Multiple sequence alignment - TraesCS5B01G263200

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 TraesCS5B01G263200 chr5B 100.000 5108 0 0 1 5108 447844470 447839363 0.000000e+00 9433.0
1 TraesCS5B01G263200 chr5B 85.268 224 33 0 1424 1647 447843017 447842794 1.110000e-56 231.0
2 TraesCS5B01G263200 chr5B 85.268 224 33 0 1454 1677 447843047 447842824 1.110000e-56 231.0
3 TraesCS5B01G263200 chr5A 93.462 3319 165 20 167 3462 476606369 476603080 0.000000e+00 4879.0
4 TraesCS5B01G263200 chr5A 87.538 995 73 20 3460 4434 476603049 476602086 0.000000e+00 1103.0
5 TraesCS5B01G263200 chr5A 86.429 280 13 10 4431 4697 476600313 476600046 3.010000e-72 283.0
6 TraesCS5B01G263200 chr5A 93.478 184 8 1 4754 4933 476599914 476599731 2.340000e-68 270.0
7 TraesCS5B01G263200 chr5A 89.381 113 7 1 4958 5070 476592682 476592575 2.480000e-28 137.0
8 TraesCS5B01G263200 chr5A 78.605 215 40 4 1484 1695 476605092 476604881 2.480000e-28 137.0
9 TraesCS5B01G263200 chr5D 95.040 2016 84 8 1454 3462 375194327 375192321 0.000000e+00 3155.0
10 TraesCS5B01G263200 chr5D 90.309 1682 101 34 1 1647 375195758 375194104 0.000000e+00 2146.0
11 TraesCS5B01G263200 chr5D 90.426 1525 93 25 3460 4945 375192290 375190780 0.000000e+00 1958.0
12 TraesCS5B01G263200 chr5D 78.505 214 42 2 1484 1695 375194327 375194116 2.480000e-28 137.0
13 TraesCS5B01G263200 chr4D 97.143 35 1 0 4968 5002 414221155 414221189 5.520000e-05 60.2
14 TraesCS5B01G263200 chr4A 97.143 35 1 0 4968 5002 225339570 225339604 5.520000e-05 60.2
15 TraesCS5B01G263200 chr2A 97.143 35 1 0 4968 5002 19248938 19248972 5.520000e-05 60.2
16 TraesCS5B01G263200 chr2A 97.143 35 1 0 4968 5002 19261607 19261641 5.520000e-05 60.2
17 TraesCS5B01G263200 chr7A 94.286 35 2 0 4968 5002 641352283 641352249 3.000000e-03 54.7
18 TraesCS5B01G263200 chr3D 96.875 32 1 0 4971 5002 378533174 378533143 3.000000e-03 54.7


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 TraesCS5B01G263200 chr5B 447839363 447844470 5107 True 3298.333333 9433 90.178667 1 5108 3 chr5B.!!$R1 5107
1 TraesCS5B01G263200 chr5A 476599731 476606369 6638 True 1334.400000 4879 87.902400 167 4933 5 chr5A.!!$R2 4766
2 TraesCS5B01G263200 chr5D 375190780 375195758 4978 True 1849.000000 3155 88.570000 1 4945 4 chr5D.!!$R1 4944

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
335 357 0.463474 GCAGCTTGTCAGATCTCCCC 60.463 60.000 0.00 0.0 0.00 4.81 F
1556 1596 1.134371 GGCCATTGAGGGTGTAGAGAC 60.134 57.143 0.00 0.0 38.09 3.36 F
1660 1730 0.032678 AGCGACTGATGATAAGGGCG 59.967 55.000 0.00 0.0 0.00 6.13 F
2409 2481 0.101219 GTTTCCGGATGATTGGCAGC 59.899 55.000 4.15 0.0 0.00 5.25 F
3467 3578 0.107508 CCGTGCATGACTCCCAAGAT 60.108 55.000 7.72 0.0 0.00 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1575 1615 0.596577 TATCATCAGTCGCTACGCCC 59.403 55.0 0.00 0.00 0.00 6.13 R
2409 2481 0.031178 GCCAAGACAGTGCCAGTTTG 59.969 55.0 0.00 0.00 0.00 2.93 R
3614 3725 0.107312 CAGGAACAGGATCAGGGCAG 60.107 60.0 0.00 0.00 0.00 4.85 R
3898 4022 0.107017 ACCATCGAGGCCCTTTGATG 60.107 55.0 16.13 16.13 43.14 3.07 R
4782 6784 0.027979 CACAAGAACTGGTGCACACG 59.972 55.0 20.43 11.11 0.00 4.49 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
111 112 8.869897 CATTCGTAAAATTCAGTTAGTCAGCTA 58.130 33.333 0.00 0.00 0.00 3.32
115 116 9.088512 CGTAAAATTCAGTTAGTCAGCTATCTT 57.911 33.333 0.00 0.00 0.00 2.40
130 131 9.425577 GTCAGCTATCTTATACTGTATTTTCCC 57.574 37.037 5.52 0.00 0.00 3.97
201 206 3.006859 TGCAACCATATGGATCGGAGTAG 59.993 47.826 28.77 3.90 38.94 2.57
225 243 3.181512 GCACTTGCATACTCTCTTGCTTC 60.182 47.826 0.00 0.00 41.59 3.86
229 251 1.472376 GCATACTCTCTTGCTTCGCCT 60.472 52.381 0.00 0.00 35.95 5.52
234 256 2.032528 TCTTGCTTCGCCTGGTGG 59.967 61.111 7.51 0.00 0.00 4.61
293 315 6.872628 TGTTCTTAGAGTCAAGTACTTCGA 57.127 37.500 4.77 4.49 39.07 3.71
295 317 6.261603 TGTTCTTAGAGTCAAGTACTTCGACA 59.738 38.462 26.08 12.82 39.07 4.35
311 333 1.654105 CGACAGTGCCGAGTTTACATC 59.346 52.381 0.00 0.00 0.00 3.06
316 338 1.732259 GTGCCGAGTTTACATCTGGTG 59.268 52.381 0.00 0.00 0.00 4.17
335 357 0.463474 GCAGCTTGTCAGATCTCCCC 60.463 60.000 0.00 0.00 0.00 4.81
336 358 1.202330 CAGCTTGTCAGATCTCCCCT 58.798 55.000 0.00 0.00 0.00 4.79
337 359 1.134461 CAGCTTGTCAGATCTCCCCTG 60.134 57.143 0.00 0.00 0.00 4.45
404 435 3.895656 CCTCATTCTCCATCCAATGCAAT 59.104 43.478 0.00 0.00 31.15 3.56
433 464 2.126189 GTCGTACACCCTCACCGC 60.126 66.667 0.00 0.00 0.00 5.68
509 540 5.652891 CACTAGGAGACACATTACCTGTACT 59.347 44.000 0.00 0.00 35.91 2.73
510 541 5.652891 ACTAGGAGACACATTACCTGTACTG 59.347 44.000 0.00 0.00 35.91 2.74
513 544 5.542635 AGGAGACACATTACCTGTACTGAAA 59.457 40.000 0.60 0.00 35.91 2.69
626 659 5.265191 AGAGAGTACTAGCTGTTTGATCCA 58.735 41.667 0.00 0.00 0.00 3.41
628 661 5.020132 AGAGTACTAGCTGTTTGATCCAGT 58.980 41.667 0.00 0.00 32.41 4.00
656 691 5.752892 TTACACTTTTACGGCATGAACAA 57.247 34.783 0.00 0.00 0.00 2.83
689 726 8.706492 TTACTTATGGTAGTCGGTAACAAATG 57.294 34.615 0.00 0.00 29.90 2.32
691 728 7.039882 ACTTATGGTAGTCGGTAACAAATGAG 58.960 38.462 0.00 0.00 29.90 2.90
693 730 5.217978 TGGTAGTCGGTAACAAATGAGTT 57.782 39.130 0.00 0.00 35.55 3.01
697 734 6.529477 GGTAGTCGGTAACAAATGAGTTAGTC 59.471 42.308 0.00 0.00 34.85 2.59
720 757 5.415701 TCAAGTGAATGCCTTACTGAAATCC 59.584 40.000 0.00 0.00 0.00 3.01
881 920 4.441495 CCATGGCATAATCATCATGATGGC 60.441 45.833 30.54 24.66 43.23 4.40
1038 1078 2.027192 CGGGGAAGAGAGAAATGACCAA 60.027 50.000 0.00 0.00 0.00 3.67
1095 1135 2.238395 AGGGAAGGAAGCTGAATCAGAC 59.762 50.000 15.38 5.53 32.44 3.51
1319 1359 2.032981 CACCGAAGCCAAGCAAAGT 58.967 52.632 0.00 0.00 0.00 2.66
1550 1590 1.922447 TGATAAGGCCATTGAGGGTGT 59.078 47.619 5.01 0.00 38.09 4.16
1551 1591 3.119319 TGATAAGGCCATTGAGGGTGTA 58.881 45.455 5.01 0.00 38.09 2.90
1552 1592 3.136443 TGATAAGGCCATTGAGGGTGTAG 59.864 47.826 5.01 0.00 38.09 2.74
1553 1593 1.668826 AAGGCCATTGAGGGTGTAGA 58.331 50.000 5.01 0.00 38.09 2.59
1554 1594 1.207791 AGGCCATTGAGGGTGTAGAG 58.792 55.000 5.01 0.00 38.09 2.43
1555 1595 1.204146 GGCCATTGAGGGTGTAGAGA 58.796 55.000 0.00 0.00 38.09 3.10
1556 1596 1.134371 GGCCATTGAGGGTGTAGAGAC 60.134 57.143 0.00 0.00 38.09 3.36
1557 1597 1.834263 GCCATTGAGGGTGTAGAGACT 59.166 52.381 0.00 0.00 38.09 3.24
1558 1598 2.419297 GCCATTGAGGGTGTAGAGACTG 60.419 54.545 0.00 0.00 38.09 3.51
1559 1599 3.099905 CCATTGAGGGTGTAGAGACTGA 58.900 50.000 0.00 0.00 0.00 3.41
1560 1600 3.708631 CCATTGAGGGTGTAGAGACTGAT 59.291 47.826 0.00 0.00 0.00 2.90
1561 1601 4.442612 CCATTGAGGGTGTAGAGACTGATG 60.443 50.000 0.00 0.00 0.00 3.07
1562 1602 3.739401 TGAGGGTGTAGAGACTGATGA 57.261 47.619 0.00 0.00 0.00 2.92
1563 1603 4.256983 TGAGGGTGTAGAGACTGATGAT 57.743 45.455 0.00 0.00 0.00 2.45
1564 1604 5.388599 TGAGGGTGTAGAGACTGATGATA 57.611 43.478 0.00 0.00 0.00 2.15
1565 1605 5.766590 TGAGGGTGTAGAGACTGATGATAA 58.233 41.667 0.00 0.00 0.00 1.75
1566 1606 5.830457 TGAGGGTGTAGAGACTGATGATAAG 59.170 44.000 0.00 0.00 0.00 1.73
1567 1607 5.144100 AGGGTGTAGAGACTGATGATAAGG 58.856 45.833 0.00 0.00 0.00 2.69
1568 1608 4.262249 GGGTGTAGAGACTGATGATAAGGC 60.262 50.000 0.00 0.00 0.00 4.35
1569 1609 4.262249 GGTGTAGAGACTGATGATAAGGCC 60.262 50.000 0.00 0.00 0.00 5.19
1570 1610 4.342378 GTGTAGAGACTGATGATAAGGCCA 59.658 45.833 5.01 0.00 0.00 5.36
1571 1611 5.011533 GTGTAGAGACTGATGATAAGGCCAT 59.988 44.000 5.01 0.00 0.00 4.40
1572 1612 5.604231 TGTAGAGACTGATGATAAGGCCATT 59.396 40.000 5.01 0.00 0.00 3.16
1573 1613 4.970711 AGAGACTGATGATAAGGCCATTG 58.029 43.478 5.01 0.00 0.00 2.82
1574 1614 4.657504 AGAGACTGATGATAAGGCCATTGA 59.342 41.667 5.01 0.00 0.00 2.57
1575 1615 4.970711 AGACTGATGATAAGGCCATTGAG 58.029 43.478 5.01 0.00 0.00 3.02
1576 1616 4.070716 GACTGATGATAAGGCCATTGAGG 58.929 47.826 5.01 0.00 41.84 3.86
1577 1617 3.181436 ACTGATGATAAGGCCATTGAGGG 60.181 47.826 5.01 0.00 38.09 4.30
1660 1730 0.032678 AGCGACTGATGATAAGGGCG 59.967 55.000 0.00 0.00 0.00 6.13
1818 1888 6.510536 TGATGACAACTCAGTAGCATATGAG 58.489 40.000 6.97 9.69 46.76 2.90
2139 2211 1.745087 ACTTTATTCTGCACATGGCCG 59.255 47.619 0.00 0.00 43.89 6.13
2409 2481 0.101219 GTTTCCGGATGATTGGCAGC 59.899 55.000 4.15 0.00 0.00 5.25
2532 2605 2.791383 TGGCAATTTTGTCAGAACCG 57.209 45.000 0.00 0.00 37.97 4.44
2549 2622 4.694037 AGAACCGTAAATTTGACCTGCTAC 59.306 41.667 0.00 0.00 0.00 3.58
2566 2639 6.874134 ACCTGCTACTTGTAAAACATGACTAG 59.126 38.462 0.00 0.00 0.00 2.57
2635 2712 1.982395 CTAGGCACTGACACCCCGA 60.982 63.158 0.00 0.00 41.52 5.14
2671 2748 2.290260 TGAGGATTCATCAACGCCAAGT 60.290 45.455 0.00 0.00 0.00 3.16
2682 2759 2.038387 ACGCCAAGTGTTGAGAAACT 57.962 45.000 0.00 0.00 0.00 2.66
2697 2774 5.385198 TGAGAAACTGTTAGGGCATTCTTT 58.615 37.500 0.00 0.00 0.00 2.52
2698 2775 5.241506 TGAGAAACTGTTAGGGCATTCTTTG 59.758 40.000 0.00 0.00 0.00 2.77
2757 2834 3.890756 TGGAAGACTGCATTTTGTGATGT 59.109 39.130 0.00 0.00 0.00 3.06
2835 2912 1.327303 TTGGCCAAACTGGTAAGCTG 58.673 50.000 17.98 0.00 40.46 4.24
3083 3160 1.871077 CGCACAGCTGAAGAATGCA 59.129 52.632 23.35 0.00 36.02 3.96
3091 3168 5.526479 CACAGCTGAAGAATGCAGTATGTAT 59.474 40.000 23.35 0.00 46.37 2.29
3096 3173 8.206867 AGCTGAAGAATGCAGTATGTATCTAAA 58.793 33.333 0.00 0.00 46.37 1.85
3103 3180 7.664082 ATGCAGTATGTATCTAAATGCAGAC 57.336 36.000 3.31 0.00 36.37 3.51
3108 3185 8.879342 AGTATGTATCTAAATGCAGACTGAAC 57.121 34.615 6.65 0.00 44.84 3.18
3142 3219 4.630111 TGGTTTGATGCTTTCAATTCCAC 58.370 39.130 15.79 7.85 43.73 4.02
3172 3249 5.585047 ACAAACTAGAATAGGGCATTTCGAC 59.415 40.000 0.00 0.00 44.97 4.20
3175 3252 2.822764 AGAATAGGGCATTTCGACGAC 58.177 47.619 0.00 0.00 0.00 4.34
3235 3312 3.131396 GTTGACACGTGAAATGACTCCT 58.869 45.455 25.01 0.00 0.00 3.69
3313 3390 1.304381 TCACAAGGATGGCCAAGGC 60.304 57.895 10.96 1.52 41.06 4.35
3319 3396 4.802051 GATGGCCAAGGCGCAGGA 62.802 66.667 10.96 0.00 43.06 3.86
3323 3400 4.722700 GCCAAGGCGCAGGAGGAA 62.723 66.667 10.83 0.00 0.00 3.36
3328 3405 2.044946 GGCGCAGGAGGAAATGGT 60.045 61.111 10.83 0.00 0.00 3.55
3329 3406 2.409870 GGCGCAGGAGGAAATGGTG 61.410 63.158 10.83 0.00 0.00 4.17
3332 3409 1.019673 CGCAGGAGGAAATGGTGATG 58.980 55.000 0.00 0.00 0.00 3.07
3333 3410 1.679944 CGCAGGAGGAAATGGTGATGT 60.680 52.381 0.00 0.00 0.00 3.06
3334 3411 2.419990 CGCAGGAGGAAATGGTGATGTA 60.420 50.000 0.00 0.00 0.00 2.29
3400 3477 4.757594 AGTTGAGTGATCTTCTCATGCTC 58.242 43.478 17.19 10.81 40.83 4.26
3447 3524 2.568956 CCATCAGGAAAGAGGTCTGTGA 59.431 50.000 0.00 0.00 36.89 3.58
3456 3533 3.566261 GGTCTGTGACCGTGCATG 58.434 61.111 0.00 0.00 43.14 4.06
3465 3576 1.003355 ACCGTGCATGACTCCCAAG 60.003 57.895 7.72 0.00 0.00 3.61
3467 3578 0.107508 CCGTGCATGACTCCCAAGAT 60.108 55.000 7.72 0.00 0.00 2.40
3476 3587 4.142609 TGACTCCCAAGATACAAGATGC 57.857 45.455 0.00 0.00 0.00 3.91
3481 3592 6.116126 ACTCCCAAGATACAAGATGCTAAAC 58.884 40.000 0.00 0.00 0.00 2.01
3487 3598 9.113838 CCAAGATACAAGATGCTAAACTGTTAT 57.886 33.333 0.00 0.00 0.00 1.89
3530 3641 6.634805 ACTATCAGATGTGGTGTAGTTGAAG 58.365 40.000 0.00 0.00 0.00 3.02
3546 3657 9.134734 TGTAGTTGAAGTTTTGAATTTTGTGTC 57.865 29.630 0.00 0.00 0.00 3.67
3605 3716 2.724977 TACTCTGCAACTTCACTCCG 57.275 50.000 0.00 0.00 0.00 4.63
3611 3722 0.599204 GCAACTTCACTCCGGACGAA 60.599 55.000 0.00 5.66 0.00 3.85
3614 3725 2.365408 ACTTCACTCCGGACGAATTC 57.635 50.000 0.00 0.00 0.00 2.17
3635 3746 1.566298 GCCCTGATCCTGTTCCTGGT 61.566 60.000 0.00 0.00 0.00 4.00
3636 3747 0.995024 CCCTGATCCTGTTCCTGGTT 59.005 55.000 0.00 0.00 0.00 3.67
3644 3755 4.351874 TCCTGTTCCTGGTTTAGTTCTG 57.648 45.455 0.00 0.00 0.00 3.02
3656 3767 4.323868 GGTTTAGTTCTGGAGGAGCTGAAT 60.324 45.833 0.00 0.00 34.50 2.57
3668 3779 3.390639 AGGAGCTGAATTCTGAGGTATGG 59.609 47.826 15.79 0.00 0.00 2.74
3689 3800 2.225255 GCCTCTCTTGCTGAAGTTGAAC 59.775 50.000 0.00 0.00 0.00 3.18
3693 3804 3.555956 TCTCTTGCTGAAGTTGAACGAAC 59.444 43.478 0.00 0.00 34.40 3.95
3696 3807 0.591659 GCTGAAGTTGAACGAACCCC 59.408 55.000 0.00 0.00 34.80 4.95
3701 3812 3.118334 TGAAGTTGAACGAACCCCTTACA 60.118 43.478 0.00 0.00 34.80 2.41
3703 3814 3.671716 AGTTGAACGAACCCCTTACATC 58.328 45.455 0.00 0.00 34.80 3.06
3706 3817 2.824936 TGAACGAACCCCTTACATCGTA 59.175 45.455 0.00 0.00 46.71 3.43
3707 3818 3.119388 TGAACGAACCCCTTACATCGTAG 60.119 47.826 0.00 0.00 46.71 3.51
3708 3819 1.135721 ACGAACCCCTTACATCGTAGC 59.864 52.381 0.00 0.00 45.69 3.58
3716 3827 1.989864 CTTACATCGTAGCGCACACAA 59.010 47.619 11.47 0.00 0.00 3.33
3726 3837 1.062258 GCGCACACAAAATGTCATGG 58.938 50.000 0.30 0.00 40.64 3.66
3729 3840 2.331194 GCACACAAAATGTCATGGAGC 58.669 47.619 0.00 0.00 40.64 4.70
3730 3841 2.288334 GCACACAAAATGTCATGGAGCA 60.288 45.455 0.00 0.00 40.64 4.26
3731 3842 3.311106 CACACAAAATGTCATGGAGCAC 58.689 45.455 0.00 0.00 40.64 4.40
3732 3843 2.297033 ACACAAAATGTCATGGAGCACC 59.703 45.455 0.00 0.00 36.54 5.01
3733 3844 4.254476 ACACAAAATGTCATGGAGCACCA 61.254 43.478 4.98 4.98 44.34 4.17
3736 3847 8.235154 ACACAAAATGTCATGGAGCACCATAC 62.235 42.308 15.81 13.74 46.30 2.39
3749 3873 5.376854 AGCACCATACTGAATTTTGTCAC 57.623 39.130 0.00 0.00 0.00 3.67
3751 3875 5.182001 AGCACCATACTGAATTTTGTCACTC 59.818 40.000 0.00 0.00 0.00 3.51
3754 3878 7.025365 CACCATACTGAATTTTGTCACTCATG 58.975 38.462 0.00 0.00 0.00 3.07
3755 3879 6.032094 CCATACTGAATTTTGTCACTCATGC 58.968 40.000 0.00 0.00 0.00 4.06
3759 3883 0.168788 ATTTTGTCACTCATGCCGCG 59.831 50.000 0.00 0.00 0.00 6.46
3783 3907 1.944035 CTTGCTTGAGCGCTTCACA 59.056 52.632 13.26 1.12 45.83 3.58
3816 3940 0.966875 TCAGCACATTCCCATGCACC 60.967 55.000 0.00 0.00 44.59 5.01
3848 3972 2.588034 GTACCGCGCCCCTTCATC 60.588 66.667 0.00 0.00 0.00 2.92
3874 3998 2.928801 TGTAGCAGAGAAAGTGGCAA 57.071 45.000 0.00 0.00 0.00 4.52
3887 4011 2.417097 GGCAAACACCAGTGGCAC 59.583 61.111 10.29 10.29 39.93 5.01
3890 4014 2.518349 AAACACCAGTGGCACCGG 60.518 61.111 18.28 18.28 34.19 5.28
3911 4035 1.000396 AGGTGCATCAAAGGGCCTC 60.000 57.895 6.46 0.00 0.00 4.70
3927 4051 2.424474 CTCGATGGTCCAGAGGAGG 58.576 63.158 0.00 0.00 29.39 4.30
3954 4078 2.750637 AGCGACGACGACCTGGAT 60.751 61.111 12.29 0.00 42.66 3.41
3987 4111 2.320781 CCCTTGATGTCCCTCTACGAT 58.679 52.381 0.00 0.00 0.00 3.73
3996 4120 1.238625 CCCTCTACGATCGGAGCTCC 61.239 65.000 23.01 23.79 0.00 4.70
4014 4138 4.473520 CCGCCCTCGCCTTGTGAT 62.474 66.667 0.00 0.00 0.00 3.06
4146 4270 0.805322 TGTTTGGCTGTTGCTTTGCG 60.805 50.000 0.00 0.00 39.59 4.85
4168 4292 0.744281 AAAGGGCGAACCAAGTGTTG 59.256 50.000 0.00 0.00 43.89 3.33
4313 4438 3.509137 TTCGCCGGTGAGCTCGTTT 62.509 57.895 18.66 0.00 0.00 3.60
4389 4519 4.455606 AGGAAAGGATGGTGAATTCGATC 58.544 43.478 0.04 2.57 0.00 3.69
4425 4555 9.601217 AAATATTAATGCGAGTATGGACCTATC 57.399 33.333 0.00 0.00 0.00 2.08
4526 6436 3.226777 CTGTATCTCTCTTCCCCGACAT 58.773 50.000 0.00 0.00 0.00 3.06
4537 6447 1.595093 CCCCGACATTTTGCACCTCC 61.595 60.000 0.00 0.00 0.00 4.30
4622 6542 1.203523 GTGGTGTCCAGCAGAGTAGAG 59.796 57.143 0.00 0.00 39.74 2.43
4658 6581 6.284891 CCTTTTGCATTTCTGAAGGGAATA 57.715 37.500 0.00 0.00 34.58 1.75
4659 6582 6.335777 CCTTTTGCATTTCTGAAGGGAATAG 58.664 40.000 0.00 0.76 34.58 1.73
4663 6586 4.943705 TGCATTTCTGAAGGGAATAGACAC 59.056 41.667 0.00 0.00 0.00 3.67
4664 6587 5.189180 GCATTTCTGAAGGGAATAGACACT 58.811 41.667 0.00 0.00 0.00 3.55
4665 6588 6.070251 TGCATTTCTGAAGGGAATAGACACTA 60.070 38.462 0.00 0.00 0.00 2.74
4666 6589 6.481644 GCATTTCTGAAGGGAATAGACACTAG 59.518 42.308 0.00 0.00 0.00 2.57
4667 6590 5.599999 TTCTGAAGGGAATAGACACTAGC 57.400 43.478 0.00 0.00 0.00 3.42
4668 6591 4.610333 TCTGAAGGGAATAGACACTAGCA 58.390 43.478 0.00 0.00 0.00 3.49
4669 6592 4.646945 TCTGAAGGGAATAGACACTAGCAG 59.353 45.833 0.00 0.00 31.59 4.24
4700 6623 1.303888 AGTGCTGTGCAAGGGATGG 60.304 57.895 0.00 0.00 41.47 3.51
4734 6715 3.770666 CATACTCTGGTCGATTGAACGT 58.229 45.455 0.00 0.00 33.14 3.99
4740 6721 2.666508 CTGGTCGATTGAACGTTGGTAG 59.333 50.000 5.00 0.00 33.14 3.18
4741 6722 2.036217 TGGTCGATTGAACGTTGGTAGT 59.964 45.455 5.00 0.00 33.14 2.73
4742 6723 3.255395 TGGTCGATTGAACGTTGGTAGTA 59.745 43.478 5.00 0.00 33.14 1.82
4782 6784 1.134965 CCTGGACTGAACGGAGATGTC 60.135 57.143 0.00 0.00 0.00 3.06
4900 6906 3.133901 TGCAATCGGAGCATTCCTTAGTA 59.866 43.478 0.00 0.00 41.67 1.82
4907 6913 3.623510 GGAGCATTCCTTAGTAGCACAAC 59.376 47.826 0.00 0.00 40.58 3.32
4945 6951 2.088950 TCGGTTCGGTTCCTTTGATC 57.911 50.000 0.00 0.00 0.00 2.92
4946 6952 1.084289 CGGTTCGGTTCCTTTGATCC 58.916 55.000 0.00 0.00 0.00 3.36
4953 6959 4.752661 CGGTTCCTTTGATCCGTAAAAA 57.247 40.909 4.35 0.00 44.96 1.94
4954 6960 5.305139 CGGTTCCTTTGATCCGTAAAAAT 57.695 39.130 4.35 0.00 44.96 1.82
4955 6961 6.425577 CGGTTCCTTTGATCCGTAAAAATA 57.574 37.500 4.35 0.00 44.96 1.40
4956 6962 6.844254 CGGTTCCTTTGATCCGTAAAAATAA 58.156 36.000 4.35 0.00 44.96 1.40
4957 6963 7.306953 CGGTTCCTTTGATCCGTAAAAATAAA 58.693 34.615 4.35 0.00 44.96 1.40
4958 6964 7.971722 CGGTTCCTTTGATCCGTAAAAATAAAT 59.028 33.333 4.35 0.00 44.96 1.40
5001 7007 9.726438 AACGATCTTATATTTCTTTATGGAGGG 57.274 33.333 0.00 0.00 0.00 4.30
5002 7008 7.824779 ACGATCTTATATTTCTTTATGGAGGGC 59.175 37.037 0.00 0.00 0.00 5.19
5003 7009 7.824289 CGATCTTATATTTCTTTATGGAGGGCA 59.176 37.037 0.00 0.00 0.00 5.36
5004 7010 9.520515 GATCTTATATTTCTTTATGGAGGGCAA 57.479 33.333 0.00 0.00 0.00 4.52
5006 7012 9.520515 TCTTATATTTCTTTATGGAGGGCAATC 57.479 33.333 0.00 0.00 0.00 2.67
5007 7013 8.650143 TTATATTTCTTTATGGAGGGCAATCC 57.350 34.615 1.21 1.21 40.03 3.01
5013 7019 2.095270 TGGAGGGCAATCCATTGGT 58.905 52.632 6.58 0.00 44.56 3.67
5014 7020 0.413037 TGGAGGGCAATCCATTGGTT 59.587 50.000 6.58 0.00 44.56 3.67
5015 7021 1.203288 TGGAGGGCAATCCATTGGTTT 60.203 47.619 6.58 0.00 44.56 3.27
5016 7022 2.043664 TGGAGGGCAATCCATTGGTTTA 59.956 45.455 6.58 0.00 44.56 2.01
5017 7023 2.695147 GGAGGGCAATCCATTGGTTTAG 59.305 50.000 1.86 0.00 39.34 1.85
5018 7024 3.627237 GGAGGGCAATCCATTGGTTTAGA 60.627 47.826 1.86 0.00 39.34 2.10
5019 7025 3.365472 AGGGCAATCCATTGGTTTAGAC 58.635 45.455 1.86 0.00 38.21 2.59
5020 7026 3.011708 AGGGCAATCCATTGGTTTAGACT 59.988 43.478 1.86 0.00 38.21 3.24
5021 7027 3.769300 GGGCAATCCATTGGTTTAGACTT 59.231 43.478 1.86 0.00 38.21 3.01
5022 7028 4.222810 GGGCAATCCATTGGTTTAGACTTT 59.777 41.667 1.86 0.00 38.21 2.66
5023 7029 5.420739 GGGCAATCCATTGGTTTAGACTTTA 59.579 40.000 1.86 0.00 38.21 1.85
5024 7030 6.405842 GGGCAATCCATTGGTTTAGACTTTAG 60.406 42.308 1.86 0.00 38.21 1.85
5025 7031 6.377146 GGCAATCCATTGGTTTAGACTTTAGA 59.623 38.462 1.86 0.00 38.21 2.10
5026 7032 7.415653 GGCAATCCATTGGTTTAGACTTTAGAG 60.416 40.741 1.86 0.00 38.21 2.43
5027 7033 7.121315 GCAATCCATTGGTTTAGACTTTAGAGT 59.879 37.037 1.86 0.00 38.21 3.24
5028 7034 9.014297 CAATCCATTGGTTTAGACTTTAGAGTT 57.986 33.333 1.86 0.00 33.50 3.01
5029 7035 8.794335 ATCCATTGGTTTAGACTTTAGAGTTC 57.206 34.615 1.86 0.00 35.88 3.01
5030 7036 7.166167 TCCATTGGTTTAGACTTTAGAGTTCC 58.834 38.462 1.86 0.00 35.88 3.62
5031 7037 7.017254 TCCATTGGTTTAGACTTTAGAGTTCCT 59.983 37.037 1.86 0.00 35.88 3.36
5032 7038 8.319146 CCATTGGTTTAGACTTTAGAGTTCCTA 58.681 37.037 0.00 0.00 35.88 2.94
5033 7039 9.372369 CATTGGTTTAGACTTTAGAGTTCCTAG 57.628 37.037 0.00 0.00 35.88 3.02
5034 7040 8.488308 TTGGTTTAGACTTTAGAGTTCCTAGT 57.512 34.615 0.00 0.00 35.88 2.57
5035 7041 9.592196 TTGGTTTAGACTTTAGAGTTCCTAGTA 57.408 33.333 0.00 0.00 35.88 1.82
5036 7042 9.765295 TGGTTTAGACTTTAGAGTTCCTAGTAT 57.235 33.333 0.00 0.00 35.88 2.12
5054 7060 9.226606 TCCTAGTATTTTATGTTTTGTCACTGG 57.773 33.333 0.00 0.00 0.00 4.00
5055 7061 7.968405 CCTAGTATTTTATGTTTTGTCACTGGC 59.032 37.037 0.00 0.00 0.00 4.85
5056 7062 6.687604 AGTATTTTATGTTTTGTCACTGGCC 58.312 36.000 0.00 0.00 0.00 5.36
5057 7063 4.329462 TTTTATGTTTTGTCACTGGCCC 57.671 40.909 0.00 0.00 0.00 5.80
5058 7064 2.969821 TATGTTTTGTCACTGGCCCT 57.030 45.000 0.00 0.00 0.00 5.19
5059 7065 2.086610 ATGTTTTGTCACTGGCCCTT 57.913 45.000 0.00 0.00 0.00 3.95
5060 7066 2.738587 TGTTTTGTCACTGGCCCTTA 57.261 45.000 0.00 0.00 0.00 2.69
5061 7067 2.303175 TGTTTTGTCACTGGCCCTTAC 58.697 47.619 0.00 0.00 0.00 2.34
5062 7068 1.265905 GTTTTGTCACTGGCCCTTACG 59.734 52.381 0.00 0.00 0.00 3.18
5063 7069 0.250553 TTTGTCACTGGCCCTTACGG 60.251 55.000 0.00 0.00 0.00 4.02
5064 7070 1.412453 TTGTCACTGGCCCTTACGGT 61.412 55.000 0.00 0.00 0.00 4.83
5065 7071 1.373812 GTCACTGGCCCTTACGGTT 59.626 57.895 0.00 0.00 0.00 4.44
5066 7072 0.250597 GTCACTGGCCCTTACGGTTT 60.251 55.000 0.00 0.00 0.00 3.27
5067 7073 0.475044 TCACTGGCCCTTACGGTTTT 59.525 50.000 0.00 0.00 0.00 2.43
5068 7074 0.879090 CACTGGCCCTTACGGTTTTC 59.121 55.000 0.00 0.00 0.00 2.29
5069 7075 0.251033 ACTGGCCCTTACGGTTTTCC 60.251 55.000 0.00 0.00 0.00 3.13
5089 7095 3.452466 CGTAAAAATAAACGGTCGGCA 57.548 42.857 0.00 0.00 35.51 5.69
5090 7096 3.808095 CGTAAAAATAAACGGTCGGCAA 58.192 40.909 0.00 0.00 35.51 4.52
5091 7097 3.599091 CGTAAAAATAAACGGTCGGCAAC 59.401 43.478 0.00 0.00 35.51 4.17
5104 7110 2.528797 GGCAACGCTTCTTCTTCGA 58.471 52.632 0.00 0.00 0.00 3.71
5105 7111 0.865769 GGCAACGCTTCTTCTTCGAA 59.134 50.000 0.00 0.00 0.00 3.71
5106 7112 1.464997 GGCAACGCTTCTTCTTCGAAT 59.535 47.619 0.00 0.00 0.00 3.34
5107 7113 2.095718 GGCAACGCTTCTTCTTCGAATT 60.096 45.455 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.227853 GCGGACACCAACAGAACCT 60.228 57.895 0.00 0.00 0.00 3.50
83 84 7.148474 GCTGACTAACTGAATTTTACGAATGGA 60.148 37.037 0.00 0.00 0.00 3.41
111 112 7.349859 TGTCCAGGGGAAAATACAGTATAAGAT 59.650 37.037 0.00 0.00 31.38 2.40
115 116 7.349859 AGAATGTCCAGGGGAAAATACAGTATA 59.650 37.037 0.00 0.00 31.38 1.47
117 118 5.491078 AGAATGTCCAGGGGAAAATACAGTA 59.509 40.000 0.00 0.00 31.38 2.74
118 119 4.292306 AGAATGTCCAGGGGAAAATACAGT 59.708 41.667 0.00 0.00 31.38 3.55
119 120 4.860022 AGAATGTCCAGGGGAAAATACAG 58.140 43.478 0.00 0.00 31.38 2.74
120 121 4.946160 AGAATGTCCAGGGGAAAATACA 57.054 40.909 0.00 0.00 31.38 2.29
121 122 5.261216 TCAAGAATGTCCAGGGGAAAATAC 58.739 41.667 0.00 0.00 31.38 1.89
128 129 2.887151 AGTTCAAGAATGTCCAGGGG 57.113 50.000 0.00 0.00 0.00 4.79
130 131 4.153117 CGAAGAAGTTCAAGAATGTCCAGG 59.847 45.833 5.50 0.00 32.36 4.45
229 251 1.304052 CCGGAATTTCCAGCCACCA 60.304 57.895 15.58 0.00 35.91 4.17
234 256 1.215382 GTTGCCCGGAATTTCCAGC 59.785 57.895 15.58 16.26 35.91 4.85
235 257 0.958382 TCGTTGCCCGGAATTTCCAG 60.958 55.000 15.58 3.96 35.91 3.86
236 258 1.073373 TCGTTGCCCGGAATTTCCA 59.927 52.632 15.58 0.00 35.91 3.53
293 315 2.612972 CCAGATGTAAACTCGGCACTGT 60.613 50.000 0.00 0.00 0.00 3.55
295 317 1.623811 ACCAGATGTAAACTCGGCACT 59.376 47.619 0.00 0.00 0.00 4.40
311 333 1.085091 GATCTGACAAGCTGCACCAG 58.915 55.000 1.02 3.50 34.12 4.00
316 338 0.463474 GGGGAGATCTGACAAGCTGC 60.463 60.000 0.00 0.00 0.00 5.25
336 358 2.029649 GCTGTACCGAAACTGGACTACA 60.030 50.000 0.00 0.00 0.00 2.74
337 359 2.230750 AGCTGTACCGAAACTGGACTAC 59.769 50.000 0.00 0.00 0.00 2.73
377 408 0.394565 GGATGGAGAATGAGGTCCCG 59.605 60.000 0.00 0.00 31.04 5.14
404 435 0.822944 TGTACGACCGTTGGACTGGA 60.823 55.000 0.00 0.00 0.00 3.86
509 540 3.318839 CCCAACAGCAACAAGAGATTTCA 59.681 43.478 0.00 0.00 0.00 2.69
510 541 3.858503 GCCCAACAGCAACAAGAGATTTC 60.859 47.826 0.00 0.00 0.00 2.17
513 544 1.251251 GCCCAACAGCAACAAGAGAT 58.749 50.000 0.00 0.00 0.00 2.75
626 659 6.439675 TGCCGTAAAAGTGTAAAAGAAACT 57.560 33.333 0.00 0.00 0.00 2.66
628 661 7.028926 TCATGCCGTAAAAGTGTAAAAGAAA 57.971 32.000 0.00 0.00 0.00 2.52
656 691 6.127140 ACCGACTACCATAAGTAAGAAGCAAT 60.127 38.462 0.00 0.00 0.00 3.56
689 726 6.091441 CAGTAAGGCATTCACTTGACTAACTC 59.909 42.308 0.00 0.00 32.32 3.01
691 728 5.932303 TCAGTAAGGCATTCACTTGACTAAC 59.068 40.000 0.00 0.00 32.32 2.34
693 730 5.738619 TCAGTAAGGCATTCACTTGACTA 57.261 39.130 0.00 0.00 32.32 2.59
697 734 5.644644 GGATTTCAGTAAGGCATTCACTTG 58.355 41.667 0.00 0.00 0.00 3.16
720 757 5.121611 TCCACTGTACTCAACATAAAATGCG 59.878 40.000 0.00 0.00 37.50 4.73
881 920 2.307098 AGAAAGTGACATCCAGGAAGGG 59.693 50.000 0.00 0.00 38.24 3.95
1038 1078 4.074970 GTTCCACTTCCACATCAGTTGAT 58.925 43.478 0.00 0.00 34.56 2.57
1095 1135 4.144297 AGGAGTCTCTAGCTGCTTCATAG 58.856 47.826 7.79 0.00 30.34 2.23
1203 1243 2.132996 TGGGCTGTTTGGCTTGGTG 61.133 57.895 0.00 0.00 41.48 4.17
1319 1359 5.594725 TCAACAGTTTTAACACCATTAGCCA 59.405 36.000 0.00 0.00 0.00 4.75
1352 1392 4.704965 AGTAACTTCCACAGTTTCTGGTC 58.295 43.478 1.90 0.00 43.89 4.02
1353 1393 4.772886 AGTAACTTCCACAGTTTCTGGT 57.227 40.909 1.90 0.00 43.89 4.00
1438 1478 1.541233 GCCCTCGGTGGACTTATCATG 60.541 57.143 0.00 0.00 38.35 3.07
1522 1562 3.117776 TCAATGGCCTTATCATCAGCAGT 60.118 43.478 3.32 0.00 0.00 4.40
1550 1590 5.840693 TCAATGGCCTTATCATCAGTCTCTA 59.159 40.000 3.32 0.00 0.00 2.43
1551 1591 4.657504 TCAATGGCCTTATCATCAGTCTCT 59.342 41.667 3.32 0.00 0.00 3.10
1552 1592 4.965814 TCAATGGCCTTATCATCAGTCTC 58.034 43.478 3.32 0.00 0.00 3.36
1553 1593 4.202440 CCTCAATGGCCTTATCATCAGTCT 60.202 45.833 3.32 0.00 0.00 3.24
1554 1594 4.070716 CCTCAATGGCCTTATCATCAGTC 58.929 47.826 3.32 0.00 0.00 3.51
1555 1595 3.181436 CCCTCAATGGCCTTATCATCAGT 60.181 47.826 3.32 0.00 0.00 3.41
1556 1596 3.418995 CCCTCAATGGCCTTATCATCAG 58.581 50.000 3.32 0.00 0.00 2.90
1557 1597 2.489619 GCCCTCAATGGCCTTATCATCA 60.490 50.000 3.32 0.00 46.11 3.07
1558 1598 2.165998 GCCCTCAATGGCCTTATCATC 58.834 52.381 3.32 0.00 46.11 2.92
1559 1599 2.299326 GCCCTCAATGGCCTTATCAT 57.701 50.000 3.32 0.00 46.11 2.45
1560 1600 3.827505 GCCCTCAATGGCCTTATCA 57.172 52.632 3.32 0.00 46.11 2.15
1568 1608 1.883084 GTCGCTACGCCCTCAATGG 60.883 63.158 0.00 0.00 0.00 3.16
1569 1609 1.141881 AGTCGCTACGCCCTCAATG 59.858 57.895 0.00 0.00 0.00 2.82
1570 1610 1.141881 CAGTCGCTACGCCCTCAAT 59.858 57.895 0.00 0.00 0.00 2.57
1571 1611 1.320344 ATCAGTCGCTACGCCCTCAA 61.320 55.000 0.00 0.00 0.00 3.02
1572 1612 1.753078 ATCAGTCGCTACGCCCTCA 60.753 57.895 0.00 0.00 0.00 3.86
1573 1613 1.299468 CATCAGTCGCTACGCCCTC 60.299 63.158 0.00 0.00 0.00 4.30
1574 1614 1.109920 ATCATCAGTCGCTACGCCCT 61.110 55.000 0.00 0.00 0.00 5.19
1575 1615 0.596577 TATCATCAGTCGCTACGCCC 59.403 55.000 0.00 0.00 0.00 6.13
1576 1616 2.320367 CTTATCATCAGTCGCTACGCC 58.680 52.381 0.00 0.00 0.00 5.68
1577 1617 2.320367 CCTTATCATCAGTCGCTACGC 58.680 52.381 0.00 0.00 0.00 4.42
1578 1618 2.320367 GCCTTATCATCAGTCGCTACG 58.680 52.381 0.00 0.00 0.00 3.51
1579 1619 2.035961 TGGCCTTATCATCAGTCGCTAC 59.964 50.000 3.32 0.00 0.00 3.58
1660 1730 2.028930 CACTGGTCTCTACACCCTCAAC 60.029 54.545 0.00 0.00 35.26 3.18
1818 1888 8.680039 ATTCCTCAATCTTCTCATCATTCTTC 57.320 34.615 0.00 0.00 0.00 2.87
2041 2111 1.708341 ACAAGCACAAGCCCAGAAAT 58.292 45.000 0.00 0.00 43.56 2.17
2409 2481 0.031178 GCCAAGACAGTGCCAGTTTG 59.969 55.000 0.00 0.00 0.00 2.93
2532 2605 9.177304 GTTTTACAAGTAGCAGGTCAAATTTAC 57.823 33.333 0.00 0.00 0.00 2.01
2582 2655 7.055667 ACCGATCAGAATATTGACATACTGT 57.944 36.000 0.00 0.00 0.00 3.55
2587 2660 9.429359 GAGAAATACCGATCAGAATATTGACAT 57.571 33.333 0.00 0.00 0.00 3.06
2635 2712 3.228188 TCCTCAACAGGAGTTTGCATT 57.772 42.857 0.00 0.00 44.75 3.56
2665 2742 3.782889 AACAGTTTCTCAACACTTGGC 57.217 42.857 0.00 0.00 35.05 4.52
2671 2748 3.569194 TGCCCTAACAGTTTCTCAACA 57.431 42.857 0.00 0.00 35.05 3.33
2676 2753 4.524328 CCAAAGAATGCCCTAACAGTTTCT 59.476 41.667 0.00 0.00 0.00 2.52
2682 2759 2.170166 CAGCCAAAGAATGCCCTAACA 58.830 47.619 0.00 0.00 0.00 2.41
2715 2792 8.796475 TCTTCCAAAGATCAATAGAAAAAGTGG 58.204 33.333 0.00 0.00 31.20 4.00
2880 2957 4.732285 AACAGAACAGCTCATAAACACG 57.268 40.909 0.00 0.00 0.00 4.49
2921 2998 1.343506 CGTCTAAACGGGCTACACAC 58.656 55.000 0.00 0.00 45.21 3.82
2954 3031 0.178767 CTGATTCACGGAGGATGGCA 59.821 55.000 0.00 0.00 0.00 4.92
3083 3160 7.928706 GGTTCAGTCTGCATTTAGATACATACT 59.071 37.037 0.00 0.00 0.00 2.12
3091 3168 3.072330 TGTGGGTTCAGTCTGCATTTAGA 59.928 43.478 0.00 0.00 0.00 2.10
3096 3173 2.165167 CAATGTGGGTTCAGTCTGCAT 58.835 47.619 0.00 0.00 0.00 3.96
3103 3180 3.817709 ACCAAAACAATGTGGGTTCAG 57.182 42.857 0.00 0.00 39.39 3.02
3108 3185 3.250521 GCATCAAACCAAAACAATGTGGG 59.749 43.478 0.00 0.00 39.39 4.61
3142 3219 5.175859 TGCCCTATTCTAGTTTGTTCTTCG 58.824 41.667 0.00 0.00 0.00 3.79
3172 3249 2.561419 TGGAAGGAGTGAACTAAGGTCG 59.439 50.000 0.00 0.00 0.00 4.79
3175 3252 4.714632 TGTTTGGAAGGAGTGAACTAAGG 58.285 43.478 0.00 0.00 0.00 2.69
3235 3312 1.059584 TGGACCAGCTTCCAACCTGA 61.060 55.000 4.57 0.00 43.04 3.86
3313 3390 1.019673 CATCACCATTTCCTCCTGCG 58.980 55.000 0.00 0.00 0.00 5.18
3319 3396 6.627087 TCTCTTCTTACATCACCATTTCCT 57.373 37.500 0.00 0.00 0.00 3.36
3323 3400 6.566079 TCCATCTCTTCTTACATCACCATT 57.434 37.500 0.00 0.00 0.00 3.16
3328 3405 4.958581 TCAGCTCCATCTCTTCTTACATCA 59.041 41.667 0.00 0.00 0.00 3.07
3329 3406 5.528043 TCAGCTCCATCTCTTCTTACATC 57.472 43.478 0.00 0.00 0.00 3.06
3332 3409 5.163364 TGGATTCAGCTCCATCTCTTCTTAC 60.163 44.000 2.39 0.00 40.43 2.34
3333 3410 4.964897 TGGATTCAGCTCCATCTCTTCTTA 59.035 41.667 2.39 0.00 40.43 2.10
3334 3411 3.779183 TGGATTCAGCTCCATCTCTTCTT 59.221 43.478 2.39 0.00 40.43 2.52
3394 3471 1.442526 GCATGTCCTTCGGGAGCATG 61.443 60.000 16.01 16.01 46.04 4.06
3400 3477 1.089920 CAAGAAGCATGTCCTTCGGG 58.910 55.000 7.24 1.79 44.56 5.14
3447 3524 1.003355 CTTGGGAGTCATGCACGGT 60.003 57.895 0.00 0.00 0.00 4.83
3456 3533 4.414337 AGCATCTTGTATCTTGGGAGTC 57.586 45.455 0.00 0.00 0.00 3.36
3503 3614 8.129496 TCAACTACACCACATCTGATAGTTAA 57.871 34.615 0.00 0.00 32.51 2.01
3504 3615 7.712204 TCAACTACACCACATCTGATAGTTA 57.288 36.000 0.00 0.00 32.51 2.24
3509 3620 5.489792 ACTTCAACTACACCACATCTGAT 57.510 39.130 0.00 0.00 0.00 2.90
3530 3641 5.005682 GCAGACCTGACACAAAATTCAAAAC 59.994 40.000 0.47 0.00 0.00 2.43
3605 3716 1.587547 GATCAGGGCAGAATTCGTCC 58.412 55.000 11.46 11.46 0.00 4.79
3611 3722 1.213926 GGAACAGGATCAGGGCAGAAT 59.786 52.381 0.00 0.00 0.00 2.40
3614 3725 0.107312 CAGGAACAGGATCAGGGCAG 60.107 60.000 0.00 0.00 0.00 4.85
3635 3746 5.249393 AGAATTCAGCTCCTCCAGAACTAAA 59.751 40.000 8.44 0.00 0.00 1.85
3636 3747 4.780021 AGAATTCAGCTCCTCCAGAACTAA 59.220 41.667 8.44 0.00 0.00 2.24
3644 3755 1.836802 ACCTCAGAATTCAGCTCCTCC 59.163 52.381 8.44 0.00 0.00 4.30
3668 3779 2.175878 TCAACTTCAGCAAGAGAGGC 57.824 50.000 0.00 0.00 33.34 4.70
3689 3800 1.849097 GCTACGATGTAAGGGGTTCG 58.151 55.000 0.00 0.00 0.00 3.95
3693 3804 0.874607 GTGCGCTACGATGTAAGGGG 60.875 60.000 9.73 0.00 0.00 4.79
3696 3807 1.624487 TGTGTGCGCTACGATGTAAG 58.376 50.000 9.73 0.00 0.00 2.34
3701 3812 1.804151 ACATTTTGTGTGCGCTACGAT 59.196 42.857 9.73 1.41 40.28 3.73
3703 3814 1.070242 TGACATTTTGTGTGCGCTACG 60.070 47.619 9.73 0.00 42.36 3.51
3706 3817 1.336148 CCATGACATTTTGTGTGCGCT 60.336 47.619 9.73 0.00 42.36 5.92
3707 3818 1.062258 CCATGACATTTTGTGTGCGC 58.938 50.000 0.00 0.00 42.36 6.09
3708 3819 2.587956 CTCCATGACATTTTGTGTGCG 58.412 47.619 0.00 0.00 42.36 5.34
3726 3837 5.182001 AGTGACAAAATTCAGTATGGTGCTC 59.818 40.000 0.00 0.00 36.16 4.26
3729 3840 6.558771 TGAGTGACAAAATTCAGTATGGTG 57.441 37.500 0.00 0.00 36.16 4.17
3730 3841 6.349611 GCATGAGTGACAAAATTCAGTATGGT 60.350 38.462 0.00 0.00 36.16 3.55
3731 3842 6.032094 GCATGAGTGACAAAATTCAGTATGG 58.968 40.000 0.00 0.00 36.16 2.74
3732 3843 6.032094 GGCATGAGTGACAAAATTCAGTATG 58.968 40.000 0.00 0.00 31.88 2.39
3733 3844 5.163723 CGGCATGAGTGACAAAATTCAGTAT 60.164 40.000 0.00 0.00 30.50 2.12
3736 3847 3.495193 CGGCATGAGTGACAAAATTCAG 58.505 45.455 0.00 0.00 30.50 3.02
3737 3848 2.351641 GCGGCATGAGTGACAAAATTCA 60.352 45.455 0.00 0.00 30.50 2.57
3738 3849 2.253603 GCGGCATGAGTGACAAAATTC 58.746 47.619 0.00 0.00 30.50 2.17
3739 3850 1.401409 CGCGGCATGAGTGACAAAATT 60.401 47.619 0.00 0.00 30.50 1.82
3740 3851 0.168788 CGCGGCATGAGTGACAAAAT 59.831 50.000 0.00 0.00 30.50 1.82
3741 3852 1.573932 CGCGGCATGAGTGACAAAA 59.426 52.632 0.00 0.00 30.50 2.44
3751 3875 4.531912 CAAGCTCTGCGCGGCATG 62.532 66.667 12.58 10.81 45.59 4.06
3783 3907 6.095160 GGAATGTGCTGATCAGATTTTTCTCT 59.905 38.462 27.04 0.64 38.60 3.10
3801 3925 2.048023 AGCGGTGCATGGGAATGTG 61.048 57.895 0.00 0.00 0.00 3.21
3848 3972 2.428890 ACTTTCTCTGCTACATCCTCCG 59.571 50.000 0.00 0.00 0.00 4.63
3861 3985 2.301346 CTGGTGTTTGCCACTTTCTCT 58.699 47.619 0.00 0.00 43.94 3.10
3874 3998 3.476031 CTCCGGTGCCACTGGTGTT 62.476 63.158 21.86 0.00 45.01 3.32
3879 4003 3.314331 ACCTCTCCGGTGCCACTG 61.314 66.667 0.00 0.00 46.80 3.66
3887 4011 0.745845 CCTTTGATGCACCTCTCCGG 60.746 60.000 0.00 0.00 39.35 5.14
3890 4014 1.034292 GGCCCTTTGATGCACCTCTC 61.034 60.000 0.00 0.00 0.00 3.20
3898 4022 0.107017 ACCATCGAGGCCCTTTGATG 60.107 55.000 16.13 16.13 43.14 3.07
3900 4024 1.602237 GACCATCGAGGCCCTTTGA 59.398 57.895 0.00 0.00 43.14 2.69
3911 4035 2.136878 CCCCTCCTCTGGACCATCG 61.137 68.421 0.00 0.00 0.00 3.84
3927 4051 3.376078 TCGTCGCTGGTGTACCCC 61.376 66.667 0.00 0.00 34.29 4.95
3954 4078 1.306997 CAAGGGGGAGCCTAGGTCA 60.307 63.158 11.31 0.00 0.00 4.02
4002 4126 1.450312 GACCCCATCACAAGGCGAG 60.450 63.158 0.00 0.00 0.00 5.03
4014 4138 0.687920 TACTGAAATGTGCGACCCCA 59.312 50.000 0.00 0.00 0.00 4.96
4146 4270 1.951602 ACACTTGGTTCGCCCTTTTAC 59.048 47.619 0.00 0.00 36.08 2.01
4168 4292 1.215382 GCAAATTCTTCACGCCCCC 59.785 57.895 0.00 0.00 0.00 5.40
4313 4438 7.624360 TGAGAAGAAGAAAAAGCAACTAACA 57.376 32.000 0.00 0.00 0.00 2.41
4389 4519 6.262273 ACTCGCATTAATATTTTACACCCAGG 59.738 38.462 0.00 0.00 0.00 4.45
4425 4555 2.754946 TCCAGCCTTTACTTACACCG 57.245 50.000 0.00 0.00 0.00 4.94
4537 6447 2.881266 CGCACAACACCAGTGACCG 61.881 63.158 4.48 0.00 39.30 4.79
4622 6542 0.877213 CAAAAGGGCAGCTGTTGTGC 60.877 55.000 16.64 0.03 40.42 4.57
4658 6581 1.595882 CTGCTGGCTGCTAGTGTCT 59.404 57.895 17.45 0.00 43.37 3.41
4659 6582 1.449246 CCTGCTGGCTGCTAGTGTC 60.449 63.158 17.45 0.00 43.37 3.67
4663 6586 1.153409 CACTCCTGCTGGCTGCTAG 60.153 63.158 17.45 8.84 43.37 3.42
4664 6587 1.610379 TCACTCCTGCTGGCTGCTA 60.610 57.895 17.45 3.45 43.37 3.49
4665 6588 2.926779 TCACTCCTGCTGGCTGCT 60.927 61.111 17.45 0.00 43.37 4.24
4666 6589 2.436292 CTCACTCCTGCTGGCTGC 60.436 66.667 9.67 9.67 43.25 5.25
4667 6590 1.375652 CACTCACTCCTGCTGGCTG 60.376 63.158 4.42 2.94 0.00 4.85
4668 6591 3.067091 CACTCACTCCTGCTGGCT 58.933 61.111 4.42 0.00 0.00 4.75
4669 6592 2.745492 GCACTCACTCCTGCTGGC 60.745 66.667 4.42 0.00 0.00 4.85
4700 6623 2.004733 AGAGTATGCCGTTAAAACCGC 58.995 47.619 0.07 0.07 34.43 5.68
4734 6715 4.131596 GTCCAGTTTGCTTGTACTACCAA 58.868 43.478 0.00 0.00 0.00 3.67
4740 6721 0.872388 CGGGTCCAGTTTGCTTGTAC 59.128 55.000 0.00 0.00 0.00 2.90
4741 6722 0.470766 ACGGGTCCAGTTTGCTTGTA 59.529 50.000 0.00 0.00 0.00 2.41
4742 6723 0.470766 TACGGGTCCAGTTTGCTTGT 59.529 50.000 0.00 0.00 0.00 3.16
4782 6784 0.027979 CACAAGAACTGGTGCACACG 59.972 55.000 20.43 11.11 0.00 4.49
4900 6906 3.278574 TGAACTTGCTAACAGTTGTGCT 58.721 40.909 12.38 0.00 0.00 4.40
4907 6913 3.120199 CCGAACCATGAACTTGCTAACAG 60.120 47.826 0.00 0.00 0.00 3.16
4975 6981 9.726438 CCCTCCATAAAGAAATATAAGATCGTT 57.274 33.333 0.00 0.00 0.00 3.85
4976 6982 7.824779 GCCCTCCATAAAGAAATATAAGATCGT 59.175 37.037 0.00 0.00 0.00 3.73
4977 6983 7.824289 TGCCCTCCATAAAGAAATATAAGATCG 59.176 37.037 0.00 0.00 0.00 3.69
4978 6984 9.520515 TTGCCCTCCATAAAGAAATATAAGATC 57.479 33.333 0.00 0.00 0.00 2.75
4980 6986 9.520515 GATTGCCCTCCATAAAGAAATATAAGA 57.479 33.333 0.00 0.00 0.00 2.10
4981 6987 8.743714 GGATTGCCCTCCATAAAGAAATATAAG 58.256 37.037 0.00 0.00 35.24 1.73
4982 6988 8.231007 TGGATTGCCCTCCATAAAGAAATATAA 58.769 33.333 0.35 0.00 40.43 0.98
4983 6989 7.764617 TGGATTGCCCTCCATAAAGAAATATA 58.235 34.615 0.35 0.00 40.43 0.86
4984 6990 6.623329 TGGATTGCCCTCCATAAAGAAATAT 58.377 36.000 0.35 0.00 40.43 1.28
4985 6991 6.024563 TGGATTGCCCTCCATAAAGAAATA 57.975 37.500 0.35 0.00 40.43 1.40
4986 6992 4.882559 TGGATTGCCCTCCATAAAGAAAT 58.117 39.130 0.35 0.00 40.43 2.17
4987 6993 4.329638 TGGATTGCCCTCCATAAAGAAA 57.670 40.909 0.35 0.00 40.43 2.52
4996 7002 1.571955 AAACCAATGGATTGCCCTCC 58.428 50.000 6.16 0.00 36.48 4.30
4997 7003 3.381590 GTCTAAACCAATGGATTGCCCTC 59.618 47.826 6.16 0.00 36.48 4.30
4998 7004 3.011708 AGTCTAAACCAATGGATTGCCCT 59.988 43.478 6.16 0.00 36.48 5.19
4999 7005 3.365472 AGTCTAAACCAATGGATTGCCC 58.635 45.455 6.16 0.00 36.48 5.36
5000 7006 5.405935 AAAGTCTAAACCAATGGATTGCC 57.594 39.130 6.16 0.00 36.48 4.52
5001 7007 7.121315 ACTCTAAAGTCTAAACCAATGGATTGC 59.879 37.037 6.16 0.00 36.48 3.56
5002 7008 8.567285 ACTCTAAAGTCTAAACCAATGGATTG 57.433 34.615 6.16 0.00 37.52 2.67
5003 7009 9.232473 GAACTCTAAAGTCTAAACCAATGGATT 57.768 33.333 6.16 2.38 33.48 3.01
5004 7010 7.829706 GGAACTCTAAAGTCTAAACCAATGGAT 59.170 37.037 6.16 0.00 33.48 3.41
5005 7011 7.017254 AGGAACTCTAAAGTCTAAACCAATGGA 59.983 37.037 6.16 0.00 33.48 3.41
5006 7012 7.168905 AGGAACTCTAAAGTCTAAACCAATGG 58.831 38.462 0.00 0.00 33.48 3.16
5007 7013 9.372369 CTAGGAACTCTAAAGTCTAAACCAATG 57.628 37.037 0.00 0.00 41.75 2.82
5008 7014 9.102453 ACTAGGAACTCTAAAGTCTAAACCAAT 57.898 33.333 0.00 0.00 41.75 3.16
5009 7015 8.488308 ACTAGGAACTCTAAAGTCTAAACCAA 57.512 34.615 0.00 0.00 41.75 3.67
5010 7016 9.765295 ATACTAGGAACTCTAAAGTCTAAACCA 57.235 33.333 0.00 0.00 41.75 3.67
5028 7034 9.226606 CCAGTGACAAAACATAAAATACTAGGA 57.773 33.333 0.00 0.00 0.00 2.94
5029 7035 7.968405 GCCAGTGACAAAACATAAAATACTAGG 59.032 37.037 0.00 0.00 0.00 3.02
5030 7036 7.968405 GGCCAGTGACAAAACATAAAATACTAG 59.032 37.037 0.00 0.00 0.00 2.57
5031 7037 7.094118 GGGCCAGTGACAAAACATAAAATACTA 60.094 37.037 4.39 0.00 0.00 1.82
5032 7038 6.295067 GGGCCAGTGACAAAACATAAAATACT 60.295 38.462 4.39 0.00 0.00 2.12
5033 7039 5.867174 GGGCCAGTGACAAAACATAAAATAC 59.133 40.000 4.39 0.00 0.00 1.89
5034 7040 5.777732 AGGGCCAGTGACAAAACATAAAATA 59.222 36.000 6.18 0.00 0.00 1.40
5035 7041 4.592778 AGGGCCAGTGACAAAACATAAAAT 59.407 37.500 6.18 0.00 0.00 1.82
5036 7042 3.964031 AGGGCCAGTGACAAAACATAAAA 59.036 39.130 6.18 0.00 0.00 1.52
5037 7043 3.571590 AGGGCCAGTGACAAAACATAAA 58.428 40.909 6.18 0.00 0.00 1.40
5038 7044 3.237268 AGGGCCAGTGACAAAACATAA 57.763 42.857 6.18 0.00 0.00 1.90
5039 7045 2.969821 AGGGCCAGTGACAAAACATA 57.030 45.000 6.18 0.00 0.00 2.29
5040 7046 2.086610 AAGGGCCAGTGACAAAACAT 57.913 45.000 6.18 0.00 0.00 2.71
5041 7047 2.303175 GTAAGGGCCAGTGACAAAACA 58.697 47.619 6.18 0.00 0.00 2.83
5042 7048 1.265905 CGTAAGGGCCAGTGACAAAAC 59.734 52.381 6.18 0.00 0.00 2.43
5043 7049 1.600023 CGTAAGGGCCAGTGACAAAA 58.400 50.000 6.18 0.00 0.00 2.44
5044 7050 3.315765 CGTAAGGGCCAGTGACAAA 57.684 52.632 6.18 0.00 0.00 2.83
5069 7075 3.452466 TGCCGACCGTTTATTTTTACG 57.548 42.857 0.00 0.00 37.50 3.18
5070 7076 3.599091 CGTTGCCGACCGTTTATTTTTAC 59.401 43.478 0.00 0.00 35.63 2.01
5071 7077 3.808095 CGTTGCCGACCGTTTATTTTTA 58.192 40.909 0.00 0.00 35.63 1.52
5072 7078 2.652795 CGTTGCCGACCGTTTATTTTT 58.347 42.857 0.00 0.00 35.63 1.94
5073 7079 1.663730 GCGTTGCCGACCGTTTATTTT 60.664 47.619 0.00 0.00 35.63 1.82
5074 7080 0.110101 GCGTTGCCGACCGTTTATTT 60.110 50.000 0.00 0.00 35.63 1.40
5075 7081 0.952010 AGCGTTGCCGACCGTTTATT 60.952 50.000 0.00 0.00 35.63 1.40
5076 7082 0.952010 AAGCGTTGCCGACCGTTTAT 60.952 50.000 0.00 0.00 35.63 1.40
5077 7083 1.559149 GAAGCGTTGCCGACCGTTTA 61.559 55.000 0.00 0.00 35.63 2.01
5078 7084 2.888998 GAAGCGTTGCCGACCGTTT 61.889 57.895 0.00 0.00 35.63 3.60
5079 7085 3.343421 GAAGCGTTGCCGACCGTT 61.343 61.111 0.00 0.00 35.63 4.44
5080 7086 3.802418 AAGAAGCGTTGCCGACCGT 62.802 57.895 0.00 0.00 35.63 4.83
5081 7087 3.011760 GAAGAAGCGTTGCCGACCG 62.012 63.158 0.00 0.00 35.63 4.79
5082 7088 1.228657 AAGAAGAAGCGTTGCCGACC 61.229 55.000 0.00 0.00 35.63 4.79
5083 7089 0.164002 GAAGAAGAAGCGTTGCCGAC 59.836 55.000 0.00 0.00 35.63 4.79
5084 7090 1.282248 CGAAGAAGAAGCGTTGCCGA 61.282 55.000 0.00 0.00 35.63 5.54
5085 7091 1.130613 CGAAGAAGAAGCGTTGCCG 59.869 57.895 0.00 0.00 37.07 5.69
5086 7092 0.865769 TTCGAAGAAGAAGCGTTGCC 59.134 50.000 0.00 0.00 45.90 4.52
5087 7093 2.882742 ATTCGAAGAAGAAGCGTTGC 57.117 45.000 3.35 0.00 45.90 4.17


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

AutoCloner maintained by Alex Coulton.