Multiple sequence alignment - TraesCS3A01G028300

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 TraesCS3A01G028300 chr3A 100.000 4584 0 0 1 4584 15085528 15090111 0.000000e+00 8466.0
1 TraesCS3A01G028300 chr3A 100.000 30 0 0 1557 1586 583696386 583696415 6.410000e-04 56.5
2 TraesCS3A01G028300 chr3D 91.308 2531 126 38 1796 4267 6014957 6012462 0.000000e+00 3369.0
3 TraesCS3A01G028300 chr3D 89.143 1354 82 30 37 1372 6016347 6015041 0.000000e+00 1626.0
4 TraesCS3A01G028300 chr3D 95.238 189 9 0 4396 4584 6012220 6012032 2.680000e-77 300.0
5 TraesCS3A01G028300 chr3B 86.270 1981 160 52 2536 4433 7609859 7611810 0.000000e+00 2049.0
6 TraesCS3A01G028300 chr3B 89.851 1547 106 20 1 1530 7606841 7608353 0.000000e+00 1940.0
7 TraesCS3A01G028300 chr3B 90.043 934 54 15 1617 2520 7608855 7609779 0.000000e+00 1173.0
8 TraesCS3A01G028300 chr3B 90.090 222 16 2 4368 4584 458275094 458274874 2.700000e-72 283.0
9 TraesCS3A01G028300 chr3B 87.215 219 22 2 4364 4577 143588456 143588673 1.270000e-60 244.0
10 TraesCS3A01G028300 chr3B 94.118 51 3 0 1578 1628 7608352 7608402 1.370000e-10 78.7
11 TraesCS3A01G028300 chr1A 88.496 226 19 3 4364 4584 514892619 514892842 2.720000e-67 267.0
12 TraesCS3A01G028300 chr1A 88.496 226 19 3 4364 4584 515148884 515149107 2.720000e-67 267.0
13 TraesCS3A01G028300 chr7A 87.556 225 22 2 4364 4583 151765296 151765073 5.890000e-64 255.0
14 TraesCS3A01G028300 chr7A 94.286 35 2 0 1557 1591 505686058 505686024 2.000000e-03 54.7
15 TraesCS3A01G028300 chr5D 87.727 220 21 2 4364 4578 171683699 171683917 7.610000e-63 252.0
16 TraesCS3A01G028300 chr4B 86.784 227 21 5 4364 4583 659670618 659670394 1.270000e-60 244.0
17 TraesCS3A01G028300 chr4B 96.875 32 1 0 1557 1588 332155534 332155503 2.000000e-03 54.7
18 TraesCS3A01G028300 chr2A 86.726 226 22 3 4364 4584 720970921 720971143 1.270000e-60 244.0
19 TraesCS3A01G028300 chr2A 100.000 28 0 0 1557 1584 703977696 703977723 8.000000e-03 52.8
20 TraesCS3A01G028300 chr1D 97.143 35 1 0 1557 1591 301353567 301353601 4.950000e-05 60.2
21 TraesCS3A01G028300 chr1D 100.000 29 0 0 1557 1585 208240398 208240426 2.000000e-03 54.7
22 TraesCS3A01G028300 chr7D 100.000 29 0 0 1557 1585 141292110 141292082 2.000000e-03 54.7
23 TraesCS3A01G028300 chr6D 100.000 29 0 0 1557 1585 363038140 363038168 2.000000e-03 54.7
24 TraesCS3A01G028300 chr6D 96.774 31 1 0 1557 1587 5831521 5831491 8.000000e-03 52.8
25 TraesCS3A01G028300 chr2D 100.000 28 0 0 1529 1556 182128131 182128158 8.000000e-03 52.8


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 TraesCS3A01G028300 chr3A 15085528 15090111 4583 False 8466.000 8466 100.000000 1 4584 1 chr3A.!!$F1 4583
1 TraesCS3A01G028300 chr3D 6012032 6016347 4315 True 1765.000 3369 91.896333 37 4584 3 chr3D.!!$R1 4547
2 TraesCS3A01G028300 chr3B 7606841 7611810 4969 False 1310.175 2049 90.070500 1 4433 4 chr3B.!!$F2 4432

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
914 930 0.098200 GTTCGGCGCATTAACTTCCC 59.902 55.0 10.83 0.0 0.00 3.97 F
1160 1183 0.035317 TCTCTGTGCGGAAACAGCAT 59.965 50.0 6.43 0.0 45.93 3.79 F
1948 2460 0.035820 TACCCTTCGCGCCTCAATTT 60.036 50.0 0.00 0.0 0.00 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1929 2441 0.035820 AAATTGAGGCGCGAAGGGTA 60.036 50.0 12.10 0.0 44.71 3.69 R
2790 3388 1.583054 ACGCTGACAGAAACAGGAAC 58.417 50.0 6.65 0.0 36.09 3.62 R
3718 4336 0.253327 AGAAGATGAACGCTTCCCCC 59.747 55.0 0.00 0.0 42.04 5.40 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
26 27 5.707298 AGAAGTTTCCATTGTCGTGATCATT 59.293 36.000 0.00 0.00 0.00 2.57
29 30 3.348647 TCCATTGTCGTGATCATTGGT 57.651 42.857 0.00 0.00 37.50 3.67
62 63 2.024414 CCCCGGGATCTTGATTTTGAC 58.976 52.381 26.32 0.00 0.00 3.18
124 125 2.492088 AGATTGTTCTGTGGATCGACGA 59.508 45.455 0.00 0.00 0.00 4.20
135 136 1.950909 GGATCGACGATGTCTCCTCTT 59.049 52.381 16.49 0.00 0.00 2.85
193 194 1.228154 GCAAAGGACCCCGTGAAGT 60.228 57.895 0.00 0.00 0.00 3.01
198 199 1.057851 AGGACCCCGTGAAGTGGAAA 61.058 55.000 0.00 0.00 0.00 3.13
280 281 2.902705 TTTGCTGTCTCCGTTGTAGT 57.097 45.000 0.00 0.00 0.00 2.73
281 282 2.433868 TTGCTGTCTCCGTTGTAGTC 57.566 50.000 0.00 0.00 0.00 2.59
294 295 2.844122 TGTAGTCGATCATGTGACCG 57.156 50.000 10.44 0.00 35.71 4.79
318 319 1.409802 GGTGGATAGTCCCTCTCGTCA 60.410 57.143 0.00 0.00 35.03 4.35
323 324 0.328592 TAGTCCCTCTCGTCACAGCT 59.671 55.000 0.00 0.00 0.00 4.24
324 325 0.328592 AGTCCCTCTCGTCACAGCTA 59.671 55.000 0.00 0.00 0.00 3.32
328 329 0.317436 CCTCTCGTCACAGCTATCGC 60.317 60.000 0.00 0.00 0.00 4.58
329 330 0.317436 CTCTCGTCACAGCTATCGCC 60.317 60.000 0.00 0.00 36.60 5.54
330 331 1.655654 CTCGTCACAGCTATCGCCG 60.656 63.158 0.00 0.00 36.60 6.46
331 332 2.102357 CGTCACAGCTATCGCCGT 59.898 61.111 0.00 0.00 36.60 5.68
332 333 1.939785 CGTCACAGCTATCGCCGTC 60.940 63.158 0.00 0.00 36.60 4.79
401 402 4.383948 CCATTGTCGACATCATCATACTCG 59.616 45.833 20.80 0.00 0.00 4.18
402 403 3.000082 TGTCGACATCATCATACTCGC 58.000 47.619 15.76 0.00 0.00 5.03
403 404 2.618709 TGTCGACATCATCATACTCGCT 59.381 45.455 15.76 0.00 0.00 4.93
404 405 3.813166 TGTCGACATCATCATACTCGCTA 59.187 43.478 15.76 0.00 0.00 4.26
445 446 0.877649 GTCATCATCATCGCCGCTGT 60.878 55.000 0.00 0.00 0.00 4.40
448 449 2.355445 ATCATCATCGCCGCTGTCGT 62.355 55.000 0.00 0.00 0.00 4.34
462 463 2.503158 TCGTTCACGATGACGCCG 60.503 61.111 0.00 0.00 44.22 6.46
476 477 4.596180 GCCGTCATTGCCGATGCG 62.596 66.667 0.00 2.88 41.78 4.73
495 496 2.369257 GATGGAGCCCGCTTCGATCA 62.369 60.000 0.00 0.00 0.00 2.92
501 502 1.927210 CCCGCTTCGATCATTGTCG 59.073 57.895 0.00 3.29 42.74 4.35
532 533 2.592574 CATCGCCGATGCCATGGT 60.593 61.111 14.88 0.00 33.05 3.55
534 535 1.301716 ATCGCCGATGCCATGGTAC 60.302 57.895 14.67 4.32 0.00 3.34
552 553 3.940640 CCATCGCCGGCATTGTCG 61.941 66.667 28.98 9.08 0.00 4.35
585 586 1.294659 GGTTGAACTCGGCAGCAGAG 61.295 60.000 19.85 19.85 41.27 3.35
612 613 1.738099 CTCTGCCGTTCCTGTTCCG 60.738 63.158 0.00 0.00 0.00 4.30
635 636 2.034687 GGGCTCAGTGGTGCATGT 59.965 61.111 10.32 0.00 35.26 3.21
653 654 2.270205 CTGCAGGTCGCCCAAGAT 59.730 61.111 5.57 0.00 41.33 2.40
662 663 4.883354 GCCCAAGATGGCCCTCGG 62.883 72.222 0.00 0.00 46.11 4.63
721 722 3.741476 GCACGCCCTTGCCAAGAG 61.741 66.667 5.89 0.00 36.42 2.85
767 768 4.038042 AGAGCGATCGATCTGGTTGATTAA 59.962 41.667 32.99 0.00 39.61 1.40
768 769 4.051922 AGCGATCGATCTGGTTGATTAAC 58.948 43.478 21.57 0.00 35.14 2.01
769 770 4.051922 GCGATCGATCTGGTTGATTAACT 58.948 43.478 21.57 0.00 36.99 2.24
794 800 2.964343 GTCTCCTGAGACGGACCTT 58.036 57.895 11.25 0.00 46.93 3.50
809 815 4.161001 ACGGACCTTCTAATTTATCCACGT 59.839 41.667 0.00 0.00 0.00 4.49
812 818 5.753921 GGACCTTCTAATTTATCCACGTCAG 59.246 44.000 0.00 0.00 0.00 3.51
844 852 3.953775 CCGGGCCTGGTTCTGTGT 61.954 66.667 23.90 0.00 0.00 3.72
868 879 3.465403 CCTGGCCCAGTCGAGGAG 61.465 72.222 10.47 0.00 34.32 3.69
876 887 1.316706 CCAGTCGAGGAGGGAGACAC 61.317 65.000 0.00 0.00 37.36 3.67
877 888 0.609406 CAGTCGAGGAGGGAGACACA 60.609 60.000 0.00 0.00 37.36 3.72
914 930 0.098200 GTTCGGCGCATTAACTTCCC 59.902 55.000 10.83 0.00 0.00 3.97
918 934 0.393808 GGCGCATTAACTTCCCTGGA 60.394 55.000 10.83 0.00 0.00 3.86
930 946 2.347490 CCTGGACCAAGACCACCG 59.653 66.667 0.00 0.00 33.57 4.94
931 947 2.516888 CCTGGACCAAGACCACCGT 61.517 63.158 0.00 0.00 33.57 4.83
932 948 1.004918 CTGGACCAAGACCACCGTC 60.005 63.158 0.00 0.00 39.50 4.79
934 950 2.048503 GACCAAGACCACCGTCCG 60.049 66.667 0.00 0.00 40.12 4.79
935 951 2.522436 ACCAAGACCACCGTCCGA 60.522 61.111 0.00 0.00 40.12 4.55
937 953 1.374252 CCAAGACCACCGTCCGAAG 60.374 63.158 0.00 0.00 40.12 3.79
952 971 2.450609 CGAAGGGGAAAAACGAGAGA 57.549 50.000 0.00 0.00 0.00 3.10
953 972 2.762745 CGAAGGGGAAAAACGAGAGAA 58.237 47.619 0.00 0.00 0.00 2.87
1130 1153 1.284785 CAGGTCTCTCTCTCTCCCTGT 59.715 57.143 0.00 0.00 35.77 4.00
1132 1155 1.564348 GGTCTCTCTCTCTCCCTGTCT 59.436 57.143 0.00 0.00 0.00 3.41
1152 1175 1.953231 CTCTGCCATCTCTGTGCGGA 61.953 60.000 0.00 0.00 38.03 5.54
1160 1183 0.035317 TCTCTGTGCGGAAACAGCAT 59.965 50.000 6.43 0.00 45.93 3.79
1187 1210 1.071699 ACCCTGACTTTTCAAGCGCTA 59.928 47.619 12.05 0.00 0.00 4.26
1372 1404 1.541379 GCCGGGTAACTCCACAATTT 58.459 50.000 2.18 0.00 38.11 1.82
1387 1419 5.721000 TCCACAATTTCTCCCAATATTGCTT 59.279 36.000 10.11 0.00 32.58 3.91
1390 1422 6.875195 CACAATTTCTCCCAATATTGCTTTGT 59.125 34.615 10.11 8.02 32.58 2.83
1442 1477 7.340743 TCCAGTTTGGATTTCTGTTCTTACAAA 59.659 33.333 0.00 0.00 42.67 2.83
1482 1517 2.606795 GCATTTGAACAGCGGCAACTTA 60.607 45.455 1.45 0.00 0.00 2.24
1490 1525 4.053469 ACAGCGGCAACTTACAAAATTT 57.947 36.364 1.45 0.00 0.00 1.82
1494 1529 4.982295 AGCGGCAACTTACAAAATTTCTTC 59.018 37.500 1.45 0.00 0.00 2.87
1498 1533 6.512297 GGCAACTTACAAAATTTCTTCCTGA 58.488 36.000 0.00 0.00 0.00 3.86
1503 1538 9.971922 AACTTACAAAATTTCTTCCTGATTCTG 57.028 29.630 0.00 0.00 0.00 3.02
1516 1551 4.290985 TCCTGATTCTGGTTTTGGGTCATA 59.709 41.667 9.18 0.00 0.00 2.15
1534 1569 9.416284 TGGGTCATAAAATTATTTCTTACTCCC 57.584 33.333 0.00 0.00 0.00 4.30
1535 1570 9.642343 GGGTCATAAAATTATTTCTTACTCCCT 57.358 33.333 0.00 0.00 0.00 4.20
1538 1573 9.555727 TCATAAAATTATTTCTTACTCCCTCCG 57.444 33.333 0.00 0.00 0.00 4.63
1539 1574 9.338622 CATAAAATTATTTCTTACTCCCTCCGT 57.661 33.333 0.00 0.00 0.00 4.69
1540 1575 7.860918 AAAATTATTTCTTACTCCCTCCGTC 57.139 36.000 0.00 0.00 0.00 4.79
1541 1576 5.548181 ATTATTTCTTACTCCCTCCGTCC 57.452 43.478 0.00 0.00 0.00 4.79
1542 1577 1.565067 TTTCTTACTCCCTCCGTCCC 58.435 55.000 0.00 0.00 0.00 4.46
1543 1578 0.682209 TTCTTACTCCCTCCGTCCCG 60.682 60.000 0.00 0.00 0.00 5.14
1544 1579 1.379576 CTTACTCCCTCCGTCCCGT 60.380 63.158 0.00 0.00 0.00 5.28
1545 1580 0.107017 CTTACTCCCTCCGTCCCGTA 60.107 60.000 0.00 0.00 0.00 4.02
1546 1581 0.331278 TTACTCCCTCCGTCCCGTAA 59.669 55.000 0.00 0.00 0.00 3.18
1547 1582 0.552848 TACTCCCTCCGTCCCGTAAT 59.447 55.000 0.00 0.00 0.00 1.89
1548 1583 0.552848 ACTCCCTCCGTCCCGTAATA 59.447 55.000 0.00 0.00 0.00 0.98
1549 1584 1.146566 ACTCCCTCCGTCCCGTAATAT 59.853 52.381 0.00 0.00 0.00 1.28
1550 1585 2.376518 ACTCCCTCCGTCCCGTAATATA 59.623 50.000 0.00 0.00 0.00 0.86
1551 1586 3.181429 ACTCCCTCCGTCCCGTAATATAA 60.181 47.826 0.00 0.00 0.00 0.98
1552 1587 3.157087 TCCCTCCGTCCCGTAATATAAC 58.843 50.000 0.00 0.00 0.00 1.89
1553 1588 2.892852 CCCTCCGTCCCGTAATATAACA 59.107 50.000 0.00 0.00 0.00 2.41
1554 1589 3.321682 CCCTCCGTCCCGTAATATAACAA 59.678 47.826 0.00 0.00 0.00 2.83
1555 1590 4.301628 CCTCCGTCCCGTAATATAACAAC 58.698 47.826 0.00 0.00 0.00 3.32
1556 1591 4.038402 CCTCCGTCCCGTAATATAACAACT 59.962 45.833 0.00 0.00 0.00 3.16
1557 1592 5.241506 CCTCCGTCCCGTAATATAACAACTA 59.758 44.000 0.00 0.00 0.00 2.24
1558 1593 6.071728 CCTCCGTCCCGTAATATAACAACTAT 60.072 42.308 0.00 0.00 0.00 2.12
1559 1594 7.121168 CCTCCGTCCCGTAATATAACAACTATA 59.879 40.741 0.00 0.00 0.00 1.31
1560 1595 8.579850 TCCGTCCCGTAATATAACAACTATAT 57.420 34.615 0.00 0.00 35.09 0.86
1561 1596 9.023962 TCCGTCCCGTAATATAACAACTATATT 57.976 33.333 3.29 3.29 43.02 1.28
1573 1608 5.740290 ACAACTATATTATGGGACGGAGG 57.260 43.478 0.00 0.00 0.00 4.30
1574 1609 4.530946 ACAACTATATTATGGGACGGAGGG 59.469 45.833 0.00 0.00 0.00 4.30
1575 1610 4.687262 ACTATATTATGGGACGGAGGGA 57.313 45.455 0.00 0.00 0.00 4.20
1576 1611 4.611367 ACTATATTATGGGACGGAGGGAG 58.389 47.826 0.00 0.00 0.00 4.30
1577 1612 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
1578 1613 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
1579 1614 2.852714 TTATGGGACGGAGGGAGTAA 57.147 50.000 0.00 0.00 0.00 2.24
1580 1615 3.339713 TTATGGGACGGAGGGAGTAAT 57.660 47.619 0.00 0.00 0.00 1.89
1673 2179 9.859427 GAATGTCAAATTTTCATATGGAACTCA 57.141 29.630 2.13 0.00 34.56 3.41
1701 2207 2.631268 CCCTTAACCCCTCCTATGTGGA 60.631 54.545 0.00 0.00 43.86 4.02
1702 2208 3.120108 CCTTAACCCCTCCTATGTGGAA 58.880 50.000 0.00 0.00 45.63 3.53
1703 2209 3.118000 CCTTAACCCCTCCTATGTGGAAC 60.118 52.174 0.00 0.00 45.63 3.62
1739 2245 6.820656 CCTGAACTATTATGTCAGCAAGTTCT 59.179 38.462 12.61 0.00 38.54 3.01
1742 2248 7.877612 TGAACTATTATGTCAGCAAGTTCTTCA 59.122 33.333 12.61 0.00 38.54 3.02
1743 2249 8.798859 AACTATTATGTCAGCAAGTTCTTCAT 57.201 30.769 0.00 0.00 0.00 2.57
1837 2346 6.090763 GGTTTTGCTTGCCTATTTATGTCAAC 59.909 38.462 0.00 0.00 0.00 3.18
1845 2354 7.099266 TGCCTATTTATGTCAACATTTCAGG 57.901 36.000 0.20 5.05 37.76 3.86
1846 2355 6.663093 TGCCTATTTATGTCAACATTTCAGGT 59.337 34.615 0.20 0.00 37.76 4.00
1865 2374 2.223377 GGTTCCAACACTTGATCGTCAC 59.777 50.000 0.00 0.00 0.00 3.67
1874 2383 6.222038 ACACTTGATCGTCACACCTAATAT 57.778 37.500 0.00 0.00 0.00 1.28
1887 2396 7.063898 GTCACACCTAATATCCATCAATCATCG 59.936 40.741 0.00 0.00 0.00 3.84
1928 2440 9.478768 TGTTCGTTTGTGAAATAGTACTGATAA 57.521 29.630 5.39 0.00 0.00 1.75
1937 2449 9.408069 GTGAAATAGTACTGATAATACCCTTCG 57.592 37.037 5.39 0.00 0.00 3.79
1938 2450 8.086522 TGAAATAGTACTGATAATACCCTTCGC 58.913 37.037 5.39 0.00 0.00 4.70
1939 2451 4.500603 AGTACTGATAATACCCTTCGCG 57.499 45.455 0.00 0.00 0.00 5.87
1941 2453 1.270147 ACTGATAATACCCTTCGCGCC 60.270 52.381 0.00 0.00 0.00 6.53
1942 2454 1.000955 CTGATAATACCCTTCGCGCCT 59.999 52.381 0.00 0.00 0.00 5.52
1943 2455 1.000506 TGATAATACCCTTCGCGCCTC 59.999 52.381 0.00 0.00 0.00 4.70
1944 2456 1.000506 GATAATACCCTTCGCGCCTCA 59.999 52.381 0.00 0.00 0.00 3.86
1945 2457 0.825410 TAATACCCTTCGCGCCTCAA 59.175 50.000 0.00 0.00 0.00 3.02
1946 2458 0.180406 AATACCCTTCGCGCCTCAAT 59.820 50.000 0.00 0.00 0.00 2.57
1947 2459 0.180406 ATACCCTTCGCGCCTCAATT 59.820 50.000 0.00 0.00 0.00 2.32
1948 2460 0.035820 TACCCTTCGCGCCTCAATTT 60.036 50.000 0.00 0.00 0.00 1.82
1949 2461 0.893727 ACCCTTCGCGCCTCAATTTT 60.894 50.000 0.00 0.00 0.00 1.82
1983 2495 2.477104 TCATCCCTGGTGCTCTATCA 57.523 50.000 0.00 0.00 0.00 2.15
1986 2498 2.254152 TCCCTGGTGCTCTATCAACT 57.746 50.000 0.00 0.00 0.00 3.16
1995 2507 4.563580 GGTGCTCTATCAACTGAGGAACAA 60.564 45.833 0.00 0.00 38.09 2.83
2049 2561 3.041946 CCCACAGCCTCCTAATAGAACT 58.958 50.000 0.00 0.00 0.00 3.01
2086 2598 3.208747 ACGGTCCAATTTCTGACTTGT 57.791 42.857 0.00 0.00 0.00 3.16
2091 2603 5.617751 CGGTCCAATTTCTGACTTGTTCATC 60.618 44.000 0.00 0.00 32.17 2.92
2135 2647 2.828520 TGGTTGAAGTGCAAAGTTCCAA 59.171 40.909 0.00 0.00 38.44 3.53
2140 2652 0.681175 AGTGCAAAGTTCCAATGGCC 59.319 50.000 0.00 0.00 0.00 5.36
2143 2655 1.070445 TGCAAAGTTCCAATGGCCAAG 59.930 47.619 10.96 5.36 0.00 3.61
2144 2656 1.344114 GCAAAGTTCCAATGGCCAAGA 59.656 47.619 10.96 4.08 0.00 3.02
2149 2661 3.575805 AGTTCCAATGGCCAAGAAAGAA 58.424 40.909 10.96 6.23 0.00 2.52
2150 2662 4.162651 AGTTCCAATGGCCAAGAAAGAAT 58.837 39.130 10.96 0.00 0.00 2.40
2327 2842 9.508642 TTGGTCAAAAGTATGTATGTACAATGA 57.491 29.630 0.00 0.00 39.99 2.57
2394 2926 9.590451 AGCTTGTGATGGTATTAAAATTTGATG 57.410 29.630 0.00 0.00 0.00 3.07
2430 2962 7.505248 TGAATATGAATAAACCAGCAGGCATAA 59.495 33.333 0.00 0.00 39.06 1.90
2483 3015 8.947055 ACAAACAAGCCCAATTCATTATAATC 57.053 30.769 0.00 0.00 0.00 1.75
2558 3154 9.471084 TTTTATTACTTAAGGAGCTTTGTTTGC 57.529 29.630 7.53 0.00 0.00 3.68
2569 3165 6.660949 AGGAGCTTTGTTTGCTTATGATAGTT 59.339 34.615 0.00 0.00 41.30 2.24
2720 3318 2.103042 AATCTCTTGCGCGGTGCTC 61.103 57.895 15.31 0.00 46.63 4.26
2739 3337 6.197096 GGTGCTCGCAGTTAATTAAAATCATG 59.803 38.462 0.00 0.00 0.00 3.07
2771 3369 4.435651 GCACTGTAAGATACGCTTTTGGTC 60.436 45.833 0.00 0.00 38.05 4.02
2790 3388 3.242739 GGTCGCAACTGCATATTAACCAG 60.243 47.826 2.12 0.00 42.21 4.00
2833 3431 4.621991 ACTATGATGTATCGCTTCCACAC 58.378 43.478 0.00 0.00 0.00 3.82
2920 3518 3.114693 GAAGAATTCACTGCAGAAGCG 57.885 47.619 23.35 5.78 46.62 4.68
2929 3527 3.127533 GCAGAAGCGGCCATCGTT 61.128 61.111 2.24 0.00 41.72 3.85
2960 3558 3.838317 TGGTCCAAGTATGTAGCTTGTCT 59.162 43.478 0.00 0.00 41.08 3.41
2961 3559 4.286032 TGGTCCAAGTATGTAGCTTGTCTT 59.714 41.667 0.00 0.00 41.08 3.01
2962 3560 5.221843 TGGTCCAAGTATGTAGCTTGTCTTT 60.222 40.000 0.00 0.00 41.08 2.52
2963 3561 5.705905 GGTCCAAGTATGTAGCTTGTCTTTT 59.294 40.000 0.00 0.00 41.08 2.27
2964 3562 6.128254 GGTCCAAGTATGTAGCTTGTCTTTTC 60.128 42.308 0.00 0.00 41.08 2.29
2965 3563 6.426937 GTCCAAGTATGTAGCTTGTCTTTTCA 59.573 38.462 0.00 0.00 41.08 2.69
2966 3564 6.995686 TCCAAGTATGTAGCTTGTCTTTTCAA 59.004 34.615 0.00 0.00 41.08 2.69
2967 3565 7.500892 TCCAAGTATGTAGCTTGTCTTTTCAAA 59.499 33.333 0.00 0.00 41.08 2.69
2968 3566 7.591426 CCAAGTATGTAGCTTGTCTTTTCAAAC 59.409 37.037 0.00 0.00 41.08 2.93
2969 3567 7.801716 AGTATGTAGCTTGTCTTTTCAAACA 57.198 32.000 0.00 0.00 0.00 2.83
2970 3568 7.865707 AGTATGTAGCTTGTCTTTTCAAACAG 58.134 34.615 0.00 0.00 0.00 3.16
2982 3580 9.179909 TGTCTTTTCAAACAGTGAATAACCTAA 57.820 29.630 0.00 0.00 45.71 2.69
2983 3581 9.447040 GTCTTTTCAAACAGTGAATAACCTAAC 57.553 33.333 0.00 0.00 45.71 2.34
2984 3582 8.626526 TCTTTTCAAACAGTGAATAACCTAACC 58.373 33.333 0.00 0.00 45.71 2.85
2985 3583 8.528044 TTTTCAAACAGTGAATAACCTAACCT 57.472 30.769 0.00 0.00 45.71 3.50
2986 3584 7.739498 TTCAAACAGTGAATAACCTAACCTC 57.261 36.000 0.00 0.00 41.47 3.85
2987 3585 5.929992 TCAAACAGTGAATAACCTAACCTCG 59.070 40.000 0.00 0.00 31.51 4.63
2988 3586 5.479124 AACAGTGAATAACCTAACCTCGT 57.521 39.130 0.00 0.00 0.00 4.18
2989 3587 6.594788 AACAGTGAATAACCTAACCTCGTA 57.405 37.500 0.00 0.00 0.00 3.43
2990 3588 6.205101 ACAGTGAATAACCTAACCTCGTAG 57.795 41.667 0.00 0.00 0.00 3.51
2991 3589 5.948162 ACAGTGAATAACCTAACCTCGTAGA 59.052 40.000 0.00 0.00 0.00 2.59
2992 3590 6.606395 ACAGTGAATAACCTAACCTCGTAGAT 59.394 38.462 0.00 0.00 33.89 1.98
2993 3591 7.776969 ACAGTGAATAACCTAACCTCGTAGATA 59.223 37.037 0.00 0.00 33.89 1.98
2994 3592 8.794553 CAGTGAATAACCTAACCTCGTAGATAT 58.205 37.037 0.00 0.00 33.89 1.63
3414 4028 6.040054 TGAAATACCATGGATCATCAGCTTTG 59.960 38.462 21.47 0.00 0.00 2.77
3424 4038 6.767902 TGGATCATCAGCTTTGTAGAATAACC 59.232 38.462 0.00 0.00 0.00 2.85
3621 4235 2.645838 TGAAAGTTTGCTCTCCTGCT 57.354 45.000 0.00 0.00 0.00 4.24
3645 4261 1.493446 TCTCGGGCCTACACTAGATGA 59.507 52.381 0.84 0.00 0.00 2.92
3702 4320 3.760151 TCTGAAATGTTGCTGGAAGATGG 59.240 43.478 0.00 0.00 34.07 3.51
3718 4336 6.714810 TGGAAGATGGGGTAATTTATTGATCG 59.285 38.462 0.00 0.00 0.00 3.69
3721 4339 4.107127 TGGGGTAATTTATTGATCGGGG 57.893 45.455 0.00 0.00 0.00 5.73
3727 4345 1.961793 TTTATTGATCGGGGGAAGCG 58.038 50.000 0.00 0.00 0.00 4.68
3778 4396 4.202182 CCATGGACAGGGCATTTTTGATAG 60.202 45.833 5.56 0.00 0.00 2.08
3837 4469 3.827008 AATCCAGCTAATGCGAGAGAA 57.173 42.857 0.00 0.00 45.42 2.87
3905 4537 7.391554 TGTTCATCTTGAGTATTCTTTTCCAGG 59.608 37.037 0.00 0.00 0.00 4.45
3921 4553 6.432403 TTTCCAGGAAATTTACTTGCCAAT 57.568 33.333 10.90 0.00 0.00 3.16
3964 4596 3.690139 TGAACAAAAACGTACCTTCTGCA 59.310 39.130 0.00 0.00 0.00 4.41
3983 4615 2.005451 CAGTGCAGATGGACAAGCTAC 58.995 52.381 7.25 0.00 38.96 3.58
3991 4623 5.297776 GCAGATGGACAAGCTACATGTAAAT 59.702 40.000 7.06 0.00 0.00 1.40
4002 4634 5.824624 AGCTACATGTAAATTGGTCAGATGG 59.175 40.000 7.06 0.00 0.00 3.51
4036 4683 4.574674 TTCAGCCAGTGTCCTATCAAAT 57.425 40.909 0.00 0.00 0.00 2.32
4067 4725 3.451141 TTGGGCACAATTCAAAGTCAC 57.549 42.857 0.00 0.00 0.00 3.67
4087 4753 2.808543 ACGGAGAAGTCAGCAATTTGAC 59.191 45.455 0.00 2.57 46.14 3.18
4132 4799 7.232941 GGCTCTTAGTCTTACCATAGGTCATTA 59.767 40.741 0.00 0.00 37.09 1.90
4166 4834 1.201647 TCGTCTCCTTAACTGCCTTCG 59.798 52.381 0.00 0.00 0.00 3.79
4225 4893 9.258629 TCATTGTCTCCATGGAAAATAAGAAAT 57.741 29.630 17.00 8.04 0.00 2.17
4277 4972 3.214328 GACAAGGTTGTGTCATCAAGGT 58.786 45.455 0.00 0.00 46.00 3.50
4288 4983 6.851609 TGTGTCATCAAGGTTAATTGTATGC 58.148 36.000 0.00 0.00 0.00 3.14
4298 4993 5.487131 AGGTTAATTGTATGCATTTGGGGTT 59.513 36.000 3.54 0.00 0.00 4.11
4307 5002 4.533919 TGCATTTGGGGTTAAGTGAATG 57.466 40.909 0.00 0.00 0.00 2.67
4311 5006 6.042143 GCATTTGGGGTTAAGTGAATGTATG 58.958 40.000 0.00 0.00 0.00 2.39
4330 5025 1.140852 TGGCAAGAAGCTGTGTACACT 59.859 47.619 25.60 6.37 44.79 3.55
4335 5030 5.385617 GCAAGAAGCTGTGTACACTATTTG 58.614 41.667 25.60 19.30 41.15 2.32
4345 5040 5.935789 TGTGTACACTATTTGTAGCCTTTCC 59.064 40.000 25.60 0.00 41.58 3.13
4445 5226 4.461781 AGCTGGATGGCAATTATATGCTTC 59.538 41.667 0.00 0.00 45.68 3.86
4446 5227 4.461781 GCTGGATGGCAATTATATGCTTCT 59.538 41.667 0.00 0.00 45.68 2.85
4456 5237 6.294675 GCAATTATATGCTTCTTGTATGGGCA 60.295 38.462 0.00 0.00 43.06 5.36
4470 5251 2.036958 TGGGCAGAATACAACCATCG 57.963 50.000 0.00 0.00 0.00 3.84
4517 5298 6.013898 TGGATGGGATGTAAATCTCTCATCTC 60.014 42.308 11.11 0.00 38.92 2.75
4522 5303 7.071572 TGGGATGTAAATCTCTCATCTCATCAA 59.928 37.037 3.29 0.00 41.98 2.57
4548 5329 8.627208 ACATGTGAACTATTTCTCAACAATCT 57.373 30.769 0.00 0.00 38.42 2.40
4569 5350 2.725008 GGATCTGCTCCGGAGTCG 59.275 66.667 31.43 21.92 33.29 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 0.247655 CGGCGAAACCAATGATCACG 60.248 55.000 0.00 0.00 39.03 4.35
26 27 2.592287 GGGACAACGGCGAAACCA 60.592 61.111 16.62 0.00 39.03 3.67
29 30 4.992511 CGGGGGACAACGGCGAAA 62.993 66.667 16.62 0.00 0.00 3.46
62 63 1.293498 CTGACGGACACCTTCTGGG 59.707 63.158 0.00 0.00 41.89 4.45
87 88 7.890503 AGAACAATCTGATACTCGAGTCGAGG 61.891 46.154 37.88 23.65 45.33 4.63
108 109 2.159366 AGACATCGTCGATCCACAGAAC 60.159 50.000 4.34 0.00 37.67 3.01
135 136 1.296392 CCACATCTGGTCCTCGCAA 59.704 57.895 0.00 0.00 32.03 4.85
177 178 1.057851 TCCACTTCACGGGGTCCTTT 61.058 55.000 0.00 0.00 0.00 3.11
281 282 2.238847 ACCACCCGGTCACATGATCG 62.239 60.000 7.58 7.58 44.71 3.69
294 295 0.031010 AGAGGGACTATCCACCACCC 60.031 60.000 0.00 0.00 41.55 4.61
323 324 2.203167 AGCGAGGAGACGGCGATA 60.203 61.111 16.62 0.00 39.26 2.92
324 325 3.893763 CAGCGAGGAGACGGCGAT 61.894 66.667 16.62 0.11 39.26 4.58
328 329 0.309302 CTACATCAGCGAGGAGACGG 59.691 60.000 0.00 0.00 0.00 4.79
329 330 1.018148 ACTACATCAGCGAGGAGACG 58.982 55.000 0.00 0.00 0.00 4.18
330 331 2.480416 CCAACTACATCAGCGAGGAGAC 60.480 54.545 0.00 0.00 0.00 3.36
331 332 1.751351 CCAACTACATCAGCGAGGAGA 59.249 52.381 0.00 0.00 0.00 3.71
332 333 1.804372 GCCAACTACATCAGCGAGGAG 60.804 57.143 0.00 0.00 0.00 3.69
387 388 3.613671 GCAGCTAGCGAGTATGATGATGT 60.614 47.826 9.55 0.00 0.00 3.06
448 449 2.646143 TGACGGCGTCATCGTGAA 59.354 55.556 36.29 14.22 41.22 3.18
462 463 1.159713 TCCATCGCATCGGCAATGAC 61.160 55.000 2.71 0.00 41.24 3.06
476 477 1.666234 GATCGAAGCGGGCTCCATC 60.666 63.158 0.00 0.00 0.00 3.51
489 490 2.504032 GGGGGCGACAATGATCGA 59.496 61.111 8.85 0.00 45.13 3.59
491 492 1.887707 GTCGGGGGCGACAATGATC 60.888 63.158 0.00 0.00 38.62 2.92
517 518 2.108157 GTACCATGGCATCGGCGA 59.892 61.111 13.87 13.87 42.47 5.54
532 533 2.203139 CAATGCCGGCGATGGGTA 60.203 61.111 23.90 1.41 0.00 3.69
534 535 3.585990 GACAATGCCGGCGATGGG 61.586 66.667 28.29 16.54 0.00 4.00
585 586 1.061485 GAACGGCAGAGACGAAAGAC 58.939 55.000 0.00 0.00 35.20 3.01
612 613 1.227380 CACCACTGAGCCCGCTATC 60.227 63.158 0.00 0.00 0.00 2.08
647 648 4.195334 CCCCGAGGGCCATCTTGG 62.195 72.222 16.60 15.16 41.55 3.61
662 663 2.513897 CGCCGGAAAGACCATCCC 60.514 66.667 5.05 0.00 38.90 3.85
704 705 3.741476 CTCTTGGCAAGGGCGTGC 61.741 66.667 25.92 3.36 44.14 5.34
733 734 3.966154 TCGATCGCTCTAGGTTTTCATC 58.034 45.455 11.09 0.00 0.00 2.92
794 800 4.746535 TGGCTGACGTGGATAAATTAGA 57.253 40.909 0.00 0.00 0.00 2.10
809 815 1.304381 GCCCAGGTTTGATGGCTGA 60.304 57.895 0.00 0.00 40.77 4.26
812 818 3.451894 CGGCCCAGGTTTGATGGC 61.452 66.667 0.00 0.00 43.26 4.40
868 879 0.250770 GGTCCAGGTTTGTGTCTCCC 60.251 60.000 0.00 0.00 0.00 4.30
876 887 0.951558 CCAGTTTCGGTCCAGGTTTG 59.048 55.000 0.00 0.00 0.00 2.93
877 888 0.549469 ACCAGTTTCGGTCCAGGTTT 59.451 50.000 0.00 0.00 32.11 3.27
914 930 1.004918 GACGGTGGTCTTGGTCCAG 60.005 63.158 0.00 0.00 40.15 3.86
918 934 2.095978 CTTCGGACGGTGGTCTTGGT 62.096 60.000 0.00 0.00 42.97 3.67
930 946 1.154197 CTCGTTTTTCCCCTTCGGAC 58.846 55.000 0.00 0.00 41.83 4.79
931 947 1.001633 CTCTCGTTTTTCCCCTTCGGA 59.998 52.381 0.00 0.00 39.68 4.55
932 948 1.001633 TCTCTCGTTTTTCCCCTTCGG 59.998 52.381 0.00 0.00 0.00 4.30
934 950 5.243207 TGTATTCTCTCGTTTTTCCCCTTC 58.757 41.667 0.00 0.00 0.00 3.46
935 951 5.237236 TGTATTCTCTCGTTTTTCCCCTT 57.763 39.130 0.00 0.00 0.00 3.95
937 953 3.374367 GCTGTATTCTCTCGTTTTTCCCC 59.626 47.826 0.00 0.00 0.00 4.81
947 966 2.722071 CCGTTCTCGCTGTATTCTCTC 58.278 52.381 0.00 0.00 35.54 3.20
952 971 1.518572 CCGCCGTTCTCGCTGTATT 60.519 57.895 0.00 0.00 35.54 1.89
953 972 2.104331 CCGCCGTTCTCGCTGTAT 59.896 61.111 0.00 0.00 35.54 2.29
1083 1105 4.335647 CTGCCCTTGCGACTGGGT 62.336 66.667 8.47 0.00 45.06 4.51
1130 1153 0.822811 GCACAGAGATGGCAGAGAGA 59.177 55.000 0.00 0.00 0.00 3.10
1132 1155 1.514553 CGCACAGAGATGGCAGAGA 59.485 57.895 0.00 0.00 0.00 3.10
1152 1175 2.040278 TCAGGGTTCTGCTATGCTGTTT 59.960 45.455 0.00 0.00 40.69 2.83
1160 1183 4.389374 CTTGAAAAGTCAGGGTTCTGCTA 58.611 43.478 0.00 0.00 39.70 3.49
1372 1404 5.475220 TCGAAAACAAAGCAATATTGGGAGA 59.525 36.000 17.02 0.00 32.02 3.71
1403 1435 6.925610 TCCAAACTGGATCAAGAATAATCG 57.074 37.500 3.42 0.00 42.67 3.34
1442 1477 2.629137 TGCAATGTCCTGACTTGCAAAT 59.371 40.909 22.82 0.00 44.34 2.32
1445 1480 3.418022 TGCAATGTCCTGACTTGCA 57.582 47.368 21.96 21.96 44.69 4.08
1446 1481 2.991190 CAAATGCAATGTCCTGACTTGC 59.009 45.455 18.90 18.90 41.43 4.01
1482 1517 6.983906 ACCAGAATCAGGAAGAAATTTTGT 57.016 33.333 0.00 0.00 0.00 2.83
1490 1525 3.140144 ACCCAAAACCAGAATCAGGAAGA 59.860 43.478 0.00 0.00 0.00 2.87
1494 1529 2.875296 TGACCCAAAACCAGAATCAGG 58.125 47.619 0.00 0.00 0.00 3.86
1516 1551 6.827251 GGACGGAGGGAGTAAGAAATAATTTT 59.173 38.462 0.00 0.00 0.00 1.82
1547 1582 8.974238 CCTCCGTCCCATAATATAGTTGTTATA 58.026 37.037 0.00 0.00 0.00 0.98
1548 1583 7.093024 CCCTCCGTCCCATAATATAGTTGTTAT 60.093 40.741 0.00 0.00 0.00 1.89
1549 1584 6.211986 CCCTCCGTCCCATAATATAGTTGTTA 59.788 42.308 0.00 0.00 0.00 2.41
1550 1585 5.012768 CCCTCCGTCCCATAATATAGTTGTT 59.987 44.000 0.00 0.00 0.00 2.83
1551 1586 4.530946 CCCTCCGTCCCATAATATAGTTGT 59.469 45.833 0.00 0.00 0.00 3.32
1552 1587 4.775780 TCCCTCCGTCCCATAATATAGTTG 59.224 45.833 0.00 0.00 0.00 3.16
1553 1588 5.019657 TCCCTCCGTCCCATAATATAGTT 57.980 43.478 0.00 0.00 0.00 2.24
1554 1589 4.045590 ACTCCCTCCGTCCCATAATATAGT 59.954 45.833 0.00 0.00 0.00 2.12
1555 1590 4.611367 ACTCCCTCCGTCCCATAATATAG 58.389 47.826 0.00 0.00 0.00 1.31
1556 1591 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
1557 1592 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
1558 1593 4.474303 TTACTCCCTCCGTCCCATAATA 57.526 45.455 0.00 0.00 0.00 0.98
1559 1594 3.339713 TTACTCCCTCCGTCCCATAAT 57.660 47.619 0.00 0.00 0.00 1.28
1560 1595 2.852714 TTACTCCCTCCGTCCCATAA 57.147 50.000 0.00 0.00 0.00 1.90
1561 1596 2.969950 CAATTACTCCCTCCGTCCCATA 59.030 50.000 0.00 0.00 0.00 2.74
1562 1597 1.768870 CAATTACTCCCTCCGTCCCAT 59.231 52.381 0.00 0.00 0.00 4.00
1563 1598 1.200519 CAATTACTCCCTCCGTCCCA 58.799 55.000 0.00 0.00 0.00 4.37
1564 1599 1.201424 ACAATTACTCCCTCCGTCCC 58.799 55.000 0.00 0.00 0.00 4.46
1565 1600 3.345508 AAACAATTACTCCCTCCGTCC 57.654 47.619 0.00 0.00 0.00 4.79
1566 1601 5.526479 GGAATAAACAATTACTCCCTCCGTC 59.474 44.000 0.00 0.00 32.44 4.79
1567 1602 5.045432 TGGAATAAACAATTACTCCCTCCGT 60.045 40.000 0.00 0.00 36.74 4.69
1568 1603 5.433526 TGGAATAAACAATTACTCCCTCCG 58.566 41.667 0.00 0.00 36.74 4.63
1569 1604 6.318900 CACTGGAATAAACAATTACTCCCTCC 59.681 42.308 0.00 0.00 36.74 4.30
1570 1605 6.183360 GCACTGGAATAAACAATTACTCCCTC 60.183 42.308 0.00 0.00 36.74 4.30
1571 1606 5.652452 GCACTGGAATAAACAATTACTCCCT 59.348 40.000 0.00 0.00 36.74 4.20
1572 1607 5.652452 AGCACTGGAATAAACAATTACTCCC 59.348 40.000 0.00 0.00 36.74 4.30
1573 1608 6.759497 AGCACTGGAATAAACAATTACTCC 57.241 37.500 0.00 0.00 37.81 3.85
1574 1609 7.538678 CACAAGCACTGGAATAAACAATTACTC 59.461 37.037 0.00 0.00 28.71 2.59
1575 1610 7.370383 CACAAGCACTGGAATAAACAATTACT 58.630 34.615 0.00 0.00 28.71 2.24
1576 1611 6.089417 GCACAAGCACTGGAATAAACAATTAC 59.911 38.462 0.00 0.00 41.58 1.89
1577 1612 6.155827 GCACAAGCACTGGAATAAACAATTA 58.844 36.000 0.00 0.00 41.58 1.40
1578 1613 4.990426 GCACAAGCACTGGAATAAACAATT 59.010 37.500 0.00 0.00 41.58 2.32
1579 1614 4.559153 GCACAAGCACTGGAATAAACAAT 58.441 39.130 0.00 0.00 41.58 2.71
1580 1615 3.976169 GCACAAGCACTGGAATAAACAA 58.024 40.909 0.00 0.00 41.58 2.83
1673 2179 3.485136 AGGAGGGGTTAAGGGAAATCAT 58.515 45.455 0.00 0.00 0.00 2.45
1701 2207 9.170734 CATAATAGTTCAGGCATAGCATATGTT 57.829 33.333 4.29 0.08 0.00 2.71
1702 2208 8.324306 ACATAATAGTTCAGGCATAGCATATGT 58.676 33.333 4.29 0.00 0.00 2.29
1703 2209 8.728337 ACATAATAGTTCAGGCATAGCATATG 57.272 34.615 0.00 0.00 0.00 1.78
1765 2271 4.335594 CCATTCGTCCTCCTTTTTGGATAC 59.664 45.833 0.00 0.00 45.16 2.24
1780 2286 5.879237 TCAAAAGTTATGATGCCATTCGTC 58.121 37.500 0.00 0.00 34.31 4.20
1837 2346 4.916983 TCAAGTGTTGGAACCTGAAATG 57.083 40.909 0.00 0.00 0.00 2.32
1845 2354 2.869801 TGTGACGATCAAGTGTTGGAAC 59.130 45.455 0.00 0.00 0.00 3.62
1846 2355 2.869801 GTGTGACGATCAAGTGTTGGAA 59.130 45.455 0.00 0.00 0.00 3.53
1865 2374 9.605275 ATTACGATGATTGATGGATATTAGGTG 57.395 33.333 0.00 0.00 0.00 4.00
1901 2410 7.956420 TCAGTACTATTTCACAAACGAACAT 57.044 32.000 0.00 0.00 0.00 2.71
1928 2440 0.180406 AATTGAGGCGCGAAGGGTAT 59.820 50.000 12.10 0.00 44.71 2.73
1929 2441 0.035820 AAATTGAGGCGCGAAGGGTA 60.036 50.000 12.10 0.00 44.71 3.69
1930 2442 0.893727 AAAATTGAGGCGCGAAGGGT 60.894 50.000 12.10 0.00 44.71 4.34
1931 2443 0.243636 AAAAATTGAGGCGCGAAGGG 59.756 50.000 12.10 0.00 46.11 3.95
1932 2444 1.335872 ACAAAAATTGAGGCGCGAAGG 60.336 47.619 12.10 0.00 0.00 3.46
1934 2446 2.095466 CCTACAAAAATTGAGGCGCGAA 60.095 45.455 12.10 0.00 0.00 4.70
1935 2447 1.466950 CCTACAAAAATTGAGGCGCGA 59.533 47.619 12.10 0.00 0.00 5.87
1936 2448 1.466950 TCCTACAAAAATTGAGGCGCG 59.533 47.619 0.00 0.00 31.90 6.86
1937 2449 3.782889 ATCCTACAAAAATTGAGGCGC 57.217 42.857 0.00 0.00 31.90 6.53
1938 2450 5.567138 AGAATCCTACAAAAATTGAGGCG 57.433 39.130 0.00 0.00 31.90 5.52
1939 2451 9.521503 GAAATAGAATCCTACAAAAATTGAGGC 57.478 33.333 0.00 0.00 31.90 4.70
1945 2457 9.942526 AGGGATGAAATAGAATCCTACAAAAAT 57.057 29.630 1.98 0.00 41.85 1.82
1946 2458 9.189156 CAGGGATGAAATAGAATCCTACAAAAA 57.811 33.333 1.98 0.00 41.85 1.94
1947 2459 7.779798 CCAGGGATGAAATAGAATCCTACAAAA 59.220 37.037 1.98 0.00 41.85 2.44
1948 2460 7.091993 ACCAGGGATGAAATAGAATCCTACAAA 60.092 37.037 1.98 0.00 41.85 2.83
1949 2461 6.389869 ACCAGGGATGAAATAGAATCCTACAA 59.610 38.462 1.98 0.00 41.85 2.41
1983 2495 4.922206 TCCAATAGCATTGTTCCTCAGTT 58.078 39.130 7.71 0.00 0.00 3.16
1986 2498 5.114764 TGATCCAATAGCATTGTTCCTCA 57.885 39.130 7.71 3.65 0.00 3.86
1995 2507 3.139770 AGCTTTCCCTGATCCAATAGCAT 59.860 43.478 0.00 0.00 0.00 3.79
2049 2561 4.142315 GGACCGTATGTAGCAGTCAAGTTA 60.142 45.833 0.00 0.00 0.00 2.24
2086 2598 4.576216 TTTGGTTTTTAGCAGCGATGAA 57.424 36.364 4.02 0.00 0.00 2.57
2091 2603 5.905480 AAATCTTTTGGTTTTTAGCAGCG 57.095 34.783 0.00 0.00 0.00 5.18
2125 2637 3.749665 TTCTTGGCCATTGGAACTTTG 57.250 42.857 6.09 0.00 0.00 2.77
2135 2647 3.167485 TGCTCAATTCTTTCTTGGCCAT 58.833 40.909 6.09 0.00 0.00 4.40
2140 2652 9.635520 AACATTATTCTGCTCAATTCTTTCTTG 57.364 29.630 0.00 0.00 0.00 3.02
2143 2655 7.490402 CCCAACATTATTCTGCTCAATTCTTTC 59.510 37.037 0.00 0.00 0.00 2.62
2144 2656 7.325694 CCCAACATTATTCTGCTCAATTCTTT 58.674 34.615 0.00 0.00 0.00 2.52
2149 2661 4.870636 TCCCCAACATTATTCTGCTCAAT 58.129 39.130 0.00 0.00 0.00 2.57
2150 2662 4.314522 TCCCCAACATTATTCTGCTCAA 57.685 40.909 0.00 0.00 0.00 3.02
2430 2962 8.949177 ACAACTGCAGAAAAATTTGAAGAAAAT 58.051 25.926 23.35 0.00 40.32 1.82
2558 3154 8.729805 AGCTTTCAAGGAAGAACTATCATAAG 57.270 34.615 0.00 0.00 0.00 1.73
2569 3165 8.177119 TGCTTAAAAATAGCTTTCAAGGAAGA 57.823 30.769 0.00 0.00 39.38 2.87
2674 3272 5.007136 GCTATCAAGTTTCATGGCTGAGTAC 59.993 44.000 0.00 0.00 31.68 2.73
2739 3337 6.696148 AGCGTATCTTACAGTGCAATAAGTAC 59.304 38.462 11.43 11.42 31.53 2.73
2771 3369 4.342772 GAACTGGTTAATATGCAGTTGCG 58.657 43.478 0.00 0.00 45.83 4.85
2790 3388 1.583054 ACGCTGACAGAAACAGGAAC 58.417 50.000 6.65 0.00 36.09 3.62
2833 3431 4.380233 GCAAGGTCATCTGGAATCTTGTTG 60.380 45.833 0.00 0.00 39.38 3.33
2920 3518 4.694037 GGACCATAATAGTTAACGATGGCC 59.306 45.833 21.72 19.68 40.68 5.36
2929 3527 9.375974 AGCTACATACTTGGACCATAATAGTTA 57.624 33.333 1.93 0.00 0.00 2.24
2963 3561 5.929992 CGAGGTTAGGTTATTCACTGTTTGA 59.070 40.000 0.00 0.00 0.00 2.69
2964 3562 5.699458 ACGAGGTTAGGTTATTCACTGTTTG 59.301 40.000 0.00 0.00 0.00 2.93
2965 3563 5.861727 ACGAGGTTAGGTTATTCACTGTTT 58.138 37.500 0.00 0.00 0.00 2.83
2966 3564 5.479124 ACGAGGTTAGGTTATTCACTGTT 57.521 39.130 0.00 0.00 0.00 3.16
2967 3565 5.948162 TCTACGAGGTTAGGTTATTCACTGT 59.052 40.000 0.00 0.00 0.00 3.55
2968 3566 6.446781 TCTACGAGGTTAGGTTATTCACTG 57.553 41.667 0.00 0.00 0.00 3.66
2969 3567 8.937207 ATATCTACGAGGTTAGGTTATTCACT 57.063 34.615 0.00 0.00 0.00 3.41
2982 3580 8.546322 TGGTGTATATCAGTATATCTACGAGGT 58.454 37.037 0.00 0.00 32.82 3.85
2983 3581 8.959705 TGGTGTATATCAGTATATCTACGAGG 57.040 38.462 0.00 0.00 32.82 4.63
2985 3583 9.338622 CCATGGTGTATATCAGTATATCTACGA 57.661 37.037 2.57 0.00 32.82 3.43
2986 3584 8.076781 GCCATGGTGTATATCAGTATATCTACG 58.923 40.741 14.67 0.00 32.82 3.51
2987 3585 8.914011 TGCCATGGTGTATATCAGTATATCTAC 58.086 37.037 14.67 0.00 30.72 2.59
2988 3586 8.914011 GTGCCATGGTGTATATCAGTATATCTA 58.086 37.037 14.67 0.00 30.72 1.98
2989 3587 7.400052 TGTGCCATGGTGTATATCAGTATATCT 59.600 37.037 14.67 0.00 30.72 1.98
2990 3588 7.555965 TGTGCCATGGTGTATATCAGTATATC 58.444 38.462 14.67 0.00 30.72 1.63
2991 3589 7.494922 TGTGCCATGGTGTATATCAGTATAT 57.505 36.000 14.67 0.00 32.87 0.86
2992 3590 6.926630 TGTGCCATGGTGTATATCAGTATA 57.073 37.500 14.67 0.00 0.00 1.47
2993 3591 5.823861 TGTGCCATGGTGTATATCAGTAT 57.176 39.130 14.67 0.00 0.00 2.12
2994 3592 5.823861 ATGTGCCATGGTGTATATCAGTA 57.176 39.130 14.67 0.00 0.00 2.74
2995 3593 4.712051 ATGTGCCATGGTGTATATCAGT 57.288 40.909 14.67 0.00 0.00 3.41
2996 3594 5.412594 GGTAATGTGCCATGGTGTATATCAG 59.587 44.000 14.67 0.00 0.00 2.90
2997 3595 5.073008 AGGTAATGTGCCATGGTGTATATCA 59.927 40.000 14.67 0.00 0.00 2.15
3385 3997 6.040166 GCTGATGATCCATGGTATTTCAGTTT 59.960 38.462 24.66 8.90 33.57 2.66
3414 4028 5.763876 ATAGAGGCCATGGGTTATTCTAC 57.236 43.478 15.13 0.00 0.00 2.59
3424 4038 3.692257 CCTGTAGAATAGAGGCCATGG 57.308 52.381 7.63 7.63 45.82 3.66
3645 4261 6.919662 CAGACACAGTTAATCAAACAATTGCT 59.080 34.615 5.05 0.00 40.83 3.91
3702 4320 4.376225 TCCCCCGATCAATAAATTACCC 57.624 45.455 0.00 0.00 0.00 3.69
3718 4336 0.253327 AGAAGATGAACGCTTCCCCC 59.747 55.000 0.00 0.00 42.04 5.40
3721 4339 4.749245 TTGAAAGAAGATGAACGCTTCC 57.251 40.909 0.00 0.00 42.04 3.46
3727 4345 5.106118 GCCTACCCTTTGAAAGAAGATGAAC 60.106 44.000 6.49 0.00 0.00 3.18
3778 4396 2.067013 GTCTTGCTGAGGGTACGAAAC 58.933 52.381 0.00 0.00 0.00 2.78
3822 4454 6.201806 GTGATTTACATTCTCTCGCATTAGCT 59.798 38.462 0.00 0.00 39.10 3.32
3833 4465 9.937175 GTAAGCCATTAAGTGATTTACATTCTC 57.063 33.333 0.00 0.00 31.95 2.87
3837 4469 7.707104 GCAGTAAGCCATTAAGTGATTTACAT 58.293 34.615 0.00 0.00 37.23 2.29
3921 4553 8.466798 TGTTCAACGAATCAACAGATAGAGATA 58.533 33.333 0.00 0.00 0.00 1.98
3964 4596 1.625315 TGTAGCTTGTCCATCTGCACT 59.375 47.619 0.00 0.00 0.00 4.40
3983 4615 5.418524 TGAACCCATCTGACCAATTTACATG 59.581 40.000 0.00 0.00 0.00 3.21
4015 4647 4.574674 ATTTGATAGGACACTGGCTGAA 57.425 40.909 0.00 0.00 0.00 3.02
4016 4648 5.894298 ATATTTGATAGGACACTGGCTGA 57.106 39.130 0.00 0.00 0.00 4.26
4017 4649 6.997655 TCTATATTTGATAGGACACTGGCTG 58.002 40.000 0.00 0.00 0.00 4.85
4018 4650 7.618019 TTCTATATTTGATAGGACACTGGCT 57.382 36.000 0.00 0.00 0.00 4.75
4019 4651 8.725148 CATTTCTATATTTGATAGGACACTGGC 58.275 37.037 0.00 0.00 0.00 4.85
4020 4652 9.784531 ACATTTCTATATTTGATAGGACACTGG 57.215 33.333 0.00 0.00 0.00 4.00
4036 4683 7.473735 TGAATTGTGCCCAAACATTTCTATA 57.526 32.000 11.17 0.00 39.48 1.31
4067 4725 2.807967 TGTCAAATTGCTGACTTCTCCG 59.192 45.455 10.75 0.00 45.03 4.63
4087 4753 3.504906 AGCCAACACAAGAAGATCACATG 59.495 43.478 0.00 0.00 0.00 3.21
4092 4759 5.241662 ACTAAGAGCCAACACAAGAAGATC 58.758 41.667 0.00 0.00 0.00 2.75
4132 4799 5.860941 AGGAGACGACTGAATATTGACAT 57.139 39.130 0.00 0.00 0.00 3.06
4166 4834 2.159881 CGATCGACAAAGGGACGAAAAC 60.160 50.000 10.26 0.00 39.38 2.43
4277 4972 8.037758 CACTTAACCCCAAATGCATACAATTAA 58.962 33.333 0.00 0.66 0.00 1.40
4288 4983 6.572519 CCATACATTCACTTAACCCCAAATG 58.427 40.000 0.00 0.00 0.00 2.32
4298 4993 5.355071 CAGCTTCTTGCCATACATTCACTTA 59.645 40.000 0.00 0.00 44.23 2.24
4307 5002 3.125316 GTGTACACAGCTTCTTGCCATAC 59.875 47.826 21.14 0.00 44.23 2.39
4311 5006 1.884235 AGTGTACACAGCTTCTTGCC 58.116 50.000 27.06 0.00 44.23 4.52
4330 5025 2.993937 CCACCGGAAAGGCTACAAATA 58.006 47.619 9.46 0.00 46.52 1.40
4345 5040 2.937469 TTATCTGCATTTTGCCACCG 57.063 45.000 0.00 0.00 44.23 4.94
4378 5079 5.924475 TTGCTAAGTGAAAAGACTACAGC 57.076 39.130 0.00 0.00 35.86 4.40
4445 5226 4.269183 TGGTTGTATTCTGCCCATACAAG 58.731 43.478 10.98 0.00 44.18 3.16
4446 5227 4.308526 TGGTTGTATTCTGCCCATACAA 57.691 40.909 7.88 7.88 42.32 2.41
4456 5237 6.946583 TCTACTATAGCCGATGGTTGTATTCT 59.053 38.462 0.00 0.00 30.70 2.40
4470 5251 5.007682 CAGTCTTCTCCCTCTACTATAGCC 58.992 50.000 0.00 0.00 0.00 3.93
4517 5298 9.121517 GTTGAGAAATAGTTCACATGTTTGATG 57.878 33.333 5.62 0.00 34.80 3.07
4518 5299 8.849168 TGTTGAGAAATAGTTCACATGTTTGAT 58.151 29.630 5.62 0.00 34.80 2.57
4522 5303 9.071276 AGATTGTTGAGAAATAGTTCACATGTT 57.929 29.630 5.62 0.00 34.80 2.71


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

AutoCloner maintained by Alex Coulton.