Multiple sequence alignment - TraesCS5D01G040500

Loading Multiple Alignment...

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 TraesCS5D01G040500 chr5D 100.000 3582 0 0 1 3582 41310709 41314290 0.000000e+00 6615.0
1 TraesCS5D01G040500 chr5D 81.008 258 37 5 1759 2006 41312003 41312258 1.010000e-45 195.0
2 TraesCS5D01G040500 chr5D 81.008 258 37 5 1295 1550 41312467 41312714 1.010000e-45 195.0
3 TraesCS5D01G040500 chr5D 81.250 144 23 4 3370 3510 528166921 528166779 2.920000e-21 113.0
4 TraesCS5D01G040500 chr5B 91.328 1649 92 28 1227 2863 35526388 35527997 0.000000e+00 2206.0
5 TraesCS5D01G040500 chr5B 90.712 323 22 3 850 1164 35526001 35526323 1.190000e-114 424.0
6 TraesCS5D01G040500 chr5B 85.930 398 43 4 3 387 35524736 35525133 2.570000e-111 412.0
7 TraesCS5D01G040500 chr5B 90.406 271 19 6 524 790 35525415 35525682 2.050000e-92 350.0
8 TraesCS5D01G040500 chr5B 81.494 308 48 7 3 305 35517947 35518250 9.930000e-61 244.0
9 TraesCS5D01G040500 chr5B 81.509 265 47 2 31 294 35514523 35514786 2.170000e-52 217.0
10 TraesCS5D01G040500 chr5B 87.603 121 9 3 414 528 35525269 35525389 6.240000e-28 135.0
11 TraesCS5D01G040500 chr5B 90.000 80 5 2 1623 1700 55039989 55039911 2.280000e-17 100.0
12 TraesCS5D01G040500 chr5A 94.614 687 22 4 2129 2812 29678333 29679007 0.000000e+00 1050.0
13 TraesCS5D01G040500 chr5A 96.008 476 13 2 1668 2137 29677674 29678149 0.000000e+00 769.0
14 TraesCS5D01G040500 chr5A 88.661 635 36 16 524 1143 29676492 29677105 0.000000e+00 741.0
15 TraesCS5D01G040500 chr5A 87.238 478 42 8 1159 1619 29677201 29677676 8.810000e-146 527.0
16 TraesCS5D01G040500 chr5A 84.515 536 72 6 3 528 29675932 29676466 1.470000e-143 520.0
17 TraesCS5D01G040500 chr5A 82.504 623 50 18 2770 3367 29679007 29679595 3.210000e-135 492.0
18 TraesCS5D01G040500 chr5A 93.976 83 3 1 524 606 29674597 29674677 1.350000e-24 124.0
19 TraesCS5D01G040500 chr5A 100.000 31 0 0 1134 1164 29677108 29677138 1.390000e-04 58.4
20 TraesCS5D01G040500 chr1D 87.063 286 35 2 2578 2863 14988416 14988699 4.460000e-84 322.0
21 TraesCS5D01G040500 chr1D 86.254 291 30 7 2578 2863 15020326 15020611 1.250000e-79 307.0
22 TraesCS5D01G040500 chr1D 92.638 163 10 1 2578 2740 14993482 14993642 2.150000e-57 233.0
23 TraesCS5D01G040500 chr1D 91.411 163 12 1 2578 2740 14998478 14998638 4.650000e-54 222.0
24 TraesCS5D01G040500 chr1D 91.411 163 12 1 2578 2740 15003480 15003640 4.650000e-54 222.0
25 TraesCS5D01G040500 chr1D 90.798 163 15 0 2578 2740 15009201 15009363 6.020000e-53 219.0
26 TraesCS5D01G040500 chr1D 90.798 163 13 1 2578 2740 14995622 14995782 2.170000e-52 217.0
27 TraesCS5D01G040500 chrUn 81.923 260 41 6 26 283 383744677 383744932 7.790000e-52 215.0
28 TraesCS5D01G040500 chr2B 85.106 141 21 0 3370 3510 557987395 557987255 1.040000e-30 145.0
29 TraesCS5D01G040500 chr3B 84.615 143 22 0 3368 3510 744633933 744634075 3.730000e-30 143.0
30 TraesCS5D01G040500 chr3B 83.333 144 24 0 3367 3510 744643079 744643222 2.240000e-27 134.0
31 TraesCS5D01G040500 chr3B 85.263 95 12 2 1601 1693 328469944 328470038 2.940000e-16 97.1
32 TraesCS5D01G040500 chr3B 85.417 96 10 4 1601 1693 632788678 632788772 2.940000e-16 97.1
33 TraesCS5D01G040500 chr3B 85.106 94 12 2 1601 1692 322357607 322357700 1.060000e-15 95.3
34 TraesCS5D01G040500 chr6B 83.453 139 23 0 3372 3510 137386990 137386852 2.900000e-26 130.0
35 TraesCS5D01G040500 chr6B 82.979 141 24 0 3370 3510 710912902 710912762 1.040000e-25 128.0
36 TraesCS5D01G040500 chr3A 83.217 143 22 1 3370 3510 449669305 449669447 2.900000e-26 130.0
37 TraesCS5D01G040500 chr3A 81.250 144 23 3 3368 3510 714369500 714369640 2.920000e-21 113.0
38 TraesCS5D01G040500 chr1A 83.453 139 23 0 3372 3510 554835657 554835519 2.900000e-26 130.0
39 TraesCS5D01G040500 chr1B 87.097 93 8 3 1623 1712 461244604 461244513 6.330000e-18 102.0
40 TraesCS5D01G040500 chr4D 85.263 95 12 2 1601 1693 249166946 249166852 2.940000e-16 97.1
41 TraesCS5D01G040500 chr2A 83.962 106 9 6 1592 1691 542655629 542655526 1.060000e-15 95.3
42 TraesCS5D01G040500 chr4A 82.857 105 13 3 1592 1692 546062301 546062198 4.930000e-14 89.8


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 TraesCS5D01G040500 chr5D 41310709 41314290 3581 False 2335.000 6615 87.338667 1 3582 3 chr5D.!!$F1 3581
1 TraesCS5D01G040500 chr5B 35524736 35527997 3261 False 705.400 2206 89.195800 3 2863 5 chr5B.!!$F2 2860
2 TraesCS5D01G040500 chr5B 35514523 35518250 3727 False 230.500 244 81.501500 3 305 2 chr5B.!!$F1 302
3 TraesCS5D01G040500 chr5A 29674597 29679595 4998 False 535.175 1050 90.939500 3 3367 8 chr5A.!!$F1 3364
4 TraesCS5D01G040500 chr1D 14993482 14998638 5156 False 224.000 233 91.615667 2578 2740 3 chr1D.!!$F5 162

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
868 5595 0.613777 CGACCTAAGGTTTGCCTCCT 59.386 55.0 0.0 0.0 46.33 3.69 F
1165 5913 0.615850 TGGTTGTGGTATCGGCATGA 59.384 50.0 0.0 0.0 0.00 3.07 F
2171 7236 0.532573 AGATAGTGCTGTGTGGGTCG 59.467 55.0 0.0 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1931 6795 0.248843 GACAGAGGCAGGAGTGAAGG 59.751 60.0 0.0 0.0 0.00 3.46 R
2433 7499 0.391130 TCGCACCATGCTCTTACCAC 60.391 55.0 0.0 0.0 42.25 4.16 R
3220 11851 0.034337 AATGTGCCAAAGCTGCCAAG 59.966 50.0 0.0 0.0 40.80 3.61 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
40 4337 1.024271 GCACCATGTCACACACACTT 58.976 50.000 0.00 0.00 38.04 3.16
42 4339 2.224079 GCACCATGTCACACACACTTAG 59.776 50.000 0.00 0.00 38.04 2.18
79 4378 2.569404 CCCTTTAGAGCCTCTCAGTGTT 59.431 50.000 0.00 0.00 32.06 3.32
128 4427 8.740123 ATGATCGAAGACCGTCTATATATTCT 57.260 34.615 0.26 0.00 42.51 2.40
145 4444 3.806625 TTCTACGGGTATAAGGTGTGC 57.193 47.619 0.00 0.00 0.00 4.57
296 4605 3.714871 GAGAGAGCTCAGCGGTGCC 62.715 68.421 17.77 3.25 40.96 5.01
314 4623 2.913578 ACGTGCGTGGGGTACTGA 60.914 61.111 0.00 0.00 0.00 3.41
316 4625 2.431942 GTGCGTGGGGTACTGACG 60.432 66.667 7.28 7.28 36.18 4.35
360 4669 0.934496 CTACGAGCCGAGAGTCTCTG 59.066 60.000 17.91 12.58 0.00 3.35
363 4672 1.021920 CGAGCCGAGAGTCTCTGTGA 61.022 60.000 17.91 0.00 0.00 3.58
371 4680 5.174395 CCGAGAGTCTCTGTGATCATTTTT 58.826 41.667 17.91 0.00 0.00 1.94
387 4696 8.966868 TGATCATTTTTGAATAAACTACTCCCC 58.033 33.333 0.00 0.00 0.00 4.81
410 4719 3.215244 CGATAAATGTTATTGTCGCGGC 58.785 45.455 2.29 2.29 37.17 6.53
411 4720 3.059868 CGATAAATGTTATTGTCGCGGCT 60.060 43.478 13.81 0.00 37.17 5.52
463 4886 2.766313 AGCTGCGACAAGTGTGAATTA 58.234 42.857 0.00 0.00 0.00 1.40
485 4908 8.950208 ATTAAAGGAAGTACTACTGATCTTGC 57.050 34.615 0.00 0.00 0.00 4.01
487 4910 5.590530 AGGAAGTACTACTGATCTTGCAG 57.409 43.478 0.00 0.00 41.63 4.41
490 4919 6.211584 AGGAAGTACTACTGATCTTGCAGAAA 59.788 38.462 0.00 0.00 39.20 2.52
521 4950 1.078214 TGGCTGCCGAGGAAGAATG 60.078 57.895 14.98 0.00 0.00 2.67
528 4957 1.811941 GCCGAGGAAGAATGACCATCC 60.812 57.143 0.00 0.00 0.00 3.51
529 4958 1.539065 CCGAGGAAGAATGACCATCCG 60.539 57.143 0.00 0.00 37.05 4.18
530 4959 1.539065 CGAGGAAGAATGACCATCCGG 60.539 57.143 0.00 0.00 37.05 5.14
557 5018 2.040544 AATCTTGCCCGGCTTCACG 61.041 57.895 11.61 0.00 0.00 4.35
651 5119 4.527583 GCGAGCCAGAGCCCAGAG 62.528 72.222 0.00 0.00 41.25 3.35
652 5120 3.847602 CGAGCCAGAGCCCAGAGG 61.848 72.222 0.00 0.00 41.25 3.69
868 5595 0.613777 CGACCTAAGGTTTGCCTCCT 59.386 55.000 0.00 0.00 46.33 3.69
871 5598 3.105283 GACCTAAGGTTTGCCTCCTCTA 58.895 50.000 0.00 0.00 46.33 2.43
948 5676 2.720750 GGTGTTCGTTTGCGCGTG 60.721 61.111 8.43 0.00 38.14 5.34
1087 5818 1.153706 AACGACGCCAAGGTATCCG 60.154 57.895 0.00 0.00 0.00 4.18
1109 5845 6.885376 TCCGTCTATCTATATCTGTTTCTCCC 59.115 42.308 0.00 0.00 0.00 4.30
1121 5857 1.874345 TTTCTCCCGTCGACAGCCTC 61.874 60.000 17.16 0.00 0.00 4.70
1164 5912 0.732571 GTGGTTGTGGTATCGGCATG 59.267 55.000 0.00 0.00 0.00 4.06
1165 5913 0.615850 TGGTTGTGGTATCGGCATGA 59.384 50.000 0.00 0.00 0.00 3.07
1168 5983 2.097466 GGTTGTGGTATCGGCATGAAAG 59.903 50.000 0.00 0.00 0.00 2.62
1185 6000 6.690530 CATGAAAGAAGTGAAAATAGGGCAA 58.309 36.000 0.00 0.00 0.00 4.52
1187 6002 7.301868 TGAAAGAAGTGAAAATAGGGCAATT 57.698 32.000 0.00 0.00 0.00 2.32
1189 6004 8.865090 TGAAAGAAGTGAAAATAGGGCAATTTA 58.135 29.630 0.00 0.00 0.00 1.40
1190 6005 9.705290 GAAAGAAGTGAAAATAGGGCAATTTAA 57.295 29.630 0.00 0.00 0.00 1.52
1191 6006 9.710900 AAAGAAGTGAAAATAGGGCAATTTAAG 57.289 29.630 0.00 0.00 0.00 1.85
1192 6007 8.650143 AGAAGTGAAAATAGGGCAATTTAAGA 57.350 30.769 0.00 0.00 0.00 2.10
1197 6016 8.188139 GTGAAAATAGGGCAATTTAAGATTCGA 58.812 33.333 0.00 0.00 0.00 3.71
1204 6023 8.463930 AGGGCAATTTAAGATTCGATTCATTA 57.536 30.769 9.78 3.51 0.00 1.90
1235 6054 4.617253 TTAGCTTCACCTCTGCTTGTAA 57.383 40.909 0.00 0.00 38.15 2.41
1238 6057 4.006319 AGCTTCACCTCTGCTTGTAATTC 58.994 43.478 0.00 0.00 32.61 2.17
1251 6070 4.319766 GCTTGTAATTCTGTCACACCTGTG 60.320 45.833 0.00 0.00 46.91 3.66
1309 6140 1.885887 TGGGAGCACCGAATGAAAAAG 59.114 47.619 0.00 0.00 44.64 2.27
1310 6141 1.402852 GGGAGCACCGAATGAAAAAGC 60.403 52.381 0.00 0.00 36.97 3.51
1311 6142 1.606606 GAGCACCGAATGAAAAAGCG 58.393 50.000 0.00 0.00 0.00 4.68
1313 6144 1.606668 AGCACCGAATGAAAAAGCGAA 59.393 42.857 0.00 0.00 0.00 4.70
1327 6160 6.803320 TGAAAAAGCGAATGAAAATAGAGCAG 59.197 34.615 0.00 0.00 0.00 4.24
1330 6163 6.985188 AAGCGAATGAAAATAGAGCAGTTA 57.015 33.333 0.00 0.00 0.00 2.24
1333 6166 6.763135 AGCGAATGAAAATAGAGCAGTTATCA 59.237 34.615 0.00 0.00 0.00 2.15
1338 6171 7.558161 TGAAAATAGAGCAGTTATCATGTGG 57.442 36.000 0.00 0.00 0.00 4.17
1349 6182 4.635765 AGTTATCATGTGGTTCGGTTCATG 59.364 41.667 0.00 0.00 38.96 3.07
1351 6184 3.133141 TCATGTGGTTCGGTTCATGAA 57.867 42.857 3.38 3.38 42.01 2.57
1360 6193 5.943416 TGGTTCGGTTCATGAATAATCTGTT 59.057 36.000 12.12 0.00 0.00 3.16
1363 6196 7.908601 GGTTCGGTTCATGAATAATCTGTTTAC 59.091 37.037 12.12 4.66 0.00 2.01
1364 6197 8.665685 GTTCGGTTCATGAATAATCTGTTTACT 58.334 33.333 12.12 0.00 0.00 2.24
1429 6262 5.579718 CCTTATGAAAAGCTGAAGATGCAG 58.420 41.667 0.00 0.00 38.91 4.41
1466 6299 0.807496 CTGCCTTGGAAGTAGCTTGC 59.193 55.000 0.00 0.00 32.43 4.01
1489 6322 1.694150 AGCTTCACTTCTGCCAGTGTA 59.306 47.619 7.46 0.00 44.10 2.90
1555 6388 8.118976 TCTAATTTCTTAGGTCTTTCTCGTCA 57.881 34.615 0.00 0.00 35.92 4.35
1588 6421 3.346315 TGATGGTGAACAGCTATGGTTG 58.654 45.455 5.64 0.00 36.18 3.77
1598 6431 2.026822 CAGCTATGGTTGTCCCTCTGTT 60.027 50.000 0.00 0.00 0.00 3.16
1616 6449 7.711339 CCCTCTGTTAAGAAATATAAGAGCGTT 59.289 37.037 0.00 0.00 30.03 4.84
1617 6450 9.099454 CCTCTGTTAAGAAATATAAGAGCGTTT 57.901 33.333 0.00 0.00 30.03 3.60
1626 6459 9.522804 AGAAATATAAGAGCGTTTAGAACTCTG 57.477 33.333 0.00 0.00 39.84 3.35
1627 6460 9.303537 GAAATATAAGAGCGTTTAGAACTCTGT 57.696 33.333 0.00 0.00 39.84 3.41
1628 6461 9.654663 AAATATAAGAGCGTTTAGAACTCTGTT 57.345 29.630 0.00 0.16 39.84 3.16
1631 6464 8.690680 ATAAGAGCGTTTAGAACTCTGTTAAG 57.309 34.615 5.05 0.00 39.84 1.85
1632 6465 6.328641 AGAGCGTTTAGAACTCTGTTAAGA 57.671 37.500 0.00 0.00 39.29 2.10
1633 6466 6.746120 AGAGCGTTTAGAACTCTGTTAAGAA 58.254 36.000 0.00 0.00 39.29 2.52
1634 6467 7.208080 AGAGCGTTTAGAACTCTGTTAAGAAA 58.792 34.615 0.00 0.00 39.29 2.52
1635 6468 7.873505 AGAGCGTTTAGAACTCTGTTAAGAAAT 59.126 33.333 0.00 0.00 39.29 2.17
1636 6469 9.136952 GAGCGTTTAGAACTCTGTTAAGAAATA 57.863 33.333 0.00 0.00 30.03 1.40
1637 6470 9.654663 AGCGTTTAGAACTCTGTTAAGAAATAT 57.345 29.630 0.00 0.00 30.03 1.28
1758 6622 4.446371 AGAGATTAACATGGGAGAAAGCG 58.554 43.478 0.00 0.00 0.00 4.68
1872 6736 1.486726 GCTGGACACCTGTAGCCTTAT 59.513 52.381 0.00 0.00 0.00 1.73
1887 6751 5.831702 AGCCTTATGAAAAGCTGAAGATG 57.168 39.130 0.00 0.00 33.41 2.90
1903 6767 6.519679 TGAAGATGCAATAATTCTTGTGCT 57.480 33.333 4.28 0.00 37.87 4.40
1912 6776 2.283145 ATTCTTGTGCTGTTCCTGCT 57.717 45.000 0.00 0.00 0.00 4.24
1931 6795 5.106673 CCTGCTTTGGTAGTAGCTTTTGTAC 60.107 44.000 0.00 0.00 38.22 2.90
1939 6803 5.868258 GGTAGTAGCTTTTGTACCTTCACTC 59.132 44.000 0.00 0.00 33.43 3.51
1945 6809 1.729586 TTGTACCTTCACTCCTGCCT 58.270 50.000 0.00 0.00 0.00 4.75
1946 6810 1.267121 TGTACCTTCACTCCTGCCTC 58.733 55.000 0.00 0.00 0.00 4.70
1947 6811 1.203187 TGTACCTTCACTCCTGCCTCT 60.203 52.381 0.00 0.00 0.00 3.69
1948 6812 1.205893 GTACCTTCACTCCTGCCTCTG 59.794 57.143 0.00 0.00 0.00 3.35
2171 7236 0.532573 AGATAGTGCTGTGTGGGTCG 59.467 55.000 0.00 0.00 0.00 4.79
2433 7499 6.546428 TTTCTCCTATAACAGACAGAAGGG 57.454 41.667 0.00 0.00 29.57 3.95
2481 7547 2.998316 GCTAAGGAGCTGGATCAGTT 57.002 50.000 0.00 0.00 45.98 3.16
2487 7553 3.300388 AGGAGCTGGATCAGTTTATCGA 58.700 45.455 0.00 0.00 33.43 3.59
2501 7567 2.325583 TATCGACATGGTTCCCAAGC 57.674 50.000 0.00 0.00 36.95 4.01
2506 7572 0.482446 ACATGGTTCCCAAGCAGGAA 59.518 50.000 7.06 0.00 42.69 3.36
2787 8945 8.447833 TCGTGAAATTAACCAGTCATTGTTATC 58.552 33.333 0.00 0.00 0.00 1.75
2788 8946 7.425309 CGTGAAATTAACCAGTCATTGTTATCG 59.575 37.037 0.00 0.00 0.00 2.92
2820 10156 4.886247 TTTGTTTAGTAGTGTGTGCACC 57.114 40.909 15.69 6.37 46.35 5.01
2823 10159 2.143008 TTAGTAGTGTGTGCACCGTG 57.857 50.000 15.69 0.00 46.35 4.94
2840 10887 2.247311 GTGCTTTTGGTACGATGCAG 57.753 50.000 0.00 0.00 30.61 4.41
2841 10888 0.521291 TGCTTTTGGTACGATGCAGC 59.479 50.000 0.00 0.00 0.00 5.25
2887 10934 7.555087 TGAAATCTTGGTTCAAAATTCTGTGT 58.445 30.769 0.00 0.00 32.13 3.72
2893 10940 7.719193 TCTTGGTTCAAAATTCTGTGTCTATCA 59.281 33.333 0.00 0.00 0.00 2.15
2913 10960 6.845758 ATCACAAGTTTGAATCATGGTGAT 57.154 33.333 0.71 0.71 39.09 3.06
2915 10962 7.053316 TCACAAGTTTGAATCATGGTGATTT 57.947 32.000 6.63 0.00 46.20 2.17
2957 11012 2.247358 AGGTGCAAATTGTAGGGTTGG 58.753 47.619 0.00 0.00 0.00 3.77
2966 11021 0.553819 TGTAGGGTTGGCAGTGGTTT 59.446 50.000 0.00 0.00 0.00 3.27
2989 11154 1.004185 CATATCAGCAAGCACAGACGC 60.004 52.381 0.00 0.00 0.00 5.19
2991 11156 2.770132 ATCAGCAAGCACAGACGCGA 62.770 55.000 15.93 0.00 36.85 5.87
2992 11157 3.038417 AGCAAGCACAGACGCGAC 61.038 61.111 15.93 6.86 36.85 5.19
3034 11259 9.085645 TCTTAAAACTACCACTCTGTATCTTCA 57.914 33.333 0.00 0.00 0.00 3.02
3057 11282 4.450053 AGTCATCTTCAGATTAGCTTGCC 58.550 43.478 0.00 0.00 31.21 4.52
3081 11306 5.689961 CGTTCCTTAAACCTTGAAACCATTG 59.310 40.000 0.00 0.00 34.11 2.82
3084 11309 5.010617 TCCTTAAACCTTGAAACCATTGCTC 59.989 40.000 0.00 0.00 0.00 4.26
3087 11312 1.247567 CCTTGAAACCATTGCTCCGT 58.752 50.000 0.00 0.00 0.00 4.69
3088 11313 1.068333 CCTTGAAACCATTGCTCCGTG 60.068 52.381 0.00 0.00 0.00 4.94
3090 11315 0.950836 TGAAACCATTGCTCCGTGTG 59.049 50.000 0.00 0.00 0.00 3.82
3091 11316 0.951558 GAAACCATTGCTCCGTGTGT 59.048 50.000 0.00 0.00 0.00 3.72
3093 11318 2.264005 AACCATTGCTCCGTGTGTAA 57.736 45.000 0.00 0.00 0.00 2.41
3095 11320 1.071699 ACCATTGCTCCGTGTGTAAGT 59.928 47.619 0.00 0.00 0.00 2.24
3096 11321 2.300723 ACCATTGCTCCGTGTGTAAGTA 59.699 45.455 0.00 0.00 0.00 2.24
3097 11322 3.055385 ACCATTGCTCCGTGTGTAAGTAT 60.055 43.478 0.00 0.00 0.00 2.12
3100 11325 2.967362 TGCTCCGTGTGTAAGTATTGG 58.033 47.619 0.00 0.00 0.00 3.16
3101 11326 2.563620 TGCTCCGTGTGTAAGTATTGGA 59.436 45.455 0.00 0.00 0.00 3.53
3103 11328 3.368116 GCTCCGTGTGTAAGTATTGGAGT 60.368 47.826 7.16 0.00 42.70 3.85
3104 11329 4.817517 CTCCGTGTGTAAGTATTGGAGTT 58.182 43.478 0.00 0.00 37.37 3.01
3105 11330 4.562082 TCCGTGTGTAAGTATTGGAGTTG 58.438 43.478 0.00 0.00 0.00 3.16
3107 11332 5.046878 TCCGTGTGTAAGTATTGGAGTTGAT 60.047 40.000 0.00 0.00 0.00 2.57
3108 11333 5.642063 CCGTGTGTAAGTATTGGAGTTGATT 59.358 40.000 0.00 0.00 0.00 2.57
3109 11334 6.814644 CCGTGTGTAAGTATTGGAGTTGATTA 59.185 38.462 0.00 0.00 0.00 1.75
3110 11335 7.494625 CCGTGTGTAAGTATTGGAGTTGATTAT 59.505 37.037 0.00 0.00 0.00 1.28
3111 11336 8.879759 CGTGTGTAAGTATTGGAGTTGATTATT 58.120 33.333 0.00 0.00 0.00 1.40
3113 11338 9.952030 TGTGTAAGTATTGGAGTTGATTATTCA 57.048 29.630 0.00 0.00 0.00 2.57
3122 11347 5.663106 TGGAGTTGATTATTCAGACTAGGCT 59.337 40.000 0.00 0.00 32.27 4.58
3154 11783 5.104569 ACATTTTGTCCAGTTTTGTTGGGAT 60.105 36.000 0.00 0.00 36.34 3.85
3155 11784 4.399004 TTTGTCCAGTTTTGTTGGGATG 57.601 40.909 0.00 0.00 36.34 3.51
3161 11790 4.526262 TCCAGTTTTGTTGGGATGTTATGG 59.474 41.667 0.00 0.00 36.34 2.74
3164 11793 6.015010 CCAGTTTTGTTGGGATGTTATGGTTA 60.015 38.462 0.00 0.00 31.87 2.85
3180 11809 8.553153 TGTTATGGTTAGGTTATCAATCCTTCA 58.447 33.333 0.00 0.00 35.51 3.02
3181 11810 9.574516 GTTATGGTTAGGTTATCAATCCTTCAT 57.425 33.333 0.00 0.00 35.51 2.57
3217 11848 7.958583 AGAAATATATCATCAGTCCCTGGTAGT 59.041 37.037 0.00 0.00 31.51 2.73
3218 11849 9.256228 GAAATATATCATCAGTCCCTGGTAGTA 57.744 37.037 0.00 0.00 31.51 1.82
3219 11850 8.830915 AATATATCATCAGTCCCTGGTAGTAG 57.169 38.462 0.00 0.00 31.51 2.57
3220 11851 2.667470 TCATCAGTCCCTGGTAGTAGC 58.333 52.381 0.00 0.00 31.51 3.58
3270 11901 1.005450 GTATCCTGGTTGCTTCCCCAA 59.995 52.381 0.00 0.00 0.00 4.12
3276 11907 1.607801 GGTTGCTTCCCCAATGAGCC 61.608 60.000 0.00 0.00 35.59 4.70
3278 11909 0.323725 TTGCTTCCCCAATGAGCCTC 60.324 55.000 0.00 0.00 35.59 4.70
3279 11910 1.454663 GCTTCCCCAATGAGCCTCC 60.455 63.158 0.00 0.00 0.00 4.30
3301 11932 5.065914 CCCACTTCAGTTCTCATTTCTCAA 58.934 41.667 0.00 0.00 0.00 3.02
3309 11940 8.103948 TCAGTTCTCATTTCTCAATTTCCTTC 57.896 34.615 0.00 0.00 0.00 3.46
3322 11953 0.884704 TTCCTTCACGGCTGCACTTC 60.885 55.000 0.50 0.00 0.00 3.01
3330 11961 1.618837 ACGGCTGCACTTCTCTTTCTA 59.381 47.619 0.50 0.00 0.00 2.10
3368 11999 4.048504 GCATTGTTGTAAGTTTGTGACCC 58.951 43.478 0.00 0.00 0.00 4.46
3369 12000 4.202111 GCATTGTTGTAAGTTTGTGACCCT 60.202 41.667 0.00 0.00 0.00 4.34
3370 12001 5.681179 GCATTGTTGTAAGTTTGTGACCCTT 60.681 40.000 0.00 0.00 0.00 3.95
3372 12003 5.986501 TGTTGTAAGTTTGTGACCCTTTT 57.013 34.783 0.00 0.00 0.00 2.27
3399 12030 9.522804 TTTTTGCGAATTGAAACTTGTATTACT 57.477 25.926 0.00 0.00 0.00 2.24
3400 12031 8.722342 TTTGCGAATTGAAACTTGTATTACTC 57.278 30.769 0.00 0.00 0.00 2.59
3401 12032 7.428282 TGCGAATTGAAACTTGTATTACTCA 57.572 32.000 0.00 0.00 0.00 3.41
3402 12033 7.866729 TGCGAATTGAAACTTGTATTACTCAA 58.133 30.769 0.00 0.00 0.00 3.02
3403 12034 8.346300 TGCGAATTGAAACTTGTATTACTCAAA 58.654 29.630 0.00 0.00 0.00 2.69
3405 12036 9.113876 CGAATTGAAACTTGTATTACTCAAACC 57.886 33.333 0.00 0.00 0.00 3.27
3406 12037 9.406828 GAATTGAAACTTGTATTACTCAAACCC 57.593 33.333 0.00 0.00 0.00 4.11
3407 12038 6.548441 TGAAACTTGTATTACTCAAACCCG 57.452 37.500 0.00 0.00 0.00 5.28
3408 12039 6.289834 TGAAACTTGTATTACTCAAACCCGA 58.710 36.000 0.00 0.00 0.00 5.14
3409 12040 6.938030 TGAAACTTGTATTACTCAAACCCGAT 59.062 34.615 0.00 0.00 0.00 4.18
3411 12042 6.045072 ACTTGTATTACTCAAACCCGATCA 57.955 37.500 0.00 0.00 0.00 2.92
3413 12044 5.018539 TGTATTACTCAAACCCGATCAGG 57.981 43.478 0.00 0.00 40.63 3.86
3414 12045 4.468510 TGTATTACTCAAACCCGATCAGGT 59.531 41.667 0.00 0.00 44.00 4.00
3423 12054 3.992943 ACCCGATCAGGTTTACAATCA 57.007 42.857 0.00 0.00 36.44 2.57
3424 12055 3.873910 ACCCGATCAGGTTTACAATCAG 58.126 45.455 0.00 0.00 36.44 2.90
3425 12056 3.517901 ACCCGATCAGGTTTACAATCAGA 59.482 43.478 0.00 0.00 36.44 3.27
3426 12057 4.122776 CCCGATCAGGTTTACAATCAGAG 58.877 47.826 0.00 0.00 38.74 3.35
3427 12058 4.122776 CCGATCAGGTTTACAATCAGAGG 58.877 47.826 0.00 0.00 34.51 3.69
3428 12059 4.141937 CCGATCAGGTTTACAATCAGAGGA 60.142 45.833 0.00 0.00 34.51 3.71
3430 12061 5.521735 CGATCAGGTTTACAATCAGAGGAAG 59.478 44.000 0.00 0.00 0.00 3.46
3431 12062 4.579869 TCAGGTTTACAATCAGAGGAAGC 58.420 43.478 0.00 0.00 0.00 3.86
3435 12524 4.762251 GGTTTACAATCAGAGGAAGCAAGT 59.238 41.667 0.00 0.00 0.00 3.16
3436 12525 5.241728 GGTTTACAATCAGAGGAAGCAAGTT 59.758 40.000 0.00 0.00 0.00 2.66
3445 12534 3.853623 GAAGCAAGTTCCACAGCAC 57.146 52.632 0.00 0.00 0.00 4.40
3446 12535 1.312815 GAAGCAAGTTCCACAGCACT 58.687 50.000 0.00 0.00 0.00 4.40
3464 12553 3.476552 CACTAGCTGGACCAGAAACAAA 58.523 45.455 26.25 2.05 32.44 2.83
3465 12554 3.251004 CACTAGCTGGACCAGAAACAAAC 59.749 47.826 26.25 5.28 32.44 2.93
3466 12555 1.692411 AGCTGGACCAGAAACAAACC 58.308 50.000 26.25 4.51 32.44 3.27
3467 12556 1.064017 AGCTGGACCAGAAACAAACCA 60.064 47.619 26.25 0.00 32.44 3.67
3469 12558 1.956477 CTGGACCAGAAACAAACCAGG 59.044 52.381 17.22 0.00 40.50 4.45
3470 12559 1.286553 TGGACCAGAAACAAACCAGGT 59.713 47.619 0.00 0.00 0.00 4.00
3471 12560 1.954382 GGACCAGAAACAAACCAGGTC 59.046 52.381 0.00 0.00 43.60 3.85
3472 12561 2.650322 GACCAGAAACAAACCAGGTCA 58.350 47.619 0.00 0.00 43.74 4.02
3474 12563 4.394729 GACCAGAAACAAACCAGGTCATA 58.605 43.478 0.00 0.00 43.74 2.15
3476 12565 4.141251 ACCAGAAACAAACCAGGTCATAGT 60.141 41.667 0.00 0.00 0.00 2.12
3478 12567 5.048713 CCAGAAACAAACCAGGTCATAGTTC 60.049 44.000 0.00 0.00 0.00 3.01
3479 12568 5.765182 CAGAAACAAACCAGGTCATAGTTCT 59.235 40.000 0.00 0.00 0.00 3.01
3480 12569 6.934645 CAGAAACAAACCAGGTCATAGTTCTA 59.065 38.462 0.00 0.00 0.00 2.10
3481 12570 6.935208 AGAAACAAACCAGGTCATAGTTCTAC 59.065 38.462 0.00 0.00 0.00 2.59
3483 12572 4.844655 ACAAACCAGGTCATAGTTCTACCT 59.155 41.667 0.00 0.00 44.54 3.08
3484 12573 5.309806 ACAAACCAGGTCATAGTTCTACCTT 59.690 40.000 0.00 0.00 41.75 3.50
3485 12574 5.678955 AACCAGGTCATAGTTCTACCTTC 57.321 43.478 0.00 0.00 41.75 3.46
3486 12575 4.031611 ACCAGGTCATAGTTCTACCTTCC 58.968 47.826 0.00 0.00 41.75 3.46
3487 12576 4.264895 ACCAGGTCATAGTTCTACCTTCCT 60.265 45.833 0.00 0.00 41.75 3.36
3490 12579 5.300792 CAGGTCATAGTTCTACCTTCCTCTC 59.699 48.000 0.00 0.00 41.75 3.20
3491 12580 5.194942 AGGTCATAGTTCTACCTTCCTCTCT 59.805 44.000 0.00 0.00 40.82 3.10
3492 12581 6.390461 AGGTCATAGTTCTACCTTCCTCTCTA 59.610 42.308 0.00 0.00 40.82 2.43
3495 12584 4.594675 AGTTCTACCTTCCTCTCTAGCA 57.405 45.455 0.00 0.00 0.00 3.49
3496 12585 4.936802 AGTTCTACCTTCCTCTCTAGCAA 58.063 43.478 0.00 0.00 0.00 3.91
3497 12586 5.334421 AGTTCTACCTTCCTCTCTAGCAAA 58.666 41.667 0.00 0.00 0.00 3.68
3498 12587 5.420739 AGTTCTACCTTCCTCTCTAGCAAAG 59.579 44.000 0.00 0.00 0.00 2.77
3499 12588 5.194473 TCTACCTTCCTCTCTAGCAAAGA 57.806 43.478 0.00 0.00 0.00 2.52
3500 12589 5.772004 TCTACCTTCCTCTCTAGCAAAGAT 58.228 41.667 0.00 0.00 32.41 2.40
3501 12590 6.912426 TCTACCTTCCTCTCTAGCAAAGATA 58.088 40.000 0.00 0.00 32.41 1.98
3502 12591 7.001674 TCTACCTTCCTCTCTAGCAAAGATAG 58.998 42.308 0.00 0.00 32.41 2.08
3504 12593 4.588528 CCTTCCTCTCTAGCAAAGATAGCT 59.411 45.833 0.00 0.00 45.77 3.32
3505 12594 5.772672 CCTTCCTCTCTAGCAAAGATAGCTA 59.227 44.000 0.00 0.00 43.25 3.32
3506 12595 6.266558 CCTTCCTCTCTAGCAAAGATAGCTAA 59.733 42.308 0.00 0.00 43.39 3.09
3507 12596 7.201956 CCTTCCTCTCTAGCAAAGATAGCTAAA 60.202 40.741 0.00 0.00 43.39 1.85
3508 12597 7.045126 TCCTCTCTAGCAAAGATAGCTAAAC 57.955 40.000 0.00 0.00 43.39 2.01
3509 12598 6.607600 TCCTCTCTAGCAAAGATAGCTAAACA 59.392 38.462 0.00 0.00 43.39 2.83
3510 12599 6.922957 CCTCTCTAGCAAAGATAGCTAAACAG 59.077 42.308 0.00 0.00 43.39 3.16
3511 12600 7.411486 TCTCTAGCAAAGATAGCTAAACAGT 57.589 36.000 0.00 0.00 43.39 3.55
3512 12601 7.841956 TCTCTAGCAAAGATAGCTAAACAGTT 58.158 34.615 0.00 0.00 43.39 3.16
3514 12603 9.757227 CTCTAGCAAAGATAGCTAAACAGTTAT 57.243 33.333 0.00 0.00 43.39 1.89
3518 12607 9.892130 AGCAAAGATAGCTAAACAGTTATAGTT 57.108 29.630 0.00 0.00 41.32 2.24
3527 12616 8.476447 AGCTAAACAGTTATAGTTCTACCTTCC 58.524 37.037 0.00 0.00 0.00 3.46
3528 12617 8.476447 GCTAAACAGTTATAGTTCTACCTTCCT 58.524 37.037 0.00 0.00 0.00 3.36
3530 12619 8.667592 AAACAGTTATAGTTCTACCTTCCTCT 57.332 34.615 0.00 0.00 0.00 3.69
3533 12622 8.780003 ACAGTTATAGTTCTACCTTCCTCTCTA 58.220 37.037 0.00 0.00 0.00 2.43
3534 12623 9.280174 CAGTTATAGTTCTACCTTCCTCTCTAG 57.720 40.741 0.00 0.00 0.00 2.43
3535 12624 9.006405 AGTTATAGTTCTACCTTCCTCTCTAGT 57.994 37.037 0.00 0.00 0.00 2.57
3539 12628 9.856162 ATAGTTCTACCTTCCTCTCTAGTAAAG 57.144 37.037 0.00 0.00 0.00 1.85
3540 12629 7.931046 AGTTCTACCTTCCTCTCTAGTAAAGA 58.069 38.462 0.00 0.00 0.00 2.52
3542 12631 9.850198 GTTCTACCTTCCTCTCTAGTAAAGATA 57.150 37.037 0.00 0.00 32.41 1.98
3545 12634 6.918033 ACCTTCCTCTCTAGTAAAGATAGCT 58.082 40.000 0.00 0.00 32.41 3.32
3546 12635 8.048016 ACCTTCCTCTCTAGTAAAGATAGCTA 57.952 38.462 0.00 0.00 32.41 3.32
3547 12636 8.504409 ACCTTCCTCTCTAGTAAAGATAGCTAA 58.496 37.037 0.00 0.00 32.41 3.09
3548 12637 9.357161 CCTTCCTCTCTAGTAAAGATAGCTAAA 57.643 37.037 0.00 0.00 32.41 1.85
3551 12640 9.344772 TCCTCTCTAGTAAAGATAGCTAAACAG 57.655 37.037 0.00 0.00 32.41 3.16
3556 12645 8.750298 TCTAGTAAAGATAGCTAAACAGTTGCT 58.250 33.333 0.00 3.75 40.43 3.91
3559 12648 9.152595 AGTAAAGATAGCTAAACAGTTGCTAAC 57.847 33.333 8.90 7.00 41.71 2.34
3563 12652 9.720769 AAGATAGCTAAACAGTTGCTAACTTTA 57.279 29.630 16.40 0.00 44.28 1.85
3564 12653 9.892130 AGATAGCTAAACAGTTGCTAACTTTAT 57.108 29.630 8.90 0.00 41.71 1.40
3568 12657 9.463443 AGCTAAACAGTTGCTAACTTTATTTTG 57.537 29.630 0.00 4.30 40.46 2.44
3569 12658 8.699749 GCTAAACAGTTGCTAACTTTATTTTGG 58.300 33.333 0.00 2.25 40.46 3.28
3570 12659 9.191995 CTAAACAGTTGCTAACTTTATTTTGGG 57.808 33.333 0.00 0.00 40.46 4.12
3573 12662 4.020573 AGTTGCTAACTTTATTTTGGGGCC 60.021 41.667 0.00 0.00 39.04 5.80
3574 12663 3.785364 TGCTAACTTTATTTTGGGGCCT 58.215 40.909 0.84 0.00 0.00 5.19
3575 12664 4.936802 TGCTAACTTTATTTTGGGGCCTA 58.063 39.130 0.84 0.00 0.00 3.93
3576 12665 4.707934 TGCTAACTTTATTTTGGGGCCTAC 59.292 41.667 0.84 0.00 0.00 3.18
3577 12666 4.201980 GCTAACTTTATTTTGGGGCCTACG 60.202 45.833 0.84 0.00 0.00 3.51
3578 12667 3.724732 ACTTTATTTTGGGGCCTACGA 57.275 42.857 0.84 0.00 0.00 3.43
3579 12668 4.036941 ACTTTATTTTGGGGCCTACGAA 57.963 40.909 0.84 0.00 0.00 3.85
3581 12670 4.401202 ACTTTATTTTGGGGCCTACGAATG 59.599 41.667 0.84 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.680555 CCTACTTGGCCACCGCATTTA 60.681 52.381 3.88 0.00 36.38 1.40
12 4303 0.327924 TGACATGGTGCCCTACTTGG 59.672 55.000 0.00 0.00 0.00 3.61
14 4305 1.064003 TGTGACATGGTGCCCTACTT 58.936 50.000 0.00 0.00 0.00 2.24
40 4337 5.818678 AAGGGCCATGTATTTATCGACTA 57.181 39.130 6.18 0.00 0.00 2.59
42 4339 6.228258 TCTAAAGGGCCATGTATTTATCGAC 58.772 40.000 6.18 0.00 0.00 4.20
79 4378 5.362717 TCGTTGCTAGAGGAAATAGGAATCA 59.637 40.000 0.00 0.00 33.85 2.57
128 4427 0.102844 GCGCACACCTTATACCCGTA 59.897 55.000 0.30 0.00 0.00 4.02
132 4431 2.536761 TATGGCGCACACCTTATACC 57.463 50.000 10.83 0.00 0.00 2.73
139 4438 4.822036 TTACATAAATATGGCGCACACC 57.178 40.909 10.83 0.00 38.00 4.16
145 4444 7.537306 GCCTACACAATTTACATAAATATGGCG 59.463 37.037 5.48 0.00 38.00 5.69
200 4500 8.341477 ACTATTCGACTGATTACTCATTTTCG 57.659 34.615 0.00 3.77 33.02 3.46
296 4605 2.736995 CAGTACCCCACGCACGTG 60.737 66.667 15.96 15.96 45.02 4.49
312 4621 2.267351 CCCAGTGGCAATTGCGTCA 61.267 57.895 23.48 14.25 43.26 4.35
314 4623 2.203480 ACCCAGTGGCAATTGCGT 60.203 55.556 23.48 12.02 43.26 5.24
338 4647 3.533774 AGAGACTCTCGGCTCGTAGAGA 61.534 54.545 19.86 11.00 46.54 3.10
360 4669 9.788960 GGGAGTAGTTTATTCAAAAATGATCAC 57.211 33.333 0.00 0.00 0.00 3.06
363 4672 8.306313 GGGGGAGTAGTTTATTCAAAAATGAT 57.694 34.615 0.00 0.00 0.00 2.45
387 4696 3.363575 CCGCGACAATAACATTTATCGGG 60.364 47.826 8.23 0.00 40.79 5.14
393 4702 5.054477 ACTATAGCCGCGACAATAACATTT 58.946 37.500 8.23 0.00 0.00 2.32
463 4886 6.211584 TCTGCAAGATCAGTAGTACTTCCTTT 59.788 38.462 0.00 0.00 38.67 3.11
490 4919 4.013728 TCGGCAGCCAGTGTAATTATTTT 58.986 39.130 13.30 0.00 0.00 1.82
494 4923 1.134521 CCTCGGCAGCCAGTGTAATTA 60.135 52.381 13.30 0.00 0.00 1.40
528 4957 1.672881 GGGCAAGATTGAGATCAACCG 59.327 52.381 0.00 0.00 38.86 4.44
529 4958 1.672881 CGGGCAAGATTGAGATCAACC 59.327 52.381 0.00 0.00 38.86 3.77
530 4959 1.672881 CCGGGCAAGATTGAGATCAAC 59.327 52.381 0.00 0.00 38.86 3.18
557 5018 1.662446 TTCGTTCGCTGGTTCGACC 60.662 57.895 0.00 0.00 38.30 4.79
634 5102 4.527583 CTCTGGGCTCTGGCTCGC 62.528 72.222 0.00 0.00 43.00 5.03
636 5104 3.478274 CCCTCTGGGCTCTGGCTC 61.478 72.222 0.00 0.00 35.35 4.70
646 5114 2.352805 GGCAAGACACCCCTCTGG 59.647 66.667 0.00 0.00 41.37 3.86
648 5116 3.322466 CGGGCAAGACACCCCTCT 61.322 66.667 0.00 0.00 45.37 3.69
688 5156 2.822399 GATCGGAATGGACGGGCT 59.178 61.111 0.00 0.00 0.00 5.19
1053 5784 3.429043 GTTGCGGACGAACTGGATA 57.571 52.632 0.00 0.00 0.00 2.59
1087 5818 7.413219 CGACGGGAGAAACAGATATAGATAGAC 60.413 44.444 0.00 0.00 0.00 2.59
1109 5845 3.753434 AGGCAGAGGCTGTCGACG 61.753 66.667 11.62 7.05 41.46 5.12
1164 5912 9.705290 TTAAATTGCCCTATTTTCACTTCTTTC 57.295 29.630 0.00 0.00 0.00 2.62
1165 5913 9.710900 CTTAAATTGCCCTATTTTCACTTCTTT 57.289 29.630 0.00 0.00 0.00 2.52
1168 5983 9.875691 AATCTTAAATTGCCCTATTTTCACTTC 57.124 29.630 0.00 0.00 0.00 3.01
1204 6023 7.177392 AGCAGAGGTGAAGCTAAACATATTTTT 59.823 33.333 0.00 0.00 36.73 1.94
1208 6027 5.365021 AGCAGAGGTGAAGCTAAACATAT 57.635 39.130 0.00 0.00 36.73 1.78
1224 6043 4.153117 GGTGTGACAGAATTACAAGCAGAG 59.847 45.833 0.00 0.00 0.00 3.35
1272 6091 7.203218 GTGCTCCCATGTTAAATAAATTCTCC 58.797 38.462 0.00 0.00 0.00 3.71
1279 6100 4.223556 TCGGTGCTCCCATGTTAAATAA 57.776 40.909 0.00 0.00 0.00 1.40
1280 6101 3.916359 TCGGTGCTCCCATGTTAAATA 57.084 42.857 0.00 0.00 0.00 1.40
1309 6140 6.948353 TGATAACTGCTCTATTTTCATTCGC 58.052 36.000 0.00 0.00 0.00 4.70
1310 6141 8.554528 ACATGATAACTGCTCTATTTTCATTCG 58.445 33.333 0.00 0.00 0.00 3.34
1311 6142 9.661187 CACATGATAACTGCTCTATTTTCATTC 57.339 33.333 0.00 0.00 0.00 2.67
1313 6144 7.776969 ACCACATGATAACTGCTCTATTTTCAT 59.223 33.333 0.00 0.00 0.00 2.57
1327 6160 4.634004 TCATGAACCGAACCACATGATAAC 59.366 41.667 0.00 0.00 42.31 1.89
1330 6163 3.348647 TCATGAACCGAACCACATGAT 57.651 42.857 0.00 0.00 42.31 2.45
1333 6166 6.038603 CAGATTATTCATGAACCGAACCACAT 59.961 38.462 11.07 0.00 0.00 3.21
1338 6171 8.665685 AGTAAACAGATTATTCATGAACCGAAC 58.334 33.333 11.07 2.13 0.00 3.95
1349 6182 9.118236 GCACAAGTGAAAGTAAACAGATTATTC 57.882 33.333 4.04 0.00 0.00 1.75
1351 6184 8.396272 AGCACAAGTGAAAGTAAACAGATTAT 57.604 30.769 4.04 0.00 0.00 1.28
1360 6193 7.067615 TCCAAATACAAGCACAAGTGAAAGTAA 59.932 33.333 4.04 0.00 0.00 2.24
1363 6196 5.830912 TCCAAATACAAGCACAAGTGAAAG 58.169 37.500 4.04 0.00 0.00 2.62
1364 6197 5.843673 TCCAAATACAAGCACAAGTGAAA 57.156 34.783 4.04 0.00 0.00 2.69
1466 6299 1.337260 ACTGGCAGAAGTGAAGCTACG 60.337 52.381 23.66 0.00 0.00 3.51
1489 6322 0.044549 ATGCCCCCAACCAAATCCAT 59.955 50.000 0.00 0.00 0.00 3.41
1588 6421 7.382759 CGCTCTTATATTTCTTAACAGAGGGAC 59.617 40.741 4.76 0.00 36.40 4.46
1660 6493 9.566432 CCCTCTGTAAAGAAATATAAGAGCATT 57.434 33.333 0.00 0.00 0.00 3.56
1661 6494 8.938883 TCCCTCTGTAAAGAAATATAAGAGCAT 58.061 33.333 0.00 0.00 0.00 3.79
1662 6495 8.319057 TCCCTCTGTAAAGAAATATAAGAGCA 57.681 34.615 0.00 0.00 0.00 4.26
1663 6496 8.425703 ACTCCCTCTGTAAAGAAATATAAGAGC 58.574 37.037 0.00 0.00 0.00 4.09
1758 6622 4.794169 ACATTCACTTTTTCATACGGTGC 58.206 39.130 0.00 0.00 0.00 5.01
1872 6736 7.833786 AGAATTATTGCATCTTCAGCTTTTCA 58.166 30.769 0.00 0.00 0.00 2.69
1887 6751 4.860907 CAGGAACAGCACAAGAATTATTGC 59.139 41.667 12.62 0.56 36.74 3.56
1903 6767 2.637872 AGCTACTACCAAAGCAGGAACA 59.362 45.455 0.00 0.00 41.32 3.18
1912 6776 6.484308 GTGAAGGTACAAAAGCTACTACCAAA 59.516 38.462 10.21 0.00 33.87 3.28
1931 6795 0.248843 GACAGAGGCAGGAGTGAAGG 59.751 60.000 0.00 0.00 0.00 3.46
1939 6803 1.681166 CCAAATCCAGACAGAGGCAGG 60.681 57.143 0.00 0.00 0.00 4.85
1945 6809 4.019411 TGCTATCAACCAAATCCAGACAGA 60.019 41.667 0.00 0.00 0.00 3.41
1946 6810 4.264253 TGCTATCAACCAAATCCAGACAG 58.736 43.478 0.00 0.00 0.00 3.51
1947 6811 4.299586 TGCTATCAACCAAATCCAGACA 57.700 40.909 0.00 0.00 0.00 3.41
1948 6812 4.641989 ACATGCTATCAACCAAATCCAGAC 59.358 41.667 0.00 0.00 0.00 3.51
2171 7236 9.651718 GGTAGATTCAAACAATGATTCGATTAC 57.348 33.333 0.00 0.00 41.29 1.89
2433 7499 0.391130 TCGCACCATGCTCTTACCAC 60.391 55.000 0.00 0.00 42.25 4.16
2464 7530 4.893524 TCGATAAACTGATCCAGCTCCTTA 59.106 41.667 0.00 0.00 34.37 2.69
2501 7567 4.113354 GCTACATAGTTCTCGGTTTCCTG 58.887 47.826 0.00 0.00 0.00 3.86
2506 7572 3.679083 GCTTGGCTACATAGTTCTCGGTT 60.679 47.826 0.00 0.00 0.00 4.44
2787 8945 7.694784 ACACTACTAAACAAAAATGAACACACG 59.305 33.333 0.00 0.00 0.00 4.49
2788 8946 8.794406 CACACTACTAAACAAAAATGAACACAC 58.206 33.333 0.00 0.00 0.00 3.82
2820 10156 0.515127 TGCATCGTACCAAAAGCACG 59.485 50.000 0.00 0.00 37.03 5.34
2823 10159 0.521291 TGCTGCATCGTACCAAAAGC 59.479 50.000 0.00 0.00 0.00 3.51
2840 10887 2.089980 ACCACAAGCTGATGATTCTGC 58.910 47.619 0.00 0.00 44.62 4.26
2841 10888 4.216902 TCAAACCACAAGCTGATGATTCTG 59.783 41.667 0.00 0.00 0.00 3.02
2887 10934 7.167535 TCACCATGATTCAAACTTGTGATAGA 58.832 34.615 0.00 0.00 0.00 1.98
2893 10940 7.274447 ACAAAATCACCATGATTCAAACTTGT 58.726 30.769 4.59 8.17 45.57 3.16
2896 10943 7.599998 GCTTACAAAATCACCATGATTCAAACT 59.400 33.333 4.59 0.00 45.57 2.66
2901 10948 9.754382 AATATGCTTACAAAATCACCATGATTC 57.246 29.630 4.59 0.00 45.57 2.52
2904 10951 9.407380 AGTAATATGCTTACAAAATCACCATGA 57.593 29.630 0.00 0.00 0.00 3.07
2913 10960 9.502091 CCTATAGGCAGTAATATGCTTACAAAA 57.498 33.333 5.67 0.00 45.75 2.44
2914 10961 8.656806 ACCTATAGGCAGTAATATGCTTACAAA 58.343 33.333 19.25 0.00 45.75 2.83
2915 10962 8.094548 CACCTATAGGCAGTAATATGCTTACAA 58.905 37.037 19.25 0.00 45.75 2.41
2957 11012 2.945008 TGCTGATATGCTAAACCACTGC 59.055 45.455 0.00 0.00 0.00 4.40
2966 11021 3.461061 GTCTGTGCTTGCTGATATGCTA 58.539 45.455 0.00 0.00 0.00 3.49
2989 11154 8.689251 TTTAAGATGACTCTCAAATACAGTCG 57.311 34.615 0.00 0.00 39.63 4.18
3034 11259 4.880696 GGCAAGCTAATCTGAAGATGACTT 59.119 41.667 0.00 0.00 39.24 3.01
3050 11275 1.202891 AGGTTTAAGGAACGGCAAGCT 60.203 47.619 0.00 0.00 39.22 3.74
3051 11276 1.244816 AGGTTTAAGGAACGGCAAGC 58.755 50.000 0.00 0.00 39.22 4.01
3057 11282 4.904253 TGGTTTCAAGGTTTAAGGAACG 57.096 40.909 0.00 0.00 39.22 3.95
3081 11306 3.187700 CTCCAATACTTACACACGGAGC 58.812 50.000 0.00 0.00 32.80 4.70
3084 11309 4.562082 TCAACTCCAATACTTACACACGG 58.438 43.478 0.00 0.00 0.00 4.94
3087 11312 9.952030 TGAATAATCAACTCCAATACTTACACA 57.048 29.630 0.00 0.00 30.99 3.72
3095 11320 8.150945 GCCTAGTCTGAATAATCAACTCCAATA 58.849 37.037 0.00 0.00 34.49 1.90
3096 11321 6.995091 GCCTAGTCTGAATAATCAACTCCAAT 59.005 38.462 0.00 0.00 34.49 3.16
3097 11322 6.156949 AGCCTAGTCTGAATAATCAACTCCAA 59.843 38.462 0.00 0.00 34.49 3.53
3100 11325 8.364142 ACATAGCCTAGTCTGAATAATCAACTC 58.636 37.037 0.00 0.00 34.49 3.01
3101 11326 8.256356 ACATAGCCTAGTCTGAATAATCAACT 57.744 34.615 0.00 2.59 34.49 3.16
3103 11328 7.510685 AGGACATAGCCTAGTCTGAATAATCAA 59.489 37.037 0.00 0.00 36.22 2.57
3104 11329 7.013220 AGGACATAGCCTAGTCTGAATAATCA 58.987 38.462 0.00 0.00 36.22 2.57
3105 11330 7.475137 AGGACATAGCCTAGTCTGAATAATC 57.525 40.000 0.00 0.00 36.22 1.75
3107 11332 7.295340 TGTAGGACATAGCCTAGTCTGAATAA 58.705 38.462 0.00 0.00 41.05 1.40
3108 11333 6.849151 TGTAGGACATAGCCTAGTCTGAATA 58.151 40.000 0.00 0.00 41.05 1.75
3109 11334 5.706447 TGTAGGACATAGCCTAGTCTGAAT 58.294 41.667 0.00 0.00 41.05 2.57
3110 11335 5.125367 TGTAGGACATAGCCTAGTCTGAA 57.875 43.478 0.00 0.00 41.05 3.02
3111 11336 4.790718 TGTAGGACATAGCCTAGTCTGA 57.209 45.455 0.00 0.00 41.05 3.27
3112 11337 6.412362 AAATGTAGGACATAGCCTAGTCTG 57.588 41.667 0.00 0.00 41.05 3.51
3113 11338 6.384305 ACAAAATGTAGGACATAGCCTAGTCT 59.616 38.462 0.00 0.00 41.05 3.24
3122 11347 7.504238 ACAAAACTGGACAAAATGTAGGACATA 59.496 33.333 0.00 0.00 37.97 2.29
3154 11783 8.553153 TGAAGGATTGATAACCTAACCATAACA 58.447 33.333 0.00 0.00 35.25 2.41
3155 11784 8.974060 TGAAGGATTGATAACCTAACCATAAC 57.026 34.615 0.00 0.00 35.25 1.89
3161 11790 9.178758 ACAAAGATGAAGGATTGATAACCTAAC 57.821 33.333 0.00 0.00 35.25 2.34
3164 11793 8.655935 AAACAAAGATGAAGGATTGATAACCT 57.344 30.769 0.00 0.00 38.23 3.50
3220 11851 0.034337 AATGTGCCAAAGCTGCCAAG 59.966 50.000 0.00 0.00 40.80 3.61
3270 11901 1.280421 GAACTGAAGTGGGAGGCTCAT 59.720 52.381 17.69 0.00 0.00 2.90
3276 11907 4.904241 AGAAATGAGAACTGAAGTGGGAG 58.096 43.478 0.00 0.00 0.00 4.30
3278 11909 4.645535 TGAGAAATGAGAACTGAAGTGGG 58.354 43.478 0.00 0.00 0.00 4.61
3279 11910 6.814506 ATTGAGAAATGAGAACTGAAGTGG 57.185 37.500 0.00 0.00 0.00 4.00
3301 11932 0.250901 AGTGCAGCCGTGAAGGAAAT 60.251 50.000 0.00 0.00 45.00 2.17
3309 11940 0.514691 GAAAGAGAAGTGCAGCCGTG 59.485 55.000 0.00 0.00 0.00 4.94
3330 11961 8.836268 ACAACAATGCAAAAACTGATTATGAT 57.164 26.923 0.00 0.00 0.00 2.45
3379 12010 9.113876 GGTTTGAGTAATACAAGTTTCAATTCG 57.886 33.333 0.00 0.00 0.00 3.34
3381 12012 8.079809 CGGGTTTGAGTAATACAAGTTTCAATT 58.920 33.333 0.00 0.00 0.00 2.32
3382 12013 7.446013 TCGGGTTTGAGTAATACAAGTTTCAAT 59.554 33.333 0.00 0.00 0.00 2.57
3383 12014 6.766944 TCGGGTTTGAGTAATACAAGTTTCAA 59.233 34.615 0.00 0.00 0.00 2.69
3385 12016 6.790285 TCGGGTTTGAGTAATACAAGTTTC 57.210 37.500 0.00 0.00 0.00 2.78
3386 12017 6.938030 TGATCGGGTTTGAGTAATACAAGTTT 59.062 34.615 0.00 0.00 0.00 2.66
3388 12019 6.045072 TGATCGGGTTTGAGTAATACAAGT 57.955 37.500 0.00 0.00 0.00 3.16
3389 12020 5.523916 CCTGATCGGGTTTGAGTAATACAAG 59.476 44.000 12.93 0.00 0.00 3.16
3392 12023 5.019785 ACCTGATCGGGTTTGAGTAATAC 57.980 43.478 21.21 0.00 35.89 1.89
3394 12025 4.569719 AACCTGATCGGGTTTGAGTAAT 57.430 40.909 29.92 8.71 46.21 1.89
3403 12034 3.517901 TCTGATTGTAAACCTGATCGGGT 59.482 43.478 21.21 21.21 42.05 5.28
3405 12036 4.122776 CCTCTGATTGTAAACCTGATCGG 58.877 47.826 0.00 0.00 39.35 4.18
3406 12037 5.011090 TCCTCTGATTGTAAACCTGATCG 57.989 43.478 0.00 0.00 0.00 3.69
3407 12038 5.295540 GCTTCCTCTGATTGTAAACCTGATC 59.704 44.000 0.00 0.00 0.00 2.92
3408 12039 5.189180 GCTTCCTCTGATTGTAAACCTGAT 58.811 41.667 0.00 0.00 0.00 2.90
3409 12040 4.041567 TGCTTCCTCTGATTGTAAACCTGA 59.958 41.667 0.00 0.00 0.00 3.86
3411 12042 4.640771 TGCTTCCTCTGATTGTAAACCT 57.359 40.909 0.00 0.00 0.00 3.50
3413 12044 5.948992 ACTTGCTTCCTCTGATTGTAAAC 57.051 39.130 0.00 0.00 0.00 2.01
3414 12045 5.473504 GGAACTTGCTTCCTCTGATTGTAAA 59.526 40.000 0.00 0.00 44.90 2.01
3415 12046 5.003804 GGAACTTGCTTCCTCTGATTGTAA 58.996 41.667 0.00 0.00 44.90 2.41
3416 12047 4.579869 GGAACTTGCTTCCTCTGATTGTA 58.420 43.478 0.00 0.00 44.90 2.41
3417 12048 3.416156 GGAACTTGCTTCCTCTGATTGT 58.584 45.455 0.00 0.00 44.90 2.71
3427 12058 1.312815 AGTGCTGTGGAACTTGCTTC 58.687 50.000 0.00 0.00 37.74 3.86
3428 12059 2.498167 CTAGTGCTGTGGAACTTGCTT 58.502 47.619 0.00 0.00 37.74 3.91
3430 12061 0.519077 GCTAGTGCTGTGGAACTTGC 59.481 55.000 0.00 0.00 41.20 4.01
3445 12534 2.814336 GGTTTGTTTCTGGTCCAGCTAG 59.186 50.000 14.64 0.00 0.00 3.42
3446 12535 2.173782 TGGTTTGTTTCTGGTCCAGCTA 59.826 45.455 14.64 1.62 0.00 3.32
3450 12539 1.286553 ACCTGGTTTGTTTCTGGTCCA 59.713 47.619 0.00 0.00 30.94 4.02
3453 12542 2.818751 TGACCTGGTTTGTTTCTGGT 57.181 45.000 0.00 0.00 37.81 4.00
3457 12546 6.148976 GGTAGAACTATGACCTGGTTTGTTTC 59.851 42.308 0.00 1.21 0.00 2.78
3458 12547 6.002082 GGTAGAACTATGACCTGGTTTGTTT 58.998 40.000 0.00 0.00 0.00 2.83
3464 12553 4.031611 GGAAGGTAGAACTATGACCTGGT 58.968 47.826 0.00 0.00 42.93 4.00
3465 12554 4.290942 AGGAAGGTAGAACTATGACCTGG 58.709 47.826 0.00 0.00 42.93 4.45
3466 12555 5.205056 AGAGGAAGGTAGAACTATGACCTG 58.795 45.833 0.00 0.00 42.93 4.00
3467 12556 5.194942 AGAGAGGAAGGTAGAACTATGACCT 59.805 44.000 0.00 0.00 45.75 3.85
3469 12558 6.206048 GCTAGAGAGGAAGGTAGAACTATGAC 59.794 46.154 0.00 0.00 0.00 3.06
3470 12559 6.126449 TGCTAGAGAGGAAGGTAGAACTATGA 60.126 42.308 0.00 0.00 0.00 2.15
3471 12560 6.065374 TGCTAGAGAGGAAGGTAGAACTATG 58.935 44.000 0.00 0.00 0.00 2.23
3472 12561 6.268855 TGCTAGAGAGGAAGGTAGAACTAT 57.731 41.667 0.00 0.00 0.00 2.12
3474 12563 4.594675 TGCTAGAGAGGAAGGTAGAACT 57.405 45.455 0.00 0.00 0.00 3.01
3476 12565 5.580998 TCTTTGCTAGAGAGGAAGGTAGAA 58.419 41.667 0.00 0.00 34.12 2.10
3478 12567 6.294508 GCTATCTTTGCTAGAGAGGAAGGTAG 60.295 46.154 11.32 1.10 41.55 3.18
3479 12568 5.536916 GCTATCTTTGCTAGAGAGGAAGGTA 59.463 44.000 11.32 0.00 41.55 3.08
3480 12569 4.343814 GCTATCTTTGCTAGAGAGGAAGGT 59.656 45.833 11.32 0.00 41.55 3.50
3481 12570 4.588528 AGCTATCTTTGCTAGAGAGGAAGG 59.411 45.833 11.32 0.00 41.55 3.46
3483 12572 7.124298 TGTTTAGCTATCTTTGCTAGAGAGGAA 59.876 37.037 11.32 0.00 41.55 3.36
3484 12573 6.607600 TGTTTAGCTATCTTTGCTAGAGAGGA 59.392 38.462 11.32 0.00 41.55 3.71
3485 12574 6.810911 TGTTTAGCTATCTTTGCTAGAGAGG 58.189 40.000 11.32 0.58 41.55 3.69
3486 12575 7.488322 ACTGTTTAGCTATCTTTGCTAGAGAG 58.512 38.462 0.00 8.24 43.61 3.20
3487 12576 7.411486 ACTGTTTAGCTATCTTTGCTAGAGA 57.589 36.000 0.00 0.00 42.89 3.10
3492 12581 9.892130 AACTATAACTGTTTAGCTATCTTTGCT 57.108 29.630 0.00 0.00 43.79 3.91
3501 12590 8.476447 GGAAGGTAGAACTATAACTGTTTAGCT 58.524 37.037 0.00 0.00 0.00 3.32
3502 12591 8.476447 AGGAAGGTAGAACTATAACTGTTTAGC 58.524 37.037 0.00 0.00 0.00 3.09
3504 12593 9.765295 AGAGGAAGGTAGAACTATAACTGTTTA 57.235 33.333 0.00 0.00 0.00 2.01
3505 12594 8.667592 AGAGGAAGGTAGAACTATAACTGTTT 57.332 34.615 0.00 0.00 0.00 2.83
3506 12595 8.117312 AGAGAGGAAGGTAGAACTATAACTGTT 58.883 37.037 0.00 0.00 0.00 3.16
3507 12596 7.645002 AGAGAGGAAGGTAGAACTATAACTGT 58.355 38.462 0.00 0.00 0.00 3.55
3508 12597 9.280174 CTAGAGAGGAAGGTAGAACTATAACTG 57.720 40.741 0.00 0.00 0.00 3.16
3509 12598 9.006405 ACTAGAGAGGAAGGTAGAACTATAACT 57.994 37.037 0.00 0.00 0.00 2.24
3514 12603 9.055689 TCTTTACTAGAGAGGAAGGTAGAACTA 57.944 37.037 0.00 0.00 0.00 2.24
3515 12604 7.931046 TCTTTACTAGAGAGGAAGGTAGAACT 58.069 38.462 0.00 0.00 0.00 3.01
3516 12605 8.756486 ATCTTTACTAGAGAGGAAGGTAGAAC 57.244 38.462 0.00 0.00 36.02 3.01
3518 12607 8.158789 GCTATCTTTACTAGAGAGGAAGGTAGA 58.841 40.741 0.00 0.00 41.55 2.59
3519 12608 8.161425 AGCTATCTTTACTAGAGAGGAAGGTAG 58.839 40.741 0.00 4.40 41.55 3.18
3520 12609 8.048016 AGCTATCTTTACTAGAGAGGAAGGTA 57.952 38.462 0.00 0.00 41.55 3.08
3524 12613 9.696572 TGTTTAGCTATCTTTACTAGAGAGGAA 57.303 33.333 0.00 0.00 41.55 3.36
3525 12614 9.344772 CTGTTTAGCTATCTTTACTAGAGAGGA 57.655 37.037 0.00 0.00 41.55 3.71
3526 12615 9.127277 ACTGTTTAGCTATCTTTACTAGAGAGG 57.873 37.037 0.00 0.00 41.55 3.69
3529 12618 9.026074 GCAACTGTTTAGCTATCTTTACTAGAG 57.974 37.037 0.00 0.00 36.02 2.43
3530 12619 8.750298 AGCAACTGTTTAGCTATCTTTACTAGA 58.250 33.333 3.79 0.00 36.73 2.43
3533 12622 9.152595 GTTAGCAACTGTTTAGCTATCTTTACT 57.847 33.333 11.81 0.00 40.23 2.24
3534 12623 9.152595 AGTTAGCAACTGTTTAGCTATCTTTAC 57.847 33.333 11.81 7.91 41.01 2.01
3535 12624 9.720769 AAGTTAGCAACTGTTTAGCTATCTTTA 57.279 29.630 19.82 4.72 43.18 1.85
3536 12625 8.622948 AAGTTAGCAACTGTTTAGCTATCTTT 57.377 30.769 19.82 11.01 43.18 2.52
3537 12626 8.622948 AAAGTTAGCAACTGTTTAGCTATCTT 57.377 30.769 19.82 19.82 45.52 2.40
3538 12627 9.892130 ATAAAGTTAGCAACTGTTTAGCTATCT 57.108 29.630 11.81 12.73 41.91 1.98
3542 12631 9.463443 CAAAATAAAGTTAGCAACTGTTTAGCT 57.537 29.630 9.84 9.84 41.91 3.32
3543 12632 8.699749 CCAAAATAAAGTTAGCAACTGTTTAGC 58.300 33.333 2.88 0.00 41.91 3.09
3545 12634 8.145122 CCCCAAAATAAAGTTAGCAACTGTTTA 58.855 33.333 2.88 0.89 41.91 2.01
3546 12635 6.989759 CCCCAAAATAAAGTTAGCAACTGTTT 59.010 34.615 2.88 3.36 41.91 2.83
3547 12636 6.521162 CCCCAAAATAAAGTTAGCAACTGTT 58.479 36.000 2.88 0.00 41.91 3.16
3548 12637 5.510690 GCCCCAAAATAAAGTTAGCAACTGT 60.511 40.000 2.88 0.77 41.91 3.55
3549 12638 4.929211 GCCCCAAAATAAAGTTAGCAACTG 59.071 41.667 2.88 0.00 41.91 3.16
3551 12640 4.020573 AGGCCCCAAAATAAAGTTAGCAAC 60.021 41.667 0.00 0.00 0.00 4.17
3553 12642 3.785364 AGGCCCCAAAATAAAGTTAGCA 58.215 40.909 0.00 0.00 0.00 3.49
3554 12643 4.201980 CGTAGGCCCCAAAATAAAGTTAGC 60.202 45.833 0.00 0.00 0.00 3.09
3556 12645 5.176741 TCGTAGGCCCCAAAATAAAGTTA 57.823 39.130 0.00 0.00 0.00 2.24
3558 12647 3.724732 TCGTAGGCCCCAAAATAAAGT 57.275 42.857 0.00 0.00 0.00 2.66
3559 12648 4.932146 CATTCGTAGGCCCCAAAATAAAG 58.068 43.478 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.