Multiple sequence alignment - TraesCS5D01G257100

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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 TraesCS5D01G257100 chr5D 100.000 6777 0 0 1 6777 363338141 363344917 0.000000e+00 12515
1 TraesCS5D01G257100 chr5D 94.428 2782 126 8 3431 6185 363179449 363182228 0.000000e+00 4252
2 TraesCS5D01G257100 chr5D 94.368 2699 75 31 1 2669 363974193 363976844 0.000000e+00 4071
3 TraesCS5D01G257100 chr5D 87.320 1806 162 33 4412 6169 363978799 363980585 0.000000e+00 2004
4 TraesCS5D01G257100 chr5D 92.723 1333 43 21 1575 2876 363177468 363178777 0.000000e+00 1875
5 TraesCS5D01G257100 chr5D 94.167 960 37 11 621 1571 363176408 363177357 0.000000e+00 1445
6 TraesCS5D01G257100 chr5D 88.629 642 46 13 2805 3433 363178735 363179362 0.000000e+00 756
7 TraesCS5D01G257100 chr5D 86.575 581 53 7 1 575 363175841 363176402 9.660000e-173 617
8 TraesCS5D01G257100 chr5D 89.796 343 24 7 6180 6521 363187370 363187702 4.860000e-116 429
9 TraesCS5D01G257100 chr5D 86.957 230 24 4 3660 3884 363977669 363977897 3.140000e-63 254
10 TraesCS5D01G257100 chr5B 94.370 2007 106 3 3904 5904 429729338 429731343 0.000000e+00 3073
11 TraesCS5D01G257100 chr5B 89.810 1580 73 26 3 1571 429818559 429820061 0.000000e+00 1945
12 TraesCS5D01G257100 chr5B 92.502 1227 55 20 361 1571 429725837 429727042 0.000000e+00 1722
13 TraesCS5D01G257100 chr5B 93.543 1115 32 17 1575 2669 429820133 429821227 0.000000e+00 1624
14 TraesCS5D01G257100 chr5B 88.142 1324 146 9 5055 6371 429823751 429825070 0.000000e+00 1565
15 TraesCS5D01G257100 chr5B 87.305 1347 140 19 5055 6379 429887585 429888922 0.000000e+00 1511
16 TraesCS5D01G257100 chr5B 87.947 1203 101 11 3903 5062 429822272 429823473 0.000000e+00 1378
17 TraesCS5D01G257100 chr5B 88.604 1132 90 13 3906 5026 429886266 429887369 0.000000e+00 1339
18 TraesCS5D01G257100 chr5B 94.083 845 18 13 1574 2401 429727119 429727948 0.000000e+00 1254
19 TraesCS5D01G257100 chr5B 82.739 1373 119 63 253 1571 429881515 429882823 0.000000e+00 1114
20 TraesCS5D01G257100 chr5B 97.239 507 14 0 1829 2335 429883151 429883657 0.000000e+00 859
21 TraesCS5D01G257100 chr5B 87.870 676 68 8 5936 6607 429731340 429732005 0.000000e+00 782
22 TraesCS5D01G257100 chr5B 87.748 555 55 5 1 555 429725297 429725838 2.670000e-178 636
23 TraesCS5D01G257100 chr5B 89.686 223 18 5 3660 3878 429822056 429822277 5.180000e-71 279
24 TraesCS5D01G257100 chr5B 79.750 400 51 16 2865 3237 429728339 429728735 5.210000e-66 263
25 TraesCS5D01G257100 chr5B 90.576 191 17 1 3673 3862 429886079 429886269 1.130000e-62 252
26 TraesCS5D01G257100 chr5B 88.601 193 18 2 3705 3897 429728902 429729090 1.470000e-56 231
27 TraesCS5D01G257100 chr5B 92.073 164 8 1 1640 1798 429882991 429883154 6.840000e-55 226
28 TraesCS5D01G257100 chr5A 91.447 1590 54 32 3 1571 464632704 464634232 0.000000e+00 2108
29 TraesCS5D01G257100 chr5A 94.675 1108 28 12 1575 2669 464634304 464635393 0.000000e+00 1690
30 TraesCS5D01G257100 chr5A 91.268 1191 96 8 5055 6242 464637883 464639068 0.000000e+00 1616
31 TraesCS5D01G257100 chr5A 89.185 1202 82 23 3902 5066 464636429 464637619 0.000000e+00 1456
32 TraesCS5D01G257100 chr5A 89.912 228 19 4 3660 3884 464636218 464636444 2.390000e-74 291
33 TraesCS5D01G257100 chr3A 89.552 402 34 7 6380 6777 638186050 638186447 2.820000e-138 503
34 TraesCS5D01G257100 chr3D 89.055 402 38 5 6380 6777 496724457 496724856 1.700000e-135 494
35 TraesCS5D01G257100 chr3D 88.806 402 40 3 6380 6777 135815199 135815599 7.900000e-134 488
36 TraesCS5D01G257100 chr7D 88.778 401 42 2 6380 6777 427634686 427635086 7.900000e-134 488
37 TraesCS5D01G257100 chr7D 88.308 402 40 6 6380 6777 269384722 269384324 6.150000e-130 475
38 TraesCS5D01G257100 chr2B 88.089 403 43 4 6380 6777 404120731 404120329 2.210000e-129 473
39 TraesCS5D01G257100 chr4D 88.491 391 41 2 6380 6767 346234581 346234970 2.860000e-128 470
40 TraesCS5D01G257100 chr3B 87.811 402 44 4 6380 6777 655807452 655807852 3.700000e-127 466
41 TraesCS5D01G257100 chr4A 87.317 410 47 3 6372 6777 137459871 137459463 1.330000e-126 464
42 TraesCS5D01G257100 chr6B 82.700 474 80 2 1846 2318 179464122 179464594 2.920000e-113 420
43 TraesCS5D01G257100 chrUn 77.632 304 57 11 1844 2141 22056738 22056440 2.510000e-39 174
44 TraesCS5D01G257100 chr2D 77.181 298 60 8 1848 2141 474750280 474749987 4.200000e-37 167


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 TraesCS5D01G257100 chr5D 363338141 363344917 6776 False 12515.000000 12515 100.000000 1 6777 1 chr5D.!!$F2 6776
1 TraesCS5D01G257100 chr5D 363974193 363980585 6392 False 2109.666667 4071 89.548333 1 6169 3 chr5D.!!$F4 6168
2 TraesCS5D01G257100 chr5D 363175841 363182228 6387 False 1789.000000 4252 91.304400 1 6185 5 chr5D.!!$F3 6184
3 TraesCS5D01G257100 chr5B 429818559 429825070 6511 False 1358.200000 1945 89.825600 3 6371 5 chr5B.!!$F2 6368
4 TraesCS5D01G257100 chr5B 429725297 429732005 6708 False 1137.285714 3073 89.274857 1 6607 7 chr5B.!!$F1 6606
5 TraesCS5D01G257100 chr5B 429881515 429888922 7407 False 883.500000 1511 89.756000 253 6379 6 chr5B.!!$F3 6126
6 TraesCS5D01G257100 chr5A 464632704 464639068 6364 False 1432.200000 2108 91.297400 3 6242 5 chr5A.!!$F1 6239

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
425 466 0.527817 GAGGACGTCGGCAACTATGG 60.528 60.000 9.92 0.0 0.00 2.74 F
760 1021 1.078567 CCTCTTGACCTGCTCCTGC 60.079 63.158 0.00 0.0 40.20 4.85 F
902 1179 1.755265 GCCCATACCACCATTCTGCAT 60.755 52.381 0.00 0.0 0.00 3.96 F
2387 3193 2.624364 AGTGCTGTTGATTGTTGCATGA 59.376 40.909 0.00 0.0 36.04 3.07 F
2955 3872 0.460311 AGATCCTACCGAAGTTGCCG 59.540 55.000 0.00 0.0 0.00 5.69 F
3669 6568 0.033366 AACATTCGTTTTGGCAGGGC 59.967 50.000 0.00 0.0 28.09 5.19 F
3807 6752 0.243907 GCTCGGTTCAGCTGTAGACA 59.756 55.000 14.67 0.0 36.38 3.41 F
4916 8616 0.110823 GCGTTGACCGTGTGATTGAC 60.111 55.000 0.00 0.0 39.32 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1711 2171 1.203287 AGGCTTACCGAAGTTCCGTAC 59.797 52.381 3.88 0.00 42.76 3.67 R
2683 3566 0.593128 CCCAACCAAAGCTGACGAAG 59.407 55.000 0.00 0.00 0.00 3.79 R
2687 3570 2.271944 AGTACCCAACCAAAGCTGAC 57.728 50.000 0.00 0.00 0.00 3.51 R
3462 4403 0.179156 ATTACTGTCGCCGTACGGTG 60.179 55.000 36.25 36.25 46.45 4.94 R
4488 8159 0.461339 GCGCGGAGGATTTGTAGGAA 60.461 55.000 8.83 0.00 0.00 3.36 R
4629 8308 0.727970 TGAAACCACACGACAAACCG 59.272 50.000 0.00 0.00 0.00 4.44 R
5560 9581 0.755686 GCCAGTACTCCCTGAGGATG 59.244 60.000 0.00 0.00 42.93 3.51 R
6694 10739 0.034477 AGTGAAAACTATGGCCCCCG 60.034 55.000 0.00 0.00 0.00 5.73 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
148 149 9.544579 AAAGTCTAACCTAAACTATACTGGACT 57.455 33.333 0.00 0.00 0.00 3.85
178 179 2.594592 GCCGAGGCACCAGTGTTT 60.595 61.111 9.58 0.00 41.49 2.83
242 243 1.515081 GAATTCACGTTTGGTCGGGA 58.485 50.000 0.00 0.00 41.60 5.14
338 343 1.806568 CACGGTTTGTGGTGTTGCT 59.193 52.632 0.00 0.00 45.21 3.91
382 387 1.597027 CGAATCGTACCATGGGGCC 60.597 63.158 18.09 0.00 37.90 5.80
415 441 1.100510 TCTATTGGGTGAGGACGTCG 58.899 55.000 9.92 0.00 0.00 5.12
425 466 0.527817 GAGGACGTCGGCAACTATGG 60.528 60.000 9.92 0.00 0.00 2.74
601 835 5.392595 GCTTCGGCAGTAAAATTGGACAATA 60.393 40.000 0.00 0.00 41.33 1.90
602 836 6.680378 GCTTCGGCAGTAAAATTGGACAATAT 60.680 38.462 0.00 0.00 41.33 1.28
603 837 6.767524 TCGGCAGTAAAATTGGACAATATT 57.232 33.333 0.00 0.00 0.00 1.28
604 838 7.867305 TCGGCAGTAAAATTGGACAATATTA 57.133 32.000 0.00 0.00 0.00 0.98
605 839 7.925993 TCGGCAGTAAAATTGGACAATATTAG 58.074 34.615 0.00 0.00 0.00 1.73
606 840 7.554835 TCGGCAGTAAAATTGGACAATATTAGT 59.445 33.333 0.00 0.00 0.00 2.24
607 841 8.832521 CGGCAGTAAAATTGGACAATATTAGTA 58.167 33.333 0.00 0.00 0.00 1.82
691 933 6.970484 TGTCATAGAAAAAGGAAGTTGAAGC 58.030 36.000 0.00 0.00 0.00 3.86
752 1013 1.918800 CCGTTCCCCCTCTTGACCT 60.919 63.158 0.00 0.00 0.00 3.85
760 1021 1.078567 CCTCTTGACCTGCTCCTGC 60.079 63.158 0.00 0.00 40.20 4.85
781 1044 3.851838 GCGTTCAAAAAGGCATTCGAGAA 60.852 43.478 0.00 0.00 43.92 2.87
785 1048 6.560251 CGTTCAAAAAGGCATTCGAGAAAAAG 60.560 38.462 0.00 0.00 0.00 2.27
902 1179 1.755265 GCCCATACCACCATTCTGCAT 60.755 52.381 0.00 0.00 0.00 3.96
927 1210 5.471456 AGTCATCACGAGCAAAAGAAGAAAT 59.529 36.000 0.00 0.00 0.00 2.17
1711 2171 3.274393 CCGGAGGCAGAAGTTATCG 57.726 57.895 0.00 0.00 46.14 2.92
2387 3193 2.624364 AGTGCTGTTGATTGTTGCATGA 59.376 40.909 0.00 0.00 36.04 3.07
2444 3283 3.181469 GGACATGATCGCAACCCTAGTAA 60.181 47.826 0.00 0.00 0.00 2.24
2445 3284 3.793559 ACATGATCGCAACCCTAGTAAC 58.206 45.455 0.00 0.00 0.00 2.50
2446 3285 3.451178 ACATGATCGCAACCCTAGTAACT 59.549 43.478 0.00 0.00 0.00 2.24
2447 3286 4.647853 ACATGATCGCAACCCTAGTAACTA 59.352 41.667 0.00 0.00 0.00 2.24
2448 3287 4.913335 TGATCGCAACCCTAGTAACTAG 57.087 45.455 0.00 0.00 34.16 2.57
2449 3288 4.275810 TGATCGCAACCCTAGTAACTAGT 58.724 43.478 0.00 0.00 32.62 2.57
2450 3289 5.439721 TGATCGCAACCCTAGTAACTAGTA 58.560 41.667 0.00 0.00 32.62 1.82
2488 3338 9.357161 AGTTTCACACTGGTGGTAATAAAAATA 57.643 29.630 5.70 0.00 45.32 1.40
2735 3618 6.076981 ACACGATTCATTGCTCTTCTTTTT 57.923 33.333 0.00 0.00 0.00 1.94
2775 3658 0.948623 TGTGGGTCGAATGTGAAGCG 60.949 55.000 0.00 0.00 0.00 4.68
2784 3667 3.376859 TCGAATGTGAAGCGGCAATTTAT 59.623 39.130 1.45 0.00 0.00 1.40
2792 3675 3.230743 AGCGGCAATTTATTGTGGTTC 57.769 42.857 1.45 0.00 39.88 3.62
2794 3677 2.669950 GCGGCAATTTATTGTGGTTCGT 60.670 45.455 0.00 0.00 39.88 3.85
2946 3863 6.654959 TCATATCTAAGGAGAGATCCTACCG 58.345 44.000 0.00 0.00 39.65 4.02
2955 3872 0.460311 AGATCCTACCGAAGTTGCCG 59.540 55.000 0.00 0.00 0.00 5.69
2984 3904 1.066071 TCGGGTTGGCGAAATCACATA 60.066 47.619 0.00 0.00 0.00 2.29
3093 4015 4.779993 ATTTCCCCCTAAGAGCAACTAG 57.220 45.455 0.00 0.00 0.00 2.57
3095 4017 1.365028 TCCCCCTAAGAGCAACTAGGT 59.635 52.381 0.00 0.00 0.00 3.08
3096 4018 2.197465 CCCCCTAAGAGCAACTAGGTT 58.803 52.381 0.00 0.00 0.00 3.50
3100 4022 4.263331 CCCCTAAGAGCAACTAGGTTTCAA 60.263 45.833 0.00 0.00 0.00 2.69
3101 4023 4.695928 CCCTAAGAGCAACTAGGTTTCAAC 59.304 45.833 0.00 0.00 0.00 3.18
3102 4024 5.305585 CCTAAGAGCAACTAGGTTTCAACA 58.694 41.667 0.00 0.00 0.00 3.33
3103 4025 5.763204 CCTAAGAGCAACTAGGTTTCAACAA 59.237 40.000 0.00 0.00 0.00 2.83
3104 4026 6.262273 CCTAAGAGCAACTAGGTTTCAACAAA 59.738 38.462 0.00 0.00 0.00 2.83
3123 4056 7.654116 TCAACAAAATTTAAACGGATTCTTCCC 59.346 33.333 0.00 0.00 39.01 3.97
3141 4074 8.527567 TTCTTCCCGCAAATAAAAATTACTTG 57.472 30.769 0.00 0.00 0.00 3.16
3153 4086 2.467566 ATTACTTGGTGTGACCCGAC 57.532 50.000 0.00 0.00 37.50 4.79
3222 4163 3.254411 GGGGCTAGATACGTGTAGGTAAC 59.746 52.174 0.00 0.00 0.00 2.50
3241 4182 5.819379 GGTAACTATGGGTTAAACCTAGCAC 59.181 44.000 11.71 10.61 41.41 4.40
3270 4211 3.573967 AGGGCACATAACAAAAACCTGAG 59.426 43.478 0.00 0.00 0.00 3.35
3271 4212 3.317150 GGCACATAACAAAAACCTGAGC 58.683 45.455 0.00 0.00 0.00 4.26
3298 4239 5.794945 CAGACGTACACCATAATGCAAAAAG 59.205 40.000 0.00 0.00 0.00 2.27
3340 4281 1.985473 TTGGTCACAGAAAGCATGCT 58.015 45.000 16.30 16.30 0.00 3.79
3433 4374 8.034313 ACTTAGCTATCCATCCACAATAGAAA 57.966 34.615 0.00 0.00 0.00 2.52
3434 4375 8.153550 ACTTAGCTATCCATCCACAATAGAAAG 58.846 37.037 0.00 0.00 0.00 2.62
3436 4377 7.141758 AGCTATCCATCCACAATAGAAAGAA 57.858 36.000 0.00 0.00 0.00 2.52
3437 4378 7.222872 AGCTATCCATCCACAATAGAAAGAAG 58.777 38.462 0.00 0.00 0.00 2.85
3439 4380 8.150945 GCTATCCATCCACAATAGAAAGAAGTA 58.849 37.037 0.00 0.00 0.00 2.24
3446 4387 8.294954 TCCACAATAGAAAGAAGTAGGAGTAG 57.705 38.462 0.00 0.00 0.00 2.57
3449 4390 9.930693 CACAATAGAAAGAAGTAGGAGTAGTTT 57.069 33.333 0.00 0.00 0.00 2.66
3542 6408 0.892755 TTACAGTGGCACCTCTACGG 59.107 55.000 15.27 0.00 39.35 4.02
3552 6418 2.642254 CCTCTACGGCGGTGGAACA 61.642 63.158 13.24 0.00 39.98 3.18
3564 6430 2.741433 TGGAACACTGGTAGCGACT 58.259 52.632 0.00 0.00 0.00 4.18
3567 6433 1.134560 GGAACACTGGTAGCGACTAGG 59.865 57.143 14.48 6.33 38.45 3.02
3568 6434 2.089980 GAACACTGGTAGCGACTAGGA 58.910 52.381 14.48 0.00 38.45 2.94
3577 6451 1.835494 AGCGACTAGGAACACTGCTA 58.165 50.000 0.00 0.00 0.00 3.49
3578 6452 1.473278 AGCGACTAGGAACACTGCTAC 59.527 52.381 0.00 0.00 0.00 3.58
3584 6458 2.092882 GGAACACTGCTACGCCGAC 61.093 63.158 0.00 0.00 0.00 4.79
3587 6461 1.802337 AACACTGCTACGCCGACTGA 61.802 55.000 0.00 0.00 0.00 3.41
3669 6568 0.033366 AACATTCGTTTTGGCAGGGC 59.967 50.000 0.00 0.00 28.09 5.19
3694 6639 0.870393 GCATTGATCGATCATGCCGT 59.130 50.000 31.30 16.33 36.36 5.68
3738 6683 2.426522 TCATAGCACAGTGGCAAAGAC 58.573 47.619 1.84 0.00 35.83 3.01
3807 6752 0.243907 GCTCGGTTCAGCTGTAGACA 59.756 55.000 14.67 0.00 36.38 3.41
3822 6767 4.407365 TGTAGACAACTGTGGAGAGATCA 58.593 43.478 0.00 0.00 0.00 2.92
3827 6772 5.078411 ACAACTGTGGAGAGATCATGTAC 57.922 43.478 0.00 0.00 0.00 2.90
3830 6775 6.609212 ACAACTGTGGAGAGATCATGTACTAT 59.391 38.462 0.00 0.00 0.00 2.12
3838 6792 9.078990 TGGAGAGATCATGTACTATTCGTATTT 57.921 33.333 0.00 0.00 0.00 1.40
3890 6848 6.320164 TCTGATACAACAAATTAATTCCCCGG 59.680 38.462 0.10 0.00 0.00 5.73
3962 7165 4.825085 GTGAGAGTAATTTTGTGGGGTGAA 59.175 41.667 0.00 0.00 0.00 3.18
4011 7215 2.156117 CGCGTGTTTTCCTAAATGACGA 59.844 45.455 0.00 0.00 35.58 4.20
4121 7362 5.945191 TGTGAAATTTCAGACATGCCATCTA 59.055 36.000 21.05 0.00 37.98 1.98
4195 7436 4.526970 AGAAACTCTTGAAGCCACTGAAA 58.473 39.130 0.00 0.00 0.00 2.69
4278 7528 1.447838 CCCGTCACTGATGAACCCG 60.448 63.158 0.00 0.00 36.31 5.28
4302 7552 1.891150 GACCACTTTCTGAGGACCGTA 59.109 52.381 0.00 0.00 0.00 4.02
4325 7575 1.521423 CAAGGACTTCGACAACGTGAC 59.479 52.381 0.00 0.00 40.69 3.67
4401 8072 8.555896 TGGTGAATAGTATTCCTAACCATACA 57.444 34.615 21.32 6.88 31.83 2.29
4461 8132 0.250513 GCGGGAAGAAGATGACCACT 59.749 55.000 0.00 0.00 0.00 4.00
4572 8247 2.363925 AGTAGCCCGGACTCCACC 60.364 66.667 0.73 0.00 0.00 4.61
4629 8308 8.728088 ATTTTGCTAATTATAAGCGTGTATGC 57.272 30.769 0.00 0.00 43.11 3.14
4709 8392 0.976641 TCCTGATGCAGTCCTTCGTT 59.023 50.000 0.00 0.00 0.00 3.85
4721 8404 4.022242 CAGTCCTTCGTTCTAACCAAGAGA 60.022 45.833 2.28 0.00 35.05 3.10
4848 8531 1.687123 GCTACGGATCCATACAGGTGT 59.313 52.381 13.41 1.03 39.02 4.16
4898 8589 0.179156 CCGCCATTGATCACTGTTGC 60.179 55.000 11.65 7.97 0.00 4.17
4902 8593 2.587956 CCATTGATCACTGTTGCGTTG 58.412 47.619 11.65 0.00 0.00 4.10
4916 8616 0.110823 GCGTTGACCGTGTGATTGAC 60.111 55.000 0.00 0.00 39.32 3.18
5045 8766 2.350057 TCGGATCGAGTTCCATCTCT 57.650 50.000 5.92 0.00 35.34 3.10
5082 9103 9.093970 CATGATACATTGATTTGATGTGCTTTT 57.906 29.630 0.00 0.00 38.17 2.27
5149 9170 2.953821 GGGGTGTCGTCGTTCGTA 59.046 61.111 0.00 0.00 40.80 3.43
5317 9338 1.071385 GAGGGCCTGATGATGATCGTT 59.929 52.381 12.95 0.00 0.00 3.85
5685 9706 0.107945 ATGAAGCTCACCGAGAAGGC 60.108 55.000 0.00 0.00 46.52 4.35
5686 9707 1.448717 GAAGCTCACCGAGAAGGCC 60.449 63.158 0.00 0.00 46.52 5.19
5780 9801 0.883833 AAATGGAGCAAAGTGAGGCG 59.116 50.000 0.00 0.00 34.54 5.52
5828 9863 6.096705 TGTTAATGGAGGATTGTTGCTTATGG 59.903 38.462 0.00 0.00 0.00 2.74
5834 9869 4.781934 AGGATTGTTGCTTATGGGTACTC 58.218 43.478 0.00 0.00 0.00 2.59
5952 9988 5.941948 AATGTAATTAGTTCATAGGCCGC 57.058 39.130 0.00 0.00 32.46 6.53
6056 10096 6.778834 ATGATTACACAAGCATCCATCAAA 57.221 33.333 0.00 0.00 35.96 2.69
6059 10099 7.036829 TGATTACACAAGCATCCATCAAATTG 58.963 34.615 0.00 0.00 0.00 2.32
6072 10112 7.936496 TCCATCAAATTGCTGTTAAGACATA 57.064 32.000 0.00 0.00 34.72 2.29
6091 10131 5.718146 ACATAAGTCTCAGTGTCACATGAG 58.282 41.667 18.75 18.75 43.53 2.90
6101 10141 1.695242 TGTCACATGAGGGGTTAACGT 59.305 47.619 0.00 0.00 0.00 3.99
6106 10146 0.690762 ATGAGGGGTTAACGTGCACT 59.309 50.000 16.19 0.00 0.00 4.40
6139 10179 5.698545 ACAAGAGACATCTACTGAGCAAAAC 59.301 40.000 0.00 0.00 33.45 2.43
6169 10209 3.695830 ATTACAGAACCACACGACCAT 57.304 42.857 0.00 0.00 0.00 3.55
6173 10213 0.036732 AGAACCACACGACCATGCAT 59.963 50.000 0.00 0.00 0.00 3.96
6174 10214 0.881118 GAACCACACGACCATGCATT 59.119 50.000 0.00 0.00 0.00 3.56
6187 10227 4.312443 ACCATGCATTGAAGCTTTTTGAG 58.688 39.130 4.52 0.00 34.99 3.02
6188 10228 4.039488 ACCATGCATTGAAGCTTTTTGAGA 59.961 37.500 4.52 0.00 34.99 3.27
6253 10294 4.427637 ACATATCTCCAGAGGCATCATCT 58.572 43.478 0.00 0.00 0.00 2.90
6275 10316 1.681166 GCAATCCTGAGCATGACAGGT 60.681 52.381 26.90 17.24 0.00 4.00
6279 10320 2.046988 TGAGCATGACAGGTGCCG 60.047 61.111 0.00 0.00 43.50 5.69
6280 10321 2.821366 GAGCATGACAGGTGCCGG 60.821 66.667 0.00 0.00 43.50 6.13
6281 10322 3.612247 GAGCATGACAGGTGCCGGT 62.612 63.158 1.90 0.00 43.50 5.28
6316 10358 1.210204 AGACATCAGCCACCACCCAT 61.210 55.000 0.00 0.00 0.00 4.00
6323 10365 2.178580 CAGCCACCACCCATAACATTT 58.821 47.619 0.00 0.00 0.00 2.32
6328 10370 3.193267 CCACCACCCATAACATTTGTCTG 59.807 47.826 0.00 0.00 0.00 3.51
6354 10396 4.581391 GAAGACCCCCTTCCTGGA 57.419 61.111 0.00 0.00 44.27 3.86
6367 10409 2.580601 CCTGGACGGTTTCGGGAGT 61.581 63.158 4.82 0.00 41.39 3.85
6384 10426 3.142174 GGAGTAGGCCATCAAATGCTAC 58.858 50.000 5.01 0.00 0.00 3.58
6391 10433 3.193267 GGCCATCAAATGCTACTTGTGAA 59.807 43.478 0.00 0.00 0.00 3.18
6392 10434 4.142093 GGCCATCAAATGCTACTTGTGAAT 60.142 41.667 0.00 0.00 0.00 2.57
6396 10438 4.475028 TCAAATGCTACTTGTGAATTGCG 58.525 39.130 0.00 0.00 0.00 4.85
6397 10439 3.492421 AATGCTACTTGTGAATTGCGG 57.508 42.857 0.00 0.00 0.00 5.69
6400 10442 1.135689 GCTACTTGTGAATTGCGGTGG 60.136 52.381 0.00 0.00 0.00 4.61
6407 10449 2.366916 TGTGAATTGCGGTGGGATTTTT 59.633 40.909 0.00 0.00 0.00 1.94
6421 10463 3.017442 GGATTTTTCCCGAAGAGGAAGG 58.983 50.000 0.00 0.00 46.44 3.46
6469 10511 7.554959 AGTATTCCTCTTACTGAGAACCAAA 57.445 36.000 0.00 0.00 45.39 3.28
6475 10517 7.974504 TCCTCTTACTGAGAACCAAAGTTATT 58.025 34.615 0.00 0.00 45.39 1.40
6479 10521 9.052759 TCTTACTGAGAACCAAAGTTATTGAAC 57.947 33.333 0.00 0.00 35.94 3.18
6486 10528 8.934023 AGAACCAAAGTTATTGAACCAATAGA 57.066 30.769 0.00 0.00 37.57 1.98
6506 10548 3.584848 AGAAGAATCACACCAAGCCTAGT 59.415 43.478 0.00 0.00 0.00 2.57
6512 10554 4.471904 TCACACCAAGCCTAGTGAATAG 57.528 45.455 4.76 0.00 37.99 1.73
6581 10623 2.820197 GGTTGTCAATCCCCTTGAACTC 59.180 50.000 0.00 0.00 45.27 3.01
6591 10636 1.308998 CCTTGAACTCGTTTGCAGGT 58.691 50.000 0.00 0.00 0.00 4.00
6607 10652 9.864034 CGTTTGCAGGTATTAAATCTAGTAATG 57.136 33.333 0.00 0.00 0.00 1.90
6609 10654 9.914834 TTTGCAGGTATTAAATCTAGTAATGGT 57.085 29.630 0.00 0.00 0.00 3.55
6673 10718 9.834628 ATTGCAGCAAGATATTTTTGATTTTTG 57.165 25.926 14.47 0.00 0.00 2.44
6674 10719 8.380743 TGCAGCAAGATATTTTTGATTTTTGT 57.619 26.923 0.00 0.00 0.00 2.83
6675 10720 9.486497 TGCAGCAAGATATTTTTGATTTTTGTA 57.514 25.926 0.00 0.00 0.00 2.41
6697 10742 9.550406 TTGTAATATGATAAAAGTAGAACCGGG 57.450 33.333 6.32 0.00 0.00 5.73
6698 10743 8.152246 TGTAATATGATAAAAGTAGAACCGGGG 58.848 37.037 6.32 0.00 0.00 5.73
6699 10744 3.918294 TGATAAAAGTAGAACCGGGGG 57.082 47.619 6.32 0.00 0.00 5.40
6700 10745 2.092807 TGATAAAAGTAGAACCGGGGGC 60.093 50.000 6.32 0.00 0.00 5.80
6701 10746 0.620030 TAAAAGTAGAACCGGGGGCC 59.380 55.000 6.32 0.00 0.00 5.80
6702 10747 1.428718 AAAAGTAGAACCGGGGGCCA 61.429 55.000 6.32 0.00 0.00 5.36
6703 10748 1.212250 AAAGTAGAACCGGGGGCCAT 61.212 55.000 6.32 0.00 0.00 4.40
6704 10749 0.326808 AAGTAGAACCGGGGGCCATA 60.327 55.000 6.32 0.00 0.00 2.74
6705 10750 0.763223 AGTAGAACCGGGGGCCATAG 60.763 60.000 6.32 0.00 0.00 2.23
6706 10751 1.052694 GTAGAACCGGGGGCCATAGT 61.053 60.000 6.32 0.00 0.00 2.12
6707 10752 0.326808 TAGAACCGGGGGCCATAGTT 60.327 55.000 6.32 4.76 0.00 2.24
6708 10753 1.212250 AGAACCGGGGGCCATAGTTT 61.212 55.000 6.32 0.00 0.00 2.66
6709 10754 0.323999 GAACCGGGGGCCATAGTTTT 60.324 55.000 6.32 0.00 0.00 2.43
6710 10755 0.323999 AACCGGGGGCCATAGTTTTC 60.324 55.000 6.32 0.00 0.00 2.29
6711 10756 1.304952 CCGGGGGCCATAGTTTTCA 59.695 57.895 4.39 0.00 0.00 2.69
6712 10757 1.035385 CCGGGGGCCATAGTTTTCAC 61.035 60.000 4.39 0.00 0.00 3.18
6713 10758 0.034477 CGGGGGCCATAGTTTTCACT 60.034 55.000 4.39 0.00 36.99 3.41
6714 10759 1.210967 CGGGGGCCATAGTTTTCACTA 59.789 52.381 4.39 0.00 39.94 2.74
6715 10760 2.745152 CGGGGGCCATAGTTTTCACTAG 60.745 54.545 4.39 0.00 38.96 2.57
6716 10761 2.508300 GGGGGCCATAGTTTTCACTAGA 59.492 50.000 4.39 0.00 38.96 2.43
6717 10762 3.433740 GGGGGCCATAGTTTTCACTAGAG 60.434 52.174 4.39 0.00 38.96 2.43
6718 10763 3.433740 GGGGCCATAGTTTTCACTAGAGG 60.434 52.174 4.39 0.00 38.96 3.69
6723 10768 5.983540 CCATAGTTTTCACTAGAGGCTTCT 58.016 41.667 3.00 3.00 38.96 2.85
6724 10769 6.045955 CCATAGTTTTCACTAGAGGCTTCTC 58.954 44.000 0.00 0.00 38.96 2.87
6726 10771 5.400066 AGTTTTCACTAGAGGCTTCTCTC 57.600 43.478 0.00 0.00 43.99 3.20
6727 10772 5.083821 AGTTTTCACTAGAGGCTTCTCTCT 58.916 41.667 0.00 0.00 43.99 3.10
6728 10773 5.542251 AGTTTTCACTAGAGGCTTCTCTCTT 59.458 40.000 0.00 0.00 43.99 2.85
6729 10774 5.398603 TTTCACTAGAGGCTTCTCTCTTG 57.601 43.478 0.00 0.00 43.99 3.02
6730 10775 4.308526 TCACTAGAGGCTTCTCTCTTGA 57.691 45.455 0.00 0.90 43.99 3.02
6731 10776 4.667573 TCACTAGAGGCTTCTCTCTTGAA 58.332 43.478 0.00 0.00 43.99 2.69
6732 10777 5.080337 TCACTAGAGGCTTCTCTCTTGAAA 58.920 41.667 0.00 0.00 43.99 2.69
6733 10778 5.047660 TCACTAGAGGCTTCTCTCTTGAAAC 60.048 44.000 0.00 0.00 43.99 2.78
6734 10779 4.835615 ACTAGAGGCTTCTCTCTTGAAACA 59.164 41.667 0.00 0.00 43.99 2.83
6735 10780 4.906747 AGAGGCTTCTCTCTTGAAACAT 57.093 40.909 0.00 0.00 43.99 2.71
6736 10781 6.665680 ACTAGAGGCTTCTCTCTTGAAACATA 59.334 38.462 0.00 0.00 43.99 2.29
6737 10782 5.976458 AGAGGCTTCTCTCTTGAAACATAG 58.024 41.667 0.00 0.00 43.99 2.23
6738 10783 4.512484 AGGCTTCTCTCTTGAAACATAGC 58.488 43.478 0.00 0.00 0.00 2.97
6739 10784 4.019860 AGGCTTCTCTCTTGAAACATAGCA 60.020 41.667 0.00 0.00 0.00 3.49
6740 10785 4.880696 GGCTTCTCTCTTGAAACATAGCAT 59.119 41.667 0.00 0.00 0.00 3.79
6741 10786 6.051717 GGCTTCTCTCTTGAAACATAGCATA 58.948 40.000 0.00 0.00 0.00 3.14
6742 10787 6.018343 GGCTTCTCTCTTGAAACATAGCATAC 60.018 42.308 0.00 0.00 0.00 2.39
6743 10788 6.292061 GCTTCTCTCTTGAAACATAGCATACG 60.292 42.308 0.00 0.00 0.00 3.06
6744 10789 5.592054 TCTCTCTTGAAACATAGCATACGG 58.408 41.667 0.00 0.00 0.00 4.02
6745 10790 5.127194 TCTCTCTTGAAACATAGCATACGGT 59.873 40.000 0.00 0.00 0.00 4.83
6746 10791 5.109210 TCTCTTGAAACATAGCATACGGTG 58.891 41.667 0.00 0.00 0.00 4.94
6747 10792 5.079689 TCTTGAAACATAGCATACGGTGA 57.920 39.130 0.00 0.00 0.00 4.02
6748 10793 5.109210 TCTTGAAACATAGCATACGGTGAG 58.891 41.667 0.00 0.00 0.00 3.51
6749 10794 4.465632 TGAAACATAGCATACGGTGAGT 57.534 40.909 0.00 0.00 0.00 3.41
6750 10795 4.180817 TGAAACATAGCATACGGTGAGTG 58.819 43.478 0.00 0.00 0.00 3.51
6751 10796 4.081917 TGAAACATAGCATACGGTGAGTGA 60.082 41.667 0.00 0.00 0.00 3.41
6752 10797 4.465632 AACATAGCATACGGTGAGTGAA 57.534 40.909 0.00 0.00 0.00 3.18
6753 10798 3.782046 ACATAGCATACGGTGAGTGAAC 58.218 45.455 0.00 0.00 0.00 3.18
6754 10799 3.194755 ACATAGCATACGGTGAGTGAACA 59.805 43.478 0.00 0.00 0.00 3.18
6755 10800 2.831685 AGCATACGGTGAGTGAACAA 57.168 45.000 0.00 0.00 0.00 2.83
6756 10801 3.120321 AGCATACGGTGAGTGAACAAA 57.880 42.857 0.00 0.00 0.00 2.83
6757 10802 3.674997 AGCATACGGTGAGTGAACAAAT 58.325 40.909 0.00 0.00 0.00 2.32
6758 10803 4.072131 AGCATACGGTGAGTGAACAAATT 58.928 39.130 0.00 0.00 0.00 1.82
6759 10804 5.242434 AGCATACGGTGAGTGAACAAATTA 58.758 37.500 0.00 0.00 0.00 1.40
6760 10805 5.121768 AGCATACGGTGAGTGAACAAATTAC 59.878 40.000 0.00 0.00 0.00 1.89
6761 10806 5.121768 GCATACGGTGAGTGAACAAATTACT 59.878 40.000 0.00 0.00 0.00 2.24
6762 10807 6.534059 CATACGGTGAGTGAACAAATTACTG 58.466 40.000 0.00 0.00 0.00 2.74
6763 10808 4.448210 ACGGTGAGTGAACAAATTACTGT 58.552 39.130 0.00 0.00 0.00 3.55
6764 10809 4.879545 ACGGTGAGTGAACAAATTACTGTT 59.120 37.500 0.00 0.00 42.23 3.16
6765 10810 5.204833 CGGTGAGTGAACAAATTACTGTTG 58.795 41.667 0.25 0.00 39.63 3.33
6766 10811 5.519722 GGTGAGTGAACAAATTACTGTTGG 58.480 41.667 0.25 0.00 39.63 3.77
6767 10812 5.298276 GGTGAGTGAACAAATTACTGTTGGA 59.702 40.000 0.25 0.00 39.63 3.53
6768 10813 6.199393 GTGAGTGAACAAATTACTGTTGGAC 58.801 40.000 0.25 0.00 39.63 4.02
6769 10814 5.883115 TGAGTGAACAAATTACTGTTGGACA 59.117 36.000 0.25 0.00 39.63 4.02
6770 10815 6.375736 TGAGTGAACAAATTACTGTTGGACAA 59.624 34.615 0.25 0.00 39.63 3.18
6771 10816 7.068103 TGAGTGAACAAATTACTGTTGGACAAT 59.932 33.333 0.25 0.00 39.63 2.71
6772 10817 8.458573 AGTGAACAAATTACTGTTGGACAATA 57.541 30.769 0.25 0.00 39.63 1.90
6773 10818 8.567948 AGTGAACAAATTACTGTTGGACAATAG 58.432 33.333 7.18 7.18 39.63 1.73
6774 10819 8.564574 GTGAACAAATTACTGTTGGACAATAGA 58.435 33.333 14.48 0.00 39.63 1.98
6775 10820 9.295825 TGAACAAATTACTGTTGGACAATAGAT 57.704 29.630 14.48 3.40 39.63 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
141 142 4.519730 CGGCTTTAGCTAGTATAGTCCAGT 59.480 45.833 1.26 0.00 41.93 4.00
142 143 4.760715 TCGGCTTTAGCTAGTATAGTCCAG 59.239 45.833 1.26 0.00 41.93 3.86
143 144 4.722220 TCGGCTTTAGCTAGTATAGTCCA 58.278 43.478 1.26 0.00 41.93 4.02
144 145 4.156373 CCTCGGCTTTAGCTAGTATAGTCC 59.844 50.000 1.26 0.00 41.93 3.85
145 146 4.379708 GCCTCGGCTTTAGCTAGTATAGTC 60.380 50.000 0.00 0.00 38.47 2.59
146 147 3.506844 GCCTCGGCTTTAGCTAGTATAGT 59.493 47.826 0.00 0.00 38.47 2.12
147 148 3.506455 TGCCTCGGCTTTAGCTAGTATAG 59.494 47.826 9.65 0.00 41.21 1.31
148 149 3.255149 GTGCCTCGGCTTTAGCTAGTATA 59.745 47.826 9.65 0.00 42.51 1.47
149 150 2.036089 GTGCCTCGGCTTTAGCTAGTAT 59.964 50.000 9.65 0.00 42.51 2.12
150 151 1.407979 GTGCCTCGGCTTTAGCTAGTA 59.592 52.381 9.65 0.00 42.51 1.82
151 152 0.175989 GTGCCTCGGCTTTAGCTAGT 59.824 55.000 9.65 0.00 42.51 2.57
152 153 0.530870 GGTGCCTCGGCTTTAGCTAG 60.531 60.000 9.65 0.37 42.51 3.42
338 343 3.727923 AGGACACCCTAATCCTAGCTAGA 59.272 47.826 22.70 8.71 43.85 2.43
382 387 2.036475 CCAATAGATGACTCACCCTCCG 59.964 54.545 0.00 0.00 0.00 4.63
415 441 2.497273 AGCAAATTCCACCATAGTTGCC 59.503 45.455 0.00 0.00 41.72 4.52
425 466 2.550606 TCGTACCAACAGCAAATTCCAC 59.449 45.455 0.00 0.00 0.00 4.02
496 729 6.825721 AGGTTCTCCAGAGCAAATTATTACTG 59.174 38.462 0.00 0.00 35.89 2.74
595 829 7.438459 ACGAGGCAGACAAATACTAATATTGTC 59.562 37.037 9.26 9.26 33.52 3.18
596 830 7.272978 ACGAGGCAGACAAATACTAATATTGT 58.727 34.615 0.00 0.00 31.07 2.71
601 835 6.466885 AGTACGAGGCAGACAAATACTAAT 57.533 37.500 0.00 0.00 0.00 1.73
602 836 5.909621 AGTACGAGGCAGACAAATACTAA 57.090 39.130 0.00 0.00 0.00 2.24
603 837 5.184479 ACAAGTACGAGGCAGACAAATACTA 59.816 40.000 0.00 0.00 0.00 1.82
604 838 4.021368 ACAAGTACGAGGCAGACAAATACT 60.021 41.667 0.00 0.00 0.00 2.12
605 839 4.243270 ACAAGTACGAGGCAGACAAATAC 58.757 43.478 0.00 0.00 0.00 1.89
606 840 4.021807 TGACAAGTACGAGGCAGACAAATA 60.022 41.667 0.00 0.00 0.00 1.40
607 841 3.244078 TGACAAGTACGAGGCAGACAAAT 60.244 43.478 0.00 0.00 0.00 2.32
608 842 2.101750 TGACAAGTACGAGGCAGACAAA 59.898 45.455 0.00 0.00 0.00 2.83
609 843 1.684450 TGACAAGTACGAGGCAGACAA 59.316 47.619 0.00 0.00 0.00 3.18
614 848 2.333291 TCGTGACAAGTACGAGGCA 58.667 52.632 0.00 0.00 44.65 4.75
691 933 0.098552 TATACGTACGTGCGTGTGGG 59.901 55.000 36.35 7.17 45.33 4.61
752 1013 0.667993 CCTTTTTGAACGCAGGAGCA 59.332 50.000 0.00 0.00 42.27 4.26
760 1021 3.536158 TCTCGAATGCCTTTTTGAACG 57.464 42.857 0.00 0.00 0.00 3.95
785 1048 9.959749 TCAAATCACAACTTGGTTTAGATTAAC 57.040 29.630 0.00 0.00 36.29 2.01
902 1179 5.134202 TCTTCTTTTGCTCGTGATGACTA 57.866 39.130 0.00 0.00 0.00 2.59
927 1210 1.229820 AGCTGGGTGGTGGTATGGA 60.230 57.895 0.00 0.00 0.00 3.41
1711 2171 1.203287 AGGCTTACCGAAGTTCCGTAC 59.797 52.381 3.88 0.00 42.76 3.67
2444 3283 6.585322 GTGAAACTGTGAATACGCTTACTAGT 59.415 38.462 0.00 0.00 0.00 2.57
2445 3284 6.584942 TGTGAAACTGTGAATACGCTTACTAG 59.415 38.462 0.00 0.00 38.04 2.57
2446 3285 6.364165 GTGTGAAACTGTGAATACGCTTACTA 59.636 38.462 0.00 0.00 38.04 1.82
2447 3286 5.176958 GTGTGAAACTGTGAATACGCTTACT 59.823 40.000 0.00 0.00 38.04 2.24
2448 3287 5.176958 AGTGTGAAACTGTGAATACGCTTAC 59.823 40.000 0.00 0.00 37.88 2.34
2449 3288 5.294356 AGTGTGAAACTGTGAATACGCTTA 58.706 37.500 0.00 0.00 37.88 3.09
2450 3289 4.127171 AGTGTGAAACTGTGAATACGCTT 58.873 39.130 0.00 0.00 37.88 4.68
2488 3338 7.486407 AAGATCCAAGCCTAAACATCAAATT 57.514 32.000 0.00 0.00 0.00 1.82
2570 3441 5.044846 GGACTTGCAGATATACCCCCATATT 60.045 44.000 0.00 0.00 0.00 1.28
2571 3442 4.475016 GGACTTGCAGATATACCCCCATAT 59.525 45.833 0.00 0.00 0.00 1.78
2683 3566 0.593128 CCCAACCAAAGCTGACGAAG 59.407 55.000 0.00 0.00 0.00 3.79
2687 3570 2.271944 AGTACCCAACCAAAGCTGAC 57.728 50.000 0.00 0.00 0.00 3.51
2750 3633 2.894765 TCACATTCGACCCACACTTAGA 59.105 45.455 0.00 0.00 0.00 2.10
2751 3634 3.313012 TCACATTCGACCCACACTTAG 57.687 47.619 0.00 0.00 0.00 2.18
2775 3658 4.747605 ACAAACGAACCACAATAAATTGCC 59.252 37.500 2.60 0.00 41.38 4.52
2784 3667 5.373981 AAACTGTAACAAACGAACCACAA 57.626 34.783 0.00 0.00 0.00 3.33
2901 3817 7.910441 ATGATTTGTGGGATCAATGTTTTTC 57.090 32.000 0.00 0.00 37.11 2.29
2905 3821 9.645128 TTAGATATGATTTGTGGGATCAATGTT 57.355 29.630 0.00 0.00 37.11 2.71
2908 3824 8.672329 TCCTTAGATATGATTTGTGGGATCAAT 58.328 33.333 0.00 0.00 37.11 2.57
2909 3825 8.044574 TCCTTAGATATGATTTGTGGGATCAA 57.955 34.615 0.00 0.00 37.11 2.57
2962 3879 2.038269 TGATTTCGCCAACCCGAGC 61.038 57.895 0.00 0.00 38.60 5.03
3026 3948 3.672767 AAAAGGACGGTCGACACTTAT 57.327 42.857 18.91 0.00 0.00 1.73
3027 3949 3.457610 AAAAAGGACGGTCGACACTTA 57.542 42.857 18.91 0.00 0.00 2.24
3032 3954 2.733552 GGACTTAAAAAGGACGGTCGAC 59.266 50.000 7.13 7.13 0.00 4.20
3034 3956 1.723003 CGGACTTAAAAAGGACGGTCG 59.277 52.381 1.43 0.00 0.00 4.79
3076 3998 1.880941 ACCTAGTTGCTCTTAGGGGG 58.119 55.000 11.09 0.00 34.13 5.40
3093 4015 8.822855 AGAATCCGTTTAAATTTTGTTGAAACC 58.177 29.630 0.00 0.00 0.00 3.27
3096 4018 9.036671 GGAAGAATCCGTTTAAATTTTGTTGAA 57.963 29.630 0.00 0.00 35.59 2.69
3123 4056 7.358848 GGTCACACCAAGTAATTTTTATTTGCG 60.359 37.037 0.00 0.00 38.42 4.85
3141 4074 2.981859 ATATGAAGTCGGGTCACACC 57.018 50.000 0.00 0.00 37.60 4.16
3192 4132 3.272574 CGTATCTAGCCCCTATACGGA 57.727 52.381 11.25 0.00 42.82 4.69
3204 4145 6.939163 ACCCATAGTTACCTACACGTATCTAG 59.061 42.308 0.00 0.00 28.80 2.43
3222 4163 4.876107 CACAGTGCTAGGTTTAACCCATAG 59.124 45.833 10.93 8.15 39.75 2.23
3226 4167 3.007614 TCTCACAGTGCTAGGTTTAACCC 59.992 47.826 10.93 0.00 39.75 4.11
3253 4194 3.957497 TGGTGCTCAGGTTTTTGTTATGT 59.043 39.130 0.00 0.00 0.00 2.29
3270 4211 2.373540 TTATGGTGTACGTCTGGTGC 57.626 50.000 0.00 0.00 0.00 5.01
3271 4212 2.607635 GCATTATGGTGTACGTCTGGTG 59.392 50.000 0.00 0.00 0.00 4.17
3371 4312 5.511234 ACGGTAAGTACTAAATCAGCGAT 57.489 39.130 15.24 0.00 0.00 4.58
3373 4314 5.229469 CAGAACGGTAAGTACTAAATCAGCG 59.771 44.000 0.00 3.82 0.00 5.18
3453 4394 2.023318 CCGTACGGTGTGGCAAAAA 58.977 52.632 26.39 0.00 0.00 1.94
3454 4395 3.733806 CCGTACGGTGTGGCAAAA 58.266 55.556 26.39 0.00 0.00 2.44
3460 4401 2.186350 TACTGTCGCCGTACGGTGTG 62.186 60.000 38.54 30.67 45.37 3.82
3461 4402 1.514678 TTACTGTCGCCGTACGGTGT 61.515 55.000 38.54 25.85 45.37 4.16
3462 4403 0.179156 ATTACTGTCGCCGTACGGTG 60.179 55.000 36.25 36.25 46.45 4.94
3542 6408 2.033194 GCTACCAGTGTTCCACCGC 61.033 63.158 0.00 0.00 34.49 5.68
3552 6418 1.817447 GTGTTCCTAGTCGCTACCAGT 59.183 52.381 0.00 0.00 0.00 4.00
3553 6419 2.093106 AGTGTTCCTAGTCGCTACCAG 58.907 52.381 0.00 0.00 0.00 4.00
3554 6420 1.816835 CAGTGTTCCTAGTCGCTACCA 59.183 52.381 0.00 0.00 0.00 3.25
3555 6421 1.469423 GCAGTGTTCCTAGTCGCTACC 60.469 57.143 0.00 0.00 0.00 3.18
3556 6422 1.473278 AGCAGTGTTCCTAGTCGCTAC 59.527 52.381 0.00 0.00 0.00 3.58
3557 6423 1.835494 AGCAGTGTTCCTAGTCGCTA 58.165 50.000 0.00 0.00 0.00 4.26
3558 6424 1.473278 GTAGCAGTGTTCCTAGTCGCT 59.527 52.381 0.00 0.00 0.00 4.93
3559 6425 1.794437 CGTAGCAGTGTTCCTAGTCGC 60.794 57.143 0.00 0.00 0.00 5.19
3560 6426 2.175530 CGTAGCAGTGTTCCTAGTCG 57.824 55.000 0.00 0.00 0.00 4.18
3577 6451 2.201022 AGTGGTCTTCAGTCGGCGT 61.201 57.895 6.85 0.00 0.00 5.68
3578 6452 1.734477 CAGTGGTCTTCAGTCGGCG 60.734 63.158 0.00 0.00 0.00 6.46
3584 6458 2.245159 TCTTGTGCAGTGGTCTTCAG 57.755 50.000 0.00 0.00 0.00 3.02
3587 6461 1.344438 TCGATCTTGTGCAGTGGTCTT 59.656 47.619 0.00 0.00 0.00 3.01
3641 6540 1.686355 AAACGAATGTTCCCAGTGCA 58.314 45.000 0.00 0.00 37.31 4.57
3669 6568 3.492313 CATGATCGATCAATGCATGCTG 58.508 45.455 30.41 17.76 40.69 4.41
3694 6639 1.735700 CGATGCCGCAGTTGAGTTAGA 60.736 52.381 0.00 0.00 0.00 2.10
3738 6683 2.688507 ACTGTCCAGAATACAAGCACG 58.311 47.619 0.40 0.00 0.00 5.34
3807 6752 7.469318 CGAATAGTACATGATCTCTCCACAGTT 60.469 40.741 0.00 0.00 0.00 3.16
3865 6819 6.320164 CCGGGGAATTAATTTGTTGTATCAGA 59.680 38.462 1.43 0.00 0.00 3.27
3937 7138 3.139397 ACCCCACAAAATTACTCTCACCA 59.861 43.478 0.00 0.00 0.00 4.17
4004 7208 1.710013 GTGACCGTCACATCGTCATT 58.290 50.000 23.95 0.00 46.22 2.57
4005 7209 3.418675 GTGACCGTCACATCGTCAT 57.581 52.632 23.95 0.00 46.22 3.06
4121 7362 4.141528 CCAGCAAGTGAGGAAGATAGGAAT 60.142 45.833 0.00 0.00 0.00 3.01
4195 7436 7.951591 ACAAGCAAAGAAATTAGGTAACACAT 58.048 30.769 0.00 0.00 41.41 3.21
4278 7528 0.966920 TCCTCAGAAAGTGGTCGGAC 59.033 55.000 0.00 0.00 32.63 4.79
4302 7552 2.350498 CACGTTGTCGAAGTCCTTGTTT 59.650 45.455 0.00 0.00 40.62 2.83
4325 7575 4.881273 TCCTTATTGATTGAACCGATGTGG 59.119 41.667 0.00 0.00 46.41 4.17
4401 8072 7.405292 TGTCCTGAAGAATCAATTAATGGAGT 58.595 34.615 0.00 0.00 34.49 3.85
4488 8159 0.461339 GCGCGGAGGATTTGTAGGAA 60.461 55.000 8.83 0.00 0.00 3.36
4572 8247 8.571336 ACTCCAATTGAAAGTTTCAGAATGTAG 58.429 33.333 17.36 15.00 41.38 2.74
4629 8308 0.727970 TGAAACCACACGACAAACCG 59.272 50.000 0.00 0.00 0.00 4.44
4709 8392 6.213397 TGTTGATGAAGGATCTCTTGGTTAGA 59.787 38.462 1.70 0.00 35.50 2.10
4721 8404 4.474651 TCCCTGTACATGTTGATGAAGGAT 59.525 41.667 2.30 0.00 33.56 3.24
4848 8531 3.318275 ACAACGAGAGACTTCTTGCTACA 59.682 43.478 0.00 0.00 38.24 2.74
4902 8593 2.476619 CAGAGTTGTCAATCACACGGTC 59.523 50.000 0.00 0.00 33.41 4.79
4916 8616 1.284657 CGAGCCTACATGCAGAGTTG 58.715 55.000 0.00 0.00 0.00 3.16
5045 8766 6.207691 TCAATGTATCATGAGACGTGAGAA 57.792 37.500 15.61 0.00 0.00 2.87
5404 9425 3.319198 GGAAGGTCGTGGGGCAGA 61.319 66.667 0.00 0.00 0.00 4.26
5551 9572 2.105128 CTGAGGATGTCGTCGCCC 59.895 66.667 0.00 0.00 33.77 6.13
5560 9581 0.755686 GCCAGTACTCCCTGAGGATG 59.244 60.000 0.00 0.00 42.93 3.51
5685 9706 2.342650 CCGTTCACCATGGGCTTGG 61.343 63.158 18.09 7.30 42.82 3.61
5686 9707 2.342650 CCCGTTCACCATGGGCTTG 61.343 63.158 18.09 5.51 45.55 4.01
5780 9801 5.876612 AAACAATTGTGCTGATCTCTCTC 57.123 39.130 12.82 0.00 0.00 3.20
5828 9863 3.662247 ACACTGCAACACTAGAGTACC 57.338 47.619 0.00 0.00 0.00 3.34
5834 9869 1.670295 TGCACAACACTGCAACACTAG 59.330 47.619 0.00 0.00 44.28 2.57
5952 9988 5.517411 TGTATATCGACAAACCGCTTACAAG 59.483 40.000 0.00 0.00 0.00 3.16
6033 10073 6.778834 TTTGATGGATGCTTGTGTAATCAT 57.221 33.333 0.00 0.00 0.00 2.45
6072 10112 2.301296 CCCTCATGTGACACTGAGACTT 59.699 50.000 24.64 0.00 41.13 3.01
6091 10131 0.320697 AGAGAGTGCACGTTAACCCC 59.679 55.000 12.01 0.00 0.00 4.95
6101 10141 5.670485 TGTCTCTTGTTTTTAGAGAGTGCA 58.330 37.500 2.98 0.00 46.43 4.57
6106 10146 9.078990 TCAGTAGATGTCTCTTGTTTTTAGAGA 57.921 33.333 0.00 0.00 44.35 3.10
6139 10179 6.091713 CGTGTGGTTCTGTAATAAGGTTTAGG 59.908 42.308 0.00 0.00 0.00 2.69
6169 10209 6.592798 CTTTTCTCAAAAAGCTTCAATGCA 57.407 33.333 0.00 0.00 43.48 3.96
6187 10227 9.893305 ATGTGTGTAGTTTGTATTAAGCTTTTC 57.107 29.630 3.20 0.00 0.00 2.29
6253 10294 3.189618 CTGTCATGCTCAGGATTGCTA 57.810 47.619 9.02 0.00 0.00 3.49
6275 10316 1.302511 GCAAAAGGAGAGACCGGCA 60.303 57.895 0.00 0.00 44.74 5.69
6279 10320 3.070748 GTCTTCAGCAAAAGGAGAGACC 58.929 50.000 0.00 0.00 39.35 3.85
6280 10321 3.733337 TGTCTTCAGCAAAAGGAGAGAC 58.267 45.455 0.00 0.00 0.00 3.36
6281 10322 4.040829 TGATGTCTTCAGCAAAAGGAGAGA 59.959 41.667 0.00 0.00 37.02 3.10
6316 10358 1.992557 AGAGGGGCCAGACAAATGTTA 59.007 47.619 4.39 0.00 0.00 2.41
6323 10365 1.158466 TCTTCAGAGGGGCCAGACA 59.842 57.895 4.39 0.00 0.00 3.41
6328 10370 3.412408 GGGGTCTTCAGAGGGGCC 61.412 72.222 0.00 0.00 0.00 5.80
6354 10396 2.653087 GGCCTACTCCCGAAACCGT 61.653 63.158 0.00 0.00 0.00 4.83
6367 10409 3.947196 CACAAGTAGCATTTGATGGCCTA 59.053 43.478 3.32 0.00 0.00 3.93
6384 10426 1.176527 ATCCCACCGCAATTCACAAG 58.823 50.000 0.00 0.00 0.00 3.16
6400 10442 3.017442 CCTTCCTCTTCGGGAAAAATCC 58.983 50.000 0.00 0.00 43.74 3.01
6407 10449 0.178915 TTCACCCTTCCTCTTCGGGA 60.179 55.000 0.00 0.00 40.55 5.14
6414 10456 5.297569 ACTATATTGCTTCACCCTTCCTC 57.702 43.478 0.00 0.00 0.00 3.71
6421 10463 8.091449 ACTTATCAGCTACTATATTGCTTCACC 58.909 37.037 0.00 0.00 37.28 4.02
6451 10493 7.878127 TCAATAACTTTGGTTCTCAGTAAGAGG 59.122 37.037 0.00 0.00 44.81 3.69
6458 10500 6.633500 TGGTTCAATAACTTTGGTTCTCAG 57.367 37.500 0.00 0.00 36.92 3.35
6469 10511 9.739276 TGTGATTCTTCTATTGGTTCAATAACT 57.261 29.630 2.58 0.00 36.14 2.24
6475 10517 5.875224 TGGTGTGATTCTTCTATTGGTTCA 58.125 37.500 0.00 0.00 0.00 3.18
6479 10521 4.096984 GGCTTGGTGTGATTCTTCTATTGG 59.903 45.833 0.00 0.00 0.00 3.16
6486 10528 3.327757 TCACTAGGCTTGGTGTGATTCTT 59.672 43.478 12.03 0.00 37.13 2.52
6506 10548 1.202746 TGTGTGTGCAGGTGCTATTCA 60.203 47.619 3.18 0.00 42.66 2.57
6512 10554 1.650912 CTCTTGTGTGTGCAGGTGC 59.349 57.895 0.00 0.00 42.50 5.01
6516 10558 2.787601 ATTTGCTCTTGTGTGTGCAG 57.212 45.000 0.00 0.00 37.66 4.41
6546 10588 1.528309 CAACCCTCTTGCCCGTGTT 60.528 57.895 0.00 0.00 0.00 3.32
6549 10591 1.990160 TTGACAACCCTCTTGCCCGT 61.990 55.000 0.00 0.00 0.00 5.28
6581 10623 9.864034 CATTACTAGATTTAATACCTGCAAACG 57.136 33.333 0.00 0.00 0.00 3.60
6647 10692 9.834628 CAAAAATCAAAAATATCTTGCTGCAAT 57.165 25.926 16.38 4.53 0.00 3.56
6648 10693 8.838365 ACAAAAATCAAAAATATCTTGCTGCAA 58.162 25.926 15.16 15.16 0.00 4.08
6649 10694 8.380743 ACAAAAATCAAAAATATCTTGCTGCA 57.619 26.923 0.00 0.00 0.00 4.41
6671 10716 9.550406 CCCGGTTCTACTTTTATCATATTACAA 57.450 33.333 0.00 0.00 0.00 2.41
6672 10717 8.152246 CCCCGGTTCTACTTTTATCATATTACA 58.848 37.037 0.00 0.00 0.00 2.41
6673 10718 7.605309 CCCCCGGTTCTACTTTTATCATATTAC 59.395 40.741 0.00 0.00 0.00 1.89
6674 10719 7.682628 CCCCCGGTTCTACTTTTATCATATTA 58.317 38.462 0.00 0.00 0.00 0.98
6675 10720 6.540083 CCCCCGGTTCTACTTTTATCATATT 58.460 40.000 0.00 0.00 0.00 1.28
6676 10721 5.514310 GCCCCCGGTTCTACTTTTATCATAT 60.514 44.000 0.00 0.00 0.00 1.78
6677 10722 4.202388 GCCCCCGGTTCTACTTTTATCATA 60.202 45.833 0.00 0.00 0.00 2.15
6678 10723 3.434596 GCCCCCGGTTCTACTTTTATCAT 60.435 47.826 0.00 0.00 0.00 2.45
6679 10724 2.092807 GCCCCCGGTTCTACTTTTATCA 60.093 50.000 0.00 0.00 0.00 2.15
6680 10725 2.569059 GCCCCCGGTTCTACTTTTATC 58.431 52.381 0.00 0.00 0.00 1.75
6681 10726 1.213678 GGCCCCCGGTTCTACTTTTAT 59.786 52.381 0.00 0.00 0.00 1.40
6682 10727 0.620030 GGCCCCCGGTTCTACTTTTA 59.380 55.000 0.00 0.00 0.00 1.52
6683 10728 1.381463 GGCCCCCGGTTCTACTTTT 59.619 57.895 0.00 0.00 0.00 2.27
6684 10729 1.212250 ATGGCCCCCGGTTCTACTTT 61.212 55.000 0.00 0.00 0.00 2.66
6685 10730 0.326808 TATGGCCCCCGGTTCTACTT 60.327 55.000 0.00 0.00 0.00 2.24
6686 10731 0.763223 CTATGGCCCCCGGTTCTACT 60.763 60.000 0.00 0.00 0.00 2.57
6687 10732 1.052694 ACTATGGCCCCCGGTTCTAC 61.053 60.000 0.00 0.00 0.00 2.59
6688 10733 0.326808 AACTATGGCCCCCGGTTCTA 60.327 55.000 0.00 0.00 0.00 2.10
6689 10734 1.212250 AAACTATGGCCCCCGGTTCT 61.212 55.000 0.00 0.00 0.00 3.01
6690 10735 0.323999 AAAACTATGGCCCCCGGTTC 60.324 55.000 0.00 0.00 0.00 3.62
6691 10736 0.323999 GAAAACTATGGCCCCCGGTT 60.324 55.000 0.00 0.00 0.00 4.44
6692 10737 1.305287 GAAAACTATGGCCCCCGGT 59.695 57.895 0.00 0.00 0.00 5.28
6693 10738 1.035385 GTGAAAACTATGGCCCCCGG 61.035 60.000 0.00 0.00 0.00 5.73
6694 10739 0.034477 AGTGAAAACTATGGCCCCCG 60.034 55.000 0.00 0.00 0.00 5.73
6695 10740 2.508300 TCTAGTGAAAACTATGGCCCCC 59.492 50.000 0.00 0.00 0.00 5.40
6696 10741 3.433740 CCTCTAGTGAAAACTATGGCCCC 60.434 52.174 0.00 0.00 0.00 5.80
6697 10742 3.809905 CCTCTAGTGAAAACTATGGCCC 58.190 50.000 0.00 0.00 0.00 5.80
6698 10743 3.118223 AGCCTCTAGTGAAAACTATGGCC 60.118 47.826 18.33 0.00 39.91 5.36
6699 10744 4.143986 AGCCTCTAGTGAAAACTATGGC 57.856 45.455 16.03 16.03 39.64 4.40
6700 10745 5.983540 AGAAGCCTCTAGTGAAAACTATGG 58.016 41.667 0.00 0.00 0.00 2.74
6715 10760 4.570369 GCTATGTTTCAAGAGAGAAGCCTC 59.430 45.833 0.00 0.00 39.72 4.70
6716 10761 4.019860 TGCTATGTTTCAAGAGAGAAGCCT 60.020 41.667 0.00 0.00 0.00 4.58
6717 10762 4.256920 TGCTATGTTTCAAGAGAGAAGCC 58.743 43.478 0.00 0.00 0.00 4.35
6718 10763 6.292061 CGTATGCTATGTTTCAAGAGAGAAGC 60.292 42.308 0.00 0.00 0.00 3.86
6719 10764 6.199908 CCGTATGCTATGTTTCAAGAGAGAAG 59.800 42.308 0.00 0.00 0.00 2.85
6720 10765 6.042777 CCGTATGCTATGTTTCAAGAGAGAA 58.957 40.000 0.00 0.00 0.00 2.87
6721 10766 5.127194 ACCGTATGCTATGTTTCAAGAGAGA 59.873 40.000 0.00 0.00 0.00 3.10
6722 10767 5.233050 CACCGTATGCTATGTTTCAAGAGAG 59.767 44.000 0.00 0.00 0.00 3.20
6723 10768 5.105513 TCACCGTATGCTATGTTTCAAGAGA 60.106 40.000 0.00 0.00 0.00 3.10
6724 10769 5.109210 TCACCGTATGCTATGTTTCAAGAG 58.891 41.667 0.00 0.00 0.00 2.85
6725 10770 5.079689 TCACCGTATGCTATGTTTCAAGA 57.920 39.130 0.00 0.00 0.00 3.02
6726 10771 4.870426 ACTCACCGTATGCTATGTTTCAAG 59.130 41.667 0.00 0.00 0.00 3.02
6727 10772 4.629634 CACTCACCGTATGCTATGTTTCAA 59.370 41.667 0.00 0.00 0.00 2.69
6728 10773 4.081917 TCACTCACCGTATGCTATGTTTCA 60.082 41.667 0.00 0.00 0.00 2.69
6729 10774 4.430007 TCACTCACCGTATGCTATGTTTC 58.570 43.478 0.00 0.00 0.00 2.78
6730 10775 4.465632 TCACTCACCGTATGCTATGTTT 57.534 40.909 0.00 0.00 0.00 2.83
6731 10776 4.181578 GTTCACTCACCGTATGCTATGTT 58.818 43.478 0.00 0.00 0.00 2.71
6732 10777 3.194755 TGTTCACTCACCGTATGCTATGT 59.805 43.478 0.00 0.00 0.00 2.29
6733 10778 3.780902 TGTTCACTCACCGTATGCTATG 58.219 45.455 0.00 0.00 0.00 2.23
6734 10779 4.465632 TTGTTCACTCACCGTATGCTAT 57.534 40.909 0.00 0.00 0.00 2.97
6735 10780 3.945981 TTGTTCACTCACCGTATGCTA 57.054 42.857 0.00 0.00 0.00 3.49
6736 10781 2.831685 TTGTTCACTCACCGTATGCT 57.168 45.000 0.00 0.00 0.00 3.79
6737 10782 4.419522 AATTTGTTCACTCACCGTATGC 57.580 40.909 0.00 0.00 0.00 3.14
6738 10783 6.147164 ACAGTAATTTGTTCACTCACCGTATG 59.853 38.462 0.00 0.00 0.00 2.39
6739 10784 6.228258 ACAGTAATTTGTTCACTCACCGTAT 58.772 36.000 0.00 0.00 0.00 3.06
6740 10785 5.603596 ACAGTAATTTGTTCACTCACCGTA 58.396 37.500 0.00 0.00 0.00 4.02
6741 10786 4.448210 ACAGTAATTTGTTCACTCACCGT 58.552 39.130 0.00 0.00 0.00 4.83
6742 10787 5.204833 CAACAGTAATTTGTTCACTCACCG 58.795 41.667 0.00 0.00 39.17 4.94
6743 10788 5.298276 TCCAACAGTAATTTGTTCACTCACC 59.702 40.000 0.00 0.00 39.17 4.02
6744 10789 6.183360 TGTCCAACAGTAATTTGTTCACTCAC 60.183 38.462 0.00 0.00 39.17 3.51
6745 10790 5.883115 TGTCCAACAGTAATTTGTTCACTCA 59.117 36.000 0.00 0.00 39.17 3.41
6746 10791 6.371809 TGTCCAACAGTAATTTGTTCACTC 57.628 37.500 0.00 0.00 39.17 3.51
6747 10792 6.767524 TTGTCCAACAGTAATTTGTTCACT 57.232 33.333 0.00 0.00 39.17 3.41
6748 10793 8.564574 TCTATTGTCCAACAGTAATTTGTTCAC 58.435 33.333 0.00 0.00 39.17 3.18
6749 10794 8.684386 TCTATTGTCCAACAGTAATTTGTTCA 57.316 30.769 0.00 0.00 39.17 3.18


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

AutoCloner maintained by Alex Coulton.