Multiple sequence alignment - TraesCS7D01G527700

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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 TraesCS7D01G527700 chr7D 100.000 4368 0 0 1 4368 622714293 622709926 0.000000e+00 8067.0
1 TraesCS7D01G527700 chr7D 79.592 98 11 7 1443 1538 561698154 561698244 1.310000e-05 62.1
2 TraesCS7D01G527700 chr7A 91.035 2309 150 27 1600 3871 719363705 719365993 0.000000e+00 3064.0
3 TraesCS7D01G527700 chr7A 85.329 1445 127 29 1 1385 719362238 719363657 0.000000e+00 1415.0
4 TraesCS7D01G527700 chr7A 88.845 251 26 2 3869 4119 719366107 719366355 1.530000e-79 307.0
5 TraesCS7D01G527700 chr7B 91.359 2060 119 28 1547 3568 720978199 720980237 0.000000e+00 2763.0
6 TraesCS7D01G527700 chr7B 88.211 950 59 21 1 928 720976297 720977215 0.000000e+00 1085.0
7 TraesCS7D01G527700 chr7B 91.501 553 41 6 3819 4368 720989191 720989740 0.000000e+00 756.0
8 TraesCS7D01G527700 chr7B 94.796 269 13 1 3560 3827 720981081 720981349 6.760000e-113 418.0
9 TraesCS7D01G527700 chr7B 87.449 247 28 2 4120 4366 705528259 705528016 9.250000e-72 281.0
10 TraesCS7D01G527700 chr7B 85.985 264 29 5 922 1182 720977548 720977806 4.300000e-70 276.0
11 TraesCS7D01G527700 chr6B 89.286 252 21 6 4117 4366 129158602 129158849 1.180000e-80 311.0
12 TraesCS7D01G527700 chr6B 88.439 173 18 1 4124 4296 127922220 127922390 1.590000e-49 207.0
13 TraesCS7D01G527700 chr3D 87.449 247 27 3 4120 4365 16494929 16494686 9.250000e-72 281.0
14 TraesCS7D01G527700 chr3D 86.000 250 30 4 4120 4368 261777493 261777248 3.350000e-66 263.0
15 TraesCS7D01G527700 chr3D 86.758 219 24 4 4151 4368 261771257 261771043 5.650000e-59 239.0
16 TraesCS7D01G527700 chr3D 86.813 182 22 2 4120 4301 4119173 4119352 7.410000e-48 202.0
17 TraesCS7D01G527700 chr2B 81.773 203 32 4 4153 4354 38273193 38273391 9.720000e-37 165.0
18 TraesCS7D01G527700 chr3B 78.824 170 19 14 1391 1544 758467293 758467125 1.000000e-16 99.0
19 TraesCS7D01G527700 chr1A 78.621 145 23 8 1407 1545 33857177 33857319 6.020000e-14 89.8
20 TraesCS7D01G527700 chr1B 78.333 120 19 5 1426 1544 579277648 579277761 2.180000e-08 71.3
21 TraesCS7D01G527700 chr2A 88.136 59 6 1 1486 1544 717197595 717197652 7.840000e-08 69.4
22 TraesCS7D01G527700 chr2A 84.058 69 11 0 1471 1539 632429987 632429919 2.820000e-07 67.6
23 TraesCS7D01G527700 chr3A 79.048 105 16 6 1436 1539 691704246 691704345 2.820000e-07 67.6
24 TraesCS7D01G527700 chr5D 81.013 79 14 1 3731 3808 445033756 445033678 1.310000e-05 62.1
25 TraesCS7D01G527700 chr5A 84.375 64 9 1 1491 1554 650638376 650638438 1.310000e-05 62.1
26 TraesCS7D01G527700 chr1D 78.652 89 16 3 1457 1544 427426225 427426311 6.100000e-04 56.5


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 TraesCS7D01G527700 chr7D 622709926 622714293 4367 True 8067.000000 8067 100.00000 1 4368 1 chr7D.!!$R1 4367
1 TraesCS7D01G527700 chr7A 719362238 719366355 4117 False 1595.333333 3064 88.40300 1 4119 3 chr7A.!!$F1 4118
2 TraesCS7D01G527700 chr7B 720976297 720981349 5052 False 1135.500000 2763 90.08775 1 3827 4 chr7B.!!$F2 3826
3 TraesCS7D01G527700 chr7B 720989191 720989740 549 False 756.000000 756 91.50100 3819 4368 1 chr7B.!!$F1 549

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
427 442 0.687354 AGAACAGCCGACAATCCACT 59.313 50.0 0.0 0.0 0.0 4.00 F
1477 2099 0.248580 ATTTGTGTGTGTGTGCTGCG 60.249 50.0 0.0 0.0 0.0 5.18 F
1502 2124 0.037975 TCGGTCGTTGTAAGGGCTTC 60.038 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1483 2105 0.037975 GAAGCCCTTACAACGACCGA 60.038 55.0 0.0 0.0 0.0 4.69 R
3004 3679 0.242825 CGGACAGCTTCTTGACGGTA 59.757 55.0 0.0 0.0 0.0 4.02 R
3490 4170 0.468226 TTCGTCATGCCACTATCCCC 59.532 55.0 0.0 0.0 0.0 4.81 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
78 85 2.338257 GCTCGCCTAGCCAGCTAG 59.662 66.667 17.97 17.97 46.25 3.42
79 86 2.338257 CTCGCCTAGCCAGCTAGC 59.662 66.667 19.23 6.62 43.35 3.42
81 88 1.743321 CTCGCCTAGCCAGCTAGCTT 61.743 60.000 16.46 3.11 41.41 3.74
82 89 1.300542 CGCCTAGCCAGCTAGCTTC 60.301 63.158 16.46 10.14 41.41 3.86
83 90 1.070615 GCCTAGCCAGCTAGCTTCC 59.929 63.158 16.46 8.96 41.41 3.46
84 91 1.365633 CCTAGCCAGCTAGCTTCCG 59.634 63.158 16.46 6.68 41.41 4.30
85 92 1.365633 CTAGCCAGCTAGCTTCCGG 59.634 63.158 16.46 14.96 41.41 5.14
161 168 3.179265 GTCCATCCGTGCGTGTCG 61.179 66.667 0.00 0.00 0.00 4.35
291 298 2.870411 GGAGCAACAACTTAACTCGTGT 59.130 45.455 0.00 0.00 0.00 4.49
427 442 0.687354 AGAACAGCCGACAATCCACT 59.313 50.000 0.00 0.00 0.00 4.00
432 447 2.027192 ACAGCCGACAATCCACTTACAT 60.027 45.455 0.00 0.00 0.00 2.29
464 486 5.501715 GTCGGCACATATGATTACTTGTTG 58.498 41.667 10.38 0.00 0.00 3.33
476 498 6.003326 TGATTACTTGTTGTCACACATGGAT 58.997 36.000 0.00 0.00 30.32 3.41
523 545 2.660552 AAGTCAACGACACGGCCG 60.661 61.111 26.86 26.86 34.60 6.13
565 587 3.406361 GCCAGCGTGTGTGTCGAG 61.406 66.667 0.00 0.00 0.00 4.04
566 588 3.406361 CCAGCGTGTGTGTCGAGC 61.406 66.667 0.00 0.00 0.00 5.03
567 589 3.756677 CAGCGTGTGTGTCGAGCG 61.757 66.667 0.00 0.00 0.00 5.03
568 590 3.961197 AGCGTGTGTGTCGAGCGA 61.961 61.111 0.00 0.00 0.00 4.93
597 619 0.956633 ATGTGTGTGCTCCTGCTTTG 59.043 50.000 0.00 0.00 40.48 2.77
604 627 1.168407 TGCTCCTGCTTTGTGAGTGC 61.168 55.000 0.00 0.00 40.48 4.40
645 672 1.373748 GCCGTGTCGCCTTAACTCA 60.374 57.895 0.00 0.00 0.00 3.41
677 704 1.262151 GTGCGCGTTACCAAGAAAGAA 59.738 47.619 8.43 0.00 0.00 2.52
681 708 1.196127 GCGTTACCAAGAAAGAACCCG 59.804 52.381 0.00 0.00 0.00 5.28
683 710 2.477754 CGTTACCAAGAAAGAACCCGTC 59.522 50.000 0.00 0.00 0.00 4.79
687 747 1.202770 CCAAGAAAGAACCCGTCCACT 60.203 52.381 0.00 0.00 0.00 4.00
788 848 2.739913 CGGGTTAACACATGACAATCGT 59.260 45.455 8.90 0.00 0.00 3.73
823 883 8.693120 ATTCGTCGATCCCTATATATATGTGT 57.307 34.615 5.44 0.00 0.00 3.72
902 962 3.491447 GCTTTGTCAAACTCCAAGTGCAT 60.491 43.478 0.00 0.00 0.00 3.96
935 1314 5.202765 TGCAATCTTGAGAGAGAGAGAGAT 58.797 41.667 0.00 0.00 34.85 2.75
943 1322 7.565029 TCTTGAGAGAGAGAGAGATAGAGAGAA 59.435 40.741 0.00 0.00 0.00 2.87
1019 1416 1.463674 ATGTGGCCCTTTTCATCGTC 58.536 50.000 0.00 0.00 0.00 4.20
1020 1417 0.608035 TGTGGCCCTTTTCATCGTCC 60.608 55.000 0.00 0.00 0.00 4.79
1021 1418 0.608035 GTGGCCCTTTTCATCGTCCA 60.608 55.000 0.00 0.00 0.00 4.02
1024 1421 1.534729 GCCCTTTTCATCGTCCACTT 58.465 50.000 0.00 0.00 0.00 3.16
1026 1423 1.732259 CCCTTTTCATCGTCCACTTCG 59.268 52.381 0.00 0.00 0.00 3.79
1039 1436 1.868498 CCACTTCGTCGTTGGCTAAAA 59.132 47.619 0.00 0.00 0.00 1.52
1080 1477 6.164176 CACTCGTAAGTTCTAATTCCACCTT 58.836 40.000 0.00 0.00 31.71 3.50
1082 1479 5.404946 TCGTAAGTTCTAATTCCACCTTCG 58.595 41.667 0.00 0.00 39.48 3.79
1087 1484 4.225267 AGTTCTAATTCCACCTTCGTCCAT 59.775 41.667 0.00 0.00 0.00 3.41
1114 1511 6.020916 GCGACAATTGATTTTCATGATCACTG 60.021 38.462 13.59 0.87 33.51 3.66
1129 1527 4.035091 TGATCACTGGTTTGAGTTTTGACG 59.965 41.667 0.00 0.00 0.00 4.35
1136 1534 7.647715 CACTGGTTTGAGTTTTGACGATAATTT 59.352 33.333 0.00 0.00 0.00 1.82
1164 1565 8.481314 AGCTAGAGATGTCATAGATTGTTTTGA 58.519 33.333 0.00 0.00 0.00 2.69
1167 1568 8.447924 AGAGATGTCATAGATTGTTTTGATGG 57.552 34.615 0.00 0.00 0.00 3.51
1186 1807 1.961394 GGGATCATGCATGCATCAAGT 59.039 47.619 30.07 15.65 33.90 3.16
1221 1842 6.806249 TGAATTAATGTCAATTTCAACTCGGC 59.194 34.615 0.00 0.00 0.00 5.54
1291 1912 0.976641 TGACCTCTGGGATGTCACAC 59.023 55.000 2.46 0.00 33.59 3.82
1301 1922 7.194112 TCTGGGATGTCACACAGAAATAATA 57.806 36.000 0.00 0.00 45.61 0.98
1307 1928 8.519526 GGATGTCACACAGAAATAATACCAAAA 58.480 33.333 0.00 0.00 0.00 2.44
1313 1934 8.455682 CACACAGAAATAATACCAAAATACCGT 58.544 33.333 0.00 0.00 0.00 4.83
1335 1956 6.404293 CCGTGGGAATCAAGTGTTAATTAAGG 60.404 42.308 0.00 0.00 0.00 2.69
1339 1960 6.458342 GGGAATCAAGTGTTAATTAAGGAGCG 60.458 42.308 0.00 0.00 0.00 5.03
1342 1963 4.757657 TCAAGTGTTAATTAAGGAGCGCAA 59.242 37.500 11.47 0.00 0.00 4.85
1344 1965 4.324267 AGTGTTAATTAAGGAGCGCAACT 58.676 39.130 11.47 3.59 0.00 3.16
1346 1967 5.935789 AGTGTTAATTAAGGAGCGCAACTTA 59.064 36.000 11.47 14.80 0.00 2.24
1368 1990 9.588096 ACTTATTACTCAAGGTTTTGAATTCCT 57.412 29.630 2.27 0.00 42.48 3.36
1389 2011 8.974060 TTCCTGTTTTAGAAATATATCGGCTT 57.026 30.769 0.00 0.00 0.00 4.35
1391 2013 7.990886 TCCTGTTTTAGAAATATATCGGCTTGT 59.009 33.333 0.00 0.00 0.00 3.16
1392 2014 9.268268 CCTGTTTTAGAAATATATCGGCTTGTA 57.732 33.333 0.00 0.00 0.00 2.41
1394 2016 9.826574 TGTTTTAGAAATATATCGGCTTGTAGT 57.173 29.630 0.00 0.00 0.00 2.73
1400 2022 9.046296 AGAAATATATCGGCTTGTAGTCTTTTG 57.954 33.333 0.00 0.00 0.00 2.44
1401 2023 7.730364 AATATATCGGCTTGTAGTCTTTTGG 57.270 36.000 0.00 0.00 0.00 3.28
1402 2024 2.178912 TCGGCTTGTAGTCTTTTGGG 57.821 50.000 0.00 0.00 0.00 4.12
1403 2025 1.165270 CGGCTTGTAGTCTTTTGGGG 58.835 55.000 0.00 0.00 0.00 4.96
1404 2026 1.544759 CGGCTTGTAGTCTTTTGGGGT 60.545 52.381 0.00 0.00 0.00 4.95
1405 2027 2.594131 GGCTTGTAGTCTTTTGGGGTT 58.406 47.619 0.00 0.00 0.00 4.11
1406 2028 2.963101 GGCTTGTAGTCTTTTGGGGTTT 59.037 45.455 0.00 0.00 0.00 3.27
1407 2029 3.386726 GGCTTGTAGTCTTTTGGGGTTTT 59.613 43.478 0.00 0.00 0.00 2.43
1408 2030 4.368315 GCTTGTAGTCTTTTGGGGTTTTG 58.632 43.478 0.00 0.00 0.00 2.44
1409 2031 4.142026 GCTTGTAGTCTTTTGGGGTTTTGT 60.142 41.667 0.00 0.00 0.00 2.83
1410 2032 5.625886 GCTTGTAGTCTTTTGGGGTTTTGTT 60.626 40.000 0.00 0.00 0.00 2.83
1411 2033 5.331876 TGTAGTCTTTTGGGGTTTTGTTG 57.668 39.130 0.00 0.00 0.00 3.33
1412 2034 5.017490 TGTAGTCTTTTGGGGTTTTGTTGA 58.983 37.500 0.00 0.00 0.00 3.18
1413 2035 5.659079 TGTAGTCTTTTGGGGTTTTGTTGAT 59.341 36.000 0.00 0.00 0.00 2.57
1414 2036 5.022282 AGTCTTTTGGGGTTTTGTTGATG 57.978 39.130 0.00 0.00 0.00 3.07
1415 2037 3.559655 GTCTTTTGGGGTTTTGTTGATGC 59.440 43.478 0.00 0.00 0.00 3.91
1416 2038 3.454082 TCTTTTGGGGTTTTGTTGATGCT 59.546 39.130 0.00 0.00 0.00 3.79
1417 2039 3.467374 TTTGGGGTTTTGTTGATGCTC 57.533 42.857 0.00 0.00 0.00 4.26
1418 2040 1.337118 TGGGGTTTTGTTGATGCTCC 58.663 50.000 0.00 0.00 0.00 4.70
1419 2041 1.133199 TGGGGTTTTGTTGATGCTCCT 60.133 47.619 0.00 0.00 0.00 3.69
1420 2042 1.546029 GGGGTTTTGTTGATGCTCCTC 59.454 52.381 0.00 0.00 0.00 3.71
1421 2043 1.200020 GGGTTTTGTTGATGCTCCTCG 59.800 52.381 0.00 0.00 0.00 4.63
1422 2044 1.200020 GGTTTTGTTGATGCTCCTCGG 59.800 52.381 0.00 0.00 0.00 4.63
1423 2045 0.881118 TTTTGTTGATGCTCCTCGGC 59.119 50.000 0.00 0.00 0.00 5.54
1424 2046 0.250684 TTTGTTGATGCTCCTCGGCA 60.251 50.000 0.00 0.00 46.63 5.69
1430 2052 4.623814 TGCTCCTCGGCATCTTTG 57.376 55.556 0.00 0.00 37.29 2.77
1431 2053 1.679311 TGCTCCTCGGCATCTTTGT 59.321 52.632 0.00 0.00 37.29 2.83
1432 2054 0.901827 TGCTCCTCGGCATCTTTGTA 59.098 50.000 0.00 0.00 37.29 2.41
1433 2055 1.486310 TGCTCCTCGGCATCTTTGTAT 59.514 47.619 0.00 0.00 37.29 2.29
1434 2056 2.139118 GCTCCTCGGCATCTTTGTATC 58.861 52.381 0.00 0.00 0.00 2.24
1435 2057 2.224161 GCTCCTCGGCATCTTTGTATCT 60.224 50.000 0.00 0.00 0.00 1.98
1436 2058 3.742640 GCTCCTCGGCATCTTTGTATCTT 60.743 47.826 0.00 0.00 0.00 2.40
1437 2059 4.446371 CTCCTCGGCATCTTTGTATCTTT 58.554 43.478 0.00 0.00 0.00 2.52
1438 2060 4.191544 TCCTCGGCATCTTTGTATCTTTG 58.808 43.478 0.00 0.00 0.00 2.77
1439 2061 3.242870 CCTCGGCATCTTTGTATCTTTGC 60.243 47.826 0.00 0.00 0.00 3.68
1440 2062 2.682856 TCGGCATCTTTGTATCTTTGCC 59.317 45.455 1.70 1.70 44.78 4.52
1441 2063 2.684881 CGGCATCTTTGTATCTTTGCCT 59.315 45.455 9.76 0.00 45.78 4.75
1442 2064 3.129287 CGGCATCTTTGTATCTTTGCCTT 59.871 43.478 9.76 0.00 45.78 4.35
1443 2065 4.380867 CGGCATCTTTGTATCTTTGCCTTT 60.381 41.667 9.76 0.00 45.78 3.11
1444 2066 5.482006 GGCATCTTTGTATCTTTGCCTTTT 58.518 37.500 4.56 0.00 44.81 2.27
1445 2067 5.934043 GGCATCTTTGTATCTTTGCCTTTTT 59.066 36.000 4.56 0.00 44.81 1.94
1471 2093 9.477484 TTTTAGTTTTGTTATTTGTGTGTGTGT 57.523 25.926 0.00 0.00 0.00 3.72
1472 2094 6.942886 AGTTTTGTTATTTGTGTGTGTGTG 57.057 33.333 0.00 0.00 0.00 3.82
1473 2095 5.347364 AGTTTTGTTATTTGTGTGTGTGTGC 59.653 36.000 0.00 0.00 0.00 4.57
1474 2096 4.710423 TTGTTATTTGTGTGTGTGTGCT 57.290 36.364 0.00 0.00 0.00 4.40
1475 2097 4.026293 TGTTATTTGTGTGTGTGTGCTG 57.974 40.909 0.00 0.00 0.00 4.41
1476 2098 2.772568 TATTTGTGTGTGTGTGCTGC 57.227 45.000 0.00 0.00 0.00 5.25
1477 2099 0.248580 ATTTGTGTGTGTGTGCTGCG 60.249 50.000 0.00 0.00 0.00 5.18
1478 2100 1.581727 TTTGTGTGTGTGTGCTGCGT 61.582 50.000 0.00 0.00 0.00 5.24
1479 2101 1.581727 TTGTGTGTGTGTGCTGCGTT 61.582 50.000 0.00 0.00 0.00 4.84
1480 2102 1.297598 GTGTGTGTGTGCTGCGTTC 60.298 57.895 0.00 0.00 0.00 3.95
1481 2103 1.449423 TGTGTGTGTGCTGCGTTCT 60.449 52.632 0.00 0.00 0.00 3.01
1482 2104 0.179097 TGTGTGTGTGCTGCGTTCTA 60.179 50.000 0.00 0.00 0.00 2.10
1483 2105 1.148310 GTGTGTGTGCTGCGTTCTAT 58.852 50.000 0.00 0.00 0.00 1.98
1484 2106 1.126846 GTGTGTGTGCTGCGTTCTATC 59.873 52.381 0.00 0.00 0.00 2.08
1485 2107 0.366871 GTGTGTGCTGCGTTCTATCG 59.633 55.000 0.00 0.00 0.00 2.92
1486 2108 0.735978 TGTGTGCTGCGTTCTATCGG 60.736 55.000 0.00 0.00 0.00 4.18
1487 2109 0.736325 GTGTGCTGCGTTCTATCGGT 60.736 55.000 0.00 0.00 0.00 4.69
1488 2110 0.457853 TGTGCTGCGTTCTATCGGTC 60.458 55.000 0.00 0.00 0.00 4.79
1489 2111 1.226575 TGCTGCGTTCTATCGGTCG 60.227 57.895 0.00 0.00 0.00 4.79
1490 2112 1.226603 GCTGCGTTCTATCGGTCGT 60.227 57.895 0.00 0.00 0.00 4.34
1491 2113 0.801067 GCTGCGTTCTATCGGTCGTT 60.801 55.000 0.00 0.00 0.00 3.85
1492 2114 0.914551 CTGCGTTCTATCGGTCGTTG 59.085 55.000 0.00 0.00 0.00 4.10
1493 2115 0.241749 TGCGTTCTATCGGTCGTTGT 59.758 50.000 0.00 0.00 0.00 3.32
1494 2116 1.468127 TGCGTTCTATCGGTCGTTGTA 59.532 47.619 0.00 0.00 0.00 2.41
1495 2117 2.095314 TGCGTTCTATCGGTCGTTGTAA 60.095 45.455 0.00 0.00 0.00 2.41
1496 2118 2.529090 GCGTTCTATCGGTCGTTGTAAG 59.471 50.000 0.00 0.00 0.00 2.34
1497 2119 3.103738 CGTTCTATCGGTCGTTGTAAGG 58.896 50.000 0.00 0.00 0.00 2.69
1498 2120 3.442100 GTTCTATCGGTCGTTGTAAGGG 58.558 50.000 0.00 0.00 0.00 3.95
1499 2121 1.406539 TCTATCGGTCGTTGTAAGGGC 59.593 52.381 0.00 0.00 0.00 5.19
1500 2122 1.407979 CTATCGGTCGTTGTAAGGGCT 59.592 52.381 0.00 0.00 0.00 5.19
1501 2123 0.611714 ATCGGTCGTTGTAAGGGCTT 59.388 50.000 0.00 0.00 0.00 4.35
1502 2124 0.037975 TCGGTCGTTGTAAGGGCTTC 60.038 55.000 0.00 0.00 0.00 3.86
1503 2125 0.320073 CGGTCGTTGTAAGGGCTTCA 60.320 55.000 0.00 0.00 0.00 3.02
1504 2126 1.674817 CGGTCGTTGTAAGGGCTTCAT 60.675 52.381 0.00 0.00 0.00 2.57
1505 2127 2.433436 GGTCGTTGTAAGGGCTTCATT 58.567 47.619 0.00 0.00 0.00 2.57
1506 2128 3.602483 GGTCGTTGTAAGGGCTTCATTA 58.398 45.455 0.00 0.00 0.00 1.90
1507 2129 4.004982 GGTCGTTGTAAGGGCTTCATTAA 58.995 43.478 0.00 0.00 0.00 1.40
1508 2130 4.638865 GGTCGTTGTAAGGGCTTCATTAAT 59.361 41.667 0.00 0.00 0.00 1.40
1509 2131 5.124936 GGTCGTTGTAAGGGCTTCATTAATT 59.875 40.000 0.00 0.00 0.00 1.40
1510 2132 6.349860 GGTCGTTGTAAGGGCTTCATTAATTT 60.350 38.462 0.00 0.00 0.00 1.82
1511 2133 7.148205 GGTCGTTGTAAGGGCTTCATTAATTTA 60.148 37.037 0.00 0.00 0.00 1.40
1512 2134 8.238631 GTCGTTGTAAGGGCTTCATTAATTTAA 58.761 33.333 0.00 0.00 0.00 1.52
1513 2135 8.794553 TCGTTGTAAGGGCTTCATTAATTTAAA 58.205 29.630 0.00 0.00 0.00 1.52
1514 2136 9.072294 CGTTGTAAGGGCTTCATTAATTTAAAG 57.928 33.333 0.00 0.00 0.00 1.85
1515 2137 8.869897 GTTGTAAGGGCTTCATTAATTTAAAGC 58.130 33.333 14.41 14.41 42.60 3.51
1519 2141 4.676061 GCTTCATTAATTTAAAGCCGCG 57.324 40.909 0.00 0.00 38.51 6.46
1520 2142 3.061205 GCTTCATTAATTTAAAGCCGCGC 60.061 43.478 0.00 0.00 38.51 6.86
1521 2143 2.710760 TCATTAATTTAAAGCCGCGCG 58.289 42.857 25.67 25.67 0.00 6.86
1522 2144 2.352034 TCATTAATTTAAAGCCGCGCGA 59.648 40.909 34.63 10.01 0.00 5.87
1523 2145 3.002862 TCATTAATTTAAAGCCGCGCGAT 59.997 39.130 34.63 17.40 0.00 4.58
1524 2146 2.376915 TAATTTAAAGCCGCGCGATG 57.623 45.000 34.63 17.45 0.00 3.84
1525 2147 0.248458 AATTTAAAGCCGCGCGATGG 60.248 50.000 34.63 16.59 0.00 3.51
1534 2156 3.577313 GCGCGATGGCCTCCTTTC 61.577 66.667 12.10 0.00 35.02 2.62
1535 2157 2.187946 CGCGATGGCCTCCTTTCT 59.812 61.111 0.00 0.00 35.02 2.52
1536 2158 1.441729 CGCGATGGCCTCCTTTCTA 59.558 57.895 0.00 0.00 35.02 2.10
1537 2159 0.179084 CGCGATGGCCTCCTTTCTAA 60.179 55.000 0.00 0.00 35.02 2.10
1538 2160 1.742411 CGCGATGGCCTCCTTTCTAAA 60.742 52.381 0.00 0.00 35.02 1.85
1539 2161 1.943340 GCGATGGCCTCCTTTCTAAAG 59.057 52.381 3.32 0.00 35.79 1.85
1540 2162 2.420129 GCGATGGCCTCCTTTCTAAAGA 60.420 50.000 3.32 0.00 38.28 2.52
1541 2163 3.873910 CGATGGCCTCCTTTCTAAAGAA 58.126 45.455 3.32 0.00 38.28 2.52
1542 2164 4.261801 CGATGGCCTCCTTTCTAAAGAAA 58.738 43.478 3.32 5.13 41.29 2.52
1543 2165 4.700213 CGATGGCCTCCTTTCTAAAGAAAA 59.300 41.667 3.32 0.00 42.72 2.29
1544 2166 5.183140 CGATGGCCTCCTTTCTAAAGAAAAA 59.817 40.000 3.32 0.00 42.72 1.94
1598 2220 9.301153 ACTAAATTTCAGCAAAACACAGTTAAG 57.699 29.630 0.00 0.00 0.00 1.85
1601 2227 4.893424 TCAGCAAAACACAGTTAAGTCC 57.107 40.909 0.00 0.00 0.00 3.85
1623 2249 4.305769 CGTTTTCATTTCAGCCAATGGAA 58.694 39.130 2.05 0.00 35.22 3.53
1630 2257 3.574284 TTCAGCCAATGGAACGAATTG 57.426 42.857 2.05 0.00 35.26 2.32
1635 2262 2.850321 CCAATGGAACGAATTGTCACG 58.150 47.619 0.00 0.00 33.93 4.35
1644 2271 7.070798 TGGAACGAATTGTCACGTAAATTTAC 58.929 34.615 16.87 16.87 41.87 2.01
1651 2278 9.820229 GAATTGTCACGTAAATTTACATGAGAA 57.180 29.630 28.03 28.03 41.22 2.87
1657 2284 8.033038 TCACGTAAATTTACATGAGAACTAGCT 58.967 33.333 20.06 0.00 31.74 3.32
1731 2364 9.825972 CCGTAATTGCTAAAATATTATGACAGG 57.174 33.333 0.00 0.00 0.00 4.00
1742 2375 8.603242 AAATATTATGACAGGACCGATGTTAC 57.397 34.615 0.00 0.00 0.00 2.50
1788 2432 6.535508 TCCAAGTTTTTGAAAATTTACACCGG 59.464 34.615 0.00 0.00 36.36 5.28
1793 2438 7.820386 AGTTTTTGAAAATTTACACCGGAAGTT 59.180 29.630 9.46 0.00 0.00 2.66
1796 2441 8.859517 TTTGAAAATTTACACCGGAAGTTTAG 57.140 30.769 9.46 0.00 0.00 1.85
1807 2452 3.270877 CGGAAGTTTAGCCATGCTTACT 58.729 45.455 0.00 0.00 40.44 2.24
1810 2460 5.429130 GGAAGTTTAGCCATGCTTACTAGT 58.571 41.667 0.00 0.00 40.44 2.57
1811 2461 6.579865 GGAAGTTTAGCCATGCTTACTAGTA 58.420 40.000 0.00 0.00 40.44 1.82
1842 2492 7.625828 ATGTTACAACCATAAGCTAGAAACC 57.374 36.000 0.00 0.00 0.00 3.27
1844 2494 7.172342 TGTTACAACCATAAGCTAGAAACCAT 58.828 34.615 0.00 0.00 0.00 3.55
1845 2495 8.322828 TGTTACAACCATAAGCTAGAAACCATA 58.677 33.333 0.00 0.00 0.00 2.74
1913 2572 1.176527 CCATGCGTGTTTCCCTGAAT 58.823 50.000 4.96 0.00 0.00 2.57
2160 2835 2.132517 TTGTGCATTGCAGCAGACGG 62.133 55.000 12.53 0.00 46.69 4.79
2163 2838 2.177531 CATTGCAGCAGACGGCAC 59.822 61.111 0.00 0.00 47.00 5.01
2203 2878 3.634568 GATTCGTCATCGTCCATCTCT 57.365 47.619 0.00 0.00 38.33 3.10
2204 2879 3.560503 GATTCGTCATCGTCCATCTCTC 58.439 50.000 0.00 0.00 38.33 3.20
2207 2882 0.312416 GTCATCGTCCATCTCTCCGG 59.688 60.000 0.00 0.00 0.00 5.14
2208 2883 1.006805 CATCGTCCATCTCTCCGGC 60.007 63.158 0.00 0.00 0.00 6.13
2209 2884 1.455773 ATCGTCCATCTCTCCGGCA 60.456 57.895 0.00 0.00 0.00 5.69
2335 3010 0.174617 CGTTCAAGCTCTCCTCCTCC 59.825 60.000 0.00 0.00 0.00 4.30
2422 3097 3.427243 CTCCTACACAATTCTCGACGAC 58.573 50.000 0.00 0.00 0.00 4.34
3121 3796 4.814294 ATCGTTGGGCGCGACCTC 62.814 66.667 34.65 23.51 41.33 3.85
3259 3934 2.444895 GAGGAGGAGTGCGGGGAT 60.445 66.667 0.00 0.00 0.00 3.85
3385 4060 4.129737 CCGTCGCCGTCCACAGAT 62.130 66.667 0.00 0.00 0.00 2.90
3408 4083 1.130186 GACGACGTCCCAAGACTAGTC 59.870 57.143 17.25 15.41 41.16 2.59
3616 5152 1.886542 GGCATTCCTCCGAAAGTGTTT 59.113 47.619 0.00 0.00 0.00 2.83
3725 5262 6.888430 AGCATCTACACGTTTTCTAACTTTG 58.112 36.000 0.00 0.00 31.89 2.77
3737 5274 9.809928 CGTTTTCTAACTTTGTGTAAAATTTCG 57.190 29.630 0.00 0.00 31.89 3.46
3752 5289 1.469335 TTTCGCCCCGAGAAGACACT 61.469 55.000 0.00 0.00 37.14 3.55
3794 5331 5.596836 AGACAAAAATGACTGCTCCAAAA 57.403 34.783 0.00 0.00 0.00 2.44
4134 5790 8.911918 TTGCTAATTCCACTAGTAGAAAACAA 57.088 30.769 7.84 7.35 0.00 2.83
4141 5797 5.995897 TCCACTAGTAGAAAACAAGCCTTTC 59.004 40.000 3.59 0.00 33.75 2.62
4145 5801 3.813724 AGTAGAAAACAAGCCTTTCGTCC 59.186 43.478 0.00 0.00 37.76 4.79
4146 5802 2.650322 AGAAAACAAGCCTTTCGTCCA 58.350 42.857 0.00 0.00 37.76 4.02
4152 5808 1.270550 CAAGCCTTTCGTCCAAAGCAT 59.729 47.619 0.00 0.00 40.40 3.79
4161 5817 1.379527 GTCCAAAGCATTAGTCCCGG 58.620 55.000 0.00 0.00 0.00 5.73
4165 5821 2.886730 AAAGCATTAGTCCCGGCCGG 62.887 60.000 37.99 37.99 0.00 6.13
4208 5864 0.036671 CCACTAGTCCCGGTTCCAAC 60.037 60.000 0.00 0.00 0.00 3.77
4227 5883 1.301322 GGCTAGGAGCGGAAGATGC 60.301 63.158 0.00 0.00 43.62 3.91
4257 5913 3.117474 TCACCTCTAGTCCCGATTCATCT 60.117 47.826 0.00 0.00 0.00 2.90
4285 5941 2.104967 CTAGTCCCGGTTGGTGATACA 58.895 52.381 0.00 0.00 34.77 2.29
4289 5945 1.170442 CCCGGTTGGTGATACAAACC 58.830 55.000 7.98 7.98 34.60 3.27
4296 5952 2.538222 TGGTGATACAAACCGGGACTA 58.462 47.619 6.32 0.00 40.86 2.59
4299 5955 3.937079 GGTGATACAAACCGGGACTAAAG 59.063 47.826 6.32 0.00 0.00 1.85
4301 5957 3.054948 TGATACAAACCGGGACTAAAGGG 60.055 47.826 6.32 0.00 0.00 3.95
4330 5986 4.767255 GCTGGCGTCAGACTGGGG 62.767 72.222 23.78 0.00 43.49 4.96
4331 5987 4.767255 CTGGCGTCAGACTGGGGC 62.767 72.222 12.86 8.19 43.49 5.80
4337 5993 4.980592 TCAGACTGGGGCCCTGCA 62.981 66.667 27.65 11.60 0.00 4.41
4353 6009 3.095347 GCAAGCCCCTCTAGTCCCG 62.095 68.421 0.00 0.00 0.00 5.14
4354 6010 2.764547 AAGCCCCTCTAGTCCCGC 60.765 66.667 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 73 1.365633 CGGAAGCTAGCTGGCTAGG 59.634 63.158 26.06 13.27 44.48 3.02
67 74 1.365633 CCGGAAGCTAGCTGGCTAG 59.634 63.158 26.06 21.27 46.41 3.42
72 79 4.899239 CCGGCCGGAAGCTAGCTG 62.899 72.222 41.82 7.45 43.05 4.24
125 132 2.294233 GACCCAAGTACGTGTCACAGTA 59.706 50.000 8.02 3.95 0.00 2.74
179 186 2.824041 CCATATATGGCGGCCGGC 60.824 66.667 41.79 41.79 41.75 6.13
206 213 1.366111 ATCCATGCGTTTTCGGTCGG 61.366 55.000 0.00 0.00 44.29 4.79
212 219 1.062587 CTGGTCGATCCATGCGTTTTC 59.937 52.381 7.11 0.00 46.12 2.29
235 242 3.181475 TGGCACGATCTATCTCAGGTTTC 60.181 47.826 0.00 0.00 0.00 2.78
427 442 1.072116 GCCGACGTGCGTACATGTAA 61.072 55.000 7.25 0.00 46.14 2.41
432 447 2.197643 TATGTGCCGACGTGCGTACA 62.198 55.000 4.09 0.00 38.77 2.90
464 486 2.980568 TCCGGTAAATCCATGTGTGAC 58.019 47.619 0.00 0.00 35.57 3.67
476 498 1.621814 AGCTAGCACAGTTCCGGTAAA 59.378 47.619 18.83 0.00 0.00 2.01
523 545 3.919973 CTGTGCCGTGCCATTTGCC 62.920 63.158 0.00 0.00 40.16 4.52
555 577 0.858583 CAACATTCGCTCGACACACA 59.141 50.000 0.00 0.00 0.00 3.72
556 578 0.859232 ACAACATTCGCTCGACACAC 59.141 50.000 0.00 0.00 0.00 3.82
558 580 2.055838 TGTACAACATTCGCTCGACAC 58.944 47.619 0.00 0.00 0.00 3.67
560 582 2.666508 ACATGTACAACATTCGCTCGAC 59.333 45.455 0.00 0.00 36.53 4.20
561 583 2.666022 CACATGTACAACATTCGCTCGA 59.334 45.455 0.00 0.00 36.53 4.04
562 584 2.411748 ACACATGTACAACATTCGCTCG 59.588 45.455 0.00 0.00 36.53 5.03
563 585 3.186409 ACACACATGTACAACATTCGCTC 59.814 43.478 0.00 0.00 36.53 5.03
564 586 3.058983 CACACACATGTACAACATTCGCT 60.059 43.478 0.00 0.00 36.53 4.93
565 587 3.225548 CACACACATGTACAACATTCGC 58.774 45.455 0.00 0.00 36.53 4.70
566 588 3.058983 AGCACACACATGTACAACATTCG 60.059 43.478 0.00 0.00 36.53 3.34
567 589 4.466828 GAGCACACACATGTACAACATTC 58.533 43.478 0.00 0.00 36.53 2.67
568 590 3.253188 GGAGCACACACATGTACAACATT 59.747 43.478 0.00 0.00 36.53 2.71
604 627 1.331756 GCACATGGATGTAAAGCGGAG 59.668 52.381 0.00 0.00 39.39 4.63
645 672 0.383949 ACGCGCACACAAAAGGAAAT 59.616 45.000 5.73 0.00 0.00 2.17
677 704 3.264964 ACATAAATGGTAAGTGGACGGGT 59.735 43.478 0.00 0.00 0.00 5.28
681 708 7.865706 ATGAAGACATAAATGGTAAGTGGAC 57.134 36.000 0.00 0.00 34.71 4.02
683 710 8.279970 TGAATGAAGACATAAATGGTAAGTGG 57.720 34.615 0.00 0.00 35.50 4.00
799 859 7.771826 TCACACATATATATAGGGATCGACGAA 59.228 37.037 0.00 0.00 0.00 3.85
800 860 7.277396 TCACACATATATATAGGGATCGACGA 58.723 38.462 9.10 0.00 0.00 4.20
803 863 7.004691 CCCTCACACATATATATAGGGATCGA 58.995 42.308 17.71 0.00 44.18 3.59
823 883 1.971149 AGATGAATGTGACCCCCTCA 58.029 50.000 0.00 0.00 0.00 3.86
861 921 0.240945 CCCGGTGAGCAACAAATGTC 59.759 55.000 0.00 0.00 0.00 3.06
867 927 2.192861 CAAAGCCCGGTGAGCAACA 61.193 57.895 0.00 0.00 0.00 3.33
902 962 9.525826 TCTCTCTCAAGATTGCAGATGTATATA 57.474 33.333 0.00 0.00 0.00 0.86
935 1314 5.604650 GGGGGAATCTTCAATCTTCTCTCTA 59.395 44.000 0.00 0.00 0.00 2.43
943 1322 2.139382 GGGAGGGGGAATCTTCAATCT 58.861 52.381 0.00 0.00 0.00 2.40
978 1375 9.309516 CACATTTGATCAAATCCCTCAAATTAG 57.690 33.333 27.08 15.28 43.51 1.73
1020 1417 4.834394 TGGTTTTAGCCAACGACGAAGTG 61.834 47.826 0.00 0.00 36.66 3.16
1021 1418 2.742530 TGGTTTTAGCCAACGACGAAGT 60.743 45.455 0.00 0.00 38.81 3.01
1024 1421 1.801771 CATGGTTTTAGCCAACGACGA 59.198 47.619 0.00 0.00 42.48 4.20
1026 1423 3.636282 AACATGGTTTTAGCCAACGAC 57.364 42.857 0.00 0.00 42.48 4.34
1039 1436 1.094785 GTGCCGATGCTAAACATGGT 58.905 50.000 0.00 0.00 39.84 3.55
1055 1452 4.329256 GGTGGAATTAGAACTTACGAGTGC 59.671 45.833 0.00 0.00 35.91 4.40
1080 1477 1.802069 TCAATTGTCGCAATGGACGA 58.198 45.000 5.13 0.00 39.83 4.20
1082 1479 4.922692 TGAAAATCAATTGTCGCAATGGAC 59.077 37.500 5.13 1.96 37.45 4.02
1087 1484 6.308524 GTGATCATGAAAATCAATTGTCGCAA 59.691 34.615 5.13 0.00 35.04 4.85
1114 1511 8.635983 GCTAAAATTATCGTCAAAACTCAAACC 58.364 33.333 0.00 0.00 0.00 3.27
1164 1565 2.302587 TGATGCATGCATGATCCCAT 57.697 45.000 36.73 21.83 36.70 4.00
1166 1567 1.961394 ACTTGATGCATGCATGATCCC 59.039 47.619 36.73 21.77 36.70 3.85
1167 1568 2.885266 AGACTTGATGCATGCATGATCC 59.115 45.455 36.73 22.14 36.70 3.36
1186 1807 9.906660 AAATTGACATTAATTCAAGCGTAAAGA 57.093 25.926 14.26 0.00 36.44 2.52
1200 1821 4.452795 TCGCCGAGTTGAAATTGACATTAA 59.547 37.500 0.00 0.00 0.00 1.40
1246 1867 0.723981 GCTCATTGCAACCTCTCGAC 59.276 55.000 0.00 0.00 42.31 4.20
1253 1874 2.480555 CCGACGCTCATTGCAACC 59.519 61.111 0.00 0.00 43.06 3.77
1269 1890 0.909610 TGACATCCCAGAGGTCACCC 60.910 60.000 7.91 0.00 46.08 4.61
1281 1902 7.624360 TTGGTATTATTTCTGTGTGACATCC 57.376 36.000 0.00 0.00 0.00 3.51
1291 1912 7.283580 TCCCACGGTATTTTGGTATTATTTCTG 59.716 37.037 0.00 0.00 0.00 3.02
1301 1922 3.443145 TGATTCCCACGGTATTTTGGT 57.557 42.857 0.00 0.00 0.00 3.67
1307 1928 3.713826 AACACTTGATTCCCACGGTAT 57.286 42.857 0.00 0.00 0.00 2.73
1313 1934 6.377146 GCTCCTTAATTAACACTTGATTCCCA 59.623 38.462 0.00 0.00 0.00 4.37
1335 1956 3.933332 ACCTTGAGTAATAAGTTGCGCTC 59.067 43.478 9.73 1.40 0.00 5.03
1339 1960 9.476202 AATTCAAAACCTTGAGTAATAAGTTGC 57.524 29.630 0.00 0.00 42.48 4.17
1342 1963 9.588096 AGGAATTCAAAACCTTGAGTAATAAGT 57.412 29.630 7.93 0.00 42.48 2.24
1344 1965 9.362151 ACAGGAATTCAAAACCTTGAGTAATAA 57.638 29.630 7.93 0.00 42.48 1.40
1346 1967 7.839680 ACAGGAATTCAAAACCTTGAGTAAT 57.160 32.000 7.93 0.00 42.48 1.89
1368 1990 9.826574 ACTACAAGCCGATATATTTCTAAAACA 57.173 29.630 0.00 0.00 0.00 2.83
1386 2008 4.142026 ACAAAACCCCAAAAGACTACAAGC 60.142 41.667 0.00 0.00 0.00 4.01
1389 2011 5.017490 TCAACAAAACCCCAAAAGACTACA 58.983 37.500 0.00 0.00 0.00 2.74
1391 2013 5.452636 GCATCAACAAAACCCCAAAAGACTA 60.453 40.000 0.00 0.00 0.00 2.59
1392 2014 4.683129 GCATCAACAAAACCCCAAAAGACT 60.683 41.667 0.00 0.00 0.00 3.24
1393 2015 3.559655 GCATCAACAAAACCCCAAAAGAC 59.440 43.478 0.00 0.00 0.00 3.01
1394 2016 3.454082 AGCATCAACAAAACCCCAAAAGA 59.546 39.130 0.00 0.00 0.00 2.52
1395 2017 3.807553 AGCATCAACAAAACCCCAAAAG 58.192 40.909 0.00 0.00 0.00 2.27
1396 2018 3.432890 GGAGCATCAACAAAACCCCAAAA 60.433 43.478 0.00 0.00 36.25 2.44
1397 2019 2.103941 GGAGCATCAACAAAACCCCAAA 59.896 45.455 0.00 0.00 36.25 3.28
1398 2020 1.691434 GGAGCATCAACAAAACCCCAA 59.309 47.619 0.00 0.00 36.25 4.12
1399 2021 1.133199 AGGAGCATCAACAAAACCCCA 60.133 47.619 0.00 0.00 36.25 4.96
1400 2022 1.546029 GAGGAGCATCAACAAAACCCC 59.454 52.381 0.00 0.00 36.25 4.95
1401 2023 1.200020 CGAGGAGCATCAACAAAACCC 59.800 52.381 0.00 0.00 36.25 4.11
1402 2024 1.200020 CCGAGGAGCATCAACAAAACC 59.800 52.381 0.00 0.00 36.25 3.27
1403 2025 1.401539 GCCGAGGAGCATCAACAAAAC 60.402 52.381 0.00 0.00 36.25 2.43
1404 2026 0.881118 GCCGAGGAGCATCAACAAAA 59.119 50.000 0.00 0.00 36.25 2.44
1405 2027 0.250684 TGCCGAGGAGCATCAACAAA 60.251 50.000 0.00 0.00 38.00 2.83
1406 2028 1.374568 TGCCGAGGAGCATCAACAA 59.625 52.632 0.00 0.00 38.00 2.83
1407 2029 3.067985 TGCCGAGGAGCATCAACA 58.932 55.556 0.00 0.00 38.00 3.33
1414 2036 2.139118 GATACAAAGATGCCGAGGAGC 58.861 52.381 0.00 0.00 0.00 4.70
1415 2037 3.742433 AGATACAAAGATGCCGAGGAG 57.258 47.619 0.00 0.00 0.00 3.69
1416 2038 4.191544 CAAAGATACAAAGATGCCGAGGA 58.808 43.478 0.00 0.00 0.00 3.71
1417 2039 3.242870 GCAAAGATACAAAGATGCCGAGG 60.243 47.826 0.00 0.00 0.00 4.63
1418 2040 3.242870 GGCAAAGATACAAAGATGCCGAG 60.243 47.826 0.00 0.00 43.26 4.63
1419 2041 2.682856 GGCAAAGATACAAAGATGCCGA 59.317 45.455 0.00 0.00 43.26 5.54
1420 2042 3.070429 GGCAAAGATACAAAGATGCCG 57.930 47.619 0.00 0.00 43.26 5.69
1445 2067 9.477484 ACACACACACAAATAACAAAACTAAAA 57.523 25.926 0.00 0.00 0.00 1.52
1446 2068 8.916654 CACACACACACAAATAACAAAACTAAA 58.083 29.630 0.00 0.00 0.00 1.85
1447 2069 7.062371 GCACACACACACAAATAACAAAACTAA 59.938 33.333 0.00 0.00 0.00 2.24
1448 2070 6.528423 GCACACACACACAAATAACAAAACTA 59.472 34.615 0.00 0.00 0.00 2.24
1449 2071 5.347364 GCACACACACACAAATAACAAAACT 59.653 36.000 0.00 0.00 0.00 2.66
1450 2072 5.347364 AGCACACACACACAAATAACAAAAC 59.653 36.000 0.00 0.00 0.00 2.43
1451 2073 5.347093 CAGCACACACACACAAATAACAAAA 59.653 36.000 0.00 0.00 0.00 2.44
1452 2074 4.861462 CAGCACACACACACAAATAACAAA 59.139 37.500 0.00 0.00 0.00 2.83
1453 2075 4.419280 CAGCACACACACACAAATAACAA 58.581 39.130 0.00 0.00 0.00 2.83
1454 2076 3.733380 GCAGCACACACACACAAATAACA 60.733 43.478 0.00 0.00 0.00 2.41
1455 2077 2.788786 GCAGCACACACACACAAATAAC 59.211 45.455 0.00 0.00 0.00 1.89
1456 2078 2.540565 CGCAGCACACACACACAAATAA 60.541 45.455 0.00 0.00 0.00 1.40
1457 2079 1.003008 CGCAGCACACACACACAAATA 60.003 47.619 0.00 0.00 0.00 1.40
1458 2080 0.248580 CGCAGCACACACACACAAAT 60.249 50.000 0.00 0.00 0.00 2.32
1459 2081 1.136356 CGCAGCACACACACACAAA 59.864 52.632 0.00 0.00 0.00 2.83
1460 2082 1.581727 AACGCAGCACACACACACAA 61.582 50.000 0.00 0.00 0.00 3.33
1461 2083 1.976478 GAACGCAGCACACACACACA 61.976 55.000 0.00 0.00 0.00 3.72
1462 2084 1.297598 GAACGCAGCACACACACAC 60.298 57.895 0.00 0.00 0.00 3.82
1463 2085 0.179097 TAGAACGCAGCACACACACA 60.179 50.000 0.00 0.00 0.00 3.72
1464 2086 1.126846 GATAGAACGCAGCACACACAC 59.873 52.381 0.00 0.00 0.00 3.82
1465 2087 1.428448 GATAGAACGCAGCACACACA 58.572 50.000 0.00 0.00 0.00 3.72
1466 2088 0.366871 CGATAGAACGCAGCACACAC 59.633 55.000 0.00 0.00 39.76 3.82
1467 2089 0.735978 CCGATAGAACGCAGCACACA 60.736 55.000 0.00 0.00 39.76 3.72
1468 2090 0.736325 ACCGATAGAACGCAGCACAC 60.736 55.000 0.00 0.00 39.76 3.82
1469 2091 0.457853 GACCGATAGAACGCAGCACA 60.458 55.000 0.00 0.00 39.76 4.57
1470 2092 1.472276 CGACCGATAGAACGCAGCAC 61.472 60.000 0.00 0.00 39.76 4.40
1471 2093 1.226575 CGACCGATAGAACGCAGCA 60.227 57.895 0.00 0.00 39.76 4.41
1472 2094 0.801067 AACGACCGATAGAACGCAGC 60.801 55.000 0.00 0.00 37.79 5.25
1473 2095 0.914551 CAACGACCGATAGAACGCAG 59.085 55.000 0.00 0.00 37.79 5.18
1474 2096 0.241749 ACAACGACCGATAGAACGCA 59.758 50.000 0.00 0.00 37.79 5.24
1475 2097 2.178474 TACAACGACCGATAGAACGC 57.822 50.000 0.00 0.00 37.79 4.84
1476 2098 3.103738 CCTTACAACGACCGATAGAACG 58.896 50.000 0.00 0.00 39.44 3.95
1477 2099 3.442100 CCCTTACAACGACCGATAGAAC 58.558 50.000 0.00 0.00 39.76 3.01
1478 2100 2.159198 GCCCTTACAACGACCGATAGAA 60.159 50.000 0.00 0.00 39.76 2.10
1479 2101 1.406539 GCCCTTACAACGACCGATAGA 59.593 52.381 0.00 0.00 39.76 1.98
1480 2102 1.407979 AGCCCTTACAACGACCGATAG 59.592 52.381 0.00 0.00 0.00 2.08
1481 2103 1.477553 AGCCCTTACAACGACCGATA 58.522 50.000 0.00 0.00 0.00 2.92
1482 2104 0.611714 AAGCCCTTACAACGACCGAT 59.388 50.000 0.00 0.00 0.00 4.18
1483 2105 0.037975 GAAGCCCTTACAACGACCGA 60.038 55.000 0.00 0.00 0.00 4.69
1484 2106 0.320073 TGAAGCCCTTACAACGACCG 60.320 55.000 0.00 0.00 0.00 4.79
1485 2107 2.109425 ATGAAGCCCTTACAACGACC 57.891 50.000 0.00 0.00 0.00 4.79
1486 2108 5.813080 ATTAATGAAGCCCTTACAACGAC 57.187 39.130 0.00 0.00 0.00 4.34
1487 2109 6.827586 AAATTAATGAAGCCCTTACAACGA 57.172 33.333 0.00 0.00 0.00 3.85
1488 2110 8.973835 TTTAAATTAATGAAGCCCTTACAACG 57.026 30.769 0.00 0.00 0.00 4.10
1489 2111 8.869897 GCTTTAAATTAATGAAGCCCTTACAAC 58.130 33.333 15.39 0.00 38.78 3.32
1490 2112 8.996024 GCTTTAAATTAATGAAGCCCTTACAA 57.004 30.769 15.39 0.00 38.78 2.41
1498 2120 3.061205 GCGCGGCTTTAAATTAATGAAGC 60.061 43.478 8.83 16.95 42.76 3.86
1499 2121 3.177643 CGCGCGGCTTTAAATTAATGAAG 59.822 43.478 24.84 0.00 0.00 3.02
1500 2122 3.102276 CGCGCGGCTTTAAATTAATGAA 58.898 40.909 24.84 0.00 0.00 2.57
1501 2123 2.352034 TCGCGCGGCTTTAAATTAATGA 59.648 40.909 31.69 0.31 0.00 2.57
1502 2124 2.710760 TCGCGCGGCTTTAAATTAATG 58.289 42.857 31.69 0.00 0.00 1.90
1503 2125 3.296628 CATCGCGCGGCTTTAAATTAAT 58.703 40.909 31.69 8.29 0.00 1.40
1504 2126 2.539953 CCATCGCGCGGCTTTAAATTAA 60.540 45.455 31.69 5.82 0.00 1.40
1505 2127 1.003331 CCATCGCGCGGCTTTAAATTA 60.003 47.619 31.69 6.44 0.00 1.40
1506 2128 0.248458 CCATCGCGCGGCTTTAAATT 60.248 50.000 31.69 0.67 0.00 1.82
1507 2129 1.355210 CCATCGCGCGGCTTTAAAT 59.645 52.632 31.69 11.39 0.00 1.40
1508 2130 2.788581 CCATCGCGCGGCTTTAAA 59.211 55.556 31.69 9.10 0.00 1.52
1509 2131 3.871574 GCCATCGCGCGGCTTTAA 61.872 61.111 31.69 9.99 46.56 1.52
1517 2139 2.644555 TAGAAAGGAGGCCATCGCGC 62.645 60.000 5.01 0.00 35.02 6.86
1518 2140 0.179084 TTAGAAAGGAGGCCATCGCG 60.179 55.000 5.01 0.00 35.02 5.87
1519 2141 1.943340 CTTTAGAAAGGAGGCCATCGC 59.057 52.381 5.01 0.00 32.40 4.58
1520 2142 3.543680 TCTTTAGAAAGGAGGCCATCG 57.456 47.619 5.01 0.00 36.67 3.84
1521 2143 6.590234 TTTTTCTTTAGAAAGGAGGCCATC 57.410 37.500 5.01 0.00 43.90 3.51
1556 2178 6.327279 AATTTAGTAATTTCGGCTATGGCC 57.673 37.500 10.66 10.66 41.76 5.36
1575 2197 7.277760 GGACTTAACTGTGTTTTGCTGAAATTT 59.722 33.333 0.00 0.00 0.00 1.82
1584 2206 6.087522 TGAAAACGGACTTAACTGTGTTTTG 58.912 36.000 5.70 0.00 39.01 2.44
1589 2211 6.491394 TGAAATGAAAACGGACTTAACTGTG 58.509 36.000 0.00 0.00 0.00 3.66
1591 2213 5.625311 GCTGAAATGAAAACGGACTTAACTG 59.375 40.000 0.00 0.00 0.00 3.16
1593 2215 4.915667 GGCTGAAATGAAAACGGACTTAAC 59.084 41.667 0.00 0.00 0.00 2.01
1596 2218 2.955660 TGGCTGAAATGAAAACGGACTT 59.044 40.909 0.00 0.00 0.00 3.01
1598 2220 3.363341 TTGGCTGAAATGAAAACGGAC 57.637 42.857 0.00 0.00 0.00 4.79
1601 2227 3.911868 TCCATTGGCTGAAATGAAAACG 58.088 40.909 0.00 0.00 39.46 3.60
1721 2354 5.871396 AGTAACATCGGTCCTGTCATAAT 57.129 39.130 0.00 0.00 0.00 1.28
1768 2410 7.528481 ACTTCCGGTGTAAATTTTCAAAAAC 57.472 32.000 0.00 0.00 0.00 2.43
1776 2420 4.828387 TGGCTAAACTTCCGGTGTAAATTT 59.172 37.500 0.00 0.00 0.00 1.82
1788 2432 8.488651 TTTACTAGTAAGCATGGCTAAACTTC 57.511 34.615 14.73 0.00 38.25 3.01
1793 2438 9.681062 ATTTTCTTTACTAGTAAGCATGGCTAA 57.319 29.630 14.73 4.63 38.25 3.09
1796 2441 7.762382 ACATTTTCTTTACTAGTAAGCATGGC 58.238 34.615 14.73 0.00 0.00 4.40
1845 2495 9.004717 GCTCTCTCTTTTGGTAAATCTAGTTTT 57.995 33.333 4.30 4.30 0.00 2.43
1860 2510 4.348168 TCAAACCCTGTAGCTCTCTCTTTT 59.652 41.667 0.00 0.00 0.00 2.27
2002 2661 0.796927 GCGACTTTTGGGAGCACTAC 59.203 55.000 0.00 0.00 0.00 2.73
2147 2822 3.425713 CGTGCCGTCTGCTGCAAT 61.426 61.111 3.02 0.00 42.00 3.56
2160 2835 1.817099 CTGCTTCCCTCCATCGTGC 60.817 63.158 0.00 0.00 0.00 5.34
2163 2838 1.523258 CTGCTGCTTCCCTCCATCG 60.523 63.158 0.00 0.00 0.00 3.84
2170 2845 2.817423 CGAATCGCTGCTGCTTCCC 61.817 63.158 14.03 0.11 36.97 3.97
2173 2848 0.742281 ATGACGAATCGCTGCTGCTT 60.742 50.000 14.03 1.75 36.97 3.91
2183 2858 3.560503 GAGAGATGGACGATGACGAATC 58.439 50.000 0.00 0.00 42.66 2.52
2184 2859 2.294791 GGAGAGATGGACGATGACGAAT 59.705 50.000 0.00 0.00 42.66 3.34
2185 2860 1.676529 GGAGAGATGGACGATGACGAA 59.323 52.381 0.00 0.00 42.66 3.85
2191 2866 1.455773 TGCCGGAGAGATGGACGAT 60.456 57.895 5.05 0.00 0.00 3.73
2194 2869 2.501610 GGTGCCGGAGAGATGGAC 59.498 66.667 5.05 0.00 0.00 4.02
2195 2870 3.147595 CGGTGCCGGAGAGATGGA 61.148 66.667 5.05 0.00 35.56 3.41
2196 2871 4.899239 GCGGTGCCGGAGAGATGG 62.899 72.222 5.05 0.00 40.19 3.51
2197 2872 4.899239 GGCGGTGCCGGAGAGATG 62.899 72.222 5.05 0.00 39.62 2.90
2422 3097 2.103934 CTCGGCTCCAGCTCGAAG 59.896 66.667 11.57 4.94 40.91 3.79
3004 3679 0.242825 CGGACAGCTTCTTGACGGTA 59.757 55.000 0.00 0.00 0.00 4.02
3408 4083 6.316390 AGCGTCTTATTTCTCCACTAAAATGG 59.684 38.462 0.00 0.00 41.57 3.16
3490 4170 0.468226 TTCGTCATGCCACTATCCCC 59.532 55.000 0.00 0.00 0.00 4.81
3681 5218 8.684520 AGATGCTCATCTAAAGAAAGATTTTGG 58.315 33.333 10.42 0.00 45.69 3.28
3725 5262 2.078392 TCTCGGGGCGAAATTTTACAC 58.922 47.619 0.00 0.00 34.74 2.90
3737 5274 1.255667 TACCAGTGTCTTCTCGGGGC 61.256 60.000 0.00 0.00 0.00 5.80
3752 5289 2.719531 TTTTGCACACACCTCTACCA 57.280 45.000 0.00 0.00 0.00 3.25
3828 5365 4.290093 AGACATATGTGGAGGCTTCTACA 58.710 43.478 17.16 17.16 46.88 2.74
3832 5369 3.879892 GGAAAGACATATGTGGAGGCTTC 59.120 47.826 14.43 6.39 0.00 3.86
3939 5595 7.085797 GCACATGCATCAATAGTAAATTTCG 57.914 36.000 0.00 0.00 41.59 3.46
4134 5790 1.620822 AATGCTTTGGACGAAAGGCT 58.379 45.000 11.35 0.00 41.41 4.58
4141 5797 1.006832 CGGGACTAATGCTTTGGACG 58.993 55.000 2.60 1.34 0.00 4.79
4145 5801 1.714899 CGGCCGGGACTAATGCTTTG 61.715 60.000 20.10 0.00 0.00 2.77
4146 5802 1.451387 CGGCCGGGACTAATGCTTT 60.451 57.895 20.10 0.00 0.00 3.51
4199 5855 1.153628 CTCCTAGCCGTTGGAACCG 60.154 63.158 0.00 0.00 31.23 4.44
4200 5856 1.449778 GCTCCTAGCCGTTGGAACC 60.450 63.158 0.00 0.00 34.48 3.62
4208 5864 1.006805 CATCTTCCGCTCCTAGCCG 60.007 63.158 0.00 0.00 38.18 5.52
4227 5883 0.526662 GACTAGAGGTGACCGTGTGG 59.473 60.000 0.00 0.00 42.84 4.17
4285 5941 0.773305 ACCCCCTTTAGTCCCGGTTT 60.773 55.000 0.00 0.00 0.00 3.27
4289 5945 1.921857 ACCACCCCCTTTAGTCCCG 60.922 63.158 0.00 0.00 0.00 5.14
4296 5952 3.914713 CCTGCCACCACCCCCTTT 61.915 66.667 0.00 0.00 0.00 3.11
4330 5986 3.411517 TAGAGGGGCTTGCAGGGC 61.412 66.667 14.52 14.52 0.00 5.19
4331 5987 1.977293 GACTAGAGGGGCTTGCAGGG 61.977 65.000 0.00 0.00 0.00 4.45
4337 5993 2.764547 GCGGGACTAGAGGGGCTT 60.765 66.667 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.