Multiple sequence alignment - TraesCS7B01G502200

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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 TraesCS7B01G502200 chr7B 100.000 4443 0 0 1 4443 750602674 750607116 0.000000e+00 8205.0
1 TraesCS7B01G502200 chr7B 83.686 1183 140 30 1872 3023 750443864 750442704 0.000000e+00 1066.0
2 TraesCS7B01G502200 chr7B 93.272 654 31 8 2951 3602 750430206 750429564 0.000000e+00 952.0
3 TraesCS7B01G502200 chr7B 87.157 693 59 14 2989 3655 750442708 750442020 0.000000e+00 760.0
4 TraesCS7B01G502200 chr7B 90.288 556 35 13 2892 3446 750415952 750415415 0.000000e+00 710.0
5 TraesCS7B01G502200 chr7B 93.172 454 22 4 2049 2500 750431018 750430572 0.000000e+00 658.0
6 TraesCS7B01G502200 chr7B 97.534 365 9 0 4079 4443 750414486 750414122 3.770000e-175 625.0
7 TraesCS7B01G502200 chr7B 85.055 455 48 14 3323 3772 750211495 750211056 3.150000e-121 446.0
8 TraesCS7B01G502200 chr7B 76.756 598 86 27 3500 4075 750415412 750414846 7.270000e-73 285.0
9 TraesCS7B01G502200 chr7D 86.709 3649 273 106 23 3603 633807635 633804131 0.000000e+00 3856.0
10 TraesCS7B01G502200 chr7D 85.870 460 31 9 3041 3484 633674820 633674379 4.050000e-125 459.0
11 TraesCS7B01G502200 chr7D 90.686 204 16 1 3129 3332 633803707 633803507 7.330000e-68 268.0
12 TraesCS7B01G502200 chr7A 90.509 2929 159 56 705 3588 732798893 732801747 0.000000e+00 3759.0
13 TraesCS7B01G502200 chr7A 84.545 1197 128 29 2333 3489 732864102 732862923 0.000000e+00 1133.0
14 TraesCS7B01G502200 chr7A 88.219 365 39 3 4077 4437 732807755 732808119 2.450000e-117 433.0
15 TraesCS7B01G502200 chr7A 88.581 289 18 10 2892 3180 732806791 732807064 1.980000e-88 337.0
16 TraesCS7B01G502200 chr7A 74.596 681 56 48 2 670 732798322 732798897 1.630000e-44 191.0
17 TraesCS7B01G502200 chr7A 81.853 259 18 10 3237 3484 733029501 733029741 1.630000e-44 191.0
18 TraesCS7B01G502200 chr3D 86.612 366 23 11 3254 3603 15609528 15609173 9.020000e-102 381.0
19 TraesCS7B01G502200 chr1D 100.000 35 0 0 4318 4352 9086576 9086610 1.030000e-06 65.8


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 TraesCS7B01G502200 chr7B 750602674 750607116 4442 False 8205 8205 100.000000 1 4443 1 chr7B.!!$F1 4442
1 TraesCS7B01G502200 chr7B 750442020 750443864 1844 True 913 1066 85.421500 1872 3655 2 chr7B.!!$R4 1783
2 TraesCS7B01G502200 chr7B 750429564 750431018 1454 True 805 952 93.222000 2049 3602 2 chr7B.!!$R3 1553
3 TraesCS7B01G502200 chr7B 750414122 750415952 1830 True 540 710 88.192667 2892 4443 3 chr7B.!!$R2 1551
4 TraesCS7B01G502200 chr7D 633803507 633807635 4128 True 2062 3856 88.697500 23 3603 2 chr7D.!!$R2 3580
5 TraesCS7B01G502200 chr7A 732798322 732801747 3425 False 1975 3759 82.552500 2 3588 2 chr7A.!!$F2 3586
6 TraesCS7B01G502200 chr7A 732862923 732864102 1179 True 1133 1133 84.545000 2333 3489 1 chr7A.!!$R1 1156
7 TraesCS7B01G502200 chr7A 732806791 732808119 1328 False 385 433 88.400000 2892 4437 2 chr7A.!!$F3 1545

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
184 220 0.173481 GCTCCCCGGAAGAAATTTGC 59.827 55.0 0.73 0.0 0.00 3.68 F
1171 1259 0.110486 TGAGAGGCACCAAAAGGGAC 59.890 55.0 0.00 0.0 41.15 4.46 F
1459 1547 0.593128 CCAAGTTTGCCAAGACCTCG 59.407 55.0 0.00 0.0 0.00 4.63 F
3019 3219 0.771127 AACCAAACTGCCCTCAGCTA 59.229 50.0 0.00 0.0 44.10 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1651 1739 0.109532 TGAAGGTGACGGCATGGAAA 59.890 50.000 0.00 0.0 0.00 3.13 R
2526 2647 1.340889 GTCCACAAGGCTGAAAATGCA 59.659 47.619 0.00 0.0 33.74 3.96 R
3443 3687 0.031178 CACTGGAACCAACAGCAAGC 59.969 55.000 0.00 0.0 39.55 4.01 R
3842 4185 0.034380 ACTCTGCTCTGCATGGCAAT 60.034 50.000 13.37 2.1 38.41 3.56 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
41 42 2.151502 TCCTTGTGCTTTGGTTTGGA 57.848 45.000 0.00 0.00 0.00 3.53
61 62 0.617535 TTGGATCCCTTCTCCTCGCA 60.618 55.000 9.90 0.00 33.69 5.10
68 69 0.826715 CCTTCTCCTCGCAGGAATCA 59.173 55.000 6.39 0.00 45.28 2.57
95 102 3.053896 CCTCCCGGCGTTTTCCAC 61.054 66.667 6.01 0.00 0.00 4.02
115 122 1.400500 CGGTTTCGATTTGGTTTCCGG 60.400 52.381 0.00 0.00 39.00 5.14
116 123 1.667756 GGTTTCGATTTGGTTTCCGGC 60.668 52.381 0.00 0.00 0.00 6.13
117 124 0.238817 TTTCGATTTGGTTTCCGGCG 59.761 50.000 0.00 0.00 0.00 6.46
118 125 2.190101 TTCGATTTGGTTTCCGGCGC 62.190 55.000 0.00 0.00 0.00 6.53
119 126 2.180769 GATTTGGTTTCCGGCGCC 59.819 61.111 19.07 19.07 0.00 6.53
120 127 3.677099 GATTTGGTTTCCGGCGCCG 62.677 63.158 41.00 41.00 39.44 6.46
139 146 4.426313 CGCCCCTTCCCCAACCTC 62.426 72.222 0.00 0.00 0.00 3.85
140 147 4.426313 GCCCCTTCCCCAACCTCG 62.426 72.222 0.00 0.00 0.00 4.63
159 191 2.125552 CGCTGCTCGAATCCACCA 60.126 61.111 0.00 0.00 41.67 4.17
165 197 1.084370 GCTCGAATCCACCACTTCCG 61.084 60.000 0.00 0.00 0.00 4.30
168 200 1.084370 CGAATCCACCACTTCCGCTC 61.084 60.000 0.00 0.00 0.00 5.03
181 217 4.637771 CGCTCCCCGGAAGAAATT 57.362 55.556 0.73 0.00 0.00 1.82
184 220 0.173481 GCTCCCCGGAAGAAATTTGC 59.827 55.000 0.73 0.00 0.00 3.68
185 221 0.817654 CTCCCCGGAAGAAATTTGCC 59.182 55.000 0.73 0.00 0.00 4.52
186 222 0.407918 TCCCCGGAAGAAATTTGCCT 59.592 50.000 0.73 0.00 0.00 4.75
187 223 1.203125 TCCCCGGAAGAAATTTGCCTT 60.203 47.619 0.73 0.00 0.00 4.35
188 224 2.041891 TCCCCGGAAGAAATTTGCCTTA 59.958 45.455 0.73 0.00 0.00 2.69
189 225 3.031013 CCCCGGAAGAAATTTGCCTTAT 58.969 45.455 0.73 0.00 0.00 1.73
190 226 3.450817 CCCCGGAAGAAATTTGCCTTATT 59.549 43.478 0.73 0.00 0.00 1.40
204 240 7.923414 TTTGCCTTATTCTTCTACTTCTTCC 57.077 36.000 0.00 0.00 0.00 3.46
220 256 0.987294 TTCCTCCTCCAGCTTTCCTG 59.013 55.000 0.00 0.00 41.41 3.86
322 360 6.338146 CGTTTCTTTCTTTCTTTTCCCCTTT 58.662 36.000 0.00 0.00 0.00 3.11
323 361 6.475727 CGTTTCTTTCTTTCTTTTCCCCTTTC 59.524 38.462 0.00 0.00 0.00 2.62
343 381 1.227383 CTTTCCCCCAATCCCTCCG 59.773 63.158 0.00 0.00 0.00 4.63
350 388 1.452108 CCAATCCCTCCGAGCAACC 60.452 63.158 0.00 0.00 0.00 3.77
403 453 1.775385 TCTATCCATCGCTGTCACCA 58.225 50.000 0.00 0.00 0.00 4.17
404 454 1.683385 TCTATCCATCGCTGTCACCAG 59.317 52.381 0.00 0.00 41.91 4.00
405 455 1.410517 CTATCCATCGCTGTCACCAGT 59.589 52.381 0.00 0.00 41.02 4.00
406 456 0.176680 ATCCATCGCTGTCACCAGTC 59.823 55.000 0.00 0.00 41.02 3.51
407 457 1.184970 TCCATCGCTGTCACCAGTCA 61.185 55.000 0.00 0.00 41.02 3.41
408 458 1.016130 CCATCGCTGTCACCAGTCAC 61.016 60.000 0.00 0.00 41.02 3.67
409 459 1.080501 ATCGCTGTCACCAGTCACG 60.081 57.895 0.00 0.00 41.02 4.35
410 460 3.406361 CGCTGTCACCAGTCACGC 61.406 66.667 0.00 0.00 41.02 5.34
411 461 3.044305 GCTGTCACCAGTCACGCC 61.044 66.667 0.00 0.00 41.02 5.68
412 462 2.357517 CTGTCACCAGTCACGCCC 60.358 66.667 0.00 0.00 33.80 6.13
413 463 3.883744 CTGTCACCAGTCACGCCCC 62.884 68.421 0.00 0.00 33.80 5.80
414 464 3.936203 GTCACCAGTCACGCCCCA 61.936 66.667 0.00 0.00 0.00 4.96
415 465 3.164977 TCACCAGTCACGCCCCAA 61.165 61.111 0.00 0.00 0.00 4.12
416 466 2.978010 CACCAGTCACGCCCCAAC 60.978 66.667 0.00 0.00 0.00 3.77
417 467 4.619227 ACCAGTCACGCCCCAACG 62.619 66.667 0.00 0.00 39.50 4.10
481 532 8.807667 AAAAAGATAGCATCACTTCTGTTTTG 57.192 30.769 0.00 0.00 27.50 2.44
482 533 5.557891 AGATAGCATCACTTCTGTTTTGC 57.442 39.130 0.00 0.00 33.88 3.68
483 534 2.693797 AGCATCACTTCTGTTTTGCG 57.306 45.000 0.00 0.00 36.89 4.85
484 535 2.221169 AGCATCACTTCTGTTTTGCGA 58.779 42.857 0.00 0.00 36.89 5.10
486 537 2.918131 GCATCACTTCTGTTTTGCGACC 60.918 50.000 0.00 0.00 0.00 4.79
487 538 1.305201 TCACTTCTGTTTTGCGACCC 58.695 50.000 0.00 0.00 0.00 4.46
488 539 1.021202 CACTTCTGTTTTGCGACCCA 58.979 50.000 0.00 0.00 0.00 4.51
502 557 2.276740 CCCATCCTCCTTGTGGCC 59.723 66.667 0.00 0.00 0.00 5.36
542 597 5.765182 CAGACCACTCAGATTACACCTTTTT 59.235 40.000 0.00 0.00 0.00 1.94
543 598 5.765182 AGACCACTCAGATTACACCTTTTTG 59.235 40.000 0.00 0.00 0.00 2.44
546 601 6.379988 ACCACTCAGATTACACCTTTTTGTTT 59.620 34.615 0.00 0.00 0.00 2.83
547 602 6.918022 CCACTCAGATTACACCTTTTTGTTTC 59.082 38.462 0.00 0.00 0.00 2.78
548 603 7.416213 CCACTCAGATTACACCTTTTTGTTTCA 60.416 37.037 0.00 0.00 0.00 2.69
549 604 7.432252 CACTCAGATTACACCTTTTTGTTTCAC 59.568 37.037 0.00 0.00 0.00 3.18
550 605 6.491394 TCAGATTACACCTTTTTGTTTCACG 58.509 36.000 0.00 0.00 0.00 4.35
600 655 2.070262 GGCTCACCTGCAATTGTTTC 57.930 50.000 7.40 0.00 34.04 2.78
613 668 6.808829 TGCAATTGTTTCTCTCTTGTCAAAT 58.191 32.000 7.40 0.00 0.00 2.32
615 670 8.412456 TGCAATTGTTTCTCTCTTGTCAAATTA 58.588 29.630 7.40 0.00 0.00 1.40
625 680 9.466497 TCTCTCTTGTCAAATTAATTATTGGCT 57.534 29.630 0.01 0.00 32.49 4.75
691 753 3.901797 CTCGGCTGTCAACCCACCC 62.902 68.421 0.00 0.00 0.00 4.61
693 755 3.897122 GGCTGTCAACCCACCCCA 61.897 66.667 0.00 0.00 0.00 4.96
694 756 2.197324 GCTGTCAACCCACCCCAA 59.803 61.111 0.00 0.00 0.00 4.12
695 757 2.200337 GCTGTCAACCCACCCCAAC 61.200 63.158 0.00 0.00 0.00 3.77
696 758 1.530655 CTGTCAACCCACCCCAACC 60.531 63.158 0.00 0.00 0.00 3.77
746 808 3.192103 AACTTCTCCGGCCACCCAC 62.192 63.158 2.24 0.00 0.00 4.61
747 809 3.636231 CTTCTCCGGCCACCCACA 61.636 66.667 2.24 0.00 0.00 4.17
748 810 3.612247 CTTCTCCGGCCACCCACAG 62.612 68.421 2.24 0.00 0.00 3.66
755 817 4.729918 GCCACCCACAGCCAGGAG 62.730 72.222 0.00 0.00 0.00 3.69
756 818 2.930019 CCACCCACAGCCAGGAGA 60.930 66.667 0.00 0.00 0.00 3.71
757 819 2.348998 CACCCACAGCCAGGAGAC 59.651 66.667 0.00 0.00 0.00 3.36
758 820 2.930562 ACCCACAGCCAGGAGACC 60.931 66.667 0.00 0.00 0.00 3.85
759 821 2.930019 CCCACAGCCAGGAGACCA 60.930 66.667 0.00 0.00 0.00 4.02
760 822 2.528818 CCCACAGCCAGGAGACCAA 61.529 63.158 0.00 0.00 0.00 3.67
761 823 1.302832 CCACAGCCAGGAGACCAAC 60.303 63.158 0.00 0.00 0.00 3.77
762 824 1.302832 CACAGCCAGGAGACCAACC 60.303 63.158 0.00 0.00 0.00 3.77
777 839 0.598065 CAACCAGGTAAGCAGCAACC 59.402 55.000 8.58 8.58 35.91 3.77
801 863 8.490311 ACCAACAAATTCCCAATCTTTTTCTTA 58.510 29.630 0.00 0.00 0.00 2.10
827 901 2.023673 CACCACATGTGTTGTTGACCT 58.976 47.619 23.79 0.00 40.26 3.85
834 908 4.142403 ACATGTGTTGTTGACCTTGACAAG 60.142 41.667 8.31 8.31 36.52 3.16
845 919 2.440539 CTTGACAAGGACGTGTAGCT 57.559 50.000 7.35 0.00 0.00 3.32
920 996 2.363306 TGGCACACATGTTTTCTCCT 57.637 45.000 0.00 0.00 0.00 3.69
921 997 2.229792 TGGCACACATGTTTTCTCCTC 58.770 47.619 0.00 0.00 0.00 3.71
923 999 1.541588 GCACACATGTTTTCTCCTCCC 59.458 52.381 0.00 0.00 0.00 4.30
926 1002 2.224867 ACACATGTTTTCTCCTCCCCTG 60.225 50.000 0.00 0.00 0.00 4.45
930 1006 3.680777 TGTTTTCTCCTCCCCTGTTTT 57.319 42.857 0.00 0.00 0.00 2.43
971 1047 7.129109 TCCACTTCAATTCAACTCGATTTAC 57.871 36.000 0.00 0.00 0.00 2.01
1002 1082 4.008933 GTGCCAGGACCGACAGCT 62.009 66.667 0.00 0.00 0.00 4.24
1018 1098 3.533547 ACAGCTCAATCTCATTCTCTGC 58.466 45.455 0.00 0.00 0.00 4.26
1025 1105 2.048444 TCTCATTCTCTGCCATTGCC 57.952 50.000 0.00 0.00 36.33 4.52
1026 1106 1.562942 TCTCATTCTCTGCCATTGCCT 59.437 47.619 0.00 0.00 36.33 4.75
1027 1107 2.025605 TCTCATTCTCTGCCATTGCCTT 60.026 45.455 0.00 0.00 36.33 4.35
1028 1108 2.758979 CTCATTCTCTGCCATTGCCTTT 59.241 45.455 0.00 0.00 36.33 3.11
1092 1180 3.238108 AGGACAAGCAGATAACAGACG 57.762 47.619 0.00 0.00 0.00 4.18
1111 1199 1.457455 CCAGCTCCTCCTCCTCCTC 60.457 68.421 0.00 0.00 0.00 3.71
1113 1201 1.625565 AGCTCCTCCTCCTCCTCCT 60.626 63.158 0.00 0.00 0.00 3.69
1114 1202 1.152546 GCTCCTCCTCCTCCTCCTC 60.153 68.421 0.00 0.00 0.00 3.71
1115 1203 1.943730 GCTCCTCCTCCTCCTCCTCA 61.944 65.000 0.00 0.00 0.00 3.86
1116 1204 0.859760 CTCCTCCTCCTCCTCCTCAT 59.140 60.000 0.00 0.00 0.00 2.90
1117 1205 0.856982 TCCTCCTCCTCCTCCTCATC 59.143 60.000 0.00 0.00 0.00 2.92
1118 1206 0.560193 CCTCCTCCTCCTCCTCATCA 59.440 60.000 0.00 0.00 0.00 3.07
1134 1222 4.216472 CCTCATCATCATTGGCAGAATCTG 59.784 45.833 5.78 5.78 34.12 2.90
1135 1223 5.043737 TCATCATCATTGGCAGAATCTGA 57.956 39.130 15.38 0.00 32.44 3.27
1136 1224 5.631119 TCATCATCATTGGCAGAATCTGAT 58.369 37.500 15.38 0.00 32.44 2.90
1137 1225 6.068670 TCATCATCATTGGCAGAATCTGATT 58.931 36.000 15.38 1.81 32.44 2.57
1171 1259 0.110486 TGAGAGGCACCAAAAGGGAC 59.890 55.000 0.00 0.00 41.15 4.46
1253 1341 1.741770 ATCGAGCTGCCCGACAAAC 60.742 57.895 8.80 0.00 38.97 2.93
1317 1405 1.531365 CCAGCAAACCAGAGGCCAA 60.531 57.895 5.01 0.00 0.00 4.52
1369 1457 3.501396 CAGTTCATGCCGCGGAAT 58.499 55.556 33.48 24.55 0.00 3.01
1384 1472 1.202580 CGGAATCTCCAGGCTTTCGAT 60.203 52.381 0.00 0.00 35.91 3.59
1390 1478 2.897350 CAGGCTTTCGATCCGGCC 60.897 66.667 0.00 0.00 44.38 6.13
1447 1535 2.486918 GTGTACCAGTACGCCAAGTTT 58.513 47.619 9.83 0.00 39.84 2.66
1459 1547 0.593128 CCAAGTTTGCCAAGACCTCG 59.407 55.000 0.00 0.00 0.00 4.63
1460 1548 1.308998 CAAGTTTGCCAAGACCTCGT 58.691 50.000 0.00 0.00 0.00 4.18
1579 1667 2.122547 AGGTCCCAGACGGTGGTT 60.123 61.111 5.44 0.00 46.37 3.67
1583 1671 0.883370 GTCCCAGACGGTGGTTGTTC 60.883 60.000 5.44 0.00 46.37 3.18
1591 1679 1.966451 GGTGGTTGTTCTGCTCGGG 60.966 63.158 0.00 0.00 0.00 5.14
1597 1685 2.032681 GTTCTGCTCGGGTGGCTT 59.967 61.111 0.00 0.00 0.00 4.35
1615 1703 1.230635 TTGGCTCGAAGCAGAAGCAC 61.231 55.000 8.71 0.00 44.75 4.40
1627 1715 3.118811 AGCAGAAGCACCTGAAGAGATAC 60.119 47.826 9.22 0.00 45.49 2.24
1657 1745 2.087248 CACCTCCAGGGGTTTCCAT 58.913 57.895 0.00 0.00 37.52 3.41
1726 1814 1.065782 GGAGGGAAGGCTGAGAAGAAC 60.066 57.143 0.00 0.00 0.00 3.01
1849 1937 3.237628 GCGCAGTTTCTTTGGATTTCTC 58.762 45.455 0.30 0.00 0.00 2.87
1852 1940 3.826466 CAGTTTCTTTGGATTTCTCGCC 58.174 45.455 0.00 0.00 0.00 5.54
1854 1942 4.022849 CAGTTTCTTTGGATTTCTCGCCTT 60.023 41.667 0.00 0.00 0.00 4.35
1855 1943 4.584743 AGTTTCTTTGGATTTCTCGCCTTT 59.415 37.500 0.00 0.00 0.00 3.11
1857 1945 6.264518 AGTTTCTTTGGATTTCTCGCCTTTAA 59.735 34.615 0.00 0.00 0.00 1.52
1858 1946 5.622770 TCTTTGGATTTCTCGCCTTTAAC 57.377 39.130 0.00 0.00 0.00 2.01
1860 1948 5.181245 TCTTTGGATTTCTCGCCTTTAACAG 59.819 40.000 0.00 0.00 0.00 3.16
1864 1952 5.998981 TGGATTTCTCGCCTTTAACAGTTAA 59.001 36.000 1.26 1.26 0.00 2.01
1865 1953 6.072893 TGGATTTCTCGCCTTTAACAGTTAAC 60.073 38.462 5.16 0.00 0.00 2.01
1868 1967 5.204409 TCTCGCCTTTAACAGTTAACTGA 57.796 39.130 36.14 16.62 46.59 3.41
1870 1969 5.694910 TCTCGCCTTTAACAGTTAACTGAAG 59.305 40.000 36.14 27.48 46.59 3.02
1875 1974 7.044314 CGCCTTTAACAGTTAACTGAAGTTTTG 60.044 37.037 36.14 20.45 46.59 2.44
2141 2248 7.589395 TGTTTATTATGCTGAACGAATGTGTT 58.411 30.769 0.00 0.00 34.02 3.32
2200 2311 7.388776 TCTGTCATTTACTCTGTTCCTCAATTG 59.611 37.037 0.00 0.00 0.00 2.32
2249 2360 5.823353 ACGGTTTGTTCGAACATAAACATT 58.177 33.333 31.57 21.30 38.95 2.71
2251 2362 5.386933 CGGTTTGTTCGAACATAAACATTGC 60.387 40.000 31.57 20.19 38.95 3.56
2512 2633 2.847441 CAGCTCATCCACATATGCAGT 58.153 47.619 1.58 0.00 0.00 4.40
2526 2647 5.894393 ACATATGCAGTAGTAGGAGTTCTGT 59.106 40.000 1.58 0.00 0.00 3.41
2527 2648 4.727507 ATGCAGTAGTAGGAGTTCTGTG 57.272 45.455 0.00 0.00 0.00 3.66
2684 2809 8.869897 CATCATTGATTATATCTTGCCAAATGC 58.130 33.333 0.00 0.00 41.77 3.56
2685 2810 7.380536 TCATTGATTATATCTTGCCAAATGCC 58.619 34.615 0.00 0.00 40.16 4.40
2686 2811 6.728089 TTGATTATATCTTGCCAAATGCCA 57.272 33.333 0.00 0.00 40.16 4.92
2941 3110 8.268850 ACTACATGGTTCAGTTAATCAACATC 57.731 34.615 0.00 0.00 37.10 3.06
3019 3219 0.771127 AACCAAACTGCCCTCAGCTA 59.229 50.000 0.00 0.00 44.10 3.32
3106 3306 1.692411 GAAAAGCAGGGTGTGAGGTT 58.308 50.000 0.00 0.00 0.00 3.50
3124 3324 2.607771 GGTTAGGTCGTGCGACTTTGTA 60.608 50.000 21.54 8.13 44.04 2.41
3127 3327 1.271379 AGGTCGTGCGACTTTGTATCA 59.729 47.619 21.54 0.00 44.04 2.15
3313 3550 7.502226 GTGATCCATTGAAATGTACCAGGATTA 59.498 37.037 0.00 0.00 34.60 1.75
3314 3551 8.226810 TGATCCATTGAAATGTACCAGGATTAT 58.773 33.333 0.00 0.00 34.60 1.28
3315 3552 9.739276 GATCCATTGAAATGTACCAGGATTATA 57.261 33.333 0.00 0.00 34.60 0.98
3441 3685 3.128415 GCAAAACAAAATTGTGGTTGGCT 59.872 39.130 17.29 0.00 41.25 4.75
3442 3686 4.380339 GCAAAACAAAATTGTGGTTGGCTT 60.380 37.500 17.29 0.00 41.25 4.35
3443 3687 4.961435 AAACAAAATTGTGGTTGGCTTG 57.039 36.364 0.00 0.00 41.31 4.01
3465 3719 1.102809 TGCTGTTGGTTCCAGTGCAG 61.103 55.000 12.30 12.30 32.41 4.41
3498 3758 0.749454 GTGTGGATGGGAGATGTGCC 60.749 60.000 0.00 0.00 33.79 5.01
3552 3823 2.159043 ACTGTCTCTCTGTGTGTGGTTG 60.159 50.000 0.00 0.00 0.00 3.77
3555 3826 1.831106 TCTCTCTGTGTGTGGTTGTGT 59.169 47.619 0.00 0.00 0.00 3.72
3575 3847 3.507233 TGTCTGTGATCCTGCAAATTTCC 59.493 43.478 0.00 0.00 0.00 3.13
3576 3848 3.091545 TCTGTGATCCTGCAAATTTCCC 58.908 45.455 0.00 0.00 0.00 3.97
3588 3860 2.403252 AATTTCCCGTGGCTACTGAG 57.597 50.000 0.00 0.00 0.00 3.35
3590 3862 1.550130 TTTCCCGTGGCTACTGAGGG 61.550 60.000 5.44 5.44 43.32 4.30
3595 3867 1.888436 CGTGGCTACTGAGGGAAGCA 61.888 60.000 0.00 0.00 38.01 3.91
3597 3869 1.762957 GTGGCTACTGAGGGAAGCATA 59.237 52.381 6.15 0.00 38.01 3.14
3629 3910 7.873719 TTTCATTATATGTTCACGGGACATT 57.126 32.000 7.82 1.20 38.58 2.71
3652 3933 5.620206 TGAGCTGTTTCTGGTATTCTCAAA 58.380 37.500 0.00 0.00 0.00 2.69
3653 3934 6.061441 TGAGCTGTTTCTGGTATTCTCAAAA 58.939 36.000 0.00 0.00 0.00 2.44
3682 3963 6.496565 TCAGAAATCTTTTAATGGCCAAAGGA 59.503 34.615 10.96 6.18 31.86 3.36
3684 3965 7.661027 CAGAAATCTTTTAATGGCCAAAGGAAA 59.339 33.333 10.96 8.10 31.86 3.13
3694 3975 3.573967 TGGCCAAAGGAAATTCTGAACTC 59.426 43.478 0.61 0.00 0.00 3.01
3707 3988 3.969287 CTGAACTCAGATCACAGGGAA 57.031 47.619 0.03 0.00 46.59 3.97
3708 3989 4.484537 CTGAACTCAGATCACAGGGAAT 57.515 45.455 0.03 0.00 46.59 3.01
3709 3990 4.440880 CTGAACTCAGATCACAGGGAATC 58.559 47.826 0.03 0.00 46.59 2.52
3710 3991 4.099633 TGAACTCAGATCACAGGGAATCT 58.900 43.478 0.00 0.00 0.00 2.40
3711 3992 4.533707 TGAACTCAGATCACAGGGAATCTT 59.466 41.667 0.00 0.00 0.00 2.40
3712 3993 5.013495 TGAACTCAGATCACAGGGAATCTTT 59.987 40.000 0.00 0.00 0.00 2.52
3717 3998 5.190330 TCAGATCACAGGGAATCTTTCATGA 59.810 40.000 0.00 0.00 0.00 3.07
3718 3999 6.062749 CAGATCACAGGGAATCTTTCATGAT 58.937 40.000 0.00 0.00 0.00 2.45
3760 4045 8.490355 GCAATACTCTTTCCAACTTTTCAAATG 58.510 33.333 0.00 0.00 0.00 2.32
3784 4069 3.949842 TGATTGGAGATCGATGCTAGG 57.050 47.619 0.54 0.00 0.00 3.02
3788 4073 1.333177 GGAGATCGATGCTAGGTGGT 58.667 55.000 0.54 0.00 0.00 4.16
3789 4074 1.689273 GGAGATCGATGCTAGGTGGTT 59.311 52.381 0.54 0.00 0.00 3.67
3790 4075 2.103263 GGAGATCGATGCTAGGTGGTTT 59.897 50.000 0.54 0.00 0.00 3.27
3792 4077 1.599542 GATCGATGCTAGGTGGTTTGC 59.400 52.381 0.54 0.00 0.00 3.68
3793 4078 0.323302 TCGATGCTAGGTGGTTTGCA 59.677 50.000 0.00 0.00 39.83 4.08
3794 4079 0.729116 CGATGCTAGGTGGTTTGCAG 59.271 55.000 0.00 0.00 38.87 4.41
3796 4081 2.676750 CGATGCTAGGTGGTTTGCAGTA 60.677 50.000 0.00 0.00 38.87 2.74
3800 4143 2.812613 GCTAGGTGGTTTGCAGTACCAA 60.813 50.000 20.48 8.10 46.62 3.67
3823 4166 2.025981 TGCCATCCAGCAGAGTATTTGT 60.026 45.455 0.00 0.00 38.00 2.83
3825 4168 3.181493 GCCATCCAGCAGAGTATTTGTTG 60.181 47.826 0.00 0.00 0.00 3.33
3835 4178 3.957497 AGAGTATTTGTTGGTGGTTTGCA 59.043 39.130 0.00 0.00 0.00 4.08
3836 4179 4.037923 AGAGTATTTGTTGGTGGTTTGCAG 59.962 41.667 0.00 0.00 0.00 4.41
3839 4182 3.512033 TTTGTTGGTGGTTTGCAGTAC 57.488 42.857 0.00 0.00 0.00 2.73
3840 4183 2.130272 TGTTGGTGGTTTGCAGTACA 57.870 45.000 0.00 0.00 0.00 2.90
3841 4184 2.447443 TGTTGGTGGTTTGCAGTACAA 58.553 42.857 0.00 0.00 36.13 2.41
3842 4185 2.826128 TGTTGGTGGTTTGCAGTACAAA 59.174 40.909 0.00 0.00 46.01 2.83
3852 4195 1.617357 TGCAGTACAAATTGCCATGCA 59.383 42.857 13.22 13.22 37.53 3.96
3853 4196 2.264813 GCAGTACAAATTGCCATGCAG 58.735 47.619 10.63 0.00 40.61 4.41
3855 4198 3.766151 CAGTACAAATTGCCATGCAGAG 58.234 45.455 0.00 0.00 40.61 3.35
3859 4202 1.203758 CAAATTGCCATGCAGAGCAGA 59.796 47.619 12.61 5.98 43.65 4.26
3860 4203 1.103803 AATTGCCATGCAGAGCAGAG 58.896 50.000 12.61 0.00 43.65 3.35
3861 4204 0.034380 ATTGCCATGCAGAGCAGAGT 60.034 50.000 12.61 2.50 43.65 3.24
3862 4205 0.614812 TTGCCATGCAGAGCAGAGTA 59.385 50.000 12.61 0.00 43.65 2.59
3863 4206 0.835276 TGCCATGCAGAGCAGAGTAT 59.165 50.000 9.24 0.00 43.65 2.12
3864 4207 1.227639 GCCATGCAGAGCAGAGTATG 58.772 55.000 5.90 0.00 43.65 2.39
3865 4208 1.474677 GCCATGCAGAGCAGAGTATGT 60.475 52.381 5.90 0.00 43.65 2.29
3866 4209 2.210961 CCATGCAGAGCAGAGTATGTG 58.789 52.381 0.00 0.00 43.65 3.21
3879 4222 6.872628 CAGAGTATGTGCCATTGTTGATAT 57.127 37.500 0.00 0.00 0.00 1.63
3880 4223 6.895898 CAGAGTATGTGCCATTGTTGATATC 58.104 40.000 0.00 0.00 0.00 1.63
3886 4229 4.395854 TGTGCCATTGTTGATATCAGACAC 59.604 41.667 15.73 9.61 0.00 3.67
3887 4230 3.947196 TGCCATTGTTGATATCAGACACC 59.053 43.478 15.73 8.74 0.00 4.16
3888 4231 3.947196 GCCATTGTTGATATCAGACACCA 59.053 43.478 15.73 7.24 0.00 4.17
3891 4234 4.558226 TTGTTGATATCAGACACCAGCT 57.442 40.909 15.73 0.00 0.00 4.24
3896 4239 3.891977 TGATATCAGACACCAGCTCCTAC 59.108 47.826 0.00 0.00 0.00 3.18
3924 4267 2.877300 GCAGAGCCTGATTCCTTGTTGA 60.877 50.000 6.40 0.00 32.44 3.18
3955 4298 2.427753 GGATGGCATCCTCGGTCC 59.572 66.667 34.15 12.12 46.19 4.46
3956 4299 2.427753 GATGGCATCCTCGGTCCC 59.572 66.667 16.75 0.00 0.00 4.46
3957 4300 3.171388 ATGGCATCCTCGGTCCCC 61.171 66.667 0.00 0.00 0.00 4.81
3960 4303 3.090532 GCATCCTCGGTCCCCCTT 61.091 66.667 0.00 0.00 0.00 3.95
3961 4304 3.108288 GCATCCTCGGTCCCCCTTC 62.108 68.421 0.00 0.00 0.00 3.46
3962 4305 2.040779 ATCCTCGGTCCCCCTTCC 60.041 66.667 0.00 0.00 0.00 3.46
3963 4306 4.772231 TCCTCGGTCCCCCTTCCG 62.772 72.222 0.00 0.00 46.93 4.30
3975 4318 1.982938 CCTTCCGTCGGACCCTCTT 60.983 63.158 15.07 0.00 0.00 2.85
3976 4319 1.542187 CCTTCCGTCGGACCCTCTTT 61.542 60.000 15.07 0.00 0.00 2.52
3988 4331 1.039233 CCCTCTTTGCCATGGCGATT 61.039 55.000 30.87 0.00 45.51 3.34
4042 4385 2.731572 CCTGACAGGCCTTTTCATGAT 58.268 47.619 8.99 0.00 0.00 2.45
4043 4386 3.094572 CCTGACAGGCCTTTTCATGATT 58.905 45.455 8.99 0.00 0.00 2.57
4044 4387 3.129988 CCTGACAGGCCTTTTCATGATTC 59.870 47.826 8.99 0.00 0.00 2.52
4045 4388 3.760151 CTGACAGGCCTTTTCATGATTCA 59.240 43.478 0.00 0.00 0.00 2.57
4046 4389 3.760151 TGACAGGCCTTTTCATGATTCAG 59.240 43.478 0.00 0.00 0.00 3.02
4047 4390 4.012374 GACAGGCCTTTTCATGATTCAGA 58.988 43.478 0.00 0.00 0.00 3.27
4048 4391 4.015084 ACAGGCCTTTTCATGATTCAGAG 58.985 43.478 0.00 0.00 0.00 3.35
4075 4418 1.138883 GATGTCGTGTCGCTGCCTA 59.861 57.895 0.00 0.00 0.00 3.93
4076 4419 0.457853 GATGTCGTGTCGCTGCCTAA 60.458 55.000 0.00 0.00 0.00 2.69
4079 4422 1.076332 GTCGTGTCGCTGCCTAAAAT 58.924 50.000 0.00 0.00 0.00 1.82
4081 4424 1.067142 TCGTGTCGCTGCCTAAAATCT 60.067 47.619 0.00 0.00 0.00 2.40
4083 4426 3.123804 CGTGTCGCTGCCTAAAATCTAT 58.876 45.455 0.00 0.00 0.00 1.98
4084 4427 4.037089 TCGTGTCGCTGCCTAAAATCTATA 59.963 41.667 0.00 0.00 0.00 1.31
4085 4428 4.743151 CGTGTCGCTGCCTAAAATCTATAA 59.257 41.667 0.00 0.00 0.00 0.98
4299 5179 2.401766 GGCGATGCACTGTGAAGGG 61.402 63.158 12.86 0.00 0.00 3.95
4302 5182 0.036952 CGATGCACTGTGAAGGGTCT 60.037 55.000 12.86 0.00 0.00 3.85
4343 5223 0.329596 AGCTTAGGGGTTGCTCCTTG 59.670 55.000 0.00 0.00 35.92 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.074951 GGTGGTGTGGGAAAGAGGG 59.925 63.158 0.00 0.00 0.00 4.30
5 6 1.602323 GATGCGGTGGTGTGGGAAA 60.602 57.895 0.00 0.00 0.00 3.13
7 8 4.028490 GGATGCGGTGGTGTGGGA 62.028 66.667 0.00 0.00 0.00 4.37
11 12 1.600636 CACAAGGATGCGGTGGTGT 60.601 57.895 4.54 0.00 0.00 4.16
41 42 0.761802 GCGAGGAGAAGGGATCCAAT 59.238 55.000 15.23 0.22 39.47 3.16
61 62 0.695803 AGGGGATTCGGCTGATTCCT 60.696 55.000 27.52 15.43 42.04 3.36
95 102 1.400500 CCGGAAACCAAATCGAAACCG 60.400 52.381 0.00 0.00 39.02 4.44
122 129 4.426313 GAGGTTGGGGAAGGGGCG 62.426 72.222 0.00 0.00 0.00 6.13
123 130 4.426313 CGAGGTTGGGGAAGGGGC 62.426 72.222 0.00 0.00 0.00 5.80
124 131 4.426313 GCGAGGTTGGGGAAGGGG 62.426 72.222 0.00 0.00 0.00 4.79
125 132 4.426313 GGCGAGGTTGGGGAAGGG 62.426 72.222 0.00 0.00 0.00 3.95
126 133 4.778143 CGGCGAGGTTGGGGAAGG 62.778 72.222 0.00 0.00 0.00 3.46
140 147 3.567797 GTGGATTCGAGCAGCGGC 61.568 66.667 0.00 0.00 41.33 6.53
145 152 0.036388 GGAAGTGGTGGATTCGAGCA 60.036 55.000 0.00 0.00 0.00 4.26
165 197 0.173481 GCAAATTTCTTCCGGGGAGC 59.827 55.000 0.00 0.00 0.00 4.70
168 200 1.266178 AAGGCAAATTTCTTCCGGGG 58.734 50.000 0.00 0.00 0.00 5.73
181 217 7.259088 AGGAAGAAGTAGAAGAATAAGGCAA 57.741 36.000 0.00 0.00 0.00 4.52
184 220 7.201965 GGAGGAGGAAGAAGTAGAAGAATAAGG 60.202 44.444 0.00 0.00 0.00 2.69
185 221 7.343316 TGGAGGAGGAAGAAGTAGAAGAATAAG 59.657 40.741 0.00 0.00 0.00 1.73
186 222 7.189794 TGGAGGAGGAAGAAGTAGAAGAATAA 58.810 38.462 0.00 0.00 0.00 1.40
187 223 6.742756 TGGAGGAGGAAGAAGTAGAAGAATA 58.257 40.000 0.00 0.00 0.00 1.75
188 224 5.594777 TGGAGGAGGAAGAAGTAGAAGAAT 58.405 41.667 0.00 0.00 0.00 2.40
189 225 5.011982 TGGAGGAGGAAGAAGTAGAAGAA 57.988 43.478 0.00 0.00 0.00 2.52
190 226 4.605183 CTGGAGGAGGAAGAAGTAGAAGA 58.395 47.826 0.00 0.00 0.00 2.87
196 232 2.037385 AAGCTGGAGGAGGAAGAAGT 57.963 50.000 0.00 0.00 0.00 3.01
204 240 2.689073 TCCAGGAAAGCTGGAGGAG 58.311 57.895 0.00 0.00 45.15 3.69
220 256 7.099764 GGGAAATCTTGATCTTTTTCCTTTCC 58.900 38.462 19.35 15.06 44.21 3.13
221 257 7.038729 AGGGGAAATCTTGATCTTTTTCCTTTC 60.039 37.037 19.35 13.33 44.21 2.62
222 258 6.789457 AGGGGAAATCTTGATCTTTTTCCTTT 59.211 34.615 19.35 11.12 44.21 3.11
223 259 6.326161 AGGGGAAATCTTGATCTTTTTCCTT 58.674 36.000 19.35 7.62 44.21 3.36
224 260 5.908590 AGGGGAAATCTTGATCTTTTTCCT 58.091 37.500 19.35 9.79 44.21 3.36
235 271 1.002857 ACAGGGGAGGGGAAATCTTG 58.997 55.000 0.00 0.00 0.00 3.02
298 334 5.515797 AGGGGAAAAGAAAGAAAGAAACG 57.484 39.130 0.00 0.00 0.00 3.60
322 360 0.924226 GAGGGATTGGGGGAAAGGGA 60.924 60.000 0.00 0.00 0.00 4.20
323 361 1.620818 GAGGGATTGGGGGAAAGGG 59.379 63.158 0.00 0.00 0.00 3.95
343 381 2.970974 GCTGGCGTCAAGGTTGCTC 61.971 63.158 0.00 0.00 0.00 4.26
431 481 2.940994 TTGTTGAACGGGATGGAAGA 57.059 45.000 0.00 0.00 0.00 2.87
467 518 1.880027 GGGTCGCAAAACAGAAGTGAT 59.120 47.619 0.00 0.00 0.00 3.06
474 525 0.804989 GAGGATGGGTCGCAAAACAG 59.195 55.000 0.00 0.00 0.00 3.16
481 532 1.450312 CACAAGGAGGATGGGTCGC 60.450 63.158 0.00 0.00 0.00 5.19
482 533 1.221840 CCACAAGGAGGATGGGTCG 59.778 63.158 0.00 0.00 36.89 4.79
483 534 1.077429 GCCACAAGGAGGATGGGTC 60.077 63.158 0.00 0.00 36.89 4.46
484 535 2.616458 GGCCACAAGGAGGATGGGT 61.616 63.158 0.00 0.00 36.89 4.51
486 537 2.124570 CGGCCACAAGGAGGATGG 60.125 66.667 2.24 0.00 36.89 3.51
487 538 1.746615 CACGGCCACAAGGAGGATG 60.747 63.158 2.24 0.00 36.89 3.51
488 539 2.671070 CACGGCCACAAGGAGGAT 59.329 61.111 2.24 0.00 36.89 3.24
563 618 8.494433 AGGTGAGCCTCTTGATTTGTAATATAA 58.506 33.333 0.00 0.00 42.67 0.98
568 623 4.326826 CAGGTGAGCCTCTTGATTTGTAA 58.673 43.478 0.00 0.00 44.97 2.41
569 624 3.869912 GCAGGTGAGCCTCTTGATTTGTA 60.870 47.826 0.00 0.00 44.97 2.41
570 625 2.787994 CAGGTGAGCCTCTTGATTTGT 58.212 47.619 0.00 0.00 44.97 2.83
571 626 1.471684 GCAGGTGAGCCTCTTGATTTG 59.528 52.381 0.00 0.00 44.97 2.32
572 627 1.074405 TGCAGGTGAGCCTCTTGATTT 59.926 47.619 0.00 0.00 44.97 2.17
577 632 1.202976 ACAATTGCAGGTGAGCCTCTT 60.203 47.619 5.05 0.00 44.97 2.85
600 655 9.512435 CAGCCAATAATTAATTTGACAAGAGAG 57.488 33.333 5.91 0.00 0.00 3.20
613 668 3.630168 TCCTGCAGCAGCCAATAATTAA 58.370 40.909 17.81 0.00 41.13 1.40
615 670 2.029623 CTCCTGCAGCAGCCAATAATT 58.970 47.619 17.81 0.00 41.13 1.40
692 754 3.305516 GGGTGGCTGCCAAGGTTG 61.306 66.667 25.23 0.00 34.18 3.77
693 755 4.621087 GGGGTGGCTGCCAAGGTT 62.621 66.667 25.23 0.00 34.18 3.50
696 758 4.601794 TGTGGGGTGGCTGCCAAG 62.602 66.667 25.23 0.00 34.18 3.61
746 808 1.002868 CTGGTTGGTCTCCTGGCTG 60.003 63.158 0.00 0.00 0.00 4.85
747 809 2.227036 CCTGGTTGGTCTCCTGGCT 61.227 63.158 0.00 0.00 37.28 4.75
748 810 2.352805 CCTGGTTGGTCTCCTGGC 59.647 66.667 0.00 0.00 37.28 4.85
757 819 0.598065 GTTGCTGCTTACCTGGTTGG 59.402 55.000 3.84 0.00 42.93 3.77
758 820 0.598065 GGTTGCTGCTTACCTGGTTG 59.402 55.000 3.84 0.00 0.00 3.77
759 821 0.184933 TGGTTGCTGCTTACCTGGTT 59.815 50.000 19.94 0.00 35.41 3.67
760 822 0.184933 TTGGTTGCTGCTTACCTGGT 59.815 50.000 19.94 4.05 35.41 4.00
761 823 0.598065 GTTGGTTGCTGCTTACCTGG 59.402 55.000 19.94 0.00 35.41 4.45
762 824 1.317613 TGTTGGTTGCTGCTTACCTG 58.682 50.000 19.94 0.00 35.41 4.00
810 879 3.128415 TGTCAAGGTCAACAACACATGTG 59.872 43.478 24.25 24.25 42.99 3.21
827 901 1.411246 ACAGCTACACGTCCTTGTCAA 59.589 47.619 0.00 0.00 0.00 3.18
834 908 1.135460 GTCCTACACAGCTACACGTCC 60.135 57.143 0.00 0.00 0.00 4.79
920 996 1.150536 AAGCGCTGAAAACAGGGGA 59.849 52.632 12.58 0.00 35.91 4.81
921 997 1.172180 TCAAGCGCTGAAAACAGGGG 61.172 55.000 12.58 0.00 35.91 4.79
930 1006 2.162208 GTGGATTCAATTCAAGCGCTGA 59.838 45.455 12.58 8.22 0.00 4.26
1000 1080 2.915349 TGGCAGAGAATGAGATTGAGC 58.085 47.619 0.00 0.00 0.00 4.26
1002 1082 3.630769 GCAATGGCAGAGAATGAGATTGA 59.369 43.478 0.00 0.00 40.72 2.57
1018 1098 5.718724 AGAAGAAGAAGAAAAGGCAATGG 57.281 39.130 0.00 0.00 0.00 3.16
1092 1180 3.160748 GGAGGAGGAGGAGCTGGC 61.161 72.222 0.00 0.00 0.00 4.85
1111 1199 4.216472 CAGATTCTGCCAATGATGATGAGG 59.784 45.833 0.00 0.00 0.00 3.86
1113 1201 5.043737 TCAGATTCTGCCAATGATGATGA 57.956 39.130 8.89 0.00 0.00 2.92
1114 1202 5.966742 ATCAGATTCTGCCAATGATGATG 57.033 39.130 8.89 0.00 0.00 3.07
1115 1203 6.068670 TCAATCAGATTCTGCCAATGATGAT 58.931 36.000 8.89 0.00 31.24 2.45
1116 1204 5.442391 TCAATCAGATTCTGCCAATGATGA 58.558 37.500 8.89 3.14 31.24 2.92
1117 1205 5.767816 TCAATCAGATTCTGCCAATGATG 57.232 39.130 8.89 1.07 31.24 3.07
1118 1206 6.549736 TCAATCAATCAGATTCTGCCAATGAT 59.450 34.615 8.89 11.56 45.06 2.45
1134 1222 6.439599 CCTCTCAGCAATCAATCAATCAATC 58.560 40.000 0.00 0.00 0.00 2.67
1135 1223 5.221263 GCCTCTCAGCAATCAATCAATCAAT 60.221 40.000 0.00 0.00 0.00 2.57
1136 1224 4.097437 GCCTCTCAGCAATCAATCAATCAA 59.903 41.667 0.00 0.00 0.00 2.57
1137 1225 3.630769 GCCTCTCAGCAATCAATCAATCA 59.369 43.478 0.00 0.00 0.00 2.57
1253 1341 3.072476 CCTGTGGTGGTGGGAGAG 58.928 66.667 0.00 0.00 0.00 3.20
1317 1405 3.971702 GGGCTGAAGGGGCTGTGT 61.972 66.667 0.00 0.00 0.00 3.72
1363 1451 1.432270 CGAAAGCCTGGAGATTCCGC 61.432 60.000 0.00 0.00 40.17 5.54
1369 1457 1.676678 CCGGATCGAAAGCCTGGAGA 61.677 60.000 0.00 0.00 33.56 3.71
1429 1517 1.196127 GCAAACTTGGCGTACTGGTAC 59.804 52.381 1.18 1.18 0.00 3.34
1447 1535 2.204461 TTCCGACGAGGTCTTGGCA 61.204 57.895 0.00 0.00 41.99 4.92
1459 1547 3.119096 GCCGCCTCTTGTTCCGAC 61.119 66.667 0.00 0.00 0.00 4.79
1460 1548 4.735132 CGCCGCCTCTTGTTCCGA 62.735 66.667 0.00 0.00 0.00 4.55
1579 1667 2.818169 AAGCCACCCGAGCAGAACA 61.818 57.895 0.00 0.00 0.00 3.18
1597 1685 1.669115 GTGCTTCTGCTTCGAGCCA 60.669 57.895 4.73 0.00 41.51 4.75
1615 1703 2.398498 CAATCGGCGTATCTCTTCAGG 58.602 52.381 6.85 0.00 0.00 3.86
1627 1715 1.520787 GGAGGTGTACCAATCGGCG 60.521 63.158 0.00 0.00 38.89 6.46
1651 1739 0.109532 TGAAGGTGACGGCATGGAAA 59.890 50.000 0.00 0.00 0.00 3.13
1657 1745 2.847234 AGGGTGAAGGTGACGGCA 60.847 61.111 0.00 0.00 0.00 5.69
1849 1937 5.668558 ACTTCAGTTAACTGTTAAAGGCG 57.331 39.130 29.83 12.10 44.12 5.52
1854 1942 8.736244 AGCTTCAAAACTTCAGTTAACTGTTAA 58.264 29.630 29.83 19.06 44.12 2.01
1855 1943 8.276252 AGCTTCAAAACTTCAGTTAACTGTTA 57.724 30.769 29.83 19.71 44.12 2.41
1857 1945 6.759497 AGCTTCAAAACTTCAGTTAACTGT 57.241 33.333 29.83 12.66 44.12 3.55
1858 1946 9.736023 AATAAGCTTCAAAACTTCAGTTAACTG 57.264 29.630 26.60 26.60 45.08 3.16
1864 1952 7.814587 GCCATAAATAAGCTTCAAAACTTCAGT 59.185 33.333 0.00 0.00 0.00 3.41
1865 1953 8.031277 AGCCATAAATAAGCTTCAAAACTTCAG 58.969 33.333 0.00 0.00 31.27 3.02
1868 1967 8.992073 CAAAGCCATAAATAAGCTTCAAAACTT 58.008 29.630 0.00 0.00 45.77 2.66
1870 1969 8.223100 CACAAAGCCATAAATAAGCTTCAAAAC 58.777 33.333 0.00 0.00 45.77 2.43
1875 1974 6.183360 GCAACACAAAGCCATAAATAAGCTTC 60.183 38.462 0.00 0.00 45.77 3.86
2141 2248 8.918202 ATAAGAAGGATAAAACACAACTGACA 57.082 30.769 0.00 0.00 0.00 3.58
2200 2311 3.733727 CCTGCGTGGTGTTCAAAAATAAC 59.266 43.478 0.00 0.00 0.00 1.89
2350 2461 3.149196 CAGACCTTGTATTTGGTGCAGT 58.851 45.455 0.00 0.00 36.59 4.40
2512 2633 6.109156 TGAAAATGCACAGAACTCCTACTA 57.891 37.500 0.00 0.00 0.00 1.82
2526 2647 1.340889 GTCCACAAGGCTGAAAATGCA 59.659 47.619 0.00 0.00 33.74 3.96
2527 2648 1.340889 TGTCCACAAGGCTGAAAATGC 59.659 47.619 0.00 0.00 33.74 3.56
2655 2778 7.368480 TGGCAAGATATAATCAATGATGACG 57.632 36.000 0.00 0.00 38.69 4.35
2686 2811 3.084039 CTGTTACAACATGAGCCATGGT 58.916 45.455 14.67 9.37 43.13 3.55
2878 3030 9.224267 GCATTTAGGACATGTTATATGACATCT 57.776 33.333 10.02 7.62 38.15 2.90
3019 3219 4.201960 CGATCGGCAGAGCTGTATATGTAT 60.202 45.833 7.38 0.00 36.18 2.29
3106 3306 2.488937 TGATACAAAGTCGCACGACCTA 59.511 45.455 18.81 5.04 45.59 3.08
3124 3324 1.392710 GGTCGACGTGAGGGGATGAT 61.393 60.000 9.92 0.00 0.00 2.45
3127 3327 2.036731 TGGTCGACGTGAGGGGAT 59.963 61.111 9.92 0.00 0.00 3.85
3315 3552 9.587772 GTCAGATGTATAATTAGCCGATGTATT 57.412 33.333 0.00 0.00 0.00 1.89
3441 3685 0.746063 CTGGAACCAACAGCAAGCAA 59.254 50.000 0.00 0.00 0.00 3.91
3442 3686 0.395586 ACTGGAACCAACAGCAAGCA 60.396 50.000 0.00 0.00 39.55 3.91
3443 3687 0.031178 CACTGGAACCAACAGCAAGC 59.969 55.000 0.00 0.00 39.55 4.01
3465 3719 5.874261 CCCATCCACACAAATAAATGGTTTC 59.126 40.000 0.00 0.00 33.37 2.78
3498 3758 4.756642 TCAGAGTATGCACAAAGAAACCAG 59.243 41.667 0.00 0.00 0.00 4.00
3552 3823 4.479619 GAAATTTGCAGGATCACAGACAC 58.520 43.478 0.00 0.00 0.00 3.67
3555 3826 3.091545 GGGAAATTTGCAGGATCACAGA 58.908 45.455 12.05 0.00 0.00 3.41
3575 3847 1.517832 CTTCCCTCAGTAGCCACGG 59.482 63.158 0.00 0.00 0.00 4.94
3576 3848 1.153549 GCTTCCCTCAGTAGCCACG 60.154 63.158 0.00 0.00 0.00 4.94
3608 3880 6.566564 GCTCAATGTCCCGTGAACATATAATG 60.567 42.308 0.00 0.00 36.35 1.90
3609 3881 5.470098 GCTCAATGTCCCGTGAACATATAAT 59.530 40.000 0.00 0.00 36.35 1.28
3622 3903 1.815003 CCAGAAACAGCTCAATGTCCC 59.185 52.381 0.00 0.00 31.50 4.46
3629 3910 4.890158 TGAGAATACCAGAAACAGCTCA 57.110 40.909 0.00 0.00 0.00 4.26
3674 3955 4.802999 CTGAGTTCAGAATTTCCTTTGGC 58.197 43.478 2.97 0.00 46.59 4.52
3694 3975 5.434408 TCATGAAAGATTCCCTGTGATCTG 58.566 41.667 0.00 0.00 0.00 2.90
3706 3987 6.853720 CAGCAACTCTGAATCATGAAAGATT 58.146 36.000 0.00 0.00 45.72 2.40
3707 3988 6.438259 CAGCAACTCTGAATCATGAAAGAT 57.562 37.500 0.00 0.00 45.72 2.40
3708 3989 5.874895 CAGCAACTCTGAATCATGAAAGA 57.125 39.130 0.00 2.72 45.72 2.52
3731 4012 7.725251 TGAAAAGTTGGAAAGAGTATTGCATT 58.275 30.769 0.00 0.00 30.43 3.56
3734 4015 8.490355 CATTTGAAAAGTTGGAAAGAGTATTGC 58.510 33.333 0.00 0.00 0.00 3.56
3739 4020 6.935167 ACACATTTGAAAAGTTGGAAAGAGT 58.065 32.000 0.00 0.00 0.00 3.24
3740 4021 7.545265 TCAACACATTTGAAAAGTTGGAAAGAG 59.455 33.333 15.93 0.00 39.84 2.85
3742 4023 7.593875 TCAACACATTTGAAAAGTTGGAAAG 57.406 32.000 15.93 0.00 39.84 2.62
3746 4031 6.538021 TCCAATCAACACATTTGAAAAGTTGG 59.462 34.615 15.93 9.41 39.84 3.77
3760 4045 3.201290 AGCATCGATCTCCAATCAACAC 58.799 45.455 0.00 0.00 0.00 3.32
3784 4069 2.403259 GCAATTGGTACTGCAAACCAC 58.597 47.619 17.90 5.53 46.56 4.16
3788 4073 2.233431 GGATGGCAATTGGTACTGCAAA 59.767 45.455 7.72 0.00 40.46 3.68
3789 4074 1.824230 GGATGGCAATTGGTACTGCAA 59.176 47.619 7.72 0.00 40.46 4.08
3790 4075 1.272369 TGGATGGCAATTGGTACTGCA 60.272 47.619 7.72 0.00 40.46 4.41
3792 4077 1.406539 GCTGGATGGCAATTGGTACTG 59.593 52.381 7.72 0.00 0.00 2.74
3793 4078 1.005805 TGCTGGATGGCAATTGGTACT 59.994 47.619 7.72 0.00 39.43 2.73
3794 4079 1.406539 CTGCTGGATGGCAATTGGTAC 59.593 52.381 7.72 0.00 41.94 3.34
3796 4081 0.040058 TCTGCTGGATGGCAATTGGT 59.960 50.000 7.72 0.00 41.94 3.67
3800 4143 3.589951 AATACTCTGCTGGATGGCAAT 57.410 42.857 0.00 0.00 41.94 3.56
3835 4178 2.165030 GCTCTGCATGGCAATTTGTACT 59.835 45.455 0.00 0.00 38.41 2.73
3836 4179 2.094597 TGCTCTGCATGGCAATTTGTAC 60.095 45.455 10.63 0.00 38.41 2.90
3839 4182 1.203758 TCTGCTCTGCATGGCAATTTG 59.796 47.619 13.37 0.00 38.41 2.32
3840 4183 1.476891 CTCTGCTCTGCATGGCAATTT 59.523 47.619 13.37 0.00 38.41 1.82
3841 4184 1.103803 CTCTGCTCTGCATGGCAATT 58.896 50.000 13.37 0.00 38.41 2.32
3842 4185 0.034380 ACTCTGCTCTGCATGGCAAT 60.034 50.000 13.37 2.10 38.41 3.56
3843 4186 0.614812 TACTCTGCTCTGCATGGCAA 59.385 50.000 13.37 5.80 38.41 4.52
3847 4190 1.598132 GCACATACTCTGCTCTGCATG 59.402 52.381 0.00 0.00 38.13 4.06
3848 4191 1.474677 GGCACATACTCTGCTCTGCAT 60.475 52.381 0.00 0.00 38.13 3.96
3849 4192 0.107993 GGCACATACTCTGCTCTGCA 60.108 55.000 0.00 0.00 36.92 4.41
3850 4193 0.107993 TGGCACATACTCTGCTCTGC 60.108 55.000 0.00 0.00 34.84 4.26
3864 4207 4.201950 GGTGTCTGATATCAACAATGGCAC 60.202 45.833 14.90 14.90 0.00 5.01
3865 4208 3.947196 GGTGTCTGATATCAACAATGGCA 59.053 43.478 16.96 7.07 0.00 4.92
3866 4209 3.947196 TGGTGTCTGATATCAACAATGGC 59.053 43.478 16.96 4.89 0.00 4.40
3867 4210 4.036027 GCTGGTGTCTGATATCAACAATGG 59.964 45.833 16.96 12.36 30.70 3.16
3870 4213 4.507710 GAGCTGGTGTCTGATATCAACAA 58.492 43.478 16.96 3.46 30.70 2.83
3871 4214 3.118629 GGAGCTGGTGTCTGATATCAACA 60.119 47.826 6.90 10.93 0.00 3.33
3872 4215 3.133721 AGGAGCTGGTGTCTGATATCAAC 59.866 47.826 6.90 8.62 0.00 3.18
3878 4221 2.541233 AGTAGGAGCTGGTGTCTGAT 57.459 50.000 0.00 0.00 0.00 2.90
3879 4222 2.310779 AAGTAGGAGCTGGTGTCTGA 57.689 50.000 0.00 0.00 0.00 3.27
3880 4223 4.437239 CAATAAGTAGGAGCTGGTGTCTG 58.563 47.826 0.00 0.00 0.00 3.51
3886 4229 2.435805 TCTGCCAATAAGTAGGAGCTGG 59.564 50.000 0.00 0.00 0.00 4.85
3887 4230 3.726607 CTCTGCCAATAAGTAGGAGCTG 58.273 50.000 0.00 0.00 0.00 4.24
3888 4231 2.103941 GCTCTGCCAATAAGTAGGAGCT 59.896 50.000 0.00 0.00 40.71 4.09
3924 4267 2.691623 ATCCTGCCTGCTGCCTCT 60.692 61.111 0.00 0.00 40.16 3.69
3956 4299 3.459063 GAGGGTCCGACGGAAGGG 61.459 72.222 20.26 0.00 31.38 3.95
3957 4300 1.542187 AAAGAGGGTCCGACGGAAGG 61.542 60.000 20.26 0.00 31.38 3.46
3958 4301 0.389948 CAAAGAGGGTCCGACGGAAG 60.390 60.000 20.26 0.00 31.38 3.46
3959 4302 1.669440 CAAAGAGGGTCCGACGGAA 59.331 57.895 20.26 0.00 31.38 4.30
3960 4303 2.939261 GCAAAGAGGGTCCGACGGA 61.939 63.158 13.88 13.88 0.00 4.69
3961 4304 2.434359 GCAAAGAGGGTCCGACGG 60.434 66.667 7.84 7.84 0.00 4.79
3962 4305 2.434359 GGCAAAGAGGGTCCGACG 60.434 66.667 0.00 0.00 0.00 5.12
3963 4306 1.026718 CATGGCAAAGAGGGTCCGAC 61.027 60.000 0.00 0.00 0.00 4.79
3964 4307 1.299648 CATGGCAAAGAGGGTCCGA 59.700 57.895 0.00 0.00 0.00 4.55
4032 4375 4.663166 CAGCAGCTCTGAATCATGAAAAG 58.337 43.478 0.00 0.00 45.72 2.27
4033 4376 4.696899 CAGCAGCTCTGAATCATGAAAA 57.303 40.909 0.00 0.00 45.72 2.29
4044 4387 1.138636 CGACATCGTCAGCAGCTCTG 61.139 60.000 0.00 6.79 44.21 3.35
4045 4388 1.138459 CGACATCGTCAGCAGCTCT 59.862 57.895 0.00 0.00 32.09 4.09
4046 4389 3.685592 CGACATCGTCAGCAGCTC 58.314 61.111 0.00 0.00 32.09 4.09
4056 4399 2.592623 TAGGCAGCGACACGACATCG 62.593 60.000 0.00 0.00 46.33 3.84
4075 4418 7.698970 CGTAACCCGCACATTTTTATAGATTTT 59.301 33.333 0.00 0.00 0.00 1.82
4076 4419 7.148205 ACGTAACCCGCACATTTTTATAGATTT 60.148 33.333 0.00 0.00 41.42 2.17
4079 4422 5.177326 ACGTAACCCGCACATTTTTATAGA 58.823 37.500 0.00 0.00 41.42 1.98
4081 4424 4.032672 CGACGTAACCCGCACATTTTTATA 59.967 41.667 0.00 0.00 41.42 0.98
4083 4426 2.157279 CGACGTAACCCGCACATTTTTA 59.843 45.455 0.00 0.00 41.42 1.52
4084 4427 1.069771 CGACGTAACCCGCACATTTTT 60.070 47.619 0.00 0.00 41.42 1.94
4085 4428 0.513820 CGACGTAACCCGCACATTTT 59.486 50.000 0.00 0.00 41.42 1.82
4299 5179 1.732259 CTGTTGCGGTATTGTGGAGAC 59.268 52.381 0.00 0.00 0.00 3.36
4302 5182 0.036164 AGCTGTTGCGGTATTGTGGA 59.964 50.000 0.00 0.00 45.42 4.02


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

AutoCloner maintained by Alex Coulton.