Multiple sequence alignment - TraesCS2D01G072500

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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 TraesCS2D01G072500 chr2D 100.000 4923 0 0 1 4923 30450621 30445699 0.000000e+00 9092
1 TraesCS2D01G072500 chr2D 82.436 2972 444 49 990 3925 22511316 22508387 0.000000e+00 2525
2 TraesCS2D01G072500 chr2D 78.356 1229 190 49 570 1761 22439846 22441035 0.000000e+00 726
3 TraesCS2D01G072500 chr2B 96.044 2022 58 6 1 2007 49902563 49900549 0.000000e+00 3271
4 TraesCS2D01G072500 chr2B 97.166 1764 48 2 1734 3496 49900546 49898784 0.000000e+00 2979
5 TraesCS2D01G072500 chr2B 85.439 2287 302 21 1734 4001 39339960 39337686 0.000000e+00 2350
6 TraesCS2D01G072500 chr2B 82.814 2409 350 37 1545 3922 39184446 39186821 0.000000e+00 2097
7 TraesCS2D01G072500 chr2B 81.042 2131 360 38 1871 3973 38034384 38036498 0.000000e+00 1657
8 TraesCS2D01G072500 chr2B 80.684 2133 366 33 1871 3973 37677759 37679875 0.000000e+00 1615
9 TraesCS2D01G072500 chr2B 82.420 1405 232 10 1871 3269 38074070 38075465 0.000000e+00 1212
10 TraesCS2D01G072500 chr2B 82.353 1411 231 12 1870 3271 38417220 38418621 0.000000e+00 1210
11 TraesCS2D01G072500 chr2B 93.092 608 41 1 3481 4087 49898767 49898160 0.000000e+00 889
12 TraesCS2D01G072500 chr2B 90.761 552 44 4 4080 4630 49897254 49896709 0.000000e+00 730
13 TraesCS2D01G072500 chr2B 78.725 1067 179 34 964 2007 39341004 39339963 0.000000e+00 669
14 TraesCS2D01G072500 chr2B 75.412 911 182 28 989 1873 38033630 38034524 2.130000e-108 403
15 TraesCS2D01G072500 chr2B 80.830 506 92 5 1370 1873 38416859 38417361 4.620000e-105 392
16 TraesCS2D01G072500 chr2B 89.691 194 17 2 2188 2378 76857683 76857490 1.370000e-60 244
17 TraesCS2D01G072500 chr2B 71.679 911 199 40 762 1644 38072900 38073779 1.080000e-46 198
18 TraesCS2D01G072500 chr2A 85.431 2320 311 21 1734 4036 24174243 24176552 0.000000e+00 2386
19 TraesCS2D01G072500 chr2A 80.720 1805 291 35 939 2725 24309429 24307664 0.000000e+00 1352
20 TraesCS2D01G072500 chr2A 78.051 1139 168 52 591 1687 24172786 24173884 1.160000e-180 643
21 TraesCS2D01G072500 chr2A 89.914 466 36 7 4175 4630 32453852 32453388 1.530000e-164 590
22 TraesCS2D01G072500 chr2A 85.646 209 25 3 3074 3277 34406309 34406517 1.070000e-51 215
23 TraesCS2D01G072500 chr7B 81.855 1488 225 23 925 2402 744137055 744138507 0.000000e+00 1210


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 TraesCS2D01G072500 chr2D 30445699 30450621 4922 True 9092.00 9092 100.00000 1 4923 1 chr2D.!!$R2 4922
1 TraesCS2D01G072500 chr2D 22508387 22511316 2929 True 2525.00 2525 82.43600 990 3925 1 chr2D.!!$R1 2935
2 TraesCS2D01G072500 chr2D 22439846 22441035 1189 False 726.00 726 78.35600 570 1761 1 chr2D.!!$F1 1191
3 TraesCS2D01G072500 chr2B 39184446 39186821 2375 False 2097.00 2097 82.81400 1545 3922 1 chr2B.!!$F2 2377
4 TraesCS2D01G072500 chr2B 49896709 49902563 5854 True 1967.25 3271 94.26575 1 4630 4 chr2B.!!$R3 4629
5 TraesCS2D01G072500 chr2B 37677759 37679875 2116 False 1615.00 1615 80.68400 1871 3973 1 chr2B.!!$F1 2102
6 TraesCS2D01G072500 chr2B 39337686 39341004 3318 True 1509.50 2350 82.08200 964 4001 2 chr2B.!!$R2 3037
7 TraesCS2D01G072500 chr2B 38033630 38036498 2868 False 1030.00 1657 78.22700 989 3973 2 chr2B.!!$F3 2984
8 TraesCS2D01G072500 chr2B 38416859 38418621 1762 False 801.00 1210 81.59150 1370 3271 2 chr2B.!!$F5 1901
9 TraesCS2D01G072500 chr2B 38072900 38075465 2565 False 705.00 1212 77.04950 762 3269 2 chr2B.!!$F4 2507
10 TraesCS2D01G072500 chr2A 24172786 24176552 3766 False 1514.50 2386 81.74100 591 4036 2 chr2A.!!$F2 3445
11 TraesCS2D01G072500 chr2A 24307664 24309429 1765 True 1352.00 1352 80.72000 939 2725 1 chr2A.!!$R1 1786
12 TraesCS2D01G072500 chr7B 744137055 744138507 1452 False 1210.00 1210 81.85500 925 2402 1 chr7B.!!$F1 1477

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
736 749 1.075212 TCCATGTTTGGCCATCAGTGA 59.925 47.619 6.09 7.36 43.29 3.41 F
1927 3028 0.181114 GTGGTAGCATCCCAGCATCA 59.819 55.000 0.00 0.00 36.85 3.07 F
2262 3363 0.573987 CGCACACAGCATCATCTACG 59.426 55.000 0.00 0.00 46.13 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2521 3624 0.104855 TGCAGAGCGATGGTGGTATC 59.895 55.0 0.0 0.0 0.00 2.24 R
3643 4807 1.037493 TGTACGCCACAGAGAACACT 58.963 50.0 0.0 0.0 31.89 3.55 R
4058 5227 0.602905 CTCGTGTTGGGAGTTGGGAC 60.603 60.0 0.0 0.0 0.00 4.46 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
199 200 5.585390 CAGCATGTTCTCAAATTACATCCC 58.415 41.667 0.00 0.00 30.45 3.85
293 304 9.842775 ATATTTCTACAGCAATGAAGAGATCAA 57.157 29.630 0.00 0.00 42.54 2.57
328 339 2.947652 CCAACTGGATTAGACCATGCAG 59.052 50.000 0.00 1.07 45.61 4.41
335 346 3.244491 GGATTAGACCATGCAGAGCTGAT 60.244 47.826 0.85 0.00 0.00 2.90
383 395 8.986929 AATCCAAGAATCAGACCCTAAATAAG 57.013 34.615 0.00 0.00 0.00 1.73
420 432 3.181483 GCATGTCATGATGAAGGAAACCC 60.181 47.826 17.24 0.00 0.00 4.11
516 528 6.155475 TGTTTAAATCTGTTCAAACCCAGG 57.845 37.500 0.00 0.00 31.38 4.45
562 574 8.846943 TGAAACTTATAAGATGCTCAAACTGA 57.153 30.769 19.38 0.00 0.00 3.41
600 612 5.479724 TCCAAATTCATGTGTATTTCTGCCA 59.520 36.000 0.00 0.00 0.00 4.92
618 630 2.704572 CCATTCTTGGCCTCGATATCC 58.295 52.381 3.32 0.00 35.85 2.59
654 667 2.143925 GTAGTCAAGTCCACAAGGTGC 58.856 52.381 0.00 0.00 35.89 5.01
736 749 1.075212 TCCATGTTTGGCCATCAGTGA 59.925 47.619 6.09 7.36 43.29 3.41
743 756 2.291209 TGGCCATCAGTGAATGTTGT 57.709 45.000 0.00 0.00 0.00 3.32
748 761 3.148412 CCATCAGTGAATGTTGTGGTCA 58.852 45.455 0.00 0.00 0.00 4.02
1436 1579 7.577426 GCATCCATGAAACTCCACTTTTATTCA 60.577 37.037 0.00 0.00 0.00 2.57
1442 1585 8.243961 TGAAACTCCACTTTTATTCATCCAAA 57.756 30.769 0.00 0.00 0.00 3.28
1443 1586 8.869109 TGAAACTCCACTTTTATTCATCCAAAT 58.131 29.630 0.00 0.00 0.00 2.32
1444 1587 9.710900 GAAACTCCACTTTTATTCATCCAAATT 57.289 29.630 0.00 0.00 0.00 1.82
1843 2382 4.090761 TCTTTCAGACAACCTCTTGCAT 57.909 40.909 0.00 0.00 0.00 3.96
1861 2400 9.896645 CTCTTGCATGGACATATACCTATAAAT 57.103 33.333 0.00 0.00 0.00 1.40
1881 2420 1.266178 TCATCTTGGAACCTGCGAGA 58.734 50.000 0.00 0.00 0.00 4.04
1927 3028 0.181114 GTGGTAGCATCCCAGCATCA 59.819 55.000 0.00 0.00 36.85 3.07
1930 3031 1.590932 GTAGCATCCCAGCATCAGTG 58.409 55.000 0.00 0.00 36.85 3.66
1948 3049 0.675083 TGTTTGCACTTCCATGCCTG 59.325 50.000 0.00 0.00 45.50 4.85
1969 3070 5.407407 TGGAGTACTTGGATCTTTCAGAC 57.593 43.478 0.00 0.00 0.00 3.51
2069 3170 7.254624 CCAAAAACAAGCTAAGCGGTAAATTTT 60.255 33.333 0.00 0.00 0.00 1.82
2070 3171 7.402811 AAAACAAGCTAAGCGGTAAATTTTC 57.597 32.000 0.00 0.00 0.00 2.29
2147 3248 2.878406 ACTGATTTGGTCGTTCAAGTGG 59.122 45.455 0.00 0.00 0.00 4.00
2262 3363 0.573987 CGCACACAGCATCATCTACG 59.426 55.000 0.00 0.00 46.13 3.51
2521 3624 8.504005 GTTTCCCACAATATTATATCTGGAACG 58.496 37.037 9.33 0.00 0.00 3.95
3028 4139 4.069232 TCAGGCTTCCCGAGTGCG 62.069 66.667 0.00 0.00 35.76 5.34
3045 4156 1.260561 TGCGTTTTTCTTCAGCTCGTC 59.739 47.619 0.00 0.00 0.00 4.20
3420 4552 7.539710 CACATATGGACAAAACTTCTTCATGTG 59.460 37.037 7.80 0.00 34.40 3.21
3445 4577 2.670414 GTCTGGCATTGACTTCTCTTCG 59.330 50.000 0.00 0.00 0.00 3.79
3454 4586 4.783764 TGACTTCTCTTCGAACATGCTA 57.216 40.909 0.00 0.00 0.00 3.49
3463 4595 4.100035 TCTTCGAACATGCTATCAGGTGAT 59.900 41.667 0.00 0.00 37.29 3.06
3496 4660 5.281193 GGAGATGGGGAATTTGAGCCATATA 60.281 44.000 0.00 0.00 0.00 0.86
3534 4698 4.036380 GTCAAACAATTTCTTGACCGGACT 59.964 41.667 9.46 0.00 43.65 3.85
3643 4807 7.279981 CAGTTAACTCGGTTATCATCATTGGAA 59.720 37.037 4.77 0.00 0.00 3.53
3735 4900 1.067071 GGACAGTTACAGAGGGAACGG 60.067 57.143 0.00 0.00 0.00 4.44
3764 4929 2.040813 AGGTCATGCACTTCCAGTTCAT 59.959 45.455 0.00 0.00 32.38 2.57
3801 4966 3.864686 CACGGGAGGAAATGCGCG 61.865 66.667 0.00 0.00 44.59 6.86
3805 4970 4.179579 GGAGGAAATGCGCGTGGC 62.180 66.667 8.43 0.00 43.96 5.01
3856 5021 1.725931 GCTGTTTCATTCGTCTTGGCG 60.726 52.381 0.00 0.00 0.00 5.69
3913 5078 1.164411 TTGGGCAGCGTGTTATTCTG 58.836 50.000 0.00 0.00 0.00 3.02
3974 5143 7.400599 AATAGTGATGATGTGAAGCAACATT 57.599 32.000 1.82 0.00 40.11 2.71
3975 5144 5.055642 AGTGATGATGTGAAGCAACATTG 57.944 39.130 1.82 0.00 40.11 2.82
4008 5177 7.693951 CACTTTAGTAATCTGCTTTTCCGATTG 59.306 37.037 0.00 0.00 0.00 2.67
4013 5182 0.516877 CTGCTTTTCCGATTGTGCGA 59.483 50.000 0.00 0.00 0.00 5.10
4044 5213 6.488683 TGTAAACTATGCTACCTTTTGTTGCT 59.511 34.615 0.00 0.00 44.65 3.91
4047 5216 6.405278 ACTATGCTACCTTTTGTTGCTTTT 57.595 33.333 0.00 0.00 44.65 2.27
4048 5217 6.215845 ACTATGCTACCTTTTGTTGCTTTTG 58.784 36.000 0.00 0.00 44.65 2.44
4054 5223 6.092122 GCTACCTTTTGTTGCTTTTGAAAAGT 59.908 34.615 17.90 0.00 41.68 2.66
4058 5227 6.578172 CCTTTTGTTGCTTTTGAAAAGTTGTG 59.422 34.615 17.90 0.00 34.83 3.33
4059 5228 6.610741 TTTGTTGCTTTTGAAAAGTTGTGT 57.389 29.167 17.90 0.00 0.00 3.72
4087 5256 4.223032 ACTCCCAACACGAGTATTCTGATT 59.777 41.667 0.00 0.00 38.82 2.57
4088 5257 5.160607 TCCCAACACGAGTATTCTGATTT 57.839 39.130 0.00 0.00 0.00 2.17
4089 5258 4.935205 TCCCAACACGAGTATTCTGATTTG 59.065 41.667 0.00 0.00 0.00 2.32
4090 5259 4.695455 CCCAACACGAGTATTCTGATTTGT 59.305 41.667 0.00 0.00 0.00 2.83
4091 5260 5.163854 CCCAACACGAGTATTCTGATTTGTC 60.164 44.000 0.00 0.00 0.00 3.18
4093 5262 6.092670 CCAACACGAGTATTCTGATTTGTCAT 59.907 38.462 0.00 0.00 0.00 3.06
4094 5263 6.653273 ACACGAGTATTCTGATTTGTCATG 57.347 37.500 0.00 0.00 0.00 3.07
4097 5266 5.877012 ACGAGTATTCTGATTTGTCATGCTT 59.123 36.000 0.00 0.00 0.00 3.91
4099 5268 7.549134 ACGAGTATTCTGATTTGTCATGCTTAA 59.451 33.333 0.00 0.00 0.00 1.85
4132 6210 5.467063 GGCGAGTAATAAATTCTCTGGAAGG 59.533 44.000 0.00 0.00 34.70 3.46
4257 6335 1.539827 GTTGACATTTTGGGAGGACCG 59.460 52.381 0.00 0.00 44.64 4.79
4274 6352 0.676466 CCGTTGGTTCTGCATAGCCA 60.676 55.000 3.41 3.41 0.00 4.75
4283 6361 4.158394 GGTTCTGCATAGCCATTTCTTTGA 59.842 41.667 0.00 0.00 0.00 2.69
4285 6363 4.334552 TCTGCATAGCCATTTCTTTGACA 58.665 39.130 0.00 0.00 0.00 3.58
4356 6434 8.780249 GTTTTTAGTGCTAGAAATGTTCCTGTA 58.220 33.333 0.00 0.00 0.00 2.74
4372 6450 6.183360 TGTTCCTGTACGTTAGGATATTGGAG 60.183 42.308 18.47 0.00 43.52 3.86
4385 6463 5.730207 AGGATATTGGAGGATATGTGCTGAT 59.270 40.000 0.00 0.00 0.00 2.90
4389 6467 2.149578 GGAGGATATGTGCTGATGTGC 58.850 52.381 0.00 0.00 0.00 4.57
4393 6471 4.639334 AGGATATGTGCTGATGTGCTAAG 58.361 43.478 0.00 0.00 0.00 2.18
4396 6474 1.445871 TGTGCTGATGTGCTAAGCTG 58.554 50.000 0.00 0.00 37.82 4.24
4448 6526 5.837979 TCCCCTTTGTGAATTCTTGATTGAA 59.162 36.000 7.05 0.00 0.00 2.69
4452 6530 6.580041 CCTTTGTGAATTCTTGATTGAAGTCG 59.420 38.462 7.05 0.00 41.98 4.18
4460 6538 4.560128 TCTTGATTGAAGTCGTCTTCCTG 58.440 43.478 17.78 4.30 46.66 3.86
4464 6542 1.040646 TGAAGTCGTCTTCCTGTGCT 58.959 50.000 17.78 0.00 46.66 4.40
4466 6544 1.795286 GAAGTCGTCTTCCTGTGCTTG 59.205 52.381 10.82 0.00 42.85 4.01
4467 6545 0.034059 AGTCGTCTTCCTGTGCTTGG 59.966 55.000 0.00 0.00 0.00 3.61
4468 6546 0.033504 GTCGTCTTCCTGTGCTTGGA 59.966 55.000 0.00 0.00 0.00 3.53
4469 6547 0.976641 TCGTCTTCCTGTGCTTGGAT 59.023 50.000 0.00 0.00 33.09 3.41
4472 6550 2.626840 GTCTTCCTGTGCTTGGATCTC 58.373 52.381 0.00 0.00 33.09 2.75
4485 6563 6.874134 GTGCTTGGATCTCTACTTTGTTTCTA 59.126 38.462 0.00 0.00 0.00 2.10
4494 6572 6.014499 TCTCTACTTTGTTTCTACCTCTTGGG 60.014 42.308 0.00 0.00 41.89 4.12
4506 6584 1.668419 CTCTTGGGATAACAAGGCCG 58.332 55.000 0.00 0.00 46.04 6.13
4507 6585 0.988832 TCTTGGGATAACAAGGCCGT 59.011 50.000 0.00 0.00 46.04 5.68
4535 6613 3.073209 TGTGTAAACCTGGGCATCACTTA 59.927 43.478 0.00 0.00 0.00 2.24
4542 6620 2.203209 GGCATCACTTAGGCCGGG 60.203 66.667 2.18 0.00 46.73 5.73
4583 6661 2.501261 ACAAAAGCCCGAGGTAGAAAC 58.499 47.619 0.00 0.00 0.00 2.78
4593 6671 3.154589 GGTAGAAACCTCAAGCCCG 57.845 57.895 0.00 0.00 43.08 6.13
4610 6688 1.202177 CCCGAGCCAACATTTGATTCG 60.202 52.381 0.00 5.55 36.64 3.34
4611 6689 1.468520 CCGAGCCAACATTTGATTCGT 59.531 47.619 9.54 0.00 35.79 3.85
4617 6695 5.331902 AGCCAACATTTGATTCGTATTTCG 58.668 37.500 0.00 0.00 41.41 3.46
4621 6699 5.138800 ACATTTGATTCGTATTTCGTCCG 57.861 39.130 0.00 0.00 40.80 4.79
4622 6700 4.033587 ACATTTGATTCGTATTTCGTCCGG 59.966 41.667 0.00 0.00 40.80 5.14
4631 6709 3.826637 TTTCGTCCGGAAAGCTAGG 57.173 52.632 5.23 0.00 39.67 3.02
4632 6710 0.248289 TTTCGTCCGGAAAGCTAGGG 59.752 55.000 5.23 0.00 39.67 3.53
4633 6711 1.610554 TTCGTCCGGAAAGCTAGGGG 61.611 60.000 5.23 0.00 0.00 4.79
4634 6712 2.189784 GTCCGGAAAGCTAGGGGC 59.810 66.667 5.23 0.00 42.19 5.80
4635 6713 2.285069 TCCGGAAAGCTAGGGGCA 60.285 61.111 0.00 0.00 44.79 5.36
4636 6714 1.921346 TCCGGAAAGCTAGGGGCAA 60.921 57.895 0.00 0.00 44.79 4.52
4637 6715 1.749258 CCGGAAAGCTAGGGGCAAC 60.749 63.158 0.00 0.00 44.79 4.17
4638 6716 1.299976 CGGAAAGCTAGGGGCAACT 59.700 57.895 0.00 0.00 44.79 3.16
4639 6717 0.539986 CGGAAAGCTAGGGGCAACTA 59.460 55.000 0.00 0.00 44.79 2.24
4640 6718 1.065709 CGGAAAGCTAGGGGCAACTAA 60.066 52.381 0.00 0.00 44.79 2.24
4641 6719 2.421529 CGGAAAGCTAGGGGCAACTAAT 60.422 50.000 0.00 0.00 44.79 1.73
4642 6720 3.632333 GGAAAGCTAGGGGCAACTAATT 58.368 45.455 0.00 0.00 44.79 1.40
4643 6721 3.381590 GGAAAGCTAGGGGCAACTAATTG 59.618 47.826 0.00 0.00 44.79 2.32
4644 6722 4.270008 GAAAGCTAGGGGCAACTAATTGA 58.730 43.478 0.00 0.00 44.79 2.57
4645 6723 3.283259 AGCTAGGGGCAACTAATTGAC 57.717 47.619 0.00 0.00 43.94 3.18
4646 6724 1.940613 GCTAGGGGCAACTAATTGACG 59.059 52.381 0.00 0.00 45.86 4.35
4647 6725 2.419574 GCTAGGGGCAACTAATTGACGA 60.420 50.000 0.00 0.00 45.86 4.20
4648 6726 2.403252 AGGGGCAACTAATTGACGAG 57.597 50.000 0.00 0.00 45.86 4.18
4649 6727 0.733150 GGGGCAACTAATTGACGAGC 59.267 55.000 0.00 0.00 45.86 5.03
4650 6728 0.373716 GGGCAACTAATTGACGAGCG 59.626 55.000 0.00 0.00 45.86 5.03
4651 6729 0.247695 GGCAACTAATTGACGAGCGC 60.248 55.000 0.00 0.00 38.15 5.92
4652 6730 0.721718 GCAACTAATTGACGAGCGCT 59.278 50.000 11.27 11.27 38.15 5.92
4653 6731 1.128692 GCAACTAATTGACGAGCGCTT 59.871 47.619 13.26 0.00 38.15 4.68
4654 6732 2.784665 GCAACTAATTGACGAGCGCTTC 60.785 50.000 13.26 6.79 38.15 3.86
4655 6733 2.656560 ACTAATTGACGAGCGCTTCT 57.343 45.000 13.26 0.00 0.00 2.85
4656 6734 2.960819 ACTAATTGACGAGCGCTTCTT 58.039 42.857 13.26 0.00 0.00 2.52
4657 6735 2.924290 ACTAATTGACGAGCGCTTCTTC 59.076 45.455 13.26 9.22 0.00 2.87
4658 6736 0.716108 AATTGACGAGCGCTTCTTCG 59.284 50.000 13.26 13.91 0.00 3.79
4659 6737 1.078759 ATTGACGAGCGCTTCTTCGG 61.079 55.000 13.26 0.00 0.00 4.30
4660 6738 2.137425 TTGACGAGCGCTTCTTCGGA 62.137 55.000 13.26 0.00 0.00 4.55
4661 6739 1.443872 GACGAGCGCTTCTTCGGAA 60.444 57.895 13.26 0.00 0.00 4.30
4670 6748 2.751166 CTTCTTCGGAAGCCTCTTCA 57.249 50.000 12.90 0.00 43.85 3.02
4671 6749 3.258971 CTTCTTCGGAAGCCTCTTCAT 57.741 47.619 12.90 0.00 43.85 2.57
4672 6750 2.680312 TCTTCGGAAGCCTCTTCATG 57.320 50.000 12.90 0.00 0.00 3.07
4673 6751 1.208052 TCTTCGGAAGCCTCTTCATGG 59.792 52.381 12.90 0.00 0.00 3.66
4674 6752 0.253044 TTCGGAAGCCTCTTCATGGG 59.747 55.000 8.59 0.00 0.00 4.00
4675 6753 0.909610 TCGGAAGCCTCTTCATGGGT 60.910 55.000 8.59 0.00 36.81 4.51
4676 6754 0.462759 CGGAAGCCTCTTCATGGGTC 60.463 60.000 8.59 0.00 33.76 4.46
4677 6755 0.620556 GGAAGCCTCTTCATGGGTCA 59.379 55.000 8.59 0.00 33.76 4.02
4678 6756 1.213926 GGAAGCCTCTTCATGGGTCAT 59.786 52.381 8.59 0.00 33.76 3.06
4679 6757 2.357569 GGAAGCCTCTTCATGGGTCATT 60.358 50.000 8.59 0.00 33.76 2.57
4680 6758 3.359950 GAAGCCTCTTCATGGGTCATTT 58.640 45.455 0.00 0.00 33.76 2.32
4681 6759 2.731572 AGCCTCTTCATGGGTCATTTG 58.268 47.619 0.00 0.00 0.00 2.32
4682 6760 1.753073 GCCTCTTCATGGGTCATTTGG 59.247 52.381 0.00 0.00 0.00 3.28
4683 6761 2.381911 CCTCTTCATGGGTCATTTGGG 58.618 52.381 0.00 0.00 0.00 4.12
4684 6762 2.381911 CTCTTCATGGGTCATTTGGGG 58.618 52.381 0.00 0.00 0.00 4.96
4685 6763 1.715931 TCTTCATGGGTCATTTGGGGT 59.284 47.619 0.00 0.00 0.00 4.95
4686 6764 1.826720 CTTCATGGGTCATTTGGGGTG 59.173 52.381 0.00 0.00 0.00 4.61
4687 6765 0.040942 TCATGGGTCATTTGGGGTGG 59.959 55.000 0.00 0.00 0.00 4.61
4688 6766 0.977108 CATGGGTCATTTGGGGTGGG 60.977 60.000 0.00 0.00 0.00 4.61
4689 6767 2.683572 GGGTCATTTGGGGTGGGC 60.684 66.667 0.00 0.00 0.00 5.36
4690 6768 2.445155 GGTCATTTGGGGTGGGCT 59.555 61.111 0.00 0.00 0.00 5.19
4691 6769 1.682344 GGTCATTTGGGGTGGGCTC 60.682 63.158 0.00 0.00 0.00 4.70
4692 6770 1.384191 GTCATTTGGGGTGGGCTCT 59.616 57.895 0.00 0.00 0.00 4.09
4693 6771 0.681243 GTCATTTGGGGTGGGCTCTC 60.681 60.000 0.00 0.00 0.00 3.20
4694 6772 1.139498 TCATTTGGGGTGGGCTCTCA 61.139 55.000 0.00 0.00 0.00 3.27
4695 6773 0.682209 CATTTGGGGTGGGCTCTCAG 60.682 60.000 0.00 0.00 0.00 3.35
4696 6774 2.505364 ATTTGGGGTGGGCTCTCAGC 62.505 60.000 0.00 0.00 41.46 4.26
4706 6784 2.582959 GCTCTCAGCCGTCGTAATG 58.417 57.895 0.00 0.00 34.48 1.90
4707 6785 0.179134 GCTCTCAGCCGTCGTAATGT 60.179 55.000 0.00 0.00 34.48 2.71
4708 6786 1.550065 CTCTCAGCCGTCGTAATGTG 58.450 55.000 0.00 0.00 0.00 3.21
4709 6787 0.457853 TCTCAGCCGTCGTAATGTGC 60.458 55.000 0.00 0.00 0.00 4.57
4710 6788 1.421410 CTCAGCCGTCGTAATGTGCC 61.421 60.000 0.00 0.00 0.00 5.01
4711 6789 1.739929 CAGCCGTCGTAATGTGCCA 60.740 57.895 0.00 0.00 0.00 4.92
4712 6790 1.089481 CAGCCGTCGTAATGTGCCAT 61.089 55.000 0.00 0.00 0.00 4.40
4713 6791 1.089481 AGCCGTCGTAATGTGCCATG 61.089 55.000 0.00 0.00 0.00 3.66
4714 6792 1.351707 CCGTCGTAATGTGCCATGC 59.648 57.895 0.00 0.00 0.00 4.06
4715 6793 1.089481 CCGTCGTAATGTGCCATGCT 61.089 55.000 0.00 0.00 0.00 3.79
4716 6794 0.726827 CGTCGTAATGTGCCATGCTT 59.273 50.000 0.00 0.00 0.00 3.91
4717 6795 1.130373 CGTCGTAATGTGCCATGCTTT 59.870 47.619 0.00 0.00 0.00 3.51
4718 6796 2.518949 GTCGTAATGTGCCATGCTTTG 58.481 47.619 0.00 0.00 0.00 2.77
4728 6806 2.559785 CATGCTTTGGACGCTTCCT 58.440 52.632 11.01 0.00 43.31 3.36
4729 6807 0.449388 CATGCTTTGGACGCTTCCTC 59.551 55.000 11.01 0.00 43.31 3.71
4730 6808 0.326264 ATGCTTTGGACGCTTCCTCT 59.674 50.000 11.01 0.00 43.31 3.69
4731 6809 0.603707 TGCTTTGGACGCTTCCTCTG 60.604 55.000 11.01 1.65 43.31 3.35
4732 6810 1.301677 GCTTTGGACGCTTCCTCTGG 61.302 60.000 11.01 0.00 43.31 3.86
4733 6811 0.321671 CTTTGGACGCTTCCTCTGGA 59.678 55.000 11.01 0.00 43.31 3.86
4734 6812 0.984230 TTTGGACGCTTCCTCTGGAT 59.016 50.000 11.01 0.00 43.31 3.41
4735 6813 0.984230 TTGGACGCTTCCTCTGGATT 59.016 50.000 11.01 0.00 43.31 3.01
4736 6814 0.984230 TGGACGCTTCCTCTGGATTT 59.016 50.000 11.01 0.00 43.31 2.17
4737 6815 1.351017 TGGACGCTTCCTCTGGATTTT 59.649 47.619 11.01 0.00 43.31 1.82
4738 6816 2.224769 TGGACGCTTCCTCTGGATTTTT 60.225 45.455 11.01 0.00 43.31 1.94
4768 6846 6.473397 TTTTTCACATGCGTTTTTGACTTT 57.527 29.167 0.00 0.00 0.00 2.66
4769 6847 6.473397 TTTTCACATGCGTTTTTGACTTTT 57.527 29.167 0.00 0.00 0.00 2.27
4770 6848 6.473397 TTTCACATGCGTTTTTGACTTTTT 57.527 29.167 0.00 0.00 0.00 1.94
4771 6849 7.582435 TTTCACATGCGTTTTTGACTTTTTA 57.418 28.000 0.00 0.00 0.00 1.52
4772 6850 6.804534 TCACATGCGTTTTTGACTTTTTAG 57.195 33.333 0.00 0.00 0.00 1.85
4773 6851 6.556212 TCACATGCGTTTTTGACTTTTTAGA 58.444 32.000 0.00 0.00 0.00 2.10
4774 6852 7.199766 TCACATGCGTTTTTGACTTTTTAGAT 58.800 30.769 0.00 0.00 0.00 1.98
4775 6853 7.167302 TCACATGCGTTTTTGACTTTTTAGATG 59.833 33.333 0.00 0.00 0.00 2.90
4776 6854 6.420604 ACATGCGTTTTTGACTTTTTAGATGG 59.579 34.615 0.00 0.00 0.00 3.51
4777 6855 5.285651 TGCGTTTTTGACTTTTTAGATGGG 58.714 37.500 0.00 0.00 0.00 4.00
4778 6856 5.163499 TGCGTTTTTGACTTTTTAGATGGGT 60.163 36.000 0.00 0.00 0.00 4.51
4779 6857 5.751509 GCGTTTTTGACTTTTTAGATGGGTT 59.248 36.000 0.00 0.00 0.00 4.11
4780 6858 6.256975 GCGTTTTTGACTTTTTAGATGGGTTT 59.743 34.615 0.00 0.00 0.00 3.27
4781 6859 7.201574 GCGTTTTTGACTTTTTAGATGGGTTTT 60.202 33.333 0.00 0.00 0.00 2.43
4782 6860 8.661257 CGTTTTTGACTTTTTAGATGGGTTTTT 58.339 29.630 0.00 0.00 0.00 1.94
4801 6879 2.580966 TTTGGGTTTTCGGGTTTTCG 57.419 45.000 0.00 0.00 0.00 3.46
4802 6880 0.102663 TTGGGTTTTCGGGTTTTCGC 59.897 50.000 0.00 0.00 0.00 4.70
4803 6881 0.752376 TGGGTTTTCGGGTTTTCGCT 60.752 50.000 0.00 0.00 0.00 4.93
4804 6882 0.386476 GGGTTTTCGGGTTTTCGCTT 59.614 50.000 0.00 0.00 0.00 4.68
4805 6883 1.202440 GGGTTTTCGGGTTTTCGCTTT 60.202 47.619 0.00 0.00 0.00 3.51
4806 6884 2.542597 GGTTTTCGGGTTTTCGCTTTT 58.457 42.857 0.00 0.00 0.00 2.27
4807 6885 2.536803 GGTTTTCGGGTTTTCGCTTTTC 59.463 45.455 0.00 0.00 0.00 2.29
4808 6886 3.180613 GTTTTCGGGTTTTCGCTTTTCA 58.819 40.909 0.00 0.00 0.00 2.69
4809 6887 2.478547 TTCGGGTTTTCGCTTTTCAC 57.521 45.000 0.00 0.00 0.00 3.18
4810 6888 0.664224 TCGGGTTTTCGCTTTTCACC 59.336 50.000 0.00 0.00 0.00 4.02
4811 6889 0.659123 CGGGTTTTCGCTTTTCACCG 60.659 55.000 0.00 0.00 0.00 4.94
4812 6890 0.318360 GGGTTTTCGCTTTTCACCGG 60.318 55.000 0.00 0.00 0.00 5.28
4813 6891 0.382873 GGTTTTCGCTTTTCACCGGT 59.617 50.000 0.00 0.00 0.00 5.28
4814 6892 1.202325 GGTTTTCGCTTTTCACCGGTT 60.202 47.619 2.97 0.00 0.00 4.44
4815 6893 2.532235 GTTTTCGCTTTTCACCGGTTT 58.468 42.857 2.97 0.00 0.00 3.27
4816 6894 2.924926 GTTTTCGCTTTTCACCGGTTTT 59.075 40.909 2.97 0.00 0.00 2.43
4817 6895 2.943449 TTCGCTTTTCACCGGTTTTT 57.057 40.000 2.97 0.00 0.00 1.94
4818 6896 2.478547 TCGCTTTTCACCGGTTTTTC 57.521 45.000 2.97 0.00 0.00 2.29
4819 6897 2.018515 TCGCTTTTCACCGGTTTTTCT 58.981 42.857 2.97 0.00 0.00 2.52
4820 6898 2.424246 TCGCTTTTCACCGGTTTTTCTT 59.576 40.909 2.97 0.00 0.00 2.52
4821 6899 3.626670 TCGCTTTTCACCGGTTTTTCTTA 59.373 39.130 2.97 0.00 0.00 2.10
4822 6900 3.972502 CGCTTTTCACCGGTTTTTCTTAG 59.027 43.478 2.97 0.00 0.00 2.18
4823 6901 3.734231 GCTTTTCACCGGTTTTTCTTAGC 59.266 43.478 2.97 4.10 0.00 3.09
4824 6902 4.499188 GCTTTTCACCGGTTTTTCTTAGCT 60.499 41.667 2.97 0.00 0.00 3.32
4825 6903 5.585820 TTTTCACCGGTTTTTCTTAGCTT 57.414 34.783 2.97 0.00 0.00 3.74
4826 6904 5.585820 TTTCACCGGTTTTTCTTAGCTTT 57.414 34.783 2.97 0.00 0.00 3.51
4827 6905 5.585820 TTCACCGGTTTTTCTTAGCTTTT 57.414 34.783 2.97 0.00 0.00 2.27
4828 6906 4.927422 TCACCGGTTTTTCTTAGCTTTTG 58.073 39.130 2.97 0.00 0.00 2.44
4829 6907 4.048504 CACCGGTTTTTCTTAGCTTTTGG 58.951 43.478 2.97 0.00 0.00 3.28
4830 6908 3.069016 ACCGGTTTTTCTTAGCTTTTGGG 59.931 43.478 0.00 0.00 0.00 4.12
4831 6909 3.554129 CCGGTTTTTCTTAGCTTTTGGGG 60.554 47.826 0.00 0.00 0.00 4.96
4832 6910 3.319689 CGGTTTTTCTTAGCTTTTGGGGA 59.680 43.478 0.00 0.00 0.00 4.81
4833 6911 4.202172 CGGTTTTTCTTAGCTTTTGGGGAA 60.202 41.667 0.00 0.00 0.00 3.97
4834 6912 5.676552 GGTTTTTCTTAGCTTTTGGGGAAA 58.323 37.500 0.00 0.00 0.00 3.13
4835 6913 6.116806 GGTTTTTCTTAGCTTTTGGGGAAAA 58.883 36.000 0.00 0.00 33.01 2.29
4836 6914 6.600032 GGTTTTTCTTAGCTTTTGGGGAAAAA 59.400 34.615 0.00 0.00 39.04 1.94
4882 6960 5.959652 AAACGTATTTGTTTTGCTTCCAC 57.040 34.783 0.00 0.00 38.89 4.02
4883 6961 3.623863 ACGTATTTGTTTTGCTTCCACG 58.376 40.909 0.00 0.00 0.00 4.94
4884 6962 3.312973 ACGTATTTGTTTTGCTTCCACGA 59.687 39.130 0.00 0.00 0.00 4.35
4885 6963 3.906008 CGTATTTGTTTTGCTTCCACGAG 59.094 43.478 0.00 0.00 0.00 4.18
4886 6964 4.319190 CGTATTTGTTTTGCTTCCACGAGA 60.319 41.667 0.00 0.00 0.00 4.04
4887 6965 4.647424 ATTTGTTTTGCTTCCACGAGAA 57.353 36.364 0.00 0.00 0.00 2.87
4888 6966 4.442375 TTTGTTTTGCTTCCACGAGAAA 57.558 36.364 0.00 0.00 32.88 2.52
4889 6967 3.414549 TGTTTTGCTTCCACGAGAAAC 57.585 42.857 0.00 0.00 32.88 2.78
4890 6968 2.750166 TGTTTTGCTTCCACGAGAAACA 59.250 40.909 0.00 0.00 35.40 2.83
4891 6969 3.105937 GTTTTGCTTCCACGAGAAACAC 58.894 45.455 0.00 0.00 30.32 3.32
4892 6970 0.934496 TTGCTTCCACGAGAAACACG 59.066 50.000 0.00 0.00 30.32 4.49
4893 6971 0.103390 TGCTTCCACGAGAAACACGA 59.897 50.000 0.00 0.00 32.88 4.35
4894 6972 1.214367 GCTTCCACGAGAAACACGAA 58.786 50.000 0.00 0.00 32.88 3.85
4895 6973 1.798813 GCTTCCACGAGAAACACGAAT 59.201 47.619 0.00 0.00 32.88 3.34
4896 6974 2.223377 GCTTCCACGAGAAACACGAATT 59.777 45.455 0.00 0.00 32.88 2.17
4897 6975 3.303791 GCTTCCACGAGAAACACGAATTT 60.304 43.478 0.00 0.00 32.88 1.82
4898 6976 4.084223 GCTTCCACGAGAAACACGAATTTA 60.084 41.667 0.00 0.00 32.88 1.40
4899 6977 4.977741 TCCACGAGAAACACGAATTTAC 57.022 40.909 0.00 0.00 34.70 2.01
4900 6978 4.624015 TCCACGAGAAACACGAATTTACT 58.376 39.130 0.00 0.00 34.70 2.24
4901 6979 5.051816 TCCACGAGAAACACGAATTTACTT 58.948 37.500 0.00 0.00 34.70 2.24
4902 6980 5.524646 TCCACGAGAAACACGAATTTACTTT 59.475 36.000 0.00 0.00 34.70 2.66
4903 6981 5.844396 CCACGAGAAACACGAATTTACTTTC 59.156 40.000 0.00 0.00 34.70 2.62
4910 6988 2.780361 CGAATTTACTTTCGCGAGCA 57.220 45.000 9.59 0.00 41.61 4.26
4911 6989 2.683061 CGAATTTACTTTCGCGAGCAG 58.317 47.619 9.59 12.38 41.61 4.24
4912 6990 2.431906 GAATTTACTTTCGCGAGCAGC 58.568 47.619 9.59 0.00 43.95 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 9.953565 ACAAGTTTAGCTAATGGAACTGTTATA 57.046 29.630 7.08 0.00 33.02 0.98
48 49 8.564574 CAACAAGTTTAGCTAATGGAACTGTTA 58.435 33.333 7.08 0.00 33.02 2.41
49 50 7.068226 ACAACAAGTTTAGCTAATGGAACTGTT 59.932 33.333 7.08 11.02 33.02 3.16
50 51 6.546034 ACAACAAGTTTAGCTAATGGAACTGT 59.454 34.615 7.08 5.15 33.02 3.55
51 52 6.970484 ACAACAAGTTTAGCTAATGGAACTG 58.030 36.000 7.08 4.55 33.02 3.16
52 53 6.770785 TGACAACAAGTTTAGCTAATGGAACT 59.229 34.615 7.08 4.85 34.03 3.01
53 54 6.966021 TGACAACAAGTTTAGCTAATGGAAC 58.034 36.000 7.08 2.35 0.00 3.62
54 55 7.575414 TTGACAACAAGTTTAGCTAATGGAA 57.425 32.000 7.08 0.00 0.00 3.53
55 56 7.422399 GTTTGACAACAAGTTTAGCTAATGGA 58.578 34.615 7.08 0.00 37.32 3.41
111 112 9.628500 GACTATCCCCAAGATTATAAACAAAGT 57.372 33.333 0.00 0.00 36.33 2.66
181 182 6.542821 AGTTCTGGGATGTAATTTGAGAACA 58.457 36.000 0.00 0.00 37.33 3.18
199 200 1.734465 GAAAGGGTCGCATGAGTTCTG 59.266 52.381 0.00 0.00 0.00 3.02
293 304 3.896888 TCCAGTTGGTTCATTTGATTGCT 59.103 39.130 0.00 0.00 36.34 3.91
364 376 4.726825 TGGGCTTATTTAGGGTCTGATTCT 59.273 41.667 0.00 0.00 0.00 2.40
383 395 0.458669 CATGCTCTTCCATGTTGGGC 59.541 55.000 0.00 0.00 38.32 5.36
582 594 6.350361 CCAAGAATGGCAGAAATACACATGAA 60.350 38.462 0.00 0.00 40.58 2.57
600 612 2.975489 ACTGGATATCGAGGCCAAGAAT 59.025 45.455 17.78 0.48 0.00 2.40
612 624 2.765122 GAAGCTCCTGCACTGGATATC 58.235 52.381 0.00 0.00 42.74 1.63
618 630 0.459237 CTACCGAAGCTCCTGCACTG 60.459 60.000 0.00 0.00 42.74 3.66
736 749 5.598005 TCTTTGGAGAATTGACCACAACATT 59.402 36.000 0.00 0.00 38.90 2.71
1120 1213 1.679139 TGCCCAAAGATTATGAGGCG 58.321 50.000 0.00 0.00 43.46 5.52
1709 2104 3.766591 TGGAGATTTCTGAGACCTGAGAC 59.233 47.826 0.00 0.00 0.00 3.36
1861 2400 1.623311 TCTCGCAGGTTCCAAGATGAA 59.377 47.619 0.00 0.00 0.00 2.57
1881 2420 6.949352 ATTTATTGGATCTCAGACGCAATT 57.051 33.333 0.00 0.00 0.00 2.32
1889 2990 7.041508 GCTACCACTCAATTTATTGGATCTCAG 60.042 40.741 3.23 0.00 38.30 3.35
1930 3031 3.502237 CAGGCATGGAAGTGCAAAC 57.498 52.632 0.00 0.00 46.81 2.93
1969 3070 4.576463 GGTACATATCCTTGCAAGAGGTTG 59.424 45.833 28.05 19.63 38.04 3.77
2262 3363 8.742554 ATTATTGTTGGACAAATCGAGAAAAC 57.257 30.769 0.00 0.00 41.96 2.43
2521 3624 0.104855 TGCAGAGCGATGGTGGTATC 59.895 55.000 0.00 0.00 0.00 2.24
2811 3922 5.904362 AGGAAGAAACCATAATGAAGTGC 57.096 39.130 0.00 0.00 0.00 4.40
3028 4139 4.489679 AATGGACGAGCTGAAGAAAAAC 57.510 40.909 0.00 0.00 0.00 2.43
3045 4156 3.803021 GCTGAGATCCAGAGCTGTAATGG 60.803 52.174 13.48 0.00 45.78 3.16
3376 4508 7.657761 CCATATGTGTATGAGTTCCCTTTAGTC 59.342 40.741 1.24 0.00 40.12 2.59
3420 4552 2.941720 GAGAAGTCAATGCCAGACATCC 59.058 50.000 0.00 0.00 38.34 3.51
3445 4577 5.349817 CGGAATATCACCTGATAGCATGTTC 59.650 44.000 0.00 0.73 40.04 3.18
3454 4586 4.483950 TCTCCTTCGGAATATCACCTGAT 58.516 43.478 0.00 0.00 38.51 2.90
3463 4595 2.787339 TCCCCATCTCCTTCGGAATA 57.213 50.000 0.00 0.00 0.00 1.75
3496 4660 9.657419 AAATTGTTTGACAAATTGAGAGACTTT 57.343 25.926 3.49 0.00 41.96 2.66
3643 4807 1.037493 TGTACGCCACAGAGAACACT 58.963 50.000 0.00 0.00 31.89 3.55
3735 4900 1.826385 AGTGCATGACCTAAGGTTGC 58.174 50.000 0.00 0.00 39.20 4.17
3801 4966 1.269778 TGATCGGATCAGAATCGCCAC 60.270 52.381 16.44 0.00 33.59 5.01
3805 4970 4.142795 ACGTAGATGATCGGATCAGAATCG 60.143 45.833 23.59 23.37 43.53 3.34
3856 5021 3.427503 CGAATGTGATAGTGGCCCAAAAC 60.428 47.826 0.00 0.00 0.00 2.43
3944 5112 8.374327 TGCTTCACATCATCACTATTAATCAG 57.626 34.615 0.00 0.00 0.00 2.90
3967 5136 3.308438 AAAGTGATCTGCCAATGTTGC 57.692 42.857 0.00 0.00 0.00 4.17
4008 5177 6.345920 AGCATAGTTTACAAATACTCGCAC 57.654 37.500 0.00 0.00 0.00 5.34
4054 5223 0.626382 TGTTGGGAGTTGGGACACAA 59.374 50.000 0.00 0.00 39.29 3.33
4058 5227 0.602905 CTCGTGTTGGGAGTTGGGAC 60.603 60.000 0.00 0.00 0.00 4.46
4059 5228 1.052124 ACTCGTGTTGGGAGTTGGGA 61.052 55.000 0.00 0.00 41.83 4.37
4087 5256 6.596106 TCGCCTTAGTAAATTAAGCATGACAA 59.404 34.615 0.00 0.00 30.84 3.18
4088 5257 6.110033 TCGCCTTAGTAAATTAAGCATGACA 58.890 36.000 0.00 0.00 30.84 3.58
4089 5258 6.258068 ACTCGCCTTAGTAAATTAAGCATGAC 59.742 38.462 0.00 0.00 30.84 3.06
4090 5259 6.346096 ACTCGCCTTAGTAAATTAAGCATGA 58.654 36.000 0.00 0.00 30.84 3.07
4091 5260 6.604735 ACTCGCCTTAGTAAATTAAGCATG 57.395 37.500 0.00 0.00 30.84 4.06
4093 5262 9.820725 TTATTACTCGCCTTAGTAAATTAAGCA 57.179 29.630 5.39 0.00 43.30 3.91
4132 6210 1.824852 CTTACCTCCCAAACCAATGGC 59.175 52.381 0.00 0.00 39.26 4.40
4209 6287 2.598589 CACCATTTTGCACCTTGATCG 58.401 47.619 0.00 0.00 0.00 3.69
4257 6335 3.445096 AGAAATGGCTATGCAGAACCAAC 59.555 43.478 7.67 3.10 35.41 3.77
4305 6383 3.751479 TGAGACTTGAGCAGTGCTAAA 57.249 42.857 19.77 16.83 39.88 1.85
4356 6434 6.574465 GCACATATCCTCCAATATCCTAACGT 60.574 42.308 0.00 0.00 0.00 3.99
4372 6450 3.188048 GCTTAGCACATCAGCACATATCC 59.812 47.826 0.00 0.00 36.85 2.59
4385 6463 1.814394 CCAATCTTGCAGCTTAGCACA 59.186 47.619 7.07 0.82 45.61 4.57
4389 6467 1.133790 GTGCCCAATCTTGCAGCTTAG 59.866 52.381 0.00 0.00 38.34 2.18
4393 6471 1.396653 ATAGTGCCCAATCTTGCAGC 58.603 50.000 0.00 0.00 38.34 5.25
4396 6474 6.464222 TGTAGTATATAGTGCCCAATCTTGC 58.536 40.000 0.00 0.00 0.00 4.01
4448 6526 0.034059 CCAAGCACAGGAAGACGACT 59.966 55.000 0.00 0.00 0.00 4.18
4452 6530 2.235898 AGAGATCCAAGCACAGGAAGAC 59.764 50.000 0.00 0.00 38.93 3.01
4460 6538 5.703130 AGAAACAAAGTAGAGATCCAAGCAC 59.297 40.000 0.00 0.00 0.00 4.40
4464 6542 7.455008 AGAGGTAGAAACAAAGTAGAGATCCAA 59.545 37.037 0.00 0.00 0.00 3.53
4466 6544 7.412853 AGAGGTAGAAACAAAGTAGAGATCC 57.587 40.000 0.00 0.00 0.00 3.36
4467 6545 7.762159 CCAAGAGGTAGAAACAAAGTAGAGATC 59.238 40.741 0.00 0.00 0.00 2.75
4468 6546 7.310734 CCCAAGAGGTAGAAACAAAGTAGAGAT 60.311 40.741 0.00 0.00 0.00 2.75
4469 6547 6.014499 CCCAAGAGGTAGAAACAAAGTAGAGA 60.014 42.308 0.00 0.00 0.00 3.10
4472 6550 6.110411 TCCCAAGAGGTAGAAACAAAGTAG 57.890 41.667 0.00 0.00 36.75 2.57
4485 6563 1.285078 GGCCTTGTTATCCCAAGAGGT 59.715 52.381 0.00 0.00 43.65 3.85
4506 6584 2.034179 GCCCAGGTTTACACACAAGAAC 59.966 50.000 0.00 0.00 0.00 3.01
4507 6585 2.303175 GCCCAGGTTTACACACAAGAA 58.697 47.619 0.00 0.00 0.00 2.52
4516 6594 3.279434 CCTAAGTGATGCCCAGGTTTAC 58.721 50.000 0.00 0.00 0.00 2.01
4544 6622 3.420893 TGTAAGCCCAACCAGAAATCTG 58.579 45.455 3.37 3.37 43.40 2.90
4545 6623 3.806949 TGTAAGCCCAACCAGAAATCT 57.193 42.857 0.00 0.00 0.00 2.40
4546 6624 4.864704 TTTGTAAGCCCAACCAGAAATC 57.135 40.909 0.00 0.00 0.00 2.17
4547 6625 5.213891 CTTTTGTAAGCCCAACCAGAAAT 57.786 39.130 0.00 0.00 0.00 2.17
4560 6638 3.604875 TCTACCTCGGGCTTTTGTAAG 57.395 47.619 0.00 0.00 34.36 2.34
4562 6640 3.557686 GGTTTCTACCTCGGGCTTTTGTA 60.558 47.826 0.00 0.00 41.53 2.41
4563 6641 2.501261 GTTTCTACCTCGGGCTTTTGT 58.499 47.619 0.00 0.00 0.00 2.83
4564 6642 1.810755 GGTTTCTACCTCGGGCTTTTG 59.189 52.381 0.00 0.00 41.53 2.44
4577 6655 0.249398 GCTCGGGCTTGAGGTTTCTA 59.751 55.000 0.00 0.00 36.47 2.10
4583 6661 2.747855 GTTGGCTCGGGCTTGAGG 60.748 66.667 7.48 0.00 36.47 3.86
4585 6663 0.539438 AAATGTTGGCTCGGGCTTGA 60.539 50.000 7.48 0.00 38.73 3.02
4593 6671 5.452302 CGAAATACGAATCAAATGTTGGCTC 59.548 40.000 0.00 0.00 45.77 4.70
4610 6688 3.121544 CCTAGCTTTCCGGACGAAATAC 58.878 50.000 1.83 0.00 39.73 1.89
4611 6689 2.101917 CCCTAGCTTTCCGGACGAAATA 59.898 50.000 1.83 0.00 39.73 1.40
4617 6695 2.189784 GCCCCTAGCTTTCCGGAC 59.810 66.667 1.83 0.00 38.99 4.79
4621 6699 2.801077 TTAGTTGCCCCTAGCTTTCC 57.199 50.000 0.00 0.00 44.23 3.13
4622 6700 4.096532 GTCAATTAGTTGCCCCTAGCTTTC 59.903 45.833 0.00 0.00 44.23 2.62
4630 6708 0.733150 GCTCGTCAATTAGTTGCCCC 59.267 55.000 0.00 0.00 35.26 5.80
4631 6709 0.373716 CGCTCGTCAATTAGTTGCCC 59.626 55.000 0.00 0.00 35.26 5.36
4632 6710 0.247695 GCGCTCGTCAATTAGTTGCC 60.248 55.000 0.00 0.00 35.26 4.52
4633 6711 0.721718 AGCGCTCGTCAATTAGTTGC 59.278 50.000 2.64 0.00 35.26 4.17
4634 6712 2.668457 AGAAGCGCTCGTCAATTAGTTG 59.332 45.455 12.06 0.00 36.65 3.16
4635 6713 2.960819 AGAAGCGCTCGTCAATTAGTT 58.039 42.857 12.06 0.00 0.00 2.24
4636 6714 2.656560 AGAAGCGCTCGTCAATTAGT 57.343 45.000 12.06 0.00 0.00 2.24
4637 6715 2.035342 CGAAGAAGCGCTCGTCAATTAG 60.035 50.000 12.06 0.00 32.54 1.73
4638 6716 1.917955 CGAAGAAGCGCTCGTCAATTA 59.082 47.619 12.06 0.00 32.54 1.40
4639 6717 0.716108 CGAAGAAGCGCTCGTCAATT 59.284 50.000 12.06 0.00 32.54 2.32
4640 6718 1.078759 CCGAAGAAGCGCTCGTCAAT 61.079 55.000 12.06 0.00 32.54 2.57
4641 6719 1.733041 CCGAAGAAGCGCTCGTCAA 60.733 57.895 12.06 0.00 32.54 3.18
4642 6720 2.126463 CCGAAGAAGCGCTCGTCA 60.126 61.111 12.06 0.00 32.54 4.35
4643 6721 1.406970 CTTCCGAAGAAGCGCTCGTC 61.407 60.000 12.06 5.48 42.97 4.20
4644 6722 1.444553 CTTCCGAAGAAGCGCTCGT 60.445 57.895 12.06 2.20 42.97 4.18
4645 6723 3.378552 CTTCCGAAGAAGCGCTCG 58.621 61.111 12.06 10.54 42.97 5.03
4652 6730 2.355108 CCATGAAGAGGCTTCCGAAGAA 60.355 50.000 12.54 0.00 0.00 2.52
4653 6731 1.208052 CCATGAAGAGGCTTCCGAAGA 59.792 52.381 12.54 0.00 0.00 2.87
4654 6732 1.661341 CCATGAAGAGGCTTCCGAAG 58.339 55.000 3.56 3.56 0.00 3.79
4655 6733 0.253044 CCCATGAAGAGGCTTCCGAA 59.747 55.000 0.00 0.00 0.00 4.30
4656 6734 0.909610 ACCCATGAAGAGGCTTCCGA 60.910 55.000 0.00 0.00 0.00 4.55
4657 6735 0.462759 GACCCATGAAGAGGCTTCCG 60.463 60.000 0.00 0.00 0.00 4.30
4658 6736 0.620556 TGACCCATGAAGAGGCTTCC 59.379 55.000 0.00 0.00 0.00 3.46
4659 6737 2.725221 ATGACCCATGAAGAGGCTTC 57.275 50.000 0.00 0.00 0.00 3.86
4660 6738 3.094572 CAAATGACCCATGAAGAGGCTT 58.905 45.455 0.00 0.00 0.00 4.35
4661 6739 2.622452 CCAAATGACCCATGAAGAGGCT 60.622 50.000 0.00 0.00 0.00 4.58
4662 6740 1.753073 CCAAATGACCCATGAAGAGGC 59.247 52.381 0.00 0.00 0.00 4.70
4663 6741 2.381911 CCCAAATGACCCATGAAGAGG 58.618 52.381 0.00 0.00 0.00 3.69
4664 6742 2.291800 ACCCCAAATGACCCATGAAGAG 60.292 50.000 0.00 0.00 0.00 2.85
4665 6743 1.715931 ACCCCAAATGACCCATGAAGA 59.284 47.619 0.00 0.00 0.00 2.87
4666 6744 1.826720 CACCCCAAATGACCCATGAAG 59.173 52.381 0.00 0.00 0.00 3.02
4667 6745 1.552023 CCACCCCAAATGACCCATGAA 60.552 52.381 0.00 0.00 0.00 2.57
4668 6746 0.040942 CCACCCCAAATGACCCATGA 59.959 55.000 0.00 0.00 0.00 3.07
4669 6747 0.977108 CCCACCCCAAATGACCCATG 60.977 60.000 0.00 0.00 0.00 3.66
4670 6748 1.391729 CCCACCCCAAATGACCCAT 59.608 57.895 0.00 0.00 0.00 4.00
4671 6749 2.857889 CCCACCCCAAATGACCCA 59.142 61.111 0.00 0.00 0.00 4.51
4672 6750 2.683572 GCCCACCCCAAATGACCC 60.684 66.667 0.00 0.00 0.00 4.46
4673 6751 1.682344 GAGCCCACCCCAAATGACC 60.682 63.158 0.00 0.00 0.00 4.02
4674 6752 0.681243 GAGAGCCCACCCCAAATGAC 60.681 60.000 0.00 0.00 0.00 3.06
4675 6753 1.139498 TGAGAGCCCACCCCAAATGA 61.139 55.000 0.00 0.00 0.00 2.57
4676 6754 0.682209 CTGAGAGCCCACCCCAAATG 60.682 60.000 0.00 0.00 0.00 2.32
4677 6755 1.693640 CTGAGAGCCCACCCCAAAT 59.306 57.895 0.00 0.00 0.00 2.32
4678 6756 3.170362 CTGAGAGCCCACCCCAAA 58.830 61.111 0.00 0.00 0.00 3.28
4679 6757 3.650950 GCTGAGAGCCCACCCCAA 61.651 66.667 0.00 0.00 34.48 4.12
4688 6766 0.179134 ACATTACGACGGCTGAGAGC 60.179 55.000 0.00 0.00 41.46 4.09
4689 6767 1.550065 CACATTACGACGGCTGAGAG 58.450 55.000 0.00 0.00 0.00 3.20
4690 6768 0.457853 GCACATTACGACGGCTGAGA 60.458 55.000 0.00 0.00 0.00 3.27
4691 6769 1.421410 GGCACATTACGACGGCTGAG 61.421 60.000 0.00 0.00 0.00 3.35
4692 6770 1.447140 GGCACATTACGACGGCTGA 60.447 57.895 0.00 0.00 0.00 4.26
4693 6771 1.739929 TGGCACATTACGACGGCTG 60.740 57.895 0.00 0.00 0.00 4.85
4694 6772 2.660206 TGGCACATTACGACGGCT 59.340 55.556 0.00 0.00 0.00 5.52
4718 6796 2.115343 AAAATCCAGAGGAAGCGTCC 57.885 50.000 11.15 11.15 45.35 4.79
4745 6823 6.473397 AAAGTCAAAAACGCATGTGAAAAA 57.527 29.167 14.43 0.00 0.00 1.94
4746 6824 6.473397 AAAAGTCAAAAACGCATGTGAAAA 57.527 29.167 14.43 0.00 0.00 2.29
4747 6825 6.473397 AAAAAGTCAAAAACGCATGTGAAA 57.527 29.167 14.43 0.00 0.00 2.69
4748 6826 7.030165 TCTAAAAAGTCAAAAACGCATGTGAA 58.970 30.769 14.43 0.00 0.00 3.18
4749 6827 6.556212 TCTAAAAAGTCAAAAACGCATGTGA 58.444 32.000 14.43 0.00 0.00 3.58
4750 6828 6.804534 TCTAAAAAGTCAAAAACGCATGTG 57.195 33.333 4.30 4.30 0.00 3.21
4751 6829 6.420604 CCATCTAAAAAGTCAAAAACGCATGT 59.579 34.615 0.00 0.00 0.00 3.21
4752 6830 6.128849 CCCATCTAAAAAGTCAAAAACGCATG 60.129 38.462 0.00 0.00 0.00 4.06
4753 6831 5.925969 CCCATCTAAAAAGTCAAAAACGCAT 59.074 36.000 0.00 0.00 0.00 4.73
4754 6832 5.163499 ACCCATCTAAAAAGTCAAAAACGCA 60.163 36.000 0.00 0.00 0.00 5.24
4755 6833 5.286438 ACCCATCTAAAAAGTCAAAAACGC 58.714 37.500 0.00 0.00 0.00 4.84
4756 6834 7.764695 AAACCCATCTAAAAAGTCAAAAACG 57.235 32.000 0.00 0.00 0.00 3.60
4780 6858 3.259902 CGAAAACCCGAAAACCCAAAAA 58.740 40.909 0.00 0.00 0.00 1.94
4781 6859 2.889852 CGAAAACCCGAAAACCCAAAA 58.110 42.857 0.00 0.00 0.00 2.44
4782 6860 1.471153 GCGAAAACCCGAAAACCCAAA 60.471 47.619 0.00 0.00 0.00 3.28
4783 6861 0.102663 GCGAAAACCCGAAAACCCAA 59.897 50.000 0.00 0.00 0.00 4.12
4784 6862 0.752376 AGCGAAAACCCGAAAACCCA 60.752 50.000 0.00 0.00 0.00 4.51
4785 6863 0.386476 AAGCGAAAACCCGAAAACCC 59.614 50.000 0.00 0.00 0.00 4.11
4786 6864 2.212869 AAAGCGAAAACCCGAAAACC 57.787 45.000 0.00 0.00 0.00 3.27
4787 6865 3.000476 GTGAAAAGCGAAAACCCGAAAAC 60.000 43.478 0.00 0.00 0.00 2.43
4788 6866 3.180613 GTGAAAAGCGAAAACCCGAAAA 58.819 40.909 0.00 0.00 0.00 2.29
4789 6867 2.479901 GGTGAAAAGCGAAAACCCGAAA 60.480 45.455 0.00 0.00 0.00 3.46
4790 6868 1.065851 GGTGAAAAGCGAAAACCCGAA 59.934 47.619 0.00 0.00 0.00 4.30
4791 6869 0.664224 GGTGAAAAGCGAAAACCCGA 59.336 50.000 0.00 0.00 0.00 5.14
4792 6870 0.659123 CGGTGAAAAGCGAAAACCCG 60.659 55.000 0.00 0.00 0.00 5.28
4793 6871 0.318360 CCGGTGAAAAGCGAAAACCC 60.318 55.000 0.00 0.00 0.00 4.11
4794 6872 0.382873 ACCGGTGAAAAGCGAAAACC 59.617 50.000 6.12 0.00 0.00 3.27
4795 6873 2.197792 AACCGGTGAAAAGCGAAAAC 57.802 45.000 8.52 0.00 0.00 2.43
4796 6874 2.943449 AAACCGGTGAAAAGCGAAAA 57.057 40.000 8.52 0.00 0.00 2.29
4797 6875 2.943449 AAAACCGGTGAAAAGCGAAA 57.057 40.000 8.52 0.00 0.00 3.46
4798 6876 2.424246 AGAAAAACCGGTGAAAAGCGAA 59.576 40.909 8.52 0.00 0.00 4.70
4799 6877 2.018515 AGAAAAACCGGTGAAAAGCGA 58.981 42.857 8.52 0.00 0.00 4.93
4800 6878 2.485266 AGAAAAACCGGTGAAAAGCG 57.515 45.000 8.52 0.00 0.00 4.68
4801 6879 3.734231 GCTAAGAAAAACCGGTGAAAAGC 59.266 43.478 8.52 7.81 0.00 3.51
4802 6880 5.183014 AGCTAAGAAAAACCGGTGAAAAG 57.817 39.130 8.52 0.70 0.00 2.27
4803 6881 5.585820 AAGCTAAGAAAAACCGGTGAAAA 57.414 34.783 8.52 0.00 0.00 2.29
4804 6882 5.585820 AAAGCTAAGAAAAACCGGTGAAA 57.414 34.783 8.52 0.00 0.00 2.69
4805 6883 5.344884 CAAAAGCTAAGAAAAACCGGTGAA 58.655 37.500 8.52 0.00 0.00 3.18
4806 6884 4.202070 CCAAAAGCTAAGAAAAACCGGTGA 60.202 41.667 8.52 0.00 0.00 4.02
4807 6885 4.048504 CCAAAAGCTAAGAAAAACCGGTG 58.951 43.478 8.52 0.00 0.00 4.94
4808 6886 3.069016 CCCAAAAGCTAAGAAAAACCGGT 59.931 43.478 0.00 0.00 0.00 5.28
4809 6887 3.554129 CCCCAAAAGCTAAGAAAAACCGG 60.554 47.826 0.00 0.00 0.00 5.28
4810 6888 3.319689 TCCCCAAAAGCTAAGAAAAACCG 59.680 43.478 0.00 0.00 0.00 4.44
4811 6889 4.948341 TCCCCAAAAGCTAAGAAAAACC 57.052 40.909 0.00 0.00 0.00 3.27
4812 6890 7.618502 TTTTTCCCCAAAAGCTAAGAAAAAC 57.381 32.000 0.00 0.00 37.93 2.43
4858 6936 6.454450 CGTGGAAGCAAAACAAATACGTTTTT 60.454 34.615 0.00 0.00 44.61 1.94
4860 6938 4.501198 CGTGGAAGCAAAACAAATACGTTT 59.499 37.500 0.00 0.00 40.79 3.60
4861 6939 4.039032 CGTGGAAGCAAAACAAATACGTT 58.961 39.130 0.00 0.00 0.00 3.99
4862 6940 3.312973 TCGTGGAAGCAAAACAAATACGT 59.687 39.130 0.00 0.00 0.00 3.57
4863 6941 3.879427 TCGTGGAAGCAAAACAAATACG 58.121 40.909 0.00 0.00 0.00 3.06
4864 6942 5.103290 TCTCGTGGAAGCAAAACAAATAC 57.897 39.130 0.00 0.00 0.00 1.89
4865 6943 5.759506 TTCTCGTGGAAGCAAAACAAATA 57.240 34.783 0.00 0.00 0.00 1.40
4866 6944 4.647424 TTCTCGTGGAAGCAAAACAAAT 57.353 36.364 0.00 0.00 0.00 2.32
4867 6945 4.170256 GTTTCTCGTGGAAGCAAAACAAA 58.830 39.130 0.00 0.00 35.62 2.83
4868 6946 3.191581 TGTTTCTCGTGGAAGCAAAACAA 59.808 39.130 7.59 0.00 41.07 2.83
4869 6947 2.750166 TGTTTCTCGTGGAAGCAAAACA 59.250 40.909 7.59 0.00 41.07 2.83
4870 6948 3.105937 GTGTTTCTCGTGGAAGCAAAAC 58.894 45.455 10.46 2.48 44.43 2.43
4871 6949 2.223157 CGTGTTTCTCGTGGAAGCAAAA 60.223 45.455 10.46 0.00 44.43 2.44
4872 6950 1.329292 CGTGTTTCTCGTGGAAGCAAA 59.671 47.619 10.46 0.00 44.43 3.68
4873 6951 0.934496 CGTGTTTCTCGTGGAAGCAA 59.066 50.000 10.46 0.00 44.43 3.91
4874 6952 0.103390 TCGTGTTTCTCGTGGAAGCA 59.897 50.000 6.41 6.41 41.61 3.91
4875 6953 1.214367 TTCGTGTTTCTCGTGGAAGC 58.786 50.000 0.00 0.00 35.16 3.86
4876 6954 4.468095 AAATTCGTGTTTCTCGTGGAAG 57.532 40.909 0.00 0.00 35.16 3.46
4877 6955 5.051816 AGTAAATTCGTGTTTCTCGTGGAA 58.948 37.500 0.00 0.00 0.00 3.53
4878 6956 4.624015 AGTAAATTCGTGTTTCTCGTGGA 58.376 39.130 0.00 0.00 0.00 4.02
4879 6957 4.985044 AGTAAATTCGTGTTTCTCGTGG 57.015 40.909 0.00 0.00 0.00 4.94
4880 6958 5.555191 CGAAAGTAAATTCGTGTTTCTCGTG 59.445 40.000 1.54 0.00 45.32 4.35
4881 6959 5.663292 CGAAAGTAAATTCGTGTTTCTCGT 58.337 37.500 1.54 0.00 45.32 4.18
4892 6970 2.159707 TGCTGCTCGCGAAAGTAAATTC 60.160 45.455 11.33 0.00 43.27 2.17
4893 6971 1.804151 TGCTGCTCGCGAAAGTAAATT 59.196 42.857 11.33 0.00 43.27 1.82
4894 6972 1.438651 TGCTGCTCGCGAAAGTAAAT 58.561 45.000 11.33 0.00 43.27 1.40
4895 6973 1.128507 CATGCTGCTCGCGAAAGTAAA 59.871 47.619 11.33 2.07 43.27 2.01
4896 6974 0.721154 CATGCTGCTCGCGAAAGTAA 59.279 50.000 11.33 4.52 43.27 2.24
4897 6975 1.083806 CCATGCTGCTCGCGAAAGTA 61.084 55.000 11.33 11.02 43.27 2.24
4898 6976 2.393768 CCATGCTGCTCGCGAAAGT 61.394 57.895 11.33 0.00 43.27 2.66
4899 6977 1.915614 AACCATGCTGCTCGCGAAAG 61.916 55.000 11.33 12.26 43.27 2.62
4900 6978 1.965930 AACCATGCTGCTCGCGAAA 60.966 52.632 11.33 0.00 43.27 3.46
4901 6979 2.358615 AACCATGCTGCTCGCGAA 60.359 55.556 11.33 0.00 43.27 4.70
4902 6980 3.120385 CAACCATGCTGCTCGCGA 61.120 61.111 9.26 9.26 43.27 5.87
4903 6981 3.425713 ACAACCATGCTGCTCGCG 61.426 61.111 0.00 0.00 43.27 5.87
4904 6982 2.177531 CACAACCATGCTGCTCGC 59.822 61.111 0.00 0.00 39.77 5.03
4905 6983 2.177531 GCACAACCATGCTGCTCG 59.822 61.111 0.00 0.00 42.62 5.03


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

AutoCloner maintained by Alex Coulton.