Multiple sequence alignment - TraesCS4D01G064500

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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 TraesCS4D01G064500 chr4D 100.000 3981 0 0 1 3981 39978743 39982723 0.000000e+00 7352.0
1 TraesCS4D01G064500 chr4B 86.469 1685 115 62 318 1947 58248697 58250323 0.000000e+00 1744.0
2 TraesCS4D01G064500 chr4B 90.828 1123 66 16 2828 3945 58251275 58252365 0.000000e+00 1469.0
3 TraesCS4D01G064500 chr4B 86.143 700 45 17 2014 2691 58250522 58251191 0.000000e+00 708.0
4 TraesCS4D01G064500 chr4B 87.402 254 21 5 1 253 58248483 58248726 8.420000e-72 281.0
5 TraesCS4D01G064500 chr4B 96.000 50 2 0 3932 3981 58252385 58252434 9.170000e-12 82.4
6 TraesCS4D01G064500 chr4A 87.209 1032 55 34 957 1964 560319562 560318584 0.000000e+00 1103.0
7 TraesCS4D01G064500 chr4A 88.150 692 47 15 2706 3378 560317606 560316931 0.000000e+00 791.0
8 TraesCS4D01G064500 chr4A 83.708 712 64 28 2014 2703 560318402 560317721 3.380000e-175 625.0
9 TraesCS4D01G064500 chr4A 84.299 656 53 24 1 631 560320377 560319747 2.650000e-166 595.0
10 TraesCS4D01G064500 chr4A 88.400 500 23 12 3472 3969 560316930 560316464 1.610000e-158 569.0
11 TraesCS4D01G064500 chr3B 81.664 589 69 20 3405 3981 730931199 730931760 1.690000e-123 453.0
12 TraesCS4D01G064500 chr3B 81.282 577 69 20 3405 3969 730850521 730851070 7.900000e-117 431.0
13 TraesCS4D01G064500 chr3A 80.599 634 80 19 3363 3981 688484869 688485474 2.180000e-122 449.0
14 TraesCS4D01G064500 chr3D 80.976 594 76 17 3363 3946 551245271 551245837 1.700000e-118 436.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G064500 chr4D 39978743 39982723 3980 False 7352.00 7352 100.0000 1 3981 1 chr4D.!!$F1 3980
1 TraesCS4D01G064500 chr4B 58248483 58252434 3951 False 856.88 1744 89.3684 1 3981 5 chr4B.!!$F1 3980
2 TraesCS4D01G064500 chr4A 560316464 560320377 3913 True 736.60 1103 86.3532 1 3969 5 chr4A.!!$R1 3968
3 TraesCS4D01G064500 chr3B 730931199 730931760 561 False 453.00 453 81.6640 3405 3981 1 chr3B.!!$F2 576
4 TraesCS4D01G064500 chr3B 730850521 730851070 549 False 431.00 431 81.2820 3405 3969 1 chr3B.!!$F1 564
5 TraesCS4D01G064500 chr3A 688484869 688485474 605 False 449.00 449 80.5990 3363 3981 1 chr3A.!!$F1 618
6 TraesCS4D01G064500 chr3D 551245271 551245837 566 False 436.00 436 80.9760 3363 3946 1 chr3D.!!$F1 583

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
846 915 0.105142 ACCACCACCACCAGAGTAGT 60.105 55.0 0.0 0.0 0.0 2.73 F
1869 2023 0.033366 GGTGGTGATTGGGTTGTTGC 59.967 55.0 0.0 0.0 0.0 4.17 F
2385 2694 0.033208 CCCTACCCACACATGCCATT 60.033 55.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1964 2118 0.037790 AAGTGGAAGCGAGAGTCAGC 60.038 55.000 2.79 2.79 0.0 4.26 R
2908 3359 0.868406 GGCAACACTTTCTCTGTCCG 59.132 55.000 0.00 0.00 0.0 4.79 R
3528 4000 1.004679 TCCAGCCCGACCGTTTTAC 60.005 57.895 0.00 0.00 0.0 2.01 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
23 24 1.021920 TCGGCGGCGAAATGAATGAA 61.022 50.000 32.93 4.55 0.00 2.57
77 90 3.712016 TGAGTACTTTATTGCCCTGCA 57.288 42.857 0.00 0.00 36.47 4.41
78 91 3.609853 TGAGTACTTTATTGCCCTGCAG 58.390 45.455 6.78 6.78 40.61 4.41
79 92 2.356069 GAGTACTTTATTGCCCTGCAGC 59.644 50.000 8.66 0.00 40.61 5.25
80 93 2.025887 AGTACTTTATTGCCCTGCAGCT 60.026 45.455 8.66 0.00 40.61 4.24
81 94 1.180029 ACTTTATTGCCCTGCAGCTG 58.820 50.000 10.11 10.11 40.61 4.24
82 95 0.179119 CTTTATTGCCCTGCAGCTGC 60.179 55.000 31.89 31.89 40.61 5.25
95 108 4.457496 GCTGCAGGAGCTACGGCA 62.457 66.667 22.95 22.95 45.21 5.69
96 109 2.510238 CTGCAGGAGCTACGGCAC 60.510 66.667 20.67 0.00 42.74 5.01
101 114 2.900273 GGAGCTACGGCACCATGA 59.100 61.111 0.00 0.00 46.21 3.07
102 115 1.447643 GGAGCTACGGCACCATGAT 59.552 57.895 0.00 0.00 46.21 2.45
103 116 0.601311 GGAGCTACGGCACCATGATC 60.601 60.000 0.00 0.00 46.21 2.92
178 191 1.332375 ACCGATCAACAAACCAACGTG 59.668 47.619 0.00 0.00 0.00 4.49
269 289 1.004918 CTTTCACGGGAAGCCGTCT 60.005 57.895 0.00 0.00 45.00 4.18
290 310 1.258676 GGTCAGAGGTCTTCTTCCGT 58.741 55.000 0.00 0.00 32.41 4.69
295 315 2.357034 GGTCTTCTTCCGTGCGCA 60.357 61.111 5.66 5.66 0.00 6.09
296 316 1.741770 GGTCTTCTTCCGTGCGCAT 60.742 57.895 15.91 0.00 0.00 4.73
297 317 1.421485 GTCTTCTTCCGTGCGCATG 59.579 57.895 22.83 22.83 0.00 4.06
298 318 2.099062 CTTCTTCCGTGCGCATGC 59.901 61.111 24.29 7.91 43.20 4.06
299 319 2.358615 TTCTTCCGTGCGCATGCT 60.359 55.556 24.29 0.00 43.34 3.79
303 323 3.300934 TTCCGTGCGCATGCTCTCT 62.301 57.895 24.29 0.00 43.34 3.10
309 329 1.742880 GCGCATGCTCTCTGGTGAA 60.743 57.895 17.13 0.00 38.39 3.18
310 330 1.094073 GCGCATGCTCTCTGGTGAAT 61.094 55.000 17.13 0.00 38.39 2.57
323 343 3.960755 TCTGGTGAATGGTGACGATAGAT 59.039 43.478 0.00 0.00 41.38 1.98
324 344 5.137551 TCTGGTGAATGGTGACGATAGATA 58.862 41.667 0.00 0.00 41.38 1.98
338 359 9.767684 GTGACGATAGATATAATTCAGAGTGAG 57.232 37.037 0.00 0.00 41.38 3.51
342 363 7.558081 CGATAGATATAATTCAGAGTGAGGGGA 59.442 40.741 0.00 0.00 39.76 4.81
343 364 8.837099 ATAGATATAATTCAGAGTGAGGGGAG 57.163 38.462 0.00 0.00 0.00 4.30
344 365 6.022315 AGATATAATTCAGAGTGAGGGGAGG 58.978 44.000 0.00 0.00 0.00 4.30
345 366 1.589414 AATTCAGAGTGAGGGGAGGG 58.411 55.000 0.00 0.00 0.00 4.30
346 367 0.327000 ATTCAGAGTGAGGGGAGGGG 60.327 60.000 0.00 0.00 0.00 4.79
347 368 1.751143 TTCAGAGTGAGGGGAGGGGT 61.751 60.000 0.00 0.00 0.00 4.95
420 446 4.391216 AGAATCGTCATCTTGAGTGCTTTG 59.609 41.667 0.00 0.00 0.00 2.77
469 499 2.105993 ACCACCTCCTTCCTGTAACAAC 59.894 50.000 0.00 0.00 0.00 3.32
481 511 3.002862 CCTGTAACAACAAAGCAACGCTA 59.997 43.478 0.00 0.00 38.25 4.26
482 512 3.942739 TGTAACAACAAAGCAACGCTAC 58.057 40.909 0.00 0.00 38.25 3.58
494 524 8.548721 ACAAAGCAACGCTACTGATAATTATAC 58.451 33.333 0.00 0.00 38.25 1.47
496 526 8.888579 AAGCAACGCTACTGATAATTATACTT 57.111 30.769 0.00 0.00 38.25 2.24
594 626 9.733556 TTGATAAGTTAAAGAAATGGCAGTAGA 57.266 29.630 0.00 0.00 0.00 2.59
597 629 7.631717 AAGTTAAAGAAATGGCAGTAGATCC 57.368 36.000 0.00 0.00 0.00 3.36
600 633 4.851639 AAGAAATGGCAGTAGATCCAGT 57.148 40.909 0.00 0.00 35.57 4.00
620 653 5.280676 CCAGTATCTAGATCCTCTCAGCTCT 60.281 48.000 8.95 0.00 0.00 4.09
631 664 4.161189 TCCTCTCAGCTCTGGAAACAATAG 59.839 45.833 0.00 0.00 42.06 1.73
632 665 3.866651 TCTCAGCTCTGGAAACAATAGC 58.133 45.455 0.00 0.00 45.30 2.97
634 667 2.305635 TCAGCTCTGGAAACAATAGCCA 59.694 45.455 0.00 0.00 45.81 4.75
635 668 3.054139 TCAGCTCTGGAAACAATAGCCAT 60.054 43.478 0.00 0.00 45.81 4.40
636 669 3.066342 CAGCTCTGGAAACAATAGCCATG 59.934 47.826 0.00 0.00 45.81 3.66
637 670 2.223665 GCTCTGGAAACAATAGCCATGC 60.224 50.000 0.00 0.00 41.34 4.06
638 671 3.018856 CTCTGGAAACAATAGCCATGCA 58.981 45.455 0.00 0.00 42.06 3.96
640 673 3.193267 TCTGGAAACAATAGCCATGCAAC 59.807 43.478 0.00 0.00 42.06 4.17
642 675 3.056678 TGGAAACAATAGCCATGCAACTG 60.057 43.478 0.00 0.00 37.44 3.16
643 676 3.056607 GGAAACAATAGCCATGCAACTGT 60.057 43.478 0.00 0.00 0.00 3.55
644 677 3.581024 AACAATAGCCATGCAACTGTG 57.419 42.857 0.00 0.00 0.00 3.66
648 717 1.533625 TAGCCATGCAACTGTGGAAC 58.466 50.000 8.28 0.00 37.72 3.62
665 734 6.538189 GTGGAACAAGAAGAAGAAGAAGAG 57.462 41.667 0.00 0.00 44.16 2.85
666 735 6.284459 GTGGAACAAGAAGAAGAAGAAGAGA 58.716 40.000 0.00 0.00 44.16 3.10
676 745 7.508977 AGAAGAAGAAGAAGAGAAGAGAGGAAA 59.491 37.037 0.00 0.00 0.00 3.13
699 768 3.641437 TGAGAAGGGAAAACAATTGCG 57.359 42.857 5.05 0.00 0.00 4.85
730 799 2.960170 GCTCTGCCTGCCAACAAG 59.040 61.111 0.00 0.00 0.00 3.16
731 800 1.601759 GCTCTGCCTGCCAACAAGA 60.602 57.895 0.00 0.00 0.00 3.02
732 801 1.584380 GCTCTGCCTGCCAACAAGAG 61.584 60.000 0.00 0.00 0.00 2.85
733 802 1.584380 CTCTGCCTGCCAACAAGAGC 61.584 60.000 0.00 0.00 0.00 4.09
734 803 2.598394 TGCCTGCCAACAAGAGCC 60.598 61.111 0.00 0.00 0.00 4.70
735 804 2.282745 GCCTGCCAACAAGAGCCT 60.283 61.111 0.00 0.00 0.00 4.58
736 805 2.338785 GCCTGCCAACAAGAGCCTC 61.339 63.158 0.00 0.00 0.00 4.70
766 835 0.738389 CGCCTGTCTCTTCTCTCCTC 59.262 60.000 0.00 0.00 0.00 3.71
767 836 1.111277 GCCTGTCTCTTCTCTCCTCC 58.889 60.000 0.00 0.00 0.00 4.30
768 837 1.341976 GCCTGTCTCTTCTCTCCTCCT 60.342 57.143 0.00 0.00 0.00 3.69
837 906 3.216292 GCACACCACCACCACCAC 61.216 66.667 0.00 0.00 0.00 4.16
838 907 2.518349 CACACCACCACCACCACC 60.518 66.667 0.00 0.00 0.00 4.61
839 908 3.018193 ACACCACCACCACCACCA 61.018 61.111 0.00 0.00 0.00 4.17
840 909 2.203337 CACCACCACCACCACCAG 60.203 66.667 0.00 0.00 0.00 4.00
843 912 2.452064 CCACCACCACCACCAGAGT 61.452 63.158 0.00 0.00 0.00 3.24
844 913 1.125093 CCACCACCACCACCAGAGTA 61.125 60.000 0.00 0.00 0.00 2.59
845 914 0.321671 CACCACCACCACCAGAGTAG 59.678 60.000 0.00 0.00 0.00 2.57
846 915 0.105142 ACCACCACCACCAGAGTAGT 60.105 55.000 0.00 0.00 0.00 2.73
847 916 0.608640 CCACCACCACCAGAGTAGTC 59.391 60.000 0.00 0.00 0.00 2.59
849 918 0.178970 ACCACCACCAGAGTAGTCGT 60.179 55.000 0.00 0.00 0.00 4.34
850 919 0.526662 CCACCACCAGAGTAGTCGTC 59.473 60.000 0.00 0.00 0.00 4.20
851 920 1.535833 CACCACCAGAGTAGTCGTCT 58.464 55.000 0.00 0.00 0.00 4.18
871 948 6.040247 CGTCTGCCAGTGACAGTATAAAATA 58.960 40.000 6.33 0.00 36.50 1.40
872 949 6.199154 CGTCTGCCAGTGACAGTATAAAATAG 59.801 42.308 6.33 0.00 36.50 1.73
873 950 7.265673 GTCTGCCAGTGACAGTATAAAATAGA 58.734 38.462 6.33 0.00 36.50 1.98
874 951 7.436673 GTCTGCCAGTGACAGTATAAAATAGAG 59.563 40.741 6.33 0.00 36.50 2.43
893 970 0.750182 GACTCTCCTCACCCTCCTCG 60.750 65.000 0.00 0.00 0.00 4.63
1005 1120 1.315690 CAGCAATCTCGCCAATGGAT 58.684 50.000 2.05 0.00 0.00 3.41
1068 1183 2.680352 GGGTCCGTCAGCCTCTCA 60.680 66.667 0.00 0.00 39.90 3.27
1079 1197 0.825410 AGCCTCTCATCTGTCTGCTG 59.175 55.000 0.00 0.00 0.00 4.41
1093 1211 3.511540 TGTCTGCTGCTTGTCTGTACTAT 59.488 43.478 0.00 0.00 0.00 2.12
1097 1215 3.515502 TGCTGCTTGTCTGTACTATCCTT 59.484 43.478 0.00 0.00 0.00 3.36
1098 1216 3.868077 GCTGCTTGTCTGTACTATCCTTG 59.132 47.826 0.00 0.00 0.00 3.61
1138 1269 0.107897 TGACTTCGTGGTGTGTGCTT 60.108 50.000 0.00 0.00 0.00 3.91
1156 1287 3.267974 GCAGGTGCAAGCACTACC 58.732 61.111 22.79 8.45 45.52 3.18
1222 1353 3.683937 GCCGCCATTGCCACAACT 61.684 61.111 0.00 0.00 0.00 3.16
1251 1382 1.142314 CTCTGCTCTGCTCTGCTCC 59.858 63.158 0.00 0.00 0.00 4.70
1252 1383 1.605971 CTCTGCTCTGCTCTGCTCCA 61.606 60.000 0.00 0.00 0.00 3.86
1305 1436 2.032071 GGGTTGGTGGTCCTCACG 59.968 66.667 0.00 0.00 46.96 4.35
1313 1444 2.435069 TGGTGGTCCTCACGTTTCTTTA 59.565 45.455 0.00 0.00 46.96 1.85
1314 1445 3.071892 TGGTGGTCCTCACGTTTCTTTAT 59.928 43.478 0.00 0.00 46.96 1.40
1340 1471 5.586243 TCTTTGGATAATCTCTGCCTTTTCG 59.414 40.000 0.00 0.00 0.00 3.46
1441 1572 2.549778 GCACTTCTCTCACTGCTTCCTT 60.550 50.000 0.00 0.00 0.00 3.36
1442 1573 3.324993 CACTTCTCTCACTGCTTCCTTC 58.675 50.000 0.00 0.00 0.00 3.46
1443 1574 2.301583 ACTTCTCTCACTGCTTCCTTCC 59.698 50.000 0.00 0.00 0.00 3.46
1444 1575 2.317371 TCTCTCACTGCTTCCTTCCT 57.683 50.000 0.00 0.00 0.00 3.36
1464 1607 8.267894 CCTTCCTCCTCTTCATTTCTTATGTTA 58.732 37.037 0.00 0.00 0.00 2.41
1468 1611 7.829211 CCTCCTCTTCATTTCTTATGTTACCAA 59.171 37.037 0.00 0.00 0.00 3.67
1477 1620 3.137544 TCTTATGTTACCAATGCCCGGAT 59.862 43.478 0.73 0.00 0.00 4.18
1490 1633 3.963129 TGCCCGGATATCTTGTTTCTTT 58.037 40.909 0.73 0.00 0.00 2.52
1491 1634 3.945285 TGCCCGGATATCTTGTTTCTTTC 59.055 43.478 0.73 0.00 0.00 2.62
1492 1635 4.200092 GCCCGGATATCTTGTTTCTTTCT 58.800 43.478 0.73 0.00 0.00 2.52
1494 1637 5.449177 GCCCGGATATCTTGTTTCTTTCTTG 60.449 44.000 0.73 0.00 0.00 3.02
1495 1638 5.880332 CCCGGATATCTTGTTTCTTTCTTGA 59.120 40.000 0.73 0.00 0.00 3.02
1496 1639 6.183360 CCCGGATATCTTGTTTCTTTCTTGAC 60.183 42.308 0.73 0.00 0.00 3.18
1497 1640 6.595716 CCGGATATCTTGTTTCTTTCTTGACT 59.404 38.462 0.00 0.00 0.00 3.41
1498 1641 7.119846 CCGGATATCTTGTTTCTTTCTTGACTT 59.880 37.037 0.00 0.00 0.00 3.01
1499 1642 8.171840 CGGATATCTTGTTTCTTTCTTGACTTC 58.828 37.037 2.05 0.00 0.00 3.01
1500 1643 8.171840 GGATATCTTGTTTCTTTCTTGACTTCG 58.828 37.037 2.05 0.00 0.00 3.79
1501 1644 5.156804 TCTTGTTTCTTTCTTGACTTCGC 57.843 39.130 0.00 0.00 0.00 4.70
1511 1654 4.330944 TCTTGACTTCGCCTTCAACTTA 57.669 40.909 0.00 0.00 0.00 2.24
1516 1659 5.757886 TGACTTCGCCTTCAACTTAATTTG 58.242 37.500 0.00 0.00 0.00 2.32
1522 1665 3.914364 GCCTTCAACTTAATTTGTCGCTG 59.086 43.478 5.56 0.00 0.00 5.18
1537 1680 4.489810 TGTCGCTGACAAAACAACATTTT 58.510 34.783 8.59 0.00 39.78 1.82
1539 1682 4.026886 GTCGCTGACAAAACAACATTTTCC 60.027 41.667 4.20 0.00 32.09 3.13
1542 1685 5.500610 CGCTGACAAAACAACATTTTCCTTG 60.501 40.000 0.00 0.00 0.00 3.61
1543 1686 5.580297 GCTGACAAAACAACATTTTCCTTGA 59.420 36.000 0.00 0.00 0.00 3.02
1545 1688 7.517259 GCTGACAAAACAACATTTTCCTTGATC 60.517 37.037 0.00 0.00 0.00 2.92
1546 1689 7.326454 TGACAAAACAACATTTTCCTTGATCA 58.674 30.769 0.00 0.00 0.00 2.92
1547 1690 7.821359 TGACAAAACAACATTTTCCTTGATCAA 59.179 29.630 8.12 8.12 0.00 2.57
1548 1691 8.735692 ACAAAACAACATTTTCCTTGATCAAT 57.264 26.923 8.96 0.00 0.00 2.57
1549 1692 9.176460 ACAAAACAACATTTTCCTTGATCAATT 57.824 25.926 8.96 0.00 0.00 2.32
1552 1695 7.967890 ACAACATTTTCCTTGATCAATTTCC 57.032 32.000 8.96 0.00 0.00 3.13
1553 1696 7.738847 ACAACATTTTCCTTGATCAATTTCCT 58.261 30.769 8.96 0.00 0.00 3.36
1554 1697 7.874528 ACAACATTTTCCTTGATCAATTTCCTC 59.125 33.333 8.96 0.00 0.00 3.71
1555 1698 7.787623 ACATTTTCCTTGATCAATTTCCTCT 57.212 32.000 8.96 0.00 0.00 3.69
1556 1699 7.834803 ACATTTTCCTTGATCAATTTCCTCTC 58.165 34.615 8.96 0.00 0.00 3.20
1557 1700 6.840780 TTTTCCTTGATCAATTTCCTCTCC 57.159 37.500 8.96 0.00 0.00 3.71
1558 1701 5.786121 TTCCTTGATCAATTTCCTCTCCT 57.214 39.130 8.96 0.00 0.00 3.69
1559 1702 5.365021 TCCTTGATCAATTTCCTCTCCTC 57.635 43.478 8.96 0.00 0.00 3.71
1583 1726 2.821991 AGGTTATATGCCTCGTCTGC 57.178 50.000 0.00 0.00 0.00 4.26
1652 1795 5.424121 TTCTTCTTTCTTGTGCTGCTAAC 57.576 39.130 0.00 0.00 0.00 2.34
1805 1953 4.313277 TGTGAGAATGAGATCCATCGTC 57.687 45.455 0.00 0.00 33.53 4.20
1806 1954 3.068732 TGTGAGAATGAGATCCATCGTCC 59.931 47.826 0.00 0.00 33.53 4.79
1807 1955 2.630098 TGAGAATGAGATCCATCGTCCC 59.370 50.000 0.00 0.00 33.53 4.46
1808 1956 2.896685 GAGAATGAGATCCATCGTCCCT 59.103 50.000 0.00 0.00 33.53 4.20
1809 1957 2.632028 AGAATGAGATCCATCGTCCCTG 59.368 50.000 0.00 0.00 33.53 4.45
1810 1958 2.094100 ATGAGATCCATCGTCCCTGT 57.906 50.000 0.00 0.00 0.00 4.00
1811 1959 1.403814 TGAGATCCATCGTCCCTGTC 58.596 55.000 0.00 0.00 0.00 3.51
1869 2023 0.033366 GGTGGTGATTGGGTTGTTGC 59.967 55.000 0.00 0.00 0.00 4.17
1873 2027 1.000274 GGTGATTGGGTTGTTGCTGAC 60.000 52.381 0.00 0.00 0.00 3.51
1874 2028 1.680735 GTGATTGGGTTGTTGCTGACA 59.319 47.619 0.00 0.00 36.19 3.58
1947 2101 1.227380 CGGCATCTGCAGGTAGGTC 60.227 63.158 15.13 0.00 44.36 3.85
1948 2102 1.227380 GGCATCTGCAGGTAGGTCG 60.227 63.158 15.13 0.00 44.36 4.79
1950 2104 0.528684 GCATCTGCAGGTAGGTCGTC 60.529 60.000 15.13 0.00 41.59 4.20
1951 2105 0.103208 CATCTGCAGGTAGGTCGTCC 59.897 60.000 15.13 0.00 0.00 4.79
1964 2118 2.828520 AGGTCGTCCTGCCTATCATATG 59.171 50.000 0.00 0.00 43.33 1.78
1967 2121 2.232208 TCGTCCTGCCTATCATATGCTG 59.768 50.000 0.00 0.00 0.00 4.41
1972 2242 3.514706 CCTGCCTATCATATGCTGACTCT 59.485 47.826 0.00 0.00 36.48 3.24
1974 2244 3.192212 TGCCTATCATATGCTGACTCTCG 59.808 47.826 0.00 0.00 36.48 4.04
1977 2247 4.082300 CCTATCATATGCTGACTCTCGCTT 60.082 45.833 0.00 0.00 36.48 4.68
1978 2248 3.361794 TCATATGCTGACTCTCGCTTC 57.638 47.619 0.00 0.00 0.00 3.86
1979 2249 2.035193 TCATATGCTGACTCTCGCTTCC 59.965 50.000 0.00 0.00 0.00 3.46
1981 2251 0.108424 ATGCTGACTCTCGCTTCCAC 60.108 55.000 0.00 0.00 0.00 4.02
1984 2254 1.606737 GCTGACTCTCGCTTCCACTTT 60.607 52.381 0.00 0.00 0.00 2.66
1985 2255 2.333014 CTGACTCTCGCTTCCACTTTC 58.667 52.381 0.00 0.00 0.00 2.62
2028 2320 2.038952 TGTGATCAACAGAGTTGGAGGG 59.961 50.000 9.72 0.00 33.78 4.30
2050 2342 1.490490 AGGACAACTTCTTCCACTGCA 59.510 47.619 0.00 0.00 33.92 4.41
2052 2344 2.291741 GGACAACTTCTTCCACTGCAAG 59.708 50.000 0.00 0.00 42.29 4.01
2110 2413 7.400339 AGTCCTAATTTTGATAGACTCACTCCA 59.600 37.037 0.00 0.00 32.17 3.86
2115 2418 8.868522 AATTTTGATAGACTCACTCCAATTCA 57.131 30.769 0.00 0.00 32.17 2.57
2122 2425 8.954950 ATAGACTCACTCCAATTCAAACTATG 57.045 34.615 0.00 0.00 0.00 2.23
2123 2426 6.176183 AGACTCACTCCAATTCAAACTATGG 58.824 40.000 0.00 0.00 0.00 2.74
2204 2513 1.332889 ATGTCTGCATCGAGGGCTCA 61.333 55.000 12.38 9.37 0.00 4.26
2332 2641 3.813529 GCTCAAGCACGACAAGTAATT 57.186 42.857 0.00 0.00 41.59 1.40
2344 2653 2.905736 ACAAGTAATTGCCCATGCCTTT 59.094 40.909 2.17 0.00 36.33 3.11
2350 2659 2.071778 TTGCCCATGCCTTTCTATCC 57.928 50.000 0.00 0.00 36.33 2.59
2351 2660 0.925558 TGCCCATGCCTTTCTATCCA 59.074 50.000 0.00 0.00 36.33 3.41
2352 2661 1.500303 TGCCCATGCCTTTCTATCCAT 59.500 47.619 0.00 0.00 36.33 3.41
2353 2662 2.165998 GCCCATGCCTTTCTATCCATC 58.834 52.381 0.00 0.00 0.00 3.51
2354 2663 2.224967 GCCCATGCCTTTCTATCCATCT 60.225 50.000 0.00 0.00 0.00 2.90
2355 2664 3.683802 CCCATGCCTTTCTATCCATCTC 58.316 50.000 0.00 0.00 0.00 2.75
2356 2665 3.560882 CCCATGCCTTTCTATCCATCTCC 60.561 52.174 0.00 0.00 0.00 3.71
2357 2666 3.560882 CCATGCCTTTCTATCCATCTCCC 60.561 52.174 0.00 0.00 0.00 4.30
2358 2667 2.057922 TGCCTTTCTATCCATCTCCCC 58.942 52.381 0.00 0.00 0.00 4.81
2359 2668 2.343625 GCCTTTCTATCCATCTCCCCT 58.656 52.381 0.00 0.00 0.00 4.79
2360 2669 2.304470 GCCTTTCTATCCATCTCCCCTC 59.696 54.545 0.00 0.00 0.00 4.30
2361 2670 2.909662 CCTTTCTATCCATCTCCCCTCC 59.090 54.545 0.00 0.00 0.00 4.30
2362 2671 2.723530 TTCTATCCATCTCCCCTCCC 57.276 55.000 0.00 0.00 0.00 4.30
2363 2672 0.793617 TCTATCCATCTCCCCTCCCC 59.206 60.000 0.00 0.00 0.00 4.81
2364 2673 0.796255 CTATCCATCTCCCCTCCCCT 59.204 60.000 0.00 0.00 0.00 4.79
2380 2689 1.635817 CCCTCCCCTACCCACACATG 61.636 65.000 0.00 0.00 0.00 3.21
2385 2694 0.033208 CCCTACCCACACATGCCATT 60.033 55.000 0.00 0.00 0.00 3.16
2390 2699 0.533491 CCCACACATGCCATTCCTTG 59.467 55.000 0.00 0.00 0.00 3.61
2405 2714 2.571212 TCCTTGCGTGTGATCTTGTTT 58.429 42.857 0.00 0.00 0.00 2.83
2411 2720 4.992688 TGCGTGTGATCTTGTTTTTCTTT 58.007 34.783 0.00 0.00 0.00 2.52
2462 2779 0.827507 GGTTCACTTGCCCCATGTGT 60.828 55.000 9.95 0.00 39.49 3.72
2465 2782 0.478072 TCACTTGCCCCATGTGTTCT 59.522 50.000 9.95 0.00 39.49 3.01
2510 2827 1.885049 TCTTGAGGGCCTTAGATGCT 58.115 50.000 7.89 0.00 0.00 3.79
2517 2834 1.346068 GGGCCTTAGATGCTGAGGTAG 59.654 57.143 0.84 0.00 39.15 3.18
2524 2841 6.459923 CCTTAGATGCTGAGGTAGGTATTTC 58.540 44.000 0.00 0.00 33.28 2.17
2581 2903 4.743151 GGTTCCTTTTCGTGTGAATTTTCC 59.257 41.667 0.00 0.00 33.20 3.13
2677 2999 0.883833 CACATGGGAAAGGTCAGTGC 59.116 55.000 0.00 0.00 0.00 4.40
2700 3022 6.098679 GCCACATTTGCAACTCACATATTTA 58.901 36.000 0.00 0.00 0.00 1.40
2703 3025 7.975058 CCACATTTGCAACTCACATATTTATGA 59.025 33.333 0.00 0.00 37.15 2.15
2760 3195 4.091549 TCTTAAGAAAAGGGCTCCGACTA 58.908 43.478 1.68 0.00 0.00 2.59
2773 3208 2.359531 CTCCGACTAACCCAGACTCATC 59.640 54.545 0.00 0.00 0.00 2.92
2777 3212 3.315749 CGACTAACCCAGACTCATCTACC 59.684 52.174 0.00 0.00 32.25 3.18
2780 3215 5.281314 ACTAACCCAGACTCATCTACCAAT 58.719 41.667 0.00 0.00 32.25 3.16
2781 3216 6.441222 ACTAACCCAGACTCATCTACCAATA 58.559 40.000 0.00 0.00 32.25 1.90
2783 3218 6.831664 AACCCAGACTCATCTACCAATATT 57.168 37.500 0.00 0.00 32.25 1.28
2784 3219 6.426646 ACCCAGACTCATCTACCAATATTC 57.573 41.667 0.00 0.00 32.25 1.75
2785 3220 5.011125 ACCCAGACTCATCTACCAATATTCG 59.989 44.000 0.00 0.00 32.25 3.34
2840 3291 4.624015 CTTTCTGATGGCATGTGTTTGTT 58.376 39.130 3.81 0.00 0.00 2.83
2844 3295 2.035704 TGATGGCATGTGTTTGTTGGTC 59.964 45.455 3.81 0.00 0.00 4.02
2971 3422 2.782222 GGTCGCTCCATCGGTGCTA 61.782 63.158 5.62 0.00 39.70 3.49
3016 3467 2.092211 GCTTCGGTGAACACTACGATTG 59.908 50.000 4.96 4.61 35.10 2.67
3032 3483 4.430908 ACGATTGTTTAGTACTAGCTGCC 58.569 43.478 2.23 0.00 0.00 4.85
3048 3499 7.879070 ACTAGCTGCCATTGATGTATTATTTG 58.121 34.615 0.00 0.00 0.00 2.32
3317 3777 4.756642 CGTCCCTATGCATGAATGTATTGT 59.243 41.667 10.16 0.00 34.85 2.71
3318 3778 5.931724 CGTCCCTATGCATGAATGTATTGTA 59.068 40.000 10.16 0.00 34.85 2.41
3319 3779 6.128553 CGTCCCTATGCATGAATGTATTGTAC 60.129 42.308 10.16 0.00 34.85 2.90
3379 3839 4.360951 AATAGTTTGTCCTTCCCGTCAA 57.639 40.909 0.00 0.00 0.00 3.18
3386 3846 3.408634 TGTCCTTCCCGTCAAAAATCTC 58.591 45.455 0.00 0.00 0.00 2.75
3604 4082 2.038557 TCCTTCTCAAAAGACTTCCCCG 59.961 50.000 0.00 0.00 0.00 5.73
3624 4102 5.107824 CCCGATATCACTATGAGATGCAAG 58.892 45.833 3.12 0.00 26.96 4.01
3632 4110 0.179000 ATGAGATGCAAGACCCGGAC 59.821 55.000 0.73 0.00 0.00 4.79
3634 4112 2.511600 GATGCAAGACCCGGACGG 60.512 66.667 0.73 3.25 37.81 4.79
3646 4124 2.566724 ACCCGGACGGTTTAGACATTTA 59.433 45.455 0.73 0.00 45.36 1.40
3656 4134 8.297470 ACGGTTTAGACATTTAGTATACAGGA 57.703 34.615 5.50 0.00 0.00 3.86
3697 4175 9.082313 ACTTGTCAAAGATAATGAAAATGACCT 57.918 29.630 0.00 0.00 36.84 3.85
3730 4208 8.301720 CACTTTAGTGTACCAACTACTATGACA 58.698 37.037 1.69 0.00 40.96 3.58
3731 4209 8.863086 ACTTTAGTGTACCAACTACTATGACAA 58.137 33.333 0.00 0.00 32.39 3.18
3732 4210 9.355215 CTTTAGTGTACCAACTACTATGACAAG 57.645 37.037 0.00 0.00 32.39 3.16
3733 4211 6.912951 AGTGTACCAACTACTATGACAAGT 57.087 37.500 0.00 0.00 0.00 3.16
3734 4212 7.299246 AGTGTACCAACTACTATGACAAGTT 57.701 36.000 0.00 0.00 33.82 2.66
3735 4213 7.152645 AGTGTACCAACTACTATGACAAGTTG 58.847 38.462 9.77 9.77 46.18 3.16
3748 4226 9.371136 ACTATGACAAGTTGACAACATATACTG 57.629 33.333 20.08 9.29 0.00 2.74
3781 4259 4.451760 GGGTAGAATCCCCCTTATGGTCTA 60.452 50.000 0.00 0.00 41.54 2.59
3873 4351 2.704725 TGCTTGAGAATTTGGTTCGC 57.295 45.000 0.00 0.00 41.84 4.70
3874 4352 2.229792 TGCTTGAGAATTTGGTTCGCT 58.770 42.857 0.00 0.00 41.84 4.93
3875 4353 2.030893 TGCTTGAGAATTTGGTTCGCTG 60.031 45.455 0.00 0.00 41.84 5.18
3876 4354 2.226437 GCTTGAGAATTTGGTTCGCTGA 59.774 45.455 0.00 0.00 41.84 4.26
3877 4355 3.119708 GCTTGAGAATTTGGTTCGCTGAT 60.120 43.478 0.00 0.00 41.84 2.90
3878 4356 4.656041 CTTGAGAATTTGGTTCGCTGATC 58.344 43.478 0.00 0.00 41.84 2.92
3879 4357 2.672874 TGAGAATTTGGTTCGCTGATCG 59.327 45.455 0.00 0.00 41.84 3.69
3880 4358 1.398390 AGAATTTGGTTCGCTGATCGC 59.602 47.619 0.23 0.23 41.84 4.58
3960 4472 3.425359 GGCTGTTGTTCGAACTCATGATG 60.425 47.826 27.32 15.00 0.00 3.07
3972 4484 7.196331 TCGAACTCATGATGTGTAAGTATCTG 58.804 38.462 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 5.759059 TCATGAAGCCCAGAGTTTTCATAT 58.241 37.500 0.00 0.00 37.98 1.78
63 64 0.179119 GCAGCTGCAGGGCAATAAAG 60.179 55.000 33.36 0.00 38.41 1.85
79 92 2.510238 GTGCCGTAGCTCCTGCAG 60.510 66.667 6.78 6.78 42.74 4.41
80 93 4.082523 GGTGCCGTAGCTCCTGCA 62.083 66.667 0.00 0.00 46.96 4.41
86 99 1.050988 AGGATCATGGTGCCGTAGCT 61.051 55.000 0.00 0.00 40.80 3.32
89 102 1.070601 CATCAGGATCATGGTGCCGTA 59.929 52.381 7.82 0.00 0.00 4.02
91 104 2.625375 CATCAGGATCATGGTGCCG 58.375 57.895 7.82 0.00 0.00 5.69
95 108 0.477204 CCAGGCATCAGGATCATGGT 59.523 55.000 7.64 0.00 0.00 3.55
96 109 0.477204 ACCAGGCATCAGGATCATGG 59.523 55.000 7.64 9.36 0.00 3.66
97 110 3.497103 TTACCAGGCATCAGGATCATG 57.503 47.619 0.00 0.00 0.00 3.07
98 111 3.718434 TCTTTACCAGGCATCAGGATCAT 59.282 43.478 0.00 0.00 0.00 2.45
99 112 3.114606 TCTTTACCAGGCATCAGGATCA 58.885 45.455 0.00 0.00 0.00 2.92
100 113 3.845781 TCTTTACCAGGCATCAGGATC 57.154 47.619 0.00 0.00 0.00 3.36
101 114 4.263905 TGTTTCTTTACCAGGCATCAGGAT 60.264 41.667 0.00 0.00 0.00 3.24
102 115 3.073798 TGTTTCTTTACCAGGCATCAGGA 59.926 43.478 0.00 0.00 0.00 3.86
103 116 3.191371 GTGTTTCTTTACCAGGCATCAGG 59.809 47.826 0.00 0.00 0.00 3.86
229 243 2.037772 CCCCGAATCCTCTGAATGTAGG 59.962 54.545 0.00 0.00 0.00 3.18
269 289 1.645710 GGAAGAAGACCTCTGACCCA 58.354 55.000 0.00 0.00 33.37 4.51
290 310 2.435410 CACCAGAGAGCATGCGCA 60.435 61.111 23.73 14.96 42.27 6.09
295 315 1.911357 TCACCATTCACCAGAGAGCAT 59.089 47.619 0.00 0.00 0.00 3.79
296 316 1.002430 GTCACCATTCACCAGAGAGCA 59.998 52.381 0.00 0.00 0.00 4.26
297 317 1.731720 GTCACCATTCACCAGAGAGC 58.268 55.000 0.00 0.00 0.00 4.09
298 318 1.546029 TCGTCACCATTCACCAGAGAG 59.454 52.381 0.00 0.00 0.00 3.20
299 319 1.627864 TCGTCACCATTCACCAGAGA 58.372 50.000 0.00 0.00 0.00 3.10
303 323 7.533289 TTATATCTATCGTCACCATTCACCA 57.467 36.000 0.00 0.00 0.00 4.17
309 329 9.249053 ACTCTGAATTATATCTATCGTCACCAT 57.751 33.333 0.00 0.00 0.00 3.55
310 330 8.515414 CACTCTGAATTATATCTATCGTCACCA 58.485 37.037 0.00 0.00 0.00 4.17
323 343 4.493618 CCCTCCCCTCACTCTGAATTATA 58.506 47.826 0.00 0.00 0.00 0.98
324 344 3.321950 CCCTCCCCTCACTCTGAATTAT 58.678 50.000 0.00 0.00 0.00 1.28
342 363 4.729856 GCGTACGCGTCAACCCCT 62.730 66.667 26.17 0.00 40.81 4.79
469 499 8.765219 AGTATAATTATCAGTAGCGTTGCTTTG 58.235 33.333 0.00 0.00 40.44 2.77
620 653 3.056678 CAGTTGCATGGCTATTGTTTCCA 60.057 43.478 0.00 0.00 0.00 3.53
631 664 0.388659 TTGTTCCACAGTTGCATGGC 59.611 50.000 0.00 0.00 35.81 4.40
632 665 1.955778 TCTTGTTCCACAGTTGCATGG 59.044 47.619 0.00 0.00 37.32 3.66
634 667 3.554934 TCTTCTTGTTCCACAGTTGCAT 58.445 40.909 0.00 0.00 0.00 3.96
635 668 2.997980 TCTTCTTGTTCCACAGTTGCA 58.002 42.857 0.00 0.00 0.00 4.08
636 669 3.627577 TCTTCTTCTTGTTCCACAGTTGC 59.372 43.478 0.00 0.00 0.00 4.17
637 670 5.586243 TCTTCTTCTTCTTGTTCCACAGTTG 59.414 40.000 0.00 0.00 0.00 3.16
638 671 5.745227 TCTTCTTCTTCTTGTTCCACAGTT 58.255 37.500 0.00 0.00 0.00 3.16
640 673 6.051717 TCTTCTTCTTCTTCTTGTTCCACAG 58.948 40.000 0.00 0.00 0.00 3.66
642 675 6.284459 TCTCTTCTTCTTCTTCTTGTTCCAC 58.716 40.000 0.00 0.00 0.00 4.02
643 676 6.485830 TCTCTTCTTCTTCTTCTTGTTCCA 57.514 37.500 0.00 0.00 0.00 3.53
644 677 7.213678 TCTTCTCTTCTTCTTCTTCTTGTTCC 58.786 38.462 0.00 0.00 0.00 3.62
648 717 7.039784 TCCTCTCTTCTCTTCTTCTTCTTCTTG 60.040 40.741 0.00 0.00 0.00 3.02
665 734 4.284746 TCCCTTCTCAACTTTCCTCTCTTC 59.715 45.833 0.00 0.00 0.00 2.87
666 735 4.235372 TCCCTTCTCAACTTTCCTCTCTT 58.765 43.478 0.00 0.00 0.00 2.85
676 745 4.499696 CGCAATTGTTTTCCCTTCTCAACT 60.500 41.667 7.40 0.00 0.00 3.16
699 768 2.821810 GAGCCTTCCTTGCTCGGC 60.822 66.667 0.00 0.00 45.05 5.54
717 786 2.598394 GGCTCTTGTTGGCAGGCA 60.598 61.111 0.00 0.00 33.00 4.75
718 787 2.282745 AGGCTCTTGTTGGCAGGC 60.283 61.111 0.00 0.00 0.00 4.85
719 788 1.676967 GGAGGCTCTTGTTGGCAGG 60.677 63.158 15.23 0.00 0.00 4.85
720 789 1.676967 GGGAGGCTCTTGTTGGCAG 60.677 63.158 15.23 0.00 0.00 4.85
721 790 1.719063 AAGGGAGGCTCTTGTTGGCA 61.719 55.000 15.23 0.00 0.00 4.92
722 791 0.540597 AAAGGGAGGCTCTTGTTGGC 60.541 55.000 15.23 0.00 0.00 4.52
723 792 2.001076 AAAAGGGAGGCTCTTGTTGG 57.999 50.000 15.23 0.00 0.00 3.77
724 793 3.486383 TGTAAAAGGGAGGCTCTTGTTG 58.514 45.455 15.23 0.00 0.00 3.33
725 794 3.756117 CTGTAAAAGGGAGGCTCTTGTT 58.244 45.455 15.23 7.27 0.00 2.83
726 795 2.553247 GCTGTAAAAGGGAGGCTCTTGT 60.553 50.000 15.23 0.00 0.00 3.16
727 796 2.087646 GCTGTAAAAGGGAGGCTCTTG 58.912 52.381 15.23 0.00 0.00 3.02
728 797 1.339151 CGCTGTAAAAGGGAGGCTCTT 60.339 52.381 15.23 3.11 41.34 2.85
729 798 0.250513 CGCTGTAAAAGGGAGGCTCT 59.749 55.000 15.23 0.00 41.34 4.09
730 799 1.369839 GCGCTGTAAAAGGGAGGCTC 61.370 60.000 5.78 5.78 41.34 4.70
731 800 1.377333 GCGCTGTAAAAGGGAGGCT 60.377 57.895 0.00 0.00 41.34 4.58
732 801 2.407428 GGCGCTGTAAAAGGGAGGC 61.407 63.158 7.64 0.00 41.34 4.70
733 802 1.026718 CAGGCGCTGTAAAAGGGAGG 61.027 60.000 7.64 0.00 41.34 4.30
734 803 0.321653 ACAGGCGCTGTAAAAGGGAG 60.322 55.000 7.64 0.00 43.46 4.30
735 804 0.321298 GACAGGCGCTGTAAAAGGGA 60.321 55.000 7.64 0.00 45.44 4.20
736 805 0.321653 AGACAGGCGCTGTAAAAGGG 60.322 55.000 7.64 0.00 45.44 3.95
766 835 2.135189 TGGGGATTGGGTCATAGAAGG 58.865 52.381 0.00 0.00 0.00 3.46
767 836 3.203040 AGTTGGGGATTGGGTCATAGAAG 59.797 47.826 0.00 0.00 0.00 2.85
768 837 3.197983 AGTTGGGGATTGGGTCATAGAA 58.802 45.455 0.00 0.00 0.00 2.10
824 893 2.367648 TCTGGTGGTGGTGGTGGT 60.368 61.111 0.00 0.00 0.00 4.16
837 906 0.453793 CTGGCAGACGACTACTCTGG 59.546 60.000 9.42 0.00 36.43 3.86
838 907 1.135546 CACTGGCAGACGACTACTCTG 60.136 57.143 23.66 0.23 38.59 3.35
839 908 1.169577 CACTGGCAGACGACTACTCT 58.830 55.000 23.66 0.00 0.00 3.24
840 909 1.135632 GTCACTGGCAGACGACTACTC 60.136 57.143 23.66 1.37 0.00 2.59
843 912 0.881796 CTGTCACTGGCAGACGACTA 59.118 55.000 28.62 19.33 38.83 2.59
844 913 1.109920 ACTGTCACTGGCAGACGACT 61.110 55.000 28.62 15.72 38.83 4.18
845 914 0.596577 TACTGTCACTGGCAGACGAC 59.403 55.000 23.66 24.47 38.83 4.34
846 915 1.545841 ATACTGTCACTGGCAGACGA 58.454 50.000 23.66 14.22 38.83 4.20
847 916 3.503827 TTATACTGTCACTGGCAGACG 57.496 47.619 23.66 11.92 38.83 4.18
849 918 7.342026 TCTCTATTTTATACTGTCACTGGCAGA 59.658 37.037 23.66 0.00 37.40 4.26
850 919 7.436673 GTCTCTATTTTATACTGTCACTGGCAG 59.563 40.741 14.16 14.16 39.67 4.85
851 920 7.124298 AGTCTCTATTTTATACTGTCACTGGCA 59.876 37.037 0.00 0.00 0.00 4.92
871 948 0.629058 GGAGGGTGAGGAGAGTCTCT 59.371 60.000 19.45 0.70 34.98 3.10
872 949 0.629058 AGGAGGGTGAGGAGAGTCTC 59.371 60.000 12.01 12.01 0.00 3.36
873 950 0.629058 GAGGAGGGTGAGGAGAGTCT 59.371 60.000 0.00 0.00 0.00 3.24
874 951 0.750182 CGAGGAGGGTGAGGAGAGTC 60.750 65.000 0.00 0.00 0.00 3.36
913 990 4.263209 TTGTTGCCTGTTGCCGCG 62.263 61.111 0.00 0.00 40.16 6.46
914 991 2.355009 CTTGTTGCCTGTTGCCGC 60.355 61.111 0.00 0.00 40.16 6.53
931 1025 1.069049 GATCTGGCTTCTCCTCTGCTC 59.931 57.143 0.00 0.00 35.26 4.26
973 1082 0.110486 ATTGCTGTTCTTGTCCGGGT 59.890 50.000 0.00 0.00 0.00 5.28
1060 1175 0.825410 CAGCAGACAGATGAGAGGCT 59.175 55.000 0.00 0.00 35.00 4.58
1068 1183 1.347050 ACAGACAAGCAGCAGACAGAT 59.653 47.619 0.00 0.00 0.00 2.90
1079 1197 3.198872 GGCAAGGATAGTACAGACAAGC 58.801 50.000 0.00 0.00 0.00 4.01
1156 1287 4.899239 GATCCTGCACCGCCTCCG 62.899 72.222 0.00 0.00 0.00 4.63
1182 1313 1.495584 GGAAGACGTCGTTGCAGCAA 61.496 55.000 10.46 2.83 0.00 3.91
1222 1353 0.328592 AGAGCAGAGACCGTGGAGTA 59.671 55.000 0.00 0.00 0.00 2.59
1251 1382 3.511146 AGAGAGCAAAGAGAAGAGAGGTG 59.489 47.826 0.00 0.00 0.00 4.00
1252 1383 3.778265 AGAGAGCAAAGAGAAGAGAGGT 58.222 45.455 0.00 0.00 0.00 3.85
1313 1444 7.968014 AAAGGCAGAGATTATCCAAAGAAAT 57.032 32.000 0.00 0.00 0.00 2.17
1314 1445 7.362056 CGAAAAGGCAGAGATTATCCAAAGAAA 60.362 37.037 0.00 0.00 0.00 2.52
1340 1471 4.002316 AGCAAGAAGAAGAAGATGCAGAC 58.998 43.478 0.00 0.00 36.30 3.51
1441 1572 7.182026 TGGTAACATAAGAAATGAAGAGGAGGA 59.818 37.037 0.00 0.00 46.17 3.71
1442 1573 7.338710 TGGTAACATAAGAAATGAAGAGGAGG 58.661 38.462 0.00 0.00 46.17 4.30
1464 1607 1.494721 ACAAGATATCCGGGCATTGGT 59.505 47.619 0.00 0.00 0.00 3.67
1468 1611 3.864789 AGAAACAAGATATCCGGGCAT 57.135 42.857 0.00 0.00 0.00 4.40
1477 1620 6.073222 GGCGAAGTCAAGAAAGAAACAAGATA 60.073 38.462 0.00 0.00 0.00 1.98
1490 1633 2.910688 AGTTGAAGGCGAAGTCAAGA 57.089 45.000 0.00 0.00 34.52 3.02
1491 1634 5.613358 ATTAAGTTGAAGGCGAAGTCAAG 57.387 39.130 0.00 0.00 34.52 3.02
1492 1635 6.183360 ACAAATTAAGTTGAAGGCGAAGTCAA 60.183 34.615 21.48 0.00 32.59 3.18
1494 1637 5.758924 ACAAATTAAGTTGAAGGCGAAGTC 58.241 37.500 21.48 0.00 32.59 3.01
1495 1638 5.560183 CGACAAATTAAGTTGAAGGCGAAGT 60.560 40.000 21.48 0.00 32.59 3.01
1496 1639 4.846137 CGACAAATTAAGTTGAAGGCGAAG 59.154 41.667 21.48 1.17 32.59 3.79
1497 1640 4.778904 CGACAAATTAAGTTGAAGGCGAA 58.221 39.130 21.48 0.00 32.59 4.70
1498 1641 3.364565 GCGACAAATTAAGTTGAAGGCGA 60.365 43.478 21.48 0.00 32.59 5.54
1499 1642 2.908626 GCGACAAATTAAGTTGAAGGCG 59.091 45.455 21.48 17.50 32.59 5.52
1500 1643 3.914364 CAGCGACAAATTAAGTTGAAGGC 59.086 43.478 21.48 18.46 32.59 4.35
1501 1644 5.147162 GTCAGCGACAAATTAAGTTGAAGG 58.853 41.667 21.48 10.79 32.09 3.46
1516 1659 4.026886 GGAAAATGTTGTTTTGTCAGCGAC 60.027 41.667 0.00 2.32 0.00 5.19
1522 1665 7.769272 TGATCAAGGAAAATGTTGTTTTGTC 57.231 32.000 0.00 0.00 0.00 3.18
1537 1680 4.164988 GGAGGAGAGGAAATTGATCAAGGA 59.835 45.833 14.54 0.00 0.00 3.36
1539 1682 4.459330 GGGAGGAGAGGAAATTGATCAAG 58.541 47.826 14.54 0.00 0.00 3.02
1542 1685 2.436173 ACGGGAGGAGAGGAAATTGATC 59.564 50.000 0.00 0.00 0.00 2.92
1543 1686 2.482494 ACGGGAGGAGAGGAAATTGAT 58.518 47.619 0.00 0.00 0.00 2.57
1545 1688 3.460857 CTACGGGAGGAGAGGAAATTG 57.539 52.381 0.00 0.00 46.53 2.32
1557 1700 2.163815 CGAGGCATATAACCTACGGGAG 59.836 54.545 0.00 0.00 37.77 4.30
1558 1701 2.165167 CGAGGCATATAACCTACGGGA 58.835 52.381 0.00 0.00 37.77 5.14
1559 1702 1.891150 ACGAGGCATATAACCTACGGG 59.109 52.381 15.06 0.00 37.77 5.28
1652 1795 7.745620 ATACCCAAACTCTGAAACTAAACTG 57.254 36.000 0.00 0.00 0.00 3.16
1805 1953 2.203998 ACAGGGACAGGGACAGGG 60.204 66.667 0.00 0.00 0.00 4.45
1806 1954 2.294078 GGACAGGGACAGGGACAGG 61.294 68.421 0.00 0.00 0.00 4.00
1807 1955 2.294078 GGGACAGGGACAGGGACAG 61.294 68.421 0.00 0.00 0.00 3.51
1808 1956 2.203938 GGGACAGGGACAGGGACA 60.204 66.667 0.00 0.00 0.00 4.02
1809 1957 2.122954 AGGGACAGGGACAGGGAC 59.877 66.667 0.00 0.00 0.00 4.46
1810 1958 2.122729 CAGGGACAGGGACAGGGA 59.877 66.667 0.00 0.00 0.00 4.20
1811 1959 2.203998 ACAGGGACAGGGACAGGG 60.204 66.667 0.00 0.00 0.00 4.45
1869 2023 1.370609 CAGCAGCAAGATCCTGTCAG 58.629 55.000 0.00 0.00 32.93 3.51
1873 2027 0.677098 ACAGCAGCAGCAAGATCCTG 60.677 55.000 3.17 0.00 45.49 3.86
1874 2028 0.677098 CACAGCAGCAGCAAGATCCT 60.677 55.000 3.17 0.00 45.49 3.24
1947 2101 2.232208 TCAGCATATGATAGGCAGGACG 59.768 50.000 11.89 0.00 38.06 4.79
1948 2102 3.260380 AGTCAGCATATGATAGGCAGGAC 59.740 47.826 19.26 19.26 40.92 3.85
1950 2104 3.514706 AGAGTCAGCATATGATAGGCAGG 59.485 47.826 11.89 3.37 40.92 4.85
1951 2105 4.674885 CGAGAGTCAGCATATGATAGGCAG 60.675 50.000 11.89 3.41 40.92 4.85
1952 2106 3.192212 CGAGAGTCAGCATATGATAGGCA 59.808 47.826 11.89 0.00 40.92 4.75
1953 2107 3.768406 CGAGAGTCAGCATATGATAGGC 58.232 50.000 6.97 0.05 40.92 3.93
1964 2118 0.037790 AAGTGGAAGCGAGAGTCAGC 60.038 55.000 2.79 2.79 0.00 4.26
1967 2121 2.333014 CTGAAAGTGGAAGCGAGAGTC 58.667 52.381 0.00 0.00 0.00 3.36
1981 2251 0.514691 GTCAGCTCGGCAACTGAAAG 59.485 55.000 3.04 0.00 44.14 2.62
1984 2254 1.005748 CAGTCAGCTCGGCAACTGA 60.006 57.895 18.09 8.71 42.83 3.41
1985 2255 0.601046 TTCAGTCAGCTCGGCAACTG 60.601 55.000 17.41 17.41 42.12 3.16
2081 2384 9.256228 AGTGAGTCTATCAAAATTAGGACTGTA 57.744 33.333 0.00 0.00 40.43 2.74
2095 2398 7.009179 AGTTTGAATTGGAGTGAGTCTATCA 57.991 36.000 0.00 0.00 34.79 2.15
2096 2399 9.039870 CATAGTTTGAATTGGAGTGAGTCTATC 57.960 37.037 0.00 0.00 0.00 2.08
2098 2401 7.180229 TCCATAGTTTGAATTGGAGTGAGTCTA 59.820 37.037 0.00 0.00 33.40 2.59
2099 2402 6.013379 TCCATAGTTTGAATTGGAGTGAGTCT 60.013 38.462 0.00 0.00 33.40 3.24
2102 2405 6.600822 ACATCCATAGTTTGAATTGGAGTGAG 59.399 38.462 0.00 0.00 41.33 3.51
2122 2425 1.300697 GCACCCGACGGATACATCC 60.301 63.158 17.49 0.00 43.65 3.51
2123 2426 1.300697 GGCACCCGACGGATACATC 60.301 63.158 17.49 0.00 0.00 3.06
2200 2509 2.352127 GGGCAGTTGTTCTTCATTGAGC 60.352 50.000 0.00 0.00 0.00 4.26
2204 2513 2.270352 TCGGGCAGTTGTTCTTCATT 57.730 45.000 0.00 0.00 0.00 2.57
2259 2568 2.181777 GCATCTCAGCACCGACGA 59.818 61.111 0.00 0.00 0.00 4.20
2292 2601 0.390866 ATCTCGTGGAAGCACTGCAG 60.391 55.000 13.48 13.48 0.00 4.41
2332 2641 0.925558 TGGATAGAAAGGCATGGGCA 59.074 50.000 0.00 0.00 43.71 5.36
2344 2653 0.793617 GGGGAGGGGAGATGGATAGA 59.206 60.000 0.00 0.00 0.00 1.98
2350 2659 2.122189 GGGAGGGGAGGGGAGATG 60.122 72.222 0.00 0.00 0.00 2.90
2351 2660 2.635315 TAGGGGAGGGGAGGGGAGAT 62.635 65.000 0.00 0.00 0.00 2.75
2352 2661 3.329217 TAGGGGAGGGGAGGGGAGA 62.329 68.421 0.00 0.00 0.00 3.71
2353 2662 2.708132 TAGGGGAGGGGAGGGGAG 60.708 72.222 0.00 0.00 0.00 4.30
2354 2663 3.040814 GTAGGGGAGGGGAGGGGA 61.041 72.222 0.00 0.00 0.00 4.81
2355 2664 4.188511 GGTAGGGGAGGGGAGGGG 62.189 77.778 0.00 0.00 0.00 4.79
2356 2665 4.188511 GGGTAGGGGAGGGGAGGG 62.189 77.778 0.00 0.00 0.00 4.30
2357 2666 3.373846 TGGGTAGGGGAGGGGAGG 61.374 72.222 0.00 0.00 0.00 4.30
2358 2667 2.040779 GTGGGTAGGGGAGGGGAG 60.041 72.222 0.00 0.00 0.00 4.30
2359 2668 2.877383 TGTGGGTAGGGGAGGGGA 60.877 66.667 0.00 0.00 0.00 4.81
2360 2669 2.691252 GTGTGGGTAGGGGAGGGG 60.691 72.222 0.00 0.00 0.00 4.79
2361 2670 1.307866 ATGTGTGGGTAGGGGAGGG 60.308 63.158 0.00 0.00 0.00 4.30
2362 2671 1.915228 CATGTGTGGGTAGGGGAGG 59.085 63.158 0.00 0.00 0.00 4.30
2363 2672 1.224592 GCATGTGTGGGTAGGGGAG 59.775 63.158 0.00 0.00 0.00 4.30
2364 2673 2.305607 GGCATGTGTGGGTAGGGGA 61.306 63.158 0.00 0.00 0.00 4.81
2380 2689 0.099436 GATCACACGCAAGGAATGGC 59.901 55.000 0.00 0.00 46.39 4.40
2385 2694 2.254546 AACAAGATCACACGCAAGGA 57.745 45.000 0.00 0.00 46.39 3.36
2390 2699 5.273944 AGAAAGAAAAACAAGATCACACGC 58.726 37.500 0.00 0.00 0.00 5.34
2405 2714 7.861372 CGAGGATAGCGTTATCTAAGAAAGAAA 59.139 37.037 17.35 0.00 37.89 2.52
2411 2720 4.388165 CGTCGAGGATAGCGTTATCTAAGA 59.612 45.833 17.35 11.47 36.67 2.10
2462 2779 4.074259 CCATGTCAAAGATGGACACAGAA 58.926 43.478 0.00 0.00 46.99 3.02
2465 2782 3.786368 TCCATGTCAAAGATGGACACA 57.214 42.857 1.91 0.00 46.99 3.72
2517 2834 6.235231 TGTGGATCTTACTGAGGAAATACC 57.765 41.667 0.00 0.00 39.35 2.73
2524 2841 3.265791 GTTGCTGTGGATCTTACTGAGG 58.734 50.000 10.19 0.00 0.00 3.86
2581 2903 1.971695 GGGGCCAAGAACGTGAAGG 60.972 63.158 4.39 0.00 0.00 3.46
2648 2970 4.827284 ACCTTTCCCATGTGTAAGAACTTG 59.173 41.667 0.00 0.00 0.00 3.16
2677 2999 7.975058 TCATAAATATGTGAGTTGCAAATGTGG 59.025 33.333 3.09 0.00 35.26 4.17
2744 3179 1.678123 GGGTTAGTCGGAGCCCTTTTC 60.678 57.143 0.00 0.00 38.12 2.29
2749 3184 1.684734 TCTGGGTTAGTCGGAGCCC 60.685 63.158 0.00 0.00 41.42 5.19
2754 3189 2.379972 AGATGAGTCTGGGTTAGTCGG 58.620 52.381 0.00 0.00 32.13 4.79
2756 3191 4.279145 TGGTAGATGAGTCTGGGTTAGTC 58.721 47.826 0.00 0.00 35.87 2.59
2760 3195 6.463049 CGAATATTGGTAGATGAGTCTGGGTT 60.463 42.308 0.00 0.00 35.87 4.11
2773 3208 7.389884 TGGCTACTACTAGACGAATATTGGTAG 59.610 40.741 2.80 1.39 29.03 3.18
2777 3212 7.204496 ACTGGCTACTACTAGACGAATATTG 57.796 40.000 0.00 0.00 29.03 1.90
2818 3257 4.247267 ACAAACACATGCCATCAGAAAG 57.753 40.909 0.00 0.00 0.00 2.62
2840 3291 3.716195 CCATCCCTGCACCGACCA 61.716 66.667 0.00 0.00 0.00 4.02
2844 3295 2.280389 CGATCCATCCCTGCACCG 60.280 66.667 0.00 0.00 0.00 4.94
2908 3359 0.868406 GGCAACACTTTCTCTGTCCG 59.132 55.000 0.00 0.00 0.00 4.79
2956 3407 2.279517 GGTAGCACCGATGGAGCG 60.280 66.667 0.00 0.00 43.81 5.03
3016 3467 5.817816 ACATCAATGGCAGCTAGTACTAAAC 59.182 40.000 3.76 0.00 0.00 2.01
3032 3483 9.356433 TGTTGAACTGCAAATAATACATCAATG 57.644 29.630 0.00 0.00 38.44 2.82
3084 3535 9.373750 CGTACATATAAATCGGTACCGTATATG 57.626 37.037 34.52 34.52 40.57 1.78
3195 3650 7.209471 TGACCAACAACCAACAATATACTTC 57.791 36.000 0.00 0.00 0.00 3.01
3201 3656 5.923733 ACTTTGACCAACAACCAACAATA 57.076 34.783 0.00 0.00 38.29 1.90
3202 3657 4.817318 ACTTTGACCAACAACCAACAAT 57.183 36.364 0.00 0.00 38.29 2.71
3204 3659 3.306364 CCAACTTTGACCAACAACCAACA 60.306 43.478 0.00 0.00 38.29 3.33
3205 3660 3.258228 CCAACTTTGACCAACAACCAAC 58.742 45.455 0.00 0.00 38.29 3.77
3206 3661 2.900546 ACCAACTTTGACCAACAACCAA 59.099 40.909 0.00 0.00 38.29 3.67
3207 3662 2.494073 GACCAACTTTGACCAACAACCA 59.506 45.455 0.00 0.00 38.29 3.67
3212 3672 4.918810 AAGATGACCAACTTTGACCAAC 57.081 40.909 0.00 0.00 0.00 3.77
3379 3839 7.722949 TTGGCTCATAATTCTTGGAGATTTT 57.277 32.000 0.00 0.00 0.00 1.82
3386 3846 6.071165 AGGTTCTTTTGGCTCATAATTCTTGG 60.071 38.462 0.00 0.00 0.00 3.61
3448 3918 1.159285 TTGTGAGCTATGTGTGCAGC 58.841 50.000 0.00 0.00 38.09 5.25
3528 4000 1.004679 TCCAGCCCGACCGTTTTAC 60.005 57.895 0.00 0.00 0.00 2.01
3534 4006 2.125512 CTTTCTCCAGCCCGACCG 60.126 66.667 0.00 0.00 0.00 4.79
3604 4082 6.105333 GGGTCTTGCATCTCATAGTGATATC 58.895 44.000 0.00 0.00 0.00 1.63
3632 4110 9.590451 TTTCCTGTATACTAAATGTCTAAACCG 57.410 33.333 4.17 0.00 0.00 4.44
3646 4124 9.668497 GTAAGGACATTTCTTTTCCTGTATACT 57.332 33.333 4.17 0.00 39.83 2.12
3656 4134 8.966868 TCTTTGACAAGTAAGGACATTTCTTTT 58.033 29.630 0.00 0.00 0.00 2.27
3664 4142 9.567776 TTTCATTATCTTTGACAAGTAAGGACA 57.432 29.630 4.82 0.00 0.00 4.02
3730 4208 6.179756 TCCATGCAGTATATGTTGTCAACTT 58.820 36.000 16.45 12.52 0.00 2.66
3731 4209 5.744171 TCCATGCAGTATATGTTGTCAACT 58.256 37.500 16.45 5.30 0.00 3.16
3732 4210 6.260714 TCATCCATGCAGTATATGTTGTCAAC 59.739 38.462 8.86 8.86 0.00 3.18
3733 4211 6.355747 TCATCCATGCAGTATATGTTGTCAA 58.644 36.000 0.00 0.00 0.00 3.18
3734 4212 5.927819 TCATCCATGCAGTATATGTTGTCA 58.072 37.500 0.00 0.00 0.00 3.58
3735 4213 5.410746 CCTCATCCATGCAGTATATGTTGTC 59.589 44.000 0.00 0.00 0.00 3.18
3736 4214 5.311265 CCTCATCCATGCAGTATATGTTGT 58.689 41.667 0.00 0.00 0.00 3.32
3737 4215 4.698780 CCCTCATCCATGCAGTATATGTTG 59.301 45.833 0.00 0.00 0.00 3.33
3748 4226 2.290577 GGGATTCTACCCTCATCCATGC 60.291 54.545 0.00 0.00 45.90 4.06
3873 4351 3.525537 ACACTTTGATACCAGCGATCAG 58.474 45.455 0.00 0.00 34.85 2.90
3874 4352 3.610040 ACACTTTGATACCAGCGATCA 57.390 42.857 0.00 0.00 0.00 2.92
3875 4353 4.154195 ACAAACACTTTGATACCAGCGATC 59.846 41.667 1.75 0.00 43.26 3.69
3876 4354 4.072131 ACAAACACTTTGATACCAGCGAT 58.928 39.130 1.75 0.00 43.26 4.58
3877 4355 3.472652 ACAAACACTTTGATACCAGCGA 58.527 40.909 1.75 0.00 43.26 4.93
3878 4356 3.498397 AGACAAACACTTTGATACCAGCG 59.502 43.478 1.75 0.00 43.26 5.18
3879 4357 4.515191 TGAGACAAACACTTTGATACCAGC 59.485 41.667 1.75 0.00 43.26 4.85
3880 4358 6.430451 GTTGAGACAAACACTTTGATACCAG 58.570 40.000 1.75 0.00 43.26 4.00


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

AutoCloner maintained by Alex Coulton.