Multiple sequence alignment - TraesCS4D01G273100

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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 TraesCS4D01G273100 chr4D 100.000 2105 0 0 1 2105 442899976 442902080 0.000000e+00 3888.0
1 TraesCS4D01G273100 chr4D 93.913 115 3 4 992 1102 102160835 102160949 9.990000e-39 171.0
2 TraesCS4D01G273100 chr4B 91.742 666 23 10 39 682 552019021 552019676 0.000000e+00 896.0
3 TraesCS4D01G273100 chr4B 90.785 293 22 5 737 1027 552019892 552020181 9.110000e-104 387.0
4 TraesCS4D01G273100 chr4B 92.593 243 17 1 1380 1622 552026148 552026389 4.300000e-92 348.0
5 TraesCS4D01G273100 chr4B 91.845 233 15 3 1106 1338 552025811 552026039 2.610000e-84 322.0
6 TraesCS4D01G273100 chr4B 94.203 207 11 1 902 1108 552025414 552025619 4.360000e-82 315.0
7 TraesCS4D01G273100 chr4B 82.131 291 29 8 1818 2105 552026551 552026821 5.840000e-56 228.0
8 TraesCS4D01G273100 chr4A 93.236 547 16 11 39 573 24763123 24762586 0.000000e+00 785.0
9 TraesCS4D01G273100 chr4A 92.969 128 5 3 988 1111 24759822 24759695 1.280000e-42 183.0
10 TraesCS4D01G273100 chr4A 93.023 43 1 2 1716 1757 102613204 102613245 6.270000e-06 62.1
11 TraesCS4D01G273100 chr2A 81.712 257 41 5 1853 2105 164603618 164603872 2.120000e-50 209.0
12 TraesCS4D01G273100 chr2A 97.143 35 1 0 1724 1758 167380608 167380642 2.260000e-05 60.2
13 TraesCS4D01G273100 chr2A 97.143 35 1 0 1723 1757 773942473 773942507 2.260000e-05 60.2
14 TraesCS4D01G273100 chr3B 81.008 258 44 5 1851 2105 55726053 55726308 1.270000e-47 200.0
15 TraesCS4D01G273100 chr6D 81.250 240 36 8 1851 2084 436264026 436264262 3.570000e-43 185.0
16 TraesCS4D01G273100 chr6D 89.130 92 9 1 683 774 155146854 155146764 1.710000e-21 113.0
17 TraesCS4D01G273100 chr6D 94.737 38 2 0 1725 1762 255445497 255445460 2.260000e-05 60.2
18 TraesCS4D01G273100 chr5D 95.413 109 2 3 991 1096 233158904 233159012 9.990000e-39 171.0
19 TraesCS4D01G273100 chr5D 95.370 108 3 2 994 1101 519411643 519411748 9.990000e-39 171.0
20 TraesCS4D01G273100 chr5D 96.000 75 3 0 683 757 74461731 74461657 2.840000e-24 122.0
21 TraesCS4D01G273100 chr7A 97.030 101 1 2 994 1093 550277072 550276973 3.590000e-38 169.0
22 TraesCS4D01G273100 chr5A 93.162 117 3 4 991 1103 321891795 321891680 1.290000e-37 167.0
23 TraesCS4D01G273100 chr5A 92.035 113 6 3 993 1103 645980652 645980763 2.800000e-34 156.0
24 TraesCS4D01G273100 chr5A 90.426 94 8 1 683 775 626964585 626964492 2.840000e-24 122.0
25 TraesCS4D01G273100 chr5B 92.793 111 4 4 992 1099 653786048 653786157 7.770000e-35 158.0
26 TraesCS4D01G273100 chr7B 94.872 78 4 0 683 760 534830221 534830144 2.840000e-24 122.0
27 TraesCS4D01G273100 chr7B 88.421 95 10 1 683 776 489323151 489323057 1.710000e-21 113.0
28 TraesCS4D01G273100 chr6A 96.000 75 3 0 683 757 616205767 616205841 2.840000e-24 122.0
29 TraesCS4D01G273100 chr6A 100.000 28 0 0 1730 1757 63601330 63601303 4.000000e-03 52.8
30 TraesCS4D01G273100 chr7D 91.667 84 7 0 683 766 163634801 163634718 1.320000e-22 117.0
31 TraesCS4D01G273100 chr7D 97.059 34 1 0 1724 1757 156686500 156686533 8.110000e-05 58.4
32 TraesCS4D01G273100 chrUn 90.805 87 6 2 683 769 97273173 97273089 4.750000e-22 115.0
33 TraesCS4D01G273100 chr2B 89.773 88 9 0 683 770 466505595 466505682 1.710000e-21 113.0
34 TraesCS4D01G273100 chr6B 81.955 133 18 5 1956 2084 659043723 659043593 7.940000e-20 108.0
35 TraesCS4D01G273100 chr6B 96.970 33 1 0 1725 1757 681076081 681076049 2.920000e-04 56.5
36 TraesCS4D01G273100 chr2D 92.500 40 3 0 1718 1757 102881855 102881894 8.110000e-05 58.4
37 TraesCS4D01G273100 chr1B 97.059 34 1 0 1724 1757 186799336 186799369 8.110000e-05 58.4


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 TraesCS4D01G273100 chr4D 442899976 442902080 2104 False 3888.00 3888 100.0000 1 2105 1 chr4D.!!$F2 2104
1 TraesCS4D01G273100 chr4B 552019021 552020181 1160 False 641.50 896 91.2635 39 1027 2 chr4B.!!$F1 988
2 TraesCS4D01G273100 chr4B 552025414 552026821 1407 False 303.25 348 90.1930 902 2105 4 chr4B.!!$F2 1203
3 TraesCS4D01G273100 chr4A 24759695 24763123 3428 True 484.00 785 93.1025 39 1111 2 chr4A.!!$R1 1072

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
560 576 0.174845 TGAGGATAGGTGGTTTCGCG 59.825 55.0 0.0 0.0 0.0 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1872 4771 0.105039 GTTGGTCGCCTCCCTGATAG 59.895 60.0 0.0 0.0 0.0 2.08 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
25 26 4.736896 GCCACGGACCACTCGGAC 62.737 72.222 0.00 0.00 35.59 4.79
26 27 4.415332 CCACGGACCACTCGGACG 62.415 72.222 0.00 0.00 40.40 4.79
423 430 3.483869 GAAGGAGGAGGCGGCCAT 61.484 66.667 23.09 6.44 0.00 4.40
477 485 1.301293 GGAGAAGGGGAAGGTGCTG 59.699 63.158 0.00 0.00 0.00 4.41
493 509 1.606531 CTGGCCTTCCCCTTGAGAG 59.393 63.158 3.32 0.00 0.00 3.20
516 532 2.040544 GGCCGATTGGGTGTCACTG 61.041 63.158 0.00 0.00 38.44 3.66
517 533 1.003839 GCCGATTGGGTGTCACTGA 60.004 57.895 0.00 0.00 38.44 3.41
518 534 1.298859 GCCGATTGGGTGTCACTGAC 61.299 60.000 0.00 1.86 38.44 3.51
519 535 0.321671 CCGATTGGGTGTCACTGACT 59.678 55.000 10.54 0.00 33.15 3.41
558 574 2.280628 GCTTGAGGATAGGTGGTTTCG 58.719 52.381 0.00 0.00 0.00 3.46
559 575 2.280628 CTTGAGGATAGGTGGTTTCGC 58.719 52.381 0.00 0.00 0.00 4.70
560 576 0.174845 TGAGGATAGGTGGTTTCGCG 59.825 55.000 0.00 0.00 0.00 5.87
653 3075 4.616604 CGGAATGAGCATGCAGAAAAGAAA 60.617 41.667 21.98 0.00 0.00 2.52
682 3108 6.329496 TCTTTGTTTTCGCAATTCAGAAACT 58.671 32.000 4.79 0.00 36.26 2.66
684 3110 6.567769 TTGTTTTCGCAATTCAGAAACTTC 57.432 33.333 4.79 1.67 36.26 3.01
685 3111 5.040635 TGTTTTCGCAATTCAGAAACTTCC 58.959 37.500 4.79 0.00 36.26 3.46
687 3113 4.909696 TTCGCAATTCAGAAACTTCCAA 57.090 36.364 0.00 0.00 0.00 3.53
688 3114 4.909696 TCGCAATTCAGAAACTTCCAAA 57.090 36.364 0.00 0.00 0.00 3.28
689 3115 5.255710 TCGCAATTCAGAAACTTCCAAAA 57.744 34.783 0.00 0.00 0.00 2.44
690 3116 5.841810 TCGCAATTCAGAAACTTCCAAAAT 58.158 33.333 0.00 0.00 0.00 1.82
691 3117 6.976088 TCGCAATTCAGAAACTTCCAAAATA 58.024 32.000 0.00 0.00 0.00 1.40
695 3272 8.866956 GCAATTCAGAAACTTCCAAAATAGATG 58.133 33.333 0.00 0.00 0.00 2.90
700 3277 6.434028 CAGAAACTTCCAAAATAGATGACCCA 59.566 38.462 0.00 0.00 0.00 4.51
707 3284 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
708 3285 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
711 3288 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
712 3289 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
713 3290 8.788325 AATAGATGACCCAACTTTGTACTAAC 57.212 34.615 0.00 0.00 0.00 2.34
715 3292 6.838382 AGATGACCCAACTTTGTACTAACTT 58.162 36.000 0.00 0.00 0.00 2.66
717 3294 8.434392 AGATGACCCAACTTTGTACTAACTTTA 58.566 33.333 0.00 0.00 0.00 1.85
718 3295 8.983702 ATGACCCAACTTTGTACTAACTTTAA 57.016 30.769 0.00 0.00 0.00 1.52
747 3336 6.544928 AATTGGGTCATCTATTTTGGAACC 57.455 37.500 0.00 0.00 37.64 3.62
751 3340 4.383770 GGGTCATCTATTTTGGAACCGAGA 60.384 45.833 0.00 0.00 0.00 4.04
753 3342 5.395324 GGTCATCTATTTTGGAACCGAGAGA 60.395 44.000 0.00 0.00 0.00 3.10
767 3356 6.349944 GGAACCGAGAGAGTAGTATGTTTCAA 60.350 42.308 0.00 0.00 0.00 2.69
800 3389 0.747255 GAACTCTGAGGCCGATGCTA 59.253 55.000 9.85 0.00 37.74 3.49
895 3488 1.889891 ACACTTTCGCAACAACAACG 58.110 45.000 0.00 0.00 0.00 4.10
916 3510 9.263538 ACAACGACAAAAGACAAGTATATGTAA 57.736 29.630 0.00 0.00 32.57 2.41
983 3621 5.716094 ACATTAAGGCATTAAAACCGAACC 58.284 37.500 7.74 0.00 34.62 3.62
1116 3948 6.916360 TTCCTTGCTTAATTTCCTGACAAT 57.084 33.333 0.00 0.00 0.00 2.71
1118 3950 8.415950 TTCCTTGCTTAATTTCCTGACAATAA 57.584 30.769 0.00 0.00 0.00 1.40
1152 3984 4.617298 GCGAGATTCTTCAGGCTATCCTAC 60.617 50.000 0.00 0.00 41.93 3.18
1163 3995 1.040646 CTATCCTACGGCTGGCAGAA 58.959 55.000 20.86 0.00 0.00 3.02
1174 4006 2.551938 GGCTGGCAGAAGAGAAGAAACT 60.552 50.000 20.86 0.00 0.00 2.66
1202 4034 5.570320 ACAGACAATACCTACTTTGGCAAT 58.430 37.500 0.00 0.00 33.09 3.56
1249 4081 1.301401 CGGTGAGAAACGGCTGGAA 60.301 57.895 0.00 0.00 0.00 3.53
1287 4119 2.109126 GTCCGGAGCCATGTTCAGC 61.109 63.158 3.06 0.00 0.00 4.26
1293 4125 0.379669 GAGCCATGTTCAGCGAATGG 59.620 55.000 0.00 0.00 43.18 3.16
1309 4141 1.608717 ATGGTCTGACTGACGCCCTC 61.609 60.000 7.85 0.00 46.24 4.30
1338 4170 4.101448 CTTGGCCCTCTCCCGTGG 62.101 72.222 0.00 0.00 0.00 4.94
1374 4216 3.680786 GCCGGGCGCTTTTCCTTT 61.681 61.111 7.64 0.00 0.00 3.11
1375 4217 3.047735 CCGGGCGCTTTTCCTTTT 58.952 55.556 7.64 0.00 0.00 2.27
1376 4218 1.365999 CCGGGCGCTTTTCCTTTTT 59.634 52.632 7.64 0.00 0.00 1.94
1378 4220 1.556591 CGGGCGCTTTTCCTTTTTGC 61.557 55.000 7.64 0.00 0.00 3.68
1383 4282 1.217001 GCTTTTCCTTTTTGCGGGTG 58.783 50.000 0.00 0.00 0.00 4.61
1388 4287 1.821216 TCCTTTTTGCGGGTGATCTC 58.179 50.000 0.00 0.00 0.00 2.75
1408 4307 3.745799 TCTTCCGTGGCATCAAGTTTAA 58.254 40.909 0.00 0.00 0.00 1.52
1412 4311 3.442273 TCCGTGGCATCAAGTTTAAATCC 59.558 43.478 0.00 0.00 0.00 3.01
1429 4328 8.573035 GTTTAAATCCAGTACCAAGTTCATTCA 58.427 33.333 0.00 0.00 0.00 2.57
1463 4362 3.323243 ACATGTTGGACGTAGCTGTAAC 58.677 45.455 0.00 0.00 0.00 2.50
1499 4398 3.792736 GCCGCCATGGGTCCAGTA 61.793 66.667 15.13 0.00 38.63 2.74
1501 4400 1.071471 CCGCCATGGGTCCAGTATC 59.929 63.158 15.13 0.00 0.00 2.24
1510 4409 1.071385 GGGTCCAGTATCAGCTGATGG 59.929 57.143 34.48 28.72 38.70 3.51
1527 4426 2.639286 GTGAAGCGTGCTTGTGGG 59.361 61.111 12.53 0.00 36.26 4.61
1540 4439 2.492088 GCTTGTGGGTTGATAGTTTCCC 59.508 50.000 0.00 0.00 40.26 3.97
1558 4457 0.245539 CCTGTCGATGTAACCCGTGT 59.754 55.000 0.00 0.00 0.00 4.49
1566 4465 2.996249 TGTAACCCGTGTTGTAACCA 57.004 45.000 0.00 0.00 35.87 3.67
1584 4483 2.209315 AGCATTTTTGCCGTGCCCT 61.209 52.632 0.00 0.00 39.62 5.19
1593 4492 1.344953 TGCCGTGCCCTAGATGGAAT 61.345 55.000 0.00 0.00 38.35 3.01
1596 4495 1.336887 CCGTGCCCTAGATGGAATACG 60.337 57.143 0.00 0.00 38.35 3.06
1643 4542 4.830826 AAAAATCTCGTTCGCTCCTTTT 57.169 36.364 0.00 0.00 0.00 2.27
1644 4543 4.406001 AAAATCTCGTTCGCTCCTTTTC 57.594 40.909 0.00 0.00 0.00 2.29
1646 4545 2.519377 TCTCGTTCGCTCCTTTTCAA 57.481 45.000 0.00 0.00 0.00 2.69
1647 4546 2.132762 TCTCGTTCGCTCCTTTTCAAC 58.867 47.619 0.00 0.00 0.00 3.18
1648 4547 2.135933 CTCGTTCGCTCCTTTTCAACT 58.864 47.619 0.00 0.00 0.00 3.16
1649 4548 2.544267 CTCGTTCGCTCCTTTTCAACTT 59.456 45.455 0.00 0.00 0.00 2.66
1650 4549 2.542595 TCGTTCGCTCCTTTTCAACTTC 59.457 45.455 0.00 0.00 0.00 3.01
1652 4551 3.363084 CGTTCGCTCCTTTTCAACTTCTC 60.363 47.826 0.00 0.00 0.00 2.87
1653 4552 3.469008 TCGCTCCTTTTCAACTTCTCA 57.531 42.857 0.00 0.00 0.00 3.27
1654 4553 4.008074 TCGCTCCTTTTCAACTTCTCAT 57.992 40.909 0.00 0.00 0.00 2.90
1655 4554 4.389374 TCGCTCCTTTTCAACTTCTCATT 58.611 39.130 0.00 0.00 0.00 2.57
1656 4555 4.821805 TCGCTCCTTTTCAACTTCTCATTT 59.178 37.500 0.00 0.00 0.00 2.32
1657 4556 5.995282 TCGCTCCTTTTCAACTTCTCATTTA 59.005 36.000 0.00 0.00 0.00 1.40
1659 4558 6.089476 GCTCCTTTTCAACTTCTCATTTAGC 58.911 40.000 0.00 0.00 0.00 3.09
1664 4563 8.137437 CCTTTTCAACTTCTCATTTAGCTTCAA 58.863 33.333 0.00 0.00 0.00 2.69
1665 4564 9.520204 CTTTTCAACTTCTCATTTAGCTTCAAA 57.480 29.630 0.00 0.00 0.00 2.69
1666 4565 9.868277 TTTTCAACTTCTCATTTAGCTTCAAAA 57.132 25.926 0.00 0.00 0.00 2.44
1672 4571 9.914131 ACTTCTCATTTAGCTTCAAAATTTACC 57.086 29.630 0.00 0.00 0.00 2.85
1673 4572 9.358872 CTTCTCATTTAGCTTCAAAATTTACCC 57.641 33.333 0.00 0.00 0.00 3.69
1674 4573 8.650143 TCTCATTTAGCTTCAAAATTTACCCT 57.350 30.769 0.00 0.00 0.00 4.34
1675 4574 9.747898 TCTCATTTAGCTTCAAAATTTACCCTA 57.252 29.630 0.00 0.00 0.00 3.53
1682 4581 7.827701 AGCTTCAAAATTTACCCTAAAGTAGC 58.172 34.615 0.00 0.00 0.00 3.58
1683 4582 7.033791 GCTTCAAAATTTACCCTAAAGTAGCC 58.966 38.462 0.00 0.00 0.00 3.93
1684 4583 7.470935 TTCAAAATTTACCCTAAAGTAGCCC 57.529 36.000 0.00 0.00 0.00 5.19
1685 4584 5.953548 TCAAAATTTACCCTAAAGTAGCCCC 59.046 40.000 0.00 0.00 0.00 5.80
1686 4585 3.851458 ATTTACCCTAAAGTAGCCCCG 57.149 47.619 0.00 0.00 0.00 5.73
1687 4586 0.832626 TTACCCTAAAGTAGCCCCGC 59.167 55.000 0.00 0.00 0.00 6.13
1688 4587 1.050421 TACCCTAAAGTAGCCCCGCC 61.050 60.000 0.00 0.00 0.00 6.13
1689 4588 2.372074 CCCTAAAGTAGCCCCGCCA 61.372 63.158 0.00 0.00 0.00 5.69
1690 4589 1.146263 CCTAAAGTAGCCCCGCCAG 59.854 63.158 0.00 0.00 0.00 4.85
1691 4590 1.523938 CTAAAGTAGCCCCGCCAGC 60.524 63.158 0.00 0.00 0.00 4.85
1692 4591 2.252072 CTAAAGTAGCCCCGCCAGCA 62.252 60.000 0.00 0.00 0.00 4.41
1702 4601 1.679139 CCCGCCAGCAATTTATCTGA 58.321 50.000 0.00 0.00 32.26 3.27
1705 4604 2.423185 CCGCCAGCAATTTATCTGAACA 59.577 45.455 0.00 0.00 32.26 3.18
1708 4607 4.614946 GCCAGCAATTTATCTGAACATCC 58.385 43.478 0.00 0.00 32.26 3.51
1716 4615 6.581388 ATTTATCTGAACATCCCTCTTCCA 57.419 37.500 0.00 0.00 0.00 3.53
1721 4620 2.242965 TGAACATCCCTCTTCCATGCAT 59.757 45.455 0.00 0.00 0.00 3.96
1728 4627 3.782523 TCCCTCTTCCATGCATTCTACTT 59.217 43.478 0.00 0.00 0.00 2.24
1737 4636 1.480954 TGCATTCTACTTCCTCCGTCC 59.519 52.381 0.00 0.00 0.00 4.79
1744 4643 2.200373 ACTTCCTCCGTCCCAAAATG 57.800 50.000 0.00 0.00 0.00 2.32
1747 4646 3.073356 ACTTCCTCCGTCCCAAAATGTAA 59.927 43.478 0.00 0.00 0.00 2.41
1749 4648 2.907696 TCCTCCGTCCCAAAATGTAAGA 59.092 45.455 0.00 0.00 0.00 2.10
1750 4649 3.521937 TCCTCCGTCCCAAAATGTAAGAT 59.478 43.478 0.00 0.00 0.00 2.40
1751 4650 3.627577 CCTCCGTCCCAAAATGTAAGATG 59.372 47.826 0.00 0.00 0.00 2.90
1752 4651 4.261801 CTCCGTCCCAAAATGTAAGATGT 58.738 43.478 0.00 0.00 0.00 3.06
1753 4652 4.658063 TCCGTCCCAAAATGTAAGATGTT 58.342 39.130 0.00 0.00 0.00 2.71
1754 4653 5.074115 TCCGTCCCAAAATGTAAGATGTTT 58.926 37.500 0.00 0.00 0.00 2.83
1755 4654 5.536916 TCCGTCCCAAAATGTAAGATGTTTT 59.463 36.000 0.00 0.00 0.00 2.43
1757 4656 6.145371 CCGTCCCAAAATGTAAGATGTTTTTG 59.855 38.462 0.00 0.00 38.28 2.44
1758 4657 6.346518 CGTCCCAAAATGTAAGATGTTTTTGC 60.347 38.462 0.00 0.00 37.60 3.68
1759 4658 6.705825 GTCCCAAAATGTAAGATGTTTTTGCT 59.294 34.615 0.00 0.00 37.60 3.91
1760 4659 7.870445 GTCCCAAAATGTAAGATGTTTTTGCTA 59.130 33.333 0.00 0.00 37.60 3.49
1761 4660 8.087750 TCCCAAAATGTAAGATGTTTTTGCTAG 58.912 33.333 0.00 0.00 37.60 3.42
1762 4661 7.331687 CCCAAAATGTAAGATGTTTTTGCTAGG 59.668 37.037 0.00 0.00 37.60 3.02
1763 4662 8.087750 CCAAAATGTAAGATGTTTTTGCTAGGA 58.912 33.333 0.00 0.00 37.60 2.94
1764 4663 9.132521 CAAAATGTAAGATGTTTTTGCTAGGAG 57.867 33.333 0.00 0.00 33.75 3.69
1765 4664 7.396540 AATGTAAGATGTTTTTGCTAGGAGG 57.603 36.000 0.00 0.00 0.00 4.30
1766 4665 5.253330 TGTAAGATGTTTTTGCTAGGAGGG 58.747 41.667 0.00 0.00 0.00 4.30
1767 4666 4.657814 AAGATGTTTTTGCTAGGAGGGA 57.342 40.909 0.00 0.00 0.00 4.20
1768 4667 4.227864 AGATGTTTTTGCTAGGAGGGAG 57.772 45.455 0.00 0.00 0.00 4.30
1771 4670 4.553330 TGTTTTTGCTAGGAGGGAGTAG 57.447 45.455 0.00 0.00 0.00 2.57
1772 4671 4.164981 TGTTTTTGCTAGGAGGGAGTAGA 58.835 43.478 0.00 0.00 0.00 2.59
1773 4672 4.783227 TGTTTTTGCTAGGAGGGAGTAGAT 59.217 41.667 0.00 0.00 0.00 1.98
1774 4673 5.119694 GTTTTTGCTAGGAGGGAGTAGATG 58.880 45.833 0.00 0.00 0.00 2.90
1775 4674 3.689872 TTGCTAGGAGGGAGTAGATGT 57.310 47.619 0.00 0.00 0.00 3.06
1776 4675 3.689872 TGCTAGGAGGGAGTAGATGTT 57.310 47.619 0.00 0.00 0.00 2.71
1778 4677 4.471548 TGCTAGGAGGGAGTAGATGTTAC 58.528 47.826 0.00 0.00 0.00 2.50
1779 4678 3.827876 GCTAGGAGGGAGTAGATGTTACC 59.172 52.174 0.00 0.00 0.00 2.85
1780 4679 3.331718 AGGAGGGAGTAGATGTTACCC 57.668 52.381 0.00 0.00 40.71 3.69
1781 4680 2.090663 AGGAGGGAGTAGATGTTACCCC 60.091 54.545 0.00 0.00 41.26 4.95
1783 4682 2.699321 GAGGGAGTAGATGTTACCCCAC 59.301 54.545 0.00 0.00 41.26 4.61
1784 4683 1.767088 GGGAGTAGATGTTACCCCACC 59.233 57.143 0.00 0.00 35.00 4.61
1785 4684 1.411612 GGAGTAGATGTTACCCCACCG 59.588 57.143 0.00 0.00 0.00 4.94
1786 4685 0.828677 AGTAGATGTTACCCCACCGC 59.171 55.000 0.00 0.00 0.00 5.68
1788 4687 0.538118 TAGATGTTACCCCACCGCAC 59.462 55.000 0.00 0.00 0.00 5.34
1789 4688 1.747745 GATGTTACCCCACCGCACC 60.748 63.158 0.00 0.00 0.00 5.01
1790 4689 3.615509 ATGTTACCCCACCGCACCG 62.616 63.158 0.00 0.00 0.00 4.94
1823 4722 4.280425 TGATTGGCAAACAAGTGCAGATAA 59.720 37.500 7.80 0.00 46.81 1.75
1833 4732 7.867445 AACAAGTGCAGATAAAATTTTACCG 57.133 32.000 12.74 5.89 0.00 4.02
1840 4739 8.583765 GTGCAGATAAAATTTTACCGTTGATTC 58.416 33.333 12.74 4.61 0.00 2.52
1848 4747 2.816204 TACCGTTGATTCAACCACGA 57.184 45.000 20.87 4.44 40.82 4.35
1897 4796 2.182030 GAGGCGACCAACTCCTCG 59.818 66.667 0.00 0.00 40.09 4.63
1904 4803 2.811317 CCAACTCCTCGTGCGCTC 60.811 66.667 9.73 3.51 0.00 5.03
1949 4850 2.511600 CCCAATCACCGCTCCGAC 60.512 66.667 0.00 0.00 0.00 4.79
1955 4856 3.822192 CACCGCTCCGACGATGGA 61.822 66.667 0.00 0.00 36.37 3.41
1956 4857 2.833582 ACCGCTCCGACGATGGAT 60.834 61.111 0.00 0.00 37.41 3.41
1957 4858 2.355126 CCGCTCCGACGATGGATG 60.355 66.667 0.00 0.00 37.41 3.51
1958 4859 2.355126 CGCTCCGACGATGGATGG 60.355 66.667 0.00 0.00 37.41 3.51
1959 4860 2.029666 GCTCCGACGATGGATGGG 59.970 66.667 0.00 0.00 37.41 4.00
1960 4861 2.797278 GCTCCGACGATGGATGGGT 61.797 63.158 0.00 0.00 37.41 4.51
1961 4862 1.068083 CTCCGACGATGGATGGGTG 59.932 63.158 0.00 0.00 37.41 4.61
1962 4863 1.380650 TCCGACGATGGATGGGTGA 60.381 57.895 0.00 0.00 31.53 4.02
1963 4864 1.068083 CCGACGATGGATGGGTGAG 59.932 63.158 0.00 0.00 0.00 3.51
1964 4865 1.068083 CGACGATGGATGGGTGAGG 59.932 63.158 0.00 0.00 0.00 3.86
1965 4866 1.447643 GACGATGGATGGGTGAGGG 59.552 63.158 0.00 0.00 0.00 4.30
1966 4867 1.002921 ACGATGGATGGGTGAGGGA 59.997 57.895 0.00 0.00 0.00 4.20
1967 4868 0.620410 ACGATGGATGGGTGAGGGAA 60.620 55.000 0.00 0.00 0.00 3.97
1968 4869 0.179045 CGATGGATGGGTGAGGGAAC 60.179 60.000 0.00 0.00 0.00 3.62
1990 4891 2.659610 GCTCTCTGCCTCCGTTGT 59.340 61.111 0.00 0.00 35.15 3.32
2026 4927 1.647084 GTGTGTTCCACGAAGGTGC 59.353 57.895 0.00 0.00 43.00 5.01
2027 4928 1.092921 GTGTGTTCCACGAAGGTGCA 61.093 55.000 0.00 0.00 43.00 4.57
2036 4937 0.740868 ACGAAGGTGCATGGATGACG 60.741 55.000 0.00 0.00 0.00 4.35
2065 4967 4.035091 GCCGGCATTTGGAATAAAATTTCC 59.965 41.667 24.80 0.00 44.60 3.13
2067 4969 5.181748 CGGCATTTGGAATAAAATTTCCCA 58.818 37.500 0.00 0.00 43.86 4.37
2075 4977 7.256494 TGGAATAAAATTTCCCAAGCTCAAT 57.744 32.000 0.00 0.00 43.86 2.57
2084 4986 1.590932 CCAAGCTCAATCCCATCTCG 58.409 55.000 0.00 0.00 0.00 4.04
2093 4995 0.962489 ATCCCATCTCGACGACATCC 59.038 55.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.736896 GTCCGAGTGGTCCGTGGC 62.737 72.222 0.00 0.00 36.30 5.01
9 10 4.415332 CGTCCGAGTGGTCCGTGG 62.415 72.222 0.00 0.00 36.30 4.94
47 48 3.203412 CTCCTCCTCGTCGTCCGG 61.203 72.222 0.00 0.00 37.11 5.14
48 49 3.203412 CCTCCTCCTCGTCGTCCG 61.203 72.222 0.00 0.00 38.13 4.79
49 50 3.519930 GCCTCCTCCTCGTCGTCC 61.520 72.222 0.00 0.00 0.00 4.79
421 428 3.853712 GCGCTAGCTCCGATGATG 58.146 61.111 13.93 0.00 41.01 3.07
477 485 1.604915 GACTCTCAAGGGGAAGGCC 59.395 63.158 0.00 0.00 0.00 5.19
516 532 1.542108 GGTGGATATGAGGCTGCAGTC 60.542 57.143 11.28 11.28 0.00 3.51
517 533 0.471617 GGTGGATATGAGGCTGCAGT 59.528 55.000 16.64 0.00 0.00 4.40
518 534 0.602106 CGGTGGATATGAGGCTGCAG 60.602 60.000 10.11 10.11 0.00 4.41
519 535 1.447217 CGGTGGATATGAGGCTGCA 59.553 57.895 0.50 0.00 0.00 4.41
559 575 4.421479 ACGGACAAGGAGCGAGCG 62.421 66.667 0.00 0.00 0.00 5.03
560 576 2.811317 CACGGACAAGGAGCGAGC 60.811 66.667 0.00 0.00 0.00 5.03
653 3075 7.147312 TCTGAATTGCGAAAACAAAGATCATT 58.853 30.769 0.00 0.00 32.27 2.57
682 3108 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
684 3110 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
685 3111 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
687 3113 9.227777 GTTAGTACAAAGTTGGGTCATCTATTT 57.772 33.333 0.00 0.00 0.00 1.40
688 3114 8.603304 AGTTAGTACAAAGTTGGGTCATCTATT 58.397 33.333 0.00 0.00 0.00 1.73
689 3115 8.147244 AGTTAGTACAAAGTTGGGTCATCTAT 57.853 34.615 0.00 0.00 0.00 1.98
690 3116 7.549147 AGTTAGTACAAAGTTGGGTCATCTA 57.451 36.000 0.00 0.00 0.00 1.98
691 3117 6.435292 AGTTAGTACAAAGTTGGGTCATCT 57.565 37.500 0.00 0.00 0.00 2.90
722 3299 7.394016 GGTTCCAAAATAGATGACCCAATTTT 58.606 34.615 0.00 0.00 33.07 1.82
723 3300 6.350949 CGGTTCCAAAATAGATGACCCAATTT 60.351 38.462 0.00 0.00 0.00 1.82
724 3301 5.127031 CGGTTCCAAAATAGATGACCCAATT 59.873 40.000 0.00 0.00 0.00 2.32
730 3307 5.661458 TCTCTCGGTTCCAAAATAGATGAC 58.339 41.667 0.00 0.00 0.00 3.06
731 3308 5.422331 ACTCTCTCGGTTCCAAAATAGATGA 59.578 40.000 0.00 0.00 0.00 2.92
732 3309 5.665459 ACTCTCTCGGTTCCAAAATAGATG 58.335 41.667 0.00 0.00 0.00 2.90
733 3310 5.941555 ACTCTCTCGGTTCCAAAATAGAT 57.058 39.130 0.00 0.00 0.00 1.98
735 3324 6.210287 ACTACTCTCTCGGTTCCAAAATAG 57.790 41.667 0.00 0.00 0.00 1.73
741 3330 4.232188 ACATACTACTCTCTCGGTTCCA 57.768 45.455 0.00 0.00 0.00 3.53
743 3332 6.192234 TGAAACATACTACTCTCTCGGTTC 57.808 41.667 0.00 0.00 0.00 3.62
800 3389 4.793071 TCAACGCGAACATTCATGAATTT 58.207 34.783 18.41 14.95 0.00 1.82
916 3510 9.716531 CATGATATTGTATACAGTCCATCACTT 57.283 33.333 13.18 0.94 30.26 3.16
983 3621 2.793933 CCATCCTGACTTGTACGTACG 58.206 52.381 20.18 15.01 0.00 3.67
1108 3940 8.397906 TCTCGCAAAAGATAAATTATTGTCAGG 58.602 33.333 0.00 0.00 0.00 3.86
1118 3950 7.680588 GCCTGAAGAATCTCGCAAAAGATAAAT 60.681 37.037 0.00 0.00 34.90 1.40
1122 3954 3.376546 GCCTGAAGAATCTCGCAAAAGAT 59.623 43.478 0.00 0.00 37.61 2.40
1128 3960 2.036475 GGATAGCCTGAAGAATCTCGCA 59.964 50.000 0.00 0.00 0.00 5.10
1152 3984 0.036952 TTCTTCTCTTCTGCCAGCCG 60.037 55.000 0.00 0.00 0.00 5.52
1163 3995 3.386078 TGTCTGTCAGCAGTTTCTTCTCT 59.614 43.478 0.00 0.00 43.05 3.10
1174 4006 5.237815 CAAAGTAGGTATTGTCTGTCAGCA 58.762 41.667 0.00 0.00 0.00 4.41
1182 4014 4.705023 ACCATTGCCAAAGTAGGTATTGTC 59.295 41.667 0.00 0.00 0.00 3.18
1183 4015 4.462483 CACCATTGCCAAAGTAGGTATTGT 59.538 41.667 0.00 0.00 0.00 2.71
1184 4016 4.142182 CCACCATTGCCAAAGTAGGTATTG 60.142 45.833 0.00 0.00 0.00 1.90
1185 4017 4.023291 CCACCATTGCCAAAGTAGGTATT 58.977 43.478 0.00 0.00 0.00 1.89
1186 4018 3.268334 TCCACCATTGCCAAAGTAGGTAT 59.732 43.478 0.00 0.00 0.00 2.73
1187 4019 2.645297 TCCACCATTGCCAAAGTAGGTA 59.355 45.455 0.00 0.00 0.00 3.08
1188 4020 1.427368 TCCACCATTGCCAAAGTAGGT 59.573 47.619 0.00 0.00 0.00 3.08
1189 4021 1.818674 GTCCACCATTGCCAAAGTAGG 59.181 52.381 0.00 0.00 0.00 3.18
1202 4034 1.067425 CCGATTACGTTCAGTCCACCA 60.067 52.381 0.00 0.00 37.88 4.17
1249 4081 3.674997 ACAGTATTGGAATGCGTCAGTT 58.325 40.909 0.00 0.00 0.00 3.16
1287 4119 1.078759 GGCGTCAGTCAGACCATTCG 61.079 60.000 0.00 0.00 44.66 3.34
1293 4125 1.608717 ATGGAGGGCGTCAGTCAGAC 61.609 60.000 9.66 0.00 44.02 3.51
1309 4141 3.211963 GCCAAGGCCTACGCATGG 61.212 66.667 15.11 15.11 43.12 3.66
1339 4171 1.093159 GCCAACTCCAAGCTGATCAG 58.907 55.000 18.84 18.84 0.00 2.90
1340 4172 0.322816 GGCCAACTCCAAGCTGATCA 60.323 55.000 0.00 0.00 0.00 2.92
1367 4209 2.556622 GAGATCACCCGCAAAAAGGAAA 59.443 45.455 0.00 0.00 0.00 3.13
1371 4213 2.162408 GGAAGAGATCACCCGCAAAAAG 59.838 50.000 0.00 0.00 0.00 2.27
1372 4214 2.159382 GGAAGAGATCACCCGCAAAAA 58.841 47.619 0.00 0.00 0.00 1.94
1373 4215 1.821216 GGAAGAGATCACCCGCAAAA 58.179 50.000 0.00 0.00 0.00 2.44
1374 4216 0.391130 CGGAAGAGATCACCCGCAAA 60.391 55.000 0.00 0.00 35.29 3.68
1375 4217 1.218047 CGGAAGAGATCACCCGCAA 59.782 57.895 0.00 0.00 35.29 4.85
1376 4218 1.982395 ACGGAAGAGATCACCCGCA 60.982 57.895 12.76 0.00 45.29 5.69
1378 4220 1.141881 CCACGGAAGAGATCACCCG 59.858 63.158 11.69 11.69 46.65 5.28
1383 4282 2.208431 CTTGATGCCACGGAAGAGATC 58.792 52.381 0.00 0.00 0.00 2.75
1388 4287 4.497473 TTTAAACTTGATGCCACGGAAG 57.503 40.909 0.00 0.00 0.00 3.46
1408 4307 5.940470 GTCTGAATGAACTTGGTACTGGATT 59.060 40.000 0.00 0.00 0.00 3.01
1412 4311 5.541845 TCAGTCTGAATGAACTTGGTACTG 58.458 41.667 5.19 0.00 34.54 2.74
1429 4328 5.482908 GTCCAACATGTACAATCTCAGTCT 58.517 41.667 0.00 0.00 0.00 3.24
1494 4393 3.464907 CTTCACCATCAGCTGATACTGG 58.535 50.000 28.27 27.20 38.26 4.00
1498 4397 1.482182 ACGCTTCACCATCAGCTGATA 59.518 47.619 28.27 10.88 33.52 2.15
1499 4398 0.251354 ACGCTTCACCATCAGCTGAT 59.749 50.000 23.75 23.75 33.52 2.90
1501 4400 1.792301 CACGCTTCACCATCAGCTG 59.208 57.895 7.63 7.63 33.52 4.24
1510 4409 1.724582 AACCCACAAGCACGCTTCAC 61.725 55.000 0.16 0.00 33.42 3.18
1527 4426 4.504858 ACATCGACAGGGAAACTATCAAC 58.495 43.478 0.00 0.00 0.00 3.18
1540 4439 1.724623 CAACACGGGTTACATCGACAG 59.275 52.381 0.85 0.00 34.87 3.51
1558 4457 2.101582 ACGGCAAAAATGCTGGTTACAA 59.898 40.909 13.64 0.00 44.95 2.41
1566 4465 0.897863 TAGGGCACGGCAAAAATGCT 60.898 50.000 0.40 0.00 39.38 3.79
1584 4483 5.925506 TGGAAACACTCGTATTCCATCTA 57.074 39.130 10.65 0.00 45.71 1.98
1622 4521 4.274950 TGAAAAGGAGCGAACGAGATTTTT 59.725 37.500 0.00 0.02 0.00 1.94
1623 4522 3.813166 TGAAAAGGAGCGAACGAGATTTT 59.187 39.130 0.00 0.00 0.00 1.82
1624 4523 3.399330 TGAAAAGGAGCGAACGAGATTT 58.601 40.909 0.00 0.00 0.00 2.17
1625 4524 3.040147 TGAAAAGGAGCGAACGAGATT 57.960 42.857 0.00 0.00 0.00 2.40
1626 4525 2.737252 GTTGAAAAGGAGCGAACGAGAT 59.263 45.455 0.00 0.00 0.00 2.75
1627 4526 2.132762 GTTGAAAAGGAGCGAACGAGA 58.867 47.619 0.00 0.00 0.00 4.04
1628 4527 2.135933 AGTTGAAAAGGAGCGAACGAG 58.864 47.619 0.00 0.00 0.00 4.18
1630 4529 2.544267 AGAAGTTGAAAAGGAGCGAACG 59.456 45.455 0.00 0.00 0.00 3.95
1631 4530 3.560068 TGAGAAGTTGAAAAGGAGCGAAC 59.440 43.478 0.00 0.00 0.00 3.95
1633 4532 3.469008 TGAGAAGTTGAAAAGGAGCGA 57.531 42.857 0.00 0.00 0.00 4.93
1634 4533 4.756084 AATGAGAAGTTGAAAAGGAGCG 57.244 40.909 0.00 0.00 0.00 5.03
1635 4534 6.072230 AGCTAAATGAGAAGTTGAAAAGGAGC 60.072 38.462 0.00 0.00 0.00 4.70
1636 4535 7.446001 AGCTAAATGAGAAGTTGAAAAGGAG 57.554 36.000 0.00 0.00 0.00 3.69
1638 4537 7.651808 TGAAGCTAAATGAGAAGTTGAAAAGG 58.348 34.615 0.00 0.00 0.00 3.11
1640 4539 9.868277 TTTTGAAGCTAAATGAGAAGTTGAAAA 57.132 25.926 0.00 0.00 0.00 2.29
1646 4545 9.914131 GGTAAATTTTGAAGCTAAATGAGAAGT 57.086 29.630 0.00 0.00 0.00 3.01
1647 4546 9.358872 GGGTAAATTTTGAAGCTAAATGAGAAG 57.641 33.333 0.00 0.00 0.00 2.85
1648 4547 9.088987 AGGGTAAATTTTGAAGCTAAATGAGAA 57.911 29.630 0.00 0.00 0.00 2.87
1649 4548 8.650143 AGGGTAAATTTTGAAGCTAAATGAGA 57.350 30.769 0.00 0.00 0.00 3.27
1656 4555 8.953313 GCTACTTTAGGGTAAATTTTGAAGCTA 58.047 33.333 0.00 0.00 0.00 3.32
1657 4556 7.093902 GGCTACTTTAGGGTAAATTTTGAAGCT 60.094 37.037 0.00 0.00 0.00 3.74
1659 4558 7.363530 GGGGCTACTTTAGGGTAAATTTTGAAG 60.364 40.741 0.00 0.00 0.00 3.02
1664 4563 4.529897 CGGGGCTACTTTAGGGTAAATTT 58.470 43.478 0.00 0.00 0.00 1.82
1665 4564 3.686405 GCGGGGCTACTTTAGGGTAAATT 60.686 47.826 0.00 0.00 0.00 1.82
1666 4565 2.158711 GCGGGGCTACTTTAGGGTAAAT 60.159 50.000 0.00 0.00 0.00 1.40
1667 4566 1.210234 GCGGGGCTACTTTAGGGTAAA 59.790 52.381 0.00 0.00 0.00 2.01
1668 4567 0.832626 GCGGGGCTACTTTAGGGTAA 59.167 55.000 0.00 0.00 0.00 2.85
1669 4568 1.050421 GGCGGGGCTACTTTAGGGTA 61.050 60.000 0.00 0.00 0.00 3.69
1670 4569 2.372890 GGCGGGGCTACTTTAGGGT 61.373 63.158 0.00 0.00 0.00 4.34
1671 4570 2.325393 CTGGCGGGGCTACTTTAGGG 62.325 65.000 0.00 0.00 0.00 3.53
1672 4571 1.146263 CTGGCGGGGCTACTTTAGG 59.854 63.158 0.00 0.00 0.00 2.69
1673 4572 1.523938 GCTGGCGGGGCTACTTTAG 60.524 63.158 0.00 0.00 0.00 1.85
1674 4573 1.843462 TTGCTGGCGGGGCTACTTTA 61.843 55.000 0.00 0.00 0.00 1.85
1675 4574 2.499303 ATTGCTGGCGGGGCTACTTT 62.499 55.000 0.00 0.00 0.00 2.66
1676 4575 2.499303 AATTGCTGGCGGGGCTACTT 62.499 55.000 0.00 0.00 0.00 2.24
1677 4576 2.499303 AAATTGCTGGCGGGGCTACT 62.499 55.000 0.00 0.00 0.00 2.57
1678 4577 0.750182 TAAATTGCTGGCGGGGCTAC 60.750 55.000 0.00 0.00 0.00 3.58
1679 4578 0.184933 ATAAATTGCTGGCGGGGCTA 59.815 50.000 0.00 0.00 0.00 3.93
1680 4579 1.076044 ATAAATTGCTGGCGGGGCT 60.076 52.632 0.00 0.00 0.00 5.19
1681 4580 1.109323 AGATAAATTGCTGGCGGGGC 61.109 55.000 0.00 0.00 0.00 5.80
1682 4581 0.670162 CAGATAAATTGCTGGCGGGG 59.330 55.000 0.00 0.00 0.00 5.73
1683 4582 1.679139 TCAGATAAATTGCTGGCGGG 58.321 50.000 0.00 0.00 33.05 6.13
1684 4583 2.423185 TGTTCAGATAAATTGCTGGCGG 59.577 45.455 0.00 0.00 33.05 6.13
1685 4584 3.763097 TGTTCAGATAAATTGCTGGCG 57.237 42.857 0.00 0.00 33.05 5.69
1686 4585 4.500375 GGGATGTTCAGATAAATTGCTGGC 60.500 45.833 0.00 0.00 33.05 4.85
1687 4586 4.891756 AGGGATGTTCAGATAAATTGCTGG 59.108 41.667 0.00 0.00 33.05 4.85
1688 4587 5.826737 AGAGGGATGTTCAGATAAATTGCTG 59.173 40.000 0.00 0.00 0.00 4.41
1689 4588 6.011122 AGAGGGATGTTCAGATAAATTGCT 57.989 37.500 0.00 0.00 0.00 3.91
1690 4589 6.238869 GGAAGAGGGATGTTCAGATAAATTGC 60.239 42.308 0.00 0.00 0.00 3.56
1691 4590 6.830324 TGGAAGAGGGATGTTCAGATAAATTG 59.170 38.462 0.00 0.00 0.00 2.32
1692 4591 6.973642 TGGAAGAGGGATGTTCAGATAAATT 58.026 36.000 0.00 0.00 0.00 1.82
1702 4601 3.053095 AGAATGCATGGAAGAGGGATGTT 60.053 43.478 0.00 0.00 0.00 2.71
1705 4604 3.979347 AGTAGAATGCATGGAAGAGGGAT 59.021 43.478 0.00 0.00 0.00 3.85
1708 4607 4.133078 GGAAGTAGAATGCATGGAAGAGG 58.867 47.826 0.00 0.00 0.00 3.69
1716 4615 2.103263 GGACGGAGGAAGTAGAATGCAT 59.897 50.000 0.00 0.00 0.00 3.96
1721 4620 2.314071 TTGGGACGGAGGAAGTAGAA 57.686 50.000 0.00 0.00 0.00 2.10
1728 4627 2.907696 TCTTACATTTTGGGACGGAGGA 59.092 45.455 0.00 0.00 0.00 3.71
1737 4636 8.087750 TCCTAGCAAAAACATCTTACATTTTGG 58.912 33.333 10.66 0.00 41.02 3.28
1744 4643 5.497474 TCCCTCCTAGCAAAAACATCTTAC 58.503 41.667 0.00 0.00 0.00 2.34
1747 4646 3.589288 ACTCCCTCCTAGCAAAAACATCT 59.411 43.478 0.00 0.00 0.00 2.90
1749 4648 4.783227 TCTACTCCCTCCTAGCAAAAACAT 59.217 41.667 0.00 0.00 0.00 2.71
1750 4649 4.164981 TCTACTCCCTCCTAGCAAAAACA 58.835 43.478 0.00 0.00 0.00 2.83
1751 4650 4.820894 TCTACTCCCTCCTAGCAAAAAC 57.179 45.455 0.00 0.00 0.00 2.43
1752 4651 4.783227 ACATCTACTCCCTCCTAGCAAAAA 59.217 41.667 0.00 0.00 0.00 1.94
1753 4652 4.362677 ACATCTACTCCCTCCTAGCAAAA 58.637 43.478 0.00 0.00 0.00 2.44
1754 4653 3.995636 ACATCTACTCCCTCCTAGCAAA 58.004 45.455 0.00 0.00 0.00 3.68
1755 4654 3.689872 ACATCTACTCCCTCCTAGCAA 57.310 47.619 0.00 0.00 0.00 3.91
1757 4656 3.827876 GGTAACATCTACTCCCTCCTAGC 59.172 52.174 0.00 0.00 0.00 3.42
1758 4657 4.409187 GGGTAACATCTACTCCCTCCTAG 58.591 52.174 0.00 0.00 35.63 3.02
1759 4658 3.141649 GGGGTAACATCTACTCCCTCCTA 59.858 52.174 0.00 0.00 38.31 2.94
1760 4659 2.090663 GGGGTAACATCTACTCCCTCCT 60.091 54.545 0.00 0.00 38.31 3.69
1761 4660 2.327373 GGGGTAACATCTACTCCCTCC 58.673 57.143 0.00 0.00 38.31 4.30
1762 4661 2.699321 GTGGGGTAACATCTACTCCCTC 59.301 54.545 0.00 0.00 37.27 4.30
1763 4662 2.628829 GGTGGGGTAACATCTACTCCCT 60.629 54.545 0.00 0.00 37.27 4.20
1764 4663 1.767088 GGTGGGGTAACATCTACTCCC 59.233 57.143 0.00 0.00 37.27 4.30
1765 4664 1.411612 CGGTGGGGTAACATCTACTCC 59.588 57.143 0.00 0.00 38.55 3.85
1766 4665 1.202498 GCGGTGGGGTAACATCTACTC 60.202 57.143 0.00 0.00 39.74 2.59
1767 4666 0.828677 GCGGTGGGGTAACATCTACT 59.171 55.000 0.00 0.00 39.74 2.57
1768 4667 0.538118 TGCGGTGGGGTAACATCTAC 59.462 55.000 0.00 0.00 39.74 2.59
1771 4670 1.747745 GGTGCGGTGGGGTAACATC 60.748 63.158 0.00 0.00 39.74 3.06
1772 4671 2.353573 GGTGCGGTGGGGTAACAT 59.646 61.111 0.00 0.00 39.74 2.71
1773 4672 4.317444 CGGTGCGGTGGGGTAACA 62.317 66.667 0.00 0.00 39.74 2.41
1798 4697 1.068895 TGCACTTGTTTGCCAATCAGG 59.931 47.619 0.00 0.00 42.25 3.86
1799 4698 2.034939 TCTGCACTTGTTTGCCAATCAG 59.965 45.455 0.00 0.00 42.25 2.90
1800 4699 2.030371 TCTGCACTTGTTTGCCAATCA 58.970 42.857 0.00 0.00 42.25 2.57
1801 4700 2.798976 TCTGCACTTGTTTGCCAATC 57.201 45.000 0.00 0.00 42.25 2.67
1802 4701 4.870123 TTATCTGCACTTGTTTGCCAAT 57.130 36.364 0.00 0.00 42.25 3.16
1803 4702 4.662468 TTTATCTGCACTTGTTTGCCAA 57.338 36.364 0.00 0.00 42.25 4.52
1805 4704 6.544038 AAATTTTATCTGCACTTGTTTGCC 57.456 33.333 0.00 0.00 42.25 4.52
1806 4705 8.009409 GGTAAAATTTTATCTGCACTTGTTTGC 58.991 33.333 13.54 0.00 43.31 3.68
1807 4706 8.213812 CGGTAAAATTTTATCTGCACTTGTTTG 58.786 33.333 17.03 0.00 0.00 2.93
1808 4707 7.923878 ACGGTAAAATTTTATCTGCACTTGTTT 59.076 29.630 17.03 0.00 0.00 2.83
1810 4709 6.977213 ACGGTAAAATTTTATCTGCACTTGT 58.023 32.000 17.03 5.12 0.00 3.16
1811 4710 7.593273 TCAACGGTAAAATTTTATCTGCACTTG 59.407 33.333 17.03 13.10 0.00 3.16
1812 4711 7.653647 TCAACGGTAAAATTTTATCTGCACTT 58.346 30.769 17.03 4.66 0.00 3.16
1813 4712 7.209471 TCAACGGTAAAATTTTATCTGCACT 57.791 32.000 17.03 3.11 0.00 4.40
1814 4713 8.460831 AATCAACGGTAAAATTTTATCTGCAC 57.539 30.769 17.03 5.40 0.00 4.57
1815 4714 8.300286 TGAATCAACGGTAAAATTTTATCTGCA 58.700 29.630 17.03 2.61 0.00 4.41
1816 4715 8.682128 TGAATCAACGGTAAAATTTTATCTGC 57.318 30.769 17.03 4.18 0.00 4.26
1823 4722 5.688176 CGTGGTTGAATCAACGGTAAAATTT 59.312 36.000 18.52 0.00 44.36 1.82
1840 4739 2.555199 GATGAGAGGGATTCGTGGTTG 58.445 52.381 0.00 0.00 0.00 3.77
1848 4747 4.953781 TTTTTCCTGGATGAGAGGGATT 57.046 40.909 0.00 0.00 0.00 3.01
1870 4769 0.325296 TGGTCGCCTCCCTGATAGTT 60.325 55.000 0.00 0.00 0.00 2.24
1871 4770 0.325296 TTGGTCGCCTCCCTGATAGT 60.325 55.000 0.00 0.00 0.00 2.12
1872 4771 0.105039 GTTGGTCGCCTCCCTGATAG 59.895 60.000 0.00 0.00 0.00 2.08
1873 4772 0.325296 AGTTGGTCGCCTCCCTGATA 60.325 55.000 0.00 0.00 0.00 2.15
1912 4811 0.670854 GCAAGAGAACCCACGACCTC 60.671 60.000 0.00 0.00 0.00 3.85
1916 4815 2.747686 GGGCAAGAGAACCCACGA 59.252 61.111 0.00 0.00 46.22 4.35
1949 4850 0.179045 GTTCCCTCACCCATCCATCG 60.179 60.000 0.00 0.00 0.00 3.84
1959 4860 4.097361 GAGCCGGGGTTCCCTCAC 62.097 72.222 2.18 0.00 42.67 3.51
1960 4861 4.332543 AGAGCCGGGGTTCCCTCA 62.333 66.667 2.18 0.00 42.67 3.86
1961 4862 3.471806 GAGAGCCGGGGTTCCCTC 61.472 72.222 2.18 0.00 42.67 4.30
1962 4863 4.012721 AGAGAGCCGGGGTTCCCT 62.013 66.667 2.18 0.00 42.67 4.20
1963 4864 3.787001 CAGAGAGCCGGGGTTCCC 61.787 72.222 2.18 0.00 41.09 3.97
1964 4865 4.475135 GCAGAGAGCCGGGGTTCC 62.475 72.222 2.18 0.00 37.23 3.62
1973 4874 0.179124 CTACAACGGAGGCAGAGAGC 60.179 60.000 0.00 0.00 44.65 4.09
1985 4886 4.541973 AAACCTAACCCTACCTACAACG 57.458 45.455 0.00 0.00 0.00 4.10
1986 4887 6.014242 ACACTAAACCTAACCCTACCTACAAC 60.014 42.308 0.00 0.00 0.00 3.32
1987 4888 6.014327 CACACTAAACCTAACCCTACCTACAA 60.014 42.308 0.00 0.00 0.00 2.41
1990 4891 5.654370 ACACACTAAACCTAACCCTACCTA 58.346 41.667 0.00 0.00 0.00 3.08
2019 4920 0.392998 ACCGTCATCCATGCACCTTC 60.393 55.000 0.00 0.00 0.00 3.46
2021 4922 1.078214 CACCGTCATCCATGCACCT 60.078 57.895 0.00 0.00 0.00 4.00
2024 4925 1.096967 GCATCACCGTCATCCATGCA 61.097 55.000 0.00 0.00 39.76 3.96
2026 4927 2.324215 GGCATCACCGTCATCCATG 58.676 57.895 0.00 0.00 0.00 3.66
2027 4928 4.885426 GGCATCACCGTCATCCAT 57.115 55.556 0.00 0.00 0.00 3.41
2036 4937 1.603236 TTCCAAATGCCGGCATCACC 61.603 55.000 40.38 4.73 35.31 4.02
2065 4967 1.139654 TCGAGATGGGATTGAGCTTGG 59.860 52.381 0.00 0.00 0.00 3.61
2067 4969 1.202463 CGTCGAGATGGGATTGAGCTT 60.202 52.381 0.00 0.00 0.00 3.74
2075 4977 0.106669 AGGATGTCGTCGAGATGGGA 60.107 55.000 9.94 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.