Multiple sequence alignment - TraesCS4A01G214700

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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 TraesCS4A01G214700 chr4A 100.000 6683 0 0 1 6683 513081798 513088480 0.000000e+00 12342.0
1 TraesCS4A01G214700 chr4A 97.948 536 9 2 1 536 15970516 15969983 0.000000e+00 928.0
2 TraesCS4A01G214700 chr4A 96.283 538 18 2 1 537 628700928 628700392 0.000000e+00 881.0
3 TraesCS4A01G214700 chr4A 95.224 335 16 0 3305 3639 513085054 513085388 1.280000e-146 531.0
4 TraesCS4A01G214700 chr4A 95.224 335 16 0 3257 3591 513085102 513085436 1.280000e-146 531.0
5 TraesCS4A01G214700 chr4A 90.074 272 24 1 950 1221 676926342 676926610 3.840000e-92 350.0
6 TraesCS4A01G214700 chr4A 95.745 47 2 0 951 997 410665994 410665948 7.190000e-10 76.8
7 TraesCS4A01G214700 chr4D 93.852 3123 141 25 537 3639 74613567 74610476 0.000000e+00 4656.0
8 TraesCS4A01G214700 chr4D 94.350 2478 87 17 3257 5731 74610759 74608332 0.000000e+00 3751.0
9 TraesCS4A01G214700 chr4D 94.256 383 19 1 3257 3639 74610807 74610428 3.470000e-162 582.0
10 TraesCS4A01G214700 chr4D 93.728 287 17 1 1319 1605 76231326 76231041 4.790000e-116 429.0
11 TraesCS4A01G214700 chr4D 89.941 169 10 4 6516 6683 74607467 74607305 1.890000e-50 211.0
12 TraesCS4A01G214700 chr4B 95.167 2959 105 12 3257 6208 106974455 106971528 0.000000e+00 4638.0
13 TraesCS4A01G214700 chr4B 95.881 1651 59 3 1990 3639 106975859 106974217 0.000000e+00 2663.0
14 TraesCS4A01G214700 chr4B 89.935 1381 65 34 580 1932 106977394 106976060 0.000000e+00 1712.0
15 TraesCS4A01G214700 chr4B 94.256 383 22 0 3257 3639 106974503 106974121 2.690000e-163 586.0
16 TraesCS4A01G214700 chr4B 94.256 383 22 0 3257 3639 106974551 106974169 2.690000e-163 586.0
17 TraesCS4A01G214700 chr4B 82.558 344 20 18 537 851 106981170 106980838 3.970000e-67 267.0
18 TraesCS4A01G214700 chr4B 81.739 345 23 19 537 851 106984919 106984585 1.110000e-62 252.0
19 TraesCS4A01G214700 chr4B 97.368 76 2 0 1916 1991 106976016 106975941 5.440000e-26 130.0
20 TraesCS4A01G214700 chr4B 94.340 53 3 0 537 589 106977451 106977399 1.540000e-11 82.4
21 TraesCS4A01G214700 chr2A 97.948 536 10 1 1 536 61816062 61815528 0.000000e+00 928.0
22 TraesCS4A01G214700 chr2A 97.020 537 15 1 1 536 59987274 59986738 0.000000e+00 902.0
23 TraesCS4A01G214700 chr2A 95.341 279 13 0 1314 1592 59582845 59583123 1.710000e-120 444.0
24 TraesCS4A01G214700 chr2A 95.745 47 2 0 951 997 703456060 703456106 7.190000e-10 76.8
25 TraesCS4A01G214700 chr1A 97.761 536 12 0 1 536 586664269 586663734 0.000000e+00 924.0
26 TraesCS4A01G214700 chr1A 96.852 540 15 2 1 539 490890067 490889529 0.000000e+00 902.0
27 TraesCS4A01G214700 chr1A 97.015 536 16 0 1 536 508121636 508121101 0.000000e+00 902.0
28 TraesCS4A01G214700 chr1A 92.233 103 4 2 1813 1912 520173505 520173404 6.990000e-30 143.0
29 TraesCS4A01G214700 chr5A 97.020 537 14 2 1 536 459344597 459345132 0.000000e+00 902.0
30 TraesCS4A01G214700 chr5A 93.204 103 3 2 1813 1912 683119788 683119687 1.500000e-31 148.0
31 TraesCS4A01G214700 chr5D 91.095 539 33 9 1 536 412201236 412201762 0.000000e+00 715.0
32 TraesCS4A01G214700 chr5D 94.077 287 15 2 1319 1605 556478512 556478228 1.030000e-117 435.0
33 TraesCS4A01G214700 chr5D 85.135 148 12 7 1768 1912 360129099 360129239 6.990000e-30 143.0
34 TraesCS4A01G214700 chr7D 96.416 279 10 0 1314 1592 572475443 572475721 1.700000e-125 460.0
35 TraesCS4A01G214700 chr7D 94.483 290 14 2 1316 1605 54880853 54881140 4.750000e-121 446.0
36 TraesCS4A01G214700 chr7D 94.138 290 15 2 1316 1605 54865438 54865725 2.210000e-119 440.0
37 TraesCS4A01G214700 chr6D 94.982 279 13 1 1314 1592 61990208 61990485 2.860000e-118 436.0
38 TraesCS4A01G214700 chr6D 92.233 103 4 2 1813 1912 372423259 372423158 6.990000e-30 143.0
39 TraesCS4A01G214700 chr6D 93.617 47 3 0 951 997 372424173 372424127 3.340000e-08 71.3
40 TraesCS4A01G214700 chr2B 90.800 250 19 2 951 1200 670845751 670845996 1.390000e-86 331.0
41 TraesCS4A01G214700 chr2B 85.135 148 12 5 1768 1912 670848045 670848185 6.990000e-30 143.0
42 TraesCS4A01G214700 chr2B 92.233 103 4 2 1813 1912 801167423 801167322 6.990000e-30 143.0
43 TraesCS4A01G214700 chr3D 91.262 103 5 2 1813 1912 96221487 96221588 3.250000e-28 137.0
44 TraesCS4A01G214700 chr2D 83.117 77 13 0 5560 5636 533084068 533084144 3.340000e-08 71.3


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 TraesCS4A01G214700 chr4A 513081798 513088480 6682 False 4468.000000 12342 96.816000 1 6683 3 chr4A.!!$F2 6682
1 TraesCS4A01G214700 chr4A 15969983 15970516 533 True 928.000000 928 97.948000 1 536 1 chr4A.!!$R1 535
2 TraesCS4A01G214700 chr4A 628700392 628700928 536 True 881.000000 881 96.283000 1 537 1 chr4A.!!$R3 536
3 TraesCS4A01G214700 chr4D 74607305 74613567 6262 True 2300.000000 4656 93.099750 537 6683 4 chr4D.!!$R2 6146
4 TraesCS4A01G214700 chr4B 106971528 106984919 13391 True 1212.933333 4638 91.722222 537 6208 9 chr4B.!!$R1 5671
5 TraesCS4A01G214700 chr2A 61815528 61816062 534 True 928.000000 928 97.948000 1 536 1 chr2A.!!$R2 535
6 TraesCS4A01G214700 chr2A 59986738 59987274 536 True 902.000000 902 97.020000 1 536 1 chr2A.!!$R1 535
7 TraesCS4A01G214700 chr1A 586663734 586664269 535 True 924.000000 924 97.761000 1 536 1 chr1A.!!$R4 535
8 TraesCS4A01G214700 chr1A 490889529 490890067 538 True 902.000000 902 96.852000 1 539 1 chr1A.!!$R1 538
9 TraesCS4A01G214700 chr1A 508121101 508121636 535 True 902.000000 902 97.015000 1 536 1 chr1A.!!$R2 535
10 TraesCS4A01G214700 chr5A 459344597 459345132 535 False 902.000000 902 97.020000 1 536 1 chr5A.!!$F1 535
11 TraesCS4A01G214700 chr5D 412201236 412201762 526 False 715.000000 715 91.095000 1 536 1 chr5D.!!$F2 535
12 TraesCS4A01G214700 chr2B 670845751 670848185 2434 False 237.000000 331 87.967500 951 1912 2 chr2B.!!$F1 961

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
782 4561 0.109272 TTCATCGTCGTCTGAGGCAC 60.109 55.000 0.00 0.0 0.00 5.01 F
846 8337 0.245539 TCTCTCGCTAAAACCCACGG 59.754 55.000 0.00 0.0 0.00 4.94 F
1169 8672 0.253207 GAGAAGGGGAAGGGGAAGGA 60.253 60.000 0.00 0.0 0.00 3.36 F
1170 8673 0.253394 AGAAGGGGAAGGGGAAGGAG 60.253 60.000 0.00 0.0 0.00 3.69 F
2431 11607 1.003839 GTCGTCAGGTGCATGGGAA 60.004 57.895 0.00 0.0 0.00 3.97 F
3293 12520 0.248012 TGCAAATGGCTCTGCATTGG 59.752 50.000 4.90 0.0 43.44 3.16 F
3593 12916 0.179059 TGCGTTGCAGAAGTCCTCAA 60.179 50.000 0.00 0.0 33.32 3.02 F
3596 12919 1.528129 GTTGCAGAAGTCCTCAAGGG 58.472 55.000 0.00 0.0 35.41 3.95 F
4757 14082 1.266989 GTTGGCTAGCTGTGTGAAACC 59.733 52.381 15.72 0.0 34.36 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1820 10843 2.202570 GCATGGCAAAGCAGAGCG 60.203 61.111 10.00 0.0 0.00 5.03 R
2118 11287 2.526888 TGGAAGGTACTCCTCGTGAT 57.473 50.000 3.08 0.0 44.35 3.06 R
3167 12346 0.675083 TCCACGTTAAGGCTCGTTGA 59.325 50.000 0.00 0.0 38.23 3.18 R
3194 12373 2.219875 CCTCTGGTGGGTCAGCTGT 61.220 63.158 14.67 0.0 34.91 4.40 R
3385 12612 0.250295 CCCTCGAGGACTTGTGCAAA 60.250 55.000 33.39 0.0 38.24 3.68 R
4455 13778 1.009900 CTCTTACCCGTCGCGCTAG 60.010 63.158 5.56 0.0 0.00 3.42 R
4717 14040 1.261619 CCAAACGACACAGTGCTCTTC 59.738 52.381 0.00 0.0 0.00 2.87 R
5519 14847 2.551912 CCACCACTCAAACCGCCAC 61.552 63.158 0.00 0.0 0.00 5.01 R
6392 15729 0.108585 TCTGGGTGAAGGCTGTGTTC 59.891 55.000 0.00 0.0 0.00 3.18 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
414 419 5.449304 CGGTTTTAGTTCAAAGTCCATCAC 58.551 41.667 0.00 0.00 0.00 3.06
565 572 4.458989 GGTGACAAAGGAACATGAATGCTA 59.541 41.667 0.00 0.00 0.00 3.49
615 636 9.597681 AGGAATAATTCTTCTTCAATGGCATAT 57.402 29.630 0.00 0.00 0.00 1.78
631 652 6.751514 TGGCATATAAATAAATAGGCACGG 57.248 37.500 3.35 0.00 40.11 4.94
632 653 6.242396 TGGCATATAAATAAATAGGCACGGT 58.758 36.000 3.35 0.00 40.11 4.83
712 741 2.980378 GCACATGCACGCACCATCA 61.980 57.895 0.00 0.00 41.59 3.07
713 742 1.804598 CACATGCACGCACCATCAT 59.195 52.632 0.00 0.00 0.00 2.45
714 743 0.248336 CACATGCACGCACCATCATC 60.248 55.000 0.00 0.00 0.00 2.92
747 776 2.677228 CCAAAGAGGGCCATCGGT 59.323 61.111 12.53 0.62 0.00 4.69
758 4534 1.817099 CCATCGGTTCTGGCTCTGC 60.817 63.158 0.00 0.00 0.00 4.26
769 4545 1.821332 GGCTCTGCCCCTTTCATCG 60.821 63.158 0.00 0.00 44.06 3.84
782 4561 0.109272 TTCATCGTCGTCTGAGGCAC 60.109 55.000 0.00 0.00 0.00 5.01
800 4579 0.533531 ACGTCCCCTTTCCGTGAAAC 60.534 55.000 0.00 0.00 32.86 2.78
846 8337 0.245539 TCTCTCGCTAAAACCCACGG 59.754 55.000 0.00 0.00 0.00 4.94
889 8380 1.832608 ACCGTGAGTGAGTGCCTCA 60.833 57.895 1.25 1.25 38.25 3.86
981 8479 1.483004 GAGGGGTTAGGTGAGAGAAGC 59.517 57.143 0.00 0.00 0.00 3.86
986 8484 2.418060 GGTTAGGTGAGAGAAGCAGAGC 60.418 54.545 0.00 0.00 0.00 4.09
1163 8666 2.003548 CCAGGGAGAAGGGGAAGGG 61.004 68.421 0.00 0.00 0.00 3.95
1167 8670 1.282653 GGGAGAAGGGGAAGGGGAAG 61.283 65.000 0.00 0.00 0.00 3.46
1168 8671 1.282653 GGAGAAGGGGAAGGGGAAGG 61.283 65.000 0.00 0.00 0.00 3.46
1169 8672 0.253207 GAGAAGGGGAAGGGGAAGGA 60.253 60.000 0.00 0.00 0.00 3.36
1170 8673 0.253394 AGAAGGGGAAGGGGAAGGAG 60.253 60.000 0.00 0.00 0.00 3.69
1171 8674 1.927569 GAAGGGGAAGGGGAAGGAGC 61.928 65.000 0.00 0.00 0.00 4.70
1172 8675 3.798511 GGGGAAGGGGAAGGAGCG 61.799 72.222 0.00 0.00 0.00 5.03
1290 8793 5.998454 ATCCTTGATTGATTTAGTGCTCG 57.002 39.130 0.00 0.00 0.00 5.03
1293 8796 1.933181 TGATTGATTTAGTGCTCGGCG 59.067 47.619 0.00 0.00 0.00 6.46
1534 9112 7.599998 GTGCCATGTTGTTTTGAAAGATTCTAT 59.400 33.333 0.00 0.00 0.00 1.98
1586 9165 3.833559 AAAGTGTTCCCCTGGATTGAT 57.166 42.857 0.00 0.00 0.00 2.57
1587 9166 3.372440 AAGTGTTCCCCTGGATTGATC 57.628 47.619 0.00 0.00 0.00 2.92
1633 9748 2.017049 GGAATTTCCTCGGTGGATGTG 58.983 52.381 8.25 0.00 45.68 3.21
1643 9758 1.131126 CGGTGGATGTGCATTCTTGAC 59.869 52.381 0.00 0.00 0.00 3.18
1674 10619 7.977789 TGACATTCTGCTTTCAACATTAGTA 57.022 32.000 0.00 0.00 0.00 1.82
1675 10620 8.032952 TGACATTCTGCTTTCAACATTAGTAG 57.967 34.615 0.00 0.00 0.00 2.57
1676 10621 7.661437 TGACATTCTGCTTTCAACATTAGTAGT 59.339 33.333 0.00 0.00 0.00 2.73
1718 10741 7.452880 TTCTTATTTCAGTTGTCCTTGATGG 57.547 36.000 0.00 0.00 37.10 3.51
1790 10813 2.637382 TGTGTCAGGGCTGAGAATTGTA 59.363 45.455 0.00 0.00 40.75 2.41
1794 10817 2.906389 TCAGGGCTGAGAATTGTACTGT 59.094 45.455 0.00 0.00 34.14 3.55
1798 10821 3.437049 GGGCTGAGAATTGTACTGTGTTC 59.563 47.826 0.00 0.00 0.00 3.18
1820 10843 7.769044 TGTTCCATTTAGCTGGTTAGAGTTATC 59.231 37.037 0.00 0.00 37.57 1.75
1985 11071 9.286170 GAGGAAGTAAAATAGAAACAAAGAGGT 57.714 33.333 0.00 0.00 0.00 3.85
2105 11274 7.920682 GCTTGGTTTCTTCTTTCTTGTGAAATA 59.079 33.333 0.00 0.00 40.85 1.40
2106 11275 9.971922 CTTGGTTTCTTCTTTCTTGTGAAATAT 57.028 29.630 0.00 0.00 40.85 1.28
2118 11287 9.540538 TTTCTTGTGAAATATCCTTTAATCCCA 57.459 29.630 0.00 0.00 37.27 4.37
2227 11396 1.221414 GCATCGCTCTATGGACAACC 58.779 55.000 0.00 0.00 0.00 3.77
2384 11560 6.994221 AGGCAGCGTCTTGTATTAATATACT 58.006 36.000 0.00 0.00 37.97 2.12
2431 11607 1.003839 GTCGTCAGGTGCATGGGAA 60.004 57.895 0.00 0.00 0.00 3.97
2471 11647 3.633986 TGTGGCAATGTGTGTTGTGAATA 59.366 39.130 0.00 0.00 0.00 1.75
2605 11784 5.774498 TGTCTACGAGCTGTGATCATATT 57.226 39.130 0.00 0.00 0.00 1.28
2635 11814 8.901748 CATTGTTAACAAGTACTTATGTGTTGC 58.098 33.333 24.22 11.70 39.47 4.17
2896 12075 1.728971 CGCTCACAATTCTCAGTGGTC 59.271 52.381 0.00 0.00 36.43 4.02
2948 12127 3.012518 TCAGCTTTTCATGCTAAGCCTC 58.987 45.455 20.91 2.84 46.10 4.70
3051 12230 2.629639 CCCCCTTGGAGGAGAGTAATGA 60.630 54.545 0.00 0.00 37.67 2.57
3058 12237 3.907474 TGGAGGAGAGTAATGAAACCACA 59.093 43.478 0.00 0.00 0.00 4.17
3160 12339 3.658351 GCTTCGGCTGTTACATGTAAG 57.342 47.619 18.56 9.22 38.08 2.34
3167 12346 3.016736 GCTGTTACATGTAAGGTGGCAT 58.983 45.455 18.56 0.00 28.09 4.40
3194 12373 4.439057 GAGCCTTAACGTGGACATGAATA 58.561 43.478 0.00 0.00 0.00 1.75
3293 12520 0.248012 TGCAAATGGCTCTGCATTGG 59.752 50.000 4.90 0.00 43.44 3.16
3324 12551 5.163405 CCTTGAGGGTTAGAGAAATCGATGA 60.163 44.000 0.00 0.00 0.00 2.92
3343 12570 3.904571 TGAAAATGACTCTGCATTGCAC 58.095 40.909 7.38 0.00 38.42 4.57
3385 12612 2.391616 TCGATGCAAATGACTCTGCT 57.608 45.000 0.00 0.00 39.38 4.24
3433 12708 1.001624 TCGATGCAAATGACTCTGCG 58.998 50.000 0.00 0.00 41.63 5.18
3472 12747 5.253330 AGGGTTAGAGAAATCGATGCAAAA 58.747 37.500 0.00 0.00 0.00 2.44
3526 12801 5.426504 AGAGAAATCGATGCAAATGACTCT 58.573 37.500 0.00 2.43 0.00 3.24
3529 12804 1.001624 TCGATGCAAATGACTCTGCG 58.998 50.000 0.00 0.00 41.63 5.18
3575 12898 5.293814 AGAGAAATCGATGCAAATGACTCTG 59.706 40.000 0.00 0.00 31.31 3.35
3593 12916 0.179059 TGCGTTGCAGAAGTCCTCAA 60.179 50.000 0.00 0.00 33.32 3.02
3596 12919 1.528129 GTTGCAGAAGTCCTCAAGGG 58.472 55.000 0.00 0.00 35.41 3.95
3601 12924 2.355209 GCAGAAGTCCTCAAGGGTTAGG 60.355 54.545 0.00 0.00 36.25 2.69
3650 12973 3.869912 GCAGAAGTCCTGTATTGCCTCAA 60.870 47.826 0.00 0.00 44.71 3.02
3755 13078 7.832503 AAACCTGTCTTCAGTTTTGAAAATG 57.167 32.000 0.00 0.00 42.48 2.32
3758 13081 6.605594 ACCTGTCTTCAGTTTTGAAAATGGTA 59.394 34.615 4.36 0.00 42.48 3.25
3871 13194 7.611855 AGCTAGTAACAATTGGCAGTCTAATTT 59.388 33.333 10.83 0.00 0.00 1.82
3952 13275 3.731867 GCATAAAGGACTTGTGCCATTCG 60.732 47.826 10.03 0.00 32.36 3.34
3976 13299 6.018913 CGTACCATGTCTAGACTAGTACACTG 60.019 46.154 29.30 19.20 34.51 3.66
4007 13330 4.630894 TTATTGGTTGCCATTCATCGTC 57.369 40.909 0.00 0.00 31.53 4.20
4062 13385 7.602517 ACATGCAAGTATTTGTTAGAGAGAC 57.397 36.000 0.00 0.00 36.65 3.36
4103 13426 9.732130 AGGTTAGAGATGGCTAATATCATTTTC 57.268 33.333 0.00 0.00 33.34 2.29
4340 13663 3.240069 CGTGGTCAAAGTAAGTAGTCCG 58.760 50.000 0.00 0.00 0.00 4.79
4354 13677 4.015764 AGTAGTCCGTCCCTAAAACTCTC 58.984 47.826 0.00 0.00 0.00 3.20
4380 13703 8.790718 CCTGATATCATTAAGCTTGCTACAATT 58.209 33.333 9.86 0.00 0.00 2.32
4389 13712 4.798574 AGCTTGCTACAATTTGTGCTTAC 58.201 39.130 12.30 7.20 0.00 2.34
4436 13759 9.912634 AGTGTGTGATTTCTGTAAATAATTTGG 57.087 29.630 0.00 0.00 35.41 3.28
4438 13761 9.689976 TGTGTGATTTCTGTAAATAATTTGGTG 57.310 29.630 0.00 0.00 35.41 4.17
4455 13778 2.749076 TGGTGATATTGCACTTGTCAGC 59.251 45.455 14.23 14.23 38.78 4.26
4476 13799 3.048941 GCGCGACGGGTAAGAGACT 62.049 63.158 12.10 0.00 0.00 3.24
4500 13823 6.223351 ACTAAGAGTACTATCACAAAGGCC 57.777 41.667 0.00 0.00 0.00 5.19
4505 13828 3.838317 AGTACTATCACAAAGGCCACTGA 59.162 43.478 5.01 0.00 0.00 3.41
4644 13967 8.366671 GTAATGTTACCTTCTCCACATATGTC 57.633 38.462 5.07 0.00 0.00 3.06
4646 13969 5.730550 TGTTACCTTCTCCACATATGTCAC 58.269 41.667 5.07 0.00 0.00 3.67
4717 14040 3.925913 CCATTTCTTTTTGTATGGGCACG 59.074 43.478 0.00 0.00 35.08 5.34
4757 14082 1.266989 GTTGGCTAGCTGTGTGAAACC 59.733 52.381 15.72 0.00 34.36 3.27
4779 14104 5.044919 ACCACCAAGAGTTATTCATGGATGA 60.045 40.000 6.01 0.00 45.51 2.92
4783 14108 7.501559 CACCAAGAGTTATTCATGGATGATCTT 59.498 37.037 6.01 0.91 45.51 2.40
4836 14161 6.815089 AGTGCAAATTTTGAATTACCACTCA 58.185 32.000 13.26 0.00 0.00 3.41
4926 14252 9.037737 CATTGATTTCAAGTTTTCAACATCTGT 57.962 29.630 0.00 0.00 39.47 3.41
4936 14262 4.548451 TTCAACATCTGTCTCTGCATCT 57.452 40.909 0.00 0.00 0.00 2.90
5336 14664 3.868077 ACAGTAGTCGTGTCGTATACCTC 59.132 47.826 0.00 0.00 0.00 3.85
5395 14723 6.012508 TCCTTTCCTGAATCACTTCCTTGTAT 60.013 38.462 0.00 0.00 0.00 2.29
5469 14797 4.289672 AGGAAGTTAAAGCTCTGGAATCCA 59.710 41.667 0.48 0.48 0.00 3.41
5717 15045 3.281727 TGTTGAGGCAGTGTTCTCTTT 57.718 42.857 13.89 0.00 0.00 2.52
5753 15081 5.959512 AGTATATGTGGAGCTCTAGAAGGT 58.040 41.667 14.64 0.00 38.79 3.50
5777 15105 4.048470 GGCAGTGGGGTTCCCTCC 62.048 72.222 7.87 0.00 45.70 4.30
5782 15110 0.778083 AGTGGGGTTCCCTCCTTTTC 59.222 55.000 7.87 0.00 45.70 2.29
5795 15123 4.280929 CCCTCCTTTTCGAAGAAAAATGGT 59.719 41.667 8.92 0.00 45.90 3.55
5940 15270 2.463553 TCGAGAATAACCGTGTAGCG 57.536 50.000 0.00 0.00 40.95 4.26
6158 15493 2.827642 GTGCATCTCTGGCCAGCC 60.828 66.667 28.91 13.16 0.00 4.85
6201 15536 1.010935 CACGTGGCTCTAGTGTGCAG 61.011 60.000 7.95 0.00 34.68 4.41
6209 15544 0.036952 TCTAGTGTGCAGCTGAAGGC 60.037 55.000 20.43 1.45 42.19 4.35
6228 15563 2.357569 GGCTTGGGTGATGAAAGGAGAT 60.358 50.000 0.00 0.00 0.00 2.75
6229 15564 2.686915 GCTTGGGTGATGAAAGGAGATG 59.313 50.000 0.00 0.00 0.00 2.90
6232 15567 4.428294 TGGGTGATGAAAGGAGATGATC 57.572 45.455 0.00 0.00 0.00 2.92
6245 15580 2.541762 GAGATGATCGGTTGCTAACTGC 59.458 50.000 3.74 0.00 43.25 4.40
6248 15583 1.134818 TGATCGGTTGCTAACTGCGAT 60.135 47.619 10.46 10.46 46.63 4.58
6251 15586 2.469826 TCGGTTGCTAACTGCGATATG 58.530 47.619 0.00 0.00 46.63 1.78
6254 15589 3.063452 CGGTTGCTAACTGCGATATGTTT 59.937 43.478 0.00 0.00 46.63 2.83
6258 15593 3.181501 TGCTAACTGCGATATGTTTTGGC 60.182 43.478 0.00 0.00 46.63 4.52
6262 15597 4.818534 ACTGCGATATGTTTTGGCTATG 57.181 40.909 0.00 0.00 0.00 2.23
6276 15611 1.745653 GGCTATGAACTTGGCCTGTTC 59.254 52.381 25.15 25.15 42.77 3.18
6322 15659 3.130280 TCTTGTGATCTGCTTGCTCAA 57.870 42.857 0.00 0.00 0.00 3.02
6325 15662 1.202794 TGTGATCTGCTTGCTCAACCA 60.203 47.619 0.00 0.00 0.00 3.67
6331 15668 2.158827 TCTGCTTGCTCAACCACTGTTA 60.159 45.455 0.00 0.00 32.09 2.41
6333 15670 2.222027 GCTTGCTCAACCACTGTTACT 58.778 47.619 0.00 0.00 32.09 2.24
6345 15682 5.057149 ACCACTGTTACTTTTCTAGCTGTG 58.943 41.667 0.00 0.00 31.08 3.66
6355 15692 1.550327 TCTAGCTGTGGACCTGTGAG 58.450 55.000 0.00 0.00 0.00 3.51
6356 15693 0.534412 CTAGCTGTGGACCTGTGAGG 59.466 60.000 0.00 0.00 42.49 3.86
6362 15699 0.326264 GTGGACCTGTGAGGCTGATT 59.674 55.000 0.00 0.00 39.63 2.57
6364 15701 1.555075 TGGACCTGTGAGGCTGATTAC 59.445 52.381 0.00 0.00 39.63 1.89
6377 15714 3.637998 CTGATTACAGCATGCCATTCC 57.362 47.619 15.66 0.15 42.53 3.01
6380 15717 2.512692 TTACAGCATGCCATTCCAGT 57.487 45.000 15.66 4.63 42.53 4.00
6381 15718 2.512692 TACAGCATGCCATTCCAGTT 57.487 45.000 15.66 0.00 42.53 3.16
6382 15719 1.180029 ACAGCATGCCATTCCAGTTC 58.820 50.000 15.66 0.00 42.53 3.01
6383 15720 1.272313 ACAGCATGCCATTCCAGTTCT 60.272 47.619 15.66 0.00 42.53 3.01
6384 15721 2.025981 ACAGCATGCCATTCCAGTTCTA 60.026 45.455 15.66 0.00 42.53 2.10
6385 15722 2.617308 CAGCATGCCATTCCAGTTCTAG 59.383 50.000 15.66 0.00 0.00 2.43
6386 15723 2.240667 AGCATGCCATTCCAGTTCTAGT 59.759 45.455 15.66 0.00 0.00 2.57
6387 15724 2.357009 GCATGCCATTCCAGTTCTAGTG 59.643 50.000 6.36 0.00 0.00 2.74
6388 15725 3.614092 CATGCCATTCCAGTTCTAGTGT 58.386 45.455 0.00 0.00 0.00 3.55
6389 15726 3.057969 TGCCATTCCAGTTCTAGTGTG 57.942 47.619 0.00 0.00 0.00 3.82
6390 15727 2.371841 TGCCATTCCAGTTCTAGTGTGT 59.628 45.455 0.00 0.00 0.00 3.72
6391 15728 3.580895 TGCCATTCCAGTTCTAGTGTGTA 59.419 43.478 0.00 0.00 0.00 2.90
6392 15729 4.184629 GCCATTCCAGTTCTAGTGTGTAG 58.815 47.826 0.00 0.00 0.00 2.74
6393 15730 4.081642 GCCATTCCAGTTCTAGTGTGTAGA 60.082 45.833 0.00 0.00 0.00 2.59
6394 15731 5.568825 GCCATTCCAGTTCTAGTGTGTAGAA 60.569 44.000 0.00 0.00 0.00 2.10
6407 15744 2.543777 TGTAGAACACAGCCTTCACC 57.456 50.000 0.00 0.00 31.89 4.02
6408 15745 1.071699 TGTAGAACACAGCCTTCACCC 59.928 52.381 0.00 0.00 31.89 4.61
6409 15746 1.071699 GTAGAACACAGCCTTCACCCA 59.928 52.381 0.00 0.00 0.00 4.51
6410 15747 0.109342 AGAACACAGCCTTCACCCAG 59.891 55.000 0.00 0.00 0.00 4.45
6411 15748 0.108585 GAACACAGCCTTCACCCAGA 59.891 55.000 0.00 0.00 0.00 3.86
6412 15749 0.773644 AACACAGCCTTCACCCAGAT 59.226 50.000 0.00 0.00 0.00 2.90
6413 15750 0.326264 ACACAGCCTTCACCCAGATC 59.674 55.000 0.00 0.00 0.00 2.75
6417 15879 2.042162 ACAGCCTTCACCCAGATCATTT 59.958 45.455 0.00 0.00 0.00 2.32
6427 15889 6.830912 TCACCCAGATCATTTTAGTATGAGG 58.169 40.000 0.00 0.00 37.91 3.86
6429 15891 6.933521 CACCCAGATCATTTTAGTATGAGGAG 59.066 42.308 0.00 0.00 37.91 3.69
6443 15905 2.497138 TGAGGAGCTCATTTGTGTGTG 58.503 47.619 17.19 0.00 35.39 3.82
6444 15906 1.198637 GAGGAGCTCATTTGTGTGTGC 59.801 52.381 17.19 0.00 38.51 4.57
6446 15908 1.542915 GGAGCTCATTTGTGTGTGCAT 59.457 47.619 17.19 0.00 40.15 3.96
6449 15911 2.055838 GCTCATTTGTGTGTGCATGTG 58.944 47.619 0.00 0.00 38.22 3.21
6452 15914 2.128821 CATTTGTGTGTGCATGTGTGG 58.871 47.619 0.00 0.00 0.00 4.17
6453 15915 1.180907 TTTGTGTGTGCATGTGTGGT 58.819 45.000 0.00 0.00 0.00 4.16
6455 15917 1.359833 GTGTGTGCATGTGTGGTGG 59.640 57.895 0.00 0.00 0.00 4.61
6456 15918 1.077140 TGTGTGCATGTGTGGTGGT 60.077 52.632 0.00 0.00 0.00 4.16
6457 15919 1.359833 GTGTGCATGTGTGGTGGTG 59.640 57.895 0.00 0.00 0.00 4.17
6458 15920 1.077140 TGTGCATGTGTGGTGGTGT 60.077 52.632 0.00 0.00 0.00 4.16
6459 15921 1.359833 GTGCATGTGTGGTGGTGTG 59.640 57.895 0.00 0.00 0.00 3.82
6461 15923 0.818852 TGCATGTGTGGTGGTGTGAG 60.819 55.000 0.00 0.00 0.00 3.51
6462 15924 0.819259 GCATGTGTGGTGGTGTGAGT 60.819 55.000 0.00 0.00 0.00 3.41
6463 15925 1.679139 CATGTGTGGTGGTGTGAGTT 58.321 50.000 0.00 0.00 0.00 3.01
6464 15926 1.334556 CATGTGTGGTGGTGTGAGTTG 59.665 52.381 0.00 0.00 0.00 3.16
6466 15928 1.003696 TGTGTGGTGGTGTGAGTTGAA 59.996 47.619 0.00 0.00 0.00 2.69
6467 15929 1.400494 GTGTGGTGGTGTGAGTTGAAC 59.600 52.381 0.00 0.00 0.00 3.18
6468 15930 1.021968 GTGGTGGTGTGAGTTGAACC 58.978 55.000 0.00 0.00 34.38 3.62
6469 15931 0.621082 TGGTGGTGTGAGTTGAACCA 59.379 50.000 0.00 0.00 41.66 3.67
6471 15933 1.676006 GGTGGTGTGAGTTGAACCAAG 59.324 52.381 0.00 0.00 45.26 3.61
6472 15934 2.639065 GTGGTGTGAGTTGAACCAAGA 58.361 47.619 0.00 0.00 45.26 3.02
6473 15935 2.614057 GTGGTGTGAGTTGAACCAAGAG 59.386 50.000 0.00 0.00 45.26 2.85
6474 15936 2.503765 TGGTGTGAGTTGAACCAAGAGA 59.496 45.455 0.00 0.00 40.97 3.10
6475 15937 3.134458 GGTGTGAGTTGAACCAAGAGAG 58.866 50.000 0.00 0.00 33.94 3.20
6477 15939 4.442706 GTGTGAGTTGAACCAAGAGAGAA 58.557 43.478 0.00 0.00 0.00 2.87
6478 15940 4.509600 GTGTGAGTTGAACCAAGAGAGAAG 59.490 45.833 0.00 0.00 0.00 2.85
6480 15942 3.711704 TGAGTTGAACCAAGAGAGAAGGT 59.288 43.478 0.00 0.00 37.20 3.50
6481 15943 4.202264 TGAGTTGAACCAAGAGAGAAGGTC 60.202 45.833 0.00 0.00 33.74 3.85
6482 15944 3.711704 AGTTGAACCAAGAGAGAAGGTCA 59.288 43.478 0.00 0.00 33.74 4.02
6483 15945 4.349342 AGTTGAACCAAGAGAGAAGGTCAT 59.651 41.667 0.00 0.00 33.74 3.06
6487 15949 4.013267 ACCAAGAGAGAAGGTCATGTTG 57.987 45.455 0.00 0.00 0.00 3.33
6488 15950 3.392616 ACCAAGAGAGAAGGTCATGTTGT 59.607 43.478 0.00 0.00 0.00 3.32
6489 15951 3.750130 CCAAGAGAGAAGGTCATGTTGTG 59.250 47.826 0.00 0.00 0.00 3.33
6490 15952 4.503817 CCAAGAGAGAAGGTCATGTTGTGA 60.504 45.833 0.00 0.00 0.00 3.58
6491 15953 5.243981 CAAGAGAGAAGGTCATGTTGTGAT 58.756 41.667 0.00 0.00 39.48 3.06
6492 15954 5.083533 AGAGAGAAGGTCATGTTGTGATC 57.916 43.478 0.00 0.00 39.48 2.92
6498 15960 4.356405 AGGTCATGTTGTGATCTGACAA 57.644 40.909 11.33 4.11 46.55 3.18
6499 15961 4.914983 AGGTCATGTTGTGATCTGACAAT 58.085 39.130 11.33 0.00 46.55 2.71
6500 15962 4.698780 AGGTCATGTTGTGATCTGACAATG 59.301 41.667 11.33 3.90 46.55 2.82
6501 15963 4.142534 GGTCATGTTGTGATCTGACAATGG 60.143 45.833 11.33 2.19 39.77 3.16
6502 15964 4.456911 GTCATGTTGTGATCTGACAATGGT 59.543 41.667 2.30 0.00 39.48 3.55
6503 15965 5.048504 GTCATGTTGTGATCTGACAATGGTT 60.049 40.000 2.30 0.00 39.48 3.67
6504 15966 5.181811 TCATGTTGTGATCTGACAATGGTTC 59.818 40.000 2.30 0.00 38.11 3.62
6505 15967 4.459330 TGTTGTGATCTGACAATGGTTCA 58.541 39.130 2.30 0.00 38.11 3.18
6506 15968 5.072055 TGTTGTGATCTGACAATGGTTCAT 58.928 37.500 2.30 0.00 38.11 2.57
6507 15969 5.535783 TGTTGTGATCTGACAATGGTTCATT 59.464 36.000 2.30 0.00 38.11 2.57
6508 15970 6.040729 TGTTGTGATCTGACAATGGTTCATTT 59.959 34.615 2.30 0.00 38.11 2.32
6509 15971 6.258230 TGTGATCTGACAATGGTTCATTTC 57.742 37.500 0.00 0.00 31.05 2.17
6510 15972 6.005823 TGTGATCTGACAATGGTTCATTTCT 58.994 36.000 0.00 0.00 31.05 2.52
6511 15973 6.072342 TGTGATCTGACAATGGTTCATTTCTG 60.072 38.462 0.00 0.00 31.05 3.02
6512 15974 6.005823 TGATCTGACAATGGTTCATTTCTGT 58.994 36.000 0.00 0.00 31.05 3.41
6513 15975 5.694231 TCTGACAATGGTTCATTTCTGTG 57.306 39.130 0.00 0.00 31.05 3.66
6514 15976 5.132502 TCTGACAATGGTTCATTTCTGTGT 58.867 37.500 0.00 0.00 31.05 3.72
6515 15977 5.239306 TCTGACAATGGTTCATTTCTGTGTC 59.761 40.000 0.00 0.00 31.05 3.67
6516 15978 5.132502 TGACAATGGTTCATTTCTGTGTCT 58.867 37.500 0.00 0.00 31.05 3.41
6517 15979 5.008911 TGACAATGGTTCATTTCTGTGTCTG 59.991 40.000 0.00 0.00 31.05 3.51
6536 15998 2.744202 CTGTGTGTGAAGGATAGCCAAC 59.256 50.000 0.00 0.00 36.29 3.77
6539 16001 3.568007 GTGTGTGAAGGATAGCCAACAAA 59.432 43.478 0.00 0.00 36.29 2.83
6543 16005 4.832266 TGTGAAGGATAGCCAACAAACAAT 59.168 37.500 0.00 0.00 36.29 2.71
6544 16006 5.163513 GTGAAGGATAGCCAACAAACAATG 58.836 41.667 0.00 0.00 36.29 2.82
6545 16007 4.220382 TGAAGGATAGCCAACAAACAATGG 59.780 41.667 0.00 0.00 39.80 3.16
6571 16033 1.733526 GTGTGGCACCAAACCTGAC 59.266 57.895 16.26 0.00 0.00 3.51
6607 16069 0.540365 AACCTGTCCATGTTGCTGGG 60.540 55.000 0.00 0.00 36.89 4.45
6638 16100 0.817634 TGGTTGCTTCACTTGGTCGG 60.818 55.000 0.00 0.00 0.00 4.79
6639 16101 0.818040 GGTTGCTTCACTTGGTCGGT 60.818 55.000 0.00 0.00 0.00 4.69
6640 16102 1.021968 GTTGCTTCACTTGGTCGGTT 58.978 50.000 0.00 0.00 0.00 4.44
6641 16103 2.215196 GTTGCTTCACTTGGTCGGTTA 58.785 47.619 0.00 0.00 0.00 2.85
6642 16104 1.873698 TGCTTCACTTGGTCGGTTAC 58.126 50.000 0.00 0.00 0.00 2.50
6643 16105 1.139256 TGCTTCACTTGGTCGGTTACA 59.861 47.619 0.00 0.00 0.00 2.41
6646 16108 2.806608 TCACTTGGTCGGTTACAGTC 57.193 50.000 0.00 0.00 0.00 3.51
6653 16115 1.338973 GGTCGGTTACAGTCACAGACA 59.661 52.381 16.83 0.00 40.08 3.41
6658 16120 3.537580 GGTTACAGTCACAGACAACCAA 58.462 45.455 11.00 0.00 36.65 3.67
6668 16130 1.948834 CAGACAACCAACACTGCATGA 59.051 47.619 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
476 483 1.888826 CGACAAAATGGGGCCCTTGTA 60.889 52.381 24.07 5.71 32.31 2.41
565 572 8.096414 CCTCATTCATGTTCCTTTTATTTTGGT 58.904 33.333 0.00 0.00 0.00 3.67
609 630 6.753107 ACCGTGCCTATTTATTTATATGCC 57.247 37.500 0.00 0.00 0.00 4.40
673 702 3.952323 GCATGAATGGATGGATAGATGGG 59.048 47.826 0.00 0.00 0.00 4.00
707 736 1.153309 TGTGCGGCAGAGATGATGG 60.153 57.895 1.18 0.00 0.00 3.51
712 741 2.435586 GCAGTGTGCGGCAGAGAT 60.436 61.111 1.18 0.00 35.86 2.75
713 742 4.687215 GGCAGTGTGCGGCAGAGA 62.687 66.667 1.18 0.00 46.21 3.10
758 4534 0.530744 TCAGACGACGATGAAAGGGG 59.469 55.000 0.00 0.00 0.00 4.79
769 4545 2.126424 GGACGTGCCTCAGACGAC 60.126 66.667 0.00 0.00 39.21 4.34
782 4561 1.562575 CGTTTCACGGAAAGGGGACG 61.563 60.000 9.71 0.00 38.08 4.79
800 4579 3.363970 CCGAGTGGTCAAAAGTCATTTCG 60.364 47.826 0.00 0.00 0.00 3.46
846 8337 4.162690 ACCGCCCCTGATTCTCGC 62.163 66.667 0.00 0.00 0.00 5.03
882 8373 2.716017 CGAGGAGGGAGTGAGGCAC 61.716 68.421 0.00 0.00 34.10 5.01
883 8374 2.363018 CGAGGAGGGAGTGAGGCA 60.363 66.667 0.00 0.00 0.00 4.75
884 8375 3.844090 GCGAGGAGGGAGTGAGGC 61.844 72.222 0.00 0.00 0.00 4.70
885 8376 2.043450 AGCGAGGAGGGAGTGAGG 60.043 66.667 0.00 0.00 0.00 3.86
886 8377 2.124693 GGAGCGAGGAGGGAGTGAG 61.125 68.421 0.00 0.00 0.00 3.51
887 8378 2.043852 GGAGCGAGGAGGGAGTGA 60.044 66.667 0.00 0.00 0.00 3.41
889 8380 2.043450 CTGGAGCGAGGAGGGAGT 60.043 66.667 0.00 0.00 0.00 3.85
893 8391 0.970937 TTACCACTGGAGCGAGGAGG 60.971 60.000 0.71 0.00 0.00 4.30
955 8453 2.024846 TCTCACCTAACCCCTCTCTCTG 60.025 54.545 0.00 0.00 0.00 3.35
981 8479 3.593834 GCCCAACAAAAAGGCTCTG 57.406 52.632 0.00 0.00 43.62 3.35
986 8484 1.542987 CCACCATGCCCAACAAAAAGG 60.543 52.381 0.00 0.00 0.00 3.11
1163 8666 1.147153 CCATTCTCCCGCTCCTTCC 59.853 63.158 0.00 0.00 0.00 3.46
1167 8670 4.918201 CCGCCATTCTCCCGCTCC 62.918 72.222 0.00 0.00 0.00 4.70
1168 8671 3.798954 CTCCGCCATTCTCCCGCTC 62.799 68.421 0.00 0.00 0.00 5.03
1169 8672 3.854669 CTCCGCCATTCTCCCGCT 61.855 66.667 0.00 0.00 0.00 5.52
1170 8673 3.798954 CTCTCCGCCATTCTCCCGC 62.799 68.421 0.00 0.00 0.00 6.13
1171 8674 2.419198 CTCTCCGCCATTCTCCCG 59.581 66.667 0.00 0.00 0.00 5.14
1172 8675 2.812619 CCCTCTCCGCCATTCTCCC 61.813 68.421 0.00 0.00 0.00 4.30
1534 9112 1.614903 CATCCAAAAGCAGAACCAGCA 59.385 47.619 0.00 0.00 0.00 4.41
1633 9748 3.018856 TGTCATCCATGGTCAAGAATGC 58.981 45.455 12.58 4.36 0.00 3.56
1643 9758 3.697542 TGAAAGCAGAATGTCATCCATGG 59.302 43.478 4.97 4.97 39.31 3.66
1687 10632 8.115490 AGGACAACTGAAATAAGAAAGATTGG 57.885 34.615 0.00 0.00 0.00 3.16
1695 10640 5.945784 CCCATCAAGGACAACTGAAATAAGA 59.054 40.000 0.00 0.00 41.22 2.10
1700 10723 2.445145 TCCCCATCAAGGACAACTGAAA 59.555 45.455 0.00 0.00 41.22 2.69
1718 10741 3.610911 CTGTGGTAAACTCTTCCATCCC 58.389 50.000 0.00 0.00 33.68 3.85
1794 10817 5.499004 ACTCTAACCAGCTAAATGGAACA 57.501 39.130 0.00 0.00 43.57 3.18
1798 10821 5.177696 GCGATAACTCTAACCAGCTAAATGG 59.822 44.000 0.00 0.00 46.47 3.16
1820 10843 2.202570 GCATGGCAAAGCAGAGCG 60.203 61.111 10.00 0.00 0.00 5.03
2009 11178 3.153130 TCGGGCATTGTTGAAATGAAGA 58.847 40.909 2.33 0.00 0.00 2.87
2105 11274 3.973973 TCCTCGTGATGGGATTAAAGGAT 59.026 43.478 0.00 0.00 0.00 3.24
2106 11275 3.380393 TCCTCGTGATGGGATTAAAGGA 58.620 45.455 0.00 0.00 0.00 3.36
2118 11287 2.526888 TGGAAGGTACTCCTCGTGAT 57.473 50.000 3.08 0.00 44.35 3.06
2334 11510 7.659186 ACCGTTAAACCAAGCAATAATTTACA 58.341 30.769 0.00 0.00 0.00 2.41
2431 11607 4.082571 GCCACAACATCTGAATAGCACTTT 60.083 41.667 0.00 0.00 0.00 2.66
2588 11767 5.262588 TGTGTAATATGATCACAGCTCGT 57.737 39.130 0.00 0.00 37.20 4.18
2896 12075 5.656480 TCAATGCACATTCCATCAAAGATG 58.344 37.500 0.00 0.07 0.00 2.90
2948 12127 7.526608 TCTATTTTAACAACCAGATTCTTGCG 58.473 34.615 0.00 0.00 0.00 4.85
3051 12230 3.203487 TGTAACCCTCTTCCTTGTGGTTT 59.797 43.478 0.00 0.00 39.81 3.27
3058 12237 4.601857 TCCATTTCTGTAACCCTCTTCCTT 59.398 41.667 0.00 0.00 0.00 3.36
3106 12285 3.243177 CGTTTTCCAAGATACTAGAGCGC 59.757 47.826 0.00 0.00 0.00 5.92
3167 12346 0.675083 TCCACGTTAAGGCTCGTTGA 59.325 50.000 0.00 0.00 38.23 3.18
3194 12373 2.219875 CCTCTGGTGGGTCAGCTGT 61.220 63.158 14.67 0.00 34.91 4.40
3293 12520 4.345854 TCTCTAACCCTCAAGGACTTCTC 58.654 47.826 0.00 0.00 39.89 2.87
3324 12551 4.202182 ACTTGTGCAATGCAGAGTCATTTT 60.202 37.500 8.73 0.00 40.08 1.82
3343 12570 2.724454 TCTCTAACCCTCGAGGACTTG 58.276 52.381 33.39 18.06 39.89 3.16
3385 12612 0.250295 CCCTCGAGGACTTGTGCAAA 60.250 55.000 33.39 0.00 38.24 3.68
3433 12708 0.390472 CCCTCGAGGACTTCTGCAAC 60.390 60.000 33.39 0.00 38.24 4.17
3439 12714 3.002038 TCTCTAACCCTCGAGGACTTC 57.998 52.381 33.39 0.00 39.89 3.01
3526 12801 1.664649 CGAGGACTTCTGCAACGCA 60.665 57.895 0.00 0.00 36.92 5.24
3529 12804 0.390472 CCCTCGAGGACTTCTGCAAC 60.390 60.000 33.39 0.00 38.24 4.17
3575 12898 0.514691 CTTGAGGACTTCTGCAACGC 59.485 55.000 0.00 0.00 0.00 4.84
3593 12916 1.843851 TGCATCGATTTCCCTAACCCT 59.156 47.619 0.00 0.00 0.00 4.34
3596 12919 5.066505 AGTCATTTGCATCGATTTCCCTAAC 59.933 40.000 0.00 0.00 0.00 2.34
3601 12924 4.595116 CAGAGTCATTTGCATCGATTTCC 58.405 43.478 0.00 0.00 0.00 3.13
3639 12962 7.391148 TTCTTATCCTTGTTTGAGGCAATAC 57.609 36.000 0.00 0.00 36.71 1.89
3650 12973 5.770162 CAGGACACCTTTTCTTATCCTTGTT 59.230 40.000 0.00 0.00 34.27 2.83
3871 13194 0.741915 GTCGCCCCAACAGTTCAAAA 59.258 50.000 0.00 0.00 0.00 2.44
3952 13275 6.238429 GCAGTGTACTAGTCTAGACATGGTAC 60.238 46.154 27.30 27.30 35.51 3.34
3976 13299 3.119173 TGGCAACCAATAATGTAAGCTGC 60.119 43.478 0.00 0.00 0.00 5.25
4007 13330 6.037940 CACACCAGATGACCTTCTGAATTATG 59.962 42.308 12.70 6.87 44.88 1.90
4062 13385 4.724399 TCTAACCTAGAGCTCAGAGATGG 58.276 47.826 17.77 10.31 0.00 3.51
4126 13449 9.077885 ACCACTTTCAAATAGTCAACACATTAT 57.922 29.630 0.00 0.00 0.00 1.28
4182 13505 9.109393 GGAGAGCATGTTTGTAAGTGAAATATA 57.891 33.333 0.00 0.00 0.00 0.86
4183 13506 7.611467 TGGAGAGCATGTTTGTAAGTGAAATAT 59.389 33.333 0.00 0.00 0.00 1.28
4184 13507 6.939730 TGGAGAGCATGTTTGTAAGTGAAATA 59.060 34.615 0.00 0.00 0.00 1.40
4185 13508 5.769662 TGGAGAGCATGTTTGTAAGTGAAAT 59.230 36.000 0.00 0.00 0.00 2.17
4186 13509 5.129634 TGGAGAGCATGTTTGTAAGTGAAA 58.870 37.500 0.00 0.00 0.00 2.69
4187 13510 4.713553 TGGAGAGCATGTTTGTAAGTGAA 58.286 39.130 0.00 0.00 0.00 3.18
4188 13511 4.350368 TGGAGAGCATGTTTGTAAGTGA 57.650 40.909 0.00 0.00 0.00 3.41
4189 13512 6.539826 TGATATGGAGAGCATGTTTGTAAGTG 59.460 38.462 0.00 0.00 0.00 3.16
4190 13513 6.540189 GTGATATGGAGAGCATGTTTGTAAGT 59.460 38.462 0.00 0.00 0.00 2.24
4191 13514 6.539826 TGTGATATGGAGAGCATGTTTGTAAG 59.460 38.462 0.00 0.00 0.00 2.34
4192 13515 6.413892 TGTGATATGGAGAGCATGTTTGTAA 58.586 36.000 0.00 0.00 0.00 2.41
4193 13516 5.988287 TGTGATATGGAGAGCATGTTTGTA 58.012 37.500 0.00 0.00 0.00 2.41
4340 13663 6.732896 TGATATCAGGAGAGTTTTAGGGAC 57.267 41.667 0.00 0.00 0.00 4.46
4354 13677 7.734924 TTGTAGCAAGCTTAATGATATCAGG 57.265 36.000 11.78 2.97 0.00 3.86
4380 13703 6.573664 AATTGCATGTCTTAGTAAGCACAA 57.426 33.333 14.85 12.32 0.00 3.33
4389 13712 9.874215 CACACTTATGATAATTGCATGTCTTAG 57.126 33.333 2.86 0.00 0.00 2.18
4436 13759 4.260538 GCTAGCTGACAAGTGCAATATCAC 60.261 45.833 7.70 0.00 37.24 3.06
4438 13761 3.060003 CGCTAGCTGACAAGTGCAATATC 60.060 47.826 13.93 0.00 0.00 1.63
4455 13778 1.009900 CTCTTACCCGTCGCGCTAG 60.010 63.158 5.56 0.00 0.00 3.42
4476 13799 6.893554 TGGCCTTTGTGATAGTACTCTTAGTA 59.106 38.462 3.32 0.00 0.00 1.82
4500 13823 7.819415 TGTCCTTCTGTATTTCAGTTATCAGTG 59.181 37.037 0.00 0.00 43.97 3.66
4505 13828 7.831193 AGCATTGTCCTTCTGTATTTCAGTTAT 59.169 33.333 0.00 0.00 43.97 1.89
4690 14013 6.495181 TGCCCATACAAAAAGAAATGGTTCTA 59.505 34.615 0.00 0.00 43.59 2.10
4691 14014 5.306678 TGCCCATACAAAAAGAAATGGTTCT 59.693 36.000 0.00 0.00 46.47 3.01
4692 14015 5.408299 GTGCCCATACAAAAAGAAATGGTTC 59.592 40.000 0.00 0.00 37.73 3.62
4717 14040 1.261619 CCAAACGACACAGTGCTCTTC 59.738 52.381 0.00 0.00 0.00 2.87
4757 14082 6.996879 AGATCATCCATGAATAACTCTTGGTG 59.003 38.462 0.00 5.34 45.55 4.17
4779 14104 6.127253 CCTGTTCATGCCCAAAAGAATAAGAT 60.127 38.462 0.00 0.00 0.00 2.40
4783 14108 4.671831 TCCTGTTCATGCCCAAAAGAATA 58.328 39.130 0.00 0.00 0.00 1.75
4869 14195 7.114529 CACTGAGCAAAGTCATCAAGAAAATTC 59.885 37.037 0.00 0.00 0.00 2.17
4879 14205 5.618056 TGAATTCACTGAGCAAAGTCATC 57.382 39.130 3.38 0.00 0.00 2.92
4926 14252 5.117406 TCTCCTAAGTACAGATGCAGAGA 57.883 43.478 0.00 0.00 0.00 3.10
4936 14262 8.758829 TCAGCAGAAATTTATCTCCTAAGTACA 58.241 33.333 0.00 0.00 0.00 2.90
5156 14483 8.380099 TGAAATATAACTGTTTCCCTACTGTGT 58.620 33.333 0.00 0.00 33.02 3.72
5336 14664 9.027129 CACAAATAAGGCAATGATCAAATACAG 57.973 33.333 0.00 0.00 0.00 2.74
5395 14723 4.574674 ATTCACAGGGTAGATTCTGCAA 57.425 40.909 4.11 0.00 34.57 4.08
5469 14797 3.884037 ACATCCCAAGACTTTCCTTGT 57.116 42.857 0.00 0.00 41.34 3.16
5519 14847 2.551912 CCACCACTCAAACCGCCAC 61.552 63.158 0.00 0.00 0.00 5.01
5731 15059 6.451393 CAACCTTCTAGAGCTCCACATATAC 58.549 44.000 10.93 0.00 0.00 1.47
5737 15065 1.276421 TGCAACCTTCTAGAGCTCCAC 59.724 52.381 10.93 0.00 0.00 4.02
5777 15105 6.668323 TCTAGCACCATTTTTCTTCGAAAAG 58.332 36.000 0.00 0.00 32.54 2.27
5782 15110 4.672801 GCCTTCTAGCACCATTTTTCTTCG 60.673 45.833 0.00 0.00 0.00 3.79
5795 15123 4.905429 TGTGTTCTTATTGCCTTCTAGCA 58.095 39.130 0.00 0.00 42.17 3.49
5940 15270 3.568538 CAGAACTACAAATGGCAGCAAC 58.431 45.455 0.00 0.00 0.00 4.17
6158 15493 0.670162 CAACCACCAGACAAGGCAAG 59.330 55.000 0.00 0.00 0.00 4.01
6201 15536 0.322816 TCATCACCCAAGCCTTCAGC 60.323 55.000 0.00 0.00 44.25 4.26
6209 15544 4.226427 TCATCTCCTTTCATCACCCAAG 57.774 45.455 0.00 0.00 0.00 3.61
6213 15548 3.181461 ACCGATCATCTCCTTTCATCACC 60.181 47.826 0.00 0.00 0.00 4.02
6228 15563 0.245266 TCGCAGTTAGCAACCGATCA 59.755 50.000 0.00 0.00 46.13 2.92
6229 15564 1.571919 ATCGCAGTTAGCAACCGATC 58.428 50.000 0.00 0.00 46.13 3.69
6232 15567 2.201732 ACATATCGCAGTTAGCAACCG 58.798 47.619 0.00 0.00 46.13 4.44
6245 15580 6.201517 CCAAGTTCATAGCCAAAACATATCG 58.798 40.000 0.00 0.00 0.00 2.92
6248 15583 4.159506 GGCCAAGTTCATAGCCAAAACATA 59.840 41.667 0.00 0.00 45.07 2.29
6251 15586 2.959516 GGCCAAGTTCATAGCCAAAAC 58.040 47.619 0.00 0.00 45.07 2.43
6258 15593 3.012518 CAGGAACAGGCCAAGTTCATAG 58.987 50.000 30.28 19.99 45.45 2.23
6262 15597 0.895559 CCCAGGAACAGGCCAAGTTC 60.896 60.000 24.93 24.93 43.49 3.01
6276 15611 2.819477 TGGCAACAGTTTTCCCAGG 58.181 52.632 0.00 0.00 46.17 4.45
6322 15659 5.057149 CACAGCTAGAAAAGTAACAGTGGT 58.943 41.667 0.00 0.00 0.00 4.16
6325 15662 5.298347 GTCCACAGCTAGAAAAGTAACAGT 58.702 41.667 0.00 0.00 0.00 3.55
6331 15668 2.706190 ACAGGTCCACAGCTAGAAAAGT 59.294 45.455 0.00 0.00 0.00 2.66
6333 15670 2.703536 TCACAGGTCCACAGCTAGAAAA 59.296 45.455 0.00 0.00 0.00 2.29
6345 15682 1.555075 TGTAATCAGCCTCACAGGTCC 59.445 52.381 0.00 0.00 37.80 4.46
6362 15699 2.025981 AGAACTGGAATGGCATGCTGTA 60.026 45.455 18.92 4.93 0.00 2.74
6364 15701 1.471119 AGAACTGGAATGGCATGCTG 58.529 50.000 18.92 1.57 0.00 4.41
6368 15705 3.009473 ACACACTAGAACTGGAATGGCAT 59.991 43.478 0.00 0.00 0.00 4.40
6388 15725 1.071699 GGGTGAAGGCTGTGTTCTACA 59.928 52.381 0.00 0.00 37.78 2.74
6389 15726 1.071699 TGGGTGAAGGCTGTGTTCTAC 59.928 52.381 0.00 0.00 0.00 2.59
6390 15727 1.347707 CTGGGTGAAGGCTGTGTTCTA 59.652 52.381 0.00 0.00 0.00 2.10
6391 15728 0.109342 CTGGGTGAAGGCTGTGTTCT 59.891 55.000 0.00 0.00 0.00 3.01
6392 15729 0.108585 TCTGGGTGAAGGCTGTGTTC 59.891 55.000 0.00 0.00 0.00 3.18
6393 15730 0.773644 ATCTGGGTGAAGGCTGTGTT 59.226 50.000 0.00 0.00 0.00 3.32
6394 15731 0.326264 GATCTGGGTGAAGGCTGTGT 59.674 55.000 0.00 0.00 0.00 3.72
6395 15732 0.325933 TGATCTGGGTGAAGGCTGTG 59.674 55.000 0.00 0.00 0.00 3.66
6396 15733 1.293062 ATGATCTGGGTGAAGGCTGT 58.707 50.000 0.00 0.00 0.00 4.40
6398 15735 3.463048 AAAATGATCTGGGTGAAGGCT 57.537 42.857 0.00 0.00 0.00 4.58
6399 15736 4.273318 ACTAAAATGATCTGGGTGAAGGC 58.727 43.478 0.00 0.00 0.00 4.35
6400 15737 7.282585 TCATACTAAAATGATCTGGGTGAAGG 58.717 38.462 0.00 0.00 30.92 3.46
6401 15738 7.443575 CCTCATACTAAAATGATCTGGGTGAAG 59.556 40.741 0.00 0.00 35.40 3.02
6402 15739 7.127186 TCCTCATACTAAAATGATCTGGGTGAA 59.873 37.037 0.00 0.00 35.40 3.18
6404 15741 6.830912 TCCTCATACTAAAATGATCTGGGTG 58.169 40.000 0.00 0.00 35.40 4.61
6406 15743 5.936956 GCTCCTCATACTAAAATGATCTGGG 59.063 44.000 0.00 0.00 35.40 4.45
6407 15744 6.767456 AGCTCCTCATACTAAAATGATCTGG 58.233 40.000 0.00 0.00 35.40 3.86
6408 15745 7.440198 TGAGCTCCTCATACTAAAATGATCTG 58.560 38.462 12.15 0.00 35.39 2.90
6409 15746 7.609097 TGAGCTCCTCATACTAAAATGATCT 57.391 36.000 12.15 0.00 35.39 2.75
6427 15889 2.030540 ACATGCACACACAAATGAGCTC 60.031 45.455 6.82 6.82 0.00 4.09
6429 15891 2.055838 CACATGCACACACAAATGAGC 58.944 47.619 0.00 0.00 0.00 4.26
6443 15905 0.819259 ACTCACACCACCACACATGC 60.819 55.000 0.00 0.00 0.00 4.06
6444 15906 1.334556 CAACTCACACCACCACACATG 59.665 52.381 0.00 0.00 0.00 3.21
6446 15908 0.615850 TCAACTCACACCACCACACA 59.384 50.000 0.00 0.00 0.00 3.72
6449 15911 1.021968 GGTTCAACTCACACCACCAC 58.978 55.000 0.00 0.00 0.00 4.16
6452 15914 2.614057 CTCTTGGTTCAACTCACACCAC 59.386 50.000 0.00 0.00 40.41 4.16
6453 15915 2.503765 TCTCTTGGTTCAACTCACACCA 59.496 45.455 0.00 0.00 38.89 4.17
6455 15917 4.060038 TCTCTCTTGGTTCAACTCACAC 57.940 45.455 0.00 0.00 0.00 3.82
6456 15918 4.443457 CCTTCTCTCTTGGTTCAACTCACA 60.443 45.833 0.00 0.00 0.00 3.58
6457 15919 4.061596 CCTTCTCTCTTGGTTCAACTCAC 58.938 47.826 0.00 0.00 0.00 3.51
6458 15920 3.711704 ACCTTCTCTCTTGGTTCAACTCA 59.288 43.478 0.00 0.00 0.00 3.41
6459 15921 4.202264 TGACCTTCTCTCTTGGTTCAACTC 60.202 45.833 0.00 0.00 33.74 3.01
6461 15923 4.073293 TGACCTTCTCTCTTGGTTCAAC 57.927 45.455 0.00 0.00 33.74 3.18
6462 15924 4.103153 ACATGACCTTCTCTCTTGGTTCAA 59.897 41.667 0.00 0.00 33.74 2.69
6463 15925 3.648067 ACATGACCTTCTCTCTTGGTTCA 59.352 43.478 0.00 0.00 33.74 3.18
6464 15926 4.278975 ACATGACCTTCTCTCTTGGTTC 57.721 45.455 0.00 0.00 33.74 3.62
6466 15928 3.392616 ACAACATGACCTTCTCTCTTGGT 59.607 43.478 0.00 0.00 36.70 3.67
6467 15929 3.750130 CACAACATGACCTTCTCTCTTGG 59.250 47.826 0.00 0.00 0.00 3.61
6468 15930 4.635223 TCACAACATGACCTTCTCTCTTG 58.365 43.478 0.00 0.00 29.99 3.02
6469 15931 4.963318 TCACAACATGACCTTCTCTCTT 57.037 40.909 0.00 0.00 29.99 2.85
6471 15933 4.869297 CAGATCACAACATGACCTTCTCTC 59.131 45.833 0.00 0.00 41.24 3.20
6472 15934 4.529769 TCAGATCACAACATGACCTTCTCT 59.470 41.667 0.00 0.00 41.24 3.10
6473 15935 4.629200 GTCAGATCACAACATGACCTTCTC 59.371 45.833 0.00 0.00 41.24 2.87
6474 15936 4.040829 TGTCAGATCACAACATGACCTTCT 59.959 41.667 0.00 0.00 41.24 2.85
6475 15937 4.318332 TGTCAGATCACAACATGACCTTC 58.682 43.478 0.00 0.00 41.24 3.46
6477 15939 4.356405 TTGTCAGATCACAACATGACCT 57.644 40.909 0.00 0.00 41.24 3.85
6478 15940 4.142534 CCATTGTCAGATCACAACATGACC 60.143 45.833 0.00 0.00 41.24 4.02
6480 15942 4.654915 ACCATTGTCAGATCACAACATGA 58.345 39.130 0.00 0.00 39.09 3.07
6481 15943 5.048573 TGAACCATTGTCAGATCACAACATG 60.049 40.000 1.03 0.00 39.09 3.21
6482 15944 5.072055 TGAACCATTGTCAGATCACAACAT 58.928 37.500 1.03 0.00 39.09 2.71
6483 15945 4.459330 TGAACCATTGTCAGATCACAACA 58.541 39.130 1.03 0.00 39.09 3.33
6487 15949 6.072286 ACAGAAATGAACCATTGTCAGATCAC 60.072 38.462 0.00 0.00 34.04 3.06
6488 15950 6.005823 ACAGAAATGAACCATTGTCAGATCA 58.994 36.000 0.00 0.00 34.04 2.92
6489 15951 6.072286 ACACAGAAATGAACCATTGTCAGATC 60.072 38.462 0.00 0.00 34.04 2.75
6490 15952 5.771666 ACACAGAAATGAACCATTGTCAGAT 59.228 36.000 0.00 0.00 34.04 2.90
6491 15953 5.132502 ACACAGAAATGAACCATTGTCAGA 58.867 37.500 0.00 0.00 34.04 3.27
6492 15954 5.240183 AGACACAGAAATGAACCATTGTCAG 59.760 40.000 9.80 3.76 34.04 3.51
6493 15955 5.008911 CAGACACAGAAATGAACCATTGTCA 59.991 40.000 9.80 0.00 34.04 3.58
6494 15956 5.009010 ACAGACACAGAAATGAACCATTGTC 59.991 40.000 0.00 0.00 34.04 3.18
6495 15957 4.889409 ACAGACACAGAAATGAACCATTGT 59.111 37.500 0.00 0.00 34.04 2.71
6496 15958 5.217393 CACAGACACAGAAATGAACCATTG 58.783 41.667 0.00 0.00 34.04 2.82
6497 15959 4.889409 ACACAGACACAGAAATGAACCATT 59.111 37.500 0.00 0.00 35.39 3.16
6498 15960 4.276678 CACACAGACACAGAAATGAACCAT 59.723 41.667 0.00 0.00 0.00 3.55
6499 15961 3.627123 CACACAGACACAGAAATGAACCA 59.373 43.478 0.00 0.00 0.00 3.67
6500 15962 3.627577 ACACACAGACACAGAAATGAACC 59.372 43.478 0.00 0.00 0.00 3.62
6501 15963 4.332543 TCACACACAGACACAGAAATGAAC 59.667 41.667 0.00 0.00 0.00 3.18
6502 15964 4.512484 TCACACACAGACACAGAAATGAA 58.488 39.130 0.00 0.00 0.00 2.57
6503 15965 4.135747 TCACACACAGACACAGAAATGA 57.864 40.909 0.00 0.00 0.00 2.57
6504 15966 4.260907 CCTTCACACACAGACACAGAAATG 60.261 45.833 0.00 0.00 0.00 2.32
6505 15967 3.879295 CCTTCACACACAGACACAGAAAT 59.121 43.478 0.00 0.00 0.00 2.17
6506 15968 3.055458 TCCTTCACACACAGACACAGAAA 60.055 43.478 0.00 0.00 0.00 2.52
6507 15969 2.499693 TCCTTCACACACAGACACAGAA 59.500 45.455 0.00 0.00 0.00 3.02
6508 15970 2.107366 TCCTTCACACACAGACACAGA 58.893 47.619 0.00 0.00 0.00 3.41
6509 15971 2.602257 TCCTTCACACACAGACACAG 57.398 50.000 0.00 0.00 0.00 3.66
6510 15972 3.554960 GCTATCCTTCACACACAGACACA 60.555 47.826 0.00 0.00 0.00 3.72
6511 15973 2.996621 GCTATCCTTCACACACAGACAC 59.003 50.000 0.00 0.00 0.00 3.67
6512 15974 2.028112 GGCTATCCTTCACACACAGACA 60.028 50.000 0.00 0.00 0.00 3.41
6513 15975 2.028112 TGGCTATCCTTCACACACAGAC 60.028 50.000 0.00 0.00 0.00 3.51
6514 15976 2.256306 TGGCTATCCTTCACACACAGA 58.744 47.619 0.00 0.00 0.00 3.41
6515 15977 2.744202 GTTGGCTATCCTTCACACACAG 59.256 50.000 0.00 0.00 0.00 3.66
6516 15978 2.105649 TGTTGGCTATCCTTCACACACA 59.894 45.455 0.00 0.00 0.00 3.72
6517 15979 2.778299 TGTTGGCTATCCTTCACACAC 58.222 47.619 0.00 0.00 0.00 3.82
6536 15998 3.933955 CCACACCAATATGCCATTGTTTG 59.066 43.478 7.21 6.47 0.00 2.93
6539 16001 1.481772 GCCACACCAATATGCCATTGT 59.518 47.619 7.21 0.00 0.00 2.71
6543 16005 2.577490 GTGCCACACCAATATGCCA 58.423 52.632 0.00 0.00 0.00 4.92
6571 16033 3.367932 CAGGTTGTGAACTGTATACGCTG 59.632 47.826 0.00 0.00 0.00 5.18
6638 16100 3.936453 TGTTGGTTGTCTGTGACTGTAAC 59.064 43.478 0.00 0.00 33.15 2.50
6639 16101 3.936453 GTGTTGGTTGTCTGTGACTGTAA 59.064 43.478 0.00 0.00 33.15 2.41
6640 16102 3.196901 AGTGTTGGTTGTCTGTGACTGTA 59.803 43.478 0.00 0.00 33.15 2.74
6641 16103 2.027192 AGTGTTGGTTGTCTGTGACTGT 60.027 45.455 0.00 0.00 33.15 3.55
6642 16104 2.352651 CAGTGTTGGTTGTCTGTGACTG 59.647 50.000 0.00 0.00 33.15 3.51
6643 16105 2.632377 CAGTGTTGGTTGTCTGTGACT 58.368 47.619 0.00 0.00 33.15 3.41
6646 16108 1.093972 TGCAGTGTTGGTTGTCTGTG 58.906 50.000 0.00 0.00 0.00 3.66
6653 16115 2.783135 CCTACTCATGCAGTGTTGGTT 58.217 47.619 0.00 0.00 36.43 3.67
6658 16120 0.251354 CTGGCCTACTCATGCAGTGT 59.749 55.000 3.32 0.00 36.43 3.55


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

AutoCloner maintained by Alex Coulton.