Multiple sequence alignment - TraesCS2D01G066400

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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 TraesCS2D01G066400 chr2D 100.000 5294 0 0 1 5294 27955835 27961128 0.000000e+00 9777.0
1 TraesCS2D01G066400 chr2D 89.864 3759 326 35 600 4324 28002144 27998407 0.000000e+00 4780.0
2 TraesCS2D01G066400 chr2D 87.726 2705 254 53 4 2682 28010168 28007516 0.000000e+00 3085.0
3 TraesCS2D01G066400 chr2D 83.889 2129 312 15 2193 4314 28417361 28415257 0.000000e+00 2002.0
4 TraesCS2D01G066400 chr2D 85.774 1434 150 34 1 1401 28095651 28094239 0.000000e+00 1469.0
5 TraesCS2D01G066400 chr2D 89.474 551 29 8 4582 5125 27976140 27975612 0.000000e+00 669.0
6 TraesCS2D01G066400 chr2D 98.551 207 3 0 4359 4565 585852672 585852466 3.010000e-97 366.0
7 TraesCS2D01G066400 chr2D 78.542 480 56 27 80 540 28002625 28002174 6.760000e-69 272.0
8 TraesCS2D01G066400 chr2D 93.750 144 7 2 4423 4566 86157123 86157264 1.150000e-51 215.0
9 TraesCS2D01G066400 chr2D 92.361 144 9 2 4423 4566 86330915 86331056 2.500000e-48 204.0
10 TraesCS2D01G066400 chr2D 84.000 200 31 1 4366 4565 580064086 580064284 1.950000e-44 191.0
11 TraesCS2D01G066400 chr2D 80.603 232 26 7 403 633 28005138 28004925 1.530000e-35 161.0
12 TraesCS2D01G066400 chr2A 92.880 4284 275 17 54 4324 30165830 30161564 0.000000e+00 6194.0
13 TraesCS2D01G066400 chr2A 85.020 3331 465 17 996 4315 30300995 30304302 0.000000e+00 3356.0
14 TraesCS2D01G066400 chr2A 84.065 3326 495 21 997 4314 30272083 30268785 0.000000e+00 3173.0
15 TraesCS2D01G066400 chr2A 86.611 2629 259 60 81 2682 30188920 30186358 0.000000e+00 2819.0
16 TraesCS2D01G066400 chr2A 90.213 705 56 12 605 1303 30212922 30212225 0.000000e+00 907.0
17 TraesCS2D01G066400 chr2A 89.349 169 15 2 4398 4566 86451751 86451916 5.370000e-50 209.0
18 TraesCS2D01G066400 chr2B 94.263 3730 158 19 638 4360 45033456 45029776 0.000000e+00 5651.0
19 TraesCS2D01G066400 chr2B 87.690 4070 424 49 285 4324 44755401 44751379 0.000000e+00 4669.0
20 TraesCS2D01G066400 chr2B 96.238 2499 91 2 1863 4360 45135922 45133426 0.000000e+00 4091.0
21 TraesCS2D01G066400 chr2B 88.954 2734 298 4 956 3688 45542365 45545095 0.000000e+00 3373.0
22 TraesCS2D01G066400 chr2B 93.281 2039 108 12 2185 4197 45667347 45669382 0.000000e+00 2979.0
23 TraesCS2D01G066400 chr2B 88.809 2091 202 20 604 2682 45041697 45039627 0.000000e+00 2536.0
24 TraesCS2D01G066400 chr2B 90.983 1841 125 18 54 1865 45137781 45135953 0.000000e+00 2442.0
25 TraesCS2D01G066400 chr2B 91.484 1456 112 4 1570 3022 45689269 45690715 0.000000e+00 1991.0
26 TraesCS2D01G066400 chr2B 90.091 1423 81 25 1 1398 45687809 45689196 0.000000e+00 1792.0
27 TraesCS2D01G066400 chr2B 83.053 1369 208 11 2948 4314 44926463 44927809 0.000000e+00 1221.0
28 TraesCS2D01G066400 chr2B 82.859 1371 207 13 2948 4314 45625117 45626463 0.000000e+00 1205.0
29 TraesCS2D01G066400 chr2B 87.845 724 41 18 4582 5294 45133393 45132706 0.000000e+00 806.0
30 TraesCS2D01G066400 chr2B 90.347 404 30 8 4893 5294 44974316 44973920 6.080000e-144 521.0
31 TraesCS2D01G066400 chr2B 85.417 384 45 9 4616 4997 44751250 44750876 6.430000e-104 388.0
32 TraesCS2D01G066400 chr2B 92.946 241 9 1 4649 4889 45029708 45029476 1.410000e-90 344.0
33 TraesCS2D01G066400 chr2B 82.597 385 51 11 4616 4997 45669980 45670351 5.110000e-85 326.0
34 TraesCS2D01G066400 chr2B 83.891 329 46 6 4671 4997 45546428 45546751 1.850000e-79 307.0
35 TraesCS2D01G066400 chr2B 93.750 160 7 3 4406 4565 139087891 139088047 2.460000e-58 237.0
36 TraesCS2D01G066400 chr2B 94.681 94 5 0 1 94 45687149 45687242 4.270000e-31 147.0
37 TraesCS2D01G066400 chr2B 90.588 85 8 0 368 452 45033672 45033588 4.330000e-21 113.0
38 TraesCS2D01G066400 chr2B 92.157 51 4 0 5071 5121 45553879 45553929 7.350000e-09 73.1
39 TraesCS2D01G066400 chr1D 96.667 210 7 0 4359 4568 488701365 488701156 3.030000e-92 350.0
40 TraesCS2D01G066400 chr3B 95.192 208 10 0 4359 4566 7497643 7497436 3.950000e-86 329.0
41 TraesCS2D01G066400 chr3B 77.723 202 43 2 4367 4567 182753710 182753910 7.200000e-24 122.0
42 TraesCS2D01G066400 chr1A 78.962 366 52 19 432 778 240953956 240953597 5.330000e-55 226.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G066400 chr2D 27955835 27961128 5293 False 9777.000000 9777 100.000000 1 5294 1 chr2D.!!$F1 5293
1 TraesCS2D01G066400 chr2D 27998407 28010168 11761 True 2074.500000 4780 84.183750 4 4324 4 chr2D.!!$R5 4320
2 TraesCS2D01G066400 chr2D 28415257 28417361 2104 True 2002.000000 2002 83.889000 2193 4314 1 chr2D.!!$R3 2121
3 TraesCS2D01G066400 chr2D 28094239 28095651 1412 True 1469.000000 1469 85.774000 1 1401 1 chr2D.!!$R2 1400
4 TraesCS2D01G066400 chr2D 27975612 27976140 528 True 669.000000 669 89.474000 4582 5125 1 chr2D.!!$R1 543
5 TraesCS2D01G066400 chr2A 30161564 30165830 4266 True 6194.000000 6194 92.880000 54 4324 1 chr2A.!!$R1 4270
6 TraesCS2D01G066400 chr2A 30300995 30304302 3307 False 3356.000000 3356 85.020000 996 4315 1 chr2A.!!$F1 3319
7 TraesCS2D01G066400 chr2A 30268785 30272083 3298 True 3173.000000 3173 84.065000 997 4314 1 chr2A.!!$R4 3317
8 TraesCS2D01G066400 chr2A 30186358 30188920 2562 True 2819.000000 2819 86.611000 81 2682 1 chr2A.!!$R2 2601
9 TraesCS2D01G066400 chr2A 30212225 30212922 697 True 907.000000 907 90.213000 605 1303 1 chr2A.!!$R3 698
10 TraesCS2D01G066400 chr2B 45039627 45041697 2070 True 2536.000000 2536 88.809000 604 2682 1 chr2B.!!$R2 2078
11 TraesCS2D01G066400 chr2B 44750876 44755401 4525 True 2528.500000 4669 86.553500 285 4997 2 chr2B.!!$R3 4712
12 TraesCS2D01G066400 chr2B 45132706 45137781 5075 True 2446.333333 4091 91.688667 54 5294 3 chr2B.!!$R5 5240
13 TraesCS2D01G066400 chr2B 45029476 45033672 4196 True 2036.000000 5651 92.599000 368 4889 3 chr2B.!!$R4 4521
14 TraesCS2D01G066400 chr2B 45542365 45546751 4386 False 1840.000000 3373 86.422500 956 4997 2 chr2B.!!$F5 4041
15 TraesCS2D01G066400 chr2B 45667347 45670351 3004 False 1652.500000 2979 87.939000 2185 4997 2 chr2B.!!$F6 2812
16 TraesCS2D01G066400 chr2B 45687149 45690715 3566 False 1310.000000 1991 92.085333 1 3022 3 chr2B.!!$F7 3021
17 TraesCS2D01G066400 chr2B 44926463 44927809 1346 False 1221.000000 1221 83.053000 2948 4314 1 chr2B.!!$F1 1366
18 TraesCS2D01G066400 chr2B 45625117 45626463 1346 False 1205.000000 1205 82.859000 2948 4314 1 chr2B.!!$F3 1366

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
636 1416 0.246635 ACAGTCACGGTATGAGGCAC 59.753 55.0 0.00 0.0 38.28 5.01 F
1130 1963 0.040067 CTTTGCTTCAAGTCCGGCAC 60.040 55.0 0.00 0.0 34.30 5.01 F
2187 3056 1.322442 GCTCCCAGCTGACAAAGTTT 58.678 50.0 17.39 0.0 38.45 2.66 F
2959 11323 2.497675 CTCTGTTCGAATTCCTCCAGGA 59.502 50.0 0.00 0.0 43.73 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1950 2819 4.974399 CCATAATTAGGGACTGGAGGTTC 58.026 47.826 10.74 0.0 41.52 3.62 R
2902 11266 5.664294 TCCAAAAGTACTGCGGTAGAATA 57.336 39.130 5.39 0.0 0.00 1.75 R
3788 12631 1.697432 TGTACCCAACTGTTCCTCCAG 59.303 52.381 0.00 0.0 38.45 3.86 R
4458 13665 1.067295 TCCCAGAATTCAGGCACACT 58.933 50.000 11.31 0.0 0.00 3.55 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
39 40 4.742201 TCGAACGCCTCCAGCTGC 62.742 66.667 8.66 0.00 40.39 5.25
50 710 0.619832 TCCAGCTGCTCCTCTCCATT 60.620 55.000 8.66 0.00 0.00 3.16
146 830 2.758737 CGCCTAGGGTTCCTCCGT 60.759 66.667 11.72 0.00 34.61 4.69
147 831 2.356780 CGCCTAGGGTTCCTCCGTT 61.357 63.158 11.72 0.00 34.61 4.44
148 832 1.521141 GCCTAGGGTTCCTCCGTTC 59.479 63.158 11.72 0.00 34.61 3.95
149 833 1.814527 CCTAGGGTTCCTCCGTTCG 59.185 63.158 0.00 0.00 34.61 3.95
150 834 1.673808 CCTAGGGTTCCTCCGTTCGG 61.674 65.000 0.00 4.74 34.61 4.30
151 835 0.682209 CTAGGGTTCCTCCGTTCGGA 60.682 60.000 13.34 13.34 34.61 4.55
152 836 0.251742 TAGGGTTCCTCCGTTCGGAA 60.252 55.000 14.79 0.00 38.18 4.30
366 1084 8.201464 TGAAATGCAGTTATCTACTCGGAATTA 58.799 33.333 0.00 0.00 33.85 1.40
553 1325 0.895100 TTCAGCGGCTCAATGGCTTT 60.895 50.000 0.00 0.00 39.32 3.51
570 1342 1.134175 CTTTGTTTGCCTTGGTGTCGT 59.866 47.619 0.00 0.00 0.00 4.34
613 1386 0.523072 GTTTGATGTGTGCTCGGCAT 59.477 50.000 1.90 0.00 41.91 4.40
633 1413 3.861276 TGTTACAGTCACGGTATGAGG 57.139 47.619 0.00 0.00 38.28 3.86
636 1416 0.246635 ACAGTCACGGTATGAGGCAC 59.753 55.000 0.00 0.00 38.28 5.01
669 1449 0.681733 ACATCCTTGTGTCGCTGTCT 59.318 50.000 0.00 0.00 33.85 3.41
670 1450 1.073964 CATCCTTGTGTCGCTGTCTG 58.926 55.000 0.00 0.00 0.00 3.51
700 1486 5.640158 TCACCTTTCCTCTTCCAGTTTTA 57.360 39.130 0.00 0.00 0.00 1.52
820 1623 2.406452 CTTGCAACACGTTCAGGGCC 62.406 60.000 0.00 0.00 0.00 5.80
882 1699 1.410083 GCATAACTCCAGGCCCATTCA 60.410 52.381 0.00 0.00 0.00 2.57
1130 1963 0.040067 CTTTGCTTCAAGTCCGGCAC 60.040 55.000 0.00 0.00 34.30 5.01
1189 2023 6.305693 GTGATGACTCACTTAACTTTTGCT 57.694 37.500 0.00 0.00 46.84 3.91
1197 2031 4.584325 TCACTTAACTTTTGCTGCTGGAAT 59.416 37.500 0.00 0.00 0.00 3.01
1387 2222 2.489938 TCCAAACCTCCATACACTGC 57.510 50.000 0.00 0.00 0.00 4.40
1424 2259 3.004752 CCTTGAAGGTAACATCCCTGG 57.995 52.381 2.25 0.00 41.41 4.45
1457 2292 5.107143 GCACTAGCAATTCTCTTAGCTATGC 60.107 44.000 5.31 5.31 38.73 3.14
1950 2819 2.743636 ACATTGGTCACTCACTACCG 57.256 50.000 0.00 0.00 38.70 4.02
2187 3056 1.322442 GCTCCCAGCTGACAAAGTTT 58.678 50.000 17.39 0.00 38.45 2.66
2902 11266 4.168101 TCCTACAAGTGGGATCTTTGAGT 58.832 43.478 0.69 0.00 35.16 3.41
2959 11323 2.497675 CTCTGTTCGAATTCCTCCAGGA 59.502 50.000 0.00 0.00 43.73 3.86
3160 11524 5.679638 GCTGTTGTGTCCAAGAAGATGTTTT 60.680 40.000 0.00 0.00 0.00 2.43
3310 11676 2.906389 AGCTCAACCTGTACTGGATCAA 59.094 45.455 24.19 6.74 0.00 2.57
3642 12008 4.820716 GCTTCTGCTCTTGATTATGTCCAT 59.179 41.667 0.00 0.00 36.03 3.41
3788 12631 1.030457 CCTGAAAGCCTGGATGATGC 58.970 55.000 0.00 0.00 36.07 3.91
4035 12879 3.024547 GCTTACCCTTCCCATTTTCTCC 58.975 50.000 0.00 0.00 0.00 3.71
4053 12899 1.486310 TCCGAATCCATGTTCCCTGAG 59.514 52.381 0.00 0.00 0.00 3.35
4056 12902 2.169352 CGAATCCATGTTCCCTGAGAGT 59.831 50.000 0.00 0.00 0.00 3.24
4334 13541 9.162764 GAATGTAGTAACATGTTCATTGTACCT 57.837 33.333 21.39 7.43 45.79 3.08
4362 13569 2.178912 TGACGAACTGGATGAAACCC 57.821 50.000 0.00 0.00 0.00 4.11
4365 13572 0.804989 CGAACTGGATGAAACCCTGC 59.195 55.000 0.00 0.00 0.00 4.85
4366 13573 1.611673 CGAACTGGATGAAACCCTGCT 60.612 52.381 0.00 0.00 0.00 4.24
4368 13575 0.038744 ACTGGATGAAACCCTGCTGG 59.961 55.000 1.89 1.89 41.37 4.85
4369 13576 1.304381 TGGATGAAACCCTGCTGGC 60.304 57.895 3.63 0.00 37.83 4.85
4371 13578 0.255890 GGATGAAACCCTGCTGGCTA 59.744 55.000 3.63 0.00 37.83 3.93
4372 13579 1.133668 GGATGAAACCCTGCTGGCTAT 60.134 52.381 3.63 0.00 37.83 2.97
4374 13581 0.034186 TGAAACCCTGCTGGCTATGG 60.034 55.000 3.63 0.00 37.83 2.74
4377 13584 0.929244 AACCCTGCTGGCTATGGATT 59.071 50.000 3.63 0.00 37.83 3.01
4379 13586 1.133668 ACCCTGCTGGCTATGGATTTC 60.134 52.381 3.63 0.00 37.83 2.17
4380 13587 1.144503 CCCTGCTGGCTATGGATTTCT 59.855 52.381 3.63 0.00 0.00 2.52
4381 13588 2.502295 CCTGCTGGCTATGGATTTCTC 58.498 52.381 0.00 0.00 0.00 2.87
4382 13589 2.158711 CCTGCTGGCTATGGATTTCTCA 60.159 50.000 0.00 0.00 0.00 3.27
4384 13591 3.949754 CTGCTGGCTATGGATTTCTCAAA 59.050 43.478 0.00 0.00 0.00 2.69
4385 13592 4.539726 TGCTGGCTATGGATTTCTCAAAT 58.460 39.130 0.00 0.00 0.00 2.32
4388 13595 6.432162 TGCTGGCTATGGATTTCTCAAATATC 59.568 38.462 0.00 0.00 0.00 1.63
4389 13596 6.432162 GCTGGCTATGGATTTCTCAAATATCA 59.568 38.462 0.00 0.00 0.00 2.15
4390 13597 7.574592 GCTGGCTATGGATTTCTCAAATATCAC 60.575 40.741 0.00 0.00 0.00 3.06
4391 13598 7.520798 TGGCTATGGATTTCTCAAATATCACT 58.479 34.615 0.00 0.00 0.00 3.41
4392 13599 8.000709 TGGCTATGGATTTCTCAAATATCACTT 58.999 33.333 0.00 0.00 0.00 3.16
4393 13600 8.854117 GGCTATGGATTTCTCAAATATCACTTT 58.146 33.333 0.00 0.00 0.00 2.66
4398 13605 9.912634 TGGATTTCTCAAATATCACTTTTGTTC 57.087 29.630 0.00 0.00 35.90 3.18
4399 13606 9.912634 GGATTTCTCAAATATCACTTTTGTTCA 57.087 29.630 0.00 0.00 35.90 3.18
4403 13610 8.746922 TCTCAAATATCACTTTTGTTCAATGC 57.253 30.769 0.00 0.00 35.90 3.56
4404 13611 8.579006 TCTCAAATATCACTTTTGTTCAATGCT 58.421 29.630 0.00 0.00 35.90 3.79
4405 13612 8.523523 TCAAATATCACTTTTGTTCAATGCTG 57.476 30.769 0.00 0.00 35.90 4.41
4406 13613 8.143193 TCAAATATCACTTTTGTTCAATGCTGT 58.857 29.630 0.00 0.00 35.90 4.40
4407 13614 9.409312 CAAATATCACTTTTGTTCAATGCTGTA 57.591 29.630 0.00 0.00 31.05 2.74
4408 13615 9.630098 AAATATCACTTTTGTTCAATGCTGTAG 57.370 29.630 0.00 0.00 0.00 2.74
4409 13616 5.437289 TCACTTTTGTTCAATGCTGTAGG 57.563 39.130 0.00 0.00 0.00 3.18
4410 13617 4.278170 TCACTTTTGTTCAATGCTGTAGGG 59.722 41.667 0.00 0.00 0.00 3.53
4411 13618 4.278170 CACTTTTGTTCAATGCTGTAGGGA 59.722 41.667 0.00 0.00 0.00 4.20
4412 13619 4.892934 ACTTTTGTTCAATGCTGTAGGGAA 59.107 37.500 0.00 0.00 0.00 3.97
4413 13620 5.010012 ACTTTTGTTCAATGCTGTAGGGAAG 59.990 40.000 0.00 0.00 0.00 3.46
4414 13621 2.436417 TGTTCAATGCTGTAGGGAAGC 58.564 47.619 0.00 0.00 41.22 3.86
4415 13622 2.040278 TGTTCAATGCTGTAGGGAAGCT 59.960 45.455 0.00 0.00 41.42 3.74
4416 13623 3.263170 TGTTCAATGCTGTAGGGAAGCTA 59.737 43.478 0.00 0.00 41.42 3.32
4417 13624 4.261801 GTTCAATGCTGTAGGGAAGCTAA 58.738 43.478 0.00 0.00 41.42 3.09
4418 13625 4.778213 TCAATGCTGTAGGGAAGCTAAT 57.222 40.909 0.00 0.00 41.42 1.73
4419 13626 4.708177 TCAATGCTGTAGGGAAGCTAATC 58.292 43.478 0.00 0.00 41.42 1.75
4420 13627 4.410228 TCAATGCTGTAGGGAAGCTAATCT 59.590 41.667 0.00 0.00 41.42 2.40
4421 13628 5.104360 TCAATGCTGTAGGGAAGCTAATCTT 60.104 40.000 0.00 0.00 41.42 2.40
4422 13629 6.099701 TCAATGCTGTAGGGAAGCTAATCTTA 59.900 38.462 0.00 0.00 41.42 2.10
4423 13630 6.694445 ATGCTGTAGGGAAGCTAATCTTAT 57.306 37.500 0.00 0.00 41.42 1.73
4424 13631 6.500589 TGCTGTAGGGAAGCTAATCTTATT 57.499 37.500 0.00 0.00 41.42 1.40
4425 13632 6.291377 TGCTGTAGGGAAGCTAATCTTATTG 58.709 40.000 0.00 0.00 41.42 1.90
4426 13633 5.180304 GCTGTAGGGAAGCTAATCTTATTGC 59.820 44.000 0.00 0.00 37.69 3.56
4427 13634 5.297547 TGTAGGGAAGCTAATCTTATTGCG 58.702 41.667 0.00 0.00 34.56 4.85
4428 13635 3.744660 AGGGAAGCTAATCTTATTGCGG 58.255 45.455 0.00 0.00 34.56 5.69
4429 13636 3.391296 AGGGAAGCTAATCTTATTGCGGA 59.609 43.478 0.00 0.00 34.56 5.54
4430 13637 4.042187 AGGGAAGCTAATCTTATTGCGGAT 59.958 41.667 0.00 0.00 34.56 4.18
4431 13638 4.762251 GGGAAGCTAATCTTATTGCGGATT 59.238 41.667 0.00 0.00 34.56 3.01
4432 13639 5.335191 GGGAAGCTAATCTTATTGCGGATTG 60.335 44.000 0.00 0.00 34.56 2.67
4433 13640 5.239525 GGAAGCTAATCTTATTGCGGATTGT 59.760 40.000 0.00 0.00 34.56 2.71
4434 13641 6.238759 GGAAGCTAATCTTATTGCGGATTGTT 60.239 38.462 0.00 0.00 34.56 2.83
4435 13642 6.699575 AGCTAATCTTATTGCGGATTGTTT 57.300 33.333 0.00 0.00 34.52 2.83
4436 13643 6.498304 AGCTAATCTTATTGCGGATTGTTTG 58.502 36.000 0.00 0.00 34.52 2.93
4437 13644 5.687285 GCTAATCTTATTGCGGATTGTTTGG 59.313 40.000 0.00 0.00 34.52 3.28
4438 13645 3.502191 TCTTATTGCGGATTGTTTGGC 57.498 42.857 0.00 0.00 0.00 4.52
4439 13646 2.822561 TCTTATTGCGGATTGTTTGGCA 59.177 40.909 0.00 0.00 0.00 4.92
4441 13648 2.540265 ATTGCGGATTGTTTGGCAAA 57.460 40.000 8.93 8.93 46.97 3.68
4442 13649 2.315925 TTGCGGATTGTTTGGCAAAA 57.684 40.000 15.29 0.00 41.90 2.44
4443 13650 1.576356 TGCGGATTGTTTGGCAAAAC 58.424 45.000 15.29 9.94 45.00 2.43
4453 13660 4.777140 GTTTGGCAAAACACTGCTTTAG 57.223 40.909 15.29 0.00 44.30 1.85
4454 13661 4.429108 GTTTGGCAAAACACTGCTTTAGA 58.571 39.130 15.29 0.00 44.30 2.10
4455 13662 4.935352 TTGGCAAAACACTGCTTTAGAT 57.065 36.364 0.00 0.00 42.25 1.98
4456 13663 4.503741 TGGCAAAACACTGCTTTAGATC 57.496 40.909 0.00 0.00 42.25 2.75
4457 13664 4.144297 TGGCAAAACACTGCTTTAGATCT 58.856 39.130 0.00 0.00 42.25 2.75
4458 13665 5.312895 TGGCAAAACACTGCTTTAGATCTA 58.687 37.500 0.00 0.00 42.25 1.98
4459 13666 5.412594 TGGCAAAACACTGCTTTAGATCTAG 59.587 40.000 2.02 0.00 42.25 2.43
4460 13667 5.412904 GGCAAAACACTGCTTTAGATCTAGT 59.587 40.000 2.02 0.00 42.25 2.57
4461 13668 6.310197 GCAAAACACTGCTTTAGATCTAGTG 58.690 40.000 17.34 17.34 43.20 2.74
4465 13672 3.868077 CACTGCTTTAGATCTAGTGTGCC 59.132 47.826 12.57 0.00 35.30 5.01
4466 13673 3.772025 ACTGCTTTAGATCTAGTGTGCCT 59.228 43.478 2.02 0.00 0.00 4.75
4467 13674 4.118410 CTGCTTTAGATCTAGTGTGCCTG 58.882 47.826 2.02 0.22 0.00 4.85
4468 13675 3.769300 TGCTTTAGATCTAGTGTGCCTGA 59.231 43.478 2.02 0.00 0.00 3.86
4469 13676 4.222810 TGCTTTAGATCTAGTGTGCCTGAA 59.777 41.667 2.02 0.00 0.00 3.02
4470 13677 5.104776 TGCTTTAGATCTAGTGTGCCTGAAT 60.105 40.000 2.02 0.00 0.00 2.57
4471 13678 5.819901 GCTTTAGATCTAGTGTGCCTGAATT 59.180 40.000 2.02 0.00 0.00 2.17
4472 13679 6.018343 GCTTTAGATCTAGTGTGCCTGAATTC 60.018 42.308 2.02 0.00 0.00 2.17
4473 13680 6.798427 TTAGATCTAGTGTGCCTGAATTCT 57.202 37.500 7.05 0.00 0.00 2.40
4474 13681 5.021033 AGATCTAGTGTGCCTGAATTCTG 57.979 43.478 7.05 6.17 0.00 3.02
4475 13682 3.616956 TCTAGTGTGCCTGAATTCTGG 57.383 47.619 23.32 23.32 37.93 3.86
4476 13683 2.237143 TCTAGTGTGCCTGAATTCTGGG 59.763 50.000 27.06 19.35 35.73 4.45
4477 13684 1.067295 AGTGTGCCTGAATTCTGGGA 58.933 50.000 27.06 23.53 35.73 4.37
4478 13685 1.637553 AGTGTGCCTGAATTCTGGGAT 59.362 47.619 27.06 11.50 37.59 3.85
4479 13686 2.042162 AGTGTGCCTGAATTCTGGGATT 59.958 45.455 27.06 14.62 37.59 3.01
4480 13687 2.424956 GTGTGCCTGAATTCTGGGATTC 59.575 50.000 27.06 18.65 37.59 2.52
4481 13688 2.309755 TGTGCCTGAATTCTGGGATTCT 59.690 45.455 27.06 0.00 37.59 2.40
4482 13689 3.523157 TGTGCCTGAATTCTGGGATTCTA 59.477 43.478 27.06 13.20 37.59 2.10
4483 13690 4.166725 TGTGCCTGAATTCTGGGATTCTAT 59.833 41.667 27.06 0.00 37.59 1.98
4484 13691 5.136105 GTGCCTGAATTCTGGGATTCTATT 58.864 41.667 27.06 0.00 37.59 1.73
4485 13692 5.009410 GTGCCTGAATTCTGGGATTCTATTG 59.991 44.000 27.06 4.12 37.59 1.90
4486 13693 4.022503 GCCTGAATTCTGGGATTCTATTGC 60.023 45.833 27.06 9.49 37.04 3.56
4487 13694 5.383476 CCTGAATTCTGGGATTCTATTGCT 58.617 41.667 20.70 0.00 37.04 3.91
4488 13695 5.472820 CCTGAATTCTGGGATTCTATTGCTC 59.527 44.000 20.70 0.00 37.04 4.26
4489 13696 5.380043 TGAATTCTGGGATTCTATTGCTCC 58.620 41.667 7.05 0.00 37.04 4.70
4490 13697 5.133322 TGAATTCTGGGATTCTATTGCTCCT 59.867 40.000 7.05 0.00 37.04 3.69
4491 13698 4.428294 TTCTGGGATTCTATTGCTCCTG 57.572 45.455 0.00 0.00 0.00 3.86
4492 13699 3.657610 TCTGGGATTCTATTGCTCCTGA 58.342 45.455 0.00 0.00 0.00 3.86
4493 13700 3.389329 TCTGGGATTCTATTGCTCCTGAC 59.611 47.826 0.00 0.00 0.00 3.51
4494 13701 3.387962 TGGGATTCTATTGCTCCTGACT 58.612 45.455 0.00 0.00 0.00 3.41
4495 13702 3.782523 TGGGATTCTATTGCTCCTGACTT 59.217 43.478 0.00 0.00 0.00 3.01
4496 13703 4.228210 TGGGATTCTATTGCTCCTGACTTT 59.772 41.667 0.00 0.00 0.00 2.66
4497 13704 5.428457 TGGGATTCTATTGCTCCTGACTTTA 59.572 40.000 0.00 0.00 0.00 1.85
4498 13705 6.101734 TGGGATTCTATTGCTCCTGACTTTAT 59.898 38.462 0.00 0.00 0.00 1.40
4499 13706 7.001073 GGGATTCTATTGCTCCTGACTTTATT 58.999 38.462 0.00 0.00 0.00 1.40
4500 13707 7.174080 GGGATTCTATTGCTCCTGACTTTATTC 59.826 40.741 0.00 0.00 0.00 1.75
4501 13708 7.936301 GGATTCTATTGCTCCTGACTTTATTCT 59.064 37.037 0.00 0.00 0.00 2.40
4502 13709 9.336171 GATTCTATTGCTCCTGACTTTATTCTT 57.664 33.333 0.00 0.00 0.00 2.52
4503 13710 8.723942 TTCTATTGCTCCTGACTTTATTCTTC 57.276 34.615 0.00 0.00 0.00 2.87
4504 13711 7.275920 TCTATTGCTCCTGACTTTATTCTTCC 58.724 38.462 0.00 0.00 0.00 3.46
4505 13712 4.908601 TGCTCCTGACTTTATTCTTCCA 57.091 40.909 0.00 0.00 0.00 3.53
4506 13713 4.579869 TGCTCCTGACTTTATTCTTCCAC 58.420 43.478 0.00 0.00 0.00 4.02
4507 13714 4.041567 TGCTCCTGACTTTATTCTTCCACA 59.958 41.667 0.00 0.00 0.00 4.17
4508 13715 5.003804 GCTCCTGACTTTATTCTTCCACAA 58.996 41.667 0.00 0.00 0.00 3.33
4509 13716 5.473504 GCTCCTGACTTTATTCTTCCACAAA 59.526 40.000 0.00 0.00 0.00 2.83
4510 13717 6.151817 GCTCCTGACTTTATTCTTCCACAAAT 59.848 38.462 0.00 0.00 0.00 2.32
4511 13718 7.309438 GCTCCTGACTTTATTCTTCCACAAATT 60.309 37.037 0.00 0.00 0.00 1.82
4512 13719 7.885297 TCCTGACTTTATTCTTCCACAAATTG 58.115 34.615 0.00 0.00 0.00 2.32
4513 13720 7.505585 TCCTGACTTTATTCTTCCACAAATTGT 59.494 33.333 0.00 0.00 0.00 2.71
4514 13721 8.792633 CCTGACTTTATTCTTCCACAAATTGTA 58.207 33.333 0.00 0.00 0.00 2.41
4518 13725 9.458374 ACTTTATTCTTCCACAAATTGTAAACG 57.542 29.630 0.00 0.00 0.00 3.60
4519 13726 9.672086 CTTTATTCTTCCACAAATTGTAAACGA 57.328 29.630 0.00 0.00 0.00 3.85
4523 13730 9.787532 ATTCTTCCACAAATTGTAAACGATATG 57.212 29.630 0.00 0.00 0.00 1.78
4524 13731 7.757526 TCTTCCACAAATTGTAAACGATATGG 58.242 34.615 0.00 0.00 0.00 2.74
4525 13732 5.885881 TCCACAAATTGTAAACGATATGGC 58.114 37.500 0.00 0.00 0.00 4.40
4526 13733 5.650266 TCCACAAATTGTAAACGATATGGCT 59.350 36.000 0.00 0.00 0.00 4.75
4527 13734 6.824196 TCCACAAATTGTAAACGATATGGCTA 59.176 34.615 0.00 0.00 0.00 3.93
4528 13735 7.500892 TCCACAAATTGTAAACGATATGGCTAT 59.499 33.333 0.00 0.00 0.00 2.97
4529 13736 8.134895 CCACAAATTGTAAACGATATGGCTATT 58.865 33.333 0.00 0.00 0.00 1.73
4530 13737 8.957028 CACAAATTGTAAACGATATGGCTATTG 58.043 33.333 0.00 0.00 0.00 1.90
4531 13738 8.682710 ACAAATTGTAAACGATATGGCTATTGT 58.317 29.630 0.00 0.00 34.03 2.71
4532 13739 9.515020 CAAATTGTAAACGATATGGCTATTGTT 57.485 29.630 0.00 0.00 41.69 2.83
4534 13741 9.515020 AATTGTAAACGATATGGCTATTGTTTG 57.485 29.630 20.68 0.00 45.42 2.93
4535 13742 7.851387 TGTAAACGATATGGCTATTGTTTGA 57.149 32.000 20.68 11.64 45.42 2.69
4536 13743 8.270080 TGTAAACGATATGGCTATTGTTTGAA 57.730 30.769 20.68 12.37 45.42 2.69
4537 13744 8.394877 TGTAAACGATATGGCTATTGTTTGAAG 58.605 33.333 20.68 0.00 45.42 3.02
4538 13745 7.624360 AAACGATATGGCTATTGTTTGAAGA 57.376 32.000 15.51 0.00 44.71 2.87
4539 13746 7.624360 AACGATATGGCTATTGTTTGAAGAA 57.376 32.000 0.00 0.00 38.33 2.52
4540 13747 7.807977 ACGATATGGCTATTGTTTGAAGAAT 57.192 32.000 0.00 0.00 29.08 2.40
4541 13748 8.902540 ACGATATGGCTATTGTTTGAAGAATA 57.097 30.769 0.00 0.00 29.08 1.75
4542 13749 9.337396 ACGATATGGCTATTGTTTGAAGAATAA 57.663 29.630 0.00 0.00 29.08 1.40
4609 13816 7.701078 TGATCAATAGTTCGCTACAGAAAGTAC 59.299 37.037 0.00 0.00 31.66 2.73
4610 13817 7.154435 TCAATAGTTCGCTACAGAAAGTACT 57.846 36.000 0.00 0.00 31.66 2.73
4612 13819 8.900781 TCAATAGTTCGCTACAGAAAGTACTAT 58.099 33.333 0.00 0.00 31.66 2.12
4613 13820 9.171701 CAATAGTTCGCTACAGAAAGTACTATC 57.828 37.037 0.00 0.00 31.66 2.08
4882 14192 4.699257 AGAGGTTTGATTGATGAAGTGCTC 59.301 41.667 0.00 0.00 0.00 4.26
4894 14204 7.043961 TGATGAAGTGCTCCTGTATTAGTAG 57.956 40.000 0.00 0.00 0.00 2.57
4895 14205 6.607600 TGATGAAGTGCTCCTGTATTAGTAGT 59.392 38.462 0.00 0.00 0.00 2.73
4896 14206 7.778382 TGATGAAGTGCTCCTGTATTAGTAGTA 59.222 37.037 0.00 0.00 0.00 1.82
4919 14229 9.233232 AGTAGTGAAAACGAAAGCAATAAAAAG 57.767 29.630 0.00 0.00 0.00 2.27
5153 14471 9.817365 GATTTGTGATATTCCGAACATAGAATG 57.183 33.333 0.00 0.00 34.60 2.67
5171 14489 5.504853 AGAATGATCACCTCTTCTTTTCCC 58.495 41.667 0.00 0.00 0.00 3.97
5183 14501 4.840115 TCTTCTTTTCCCATGCTCCAAATT 59.160 37.500 0.00 0.00 0.00 1.82
5188 14506 0.906775 CCCATGCTCCAAATTGCCTT 59.093 50.000 0.00 0.00 0.00 4.35
5271 14589 6.207614 GGCAACAATAATTCTAGAGATTCCCC 59.792 42.308 0.00 0.00 0.00 4.81
5272 14590 6.207614 GCAACAATAATTCTAGAGATTCCCCC 59.792 42.308 0.00 0.00 0.00 5.40
5273 14591 7.290061 CAACAATAATTCTAGAGATTCCCCCA 58.710 38.462 0.00 0.00 0.00 4.96
5275 14593 8.061890 ACAATAATTCTAGAGATTCCCCCAAT 57.938 34.615 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 2.547642 GCGAGGAATGAATGGAGAGGAG 60.548 54.545 0.00 0.00 0.00 3.69
50 710 1.612146 TGGAGGTGGCGAGGAATGA 60.612 57.895 0.00 0.00 0.00 2.57
140 824 1.445582 CCGAAGTTCCGAACGGAGG 60.446 63.158 15.34 9.59 46.06 4.30
146 830 2.098233 GCGCATCCGAAGTTCCGAA 61.098 57.895 0.30 0.00 36.29 4.30
147 831 2.508439 GCGCATCCGAAGTTCCGA 60.508 61.111 0.30 0.00 36.29 4.55
148 832 2.802667 CTGCGCATCCGAAGTTCCG 61.803 63.158 12.24 0.00 35.32 4.30
149 833 3.093278 CTGCGCATCCGAAGTTCC 58.907 61.111 12.24 0.00 35.32 3.62
553 1325 1.098712 GGACGACACCAAGGCAAACA 61.099 55.000 0.00 0.00 0.00 2.83
570 1342 1.075601 AGGATGAACAAGCCAAGGGA 58.924 50.000 0.00 0.00 0.00 4.20
613 1386 2.094390 GCCTCATACCGTGACTGTAACA 60.094 50.000 0.00 0.00 32.22 2.41
633 1413 3.858238 GGATGTTGTAAGACTAGTCGTGC 59.142 47.826 19.95 18.69 34.09 5.34
636 1416 5.573282 CACAAGGATGTTGTAAGACTAGTCG 59.427 44.000 17.07 0.58 37.82 4.18
669 1449 7.237982 TGGAAGAGGAAAGGTGAATTATTTCA 58.762 34.615 0.00 0.00 39.54 2.69
670 1450 7.394641 ACTGGAAGAGGAAAGGTGAATTATTTC 59.605 37.037 0.00 0.00 37.43 2.17
792 1583 2.218603 ACGTGTTGCAAGGGTAAAGAG 58.781 47.619 0.00 0.00 0.00 2.85
820 1623 1.000060 CAAACAATGGTGGGCTGTCTG 60.000 52.381 0.00 0.00 0.00 3.51
882 1699 2.514458 AAGGATTTGTCTGCCGGAAT 57.486 45.000 5.05 0.00 0.00 3.01
1130 1963 4.455606 GATGTCAAGGGGATAAGAGTTGG 58.544 47.826 0.00 0.00 0.00 3.77
1189 2023 1.559368 CAAATGACCCCATTCCAGCA 58.441 50.000 0.00 0.00 41.84 4.41
1197 2031 2.988684 GTGCCGCAAATGACCCCA 60.989 61.111 0.00 0.00 0.00 4.96
1308 2143 5.427378 TCATTATCAGCAAGGTTCATCGAA 58.573 37.500 0.00 0.00 0.00 3.71
1387 2222 5.261209 TCAAGGTTGTTGTTGGAAAGATG 57.739 39.130 0.00 0.00 0.00 2.90
1424 2259 4.518249 AGAATTGCTAGTGCCTAAGGAAC 58.482 43.478 0.00 0.00 38.71 3.62
1457 2292 7.732840 CTGTAAGAGTGTTGTTTCCAAGATTGG 60.733 40.741 5.18 5.18 43.58 3.16
1950 2819 4.974399 CCATAATTAGGGACTGGAGGTTC 58.026 47.826 10.74 0.00 41.52 3.62
2902 11266 5.664294 TCCAAAAGTACTGCGGTAGAATA 57.336 39.130 5.39 0.00 0.00 1.75
3269 11634 5.907207 AGCTGATAGTATGAAGCGAAGAAA 58.093 37.500 8.19 0.00 40.63 2.52
3310 11676 6.943718 TCGGACTTGAACCTACCAAAATAAAT 59.056 34.615 0.00 0.00 0.00 1.40
3642 12008 3.071312 TCAAAGGAGGCGTTAGTTGGTTA 59.929 43.478 0.00 0.00 0.00 2.85
3788 12631 1.697432 TGTACCCAACTGTTCCTCCAG 59.303 52.381 0.00 0.00 38.45 3.86
4035 12879 2.169352 ACTCTCAGGGAACATGGATTCG 59.831 50.000 0.00 0.00 0.00 3.34
4053 12899 1.941294 TCTAGAATCTCCGCGACACTC 59.059 52.381 8.23 0.00 0.00 3.51
4056 12902 1.880675 GGATCTAGAATCTCCGCGACA 59.119 52.381 8.23 0.00 0.00 4.35
4334 13541 8.826710 GTTTCATCCAGTTCGTCATATTGATAA 58.173 33.333 0.00 0.00 0.00 1.75
4336 13543 6.260936 GGTTTCATCCAGTTCGTCATATTGAT 59.739 38.462 0.00 0.00 0.00 2.57
4362 13569 3.204306 TGAGAAATCCATAGCCAGCAG 57.796 47.619 0.00 0.00 0.00 4.24
4365 13572 7.664731 AGTGATATTTGAGAAATCCATAGCCAG 59.335 37.037 0.00 0.00 32.38 4.85
4366 13573 7.520798 AGTGATATTTGAGAAATCCATAGCCA 58.479 34.615 0.00 0.00 32.38 4.75
4372 13579 9.912634 GAACAAAAGTGATATTTGAGAAATCCA 57.087 29.630 6.05 0.00 39.56 3.41
4377 13584 9.195411 GCATTGAACAAAAGTGATATTTGAGAA 57.805 29.630 6.05 0.00 39.56 2.87
4379 13586 8.644619 CAGCATTGAACAAAAGTGATATTTGAG 58.355 33.333 6.05 0.00 39.56 3.02
4380 13587 8.143193 ACAGCATTGAACAAAAGTGATATTTGA 58.857 29.630 6.05 0.00 39.56 2.69
4381 13588 8.301730 ACAGCATTGAACAAAAGTGATATTTG 57.698 30.769 0.00 0.00 42.18 2.32
4382 13589 9.630098 CTACAGCATTGAACAAAAGTGATATTT 57.370 29.630 0.00 0.00 0.00 1.40
4384 13591 7.148018 CCCTACAGCATTGAACAAAAGTGATAT 60.148 37.037 0.00 0.00 0.00 1.63
4385 13592 6.150976 CCCTACAGCATTGAACAAAAGTGATA 59.849 38.462 0.00 0.00 0.00 2.15
4388 13595 4.278170 TCCCTACAGCATTGAACAAAAGTG 59.722 41.667 0.00 0.00 0.00 3.16
4389 13596 4.469657 TCCCTACAGCATTGAACAAAAGT 58.530 39.130 0.00 0.00 0.00 2.66
4390 13597 5.452078 TTCCCTACAGCATTGAACAAAAG 57.548 39.130 0.00 0.00 0.00 2.27
4391 13598 4.261994 GCTTCCCTACAGCATTGAACAAAA 60.262 41.667 0.00 0.00 37.22 2.44
4392 13599 3.255642 GCTTCCCTACAGCATTGAACAAA 59.744 43.478 0.00 0.00 37.22 2.83
4393 13600 2.819608 GCTTCCCTACAGCATTGAACAA 59.180 45.455 0.00 0.00 37.22 2.83
4394 13601 2.040278 AGCTTCCCTACAGCATTGAACA 59.960 45.455 0.00 0.00 39.99 3.18
4395 13602 2.716217 AGCTTCCCTACAGCATTGAAC 58.284 47.619 0.00 0.00 39.99 3.18
4396 13603 4.568072 TTAGCTTCCCTACAGCATTGAA 57.432 40.909 0.00 0.00 39.99 2.69
4397 13604 4.410228 AGATTAGCTTCCCTACAGCATTGA 59.590 41.667 0.00 0.00 39.99 2.57
4398 13605 4.712476 AGATTAGCTTCCCTACAGCATTG 58.288 43.478 0.00 0.00 39.99 2.82
4399 13606 5.379706 AAGATTAGCTTCCCTACAGCATT 57.620 39.130 0.00 0.00 39.99 3.56
4400 13607 6.694445 ATAAGATTAGCTTCCCTACAGCAT 57.306 37.500 0.00 0.00 39.99 3.79
4401 13608 6.291377 CAATAAGATTAGCTTCCCTACAGCA 58.709 40.000 0.00 0.00 39.99 4.41
4402 13609 5.180304 GCAATAAGATTAGCTTCCCTACAGC 59.820 44.000 0.00 0.00 38.05 4.40
4403 13610 5.406780 CGCAATAAGATTAGCTTCCCTACAG 59.593 44.000 0.00 0.00 38.05 2.74
4404 13611 5.297547 CGCAATAAGATTAGCTTCCCTACA 58.702 41.667 0.00 0.00 38.05 2.74
4405 13612 4.691216 CCGCAATAAGATTAGCTTCCCTAC 59.309 45.833 0.00 0.00 38.05 3.18
4406 13613 4.591498 TCCGCAATAAGATTAGCTTCCCTA 59.409 41.667 0.00 0.00 38.05 3.53
4407 13614 3.391296 TCCGCAATAAGATTAGCTTCCCT 59.609 43.478 0.00 0.00 38.05 4.20
4408 13615 3.740115 TCCGCAATAAGATTAGCTTCCC 58.260 45.455 0.00 0.00 38.05 3.97
4409 13616 5.239525 ACAATCCGCAATAAGATTAGCTTCC 59.760 40.000 0.00 0.00 38.05 3.46
4410 13617 6.305693 ACAATCCGCAATAAGATTAGCTTC 57.694 37.500 0.00 0.00 38.05 3.86
4411 13618 6.699575 AACAATCCGCAATAAGATTAGCTT 57.300 33.333 0.00 0.00 40.68 3.74
4412 13619 6.460123 CCAAACAATCCGCAATAAGATTAGCT 60.460 38.462 0.00 0.00 31.55 3.32
4413 13620 5.687285 CCAAACAATCCGCAATAAGATTAGC 59.313 40.000 0.00 0.00 31.55 3.09
4414 13621 5.687285 GCCAAACAATCCGCAATAAGATTAG 59.313 40.000 0.00 0.00 31.55 1.73
4415 13622 5.126222 TGCCAAACAATCCGCAATAAGATTA 59.874 36.000 0.00 0.00 31.55 1.75
4416 13623 4.081752 TGCCAAACAATCCGCAATAAGATT 60.082 37.500 0.00 0.00 32.95 2.40
4417 13624 3.446873 TGCCAAACAATCCGCAATAAGAT 59.553 39.130 0.00 0.00 0.00 2.40
4418 13625 2.822561 TGCCAAACAATCCGCAATAAGA 59.177 40.909 0.00 0.00 0.00 2.10
4419 13626 3.229276 TGCCAAACAATCCGCAATAAG 57.771 42.857 0.00 0.00 0.00 1.73
4420 13627 3.667497 TTGCCAAACAATCCGCAATAA 57.333 38.095 0.00 0.00 36.36 1.40
4421 13628 3.667497 TTTGCCAAACAATCCGCAATA 57.333 38.095 0.00 0.00 40.63 1.90
4422 13629 2.540265 TTTGCCAAACAATCCGCAAT 57.460 40.000 0.00 0.00 40.63 3.56
4423 13630 1.936547 GTTTTGCCAAACAATCCGCAA 59.063 42.857 8.45 0.00 41.85 4.85
4424 13631 1.576356 GTTTTGCCAAACAATCCGCA 58.424 45.000 8.45 0.00 41.85 5.69
4432 13639 4.429108 TCTAAAGCAGTGTTTTGCCAAAC 58.571 39.130 14.50 6.46 45.18 2.93
4433 13640 4.727507 TCTAAAGCAGTGTTTTGCCAAA 57.272 36.364 14.50 0.00 45.18 3.28
4434 13641 4.584325 AGATCTAAAGCAGTGTTTTGCCAA 59.416 37.500 14.50 0.00 45.18 4.52
4435 13642 4.144297 AGATCTAAAGCAGTGTTTTGCCA 58.856 39.130 14.50 0.00 45.18 4.92
4436 13643 4.773323 AGATCTAAAGCAGTGTTTTGCC 57.227 40.909 14.50 2.20 45.18 4.52
4437 13644 6.073003 ACACTAGATCTAAAGCAGTGTTTTGC 60.073 38.462 18.43 2.65 45.62 3.68
4438 13645 7.293745 CACACTAGATCTAAAGCAGTGTTTTG 58.706 38.462 20.63 10.05 45.62 2.44
4439 13646 6.073003 GCACACTAGATCTAAAGCAGTGTTTT 60.073 38.462 20.63 9.99 45.62 2.43
4440 13647 5.409826 GCACACTAGATCTAAAGCAGTGTTT 59.590 40.000 20.63 3.49 45.62 2.83
4441 13648 4.932200 GCACACTAGATCTAAAGCAGTGTT 59.068 41.667 20.63 8.09 45.62 3.32
4443 13650 3.868077 GGCACACTAGATCTAAAGCAGTG 59.132 47.826 17.34 17.34 41.83 3.66
4444 13651 3.772025 AGGCACACTAGATCTAAAGCAGT 59.228 43.478 3.57 0.00 0.00 4.40
4445 13652 4.118410 CAGGCACACTAGATCTAAAGCAG 58.882 47.826 3.57 0.00 0.00 4.24
4446 13653 3.769300 TCAGGCACACTAGATCTAAAGCA 59.231 43.478 3.57 0.00 0.00 3.91
4447 13654 4.392921 TCAGGCACACTAGATCTAAAGC 57.607 45.455 3.57 5.52 0.00 3.51
4448 13655 7.224362 CAGAATTCAGGCACACTAGATCTAAAG 59.776 40.741 8.44 1.94 0.00 1.85
4449 13656 7.044181 CAGAATTCAGGCACACTAGATCTAAA 58.956 38.462 8.44 0.00 0.00 1.85
4450 13657 6.407412 CCAGAATTCAGGCACACTAGATCTAA 60.407 42.308 8.44 0.00 0.00 2.10
4451 13658 5.069648 CCAGAATTCAGGCACACTAGATCTA 59.930 44.000 8.44 1.69 0.00 1.98
4452 13659 4.141756 CCAGAATTCAGGCACACTAGATCT 60.142 45.833 8.44 0.00 0.00 2.75
4453 13660 4.125703 CCAGAATTCAGGCACACTAGATC 58.874 47.826 8.44 0.00 0.00 2.75
4454 13661 3.118112 CCCAGAATTCAGGCACACTAGAT 60.118 47.826 11.31 0.00 0.00 1.98
4455 13662 2.237143 CCCAGAATTCAGGCACACTAGA 59.763 50.000 11.31 0.00 0.00 2.43
4456 13663 2.237143 TCCCAGAATTCAGGCACACTAG 59.763 50.000 11.31 0.00 0.00 2.57
4457 13664 2.265367 TCCCAGAATTCAGGCACACTA 58.735 47.619 11.31 0.00 0.00 2.74
4458 13665 1.067295 TCCCAGAATTCAGGCACACT 58.933 50.000 11.31 0.00 0.00 3.55
4459 13666 2.134789 ATCCCAGAATTCAGGCACAC 57.865 50.000 11.31 0.00 0.00 3.82
4460 13667 2.309755 AGAATCCCAGAATTCAGGCACA 59.690 45.455 11.31 0.00 37.98 4.57
4461 13668 3.010200 AGAATCCCAGAATTCAGGCAC 57.990 47.619 11.31 2.85 37.98 5.01
4462 13669 5.135383 CAATAGAATCCCAGAATTCAGGCA 58.865 41.667 11.31 0.00 37.98 4.75
4463 13670 4.022503 GCAATAGAATCCCAGAATTCAGGC 60.023 45.833 11.31 0.00 37.98 4.85
4464 13671 5.383476 AGCAATAGAATCCCAGAATTCAGG 58.617 41.667 9.87 9.87 37.98 3.86
4465 13672 5.472820 GGAGCAATAGAATCCCAGAATTCAG 59.527 44.000 8.44 0.00 37.98 3.02
4466 13673 5.133322 AGGAGCAATAGAATCCCAGAATTCA 59.867 40.000 8.44 0.00 37.98 2.57
4467 13674 5.472820 CAGGAGCAATAGAATCCCAGAATTC 59.527 44.000 0.00 0.00 36.16 2.17
4468 13675 5.133322 TCAGGAGCAATAGAATCCCAGAATT 59.867 40.000 0.00 0.00 33.30 2.17
4469 13676 4.662179 TCAGGAGCAATAGAATCCCAGAAT 59.338 41.667 0.00 0.00 33.30 2.40
4470 13677 4.040047 TCAGGAGCAATAGAATCCCAGAA 58.960 43.478 0.00 0.00 33.30 3.02
4471 13678 3.389329 GTCAGGAGCAATAGAATCCCAGA 59.611 47.826 0.00 0.00 33.30 3.86
4472 13679 3.390639 AGTCAGGAGCAATAGAATCCCAG 59.609 47.826 0.00 0.00 33.30 4.45
4473 13680 3.387962 AGTCAGGAGCAATAGAATCCCA 58.612 45.455 0.00 0.00 33.30 4.37
4474 13681 4.429854 AAGTCAGGAGCAATAGAATCCC 57.570 45.455 0.00 0.00 33.30 3.85
4475 13682 7.936301 AGAATAAAGTCAGGAGCAATAGAATCC 59.064 37.037 0.00 0.00 0.00 3.01
4476 13683 8.900983 AGAATAAAGTCAGGAGCAATAGAATC 57.099 34.615 0.00 0.00 0.00 2.52
4477 13684 9.336171 GAAGAATAAAGTCAGGAGCAATAGAAT 57.664 33.333 0.00 0.00 0.00 2.40
4478 13685 7.770897 GGAAGAATAAAGTCAGGAGCAATAGAA 59.229 37.037 0.00 0.00 0.00 2.10
4479 13686 7.092891 TGGAAGAATAAAGTCAGGAGCAATAGA 60.093 37.037 0.00 0.00 0.00 1.98
4480 13687 7.011857 GTGGAAGAATAAAGTCAGGAGCAATAG 59.988 40.741 0.00 0.00 0.00 1.73
4481 13688 6.823689 GTGGAAGAATAAAGTCAGGAGCAATA 59.176 38.462 0.00 0.00 0.00 1.90
4482 13689 5.649831 GTGGAAGAATAAAGTCAGGAGCAAT 59.350 40.000 0.00 0.00 0.00 3.56
4483 13690 5.003804 GTGGAAGAATAAAGTCAGGAGCAA 58.996 41.667 0.00 0.00 0.00 3.91
4484 13691 4.041567 TGTGGAAGAATAAAGTCAGGAGCA 59.958 41.667 0.00 0.00 0.00 4.26
4485 13692 4.579869 TGTGGAAGAATAAAGTCAGGAGC 58.420 43.478 0.00 0.00 0.00 4.70
4486 13693 7.693969 ATTTGTGGAAGAATAAAGTCAGGAG 57.306 36.000 0.00 0.00 0.00 3.69
4487 13694 7.505585 ACAATTTGTGGAAGAATAAAGTCAGGA 59.494 33.333 0.15 0.00 0.00 3.86
4488 13695 7.661040 ACAATTTGTGGAAGAATAAAGTCAGG 58.339 34.615 0.15 0.00 0.00 3.86
4492 13699 9.458374 CGTTTACAATTTGTGGAAGAATAAAGT 57.542 29.630 12.30 0.00 29.34 2.66
4493 13700 9.672086 TCGTTTACAATTTGTGGAAGAATAAAG 57.328 29.630 12.30 0.00 29.34 1.85
4497 13704 9.787532 CATATCGTTTACAATTTGTGGAAGAAT 57.212 29.630 12.30 6.19 29.34 2.40
4498 13705 8.240682 CCATATCGTTTACAATTTGTGGAAGAA 58.759 33.333 12.30 0.00 29.34 2.52
4499 13706 7.627513 GCCATATCGTTTACAATTTGTGGAAGA 60.628 37.037 12.30 8.29 29.34 2.87
4500 13707 6.472163 GCCATATCGTTTACAATTTGTGGAAG 59.528 38.462 12.30 3.50 29.34 3.46
4501 13708 6.151985 AGCCATATCGTTTACAATTTGTGGAA 59.848 34.615 12.30 4.47 0.00 3.53
4502 13709 5.650266 AGCCATATCGTTTACAATTTGTGGA 59.350 36.000 12.30 4.90 0.00 4.02
4503 13710 5.890334 AGCCATATCGTTTACAATTTGTGG 58.110 37.500 12.30 2.82 0.00 4.17
4504 13711 8.957028 CAATAGCCATATCGTTTACAATTTGTG 58.043 33.333 12.30 0.00 0.00 3.33
4505 13712 8.682710 ACAATAGCCATATCGTTTACAATTTGT 58.317 29.630 7.30 7.30 0.00 2.83
4506 13713 9.515020 AACAATAGCCATATCGTTTACAATTTG 57.485 29.630 0.00 0.00 0.00 2.32
4508 13715 9.515020 CAAACAATAGCCATATCGTTTACAATT 57.485 29.630 0.00 0.00 0.00 2.32
4509 13716 8.898761 TCAAACAATAGCCATATCGTTTACAAT 58.101 29.630 0.00 0.00 0.00 2.71
4510 13717 8.270080 TCAAACAATAGCCATATCGTTTACAA 57.730 30.769 0.00 0.00 0.00 2.41
4511 13718 7.851387 TCAAACAATAGCCATATCGTTTACA 57.149 32.000 0.00 0.00 0.00 2.41
4512 13719 8.609176 TCTTCAAACAATAGCCATATCGTTTAC 58.391 33.333 0.00 0.00 0.00 2.01
4513 13720 8.725405 TCTTCAAACAATAGCCATATCGTTTA 57.275 30.769 0.00 0.00 0.00 2.01
4514 13721 7.624360 TCTTCAAACAATAGCCATATCGTTT 57.376 32.000 0.00 0.00 0.00 3.60
4515 13722 7.624360 TTCTTCAAACAATAGCCATATCGTT 57.376 32.000 0.00 0.00 0.00 3.85
4516 13723 7.807977 ATTCTTCAAACAATAGCCATATCGT 57.192 32.000 0.00 0.00 0.00 3.73
4571 13778 8.551205 GCGAACTATTGATCACTCATATTTTCA 58.449 33.333 0.00 0.00 0.00 2.69
4572 13779 8.768955 AGCGAACTATTGATCACTCATATTTTC 58.231 33.333 0.00 0.00 0.00 2.29
4573 13780 8.668510 AGCGAACTATTGATCACTCATATTTT 57.331 30.769 0.00 0.00 0.00 1.82
4574 13781 9.197694 GTAGCGAACTATTGATCACTCATATTT 57.802 33.333 0.00 0.00 0.00 1.40
4575 13782 8.360390 TGTAGCGAACTATTGATCACTCATATT 58.640 33.333 0.00 0.00 0.00 1.28
4576 13783 7.886338 TGTAGCGAACTATTGATCACTCATAT 58.114 34.615 0.00 0.00 0.00 1.78
4577 13784 7.228706 TCTGTAGCGAACTATTGATCACTCATA 59.771 37.037 0.00 0.00 0.00 2.15
4578 13785 6.039829 TCTGTAGCGAACTATTGATCACTCAT 59.960 38.462 0.00 0.00 0.00 2.90
4579 13786 5.357032 TCTGTAGCGAACTATTGATCACTCA 59.643 40.000 0.00 0.00 0.00 3.41
4580 13787 5.822278 TCTGTAGCGAACTATTGATCACTC 58.178 41.667 0.00 0.00 0.00 3.51
4586 13793 7.154435 AGTACTTTCTGTAGCGAACTATTGA 57.846 36.000 0.00 0.00 0.00 2.57
4639 13865 3.243941 TGCCATACATACACGGATACACC 60.244 47.826 0.00 0.00 0.00 4.16
4640 13866 3.985008 TGCCATACATACACGGATACAC 58.015 45.455 0.00 0.00 0.00 2.90
4642 13868 5.994887 TTTTGCCATACATACACGGATAC 57.005 39.130 0.00 0.00 0.00 2.24
4643 13869 6.995686 AGAATTTTGCCATACATACACGGATA 59.004 34.615 0.00 0.00 0.00 2.59
4645 13871 5.189928 AGAATTTTGCCATACATACACGGA 58.810 37.500 0.00 0.00 0.00 4.69
4646 13872 5.499139 AGAATTTTGCCATACATACACGG 57.501 39.130 0.00 0.00 0.00 4.94
4647 13873 6.321717 ACAAGAATTTTGCCATACATACACG 58.678 36.000 1.74 0.00 0.00 4.49
4695 14004 9.403583 GGGAGAAAAACACCTTCATATATACAA 57.596 33.333 0.00 0.00 0.00 2.41
4796 14106 7.759489 TTTGAATGTTATAGTGTCAGCCTTT 57.241 32.000 0.00 0.00 0.00 3.11
4799 14109 6.072175 TGGTTTTGAATGTTATAGTGTCAGCC 60.072 38.462 0.00 0.00 0.00 4.85
4882 14192 9.630098 TTTCGTTTTCACTACTACTAATACAGG 57.370 33.333 0.00 0.00 0.00 4.00
4894 14204 9.228636 TCTTTTTATTGCTTTCGTTTTCACTAC 57.771 29.630 0.00 0.00 0.00 2.73
4895 14205 9.445786 CTCTTTTTATTGCTTTCGTTTTCACTA 57.554 29.630 0.00 0.00 0.00 2.74
4896 14206 8.188139 TCTCTTTTTATTGCTTTCGTTTTCACT 58.812 29.630 0.00 0.00 0.00 3.41
5049 14364 8.958043 CATTTCTGAACTTCCTTTTTAGTTTCG 58.042 33.333 0.00 0.00 34.88 3.46
5136 14454 7.233553 AGAGGTGATCATTCTATGTTCGGAATA 59.766 37.037 10.08 0.00 32.88 1.75
5137 14455 6.042552 AGAGGTGATCATTCTATGTTCGGAAT 59.957 38.462 10.08 0.00 32.88 3.01
5153 14471 3.379688 GCATGGGAAAAGAAGAGGTGATC 59.620 47.826 0.00 0.00 0.00 2.92
5171 14489 6.989659 AGATTATAAGGCAATTTGGAGCATG 58.010 36.000 0.00 0.00 0.00 4.06
5183 14501 8.424918 CCTTGTTAGAAGAGAGATTATAAGGCA 58.575 37.037 0.00 0.00 0.00 4.75
5226 14544 4.176271 GCCATCAACCTTCTTGCAAATAC 58.824 43.478 0.00 0.00 0.00 1.89
5232 14550 2.070262 GTTGCCATCAACCTTCTTGC 57.930 50.000 0.00 0.00 45.15 4.01


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

AutoCloner maintained by Alex Coulton.