Multiple sequence alignment - TraesCS2A01G572800

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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 TraesCS2A01G572800 chr2A 100.000 3625 0 0 1 3625 768675637 768679261 0.000000e+00 6695.0
1 TraesCS2A01G572800 chr2A 84.161 1288 150 33 1574 2828 768716095 768717361 0.000000e+00 1199.0
2 TraesCS2A01G572800 chr2A 85.294 68 10 0 1862 1929 769145224 769145291 1.810000e-08 71.3
3 TraesCS2A01G572800 chr2D 94.916 1377 59 9 1462 2831 643800678 643802050 0.000000e+00 2145.0
4 TraesCS2A01G572800 chr2D 85.465 1087 111 31 1765 2828 643836741 643837803 0.000000e+00 1088.0
5 TraesCS2A01G572800 chr2D 85.759 955 94 16 395 1341 643799762 643800682 0.000000e+00 972.0
6 TraesCS2A01G572800 chr2D 90.805 174 15 1 1575 1747 643831176 643831349 7.830000e-57 231.0
7 TraesCS2A01G572800 chr2D 90.385 104 10 0 1471 1574 643830982 643831085 1.760000e-28 137.0
8 TraesCS2A01G572800 chr2B 87.213 915 91 12 388 1300 793322863 793321973 0.000000e+00 1018.0
9 TraesCS2A01G572800 chr2B 92.484 612 40 5 2060 2666 793314596 793313986 0.000000e+00 870.0
10 TraesCS2A01G572800 chr2B 89.897 485 20 13 1462 1946 793296175 793295720 6.700000e-167 597.0
11 TraesCS2A01G572800 chr2B 87.887 388 44 1 1 388 793323378 793322994 1.530000e-123 453.0
12 TraesCS2A01G572800 chr2B 85.465 344 39 8 1704 2037 793321950 793321608 7.450000e-92 348.0
13 TraesCS2A01G572800 chr2B 93.909 197 12 0 1145 1341 793296367 793296171 7.610000e-77 298.0
14 TraesCS2A01G572800 chr2B 92.105 190 6 5 2566 2747 793281009 793280821 3.590000e-65 259.0
15 TraesCS2A01G572800 chr2B 100.000 124 0 0 1343 1466 598960972 598960849 2.820000e-56 230.0
16 TraesCS2A01G572800 chr2B 94.776 134 5 2 2703 2834 793313983 793313850 1.320000e-49 207.0
17 TraesCS2A01G572800 chr2B 85.294 68 10 0 1862 1929 793034776 793034709 1.810000e-08 71.3
18 TraesCS2A01G572800 chr7B 86.203 819 70 26 2831 3624 56385242 56384442 0.000000e+00 846.0
19 TraesCS2A01G572800 chr7B 89.501 581 53 8 2832 3408 595680051 595680627 0.000000e+00 728.0
20 TraesCS2A01G572800 chr7B 77.055 584 93 32 2836 3409 23973454 23972902 7.610000e-77 298.0
21 TraesCS2A01G572800 chr7B 97.015 134 2 2 1343 1474 46022946 46022813 1.310000e-54 224.0
22 TraesCS2A01G572800 chr7B 95.035 141 3 4 1334 1472 295083300 295083162 6.090000e-53 219.0
23 TraesCS2A01G572800 chr5B 86.191 659 56 21 2989 3624 480300383 480301029 0.000000e+00 680.0
24 TraesCS2A01G572800 chr5B 89.597 298 27 4 2951 3246 470193754 470194049 3.420000e-100 375.0
25 TraesCS2A01G572800 chr5B 91.391 151 12 1 2829 2978 480300126 480300276 4.740000e-49 206.0
26 TraesCS2A01G572800 chr5B 78.355 231 35 9 388 609 422119766 422119990 6.310000e-28 135.0
27 TraesCS2A01G572800 chr4A 76.884 584 94 32 2836 3409 709968814 709969366 3.540000e-75 292.0
28 TraesCS2A01G572800 chr4A 78.509 228 36 9 388 609 549922035 549922255 1.760000e-28 137.0
29 TraesCS2A01G572800 chr7A 83.934 305 39 7 3106 3409 105629818 105629523 2.130000e-72 283.0
30 TraesCS2A01G572800 chr7A 94.891 137 7 0 1330 1466 220543488 220543624 7.880000e-52 215.0
31 TraesCS2A01G572800 chr1B 83.388 307 44 7 3106 3409 653824387 653824085 9.910000e-71 278.0
32 TraesCS2A01G572800 chr1B 86.893 206 23 4 3273 3477 602230735 602230533 1.010000e-55 228.0
33 TraesCS2A01G572800 chr6D 97.710 131 1 2 1343 1471 435990515 435990645 1.310000e-54 224.0
34 TraesCS2A01G572800 chr6D 88.112 143 14 3 388 528 39061831 39061690 2.240000e-37 167.0
35 TraesCS2A01G572800 chr6D 84.722 144 14 2 473 608 89701004 89700861 1.760000e-28 137.0
36 TraesCS2A01G572800 chr3B 95.683 139 6 0 1330 1468 378689156 378689294 1.310000e-54 224.0
37 TraesCS2A01G572800 chr3D 96.296 135 5 0 1334 1468 261156866 261157000 4.710000e-54 222.0
38 TraesCS2A01G572800 chr4D 94.964 139 5 2 1333 1471 106682383 106682247 2.190000e-52 217.0
39 TraesCS2A01G572800 chr6B 90.506 158 13 2 1330 1486 269692970 269692814 1.320000e-49 207.0
40 TraesCS2A01G572800 chr5A 82.888 187 27 4 395 578 591675553 591675737 2.900000e-36 163.0
41 TraesCS2A01G572800 chr3A 81.006 179 29 4 397 573 127979587 127979412 1.760000e-28 137.0
42 TraesCS2A01G572800 chr1D 80.114 176 28 6 388 559 461083505 461083333 1.370000e-24 124.0
43 TraesCS2A01G572800 chr4B 76.549 226 46 5 391 609 29933219 29932994 2.290000e-22 117.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G572800 chr2A 768675637 768679261 3624 False 6695.000000 6695 100.0000 1 3625 1 chr2A.!!$F1 3624
1 TraesCS2A01G572800 chr2A 768716095 768717361 1266 False 1199.000000 1199 84.1610 1574 2828 1 chr2A.!!$F2 1254
2 TraesCS2A01G572800 chr2D 643799762 643802050 2288 False 1558.500000 2145 90.3375 395 2831 2 chr2D.!!$F2 2436
3 TraesCS2A01G572800 chr2D 643836741 643837803 1062 False 1088.000000 1088 85.4650 1765 2828 1 chr2D.!!$F1 1063
4 TraesCS2A01G572800 chr2B 793321608 793323378 1770 True 606.333333 1018 86.8550 1 2037 3 chr2B.!!$R6 2036
5 TraesCS2A01G572800 chr2B 793313850 793314596 746 True 538.500000 870 93.6300 2060 2834 2 chr2B.!!$R5 774
6 TraesCS2A01G572800 chr2B 793295720 793296367 647 True 447.500000 597 91.9030 1145 1946 2 chr2B.!!$R4 801
7 TraesCS2A01G572800 chr7B 56384442 56385242 800 True 846.000000 846 86.2030 2831 3624 1 chr7B.!!$R3 793
8 TraesCS2A01G572800 chr7B 595680051 595680627 576 False 728.000000 728 89.5010 2832 3408 1 chr7B.!!$F1 576
9 TraesCS2A01G572800 chr7B 23972902 23973454 552 True 298.000000 298 77.0550 2836 3409 1 chr7B.!!$R1 573
10 TraesCS2A01G572800 chr5B 480300126 480301029 903 False 443.000000 680 88.7910 2829 3624 2 chr5B.!!$F3 795
11 TraesCS2A01G572800 chr4A 709968814 709969366 552 False 292.000000 292 76.8840 2836 3409 1 chr4A.!!$F2 573

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
449 581 0.033504 GCGTTCACTGGGAAGAGACA 59.966 55.0 0.00 0.0 35.82 3.41 F
1005 1145 0.036858 GCTAGGAAGGATCGATGGCC 60.037 60.0 0.54 0.0 0.00 5.36 F
1354 1494 0.043637 AAGTATCCCCTCCGTCCCAA 59.956 55.0 0.00 0.0 0.00 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1448 1588 0.042131 ACATACTCCCTCCGTCCCAA 59.958 55.0 0.00 0.0 0.00 4.12 R
2471 2639 0.112606 TGGTCTCGTTGAGGAGGAGT 59.887 55.0 1.35 0.0 40.37 3.85 R
2861 3055 0.396556 TGGTGGAGATAGGCGCTGTA 60.397 55.0 7.64 0.0 0.00 2.74 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
30 31 8.978874 ATTGTCACCATCTAAGTAATGCAATA 57.021 30.769 0.00 0.00 0.00 1.90
32 33 8.978874 TGTCACCATCTAAGTAATGCAATAAT 57.021 30.769 0.00 0.00 0.00 1.28
79 80 7.399634 TGGAGTAAAACTCTAGGGTAATTTGG 58.600 38.462 0.00 0.00 44.46 3.28
81 82 8.542926 GGAGTAAAACTCTAGGGTAATTTGGTA 58.457 37.037 0.00 0.00 44.46 3.25
119 120 9.914131 CTTACTCCATTATTGATCGATGTCTTA 57.086 33.333 0.54 0.00 0.00 2.10
131 132 9.816354 TTGATCGATGTCTTATTTCACATAAGA 57.184 29.630 0.54 0.96 38.04 2.10
132 133 9.987272 TGATCGATGTCTTATTTCACATAAGAT 57.013 29.630 0.54 0.00 41.13 2.40
168 169 7.421530 TTGTTGTAGAGAGAATTGCTTGTAC 57.578 36.000 0.00 0.00 0.00 2.90
169 170 6.521162 TGTTGTAGAGAGAATTGCTTGTACA 58.479 36.000 0.00 0.00 0.00 2.90
176 177 6.091441 AGAGAGAATTGCTTGTACATCGTTTC 59.909 38.462 0.00 0.00 0.00 2.78
177 178 5.934625 AGAGAATTGCTTGTACATCGTTTCT 59.065 36.000 0.00 2.56 0.00 2.52
183 184 5.474825 TGCTTGTACATCGTTTCTCATACA 58.525 37.500 0.00 0.00 0.00 2.29
184 185 6.106003 TGCTTGTACATCGTTTCTCATACAT 58.894 36.000 0.00 0.00 0.00 2.29
241 242 8.773404 TTCTTACTGCAAACCTCTATACTTTC 57.227 34.615 0.00 0.00 0.00 2.62
248 249 5.747675 GCAAACCTCTATACTTTCGACCTAC 59.252 44.000 0.00 0.00 0.00 3.18
251 252 5.513233 ACCTCTATACTTTCGACCTACCAA 58.487 41.667 0.00 0.00 0.00 3.67
252 253 6.134754 ACCTCTATACTTTCGACCTACCAAT 58.865 40.000 0.00 0.00 0.00 3.16
262 263 6.978343 TTCGACCTACCAATTTTATGAGTG 57.022 37.500 0.00 0.00 0.00 3.51
306 307 3.373001 GGGGAGGGAATCATCATGAAACA 60.373 47.826 0.00 0.00 0.00 2.83
312 313 5.124457 AGGGAATCATCATGAAACAGAAACG 59.876 40.000 0.00 0.00 0.00 3.60
332 333 5.952347 ACGAGGGGAATAAACTACAATCT 57.048 39.130 0.00 0.00 0.00 2.40
333 334 5.671493 ACGAGGGGAATAAACTACAATCTG 58.329 41.667 0.00 0.00 0.00 2.90
336 337 4.794067 AGGGGAATAAACTACAATCTGGGT 59.206 41.667 0.00 0.00 0.00 4.51
338 339 5.955959 GGGGAATAAACTACAATCTGGGTTT 59.044 40.000 0.00 0.00 34.09 3.27
343 344 7.703058 ATAAACTACAATCTGGGTTTGGAAG 57.297 36.000 0.00 0.00 32.75 3.46
344 345 4.034285 ACTACAATCTGGGTTTGGAAGG 57.966 45.455 0.00 0.00 0.00 3.46
378 379 6.210078 TCGAAGAAAGAAGTGAGAAGAGAAC 58.790 40.000 0.00 0.00 0.00 3.01
383 384 4.674281 AGAAGTGAGAAGAGAACGGTTT 57.326 40.909 0.00 0.00 0.00 3.27
403 535 3.401033 TCACTGCTCGGATTTTTCTGA 57.599 42.857 0.00 0.00 0.00 3.27
428 560 9.502557 GAATTTATTTCAGGCCTTCTGGCGATT 62.503 40.741 0.00 0.00 45.80 3.34
449 581 0.033504 GCGTTCACTGGGAAGAGACA 59.966 55.000 0.00 0.00 35.82 3.41
464 596 2.619177 AGAGACATTCCCGATGACTACG 59.381 50.000 0.00 0.00 40.14 3.51
497 630 3.124297 GGCAACTTCGTCAATCTCAAGAG 59.876 47.826 0.00 0.00 0.00 2.85
504 637 2.606725 CGTCAATCTCAAGAGGATGTGC 59.393 50.000 0.00 0.00 0.00 4.57
512 645 1.841302 AAGAGGATGTGCCGGCTCAA 61.841 55.000 32.53 16.47 43.43 3.02
520 653 2.279784 GCCGGCTCAATCTCTCGG 60.280 66.667 22.15 0.00 43.13 4.63
528 661 1.480137 CTCAATCTCTCGGAGGTGCTT 59.520 52.381 4.96 0.00 0.00 3.91
559 693 1.198867 GGTGTGTGCATGCGTTCATAA 59.801 47.619 14.09 2.95 0.00 1.90
560 694 2.351253 GGTGTGTGCATGCGTTCATAAA 60.351 45.455 14.09 0.68 0.00 1.40
578 712 7.832503 TCATAAAGATGAGTGTATGTGTGTG 57.167 36.000 0.00 0.00 37.15 3.82
603 743 3.994204 TGAGCGTCTGTACTGTGTTAA 57.006 42.857 0.00 0.00 0.00 2.01
672 812 3.633525 CCAAAGCTAGGCAATTGCATCTA 59.366 43.478 30.32 21.04 44.36 1.98
676 816 4.785301 AGCTAGGCAATTGCATCTAGAAA 58.215 39.130 31.48 13.31 44.36 2.52
683 823 7.163441 AGGCAATTGCATCTAGAAAACAAAAT 58.837 30.769 30.32 0.00 44.36 1.82
684 824 7.118680 AGGCAATTGCATCTAGAAAACAAAATG 59.881 33.333 30.32 6.95 44.36 2.32
710 850 5.664908 AGAAGAGAAAGGAAGATGCTCCATA 59.335 40.000 0.00 0.00 38.02 2.74
715 855 4.696479 AAGGAAGATGCTCCATATTCGT 57.304 40.909 6.52 4.75 41.31 3.85
774 914 6.907741 TCTTAGATGATCATGTCACGATCTC 58.092 40.000 14.30 5.62 40.28 2.75
794 934 8.281194 CGATCTCAATTAATGAAATGAGTGAGG 58.719 37.037 7.61 0.00 36.60 3.86
847 987 2.095059 CAGGGCATTTCGGTCTTTTCAG 60.095 50.000 0.00 0.00 0.00 3.02
868 1008 1.896465 CCTCTCCCTCCATTATCGGTC 59.104 57.143 0.00 0.00 0.00 4.79
870 1010 1.219469 TCTCCCTCCATTATCGGTCCA 59.781 52.381 0.00 0.00 0.00 4.02
871 1011 1.344763 CTCCCTCCATTATCGGTCCAC 59.655 57.143 0.00 0.00 0.00 4.02
872 1012 0.396811 CCCTCCATTATCGGTCCACC 59.603 60.000 0.00 0.00 0.00 4.61
873 1013 1.424638 CCTCCATTATCGGTCCACCT 58.575 55.000 0.00 0.00 0.00 4.00
910 1050 3.634397 TCTCCAACCCTGAAGCTATTG 57.366 47.619 0.00 0.00 0.00 1.90
965 1105 2.159028 GGAAGACACACTCCCAGATAGC 60.159 54.545 0.00 0.00 0.00 2.97
994 1134 6.148811 GCAGTACTGATAGTAGAGCTAGGAAG 59.851 46.154 27.08 0.00 32.26 3.46
996 1136 5.915744 ACTGATAGTAGAGCTAGGAAGGA 57.084 43.478 0.00 0.00 32.45 3.36
1005 1145 0.036858 GCTAGGAAGGATCGATGGCC 60.037 60.000 0.54 0.00 0.00 5.36
1027 1167 1.811941 GCAGTAGAGCAATGGTAGCCC 60.812 57.143 0.00 0.00 0.00 5.19
1032 1172 1.142465 AGAGCAATGGTAGCCCTGATG 59.858 52.381 0.00 0.00 0.00 3.07
1044 1184 1.693640 CCTGATGGGGCTTGTCCTT 59.306 57.895 0.00 0.00 34.39 3.36
1074 1214 2.668212 TTCCCAGCGGCTTTGTCG 60.668 61.111 0.00 0.00 0.00 4.35
1079 1219 2.357517 AGCGGCTTTGTCGTCCAG 60.358 61.111 0.00 0.00 31.29 3.86
1107 1247 3.616076 CGGATCAGCTTATCTCCATGACC 60.616 52.174 7.79 0.00 0.00 4.02
1336 1476 3.520317 TCAAGCTTCCTCCGGGTAATTAA 59.480 43.478 0.00 0.00 0.00 1.40
1337 1477 3.840124 AGCTTCCTCCGGGTAATTAAG 57.160 47.619 0.00 0.00 0.00 1.85
1338 1478 3.113043 AGCTTCCTCCGGGTAATTAAGT 58.887 45.455 0.00 0.00 0.00 2.24
1339 1479 4.292643 AGCTTCCTCCGGGTAATTAAGTA 58.707 43.478 0.00 0.00 0.00 2.24
1340 1480 4.906060 AGCTTCCTCCGGGTAATTAAGTAT 59.094 41.667 0.00 0.00 0.00 2.12
1341 1481 5.011840 AGCTTCCTCCGGGTAATTAAGTATC 59.988 44.000 0.00 0.00 0.00 2.24
1342 1482 5.791666 CTTCCTCCGGGTAATTAAGTATCC 58.208 45.833 0.00 1.97 0.00 2.59
1343 1483 4.162651 TCCTCCGGGTAATTAAGTATCCC 58.837 47.826 6.65 8.21 35.22 3.85
1344 1484 3.262660 CCTCCGGGTAATTAAGTATCCCC 59.737 52.174 6.65 2.95 35.11 4.81
1345 1485 4.165760 CTCCGGGTAATTAAGTATCCCCT 58.834 47.826 6.65 0.00 35.11 4.79
1346 1486 4.162651 TCCGGGTAATTAAGTATCCCCTC 58.837 47.826 6.65 0.00 35.11 4.30
1347 1487 3.262660 CCGGGTAATTAAGTATCCCCTCC 59.737 52.174 6.65 0.00 35.11 4.30
1348 1488 3.056322 CGGGTAATTAAGTATCCCCTCCG 60.056 52.174 6.65 1.37 35.11 4.63
1349 1489 3.906218 GGGTAATTAAGTATCCCCTCCGT 59.094 47.826 0.48 0.00 32.66 4.69
1350 1490 4.020751 GGGTAATTAAGTATCCCCTCCGTC 60.021 50.000 0.48 0.00 32.66 4.79
1351 1491 4.020751 GGTAATTAAGTATCCCCTCCGTCC 60.021 50.000 0.00 0.00 0.00 4.79
1352 1492 2.092598 TTAAGTATCCCCTCCGTCCC 57.907 55.000 0.00 0.00 0.00 4.46
1353 1493 0.935942 TAAGTATCCCCTCCGTCCCA 59.064 55.000 0.00 0.00 0.00 4.37
1354 1494 0.043637 AAGTATCCCCTCCGTCCCAA 59.956 55.000 0.00 0.00 0.00 4.12
1355 1495 0.043637 AGTATCCCCTCCGTCCCAAA 59.956 55.000 0.00 0.00 0.00 3.28
1356 1496 0.913924 GTATCCCCTCCGTCCCAAAA 59.086 55.000 0.00 0.00 0.00 2.44
1357 1497 1.493446 GTATCCCCTCCGTCCCAAAAT 59.507 52.381 0.00 0.00 0.00 1.82
1358 1498 1.007607 ATCCCCTCCGTCCCAAAATT 58.992 50.000 0.00 0.00 0.00 1.82
1359 1499 0.330267 TCCCCTCCGTCCCAAAATTC 59.670 55.000 0.00 0.00 0.00 2.17
1360 1500 0.331616 CCCCTCCGTCCCAAAATTCT 59.668 55.000 0.00 0.00 0.00 2.40
1361 1501 1.272480 CCCCTCCGTCCCAAAATTCTT 60.272 52.381 0.00 0.00 0.00 2.52
1362 1502 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
1363 1503 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
1364 1504 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
1365 1505 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
1366 1506 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
1367 1507 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
1368 1508 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
1369 1509 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
1370 1510 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
1371 1511 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
1372 1512 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
1373 1513 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
1374 1514 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
1375 1515 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
1376 1516 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
1384 1524 9.582431 TCTTGTCTTAGATTTGTCTAAATACGG 57.418 33.333 0.26 0.99 36.66 4.02
1385 1525 9.582431 CTTGTCTTAGATTTGTCTAAATACGGA 57.418 33.333 0.26 0.00 36.66 4.69
1387 1527 9.529325 TGTCTTAGATTTGTCTAAATACGGATG 57.471 33.333 0.26 0.00 36.66 3.51
1388 1528 9.530633 GTCTTAGATTTGTCTAAATACGGATGT 57.469 33.333 0.26 0.00 36.66 3.06
1395 1535 9.832445 ATTTGTCTAAATACGGATGTATCAAGT 57.168 29.630 0.00 0.00 40.42 3.16
1396 1536 8.867112 TTGTCTAAATACGGATGTATCAAGTC 57.133 34.615 0.00 0.00 40.42 3.01
1397 1537 8.002984 TGTCTAAATACGGATGTATCAAGTCA 57.997 34.615 0.00 0.00 40.42 3.41
1398 1538 7.919091 TGTCTAAATACGGATGTATCAAGTCAC 59.081 37.037 0.00 0.00 40.42 3.67
1399 1539 7.919091 GTCTAAATACGGATGTATCAAGTCACA 59.081 37.037 0.00 0.00 40.42 3.58
1400 1540 8.638873 TCTAAATACGGATGTATCAAGTCACAT 58.361 33.333 0.00 0.00 40.42 3.21
1401 1541 9.261180 CTAAATACGGATGTATCAAGTCACATT 57.739 33.333 0.00 0.00 40.42 2.71
1402 1542 8.506168 AAATACGGATGTATCAAGTCACATTT 57.494 30.769 0.00 0.00 40.42 2.32
1403 1543 8.506168 AATACGGATGTATCAAGTCACATTTT 57.494 30.769 0.00 0.00 40.42 1.82
1404 1544 9.607988 AATACGGATGTATCAAGTCACATTTTA 57.392 29.630 0.00 0.00 40.42 1.52
1405 1545 7.539712 ACGGATGTATCAAGTCACATTTTAG 57.460 36.000 0.00 0.00 35.55 1.85
1406 1546 7.103641 ACGGATGTATCAAGTCACATTTTAGT 58.896 34.615 0.00 0.00 35.55 2.24
1407 1547 8.255206 ACGGATGTATCAAGTCACATTTTAGTA 58.745 33.333 0.00 0.00 35.55 1.82
1408 1548 9.261180 CGGATGTATCAAGTCACATTTTAGTAT 57.739 33.333 0.00 0.00 35.55 2.12
1439 1579 8.234136 ACATCCGTATCTAGACAAATGTAAGA 57.766 34.615 0.00 1.82 0.00 2.10
1440 1580 8.136165 ACATCCGTATCTAGACAAATGTAAGAC 58.864 37.037 0.00 0.00 0.00 3.01
1441 1581 7.634671 TCCGTATCTAGACAAATGTAAGACA 57.365 36.000 0.00 0.00 0.00 3.41
1442 1582 8.058667 TCCGTATCTAGACAAATGTAAGACAA 57.941 34.615 0.00 0.00 0.00 3.18
1443 1583 8.188799 TCCGTATCTAGACAAATGTAAGACAAG 58.811 37.037 0.00 0.00 0.00 3.16
1444 1584 8.188799 CCGTATCTAGACAAATGTAAGACAAGA 58.811 37.037 0.00 0.00 0.00 3.02
1445 1585 9.569167 CGTATCTAGACAAATGTAAGACAAGAA 57.431 33.333 0.00 0.00 0.00 2.52
1452 1592 8.143835 AGACAAATGTAAGACAAGAATTTTGGG 58.856 33.333 7.26 0.00 31.16 4.12
1453 1593 8.017418 ACAAATGTAAGACAAGAATTTTGGGA 57.983 30.769 7.26 0.00 31.16 4.37
1454 1594 7.926018 ACAAATGTAAGACAAGAATTTTGGGAC 59.074 33.333 7.26 0.00 31.16 4.46
1455 1595 5.682943 TGTAAGACAAGAATTTTGGGACG 57.317 39.130 5.68 0.00 0.00 4.79
1456 1596 4.517453 TGTAAGACAAGAATTTTGGGACGG 59.483 41.667 0.00 0.00 0.00 4.79
1457 1597 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
1458 1598 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
1459 1599 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
1460 1600 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
1528 1668 8.442374 AGGTCTAACTTTATGGGTTTAGTTCAA 58.558 33.333 0.00 0.00 33.28 2.69
1542 1682 7.415877 GGGTTTAGTTCAATGTTACACTTGTGT 60.416 37.037 11.30 11.30 0.00 3.72
1550 1690 2.942376 TGTTACACTTGTGTCTTGCCAG 59.058 45.455 9.85 0.00 0.00 4.85
1557 1697 3.319122 ACTTGTGTCTTGCCAGATTTTCC 59.681 43.478 0.00 0.00 0.00 3.13
1586 1726 9.251440 GCCATGGCCATATATATATGATTCAAT 57.749 33.333 27.24 14.96 42.05 2.57
1604 1744 1.454572 ATTCTTGCCGCACTTGTGCA 61.455 50.000 22.97 6.71 34.41 4.57
1623 1764 5.047448 TGTGCAGCCAATTTGTACATTACAT 60.047 36.000 0.00 0.00 36.46 2.29
1627 1768 7.117523 TGCAGCCAATTTGTACATTACATTTTC 59.882 33.333 0.00 0.00 38.68 2.29
2025 2181 6.619801 AAACTTCCTTAAGTGTTGCTACTG 57.380 37.500 0.97 0.00 45.37 2.74
2197 2365 1.683365 CCCCCACCTTCAGCATTGG 60.683 63.158 0.00 0.00 0.00 3.16
2284 2452 2.378038 GCATACCATTGGGAAAGCTCA 58.622 47.619 7.78 0.00 38.05 4.26
2387 2555 3.236003 GAACCGGCGTCAGGACCTT 62.236 63.158 6.01 0.00 0.00 3.50
2459 2627 0.197661 AGGGGAAGGGGGTTCTTACA 59.802 55.000 0.00 0.00 35.25 2.41
2471 2639 2.063266 GTTCTTACATCCGACGTGCAA 58.937 47.619 0.00 0.00 0.00 4.08
2591 2759 1.613630 GCTCCAGGGACCTCAAGGA 60.614 63.158 2.30 0.00 38.94 3.36
2646 2814 3.314635 GTCTCATCGTACGTCCAACCTAT 59.685 47.826 16.05 0.00 0.00 2.57
2647 2815 3.562973 TCTCATCGTACGTCCAACCTATC 59.437 47.826 16.05 0.00 0.00 2.08
2811 3005 8.601476 CCCTTTATCACACGAAATTTACTACTC 58.399 37.037 0.00 0.00 0.00 2.59
2861 3055 3.312421 CCATTTACATTCGCGTTCCATCT 59.688 43.478 5.77 0.00 0.00 2.90
2880 3074 0.396556 TACAGCGCCTATCTCCACCA 60.397 55.000 2.29 0.00 0.00 4.17
2885 3079 1.832912 GCCTATCTCCACCACCCAG 59.167 63.158 0.00 0.00 0.00 4.45
2978 3174 1.831106 TGCATGTCAGGTAGTAGGTGG 59.169 52.381 0.00 0.00 0.00 4.61
2980 3176 2.159085 GCATGTCAGGTAGTAGGTGGAC 60.159 54.545 0.00 0.00 0.00 4.02
3097 3390 6.293298 GCACACAAACATGATTTAAATGCCAA 60.293 34.615 5.17 0.00 0.00 4.52
3100 3393 8.848182 ACACAAACATGATTTAAATGCCAAAAT 58.152 25.926 5.17 0.00 0.00 1.82
3141 3434 9.635520 TTGTTTAAATTGGTTTGAAAGAACGTA 57.364 25.926 0.00 0.00 0.00 3.57
3214 3507 6.405538 ACTTTGCCATGAAAAACAGAAGAAA 58.594 32.000 0.00 0.00 0.00 2.52
3221 3514 8.066000 GCCATGAAAAACAGAAGAAATTTTGAG 58.934 33.333 0.00 0.00 0.00 3.02
3326 3620 7.832685 ACTCAAAGAACTTTAGGTTTTACTGGT 59.167 33.333 0.00 0.00 38.41 4.00
3357 3651 6.925165 TCAAAAGTTCTTCTGATTTTCATGGC 59.075 34.615 0.00 0.00 0.00 4.40
3361 3655 6.819284 AGTTCTTCTGATTTTCATGGCAAAA 58.181 32.000 0.00 0.00 0.00 2.44
3366 3660 7.601130 TCTTCTGATTTTCATGGCAAAATTCAG 59.399 33.333 20.30 20.30 36.33 3.02
3373 3667 5.471556 TCATGGCAAAATTCAGACACATT 57.528 34.783 0.00 0.00 0.00 2.71
3426 3722 5.073428 TGTGATTGGTGGTTAGTTATGCAA 58.927 37.500 0.00 0.00 0.00 4.08
3498 3794 5.789574 AGTATTAATCTGTTCACCCCCAA 57.210 39.130 0.00 0.00 0.00 4.12
3510 3806 4.390129 TCACCCCCAAAGTAATTAGCAA 57.610 40.909 0.00 0.00 0.00 3.91
3511 3807 4.941713 TCACCCCCAAAGTAATTAGCAAT 58.058 39.130 0.00 0.00 0.00 3.56
3514 3810 4.466015 ACCCCCAAAGTAATTAGCAATGTG 59.534 41.667 0.00 0.00 0.00 3.21
3526 3822 9.599322 GTAATTAGCAATGTGAGTTATGCATAC 57.401 33.333 5.74 0.00 41.18 2.39
3527 3823 7.806409 ATTAGCAATGTGAGTTATGCATACA 57.194 32.000 5.74 3.56 41.18 2.29
3528 3824 7.622893 TTAGCAATGTGAGTTATGCATACAA 57.377 32.000 5.74 0.00 41.18 2.41
3529 3825 6.127810 AGCAATGTGAGTTATGCATACAAG 57.872 37.500 5.74 2.40 41.18 3.16
3530 3826 5.882000 AGCAATGTGAGTTATGCATACAAGA 59.118 36.000 5.74 0.00 41.18 3.02
3531 3827 6.037940 AGCAATGTGAGTTATGCATACAAGAG 59.962 38.462 5.74 0.00 41.18 2.85
3532 3828 6.037500 GCAATGTGAGTTATGCATACAAGAGA 59.962 38.462 5.74 0.00 38.63 3.10
3536 3832 8.032952 TGTGAGTTATGCATACAAGAGAAAAG 57.967 34.615 5.74 0.00 0.00 2.27
3537 3833 6.963805 GTGAGTTATGCATACAAGAGAAAAGC 59.036 38.462 5.74 0.00 0.00 3.51
3538 3834 6.094048 TGAGTTATGCATACAAGAGAAAAGCC 59.906 38.462 5.74 0.00 0.00 4.35
3540 3836 4.708726 ATGCATACAAGAGAAAAGCCAC 57.291 40.909 0.00 0.00 0.00 5.01
3545 3858 5.175673 GCATACAAGAGAAAAGCCACAAAAC 59.824 40.000 0.00 0.00 0.00 2.43
3594 3908 0.326264 ATGCGGAGGAAAAGCTGACT 59.674 50.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 3.431415 TCCATATAGTAGCGCATGTCCT 58.569 45.455 11.47 0.00 0.00 3.85
154 155 6.128553 TGAGAAACGATGTACAAGCAATTCTC 60.129 38.462 22.07 22.07 40.21 2.87
160 161 5.474825 TGTATGAGAAACGATGTACAAGCA 58.525 37.500 0.00 0.00 0.00 3.91
161 162 6.589830 ATGTATGAGAAACGATGTACAAGC 57.410 37.500 0.00 0.00 0.00 4.01
176 177 8.137437 GGTGACCCAAATTTATCAATGTATGAG 58.863 37.037 0.00 0.00 42.53 2.90
177 178 7.617329 TGGTGACCCAAATTTATCAATGTATGA 59.383 33.333 0.00 0.00 39.29 2.15
183 184 4.162131 GCCTGGTGACCCAAATTTATCAAT 59.838 41.667 0.00 0.00 41.27 2.57
184 185 3.513515 GCCTGGTGACCCAAATTTATCAA 59.486 43.478 0.00 0.00 41.27 2.57
241 242 4.574828 CCCACTCATAAAATTGGTAGGTCG 59.425 45.833 0.00 0.00 0.00 4.79
248 249 5.937975 ATGGTTCCCACTCATAAAATTGG 57.062 39.130 0.00 0.00 35.80 3.16
251 252 4.162131 GCCAATGGTTCCCACTCATAAAAT 59.838 41.667 0.00 0.00 35.80 1.82
252 253 3.513515 GCCAATGGTTCCCACTCATAAAA 59.486 43.478 0.00 0.00 35.80 1.52
262 263 1.396653 CTCAGATGCCAATGGTTCCC 58.603 55.000 0.00 0.00 0.00 3.97
287 288 6.558909 GTTTCTGTTTCATGATGATTCCCTC 58.441 40.000 0.00 0.00 0.00 4.30
299 300 3.502123 TTCCCCTCGTTTCTGTTTCAT 57.498 42.857 0.00 0.00 0.00 2.57
306 307 5.750352 TGTAGTTTATTCCCCTCGTTTCT 57.250 39.130 0.00 0.00 0.00 2.52
312 313 5.104067 ACCCAGATTGTAGTTTATTCCCCTC 60.104 44.000 0.00 0.00 0.00 4.30
332 333 1.228429 CGCCTTCCTTCCAAACCCA 60.228 57.895 0.00 0.00 0.00 4.51
333 334 2.636412 GCGCCTTCCTTCCAAACCC 61.636 63.158 0.00 0.00 0.00 4.11
336 337 1.152830 AAGGCGCCTTCCTTCCAAA 59.847 52.632 35.84 0.00 42.55 3.28
343 344 0.953960 TTTCTTCGAAGGCGCCTTCC 60.954 55.000 46.84 34.02 47.00 3.46
344 345 0.444260 CTTTCTTCGAAGGCGCCTTC 59.556 55.000 45.39 45.39 46.41 3.46
378 379 1.156736 AAATCCGAGCAGTGAAACCG 58.843 50.000 0.00 0.00 37.80 4.44
383 384 3.401033 TCAGAAAAATCCGAGCAGTGA 57.599 42.857 0.00 0.00 0.00 3.41
428 560 0.756294 TCTCTTCCCAGTGAACGCAA 59.244 50.000 0.00 0.00 0.00 4.85
449 581 1.068741 GCCTTCGTAGTCATCGGGAAT 59.931 52.381 0.00 0.00 0.00 3.01
464 596 0.169009 GAAGTTGCCACGATGCCTTC 59.831 55.000 0.00 0.00 0.00 3.46
497 630 1.153086 AGATTGAGCCGGCACATCC 60.153 57.895 31.54 21.53 0.00 3.51
504 637 1.361993 CTCCGAGAGATTGAGCCGG 59.638 63.158 0.00 0.00 41.36 6.13
512 645 3.074687 TCCTATAAGCACCTCCGAGAGAT 59.925 47.826 0.00 0.00 0.00 2.75
520 653 3.574826 CACCCTACTCCTATAAGCACCTC 59.425 52.174 0.00 0.00 0.00 3.85
528 661 3.391799 TGCACACACCCTACTCCTATA 57.608 47.619 0.00 0.00 0.00 1.31
559 693 4.960938 ACACACACACATACACTCATCTT 58.039 39.130 0.00 0.00 0.00 2.40
560 694 4.607293 ACACACACACATACACTCATCT 57.393 40.909 0.00 0.00 0.00 2.90
578 712 2.218759 CACAGTACAGACGCTCAAACAC 59.781 50.000 0.00 0.00 0.00 3.32
672 812 9.408648 TCCTTTCTCTTCTACATTTTGTTTTCT 57.591 29.630 0.00 0.00 0.00 2.52
676 816 8.980481 TCTTCCTTTCTCTTCTACATTTTGTT 57.020 30.769 0.00 0.00 0.00 2.83
683 823 5.105146 GGAGCATCTTCCTTTCTCTTCTACA 60.105 44.000 0.00 0.00 34.27 2.74
684 824 5.105146 TGGAGCATCTTCCTTTCTCTTCTAC 60.105 44.000 0.00 0.00 38.12 2.59
687 827 4.213564 TGGAGCATCTTCCTTTCTCTTC 57.786 45.455 0.00 0.00 38.12 2.87
710 850 8.616942 CGTGATAAGATCAGGATAGATACGAAT 58.383 37.037 3.61 0.00 45.37 3.34
744 884 9.166173 TCGTGACATGATCATCTAAGAAAATTT 57.834 29.630 4.86 0.00 40.28 1.82
751 891 6.675987 TGAGATCGTGACATGATCATCTAAG 58.324 40.000 30.31 0.00 41.84 2.18
762 902 9.112725 TCATTTCATTAATTGAGATCGTGACAT 57.887 29.630 0.00 0.00 35.27 3.06
802 942 9.859427 CTGGTTTAGATTTAATTTCAATCAGCA 57.141 29.630 10.93 6.67 33.67 4.41
804 944 9.807649 CCCTGGTTTAGATTTAATTTCAATCAG 57.192 33.333 10.93 0.00 33.67 2.90
823 963 0.112412 AAGACCGAAATGCCCTGGTT 59.888 50.000 0.00 0.00 34.12 3.67
824 964 0.112412 AAAGACCGAAATGCCCTGGT 59.888 50.000 0.00 0.00 37.44 4.00
847 987 0.610687 CCGATAATGGAGGGAGAGGC 59.389 60.000 0.00 0.00 0.00 4.70
868 1008 2.829023 TGAGAAAGGGTAGGTAGGTGG 58.171 52.381 0.00 0.00 0.00 4.61
870 1010 4.961585 AGATTGAGAAAGGGTAGGTAGGT 58.038 43.478 0.00 0.00 0.00 3.08
871 1011 4.345547 GGAGATTGAGAAAGGGTAGGTAGG 59.654 50.000 0.00 0.00 0.00 3.18
872 1012 4.962995 TGGAGATTGAGAAAGGGTAGGTAG 59.037 45.833 0.00 0.00 0.00 3.18
873 1013 4.955335 TGGAGATTGAGAAAGGGTAGGTA 58.045 43.478 0.00 0.00 0.00 3.08
910 1050 8.621286 CAGGATGGTGTTATTTATAACTCAACC 58.379 37.037 17.34 17.34 42.32 3.77
938 1078 1.891150 GGGAGTGTGTCTTCCTTACGA 59.109 52.381 0.00 0.00 38.77 3.43
994 1134 0.320247 CTACTGCAGGCCATCGATCC 60.320 60.000 19.93 0.00 0.00 3.36
996 1136 0.678395 CTCTACTGCAGGCCATCGAT 59.322 55.000 19.93 0.00 0.00 3.59
1005 1145 2.208431 GCTACCATTGCTCTACTGCAG 58.792 52.381 13.48 13.48 44.27 4.41
1027 1167 1.318158 GCAAGGACAAGCCCCATCAG 61.318 60.000 0.00 0.00 37.37 2.90
1042 1182 4.157958 GAAGAGCAGCGCGGCAAG 62.158 66.667 33.13 8.79 35.83 4.01
1065 1205 3.423154 CGCCTGGACGACAAAGCC 61.423 66.667 0.00 0.00 34.06 4.35
1079 1219 3.537206 ATAAGCTGATCCGGCCGCC 62.537 63.158 22.85 11.70 36.20 6.13
1107 1247 0.756294 TATGGTACTGGCCATCGGTG 59.244 55.000 5.51 0.00 45.47 4.94
1336 1476 0.043637 TTTGGGACGGAGGGGATACT 59.956 55.000 0.00 0.00 0.00 2.12
1337 1477 0.913924 TTTTGGGACGGAGGGGATAC 59.086 55.000 0.00 0.00 0.00 2.24
1338 1478 1.901648 ATTTTGGGACGGAGGGGATA 58.098 50.000 0.00 0.00 0.00 2.59
1339 1479 1.007607 AATTTTGGGACGGAGGGGAT 58.992 50.000 0.00 0.00 0.00 3.85
1340 1480 0.330267 GAATTTTGGGACGGAGGGGA 59.670 55.000 0.00 0.00 0.00 4.81
1341 1481 0.331616 AGAATTTTGGGACGGAGGGG 59.668 55.000 0.00 0.00 0.00 4.79
1342 1482 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
1343 1483 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
1344 1484 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
1345 1485 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
1346 1486 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
1347 1487 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
1348 1488 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
1349 1489 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
1350 1490 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
1358 1498 9.582431 CCGTATTTAGACAAATCTAAGACAAGA 57.418 33.333 9.81 0.00 45.93 3.02
1359 1499 9.582431 TCCGTATTTAGACAAATCTAAGACAAG 57.418 33.333 9.81 3.88 45.93 3.16
1361 1501 9.529325 CATCCGTATTTAGACAAATCTAAGACA 57.471 33.333 9.81 0.00 45.93 3.41
1362 1502 9.530633 ACATCCGTATTTAGACAAATCTAAGAC 57.469 33.333 0.00 0.83 45.93 3.01
1369 1509 9.832445 ACTTGATACATCCGTATTTAGACAAAT 57.168 29.630 0.00 0.00 38.48 2.32
1370 1510 9.309516 GACTTGATACATCCGTATTTAGACAAA 57.690 33.333 0.00 0.00 38.48 2.83
1371 1511 8.471609 TGACTTGATACATCCGTATTTAGACAA 58.528 33.333 0.00 0.00 38.48 3.18
1372 1512 7.919091 GTGACTTGATACATCCGTATTTAGACA 59.081 37.037 0.00 0.00 38.48 3.41
1373 1513 7.919091 TGTGACTTGATACATCCGTATTTAGAC 59.081 37.037 0.00 0.00 38.48 2.59
1374 1514 8.002984 TGTGACTTGATACATCCGTATTTAGA 57.997 34.615 0.00 0.00 38.48 2.10
1375 1515 8.818141 ATGTGACTTGATACATCCGTATTTAG 57.182 34.615 0.00 0.00 38.48 1.85
1376 1516 9.607988 AAATGTGACTTGATACATCCGTATTTA 57.392 29.630 0.00 0.00 38.48 1.40
1377 1517 8.506168 AAATGTGACTTGATACATCCGTATTT 57.494 30.769 0.00 0.00 38.48 1.40
1378 1518 8.506168 AAAATGTGACTTGATACATCCGTATT 57.494 30.769 0.00 0.00 38.48 1.89
1379 1519 9.261180 CTAAAATGTGACTTGATACATCCGTAT 57.739 33.333 0.00 0.00 41.16 3.06
1380 1520 8.255206 ACTAAAATGTGACTTGATACATCCGTA 58.745 33.333 0.00 0.00 36.56 4.02
1381 1521 7.103641 ACTAAAATGTGACTTGATACATCCGT 58.896 34.615 0.00 0.00 36.56 4.69
1382 1522 7.539712 ACTAAAATGTGACTTGATACATCCG 57.460 36.000 0.00 0.00 36.56 4.18
1413 1553 9.346005 TCTTACATTTGTCTAGATACGGATGTA 57.654 33.333 11.94 11.94 32.86 2.29
1414 1554 8.136165 GTCTTACATTTGTCTAGATACGGATGT 58.864 37.037 13.29 13.29 34.19 3.06
1415 1555 8.135529 TGTCTTACATTTGTCTAGATACGGATG 58.864 37.037 0.00 0.85 0.00 3.51
1416 1556 8.234136 TGTCTTACATTTGTCTAGATACGGAT 57.766 34.615 0.00 0.00 0.00 4.18
1417 1557 7.634671 TGTCTTACATTTGTCTAGATACGGA 57.365 36.000 0.00 0.00 0.00 4.69
1418 1558 8.188799 TCTTGTCTTACATTTGTCTAGATACGG 58.811 37.037 0.00 0.00 0.00 4.02
1419 1559 9.569167 TTCTTGTCTTACATTTGTCTAGATACG 57.431 33.333 0.00 0.00 0.00 3.06
1426 1566 8.143835 CCCAAAATTCTTGTCTTACATTTGTCT 58.856 33.333 0.00 0.00 27.14 3.41
1427 1567 8.141268 TCCCAAAATTCTTGTCTTACATTTGTC 58.859 33.333 0.00 0.00 27.14 3.18
1428 1568 7.926018 GTCCCAAAATTCTTGTCTTACATTTGT 59.074 33.333 0.00 0.00 27.14 2.83
1429 1569 7.114811 CGTCCCAAAATTCTTGTCTTACATTTG 59.885 37.037 0.00 0.00 0.00 2.32
1430 1570 7.145323 CGTCCCAAAATTCTTGTCTTACATTT 58.855 34.615 0.00 0.00 0.00 2.32
1431 1571 6.294508 CCGTCCCAAAATTCTTGTCTTACATT 60.295 38.462 0.00 0.00 0.00 2.71
1432 1572 5.183140 CCGTCCCAAAATTCTTGTCTTACAT 59.817 40.000 0.00 0.00 0.00 2.29
1433 1573 4.517453 CCGTCCCAAAATTCTTGTCTTACA 59.483 41.667 0.00 0.00 0.00 2.41
1434 1574 4.758165 TCCGTCCCAAAATTCTTGTCTTAC 59.242 41.667 0.00 0.00 0.00 2.34
1435 1575 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
1436 1576 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
1437 1577 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
1438 1578 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
1439 1579 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
1440 1580 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
1441 1581 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
1442 1582 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
1443 1583 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
1444 1584 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
1445 1585 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
1446 1586 1.557832 CATACTCCCTCCGTCCCAAAA 59.442 52.381 0.00 0.00 0.00 2.44
1447 1587 1.200519 CATACTCCCTCCGTCCCAAA 58.799 55.000 0.00 0.00 0.00 3.28
1448 1588 0.042131 ACATACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
1449 1589 0.928505 TACATACTCCCTCCGTCCCA 59.071 55.000 0.00 0.00 0.00 4.37
1450 1590 2.077687 TTACATACTCCCTCCGTCCC 57.922 55.000 0.00 0.00 0.00 4.46
1451 1591 3.196254 TGTTTTACATACTCCCTCCGTCC 59.804 47.826 0.00 0.00 0.00 4.79
1452 1592 4.460948 TGTTTTACATACTCCCTCCGTC 57.539 45.455 0.00 0.00 0.00 4.79
1453 1593 4.224370 ACATGTTTTACATACTCCCTCCGT 59.776 41.667 0.00 0.00 36.53 4.69
1454 1594 4.766375 ACATGTTTTACATACTCCCTCCG 58.234 43.478 0.00 0.00 36.53 4.63
1455 1595 6.657541 TCAAACATGTTTTACATACTCCCTCC 59.342 38.462 21.10 0.00 36.53 4.30
1456 1596 7.681939 TCAAACATGTTTTACATACTCCCTC 57.318 36.000 21.10 0.00 36.53 4.30
1457 1597 8.650143 AATCAAACATGTTTTACATACTCCCT 57.350 30.769 21.10 0.00 36.53 4.20
1458 1598 7.696453 CGAATCAAACATGTTTTACATACTCCC 59.304 37.037 21.10 2.56 36.53 4.30
1459 1599 8.234546 ACGAATCAAACATGTTTTACATACTCC 58.765 33.333 21.10 3.73 36.53 3.85
1528 1668 3.550820 TGGCAAGACACAAGTGTAACAT 58.449 40.909 5.74 0.00 45.05 2.71
1542 1682 2.308570 TGGCTAGGAAAATCTGGCAAGA 59.691 45.455 0.00 0.00 42.08 3.02
1550 1690 2.071778 TGGCCATGGCTAGGAAAATC 57.928 50.000 34.70 16.05 41.60 2.17
1557 1697 9.610705 GAATCATATATATATGGCCATGGCTAG 57.389 37.037 34.70 14.62 40.35 3.42
1604 1744 7.906327 AGGAAAATGTAATGTACAAATTGGCT 58.094 30.769 0.00 0.00 42.76 4.75
1623 1764 5.373222 TCAGCTAAGTGTGCTAAAGGAAAA 58.627 37.500 0.00 0.00 38.92 2.29
1627 1768 4.569943 TCTTCAGCTAAGTGTGCTAAAGG 58.430 43.478 0.00 0.00 36.66 3.11
1955 2109 4.481368 TCCAAAAGTGACATACCGCTAT 57.519 40.909 0.00 0.00 0.00 2.97
2058 2222 7.379529 GCATTAAAGCATATGATTTAGCGTGTT 59.620 33.333 21.60 1.61 37.23 3.32
2108 2275 1.206132 CTACCGAGTGGCACATGGTAA 59.794 52.381 29.10 18.63 44.52 2.85
2284 2452 3.434319 CGCTGAAGGTGGCGCAAT 61.434 61.111 10.83 0.00 44.64 3.56
2459 2627 1.215647 GAGGAGTTGCACGTCGGAT 59.784 57.895 0.00 0.00 0.00 4.18
2471 2639 0.112606 TGGTCTCGTTGAGGAGGAGT 59.887 55.000 1.35 0.00 40.37 3.85
2646 2814 1.597854 CAGGCAGCAAACACCTCGA 60.598 57.895 0.00 0.00 0.00 4.04
2647 2815 2.949106 CAGGCAGCAAACACCTCG 59.051 61.111 0.00 0.00 0.00 4.63
2666 2840 2.848694 TCCCATCTGAAGGAAGCAGAAT 59.151 45.455 0.00 0.00 44.71 2.40
2811 3005 6.259550 ACCGTACAGTTTGTAAGTACTAGG 57.740 41.667 0.00 0.00 34.21 3.02
2861 3055 0.396556 TGGTGGAGATAGGCGCTGTA 60.397 55.000 7.64 0.00 0.00 2.74
2880 3074 1.992519 GATCATGGGCAGCTCTGGGT 61.993 60.000 0.00 0.00 0.00 4.51
2885 3079 0.942962 CTTTCGATCATGGGCAGCTC 59.057 55.000 0.00 0.00 0.00 4.09
2978 3174 3.338249 TGCAAGAATCTAGCAACAGGTC 58.662 45.455 0.00 0.00 34.97 3.85
2980 3176 3.693085 ACATGCAAGAATCTAGCAACAGG 59.307 43.478 0.00 0.00 42.15 4.00
3039 3332 5.134339 AGCCACCATCAAAGATAATAAGGGA 59.866 40.000 0.00 0.00 0.00 4.20
3221 3514 9.807649 AACAGTTATGAGATATGCCAAAATTTC 57.192 29.630 0.00 0.00 0.00 2.17
3225 3518 7.936496 TCAACAGTTATGAGATATGCCAAAA 57.064 32.000 0.00 0.00 0.00 2.44
3357 3651 9.770503 CTCTATGAAGAATGTGTCTGAATTTTG 57.229 33.333 0.00 0.00 36.40 2.44
3361 3655 8.538701 AGAACTCTATGAAGAATGTGTCTGAAT 58.461 33.333 0.00 0.00 36.40 2.57
3366 3660 9.862371 TCTTAAGAACTCTATGAAGAATGTGTC 57.138 33.333 1.68 0.00 0.00 3.67
3477 3773 5.949952 ACTTTGGGGGTGAACAGATTAATAC 59.050 40.000 0.00 0.00 0.00 1.89
3478 3774 6.147437 ACTTTGGGGGTGAACAGATTAATA 57.853 37.500 0.00 0.00 0.00 0.98
3479 3775 5.010708 ACTTTGGGGGTGAACAGATTAAT 57.989 39.130 0.00 0.00 0.00 1.40
3480 3776 4.463050 ACTTTGGGGGTGAACAGATTAA 57.537 40.909 0.00 0.00 0.00 1.40
3481 3777 5.586155 TTACTTTGGGGGTGAACAGATTA 57.414 39.130 0.00 0.00 0.00 1.75
3482 3778 4.463050 TTACTTTGGGGGTGAACAGATT 57.537 40.909 0.00 0.00 0.00 2.40
3483 3779 4.675063 ATTACTTTGGGGGTGAACAGAT 57.325 40.909 0.00 0.00 0.00 2.90
3498 3794 8.279970 TGCATAACTCACATTGCTAATTACTT 57.720 30.769 0.00 0.00 36.10 2.24
3510 3806 8.565896 TTTTCTCTTGTATGCATAACTCACAT 57.434 30.769 8.28 0.00 0.00 3.21
3511 3807 7.361201 GCTTTTCTCTTGTATGCATAACTCACA 60.361 37.037 8.28 1.00 0.00 3.58
3514 3810 6.094048 TGGCTTTTCTCTTGTATGCATAACTC 59.906 38.462 8.28 0.00 0.00 3.01
3526 3822 3.115554 CGGTTTTGTGGCTTTTCTCTTG 58.884 45.455 0.00 0.00 0.00 3.02
3527 3823 3.020984 TCGGTTTTGTGGCTTTTCTCTT 58.979 40.909 0.00 0.00 0.00 2.85
3528 3824 2.618709 CTCGGTTTTGTGGCTTTTCTCT 59.381 45.455 0.00 0.00 0.00 3.10
3529 3825 2.858646 GCTCGGTTTTGTGGCTTTTCTC 60.859 50.000 0.00 0.00 0.00 2.87
3530 3826 1.067060 GCTCGGTTTTGTGGCTTTTCT 59.933 47.619 0.00 0.00 0.00 2.52
3531 3827 1.202359 TGCTCGGTTTTGTGGCTTTTC 60.202 47.619 0.00 0.00 0.00 2.29
3532 3828 0.820871 TGCTCGGTTTTGTGGCTTTT 59.179 45.000 0.00 0.00 0.00 2.27
3536 3832 1.080569 CCATGCTCGGTTTTGTGGC 60.081 57.895 0.00 0.00 0.00 5.01
3537 3833 0.958091 TTCCATGCTCGGTTTTGTGG 59.042 50.000 0.00 0.00 0.00 4.17
3538 3834 1.068333 CCTTCCATGCTCGGTTTTGTG 60.068 52.381 0.00 0.00 0.00 3.33
3540 3836 0.527565 CCCTTCCATGCTCGGTTTTG 59.472 55.000 0.00 0.00 0.00 2.44
3545 3858 1.098050 CTTTTCCCTTCCATGCTCGG 58.902 55.000 0.00 0.00 0.00 4.63
3580 3893 2.498167 TCTGCAAGTCAGCTTTTCCTC 58.502 47.619 0.00 0.00 42.56 3.71
3594 3908 3.745480 GCCACAGGCTATAGATTCTGCAA 60.745 47.826 3.21 0.00 46.69 4.08


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

AutoCloner maintained by Alex Coulton.