 6745 9.737427 CGTATGTAGTCACTTATTGAAATCTCT 57.263 33.333 0.00 0.00 35.39 3.10
5223 6746 8.969267 CCGTATGTAGTCACTTATTGAAATCTC 58.031 37.037 0.00 0.00 35.39 2.75
5224 6747 8.692710 TCCGTATGTAGTCACTTATTGAAATCT 58.307 33.333 0.00 0.00 35.39 2.40
5225 6748 8.867112 TCCGTATGTAGTCACTTATTGAAATC 57.133 34.615 0.00 0.00 35.39 2.17
5226 6749 7.438459 GCTCCGTATGTAGTCACTTATTGAAAT 59.562 37.037 0.00 0.00 35.39 2.17
5227 6750 6.755141 GCTCCGTATGTAGTCACTTATTGAAA 59.245 38.462 0.00 0.00 35.39 2.69
5228 6751 6.127563 TGCTCCGTATGTAGTCACTTATTGAA 60.128 38.462 0.00 0.00 35.39 2.69
5229 6752 5.358725 TGCTCCGTATGTAGTCACTTATTGA 59.641 40.000 0.00 0.00 0.00 2.57
5230 6753 5.588240 TGCTCCGTATGTAGTCACTTATTG 58.412 41.667 0.00 0.00 0.00 1.90
5231 6754 5.847111 TGCTCCGTATGTAGTCACTTATT 57.153 39.130 0.00 0.00 0.00 1.40
5232 6755 5.847111 TTGCTCCGTATGTAGTCACTTAT 57.153 39.130 0.00 0.00 0.00 1.73
5233 6756 5.648178 TTTGCTCCGTATGTAGTCACTTA 57.352 39.130 0.00 0.00 0.00 2.24
5234 6757 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
5235 6758 4.495422 CTTTTGCTCCGTATGTAGTCACT 58.505 43.478 0.00 0.00 0.00 3.41
5236 6759 3.617263 CCTTTTGCTCCGTATGTAGTCAC 59.383 47.826 0.00 0.00 0.00 3.67
5237 6760 3.512329 TCCTTTTGCTCCGTATGTAGTCA 59.488 43.478 0.00 0.00 0.00 3.41
5238 6761 4.119442 TCCTTTTGCTCCGTATGTAGTC 57.881 45.455 0.00 0.00 0.00 2.59
5239 6762 4.546829 TTCCTTTTGCTCCGTATGTAGT 57.453 40.909 0.00 0.00 0.00 2.73
5240 6763 5.116180 TCATTCCTTTTGCTCCGTATGTAG 58.884 41.667 0.00 0.00 0.00 2.74
5241 6764 5.092554 TCATTCCTTTTGCTCCGTATGTA 57.907 39.130 0.00 0.00 0.00 2.29
5242 6765 3.950397 TCATTCCTTTTGCTCCGTATGT 58.050 40.909 0.00 0.00 0.00 2.29
5243 6766 4.963276 TTCATTCCTTTTGCTCCGTATG 57.037 40.909 0.00 0.00 0.00 2.39
5244 6767 5.297776 CAGATTCATTCCTTTTGCTCCGTAT 59.702 40.000 0.00 0.00 0.00 3.06
5245 6768 4.635765 CAGATTCATTCCTTTTGCTCCGTA 59.364 41.667 0.00 0.00 0.00 4.02
5246 6769 3.441572 CAGATTCATTCCTTTTGCTCCGT 59.558 43.478 0.00 0.00 0.00 4.69
5247 6770 3.733077 GCAGATTCATTCCTTTTGCTCCG 60.733 47.826 0.00 0.00 0.00 4.63
5248 6771 3.194116 TGCAGATTCATTCCTTTTGCTCC 59.806 43.478 0.00 0.00 0.00 4.70
5249 6772 4.082354 AGTGCAGATTCATTCCTTTTGCTC 60.082 41.667 0.00 0.00 0.00 4.26
5250 6773 3.830755 AGTGCAGATTCATTCCTTTTGCT 59.169 39.130 0.00 0.00 0.00 3.91
5251 6774 4.082354 AGAGTGCAGATTCATTCCTTTTGC 60.082 41.667 0.00 0.00 0.00 3.68
5252 6775 5.640189 AGAGTGCAGATTCATTCCTTTTG 57.360 39.130 0.00 0.00 0.00 2.44
5253 6776 7.765695 TTTAGAGTGCAGATTCATTCCTTTT 57.234 32.000 0.00 0.00 0.00 2.27
5254 6777 7.765695 TTTTAGAGTGCAGATTCATTCCTTT 57.234 32.000 0.00 0.00 0.00 3.11
5255 6778 7.951347 ATTTTAGAGTGCAGATTCATTCCTT 57.049 32.000 0.00 0.00 0.00 3.36
5256 6779 9.064706 CATATTTTAGAGTGCAGATTCATTCCT 57.935 33.333 0.00 0.00 0.00 3.36
5257 6780 8.844244 ACATATTTTAGAGTGCAGATTCATTCC 58.156 33.333 0.00 0.00 0.00 3.01
5258 6781 9.875675 GACATATTTTAGAGTGCAGATTCATTC 57.124 33.333 0.00 0.00 0.00 2.67
5259 6782 9.624373 AGACATATTTTAGAGTGCAGATTCATT 57.376 29.630 0.00 0.00 0.00 2.57
5291 6814 8.685427 TTTCAAATGAACTACCACATATGGATG 58.315 33.333 7.80 0.00 40.19 3.51
5292 6815 8.821686 TTTCAAATGAACTACCACATATGGAT 57.178 30.769 7.80 0.00 40.19 3.41
5293 6816 8.821686 ATTTCAAATGAACTACCACATATGGA 57.178 30.769 7.80 0.00 40.19 3.41
5294 6817 8.906867 AGATTTCAAATGAACTACCACATATGG 58.093 33.333 7.80 0.00 42.08 2.74
5295 6818 9.941664 GAGATTTCAAATGAACTACCACATATG 57.058 33.333 0.00 0.00 33.13 1.78
5296 6819 9.911788 AGAGATTTCAAATGAACTACCACATAT 57.088 29.630 0.00 0.00 33.13 1.78
5298 6821 9.739276 TTAGAGATTTCAAATGAACTACCACAT 57.261 29.630 0.00 0.00 33.13 3.21
5299 6822 9.567776 TTTAGAGATTTCAAATGAACTACCACA 57.432 29.630 0.00 0.00 33.13 4.17
5324 6847 9.025041 CCCTCTGTTCCTAAATATTTGTCTTTT 57.975 33.333 11.05 0.00 0.00 2.27
5325 6848 8.390921 TCCCTCTGTTCCTAAATATTTGTCTTT 58.609 33.333 11.05 0.00 0.00 2.52
5326 6849 7.928873 TCCCTCTGTTCCTAAATATTTGTCTT 58.071 34.615 11.05 0.00 0.00 3.01
5327 6850 7.182930 ACTCCCTCTGTTCCTAAATATTTGTCT 59.817 37.037 11.05 0.00 0.00 3.41
5328 6851 7.339482 ACTCCCTCTGTTCCTAAATATTTGTC 58.661 38.462 11.05 0.00 0.00 3.18
5329 6852 7.272144 ACTCCCTCTGTTCCTAAATATTTGT 57.728 36.000 11.05 0.00 0.00 2.83
5330 6853 8.487028 AGTACTCCCTCTGTTCCTAAATATTTG 58.513 37.037 11.05 1.40 0.00 2.32
5331 6854 8.487028 CAGTACTCCCTCTGTTCCTAAATATTT 58.513 37.037 5.89 5.89 0.00 1.40
5332 6855 7.624077 ACAGTACTCCCTCTGTTCCTAAATATT 59.376 37.037 0.00 0.00 41.33 1.28
5333 6856 7.133483 ACAGTACTCCCTCTGTTCCTAAATAT 58.867 38.462 0.00 0.00 41.33 1.28
5334 6857 6.500336 ACAGTACTCCCTCTGTTCCTAAATA 58.500 40.000 0.00 0.00 41.33 1.40
5335 6858 5.342866 ACAGTACTCCCTCTGTTCCTAAAT 58.657 41.667 0.00 0.00 41.33 1.40
5336 6859 4.748701 ACAGTACTCCCTCTGTTCCTAAA 58.251 43.478 0.00 0.00 41.33 1.85
5337 6860 4.399483 ACAGTACTCCCTCTGTTCCTAA 57.601 45.455 0.00 0.00 41.33 2.69
5343 6866 4.409247 ACTTCAAAACAGTACTCCCTCTGT 59.591 41.667 0.00 0.00 45.21 3.41
5344 6867 4.962155 ACTTCAAAACAGTACTCCCTCTG 58.038 43.478 0.00 0.00 37.65 3.35
5345 6868 5.839606 ACTACTTCAAAACAGTACTCCCTCT 59.160 40.000 0.00 0.00 0.00 3.69
5346 6869 6.099159 ACTACTTCAAAACAGTACTCCCTC 57.901 41.667 0.00 0.00 0.00 4.30
5347 6870 6.781507 ACTACTACTTCAAAACAGTACTCCCT 59.218 38.462 0.00 0.00 0.00 4.20
5348 6871 6.990798 ACTACTACTTCAAAACAGTACTCCC 58.009 40.000 0.00 0.00 0.00 4.30
5349 6872 9.404348 GTTACTACTACTTCAAAACAGTACTCC 57.596 37.037 0.00 0.00 0.00 3.85
5467 6990 6.552445 AGTCTCAACAATAGTAGCCTGAAT 57.448 37.500 0.00 0.00 0.00 2.57
5479 7002 3.539604 GCCAGATGCTAGTCTCAACAAT 58.460 45.455 0.00 0.00 36.87 2.71
5548 7071 6.717540 TCCTCTCCATCTCAAATACTAGCTAC 59.282 42.308 0.00 0.00 0.00 3.58
5549 7072 6.853490 TCCTCTCCATCTCAAATACTAGCTA 58.147 40.000 0.00 0.00 0.00 3.32
5550 7073 5.710646 TCCTCTCCATCTCAAATACTAGCT 58.289 41.667 0.00 0.00 0.00 3.32
5605 7128 3.215975 AGATAGTCGTTCACCTCTAGGC 58.784 50.000 0.00 0.00 39.32 3.93
5606 7129 7.513371 AAATAGATAGTCGTTCACCTCTAGG 57.487 40.000 0.00 0.00 42.17 3.02
5607 7130 9.881529 GTAAAATAGATAGTCGTTCACCTCTAG 57.118 37.037 0.00 0.00 0.00 2.43
5608 7131 8.844244 GGTAAAATAGATAGTCGTTCACCTCTA 58.156 37.037 0.00 0.00 0.00 2.43
5715 7238 3.994392 TCTGCCGAAACAGAGTAATGAAC 59.006 43.478 0.00 0.00 41.72 3.18
5732 7255 0.531974 TCGGCCATAATCGTTCTGCC 60.532 55.000 2.24 0.00 35.55 4.85
5745 7268 1.303236 CAAATCCCACTGTCGGCCA 60.303 57.895 2.24 0.00 0.00 5.36
5764 7287 6.377146 GGAGCAACCAATTAAGTCCTGAATAA 59.623 38.462 0.00 0.00 38.79 1.40
5862 7385 3.057174 ACAGAGTGATCGACTGACCTTTC 60.057 47.826 16.54 0.00 33.83 2.62
5896 7419 7.550551 TGTTGAGATGCTGAACTAAGAATAAGG 59.449 37.037 0.00 0.00 29.40 2.69
5975 7498 4.579340 CCAATCATCATTCCAAGACTCCAG 59.421 45.833 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.