Multiple sequence alignment - TraesCS3A01G338100

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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 TraesCS3A01G338100 chr3A 100.000 7119 0 0 1 7119 584937540 584930422 0.000000e+00 13147.0
1 TraesCS3A01G338100 chr3A 92.632 190 13 1 3395 3583 671642925 671642736 9.100000e-69 272.0
2 TraesCS3A01G338100 chr3D 94.007 3020 121 27 3575 6578 443710578 443707603 0.000000e+00 4519.0
3 TraesCS3A01G338100 chr3D 97.790 1131 24 1 2284 3413 443711707 443710577 0.000000e+00 1949.0
4 TraesCS3A01G338100 chr3D 90.937 971 39 16 285 1252 443713803 443712879 0.000000e+00 1260.0
5 TraesCS3A01G338100 chr3D 92.601 892 34 10 1327 2194 443712775 443711892 0.000000e+00 1253.0
6 TraesCS3A01G338100 chr3D 91.701 482 34 4 6632 7109 443707371 443706892 0.000000e+00 664.0
7 TraesCS3A01G338100 chr3D 96.035 227 4 1 1 222 443714295 443714069 1.460000e-96 364.0
8 TraesCS3A01G338100 chr3B 91.702 3290 144 41 3861 7074 581705047 581701811 0.000000e+00 4444.0
9 TraesCS3A01G338100 chr3B 98.523 880 13 0 2534 3413 581706336 581705457 0.000000e+00 1554.0
10 TraesCS3A01G338100 chr3B 87.219 1377 64 40 1 1330 581710350 581709039 0.000000e+00 1465.0
11 TraesCS3A01G338100 chr3B 95.251 737 30 4 1483 2216 581707545 581706811 0.000000e+00 1162.0
12 TraesCS3A01G338100 chr3B 98.276 290 5 0 3575 3864 581705458 581705169 6.370000e-140 508.0
13 TraesCS3A01G338100 chr3B 93.836 292 15 3 2272 2561 581706783 581706493 3.050000e-118 436.0
14 TraesCS3A01G338100 chr3B 95.000 100 2 3 1401 1499 581707711 581707614 3.440000e-33 154.0
15 TraesCS3A01G338100 chr3B 93.506 77 5 0 1327 1403 581708967 581708891 1.620000e-21 115.0
16 TraesCS3A01G338100 chr3B 80.147 136 19 7 887 1019 391143558 391143428 2.110000e-15 95.3
17 TraesCS3A01G338100 chr1D 95.628 183 5 2 3412 3592 178466306 178466487 2.510000e-74 291.0
18 TraesCS3A01G338100 chr1D 84.951 206 31 0 3195 3400 403051502 403051707 7.240000e-50 209.0
19 TraesCS3A01G338100 chr4D 97.059 170 5 0 3411 3580 75782052 75782221 3.250000e-73 287.0
20 TraesCS3A01G338100 chr4D 97.041 169 5 0 3409 3577 452926302 452926134 1.170000e-72 285.0
21 TraesCS3A01G338100 chr4D 96.512 172 5 1 3412 3583 93338206 93338036 4.200000e-72 283.0
22 TraesCS3A01G338100 chr4D 78.605 215 38 5 864 1075 109359858 109359649 1.250000e-27 135.0
23 TraesCS3A01G338100 chr6D 96.023 176 5 1 3409 3582 389700708 389700533 1.170000e-72 285.0
24 TraesCS3A01G338100 chr5A 96.512 172 6 0 3412 3583 290391861 290391690 1.170000e-72 285.0
25 TraesCS3A01G338100 chr7B 95.455 176 8 0 3409 3584 427701763 427701938 1.510000e-71 281.0
26 TraesCS3A01G338100 chr2D 94.536 183 7 3 3398 3579 135284992 135284812 5.440000e-71 279.0
27 TraesCS3A01G338100 chr1A 84.466 206 32 0 3195 3400 498166138 498166343 3.370000e-48 204.0
28 TraesCS3A01G338100 chr1A 73.118 651 138 24 2508 3144 498165239 498165866 1.570000e-46 198.0
29 TraesCS3A01G338100 chr1B 83.981 206 33 0 3195 3400 541002790 541002995 1.570000e-46 198.0
30 TraesCS3A01G338100 chr1B 81.871 171 30 1 3966 4136 541003293 541003462 7.440000e-30 143.0
31 TraesCS3A01G338100 chr4B 79.358 218 37 4 861 1075 167347557 167347769 5.750000e-31 147.0
32 TraesCS3A01G338100 chr4B 80.882 136 18 7 887 1019 85872630 85872500 4.540000e-17 100.0
33 TraesCS3A01G338100 chr4B 80.916 131 17 6 892 1019 85897041 85896916 5.880000e-16 97.1
34 TraesCS3A01G338100 chr2B 77.698 139 20 4 887 1019 368943426 368943559 2.750000e-09 75.0


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 TraesCS3A01G338100 chr3A 584930422 584937540 7118 True 13147.000000 13147 100.000000 1 7119 1 chr3A.!!$R1 7118
1 TraesCS3A01G338100 chr3D 443706892 443714295 7403 True 1668.166667 4519 93.845167 1 7109 6 chr3D.!!$R1 7108
2 TraesCS3A01G338100 chr3B 581701811 581710350 8539 True 1229.750000 4444 94.164125 1 7074 8 chr3B.!!$R2 7073
3 TraesCS3A01G338100 chr1A 498165239 498166343 1104 False 201.000000 204 78.792000 2508 3400 2 chr1A.!!$F1 892

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
799 1013 0.095417 GAAACCGCATCTTCTCGTGC 59.905 55.000 0.00 0.0 37.97 5.34 F
1117 1353 0.890683 CATTTGGACTCCAGGGTTGC 59.109 55.000 0.00 0.0 33.81 4.17 F
3111 5005 2.262423 GCATAGGGCGAGGAATTCTT 57.738 50.000 5.23 0.0 0.00 2.52 F
4486 6727 0.032615 AAGCCACAAAGAACCCACCA 60.033 50.000 0.00 0.0 0.00 4.17 F
5307 7576 1.202382 GGTCATACCCTACACGCACTC 60.202 57.143 0.00 0.0 30.04 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2645 4533 2.500509 GACAGATGGAGATGTCGGAC 57.499 55.00 0.00 0.0 36.76 4.79 R
3153 5047 5.545658 ACGGACAATTAGTTACAGCAATG 57.454 39.13 0.00 0.0 0.00 2.82 R
4589 6830 0.253327 AGGGCCTCTTTGGTTCGATC 59.747 55.00 0.00 0.0 38.35 3.69 R
6025 8299 0.603975 GAGGTGTTGGAGAGGCACAC 60.604 60.00 0.00 0.0 40.16 3.82 R
6556 8839 0.033405 CCCCCTCAACGGAGAGTAGA 60.033 60.00 5.78 0.0 44.26 2.59 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
31 32 3.870633 ATTATATCCTTCTCGCCCGAC 57.129 47.619 0.00 0.00 0.00 4.79
54 55 2.341846 TTCCGGGATCATGTAAAGGC 57.658 50.000 0.00 0.00 0.00 4.35
78 79 1.212229 GGTCGACGTCTGTCCCTTC 59.788 63.158 14.70 0.00 42.37 3.46
219 225 1.074951 CACTTTCTCCCCACCACCC 59.925 63.158 0.00 0.00 0.00 4.61
319 528 2.048222 GCAGCAGCACGGACAGTA 60.048 61.111 0.00 0.00 41.58 2.74
320 529 2.383527 GCAGCAGCACGGACAGTAC 61.384 63.158 0.00 0.00 41.58 2.73
321 530 1.290324 CAGCAGCACGGACAGTACT 59.710 57.895 0.00 0.00 0.00 2.73
322 531 0.526211 CAGCAGCACGGACAGTACTA 59.474 55.000 0.00 0.00 0.00 1.82
323 532 0.526662 AGCAGCACGGACAGTACTAC 59.473 55.000 0.00 0.00 0.00 2.73
446 655 3.191539 CTCCTTCCGCTGCGCTTC 61.192 66.667 18.00 0.00 0.00 3.86
702 911 4.809513 GAGGTTCCCTCCAGGCTA 57.190 61.111 0.00 0.00 44.36 3.93
703 912 3.007581 GAGGTTCCCTCCAGGCTAA 57.992 57.895 0.00 0.00 44.36 3.09
764 978 4.867599 GGTCCGTCGGATCGTGCC 62.868 72.222 18.75 9.77 32.73 5.01
784 998 0.810426 GAGGAAGATCGGCCCGAAAC 60.810 60.000 11.19 7.83 39.99 2.78
799 1013 0.095417 GAAACCGCATCTTCTCGTGC 59.905 55.000 0.00 0.00 37.97 5.34
896 1131 4.983215 TGTTACTTATGTGAACACTGCG 57.017 40.909 6.51 0.00 0.00 5.18
904 1139 3.541071 TGTGAACACTGCGATGATTTG 57.459 42.857 6.51 0.00 0.00 2.32
1011 1246 3.341043 CAATCGATGGCCTCCGCG 61.341 66.667 3.32 0.00 35.02 6.46
1063 1298 1.606668 TCTGTTTCCGCAACCACATTC 59.393 47.619 0.00 0.00 33.97 2.67
1066 1301 1.336755 GTTTCCGCAACCACATTCTGT 59.663 47.619 0.00 0.00 0.00 3.41
1078 1313 7.301054 CAACCACATTCTGTAGAGATGAAAAC 58.699 38.462 0.00 0.00 0.00 2.43
1084 1320 8.025445 ACATTCTGTAGAGATGAAAACAATTGC 58.975 33.333 5.05 0.00 0.00 3.56
1090 1326 6.600882 AGAGATGAAAACAATTGCCTTCAT 57.399 33.333 24.82 24.82 40.36 2.57
1104 1340 5.389859 TGCCTTCATCAAACTACATTTGG 57.610 39.130 0.00 0.00 46.65 3.28
1117 1353 0.890683 CATTTGGACTCCAGGGTTGC 59.109 55.000 0.00 0.00 33.81 4.17
1246 1482 6.267070 TGAAAATACCTTTGGACGTTGTTTC 58.733 36.000 0.00 0.00 0.00 2.78
1267 1503 7.016072 TGTTTCCATCCCATGTTTTAGATTGTT 59.984 33.333 0.00 0.00 0.00 2.83
1393 1706 5.736951 TCACCAAATTGTTCCCTAATTGG 57.263 39.130 0.00 0.00 0.00 3.16
1442 2942 3.148412 GGGCGAGTTTTACCCAAAAGTA 58.852 45.455 0.00 0.00 43.64 2.24
1443 2943 3.760151 GGGCGAGTTTTACCCAAAAGTAT 59.240 43.478 0.00 0.00 43.64 2.12
1444 2944 4.380128 GGGCGAGTTTTACCCAAAAGTATG 60.380 45.833 0.00 0.00 43.64 2.39
1445 2945 4.456566 GGCGAGTTTTACCCAAAAGTATGA 59.543 41.667 0.00 0.00 37.41 2.15
1446 2946 5.124936 GGCGAGTTTTACCCAAAAGTATGAT 59.875 40.000 0.00 0.00 37.41 2.45
1447 2947 6.027749 GCGAGTTTTACCCAAAAGTATGATG 58.972 40.000 0.00 0.00 37.41 3.07
1448 2948 6.349033 GCGAGTTTTACCCAAAAGTATGATGT 60.349 38.462 0.00 0.00 37.41 3.06
1515 3099 5.345741 CCATTCCATTTTCGAAACATGACAC 59.654 40.000 23.13 0.00 0.00 3.67
1587 3193 5.698545 AGAGATTAATATGAAGCTCCGCAAC 59.301 40.000 13.50 0.00 41.74 4.17
1614 3220 6.150140 GTCATTAAATGAGCCTCACAGTTCTT 59.850 38.462 0.00 0.00 40.53 2.52
1615 3221 7.334421 GTCATTAAATGAGCCTCACAGTTCTTA 59.666 37.037 0.00 0.00 40.53 2.10
1669 3275 8.154649 TCCAGAAATCTTTAGTTTGTCTTGAC 57.845 34.615 0.00 0.00 0.00 3.18
2018 3625 5.394005 CCAACAGACTAGATTCTCCACTCTG 60.394 48.000 0.00 0.00 0.00 3.35
2109 3716 4.463891 ACATGGATGATTTTGTTCCACCTC 59.536 41.667 0.00 0.00 42.09 3.85
2144 3751 7.060421 CAGATATTTATGTGTTGGGGTAGGTT 58.940 38.462 0.00 0.00 0.00 3.50
2158 3766 4.525100 GGGGTAGGTTTTGCACTGATTTTA 59.475 41.667 0.00 0.00 0.00 1.52
2184 3792 8.553459 AATAGATACAGAAATATTCCTTGCCG 57.447 34.615 0.00 0.00 0.00 5.69
2321 4024 6.915544 TCTCATCTACAAGATTCAATGCAC 57.084 37.500 0.00 0.00 31.32 4.57
2400 4103 6.366877 ACACGTTTAGTATTTGTATTCAGCGT 59.633 34.615 0.00 0.00 0.00 5.07
2430 4133 4.352595 TCCTGGATTCCTGGTTTACTTTCA 59.647 41.667 23.58 3.27 42.31 2.69
2434 4137 5.768164 TGGATTCCTGGTTTACTTTCAAGTC 59.232 40.000 3.95 0.00 40.37 3.01
2453 4156 7.603651 TCAAGTCTCAAGAGTATTTAGTGGAC 58.396 38.462 0.00 0.00 0.00 4.02
2454 4157 6.532988 AGTCTCAAGAGTATTTAGTGGACC 57.467 41.667 0.00 0.00 0.00 4.46
2491 4195 8.215736 ACATTGATCTCCATGACATCAATTCTA 58.784 33.333 17.41 0.73 39.20 2.10
2620 4508 2.399356 GCACTAAACCGGCCAGCTC 61.399 63.158 0.00 0.00 0.00 4.09
2645 4533 5.490139 AATGATACCAATGTCTTTCAGCG 57.510 39.130 0.00 0.00 0.00 5.18
3111 5005 2.262423 GCATAGGGCGAGGAATTCTT 57.738 50.000 5.23 0.00 0.00 2.52
3153 5047 5.295540 GGTCAGGACTAAATCAGATTGAAGC 59.704 44.000 0.00 0.00 0.00 3.86
3411 5526 7.015974 TGAGCATGAGTAAGAATCTGGTGATAT 59.984 37.037 0.00 0.00 31.70 1.63
3412 5527 8.427902 AGCATGAGTAAGAATCTGGTGATATA 57.572 34.615 0.00 0.00 31.70 0.86
3413 5528 8.310382 AGCATGAGTAAGAATCTGGTGATATAC 58.690 37.037 0.00 0.00 31.70 1.47
3414 5529 8.310382 GCATGAGTAAGAATCTGGTGATATACT 58.690 37.037 0.00 0.00 33.41 2.12
3415 5530 9.853555 CATGAGTAAGAATCTGGTGATATACTC 57.146 37.037 8.36 8.36 39.98 2.59
3416 5531 8.410673 TGAGTAAGAATCTGGTGATATACTCC 57.589 38.462 11.34 0.00 39.52 3.85
3417 5532 7.451877 TGAGTAAGAATCTGGTGATATACTCCC 59.548 40.741 11.34 0.00 39.52 4.30
3418 5533 7.540183 AGTAAGAATCTGGTGATATACTCCCT 58.460 38.462 0.00 0.00 28.97 4.20
3419 5534 6.926630 AAGAATCTGGTGATATACTCCCTC 57.073 41.667 0.00 0.00 31.70 4.30
3420 5535 5.337788 AGAATCTGGTGATATACTCCCTCC 58.662 45.833 0.00 0.00 31.70 4.30
3421 5536 3.156288 TCTGGTGATATACTCCCTCCG 57.844 52.381 0.00 0.00 0.00 4.63
3422 5537 2.445905 TCTGGTGATATACTCCCTCCGT 59.554 50.000 0.00 0.00 0.00 4.69
3423 5538 3.117246 TCTGGTGATATACTCCCTCCGTT 60.117 47.826 0.00 0.00 0.00 4.44
3424 5539 3.228453 TGGTGATATACTCCCTCCGTTC 58.772 50.000 0.00 0.00 0.00 3.95
3425 5540 2.561858 GGTGATATACTCCCTCCGTTCC 59.438 54.545 0.00 0.00 0.00 3.62
3426 5541 3.498334 GTGATATACTCCCTCCGTTCCT 58.502 50.000 0.00 0.00 0.00 3.36
3427 5542 4.508047 GGTGATATACTCCCTCCGTTCCTA 60.508 50.000 0.00 0.00 0.00 2.94
3428 5543 5.075493 GTGATATACTCCCTCCGTTCCTAA 58.925 45.833 0.00 0.00 0.00 2.69
3429 5544 5.537674 GTGATATACTCCCTCCGTTCCTAAA 59.462 44.000 0.00 0.00 0.00 1.85
3430 5545 6.210984 GTGATATACTCCCTCCGTTCCTAAAT 59.789 42.308 0.00 0.00 0.00 1.40
3431 5546 7.395489 GTGATATACTCCCTCCGTTCCTAAATA 59.605 40.741 0.00 0.00 0.00 1.40
3432 5547 8.120538 TGATATACTCCCTCCGTTCCTAAATAT 58.879 37.037 0.00 0.00 0.00 1.28
3433 5548 9.638176 GATATACTCCCTCCGTTCCTAAATATA 57.362 37.037 0.00 0.00 0.00 0.86
3435 5550 6.607004 ACTCCCTCCGTTCCTAAATATATG 57.393 41.667 0.00 0.00 0.00 1.78
3436 5551 6.082707 ACTCCCTCCGTTCCTAAATATATGT 58.917 40.000 0.00 0.00 0.00 2.29
3437 5552 6.210984 ACTCCCTCCGTTCCTAAATATATGTC 59.789 42.308 0.00 0.00 0.00 3.06
3438 5553 6.320518 TCCCTCCGTTCCTAAATATATGTCT 58.679 40.000 0.00 0.00 0.00 3.41
3439 5554 6.785963 TCCCTCCGTTCCTAAATATATGTCTT 59.214 38.462 0.00 0.00 0.00 3.01
3440 5555 7.291651 TCCCTCCGTTCCTAAATATATGTCTTT 59.708 37.037 0.00 0.00 0.00 2.52
3441 5556 7.937394 CCCTCCGTTCCTAAATATATGTCTTTT 59.063 37.037 0.00 0.00 0.00 2.27
3442 5557 9.338622 CCTCCGTTCCTAAATATATGTCTTTTT 57.661 33.333 0.00 0.00 0.00 1.94
3476 5591 3.900971 TGGACTACCACATACGGATGTA 58.099 45.455 14.23 0.00 44.82 2.29
3477 5592 4.476297 TGGACTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
3478 5593 5.633117 TGGACTACCACATACGGATGTATA 58.367 41.667 14.23 8.27 44.82 1.47
3479 5594 6.250711 TGGACTACCACATACGGATGTATAT 58.749 40.000 14.23 4.37 44.82 0.86
3480 5595 7.404481 TGGACTACCACATACGGATGTATATA 58.596 38.462 14.23 5.36 44.82 0.86
3481 5596 7.555195 TGGACTACCACATACGGATGTATATAG 59.445 40.741 14.23 16.35 44.82 1.31
3482 5597 7.772292 GGACTACCACATACGGATGTATATAGA 59.228 40.741 22.62 5.04 44.82 1.98
3483 5598 8.503458 ACTACCACATACGGATGTATATAGAC 57.497 38.462 22.62 0.00 44.82 2.59
3484 5599 8.105197 ACTACCACATACGGATGTATATAGACA 58.895 37.037 22.62 2.07 44.82 3.41
3485 5600 7.154435 ACCACATACGGATGTATATAGACAC 57.846 40.000 14.23 0.00 44.82 3.67
3486 5601 6.717997 ACCACATACGGATGTATATAGACACA 59.282 38.462 14.23 0.00 44.82 3.72
3487 5602 7.396339 ACCACATACGGATGTATATAGACACAT 59.604 37.037 14.23 0.00 44.82 3.21
3488 5603 8.251026 CCACATACGGATGTATATAGACACATT 58.749 37.037 14.23 0.00 44.82 2.71
3489 5604 9.639601 CACATACGGATGTATATAGACACATTT 57.360 33.333 14.23 0.00 44.82 2.32
3516 5631 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
3517 5632 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
3518 5633 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
3519 5634 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
3520 5635 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
3521 5636 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
3522 5637 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
3523 5638 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
3524 5639 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
3525 5640 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
3526 5641 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
3527 5642 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
3528 5643 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
3529 5644 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
3530 5645 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
3531 5646 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
3532 5647 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
3533 5648 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
3534 5649 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
3535 5650 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
3536 5651 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
3537 5652 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
3538 5653 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
3539 5654 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
3540 5655 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
3541 5656 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
3542 5657 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
3543 5658 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
3544 5659 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
3546 5661 9.778741 ATGTAGTCACTTGTTGAAATCTCTAAA 57.221 29.630 0.00 0.00 35.39 1.85
3547 5662 9.607988 TGTAGTCACTTGTTGAAATCTCTAAAA 57.392 29.630 0.00 0.00 35.39 1.52
3550 5665 9.396022 AGTCACTTGTTGAAATCTCTAAAAAGA 57.604 29.630 0.00 0.00 35.39 2.52
3551 5666 9.439537 GTCACTTGTTGAAATCTCTAAAAAGAC 57.560 33.333 0.00 0.00 35.39 3.01
3552 5667 9.173021 TCACTTGTTGAAATCTCTAAAAAGACA 57.827 29.630 0.00 0.00 0.00 3.41
3553 5668 9.787532 CACTTGTTGAAATCTCTAAAAAGACAA 57.212 29.630 0.00 0.00 0.00 3.18
3570 5685 8.904099 AAAAGACAAATATATAGGAACGGAGG 57.096 34.615 0.00 0.00 0.00 4.30
3571 5686 6.607004 AGACAAATATATAGGAACGGAGGG 57.393 41.667 0.00 0.00 0.00 4.30
3572 5687 6.320518 AGACAAATATATAGGAACGGAGGGA 58.679 40.000 0.00 0.00 0.00 4.20
3573 5688 6.437793 AGACAAATATATAGGAACGGAGGGAG 59.562 42.308 0.00 0.00 0.00 4.30
3649 5764 6.599356 TGCACTGTTTATCTCAGTAAGGTA 57.401 37.500 0.00 0.00 43.14 3.08
4303 6543 1.021390 AAGATTGAGCGGCTGTTCGG 61.021 55.000 7.50 0.00 0.00 4.30
4317 6557 3.518590 CTGTTCGGTACACCATAAGGAC 58.481 50.000 0.00 0.00 38.69 3.85
4486 6727 0.032615 AAGCCACAAAGAACCCACCA 60.033 50.000 0.00 0.00 0.00 4.17
4589 6830 9.936759 AGTAGAATCCTAGAAAAACTCTTTGAG 57.063 33.333 0.00 0.00 35.41 3.02
4949 7214 5.297029 GCACTAAACAGAAAGACAAAGAGGT 59.703 40.000 0.00 0.00 0.00 3.85
4951 7216 6.316390 CACTAAACAGAAAGACAAAGAGGTGT 59.684 38.462 0.00 0.00 0.00 4.16
4987 7252 3.820467 ACATGAAAATCGGTGCTGAAGAA 59.180 39.130 0.00 0.00 0.00 2.52
5037 7302 4.357918 AAGGTACTGCACTTCTTCACAT 57.642 40.909 0.00 0.00 40.86 3.21
5038 7303 3.668447 AGGTACTGCACTTCTTCACATG 58.332 45.455 0.00 0.00 37.18 3.21
5098 7363 4.258543 TGGCATAGTAACTAAACAGGTGC 58.741 43.478 0.00 0.00 0.00 5.01
5145 7410 3.630312 ACGATATCCCATTTTGGTTTCCG 59.370 43.478 0.00 0.00 35.17 4.30
5168 7433 5.413213 CGGTTAGGTAACAACAATGGAATCA 59.587 40.000 2.44 0.00 37.92 2.57
5200 7465 8.140628 ACATGATGCATTGTTGTTTAACTACAA 58.859 29.630 22.40 22.40 44.95 2.41
5203 7468 9.371136 TGATGCATTGTTGTTTAACTACAAAAA 57.629 25.926 23.51 14.70 44.30 1.94
5297 7566 1.345415 ACGTGAAAACGGTCATACCCT 59.655 47.619 3.09 0.00 33.75 4.34
5307 7576 1.202382 GGTCATACCCTACACGCACTC 60.202 57.143 0.00 0.00 30.04 3.51
5369 7638 2.181125 TCCATTTTGCAGGCACATCAT 58.819 42.857 0.00 0.00 0.00 2.45
5374 7643 1.317431 TTGCAGGCACATCATGGAGC 61.317 55.000 0.00 0.00 0.00 4.70
5475 7744 7.658179 GAATCGTGCATAGATTCTATTTGGA 57.342 36.000 26.85 0.00 46.22 3.53
5476 7745 7.426929 AATCGTGCATAGATTCTATTTGGAC 57.573 36.000 12.71 6.24 33.45 4.02
5563 7832 9.753674 AAGGATAATGTCTAGTTTTCATTCCAA 57.246 29.630 0.00 0.00 34.35 3.53
5730 8003 5.587844 GTCTATGACAGGATGAAGCAACAAT 59.412 40.000 0.00 0.00 39.69 2.71
5734 8007 4.828939 TGACAGGATGAAGCAACAATCTTT 59.171 37.500 0.00 0.00 39.69 2.52
5797 8070 4.978083 ATGCACATGATGTTCTTTCCTC 57.022 40.909 0.00 0.00 0.00 3.71
5813 8086 3.795623 TCCTCCTTTCTACCGATTTCG 57.204 47.619 0.00 0.00 39.44 3.46
5814 8087 3.094572 TCCTCCTTTCTACCGATTTCGT 58.905 45.455 0.00 0.00 37.74 3.85
5845 8118 3.246226 GTGTCTTGCAACTGTGTACTCTG 59.754 47.826 0.00 0.00 0.00 3.35
6025 8299 2.100631 GGCACACTGGGATTCGTCG 61.101 63.158 0.00 0.00 0.00 5.12
6052 8326 2.168106 CTCTCCAACACCTCCAGATCAG 59.832 54.545 0.00 0.00 0.00 2.90
6097 8371 3.354948 TGCTGTTATCTGAGCAACCAT 57.645 42.857 0.00 0.00 42.22 3.55
6105 8379 2.715046 TCTGAGCAACCATGATGTTCC 58.285 47.619 11.00 0.00 0.00 3.62
6137 8411 0.542702 ACCTTGGGCCCATGTTGAAG 60.543 55.000 29.23 19.04 0.00 3.02
6158 8433 6.479990 TGAAGATAACTTGTAAGATGGATGCG 59.520 38.462 0.00 0.00 36.39 4.73
6166 8441 0.882042 AAGATGGATGCGCGATGACC 60.882 55.000 12.10 7.75 0.00 4.02
6201 8476 3.587951 CTCAGATCCATTCTCCCCATGAT 59.412 47.826 0.00 0.00 29.93 2.45
6216 8491 4.221482 CCCCATGATGTAGATCGAGATCAA 59.779 45.833 17.44 4.27 40.22 2.57
6239 8514 6.505048 AAATGGTCAGATCTCATATGGTGA 57.495 37.500 2.13 2.46 35.05 4.02
6265 8540 5.030147 ACTAGATTGGGTATGTGTCCTTCA 58.970 41.667 0.00 0.00 0.00 3.02
6268 8543 4.474651 AGATTGGGTATGTGTCCTTCATCA 59.525 41.667 0.00 0.00 0.00 3.07
6326 8601 6.992123 CCTAACACTCTTAATATGGCATGTGA 59.008 38.462 10.98 0.00 0.00 3.58
6336 8611 2.127271 TGGCATGTGACCTGGTTATG 57.873 50.000 0.00 7.93 0.00 1.90
6364 8639 6.700960 TCAATTGAATGGTTTGACATGTTCAC 59.299 34.615 5.45 0.00 32.26 3.18
6379 8654 4.252971 TGTTCACTTGGTAGAGCTACAC 57.747 45.455 9.62 0.00 37.78 2.90
6386 8661 5.578727 CACTTGGTAGAGCTACACATTCTTC 59.421 44.000 9.62 0.00 37.78 2.87
6387 8662 5.246203 ACTTGGTAGAGCTACACATTCTTCA 59.754 40.000 9.62 0.00 37.78 3.02
6388 8663 5.939764 TGGTAGAGCTACACATTCTTCAT 57.060 39.130 9.62 0.00 37.78 2.57
6389 8664 5.664457 TGGTAGAGCTACACATTCTTCATG 58.336 41.667 9.62 0.00 37.78 3.07
6414 8689 0.524414 TCGTACCACTGTCCACATCG 59.476 55.000 0.00 0.00 0.00 3.84
6420 8695 2.124983 CTGTCCACATCGCCCCAG 60.125 66.667 0.00 0.00 0.00 4.45
6452 8735 4.201990 ACTCTTATTACCGAACCAGTAGCG 60.202 45.833 0.00 0.00 0.00 4.26
6552 8835 5.174037 TCCTCGAATTCAAATACCACCTT 57.826 39.130 6.22 0.00 0.00 3.50
6556 8839 7.832187 TCCTCGAATTCAAATACCACCTTTATT 59.168 33.333 6.22 0.00 0.00 1.40
6613 8924 3.554934 TCTCTCTCTCTCTCTGGATTGC 58.445 50.000 0.00 0.00 0.00 3.56
6649 9110 8.432805 CACTATGGATACTATTTTCCTCCACTT 58.567 37.037 0.00 0.00 38.74 3.16
6665 9126 4.315803 TCCACTTCGGAGACAGAAAATTC 58.684 43.478 0.00 0.00 39.64 2.17
6683 9145 6.906157 AAATTCCACAATCACTTCACAGAT 57.094 33.333 0.00 0.00 0.00 2.90
6707 9169 2.222027 CCGACCTCTTTCACAAGCTTT 58.778 47.619 0.00 0.00 0.00 3.51
6786 9249 5.870706 AGAGTAACAAGCTTTAAGGCTCTT 58.129 37.500 13.02 9.63 42.24 2.85
6790 9253 4.367039 ACAAGCTTTAAGGCTCTTACCA 57.633 40.909 13.02 0.00 42.24 3.25
6795 9258 3.119955 GCTTTAAGGCTCTTACCAAACCG 60.120 47.826 1.67 0.00 0.00 4.44
6819 9282 0.449388 CTTGGTGGAGCTCAAATCGC 59.551 55.000 17.19 4.32 0.00 4.58
6829 9292 1.064654 GCTCAAATCGCTCCATCCAAC 59.935 52.381 0.00 0.00 0.00 3.77
6868 9331 3.760580 AATCTGACCCCATCGATTCTC 57.239 47.619 0.00 0.00 29.96 2.87
6872 9335 0.106894 GACCCCATCGATTCTCACCC 59.893 60.000 0.00 0.00 0.00 4.61
6879 9342 3.307269 CCATCGATTCTCACCCTATGCAT 60.307 47.826 3.79 3.79 0.00 3.96
6926 9389 2.310647 GGGGGAAACAATGGAGAAGGTA 59.689 50.000 0.00 0.00 0.00 3.08
6981 9444 3.495100 CCTCACTTAGATGGGAAATCGGG 60.495 52.174 0.00 0.00 0.00 5.14
7010 9473 3.119849 GGGATGAACTTGGATGTCAAACG 60.120 47.826 0.00 0.00 34.56 3.60
7011 9474 3.751175 GGATGAACTTGGATGTCAAACGA 59.249 43.478 0.00 0.00 34.56 3.85
7012 9475 4.396166 GGATGAACTTGGATGTCAAACGAT 59.604 41.667 0.00 0.00 34.56 3.73
7018 9481 4.333649 ACTTGGATGTCAAACGATATGCAG 59.666 41.667 0.00 0.00 34.66 4.41
7027 9490 2.542766 ACGATATGCAGCAAAAACCG 57.457 45.000 0.00 1.80 0.00 4.44
7032 9495 2.352503 ATGCAGCAAAAACCGACATC 57.647 45.000 0.00 0.00 0.00 3.06
7041 9504 4.429108 CAAAAACCGACATCCAGTTGTTT 58.571 39.130 0.00 0.00 37.19 2.83
7100 9567 5.719085 TCCCACTTATTTATGCATGTTGGTT 59.281 36.000 10.16 0.00 0.00 3.67
7109 9576 1.340889 TGCATGTTGGTTGCTTCTTCC 59.659 47.619 0.00 0.00 40.77 3.46
7110 9577 1.666888 GCATGTTGGTTGCTTCTTCCG 60.667 52.381 0.00 0.00 37.14 4.30
7111 9578 1.608590 CATGTTGGTTGCTTCTTCCGT 59.391 47.619 0.00 0.00 0.00 4.69
7112 9579 1.757682 TGTTGGTTGCTTCTTCCGTT 58.242 45.000 0.00 0.00 0.00 4.44
7113 9580 1.673920 TGTTGGTTGCTTCTTCCGTTC 59.326 47.619 0.00 0.00 0.00 3.95
7114 9581 1.947456 GTTGGTTGCTTCTTCCGTTCT 59.053 47.619 0.00 0.00 0.00 3.01
7115 9582 2.341846 TGGTTGCTTCTTCCGTTCTT 57.658 45.000 0.00 0.00 0.00 2.52
7116 9583 2.218603 TGGTTGCTTCTTCCGTTCTTC 58.781 47.619 0.00 0.00 0.00 2.87
7117 9584 1.194772 GGTTGCTTCTTCCGTTCTTCG 59.805 52.381 0.00 0.00 39.52 3.79
7118 9585 0.865769 TTGCTTCTTCCGTTCTTCGC 59.134 50.000 0.00 0.00 38.35 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 4.067896 CCTTTACATGATCCCGGAATCAG 58.932 47.826 9.95 4.13 38.96 2.90
54 55 4.813526 CAGACGTCGACCCGCTCG 62.814 72.222 10.58 0.00 44.44 5.03
311 520 7.432869 ACATCTAGTAGTAGTAGTACTGTCCG 58.567 42.308 22.76 13.34 39.96 4.79
312 521 9.912634 CTACATCTAGTAGTAGTAGTACTGTCC 57.087 40.741 22.76 7.83 44.24 4.02
392 601 4.962836 ACACTGTGGCAGGCAGGC 62.963 66.667 13.09 0.00 44.50 4.85
393 602 2.670934 GACACTGTGGCAGGCAGG 60.671 66.667 9.20 0.00 38.22 4.85
394 603 2.670934 GGACACTGTGGCAGGCAG 60.671 66.667 16.72 3.75 39.67 4.85
395 604 4.624364 CGGACACTGTGGCAGGCA 62.624 66.667 16.72 0.00 35.51 4.75
446 655 2.423538 CCTTTAAACCAATGCGGGAGAG 59.576 50.000 0.00 0.00 40.22 3.20
621 830 3.437795 CCAGCCAAGAAGCAGCGG 61.438 66.667 0.00 0.00 34.23 5.52
622 831 3.437795 CCCAGCCAAGAAGCAGCG 61.438 66.667 0.00 0.00 34.23 5.18
623 832 1.905354 AACCCAGCCAAGAAGCAGC 60.905 57.895 0.00 0.00 34.23 5.25
696 905 2.039879 ACACCCACCTTTAGTTAGCCTG 59.960 50.000 0.00 0.00 0.00 4.85
700 909 7.864379 CGTATGTATACACCCACCTTTAGTTAG 59.136 40.741 7.96 0.00 32.87 2.34
701 910 7.341769 ACGTATGTATACACCCACCTTTAGTTA 59.658 37.037 7.96 0.00 32.87 2.24
702 911 6.155049 ACGTATGTATACACCCACCTTTAGTT 59.845 38.462 7.96 0.00 32.87 2.24
703 912 5.658190 ACGTATGTATACACCCACCTTTAGT 59.342 40.000 7.96 0.00 32.87 2.24
741 955 1.449070 GATCCGACGGACCCCAAAC 60.449 63.158 21.02 1.40 32.98 2.93
764 978 2.292794 TTTCGGGCCGATCTTCCTCG 62.293 60.000 31.59 0.00 35.23 4.63
777 991 1.421410 CGAGAAGATGCGGTTTCGGG 61.421 60.000 0.00 0.00 36.79 5.14
784 998 1.880340 GAGGCACGAGAAGATGCGG 60.880 63.158 0.00 0.00 43.02 5.69
799 1013 1.654317 GCTGACAGAGAATGCAGAGG 58.346 55.000 6.65 0.00 36.02 3.69
874 1109 5.234752 TCGCAGTGTTCACATAAGTAACAT 58.765 37.500 5.74 0.00 35.72 2.71
896 1131 7.543172 TGTTAAAGAATCTGCAAGCAAATCATC 59.457 33.333 0.00 0.00 0.00 2.92
904 1139 7.823149 ATCAAATGTTAAAGAATCTGCAAGC 57.177 32.000 0.00 0.00 0.00 4.01
993 1228 3.654020 GCGGAGGCCATCGATTGC 61.654 66.667 19.65 12.86 0.00 3.56
1011 1246 2.562738 CACCTTCATTTTTCCCTCACCC 59.437 50.000 0.00 0.00 0.00 4.61
1019 1254 8.743714 AGAATTACCATCTCACCTTCATTTTTC 58.256 33.333 0.00 0.00 0.00 2.29
1063 1298 6.506500 AGGCAATTGTTTTCATCTCTACAG 57.493 37.500 7.40 0.00 0.00 2.74
1066 1301 7.707624 ATGAAGGCAATTGTTTTCATCTCTA 57.292 32.000 22.77 7.42 35.91 2.43
1078 1313 7.894376 AAATGTAGTTTGATGAAGGCAATTG 57.106 32.000 0.00 0.00 0.00 2.32
1117 1353 2.197605 ACCGAAAAGTTTGGGGCGG 61.198 57.895 14.22 14.22 39.97 6.13
1123 1359 3.115554 CTCCTTTGCACCGAAAAGTTTG 58.884 45.455 0.00 0.00 33.61 2.93
1246 1482 6.459573 CCGTAACAATCTAAAACATGGGATGG 60.460 42.308 0.00 0.00 33.60 3.51
1267 1503 4.091549 AGGTTTTAGACTCATGTCCCGTA 58.908 43.478 0.00 0.00 43.91 4.02
1340 1653 8.905103 TTGCTTCACTAAAGTTAGTTTTCAAC 57.095 30.769 0.85 0.00 41.82 3.18
1393 1706 6.918892 AAATTTGAAGTGGTTAAACTTGCC 57.081 33.333 0.00 0.00 40.48 4.52
1442 2942 8.767085 GTTTGTCAATCAATTTTGTCACATCAT 58.233 29.630 0.00 0.00 35.84 2.45
1443 2943 7.224362 GGTTTGTCAATCAATTTTGTCACATCA 59.776 33.333 0.00 0.00 35.84 3.07
1444 2944 7.439056 AGGTTTGTCAATCAATTTTGTCACATC 59.561 33.333 0.00 0.00 35.84 3.06
1445 2945 7.225145 CAGGTTTGTCAATCAATTTTGTCACAT 59.775 33.333 0.00 0.00 35.84 3.21
1446 2946 6.534436 CAGGTTTGTCAATCAATTTTGTCACA 59.466 34.615 0.00 0.00 35.84 3.58
1447 2947 6.509997 GCAGGTTTGTCAATCAATTTTGTCAC 60.510 38.462 0.00 0.00 35.84 3.67
1448 2948 5.523188 GCAGGTTTGTCAATCAATTTTGTCA 59.477 36.000 0.00 0.00 35.84 3.58
1583 3189 4.156556 TGAGGCTCATTTAATGACTGTTGC 59.843 41.667 14.43 5.65 35.06 4.17
1587 3193 4.940046 ACTGTGAGGCTCATTTAATGACTG 59.060 41.667 21.84 11.05 35.06 3.51
1669 3275 8.559536 ACGACACATTTAATTCCTGCTATTATG 58.440 33.333 0.00 0.00 0.00 1.90
1843 3450 9.567848 GTTTGAATTAAAGACAGACAAGAAACA 57.432 29.630 0.00 0.00 0.00 2.83
2018 3625 8.134905 AGACAAAAATTCTGTTCAATGAAAGC 57.865 30.769 0.00 0.00 0.00 3.51
2158 3766 9.003658 CGGCAAGGAATATTTCTGTATCTATTT 57.996 33.333 0.00 0.00 0.00 1.40
2170 3778 8.691661 ATTAGTAATGTCGGCAAGGAATATTT 57.308 30.769 0.00 0.00 0.00 1.40
2179 3787 5.064198 GCAGTGTAATTAGTAATGTCGGCAA 59.936 40.000 0.00 0.00 0.00 4.52
2184 3792 7.005062 CACAGGCAGTGTAATTAGTAATGTC 57.995 40.000 1.31 0.00 43.40 3.06
2258 3866 9.449896 TGTGTTAAACATTAGGGAGGGTATATA 57.550 33.333 0.00 0.00 32.36 0.86
2259 3867 8.339720 TGTGTTAAACATTAGGGAGGGTATAT 57.660 34.615 0.00 0.00 32.36 0.86
2260 3868 7.752518 TGTGTTAAACATTAGGGAGGGTATA 57.247 36.000 0.00 0.00 32.36 1.47
2261 3869 6.645884 TGTGTTAAACATTAGGGAGGGTAT 57.354 37.500 0.00 0.00 32.36 2.73
2295 3998 7.909121 GTGCATTGAATCTTGTAGATGAGAAAG 59.091 37.037 0.00 0.00 34.65 2.62
2321 4024 9.750125 AAGGATTACTTTTAACTTTTTCAGCTG 57.250 29.630 7.63 7.63 35.35 4.24
2400 4103 8.787818 AGTAAACCAGGAATCCAGGATTAATTA 58.212 33.333 18.16 5.84 31.54 1.40
2430 4133 6.726764 AGGTCCACTAAATACTCTTGAGACTT 59.273 38.462 4.49 0.00 0.00 3.01
2434 4137 7.334671 GGAAAAGGTCCACTAAATACTCTTGAG 59.665 40.741 0.00 0.00 46.97 3.02
2453 4156 7.466746 TGGAGATCAATGTTAAAGGAAAAGG 57.533 36.000 0.00 0.00 0.00 3.11
2454 4157 8.742777 TCATGGAGATCAATGTTAAAGGAAAAG 58.257 33.333 0.00 0.00 0.00 2.27
2620 4508 7.073883 CGCTGAAAGACATTGGTATCATTATG 58.926 38.462 0.00 0.00 34.07 1.90
2645 4533 2.500509 GACAGATGGAGATGTCGGAC 57.499 55.000 0.00 0.00 36.76 4.79
3153 5047 5.545658 ACGGACAATTAGTTACAGCAATG 57.454 39.130 0.00 0.00 0.00 2.82
3411 5526 7.243824 ACATATATTTAGGAACGGAGGGAGTA 58.756 38.462 0.00 0.00 0.00 2.59
3412 5527 6.082707 ACATATATTTAGGAACGGAGGGAGT 58.917 40.000 0.00 0.00 0.00 3.85
3413 5528 6.437793 AGACATATATTTAGGAACGGAGGGAG 59.562 42.308 0.00 0.00 0.00 4.30
3414 5529 6.320518 AGACATATATTTAGGAACGGAGGGA 58.679 40.000 0.00 0.00 0.00 4.20
3415 5530 6.607004 AGACATATATTTAGGAACGGAGGG 57.393 41.667 0.00 0.00 0.00 4.30
3416 5531 8.904099 AAAAGACATATATTTAGGAACGGAGG 57.096 34.615 0.00 0.00 0.00 4.30
3440 5555 9.967451 TGTGGTAGTCCATTTGAAATCTATAAA 57.033 29.630 0.00 0.00 46.20 1.40
3443 5558 9.561069 GTATGTGGTAGTCCATTTGAAATCTAT 57.439 33.333 0.00 0.00 46.20 1.98
3444 5559 7.709182 CGTATGTGGTAGTCCATTTGAAATCTA 59.291 37.037 0.00 0.00 46.20 1.98
3445 5560 6.538742 CGTATGTGGTAGTCCATTTGAAATCT 59.461 38.462 0.00 0.00 46.20 2.40
3446 5561 6.238374 CCGTATGTGGTAGTCCATTTGAAATC 60.238 42.308 0.00 0.00 46.20 2.17
3447 5562 5.588648 CCGTATGTGGTAGTCCATTTGAAAT 59.411 40.000 0.00 0.00 46.20 2.17
3448 5563 4.938832 CCGTATGTGGTAGTCCATTTGAAA 59.061 41.667 0.00 0.00 46.20 2.69
3449 5564 4.223255 TCCGTATGTGGTAGTCCATTTGAA 59.777 41.667 0.00 0.00 46.20 2.69
3450 5565 3.770388 TCCGTATGTGGTAGTCCATTTGA 59.230 43.478 0.00 0.00 46.20 2.69
3451 5566 4.131649 TCCGTATGTGGTAGTCCATTTG 57.868 45.455 0.00 0.00 46.20 2.32
3452 5567 4.163458 ACATCCGTATGTGGTAGTCCATTT 59.837 41.667 0.00 0.00 44.79 2.32
3453 5568 3.709653 ACATCCGTATGTGGTAGTCCATT 59.290 43.478 0.00 0.00 44.79 3.16
3454 5569 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
3455 5570 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.00 0.00 44.79 4.02
3456 5571 6.770746 ATATACATCCGTATGTGGTAGTCC 57.229 41.667 3.56 0.00 45.99 3.85
3457 5572 8.610896 GTCTATATACATCCGTATGTGGTAGTC 58.389 40.741 3.56 0.00 45.99 2.59
3458 5573 8.105197 TGTCTATATACATCCGTATGTGGTAGT 58.895 37.037 3.56 0.00 45.99 2.73
3459 5574 8.396390 GTGTCTATATACATCCGTATGTGGTAG 58.604 40.741 3.56 3.93 45.99 3.18
3460 5575 7.884354 TGTGTCTATATACATCCGTATGTGGTA 59.116 37.037 3.56 0.00 45.99 3.25
3461 5576 6.717997 TGTGTCTATATACATCCGTATGTGGT 59.282 38.462 3.56 0.00 45.99 4.16
3462 5577 7.153217 TGTGTCTATATACATCCGTATGTGG 57.847 40.000 3.56 0.00 45.99 4.17
3463 5578 9.639601 AAATGTGTCTATATACATCCGTATGTG 57.360 33.333 3.56 0.00 45.99 3.21
3479 5594 9.856488 GTGAATCTACACTCTAAAATGTGTCTA 57.144 33.333 1.91 0.00 44.94 2.59
3480 5595 8.589338 AGTGAATCTACACTCTAAAATGTGTCT 58.411 33.333 1.91 0.00 46.36 3.41
3481 5596 8.764524 AGTGAATCTACACTCTAAAATGTGTC 57.235 34.615 1.91 0.00 46.36 3.67
3494 5609 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
3495 5610 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
3496 5611 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
3497 5612 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
3498 5613 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
3499 5614 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
3500 5615 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
3501 5616 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
3502 5617 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
3503 5618 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
3504 5619 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
3505 5620 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
3506 5621 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
3507 5622 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
3508 5623 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
3509 5624 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
3510 5625 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
3511 5626 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
3512 5627 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
3513 5628 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
3514 5629 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
3515 5630 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
3516 5631 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
3517 5632 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
3518 5633 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
3520 5635 9.778741 TTTAGAGATTTCAACAAGTGACTACAT 57.221 29.630 0.00 0.00 35.39 2.29
3521 5636 9.607988 TTTTAGAGATTTCAACAAGTGACTACA 57.392 29.630 0.00 0.00 35.39 2.74
3524 5639 9.396022 TCTTTTTAGAGATTTCAACAAGTGACT 57.604 29.630 0.00 0.00 35.39 3.41
3525 5640 9.439537 GTCTTTTTAGAGATTTCAACAAGTGAC 57.560 33.333 0.00 0.00 35.39 3.67
3526 5641 9.173021 TGTCTTTTTAGAGATTTCAACAAGTGA 57.827 29.630 0.00 0.00 0.00 3.41
3527 5642 9.787532 TTGTCTTTTTAGAGATTTCAACAAGTG 57.212 29.630 0.00 0.00 0.00 3.16
3544 5659 9.338622 CCTCCGTTCCTATATATTTGTCTTTTT 57.661 33.333 0.00 0.00 0.00 1.94
3545 5660 7.937394 CCCTCCGTTCCTATATATTTGTCTTTT 59.063 37.037 0.00 0.00 0.00 2.27
3546 5661 7.291651 TCCCTCCGTTCCTATATATTTGTCTTT 59.708 37.037 0.00 0.00 0.00 2.52
3547 5662 6.785963 TCCCTCCGTTCCTATATATTTGTCTT 59.214 38.462 0.00 0.00 0.00 3.01
3548 5663 6.320518 TCCCTCCGTTCCTATATATTTGTCT 58.679 40.000 0.00 0.00 0.00 3.41
3549 5664 6.210984 ACTCCCTCCGTTCCTATATATTTGTC 59.789 42.308 0.00 0.00 0.00 3.18
3550 5665 6.082707 ACTCCCTCCGTTCCTATATATTTGT 58.917 40.000 0.00 0.00 0.00 2.83
3551 5666 6.607004 ACTCCCTCCGTTCCTATATATTTG 57.393 41.667 0.00 0.00 0.00 2.32
3553 5668 9.589461 CATATACTCCCTCCGTTCCTATATATT 57.411 37.037 0.00 0.00 0.00 1.28
3554 5669 8.956860 TCATATACTCCCTCCGTTCCTATATAT 58.043 37.037 0.00 0.00 0.00 0.86
3555 5670 8.341022 TCATATACTCCCTCCGTTCCTATATA 57.659 38.462 0.00 0.00 0.00 0.86
3556 5671 7.222180 TCATATACTCCCTCCGTTCCTATAT 57.778 40.000 0.00 0.00 0.00 0.86
3557 5672 6.647461 TCATATACTCCCTCCGTTCCTATA 57.353 41.667 0.00 0.00 0.00 1.31
3558 5673 5.531753 TCATATACTCCCTCCGTTCCTAT 57.468 43.478 0.00 0.00 0.00 2.57
3559 5674 5.531753 ATCATATACTCCCTCCGTTCCTA 57.468 43.478 0.00 0.00 0.00 2.94
3560 5675 3.897657 TCATATACTCCCTCCGTTCCT 57.102 47.619 0.00 0.00 0.00 3.36
3561 5676 4.283722 ACAATCATATACTCCCTCCGTTCC 59.716 45.833 0.00 0.00 0.00 3.62
3562 5677 5.470047 ACAATCATATACTCCCTCCGTTC 57.530 43.478 0.00 0.00 0.00 3.95
3563 5678 5.836898 TGTACAATCATATACTCCCTCCGTT 59.163 40.000 0.00 0.00 0.00 4.44
3564 5679 5.391256 TGTACAATCATATACTCCCTCCGT 58.609 41.667 0.00 0.00 0.00 4.69
3565 5680 5.977489 TGTACAATCATATACTCCCTCCG 57.023 43.478 0.00 0.00 0.00 4.63
3566 5681 7.179338 ACAGATGTACAATCATATACTCCCTCC 59.821 40.741 0.00 0.00 0.00 4.30
3567 5682 8.128322 ACAGATGTACAATCATATACTCCCTC 57.872 38.462 0.00 0.00 0.00 4.30
3568 5683 8.497910 AACAGATGTACAATCATATACTCCCT 57.502 34.615 0.00 0.00 0.00 4.20
3569 5684 7.819900 GGAACAGATGTACAATCATATACTCCC 59.180 40.741 0.00 0.00 0.00 4.30
3570 5685 8.589338 AGGAACAGATGTACAATCATATACTCC 58.411 37.037 0.00 0.00 0.00 3.85
3571 5686 9.988815 AAGGAACAGATGTACAATCATATACTC 57.011 33.333 0.00 0.00 0.00 2.59
3572 5687 9.770097 CAAGGAACAGATGTACAATCATATACT 57.230 33.333 0.00 0.00 0.00 2.12
3573 5688 9.547753 ACAAGGAACAGATGTACAATCATATAC 57.452 33.333 0.00 0.00 0.00 1.47
3649 5764 6.382859 GGTAGTTCAAATCCCCAAACCATATT 59.617 38.462 0.00 0.00 0.00 1.28
3852 5967 9.558396 TTTTCGGATTTCTTTAGTAGTACCAAA 57.442 29.630 0.00 0.00 0.00 3.28
4145 6385 9.965824 CTTGTCATGGAACTACTTAAAATTGTT 57.034 29.630 0.00 0.00 0.00 2.83
4283 6523 0.798776 CGAACAGCCGCTCAATCTTT 59.201 50.000 0.00 0.00 0.00 2.52
4303 6543 8.732746 ATTTCTATGTTGTCCTTATGGTGTAC 57.267 34.615 0.00 0.00 34.23 2.90
4317 6557 6.183347 ACCTCTTGGGAAGATTTCTATGTTG 58.817 40.000 0.00 0.00 36.82 3.33
4352 6593 1.273594 GCAAAGCTTTTGTGCACGC 59.726 52.632 9.53 9.42 38.19 5.34
4373 6614 3.552604 TGGCATGCTTAACGAAAAGAC 57.447 42.857 18.92 0.00 0.00 3.01
4496 6737 4.280929 GCAACCAATAGGACTTTTGGACTT 59.719 41.667 22.70 9.16 42.04 3.01
4497 6738 3.826729 GCAACCAATAGGACTTTTGGACT 59.173 43.478 22.70 10.31 42.04 3.85
4498 6739 3.572255 TGCAACCAATAGGACTTTTGGAC 59.428 43.478 22.70 13.97 42.04 4.02
4499 6740 3.838565 TGCAACCAATAGGACTTTTGGA 58.161 40.909 22.70 3.40 42.04 3.53
4500 6741 4.599047 TTGCAACCAATAGGACTTTTGG 57.401 40.909 16.67 16.67 44.06 3.28
4589 6830 0.253327 AGGGCCTCTTTGGTTCGATC 59.747 55.000 0.00 0.00 38.35 3.69
4776 7041 8.440833 AGTTCAATTACTTAAGACGTATGCAAC 58.559 33.333 10.09 2.77 0.00 4.17
4949 7214 7.451501 TTTTCATGTCAGCATTAGATGAACA 57.548 32.000 0.00 0.00 42.59 3.18
4951 7216 7.412063 CGATTTTCATGTCAGCATTAGATGAA 58.588 34.615 0.00 0.00 42.59 2.57
4987 7252 6.206048 CCTTATTCTTGTCCGTTGGTAAAAGT 59.794 38.462 0.00 0.00 0.00 2.66
5037 7302 6.899393 AAGATTTAGAAAATGACCACTGCA 57.101 33.333 0.00 0.00 0.00 4.41
5038 7303 7.370383 TGAAAGATTTAGAAAATGACCACTGC 58.630 34.615 0.00 0.00 0.00 4.40
5080 7345 6.870769 ACATACGCACCTGTTTAGTTACTAT 58.129 36.000 0.00 0.00 0.00 2.12
5084 7349 5.136816 TGACATACGCACCTGTTTAGTTA 57.863 39.130 0.00 0.00 0.00 2.24
5085 7350 3.997762 TGACATACGCACCTGTTTAGTT 58.002 40.909 0.00 0.00 0.00 2.24
5086 7351 3.671008 TGACATACGCACCTGTTTAGT 57.329 42.857 0.00 0.00 0.00 2.24
5087 7352 3.370978 CCTTGACATACGCACCTGTTTAG 59.629 47.826 0.00 0.00 0.00 1.85
5088 7353 3.331150 CCTTGACATACGCACCTGTTTA 58.669 45.455 0.00 0.00 0.00 2.01
5089 7354 2.151202 CCTTGACATACGCACCTGTTT 58.849 47.619 0.00 0.00 0.00 2.83
5098 7363 4.394920 ACTTTGTATTGGCCTTGACATACG 59.605 41.667 3.32 0.00 0.00 3.06
5145 7410 6.827586 TGATTCCATTGTTGTTACCTAACC 57.172 37.500 0.00 0.00 35.37 2.85
5297 7566 1.320344 CCAGGGCTAGAGTGCGTGTA 61.320 60.000 0.00 0.00 0.00 2.90
5307 7576 2.950781 TCTGTATGAGTCCAGGGCTAG 58.049 52.381 0.00 0.00 0.00 3.42
5374 7643 4.219033 GTGTTATTTTGTGGAAGCTCACG 58.781 43.478 1.53 0.00 40.31 4.35
5467 7736 5.384787 GGTTTTTAACCGTCGTCCAAATAG 58.615 41.667 0.00 0.00 42.62 1.73
5468 7737 5.355467 GGTTTTTAACCGTCGTCCAAATA 57.645 39.130 0.00 0.00 42.62 1.40
5469 7738 4.227512 GGTTTTTAACCGTCGTCCAAAT 57.772 40.909 0.00 0.00 42.62 2.32
5563 7832 3.810310 TTTGGACTGCGTTGGAAAAAT 57.190 38.095 0.00 0.00 0.00 1.82
5706 7979 4.507710 TGTTGCTTCATCCTGTCATAGAC 58.492 43.478 0.00 0.00 0.00 2.59
5707 7980 4.824479 TGTTGCTTCATCCTGTCATAGA 57.176 40.909 0.00 0.00 0.00 1.98
5708 7981 5.821470 AGATTGTTGCTTCATCCTGTCATAG 59.179 40.000 0.00 0.00 0.00 2.23
5709 7982 5.748402 AGATTGTTGCTTCATCCTGTCATA 58.252 37.500 0.00 0.00 0.00 2.15
5710 7983 4.597004 AGATTGTTGCTTCATCCTGTCAT 58.403 39.130 0.00 0.00 0.00 3.06
5711 7984 4.025040 AGATTGTTGCTTCATCCTGTCA 57.975 40.909 0.00 0.00 0.00 3.58
5712 7985 5.382618 AAAGATTGTTGCTTCATCCTGTC 57.617 39.130 0.00 0.00 0.00 3.51
5713 7986 5.796424 AAAAGATTGTTGCTTCATCCTGT 57.204 34.783 0.00 0.00 0.00 4.00
5753 8026 2.100584 TCAAAATGCTCGTGGCTTGTTT 59.899 40.909 5.00 2.12 42.39 2.83
5784 8057 4.870991 CGGTAGAAAGGAGGAAAGAACATC 59.129 45.833 0.00 0.00 0.00 3.06
5797 8070 3.777478 TGCTACGAAATCGGTAGAAAGG 58.223 45.455 7.81 0.00 44.95 3.11
5813 8086 3.003689 AGTTGCAAGACACACAATGCTAC 59.996 43.478 0.00 0.00 42.27 3.58
5814 8087 3.003585 CAGTTGCAAGACACACAATGCTA 59.996 43.478 0.00 0.00 39.49 3.49
5877 8151 2.936919 TCCATCCACCTATGTGCATC 57.063 50.000 0.00 0.00 41.35 3.91
6025 8299 0.603975 GAGGTGTTGGAGAGGCACAC 60.604 60.000 0.00 0.00 40.16 3.82
6097 8371 2.068915 TGCCTCAGCAGGAACATCA 58.931 52.632 0.00 0.00 46.52 3.07
6137 8411 4.376413 CGCGCATCCATCTTACAAGTTATC 60.376 45.833 8.75 0.00 0.00 1.75
6158 8433 0.946221 GGATGTCATCGGGTCATCGC 60.946 60.000 6.74 0.00 38.86 4.58
6166 8441 2.230992 GGATCTGAGAGGATGTCATCGG 59.769 54.545 6.74 0.00 37.93 4.18
6201 8476 6.096846 TCTGACCATTTTGATCTCGATCTACA 59.903 38.462 8.25 0.00 38.60 2.74
6216 8491 6.126681 TGTCACCATATGAGATCTGACCATTT 60.127 38.462 0.00 0.00 38.28 2.32
6239 8514 4.783227 AGGACACATACCCAATCTAGTTGT 59.217 41.667 0.00 0.00 36.01 3.32
6268 8543 4.853142 TAGATGGCGGCGGGGAGT 62.853 66.667 9.78 0.00 0.00 3.85
6326 8601 5.185635 CCATTCAATTGACACATAACCAGGT 59.814 40.000 7.89 0.00 0.00 4.00
6359 8634 4.252971 TGTGTAGCTCTACCAAGTGAAC 57.747 45.455 0.00 0.00 35.26 3.18
6364 8639 5.724328 TGAAGAATGTGTAGCTCTACCAAG 58.276 41.667 0.00 0.00 35.26 3.61
6379 8654 5.289675 GTGGTACGAAGAGACATGAAGAATG 59.710 44.000 0.00 0.00 42.48 2.67
6386 8661 3.502920 GACAGTGGTACGAAGAGACATG 58.497 50.000 0.00 0.00 0.00 3.21
6387 8662 2.492484 GGACAGTGGTACGAAGAGACAT 59.508 50.000 0.00 0.00 0.00 3.06
6388 8663 1.884579 GGACAGTGGTACGAAGAGACA 59.115 52.381 0.00 0.00 0.00 3.41
6389 8664 1.884579 TGGACAGTGGTACGAAGAGAC 59.115 52.381 0.00 0.00 0.00 3.36
6414 8689 1.501582 AGAGTTAGGATCACTGGGGC 58.498 55.000 0.00 0.00 0.00 5.80
6420 8695 6.922407 GGTTCGGTAATAAGAGTTAGGATCAC 59.078 42.308 0.00 0.00 0.00 3.06
6452 8735 3.521560 TGATATTCGGCAAGTCACACTC 58.478 45.455 0.00 0.00 0.00 3.51
6465 8748 7.412137 TCACACTTGCTATCATTGATATTCG 57.588 36.000 6.82 0.00 0.00 3.34
6552 8835 3.958798 CCCCTCAACGGAGAGTAGAATAA 59.041 47.826 5.78 0.00 44.26 1.40
6556 8839 0.033405 CCCCCTCAACGGAGAGTAGA 60.033 60.000 5.78 0.00 44.26 2.59
6585 8890 0.846693 AGAGAGAGAGAGAGAGGGGC 59.153 60.000 0.00 0.00 0.00 5.80
6649 9110 3.762407 TGTGGAATTTTCTGTCTCCGA 57.238 42.857 0.00 0.00 0.00 4.55
6658 9119 6.738114 TCTGTGAAGTGATTGTGGAATTTTC 58.262 36.000 0.00 0.00 0.00 2.29
6659 9120 6.713762 TCTGTGAAGTGATTGTGGAATTTT 57.286 33.333 0.00 0.00 0.00 1.82
6665 9126 4.396166 GGGTTATCTGTGAAGTGATTGTGG 59.604 45.833 0.00 0.00 0.00 4.17
6683 9145 2.549349 GCTTGTGAAAGAGGTCGGGTTA 60.549 50.000 0.00 0.00 0.00 2.85
6721 9183 6.933514 AAATGGTTTGGTCATATTGGTTCT 57.066 33.333 0.00 0.00 0.00 3.01
6724 9187 7.124147 CCTTCTAAATGGTTTGGTCATATTGGT 59.876 37.037 0.00 0.00 0.00 3.67
6790 9253 2.593436 CCACCAAGCGACCGGTTT 60.593 61.111 9.42 0.00 31.41 3.27
6819 9282 2.154462 AGTTGCTTTCGTTGGATGGAG 58.846 47.619 0.00 0.00 0.00 3.86
6829 9292 7.427606 GTCAGATTTGATCATAAGTTGCTTTCG 59.572 37.037 0.00 0.00 35.39 3.46
6879 9342 7.827729 CCTCTATAATCCATCAATTGCATGAGA 59.172 37.037 15.30 11.99 31.76 3.27
6936 9399 5.376625 GGCAAGTAACCATGGATCTATGAA 58.623 41.667 21.47 3.02 0.00 2.57
6939 9402 3.983410 AGGGCAAGTAACCATGGATCTAT 59.017 43.478 21.47 0.00 0.00 1.98
6957 9420 3.481453 GATTTCCCATCTAAGTGAGGGC 58.519 50.000 0.00 0.00 44.69 5.19
6981 9444 3.085952 TCCAAGTTCATCCCCACAATC 57.914 47.619 0.00 0.00 0.00 2.67
7010 9473 3.485947 TGTCGGTTTTTGCTGCATATC 57.514 42.857 1.84 0.00 0.00 1.63
7011 9474 3.181487 GGATGTCGGTTTTTGCTGCATAT 60.181 43.478 1.84 0.00 0.00 1.78
7012 9475 2.163412 GGATGTCGGTTTTTGCTGCATA 59.837 45.455 1.84 0.00 0.00 3.14
7018 9481 2.223711 ACAACTGGATGTCGGTTTTTGC 60.224 45.455 0.00 0.00 42.69 3.68
7027 9490 3.255888 GGGAAAGGAAACAACTGGATGTC 59.744 47.826 0.00 0.00 31.81 3.06
7032 9495 2.239400 GAGGGGAAAGGAAACAACTGG 58.761 52.381 0.00 0.00 0.00 4.00
7100 9567 2.528797 GCGAAGAACGGAAGAAGCA 58.471 52.632 0.00 0.00 42.83 3.91


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

AutoCloner maintained by Alex Coulton.